Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011221.1 Corchorus capsularis cultivar CVL-1 contig11242, whole genome shotgun sequence
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: 135932
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:788 original size:5 final size:5
Alignment explanation
Indices: 778--804 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
768 GTGTACACGG
778 GACAC GACAC GACAC GACAC GACAC GA
1 GACAC GACAC GACAC GACAC GACAC GA
805 TTAAGCCGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.37, G:0.22, T:0.00
Consensus pattern (5 bp):
GACAC
Found at i:1693 original size:44 final size:44
Alignment explanation
Indices: 1640--1723 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
1630 ATATGGTCAG
* *
1640 GATGATGCTTGATATGAATATTTGACCGCTTAATGTTGTCGGCC
1 GATGATGCTTGATATGAATATTTAACCACTTAATGTTGTCGGCC
*
1684 GATGATGCTTGATCTGAATATTTAACCACTTAATGTTGTC
1 GATGATGCTTGATATGAATATTTAACCACTTAATGTTGTC
1724 CGTTATTAGG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.38
Consensus pattern (44 bp):
GATGATGCTTGATATGAATATTTAACCACTTAATGTTGTCGGCC
Found at i:3928 original size:17 final size:18
Alignment explanation
Indices: 3888--3928 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
3878 CACCCAAAAA
*
3888 TTCGGGTCATTTTTTGGG
1 TTCGGGTCATGTTTTGGG
*
3906 TT-GGGTCA-GTTTTGGT
1 TTCGGGTCATGTTTTGGG
3922 TTCGGGT
1 TTCGGGT
3929 TGGGCGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 8 0.40
17 10 0.50
18 2 0.10
ACGTcount: A:0.05, C:0.10, G:0.37, T:0.49
Consensus pattern (18 bp):
TTCGGGTCATGTTTTGGG
Found at i:4632 original size:26 final size:26
Alignment explanation
Indices: 4590--4644 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
4580 TGGATCTTCT
*
4590 TTCAATAATTTCCCAATAACTGGGTC
1 TTCAATAATTTCCCAATAACTGGATC
* *
4616 TTCAATAA-TTCTGCAATAATTGGATC
1 TTCAATAATTTC-CCAATAACTGGATC
4642 TTC
1 TTC
4645 TTTGAAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 3 0.12
26 22 0.88
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (26 bp):
TTCAATAATTTCCCAATAACTGGATC
Found at i:4752 original size:16 final size:16
Alignment explanation
Indices: 4731--4765 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
4721 ATCTGAAATA
4731 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
4747 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
4763 CTT
1 CTT
4766 TCTGAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Found at i:5597 original size:79 final size:81
Alignment explanation
Indices: 5510--5680 Score: 253
Period size: 78 Copynumber: 2.1 Consensus size: 81
5500 ACGTAGTTCA
* *
5510 TTTTTTTTTGTGCTCTAAGTTTTGCCTAAG-TCGTCCTTTGCAGGATTTTCAACTTAGCGA-GC-
1 TTTTTTTTTTTGCTCTAACTTTTGCCTAAGCT-GTCCTTTGCAGGATTTTCAACTTAGCGAGGCA
5572 GTT-TTT-TTTCTTCTT
65 GTTCTTTCTTTCTTCTT
5587 TTTCTTTTTTTTGCTCTAACTTTTGCCTAAGCTGTCCTTTGCAGGATTTTCAACTTAGCGAGGCA
1 TTT-TTTTTTTTGCTCTAACTTTTGCCTAAGCTGTCCTTTGCAGGATTTTCAACTTAGCGAGGCA
*
5652 TTTCTTTCTTTCTTCTT
65 GTTCTTTCTTTCTTCTT
5669 TTTTTTTCTTTT
1 TTTTTTT-TTTT
5681 TTTGGTGTGC
Statistics
Matches: 84, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
77 3 0.04
78 53 0.63
79 3 0.04
80 2 0.02
81 7 0.08
82 16 0.19
ACGTcount: A:0.12, C:0.19, G:0.14, T:0.54
Consensus pattern (81 bp):
TTTTTTTTTTTGCTCTAACTTTTGCCTAAGCTGTCCTTTGCAGGATTTTCAACTTAGCGAGGCAG
TTCTTTCTTTCTTCTT
Found at i:7718 original size:26 final size:26
Alignment explanation
Indices: 7676--7730 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
