Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold167
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: 4199719
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 197959 characters in sequence are not A, C, G, or T
File 12 of 22
Found at i:1620872 original size:17 final size:16
Alignment explanation
Indices: 1620817--1620871 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 16
1620807 TTTTTATGTT
1620817 AATAATATAAATATGTA
1 AATAATATAAATAT-TA
1620834 AATAATATAAATATTA
1 AATAATATAAATATTA
*
1620850 ACATATTATAAATGATTA
1 A-ATAATATAAAT-ATTA
1620868 AATA
1 AATA
1620872 TGTTAAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
16 3 0.09
17 27 0.77
18 5 0.14
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (16 bp):
AATAATATAAATATTA
Found at i:1620928 original size:33 final size:33
Alignment explanation
Indices: 1620891--1621004 Score: 105
Period size: 33 Copynumber: 3.5 Consensus size: 33
1620881 TTTATCGTAA
1620891 ATATTTATATGTATTAAATATATTAATTTA-ATT
1 ATATTTATAT-TATTAAATATATTAATTTATATT
*
1620924 ATATTTAAATATT-TTAAATTATATTTA-TTATATT
1 ATATTT--ATATTATTAAA-TATATTAATTTATATT
* *
1620958 A-ATTTTTATT-TATAAATATATTATATTTATATC
1 ATATTTATATTAT-TAAATATATTA-ATTTATATT
1620991 ATATTTA-ATTATTA
1 ATATTTATATTATTA
1621005 CATCTATCTC
Statistics
Matches: 67, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
31 11 0.16
32 5 0.07
33 30 0.45
34 17 0.25
35 4 0.06
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (33 bp):
ATATTTATATTATTAAATATATTAATTTATATT
Found at i:1620952 original size:24 final size:24
Alignment explanation
Indices: 1620895--1620952 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
1620885 TCGTAAATAT
* *
1620895 TTATATGTA-TTAAATATATTAAT
1 TTATATTTATTTAAATATATTAAA
*
1620918 TTA-ATTATATTTAAATATTTTAAA
1 TTATATT-TATTTAAATATATTAAA
1620942 TTATATTTATT
1 TTATATTTATT
1620953 ATATTAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 2 0.07
23 5 0.17
24 19 0.66
25 3 0.10
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TTATATTTATTTAAATATATTAAA
Found at i:1622421 original size:17 final size:17
Alignment explanation
Indices: 1622367--1622424 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
1622357 AAATTTTAAA
* *
1622367 ATAATATAAATATAGAAT
1 ATAAAATAAA-ATATAAT
* **
1622385 AAAAAATAAAATATTTT
1 ATAAAATAAAATATAAT
*
1622402 ATAAAATTAAATATAAT
1 ATAAAATAAAATATAAT
1622419 ATAAAA
1 ATAAAA
1622425 ATATGTTAAA
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
17 23 0.74
18 8 0.26
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
ATAAAATAAAATATAAT
Found at i:1622422 original size:29 final size:26
Alignment explanation
Indices: 1622387--1622455 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 26
1622377 TATAGAATAA
1622387 AAAATAAAATATTTTATAAAATTAAAT
1 AAAATAAAATATTTTA-AAAATTAAAT
* *
1622414 ATAATATAAAAATATGTTAAAATTTAAAT
1 A-AA-AT-AAAATATTTTAAAAATTAAAT
*
1622443 AAAATAAATTATT
1 AAAATAAAATATT
1622456 AATATTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
26 6 0.17
27 3 0.09
28 4 0.11
29 12 0.34
30 10 0.29
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (26 bp):
AAAATAAAATATTTTAAAAATTAAAT
Found at i:1632180 original size:17 final size:17
Alignment explanation
Indices: 1632158--1632190 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1632148 GTTTTATTTC
1632158 ATTTTTTTAAAATTTTT
1 ATTTTTTTAAAATTTTT
*
1632175 ATTTTTTTATAATTTT
1 ATTTTTTTAAAATTTT
1632191 ATATATTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTTTTTAAAATTTTT
Found at i:1632190 original size:16 final size:16
Alignment explanation
Indices: 1632153--1632192 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
1632143 AAATAGTTTT
*
1632153 ATTTCATTTTTTTAAA
1 ATTTTATTTTTTTAAA
*
1632169 ATTTTTATTTTTTTATA
1 A-TTTTATTTTTTTAAA
1632186 ATTTTAT
1 ATTTTAT
1632193 ATATTTCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTTTATTTTTTTAAA
Found at i:1632809 original size:29 final size:28
Alignment explanation
Indices: 1632768--1632827 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
1632758 TAGAGTTCAG
* *
1632768 TTTTATATTTAAA-ATATTTATAATAATAT
1 TTTTATAATTAAATA-ATTTA-AATAAAAT
1632797 TTTTATAATTAAATAATTTAAATAAAAT
1 TTTTATAATTAAATAATTTAAATAAAAT
1632825 TTT
1 TTT
1632828 ATTTAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 10 0.36
29 17 0.61
30 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TTTTATAATTAAATAATTTAAATAAAAT
Found at i:1632811 original size:28 final size:29
Alignment explanation
Indices: 1632768--1632827 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
1632758 TAGAGTTCAG
* *
1632768 TTTTATATTTAAAAT-ATTTATAATAATAT
1 TTTTATAATTAAAATAATTTA-AATAAAAT
1632797 TTTTATAATT-AAATAATTTAAATAAAAT
1 TTTTATAATTAAAATAATTTAAATAAAAT
1632825 TTT
1 TTT
1632828 ATTTAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TTTTATAATTAAAATAATTTAAATAAAAT
Found at i:1632824 original size:14 final size:14
Alignment explanation
Indices: 1632777--1632829 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
1632767 GTTTTATATT
1632777 TAAAATATTTATAA
1 TAAAATATTTATAA
* *
1632791 TAATATTTTTATAA
1 TAAAATATTTATAA
*
1632805 TTAAATAATTTA-AA
1 TAAAAT-ATTTATAA
1632819 TAAAAT-TTTAT
1 TAAAATATTTAT
1632830 TTAATTTATT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
12 4 0.13
14 23 0.74
15 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TAAAATATTTATAA
Found at i:1634311 original size:18 final size:18
Alignment explanation
Indices: 1634288--1634322 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1634278 ATCTAATTAA
1634288 AATTTTAA-AAATATAAAT
1 AATTTTAATAAA-ATAAAT
1634306 AATTTTAATAAAATAAA
1 AATTTTAATAAAATAAA
1634323 ATAAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATTTTAATAAAATAAAT
Found at i:1639664 original size:2 final size:2
Alignment explanation
Indices: 1639659--1639687 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1639649 TATATATCCA
1639659 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1639688 AATAAAAATT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1642451 original size:25 final size:29
Alignment explanation
Indices: 1642391--1642454 Score: 98
Period size: 28 Copynumber: 2.3 Consensus size: 29
1642381 AATATAACAC
1642391 ATAAAAAATAATATAAATTATTAATATAT
1 ATAAAAAATAATATAAATTATTAATATAT
*
1642420 ATAAAAAAT-ATATAAATTATT-ATCTAT
1 ATAAAAAATAATATAAATTATTAATATAT
1642447 -TAAAAAAT
1 ATAAAAAAT
1642455 TATCAGACTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 8 0.24
27 5 0.15
28 12 0.35
29 9 0.26
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (29 bp):
ATAAAAAATAATATAAATTATTAATATAT
Found at i:1643570 original size:22 final size:22
Alignment explanation
Indices: 1643545--1643588 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1643535 ATGTTTATTT
*
1643545 AGACAAAGTACAACTTTACTTC
1 AGACAAAGTACAACATTACTTC
1643567 AGACAAAGTACAACATTACTTC
1 AGACAAAGTACAACATTACTTC
1643589 CGAACTCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.25
Consensus pattern (22 bp):
AGACAAAGTACAACATTACTTC
Found at i:1643928 original size:2 final size:2
Alignment explanation
Indices: 1643921--1643946 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1643911 AAAATAAATA
1643921 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
1643947 CCAGTGTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1645942 original size:14 final size:15
Alignment explanation
Indices: 1645919--1645951 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1645909 ATTCAATTGA
1645919 TTTAAAATTTAA-AT
1 TTTAAAATTTAAGAT
*
1645933 TTTAATATTTAAGAT
1 TTTAAAATTTAAGAT
1645948 TTTA
1 TTTA
1645952 TTTTATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTTAAAATTTAAGAT
Found at i:1646032 original size:2 final size:2
Alignment explanation
Indices: 1646025--1646065 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1646015 ATGTTGGTTT
1646025 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1646066 CCTCTTTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1647304 original size:17 final size:18
Alignment explanation
Indices: 1647282--1647321 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
1647272 AAAAATAAAA
*
1647282 TTAATAAAAGTTT-TATT
1 TTAATAAAAATTTATATT
1647299 TTAATAAAAATTTATATT
1 TTAATAAAAATTTATATT
1647317 TTAAT
1 TTAAT
1647322 TTTTTTATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TTAATAAAAATTTATATT
