Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr1
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: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 91 of 109
Found at i:28925167 original size:82 final size:82
Alignment explanation
Indices: 28925081--28925334 Score: 307
Period size: 82 Copynumber: 3.1 Consensus size: 82
28925071 TTAGAAATGC
* * * * *
28925081 CGCTAAAGATCCGAGAATTAGCAGCGCTTGTATAAAAACGCCGCTAAAGACCCGAGCATTAGCGG
1 CGCTAAAGATCCGAGCATTAGCGGCGCTTGTACAAAAACGCCGCTAAAGATCCGAGCATTAGCGA
*
28925146 CGCATAGACAAAAACGT
66 CGCATAGACAAAAACGA
* * * * * *
28925163 CGCTAAAGACCCGAGCATTAGCGGCGCATAG-ACAAAAACGCTGCTAAAGATCTGAGAATTAGCA
1 CGCTAAAGATCCGAGCATTAGCGGCGC-TTGTACAAAAACGCCGCTAAAGATCCGAGCATTAGCG
28925227 ACGCATAGACAAAAAC-A
65 ACGCATAGACAAAAACGA
* *
28925244 CAGCTAAAGATCCGAGCATTAGCGGCGCTT-TCACAAAAACGCCGCGAAAGATCGGAGCATTAGC
1 C-GCTAAAGATCCGAGCATTAGCGGCGCTTGT-ACAAAAACGCCGCTAAAGATCCGAGCATTAGC
* * *
28925308 GACGCTTACACAAAAACGC
64 GACGCATAGACAAAAACGA
28925327 CGCTAAAG
1 CGCTAAAG
28925335 GTTTAAAAAA
Statistics
Matches: 145, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
81 2 0.01
82 140 0.97
83 3 0.02
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (82 bp):
CGCTAAAGATCCGAGCATTAGCGGCGCTTGTACAAAAACGCCGCTAAAGATCCGAGCATTAGCGA
CGCATAGACAAAAACGA
Found at i:28925209 original size:123 final size:123
Alignment explanation
Indices: 28925079--28925334 Score: 334
Period size: 123 Copynumber: 2.1 Consensus size: 123
28925069 AGTTAGAAAT
* * * * *
28925079 GCCGCTAAAGATCCGAGAATTAGCAGCGC-TTGTATAAAAACGCCGCTAAAGACCCGAGCATTAG
1 GCCGCTAAAGATCCGAGAATTAGCAACGCATAG-ACAAAAACACAGCTAAAGACCCGAGCATTAG
* * * * *
28925143 CGGCGCATAGACAAAAACGTCGCTAAAGACCCGAGCATTAGCGGCGCATAGACAAAAAC
65 CGGCGCATACACAAAAACGCCGCGAAAGACCCGAGCATTAGCGACGCATACACAAAAAC
* * *
28925202 GCTGCTAAAGATCTGAGAATTAGCAACGCATAGACAAAAACACAGCTAAAGATCCGAGCATTAGC
1 GCCGCTAAAGATCCGAGAATTAGCAACGCATAGACAAAAACACAGCTAAAGACCCGAGCATTAGC
* * * * *
28925267 GGCGCTTTCACAAAAACGCCGCGAAAGATCGGAGCATTAGCGACGCTTACACAAAAAC
66 GGCGCATACACAAAAACGCCGCGAAAGACCCGAGCATTAGCGACGCATACACAAAAAC
28925325 GCCGCTAAAG
1 GCCGCTAAAG
28925335 GTTTAAAAAA
Statistics
Matches: 113, Mismatches: 19, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
123 111 0.98
124 2 0.02
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.14
Consensus pattern (123 bp):
GCCGCTAAAGATCCGAGAATTAGCAACGCATAGACAAAAACACAGCTAAAGACCCGAGCATTAGC
GGCGCATACACAAAAACGCCGCGAAAGACCCGAGCATTAGCGACGCATACACAAAAAC
Found at i:28925465 original size:40 final size:40
Alignment explanation
Indices: 28925391--28925489 Score: 103
Period size: 40 Copynumber: 2.5 Consensus size: 40
28925381 GGCGCTTTAT
* * ** *
28925391 ATAAAACGCCGCTAATTC-CTATTTTTAGCGGCGCTTCCGG
1 ATAAATCGCCGCTAATGCTCTACCTTTAGCAGCGCTT-CGG
*
28925431 AT-AATCGCCGCTAATGCTCTACCTTTAGCAGCGCTTTGG
1 ATAAATCGCCGCTAATGCTCTACCTTTAGCAGCGCTTCGG
* *
28925470 CTAAATCACCGCTAATGCTC
1 ATAAATCGCCGCTAATGCTC
28925490 GATTTTTTGT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
39 16 0.33
40 33 0.67
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.29
Consensus pattern (40 bp):
ATAAATCGCCGCTAATGCTCTACCTTTAGCAGCGCTTCGG
Found at i:28926383 original size:3 final size:3
Alignment explanation
Indices: 28926377--28926431 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
28926367 ATAATATTAA
28926377 TAC TAC TAC TAC TAC TAC TAC TAC -AC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
28926424 TAC TAC TA
1 TAC TAC TA
28926432 ATAATAATAA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TAC
Found at i:28928866 original size:3 final size:3
Alignment explanation
Indices: 28928858--28928911 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
28928848 TATTTTTAAC
28928858 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28928906 ATT ATT
1 ATT ATT
28928912 NNNNNNNNNN
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:28929466 original size:20 final size:21
Alignment explanation
Indices: 28929428--28929473 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
28929418 AATCTATGTA
*
28929428 TATATACATGCTTACATATTCT
1 TATATACATGCGTA-ATATTCT
*
28929450 TATATACATGCGT-ATATTTT
1 TATATACATGCGTAATATTCT
28929470 TATA
1 TATA
28929474 CTTTATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
22 12 0.55
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.48
Consensus pattern (21 bp):
TATATACATGCGTAATATTCT
Found at i:28929645 original size:18 final size:19
Alignment explanation
Indices: 28929600--28929647 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
28929590 GTTTAAGTGC
* *
28929600 TTTAATTTTTATTTATTTA
1 TTTACTTTTTATTTATTGA
*
28929619 TTTAC-TTTTATTTGTTGA
1 TTTACTTTTTATTTATTGA
28929637 TTT-CTTTTTAT
1 TTTACTTTTTAT
28929648 CATATATTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 1 0.04
18 20 0.80
19 4 0.16
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.73
Consensus pattern (19 bp):
TTTACTTTTTATTTATTGA
Found at i:28930201 original size:9 final size:9
Alignment explanation
Indices: 28930187--28930216 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
28930177 TTAAACGAAG
28930187 CGAGTTATT
1 CGAGTTATT
*
28930196 CGAGTTAAT
1 CGAGTTATT
28930205 CGAGTTATT
1 CGAGTTATT
28930214 CGA
1 CGA
28930217 ATCAACTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (9 bp):
CGAGTTATT
Found at i:28940054 original size:37 final size:37
Alignment explanation
Indices: 28940004--28940080 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
28939994 CAACGCAGAG
* *
28940004 TTTGATTTTGAAAGACAAAAGTGCACAATGCTTTCCA
1 TTTGATTTCGAAAGACAAAAGTACACAATGCTTTCCA
*
28940041 TTTGATTTCGAAAGACAGAAGTACACAATGCTTTCCA
1 TTTGATTTCGAAAGACAAAAGTACACAATGCTTTCCA
28940078 TTT
1 TTT
28940081 TTCTCAACAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Consensus pattern (37 bp):
TTTGATTTCGAAAGACAAAAGTACACAATGCTTTCCA
Found at i:28940574 original size:25 final size:25
Alignment explanation
Indices: 28940540--28940589 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
28940530 CAGGTAAGGC
* *
28940540 TCCTTCTTCTTCTTCCGTTCTTCAT
1 TCCTTCTTCTCCTTCCATTCTTCAT
* *
28940565 TCCTTTTTCTCCTTCTATTCTTCAT
1 TCCTTCTTCTCCTTCCATTCTTCAT
28940590 CTTCTCTTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.06, C:0.34, G:0.02, T:0.58
Consensus pattern (25 bp):
TCCTTCTTCTCCTTCCATTCTTCAT
Found at i:28940793 original size:11 final size:11
Alignment explanation
Indices: 28940777--28940802 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28940767 TTGCTGGATG
28940777 ATATTTTGGTT
1 ATATTTTGGTT
28940788 ATATTTTGGTT
1 ATATTTTGGTT
28940799 ATAT
1 ATAT
28940803 ACAGATGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (11 bp):
ATATTTTGGTT
Found at i:28942884 original size:22 final size:20
Alignment explanation
Indices: 28942841--28942879 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28942831 TAATTTAAAA
28942841 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
28942861 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
28942880 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:28942984 original size:14 final size:15
Alignment explanation
Indices: 28942962--28943071 Score: 57
Period size: 14 Copynumber: 6.9 Consensus size: 15
28942952 CAATCAAACA
28942962 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
28942976 CCAGCAAATCATTTT
1 CCAGAAAATCATTTT
*
28942991 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
28943011 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
*
28943025 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
28943045 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
28943059 ACGGAAAA-CATTT
1 CCAGAAAATCATTT
28943072 CACTGCCAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 26
0.69 0.07 0.24
Matches are distributed among these distances:
14 30 0.40
15 17 0.23
16 2 0.03
18 2 0.03
19 6 0.08
20 18 0.24
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:28943010 original size:20 final size:20
Alignment explanation
Indices: 28942985--28943051 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
28942975 TCCAGCAAAT
28942985 CATTTTACAGAAAAGTAAAA
1 CATTTTACAGAAAAGTAAAA
*
28943005 CATTTTCCAG-AAA-T----
1 CATTTTACAGAAAAGTAAAA
28943019 CATTTTACAGAAAAGTAAAA
1 CATTTTACAGAAAAGTAAAA
*
28943039 CATTTTCCAGAAA
1 CATTTTACAGAAA
28943052 TCATTTTACG
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
14 9 0.24
15 3 0.08
16 1 0.03
18 1 0.03
19 3 0.08
20 21 0.55
ACGTcount: A:0.48, C:0.15, G:0.09, T:0.28
Consensus pattern (20 bp):
CATTTTACAGAAAAGTAAAA
Found at i:28943023 original size:34 final size:34
Alignment explanation
Indices: 28942966--28943066 Score: 175
Period size: 34 Copynumber: 2.9 Consensus size: 34
28942956 CAAACACCAG
*
28942966 AAAATATTTTCCAGCAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAG-AAATCATTTTACAGAAAAGT
28943001 AAAACATTTTCCAGAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGAAATCATTTTACAGAAAAGT
*
28943035 AAAACATTTTCCAGAAATCATTTTACGGAAAA
1 AAAACATTTTCCAGAAATCATTTTACAGAAAA
28943067 CATTTCACTG
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
34 51 0.80
35 13 0.20
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.30
Consensus pattern (34 bp):
AAAACATTTTCCAGAAATCATTTTACAGAAAAGT
Found at i:28949107 original size:31 final size:30
Alignment explanation
Indices: 28949071--28949145 Score: 78
Period size: 31 Copynumber: 2.5 Consensus size: 30
28949061 TTATAATTTG
* **
28949071 GTCACTAAATTATTTGAAAGTTTGCATTTAA
1 GTCACTAAACTATTCAAAAGTTT-CATTTAA
* * *
28949102 GTCACTGAACTGTTCAAAAGTTTTATTTAA
1 GTCACTAAACTATTCAAAAGTTTCATTTAA
*
28949132 GTCACTAAGCTATT
1 GTCACTAAACTATT
28949146 AGTTTTCTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
30 17 0.49
31 18 0.51
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (30 bp):
GTCACTAAACTATTCAAAAGTTTCATTTAA
Found at i:28950571 original size:25 final size:25
Alignment explanation
Indices: 28950517--28950579 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 25
28950507 ATAACGAGAC
28950517 TATTTAAAAAAATTAATTAATTATT
1 TATTTAAAAAAATTAATTAATTATT
*
28950542 T-TTTATAAAAAATGTATTTATATTTATT
1 TATTTA-AAAAAAT-TAATTA-A-TTATT
28950570 TAATTTAAAA
1 T-ATTTAAAA
28950580 CCGGTCCTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
24 4 0.13
25 8 0.26
26 5 0.16
27 1 0.03
28 6 0.19
29 3 0.10
30 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TATTTAAAAAAATTAATTAATTATT
Found at i:28954232 original size:2 final size:2
Alignment explanation
Indices: 28954225--28954252 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28954215 TCTTCGTTTG
28954225 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
28954253 TTTCTTCTTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:28976045 original size:29 final size:28
Alignment explanation
Indices: 28975903--28976053 Score: 106
Period size: 29 Copynumber: 5.2 Consensus size: 28
28975893 ACAAAAATAT
* *
28975903 AAATTACATTTTAGCCCCTAAACTTTTCAA
1 AAATTACATTTT-GCCCCTATA-TTTTCTA
*
28975933 AAATTACATTTTGACCCCTATTTTTTCTA
1 AAATTACATTTTG-CCCCTATATTTTCTA
* ** * * *
28975962 AATTTACATATTAACCCATAATAATTTGT-
