Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold273
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1282806
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 8 of 9
Found at i:1126232 original size:20 final size:20
Alignment explanation
Indices: 1126207--1126259 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
1126197 TCCCGTAGCC
1126207 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCATA
1126227 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCATA
1126247 ATGTATCGATACA
1 ATGTATCGATACA
1126260 TTGATTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAATTCATA
Found at i:1126386 original size:20 final size:20
Alignment explanation
Indices: 1126361--1126420 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
1126351 CTGTCAGTTT
1126361 CATGTATCGATACAATTATC
1 CATGTATCGATACAATTATC
*
1126381 CATGTATCGATACAATGAT-
1 CATGTATCGATACAATTATC
1126400 CATGTATCGATACAATATATC
1 CATGTATCGATACAAT-TATC
1126421 GATACAAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 16 0.44
20 20 0.56
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTATC
Found at i:1126442 original size:20 final size:20
Alignment explanation
Indices: 1126417--1126465 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1126407 CGATACAATA
1126417 TATCGATACAAA-ACATAATG
1 TATCGATACAAATACAT-ATG
*
1126437 TATCGATACAAATACCTATG
1 TATCGATACAAATACATATG
1126457 TATCGATAC
1 TATCGATAC
1126466 TTTGAAGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 24 0.89
21 3 0.11
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (20 bp):
TATCGATACAAATACATATG
Found at i:1126747 original size:110 final size:110
Alignment explanation
Indices: 1126554--1126774 Score: 433
Period size: 110 Copynumber: 2.0 Consensus size: 110
1126544 AGAAAATTAC
1126554 TTAGAACATGTTTTTAGAGTAATTTTGAGTGAATAAAACTTGTTTACGATTTTTCAAACATTTTT
1 TTAGAACATGTTTTTAGAGTAATTTTGAGTGAATAAAACTTGTTTACGATTTTTCAAACATTTTT
*
1126619 CGGTTTTATTCAATCTTTGTTATATAAAAACCAAGATGCTAACAA
66 CGATTTTATTCAATCTTTGTTATATAAAAACCAAGATGCTAACAA
1126664 TTAGAACATGTTTTTAGAGTAATTTTGAGTGAATAAAACTTGTTTACGATTTTTCAAACATTTTT
1 TTAGAACATGTTTTTAGAGTAATTTTGAGTGAATAAAACTTGTTTACGATTTTTCAAACATTTTT
1126729 CGATTTTATTCAATCTTTGTTATATAAAAACCAAGATGCTAACAA
66 CGATTTTATTCAATCTTTGTTATATAAAAACCAAGATGCTAACAA
1126774 T
1 T
1126775 CCCCAATATG
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 110 1.00
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (110 bp):
TTAGAACATGTTTTTAGAGTAATTTTGAGTGAATAAAACTTGTTTACGATTTTTCAAACATTTTT
CGATTTTATTCAATCTTTGTTATATAAAAACCAAGATGCTAACAA
Found at i:1128726 original size:16 final size:16
Alignment explanation
Indices: 1128701--1128732 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1128691 TGACGAGACA
*
1128701 AATATTTTTTGCTTAT
1 AATATATTTTGCTTAT
1128717 AATATATTTTGCTTAT
1 AATATATTTTGCTTAT
1128733 GGTGTCATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.59
Consensus pattern (16 bp):
AATATATTTTGCTTAT
Found at i:1128899 original size:49 final size:49
Alignment explanation
Indices: 1128810--1128917 Score: 119
Period size: 49 Copynumber: 2.2 Consensus size: 49
1128800 GCGATCGCAT
* **
1128810 CACCGT-AGTCCAATCGATTAGGTGACTGTTTATATCAGCACGATCACGC
1 CACCGTGA-TCCAATCGATTAGGTGACAGTCCATATCAGCACGATCACGC
* * * *
1128859 CACCGTGATCCAATCGGTTAGGTGACAGTCCATGTTAGCACGATCGCGC
1 CACCGTGATCCAATCGATTAGGTGACAGTCCATATCAGCACGATCACGC
* *
1128908 TACTGTGATC
1 CACCGTGATC
1128918 TAGTCAACAG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 48 0.98
50 1 0.02
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (49 bp):
CACCGTGATCCAATCGATTAGGTGACAGTCCATATCAGCACGATCACGC
Found at i:1130121 original size:20 final size:20
Alignment explanation
Indices: 1130082--1130121 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1130072 TATTAAAATA
* *
1130082 TTATTTTTATACTTATATTT
1 TTATTTTTATAATTAAATTT
1130102 TTATTTTTATAATTAAATTT
1 TTATTTTTATAATTAAATTT
1130122 AAAAAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTTTATAATTAAATTT
Found at i:1130487 original size:22 final size:22
Alignment explanation
Indices: 1130444--1130489 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1130434 GATTCGAATT
*
1130444 AATTTAAAAAGTTAAAAGTTTA
1 AATTTAAAAAATTAAAAGTTTA
*
1130466 AATTTAAATAAATTCAAA-TTTA
1 AATTTAAA-AAATTAAAAGTTTA
1130488 AA
1 AA
1130490 AAATTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (22 bp):
AATTTAAAAAATTAAAAGTTTA
Found at i:1130500 original size:16 final size:16
Alignment explanation
Indices: 1130457--1130510 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
1130447 TTAAAAAGTT
*
1130457 AAAAGTTTAAATTTAA
1 AAAATTTTAAATTTAA
*
1130473 ATAAA-TTCAAATTTAA
1 A-AAATTTTAAATTTAA
*
1130489 AAAATTTTAAATCTGAA
1 AAAATTTTAAAT-TTAA
1130506 AAAAT
1 AAAAT
1130511 AAAAACCCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 3 0.09
16 18 0.56
17 11 0.34
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (16 bp):
AAAATTTTAAATTTAA
Found at i:1130773 original size:23 final size:23
Alignment explanation
Indices: 1130728--1130773 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1130718 TTTATGAACA
* *
1130728 TATATTTATAATTTTTATACAAT
1 TATATTCATAATTGTTATACAAT
1130751 TATATTCATAATGTGTTAT-CAAT
1 TATATTCATAAT-TGTTATACAAT
1130774 ATAATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (23 bp):
TATATTCATAATTGTTATACAAT
Found at i:1131202 original size:15 final size:15
Alignment explanation
Indices: 1131182--1131211 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1131172 TACAACATCC
1131182 AAATAAAATATATTT
1 AAATAAAATATATTT
1131197 AAATAAAATATATTT
1 AAATAAAATATATTT
1131212 TTCAAATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATAAAATATATTT
Found at i:1131937 original size:15 final size:16
Alignment explanation
Indices: 1131898--1131938 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1131888 TATTTATAAA
1131898 AATATTTATTAATTTTT
1 AATATTT-TTAATTTTT
*
1131915 AA-AATTTTAA-TTTT
1 AATATTTTTAATTTTT
1131929 AATATTTTTA
1 AATATTTTTA
1131939 TTATTATGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 6 0.29
15 10 0.48
16 3 0.14
17 2 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AATATTTTTAATTTTT
Found at i:1132105 original size:22 final size:22
Alignment explanation
Indices: 1132080--1132121 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1132070 AACTCATATC
*
1132080 TAAAATTATTTAAATTTAAATT
1 TAAAATTAATTAAATTTAAATT
1132102 TAAAATTAATTAAATTTAAA
1 TAAAATTAATTAAATTTAAA
1132122 AATATCCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAAATTAATTAAATTTAAATT
Found at i:1133907 original size:37 final size:34
Alignment explanation
Indices: 1133824--1133907 Score: 82
Period size: 37 Copynumber: 2.4 Consensus size: 34
1133814 TTTTATGAAT
*
1133824 AATTAAAAATTAAATAAAAATTTTGATTTGATCA
1 AATTAAAAATTAAATAAAAATTTTGAATTGATCA
* * *
1133858 AATTTAATTTAAA-TAATTATAAATTTTTAATTGAT-A
1 AA-TTAA---AAATTAAATAAAAATTTTGAATTGATCA
1133894 AATTAAAAATTAAA
1 AATTAAAAATTAAA
1133908 CCAAATAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
32 3 0.08
33 3 0.08
34 2 0.05
35 8 0.20
36 3 0.08
37 18 0.45
38 3 0.08
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.42
Consensus pattern (34 bp):
AATTAAAAATTAAATAAAAATTTTGAATTGATCA
Found at i:1133955 original size:16 final size:16
Alignment explanation
Indices: 1133936--1133967 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1133926 ATTAACATTA
1133936 TAATAAAAATCAAATT
1 TAATAAAAATCAAATT
1133952 TAATAAAAATCAAATT
1 TAATAAAAATCAAATT
1133968 AAACATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (16 bp):
TAATAAAAATCAAATT
Found at i:1134313 original size:13 final size:14
Alignment explanation
Indices: 1134281--1134317 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
1134271 ACGTGGCAGG
1134281 TTTTATTTTATTCT
1 TTTTATTTTATTCT
1134295 TTTTATTTT-TT-T
1 TTTTATTTTATTCT
1134307 TTGTTATTTTA
1 TT-TTATTTTA
1134318 AAGAAATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.14
13 9 0.43
14 9 0.43
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.81
Consensus pattern (14 bp):
TTTTATTTTATTCT
Found at i:1134404 original size:13 final size:14
Alignment explanation
Indices: 1134386--1134421 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
1134376 AAAATTTTTA
1134386 ATTATTTTT-AATT
1 ATTATTTTTAAATT
1134399 ATTATTTTTAAATT
1 ATTATTTTTAAATT
1134413 ATATATTTT
1 AT-TATTTT
1134422 AAGAGTTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 9 0.43
14 6 0.29
15 6 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTATTTTTAAATT
Found at i:1140481 original size:17 final size:18
Alignment explanation
Indices: 1140459--1140492 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1140449 ATTTTTTATT
*
1140459 ATTAAAT-AATAATTTAA
1 ATTAAATCAAAAATTTAA
1140476 ATTAAATCAAAAATTTA
1 ATTAAATCAAAAATTTA
1140493 TAAAAATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTAAATCAAAAATTTAA
Found at i:1141224 original size:2 final size:2
Alignment explanation
Indices: 1141217--1141242 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1141207 ACATACATAC
1141217 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1141243 TAAATACATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1144296 original size:21 final size:19
Alignment explanation
Indices: 1144272--1144310 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
1144262 TTCCTTTAAT
1144272 ATAAAAAAGGATAATAATTTG
1 ATAAAAAA-GATAA-AATTTG
*
1144293 ATAACAAAGATAAAATTT
1 ATAAAAAAGATAAAATTT
1144311 ACAAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 5 0.29
21 7 0.41
ACGTcount: A:0.59, C:0.03, G:0.10, T:0.28
Consensus pattern (19 bp):
ATAAAAAAGATAAAATTTG
Found at i:1146857 original size:22 final size:21
Alignment explanation
Indices: 1146830--1146870 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
1146820 AAATTAAAAT
1146830 TATTTTA-ATATTAATATTTATA
1 TATTTTATA-ATTAA-ATTTATA
1146852 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
1146871 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 12 0.67
23 1 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:1146883 original size:35 final size:35
Alignment explanation
Indices: 1146842--1146908 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
1146832 TTTTAATATT
1146842 AATATTTATATATT-TTATAAT-TAAATTTAAATAAA
1 AATATTTATA-ATTATTA-AATATAAATTTAAATAAA
* *
1146877 AATATTTTTAATTATTAAATATTAATTTAAAT
1 AATATTTATAATTATTAAATATAAATTTAAAT
1146909 TAAATTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 6 0.21
35 22 0.79
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (35 bp):
AATATTTATAATTATTAAATATAAATTTAAATAAA
Found at i:1148109 original size:28 final size:29
Alignment explanation
Indices: 1148050--1148106 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
1148040 AATTCAAAAA
*
1148050 TAAAATTTAATTAAATTAAAAAATTATTT
1 TAAAATTTAATTAAATTAAAAAATAATTT
* *
1148079 TAAAA-TTAA-TATATTAATAAATAATTT
1 TAAAATTTAATTAAATTAAAAAATAATTT
1148106 T
1 T
1148107 TAATAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 16 0.64
28 4 0.16
29 5 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TAAAATTTAATTAAATTAAAAAATAATTT
Found at i:1148193 original size:39 final size:38
Alignment explanation
Indices: 1148116--1148208 Score: 107
Period size: 39 Copynumber: 2.4 Consensus size: 38
1148106 TTAATAAAAT
* * **
1148116 AAAAATTAAATTAATTAAATTTAAAAAATTTTGTATTA
1 AAAAATTAAATTAAATAAATATAAAAAATTTTAAATTA
1148154 AAAAATTAATAATTAAATAAA-ATAAAAAATTTTAAATTA
1 AAAAATT-A-AATTAAATAAATATAAAAAATTTTAAATTA
*
1148193 AAAAATAAAATGTAAA
1 AAAAATTAAAT-TAAA
1148209 AGTCACATAG
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
37 3 0.06
38 12 0.26
39 22 0.47
40 10 0.21
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (38 bp):
AAAAATTAAATTAAATAAATATAAAAAATTTTAAATTA
Found at i:1148208 original size:19 final size:18
Alignment explanation
Indices: 1148150--1148208 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 18
1148140 AAAATTTTGT
1148150 ATTAAAAAATTAATAATTAA
1 ATTAAAAAA-TAA-AATTAA
1148170 A-TAAAATAA-AAAATTTTAA
1 ATTAAAA-AATAAAA--TTAA
1148189 ATTAAAAAATAAAATGTAA
1 ATTAAAAAATAAAAT-TAA
1148208 A
1 A
1148209 AGTCACATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
17 2 0.06
18 3 0.09
19 16 0.48
20 12 0.36
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (18 bp):
ATTAAAAAATAAAATTAA
Found at i:1151660 original size:22 final size:22
Alignment explanation
Indices: 1151629--1151675 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1151619 AGAAAGGGAA
**
1151629 AAAAAAGAAGGAATGAAAGAAG
1 AAAAAAGAAGGAAAAAAAGAAG
*
1151651 AAAAAGGAAGGAAAAAAAGAAG
1 AAAAAAGAAGGAAAAAAAGAAG
1151673 AAA
1 AAA
1151676 GAAAAAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (22 bp):
AAAAAAGAAGGAAAAAAAGAAG
Found at i:1151687 original size:35 final size:35
Alignment explanation
Indices: 1151622--1151690 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
1151612 AGGGAGAAGA
* * *
1151622 AAGGGAAAAAAAAGAAGGAATGAAAGAAGAAAAAGG
1 AAGGAAAAAAAAAGAAAGAA-GAAAAAAGAAAAAGG
1151658 AAGGAAAAAAAGAAGAAAGAA-AAAAAAGAAAAA
1 AAGGAAAAAAA-AAGAAAGAAGAAAAAAGAAAAA
1151691 AGTAGCTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 11 0.38
36 10 0.34
37 8 0.28
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.01
Consensus pattern (35 bp):
AAGGAAAAAAAAAGAAAGAAGAAAAAAGAAAAAGG
Found at i:1156358 original size:74 final size:70
Alignment explanation
Indices: 1156232--1156438 Score: 254
Period size: 72 Copynumber: 2.9 Consensus size: 70
1156222 GTCATCGAGC
* *
1156232 TAAAAATTTAAACTCGTATAATCAAATAAAAATAAATATTAAATTTCTACAAATAAAAATAAATT
1 TAAAAATTTAAATTCGTATAATCAAATAAAAATAAAT-TTAAATTTTTACAAATAAAAATAAATT
1156297 ACACCA
65 ACACCA
* * * *
1156303 TAAAAAATTTAAATTCGTATAATTATACTTAAAAAATATATTTAAATTTTTACAAATTAAAATAA
1 T-AAAAATTTAAATTCGTATAATCA-A-AT-AAAAATAAATTTAAATTTTTACAAATAAAAATAA
* *
1156368 ATTATACCC
62 ATTACACCA
** * *
1156377 T-AAAATTTAAATTCACATAATCAAATAAAAATAAATTTAAACTTTTACAATTAAAAATAAAT
1 TAAAAATTTAAATTCGTATAATCAAATAAAAATAAATTTAAATTTTTACAAATAAAAATAAAT
1156439 ATACCTTTAA
Statistics
Matches: 116, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
69 32 0.28
70 1 0.01
71 2 0.02
72 40 0.34
73 1 0.01
74 31 0.27
75 9 0.08
ACGTcount: A:0.56, C:0.09, G:0.01, T:0.34
Consensus pattern (70 bp):
TAAAAATTTAAATTCGTATAATCAAATAAAAATAAATTTAAATTTTTACAAATAAAAATAAATTA
CACCA
Found at i:1161879 original size:32 final size:33
Alignment explanation
Indices: 1161813--1161880 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 33
1161803 TTCAACGATT
* *
1161813 TGTATCGATACATAAAGTGTTGTGTCGATGCAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
1161846 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1161878 TGT
1 TGT
1161881 TAGCTACTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 19 0.59
33 13 0.41
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.37
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1161938 original size:13 final size:13
