Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 393 of 438
Found at i:122504402 original size:26 final size:25
Alignment explanation
Indices: 122504379--122504427 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
122504369 AAAGTTAACC
*
122504379 AGTTTAAT-ATTTTTAATTTTTTAA
1 AGTTTAATAATTTTTAATTGTTTAA
*
122504403 AGTTTTATGAATTTTTAATTGTTTA
1 AGTTTAAT-AATTTTTAATTGTTTA
122504428 TTTAATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
26 14 0.67
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (25 bp):
AGTTTAATAATTTTTAATTGTTTAA
Found at i:122511696 original size:13 final size:13
Alignment explanation
Indices: 122511678--122511703 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
122511668 GGACATAATG
122511678 AAAAAAAGAAAGA
1 AAAAAAAGAAAGA
122511691 AAAAAAAGAAAGA
1 AAAAAAAGAAAGA
122511704 GTAGACAGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAGA
Found at i:122513947 original size:2 final size:2
Alignment explanation
Indices: 122513940--122513972 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
122513930 ATAAATCTGA
122513940 AT AT AT AT 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 AT AT AT AT A
122513973 AAAGGAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:122519598 original size:3 final size:3
Alignment explanation
Indices: 122519590--122519648 Score: 109
Period size: 3 Copynumber: 19.3 Consensus size: 3
122519580 TAGCTATGGA
122519590 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
122519638 AAT AAT GAAT A
1 AAT AAT -AAT A
122519649 TGAAAAATAT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 52 0.95
4 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:122520244 original size:2 final size:2
Alignment explanation
Indices: 122520227--122520262 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
122520217 ATCCCAGTTT
*
122520227 TA TA -A TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
122520263 TTGTTATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:122525482 original size:6 final size:6
Alignment explanation
Indices: 122525463--122525492 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
122525453 CAATGGCTCA
*
122525463 TAGTCC TAGCCC TAGTCC TAGTCC TAGTCC
1 TAGTCC TAGTCC TAGTCC TAGTCC TAGTCC
122525493 CAGAGCTGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.37, G:0.17, T:0.30
Consensus pattern (6 bp):
TAGTCC
Found at i:122529164 original size:151 final size:150
Alignment explanation
Indices: 122528891--122529193 Score: 446
Period size: 151 Copynumber: 2.0 Consensus size: 150
122528881 ATTTGATCTA
* *
122528891 AGTCATTTTGTTATGTTAATATACGTGATTAGAGATGGATTTAATTACAATATATGTAACAAAAG
1 AGTCATTTGGTTATGTTAATATACGTAATTAGAGATGGATTTAATTACAATATATGTAACAAAAG
* * *
122528956 TCGCATTGGTGCTATGTTAACATGGTTAATGAACAAGATTGTTTGGAATACCTTTTGGATATGAT
66 TCACATTGATGCTATGTTAACATGGTTAATGAACAAGATTGTTCGGAATACCTTTTGGATATGAT
122529021 AGAAAGATTTTGAGCTCATG
131 AGAAAGATTTTGAGCTCATG
* * * *
122529041 AGTCATTTGGTTATGTTGATATACGATAATTTTG-GATGGATTTAGTTACAATATATGTAACGAA
1 AGTCATTTGGTTATGTTAATATACG-TAA-TTAGAGATGGATTTAATTACAATATATGTAACAAA
* * * *
122529105 AGTCACATTGATTCTATGTTAACATGGTTATTGGACGAGATTGTTCGGAATACCTTTTGGATATG
64 AGTCACATTGATGCTATGTTAACATGGTTAATGAACAAGATTGTTCGGAATACCTTTTGGATATG
* *
122529170 ATAGTAAGATTTTGAGCTTATG
129 ATAGAAAGATTTTGAGCTCATG
122529192 AG
1 AG
122529194 GTTATATAAT
Statistics
Matches: 136, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
150 23 0.17
151 110 0.81
152 3 0.02
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (150 bp):
AGTCATTTGGTTATGTTAATATACGTAATTAGAGATGGATTTAATTACAATATATGTAACAAAAG
TCACATTGATGCTATGTTAACATGGTTAATGAACAAGATTGTTCGGAATACCTTTTGGATATGAT
AGAAAGATTTTGAGCTCATG
Found at i:122531853 original size:40 final size:40
Alignment explanation
Indices: 122531809--122531994 Score: 218
Period size: 40 Copynumber: 4.7 Consensus size: 40
122531799 GCTACTCATT
* * *
122531809 CAAATACCTTCGGGACATAGCCCGG-TTATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
122531849 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
122531889 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACCCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * *
122531929 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
122531970 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
122531995 CATCATTCGA
Statistics
Matches: 130, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
39 3 0.02
40 115 0.88
41 12 0.09
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:122539922 original size:40 final size:40
Alignment explanation
Indices: 122539857--122540035 Score: 215
Period size: 40 Copynumber: 4.5 Consensus size: 40
122539847 CTCGTTCAAA
* *
122539857 CCTTCGGGACATAGCCC-G-TTATAGTAGCTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACAAATG
*
122539896 CCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATG
*
122539936 CCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCACAAATG
1 CCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCACAAATG
* * * *
122539976 CCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACAAA-G
1 CCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCACAAATG
122540016 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAGCCCGGA
122540036 CATCATTCGA
Statistics
Matches: 126, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
39 18 0.14
40 95 0.75
41 13 0.10
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATG
Found at i:122542230 original size:26 final size:25
Alignment explanation
Indices: 122542162--122542240 Score: 142
Period size: 25 Copynumber: 3.2 Consensus size: 25
122542152 TGATACAAAT
122542162 TGATAATGGTTAGGTAAATGTTCCA
1 TGATAATGGTTAGGTAAATGTTCCA
122542187 TGATAATGGTTAGGTAAATGTTCCA
1 TGATAATGGTTAGGTAAATGTTCCA
122542212 TGATAATGGGTTAGGTAAATGTT-CA
1 TGATAAT-GGTTAGGTAAATGTTCCA
122542237 TGAT
1 TGAT
122542241 GGGATTTCAT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
25 38 0.72
26 15 0.28
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (25 bp):
TGATAATGGTTAGGTAAATGTTCCA
Found at i:122549263 original size:26 final size:26
Alignment explanation
Indices: 122549201--122549281 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
122549191 TGATACAAAT
122549201 TGATAATGGGTTAGGTAAATGTT-CA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
122549226 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
122549252 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
122549278 TGAT
1 TGAT
122549282 GGGCATTTCA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
25 22 0.42
26 31 0.58
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:122552784 original size:35 final size:35
Alignment explanation
Indices: 122552738--122552805 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
122552728 ATGTCCATGT
122552738 CCTTGCCCGTGTGGCTCACATGGCCTAGACACACG
1 CCTTGCCCGTGTGGCTCACATGGCCTAGACACACG
122552773 CCTTGCCCGTGTGGCTCACATGGCCTAGACACA
1 CCTTGCCCGTGTGGCTCACATGGCCTAGACACA
122552806 TGCCCATGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.18, C:0.37, G:0.25, T:0.21
Consensus pattern (35 bp):
CCTTGCCCGTGTGGCTCACATGGCCTAGACACACG
Found at i:122552895 original size:42 final size:42
Alignment explanation
Indices: 122552773--122552899 Score: 164
Period size: 42 Copynumber: 3.0 Consensus size: 42
122552763 TAGACACACG
* * * *
122552773 CCTTGCCCGTGTGGCTCACATGGCCTAGACACATGCCCATGT
1 CCTTGCCCGTGTGACTCACACGGCCTGGACACATGCTCATGT
* * *
122552815 CCTTGCCCGTGTGACTCACACAGCTTGGACACACGCTCATGT
1 CCTTGCCCGTGTGACTCACACGGCCTGGACACATGCTCATGT
* * *
122552857 CCTTACCCGTGTGACTCACACGGCCTGGAAAAATGCTCATGT
1 CCTTGCCCGTGTGACTCACACGGCCTGGACACATGCTCATGT
122552899 C
1 C
122552900 TCTGGCTGTG
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.20, C:0.35, G:0.22, T:0.24
Consensus pattern (42 bp):
CCTTGCCCGTGTGACTCACACGGCCTGGACACATGCTCATGT
Found at i:122556701 original size:37 final size:37
Alignment explanation
Indices: 122556627--122556735 Score: 155
Period size: 37 Copynumber: 2.9 Consensus size: 37
122556617 CACGACAATC
* * *
122556627 GCTCATAAGAGCTAATCCACATGAATAACATGCCAGAT
1 GCTCATAAGAGCTAGTCCACCTG-ATAACACGCCAGAT
*
122556665 GCTCATAAGAGCTAGTCCACCCGATAACACGCCAGAT
1 GCTCATAAGAGCTAGTCCACCTGATAACACGCCAGAT
* *
122556702 GCTCATAAGAGCTAGTCCAACTGAAAACACGCCA
1 GCTCATAAGAGCTAGTCCACCTGATAACACGCCA
122556736 AAACAAGGAG
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
37 44 0.69
38 20 0.31
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.17
Consensus pattern (37 bp):
GCTCATAAGAGCTAGTCCACCTGATAACACGCCAGAT
Found at i:122573193 original size:13 final size:13
Alignment explanation
Indices: 122573175--122573200 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
122573165 GGCGTGTTAG
122573175 TTCACACGACCGT
1 TTCACACGACCGT
122573188 TTCACACGACCGT
1 TTCACACGACCGT
122573201 GTCTGGCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.38, G:0.15, T:0.23
Consensus pattern (13 bp):
TTCACACGACCGT
Found at i:122579673 original size:20 final size:20
Alignment explanation
Indices: 122579648--122579685 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
122579638 GTTTATTCGC
*
122579648 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
122579668 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
122579686 TTTGGATGTG
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:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:122581347 original size:28 final size:28
Alignment explanation
Indices: 122581315--122581383 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
122581305 GCGTAGATCA
*
122581315 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAACAAAATTAC
*
122581343 CGAAATTACCCCTAAATAACAAAATTAC
1 CGAAATTACCCCTAAAGAACAAAATTAC
122581371 C--AATATACCCCTA
1 CGAAAT-TACCCCTA
122581384 GGGTTTAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 3 0.08
27 8 0.21
28 27 0.71
ACGTcount: A:0.46, C:0.28, G:0.06, T:0.20
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAACAAAATTAC
Found at i:122584019 original size:6 final size:6
Alignment explanation
Indices: 122584008--122584049 Score: 57
Period size: 6 Copynumber: 6.5 Consensus size: 6
122583998 TCCTCTTATC
122584008 TTTTTA TTTTTA TTTTTTTA TTTTTA TTTTTA TTTTTCA TTT
1 TTTTTA TTTTTA --TTTTTA TTTTTA TTTTTA TTTTT-A TTT
122584050 CAATTTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
6 23 0.70
7 4 0.12
8 6 0.18
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:122584025 original size:14 final size:14
Alignment explanation
