Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3
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: 6198200
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 200361 characters in sequence are not A, C, G, or T
File 10 of 32
Found at i:1197551 original size:23 final size:23
Alignment explanation
Indices: 1197507--1197570 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
1197497 TATAATATAT
*
1197507 ATATATTATTAAAAAATTTGAAA
1 ATATATTATTAAAAAATATGAAA
*
1197530 ATATATTA-TAAATATATATGAAA
1 ATATATTATTAAA-AAATATGAAA
*
1197553 A-A-AGTATTTAAAAAATAT
1 ATATATTA-TTAAAAAATAT
1197571 AGTAAACTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
21 3 0.09
22 10 0.29
23 21 0.62
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.38
Consensus pattern (23 bp):
ATATATTATTAAAAAATATGAAA
Found at i:1198260 original size:18 final size:18
Alignment explanation
Indices: 1198231--1198274 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1198221 AAATTCATCA
* *
1198231 TTTTAAAGTTTTAATTTT
1 TTTTAAATTTTTAATCTT
*
1198249 TTTTAAATTTTTCATCTT
1 TTTTAAATTTTTAATCTT
*
1198267 TTTCAAAT
1 TTTTAAAT
1198275 AAAGATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTTAAATTTTTAATCTT
Found at i:1198435 original size:6 final size:6
Alignment explanation
Indices: 1198424--1198448 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1198414 ATTTATTTAA
1198424 TTATTT TTATTT TTATTT TTATTT T
1 TTATTT TTATTT TTATTT TTATTT T
1198449 ATCCTCACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:1198672 original size:18 final size:17
Alignment explanation
Indices: 1198651--1198693 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
1198641 TTAAATTAAT
1198651 TTTATTAATTCAATTTTC
1 TTTATTAATT-AATTTTC
* *
1198669 TTTATATGATTAATTTTT
1 TTTAT-TAATTAATTTTC
1198687 TTTATTA
1 TTTATTA
1198694 TTTATTTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.05
18 16 0.76
19 4 0.19
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTATTAATTAATTTTC
Found at i:1200400 original size:146 final size:144
Alignment explanation
Indices: 1200185--1200522 Score: 330
Period size: 144 Copynumber: 2.3 Consensus size: 144
1200175 GTTTTGGTTC
* * * * *
1200185 TATAGGAACTGTTTTATAATTTTGTTCA-ATTTTTTTAAACTTATTTAAAAGTGTTATTAGGTTC
1 TATAGGAACTGTTTAATAATTTT-TTTAGA-TTTTTTAAGCTCATTTAAAAGTGCTATTAGGTTC
* * * * **
1200249 GTTGAAACTTA-TGAGTTCAAAAAAATA-ATTTTTTTTCTTAATTTTT-AGACCACT-TACGGGT
64 GTTGAAACATATTG-GTT--AAAAAATACA-ATATTTCCTTAATTTTTAAG-CCA-TGTAAAGGT
* * *
1200310 TGTTTTGGTTTATGACAGCATT
123 TGTTTTGGTTCATGACAACATA
* * * *
1200332 TATAGGAATTGTTTAATAATTTTTTTAGATTTTTTAAGCACATTTAGAAGTGCTCTTAGGTT-GT
1 TATAGGAACTGTTTAATAATTTTTTTAGATTTTTTAAGCTCATTTAAAAGTGCTATTAGGTTCG-
*
1200396 TTGAAACATATTGGTTAAAAATTACAATATTTCCTTAATTTTTAAGCCATGTAAAGGTTGTTTTG
65 TTGAAACATATTGGTTAAAAAATACAATATTTCCTTAATTTTTAAGCCATGTAAAGGTTGTTTTG
*
1200461 GTTCATGGCAACATA
130 GTTCATGACAACATA
* * *
1200476 TATAAGG-ACTATTTAATAATTTTTCTGGATTTTTTAAGCTCATTTAA
1 TAT-AGGAACTGTTTAATAATTTTTTTAGATTTTTTAAGCTCATTTAA
1200523 GAGTATTTTT
Statistics
Matches: 158, Mismatches: 26, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
143 1 0.01
144 84 0.53
145 7 0.04
146 42 0.27
147 24 0.15
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.46
Consensus pattern (144 bp):
TATAGGAACTGTTTAATAATTTTTTTAGATTTTTTAAGCTCATTTAAAAGTGCTATTAGGTTCGT
TGAAACATATTGGTTAAAAAATACAATATTTCCTTAATTTTTAAGCCATGTAAAGGTTGTTTTGG
TTCATGACAACATA
Found at i:1201122 original size:28 final size:28
Alignment explanation
Indices: 1201065--1201148 Score: 98
Period size: 29 Copynumber: 3.0 Consensus size: 28
1201055 AAAGTTTGTC
* * *
1201065 AAATGATAATTTCAAAAAATTTAAGGGTTA
1 AAATG-TAATTTTAAAAAGTTTAA-AGTTA
*
1201095 GAATGTAATTTTAAAAAGTTTAAAGTTA
1 AAATGTAATTTTAAAAAGTTTAAAGTTA
*
1201123 AAATGTAACTTT-AAAAGTTTAAAGTT
1 AAATGTAATTTTAAAAAGTTTAAAGTT
1201149 TTAGCAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
27 14 0.29
28 14 0.29
29 16 0.33
30 4 0.08
ACGTcount: A:0.48, C:0.02, G:0.13, T:0.37
Consensus pattern (28 bp):
AAATGTAATTTTAAAAAGTTTAAAGTTA
Found at i:1201146 original size:27 final size:28
Alignment explanation
Indices: 1201065--1201148 Score: 91
Period size: 27 Copynumber: 3.0 Consensus size: 28
1201055 AAAGTTTGTC
* *
1201065 AAATGATAA-TTTCAAAAAATTTAAGGGTTA
1 AAATG-TAACTTT-AAAAAGTTTAA-AGTTA
* *
1201095 GAATGTAATTTTAAAAAGTTTAAAGTTA
1 AAATGTAACTTTAAAAAGTTTAAAGTTA
1201123 AAATGTAACTTT-AAAAGTTTAAAGTT
1 AAATGTAACTTTAAAAAGTTTAAAGTT
1201149 TTAGCAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
27 14 0.29
28 14 0.29
29 13 0.27
30 7 0.15
ACGTcount: A:0.48, C:0.02, G:0.13, T:0.37
Consensus pattern (28 bp):
AAATGTAACTTTAAAAAGTTTAAAGTTA
Found at i:1205055 original size:201 final size:199
Alignment explanation
Indices: 1204670--1205060 Score: 527
Period size: 201 Copynumber: 2.0 Consensus size: 199
1204660 CTCTTATCTT
* * * *
1204670 TTATAAATTTTCTGTTCAAGCGTTAAATTCTTACAGTCTCTTTCCTATAGATTTAGGCGAGCATA
1 TTATAAATTTTCTGTTCAAACGTTAAATTCTTACAGTCTCTTTCCTATAGATTTAAGCAAACATA
* * * *
1204735 AACTGAAATGGATTTAACAGAAGTTAGAAAATAGATATCTGAAACAACTGTGGACTTTTATTAAA
66 AACTGAAATGAATTGAACAGAAGTTAGAAAATAGATATCTAAAACAACTGTGGACTTCTATTAAA
* * *
1204800 ATGCTAGAGAGAACCTGCAGATCCTAATTGTTGCATATATCAGTTTGTAATTCTGTTGCTCATAT
131 ATACTAGAGAGAACCTGCAGATCCTAATTGTTGCACACATCAGTTTGTAATTCTGTTGCTCATAT
1204865 TTTC
196 TTTC
* * * * *
1204869 TTATAAATTTTCTTTTCAAATGTTAAAATTCTTAC-GTTTTTTTTTCCTATAGATTTAAGCAAAT
1 TTATAAATTTTCTGTTCAAACGTT-AAATTCTTACAG--TCTCTTTCCTATAGATTTAAGCAAAC
* * * *
1204933 ATAAACTGCAATGAATTGAA-AGGAAGTTAGAAAATAGCTATCTAAAATAACCT-TGGACTTCTG
63 ATAAACTGAAATGAATTGAACA-GAAGTTAGAAAATAGATATCTAAAACAA-CTGTGGACTTCTA
*
1204996 TTAAAATACTAGAGAGAACCTGCAGATCCTAGTTGTTGCACACATCAGTTTGTAATTCTGTTGCT
126 TTAAAATACTAGAGAGAACCTGCAGATCCTAATTGTTGCACACATCAGTTTGTAATTCTGTTGCT
1205061 TCTGCATGGT
Statistics
Matches: 166, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
199 22 0.13
200 11 0.07
201 131 0.79
202 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (199 bp):
TTATAAATTTTCTGTTCAAACGTTAAATTCTTACAGTCTCTTTCCTATAGATTTAAGCAAACATA
AACTGAAATGAATTGAACAGAAGTTAGAAAATAGATATCTAAAACAACTGTGGACTTCTATTAAA
ATACTAGAGAGAACCTGCAGATCCTAATTGTTGCACACATCAGTTTGTAATTCTGTTGCTCATAT
TTTC
Found at i:1210361 original size:28 final size:29
Alignment explanation
Indices: 1210330--1210399 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 29
1210320 TATTTTGATG
**
1210330 TATTTATATATTTGTATTATATTTATAT-
1 TATTTATATATTTGTATTATAACTATATA
* *
1210358 TATTT-TTTATGTTGTATTTTAACTATATA
1 TATTTATATAT-TTGTATTATAACTATATA
*
1210387 TATATATATATTT
1 TATTTATATATTT
1210400 ATATGTGTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
27 4 0.12
28 19 0.58
29 6 0.18
30 4 0.12
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.63
Consensus pattern (29 bp):
TATTTATATATTTGTATTATAACTATATA
Found at i:1210405 original size:36 final size:33
Alignment explanation
Indices: 1210347--1210414 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 33
1210337 ATATTTGTAT
* *
1210347 TATATTTATATTATTTTTTATGTTGTATTTTAAC
1 TATATATATATTATTTTATATG-TGTATTTTAAC
*
1210381 TATATATATATATATATTTATATGTGTGTTTTAA
1 TATATATATAT-TAT-TTTATATGTGTATTTTAA
1210415 TTTATATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 10 0.34
35 12 0.41
36 7 0.24
ACGTcount: A:0.31, C:0.01, G:0.07, T:0.60
Consensus pattern (33 bp):
TATATATATATTATTTTATATGTGTATTTTAAC
Found at i:1210421 original size:36 final size:34
Alignment explanation
Indices: 1210345--1210421 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
1210335 ATATATTTGT
* *
1210345 ATTATATTTATATTATTTTTTATGTTGTATTTTA
1 ATTATATATATATTATTTTATATGTTGTATTTTA
* *
1210379 ACTATATATATATATATATTTATATG-TGTGTTTTA
1 ATTATATATATAT-TAT-TTTATATGTTGTATTTTA
1210414 ATT-TATAT
1 ATTATATAT
1210422 TTTGCATAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
34 16 0.44
35 13 0.36
36 7 0.19
ACGTcount: A:0.31, C:0.01, G:0.06, T:0.61
Consensus pattern (34 bp):
ATTATATATATATTATTTTATATGTTGTATTTTA
Found at i:1211034 original size:14 final size:14
Alignment explanation
Indices: 1211015--1211086 Score: 78
Period size: 14 Copynumber: 5.1 Consensus size: 14
1211005 TATTTCTGTC
1211015 AAAAAAAGAAAGAA
1 AAAAAAAGAAAGAA
1211029 AAAAAAAGAAAGAA
1 AAAAAAAGAAAGAA
**
1211043 AGAAAGGAGAAA-AA
1 A-AAAAAAGAAAGAA
1211057 AATAAAAAGGAAAG-A
1 AA-AAAAA-GAAAGAA
1211072 AAAAAAAGAAA-AA
1 AAAAAAAGAAAGAA
1211085 AA
1 AA