1 AAATTACAT-TTTGCCCCT-ATATTTTCTA
* * * *
28975991 AAATTACATTTGGGCCCTAAACTTTCTA
1 AAATTACATTTTGCCCCTATATTTTCTA
*
28976019 GAAATTACATTTTGGCCCTATATTTTCCTA
1 -AAATTACATTTTGCCCCTATATTTT-CTA
28976049 AAATT
1 AAATT
28976054 GCACTTTTAC
Statistics
Matches: 94, Mismatches: 21, Indels: 13
0.73 0.16 0.10
Matches are distributed among these distances:
27 6 0.06
28 5 0.05
29 54 0.57
30 29 0.31
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41
Consensus pattern (28 bp):
AAATTACATTTTGCCCCTATATTTTCTA
Found at i:28976449 original size:20 final size:20
Alignment explanation
Indices: 28976412--28976450 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28976402 TTTTTAAGTA
*
28976412 TTTTTTATTTTGTATTTATG
1 TTTTTTATTTTATATTTATG
28976432 TTTTTTAATTTTAT-TTTAT
1 TTTTTT-ATTTTATATTTAT
28976451 TTTATTCGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (20 bp):
TTTTTTATTTTATATTTATG
Found at i:28976761 original size:18 final size:18
Alignment explanation
Indices: 28976738--28976784 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
28976728 AAACTAATCG
28976738 TGTTTCAAAAATTT-TCA
1 TGTTTCAAAAATTTCTCA
*
28976755 TGTTTTC-AAAATTTCTCG
1 TG-TTTCAAAAATTTCTCA
28976773 TGTTTCAAAAAT
1 TGTTTCAAAAAT
28976785 AATAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.47
Consensus pattern (18 bp):
TGTTTCAAAAATTTCTCA
Found at i:28976891 original size:21 final size:22
Alignment explanation
Indices: 28976849--28976891 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
28976839 CGTAATTTAT
**
28976849 CAAAATTTTTGTGTTTTTAAAA
1 CAAAATTTTTGTGTTTCAAAAA
28976871 CAAAA-TTTTGTGTTTCAAAAA
1 CAAAATTTTTGTGTTTCAAAAA
28976892 TTTTCGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (22 bp):
CAAAATTTTTGTGTTTCAAAAA
Found at i:28976997 original size:57 final size:57
Alignment explanation
Indices: 28976883--28977024 Score: 198
Period size: 57 Copynumber: 2.5 Consensus size: 57
28976873 AAATTTTGTG
* **
28976883 TTTCAAAAATTTTCGTATTTTC-AAAAAAATTTCCCATGTTTTCAAAAATTCCCGTA
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAAAATCCCATGTTTTCAAAAATTCCCGTA
* * *
28976939 TTTCAAAAATTTTCTTGTTTTCAGAAAAAAAAAT-CCGTGTTTTCAAAAATTCCGGTA
1 TTTCAAAAATTTTCGTGTTTTCA-AAAAAAAAATCCCATGTTTTCAAAAATTCCCGTA
*
28976996 TTTCAAAAAATTTCGTGTTTTCAAAAAAA
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAA
28977025 TTTCATGTTT
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
56 26 0.34
57 42 0.55
58 8 0.11
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (57 bp):
TTTCAAAAATTTTCGTGTTTTCAAAAAAAAAATCCCATGTTTTCAAAAATTCCCGTA
Found at i:28977130 original size:71 final size:66
Alignment explanation
Indices: 28976965--28977272 Score: 206
Period size: 71 Copynumber: 4.4 Consensus size: 66
28976955 GTTTTCAGAA
* * *
28976965 AAAAAAATCCGTGTTTTCAAAAATTCCGGTATTTCAAAAAATTTCGTGTTTTCAAAAAAATTTCA
1 AAAAAAATTCGTGTTTTCAAAAATT-CGGTATTTCAAAAATTTTCATGTTTTC---AAAATTTC-
28977030 T-GT-T
61 TGGTGT
** *
28977034 TCAAAAATCCTCGTTTTTTCAAAAATTCCGGTATTTCAAAAATTTTCATGTTTTCAAAATTTCTG
1 AAAAAAAT--TCGTGTTTTCAAAAATT-CGGTATTTCAAAAATTTTCATGTTTTCAAAATTTCTG
28977099 GTGAT
63 GTG-T
** * ** * * *
28977104 AAAAAAATTCGTGTTTTCAAAGAAAATTTTGTGTTTCAAAAATCCTCTTGTTTTCAAAAATTCCG
1 AAAAAAATTCGTGTTTTC--A-AAAATTCGGTATTTCAAAAATTTTCATGTTTTCAAAATTTCTG
28977169 GTGTTTT
63 GTG---T
** ** * *
28977176 AAAAATTTTCGTGTTTTCAAAAAAATTTTGTATTTAAAAAATTTTCATGTTTTCAAAAAATTCTC
1 AAAAAAATTCGTGTTTTC--AAAAATTCGGTATTTCAAAAATTTTCATGTTTTC-AAAATTTCT-
*
28977241 GTGTTT
62 G-GTGT
* *
28977247 TAAAAATTTCCGTGTTTTCAAAAATT
1 AAAAAAATT-CGTGTTTTCAAAAATT
28977273 TTCATGTTTT
Statistics
Matches: 196, Mismatches: 29, Indels: 27
0.78 0.12 0.11
Matches are distributed among these distances:
67 1 0.01
68 19 0.10
69 6 0.03
70 47 0.24
71 83 0.42
72 37 0.19
73 1 0.01
74 2 0.01
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.42
Consensus pattern (66 bp):
AAAAAAATTCGTGTTTTCAAAAATTCGGTATTTCAAAAATTTTCATGTTTTCAAAATTTCTGGTG
T
Found at i:28977132 original size:105 final size:104
Alignment explanation
Indices: 28977000--28977197 Score: 317
Period size: 105 Copynumber: 1.9 Consensus size: 104
28976990 CCGGTATTTC
*
28977000 AAAAAATTTCGTGTTTTCAAAAAAATTTCATGTTTCAAAAATCCTCGTT-TTTTCAAAAATTCCG
1 AAAAAAATTCGTGTTTTCAAAAAAATTTCATGTTTCAAAAATCCTC-TTGTTTTCAAAAATTCCG
28977064 GTATTTCAAAAATTTTCATGTTTTCAAAATTTCTGGTGAT
65 GTATTTCAAAAATTTTCATGTTTTCAAAATTTCTGGTGAT
**
28977104 AAAAAAATTCGTGTTTTCAAAGAAAATTTTGTGTTTCAAAAATCCTCTTGTTTTCAAAAATTCCG
1 AAAAAAATTCGTGTTTTCAAA-AAAATTTCATGTTTCAAAAATCCTCTTGTTTTCAAAAATTCCG
* * *
28977169 GTGTTTTAAAAATTTTCGTGTTTTCAAAA
65 GTATTTCAAAAATTTTCATGTTTTCAAAA
28977198 AAATTTTGTA
Statistics
Matches: 86, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
104 22 0.26
105 64 0.74
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.42
Consensus pattern (104 bp):
AAAAAAATTCGTGTTTTCAAAAAAATTTCATGTTTCAAAAATCCTCTTGTTTTCAAAAATTCCGG
TATTTCAAAAATTTTCATGTTTTCAAAATTTCTGGTGAT
Found at i:28977281 original size:35 final size:35
Alignment explanation
Indices: 28976974--28977339 Score: 250
Period size: 35 Copynumber: 10.3 Consensus size: 35
28976964 AAAAAAAATC
* *
28976974 CGTGTTTTCAAAAA-TTCCG-GTATTTCAAAAAATTT
1 CGTGTTTTCAAAAATTTTCGTGT-TTT-AAAAATTTT
* * * **
28977009 CGTGTTTTCAAAAAAATTTCATGTTTCAAAAATCCT
1 CGTGTTTTC-AAAAATTTTCGTGTTTTAAAAATTTT
* *
28977045 CGTTTTTTCAAAAA-TTCCG-GTATTTCAAAAATTTT
1 CGTGTTTTCAAAAATTTTCGTGT-TTT-AAAAATTTT
* ** **
28977080 CATGTTTTC-AAAA-TTTC-TGGTGATAAAAAAATT
1 CGTGTTTTCAAAAATTTTCGT-GTTTTAAAAATTTT
* **
28977113 CGTGTTTTCAAAGAAAATTTT-GTGTTTCAAAAATCCT
1 CGTGTTTTC--A-AAAATTTTCGTGTTTTAAAAATTTT
* *
28977150 CTTGTTTTCAAAAA-TTCCGGTGTTTTAAAAATTTT
1 CGTGTTTTCAAAAATTTTC-GTGTTTTAAAAATTTT
* *
28977185 CGTGTTTTCAAAAAAATTTT-GTATTTAAAAAATTTT
1 CGTGTTTTC--AAAAATTTTCGTGTTTTAAAAATTTT
* * *
28977221 CATGTTTTCAAAAAATTCTCGTGTTTTAAAAATTTC
1 CGTGTTTTC-AAAAATTTTCGTGTTTTAAAAATTTT
* * *
28977257 CGTGTTTTCAAAAATTTTCATGTTTTTAAGAATTAT
1 CGTGTTTTCAAAAATTTTCGTG-TTTTAAAAATTTT
* * *
28977293 CGTG-TCTCTAAAATTCTCGTGTTTTAAAAATTTTT
1 CGTGTTTTCAAAAATTTTCGTGTTTTAAAAA-TTTT
28977328 CGTGTTTTCAAA
1 CGTGTTTTCAAA
28977340 GAAAATAATT
Statistics
Matches: 255, Mismatches: 54, Indels: 43
0.72 0.15 0.12
Matches are distributed among these distances:
33 19 0.07
34 25 0.10
35 92 0.36
36 81 0.32
37 30 0.12
38 8 0.03
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (35 bp):
CGTGTTTTCAAAAATTTTCGTGTTTTAAAAATTTT
Found at i:28977283 original size:19 final size:18
Alignment explanation
Indices: 28976872--28977339 Score: 267
Period size: 18 Copynumber: 26.1 Consensus size: 18
28976862 TTTTTAAAAC
28976872 AAAATTTT-GTG-TTTCA
1 AAAATTTTCGTGTTTTCA
*
28976888 AAAATTTTCGTATTTTCAAA
1 AAAATTTTCGTGTTTTC--A
* *
28976908 AAAATTTCCCATGTTTTCA
1 AAAATTT-TCGTGTTTTCA
** *
28976927 AAAATTCCCGT-ATTTCA
1 AAAATTTTCGTGTTTTCA
*
28976944 AAAATTTTCTTGTTTTCAGAAA
1 AAAATTTTCGTGTTTTC----A
** *
28976966 AAAAAATCCGTGTTTTCA
1 AAAATTTTCGTGTTTTCA
*
28976984 AAAA-TTCCG-GTATTTCA
1 AAAATTTTCGTGT-TTTCA
*
28977001 AAAAATTTCGTGTTTTCAA
1 AAAATTTTCGTGTTTTC-A
* *
28977020 AAAAATTTCATG-TTTCA
1 AAAATTTTCGTGTTTTCA
** *
28977037 AAAATCCTCGTTTTTTCA
1 AAAATTTTCGTGTTTTCA
*
28977055 AAAA-TTCCG-GTATTTCA
1 AAAATTTTCGTGT-TTTCA
*
28977072 AAAATTTTCATGTTTTC-
1 AAAATTTTCGTGTTTTCA
**
28977089 AAAA-TTTC-TGGTGAT-A
1 AAAATTTTCGT-GTTTTCA
**
28977105 AAAAAATTCGTGTTTTCAAA
1 AAAATTTTCGTGTTTTC--A
28977125 GAAAATTTT-GTG-TTTCA
1 -AAAATTTTCGTGTTTTCA
** *
28977142 AAAATCCTCTTGTTTTCA
1 AAAATTTTCGTGTTTTCA
*
28977160 AAAA-TTCCGGTGTTTT-A
1 AAAATTTTC-GTGTTTTCA
28977177 AAAATTTTCGTGTTTTCAAA
1 AAAATTTTCGTGTTTTC--A
* *
28977197 AAAATTTT-GT-ATTTAA
1 AAAATTTTCGTGTTTTCA
*
28977213 AAAATTTTCATGTTTTCAA
1 AAAATTTTCGTGTTTTC-A
*
28977232 AAAATTCTCGTGTTTT-A
1 AAAATTTTCGTGTTTTCA
*
28977249 AAAATTTCCGTGTTTTCA
1 AAAATTTTCGTGTTTTCA
* *
28977267 AAAATTTTCATGTTTTTA
1 AAAATTTTCGTGTTTTCA
* * * *
28977285 AGAATTATCGTG-TCTCT
1 AAAATTTTCGTGTTTTCA
*
28977302 AAAATTCTCGTGTTTT-A
1 AAAATTTTCGTGTTTTCA
28977319 AAAATTTTTCGTGTTTTCA
1 AAAA-TTTTCGTGTTTTCA
28977338 AA
1 AA
28977340 GAAAATAATT
Statistics
Matches: 345, Mismatches: 67, Indels: 77
0.71 0.14 0.16
Matches are distributed among these distances:
15 1 0.00
16 37 0.11
17 105 0.30
18 107 0.31
19 47 0.14
20 21 0.06
21 13 0.04
22 14 0.04
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.44
Consensus pattern (18 bp):
AAAATTTTCGTGTTTTCA
Found at i:28977381 original size:36 final size:37
Alignment explanation
Indices: 28977312--28977381 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 37
28977302 AAAATTCTCG
* * * * *
28977312 TGTTTTAAAAATTTTTCGTGTTTTCAAAGAAAATAAT
1 TGTTTCAAAAATTCTTCGTGGTTTAAAACAAAATAAT
28977349 TGTTTCAAAAA-TCTTCGTGGTTTAAAACAAAAT
1 TGTTTCAAAAATTCTTCGTGGTTTAAAACAAAAT
28977382 TCTCGTATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
36 18 0.64
37 10 0.36
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (37 bp):
TGTTTCAAAAATTCTTCGTGGTTTAAAACAAAATAAT
Found at i:28978934 original size:7 final size:7
Alignment explanation
Indices: 28978918--28978948 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
28978908 ATTTAATTTG
28978918 TTTT-GA
1 TTTTCGA
28978924 TTTTCGA
1 TTTTCGA
28978931 TTTTCGA
1 TTTTCGA
28978938 TTTTCGA
1 TTTTCGA
28978945 TTTT
1 TTTT
28978949 ACAAACTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 20 0.83
ACGTcount: A:0.13, C:0.10, G:0.13, T:0.65
Consensus pattern (7 bp):
TTTTCGA
Found at i:28992270 original size:42 final size:43
Alignment explanation
Indices: 28992206--28992298 Score: 170
Period size: 42 Copynumber: 2.2 Consensus size: 43
28992196 TGTTTATCTC
*
28992206 TTTGAGGTGTTGCAGTTGAAAAGATAAGTTTCACGTGTC-AAA
1 TTTGTGGTGTTGCAGTTGAAAAGATAAGTTTCACGTGTCGAAA
28992248 TTTGTGGTGTTGCAGTTGAAAAGATAAGTTTCACGTGTCGAAA
1 TTTGTGGTGTTGCAGTTGAAAAGATAAGTTTCACGTGTCGAAA
28992291 TTTGTGGT
1 TTTGTGGT
28992299 TTGGGACAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 38 0.78
43 11 0.22
ACGTcount: A:0.27, C:0.09, G:0.28, T:0.37
Consensus pattern (43 bp):
TTTGTGGTGTTGCAGTTGAAAAGATAAGTTTCACGTGTCGAAA
Found at i:28992864 original size:217 final size:218
Alignment explanation
Indices: 28992605--28993039 Score: 863
Period size: 217 Copynumber: 2.0 Consensus size: 218
28992595 TTTTGTTTTA
28992605 ACATATAATAATTATTTACCTATCTTTTTAATAGGAAAAAGAAAACGCAATTTAATTTAAGTGAA
1 ACATATAATAATTATTTACCTATCTTTTTAATAGGAAAAAGAAAACGCAATTTAATTTAAGTGAA
28992670 AATTATCTTAGTGAAAATTCATGAAATTAGTAGAAACTGAGACATATTAGGCAGTGTTCTAGAAA
66 AATTATCTTAGTGAAAATTCATGAAATTAGTAGAAACTGAGACATATTAGGCAGTGTTCTAGAAA
28992735 AAGACGATGAAAAAACAAAGACAAGTCACTGTTTTGTCTTGAAACGGAGAGGATTTTAATCGGAG
131 AAGACGATGAAAAAACAAAGACAAGTCACTGTTTTGTCTTGAAACGGAGAGGATTTTAATCGGAG
28992800 AATGAACGCCACTTCTCAATGGT
196 AATGAACGCCACTTCTCAATGGT
28992823 ACATATAAT-ATTATTTACCTATCTTTTTAATAGGAAAAAGAAAACGCAATTTAATTTAAGTGAA
1 ACATATAATAATTATTTACCTATCTTTTTAATAGGAAAAAGAAAACGCAATTTAATTTAAGTGAA
28992887 AATTATCTTAGTGAAAATTCATGAAATTAGTAGAAACTGAGACATATTAGGCAGTGTTCTAGAAA
66 AATTATCTTAGTGAAAATTCATGAAATTAGTAGAAACTGAGACATATTAGGCAGTGTTCTAGAAA
28992952 AAGACGATGAAAAAACAAAGACAAGTCACTGTTTTGTCTTGAAACGGAGAGGATTTTAATCGGAG