Alignment explanation
Indices: 1161920--1161944 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1161910 ATTACTCAAA
1161920 TGTATCGATACAT
1 TGTATCGATACAT
1161933 TGTATCGATACA
1 TGTATCGATACA
1161945 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1161996 original size:52 final size:52
Alignment explanation
Indices: 1161953--1162081 Score: 204
Period size: 52 Copynumber: 2.5 Consensus size: 52
1161943 CACTGATCTT
* * *
1161953 TGTATCAATACATGCAGGCAAATTTGCCCATATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
1162005 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1162057 TGTATCGATATATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1162082 TCATATTTCG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1166649 original size:21 final size:21
Alignment explanation
Indices: 1166623--1166665 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1166613 AAATTTTCAC
*
1166623 TCTCTCTCTACACTCTAAAAT
1 TCTCTCACTACACTCTAAAAT
* *
1166644 TCTCTCACTTCTCTCTAAAAT
1 TCTCTCACTACACTCTAAAAT
1166665 T
1 T
1166666 TTATAAATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.33, G:0.00, T:0.42
Consensus pattern (21 bp):
TCTCTCACTACACTCTAAAAT
Found at i:1166979 original size:7 final size:7
Alignment explanation
Indices: 1166967--1167004 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
1166957 AAAATGTTTG
1166967 TATTGAT
1 TATTGAT
1166974 TATTGAT
1 TATTGAT
1166981 TATTGAT
1 TATTGAT
*
1166988 TATTTAT
1 TATTGAT
1166995 T-TTG-T
1 TATTGAT
1167000 TATTG
1 TATTG
1167005 TTTAGGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 2 0.07
6 5 0.18
7 21 0.75
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.63
Consensus pattern (7 bp):
TATTGAT
Found at i:1171846 original size:15 final size:15
Alignment explanation
Indices: 1171828--1171868 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1171818 TGATCCTGTC
*
1171828 CATCCACCACTCGTG
1 CATCCACCACCCGTG
*
1171843 CATCCACAACCCGTG
1 CATCCACCACCCGTG
1171858 CATCCACCACC
1 CATCCACCACC
1171869 TGTTTACTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.24, C:0.51, G:0.10, T:0.15
Consensus pattern (15 bp):
CATCCACCACCCGTG
Found at i:1172021 original size:27 final size:27
Alignment explanation
Indices: 1171968--1172021 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1171958 CATCATATTT
* **
1171968 CCCTACTCAATCTCCATACCCGTCATA
1 CCCTACTCAACCTCCATACCCAACATA
1171995 CCCTACTCAACCTCCATACCCAACATA
1 CCCTACTCAACCTCCATACCCAACATA
1172022 TCTTGCCACG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.30, C:0.46, G:0.02, T:0.22
Consensus pattern (27 bp):
CCCTACTCAACCTCCATACCCAACATA
Found at i:1172955 original size:20 final size:20
Alignment explanation
Indices: 1172926--1172974 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1172916 ATTAGGGTTT
*
1172926 CTTTCATTTGAATGCTTTTG
1 CTTTCTTTTGAATGCTTTTG
1172946 CTTTCTTTTGAATGCTTTTG
1 CTTTCTTTTGAATGCTTTTG
1172966 CTTTCTTTT
1 CTTTCTTTT
1172975 TTTTATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.10, C:0.16, G:0.12, T:0.61
Consensus pattern (20 bp):
CTTTCTTTTGAATGCTTTTG
Found at i:1181374 original size:21 final size:22
Alignment explanation
Indices: 1181345--1181390 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1181335 TGTTCAAACA
** *
1181345 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1181367 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1181388 AGT
1 AGT
1181391 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:1186950 original size:2 final size:2
Alignment explanation
Indices: 1186943--1186971 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1186933 ACTACCTTCA
1186943 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1186972 AATCGTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1189087 original size:20 final size:21
Alignment explanation
Indices: 1189054--1189092 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1189044 TGCAGCTATA
*
1189054 TTTTTCATTATTTGTTATTAT
1 TTTTTCATTATTTGCTATTAT
*
1189075 TTTTTC-TTGTTTGCTATT
1 TTTTTCATTATTTGCTATT
1189093 TGTTTGGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.13, C:0.08, G:0.08, T:0.72
Consensus pattern (21 bp):
TTTTTCATTATTTGCTATTAT
Found at i:1190571 original size:6 final size:7
Alignment explanation
Indices: 1190479--1190569 Score: 87
Period size: 7 Copynumber: 12.9 Consensus size: 7
1190469 TCAAATGAAA
1190479 AAATTTT
1 AAATTTT
1190486 AAATTTT
1 AAATTTT
1190493 AAAATTTT
1 -AAATTTT
**
1190501 AAAATCAT
1 -AAATTTT
1190509 AAATTTT
1 AAATTTT
1190516 AAATTTT
1 AAATTTT
1190523 AAATTTT
1 AAATTTT
1190530 AAATTTT
1 AAATTTT
* *
1190537 AAAATTC
1 AAATTTT
*
1190544 AAA-TGT
1 AAATTTT
*
1190550 AAA-TTA
1 AAATTTT
1190556 AAATTTTT
1 AAA-TTTT
1190564 AAATTT
1 AAATTT
1190570 AACTTAATAG
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
6 8 0.11
7 44 0.63
8 18 0.26
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (7 bp):
AAATTTT
Found at i:1192787 original size:2 final size:2
Alignment explanation
Indices: 1192780--1192811 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1192770 ACAACCTTAA
1192780 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1192812 TGCAAATCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1196046 original size:21 final size:21
Alignment explanation
Indices: 1196000--1196047 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1195990 ATTTAGATGT
* *
1196000 TAAA-TTAAAAAAATTTAATT
1 TAAATTTAAAAAAATTCAATA
*
1196020 TAAATTTAAACAAATTCAATA
1 TAAATTTAAAAAAATTCAATA
*
1196041 TCAATTT
1 TAAATTT
1196048 TGAGTTACTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAAAAAAATTCAATA
Found at i:1197495 original size:46 final size:46
Alignment explanation
Indices: 1197419--1197510 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
1197409 ACACAAGTTC
* *
1197419 ACATAGTCTGTTGCAGAAAATAGACCATGTCTTAGAAACCTTGCAT
1 ACATAGTCCGTTGCAGAAAACAGACCATGTCTTAGAAACCTTGCAT
*
1197465 ACATCGTCCGTTGCAGAAAACAGACCATGTCTTAGAAACCTTGCAT
1 ACATAGTCCGTTGCAGAAAACAGACCATGTCTTAGAAACCTTGCAT
1197511 GAAGCAAAGC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (46 bp):
ACATAGTCCGTTGCAGAAAACAGACCATGTCTTAGAAACCTTGCAT
Found at i:1202652 original size:21 final size:21
Alignment explanation
Indices: 1202626--1202668 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1202616 AAATTTTCAC
*
1202626 TCTCTCTCTACACTCTAAAAT
1 TCTCTCACTACACTCTAAAAT
* *
1202647 TCTCTCACTTCTCTCTAAAAT
1 TCTCTCACTACACTCTAAAAT
1202668 T
1 T
1202669 TTATAAATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.33, G:0.00, T:0.42
Consensus pattern (21 bp):
TCTCTCACTACACTCTAAAAT
Found at i:1202756 original size:26 final size:27
Alignment explanation
Indices: 1202727--1202784 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
1202717 TAATATTTAT
1202727 TTTTTAGCCGTT-AAATTGT-ATTATTA
1 TTTTTAG-CGTTAAAATTGTAATTATTA
* * *
1202753 TTTTTTGTGTTAAAATTTTAATTATTA
1 TTTTTAGCGTTAAAATTGTAATTATTA
1202780 TTTTT
1 TTTTT
1202785 TTAATAGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 3 0.11
26 12 0.44
27 12 0.44
ACGTcount: A:0.26, C:0.03, G:0.09, T:0.62
Consensus pattern (27 bp):
TTTTTAGCGTTAAAATTGTAATTATTA
Found at i:1202927 original size:15 final size:15
Alignment explanation
Indices: 1202907--1202946 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1202897 TATTATGTGG
1202907 AATTAGGTTTA-GCGT
1 AATTA-GTTTAGGCGT
*
1202922 AATTAGTTTAGGGGT
1 AATTAGTTTAGGCGT
1202937 AATTAGTTTA
1 AATTAGTTTA
1202947 AAGCCTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.30, C:0.03, G:0.25, T:0.42
Consensus pattern (15 bp):
AATTAGTTTAGGCGT
Found at i:1207819 original size:15 final size:15
Alignment explanation
Indices: 1207801--1207848 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
1207791 CACTACCGAT
*
1207801 CCTGTCCATCCACCA
1 CCTGTGCATCCACCA
*
1207816 CCTGTGCATCCACAA
1 CCTGTGCATCCACCA
*
1207831 CCCGTGCATCCACCA
1 CCTGTGCATCCACCA
1207846 CCT
1 CCT
1207849 ATTTACCCAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.21, C:0.50, G:0.10, T:0.19
Consensus pattern (15 bp):
CCTGTGCATCCACCA
Found at i:1208305 original size:44 final size:44
Alignment explanation
Indices: 1208256--1208368 Score: 208
Period size: 44 Copynumber: 2.6 Consensus size: 44
1208246 ATTATAATTA
*
1208256 TTGATAGTAGTAATGTGAAATATGCAGATATCTCGAATTAGTTG
1 TTGATAGTAATAATGTGAAATATGCAGATATCTCGAATTAGTTG
*
1208300 TTGATAGTAATAATGTGAAATATGCAGATATCTCGGATTAGTTG
1 TTGATAGTAATAATGTGAAATATGCAGATATCTCGAATTAGTTG
1208344 TTGATAGTAATAATGTGAAATATGC
1 TTGATAGTAATAATGTGAAATATGC
1208369 TGAAATATTT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 67 1.00
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.36
Consensus pattern (44 bp):
TTGATAGTAATAATGTGAAATATGCAGATATCTCGAATTAGTTG
Found at i:1211893 original size:19 final size:19
Alignment explanation
Indices: 1211867--1211908 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1211857 GTTAAAAACT
1211867 TTTA-AAATTTATAAATTA
1 TTTACAAATTTATAAATTA
* *
1211885 TTTACAAATTTATTAGTTA
1 TTTACAAATTTATAAATTA
1211904 TTTAC
1 TTTAC
1211909 TTTTAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTACAAATTTATAAATTA
Found at i:1212111 original size:27 final size:27
Alignment explanation
Indices: 1212055--1212111 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
1212045 AAATTTTATA
* *
1212055 TTAATATTTATATATTATAATTAAATT
1 TTAATATTTATATATTATAAATAAAAT
1212082 TTAATATTT-TA-ATTATTAAATAATAAT
1 TTAATATTTATATATTA-TAAATAA-AAT
1212109 TTA
1 TTA
1212112 GGTGAATGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 4 0.15
26 8 0.31
27 14 0.54
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTAATATTTATATATTATAAATAAAAT
Found at i:1212531 original size:2 final size:2
Alignment explanation
Indices: 1212524--1212563 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1212514 CCGACTAGCC
1212524 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1212564 AACGGTATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1212705 original size:24 final size:24
Alignment explanation
Indices: 1212678--1212728 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
1212668 TTATGTTATA
1212678 ATTAAA-AATATATTTTAATTTTTT
1 ATTAAATAAT-TATTTTAATTTTTT
*
1212702 ATTAAATTAATTATTTTTATTTTTT
1 ATTAAA-TAATTATTTTAATTTTTT
1212727 AT
1 AT
1212729 ATTTAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 6 0.25
25 15 0.62
26 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
ATTAAATAATTATTTTAATTTTTT
Found at i:1212738 original size:25 final size:26
Alignment explanation
Indices: 1212673--1212739 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
1212663 AATCTTTATG
* *
1212673 TTATAATTAAAAATATATTTTAATTT
1 TTATATTTAAAATTATATTTTAATTT
* *
1212699 TT-TATTAAATTAATTAT-TTTTATTTT
1 TTATATTTAA--AATTATATTTTAATTT
1212725 TTATATTTAAAATTA
1 TTATATTTAAAATTA
1212740 AAATAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
25 10 0.30
26 12 0.36
27 11 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TTATATTTAAAATTATATTTTAATTT
Found at i:1214065 original size:63 final size:64
Alignment explanation
Indices: 1213965--1214090 Score: 175
Period size: 63 Copynumber: 2.0 Consensus size: 64
1213955 ATTACCCCAC
* **
1213965 CTGCAACCAATCAACAATAAAATTCAGCTTTGTCGACTACCAACCGAGCTAAACAGTCAGGCAT
1 CTGCAACCAAGCAACAATAAAATTCAGCTTTACCGACTACCAACCGAGCTAAACAGTCAGGCAT
* * *
1214029 CTGCAACCAAGCAA-AATGAAATTCAG-TTTCACCGACTACCAACTGAGCTAAAGAGTCAGGCA
1 CTGCAACCAAGCAACAATAAAATTCAGCTTT-ACCGACTACCAACCGAGCTAAACAGTCAGGCA
1214091 AAATGATTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
62 3 0.05
63 39 0.71
64 13 0.24
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.19
Consensus pattern (64 bp):
CTGCAACCAAGCAACAATAAAATTCAGCTTTACCGACTACCAACCGAGCTAAACAGTCAGGCAT
Found at i:1214532 original size:21 final size:23
Alignment explanation
Indices: 1214495--1214537 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
1214485 ATTTAGTCGA
1214495 TAAATTAATATAAAAATTTAAAT
1 TAAATTAATATAAAAATTTAAAT
1214518 TAAATT-ATA-AAAAATTTAAA
1 TAAATTAATATAAAAATTTAAA
1214538 AAATAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 11 0.55
22 3 0.15
23 6 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
TAAATTAATATAAAAATTTAAAT
Found at i:1217038 original size:24 final size:24
Alignment explanation
Indices: 1217011--1217060 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1217001 TGACTTATAC
1217011 AAATAATAATAAATTGTCACATGT
1 AAATAATAATAAATTGTCACATGT
1217035 AAATAATAATAAATTGTCACATGT
1 AAATAATAATAAATTGTCACATGT
1217059 AA
1 AA
1217061 GGGGATACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (24 bp):
AAATAATAATAAATTGTCACATGT
Found at i:1217742 original size:21 final size:21
Alignment explanation
Indices: 1217703--1217742 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1217693 ATGAATTCAA
*
1217703 AATAAAAATAATGACAATATG
1 AATAAAAATAATGAAAATATG
1217724 AATATAAAATAAT-AAAATA
1 AATA-AAAATAATGAAAATA
1217743 AGACAAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.25
Consensus pattern (21 bp):
AATAAAAATAATGAAAATATG
Found at i:1218143 original size:20 final size:20
Alignment explanation
Indices: 1218118--1218156 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1218108 TGATAGCTCA
*
1218118 AATTTTGGCCTTGAAAAATT
1 AATTTTGGCCTTAAAAAATT
*
1218138 AATTTTGGCTTTAAAAAAT
1 AATTTTGGCCTTAAAAAAT
1218157 GGTTTTTGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (20 bp):
AATTTTGGCCTTAAAAAATT
Found at i:1218442 original size:19 final size:20
Alignment explanation
Indices: 1218410--1218447 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1218400 AAAGTATAAC
1218410 AACTTAAAAAAAAA-AAAAG
1 AACTTAAAAAAAAAGAAAAG
**
1218429 AACTTAAATGAAAAGAAAA
1 AACTTAAAAAAAAAGAAAA
1218448 TGAGATGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.13
Consensus pattern (20 bp):
AACTTAAAAAAAAAGAAAAG
Found at i:1218527 original size:6 final size:6
Alignment explanation
Indices: 1218516--1218558 Score: 50
Period size: 6 Copynumber: 6.7 Consensus size: 6
1218506 ATATAAACTG
*
1218516 CTTTTC CTTTTC CTTTTC CTTTTTC TCTTATTT CTTTTC CTTT
1 CTTTTC CTTTTC CTTTTC C-TTTTC -CTT-TTC CTTTTC CTTT
1218559 GTTTTTTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 19 0.59
7 10 0.31
8 3 0.09
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (6 bp):
CTTTTC
Found at i:1218936 original size:38 final size:38
Alignment explanation
Indices: 1218861--1218935 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 38
1218851 CATGAATGAC
*
1218861 AAAAAATAATCTAATGGTAGCCAACAAGTTTTAAAAAT
1 AAAAAATAATCTAATGATAGCCAACAAGTTTTAAAAAT
* * * *
1218899 AAAAAATTAATCTAATTATTGCCAACATGTTTGAAAA
1 AAAAAA-TAATCTAATGATAGCCAACAAGTTTTAAAA
1218936 TTCAACCTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
38 6 0.19
39 25 0.81
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (38 bp):
AAAAAATAATCTAATGATAGCCAACAAGTTTTAAAAAT
Found at i:1221344 original size:149 final size:146
Alignment explanation