1211087 TTATGTATTC
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
13 8 0.16
14 26 0.53
15 15 0.31
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (14 bp):
AAAAAAAGAAAGAA
Found at i:1211070 original size:30 final size:27
Alignment explanation
Indices: 1211015--1211087 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 27
1211005 TATTTCTGTC
1211015 AAAAAAAGAAAGAAAA-AAAAAGAAAGA
1 AAAAAAAGAAA-AAAATAAAAAGAAAGA
*
1211042 AAGAAAGGAGAAAAAAATAAAAAGGAAAGA
1 AA-AAA-AAGAAAAAAATAAAAA-GAAAGA
1211072 AAAAAAAGAAAAAAAT
1 AAAAAAAGAAAAAAAT
1211088 TATGTATTCG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
27 2 0.05
28 17 0.43
29 13 0.32
30 8 0.20
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (27 bp):
AAAAAAAGAAAAAAATAAAAAGAAAGA
Found at i:1211085 original size:22 final size:21
Alignment explanation
Indices: 1211015--1211086 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 21
1211005 TATTTCTGTC
1211015 AAAAAAAGAAAGAAAAAAAAAG
1 AAAAAAAGAAAG-AAAAAAAAG
*
1211037 AAAGAAAGAAAGGAGAAAAAAA-
1 AAAAAAAGAAA-GA-AAAAAAAG
* *
1211059 TAAAAAGGAAAGAAAAAAAAG
1 AAAAAAAGAAAGAAAAAAAAG
1211080 AAAAAAA
1 AAAAAAA
1211087 TTATGTATTC
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
20 7 0.17
21 7 0.17
22 19 0.46
23 8 0.20
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (21 bp):
AAAAAAAGAAAGAAAAAAAAG
Found at i:1211707 original size:23 final size:24
Alignment explanation
Indices: 1211676--1211723 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
1211666 TTGTATCATA
1211676 TTTATATTATTTTTTATGCTGTGT
1 TTTATATTATTTTTTATGCTGTGT
*
1211700 TTTA-ATTATTTTTTATGTTGTGT
1 TTTATATTATTTTTTATGCTGTGT
1211723 T
1 T
1211724 CATGTCGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.17, C:0.02, G:0.12, T:0.69
Consensus pattern (24 bp):
TTTATATTATTTTTTATGCTGTGT
Found at i:1211877 original size:15 final size:15
Alignment explanation
Indices: 1211859--1211911 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 15
1211849 TCAATTGGTG
1211859 ATATTTTTTATATAA
1 ATATTTTTTATATAA
* *
1211874 ATA-TTTATATATTA
1 ATATTTTTTATATAA
1211888 ATAATTTATTTTATATAA
1 AT-A-TT-TTTTATATAA
1211906 ATATTT
1 ATATTT
1211912 ATATATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
14 11 0.37
15 5 0.17
16 2 0.07
17 2 0.07
18 10 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATATTTTTTATATAA
Found at i:1211890 original size:14 final size:14
Alignment explanation
Indices: 1211867--1211917 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
1211857 TGATATTTTT
1211867 TATATAAATATTTA
1 TATATAAATATTTA
*
1211881 TATATTAATAATTTA
1 TATATAAAT-ATTTA
1211896 TTTTATATAAATATTTA
1 ---TATATAAATATTTA
1211913 TATAT
1 TATAT
1211918 TTTTATCATG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 13 0.42
15 5 0.16
17 5 0.16
18 8 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATATAAATATTTA
Found at i:1212013 original size:35 final size:34
Alignment explanation
Indices: 1211934--1212014 Score: 94
Period size: 35 Copynumber: 2.4 Consensus size: 34
1211924 CATGTTCATA
*
1211934 TTAT-TTTTATA-TCACATTATATTTTAATTATT
1 TTATATTTTATATTCACATTATATCTTAATTATT
* * *
1211966 TTTTAATATTATATTCATATTATATCTTAATTTATT
1 TTAT-ATTTTATATTCACATTATATCTTAA-TTATT
1212002 TTATATTTTATAT
1 TTATATTTTATAT
1212015 AAATTTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
32 3 0.08
34 6 0.15
35 22 0.56
36 8 0.21
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (34 bp):
TTATATTTTATATTCACATTATATCTTAATTATT
Found at i:1212019 original size:22 final size:22
Alignment explanation
Indices: 1211894--1212020 Score: 54
Period size: 22 Copynumber: 5.7 Consensus size: 22
1211884 ATTAATAATT
1211894 TATTTTATATAAA--TATTTATA
1 TATTTTATATAAATTTATTT-TA
* *
1211915 TATTTT-TAT-CATGTTCATATTA
1 TATTTTATATAAAT-TT-ATTTTA
*
1211937 T-TTTTATATCACATTATATTTTAA
1 TATTTTATAT-AAATT-TATTTT-A
*
1211961 TTATTTT-T-T-AATATTATATTCA
1 -TATTTTATATAAAT-TTAT-TTTA
* * *
1211983 TATTATATCTTAATTTATTTTA
1 TATTTTATATAAATTTATTTTA
1212005 TATTTTATATAAATTT
1 TATTTTATATAAATTT
1212021 TTATATAATT
Statistics
Matches: 80, Mismatches: 10, Indels: 31
0.66 0.08 0.26
Matches are distributed among these distances:
19 1 0.01
20 3 0.04
21 15 0.19
22 30 0.38
23 16 0.20
24 9 0.11
25 2 0.03
26 4 0.05
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.61
Consensus pattern (22 bp):
TATTTTATATAAATTTATTTTA
Found at i:1212038 original size:27 final size:27
Alignment explanation
Indices: 1212006--1212094 Score: 69
Period size: 29 Copynumber: 3.3 Consensus size: 27
1211996 TTTATTTTAT
1212006 ATTTTATATAAATTTTTATATAATTAA
1 ATTTTATATAAATTTTTATATAATTAA
* *
1212033 ATTTTAAATTTAAATTTATT-TATTAAAT-A
1 ATTTT--ATATAAATTT-TTATA-TAATTAA
* *
1212062 TTTTTAAATAAA-TTTTAT-TAATTATA
1 ATTTTATATAAATTTTTATATAATTA-A
1212088 ATTTTAT
1 ATTTTAT
1212095 TTAATTAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 15
0.67 0.11 0.21
Matches are distributed among these distances:
24 4 0.09
25 2 0.04
26 9 0.19
27 10 0.21
29 16 0.34
30 6 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTTTATATAAATTTTTATATAATTAA
Found at i:1212065 original size:44 final size:47
Alignment explanation
Indices: 1212015--1212124 Score: 117
Period size: 43 Copynumber: 2.4 Consensus size: 47
1212005 TATTTTATAT
1212015 AAATTTTTATATAATTAAATTTTA-AATT-TAAATTTATTT-ATTAA
1 AAATTTTTATATAATTAAATTTTATAATTATAAATTTATTTAATTAA
* *
1212059 ATA-TTTT-TA-AA-TAAATTTTATTAATTATAATTTTATTTAATTAA
1 AAATTTTTATATAATTAAATTTTA-TAATTATAAATTTATTTAATTAA
* *
1212103 AAATTTTATAAATAATAAAATT
1 AAATTTT-TATATAATTAAATT
1212125 CGAGAGGAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
40 9 0.17
41 2 0.04
42 6 0.12
43 14 0.27
44 9 0.17
45 3 0.06
46 1 0.02
47 1 0.02
48 2 0.04
49 5 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (47 bp):
AAATTTTTATATAATTAAATTTTATAATTATAAATTTATTTAATTAA
Found at i:1216920 original size:31 final size:33
Alignment explanation
Indices: 1216885--1216986 Score: 84
Period size: 31 Copynumber: 3.0 Consensus size: 33
1216875 AATTAATTTA
*
1216885 TATATTTATATCATT-TTTATATT-TA-AAATAT
1 TATATTTAT-TAATTATTTATATTATATAAATAT
* *
1216916 TATATATATTAATTATTTATATTATATAAATTT
1 TATATTTATTAATTATTTATATTATATAAATAT
* *
1216949 TAATTTATTTATTTATTATTTTTATATTATATTAATAT
1 T-A--TATTTATTAATTA--TTTATATTATATAAATAT
1216987 CCATGGAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
30 4 0.07
31 16 0.29
32 2 0.04
33 6 0.11
34 1 0.02
36 11 0.20
38 16 0.29
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (33 bp):
TATATTTATTAATTATTTATATTATATAAATAT
Found at i:1216935 original size:17 final size:17
Alignment explanation
Indices: 1216872--1216947 Score: 59
Period size: 17 Copynumber: 4.4 Consensus size: 17
1216862 TAATTAATTA
1216872 ATTAATTAATTTATATAT
1 ATTAATT-ATTTATATAT
* *
1216890 -TTATATCATTTTTATAT
1 ATTA-ATTATTTATATAT
*
1216907 -TTAA-AATATTATATAT
1 ATTAATTAT-TTATATAT
1216923 ATTAATTATTTATATTAT
1 ATTAATTATTTATA-TAT
*
1216941 ATAAATT
1 ATTAATT
1216948 TTAATTTATT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
15 2 0.04
16 8 0.17
17 24 0.51
18 13 0.28
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTAATTATTTATATAT
Found at i:1216951 original size:24 final size:23
Alignment explanation
Indices: 1216912--1216964 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
1216902 TATATTTAAA
1216912 ATATTATATATATTAA-TTATTT
1 ATATTATATATATTAATTTATTT
*
1216934 ATATTATATAAATTTTAATTTATTT
1 ATATTATAT--ATATTAATTTATTT
1216959 AT-TTAT
1 ATATTAT
1216965 TATTTTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 9 0.33
24 10 0.37
25 8 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATATTATATATATTAATTTATTT
Found at i:1222650 original size:17 final size:15
Alignment explanation
Indices: 1222616--1222663 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
1222606 CTGACAATAA
*
1222616 TATATTATTTTATAT
1 TATATTATTTTAAAT
1222631 TATATTATATTTAAAT
1 TATATTAT-TTTAAAT
*
1222647 T-TATAATTTTAATAT
1 TATATTATTTTAA-AT
1222662 TA
1 TA
1222664 AAAAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 5 0.18
15 16 0.57
16 7 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATATTATTTTAAAT
Found at i:1223144 original size:19 final size:19
Alignment explanation
Indices: 1223111--1223156 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1223101 AAATAAAAAA
*
1223111 TATTTTTTAATA-TTTACT
1 TATTTTTTAAAATTTTACT
1223129 TATTTTTTGAAAATTTTACT
1 TATTTTTT-AAAATTTTACT
1223149 T-TTTTTTA
1 TATTTTTTA
