Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 4 of 290
Found at i:1181072 original size:64 final size:64
Alignment explanation
Indices: 1180971--1181101 Score: 217
Period size: 64 Copynumber: 2.0 Consensus size: 64
1180961 AGGTCATCCA
* * *
1180971 TTAATAAGAGTCTCAACTAAGTTGGGGAATTACTAAAAAAAGATCAATTTTTAACAAAAATAAG
1 TTAATAAGAGACTCAACTAAGTTAGGGAATTACTAAAAAAAGATCAAATTTTAACAAAAATAAG
* *
1181035 TTAATCAGAGACTCAACTAAGTTAGGGAATTATTAAAAAAAGATCAAATTTTAACAAAAATAAG
1 TTAATAAGAGACTCAACTAAGTTAGGGAATTACTAAAAAAAGATCAAATTTTAACAAAAATAAG
1181099 TTA
1 TTA
1181102 TATGAATATG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.28
Consensus pattern (64 bp):
TTAATAAGAGACTCAACTAAGTTAGGGAATTACTAAAAAAAGATCAAATTTTAACAAAAATAAG
Found at i:1187885 original size:21 final size:22
Alignment explanation
Indices: 1187860--1187900 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1187850 TTATTATTTT
1187860 ATAATAAAAATA-GAAAAATAA
1 ATAATAAAAATAGGAAAAATAA
*
1187881 ATAATCAAAATAGGAAAAAT
1 ATAATAAAAATAGGAAAAAT
1187901 TAGTTGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.20
Consensus pattern (22 bp):
ATAATAAAAATAGGAAAAATAA
Found at i:1193966 original size:3 final size:3
Alignment explanation
Indices: 1193958--1193989 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1193948 AAAAATTATT
1193958 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1193990 GATTGTGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1198523 original size:17 final size:16
Alignment explanation
Indices: 1198488--1198518 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1198478 TGTTGAGGAT
1198488 TTTAGTTTTTTTTTTA
1 TTTAGTTTTTTTTTTA
1198504 TTTA-TTTTTTTTTTA
1 TTTAGTTTTTTTTTTA
1198519 GATTTTAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.84
Consensus pattern (16 bp):
TTTAGTTTTTTTTTTA
Found at i:1200171 original size:21 final size:21
Alignment explanation
Indices: 1200129--1200171 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1200119 GTTTCGAAGG
**
1200129 ATTTATGTCTGTAATCTGTAA
1 ATTTATGTCTGTAATCCATAA
* *
1200150 ATTTATGTTTGTTATCCATAA
1 ATTTATGTCTGTAATCCATAA
1200171 A
1 A
1200172 AATAATAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (21 bp):
ATTTATGTCTGTAATCCATAA
Found at i:1213432 original size:12 final size:12
Alignment explanation
Indices: 1213410--1213438 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1213400 TAATAATAAA
1213410 TTAAT-GTTTAT
1 TTAATAGTTTAT
1213421 TTAATAGTTTAT
1 TTAATAGTTTAT
1213433 TTAATA
1 TTAATA
1213439 TAATAATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (12 bp):
TTAATAGTTTAT
Found at i:1214748 original size:3 final size:3
Alignment explanation
Indices: 1214740--1214766 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1214730 TTTTGAGACA
1214740 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1214767 TGACTAACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1214825 original size:28 final size:30
Alignment explanation
Indices: 1214766--1214825 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 30
1214756 TTATTATTAT
* *
1214766 TTGACTAACTGACTTTATTACATTTACTTA
1 TTGACTAACTGAATTTATTACATTTACATA
1214796 TTGACTAA-TGAATTT-TTA-ACTTTACATA
1 TTGACTAACTGAATTTATTACA-TTTACATA
1214824 TT
1 TT
1214826 ATGTTGGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 1 0.04
28 12 0.44
29 6 0.22
30 8 0.30
ACGTcount: A:0.32, C:0.13, G:0.07, T:0.48
Consensus pattern (30 bp):
TTGACTAACTGAATTTATTACATTTACATA
Found at i:1222154 original size:22 final size:23
Alignment explanation
Indices: 1222127--1222183 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
1222117 TTTAATATTT
*
1222127 TAAAAATTATATTTTTACTATCA
1 TAAAAATTACATTTTTACTATCA
*
1222150 TAAAAATTACATTTTTACTATTA
1 TAAAAATTACATTTTTACTATCA
1222173 TAAAAATTACA
1 TAAAAATTACA
1222184 ATTTAATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAAAATTACATTTTTACTATCA
Found at i:1229992 original size:19 final size:19
Alignment explanation
Indices: 1229954--1229994 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1229944 ATCAGCATGA
*
1229954 GGTACACGTGTTATTATTT
1 GGTACACGTGTTACTATTT
*
1229973 GGTACACGTGTTACTGTTT
1 GGTACACGTGTTACTATTT
1229992 GGT
1 GGT
1229995 TATTTCCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.12, G:0.27, T:0.44
Consensus pattern (19 bp):
GGTACACGTGTTACTATTT
Found at i:1235467 original size:16 final size:16
Alignment explanation
Indices: 1235432--1235464 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1235422 TTAATTTTTT
*
1235432 AATTTAAAATATATAA
1 AATTCAAAATATATAA
1235448 AATTCAAAAT-TATAA
1 AATTCAAAATATATAA
1235463 AA
1 AA
1235465 ATTATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTCAAAATATATAA
Found at i:1235481 original size:20 final size:19
Alignment explanation
Indices: 1235453--1235490 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1235443 TATAAAATTC
*
1235453 AAAATTATAAAAATTATTTA
1 AAAACTATAAAAA-TATTTA
1235473 AAAACTATAAAAATATTT
1 AAAACTATAAAAATATTT
1235491 TTAAATGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAACTATAAAAATATTTA
Found at i:1275873 original size:20 final size:20
Alignment explanation
Indices: 1275841--1275883 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
1275831 TTCAAAATAA
1275841 TTATTTTAGGTTG-AGATTAT
1 TTATTTTAGGTTGAAG-TTAT
1275861 TTATTTT-GAGTTGAAGTTAT
1 TTATTTTAG-GTTGAAGTTAT
1275881 TTA
1 TTA
1275884 AATTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 1 0.05
20 18 0.86
21 2 0.10
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.56
Consensus pattern (20 bp):
TTATTTTAGGTTGAAGTTAT
Found at i:1282150 original size:13 final size:13
Alignment explanation
Indices: 1282132--1282204 Score: 53
Period size: 13 Copynumber: 5.6 Consensus size: 13
1282122 TTATGTTTAG
1282132 TATATTATTATAT
1 TATATTATTATAT
1282145 TATATTATTATA-
1 TATATTATTATAT
* **
1282157 TA-ATAAAGATAT
1 TATATTATTATAT
* *
1282169 TTTATGTTTTA-AT
1 TATAT-TATTATAT
1282182 TATATTATATTATAT
1 TATA-T-TATTATAT
1282197 TATATTAT
1 TATATTAT
1282205 ATAAACTAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
11 6 0.14
12 3 0.07
13 22 0.50
14 7 0.16
15 6 0.14
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.58
Consensus pattern (13 bp):
TATATTATTATAT
Found at i:1282190 original size:5 final size:5
Alignment explanation
Indices: 1282180--1282206 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1282170 TTATGTTTTA
1282180 ATTAT ATTAT ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT AT
1282207 AAACTAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:1283495 original size:15 final size:15
Alignment explanation
Indices: 1283475--1283531 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
1283465 CGATGAATTT
*
1283475 ATTGAATTTATATTG
1 ATTGAAATTATATTG
*
1283490 ATTGAAATTATTTTG
1 ATTGAAATTATATTG
1283505 ATTGAAATTATATTG
1 ATTGAAATTATATTG
1283520 ATTG-AATTATAT
1 ATTGAAATTATAT
1283532 AATATATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
14 8 0.21
15 31 0.79
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (15 bp):
ATTGAAATTATATTG
Found at i:1283942 original size:23 final size:21
Alignment explanation
Indices: 1283916--1283967 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
1283906 ATGCACTTTA
1283916 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA--TCAGGCACCTCG
*
1283939 TGTGTTGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
1283960 TGTGTCGT
1 TGTGTCGT
1283968 TTTAGACACT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 19 0.70
23 8 0.30
ACGTcount: A:0.12, C:0.23, G:0.29, T:0.37
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:1285343 original size:13 final size:13
Alignment explanation
Indices: 1285327--1285351 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1285317 ATATTCCCAC
1285327 ATTATTTTGTATG
1 ATTATTTTGTATG
1285340 ATTATTTTGTAT
1 ATTATTTTGTAT
1285352 ATAAATGGTA
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:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (13 bp):
ATTATTTTGTATG
Found at i:1288590 original size:28 final size:28
Alignment explanation
Indices: 1288559--1288620 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
1288549 TAGTATAATC
* * *
1288559 GATTAACTGTTTGAAATTAAAATACCGA
1 GATTAACCGTTTCAAATTAAAATACAGA
*
1288587 GATTAACCGTTTCAAATTAAAATATAGA
