Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 182 of 196
Found at i:53392318 original size:15 final size:15
Alignment explanation
Indices: 53392294--53392331 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
53392284 GTTTTTAGTC
53392294 TATT-TTATTAATTT
1 TATTATTATTAATTT
* *
53392308 TGTTATTATTATTTT
1 TATTATTATTAATTT
53392323 TATTATTAT
1 TATTATTAT
53392332 ATTATATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TATTATTATTAATTT
Found at i:53392325 original size:12 final size:12
Alignment explanation
Indices: 53392296--53392346 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 12
53392286 TTTTAGTCTA
53392296 TTTTATTAATT-T
1 TTTTATT-ATTAT
*
53392308 TGTTATTATTAT
1 TTTTATTATTAT
53392320 TTTTATTATTAT
1 TTTTATTATTAT
53392332 ATTATATATTATTAT
1 -TT-T-TATTATTAT
53392347 ACCTACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
11 3 0.09
12 18 0.55
13 2 0.06
14 1 0.03
15 9 0.27
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:53392341 original size:15 final size:13
Alignment explanation
Indices: 53392310--53392347 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
53392300 ATTAATTTTG
53392310 TTATTATTAT-TT
1 TTATTATTATATT
53392322 TTATTATTATATT
1 TTATTATTATATT
53392335 ATATATTATTATA
1 -T-TATTATTATA
53392348 CCTACATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.43
13 2 0.09
14 1 0.04
15 10 0.43
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATTATTATATT
Found at i:53395442 original size:33 final size:32
Alignment explanation
Indices: 53395298--53395450 Score: 99
Period size: 33 Copynumber: 4.6 Consensus size: 32
53395288 AGTGCCACAA
* * *
53395298 CCCAATTATGATCTTATCATCAGAATGCCATAG
1 CCCAACTATGGTCTTA-CATCAGAATGTCATAG
* * *
53395331 CCCAACTATGGTCTTACATATAAACACTGTCATGG
1 CCCAACTATGGTCTTACAT-CAGA-A-TGTCATAG
* * * * * *
53395366 TCCAACCATGGTCTTACGTTCATAGTGTCATAA
1 CCCAACTATGGTCTTAC-ATCAGAATGTCATAG
**
53395399 CCCAGTTATGGTCTTATCATCAGAATGTCATAG
1 CCCAACTATGGTCTTA-CATCAGAATGTCATAG
* * *
53395432 CTCAGCTATGGTTTTACAT
1 CCCAACTATGGTCTTACAT
53395451 ATAAACACTG
Statistics
Matches: 90, Mismatches: 25, Indels: 11
0.71 0.20 0.09
Matches are distributed among these distances:
32 6 0.07
33 58 0.64
34 2 0.02
35 23 0.26
36 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.33
Consensus pattern (32 bp):
CCCAACTATGGTCTTACATCAGAATGTCATAG
Found at i:53395467 original size:101 final size:101
Alignment explanation
Indices: 53395279--53395517 Score: 354
Period size: 101 Copynumber: 2.4 Consensus size: 101
53395269 AATTCATCCT
* * *
53395279 TTACATTC-TAGTGCCACAACCCAATTATGATCTTATCATCAGAATGCCATAGCCCAACTATGGT
1 TTACATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGT
53395343 CTTACATATAAACACTGTCATGGTCCAACCATGGTC
66 CTTACATATAAACACTGTCATGGTCCAACCATGGTC
* * * * *
53395379 TTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATCATCAGAATGTCATAGCTCAGCTATGGT
1 TTACATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGT
* * *
53395444 TTTACATATAAACACTGTTATGGTCCAACCATGGTG
66 CTTACATATAAACACTGTCATGGTCCAACCATGGTC
* *
53395480 TTACATTCATAGAGCCATAACCTAGTTATGGTCTTATC
1 TTACATTCATAGTGCCATAACCCAGTTATGGTCTTATC
53395518 TGTCAATTCA
Statistics
Matches: 123, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
100 7 0.06
101 116 0.94
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (101 bp):
TTACATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGT
CTTACATATAAACACTGTCATGGTCCAACCATGGTC
Found at i:53397431 original size:29 final size:29
Alignment explanation
Indices: 53397389--53397447 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
53397379 TATCAACTAT
* * *
53397389 TTAAACTAGTTAATTACATTATAAAAATA
1 TTAAACTAATTAATAACATAATAAAAATA
*
53397418 TTAAATTAATTAATAACATAATAAAAATA
1 TTAAACTAATTAATAACATAATAAAAATA
53397447 T
1 T
53397448 AGAGATAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAAACTAATTAATAACATAATAAAAATA
Found at i:53397738 original size:23 final size:24
Alignment explanation
Indices: 53397686--53397740 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
53397676 GGTAGTCTTT
*
53397686 TAAAAAGATTGTTTTAATTTTTTAA
1 TAAAAA-ATTGTTTTAATTTTATAA
*
53397711 GAAAAAA-TGTTTT-ATTTTATATA
1 TAAAAAATTGTTTTAATTTTATA-A
53397734 TAAAAAA
1 TAAAAAA
53397741 AGATAAAGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 7 0.27
23 13 0.50
24 1 0.04
25 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (24 bp):
TAAAAAATTGTTTTAATTTTATAA
Found at i:53398454 original size:14 final size:14
Alignment explanation
Indices: 53398436--53398475 Score: 50
Period size: 12 Copynumber: 3.1 Consensus size: 14
53398426 AATAATAAAA
53398436 ATATAATTTTATAT
1 ATATAATTTTATAT
*
53398450 TTATAA-TTTATA-
1 ATATAATTTTATAT
53398462 AT-TAATTTTATAT
1 ATATAATTTTATAT
53398475 A
1 A
53398476 AAAATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
11 3 0.14
12 7 0.32
13 7 0.32
14 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATATAATTTTATAT
Found at i:53398455 original size:25 final size:25
Alignment explanation
Indices: 53398427--53398474 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
53398417 AAATAATAAA
53398427 ATAA-TAAAAATATAATTTTATATTT
1 ATAATTAAAAAT-TAATTTTATATTT
* *
53398452 ATAATTTATAATTAATTTTATAT
1 ATAATTAAAAATTAATTTTATAT
53398475 AAAAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATAATTAAAAATTAATTTTATATTT
Found at i:53401174 original size:29 final size:31
Alignment explanation
Indices: 53401105--53401179 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 31
53401095 ATATTTTTCC
*
53401105 ATAT-ATTAATATAAACACGGTTTTCTCATT
1 ATATAATTAATATAAACACGGTTTTCTCATA
* ** *
53401135 ATATATTTAATATAAACA-TTTTTTTTCATA
1 ATATAATTAATATAAACACGGTTTTCTCATA
53401165 AT-TAATTAATATAAA
1 ATATAATTAATATAAA
53401180 AATGTTCCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 12 0.32
30 14 0.37
31 12 0.32
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.47
Consensus pattern (31 bp):
ATATAATTAATATAAACACGGTTTTCTCATA
Found at i:53408508 original size:2 final size:2
Alignment explanation
Indices: 53408501--53408537 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
53408491 GATGGTACAT
53408501 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
53408538 GCATCCTTTT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:53418263 original size:13 final size:14
Alignment explanation
Indices: 53418220--53418269 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
53418210 TGATCTTTTG
* *
53418220 GTTTAGAGTTTCAA
1 GTTTAGATTTTGAA
*
53418234 GTTTCA-AATTTGAA
1 GTTT-AGATTTTGAA
53418248 GTTTAGATTTTG-A
1 GTTTAGATTTTGAA
53418261 GTTTAGATT
1 GTTTAGATT
53418270 CTAAGTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 11 0.35
14 19 0.61
15 1 0.03
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.48
Consensus pattern (14 bp):
GTTTAGATTTTGAA
Found at i:53420225 original size:188 final size:188
Alignment explanation
Indices: 53419978--53420345 Score: 445
Period size: 188 Copynumber: 2.0 Consensus size: 188
53419968 CTTTTATTTA
* * ** *
53419978 ATATGAAAAAATATTTAGTATACTGTCTGTGGAGTTTTTAAACTCCACAGGTCGGGTCAA-AGGT
1 ATATGAAAAAATATTTAGTACACTGTCTATGGAGTTTTTAAACTCCACAAATAGGGTCAAGA-GT
* * * * * **
53420042 TGACAAGTGTTCTATAAGAATATAGTAAAATATTTTAA-AAAATAGACACATGGTAATTTTTTAA
65 TAACAAGTGTCCTATAAGAATATAGTAAAATATTTAAATAAAACAAACACATGACAATTTTTTAA
*
53420106 GGCTACTTATAGAATAAAAAAAAGTACACTACCAGTGAACCAATTACTAACCTATTTAAT
130 GGCTACTTATAGAATAAAAAAAA-TACACTACCAATGAACCAATTACTAACCTATTTAAT
* * *
53420166 ATATGAAATAATATTTGGTACACTGT-TAATGGAGTTTTTAAACTTCACAAATAGGGTCAAGAGT
1 ATATGAAAAAATATTTAGTACACTGTCT-ATGGAGTTTTTAAACTCCACAAATAGGGTCAAGAGT
* ** *
53420230 TAACAAGTGTCCTATAGGGGTATAGTAAAATATTTAAATAAAACAAACACATTACAATTTTTTAA
65 TAACAAGTGTCCTATAAGAATATAGTAAAATATTTAAATAAAACAAACACATGACAATTTTTTAA
* * * * * * *
53420295 GGTTGCTTGTGGAATAAAAAAAATACATTATCAATGTACCAATTACTAACC
130 GGCTACTTATAGAATAAAAAAAATACACTACCAATGAACCAATTACTAACC
53420346 CTTAATATAT
Statistics
Matches: 150, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
187 1 0.01
188 108 0.72
189 41 0.27
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (188 bp):
ATATGAAAAAATATTTAGTACACTGTCTATGGAGTTTTTAAACTCCACAAATAGGGTCAAGAGTT
AACAAGTGTCCTATAAGAATATAGTAAAATATTTAAATAAAACAAACACATGACAATTTTTTAAG
GCTACTTATAGAATAAAAAAAATACACTACCAATGAACCAATTACTAACCTATTTAAT
Found at i:53421127 original size:38 final size:39
Alignment explanation
Indices: 53421084--53421174 Score: 98
Period size: 38 Copynumber: 2.4 Consensus size: 39
53421074 AATTTATTTT
* ***
53421084 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA-T-A
1 AAAAATTAAAAAAAATATTTTAAAAAT-TAAAAAAATTAA
*
53421122 AAAAA-TAATAAAAAATATTTTTAAAATTAAAAAAATTAA
1 AAAAATTAA-AAAAAATATTTTAAAAATTAAAAAAATTAA
53421161 AAAAATTAAAAAAA
1 AAAAATTAAAAAAA
53421175 TTTAAAAGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
37 8 0.18
38 22 0.50
39 11 0.25
40 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (39 bp):
AAAAATTAAAAAAAATATTTTAAAAATTAAAAAAATTAA
Found at i:53421165 original size:10 final size:9
Alignment explanation
Indices: 53421144--53421181 Score: 67
Period size: 9 Copynumber: 4.1 Consensus size: 9
53421134 AAATATTTTT
53421144 AAAATTAAA
1 AAAATTAAA
53421153 AAAATTAAA
1 AAAATTAAA
53421162 AAAATTAAA
1 AAAATTAAA
53421171 AAAATTTAAA
1 AAAA-TTAAA
53421181 A
1 A
53421182 GATTTATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
9 22 0.79
10 6 0.21
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAATTAAA
Found at i:53421186 original size:9 final size:9
Alignment explanation
Indices: 53421144--53421187 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
53421134 AAATATTTTT
*
53421144 AAAATTAAA
1 AAAATTTAA
*
53421153 AAAATTAAA
1 AAAATTTAA
*
53421162 AAAATTAAA
1 AAAATTTAA
53421171 AAAATTTAA
1 AAAATTTAA
*
53421180 AAGATTTA
1 AAAATTTA
53421188 TTATATCGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (9 bp):
AAAATTTAA
Found at i:53426672 original size:16 final size:16
Alignment explanation
Indices: 53426651--53426681 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53426641 TATTAAAATT
*
53426651 TATATTTTTGTATAAA
1 TATATTTATGTATAAA
53426667 TATATTTATGTATAA
1 TATATTTATGTATAA
53426682 TTGAGGTATA
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:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (16 bp):