131 AAGACGATGAAAAAACAAAGACAAGTCACTGTTTTGTCTTGAAACGGAGAGGATTTTAATCGGAG
28993017 AATGAACGCCACTTCTCAATGGT
196 AATGAACGCCACTTCTCAATGGT
28993040 GTGTGCAGGT
Statistics
Matches: 217, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
217 208 0.96
218 9 0.04
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (218 bp):
ACATATAATAATTATTTACCTATCTTTTTAATAGGAAAAAGAAAACGCAATTTAATTTAAGTGAA
AATTATCTTAGTGAAAATTCATGAAATTAGTAGAAACTGAGACATATTAGGCAGTGTTCTAGAAA
AAGACGATGAAAAAACAAAGACAAGTCACTGTTTTGTCTTGAAACGGAGAGGATTTTAATCGGAG
AATGAACGCCACTTCTCAATGGT
Found at i:29006799 original size:33 final size:33
Alignment explanation
Indices: 29006727--29006798 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
29006717 CTTAGTCACC
*
29006727 AAAAATTTCAAATATCAAAATGTTAATCGCCAAAT
1 AAAAATTT--AATATCAAAATGTTAATCGACAAAT
* *
29006762 AAAAATTTAATATCAAAATGTTAGT-GATAAAT
1 AAAAATTTAATATCAAAATGTTAATCGACAAAT
29006794 AAAAA
1 AAAAA
29006799 ACTTTTATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 10 0.29
33 16 0.47
35 8 0.24
ACGTcount: A:0.56, C:0.08, G:0.07, T:0.29
Consensus pattern (33 bp):
AAAAATTTAATATCAAAATGTTAATCGACAAAT
Found at i:29014002 original size:90 final size:90
Alignment explanation
Indices: 29013849--29014024 Score: 212
Period size: 90 Copynumber: 2.0 Consensus size: 90
29013839 GAGGTTTTAC
* * * * * *
29013849 ATACCGGTATGGCGATGTGATTTGCTTCTTTGACATCTGGCATGCTTATTTAACTTCTGTTGCAA
1 ATACCAGTATGGCAATGTGATTTGCTTCTTTGACATATGGCATACTTATGTAACTTCGGTTGCAA
29013914 GTTGGTACT-GTGCGGATTCATGCTT
66 GTTGGTA-TAGTGCGGATTCATGCTT
* ** *
29013939 ATACCAGTATGGTAATGTGATTTGCTTCTTTGACATATGGTGTACTTGTGTAAC-TCGGGTTGCA
1 ATACCAGTATGGCAATGTGATTTGCTTCTTTGACATATGGCATACTTATGTAACTTC-GGTTGCA
* *
29014003 TGTTGGTATAGTGCTGATTCAT
65 AGTTGGTATAGTGCGGATTCAT
29014025 ATCACTCAAA
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
89 3 0.04
90 69 0.96
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.40
Consensus pattern (90 bp):
ATACCAGTATGGCAATGTGATTTGCTTCTTTGACATATGGCATACTTATGTAACTTCGGTTGCAA
GTTGGTATAGTGCGGATTCATGCTT
Found at i:29014359 original size:1 final size:1
Alignment explanation
Indices: 29014353--29014386 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
29014343 ATTCTTCTTC
29014353 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
29014387 GCACTCGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:29033266 original size:40 final size:40
Alignment explanation
Indices: 29033189--29033322 Score: 196
Period size: 40 Copynumber: 3.3 Consensus size: 40
29033179 AGCGGCACTT
** *
29033189 TTAGCGGCGTTTGGAGCAAAAACGCTGCTAAAGAGTGAGCA
1 TTAGCGGCGTTTAAAG-AAAAGCGCTGCTAAAGAGTGAGCA
*
29033230 TTAGCGGCGTTTAAAGAAAAGCGCCGCTAAAGAGTGAGCA
1 TTAGCGGCGTTTAAAGAAAAGCGCTGCTAAAGAGTGAGCA
* *
29033270 TTAGTGGCGTTTAAGGAAAAGCGCTGCTAAAGAGTGAGCA
1 TTAGCGGCGTTTAAAGAAAAGCGCTGCTAAAGAGTGAGCA
*
29033310 TTAGCAGCGTTTA
1 TTAGCGGCGTTTA
29033323 TAAAAAACAC
Statistics
Matches: 84, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 70 0.83
41 14 0.17
ACGTcount: A:0.32, C:0.16, G:0.31, T:0.22
Consensus pattern (40 bp):
TTAGCGGCGTTTAAAGAAAAGCGCTGCTAAAGAGTGAGCA
Found at i:29033548 original size:112 final size:114
Alignment explanation
Indices: 29033269--29033637 Score: 566
Period size: 113 Copynumber: 3.3 Consensus size: 114
29033259 AAGAGTGAGC
** * * * *
29033269 ATTAGTGGCGTTTAAGGAAAAGCGCTGCTAAAGAGTGAGCATTAGCAGCGTTTATAAAAAACACC
1 ATTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
*
29033334 -AGAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGGA
66 GAAAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGGA
*
29033382 ATTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTAT-AAGAACGCC
1 ATTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
*
29033446 GAAAAATAATACACCCAGACGATGCCGTTTTGTGGCCTTT-GGGGGGGA
66 GAAAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGGA
* *
29033494 ATTAGTGGTGTTTATTGTAAAGCGTCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
1 ATTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
* * * *
29033559 G-CAACTAATATACCCAGACGGTGCCGTTTTGTGTCCTTTGGGGGGGGA
66 GAAAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGGA
*
29033607 ATTAGTGGCGTTTTTTGTAAAGCGCCGCTAA
1 ATTAGTGGCGTTTATTGTAAAGCGCCGCTAA
29033638 TCTAGGTGTT
Statistics
Matches: 233, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
112 101 0.43
113 132 0.57
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (114 bp):
ATTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
GAAAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGGA
Found at i:29035093 original size:88 final size:84
Alignment explanation
Indices: 29034929--29035227 Score: 438
Period size: 84 Copynumber: 3.5 Consensus size: 84
29034919 TAAACTTTTG
*
29034929 GTGGCGTTTTTAGGAAAACGCCACAAATAATGCAATTCCAGACCACGAAAACGGTGTCGTTTCTG
1 GTGGCGTTTTTAGAAAAACGCCACAAATAATGCAATTCCAGACCACGAAAACGGTGTCGTTTCTG
*
29034994 TTCATAGCTGTAATATTTA
66 TTCACAGCTGTAATATTTA
* * *
29035013 GTGGCGTTTTTATAAAAATGCCACAAACAATGCAATTATTCCAGACCACGTAAAACGGTGTCGTT
1 GTGGCGTTTTTAGAAAAACGCCACAAATAATGC-A--ATTCCAGACCACG-AAAACGGTGTCGTT
29035078 TCTGTTCACAGCTGTAATATTTA
62 TCTGTTCACAGCTGTAATATTTA
* *
29035101 GTGGCGTTTTTAGGAAAACGCCATAAATAATGCAATTCCAGACCACGAAAACGGTGTCGTTTCTG
1 GTGGCGTTTTTAGAAAAACGCCACAAATAATGCAATTCCAGACCACGAAAACGGTGTCGTTTCTG
*
29035166 TTCACAGCTGTAATATTTT
66 TTCACAGCTGTAATATTTA
** * *
29035185 GTGGCGTTTTTTA-TTAAACGCCACAAAAAATGCAATTTCAGAC
1 GTGGCG-TTTTTAGAAAAACGCCACAAATAATGCAATTCCAGAC
29035228 TAACAAAACA
Statistics
Matches: 194, Mismatches: 16, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
84 96 0.49
85 20 0.10
87 14 0.07
88 64 0.33
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (84 bp):
GTGGCGTTTTTAGAAAAACGCCACAAATAATGCAATTCCAGACCACGAAAACGGTGTCGTTTCTG
TTCACAGCTGTAATATTTA
Found at i:29035724 original size:15 final size:15
Alignment explanation
Indices: 29035706--29035775 Score: 94
Period size: 15 Copynumber: 4.9 Consensus size: 15
29035696 TATTTAGCAA
29035706 TTTAGGAAAAATTTG
1 TTTAGGAAAAATTTG
29035721 TTTAGGAAAAATTTG
1 TTTAGGAAAAATTTG
29035736 TTTAGGAAAAATTTG
1 TTTAGGAAAAATTTG
**
29035751 ----GGAATTATTTG
1 TTTAGGAAAAATTTG
29035762 TTTAGGAAAAATTT
1 TTTAGGAAAAATTT
29035776 TGTCTATATA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
11 9 0.19
15 38 0.81
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (15 bp):
TTTAGGAAAAATTTG
Found at i:29035754 original size:26 final size:27
Alignment explanation
Indices: 29035706--29035775 Score: 88
Period size: 26 Copynumber: 2.5 Consensus size: 27
29035696 TATTTAGCAA
29035706 TTTAGGAAAAATTTGTTTAGGAAAAATTTG
1 TTTAGGAAAAATTTG--T-GGAAAAATTTG
**
29035736 TTTAGGAAAAATTTG-GGAATTATTTG
1 TTTAGGAAAAATTTGTGGAAAAATTTG
29035762 TTTAGGAAAAATTT
1 TTTAGGAAAAATTT
29035776 TGTCTATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 23 0.61
30 15 0.39
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (27 bp):
TTTAGGAAAAATTTGTGGAAAAATTTG
Found at i:29037237 original size:17 final size:17
Alignment explanation
Indices: 29037215--29037258 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
29037205 GTTAAATTTA
*
29037215 TTACTAAAATACATTAC
1 TTACTAAAATAAATTAC
29037232 TTACTAAAATAAATTAC
1 TTACTAAAATAAATTAC
29037249 TTACTAAAAT
1 TTACTAAAAT
29037259 TTGTTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (17 bp):
TTACTAAAATAAATTAC
Found at i:29037268 original size:23 final size:23
Alignment explanation
Indices: 29037241--29037286 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
29037231 CTTACTAAAA
*
29037241 TAAA-TTACTTACTAAAATTTGTT
1 TAAATTTA-TTACTAAAATATGTT
*
29037264 TAAATTTATTACTTAAATATGTT
1 TAAATTTATTACTAAAATATGTT
29037287 ACTTAAATNN
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (23 bp):
TAAATTTATTACTAAAATATGTT
Found at i:29044774 original size:42 final size:41
Alignment explanation
Indices: 29044722--29044885 Score: 132
Period size: 42 Copynumber: 3.9 Consensus size: 41
29044712 ATTTTTGTAT
* *
29044722 AAAAGCGCCACTAAAGAACATGTTCTTTCGCAGCGTTTGTAA
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCAGCGTTTG-AA
* * *
29044764 AAAAATGCCACTAAAGACCATGTTCTTTAG-AGGCGCTTAGAA
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCA-GCG-TTTGAA
* * * * ***
29044806 AAAAACACCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCC
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCAGCG-TTTGAA
** * * *
29044848 TTAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTT
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCAGCGTTT
29044886 TTTTCTAAAC
Statistics
Matches: 98, Mismatches: 21, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
41 4 0.04
42 91 0.93
43 3 0.03
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (41 bp):
AAAAACGCCACTAAAGAACATGTTCTTTAGCAGCGTTTGAA
Found at i:29044873 original size:84 final size:82
Alignment explanation
Indices: 29044774--29045026 Score: 290
Period size: 84 Copynumber: 3.0 Consensus size: 82
29044764 AAAAATGCCA
* * **** *
29044774 CTAAAGACCATGTTCTTTAGAGGCGCTTAGAAAAAAACACCGCTAAAGAACATGATCTTTAGCGG
1 CTAAAGAACATGTTCTTTAGAGGCGTTTTTTTAAAAACGCCGCTAAAGAACATGATCTTTAGCGG
29044839 CGTTTTTCCTTAAGCGCCG
66 CGTTTTT--TTAAGCGCCG
* ** * *
29044858 CTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAACGCCGCTAAAGAACGTGGTCTTTAGCGG
1 CTAAAGAACATGTTCTTTAGAGGCGTTTTTTTAAAAACGCCGCTAAAGAACATGATCTTTAGCGG
29044923 CGTTTTTTTACAAGCGCCG
66 CGTTTTTTT--AAGCGCCG
* * * * * *
29044942 CTAAAGAACATGGTCTTTAGTGGCATTTTTTTACAAACGCCGCGAAAGAACATGTTCTTTAGCGG
1 CTAAAGAACATGTTCTTTAGAGGCGTTTTTTTAAAAACGCCGCTAAAGAACATGATCTTTAGCGG
29045007 CGTTTTTTTCTAAGCGCCG
66 CG-TTTTTT-TAAGCGCCG
29045026 C
1 C
29045027 NNNNNNNNNN
Statistics
Matches: 145, Mismatches: 20, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
82 2 0.01
84 136 0.94
85 6 0.04
86 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (82 bp):
CTAAAGAACATGTTCTTTAGAGGCGTTTTTTTAAAAACGCCGCTAAAGAACATGATCTTTAGCGG
CGTTTTTTTAAGCGCCG
Found at i:29044886 original size:42 final size:40
Alignment explanation
Indices: 29044813--29045026 Score: 257
Period size: 42 Copynumber: 5.1 Consensus size: 40
29044803 GAAAAAAACA
*
29044813 CCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCCTTAAGCG
1 CCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT--TTAAGCG
* *
29044855 CCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAACG
1 CCGCTAAAGAACATGGTCTTTAGCGGCG-TTTTTT-TAAGCG
*
29044897 CCGCTAAAGAACGTGGTCTTTAGCGGCGTTTTTTTACAAGCG
1 CCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTT--AAGCG
* * *
29044939 CCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTTACAAACG
1 CCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTT--AAGCG
* *
29044981 CCGCGAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAGCG
1 CCGCTAAAGAACATGGTCTTTAGCGGCG-TTTTTT-TAAGCG
29045023 CCGC
1 CCGC
29045027 NNNNNNNNNN
Statistics
Matches: 152, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
40 1 0.01
41 7 0.05
42 132 0.87
43 11 0.07
44 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.32
Consensus pattern (40 bp):
CCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTAAGCG
Found at i:29049196 original size:2 final size:2
Alignment explanation
Indices: 29049155--29049183 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29049145 TATTTACAAA
29049155 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 A
29049184 AGGATGATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29052462 original size:21 final size:22
Alignment explanation
Indices: 29052433--29052493 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
29052423 GTGGACGGTC
29052433 ATATCATATTTATATGT-A-TGTA
1 ATAT-ATATTTATAT-TAACTGTA
*
29052455 ATATATA-TTATGTTAACTGTA
1 ATATATATTTATATTAACTGTA
29052476 ATATATATGTTATATTAA
1 ATATATAT-TTATATTAA
29052494 ACTATTATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
19 1 0.03
20 6 0.18
21 14 0.42
22 4 0.12
23 8 0.24
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.49
Consensus pattern (22 bp):
ATATATATTTATATTAACTGTA
Found at i:29054552 original size:25 final size:24
Alignment explanation
Indices: 29054481--29054565 Score: 91
Period size: 25 Copynumber: 3.5 Consensus size: 24
29054471 ACAATATATA
*
29054481 TATATATATATATATGCATTTTTT
1 TATATATATATATACGCATTTTTT
* * * * *
29054505 TATGTAT-TAAACACACATATTTT
1 TATATATATATATACGCATTTTTT
29054528 TATATATAATATATACGCATTTTTT
1 TATATAT-ATATATACGCATTTTTT
*
29054553 TAAATATATATAT
1 TATATATATATAT
29054566 TTTTTAAAGC
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
23 17 0.36
24 12 0.26
25 18 0.38
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.51
Consensus pattern (24 bp):
TATATATATATATACGCATTTTTT
Found at i:29058537 original size:20 final size:20
Alignment explanation
Indices: 29058512--29058552 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
29058502 GCAAATGTTC
*
29058512 TTTCATT-CTTTACGATTTTT
1 TTTCATTCCTTCA-GATTTTT
29058532 TTTCATTCCTTCAGATTTTT
1 TTTCATTCCTTCAGATTTTT
29058552 T
1 T
29058553 CTGCCAAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.15, C:0.17, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTCATTCCTTCAGATTTTT
Found at i:29059391 original size:60 final size:58
Alignment explanation
Indices: 29059298--29059414 Score: 207
Period size: 60 Copynumber: 2.0 Consensus size: 58
29059288 GAGGGAAATG
*
29059298 GATGCCAAATTGGGTGGAACCTTATGATTATAGAGAAGGTTTTTTTTCCAAAGGAGCTTA
1 GATGCCAAATTGGGTGGAACCTTATGATTATAGAGAA-GCTTTTTTT-CAAAGGAGCTTA
29059358 GATGCCAAATTGGGTGGAACCTTATGATTATAGAGAAGCTTTTTTTCAAAGGAGCTT
1 GATGCCAAATTGGGTGGAACCTTATGATTATAGAGAAGCTTTTTTTCAAAGGAGCTT
29059415 TGATTTTCAG
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
58 11 0.20
59 8 0.14
60 37 0.66
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (58 bp):
GATGCCAAATTGGGTGGAACCTTATGATTATAGAGAAGCTTTTTTTCAAAGGAGCTTA
Found at i:29059582 original size:7 final size:7
Alignment explanation
Indices: 29059557--29059598 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
29059547 AGTGATGTGA
29059557 AAAAATG
1 AAAAATG
29059564 AAAAGATG
1 AAAA-ATG
29059572 -AAAATG
1 AAAAATG
29059578 AAAAATG
1 AAAAATG
29059585 AAAAA-G
1 AAAAATG
29059591 TAAAAATG
1 -AAAAATG
29059599 GAGAGGCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 4 0.13
7 23 0.74
8 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:29059596 original size:21 final size:21
Alignment explanation
Indices: 29059557--29059598 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29059547 AGTGATGTGA
*
29059557 AAAAATGAAAAGATGAAAATG
1 AAAAATGAAAAGATAAAAATG
29059578 AAAAATGAAAA-AGTAAAAATG
1 AAAAATGAAAAGA-TAAAAATG
29059599 GAGAGGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (21 bp):
AAAAATGAAAAGATAAAAATG
Found at i:29061468 original size:44 final size:44
Alignment explanation
Indices: 29061412--29061865 Score: 142
Period size: 44 Copynumber: 10.3 Consensus size: 44
29061402 ACTGGCGTGA
*
29061412 AGTAGATCGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
** ** * ** * ** * *
29061456 AACAGATTGAAGATGGCAGATTTTGCCTCCCTGAGGTTGCAGCGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCT-AAGCAGTAGTGG
* * * ** * **
29061501 AGTATATTGAAGCCAGTA-A-TTC-TATCTCCCTGGGCAGCAGTAT
1 AGTAGATTGAAG--ATTACAGATCTTATCTCCCTAAGCAGTAGTGG
* *
29061544 AATAGATTGAAGATTACAGATCTTATCTCCCTAAGTAGTAGTGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
* * ** * * *
29061588 AGCAGATCGAAGATGGC-GAATTTTACCTCCCTGAG--GTTACAGTGG
1 AGTAGATTGAAGATTACAG-ATCTTATCTCCCTAAGCAG-T--AGTGG
* * * * * **
29061633 AGTACATTGAAGCCAGTA-A-TTC-TATCTCCCTAGGCAGCAGTAT
1 AGTAGATTGAAG--ATTACAGATCTTATCTCCCTAAGCAGTAGTGG
* *
29061676 AATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAATGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
* ** ** * * * ** *
29061720 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTGCAGTGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCT-AAGCAGTAGTGG
* * * * * **
29061765 AGTACATTGAAGCCAGTA-A-TTC-TATCTCTC-AGGGCAACAGTGG
1 AGTAGATTGAAG--ATTACAGATCTTATCTCCCTA-AGCAGTAGTGG
* * *
29061808 AATAGATTGAATATTACAGATCTTATCTCCTTAAGCAGTAGTGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
* *
29061852 AGCAGATCGAAGAT
1 AGTAGATTGAAGAT
29061866 GGTGGATTTT
Statistics
Matches: 273, Mismatches: 111, Indels: 52
0.63 0.25 0.12
Matches are distributed among these distances:
41 9 0.03
42 5 0.02
43 54 0.20
44 150 0.55
45 49 0.18
46 3 0.01
47 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (44 bp):
AGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
Found at i:29061584 original size:132 final size:132
Alignment explanation
Indices: 29061414--29061929 Score: 818
Period size: 132 Copynumber: 3.9 Consensus size: 132
29061404 TGGCGTGAAG
* * *
29061414 TAGATCGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAACAGATTGAAGATGGCAGATTT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTT
* * * *
29061479 TGCCTCCCTGAGGTTGCAGCGGAGTATATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTAT
66 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTAT
29061544 AA
131 AA
*
29061546 TAGATTGAAGATTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGATGGC-GAATT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAG-ATT
*
29061610 TTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTAGGCAGCAGTA
65 TTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTA
29061675 TAA
130 TAA
* *
29061678 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAATGGAGCAGATCAAAGATGGCAGATTT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTT
* * * * **
29061743 TACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTATCTCTCAGGGCAACAGTGG
66 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTAT
29061808 AA
131 AA
* * **
29061810 TAGATTGAATATTACAGATCTTATCTCCTTAAGCAGTAGTGGAGCAGATCGAAGATGGTGGATTT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTT
*
29061875 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTAACTCCCTGG
66 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGG
29061930 TCGGAGTAGA
Statistics
Matches: 353, Mismatches: 29, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
131 1 0.00
132 351 0.99
133 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (132 bp):
TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTT
TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTAT
AA
Found at i:29062938 original size:22 final size:19
Alignment explanation
Indices: 29062895--29062935 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
29062885 GTGAATTTCA
29062895 TCTTAGTTTTTTTTTTATT
1 TCTTAGTTTTTTTTTTATT
*
29062914 TCTTTGTTTGTTTTATTTATT
1 TCTTAGTTT-TTTT-TTTATT
29062935 T
1 T
29062936 TCTGATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 4 0.21
21 7 0.37
ACGTcount: A:0.10, C:0.05, G:0.07, T:0.78
Consensus pattern (19 bp):
TCTTAGTTTTTTTTTTATT
Found at i:29066775 original size:29 final size:29
Alignment explanation
Indices: 29066733--29066791 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
29066723 CATGATTTTC
29066733 CATTTGCACCTCTCGTCGCGCATTGCGTA
1 CATTTGCACCTCTCGTCGCGCATTGCGTA
* *
29066762 CATTTGTACCTCTCGTCGTGCATTGCGTA
1 CATTTGCACCTCTCGTCGCGCATTGCGTA
29066791 C
1 C
29066792 TTTCCCTCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.14, C:0.32, G:0.20, T:0.34
Consensus pattern (29 bp):
CATTTGCACCTCTCGTCGCGCATTGCGTA
Found at i:29067194 original size:18 final size:18
Alignment explanation
Indices: 29067159--29067197 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29067149 TCCGTTGCCC
*
29067159 CTTCTTCCTCGGCTGCAT
1 CTTCTTCCTCAGCTGCAT
29067177 CTTCTTCCTCAG-TGGCAT
1 CTTCTTCCTCAGCT-GCAT
29067195 CTT
1 CTT
29067198 TATTTTCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.08, C:0.36, G:0.15, T:0.41
Consensus pattern (18 bp):
CTTCTTCCTCAGCTGCAT
Found at i:29078492 original size:15 final size:15
Alignment explanation
Indices: 29078472--29078502 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29078462 TTTGTATAGT
29078472 TTACATCTTGCTCAC
1 TTACATCTTGCTCAC
29078487 TTACATCTTGCTCAC
1 TTACATCTTGCTCAC
29078502 T
1 T
29078503 CTACTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.32, G:0.06, T:0.42
Consensus pattern (15 bp):
TTACATCTTGCTCAC
Found at i:29083582 original size:86 final size:87
Alignment explanation
Indices: 29083476--29083640 Score: 287
Period size: 86 Copynumber: 1.9 Consensus size: 87
29083466 ATCGACCCCA
*
29083476 AAAATTTTCTAGAAATGACTATCCAAAGATCATGAGAAGTCGTCACCTTTACATGTCTCTAACAG
1 AAAATTTTCTAGAAATGACTATCCAAAGATCATGAAAAGTCGTCACCTTTACATGTCTCTAACAG
29083541 CAAACTAAATCAACTAAAAAAG
66 CAAACTAAATCAACTAAAAAAG
* * *
29083563 AAAA-TTTCTAGAAATGACTATGCACAGATCATGAAAAGTCGTCACCTTTACATGTGTCTAACAG
1 AAAATTTTCTAGAAATGACTATCCAAAGATCATGAAAAGTCGTCACCTTTACATGTCTCTAACAG
29083627 CAAACTAAATCAAC
66 CAAACTAAATCAAC
29083641 CCAAAGGATA
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
86 70 0.95
87 4 0.05
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.25
Consensus pattern (87 bp):
AAAATTTTCTAGAAATGACTATCCAAAGATCATGAAAAGTCGTCACCTTTACATGTCTCTAACAG
CAAACTAAATCAACTAAAAAAG
Found at i:29095190 original size:11 final size:12
Alignment explanation
Indices: 29095172--29095202 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
29095162 CTTTTGTAGA
29095172 TCATTTTCTTTT
1 TCATTTTCTTTT
29095184 T-ATTTTCTTTT
1 TCATTTTCTTTT
29095195 TCATTTTC
1 TCATTTTC
29095203 CCTCTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.74
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:29095208 original size:16 final size:16
Alignment explanation
Indices: 29095189--29095219 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29095179 CTTTTTATTT
29095189 TCTTTTTCATTTTCCC
1 TCTTTTTCATTTTCCC
*
29095205 TCTTTTTCTTTTTCC
1 TCTTTTTCATTTTCC
29095220 TATCCTAGCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (16 bp):
TCTTTTTCATTTTCCC
Found at i:29095506 original size:40 final size:41
Alignment explanation
Indices: 29095462--29095547 Score: 147
Period size: 40 Copynumber: 2.1 Consensus size: 41
29095452 TGATTTCAGT
29095462 TTTTTTCAAGCTTAAATTCATAGCTAATTTTTG-GGTTTTC
1 TTTTTTCAAGCTTAAATTCATAGCTAATTTTTGAGGTTTTC
* *
29095502 TTTTTTCAAGCTTAAATTCATAGGTAATTTTTGAGTTTTTC
1 TTTTTTCAAGCTTAAATTCATAGCTAATTTTTGAGGTTTTC
29095543 TTTTT
1 TTTTT