Found at i:1647991 original size:21 final size:21
Alignment explanation
Indices: 1647966--1648006 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1647956 AAATTTAAAA
1647966 ATATTTTAT-ATTAATATTTAT
1 ATATTTTATAATTAA-ATTTAT
1647987 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
1648007 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:1649999 original size:13 final size:14
Alignment explanation
Indices: 1649981--1650013 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1649971 ACATTATAAT
1649981 TTTTAATATTTT-A
1 TTTTAATATTTTAA
1649994 TTTTAA-ATTTTAA
1 TTTTAATATTTTAA
1650007 TTTTAAT
1 TTTTAAT
1650014 TATTCCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTAATATTTTAA
Found at i:1653995 original size:14 final size:14
Alignment explanation
Indices: 1653948--1653996 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
1653938 AAAAGAAGTG
1653948 TTTTAATTTTTATA
1 TTTTAATTTTTATA
*
1653962 TTATTAA-ATTTAGTA
1 TT-TTAATTTTTA-TA
1653977 TTTTAATTTTTATA
1 TTTTAATTTTTATA
*
1653991 CTTTAA
1 TTTTAA
1653997 AATTATAGCG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (14 bp):
TTTTAATTTTTATA
Found at i:1654528 original size:3 final size:3
Alignment explanation
Indices: 1654522--1654559 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1654512 AGAGATGTTG
1654522 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 TT
1654560 GGGGTAATAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1657694 original size:3 final size:3
Alignment explanation
Indices: 1657686--1657716 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1657676 TTTTATCCTA
1657686 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1657717 GCTAATTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1658454 original size:9 final size:9
Alignment explanation
Indices: 1658442--1658475 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1658432 TTATTATTTA
1658442 AAATATTAT
1 AAATATTAT
1658451 AAAT-TTAT
1 AAATATTAT
1658459 ATAATATTAT
1 A-AATATTAT
1658469 AAATATT
1 AAATATT
1658476 TTTTATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 5 0.22
9 13 0.57
10 5 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
AAATATTAT
Found at i:1658529 original size:24 final size:24
Alignment explanation
Indices: 1658473--1658542 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
1658463 TATTATAAAT
* *
1658473 ATTTTTTATATTTTTATATTCATTTC
1 ATTTTTTATA-TTTTAT-TTCAATTA
*
1658499 ATGTTTTTATATTTTATTTTAATTA
1 AT-TTTTTATATTTTATTTCAATTA
* *
1658524 ATTTTTAATATTATATTTC
1 ATTTTTTATATTTTATTTC
1658543 TGTTATTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
24 14 0.38
25 7 0.19
26 8 0.22
27 8 0.22
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.67
Consensus pattern (24 bp):
ATTTTTTATATTTTATTTCAATTA
Found at i:1658704 original size:37 final size:38
Alignment explanation
Indices: 1658643--1658722 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 38
1658633 ATTTGTATCA
* * * * * *
1658643 TATTTATTTTATTTTTTGTATTATGTTTTAATTATTTT
1 TATTTATGTTATTGTTTATATTATGTCTCAATTAATTT
1658681 TATTTATGTTA-TGTTTATATTATGTCTCAATTAATTT
1 TATTTATGTTATTGTTTATATTATGTCTCAATTAATTT
1658718 TATTT
1 TATTT
1658723 TTTGTATAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 26 0.72
38 10 0.28
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.68
Consensus pattern (38 bp):
TATTTATGTTATTGTTTATATTATGTCTCAATTAATTT
Found at i:1659132 original size:321 final size:322
Alignment explanation
Indices: 1658561--1659158 Score: 682
Period size: 321 Copynumber: 1.9 Consensus size: 322
1658551 TTCATATATA
* * * *
1658561 TAAAGTATTAAAAATTTATATAAATTTTTACACGTTAATTATTCGTTTATATATATTTTGACATA
1 TAAAGTATTAAAAATTTATATAAATTTTTACACATCAATAATTAGTTTATATATATTTTGACATA
* * ** * *
1658626 TTCATATATTTGTATCATATTTATTTTATTTTTTGTATTATGTTTTAATTATTTTTATTTATGTT
66 TTCATATATTTGTATCATATATATTGTATTTTTTACATTATATTTTAATTATTTTTATATATGTT
* * * ** *
1658691 ATGTTTATATTATGTCTCAATTAATTTTATTTTTTGTATAATTTGATCATTGTAATTTAATTTTA
131 ATATTTATATTATGTCTCAATTAATCTTATATTTTACATAATTTGATCATTATAATTTAATTTTA
** * * * *
1658756 AGAAAATTCGTATTTATATAAAGTTCGTATTCTATTTCAATTCATGAATATTTTACTTAATTTAT
196 AGAAAATTAATATTTATATAAAGTTCGTAGTCTATCTCAATTCATAAATATTTTACATAATTTAT
*
1658821 CGCAGTAATTCAATTTAACAAAAATTTTGTGTGTAATGACATGATCATGTTATTTTTGGTGTG
261 CACAGTAA-TCAATTTAACAAAAATTTTGTGTGTAATGACATGATCATGTTATTTTTGGTGTG
* ** * *
1658884 TAAAGTATTATAAATTTATATAAATTTTTTGACATCAATAATTAGTATTATGTATATTTTGATAT
1 TAAAGTATTAAAAATTTATATAAATTTTTACACATCAATAATTAGT-TTATATATATTTTGACAT
* *
1658949 ATTTATATA-TT-TAT-AT-TATATTCGTATTTTTTACA-TAGTATTTTAATTATTTTTCTATAT
65 ATTCATATATTTGTATCATATATATT-GTATTTTTTACATTA-TATTTTAATTATTTTTATATAT
* *
1659009 -TT-TATTTATA-TAGTGTCTCGATTTATCTTATATTTTACATAATTT-ATCATTATAATTTAA-
128 GTTATATTTATATTA-TGTCTCAATTAATCTTATATTTTACATAATTTGATCATTATAATTTAAT
* *
1659069 TTTAGAGAAAATTTTAAATATTTATATCATA-TT-GT-GTCATATCTCAATTTATAATATATTTT
192 TTTA-AGAAAA--TT-AATATTTATAT-AAAGTTCGTAGTC-TATCTCAATTCATAA-ATATTTT
*
1659131 ACATAATTTATCATAGTAATCAATTTAA
250 ACATAATTTATCACAGTAATCAATTTAA
1659159 ATTTTTTTTG
Statistics
Matches: 229, Mismatches: 35, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
317 4 0.02
318 22 0.10
319 35 0.15
320 34 0.15
321 64 0.28
322 5 0.02
323 41 0.18
324 24 0.10
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.53
Consensus pattern (322 bp):
TAAAGTATTAAAAATTTATATAAATTTTTACACATCAATAATTAGTTTATATATATTTTGACATA
TTCATATATTTGTATCATATATATTGTATTTTTTACATTATATTTTAATTATTTTTATATATGTT
ATATTTATATTATGTCTCAATTAATCTTATATTTTACATAATTTGATCATTATAATTTAATTTTA
AGAAAATTAATATTTATATAAAGTTCGTAGTCTATCTCAATTCATAAATATTTTACATAATTTAT
CACAGTAATCAATTTAACAAAAATTTTGTGTGTAATGACATGATCATGTTATTTTTGGTGTG
Found at i:1659287 original size:11 final size:11
Alignment explanation
Indices: 1659271--1659341 Score: 56
Period size: 11 Copynumber: 6.2 Consensus size: 11
1659261 TTAATACGTT
1659271 TTATATTTATA
1 TTATATTTATA
*
1659282 TTATATTTATC
1 TTATATTTATA
*
1659293 TTATTTTTATGCAGTA
1 TTA-TATT-T--A-TA
1659309 TTATATTT-TA
1 TTATATTTATA
*
1659319 TT-TTTTTATA
1 TTATATTTATA
1659329 TTATATTTATA
1 TTATATTTATA
1659340 TT
1 TT
1659342 GTATCTCAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
9 4 0.09
10 8 0.17
11 22 0.47
12 3 0.06
13 1 0.02
14 1 0.02
15 4 0.09
16 4 0.09
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (11 bp):
TTATATTTATA
Found at i:1659440 original size:17 final size:16
Alignment explanation
Indices: 1659413--1659446 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1659403 TCAGTTACAT
*
1659413 AAAATTTTAAATTATA
1 AAAATTTTAAATAATA
1659429 AAAATATTTAAATAATA
1 AAAAT-TTTAAATAATA
1659446 A
1 A
1659447 TTATTTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATTTTAAATAATA
Found at i:1659489 original size:22 final size:21
Alignment explanation
Indices: 1659449--1659499 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
1659439 AATAATAATT
1659449 ATTTAATATAATTTAATTTAA
1 ATTTAATATAATTTAATTTAA
1659470 ATTT-ATATAATTATTAATTT-A
1 ATTTAATATAA-T-TTAATTTAA
*
1659491 ATTAAATAT
1 ATTTAATAT
1659500 TTATAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.23
21 9 0.35
22 11 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTAATATAATTTAATTTAA
Found at i:1659504 original size:26 final size:27
Alignment explanation
Indices: 1659453--1659512 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
1659443 ATAATTATTT
1659453 AATA-TAATTTAATTTAAATTTATATA
1 AATATTAATTTAATTTAAATTTATATA
*
1659479 ATTATTAATTTAA-TTAAATATT-TATA
1 AATATTAATTTAATTTAAAT-TTATATA
1659505 AATATTAA
1 AATATTAA
1659513 AAATCTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 20 0.67
27 10 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
AATATTAATTTAATTTAAATTTATATA
Found at i:1660405 original size:23 final size:22
Alignment explanation
Indices: 1660385--1660433 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1660375 AAAATATTAA
1660385 AAATATTTTTAT-ATTAATATT
1 AAATATTTTTATAATTAATATT
*
1660406 ATATATTTTTATAATTAA-ATTT
1 AAATATTTTTATAATTAATA-TT
1660428 AAATAT
1 AAATAT
1660434 AACTTAATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AAATATTTTTATAATTAATATT
Found at i:1661067 original size:23 final size:23
Alignment explanation
Indices: 1661005--1661069 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 23