TATATTTATGTATAAA
Found at i:53427267 original size:12 final size:12
Alignment explanation
Indices: 53427252--53427278 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
53427242 TAAATTTCAA
53427252 TTTAAAATTAAT
1 TTTAAAATTAAT
53427264 TTTAAAATTAAT
1 TTTAAAATTAAT
53427276 TTT
1 TTT
53427279 TTTTAGTACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTAAAATTAAT
Found at i:53427677 original size:58 final size:61
Alignment explanation
Indices: 53427582--53427713 Score: 155
Period size: 58 Copynumber: 2.2 Consensus size: 61
53427572 TTTTATTGGC
* * * * * *
53427582 ATAATAACAAATTTAGCCCTCCAATGTTTACAGATTCTATCAAATTGGTCTTAATTC-TAAA
1 ATAATAA-AAAATTAGCCCTCCAATCTTTACACATTCTATCAAATTAGCCATAATTCTTAAA
*
53427643 ATAATAAAAAATTAGCCCT-CAA-CTTTACACATTCTATCAATTTAGCCATAATTCTTAAA
1 ATAATAAAAAATTAGCCCTCCAATCTTTACACATTCTATCAAATTAGCCATAATTCTTAAA
53427702 ATTAA-AAAAAAT
1 A-TAATAAAAAAT
53427714 ATATTTAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
58 26 0.42
59 15 0.24
60 14 0.23
61 7 0.11
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.34
Consensus pattern (61 bp):
ATAATAAAAAATTAGCCCTCCAATCTTTACACATTCTATCAAATTAGCCATAATTCTTAAA
Found at i:53427776 original size:20 final size:20
Alignment explanation
Indices: 53427734--53427781 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
53427724 ATTCATTTTC
* **
53427734 TATAAAAATACACACTATTT
1 TATAAAAATACACACAAAAT
*
53427754 TATAAAAATACATACAAAAT
1 TATAAAAATACACACAAAAT
53427774 TATAAAAA
1 TATAAAAA
53427782 ATGAATATCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.29
Consensus pattern (20 bp):
TATAAAAATACACACAAAAT
Found at i:53434208 original size:29 final size:30
Alignment explanation
Indices: 53434166--53434227 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
53434156 TATATTTTTA
*
53434166 ATTTTTAAAGGATTAGA-TCAAAATTTTATC
1 ATTTTTAAAGGATTAAAGT-AAAATTTTATC
* *
53434196 ATTTTTGAA-GATTAAAGTATAATTTTATC
1 ATTTTTAAAGGATTAAAGTAAAATTTTATC
53434225 ATT
1 ATT
53434228 ACTAATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.47
Consensus pattern (30 bp):
ATTTTTAAAGGATTAAAGTAAAATTTTATC
Found at i:53437597 original size:25 final size:24
Alignment explanation
Indices: 53437569--53437686 Score: 105
Period size: 25 Copynumber: 4.8 Consensus size: 24
53437559 TCTCGTTTAA
*
53437569 TGGCTCTCACGAGCTTCCCGATATT
1 TGGCTCTCATGAGCTTCCCGAT-TT
* * *
53437594 TGGCTCTTATGAGCTTCTCGATTAG
1 TGGCTCTCATGAGCTTCCCGATT-T
*
53437619 TGGCTCTCTTGAGCTTCCCG-TTT
1 TGGCTCTCATGAGCTTCCCGATTT
*
53437642 ATGGCTCGT-ATGAGCTTCCCGATAAT
1 -TGGCTC-TCATGAGCTTCCCGAT-TT
* *
53437668 TGGCTCGCAAGAGCTTCCC
1 TGGCTCTCATGAGCTTCCC
53437687 ATTACATGGC
Statistics
Matches: 75, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
24 20 0.27
25 54 0.72
26 1 0.01
ACGTcount: A:0.15, C:0.28, G:0.23, T:0.34
Consensus pattern (24 bp):
TGGCTCTCATGAGCTTCCCGATTT
Found at i:53437605 original size:50 final size:49
Alignment explanation
Indices: 53437546--53437686 Score: 153
Period size: 50 Copynumber: 2.9 Consensus size: 49
53437536 TCCATTATTA
*
53437546 GCTCTTATGAG-TATCTCGTTTAATGGCTCTCACGAGCTTCCCGATATT-TG
1 GCTCTTATGAGCT-TCTCGATTAATGGCTCTCACGAGCTTCCCG-T-TTATG
* **
53437596 GCTCTTATGAGCTTCTCGATTAGTGGCTCTCTTGAGCTTCCCGTTTATG
1 GCTCTTATGAGCTTCTCGATTAATGGCTCTCACGAGCTTCCCGTTTATG
* * * *
53437645 GCTCGTATGAGCTTCCCGA-TAATTGGCTCGCAAGAGCTTCCC
1 GCTCTTATGAGCTTCTCGATTAA-TGGCTCTCACGAGCTTCCC
53437687 ATTACATGGC
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
48 4 0.05
49 36 0.46
50 37 0.47
51 1 0.01
ACGTcount: A:0.16, C:0.26, G:0.22, T:0.35
Consensus pattern (49 bp):
GCTCTTATGAGCTTCTCGATTAATGGCTCTCACGAGCTTCCCGTTTATG
Found at i:53437672 original size:49 final size:49
Alignment explanation
Indices: 53437569--53437711 Score: 144
Period size: 49 Copynumber: 2.9 Consensus size: 49
53437559 TCTCGTTTAA
* * * *
53437569 TGGCTCTCACGAGCTTCCCGATATT-TGGCTCTTATGAGCTTCTCGATTAG
1 TGGCTCTCAAGAGCTTCCCG-T-TTATGGCTCGTATGAGCTTCCCGATAAG
** *
53437619 TGGCTCTCTTGAGCTTCCCGTTTATGGCTCGTATGAGCTTCCCGATAAT
1 TGGCTCTCAAGAGCTTCCCGTTTATGGCTCGTATGAGCTTCCCGATAAG
* * * * *
53437668 TGGCTCGCAAGAGCTTCCCATTACATGGCTCGAAAGAGCTTCCC
1 TGGCTCTCAAGAGCTTCCCGTT-TATGGCTCGTATGAGCTTCCC
53437712 ATTTACATGC
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
48 2 0.03
49 40 0.51
50 36 0.46
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.32
Consensus pattern (49 bp):
TGGCTCTCAAGAGCTTCCCGTTTATGGCTCGTATGAGCTTCCCGATAAG
Found at i:53437696 original size:25 final size:25
Alignment explanation
Indices: 53437629--53437724 Score: 92
Period size: 25 Copynumber: 3.9 Consensus size: 25
53437619 TGGCTCTCTT
* * * *
53437629 GAGCTTCCCGTT-TATGGCTCGTAT
1 GAGCTTCCCATTACATGGCTCGAAA
*
53437653 GAGCTTCCCGA-TA-ATTGGCTCGCAA
1 GAGCTTCCC-ATTACA-TGGCTCGAAA
53437678 GAGCTTCCCATTACATGGCTCGAAA
1 GAGCTTCCCATTACATGGCTCGAAA
53437703 GAGCTTCCCATTTACAT-GCTCG
1 GAGCTTCCCA-TTACATGGCTCG
53437725 TATAGGCATA
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
24 12 0.19
25 43 0.69
26 7 0.11
ACGTcount: A:0.21, C:0.28, G:0.22, T:0.29
Consensus pattern (25 bp):
GAGCTTCCCATTACATGGCTCGAAA
Found at i:53439313 original size:25 final size:24
Alignment explanation
Indices: 53439285--53439451 Score: 79
Period size: 25 Copynumber: 6.7 Consensus size: 24
53439275 CACATAAATG
**
53439285 GGAAGCTCATGTGAGCCATGTAACA
1 GGAAGCTCATAAGAGCCAT-TAACA
*
53439310 GGAAGCTTCA-AAGAGCCATTAACG
1 GGAAGC-TCATAAGAGCCATTAACA
* * *
53439334 GGAAGCTCATACGAGCCAATATC-
1 GGAAGCTCATAAGAGCCATTAACA
*** ** *
53439357 GAGAAGCTCCGGAGAGAAAATTAATCG
1 G-GAAGCTCATAAGAG-CCATTAA-CA
* *
53439384 GGAAGCTCATGAAAGAGCCTTTAATCG
1 GGAAGCTCAT--AAGAGCCATTAA-CA
*
53439411 GGAAGCTCCA-AAGAGCCATATATCA
1 GGAAGCT-CATAAGAGCCAT-TAACA
*
53439436 GGACGCTCATAAGAGC
1 GGAAGCTCATAAGAGC
53439452 TGCGGTGTGT
Statistics
Matches: 107, Mismatches: 24, Indels: 22
0.70 0.16 0.14
Matches are distributed among these distances:
23 4 0.04
24 32 0.30
25 37 0.35
26 13 0.12
27 15 0.14
28 6 0.06
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (24 bp):
GGAAGCTCATAAGAGCCATTAACA
Found at i:53439337 original size:24 final size:24
Alignment explanation
Indices: 53439297--53439429 Score: 79
Period size: 24 Copynumber: 5.3 Consensus size: 24
53439287 AAGCTCATGT
*
53439297 GAGCCATGTAACAGGAAGCTTCAAA
1 GAGCCAT-TAACGGGAAGCTTCAAA
*
53439322 GAGCCATTAACGGGAAGC-TCATAC
1 GAGCCATTAACGGGAAGCTTCA-AA
* * * * **
53439346 GAGCCAATATCGAGAAGCTCCGGA
1 GAGCCATTAACGGGAAGCTTCAAA
** *
53439370 GAGAAAATTAATCGGGAAGCTCATGAAA
1 GAG-CCATTAA-CGGGAAGCT--TCAAA
* *
53439398 GAGCCTTTAATCGGGAAGCTCCAAA
1 GAGCCATTAA-CGGGAAGCTTCAAA
53439423 GAGCCAT
1 GAGCCAT
53439430 ATATCAGGAC
Statistics
Matches: 78, Mismatches: 24, Indels: 12
0.68 0.21 0.11
Matches are distributed among these distances:
23 3 0.04
24 29 0.37
25 20 0.26
26 8 0.10
27 14 0.18
28 4 0.05
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.17
Consensus pattern (24 bp):
GAGCCATTAACGGGAAGCTTCAAA
Found at i:53439529 original size:24 final size:24
Alignment explanation
Indices: 53439502--53439566 Score: 58
Period size: 25 Copynumber: 2.7 Consensus size: 24
53439492 GGATGCTCTA
*
53439502 AAGAGCTATTAACGGGAAGCTCGC
1 AAGAGCTATTAACGGGAAGCTCAC
* * * *
53439526 AAGAACCATATAATGGGAAGCTCAT
1 AAGAGCTAT-TAACGGGAAGCTCAC
* *
53439551 GAGAGCTAATAACGGG
1 AAGAGCTATTAACGGG
53439567 GCACTCTTTT
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
24 13 0.43
25 17 0.57
ACGTcount: A:0.38, C:0.17, G:0.28, T:0.17
Consensus pattern (24 bp):
AAGAGCTATTAACGGGAAGCTCAC
Found at i:53442634 original size:35 final size:34
Alignment explanation
Indices: 53442546--53442642 Score: 113
Period size: 35 Copynumber: 2.8 Consensus size: 34
53442536 AATATTCGCG
* *
53442546 CCCAGCGCTAGTCGGATAAACCGACGAATGTGTG
1 CCCAGCGCTAGTCGGATAAACCGACGAAAGTGTA
* * ** *
53442580 CCCAACACTAGTCAAATAAACTGACGAAAGTTGTA
1 CCCAGCGCTAGTCGGATAAACCGACGAAAG-TGTA
*
53442615 CCCAGCGCTAGTCGGATAAACCAACGAA
1 CCCAGCGCTAGTCGGATAAACCGACGAA
53442643 TAATTAGTGA
Statistics
Matches: 49, Mismatches: 13, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
34 24 0.49
35 25 0.51
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.16
Consensus pattern (34 bp):
CCCAGCGCTAGTCGGATAAACCGACGAAAGTGTA
Found at i:53445011 original size:5 final size:5
Alignment explanation
Indices: 53444990--53445022 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
53444980 AGTTAAGCTA
*
53444990 TATAT TATA- TATGT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATA
53445023 AAAGAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 22 0.88
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:53446007 original size:25 final size:25
Alignment explanation
Indices: 53445979--53446036 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
53445969 ACTTTACCGC
* * **
53445979 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTACTAACACGTCAGT
*
53446004 GCTCTTTGATTACTAACACGTCAGT
1 GCTCTCTGATTACTAACACGTCAGT
53446029 GCTCTCTG
1 GCTCTCTG
53446037 TTTAGCAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (25 bp):
GCTCTCTGATTACTAACACGTCAGT
Found at i:53446056 original size:22 final size:22
Alignment explanation
Indices: 53446024--53446082 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
53446014 TACTAACACG
53446024 TCAGTGCTCTCTGTTTAGCAAA
1 TCAGTGCTCTCTGTTTAGCAAA
* **
53446046 TCTA-TGCTCTCTGTATAGCACT
1 TC-AGTGCTCTCTGTTTAGCAAA
53446068 TCAGTGCTCTCTGTT
1 TCAGTGCTCTCTGTT
53446083 CATTAATGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.03
22 29 0.94
23 1 0.03
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.41
Consensus pattern (22 bp):
TCAGTGCTCTCTGTTTAGCAAA
Found at i:53448141 original size:42 final size:42
Alignment explanation
Indices: 53448082--53448170 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
53448072 CTATTTCGTC
** * *
53448082 CACACGGGTAGAGACACAGGCATGTGTCTCAACTGTGTGTGA
1 CACACGGCCAGAGACACAGACATGTGTCTCAACTGTGTGTCA
* *
53448124 CACACGGCCAGAGACACAGACGTGTGTCTCAGCTGTGTGTCA
1 CACACGGCCAGAGACACAGACATGTGTCTCAACTGTGTGTCA
53448166 CACAC
1 CACAC
53448171 AGCTAGGCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.26, C:0.27, G:0.28, T:0.19
Consensus pattern (42 bp):
CACACGGCCAGAGACACAGACATGTGTCTCAACTGTGTGTCA
Found at i:53452892 original size:2 final size:2
Alignment explanation