1223157 GATAACAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 9 0.36
19 9 0.36
20 7 0.28
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTTTTTAAAATTTTACT
Found at i:1223493 original size:33 final size:32
Alignment explanation
Indices: 1223425--1223494 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
1223415 ATTATAAATC
* * *
1223425 TATACAAATTTTATTATTTTAATAATTAATTT
1 TATAAAAATTTTATCATATTAATAATTAATTT
*
1223457 TATAAAAATTTTATCATATTCATAAATT-ATTAT
1 TATAAAAATTTTATCATATTAAT-AATTAATT-T
1223490 TATAA
1 TATAA
1223495 TTATATTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 22 0.69
33 10 0.31
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (32 bp):
TATAAAAATTTTATCATATTAATAATTAATTT
Found at i:1225250 original size:30 final size:29
Alignment explanation
Indices: 1225214--1225275 Score: 72
Period size: 32 Copynumber: 2.1 Consensus size: 29
1225204 TATATTTTAA
*
1225214 TAATATA-ATATTTTTTTAATAATAAACTAT
1 TAATATACATATTATTTTAATAA-AAA-TAT
*
1225244 TAATATAGCTTATTATTTTAATAAAAATAT
1 TAATATA-CATATTATTTTAATAAAAATAT
1225274 TA
1 TA
1225276 TTTAATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 12 0.43
31 3 0.11
32 13 0.46
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (29 bp):
TAATATACATATTATTTTAATAAAAATAT
Found at i:1225292 original size:18 final size:16
Alignment explanation
Indices: 1225254--1225296 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 16
1225244 TAATATAGCT
1225254 TATTATTTTAATAAAAA
1 TATTA-TTTAATAAAAA
1225271 TATTATTTAATAAAATAA
1 TATTATTTAAT-AAA-AA
1225289 TATTATTT
1 TATTATTT
1225297 TAATGATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.25
17 8 0.33
18 10 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATTATTTAATAAAAA
Found at i:1225307 original size:21 final size:19
Alignment explanation
Indices: 1225254--1225308 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 19
1225244 TAATATAGCT
*
1225254 TATTATTTTA-ATAAA-AA
1 TATTATTTAATATAAATAA
1225271 TATTATTTAATA-AAATAA
1 TATTATTTAATATAAATAA
1225289 TATTATTTTAATGATAAATA
1 TATTA-TTTAAT-ATAAATA
1225309 GTAACCTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 12 0.38
18 8 0.25
19 6 0.19
20 1 0.03
21 5 0.16
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TATTATTTAATATAAATAA
Found at i:1225308 original size:18 final size:17
Alignment explanation
Indices: 1225254--1225300 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 17
1225244 TAATATAGCT
1225254 TATTATTTTAATAAAAA
1 TATTATTTTAATAAAAA
1225271 TATTA-TTTAATAAAATAA
1 TATTATTTTAAT-AAA-AA
1225289 TATTATTTTAAT
1 TATTATTTTAAT
1225301 GATAAATAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.22
17 8 0.30
18 7 0.26
19 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTATTTTAATAAAAA
Found at i:1225823 original size:25 final size:25
Alignment explanation
Indices: 1225795--1225842 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1225785 GATTAAAATA
1225795 TTAATATTTTAAAAATAAATAATTT
1 TTAATATTTTAAAAATAAATAATTT
* *
1225820 TTAATATTTTAATAATTAATAAT
1 TTAATATTTTAAAAATAAATAAT
1225843 AAAATATCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TTAATATTTTAAAAATAAATAATTT
Found at i:1228656 original size:20 final size:20
Alignment explanation
Indices: 1228631--1228669 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1228621 ACCCATGAAA
1228631 GCTTGGGTTTTGAGATCTAT
1 GCTTGGGTTTTGAGATCTAT
1228651 GCTTGGGTTTTGAGATCTA
1 GCTTGGGTTTTGAGATCTA
1228670 CGGAGGTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.10, G:0.31, T:0.44
Consensus pattern (20 bp):
GCTTGGGTTTTGAGATCTAT
Found at i:1229052 original size:21 final size:20
Alignment explanation
Indices: 1229028--1229090 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 20
1229018 TTTGAATTTT
1229028 ATTTAATTATTATTAAATTAA
1 ATTTAA-TATTATTAAATTAA
1229049 ATTT-A-A--A-TAAATTAA
1 ATTTAATATTATTAAATTAA
1229064 ATTTAAATATT-TTAATATTAA
1 ATTT-AATATTATTAA-ATTAA
1229085 ATTTAA
1 ATTTAA
1229091 ATAATTTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 15
0.70 0.00 0.30
Matches are distributed among these distances:
15 12 0.34
16 1 0.03
17 1 0.03
18 2 0.06
20 6 0.17
21 13 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTAATATTATTAAATTAA
Found at i:1229078 original size:15 final size:15
Alignment explanation
Indices: 1229041--1229072 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1229031 TAATTATTAT
1229041 TAAATTAAATTTAAA
1 TAAATTAAATTTAAA
1229056 TAAATTAAATTTAAA
1 TAAATTAAATTTAAA
1229071 TA
1 TA
1229073 TTTTAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAATTAAATTTAAA
Found at i:1229091 original size:21 final size:21
Alignment explanation
Indices: 1229059--1229098 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1229049 ATTTAAATAA
*
1229059 ATTAAATTTAAATATTTTAAT
1 ATTAAATTTAAATAATTTAAT
1229080 ATTAAATTTAAATAATTTA
1 ATTAAATTTAAATAATTTA
1229099 TAAATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTAAATTTAAATAATTTAAT
Found at i:1229222 original size:7 final size:6
Alignment explanation
Indices: 1229205--1229229 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1229195 AAATTAATTT
1229205 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
1229230 TAAATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:1229241 original size:6 final size:6
Alignment explanation
Indices: 1229232--1229263 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1229222 ATAAAAATTA
1229232 AATTTT AATTTT AATTTT AATTTT AATTTT AA
1 AATTTT AATTTT AATTTT AATTTT AATTTT AA
1229264 AATTTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
AATTTT
Found at i:1229275 original size:18 final size:18
Alignment explanation
Indices: 1229192--1229284 Score: 55
Period size: 18 Copynumber: 5.1 Consensus size: 18
1229182 TAATTTTTAT
1229192 TTTAAATTAATTTTAAAA
1 TTTAAATTAATTTTAAAA
* * * ***
1229210 ATAAAAATAAAAATAAAA
1 TTTAAATTAATTTTAAAA
* *
1229228 ATTAAATTTTAATTTT-AAT
1 TTTAAA--TTAATTTTAAAA
*
1229247 TTTAATTTTAATTTTAAAA
1 TTTAA-ATTAATTTTAAAA
*
1229266 TTTAAATTAA-ATTAAAA
1 TTTAAATTAATTTTAAAA
1229283 TT
1 TT
1229285 GAATTCTAAT
Statistics
Matches: 54, Mismatches: 17, Indels: 9
0.68 0.21 0.11
Matches are distributed among these distances:
17 8 0.15
18 29 0.54
19 13 0.24
20 4 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTAAATTAATTTTAAAA
Found at i:1235941 original size:69 final size:69
Alignment explanation
Indices: 1235827--1235968 Score: 223
Period size: 69 Copynumber: 2.1 Consensus size: 69
1235817 AAAAGCTACT
* * *
1235827 AGAAACTATACCTTATTGTTTATTTTCCAAAATTAAAAATGTATCCAGATATTTGGAAATTAAAA
1 AGAAACTATACCTTATTGTTCATTTTCCAAAATTAAAAATATATCCAGATATTTGGAAATCAAAA
1235892 TACA
66 TACA
* *
1235896 AGAAACTATACCTTATTGTTCATTTTCCAAAA-TGAAAATCATATCCCGATATTTGGAAATCAAA
1 AGAAACTATACCTTATTGTTCATTTTCCAAAATTAAAAAT-ATATCCAGATATTTGGAAATCAAA
1235960 ATACA
65 ATACA
1235965 AGAA
1 AGAA
1235969 CTAATTCATT
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
68 6 0.09
69 61 0.91
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (69 bp):
AGAAACTATACCTTATTGTTCATTTTCCAAAATTAAAAATATATCCAGATATTTGGAAATCAAAA
TACA
Found at i:1239310 original size:15 final size:15
Alignment explanation
Indices: 1239286--1239315 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1239276 TATGCAAGTG
*
1239286 AAGTTTTTATCTTTT
1 AAGTTGTTATCTTTT
1239301 AAGTTGTTATCTTTT
1 AAGTTGTTATCTTTT
1239316 CTTGGCTTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.63
Consensus pattern (15 bp):
AAGTTGTTATCTTTT
Found at i:1246142 original size:19 final size:18
Alignment explanation
Indices: 1246120--1246164 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 18
1246110 TTATTTTTTA
1246120 TTATTTAAAATATTATAAT
1 TTATTTAAAAT-TTATAAT
*
1246139 TTATATATAAAATTTATATT
1 TTAT-T-TAAAATTTATAAT
1246159 TTATTT
1 TTATTT
1246165 TATTTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 1 0.04
19 5 0.22
20 11 0.48
21 6 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATTTAAAATTTATAAT
Found at i:1247174 original size:19 final size:18
Alignment explanation
Indices: 1247087--1247170 Score: 66
Period size: 19 Copynumber: 4.6 Consensus size: 18
1247077 GCCACCCTCA
*
1247087 TTATATAATTTTATAAATAT
1 TTATAT-ATATTATAAA-AT
* * *
1247107 ATACATAAATTAT-AAAT
1 TTATATATATTATAAAAT
1247124 TT-TATATATTATAAAAT
1 TTATATATATTATAAAAT
*
1247141 TCACTCATATA-TATAAAAT
1 TTA-T-ATATATTATAAAAT
1247160 TTATATATATT
1 TTATATATATT
1247171 TATACAACTA