1660995 TTAGTAAAGT
1661005 TTATATAATTTTATGTTAAAAAA
1 TTATATAATTTTATGTTAAAAAA
* *
1661028 --ATCATAGAGTTTGTGTTAAAAAA
1 TTAT-ATA-ATTTTATGTTAAAAAA
1661051 TTATATAATTTTATGTTAA
1 TTATATAATTTTATGTTAA
1661070 TTTTTCTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
21 2 0.06
22 3 0.09
23 24 0.71
24 3 0.09
25 2 0.06
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (23 bp):
TTATATAATTTTATGTTAAAAAA
Found at i:1662390 original size:27 final size:26
Alignment explanation
Indices: 1662355--1662405 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
1662345 TAATTTTAAG
*
1662355 TAAATTAAAAATGTTTAACTATTTATT
1 TAAAATAAAAATGTTTAACT-TTTATT
*
1662382 TAAAATAAAAATTTTTAACTTTTA
1 TAAAATAAAAATGTTTAACTTTTA
1662406 AATATATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (26 bp):
TAAAATAAAAATGTTTAACTTTTATT
Found at i:1663291 original size:16 final size:15
Alignment explanation
Indices: 1663270--1663299 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
1663260 ATAATATTAT
1663270 AATTAATATATTAAAA
1 AATTAAT-TATTAAAA
1663286 AATTAATTATTAAA
1 AATTAATTATTAAA
1663300 TTTAATAATA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATTAATTATTAAAA
Found at i:1663496 original size:13 final size:12
Alignment explanation
Indices: 1663471--1663506 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1663461 GTTTTACATT
1663471 AATAAAATATAA
1 AATAAAATATAA
1663483 AATAAAACTATAA
1 AATAAAA-TATAA
*
1663496 AATTAAATATA
1 AATAAAATATA
1663507 TATAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (12 bp):
AATAAAATATAA
Found at i:1663537 original size:25 final size:24
Alignment explanation
Indices: 1663475--1663542 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 24
1663465 TACATTAATA
* * *
1663475 AAATATAAAATAAAACTATAAAATT
1 AAATAT-ATATAAAATTAAAAAATT
*
1663500 AAATATATATAAATTTAAAAAATT
1 AAATATATATAAAATTAAAAAATT
*
1663524 ATATCATATATAAAATTAA
1 AAAT-ATATATAAAATTAA
1663543 TTTTATTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
24 17 0.47
25 19 0.53
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (24 bp):
AAATATATATAAAATTAAAAAATT
Found at i:1665561 original size:28 final size:27
Alignment explanation
Indices: 1665515--1665600 Score: 79
Period size: 28 Copynumber: 3.0 Consensus size: 27
1665505 TTAAGATTTC
1665515 AAAA-AAAAATTATATTATTATATATTAT
1 AAAATAAAAA-TATA-TATTATATATTAT
*
1665543 AAAATAAAAATGATATATTATATAATTTT
1 AAAATAAAAAT-ATATATTATAT-ATTAT
1665572 AAATTATTAAAAAT-TATATTATAT-TTAT
1 AAA--A-TAAAAATATATATTATATATTAT
1665600 A
1 A
1665601 TTTATAAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
28 17 0.34
29 15 0.30
30 10 0.20
31 1 0.02
32 7 0.14
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (27 bp):
AAAATAAAAATATATATTATATATTAT
Found at i:1665563 original size:36 final size:34
Alignment explanation
Indices: 1665523--1665610 Score: 82
Period size: 36 Copynumber: 2.7 Consensus size: 34
1665513 TCAAAAAAAA
1665523 ATTATATTATTATATATTATAAAATAAAAATGATAT
1 ATTATATTATTATATATTATAAAATAAAAAT--TAT
* * *
1665559 ATTATATAATTTTAAATTAT----TAAAAATTAT
1 ATTATATTATTATATATTATAAAATAAAAATTAT
1665589 ATTATA-T-TTATAT-TTATAAAAT
1 ATTATATTATTATATATTATAAAAT
1665611 TTTAATTAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
27 4 0.10
28 4 0.10
30 9 0.21
31 1 0.02
32 7 0.17
36 17 0.40
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (34 bp):
ATTATATTATTATATATTATAAAATAAAAATTAT
Found at i:1666301 original size:22 final size:24
Alignment explanation
Indices: 1666266--1666311 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
1666256 GCTCCGTTTG
*
1666266 TTTAAATTACTA-TTTATA-AAAT
1 TTTAAAATACTATTTTATATAAAT
*
1666288 TTTAAAATATTATTTTATATAAAT
1 TTTAAAATACTATTTTATATAAAT
1666312 ATTTTTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.50
23 6 0.30
24 4 0.20
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTAAAATACTATTTTATATAAAT
Found at i:1667114 original size:48 final size:48
Alignment explanation
Indices: 1667033--1667137 Score: 149
Period size: 48 Copynumber: 2.2 Consensus size: 48
1667023 TTTTATTCCT
*
1667033 ATTGCGTGACAAAAAATTTCGTTCAGATACTTATATTTAGATTCATTA
1 ATTGAGTGACAAAAAATTTCGTTCAGATACTTATATTTAGATTCATTA
* * *
1667081 ATTGAGTGACAAAAAATTTTGTTCTA-ATTCTTATATTTAGATTCATTT
1 ATTGAGTGACAAAAAATTTCGTTC-AGATACTTATATTTAGATTCATTA
*
1667129 ATTAAGTGA
1 ATTGAGTGA
1667138 ATTGAAGTGA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
48 50 0.98
49 1 0.02
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (48 bp):
ATTGAGTGACAAAAAATTTCGTTCAGATACTTATATTTAGATTCATTA
Found at i:1667210 original size:15 final size:15
Alignment explanation
Indices: 1667175--1667210 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1667165 TTAAATTACG
1667175 TTATTTTAAATTTTT
1 TTATTTTAAATTTTT
**
1667190 AAATTTTAAATTTTT
1 TTATTTTAAATTTTT
1667205 TTATTT
1 TTATTT
1667211 AAGTAATTTC
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTATTTTAAATTTTT
Found at i:1667867 original size:21 final size:20
Alignment explanation
Indices: 1667837--1667894 Score: 55
Period size: 22 Copynumber: 2.8 Consensus size: 20
1667827 TTTATTTATT
* *
1667837 TTTTAGTTTAATTTGTTATA
1 TTTTAATTTAATTTGTTAAA
1667857 TTTTAAATTTAAATTAT-TTAAA
1 TTTT-AATTT-AATT-TGTTAAA
*
1667879 TTTTAATTTATTTTGT
1 TTTTAATTTAATTTGT
1667895 ATTTAAATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 1 0.03
20 8 0.26
21 9 0.29
22 12 0.39
23 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (20 bp):
TTTTAATTTAATTTGTTAAA
Found at i:1667874 original size:16 final size:16
Alignment explanation
Indices: 1667855--1667902 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1667845 TAATTTGTTA
1667855 TATTTTAAATTTAAAT
1 TATTTTAAATTTAAAT
*
1667871 TA-TTTAAATTTTAATT
1 TATTTTAAA-TTTAAAT
**
1667887 TATTTTGTATTTAAAT
1 TATTTTAAATTTAAAT
1667903 CAATTGAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 6 0.23
16 16 0.62
17 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TATTTTAAATTTAAAT
Found at i:1667883 original size:42 final size:39
Alignment explanation
Indices: 1667817--1667894 Score: 93
Period size: 42 Copynumber: 1.9 Consensus size: 39
1667807 TTATTTTAAG
** *
1667817 ATTTTAAATTTTTATTTATTTTTTAGTTTAATTTGTTAT
1 ATTTTAAATTTTTATTTAAATTTTAATTTAATTTGTTAT
*
1667856 ATTTTAAATTTAAATTATTTAAATTTTAATTTATTTTGT
1 ATTTTAAATTT---TTATTTAAATTTTAATTTAATTTGT
1667895 ATTTAAATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 11 0.34
42 21 0.66
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (39 bp):
ATTTTAAATTTTTATTTAAATTTTAATTTAATTTGTTAT
Found at i:1669137 original size:23 final size:21
Alignment explanation
Indices: 1669104--1669150 Score: 51
Period size: 23 Copynumber: 2.1 Consensus size: 21
1669094 TTAAACATAT
*
1669104 TTTTATATAAATATT-TATAAA
1 TTTTATATAAA-ATTAAATAAA
1669125 TTTTATAATTAAAATTAAATAAA
1 TTTTAT-A-TAAAATTAAATAAA
1669148 TTT
1 TTT
1669151 ATTTTTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 6 0.27
22 4 0.18
23 12 0.55
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTATATAAAATTAAATAAA
Found at i:1669570 original size:12 final size:13
Alignment explanation
Indices: 1669552--1669582 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
1669542 ACCTTCATCA
1669552 AATTATAAATAAT
1 AATTATAAATAAT
1669565 -ATTATAAATAAT
1 AATTATAAATAAT
1669577 AATTAT
1 AATTAT
1669583 TTTCTTTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AATTATAAATAAT
Found at i:1678204 original size:28 final size:26
Alignment explanation
Indices: 1678173--1678261 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 26
1678163 TTAAAATTTG
1678173 ATTTAATTATAAATTAAAAGTTAAGATT
1 ATTTAA-TATAAATTAAAAGTTAA-ATT
* * *
1678201 ATTTTAGTATAAGTTAAAAATTATAAATTT
1 A-TTTAATATAAATT-AAAAGT-TAAA-TT
1678231 ATTTTAATATAAATTAAAAGTTAAATT
1 A-TTTAATATAAATTAAAAGTTAAATT
1678258 -TTTA
1 ATTTA
1678262 TCTGATTGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
25 4 0.08
27 2 0.04
28 12 0.24
29 15 0.29
30 18 0.35
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (26 bp):
ATTTAATATAAATTAAAAGTTAAATT
Found at i:1678262 original size:30 final size:28
Alignment explanation
Indices: 1678166--1678258 Score: 100
Period size: 29 Copynumber: 3.2 Consensus size: 28
1678156 AATTATTTTA
1678166 AAATTTGA-TTTAATTATAAATTAAAAGTT
1 AAATTT-ATTTTAA-TATAAATTAAAAGTT
* * *
1678195 AAGA-TTATTTTAGTATAAGTTAAAAATTAT