7666 TGGATCTTCT
*
7676 TTCAATAATTTCCCAATAACTGGGTC
1 TTCAATAATTTCCCAATAACTGGATC
* *
7702 TTCAATAA-TTCTGCAATAATTGGATC
1 TTCAATAATTTC-CCAATAACTGGATC
7728 TTC
1 TTC
7731 TTTGAAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 3 0.12
26 22 0.88
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (26 bp):
TTCAATAATTTCCCAATAACTGGATC
Found at i:8592 original size:26 final size:26
Alignment explanation
Indices: 8550--8604 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
8540 TGGATCTTCT
*
8550 TTCAATAATTTCCCAATAACTGGGTC
1 TTCAATAATTTCCCAATAACTGGATC
* *
8576 TTCAATAA-TTCTGCAATAATTGGATC
1 TTCAATAATTTC-CCAATAACTGGATC
8602 TTC
1 TTC
8605 TTTGAAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 3 0.12
26 22 0.88
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (26 bp):
TTCAATAATTTCCCAATAACTGGATC
Found at i:8713 original size:16 final size:17
Alignment explanation
Indices: 8692--8727 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
8682 TCTGAAATAC
8692 TTCAGAGCTTTTCTG-T
1 TTCAGAGCTTTTCTGCT
8708 TTCAGAGCTTTTCTGCT
1 TTCAGAGCTTTTCTGCT
8725 TTC
1 TTC
8728 TGAATTGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.11, C:0.22, G:0.17, T:0.50
Consensus pattern (17 bp):
TTCAGAGCTTTTCTGCT
Found at i:9535 original size:28 final size:28
Alignment explanation
Indices: 9504--9557 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
9494 TAAATACCTG
9504 TCACAATTTCCTCCTACCAGAATATATA
1 TCACAATTTCCTCCTACCAGAATATATA
*
9532 TCACAGTTTCCTCCTACCAGAATATA
1 TCACAATTTCCTCCTACCAGAATATA
9558 AATACCTGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.31
Consensus pattern (28 bp):
TCACAATTTCCTCCTACCAGAATATATA
Found at i:18124 original size:16 final size:16
Alignment explanation
Indices: 18050--18187 Score: 102
Period size: 16 Copynumber: 8.6 Consensus size: 16
18040 TGGGTTATCA
* *
18050 GGTTCGGGTCATTTCG
1 GGTTCGGGTTAATTCG
* *
18066 GGTTCGGGTTTGAGTCG
1 GGTTCGGG-TTAATTCG
* *
18083 GGTTCGGGTTGGATTTG
1 GGTTCGGGTT-AATTCG
*
18100 GG-TCAGGTTAATTCG
1 GGTTCGGGTTAATTCG
*
18115 GGTTCGGGTTAATTTG
1 GGTTCGGGTTAATTCG
* * *
18131 GG-TCAGATTAATTCA
1 GGTTCGGGTTAATTCG
*
18146 GGTTCGGGTTAAATT-T
1 GGTTCGGGTT-AATTCG
* *
18162 GGATCAGGTTAATTCG
1 GGTTCGGGTTAATTCG
18178 GGTTCGGGTT
1 GGTTCGGGTT
18188 CTGTTTGGGT
Statistics
Matches: 93, Mismatches: 23, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
15 21 0.23
16 50 0.54
17 22 0.24
ACGTcount: A:0.14, C:0.11, G:0.37, T:0.38
Consensus pattern (16 bp):
GGTTCGGGTTAATTCG
Found at i:18133 original size:31 final size:32
Alignment explanation
Indices: 18080--18187 Score: 164
Period size: 32 Copynumber: 3.4 Consensus size: 32
18070 CGGGTTTGAG
**
18080 TCGGGTTCGGGTTGGATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTAAATTTGGGTCAGGTTAAT
*
18112 TCGGGTTCGGGTT-AATTTGGGTCAGATTAAT
1 TCGGGTTCGGGTTAAATTTGGGTCAGGTTAAT
* *
18143 TCAGGTTCGGGTTAAATTTGGATCAGGTTAAT
1 TCGGGTTCGGGTTAAATTTGGGTCAGGTTAAT
18175 TCGGGTTCGGGTT
1 TCGGGTTCGGGTT
18188 CTGTTTGGGT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
31 28 0.41
32 41 0.59
ACGTcount: A:0.17, C:0.10, G:0.35, T:0.38
Consensus pattern (32 bp):
TCGGGTTCGGGTTAAATTTGGGTCAGGTTAAT
Found at i:18356 original size:16 final size:16
Alignment explanation
Indices: 18343--18462 Score: 123
Period size: 16 Copynumber: 7.5 Consensus size: 16
18333 AATTTTCGAA
18343 TTCGGGTTTTTTCGGG
1 TTCGGGTTTTTTCGGG
* * *
18359 TTTGAGCTTTTTCGGG
1 TTCGGGTTTTTTCGGG
18375 TTCGGGTTTTTTCGGG
1 TTCGGGTTTTTTCGGG
* *** *