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
16 8 0.16
17 13 0.26
18 4 0.08
19 16 0.32
20 9 0.18
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (18 bp):
TTATATATATTATAAAAT
Found at i:1247453 original size:16 final size:16
Alignment explanation
Indices: 1247415--1247445 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1247405 TTTAGATTCC
1247415 TATAAAAGAAAAAAAA
1 TATAAAAGAAAAAAAA
1247431 TATAAAAGAAAAAAA
1 TATAAAAGAAAAAAA
1247446 TTCAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.13
Consensus pattern (16 bp):
TATAAAAGAAAAAAAA
Found at i:1247454 original size:17 final size:16
Alignment explanation
Indices: 1247418--1247468 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1247408 AGATTCCTAT
* *
1247418 AAAAGAAAAAAAATAT
1 AAAAGAAAAAAATTAA
1247434 AAAAGAAAAAAATTCAA
1 AAAAGAAAAAAATT-AA
**
1247451 AAAATTAAAAAATTAA
1 AAAAGAAAAAAATTAA
1247467 AA
1 AA
1247469 TTTTAAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 17 0.57
17 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (16 bp):
AAAAGAAAAAAATTAA
Found at i:1247468 original size:24 final size:24
Alignment explanation
Indices: 1247424--1247486 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 24
1247414 CTATAAAAGA
1247424 AAAAAAATATAAAAGAAAAAA-ATT
1 AAAAAAAT-TAAAAGAAAAAATATT
* *
1247448 CAAAAAATTAAAA-AATTAAAATTTT
1 AAAAAAATTAAAAGAA--AAAATATT
1247473 AAAAATAATTAAAA
1 AAAAA-AATTAAAA
1247487 TATTTTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
22 2 0.06
23 5 0.16
24 11 0.34
25 6 0.19
26 8 0.25
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAAAAATTAAAAGAAAAAATATT
Found at i:1248064 original size:2 final size:2
Alignment explanation
Indices: 1248057--1248093 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1248047 TCTTACTAAA
1248057 AT AT AT AT 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 AT AT AT AT A
1248094 AACAAATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1252782 original size:3 final size:3
Alignment explanation
Indices: 1252774--1252799 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1252764 AGAATCTGAG
1252774 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
1252800 CGAGAGATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:1255697 original size:108 final size:108
Alignment explanation
Indices: 1255562--1256226 Score: 1084
Period size: 108 Copynumber: 6.2 Consensus size: 108
1255552 TACATGGTAT
* *
1255562 AAGAAATTTTACTTTGCTTCACATGAATCTATTAAAAAAAAGTGTCAATTTTAAGCCACCAAGTG
1 AAGAAAATTTACTTTGCTTCACATGAATCTATTAAAAAAAAGTGTCAATTTTAAGCCATCAAGTG
*
1255627 AGAGAGAAAAAGATTGAAAATTCATAATTGTCAAATTAATCCC
66 AGAGAGAAAAAGATTGAAAATTCACAATTGTCAAATTAATCCC
* * * *
1255670 AAGAAAATTTACTTTGCTTGACATGAATCTATTTAAAAAAAGTATCAATTTTAAGCCACCAAGT-
1 AAGAAAATTTACTTTGCTTCACATGAATCTATTAAAAAAAAGTGTCAATTTTAAGCCATCAAGTG
*
1255734 AGGAGAGAAAAAGATTGAAAATTCACAATTGTCAAATTAATCTC
66 A-GAGAGAAAAAGATTGAAAATTCACAATTGTCAAATTAATCCC
*
1255778 AAGAAAATTTACTTTGCTTCACATGAATCTATTAAAAAAAAGTGTCAATTTTAAGCAATCAAGTG
1 AAGAAAATTTACTTTGCTTCACATGAATCTATTAAAAAAAAGTGTCAATTTTAAGCCATCAAGTG
1255843 AGAGAGAAAAAGATTGAAAATTCACAATTGTCAAATTAATCCC
66 AGAGAGAAAAAGATTGAAAATTCACAATTGTCAAATTAATCCC
* * * *
1255886 AAGAAAATTTACTTTACTTCACATGAATCTATTAAAAGAAAGTATTAATTTTAAGCCATCAAGTG
1 AAGAAAATTTACTTTGCTTCACATGAATCTATTAAAAAAAAGTGTCAATTTTAAGCCATCAAGTG
*
1255951 AGAGAGAAAAAGATTAAAAATTCACAATTGTCAAATTAATCCC
66 AGAGAGAAAAAGATTGAAAATTCACAATTGTCAAATTAATCCC
*
1255994 AAGAAAATTTGCTTTGCTTCACATGAATCTATTAAAAAAAAGTGTCAATTTTAAGCCATCAAGTG
1 AAGAAAATTTACTTTGCTTCACATGAATCTATTAAAAAAAAGTGTCAATTTTAAGCCATCAAGTG
* * *
1256059 GGAGAGAAAAAGATTAAAAATTCACAATCGTCAAATTAATCCC
66 AGAGAGAAAAAGATTGAAAATTCACAATTGTCAAATTAATCCC
*
1256102 AAAAAAATTTACTTTGCTTCACATGAATCTATT-AAAAAAA-TGTCAATTTTAAGCCATCAAGTG
1 AAGAAAATTTACTTTGCTTCACATGAATCTATTAAAAAAAAGTGTCAATTTTAAGCCATCAAGTG
* * * *
1256165 GGAGAGAAAAAGATTGAAAATTCATAATTATCAAATTAATCTC
66 AGAGAGAAAAAGATTGAAAATTCACAATTGTCAAATTAATCCC
*
1256208 AAAAAAATTTACTTTGCTT
1 AAGAAAATTTACTTTGCTT
1256227 AAAAAAAAAT
Statistics
Matches: 523, Mismatches: 32, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
106 80 0.15
107 8 0.02
108 434 0.83
109 1 0.00
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (108 bp):
AAGAAAATTTACTTTGCTTCACATGAATCTATTAAAAAAAAGTGTCAATTTTAAGCCATCAAGTG
AGAGAGAAAAAGATTGAAAATTCACAATTGTCAAATTAATCCC
Found at i:1256483 original size:36 final size:36
Alignment explanation
Indices: 1256446--1256534 Score: 96
Period size: 36 Copynumber: 2.5 Consensus size: 36
1256436 AAAAATTTTA
** *
1256446 TTTATATAAATTTTTATATATTAATA-ATTTTTATTAT
1 TTTATAT-AATTTAAAT-TATTAATATATTTATATTAT
*
1256483 TTTATATAATTTAAATTATTTATATATTTATATTAT
1 TTTATATAATTTAAATTATTAATATATTTATATTAT
1256519 TTT-TAT-ATTT-AATTAT
1 TTTATATAATTTAAATTAT
1256535 ATAACTTCTG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
33 6 0.13
34 4 0.09
35 10 0.21
36 20 0.43
37 7 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (36 bp):
TTTATATAATTTAAATTATTAATATATTTATATTAT
Found at i:1256485 original size:25 final size:25
Alignment explanation
Indices: 1256457--1256515 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 25
1256447 TTATATAAAT
1256457 TTTTATAT-ATTAATAATT-TTTATTA
1 TTTTATATAATTAA-AATTATTTA-TA
*
1256482 TTTTATATAATTTAAATTATTTATA
1 TTTTATATAATTAAAATTATTTATA
1256507 TATTTATAT
1 T-TTTATAT
1256516 TATTTTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 15 0.50
26 15 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTTATATAATTAAAATTATTTATA
Found at i:1256485 original size:26 final size:26
Alignment explanation
Indices: 1256455--1256515 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
1256445 ATTTATATAA
1256455 ATTTTTATAT-ATTAATAATT-TTTAT
1 ATTTTTATATAATTAA-AATTATTTAT
*
1256480 -TATTTTATATAATTTAAATTATTTAT
1 AT-TTTTATATAATTAAAATTATTTAT
*
1256506 ATATTTATAT
1 ATTTTTATAT
1256516 TATTTTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
24 1 0.03
25 12 0.40
26 16 0.53
27 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
ATTTTTATATAATTAAAATTATTTAT
Found at i:1256526 original size:19 final size:19
Alignment explanation
Indices: 1256446--1256534 Score: 84
Period size: 17 Copynumber: 5.0 Consensus size: 19
1256436 AAAAATTTTA
*
1256446 TTTATATAAATTTTTA-TAT
1 TTTATAT-AATTTATATTAT
* *
1256465 ATTA-ATAATTTTTATTAT
1 TTTATATAATTTATATTAT
*
1256483 TTTATATAATTTAAATTA-
1 TTTATATAATTTATATTAT
1256501 TTTATAT-ATTTATATTAT
1 TTTATATAATTTATATTAT
1256519 TTT-TAT-ATTTA-ATTAT
1 TTTATATAATTTATATTAT
1256535 ATAACTTCTG
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
16 5 0.08
17 25 0.40
18 18 0.29
19 14 0.23
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTATATAATTTATATTAT
Found at i:1258801 original size:19 final size:19
Alignment explanation
Indices: 1258774--1258829 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
1258764 ATTTGATTAA
*
1258774 TTATAATTTAAAATTTATT
1 TTATTATTTAAAATTTATT
* *
1258793 TTATTATTTTAAATGTATT
1 TTATTATTTAAAATTTATT
** *
1258812 AAAATA-TTAAAATTTATT
1 TTATTATTTAAAATTTATT
1258830 AATATTTATA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 10 0.34
19 19 0.66
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TTATTATTTAAAATTTATT
Found at i:1259738 original size:20 final size:20
Alignment explanation
Indices: 1259684--1259738 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
1259674 AGAAATTGAT
1259684 TTAA-TTAATTTAAATTAAA
1 TTAAGTTAATTTAAATTAAA
**
1259703 TTAAGTTAATAAAAATTAAA
1 TTAAGTTAATTTAAATTAAA
* * *
1259723 TTGATTTGATTTAAAT
1 TTAAGTTAATTTAAAT
1259739 AATTATTTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
TTAAGTTAATTTAAATTAAA
Found at i:1259748 original size:12 final size:12
Alignment explanation
Indices: 1259731--1259768 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
1259721 AATTGATTTG
1259731 ATTTAAATAATT
1 ATTTAAATAATT
1259743 ATTTAAATAATT
1 ATTTAAATAATT
*
1259755 A--TAAAAAATT
1 ATTTAAATAATT
1259765 ATTT
1 ATTT
1259769 TAATTTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
10 9 0.39
12 14 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATTTAAATAATT
Found at i:1259764 original size:22 final size:24
Alignment explanation
Indices: 1259734--1259784 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1259724 TGATTTGATT
*
1259734 TAAATAATTA-TTTAA-ATAATTA
1 TAAAAAATTATTTTAATATAATTA
*
1259756 TAAAAAATTATTTTAATTTAATTA
1 TAAAAAATTATTTTAATATAATTA
1259780 TAAAA
