Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 182 of 292
Found at i:54246594 original size:19 final size:18
Alignment explanation
Indices: 54246572--54246624 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
54246562 CTGTCACCAA
54246572 ATTCTGATTCTGATTTTGG
1 ATTCTGATTCTGATTTT-G
*
54246591 ATTCTGATTCTG-TCACTTG
1 ATTCTGATTCTGAT--TTTG
54246610 ATTCTGATTCTGATT
1 ATTCTGATTCTGATT
54246625 CTCATTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 1 0.03
19 25 0.86
20 3 0.10
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.51
Consensus pattern (18 bp):
ATTCTGATTCTGATTTTG
Found at i:54249315 original size:37 final size:37
Alignment explanation
Indices: 54249261--54249378 Score: 157
Period size: 37 Copynumber: 3.2 Consensus size: 37
54249251 CTATGCAGCA
**
54249261 GATGCACGGGGCCAAGGCGATGGAGGAGATGGGTTGC
1 GATGCACGGGGAGAAGGCGATGGAGGAGATGGGTTGC
* * *
54249298 GATGCATGGGGTGAAGGCGATGGAAGG-GATGGTTTGC
1 GATGCACGGGGAGAAGGCGATGG-AGGAGATGGGTTGC
*
54249335 GATGCACGGGGAGAAGGCGACGGAGGAGATGGGTTGC
1 GATGCACGGGGAGAAGGCGATGGAGGAGATGGGTTGC
*
54249372 AATGCAC
1 GATGCAC
54249379 AGGAGATTTG
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
36 3 0.04
37 64 0.91
38 3 0.04
ACGTcount: A:0.24, C:0.14, G:0.47, T:0.15
Consensus pattern (37 bp):
GATGCACGGGGAGAAGGCGATGGAGGAGATGGGTTGC
Found at i:54250202 original size:15 final size:15
Alignment explanation
Indices: 54250179--54250210 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
54250169 AAATAATAAT
54250179 TTATATATATTTATC
1 TTATATATATTTATC
*
54250194 TTATTTATATTTATC
1 TTATATATATTTATC
54250209 TT
1 TT
54250211 CTAAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATATATATTTATC
Found at i:54251301 original size:105 final size:105
Alignment explanation
Indices: 54251119--54251308 Score: 292
Period size: 105 Copynumber: 1.8 Consensus size: 105
54251109 CTCTATAACC
* * * *
54251119 ACTTTTGCGGCGTTATTATAGAAGCGCCGCTAATTCTTATATATTGCGGCGTTTTTAGTAAAATG
1 ACTTTTGCGGCGTTATTAAAGAAGCGCCGCTAATTCTAATATATTGCGGCGTTTTAAGTAAAACG
*
54251184 CCACTAATGCCTCTATAGCTACGTCGTCGTTTCTCTCAAG
66 CCACAAATGCCTCTATAGCTACGTCGTCGTTTCTCTCAAG
* * *
54251224 ACTTTTGCGGCGTT-TCTAAAGAAGCGTCGTTAATTCTAATATATTGTGGCGTTTTAAGTAAAAC
1 ACTTTTGCGGCGTTAT-TAAAGAAGCGCCGCTAATTCTAATATATTGCGGCGTTTTAAGTAAAAC
54251288 GCCACAAATGCCTCTATAGCT
65 GCCACAAATGCCTCTATAGCT
54251309 CATTAACATA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
104 1 0.01
105 75 0.99
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (105 bp):
ACTTTTGCGGCGTTATTAAAGAAGCGCCGCTAATTCTAATATATTGCGGCGTTTTAAGTAAAACG
CCACAAATGCCTCTATAGCTACGTCGTCGTTTCTCTCAAG
Found at i:54252234 original size:62 final size:62
Alignment explanation
Indices: 54252160--54252284 Score: 169
Period size: 62 Copynumber: 2.0 Consensus size: 62
54252150 TTTTTAACAG
* * * *
54252160 TATAAACCTTTTTTTGTTGTATTATATAGGTTTTGAGAAGTTGATGTCATGTTTATGTTATT
1 TATAAACCTTTTTATGTTGTATTATATAGATTTTGAGAAGTTCATATCATGTTTATGTTATT
* * * **
54252222 TATAAACCTTTTTATGTTGTTTTATATTGATTTTGAGATGTTCATATTGTGTTTATGTTATT
1 TATAAACCTTTTTATGTTGTATTATATAGATTTTGAGAAGTTCATATCATGTTTATGTTATT
54252284 T
1 T
54252285 TTATGTCATA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.23, C:0.05, G:0.16, T:0.56
Consensus pattern (62 bp):
TATAAACCTTTTTATGTTGTATTATATAGATTTTGAGAAGTTCATATCATGTTTATGTTATT
Found at i:54255112 original size:90 final size:90
Alignment explanation
Indices: 54254913--54255112 Score: 206
Period size: 90 Copynumber: 2.2 Consensus size: 90
54254903 TAAGACGGGT
* * * * * *
54254913 TTGATGAATTCAGCAGATTTATAGGATGAACTACTAGAAGCTCTTAATGATTTCATAGCCTAAGG
1 TTGATGAATTCATCAAATTTATAAGATGAACCACTAGAAGCTCTTAATGAATTCATAGCCTAAGC
* * * *
54254978 TTTTGGTGGTCCTATTGAGACATAC
66 TTTGGGTGGTCCCAGTGAGACAGAC
* * ** * * *
54255003 TTGATGAA-CCTGTTGAATTTATAAGATGAGCCACTA-AATGTTCTTAATGAATTCATATCCTAA
1 TTGATGAATTC-ATCAAATTTATAAGATGAACCACTAGAA-GCTCTTAATGAATTCATAGCCTAA
*
54255066 GCTTTGGGTGGTCCCAGTGAGACGGAC
64 GCTTTGGGTGGTCCCAGTGAGACAGAC
54255093 TTGATGAATTCATCAAATTT
1 TTGATGAATTCATCAAATTT
54255113 TTTAAACTGA
Statistics
Matches: 85, Mismatches: 22, Indels: 6
0.75 0.19 0.05
Matches are distributed among these distances:
89 3 0.04
90 81 0.95
91 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.34
Consensus pattern (90 bp):
TTGATGAATTCATCAAATTTATAAGATGAACCACTAGAAGCTCTTAATGAATTCATAGCCTAAGC
TTTGGGTGGTCCCAGTGAGACAGAC
Found at i:54255596 original size:28 final size:28
Alignment explanation
Indices: 54255552--54255659 Score: 121
Period size: 28 Copynumber: 3.9 Consensus size: 28
54255542 AATATGACCG
* * *
54255552 TTACAATATAACCGTTGGAATCT-AAGTA
1 TTACAATATGACTGTTGGAATCTGGA-TA
* *
54255580 TTACAATATGACTGTTGGAATCTGGTTG
1 TTACAATATGACTGTTGGAATCTGGATA
*
54255608 TTACAATAT-AGCTGTTGGAATCTGGACA
1 TTACAATATGA-CTGTTGGAATCTGGATA
*
54255636 TTACAATATGACTGTTGGGATCTG
1 TTACAATATGACTGTTGGAATCTG
54255660 ACCGTTGCAA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
27 1 0.01
28 66 0.97
29 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (28 bp):
TTACAATATGACTGTTGGAATCTGGATA
Found at i:54255670 original size:28 final size:27
Alignment explanation
Indices: 54255550--54255673 Score: 108
Period size: 28 Copynumber: 4.4 Consensus size: 27
54255540 AAAATATGAC
* *
54255550 CGTTACAATATAACCGTTGGAATCT-A
1 CGTTACAATATGACTGTTGGAATCTGA
* *
54255576 AGTATTACAATATGACTGTTGGAATCTGGT
1 CG--TTACAATATGACTGTTGGAATCT-GA
*
54255606 TGTTACAATAT-AGCTGTTGGAATCTGGA
1 CGTTACAATATGA-CTGTTGGAATCT-GA
* *
54255634 CATTACAATATGACTGTTGGGATCTGA
1 CGTTACAATATGACTGTTGGAATCTGA
*
54255661 CCGTTGCAATATG
1 -CGTTACAATATG
54255674 GTCGTTAATT
Statistics
Matches: 80, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
26 1 0.01
27 3 0.04
28 74 0.93
29 1 0.01
30 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.34
Consensus pattern (27 bp):
CGTTACAATATGACTGTTGGAATCTGA
Found at i:54255671 original size:56 final size:56
Alignment explanation
Indices: 54255546--54255672 Score: 157
Period size: 56 Copynumber: 2.3 Consensus size: 56
54255536 TGCAAAAATA
*
54255546 TGACCGTTACAATATAACCGTTGGAATCTAAGTATTACAATATGACTGTTGGAATC
1 TGACCGTTACAATATAACCGTTGGAATCTAAGCATTACAATATGACTGTTGGAATC
*** * * * *
54255602 TGGTTGTTACAATATAGCTGTTGGAATCT-GGACATTACAATATGACTGTTGGGATC
1 TGACCGTTACAATATAACCGTTGGAATCTAAG-CATTACAATATGACTGTTGGAATC
*
54255658 TGACCGTTGCAATAT
1 TGACCGTTACAATAT
54255673 GGTCGTTAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
55 1 0.02
56 57 0.98
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (56 bp):
TGACCGTTACAATATAACCGTTGGAATCTAAGCATTACAATATGACTGTTGGAATC
Found at i:54257470 original size:2 final size:2
Alignment explanation
Indices: 54257463--54257487 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54257453 AGATAGGTTA
54257463 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
54257488 AACTTTTCTT
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:54257801 original size:27 final size:28
Alignment explanation
Indices: 54257761--54257830 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
54257751 TACTCTTTAA
* *
54257761 AATTTTAAATTTAACTTTTT-TATT-TTT
1 AATTTTAAAATTAAATTTTTAT-TTGTTT
*
54257788 ATTTTTAAAATTAAATTTTTATTTGTTT
1 AATTTTAAAATTAAATTTTTATTTGTTT
*
54257816 AATTTAAAAATTAAA
1 AATTTTAAAATTAAA
54257831 GTTGAATTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 19 0.53
28 17 0.47
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (28 bp):
AATTTTAAAATTAAATTTTTATTTGTTT
Found at i:54257807 original size:28 final size:28
Alignment explanation
Indices: 54257761--54257830 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
54257751 TACTCTTTAA
* *
54257761 AATTTT-AAATTTAACTTTT-TTATTTTT
1 AATTTTAAAATTAAACTTTTATT-TGTTT
* *
54257788 ATTTTTAAAATTAAATTTTTATTTGTTT
1 AATTTTAAAATTAAACTTTTATTTGTTT
*
54257816 AATTTAAAAATTAAA
1 AATTTTAAAATTAAA
54257831 GTTGAATTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
27 5 0.14
28 28 0.80
29 2 0.06
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (28 bp):
AATTTTAAAATTAAACTTTTATTTGTTT
Found at i:54260535 original size:40 final size:40
Alignment explanation
Indices: 54260490--54260619 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
54260480 CGGAATACAA
54260490 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* ** *
54260530 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
54260570 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
54260610 CCGGATATAA
1 CCGGATATAA
54260620 TTTCCAGCAT
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 3 0.04
