Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 182 of 182
Found at i:55662260 original size:2 final size:2
Alignment explanation
Indices: 55662255--55662282 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55662245 ATATATAAAT
55662255 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
55662283 CAGAAGGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:55665866 original size:6 final size:6
Alignment explanation
Indices: 55665867--55665900 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
55665857 TTCTTTTTCT
55665867 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
55665901 ATTACATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:55666312 original size:31 final size:31
Alignment explanation
Indices: 55666267--55666340 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
55666257 TGTACGTTAG
*
55666267 TTAGTT-GATGACCAAAAAGACAAAATT-TAA
1 TTAGTTGGGTGACCAAAAA-ACAAAATTATAA
* *
55666297 TTAGTTGGGTGACCAAAAAATAAATTTATAA
1 TTAGTTGGGTGACCAAAAAACAAAATTATAA
*
55666328 ATAGTTGGGTGAC
1 TTAGTTGGGTGAC
55666341 TACTAATGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 12 0.32
31 26 0.68
ACGTcount: A:0.43, C:0.08, G:0.19, T:0.30
Consensus pattern (31 bp):
TTAGTTGGGTGACCAAAAAACAAAATTATAA
Found at i:55669589 original size:22 final size:22
Alignment explanation
Indices: 55669559--55669602 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
55669549 AACACTCCTT
*
55669559 TAAATAATAAATAAGAAATAAG
1 TAAACAATAAATAAGAAATAAG
55669581 TAAACAATAAATAAGAAATAAG
1 TAAACAATAAATAAGAAATAAG
55669603 GGGTTCTCTT
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:0.68, C:0.02, G:0.09, T:0.20
Consensus pattern (22 bp):
TAAACAATAAATAAGAAATAAG
Found at i:55669600 original size:11 final size:11
Alignment explanation
Indices: 55669564--55669601 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
55669554 TCCTTTAAAT
55669564 AATAAATAAGA
1 AATAAATAAGA
*
55669575 AATAAGTAA-A
1 AATAAATAAGA
55669585 CAATAAATAAGA
1 -AATAAATAAGA
55669597 AATAA
1 AATAA
55669602 GGGGTTCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 1 0.04
11 21 0.91
12 1 0.04
ACGTcount: A:0.71, C:0.03, G:0.08, T:0.18
Consensus pattern (11 bp):
AATAAATAAGA
Found at i:55669602 original size:7 final size:7
Alignment explanation
Indices: 55669560--55669602 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
55669550 ACACTCCTTT
*
55669560 AAATAAT
1 AAATAAG
55669567 AAATAAG
1 AAATAAG
55669574 AAATAAG
1 AAATAAG
* *
55669581 TAAACAAT
1 -AAATAAG
55669589 AAATAAG
1 AAATAAG
55669596 AAATAAG
1 AAATAAG
55669603 GGGTTCTCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
7 25 0.83
8 5 0.17
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.19
Consensus pattern (7 bp):
AAATAAG
Found at i:55672177 original size:25 final size:26
Alignment explanation
Indices: 55672149--55672209 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
55672139 TACGTGTTTT
55672149 TTTAATAATTATATA-TTTTA-AAAAA
1 TTTAATAATTATA-ACTTTTACAAAAA
*
55672174 TTTAA-AATTTTAACTTTTACAAAAA
1 TTTAATAATTATAACTTTTACAAAAA
*
55672199 ATTAATTAATT
1 TTTAA-TAATT
55672210 GTTGACATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
23 1 0.03
24 11 0.37
25 14 0.47
27 4 0.13
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (26 bp):
TTTAATAATTATAACTTTTACAAAAA
Found at i:55680670 original size:21 final size:21
Alignment explanation
Indices: 55680644--55680684 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
55680634 AGACGAGCAA
* *
55680644 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
55680665 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
55680685 TTGAGCAGAT
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:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:55682623 original size:16 final size:16
Alignment explanation
Indices: 55682590--55682623 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55682580 GGAGATTGTT
* *
55682590 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
55682606 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
55682622 AA
1 AA
55682624 TACAAAGTGG
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:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:55686434 original size:7 final size:7
Alignment explanation
Indices: 55686424--55686450 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
55686414 CACTTAATTA
55686424 TTAAAAT
1 TTAAAAT
55686431 TTAAAAT
1 TTAAAAT
55686438 TTAAAAT
1 TTAAAAT
55686445 TTAAAA
1 TTAAAA
55686451 ATAAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TTAAAAT
Found at i:55687847 original size:21 final size:22
Alignment explanation
Indices: 55687814--55687854 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
55687804 TTATATTAAT
*
55687814 TTTTTAAAGATTATTTTTAAAA
1 TTTTTAAAGATTATTGTTAAAA
*
55687836 TTTTTATA-ATTATTGTTAA
1 TTTTTAAAGATTATTGTTAA
55687855 GAAAAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (22 bp):