Indices: 53452885--53452914 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
53452875 GTTAGAATAA
*
53452885 GT GT GT GT GT GT GT GT GT GT GT AT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
53452915 ATCAATATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
GT
Found at i:53470813 original size:24 final size:24
Alignment explanation
Indices: 53470786--53470835 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
53470776 GAGATTGTTT
*
53470786 TTATTAACCTTTTATACTATTAAA
1 TTATTAACCTTTTATACTATAAAA
* **
53470810 TTATTCATTTTTTATACTATAAAA
1 TTATTAACCTTTTATACTATAAAA
53470834 TT
1 TT
53470836 GTAATCTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (24 bp):
TTATTAACCTTTTATACTATAAAA
Found at i:53472582 original size:19 final size:19
Alignment explanation
Indices: 53472558--53472611 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
53472548 TGAACCTCAG
53472558 TTCAAGTTTAGGGTTT-GA
1 TTCAAGTTTAGGGTTTAGA
*
53472576 CTTCAAGTTTAGGATTTAGA
1 -TTCAAGTTTAGGGTTTAGA
*
53472596 TTCAATGTTCAGGGTT
1 TTCAA-GTTTAGGGTT
53472612 AAAAAGATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 20 0.67
20 10 0.33
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.43
Consensus pattern (19 bp):
TTCAAGTTTAGGGTTTAGA
Found at i:53478165 original size:21 final size:21
Alignment explanation
Indices: 53478127--53478166 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
53478117 ATTGACATCT
*
53478127 TTTTTTTAACAAGTTAATAAA
1 TTTTTTTAACAAGATAATAAA
53478148 TTTTTTTATACAA-ATAATA
1 TTTTTTTA-ACAAGATAATA
53478167 TAAAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (21 bp):
TTTTTTTAACAAGATAATAAA
Found at i:53478607 original size:18 final size:19
Alignment explanation
Indices: 53478576--53478613 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
53478566 AAAAAGACGA
53478576 AGTTAATAAATATAAATAT
1 AGTTAATAAATATAAATAT
* *
53478595 AGTT-ATAATTATAATTAT
1 AGTTAATAAATATAAATAT
53478613 A
1 A
53478614 AATATTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (19 bp):
AGTTAATAAATATAAATAT
Found at i:53484137 original size:64 final size:64
Alignment explanation
Indices: 53484007--53484130 Score: 164
Period size: 61 Copynumber: 2.0 Consensus size: 64
53483997 TTGGTACACT
* * ** *
53484007 TATTTTCTGGTCGCTTTATAAATATTAGTTTTCTTTTTTTTTTTAAATCTAAATTTGAAAAAATA
1 TATTTTCTGGTCGCTTTATAAATATAAG-TTTCTTATTTTTTAAAAATCTAAATATGAAAAAATA
*
53484072 TATTTT-TGGTGGCTTTATAAATATAAG-TT-TTATTTTTTAAAAATCTAAATATGAAAAAA
1 TATTTTCTGGTCGCTTTATAAATATAAGTTTCTTATTTTTTAAAAATCTAAATATGAAAAAA
53484131 AAATATAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
61 26 0.49
62 2 0.04
64 19 0.36
65 6 0.11
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (64 bp):
TATTTTCTGGTCGCTTTATAAATATAAGTTTCTTATTTTTTAAAAATCTAAATATGAAAAAATA
Found at i:53487433 original size:11 final size:11
Alignment explanation
Indices: 53487419--53487443 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53487409 AAAAACTTCA
53487419 TAAAATATTTT
1 TAAAATATTTT
53487430 TAAAATATTTT
1 TAAAATATTTT
53487441 TAA
1 TAA
53487444 TTGATATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TAAAATATTTT
Found at i:53497593 original size:47 final size:46
Alignment explanation
Indices: 53497542--53497631 Score: 135
Period size: 47 Copynumber: 1.9 Consensus size: 46
53497532 ATTAAAAAAT
* *
53497542 AAATAAAATATAGTTATAAACAATTAAAAATCTTTAAAAAAAATAAA
1 AAATAAAAAATAGCTATAAACAATTAAAAATC-TTAAAAAAAATAAA
* *
53497589 AAATAAAAAATAGCTATAAAGAATTAAAAATCTTAAAAGAAAT
1 AAATAAAAAATAGCTATAAACAATTAAAAATCTTAAAAAAAAT
53497632 CTCGGTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 10 0.26
47 29 0.74
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (46 bp):
AAATAAAAAATAGCTATAAACAATTAAAAATCTTAAAAAAAATAAA
Found at i:53497670 original size:16 final size:17
Alignment explanation
Indices: 53497643--53497679 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
53497633 TCGGTTTTAA
*
53497643 TTTTTTCTCAAAAATAG
1 TTTTTTCTCAAAAATAC
53497660 TTTTTTC-CAAAAATAC
1 TTTTTTCTCAAAAATAC
53497676 TTTT
1 TTTT
53497680 AAAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.32, C:0.14, G:0.03, T:0.51
Consensus pattern (17 bp):
TTTTTTCTCAAAAATAC
Found at i:53506814 original size:23 final size:23
Alignment explanation
Indices: 53506786--53506842 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
53506776 TTTAATATAT
*
53506786 ATATATATATAAATATATGAATTTA
1 ATATAAAT-TAAATATAT-AATTTA
*
53506811 ATATAAATTCAATATATAATTTTA
1 ATATAAATTAAATATATAA-TTTA
*
53506835 CTATAAAT
1 ATATAAAT
53506843 AAACTTGGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 2 0.07
24 19 0.68
25 7 0.25
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (23 bp):
ATATAAATTAAATATATAATTTA
Found at i:53506825 original size:24 final size:24
Alignment explanation
Indices: 53506797--53506842 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
53506787 TATATATATA
53506797 AATATATGAA-TTTAATATAAATTC
1 AATATAT-AATTTTAATATAAATTC
*
53506821 AATATATAATTTTACTATAAAT
1 AATATATAATTTTAATATAAAT
53506843 AAACTTGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (24 bp):
AATATATAATTTTAATATAAATTC
Found at i:53507797 original size:3 final size:3
Alignment explanation
Indices: 53507769--53507831 Score: 51
Period size: 3 Copynumber: 21.3 Consensus size: 3
53507759 CAGACGGTAG
* * * *
53507769 AGA AGA A-A AAA AGA GAGAA AGG AGA AGA AG- AGA AGG AGA AGG AGA
1 AGA AGA AGA AGA AGA -AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA
53507814 AGA AGA AG- AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA A
53507832 AAAAAAAAGG
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
2 6 0.12
3 37 0.77
4 4 0.08
5 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:53507829 original size:20 final size:20
Alignment explanation
Indices: 53507768--53507829 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
53507758 CCAGACGGTA
* *
53507768 GAGAAGAAAAAAAGAGAGAAAG
1 GAGAAGAAGAAGAGA-AG-AAG
*
53507790 GAGAAGAAG-AGAAGGAGAAG
1 GAGAAGAAGAAG-AGAAGAAG
53507810 GAGAAGAAGAAGAGAAGAAG
1 GAGAAGAAGAAGAGAAGAAG
53507830 AAAAAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 19 0.56
21 5 0.15
22 10 0.29
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (20 bp):
GAGAAGAAGAAGAGAAGAAG
Found at i:53508023 original size:22 final size:20
Alignment explanation
Indices: 53507996--53508076 Score: 94
Period size: 19 Copynumber: 4.0 Consensus size: 20
53507986 TAGATTAGAA
*
53507996 TTTTGTATGAATATTTTAAATT
1 TTTTGTATGAATATTAT-AA-T
53508018 TTTTGTATGAATATTATAAT
1 TTTTGTATGAATATTATAAT
*
53508038 TTTT-TATGAATATTGTAA-
1 TTTTGTATGAATATTATAAT
* *
53508056 TGTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTATAAT
53508076 T
1 T
53508077 ATTTTATAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.06
19 27 0.50
20 6 0.11
21 2 0.04
22 16 0.30
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (20 bp):
TTTTGTATGAATATTATAAT
Found at i:53508040 original size:41 final size:38
Alignment explanation
Indices: 53507989--53508076 Score: 104
Period size: 41 Copynumber: 2.2 Consensus size: 38
53507979 TATAGTTTAG
* * *
53507989 ATTAGAATTTTGTATGAATATTTTAAATTTTTTGTATGAAT
1 ATTATAATTTTGTATGAATATTGT-AA--TGTTGTATGAAT
*
53508030 ATTATAATTTTTTATGAATATTGTAATGTTGTATGAAT
1 ATTATAATTTTGTATGAATATTGTAATGTTGTATGAAT
*
53508068 ATTGTAATT
1 ATTATAATT
53508077 ATTTTATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
38 19 0.45
40 2 0.05
41 21 0.50
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (38 bp):
ATTATAATTTTGTATGAATATTGTAATGTTGTATGAAT
Found at i:53508045 original size:19 final size:19
Alignment explanation
Indices: 53507989--53508083 Score: 91
Period size: 19 Copynumber: 4.8 Consensus size: 19
53507979 TATAGTTTAG
* *
53507989 ATTAGAATTTTGTATGAAT
1 ATTATAATTTTTTATGAAT
*
53508008 ATTTTAAATTTTTTGTATGAAT
1 ATTAT-AA-TTTTT-TATGAAT
53508030 ATTATAATTTTTTATGAAT
1 ATTATAATTTTTTATGAAT
* * *
53508049 ATTGTAATGTTGTATGAAT
1 ATTATAATTTTTTATGAAT
*
53508068 ATTGTAATTATTTTAT
1 ATTATAATT-TTTTAT
53508084 AATTAAATTT
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
19 34 0.54
20 12 0.19
21 6 0.10
22 11 0.17
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.55
Consensus pattern (19 bp):
ATTATAATTTTTTATGAAT
Found at i:53508135 original size:22 final size:23
Alignment explanation
Indices: 53508110--53508313 Score: 120
Period size: 27 Copynumber: 8.4 Consensus size: 23
53508100 ATAGTTTTGG
53508110 ATTAGTAA-TTTTTTGTATGAAT
1 ATTAGTAATTTTTTTGTATGAAT
53508132 ATTA-TAATTTTTTTGTATGAAT
1 ATTAGTAATTTTTTTGTATGAAT
*
53508154 ACT-GTAATATTATAGTTTTGTATGAAT
1 ATTAGT-A-ATT-T--TTTTGTATGAAT
* *
53508181 ATT-GCAATTTTTTAATTTTATATGAAT
1 ATTAGTAA---TTT--TTTTGTATGAAT
*
53508208 ATTA-TATTTTTTTTGTATGAAT
1 ATTAGTAATTTTTTTGTATGAAT
53508230 ATT-GTAATATTATAATTTTGTATGAAT
1 ATTAGT-A-ATT-T--TTTTGTATGAAT
*
53508257 ATTA-CAATTTTTTTGTATGAAT
1 ATTAGTAATTTTTTTGTATGAAT
53508279 ATT-GTAATATTGTAATTTTGTATGAAT
1 ATTAGT-A-ATT-T--TTTTGTATGAAT
53508306 ATT-GTAAT
1 ATTAGTAAT
53508314 GTGGGGATAT
Statistics
Matches: 147, Mismatches: 11, Indels: 45
0.72 0.05 0.22
Matches are distributed among these distances:
21 3 0.02
22 51 0.35
23 3 0.02
24 12 0.08
25 9 0.06
26 3 0.02
27 64 0.44
28 2 0.01
ACGTcount: A:0.33, C:0.01, G:0.11, T:0.54
Consensus pattern (23 bp):
ATTAGTAATTTTTTTGTATGAAT
Found at i:53508177 original size:27 final size:26
Alignment explanation
Indices: 53508142--53508313 Score: 182
Period size: 27 Copynumber: 6.8 Consensus size: 26
53508132 ATTATAATTT
* *
53508142 TTTTGTATGAATACTGTAATATTATAG
1 TTTTGTATGAATATTGTAATATT-TAA
* *
53508169 TTTTGTATGAATATTGCAATTTTTTAA
1 TTTTGTATGAATATTGTAA-TATTTAA
* *
53508196 TTTTATATGAATA-T-T-ATATTT-T
1 TTTTGTATGAATATTGTAATATTTAA
53508218 TTTTGTATGAATATTGTAATATTATAA
1 TTTTGTATGAATATTGTAATATT-TAA
53508245 TTTTGTATGAATA-T-TACA-ATTT--
1 TTTTGTATGAATATTGTA-ATATTTAA
53508267 TTTTGTATGAATATTGTAATATTGTAA
1 TTTTGTATGAATATTGTAATATT-TAA
53508294 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
53508314 GTGGGGATAT
Statistics
Matches: 122, Mismatches: 10, Indels: 26
0.77 0.06 0.16
Matches are distributed among these distances:
22 25 0.20
23 7 0.06
24 8 0.07
25 11 0.09
26 4 0.03
27 64 0.52
28 3 0.02
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.54
Consensus pattern (26 bp):
TTTTGTATGAATATTGTAATATTTAA
