Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold221
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: 2539808
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 14 of 19
Found at i:1677795 original size:15 final size:15
Alignment explanation
Indices: 1677775--1677821 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
1677765 AATATATTAA
1677775 AATTTATATAAATAT
1 AATTTATATAAATAT
*
1677790 AATTTATTTTAAATAT
1 AATTTA-TATAAATAT
1677806 AA-TTATGATAAA-AT
1 AATTTAT-ATAAATAT
1677820 AA
1 AA
1677822 AATATATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 5 0.18
15 13 0.46
16 10 0.36
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
AATTTATATAAATAT
Found at i:1684269 original size:18 final size:17
Alignment explanation
Indices: 1684222--1684274 Score: 60
Period size: 18 Copynumber: 3.3 Consensus size: 17
1684212 AAATATTTTA
1684222 AAATTTATAT--AATAT
1 AAATTTATATAAAATAT
*
1684237 AAA-TTAT-TAATATAT
1 AAATTTATATAAAATAT
1684252 AAATTTGATATAAAATAT
1 AAATTT-ATATAAAATAT
1684270 AAATT
1 AAATT
1684275 AAATAGGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
13 1 0.03
14 4 0.13
15 10 0.32
16 2 0.06
17 2 0.06
18 12 0.39
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
AAATTTATATAAAATAT
Found at i:1685117 original size:16 final size:16
Alignment explanation
Indices: 1685098--1685131 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1685088 AACTTTTTTT
* *
1685098 ATTATTAATATTAATA
1 ATTATTAACAATAATA
1685114 ATTATTAACAATAATA
1 ATTATTAACAATAATA
1685130 AT
1 AT
1685132 AGCTATTATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTATTAACAATAATA
Found at i:1686911 original size:20 final size:21
Alignment explanation
Indices: 1686865--1686912 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1686855 ATAAATGTAT
*
1686865 TAAAT-TTTTTAAAAAAATTA
1 TAAATATTTATAAAAAAATTA
* *
1686885 TATATATTTATAAAAACATTA
1 TAAATATTTATAAAAAAATTA
1686906 -AAATATT
1 TAAATATT
1686913 ATATCCTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAATATTTATAAAAAAATTA
Found at i:1687181 original size:28 final size:28
Alignment explanation
Indices: 1687150--1687260 Score: 86
Period size: 28 Copynumber: 3.9 Consensus size: 28
1687140 TAGATATTCA
1687150 TTATA-TTAT-TATTATGTTTAATATATTT
1 TTATATTTATATA-TAT-TTTAATATATTT
*
1687178 TTATGTTTATATATATTTTAATATATTAT
1 TTATATTTATATATATTTTAATATATT-T
* *
1687207 TAATTTATATTATATAAAATTTTAA-ATATTT
1 T--TATAT-TTATAT-ATATTTTAATATATTT
* *
1687238 ATATATTTATAT-TATTTTTATAT
1 TTATATTTATATATATTTTAATAT
1687261 TATATTATAG
Statistics
Matches: 67, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
26 6 0.09
27 2 0.03
28 21 0.31
29 13 0.19
30 2 0.03
31 4 0.06
32 11 0.16
33 8 0.12
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (28 bp):
TTATATTTATATATATTTTAATATATTT
Found at i:1687191 original size:18 final size:18
Alignment explanation
Indices: 1687150--1687196 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
1687140 TAGATATTCA
*
1687150 TTATAT-TATTATTATGT
1 TTATATATATTTTTATGT
1687167 TTA-ATATATTTTTATGT
1 TTATATATATTTTTATGT
1687184 TTATATATATTTT
1 TTATATATATTTT
1687197 AATATATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 2 0.07
17 16 0.59
18 9 0.33
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (18 bp):
TTATATATATTTTTATGT
Found at i:1687229 original size:33 final size:32
Alignment explanation
Indices: 1687184--1687252 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 32
1687174 ATTTTTATGT
*
1687184 TTATATATATTTT-AATATATTAT-TAATTTATA
1 TTATATAAATTTTAAATAT-TTATAT-ATTTATA
1687216 TTATATAAAATTTTAAATATTTATATATTTATA
1 TTATAT-AAATTTTAAATATTTATATATTTATA
1687249 TTAT
1 TTAT
1687253 TTTTATATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
32 6 0.18
33 21 0.64
34 6 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
TTATATAAATTTTAAATATTTATATATTTATA
Found at i:1688445 original size:20 final size:19
Alignment explanation
Indices: 1688402--1688445 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
1688392 TATATATTTG
**
1688402 ATATAAATATTTTTAAATT
1 ATATAAATATTTTTAAAAA
*
1688421 TTATAATATATTTTTAAAAA
1 ATATAA-ATATTTTTAAAAA
1688441 ATATA
1 ATATA
1688446 CTTTTAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATAAATATTTTTAAAAA
Found at i:1689517 original size:40 final size:38
Alignment explanation
Indices: 1689487--1689560 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
1689477 ATTATTTAAA
*
1689487 TAATA-AAAAATATTTTATTTAATTTTAATTATAAATAT
1 TAATATAAAAATAATTT-TTTAATTTTAATTATAAATAT
*
1689525 TAATATAAAAATAATTTTTTAATTTT-ATTTTAAATA
1 TAATATAAAAATAATTTTTTAATTTTAATTATAAATA
1689561 AAAAATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
37 9 0.27
38 14 0.42
39 10 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (38 bp):
TAATATAAAAATAATTTTTTAATTTTAATTATAAATAT
Found at i:1691400 original size:23 final size:22
Alignment explanation
Indices: 1691363--1691414 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
1691353 TTTAAATTTT
*
1691363 TTTGTCT-AAGCTCAAATTAGG
1 TTTGTCTAAAGCTCAAATTAGA
1691384 TTTGTCTAAAAGCTCAAATTAGA
1 TTTGTCT-AAAGCTCAAATTAGA
*
1691407 TCTGTCTA
1 TTTGTCTA
1691415 TAAACTCGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 7 0.26
22 1 0.04
23 19 0.70
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (22 bp):
TTTGTCTAAAGCTCAAATTAGA
Found at i:1692873 original size:2 final size:2
Alignment explanation
Indices: 1692866--1692890 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1692856 TTACATTTTA
1692866 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 A
1692891 AGCTACATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1696466 original size:32 final size:33
Alignment explanation
Indices: 1696408--1696487 Score: 108
Period size: 32 Copynumber: 2.4 Consensus size: 33
1696398 TAATAAAAAA
* *
1696408 ATAATATAAATATATAAATATGTCAAAATTTAT
1 ATAAAATAAATATATAAATATATCAAAATTTAT
*
1696441 ATAAAATAAAT-TATTAATATATCAAAATTTAT
1 ATAAAATAAATATATAAATATATCAAAATTTAT
1696473 ATAAATATATAATAT
1 ATAAA-ATA-AATAT
1696488 TTTGAAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
32 24 0.59
33 13 0.32
34 3 0.07
35 1 0.02
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (33 bp):
ATAAAATAAATATATAAATATATCAAAATTTAT
Found at i:1696481 original size:20 final size:19
Alignment explanation
Indices: 1696418--1696482 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 19
1696408 ATAATATAAA
*
1696418 TATATAAATATGTCAAAATT
1 TATAT-AATATATCAAAATT
1696438 TATATAA-A-AT--AAA-T
1 TATATAATATATCAAAATT
1696452 TAT-TAATATATCAAAATT
1 TATATAATATATCAAAATT
1696470 TATATAAATATAT
1 TATAT-AATATAT
1696483 AATATTTTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
13 3 0.08
14 5 0.14
15 5 0.14
17 4 0.11
18 5 0.14
19 3 0.08
20 12 0.32
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (19 bp):
TATATAATATATCAAAATT
Found at i:1699826 original size:31 final size:31
Alignment explanation
Indices: 1699791--1699855 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
1699781 TTTATTTAAA
1699791 TTTAATTATAAATATTAATA-TAAAATAATTT
1 TTTAA-TATAAATATTAATAGTAAAATAATTT
* * * *
1699822 TTTAATATTATTTTTAATAGTAAAATAGTTT
1 TTTAATATAAATATTAATAGTAAAATAATTT
1699853 TTT
1 TTT
1699856 GGATAACCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 11 0.38
31 18 0.62
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (31 bp):
TTTAATATAAATATTAATAGTAAAATAATTT
Found at i:1700060 original size:2 final size:2
Alignment explanation
Indices: 1700017--1700043 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1700007 ATTCGGAGTA
1700017 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 A
1700044 ATAGGAGAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1701184 original size:20 final size:19
Alignment explanation
Indices: 1701161--1701225 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
1701151 ATAATATAAA
