Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 200 of 207
Found at i:60168419 original size:62 final size:56
Alignment explanation
Indices: 60168343--60168482 Score: 145
Period size: 57 Copynumber: 2.4 Consensus size: 56
60168333 AATTGATGGT
*
60168343 AAAAAGGATCTAGCCCGGACGAGTGATCTTATCCTGACATAGCCCTCCCGAATAATATGTGTG
1 AAAAA-GATCTAGCCCGGACGAGTGATC---T--TGACATAGCCCTCCCGAAGAATATGTG-G
* * * *
60168406 AAAAAGATCTAGCCTGGATGGGTGATCTTGATATAGCCCTCCCGAAGAATATGTGG
1 AAAAAGATCTAGCCCGGACGAGTGATCTTGACATAGCCCTCCCGAAGAATATGTGG
* *
60168462 AAAATGGATTTAGCCCGGACG
1 AAAA-AGATCTAGCCCGGACG
60168483 GGTAATCTGA
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
56 5 0.07
57 37 0.55
59 1 0.01
62 19 0.28
63 5 0.07
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.24
Consensus pattern (56 bp):
AAAAAGATCTAGCCCGGACGAGTGATCTTGACATAGCCCTCCCGAAGAATATGTGG
Found at i:60168476 original size:57 final size:57
Alignment explanation
Indices: 60168381--60168490 Score: 150
Period size: 57 Copynumber: 1.9 Consensus size: 57
60168371 TTATCCTGAC
* * * *
60168381 ATAGCCCTCCCGAATAATATGTGTGAAAAAGATCTAGCCTGGATGGGTGATCTTGAT
1 ATAGCCCTCCCGAAGAATATGTGTGAAAAAGATCTAGCCCGGACGGGTAATCTTGAT
* *
60168438 ATAGCCCTCCCGAAGAATATGTG-GAAAATGGATTTAGCCCGGACGGGTAATCT
1 ATAGCCCTCCCGAAGAATATGTGTGAAAA-AGATCTAGCCCGGACGGGTAATCT
60168491 GAATTAGGGT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
56 5 0.11
57 41 0.89
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (57 bp):
ATAGCCCTCCCGAAGAATATGTGTGAAAAAGATCTAGCCCGGACGGGTAATCTTGAT
Found at i:60168672 original size:67 final size:67
Alignment explanation
Indices: 60168559--60168689 Score: 235
Period size: 67 Copynumber: 2.0 Consensus size: 67
60168549 TTGACGTTGC
* *
60168559 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCTT
1 AGGGAATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGAGGGAGTGTGCTCTCTT
60168624 GT
66 GT
*
60168626 AGGGAATTTAGCCTGGACTGGTAATCCTGCTGTAAGAAATGAGGTTCGAGGGAGTGTGCTCTCT
1 AGGGAATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGAGGGAGTGTGCTCTCT
60168690 AAATTGGAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.21, C:0.17, G:0.34, T:0.28
Consensus pattern (67 bp):
AGGGAATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGAGGGAGTGTGCTCTCTT
GT
Found at i:60176030 original size:34 final size:34
Alignment explanation
Indices: 60175987--60176054 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
60175977 TTCAGGGAAT
60175987 GCAACAAATCTACTAGGACGGACTTATAAACATC
1 GCAACAAATCTACTAGGACGGACTTATAAACATC
60176021 GCAACAAATCTACTAGGACGGACTTATAAACATC
1 GCAACAAATCTACTAGGACGGACTTATAAACATC
60176055 CCAATAGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.21
Consensus pattern (34 bp):
GCAACAAATCTACTAGGACGGACTTATAAACATC
Found at i:60177275 original size:30 final size:30
Alignment explanation
Indices: 60177231--60177293 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
60177221 ACTTAACAAG
60177231 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* * *
60177261 CAAATGTCTTTAAAATGATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
60177291 CAA
1 CAA
60177294 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.56, C:0.14, G:0.05, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:60183954 original size:31 final size:30
Alignment explanation
Indices: 60183911--60183968 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
60183901 TTCTCAACCC
*
60183911 TAATGTAGGAACAATTGTCAAATTCAAGTCT
1 TAATATAGGAACAATTG-CAAATTCAAGTCT
*
60183942 TAATATAGGAACAATTGCAAGTTCAAG
1 TAATATAGGAACAATTGCAAATTCAAG
60183969 GACTAACTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (30 bp):
TAATATAGGAACAATTGCAAATTCAAGTCT
Found at i:60188334 original size:32 final size:31
Alignment explanation
Indices: 60188298--60188377 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
60188288 AAATATTTTT
* **
60188298 CAGATCTATATCATGAAAATTATATCCATTAA
1 CAGATCTATAACATGAAAA-TATATCCACAAA
* * *
60188330 CAGATCTAAAACATGAAGATATATTCACAAA
1 CAGATCTATAACATGAAAATATATCCACAAA
60188361 CAGATCTATAACATGAA
1 CAGATCTATAACATGAA
60188378 GTTATATACC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 25 0.61
32 16 0.39
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.28
Consensus pattern (31 bp):
CAGATCTATAACATGAAAATATATCCACAAA
Found at i:60191277 original size:27 final size:27
Alignment explanation
Indices: 60191231--60191294 Score: 69
Period size: 30 Copynumber: 2.3 Consensus size: 27
60191221 ATAATTTTTG
* *
60191231 AATTTTTTTTCTCATTTC-TTTTTA-T
1 AATTTTTTTTCACATCTCTTTTTTACT
60191256 AATTTTTTTGTCAACATCTCTTTTTTAGCT
1 AATTTTTTT-TC-ACATCTCTTTTTTA-CT
60191286 AATTTTTTT
1 AATTTTTTT
60191295 AACAGGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 9 0.28
26 2 0.06
27 5 0.16
28 6 0.19
30 10 0.31
ACGTcount: A:0.19, C:0.12, G:0.03, T:0.66
Consensus pattern (27 bp):
AATTTTTTTTCACATCTCTTTTTTACT
Found at i:60193410 original size:5 final size:5
Alignment explanation
Indices: 60193400--60193428 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
60193390 ATACTTGCTA
60193400 TATTT TATTT TATTT TATTT TATTT TATT
1 TATTT TATTT TATTT TATTT TATTT TATT
60193429 GAAAAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:60196085 original size:11 final size:11
Alignment explanation
Indices: 60196069--60196096 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
60196059 GAGGAAAAAG
60196069 ATAAAAATAAA
1 ATAAAAATAAA
60196080 ATAAAAATAAA
1 ATAAAAATAAA
60196091 ATAAAA
1 ATAAAA
60196097 CTAACCTCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
ATAAAAATAAA
Found at i:60219598 original size:15 final size:14
Alignment explanation
Indices: 60219549--60219604 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
60219539 AAATGACTAT
*
60219549 ATATAAA-TAAATA
1 ATATAAATTAAAAA
**
60219562 ATATAAATTACTAA
1 ATATAAATTAAAAA
60219576 ATATTAAATTAAAAA
1 ATA-TAAATTAAAAA
60219591 GATATAAATATAAA
1 -ATATAAAT-TAAA
60219605 TTATTAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
13 7 0.21
14 6 0.18
15 14 0.41
16 7 0.21
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (14 bp):
ATATAAATTAAAAA
Found at i:60229392 original size:28 final size:29
Alignment explanation
Indices: 60229360--60229426 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 29
60229350 GAGACTTTCC
* *
60229360 TTTTAATTCTTGACTAG-AGCTTATTCAA
1 TTTTAATGCTTCACTAGAAGCTTATTCAA
* *
60229388 TTTT-ATGCTTCAGTTGAAGCTTATTCAA
1 TTTTAATGCTTCACTAGAAGCTTATTCAA
60229416 TTTT-ATGCTTC
1 TTTTAATGCTTC
60229427 GGTTGAAAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 8 0.24
28 26 0.76
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.49
Consensus pattern (29 bp):
TTTTAATGCTTCACTAGAAGCTTATTCAA
Found at i:60229431 original size:28 final size:28
Alignment explanation
Indices: 60229377--60229433 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
60229367 TCTTGACTAG
60229377 AGCTTATTCAATTTTATGCTTCAGTTGA
1 AGCTTATTCAATTTTATGCTTCAGTTGA
*
60229405 AGCTTATTCAATTTTATGCTTCGGTTGA
1 AGCTTATTCAATTTTATGCTTCAGTTGA
60229433 A
1 A
60229434 AGCCAATCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.46
Consensus pattern (28 bp):
AGCTTATTCAATTTTATGCTTCAGTTGA
Found at i:60240457 original size:95 final size:95
Alignment explanation
Indices: 60240294--60240483 Score: 346
Period size: 95 Copynumber: 2.0 Consensus size: 95
60240284 GGTCTAGGTT
60240294 TCTTCACTACTGGTGAAGAATCTAAGAGAAGACTAAGAACAACAATGTTGAAACTACATATAAAC
1 TCTTCACTACTGGTGAAGAATCTAAGAGAAGACTAAGAACAACAATGTTGAAACTACATATAAAC
60240359 CCACAAAAACTAGGTAGGTTTATGACAACA
66 CCACAAAAACTAGGTAGGTTTATGACAACA
* *
60240389 TCTTCACTACTGGTGAAGAATCTAAGGGAAGAC-ATAGAACAATAATGTTGAAACTACATATAAA
1 TCTTCACTACTGGTGAAGAATCTAAGAGAAGACTA-AGAACAACAATGTTGAAACTACATATAAA
60240453 CCCACAAAAACTAGGTAGGTTTATGACAACA
65 CCCACAAAAACTAGGTAGGTTTATGACAACA
60240484 CAACAATACC
Statistics
Matches: 92, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
94 1 0.01
95 91 0.99
ACGTcount: A:0.44, C:0.17, G:0.16, T:0.23
Consensus pattern (95 bp):
TCTTCACTACTGGTGAAGAATCTAAGAGAAGACTAAGAACAACAATGTTGAAACTACATATAAAC
CCACAAAAACTAGGTAGGTTTATGACAACA
Found at i:60257449 original size:25 final size:26
Alignment explanation
Indices: 60257415--60257463 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
60257405 CTGTTTTGAC
60257415 CAAATATCTAGAAA-CAAA-TTAATGT
1 CAAATATCTA-AAATCAAACTTAATGT
*
60257440 CAAATTTCTAAAATCAAACTTAAT
1 CAAATATCTAAAATCAAACTTAAT
60257464 AAAAAGGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 13 0.62
26 5 0.24
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.31
Consensus pattern (26 bp):
CAAATATCTAAAATCAAACTTAATGT
Found at i:60257917 original size:17 final size:17
Alignment explanation
Indices: 60257895--60257927 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
60257885 TATTTAATTT
60257895 TTATTT-ATAAATATATA
1 TTATTTAAT-AATATATA
60257912 TTATTTAATAATATAT
1 TTATTTAATAATATAT
60257928 TTGTTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATTTAATAATATATA
Found at i:60258075 original size:23 final size:21
Alignment explanation
Indices: 60258036--60258078 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
60258026 AAGGAGGAAT
*
60258036 TATAAAAAATTCTAAATATTG
1 TATAAAAAATTATAAATATTG
60258057 TATAAAAAATTAATAAAATATT
1 TATAAAAAATT-AT-AAATATT
60258079 TTAAACATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 1 0.05
23 7 0.37
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
TATAAAAAATTATAAATATTG
Found at i:60265181 original size:26 final size:26
Alignment explanation