Indices: 1220922--1224762 Score: 1374
Period size: 146 Copynumber: 26.2 Consensus size: 146
1220912 ATATATATTA
* * * * * * *
1220922 AAACTTCTACAAATAGAACTAAATTGTAGCTTTAAAAATTTAAA-TTCATATAATCATA-TCAAA
1 AAACTTTTACAAATAAAAATAAATTATA-CCTTAAAAATTTAAACTT-ATATAATTATACCCAAA
* * * *
1220985 TAAACAAATTTAAACTAT-TATAAATAAAGATAAA-TATTAAC-TTAAAAATTTAAACTCGTATA
64 -AAATAAATTTAAACT-TCTACAAATAAAAATAAATTA-T-ACTTTAAAAATTTAAACTCATATA
* *
1221047 TTCATACTCAAAAAATAAATTT
125 ATCATACCCAAAAAATAAATTT
* * * * *
1221069 AAACTTCTACAAATAAAAATAAATTATACCTTTAAAATTTAAACATGTATAATTTTAAACCCCAA
1 AAACTTTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTTATATAA--TTATA-CCCAA
* ** *
1221134 AATATAAATTT-AACTTCTACAAATAAAAATAAATTATACACTAAAAATTTAAACTCGTATAATC
63 AAAATAAATTTAAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTCATATAATC
* ** *
1221198 ATACCTAAAAAGCAAATAT
128 ATACCCAAAAAATAAATTT
** * * * * *
1221217 AAACTTCCAAAAAGAGAAATAAATTATAGCTTAAAAGATTTAAACTCATATAATTATACCCAAAA
1 AAACTTTTACAAATAAAAATAAATTATACCTTAAAA-ATTTAAACTTATATAATTATACCC-AAA
* * ** * * *
1221282 AAATCAAATGTAAACTACTATGAATAAAAATAAATAATACTTTAAAACTTTAAACTCATATAATT
64 AAAT-AAATTTAAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTCATATAATC
1221347 ATACCCAAAAAATAAATTT
128 ATACCCAAAAAATAAATTT
* * * * * *
1221366 AAACTTTTACAAATAATAATAAATTATACATTCAAAAATTTACACTTGTATAATCCCAAACCCTA
1 AAACTTTTACAAATAAAAATAAATTATACCTT-AAAAATTTAAACTTATATAAT--TATACCC-A
* * * *
1221431 AAAAATAAATTTTAACATCTAC-AATAAAAATAAATTATACTTTAAAAATTTAAACTCCTATTAT
62 AAAAATAAATTTAAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTCATATAAT
* * * *
1221495 TATA-CCTAAAAACAAATAT
127 CATACCCAAAAAATAAATTT
* * * * *
1221514 AAACTTTTACAAATAAAGATAAATAATATCC-TAAAAATTTAAACATGTATAATTA-A-CCTAAA
1 AAACTTTTACAAATAAAAATAAATTATA-CCTTAAAAATTTAAACTTATATAATTATACCCAAAA
* * * * *
1221576 AATAAATTTAAGCTTCTACAAATAAAGATAAATAATA-TCCTAAAAATTTAAA-T-ATGTTTAAT
65 AATAAATTTAAACTTCTACAAATAAAAATAAATTATACT-TTAAAAATTTAAACTCA--TATAAT
1221638 CA-ACCC-AAAAATAAATTT
127 CATACCCAAAAAATAAATTT
* * *
1221656 AAACTTTTATAAATAAAAATAAATTATACCTTAAAAAATTTAAACTTATTTAATTCTAAGCCCAA
1 AAACTTTTACAAATAAAAATAAATTATACCTT-AAAAATTTAAACTTATATAATTAT-A-CCCAA
* * * *
1221721 AAAATAAATTTTAACTTTTACAAATAAAATTAAAGTATAAC-TTAAAAATTTAAACTCATATAAT
63 AAAATAAATTTAAACTTCTACAAATAAAAATAAATTAT-ACTTTAAAAATTTAAACTCATATAAT
* *
1221785 CATACCC-AATAACAAATTT
127 CATACCCAAAAAATAAATTT
* * * * * *
1221804 AAACTTTTACGAATAAACATAAATGATACCCTGAAAATTTAAACTTATATAA-TAAACCCTAAAA
1 AAACTTTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTTATATAATTATACCC-AAAA
* * * *
1221868 AATAAATTTAAACTTCTACAAATAAAAATAAATTATATCATCACAAA-TTAAACTCATATAACCA
65 AATAAATTTAAACTTCTACAAATAAAAATAAATTATA-CTTTAAAAATTTAAACTCATATAATCA
*
1221932 TACCAAAAAAATAAATTT
129 TACCCAAAAAATAAATTT
** * ** **
1221950 AAACTTTTATGAATAAAAATAAATTATACTTTAAAAATTTAAACTTGCATAGCTATACCCAAAAA
1 AAACTTTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTTATATAATTATACCCAAAAA
* * * * * **
1222015 ATAAATTTAAACTTCTACAAATATAGATAAGTTATACTCTAAGAACCTAAACTCATATAATCA-A
66 ATAAATTTAAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTCATATAATCATA
1222079 CCCAAAAAATAAATTT
131 CCCAAAAAATAAATTT
* * * * * *
1222095 AAACTTCTACAAATAAAAATAAATTATACCATCAAAAATTTAAAAATAAAAATAAATTAT--GCA
1 AAACTTTTACAAATAAAAATAAATTATACC-TTAAAAATTT-AAACT-TATAT-AATTATACCCA
*** * * ** * * * *
1222158 ATTGA-AAATTTAAA-TTCATATAATCATATCAAA-AAACCACA-TTTAAAATTTTACAAATAAA
62 AAAAATAAATTTAAACTTC-TACAA--ATA-AAAATAAATTATACTTTAAAAATTTA-AACT-CA
* * **
1222219 AATAAATTATA-CCTTAAAAT--ATTT
121 TAT-AATCATACCCAAAAAATAAATTT
* * * * *
1222243 AAACTCGTTA-AATCATGCTGAAAAACAAATTTAAACTTCTAAAAA--TAAA--TAT-TAAATAA
1 AAACT-TTTACAA--A---T-AAAAATAAA-TTATACCT-TAAAAATTTAAACTTATAT-AATTA
* * * * *
1222302 TA---ACATAA-AAATTTAAACTCATATAATCAAACCAAAAACTAAATTTAAACTTGTACAAAA-
56 TACCCAAAAAATAAATTTAAACT--TCT-A-CAAA-TAAAAA-TAAA-TTATACTT-TA-AAAAT
* ****
1222362 --AAA---ATA-AATTATA--CTTTCAA-AAATTT
112 TTAAACTCATATAATCATACCCAAAAAATAAATTT
* * * * * * *
1222388 AAACTCATATAATCATACTTAGAAAACACATTTAAACTTTTAAAAA-TCAAA---ATA-AATTAT
1 AAACT--T-TTA-CA-A-ATA-AAAATA-AATTATAC-CTTAAAAATTTAAACTTATATAATTAT
* ** ** * * *
1222448 ACTCCAAAAATTTAAATTTGCA-TAAT-CAAGA-AAAAATAAATTTAAAATTCTACAAA--TAAA
57 AC-CCAAAAA-ATAAATTTAAACTTCTACAA-ATAAAAATAAA-TTATACTT-TAAAAATTTAAA
** * * ** *
1222508 -AAATAT-ATTATACTTTCAAAATTTAAACTCAT
117 CTCATATAATCATAC--CCAAAAAATAAA-T-TT
* * * * * * *
1222540 ATAA-TCATTAC--TTACAAATAAATTTATACTTCTACAAAA--AAAAC--AAATAA-TAT-CTT
1 A-AACT-TTTACAAATAAAAATAAA-TTATACCT-TA-AAAATTTAAACTTATATAATTATAC-C
* * * ** * * * * *
1222596 C---AATTAAA-CT-AA-TTTTATGAATAAAAATAAATTATATCATCACAAA-TCAAACTCGTAT
60 CAAAAAATAAATTTAAACTTCTACAAATAAAAATAAATTATA-CTTTAAAAATTTAAACTCATAT
* *
1222654 AATCATACCCAAAAAGTACATTT
124 AATCATACCCAAAAAATAAATTT
* ** ** * *
1222677 AAACTTCTATGAATAAAAATAAATTATACCTTAAAAATTGT-AACTCGTATAACTATACCTAAAA
1 AAACTTTTACAAATAAAAATAAATTATACCTTAAAAATT-TAAACTTATATAATTATACCCAAAA
* * * * * * * *
1222741 AATAAATTTAAACTTCTACGAATATAGATAAGTTATACTCTAAGAACTTAAACTCACATAATCA-
65 AATAAATTTAAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTCATATAATCAT
*
1222805 ACGCAAAAAATAAATTT
130 ACCCAAAAAATAAATTT
* * * * * ** * *
1222822 GAACATTTACAAA-AAAAAT-TA-TATA-ATAAAAAATTTAAACCCATATAATCAAACCC-AAAA
1 AAACTTTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTTATATAATTATACCCAAAAA
** * *
1222882 GCACATTTAAAC-TCTTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTCGTATAA-CTA
66 ATAAATTTAAACTTC-TACAAATAAAAATAAATTATACTTTAAAAATTTAAACTCATATAATC-A
1222945 TACCCAAAAAATAAATTT
129 TACCCAAAAAATAAATTT
* * * * * * * * *
1222963 AAACTTCTACAAATATAGATAAGTTATA-CTCTAAGAACTTAAACTCATATAATCA-ACCTAAAA
1 AAACTTTTACAAATAAAAATAAATTATACCT-TAAAAATTTAAACTTATATAATTATACCCAAAA
* * * * *
1223026 AATAAATTTAAACTTTTACAAATAAAAATAAATTATACCATAAAAAATTCAAACTCATATAATAA
65 AATAAATTTAAACTTCTACAAATAAAAATAAATTATA-CTTTAAAAATTTAAACTCATATAATCA
* *
1223091 TACCC-AAAAACACATTT
129 TACCCAAAAAATAAATTT
* * * * ** * *
1223108 AAACTCTTACAAATAAAAATAAATGATTCAATCGAAAATTTAAA-TTCATACAATCATA-CCAAA
1 AAACTTTTACAAATAAAAATAAATTATAC-CTTAAAAATTTAAACTT-ATATAATTATACCCAAA
* * * * * *
1223171 AAATTATATTTAAACTTCTATAAATAAAAATAAATCATACCTTAAAAATTTAAATTCGT-TAAAT
64 AAA-TAAATTTAAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTCATAT-AAT
* * *
1223235 CAT--GCTAAAAACAAATTT
127 CATACCCAAAAAATAAATTT
* * * * * * * * *
1223253 AAACTTCTAAAAATATAGATAAATAATAACC-TAAAAATTTAAACTCATATAATCA-AACTAAAA
1 AAACTTTTACAAATAAAAATAAATTAT-ACCTTAAAAATTTAAACTTATATAATTATACCCAAAA
* *
1223316 AATAAATTTAAACTTGTACAAATAAAAATAAATTATACATTTAAAAATTTAAACTTATATAATCA
65 AATAAATTTAAACTTCTACAAATAAAAATAAATTATAC-TTTAAAAATTTAAACTCATATAATCA
** * *
1223381 TACTTAAAAAACACATTT
129 TACCCAAAAAATAAATTT
* * ** * **
1223399 AAACTTTTAAAAATCAAAATAAATTATA-CTCTAAAAATTTAAA-TTCGCATAATCA-A--GTAA
1 AAACTTTTACAAATAAAAATAAATTATACCT-TAAAAATTTAAACTT-ATATAATTATACCCAAA
* * * * *
1223459 AAATAAATTTAAACTTTTATAAATAAAAA-AATATTATACCTTCAAAATTTAAACTCGTATAATC
64 AAATAAATTTAAACTTCTACAAATAAAAATAA-ATTATACTTTAAAAATTTAAACTCATATAATC
** *
1223523 ATTA-CTTATAAATAAATTT
128 A-TACCCAAAAAATAAATTT
* * * * *
1223542 ATACTTCTACAAATAAAAATAAATAATACCTT--CAA-TTAAAC-TA-AT-TTTATGA---ATAA
1 AAACTTTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTTATATAATTAT-ACCCA-AA
* * * * ** *
1223598 AAATAAA-TTATACTT-TAAAAATTTAAACTCCTATTAT-CGTACCTAAAAATAAATATAAACTT
64 AAATAAATTTAAACTTCTACAAA-TAAAAAT-AAATTATAC-T--TTAAAAAT---T-TAAAC-T
* *
1223660 C-TACAA--ATA---AAGATAAATAATATCCT
119 CATATAATCATACCCAA-A-AAATAA-AT-TT
** * * ** * * * ** ** * *
1223686 AAAAATTTA-AATATGTATAATAAACCAAAAACAATTTAAGCTTCTACAAACAAAGATAAATAAT
1 AAACTTTTACAA-AT-AAAAATAAA--TTATAC-CTTAAAAATT-T--AAACTTATAT-AATTAT
* * * ** ** * * *
1223750 ACCCTAAAAATTTAAATATATA-TAAT-CAACCCAAAAACAAATTTAAACTTTTATAAA--TAAA
57 ACCC-AAAAA-ATAAATTTAAACTTCTACAA-ATAAAAATAAA-TTATAC-TTTAAAAATTTAAA
* * * * **
1223811 --AATA-AATTACATCTTAAAAAT---TTT
117 CTCATATAATCATACCCAAAAAATAAATTT
* * * * * *
1223835 AAACTTATTTAATTCTAAACCCAAAAAATAAATTTTAACTTTTACAAA--TAAA--AATA-AAAT
1 AAAC-T-TTT-A--C-AAA---TAAAAATAAATTAT-AC-CTTAAAAATTTAAACTTATATAATT
* **
1223895 ATACCCTAAAAATTTAAACTCGTATAATCATACCTAATAACAAATTTAAACTTATGCGAACATAA
55 ATACCC-AAAAA-ATAAA-T--T-T-A--A-A-CTTCT-ACAAA--T--A---A----AA-ATAA
* * * * *
1223960 ATGATACCTTGAAAATTTAAACTTATATAAT-AAACCCTAAAAAATAAATTT
96 ATTATACTTTAAAAATTTAAACTCATATAATCATACCC-AAAAAATAAATTT
* * * * * * * *
1224011 AAACTTCTATAAACAAAAATAAATTATATCATTACAAA-TTAAACTCATATAATCATACCAAAAA
1 AAACTTTTACAAATAAAAATAAATTATA-CCTTAAAAATTTAAACTTATATAATTATACCCAAAA
* * ** * *
1224075 AATACATTTAAACTTTTATGAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAA-CTA
65 AATAAATTTAAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTCATATAATC-A
1224139 TACCCAAAAAATAAATTT
129 TACCCAAAAAATAAATTT
* * * * * ** * *
1224157 AAACTTCTATAAA-AATAGATAAGTTATA-CTCTAAGAACCTAAACTCATATAATCA-ACCCAAA
1 AAACTTTTACAAATAA-AAATAAATTATACCT-TAAAAATTTAAACTTATATAATTATACCCAAA
* * *
1224219 AAATAAATTTAAACTTCTACAAATAAAAATAAATTATACTATCAAAAATGTAAACTCATATAACC
64 AAATAAATTTAAACTTCTACAAATAAAAATAAATTATACT-TTAAAAATTTAAACTCATATAATC
*
1224284 ATACCTAAAAACAT--ATTT
128 ATACCCAAAAA-ATAAATTT
* * * ** *
1224302 AAACTCTTACAAATAAAAATAAATTATGCAATCGAAAATTTAAA-TTCATATAATCATA-CCAAA
1 AAACTTTTACAAATAAAAATAAATTATAC-CTTAAAAATTTAAACTT-ATATAATTATACCCAAA
* * * *
1224365 AAATCATATTTAAACTTCTACAAATAAAAATAAATTATACCTTAAAAATTTAAATTCGT-TAAAT
64 AAAT-AAATTTAAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTCATAT-AAT
* **
1224429 CAT-GCTGAAAAATAAATTT
127 CATACCCAAAAAATAAATTT
* * * * * * * *
1224448 AAACTTCTAAAAATAAAGATAAATAATAACC-TAAAAATTTAAACTCATATAATCA-AACTAAAA
1 AAACTTTTACAAATAAAAATAAATTAT-ACCTTAAAAATTTAAACTTATATAATTATACCCAAAA
* * * *
1224511 AATAAATTTAAACTTGTATAATTAAAAATAAATTATACCTTCAAAAATTTAAACTCATATAATCA
65 AATAAATTTAAACTTCTACAAATAAAAATAAATTATA-CTTTAAAAATTTAAACTCATATAATCA
** *
1224576 TACTTAAAAAATACATTT
129 TACCCAAAAAATAAATTT
* ** * *
1224594 AAACTTTTAAAAATCAAAAATAAATTATA-CTCTAAAAATTTAAA-TTCGCATAATCA-A--GAA
1 AAACTTTTACAAAT-AAAAATAAATTATACCT-TAAAAATTTAAACTT-ATATAATTATACCCAA
* * * * * * *
1224654 AAAATAAATTTAAACTTATACAAATAAAAAATATATTATGCCTTCAAAACTTAAACTCGTATAAT
63 AAAATAAATTTAAACTTCTACAAAT-AAAAATAAATTATACTTTAAAAATTTAAACTCATATAAT
** *
1224719 CAATA-CTTACAAATAAATTT
127 C-ATACCCAAAAAATAAATTT
* **
1224739 ATACTTCAACAAATAAAAATAAAT
1 AAACTTTTACAAATAAAAATAAAT
1224763 AATATCTTTA
Statistics
Matches: 2794, Mismatches: 609, Indels: 585
0.70 0.15 0.15
Matches are distributed among these distances:
135 4 0.00
136 6 0.00
137 20 0.01
138 37 0.01
139 45 0.02
140 69 0.02
141 66 0.02
142 77 0.03
143 178 0.06
144 188 0.07
145 517 0.19
146 565 0.20
147 307 0.11
148 210 0.08
149 195 0.07
150 42 0.02
151 39 0.01
152 14 0.01
153 9 0.00
154 24 0.01
155 17 0.01
156 11 0.00
157 12 0.00
158 6 0.00
159 6 0.00
160 11 0.00
161 15 0.01
162 8 0.00
163 1 0.00
164 1 0.00
165 2 0.00
166 8 0.00
167 18 0.01
168 8 0.00
169 14 0.01
170 18 0.01
172 6 0.00
173 10 0.00
174 2 0.00
175 1 0.00
176 7 0.00
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.31
Consensus pattern (146 bp):
AAACTTTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTTATATAATTATACCCAAAAA
ATAAATTTAAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTCATATAATCATA
CCCAAAAAATAAATTT
Found at i:1221749 original size:290 final size:287
Alignment explanation
Indices: 1220922--1222138 Score: 1211
Period size: 290 Copynumber: 4.1 Consensus size: 287
1220912 ATATATATTA
* * * * * * *
1220922 AAACTTCTACAAATAGAACTAAATTGTAGCTTTAAAAATTTAAATTCATATAATCATA-TCAAAT
1 AAACTTCTACAAATA-AAATAAATTATA-C-CTAAAAATTTAAACT-ATATAATTA-ACCCTAA-
* * * * * * *
1220986 AAACAAATTTAAACTAT-TATAAATAAAGATAAATATTAACTTAAAAATTTAAACTCGTATATTC
60 AAATAAATTTAAACT-TCTACAAATAAAAATAAATAATATCTTAAAAATTTAAACTCATATAATC
* * *
1221050 ATACTCAAAAAATAAATTTAAACTTCTACAAATAAAAATAAATTATACCTTTAAAATTTAAACAT
124 ATAC-CAAAAAATAAATTTAAACTTTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTT
* * *
1221115 GTATAATTTTAAACCCCAAAATATAAA-TTTAACTTCTACAAATAAAAATAAATTATACACTAAA
188 GTATAATTCT-AA-CCCAAAAAATAAATTTTAACTTCTACAAATAAAAATAAATTATACTCTAAA
*
1221179 AATTTAAACTCGTATAATCATACCTAAAAAGCAAATAT
251 AATTTAAACTCATATAATCATACCTAAAAA-CAAATAT
* * * * *
1221217 AAACTTCCAAAAAGAGAAATAAATTATAGCTTAAAAGATTTAAACTCATATAATTATACCCAAAA
1 AAACTTCTACAAATA-AAATAAATTATA-CCTAAAA-ATTTAAACT-ATATAATTA-ACCC-TAA
* * ** *
1221282 AAATCAAATGTAAACTACTATGAATAAAAATAAATAATA-CTTTAAAACTTTAAACTCATATAAT
60 AAAT-AAATTTAAACTTCTACAAATAAAAATAAATAATATC-TTAAAAATTTAAACTCATATAAT
* * * *
1221346 TATACCCAAAAAATAAATTTAAACTTTTACAAATAATAATAAATTATACATTCAAAAATTTACAC
123 CATA-CCAAAAAATAAATTTAAACTTTTACAAATAAAAATAAATTATACCTT-AAAAATTTAAAC
* * * *
1221411 TTGTATAATCCCAAACCCTAAAAAATAAATTTTAACATCTAC-AATAAAAATAAATTATACTTTA
186 TTGTATAAT-TCTAACCC-AAAAAATAAATTTTAACTTCTACAAATAAAAATAAATTATACTCTA
* * *
1221475 AAAATTTAAACTCCTATTATTATACCTAAAAACAAATAT
249 AAAATTTAAACTCATATAATCATACCTAAAAACAAATAT
* * *
1221514 AAACTTTTACAAATAAAGATAAATAATATCCTAAAAATTTAAACATGTATAATTAA-CCTAAAAA
1 AAACTTCTACAAATAAA-ATAAATTATA-CCTAAAAATTTAAAC-TATATAATTAACCCTAAAAA
* * * *
1221578 TAAATTTAAGCTTCTACAAATAAAGATAAATAATATCCTAAAAATTTAAA-T-ATGTTTAATCA-
63 TAAATTTAAACTTCTACAAATAAAAATAAATAATATCTTAAAAATTTAAACTCA--TATAATCAT
* * *
1221640 ACCCAAAAATAAATTTAAACTTTTATAAATAAAAATAAATTATACCTTAAAAAATTTAAACTTAT
126 ACCAAAAAATAAATTTAAACTTTTACAAATAAAAATAAATTATACCTT-AAAAATTTAAACTTGT
* * * *
1221705 TTAATTCTAAGCCCAAAAAATAAATTTTAACTTTTACAAATAAAATTAAAGTATAACT-TAAAAA
190 ATAATTCTAA-CCCAAAAAATAAATTTTAACTTCTACAAATAAAAATAAATTAT-ACTCTAAAAA
* * *
1221769 TTTAAACTCATATAATCATACCCAATAACAAATTT
253 TTTAAACTCATATAATCATACCTAAAAACAAATAT
* * * * *
1221804 AAACTTTTACGAATAAACATAAATGATACCCTGAAAATTTAAACTTATATAATAAACCCTAAAAA
1 AAACTTCTACAAATAAA-ATAAATTATA-CCTAAAAATTTAAAC-TATATAATTAACCCT-AAAA
* * * *
1221869 ATAAATTTAAACTTCTACAAATAAAAATAAATTATATCATCACAAA-TTAAACTCATATAACCAT
62 ATAAATTTAAACTTCTACAAATAAAAATAAATAATATC-TTAAAAATTTAAACTCATATAATCAT
** * *
1221933 ACCAAAAAAATAAATTTAAACTTTTATGAATAAAAATAAATTATACTTTAAAAATTTAAACTTGC
126 ACC-AAAAAATAAATTTAAACTTTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTTGT
* * * * * * *
1221998 AT-A-GCTATACCCAAAAAATAAATTTAAACTTCTACAAATATAGATAAGTTATACTCTAAGAAC
190 ATAATTCTA-ACCCAAAAAATAAATTTTAACTTCTACAAATAAAAATAAATTATACTCTAAAAAT
* * * *
1222061 CTAAACTCATATAATCA-ACCCAAAAAATAAATTT
254 TTAAACTCATATAATCATA-CCTAAAAACAAATAT
1222095 AAACTTCTACAAATAAAAATAAATTATACCATCAAAAATTTAAA
1 AAACTTCTACAAAT-AAAATAAATTATACC-T-AAAAATTTAAA
1222139 AATAAAAATA
Statistics
Matches: 777, Mismatches: 113, Indels: 67
0.81 0.12 0.07
Matches are distributed among these distances:
289 24 0.03
290 168 0.22
291 102 0.13
292 110 0.14
293 30 0.04
294 51 0.07
295 45 0.06
296 23 0.03
297 134 0.17
298 79 0.10
299 11 0.01
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.31
Consensus pattern (287 bp):
AAACTTCTACAAATAAAATAAATTATACCTAAAAATTTAAACTATATAATTAACCCTAAAAATAA