1 GATTAACCGTTTCAAATTAAAATACAGA
1288615 GATTAA
1 GATTAA
1288621 ATCTTAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (28 bp):
GATTAACCGTTTCAAATTAAAATACAGA
Found at i:1293064 original size:9 final size:9
Alignment explanation
Indices: 1293050--1293076 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1293040 ATAATTACAT
1293050 ATATATATA
1 ATATATATA
1293059 ATATATATA
1 ATATATATA
1293068 ATATATATA
1 ATATATATA
1293077 TTTTGATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
ATATATATA
Found at i:1293556 original size:17 final size:17
Alignment explanation
Indices: 1293517--1293558 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1293507 TGATGAAAAC
*
1293517 ATTTTTTATTGTTTTCT
1 ATTTTTTATTATTTTCT
*
1293534 AATTTTTATATATTTT-T
1 ATTTTTTAT-TATTTTCT
1293551 ATTTTTTA
1 ATTTTTTA
1293559 AAAATCATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (17 bp):
ATTTTTTATTATTTTCT
Found at i:1303792 original size:72 final size:72
Alignment explanation
Indices: 1303675--1303887 Score: 363
Period size: 72 Copynumber: 3.0 Consensus size: 72
1303665 GAGCAAGAAA
*
1303675 AGACCCCTTACTATAGTAAGGGGCCCTTTCTTGCAGGATGCCGGGTGCGCAGGAACGCCCAACCT
1 AGACCCCTTACTATAGTAAGGGGCCATTTCTTGCAGGATGCCGGGTGCGCAGGAACGCCCAACCT
1303740 ATACCTC
66 ATACCTC
* * * * *
1303747 AGACCCCTTACTATAGTAAGGGGCCTTTTCTTCCAAGATGCCGGGTGCACAAGAACGCCCAACCT
1 AGACCCCTTACTATAGTAAGGGGCCATTTCTTGCAGGATGCCGGGTGCGCAGGAACGCCCAACCT
1303812 ATACCTC
66 ATACCTC
*
1303819 AGACCCCTTACTATAGTAAGGGGCCATTTCTTGTAGGATGCCGGGTGCGCAGGAACGCCCAACCT
1 AGACCCCTTACTATAGTAAGGGGCCATTTCTTGCAGGATGCCGGGTGCGCAGGAACGCCCAACCT
1303884 ATAC
66 ATAC
1303888 AAGAGATTTC
Statistics
Matches: 130, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 130 1.00
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.22
Consensus pattern (72 bp):
AGACCCCTTACTATAGTAAGGGGCCATTTCTTGCAGGATGCCGGGTGCGCAGGAACGCCCAACCT
ATACCTC
Found at i:1307476 original size:23 final size:24
Alignment explanation
Indices: 1307445--1307489 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1307435 TTCGAGAATT
*
1307445 ATTTGAATAAATAATTA-AAAATA
1 ATTTAAATAAATAATTAGAAAATA
*
1307468 ATTTAAATAAGTAATTAGAAAA
1 ATTTAAATAAATAATTAGAAAA
1307490 GACTTGAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (24 bp):
ATTTAAATAAATAATTAGAAAATA
Found at i:1313621 original size:180 final size:178
Alignment explanation
Indices: 1313124--1313817 Score: 755
Period size: 180 Copynumber: 4.0 Consensus size: 178
1313114 CAAAGCTGTC
* *
1313124 AAAAATGACCCAATTTCTAAATTAAAACAAATAG-AAATACAAAGTACACAATTTTTTTCAAATA
1 AAAAATGACCCAATTTCTAAATTAAAACACATAGAAAATACAAAGTAAAC-ATTTTTTTCAAATA
* * * * * *
1313188 CCCTTTGTACATTTTTTTTATAAACCTTATTAATTATTTA-AACTTTTTCCAGTACTTTCTCAGG
65 CCCTTTGTACAATTTTTAT-TAAACCTTATTAATT-TCTACAAC-TTCTCCACTACTTTCTCAGC
*
1313252 AAACAAACACCAAATAATGGTGGGTAATTAAAGAGTACCTCAAAGCTGCC-A
127 AAACAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAAGCTGCCAA
* * * * * *
1313303 AAAAATGACCAAATTTCTAAATTAAAACACATAGAAAACACAAAGCAAGCA-CTTCTTCAAATAC
1 AAAAATGACCCAATTTCTAAATTAAAACACATAGAAAATACAAAGTAAACATTTTTTTCAAATAC
* * * * * * *
1313367 CGTTTGCAGAATATTTTA-TAAACCTTACTAATTTGTACAACTTCCCCTCTACTTTCTCAGCAAA
66 CCTTTGTACAAT-TTTTATTAAACCTTATTAATTTCTACAACTTCTCCACTACTTTCTCAGCAAA
* * * *
1313431 CAAACACCAAGTAATGGCGGGTAATTAAAGAGTACCACAAAACCGCCAA
130 CAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAAGCTGCCAA
* * * *
1313480 AAAAAGGACCCAATTTCTAATTTAAAACACATACAAAATACAAAGTAAACATTTTTTTTCTAATA
1 AAAAATGACCCAATTTCTAAATTAAAACACATAGAAAATACAAAGTAAACA-TTTTTTTCAAATA
* *
1313545 CCCTTTGTATAATTTTTATTAAACCTTATTAATTTCAACAACTTCTCCGACTACTTTCTCAGCAA
65 CCCTTTGTACAATTTTTATTAAACCTTATTAATTTCTACAACTTCTCC-ACTACTTTCTCAGCAA
* * *
1313610 ACAAACACCAAGTAATGGTGAGTAATTAAAAAGCACCTCAAAGCTGCCAA
129 ACAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAAGCTGCCAA
*
1313660 AAAAATGACCCAATTTCTAAATTCAAACACATAG-----A-AAA-T--AC---TTTTTCAAATAC
1 AAAAATGACCCAATTTCTAAATTAAAACACATAGAAAATACAAAGTAAACATTTTTTTCAAATAC
* * * *
1313713 CCTTTGCT-C-ATTTTT-TTATGAACCTTATTAAATTGT-TAACTTTTCCCACTACTTTCTCAGC
66 CCTTTG-TACAATTTTTATTA--AACCTTATTAATTTCTACAACTTCT-CCACTACTTTCTCAGC
* * *
1313774 AAACAAACACCAAGTAATGATGGCTAACTAAAGAGTACCTCAAA
127 AAACAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAA
1313818 CAAGGCCATC
Statistics
Matches: 436, Mismatches: 67, Indels: 37
0.81 0.12 0.07
Matches are distributed among these distances:
165 3 0.01
166 64 0.15
167 32 0.07
168 1 0.00
171 2 0.00
173 1 0.00
174 3 0.01
175 1 0.00
176 63 0.14
177 62 0.14
178 24 0.06
179 81 0.19
180 99 0.23
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.30
Consensus pattern (178 bp):
AAAAATGACCCAATTTCTAAATTAAAACACATAGAAAATACAAAGTAAACATTTTTTTCAAATAC
CCTTTGTACAATTTTTATTAAACCTTATTAATTTCTACAACTTCTCCACTACTTTCTCAGCAAAC
AAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAAGCTGCCAA
Found at i:1332420 original size:5 final size:5
Alignment explanation
Indices: 1332405--1332443 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
1332395 TCTCTTTATT
1332405 TTTTCA TTTTA TTTTA TTTTA TTTGT- TTTTA TTTTA TTT
1 TTTT-A TTTTA TTTTA TTTTA TTT-TA TTTTA TTTTA TTT
1332444 ACCATATTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
4 1 0.03
5 25 0.81
6 5 0.16
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:1333331 original size:6 final size:6
Alignment explanation
Indices: 1333320--1333346 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1333310 CTTTGAATTT
1333320 TTTTAA TTTTAA TTTTAA TTTTAA TTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTT
1333347 CAATCAAGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTAA
Found at i:1339939 original size:16 final size:17
Alignment explanation
Indices: 1339911--1339943 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1339901 AATTAAAATG
1339911 TAATTTCATATTTTTAT
1 TAATTTCATATTTTTAT
1339928 TAATTT-ATATTTTTAT
1 TAATTTCATATTTTTAT
1339944 GGTTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
TAATTTCATATTTTTAT
Found at i:1351804 original size:19 final size:19
Alignment explanation
Indices: 1351782--1351820 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1351772 TAGATAGATG
1351782 ATAATTGAATTAAGGTTGT
1 ATAATTGAATTAAGGTTGT
1351801 ATAATTGAATTAAGGTTGT
1 ATAATTGAATTAAGGTTGT
1351820 A
1 A
1351821 CTCTTTGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (19 bp):
ATAATTGAATTAAGGTTGT
Found at i:1357469 original size:3 final size:3
Alignment explanation
Indices: 1357461--1357499 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1357451 AGTATAAAGG
1357461 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1357500 ACTGTGAGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1359637 original size:38 final size:38
Alignment explanation
Indices: 1359524--1359639 Score: 144
Period size: 38 Copynumber: 3.1 Consensus size: 38
1359514 ATTCTTACAT
* * * *
1359524 TAAATCGATAAATCCAATTCAATCTAAAATATAAAAGA
1 TAAATCAATAAATCTAATTCAATCCAAAATATAAAAGG
* * *
1359562 TTAATCAATAAAT-TCGATTCAATTCAAAATATAAAAGG
1 TAAATCAATAAATCT-AATTCAATCCAAAATATAAAAGG
*
1359600 TAAATCAATAAATCTAATTCGATCCAAAATATAAAAGG
1 TAAATCAATAAATCTAATTCAATCCAAAATATAAAAGG
1359638 TA
1 TA
1359640 GAATAAAAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
38 64 0.98
39 1 0.02
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (38 bp):
TAAATCAATAAATCTAATTCAATCCAAAATATAAAAGG
Found at i:1361398 original size:18 final size:18
Alignment explanation
Indices: 1361348--1361398 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1361338 AAAAAAAAAA
* *
1361348 TAGTAATAATAAAAGGGT
1 TAGTAATAATAGAGGGGT
* *
1361366 TAGTTCATCAT-GAGGGGT
1 TAG-TAATAATAGAGGGGT
1361384 TAGTAATAATAGAGG
1 TAGTAATAATAGAGG
1361399 CACTTGGTGG
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
17 5 0.20
18 15 0.60
19 5 0.20
ACGTcount: A:0.39, C:0.04, G:0.27, T:0.29
Consensus pattern (18 bp):
TAGTAATAATAGAGGGGT
Found at i:1362668 original size:18 final size:18
Alignment explanation
Indices: 1362632--1362670 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1362622 ATTATATCAG
1362632 TAAAATTTAATTCGAATT
1 TAAAATTTAATTCGAATT
*
1362650 TAAATATTTAATTCGATTT
1 TAAA-ATTTAATTCGAATT
1362669 TA
1 TA
1362671 TTATAAAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (18 bp):