1 TAAAA
1259785 TATATAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.36
23 5 0.20
24 11 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TAAAAAATTATTTTAATATAATTA
Found at i:1259781 original size:24 final size:23
Alignment explanation
Indices: 1259726--1259784 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
1259716 AATTAAATTG
* *
1259726 ATTTGATT-TAAATAATTATTTA
1 ATTTAATTATAAAAAATTATTTA
*
1259748 A-ATAATTATAAAAAATTATTTTA
1 ATTTAATTATAAAAAATTA-TTTA
1259771 ATTTAATTATAAAA
1 ATTTAATTATAAAA
1259785 TATATAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 4 0.13
22 10 0.33
23 5 0.17
24 11 0.37
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTTAATTATAAAAAATTATTTA
Found at i:1262561 original size:20 final size:20
Alignment explanation
Indices: 1262524--1262562 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1262514 TTTAAGGCTT
*
1262524 TATTTAGTTGATATTTTTAC
1 TATTTAGTTGATACTTTTAC
**
1262544 TATTTAGTTTTTACTTTTA
1 TATTTAGTTGATACTTTTA
1262563 TTTATTAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.05, G:0.08, T:0.64
Consensus pattern (20 bp):
TATTTAGTTGATACTTTTAC
Found at i:1267585 original size:18 final size:18
Alignment explanation
Indices: 1267562--1267600 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1267552 AATATATGTC
1267562 ATTAATATGT-GAATTGAA
1 ATTAATAT-TCGAATTGAA
1267580 ATTAATATTCGAATTGAA
1 ATTAATATTCGAATTGAA
1267598 ATT
1 ATT
1267601 GAACATAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.41
Consensus pattern (18 bp):
ATTAATATTCGAATTGAA
Found at i:1267909 original size:19 final size:20
Alignment explanation
Indices: 1267868--1267911 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1267858 TTAAAAATTT
* * *
1267868 AAATTTTAATATATATAATA
1 AAATTTAAAAATATATAAAA
1267888 AAATTTAAAAATAT-TAAAA
1 AAATTTAAAAATATATAAAA
1267907 AAATT
1 AAATT
1267912 AAATTTAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATTTAAAAATATATAAAA
Found at i:1268539 original size:15 final size:16
Alignment explanation
Indices: 1268511--1268540 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1268501 AGATCAAATC
1268511 AAATTATGATTAAAAA
1 AAATTATGATTAAAAA
1268527 AAATTAT-ATTAAAA
1 AAATTATGATTAAAA
1268541 TTTGATTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
AAATTATGATTAAAAA
Found at i:1272309 original size:3 final size:3
Alignment explanation
Indices: 1272301--1272341 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1272291 AAGTCTTTTC
1272301 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1272342 TAACTATACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1272574 original size:3 final size:3
Alignment explanation
Indices: 1272566--1272622 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
1272556 ATTACTTAAA
*
1272566 AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1272614 AAT AAT AAT
1 AAT AAT AAT
1272623 CTTGATTTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1274755 original size:2 final size:2
Alignment explanation
Indices: 1274742--1274811 Score: 50
Period size: 2 Copynumber: 35.0 Consensus size: 2
1274732 CGGCCAAAGG
* * * * * * *
1274742 TA TA TG TA TA TA TA TA TG TA TA TA CA TA TA CA TG TG TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
1274784 TA TA TA TA TA TA CA CA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1274812 CCAACATACA
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (2 bp):
TA
Found at i:1274782 original size:32 final size:32
Alignment explanation
Indices: 1274746--1274806 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
1274736 CAAAGGTATA
* *
1274746 TGTATATATATATGTATATACATATACATGTG
1 TGTATATATATATATATACACATATACATGTG
1274778 TGTATATATATATATATACACATATACAT
1 TGTATATATATATATATACACATATACAT
1274807 ATATACCAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (32 bp):
TGTATATATATATATATACACATATACATGTG
Found at i:1280723 original size:20 final size:18
Alignment explanation
Indices: 1280688--1280741 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 18
1280678 TTAATTTAGG
1280688 TTAAATTT--AAA-ATTT
1 TTAAATTTAAAAATATTT
*
1280703 TTAATTTTAAATAATATTT
1 TTAAATTTAAA-AATATTT
1280722 TTAAATTTAAAAATATTT
1 TTAAATTTAAAAATATTT
1280740 TT
1 TT
1280742 TATTTAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
15 7 0.21
17 1 0.03
18 11 0.33
19 14 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAAATTTAAAAATATTT
Found at i:1280742 original size:20 final size:19
Alignment explanation
Indices: 1280699--1280750 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
1280689 TAAATTTAAA
*
1280699 ATTTTTAATTTTAAATAAT
1 ATTTTTAAATTTAAATAAT
1280718 ATTTTTAAATTTAAA-AAT
1 ATTTTTAAATTTAAATAAT
*
1280736 ATTTTT-TATTTAAAT
1 ATTTTTAAATTTAAAT
1280751 TTAATTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 7 0.23
18 9 0.30
19 14 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTTTAAATTTAAATAAT
Found at i:1281100 original size:21 final size:22
Alignment explanation
Indices: 1281039--1281100 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 22
1281029 AAAACTTGAC
* *
1281039 AAAAAAATTCAAAATATATAAT
1 AAAAATATTCAAAATAAATAAT
* *
1281061 AAACAATATT-TAAA-GAATAAT
1 AAA-AATATTCAAAATAAATAAT
1281082 -AAAATATTCAAAATAAATA
1 AAAAATATTCAAAATAAATA
1281101 CAAATAATGT
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 6 0.19
20 5 0.16
21 9 0.29
22 6 0.19
23 5 0.16
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAAATATTCAAAATAAATAAT
Found at i:1281941 original size:2 final size:2
Alignment explanation
Indices: 1281929--1281968 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
1281919 AGTGTTTAAA
* * *
1281929 AT AT AT TT AT AT AT AT GT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1281969 TTGTGTGCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (2 bp):
AT
Found at i:1282111 original size:5 final size:5
Alignment explanation
Indices: 1282096--1282148 Score: 63
Period size: 5 Copynumber: 10.2 Consensus size: 5
1282086 AAATATATTT
*
1282096 ATATGA ATATA ATAT- ATATA AAATA ATTATA ATATA ATATA ATATAA
1 ATAT-A ATATA ATATA ATATA ATATA A-TATA ATATA ATATA ATAT-A
1282143 ATATA A
1 ATATA A
1282149 ATTATAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
4 4 0.10
5 25 0.60
6 13 0.31
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:1282125 original size:28 final size:28
Alignment explanation
Indices: 1282081--1282158 Score: 85
Period size: 25 Copynumber: 2.9 Consensus size: 28
1282071 TACATAAATA
*
1282081 ATAT-TAAATATATTTATATGAATATAAT
1 ATATATAAATATAATTATAT-AATATAAT
1282109 ATATATAAA-ATAA-T-TATAATATAAT
1 ATATATAAATATAATTATATAATATAAT
1282134 ATAATATAAATATAAATTATA-AATA
1 AT-ATATAAATAT-AATTATATAATA
1282159 AAACATGAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
25 10 0.23
26 10 0.23
27 3 0.07
28 9 0.21
29 9 0.21
30 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (28 bp):
ATATATAAATATAATTATATAATATAAT
Found at i:1282832 original size:31 final size:31
Alignment explanation
Indices: 1282761--1282848 Score: 77
Period size: 31 Copynumber: 2.7 Consensus size: 31
1282751 GACCTAGTTT
* * * *
1282761 AAATTATTATTAAATAATAAAATTTTTATTTAA
1 AAATAATT-TTAAA-AATAAAATATTAATATAA
**
1282794 ATTTAATTTTAAAAATAAAATATTAATATAA
1 AAATAATTTTAAAAATAAAATATTAATATAA
*
1282825 AAATAATTTTTTAAAATAATAATA
1 AAATAA-TTTTAAAAATAA-AATA
1282849 AAATTTTAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
31 19 0.43
32 16 0.36
33 9 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
AAATAATTTTAAAAATAAAATATTAATATAA
Found at i:1282855 original size:19 final size:19
Alignment explanation
Indices: 1282803--1282858 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
1282793 AATTTAATTT
* *
1282803 TAAAAATAAAATATTAATA
1 TAAAAATAAAATTTTAAAA
**
1282822 TAAAAATAATTTTTTAAAA
1 TAAAAATAAAATTTTAAAA
*
1282841 TAATAATAAAATTTTAAA
1 TAAAAATAAAATTTTAAA
1282859 TTTAACAATA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAATAAAATTTTAAAA
Found at i:1283066 original size:2 final size:2
Alignment explanation
Indices: 1283059--1283094 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1283049 GTAAAGAAGC
1283059 AT AT 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 AT AT
1283095 TAATTATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1283457 original size:27 final size:28
Alignment explanation
Indices: 1283426--1283485 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
1283416 TAAGATTATC
* *