29095548 CTTCTTTGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
40 32 0.74
41 11 0.26
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.56
Consensus pattern (41 bp):
TTTTTTCAAGCTTAAATTCATAGCTAATTTTTGAGGTTTTC
Found at i:29096920 original size:7 final size:7
Alignment explanation
Indices: 29096908--29096938 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
29096898 ATGTAATAAC
29096908 TTAAAAA
1 TTAAAAA
29096915 TTAAAAA
1 TTAAAAA
29096922 TTAAAAA
1 TTAAAAA
*
29096929 TTAAACA
1 TTAAAAA
29096936 TTA
1 TTA
29096939 TAGTGCACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (7 bp):
TTAAAAA
Found at i:29097611 original size:9 final size:9
Alignment explanation
Indices: 29097599--29097637 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
29097589 AAAATTATAA
29097599 AAAAAACAT
1 AAAAAACAT
*
29097608 AAAAAACGT
1 AAAAAACAT
*
29097617 AAAAAAGAT
1 AAAAAACAT
29097626 AAAAAACA-
1 AAAAAACAT
29097634 AAAA
1 AAAA
29097638 GAATATGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
8 4 0.15
9 22 0.85
ACGTcount: A:0.79, C:0.08, G:0.05, T:0.08
Consensus pattern (9 bp):
AAAAAACAT
Found at i:29098568 original size:6 final size:6
Alignment explanation
Indices: 29098559--29098583 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29098549 TTATCTTTCC
29098559 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
29098584 CACTGTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:29099275 original size:3 final size:3
Alignment explanation
Indices: 29099262--29099352 Score: 116
Period size: 3 Copynumber: 30.7 Consensus size: 3
29099252 TTATTTACTC
* * *
29099262 ATT ATT A-T ATT ATT -GT ATT A-T ACT ATT AGTT TTGT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT AT-T ATT ATT ATT
29099306 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
29099353 NNNNNNNNNN
Statistics
Matches: 78, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
2 5 0.06
3 69 0.88
4 4 0.05
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:29100242 original size:8 final size:8
Alignment explanation
Indices: 29100231--29100271 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
29100221 TATTTGCTTG
29100231 ATTCATTT
1 ATTCATTT
29100239 ATTCATTT
1 ATTCATTT
*
29100247 ATTTATTT
1 ATTCATTT
*
29100255 ATCCATTCT
1 ATTCATT-T
29100264 ATTCATTT
1 ATTCATTT
29100272 TCACTCAGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (8 bp):
ATTCATTT
Found at i:29102010 original size:19 final size:18
Alignment explanation
Indices: 29101969--29102011 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
29101959 GTCTCTTTTT
29101969 TGCATTCATTTCATGCATC
1 TGCATTCATTTCATGCA-C
29101988 TGCATTGCATTTCATTGCA-
1 TGCATT-CATTTCA-TGCAC
29102007 TGCAT
1 TGCAT
29102012 CAAATTTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 11 0.50
20 7 0.32
21 4 0.18
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (18 bp):
TGCATTCATTTCATGCAC
Found at i:29104637 original size:9 final size:9
Alignment explanation
Indices: 29104625--29104689 Score: 58
Period size: 9 Copynumber: 6.6 Consensus size: 9
29104615 AAAAAATTTC
29104625 AAAAAATAA
1 AAAAAATAA
*
29104634 AAAAAATCA
1 AAAAAATAA
29104643 AAAAAATCAAA
1 AAAAAAT--AA
*
29104654 AAAAAATCA
1 AAAAAATAA
29104663 AAAAAATCAAA
1 AAAAAAT--AA
29104674 AATCAAAATAA
1 AA--AAAATAA
29104685 AAAAA
1 AAAAA
29104690 TCAAAGTCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
9 26 0.57
11 15 0.33
13 5 0.11
ACGTcount: A:0.82, C:0.08, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAATAA
Found at i:29104637 original size:17 final size:17
Alignment explanation
Indices: 29104613--29104694 Score: 73
Period size: 19 Copynumber: 4.8 Consensus size: 17
29104603 GTTCAGACTC
29104613 AAAAAAAATTTCAAAAAAT
1 AAAAAAAA--TCAAAAAAT
29104632 AAAAAAAATCAAAAAAAT
1 AAAAAAAATC-AAAAAAT
29104650 CAAAAAAAAATCAAAAAA-
1 --AAAAAAAATCAAAAAAT
**
29104668 ATCAAAAATC--AAAAT
1 AAAAAAAATCAAAAAAT
29104683 -AAAAAAATCAAA
1 AAAAAAAATCAAA
29104695 GTCAAAAATA
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
14 11 0.21
16 9 0.17
17 2 0.04
18 7 0.13
19 14 0.26
20 10 0.19
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.13
Consensus pattern (17 bp):
AAAAAAAATCAAAAAAT
Found at i:29104661 original size:20 final size:20
Alignment explanation
Indices: 29104611--29104694 Score: 104
Period size: 20 Copynumber: 4.2 Consensus size: 20
29104601 GAGTTCAGAC
*
29104611 TCAAAAAAAATTTC-AAAAAA
1 TCAAAAAAAA-ATCAAAAAAA
29104631 T--AAAAAAAATCAAAAAAA
1 TCAAAAAAAAATCAAAAAAA
29104649 TCAAAAAAAAATCAAAAAAA
1 TCAAAAAAAAATCAAAAAAA
29104669 TCAAAAATCAAAAT-AAAAAAA
1 TCAAAAA--AAAATCAAAAAAA
29104690 TCAAA
1 TCAAA
29104695 GTCAAAAATA
Statistics
Matches: 58, Mismatches: 1, Indels: 9
0.85 0.01 0.13
Matches are distributed among these distances:
17 2 0.03
18 14 0.24
20 25 0.43
21 12 0.21
22 5 0.09
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (20 bp):
TCAAAAAAAAATCAAAAAAA
Found at i:29104688 original size:29 final size:29
Alignment explanation
Indices: 29104625--29104694 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
29104615 AAAAAATTTC
*
29104625 AAAAAATAAAAAAAATCAAAAAAATC-AAA
1 AAAAAATCAAAAAAATC-AAAAAATCAAAA
29104654 AAAAAATCAAAAAAATC-AAAAATCAAAATA
1 AAAAAATCAAAAAAATCAAAAAATC-AAA-A
29104684 AAAAAATCAAA
1 AAAAAATCAAA
29104695 GTCAAAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
27 7 0.19
29 18 0.49
30 12 0.32
ACGTcount: A:0.80, C:0.09, G:0.00, T:0.11
Consensus pattern (29 bp):
AAAAAATCAAAAAAATCAAAAAATCAAAA
Found at i:29104701 original size:13 final size:13
Alignment explanation
Indices: 29104644--29104703 Score: 52
Period size: 14 Copynumber: 4.5 Consensus size: 13
29104634 AAAAAATCAA
29104644 AAAAATCAAAA--
1 AAAAATCAAAATC
29104655 AAAAATCAAAAAAATC
1 AAAAATC---AAAATC
*
29104671 AAAAATCAAAATAA
1 AAAAATCAAAAT-C
*
29104685 AAAAATCAAAGTC
1 AAAAATCAAAATC
29104698 AAAAAT
1 AAAAAT
29104704 AGGAGAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
11 7 0.17
13 11 0.28
14 15 0.38
16 7 0.17
ACGTcount: A:0.75, C:0.10, G:0.02, T:0.13
Consensus pattern (13 bp):
AAAAATCAAAATC
Found at i:29104702 original size:14 final size:14
Alignment explanation
Indices: 29104636--29104694 Score: 61
Period size: 16 Copynumber: 4.2 Consensus size: 14
29104626 AAAAATAAAA
29104636 AAAATCAAAAAAATC
1 AAAAT-AAAAAAATC
29104651 --AA-AAAAAAATC
1 AAAATAAAAAAATC
*
29104662 AAAAAAATCAAAAATC
1 AAAATAA--AAAAATC
29104678 AAAATAAAAAAATC
1 AAAATAAAAAAATC
29104692 AAA
1 AAA
29104695 GTCAAAAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
11 9 0.24
13 4 0.11
14 12 0.32
16 13 0.34
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAATAAAAAAATC
Found at i:29104703 original size:27 final size:26
Alignment explanation
Indices: 29104625--29104687 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
29104615 AAAAAATTTC
*
29104625 AAAAAATA-AAAAAAATCAAAAAAATCA
1 AAAAAAAACAAAAAAATC--AAAAATCA
29104652 AAAAAAAATCAAAAAAATCAAAAATCA
1 AAAAAAAA-CAAAAAAATCAAAAATCA
29104679 AAATAAAAA
1 AAA-AAAAA
29104688 AATCAAAGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 18 0.56
28 5 0.16
29 9 0.28
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.11
Consensus pattern (26 bp):
AAAAAAAACAAAAAAATCAAAAATCA
Found at i:29104704 original size:21 final size:21
Alignment explanation
Indices: 29104635--29104703 Score: 81
Period size: 20 Copynumber: 3.3 Consensus size: 21
29104625 AAAAAATAAA
*
29104635 AAAAATCAAAAAAATCAAA-A
1 AAAAATCAAAAAAATCAAATC
29104655 AAAAATCAAAAAAATCAAAAATC
1 AAAAATCAAAAAAATC--AAATC
29104678 -AAAAT-AAAAAAATCAAAGTC
1 AAAAATCAAAAAAATCAAA-TC
29104698 AAAAAT
1 AAAAAT
29104704 AGGAGAAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
19 3 0.07
20 18 0.42
21 14 0.33
22 8 0.19
ACGTcount: A:0.75, C:0.10, G:0.01, T:0.13
Consensus pattern (21 bp):
AAAAATCAAAAAAATCAAATC
Found at i:29106847 original size:86 final size:87
Alignment explanation
Indices: 29106651--29107292 Score: 823
Period size: 87 Copynumber: 7.4 Consensus size: 87
29106641 ATGAAGTTGC
* * * * *
29106651 AGATCTTGCCTTCCTGCATTGACAGTGAAGCAGATTGAAGACACAAA-CCTTGTCTCTC-TCGGT
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCCT-TCATTGGT
* *
29106714 TG-TGATGGAGCTGGTTGAAGACAAA
63 TGCAG-TGGAGCTGGTTAAAGACAAA
*
29106739 AGATCTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAAGCCTTGCCTTCATTGGTTGC
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCATTGGTTGC
**
29106804 AGTGGAGCTGGTTAAAGA-AGC
66 AGTGGAGCTGGTTAAAGACAAA
*
29106825 AGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCATTGGTTGC
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCATTGGTTGC
*
29106890 AGTGGAGTTGGTTAAAGACAAA
66 AGTGGAGCTGGTTAAAGACAAA
* * * *
29106912 AGATCTTGCCTTCCTGCATTAATAACGAAGCAGATCGAAAAAAAAGTCTTGCCTTCATTGGTTGC
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCATTGGTTGC
**
29106977 AGTGGAGCTGGTTAAAGA-AGC
66 AGTGGAGCTGGTTAAAGACAAA
* * *
29106998 AGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAACCTTGCCTTCATTGGTTTC
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCATTGGTTGC
29107063 AGTGGAGCTGGTTAAAGACAAA
66 AGTGGAGCTGGTTAAAGACAAA
* * * *
29107085 AGATCTTGCCTTCCTGCATTAATAACGAAGCAGATCGAAAAAAAAGTCTTGCCTTCATTGGTTGC
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCATTGGTTGC
29107150 AGTGGAGCTGGTTAAAGACAAA
66 AGTGGAGCTGGTTAAAGACAAA
* * * * **
29107172 AGATCTTGTCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACACAAA-CCTTGCCTTTC-CCGGT
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCC-TTCATTGGT
* * * *
29107235 TG-TGATAGAGCTGGTTGAAGACAAC
63 TGCAG-TGGAGCTGGTTAAAGACAAA
* *
29107260 AGATCTTGCCTTCCTACATTGACAGCGAAGCAG
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAG
29107293 GTCAAGGACA
Statistics
Matches: 489, Mismatches: 56, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
86 165 0.34
87 222 0.45
88 95 0.19
89 7 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (87 bp):
AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCATTGGTTGC
AGTGGAGCTGGTTAAAGACAAA
Found at i:29106941 original size:173 final size:173
Alignment explanation
Indices: 29106649--29107279 Score: 903
Period size: 173 Copynumber: 3.6 Consensus size: 173
29106639 CAATGAAGTT
* * * *
29106649 GCAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGATTGAAGACACAAACCTTGTCTCTCTCGGT
1 GCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAGACACAAACCTTGCCT-TCTCGGT
* * *
29106714 TGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAA
65 TGAGATGGAGCTGGTTAAAGACAAAAGATCTTGCCTTCCTGCATTAATAACGAAGCAGATCGAAA
* *
29106779 ACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAA
130 AAAAAGTCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAA
* *
29106823 GCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCCTTCATTGG
1 GCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAGACACAAA-CCTTGCCTTC-TCGG
*
29106886 TTGCAG-TGGAGTTGGTTAAAGACAAAAGATCTTGCCTTCCTGCATTAATAACGAAGCAGATCGA
64 TTG-AGATGGAGCTGGTTAAAGACAAAAGATCTTGCCTTCCTGCATTAATAACGAAGCAGATCGA
29106950 AAAAAAAGTCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAA
128 AAAAAAAGTCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAA
* * *