TTTTTAAAGATTATTGTTAAAA
Found at i:55688679 original size:30 final size:30
Alignment explanation
Indices: 55688643--55688703 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
55688633 ACCTAGTGAC
55688643 TTAAAT-AAAATATTTCGAATAGTTTAATGA
1 TTAAATAAAAATA-TTCGAATAGTTTAATGA
*
55688673 TTAAATAAAAATATTCGAATAGTTTAGTGA
1 TTAAATAAAAATATTCGAATAGTTTAATGA
55688703 T
1 T
55688704 CATTTTGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 23 0.79
31 6 0.21
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.39
Consensus pattern (30 bp):
TTAAATAAAAATATTCGAATAGTTTAATGA
Found at i:55695599 original size:14 final size:14
Alignment explanation
Indices: 55695570--55695618 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
55695560 AAAAATTAAT
*
55695570 ATTTTTAATAATTTA
1 ATTTTTAAT-ACTTA
55695585 ATTTTTAATACTTA
1 ATTTTTAATACTTA
*
55695599 ATTTTTCAACACTT-
1 ATTTTT-AATACTTA
55695613 ATTTTT
1 ATTTTT
55695619 TCAACAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
14 16 0.52
15 15 0.48
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTTTTAATACTTA
Found at i:55695619 original size:15 final size:15
Alignment explanation
Indices: 55695582--55695624 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
55695572 TTTTAATAAT
*
55695582 TTAATTTTT-AATAC
1 TTAATTTTTCAACAC
55695596 TTAATTTTTCAACAC
1 TTAATTTTTCAACAC
*
55695611 TTATTTTTTCAACA
1 TTAATTTTTCAACA
55695625 AATAGCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATTTTTCAACAC
Found at i:55697573 original size:30 final size:29
Alignment explanation
Indices: 55697537--55697598 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 29
55697527 TATTATTTTG
*
55697537 AAAAATATATAAAAGCCTATAATATATATA
1 AAAAATATATAAAAACCTATAAT-TATATA
* *
55697567 AAAAATATATAAAAACGTATAATTTTATA
1 AAAAATATATAAAAACCTATAATTATATA
55697596 AAA
1 AAA
55697599 GTATGTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (29 bp):
AAAAATATATAAAAACCTATAATTATATA
Found at i:55697643 original size:23 final size:24
Alignment explanation
Indices: 55697606--55697661 Score: 80
Period size: 23 Copynumber: 2.3 Consensus size: 24
55697596 AAAGTATGTA
55697606 TTATAAAAAATTATAGTA-TATAAAT
1 TTAT-AAAAATTATA-TATTATAAAT
55697631 TTATAAAAA-TATATATTATAAAT
1 TTATAAAAATTATATATTATAAAT
55697654 TTATAAAA
1 TTATAAAA
55697662 TGTATTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 2 0.07
23 19 0.63
24 5 0.17
25 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
TTATAAAAATTATATATTATAAAT
Found at i:55703334 original size:47 final size:47
Alignment explanation
Indices: 55703280--55703373 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
55703270 TCATGCATGT
55703280 AAATTTTTAAAATCGGTTCAATATCT-TCATCATATTGATCTAAAAAG
1 AAATTTTTAAAATCGGTTCAATATCTCT-ATCATATTGATCTAAAAAG
55703327 AAATTTTTAAAATCGGTTCAATATCTCTATCATATTGATCTAAAAAG
1 AAATTTTTAAAATCGGTTCAATATCTCTATCATATTGATCTAAAAAG
55703374 GTGTATATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
47 45 0.98
48 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (47 bp):
AAATTTTTAAAATCGGTTCAATATCTCTATCATATTGATCTAAAAAG
Found at i:55704520 original size:16 final size:16
Alignment explanation
Indices: 55704499--55704529 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
55704489 AAAATCCTCA
55704499 ACTCTTTCATCGAATG
1 ACTCTTTCATCGAATG
55704515 ACTCTTTCATCGAAT
1 ACTCTTTCATCGAAT
55704530 AATATTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.39
Consensus pattern (16 bp):
ACTCTTTCATCGAATG
Found at i:55706189 original size:16 final size:17
Alignment explanation
Indices: 55706157--55706189 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
55706147 TAACCAAACA
55706157 TAAAACAAGAACACACAC
1 TAAAACAAG-ACACACAC
55706175 TAAAACAAG-CACACA
1 TAAAACAAGACACACA
55706190 AAGCAGATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.61, C:0.27, G:0.06, T:0.06
Consensus pattern (17 bp):
TAAAACAAGACACACAC
Found at i:55709351 original size:29 final size:29
Alignment explanation
Indices: 55709291--55709351 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
55709281 GGCCTATTTC
** *
55709291 CCTAATTAATTTTAAAACGGGCCTAAATG
1 CCTAATTAATTAAAAAACGGGCCTAAAGG
*
55709320 CCTAATTAATTAAAAAAAC-GGCCTATAGG
1 CCTAATTAATT-AAAAAACGGGCCTAAAGG
55709349 CCT
1 CCT
55709352 TACTTTGCCC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (29 bp):
CCTAATTAATTAAAAAACGGGCCTAAAGG
Found at i:55709811 original size:20 final size:22
Alignment explanation
Indices: 55709772--55709811 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
55709762 CAAAATTAAT
*
55709772 AAACTTTTATTATGAATTAGAC
1 AAACTTTAATTATGAATTAGAC
55709794 AAACTTTAATT-T-AATTAG
1 AAACTTTAATTATGAATTAG
55709812 TAGTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 1 0.06
22 10 0.59
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.42
Consensus pattern (22 bp):
AAACTTTAATTATGAATTAGAC
Found at i:55714295 original size:30 final size:31