40 73 0.96
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:54268538 original size:40 final size:40
Alignment explanation
Indices: 54268493--54268659 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
54268483 CGGAATACAA
54268493 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* ** *
54268533 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
54268573 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
*** * * * *
54268613 CCGGATATAATTTCCAGCA-TAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
54268652 CCGGATAT
1 CCGGATAT
54268660 CATTCAATTG
Statistics
Matches: 105, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
39 25 0.24
40 80 0.76
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:54278088 original size:20 final size:19
Alignment explanation
Indices: 54278052--54278090 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
54278042 CTTTAGGATT
*
54278052 TATTTTTTTTTCCTTCTTC
1 TATTTTTTATTCCTTCTTC
54278071 TATTTTTTATT-CTT-TTC
1 TATTTTTTATTCCTTCTTC
54278088 TAT
1 TAT
54278091 CCTTCTCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 3 0.16
19 10 0.53
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTTTTTATTCCTTCTTC
Found at i:54279423 original size:20 final size:20
Alignment explanation
Indices: 54279393--54279437 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
54279383 CTGTTTTATT
54279393 ATGGG-CCAACTGTATTAAA
1 ATGGGCCCAACTGTATTAAA
* *
54279412 ATGGGCCCAACTGTGTTAAT
1 ATGGGCCCAACTGTATTAAA
54279432 ATGGGC
1 ATGGGC
54279438 AAGACCCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (20 bp):
ATGGGCCCAACTGTATTAAA
Found at i:54279506 original size:28 final size:27
Alignment explanation
Indices: 54279466--54279518 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
54279456 ACTTGTAATA
* *
54279466 GGGCTATGGCCCAGATTAATATTGATAT
1 GGGCTAAGGCCCAG-TTAACATTGATAT
54279494 GGGCTAAGGCCCAGTTAACATTGAT
1 GGGCTAAGGCCCAGTTAACATTGAT
54279519 TTCTGAATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.28
Consensus pattern (27 bp):
GGGCTAAGGCCCAGTTAACATTGATAT
Found at i:54285253 original size:3 final size:3
Alignment explanation
Indices: 54285247--54285277 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
54285237 TGGTGGTGGT
54285247 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA G
54285278 AAGTCTCATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:54285534 original size:42 final size:43
Alignment explanation
Indices: 54285436--54285536 Score: 134
Period size: 43 Copynumber: 2.4 Consensus size: 43
54285426 ATATCCCATA
*
54285436 ATAATATCCTATAATATCCTATTAGGAATAAAATTTCTAAGAG
1 ATAATATCCTATAATATCCTATTAGGAATAAAATTTCTAAAAG
* * * *
54285479 ATAATATCTTATAATATCTTTTTAGGAAT-CAATTTGCTAAAAG
1 ATAATATCCTATAATATCCTATTAGGAATAAAATTT-CTAAAAG
54285522 AT-ATATCCTATAATA
1 ATAATATCCTATAATA
54285537 ATATCTTAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
42 17 0.33
43 34 0.67
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.39
Consensus pattern (43 bp):
ATAATATCCTATAATATCCTATTAGGAATAAAATTTCTAAAAG
Found at i:54287136 original size:9 final size:9
Alignment explanation
Indices: 54287122--54287146 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
54287112 TTTATATAGG
54287122 GAGAGTTTA
1 GAGAGTTTA
54287131 GAGAGTTTA
1 GAGAGTTTA
54287140 GAGAGTT
1 GAGAGTT
54287147 CAATTATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (9 bp):
GAGAGTTTA
Found at i:54287316 original size:20 final size:18
Alignment explanation
Indices: 54287264--54287317 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
54287254 ATATAAAAGA
54287264 TAAATATTAAATTAA-AT
1 TAAATATTAAATTAATAT
54287281 TAAATATTAAGA-TAATCACT
1 TAAATATTAA-ATTAAT-A-T
*
54287301 TCAATATTAAATTAATA
1 TAAATATTAAATTAATA
54287318 AAATACTATC
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
17 13 0.42
18 1 0.03
19 3 0.10
20 14 0.45
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.39
Consensus pattern (18 bp):
TAAATATTAAATTAATAT
Found at i:54287375 original size:68 final size:70
Alignment explanation
Indices: 54287233--54287377 Score: 170
Period size: 68 Copynumber: 2.1 Consensus size: 70
54287223 ATATTAAATC
* * *
54287233 TATTAAATTAATAGAATACTTATATAAAAGATAAATATTAAATTAAATTAAATATTAAGATAATC
1 TATTAAATTAATAAAATAC-T-TATAAAAGATAAATATTAAATTAAATTAAATATTAAAATAATA
**
54287298 ACTTCAA
64 AAATCAA
* * *
54287305 TATTAAATTAATAAAATAC-TAT-CAAGATAAGTATTAAATTAAATTTAATATTAAAACTAATAA
1 TATTAAATTAATAAAATACTTATAAAAGATAAATATTAAATTAAATTAAATATTAAAA-TAATAA
54287368 AAT-AA
65 AATCAA
54287373 TATTA
1 TATTA
54287378 TTTTTGAAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
68 37 0.58
69 9 0.14
72 18 0.28
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (70 bp):
TATTAAATTAATAAAATACTTATAAAAGATAAATATTAAATTAAATTAAATATTAAAATAATAAA
ATCAA
Found at i:54290926 original size:41 final size:41
Alignment explanation
Indices: 54290881--54290998 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
54290871 TGAAAGATAA
54290881 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
54290922 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
54290952 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
54290993 ATGTAG
1 ATGTAG
54290999 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:54290937 original size:71 final size:71
Alignment explanation
Indices: 54290849--54291012 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
54290839 GAGATGTATC
54290849 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
54290914 AGGACA
66 AGGACA
54290920 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
54290985 AGGACA
66 AGGACA
54290991 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
54291013 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:54297836 original size:41 final size:41
Alignment explanation
Indices: 54297791--54297908 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
54297781 TGAAAGATAA
54297791 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
54297832 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
54297862 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
54297903 ATGTAG
1 ATGTAG
54297909 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:54297847 original size:71 final size:71
Alignment explanation
Indices: 54297759--54297922 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
54297749 GAGATGTATC
54297759 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
54297824 AGGACA
66 AGGACA
54297830 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
54297895 AGGACA
66 AGGACA
54297901 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
54297923 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:54305413 original size:41 final size:41
Alignment explanation
Indices: 54305368--54305485 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
54305358 TGAAAGATAA
54305368 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
54305409 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
54305439 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
54305480 ATGTAG
1 ATGTAG
54305486 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:54305424 original size:71 final size:71
Alignment explanation
Indices: 54305336--54305499 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
54305326 GAGATGTATC
54305336 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
54305401 AGGACA
66 AGGACA
54305407 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
54305472 AGGACA
66 AGGACA
54305478 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
54305500 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:54307049 original size:8 final size:7
Alignment explanation
Indices: 54307014--54307050 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
54307004 ATAATATGAG
54307014 TAAACCC
1 TAAACCC
54307021 TAAACCC
1 TAAACCC
*
54307028 TAAACCT
1 TAAACCC
54307035 TAAACCC
1 TAAACCC
54307042 TAAAACCC
1 T-AAACCC
54307050 T
1 T
54307051 TAGGACAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.43, C:0.38, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:54310260 original size:26 final size:26
Alignment explanation
Indices: 54310214--54310265 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
54310204 ATTTTAATCC
*
54310214 TTTACTTTATTTTATTGTTTAATTTA
1 TTTACTTTATTTGATTGTTTAATTTA
* *
54310240 TTTATTTTATTATGATT-TTTACTTTA
1 TTTACTTTATT-TGATTGTTTAATTTA
54310266 AATTTTGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (26 bp):
TTTACTTTATTTGATTGTTTAATTTA