Found at i:53508208 original size:76 final size:76
Alignment explanation
Indices: 53508120--53508269 Score: 255
Period size: 76 Copynumber: 2.0 Consensus size: 76
53508110 ATTAGTAATT
* * *
53508120 TTTTGTATGAATATTATAATTTTTTTGTATGAATACTGTAATATTATAGTTTTGTATGAATATTG
1 TTTTATATGAATATTATAATTTTTTTGTATGAATACTGTAATATTATAATTTTGTATGAATATTA
53508185 CAATTTTTTAA
66 CAATTTTTTAA
* *
53508196 TTTTATATGAATATTATATTTTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTA
1 TTTTATATGAATATTATAATTTTTTTGTATGAATACTGTAATATTATAATTTTGTATGAATATTA
53508261 CAATTTTTT
66 CAATTTTTT
53508270 TGTATGAATA
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 69 1.00
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (76 bp):
TTTTATATGAATATTATAATTTTTTTGTATGAATACTGTAATATTATAATTTTGTATGAATATTA
CAATTTTTTAA
Found at i:53508222 original size:49 final size:49
Alignment explanation
Indices: 53508169--53508308 Score: 217
Period size: 49 Copynumber: 2.9 Consensus size: 49
53508159 AATATTATAG
* * * * * *
53508169 TTTTGTATGAATATTGCAATTTTTTAATTTTATATGAATATTATATTTT
1 TTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTACAATTT
53508218 TTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTACAATTT
1 TTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTACAATTT
*
53508267 TTTTGTATGAATATTGTAATATTGTAATTTTGTATGAATATT
1 TTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATT
53508309 GTAATGTGGG
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 84 1.00
ACGTcount: A:0.32, C:0.01, G:0.11, T:0.56
Consensus pattern (49 bp):
TTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTACAATTT
Found at i:53508259 original size:19 final size:19
Alignment explanation
Indices: 53508235--53508292 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 19
53508225 TGAATATTGT
53508235 AATATTATAATTTTGTATG
1 AATATTATAATTTTGTATG
*
53508254 AATATTACAATTTTTTTGTATG
1 AATATTATAA---TTTTGTATG
* *
53508276 AATATTGTAATATTGTA
1 AATATTATAATTTTGTA
53508293 ATTTTGTATG
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
19 15 0.47
22 17 0.53
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (19 bp):
AATATTATAATTTTGTATG
Found at i:53508298 original size:76 final size:73
Alignment explanation
Indices: 53508120--53508313 Score: 232
Period size: 76 Copynumber: 2.6 Consensus size: 73
53508110 ATTAGTAATT
* * *
53508120 TTTTGTATGAATATTATAATTT-TTTTGTATGAATACTGTAATATTATAGTTTTGTATGAATATT
1 TTTTATATGAATATTAT-ATTTATTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATT
*
53508184 GCAATTTTTTAA
65 ACAA--TTTT-A
*
53508196 TTTTATATGAATATTATATTTTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTA
1 TTTTATATGAATATTATATTTATTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTA
53508261 CAA-TTT-
66 CAATTTTA
*
53508267 TTTTGTATGAATATTGTAATATTGTAATTTTGTATGAATATTGTAAT
1 TTTTATATGAATA-T-T-ATATT-T-ATTTTGTATGAATATTGTAAT
53508314 GTGGGGATAT
Statistics
Matches: 106, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
71 12 0.11
72 1 0.01
73 4 0.04
74 5 0.05
75 5 0.05
76 79 0.75
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (73 bp):
TTTTATATGAATATTATATTTATTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTA
CAATTTTA
Found at i:53508719 original size:16 final size:15
Alignment explanation
Indices: 53508693--53508740 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
53508683 GTTAACTCAT
*
53508693 TTAATTTTTATATGA
1 TTAAATTTTATATGA
* *
53508708 TGTAACTTTTATATAA
1 T-TAAATTTTATATGA
*
53508724 TTAAATTTTATTTGA
1 TTAAATTTTATATGA
53508739 TT
1 TT
53508741 TTGTATTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.58
Consensus pattern (15 bp):
TTAAATTTTATATGA
Found at i:53510368 original size:6 final size:6
Alignment explanation
Indices: 53510357--53510397 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
53510347 GTATCATGCA
* *
53510357 CCAGAG CCAGAG CCAAAG CCAGAG CCAGAG CCAGAG GCAGA
1 CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGA
53510398 ACTACATTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.37, C:0.32, G:0.32, T:0.00
Consensus pattern (6 bp):
CCAGAG
Found at i:53513432 original size:22 final size:21
Alignment explanation
Indices: 53513397--53513448 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 21
53513387 ACCTAATTTT
*
53513397 TTTTCTTCTTTTCCTTCCTTC
1 TTTTCTTCTCTTCCTTCCTTC
53513418 TTTTCTTCTGCTTCCTTCCTTC
1 TTTTCTTCT-CTTCCTTCCTTC
53513440 TTTTCTTCT
1 TTTTCTTCT
53513449 TTCTTCTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 9 0.31
22 20 0.69
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTCTTCTCTTCCTTCCTTC
Found at i:53513630 original size:20 final size:21
Alignment explanation
Indices: 53513605--53513643 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
53513595 GGAAAAGTAT
53513605 AAAATTA-TATTTTATTCAAA
1 AAAATTATTATTTTATTCAAA
53513625 AAAATTATTATTTTATTCA
1 AAAATTATTATTTTATTCA
53513644 TTGGCGCCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAATTATTATTTTATTCAAA
Found at i:53515899 original size:112 final size:105
Alignment explanation
Indices: 53515763--53516199 Score: 512
Period size: 112 Copynumber: 4.2 Consensus size: 105
53515753 TAAGTCCTAT
*
53515763 AAATTTTTTTTTATTTTTTTGTATTTTTATATCTAATTCTGACACGAAAAAAAGGAAATTTTTTT
1 AAATTTTTTTTTATTTTTTTGTATTTTTATATCTGATTCTGACACGAAAAAAA-GAAA-TTTTTT
* *
53515828 TTACTGTGT-ACTGGGTGCTGGCAATTGACAGGCCAGCACCCAAAA
64 TTACTGT-TCACTGGGTGCCGGCCATTGACAGGCCAGCACCC---A
*
53515873 AAATTTTGTTTTTATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAGAATAATTT
1 AAATTTT-TTTTTATTTTTTT-GTATTTTTATATCTGATTCTGACACG-AAAAAAAGAA-ATTTT
53515938 TTTTACTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCC-
62 TTTTACTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCCA
*
53515981 AAA-TTTTTTTTATTTTTTTGTATTTTTATATCTGATTCTGACACGAAAAGAA-AAA-----TTT
1 AAATTTTTTTTTATTTTTTTGTATTTTTATATCTGATTCTGACACGAAAAAAAGAAATTTTTTTT
53516039 ACTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCCA
66 ACTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCCA
*
53516079 AAATTTTTTTTTAATTTTTTTTTCGTATTTTTATATCTGACTCTGACACG-AAAAAA-AAA----
1 AAATTTTTTTTT-A--TTTTTTT-GTATTTTTATATCTGATTCTGACACGAAAAAAAGAAATTTT
* * * * *
53516138 -TTTACTATTTACTTGGTGCCAGCCATTGACAGGCTAGCA-CCA
62 TTTTACTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCCA
* *
53516180 AATTTTTTTTTTCTTTTTTT
1 AAATTTTTTTTTATTTTTTT
53516200 CTTTTTTGTA
Statistics
Matches: 302, Mismatches: 14, Indels: 34
0.86 0.04 0.10
Matches are distributed among these distances:
97 42 0.14
98 10 0.03
99 8 0.03
100 1 0.00
101 14 0.05
102 50 0.17
103 27 0.09
104 6 0.02
105 26 0.09
106 13 0.04
107 3 0.01
108 3 0.01
110 7 0.02
111 14 0.05
112 70 0.23
113 8 0.03
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (105 bp):
AAATTTTTTTTTATTTTTTTGTATTTTTATATCTGATTCTGACACGAAAAAAAGAAATTTTTTTT
ACTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCCA
Found at i:53517090 original size:31 final size:31
Alignment explanation
Indices: 53517052--53517111 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
53517042 CAACTTAACA
53517052 AACAAATGCCTCTAAAATAATAAAAAATTTT
1 AACAAATGCCTCTAAAATAATAAAAAATTTT
* * *
53517083 AACAAATGTCTTTAAAATAATAATAAATT
1 AACAAATGCCTCTAAAATAATAAAAAATT
53517112 AACAATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.32
Consensus pattern (31 bp):
AACAAATGCCTCTAAAATAATAAAAAATTTT
Found at i:53517469 original size:14 final size:14
Alignment explanation
Indices: 53517428--53517470 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
53517418 CAGCCAAGTA
*
53517428 AATTAATTGATTTTT
1 AATTAATTGA-ATTT
* *
53517443 AATTAAATAAATTT
1 AATTAATTGAATTT
53517457 AATTAATTGAATTT
1 AATTAATTGAATTT
53517471 TCTAAATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (14 bp):
AATTAATTGAATTT
Found at i:53519040 original size:30 final size:30
Alignment explanation
Indices: 53519006--53519070 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
53518996 CAACTTAACA
53519006 AACAAAT-ACATCTAAAATAATAACAAAATT
1 AACAAATGAC-TCTAAAATAATAACAAAATT
* *
53519036 AACAAATGTCTTTAAAATAATAACAAAATT
1 AACAAATGACTCTAAAATAATAACAAAATT
53519066 AACAA
1 AACAA
53519071 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.25
Consensus pattern (30 bp):
AACAAATGACTCTAAAATAATAACAAAATT
Found at i:53527771 original size:17 final size:18
Alignment explanation
Indices: 53527727--53527771 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 18
53527717 ATTTATTTTC
53527727 TTATTTATTGTTCTAAATT
1 TTATTTATTGTTCT-AATT
53527746 TTAATTTATTGTTCT-ATT
1 TT-ATTTATTGTTCTAATT
53527764 TTATTTAT
1 TTATTTAT
53527772 CTTAGTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.24
18 5 0.20
19 2 0.08
20 12 0.48
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (18 bp):
TTATTTATTGTTCTAATT
Found at i:53534300 original size:13 final size:14
Alignment explanation
Indices: 53534274--53534315 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
53534264 TTAACTAATC
53534274 ATTTATTATTTTCA
1 ATTTATTATTTTCA
53534288 ATTTATT-TTTTCA
1 ATTTATTATTTTCA
*
53534301 A-ATATGTATTTTCA
1 ATTTAT-TATTTTCA
53534315 A
1 A
53534316 CCCCAAAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 3 0.12
13 8 0.32
14 14 0.56
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (14 bp):
ATTTATTATTTTCA
Found at i:53592350 original size:24 final size:24
Alignment explanation
Indices: 53592305--53592356 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
53592295 GACTTCCGCA
*
53592305 GCTGTTGCAATAGCAGCAGCTGCT
1 GCTGTTGCAATAGCAGCAGCTGCG
* *
53592329 GCTGTTGCAA-AGGCTGCGGCTGCG
1 GCTGTTGCAATA-GCAGCAGCTGCG
53592353 GCTG
1 GCTG
53592357 CCAATGTCGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.15, C:0.25, G:0.37, T:0.23
Consensus pattern (24 bp):
GCTGTTGCAATAGCAGCAGCTGCG
Found at i:53602307 original size:23 final size:25
Alignment explanation
Indices: 53602276--53602322 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
53602266 ATAATAAGAA
53602276 GAAGAAGAAG-AAGAAA-AATAAAT
1 GAAGAAGAAGAAAGAAAGAATAAAT
*
53602299 GAAGTAGAAGTAAAGAAAGAATAA
1 GAAGAAGAAG-AAAGAAAGAATAA
53602323 GAAAACTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
25 6 0.30
26 5 0.25
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (25 bp):
GAAGAAGAAGAAAGAAAGAATAAAT
Found at i:53602307 original size:26 final size:26
Alignment explanation