TAAAATTTAATTCGAATT
Found at i:1364002 original size:16 final size:15
Alignment explanation
Indices: 1363978--1364008 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1363968 TTTTAGGCGG
1363978 ATTTCATTTATTTTT
1 ATTTCATTTATTTTT
1363993 ATTTCAATTTATTTTT
1 ATTTC-ATTTATTTTT
1364009 TGAGTCTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTCATTTATTTTT
Found at i:1368906 original size:19 final size:19
Alignment explanation
Indices: 1368876--1368946 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 19
1368866 TTAGAAATTT
1368876 TTTTGAAATTTTTATAAATA
1 TTTT-AAATTTTTATAAATA
* *
1368896 TTTTGAA-TTTTAAAAATTA
1 TTTTAAATTTTTATAAA-TA
1368915 TTTTAAATTTTT-TAAAATAA
1 TTTTAAATTTTTAT-AAAT-A
1368935 TTTTAAATTTTT
1 TTTTAAATTTTT
1368947 GTTGAAAGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
18 8 0.19
19 11 0.26
20 24 0.56
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (19 bp):
TTTTAAATTTTTATAAATA
Found at i:1368906 original size:39 final size:39
Alignment explanation
Indices: 1368863--1368945 Score: 107
Period size: 39 Copynumber: 2.1 Consensus size: 39
1368853 CTTCACATAT
* * *
1368863 ATTTTAGAAATTTTTTTGAAA-TTTTTATAAAT-ATTTTGA
1 ATTTTAAAAATTATTTT-AAATTTTTTA-AAATAATTTTAA
1368902 ATTTTAAAAATTATTTTAAATTTTTTAAAATAATTTTAA
1 ATTTTAAAAATTATTTTAAATTTTTTAAAATAATTTTAA
1368941 ATTTT
1 ATTTT
1368946 TGTTGAAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
38 7 0.18
39 32 0.82
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (39 bp):
ATTTTAAAAATTATTTTAAATTTTTTAAAATAATTTTAA
Found at i:1370648 original size:13 final size:14
Alignment explanation
Indices: 1370630--1370669 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
1370620 ATTGAAAGTC
1370630 TTTTTAATAAATA-
1 TTTTTAATAAATAT
1370643 TTTTTAA-AAATAT
1 TTTTTAATAAATAT
1370656 TTTTTAAGTAAATA
1 TTTTTAA-TAAATA
1370670 AAAATTACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.21
13 14 0.58
15 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
TTTTTAATAAATAT
Found at i:1371740 original size:29 final size:30
Alignment explanation
Indices: 1371647--1371748 Score: 111
Period size: 29 Copynumber: 3.5 Consensus size: 30
1371637 ATGTGTATAT
*
1371647 TATATGCGAGCCTATATGTGAACCTTAGAA
1 TATATGCAAGCCTATATGTGAACCTTAGAA
** *
1371677 T-TATGCAAGGTTATATGTGAACCTTAGGA
1 TATATGCAAGCCTATATGTGAACCTTAGAA
* * *
1371706 -ACATGCAAGCCTACATGTGAACCCTA-AA
1 TATATGCAAGCCTATATGTGAACCTTAGAA
*
1371734 TATATGCGAGCCTAT
1 TATATGCAAGCCTAT
1371749 GTGCGAAATC
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
28 1 0.02
29 55 0.96
30 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (30 bp):
TATATGCAAGCCTATATGTGAACCTTAGAA
Found at i:1373780 original size:24 final size:24
Alignment explanation
Indices: 1373744--1373789 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1373734 GGGTCAACAT
1373744 TGGCACTAAGTGTACGGATTTGAA
1 TGGCACTAAGTGTACGGATTTGAA
* * *
1373768 TGGCACTATGTGTGCTGATTTG
1 TGGCACTAAGTGTACGGATTTG
1373790 GATGTCAATA
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:0.22, C:0.13, G:0.30, T:0.35
Consensus pattern (24 bp):
TGGCACTAAGTGTACGGATTTGAA
Found at i:1383001 original size:14 final size:15
Alignment explanation
Indices: 1382974--1383004 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1382964 TTATTTTTAC
1382974 AAATTTTCAAAAAAT
1 AAATTTTCAAAAAAT
1382989 AAATTTT-AAAAAAT
1 AAATTTTCAAAAAAT
1383003 AA
1 AA
1383005 TACGAACGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATTTTCAAAAAAT
Found at i:1389894 original size:3 final size:3
Alignment explanation
Indices: 1389881--1389910 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1389871 TGATGATGAT
*
1389881 GAA GAA AAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1389911 AATTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1396839 original size:3 final size:3
Alignment explanation
Indices: 1396828--1396891 Score: 85
Period size: 3 Copynumber: 21.3 Consensus size: 3
1396818 CAACAATACC
* * *
1396828 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
1396873 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
1396892 GCAAAAGTAC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 1 0.02
3 52 0.98
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1398225 original size:39 final size:38
Alignment explanation
Indices: 1398179--1398294 Score: 123
Period size: 39 Copynumber: 3.1 Consensus size: 38
1398169 TAGTTTCTTT
* * *
1398179 TGTCTGCTCCGCTATTGCTTAGAGAGATGAGACTTGATG
1 TGTCTGCTCCACTACTGCTTAG-GAGATAAGACTTGATG
*
1398218 TGTCTGCTCCACTACTACTTAGGGAGATAAGATCTCT--T-
1 TGTCTGCTCCACTACTGCTTA-GGAGATAAGA-CT-TGATG
*
1398256 CGTCTGCT-CACTACTGCTTAGGAGATAAGACTTGATG
1 TGTCTGCTCCACTACTGCTTAGGAGATAAGACTTGATG
1398293 TG
1 TG
1398295 ATCCACTCTG
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
34 1 0.02
35 2 0.03
36 11 0.17
37 12 0.19
38 7 0.11
39 27 0.42
40 3 0.05
41 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (38 bp):
TGTCTGCTCCACTACTGCTTAGGAGATAAGACTTGATG
Found at i:1398366 original size:44 final size:44
Alignment explanation
Indices: 1398305--1398673 Score: 182
Period size: 44 Copynumber: 8.5 Consensus size: 44
1398295 ATCCACTCTG
* * * * *
1398305 CTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCA
1 CTGTAACTTCAGGGAGATAAGATCCTTTACTTTGATCTGCTCCA
* ** * * *
1398349 CTGTAACTTCAGGGAGATAGGATAGTGT-CTTCGATCTGCTCCG
1 CTGTAACTTCAGGGAGATAAGATCCTTTACTTTGATCTGCTCCA
** **
1398392 CTGTAA-TCTCAGGGAGATAAGAT-CTCTGGCTTCAATCTGCTCCA
1 CTGTAACT-TCAGGGAGATAAGATCCT-TTACTTTGATCTGCTCCA
* * * **
1398436 CTGTAACCTCAGGGAGATAAGATCCGAAATT-CTTTGGTCTATTCCA
1 CTGTAACTTCAGGGAGATAAGATCC---TTTACTTTGATCTGCTCCA
* * * *
1398482 CTGTAA-TCTCAGGGAGATAAGA-CC-TGA-TGTGATCTTCTCTA
1 CTGTAACT-TCAGGGAGATAAGATCCTTTACTTTGATCTGCTCCA
*
1398523 CTGTAACTTCAGGGAGATAAGATCCTTTA-----ATCCGCTCCA
1 CTGTAACTTCAGGGAGATAAGATCCTTTACTTTGATCTGCTCCA
* * * * * *
1398562 TTGTAA-TCTCAAGGAGATAGGATTACTAT-CTTTGATCTGCTCCG
1 CTGTAACT-TCAGGGAGATAAGA-TCCTTTACTTTGATCTGCTCCA
* *
1398606 CTGTAA-TCTCAGGGAGATAAGAT-CTGAAATT-CTTTGGTCTGTTCCA
1 CTGTAACT-TCAGGGAGATAAGATCCT----TTACTTTGATCTGCTCCA
1398652 CTGTAA-TCTCAGGGAGATAAGA
1 CTGTAACT-TCAGGGAGATAAGA
1398674 CCTGTATAAT
Statistics
Matches: 251, Mismatches: 50, Indels: 46
0.72 0.14 0.13
Matches are distributed among these distances:
38 1 0.00
39 24 0.10
40 4 0.02
41 30 0.12
42 7 0.03
43 33 0.13
44 83 0.33
45 3 0.01
46 65 0.26
47 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (44 bp):
CTGTAACTTCAGGGAGATAAGATCCTTTACTTTGATCTGCTCCA
Found at i:1398495 original size:46 final size:45
Alignment explanation
Indices: 1398432--1398673 Score: 149
Period size: 46 Copynumber: 5.6 Consensus size: 45
1398422 TTCAATCTGC
*
1398432 TCCACTGTAACCTCAGGGAGATAAGATCCGAAATTCTTTGGTCTAT
1 TCCACTGTAATCTCAGGGAGATAAGATCCGAAATTCTTTGGTCT-T
* *
1398478 TCCACTGTAATCTCAGGGAGATAAGA-CCTG--A---TGTGATCTT
1 TCCACTGTAATCTCAGGGAGATAAGATCC-GAAATTCTTTGGTCTT
* ** *
1398518 CTCTACTGTAA-CTTCAGGGAGATAAGATCCTTTAA-TC---CG-C--
1 -TCCACTGTAATC-TCAGGGAGATAAGATCC-GAAATTCTTTGGTCTT
* * * * * * *
1398558 TCCATTGTAATCTCAAGGAGATAGGAT---TACTATCTTTGATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCGAAAT-TCTTTGGTCT-T
* *
1398602 TCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGT
1 TCCACTGTAATCTCAGGGAGATAAGATCCGAAATTCTTTGGTCT-T
1398648 TCCACTGTAATCTCAGGGAGATAAGA
1 TCCACTGTAATCTCAGGGAGATAAGA
1398674 CCTGTATAAT
Statistics
Matches: 152, Mismatches: 23, Indels: 42
0.70 0.11 0.19
Matches are distributed among these distances:
35 2 0.01
37 2 0.01
39 21 0.14
40 3 0.02
41 30 0.20
42 4 0.03
44 25 0.16
45 2 0.01
46 61 0.40
47 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (45 bp):
TCCACTGTAATCTCAGGGAGATAAGATCCGAAATTCTTTGGTCTT
Found at i:1411466 original size:3 final size:3
Alignment explanation
Indices: 1411455--1411515 Score: 79
Period size: 3 Copynumber: 20.3 Consensus size: 3
1411445 CAACAATACC
* * *
1411455 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
1411500 AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
1411516 GCAAAAGTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 1 0.02
3 49 0.98
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1418040 original size:30 final size:30
Alignment explanation
Indices: 1418006--1418065 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1417996 CAAATGGTCA