1283426 TAAAAGATAAT-TAAATATAT-TATAAAA
1 TAAAA-ATAATATAAACATATAAATAAAA
*
1283453 TAAAAATATTATAAACATATAAATAAAA
1 TAAAAATAATATAAACATATAAATAAAA
1283481 TAAAA
1 TAAAA
1283486 TTTATAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 4 0.14
27 13 0.46
28 11 0.39
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (28 bp):
TAAAAATAATATAAACATATAAATAAAA
Found at i:1283461 original size:16 final size:17
Alignment explanation
Indices: 1283437--1283477 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
1283427 AAAAGATAAT
*
1283437 TAAATATATTATAAA-A
1 TAAAAATATTATAAACA
1283453 TAAAAATATTATAAACA
1 TAAAAATATTATAAACA
*
1283470 TATAAATA
1 TAAAAATA
1283478 AAATAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAAATATTATAAACA
Found at i:1283479 original size:28 final size:25
Alignment explanation
Indices: 1283438--1283498 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 25
1283428 AAAGATAATT
*
1283438 AAATATATTATAAAATAAAAATATTATA
1 AAATATA-AATAAAAT-AAAAT-TTATA
1283466 AACATATAAATAAAATAAAATTTATA
1 AA-ATATAAATAAAATAAAATTTATA
1283492 AAATATA
1 AAATATA
1283499 TATTATTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
25 5 0.16
26 7 0.23
27 5 0.16
28 9 0.29
29 5 0.16
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (25 bp):
AAATATAAATAAAATAAAATTTATA
Found at i:1283499 original size:27 final size:28
Alignment explanation
Indices: 1283437--1283500 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
1283427 AAAAGATAAT
*
1283437 TAAATATAT-TATAAAATAAAAATATTA
1 TAAATATATAAATAAAATAAAAATATTA
*
1283464 TAAACATATAAATAAAAT-AAAAT-TTA
1 TAAATATATAAATAAAATAAAAATATTA
1283490 TAAAATATATA
1 T-AAATATATA
1283501 TTATTAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 4 0.12
27 21 0.66
28 7 0.22
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (28 bp):
TAAATATATAAATAAAATAAAAATATTA
Found at i:1283509 original size:27 final size:29
Alignment explanation
Indices: 1283440--1283509 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 29
1283430 AGATAATTAA
1283440 ATATATTATAAAATAAAAATATTATAAACAT
1 ATATATTAT-AAAT-AAAATATTATAAACAT
*
1283471 ATA-AATA-AAATAAAAT-TTATAAA-AT
1 ATATATTATAAATAAAATATTATAAACAT
*
1283496 ATATATTATTAATA
1 ATATATTATAAATA
1283510 TATTAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
25 5 0.15
26 10 0.29
27 9 0.26
28 4 0.12
30 3 0.09
31 3 0.09
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (29 bp):
ATATATTATAAATAAAATATTATAAACAT
Found at i:1283538 original size:18 final size:18
Alignment explanation
Indices: 1283486--1283539 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 18
1283476 TAAAATAAAA
*
1283486 TTTATA-AAATATATATT
1 TTTATATAAATATAAATT
* *
1283503 ATTA-ATATAT-TAAA-T
1 TTTATATAAATATAAATT
1283518 TTTATATAAATATAAATT
1 TTTATATAAATATAAATT
1283536 TTTA
1 TTTA
1283540 AATATGATCT
Statistics
Matches: 28, Mismatches: 5, Indels: 7
0.70 0.12 0.17
Matches are distributed among these distances:
15 4 0.14
16 9 0.32
17 10 0.36
18 5 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTATATAAATATAAATT
Found at i:1283541 original size:14 final size:15
Alignment explanation
Indices: 1283478--1283544 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 15
1283468 CATATAAATA
*
1283478 AAATA-AAATTTATA
1 AAATATAAATTTATT
*
1283492 AAATATATA-TTATT
1 AAATATAAATTTATT
1283506 AATATATTAAATTTTATAT
1 AA-ATA-TAAA-TTTAT-T
1283525 AAATATAAATTT-TT
1 AAATATAAATTTATT
1283539 AAATAT
1 AAATAT
1283545 GATCTTAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
14 18 0.41
15 6 0.14
16 6 0.14
17 4 0.09
18 7 0.16
19 3 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AAATATAAATTTATT
Found at i:1283581 original size:11 final size:11
Alignment explanation
Indices: 1283550--1283584 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
1283540 AATATGATCT
*
1283550 TAATATAAAAA
1 TAATATAAATA
1283561 TAATATAAATA
1 TAATATAAATA
1283572 TAATATAAATA
1 TAATATAAATA
1283583 TA
1 TA
1283585 TTAATTAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TAATATAAATA
Found at i:1283794 original size:24 final size:25
Alignment explanation
Indices: 1283756--1283804 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
1283746 AATACATGTA
1283756 TTAACTATATCATATTAATTATATT
1 TTAACTATATCATATTAATTATATT
* *
1283781 TTAA-TATATTATATTATTTATATT
1 TTAACTATATCATATTAATTATATT
1283805 ATTATAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (25 bp):
TTAACTATATCATATTAATTATATT
Found at i:1283795 original size:5 final size:5
Alignment explanation
Indices: 1283761--1283806 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
1283751 ATGTATTAAC
* * *
1283761 TATAT CATAT TA-AT TATAT TTTAA TATAT TATAT TAT-T TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
1283807 TATAAAATGA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
4 8 0.24
5 25 0.76
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:1284546 original size:16 final size:15
Alignment explanation
Indices: 1284502--1284583 Score: 52
Period size: 15 Copynumber: 5.8 Consensus size: 15
1284492 CAAATAATTT
*
1284502 AAAATATAATAAAAA
1 AAAATATAATATAAA
1284517 ATAAAT-TAAT-TAAA
1 A-AAATATAATATAAA
1284531 AAAATTATAATAT-AA
1 AAAA-TATAATATAAA
* **
1284546 ATAAT-TAATATATT
1 AAAATATAATATAAA
*
1284560 AAAAT-T--TATATA
1 AAAATATAATATAAA
1284572 AAAATATAATAT
1 AAAATATAATAT
1284584 TTAAAATATA
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
12 10 0.19
13 10 0.19
14 11 0.21
15 17 0.32
16 5 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAATATAATATAAA
Found at i:1284569 original size:25 final size:26
Alignment explanation
Indices: 1284531--1284590 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 26
1284521 ATTAATTAAA
1284531 AAAATTATAATATAAATAAT-TAATATATT
1 AAAATT-T-ATATAAA-AATATAATAT-TT
1284560 AAAATTTATATAAAAATATAATATTT
1 AAAATTTATATAAAAATATAATATTT
1284586 AAAAT
1 AAAAT
1284591 ATAATTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 10 0.33
27 13 0.43
28 1 0.03
29 6 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
AAAATTTATATAAAAATATAATATTT
Found at i:1284575 original size:12 final size:13
Alignment explanation
Indices: 1284530--1284576 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
1284520 AATTAATTAA
1284530 AAAAATTATAATAT
1 AAAAATTAT-ATAT
1284544 AAATAATTAATATAT
1 AAA-AATT-ATATAT
*
1284559 TAAAATT-TATAT
1 AAAAATTATATAT
1284571 AAAAAT
1 AAAAAT
1284577 ATAATATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 10 0.34
14 7 0.24
15 10 0.34
16 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAAATTATATAT
Found at i:1286307 original size:25 final size:25
Alignment explanation
Indices: 1286279--1286326 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1286269 AAGATTAGTA
*
1286279 TTTAA-TATATTAACAGTATAAATTT
1 TTTAACTATATAAACAG-ATAAATTT
*
1286304 TTTAACTTTATAAACAGATAAAT
1 TTTAACTATATAAACAGATAAAT
1286327 AATTTACCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (25 bp):
TTTAACTATATAAACAGATAAATTT
Found at i:1286617 original size:17 final size:17
Alignment explanation
Indices: 1286576--1286623 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
1286566 TTATATTTTA
1286576 AAATTTAATAAAAATATT
1 AAATTTAAT-AAAATATT
1286594 AAA-TTAATAAAA-ATT
1 AAATTTAATAAAATATT
1286609 AAATTTTAA-AAAATA
1 AAA-TTTAATAAAATA
1286624 AAGATATCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 6 0.22
16 8 0.30
17 10 0.37
18 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATTTAATAAAATATT
Found at i:1290065 original size:13 final size:15
Alignment explanation
Indices: 1290035--1290071 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1290025 GTTAATTGCA
1290035 TAAATAATTTTTATAT
1 TAAAT-ATTTTTATAT
1290051 T-AATATTTTTA-AT
1 TAAATATTTTTATAT
1290064 TAAATATT
1 TAAATATT
1290072 AAAATAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.15
14 13 0.65
15 3 0.15
16 1 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TAAATATTTTTATAT
Found at i:1290072 original size:20 final size:20
Alignment explanation
Indices: 1290047--1290121 Score: 68
Period size: 22 Copynumber: 3.8 Consensus size: 20
1290037 AATAATTTTT
*
1290047 ATATTAATATTTTTAATTAA
1 ATATTAATAATTTTAATTAA
*
1290067 ATATTAAAATAATTTTATTTAA
1 ATATT--AATAATTTTAATTAA
1290089 ATAATT-ATAATTTT-ATT-A
1 AT-ATTAATAATTTTAATTAA
1290107 A-ATTAATAATATTTA
1 ATATTAATAAT-TTTA
1290122 TAATAATATT
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
16 3 0.07
17 5 0.11
18 5 0.11
19 2 0.04