Indices: 122584003--122584038 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
122583993 TTGAATCCTC
*
122584003 TTATCTTTTTATTT
1 TTATTTTTTTATTT
122584017 TTATTTTTTTATTT
1 TTATTTTTTTATTT
122584031 TTATTTTT
1 TTATTTTT
122584039 ATTTTTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (14 bp):
TTATTTTTTTATTT
Found at i:122589358 original size:29 final size:29
Alignment explanation
Indices: 122589326--122589383 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
122589316 TATTATTCTG
122589326 GAATAATATATTTAATAGATGAGAATAAA
1 GAATAATATATTTAATAGATGAGAATAAA
122589355 GAATAATATATTTAATAGATGAGAATAAA
1 GAATAATATATTTAATAGATGAGAATAAA
122589384 TTCTATCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (29 bp):
GAATAATATATTTAATAGATGAGAATAAA
Found at i:122589889 original size:18 final size:19
Alignment explanation
Indices: 122589855--122589890 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
122589845 TGCAAATGAA
*
122589855 TATTTCACAATTTCATTTC
1 TATTTCACAATTCCATTTC
122589874 TATTTC-CAATTCCATTT
1 TATTTCACAATTCCATTT
122589891 TGAGAAATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTTCACAATTCCATTTC
Found at i:122589995 original size:18 final size:19
Alignment explanation
Indices: 122589968--122590006 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
122589958 TAATGTTTTC
*
122589968 CATTTCTTTC-TTTTTATT
1 CATTTCTTTCATTTTAATT
*
122589986 CATTTTTTTCATTTTAATT
1 CATTTCTTTCATTTTAATT
122590005 CA
1 CA
122590007 AACATGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (19 bp):
CATTTCTTTCATTTTAATT
Found at i:122599490 original size:18 final size:18
Alignment explanation
Indices: 122599467--122599508 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
122599457 TGTCTTTCTC
122599467 ACAATGTAAACGTTCTTT
1 ACAATGTAAACGTTCTTT
122599485 ACAATGTAAACGTTCTTT
1 ACAATGTAAACGTTCTTT
122599503 ACAATG
1 ACAATG
122599509 CCACTTATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (18 bp):
ACAATGTAAACGTTCTTT
Found at i:122602469 original size:3 final size:3
Alignment explanation
Indices: 122602461--122602485 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
122602451 GGTATAAATG
122602461 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
122602486 GAGGAACCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:122609496 original size:15 final size:15
Alignment explanation
Indices: 122609473--122609514 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
122609463 GAAGCCCAGA
*
122609473 ATAAGGAAATCTAAG
1 ATAAGGAAATCCAAG
* *
122609488 ATAAAGAAATCCATG
1 ATAAGGAAATCCAAG
122609503 ATAAGGAAATCC
1 ATAAGGAAATCC
122609515 CATTTACAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.52, C:0.12, G:0.17, T:0.19
Consensus pattern (15 bp):
ATAAGGAAATCCAAG
Found at i:122612519 original size:38 final size:38
Alignment explanation
Indices: 122612476--122612854 Score: 227
Period size: 38 Copynumber: 9.0 Consensus size: 38
122612466 TTTCAAATTA
*
122612476 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
1 ACATGTATAACCGTGGTATATCCACTTAGCACCACGTT
* *
122612514 ACATGTTTAACCGTGGTATATCCACTTAGCACCATGTTAAT
1 ACATGTATAACCGTGGTATATCCACTTAGCACCACG-T--T
* * * *
122612555 GAATCAATATATGTAACCGTAGCATATCCACTTAGAACCACGTT
1 --A-C-ATGTA--TAACCGTGGTATATCCACTTAGCACCACGTT
* * *
122612599 ACAGGTTTAACCATGGTATATCCACTTAGCACCACGTTAAT
1 ACATGTATAACCGTGGTATATCCACTTAGCACCACG-T--T
* *
122612640 GAATCAATATATGTAACCGTGGTATATCCACTTAGCACCATGTT
1 --A-C-ATGTA--TAACCGTGGTATATCCACTTAGCACCACGTT
* * *
122612684 ACATGTTTAACCGTGGTACATCCACTTAACACCACGTTAAT
1 ACATGTATAACCGTGGTATATCCACTTAGCACCACG-T--T
* *
122612725 GAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
1 --A-C-ATGTA--TAACCGTGGTATATCCACTTAGCACCACGTT
** * *
122612769 ACATGTATCAATATGTGTAATTGTGGTATATCCACTTAGCAACACTTT
1 ACATG------TA----TAACCGTGGTATATCCACTTAGCACCACGTT
*
122612817 ACATGTATAACCGTGGTATATTCACTTAGCACCACGTT
1 ACATGTATAACCGTGGTATATCCACTTAGCACCACGTT
122612855 TATCCATTCC
Statistics
Matches: 264, Mismatches: 42, Indels: 70
0.70 0.11 0.19
Matches are distributed among these distances:
38 110 0.42
39 3 0.01
40 7 0.03
41 6 0.02
42 5 0.02
43 3 0.01
44 6 0.02
45 8 0.03
46 5 0.02
47 78 0.30
48 33 0.12
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (38 bp):
ACATGTATAACCGTGGTATATCCACTTAGCACCACGTT
Found at i:122612580 original size:85 final size:85
Alignment explanation
Indices: 122612483--122612774 Score: 503
Period size: 85 Copynumber: 3.4 Consensus size: 85
122612473 TTAACATGTA
122612483 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTTAGCACCA
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTTAGCACCA
*
122612548 TGTTAATGAATCAATATATG
66 CGTTAATGAATCAATATATG
* * * *
122612568 TAACCGTAGCATATCCACTTAGAACCACGTTACAGGTTTAACCATGGTATATCCACTTAGCACCA
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTTAGCACCA
122612633 CGTTAATGAATCAATATATG
66 CGTTAATGAATCAATATATG
* * * *
122612653 TAACCGTGGTATATCCACTTAGCACCATGTTACATGTTTAACCGTGGTACATCCACTTAACACCA
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTTAGCACCA
122612718 CGTTAATGAATCAATATATG
66 CGTTAATGAATCAATATATG
122612738 TAACCGTGGCATATCCACTTAGCACCACGTTACATGT
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGT
122612775 ATCAATATGT
Statistics
Matches: 192, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 192 1.00
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (85 bp):
TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTTAGCACCA
CGTTAATGAATCAATATATG
Found at i:122612800 original size:48 final size:48
Alignment explanation
Indices: 122612691--122612824 Score: 180
Period size: 48 Copynumber: 2.8 Consensus size: 48
122612681 GTTACATGTT
* * *
122612691 TAACCGTGGTACATCCACTTAACACCACGTTA-ATGAATCAATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
* *
122612738 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
** * *
122612786 TAATTGTGGTATATCCACTTAGCAACACTTTACATGTAT
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGTAT
122612825 AACCGTGGTA
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
47 29 0.38
48 47 0.62
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.31
Consensus pattern (48 bp):
TAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
Found at i:122612843 original size:133 final size:132
Alignment explanation
Indices: 122612606--122612854 Score: 374
Period size: 133 Copynumber: 1.9 Consensus size: 132
122612596 GTTACAGGTT
*
122612606 TAACCATGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGTATATCCAC
1 TAACCATGGCATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGTATATCCAC
* *
122612671 TTAGCACCATGTTACATGTTTAACCGTGGTACATCCACTTAACACCACGTTAATGAATCAATATA
66 TTAGCAACATGTTACATGTATAACCGTGGTACATCCACTTAACACCACGTTAATGAATCAATATA
122612736 TG
131 TG
* * * **
122612738 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTGTAATTGTGGTATATCCA
1 TAACCATGGCATATCCACTTAGCACCACGTTA-ATGAATCAATATATGTAACCGTGGTATATCCA
* * *
122612803 CTTAGCAACACT-TTACATGTATAACCGTGGTATATTCACTTAGCACCACGTT
65 CTTAGCAACA-TGTTACATGTATAACCGTGGTACATCCACTTAACACCACGTT
122612855 TATCCATTCC
Statistics
Matches: 104, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
132 30 0.29
133 73 0.70
134 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (132 bp):
TAACCATGGCATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGTATATCCAC
TTAGCAACATGTTACATGTATAACCGTGGTACATCCACTTAACACCACGTTAATGAATCAATATA
TG
Found at i:122617806 original size:17 final size:17
Alignment explanation
Indices: 122617792--122617825 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
122617782 CAGAAAGATC
122617792 TGAATCTGCGAAAGAGA
1 TGAATCTGCGAAAGAGA
122617809 TGAATCTGCGAAAGAGA
1 TGAATCTGCGAAAGAGA
122617826 AAATGGTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.29, T:0.18
Consensus pattern (17 bp):
TGAATCTGCGAAAGAGA
Found at i:122619787 original size:12 final size:13
Alignment explanation
Indices: 122619770--122619807 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
122619760 ATCCTGGAAT
122619770 ATTAAG-ACAAGA
1 ATTAAGAACAAGA
*
122619782 ATTAAGAACACATA
1 ATTAAGAACA-AGA
122619796 ATTAAGAACAAG
1 ATTAAGAACAAG
122619808 TCAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 6 0.27
13 4 0.18
14 12 0.55
ACGTcount: A:0.58, C:0.11, G:0.13, T:0.18
Consensus pattern (13 bp):
ATTAAGAACAAGA
Found at i:122627177 original size:47 final size:47
Alignment explanation
Indices: 122627114--122627783 Score: 1090
Period size: 47 Copynumber: 14.3 Consensus size: 47
122627104 CCCTTCGGGA
* * * *
122627114 CTTATCACATTTATACACTTTCACATCCATCACATTGACCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * * *
122627161 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
122627208 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
122627255 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
122627302 CTTGTCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
122627349 TTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
122627396 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
122627443 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
122627490 CTTGTCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
122627537 TTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
122627584 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
122627631 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
122627678 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
122627725 CTTGTCACATATATACACTTTCACATTCATC-CATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
122627771 CTTATCACATATA
1 CTTATCACATATA
122627784 CATATCTTGT
Statistics
Matches: 577, Mismatches: 46, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
46 26 0.05
47 551 0.95
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
Found at i:122627640 original size:22 final size:22
Alignment explanation
Indices: 122627612--122627687 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
122627602 TTTCACATTC
122627612 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
122627634 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
122627658 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
122627681 ATCACAT
1 ATCACAT
122627688 ATATACACTT
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 18 0.46
23 5 0.13
24 5 0.13
25 11 0.28
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:122634535 original size:19 final size:20
Alignment explanation
Indices: 122634511--122634549 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