1418006 TTGAACTATTTAAAAGTTTTCATTTAAGTC
1 TTGAACTATTTAAAAGTTTTCATTTAAGTC
* *
1418036 TTGAACTATTTGAAAGTTTTTATTTAAGTC
1 TTGAACTATTTAAAAGTTTTCATTTAAGTC
1418066 ACTAGATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (30 bp):
TTGAACTATTTAAAAGTTTTCATTTAAGTC
Found at i:1423875 original size:14 final size:13
Alignment explanation
Indices: 1423834--1423884 Score: 54
Period size: 12 Copynumber: 4.0 Consensus size: 13
1423824 TTGCATCTAC
1423834 TTCAAA-ATTAAA
1 TTCAAATATTAAA
*
1423846 TAT-AAATAAT-AA
1 T-TCAAATATTAAA
1423858 TTCAAATATCTAAA
1 TTCAAATAT-TAAA
1423872 TTCAAATATTAAA
1 TTCAAATATTAAA
1423885 AAATATCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
11 1 0.03
12 12 0.38
13 8 0.25
14 11 0.34
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (13 bp):
TTCAAATATTAAA
Found at i:1424562 original size:22 final size:22
Alignment explanation
Indices: 1424537--1424585 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1424527 TTAATATTTG
*
1424537 AAATTT-TTTAAATAAAATTAAA
1 AAATTTATTT-AATAAAATGAAA
*
1424559 AAATTTATTTACTAAAATGAAA
1 AAATTTATTTAATAAAATGAAA
1424581 AAATT
1 AAATT
1424586 GCATGATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
AAATTTATTTAATAAAATGAAA
Found at i:1425503 original size:21 final size:21
Alignment explanation
Indices: 1425479--1425519 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1425469 CAAAAAGAAC
1425479 TTTATTTTATTTAAAGGTTCA
1 TTTATTTTATTTAAAGGTTCA
*
1425500 TTTATTTTGTTTAAAGGTTC
1 TTTATTTTATTTAAAGGTTC
1425520 GACCAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.12, T:0.59
Consensus pattern (21 bp):
TTTATTTTATTTAAAGGTTCA
Found at i:1425916 original size:15 final size:15
Alignment explanation
Indices: 1425896--1425930 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1425886 AAATTAATCG
* *
1425896 AATGTGATTTTTTGT
1 AATGTGATTATTAGT
1425911 AATGTGATTATTAGT
1 AATGTGATTATTAGT
1425926 AATGT
1 AATGT
1425931 AATTGTCGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (15 bp):
AATGTGATTATTAGT
Found at i:1429430 original size:60 final size:59
Alignment explanation
Indices: 1429362--1429514 Score: 161
Period size: 60 Copynumber: 2.6 Consensus size: 59
1429352 TCATCTAGTT
* * *
1429362 ACCAAAAAGGAAAAATTA-AATAGTT-AGATGACTATTTTATAATTTTTCATAGTTAGATG
1 ACCAAAAAAG-AAAATTACAATAGTTGAG-TGACTATTTTATAACTTTTCATAATTAGATG
* * * *
1429421 ACTAAAAAAGAAATTTACTAATAGTTGAGTGACTATTTTGTCACTTTTCATAATTAGATG
1 ACCAAAAAAGAAAATTAC-AATAGTTGAGTGACTATTTTATAACTTTTCATAATTAGATG
*
1429481 ACC-AAAAAG-AAATATATCAATAGTTGGGTGACTA
1 ACCAAAAAAGAAAAT-TA-CAATAGTTGAGTGACTA
1429515 CTAGTGTAGT
Statistics
Matches: 79, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
58 9 0.11
59 31 0.39
60 37 0.47
61 2 0.03
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.34
Consensus pattern (59 bp):
ACCAAAAAAGAAAATTACAATAGTTGAGTGACTATTTTATAACTTTTCATAATTAGATG
Found at i:1433415 original size:2 final size:2
Alignment explanation
Indices: 1433408--1433437 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1433398 AGGACTCATT
*
1433408 AG AG AG AG AG AG AG CG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1433438 CCTGATCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1440594 original size:3 final size:3
Alignment explanation
Indices: 1440586--1440618 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1440576 GTGGGGTCTT
1440586 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1440619 CCTGCTAGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1440668 original size:27 final size:27
Alignment explanation
Indices: 1440630--1440685 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
1440620 CTGCTAGACT
1440630 CATAGCCAAAACTTCCCAACTTAACCC
1 CATAGCCAAAACTTCCCAACTTAACCC
*
1440657 CATAGCCAAAACTTCCCAGCTTAACCC
1 CATAGCCAAAACTTCCCAACTTAACCC
1440684 CA
1 CA
1440686 CATACATCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.41, G:0.05, T:0.18
Consensus pattern (27 bp):
CATAGCCAAAACTTCCCAACTTAACCC
Found at i:1444469 original size:17 final size:17
Alignment explanation
Indices: 1444447--1444487 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1444437 GATTTGATCA
*
1444447 ATTTAAATCTT-ATTTTG
1 ATTTAAATCTTGA-ATTG
1444464 ATTTAAA-CTTGAATTG
1 ATTTAAATCTTGAATTG
1444480 ATTTAAAT
1 ATTTAAAT
1444488 TCAAAATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (17 bp):
ATTTAAATCTTGAATTG
Found at i:1447928 original size:24 final size:25
Alignment explanation
Indices: 1447881--1447928 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
1447871 ATTAAAATTG
* *
1447881 TAAGTGGATATTATTTTTTTAAATAA
1 TAAGTGGATA-TATTTATTCAAATAA
1447907 TAAGTGGATA-ATTTATTCAAAT
1 TAAGTGGATATATTTATTCAAAT
1447929 TACTAAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
26 10 0.50
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (25 bp):
TAAGTGGATATATTTATTCAAATAA
Found at i:1450422 original size:21 final size:21
Alignment explanation
Indices: 1450387--1450427 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1450377 TTTGTAATGT
* *
1450387 TATTAATTCATTTATGTTTTA
1 TATTAATTCAATTATATTTTA
*
1450408 TATTAATTTAATTATATTTT
1 TATTAATTCAATTATATTTT
1450428 GTAACTGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (21 bp):
TATTAATTCAATTATATTTTA
Found at i:1458958 original size:21 final size:21
Alignment explanation
Indices: 1458934--1458984 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
1458924 GGCTCAAACA
1458934 TATTATTT-TTAATATT-TTATT
1 TATTATTTATT-AT-TTATTATT
1458955 TATTATTTATTATTTATTATT
1 TATTATTTATTATTTATTATT
1458976 TATTATTTA
1 TATTATTTA
1458985 GTCATTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TATTATTTATTATTTATTATT
Found at i:1458962 original size:7 final size:7
Alignment explanation
Indices: 1458950--1458984 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
1458940 TTTTAATATT
1458950 TTATTTA
1 TTATTTA
1458957 TTATTTA
1 TTATTTA
1458964 TTATTTA
1 TTATTTA
1458971 TTATTTA
1 TTATTTA
1458978 TTATTTA
1 TTATTTA
1458985 GTCATTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTATTTA
Found at i:1459443 original size:22 final size:23
Alignment explanation
Indices: 1459415--1459461 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1459405 AATTTAAATT
1459415 ATAATAAAAGTGTAATTTAACATGG
1 ATAA-AAAA-TGTAATTTAACATGG
*
1459440 ATAAAAAATGTCATTTAACATG
1 ATAAAAAATGTAATTTAACATG
1459462 TACGGATGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.62
24 4 0.19
25 4 0.19
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.32
Consensus pattern (23 bp):
ATAAAAAATGTAATTTAACATGG
Found at i:1460295 original size:32 final size:32
Alignment explanation
Indices: 1460241--1460301 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
1460231 CTGACCCAAA
* * * *
1460241 AAACCCAATACACAGAAGCCCAAACCCCTTAC
1 AAACCCAAAACACAAAACCCCAAAACCCTTAC
*
1460273 AAACCCAAAACCCAAAACCCCAAAACCCT
1 AAACCCAAAACACAAAACCCCAAAACCCT
1460302 AATCAGCCGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.48, C:0.43, G:0.03, T:0.07
Consensus pattern (32 bp):
AAACCCAAAACACAAAACCCCAAAACCCTTAC
Found at i:1461395 original size:20 final size:21
Alignment explanation
Indices: 1461353--1461397 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1461343 TTTTGTTGTT
*
1461353 TATTCTTATTTTCTTATTAAA
1 TATTCTTATTATCTTATTAAA
1461374 TATTCTTATTAT-TTA-TATAA
1 TATTCTTATTATCTTATTA-AA
1461394 TATT
1 TATT
1461398 AGTACCATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 2 0.09
20 9 0.41
21 11 0.50
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTCTTATTATCTTATTAAA
Found at i:1461435 original size:3 final size:3
Alignment explanation
Indices: 1461429--1461471 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
1461419 GTTGTTCTTC
*
1461429 TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TGTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
1461472 GTTTATGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1461703 original size:15 final size:15
Alignment explanation
Indices: 1461670--1461708 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1461660 TTTAATGTCG
*
1461670 TATTATTATGTTTTAA
1 TATTA-TATATTTTAA
*
1461686 TATTATATATTTTCA
1 TATTATATATTTTAA
1461701 TATTATAT
1 TATTATAT
1461709 TATATACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (15 bp):