1701161 TATATGAATATATCAAAATT
1 TATAT-AATATATCAAAATT
1701181 TATATAA-A-AT--AAA-T
1 TATATAATATATCAAAATT
1701195 TAT-TAATATATCAAAATT
1 TATATAATATATCAAAATT
1701213 TATATAAATATAT
1 TATAT-AATATAT
1701226 ATTATTTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 3 0.08
14 5 0.13
15 5 0.13
17 5 0.13
18 5 0.13
19 3 0.08
20 12 0.32
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (19 bp):
TATATAATATATCAAAATT
Found at i:1701207 original size:32 final size:32
Alignment explanation
Indices: 1701151--1701231 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 32
1701141 AATATAAAAA
* *
1701151 ATAATATAAATATATGAATATATCAAAATTTAT
1 ATAAAATAAAT-TATTAATATATCAAAATTTAT
1701184 ATAAAATAAATTATTAATATATCAAAATTTAT
1 ATAAAATAAATTATTAATATATCAAAATTTAT
*
1701216 ATAAATATATATTATT
1 ATAAA-ATAAATTATT
1701232 TTAAAAATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
32 25 0.57
33 19 0.43
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (32 bp):
ATAAAATAAATTATTAATATATCAAAATTTAT
Found at i:1701239 original size:18 final size:17
Alignment explanation
Indices: 1701218--1701262 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
1701208 AAATTTATAT
* *
1701218 AAATATATATTATTTTAA
1 AAATA-ATATTATATGAA
1701236 AAATAATTATTATATGAA
1 AAATAA-TATTATATGAA
1701254 AAATAATAT
1 AAATAATAT
1701263 GAATACGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
AAATAATATTATATGAA
Found at i:1704538 original size:31 final size:31
Alignment explanation
Indices: 1704503--1704567 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
1704493 TTTATTTAAA
1704503 TTTAATTATAAATATTAATA-TAAAATAATTT
1 TTTAA-TATAAATATTAATAGTAAAATAATTT
* * * *
1704534 TTTAATATTATTTTTAATAGTAAAATAGTTT
1 TTTAATATAAATATTAATAGTAAAATAATTT
1704565 TTT
1 TTT
1704568 GGATAACCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 11 0.38
31 18 0.62
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (31 bp):
TTTAATATAAATATTAATAGTAAAATAATTT
Found at i:1704775 original size:2 final size:2
Alignment explanation
Indices: 1704727--1704758 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1704717 TAATTCGGAG
1704727 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1704759 ATAGGAGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1705899 original size:20 final size:19
Alignment explanation
Indices: 1705876--1705940 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
1705866 ATAATATAAA
1705876 TATATGAATATATCAAAATT
1 TATAT-AATATATCAAAATT
1705896 TATATAA-A-AT--AAA-T
1 TATATAATATATCAAAATT
1705910 TAT-TAATATATCAAAATT
1 TATATAATATATCAAAATT
1705928 TATATAAATATAT
1 TATAT-AATATAT
1705941 ATTATTTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 3 0.08
14 5 0.13
15 5 0.13
17 5 0.13
18 5 0.13
19 3 0.08
20 12 0.32
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (19 bp):
TATATAATATATCAAAATT
Found at i:1705922 original size:32 final size:32
Alignment explanation
Indices: 1705866--1705946 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 32
1705856 AATATAAAAA
* *
1705866 ATAATATAAATATATGAATATATCAAAATTTAT
1 ATAAAATAAAT-TATTAATATATCAAAATTTAT
1705899 ATAAAATAAATTATTAATATATCAAAATTTAT
1 ATAAAATAAATTATTAATATATCAAAATTTAT
*
1705931 ATAAATATATATTATT
1 ATAAA-ATAAATTATT
1705947 TTAAAAATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
32 25 0.57
33 19 0.43
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (32 bp):
ATAAAATAAATTATTAATATATCAAAATTTAT
Found at i:1705954 original size:18 final size:17
Alignment explanation
Indices: 1705933--1705977 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
1705923 AAATTTATAT
* *
1705933 AAATATATATTATTTTAA
1 AAATA-ATATTATATGAA
1705951 AAATAATTATTATATGAA
1 AAATAA-TATTATATGAA
1705969 AAATAATAT
1 AAATAATAT
1705978 GAATACGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
AAATAATATTATATGAA
Found at i:1709254 original size:31 final size:31
Alignment explanation
Indices: 1709219--1709283 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
1709209 TTTATTTAAA
1709219 TTTAATTATAAATATTAATA-TAAAATAATTT
1 TTTAA-TATAAATATTAATAGTAAAATAATTT
* * *
1709250 TTTAATATTATTTTTAATAGTAAAATAATTT
1 TTTAATATAAATATTAATAGTAAAATAATTT
1709281 TTT
1 TTT
1709284 TAAGATAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 11 0.37
31 19 0.63
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (31 bp):
TTTAATATAAATATTAATAGTAAAATAATTT
Found at i:1709256 original size:18 final size:18
Alignment explanation
Indices: 1709233--1709283 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 18
1709223 ATTATAAATA
1709233 TTAATATAAAATAATTTT
1 TTAATATAAAATAATTTT
1709251 TTAATAT----T-A-TTT
1 TTAATATAAAATAATTTT
1709263 TTAATAGTAAAATAATTTT
1 TTAATA-TAAAATAATTTT
1709282 TT
1 TT
1709284 TAAGATAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 13
0.67 0.00 0.33
Matches are distributed among these distances:
12 9 0.35
13 2 0.08
14 1 0.04
17 1 0.04
18 8 0.31
19 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
TTAATATAAAATAATTTT
Found at i:1711537 original size:14 final size:15
Alignment explanation
Indices: 1711510--1711542 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1711500 AAGAAAATTT
*
1711510 TTAAAAATACAAAAG
1 TTAAAAATACAAAAC
1711525 TTAAAAATA-AAAAC
1 TTAAAAATACAAAAC
1711539 TTAA
1 TTAA
1711543 GTGGTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.67, C:0.06, G:0.03, T:0.24
Consensus pattern (15 bp):
TTAAAAATACAAAAC
Found at i:1711686 original size:254 final size:257
Alignment explanation
Indices: 1711379--1711890 Score: 861
Period size: 258 Copynumber: 2.0 Consensus size: 257
1711369 ATATTATTCT
*
1711379 AAAATTAAAATTTAAAAATAAAATATTATTTTAATATTTTAATACGAGTTAAGTA-GAAATATTA
1 AAAATTAAAATTTAAAAATAAAATATTACTTTAATATTTTAATACGAGTTAAGTATG-AATATTA
1711443 AATCAATCTACCATATAAACCAACATTAAC-ATAT-TTTAAGAATAAATTAAAACTTAAAAGAAA
65 AATCAATCTACCATATAAACCAACATTAACAATATATTTAAGAATAAATTAAAACTTAAAAGAAA
*
1711506 ATTTTTAAAAATACAAAAGTTAAAAATAAAAACTTAAGTGGTTTAGTACCTACCACGTATCAGGT
130 ATTTTAAAAAATACAAAAGTTAAAAATAAAAACTTAAGTGGTTTAGTACCTACCACGTATCAGGT
* *
1711571 AAAAGGTCTGACATGTATCAGACTCTAACCTCTTGATTTATATAAATTTATATAAAAATAACG
195 AAAAAGTCTGACATGTATCAAACTCTAACCTCTTGATTTATATAAATTTATATAAAAATAACG
* *
1711634 AAAATTAAAATTTAAAAATAAAA-ATTGCTTTAATATTTTAATGCGAGTTAAGTATGAATATTAA
1 AAAATTAAAATTTAAAAATAAAATATTACTTTAATATTTTAATACGAGTTAAGTATGAATATTAA
* * *
1711698 ATCAATCTACTATATGAACCAACATTAACATATATAATTTAAGAATAAATTAAAACTTAAAAGAG
66 ATCAATCTACCATATAAACCAACATTAACA-ATAT-ATTTAAGAATAAATTAAAACTTAAAAGAA
* *
1711763 AATTTTAAAAAATACAAAAGTTAAAAATAAAAACTTAAGTGGTTTAGTACCTATCACGTATTAGG
129 AATTTTAAAAAATACAAAAGTTAAAAATAAAAACTTAAGTGGTTTAGTACCTACCACGTATCAGG
*
1711828 TAAAAAGTCTGACATGTATCAAATTCTAACCTCTTGATTTATATAAATTTATATAAAAATAAC
194 TAAAAAGTCTGACATGTATCAAACTCTAACCTCTTGATTTATATAAATTTATATAAAAATAAC
1711891 ATGAAAATAA
Statistics
Matches: 240, Mismatches: 12, Indels: 7
0.93 0.05 0.03
Matches are distributed among these distances:
254 63 0.26
255 24 0.10
256 4 0.02
258 149 0.62
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (257 bp):
AAAATTAAAATTTAAAAATAAAATATTACTTTAATATTTTAATACGAGTTAAGTATGAATATTAA
ATCAATCTACCATATAAACCAACATTAACAATATATTTAAGAATAAATTAAAACTTAAAAGAAAA
TTTTAAAAAATACAAAAGTTAAAAATAAAAACTTAAGTGGTTTAGTACCTACCACGTATCAGGTA
AAAAGTCTGACATGTATCAAACTCTAACCTCTTGATTTATATAAATTTATATAAAAATAACG
Found at i:1712100 original size:18 final size:17
Alignment explanation
Indices: 1712077--1712110 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1712067 TGTAAAAAAA
1712077 TTTATAAAAATATAATAT
1 TTTATAAAAA-ATAATAT
1712095 TTTATAAAAAATAATA
1 TTTATAAAAAATAATA
1712111 CAAATATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTATAAAAAATAATAT
Found at i:1712103 original size:17 final size:18
Alignment explanation
Indices: 1712077--1712110 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1712067 TGTAAAAAAA
*
1712077 TTTATAAAAATATAATAT
1 TTTATAAAAAAATAATAT