1 AA-ATTTATTTTAATATAAATT-AAAAGT-T
1678225 AAATTTATTTTAATATAAATTAAAAGTT
1 AAATTTATTTTAATATAAATTAAAAGTT
1678253 AAATTT
1 AAATTT
1678259 TTATCTGATT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
28 15 0.28
29 19 0.36
30 19 0.36
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (28 bp):
AAATTTATTTTAATATAAATTAAAAGTT
Found at i:1679620 original size:24 final size:24
Alignment explanation
Indices: 1679593--1679644 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
1679583 CAAAAGGAAA
1679593 AGGAAGAAAGAAGTCAATTTCTAG
1 AGGAAGAAAGAAGTCAATTTCTAG
1679617 AGGAAGAAAGAAGTCAATTTCTAG
1 AGGAAGAAAGAAGTCAATTTCTAG
1679641 -GGAA
1 AGGAA
1679645 AAGGACTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.46, C:0.08, G:0.27, T:0.19
Consensus pattern (24 bp):
AGGAAGAAAGAAGTCAATTTCTAG
Found at i:1682407 original size:29 final size:29
Alignment explanation
Indices: 1682374--1682430 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1682364 GATTTTAAAT
*
1682374 AGTAATA-TTATTAATATAAATATTAAAAG
1 AGTAATATTTATTAACA-AAATATTAAAAG
*
1682403 AGTAATATTTATTAGCAAAATATTAAAA
1 AGTAATATTTATTAACAAAATATTAAAA
1682431 AATATTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (29 bp):
AGTAATATTTATTAACAAAATATTAAAAG
Found at i:1683351 original size:5 final size:5
Alignment explanation
Indices: 1683341--1683401 Score: 56
Period size: 5 Copynumber: 12.4 Consensus size: 5
1683331 ATCATATTTA
* * *
1683341 TATAT TATAT TATAT TATAATT TATAT TATAT AATAT TAAAA TAT-T TAT-T
1 TATAT TATAT TATAT TAT-A-T TATAT TATAT TATAT TATAT TATAT TATAT
1683391 TAT-T TATAT TA
1 TATAT TATAT TA
1683402 AGTTTGATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
4 11 0.23
5 30 0.64
6 2 0.04
7 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:1683369 original size:22 final size:21
Alignment explanation
Indices: 1683341--1683415 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 21
1683331 ATCATATTTA
1683341 TATATTATATTATATTATAATT
1 TATATTATATTATATTA-AATT
*
1683363 TATATTATATAATATTAAAATAT
1 TATATTATATTATATT-AAAT-T
*
1683386 T-TATT-TATTTATATTAAGTT
1 TATATTATA-TTATATTAAATT
1683406 TGATATTATA
1 T-ATATTATA
1683416 AAATTTGATC
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
20 2 0.05
21 5 0.11
22 32 0.73
23 5 0.11
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
TATATTATATTATATTAAATT
Found at i:1683690 original size:13 final size:13
Alignment explanation
Indices: 1683672--1683713 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1683662 GTTATATATA
1683672 TATATTTATATTT
1 TATATTTATATTT
*
1683685 TATATTT-TAATAT
1 TATATTTAT-ATTT
*
1683698 TATATTAATATTT
1 TATATTTATATTT
1683711 TAT
1 TAT
1683714 GTTCTACCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 1 0.04
13 22 0.92
14 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATATTTATATTT
Found at i:1884313 original size:21 final size:21
Alignment explanation
Indices: 1884289--1884330 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1884279 TTTACTAAAT
*
1884289 AAATATTAGATTTATAAGAAA
1 AAATATTAGAATTATAAGAAA
* *
1884310 AAATTTTAGAATTATTAGAAA
1 AAATATTAGAATTATAAGAAA
1884331 TAAAAATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.36
Consensus pattern (21 bp):
AAATATTAGAATTATAAGAAA
Found at i:1884644 original size:38 final size:38
Alignment explanation
Indices: 1884602--1884686 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 38
1884592 CATCAAATTC
* * * *
1884602 AATTAAATTCTCTAATCACTAATTA-CTAATTAAATTTA
1 AATTAAATTATCTAATAACCAATCATC-AATTAAATTTA
* *
1884640 AATTAAATAATTTAATAACCAATCATCAATTAAATTTA
1 AATTAAATTATCTAATAACCAATCATCAATTAAATTTA
1884678 AATTAAATT
1 AATTAAATT
1884687 TATTAATTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
38 38 0.97
39 1 0.03
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (38 bp):
AATTAAATTATCTAATAACCAATCATCAATTAAATTTA
Found at i:1885266 original size:23 final size:22
Alignment explanation
Indices: 1885201--1885266 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 22
1885191 AAATAATATT
* *
1885201 TTTTACATAATATTAAATAATA
1 TTTTAAATAATATTAAATTATA
1885223 TTTTAAATAAT-TTCAATATTATCA
1 TTTTAAATAATATT-AA-ATTAT-A
1885247 -TTTAAATAATATTATAATTA
1 TTTTAAATAATATTA-AATTA
1885267 AAAATTAGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
21 2 0.05
22 12 0.32
23 19 0.51
24 4 0.11
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTTAAATAATATTAAATTATA
Found at i:1888327 original size:57 final size:57
Alignment explanation
Indices: 1888220--1888329 Score: 161
Period size: 56 Copynumber: 2.0 Consensus size: 57
1888210 AAAATAGTGA
* *
1888220 ACAAGAATGGTAAAATGCGAAGAAAATGAAGTTATATACATATACATATATATATAT
1 ACAAGAATGGTAAAATGAGAAGAAAATGAAGTTATACACATATACATATATATATAT
* * *
1888277 ACAAGAATGGTAAAATGAGAA-AAAATGAAGTTTTACATATATATAT-TATATAT
1 ACAAGAATGGTAAAATGAGAAGAAAATGAAGTTATACACATATACATATATATAT
1888330 TATTAAAGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
55 7 0.15
56 21 0.44
57 20 0.42
ACGTcount: A:0.51, C:0.05, G:0.14, T:0.30
Consensus pattern (57 bp):
ACAAGAATGGTAAAATGAGAAGAAAATGAAGTTATACACATATACATATATATATAT
Found at i:1892314 original size:20 final size:18
Alignment explanation
Indices: 1892269--1892316 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1892259 ACTTGTGTCT
* *
1892269 ATTTTTATTTATTTTTAC
1 ATTTTTATATATTTTCAC
1892287 ATTTTTATATATTTTACAC
1 ATTTTTATATATTTT-CAC
1892306 ATATTTTATAT
1 AT-TTTTATAT
1892317 TTTATAATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 14 0.54
19 4 0.15
20 8 0.31
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTTTATATATTTTCAC
Found at i:1898541 original size:3 final size:3
Alignment explanation
Indices: 1898490--1898526 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1898480 AAGTATTGAA
1898490 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
1898527 CTTGGAATTA
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:1905160 original size:19 final size:17
Alignment explanation
Indices: 1905120--1905160 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
1905110 AAAAATATTA
1905120 TATTTA-TTAAAAAAAC
1 TATTTATTTAAAAAAAC
1905136 TA-TTATTTAAATAAATAC
1 TATTTATTTAAA-AAA-AC
1905154 TATTTAT
1 TATTTAT
1905161 CTAATGTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.14
16 7 0.33
17 3 0.14
18 4 0.19
19 4 0.19
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (17 bp):
TATTTATTTAAAAAAAC
Found at i:1905445 original size:90 final size:90
Alignment explanation
Indices: 1905340--1905521 Score: 337
Period size: 90 Copynumber: 2.0 Consensus size: 90
1905330 TAAACTAATA
1905340 AATTTTAATTATAAATTTTTCTATGAAAATATATAATATTAATTTATTACAAAGATATTATTCAC
1 AATTTTAATTATAAATTTTTCTATGAAAATATATAATATTAATTTATTACAAAGATATTATTCAC
*
1905405 TTAAAATTAAGTAGTATGAGAAAGG
66 TTAAAATTAAGTAGTATCAGAAAGG
*
1905430 AATTTTAATTATAAATTTTTCTATGAAAATATATAATATTAATTTATTACAAAGTTATTATTCAC
1 AATTTTAATTATAAATTTTTCTATGAAAATATATAATATTAATTTATTACAAAGATATTATTCAC
*
1905495 TTATAATTAAGTAGTATCAGAAAGG
66 TTAAAATTAAGTAGTATCAGAAAGG
1905520 AA
1 AA
1905522 AACAATTTTT
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (90 bp):
AATTTTAATTATAAATTTTTCTATGAAAATATATAATATTAATTTATTACAAAGATATTATTCAC
TTAAAATTAAGTAGTATCAGAAAGG
Found at i:1906536 original size:23 final size:22
Alignment explanation
Indices: 1906504--1906574 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 22
1906494 TTATTTAAAT
*
1906504 AATACTATTTATATAATATTAA
1 AATATTATTTATATAATATTAA
1906526 ACATATTATTTAATAGTAATATT-A
1 A-ATATTATTT-ATA-TAATATTAA
*
1906550 AATTTTATTTA-ATAATATTACA
1 AATATTATTTATATAATATTA-A
1906572 AAT
1 AAT
1906575 TAATTTGATT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
20 7 0.17
21 1 0.02
22 6 0.14
23 16 0.38
24 5 0.12
25 7 0.17
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (22 bp):
AATATTATTTATATAATATTAA
Found at i:1906565 original size:26 final size:27
Alignment explanation
Indices: 1906536--1906593 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
1906526 ACATATTATT
* *
1906536 TAATAGTA-ATATTAAATTTTATTTA-A
1 TAATAGTACAAATT-AATTTGATTTACA
*
1906562 TAATATTACAAATTAATTTGATTTACA
1 TAATAGTACAAATTAATTTGATTTACA
1906589 TAATA
1 TAATA
1906594 TTATAATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 17 0.63
27 10 0.37
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (27 bp):
TAATAGTACAAATTAATTTGATTTACA
Found at i:1907205 original size:3 final size:3