Found at i:54310600 original size:18 final size:17
Alignment explanation
Indices: 54310569--54310610 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
54310559 TTTATGTGCA
54310569 TATTTTTTCATTATTAT
1 TATTTTTTCATTATTAT
*
54310586 TATTATTTTCTTTATTATT
1 TATT-TTTTCATTATTA-T
54310605 TATTTT
1 TATTTT
54310611 ATTTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 4 0.18
18 13 0.59
19 5 0.23
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (17 bp):
TATTTTTTCATTATTAT
Found at i:54310604 original size:21 final size:20
Alignment explanation
Indices: 54310569--54310617 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
54310559 TTTATGTGCA
54310569 TATTTTTTCATTA-TTATTAT
1 TATTTTTTCATTATTTATT-T
*
54310589 TATTTTCTTTATTATTTATTT
1 TATTTT-TTCATTATTTATTT
54310610 TATTTTTT
1 TATTTTTT
54310618 ATTGTTCATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 8 0.31
21 13 0.50
22 5 0.19
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (20 bp):
TATTTTTTCATTATTTATTT
Found at i:54310609 original size:16 final size:16
Alignment explanation
Indices: 54310582--54310620 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
54310572 TTTTTCATTA
*
54310582 TTATTA-TTATTTTCT
1 TTATTATTTATTTTAT
54310597 TTATTATTTATTTTAT
1 TTATTATTTATTTTAT
*
54310613 TTTTTATT
1 TTATTATT
54310621 GTTCATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (16 bp):
TTATTATTTATTTTAT
Found at i:54310618 original size:12 final size:12
Alignment explanation
Indices: 54310579--54310620 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
54310569 TATTTTTTCA
54310579 TTATTATTATTAT
1 TTATT-TTATTAT
54310592 TT-TCTTTATTAT
1 TTAT-TTTATTAT
*
54310604 TTATTTTATTTT
1 TTATTTTATTAT
54310616 TTATT
1 TTATT
54310621 GTTCATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 22 0.85
13 4 0.15
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (12 bp):
TTATTTTATTAT
Found at i:54312888 original size:21 final size:21
Alignment explanation
Indices: 54312862--54312906 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
54312852 ATAATTAGAA
*
54312862 TAATTAGAATT-ATTTCTTTAT
1 TAATTAAAATTCATTT-TTTAT
*
54312883 TAATTAAAATTCATTTTTTTT
1 TAATTAAAATTCATTTTTTAT
54312904 TAA
1 TAA
54312907 AAATCATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (21 bp):
TAATTAAAATTCATTTTTTAT
Found at i:54315092 original size:17 final size:18
Alignment explanation
Indices: 54315052--54315095 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
54315042 GTTTTTGCAG
54315052 ATTTGATTTTAATACTTTA
1 ATTT-ATTTTAATACTTTA
* *
54315071 CTTTATTTTATTA-TTTA
1 ATTTATTTTAATACTTTA
54315088 ATTTATTT
1 ATTTATTT
54315096 ATTTTATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 11 0.50
18 8 0.36
19 3 0.14
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (18 bp):
ATTTATTTTAATACTTTA
Found at i:54315113 original size:21 final size:21
Alignment explanation
Indices: 54315067--54315118 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 21
54315057 ATTTTAATAC
54315067 TTTACTTTATTTTATTATTTAA
1 TTTACTTTATTTTATTATTT-A
54315089 TTTA-TTTATTTTATTATGATT-
1 TTTACTTTATTTTATTAT--TTA
54315110 TTTACTTTA
1 TTTACTTTA
54315119 AATTTTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 17 0.63
22 8 0.30
23 2 0.07
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTACTTTATTTTATTATTTA
Found at i:54315371 original size:4 final size:4
Alignment explanation
Indices: 54315350--54315386 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
54315340 TTTTCCTCAA
* *
54315350 TATT CATT TATG TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT T
54315387 TCTTTATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (4 bp):
TATT
Found at i:54315457 original size:18 final size:18
Alignment explanation
Indices: 54315431--54315468 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
54315421 CATGCGCATA
*
54315431 TTTTGTCATTATTATTAT
1 TTTTATCATTATTATTAT
54315449 TTTTATCATTATTATTAT
1 TTTTATCATTATTATTAT
54315467 TT
1 TT
54315469 ACTTTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTTATCATTATTATTAT
Found at i:54315461 original size:15 final size:14
Alignment explanation
Indices: 54315441--54315480 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
54315431 TTTTGTCATT
54315441 ATTATTATTTTTATC
1 ATTATTATTTTTA-C
54315456 ATTATTATTATTTAC
1 ATTATTATT-TTTAC
*
54315471 TTTATTATTT
1 ATTATTATTT
54315481 ACTTTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 1 0.04
15 18 0.78
16 4 0.17
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTATTATTTTTAC
Found at i:54315475 original size:12 final size:12
Alignment explanation
Indices: 54315460--54315488 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
54315450 TTTATCATTA
54315460 TTATTATTTACT
1 TTATTATTTACT
54315472 TTATTATTTACT
1 TTATTATTTACT
54315484 TTATT
1 TTATT
54315489 TTTTTATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATTATTTACT
Found at i:54316817 original size:29 final size:29
Alignment explanation
Indices: 54316761--54316818 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
54316751 TTTTTTCAAA
*
54316761 TTACAAAAATAGGCCAAATTTTTGAAAAT
1 TTACAAAAATAGGCCAAATTTTGGAAAAT
* *
54316790 TTACAAGAATGGGCC-AATTTTGGTAAAAT
1 TTACAAAAATAGGCCAAATTTTGG-AAAAT
54316819 GCTTACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (29 bp):
TTACAAAAATAGGCCAAATTTTGGAAAAT
Found at i:54318857 original size:24 final size:24
Alignment explanation
Indices: 54318829--54318880 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
54318819 TTAGTAAGTC
* *
54318829 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* * *
54318853 AAATATATTATATTAATAAATACT
1 AAATAAACTATACTAATAAATACT
54318877 AAAT
1 AAAT
54318881 CTTTTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:54320820 original size:24 final size:24
Alignment explanation
Indices: 54320792--54320841 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
54320782 TTAGTAGGTC
* *
54320792 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
54320816 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
54320840 AA
1 AA
54320842 TTTTTCTACA
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:0.54, C:0.10, G:0.04, T:0.32
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:54347345 original size:64 final size:64
Alignment explanation
Indices: 54347263--54347398 Score: 148
Period size: 64 Copynumber: 2.1 Consensus size: 64
54347253 ATATTAGTGC
* * *
54347263 AGGATTCACATGGGCCAAGGACACAGA-CGTGTATCTAAGCCATGTAACTCACTATTTACAAAAT
1 AGGA-TCACACGGACCAAGGACA-AGAGCGTGTATCCAAGCCATGTAACTCACTATTTACAAAAT
*
54347327 T
64 A
* * * * * * *
54347328 AGGATCACACGGACCAAGGACATGAGCTTGTGTCCAGGTCGTGTGACTCACTATTTACAAAATA
1 AGGATCACACGGACCAAGGACAAGAGCGTGTATCCAAGCCATGTAACTCACTATTTACAAAATA
54347392 AGGATCA
1 AGGATCA
54347399 TTGTAGCACC
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
63 2 0.03
64 53 0.90
65 4 0.07
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (64 bp):
AGGATCACACGGACCAAGGACAAGAGCGTGTATCCAAGCCATGTAACTCACTATTTACAAAATA
Found at i:54348365 original size:27 final size:27
Alignment explanation
Indices: 54348310--54348448 Score: 162
Period size: 27 Copynumber: 5.2 Consensus size: 27
54348300 AGCATGGCTG
* *
54348310 CCAGA-ACAGATAATGTGACAGAGTCA
1 CCAGATACAGATAATGTGGCAGAGCCA
54348336 CCAGATACA-ATAATCGTGGCAGAGCCA
1 CCAGATACAGATAAT-GTGGCAGAGCCA
54348363 CCAGA-ACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
*
54348390 CCAGAT-CAGATATTTGTGGCAGAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
* *
54348417 CCAGAT-CAGATATTTGTGGCATAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
54348444 CCAGA
1 CCAGA
54348449 ACGCTTTCTC
Statistics
Matches: 104, Mismatches: 4, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
26 13 0.12
27 89 0.86
28 2 0.02
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (27 bp):
CCAGATACAGATAATGTGGCAGAGCCA
Found at i:54348392 original size:54 final size:54
Alignment explanation
Indices: 54348310--54348448 Score: 192
Period size: 54 Copynumber: 2.6 Consensus size: 54
54348300 AGCATGGCTG
* *
54348310 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACA-ATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* *
54348363 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
* * *
54348417 CCAGATCAGATATTTGTGGCATAGCCACCAGA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGA
54348449 ACGCTTTCTC
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
53 14 0.18
54 63 0.82
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (54 bp):
CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:54350102 original size:26 final size:26
Alignment explanation
Indices: 54350066--54350175 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
54350056 CATGAAATTC
54350066 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
54350092 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
54350118 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
54350144 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
54350170 TTATCA
1 TTATCA
54350176 ATTTGTATCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:54356343 original size:32 final size:32
Alignment explanation
Indices: 54356307--54356369 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
54356297 CTAGCTGATC
* ** * *
54356307 TTAGAATCAATATTAGTTGGGCCTATCCCATA
1 TTAGAACCAATACCAGTTGCGCCTAGCCCATA
54356339 TTAGAACCAATACCAGTTGCGCCTAGCCCAT
1 TTAGAACCAATACCAGTTGCGCCTAGCCCAT
54356370 TTCAATATCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (32 bp):
TTAGAACCAATACCAGTTGCGCCTAGCCCATA
Found at i:54356523 original size:23 final size:23
Alignment explanation
Indices: 54356490--54356536 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
54356480 ACTTACAGTG
* *
54356490 TTAGCATCGGTTGCGGCACTAAC
1 TTAGCACCGGTTGCAGCACTAAC
*
54356513 TTAGCACCGGTTGTAGCACTAAC
1 TTAGCACCGGTTGCAGCACTAAC
54356536 T
1 T
54356537 AGAATCCCGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (23 bp):
TTAGCACCGGTTGCAGCACTAAC
Found at i:54356769 original size:27 final size:27
Alignment explanation
Indices: 54356727--54356817 Score: 137
Period size: 27 Copynumber: 3.4 Consensus size: 27
54356717 AGGCATAATC
*
54356727 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
* *
54356754 GTCATTTTACCCTACATGGGTATTACA
1 GTCATTTTACCCTACAGGGGTATTACG
* *
54356781 GTCATTTTACCCTATAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
54356808 GTCATTTTAC
1 GTCATTTTAC
54356818 TAATTTTGAG
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGTATTACG
Found at i:54383849 original size:19 final size:20
Alignment explanation
Indices: 54383825--54383873 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
54383815 ACAAAACATG
54383825 TTAACATGAATTAA-ATAAA
1 TTAACATGAATTAATATAAA
54383844 TTAACATGAATTAATATAAA
1 TTAACATGAATTAATATAAA
54383864 TTAACATGAA
1 TTAACATGAA
54383874 AATCATGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (20 bp):
TTAACATGAATTAATATAAA
Found at i:54383855 original size:10 final size:10
Alignment explanation
Indices: 54383825--54383873 Score: 64
Period size: 10 Copynumber: 5.0 Consensus size: 10
54383815 ACAAAACATG
54383825 TTAACATGAA
1 TTAACATGAA
*
54383835 TTAA-ATAAA
1 TTAACATGAA
54383844 TTAACATGAA
1 TTAACATGAA
* *
54383854 TTAATATAAA
1 TTAACATGAA
54383864 TTAACATGAA
1 TTAACATGAA
54383874 AATCATGTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
9 8 0.25
10 24 0.75
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (10 bp):
TTAACATGAA
Found at i:54386260 original size:26 final size:25
Alignment explanation
Indices: 54386231--54386301 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 25
54386221 AATAAAAAAC
54386231 AAACAAAGAAGAAAAAGAAAAAAGAA
1 AAACAAAG-AGAAAAAGAAAAAAGAA
* * *
54386257 AAACGAATGAGAAAAATAAAGAAGAA
1 AAAC-AAAGAGAAAAAGAAAAAAGAA
* *
54386283 GAACGAAGGAGAAAAAGAA
1 AAAC-AAAGAGAAAAAGAA
54386302 CGAAGGAGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 35 0.92
27 3 0.08
ACGTcount: A:0.72, C:0.04, G:0.21, T:0.03
Consensus pattern (25 bp):
AAACAAAGAGAAAAAGAAAAAAGAA
Found at i:54386282 original size:13 final size:13
Alignment explanation
Indices: 54386235--54386306 Score: 58
Period size: 13 Copynumber: 5.5 Consensus size: 13
54386225 AAAAACAAAC
54386235 AAAGAAGAAAAAG
1 AAAGAAGAAAAAG
*
54386248 AAAAAAGAAAAACG
1 AAAGAAGAAAAA-G
* *
54386262 AATG-AGAAAAAT
1 AAAGAAGAAAAAG
*
54386274 AAAGAAGAAGAACG
1 AAAGAAGAA-AAAG
*
54386288 -AAGGAGAAAAAG
1 AAAGAAGAAAAAG
*
54386300 AACGAAG
1 AAAGAAG
54386307 GAGAAAAAGA
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
12 6 0.14
13 33 0.75
14 5 0.11
ACGTcount: A:0.69, C:0.04, G:0.24, T:0.03
Consensus pattern (13 bp):
AAAGAAGAAAAAG
Found at i:54386306 original size:26 final size:26
Alignment explanation
Indices: 54386240--54386311 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 26
54386230 CAAACAAAGA
* * *
54386240 AGAAAAAGAAAAAAGAAAAACGAATG
1 AGAAAAAGAAAGAAGAAGAACGAAGG
*
54386266 AGAAAAATAAAGAAGAAGAACGAAGG
1 AGAAAAAGAAAGAAGAAGAACGAAGG
* *
54386292 AGAAAAAGAACGAAGGAGAA
1 AGAAAAAGAAAGAAGAAGAA
54386312 AAAGAACTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.68, C:0.04, G:0.25, T:0.03
Consensus pattern (26 bp):
AGAAAAAGAAAGAAGAAGAACGAAGG
Found at i:54386331 original size:14 final size:16
Alignment explanation
Indices: 54386276--54386328 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
54386266 AGAAAAATAA
*
54386276 AGAAGAAGAACGAAGG
1 AGAAAAAGAACGAAGG
54386292 AGAAAAAGAACGAAGG
1 AGAAAAAGAACGAAGG
*
54386308 AGAAAAAGAACTAAGG
1 AGAAAAAGAACGAAGG
54386324 A-AAAA
1 AGAAAA
54386329 GAATAAAGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
15 4 0.11
16 31 0.89
ACGTcount: A:0.64, C:0.06, G:0.28, T:0.02
Consensus pattern (16 bp):
AGAAAAAGAACGAAGG
Found at i:54386562 original size:27 final size:27
Alignment explanation
Indices: 54386532--54386586 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
54386522 ATGGATAAGG
*
54386532 ATAGTTTTTAAAATAATAAAGTTTTTA
1 ATAGTTTTTAAAATAATAAAGCTTTTA
54386559 ATAGTTTTTAAAATAATAAAGCTTTTA
1 ATAGTTTTTAAAATAATAAAGCTTTTA
54386586 A
1 A
54386587 CGATACGACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (27 bp):
ATAGTTTTTAAAATAATAAAGCTTTTA
Found at i:54387569 original size:20 final size:21
Alignment explanation
Indices: 54387523--54387575 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
54387513 TACTAATTAC
54387523 AAATATTTAATAATTATATTT
1 AAATATTTAATAATTATATTT
54387544 AAATATTTAA-AA-TATAGTTT
1 AAATATTTAATAATTATA-TTT
*
54387564 ATATATTCTAAT
1 AAATATT-TAAT
54387576 TAAATTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 4 0.14
20 11 0.39
21 13 0.46
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
AAATATTTAATAATTATATTT
Found at i:54388215 original size:20 final size:19
Alignment explanation
Indices: 54388177--54388213 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
54388167 AAAATAAAAT
54388177 AAAATTTAAAATATTTATA
1 AAAATTTAAAATATTTATA
*
54388196 AAAATTTCAAA-ATTTATA
1 AAAATTTAAAATATTTATA
54388214 TATTTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATTTAAAATATTTATA
Found at i:54388730 original size:21 final size:21
Alignment explanation
Indices: 54388691--54388730 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
54388681 ATTATTTATT
*
54388691 ATATGTTATTTTGAAACATAA
1 ATATGTTATTTTAAAACATAA
54388712 ATATG-TATTTTAAATACAT
1 ATATGTTATTTTAAA-ACAT
54388731 GATTTCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
ATATGTTATTTTAAAACATAA
Found at i:54388868 original size:16 final size:16
Alignment explanation
Indices: 54388827--54388868 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
54388817 TATGGTACTA
54388827 ATATTTTTATATAATT
1 ATATTTTTATATAATT
*
54388843 AAATTTTTATAT-ATCT
1 ATATTTTTATATAAT-T
*
54388859 ATATTGTTAT
1 ATATTTTTAT
54388869 TTAAGCCTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 2 0.09
16 20 0.91
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (16 bp):
ATATTTTTATATAATT
Found at i:54389517 original size:2 final size:2
Alignment explanation
Indices: 54389510--54389551 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
54389500 CCAAATACAA
54389510 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54389552 GGGCGTAACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54399601 original size:39 final size:39
Alignment explanation
Indices: 54399517--54399706 Score: 310
Period size: 39 Copynumber: 4.9 Consensus size: 39
54399507 TATGGTAACC
* * * *
54399517 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCATAGCT
* *
54399557 TGCACAATTGCCTTCGGGCTTAGCCCGGGTATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
54399596 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
54399635 CGCACAATTGCCTTCGGGCTTAGCCCGG-TATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
54399673 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
54399707 CTCGAACATT
Statistics
Matches: 141, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
38 38 0.27
39 87 0.62
40 16 0.11
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.25