122634501 ATAAAATATA
*
122634511 TTTAATATATTTA-ACATTT
1 TTTAATATATATATACATTT
*
122634530 TTTAATTTATATATACATTT
1 TTTAATATATATATACATTT
122634550 CAAATCCGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAATATATATATACATTT
Found at i:122646506 original size:26 final size:25
Alignment explanation
Indices: 122646477--122646532 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
122646467 AATTATACTT
*
122646477 ATTTATATTCTTGTTGAAAATTCTAA
1 ATTTATATTCTTATT-AAAATTCTAA
* * *
122646503 ATTTATTTTTTTATTAAAATTTTAA
1 ATTTATATTCTTATTAAAATTCTAA
122646528 ATTTA
1 ATTTA
122646533 AAAACAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.57
Consensus pattern (25 bp):
ATTTATATTCTTATTAAAATTCTAA
Found at i:122657260 original size:22 final size:22
Alignment explanation
Indices: 122657234--122657281 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
122657224 CCTGAGTTGT
122657234 ATGTTTCTTTGATAAGTTGATC
1 ATGTTTCTTTGATAAGTTGATC
122657256 ATGTTTCTTTGATAAGTTGATC
1 ATGTTTCTTTGATAAGTTGATC
122657278 -TGTT
1 ATGTT
122657282 GTGGTTCGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.21, C:0.08, G:0.19, T:0.52
Consensus pattern (22 bp):
ATGTTTCTTTGATAAGTTGATC
Found at i:122661621 original size:21 final size:21
Alignment explanation
Indices: 122661595--122661647 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
122661585 GTGGACCGCT
* *
122661595 GTGAGATTAGTTACTGTAGTG
1 GTGAGATTAGATACTGTAGCG
*
122661616 GTGAGATTGGATACTGTAGCG
1 GTGAGATTAGATACTGTAGCG
*
122661637 GTAAGATTAGA
1 GTGAGATTAGA
122661648 AACAATGGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.06, G:0.34, T:0.32
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGCG
Found at i:122664427 original size:18 final size:18
Alignment explanation
Indices: 122664406--122664446 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
122664396 TCAAATGGAC
122664406 ATGCCGCCCGGCATGGTA
1 ATGCCGCCCGGCATGGTA
122664424 ATGCCGCCCGGCATGGTA
1 ATGCCGCCCGGCATGGTA
122664442 ATGCC
1 ATGCC
122664447 ACCAGGCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.34, G:0.32, T:0.17
Consensus pattern (18 bp):
ATGCCGCCCGGCATGGTA
Found at i:122665157 original size:26 final size:26
Alignment explanation
Indices: 122665127--122665178 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
122665117 TAAAAAAAGT
122665127 TAACATTTTAACCTTGCTAACGTGGG
1 TAACATTTTAACCTTGCTAACGTGGG
122665153 TAACATTTTAACCTTGCTAACGTGGG
1 TAACATTTTAACCTTGCTAACGTGGG
122665179 ATACAAGTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (26 bp):
TAACATTTTAACCTTGCTAACGTGGG
Found at i:122669663 original size:5 final size:5
Alignment explanation
Indices: 122669655--122669683 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
122669645 TCTTAATATA
122669655 ATTAT ATTAT ATTAT ATTAT ATTAT ATTA
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTA
122669684 AAAGATTTTT
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:122675239 original size:3 final size:3
Alignment explanation
Indices: 122675231--122675267 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
122675221 TAATAAAGTC
*
122675231 ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
122675268 GTATATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:122675274 original size:2 final size:2
Alignment explanation
Indices: 122675260--122675314 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
122675250 TTATTGTTAT
*
122675260 TA TA TA T- TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
122675301 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
122675315 AGTAAAACAA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:122677483 original size:46 final size:46
Alignment explanation
Indices: 122677416--122677663 Score: 372
Period size: 46 Copynumber: 5.4 Consensus size: 46
122677406 CGCGGGAGTG
*
122677416 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCCTGGT
1 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGT
*
122677462 TGAAAGATACCATGGCAACCTGATATGAAGTGTGTAAGACCATGGT
1 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGT
*
122677508 TGAAAGATACCACGGCAACCTGATATGAAATGTGTAAGACCAT-GT
1 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGT
* **
122677553 TGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGT
1 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGT
* * * ** *
122677599 TGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATAGT
1 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGT
*
122677645 TGAAAGATACCATGACAAC
1 TGAAAGATACCATGGCAAC
122677664 ATGACAGAAA
Statistics
Matches: 189, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 41 0.22
46 148 0.78
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (46 bp):
TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGT
Found at i:122677490 original size:25 final size:25
Alignment explanation
Indices: 122677416--122677490 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
122677406 CGCGGGAGTG
122677416 TGAAAGATACCATGGCAACCTGATA
1 TGAAAGATACCATGGCAACCTGATA
* * *
122677441 TGAAATGTGTA--A--G-ACCCTGGT-
1 TGAAA-G-ATACCATGGCAACCTGATA
122677462 TGAAAGATACCATGGCAACCTGATA
1 TGAAAGATACCATGGCAACCTGATA
122677487 TGAA
1 TGAA
122677491 GTGTGTAAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 16
0.62 0.10 0.28
Matches are distributed among these distances:
19 2 0.06
20 1 0.03
21 6 0.17
22 6 0.17
23 2 0.06
24 6 0.17
25 10 0.28
26 1 0.03
27 2 0.06
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (25 bp):
TGAAAGATACCATGGCAACCTGATA
Found at i:122677596 original size:91 final size:92
Alignment explanation
Indices: 122677416--122677663 Score: 372
Period size: 91 Copynumber: 2.7 Consensus size: 92
122677406 CGCGGGAGTG
* *
122677416 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCCTGGTTGAAAGATACCATGGCAAC
1 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGCAAC
* **
122677481 CTGATATGAAGTGTGTAAGACCATGGT
66 CTGATATGAAATGAATAAGACCATGGT
*
122677508 TGAAAGATACCACGGCAACCTGATATGAAATGTGTAAGACCAT-GTTGAAAGATACCATGGCAAC
1 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGCAAC
*
122677572 GTGATATGAAATGAATAAGACCATGGT
66 CTGATATGAAATGAATAAGACCATGGT
* * * ** *
122677599 TGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATAGTTGAAAGATACCATGACAAC
1 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGCAAC
122677664 ATGACAGAAA
Statistics
Matches: 142, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
91 81 0.57
92 61 0.43
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (92 bp):
TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGCAAC
CTGATATGAAATGAATAAGACCATGGT
Found at i:122677676 original size:137 final size:140
Alignment explanation
Indices: 122677416--122677711 Score: 384
Period size: 137 Copynumber: 2.1 Consensus size: 140
122677406 CGCGGGAGTG
** *
122677416 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCCTGGTTGAAAGATACCATGGCAAC
1 TGAAAGATACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* ** ** * * * *
122677481 CTGATATGAAGTGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTGATATGAAATG-T-GTA
66 CTGACATGAAAAGAATAAGACCATAGTTGAAAGATACCACGACAACATGACATGAAATGATAGTA
122677544 AGACCAT-GT
131 AGACCATAGT
*
122677553 TGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 TGAAAGATACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* *
122677618 GTGACATGAAAAGAATAAGACCATAGTTGAAAGATACCATGACAACATGACA-GAAAATGAATGA
66 CTGACATGAAAAGAATAAGACCATAGTTGAAAGATACCACGACAACATGACATG-AAATG-AT-A
122677682 GTAAGACCATAGT
128 GTAAGACCATAGT
* *
122677695 TGAAAGACACTATGGCA
1 TGAAAGATACCATGGCA
122677712 TCATGTCAAA
Statistics
Matches: 136, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
136 1 0.01
137 107 0.79
139 1 0.01
141 10 0.07
142 17 0.12
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.21
Consensus pattern (140 bp):
TGAAAGATACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
CTGACATGAAAAGAATAAGACCATAGTTGAAAGATACCACGACAACATGACATGAAATGATAGTA
AGACCATAGT
Found at i:122677723 original size:92 final size:89
Alignment explanation
Indices: 122677416--122677711 Score: 243
Period size: 91 Copynumber: 3.2 Consensus size: 89
122677406 CGCGGGAGTG
* * * ** * *
122677416 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCCTGGTTGAAAGATACCATGGCAAC
1 TGAAAGACACCATGGCAA-CT-ACATGAAAAGAATAAGACCAT-GTTGAAAGATACCATGACAAC
* * * ** *
122677481 CTGATATGAAGTGTGTAAGACCATGGT
63 ATGACATGAAATGAATAAGACCATAGT
* * * * ** * *
122677508 TGAAAGATACCACGGCAACCTGATATGAAATGTGTAAGACCATGTTGAAAGATACCATGGCAACG
1 TGAAAGACACCATGGCAA-CT-ACATGAAAAGAATAAGACCATGTTGAAAGATACCATGACAACA
* *
122677573 TGATATGAAATGAATAAGACCATGGT
64 TGACATGAAATGAATAAGACCATAGT
*
122677599 TGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATAGTTGAAAGATACCATGACAAC
1 TGAAAGACACCATGGCAAC-T-ACATGAAAAGAATAAGACCAT-GTTGAAAGATACCATGACAAC
122677664 ATGACA-GAAAATGAATGAGTAAGACCATAGT
63 ATGACATG-AAATG-A--A-TAAGACCATAGT
*
122677695 TGAAAGACACTATGGCA
1 TGAAAGACACCATGGCA
122677712 TCATGTCAAA
Statistics
Matches: 180, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
90 1 0.01
91 81 0.45
92 70 0.39
93 1 0.01
95 1 0.01
96 26 0.14
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.21
Consensus pattern (89 bp):
TGAAAGACACCATGGCAACTACATGAAAAGAATAAGACCATGTTGAAAGATACCATGACAACATG
ACATGAAATGAATAAGACCATAGT
Found at i:122680277 original size:196 final size:196
Alignment explanation
Indices: 122679931--122680325 Score: 736
Period size: 196 Copynumber: 2.0 Consensus size: 196
122679921 TAATGTGAGC
*
122679931 TTTGTGAAGTTTGATGATATTAAATGAAAGATATGTGTTAGATTACTAAGTTTTATCTTTAAATT
1 TTTGTGAAGTTTGATGATAGTAAATGAAAGATATGTGTTAGATTACTAAGTTTTATCTTTAAATT
122679996 GTTTATGAATTTGAGTAATTTGGGCTAAATTGTGAAATTTGTAAATTGAGGGACTAAAATGTGAA
66 GTTTATGAATTTGAGTAATTTGGGCTAAATTGTGAAATTTGTAAATTGAGGGACTAAAATGTGAA
* *
122680061 ATAAATGAAATATGTGGACTTTTATGAGTGCTATGAATATTCGTCTAGGCATGTGTACAAAGAAA
131 ATAAATGAAATATGTGGACTTGTATGAGTGCTATGAATATTCGTCTAGGCATGCGTACAAAGAAA
122680126 T
196 T
* *
122680127 TTTGTTAAGTTTGATGATAGTAAATGAAAGATATGTGTTAGATTACTAAGTTTTATCTTTGAATT
1 TTTGTGAAGTTTGATGATAGTAAATGAAAGATATGTGTTAGATTACTAAGTTTTATCTTTAAATT
122680192 GTTTATGAATTTGAGTAATTTGGGCTAAATTGTGAAATTTGTAAATTGAGGGACTAAAATGTGAA
66 GTTTATGAATTTGAGTAATTTGGGCTAAATTGTGAAATTTGTAAATTGAGGGACTAAAATGTGAA
*
122680257 ATAAATGAAATATTTGGACTTGTATGAGTGCTATGAATATTCGTCTAGGCATGCGTACAAAGAAA
131 ATAAATGAAATATGTGGACTTGTATGAGTGCTATGAATATTCGTCTAGGCATGCGTACAAAGAAA
122680322 T
196 T
122680323 TTT
1 TTT
122680326 ATGTATTTTG
Statistics