Alignment explanation
Indices: 1907197--1907241 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1907187 GTGTTTTTTC
1907197 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1907242 AATTCAGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:1907998 original size:28 final size:28
Alignment explanation
Indices: 1907934--1907988 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
1907924 CAAATGTCAC
1907934 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
1907962 CCTTTGTATTTGTCAAATATGGTGGTT
1 CCTTTGTATTTGTCAAATATGGTGGTT
1907989 ATTTTTGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.11, G:0.22, T:0.49
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTGGTTT
Found at i:1908029 original size:24 final size:24
Alignment explanation
Indices: 1907970--1908038 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
1907960 TTCCTTTGTA
* * *
1907970 TTTGTCAAATATGGTGGTTATTTTTG
1 TTTGTCAAAAATGGTGG--CTTGTTG
* *
1907996 TATGTAAAAAATGGTGGCTTGTTG
1 TTTGTCAAAAATGGTGGCTTGTTG
*
1908020 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAAATGGTGGCT
1908039 AATTTTTATT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
24 21 0.60
26 14 0.40
ACGTcount: A:0.23, C:0.06, G:0.26, T:0.45
Consensus pattern (24 bp):
TTTGTCAAAAATGGTGGCTTGTTG
Found at i:1910591 original size:21 final size:22
Alignment explanation
Indices: 1910562--1910607 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1910552 TGTTCAGACA
** *
1910562 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1910584 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1910605 AGT
1 AGT
1910608 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:1912576 original size:28 final size:28
Alignment explanation
Indices: 1912512--1912566 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
1912502 CAAATGCCAC
1912512 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
1912540 CCTTTGTATTTGTCAAATATGGTGGTT
1 CCTTTGTATTTGTCAAATATGGTGGTT
1912567 ATTTTTGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.11, G:0.22, T:0.49
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTGGTTT
Found at i:1912607 original size:24 final size:24
Alignment explanation
Indices: 1912548--1912616 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
1912538 TTCCTTTGTA
* * *
1912548 TTTGTCAAATATGGTGGTTATTTTTG
1 TTTGTCAAAAATGGTGG--CTTGTTG
* *
1912574 TATGTAAAAAATGGTGGCTTGTTG
1 TTTGTCAAAAATGGTGGCTTGTTG
*
1912598 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAAATGGTGGCT
1912617 AATTTTTATT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
24 21 0.60
26 14 0.40
ACGTcount: A:0.23, C:0.06, G:0.26, T:0.45
Consensus pattern (24 bp):
TTTGTCAAAAATGGTGGCTTGTTG
Found at i:1917507 original size:3 final size:3
Alignment explanation
Indices: 1917499--1917558 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
1917489 ACGTATTGAA
1917499 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1917547 TAT TAT TAT TAT
1 TAT TAT TAT TAT
1917559 CCTTGCAATT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1923486 original size:35 final size:32
Alignment explanation
Indices: 1923447--1923519 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 32
1923437 CAAACCATTC
1923447 AAAAATAAAGTTCAGTGATAAAATTTAATAAAAAT
1 AAAAATAAA-TT-AGTGATAAAATTTAAT-AAAAT
* *
1923482 AAAAAT---TTAGTGATAAAATTTAATCATAT
1 AAAAATAAATTAGTGATAAAATTTAATAAAAT
1923511 AAAAATAAA
1 AAAAATAAA
1923520 ATAAAATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
29 9 0.27
30 16 0.48
31 2 0.06
35 6 0.18
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (32 bp):
AAAAATAAATTAGTGATAAAATTTAATAAAAT
Found at i:1923496 original size:30 final size:29
Alignment explanation
Indices: 1923447--1923505 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
1923437 CAAACCATTC
*
1923447 AAAAATAAAGTTCAGTGATAAAATTTAAT
1 AAAAATAAAATTCAGTGATAAAATTTAAT
*
1923476 AAAAATAAAAATTTAGTGATAAAATTTAAT
1 AAAAAT-AAAATTCAGTGATAAAATTTAAT
1923506 CATATAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (29 bp):
AAAAATAAAATTCAGTGATAAAATTTAAT
Found at i:1925646 original size:13 final size:13
Alignment explanation
Indices: 1925628--1925754 Score: 59
Period size: 13 Copynumber: 9.8 Consensus size: 13
1925618 TAATACTGTT
1925628 TATTATTAAATAA
1 TATTATTAAATAA
* *
1925641 TATTATTTAATAG
1 TATTATTAAATAA
*
1925654 TAATATTAAAT--
1 TATTATTAAATAA
*
1925665 T-TTATTTAATAA
1 TATTATTAAATAA
* *
1925677 TACTA-CAAATTAA
1 TATTATTAAA-TAA
*
1925690 TATGATTTAAATAA
1 TATTA-TTAAATAA
*
1925704 TATTA-TAATTTAA
1 TATTATTAA-ATAA
*
1925717 TAAAATATTAAATAA
1 T--ATTATTAAATAA
* *
1925732 TATAATTGAA-AA
1 TATTATTAAATAA
*
1925744 TATTAATAAAT
1 TATTATTAAAT
1925755 TGTTATTAAA
Statistics
Matches: 81, Mismatches: 22, Indels: 22
0.65 0.18 0.18
Matches are distributed among these distances:
10 7 0.09
11 1 0.01
12 15 0.19
13 38 0.47
14 7 0.09
15 10 0.12
16 3 0.04
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (13 bp):
TATTATTAAATAA
Found at i:1925649 original size:20 final size:21
Alignment explanation
Indices: 1925607--1925649 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1925597 TATTAAAAAA
*
1925607 TATTATTTAAATAATACTGTT
1 TATTATTTAAATAATACTATT
*
1925628 TATTA-TTAAATAATATTATT
1 TATTATTTAAATAATACTATT
1925648 TA
1 TA
1925650 ATAGTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
TATTATTTAAATAATACTATT
Found at i:1925660 original size:26 final size:25
Alignment explanation
Indices: 1925631--1925708 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 25
1925621 TACTGTTTAT
1925631 TATTAAATAATATTATTTAATAGTAA
1 TATTAAATAATATTATTTAATA-TAA
*
1925657 TATTAAAT--T-TTATTTAATAATAC
1 TATTAAATAATATTATTTAAT-ATAA
* *
1925680 TA-CAAATTAATATGATTTAA-ATAA
1 TATTAAA-TAATATTATTTAATATAA
1925704 TATTA
1 TATTA
1925709 TAATTTAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 13
0.69 0.08 0.22
Matches are distributed among these distances:
22 3 0.07
23 14 0.34
24 7 0.17
25 2 0.05
26 15 0.37
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (25 bp):
TATTAAATAATATTATTTAATATAA
Found at i:1925702 original size:27 final size:27
Alignment explanation
Indices: 1925668--1925733 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
1925658 ATTAAATTTT
**
1925668 ATTT-AATAATACTACAAATTAATATG
1 ATTTAAATAATACTACAAATTAATAAA
* * *
1925694 ATTTAAATAATATTATAATTTAATAAA
1 ATTTAAATAATACTACAAATTAATAAA
1925721 ATATTAAATAATA
1 AT-TTAAATAATA
1925734 TAATTGAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 4 0.12
27 19 0.58
28 10 0.30
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.41
Consensus pattern (27 bp):
ATTTAAATAATACTACAAATTAATAAA
Found at i:1926215 original size:2 final size:2
Alignment explanation
Indices: 1926208--1926244 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1926198 ATCTCAGAGT
1926208 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1926245 TCTTCTGTTT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1930974 original size:21 final size:21
Alignment explanation
Indices: 1930941--1930981 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1930931 TTTGGTATTG
1930941 TTACCATTAATATAATTTTGT
1 TTACCATTAATATAATTTTGT
* *
1930962 TTACCTTTGATATAATTTTG
1 TTACCATTAATATAATTTTG
1930982 GTGACATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.54
Consensus pattern (21 bp):
TTACCATTAATATAATTTTGT
Found at i:1933853 original size:19 final size:20
Alignment explanation
Indices: 1933829--1933870 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
1933819 GTTTATTGTG
1933829 TGATACTAAGTAGAAT-ATA
1 TGATACTAAGTAGAATAATA
1933848 TGATACTAAGTAGAATAATA
1 TGATACTAAGTAGAATAATA
1933868 TGA
1 TGA
1933871 CTTTAATGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.31
Consensus pattern (20 bp):
TGATACTAAGTAGAATAATA
Found at i:1934531 original size:2 final size:2
Alignment explanation
Indices: 1934524--1934563 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1934514 ATGTTAGTTG
1934524 AT AT 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 AT AT
1934564 CATCACATGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1935479 original size:11 final size:12
Alignment explanation
Indices: 1935437--1935493 Score: 61
Period size: 12 Copynumber: 5.1 Consensus size: 12
1935427 CTAACAACTG
1935437 TTATCAAAATTA
1 TTATCAAAATTA
*