Indices: 60265152--60265211 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 26
60265142 TTTCTTTTGT
60265152 TTTGGGTTT-GTTTGGGTTATTGAG-T-A
1 TTTGGGTTTAG-TTGGGTT-TTG-GCTGA
60265178 TTT-GGTTTAGTTGGGTTTTGGCTGA
1 TTTGGGTTTAGTTGGGTTTTGGCTGA
60265203 TTTGGGTTT
1 TTTGGGTTT
60265212 TAGGTTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
23 1 0.03
24 4 0.13
25 16 0.53
26 9 0.30
ACGTcount: A:0.08, C:0.02, G:0.35, T:0.55
Consensus pattern (26 bp):
TTTGGGTTTAGTTGGGTTTTGGCTGA
Found at i:60265197 original size:16 final size:16
Alignment explanation
Indices: 60265178--60265220 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
60265168 TTATTGAGTA
60265178 TTTGGTTTAGTTGGGT
1 TTTGGTTTAGTTGGGT
* * *
60265194 TTTGGCTGATTTGGGT
1 TTTGGTTTAGTTGGGT
60265210 TTTAGGTTTAG
1 TTT-GGTTTAG
60265221 GCCTGCTATT
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.09, C:0.02, G:0.35, T:0.53
Consensus pattern (16 bp):
TTTGGTTTAGTTGGGT
Found at i:60269574 original size:32 final size:32
Alignment explanation
Indices: 60269535--60269597 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
60269525 TCCTTAATGT
60269535 TTTTTGTTTTACTAGAGCACTATTGTAGGTTG
1 TTTTTGTTTTACTAGAGCACTATTGTAGGTTG
60269567 TTTTTGTTTTACTAGAGCACTATTGTAGGTT
1 TTTTTGTTTTACTAGAGCACTATTGTAGGTT
60269598 TGAAGGCATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.19, C:0.10, G:0.21, T:0.51
Consensus pattern (32 bp):
TTTTTGTTTTACTAGAGCACTATTGTAGGTTG
Found at i:60283221 original size:87 final size:87
Alignment explanation
Indices: 60283075--60283250 Score: 343
Period size: 87 Copynumber: 2.0 Consensus size: 87
60283065 GTCAAAACTC
*
60283075 AAGAAAATAGAAAGGGGAAGTCAAGTATTTCTAATTTTGTAAAACACATACAATGCCATTTTTAT
1 AAGAAAATAGAAAGGAGAAGTCAAGTATTTCTAATTTTGTAAAACACATACAATGCCATTTTTAT
60283140 TCATAATTCTTTTTCAACCTTT
66 TCATAATTCTTTTTCAACCTTT
60283162 AAGAAAATAGAAAGGAGAAGTCAAGTATTTCTAATTTTGTAAAACACATACAATGCCATTTTTAT
1 AAGAAAATAGAAAGGAGAAGTCAAGTATTTCTAATTTTGTAAAACACATACAATGCCATTTTTAT
60283227 TCATAATTCTTTTTCAACCTTT
66 TCATAATTCTTTTTCAACCTTT
60283249 AA
1 AA
60283251 ATTAAAGGAA
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (87 bp):
AAGAAAATAGAAAGGAGAAGTCAAGTATTTCTAATTTTGTAAAACACATACAATGCCATTTTTAT
TCATAATTCTTTTTCAACCTTT
Found at i:60283793 original size:17 final size:18
Alignment explanation
Indices: 60283752--60283790 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
60283742 TTCTCATTTT
*
60283752 TTTTAAATATTTTTTTAA
1 TTTTAAATATTTTTATAA
60283770 TTTTAAAT-TTATTTATAA
1 TTTTAAATATT-TTTATAA
60283788 TTT
1 TTT
60283791 AAAAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTAAATATTTTTATAA
Found at i:60284581 original size:27 final size:27
Alignment explanation
Indices: 60284551--60284610 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
60284541 ATAGGTGGTG
*
60284551 CCTATCC-AGTAGGCGCCACTGGTGACT
1 CCTATCCGA-TAGGCGCCACGGGTGACT
* * *
60284578 CCTATTCGATAGGTGCCTCGGGTGACT
1 CCTATCCGATAGGCGCCACGGGTGACT
60284605 CCTATC
1 CCTATC
60284611 AATAAAAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.17, C:0.32, G:0.25, T:0.27
Consensus pattern (27 bp):
CCTATCCGATAGGCGCCACGGGTGACT
Found at i:60284831 original size:99 final size:102
Alignment explanation
Indices: 60284647--60284897 Score: 330
Period size: 99 Copynumber: 2.5 Consensus size: 102
60284637 ATTACATTAC
* *
60284647 AAAAAATTTACATTAATAAAAAATCACAAAACACTAAACTAAACTCTAACAATTTATATAACTTA
1 AAAAAATTTACATTACTAAAAAATCACAAAACAC---A--AAACACTAACAATTTATATAACTTA
** **
60284712 ATCATAAATTTTTAACAAAATAACTATAAAATTATTTTTTAA
61 ATCATAAATTACTAACAAAATAACTATAAAAACATTTTTTAA
* *
60284754 AAAAAATTT-CATTACTAAAAAATCACAAATCACAAAACACTAACAATTTATA-AAC-TAATTAT
1 AAAAAATTTACATTACTAAAAAATCACAAAACACAAAACACTAACAATTTATATAACTTAATCAT
*
60284816 AAATTACTGACAAAATAACTATAAAAACATTTTTTAA
66 AAATTACTAACAAAATAACTATAAAAACATTTTTTAA
* *
60284853 AAATATTTTACATTACTAAAAAATCACAAAACACAAAA-ACTAACA
1 AAAAAATTTACATTACTAAAAAATCACAAAACACAAAACACTAACA
60284898 TAAATTACTA
Statistics
Matches: 131, Mismatches: 12, Indels: 10
0.86 0.08 0.07
Matches are distributed among these distances:
99 52 0.40
100 30 0.23
101 17 0.13
103 1 0.01
106 22 0.17
107 9 0.07
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.30
Consensus pattern (102 bp):
AAAAAATTTACATTACTAAAAAATCACAAAACACAAAACACTAACAATTTATATAACTTAATCAT
AAATTACTAACAAAATAACTATAAAAACATTTTTTAA
Found at i:60287706 original size:82 final size:82
Alignment explanation
Indices: 60287569--60287734 Score: 323
Period size: 82 Copynumber: 2.0 Consensus size: 82
60287559 ACTAGTTTGT
60287569 TGAAGTAACACTTTGTCCCTTTGGATAAGCTTTTTCTTGAATTACCCTTGAATAAACTTGATGCA
1 TGAAGTAACACTTTGTCCCTTTGGATAAGCTTTTTCTTGAATTACCCTTGAATAAACTTGATGCA
60287634 AACGAACAATGGGAGAG
66 AACGAACAATGGGAGAG
*
60287651 TGAAGTAACACTTTGTCCCTTTGGATTAGCTTTTTCTTGAATTACCCTTGAATAAACTTGATGCA
1 TGAAGTAACACTTTGTCCCTTTGGATAAGCTTTTTCTTGAATTACCCTTGAATAAACTTGATGCA
60287716 AACGAACAATGGGAGAG
66 AACGAACAATGGGAGAG
60287733 TG
1 TG
60287735 GACTAAGGGA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 83 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Consensus pattern (82 bp):
TGAAGTAACACTTTGTCCCTTTGGATAAGCTTTTTCTTGAATTACCCTTGAATAAACTTGATGCA
AACGAACAATGGGAGAG
Found at i:60292910 original size:24 final size:25
Alignment explanation
Indices: 60292883--60292952 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 25
60292873 CAGCTCGAAA
60292883 GAGCTTCTC-GTTATTAGCTCTCAT
1 GAGCTTCTCTGTTATTAGCTCTCAT
* * *
60292907 GAGCTT-TCTGTTATATGGTTCTTAT
1 GAGCTTCTCTGTTAT-TAGCTCTCAT
*
60292932 GAGCTTC-CTGTTAATAGCTCT
1 GAGCTTCTCTGTTATTAGCTCT
60292953 TTAAGGCATC
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
23 2 0.05
24 16 0.43
25 19 0.51
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (25 bp):
GAGCTTCTCTGTTATTAGCTCTCAT
Found at i:60293100 original size:25 final size:24
Alignment explanation
Indices: 60293029--60293108 Score: 79
Period size: 27 Copynumber: 3.2 Consensus size: 24
60293019 TCGTTATATA
* *
60293029 GCTCTTCGGAGCTTCCCGACTAAAG
1 GCTCTTCGGAGCTTCCC-AATAATG
**
60293054 GCTCTTTTATGAGCTTCCCAATTAATG
1 GCTC--TTCGGAGCTTCCCAA-TAATG
*
60293081 GCTCTTCGGAGCTTCCCAATATTG
1 GCTCTTCGGAGCTTCCCAATAATG
60293105 GCTC
1 GCTC
60293109 GCTTGAACCT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
24 8 0.18
25 17 0.38
26 1 0.02
27 19 0.42
ACGTcount: A:0.19, C:0.29, G:0.20, T:0.33
Consensus pattern (24 bp):
GCTCTTCGGAGCTTCCCAATAATG
Found at i:60293156 original size:49 final size:48
Alignment explanation
Indices: 60293089--60293208 Score: 134
Period size: 49 Copynumber: 2.4 Consensus size: 48
60293079 TGGCTCTTCG
* * * * **
60293089 GAGCTTCCCAATATTGGCTCGCTTGAACCTTCCTGTT-ATGTGCTCGTAT
1 GAGCTTCCCATTAATGGCTCGCTGGAA-CTTCCCGTTAATG-GCTCACAT
*
60293138 GAGCTTCCCATTAATGGCTCTCTGGAACTTCCCGTTACATGGCTCACAT
1 GAGCTTCCCATTAATGGCTCGCTGGAACTTCCCGTTA-ATGGCTCACAT
60293187 GAGCTTCCCATTATATGGCTCG
1 GAGCTTCCCATTA-ATGGCTCG
60293209 AGAGATAGCT
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
48 8 0.13
49 42 0.70
50 10 0.17
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.33
Consensus pattern (48 bp):
GAGCTTCCCATTAATGGCTCGCTGGAACTTCCCGTTAATGGCTCACAT
Found at i:60293193 original size:25 final size:24
Alignment explanation
Indices: 60293136--60293207 Score: 83
Period size: 25 Copynumber: 2.9 Consensus size: 24
60293126 ATGTGCTCGT
*
60293136 ATGAGCTTCCCATTAATGGCTCTC
1 ATGAGCTTCCCATTAATGGCTCAC
* *
60293160 -TGGAACTTCCCGTTACATGGCTCAC
1 AT-GAGCTTCCCATTA-ATGGCTCAC
60293185 ATGAGCTTCCCATTATATGGCTC
1 ATGAGCTTCCCATTA-ATGGCTC
60293208 GAGAGATAGC
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
23 1 0.03
24 11 0.28
25 26 0.67
26 1 0.03
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (24 bp):
ATGAGCTTCCCATTAATGGCTCAC
Found at i:60297430 original size:16 final size:16
Alignment explanation
Indices: 60297405--60297436 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
60297395 TCCAAAAATT
*
60297405 GTAAACAAAATAAAAA
1 GTAAAAAAAATAAAAA
60297421 GTAAAAAAAATAAAAA
1 GTAAAAAAAATAAAAA
60297437 ATCTAGATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.03, G:0.06, T:0.12
Consensus pattern (16 bp):
GTAAAAAAAATAAAAA
Found at i:60298630 original size:26 final size:26
Alignment explanation
Indices: 60298592--60298647 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
60298582 TAGGGAGAAT
*
60298592 AAGT-AAAACCCTTATTGAATCATAG
1 AAGTCAAAAACCTTATTGAATCATAG
* *
60298617 AAGTCAAAAACCTTGTTGAATCGTAG
1 AAGTCAAAAACCTTATTGAATCATAG
60298643 AAGTC
1 AAGTC
60298648 TATTTCAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 4 0.15
26 23 0.85
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (26 bp):
AAGTCAAAAACCTTATTGAATCATAG
Found at i:60302330 original size:11 final size:11
Alignment explanation
Indices: 60302314--60302353 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
60302304 CTCCCACAAC
60302314 TAAAATAAAAA
1 TAAAATAAAAA
*
60302325 TAAAATAGAAA
1 TAAAATAAAAA
60302336 TAAAATAATAAA
1 TAAAATAA-AAA
*
60302348 CAAAAT
1 TAAAAT
60302354 CTTCTATACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (11 bp):
TAAAATAAAAA
Found at i:60305497 original size:19 final size:21
Alignment explanation
Indices: 60305461--60305501 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
60305451 TTCTTTGCTC
60305461 TTTTGCTTCGAGTTTGCTTTTG
1 TTTTGCTTCGAG-TTGCTTTTG
60305483 TTTTGCTTC-AG-TGCTTTTG
1 TTTTGCTTCGAGTTGCTTTTG
60305502 AGAATTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
21 2 0.11
22 9 0.47
ACGTcount: A:0.05, C:0.15, G:0.22, T:0.59
Consensus pattern (21 bp):