ATTTAAACTTCTACAAATAAAAATAAATAATATCTTAAAAATTTAAACTCATATAATCATACCAA
AAAATAAATTTAAACTTTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTTGTATAATT
CTAACCCAAAAAATAAATTTTAACTTCTACAAATAAAAATAAATTATACTCTAAAAATTTAAACT
CATATAATCATACCTAAAAACAAATAT
Found at i:1221919 original size:73 final size:72
Alignment explanation
Indices: 1220922--1223570 Score: 971
Period size: 73 Copynumber: 36.4 Consensus size: 72
1220912 ATATATATTA
* * * * *
1220922 AAACTTCTACAAATAGAACTAAATTGTAGCTTTAAAAATTTAAA-TTCATATAATCATA-TCAAA
1 AAACTTCTACAAATAAAAATAAATTATA-CTTTAAAAATTTAAACTT-ATATAAT-AAACCCAAA
*
1220985 TAAACAAATTT
63 -AAATAAATTT
* * ** * * *
1220996 AAACTAT-TATAAATAAAGATAAA-TATTAAC-TTAAAAATTTAAACTCGTATATTCATACTCAA
1 AAACT-TCTACAAATAAAAATAAATTA-T-ACTTTAAAAATTTAAACTTATATAAT-AAACCCAA
1221058 AAAATAAATTT
62 AAAATAAATTT
**
1221069 AAACTTCTACAAATAAAAATAAATTATACCTTT-AAAATTTAAACATGTATAATTTTAAACCCCA
1 AAACTTCTACAAATAAAAATAAATTATA-CTTTAAAAATTTAAAC-T-TAT-ATAATAAA-CCCA
*
1221133 AAATATAAATTT
61 AAAAATAAATTT
** ** * *
1221145 -AACTTCTACAAATAAAAATAAATTATACACTAAAAATTTAAACTCGTATAATCATACCTAAAAA
1 AAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTTATATAAT-AAACCCAAAAA
** *
1221209 GCAAATAT
65 ATAAATTT
* * * * * *
1221217 AAACTTCCAAAAAGAGAAATAAATTATAGC-TTAAAAGATTTAAACTCATATAATTATACCCAAA
1 AAACTTCTACAAATAAAAATAAATTATA-CTTTAAAA-ATTTAAACTTATATAA-TAAACCC-AA
*
1221281 AAAATCAAATGT
62 AAAAT-AAATTT
* ** * * * *
1221293 AAACTACTATGAATAAAAATAAATAATACTTTAAAACTTTAAACTCATATAATTATACCCAAAAA
1 AAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTTATATAA-TAAACCCAAAAA
1221358 ATAAATTT
65 ATAAATTT
* * * * *
1221366 AAACTTTTACAAATAATAATAAATTATACATTCAAAAATTTACACTTGTATAATCCCAAACCCTA
1 AAACTTCTACAAATAAAAATAAATTATAC-TTTAAAAATTTAAACTTATATAAT---AAACCC-A
1221431 AAAAATAAATTT
61 AAAAATAAATTT
* * * * *
1221443 TAACATCTAC-AATAAAAATAAATTATACTTTAAAAATTTAAACTCCTAT-TATTATA-CCTAAA
1 AAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACT--TATATAATAAACCCAAAA
* *
1221505 AACAAATAT
64 AATAAATTT
* * * * * * * *
1221514 AAACTTTTACAAATAAAGATAAATAATA-TCCTAAAAATTTAAACATGTATAATTAA-CCTAAAA
1 AAACTTCTACAAATAAAAATAAATTATACT-TTAAAAATTTAAACTTATATAATAAACCCAAAAA
1221577 ATAAATTT
65 ATAAATTT
* * * * * * *
1221585 AAGCTTCTACAAATAAAGATAAATAATA-TCCTAAAAATTTAAA-TATGTTTAATCAACCC-AAA
1 AAACTTCTACAAATAAAAATAAATTATACT-TTAAAAATTTAAACT-TATATAATAAACCCAAAA
1221647 AATAAATTT
64 AATAAATTT
* * * * *
1221656 AAACTTTTATAAATAAAAATAAATTATACCTTAAAAAATTTAAACTTATTTAATTCTAAGCCCAA
1 AAACTTCTACAAATAAAAATAAATTATA-CTTTAAAAATTTAAACTTATATAA---TAAACCCAA
1221721 AAAATAAATTT
62 AAAATAAATTT
* * * * * * *
1221732 TAACTTTTACAAATAAAATTAAAGTATAAC-TTAAAAATTTAAACTCATATAATCATACCC-AAT
1 AAACTTCTACAAATAAAAATAAATTAT-ACTTTAAAAATTTAAACTTATATAAT-AAACCCAAAA
*
1221795 AACAAATTT
64 AATAAATTT
* * * * ** *
1221804 AAACTTTTACGAATAAACATAAATGATACCCTGAAAATTTAAACTTATATAATAAACCCTAAAAA
1 AAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTTATATAATAAACCC-AAAAA
1221869 ATAAATTT
65 ATAAATTT
* * * * * * *
1221877 AAACTTCTACAAATAAAAATAAATTATATCATCACAAA-TTAAACTCATATAACCATACCAAAAA
1 AAACTTCTACAAATAAAAATAAATTATA-CTTTAAAAATTTAAACTTATATAA-TAAACCCAAAA
1221941 AATAAATTT
64 AATAAATTT
* ** ** * *
1221950 AAACTTTTATGAATAAAAATAAATTATACTTTAAAAATTTAAACTTGCATAGCTATACCCAAAAA
1 AAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTTATATA-ATAAACCCAAAAA
1222015 ATAAATTT
65 ATAAATTT
* * * * * ** * *
1222023 AAACTTCTACAAATATAGATAAGTTATACTCTAAGAACCTAAACTCATATAATCAACCCAAAAAA
1 AAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTTATATAATAAACCCAAAAAA
1222088 TAAATTT
66 TAAATTT
* * ** * ** **
1222095 AAACTTCTACAAATAAAAATAAATTATACCATCAAAAATTTAAAAATA-AAAATAAA-TTATGCA
1 AAACTTCTACAAATAAAAATAAATTATA-CTTTAAAAATTTAAACTTATATAATAAACCCA-AAA
*
1222158 ATTGAAAATTT
64 AAT--AAATTT
* * ** * * * * * *
1222169 AAA-TTCATATAATCATATCAAA-AAACCACA-TTTAAAATTTTACAAATAAAAATAAATTATA-
1 AAACTTC-TACAA--ATA-AAAATAAATTATACTTTAAAAATTTA-AACT-TATAT-AA-TAAAC
**
1222230 CCTTAAAAT--ATTT
58 CCAAAAAATAAATTT
* * * *
1222243 AAAC-TCGTTA-AATCATGCTGAAAAACAAATTTAAACTTCTAAAAA--TAAATATTAAATAAT-
1 AAACTTC--TACAA--A---T-AAAAATAAA-TTATACTT-TAAAAATTTAAA-CTTATATAATA
*
1222303 AA--C--ATAA-AAATTT
55 AACCCAAAAAATAAATTT
* * * * * * **
1222316 AAACTCATATAATCAAACCAAAAACTAAATTTAAACTTGTACAAAA---AAA-ATAAATTATACT
1 AAACT--TCT-A-CAAA-TAAAAA-TAAA-TTATACTT-TA-AAAATTTAAACTTATATAATAAA
** * *
1222377 TTCAAAAATTTAAACTCAT
57 CCCAAAAA-ATAAA-T-TT
* * * * * *
1222396 ATAA--TCATAC--TTAGAAAACACATTTAAACTTTTAAAAA-TCAAA---ATA-AATTATACTC
1 A-AACTTC-TACAAATA-AAAATA-AATTATAC-TTTAAAAATTTAAACTTATATAA-TAAAC-C
*
1222452 CAAAAATTTAAATTT
59 CAAAAA-ATAAATTT
** ** * * * * ** * ****
1222467 GCA-TAAT-CAAGA-AAAAATAAATTTAAAATTCTACAAA-TAAAAAATATATTATACTTTCAAA
1 AAACTTCTACAA-ATAAAAATAAA-TTATACTT-TAAAAATTTAAACTTATATAATAAACCCAAA
**
1222528 ATTTAAACTCATAT
63 AAATAAA-T--T-T
* * * * * * * *
1222542 AATCAT-TAC--TTACAAATAAATTTATACTTCTACAAAA--AAAAC--AAATAAT-ATCTTC--
1 AAACTTCTACAAATAAAAATAAA-TTATACTT-TA-AAAATTTAAACTTATATAATAAAC-CCAA
* *
1222597 -AATTAAA-CT
62 AAAATAAATTT
* ** * * * * ** *
1222606 -AA-TTTTATGAATAAAAATAAATTATATCATCACAAA-TCAAACTCGTATAATCATACCCAAAA
1 AAACTTCTACAAATAAAAATAAATTATA-CTTTAAAAATTTAAACTTATATAAT-AAACCCAAAA
* *
1222668 AGTACATTT
64 AATAAATTT
** * ** * *
1222677 AAACTTCTATGAATAAAAATAAATTATACCTTAAAAATTGT-AACTCGTATAACTATACCTAAAA
1 AAACTTCTACAAATAAAAATAAATTATACTTTAAAAATT-TAAACTTATATAA-TAAACCCAAAA
1222741 AATAAATTT
64 AATAAATTT
* * * * * * * * * * *
1222750 AAACTTCTACGAATATAGATAAGTTATACTCTAAGAACTTAAACTCACATAATCAACGCAAAAAA
1 AAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTTATATAATAAACCCAAAAAA
1222815 TAAATTT
66 TAAATTT
* * * * **
1222822 GAACATT-TACAAA-AAAAAT-TA-TATA-ATAAAAAATTTAAACCCATATAATCAAACCC-AAA
1 AAAC-TTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTTATATAAT-AAACCCAAAA
** *
1222881 AGCACATTT
64 AATAAATTT
** *
1222890 AAAC-TCTTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTCGTATAACTATACCCAAAA
1 AAACTTC-TACAAATAAAAATAAATTATACTTTAAAAATTTAAACTTATATAA-TAAACCCAAAA
1222954 AATAAATTT
64 AATAAATTT
* * * * * * * * *
1222963 AAACTTCTACAAATATAGATAAGTTATACTCTAAGAACTTAAACTCATATAATCAACCTAAAAAA
1 AAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTTATATAATAAACCCAAAAAA
1223028 TAAATTT
66 TAAATTT
* * * * *
1223035 AAACTTTTACAAATAAAAATAAATTATACCATAAAAAATTCAAACTCATATAATAATACCC-AAA
1 AAACTTCTACAAATAAAAATAAATTATA-CTTTAAAAATTTAAACTTATATAATAA-ACCCAAAA
* *
1223099 AACACATTT
64 AATAAATTT
* * * ** * *
1223108 AAAC-TCTTACAAATAAAAATAAATGATTCAATCGAAAATTTAAA-TTCATACAATCATA-CCAA
1 AAACTTC-TACAAATAAAAATAAATTATAC-TTTAAAAATTTAAACTT-ATATAAT-AAACCCAA
*
1223170 AAAATTATATTT
62 AAAA-TAAATTT
* * * * * ** *
1223182 AAACTTCTATAAATAAAAATAAATCATACCTTAAAAATTTAAA-TTCGT-TAA-ATCATGCTAAA
1 AAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTT-ATATAATA-AACCCAAAA
*
1223244 AACAAATTT
64 AATAAATTT
* * * * * * *
1223253 AAACTTCTAAAAATATAGATAAATAATAAC-CTAAAAATTTAAACTCATATAATCAAA-CTAAAA
1 AAACTTCTACAAATAAAAATAAATTAT-ACTTTAAAAATTTAAACTTATATAAT-AAACCCAAAA
1223316 AATAAATTT
64 AATAAATTT
* * **
1223325 AAACTTGTACAAATAAAAATAAATTATACATTTAAAAATTTAAACTTATATAATCATACTTAAAA
1 AAACTTCTACAAATAAAAATAAATTATAC-TTTAAAAATTTAAACTTATATAAT-AAACCCAAAA
* *
1223390 AACACATTT
64 AATAAATTT
* * * * ** * **
1223399 AAACTTTTAAAAATCAAAATAAATTATACTCTAAAAATTTAAA-TTCGCATAATCAA--GTAAAA
1 AAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTT-ATATAATAAACCCAAAAA
1223461 ATAAATTT
65 ATAAATTT
* * * * ** * ** *
1223469 AAACTTTTATAAATAAAAA-AATATTATACCTTCAAAATTTAAACTCGTATAATCATTA-CTTAT
1 AAACTTCTACAAATAAAAATAA-ATTATACTTTAAAAATTTAAACTTATATAAT-A-AACCCAAA
1223532 AAATAAATTT
63 AAATAAATTT
* *
1223542 ATACTTCTACAAATAAAAATAAATAATAC
1 AAACTTCTACAAATAAAAATAAATTATAC
1223571 CTTCAATTAA
Statistics
Matches: 1967, Mismatches: 431, Indels: 355
0.71 0.16 0.13
Matches are distributed among these distances:
62 1 0.00
63 6 0.00
64 11 0.01
65 11 0.01
66 6 0.00
67 1 0.00
68 36 0.02
69 26 0.01
70 81 0.04
71 198 0.10
72 359 0.18
73 662 0.34
74 240 0.12
75 126 0.06
76 126 0.06
77 37 0.02
78 19 0.01
79 10 0.01
80 4 0.00
81 7 0.00
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.31
Consensus pattern (72 bp):
AAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTTATATAATAAACCCAAAAAA
TAAATTT
Found at i:1222166 original size:33 final size:33
Alignment explanation
Indices: 1222105--1222171 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1222095 AAACTTCTAC
*
1222105 AAATAAAAATAAATTATACCATCAAAAATTTAA
1 AAATAAAAATAAATTATACAATCAAAAATTTAA
* **
1222138 AAATAAAAATAAATTATGCAATTGAAAATTTAA
1 AAATAAAAATAAATTATACAATCAAAAATTTAA
1222171 A
1 A
1222172 TTCATATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.28
Consensus pattern (33 bp):
AAATAAAAATAAATTATACAATCAAAAATTTAA
Found at i:1222171 original size:146 final size:146
Alignment explanation
Indices: 1220922--1222151 Score: 618
Period size: 148 Copynumber: 8.4 Consensus size: 146
1220912 ATATATATTA
* * * * * * * * *
1220922 AAACTTCTACAAATAGAACTAAATTGTAGCTTTAAAAATTTAAATTCATAT-AATCATA-TCAAA
1 AAACTTCTACAAATAAAAATAAATTATA-CATCAAAAATTTAAAATAAAATAAAT-ATACCCAAA
* * * * * * *
1220985 TAAACAAATTTAAACTAT-TATAAATAAAGATAAA-TATTAACTTAA-AAATTTAAACTCGTATA
64 -AAATAAATTTAAACT-TCTACAAATAAAAATAAATTA-TATCATAACAAA-CTAAACTCATATA
**
1221047 TTCATACTC-AAAAAATAAATTT
125 ACCATAC-CAAAAAAATAAATTT
* ** * ** *
1221069 AAACTTCTACAAATAAAAATAAATTATACCTTTAAAATTTAAACATGTATAAT-TTTAAACCCCA
1 AAACTTCTACAAATAAAAATAAATTATACATCAAAAATTTAAA-A--TAAAATAAATATA-CCCA
* * *
1221133 AAATATAAATTT-AACTTCTACAAATAAAAATAAATTATA-CACTAA-AAATTTAAACTCGTATA
62 AAAAATAAATTTAAACTTCTACAAATAAAAATAAATTATATCA-TAACAAA-CTAAACTCATATA
* * ** *
1221195 ATCATACCTAAAAAGCAAATAT
125 ACCATACCAAAAAAATAAATTT
* * * * * * * * *
1221217 AAACTTCCAAAAAGAGAAATAAATTATAGC-TTAAAAGATTTAAACTCATATAATTATACCCAAA
1 AAACTTCTACAAATAAAAATAAATTATA-CATCAAAA-ATTTAAAATAAAATAAATATACCC-AA
* * ** * * *
1221281 AAAATCAAATGTAAACTACTATGAATAAAAATAAATAATA-CTTTA-AAACTTTAAACTCATATA
63 AAAAT-AAATTTAAACTTCTACAAATAAAAATAAATTATATCATAACAAAC--TAAACTCATATA
** *
1221344 ATTATACCCAAAAAATAAATTT
125 ACCATACCAAAAAAATAAATTT
* * * * *** *
1221366 AAACTTTTACAAATAATAATAAATTATACATTCAAAAATTTACACTTGTAT-AATCCCAAACCCT
1 AAACTTCTACAAATAAAAATAAATTATACA-TCAAAAATTTAAAATAAAATAAAT---ATACCC-
* * * * *
1221430 AAAAAATAAATTTTAACATCTAC-AATAAAAATAAATTATA-CTTTAA-AAATTTAAACTCCTAT
61 AAAAAATAAATTTAAACTTCTACAAATAAAAATAAATTATATC-ATAACAAA-CTAAACTCATAT
* ** * * *
1221492 TATTATACC-TAAAAACAAATAT
124 AACCATACCAAAAAAATAAATTT
* * * * ** * *
1221514 AAACTTTTACAAATAAAGATAAATAATATCCT-AAAAATTTAAACAT-GTAT-AAT-TAACCTAA
1 AAACTTCTACAAATAAAAATAAATTATA-CATCAAAAATTTAAA-ATAAAATAAATATACCCAAA
* * * * * *
1221575 AAATAAATTTAAGCTTCTACAAATAAAGATAAATAATATCCTAA-AAATTTAAA-T-ATGTTTAA
64 AAATAAATTTAAACTTCTACAAATAAAAATAAATTATATCATAACAAA-CTAAACTCA--TATAA
* *
1221637 TCA-ACC-CAAAAATAAATTT
126 CCATACCAAAAAAATAAATTT
* * * * * * ** * *
1221656 AAACTTTTATAAATAAAAATAAATTATACCTTAAAAAATTTAAACTTATTTAATTCTAAGCCCAA
1 AAACTTCTACAAATAAAAATAAATTATA-CATCAAAAATTTAAAATAAAATAAATAT-A-CCCAA
* * * * * * * *
1221721 AAAATAAATTTTAACTTTTACAAATAAAATTAAAGTATAACTTAA-AAATTTAAACTCATATAAT
63 AAAATAAATTTAAACTTCTACAAATAAAAATAAATTATATCATAACAAA-CTAAACTCATATAAC
* * *
1221785 CATACC-CAATAACAAATTT
127 CATACCAAAAAAATAAATTT
* * * * * * * * * *
1221804 AAACTTTTACGAATAAACATAAATGATAC-CCTGAAAATTTAAACTTATAT-AATAAACCCTAAA
1 AAACTTCTACAAATAAAAATAAATTATACATC-AAAAATTTAAAATAAAATAAATATACCC-AAA
* *
1221867 AAATAAATTTAAACTTCTACAAATAAAAATAAATTATATCATCACAAATTAAACTCATATAACCA
64 AAATAAATTTAAACTTCTACAAATAAAAATAAATTATATCATAACAAACTAAACTCATATAACCA
1221932 TACCAAAAAAATAAATTT
129 TACCAAAAAAATAAATTT
* ** * * * *** **
1221950 AAACTTTTATGAATAAAAATAAATTATACTTTAAAAATTTAAACTTGCATAGCTATACCCAAAAA
1 AAACTTCTACAAATAAAAATAAATTATACATCAAAAATTTAAAATAAAATAAATATACCCAAAAA
* * * * * *
1222015 ATAAATTTAAACTTCTACAAATATAGATAAGTTATACTC-TAAGAACCTAAACTCATATAATCA-
66 ATAAATTTAAACTTCTACAAATAAAAATAAATTATA-TCATAACAAACTAAACTCATATAACCAT
*
1222078 ACCCAAAAAATAAATTT
130 ACCAAAAAAATAAATTT
1222095 AAACTTCTACAAATAAAAATAAATTATACCATCAAAAATTTAAAAATAAAAATAAAT
1 AAACTTCTACAAATAAAAATAAATTATA-CATCAAAAATTT-AAAAT-AAAATAAAT
1222152 TATGCAATTG
Statistics
Matches: 862, Mismatches: 172, Indels: 97
0.76 0.15 0.09
Matches are distributed among these distances:
142 61 0.07
143 48 0.06
144 6 0.01
145 103 0.12
146 143 0.17
147 139 0.16
148 180 0.21
149 144 0.17
150 26 0.03
151 12 0.01
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.31
Consensus pattern (146 bp):
AAACTTCTACAAATAAAAATAAATTATACATCAAAAATTTAAAATAAAATAAATATACCCAAAAA
ATAAATTTAAACTTCTACAAATAAAAATAAATTATATCATAACAAACTAAACTCATATAACCATA
CCAAAAAAATAAATTT
Found at i:1222377 original size:24 final size:23
Alignment explanation
Indices: 1222335--1222384 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
1222325 TAATCAAACC
*
1222335 AAAAACTAAATTTAAACTTGTACAA
1 AAAAAATAAATTTAAACTT-T-CAA
*
1222360 AAAAAATAAA-TTATACTTTCAA
1 AAAAAATAAATTTAAACTTTCAA
1222382 AAA
1 AAA
1222385 TTTAAACTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 6 0.26
23 1 0.04
24 7 0.30
25 9 0.39
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.28
Consensus pattern (23 bp):
AAAAAATAAATTTAAACTTTCAA
Found at i:1222458 original size:145 final size:144
Alignment explanation
Indices: 1222162--1222578 Score: 447
Period size: 145 Copynumber: 2.9 Consensus size: 144
1222152 TATGCAATTG
* * * *
1222162 AAAATTTAAATTCATATAATCATATCAAAAAACCACATTTAAAATTTTACAAATAAAAATAAATT
1 AAAATTTAAATTCATATAATCA-AAC-AAAAACTAAATTTAAAATTCTACAAA-AAAAATAAATT
* * * *
1222227 ATACCTT-AAAATATTTAAACTCGT-TAAATCATGCTGAAAAACAAATTTAAACTTCTAAAAATA
63 ATACTTTCAAAA-ATTTAAACTCATAT-AATCATACTTAAAAACAAATTTAAACTTCTAAAAATA
1222290 AATATTAAATAATAACATA
126 AATATTAAATAATAACATA
* * *
1222309 AAAATTTAAACTCATATAATCAAACCAAAAACTAAATTTAAACTTGTACAAAAAAAATAAATTAT
1 AAAATTTAAATTCATATAATCAAA-CAAAAACTAAATTTAAAATTCTACAAAAAAAATAAATTAT
* *
1222374 ACTTTCAAAAATTTAAACTCATATAATCATACTTAGAAAACACATTTAAACTTTTAAAAATCAAA
65 ACTTTCAAAAATTTAAACTCATATAATCATACTTA-AAAACAAATTTAAACTTCTAAAAAT-AAA
*
1222439 -A-TAAATTAT-AC-TCCA
128 TATTAAATAATAACAT--A
*** *
1222454 AAAATTTAAATTTGCATAATCAAGA-AAAAA-TAAATTTAAAATTCTACAAATAAAAAATATATT
1 AAAATTTAAATTCATATAATCAA-ACAAAAACTAAATTTAAAATTCTAC-AA-AAAAAATAAATT
* * *
1222517 ATACTTTC-AAAATTTAAACTCATATAATCATTACTTACAAATAAATTTATACTTCTACAAAA
63 ATACTTTCAAAAATTTAAACTCATATAATCA-TACTTAAAAACAAATTTAAACTTCTA-AAAA
1222579 AAAACAAATA
Statistics
Matches: 233, Mismatches: 25, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
143 16 0.07
144 46 0.20
145 93 0.40
146 53 0.23
147 25 0.11
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (144 bp):
AAAATTTAAATTCATATAATCAAACAAAAACTAAATTTAAAATTCTACAAAAAAAATAAATTATA
CTTTCAAAAATTTAAACTCATATAATCATACTTAAAAACAAATTTAAACTTCTAAAAATAAATAT
TAAATAATAACATA
Found at i:1222890 original size:213 final size:217
Alignment explanation
Indices: 1222615--1223497 Score: 811