Matches: 193, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
196 193 1.00
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.39
Consensus pattern (196 bp):
TTTGTGAAGTTTGATGATAGTAAATGAAAGATATGTGTTAGATTACTAAGTTTTATCTTTAAATT
GTTTATGAATTTGAGTAATTTGGGCTAAATTGTGAAATTTGTAAATTGAGGGACTAAAATGTGAA
ATAAATGAAATATGTGGACTTGTATGAGTGCTATGAATATTCGTCTAGGCATGCGTACAAAGAAA
T
Found at i:122680912 original size:43 final size:43
Alignment explanation
Indices: 122680759--122680913 Score: 126
Period size: 43 Copynumber: 3.6 Consensus size: 43
122680749 TGTTATTGTA
* * *
122680759 TAAGACCATGTT-TGGGATGTTGGCATCGACT-TATGATTTACGTG
1 TAAGACCACGTTCT-GGACGTTGGCATCGA-TATTTGA-TTACGTG
*
122680803 TAAGACCACGTT-TGAGACGTTGGCATCG-TATTTGATTTCGTG
1 TAAGACCACGTTCTG-GACGTTGGCATCGATATTTGATTACGTG
* * *
122680845 TAAAACC-C-TGTCTGG-CATAGTGGCATCGATATTTGATTACATG
1 TAAGACCACGT-TCTGGACGT--TGGCATCGATATTTGATTACGTG
*
122680888 TAAGACCACGTTCAGGACGTTGGCAT
1 TAAGACCACGTTCTGGACGTTGGCAT
122680914 TGTACGACAT
Statistics
Matches: 90, Mismatches: 11, Indels: 21
0.74 0.09 0.17
Matches are distributed among these distances:
40 3 0.03
41 3 0.03
42 23 0.26
43 29 0.32
44 29 0.32
45 3 0.03
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (43 bp):
TAAGACCACGTTCTGGACGTTGGCATCGATATTTGATTACGTG
Found at i:122684275 original size:26 final size:26
Alignment explanation
Indices: 122684239--122684296 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
122684229 TGCCTATGTG
122684239 ATTGATTCGAAAATGTCAGAAAAGAA
1 ATTGATTCGAAAATGTCAGAAAAGAA
122684265 ATTGATTCGAAAATGTCAGAAAAGAA
1 ATTGATTCGAAAATGTCAGAAAAGAA
122684291 AGTTGA
1 A-TTGA
122684297 ATCAGTACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 27 0.87
27 4 0.13
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.24
Consensus pattern (26 bp):
ATTGATTCGAAAATGTCAGAAAAGAA
Found at i:122688565 original size:43 final size:43
Alignment explanation
Indices: 122688494--122688578 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
122688484 GTTGGCATCG
* * ***
122688494 TATTTGATTTCGTGTAAGACCTTGTCTGGGACAATAGCATTGA
1 TATTTGATTACATGTAAGACCACATCTGGGACAATAGCATTGA
**
122688537 TATTTGATTACATGTAAGACCACATCTGGGACGTTAGCATTG
1 TATTTGATTACATGTAAGACCACATCTGGGACAATAGCATTG
122688579 TACGAGATTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.35
Consensus pattern (43 bp):
TATTTGATTACATGTAAGACCACATCTGGGACAATAGCATTGA
Found at i:122691253 original size:21 final size:21
Alignment explanation
Indices: 122691195--122691291 Score: 61
Period size: 21 Copynumber: 4.6 Consensus size: 21
122691185 GAAGCTCGAA
* * *
122691195 AGCTGAATAGAACCTCATAAG
1 AGCTGAACAGAAACTCGTAAG
*
122691216 AGCTGAACAGGAACTCGTAAG
1 AGCTGAACAGAAACTCGTAAG
* *
122691237 AGTTGAACA-AAAGCTCGAAAG
1 AGCTGAACAGAAA-CTCGTAAG
* * ** *
122691258 AACTAAACAGAGGCTCGAAAG
1 AGCTGAACAGAAACTCGTAAG
* *
122691279 AGCTAAATAGAAA
1 AGCTGAACAGAAA
122691292 GTAAAACACA
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
20 2 0.03
21 55 0.95
22 1 0.02
ACGTcount: A:0.46, C:0.16, G:0.23, T:0.14
Consensus pattern (21 bp):
AGCTGAACAGAAACTCGTAAG
Found at i:122694214 original size:11 final size:11
Alignment explanation
Indices: 122694172--122694207 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
122694162 GAAAAGGTAA
*
122694172 ATTGATTGATT
1 ATTGTTTGATT
122694183 ATTGTTTGATT
1 ATTGTTTGATT
122694194 ATTGTTTGATT
1 ATTGTTTGATT
122694205 ATT
1 ATT
122694208 TCTTGATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.22, C:0.00, G:0.17, T:0.61
Consensus pattern (11 bp):
ATTGTTTGATT
Found at i:122694602 original size:39 final size:40
Alignment explanation
Indices: 122694545--122694632 Score: 101
Period size: 39 Copynumber: 2.2 Consensus size: 40
122694535 ATACTTTTAA
* * *
122694545 AATC-AGTGAAAATGATTTTAAC-CAAGCCAAATGA-TTTC
1 AATCAAGTTAAAATCATTTTAACAC-AGCAAAATGATTTTC
*
122694583 AATCAAGTTAAAATCATTTTAACACATCAAAATGATTTTC
1 AATCAAGTTAAAATCATTTTAACACAGCAAAATGATTTTC
*
122694623 AAACAAGTTA
1 AATCAAGTTA
122694633 GAATTGCTCC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 4 0.10
39 24 0.57
40 14 0.33
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (40 bp):
AATCAAGTTAAAATCATTTTAACACAGCAAAATGATTTTC
Found at i:122694620 original size:19 final size:19
Alignment explanation
Indices: 122694553--122694621 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 19
122694543 AAAATCAGTG
*
122694553 AAAATGATTTTAAC-CAAGC
1 AAAATGATTTTAACAC-ATC
* * *
122694572 CAAATGATTTCAATCA-AGTT
1 AAAATGATTTTAA-CACA-TC
*
122694592 AAAATCATTTTAACACATC
1 AAAATGATTTTAACACATC
122694611 AAAATGATTTT
1 AAAATGATTTT
122694622 CAAACAAGTT
Statistics
Matches: 37, Mismatches: 9, Indels: 8
0.69 0.17 0.15
Matches are distributed among these distances:
19 25 0.68
20 12 0.32
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (19 bp):
AAAATGATTTTAACACATC
Found at i:122700846 original size:40 final size:38
Alignment explanation
Indices: 122700763--122700846 Score: 89
Period size: 37 Copynumber: 2.2 Consensus size: 38
122700753 TTTATATATA
* *
122700763 TATATATATGGTAAATAGTATTATGATAATTGTTCTTT
1 TATATATACGGTAAATAATATTATGATAATTGTTCTTT
* * *
122700801 AATATATACGGT-AGTAATATTATGGTAATTGCTCTCTCTT
1 TATATATACGGTAAATAATATTATGATAATTG-T-TCT-TT
122700841 TATATA
1 TATATA
122700847 GTAATTTCAC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
37 16 0.43
38 11 0.30
39 3 0.08
40 7 0.19
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.46
Consensus pattern (38 bp):
TATATATACGGTAAATAATATTATGATAATTGTTCTTT
Found at i:122703196 original size:39 final size:36
Alignment explanation
Indices: 122703121--122703193 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
122703111 TATTTCATCT
122703121 AGCCTTAGTTGGCTTCTTCTCATACTATGCCACAAC
1 AGCCTTAGTTGGCTTCTTCTCATACTATGCCACAAC
122703157 AGCCTTAGTTGGCTTCTTCTCATACTATGCCACAAC
1 AGCCTTAGTTGGCTTCTTCTCATACTATGCCACAAC
122703193 A
1 A
122703194 ACATTCTTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (36 bp):
AGCCTTAGTTGGCTTCTTCTCATACTATGCCACAAC
Found at i:122706145 original size:36 final size:35
Alignment explanation
Indices: 122706098--122706172 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 35
122706088 CTTATTACAT
* **
122706098 TGTTTGTGAACATGTTCAATTATATGTTCATGAACA
1 TGTTTGAGAACATGTTCAATTA-ATGTTCACAAACA
**
122706134 TGTTTGAGAACATGTTCGTTTAATGTTCACAAACA
1 TGTTTGAGAACATGTTCAATTAATGTTCACAAACA
122706169 TGTT
1 TGTT
122706173 CGTTTAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 15 0.44
36 19 0.56
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.41
Consensus pattern (35 bp):
TGTTTGAGAACATGTTCAATTAATGTTCACAAACA
Found at i:122717205 original size:58 final size:57
Alignment explanation
Indices: 122717142--122717306 Score: 172
Period size: 58 Copynumber: 2.9 Consensus size: 57
122717132 TTTTTATACT
* * * *
122717142 ATTATATATTATGATTT-TTTAATT-CATTTAATAATAATTATATTAAGAATTTTATTAA
1 ATTATATATTAT--TTTATTAAATTACATTTAATAATAATCATATTAA-AATATGATTAA
* * *
122717200 ATTATATATTATTTTATTAAATTATATTTAGTAATAATCATGTTAAAATATGATTAA
1 ATTATATATTATTTTATTAAATTACATTTAATAATAATCATATTAAAATATGATTAA
* * ** *
122717257 ATTATTTATTATTTTTATTAAAATATTTTTAATAATAATCTTATTAAAAT
1 ATTATATATTA-TTTTATTAAATTACATTTAATAATAATCATATTAAAAT
122717307 TTAATAATAA
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
56 3 0.03
57 25 0.27
58 63 0.69
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (57 bp):
ATTATATATTATTTTATTAAATTACATTTAATAATAATCATATTAAAATATGATTAA
Found at i:122717320 original size:25 final size:26
Alignment explanation
Indices: 122717271--122717320 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
122717261 TTTATTATTT
**
122717271 TTATTAAAATATTTTTAATAATAATC
1 TTATTAAAATATTAATAATAATAATC
122717297 TTATTAAAAT-TTAATAATAATAAT
1 TTATTAAAATATTAATAATAATAAT
122717321 AATAATCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
TTATTAAAATATTAATAATAATAATC
Found at i:122717503 original size:12 final size:11
Alignment explanation
Indices: 122717439--122717504 Score: 57
Period size: 12 Copynumber: 5.7 Consensus size: 11
122717429 AATAATAATT
122717439 TTATATTAAAA
1 TTATATTAAAA
122717450 TTATTATT-AAA
1 TTA-TATTAAAA
122717461 -TATTATTAATAA
1 TTA-TATTAA-AA
122717473 TTATATTAATAA
1 TTATATTAA-AA
122717485 TGT-TATTAAAA
1 T-TATATTAAAA
122717496 TATATATTA
1 T-TATATTA
122717505 TTTTATTAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
10 7 0.15
11 11 0.23
12 27 0.56
13 3 0.06
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (11 bp):
TTATATTAAAA
Found at i:122717770 original size:16 final size:16
Alignment explanation
Indices: 122717749--122717798 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
122717739 AAATTACTGG
122717749 TTACAGCTCTATTCCA
1 TTACAGCTCTATTCCA
* *
122717765 TTACAGTTCTATTCAA
1 TTACAGCTCTATTCCA
*
122717781 TTACAGCCCTATTCCA
1 TTACAGCTCTATTCCA
122717797 TT
1 TT
122717799 GCAGTAAACC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.26, C:0.28, G:0.06, T:0.40
Consensus pattern (16 bp):
TTACAGCTCTATTCCA
Found at i:122723362 original size:25 final size:23
Alignment explanation
Indices: 122723310--122723364 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
122723300 TATAAATAGT
122723310 AATAGTGTTAGAAATATACTATA
1 AATAGTGTTAGAAATATACTATA
* *
122723333 TATAGTGTTTGAAGTATATAC-ATAA
1 AATAGTGTTAGAA--ATATACTAT-A
122723358 AATAGTG
1 AATAGTG
122723365 AAAATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.42
24 2 0.08
25 13 0.50
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (23 bp):
AATAGTGTTAGAAATATACTATA
Found at i:122723461 original size:25 final size:26
Alignment explanation
Indices: 122723433--122723482 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
122723423 AAAAAATGTA
*
122723433 ATAATATAGTGTAAAA-A-ATACATAC
1 ATAATATAAT-TAAAATATATACATAC
122723458 ATAATATAATTAAAATATATACATA
1 ATAATATAATTAAAATATATACATA
122723483 AGATAACATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 5 0.23
25 10 0.45
26 7 0.32
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.32
Consensus pattern (26 bp):
ATAATATAATTAAAATATATACATAC
Found at i:122723472 original size:22 final size:22
Alignment explanation
Indices: 122723447--122723488 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
122723437 TATAGTGTAA
*
122723447 AAAATACATACATAATATAATT
1 AAAATACATACATAAGATAATT
*
122723469 AAAATATATACATAAGATAA
1 AAAATACATACATAAGATAA
122723489 CATGTAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAATACATACATAAGATAATT
Found at i:122723533 original size:25 final size:25
Alignment explanation