TTTTGCTTCGAGTTGCTTTTG
Found at i:60308445 original size:31 final size:29
Alignment explanation
Indices: 60308408--60308507 Score: 94
Period size: 31 Copynumber: 3.3 Consensus size: 29
60308398 TATTTGGTTT
60308408 AAGTATCAAATTGAATATTAAAGCAAAACTC
1 AAGTATCAAATTGAATATTAAA-CAAAA-TC
* * *
60308439 AAGTATCAAATTGAGATAATAAA-AAATTT
1 AAGTATCAAATTGA-ATATTAAACAAAATC
* * *
60308468 AAATACCGAATTGAATATTAAAATCAAAATC
1 AAGTATCAAATTGAATATT-AAA-CAAAATC
60308499 AAGTATCAA
1 AAGTATCAA
60308508 CGGATATATT
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
28 4 0.08
29 15 0.28
30 3 0.06
31 24 0.45
32 7 0.13
ACGTcount: A:0.54, C:0.10, G:0.09, T:0.27
Consensus pattern (29 bp):
AAGTATCAAATTGAATATTAAACAAAATC
Found at i:60308540 original size:13 final size:13
Alignment explanation
Indices: 60308522--60308548 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
60308512 TATATTAACC
60308522 CTTAATGAAGTTA
1 CTTAATGAAGTTA
60308535 CTTAATGAAGTTA
1 CTTAATGAAGTTA
60308548 C
1 C
60308549 CAAGCATAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (13 bp):
CTTAATGAAGTTA
Found at i:60311823 original size:20 final size:20
Alignment explanation
Indices: 60311781--60311824 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
60311771 CAAAACCTTG
* *
60311781 AACCCTAACACTAAATTCAA
1 AACCCGAACACTAAACTCAA
* *
60311801 AACCCGAACCCTAAACTCTA
1 AACCCGAACACTAAACTCAA
60311821 AACC
1 AACC
60311825 TTAAATTCGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.36, G:0.02, T:0.16
Consensus pattern (20 bp):
AACCCGAACACTAAACTCAA
Found at i:60311900 original size:21 final size:21
Alignment explanation
Indices: 60311876--60311916 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
60311866 GGGTTTTGGA
*
60311876 TTTAAGGCTCGAAGTTTAGGG
1 TTTAAGGCTCAAAGTTTAGGG
60311897 TTTAAGGCTCAAAGTTTAGG
1 TTTAAGGCTCAAAGTTTAGG
60311917 ATAAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.10, G:0.29, T:0.34
Consensus pattern (21 bp):
TTTAAGGCTCAAAGTTTAGGG
Found at i:60319223 original size:4 final size:4
Alignment explanation
Indices: 60319214--60319246 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
60319204 TGATGAACAC
60319214 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
60319247 AGATAAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:60320844 original size:22 final size:21
Alignment explanation
Indices: 60320819--60320863 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
60320809 TTGGTTGTAA
60320819 TTGGGTTAGGTCTAGGTTGGGT
1 TTGGGTTAGGTCTA-GTTGGGT
* * *
60320841 TTGGTTTTGGTCTATTTGGGT
1 TTGGGTTAGGTCTAGTTGGGT
60320862 TT
1 TT
60320864 TGGGCCTCGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.07, C:0.04, G:0.38, T:0.51
Consensus pattern (21 bp):
TTGGGTTAGGTCTAGTTGGGT
Found at i:60321298 original size:50 final size:50
Alignment explanation
Indices: 60321235--60321996 Score: 544
Period size: 50 Copynumber: 15.2 Consensus size: 50
60321225 TAGTTAACTA
* * * **
60321235 CAATGTCGGGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTG
1 CAATGTCAGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTTTTTAATTG
* * * * * ** *
60321285 CAATATCGGGGAAGCCAGATTCACCGTTGTAGCTTCAATCTATTCCACTG
1 CAATGTCAGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTTTTTAATTG
* * * *
60321335 CACA-GCCAAGGAAGCAAGATTCGCCATTGTGGCTTCAATCTTTTTAATTG
1 CA-ATGTCAGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTTTTTAATTG
* * * * ** *
60321385 CAATGTCGGGGAAGCAAGATTCGTCGTTGTAGTTTCAATCTGTTCCACTG
1 CAATGTCAGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTTTTTAATTG
**** * * **
60321435 CACCACCAGGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTG
1 CAATGTCAGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTTTTTAATTG
* * * * *
60321485 CAATGTC-GAGAAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTTCACTG
1 CAATGTCAG-GGAAGCAAGATTCGCCGTTGTAGCTTCAATCTTTTTAATTG
* * * **
60321535 CACTG-CTAGGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTG
1 CAATGTC-AGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTTTTTAATTG
* * * * * * ** *
60321585 CAATGTCGGGGAAGTAAGATTCACTGTTGTAGCTCCAATCTGTTCCACTG
1 CAATGTCAGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTTTTTAATTG
** * * * *
60321635 CACCGCCAGGGAAGTAAGATTCGCCGTTGCAGCTTCAATATTTTTAATTG
1 CAATGTCAGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTTTTTAATTG
* * ** ** *
60321685 GAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGCTCCACTG
1 CAATGTCAGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTTTTTAATTG
**** * * * *
60321735 CACCACCAGGGAAGTAAGATTTGCCGTTGT-GAATTCAACCTTTTTAATTG
1 CAATGTCAGGGAAGCAAGATTCGCCGTTGTAG-CTTCAATCTTTTTAATTG
* * * ** * ** * *
60321785 CAATGTCGGGGAAGCAACATTCACTATTGTAGCTTCAATCTGTTCCACTA
1 CAATGTCAGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTTTTTAATTG
* * *
60321835 C-ATCGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTG
1 CAAT-GTCAGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTTTTTAATTG
* * ** *
60321885 CAATGTCAGGGAAGCAAGATTCGCCGTTGTAGTTTCAATCTGTTCCATTA
1 CAATGTCAGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTTTTTAATTG
** * * * * * *
60321935 CACCGCCAGAGAAGTAAGATTTGCCATTGTGGCTTCAATCTTTTTTAATTG
1 CAATGTCAGGGAAGCAAGATTCGCCGTTGTAGCTTCAATC-TTTTTAATTG
*
60321986 CAATCTCAGGG
1 CAATGTCAGGG
60321997 GTATGAGTAA
Statistics
Matches: 523, Mismatches: 178, Indels: 21
0.72 0.25 0.03
Matches are distributed among these distances:
49 6 0.01
50 499 0.95
51 18 0.03
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (50 bp):
CAATGTCAGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTTTTTAATTG
Found at i:60321422 original size:100 final size:100
Alignment explanation
Indices: 60321243--60321989 Score: 1005
Period size: 100 Copynumber: 7.5 Consensus size: 100
60321233 TACAATGTCG
* * * *
60321243 GGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATATCGGGGAAGCCAGATTCA
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCG
*
60321308 CCGTTGTAGCTTCAATCTATTCCACTGCACAGCCA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACAGCCA
* * * *
60321343 AGGAAGCAAGATTCGCCATTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCG
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCG
* *
60321408 TCGTTGTAGTTTCAATCTGTTCCACTGCACCA-CCA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCA-CAGCCA
* * *
60321443 GGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGAGAAAGCAAGATTCG
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCG
* * * *
60321508 CTGTTGTAGCTTCAATCTGTTTCACTGCACTGCTA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACAGCCA
* * *
60321543 GGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGTAAGATTCA
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCG
* * *
60321608 CTGTTGTAGCTCCAATCTGTTCCACTGCACCGCCA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACAGCCA
* * *
60321643 GGGAAGTAAGATTCGCCGTTGCAGCTTCAATATTTTTAATTGGAATGTCGGGGAAGCAAGATTCG
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCG
*
60321708 CCGTTGTAGCTTCAATCTGCTCCACTGCACCA-CCA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCA-CAGCCA
* * ** * * *
60321743 GGGAAGTAAGATTTGCCGTTGTGAATTCAACCTTTTTAATTGCAATGTCGGGGAAGCAACATTCA
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCG
** *
60321808 CTATTGTAGCTTCAATCTGTTCCACTACATC-GCCA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCA-CAGCCA
* *
60321843 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATTCG
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCG
* * * *
60321908 CCGTTGTAGTTTCAATCTGTTCCATTACACCGCCA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACAGCCA
* * * *
60321943 GAGAAGTAAGATTTGCCATTGTGGCTTCAATCTTTTTTAATTGCAAT
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATC-TTTTTAATTGCAAT
60321990 CTCAGGGGTA
Statistics
Matches: 570, Mismatches: 71, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
99 2 0.00
100 551 0.97
101 17 0.03
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (100 bp):
GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCG
CCGTTGTAGCTTCAATCTGTTCCACTGCACAGCCA
Found at i:60322162 original size:15 final size:15
Alignment explanation
Indices: 60322122--60322162 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
60322112 TAACTAGATG
60322122 TGTATGAATGATATT
1 TGTATGAATGATATT
*
60322137 TGCATTGAATGATATT
1 TGTA-TGAATGATATT
60322153 TGTATGAATG
1 TGTATGAATG
60322163 CAAAATGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.32, C:0.02, G:0.22, T:0.44
Consensus pattern (15 bp):
TGTATGAATGATATT
Found at i:60322923 original size:7 final size:7
Alignment explanation
Indices: 60322887--60322935 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 7
60322877 TGGCCTCTCC
60322887 TTTTCTT
1 TTTTCTT
*
60322894 TTTTCGT
1 TTTTCTT
*
60322901 TCTTC--
1 TTTTCTT
60322906 TTTTC-T
1 TTTTCTT
60322912 TTTTCTT
1 TTTTCTT
60322919 TTTTCTT
1 TTTTCTT
60322926 TTTTCTT
1 TTTTCTT
60322933 TTT
1 TTT
60322936 ATTTCTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
5 4 0.11
6 5 0.14
7 28 0.76
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (7 bp):
TTTTCTT
Found at i:60322947 original size:13 final size:12
Alignment explanation
Indices: 60322886--60322948 Score: 54
Period size: 13 Copynumber: 5.1 Consensus size: 12
60322876 TTGGCCTCTC
*
60322886 CTTTTCTTTTTT
1 CTTTTTTTTTTT
* * *
60322898 CGTTCTTCTTTT
1 CTTTTTTTTTTT
60322910 CTTTTTCTTTTTT
1 CTTTTT-TTTTTT
60322923 CTTTTTTCTTTTT
1 CTTTTTT-TTTTT
* *
60322936 ATTTCTTTTTTT
1 CTTTTTTTTTTT
60322948 C
1 C
60322949 AAGTGAAGTA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