TATTATATATTTTAA
Found at i:1474605 original size:71 final size:71
Alignment explanation
Indices: 1474477--1474615 Score: 206
Period size: 71 Copynumber: 2.0 Consensus size: 71
1474467 AATTTTTACT
* * *
1474477 TTTCCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAATACACGTTAAGGTAATTTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTAAGGTAATTTCAA
1474542 TTTATG
66 TTTATG
** * * *
1474548 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTAAGGTAATTTCAA
1474613 TTT
66 TTT
1474616 CTACTTTCCA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
71 60 1.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (71 bp):
TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTAAGGTAATTTCAA
TTTATG
Found at i:1474704 original size:55 final size:52
Alignment explanation
Indices: 1474633--1474836 Score: 295
Period size: 55 Copynumber: 3.8 Consensus size: 52
1474623 CCAATTCCTG
* *
1474633 TTTTTCAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTTTCAATTTAT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTT-T
1474686 ATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCT
1 -TTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTT-T
*
1474741 GTTTTTCAAAAAGCAACTCATATTGCGAGAGGTGAGTTGTA-CCTTTTAATTTT
1 -TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTG-AGCCTTTTAATTTT
* *
1474794 GTTTTCAAAAATCAAC-CATATTGCGAGAAGTGAGTTGAGCCTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT
1474837 AGGTCATATG
Statistics
Matches: 139, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
50 1 0.01
51 24 0.17
52 14 0.10
53 1 0.01
54 48 0.35
55 51 0.37
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.37
Consensus pattern (52 bp):
TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTT
Found at i:1474776 original size:54 final size:54
Alignment explanation
Indices: 1474625--1474836 Score: 315
Period size: 54 Copynumber: 4.0 Consensus size: 54
1474615 TCTACTTTCC
* * *
1474625 AATTCCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTTTC
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
* *
1474679 AATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
1 AATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
*
1474734 AATTTCTGTTTTTCAAAAAGCAACTCATATTGCGAGAGGTGAGTTGTA-CCTTTT
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTG-AGCCTTTT
*
1474788 AATTT-TG-TTTTCAAAAATCAAC-CATATTGCGAGAAGTGAGTTGAGCCTT
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT
1474837 AGGTCATATG
Statistics
Matches: 145, Mismatches: 10, Indels: 9
0.88 0.06 0.05
Matches are distributed among these distances:
50 1 0.01
51 24 0.17
52 14 0.10
53 2 0.01
54 53 0.37
55 51 0.35
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (54 bp):
AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
Found at i:1475635 original size:32 final size:32
Alignment explanation
Indices: 1475581--1475641 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
1475571 CTGACCCACA
* * * *
1475581 AAACCCAATACACAGAAGCCCAAACCCCTTAC
1 AAACCCAAAACACAAAACCCCAAAACCCTTAC
*
1475613 AAACCCAAAACCCAAAACCCCAAAACCCT
1 AAACCCAAAACACAAAACCCCAAAACCCT
1475642 AATCAGCCGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.48, C:0.43, G:0.03, T:0.07
Consensus pattern (32 bp):
AAACCCAAAACACAAAACCCCAAAACCCTTAC
Found at i:1476700 original size:20 final size:21
Alignment explanation
Indices: 1476658--1476702 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1476648 TTTTGTTGTT
*
1476658 TATTCTTATTTTCTTATTAAA
1 TATTCTTATTATCTTATTAAA
1476679 TATTCTTATTAT-TTA-TATAA
1 TATTCTTATTATCTTATTA-AA
1476699 TATT
1 TATT
1476703 AGTACCATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 2 0.09
20 9 0.41
21 11 0.50
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTCTTATTATCTTATTAAA
Found at i:1476737 original size:3 final size:3
Alignment explanation
Indices: 1476731--1476764 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
1476721 ATTGTTCTTC
*
1476731 TTA TTA TTA TTA TTA CTA TTA TTA TTA TGTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
1476765 GTTTATGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1476996 original size:15 final size:15
Alignment explanation
Indices: 1476963--1477001 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1476953 TTTAATGTCG
*
1476963 TATTATTATGTTTTAA
1 TATTA-TATATTTTAA
*
1476979 TATTATATATTTTCA
1 TATTATATATTTTAA
1476994 TATTATAT
1 TATTATAT
1477002 TATATACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (15 bp):
TATTATATATTTTAA
Found at i:1481083 original size:16 final size:16
Alignment explanation
Indices: 1481064--1481095 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1481054 AAAATTTTCT
1481064 ATTCAAATCATTTTAA
1 ATTCAAATCATTTTAA
*
1481080 ATTCACATCATTTTAA
1 ATTCAAATCATTTTAA
1481096 CTTGTTTTGG
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:0.41, C:0.16, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTCAAATCATTTTAA
Found at i:1483191 original size:16 final size:17
Alignment explanation
Indices: 1483170--1483207 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
1483160 TTTTGGATTC
1483170 GAGTTTAAGTT-ATTTT
1 GAGTTTAAGTTAATTTT
1483186 GAGTTTAAGTTAATTTT
1 GAGTTTAAGTTAATTTT
*
1483203 TAGTT
1 GAGTT
1483208 CGAATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.55
Consensus pattern (17 bp):
GAGTTTAAGTTAATTTT
Found at i:1483439 original size:17 final size:17
Alignment explanation
Indices: 1483419--1483454 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1483409 TCACTTTGAG
*
1483419 TTCAAATTTACTCAGGT
1 TTCAAATTTACTCAAGT
*
1483436 TTCAAGTTTACTCAAGT
1 TTCAAATTTACTCAAGT
1483453 TT
1 TT
1483455 GTTAGTTGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (17 bp):
TTCAAATTTACTCAAGT
Found at i:1486804 original size:24 final size:24
Alignment explanation
Indices: 1486777--1486828 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1486767 TTAGTAAGTC
*
1486777 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1486801 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1486825 AAAT
1 AAAT
1486829 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1488774 original size:24 final size:24
Alignment explanation
Indices: 1488747--1488798 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1488737 TTAGTAAGTC
*
1488747 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1488771 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1488795 AAAT
1 AAAT
1488799 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1490828 original size:21 final size:21
Alignment explanation
Indices: 1490803--1490865 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
1490793 CATTTAAGAG
1490803 AAAAATAACTATAAACCTTAA
1 AAAAATAACTATAAACCTTAA
* *
1490824 AAAAATAA-TAT-TA--TTGAG
1 AAAAATAACTATAAACCTT-AA
*
1490842 AAAATTAACTATAAACCTTAA
1 AAAAATAACTATAAACCTTAA
1490863 AAA
1 AAA
1490866 TTGACATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
17 2 0.06
18 8 0.25
19 4 0.12
20 4 0.12
21 12 0.38
22 2 0.06
ACGTcount: A:0.60, C:0.10, G:0.03, T:0.27
Consensus pattern (21 bp):
AAAAATAACTATAAACCTTAA
Found at i:1490884 original size:38 final size:39
Alignment explanation
Indices: 1490803--1490884 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 39
1490793 CATTTAAGAG
* **
1490803 AAAAA-TAACTATAAACCTTAAAAAAATAATATTATTGA
1 AAAAATTAACTATAAACCTTAAAAAAATAACATTATAAA
* * *
1490841 GAAAATTAACTATAAACCTT-AAAAATTGACATTATAAA
1 AAAAATTAACTATAAACCTTAAAAAAATAACATTATAAA
1490879 AAAAAT
1 AAAAAT
1490885 AAATTTACAC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
38 22 0.61
39 14 0.39
ACGTcount: A:0.60, C:0.09, G:0.04, T:0.28
Consensus pattern (39 bp):
AAAAATTAACTATAAACCTTAAAAAAATAACATTATAAA
Found at i:1491816 original size:11 final size:10
Alignment explanation
Indices: 1491789--1491825 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 10
1491779 CATGTATCAT
1491789 TATA-TTAAA
1 TATATTTAAA
1491798 T-TATTTAAA
1 TATATTTAAA
1491807 TATAATTTAAA
1 TAT-ATTTAAA
1491818 TATATTTA
1 TATATTTA
1491826 TTTTTTTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 2 0.08
9 7 0.28
10 6 0.24
11 10 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
TATATTTAAA
Found at i:1493871 original size:3 final size:3
Alignment explanation
Indices: 1493856--1493947 Score: 53