18391 TTTGAACTTTTTCAGG
1 TTCGGGTTTTTTCGGG
*
18407 TTCGTGTTTTTTCGGG
1 TTCGGGTTTTTTCGGG
* * *
18423 TTTGAGCTTTTTCGGG
1 TTCGGGTTTTTTCGGG
18439 TTCGGGTTTTTTCGGG
1 TTCGGGTTTTTTCGGG
*
18455 TTCAGGTT
1 TTCGGGTT
18463 CAGGCGGGTT
Statistics
Matches: 81, Mismatches: 23, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 81 1.00
ACGTcount: A:0.05, C:0.12, G:0.32, T:0.51
Consensus pattern (16 bp):
TTCGGGTTTTTTCGGG
Found at i:18379 original size:32 final size:32
Alignment explanation
Indices: 18343--18456 Score: 201
Period size: 32 Copynumber: 3.6 Consensus size: 32
18333 AATTTTCGAA
18343 TTCGGGTTTTTTCGGGTTTGAGCTTTTTCGGG
1 TTCGGGTTTTTTCGGGTTTGAGCTTTTTCGGG
* *
18375 TTCGGGTTTTTTCGGGTTTGAACTTTTTCAGG
1 TTCGGGTTTTTTCGGGTTTGAGCTTTTTCGGG
*
18407 TTCGTGTTTTTTCGGGTTTGAGCTTTTTCGGG
1 TTCGGGTTTTTTCGGGTTTGAGCTTTTTCGGG
18439 TTCGGGTTTTTTCGGGTT
1 TTCGGGTTTTTTCGGGTT
18457 CAGGTTCAGG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 76 1.00
ACGTcount: A:0.04, C:0.12, G:0.32, T:0.52
Consensus pattern (32 bp):
TTCGGGTTTTTTCGGGTTTGAGCTTTTTCGGG
Found at i:18535 original size:15 final size:16
Alignment explanation
Indices: 18515--18544 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18505 CGGAATCGGG
18515 TTTTCGGG-CGGGTTT
1 TTTTCGGGTCGGGTTT
18530 TTTTCGGGTCGGGTT
1 TTTTCGGGTCGGGTT
18545 CACTTTGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.00, C:0.13, G:0.40, T:0.47
Consensus pattern (16 bp):
TTTTCGGGTCGGGTTT
Found at i:24459 original size:34 final size:35
Alignment explanation
Indices: 24310--24574 Score: 272
Period size: 35 Copynumber: 7.6 Consensus size: 35
24300 TTCTTACTAA
* * *
24310 ACTTAATTACCCTGAATTAAGTCGA-TCAATGACTT
1 ACTTAATTACCCTGAATTAAGT-TACTTACTGACTT
*
24345 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTC
1 ACTTAATTACCCTGAATTAAGTT-ACTTACTGACTT
*
24380 ACTTAATTACCCTGAATTAAAGTTGA-TTACTGACTC
1 ACTTAATTACCCTGAATT-AAGTT-ACTTACTGACTT
* * * *
24416 ACTTAATTACCTTCAATTAAATTACTTA-TTACTT
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACTT
*
24450 ACTTAATTACCCTGAATTAAGTTACTTA-TTACTT
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACTT
*
24484 GCTTAATTACCCTGAATTAAGTTACTTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACTT
** * ** *
24519 GTTTAATTACACTGAATTAAACTA-TTCACTGACCT
1 ACTTAATTACCCTGAATTAAGTTACTT-ACTGACTT
* *
24554 ACTTAATTATCCTAAATTAAG
1 ACTTAATTACCCTGAATTAAG
24575 CCTTATTACT
Statistics
Matches: 200, Mismatches: 25, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
34 65 0.32
35 102 0.51
36 33 0.17
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.39
Consensus pattern (35 bp):
ACTTAATTACCCTGAATTAAGTTACTTACTGACTT
Found at i:28457 original size:36 final size:36
Alignment explanation
Indices: 28410--28702 Score: 145
Period size: 36 Copynumber: 8.2 Consensus size: 36
28400 GAGAATAAAT
* * * *
28410 CACCCTGGATCATTCCGAACTGAACTGAAGAATGAC
1 CACCCTCGATCATACCGAACTAAACTGAAGAAAGAC
* *
28446 CACCCTCGATCATACCG-ACGCAAACCGAAGAAAGAC
1 CACCCTCGATCATACCGAAC-TAAACTGAAGAAAGAC
* * * *
28482 CACCCTGGGTCA-ACTGAAATAAACTGAA-AAACGAC
1 CACCCTCGATCATACCGAACTAAACTGAAGAAA-GAC
28517 CACCCTCGATCATTA-C-AACATAAACTGAAGAAAGAC
1 CACCCTCGATCA-TACCGAAC-TAAACTGAAGAAAGAC
* * * * * * *
28553 CATCCTCGGTTA-ACTGAAATAAGCTGAAGAACGAC
1 CACCCTCGATCATACCGAACTAAACTGAAGAAAGAC
* * * * *
28588 TACCCTCGATCCTTCTGACAC-AAACTAAAGGAAA-AC
1 CACCCTCGATCATACCGA-ACTAAACTGAA-GAAAGAC
* * * * * * *
28624 CGCCCTGGGTCA-ACTGAAATGAACTGAAAAAACGAC
1 CACCCTCGATCATACCGAACTAAACTGAAGAAA-GAC