12 18 0.46
13 21 0.54
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (12 bp):
CTTTTTTTTTTT
Found at i:60322947 original size:20 final size:20
Alignment explanation
Indices: 60322900--60322939 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
60322890 TCTTTTTTCG
*
60322900 TTCTTCTTTTCTTTTTCTTTT
1 TTCTT-TTTTCTTTTTATTTT
60322921 TTCTTTTTTCTTTTTATTT
1 TTCTTTTTTCTTTTTATTT
60322940 CTTTTTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (20 bp):
TTCTTTTTTCTTTTTATTTT
Found at i:60322948 original size:25 final size:25
Alignment explanation
Indices: 60322888--60322946 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
60322878 GGCCTCTCCT
*
60322888 TTTCTTTTTTCGTTCTTCTTTTCTT
1 TTTCTTTTTTCGTTCTTCTTTTCTA
* *
60322913 TTTCTTTTTTCTTTTTTCTTTT-TA
1 TTTCTTTTTTCGTTCTTCTTTTCTA
60322937 TTTCTTTTTT
1 TTTCTTTTTT
60322947 TCAAGTGAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
24 11 0.35
25 20 0.65
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (25 bp):
TTTCTTTTTTCGTTCTTCTTTTCTA
Found at i:60326172 original size:24 final size:25
Alignment explanation
Indices: 60326145--60326197 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
60326135 GGCCTTTTCG
*
60326145 TGAAATTTAATACAAATG-ATGCAA
1 TGAAATGTAATACAAATGCATGCAA
* * *
60326169 TGAAATGTAATGCAGATGCATGGAA
1 TGAAATGTAATACAAATGCATGCAA
60326194 TGAA
1 TGAA
60326198 TGCAAAAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.45, C:0.08, G:0.21, T:0.26
Consensus pattern (25 bp):
TGAAATGTAATACAAATGCATGCAA
Found at i:60331095 original size:25 final size:23
Alignment explanation
Indices: 60331046--60331240 Score: 86
Period size: 25 Copynumber: 8.0 Consensus size: 23
60331036 CGAGCCCTAT
** *
60331046 ATAACAGGAAGCTCATGTGATCC
1 ATAACAGGAAGCTCATAAGAGCC
*
60331069 ATGTAACAGAAAGCTCATAAGAGCC
1 A--TAACAGGAAGCTCATAAGAGCC
*
60331094 ATAATCGGGAAGCTCATAAGAGCC
1 ATAA-CAGGAAGCTCATAAGAGCC
* * * *
60331118 AATTATCGGGAAGCTCCA-GAGAGTCA
1 -A-TAACAGGAAGCT-CATAAGAG-CC
*** *
60331144 ATTATTGGGAAGCTCATACGAGCC
1 A-TAACAGGAAGCTCATAAGAGCC
* *
60331168 ATAAACGGGAAGCTCATAAGAGCTAA
1 AT-AACAGGAAGCTCATAAGAGC--C
* *
60331194 ATAACGGGAAGCTCATGAGAGCC
1 ATAACAGGAAGCTCATAAGAGCC
* * *
60331217 TATTATCGGGACGCTCATAAGAGC
1 -A-TAACAGGAAGCTCATAAGAGC
60331241 TATGGTGTGT
Statistics
Matches: 137, Mismatches: 22, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
23 5 0.04
24 39 0.28
25 86 0.63
26 7 0.05
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (23 bp):
ATAACAGGAAGCTCATAAGAGCC
Found at i:60331132 original size:49 final size:48
Alignment explanation
Indices: 60331079--60331240 Score: 175
Period size: 50 Copynumber: 3.3 Consensus size: 48
60331069 ATGTAACAGA
*
60331079 AAGCTCATAAGAGCCATAATCGGGAAGCTCATAAGAGCCAATTATCGGG
1 AAGCTCATAAGAGCAATAATCGGGAAGCTCATAAGAGCC-ATTATCGGG
* * * * * *
60331128 AAGCTCCA-GAGAGTCAATTATTGGGAAGCTCATACGAGCCATAAACGGG
1 AAGCT-CATAAGAG-CAATAATCGGGAAGCTCATAAGAGCCATTATCGGG
*
60331177 AAGCTCATAAGAGCTAAATAA-CGGGAAGCTCATGAGAGCCTATTATCGGG
1 AAGCTCATAAGAGC--AATAATCGGGAAGCTCATAAGAGCC-ATTATCGGG
*
60331227 ACGCTCATAAGAGC
1 AAGCTCATAAGAGC
60331241 TATGGTGTGT
Statistics
Matches: 92, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
48 3 0.03
49 41 0.45
50 48 0.52
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (48 bp):
AAGCTCATAAGAGCAATAATCGGGAAGCTCATAAGAGCCATTATCGGG
Found at i:60331157 original size:74 final size:74
Alignment explanation
Indices: 60331079--60331240 Score: 227
Period size: 74 Copynumber: 2.2 Consensus size: 74
60331069 ATGTAACAGA
* * * *
60331079 AAGCTCATAAGAGCCATAATCGGGAAGCTCATAAGAGCCAATTATCGGGAAGCTCCA-GAGAGTC
1 AAGCTCATAAGAGCCATAAACGGGAAGCTCATAAGAGCCAAATAACGGGAAGCT-CATGAGAGCC
*
60331143 AATTATTGGG
65 AATTATCGGG
* * *
60331153 AAGCTCATACGAGCCATAAACGGGAAGCTCATAAGAGCTAAATAACGGGAAGCTCATGAGAGCCT
1 AAGCTCATAAGAGCCATAAACGGGAAGCTCATAAGAGCCAAATAACGGGAAGCTCATGAGAGCCA
60331218 ATTATCGGG
66 ATTATCGGG
*
60331227 ACGCTCATAAGAGC
1 AAGCTCATAAGAGC
60331241 TATGGTGTGT
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
73 2 0.03
74 75 0.97
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (74 bp):
AAGCTCATAAGAGCCATAAACGGGAAGCTCATAAGAGCCAAATAACGGGAAGCTCATGAGAGCCA
ATTATCGGG
Found at i:60331239 original size:50 final size:48
Alignment explanation
Indices: 60331079--60331242 Score: 156
Period size: 49 Copynumber: 3.3 Consensus size: 48
60331069 ATGTAACAGA
*
60331079 AAGCTCATAAGAGC--CATAATCGGGAAGCTCATAAGAGCCAATTATCGGG
1 AAGCTCATAAGAGCTAAATAA-CGGGAAGCTCAT-AGAGCC-ATTATCGGG
* * ** * *
60331128 AAGCTCCA-GAGAG-TCAATTATTGGGAAGCTCATACGAGCCATAAACGGG
1 AAGCT-CATAAGAGCT-AAATAACGGGAAGCTCATA-GAGCCATTATCGGG
60331177 AAGCTCATAAGAGCTAAATAACGGGAAGCTCATGAGAGCCTATTATCGGG
1 AAGCTCATAAGAGCTAAATAACGGGAAGCTCAT-AGAGCC-ATTATCGGG
*
60331227 ACGCTCATAAGAGCTA
1 AAGCTCATAAGAGCTA
60331243 TGGTGTGTCC
Statistics
Matches: 92, Mismatches: 14, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
48 2 0.02
49 46 0.50
50 42 0.46
51 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (48 bp):
AAGCTCATAAGAGCTAAATAACGGGAAGCTCATAGAGCCATTATCGGG
Found at i:60333421 original size:31 final size:32
Alignment explanation
Indices: 60333383--60333450 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
60333373 TTCAAAATCC
** *
60333383 AAAAAGTACA-ATGACTAAATTTGA-CTAATTA
1 AAAAAGTACAGA-GACTAAAAATGATCAAATTA
60333414 AAAAAGTACAGAGACTAAAAATGATCAAATTA
1 AAAAAGTACAGAGACTAAAAATGATCAAATTA
60333446 AAAAA
1 AAAAA
60333451 TAAAGACCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 20 0.62
32 12 0.38
ACGTcount: A:0.59, C:0.09, G:0.10, T:0.22
Consensus pattern (32 bp):
AAAAAGTACAGAGACTAAAAATGATCAAATTA
Found at i:60335822 original size:16 final size:17
Alignment explanation
Indices: 60335801--60335832 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
60335791 TGTTCATACT
60335801 AAAAAGAAAA-GAAAAC
1 AAAAAGAAAAGGAAAAC
60335817 AAAAAGAAAAGGAAAA
1 AAAAAGAAAAGGAAAA
60335833 GCCTTACTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAGGAAAAC
Found at i:60336573 original size:3 final size:3
Alignment explanation
Indices: 60336555--60336636 Score: 65
Period size: 3 Copynumber: 26.7 Consensus size: 3
60336545 TAATGTGTGC
* * * *
60336555 TAT TATT TAT TTT TAT TAT TAT TAT ATAT TAT TAT TAA CAC TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
* * * * *
60336602 AAT TAT TAT TAG CAT TAT TAT TAC TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
60336637 AATACCTTTT
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
3 55 0.90
4 6 0.10
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:60336608 original size:21 final size:22
Alignment explanation
Indices: 60336574--60336637 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
60336564 TTTTTATTAT
60336574 TATTATATATTATTATTAACAC
1 TATTATATATTATTATTAACAC
* *
60336596 TATTATA-ATTATTATTAGCAT
1 TATTATATATTATTATTAACAC
*
60336617 TATTATTACTAATATTATTAA
1 TATTA-TA-TATTATTATTAA
60336638 ATACCTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 17 0.49
22 9 0.26
24 9 0.26
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.52
Consensus pattern (22 bp):
TATTATATATTATTATTAACAC
Found at i:60336856 original size:36 final size:40
Alignment explanation
Indices: 60336816--60336906 Score: 100
Period size: 42 Copynumber: 2.3 Consensus size: 40
60336806 AAGTACGTAC
60336816 ATATATATATACATT-TTTT-T-TT-GAATTTGTATAAGT
1 ATATATATATACATTGTTTTGTGTTAGAATTTGTATAAGT
* *
60336852 ATATATATATGCACATTGTTTTGTGTTAGAATTTTTATAATT
1 ATATATATAT--ACATTGTTTTGTGTTAGAATTTGTATAAGT
* *
60336894 ATGTACATATACA
1 ATATATATATACA
60336907 AGTTCTTATA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
36 10 0.22
38 5 0.11
39 4 0.09
40 4 0.09
41 2 0.04
42 20 0.44
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (40 bp):
ATATATATATACATTGTTTTGTGTTAGAATTTGTATAAGT
Found at i:60345363 original size:21 final size:21
Alignment explanation
Indices: 60345333--60345377 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
60345323 TTGAGCCATG
*
60345333 TTTGGCCTAGAATTTTTGTAA
1 TTTGGACTAGAATTTTTGTAA
* *
60345354 TTTGGACTAGACTTTTTTTAA
1 TTTGGACTAGAATTTTTGTAA
60345375 TTT
1 TTT
60345378 TAATTTGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.09, G:0.16, T:0.53
Consensus pattern (21 bp):
TTTGGACTAGAATTTTTGTAA
Found at i:60346014 original size:21 final size:21
Alignment explanation
Indices: 60345988--60346030 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
60345978 TTTGGGTGGA
60345988 TCAGCTCTCACGAGCTTTTGT
1 TCAGCTCTCACGAGCTTTTGT
60346009 TCAGCTCTCACGAGCTTTTGT
1 TCAGCTCTCACGAGCTTTTGT
60346030 T
1 T
60346031 GGCATGTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.19, T:0.40
Consensus pattern (21 bp):
TCAGCTCTCACGAGCTTTTGT
Found at i:60348132 original size:15 final size:14
Alignment explanation
Indices: 60348102--60348137 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
60348092 GACTCTATTT
*
60348102 TAATTATATTAGGA
1 TAATTATATTAAGA
60348116 TAATTACTATTAAGA
1 TAATTA-TATTAAGA
60348131 TAATTAT
1 TAATTAT
60348138 TAAGGATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (14 bp):
TAATTATATTAAGA
Found at i:60351139 original size:20 final size:20
Alignment explanation
Indices: 60351102--60351140 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
60351092 TATGCAAAAT
*
60351102 AGGCTATCTGGGAATTAGGA
1 AGGCTATCTGAGAATTAGGA
* *
60351122 AGGCTATGTGAGATTTAGG
1 AGGCTATCTGAGAATTAGG
60351141 GGCTTCTATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.08, G:0.36, T:0.28
Consensus pattern (20 bp):