Alignment explanation
Indices: 55714232--55714298 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
55714222 ATATGTTGAT
** *
55714232 AGTCCTTATACTTTGATAAAATTTGAGATTA
1 AGTCCTTATACTTTGATAAAATTAAAAATTA
55714263 AGTCCTTATA-TTT-ATAAAAGTTAAAAATTA
1 AGTCCTTATACTTTGATAAAA-TTAAAAATTA
55714293 AGTCCT
1 AGTCCT
55714299 CCTAGTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 6 0.19
30 16 0.50
31 10 0.31
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.40
Consensus pattern (31 bp):
AGTCCTTATACTTTGATAAAATTAAAAATTA
Found at i:55716768 original size:9 final size:9
Alignment explanation
Indices: 55716750--55716796 Score: 85
Period size: 9 Copynumber: 5.2 Consensus size: 9
55716740 TTGAGTTTTC
55716750 TAATTCGAA
1 TAATTCGAA
*
55716759 TAACTCGAA
1 TAATTCGAA
55716768 TAATTCGAA
1 TAATTCGAA
55716777 TAATTCGAA
1 TAATTCGAA
55716786 TAATTCGAA
1 TAATTCGAA
55716795 TA
1 TA
55716797 TCAAAATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.32
Consensus pattern (9 bp):
TAATTCGAA
Found at i:55716873 original size:21 final size:21
Alignment explanation
Indices: 55716832--55716874 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
55716822 ACCCCAAACT
* *
55716832 CCCAAACCTTTTTACTTTTCC
1 CCCAAAACTTTTTACTCTTCC
55716853 CCCAAAAC-TTTTACTCCTTCC
1 CCCAAAACTTTTTACT-CTTCC
55716874 C
1 C
55716875 ACTTCCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (21 bp):
CCCAAAACTTTTTACTCTTCC
Found at i:55718944 original size:12 final size:12
Alignment explanation
Indices: 55718920--55718955 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
55718910 TGACCTGCCC
55718920 ATATTACTTTTTT
1 ATATTA-TTTTTT
55718933 ATATTATTTTTT
1 ATATTATTTTTT
*
55718945 ATATAATTTTT
1 ATATTATTTTT
55718956 AAATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 16 0.73
13 6 0.27
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (12 bp):
ATATTATTTTTT
Found at i:55719009 original size:25 final size:24
Alignment explanation
Indices: 55718981--55719028 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
55718971 ATCAAAAATA
*
55718981 CCAAAAATATT-AAATTAAATATTTC
1 CCAAAAA-ATTGAAAATAAA-ATTTC
55719006 CCAAAAAATTGAAAATAAAATTT
1 CCAAAAAATTGAAAATAAAATTT
55719029 TAAAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (24 bp):
CCAAAAAATTGAAAATAAAATTTC
Found at i:55727029 original size:51 final size:51
Alignment explanation
Indices: 55726878--55727185 Score: 422
Period size: 51 Copynumber: 6.2 Consensus size: 51
55726868 CTTACGTATG
*
55726878 ATCACTTATCACTTGTC-CTTGATCAGATAAGTGTAGCT-AAGCTACCACTT
1 ATCACTTGTCACTTGTCAC-TGATCAGATAAGTGTAGCTAAAGCTACCACTT
* * *
55726928 ATCACTTGCCGCTTGTCACTGATCAGATAAGTGTAGCTAATGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
*
55726979 ATCACTTG-C-C--G---CTGATCAGATAAGTGTAGCTGAAA-CTATCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCT-AAAGCTACCACTT
*
55727023 ATCACTTGTCACTTGTCACTGATTAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* * *
55727074 ATCACTTGCCGCTTGTCACTGATCAGATAAGTGTAGCTGAAA-CTATCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCT-AAAGCTACCACTT
*
55727125 ATCACTTGTCACTTGTCACTGATTAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
55727176 ATCACTTGTC
1 ATCACTTGTC
55727186 CCTGATCAGA
Statistics
Matches: 229, Mismatches: 16, Indels: 25
0.85 0.06 0.09
Matches are distributed among these distances:
44 36 0.16
45 3 0.01
46 1 0.00
47 1 0.00
48 1 0.00
49 1 0.00
50 40 0.17
51 143 0.62
52 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.32
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
Found at i:55727053 original size:95 final size:95
Alignment explanation
Indices: 55726880--55727195 Score: 474
Period size: 102 Copynumber: 3.3 Consensus size: 95
55726870 TACGTATGAT
* * * * *
55726880 CACTTATCACTTGTCCTTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTGCCGCTTGT
1 CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCTGAAACTATCACTTATCACTTGTCACTTGT
* *
55726944 CACTGATCAGATAAGTGTAGCTAATGCTAC
66 CACTGATTAGATAAGTGTAGCTAAAGCTAC
55726974 CACTTATCACTTG-CCGCTGATCAGATAAGTGTAGCTGAAACTATCACTTATCACTTGTCACTTG
1 CACTTATCACTTGTCC-CTGATCAGATAAGTGTAGCTGAAACTATCACTTATCACTTGTCACTTG
55727038 TCACTGATTAGATAAGTGTAGCTAAAGCTAC
65 TCACTGATTAGATAAGTGTAGCTAAAGCTAC
*
55727069 CACTTATCACTTGCCGCTTGTCACTGATCAGATAAGTGTAGCTGAAACTATCACTTATCACTTGT
1 CACTTATCA-------CTTGTCCCTGATCAGATAAGTGTAGCTGAAACTATCACTTATCACTTGT
55727134 CACTTGTCACTGATTAGATAAGTGTAGCTAAAGCTAC
59 CACTTGTCACTGATTAGATAAGTGTAGCTAAAGCTAC
55727171 CACTTATCACTTGTCCCTGATCAGA
1 CACTTATCACTTGTCCCTGATCAGA
55727196 AGTACTCAAA
Statistics
Matches: 203, Mismatches: 9, Indels: 19
0.88 0.04 0.08
Matches are distributed among these distances:
93 2 0.01
94 32 0.16
95 76 0.37
102 92 0.45
103 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (95 bp):
CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCTGAAACTATCACTTATCACTTGTCACTTGT