Period size: 213 Copynumber: 4.1 Consensus size: 217
1222605 TAATTTTATG
* * * * * *
1222615 AATAAAAATAAATTATATCATCACAAA-TCAAACTCGTATAATCATACCCAAAAAGTACATTTAA
1 AATAAAAATAAATTATA-CATAAAAAATTCAAACCCATATAATCAAACCC-AAAAGCACATTTAA
** *
1222679 ACT-TCTATGAATAAAAATAAATTATACCTTAAAAATTGT-AACTCGTATAACTATACCTAAAAA
64 ACTCT-TACAAATAAAAATAAATTATACCTTAAAAATT-TAAACTCGTATAACTATACCCAAAAA
*
1222742 ATAAATTTAAACTTCTACGAATATAGATAAGTTATACTCTAAGAACTTAAACTCACATAATCAAC
127 ATAAATTTAAACTTCTACAAATATAGATAAGTTATACTCTAAGAACTTAAACTCACATAATCAAC
*
1222807 GC-AAAAAATAAATTTGAACATTTACA
192 -CTAAAAAATAAATTTAAACATTTACA
* *
1222833 AA-AAAAAT-TA-TATA-ATAAAAAATTTAAACCCATATAATCAAACCCAAAAGCACATTTAAAC
1 AATAAAAATAAATTATACATAAAAAATTCAAACCCATATAATCAAACCCAAAAGCACATTTAAAC
*
1222894 TCTTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTCGTATAACTATACCCAAAAAATAA
66 TCTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAACTATACCCAAAAAATAA
*
1222959 ATTTAAACTTCTACAAATATAGATAAGTTATACTCTAAGAACTTAAACTCATATAATCAACCTAA
131 ATTTAAACTTCTACAAATATAGATAAGTTATACTCTAAGAACTTAAACTCACATAATCAACCTAA
*
1223024 AAAATAAATTTAAACTTTTACA
196 AAAATAAATTTAAACATTTACA
* *
1223046 AATAAAAATAAATTATACCATAAAAAATTCAAACTCATATAAT-AATACCCAAAAACACATTTAA
1 AATAAAAATAAATTATA-CATAAAAAATTCAAACCCATATAATCAA-ACCCAAAAGCACATTTAA
* * * ** * * *
1223110 ACTCTTACAAATAAAAATAAATGATTCAATCGAAAATTTAAATTCATACAA-TCATA-CCAAAAA
64 ACTCTTACAAATAAAAATAAATTATAC-CTTAAAAATTTAAACTCGTATAACT-ATACCCAAAAA
* * * * * * * * * **
1223173 ATTATATTTAAACTTCTATAAATAAAAATAAATCATAC-CTTAAAAATTTAAATTC-GTTAAATC
127 A-TAAATTTAAACTTCTACAAATATAGATAAGTTATACTC-TAAGAACTTAAACTCACAT-AATC
** * *
1223236 ATGCT-AAAAACAAATTTAAAC-TTCTAAA
189 AACCTAAAAAATAAATTTAAACATT-TACA
* * * * * * ** ** *
1223264 AATATAGATAAATAATAACCT-AAAAATTTAAACTCATATAATCAAACTAAAAAATAAATTTAAA
1 AATAAAAATAAATTAT-ACATAAAAAATTCAAACCCATATAATCAAACCCAAAAGCACATTTAAA
* ** **
1223328 CT-TGTACAAATAAAAATAAATTATACATTTAAAAATTTAAACTTATATAA-TCATACTTAAAAA
65 CTCT-TACAAATAAAAATAAATTATAC-CTTAAAAATTTAAACTCGTATAACT-ATACCCAAAAA
* * * * * * * * * *
1223391 ACACATTTAAACTTTTAAAAATCA-AAATAAATTATACTCTAAAAATTTAAATTCGCATAATCAA
127 ATAAATTTAAACTTCTACAAAT-ATAGATAAGTTATACTCTAAGAACTTAAACTCACATAATCAA
* * *
1223455 -GT-AAAAATAAATTTAAACTTTTATA
191 CCTAAAAAATAAATTTAAACATTTACA
1223480 AATAAAAA-AATATTATAC
1 AATAAAAATAA-ATTATAC
1223498 CTTCAAAATT
Statistics
Matches: 564, Mismatches: 76, Indels: 53
0.81 0.11 0.08
Matches are distributed among these distances:
212 2 0.00
213 161 0.29
214 25 0.04
215 9 0.02
216 35 0.06
217 141 0.25
218 121 0.21
219 70 0.12
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.30
Consensus pattern (217 bp):
AATAAAAATAAATTATACATAAAAAATTCAAACCCATATAATCAAACCCAAAAGCACATTTAAAC
TCTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAACTATACCCAAAAAATAA
ATTTAAACTTCTACAAATATAGATAAGTTATACTCTAAGAACTTAAACTCACATAATCAACCTAA
AAAATAAATTTAAACATTTACA
Found at i:1223365 original size:217 final size:215
Alignment explanation
Indices: 1222644--1223570 Score: 803
Period size: 217 Copynumber: 4.3 Consensus size: 215
1222634 ATCACAAATC
* * * * ** *
1222644 AAACTCGTATAATCATACCCAAAAAGTACATTTAAACT-TCTATGAATAAAAATAAATTATAC-C
1 AAACTCATATAATCAAACCCAAAAA-CAAATTTAAACTCT-TACAAATAAAAATAAATTATACAT
* * ** * *
1222707 TTAAAAATTGT-AACTCGTATAA-CTATACCTAAAAAATAAATTTAAACTTCTACGAATATAGAT
64 TTAAAAATT-TAAATTCATATAATC-ATACC-AAAAAATAAATTTAAACTTCTAAAAATAAAAAT
* * * * ** * * * *
1222770 AAGTTATACTCTAAGAACTTAAACTCACATAATCAACGCAAAAAATAAATTTGAACATTTACAAA
126 AAATTATACTCTAAAAATTTAAATTCGTATAATCAA-GCTAAAAATAAATTTAAACTTTTAAAAA
* *
1222835 -AAA-AATTATATAA-TA-AAAAATTT
190 TAAATAAATA-ATAACCATAAAAATTT
* * *
1222858 AAACCCATATAATCAAACCCAAAAGCACATTTAAACTCTTACAAATAAAAATAAATTATAC-TTT
1 AAACTCATATAATCAAACCCAAAAACAAATTTAAACTCTTACAAATAAAAATAAATTATACATTT
* * * * * *
1222922 AAAAATTTAAACTCGTATAA-CTATACCCAAAAAATAAATTTAAACTTCTACAAATATAGATAAG
66 AAAAATTTAAATTCATATAATC-ATA-CCAAAAAATAAATTTAAACTTCTAAAAATAAAAATAAA
* * * * * *
1222986 TTATACTCTAAGAACTTAAACTCATATAATCAACCTAAAAAATAAATTTAAACTTTTACAAATAA
129 TTATACTCTAAAAATTTAAATTCGTATAATCAAGCT-AAAAATAAATTTAAACTTTTA-AAA-AT
* *
1223051 AAATAAATTAT-ACCATAAAAAATTC
191 AAATAAATAATAACCAT-AAAAATTT
* * * *
1223076 AAACTCATATAAT-AATACCCAAAAACACATTTAAACTCTTACAAATAAAAATAAATGATTCAAT
1 AAACTCATATAATCAA-ACCCAAAAACAAATTTAAACTCTTACAAATAAAAATAAATTATACATT
** * * *
1223140 CGAAAATTTAAATTCATACAATCATACCAAAAAATTATATTTAAACTTCTATAAATAAAAATAAA
65 TAAAAATTTAAATTCATATAATCATACCAAAAAA-TAAATTTAAACTTCTAAAAATAAAAATAAA
* * * *
1223205 TCATAC-CTTAAAAATTTAAATTCGT-TAAATCATGCTAAAAACAAATTTAAACTTCTAAAAATA
129 TTATACTC-TAAAAATTTAAATTCGTAT-AATCAAGCTAAAAATAAATTTAAACTTTTAAAAATA
1223268 TAGATAAATAATAACC-TAAAAATTT
192 -A-ATAAATAATAACCATAAAAATTT
** *
1223293 AAACTCATATAATCAAACTAAAAAATAAATTTAAACT-TGTACAAATAAAAATAAATTATACATT
1 AAACTCATATAATCAAACCCAAAAACAAATTTAAACTCT-TACAAATAAAAATAAATTATACATT
* * * * *
1223357 TAAAAATTTAAACTT-ATATAATCATACTTAAAAAACACATTTAAACTTTTAAAAATCAAAATAA
65 TAAAAATTTAAA-TTCATATAATCATAC-CAAAAAATAAATTTAAACTTCTAAAAATAAAAATAA
* *
1223421 ATTATACTCTAAAAATTTAAATTCGCATAATCAAG-TAAAAATAAATTTAAACTTTTATAAATAA
128 ATTATACTCTAAAAATTTAAATTCGTATAATCAAGCTAAAAATAAATTTAAACTTTTAAAAATAA
* * * *
1223485 AAAAATATTATACCTTCAAAATTT
193 ATAAATAATA-ACCATAAAAATTT
* * ** * * * *
1223509 AAACTCGTATAATCATTACTTATAAATAAATTTATACT-TCTACAAATAAAAATAAATAATAC
1 AAACTCATATAATCA-AACCCAAAAACAAATTTAAACTCT-TACAAATAAAAATAAATTATAC
1223571 CTTCAATTAA
Statistics
Matches: 606, Mismatches: 78, Indels: 55
0.82 0.11 0.07
Matches are distributed among these distances:
212 2 0.00
213 142 0.23
214 34 0.06
215 6 0.01
216 56 0.09
217 181 0.30
218 111 0.18
219 73 0.12
220 1 0.00
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.31
Consensus pattern (215 bp):
AAACTCATATAATCAAACCCAAAAACAAATTTAAACTCTTACAAATAAAAATAAATTATACATTT
AAAAATTTAAATTCATATAATCATACCAAAAAATAAATTTAAACTTCTAAAAATAAAAATAAATT
ATACTCTAAAAATTTAAATTCGTATAATCAAGCTAAAAATAAATTTAAACTTTTAAAAATAAATA
AATAATAACCATAAAAATTT
Found at i:1223677 original size:112 final size:113
Alignment explanation
Indices: 1223473--1223681 Score: 296
Period size: 113 Copynumber: 1.9 Consensus size: 113
1223463 AAATTTAAAC
* * * * *
1223473 TTTTATAAATAAAAAAATATTATACCTTCAAAATTTAAACTCGTATAATCATTACTTATAAATAA
1 TTTTATAAATAAAAAAATATTATACCTTAAAAATTTAAACTCCTATAATCAGTACCTAAAAATAA
* *
1223538 ATTTATACTTCTACAAATAAAAATAAATAATACCTTCAATTAAACTAA
66 ATATAAACTTCTACAAATAAAAATAAATAATACCTTCAATTAAACTAA
* * *
1223586 TTTTATGAATAAAAATAA-ATTATACTTTAAAAATTTAAACTCCTATTATC-GTACCTAAAAATA
1 TTTTATAAATAAAAA-AATATTATACCTTAAAAATTTAAACTCCTATAATCAGTACCTAAAAATA
*
1223649 AATATAAACTTCTACAAATAAAGATAAATAATA
65 AATATAAACTTCTACAAATAAAAATAAATAATA
1223682 TCCTAAAAAT
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
112 40 0.48
113 42 0.50
114 2 0.02
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.35
Consensus pattern (113 bp):
TTTTATAAATAAAAAAATATTATACCTTAAAAATTTAAACTCCTATAATCAGTACCTAAAAATAA
ATATAAACTTCTACAAATAAAAATAAATAATACCTTCAATTAAACTAA
Found at i:1224054 original size:73 final size:71
Alignment explanation
Indices: 1223593--1224762 Score: 893
Period size: 73 Copynumber: 16.2 Consensus size: 71
1223583 TAATTTTATG
* * * ** * *
1223593 AATAAAAATAAATTATACTTTAAAAATTTAAACTCCTATTATCGTACCTAAAAATAAATATAAAC
1 AATAAAAATAAATTATACCTTAAAAATTTAAACTCATATAAT-AAACCAAAAAATAAATTTAAAC
1223658 TTCTACA
65 TTCTACA
* * *
1223665 AATAAAGATAAATAATATCC-TAAAAATTTAAA-T-ATGTATAATAAACC-AAAAA-CAATTTAA
1 AATAAAAATAAATTATA-CCTTAAAAATTTAAACTCA--TATAATAAACCAAAAAATAAATTTAA
*
1223725 GCTTCTACA
63 ACTTCTACA
* * * * * * * *
1223734 AACAAAGATAAATAATACCCTAAAAATTTAAA-TATATATAATCAACCCAAAAACAAATTTAAAC
1 AATAAAAATAAATTATACCTTAAAAATTTAAACT-CATATAATAAACCAAAAAATAAATTTAAAC
* *
1223798 TTTTATA
65 TTCTACA
* * * *
1223805 AATAAAAATAAATTACATCTTAAAAATTTTAAACTTATTTAATTCTAAACCCAAAAAATAAATTT
1 AATAAAAATAAATTATACCTTAAAAA-TTTAAACTCATATAA---TAAA-CCAAAAAATAAATTT
* *
1223870 TAACTTTTACA
61 AAACTTCTACA
* * * * * * *
1223881 AATAAAAATAAAATATACCCTAAAAATTTAAACTCGTATAATCATACCTAATAACAAATTTAAAC
1 AATAAAAATAAATTATACCTTAAAAATTTAAACTCATATAAT-AAACCAAAAAATAAATTTAAAC
* *
1223946 TTATGC-
65 TTCTACA
* * * * *
1223952 ---GAACATAAATGATACCTTGAAAATTTAAACTTATATAATAAACCCTAAAAAATAAATTTAAA
1 AATAAAAATAAATTATACCTTAAAAATTTAAACTCATATAATAAA-CC-AAAAAATAAATTTAAA
*
1224014 CTTCTATA
64 CTTCTACA
* * * * *
1224022 AACAAAAATAAATTATATCATTACAAA-TTAAACTCATATAATCATACCAAAAAAATACATTTAA
1 AATAAAAATAAATTATA-CCTTAAAAATTTAAACTCATATAAT-AAACC-AAAAAATAAATTTAA
* **
1224086 ACTTTTATG
63 ACTTCTACA
* *
1224095 AATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAACTATACCCAAAAAATAAATTTAAA
1 AATAAAAATAAATTATACCTTAAAAATTTAAACTCATATAA-TA-AACCAAAAAATAAATTTAAA
*
1224160 CTTCTATA
64 CTTCTACA
* * * ** *
1224168 AA-AATAGATAAGTTATA-CTCTAAGAACCTAAACTCATATAATCAACCCAAAAAATAAATTTAA
1 AATAA-AAATAAATTATACCT-TAAAAATTTAAACTCATATAAT-AAACCAAAAAATAAATTTAA
1224231 ACTTCTACA
63 ACTTCTACA
* * * * * *
1224240 AATAAAAATAAATTATA-CTATCAAAAATGTAAACTCATATAACCATACCTAAAAACATATTTAA
1 AATAAAAATAAATTATACCT-T-AAAAATTTAAACTCATATAA-TAAACCAAAAAATAAATTTAA
1224304 AC-TCTTACA
63 ACTTC-TACA
* * ** * * *
1224313 AATAAAAATAAATTATGCAATCGAAAATTTAAATTCATATAATCATACCAAAAAATCATATTTAA
1 AATAAAAATAAATTATAC-CTTAAAAATTTAAACTCATATAAT-AAACCAAAAAAT-AAATTTAA
1224378 ACTTCTACA
63 ACTTCTACA
* * ** **
1224387 AATAAAAATAAATTATACCTTAAAAATTTAAATTCGT-TAAATCATGCTGAAAAATAAATTTAAA
1 AATAAAAATAAATTATACCTTAAAAATTTAAACTCATAT-AAT-AAACCAAAAAATAAATTTAAA
*
1224451 CTTCTAAA
64 CTTCTACA
* * *
1224459 AATAAAGATAAATAATAACC-TAAAAATTTAAACTCATATAATCAAACTAAAAAATAAATTTAAA
1 AATAAAAATAAATTAT-ACCTTAAAAATTTAAACTCATATAAT-AAACCAAAAAATAAATTTAAA
* *
1224523 CTTGTATA
64 CTTCTACA
* * * *
1224531 ATTAAAAATAAATTATACCTTCAAAAATTTAAACTCATATAATCATACTTAAAAAATACATTTAA
1 AATAAAAATAAATTATACCTT-AAAAATTTAAACTCATATAAT-AAAC-CAAAAAATAAATTTAA
* *
1224596 ACTTTTAAA
63 ACTTCTACA
* ** * *
1224605 AATCAAAAATAAATTATA-CTCTAAAAATTTAAATTCGCATAATCAA-GAAAAAATAAATTTAAA
1 AAT-AAAAATAAATTATACCT-TAAAAATTTAAACTCATATAATAAACCAAAAAATAAATTTAAA
*
1224668 CTTATACA
64 CTTCTACA
* * * * * ** * *
1224676 AATAAAAAATATATTATGCCTTCAAAACTTAAACTCGTATAATCAATACTTACAAATAAATTTAT
1 AAT-AAAAATAAATTATACCTTAAAAATTTAAACTCATATAAT-AA-ACCAAAAAATAAATTTAA
*
1224741 ACTTCAACA
63 ACTTCTACA
1224750 AATAAAAATAAAT
1 AATAAAAATAAAT
1224763 AATATCTTTA
Statistics
Matches: 891, Mismatches: 157, Indels: 99
0.78 0.14 0.09
Matches are distributed among these distances:
67 2 0.00
68 35 0.04
69 70 0.08
70 10 0.01
71 95 0.11
72 210 0.24
73 284 0.32
74 108 0.12
75 33 0.04
76 44 0.05
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.31
Consensus pattern (71 bp):
AATAAAAATAAATTATACCTTAAAAATTTAAACTCATATAATAAACCAAAAAATAAATTTAAACT
TCTACA
Found at i:1224304 original size:218 final size:214
Alignment explanation
Indices: 1223593--1224762 Score: 1000
Period size: 219 Copynumber: 5.4 Consensus size: 214
1223583 TAATTTTATG
* * * * *
1223593 AATAAAAATAAATTATACTTTAAAAATTTAAACTCCTATTATCGTACCT-AAAAATAAATATAAA
1 AATAAAAATAAATTATACTTCAAAAATTTAAACTCATATAATCATACCTAAAAAAT-AATTTAAA
* * * * *
1223657 CTTCTACAAATAAAGATAAATAATATCC-TAAAAATTTAAA-TATGTATAAT-AAACC-AAAAA-
65 CTTTTACAAATAAAAATAAATTATA-CCTTAAAAATTTAAACT-CGTATAATCATACCAAAAAAT
* * * * * *
1223717 CAATTTAAGCTTCTACAAACAAAGATAAATAATACCCTAAAAATTTAAA-TATATATAATCAACC
128 AAATTTAAACTTCTATAAA-AAAAATAAATTATA-CCTAAAAATTTAAACT-CATATAATCAACC
* * *
1223781 C-AAAAACAAATTTAAACTTTTATA
190 CAAAAAATAAATTTAAACTTCTACA
* * * * *
1223805 AATAAAAATAAATTACATCTT-AAAAATTTTAAACTTATTTAATTCTAAACCCAAAAAATAAATT
1 AATAAAAATAAATTATA-CTTCAAAAA-TTTAAACTCATATAA-TC-ATACCTAAAAAAT-AATT
* * * * *
1223869 TTAACTTTTACAAATAAAAATAAAATATACCCTAAAAATTTAAACTCGTATAATCATACCTAATA
61 TAAACTTTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATACCAAAAA
* *** * * * * *
1223934 ACAAATTTAAAC-T-TAT-GCGAACATAAATGATACCTTGAAAATTTAAACTTATATAATAAACC
126 ATAAATTTAAACTTCTATAAAAAAAATAAATTATACC-TAAAAATTTAAACTCATATAATCAACC
*
1223996 CTAAAAAATAAATTTAAACTTCTATA
190 C-AAAAAATAAATTTAAACTTCTACA
* * *
1224022 AACAAAAATAAATTATATCATT-ACAAA-TTAAACTCATATAATCATACCAAAAAAATACATTTA
1 AATAAAAATAAATTATA-C-TTCAAAAATTTAAACTCATATAATCATACCTAAAAAATA-ATTTA
**
1224085 AACTTTTATGAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAA-CTATACCCAAAAA
63 AACTTTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATC-ATA-CCAAAAA
* * * **
1224149 ATAAATTTAAACTTCTATAAAAATAGATAAGTTATACTCTAAGAACCTAAACTCATATAATCAAC
126 ATAAATTTAAACTTCTATAAAAA-AAATAAATTATAC-CTAAAAATTTAAACTCATATAATCAAC
1224214 CCAAAAAATAAATTTAAACTTCTACA
189 CCAAAAAATAAATTTAAACTTCTACA
* *
1224240 AATAAAAATAAATTATACTATCAAAAATGTAAACTCATATAACCATACCTAAAAACAT-ATTTAA
1 AATAAAAATAAATTATACT-TCAAAAATTTAAACTCATATAATCATACCTAAAAA-ATAATTTAA
* * * ** * *
1224304 ACTCTTACAAATAAAAATAAATTATGCAATCGAAAATTTAAATTCATATAATCATACCAAAAAAT
64 ACTTTTACAAATAAAAATAAATTATAC-CTTAAAAATTTAAACTCGTATAATCATACCAAAAAAT
* * * * **
1224369 CATATTTAAACTTCTACAAATAAAAATAAATTATACCTTAAAAATTTAAATTCGT-TAAATCATG
128 -AAATTTAAACTTCTATAAA-AAAAATAAATTATACC-TAAAAATTTAAACTCATAT-AATCAAC
** *
1224433 CTGAAAAATAAATTTAAACTTCTAAA
189 CCAAAAAATAAATTTAAACTTCTACA
* * * *
1224459 AATAAAGATAAATAATAACCT-AAAAATTTAAACTCATATAATCA-AACTAAAAAATAAATTTAA
1 AATAAAAATAAATTAT-ACTTCAAAAATTTAAACTCATATAATCATACCTAAAAAAT-AATTTAA
* * * * *
1224522 ACTTGTATAATTAAAAATAAATTATACCTTCAAAAATTTAAACTCATATAATCATACTTAAAAAA
64 ACTTTTACAAATAAAAATAAATTATACCTT-AAAAATTTAAACTCGTATAATCATAC-CAAAAAA
* * * * **
1224587 TACATTTAAACTTTTAAAAATCAAAAATAAATTATACTCTAAAAATTTAAATTCGCATAATCAA-
127 TAAATTTAAACTTCTATAAA--AAAAATAAATTATAC-CTAAAAATTTAAACTCATATAATCAAC
* *
1224651 -GAAAAAATAAATTTAAACTTATACA
189 CCAAAAAATAAATTTAAACTTCTACA
* * * * * *
1224676 AATAAAAAATATATTATGCCTTC-AAAACTTAAACTCGTATAATCAATA-CTTACAAATAAATTT
1 AAT-AAAAATAAATTAT-ACTTCAAAAATTTAAACTCATATAATC-ATACCTAAAAAAT-AATTT
* **
1224739 ATACTTCAACAAATAAAAATAAAT
62 AAACTTTTACAAATAAAAATAAAT
1224763 AATATCTTTA
Statistics
Matches: 787, Mismatches: 126, Indels: 83
0.79 0.13 0.08
Matches are distributed among these distances:
212 21 0.03
213 16 0.02
214 69 0.09
215 58 0.07
216 70 0.09
217 83 0.11
218 215 0.27
219 244 0.31
220 11 0.01
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.31
Consensus pattern (214 bp):
AATAAAAATAAATTATACTTCAAAAATTTAAACTCATATAATCATACCTAAAAAATAATTTAAAC
TTTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATACCAAAAAATAAA
TTTAAACTTCTATAAAAAAAATAAATTATACCTAAAAATTTAAACTCATATAATCAACCCAAAAA
ATAAATTTAAACTTCTACA
Found at i:1224378 original size:977 final size:975
Alignment explanation
Indices: 1222138--1225554 Score: 3180
Period size: 977 Copynumber: 3.5 Consensus size: 975
1222128 AAAAATTTAA
* * ** * * * ** *
1222138 AAATAAAAATAAATTATGCAATTGAAAATTTAAATTCATATAATCATATCAAAAAACCACATTTA
1 AAATAAAAATAAATGATACAATCAAAAATTTAAACTCATACAATCATACCAAAAAATTAAATTTA
* * * * ** * * **
1222203 AAATTTTACAAATAAAAATAAATTATACCTTAAAATATTTAAACTCGTTAAATCATGCTGAAAAA
66 AACTTCTATAAATAAAAATAAATCATACCTTAAAA-ACCTAAACTCATTAAATCA-CCCAAAAAA