AGGCTATCTGAGAATTAGGA
Found at i:60354638 original size:31 final size:31
Alignment explanation
Indices: 60354598--60354681 Score: 102
Period size: 31 Copynumber: 2.7 Consensus size: 31
60354588 GCAACCCAAT
60354598 TTTTATTTTTATTTATTTATTTATTTA-TTTA
1 TTTTATTTTTATTTATTTATTTA-TTACTTTA
*
60354629 TTTTGTTTTT-TTTACTTTATTTATTACTTTA
1 TTTTATTTTTATTTA-TTTATTTATTACTTTA
*
60354660 TTTTATTATTTA-TTACTTATTT
1 TTTTATT-TTTATTTATTTATTT
60354682 GGATATTAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
30 7 0.15
31 33 0.72
32 6 0.13
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.75
Consensus pattern (31 bp):
TTTTATTTTTATTTATTTATTTATTACTTTA
Found at i:60354647 original size:5 final size:4
Alignment explanation
Indices: 60354605--60354673 Score: 67
Period size: 4 Copynumber: 17.5 Consensus size: 4
60354595 AATTTTTATT
60354605 TTTA TTTA TTTA TTTA TTTA TTTA TTT- TGTT- TTT- TTTA CTTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA -TTTA TTTA
60354652 -TTA CTTTA TTT- TATTA TTTA TT
1 TTTA -TTTA TTTA T-TTA TTTA TT
60354674 ACTTATTTGG
Statistics
Matches: 58, Mismatches: 0, Indels: 14
0.81 0.00 0.19
Matches are distributed among these distances:
3 10 0.17
4 40 0.69
5 8 0.14
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:60356620 original size:15 final size:15
Alignment explanation
Indices: 60356595--60356629 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
60356585 GACTCTATTT
*
60356595 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
60356609 TAATTAATATTAAGA
1 TAATTAATATTAAGA
60356624 TAATTA
1 TAATTA
60356630 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:60359388 original size:3 final size:3
Alignment explanation
Indices: 60359382--60359421 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
60359372 TCTCTAACTC
60359382 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
60359422 GCTTTATACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:60360282 original size:29 final size:26
Alignment explanation
Indices: 60360216--60360301 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 26
60360206 ACACTTTTTC
* *
60360216 TTTTTCTAATTTGGTATCTAATTTTT
1 TTTTTCTAATTTGGTACCTAATCTTT
60360242 TTTTGTCTAATTTGGTACCTATGATACTTT
1 TTTT-TCTAATTTGGTACCTA--AT-CTTT
* * *
60360272 TTTTTCTAATTTAGTACCTAAGCTTG
1 TTTTTCTAATTTGGTACCTAATCTTT
60360298 TTTT
1 TTTT
60360302 GTTGTCCAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
26 11 0.22
27 16 0.31
29 17 0.33
30 7 0.14
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.58
Consensus pattern (26 bp):
TTTTTCTAATTTGGTACCTAATCTTT
Found at i:60385483 original size:24 final size:24
Alignment explanation
Indices: 60385454--60385515 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
60385444 TCAAAGAAGT
*
60385454 TGATAGTAATAGTGCAAGCTATGA
1 TGATAGTAATAGTGCAAACTATGA
60385478 TGATAGTAATAGTGCAAACTATGA
1 TGATAGTAATAGTGCAAACTATGA
*
60385502 TGATAGTGATAGTG
1 TGATAGTAATAGTG
60385516 AACTTTTTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (24 bp):
TGATAGTAATAGTGCAAACTATGA
Found at i:60390825 original size:26 final size:26
Alignment explanation
Indices: 60390789--60390842 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
60390779 TTCATCTCTC
60390789 CTAGGTATTTAGAAAATTAGTTAATG
1 CTAGGTATTTAGAAAATTAGTTAATG
*
60390815 CTAGGTATTTAGAAAATTAGTTCATG
1 CTAGGTATTTAGAAAATTAGTTAATG
60390841 CT
1 CT
60390843 TGAAAATAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.39
Consensus pattern (26 bp):
CTAGGTATTTAGAAAATTAGTTAATG
Found at i:60393399 original size:40 final size:39
Alignment explanation
Indices: 60393327--60393403 Score: 93
Period size: 39 Copynumber: 1.9 Consensus size: 39
60393317 GTCCCAAAAT
* * *
60393327 TATTATTTTAGAAAATTTTAAACTTTTAACTTTCTTTATA
1 TATTATTTTAAAAAAATTAAAACTTTTAACTTT-TTTATA
*
60393367 TATTA-TTTAAAAAAATTAAAATTTTTATACTTTTTTA
1 TATTATTTTAAAAAAATTAAAACTTTTA-ACTTTTTTA
60393404 GAAATATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 22 0.69
40 10 0.31
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.55
Consensus pattern (39 bp):
TATTATTTTAAAAAAATTAAAACTTTTAACTTTTTTATA
Found at i:60400354 original size:6 final size:6
Alignment explanation
Indices: 60400343--60400375 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
60400333 TCAATACATA
60400343 TATATT TATATT TATATT TATATT TATATT TAT
1 TATATT TATATT TATATT TATATT TATATT TAT
60400376 TACCTGATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:60401201 original size:15 final size:14
Alignment explanation
Indices: 60401181--60401218 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
60401171 GTTTTTTAAG
60401181 ATTATAATATTTTAT
1 ATTATAATATTTT-T
*
60401196 ATTATATTATTTTT
1 ATTATAATATTTTT
60401210 A-TATAATAT
1 ATTATAATAT
60401219 ATAATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 7 0.33
14 2 0.10
15 12 0.57
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTATAATATTTTT
Found at i:60403274 original size:13 final size:13
Alignment explanation
Indices: 60403258--60403302 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
60403248 TTCATTACTA
60403258 TTATATTATTATT
1 TTATATTATTATT
60403271 TTATATTATTAGTT
1 TTATATTATTA-TT
* *
60403285 TTGTACTATTATT
1 TTATATTATTATT
60403298 ATTAT
1 -TTAT
60403303 TATGTTTCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 13 0.48
14 14 0.52
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (13 bp):
TTATATTATTATT
Found at i:60405131 original size:13 final size:13
Alignment explanation
Indices: 60405113--60405139 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
60405103 ACTAATTGTC
60405113 ATTATTAAATATG
1 ATTATTAAATATG
60405126 ATTATTAAATATG
1 ATTATTAAATATG
60405139 A
1 A
60405140 AAGATAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (13 bp):
ATTATTAAATATG
Found at i:60406102 original size:59 final size:60
Alignment explanation
Indices: 60405997--60406120 Score: 214
Period size: 59 Copynumber: 2.1 Consensus size: 60
60405987 ATTAAGCATT
60405997 AAAACATGAATTTAAGTGATTATAAGTATAAAATTCACAATAAACATCAAATAATCACTC
1 AAAACATGAATTTAAGTGATTATAAGTATAAAATTCACAATAAACATCAAATAATCACTC
* * *
60406057 AAAA-ATGTATTTAAGTGATTATGAGTATAAAATTCACAATTAACATCAAATAATCACTC
1 AAAACATGAATTTAAGTGATTATAAGTATAAAATTCACAATAAACATCAAATAATCACTC
60406116 AAAAC
1 AAAAC
60406121 GCATTAAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 56 0.93
60 4 0.07
ACGTcount: A:0.51, C:0.13, G:0.07, T:0.29
Consensus pattern (60 bp):
AAAACATGAATTTAAGTGATTATAAGTATAAAATTCACAATAAACATCAAATAATCACTC
Found at i:60406781 original size:21 final size:21
Alignment explanation
Indices: 60406756--60406807 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
60406746 AAAATATTAA
*
60406756 GATAATTATATATAAAATTTT
1 GATAATTATATATAAAAATTT
* *
60406777 GATAAATAAAATATAAAAATTT
1 GAT-AATTATATATAAAAATTT
60406799 -ATTAATTAT
1 GA-TAATTAT
60406808 TAATTATTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (21 bp):
GATAATTATATATAAAAATTT
Found at i:60409768 original size:2 final size:2
Alignment explanation
Indices: 60409761--60409790 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
60409751 CAATATAAAA
60409761 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
60409791 TGCACTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60412948 original size:19 final size:18
Alignment explanation
Indices: 60412890--60413034 Score: 95
Period size: 18 Copynumber: 8.0 Consensus size: 18
60412880 ACACGAGAAC
60412890 TTTGAAACAC-AATAATAATT
1 TTTGAAACACGAA-AAT--TT
*
60412910 TTTGAAAACACGAAGA-TT
1 TTTG-AAACACGAAAATTT
60412928 TTTGAAACACGAAAATTT
1 TTTGAAACACGAAAATTT
* *
60412946 TTTGAAAACACGGAATTTT
1 TTTG-AAACACGAAAATTT
* *
60412965 TTTGAAAACAAGGAAA-TT
1 TTTG-AAACACGAAAATTT
* * * *
60412983 TTCGATACATGAGAATTT
1 TTTGAAACACGAAAATTT
*
60413001 TTTG--ACACGAAAA-AT
1 TTTGAAACACGAAAATTT
60413016 TTTGAAAACACGAAAATTT
1 TTTG-AAACACGAAAATTT
60413035 CGAAAACATG
Statistics
Matches: 100, Mismatches: 16, Indels: 19
0.74 0.12 0.14
Matches are distributed among these distances:
15 5 0.05
16 7 0.07
17 17 0.17
18 31 0.31
19 27 0.27
20 4 0.04
21 7 0.07
22 2 0.02
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.32
Consensus pattern (18 bp):
TTTGAAACACGAAAATTT
Found at i:60412953 original size:36 final size:38
Alignment explanation
Indices: 60412890--60412975 Score: 108
Period size: 36 Copynumber: 2.3 Consensus size: 38
60412880 ACACGAGAAC
60412890 TTTGAAACACAATAATAATTTTTGAAAACAC-GAAGATT
1 TTTGAAACACAATAAT-ATTTTTGAAAACACGGAAGATT
**
60412928 TTTGAAACACGAA-AAT-TTTTTGAAAACACGGAATTTT
1 TTTGAAACAC-AATAATATTTTTGAAAACACGGAAGATT
60412965 TTTGAAA-ACAA
1 TTTGAAACACAA
60412976 GGAAATTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
35 2 0.05
36 15 0.34
37 12 0.27
38 13 0.30
39 2 0.05
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (38 bp):
TTTGAAACACAATAATATTTTTGAAAACACGGAAGATT
Found at i:60413108 original size:28 final size:28
Alignment explanation
Indices: 60413076--60413132 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 28
60413066 TTTTTTAAAA
60413076 AAAACACGAGAA-TTTTTTTGAAAACACG
1 AAAACACGA-AATTTTTTTTGAAAACACG
* *
60413104 AAAACATGAAA---ATTTTGAAAACACG
1 AAAACACGAAATTTTTTTTGAAAACACG
60413129 AAAA
1 AAAA
60413133 TTTTTGAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 17 0.63
27 2 0.07
28 8 0.30
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.21
Consensus pattern (28 bp):
AAAACACGAAATTTTTTTTGAAAACACG
Found at i:60413155 original size:18 final size:18
Alignment explanation
Indices: 60412906--60413154 Score: 116