Period size: 3 Copynumber: 30.7 Consensus size: 3
1493846 CTTACTTCCT
* * * * *
1493856 TCA TCA TCC TCA TCA TCG TCA TCG TCA TC- TCCA TCT TCA TCT TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T-CA TCA TCA TCA TCA
* * * * * *
1493901 TCC TCA TCA TCC TCG TCC TCA TCC TCG TCCA -CA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T-CA TCA TCA TCA TCA TCA
1493946 TC
1 TC
1493948 TCCTATCTCT
Statistics
Matches: 66, Mismatches: 19, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
2 3 0.05
3 61 0.92
4 2 0.03
ACGTcount: A:0.20, C:0.41, G:0.04, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:1493947 original size:12 final size:12
Alignment explanation
Indices: 1493856--1493947 Score: 62
Period size: 12 Copynumber: 7.7 Consensus size: 12
1493846 CTTACTTCCT
* *
1493856 TCATCATCCTCA
1 TCATCATCATCG
*
1493868 TCATCGTCATCG
1 TCATCATCATCG
*
1493880 TCATC-TCCATCT
1 TCATCAT-CATCG
* *
1493892 TCATCTTCATCC
1 TCATCATCATCG
*
1493904 TCATCATCCTCG
1 TCATCATCATCG
* *
1493916 TCCTCATCCTCG
1 TCATCATCATCG
*
1493928 TCCA-CATCATCA
1 T-CATCATCATCG
1493940 TCATCATC
1 TCATCATC
1493948 TCCTATCTCT
Statistics
Matches: 64, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
11 3 0.05
12 59 0.92
13 2 0.03
ACGTcount: A:0.20, C:0.41, G:0.04, T:0.35
Consensus pattern (12 bp):
TCATCATCATCG
Found at i:1501021 original size:28 final size:28
Alignment explanation
Indices: 1500988--1501089 Score: 114
Period size: 28 Copynumber: 3.4 Consensus size: 28
1500978 AACTTAAGAA
1500988 ATTTTACATATTCAAATAGGACTCATAT
1 ATTTTACATATTCAAATAGGACTCATAT
* * * *
1501016 ATTTTACATATTTATACGATAAGGAACTTAAGAA
1 ATTTTACATATTCA-A--AT-AGG-AC-TCATAT
1501050 ATTTTACATATTCAAATAGGACTCATAT
1 ATTTTACATATTCAAATAGGACTCATAT
1501078 ATTTTACATATT
1 ATTTTACATATT
1501090 TATACGATTG
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
28 28 0.47
29 3 0.05
30 3 0.05
31 4 0.07
32 3 0.05
33 3 0.05
34 16 0.27
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (28 bp):
ATTTTACATATTCAAATAGGACTCATAT
Found at i:1501042 original size:62 final size:62
Alignment explanation
Indices: 1500972--1501097 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
1500962 ATATTTGCAA
1500972 ATAAGGAACTTAAGAAATTTTACATATTCAAATAGGACTCATATATTTTACATATTTATACG
1 ATAAGGAACTTAAGAAATTTTACATATTCAAATAGGACTCATATATTTTACATATTTATACG
1501034 ATAAGGAACTTAAGAAATTTTACATATTCAAATAGGACTCATATATTTTACATATTTATACG
1 ATAAGGAACTTAAGAAATTTTACATATTCAAATAGGACTCATATATTTTACATATTTATACG
1501096 AT
1 AT
1501098 TGAGTCTTTG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (62 bp):
ATAAGGAACTTAAGAAATTTTACATATTCAAATAGGACTCATATATTTTACATATTTATACG
Found at i:1501059 original size:34 final size:31
Alignment explanation
Indices: 1500969--1501067 Score: 114
Period size: 28 Copynumber: 3.2 Consensus size: 31
1500959 TTAATATTTG
1500969 CAAATAAGGAACTTAAGAAATTTTACATATT
1 CAAATAAGGAACTTAAGAAATTTTACATATT
* * *
1501000 CAAAT-AGG-AC-TCATATATTTTACATATT
1 CAAATAAGGAACTTAAGAAATTTTACATATT
*
1501028 TATACGATAAGGAACTTAAGAAATTTTACATATT
1 CA-A--ATAAGGAACTTAAGAAATTTTACATATT
1501062 CAAATA
1 CAAATA
1501068 GGACTCATAT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
28 16 0.30
29 3 0.06
30 3 0.06
31 10 0.19
32 3 0.06
33 3 0.06
34 16 0.30
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (31 bp):
CAAATAAGGAACTTAAGAAATTTTACATATT
Found at i:1506835 original size:18 final size:18
Alignment explanation
Indices: 1506812--1506846 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1506802 ATATCTTGTC
* *
1506812 TATAAATAATTTTAAAAT
1 TATAAAAAATTATAAAAT
1506830 TATAAAAAATTATAAAA
1 TATAAAAAATTATAAAA
1506847 AGTCATAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TATAAAAAATTATAAAAT
Found at i:1508132 original size:11 final size:10
Alignment explanation
Indices: 1508066--1508131 Score: 53
Period size: 10 Copynumber: 6.3 Consensus size: 10
1508056 TAAACGTGTA
1508066 TTTATATAATT
1 TTTA-ATAATT
1508077 TTT-ATAATT
1 TTTAATAATT
* *
1508086 GTTAAAAATGT
1 TTTAATAAT-T
*
1508097 TTCTCATAAATT
1 TT-TAAT-AATT
*
1508109 TTTATTAATT
1 TTTAATAATT
1508119 TTTAATAATT
1 TTTAATAATT
1508129 TTT
1 TTT
1508132 TTTTTTGAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
9 8 0.19
10 20 0.47
11 7 0.16
12 5 0.12
13 3 0.07
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (10 bp):
TTTAATAATT
Found at i:1509102 original size:15 final size:16
Alignment explanation
Indices: 1509082--1509114 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1509072 TGGTTGGAGG
*
1509082 AAAAAAATAGAA-AAA
1 AAAAAAAAAGAAGAAA
1509097 AAAAAAAAAGAAGAAA
1 AAAAAAAAAGAAGAAA
1509113 AA
1 AA
1509115 TGAAGTGTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (16 bp):
AAAAAAAAAGAAGAAA
Found at i:1511108 original size:54 final size:53
Alignment explanation
Indices: 1511050--1511163 Score: 201
Period size: 54 Copynumber: 2.1 Consensus size: 53
1511040 ATTACAAAGA
1511050 TATTTTCTAATTATGTAAAAAATAGACAAGATAAAAATGGGATTTCATATTTTT
1 TATTTTCTAATTATGTAAAAAATAGACAAGATAAAAATGGGATTTCATA-TTTT
* *
1511104 TATTTTCTAATTATGTAAAAAATAGACAAGATAGAAATGGTATTTCATATTTT
1 TATTTTCTAATTATGTAAAAAATAGACAAGATAAAAATGGGATTTCATATTTT
1511157 TATTTTC
1 TATTTTC
1511164 CAAAATTGAG
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
53 11 0.19
54 47 0.81
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (53 bp):
TATTTTCTAATTATGTAAAAAATAGACAAGATAAAAATGGGATTTCATATTTT
Found at i:1511444 original size:47 final size:47
Alignment explanation
Indices: 1511370--1511459 Score: 126
Period size: 47 Copynumber: 1.9 Consensus size: 47
1511360 AGTATTTTCT
* * *
1511370 GTCAAAATTTGCCATCAATACAGCTATGCTATCATACTAACTTTAGA
1 GTCAAAATTTACCATCAATACACCTATGCAATCATACTAACTTTAGA
* * *
1511417 GTCAAAATTTACCATCAATGCACCTATGCAATGATATTAACTT
1 GTCAAAATTTACCATCAATACACCTATGCAATCATACTAACTT
1511460 CCAGAAGCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 37 1.00
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (47 bp):
GTCAAAATTTACCATCAATACACCTATGCAATCATACTAACTTTAGA
Found at i:1518661 original size:31 final size:31
Alignment explanation
Indices: 1518626--1518691 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
1518616 TTTTTAACTA
* *
1518626 AATTTGATCATCAACCTTTTAAAAAGAATCG
1 AATTTGACCATCAACCTTTCAAAAAGAATCG
* *
1518657 AATTTGACCATCAATCTTTCAAAAAGAGTCG
1 AATTTGACCATCAACCTTTCAAAAAGAATCG
1518688 AATT
1 AATT
1518692 GTTGTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.32
Consensus pattern (31 bp):
AATTTGACCATCAACCTTTCAAAAAGAATCG
Found at i:1521399 original size:22 final size:23
Alignment explanation
Indices: 1521374--1521425 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
1521364 CGACCTGGTT
1521374 GTTTCGCTGATGTGTTATTG-TA
1 GTTTCGCTGATGTGTTATTGTTA
* * * *
1521396 GTTTTGGTGTTGTTTTATTGTTA
1 GTTTCGCTGATGTGTTATTGTTA
1521419 -TTTCGCT
1 GTTTCGCT
1521426 ATTATATTTC
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.10, C:0.08, G:0.25, T:0.58
Consensus pattern (23 bp):
GTTTCGCTGATGTGTTATTGTTA
Found at i:1521981 original size:25 final size:25
Alignment explanation
Indices: 1521947--1521995 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
1521937 ATATCGATAA
1521947 ATTTTATGTACAATTCATGAAAAAC
1 ATTTTATGTACAATTCATGAAAAAC
1521972 ATTTTATGTACAATTCATGAAAAA
1 ATTTTATGTACAATTCATGAAAAA
1521996 TATTAACTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (25 bp):
ATTTTATGTACAATTCATGAAAAAC
Found at i:1523685 original size:28 final size:30
Alignment explanation
Indices: 1523645--1523700 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
1523635 TATATTATTA
* **
1523645 ATTTTATGTTTTATGATA-TAAAAATAAAT
1 ATTTTATGATTTAAAATAGTAAAAATAAAT
1523674 ATTTTAT-ATTTAAAATAGTAAAAATAA
1 ATTTTATGATTTAAAATAGTAAAAATAA
1523701 TTTAAAAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (30 bp):
ATTTTATGATTTAAAATAGTAAAAATAAAT
Found at i:1524136 original size:207 final size:204
Alignment explanation
Indices: 1523727--1524137 Score: 795
Period size: 207 Copynumber: 2.0 Consensus size: 204
1523717 TTGTTATATT
1523727 TTAAAAATATTAATGAAAAAATTCATAAAAAATTACCAGACAATATTAAATAAATTATAAAATAA
1 TTAAAAATATTAATGAAAAAATTCATAAAAAATTACCAGACAATATTAAATAAATTATAAAATAA
1523792 TGCTCATTTTATCAAAATAAATTTAAAAAATTAAAAAAAAATTTAACCAACCCAACCTAATCCAG
66 TGCTCATTTTATCAAAATAAATTTAAAAAATTAAAAAAAAATTTAACCAACCCAACCTAATCCAG