** ** *
28660 CATTCTCGATCATTTCGGACTAAACTGAAGAAAAGAC
1 CACCCTCGATCATACCGAACTAAACTGAAG-AAAGAC
28697 CACCCT
1 CACCCT
28703 TGGTCATTGG
Statistics
Matches: 183, Mismatches: 57, Indels: 33
0.67 0.21 0.12
Matches are distributed among these distances:
34 8 0.04
35 58 0.32
36 89 0.49
37 25 0.14
38 3 0.02
ACGTcount: A:0.39, C:0.28, G:0.16, T:0.17
Consensus pattern (36 bp):
CACCCTCGATCATACCGAACTAAACTGAAGAAAGAC
Found at i:28522 original size:35 final size:35
Alignment explanation
Indices: 28479--28661 Score: 115
Period size: 35 Copynumber: 5.1 Consensus size: 35
28469 ACCGAAGAAA
*
28479 GACCACCCTGGGTCAACTGAAATAAACTGAAAAAC
1 GACCACCCTCGGTCAACTGAAATAAACTGAAAAAC
*
28514 GACCACCCTCGATCATTAC--AACATAAACTGAAGAAA-
1 GACCACCCTCGGTCA--ACTGAA-ATAAACTGAA-AAAC
* * * *
28550 GACCATCCTCGGTTAACTGAAATAAGCTGAAGAAC
1 GACCACCCTCGGTCAACTGAAATAAACTGAAAAAC
* * ** * *
28585 GACTACCCTCGATCCTTCTGACACAAACT-AAAGGAA-
1 GACCACCCTCGGT-CAACTGAAATAAACTGAAA--AAC
* * * *
28621 AACCGCCCTGGGTCAACTGAAATGAACTGAAAAAAC
1 GACCACCCTCGGTCAACTGAAATAAACTG-AAAAAC
28657 GACCA
1 GACCA
28662 TTCTCGATCA
Statistics
Matches: 106, Mismatches: 29, Indels: 25
0.66 0.18 0.16
Matches are distributed among these distances:
34 4 0.04
35 48 0.45
36 44 0.42
37 10 0.09
ACGTcount: A:0.40, C:0.27, G:0.16, T:0.16
Consensus pattern (35 bp):
GACCACCCTCGGTCAACTGAAATAAACTGAAAAAC
Found at i:28527 original size:71 final size:72
Alignment explanation
Indices: 28432--28708 Score: 285
Period size: 71 Copynumber: 3.9 Consensus size: 72
28422 TTCCGAACTG
* * * *
28432 AACTGAAGAATGACCACCCTCGATCA-TACCGACGCAAACCGAAGAAAGACCACCCTGGGTCAAC
1 AACTGAAAAACGACCACCCTCGATCATTACCGACACAAACTGAAGAAAGACCACCCTGGGTCAAC
28496 TGAAATA
66 TGAAATA
* * * * *
28503 AACTGAAAAACGACCACCCTCGATCATTA-CAACATAAACTGAAGAAAGACCATCCTCGGTTAAC
1 AACTGAAAAACGACCACCCTCGATCATTACCGACACAAACTGAAGAAAGACCACCCTGGGTCAAC
28567 TGAAATA
66 TGAAATA
* * * * * * *
28574 AGCTGAAGAACGACTACCCTCGATCCTT-CTGACACAAACTAAAGGAAA-ACCGCCCTGGGTCAA
1 AACTGAAAAACGACCACCCTCGATCATTACCGACACAAACTGAA-GAAAGACCACCCTGGGTCAA
*
28637 CTGAAATG
65 CTGAAATA
** * * * *
28645 AACTGAAAAAACGACCATTCTCGATCATTTCGGAC-TAAACTGAAGAAAAGACCACCCTTGGTCA
1 AACTG-AAAAACGACCACCCTCGATCATTACCGACACAAACTGAAG-AAAGACCACCCTGGGTCA
28709 TTGGAGCATT
Statistics
Matches: 166, Mismatches: 33, Indels: 12
0.79 0.16 0.06
Matches are distributed among these distances:
71 116 0.70
72 34 0.20
73 16 0.10
ACGTcount: A:0.39, C:0.27, G:0.17, T:0.17
Consensus pattern (72 bp):
AACTGAAAAACGACCACCCTCGATCATTACCGACACAAACTGAAGAAAGACCACCCTGGGTCAAC
TGAAATA
Found at i:28642 original size:142 final size:144
Alignment explanation
Indices: 28434--28698 Score: 358
Period size: 142 Copynumber: 1.9 Consensus size: 144
28424 CCGAACTGAA
* * *
28434 CTGAAGAATGACCACCCTCGATCATACCGACGCAAACCGAAGAAAGACCACCCTGGGTCAACTGA
1 CTGAAGAACGACCACCCTCGATCATACCGACACAAACCAAAGAAAGACCACCCTGGGTCAACTGA
28499 AATAAACTG-AAAAACGACCACCCTCGATCATTAC-AACATAAACTGAAG-AAAGACCATCCTCG
66 AATAAACTGAAAAAACGACCACCCTCGATCATTACGAAC-TAAACTGAAGAAAAGACCATCCTCG
28561 GTTAACTGAAATAAG
130 GTTAACTGAAATAAG
* * * * * *
28576 CTGAAGAACGACTACCCTCGATCCTTCTGACACAAACTAAAGGAAA-ACCGCCCTGGGTCAACTG
1 CTGAAGAACGACCACCCTCGATCATACCGACACAAACCAAA-GAAAGACCACCCTGGGTCAACTG
* ** * *
28640 AAATGAACTGAAAAAACGACCATTCTCGATCATTTCGGACTAAACTGAAGAAAAGACCA
65 AAATAAACTGAAAAAACGACCACCCTCGATCATTACGAACTAAACTGAAGAAAAGACCA
28699 CCCTTGGTCA
Statistics
Matches: 105, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
142 59 0.56
143 36 0.34