Period size: 18 Copynumber: 13.4 Consensus size: 18
60412896 ACACAATAAT
60412906 AATTTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
*
60412924 GATTTTTG-AAACACGAA
1 AATTTTTGAAAACACGAA
60412941 AATTTTTTGAAAACACGGAA
1 AA-TTTTTGAAAACAC-GAA
** * *
60412961 TTTTTTTGAAAACAAGGA
1 AATTTTTGAAAACACGAA
* * *
60412979 AATTTTCG-ATACATGAGA
1 AATTTTTGAAAACACGA-A
*
60412997 ATTTTTTG---ACACGAA
1 AATTTTTGAAAACACGAA
*
60413012 AAATTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
* * *
60413030 AA-TTTCGAAAACATGTA
1 AATTTTTGAAAACACGAA
** * *
60413047 TTTTTTTTAAAACATGAA
1 AATTTTTGAAAACACGAA
** *
60413065 TTTTTTTAAAAAAAACACGAGA
1 AATTTTT---GAAAACACGA-A
*
60413087 ATTTTTTTGAAAACACGAAA
1 A-ATTTTTGAAAACACG-AA
60413107 ACATGAAAATTTTGAAAACACGAA
1 A-AT-----TTTTGAAAACACGAA
*
60413131 AATTTTTG-AAACACGAG
1 AATTTTTGAAAACACGAA
60413148 AATTTTT
1 AATTTTT
60413155 TTTTAAAACA
Statistics
Matches: 180, Mismatches: 32, Indels: 39
0.72 0.13 0.16
Matches are distributed among these distances:
15 7 0.04
16 5 0.03
17 42 0.23
18 60 0.33
19 18 0.10
20 14 0.08
21 9 0.05
22 1 0.01
23 8 0.04
24 3 0.02
25 13 0.07
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:60413180 original size:28 final size:29
Alignment explanation
Indices: 60413139--60413194 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 29
60413129 AAAATTTTTG
60413139 AAACACGAGAATTTTTTTTTAAAACACGA
1 AAACACGAGAATTTTTTTTTAAAACACGA
60413168 AAACACGA-AATTTTTTTTTAAAACACG
1 AAACACGAGAATTTTTTTTTAAAACACG
60413195 GGAATTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (29 bp):
AAACACGAGAATTTTTTTTTAAAACACGA
Found at i:60413208 original size:18 final size:18
Alignment explanation
Indices: 60413181--60413246 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 18
60413171 CACGAAATTT
* *
60413181 TTTTTTAAAACACGGGAA
1 TTTTTGAAAACACGAGAA
*
60413199 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAGAA
* **
60413217 TTTTT-TATTCACGAGAA
1 TTTTTGAAAACACGAGAA
60413234 TTTTTG-AAACACG
1 TTTTTGAAAACACG
60413247 GATTTTTTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
17 18 0.47
18 20 0.53
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (18 bp):
TTTTTGAAAACACGAGAA
Found at i:60413246 original size:17 final size:17
Alignment explanation
Indices: 60413182--60413246 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 17
60413172 ACGAAATTTT
* *
60413182 TTTTTAAAACACGGGAA
1 TTTTTGAAACACGAGAA
*
60413199 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAGAA
* **
60413217 TTTTTTATTCACGAGAA
1 TTTTTGAAACACGAGAA
60413234 TTTTTGAAACACG
1 TTTTTGAAACACG
60413247 GATTTTTTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
17 23 0.62
18 14 0.38
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (17 bp):
TTTTTGAAACACGAGAA
Found at i:60413331 original size:17 final size:18
Alignment explanation
Indices: 60413309--60413356 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
60413299 TATTATTATT
60413309 ATTTTGAAACACGTG-AA
1 ATTTTGAAACACGTGAAA
60413326 ATTTTGAAGACA--TGAAA
1 ATTTTGAA-ACACGTGAAA
60413343 ATTTTTGAAACACG
1 A-TTTTGAAACACG
60413357 ATTTTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.08
17 14 0.54
18 10 0.38
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (18 bp):
ATTTTGAAACACGTGAAA
Found at i:60413503 original size:20 final size:20
Alignment explanation
Indices: 60413474--60413511 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
60413464 GGGATTCTAA
60413474 TAAAACACGAGAATTTTTAT
1 TAAAACACGAGAATTTTTAT
* *
60413494 TAAAATACGAGGATTTTT
1 TAAAACACGAGAATTTTT
60413512 GAATATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (20 bp):
TAAAACACGAGAATTTTTAT
Found at i:60414013 original size:29 final size:29
Alignment explanation
Indices: 60413948--60414013 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
60413938 TAGTTTTTTT
*
60413948 TTTCTTT-TTTCTTTCTTTCTTTTTCCCC
1 TTTCTTTCTTTCCTTCTTTCTTTTTCCCC
*
60413976 TTT-TCTTCTTTCCTTC-TTCTTTTTCTTCC
1 TTTCT-TTCTTTCCTTCTTTCTTTTTC-CCC
60414005 TTTCTTTCT
1 TTTCTTTCT
60414014 CCCCGATCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
27 1 0.03
28 14 0.44
29 16 0.50
30 1 0.03
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (29 bp):
TTTCTTTCTTTCCTTCTTTCTTTTTCCCC
Found at i:60414552 original size:29 final size:30
Alignment explanation
Indices: 60414519--60414635 Score: 105
Period size: 30 Copynumber: 3.9 Consensus size: 30
60414509 TGTAATTTTT
*
60414519 AGAAAATTT-AGGATTAAAATGAAATTTAA
1 AGAAAATTTAAGGGTTAAAATGAAATTTAA
* * *
60414548 TGAAAGTTTAAGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTAAGGGT-TAAAATGAAATTTAA
* *
60414578 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTTAAGGGTTAAAATGAAATTTAA
* * * *
60414607 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTAAGGGTTAAAATGAAATTT
60414636 TTATTTTTTA
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
29 12 0.16
30 60 0.82
31 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.30
Consensus pattern (30 bp):
AGAAAATTTAAGGGTTAAAATGAAATTTAA
Found at i:60414574 original size:30 final size:30
Alignment explanation
Indices: 60414534--60414635 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
60414524 ATTTAGGATT
*
60414534 AAAATGAAATTTAATGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* *
60414564 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* *
60414594 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAAGGGTC
*
60414624 AAAATGCAATTT
1 AAAATGAAATTT
60414636 TTATTTTTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 2 0.03
30 61 0.97
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAAGGGTC
Found at i:60414658 original size:16 final size:17
Alignment explanation
Indices: 60414633--60414668 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
60414623 CAAAATGCAA
60414633 TTTTTATTTTTT-AAAT
1 TTTTTATTTTTTGAAAT
*
60414649 TTTTTTTTTTTTGAAAT
1 TTTTTATTTTTTGAAAT
60414666 TTT
1 TTT
60414669 GAAAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTTTATTTTTTGAAAT
Found at i:60414659 original size:17 final size:17
Alignment explanation
Indices: 60414633--60414668 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
60414623 CAAAATGCAA
*
60414633 TTTTTATTTTTTAAATT
1 TTTTTATTTTTGAAATT
*
60414650 TTTTTTTTTTTGAAATT
1 TTTTTATTTTTGAAATT
60414667 TT
1 TT
60414669 GAAAATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTTTATTTTTGAAATT
Found at i:60415040 original size:14 final size:14
Alignment explanation
Indices: 60415004--60415054 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
60414994 GAGTTGATTT
*
60415004 TTGAAAAATATAAA
1 TTGAAAAATAGAAA
*
60415018 TTGAAAAAAACAGAAA
1 TTG--AAAAATAGAAA
*
60415034 TTGAAAAGTAGAAA
1 TTGAAAAATAGAAA
60415048 TT-AAAAA
1 TTGAAAAA
60415055 GACCTCAGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
13 4 0.13
14 14 0.47
16 12 0.40
ACGTcount: A:0.65, C:0.02, G:0.12, T:0.22
Consensus pattern (14 bp):
TTGAAAAATAGAAA
Found at i:60415164 original size:73 final size:73
Alignment explanation
Indices: 60415077--60415487 Score: 406
Period size: 73 Copynumber: 5.5 Consensus size: 73
60415067 TGAGCCGAGA
* *
60415077 CTCAACTCACCTCTCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATTACCTCAGCGTG
60415142 TCTTGAGG
66 TCTTGAGG
*
60415150 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATTACCTCAGCGTG
60415215 T-TCTGAGG
66 TCT-TGAGG
60415223 CTCAACTCACCTCTCGCAATATGAGTTGA-TTTT-AAAAACAGAAATTAAAAACCAGAAATTGAA
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT--------GAAATT--A
** ** *
60415286 AATACCTCAGTGT-GTGA-G
56 CCT-CAGC-GTGTCTTGAGG
* * * ** * * **
60415304 C-CAAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTGATGAACATAAATTAAAACCACCT
1 CTCAA--CTC-----ACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATTACCT
*
60415368 CAGCGTGTCCTGAGG
59 CAGCGTGTCTTGAGG
*
60415383 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTGAAATTACCTCAGC--G
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATTACCTCAGCGTG
60415446 TCTTGAGG
66 TCTTGAGG
*
60415454 CTCAACTCACTTCTCGCAATATGAGTTGATTTTT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTT
60415488 TTGAAACATA
Statistics
Matches: 281, Mismatches: 32, Indels: 52
0.77 0.09 0.14
Matches are distributed among these distances:
71 53 0.19
72 5 0.02
73 144 0.51
77 4 0.01
78 8 0.03
79 10 0.04
80 6 0.02
81 7 0.02
82 8 0.03
83 4 0.01
87 18 0.06
88 4 0.01
89 10 0.04
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (73 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATTACCTCAGCGTG
TCTTGAGG
Found at i:60415272 original size:13 final size:14
Alignment explanation
Indices: 60415254--60415287 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
60415244 TGAGTTGATT
60415254 TTAAAAA-CAGAAA
1 TTAAAAACCAGAAA
60415267 TTAAAAACCAGAAA
1 TTAAAAACCAGAAA
*
60415281 TTGAAAA
1 TTAAAAA
60415288 TACCTCAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.18
Consensus pattern (14 bp):
TTAAAAACCAGAAA
Found at i:60415615 original size:72 final size:73
Alignment explanation
Indices: 60415497--60415638 Score: 223
Period size: 72 Copynumber: 2.0 Consensus size: 73
60415487 TTTGAAACAT
* * *
60415497 AAATTAAAAAAACGAAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAAT
1 AAATTAAAAAAACAAAAATTGAAAATACCTCAGCATGCCCCGAGGCTCAACTCACCTCTCGCAAT
60415562 ATGAGTTG
66 ATGAGTTG
* * *
60415570 AAATT-AAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAAT
1 AAATTAAAAAAACAAAAATTGAAAATACCTCAGCATGCCCCGAGGCTCAACTCACCTCTCGCAAT
60415634 ATGAG
66 ATGAG
60415639 CTGATTTTGA
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