1523857 TCAGCAAAAAAGGCAAAAGTCCACTCAGAAGCCATAAAAACAAAACGGTGCCGTATAAGTAACAA
131 TCAGCAAAAAAGGCAAAAGTCCACTCAGAAGCCATAAAAACAAAACGGTGCCGTATAAGTAACAA
1523922 GAAAAGAGA
196 GAAAAGAGA
1523931 TTAAAAATATTAATGAAAAAATTCATAAAAAATTACCAGACAATATTAAATAAATTATAAAATAA
1 TTAAAAATATTAATGAAAAAATTCATAAAAAATTACCAGACAATATTAAATAAATTATAAAATAA
1523996 TGCTCATTTTATCAAAATAAATTTAAAAAATTAAAAAAAAAAAATTTAACCAACCCAACCTAATC
66 TGCTCATTTTATCAAAATAAATTTAAAAAATT---AAAAAAAAATTTAACCAACCCAACCTAATC
1524061 CAGTCAGCAAAAAAGGCAAAAGTCCACTCAGAAGCCATAAAAACAAAACGGTGCCGTATAAGTAA
128 CAGTCAGCAAAAAAGGCAAAAGTCCACTCAGAAGCCATAAAAACAAAACGGTGCCGTATAAGTAA
1524126 CAAGAAAAGAGA
193 CAAGAAAAGAGA
1524138 GGCAAATTTT
Statistics
Matches: 204, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
204 97 0.48
207 107 0.52
ACGTcount: A:0.55, C:0.15, G:0.09, T:0.22
Consensus pattern (204 bp):
TTAAAAATATTAATGAAAAAATTCATAAAAAATTACCAGACAATATTAAATAAATTATAAAATAA
TGCTCATTTTATCAAAATAAATTTAAAAAATTAAAAAAAAATTTAACCAACCCAACCTAATCCAG
TCAGCAAAAAAGGCAAAAGTCCACTCAGAAGCCATAAAAACAAAACGGTGCCGTATAAGTAACAA
GAAAAGAGA
Found at i:1524257 original size:15 final size:16
Alignment explanation
Indices: 1524228--1524270 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
1524218 TATAGAAAGG
* *
1524228 AAAAGAAAAACTAA-T
1 AAAAAAAAAAATAATT
*
1524243 AACAAAAAAAATAATT
1 AAAAAAAAAAATAATT
1524259 AAAAAAAAAAAT
1 AAAAAAAAAAAT
1524271 CCTTTGCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (16 bp):
AAAAAAAAAAATAATT
Found at i:1524547 original size:10 final size:10
Alignment explanation
Indices: 1524532--1524567 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
1524522 CCCTCTCTAG
1524532 TATTTTTATT
1 TATTTTTATT
1524542 TATTTTT-TT
1 TATTTTTATT
*
1524551 AATTTTTATT
1 TATTTTTATT
1524561 TATTTTT
1 TATTTTT
1524568 CGTCGATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
TATTTTTATT
Found at i:1525843 original size:41 final size:42
Alignment explanation
Indices: 1525755--1525852 Score: 171
Period size: 42 Copynumber: 2.4 Consensus size: 42
1525745 GAATGAACCG
*
1525755 TACATCTTATTATTGATGATAAGATTGAACTTTGAGAAACTA
1 TACATCTTGTTATTGATGATAAGATTGAACTTTGAGAAACTA
1525797 TACATCTTGTTATTGATGATAAGATTGAAC-TTGAGAAACTA
1 TACATCTTGTTATTGATGATAAGATTGAACTTTGAGAAACTA
*
1525838 TACATCTCGTTATTG
1 TACATCTTGTTATTG
1525853 GTTTAAAGTT
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
41 25 0.46
42 29 0.54
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (42 bp):
TACATCTTGTTATTGATGATAAGATTGAACTTTGAGAAACTA
Found at i:1537270 original size:21 final size:21
Alignment explanation
Indices: 1537235--1537330 Score: 111
Period size: 21 Copynumber: 4.5 Consensus size: 21
1537225 AGGCAGTTTA
1537235 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA--TCAGGCACCTCG
* *
1537258 TGTGTCGTATCAGACACCTTG
1 TGTGTCGTATCAGGCACCTCG
1537279 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
* * * **
1537300 TGTGTCGTTTTAGGCACTTTA
1 TGTGTCGTATCAGGCACCTCG
1537321 TGTGTCGTAT
1 TGTGTCGTAT
1537331 ACTGATCAGG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
21 54 0.86
23 9 0.14
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.38
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:1537294 original size:42 final size:42
Alignment explanation
Indices: 1537232--1537330 Score: 135
Period size: 42 Copynumber: 2.3 Consensus size: 42
1537222 ATCAGGCAGT
1537232 TTATGTGTCGTATTTCAGGCACCTCGTGTGTCGTATCAGACACC
1 TTATGTGTCGTA--TCAGGCACCTCGTGTGTCGTATCAGACACC
* * * * *
1537276 TTGTGTGTCGTATCAGGCACCTCGTGTGTCGTTTTAGGCACT
1 TTATGTGTCGTATCAGGCACCTCGTGTGTCGTATCAGACACC
1537318 TTATGTGTCGTAT
1 TTATGTGTCGTAT
1537331 ACTGATCAGG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
42 38 0.78
44 11 0.22
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.38
Consensus pattern (42 bp):
TTATGTGTCGTATCAGGCACCTCGTGTGTCGTATCAGACACC
Found at i:1542751 original size:51 final size:51
Alignment explanation
Indices: 1542673--1542776 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
1542663 AAATGTTGGG
*
1542673 TACATTTTAATTTGCATTAGAACCAGAAGGGAAATGCAGGGAGGTTTAGAA
1 TACATTTTAATTTGCATTAGAACCAGAAGGGAAAGGCAGGGAGGTTTAGAA
*
1542724 TACATTTTAATTTGCATTAGAATCAGAAGGGAAAGGCAGGGAGGTTTAGAA
1 TACATTTTAATTTGCATTAGAACCAGAAGGGAAAGGCAGGGAGGTTTAGAA
1542775 TA
1 TA
1542777 ATAGCTGTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.28
Consensus pattern (51 bp):
TACATTTTAATTTGCATTAGAACCAGAAGGGAAAGGCAGGGAGGTTTAGAA
Found at i:1546258 original size:21 final size:21
Alignment explanation
Indices: 1546232--1546273 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1546222 ATGAATCGCA
*
1546232 AAGGATCAGCAGATTAAAAAC
1 AAGGATCAGCAGATCAAAAAC
1546253 AAGGATCAGCAGATCAAAAAC
1 AAGGATCAGCAGATCAAAAAC
1546274 TTACTTAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.17, G:0.19, T:0.12
Consensus pattern (21 bp):
AAGGATCAGCAGATCAAAAAC
Found at i:1555612 original size:15 final size:15
Alignment explanation
Indices: 1555592--1555622 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1555582 ATCTAAATGC
1555592 GAAGAAGAAAGAAAA
1 GAAGAAGAAAGAAAA
*
1555607 GAAGAAGAAGGAAAA
1 GAAGAAGAAAGAAAA
1555622 G
1 G
1555623 TAGCTACGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (15 bp):
GAAGAAGAAAGAAAA
Found at i:1564500 original size:46 final size:46
Alignment explanation
Indices: 1564445--1564800 Score: 375
Period size: 46 Copynumber: 7.8 Consensus size: 46
1564435 GCTTTCTGAA
* * *
1564445 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATAGGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACAGGAC
* * * * * ** *
1564491 ATAAAATGTGTAAGGCCATGGTTGAAAGACACCATCGCAACATAAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACAGGAC
* *
1564537 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACAGGAC
* *
1564583 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC-GTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACAG-GAC
* * * *
1564629 ATGAAAAGAATAAGACAATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACAGGAC
* * * *
1564675 -GGAAATGAATAAGACCATGGTTG--A-ATACCATGGCAA-TGTAAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACAG-GAC
* * **
1564717 ATGAAATGAATAAGACCATGGTTGAAGGATACCATGGCAACCTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACAGGAC
* * *
1564763 A-GAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
1564801 TCATGTTGAA
Statistics
Matches: 265, Mismatches: 37, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
42 14 0.05
43 23 0.09
45 53 0.20
46 175 0.66
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACAGGAC
Found at i:1564602 original size:92 final size:92
Alignment explanation
Indices: 1564445--1564800 Score: 416
Period size: 92 Copynumber: 3.9 Consensus size: 92
1564435 GCTTTCTGAA
** * * *
1564445 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATAGGATATAAAATGTGTAAGGCCAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACAGGATATAAAATGAGTAAGACCAT
* * *
1564510 GGTTGAAAGACACCATCGCAACATAAT
66 GGTTGAAAGACACCATGGCAACGTAAC
** *
1564537 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGATATAAAATGTGTAAGACCAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACAGGATATAAAATGAGTAAGACCAT
* *
1564602 GGTTGAAAGATACCATGGCAACGTGAC
66 GGTTGAAAGACACCATGGCAACGTAAC
* * * *** *
1564629 ATGAAAAGAATAAGACAATGGTTGAAAGATACCATGGCAACATGA-CGGAAATGAATAAGACCAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACAGGATATAAAATGAGTAAGACCAT
* *
1564693 GGTTG--A-ATACCATGGCAATGTAAC
66 GGTTGAAAGACACCATGGCAACGTAAC
* ** * *
1564717 ATGAAATGAATAAGACCATGGTTGAAGGATACCATGGCAACCTGACA-GAAATGAGTAAGACCAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACAGGATATAAAATGAGTAAGACCAT
* *
1564781 AGTTGAAAGACACTATGGCA
66 GGTTGAAAGACACCATGGCA
1564801 TCATGTTGAA
Statistics
Matches: 232, Mismatches: 28, Indels: 9
0.86 0.10 0.03
Matches are distributed among these distances:
88 77 0.33
89 1 0.00
90 1 0.00
91 28 0.12
92 125 0.54
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (92 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACAGGATATAAAATGAGTAAGACCAT
GGTTGAAAGACACCATGGCAACGTAAC
Found at i:1566231 original size:15 final size:15
Alignment explanation
Indices: 1566183--1566234 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
1566173 ACTATAAAAC
*
1566183 ATTTAATATTAATAT
1 ATTTATTATTAATAT