144 10 0.10
ACGTcount: A:0.40, C:0.27, G:0.17, T:0.17
Consensus pattern (144 bp):
CTGAAGAACGACCACCCTCGATCATACCGACACAAACCAAAGAAAGACCACCCTGGGTCAACTGA
AATAAACTGAAAAAACGACCACCCTCGATCATTACGAACTAAACTGAAGAAAAGACCATCCTCGG
TTAACTGAAATAAG
Found at i:28952 original size:34 final size:35
Alignment explanation
Indices: 28904--28999 Score: 124
Period size: 34 Copynumber: 2.8 Consensus size: 35
28894 TTTGAAAGCA
*
28904 ACTGAAGAA-AGACCGCCCTGGGTCAATTGAAA-TT
1 ACTGAA-AAGAGACCGCCCTGGGTCAATTAAAATTT
* *
28938 ATTGAAAAGAGACCGCCCTGGATCAATTAAAATTT
1 ACTGAAAAGAGACCGCCCTGGGTCAATTAAAATTT
**
28973 ACTGAACGGAGACCGCCCTGGGTCAAT
1 ACTGAAAAGAGACCGCCCTGGGTCAAT
29000 CAACTGAATG
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
33 2 0.04
34 26 0.49
35 25 0.47
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (35 bp):
ACTGAAAAGAGACCGCCCTGGGTCAATTAAAATTT
Found at i:29997 original size:16 final size:16
Alignment explanation
Indices: 29976--30012 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
29966 GAGCTTCTTT
29976 TTTTTCTTCTTCTTCC
1 TTTTTCTTCTTCTTCC
* *
29992 TTTTTCTTTTTCTTTC
1 TTTTTCTTCTTCTTCC
30008 TTTTT
1 TTTTT
30013 TATGCACTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTCTTCTTCTTCC
Found at i:30340 original size:7 final size:6
Alignment explanation
Indices: 30325--30383 Score: 66
Period size: 6 Copynumber: 9.5 Consensus size: 6
30315 TTCCTTTTAC
* *
30325 TTTCTT TTTCAAT TTTCAT TTTCAT TTTCAT TTTCAC TTTCAT TTCATCAT
1 TTTCAT TTTC-AT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TT--TCAT
30376 TTTC-T TTT
1 TTTCAT TTT
30384 TTTTTTCGCT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
5 4 0.09
6 32 0.68
7 5 0.11
8 6 0.13
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.66
Consensus pattern (6 bp):
TTTCAT
Found at i:30340 original size:18 final size:18
Alignment explanation
Indices: 30313--30379 Score: 73
Period size: 18 Copynumber: 3.6 Consensus size: 18
30303 ATACCTTCGT
* *
30313 TTTTCCTTTT-ACTTTCT
1 TTTTCATTTTCACTTTCA
*
30330 TTTTCAATTTTCATTTTCA
1 TTTTC-ATTTTCACTTTCA
30349 TTTTCATTTTCACTTTCA
1 TTTTCATTTTCACTTTCA
30367 TTTCATCATTTTC
1 TTT--TCATTTTC
30380 TTTTTTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
17 5 0.12
18 19 0.45
19 10 0.24
20 8 0.19
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTCATTTTCACTTTCA
Found at i:30747 original size:14 final size:14
Alignment explanation
Indices: 30711--30747 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
30701 TGAAAACAAA
30711 TTTTTGAAATCATT
1 TTTTTGAAATCATT
**
30725 TTTGAGAAATCATT
1 TTTTTGAAATCATT
30739 TTTTTGAAA
1 TTTTTGAAA
30748 AATCTTTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (14 bp):
TTTTTGAAATCATT
Found at i:31111 original size:2 final size:2
Alignment explanation
Indices: 31104--31136 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
31094 GAACAGCAGA
31104 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31137 CAAAAAGCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44797 original size:183 final size:183
Alignment explanation
Indices: 44463--44872 Score: 501
Period size: 183 Copynumber: 2.2 Consensus size: 183
44453 CTAAACCCCT
* * * * *
44463 TGATTTTCGGCTTAATTAA-CTAATTTTGCCTAAATCACAAAAACTCTAATTCACCAAGCAAGCT
1 TGATTTTAGGCTTAATTAATC-AATTTGGCCAAAATCACAAGAACCCTAATTCACCAAGCAAGCT
44527 AATTTGCCGCCTATATTGCAATTTTTGCAAAAAAGGGCTCGACTCATTAGGGGTAGCTTGGTTCA
65 AATTTGCCGCCTATATTGCAATTTTTGCAAAAAAGGGCTCGACTCATTAGGGGTAGCTTGGTTCA
* * * *
44592 TTAAATTGGGCTTATGTTCATGTGATAT-AGCCT-AGTTTAAAGGGTTTAACCTAC