72 58 0.92
73 5 0.08
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (73 bp):
AAATTAAAAAAACAAAAATTGAAAATACCTCAGCATGCCCCGAGGCTCAACTCACCTCTCGCAAT
ATGAGTTG
Found at i:60415805 original size:72 final size:72
Alignment explanation
Indices: 60415669--60415993 Score: 480
Period size: 72 Copynumber: 4.5 Consensus size: 72
60415659 ATTAAAAGGT
* * * *
60415669 TCAACCCACCTCTCGTAATATGAGTTG-ATTCTTGACAAACAGAAATTGAAATTACCTCATCGTG
1 TCAACTCACCTCTCGCAATATGAGTTGAATT-TTGA-AAACAAAAATTGAAATTACCTCAACGTG
60415733 TCCTGAGGC
64 TCCTGAGGC
60415742 TCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAACGTGTC
1 TCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAACGTGTC
*
60415807 TTGAGGC
66 CTGAGGC
**
60415814 TCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAACGTGTC
1 TCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAACGTGTC
*
60415879 TTGAGGC
66 CTGAGGC
** *
60415886 TCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAACAGAAATTGAAAATTACCTC-ACGTG-
1 TCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTG-AAATTACCTCAACGTGT
60415948 CCTTGAGGC
65 CC-TGAGGC
60415957 TCAACTCACCTCTCGCAATATGAGTTG-ATTTTGAAAA
1 TCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAA
60415994 GCATAGATTG
Statistics
Matches: 237, Mismatches: 11, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
70 7 0.03
71 50 0.21
72 148 0.62
73 29 0.12
74 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (72 bp):
TCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAACGTGTC
CTGAGGC
Found at i:60416006 original size:14 final size:14
Alignment explanation
Indices: 60415987--60416021 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
60415977 TGAGTTGATT
* *
60415987 TTGAAAAGCATAGA
1 TTGAAAAACATAAA
60416001 TTGAAAAACATAAA
1 TTGAAAAACATAAA
60416015 TTGAAAA
1 TTGAAAA
60416022 TACCTCAGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.57, C:0.06, G:0.14, T:0.23
Consensus pattern (14 bp):
TTGAAAAACATAAA
Found at i:60416141 original size:73 final size:72
Alignment explanation
Indices: 60416001--60416230 Score: 322
Period size: 70 Copynumber: 3.2 Consensus size: 72
60415991 AAAGCATAGA
* *
60416001 TTGAAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATA
1 TTGAAAAACAAAAATTGAAAATACCTCAGC--GTGA-CCTGAGGCTCAACTCACCTCTCGCAATA
60416065 TGAGTTGATTT
63 TGAGTTGA-TT
* **
60416076 TTGAAAAACAAAAATTGAAATTACCTCAGCGTGTTCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAAAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGA
60416141 GTTGATT
66 GTTGATT
* * **
60416148 TT--AAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCATTTCTCGCAATATGA
1 TTGAAAAACAAAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGA
60416211 GTTGATT
66 GTTGATT
60416218 TTGAAAAACAAAA
1 TTGAAAAACAAAA
60416231 TTAAAAGGCT
Statistics
Matches: 140, Mismatches: 12, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
70 64 0.46
72 13 0.09
73 35 0.25
75 28 0.20
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (72 bp):
TTGAAAAACAAAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATT
Found at i:60416212 original size:231 final size:231
Alignment explanation
Indices: 60415809--60416224 Score: 685
Period size: 231 Copynumber: 1.8 Consensus size: 231
60415799 AACGTGTCTT
**
60415809 GAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAAC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAAC
** *
60415874 GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAACAGAAATTGAAAATTA
66 GTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTAAAACAGAAATTGAAAATTA
*
60415939 CCTCACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAGCATAGATTG
131 CCTCACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAGCATAGATTG
60416004 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC
196 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC
* * *
60416040 GAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAACAAAAATTGAAATTACCTCAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTG-AAAACAAAAATTGAAATTACCTCAA
60416105 CGTGT-TCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTAAAACAGAAATTGAAAA-
65 CGTGTCT-TGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTAAAACAGAAATTGAAAAT
**
60416167 TACCTCAGCGTGCCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAA
129 TACCTCA-CGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAA
60416225 ACAAAATTAA
Statistics
Matches: 171, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
230 7 0.04
231 104 0.61
232 60 0.35
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (231 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAAC
GTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTAAAACAGAAATTGAAAATTA
CCTCACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAGCATAGATTG
AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC
Found at i:60416384 original size:116 final size:118
Alignment explanation
Indices: 60416114--60416463 Score: 544
Period size: 116 Copynumber: 2.9 Consensus size: 118
60416104 GCGTGTTCTG
* * *
60416114 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAACAGAAATTGAAAATACCTCAGCGTG
1 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACAGAAATT-AAAATACCTCAGCGTG
*
60416179 CCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAATTAAA
64 CCC-GAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAA-AAAATTAAA
*
60416236 AGGCTTAACTCACCACTCGCAATATGAGTCAATTTAAAACA-AAATTAAAATACCTCAGCGTG-C
1 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACAGAAATTAAAATACCTCAGCGTGCC
*
60416299 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAAAAAATTAAA
66 CGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAAAAAATTAAA
* * *
60416352 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGC
1 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACAGAAA-TTAAAATACCTCAGCGTG-
60416417 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT-AAAAAAA
64 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAAAA
60416464 TTAAAATACC
Statistics
Matches: 214, Mismatches: 10, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
116 49 0.23
117 44 0.21
118 18 0.08
119 23 0.11
120 43 0.20
121 11 0.05
122 26 0.12
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (118 bp):
AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACAGAAATTAAAATACCTCAGCGTGCC
CGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAAAAAATTAAA
Found at i:60416497 original size:66 final size:69
Alignment explanation
Indices: 60416352--60416522 Score: 213
Period size: 66 Copynumber: 2.5 Consensus size: 69
60416342 AAAAATTAAA
* * ** * **
60416352 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGC
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAACATAAACTAAAAATACCTCAACGTGC
60416417 CCCG
66 CCCG
* *
60416421 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAA-A-AAA-TTAAAATACCTCAACGTGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAACATAAACTAAAAATACCTCAACGTGC
**
60416483 CTTG
66 CCCG
*
60416487 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT
60416523 CCTTGGAAAG
Statistics
Matches: 90, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
66 52 0.58
67 3 0.03
68 1 0.01
69 34 0.38
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (69 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAACATAAACTAAAAATACCTCAACGTGC
CCCG
Found at i:60428242 original size:19 final size:18
Alignment explanation
Indices: 60428184--60428328 Score: 95
Period size: 18 Copynumber: 8.0 Consensus size: 18
60428174 ACACGAGAAC
60428184 TTTGAAACAC-AATAATAATT
1 TTTGAAACACGAA-AAT--TT
*
60428204 TTTGAAAACACGAAGA-TT
1 TTTG-AAACACGAAAATTT
60428222 TTTGAAACACGAAAATTT
1 TTTGAAACACGAAAATTT
* *
60428240 TTTGAAAACACGGAATTTT
1 TTTG-AAACACGAAAATTT
* *
60428259 TTTGAAAACAAGGAAA-TT
1 TTTG-AAACACGAAAATTT
* * * *
60428277 TTCGATACATGAGAATTT
1 TTTGAAACACGAAAATTT
*
60428295 TTTG--ACACGAAAA-AT
1 TTTGAAACACGAAAATTT
60428310 TTTGAAAACACGAAAATTT
1 TTTG-AAACACGAAAATTT
60428329 CGAAAACATG
Statistics
Matches: 100, Mismatches: 16, Indels: 19
0.74 0.12 0.14
Matches are distributed among these distances:
15 5 0.05
16 7 0.07
17 17 0.17
18 31 0.31
19 27 0.27
20 4 0.04
21 7 0.07
22 2 0.02
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.32
Consensus pattern (18 bp):
TTTGAAACACGAAAATTT
Found at i:60428247 original size:36 final size:38
Alignment explanation
Indices: 60428184--60428269 Score: 108
Period size: 36 Copynumber: 2.3 Consensus size: 38
60428174 ACACGAGAAC
60428184 TTTGAAACACAATAATAATTTTTGAAAACAC-GAAGATT
1 TTTGAAACACAATAAT-ATTTTTGAAAACACGGAAGATT
**
60428222 TTTGAAACACGAA-AAT-TTTTTGAAAACACGGAATTTT
1 TTTGAAACAC-AATAATATTTTTGAAAACACGGAAGATT
60428259 TTTGAAA-ACAA
1 TTTGAAACACAA
60428270 GGAAATTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
35 2 0.05
36 15 0.34
37 12 0.27
38 13 0.30
39 2 0.05
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (38 bp):
TTTGAAACACAATAATATTTTTGAAAACACGGAAGATT
Found at i:60428449 original size:18 final size:18
Alignment explanation
Indices: 60428200--60428448 Score: 109
Period size: 17 Copynumber: 13.4 Consensus size: 18
60428190 ACACAATAAT
60428200 AATTTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
*
60428218 GATTTTTG-AAACACGAA
1 AATTTTTGAAAACACGAA
60428235 AATTTTTTGAAAACACGGAA
1 AA-TTTTTGAAAACAC-GAA
** * *
60428255 TTTTTTTGAAAACAAGGA
1 AATTTTTGAAAACACGAA
* * *
60428273 AATTTTCG-ATACATGAGA
1 AATTTTTGAAAACACGA-A
*
60428291 ATTTTTTG---ACACGAA
1 AATTTTTGAAAACACGAA
*
60428306 AAATTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