CACTGATTAGATAAGTGTAGCTAAAGCTAC
Found at i:55730854 original size:31 final size:30
Alignment explanation
Indices: 55730757--55730858 Score: 105
Period size: 31 Copynumber: 3.3 Consensus size: 30
55730747 AAAAACCATA
* *
55730757 AAGTTTAGGCCTTAATGTGGGAACAATTATC
1 AAGTTCAGGCCTCAATGT-GGAACAATTATC
* * * * *
55730788 AAGCTCAAGCCCCAATGTGGAAACAATCATT
1 AAGTTCAGGCCTCAATGTGG-AACAATTATC
*
55730819 AAGTTCAGGCCTCAATGTGAGAACAATTGTC
1 AAGTTCAGGCCTCAATGTG-GAACAATTATC
55730850 AAGTTCAGG
1 AAGTTCAGG
55730859 GATTAACTTG
Statistics
Matches: 56, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
30 2 0.04
31 53 0.95
32 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (30 bp):
AAGTTCAGGCCTCAATGTGGAACAATTATC
Found at i:55734034 original size:29 final size:29
Alignment explanation
Indices: 55733984--55734040 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
55733974 TCCAATCCTA
*
55733984 TGTACATGCATAATTACAAAATTCATGCT
1 TGTACATGCATAATTACAAAATACATGCT
* *
55734013 TGTACATGCGTTAA-TACCAAATACATGC
1 TGTACATGC-ATAATTACAAAATACATGC
55734041 ATCTAATCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (29 bp):
TGTACATGCATAATTACAAAATACATGCT
Found at i:55745168 original size:25 final size:21
Alignment explanation
Indices: 55745123--55745164 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
55745113 TCTCTATAAT
55745123 CACTTCATCCTAAAAAAAGAA
1 CACTTCATCCTAAAAAAAGAA
55745144 CACTTCATCCTAAAAAAAGAA
1 CACTTCATCCTAAAAAAAGAA
55745165 AGAAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.05, T:0.19
Consensus pattern (21 bp):
CACTTCATCCTAAAAAAAGAA
Found at i:55746384 original size:24 final size:24
Alignment explanation
Indices: 55746351--55746430 Score: 79
Period size: 26 Copynumber: 3.2 Consensus size: 24
55746341 TAAACATTAA
* **
55746351 AAAATGTTAAAAATTACTATATAT
1 AAAATTTTAAAAATTAAAATATAT
*
55746375 AAAATTTTAATAAATAAAAAATATAT
1 AAAATTTTAA-AAAT-TAAAATATAT
*
55746401 AACATTATTAAAAATTAAAATAATAT
1 AAAATT-TTAAAAATTAAAAT-ATAT
55746427 AAAA
1 AAAA
55746431 ATATTTATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
24 9 0.20
25 9 0.20
26 23 0.51
27 4 0.09
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (24 bp):
AAAATTTTAAAAATTAAAATATAT
Found at i:55746398 original size:26 final size:27
Alignment explanation
Indices: 55746369--55746437 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
55746359 AAAAATTACT
55746369 ATATATAAAATTTTAATAAA-TAAAA-A
1 ATATATAAAATTTTAA-AAATTAAAATA
*
55746395 ATATATAACATTATTAAAAATTAAAATA
1 ATATATAAAATT-TTAAAAATTAAAATA
55746423 ATATA-AAAATATTTA
1 ATATATAAAAT-TTTA
55746438 TATTTTTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
26 14 0.38
27 16 0.43
28 7 0.19
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (27 bp):
ATATATAAAATTTTAAAAATTAAAATA
Found at i:55747595 original size:22 final size:23
Alignment explanation
Indices: 55747555--55747598 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
55747545 AAGAATCCGA
*
55747555 AATTAAACTATATATTTTTACAAG
1 AATTAAAC-ATATAATTTTACAAG
55747579 AATTAAA-ATATAATTTTACA
1 AATTAAACATATAATTTTACA
55747599 GTTTTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
24 7 0.37
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (23 bp):
AATTAAACATATAATTTTACAAG
Found at i:55749225 original size:8 final size:8
Alignment explanation
Indices: 55749212--55749239 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
55749202 TGTTAAAAAA
55749212 ATATTATT
1 ATATTATT
55749220 ATATTATT
1 ATATTATT
55749228 ATATTATT
1 ATATTATT
55749236 ATAT
1 ATAT
55749240 GTATATAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
ATATTATT
Found at i:55750399 original size:25 final size:24
Alignment explanation
Indices: 55750332--55750463 Score: 153
Period size: 25 Copynumber: 5.5 Consensus size: 24
55750322 ACTTTAGCGC
*
55750332 GCTCTCTGATATTAGTACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
55750356 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
55750380 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGA-TATTAGCACGTTGGT
* ***
55750405 GCTCACTGATATTTAGCACGGCAGT
1 GCTCTCTGATA-TTAGCACGTTGGT
* * *
55750430 ACTCTCTG-T-TTAGCACATTTGT
1 GCTCTCTGATATTAGCACGTTGGT
55750452 GCTCTCTG-TATT
1 GCTCTCTGATATT
55750464 TGTTCCGTAT
Statistics
Matches: 93, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
22 17 0.18
23 2 0.02
24 35 0.38
25 39 0.42
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.39
Consensus pattern (24 bp):
GCTCTCTGATATTAGCACGTTGGT
Found at i:55750953 original size:17 final size:17
Alignment explanation
Indices: 55750931--55750964 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
55750921 ATGTGGCATG
*
55750931 TACCTAGGTAATGTATA
1 TACCTAAGTAATGTATA
*
55750948 TACCTAAGTGATGTATA
1 TACCTAAGTAATGTATA
55750965 GGGATTAGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (17 bp):
TACCTAAGTAATGTATA
Found at i:55753212 original size:25 final size:24
Alignment explanation