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
Found at i:54399698 original size:77 final size:78
Alignment explanation
Indices: 54399517--54399707 Score: 321
Period size: 77 Copynumber: 2.4 Consensus size: 78
54399507 TATGGTAACC
* * *
54399517 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTTGCACAATTGCCTTCGGGCTTAGCC
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
54399582 CGGGTATCATAGCT
65 CGGGTATCATAGCT
* *
54399596 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTGCCTTCGGGCTTAGCCC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCCC
54399661 -GGTATCATAGCT
66 GGGTATCATAGCT
54399673 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
54399708 TCGAACATTC
Statistics
Matches: 106, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
77 46 0.43
78 43 0.41
79 17 0.16
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.25
Consensus pattern (78 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCCC
GGGTATCATAGCT
Found at i:54404496 original size:40 final size:40
Alignment explanation
Indices: 54404388--54404557 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
54404378 CGGGATTTAA
* * * * *
54404388 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
54404428 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
54404468 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
54404508 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
54404548 CCGGATATAT
1 CCGGATATAT
54404558 TTCCAATGTT
Statistics
Matches: 113, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
39 1 0.01
40 112 0.99
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:54411678 original size:40 final size:40
Alignment explanation
Indices: 54411570--54411779 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
54411560 CGGGATTTAA
* * * * *
54411570 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
54411610 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
54411650 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
54411690 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
54411730 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
54411770 CCGGATATAT
1 CCGGATATAT
54411780 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:54415848 original size:39 final size:39
Alignment explanation
Indices: 54415764--54415993 Score: 370
Period size: 39 Copynumber: 5.9 Consensus size: 39
54415754 TATGGTAACC
* * ** * *
54415764 CGCACAAATGCCTTCGGGACTTAACCCGAATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGGTATCATAGCT
*
54415804 CGCACAATTTCCTTCGGGCTTAGCCCGGGTATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGGTATCATAGCT
* *
54415843 TGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGGTATCATAGCT
54415882 CGCACAATTGCCTTCGGGCTTAGCCCGGGTATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGGTATCATAGCT
54415921 CGCACAATTGCCTTCGGGCTTAGCCCGGGTATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGGTATCATAGCT
54415960 CGCACAATTGCCTTCGGGCTTAGCCCGGGTATCA
1 CGCACAATTGCCTTCGGGCTTAGCCCGGGTATCA
54415994 CTCGAACATT
Statistics
Matches: 178, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 162 0.91
40 16 0.09
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.25
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGGTATCATAGCT
Found at i:54436242 original size:84 final size:83
Alignment explanation
Indices: 54436134--54436299 Score: 278
Period size: 84 Copynumber: 2.0 Consensus size: 83
54436124 ATTTGTTCCT
* *
54436134 ATACGAAGAAGGAACGATCCTAAGAAGTCAATGCCCTATACGTCGAATAATTCAATCTCTAAAAT
1 ATACGAAGAAGGAACGATCCTAAGAAGTCAATGCCCCATACGTCGAATAATTCAATCTCCAAAAT
54436199 GTTTGTCAAGCGCATCTC
66 GTTTGTCAAGCGCATCTC
* *
54436217 ATACGAAGAAGGGAACGGTCCTAAGAAGTCAGTGCCCCATACGTCGAATAATTCAATCTCCAAAA
1 ATACGAAGAA-GGAACGATCCTAAGAAGTCAATGCCCCATACGTCGAATAATTCAATCTCCAAAA
*
54436282 TGTTTGTCAAGGGCATCT
65 TGTTTGTCAAGCGCATCT
54436300 AATTCCTCCT
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
83 10 0.13
84 67 0.87
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (83 bp):
ATACGAAGAAGGAACGATCCTAAGAAGTCAATGCCCCATACGTCGAATAATTCAATCTCCAAAAT
GTTTGTCAAGCGCATCTC
Found at i:54442532 original size:13 final size:14
Alignment explanation
Indices: 54442511--54442543 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
54442501 TTTATTAATG
54442511 AAATATATTAAA-AT
1 AAAT-TATTAAATAT
54442525 AAATTATTAAATAT
1 AAATTATTAAATAT
54442539 AAATT
1 AAATT
54442544 TATATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATTATTAAATAT
Found at i:54443476 original size:16 final size:16
Alignment explanation
Indices: 54443455--54443486 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
54443445 CTAATTGATT
54443455 CTTCAAAAACACTGTC
1 CTTCAAAAACACTGTC
54443471 CTTCAAAAACACTGTC
1 CTTCAAAAACACTGTC
54443487 ACTCCCCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.06, T:0.25
Consensus pattern (16 bp):
CTTCAAAAACACTGTC
Found at i:54446849 original size:14 final size:14
Alignment explanation
Indices: 54446832--54446858 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54446822 AAGGTATAGT
54446832 TTTGTGTTGTTTTG
1 TTTGTGTTGTTTTG
54446846 TTTGTGTTGTTTT
1 TTTGTGTTGTTTT
54446859 AATTTAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.26, T:0.74
Consensus pattern (14 bp):
TTTGTGTTGTTTTG
Found at i:54453447 original size:14 final size:14
Alignment explanation
Indices: 54453430--54453456 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54453420 GAGGTATAGT
54453430 TTTGTGTTGTTTTG
1 TTTGTGTTGTTTTG
54453444 TTTGTGTTGTTTT
1 TTTGTGTTGTTTT
54453457 AATTTAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.26, T:0.74
Consensus pattern (14 bp):
TTTGTGTTGTTTTG
Found at i:54454255 original size:21 final size:21
Alignment explanation
Indices: 54454229--54454308 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
54454219 GTCCTTGGTC
*
54454229 CACACGGTTGTGTGCCTCAGT
1 CACACGGCTGTGTGCCTCAGT
* **
54454250 CACACGGCTATGTGCCTCTCCT
1 CACACGGCTGTGTGCCTC-AGT
* *
54454272 CACACGGGC-GTGTACCTCAGC
1 CACAC-GGCTGTGTGCCTCAGT
*
54454293 CACACGGCTCTGTGCC
1 CACACGGCTGTGTGCC
54454309 CCTCCTCATA
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
20 3 0.07
21 26 0.58
22 13 0.29
23 3 0.07
ACGTcount: A:0.15, C:0.38, G:0.25, T:0.23
Consensus pattern (21 bp):
CACACGGCTGTGTGCCTCAGT
Found at i:54454290 original size:43 final size:43
Alignment explanation
Indices: 54454229--54454325 Score: 122
Period size: 43 Copynumber: 2.3 Consensus size: 43
54454219 GTCCTTGGTC
** * * *
54454229 CACACGGTTGTGTGCCTCAGTCACACGGCTATGTGCCTCTCCT
1 CACACGGGCGTGTACCTCAGCCACACGGCTATGTGCCCCTCCT
*
54454272 CACACGGGCGTGTACCTCAGCCACACGGCTCTGTGCCCCTCCT
1 CACACGGGCGTGTACCTCAGCCACACGGCTATGTGCCCCTCCT
* *
54454315 CATACAGGCGT
1 CACACGGGCGT
54454326 TTGACCTTCT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.15, C:0.38, G:0.24, T:0.23
Consensus pattern (43 bp):
CACACGGGCGTGTACCTCAGCCACACGGCTATGTGCCCCTCCT
Found at i:54457265 original size:18 final size:18
Alignment explanation
Indices: 54457230--54457274 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
54457220 GATTGAGATA
*
54457230 TATGTATGAGTTTGATTAT
1 TATGTAT-AGTTTAATTAT
54457249 TATGTATAGTTTAATTAT
1 TATGTATAGTTTAATTAT
54457267 TATGTATA
1 TATGTATA
54457275 ATTATCGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (18 bp):
TATGTATAGTTTAATTAT
Found at i:54457444 original size:25 final size:25
Alignment explanation
Indices: 54457410--54457466 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
54457400 GGACTCACCA
* *
54457410 CAGCTCGTATGACCTTATTGATTTG
1 CAGCTCGTATGAACTTACTGATTTG
*
54457435 CAGCTCGTATGAACTTACTGATTTT
1 CAGCTCGTATGAACTTACTGATTTG
54457460 CAGCTCG
1 CAGCTCG
54457467 GAAGAGCTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (25 bp):
CAGCTCGTATGAACTTACTGATTTG
Found at i:54457476 original size:25 final size:25
Alignment explanation
Indices: 54457423--54457476 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
54457413 CTCGTATGAC
* * *
54457423 CTTATTGATTTGCAGCTCGTATGAA
1 CTTACTGATTTGCAGCTCGGAAGAA
* *
54457448 CTTACTGATTTTCAGCTCGGAAGAG
1 CTTACTGATTTGCAGCTCGGAAGAA
54457473 CTTA
1 CTTA
54457477 TTGTTTATCG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (25 bp):
CTTACTGATTTGCAGCTCGGAAGAA
Found at i:54461972 original size:40 final size:40
Alignment explanation
Indices: 54461873--54462089 Score: 264
Period size: 40 Copynumber: 5.5 Consensus size: 40
54461863 GGATGATAAT
*