Indices: 122723505--122723637 Score: 84
Period size: 25 Copynumber: 5.6 Consensus size: 25
122723495 GAAAAAAATT
122723505 ATATATAAATAATATAGTATTAAAG
1 ATATATAAATAATATAGTATTAAAG
* * *
122723530 ATATATACATAAAATAGTA-TAATAT
1 ATATATAAATAATATAGTATTAA-AG
** * *
122723555 ATATATACGTAATATAGAATT-TAG
1 ATATATAAATAATATAGTATTAAAG
** *
122723579 A-ATATACCTAATATA-T-TAAAAG
1 ATATATAAATAATATAGTATTAAAG
*
122723601 A-ATATATAATAATATAATATT-AAG
1 ATATATA-AATAATATAGTATTAAAG
*
122723625 AAATAT-AATAATA
1 ATATATAAATAATA
122723638 ACAAAAAAAA
Statistics
Matches: 86, Mismatches: 15, Indels: 16
0.74 0.13 0.14
Matches are distributed among these distances:
21 1 0.01
22 8 0.09
23 27 0.31
24 10 0.12
25 39 0.45
26 1 0.01
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (25 bp):
ATATATAAATAATATAGTATTAAAG
Found at i:122723613 original size:23 final size:23
Alignment explanation
Indices: 122723587--122723637 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
122723577 AGAATATACC
*
122723587 TAATATATTA-AAAGAATATATAA
1 TAATATAATATAAAGAA-ATATAA
*
122723610 TAATATAATATTAAGAAATATAA
1 TAATATAATATAAAGAAATATAA
122723633 TAATA
1 TAATA
122723638 ACAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (23 bp):
TAATATAATATAAAGAAATATAA
Found at i:122723957 original size:16 final size:16
Alignment explanation
Indices: 122723919--122723957 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
122723909 TCTCAAAAAA
*
122723919 AAAAACTAGCCTCTCC
1 AAAAACTAGCCTCTAC
*
122723935 AAAAACTAGCCTTTAC
1 AAAAACTAGCCTCTAC
*
122723951 AATAACT
1 AAAAACT
122723958 CTTCTCCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.28, G:0.05, T:0.23
Consensus pattern (16 bp):
AAAAACTAGCCTCTAC
Found at i:122724152 original size:30 final size:30
Alignment explanation
Indices: 122724116--122724183 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
122724106 AGGTACAAGT
122724116 GGTGGTGGAGCAAGTGTGGCTAATGGAGTA
1 GGTGGTGGAGCAAGTGTGGCTAATGGAGTA
* *
122724146 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTT
1 GGTGGTGGAGCAAGTGTGGCTAATGGAGTA
122724176 GGTGGTGG
1 GGTGGTGG
122724184 CAAAGGCTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.18, C:0.06, G:0.51, T:0.25
Consensus pattern (30 bp):
GGTGGTGGAGCAAGTGTGGCTAATGGAGTA
Found at i:122724953 original size:88 final size:85
Alignment explanation
Indices: 122724817--122725021 Score: 223
Period size: 87 Copynumber: 2.4 Consensus size: 85
122724807 TCCTGAGCTT
* * *
122724817 AACTCATTTCTCGCAATATGAA-TTGACTCTTTAAAACTAAACATTAAAAACAGAAATTGAAAAT
1 AACTCACTTCTCGCAATAT-AAGTTGA-TTTTTAAAACAAAACATT-AAAACAGAAATTGAAAAT
*
122724881 AGCTCAGCACGTGAGCCAAGGCTC
63 ACCTCAGCACGTGA-CCAAGGCTC
** **
122724905 AACTCACTTCTCGCAATATAAGTTGATTTTTAAAACAAAATTTGTAAAACAGATTTTGAAAATAC
1 AACTCACTTCTCGCAATATAAGTTGATTTTTAAAACAAAACAT-TAAAACAGAAATTGAAAATAC
* * * *
122724970 CTCGGTATGTGACCGAGGCTC
65 CTCAGCACGTGACCAAGGCTC
* * *
122724991 AACTCACCTCTCGTAATATGAGTTGATTTTT
1 AACTCACTTCTCGCAATATAAGTTGATTTTT
122725022 GCAAAGCATA
Statistics
Matches: 100, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
86 36 0.36
87 41 0.41
88 23 0.23
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (85 bp):
AACTCACTTCTCGCAATATAAGTTGATTTTTAAAACAAAACATTAAAACAGAAATTGAAAATACC
TCAGCACGTGACCAAGGCTC
Found at i:122725015 original size:86 final size:87
Alignment explanation
Indices: 122724795--122725021 Score: 246
Period size: 86 Copynumber: 2.6 Consensus size: 87
122724785 TTATTCTTTA
* * * * *
122724795 CTCGGTATGTGATCCTGA-GCTTAACTCATTTCTCGCAATATGAATTGACTCTTTAAAACTAAAC
1 CTCGGTATGTGAGCC-GAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTAAAACTAAAC
*
122724859 ATTAAAAACAGAAATTGAAAATAG
64 ATTAAAAACAGAAATTGAAAATAC
* * * * *
122724883 CTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATAAGTTGATTTTTAAAAC-AAA-AT
1 CTCGGTATGTGAGCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACTAAACA-
* **
122724946 TTGTAAAACAGATTTTGAAAATAC
65 TT-AAAAACAGAAATTGAAAATAC
* *
122724970 CTCGGTATGTGA-CCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTT
1 CTCGGTATGTGAGCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT
122725022 GCAAAGCATA
Statistics
Matches: 115, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
85 1 0.01
86 41 0.36
87 36 0.31
88 37 0.32
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.31
Consensus pattern (87 bp):
CTCGGTATGTGAGCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACTAAACAT
TAAAAACAGAAATTGAAAATAC
Found at i:122725117 original size:102 final size:102
Alignment explanation
Indices: 122724960--122725148 Score: 301
Period size: 102 Copynumber: 1.8 Consensus size: 102
122724950 AAAACAGATT
* *
122724960 TTGAAAATACCTCGGTATGTGACCGAGGCTCAACTCACCTCTCGTAATATGAGTTGA-TTTTTG-
1 TTGAAAATACCTCGGCATGTGACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGA
122725023 CAAAGCATAAATTGAAAAAAAAAATAAAAAAAAATCAA
66 CAAA-CATAAATTGAAAAAAAAAATAAAAAAAAATCAA
* *
122725061 TTGAAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
1 TTGAAAATACCTCGGCATGTGA-CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTT
122725126 GACAAACATAAATTGAAAAAAAA
64 GACAAACATAAATTGAAAAAAAA
122725149 GAAATTGAAA
Statistics
Matches: 80, Mismatches: 4, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
101 20 0.25
102 33 0.41
104 23 0.29
105 4 0.05
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.28
Consensus pattern (102 bp):
TTGAAAATACCTCGGCATGTGACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGA
CAAACATAAATTGAAAAAAAAAATAAAAAAAAATCAA
Found at i:122725146 original size:90 final size:90
Alignment explanation
Indices: 122725059--122725413 Score: 397
Period size: 90 Copynumber: 4.0 Consensus size: 90
122725049 AAAAAAAATC
* *
122725059 AATTGAAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTT
1 AATTGAAAATACCTCAGCGTGT-ATCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTT
*
122725123 TTTGACAA-ACATAAATTGAAAAAAAAGA
65 TTTGA-AACACAGAAATTG--AAAAAAGA
* * * *
122725151 AATTGAAAATATCTCAGCGTGT-CCTGAGGCTGAACTCACCTCTCGCAATATGAGTTGA-TTTTT
1 AATTGAAAATACCTCAGCGTGTATCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTT
* *
122725214 TGGAAAAACA-AAATTTGAAAAACAGA
66 TTGAAACACAGAAA-TTGAAAAA-AGA
* * *
122725240 ATTTGAAAATACCTCAGCGTGTGAGTC-AAGGCTCAACTCACC-ATCGCAATATGAGCTGATTTT
1 AATTGAAAATACCTCAGCGTGT-A-TCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTT
*
122725303 TTTTGAAACACAGAAATTGAAGAACAGA
64 TTTTGAAACACAGAAATTGAA-AAAAGA
* * * *
122725331 AATGGAAAACACCTCAGC--GTCT-TGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTT
1 AATTGAAAATACCTCAGCGTGTATCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTT
*
122725393 TTGAAAGACAGAAATTGAAAA
66 TTGAAACACAGAAATTGAAAA
122725414 TACCTCAACG
Statistics
Matches: 229, Mismatches: 23, Indels: 27
0.82 0.08 0.10
Matches are distributed among these distances:
87 16 0.07
88 45 0.20
89 30 0.13
90 63 0.28
91 49 0.21
92 26 0.11
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (90 bp):
AATTGAAAATACCTCAGCGTGTATCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTT
TTGAAACACAGAAATTGAAAAAAGA
Found at i:122725248 original size:13 final size:14
Alignment explanation
Indices: 122725216--122725248 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
122725206 TGATTTTTTG
122725216 GAAAAACAAAATTT
1 GAAAAACAAAATTT
*
122725230 GAAAAACAGAATTT
1 GAAAAACAAAATTT
122725244 GAAAA
1 GAAAA
122725249 TACCTCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.64, C:0.06, G:0.12, T:0.18
Consensus pattern (14 bp):
GAAAAACAAAATTT
Found at i:122725281 original size:181 final size:165
Alignment explanation
Indices: 122725059--122725617 Score: 507
Period size: 146 Copynumber: 3.4 Consensus size: 165
122725049 AAAAAAAATC
*
122725059 AATTGAAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AATTGAAAATACCTCAGCGTGTGATC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
* * * * *
122725124 TTGACAAACATAAATTGAAAAAAAAGAAATTGAAAATATCTCAGCGTGTCCTGAGGCTGAACTCA
65 TTGACAAACAAAAATTGAAAAAAAAGAAATGGAAAACACCTCAGC--GTCCTGAGGCTCAACTCA
*
122725189 CCTCTCGCAATATGAGTTGATTTTTTGGAAAAACAAAATTTGAAAAACAGA
128 CCTCTCGCAATATGAGCTGA-TTTTT------------TTTGAAAAACAGA
* * * *
122725240 ATTTGAAAATACCTCAGCGTGTGAGTCAAGGCTCAACTCACC-ATCGCAATATGAGCTGATTTTT
1 AATTGAAAATACCTCAGCGTGTGA-TCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTT
* * * * *
122725304 TTTGA-AACACAGAAATTG-AAGAACAGAAATGGAAAACACCTCAGCGTCTTGAGGTTCAACTCA
64 TTTGACAA-ACAAAAATTGAAAAAAAAGAAATGGAAAACACCTCAGCGTCCTGAGGCTCAACTCA
*
122725367 CCTCTCGCAATATGAGCTGATTTTTTTTGAAAGACAGA
128 CCTCTCGCAATATGAGCTGATTTTTTTTGAAAAACAGA
* * *
122725405 AATTGAAAATACCTCAACGTGT-CTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTT
1 AATTGAAAATACCTCAGCGTGTGATCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
* * *
122725467 TGACAAACAAAAATT---------GAAAT------TACCTCAGCGTCTTGAGGTTCAACTCACCT
66 TGACAAACAAAAATTGAAAAAAAAGAAATGGAAAACACCTCAGCGTCCTGAGGCTCAACTCACCT
* * *
122725517 ATCGCAATATGAGTTGA-TTTTTTTGAAAAACAAA
131 CTCGCAATATGAGCTGATTTTTTTTGAAAAACAGA
* * * * *
122725551 AATTGAAAATACCTCAACGTGT-CTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTT
1 AATTGAAAATACCTCAGCGTGTGATCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
122725615 TGA
66 TGA
122725618 AATTACCTCA
Statistics
Matches: 340, Mismatches: 31, Indels: 47
0.81 0.07 0.11
Matches are distributed among these distances:
146 71 0.21
147 44 0.13
148 7 0.02
153 5 0.01
161 15 0.04
162 2 0.01
163 15 0.04
164 15 0.04
165 32 0.09
177 5 0.01
178 34 0.10
180 39 0.11
181 54 0.16
182 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (165 bp):
AATTGAAAATACCTCAGCGTGTGATCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
TGACAAACAAAAATTGAAAAAAAAGAAATGGAAAACACCTCAGCGTCCTGAGGCTCAACTCACCT
CTCGCAATATGAGCTGATTTTTTTTGAAAAACAGA
Found at i:122725610 original size:146 final size:146
Alignment explanation
Indices: 122725341--122725816 Score: 669
Period size: 146 Copynumber: 3.3 Consensus size: 146
122725331 AATGGAAAAC
* * * * *
122725341 ACCTCAGCGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTTGAAAGACAGAA
1 ACCTCAGCGTCCTGAGGCTCAACTCACCTATCGCAATATGAGTTGA-TTTTTTTGAAAAACAGAA
122725406 ATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAC
65 ATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAC
122725471 AAACAAAAATTGAAATT
130 AAACAAAAATTGAAATT
* * *
122725488 ACCTCAGCGTCTTGAGGTTCAACTCACCTATCGCAATATGAGTTGATTTTTTTGAAAAACAAAAA
1 ACCTCAGCGTCCTGAGGCTCAACTCACCTATCGCAATATGAGTTGATTTTTTTGAAAAACAGAAA
* *