1712095 TTTAT-AAAAAATAATA
1 TTTATAAAAAAATAATA
1712111 CAAATATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TTTATAAAAAAATAATAT
Found at i:1712440 original size:28 final size:27
Alignment explanation
Indices: 1712400--1712455 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
1712390 ATATGATAAA
* * *
1712400 AAAATTATTAAAATATAATACTAAATAT
1 AAAATAATAAAAAAATAAT-CTAAATAT
*
1712428 AAAATAATAAAAAAATAATTTAAATAT
1 AAAATAATAAAAAAATAATCTAAATAT
1712455 A
1 A
1712456 TGAATATATC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (27 bp):
AAAATAATAAAAAAATAATCTAAATAT
Found at i:1712502 original size:32 final size:33
Alignment explanation
Indices: 1712448--1712511 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1712438 AAAAATAATT
1712448 TAAATATATGAATATATCAAAATTTATATAAAA
1 TAAATATATGAATATATCAAAATTTATATAAAA
* * *
1712481 TAAAT-TATTAATGTATTAAAATTTATATAAA
1 TAAATATATGAATATATCAAAATTTATATAAA
1712512 TATTTAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 23 0.82
33 5 0.18
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (33 bp):
TAAATATATGAATATATCAAAATTTATATAAAA
Found at i:1712627 original size:19 final size:21
Alignment explanation
Indices: 1712603--1712641 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1712593 ATAGGTTTCA
1712603 TTTA-TTTTTTAAAT-TATTT
1 TTTATTTTTTTAAATATATTT
1712622 TTTATTTTTTTAAATATATT
1 TTTATTTTTTTAAATATATT
1712642 CTAAGTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTATTTTTTTAAATATATTT
Found at i:1712897 original size:30 final size:30
Alignment explanation
Indices: 1712863--1712925 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
1712853 AATTCAATTA
* *
1712863 TATATTAATTTTAAAATGAATATATTAA-AT
1 TATATTAA-TTCAAAATAAATATATTAATAT
* *
1712893 TATATTTATTCAAAATAAATTTATTAATAT
1 TATATTAATTCAAAATAAATATATTAATAT
1712923 TAT
1 TAT
1712926 TTTCAAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (30 bp):
TATATTAATTCAAAATAAATATATTAATAT
Found at i:1712959 original size:17 final size:17
Alignment explanation
Indices: 1712937--1712978 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1712927 TTCAAATAAT
1712937 AAAAAAATT-ATTAAAAC
1 AAAAAAATTGA-TAAAAC
* *
1712954 AAAAAACTTGATAAAAT
1 AAAAAAATTGATAAAAC
1712971 AAAAAAAT
1 AAAAAAAT
1712979 ATTTTTATCC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.21
Consensus pattern (17 bp):
AAAAAAATTGATAAAAC
Found at i:1714969 original size:22 final size:23
Alignment explanation
Indices: 1714921--1714970 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
1714911 AATATTTTTT
* *
1714921 ATTTTTTAAAACAAATAAAGATC
1 ATTTTTTAAAACAAATAAACATA
1714944 ATTTTTTAAAA-AAA-AAACATA
1 ATTTTTTAAAACAAATAAACATA
*
1714965 AATTTT
1 ATTTTT
1714971 GAACTTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.42
22 3 0.12
23 11 0.46
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (23 bp):
ATTTTTTAAAACAAATAAACATA
Found at i:1715115 original size:2 final size:2
Alignment explanation
Indices: 1715108--1715142 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1715098 GATTTTCAAA
* *
1715108 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1715143 AATAAAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1715129 original size:16 final size:16
Alignment explanation
Indices: 1715108--1715142 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1715098 GATTTTCAAA
1715108 ATATATATATATACAT
1 ATATATATATATACAT
1715124 ATATATATATATACAT
1 ATATATATATATACAT
1715140 ATA
1 ATA
1715143 AATAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATATATATATACAT
Found at i:1715523 original size:16 final size:14
Alignment explanation
Indices: 1715489--1715529 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
1715479 TTTCATATTT
*
1715489 TTTCTTTTTTTTTC
1 TTTCTTTCTTTTTC
1715503 TTTCTTTCTTTTTC
1 TTTCTTTCTTTTTC
1715517 ATCTTCTTTCTTT
1 -T-TTCTTTCTTT
1715530 CTTTTTTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 13 0.54
15 1 0.04
16 10 0.42
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTCTTTCTTTTTC
Found at i:1716828 original size:32 final size:32
Alignment explanation
Indices: 1716765--1717201 Score: 706
Period size: 32 Copynumber: 13.8 Consensus size: 32
1716755 AAAATGGTGA
* * * **
1716765 TTTGAAAAGGGGTGCCACTGACTTGCATGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
1716797 TTTTAAATGGGTTACCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
1716829 TTTGAAAAGGGTCGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1716861 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1716893 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1716925 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1716957 TTTGAAATGGGTTGCCATCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1716989 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1717021 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1717053 TTTGAAATGGGTTGCCACCGAC---T-T-GGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1717080 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1717112 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1717144 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
1717176 TTTGAAATGGG-TGCCACAGAGTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
1717202 GATTTAAAAG
Statistics
Matches: 379, Mismatches: 21, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
27 25 0.07
28 1 0.00
29 1 0.00
30 1 0.00
31 14 0.04
32 337 0.89
ACGTcount: A:0.17, C:0.19, G:0.34, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:1717219 original size:27 final size:27
Alignment explanation
Indices: 1717184--1717702 Score: 822
Period size: 27 Copynumber: 19.0 Consensus size: 27
1717174 GCTTTGAAAT
* *
1717184 GGGTGCCACAGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
**
1717211 GGACGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1717238 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1717265 GGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1717292 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1717319 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1717346 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
1717374 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1717401 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
*
1717429 GGGTGCCACGGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1717456 GGGTGCCACGGAGTTATGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1717483 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
*
1717511 GGGTGCCACGGAATTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1717538 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1717565 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1717592 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1717619 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
1717647 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1717674 GGATGCCACAGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
1717702 G
1 G
1717703 AAAATGCCAC
Statistics
Matches: 455, Mismatches: 32, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
27 349 0.77
28 106 0.23
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.23
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:1717702 original size:273 final size:272
Alignment explanation
Indices: 1717184--1717702 Score: 934
Period size: 273 Copynumber: 1.9 Consensus size: 272
1717174 GCTTTGAAAT
*
1717184 GGGTGCCACAGAGTTGTGGATTTAAAAGGACGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACAGAGTTATGGATTTAAAAGGACGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
* *
1717249 AGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGTCTTAAAAGGGTGCCACGGAGTTGTGGACT
66 AATTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACT
1717314 TAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTG
131 TAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTG
*
1717379 CCACAGAGTTGTGGACTTAAAAGAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTT
196 CCACAGAGTTGTGGACTTAAAAGAGATGCCACAGAGTTATGGACTTAAAAGGGTGCCACGGAGTT
1717444 GTGGATTTAAAA
261 GTGGATTTAAAA
* *
1717456 GGGTGCCACGGAGTTATGG-TCTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC
1 GGGTGCCACAGAGTTATGGAT-TTAAAA-GGACGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC
1717520 GGAATTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGA
64 GGAATTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGA
1717585 CTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG
129 CTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG
*
1717650 TGCCACAGAGTTGTGGACTTAAAAG-GATGCCACAGAGTTGTGGACTTTAAAAG
194 TGCCACAGAGTTGTGGACTTAAAAGAGATGCCACAGAGTTATGGAC-TTAAAAG
1717703 AAAATGCCAC
Statistics
Matches: 237, Mismatches: 7, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
271 1 0.00
272 41 0.17
273 195 0.82
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.23
Consensus pattern (272 bp):
GGGTGCCACAGAGTTATGGATTTAAAAGGACGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
AATTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACT
TAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTG
CCACAGAGTTGTGGACTTAAAAGAGATGCCACAGAGTTATGGACTTAAAAGGGTGCCACGGAGTT
GTGGATTTAAAA
Found at i:1723599 original size:12 final size:12
Alignment explanation
Indices: 1723582--1723606 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1723572 AATAATCATC
1723582 ATAATGACAAGT
1 ATAATGACAAGT
1723594 ATAATGACAAGT
1 ATAATGACAAGT
1723606 A
1 A
1723607 AAAGAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (12 bp):
ATAATGACAAGT
Found at i:1724979 original size:23 final size:23
Alignment explanation
Indices: 1724930--1724980 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
1724920 AATATTTTTT
* * *
1724930 ATTTTTTAAAACAAATAAAGATC
1 ATTTTTTAAAACAAAAAAACATA
1724953 ATTTTTTAAAA-AAAAAAACATA
1 ATTTTTTAAAACAAAAAAACATA
*
1724975 AATTTT
1 ATTTTT
1724981 GAACTTTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (23 bp):
ATTTTTTAAAACAAAAAAACATA
Found at i:1725136 original size:14 final size:14
Alignment explanation
Indices: 1725117--1725147 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1725107 GATTTTCAAA
1725117 ATATATATATACAT
1 ATATATATATACAT
1725131 ATATATATATACAT
1 ATATATATATACAT
1725145 ATA
1 ATA
1725148 AATAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATATATATACAT
Found at i:1725532 original size:10 final size:11
Alignment explanation
Indices: 1725519--1725569 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
1725509 CCATTTCATA
1725519 TTTTTTCTTT-
1 TTTTTTCTTTC
1725529 TTTTTTCTTTC
1 TTTTTTCTTTC
*
1725540 TTTCTTCTTCATC
1 TTTTTTCTT--TC
*
1725553 TTCTTTCTTTC
1 TTTTTTCTTTC
1725564 TTTTTT
1 TTTTTT
1725570 ACCTAACTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
10 10 0.29
11 15 0.44
13 9 0.26
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:1729105 original size:22 final size:22
Alignment explanation
Indices: 1729080--1729121 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1729070 TATATTCACT
* *
1729080 TAACACACCTAATATGTTTATC
1 TAACAAACCTAATATATTTATC
1729102 TAACAAACCTAATATATTTA
1 TAACAAACCTAATATATTTA
1729122 CTTAATACAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.36
Consensus pattern (22 bp):
TAACAAACCTAATATATTTATC
Found at i:1729174 original size:12 final size:12
Alignment explanation
Indices: 1729157--1729181 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1729147 ATATATTGCT
1729157 CACTTAACATAC
1 CACTTAACATAC
1729169 CACTTAACATAC
1 CACTTAACATAC
1729181 C
1 C
1729182 TAATATGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.36, G:0.00, T:0.24
Consensus pattern (12 bp):
CACTTAACATAC
Found at i:1730015 original size:25 final size:26
Alignment explanation
Indices: 1729979--1730038 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 26
1729969 CTTCATTTAC
* *
1729979 AATTTGTTAATTTTTA-TTAATAAA-A
1 AATTT-TTAATTATTATTTAATAATAA
1730004 AATTTTTAAATTATTATTTAATAATAA
1 AATTTTT-AATTATTATTTAATAATAA
1730031 AATATTTT
1 AAT-TTTT
1730039 TATTTAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 2 0.07
25 12 0.41
26 7 0.24
27 4 0.14
28 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
AATTTTTAATTATTATTTAATAATAA
Found at i:1730049 original size:27 final size:29
Alignment explanation
Indices: 1729991--1730060 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 29
1729981 TTTGTTAATT
* *
1729991 TTTATTAATAAAAAATTTTTAAATTATTA
1 TTTAATAATAAAAAATTTTTAAATTATAA
* *
1730020 TTTAATAATAAAATATTTTT-ATTTA-AA
1 TTTAATAATAAAAAATTTTTAAATTATAA
*
1730047 TTTAATTATAAAAA
1 TTTAATAATAAAAA
1730061 TATATAAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 13 0.37
28 4 0.11
29 18 0.51
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
TTTAATAATAAAAAATTTTTAAATTATAA
Found at i:1730402 original size:28 final size:27
Alignment explanation
Indices: 1730347--1730417 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
1730337 GCCACCCATT
1730347 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
1730374 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
1730402 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
1730418 AGGCTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:1730519 original size:20 final size:20
Alignment explanation
Indices: 1730494--1730539 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1730484 AAATAGAGGC
*
1730494 TCCCTCCTCCATCTCAAGTA
1 TCCCTCATCCATCTCAAGTA
* **
1730514 TCCCTCATCCCTCTCTTGTA
1 TCCCTCATCCATCTCAAGTA
1730534 TCCCTC
1 TCCCTC
1730540 TTCAATTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.13, C:0.48, G:0.04, T:0.35
Consensus pattern (20 bp):
TCCCTCATCCATCTCAAGTA
Found at i:1733020 original size:21 final size:22
Alignment explanation
Indices: 1732991--1733036 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1732981 TGTTCAGACA
** *
1732991 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1733013 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1733034 AGT
1 AGT
1733037 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:1734954 original size:27 final size:27
Alignment explanation
Indices: 1734920--1734990 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
1734910 GCCACCCATT
1734920 TGTTTGTCAAAAATGGTGGTTAT-TTTG
1 TGTTTGTCAAAAATGGTGGTT-TCTTTG
*
1734947 TGTTTGTCAAAAATAGTGGTTTCCTTTG
1 TGTTTGTCAAAAATGGTGGTTT-CTTTG
* *
1734975 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
1734991 AGGCTTGCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
28 17 0.45
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTTCTTTG
Found at i:1735657 original size:16 final size:17
Alignment explanation
Indices: 1735636--1735669 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1735626 ATTTTTATAA
*
1735636 TTTTAT-TTAAAATATT
1 TTTTATATTAAAAAATT
1735652 TTTTATATTAAAAAATT
1 TTTTATATTAAAAAATT
1735669 T
1 T
1735670 ATAAACATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTATATTAAAAAATT
Found at i:1736150 original size:21 final size:21
Alignment explanation
Indices: 1736126--1736183 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1736116 TTTGTTTTCA
1736126 ATTTTA-ATTTTTAAAATTATT
1 ATTTTATA-TTTTAAAATTATT
*
1736147 ATTTTATCTTTTAAAA-TATT
1 ATTTTATATTTTAAAATTATT
*
1736167 -TTATATATTTTAAAATT
1 ATTTTATATTTTAAAATT
1736184 TATGATTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 13 0.41
20 5 0.16
21 14 0.44
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTATATTTTAAAATTATT
Found at i:1736170 original size:22 final size:21
Alignment explanation
Indices: 1736126--1736183 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 21
1736116 TTTGTTTTCA
1736126 ATTTTAATTTTTAAAATTATT
1 ATTTTAATTTTTAAAATTATT
1736147 ATTTT-ATCTTTTAAAA-TATT