54461873 CGGGCTAAGTCCCGAAGGCATTT-TGCGCTAGTGACTAGT-TC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTA-TATC
* * *
54461914 CGAGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
*
54461954 CGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
*
54461994 CGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
* * *
54462034 CGGGCTATGTCCCGAAGGCA-TTGAGCAAG-TAGCTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATC
* *
54462073 C-GGTTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGG
54462090 TACTTGGCTT
Statistics
Matches: 156, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
38 15 0.10
39 14 0.09
40 101 0.65
41 22 0.14
42 4 0.03
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
Found at i:54470754 original size:29 final size:29
Alignment explanation
Indices: 54470688--54470758 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
54470678 CTTAATAATC
*
54470688 AACCACGCACACTTAGTGCCATGTACTTTA
1 AACC-CGCACACTTAGTGCCATGCACTTTA
*
54470718 AACTCGCACACTTAGTGCCATGCA-TTTCA
1 AACCCGCACACTTAGTGCCATGCACTTT-A
*
54470747 AGCCCGCACACT
1 AACCCGCACACT
54470759 AATCTCACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 3 0.08
29 30 0.83
30 3 0.08
ACGTcount: A:0.28, C:0.34, G:0.14, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCACTTTA
Found at i:54471413 original size:2 final size:2
Alignment explanation
Indices: 54471395--54471456 Score: 106
Period size: 2 Copynumber: 31.0 Consensus size: 2
54471385 TGATGGCCGA
* *
54471395 AT AT GT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54471437 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
54471457 CAGCTATACT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54473299 original size:40 final size:40
Alignment explanation
Indices: 54473199--54473416 Score: 257
Period size: 40 Copynumber: 5.5 Consensus size: 40
54473189 TGGATGATAA
* *
54473199 CCGGGCTAAGTCCCGAAGGCATTT-TGCGCTAGTAAATAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTA-TAT
* *
54473240 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
54473280 CCTGGCTAAGTCCCAAAGGCATTTGTACGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
54473320 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
54473360 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
54473399 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
54473417 TACTTGGCTT
Statistics
Matches: 156, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
38 15 0.10
39 15 0.10
40 98 0.63
41 24 0.15
42 4 0.03
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:54476299 original size:31 final size:31
Alignment explanation
Indices: 54476255--54476400 Score: 258
Period size: 31 Copynumber: 4.7 Consensus size: 31
54476245 TTAGTCTTGA
* *
54476255 CATAT-ACTCGGCCGAAGCCTTTCCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
54476285 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
54476316 CATATCACTGGGCCGAATCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
54476347 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
54476378 CATATCACTGGGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
54476401 ACTGTAAACG
Statistics
Matches: 111, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
30 5 0.05
31 106 0.95
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:54476518 original size:41 final size:42
Alignment explanation
Indices: 54476424--54476556 Score: 250
Period size: 42 Copynumber: 3.2 Consensus size: 42
54476414 TGGCCCTTAG
*
54476424 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
54476466 GCCCATTTCAATATCACATGTAATGTCAATGAATGT-TGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
54476507 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
54476549 GCCCATTT
1 GCCCATTT
54476557 GGGGAGACTA
Statistics
Matches: 89, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
41 41 0.46
42 48 0.54
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
Found at i:54476732 original size:25 final size:25
Alignment explanation
Indices: 54476704--54476773 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
54476694 CTCTTTTAAT
54476704 AACTGGGGCAAAGCCC-TTTCTGATA
1 AACTGGGGCAAAGCCCTTTTC-GATA
*
54476729 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
54476754 AACTGGGGCAGAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
54476774 AGCACTTCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
25 38 0.90
26 4 0.10
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:54477768 original size:55 final size:53
Alignment explanation
Indices: 54477678--54477833 Score: 152
Period size: 55 Copynumber: 2.9 Consensus size: 53
54477668 TTTCATCCTA
* * * * * *
54477678 CAAGGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTGTTAAC
1 CAAGGGTATTTTGATAATTTTACAAATCAAGGGTATTTCAGTAATTTGTAAAC
* * * *
54477731 CAATGGTATTTCT-ATAATTTTTAGAAAGTCAAGGGTATTTCTGTAATTTTGTAAAT
1 CAAGGGTATTT-TGATAA-TTTTACAAA-TCAAGGGTATTTCAGTAA-TTTGTAAAC
* * *
54477787 CAAGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTT
1 CAAGGGTATTTTGATAATTTTACAAATCAAGGGTATTTCAGTAATTT
54477834 CATAAACTTG
Statistics
Matches: 83, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
53 15 0.18
54 23 0.28
55 25 0.30
56 20 0.24
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.40
Consensus pattern (53 bp):
CAAGGGTATTTTGATAATTTTACAAATCAAGGGTATTTCAGTAATTTGTAAAC
Found at i:54477797 original size:27 final size:27
Alignment explanation
Indices: 54477705--54477833 Score: 120
Period size: 27 Copynumber: 4.7 Consensus size: 27
54477695 ATCTACAAAC
* * *
54477705 CAAGGGTATTTCAGTAA-TTTGTTAAC
1 CAAGGGTATTTCTGTAATTTTGTAAAT
* *
54477731 CAATGGTATTTCTATAATTTT-TAGAAAGT
1 CAAGGGTATTTCTGTAATTTTGT--AAA-T
54477760 CAAGGGTATTTCTGTAATTTTGTAAAT
1 CAAGGGTATTTCTGTAATTTTGTAAAT
**
54477787 CAAGGGTATTT-TGGTAATTTTACAAAT
1 CAAGGGTATTTCT-GTAATTTTGTAAAT
* *
54477814 TAAGGGTATTTCGGTAATTT
1 CAAGGGTATTTCTGTAATTT
54477834 CATAAACTTG
Statistics
Matches: 85, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
26 16 0.19
27 44 0.52
28 5 0.06
29 19 0.22
30 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.43
Consensus pattern (27 bp):
CAAGGGTATTTCTGTAATTTTGTAAAT
Found at i:54477889 original size:26 final size:26
Alignment explanation
Indices: 54477790--54477912 Score: 147
Period size: 27 Copynumber: 4.6 Consensus size: 26
54477780 TGTAAATCAA
* *
54477790 GGGTATTTTGGTAATTTTACAAATTAA
1 GGGTA-TTTGGTAATTTTACAAACTAG
* * *
54477817 GGGTATTTCGGTAATTTCATAAACTTG
1 GGGTATTT-GGTAATTTTACAAACTAG
*
54477844 TGGTATTTCGGTAATTTTACAAACTAG
1 GGGTATTT-GGTAATTTTACAAACTAG
*
54477871 GGGTATTTGGTAATTTTACAAATTAG
1 GGGTATTTGGTAATTTTACAAACTAG
54477897 GGGTATTTTGGTAATT
1 GGGTA-TTTGGTAATT
54477913 CTATCCTACA
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
26 25 0.30
27 58 0.70
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (26 bp):
GGGTATTTGGTAATTTTACAAACTAG
Found at i:54477901 original size:80 final size:81
Alignment explanation
Indices: 54477764--54477912 Score: 221
Period size: 80 Copynumber: 1.9 Consensus size: 81
54477754 GAAAGTCAAG
* **
54477764 GGTATTTCTGTAATTTTGTAAATCAAGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGT
1 GGTATTTCGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGT
54477829 AATTTCATAAACTTGT
66 AATTTCATAAACTTGT
* * *
54477845 GGTATTTCGGTAATTTTACAAA-CTAGGGGTA-TTTGGTAATTTTACAAATTAGGGGTATTTTGG
1 GGTATTTCGGTAATTTTACAAATC-AAGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGG
54477908 TAATT
65 TAATT
54477913 CTATCCTACA
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
80 36 0.59
81 25 0.41
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.44
Consensus pattern (81 bp):
GGTATTTCGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGT
AATTTCATAAACTTGT
Found at i:54477929 original size:80 final size:80
Alignment explanation
Indices: 54477760--54477954 Score: 209
Period size: 80 Copynumber: 2.4 Consensus size: 80
54477750 TTTAGAAAGT
* **
54477760 CAAGGGTATTTCTGTAATTTTGTAAATCAAGGGTATTTTGGTAATTTTACAAATTAAGGGTATTT
1 CAAGGGTATTTCAGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAATTAAGGGTATTT
54477825 CGGTAATTTCATAAA
66 CGGTAATTTCATAAA
** * * *
54477840 CTTGTGGTATTTCGGTAATTTTACAAA-CTAGGGGTA-TTTGGTAATTTTACAAATTAGGGGTAT
1 CAAG-GGTATTTCAGTAATTTTACAAATC-AAGGGTATTTTGGTAATTTTACAAATTAAGGGTAT
* **
54477903 TTTGGTAA-TTCTATCCTA
64 TTCGGTAATTTC-AT-AAA
* *
54477921 CAAGGGTATTTCAGTAATTTCAC-AATCGAGGGTA
1 CAAGGGTATTTCAGTAATTTTACAAATCAAGGGTA
54477955 AAACGGTAAT
Statistics
Matches: 94, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