Indices: 53602273--53602322 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
53602263 TTAATAATAA
53602273 GAAGAAGAAGAAGAAGAAA-AATAAAT
1 GAAGAAGAAGAA-AAGAAAGAATAAAT
* *
53602299 GAAGTAGAAGTAAAGAAAGAATAA
1 GAAGAAGAAGAAAAGAAAGAATAA
53602323 GAAAACTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.66, C:0.00, G:0.24, T:0.10
Consensus pattern (26 bp):
GAAGAAGAAGAAAAGAAAGAATAAAT
Found at i:53604434 original size:43 final size:43
Alignment explanation
Indices: 53604373--53604458 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
53604363 TGTTTCAATA
53604373 ATTAATGAATTAAATTAATTATGATTTGGTTGAATATTGTAAC
1 ATTAATGAATTAAATTAATTATGATTTGGTTGAATATTGTAAC
53604416 ATTAATGAATTAAATTAATTATGATTTGGTTGAATATTGTAAC
1 ATTAATGAATTAAATTAATTATGATTTGGTTGAATATTGTAAC
53604459 CTCCTCAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.44
Consensus pattern (43 bp):
ATTAATGAATTAAATTAATTATGATTTGGTTGAATATTGTAAC
Found at i:53605214 original size:17 final size:17
Alignment explanation
Indices: 53605189--53605222 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53605179 CTTAAGATGT
53605189 ATGTATATTTTGATTTA
1 ATGTATATTTTGATTTA
* *
53605206 ATGTTTATTTTTATTTA
1 ATGTATATTTTGATTTA
53605223 TAATCTCTTA
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:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (17 bp):
ATGTATATTTTGATTTA
Found at i:53607611 original size:39 final size:41
Alignment explanation
Indices: 53607548--53607637 Score: 130
Period size: 39 Copynumber: 2.2 Consensus size: 41
53607538 TTAAAAGTAT
* *
53607548 TTATATTAAAAAAAACTACCATAAATATAATAAATGTTTTA
1 TTATATTAAAAAAAACTACAATAAATATAATAAATATTTTA
*
53607589 TTATATTAAAAAACAC-A-AATAAATATAATAAATATTTTA
1 TTATATTAAAAAAAACTACAATAAATATAATAAATATTTTA
*
53607628 TTGTATTAAA
1 TTATATTAAA
53607638 TATAAAATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 29 0.64
40 1 0.02
41 15 0.33
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (41 bp):
TTATATTAAAAAAAACTACAATAAATATAATAAATATTTTA
Found at i:53613381 original size:18 final size:19
Alignment explanation
Indices: 53613358--53613393 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
53613348 TATAATTAAA
53613358 AAATAA-AATTTTTAATAT
1 AAATAATAATTTTTAATAT
*
53613376 AAATAATTATTTTTAATA
1 AAATAATAATTTTTAATA
53613394 GTAGTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATAATAATTTTTAATAT
Found at i:53614598 original size:7 final size:7
Alignment explanation
Indices: 53614584--53614615 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
53614574 GGTTTGGACT
53614584 TTGG-AC
1 TTGGCAC
53614590 TTGGCAC
1 TTGGCAC
53614597 TTGGCAC
1 TTGGCAC
53614604 TTGGCAC
1 TTGGCAC
53614611 TTGGC
1 TTGGC
53614616 TTTATAATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.16
7 21 0.84
ACGTcount: A:0.12, C:0.25, G:0.31, T:0.31
Consensus pattern (7 bp):
TTGGCAC
Found at i:53616296 original size:14 final size:14
Alignment explanation
Indices: 53616261--53616302 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
53616251 TTCCATGTCA
* *
53616261 ATTTATTCAAGAA-
1 ATTTATTTAAAAAT
53616274 ATTTATTTAAAAAT
1 ATTTATTTAAAAAT
*
53616288 ATTTTTTTAAAAAT
1 ATTTATTTAAAAAT
53616302 A
1 A
53616303 ATAAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (14 bp):
ATTTATTTAAAAAT
Found at i:53617036 original size:34 final size:35
Alignment explanation
Indices: 53616992--53617058 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
53616982 CAGTAAAATA
*
53616992 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
53617026 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
53617059 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:53623577 original size:33 final size:32
Alignment explanation
Indices: 53623535--53623713 Score: 117
Period size: 27 Copynumber: 5.5 Consensus size: 32
53623525 ATACGGTAGG
53623535 ATCAGCACTTAGCAACCACCAATGAGTCGGGGA
1 ATCAGCACTTAGCAACCACCAATGA-TCGGGGA
*
53623568 ATCAGCACTTAGCAACC-CC--T--TGGGGGA
1 ATCAGCACTTAGCAACCACCAATGATCGGGGA
* * *
53623595 ATCAGCACTTAGCAACCCCCTTTACATTTAAAATACGATGGA
1 ATCAGCACTTAGCAACCACC---A-A--T--GAT-CG-GGGA
*
53623637 ATCAGCACTTAGCAACCACCAATGATTCGAGGA
1 ATCAGCACTTAGCAACCACCAATGA-TCGGGGA
*
53623670 ATCAGCACTTAGCAACC-CC--T--TGGGGGA
1 ATCAGCACTTAGCAACCACCAATGATCGGGGA
*
53623697 ATCAACACTTAGCAACC
1 ATCAGCACTTAGCAACC
53623714 CCCTTTATAT
Statistics
Matches: 121, Mismatches: 9, Indels: 38
0.72 0.05 0.23
Matches are distributed among these distances:
27 44 0.36
28 2 0.02
30 2 0.02
32 4 0.03
33 37 0.31
34 3 0.02
35 1 0.01
36 2 0.02
38 1 0.01
39 1 0.01
40 1 0.01
41 1 0.01
42 22 0.18
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (32 bp):
ATCAGCACTTAGCAACCACCAATGATCGGGGA
Found at i:53623643 original size:102 final size:102
Alignment explanation
Indices: 53623489--53623720 Score: 378
Period size: 102 Copynumber: 2.3 Consensus size: 102
53623479 CAGTGATTCA
* * *
53623489 GGGAATCAGCACTTAGCAA-CCCCTTTCATATTTAAGATACGGTAGGATCAGCACTTAGCAACCA
1 GGGAATCAGCACTTAGCAACCCCCTTT-ACATTTAAAATACGATAGGATCAGCACTTAGCAACCA
*
53623553 CCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTGG
65 CCAATGAGTCGAGGAATCAGCACTTAGCAACCCCTTGG
53623591 GGGAATCAGCACTTAGCAACCCCCTTTACATTTAAAATACGAT-GGAATCAGCACTTAGCAACCA
1 GGGAATCAGCACTTAGCAACCCCCTTTACATTTAAAATACGATAGG-ATCAGCACTTAGCAACCA
*
53623655 CCAATGATTCGAGGAATCAGCACTTAGCAACCCCTTGG
65 CCAATGAGTCGAGGAATCAGCACTTAGCAACCCCTTGG
*
53623693 GGGAATCAACACTTAGCAACCCCCTTTA
1 GGGAATCAGCACTTAGCAACCCCCTTTA
53623721 TATTCAATGT
Statistics
Matches: 122, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
101 2 0.02
102 113 0.93
103 7 0.06
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.22
Consensus pattern (102 bp):
GGGAATCAGCACTTAGCAACCCCCTTTACATTTAAAATACGATAGGATCAGCACTTAGCAACCAC
CAATGAGTCGAGGAATCAGCACTTAGCAACCCCTTGG
Found at i:53632664 original size:91 final size:88
Alignment explanation
Indices: 53632539--53632727 Score: 299
Period size: 91 Copynumber: 2.1 Consensus size: 88
53632529 TTGATTTTAG
*
53632539 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAACAATTTATTATTAAGAATTTTATGAAA-T-TATAT-ATTATTAAATTAT
* *
53632604 ATTTAATATTAATTATTTTAAATTGTA
63 ATGTAATATT-ATTATTTTAAATTATA
53632631 TAAATTCATATAAGAA-AATTTATTATTAAGAATTTTATGAAATTATATATTATTAAATTATATG
1 TAAATTCATATAAGAACAATTTATTATTAAGAATTTTATGAAATTATATATTATTAAATTATATG
53632695 TAATATTATTATTTTAAATTATA
66 TAATATTATTATTTTAAATTATA
*
53632718 CAAATTCATA
1 TAAATTCATA
53632728 AAATATAATT
Statistics
Matches: 93, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
87 24 0.26
88 22 0.24
89 5 0.05
90 1 0.01
91 25 0.27
92 16 0.17
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (88 bp):
TAAATTCATATAAGAACAATTTATTATTAAGAATTTTATGAAATTATATATTATTAAATTATATG
TAATATTATTATTTTAAATTATA
Found at i:53632666 original size:44 final size:44
Alignment explanation
Indices: 53632539--53632677 Score: 122
Period size: 47 Copynumber: 3.0 Consensus size: 44
53632529 TTGATTTTAG
*
53632539 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTA
1 TAAATTCATATAAGAA-AATTTATTATTAAGAATTTTA-GAAATTA
* * * ** *
53632585 TATA-TCATTATTAA-ATTATATTTAATATTAATTATTTTA-AATTGTA
1 TAAATTCA-TA-TAAGA--AAATTTATTATTAAGAATTTTAGAAAT-TA
53632631 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTA
1 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTA-GAAATTA
53632676 TA
1 TA
53632678 TATTATTAAA
Statistics
Matches: 71, Mismatches: 13, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
44 18 0.25
45 13 0.18
46 17 0.24
47 22 0.31
48 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (44 bp):
TAAATTCATATAAGAAAATTTATTATTAAGAATTTTAGAAATTA
Found at i:53632689 original size:25 final size:26
Alignment explanation
Indices: 53632650--53632717 Score: 79
Period size: 25 Copynumber: 2.6 Consensus size: 26
53632640 ATAAGAAAAT
*
53632650 TTATTATTAAGAATTTTATG-AA-ATTA
1 TTATTATT-A-AATTATATGTAATATTA
53632676 TATATTATTAAATTATATGTAATATTA
1 T-TATTATTAAATTATATGTAATATTA
53632703 TTATT-TTAAATTATA
1 TTATTATTAAATTATA
53632718 CAAATTCATA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
25 18 0.47
26 8 0.21
27 12 0.32
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (26 bp):
TTATTATTAAATTATATGTAATATTA
Found at i:53632702 original size:44 final size:45
Alignment explanation
Indices: 53632558--53632702 Score: 129
Period size: 44 Copynumber: 3.2 Consensus size: 45
53632548 ATAAGAACAT
*
53632558 TTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TTTAATATTAAGAATTTTATGAAA-TATATAT-ATTATTAAATTATA
** * * * *
53632605 TTTAATATTAATTATTTTA--AATTGTATAAATTCATATAAGA--AAA
1 TTTAATATTAAGAATTTTATGAAATATATATATT-AT-TAA-ATTATA
*
53632649 TTTATTATTAAGAATTTTATGAAAT-TATATATTATTAAATTATA
1 TTTAATATTAAGAATTTTATGAAATATATATATTATTAAATTATA
*
53632693 TGTAATATTA
1 TTTAATATTA
53632703 TTATTTTAAA
Statistics
Matches: 76, Mismatches: 15, Indels: 17
0.70 0.14 0.16
Matches are distributed among these distances:
42 1 0.01
43 6 0.08
44 37 0.49
45 12 0.16
46 4 0.05
47 16 0.21
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (45 bp):
TTTAATATTAAGAATTTTATGAAATATATATATTATTAAATTATA
Found at i:53632783 original size:46 final size:47
Alignment explanation
Indices: 53632661--53632783 Score: 108
Period size: 46 Copynumber: 2.6 Consensus size: 47
53632651 TATTATTAAG
* * *
53632661 AATTTTATGAAATTATATATTATTAAATTATATGTAATATTATTATTTTA
1 AATTTTATCAAATCATATATT-TT-AATTATATGT-ATATAATTATTTTA
* * * *
53632711 AATTATA-CAAATTCATAAAATATAATTAT-TAGT-TATAATTATTTTA
1 AATTTTATCAAA-TCATATATTTTAATTATAT-GTATATAATTATTTTA
*
53632757 AATTTTATTAAATCATATATTTTAATT
1 AATTTTATCAAATCATATATTTTAATT
53632784 TAAATATATT
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
46 30 0.52
47 4 0.07
48 8 0.14
49 4 0.07
50 12 0.21
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (47 bp):
AATTTTATCAAATCATATATTTTAATTATATGTATATAATTATTTTA
Found at i:53632913 original size:14 final size:14
Alignment explanation
Indices: 53632881--53632931 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
53632871 TTAAGAATTT
* *
53632881 TATTAAATTATATA
1 TATTTAATTATAAA
53632895 T-TTTAATTATAAA
1 TATTTAATTATAAA
* *
53632908 TATTTAATAATAAT
1 TATTTAATTATAAA
53632922 TATGTTAATT
1 TAT-TTAATT
53632932 TATATTTTAC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 11 0.37
14 14 0.47
15 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (14 bp):