Indices: 55753184--55753253 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 24
55753174 GTTTTTTAAT
55753184 TTTTATAATATATCATATTAAATTA
1 TTTTATAATATATCATATTAAA-TA
*
55753209 TTTT-TACATAT-TACATATTATATA
1 TTTTATA-ATATAT-CATATTAAATA
*
55753233 ATTTATAATATAT-ATAATTAA
1 TTTTATAATATATCAT-ATTAA
55753254 TAGACTTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
23 2 0.05
24 16 0.43
25 19 0.51
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTTATAATATATCATATTAAATA
Found at i:55754740 original size:30 final size:32
Alignment explanation
Indices: 55754688--55754765 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 32
55754678 CATTTTTTAA
55754688 TAAACATTAAAAATATTTTAAAAA-TAAAAAAT
1 TAAA-ATTAAAAATATTTTAAAAATTAAAAAAT
*
55754720 TAAAATTAAAAGTA-TTTAAAAATTAAAAAAT
1 TAAAATTAAAAATATTTTAAAAATTAAAAAAT
* *
55754751 AAAAATAAAAAATAT
1 TAAAATTAAAAATAT
55754766 ATATTTATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
30 8 0.20
31 28 0.70
32 4 0.10
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (32 bp):
TAAAATTAAAAATATTTTAAAAATTAAAAAAT
Found at i:55755087 original size:24 final size:25
Alignment explanation
Indices: 55755011--55755088 Score: 69
Period size: 24 Copynumber: 3.3 Consensus size: 25
55755001 GTCATCATCT
55755011 CAAAATTAAATAAA-AAAT-TATTA
1 CAAAATTAAATAAATAAATATATTA
* * *
55755034 -ATAAATTTAAATATATATATA-ATAA
1 CA-AAA-TTAAATAAATAAATATATTA
55755059 C-AAA-TAAATAAATAAATATATTA
1 CAAAATTAAATAAATAAATATATTA
55755082 CAAAATT
1 CAAAATT
55755089 TAAAAAAACT
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 13 0.32
23 7 0.17
24 14 0.34
25 7 0.17
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (25 bp):
CAAAATTAAATAAATAAATATATTA
Found at i:55768768 original size:30 final size:30
Alignment explanation
Indices: 55768734--55768791 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
55768724 ACGCGTGTTA
55768734 TTATTAATTTTAAATACTATATTT-TATTAT
1 TTATTAATTTTAAATA-TATATTTATATTAT
*
55768764 TTATTATTTTTAAATATATATTTATATT
1 TTATTAATTTTAAATATATATTTATATT
55768792 TTAAATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (30 bp):
TTATTAATTTTAAATATATATTTATATTAT
Found at i:55768806 original size:20 final size:18
Alignment explanation
Indices: 55768767--55768802 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
55768757 TTATTATTTA
*
55768767 TTATTTTTAAATATATAT
1 TTATTTTTAAATAAATAT
55768785 TTATATTTTAAATAAATA
1 TTAT-TTTTAAATAAATA
55768803 ATTTTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTATTTTTAAATAAATAT
Found at i:55774767 original size:2 final size:2
Alignment explanation
Indices: 55774760--55774784 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55774750 AAGATGTTAC
55774760 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
55774785 GAATTGGATG
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:55776943 original size:26 final size:27
Alignment explanation
Indices: 55776914--55776966 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
55776904 TCATTAGTTC
* *
55776914 AATTATCGGTTCAATCAATCT-ATATT
1 AATTATCAGATCAATCAATCTAATATT
*
55776940 AATTCTCAGATCAATCAATCTAATATT
1 AATTATCAGATCAATCAATCTAATATT
55776967 TCTCTCTAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.40
Consensus pattern (27 bp):
AATTATCAGATCAATCAATCTAATATT
Found at i:55783494 original size:24 final size:23
Alignment explanation
Indices: 55783467--55783516 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
55783457 TAATATATAT
*
55783467 AATATTATCTAAATTAATTTTTCA
1 AATATT-TCTAAATTAAATTTTCA
* *
55783491 AATATTTTTATATTAAATTTTCA
1 AATATTTCTAAATTAAATTTTCA
55783514 AAT
1 AAT
55783517 CAAATTCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTCTAAATTAAATTTTCA
Found at i:55784310 original size:20 final size:20
Alignment explanation
Indices: 55784264--55784313 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
55784254 TTACATCAGT
** *
55784264 TTTTTTTCTCTTGAATTTTA
1 TTTTTTTCAGTTGAATTTAA
* *
55784284 GTATTTTCAGTTGAATTTAA
1 TTTTTTTCAGTTGAATTTAA
55784304 TTTTTTTCAG
1 TTTTTTTCAG
55784314 GAAGAAAATG
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.08, G:0.10, T:0.62
Consensus pattern (20 bp):
TTTTTTTCAGTTGAATTTAA
Found at i:55791111 original size:20 final size:19
Alignment explanation
Indices: 55791066--55791107 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
55791056 TGAAAGAAAT
*
55791066 AAAA-ATTTAAAAATTATG
1 AAAATATTTAAAAAATATG
55791084 AAAATATTTAAAAAA-ATAG
1 AAAATATTTAAAAAATAT-G
55791103 AAAAT
1 AAAAT
55791108 TATTAAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
AAAATATTTAAAAAATATG
Found at i:55791208 original size:20 final size:21
Alignment explanation
Indices: 55791171--55791210 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
55791161 TAAAAATTGT
55791171 AAAACAAATTAAAAATATATG
1 AAAACAAATTAAAAATATATG
* *
55791192 AAAA-AAATTATATATATAT
1 AAAACAAATTAAAAATATAT