1935449 TTA-C-GAA-TA
1 TTATCAAAATTA
1935458 TTATCAAAATTA
1 TTATCAAAATTA
1935470 TTAT-AAAATTA
1 TTATCAAAATTA
1935481 -TATCAATAATTA
1 TTATCAA-AATTA
1935493 T
1 T
1935494 AAAAAAAATC
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
9 5 0.14
10 6 0.16
11 12 0.32
12 14 0.38
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (12 bp):
TTATCAAAATTA
Found at i:1935494 original size:12 final size:11
Alignment explanation
Indices: 1935459--1935577 Score: 60
Period size: 11 Copynumber: 11.3 Consensus size: 11
1935449 TTACGAATAT
1935459 TATCAAAATTA
1 TATCAAAATTA
1935470 TTAT-AAAATTA
1 -TATCAAAATTA
1935481 TATCAATAATTA
1 TATCAA-AATTA
**
1935493 TA--AAAAAAA
1 TATCAAAATTA
*
1935502 TCTCAAAATT-
1 TATCAAAATTA
*
1935512 TCATCATAATT-
1 T-ATCAAAATTA
* *
1935523 TTTAAAAATTA
1 TATCAAAATTA
1935534 TATCAAATATTA
1 TATCAAA-ATTA
*
1935546 -AT-AAAA-AA
1 TATCAAAATTA
1935554 TATC-AAA-TA
1 TATCAAAATTA
1935563 TTATCAAAATTA
1 -TATCAAAATTA
1935575 TAT
1 TAT
1935578 AAACTGTCGT
Statistics
Matches: 81, Mismatches: 14, Indels: 25
0.68 0.12 0.21
Matches are distributed among these distances:
8 1 0.01
9 11 0.14
10 19 0.23
11 34 0.42
12 16 0.20
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.38
Consensus pattern (11 bp):
TATCAAAATTA
Found at i:1936043 original size:22 final size:22
Alignment explanation
Indices: 1935991--1936044 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
1935981 ATGCTTATAG
*
1935991 ATATTA-TTTAAAAATTATTTA
1 ATATTATTTTAAAAATAATTTA
* *
1936012 ATTATAATTTTAAAAATAATTTT
1 A-TATTATTTTAAAAATAATTTA
1936035 ATATTATTTT
1 ATATTATTTT
1936045 TACTAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 1 0.04
22 12 0.44
23 14 0.52
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATATTATTTTAAAAATAATTTA
Found at i:1936439 original size:2 final size:2
Alignment explanation
Indices: 1936424--1936465 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1936414 TTACACAAAA
* *
1936424 AT AT AT GT AC 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 AT AT AT
1936466 TCTGCAAGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1942278 original size:16 final size:16
Alignment explanation
Indices: 1942232--1942278 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1942222 AATCCGAAAT
* *
1942232 AGCCCGAACTCGAGAC
1 AGCCCGAACTCAAGAA
*
1942248 AGCTCGAAC-CTAAGAA
1 AGCCCGAACTC-AAGAA
1942264 AGCCCGAACTCAAGA
1 AGCCCGAACTCAAGA
1942279 GAACCTGAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 1 0.04
16 23 0.92
17 1 0.04
ACGTcount: A:0.38, C:0.32, G:0.21, T:0.09
Consensus pattern (16 bp):
AGCCCGAACTCAAGAA
Found at i:1942783 original size:16 final size:15
Alignment explanation
Indices: 1942762--1942791 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1942752 ATGTTACATT
1942762 TAGAATAGCAATATAG
1 TAGAATAG-AATATAG
1942778 TAGAATAGAATATA
1 TAGAATAGAATATA
1942792 AAGTTAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.03, G:0.17, T:0.27
Consensus pattern (15 bp):
TAGAATAGAATATAG
Found at i:1943744 original size:16 final size:16
Alignment explanation
Indices: 1943719--1943780 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
1943709 AATCCTGAAT
*
1943719 AAATTTAAATCCAAAA
1 AAATTCAAATCCAAAA
1943735 AAATTCAAATCCAAATA
1 AAATTCAAATCCAAA-A
* *
1943752 AAATT-AAATCTAAAT
1 AAATTCAAATCCAAAA
* *
1943767 GAATTCAAACCCAA
1 AAATTCAAATCCAA
1943781 TCCTATCTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
15 4 0.11
16 28 0.74
17 6 0.16
ACGTcount: A:0.58, C:0.16, G:0.02, T:0.24
Consensus pattern (16 bp):
AAATTCAAATCCAAAA
Found at i:1943753 original size:32 final size:32
Alignment explanation
Indices: 1943716--1943780 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
1943706 CTAAATCCTG
* *
1943716 AATAAATTTAAATCCAAAAAAATTCAAATCCA
1 AATAAAATTAAATCCAAAAAAATTCAAACCCA
* **
1943748 AATAAAATTAAATCTAAATGAATTCAAACCCA
1 AATAAAATTAAATCCAAAAAAATTCAAACCCA
1943780 A
1 A
1943781 TCCTATCTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.58, C:0.15, G:0.02, T:0.25
Consensus pattern (32 bp):
AATAAAATTAAATCCAAAAAAATTCAAACCCA
Found at i:1947453 original size:19 final size:20
Alignment explanation
Indices: 1947429--1947470 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
1947419 GTTTATTGTG
1947429 TGATACTAAGTAGAAT-ATA
1 TGATACTAAGTAGAATAATA
1947448 TGATACTAAGTAGAATAATA
1 TGATACTAAGTAGAATAATA
1947468 TGA
1 TGA
1947471 CTTTAATGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.31
Consensus pattern (20 bp):
TGATACTAAGTAGAATAATA
Found at i:1949475 original size:11 final size:12
Alignment explanation
Indices: 1949448--1949476 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1949438 TTTTATTTTA
1949448 ATAAAAAATTAT
1 ATAAAAAATTAT
1949460 ATAAAAAATTAT
1 ATAAAAAATTAT
1949472 -TAAAA
1 ATAAAA
1949477 TTATATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
ATAAAAAATTAT
Found at i:1949507 original size:21 final size:21
Alignment explanation
Indices: 1949483--1949528 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1949473 AAAATTATAT
1949483 CAAAGGTTAACAAAACTATTA
1 CAAAGGTTAACAAAACTATTA
* ** *
1949504 CAAATGTTATTAAAATTATTA
1 CAAAGGTTAACAAAACTATTA
1949525 CAAA
1 CAAA
1949529 ATTATACCAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (21 bp):
CAAAGGTTAACAAAACTATTA
Found at i:1950473 original size:2 final size:2
Alignment explanation
Indices: 1950458--1950505 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
1950448 TTACACAAAA
* *
1950458 AT AT AT GT AC 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 AT AT AT
1950500 AT AT AT
1 AT AT AT
1950506 TCTGCCATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1952650 original size:21 final size:21
Alignment explanation
Indices: 1952626--1952665 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1952616 TTTGGTATTG
1952626 TTACCATTAATATAATTTTAT
1 TTACCATTAATATAATTTTAT
* *
1952647 TTACCTTTGATATAATTTT
1 TTACCATTAATATAATTTT
1952666 GGTAACATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.55
Consensus pattern (21 bp):
TTACCATTAATATAATTTTAT
Found at i:1953839 original size:59 final size:59
Alignment explanation
Indices: 1953772--1953884 Score: 172
Period size: 59 Copynumber: 1.9 Consensus size: 59
1953762 TCAAAATCTC
*
1953772 TTAATTTAAAAGATTTAAATTAAATAGTGATGCATTAGTCCTTAATCTAAAGGAATCCT
1 TTAATTTAAAAGATTTAAATTAAATAGTGATGCACTAGTCCTTAATCTAAAGGAATCCT
* ** * *
1953831 TTAATTTAAAGGATTTAAATTAGTTAGTGATGTACTAGTCTTTAATCTAAAGGA
1 TTAATTTAAAAGATTTAAATTAAATAGTGATGCACTAGTCCTTAATCTAAAGGA
1953885 TTTAAATTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 48 1.00
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (59 bp):
TTAATTTAAAAGATTTAAATTAAATAGTGATGCACTAGTCCTTAATCTAAAGGAATCCT
Found at i:1954110 original size:33 final size:33
Alignment explanation
Indices: 1954045--1954111 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
1954035 TTTGAGATCT
* *
1954045 TGAAATTATTTTTTTCTATTCAATCTTCATTGC
1 TGAAATTATTTTTTTCTAATCAATCTTAATTGC
* *
1954078 TGAAATTCTTCTTTTTCTAAT-AGTCTTAATTGC
1 TGAAATTATT-TTTTTCTAATCAATCTTAATTGC
1954111 T
1 T
1954112 TCCTTTCAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 20 0.69
34 9 0.31
ACGTcount: A:0.24, C:0.15, G:0.07, T:0.54
Consensus pattern (33 bp):
TGAAATTATTTTTTTCTAATCAATCTTAATTGC
Found at i:1960315 original size:19 final size:20
Alignment explanation
Indices: 1960287--1960328 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1960277 GTTTATTGTG
1960287 TGATACTAAGTAAAAT-ATA
1 TGATACTAAGTAAAATAATA
* *
1960306 TGATAGTAAGTAGAATAATA
1 TGATACTAAGTAAAATAATA
1960326 TGA
1 TGA
1960329 CTTTAATGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.50, C:0.02, G:0.17, T:0.31
Consensus pattern (20 bp):
TGATACTAAGTAAAATAATA
Found at i:1962348 original size:11 final size:11
Alignment explanation
Indices: 1962332--1962462 Score: 50
Period size: 11 Copynumber: 12.4 Consensus size: 11
1962322 AAACTATTAT
1962332 AAATTATATCA
1 AAATTATATCA
1962343 AAATTAT-TACA
1 AAATTATAT-CA
*
1962354 AAATTATAGCA
1 AAATTATATCA
*
1962365 ATAATT-T-CCAA
1 A-AATTATATC-A
** *
1962376 AAAAAATCTCA
1 AAATTATATCA
1962387 AAATT-TCATCA
1 AAATTAT-ATCA
* *
1962398 CAATT-TATTA
1 AAATTATATCA
*
1962408 AAATTATATTA
1 AAATTATATCA
1962419 AATATTA-AT-A
1 AA-ATTATATCA
*
1962429 AAA-CATATC-
1 AAATTATATCA
1962438 AAA-TATTATCA
1 AAATTA-TATCA
1962449 AAATTATAT-A