122725553 TTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTT----
66 TTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACA
122725614 --------TTGAAATT
131 AACAAAAATTGAAATT
* *
122725622 ACCTCAACGTGTCCTGAGGCTCAACTCACTTATCGCAATATGAGTTGATTTTTTTG-AAAACAGA
1 ACCTC-A-GCGTCCTGAGGCTCAACTCACCTATCGCAATATGAGTTGATTTTTTTGAAAAACAGA
*
122725686 AATTGAAAATACCTC-A-GTGTCTTGAGGCTCAACTCACCTCTTGCAATATGAGTTGA-TTTTGA
64 AATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
122725748 CAAACAAAAATTGAAATT
129 CAAACAAAAATTGAAATT
*
122725766 ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 ACCTCAGC--GTCCTGAGGCTCAACTCACCTATCGCAATATGAGTTGATTT
122725817 GAAAAGTAGA
Statistics
Matches: 296, Mismatches: 17, Indels: 35
0.85 0.05 0.10
Matches are distributed among these distances:
132 4 0.01
133 37 0.12
134 14 0.05
135 23 0.08
136 44 0.15
142 1 0.00
143 1 0.00
144 52 0.18
146 76 0.26
147 44 0.15
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (146 bp):
ACCTCAGCGTCCTGAGGCTCAACTCACCTATCGCAATATGAGTTGATTTTTTTGAAAAACAGAAA
TTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACA
AACAAAAATTGAAATT
Found at i:122725648 original size:61 final size:61
Alignment explanation
Indices: 122725553--122725681 Score: 204
Period size: 61 Copynumber: 2.1 Consensus size: 61
122725543 AAAACAAAAA
* * *
122725553 TTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTT
1 TTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTATCGCAATATGAGCTGATTTTT
* * *
122725614 TTGAAATTACCTCAACGTGTCCTGAGGCTCAACTCACTTATCGCAATATGAGTTGATTTTT
1 TTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTATCGCAATATGAGCTGATTTTT
122725675 TTGAAAA
1 TTGAAAA
122725682 CAGAAATTGA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (61 bp):
TTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTATCGCAATATGAGCTGATTTTT
Found at i:122725715 original size:72 final size:74
Alignment explanation
Indices: 122725614--122725816 Score: 299
Period size: 72 Copynumber: 2.8 Consensus size: 74
122725604 GCTGATTTTT
* *
122725614 TTGAAATTACCTCAACGTGTCCTGAGGCTCAACTCACTTATCGCAATATGAGTTGATTTTTTTGA
1 TTGAAATTACCTC-ACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA
*
122725679 -AAACAGAAA
65 CAAACAAAAA
* * *
122725688 TTGAAAATACCTCA-GTGTCTTGAGGCTCAACTCACCTCTTGCAATATGAGTTGA---TTTTGAC
1 TTGAAATTACCTCACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAC
122725749 AAACAAAAA
66 AAACAAAAA
122725758 TTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 TTGAAATTACCTCA-CGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
122725817 GAAAAGTAGA
Statistics
Matches: 114, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
69 6 0.05
70 21 0.18
72 74 0.65
73 1 0.01
74 12 0.11
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (74 bp):
TTGAAATTACCTCACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAC
AAACAAAAA
Found at i:122725954 original size:14 final size:13
Alignment explanation
Indices: 122725919--122725962 Score: 70
Period size: 13 Copynumber: 3.3 Consensus size: 13
122725909 TTGATTTTTG
122725919 AAAAACAGAAATT
1 AAAAACAGAAATT
*
122725932 AAAAGCAGAAATT
1 AAAAACAGAAATT
122725945 GAAAAACAGAAATT
1 -AAAAACAGAAATT
122725959 AAAA
1 AAAA
122725963 TACCTCGGCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.68, C:0.07, G:0.11, T:0.14
Consensus pattern (13 bp):
AAAAACAGAAATT
Found at i:122725963 original size:99 final size:97
Alignment explanation
Indices: 122725744--122726106 Score: 435
Period size: 99 Copynumber: 3.8 Consensus size: 97
122725734 TGAGTTGATT
* * * *
122725744 TTGACAAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
* * *
122725809 GTTGA--TTTGAAAAGTAGAATTTGTAAGGAAAAAA
66 GTTGATTTTTGAAAAGCAGAA-AT-TAA-G-AGAAA
122725843 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
*
122725908 GTTGATTTTTGAAAAACAGAAATTAAAAGCAGAAA
66 GTTGATTTTTGAAAAGCAGAAATT--AAG-AGAAA
* *
122725943 TTGAAAAACAGAAATT-AAAATACCTCGGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
*
122726007 GTTGATTTTTGAAAAGCATAAATT----G--A
66 GTTGATTTTTGAAAAGCAGAAATTAAGAGAAA
* * *
122726033 ---AAAAACGGAAATTGAAAATACCTCAGCGTGTGACCTGAGGCCCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAATACCTCAGC--GTGCCCTGAGGCTCAACTCACCTCTCGCAATAT
122726095 GAGTTGATTTTT
64 GAGTTGATTTTT
122726107 TTGAAAGATA
Statistics
Matches: 239, Mismatches: 18, Indels: 23
0.85 0.06 0.08
Matches are distributed among these distances:
87 12 0.05
88 12 0.05
90 43 0.18
92 1 0.00
99 135 0.56
100 22 0.09
101 14 0.06
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (97 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTTGAAAAGCAGAAATTAAGAGAAA
Found at i:122726087 original size:90 final size:86
Alignment explanation
Indices: 122725932--122726106 Score: 260
Period size: 90 Copynumber: 2.0 Consensus size: 86
122725922 AACAGAAATT
* *
122725932 AAAAGCAGAAATTGAAAAACAGAAATTAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACCTCT
1 AAAAGCAGAAATTGAAAAACAGAAATTAAAATACCTCGGCGTGACCCGAGGCCCAACTCACCTCT
122725997 CGCAATATGAGTTGATTTTTG
66 CGCAATATGAGTTGATTTTTG
* * * *
122726018 AAAAGCATAAATTGAAAAAACGGAAATTGAAAATACCTCAGCGTGTGACCTGAGGCCCAACTCAC
1 AAAAGCAGAAATTG-AAAAACAGAAATT-AAAATACCTC-G-GCGTGACCCGAGGCCCAACTCAC
122726083 CTCTCGCAATATGAGTTGATTTTT
62 CTCTCGCAATATGAGTTGATTTTT
122726107 TTGAAAGATA
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
86 13 0.16
87 12 0.15
88 10 0.13
89 1 0.01
90 43 0.54
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (86 bp):
AAAAGCAGAAATTGAAAAACAGAAATTAAAATACCTCGGCGTGACCCGAGGCCCAACTCACCTCT
CGCAATATGAGTTGATTTTTG
Found at i:122737207 original size:16 final size:16
Alignment explanation
Indices: 122737169--122737207 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
122737159 TCTTCAAAAA
*
122737169 AAAAACTAGCCTCTCC
1 AAAAACTAGCCTCTAC
*
122737185 AAAAACTAGCCTTTAC
1 AAAAACTAGCCTCTAC
*
122737201 AATAACT
1 AAAAACT
122737208 CTTCTCCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.28, G:0.05, T:0.23
Consensus pattern (16 bp):
AAAAACTAGCCTCTAC
Found at i:122737402 original size:30 final size:30
Alignment explanation
Indices: 122737365--122737463 Score: 171
Period size: 30 Copynumber: 3.3 Consensus size: 30
122737355 TAGGTACAAG
*
122737365 TGGTGGTGGAGCAAGTGTGGCTAATGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
*
122737395 AGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
*
122737425 TGGTAGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
122737455 TGGTGGTGG
1 TGGTGGTGG
122737464 CAAAGGCTAG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.18, C:0.06, G:0.49, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:122737423 original size:18 final size:18
Alignment explanation
Indices: 122737400--122737453 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
122737390 GGAGTAGGTG
122737400 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
122737418 GT-G-G--AGT-TGG-TA
1 GTGGAGCAAGTGTGGCTA
122737430 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
122737448 GTGGAG
1 GTGGAG
122737454 TTGGTGGTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
12 4 0.13
13 4 0.13
14 4 0.13
16 4 0.13
17 4 0.13
18 10 0.33
ACGTcount: A:0.20, C:0.07, G:0.48, T:0.24
Consensus pattern (18 bp):
GTGGAGCAAGTGTGGCTA
Found at i:122744871 original size:58 final size:55
Alignment explanation
Indices: 122744808--122744974 Score: 167
Period size: 58 Copynumber: 2.9 Consensus size: 55
122744798 TTTTTATACT
*
122744808 ATTATATATTATGATTTTTTAATTTATTTAATAATAATTATATTAAGAATTTTATTAA
1 ATTATATATTAT--TTTTTTAATTTATTTAATAATAATTATATTAA-AATTTGATTAA
* * * * *
122744866 ATTATATATTATTTTATTAAATTATATTTAGTAATAATCATGTTAAAATATGATTAA
1 ATTATATATTATTTT-TTTAATT-TATTTAATAATAATTATATTAAAATTTGATTAA
*
122744923 ATTATTTATTATTTTTATTAAAATATT-TTTAATAATAATCT-TATTAAAATTT
1 ATTATATATTATTTTT-TT--AAT-TTATTTAATAATAAT-TATATTAAAATTT
122744975 AATAATAATA
Statistics
Matches: 90, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
56 4 0.04
57 30 0.33
58 51 0.57
59 4 0.04
60 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (55 bp):
ATTATATATTATTTTTTTAATTTATTTAATAATAATTATATTAAAATTTGATTAA
Found at i:122745112 original size:12 final size:13
Alignment explanation
Indices: 122745084--122745144 Score: 60
Period size: 12 Copynumber: 4.9 Consensus size: 13
122745074 ATGTTCTTAA
*
122745084 TAATAATTTTATAT
1 TAATAATTAT-TAT
122745098 TAA-AATTATTAT
1 TAATAATTATTAT
122745110 T-A-AA-TATTAT
1 TAATAATTATTAT
122745120 TAATAATTA-TAT
1 TAATAATTATTAT
122745132 TAATAAGTTATTA
1 TAATAA-TTATTA
122745145 AAATATATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
10 7 0.17
11 4 0.10
12 15 0.37
13 10 0.24
14 5 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (13 bp):
TAATAATTATTAT
Found at i:122745142 original size:23 final size:21
Alignment explanation
Indices: 122745095--122745156 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 21
122745085 AATAATTTTA
122745095 TATTAAAATTATTATTAAATAT
1 TATTAAAATTA-TATTAAATAT
122745117 TATTAATAATTATATT-AATAAGT
1 TATTAA-AATTATATTAAAT-A-T
122745140 TATTAAAATATATATTA
1 TATTAAAAT-TATATTA
122745157 TTTTATTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
21 3 0.09
22 14 0.40
23 18 0.51
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TATTAAAATTATATTAAATAT
Found at i:122745155 original size:12 final size:11
Alignment explanation
Indices: 122745092--122745156 Score: 55
Period size: 12 Copynumber: 5.7 Consensus size: 11
122745082 AATAATAATT
122745092 TTATATTAAAA
1 TTATATTAAAA
122745103 TTATTATT-AAA
1 TTA-TATTAAAA
122745114 -TATTATTAATAA
1 TTA-TATTAA-AA
122745126 TTATATTAATAA
1 TTATATTAA-AA
*
122745138 GT-TATTAAAA
1 TTATATTAAAA
122745148 TATATATTA
1 T-TATATTA
122745157 TTTTATTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
10 9 0.20
11 14 0.30
12 21 0.46
13 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (11 bp):
TTATATTAAAA
Found at i:122745411 original size:44 final size:46
Alignment explanation
Indices: 122745341--122745434 Score: 138
Period size: 44 Copynumber: 2.1 Consensus size: 46
122745331 ATTACAACAT
*
122745341 CATTCCATTCAACTAAACACAAGAATT-CT-ATTACAGCTCTATTC
1 CATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTATTC
***
122745385 CATTCCATTCAACCAAACAGTTGAATTACTGATTACAGCTCTATTC
1 CATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTATTC
122745431 CATT
1 CATT
122745435 ACAGCTCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 23 0.52
45 2 0.05
46 19 0.43
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (46 bp):
CATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTATTC
Found at i:122745437 original size:16 final size:16
Alignment explanation
Indices: 122745416--122745470 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
122745406 TGAATTACTG
122745416 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
122745432 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
*
122745448 ATTACAGCCCTATTCC
1 ATTACAGCTCTATTCC
122745464 ATTACAG
1 ATTACAG
122745471 TGAACCAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.35
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:122745656 original size:14 final size:13
Alignment explanation
Indices: 122745637--122745676 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
122745627 ATTTTTATTT
*
122745637 AAAAAATTGACGTA
1 AAAAAATTGAC-AA
122745651 AAAAAATTGACAA
1 AAAAAATTGACAA
*
122745664 AAAAAATTAACAA
1 AAAAAATTGACAA
122745677 TGTTAACAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.68, C:0.07, G:0.07, T:0.17
Consensus pattern (13 bp):
AAAAAATTGACAA
Found at i:122745835 original size:15 final size:15
Alignment explanation
Indices: 122745780--122745836 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
122745770 TTTATACTAC
*
122745780 AAAACATTTATTATT
1 AAAATATTTATTATT
* *
122745795 AATATATTCATAATTATA
1 AAAATATT--T-ATTATT
122745813 ATAAATATTTATTATT
1 A-AAATATTTATTATT
122745829 AAAATATT
1 AAAATATT
122745837 AATATTGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 13 0.39
16 6 0.18
17 2 0.06
18 6 0.18
19 6 0.18
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:122745897 original size:15 final size:16
Alignment explanation
Indices: 122745877--122745907 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
122745867 AAGAAAATTG
122745877 TTTAAAA-TTATTATT
1 TTTAAAATTTATTATT
122745892 TTTAAAATTTATTATT
1 TTTAAAATTTATTATT
122745908 AATGTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAAAATTTATTATT
Found at i:122746319 original size:53 final size:53
Alignment explanation
Indices: 122746262--122746364 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
122746252 AGAAAAATAT
* * *
122746262 AGAAAATATTTTATGTGAAACAAATAGAACTTAATGGTTGAATGTAAAAATGC
1 AGAAAATATTTTATATGAAACAAATAGAACCTAATGATTGAATGTAAAAATGC
* *
122746315 AGAAAATATTTTCTATGAAACAAATATAACCTAATGATTGAATGTAAAAA
1 AGAAAATATTTTATATGAAACAAATAGAACCTAATGATTGAATGTAAAAA
122746365 CAATGTAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.30
Consensus pattern (53 bp):
AGAAAATATTTTATATGAAACAAATAGAACCTAATGATTGAATGTAAAAATGC
Found at i:122747209 original size:2 final size:2
Alignment explanation
Indices: 122747196--122747225 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
122747186 AGGTAGCTAC
*
122747196 AT AT AC 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
122747226 GTTAAAAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:122747659 original size:2 final size:2
Alignment explanation
Indices: 122747652--122747686 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
122747642 CCTTTCAAAT
122747652 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
122747687 TTTATTACCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:122776801 original size:45 final size:43
Alignment explanation
Indices: 122776751--122776899 Score: 126
Period size: 45 Copynumber: 3.4 Consensus size: 43
122776741 AACTTTAAAT
* * *
122776751 CCCTAAGCAGTAGGGTAACACGCTGAAGATTTACGGATCTTATC
1 CCCTAAGCAGTAGGGTAACA-GCTGAAGATTTACAGACCTTAAC
* * * * *
122776795 ACCCTAAGCAGTAGGGAAACAGATCGAAGA-TGA-TGAGCTTTAACC
1 -CCCTAAGCAGTAGGGTAACAGCT-GAAGATTTACAGA-CCTTAA-C
* *
122776840 CCCTAAGCAGTAAGGTAACAAGC-CAA-ATTTACAGACCTTAAC
1 CCCTAAGCAGTAGGGTAAC-AGCTGAAGATTTACAGACCTTAAC
122776882 CCCTAAGCAGTAGGGTAA
1 CCCTAAGCAGTAGGGTAA
122776900 TAGGTTGAAA
Statistics
Matches: 83, Mismatches: 15, Indels: 15
0.73 0.13 0.13
Matches are distributed among these distances:
42 19 0.23
43 11 0.13
44 26 0.31
45 27 0.33
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (43 bp):
CCCTAAGCAGTAGGGTAACAGCTGAAGATTTACAGACCTTAAC
Found at i:122777258 original size:129 final size:128
Alignment explanation
Indices: 122776990--122777337 Score: 491
Period size: 129 Copynumber: 2.7 Consensus size: 128
122776980 TGCAGTGAAG
*
122776990 CAGGCTGAATTTACAGATTTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGAGCTTT
1 CAGGCTGAATTTACAGA-TTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGGGC-TT
* * *
122777055 AACCCCTTAAGTAGTAGGGTAACAAGCCAAATTTACAGACCTTAACCCCCTAAGCAGTAGGGTAA
64 AACCCCCTAAGCAGTAGGGTAACAAGCCAAATTTACAGACCTTAAACCCCTAAGCAGTAGGGTAA
* *
122777120 TAGGCTGAATTTATAGATATTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGGGCTTA
1 CAGGCTGAATTTACAGAT-TTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGGGCTTA
*
122777185 ACCCCCTAAGCAGTAGAGTAACAAGCCAAATTTACAGACCTTAAACCCCTAAGCAGTAGGGTAA
65 ACCCCCTAAGCAGTAGGGTAACAAGCCAAATTTACAGACCTTAAACCCCTAAGCAGTAGGGTAA
* * * * * ** *
122777249 CAGGTTGAATTCACAGATCTAAACCCCTAAGC-GATAGGGAAACAGATCGATGATGACAAGCCTT
1 CAGGCTGAATTTACAGATTTAACCCCCTAAGCAG-TAGGGAAACAGATCGAAGATGA-TGGGCTT
*
122777313 AAACCCCTAAGCAGTAAGGGTAACA
64 AACCCCCTAAGCAGT-AGGGTAACA
122777338 GGTTAAAAAT
Statistics
Matches: 195, Mismatches: 19, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
127 1 0.01
128 33 0.17
129 96 0.49
130 65 0.33
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (128 bp):
CAGGCTGAATTTACAGATTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGGGCTTAA
CCCCCTAAGCAGTAGGGTAACAAGCCAAATTTACAGACCTTAAACCCCTAAGCAGTAGGGTAA
Found at i:122777265 original size:43 final size:43
Alignment explanation
Indices: 122776996--122777340 Score: 218
Period size: 43 Copynumber: 8.0 Consensus size: 43
122776986 GAAGCAGGCT
** * * *
122776996 GAATTTACAGATTTTAACCCCCTAAGCAGTAGGGAAACAGATC
1 GAATTTACAGACCTTAAACCCCTAAGCAGTAGGGTAACAGGTC
* * * * * * * *
122777039 GAAGATGA-TGAGCTTTAACCCCTTAAGTAGTAGGGTAACAAGCC
1 GAA-TTTACAGACCTTAAACCCC-TAAGCAGTAGGGTAACAGGTC
* * *
122777083 AAATTTACAGACCTTAACCCCCTAAGCAGTAGGGTAATAGG-C
1 GAATTTACAGACCTTAAACCCCTAAGCAGTAGGGTAACAGGTC
* ** * * *
122777125 TGAATTTATAGATATTAACCCCCTAAGCAGTAGGGAAACAGATC
1 -GAATTTACAGACCTTAAACCCCTAAGCAGTAGGGTAACAGGTC
* * * ** * * * *
122777169 GAAGATGA-TGGGCTTAACCCCCTAAGCAGTAGAGTAACAAGCC
1 GAA-TTTACAGACCTTAAACCCCTAAGCAGTAGGGTAACAGGTC
* *
122777212 AAATTTACAGACCTTAAACCCCTAAGCAGTAGGGTAACAGGTT
1 GAATTTACAGACCTTAAACCCCTAAGCAGTAGGGTAACAGGTC
* * * *
122777255 GAATTCACAGATC-TAAACCCCTAAGC-GATAGGGAAACAGATC
1 GAATTTACAGACCTTAAACCCCTAAGCAG-TAGGGTAACAGGTC
*
122777297 G-ATGATGACA-AGCCTTAAACCCCTAAGCAGTAAGGGTAACAGGT
1 GAAT--TTACAGA-CCTTAAACCCCTAAGCAGT-AGGGTAACAGGT
122777341 TAAAAATCAA
Statistics
Matches: 227, Mismatches: 61, Indels: 26
0.72 0.19 0.08
Matches are distributed among these distances:
41 3 0.01
42 29 0.13
43 137 0.60
44 47 0.21
45 11 0.05
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (43 bp):
GAATTTACAGACCTTAAACCCCTAAGCAGTAGGGTAACAGGTC
Found at i:122777757 original size:24 final size:23
Alignment explanation
Indices: 122777705--122777758 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
122777695 TTTTGGGCCC
* *
122777705 AAACCCCTAAACCCACTAAGCCA
1 AAACCCCAAAACCCACTAACCCA
*
122777728 ACAACCCCAAAACCTACTAAACCCA
1 A-AACCCCAAAACCCACT-AACCCA
122777753 AAACCC
1 AAACCC
122777759 AACAGCAGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 1 0.04
24 19 0.73
25 6 0.23
ACGTcount: A:0.46, C:0.44, G:0.02, T:0.07
Consensus pattern (23 bp):
AAACCCCAAAACCCACTAACCCA
Found at i:122779239 original size:2 final size:2
Alignment explanation
Indices: 122779232--122779274 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
122779222 TTAATATCTC
* * *
122779232 AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT -T AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
122779273 AT
1 AT
122779275 TTTCCTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (2 bp):
AT
Found at i:122782370 original size:46 final size:47
Alignment explanation
Indices: 122782320--122782441 Score: 160
Period size: 46 Copynumber: 2.7 Consensus size: 47
122782310 GCCATAGTGT
* * *
122782320 CTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTAC
1 CTTTCAACCATGGTCTTACTCATTTTCATATCACGTTGCCATGGTAC
** *
122782366 CTTTCAACCATGGTCTTGTTCA-TTTCATATCACGTTGCCATGGTAT
1 CTTTCAACCATGGTCTTACTCATTTTCATATCACGTTGCCATGGTAC
*
122782412 CTTTCAACCATGGTCTTACACA-TTTCATAT
1 CTTTCAACCATGGTCTTACTCATTTTCATAT
122782442 AAGAGAGCAC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
45 4 0.06
46 62 0.94
ACGTcount: A:0.20, C:0.25, G:0.13, T:0.42
Consensus pattern (47 bp):
CTTTCAACCATGGTCTTACTCATTTTCATATCACGTTGCCATGGTAC
Found at i:122787882 original size:44 final size:44
Alignment explanation
Indices: 122787834--122788048 Score: 111
Period size: 44 Copynumber: 5.1 Consensus size: 44
122787824 ACAGTAGCAG
122787834 AACAGATCGAAGACAGTAAGCCTTAACTCCCTAAGTAGTAGGGT
1 AACAGATCGAAGACAGTAAGCCTTAACTCCCTAAGTAGTAGGGT
* * * * *
122787878 AACAG-GC-TAGAAAGTACAG----ATCTCCCCTAAATAGTAGTGG-
1 AACAGATCGAAGACAGTA-AGCCTTAACT-CCCTAAGTAGTAG-GGT
* * *
122787918 AGA-AGATCAAAGACAATAAGCCTTAACTCCCTAAGCAGTAGGGT
1 A-ACAGATCGAAGACAGTAAGCCTTAACTCCCTAAGTAGTAGGGT
* * * **
122787962 AACAGGTTAGAA-A-A-TACAGATCTT---T-CCTAAACAGTAGCGG-
1 AACA-GATCGAAGACAGTA-AG-CCTTAACTCCCTAAGTAGTAG-GGT
* *
122788002 AGCAGATCGAAGATAGTAAGCCTTAACTCCCTAAGTAGTAGGGT
1 AACAGATCGAAGACAGTAAGCCTTAACTCCCTAAGTAGTAGGGT
122788046 AAC
1 AAC
122788049 CGGCTAGAAG
Statistics
Matches: 123, Mismatches: 24, Indels: 48
0.63 0.12 0.25
Matches are distributed among these distances:
39 8 0.07
40 33 0.27
41 12 0.10
42 17 0.14
43 12 0.10
44 34 0.28
45 7 0.06
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (44 bp):
AACAGATCGAAGACAGTAAGCCTTAACTCCCTAAGTAGTAGGGT
Found at i:122788088 original size:84 final size:84
Alignment explanation
Indices: 122787344--122788098 Score: 874
Period size: 84 Copynumber: 8.9 Consensus size: 84
122787334 CAAGACAGCG
* * * * *
122787344 AGCCTTAACCCCCTAAGCAGTGGGGTAATAGGC-AGGAAAATATAGATCTCCCTTAAACAGTAGT
1 AGCCTTAACTCCCTAAGCAGTAGGGTAACAGGCTA-GAAAATACAGATCTCCCCTAAACAGTAGT
** * *
122787408 ATAGAAAATCGAAGATAGTA
65 GGAGCAGATCGAAGATAGTA
* *
122787428 AGCCTTAACTCCCTAAGCAGTAGGGTAACCGGTTAGAAAATACAGATCTCCCCTAAACAGTAGTG
1 AGCCTTAACTCCCTAAGCAGTAGGGTAACAGGCTAGAAAATACAGATCTCCCCTAAACAGTAGTG
*
122787493 GAGCAGATCGAAG-TCAGCA
66 GAGCAGATCGAAGAT-AGTA
* * *
122787512 AGCCTTAACTCCCTAAGCGGTACGGTAACAGGCTAAAAAAAATACAGATCTCCCCTAAACAGTAG
1 AGCCTTAACTCCCTAAGCAGTAGGGTAACAGGCT--AGAAAATACAGATCTCCCCTAAACAGTAG
* *
122787577 TGGAACAGATCGAAG-TCAGCA