130 TCAAATTAGGATTATATTCATGTGATATGA-CCTAAGTTTAAAGGGTTT-ACCTAC
* * * *
44646 TTATTTTAGGCTTAATTAATCAATTTGGCCAAAATCACAAGAACCCTAATTTATCAAGCTAGCTA
1 TGATTTTAGGCTTAATTAATCAATTTGGCCAAAATCACAAGAACCCTAATTCACCAAGCAAGCTA
* * *
44711 ATTTGCCGCC-A-AGTTGCAATTTTTGCAAAAAAGGGCTCGAC-CTATTAGGGTTTGCTTGATTT
66 ATTTGCCGCCTATA-TTGCAATTTTTGCAAAAAAGGGCTCGACTC-ATTAGGGGTAGCTTG-GTT
* **
44773 CATCAAATTAGGATTATATTCATGTGATATGACCTAATTTTGGAGGGTTTACCTAC
128 CATCAAATTAGGATTATATTCATGTGATATGACCTAAGTTTAAAGGGTTTACCTAC
* * *
44829 TGATTTTTGGC-TAATTTAATCAATTAGGCCGAAAATTACAAGAA
1 TGATTTTAGGCTTAA-TTAATCAATTTGGCC-AAAATCACAAGAA
44873 ATTACAAAAC
Statistics
Matches: 196, Mismatches: 23, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
181 2 0.01
182 45 0.23
183 124 0.63
184 25 0.13
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (183 bp):
TGATTTTAGGCTTAATTAATCAATTTGGCCAAAATCACAAGAACCCTAATTCACCAAGCAAGCTA
ATTTGCCGCCTATATTGCAATTTTTGCAAAAAAGGGCTCGACTCATTAGGGGTAGCTTGGTTCAT
CAAATTAGGATTATATTCATGTGATATGACCTAAGTTTAAAGGGTTTACCTAC
Found at i:51126 original size:35 final size:34
Alignment explanation
Indices: 50875--51186 Score: 322
Period size: 35 Copynumber: 8.9 Consensus size: 34
50865 TTCTTACTAA
* * *
50875 ACTTAATTACCCTGAATTAAGTCGATCAATGACTT
1 ACTTAATTACCCTGAATTAAGT-TATTACTGACTT
*
50910 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTT-ATTACTGACTT
* *
50945 ACTTAATTACCCTGAATTAAATTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTT-ATTACTGACTT
*
50980 ACTTAATTACCCTGAATTAAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATT-AAGTT-ATTACTGACTT
* *
51016 ACTTAATTACCCTGAATTAAATTACTTA-TTACTT
1 ACTTAATTACCCTGAATTAAGTTA-TTACTGACTT
* * *
51050 ACTTAATTGCCCCGAATTAAGTTACTTA-TTACTT
1 ACTTAATTACCCTGAATTAAGTTA-TTACTGACTT
*
51084 GCTTAATTACCCTGAATTAAGTTACTTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTA-TTACTGACTT
** * ** *
51119 GTTTAATTACACTGAATTAAACTATTCACTGACCT
1 ACTTAATTACCCTGAATTAAGTTATT-ACTGACTT
* *
51154 ACTTAATTATCCTAAATTAAGCCTTATTACTGA
1 ACTTAATTACCCTGAATTAAG--TTATTACTGA
51187 TTCATCTTTT
Statistics
Matches: 242, Mismatches: 28, Indels: 13
0.86 0.10 0.05
Matches are distributed among these distances:
34 63 0.26
35 136 0.56
36 39 0.16
37 4 0.02
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (34 bp):
ACTTAATTACCCTGAATTAAGTTATTACTGACTT
Found at i:56628 original size:2 final size:2
Alignment explanation
Indices: 56623--56647 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56613 GGTTTTTTTC
56623 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
56648 GTTTAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58039 original size:12 final size:12
Alignment explanation
Indices: 58024--58049 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
58014 GCAAAAAGAC
58024 AAAAAAAAATCA
1 AAAAAAAAATCA
58036 AAAAAAAAATCA
1 AAAAAAAAATCA
58048 AA
1 AA
58050 TCTTCAGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.08, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAAAAAAATCA
Found at i:59851 original size:49 final size:49
Alignment explanation
Indices: 59778--59907 Score: 156
Period size: 49 Copynumber: 2.6 Consensus size: 49
59768 CAGTGTGATT
* *
59778 GAAGAAAATTAAGATAAGTAAATCTTAATTCAGCAAAAT-TAGGGAAAATA
1 GAAG-AAATTAAGAGAAGTAAATCTTAATTCAGCAAAATGAAGGG-AAATA
** * *
59828 GAAGAAATTAAGAGAAGTAAATCTTAATTCAGTGAAATGAATGGACATA
1 GAAGAAATTAAGAGAAGTAAATCTTAATTCAGCAAAATGAAGGGAAATA
*
59877 -AAGGAAATTAAGAGAAGTGAATCTTAATTCA
1 GAA-GAAATTAAGAGAAGTAAATCTTAATTCA