1 ATTTTAAT-TTTTAAAATTATT
*
1736167 -TTAT-ATATTTTAAAATT
1 ATTTTAAT-TTTTAAAATT
1736184 TATGATTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
19 13 0.39
20 7 0.21
21 13 0.39
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTAATTTTTAAAATTATT
Found at i:1736237 original size:12 final size:12
Alignment explanation
Indices: 1736208--1736251 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
1736198 TTAGTTAAAA
1736208 ATTAAAA-AATT
1 ATTAAAATAATT
**
1736219 AAAAAAATAATT
1 ATTAAAATAATT
1736231 ATTAAAATAATT
1 ATTAAAATAATT
*
1736243 ATTATAATA
1 ATTAAAATA
1736252 TTAAACATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 5 0.19
12 22 0.81
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
ATTAAAATAATT
Found at i:1736489 original size:11 final size:10
Alignment explanation
Indices: 1736467--1736526 Score: 53
Period size: 9 Copynumber: 6.6 Consensus size: 10
1736457 TAACTTAATA
1736467 ATTTA-ATA-
1 ATTTATATAT
1736475 ATTTATATCAT
1 ATTTATAT-AT
1736486 ATTTATATAT
1 ATTTATATAT
1736496 ATTT-TA-A-
1 ATTTATATAT
*
1736503 AATTAT-TAT
1 ATTTATATAT
1736512 ATTTATATA-
1 ATTTATATAT
1736521 ATTTAT
1 ATTTAT
1736527 TTTTAATAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
7 3 0.07
8 8 0.19
9 15 0.35
10 9 0.21
11 8 0.19
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (10 bp):
ATTTATATAT
Found at i:1736544 original size:13 final size:14
Alignment explanation
Indices: 1736467--1736545 Score: 54
Period size: 15 Copynumber: 5.4 Consensus size: 14
1736457 TAACTTAATA
1736467 ATTTAATAATTTAT
1 ATTTAATAATTTAT
* * * *
1736481 ATCATATTTATATAT
1 AT-TTAATAATTTAT
1736496 ATTTTAA-AATTATTAT
1 A-TTTAATAA-T-TTAT
1736512 ATTTATATAATTTAT
1 ATTTA-ATAATTTAT
*
1736527 TTTTAATAATTT-T
1 ATTTAATAATTTAT
1736540 ATTTAA
1 ATTTAA
1736546 AATATTTTTT
Statistics
Matches: 49, Mismatches: 10, Indels: 13
0.68 0.14 0.18
Matches are distributed among these distances:
13 6 0.12
14 10 0.20
15 24 0.49
16 7 0.14
17 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTTAATAATTTAT
Found at i:1736599 original size:19 final size:18
Alignment explanation
Indices: 1736577--1736628 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
1736567 TATGTAAATA
1736577 TAAATTTAATATAAATTAT
1 TAAATTTAATATAAATT-T
* *
1736596 TAAATATATTA-AAATTT
1 TAAATTTAATATAAATTT
*
1736613 TAAATATAAATATAAA
1 TAAAT-TTAATATAAA
1736629 ATATATGTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 6 0.23
18 8 0.31
19 12 0.46
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAATTTAATATAAATTT
Found at i:1736791 original size:24 final size:24
Alignment explanation
Indices: 1736730--1736791 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
1736720 GCCATATACA
*
1736730 TATATAATATATA-TTAAATATAT
1 TATATAATATTTATTTAAATATAT
* *
1736753 TTTATTAAT-TATATTTAAATATAT
1 TATA-TAATATTTATTTAAATATAT
*
1736777 TATATCATATTTATT
1 TATATAATATTTATT
1736792 ATATTATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
23 10 0.31
24 22 0.69
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TATATAATATTTATTTAAATATAT
Found at i:1736793 original size:14 final size:14
Alignment explanation
Indices: 1736774--1736803 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1736764 TATTTAAATA
1736774 TATTATATCATATT
1 TATTATATCATATT
*
1736788 TATTATATTATATT
1 TATTATATCATATT
1736802 TA
1 TA
1736804 CCTTTATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (14 bp):
TATTATATCATATT
Found at i:1736796 original size:5 final size:5
Alignment explanation
Indices: 1736730--1736801 Score: 55
Period size: 5 Copynumber: 15.2 Consensus size: 5
1736720 GCCATATACA
* * * *
1736730 TATAT AATA- TATAT TA-AA TATAT TTTAT TA-AT TATAT T-TAAA TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT-AT TATAT
*
1736777 TATAT CATAT T-TAT TATAT TATAT T
1 TATAT TATAT TATAT TATAT TATAT T
1736802 TACCTTTATA
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
4 15 0.29
5 35 0.69
6 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:1737132 original size:2 final size:2
Alignment explanation
Indices: 1737125--1737182 Score: 57
Period size: 2 Copynumber: 29.5 Consensus size: 2
1737115 ATAAGAATGT
* * * *
1737125 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TG TA CTA AA AA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
1737167 T- TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1737183 TAAAATTATG
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
1 2 0.04
2 45 0.92
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1739182 original size:16 final size:15
Alignment explanation
Indices: 1739146--1739186 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
1739136 TAATATTAAA
1739146 AATAAATATTATTTT
1 AATAAATATTATTTT
1739161 AA-AAAT-TTATTTTT
1 AATAAATATTA-TTTT
1739175 ATATAAATATTA
1 A-ATAAATATTA
1739187 ATATATCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.14
14 9 0.41
15 3 0.14
16 4 0.18
17 3 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AATAAATATTATTTT
Found at i:1739235 original size:2 final size:2
Alignment explanation
Indices: 1739228--1739252 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1739218 GCTCCAATCA
1739228 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 A
1739253 CCCTAAACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1740254 original size:13 final size:13
Alignment explanation
Indices: 1740236--1740260 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1740226 TTTTTTTTAA
1740236 AATATTTATATTT
1 AATATTTATATTT
1740249 AATATTTATATT
1 AATATTTATATT
1740261 CGATACATGT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:1741572 original size:2 final size:2
Alignment explanation
Indices: 1741565--1741603 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1741555 CTCCAAGTTC
*
1741565 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1741604 AAGTTTATCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1742333 original size:17 final size:17
Alignment explanation
Indices: 1742311--1742362 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
1742301 CTTGAGATGC
1742311 AATTATATATATTT-TTT
1 AATTATAT-TATTTATTT
1742328 AATTATATTATTTATTT
1 AATTATATTATTTATTT
*
1742345 -ATT-TATTA-ATATTT
1 AATTATATTATTTATTT
1742359 AATT
1 AATT
1742363 CAAAATATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.16
15 8 0.25
16 8 0.25
17 11 0.34
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
AATTATATTATTTATTT
Found at i:1742957 original size:2 final size:2
Alignment explanation
Indices: 1742950--1743002 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1742940 CACTTAATTT
1742950 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1742992 TA TA TA TA TA T
1 TA TA TA TA TA T
1743003 TGGTATGAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1743505 original size:2 final size:2
Alignment explanation
Indices: 1743498--1743530 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1743488 TGAGAAATTG
1743498 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1743531 GTTTATAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1744380 original size:26 final size:29
Alignment explanation
Indices: 1744351--1744432 Score: 82
Period size: 33 Copynumber: 2.8 Consensus size: 29
1744341 TTTAAAATTT
1744351 TAAAAAATA-AAT-TATT-TATATTATTA
1 TAAAAAATATAATATATTATATATTATTA
*
1744377 TAAAAAATATTATATATTATATATTATAATA
1 TAAAAAATATAATATATTATATATTAT--TA
1744408 TATAATAGAA-ATAATATATTATATA
1 TA-AA-A-AATATAATATATTATATA
1744433 ATTTTAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
26 9 0.20
27 2 0.04
28 4 0.09
29 8 0.17
31 4 0.09
32 2 0.04
33 15 0.33
34 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (29 bp):
TAAAAAATATAATATATTATATATTATTA
Found at i:1744395 original size:7 final size:7
Alignment explanation
Indices: 1744383--1744432 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
1744373 ATTATAAAAA