* * *
60428324 AA-TTTCGAAAACATG-T
1 AATTTTTGAAAACACGAA
* * *
60428340 ATTTTTTTAAAACATGAA
1 AATTTTTGAAAACACGAA
** *
60428358 TTTTTTTTTAAAAAAACACGAGA
1 --AATTTTT--GAAAACACGA-A
*
60428381 ATTTTTTTGAAAACACGAAA
1 A-ATTTTTGAAAACACG-AA
60428401 ACATGAAAATTTTGAAAACACGAA
1 A-AT-----TTTTGAAAACACGAA
*
60428425 AATTTTTG-AAACACGAG
1 AATTTTTGAAAACACGAA
60428442 AATTTTT
1 AATTTTT
60428449 TTTTAAAACA
Statistics
Matches: 178, Mismatches: 32, Indels: 43
0.70 0.13 0.17
Matches are distributed among these distances:
15 7 0.04
16 6 0.03
17 52 0.29
18 41 0.23
19 18 0.10
20 20 0.11
21 1 0.01
22 14 0.08
23 3 0.02
24 3 0.02
25 13 0.07
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.33
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:60428476 original size:29 final size:29
Alignment explanation
Indices: 60428433--60428489 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
60428423 AAAATTTTTG
60428433 AAACACGAGAATTTTTTTTTAAAACACGA
1 AAACACGAGAATTTTTTTTTAAAACACGA
60428462 AAACACGA-AATTTTTTTTTTAAAACACG
1 AAACACGAGAA-TTTTTTTTTAAAACACG
60428490 GGAATTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 2 0.07
29 25 0.93
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (29 bp):
AAACACGAGAATTTTTTTTTAAAACACGA
Found at i:60428513 original size:18 final size:18
Alignment explanation
Indices: 60428476--60428516 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
60428466 ACGAAATTTT
* **
60428476 TTTTTTAAAACACGGGAA
1 TTTTTGAAAACACGAAAA
60428494 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
60428512 TTTTT
1 TTTTT
60428517 TATTCACGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:60428625 original size:17 final size:18
Alignment explanation
Indices: 60428603--60428650 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
60428593 TATTATTATT
60428603 ATTTTGAAACACGTG-AA
1 ATTTTGAAACACGTGAAA
60428620 ATTTTGAAGACA--TGAAA
1 ATTTTGAA-ACACGTGAAA
60428637 ATTTTTGAAACACG
1 A-TTTTGAAACACG
60428651 ATTTTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.08
17 14 0.54
18 10 0.38
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (18 bp):
ATTTTGAAACACGTGAAA
Found at i:60428797 original size:20 final size:20
Alignment explanation
Indices: 60428768--60428805 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
60428758 GGGATTCTAA
60428768 TAAAACACGAGAATTTTTAT
1 TAAAACACGAGAATTTTTAT
* *
60428788 TAAAATACGAGGATTTTT
1 TAAAACACGAGAATTTTT
60428806 GAATATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (20 bp):
TAAAACACGAGAATTTTTAT
Found at i:60429239 original size:11 final size:11
Alignment explanation
Indices: 60429223--60429262 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
60429213 TGGCCTGCTA
60429223 TTTTTTTTCTT
1 TTTTTTTTCTT
60429234 TTTTTTTTCTT
1 TTTTTTTTCTT
*
60429245 TTTTCTTTCTT
1 TTTTTTTTCTT
*
60429256 TCTTTTT
1 TTTTTTT
60429263 CCCCTTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:60429304 original size:29 final size:29
Alignment explanation
Indices: 60429239--60429304 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
60429229 TTCTTTTTTT
*
60429239 TTTCTTT-TTTCTTTCTTTCTTTTTCCCC
1 TTTCTTTCTTTCCTTCTTTCTTTTTCCCC
*
60429267 TTT-TCTTCTTTCCTTC-TTCTTTTTCTTCC
1 TTTCT-TTCTTTCCTTCTTTCTTTTTC-CCC
60429296 TTTCTTTCT
1 TTTCTTTCT
60429305 CCCCGATCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
27 1 0.03
28 14 0.44
29 16 0.50
30 1 0.03
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (29 bp):
TTTCTTTCTTTCCTTCTTTCTTTTTCCCC
Found at i:60429846 original size:29 final size:30
Alignment explanation
Indices: 60429813--60429929 Score: 105
Period size: 30 Copynumber: 3.9 Consensus size: 30
60429803 TGTAATTTTT
*
60429813 AGAAAATTT-AGGATTAAAATGAAATTTAA
1 AGAAAATTTAAGGGTTAAAATGAAATTTAA
* * *
60429842 TGAAAGTTTAAGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTAAGGGT-TAAAATGAAATTTAA
* *
60429872 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTTAAGGGTTAAAATGAAATTTAA
* * * *
60429901 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTAAGGGTTAAAATGAAATTT
60429930 TTATTTTTTA
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
29 12 0.16
30 60 0.82
31 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.30
Consensus pattern (30 bp):
AGAAAATTTAAGGGTTAAAATGAAATTTAA
Found at i:60429868 original size:30 final size:30
Alignment explanation
Indices: 60429828--60429929 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
60429818 ATTTAGGATT
*
60429828 AAAATGAAATTTAATGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* *
60429858 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* *
60429888 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAAGGGTC
*
60429918 AAAATGCAATTT
1 AAAATGAAATTT
60429930 TTATTTTTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 2 0.03
30 61 0.97
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAAGGGTC
Found at i:60429945 original size:15 final size:16
Alignment explanation
Indices: 60429925--60429961 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
60429915 GTCAAAATGC
60429925 AATTTTTATTTT-TT-A
1 AATTTTT-TTTTATTGA
60429940 AATTTTTTTTTATTGA
1 AATTTTTTTTTATTGA
60429956 AATTTT
1 AATTTT
60429962 GAAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 9 0.45
16 7 0.35
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
AATTTTTTTTTATTGA
Found at i:60430631 original size:13 final size:13
Alignment explanation
Indices: 60430613--60430639 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
60430603 ACTAATTGTC
60430613 ATTATTAAATATG
1 ATTATTAAATATG
60430626 ATTATTAAATATG
1 ATTATTAAATATG
60430639 A
1 A
60430640 AAGATAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (13 bp):
ATTATTAAATATG
Found at i:60431602 original size:59 final size:60
Alignment explanation
Indices: 60431497--60431620 Score: 214
Period size: 59 Copynumber: 2.1 Consensus size: 60
60431487 ATTAAGCATT
60431497 AAAACATGAATTTAAGTGATTATAAGTATAAAATTCACAATAAACATCAAATAATCACTC
1 AAAACATGAATTTAAGTGATTATAAGTATAAAATTCACAATAAACATCAAATAATCACTC
* * *
60431557 AAAA-ATGTATTTAAGTGATTATGAGTATAAAATTCACAATTAACATCAAATAATCACTC
1 AAAACATGAATTTAAGTGATTATAAGTATAAAATTCACAATAAACATCAAATAATCACTC
60431616 AAAAC
1 AAAAC
60431621 GCATTAAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 56 0.93
60 4 0.07
ACGTcount: A:0.51, C:0.13, G:0.07, T:0.29
Consensus pattern (60 bp):
AAAACATGAATTTAAGTGATTATAAGTATAAAATTCACAATAAACATCAAATAATCACTC
Found at i:60432280 original size:21 final size:21
Alignment explanation
Indices: 60432255--60432306 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
60432245 AAAATATTAA
*
60432255 GATAATTATATATAAAATTTT
1 GATAATTATATATAAAAATTT
* *
60432276 GATAAATAAAATATAAAAATTT
1 GAT-AATTATATATAAAAATTT
60432298 -ATTAATTAT
1 GA-TAATTAT
60432307 TAATTATTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (21 bp):
GATAATTATATATAAAAATTT
Found at i:60443530 original size:6 final size:6
Alignment explanation
Indices: 60443519--60443547 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
60443509 GAATACAACC
60443519 ATTTAT ATTTAT ATTTAT ATTTAT ATTTA
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTA
60443548 ATTATTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATTTAT
Found at i:60450187 original size:22 final size:21
Alignment explanation
Indices: 60450162--60450231 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 21
60450152 AATTACATAG
60450162 AATTTTACTCTTAATAAACATT
1 AATTTTA-TCTTAATAAACATT
*
60450184 AATTTTAAT-GTATATCAAACTATT
1 AATTTT-ATCTTA-AT-AAAC-ATT
60450208 --TTTTATCTTAATAAACATT
1 AATTTTATCTTAATAAACATT
*
60450227 CATTT
1 AATTT
60450232 AATAATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 15
0.70 0.04 0.27
Matches are distributed among these distances:
19 3 0.08
20 4 0.10
21 9 0.23
22 15 0.38
23 5 0.13
24 3 0.08
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.49
Consensus pattern (21 bp):
AATTTTATCTTAATAAACATT
Found at i:60450909 original size:14 final size:14
Alignment explanation
Indices: 60450874--60450912 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
60450864 TATCGTGTAA
*
60450874 AATAGAAATCAAAT
1 AATAGAATTCAAAT
60450888 AATAGAATTCAAAT
1 AATAGAATTCAAAT
60450902 AATAGAATTCA
1 AATAGAATTCA
60450913 TTATAGGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.26
Consensus pattern (14 bp):
AATAGAATTCAAAT
Found at i:60451355 original size:9 final size:9
Alignment explanation
Indices: 60451341--60451368 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
60451331 GATTATCTAA
60451341 TTTTTGCTC
1 TTTTTGCTC
60451350 TTTTTGCTC
1 TTTTTGCTC
60451359 TTTTTGCTC
1 TTTTTGCTC
60451368 T
1 T
60451369 CAAATGCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.21, G:0.11, T:0.68
Consensus pattern (9 bp):
TTTTTGCTC
Found at i:60457476 original size:20 final size:20
Alignment explanation
Indices: 60457447--60457493 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
60457437 CATTCAAACA
60457447 CTAGAAAAGTAAATCATTTT
1 CTAGAAAAGTAAATCATTTT
*
60457467 CTAGAGAAGTAAATCATTTT
1 CTAGAAAAGTAAATCATTTT
60457487 CTAGAAA
1 CTAGAAA
60457494 TCATTTTCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (20 bp):
CTAGAAAAGTAAATCATTTT
Found at i:60457496 original size:14 final size:13
Alignment explanation
Indices: 60457477--60457506 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
60457467 CTAGAGAAGT
60457477 AAATCATTTTCTAG
1 AAATCATTTTCT-G
60457491 AAATCATTTTCTG
1 AAATCATTTTCTG
60457504 AAA
1 AAA
60457507 AACATTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (13 bp):
AAATCATTTTCTG
Done.