64 TGGAGCAGATCGAAGAT-AGTA
* * *
122787598 AGCCTTAAC-CCCTTAAGCAATAGGGTAACAGGCTAAAAAAAATACAGATCTCCCCTAATCAGTA
1 AGCCTTAACTCCC-TAAGCAGTAGGGTAACAGGCT--AGAAAATACAGATCTCCCCTAAACAGTA
* * *
122787662 ATGGAACAGATCGAAG-TCAGGA
63 GTGGAGCAGATCGAAGAT-AGTA
* * * * **
122787684 AGCCTTAAC-CCTTTAAGCAGTAGCGTAACAGGCTAAAAAATACAGATCTCTCCTAAACAGTAAC
1 AGCCTTAACTCC-CTAAGCAGTAGGGTAACAGGCTAGAAAATACAGATCTCCCCTAAACAGTAGT
* * *
122787748 GGAGCAGATCGAAAACAGCA
65 GGAGCAGATCGAAGATAGTA
* * * **
122787768 AGCCTTAACTCTCTAAGTAGTAGGGTAATAGGCTAGAAAATACAGATCTCCCCTAAACAGTAGCA
1 AGCCTTAACTCCCTAAGCAGTAGGGTAACAGGCTAGAAAATACAGATCTCCCCTAAACAGTAGTG
* *
122787833 GAACAGATCGAAGACAGTA
66 GAGCAGATCGAAGATAGTA
* * *
122787852 AGCCTTAACTCCCTAAGTAGTAGGGTAACAGGCTAGAAAGTACAGATCTCCCCTAAATAGTAGTG
1 AGCCTTAACTCCCTAAGCAGTAGGGTAACAGGCTAGAAAATACAGATCTCCCCTAAACAGTAGTG
* * * *
122787917 GAGAAGATCAAAGACAATA
66 GAGCAGATCGAAGATAGTA
* ** *
122787936 AGCCTTAACTCCCTAAGCAGTAGGGTAACAGGTTAGAAAATACAGATCTTTCCTAAACAGTAGCG
1 AGCCTTAACTCCCTAAGCAGTAGGGTAACAGGCTAGAAAATACAGATCTCCCCTAAACAGTAGTG
122788001 GAGCAGATCGAAGATAGTA
66 GAGCAGATCGAAGATAGTA
* * * * *
122788020 AGCCTTAACTCCCTAAGTAGTAGGGTAACCGGCTAGAAGATACAAATCTCCCCTAAAAAGTAGTG
1 AGCCTTAACTCCCTAAGCAGTAGGGTAACAGGCTAGAAAATACAGATCTCCCCTAAACAGTAGTG
*
122788085 GAGCAGATTGAAGA
66 GAGCAGATCGAAGA
122788099 CAAGTTCCTA
Statistics
Matches: 586, Mismatches: 77, Indels: 16
0.86 0.11 0.02
Matches are distributed among these distances:
83 1 0.00
84 426 0.73
85 5 0.01
86 154 0.26
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (84 bp):
AGCCTTAACTCCCTAAGCAGTAGGGTAACAGGCTAGAAAATACAGATCTCCCCTAAACAGTAGTG
GAGCAGATCGAAGATAGTA
Found at i:122790648 original size:125 final size:125
Alignment explanation
Indices: 122790278--122790688 Score: 466
Period size: 125 Copynumber: 3.2 Consensus size: 125
122790268 GGTCCAAGAA
* * * * * *
122790278 ATCGTGCCTAATCGTGTTGGGTTTTGATTTTTTCGTTCAGCTAAAATGCGGAATATCCTTTGGAA
1 ATCGTGCCCAATCGTGCTGGGTTTCGATTTTTTCATTCAACTAAAATACGGAATATCCTTT-GAA
** * *
122790343 ATTTTGTCCAT-TTTTTTTAAATTAAAATGAGGCAATATTTCGTATTTGGGGAGTTTGAGAG
65 ATTTCATCCATGTTTTCTTAAATTAAAATGAGGCAATATTTCGTATTT-GGAAGTTTGAGAG
* * *
122790404 ATCGTGCCCAATCGTGCTGGGTTTCAAATTTTTTTCATTCGACTAAAATATGGAATATCCTTTTT
1 ATCGTGCCCAATCGTGCTGGGTTTC-GA-TTTTTTCATTCAACTAAAATACGGAATATCC---TT
* * * * *
122790469 TGAAATTTCATTCAAGTTTTCTTAAACTAAAACGAGGCAATATTTTGTATTTGGAAGTTTGAGAG
61 TGAAATTTCATCCATGTTTTCTTAAATTAAAATGAGGCAATATTTCGTATTTGGAAGTTTGAGAG
* * ** *
122790534 ATCGTGCCCAATCGTGCTGAGTTTCGA-TTTTTCATTCAACTAAGATACAAAATATCCTTTCAAC
1 ATCGTGCCCAATCGTGCTGGGTTTCGATTTTTTCATTCAACTAAAATACGGAATATCCTTTGAA-
* * * * *
122790598 ATTTCATCCATGTTTTCTTAAATTAAAATGAGGTAATATTTCGTATTTGGAAATTCGATAA
65 ATTTCATCCATGTTTTCTTAAATTAAAATGAGGCAATATTTCGTATTTGGAAGTTTGAGAG
* *
122790659 ATCATGCCCAATCGTGCTGGGTTGCGATTT
1 ATCGTGCCCAATCGTGCTGGGTTTCGATTT
122790689 ACTGTTTGGC
Statistics
Matches: 238, Mismatches: 39, Indels: 16
0.81 0.13 0.05
Matches are distributed among these distances:
124 5 0.02
125 75 0.32
126 24 0.10
127 26 0.11
128 26 0.11
129 1 0.00
130 46 0.19
131 35 0.15
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.40
Consensus pattern (125 bp):
ATCGTGCCCAATCGTGCTGGGTTTCGATTTTTTCATTCAACTAAAATACGGAATATCCTTTGAAA
TTTCATCCATGTTTTCTTAAATTAAAATGAGGCAATATTTCGTATTTGGAAGTTTGAGAG
Found at i:122791423 original size:2 final size:2
Alignment explanation
Indices: 122791416--122791443 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
122791406 GGGTTTTAAA
122791416 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
122791444 TTTGATACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:122794119 original size:18 final size:19
Alignment explanation
Indices: 122794096--122794135 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
122794086 CAAGTGTATG
*
122794096 GTAAAAATAAT-TACATGT
1 GTAAAAATAATATACATAT
122794114 GTAAAAATAATATACATAT
1 GTAAAAATAATATACATAT
122794133 GTA
1 GTA
122794136 TATAATAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.33
Consensus pattern (19 bp):
GTAAAAATAATATACATAT
Found at i:122794182 original size:5 final size:5
Alignment explanation
Indices: 122794168--122794212 Score: 83
Period size: 5 Copynumber: 9.2 Consensus size: 5
122794158 AATATTTAAG
122794168 TATA- TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT T
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT T
122794213 GTTATAATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.10
5 36 0.90
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:122805034 original size:23 final size:23
Alignment explanation
Indices: 122804991--122805037 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
122804981 TATAACAATA
*
122804991 TTTTAATTTAATATATTTAATTT
1 TTTTAATTTAATATATATAATTT
*
122805014 TTTTAATTTAACTCTA-ATAATTT
1 TTTTAATTTAA-TATATATAATTT
122805037 T
1 T
122805038 ACTCAACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTAATTTAATATATATAATTT
Found at i:122806766 original size:19 final size:18
Alignment explanation
Indices: 122806738--122806775 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
122806728 GGTTAAATTG
122806738 TTCTTCTTTTTTTTCTTTT
1 TTCTTCTTTTTTTT-TTTT
122806757 TTCTT-TTTTTTTTTTTT
1 TTCTTCTTTTTTTTTTTT
122806774 TT
1 TT
122806776 GGGGGGGGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
18 8 0.42
19 5 0.26
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (18 bp):
TTCTTCTTTTTTTTTTTT
Found at i:122806774 original size:16 final size:16
Alignment explanation
Indices: 122806741--122806773 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
122806731 TAAATTGTTC
122806741 TTCTTTTTTTTCTTTT
1 TTCTTTTTTTTCTTTT
122806757 TTCTTTTTTTT-TTTT
1 TTCTTTTTTTTCTTTT
122806772 TT
1 TT
122806774 TTGGGGGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (16 bp):
TTCTTTTTTTTCTTTT
Found at i:122808416 original size:41 final size:41
Alignment explanation
Indices: 122808371--122808461 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 41
122808361 AGGTGGAATG
* * *
122808371 TAGAAAAATACTTCTAACTTGAAGCGCTTTCAGGTAAAATA
1 TAGAAAAACACTTCTAACTGGAAGCACTTTCAGGTAAAATA
* * * * *
122808412 TAGAAAAACACTTTTTACTGGAAGTACTTTTAGGTGAAATA
1 TAGAAAAACACTTCTAACTGGAAGCACTTTCAGGTAAAATA
122808453 TAGAAAAAC
1 TAGAAAAAC
122808462 GCTTTCAGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (41 bp):
TAGAAAAACACTTCTAACTGGAAGCACTTTCAGGTAAAATA
Found at i:122811731 original size:44 final size:45
Alignment explanation
Indices: 122811643--122811769 Score: 139
Period size: 44 Copynumber: 2.8 Consensus size: 45
122811633 AGAACAAAAA
*
122811643 TGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGGAT
1 TGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGGAT
* * *
122811689 TGAGCCATGTAAGTCTATATT-ATATATGGCATTGGAGACAGGAA
1 TGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGGAT
* ** * * *
122811733 TAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 TGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
122811770 CAGGATATTG
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
44 35 0.52
45 1 0.01
46 31 0.46
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.29
Consensus pattern (45 bp):
TGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGGAT
Found at i:122813901 original size:6 final size:6
Alignment explanation
Indices: 122813890--122813916 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
122813880 GAGCCTCCGA
122813890 TTGGGG TTGGGG TTGGGG TTGGGG TTG
1 TTGGGG TTGGGG TTGGGG TTGGGG TTG
122813917 TGGTCTTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.63, T:0.37
Consensus pattern (6 bp):
TTGGGG
Found at i:122815971 original size:13 final size:13
Alignment explanation
Indices: 122815953--122815992 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
122815943 GAATTAATTT
122815953 TTAATAAAAAATA
1 TTAATAAAAAATA
122815966 TTAATAAAAAAT-
1 TTAATAAAAAATA
*
122815978 CTAATAAAAAATA
1 TTAATAAAAAATA
122815991 TT
1 TT
122815993 TTTAAGAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (13 bp):
TTAATAAAAAATA
Found at i:122815982 original size:12 final size:13
Alignment explanation
Indices: 122815954--122815990 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
122815944 AATTAATTTT
*
122815954 TAATAAAAAATAT
1 TAATAAAAAATAC
122815967 TAATAAAAAAT-C
1 TAATAAAAAATAC
122815979 TAATAAAAAATA
1 TAATAAAAAATA
122815991 TTTTTAAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (13 bp):
TAATAAAAAATAC
Found at i:122820305 original size:3 final size:3
Alignment explanation
Indices: 122820297--122820321 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
122820287 TCAGAAGCAC
122820297 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
122820322 AGTATTTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:122822588 original size:14 final size:14
Alignment explanation
Indices: 122822569--122822607 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
122822559 TCTCTTTCAG
*
122822569 GTTTTGAATTTTTA
1 GTTTTGAATTTTAA
*
122822583 GTTTTGGATTTTAA
1 GTTTTGAATTTTAA
*
122822597 TTTTTGAATTT
1 GTTTTGAATTT
122822608 CGAGTTTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.64
Consensus pattern (14 bp):
GTTTTGAATTTTAA
Found at i:122829566 original size:19 final size:20
Alignment explanation
Indices: 122829532--122829574 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
122829522 CCTCTTTTTT
*
122829532 CATT-CATTTCATTCATCTG
1 CATTACATTTCATTCATATG
122829551 CATTACATTTCA-TCATATG
1 CATTACATTTCATTCATATG
122829570 CATTA
1 CATTA
122829575 AGTTTCATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (20 bp):
CATTACATTTCATTCATATG
Found at i:122837747 original size:45 final size:44
Alignment explanation
Indices: 122837597--122837755 Score: 142
Period size: 44 Copynumber: 3.6 Consensus size: 44
122837587 TATCGTGATG
* * * * **
122837597 AATCTTATCTCCCTGAAGTTGCAGTTG-AGTAGATTAAAGCCACA
1 AATCTCATCTCCCTGAAGTTGCAG-TGAAGCAAATTGAAGATACA
* * ** * *
122837641 AACCTTATCTCCCTGAAGTCACAGT-AGAGCAAGTTGAAGTTACA
1 AATCTCATCTCCCTGAAGTTGCAGTGA-AGCAAATTGAAGATACA
* *
122837685 AATCTCATCTCCCTGAAGTTGTAGTGAAGCAAATTGAAGATAGCG
1 AATCTCATCTCCCTGAAGTTGCAGTGAAGCAAATTGAAGATA-CA
*
122837730 AATCTCATTTCCCTGAAGTTGCAGTG
1 AATCTCATCTCCCTGAAGTTGCAGTG
122837756 GAACGGATTA
Statistics
Matches: 92, Mismatches: 19, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
43 1 0.01
44 65 0.71
45 26 0.28
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (44 bp):
AATCTCATCTCCCTGAAGTTGCAGTGAAGCAAATTGAAGATACA
Done.