1 AAATTATATCA
1962459 AAAT
1 AAAT
1962463 CAAAATTATA
Statistics
Matches: 93, Mismatches: 13, Indels: 29
0.69 0.10 0.21
Matches are distributed among these distances:
8 1 0.01
9 7 0.08
10 24 0.26
11 50 0.54
12 11 0.12
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.35
Consensus pattern (11 bp):
AAATTATATCA
Found at i:1962466 original size:16 final size:16
Alignment explanation
Indices: 1962445--1962476 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1962435 ATCAAATATT
1962445 ATCAAAATTATATAAA
1 ATCAAAATTATATAAA
1962461 ATCAAAATTATATAAA
1 ATCAAAATTATATAAA
1962477 CTGTTGTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (16 bp):
ATCAAAATTATATAAA
Found at i:1962940 original size:23 final size:22
Alignment explanation
Indices: 1962892--1962941 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
1962882 ATAGATGTAA
*
1962892 TTTAAAAATTATTTAATTATAAT
1 TTTAAAAATAATTTAATTAT-AT
1962915 TTTAAAAATAATTTTATATTAT-T
1 TTTAAAAATAA-TTTA-ATTATAT
1962938 TTTA
1 TTTA
1962942 CTAAATTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 15 0.62
24 4 0.17
25 5 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTAAAAATAATTTAATTATAT
Found at i:1963339 original size:2 final size:2
Alignment explanation
Indices: 1963324--1963359 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1963314 TTACACAAAA
* *
1963324 AT AT AT GT AC 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
1963360 TCTGCAAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1966849 original size:37 final size:40
Alignment explanation
Indices: 1966769--1966907 Score: 119
Period size: 37 Copynumber: 3.5 Consensus size: 40
1966759 TCGGTTTTAA
* * *
1966769 CCGTGCCACCGGTTAAGAATA-A-TAGTTTTTGTTTCGA-T
1 CCGTGCCACC-GATAAGAATATAGTAGTTTTTGTTCCAACT
*
1966807 CCGTGCTACCGATAA-AAT-TAGTAGTTTTTGTTCCAACT
1 CCGTGCCACCGATAAGAATATAGTAGTTTTTGTTCCAACT
* * *
1966845 -CGTGCCACGGGTAAGAATAATAGTAGTTTTTGTTCCAACCCAC
1 CCGTGCCACCGATAAGAAT-ATAGTAGTTTTTGTTCCAA--C-T
*
1966888 CCATGCCACCGATAAGAATA
1 CCGTGCCACCGATAAGAATA
1966908 GCAATTTTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 15
0.75 0.10 0.14
Matches are distributed among these distances:
36 4 0.05
37 28 0.35
38 13 0.16
40 18 0.22
42 1 0.01
43 1 0.01
44 15 0.19
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (40 bp):
CCGTGCCACCGATAAGAATATAGTAGTTTTTGTTCCAACT
Found at i:1970840 original size:22 final size:22
Alignment explanation
Indices: 1970798--1970841 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1970788 ACCTTCTCTT
*
1970798 CAAAAAAAAAAAGGAAAAAAAA
1 CAAAAAAAAAAAGCAAAAAAAA
*
1970820 CAAAAAACAAAA-CAAAGAAAAA
1 CAAAAAAAAAAAGCAAA-AAAAA
1970842 GAGAGAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (22 bp):
CAAAAAAAAAAAGCAAAAAAAA
Found at i:1971960 original size:55 final size:55
Alignment explanation
Indices: 1971850--1972673 Score: 1252
Period size: 55 Copynumber: 15.0 Consensus size: 55
1971840 GATGCTTTTT
*
1971850 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGCGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACA
*
1971906 CCTCTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
* * *
1971961 CCTTTCAAAGCCCACCCAAGTTGGTGGCATTTTCCAGTCCTTAAGGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
*
1972016 CCTCTT-AAAGCCCACACAAGTTGGTGGCATCTTT-CAGTCCCCAAAGAGCAGGACA
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCAT-TTTCCAGTCCTCAAAGAGCAGGACA
* *
1972071 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGGCA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
*
1972126 CCTTTCAAAGCCCACCCAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
* *
1972181 CCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCCCAAAGAGCAGGACA
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACA
*
1972236 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
1972291 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
* *
1972346 CCTCTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
* * *
1972401 CCTTTCAAAGCCCACCCAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGTAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
* *
1972456 CCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCCCAAAGAGCAGGACA
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACA
*
1972511 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
* * *
1972566 CCTCTT-AAAGCCCACGCAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACG
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACA
* * * *
1972621 CCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-TACTCCTCAATGAGCAGGA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGA
1972674 TACACTTTAT
Statistics
Matches: 709, Mismatches: 44, Indels: 31
0.90 0.06 0.04
Matches are distributed among these distances:
54 17 0.02
55 644 0.91
56 48 0.07
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (55 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
Found at i:1972297 original size:26 final size:26
Alignment explanation
Indices: 1972208--1972297 Score: 65
Period size: 26 Copynumber: 3.3 Consensus size: 26
1972198 AAGTTGGTGG
*
1972208 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * **
1972234 CACCTTTCAAAGCCCACACAAGTTGGTGG-
1 CACCTTTC--AGTCCACA-AAG-AGCAGGA
** *
1972263 CATTTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
1972289 CACCTTTCA
1 CACCTTTCA
1972298 AAGCCCACAC
Statistics
Matches: 45, Mismatches: 14, Indels: 10
0.65 0.20 0.14
Matches are distributed among these distances:
25 3 0.07
26 18 0.40
27 6 0.13
28 6 0.13
29 9 0.20
30 3 0.07
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (26 bp):
CACCTTTCAGTCCACAAAGAGCAGGA
Found at i:1973507 original size:19 final size:19
Alignment explanation
Indices: 1973483--1973550 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1973473 AATTCAACAA
1973483 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1973502 TTTGTATCGATAC---A--
1 TTTGTATCGATACATAAGT
1973516 -TTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1973534 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1973551 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 12 0.28
16 2 0.05
19 29 0.67
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1973520 original size:32 final size:32
Alignment explanation
Indices: 1973484--1973548 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
1973474 ATTCAACAAT
*
1973484 TTGTATCGATACATAAGTTTTGTATCGATACA
1 TTGTATCGATACATAAGTATTGTATCGATACA
1973516 TTGTATCGATACATAAGTATTGTATCGATACA
1 TTGTATCGATACATAAGTATTGTATCGATACA
1973548 T
1 T
1973549 AATTAGCTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.40
Consensus pattern (32 bp):
TTGTATCGATACATAAGTATTGTATCGATACA
Found at i:1973521 original size:13 final size:13
Alignment explanation
Indices: 1973503--1973529 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1973493 TACATAAGTT
1973503 TTGTATCGATACA
1 TTGTATCGATACA
1973516 TTGTATCGATACA
1 TTGTATCGATACA
1973529 T
1 T
1973530 AAGTATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1973608 original size:13 final size:13
Alignment explanation
Indices: 1973590--1973615 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1973580 CATTTTTCTG
1973590 TGTATCGATACAT
1 TGTATCGATACAT
1973603 TGTATCGATACAT
1 TGTATCGATACAT
1973616 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1973612 original size:33 final size:33
Alignment explanation
Indices: 1973570--1973636 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1973560 GCCAAGGAAA
***
1973570 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1973603 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1973636 T
1 T
1973637 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1976103 original size:27 final size:28
Alignment explanation
Indices: 1976073--1976148 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
1976063 AATTTTCACA
1976073 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
1976100 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
***
1976128 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1976149 ACTTTATCTC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 24 0.55
28 20 0.45
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:1976301 original size:54 final size:51
Alignment explanation
Indices: 1975968--1976303 Score: 225