1744383 ATATTAT
1 ATATTAT
1744390 ATATTAT
1 ATATTAT
1744397 ATATTAT
1 ATATTAT
1744404 A-A-TAT
1 ATATTAT
* *
1744409 ATAATAG
1 ATATTAT
* *
1744416 AAATAAT
1 ATATTAT
1744423 ATATTAT
1 ATATTAT
1744430 ATA
1 ATA
1744433 ATTTTAAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
5 4 0.12
6 2 0.06
7 28 0.82
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (7 bp):
ATATTAT
Found at i:1744711 original size:173 final size:173
Alignment explanation
Indices: 1744422--1744768 Score: 631
Period size: 173 Copynumber: 2.0 Consensus size: 173
1744412 ATAGAAATAA
1744422 TATATTATATAATTTTAAAATATTATATAAATATATTTTACTTGTATTATATGCAAAATATAATT
1 TATATTATATAATTTTAAAATATTATATAAATATATTTTACTTGTATTATATGCAAAATATAATT
1744487 AAAAATAAAGTTAAAAAAGTTAATTAGTTCAATCTATTCCATTATCAATTTTAAAAATCAATAAC
66 AAAAATAAAGTTAAAAAAGTTAATTAGTTCAATCTATTCCATTATCAATTTTAAAAATCAATAAC
* *
1744552 TTACTAAACGACCTGAATAAATTATTTTTTAAAATTAATTAAT
131 ATACTAAACGACATGAATAAATTATTTTTTAAAATTAATTAAT
1744595 TATATTATATAATTTTAAAATATTATATAAATATATTTTACTTGTATTATATGCAAAATATAATT
1 TATATTATATAATTTTAAAATATTATATAAATATATTTTACTTGTATTATATGCAAAATATAATT
* *
1744660 AAAAATAAAGTTAAAAGAGTTAATTAGTTCAATCTATTCGATTATCAATTTTAAAAATCAATAAC
66 AAAAATAAAGTTAAAAAAGTTAATTAGTTCAATCTATTCCATTATCAATTTTAAAAATCAATAAC
* * *
1744725 ATACTGAACTATATGAATAAATTATTTTTTAAAATTAATTAAT
131 ATACTAAACGACATGAATAAATTATTTTTTAAAATTAATTAAT
1744768 T
1 T
1744769 TCAAAACTGA
Statistics
Matches: 167, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
173 167 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (173 bp):
TATATTATATAATTTTAAAATATTATATAAATATATTTTACTTGTATTATATGCAAAATATAATT
AAAAATAAAGTTAAAAAAGTTAATTAGTTCAATCTATTCCATTATCAATTTTAAAAATCAATAAC
ATACTAAACGACATGAATAAATTATTTTTTAAAATTAATTAAT
Found at i:1749061 original size:21 final size:21
Alignment explanation
Indices: 1749015--1749064 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1749005 AAAAATAAAA
*
1749015 AAATTATAAATTTCAAGGTTT
1 AAATTATAAATTTCAAAGTTT
1749036 AAATTATAAATTT-ATTAAGTTT
1 AAATTATAAATTTCA--AAGTTT
1749058 -AATTATA
1 AAATTATA
1749065 TGAATAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 20 0.77
22 5 0.19
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (21 bp):
AAATTATAAATTTCAAAGTTT
Found at i:1749470 original size:11 final size:12
Alignment explanation
Indices: 1749454--1749494 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
1749444 CATATCTAAT
1749454 AAAGAAAATAA-
1 AAAGAAAATAAG
*
1749465 AAAGAAAA-AAT
1 AAAGAAAATAAG
*
1749476 AAAGAAATTAAG
1 AAAGAAAATAAG
1749488 AAAGAAA
1 AAAGAAA
1749495 TTAGGTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 2 0.08
11 15 0.58
12 9 0.35
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (12 bp):
AAAGAAAATAAG
Found at i:1749476 original size:22 final size:23
Alignment explanation
Indices: 1749451--1749494 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1749441 AATCATATCT
1749451 AATAAAGAAAATAA-AAAGAAAA
1 AATAAAGAAAATAAGAAAGAAAA
*
1749473 AATAAAGAAATTAAGAAAGAAA
1 AATAAAGAAAATAAGAAAGAAA
1749495 TTAGGTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (23 bp):
AATAAAGAAAATAAGAAAGAAAA
Found at i:1750387 original size:2 final size:2
Alignment explanation
Indices: 1750380--1750426 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1750370 ATAGATCCTC
1750380 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1750422 TA TA T
1 TA TA T
1750427 GGAGAAAACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1750532 original size:2 final size:2
Alignment explanation
Indices: 1750525--1750553 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1750515 AACAGAGTTT
1750525 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1750554 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1750558 original size:2 final size:2
Alignment explanation
Indices: 1750553--1750590 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1750543 ACACACACAC
*
1750553 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1750591 TTCTGGTGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1751440 original size:18 final size:19
Alignment explanation
Indices: 1751417--1751452 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1751407 AATTAGATTA
1751417 ATCAAAA-TCTAATAAAAT
1 ATCAAAATTCTAATAAAAT
*
1751435 ATCAAAATTTTAATAAAA
1 ATCAAAATTCTAATAAAA
1751453 AAATATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
ATCAAAATTCTAATAAAAT
Found at i:1751527 original size:38 final size:38
Alignment explanation
Indices: 1751479--1751602 Score: 118
Period size: 38 Copynumber: 3.4 Consensus size: 38
1751469 GAAAAAAACA
*
1751479 CATATAATATTTAATAAATATGTAAATATATTAAAATT
1 CATAAAATATTTAATAAATATGTAAATATATTAAAATT
*
1751517 CATAAAATATTTAATGAAA-ATGTAAGTATATTAAAATT
1 CATAAAATATTTAAT-AAATATGTAAATATATTAAAATT
* **
1751555 TATTTAATA-TTAAT---TAT-T-AATATATTAAAATT
1 CATAAAATATTTAATAAATATGTAAATATATTAAAATT
* *
1751587 TATATAAATATATAAT
1 CATA-AAATATTTAAT
1751603 GAATTATTCA
Statistics
Matches: 73, Mismatches: 9, Indels: 12
0.78 0.10 0.13
Matches are distributed among these distances:
32 16 0.22
33 5 0.07
34 6 0.08
37 5 0.07
38 38 0.52
39 3 0.04
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (38 bp):
CATAAAATATTTAATAAATATGTAAATATATTAAAATT
Found at i:1751566 original size:17 final size:18
Alignment explanation
Indices: 1751543--1751599 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 18
1751533 AAAATGTAAG
*
1751543 TATATTAAAATTTATTTA
1 TATATTAAAATTTATTAA
1751561 -ATATT--AA-TTATTAA
1 TATATTAAAATTTATTAA
1751575 TATATTAAAATTTATATAAA
1 TATATTAAAATTTAT-T-AA
1751595 TATAT
1 TATAT
1751600 AATGAATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
14 6 0.19
15 7 0.22
17 7 0.22
18 4 0.12
19 1 0.03
20 7 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATATTAAAATTTATTAA
Found at i:1754407 original size:23 final size:21
Alignment explanation
Indices: 1754372--1754414 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
1754362 GGATACTGTT
*
1754372 TATATTTATATTATATTAATA
1 TATATTTATATTATAATAATA
1754393 TATATTATCATATTATAATAAT
1 TATATT-T-ATATTATAATAAT
1754415 GTTTAAGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 1 0.05
23 12 0.63
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
TATATTTATATTATAATAATA
Found at i:1754470 original size:32 final size:29
Alignment explanation
Indices: 1754433--1754500 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 29
1754423 CATTTTATAT
1754433 TTATATTAATTTTGATATGTTA-ATAATTCGTA
1 TTATATTAATTTT-A-AT-TTATAT-ATTCGTA
*
1754465 TTATATAAATTTTAATTTATATATTCGTA
1 TTATATTAATTTTAATTTATATATTCGTA
*
1754494 TCATATT
1 TTATATT
1754501 TCTGTCATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
29 15 0.47
30 4 0.12
31 1 0.03
32 12 0.38
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.54
Consensus pattern (29 bp):
TTATATTAATTTTAATTTATATATTCGTA
Found at i:1754965 original size:27 final size:27
Alignment explanation
Indices: 1754935--1754994 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
1754925 TCCACGTCCT
*
1754935 CCACCACGACCACCTCCGTATCCGCCA
1 CCACCACGACCACCTCCATATCCGCCA
* ** * *
1754962 CCACCTCTTCCTCCTCCATGTCCGCCA
1 CCACCACGACCACCTCCATATCCGCCA
1754989 CCACCA
1 CCACCA
1754995 TAACCTCCCC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.18, C:0.57, G:0.08, T:0.17
Consensus pattern (27 bp):
CCACCACGACCACCTCCATATCCGCCA
Found at i:1755060 original size:18 final size:18
Alignment explanation
Indices: 1755039--1755075 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1755029 CGCCGCCGCC
*
1755039 ATGTCCTCCGCCACCATA
1 ATGTCCTCCACCACCATA
1755057 ATGTCCTCCACCACCATA
1 ATGTCCTCCACCACCATA
1755075 A
1 A
1755076 CCACCACCGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.43, G:0.08, T:0.22
Consensus pattern (18 bp):
ATGTCCTCCACCACCATA
Found at i:1755110 original size:31 final size:30
Alignment explanation