20 13 0.28
22 15 0.33
23 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATATTAATAATTTTAATTAA
Found at i:1290150 original size:26 final size:29
Alignment explanation
Indices: 1290090--1290154 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 29
1290080 TTTATTTAAA
* *
1290090 TAATTATAATTTTATTAAATTAATAATAT
1 TAATAATAATATTATTAAATTAATAATAT
*
1290119 TTATAATAATATTATTAAA-T-A-AATAT
1 TAATAATAATATTATTAAATTAATAATAT
1290145 TAATAA-AATA
1 TAATAATAATA
1290155 AAAATATCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 4 0.12
26 10 0.31
27 1 0.03
28 1 0.03
29 16 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TAATAATAATATTATTAAATTAATAATAT
Found at i:1290170 original size:25 final size:25
Alignment explanation
Indices: 1290142--1290205 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
1290132 ATTAAATAAA
1290142 TATTAATAAAATAAAAAT-ATCATAT
1 TATTAATAAAATAAAAATCAT-ATAT
*
1290167 TATTATTTAAAA-AAAAATCATATAT
1 TATTA-ATAAAATAAAAATCATATAT
*
1290192 TA-TAATAAATTAAA
1 TATTAATAAAATAAA
1290206 TTAAAAAGCC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
23 4 0.12
24 5 0.15
25 17 0.52
26 7 0.21
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (25 bp):
TATTAATAAAATAAAAATCATATAT
Found at i:1290173 original size:28 final size:26
Alignment explanation
Indices: 1290142--1290205 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 26
1290132 ATTAAATAAA
1290142 TATTAATAAAATAAAAATATCATATTAT
1 TATTAATAAAATAAAAA-ATCATA-TAT
1290170 TATT--T-AAA-AAAAAATCATATAT
1 TATTAATAAAATAAAAAATCATATAT
*
1290192 TA-TAATAAATTAAA
1 TATTAATAAAATAAA
1290206 TTAAAAAGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
21 1 0.03
22 5 0.16
23 7 0.23
24 7 0.23
25 6 0.19
26 1 0.03
28 4 0.13
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (26 bp):
TATTAATAAAATAAAAAATCATATAT
Found at i:1298035 original size:30 final size:31
Alignment explanation
Indices: 1297988--1298048 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
1297978 GATATTTAAT
**
1297988 AAAATTTAAATAAAAATATTATTTTTAAAAA
1 AAAATTTAAATAAAAATATTACGTTTAAAAA
1298019 AAAATTTAAA-AAAAATATTACGTTTAAAAA
1 AAAATTTAAATAAAAATATTACGTTTAAAAA
1298049 TTGAGTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 18 0.64
31 10 0.36
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (31 bp):
AAAATTTAAATAAAAATATTACGTTTAAAAA
Found at i:1298191 original size:32 final size:31
Alignment explanation
Indices: 1298145--1298211 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 31
1298135 CGATTTATTT
1298145 TTATAATTATATCATATAAAAAATAT-ATAATA
1 TTATAATTATATCAT-TAAAAAATATGATAA-A
*
1298177 TTATAA-TATAATCATTCAAAAATATGATAAA
1 TTATAATTAT-ATCATTAAAAAATATGATAAA
1298208 TTAT
1 TTAT
1298212 TTATATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
31 17 0.53
32 15 0.47
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (31 bp):
TTATAATTATATCATTAAAAAATATGATAAA
Found at i:1298984 original size:9 final size:9
Alignment explanation
Indices: 1298946--1298986 Score: 52
Period size: 8 Copynumber: 4.8 Consensus size: 9
1298936 TATTATTTTA
1298946 TTAATA-TT
1 TTAATATTT
1298954 TTAA-ATTT
1 TTAATATTT
1298962 TTAAT-TTT
1 TTAATATTT
1298970 TATAATATTT
1 T-TAATATTT
1298980 TTAATAT
1 TTAATAT
1298987 AAATTATTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
7 1 0.03
8 14 0.48
9 10 0.34
10 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TTAATATTT
Found at i:1299456 original size:27 final size:27
Alignment explanation
Indices: 1299420--1299488 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
1299410 AATTTTTATA
*
1299420 TTTATCAAAAAT-GATAGTT-TTTTTGTG
1 TTTATAAAAAATAG-TAGTTCTTTTT-TG
*
1299447 TTTGTAAAAAATAGTAGTTCTTTTTTG
1 TTTATAAAAAATAGTAGTTCTTTTTTG
1299474 TTTATAAAAAATAGT
1 TTTATAAAAAATAGT
1299489 GATTTGTTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 31 0.84
28 6 0.16
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (27 bp):
TTTATAAAAAATAGTAGTTCTTTTTTG
Found at i:1302085 original size:21 final size:22
Alignment explanation
Indices: 1302043--1302088 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1302033 TATTCAGACA
* *
1302043 AGTAGTACTCCACAGCAAGTGG
1 AGTAGTACTCCAAAACAAGTGG
*
1302065 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAAGTGG
1302086 AGT
1 AGT
1302089 TTTAACATAT
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:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAAGTGG
Found at i:1304842 original size:31 final size:30
Alignment explanation
Indices: 1304759--1304842 Score: 93
Period size: 32 Copynumber: 2.8 Consensus size: 30
1304749 CATAATTATA
*
1304759 TTTAAAATATTT-TATATT-TTATATAAAT
1 TTTAAAATATTTATATATTCATATATAAAT
* *
1304787 TTTAATAA-ATTAAAATAATTCATATCATAAAT
1 TTTAA-AATATTTATAT-ATTCATAT-ATAAAT
1304819 TTTAAAATATTTATATATTCATAT
1 TTTAAAATATTTATATATTCATAT
1304843 TATATCTTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
28 8 0.18
29 4 0.09
30 3 0.07
31 13 0.29
32 17 0.38
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (30 bp):
TTTAAAATATTTATATATTCATATATAAAT
Found at i:1308054 original size:23 final size:23
Alignment explanation
Indices: 1308028--1308071 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1308018 TATAATAATT
1308028 TTTAAAATAT-AATATTTAATAAA
1 TTTAAAATATAAATA-TTAATAAA
*
1308051 TTTAAAATTTAAATATTAATA
1 TTTAAAATATAAATATTAATA
1308072 TTTATAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTAAAATATAAATATTAATAAA
Found at i:1308525 original size:27 final size:27
Alignment explanation
Indices: 1308468--1308526 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
1308458 AGTTGCTTTC
* ** *
1308468 ATTA-ATTTTAAAATAAAATATTTAAT
1 ATTATATTATAAAATAAAATAACTAAA
*
1308494 TTTATATTATAAAATAAAATAACTAAA
1 ATTATATTATAAAATAAAATAACTAAA
1308521 ATTATA
1 ATTATA
1308527 ATTTGATTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 3 0.12
27 23 0.88
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
ATTATATTATAAAATAAAATAACTAAA
Found at i:1308606 original size:40 final size:41
Alignment explanation
Indices: 1308530--1308607 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
1308520 AATTATAATT
*
1308530 TGATTTTTAAATCTAATAAATCTAATAAAATAAAATAATCA
1 TGATTTTTAAATCTAATAAATCAAATAAAATAAAATAATCA
* * *
1308571 TGATTTTT-AATCT-GTAAATTCAAATCAAATCAAATAA
1 TGATTTTTAAATCTAATAAA-TCAAATAAAATAAAATAA
1308608 ATCTAATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 4 0.12
40 20 0.62
41 8 0.25
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (41 bp):
TGATTTTTAAATCTAATAAATCAAATAAAATAAAATAATCA
Found at i:1308664 original size:16 final size:16
Alignment explanation
Indices: 1308634--1308672 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1308624 AATTAAAATT
* *
1308634 AAATAAATTTTAATAA
1 AAATTAATTTAAATAA
*
1308650 ATATTAATTTAAATAA
1 AAATTAATTTAAATAA
1308666 AAATTAA
1 AAATTAA
1308673 ATACTATAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATTAATTTAAATAA
Found at i:1309394 original size:18 final size:20
Alignment explanation
Indices: 1309355--1309393 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1309345 AGATTGGATT
1309355 ATATATTTTAATTAATAAAA
1 ATATATTTTAATTAATAAAA
*
1309375 ATAT-TTTTATTTAATAAAA
1 ATATATTTTAATTAATAAAA
1309394 TTATGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATATTTTAATTAATAAAA
Found at i:1310171 original size:31 final size:30
Alignment explanation
Indices: 1310107--1310215 Score: 89
Period size: 31 Copynumber: 3.6 Consensus size: 30
1310097 AATTGATATA
* *
1310107 TATCATTATATTTTTAGATTAAAAGTAAA-TT
1 TATCATTATA-TTTTA-ATTAATATTAAATTT
1310138 TATCATTATATTTTAATTCAATATTAAATTT
1 TATCATTATATTTTAATT-AATATTAAATTT
* * * *
1310169 TATTATTTTATTTTTATT--TGATTGAATTT
1 TATCATTATATTTTAATTAAT-ATTAAATTT
* *
1310198 TACCATTAAATTTTAATT
1 TATCATTATATTTTAATT
1310216 TTTGATACTT
Statistics
Matches: 64, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
28 1 0.02
29 24 0.38
30 12 0.19
31 27 0.42
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.56
Consensus pattern (30 bp):
TATCATTATATTTTAATTAATATTAAATTT
Found at i:1310834 original size:23 final size:24
Alignment explanation
Indices: 1310763--1310836 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 24
1310753 ATTCATCTAC
* *
1310763 TTAAATTATTATTTAAAA-T-ATA
1 TTAAAATATTATTTAAAATTAAAA
* * *
1310785 TTAAAATATTATTTTATATTAATA
1 TTAAAATATTATTTAAAATTAAAA
*
1310809 TTAATATATT-TTTAAAATTAAAA
1 TTAAAATATTATTTAAAATTAAAA
1310832 TTAAA
1 TTAAA