29106996 GCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACA-AAACCTTGCCTTCATTGGT
1 GCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAGACACAAACCTTGCCTTC-TCGG-
*
29107060 TTCAG-TGGAGCTGGTTAAAGACAAAAGATCTTGCCTTCCTGCATTAATAACGAAGCAGATCGAA
64 TTGAGATGGAGCTGGTTAAAGACAAAAGATCTTGCCTTCCTGCATTAATAACGAAGCAGATCGAA
29107124 AAAAAAGTCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGACA
129 AAAAAAGTCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGA-A
** * * * * *
29107170 AAAGATCTTGTCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACACAAACCTTGCCTTTCCCGGT
1 GCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAGACACAAACCTTGCC-TTCTCGGT
* * * * *
29107235 TGTGATAGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTACATT
65 TGAGATGGAGCTGGTTAAAGACAAAAGATCTTGCCTTCCTGCATT
29107280 GACAGCGAAG
Statistics
Matches: 417, Mismatches: 30, Indels: 19
0.89 0.06 0.04
Matches are distributed among these distances:
172 7 0.02
173 273 0.65
174 85 0.20
175 49 0.12
176 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (173 bp):
GCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAGACACAAACCTTGCCTTCTCGGTT
GAGATGGAGCTGGTTAAAGACAAAAGATCTTGCCTTCCTGCATTAATAACGAAGCAGATCGAAAA
AAAAGTCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAA
Found at i:29107213 original size:45 final size:45
Alignment explanation
Indices: 29106651--29107295 Score: 198
Period size: 43 Copynumber: 14.8 Consensus size: 45
29106641 ATGAAGTTGC
* * *
29106651 AGATCTTGCCTTCCTGCATTGACAGTGAAGCAGATTGAAGACACA
1 AGATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACAAA
* * * ** * * *
29106696 A-ACCTTGTC-TCTCT-CGGTTGTGA-TGGAGCTGGTTGAAGACAAA
1 AGATCTTGCCTTC-CTGC-ATTGACAGTGAAGCAGGTCGAAGACAAA
* ** * *
29106739 AGATCTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAAAC-AA
1 AGATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACAAA
* * * * * ** **
29106783 AG-CCTTGCCTTCATTG-GTTG-CAGTGGAGCTGGTTAAAGA-AGC
1 AGATCTTGCCTTC-CTGCATTGACAGTGAAGCAGGTCGAAGACAAA
* * * * *
29106825 AGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAAC-AA
1 AGATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACAAA
* * * * ** **
29106869 AG-CCTTGCCTTCATTG-GTTG-CAGTGGAGTTGGTTAAAGACAAA
1 AGATCTTGCCTTC-CTGCATTGACAGTGAAGCAGGTCGAAGACAAA
* * ** * *
29106912 AGATCTTGCCTTCCTGCATTAATAACGAAGCAGATCGAA-AAAAA
1 AGATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACAAA
* * * * ** **
29106956 AG-TCTTGCCTTCATTG-GTTG-CAGTGGAGCTGGTTAAAGA-AGC
1 AGATCTTGCCTTC-CTGCATTGACAGTGAAGCAGGTCGAAGACAAA
* * * * *
29106998 AGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAAC-AA
1 AGATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACAAA
* * * * * * **
29107042 A-ACCTTGCCTTCATTG-GTT-TCAGTGGAGCTGGTTAAAGACAAA
1 AGATCTTGCCTTC-CTGCATTGACAGTGAAGCAGGTCGAAGACAAA
* * ** * *
29107085 AGATCTTGCCTTCCTGCATTAATAACGAAGCAGATCGAA-AAAAA
1 AGATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACAAA
* * * * **
29107129 AG-TCTTGCCTTCATTG-GTTG-CAGTGGAGCTGGTTAAAGACAAA
1 AGATCTTGCCTTC-CTGCATTGACAGTGAAGCAGGTCGAAGACAAA
* *
29107172 AGATCTTGTCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACACA
1 AGATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACAAA
* * * ** * * *
29107217 A-ACCTTGCCTTTCCCG-GTTGTGA-T-AGAGCTGGTTGAAGACAAC
1 AGATCTTGCC-TTCCTGCATTGACAGTGA-AGCAGGTCGAAGACAAA
* *
29107260 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGGTC
1 AGATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTC
29107296 AAGGACACGA
Statistics
Matches: 403, Mismatches: 158, Indels: 78
0.63 0.25 0.12
Matches are distributed among these distances:
42 64 0.16
43 144 0.36
44 132 0.33
45 62 0.15
46 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (45 bp):
AGATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACAAA
Found at i:29107256 original size:43 final size:43
Alignment explanation
Indices: 29107208--29107345 Score: 102
Period size: 44 Copynumber: 3.2 Consensus size: 43
29107198 GAAGCAGGTC
29107208 GAAGACACAAACCTTGCCTTTCCCGGTTGTGATAGAGCTGGTT
1 GAAGACACAAACCTTGCCTTTCCCGGTTGTGATAGAGCTGGTT
* * * ** ** *
29107251 GAAGACAACAGATCTTGCC-TTCCTAC-ATTGACAGCGAAGCAGG-T
1 GAAGAC-ACAAACCTTGCCTTTCC--CGGTTGTGATAG-AGCTGGTT
* * * *
29107295 CAAGGACACGAACCTTGCCTCTCCCGGTTGTGATGGAGCTGGTT
1 GAA-GACACAAACCTTGCCTTTCCCGGTTGTGATAGAGCTGGTT
29107339 GAAGACA
1 GAAGACA
29107346 AAAGATTTTT
Statistics
Matches: 67, Mismatches: 20, Indels: 16
0.65 0.19 0.16
Matches are distributed among these distances:
43 20 0.30
44 35 0.52
45 12 0.18
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (43 bp):
GAAGACACAAACCTTGCCTTTCCCGGTTGTGATAGAGCTGGTT
Found at i:29107380 original size:88 final size:88
Alignment explanation
Indices: 29106659--29107391 Score: 322
Period size: 87 Copynumber: 8.4 Consensus size: 88
29106649 GCAGATCTTG
* * * *
29106659 CCTTCCTG-CATTGACAGTGAAGCAGATTGAAGACACAAACCTTGTCTCTCTCGGTTGTGATGGA
1 CCTTCCTGACATTGACAGTGAAGCAG-GTCAAGACACAAACCTTGCCTCTCCCGGTTGTGATGGA
* *
29106723 GCTGGTTGAAGACAAAAGATCTTG
65 GCTGGTTGAAGACAAAAGATTTTT
* ** * ** *
29106747 CCTTCCTG-CATTAACAACGAAGCAGATCGAA-A-ACAAAGCCTTGCCT-TCATTGGTTG-CAGT
1 CCTTCCTGACATTGACAGTGAAGCAGGTC-AAGACACAAA-CCTTGCCTCTC-CCGGTTGTGA-T
* ** * *
29106807 GGAGCTGGTTAAAGA-AGCAGATCTTG
62 GGAGCTGGTTGAAGACAAAAGATTTTT
* * * * ** *
29106833 CCTTCCTG-CGTTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCCT-TCATTGGTTG-CAGT
1 CCTTCCTGACATTGACAGTGAAGCAGGTC-AAGACACAAA-CCTTGCCTCTC-CCGGTTGTGA-T
* * * *
29106893 GGAGTTGGTTAAAGACAAAAGATCTTG
62 GGAGCTGGTTGAAGACAAAAGATTTTT
* * ** * * * ** *
29106920 CCTTCCTG-CATTAATAACGAAGCAGATCGAA-A-AAAAAGTCTTGCCT-TCATTGGTTG-CAGT
1 CCTTCCTGACATTGACAGTGAAGCAGGTC-AAGACACAAA-CCTTGCCTCTC-CCGGTTGTGA-T
* ** * *
29106980 GGAGCTGGTTAAAGA-AGCAGATCTTG
62 GGAGCTGGTTGAAGACAAAAGATTTTT
* * * * * ** *
29107006 CCTTCCTG-CGTTAACAGCGAAGCAGATCGAAAACA-AAACCTTGCCT-TCATTGGTT-TCAGTG
1 CCTTCCTGACATTGACAGTGAAGCAGGTC-AAGACACAAACCTTGCCTCTC-CCGGTTGTGA-TG
* * *
29107067 GAGCTGGTTAAAGACAAAAGATCTTG
63 GAGCTGGTTGAAGACAAAAGATTTTT
* * ** * * * ** *
29107093 CCTTCCTG-CATTAATAACGAAGCAGATCGAA-A-AAAAAGTCTTGCCT-TCATTGGTTG-CAGT
1 CCTTCCTGACATTGACAGTGAAGCAGGTC-AAGACACAAA-CCTTGCCTCTC-CCGGTTGTGA-T
* *
29107153 GGAGCTGGTTAAAGACAAAAGATCTTGT
62 GGAGCTGGTTGAAGACAAAAGAT-TTTT
* *
29107181 -CTTCCTG-CATTGACAGTGAAGCAGGTCGAAGACACAAACCTTGCCTTTCCCGGTTGTGATAGA
1 CCTTCCTGACATTGACAGTGAAGCAGGTC-AAGACACAAACCTTGCCTCTCCCGGTTGTGATGGA
* * *
29107244 GCTGGTTGAAGACAACAGATCTTG
65 GCTGGTTGAAGACAAAAGATTTTT
* *
29107268 CCTTCCT-ACATTGACAGCGAAGCAGGTCAAGGACACGAACCTTGCCTCTCCCGGTTGTGATGGA
1 CCTTCCTGACATTGACAGTGAAGCAGGTCAA-GACACAAACCTTGCCTCTCCCGGTTGTGATGGA
29107332 GCTGGTTGAAGACAAAAGATTTTT
65 GCTGGTTGAAGACAAAAGATTTTT
* * * * *
29107356 CCTCCCTGAGATT-ACAATGGAGCAGATCAAAGACAC
1 CCTTCCTGACATTGACAGTGAAGCAGGTC-AAGACAC
29107392 TATCATATCT
Statistics
Matches: 557, Mismatches: 66, Indels: 44
0.84 0.10 0.07
Matches are distributed among these distances:
85 1 0.00
86 165 0.30
87 220 0.39
88 158 0.28
89 13 0.02
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.25
Consensus pattern (88 bp):
CCTTCCTGACATTGACAGTGAAGCAGGTCAAGACACAAACCTTGCCTCTCCCGGTTGTGATGGAG
CTGGTTGAAGACAAAAGATTTTT
Found at i:29107659 original size:129 final size:128
Alignment explanation
Indices: 29107397--29107684 Score: 348
Period size: 129 Copynumber: 2.2 Consensus size: 128
29107387 GACACTATCA
* *
29107397 TATCTCCCTGAAG-TTACAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGT
1 TATCTCCCT-AAGATTACAGTGGAGTGGATTAAAATAAAAGATCTTATCTCTCTGAAG-TACAGC
* * * *
29107461 AGAGTAGATCGTGCCAGATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGTTAGTAATCC
64 AGAGTAGATCGCGCCAGATCTTATCTACCTAAGATTACAGCGGAACAGACTGAAGTTAGTAATCC
* * *
29107526 TATCTCTCTAAGATTACAGTGGAGTGGATTAAAATGAATGATCTTATCTCTCTGAAG-ACAGCAG
1 TATCTCCCTAAGATTACAGTGGAGTGGATTAAAATAAAAGATCTTATCTCTCTGAAGTACAGCAG
* * * * *
29107590 AGTAGATCGCGTCAGGTCTTATTTACCTGAGATTACAGTGGAACAGACTGAAGATT-GTCAGATC
66 AGTAGATCGCGCCAGATCTTATCTACCTAAGATTACAGCGGAACAGACTGAAG-TTAGT-A-ATC
*
29107654 T
128 C
* * *
29107655 TATCTCCCTGAGATTACAGCGGAGTAGATT
1 TATCTCCCTAAGATTACAGTGGAGTGGATT
29107685 GAAGCTGGTA
Statistics
Matches: 136, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
127 52 0.38
128 6 0.04
129 78 0.57
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.30
Consensus pattern (128 bp):
TATCTCCCTAAGATTACAGTGGAGTGGATTAAAATAAAAGATCTTATCTCTCTGAAGTACAGCAG
AGTAGATCGCGCCAGATCTTATCTACCTAAGATTACAGCGGAACAGACTGAAGTTAGTAATCC
Found at i:29107850 original size:175 final size:175
Alignment explanation
Indices: 29107475--29108152 Score: 1094
Period size: 175 Copynumber: 3.9 Consensus size: 175
29107465 TAGATCGTGC
* * * *
29107475 CAGATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCTCTAAGAT
1 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGAT
* **
29107540 TACAGTGGAGTGGATTAAAATGAATGATCTTATCTCTCTGAAG--ACAGCAGAGTAGATCGCGTC
66 TACAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTC
* * *
29107603 AGGTCTTATTTACCTGAGATTACAGTGGAAC-AGACTGA-AGATTGT
131 AGGTCTTATTTCCCTGAGATTACAGTGGAACAAGCCGGAGA-ATT-T
* *
29107648 CAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTGGTAATCCTATCTCCCTGAGAT
1 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGAT
29107713 TACAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTC
66 TACAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTC
29107778 AGGTCTTATTTCCCTGAGATTACAGTGGAACAAGCCGGAGAATTT
131 AGGTCTTATTTCCCTGAGATTACAGTGGAACAAGCCGGAGAATTT
* *
29107823 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTTCCTGAGAT
1 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGAT
*
29107888 TACAGTGGAGTGGATTAAAACCAATGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTC
66 TACAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTC
29107953 AGGTCTTATTTCCCTGAGATTACAGTGGAACAAGCCGGAGAATTT
131 AGGTCTTATTTCCCTGAGATTACAGTGGAACAAGCCGGAGAATTT
* *
29107998 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCTTATCTCCCTGATAT
1 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGAT
* * * ***
29108063 TACAGTGGAGCGGATTAAAACCAAGGATCTTATCCCTCTGAAGTTACAGTAGAGTAGATCGTACC
66 TACAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTC
*
29108128 AGGTCTTATCTCCCTGAGATTACAG
131 AGGTCTTATTTCCCTGAGATTACAG
29108153 CGGAGCAGAT
Statistics
Matches: 472, Mismatches: 29, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
173 99 0.21
175 364 0.77
176 8 0.02
177 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (175 bp):
CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGAT
TACAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTC
AGGTCTTATTTCCCTGAGATTACAGTGGAACAAGCCGGAGAATTT
Found at i:29108154 original size:129 final size:129
Alignment explanation
Indices: 29108002--29108290 Score: 443
Period size: 129 Copynumber: 2.2 Consensus size: 129
29107992 GAATTTCAGA
* * *
29108002 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCTTATCTCCCTGATATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGCTAGTAATCCTATCTCCCTGAGATTACA
* ** *
29108067 GTGGAGCGGATTAAAACCAAGGATCTTATCCCTCTGAAGTTACAGTAGAGTAGATCGTACCAGG