TATTTAATTATAAA
Found at i:53632921 original size:53 final size:53
Alignment explanation
Indices: 53632864--53633043 Score: 132
Period size: 53 Copynumber: 3.2 Consensus size: 53
53632854 ATATAAGAAT
53632864 ATAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAAATATTTAATA
1 ATAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAAATATTTAATA
* * * * *
53632917 ATAATTATGT--TAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATGTAAGA
1 ATAATTAT-TAAGAATTT-TA--TTA-A--ATTATATATT-TTAATT-A-TAAA-T-AT-T--TA
53632980 ATA
51 ATA
* *
53632983 TTAATTATTAAGAATTTTA-TAAATTATATAATTTAATTATAATATATTTAATA
1 ATAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAA-ATATTTAATA
53633036 ATAATTAT
1 ATAATTAT
53633044 GTTTAAATAT
Statistics
Matches: 96, Mismatches: 13, Indels: 36
0.66 0.09 0.25
Matches are distributed among these distances:
52 5 0.05
53 21 0.22
54 1 0.01
55 4 0.04
56 3 0.03
57 4 0.04
58 11 0.11
59 8 0.08
60 9 0.09
61 4 0.04
62 2 0.02
63 4 0.04
64 1 0.01
65 1 0.01
66 13 0.14
67 5 0.05
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (53 bp):
ATAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAAATATTTAATA
Found at i:53632955 original size:118 final size:119
Alignment explanation
Indices: 53632744--53633051 Score: 448
Period size: 118 Copynumber: 2.6 Consensus size: 119
53632734 AATTATTAGT
* * *
53632744 TATAATTATTTTA-AATTTTATTAAATCATATATTTTAATT-TAAATATATTTAATATTAATTAT
1 TATAATTA-TTAAGAATTTTATTAAATTATATATTTTAATTAT-AATATATTTAATAATAATTAT
* *
53632807 -TTCAAATTTTCTTTTATAGTATCATATATTATGATTTGAATAAATTCATATAAGAA
64 GTT-AAATTTTATTTTACAGTATCATATATTATGATTTGAATAAATTCATATAAGAA
53632863 TATAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAA-ATATTTAATAATAATTATGT
1 TATAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGT
* *
53632927 T-AATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATGTAAGAA
66 TAAATTT-TATTTTACAGTATCATATATTATGATTTGAATAAATTCATATAAGAA
*
53632981 TATTAATTATTAAGAATTTTA-TAAATTATATAATTTAATTATAATATATTTAATAATAATTATG
1 TA-TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG
53633045 TTTAAAT
65 -TTAAAT
53633052 ATGATTAAAT
Statistics
Matches: 173, Mismatches: 8, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
117 5 0.03
118 87 0.50
119 75 0.43
120 3 0.02
121 3 0.02
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.50
Consensus pattern (119 bp):
TATAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGT
TAAATTTTATTTTACAGTATCATATATTATGATTTGAATAAATTCATATAAGAA
Found at i:53633178 original size:18 final size:17
Alignment explanation
Indices: 53633150--53633184 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53633140 ATTATTAAGA
*
53633150 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
53633167 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
53633185 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:53633189 original size:155 final size:156
Alignment explanation
Indices: 53632984--53633297 Score: 533
Period size: 155 Copynumber: 2.0 Consensus size: 156
53632974 GTAAGAATAT
*
53632984 TAATTATTAAGAATTTTATAAATTATATAATTTAATTATAATATATTTAATAATAATTATGTTTA
1 TAATTATTAAGAATTTTATAAATTATATAATTTAATTAAAATATATTTAATAATAATTATGTTTA
*
53633049 AATATGATTAAATTATTTATTACTGATATTAATAATCTTATTAAAATTTAAATAACAATAAC-A-
66 AATATGATTAAATTATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAT
*
53633112 AATAATTTACCAAAACAAATTTCTGC
131 AATAATTTACCAAAACAAATTTATGC
*
53633138 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTA-TAAATTATATAATTTAATTAAAATATATTTAATAATAATTATGTTT
* *
53633203 AAATATGGTTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
65 AAATATGATTAAATTATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
* *
53633268 TAATCATTTACCCAAACAAATTTATGC
130 TAATAATTTACCAAAACAAATTTATGC
53633295 TAA
1 TAA
53633298 GGGTATTCTA
Statistics
Matches: 149, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
154 18 0.12
155 104 0.70
156 1 0.01
157 26 0.17
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.44
Consensus pattern (156 bp):
TAATTATTAAGAATTTTATAAATTATATAATTTAATTAAAATATATTTAATAATAATTATGTTTA
AATATGATTAAATTATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAT
AATAATTTACCAAAACAAATTTATGC
Found at i:53633400 original size:44 final size:45
Alignment explanation
Indices: 53633345--53633439 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 45
53633335 TTACATCTAT
53633345 ATTACATTCAACCAAACACAGGA-TTACTATTACACCTCTATTCC
1 ATTACATTCAACCAAACACAGGATTTACTATTACACCTCTATTCC
*** *
53633389 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACACAGGATTTACTATTACACCTCTATTCC
53633434 ATTACA
1 ATTACA
53633440 CCTCTAATCC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 20 0.43
45 26 0.57
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (45 bp):
ATTACATTCAACCAAACACAGGATTTACTATTACACCTCTATTCC
Found at i:53633439 original size:16 final size:16
Alignment explanation
Indices: 53633418--53633455 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
53633408 TTGATTTGCT
*
53633418 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
53633434 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
53633450 AATACA
1 ATTACA
53633456 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:53649283 original size:16 final size:16
Alignment explanation
Indices: 53649264--53649294 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53649254 TCCCACGTTA
*
53649264 GGTTTTGGGTTTTTAG
1 GGTTTAGGGTTTTTAG
53649280 GGTTTAGGGTTTTTA
1 GGTTTAGGGTTTTTA
53649295 AAGTTTTGGA
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:0.10, C:0.00, G:0.35, T:0.55
Consensus pattern (16 bp):
GGTTTAGGGTTTTTAG
Found at i:53649599 original size:49 final size:49
Alignment explanation
Indices: 53649543--53649689 Score: 251
Period size: 49 Copynumber: 3.0 Consensus size: 49
53649533 CGTTTTTGAG
53649543 CAAATAATAT-ACAAATATTCAAAATAAACTATTTTGTATTTTATTACAT
1 CAAATAATATCA-AAATATTCAAAATAAACTATTTTGTATTTTATTACAT
* *
53649592 CAAATAATATCAAAATATTCAAAATAAACTATTTTATATTTTATTATAT
1 CAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTTATTACAT
*
53649641 CAAATAATATCAAAATATTCAAATTAAACTATTTTGTATTTTATTACAT
1 CAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTTATTACAT
53649690 TAATATAAAC
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
49 91 0.99
50 1 0.01
ACGTcount: A:0.47, C:0.10, G:0.01, T:0.42
Consensus pattern (49 bp):
CAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTTATTACAT
Found at i:53650502 original size:9 final size:9
Alignment explanation
Indices: 53650490--53650515 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
53650480 TCTCCTCCCT
53650490 AATTTCACA
1 AATTTCACA
53650499 AATTTCACA
1 AATTTCACA
53650508 AATTTCAC
1 AATTTCAC
53650516 TTTCACACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (9 bp):
AATTTCACA
Found at i:53654350 original size:24 final size:24
Alignment explanation
Indices: 53654293--53654351 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
53654283 GGTTTAATGC
* *
53654293 AAATGGAGATATTTTGGAGAGATG
1 AAATGGATATATTTTGGAAAGATG
*
53654317 AAATGAATATATTTTGGAAAGATG
1 AAATGGATATATTTTGGAAAGATG
53654341 AAATGGATATA
1 AAATGGATATA
53654352 AATGGAGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (24 bp):
AAATGGATATATTTTGGAAAGATG
Found at i:53654443 original size:20 final size:19
Alignment explanation
Indices: 53654417--53654481 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
53654407 AATATTTTTA
53654417 ATTATGTAGTGATTCAAAG
1 ATTATGTAGTGATTCAAAG
* ***
53654436 ACTTATGTAAT-ATTTTTA-
1 A-TTATGTAGTGATTCAAAG
53654454 ATTATGTAGTGATTCAAAG
1 ATTATGTAGTGATTCAAAG
53654473 ATTTATGTA
1 A-TTATGTA
53654482 ATGTTTTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 7
0.69 0.16 0.14
Matches are distributed among these distances:
17 8 0.24
18 5 0.15
19 6 0.18
20 15 0.44
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (19 bp):
ATTATGTAGTGATTCAAAG
Found at i:53654446 original size:37 final size:37
Alignment explanation
Indices: 53654392--53654504 Score: 192
Period size: 37 Copynumber: 3.1 Consensus size: 37
53654382 TTATGTTTTA
*
53654392 ATTC-AAGACTTGTGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
53654428 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
* *
53654465 ATTCAAAGATTTATGTAATGTTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
53654502 ATT
1 ATT
53654505 TAATTCGGGT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 4 0.05
37 69 0.95
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (37 bp):
ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
Found at i:53654460 original size:17 final size:17
Alignment explanation
Indices: 53654404--53654498 Score: 55
Period size: 17 Copynumber: 5.2 Consensus size: 17
53654394 TCAAGACTTG
53654404 TGTAATATTTTTAATTA
1 TGTAATATTTTTAATTA
* ***
53654421 TGTAGTGATTCAAAGACTTA
1 TGTAAT-ATTTTTA-A-TTA
53654441 TGTAATATTTTTAATTA
1 TGTAATATTTTTAATTA
* ***
53654458 TGTAGTGATTCAAAGATTTA
1 TGTAAT-ATTTTTA-A-TTA
*
53654478 TGTAATGTTTTTAATTA
1 TGTAATATTTTTAATTA
53654495 TGTA
1 TGTA
53654499 GTGATTTAAT
Statistics
Matches: 55, Mismatches: 17, Indels: 12
0.65 0.20 0.14
Matches are distributed among these distances:
17 20 0.36
18 10 0.18
19 9 0.16
20 16 0.29
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.49
Consensus pattern (17 bp):
TGTAATATTTTTAATTA
Found at i:53654519 original size:9 final size:9
Alignment explanation
Indices: 53654505--53654623 Score: 139
Period size: 9 Copynumber: 12.6 Consensus size: 9
53654495 TGTAGTGATT
53654505 TAATTCGGG
1 TAATTCGGG
53654514 TAATTCGGG
1 TAATTCGGG
53654523 TAATTTTCGGG
1 TAA--TTCGGG
*
53654534 TAATTTTCGAG
1 TAA--TTCGGG
53654545 TAATTCGGG
1 TAATTCGGG
*
53654554 TAATTTGGG
1 TAATTCGGG
53654563 TAATTTTCGGG
1 TAA--TTCGGG
53654574 TAATTCGGG
1 TAATTCGGG
53654583 TAATTCGGG
1 TAATTCGGG
* **
53654592 TAAGTCAAG
1 TAATTCGGG
53654601 TAATTCGGG
1 TAATTCGGG
53654610 TAATTCGGG
1 TAATTCGGG
53654619 TAATT
1 TAATT
53654624 TTTAACCAAA
Statistics
Matches: 96, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
9 69 0.72
11 27 0.28
ACGTcount: A:0.24, C:0.09, G:0.29, T:0.38
Consensus pattern (9 bp):
TAATTCGGG
Found at i:53654761 original size:28 final size:27
Alignment explanation
Indices: 53654729--53654794 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 27