59908 ATGAAATTAA
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
48 2 0.03
49 62 0.87
50 7 0.10
ACGTcount: A:0.51, C:0.06, G:0.18, T:0.25
Consensus pattern (49 bp):
GAAGAAATTAAGAGAAGTAAATCTTAATTCAGCAAAATGAAGGGAAATA
Found at i:61133 original size:36 final size:36
Alignment explanation
Indices: 61082--61220 Score: 165
Period size: 36 Copynumber: 3.8 Consensus size: 36
61072 TAAGTAAAAA
* * *
61082 AAAGAAAAGATTGGCTTAGTTTCAAGGAAACTAGGT
1 AAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGT
*
61118 AAAGAAAAGACTGGCTTAATTTCAAGGAAATTAAGT
1 AAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGT
*
61154 -AA-AAAAGACTAGCTTAATTTCAAGAAAGGAAATTAGGT
1 AAAGAAAAGACTGGCTTAATTTC----AAGGAAATTAGGT
* *
61192 AAAGAAAAGATTGGCTTAATTTCGAGGAA
1 AAAGAAAAGACTGGCTTAATTTCAAGGAA
61221 GCAAAGACTT
Statistics
Matches: 88, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
34 18 0.20
35 2 0.02
36 37 0.42
38 12 0.14
39 2 0.02
40 17 0.19
ACGTcount: A:0.46, C:0.08, G:0.22, T:0.24
Consensus pattern (36 bp):
AAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGT
Found at i:61267 original size:36 final size:36
Alignment explanation
Indices: 61220--61347 Score: 143
Period size: 36 Copynumber: 3.5 Consensus size: 36
61210 ATTTCGAGGA
* *
61220 AGCAAAGACTTAATTTCGCAAGAATTAAGTAAAATT
1 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATC
*
61256 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAGTC
1 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATC
* * *
61292 AGCAAAGATTTAA-TCCA-AAGATGATTAAGTAATATC
1 AGCAAAGACTTAATTTCACAAGA--ATTAAGTAAAATC
*
61328 AGACAAAGGGCTTAATTTCA
1 AG-CAAA-GACTTAATTTCA
61348 AGGAAATTAG
Statistics
Matches: 77, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
34 4 0.05
35 3 0.04
36 58 0.75
37 4 0.05
38 5 0.06
39 3 0.04
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (36 bp):
AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATC
Found at i:61407 original size:47 final size:47
Alignment explanation
Indices: 61338--61466 Score: 240
Period size: 47 Copynumber: 2.7 Consensus size: 47
61328 AGACAAAGGG
61338 CTTAATTTCAAGGAAATTAGGCAAAAGAAGACTGAAAGACTGACTGA
1 CTTAATTTCAAGGAAATTAGGCAAAAGAAGACTGAAAGACTGACTGA
61385 CTTAATTTCAAGGAAATTAGGCAAAAGAAGACTGAAAGACTGACTGA
1 CTTAATTTCAAGGAAATTAGGCAAAAGAAGACTGAAAGACTGACTGA
*
61432 CTTAATTTCAAGGAAATTAGGTAAAAAGAAGACTG
1 CTTAATTTCAAGGAAATTAGG-CAAAAGAAGACTG
61467 GCTTAATTTC
Statistics
Matches: 80, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
47 68 0.85
48 12 0.15
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (47 bp):
CTTAATTTCAAGGAAATTAGGCAAAAGAAGACTGAAAGACTGACTGA
Found at i:61472 original size:36 final size:36
Alignment explanation
Indices: 61426--61607 Score: 248
Period size: 36 Copynumber: 5.1 Consensus size: 36
61416 CTGAAAGACT
*
61426 GACTGACTTAATTTCAAGGAAATTAGGTAAAAAGAA
1 GACTGGCTTAATTTCAAGGAAATTAGGTAAAAAGAA
61462 GACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA-AA
1 GACTGGCTTAATTTCAAGGAAATTAGGTAAA-AAGAA
61498 GACTGGCTTAATTTCAAGGAAATTAGGT--AAAGATA
1 GACTGGCTTAATTTCAAGGAAATTAGGTAAAAAGA-A
* * *
61533 GACTGGC-TAGTTTCAAGGAAACTAGGTAAAGA-AA
1 GACTGGCTTAATTTCAAGGAAATTAGGTAAAAAGAA
* *
61567 GACTAGCTTAATTTCAAGGAAATTAAGTAAAAAGACA
1 GACTGGCTTAATTTCAAGGAAATTAGGTAAAAAGA-A
61604 GACT
1 GACT
61608 TAATTTCAAA
Statistics
Matches: 129, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
33 2 0.02
34 27 0.21
35 30 0.23
36 63 0.49
37 7 0.05