*
1566198 ATTTATATTTGTTATATAT
1 A-TT-TA-TTATTA-ATAT
1566217 ATTTATTATTAATAT
1 ATTTATTATTAATAT
1566232 ATT
1 ATT
1566235 AATATATGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 8 0.27
16 7 0.23
17 4 0.13
18 6 0.20
19 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:1566323 original size:15 final size:17
Alignment explanation
Indices: 1566280--1566333 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 17
1566270 TAAAATCTAT
*
1566280 TATTAAAATA-AAATTA
1 TATTAAAAAATAAATTA
* **
1566296 TAATATTAAAT-AATT-
1 TATTAAAAAATAAATTA
1566311 TATTAAAAAATAAATTA
1 TATTAAAAAATAAATTA
1566328 TATTAA
1 TATTAA
1566334 TCATTTATAA
Statistics
Matches: 28, Mismatches: 7, Indels: 5
0.70 0.17 0.12
Matches are distributed among these distances:
15 8 0.29
16 14 0.50
17 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TATTAAAAAATAAATTA
Found at i:1566344 original size:27 final size:28
Alignment explanation
Indices: 1566279--1566359 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 28
1566269 TTAAAATCTA
* *
1566279 TTATTAAAATAAAATTATAATATTAAATAAT
1 TTATT-AAAT-AAATAATTATATT-AATAAT
*
1566310 TTATTAAA-AAATAAATTATATTAATCAT
1 TTATTAAATAAAT-AATTATATTAATAAT
*
1566338 TTA-TAAATAAATTATTATATTA
1 TTATTAAATAAATAATTATATTA
1566360 TTAAATATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
27 13 0.30
28 16 0.36
29 7 0.16
30 3 0.07
31 5 0.11
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (28 bp):
TTATTAAATAAATAATTATATTAATAAT
Found at i:1583772 original size:8 final size:8
Alignment explanation
Indices: 1583759--1583788 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1583749 CTTTTTCTTT
1583759 TATTTTTA
1 TATTTTTA
1583767 TATTTTTA
1 TATTTTTA
1583775 TATTTTTA
1 TATTTTTA
1583783 -ATTTTT
1 TATTTTT
1583789 TTTTTTTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TATTTTTA
Found at i:1593418 original size:13 final size:13
Alignment explanation
Indices: 1593400--1593424 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1593390 AGTTTGATTT
1593400 AGTTTTTGAGTCG
1 AGTTTTTGAGTCG
1593413 AGTTTTTGAGTC
1 AGTTTTTGAGTC
1593425 AAATCAATTC
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:0.16, C:0.08, G:0.28, T:0.48
Consensus pattern (13 bp):
AGTTTTTGAGTCG
Found at i:1594131 original size:3 final size:3
Alignment explanation
Indices: 1594123--1594173 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
1594113 ATTAAGTTGG
1594123 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1594171 ATT
1 ATT
1594174 CACATCGACT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1594356 original size:4 final size:4
Alignment explanation
Indices: 1594347--1594371 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1594337 TACACGACAA
1594347 TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT T
1594372 CAGATCCTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:1594991 original size:13 final size:13
Alignment explanation
Indices: 1594973--1594997 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1594963 TATTTTAATA
1594973 TTATTTTGTGTGT
1 TTATTTTGTGTGT
1594986 TTATTTTGTGTG
1 TTATTTTGTGTG
1594998 CATTCGATGG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:1596732 original size:41 final size:41
Alignment explanation
Indices: 1596525--1596721 Score: 317
Period size: 41 Copynumber: 4.8 Consensus size: 41
1596515 TTTATCGTTA
* * * *
1596525 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1596566 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1596607 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1596648 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
1596689 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
1596722 AAGAGCCGGT
Statistics
Matches: 148, Mismatches: 4, Indels: 8
0.93 0.03 0.05
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 143 0.97
42 2 0.01
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:1596995 original size:32 final size:31
Alignment explanation
Indices: 1596940--1597003 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 31
1596930 ATATGTATAT
1596940 ATATATATATATGTTGCATTCGGCATAGGTG
1 ATATATATATATGTTGCATTCGGCATAGGTG
* *
1596971 ATATATTTATGTGTATGCATTCGGCATAGGTG
1 ATATATATATATGT-TGCATTCGGCATAGGTG
1597003 A
1 A
1597004 AAATAAGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 12 0.40
32 18 0.60
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.39
Consensus pattern (31 bp):
ATATATATATATGTTGCATTCGGCATAGGTG
Found at i:1602663 original size:13 final size:13
Alignment explanation
Indices: 1602645--1602669 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1602635 TATTTTAATA
1602645 TTATTTTGTGTGT
1 TTATTTTGTGTGT
1602658 TTATTTTGTGTG
1 TTATTTTGTGTG
1602670 CATTCGATGT
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:1604322 original size:81 final size:81
Alignment explanation
Indices: 1604187--1604338 Score: 236
Period size: 81 Copynumber: 1.9 Consensus size: 81
1604177 TTTATCGTTA
* * *
1604187 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATTATTCAGACTATAAGTC
1 GTGACACAATTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGAAATTATTCAGACTATAAGTC
1604252 TAGCAGCTTAATGCCG
66 TAGCAGCTTAATGCCG
*
1604268 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGACACA-T-TTCAGACTATAAG
1 GTGACACAATTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGA-A-ATTATTCAGACTATAAG
1604331 TCTAGCAG
64 TCTAGCAG
1604339 GCTAAGAGCC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
81 62 0.95
82 2 0.03
83 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (81 bp):
GTGACACAATTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGAAATTATTCAGACTATAAGTC
TAGCAGCTTAATGCCG
Found at i:1604352 original size:41 final size:41
Alignment explanation
Indices: 1604187--1604341 Score: 235
Period size: 41 Copynumber: 3.8 Consensus size: 41
1604177 TTTATCGTTA
* * * *
1604187 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1604228 GTGA-A-ATTATTCAGACTATAAGTCTAGCA-GCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1604268 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1604309 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
1604342 AAGAGCCGGT
Statistics
Matches: 106, Mismatches: 3, Indels: 10
0.89 0.03 0.08
Matches are distributed among these distances:
39 1 0.01
40 36 0.34
41 68 0.64
42 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:1604615 original size:32 final size:31
Alignment explanation
Indices: 1604560--1604623 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 31
1604550 ATATGTATAT
1604560 ATATATATATATGTTGCATTCGGCATAGGTG
1 ATATATATATATGTTGCATTCGGCATAGGTG
* *
1604591 ATATATTTATGTGTATGCATTCGGCATAGGTG
1 ATATATATATATGT-TGCATTCGGCATAGGTG
1604623 A
1 A
1604624 AAATAAGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 12 0.40
32 18 0.60
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.39
Consensus pattern (31 bp):
ATATATATATATGTTGCATTCGGCATAGGTG
Found at i:1611056 original size:43 final size:45
Alignment explanation
Indices: 1611006--1611098 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 45
1610996 AAGTATAAAC
* *
1611006 TTAAAAAA-ATAATATTATTTTCTTCAATA-TAAAAATAAAATAA
1 TTAAAAAAGATAATATTATTTGCTTCAAGATTAAAAATAAAATAA
* * * *
1611049 TTAAAAAAGTTAATTTTATTTGCTTCAAGATTAAATATAAAATGA
1 TTAAAAAAGATAATATTATTTGCTTCAAGATTAAAAATAAAATAA
1611094 TTAAA
1 TTAAA
1611099 TTAAATTTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 8 0.19
44 17 0.40
45 17 0.40
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (45 bp):
TTAAAAAAGATAATATTATTTGCTTCAAGATTAAAAATAAAATAA
Found at i:1611996 original size:60 final size:59
Alignment explanation
Indices: 1611941--1612061 Score: 138
Period size: 59 Copynumber: 2.1 Consensus size: 59
1611931 TAAAAAAGAC
* *
1611941 AAAATA-GAATAGTTGAGTAATTATTTTTGTAATTTTTCATAATTGAGTGCTAAAAATAA
1 AAAATATGAATAGTTGAGTAATCA-TTTTATAATTTTTCATAATTGAGTGCTAAAAATAA
* * * * * *
1612000 AGATTATTAATTGTTGAGTAATCATTTTATAATTTTTCATAATT-AGGTACCAAAAATAA
1 AAAATATGAATAGTTGAGTAATCATTTTATAATTTTTCATAATTGA-GTGCTAAAAATAA
1612059 AAA
1 AAA
1612062 TAAAATCATA
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
58 1 0.02
59 36 0.71
60 14 0.27
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (59 bp):
AAAATATGAATAGTTGAGTAATCATTTTATAATTTTTCATAATTGAGTGCTAAAAATAA
Done.