*
1222268 CAAATTTAAACTTCTAAAAATAAATATTAAATAATAACAT-AAAAATTTAAACTCATATAATCAA
129 CAAATTTAAACTTCTAAAAATAAA-AATAAATAAT-ACATCAAAAATTTAAACTCATATAATC-A
* * *
1222332 ACC-AAAAACTAAATTTAAACTTGTACAAA-AAAAATAAATTATACTTTCAAAAATTTAAACTCA
191 ACCTAAAAAC-ATATTTAAACTTGTACAAATAAAAATAAATTATACATTCAAAAATTTAAATTCA
* *
1222395 TATAATCATACTTAGAAAACACATTTAAACTTTTAAAAATCAAAATAAATTATACTCCAAAAATT
255 TATAATCATACTTAAAAAACACATTTAAACTTTTAAAAATCAAAATAAATTATACTCTAAAAATT
* * * * *
1222460 TAAATTTGCATAATCAAGAAAAAATAAATTTAAAATTCTACAAATAAAAAATATATTATACTTTC
320 TAAATTCGCATAATCAAGTAAAAATAAATTTAAACTTCTAAAAATAAAAAA-ATATTATACCTTC
* *
1222525 AAAATTTAAACTCATATAATCATTACTTACAAATAAATTTATACTTCTACAAA-AAAAACAAATA
384 AAAATTTAAACTCATATAATCATTACTTAAAAATAAATTTATACTTCTACAAATAAAAATAAATA
* * *
1222589 ATATCTTCAATTAAACTAATTTTATGAATAAAAATAAATTATATCATCACAAATCAAACTCGTAT
449 ATACCTTCAATTAAACTAATTTTATGAATAAAAATAAATTATATCATCAAAAATCAAACTCCTAT
* * ** *
1222654 AATCATACCCAAAAAGTACATTTAAACTTCTATGAATAAAAATAAATTATACCTTAAAAATTGTA
514 AATCATACCCAAAAAGTAAATATAAACTTCTACAAATAAAAATAAATAATACCTTAAAAATTGTA
* * * * * * * *
1222719 ACTCGTATAACTATACCTAAAAAATAAATTTAAACTTCTACGAATATAGATAAGTTATACTCTAA
579 AATCGTATAACTAAACC-AAAAAATAAATTTAAACTTCTACAAACAAAGATAAATAATACCCTAA
* * * *
1222784 GAACTTAAACTCACATAATCAACGCAAAAAATAAATTTGAACATTTACAAAAAAAATTATATAAT
643 AAACTTAAACTCACATAATCAACGCAAAAAACAAATTTAAACATTTACAAAAAAAATAATATAAT
* * *
1222849 AAAAAATTTAAACCCATATAATCAAACCCAAAAGCACATTTAAACTCTTACAAATAAAAATAAAT
708 AAAAAATTTAAACCCATATAATCAAACCCAAAAACAAATTTAAACTCTTACAAATAAAAATAAAA
** * * *
1222914 TATACTTTAAAAATTTAAACTCGTATAACTATACCCAAAAAATAAATTTAAACTTCTACAAATAT
773 TATACCCTAAAAATTTAAACTCGTATAACTATACCCAAAAAACAAATTTAAACTTATACAAACAT
* * *
1222979 AGATAAGTTATACTCTAAGAACTTAAACTCATATAATCAACCTAAAAAATAAATTTAAACTTTTA
838 A-ATAAGTGATACTCTAAGAACTTAAACTCATATAATAAACCTAAAAAATAAATTTAAACTTCTA
* *
1223044 CAAATAAAAATAAATTATACCATAAAAAATTCAAACTCATATAATAATACCCAAAAACACATTTA
902 CAAACAAAAATAAATTATACCATAAAAAATTCAAACTCATATAATAATACCAAAAAACACATTTA
1223109 AACTCTTAC
967 AACTCTTAC
* * * *
1223118 AAATAAAAATAAATGATTCAATCGAAAATTTAAATTCATACAATCATACCAAAAAATTATATTTA
1 AAATAAAAATAAATGATACAATCAAAAATTTAAACTCATACAATCATACCAAAAAATTAAATTTA
** * * ** *
1223183 AACTTCTATAAATAAAAATAAATCATACCTTAAAAATTTAAATTCGTTAAATCATGCTAAAAACA
66 AACTTCTATAAATAAAAATAAATCATACCTTAAAAACCTAAACTCATTAAATCACCCAAAAAACA
* * * *
1223248 AATTTAAACTTCTAAAAATATAGATAAATAATA-ACCTAAAAATTTAAACTCATATAATCAAACT
131 AATTTAAACTTCTAAAAATAAAAATAAATAATACATC-AAAAATTTAAACTCATATAATCAACCT
*
1223312 AAAAA-ATAAATTTAAACTTGTACAAATAAAAATAAATTATACATTTAAAAATTTAAACTT-ATA
195 AAAAACAT--ATTTAAACTTGTACAAATAAAAATAAATTATACATTCAAAAATTTAAA-TTCATA
1223375 TAATCATACTTAAAAAACACATTTAAACTTTTAAAAATCAAAATAAATTATACTCTAAAAATTTA
257 TAATCATACTTAAAAAACACATTTAAACTTTTAAAAATCAAAATAAATTATACTCTAAAAATTTA
* *
1223440 AATTCGCATAATCAAGTAAAAATAAATTTAAACTTTTATAAATAAAAAAATATTATACCTTCAAA
322 AATTCGCATAATCAAGTAAAAATAAATTTAAACTTCTAAAAATAAAAAAATATTATACCTTCAAA
* *
1223505 ATTTAAACTCGTATAATCATTACTTATAAATAAATTTATACTTCTACAAATAAAAATAAATAATA
387 ATTTAAACTCATATAATCATTACTTAAAAATAAATTTATACTTCTACAAATAAAAATAAATAATA
* * * *
1223570 CCTTCAATTAAACTAATTTTATGAATAAAAATAAATTATA-CTTTAAAAATTTAAACTCCTATTA
452 CCTTCAATTAAACTAATTTTATGAATAAAAATAAATTATATCATCAAAAA-TCAAACTCCTATAA
* * *
1223634 TCGTACCTAAAAA-TAAATATAAACTTCTACAAATAAAGATAAATAATATCC-TAAAAATT-TAA
516 TCATACCCAAAAAGTAAATATAAACTTCTACAAATAAAAATAAATAATA-CCTTAAAAATTGTAA
* * *
1223696 ATATGTATAA-TAAACC-AAAAA-CAATTTAAGCTTCTACAAACAAAGATAAATAATACCCTAAA
580 AT-CGTATAACTAAACCAAAAAATAAATTTAAACTTCTACAAACAAAGATAAATAATACCCTAAA
* * * * * *
1223758 AATTTAAA-TATATATAATCAAC-CCAAAAACAAATTTAAACTTTTATAAATAAAAATAA-ATTA
644 AACTTAAACT-CACATAATCAACGCAAAAAACAAATTTAAACATTTACAAA-AAAAATAATA-TA
* ** * * * *
1223820 CATCTTAAAAATTTTAAACTTATTTAATTCTAAACCCAAAAAATAAATTTTAACTTTTACAAATA
706 -A---TAAAAAATTTAAACCCATATAA-TC-AAACCC-AAAAACAAATTTAAACTCTTACAAATA
* *
1223885 AAAATAAAATATACCCTAAAAATTTAAACTCGTATAA-TCATA-CCTAATAACAAATTTAAACTT
764 AAAATAAAATATACCCTAAAAATTTAAACTCGTATAACT-ATACCCAAAAAACAAATTTAAACTT
* * * *
1223948 ATGCGAACAT-A-AA-TGATAC-CTTGAA-AATTTAAACTTATATAATAAACCCTAAAAAATAAA
828 ATACAAACATAATAAGTGATACTC-T-AAGAACTTAAACTCATATAATAAA-CCTAAAAAATAAA
* * * * *
1224008 TTTAAACTTCTATAAACAAAAATAAATTATATCATTACAAATT-AAACTCATATAATCATACCAA
890 TTTAAACTTCTACAAACAAAAATAAATTATACCATAAAAAATTCAAACTCATATAATAATACC-A
* * *
1224072 AAAAATACATTTAAACTTTTAT
954 AAAAACACATTTAAACTCTTAC
* * * * * *
1224094 GAATAAAAATAAATTATAC-CTTAAAAATTTAAACTCGTATAA-CTATACCCAAAAAA-TAAATT
1 AAATAAAAATAAATGATACAATCAAAAATTTAAACTCATACAATC-ATA-CCAAAAAATTAAATT
* * * *
1224156 TAAACTTCTATAAA-AATAGATAAGTTATA-CTCTAAGAACCTAAACTCA-TATAATCAACCCAA
64 TAAACTTCTATAAATAA-AAATAAATCATACCT-TAAAAACCTAAACTCATTA-AATC-ACCCAA
* * * * *
1224218 AAAATAAATTTAAACTTCTACAAATAAAAATAAATTATACTATCAAAAATGTAAACTCATATAAC
125 AAAACAAATTTAAACTTCTAAAAATAAAAATAAATAATAC-ATCAAAAATTTAAACTCATATAAT
* * *
1224283 CATACCTAAAAACATATTTAAACTCT-TACAAATAAAAATAAATTATGCAATCGAAAATTTAAAT
189 CA-ACCTAAAAACATATTTAAACT-TGTACAAATAAAAATAAATTATACATTCAAAAATTTAAAT
* * * * *
1224347 TCATATAATCATAC-CAAAAAATCATATTTAAACTTCTACAAATAAAAATAAATTATAC-CTTAA
252 TCATATAATCATACTTAAAAAA-CACATTTAAACTTTTAAAAATCAAAATAAATTATACTC-TAA
* * *
1224410 AAATTTAAATTCG-TTAAATCATGCTGAAAAATAAATTTAAACTTCTAAAAATAAAGATAAATAA
315 AAATTTAAATTCGCAT-AATCAAG-T-AAAAATAAATTTAAACTTCTAAAAATAAA-A-AAATAT
* * * * * * *
1224474 TA-ACC-TAAAAATTTAAACTCATATAATCA-AACTAAAAAATAAATTTAAACTTGTATAATTAA
375 TATACCTTCAAAATTTAAACTCATATAATCATTACTTAAAAATAAATTTATACTTCTACAAATAA
* * * * *
1224536 AAATAAATTATACCTTCAAAAATTTAAACTCATATAATCATACTTAAAAAATACATTTAAACTTT
440 AAATAAATAATACCTTC---AA-TTAAACT-A-AT--T-TTA-TGAATAAA-A-A--TAAA-TTA
** * ** * *
1224601 TAAAAATCAAAAAT-AAATTATACTCTAAAAATTTAAATTCGCATAATCAAGAAAAAATAAATTT
490 T-ATCATCAAAAATCAAA--CT-C-CT----A--T-AA-T--CAT-A-C-CCAAAAAGTAAATAT
* * * * * * **
1224665 AAACTTATACAAATAAAAAATATATTATGCCTTCAAAACT-TAAACTCGTATAA-TCAATACTTA
537 AAACTTCTACAAAT-AAAAATAAATAATACCTTAAAAATTGTAAA-TCGTATAACT-AA-ACCAA
* * * * *
1224728 CAAATAAATTTATACTTCAACAAATAAAAATAAATAATA---T-----CTT----T-A-AT--T-
598 AAAATAAATTTAAACTTCTACAAACAAAGATAAATAATACCCTAAAAACTTAAACTCACATAATC
* * ** * * * * * * * *
1224776 --------AAACTAATTTTATGA-ATA-AAAATAAATTATATCATCACAAA-TTAAACTCGTATA
663 AACGCAAAAAACAAATTTAAACATTTACAAAAAAAATAATATAATAAAAAATTTAAACCCATATA
* * * ** * * *
1224830 ATCATACCCAAAAAATAAATTTAAACTTTTATGAATTAAAATAAATTATACCTTAAAAATTTAAA
728 ATCAAACCC-AAAAACAAATTTAAACTCTTACAAATAAAAATAAAATATACCCTAAAAATTTAAA
* * * * *
1224895 CTCATATAACTATACCCAAAAAATAAATTTAAACTTCTACAAATATAGATAAGTTATACTCTAAG
792 CTCGTATAACTATACCCAAAAAACAAATTTAAACTTATACAAACATA-ATAAGTGATACTCTAAG
* * *
1224960 AACTTAAACTCATATAATCAACCCAAAAAATAAATTTAAACTTCTACAAATAAAAATAAATTATA
856 AACTTAAACTCATATAATAAACCTAAAAAATAAATTTAAACTTCTACAAACAAAAATAAATTATA
* * * * *
1225025 CCATCAAAAATTTAAACTCACATAATCATACCCAAAAACACATTTAAACTCTTAC
921 CCATAAAAAATTCAAACTCATATAATAATACCAAAAAACACATTTAAACTCTTAC
* * * * * ** *
1225080 AAATAAAAATAAATTATACAATAAAAAATTTAAATTCATATAATCATAACAAAAAACCACATTTA
1 AAATAAAAATAAATGATACAATCAAAAATTTAAACTCATACAATCATACCAAAAAATTAAATTTA
* * * ** * * **
1225145 AACTTCTACAAATAAAAATAAATTATATCTTAAAAATTTAAACTCGTTAAATCATGCTGAAAAAC
66 AACTTCTATAAATAAAAATAAATCATACCTTAAAAACCTAAACTCATTAAATCA-CCCAAAAAAC
* * * * *
1225210 AAATTTAAATTTCTAAAAATTAAGATAAATAATA-ACCTAAAAATTTAAACTCATATAATCAAAC
130 AAATTTAAACTTCTAAAAATAAAAATAAATAATACATC-AAAAATTTAAACTCATATAATCAACC
* * *
1225274 TAAAAA-ATAAATTTAAACTTGTACAAATAAAAATAAATTATACCTTCAAAAATTTAAACTCTTA
194 TAAAAACAT--ATTTAAACTTGTACAAATAAAAATAAATTATACATTCAAAAATTTAAATTCATA
* *
1225338 TAATCATACTTAGAAAACACATTTAAACTTTTAAAAATCAAAATAAATTGTACTCTAAAAATTTA
257 TAATCATACTTAAAAAACACATTTAAACTTTTAAAAATCAAAATAAATTATACTCTAAAAATTTA
*
1225403 AATTCGCATAATCAAG---CAA-AAA--T--A-----AAAAAT------ATATTATACCTTCAAA
322 AATTCGCATAATCAAGTAAAAATAAATTTAAACTTCTAAAAATAAAAAAATATTATACCTTCAAA
* * * *
1225449 ATTTAAACTCGTATAATCATTACTTACAAATAAATTTATACTTCAAAAAATAAAAATAAATAATA
387 ATTTAAACTCATATAATCATTACTTAAAAATAAATTTATACTTCTACAAATAAAAATAAATAATA
1225514 CCTTCAATTAAACTAATTTTATGAATAAAAATAAATTATAT
452 CCTTCAATTAAACTAATTTTATGAATAAAAATAAATTATAT
1225555 TTTAAAATAA
Statistics
Matches: 2026, Mismatches: 297, Indels: 258
0.78 0.12 0.10
Matches are distributed among these distances:
950 1 0.00
951 3 0.00
952 4 0.00
954 1 0.00
955 1 0.00
956 6 0.00
957 2 0.00
958 1 0.00
960 2 0.00
961 1 0.00
962 7 0.00
963 7 0.00
964 3 0.00
965 22 0.01
966 41 0.02
971 6 0.00
972 24 0.01
973 58 0.03
974 14 0.01
975 107 0.05
976 158 0.08
977 312 0.15
978 299 0.15
979 101 0.05
980 154 0.08
981 11 0.01
982 73 0.04
983 28 0.01
984 15 0.01
985 16 0.01
986 229 0.11
987 151 0.07
988 15 0.01
989 8 0.00
990 5 0.00
991 2 0.00
992 14 0.01
993 6 0.00
994 2 0.00
995 7 0.00
996 1 0.00
997 2 0.00
1000 1 0.00
1001 1 0.00
1002 2 0.00
1003 2 0.00
1004 1 0.00
1005 2 0.00
1007 2 0.00
1008 3 0.00
1009 1 0.00
1010 5 0.00
1011 21 0.01
1012 27 0.01
1013 4 0.00
1014 2 0.00
1015 4 0.00
1016 28 0.01
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.31
Consensus pattern (975 bp):
AAATAAAAATAAATGATACAATCAAAAATTTAAACTCATACAATCATACCAAAAAATTAAATTTA
AACTTCTATAAATAAAAATAAATCATACCTTAAAAACCTAAACTCATTAAATCACCCAAAAAACA
AATTTAAACTTCTAAAAATAAAAATAAATAATACATCAAAAATTTAAACTCATATAATCAACCTA
AAAACATATTTAAACTTGTACAAATAAAAATAAATTATACATTCAAAAATTTAAATTCATATAAT
CATACTTAAAAAACACATTTAAACTTTTAAAAATCAAAATAAATTATACTCTAAAAATTTAAATT
CGCATAATCAAGTAAAAATAAATTTAAACTTCTAAAAATAAAAAAATATTATACCTTCAAAATTT
AAACTCATATAATCATTACTTAAAAATAAATTTATACTTCTACAAATAAAAATAAATAATACCTT
CAATTAAACTAATTTTATGAATAAAAATAAATTATATCATCAAAAATCAAACTCCTATAATCATA
CCCAAAAAGTAAATATAAACTTCTACAAATAAAAATAAATAATACCTTAAAAATTGTAAATCGTA
TAACTAAACCAAAAAATAAATTTAAACTTCTACAAACAAAGATAAATAATACCCTAAAAACTTAA
ACTCACATAATCAACGCAAAAAACAAATTTAAACATTTACAAAAAAAATAATATAATAAAAAATT
TAAACCCATATAATCAAACCCAAAAACAAATTTAAACTCTTACAAATAAAAATAAAATATACCCT
AAAAATTTAAACTCGTATAACTATACCCAAAAAACAAATTTAAACTTATACAAACATAATAAGTG
ATACTCTAAGAACTTAAACTCATATAATAAACCTAAAAAATAAATTTAAACTTCTACAAACAAAA
ATAAATTATACCATAAAAAATTCAAACTCATATAATAATACCAAAAAACACATTTAAACTCTTAC
Found at i:1224846 original size:768 final size:747
Alignment explanation
Indices: 1224025--1225554 Score: 2529
Period size: 768 Copynumber: 2.0 Consensus size: 747
1224015 TTCTATAAAC
* *
1224025 AAAAATAAATTATATCATTACAAATTAAACTCATATAATCATACCAAAAAAATACATTTAAACTT
1 AAAAATAAATTATATCATCACAAATTAAACTCATATAATCATACCAAAAAAATAAATTTAAACTT
*
1224090 TTATGAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAACTATACCCAAAAAATAAAT
66 TTATGAATAAAAATAAATTATACCTTAAAAATTTAAACTCATATAACTATACCCAAAAAATAAAT
*
1224155 TTAAACTTCTATAAAAATAGATAAGTTATACTCTAAGAACCTAAACTCATATAATCAACCCAAAA
131 TTAAACTTCTACAAAAATAGATAAGTTATACTCTAAGAACCTAAACTCATATAATCAACCCAAAA
* *
1224220 AATAAATTTAAACTTCTACAAATAAAAATAAATTATACTATCAAAAATGTAAACTCATATAACCA
196 AATAAATTTAAACTTCTACAAATAAAAATAAATTATACCATCAAAAATGTAAACTCACATAACCA
* * * **
1224285 TACCTAAAAACATATTTAAACTCTTACAAATAAAAATAAATTATGCAATCGAAAATTTAAATTCA
261 TACCCAAAAACACATTTAAACTCTTACAAATAAAAATAAATTATACAATAAAAAATTTAAATTCA
* * *
1224350 TATAATCATACCAAAAAATCATATTTAAACTTCTACAAATAAAAATAAATTATACCTTAAAAATT
326 TATAATCATAACAAAAAACCACATTTAAACTTCTACAAATAAAAATAAATTATACCTTAAAAATT
* *
1224415 TAAATTCGTTAAATCATGCTGAAAAATAAATTTAAACTTCTAAAAATAAAGATAAATAATAACCT
391 TAAACTCGTTAAATCATGCTGAAAAACAAATTTAAACTTCTAAAAATAAAGATAAATAATAACCT
* *
1224480 AAAAATTTAAACTCATATAATCAAACTAAAAAATAAATTTAAACTTGTATAATTAAAAATAAATT
456 AAAAATTTAAACTCATATAATCAAACTAAAAAATAAATTTAAACTTGTACAAATAAAAATAAATT
*
1224545 ATACCTTCAAAAATTTAAACTCATATAATCATACTTAAAAAATACATTTAAACTTTTAAAAATCA
521 ATACCTTCAAAAATTTAAACTCATATAATCATACTTAAAAAACACATTTAAACTTTTAAAAATC-
1224610 AAAATAAATTATACTCTAAAAATTTAAATTCGCATAATCAAGAAAAAATAAATTTAAACTTATAC
585 AAAATAAATTATACTCTAAAAATTTAAATTCGCATAATCAAG----------------C--A-A-
*
1224675 AAATAAAAAATATATTATGCCTTCAAAACTTAAACTCGTATAATCAATACTTACAAATAAATTTA
630 AAATAAAAAATATATTATACCTTCAAAACTTAAACTCGTATAATCAATACTTACAAATAAATTTA
* * *
1224740 TACTTCAACAAATAAAAATAAATAATATCTTTAATTAAACTAATTTTATGAAT
695 TACTTCAAAAAATAAAAATAAATAATACCTTCAATTAAACTAATTTTATGAAT
* *
1224793 AAAAATAAATTATATCATCACAAATTAAACTCGTATAATCATACCCAAAAAATAAATTTAAACTT
1 AAAAATAAATTATATCATCACAAATTAAACTCATATAATCATACCAAAAAAATAAATTTAAACTT
*
1224858 TTATGAATTAAAATAAATTATACCTTAAAAATTTAAACTCATATAACTATACCCAAAAAATAAAT
66 TTATGAATAAAAATAAATTATACCTTAAAAATTTAAACTCATATAACTATACCCAAAAAATAAAT
* *
1224923 TTAAACTTCTACAAATATAGATAAGTTATACTCTAAGAACTTAAACTCATATAATCAACCCAAAA
131 TTAAACTTCTACAAAAATAGATAAGTTATACTCTAAGAACCTAAACTCATATAATCAACCCAAAA
* *
1224988 AATAAATTTAAACTTCTACAAATAAAAATAAATTATACCATCAAAAATTTAAACTCACATAATCA
196 AATAAATTTAAACTTCTACAAATAAAAATAAATTATACCATCAAAAATGTAAACTCACATAACCA
1225053 TACCCAAAAACACATTTAAACTCTTACAAATAAAAATAAATTATACAATAAAAAATTTAAATTCA
261 TACCCAAAAACACATTTAAACTCTTACAAATAAAAATAAATTATACAATAAAAAATTTAAATTCA
*
1225118 TATAATCATAACAAAAAACCACATTTAAACTTCTACAAATAAAAATAAATTATATCTTAAAAATT
326 TATAATCATAACAAAAAACCACATTTAAACTTCTACAAATAAAAATAAATTATACCTTAAAAATT
* *
1225183 TAAACTCGTTAAATCATGCTGAAAAACAAATTTAAATTTCTAAAAATTAAGATAAATAATAACCT
391 TAAACTCGTTAAATCATGCTGAAAAACAAATTTAAACTTCTAAAAATAAAGATAAATAATAACCT
1225248 AAAAATTTAAACTCATATAATCAAACTAAAAAATAAATTTAAACTTGTACAAATAAAAATAAATT
456 AAAAATTTAAACTCATATAATCAAACTAAAAAATAAATTTAAACTTGTACAAATAAAAATAAATT
* *
1225313 ATACCTTCAAAAATTTAAACTCTTATAATCATACTTAGAAAACACATTTAAACTTTTAAAAATCA
521 ATACCTTCAAAAATTTAAACTCATATAATCATACTTAAAAAACACATTTAAACTTTTAAAAATCA
*
1225378 AAATAAATTGTACTCTAAAAATTTAAATTCGCATAATCAAGCAAAAATAAAAAATATATTATACC
586 AAATAAATTATACTCTAAAAATTTAAATTCGCATAATCAAGCAAAAATAAAAAATATATTATACC
* *
1225443 TTCAAAATTTAAACTCGTATAATCATTACTTACAAATAAATTTATACTTCAAAAAATAAAAATAA
651 TTCAAAACTTAAACTCGTATAATCAATACTTACAAATAAATTTATACTTCAAAAAATAAAAATAA
1225508 ATAATACCTTCAATTAAACTAATTTTATGAAT
716 ATAATACCTTCAATTAAACTAATTTTATGAAT
1225540 AAAAATAAATTATAT
1 AAAAATAAATTATAT
1225555 TTTAAAATAA
Statistics
Matches: 724, Mismatches: 38, Indels: 21
0.92 0.05 0.03
Matches are distributed among these distances:
747 127 0.18
748 1 0.00
749 1 0.00
751 1 0.00
767 41 0.06
768 553 0.76
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.31
Consensus pattern (747 bp):
AAAAATAAATTATATCATCACAAATTAAACTCATATAATCATACCAAAAAAATAAATTTAAACTT
TTATGAATAAAAATAAATTATACCTTAAAAATTTAAACTCATATAACTATACCCAAAAAATAAAT
TTAAACTTCTACAAAAATAGATAAGTTATACTCTAAGAACCTAAACTCATATAATCAACCCAAAA
AATAAATTTAAACTTCTACAAATAAAAATAAATTATACCATCAAAAATGTAAACTCACATAACCA
TACCCAAAAACACATTTAAACTCTTACAAATAAAAATAAATTATACAATAAAAAATTTAAATTCA
TATAATCATAACAAAAAACCACATTTAAACTTCTACAAATAAAAATAAATTATACCTTAAAAATT
TAAACTCGTTAAATCATGCTGAAAAACAAATTTAAACTTCTAAAAATAAAGATAAATAATAACCT
AAAAATTTAAACTCATATAATCAAACTAAAAAATAAATTTAAACTTGTACAAATAAAAATAAATT
ATACCTTCAAAAATTTAAACTCATATAATCATACTTAAAAAACACATTTAAACTTTTAAAAATCA
AAATAAATTATACTCTAAAAATTTAAATTCGCATAATCAAGCAAAAATAAAAAATATATTATACC