Period size: 51 Copynumber: 6.4 Consensus size: 51
1975958 AATTCTCCAC
* * * * *
1975968 AATCGGGGATATTCCAACTCCGATTTTATTTTCAAGACACTAA-TTTTCTAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTC-AT
* * *
1976019 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAATAACACCAAATTTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCC-AA-AACACCAATTTTTCAT
* * ** * * *
1976072 AATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGTTATTTC-C
1 AATCGGGGATACTCCAACCCCGATTTTAT-TTC--CAAAACACCAA-----TT-TTTCAT
* * * * ***
1976129 GA--GGGGATACTCCAACCCCGACTTTATCTCCAAAATATTGATTTTTCAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCAT
* * *
1976178 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCTCTTT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTT-TC-AT
* *
1976231 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAAATACCAATTTTTCAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCC---AAAACACCAATTTTTCAT
*
1976285 AATCGAGGATACTCCAACC
1 AATCGGGGATACTCCAACC
1976304 TCGTTATTTC
Statistics
Matches: 221, Mismatches: 42, Indels: 41
0.73 0.14 0.13
Matches are distributed among these distances:
48 4 0.02
49 3 0.01
51 70 0.32
52 12 0.05
53 60 0.27
54 26 0.12
55 20 0.09
56 15 0.07
57 7 0.03
58 4 0.02
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (51 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCAT
Found at i:1976322 original size:28 final size:29
Alignment explanation
Indices: 1976286--1976362 Score: 95
Period size: 28 Copynumber: 2.7 Consensus size: 29
1976276 ATTTTTCATA
* * *
1976286 ATCGAGGATACTCCAACCTCGTTA-TTTC
1 ATCGGGGATACTCCAACCCCGTTACTTCC
*
1976314 ATCGGGGATACTCCAACCCCTTTACTTCC
1 ATCGGGGATACTCCAACCCCGTTACTTCC
*
1976343 A-AGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1976363 GCTTTATTCC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 38 0.90
29 4 0.10
ACGTcount: A:0.25, C:0.34, G:0.17, T:0.25
Consensus pattern (29 bp):
ATCGGGGATACTCCAACCCCGTTACTTCC
Found at i:1976358 original size:214 final size:210
Alignment explanation
Indices: 1975968--1976413 Score: 660
Period size: 214 Copynumber: 2.1 Consensus size: 210
1975958 AATTCTCCAC
* * * *
1975968 AATCGGGGATATTCCAACTCCGATTTTATTTTCAAGACACTAATTTTCTATAATCGGGGATACTC
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
* *
1976033 CAACTCCGATTTTATTTCCAAATAACACCAAATTTTCACAATCGGGGATACTCCAACCCCGTTAA
66 CAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCCCGTTAA
* *
1976098 TCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTA-TCTCCAA
131 TCATCGGGGATACTCCAACCCCGTTACTTCCAAGGGGATACTCCAACCCCGACTTTATTC-CCAA
*
1976162 AATATTGATTTTTCAT
195 AATATTGATTTCTCAT
* *
1976178 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCTCTTTAATCGGGGATAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAA-TTT-TCTATAATCGGGGATAC
* * * *
1976243 TCCAACTCCGATTTTATTTCCAAAAAAATACCAATTTTTCATAATCGAGGATACTCCAACCTCGT
64 TCCAACTCCGATTTTATTTCC-AAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCCCGT
* * *
1976308 TATTTCATCGGGGATACTCCAACCCCTTTACTTCCAAGGGGATACTCCAACCCCGGCTTTATTCC
128 TA-ATCATCGGGGATACTCCAACCCCGTTACTTCCAAGGGGATACTCCAACCCCGACTTTATTCC
1976373 CAAAATATTGATTTCTCAT
192 CAAAATATTGATTTCTCAT
* *
1976392 AATTGGGGATACTCCAATCCCG
1 AATCGGGGATACTCCAACCCCG
1976414 TTATTTTCGA
Statistics
Matches: 211, Mismatches: 20, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
210 38 0.18
211 3 0.01
212 37 0.18
213 39 0.18
214 92 0.44
215 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (210 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
CAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCCCGTTAA
TCATCGGGGATACTCCAACCCCGTTACTTCCAAGGGGATACTCCAACCCCGACTTTATTCCCAAA
ATATTGATTTCTCAT
Found at i:1976378 original size:107 final size:107
Alignment explanation
Indices: 1976023--1976436 Score: 358
Period size: 107 Copynumber: 3.9 Consensus size: 107
1976013 TTCTATAATC
* * * * *
1976023 GGGGATACTCCAACTCCGATTTTATTTCCAAATAACACCAAATTTTCACAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAA-AATACCAATTTTTCATAATCGGGGATACTCCA
* * * * *
1976088 ACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGA
65 ACCCCGTTATTTATCGGGGATACTCCAACCCCTTTACTTCCAA
* ***
1976131 GGGGATACTCCAACCCCGACTTTATCTCC-AAAATATTGATTTTTCATAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTTTCATAATCGGGGATACTCCAA
* ***** * * * **
1976195 CCCCGGT-TTTATTTTCAAAACACCAA----TTTTCTCTTTAA
66 CCCCGTTATTTATCGGGGATACTCCAACCCCTTTACT-TCCAA
* * *
1976233 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAAATACCAATTTTTCATAATCGAGGATACT
1 --GGGGATACTCCAACCCCGACTTTATTTCC--AAAAATACCAATTTTTCATAATCGGGGATACT
*
1976298 CCAACCTCGTTATTTCATCGGGGATACTCCAACCCCTTTACTTCCAA
62 CCAACCCCGTTATTT-ATCGGGGATACTCCAACCCCTTTACTTCCAA
* * *** * *
1976345 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTTTCATAATCGGGGATACTCCAA
*
1976409 TCCCGTTATTT-TCGAGGAGATACTCCAA
66 CCCCGTTATTTATCG-GG-GATACTCCAA
1976437 TCTCGATTTA
Statistics
Matches: 236, Mismatches: 56, Indels: 29
0.74 0.17 0.09
Matches are distributed among these distances:
101 3 0.01
102 2 0.01
104 26 0.11
105 13 0.06
106 35 0.15
107 86 0.36
108 29 0.12
109 13 0.06
110 21 0.09
112 3 0.01
113 5 0.02
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.31
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTTTCATAATCGGGGATACTCCAA
CCCCGTTATTTATCGGGGATACTCCAACCCCTTTACTTCCAA
Found at i:1978238 original size:19 final size:20
Alignment explanation
Indices: 1978210--1978251 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
1978200 GTTTATTGTG
1978210 TGATACTAAGTAGAAT-ATA
1 TGATACTAAGTAGAATAATA
*
1978229 TGATAGTAAGTAGAATAATA
1 TGATACTAAGTAGAATAATA
1978249 TGA
1 TGA
1978252 CTTTAATGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.48, C:0.02, G:0.19, T:0.31
Consensus pattern (20 bp):
TGATACTAAGTAGAATAATA
Found at i:1980267 original size:20 final size:21
Alignment explanation
Indices: 1980242--1980281 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1980232 TATTTTAGTA
1980242 TAAAATTATAT-AAAAATTAT
1 TAAAATTATATCAAAAATTAT
*
1980262 TAAAATTTTATCAAAAATTA
1 TAAAATTATATCAAAAATTA
1980282 ACAAAACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAATTATATCAAAAATTAT
Found at i:1980287 original size:21 final size:20
Alignment explanation
Indices: 1980243--1980322 Score: 56
Period size: 21 Copynumber: 3.9 Consensus size: 20
1980233 ATTTTAGTAT
**
1980243 AAAATTATATAAAAATTATT
1 AAAATTATATAAAAATTAAC
*
1980263 AAAATTTTATCAAAAATTAAC
1 AAAATTATAT-AAAAATTAAC
* * *
1980284 AAAACTAT-TACAAATGTTATC
1 AAAATTATATA-AAA-ATTAAC
1980305 AAAATTAT-TACAAAATTA
1 AAAATTATATA-AAAATTA
1980323 TATCAATAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 1 0.02
20 16 0.33
21 31 0.65
ACGTcount: A:0.56, C:0.07, G:0.01, T:0.35
Consensus pattern (20 bp):
AAAATTATATAAAAATTAAC
Found at i:1980430 original size:11 final size:11
Alignment explanation
Indices: 1980243--1980433 Score: 69
Period size: 11 Copynumber: 18.3 Consensus size: 11
1980233 ATTTTAGTAT
*
1980243 AAAATTATATA
1 AAAATTATATC
1980254 AAAATTAT-T-
1 AAAATTATATC
*
1980263 AAAATTTTATC
1 AAAATTATATC
1980274 AAAAATTA-A-C
1 -AAAATTATATC
*
1980284 AAAACTAT-T-
1 AAAATTATATC
1980293 ACAAATGT-TATC
1 A-AAAT-TATATC
1980305 AAAATTAT-TAC
1 AAAATTATAT-C
1980316 AAAATTATATC
1 AAAATTATATC
**
1980327 AATAATTACCT-
1 AA-AATTATATC
* *
1980338 AAAA-AATCTC
1 AAAATTATATC
*
1980348 AAAATT-TATT
1 AAAATTATATC
1980358 AAAATT-TCATC
1 AAAATTAT-ATC
*
1980369 ATAAGTTAT-T-
1 A-AAATTATATC
1980379 AAAATTATATC
1 AAAATTATATC
1980390 AAATATTA-AT-
1 AAA-ATTATATC
**
1980400 AAAAAAAT-TC
1 AAAATTATATC
1980410 -AAA-TATTATC
1 AAAATTA-TATC
1980420 AAAATTATATC
1 AAAATTATATC
1980431 AAA
1 AAA
1980434 TGTTTGTATA
Statistics
Matches: 136, Mismatches: 17, Indels: 54
0.66 0.08 0.26
Matches are distributed among these distances:
8 1 0.01
9 30 0.22
10 31 0.23
11 49 0.36
12 24 0.18
13 1 0.01
ACGTcount: A:0.54, C:0.09, G:0.01, T:0.36
Consensus pattern (11 bp):
AAAATTATATC
Found at i:1986537 original size:16 final size:16
Alignment explanation
Indices: 1986516--1986546 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1986506 CACTTGAAAC
1986516 AGTTAAACAATTAAAG
1 AGTTAAACAATTAAAG
*
1986532 AGTTAAATAATTAAA
1 AGTTAAACAATTAAA
1986547 AATTTGAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.03, G:0.10, T:0.29
Consensus pattern (16 bp):
AGTTAAACAATTAAAG
Done.