Indices: 1755057--1755130 Score: 130
Period size: 31 Copynumber: 2.4 Consensus size: 30
1755047 CGCCACCATA
*
1755057 ATGTCCTCCACCACCATAACCACCACCGCC
1 ATGTCCTCCACCACCATAACCACCACCACC
1755087 ATGTCCTCCACCACCTATAACCACCACCACC
1 ATGTCCTCCACCACC-ATAACCACCACCACC
1755118 ATGTCCTCCACCA
1 ATGTCCTCCACCA
1755131 TAGCCACCAC
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 15 0.36
31 27 0.64
ACGTcount: A:0.27, C:0.51, G:0.05, T:0.16
Consensus pattern (30 bp):
ATGTCCTCCACCACCATAACCACCACCACC
Found at i:1755130 original size:15 final size:15
Alignment explanation
Indices: 1755019--1755130 Score: 89
Period size: 15 Copynumber: 7.2 Consensus size: 15
1755009 CCCATGTCCT
* *
1755019 CCACCATGTCCGCCG
1 CCACCATGTCCTCCA
* *
1755034 CCGCCATGTCCTCCG
1 CCACCATGTCCTCCA
1755049 CCACCATAATGTCCTCCA
1 CCACC---ATGTCCTCCA
** *
1755067 CCACCATAACCACCA
1 CCACCATGTCCTCCA
*
1755082 CCGCCATGTCCTCCA
1 CCACCATGTCCTCCA
** *
1755097 CCACCTATAACCACCA
1 CCACC-ATGTCCTCCA
1755113 CCACCATGTCCTCCA
1 CCACCATGTCCTCCA
1755128 CCA
1 CCA
1755131 TAGCCACCAC
Statistics
Matches: 75, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
15 49 0.65
16 12 0.16
18 14 0.19
ACGTcount: A:0.23, C:0.52, G:0.09, T:0.16
Consensus pattern (15 bp):
CCACCATGTCCTCCA
Found at i:1755143 original size:15 final size:15
Alignment explanation
Indices: 1755064--1755143 Score: 60
Period size: 15 Copynumber: 5.5 Consensus size: 15
1755054 ATAATGTCCT
*
1755064 CCACCACCATAACCA
1 CCACCACCATAGCCA
* *
1755079 CCACCGCCAT-GTCCT
1 CCACCACCATAG-CCA
*
1755094 CCACCACCTATAACCA
1 CCACCACC-ATAGCCA
*
1755110 CCACCACCAT-G--T
1 CCACCACCATAGCCA
*
1755122 CCTCCACCATAGCCA
1 CCACCACCATAGCCA
1755137 CCACCAC
1 CCACCAC
1755144 GCCCTCCATC
Statistics
Matches: 48, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
12 9 0.19
13 1 0.02
15 26 0.54
16 12 0.25
ACGTcount: A:0.29, C:0.54, G:0.05, T:0.12
Consensus pattern (15 bp):
CCACCACCATAGCCA
Found at i:1758433 original size:14 final size:14
Alignment explanation
Indices: 1758416--1758456 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 14
1758406 ATAAATCTTT
1758416 AAATATAAATATAA
1 AAATATAAATATAA
1758430 AAATATAATATTATAA
1 AAATATAA-A-TATAA
*
1758446 ATATATAAATA
1 AAATATAAATA
1758457 AATTTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 10 0.42
15 2 0.08
16 12 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AAATATAAATATAA
Found at i:1761087 original size:21 final size:21
Alignment explanation
Indices: 1761052--1761111 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
1761042 TTTTTTTAAT
1761052 TTAA-TAAAA-TAAAATTATA
1 TTAATTAAAATTAAAATTATA
1761071 TTAATTAAAATTAAAATTTTATA
1 TTAATTAAAATTAAAA--TTATA
1761094 TT--TTAATAATTAAAATTA
1 TTAATTAA-AATTAAAATTA
1761112 AGTCGAATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
19 4 0.11
20 8 0.22
21 9 0.25
22 8 0.22
23 7 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTAATTAAAATTAAAATTATA
Found at i:1761107 original size:22 final size:22
Alignment explanation
Indices: 1761066--1761110 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1761056 TAAAATAAAA
1761066 TTATATTAATTAAAATTAAAATT
1 TTATATT-ATTAAAATTAAAATT
1761089 TTATATT-TTAATAATTAAAATT
1 TTATATTATTAA-AATTAAAATT
1761111 AAGTCGAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.19
22 10 0.48
23 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTATATTATTAAAATTAAAATT
Found at i:1762289 original size:18 final size:18
Alignment explanation
Indices: 1762234--1762314 Score: 55
Period size: 18 Copynumber: 4.6 Consensus size: 18
1762224 AGAGCATTAT
* *
1762234 ATATTTATATGAATTTTG
1 ATATTTATATAAATTTTA
1762252 ATATATTA-AT-AA-TTT-
1 ATAT-TTATATAAATTTTA
1762267 A-ATTTATATAAATTTTA
1 ATATTTATATAAATTTTA
* *
1762284 ATATTTTTATATATTTATA
1 ATATTTATATAAATTT-TA
1762303 TTATATTTATAT
1 --ATATTTATAT
1762315 TATTTTTTAC
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
13 3 0.06
14 4 0.08
15 3 0.06
16 6 0.12
17 3 0.06
18 18 0.35
19 5 0.10
21 9 0.18
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
ATATTTATATAAATTTTA
Found at i:1762309 original size:11 final size:11
Alignment explanation
Indices: 1762284--1762335 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
1762274 ATAAATTTTA
*
1762284 ATATTTTTA-T
1 ATATTTATATT
1762294 ATATTTATATT
1 ATATTTATATT
1762305 ATATTTATATT
1 ATATTTATATT
* *
1762316 ATTTTTTACATT
1 A-TATTTATATT
1762328 ATATTTAT
1 ATATTTAT
1762336 TTCGTGTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
10 8 0.23
11 18 0.51
12 9 0.26
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
ATATTTATATT
Found at i:1762595 original size:22 final size:22
Alignment explanation
Indices: 1762546--1762595 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1762536 ATTATTTTTA
1762546 TTTAAATTTAATTATAAAATAT
1 TTTAAATTTAATTATAAAATAT
** *
1762568 ACTAAATATTAA-TATAAAATTT
1 TTTAAAT-TTAATTATAAAATAT
1762590 TTTAAA
1 TTTAAA
1762596 AATATTTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
TTTAAATTTAATTATAAAATAT
Found at i:1763936 original size:2 final size:2
Alignment explanation
Indices: 1763929--1763957 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1763919 TATCGAATAA
1763929 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1763958 AATTATATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1764992 original size:18 final size:19
Alignment explanation
Indices: 1764969--1765007 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1764959 CTAATTTATT
1764969 AAAATAT-TAATTATATAA
1 AAAATATATAATTATATAA
*
1764987 AAAATATATAATTATTTAA
1 AAAATATATAATTATATAA
1765006 AA
1 AA
1765008 TAAATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATATATAATTATATAA
Found at i:1765008 original size:17 final size:17
Alignment explanation
Indices: 1764960--1765009 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
1764950 ATTTAATAGC
1764960 TAATT-TATTAAAATAT
1 TAATTATATTAAAATAT
*
1764976 TAATTATATAAAAAATAT
1 TAATTATAT-TAAAATAT
1764994 ATAATTAT-TTAAAATA
1 -TAATTATATTAAAATA
1765010 AATTTAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 5 0.17
17 9 0.31
18 8 0.28
19 7 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATATTAAAATAT
Found at i:1765017 original size:19 final size:18
Alignment explanation
Indices: 1764969--1765023 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
1764959 CTAATTTATT
1764969 AAAATATTAATTATATAAA
1 AAAAT-TTAATTATATAAA
* *
1764988 AAATATATAATTATTTAAA
1 AAA-ATTTAATTATATAAA
*
1765007 ATAAATTTAATTTTATA
1 A-AAATTTAATTATATA
1765024 CTAATATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 25 0.86
20 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAATTTAATTATATAAA
Found at i:1765340 original size:18 final size:17
Alignment explanation
Indices: 1765306--1765350 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
1765296 ATTTGATTTG
*
1765306 ATTTAATTTAAATTATT
1 ATTTAATTTAAAATATT
1765323 ATTTAATATTAAAATATT
1 ATTTAAT-TTAAAATATT
1765341 -TTT-ATTTAAA
1 ATTTAATTTAAA
1765351 TTTAATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 5 0.19
16 2 0.08
17 10 0.38
18 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTAATTTAAAATATT
Found at i:1765395 original size:19 final size:21
Alignment explanation
Indices: 1765347--1765397 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1765337 TATTTTTATT
1765347 TAAATTTAAT-TAAAAATATA
1 TAAATTTAATATAAAAATATA
1765367 TAAATTTAATATAAAAATA-A
1 TAAATTTAATATAAAAATATA
*
1765387 T-ATTTTAATAT
1 TAAATTTAATAT
1765398 TATTATGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 9 0.31
20 12 0.41
21 8 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAATTTAATATAAAAATATA
Found at i:1767405 original size:3 final size:3
Alignment explanation
Indices: 1767397--1767433 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1767387 TATCATGTTA