TTCAAAACTTAAACTCGTATAATCAATACTTACAAATAAATTTATACTTCAAAAAATAAAAATAA
ATAATACCTTCAATTAAACTAATTTTATGAAT
Found at i:1225004 original size:72 final size:73
Alignment explanation
Indices: 1224790--1225404 Score: 624
Period size: 73 Copynumber: 8.4 Consensus size: 73
1224780 TAATTTTATG
* * * *
1224790 AATAAAAATAAATTATATCATCACAAA-TTAAACTCGTATAATCATACCCAAAAAATAAATTTAA
1 AATAAAAATAAATTATA-CCTTAAAAATTTAAACTCATATAATCATACCCAAAAAATAAATTTAA
* **
1224854 ACTTTTATG
65 ACTTCTACA
*
1224863 AATTAAAATAAATTATACCTTAAAAATTTAAACTCATATAA-CTATACCCAAAAAATAAATTTAA
1 AATAAAAATAAATTATACCTTAAAAATTTAAACTCATATAATC-ATACCCAAAAAATAAATTTAA
1224927 ACTTCTACA
65 ACTTCTACA
* * * * *
1224936 AATATAGATAAGTTATA-CTCTAAGAACTTAAACTCATATAATCA-ACCCAAAAAATAAATTTAA
1 AATAAAAATAAATTATACCT-TAAAAATTTAAACTCATATAATCATACCCAAAAAATAAATTTAA
1224999 ACTTCTACA
65 ACTTCTACA
* * * *
1225008 AATAAAAATAAATTATACCATCAAAAATTTAAACTCACATAATCATACCC-AAAAACACATTTAA
1 AATAAAAATAAATTATACC-TTAAAAATTTAAACTCATATAATCATACCCAAAAAATAAATTTAA
1225072 AC-TCTTACA
65 ACTTC-TACA
* * * * * *
1225081 AATAAAAATAAATTATACAATAAAAAATTTAAATTCATATAATCATA-ACAAAAAACCACATTTA
1 AATAAAAATAAATTATAC-CTTAAAAATTTAAACTCATATAATCATACCCAAAAAA-TAAATTTA
1225145 AACTTCTACA
64 AACTTCTACA
* * * ** *
1225155 AATAAAAATAAATTATATCTTAAAAATTTAAACTCGT-TAAATCAT-GCTGAAAAACAAATTTAA
1 AATAAAAATAAATTATACCTTAAAAATTTAAACTCATAT-AATCATACCCAAAAAATAAATTTAA
* *
1225218 ATTTCTAAA
65 ACTTCTACA
* * * * *
1225227 AATTAAGATAAATAATAACC-TAAAAATTTAAACTCATATAATCA-AACTAAAAAATAAATTTAA
1 AATAAAAATAAATTAT-ACCTTAAAAATTTAAACTCATATAATCATACCCAAAAAATAAATTTAA
*
1225290 ACTTGTACA
65 ACTTCTACA
* ** * * *
1225299 AATAAAAATAAATTATACCTTCAAAAATTTAAACTCTTATAATCATACTTAGAAAACACATTTAA
1 AATAAAAATAAATTATACCTT-AAAAATTTAAACTCATATAATCATACCCAAAAAATAAATTTAA
* *
1225364 ACTTTTAAA
65 ACTTCTACA
* *
1225373 AATCAAAATAAATTGTA-CTCTAAAAATTTAAA
1 AATAAAAATAAATTATACCT-TAAAAATTTAAA
1225405 TTCGCATAAT
Statistics
Matches: 458, Mismatches: 63, Indels: 42
0.81 0.11 0.07
Matches are distributed among these distances:
71 3 0.01
72 139 0.30
73 239 0.52
74 75 0.16
75 2 0.00
ACGTcount: A:0.54, C:0.14, G:0.02, T:0.30
Consensus pattern (73 bp):
AATAAAAATAAATTATACCTTAAAAATTTAAACTCATATAATCATACCCAAAAAATAAATTTAAA
CTTCTACA
Found at i:1225024 original size:218 final size:219
Alignment explanation
Indices: 1224790--1225404 Score: 667
Period size: 218 Copynumber: 2.8 Consensus size: 219
1224780 TAATTTTATG
* * *
1224790 AATAAAAATAAATTATATCATCACAAA-TTAAACTCGTATAATCATACCCAAAAAATAAATTTAA
1 AATAAAAATAAATTATAACATCAAAAATTTAAACTCATATAATCATACCCAAAAAATAAATTTAA
** * *
1224854 ACTTTTATGAATTAAAATAAATTATACCTTAAAAATTTAAACTCATATAA-CTATACCCAAAAAA
66 ACTTTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCATATAATC-ATA-ACAAAAAA
* * * * *
1224918 -TAAATTTAAACTTCTACAAATATAGATAAGTTATA-CTCTAAGAACTTAAACTCA-TATAATCA
129 CCAAATTTAAACTTCTACAAATAAAAATAAATTATATCT-TAAAAACTTAAACTCATTA-AATCA
* *
1224980 ACCCAAAAAATAAATTTAAACTTCTACA
192 ACCCAAAAAACAAATTTAAACTTCTAAA
* * * *
1225008 AATAAAAATAAATTATACCATCAAAAATTTAAACTCACATAATCATACCC-AAAAACACATTTAA
1 AATAAAAATAAATTATAACATCAAAAATTTAAACTCATATAATCATACCCAAAAAATAAATTTAA
* * * *
1225072 ACTCTTACAAATAAAAATAAATTATACAATAAAAAATTTAAATTCATATAATCATAACAAAAAAC
66 ACTTTTACAAATAAAAATAAATTATAC-CTTAAAAATTTAAACTCATATAATCATAACAAAAAAC
* * * **
1225137 CACATTTAAACTTCTACAAATAAAAATAAATTATATCTTAAAAATTTAAACTCGTTAAATCATGC
130 CAAATTTAAACTTCTACAAATAAAAATAAATTATATCTTAAAAACTTAAACTCATTAAATCAACC
** *
1225202 TGAAAAACAAATTTAAATTTCTAAA
195 CAAAAAACAAATTTAAACTTCTAAA
* * * * * *
1225227 AATTAAGATAAATAATAACCT-AAAAATTTAAACTCATATAATCA-AACTAAAAAATAAATTTAA
1 AATAAAAATAAATTATAACATCAAAAATTTAAACTCATATAATCATACCCAAAAAATAAATTTAA
* * *
1225290 ACTTGTACAAATAAAAATAAATTATACCTTCAAAAATTTAAACTCTTATAATCAT-ACTTAGAAA
66 ACTTTTACAAATAAAAATAAATTATACCTT-AAAAATTTAAACTCATATAATCATAAC--AAAAA
* * * * * *
1225354 A-CACATTTAAACTTTTAAAAATCAAAATAAATTGTA-CTCTAAAAATTTAAA
128 ACCAAATTTAAACTTCTACAAATAAAAATAAATTATATCT-TAAAAACTTAAA
1225405 TTCGCATAAT
Statistics
Matches: 336, Mismatches: 50, Indels: 22
0.82 0.12 0.05
Matches are distributed among these distances:
217 7 0.02
218 191 0.57
219 133 0.40
220 5 0.01
ACGTcount: A:0.54, C:0.14, G:0.02, T:0.30
Consensus pattern (219 bp):
AATAAAAATAAATTATAACATCAAAAATTTAAACTCATATAATCATACCCAAAAAATAAATTTAA
ACTTTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCATATAATCATAACAAAAAACC
AAATTTAAACTTCTACAAATAAAAATAAATTATATCTTAAAAACTTAAACTCATTAAATCAACCC
AAAAAACAAATTTAAACTTCTAAA
Found at i:1225263 original size:291 final size:290
Alignment explanation
Indices: 1224790--1225424 Score: 789
Period size: 291 Copynumber: 2.2 Consensus size: 290
1224780 TAATTTTATG
* * * *
1224790 AATAAAAATAAATTATATCATCACAAA-TTAAACTCGTATAATCATACCCAAAAAATAAATTTAA
1 AATAAAAATAAATTATA-CAT-AAAAATTTAAATTCGTATAATCATA-ACAAAAAACAAATTTAA
* ** * * *
1224854 ACTTTTATGAATTAAAATAAATTATACCTTAAAAATTTAAACTCATATAACTATACCCAAAAAAT
63 ACTTCTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCATATAAATATACCCAAAAAAC
* * * * *
1224919 AAATTTAAACTTCTACAAATATAGATAAGTTATACTCTAAGAACTTAAACTCATATAATCAACCC
128 AAATTTAAACTTCTAAAAATATAGATAAATAATACTCTAAAAACTTAAACTCATATAATCAAACC
1224984 AAAAAATAAATTTAAACTTCTACAAATAAAAATAAATTATACCATCAAAAATTTAAACTCACATA
193 AAAAAATAAATTTAAACTTCTACAAATAAAAATAAATTATACCATCAAAAATTTAAACTCACATA
*
1225049 ATCATACCCA-AAAACACATTTAAACTCTTACA
258 ATCATACCCAGAAAACACATTTAAACTCTTAAA
* *
1225081 AATAAAAATAAATTATACAATAAAAAATTTAAATTCATATAATCATAACAAAAAACCACATTTAA
1 AATAAAAATAAATTATAC-AT-AAAAATTTAAATTCGTATAATCATAACAAAAAA-CAAATTTAA
* * * **
1225146 ACTTCTACAAATAAAAATAAATTATATCTTAAAAATTTAAACTCGT-TAAATCAT-GCTGAAAAA
63 ACTTCTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCATATAAAT-ATACCCAAAAAA
* *
1225209 CAAATTTAAATTTCTAAAAAT-TAAGATAAATAATAAC-CTAAAAATTTAAACTCATATAATCAA
127 CAAATTTAAACTTCTAAAAATAT-AGATAAATAAT-ACTCTAAAAACTTAAACTCATATAATCAA
* * * **
1225272 ACTAAAAAATAAATTTAAACTTGTACAAATAAAAATAAATTATACCTTCAAAAATTTAAACTCTT
190 ACCAAAAAATAAATTTAAACTTCTACAAATAAAAATAAATTATACCATCAAAAATTTAAACTCAC
** *
1225337 ATAATCATACTTAGAAAACACATTTAAACTTTTAAA
255 ATAATCATACCCAGAAAACACATTTAAACTCTTAAA
* * * * *
1225373 AATCAAAATAAATTGTACTCTAAAAATTTAAATTCGCATAATCA-AGCAAAAA
1 AATAAAAATAAATTATAC-ATAAAAATTTAAATTCGTATAATCATAACAAAAA
1225425 TAAAAAATAT
Statistics
Matches: 296, Mismatches: 41, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
290 9 0.03
291 182 0.61
292 105 0.35
ACGTcount: A:0.54, C:0.14, G:0.02, T:0.30
Consensus pattern (290 bp):
AATAAAAATAAATTATACATAAAAATTTAAATTCGTATAATCATAACAAAAAACAAATTTAAACT
TCTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCATATAAATATACCCAAAAAACAAA
TTTAAACTTCTAAAAATATAGATAAATAATACTCTAAAAACTTAAACTCATATAATCAAACCAAA
AAATAAATTTAAACTTCTACAAATAAAAATAAATTATACCATCAAAAATTTAAACTCACATAATC
ATACCCAGAAAACACATTTAAACTCTTAAA
Found at i:1225569 original size:22 final size:25
Alignment explanation
Indices: 1225537--1225618 Score: 109
Period size: 24 Copynumber: 3.4 Consensus size: 25
1225527 TAATTTTATG
1225537 AATAAAAATAAATTATA-TTTTA-A
1 AATAAAAATAAATTATATTTTTACA
1225560 AAT-AAAATAAATTTATATTTTTACA
1 AATAAAAATAAA-TTATATTTTTACA
*
1225585 AATAAAAATAAA-TAAATTTTTACA
1 AATAAAAATAAATTATATTTTTACA
*
1225609 AATAATAATA
1 AATAAAAATA
1225619 CTTTAAAATA
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
22 8 0.15
23 8 0.15
24 25 0.47
25 4 0.08
26 8 0.15
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
AATAAAAATAAATTATATTTTTACA
Found at i:1225575 original size:40 final size:40
Alignment explanation
Indices: 1225497--1225575 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 40
1225487 TACTTCAAAA
* * * *
1225497 AATAAAAATAAATAATACCTTCAATTAAACTAATTTTATG
1 AATAAAAATAAATAATACCTTAAAATAAAATAAATTTATG
* **
1225537 AATAAAAATAAATTATATTTTAAAATAAAATAAATTTAT
1 AATAAAAATAAATAATACCTTAAAATAAAATAAATTTAT
1225576 ATTTTTACAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.37
Consensus pattern (40 bp):
AATAAAAATAAATAATACCTTAAAATAAAATAAATTTATG
Found at i:1225878 original size:19 final size:20
Alignment explanation
Indices: 1225841--1225878 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1225831 TTTATAAAAG
*
1225841 TTTATTTTCATTTAAAATTT
1 TTTATTTTCATTAAAAATTT
1225861 TTTATTTT-ATTAAAAATT
1 TTTATTTTCATTAAAAATT
1225879 AAAAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTATTTTCATTAAAAATTT
Found at i:1226188 original size:14 final size:15
Alignment explanation
Indices: 1226148--1226188 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1226138 AAAATGTTCA
* *
1226148 TAAAAAAATATATTT
1 TAAAAATATTTATTT
1226163 TAAAAATATTTATTT
1 TAAAAATATTTATTT
1226178 TAAAAAT-TTTA
1 TAAAAATATTTA
1226189 AAAAATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 4 0.17
15 20 0.83
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TAAAAATATTTATTT
Found at i:1230489 original size:24 final size:24
Alignment explanation
Indices: 1230438--1230483 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1230428 TCATAAATAC
* *
1230438 TAAACGAATATGTTTATGAACAAA
1 TAAACGAACATATTTATGAACAAA
*
1230462 TAAACGAACATATTTGTGAACA
1 TAAACGAACATATTTATGAACA
1230484 TTTAAATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28
Consensus pattern (24 bp):
TAAACGAACATATTTATGAACAAA
Found at i:1230641 original size:23 final size:21
Alignment explanation
Indices: 1230615--1230664 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1230605 AATCAAACAA
*
1230615 TAAACTAGTTTTAAATCAATTAT
1 TAAA-TAGCTTTAAAT-AATTAT
1230638 TAAATAGCTTTAAATAATT-T
1 TAAATAGCTTTAAATAATTAT
1230658 ATAAATA
1 -TAAATA
1230665 AATTTCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 10 0.40
22 10 0.40
23 4 0.16
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (21 bp):
TAAATAGCTTTAAATAATTAT
Found at i:1230662 original size:21 final size:21
Alignment explanation
Indices: 1230614--1230664 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
1230604 TAATCAAACA
*
1230614 ATAAACTAGTTTTAAATCAATT
1 ATAAA-TAGCTTTAAATCAATT
1230636 ATTAAATAGCTTTAAAT-AATTT
1 A-TAAATAGCTTTAAATCAA-TT
1230658 ATAAATA
1 ATAAATA
1230665 AATTTCTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 8 0.31
22 14 0.54
23 4 0.15
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (21 bp):
ATAAATAGCTTTAAATCAATT
Found at i:1231463 original size:22 final size:21
Alignment explanation
Indices: 1231424--1231471 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
1231414 CGTGTTCATG
*
1231424 TTATTTTTGTATTATATTCTAA
1 TTATTTTTGTAATATATT-TAA
*
1231446 TTATTTTT-TAATATTATTTTA
1 TTATTTTTGTAATA-TATTTAA
1231467 TTATT
1 TTATT
1231472 GATTTCAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (21 bp):
TTATTTTTGTAATATATTTAA
Found at i:1231758 original size:22 final size:23
Alignment explanation
Indices: 1231719--1231772 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
1231709 TCATGTTATG
1231719 TTTATATTATTTTTATATCGTAT
1 TTTATATTATTTTTATATCGTAT
*
1231742 TTTA-ATT-TTTTTCATATTGTAT
1 TTTATATTATTTTT-ATATCGTAT
1231764 GTTTCATAT
1 -TTT-ATAT
1231773 CTCAATTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 5 0.19
22 11 0.42
23 7 0.27
24 1 0.04
25 2 0.08
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.65
Consensus pattern (23 bp):
TTTATATTATTTTTATATCGTAT
Found at i:1232644 original size:24 final size:24
Alignment explanation
Indices: 1232617--1232671 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
1232607 GGTTTTTTTT
*
1232617 TTGTTTATCAAAAATT-GTGGCTTA
1 TTGTTTATC-AAAATTGGTGGCTAA
*
1232641 TTGTTTGTCAAAATTGGTGGCTAA
1 TTGTTTATCAAAATTGGTGGCTAA
1232665 TT-TTTAT
1 TTGTTTAT
1232672 TGCAAAATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.49
Consensus pattern (24 bp):
TTGTTTATCAAAATTGGTGGCTAA
Found at i:1235229 original size:21 final size:22
Alignment explanation
Indices: 1235200--1235245 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1235190 TGTTCAGACA
* *
1235200 AGTAGTACTCCACAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1235222 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1235243 AGT
1 AGT
1235246 TTCAACAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:1236109 original size:42 final size:41
Alignment explanation
Indices: 1236062--1236160 Score: 118
Period size: 36 Copynumber: 2.5 Consensus size: 41
1236052 CCAACCTAAG
1236062 TCTATTGAATTGGTAAAACCCTAAATTGGTAATGAAACTACC
1 TCTATTGAATTGGT-AAACCCTAAATTGGTAATGAAACTACC
* *
1236104 TCTATTG-ATT--T--ACCCTAAATTGGTGATGAAACTATC
1 TCTATTGAATTGGTAAACCCTAAATTGGTAATGAAACTACC
*
1236140 TCTATTGACTTGGTAAGACCC
1 TCTATTGAATTGGTAA-ACCC
1236161 ATGCTTTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
36 30 0.62
37 2 0.04
39 2 0.04
41 3 0.06
42 11 0.23
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (41 bp):
TCTATTGAATTGGTAAACCCTAAATTGGTAATGAAACTACC
Found at i:1236119 original size:36 final size:36
Alignment explanation
Indices: 1236079--1236147 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
1236069 AATTGGTAAA
1236079 ACCCTAAATTGGTAATGAAACTACCTCTATTGATTT
1 ACCCTAAATTGGTAATGAAACTACCTCTATTGATTT
* *
1236115 ACCCTAAATTGGTGATGAAACTATCTCTATTGA
1 ACCCTAAATTGGTAATGAAACTACCTCTATTGA
1236148 CTTGGTAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (36 bp):
ACCCTAAATTGGTAATGAAACTACCTCTATTGATTT
Found at i:1237909 original size:44 final size:44
Alignment explanation
Indices: 1237792--1237914 Score: 169
Period size: 43 Copynumber: 2.8 Consensus size: 44
1237782 TTGTTAGAAT
* *
1237792 TTGGGTGGCTATGCCAA-TCTACAGAAAAATAAATAAATATGCAA
1 TTGGGTGGCTATGCCAATTC-ACGGAAAAATAAATAAATATACAA
* * *
1237836 TTGGG-GGCTATGCTAATCCACGAAAAAATAAATAAATATACAA
1 TTGGGTGGCTATGCCAATTCACGGAAAAATAAATAAATATACAA
*
1237879 TTGGGTGGTTATGCCAATTCACGGAAAAATAAATAA
1 TTGGGTGGCTATGCCAATTCACGGAAAAATAAATAA
1237915 TAAAAACACC
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
43 36 0.53
44 32 0.47
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (44 bp):
TTGGGTGGCTATGCCAATTCACGGAAAAATAAATAAATATACAA
Found at i:1242622 original size:44 final size:43
Alignment explanation
Indices: 1242559--1242682 Score: 203
Period size: 44 Copynumber: 2.8 Consensus size: 43
1242549 TTGTTAGAAT
1242559 TTGGGTGGCTATGCCAATCCACAGAAAAATAAATAAATATGCAA
1 TTGGGTGGCTATGCCAATCCAC-GAAAAATAAATAAATATGCAA
*
1242603 TTGGGTAGCTATGCCAATCCACGAAAAAATAAATAAATATGCAA
1 TTGGGTGGCTATGCCAATCCACG-AAAAATAAATAAATATGCAA
*
1242647 TTGGGTGGCTATGCCAATTCACGGAAAAATAAATAA
1 TTGGGTGGCTATGCCAATCCAC-GAAAAATAAATAA
1242683 TAAAAACACT
Statistics
Matches: 75, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
43 1 0.01
44 73 0.97
45 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (43 bp):
TTGGGTGGCTATGCCAATCCACGAAAAATAAATAAATATGCAA
Found at i:1245582 original size:2 final size:2
Alignment explanation
Indices: 1245575--1245613 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1245565 TATACACATC
1245575 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1245614 CAATGCCTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1245935 original size:16 final size:16