79 10 0.11
80 56 0.60
81 28 0.30
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.40
Consensus pattern (80 bp):
CAAGGGTATTTCAGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAATTAAGGGTATTT
CGGTAATTTCATAAA
Found at i:54477981 original size:27 final size:27
Alignment explanation
Indices: 54477944--54478149 Score: 198
Period size: 27 Copynumber: 7.3 Consensus size: 27
54477934 GTAATTTCAC
* *
54477944 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTCTGTA
*
54477971 AA-CTGAGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAATGGTAATTCTGTA
*
54477998 AATTGAGGGTAAAACTGTAATTCTGTAATTCTGTA
1 AATCGAGGGTAAAA-TG-------GTAATTCTGTA
* *
54478033 AATCGAGAGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTCTGTA
* * *
54478060 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTCTGTA
* * *
54478087 AATCGATGGTGAAATGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTCTGTA
**
54478114 AATCGAGGGTAAAATGGTAATTCTACA
1 AATCGAGGGTAAAATGGTAATTCTGTA
54478141 AATCGAGGG
1 AATCGAGGG
54478150 CATTTCAGTA
Statistics
Matches: 149, Mismatches: 20, Indels: 20
0.79 0.11 0.11
Matches are distributed among these distances:
26 1 0.01
27 122 0.82
28 2 0.01
34 2 0.01
35 22 0.15
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (27 bp):
AATCGAGGGTAAAATGGTAATTCTGTA
Found at i:54478001 original size:107 final size:107
Alignment explanation
Indices: 54477773--54478006 Score: 231
Period size: 107 Copynumber: 2.2 Consensus size: 107
54477763 GGGTATTTCT
* * * * * *
54477773 GTAATTTTGTAAATCAAGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCATA
1 GTAATTTTGTAAATTAGGGGTATTTTGGTAATTCTACAAATCAAGGGTATTTCAGTAATTTCACA
** *** **
54477838 AACTTGTGGTATTTCGGTAATTTTACAAACTAGGGGTATTTG
66 AACGAGTGGTAAAACGGTAATTTTACAAACTAGGGGTAAATG
** **
54477880 GTAATTTTACAAATTAGGGGTATTTTGGTAATTCTATCCTA-CAAGGGTATTTCAGTAATTTCAC
1 GTAATTTTGTAAATTAGGGGTATTTTGGTAATTCTA-CAAATCAAGGGTATTTCAGTAATTTCAC
* **
54477944 AATCGAG-GGTAAAACGGTAATTTTGTAAACT-GAGGGTAAAATG
65 AAACGAGTGGTAAAACGGTAATTTTACAAACTAG-GGGT-AAATG
54477987 GTAATTTTGTAAATTGAGGG
1 GTAATTTTGTAAATT-AGGG
54478007 TAAAACTGTA
Statistics
Matches: 101, Mismatches: 22, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
105 1 0.01
106 23 0.23
107 71 0.70
108 6 0.06
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (107 bp):
GTAATTTTGTAAATTAGGGGTATTTTGGTAATTCTACAAATCAAGGGTATTTCAGTAATTTCACA
AACGAGTGGTAAAACGGTAATTTTACAAACTAGGGGTAAATG
Found at i:54478027 original size:35 final size:35
Alignment explanation
Indices: 54477987--54478056 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
54477977 GGGTAAAATG
* * *
54477987 GTAATTTTGTAAATTGAGGGTAAAACT-GTAATTCT
1 GTAATTCTGTAAATCGAGAGTAAAA-TGGTAATTCT
54478022 GTAATTCTGTAAATCGAGAGTAAAATGGTAATTCT
1 GTAATTCTGTAAATCGAGAGTAAAATGGTAATTCT
54478057 ATAAATCGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 1 0.03
35 30 0.97
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.37
Consensus pattern (35 bp):
GTAATTCTGTAAATCGAGAGTAAAATGGTAATTCT
Found at i:54487405 original size:25 final size:26
Alignment explanation
Indices: 54487350--54487405 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
54487340 GGCTCACCAC
54487350 AGCTCGTATGAGCTTACCAATTTGCA
1 AGCTCGTATGAGCTTACCAATTTGCA
* *
54487376 A-CTCGTATGAGCTTACCGATTT-TA
1 AGCTCGTATGAGCTTACCAATTTGCA
54487400 AGCTCG
1 AGCTCG
54487406 AAGAAGCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 2 0.07
25 24 0.89
26 1 0.04
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (26 bp):
AGCTCGTATGAGCTTACCAATTTGCA
Found at i:54488561 original size:64 final size:64
Alignment explanation
Indices: 54488455--54488591 Score: 220
Period size: 64 Copynumber: 2.1 Consensus size: 64
54488445 CCATATGTGA
* * ** *
54488455 CACATGGCCAGGTGACATGTCCGTGTGTCCCCTGATACTTCTATAGAAATCAAGTCAGTAGCTT
1 CACACGGCCAGATGACACATCCGTGTGTCCCCTGATACTTCTATAGAAATCAAGCCAGTAGCTT
*
54488519 CACACGGCCAGATGACACATCCGTGTGTCCCGTGATACTTCTATAGAAATCAAGCCAGTAGCTT
1 CACACGGCCAGATGACACATCCGTGTGTCCCCTGATACTTCTATAGAAATCAAGCCAGTAGCTT
54488583 CACACGGCC
1 CACACGGCC
54488592 TATCACACGG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (64 bp):
CACACGGCCAGATGACACATCCGTGTGTCCCCTGATACTTCTATAGAAATCAAGCCAGTAGCTT
Found at i:54489029 original size:34 final size:33
Alignment explanation
Indices: 54488980--54489065 Score: 106
Period size: 34 Copynumber: 2.6 Consensus size: 33
54488970 ACCAACACAA
* * *
54488980 ATATATTATACATATAACATCCATGCATC-CAAAT
1 ATATATTTTATATATAACACCCATGCA-CGC-AAT
54489014 ATATATTTTATATATAACACCCATGCACGCAAT
1 ATATATTTTATATATAACACCCATGCACGCAAT
54489047 ATATA--TTATATATAACACC
1 ATATATTTTATATATAACACC
54489066 AAAACCCATA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
31 14 0.29
33 9 0.19
34 25 0.52
ACGTcount: A:0.43, C:0.20, G:0.03, T:0.34
Consensus pattern (33 bp):
ATATATTTTATATATAACACCCATGCACGCAAT
Found at i:54505914 original size:23 final size:23
Alignment explanation
Indices: 54505886--54505933 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
54505876 AGCATTTCAA
54505886 AATAGATAACATAAATTGCATTT
1 AATAGATAACATAAATTGCATTT
54505909 AATAGATAACATAAATTGCATTT
1 AATAGATAACATAAATTGCATTT
54505932 AA
1 AA
54505934 AGCATCATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.33
Consensus pattern (23 bp):
AATAGATAACATAAATTGCATTT
Found at i:54510712 original size:5 final size:5
Alignment explanation
Indices: 54510697--54510736 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
54510687 TGTTGATTAA
*
54510697 ATATT AAATT ATA-T -TATT ATATT ATATT ATATT ATATT AT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT AT
54510737 TATAAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 2 0.06
4 2 0.06
5 27 0.87
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:54510717 original size:8 final size:8
Alignment explanation
Indices: 54510704--54510740 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
54510694 TAAATATTAA
54510704 ATTATATT
1 ATTATATT
54510712 ATTATATT
1 ATTATATT
54510720 A-TAT-TAT
1 ATTATAT-T
54510727 ATTATATT
1 ATTATATT
54510735 ATTATA
1 ATTATA
54510741 AATAAACTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
6 1 0.04
7 5 0.19
8 19 0.73
9 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
ATTATATT
Found at i:54510720 original size:13 final size:13
Alignment explanation
Indices: 54510698--54510740 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
54510688 GTTGATTAAA
*
54510698 TATTAAATTATAT
1 TATTATATTATAT
54510711 TATTATA-T-TA-
1 TATTATATTATAT
54510721 TATTATATTATAT
1 TATTATATTATAT
54510734 TATTATA
1 TATTATA
54510741 AATAAACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 7 0.27
11 3 0.12
12 3 0.12
13 13 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTATATTATAT
Found at i:54510737 original size:18 final size:17
Alignment explanation
Indices: 54510692--54510740 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
54510682 TTTTATGTTG
* *
54510692 ATTAAATATTAAATTAT
1 ATTATATATTATATTAT
54510709 ATTATTATATTATATTAT
1 ATTA-TATATTATATTAT
54510727 ATTATATTATTATA
1 ATTATA-TATTATA
54510741 AATAAACTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 6 0.21
18 22 0.79
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTATATATTATATTAT
Found at i:54511234 original size:3 final size:3
Alignment explanation
Indices: 54511226--54511275 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
54511216 AATTGTATAG
54511226 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
54511274 AT
1 AT
54511276 TATTATTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:54511280 original size:3 final size:3
Alignment explanation
Indices: 54511274--54511320 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
54511264 AATAATAATA
54511274 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
54511321 AAGATATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:54512313 original size:21 final size:21
Alignment explanation
Indices: 54512234--54512314 Score: 99
Period size: 21 Copynumber: 3.8 Consensus size: 21
54512224 GCATGGCTGA
54512234 TCAGGCACTTTATGTGTTGTAT
1 TCAGGCACTTTATGTGTTGT-T
* *
54512256 TCAAGCACTTTATGTGTCGTT
1 TCAGGCACTTTATGTGTTGTT
* * **
54512277 TTAGGCACCTCGTGTGTTGTT
1 TCAGGCACTTTATGTGTTGTT
54512298 TCAGGCACTTTATGTGT
1 TCAGGCACTTTATGTGT
54512315 CGTATACTGC
Statistics
Matches: 47, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
21 29 0.62
22 18 0.38
ACGTcount: A:0.16, C:0.17, G:0.23, T:0.43
Consensus pattern (21 bp):
TCAGGCACTTTATGTGTTGTT