1767397 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1767434 GCACTTGACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1768167 original size:3 final size:3
Alignment explanation
Indices: 1768159--1768188 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1768149 ATCAAATTGG
1768159 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1768189 TAATTAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1768392 original size:37 final size:38
Alignment explanation
Indices: 1768342--1768417 Score: 136
Period size: 37 Copynumber: 2.0 Consensus size: 38
1768332 GTTTTAACAT
1768342 GCTCCCTCATATATACAAGCCAGA-TAGATGGTTAATA
1 GCTCCCTCATATATACAAGCCAGACTAGATGGTTAATA
*
1768379 GCTCCCTCATATATACAAGCCAGACTAGTTGGTTAATA
1 GCTCCCTCATATATACAAGCCAGACTAGATGGTTAATA
1768417 G
1 G
1768418 ACTTACACGT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 24 0.65
38 13 0.35
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (38 bp):
GCTCCCTCATATATACAAGCCAGACTAGATGGTTAATA
Found at i:1769058 original size:2 final size:2
Alignment explanation
Indices: 1769051--1769084 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1769041 CAACAACAAT
1769051 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1769085 ATGAAACAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1771348 original size:19 final size:21
Alignment explanation
Indices: 1771301--1771346 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
1771291 ATTTAAATCG
1771301 AATATAAATATTTAAAAAAAT
1 AATATAAATATTTAAAAAAAT
1771322 AATATAAATATTTAAAAAAAT
1 AATATAAATATTTAAAAAAAT
1771343 AATA
1 AATA
1771347 AAGAGTCTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AATATAAATATTTAAAAAAAT
Found at i:1771876 original size:27 final size:27
Alignment explanation
Indices: 1771838--1771893 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
1771828 ATGAATATAA
1771838 AATAAAAAAATAATAATAATATAATAT
1 AATAAAAAAATAATAATAATATAATAT
* * *
1771865 AATATAAAAATAATATTAATATTATAT
1 AATAAAAAAATAATAATAATATAATAT
1771892 AA
1 AA
1771894 ATAGACTTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (27 bp):
AATAAAAAAATAATAATAATATAATAT
Found at i:1771884 original size:6 final size:5
Alignment explanation
Indices: 1771826--1771893 Score: 50
Period size: 5 Copynumber: 13.2 Consensus size: 5
1771816 TAACATATTC
* *
1771826 ATATGA ATATA AAATA A-A-A AAATA ATAATA ATATA ATATA ATATAA
1 ATAT-A ATATA ATATA ATATA ATATA AT-ATA ATATA ATATA ATAT-A
* *
1771872 AAATA ATATTA ATATT ATATA A
1 ATATA ATA-TA ATATA ATATA A
1771894 ATAGACTTAC
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
3 2 0.04
4 2 0.04
5 29 0.57
6 18 0.35
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (5 bp):
ATATA
Found at i:1771980 original size:21 final size:22
Alignment explanation
Indices: 1771954--1771998 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1771944 TTCTATATAT
1771954 TTTAAAT-ATTTTATAATTAAA
1 TTTAAATAATTTTATAATTAAA
*
1771975 TTTAAATAAATTTTATTATTAAA
1 TTTAAAT-AATTTTATAATTAAA
1771998 T
1 T
1771999 AGTATTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
23 14 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTAAATAATTTTATAATTAAA
Found at i:1772115 original size:17 final size:17
Alignment explanation
Indices: 1772095--1772148 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
1772085 ATATACAAAT
1772095 ATATTAAAATTTATATA
1 ATATTAAAATTTATATA
1772112 ATA-T-AAA-TTAT-TA
1 ATATTAAAATTTATATA
1772125 ATATGTCAAAATTTATATA
1 ATAT-T-AAAATTTATATA
1772144 GATAT
1 -ATAT
1772149 ATAATATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
13 5 0.17
14 4 0.13
15 4 0.13
16 1 0.03
17 6 0.20
18 4 0.13
19 2 0.07
20 4 0.13
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (17 bp):
ATATTAAAATTTATATA
Found at i:1772149 original size:33 final size:34
Alignment explanation
Indices: 1772076--1772155 Score: 101
Period size: 32 Copynumber: 2.4 Consensus size: 34
1772066 CTAAACGATC
*
1772076 TAGATATAAATATACAAATATATTAAAATTTATA
1 TAGATATAAATATACAAATATATCAAAATTTATA
** *
1772110 TA-ATATAAAT-TATTAATATGTCAAAATTTATA
1 TAGATATAAATATACAAATATATCAAAATTTATA
1772142 TAGATATATAATAT
1 TAGATATA-AATAT
1772156 TTTAAGTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
32 20 0.51
33 13 0.33
34 5 0.13
35 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.41
Consensus pattern (34 bp):
TAGATATAAATATACAAATATATCAAAATTTATA
Found at i:1773675 original size:7 final size:7
Alignment explanation
Indices: 1773663--1773696 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
1773653 TAAATTTAAT
1773663 TATAAAA
1 TATAAAA
1773670 TATAAAA
1 TATAAAA
1773677 TATAAAA
1 TATAAAA
*
1773684 TAT-TAA
1 TATAAAA
1773690 TATAAAA
1 TATAAAA
1773697 ATATTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
TATAAAA
Found at i:1773697 original size:14 final size:15
Alignment explanation
Indices: 1773654--1773701 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 15
1773644 ATTTTCATTT
1773654 AAAT-TTAAT-TATA
1 AAATATTAATATATA
*
1773667 AAATA-TAAAATATA
1 AAATATTAATATATA
1773681 AAATATTAATATA-A
1 AAATATTAATATATA
1773695 AAATATT
1 AAATATT
1773702 TTTTTAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 7 0.23
14 17 0.57
15 6 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATATTAATATATA
Found at i:1774832 original size:19 final size:20
Alignment explanation
Indices: 1774796--1774846 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
1774786 TTTAATTTAA
1774796 TTTTAAAATATATAAATAAT
1 TTTTAAAATATATAAATAAT
* * *
1774816 TTTTAAAA-ATTTTAATACT
1 TTTTAAAATATATAAATAAT
1774835 TTTTAACAATAT
1 TTTTAA-AATAT
1774847 TTTGAGCTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 14 0.54
20 10 0.38
21 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTTAAAATATATAAATAAT
Found at i:1776898 original size:11 final size:11
Alignment explanation
Indices: 1776882--1776915 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1776872 TTTATTTTTA
1776882 AATATAATTAT
1 AATATAATTAT
*
1776893 AATATAAATAT
1 AATATAATTAT
*
1776904 AATATCATTAT
1 AATATAATTAT
1776915 A
1 A
1776916 TGAATTATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (11 bp):
AATATAATTAT
Found at i:1777095 original size:6 final size:6
Alignment explanation
Indices: 1777084--1777108 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1777074 ATATTAAAAT
1777084 TTTATA TTTATA TTTATA TTTATA T
1 TTTATA TTTATA TTTATA TTTATA T
1777109 AAAATATTTT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTATA
Found at i:1779262 original size:3 final size:3
Alignment explanation
Indices: 1779254--1779297 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1779244 TATTCAACTG
1779254 TTA 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 TTA TT
1779298 TTTGGCATTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1780466 original size:15 final size:15
Alignment explanation
Indices: 1780446--1780503 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 15
1780436 GTCATAATAG
1780446 TATTTAATAAATTTA
1 TATTTAATAAATTTA
1780461 TATTTAAATAAATTTTAA
1 TATTT-AATAAA-TTT-A
1780479 TATTTTAAT-AATTTA
1 TA-TTTAATAAATTTA
*
1780494 TATTTTATAA
1 TATTTAATAA
1780504 TCTATTTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 5 0.14
15 9 0.24
16 9 0.24
17 5 0.14
18 6 0.16
19 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTTAATAAATTTA
Found at i:1780492 original size:33 final size:32
Alignment explanation
Indices: 1780448--1780534 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 32
1780438 CATAATAGTA
1780448 TTTAATAAATTTATATTTA-AATAAATTTTAATAT
1 TTTAAT-AATTTATATTTATAATAAATTTT-A-AT
**
1780482 TTTAATAATTTATATTTTATAATCTATTTTAAT
1 TTTAATAATTTATA-TTTATAATAAATTTTAAT
* *
1780515 TATAATTATTTATATTTATA
1 TTTAATAATTTATATTTATA
1780535 TCATATAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
32 6 0.13
33 22 0.47
34 11 0.23
35 8 0.17
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (32 bp):
TTTAATAATTTATATTTATAATAAATTTTAAT
Done.