66 GTGGAGCGGATTAAAACAAAGGATCTTATCCCTCTGAAGTTACAACAGAGTAGATCGCACCAGG
29108131 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGCTAGTAATCCTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGCTAGTAATCCTATCTCCCTGAGATTACA
* * * * *
29108196 GTGGAGCGGATTAAAATAAATGATCTTATCTCTTTGAAGTTACAACAGAGTAGATCGCATCAGG
66 GTGGAGCGGATTAAAACAAAGGATCTTATCCCTCTGAAGTTACAACAGAGTAGATCGCACCAGG
* * *
29108260 TCTTATCTCTCTGAGATTACAGTGGAACAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGA
29108291 CCGAGGGATT
Statistics
Matches: 145, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
129 145 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (129 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGCTAGTAATCCTATCTCCCTGAGATTACA
GTGGAGCGGATTAAAACAAAGGATCTTATCCCTCTGAAGTTACAACAGAGTAGATCGCACCAGG
Found at i:29108202 original size:44 final size:44
Alignment explanation
Indices: 29107357--29108202 Score: 270
Period size: 44 Copynumber: 19.5 Consensus size: 44
29107347 AAGATTTTTC
* * * *
29107357 CTCCCTGAGATTACAATGGAGCAGATCAAAGAC-ACT-ATCATAT
1 CTCCCTGAGATTACAGTGGAGCAGATCGAAG-CTAGTAATCTTAT
* * ** **
29107400 CTCCCTGA-AGTTACAGTGGAGCGGAT-TAAAATAAAAGATCTTAT
1 CTCCCTGAGA-TTACAGTGGAGCAGATCGAAGCTAGTA-ATCTTAT
* * * * *
29107444 CTCTCTGA-AGTTACAGTAGAGTAGATCG-TGCCAG--ATCTTAT
1 CTCCCTGAGA-TTACAGTGGAGCAGATCGAAGCTAGTAATCTTAT
* * * * *
29107485 CTCCCTAAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTAT
1 CTCCCTGAGATTACAGTGGAGCAGATCGAAGCTAGTAATCTTAT
* * ** * ** * *
29107529 CTCTCTAAGATTACAGTGGAGTGGAT-TAAAATGAATGATCTTAT
1 CTCCCTGAGATTACAGTGGAGCAGATCGAAGCT-AGTAATCTTAT
* * ** * * *
29107573 CTCTCTGA-A-GACAGCAGAGTAGATCG-CG-TCAG--GTCTTAT
1 CTCCCTGAGATTACAGTGGAGCAGATCGAAGCT-AGTAATCTTAT
* * * * *
29107612 TTACCTGAGATTACAGTGGAACAGA-CTGAAGATTGTCAGATCTTAT
1 CTCCCTGAGATTACAGTGGAGCAGATC-GAAGCTAGT-A-ATCTTAT
* * * * *
29107658 CTCCCTGAGATTACAGCGGAGTAGATTGAAGCTGGTAATCCTAT
1 CTCCCTGAGATTACAGTGGAGCAGATCGAAGCTAGTAATCTTAT
* ** * * * *
29107702 CTCCCTGAGATTACAGTGGAGCGGATTAAAACCAATGATCTTAT
1 CTCCCTGAGATTACAGTGGAGCAGATCGAAGCTAGTAATCTTAT
* ** * * *
29107746 CTCTCTGA-AGTTACAGCAGAGTAGATCG-CG-TCAG--GTCTTAT
1 CTCCCTGAGA-TTACAGTGGAGCAGATCGAAGCT-AGTAATCTTAT
* * * * * *
29107787 TTCCCTGAGATTACAGTGGAACA-AGCCGGAG-AATTTCAGATCTTAT
1 CTCCCTGAGATTACAGTGGAGCAGA-TCGAAGCTA-GT-A-ATCTTAT
* * * *
29107833 CTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTAT
1 CTCCCTGAGATTACAGTGGAGCAGATCGAAGCTAGTAATCTTAT
* ** ** * * * *
29107877 CTTCCTGAGATTACAGTGGAGTGGATTAAAACCAATGATCTTAT
1 CTCCCTGAGATTACAGTGGAGCAGATCGAAGCTAGTAATCTTAT
* ** * * *
29107921 CTCTCTGA-AGTTACAGCAGAGTAGATCG-CG-TCAG--GTCTTAT
1 CTCCCTGAGA-TTACAGTGGAGCAGATCGAAGCT-AGTAATCTTAT
* * * * * *
29107962 TTCCCTGAGATTACAGTGGAACA-AGCCGGAG-AATTTCAGATCTTAT
1 CTCCCTGAGATTACAGTGGAGCAGA-TCGAAGCTA-GT-A-ATCTTAT
* *
29108008 CTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCTTAT
1 CTCCCTGAGATTACAGTGGAGCAGATCGAAGCTAGTAATCTTAT
* * ** * * *
29108052 CTCCCTGATATTACAGTGGAGCGGATTAAAACCAAG-GATCTTAT
1 CTCCCTGAGATTACAGTGGAGCAGA-TCGAAGCTAGTAATCTTAT
* * * * *
29108096 C-CCTCTGA-AGTTACAGTAGAGTAGATCGTA-CCAG--GTCTTAT
1 CTCC-CTGAGA-TTACAGTGGAGCAGATCGAAGCTAGTAATCTTAT
* *
29108137 CTCCCTGAGATTACAGCGGAGCAGATCGAAGCTAGTAATCCTAT
1 CTCCCTGAGATTACAGTGGAGCAGATCGAAGCTAGTAATCTTAT
29108181 CTCCCTGAGATTACAGTGGAGC
1 CTCCCTGAGATTACAGTGGAGC
29108203 GGATTAAAAT
Statistics
Matches: 573, Mismatches: 177, Indels: 105
0.67 0.21 0.12
Matches are distributed among these distances:
39 11 0.02
40 4 0.01
41 114 0.20
42 34 0.06
43 36 0.06
44 268 0.47
45 9 0.02
46 93 0.16
47 4 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
CTCCCTGAGATTACAGTGGAGCAGATCGAAGCTAGTAATCTTAT
Found at i:29109026 original size:6 final size:6
Alignment explanation
Indices: 29109017--29109041 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29109007 TTATCTTTCC
29109017 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
29109042 CACTGTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:29109734 original size:3 final size:3
Alignment explanation
Indices: 29109726--29109767 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
29109716 TTATTTTCTC
*
29109726 ATT ATT ATT A-T ATT A-T ATT -GT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
29109768 TTAATTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 5 0.15
3 29 0.85
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:29109762 original size:30 final size:28
Alignment explanation
Indices: 29109710--29109774 Score: 78
Period size: 30 Copynumber: 2.3 Consensus size: 28
29109700 TATTTTCTTT
*
29109710 TTATATTTATTTTCTCATTATTATTATA
1 TTATATTTATTTTATCATTATTATTATA
* *
29109738 TTATATTGTATTATTATTATTATTATTATT
1 TTATATT-TATT-TTATCATTATTATTATA
29109768 TTA-ATTT
1 TTATATTT
29109775 CTTGTATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 8 0.25
29 7 0.22
30 17 0.53
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (28 bp):
TTATATTTATTTTATCATTATTATTATA
Found at i:29110110 original size:8 final size:8
Alignment explanation
Indices: 29110099--29110139 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
29110089 TATTTGCTTG
29110099 ATTCATTT
1 ATTCATTT
29110107 ATTCATTT
1 ATTCATTT
*
29110115 ATTTATTT
1 ATTCATTT
*
29110123 ATCCATTCT
1 ATTCATT-T
29110132 ATTCATTT
1 ATTCATTT
29110140 TCACTCAGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (8 bp):
ATTCATTT
Found at i:29117777 original size:31 final size:31
Alignment explanation
Indices: 29117742--29117806 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
29117732 TACAAAATGA
29117742 TCACTGAACTA-TTCAAGA-TTTTTCATTTAAG
1 TCACTGAACTATTTCAA-ACTTTTT-ATTTAAG
*
29117773 TCACTGAACTATTTGAAACTTTTTATTTAAG
1 TCACTGAACTATTTCAAACTTTTTATTTAAG
29117804 TCA
1 TCA
29117807 TTAGGCCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 22 0.71
32 9 0.29
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.43
Consensus pattern (31 bp):
TCACTGAACTATTTCAAACTTTTTATTTAAG
Found at i:29118688 original size:2 final size:2
Alignment explanation
Indices: 29118681--29118720 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
29118671 GAAGAAGAAA
29118681 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
29118721 GAAAATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29126200 original size:184 final size:184
Alignment explanation
Indices: 29125849--29126216 Score: 587
Period size: 184 Copynumber: 2.0 Consensus size: 184
29125839 TTTTTAACTG
* * *
29125849 TAGACATGGATGAAATTTTTAATAGAAAAGACTAGTTCACTCTTTGATTACTGTACAAGGACAAA
1 TAGAAATGGATGAAATTTTTAATAGAAAAGACCAGTTCACGCTTTGATTACTGTACAAGGACAAA
* * * *
29125914 TTTGCCCATTTTTTGTACAAAGGCCTCTATTGTACTTTTACTAAATAAATCATAGGTTTCAGATT
66 TTTGCCCATTTTTTGTACAAAGGCCTCCATGGTAC-TTTA-TAAATAAAACATAGGTTTCAGATA
29125979 GAAAATGTTATTGGACATTTAACATTCTTGAATACTTTCATATGTCTCTTTTTTTAA
129 GAAAATGTTATTGGACATTTAACATTCTTGAATACTTTCATATGTCT-TTTTTTTAA
* *
29126036 TAGAAATGGATGAAATTTTTATTAGAAAGGACCAGTTCACGCTTTGATTTACTGTACAAGGACAA
1 TAGAAATGGATGAAATTTTTAATAGAAAAGACCAGTTCACGCTTTGA-TTACTGTACAAGGACAA
*
29126101 ATTTGCCCATTTTTTGTACAAAGGCCTCCATGGTAC-TT-TGAATAAAACATAGGTTTCAGATAG
65 ATTTGCCCATTTTTTGTACAAAGGCCTCCATGGTACTTTATAAATAAAACATAGGTTTCAGATAG
*
29126164 AAAATGTTATTGGACATTTAACATTCTTGAATACTTTCATGTGTCTTTTTTTT
130 AAAATGTTATTGGACATTTAACATTCTTGAATACTTTCATATGTCTTTTTTTT
29126217 CTTTTTTCTT
Statistics
Matches: 169, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
183 7 0.04
184 67 0.40
186 2 0.01
187 42 0.25
188 51 0.30
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (184 bp):
TAGAAATGGATGAAATTTTTAATAGAAAAGACCAGTTCACGCTTTGATTACTGTACAAGGACAAA
TTTGCCCATTTTTTGTACAAAGGCCTCCATGGTACTTTATAAATAAAACATAGGTTTCAGATAGA
AAATGTTATTGGACATTTAACATTCTTGAATACTTTCATATGTCTTTTTTTTAA
Found at i:29141106 original size:28 final size:26
Alignment explanation
Indices: 29141075--29141132 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
29141065 ACAACAAAAC
29141075 AAAGAGGCAAGTGCACACAAGTCCAGCA
1 AAAGAGG-AAGT-CACACAAGTCCAGCA
** * *
29141103 AAAGTTGAGGTTACACAAGTCCAGCA
1 AAAGAGGAAGTCACACAAGTCCAGCA
29141129 AAAG
1 AAAG
29141133 TTGAGGTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 18 0.69
27 3 0.12
28 5 0.19
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (26 bp):
AAAGAGGAAGTCACACAAGTCCAGCA
Found at i:29141118 original size:26 final size:26
Alignment explanation
Indices: 29141089--29141140 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
29141079 AGGCAAGTGC
29141089 ACACAAGTCCAGCAAAAGTTGAGGTT
1 ACACAAGTCCAGCAAAAGTTGAGGTT
29141115 ACACAAGTCCAGCAAAAGTTGAGGTT
1 ACACAAGTCCAGCAAAAGTTGAGGTT
29141141 CAAGTATTCT
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:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (26 bp):
ACACAAGTCCAGCAAAAGTTGAGGTT
Found at i:29165186 original size:22 final size:22
Alignment explanation
Indices: 29165161--29165202 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
29165151 CATCCTACAA
*
29165161 TCATTTAGAAACTATTTGTGTG
1 TCATTTAAAAACTATTTGTGTG
29165183 TCATTTAAAAACTATTTGTG
1 TCATTTAAAAACTATTTGTG
29165203 GGTGATCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (22 bp):
TCATTTAAAAACTATTTGTGTG
Found at i:29165462 original size:21 final size:20
Alignment explanation
Indices: 29165412--29165463 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
29165402 ATGTCGTCCT
* *
29165412 CTAAATAGCCCAAAATCACT
1 CTAAATATCCCAAAATCACC
*
29165432 CTAAATTATCCCCAAATCACCC
1 CTAAA-TATCCCAAAATCA-CC
29165454 CTAAATATCC
1 CTAAATATCC
29165464 ACAGAACTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 16 0.59
22 6 0.22
ACGTcount: A:0.40, C:0.35, G:0.02, T:0.23
Consensus pattern (20 bp):
CTAAATATCCCAAAATCACC
Found at i:29166007 original size:15 final size:17
Alignment explanation
Indices: 29165977--29166009 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
29165967 TATAAAAAAC
29165977 AAAAAATATATATAAAT
1 AAAAAATATATATAAAT
29165994 AAAAAATA-AT-TAAAT
1 AAAAAATATATATAAAT
29166009 A
1 A
29166010 GTATCTGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAAAATATATATAAAT
Found at i:29171293 original size:23 final size:23
Alignment explanation
Indices: 29171238--29171293 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
29171228 TTAGGAGTCA
*
29171238 AAAATATAATTTTATAATTTATT
1 AAAATATAAATTTATAATTTATT
*
29171261 AATATATAAATTTATAATTT-TAT
1 AAAATATAAATTTATAATTTAT-T
*
29171284 AAAATTTAAA
1 AAAATATAAA
29171294 GGAGCGAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 1 0.04
23 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAATATAAATTTATAATTTATT
Found at i:29181614 original size:2 final size:2
Alignment explanation
Indices: 29181607--29181659 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
29181597 AAATGATTAA
*
29181607 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC GC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
29181649 AC AC AC AC AC A
1 AC AC AC AC AC A
29181660 TATATATATA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.49, G:0.02, T:0.00
Consensus pattern (2 bp):
AC
Found at i:29183917 original size:31 final size:31
Alignment explanation