Found at i:54512665 original size:40 final size:40
Alignment explanation
Indices: 54512588--54512665 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
54512578 CGTTAGGATA
* ***
54512588 AAAAACGCCGCTATAGATCTAGCATTAGCGGTGCTTTTTG
1 AAAAACGCCGCTATAGATCTACCATTAGCGACACTTTTTG
*
54512628 AAAAACGCCGCTATAGGT-TGACCATTAGCGACACTTTT
1 AAAAACGCCGCTATAGATCT-ACCATTAGCGACACTTTT
54512666 CAAAAATACC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 1 0.03
40 31 0.97
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (40 bp):
AAAAACGCCGCTATAGATCTACCATTAGCGACACTTTTTG
Found at i:54512775 original size:75 final size:75
Alignment explanation
Indices: 54512677--54512825 Score: 235
Period size: 75 Copynumber: 2.0 Consensus size: 75
54512667 AAAAATACCG
* * *
54512677 CAAAAAAATTAAGCACAACGTCGTCGTTTTATGTTGAGCTTTAGTGGCATTAGAGACGCTTTTTG
1 CAAAAAAATTAAGCACAACGTCGTCATTTTATGTTGAGCTTTAGTGGAACTAGAGACGCTTTTTG
54512742 AAAAACGCCT
66 AAAAACGCCT
* * * *
54512752 CAAAAAAATTAAGCACAATGTCGTTATTTTATGTTGAGCTTTAGTGGAACTAGCGGCGCTTTTTG
1 CAAAAAAATTAAGCACAACGTCGTCATTTTATGTTGAGCTTTAGTGGAACTAGAGACGCTTTTTG
54512817 AAAAACGCC
66 AAAAACGCC
54512826 ACTATAGATC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (75 bp):
CAAAAAAATTAAGCACAACGTCGTCATTTTATGTTGAGCTTTAGTGGAACTAGAGACGCTTTTTG
AAAAACGCCT
Found at i:54513188 original size:14 final size:14
Alignment explanation
Indices: 54513171--54513209 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
54513161 ATCATTATAG
54513171 TTTAGGGTTTATGA
1 TTTAGGGTTTATGA
*
54513185 TTTAGGGTATATGA
1 TTTAGGGTTTATGA
*
54513199 TTTAAGGTTTA
1 TTTAGGGTTTA
54513210 AGGTTTAGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (14 bp):
TTTAGGGTTTATGA
Found at i:54513207 original size:28 final size:29
Alignment explanation
Indices: 54513171--54513238 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 29
54513161 ATCATTATAG
* *
54513171 TTTAGGGTTTATGATTTAGG-GTATATGA-
1 TTTAAGGTTTAAGATTTAGGAGT-TATGAT
* *
54513199 TTTAAGGTTTAAGGTTTAGGAGTTATTAT
1 TTTAAGGTTTAAGATTTAGGAGTTATGAT
54513228 TTTAAGGTTTA
1 TTTAAGGTTTA
54513239 GGGATTACAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 21 0.62
29 13 0.38
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (29 bp):
TTTAAGGTTTAAGATTTAGGAGTTATGAT
Found at i:54517471 original size:39 final size:38
Alignment explanation
Indices: 54517428--54517565 Score: 118
Period size: 39 Copynumber: 3.5 Consensus size: 38
54517418 ACTTAAGGTT
54517428 CGCAGGCTATGTGCTGGAATTATAACCGGACTTAAAGT-C
1 CGCAGGCT-TGTGCTGGAATTAT-ACCGGACTTAAAGTCC
* * * *
54517467 CGCAGGCTACGTGCTGGAAATATGTCCGGGC-TAAAGTCC
1 CGCAGGCT-TGTGCTGGAATTAT-ACCGGACTTAAAGTCC
* * * ** *
54517506 CGCAGGCTTCGAGCTGGTATTATACTGGGTTTAAATTCC
1 CGCAGGCTT-GTGCTGGAATTATACCGGACTTAAAGTCC
54517545 CGCAGGCTTGTGCTGGTAATT
1 CGCAGGCTTGTGCTGG-AATT
54517566 GGTTTCAAGT
Statistics
Matches: 80, Mismatches: 15, Indels: 8
0.78 0.15 0.08
Matches are distributed among these distances:
38 16 0.20
39 64 0.80
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (38 bp):
CGCAGGCTTGTGCTGGAATTATACCGGACTTAAAGTCC
Found at i:54518524 original size:21 final size:21
Alignment explanation
Indices: 54518498--54518574 Score: 109
Period size: 21 Copynumber: 3.6 Consensus size: 21
54518488 GTGTTACAGG
54518498 TTAAGGTTTAGGGTTTGATGT
1 TTAAGGTTTAGGGTTTGATGT
*
54518519 TTAAGGTTTAGGGGTTGATGT
1 TTAAGGTTTAGGGTTTGATGT
* *
54518540 TTAAGGTTTAGGGGTTTAAGGGT
1 TTAAGGTTTA-GGGTTTGA-TGT
54518563 TTAAGGTTTAGG
1 TTAAGGTTTAGG
54518575 AGATAATGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
21 30 0.60
22 8 0.16
23 12 0.24
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.43
Consensus pattern (21 bp):
TTAAGGTTTAGGGTTTGATGT
Found at i:54518570 original size:15 final size:15
Alignment explanation
Indices: 54518517--54518572 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
54518507 AGGGTTTGAT
54518517 GTTTAAGGTTT-AGG
1 GTTTAAGGTTTAAGG
* * *
54518531 GGTTGATGTTTAA-G
1 GTTTAAGGTTTAAGG
*
54518545 GTTTAGGGGTTTAAGG
1 GTTTA-AGGTTTAAGG
54518561 GTTTAAGGTTTA
1 GTTTAAGGTTTA
54518573 GGAGATAATG
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
14 12 0.39
15 13 0.42
16 6 0.19
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.43
Consensus pattern (15 bp):
GTTTAAGGTTTAAGG
Found at i:54518599 original size:44 final size:42
Alignment explanation
Indices: 54518496--54518601 Score: 122
Period size: 44 Copynumber: 2.5 Consensus size: 42
54518486 GGGTGTTACA
* * * * *
54518496 GGTTAAGGTTTAGGGTTTGATGTTTAAGGTTTAGGGGTTGAT
1 GGTTAAGGTTTAGGGTTTAAGGTTTAAGGTTTAGGAGATAAT
*
54518538 GTTTAAGGTTTAGGGGTTTAAGGGTTTAAGGTTTAGGAGATAAT
1 GGTTAAGGTTTA-GGGTTTAA-GGTTTAAGGTTTAGGAGATAAT
*
54518582 GGTTAGGGATTTAGGGTTTA
1 GGTTAAGG-TTTAGGGTTTA
54518602 GATTAATTAG
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
42 11 0.21
43 7 0.13
44 31 0.58
45 4 0.08
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.41
Consensus pattern (42 bp):
GGTTAAGGTTTAGGGTTTAAGGTTTAAGGTTTAGGAGATAAT
Found at i:54518733 original size:16 final size:16
Alignment explanation
Indices: 54518714--54518744 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54518704 ATATTAAATA
54518714 ATTTCAAATTCTAAAG
1 ATTTCAAATTCTAAAG
*
54518730 ATTTCAAATTTTAAA
1 ATTTCAAATTCTAAA
54518745 TAATTTTCAA
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:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (16 bp):
ATTTCAAATTCTAAAG
Found at i:54518749 original size:26 final size:25
Alignment explanation
Indices: 54518720--54518776 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
54518710 AATAATTTCA
54518720 AATTCTAAAGATTTCAAATTTTAAAT
1 AATTCTAAAGATTTC-AATTTTAAAT
* * *
54518746 AATTTTCAAGATTTCAATTTTATAT
1 AATTCTAAAGATTTCAATTTTAAAT
54518771 AATTCT
1 AATTCT
54518777 TTTAAATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 14 0.52
26 13 0.48
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (25 bp):
AATTCTAAAGATTTCAATTTTAAAT
Found at i:54519009 original size:12 final size:12
Alignment explanation
Indices: 54518992--54519017 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54518982 GAAACGCCAT
54518992 AATTTTATCCCC
1 AATTTTATCCCC
54519004 AATTTTATCCCC
1 AATTTTATCCCC
54519016 AA
1 AA
54519018 CCTAGATACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (12 bp):
AATTTTATCCCC
Found at i:54519091 original size:17 final size:17
Alignment explanation
Indices: 54519053--54519091 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
54519043 TTTTCCCCTA
54519053 AAAATTTTCCCCAAACC
1 AAAATTTTCCCCAAACC
* * *
54519070 TAAATTTTCCCTAAATC
1 AAAATTTTCCCCAAACC
54519087 AAAAT
1 AAAAT
54519092 CCCAACCCAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATTTTCCCCAAACC
Found at i:54519242 original size:16 final size:16
Alignment explanation
Indices: 54519221--54519261 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
54519211 TTTTTGTCAT
54519221 ATTCTTCTCGGTTCTC
1 ATTCTTCTCGGTTCTC
54519237 ATTCTTCTCGGTTCTC
1 ATTCTTCTCGGTTCTC
54519253 ATTCTTCTC
1 ATTCTTCTC
54519262 TTTTGGCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.07, C:0.32, G:0.10, T:0.51
Consensus pattern (16 bp):
ATTCTTCTCGGTTCTC
Found at i:54520194 original size:14 final size:14
Alignment explanation
Indices: 54520175--54520204 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
54520165 TTCCTTTTAT
54520175 GAAAGCGAGACCCC
1 GAAAGCGAGACCCC
54520189 GAAAGCGAGACCCC
1 GAAAGCGAGACCCC
54520203 GA
1 GA
54520205 GGACTCCGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.33, G:0.30, T:0.00
Consensus pattern (14 bp):
GAAAGCGAGACCCC
Found at i:54521131 original size:17 final size:18
Alignment explanation
Indices: 54521109--54521148 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
54521099 GACATAGGCT
*
54521109 AGAGTAGTTGATG-TCGA
1 AGAGTAGTTCATGCTCGA
*
54521126 AGAGTAGTTCATGCTCTA
1 AGAGTAGTTCATGCTCGA
54521144 AGAGT
1 AGAGT
54521149 GACAGTGACG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (18 bp):
AGAGTAGTTCATGCTCGA
Found at i:54529012 original size:35 final size:34
Alignment explanation
Indices: 54528973--54529038 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
54528963 TAATTGTGTT
*
54528973 ATTAATTTCTTAT-TTTAAGTTCTAAATTTAAATTC
1 ATTAATTT-TTATATTT-AGTTCTAAAGTTAAATTC
*
54529008 ATTAATTTTTATATTTAGTTTTAAAGTTAAA
1 ATTAATTTTTATATTTAGTTCTAAAGTTAAA
54529039 ATTTTAATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 17 0.61
35 11 0.39
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (34 bp):
ATTAATTTTTATATTTAGTTCTAAAGTTAAATTC
Done.