53654719 AAAATTCGGT
53654729 TCGGTTAACGGTTA-AAAAATTTGAGAGG
1 TCGGTTAACGGTTACAAAAATTT-AG-GG
* *
53654757 TCGGTTAATTCGGTTACAAGAATTTCGGG
1 TCGGTTAA--CGGTTACAAAAATTTAGGG
53654786 TCGGTTAAC
1 TCGGTTAAC
53654795 CGACTGAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
27 1 0.03
28 8 0.24
29 10 0.30
30 7 0.21
31 7 0.21
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (27 bp):
TCGGTTAACGGTTACAAAAATTTAGGG
Found at i:53656765 original size:11 final size:10
Alignment explanation
Indices: 53656739--53656780 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
53656729 AAATATGGAT
53656739 TTGAGAGAAA
1 TTGAGAGAAA
*
53656749 TTGAGAGCAAT
1 TTGAGAG-AAA
53656760 TTGAGAGGAAA
1 TTGAGA-GAAA
53656771 TTGAGA-AAA
1 TTGAGAGAAA
53656780 T
1 T
53656781 AATTGAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 4 0.14
10 7 0.25
11 16 0.57
12 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.29, T:0.24
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:53662615 original size:6 final size:6
Alignment explanation
Indices: 53662604--53662651 Score: 78
Period size: 6 Copynumber: 7.8 Consensus size: 6
53662594 TAAACTTATT
*
53662604 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA AAAGTAA ATATA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATA-TAA ATATA
53662652 TTATAAATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
6 34 0.87
7 5 0.13
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (6 bp):
ATATAA
Found at i:53662703 original size:18 final size:19
Alignment explanation
Indices: 53662667--53662704 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
53662657 AATTATATTA
* *
53662667 TTATATAATGCTTGTAAAT
1 TTATATAATACTTGCAAAT
53662686 TTATA-AATACTTGCAAAT
1 TTATATAATACTTGCAAAT
53662704 T
1 T
53662705 ATTTTAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (19 bp):
TTATATAATACTTGCAAAT
Found at i:53664140 original size:21 final size:21
Alignment explanation
Indices: 53664097--53664158 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
53664087 CGAATACGCC
53664097 AACAGAAGCTCG-AA-AGCTG
1 AACAGAAGCTCGTAAGAGCTG
* *
53664116 AACAGAAGCTTGTAAGAGCTT
1 AACAGAAGCTCGTAAGAGCTG
* *
53664137 AACAAAAGCTCATAAGAGCTG
1 AACAGAAGCTCGTAAGAGCTG
53664158 A
1 A
53664159 CCACCCAATC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 11 0.31
20 2 0.06
21 22 0.63
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGCTG
Found at i:53677576 original size:20 final size:22
Alignment explanation
Indices: 53677529--53677578 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
53677519 TTTAGGTTTT
*
53677529 AAAATTAATATGATGAAAATTC
1 AAAATTAATATGATGAAAATTA
* *
53677551 ATAATTAA-CTGAT-AAAATTA
1 AAAATTAATATGATGAAAATTA
53677571 AAAATTAA
1 AAAATTAA
53677579 ATTTTTTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 13 0.54
21 4 0.17
22 7 0.29
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (22 bp):
AAAATTAATATGATGAAAATTA
Found at i:53681414 original size:3 final size:3
Alignment explanation
Indices: 53681406--53681436 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
53681396 GGGAAGAACA
53681406 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
53681437 CTGGAGCTTT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:53695284 original size:22 final size:22
Alignment explanation
Indices: 53695253--53695302 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
53695243 GGTATTTGTT
*
53695253 TGTTAAATTGCATCTATCTTAA
1 TGTTATATTGCATCTATCTTAA
53695275 TGTTATATTGCATCTATCTTAA
1 TGTTATATTGCATCTATCTTAA
53695297 TGTTAT
1 TGTTAT
53695303 TTAAGTATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.50
Consensus pattern (22 bp):
TGTTATATTGCATCTATCTTAA
Found at i:53699172 original size:19 final size:20
Alignment explanation
Indices: 53699135--53699174 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
53699125 TCTTTTCGCA
* *
53699135 TTCATTTCATGCATTTGCAT
1 TTCATTACATGCATATGCAT
53699155 TTCATTACAT-CATATGCAT
1 TTCATTACATGCATATGCAT
53699174 T
1 T
53699175 AGACACCGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (20 bp):
TTCATTACATGCATATGCAT
Found at i:53701988 original size:14 final size:13
Alignment explanation
Indices: 53701969--53702025 Score: 55
Period size: 14 Copynumber: 4.4 Consensus size: 13
53701959 TTGAGTCGTA
53701969 AAAAATGATGAAAT
1 AAAAATGA-GAAAT
*
53701983 AAAAATGAAAAAGT
1 AAAAATGAGAAA-T
* *
53701997 GAAAATAAGAAAT
1 AAAAATGAGAAAT
53702010 AAAAATG-GAAA-
1 AAAAATGAGAAAT
53702021 AAAAA
1 AAAAA
53702026 AAGAAAATGA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
11 5 0.14
12 4 0.11
13 9 0.25
14 18 0.50
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (13 bp):
AAAAATGAGAAAT
Found at i:53702002 original size:20 final size:20
Alignment explanation
Indices: 53701979--53702032 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
53701969 AAAAATGATG
53701979 AAATAAAAATGAAAAA-GTGA
1 AAATAAAAATGAAAAATG-GA
53701999 AAATAAGAAAT-AAAAATGGA
1 AAATAA-AAATGAAAAATGGA
*
53702019 AAA-AAAAAAGAAAA
1 AAATAAAAATGAAAA
53702033 TGAGAGGCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 3 0.10
19 6 0.20
20 16 0.53
21 5 0.17
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (20 bp):
AAATAAAAATGAAAAATGGA
Found at i:53703384 original size:44 final size:44
Alignment explanation
Indices: 53703333--53703701 Score: 380
Period size: 44 Copynumber: 8.3 Consensus size: 44
53703323 TACTGGTAGC
* * * *
53703333 GAAGTAGATCGAAGAAAAAAGTTCTTGTCTTCATGTATTGGCGC
1 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* * * *** *
53703377 GAAGTAGATCGAATAAAGCAGATCTTGTCTCCCCATACTGGTGGT
1 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG-CGT
* *
53703422 GGAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* * *
53703466 GAAGTAGATCGAAGAAAGCTGATATTGTCTTCATGTACTGGCGT
1 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* * * * *** * *
53703510 GAAGTAGATCAAAGATACCAGATCTTATCTTCCCATACTGGTGGC
1 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG-CGT
53703555 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
1 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* * *** *
53703599 GAAGTAGATCAAAG-AAACAGATCTTGTCTCCCCATACTGGTGGT
1 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG-CGT
* * * *
53703643 GGAGTAGATTGAAGAAAATAGATCTTATCTTCATGTACTGGCGT
1 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
*
53703687 GAAGTAGATCAAAGA
1 GAAGTAGATCGAAGA
53703702 TAGCAGGTCC
Statistics
Matches: 257, Mismatches: 64, Indels: 8
0.78 0.19 0.02
Matches are distributed among these distances:
43 22 0.09
44 146 0.57
45 89 0.35
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.28
Consensus pattern (44 bp):
GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
Found at i:53703412 original size:89 final size:89
Alignment explanation
Indices: 53703307--53703627 Score: 297
Period size: 89 Copynumber: 3.6 Consensus size: 89
53703297 GACAAGCAGT
* *
53703307 AGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAGAAAAAAGTTCTTGTCTTCATGTATT
1 AGATCTTGTCTCCCCATACTGGTAGCGAAGTAGATCGAAGAAAAAAGATCTTGTCTTCATGTATT
*
53703372 GGCGCGAAGTAGATCGAATAAAGC
66 GGCGCGAAGTAGATCGAAGAAAGC
* * * *
53703396 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATT
1 AGATCTTGTCTCCCCATACTGGTAGCGAAGTAGATCGAAGAAAAAAGATCTTGTCTTCATGTATT
*
53703461 GGCGTGAAGTAGATCGAAGAAAGC
66 GGCGCGAAGTAGATCGAAGAAAGC
* * * *** * * * * ** * *** *
53703485 TGATATTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGATACCAGATCTTATCTTCCCATACT
1 AGATCTTGTCTCCCCATACTGGTAGCGAAGTAGATCGAAGAAAAAAGATCTTGTCTTCATGTATT
* *
53703549 GGTGGCGAAGTAGATCGAAGAAAAC
66 GG-CGCGAAGTAGATCGAAGAAAGC
* *** * * * *
53703574 AGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAG-AAACAGATCTTGTCT
1 AGATCTTGTCTCCCCATACTGGTAGCGAAGTAGATCGAAGAAAAAAGATCTTGTCT
53703628 CCCCATACTG
Statistics
Matches: 199, Mismatches: 32, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
88 46 0.23
89 153 0.77
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (89 bp):
AGATCTTGTCTCCCCATACTGGTAGCGAAGTAGATCGAAGAAAAAAGATCTTGTCTTCATGTATT
GGCGCGAAGTAGATCGAAGAAAGC
Found at i:53703494 original size:133 final size:133
Alignment explanation
Indices: 53703333--53703615 Score: 413
Period size: 133 Copynumber: 2.1 Consensus size: 133
53703323 TACTGGTAGC
* * * * * *
53703333 GAAGTAGATCGAAGAAAAAAGTTCTTGTCTTCATGTATTGGCGCGAAGTAGATCGAATAAAGCAG
1 GAAGTAGATCGAAGAAAAAAGATATTGTCTTCATGTACTGGCGCGAAGTAGATCAAAGAAACCAG
* * * *
53703398 ATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGG
66 ATCTTATCTCCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG
53703463 CGT
131 CGT
*** * *
53703466 GAAGTAGATCGAAGAAAGCTGATATTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAG
1 GAAGTAGATCGAAGAAAAAAGATATTGTCTTCATGTACTGGCGCGAAGTAGATCAAAGAAACCAG
*
53703531 ATCTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG
66 ATCTTATCTCCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG
53703596 CGT
131 CGT
*
53703599 GAAGTAGATCAAAGAAA
1 GAAGTAGATCGAAGAAA
53703616 CAGATCTTGT
Statistics
Matches: 133, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
133 133 1.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (133 bp):
GAAGTAGATCGAAGAAAAAAGATATTGTCTTCATGTACTGGCGCGAAGTAGATCAAAGAAACCAG
ATCTTATCTCCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG
CGT
Found at i:53703649 original size:133 final size:133
Alignment explanation
Indices: 53703371--53703674 Score: 385
Period size: 133 Copynumber: 2.3 Consensus size: 133
53703361 CTTCATGTAT
* * * * * * * *
53703371 TGGCGCGAAGTAGATCGAATAAAGCAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAG
1 TGGCGTGAAGTAGATCAAAGAAAACAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAG
* * * * **
53703436 AAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCTGATATTGTCTTCATG
66 AAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAGCAGATATTGTCTCCACA
53703501 TAC
131 TAC
* *
53703504 TGGCGTGAAGTAGATCAAAGATACCAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAG
1 TGGCGTGAAGTAGATCAAAGAAAACAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAG
* *
53703569 AAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAA-CAGATCTTGTCTCCCCA
66 AAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAGCAGATATTGTCTCCACA
53703633 TAC
131 TAC
* * ** *