Indices: 29183882--29183947 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
29183872 CTTAACATTC
* * *
29183882 CAATAACTTAAATTAAAATTTTTGAATAGTT
1 CAATAACTTAAATGAAAATTTTTAAATAATT
29183913 CAATAACTTAAATGAAAATTTTTAAATAATT
1 CAATAACTTAAATGAAAATTTTTAAATAATT
29183944 CAAT
1 CAAT
29183948 GATCATTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (31 bp):
CAATAACTTAAATGAAAATTTTTAAATAATT
Found at i:29184633 original size:20 final size:21
Alignment explanation
Indices: 29184603--29184644 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
29184593 AAATGATAAC
* *
29184603 AGAACACAACAATAAAATAGT
1 AGAACACAACAACAAAACAGT
29184624 AGAA-ACAACAACAAAACAGT
1 AGAACACAACAACAAAACAGT
29184644 A
1 A
29184645 AAAATAGCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.64, C:0.17, G:0.10, T:0.10
Consensus pattern (21 bp):
AGAACACAACAACAAAACAGT
Found at i:29185256 original size:28 final size:29
Alignment explanation
Indices: 29185225--29185282 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
29185215 CGCTCACCTG
* * *
29185225 AAAATCAGCAATTTAACATTTTATA-ATA
1 AAAATCAACAATTCAACAATTTATATATA
*
29185253 AAAATTAACAATTCAACAATTTATATATA
1 AAAATCAACAATTCAACAATTTATATATA
29185282 A
1 A
29185283 CAAAATAGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.34
Consensus pattern (29 bp):
AAAATCAACAATTCAACAATTTATATATA
Found at i:29196995 original size:33 final size:33
Alignment explanation
Indices: 29196953--29197021 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
29196943 ATTTGTCACA
29196953 TTAGATTTTAGGAATAGCAAAAACTTAATAAAT
1 TTAGATTTTAGGAATAGCAAAAACTTAATAAAT
*
29196986 TTAGATTTTAGGAATGGCAAAAACTTAATAAAT
1 TTAGATTTTAGGAATAGCAAAAACTTAATAAAT
29197019 TTA
1 TTA
29197022 ACCGTTAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (33 bp):
TTAGATTTTAGGAATAGCAAAAACTTAATAAAT
Found at i:29201087 original size:17 final size:18
Alignment explanation
Indices: 29201055--29201093 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
29201045 ACGGTAGCTT
* *
29201055 TTTCAACCGCTAAAAAGA
1 TTTCAACAGCTAAAAAAA
29201073 TTTCAACAG-TAAAAAAA
1 TTTCAACAGCTAAAAAAA
29201090 TTTC
1 TTTC
29201094 TTATATAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (18 bp):
TTTCAACAGCTAAAAAAA
Found at i:29207102 original size:29 final size:29
Alignment explanation
Indices: 29207060--29207120 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
29207050 TTTTTACAAT
29207060 TTATGCATTTTAGTCTCTATAGAAAAAAA
1 TTATGCATTTTAGTCTCTATAGAAAAAAA
29207089 TTATGCATTTTAGTCTCTATAGAAAAAAA
1 TTATGCATTTTAGTCTCTATAGAAAAAAA
29207118 TTA
1 TTA
29207121 ATAATTGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (29 bp):
TTATGCATTTTAGTCTCTATAGAAAAAAA
Found at i:29208519 original size:32 final size:31
Alignment explanation
Indices: 29208474--29208569 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
29208464 CTTAGATAAT
29208474 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
29208505 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
29208537 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
29208568 TT
1 TT
29208570 GTAATTTGGC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:29208988 original size:29 final size:28
Alignment explanation
Indices: 29208946--29209010 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 28
29208936 CTTATTCTTT
29208946 AAAAAAAACAAAAAAAGCAAAAAAGCGCA
1 AAAAAAAAC-AAAAAAGCAAAAAAGCGCA
29208975 AAAAAAAAGC-AAAAAGCAAAAAAGCGCA
1 AAAAAAAA-CAAAAAAGCAAAAAAGCGCA
29209003 AAAAAAAA
1 AAAAAAAA
29209011 AGTTGCCTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
28 26 0.74
29 8 0.23
30 1 0.03
ACGTcount: A:0.77, C:0.12, G:0.11, T:0.00
Consensus pattern (28 bp):
AAAAAAAACAAAAAAGCAAAAAAGCGCA
Found at i:29209012 original size:29 final size:28
Alignment explanation
Indices: 29208957--29209010 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
29208947 AAAAAAACAA
29208957 AAAAAGCAAAAAAGCGCAAAAAAAAAGC
1 AAAAAGCAAAAAAGCGCAAAAAAAAAGC
29208985 AAAAAGCAAAAAAGCGCAAAAAAAAA
1 AAAAAGCAAAAAAGCGCAAAAAAAAA
29209011 AGTTGCCTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.74, C:0.13, G:0.13, T:0.00
Consensus pattern (28 bp):
AAAAAGCAAAAAAGCGCAAAAAAAAAGC
Found at i:29209590 original size:44 final size:45
Alignment explanation
Indices: 29209527--29209613 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 45
29209517 ATACCTTATT
* *
29209527 CATTATACCTTACTGCCATGACGTCTTTCATCCATGGTCTTACAC
1 CATTATACCTTACTACCATGACATCTTTCATCCATGGTCTTACAC
*
29209572 CATT-TACCTTTCTACCATGACATCTTTCATCCATGGTCTTAC
1 CATTATACCTTACTACCATGACATCTTTCATCCATGGTCTTAC
29209614 GTGTAACACC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 35 0.90
45 4 0.10
ACGTcount: A:0.22, C:0.31, G:0.09, T:0.38
Consensus pattern (45 bp):
CATTATACCTTACTACCATGACATCTTTCATCCATGGTCTTACAC
Found at i:29211053 original size:11 final size:11
Alignment explanation
Indices: 29211037--29211061 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29211027 TTCAATTCAA
29211037 ATAATCAATAT
1 ATAATCAATAT
29211048 ATAATCAATAT
1 ATAATCAATAT
29211059 ATA
1 ATA
29211062 TACCAATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATCAATAT
Found at i:29211789 original size:12 final size:13
Alignment explanation
Indices: 29211767--29211799 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
29211757 CTAATTTCTT
29211767 CTTTCTTTCTTTC
1 CTTTCTTTCTTTC
*
29211780 CTTT-TTTCTTTT
1 CTTTCTTTCTTTC
29211792 CTTTCTTT
1 CTTTCTTT
29211800 TTCTCCCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
CTTTCTTTCTTTC
Found at i:29211789 original size:16 final size:16
Alignment explanation
Indices: 29211761--29211801 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
29211751 AAAACCCTAA
*
29211761 TTTCTTCTTTC-TTTC
1 TTTCTTTTTTCTTTTC
29211776 TTTCCTTTTTTCTTTTC
1 TTT-CTTTTTTCTTTTC
29211793 TTTCTTTTT
1 TTTCTTTTT
29211802 CTCCCTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 3 0.13
16 13 0.57
17 7 0.30
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTCTTTTTTCTTTTC
Found at i:29211803 original size:10 final size:10
Alignment explanation
Indices: 29211761--29211852 Score: 51
Period size: 10 Copynumber: 8.8 Consensus size: 10
29211751 AAAACCCTAA
29211761 TTTCTTCTTTC
1 TTTCTT-TTTC
*
29211772 TTTCTTTCCTTT
1 TTTCTTT--TTC
29211784 TTTC-TTTTC
1 TTTCTTTTTC
29211793 TTTCTTTTTC
1 TTTCTTTTTC
** *
29211803 TCCCTATTTC
1 TTTCTTTTTC
* *
29211813 GTTTCTATTCTG
1 -TTTCT-TTTTC
* *
29211825 TTTCTTTCTA
1 TTTCTTTTTC
*
29211835 TTTCTTTTTG
1 TTTCTTTTTC
29211845 TTTCTTTT
1 TTTCTTTT
29211853 ATTTATTATA
Statistics
Matches: 63, Mismatches: 13, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
9 6 0.10
10 33 0.52
11 16 0.25
12 8 0.13
ACGTcount: A:0.03, C:0.22, G:0.03, T:0.72
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:29211828 original size:16 final size:16
Alignment explanation
Indices: 29211809--29211849 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
29211799 TTTCTCCCTA
29211809 TTTCGTTTCTA-TTCT
1 TTTCGTTTCTATTTCT
29211824 GTTTC-TTTCTATTTCT
1 -TTTCGTTTCTATTTCT
*
29211840 TTTTGTTTCT
1 TTTCGTTTCT
29211850 TTTATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.05, C:0.17, G:0.07, T:0.71
Consensus pattern (16 bp):
TTTCGTTTCTATTTCT
Found at i:29211829 original size:26 final size:25
Alignment explanation
Indices: 29211784--29211838 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
29211774 TCTTTCCTTT
* *
29211784 TTTCTTTTCTTTCTTTTTCTCCCTA
1 TTTCGTTTCTTTCTGTTTCTCCCTA
**
29211809 TTTCGTTTCTATTCTGTTTCTTTCTA
1 TTTCGTTTCT-TTCTGTTTCTCCCTA
29211835 TTTC
1 TTTC
29211839 TTTTTGTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.05, C:0.24, G:0.04, T:0.67
Consensus pattern (25 bp):
TTTCGTTTCTTTCTGTTTCTCCCTA
Found at i:29211832 original size:20 final size:20
Alignment explanation
Indices: 29211814--29211856 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
29211804 CCCTATTTCG
29211814 TTTCTATTCTGTTTCTTTCTA
1 TTTCT-TTCTGTTTCTTTCTA
*
29211835 TTTCTTTTTGTTTCTTT-TA
1 TTTCTTTCTGTTTCTTTCTA
29211854 TTT
1 TTT
29211857 ATTATATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 11 0.52
21 5 0.24
ACGTcount: A:0.07, C:0.14, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTCTTTCTGTTTCTTTCTA
Found at i:29216730 original size:17 final size:16
Alignment explanation
Indices: 29216706--29216776 Score: 56
Period size: 17 Copynumber: 4.2 Consensus size: 16
29216696 TCATGGTTAA
29216706 TTTT-TTTTTATAATT
1 TTTTATTTTTATAATT
*
29216721 TTTGTATTTTTGTAA-T
1 TTT-TATTTTTATAATT
*
29216737 TTTAATATTTTATAAACTT
1 TTTTAT-TTTTAT-AA-TT
*
29216756 TTTTAATTTTTAAAATT
1 TTTT-ATTTTTATAATT
29216773 TTTT
1 TTTT
29216777 TAAAAATAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
15 5 0.11
16 10 0.23
17 16 0.36
18 2 0.05
19 9 0.20
20 2 0.05
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.69
Consensus pattern (16 bp):
TTTTATTTTTATAATT
Found at i:29216765 original size:8 final size:9
Alignment explanation
Indices: 29216710--29216775 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
29216700 GGTTAATTTT
29216710 TTTTTATAA
1 TTTTTATAA
*
29216719 TTTTTGT-A
1 TTTTTATAA
*
29216727 TTTTTGTAA
1 TTTTTATAA
*
29216736 TTTTAAT-A
1 TTTTTATAA
29216744 -TTTTATAAA
1 TTTTTAT-AA
29216753 CTTTTT-TAA
1 -TTTTTATAA
*
29216762 TTTTTAAAA
1 TTTTTATAA
29216771 TTTTT
1 TTTTT
29216776 TTAAAAATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
7 5 0.11
8 14 0.30
9 22 0.48
10 1 0.02
11 4 0.09
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.67
Consensus pattern (9 bp):
TTTTTATAA
Found at i:29216776 original size:18 final size:20
Alignment explanation
Indices: 29216736--29216779 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
29216726 ATTTTTGTAA
29216736 TTTTAATATTTTATAAACTT
1 TTTTAATATTTTATAAACTT
*
29216756 TTTTAAT-TTTTA-AAATTT
1 TTTTAATATTTTATAAACTT
29216774 TTTTAA
1 TTTTAA
29216780 AAATAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.48
19 5 0.22
20 7 0.30
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTAATATTTTATAAACTT
Found at i:29217768 original size:33 final size:32
Alignment explanation
Indices: 29217674--29217779 Score: 137
Period size: 33 Copynumber: 3.3 Consensus size: 32
29217664 TTTAGTGTTC
*
29217674 TTTTT-AAAAATTAATTAAATTT--GTTTAGA
1 TTTTTAAAAAATTAATTAAATTTGGGTTTAGT
*
29217703 GTTTTAAATAAATTAATTAAATTTGGGTTTAGT
1 TTTTTAAA-AAATTAATTAAATTTGGGTTTAGT
29217736 TTTTTAAGAAAATTAATTAAATTTGGGTTTAGT
1 TTTTTAA-AAAATTAATTAAATTTGGGTTTAGT
*
29217769 TCTTTTTAAAA
1 T-TTTTAAAAA
29217780 TAAGGGTCTG
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
29 4 0.06
30 2 0.03
31 15 0.22
33 40 0.60
34 6 0.09
ACGTcount: A:0.38, C:0.01, G:0.11, T:0.50
Consensus pattern (32 bp):
TTTTTAAAAAATTAATTAAATTTGGGTTTAGT
Found at i:29217820 original size:14 final size:14
Alignment explanation
Indices: 29217801--29217840 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
29217791 TTGATTGGCT
29217801 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
29217815 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
29217829 GGAAAATGTTTT
1 GTAAAATGTTTT
29217841 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Done.