55791211 ATATATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (21 bp):
AAAACAAATTAAAAATATATG
Found at i:55791602 original size:19 final size:18
Alignment explanation
Indices: 55791574--55791615 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
55791564 TGTTTTTGTT
* *
55791574 ATTTTAATATTTTTTGAA
1 ATTTTAATATATTTTAAA
55791592 ATTTTATATATATTTTAAA
1 ATTTTA-ATATATTTTAAA
55791611 ATTTT
1 ATTTT
55791616 GTACATCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
ATTTTAATATATTTTAAA
Found at i:55793370 original size:15 final size:16
Alignment explanation
Indices: 55793342--55793372 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
55793332 ACCACTTTTT
55793342 TGGCCCGAGCCCGGCC
1 TGGCCCGAGCCCGGCC
55793358 TGGCCCG-GCCCGGCC
1 TGGCCCGAGCCCGGCC
55793373 CGATATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.03, C:0.52, G:0.39, T:0.06
Consensus pattern (16 bp):
TGGCCCGAGCCCGGCC
Found at i:55793424 original size:19 final size:18
Alignment explanation
Indices: 55793392--55793513 Score: 113
Period size: 19 Copynumber: 6.6 Consensus size: 18
55793382 AAATATATTT
55793392 ATTTTAAAAT-TTTTTTA
1 ATTTTAAAATATTTTTTA
55793409 ATTTTAAAATATTTTTAAATA
1 ATTTTAAAATATTTTT---TA
* ****
55793430 CTTTTTTCTTATTTTTTA
1 ATTTTAAAATATTTTTTA
**
55793448 ATTTTAAAATGATTTTAAA
1 ATTTTAAAAT-ATTTTTTA
55793467 ATTTTAAAAT-TTTTTTA
1 ATTTTAAAATATTTTTTA
55793484 ATTTTAAAATATTTTTTA
1 ATTTTAAAATATTTTTTA
*
55793502 CTTTTTAAAATA
1 -ATTTTAAAATA
55793514 AATTTTTGGT
Statistics
Matches: 83, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
17 25 0.30
18 19 0.23
19 26 0.31
21 13 0.16
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (18 bp):
ATTTTAAAATATTTTTTA
Found at i:55799309 original size:24 final size:25
Alignment explanation
Indices: 55799263--55799314 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
55799253 TAGAAATGAA
* *
55799263 AAATAAATTAATTTAGATAATATTT
1 AAATAAATTAATATAGATAATATAT
* *
55799288 AAATAATTTAATATA-ATTATATAT
1 AAATAAATTAATATAGATAATATAT
55799312 AAA
1 AAA
55799315 ATATACATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
AAATAAATTAATATAGATAATATAT
Found at i:55806951 original size:2 final size:2
Alignment explanation
Indices: 55806940--55806987 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
55806930 TCAACACCAA
55806940 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
55806981 TC TC TC T
1 TC TC TC T
55806988 ATTTTGTTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:55814461 original size:22 final size:21
Alignment explanation
Indices: 55814427--55814469 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
55814417 CTTGAAATTT
* *
55814427 ATAAATTTTATTTTACTTAAAA
1 ATAAAATTAATTTTAC-TAAAA
55814449 ATAAAATTAATTTTACTAAAA
1 ATAAAATTAATTTTACTAAAA
55814470 TTTGAAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAAAATTAATTTTACTAAAA
Found at i:55822262 original size:13 final size:13
Alignment explanation
Indices: 55822244--55822270 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55822234 TGTGAGATTC
55822244 ATCTATAATTGTG
1 ATCTATAATTGTG
55822257 ATCTATAATTGTG
1 ATCTATAATTGTG
55822270 A
1 A
55822271 ACAATATGCT
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:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (13 bp):
ATCTATAATTGTG
Found at i:55827695 original size:37 final size:37
Alignment explanation
Indices: 55827645--55827720 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
55827635 ATCATTCGGT
55827645 CTTGGAATCAAATTCCAATCTAATAGGATCAATATTC
1 CTTGGAATCAAATTCCAATCTAATAGGATCAATATTC
* * *
55827682 CTTGGAATCAAATTCCAGTTTAATAGTATCAATATTC
1 CTTGGAATCAAATTCCAATCTAATAGGATCAATATTC
55827719 CT
1 CT
55827721 ACACCAAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (37 bp):
CTTGGAATCAAATTCCAATCTAATAGGATCAATATTC
Found at i:55829606 original size:12 final size:13
Alignment explanation
Indices: 55829589--55829618 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
55829579 TCGAGGAAGG
55829589 AAGGGTGATAT-T
1 AAGGGTGATATAT
55829601 AAGGGTGATATAT
1 AAGGGTGATATAT
55829614 AAGGG
1 AAGGG
55829619 GCTTCCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.27
Consensus pattern (13 bp):
AAGGGTGATATAT
Found at i:55834315 original size:21 final size:22
Alignment explanation
Indices: 55834286--55834332 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
55834276 CAGAAGGAGT
*
55834286 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
55834308 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
55834329 GAGT
1 GAGT
55834333 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:55839993 original size:21 final size:21
Alignment explanation
Indices: 55839967--55840007 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
55839957 ATCTGCTCAA
* *
55839967 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
55839988 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
55840008 TTGCTCGTCT