Alignment explanation
Indices: 1245922--1245958 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1245912 GAAGAAAATT
1245922 GAAAACATGAAAAAGA
1 GAAAACATGAAAAAGA
*
1245938 GAAAACGTGAAAAAGA
1 GAAAACATGAAAAAGA
*
1245954 TAAAA
1 GAAAA
1245959 AAAAAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.68, C:0.05, G:0.19, T:0.08
Consensus pattern (16 bp):
GAAAACATGAAAAAGA
Found at i:1247604 original size:18 final size:19
Alignment explanation
Indices: 1247559--1247604 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
1247549 ATTAAAAATA
*
1247559 TTAAAAAAATTATTAATTT
1 TTAAAAAAATAATTAATTT
* *
1247578 TT-AATAAATAATT-GTTT
1 TTAAAAAAATAATTAATTT
1247595 TTAAAAAAAT
1 TTAAAAAAAT
1247605 TAAAATACTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 5 0.23
18 15 0.68
19 2 0.09
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
TTAAAAAAATAATTAATTT
Found at i:1248015 original size:15 final size:16
Alignment explanation
Indices: 1247991--1248020 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1247981 TTTTTTAAAT
1247991 GAAAATTTTAAAAAAC
1 GAAAATTTTAAAAAAC
1248007 GAAAA-TTTAAAAAA
1 GAAAATTTTAAAAAA
1248021 ATTCTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.23
Consensus pattern (16 bp):
GAAAATTTTAAAAAAC
Found at i:1248021 original size:16 final size:16
Alignment explanation
Indices: 1247991--1248021 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1247981 TTTTTTAAAT
*
1247991 GAAAATTTTAAAAAAC
1 GAAAATTTAAAAAAAC
1248007 GAAAATTTAAAAAAA
1 GAAAATTTAAAAAAA
1248022 TTCTTTTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.23
Consensus pattern (16 bp):
GAAAATTTAAAAAAAC
Found at i:1249362 original size:21 final size:22
Alignment explanation
Indices: 1249328--1249387 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 22
1249318 GATATCGGTC
1249328 AATT-AAATTAATAATAA-AAAT
1 AATTAAAATT-ATAATAATAAAT
*
1249349 AATTAAAATTATAA-AATTAAT
1 AATTAAAATTATAATAATAAAT
1249370 AATTATAATATTATAATA
1 AATTA-AA-ATTATAATA
1249388 TGATCATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 7 0.21
23 7 0.21
24 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AATTAAAATTATAATAATAAAT
Found at i:1251028 original size:16 final size:16
Alignment explanation
Indices: 1251007--1251057 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
1250997 TTTCGATTAT
1251007 TTTTGAGTTTGAGTCA
1 TTTTGAGTTTGAGTCA
*
1251023 TTTTGAGTTTGGGTCA
1 TTTTGAGTTTGAGTCA
* * *
1251039 TTTCGAGTTCGAATCA
1 TTTTGAGTTTGAGTCA
1251055 TTT
1 TTT
1251058 CGGGTTCGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.18, C:0.10, G:0.24, T:0.49
Consensus pattern (16 bp):
TTTTGAGTTTGAGTCA
Found at i:1251090 original size:16 final size:16
Alignment explanation
Indices: 1251036--1251084 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
1251026 TGAGTTTGGG
*
1251036 TCATTTCGAGTTCGAA
1 TCATTTCGGGTTCGAA
1251052 TCATTTCGGGTTCGAA
1 TCATTTCGGGTTCGAA
1251068 TCATTTCGGGTTCGAA
1 TCATTTCGGGTTCGAA
1251084 T
1 T
1251085 TGTTTCTCGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.39
Consensus pattern (16 bp):
TCATTTCGGGTTCGAA
Found at i:1251104 original size:32 final size:32
Alignment explanation
Indices: 1251011--1251108 Score: 88
Period size: 32 Copynumber: 3.1 Consensus size: 32
1251001 GATTATTTTT
* * * *
1251011 GAGTTTGAGTCATTTTGAGTTTGGGTCATTTC
1 GAGTTCGAATCATTTCGCGTTTGGGTCATTTC
* * **
1251043 GAGTTCGAATCATTTCGGGTTCGAATCATTTC
1 GAGTTCGAATCATTTCGCGTTTGGGTCATTTC
* ** *
1251075 GGGTTCGAATTGTTTCTCGTTTGGGTCATTTC
1 GAGTTCGAATCATTTCGCGTTTGGGTCATTTC
1251107 GA
1 GA
1251109 ATTCAGGTCA
Statistics
Matches: 50, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.16, C:0.14, G:0.27, T:0.43
Consensus pattern (32 bp):
GAGTTCGAATCATTTCGCGTTTGGGTCATTTC
Found at i:1252593 original size:50 final size:50
Alignment explanation
Indices: 1252533--1252767 Score: 346
Period size: 50 Copynumber: 4.7 Consensus size: 50
1252523 TATACTTAGA
* * *
1252533 GTCAACAATTATGGCTACCTTTCTCTATTGTCAAAGGTTGGTGAATAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
1252583 ATCAACAATTATGGTCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
1252633 GTCAACAATTATGGCCACCTC-CATCTATTGTCAAAGGTTGGTGAAAAATC
1 GTCAACAATTATGGCCACCTCTC-TCTATTGTCAAAGGTTGGTGAAGAATC
* *
1252683 GTCAACAATTATGACCACCTCTCTCTATTATCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
1252733 GTCAATAATTGTGGCCACCTCTCTCTATTATCAAA
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAA
1252768 TGTACTTTTC
Statistics
Matches: 168, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
49 1 0.01
50 166 0.99
51 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:1257319 original size:11 final size:11
Alignment explanation
Indices: 1257303--1257332 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1257293 TTCTCTTCAA
*
1257303 AAAAAAAAAAG
1 AAAAAAAAAAC
1257314 AAAAAAAAAAC
1 AAAAAAAAAAC
1257325 AAAAAAAA
1 AAAAAAAA
1257333 CAAAACAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.93, C:0.03, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:1257321 original size:15 final size:15
Alignment explanation
Indices: 1257301--1257363 Score: 65
Period size: 15 Copynumber: 4.3 Consensus size: 15
1257291 CATTCTCTTC
1257301 AAAAAAAAAAAAGAA
1 AAAAAAAAAAAAGAA
*
1257316 AAAAAAAACAAA-AA
1 AAAAAAAAAAAAGAA
* *
1257330 AAACAAAACAAAGAA
1 AAAAAAAAAAAAGAA
* * *
1257345 AAAGAGAGAAAAGAA
1 AAAAAAAAAAAAGAA
1257360 AAAA
1 AAAA
1257364 CCTACTTAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
14 13 0.32
15 27 0.68
ACGTcount: A:0.86, C:0.05, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAGAA
Found at i:1258413 original size:55 final size:55
Alignment explanation
Indices: 1258324--1258895 Score: 854
Period size: 55 Copynumber: 10.4 Consensus size: 55
1258314 TCCTTCCGCC
*
1258324 TTTCAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCA-T
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACT
*
1258378 TTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-T
1 TTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACT
1258433 TTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-T
1 TTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACT
* *
1258488 TTTCCAGTCCTCAACGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACC
1 TTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACT
* *
1258544 TTTCAGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACT
1258599 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-T
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACT
*
1258653 TTTCCAGTCCTCAAAGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-T
1 TTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACT
*
1258708 TTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACC
1 TTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACT
* * * * *
1258764 TTTCATTCCCCAAAGAGCAGGACACTTTTCAAAGCCCACACAAGTGGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACT
* *
1258819 TTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACT
* * *
1258874 TTTTACTCCTCAATGAGCAGGA
1 TTTCAGTCCTCAAAGAGCAGGA
1258896 TACAATTTAT
Statistics
Matches: 484, Mismatches: 26, Indels: 15
0.92 0.05 0.03
Matches are distributed among these distances:
54 10 0.02
55 464 0.96
56 10 0.02
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (55 bp):
TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACT
Found at i:1258599 original size:29 final size:29
Alignment explanation
Indices: 1258511--1258599 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
1258501 ACGAGCAGGA
1258511 CACCTCTTAAAGCCCACACAAGTTGGTGG
1 CACCTCTTAAAGCCCACACAAGTTGGTGG
* * **
1258540 CACCT-TT-CAGTCCC-CA-AAG-AGCAGG
1 CACCTCTTAAAG-CCCACACAAGTTGGTGG
1258565 ACACCTCTTAAAGCCCACACAAGTTGGTGG
1 -CACCTCTTAAAGCCCACACAAGTTGGTGG
1258595 CACCT
1 CACCT
1258600 TTCAGTCCTC
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 3 0.07
26 8 0.18
27 9 0.20
28 9 0.20
29 13 0.29
30 3 0.07
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (29 bp):
CACCTCTTAAAGCCCACACAAGTTGGTGG
Found at i:1258625 original size:26 final size:26
Alignment explanation
Indices: 1258540--1258629 Score: 74
Period size: 26 Copynumber: 3.3 Consensus size: 26
1258530 AAGTTGGTGG
*
1258540 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
1258566 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
1258595 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
1258621 CACCTTTCA
1 CACCTTTCA
1258630 AAGCCCACAC
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
25 3 0.06
26 17 0.36
27 8 0.17
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (26 bp):
CACCTTTCAGTCCACAAAGAGCAGGA
Found at i:1259508 original size:15 final size:15
Alignment explanation
Indices: 1259488--1259529 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 15
1259478 GATAAAGTGT
1259488 TTGAAAAAAAAAAAA
1 TTGAAAAAAAAAAAA
1259503 TTG---AAAAAAAAA
1 TTGAAAAAAAAAAAA
1259515 TTGAAAAAAAAAAAA
1 TTGAAAAAAAAAAAA
1259530 AAAATTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 12 0.50
15 12 0.50
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (15 bp):
TTGAAAAAAAAAAAA
Found at i:1259511 original size:12 final size:12
Alignment explanation
Indices: 1259494--1259526 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
1259484 GTGTTTGAAA
1259494 AAAAAAAAATTG
1 AAAAAAAAATTG
1259506 AAAAAAAAATTG
1 AAAAAAAAATTG
1259518 AAAAAAAAA
1 AAAAAAAAA
1259527 AAAAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:1259562 original size:21 final size:21
Alignment explanation
Indices: 1259538--1259594 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1259528 AAAAAATTTA
1259538 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
1259559 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
1259580 AATGTATCGATACAT
1 AATGTATCGATACAT
1259595 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:1259674 original size:19 final size:19
Alignment explanation
Indices: 1259650--1259717 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1259640 AATTCAACAA
1259650 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1259669 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1259684 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1259701 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1259718 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1259689 original size:13 final size:13
Alignment explanation
Indices: 1259671--1259695 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1259661 ACATAAGTTT
1259671 TGTATCGATACAA
1 TGTATCGATACAA
1259684 TGTATCGATACA
1 TGTATCGATACA
1259696 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1259693 original size:32 final size:32
Alignment explanation
Indices: 1259652--1259714 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1259642 TTCAACAATT
*
1259652 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1259684 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1259715 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1259775 original size:13 final size:13
Alignment explanation
Indices: 1259757--1259782 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1259747 CATTTTTCTG
1259757 TGTATCGATACAT
1 TGTATCGATACAT
1259770 TGTATCGATACAT
1 TGTATCGATACAT
1259783 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1259779 original size:33 final size:33
Alignment explanation
Indices: 1259737--1259803 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1259727 GCCAAGGAAA
***
1259737 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1259770 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1259803 T
1 T
1259804 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1262326 original size:28 final size:27
Alignment explanation
Indices: 1262259--1262329 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
1262249 CTTCACAATC
* *
1262259 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
1262286 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
1262314 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
1262330 TGACTTTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:1262374 original size:51 final size:50
Alignment explanation
Indices: 1262314--1262484 Score: 180
Period size: 51 Copynumber: 3.3 Consensus size: 50
1262304 TTATTTCTGA
* * *
1262314 GGGGATACTCCAACCCTGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCC-GATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
1262365 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAA-CCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
* * *
1262418 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAA-CCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
1262470 GAGGATACTCCAACC
1 GGGGATACTCCAACC
1262485 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 19, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
51 33 0.34
52 21 0.22
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (50 bp):
GGGGATACTCCAACCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:1262477 original size:105 final size:104
Alignment explanation
Indices: 1262145--1262484 Score: 255
Period size: 105 Copynumber: 3.2 Consensus size: 104
1262135 CTCAATTCTC
* * * * ** *
1262145 CACAATCGAGGATATTCCAACTCCGATTTTACTTTCAAAACATTAATTT-T-CTATAATCGGGGA
1 CACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTCCTTTAATCGGGGA
*
1262208 TACTCCAACTCCGATTTTATTTCCAAAAAAAACACCAATTTCTT
66 TACTCCAA-TCCGATTTTATTTCC---AAAAATACCAATTT-TT
* * * ** * * * * * *
1262252 CACAATCGGGGACACTCCAACCCC-G-TTAATCATCGGGGATACTCCAA---CCCCGTTATTTCT
1 CACAATCGAGGATACTCCAACCCCGGTTTTATTTTC---AAAACACCAATTTCTCCTTTA-ATC-
* * * * *
1262312 GAGGGGATACTCCAACCCTGACTTTATTTTC-AAAATATCGATTTTT
61 --GGGGATACTCCAATCC-GATTTTATTTCCAAAAATACCAATTTTT
* * *
1262358 CATAATCGGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATCGGGGA
1 CACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTCCTTTAATCGGGGA
1262423 TACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTT
66 TACTCCAA-TCCGATTTTATTTCCAAAAATACCAATTTTT
1262463 CACAATCGAGGATACTCCAACC
1 CACAATCGAGGATACTCCAACC
1262485 TCGTTATTTC
Statistics
Matches: 173, Mismatches: 43, Indels: 36
0.69 0.17 0.14
Matches are distributed among these distances:
104 23 0.13
105 46 0.27
106 24 0.14
107 36 0.21
108 19 0.11
110 2 0.01
111 23 0.13
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.31
Consensus pattern (104 bp):
CACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTCCTTTAATCGGGGA
TACTCCAATCCGATTTTATTTCCAAAAATACCAATTTTT
Found at i:1262503 original size:28 final size:28
Alignment explanation
Indices: 1262467--1262548 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
1262457 ATTTTTCACA
*
1262467 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
1262495 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
1262523 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
1262549 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Done.