53703636 TGGTGGTGGAGTAGATTGAAGAAAATAGATCTTATCTTC
1 TGG-CGTGAAGTAGATCAAAGAAAACAGATCTTATCTTC
53703675 ATGTACTGGC
Statistics
Matches: 146, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
132 17 0.12
133 129 0.88
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.28
Consensus pattern (133 bp):
TGGCGTGAAGTAGATCAAAGAAAACAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAG
AAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAGCAGATATTGTCTCCACA
TAC
Found at i:53703831 original size:221 final size:221
Alignment explanation
Indices: 53703307--53703834 Score: 546
Period size: 221 Copynumber: 2.4 Consensus size: 221
53703297 GACAAGCAGT
* * * * * * *
53703307 AGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAGAAAA-AAGTTCTTGTCTTCATGTAT
1 AGATCTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAA-ATCTTATCTCCATGAAC
* * * * * *
53703371 TGGCGCGAAGTAGATCGAATAAAGCAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAG
65 AGGAGTGAAGCAGATCAAAGAAA-CAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAG
* * * * * * *
53703436 AAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCTGATATTGTCTTCATG
129 AAAACAGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAGCAGATACTGTCTCCATA
* *
53703501 TACTGGCGTGAAGTAGATCAAAGATACC
194 TACTCGCGTGAAGGAGATCAAAGATACC
* * * * *
53703529 AGATCTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACT
1 AGATCTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAAATCTTATCTCCATGAACA
* * *
53703594 GGCGTGAAGTAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATTGAAGAA
66 GGAGTGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAA
* * * * *
53703659 AATAGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGGTCCTGTCTCCCTATA
131 AACAGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAGCAGATACTGTCTCCATATA
* * *
53703724 -TCG-GTAGCAAAGGGGATCGAATATA-C
196 CTCGCGT-G--AAGGAGATCAAAGATACC
* * * * *
53703750 ATATTTTATCTTCCCATACTGGTGGCGAAAG-AGATTGAGGAAAACAAATCTTATCTCCCT-AAG
1 AGATCTTATCTTCCCATACTGGTGGCG-AAGTAGATCGAAGAAAACAAATCTTATCTCCATGAA-
* *
53703813 CAGTAGTGGAGCAGATCAAAGA
64 CAGGAGTGAAGCAGATCAAAGA
53703835 TGGCAGATTT
Statistics
Matches: 260, Mismatches: 40, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
219 2 0.01
220 4 0.02
221 161 0.62
222 92 0.35
223 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.27
Consensus pattern (221 bp):
AGATCTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAAATCTTATCTCCATGAACA
GGAGTGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAA
AACAGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAGCAGATACTGTCTCCATATA
CTCGCGTGAAGGAGATCAAAGATACC
Found at i:53703950 original size:132 final size:131
Alignment explanation
Indices: 53703797--53704408 Score: 847
Period size: 132 Copynumber: 4.6 Consensus size: 131
53703787 AGGAAAACAA
* *
53703797 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTGC
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG-AGATTTTACCTCCCTGAGGTTAC
* *
53703862 AGTGGAGTATATTGAAGCCAGTAATTCTA-CTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTT
65 AGTGGAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTA
53703926 CAG
129 CAG
* * * * *
53703929 ATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTAC
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGAG-ATTTTACCTCCCTGAGGTTAC
*
53703994 AGTGGAATACATTGAAGCCAGTAATTCTAAT-TCCGC-GGGCAGCAGTGGAATAGATTGAAGATT
65 AGTGGAGTACATTGAAGCCAGTAATTCT-ATCTCC-CTGGGCAGCAGTGGAATAGATTGAAGATT
*
53704057 TCAG
128 ACAG
** * * * * *
53704061 ATCTTGCCTTCCT--GCATAGACAGTGAAGCAGATCGAAGATGGTGAATTTTACCTCCCTGTGGT
1 ATCTTATCTCCCTAAGC--AG-TAGTGGAGCAGATCGAAGATGGAG-ATTTTACCTCCCTGAGGT
* * *
53704124 TACAGTGGAGTACATTAAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGAG
62 TACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGAT
53704189 TACAG
127 TACAG
*
53704194 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGGATTTTACCTCCCTGAGGTTAC
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG-AGATTTTACCTCCCTGAGGTTAC
*
53704259 AGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAAATTAC
65 AGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTAC
53704324 AG
130 AG
* * * *
53704326 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAATATGACAGATTTTACCTCCCTGAAGTTAC
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATG-GAGATTTTACCTCCCTGAGGTTAC
53704391 AGTGGAGTACATTGAAGC
65 AGTGGAGTACATTGAAGC
53704409 TAATCCTATC
Statistics
Matches: 433, Mismatches: 34, Indels: 26
0.88 0.07 0.05
Matches are distributed among these distances:
130 2 0.00
131 1 0.00
132 313 0.72
133 115 0.27
135 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (131 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGAGATTTTACCTCCCTGAGGTTACA
GTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACA
G
Found at i:53704148 original size:265 final size:265
Alignment explanation
Indices: 53703817--53704408 Score: 820
Period size: 265 Copynumber: 2.2 Consensus size: 265
53703807 CCTAAGCAGT
* * * *
53703817 AGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTGCAGTGGAGTATATTGAAGCCA
1 AGTGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTAAAGCCA
* * * *
53703882 GTAATTCTA-CTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCCAAGC
66 GTAATTCTATC-TCCCTGGGCAACAGTGGAATAGATTGAAGAGTACAGATCTTATCTCCCCAAGC
*
53703946 AGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAATACATTGAAG
130 AGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTACAGTGGAATACATTGAAG
* *
53704011 CCAGTAATTCTAAT-TCCGC-GGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGCCTTCCT
195 CCAGTAATTCT-ATCTCC-CTGGGCAGCAGTGGAATAGATTGAAAATTACAGATCTTGCCTTCCT
53704074 GCATAGAC
258 GCATAGAC
* * *
53704082 AGTGAAGCAGATCGAAGATGG-TGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTAAAGCC
1 AGTGAAGCAGATCAAAGATGGCAG-ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTAAAGCC
*
53704146 AGTAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGAGTACAGATCTTATCTCCCTAAGC
65 AGTAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGAGTACAGATCTTATCTCCCCAAGC
* * *
53704211 AGTAGTGGAGCAGATCGAAGATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAG
130 AGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTACAGTGGAATACATTGAAG
** *
53704276 CCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAAATTACAGATCTTATCTCCCT--
195 CCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAAATTACAGATCTTGCCTTCCTGC
*
53704339 A-AGCAGT
260 ATAG-A-C
* * * * * * *
53704346 AGTGGAGTAGATCGAATATGACAGATTTTACCTCCCTGAAGTTACAGTGGAGTACATTGAAGC
1 AGTGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTAAAGC
53704409 TAATCCTATC
Statistics
Matches: 290, Mismatches: 30, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
262 2 0.01
263 2 0.01
264 57 0.20
265 228 0.79
266 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (265 bp):
AGTGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTAAAGCCA
GTAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGAGTACAGATCTTATCTCCCCAAGCA
GTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTACAGTGGAATACATTGAAGC
CAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAAATTACAGATCTTGCCTTCCTGCA
TAGAC
Found at i:53704202 original size:44 final size:43
Alignment explanation
Indices: 53704154--53704338 Score: 124
Period size: 44 Copynumber: 4.2 Consensus size: 43
53704144 CCAGTAATTC
53704154 TATCTCCCTGGGCAACAGTGGAATAGATTGAAGAGTACAGATCT
1 TATCTCCCTGGGCAACAGTGGAATAGATTGAAGAGTA-AGATCT
** ** ** * * *
53704198 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGT-GGATTT
1 TATCTCCCTGGGCAACAGTGGAATAGATTGAAGA--GTAAGATCT
* ** * * *
53704242 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA-TTC-
1 TATCTCCCTG-GGCAACAGTGGAATAGATTGAAG--AGTAAGATCT
* * *
53704286 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAAATTACAGATCT
1 TATCTCCCTGGGCAACAGTGGAATAGATTGAAGAGTA-AGATCT
53704330 TATCTCCCT
1 TATCTCCCT
53704339 AAGCAGTAGT
Statistics
Matches: 101, Mismatches: 31, Indels: 18
0.67 0.21 0.12
Matches are distributed among these distances:
41 3 0.03
42 1 0.01
43 19 0.19
44 57 0.56
45 18 0.18
46 2 0.02
47 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (43 bp):
TATCTCCCTGGGCAACAGTGGAATAGATTGAAGAGTAAGATCT
Found at i:53704350 original size:44 final size:44
Alignment explanation
Indices: 53704286--53704382 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 44
53704276 CCAGTAATTC
** * *
53704286 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAAATTACAGATCT
1 TATCTCCCTAAGCAGCAGTGGAATAGATCGAAAATGACAGATCT
* * * *
53704330 TATCTCCCTAAGCAGTAGTGGAGTAGATCGAATATGACAGATTT
1 TATCTCCCTAAGCAGCAGTGGAATAGATCGAAAATGACAGATCT
*
53704374 TACCTCCCT
1 TATCTCCCT
53704383 GAAGTTACAG
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (44 bp):
TATCTCCCTAAGCAGCAGTGGAATAGATCGAAAATGACAGATCT
Found at i:53712974 original size:21 final size:21
Alignment explanation
Indices: 53712948--53713000 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
53712938 CGCTATTTTT
* *
53712948 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAATAACC
** *
53712969 AATCTCACTACTACAATAACT
1 AATCTCACCGCTACAATAACC
53712990 AATCTCACCGC
1 AATCTCACCGC
53713001 CACCGCTGTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.36, G:0.06, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAATAACC
Found at i:53716364 original size:36 final size:32
Alignment explanation
Indices: 53716324--53716388 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 32
53716314 TTTGATCCTA
53716324 CTCAATAAATAATTTTAATTTTTCATCCAAGTCTAG
1 CTCAATAAA-AATTTT--TTTTT-ATCCAAGTCTAG
*
53716360 CTCAATAAAACTTTTTTTTTATCCAAGTC
1 CTCAATAAAAATTTTTTTTTATCCAAGTC
53716389 ATATTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 9 0.32
33 5 0.18
35 5 0.18
36 9 0.32
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.43
Consensus pattern (32 bp):
CTCAATAAAAATTTTTTTTTATCCAAGTCTAG
Found at i:53718044 original size:18 final size:19
Alignment explanation
Indices: 53718021--53718058 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
53718011 TTTCAAGAAA
53718021 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAGAATTTT
53718039 TATAAATATTTAGAATTTT
1 TATAAATATTTAGAATTTT
53718058 T
1 T
53718059 TTTATTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Done.