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:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:55846081 original size:27 final size:27
Alignment explanation
Indices: 55846043--55846096 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
55846033 TAGATTCTTC
**
55846043 CTAATATCTTCTACATGGAGTATATTG
1 CTAATATCTTCTACATAAAGTATATTG
*
55846070 CTAATATCTTCTGCATAAAGTATATTG
1 CTAATATCTTCTACATAAAGTATATTG
55846097 TTAAGGGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (27 bp):
CTAATATCTTCTACATAAAGTATATTG
Found at i:55846947 original size:17 final size:17
Alignment explanation
Indices: 55846925--55846958 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
55846915 ATCCACTAAT
*
55846925 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
55846942 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
55846959 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:55851586 original size:17 final size:17
Alignment explanation
Indices: 55851564--55851597 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
55851554 ATCCACTAAT
*
55851564 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
55851581 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
55851598 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:55856101 original size:24 final size:24
Alignment explanation
Indices: 55856073--55856125 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
55856063 ATTCGTACGT
** *
55856073 TAAATAAATTATGCTAATAAATGC
1 TAAATAAATTAAACTAATAAATAC
*
55856097 TAAATATATTAAACTAATAAATAC
1 TAAATAAATTAAACTAATAAATAC
55856121 TAAAT
1 TAAAT
55856126 CTTTTAGGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.34
Consensus pattern (24 bp):
TAAATAAATTAAACTAATAAATAC
Found at i:55857189 original size:22 final size:21
Alignment explanation
Indices: 55857123--55857192 Score: 86
Period size: 23 Copynumber: 3.2 Consensus size: 21
55857113 TCATCCTAAA
*
55857123 CCAAGCCTAAACCAACCTAGC
1 CCAATCCTAAACCAACCTAGC
55857144 CCAATACCCTAAACCAACCTAGC
1 CCAAT--CCTAAACCAACCTAGC
* *
55857167 CCAATCCTAAAACTACCTGAGC
1 CCAATCCTAAACCAACCT-AGC
55857189 CCAA
1 CCAA
55857193 ATTTTAAAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 15 0.35
22 7 0.16
23 21 0.49
ACGTcount: A:0.39, C:0.41, G:0.07, T:0.13
Consensus pattern (21 bp):
CCAATCCTAAACCAACCTAGC
Found at i:55870373 original size:44 final size:44
Alignment explanation
Indices: 55870306--55870548 Score: 184
Period size: 44 Copynumber: 5.5 Consensus size: 44
55870296 AAGTCATTAA
* * * * *
55870306 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAT
1 AGCAGATCCTATCTTCCTATATTGGCATGAAGTAGATCGAAGAT
* * * *
55870350 ATCAGATCCTATCTTCCTATATTGGTAAGAAGTGGATCGAAGAT
1 AGCAGATCCTATCTTCCTATATTGGCATGAAGTAGATCGAAGAT
* * * *** *
55870394 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
1 AGCAGATCCTATCTTCCTATATTGG-CATGAAGTAGATCGAAGAT
* * * * * *
55870438 AGCAGATCTTGTCTTCATGTGTTGGCATGAAGTAGATCAAAGAT
1 AGCAGATCCTATCTTCCTATATTGGCATGAAGTAGATCGAAGAT
* ** * * *
55870482 AGCAGGTCCTATCTTCCTATATTGATAGGAAGTGGATCCAAGAT
1 AGCAGATCCTATCTTCCTATATTGGCATGAAGTAGATCGAAGAT
* * *
55870526 -GCAGATCTTGTCTTCCCATATTG
1 AGCAGATCCTATCTTCCTATATTG
55870549 ATGGCGAAGT
Statistics
Matches: 155, Mismatches: 42, Indels: 5
0.77 0.21 0.02
Matches are distributed among these distances:
43 39 0.25
44 96 0.62
45 20 0.13
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (44 bp):
AGCAGATCCTATCTTCCTATATTGGCATGAAGTAGATCGAAGAT
Found at i:55870453 original size:88 final size:88
Alignment explanation
Indices: 55870306--55870548 Score: 231
Period size: 88 Copynumber: 2.8 Consensus size: 88
55870296 AAGTCATTAA
* * * * * * *
55870306 AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATATCAGATCCTATCTTCCTAT
1 AGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCCTAT
* * *
55870370 ATTGGTAAGAAGTGGATCGAAGAT
65 ATTGGCAAGAAGTAGATCAAAGAT
* * * *
55870394 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGT
1 AGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCCTAT
* *
55870458 GTTGGCATGAAGTAGATCAAAGAT
65 ATTGGCAAGAAGTAGATCAAAGAT
* * * * * * * *
55870482 AGCAGGTCCTATCTTCCTATATTGATAGGAAGTGGATCCAAG-ATGCAGATCTTGTCTTCCCATA
1 AGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCCTATA
55870546 TTG
66 TTG
55870549 ATGGCGAAGT
Statistics
Matches: 124, Mismatches: 29, Indels: 5
0.78 0.18 0.03
Matches are distributed among these distances:
87 41 0.33
88 62 0.50
89 21 0.17
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (88 bp):
AGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCCTATA
TTGGCAAGAAGTAGATCAAAGAT
Found at i:55870541 original size:132 final size:132
Alignment explanation
Indices: 55870304--55870563 Score: 439
Period size: 132 Copynumber: 2.0 Consensus size: 132
55870294 TGAAGTCATT
* * *
55870304 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATATCAGATCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAGATCCTATCTTCCTA
* * *