1310837 TAAAATTATT
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
22 15 0.36
23 15 0.36
24 12 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TTAAAATATTATTTAAAATTAAAA
Found at i:1314465 original size:11 final size:11
Alignment explanation
Indices: 1314431--1314468 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1314421 TAAATTATTG
*
1314431 AATTGAATT-A
1 AATTTAATTAA
1314441 AATTTAAATTAA
1 AATTT-AATTAA
1314453 AATTTAATTAA
1 AATTTAATTAA
1314464 AATTT
1 AATTT
1314469 TTTAAATTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 4 0.16
11 15 0.60
12 6 0.24
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (11 bp):
AATTTAATTAA
Found at i:1315892 original size:2 final size:2
Alignment explanation
Indices: 1315887--1315917 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1315877 CCTTTTTTTA
1315887 AT 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 AT A
1315918 AGAGAAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1316139 original size:2 final size:2
Alignment explanation
Indices: 1316132--1316158 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1316122 TAGGTTGGTT
1316132 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 T
1316159 GATCCGTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1316634 original size:37 final size:38
Alignment explanation
Indices: 1316567--1316688 Score: 162
Period size: 38 Copynumber: 3.2 Consensus size: 38
1316557 CTGATTACCC
1316567 CTATAATTTTTGTTTCATGCAAATGAGTTTTAATTGGTA
1 CTATAATTTTTGTTTCATGCAAATG-GTTTTAATTGGTA
*
1316606 C-ATAATTTTT-TTTCTTGCAAATTGGTTTTAATTGGT-
1 CTATAATTTTTGTTTCATGCAAA-TGGTTTTAATTGGTA
*
1316642 CTATAATTTTTGTTCCATGCAAATGGATTTTAATTGGTA
1 CTATAATTTTTGTTTCATGCAAATGG-TTTTAATTGGTA
*
1316681 -TGTAATTT
1 CTATAATTT
1316689 AATTGGAAAC
Statistics
Matches: 74, Mismatches: 4, Indels: 11
0.83 0.04 0.12
Matches are distributed among these distances:
36 1 0.01
37 34 0.46
38 38 0.51
39 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.15, T:0.51
Consensus pattern (38 bp):
CTATAATTTTTGTTTCATGCAAATGGTTTTAATTGGTA
Found at i:1317382 original size:11 final size:11
Alignment explanation
Indices: 1317363--1317396 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1317353 ATAAGTTATG
*
1317363 TATTCATATTA
1 TATTAATATTA
1317374 TATTAATATTA
1 TATTAATATTA
*
1317385 TATTTATATTA
1 TATTAATATTA
1317396 T
1 T
1317397 CTTCGTGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TATTAATATTA
Found at i:1320919 original size:34 final size:34
Alignment explanation
Indices: 1320849--1321064 Score: 229
Period size: 34 Copynumber: 6.4 Consensus size: 34
1320839 CTCTGAAAAC
* *
1320849 TGTTGATTAAATG-GTGATTTGGTAGTTTACCGT
1 TGTTGATTAAATGAGTGATTTGGTAGCTTACCAT
* * * **
1320882 TGTTGATTAAATGAGTGATTTGATGGTTTGTCAT
1 TGTTGATTAAATGAGTGATTTGGTAGCTTACCAT
* * * *
1320916 TGTTGACTAAATGAGAGATTTGGTAACCTACCAT
1 TGTTGATTAAATGAGTGATTTGGTAGCTTACCAT
** *
1320950 TGTTGATTAAATGAGAAATTTGATAGCTTACCAT
1 TGTTGATTAAATGAGTGATTTGGTAGCTTACCAT
* * *
1320984 TATTGATTAAATAAGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGAGTGATTTGGTAGCTTACCAT
* * *
1321018 TGTTGACTAAATGA-TAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGAGT-GATTTGGTAGCTTACCAT
1321052 TGTTGATTAAATG
1 TGTTGATTAAATG
1321065 GTAGTTTTTA
Statistics
Matches: 149, Mismatches: 32, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
33 14 0.09
34 135 0.91
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.41
Consensus pattern (34 bp):
TGTTGATTAAATGAGTGATTTGGTAGCTTACCAT
Found at i:1321024 original size:102 final size:101
Alignment explanation
Indices: 1320849--1321065 Score: 281
Period size: 102 Copynumber: 2.1 Consensus size: 101
1320839 CTCTGAAAAC
** * * * * * * **
1320849 TGTTGATTAAATGGTGATTTGGTAGTTTACCGTTGTTGATTAAATGAGTGATTTGATGGTTTGTC
1 TGTTGATTAAATGGAAATTTGATAGCTTACCATTATTGATTAAATAAGTGATTTGATGGCTTACC
1320914 ATTGTTGACTAAATGAGAGATTTGGTAACCTACCAT
66 ATTGTTGACTAAATGAGAGATTTGGTAACCTACCAT
*
1320950 TGTTGATTAAATGAGAAATTTGATAGCTTACCATTATTGATTAAATAAGTGATTTGGTGGCTTAC
1 TGTTGATTAAATG-GAAATTTGATAGCTTACCATTATTGATTAAATAAGTGATTTGATGGCTTAC
* *** *
1321015 CATTGTTGACTAAATGATAGATTTGGTAGGTTGCCAT
65 CATTGTTGACTAAATGAGAGATTTGGTAACCTACCAT
1321052 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1321066 TAGTTTTTAC
Statistics
Matches: 99, Mismatches: 16, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
101 14 0.14
102 85 0.86
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.41
Consensus pattern (101 bp):
TGTTGATTAAATGGAAATTTGATAGCTTACCATTATTGATTAAATAAGTGATTTGATGGCTTACC
ATTGTTGACTAAATGAGAGATTTGGTAACCTACCAT
Found at i:1322946 original size:171 final size:171
Alignment explanation
Indices: 1322661--1323002 Score: 675
Period size: 171 Copynumber: 2.0 Consensus size: 171
1322651 AAATCTATAC
1322661 ATGCTTAAAGGAGAGACATTGCAGGAGGCAGACGCATCTGTTGCGACAATCAGTTCGGATGAAGA
1 ATGCTTAAAGGAGAGACATTGCAGGAGGCAGACGCATCTGTTGCGACAATCAGTTCGGATGAAGA
1322726 ATCAACAATGATGTGGCATCGTAGATTGGGCCATATGTCAGAACGAGGTATAAAGATTCTATCTG
66 ATCAACAATGATGTGGCATCGTAGATTGGGCCATATGTCAGAACGAGGTATAAAGATTCTATCTG
1322791 ATAGTGGATTGCTTCCTGGACTCAAAACAGTAAGCCTACCT
131 ATAGTGGATTGCTTCCTGGACTCAAAACAGTAAGCCTACCT
1322832 ATGCTTAAAGGAGAGACATTGCAGGAGGCAGACGCATCTGTTGCGACAATCAGTTCGGATGAAGA
1 ATGCTTAAAGGAGAGACATTGCAGGAGGCAGACGCATCTGTTGCGACAATCAGTTCGGATGAAGA
1322897 ATCAACAATGATGTGGCATCGTAGATTGGGCCATATGTCAGAACGAGGTATAAAGATTCTATCTG
66 ATCAACAATGATGTGGCATCGTAGATTGGGCCATATGTCAGAACGAGGTATAAAGATTCTATCTG
*
1322962 ATAGTGGATTGCTTCTTGGACTCAAAACAGTAAGCCTACCT
131 ATAGTGGATTGCTTCCTGGACTCAAAACAGTAAGCCTACCT
1323003 TTCTGTGAGC
Statistics
Matches: 170, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
171 170 1.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (171 bp):
ATGCTTAAAGGAGAGACATTGCAGGAGGCAGACGCATCTGTTGCGACAATCAGTTCGGATGAAGA
ATCAACAATGATGTGGCATCGTAGATTGGGCCATATGTCAGAACGAGGTATAAAGATTCTATCTG
ATAGTGGATTGCTTCCTGGACTCAAAACAGTAAGCCTACCT
Found at i:1325700 original size:34 final size:34
Alignment explanation
Indices: 1325643--1325860 Score: 287
Period size: 34 Copynumber: 6.4 Consensus size: 34
1325633 AAGTGGGAGA
*
1325643 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1325676 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1325710 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
1325744 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1325778 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1325812 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
1325846 ATTGTTGATTAAATG
1 ATTGTTGATTAAATG
1325861 ATGGTTTTTA
Statistics
Matches: 161, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
33 17 0.11
34 144 0.89
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:1325786 original size:102 final size:102
Alignment explanation
Indices: 1325643--1325861 Score: 350
Period size: 102 Copynumber: 2.2 Consensus size: 102
1325633 AAGTGGGAGA
** * * *
1325643 ATTGTTGATTAAATG-GTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTT
1 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
*
1325707 GCCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1325744 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * *
1325809 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
66 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1325846 ATTGTTGATTAAATGA
1 ATTGTTGATTAAATGA
1325862 TGGTTTTTAC
Statistics
Matches: 108, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
101 15 0.14
102 93 0.86
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (102 bp):
ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:1326248 original size:4 final size:4
Alignment explanation
Indices: 1326239--1326266 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1326229 ATTGACCACA
1326239 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1326267 GCAACGGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:1326671 original size:15 final size:16
Alignment explanation
Indices: 1326634--1326690 Score: 64
Period size: 15 Copynumber: 3.6 Consensus size: 16
1326624 TTTTATATAA
* *
1326634 AAAATTATAATTAAGTA
1 AAAATTATAAATAA-TT
1326651 AAAATTATAAAT-ATT
1 AAAATTATAAATAATT
1326666 AAAATT-TAAATAATT
1 AAAATTATAAATAATT
*
1326681 TAAATTATAA
1 AAAATTATAA
1326691 TTAAAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 5 0.14
15 15 0.43
16 4 0.11
17 11 0.31
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
AAAATTATAAATAATT
Done.