55870369 TATTGGTAAGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
66 TATTGATAAGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGATGGCGAAGTAGATCGA
55870434 AG
131 AG
* *
55870436 AAAGCAGATCTTGTCTTCATGTGTTGGCATGAAGTAGATCAAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAGATCCTATCTTCCTA
*
55870501 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGATGGCGAAGTAGATC
66 TATTGATAAGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGATGGCGAAGTAGATC
55870564 TAAATTCGTA
Statistics
Matches: 119, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 119 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (132 bp):
AAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAGATCCTATCTTCCTA
TATTGATAAGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGATGGCGAAGTAGATCGA
AG
Found at i:55870604 original size:24 final size:24
Alignment explanation
Indices: 55870577--55870629 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
55870567 ATTCGTACGT
** *
55870577 TAAATAAATTATGCTAATAAATGC
1 TAAATAAATTAAACTAATAAATAC
*
55870601 TAAATATATTAAACTAATAAATAC
1 TAAATAAATTAAACTAATAAATAC
55870625 TAAAT
1 TAAAT
55870630 CTTTTAGGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.34
Consensus pattern (24 bp):
TAAATAAATTAAACTAATAAATAC
Found at i:55870773 original size:44 final size:44
Alignment explanation
Indices: 55870718--55871050 Score: 208
Period size: 44 Copynumber: 7.5 Consensus size: 44
55870708 CACTTGGTAG
* *
55870718 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGC
1 GAAGTAGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGT
* *** **
55870762 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CAT
1 GAAGTAGATCGAAG-ATGCAGATCTTGTCTTCCCATATTGGTGGT
* * * * *
55870806 GAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTC-TATTGATAG-
1 GAAGTAGATCGAAGAT-GCAGATCTTGTCTTCC-CATATTGGTGGT
* * * *
55870850 GAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGATGGC
1 GAAGTAGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGT
* * *** *
55870894 GAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGG-CGT
1 GAAGTAGATCGAAG-ATGCAGATCTTGTCTTCCCATATTGGTGGT
* * * * * * * * *
55870938 GAAGTAGATCAAAGATAACAGGTCCTATCTTCCTATAATGAATTG-
1 GAAGTAGATCGAAGAT-GCAGATCTTGTCTTCCCATATTG-GTGGT
* * * ** * *
55870983 GAAGTGGATCGACGACGCAGATCAAGTCTTCCCATACTAGTGGT
1 GAAGTAGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGT
*
55871027 GAAGTAGATCGAAGAAAGCAGATC
1 GAAGTAGATCGAAG-ATGCAGATC
55871051 GACGATGGCA
Statistics
Matches: 215, Mismatches: 62, Indels: 23
0.72 0.21 0.08
Matches are distributed among these distances:
42 1 0.00
43 25 0.12
44 125 0.58
45 63 0.29
46 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.27
Consensus pattern (44 bp):
GAAGTAGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGT
Found at i:55870953 original size:132 final size:133
Alignment explanation
Indices: 55870715--55871050 Score: 514
Period size: 132 Copynumber: 2.5 Consensus size: 133
55870705 GCACACTTGG
*
55870715 TAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
1 TAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGATGGCGAAGTAGATCGAAGAAAG
* * * *
55870780 CAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTCTATT
66 CAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAACAGGTCCTATCTTCCTATAAT
55870845 G-A
131 GAA
* *
55870847 TAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGATGGCGAAGTAGATCGCAGAAAG
1 TAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGATGGCGAAGTAGATCGAAGAAAG
*
55870912 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAACAGGTCCTATCTTCCTATAAT
66 CAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAACAGGTCCTATCTTCCTATAAT
55870977 GAA
131 GAA
* * * ** * *
55870980 TTGGAAGTGGATCGACGACGCAGATCAAGTCTTCCCATACT-AGTGGTGAAGTAGATCGAAGAAA
1 TAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGA-TGGCGAAGTAGATCGAAGAAA
55871044 GCAGATC
65 GCAGATC
55871051 GACGATGGCA
Statistics
Matches: 185, Mismatches: 17, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
132 124 0.67
133 61 0.33
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.27
Consensus pattern (133 bp):
TAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGATGGCGAAGTAGATCGAAGAAAG
CAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAACAGGTCCTATCTTCCTATAAT
GAA
Found at i:55872353 original size:22 final size:21
Alignment explanation
Indices: 55872287--55872356 Score: 86
Period size: 23 Copynumber: 3.2 Consensus size: 21
55872277 TCATCCTAAA
*
55872287 CCAAGCCTAAACCAACCTAGC
1 CCAATCCTAAACCAACCTAGC
55872308 CCAATACCCTAAACCAACCTAGC
1 CCAAT--CCTAAACCAACCTAGC
* *
55872331 CCAATCCTAAAACTACCTGAGC
1 CCAATCCTAAACCAACCT-AGC
55872353 CCAA
1 CCAA
55872357 ATTTTAAAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 15 0.35
22 7 0.16
23 21 0.49
ACGTcount: A:0.39, C:0.41, G:0.07, T:0.13
Consensus pattern (21 bp):
CCAATCCTAAACCAACCTAGC
Done.