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (36 bp):
GACTGGCTTAATTTCAAGGAAATTAGGTAAAAAGAA
Found at i:61597 original size:69 final size:70
Alignment explanation
Indices: 61432--61621 Score: 269
Period size: 69 Copynumber: 2.7 Consensus size: 70
61422 GACTGACTGA
*
61432 CTTAATTTCAAGGAAATTAGGTAAAAAGAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAAA
1 CTTAATTTCAAGGAAATTAGGT--AAAGAAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAAA
*
61497 AGACTGG
64 AGACTAG
*
61504 CTTAATTTCAAGGAAATTAGGTAAAGATAGACTGGC-TAGTTTCAAGGAAACTAGGTAAAG-AAA
1 CTTAATTTCAAGGAAATTAGGTAAAGA-AGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAAAA
61567 GACTAG
65 GACTAG
* * * *
61573 CTTAATTTCAAGGAAATTAAGTAAA-AAGACAGACTTAATTTCAAAGAAA
1 CTTAATTTCAAGGAAATTAGGTAAAGAAGACTGGCTTAATTTCAAGGAAA
61622 GAAATTAATT
Statistics
Matches: 108, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
67 6 0.06
68 13 0.12
69 32 0.30
70 27 0.25
71 8 0.07
72 22 0.20
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.25
Consensus pattern (70 bp):
CTTAATTTCAAGGAAATTAGGTAAAGAAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAAAAG
ACTAG
Found at i:70994 original size:11 final size:11
Alignment explanation
Indices: 70959--70988 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
70949 ATAAAACAAA
*
70959 TATAAAATAAT
1 TATAAATTAAT
70970 TATAAATTAAT
1 TATAAATTAAT
70981 TATAAATT
1 TATAAATT
70989 TGTTATGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATAAATTAAT
Found at i:79941 original size:33 final size:33
Alignment explanation
Indices: 79902--79968 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
79892 CTTTGATGCA
79902 TTCTTTACCTCGCACTTCTAGTAAAAAG-CCTTC
1 TTCTTTACCTCGCACTTCTAGT-AAAAGCCCTTC
* * *
79935 TTCTTTACCTTGCTCTTCTTGTAAAAGCCCTTC
1 TTCTTTACCTCGCACTTCTAGTAAAAGCCCTTC
79968 T
1 T
79969 GCGCTCCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 5 0.17
33 25 0.83
ACGTcount: A:0.19, C:0.30, G:0.09, T:0.42
Consensus pattern (33 bp):
TTCTTTACCTCGCACTTCTAGTAAAAGCCCTTC
Found at i:85531 original size:19 final size:19
Alignment explanation
Indices: 85507--85545 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
85497 ATTACCTGAG
85507 TGGCTCTCTTTCCGTCGAT
1 TGGCTCTCTTTCCGTCGAT
85526 TGGCTCTCTTTCCGTCGAT
1 TGGCTCTCTTTCCGTCGAT
85545 T
1 T
85546 TCTCTTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.05, C:0.31, G:0.21, T:0.44
Consensus pattern (19 bp):
TGGCTCTCTTTCCGTCGAT
Found at i:85551 original size:16 final size:17
Alignment explanation
Indices: 85511--85552 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
85501 CCTGAGTGGC
85511 TCTCTTTCCGTCGATTGG
1 TCTCTTTCCGTCGATT-G
85529 CTCTCTTTCCGTCGATT-
1 -TCTCTTTCCGTCGATTG
85546 TCTCTTT
1 TCTCTTT
85553 GATTCCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.30
19 16 0.70
ACGTcount: A:0.05, C:0.31, G:0.14, T:0.50
Consensus pattern (17 bp):
TCTCTTTCCGTCGATTG
Found at i:96452 original size:15 final size:16
Alignment explanation
Indices: 96421--96453 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
96411 AATTTAAAGA
*
96421 AAAATTAAATCTAACT
1 AAAAGTAAATCTAACT
96437 AAAAGTAAAT-TAACT
1 AAAAGTAAATCTAACT
96452 AA
1 AA
96454 GAGAGCAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.61, C:0.09, G:0.03, T:0.27
Consensus pattern (16 bp):
AAAAGTAAATCTAACT
Found at i:97944 original size:20 final size:21
Alignment explanation
Indices: 97906--97944 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
97896 TAGAAAATAA
*
97906 GGTAAAAATGCATATAAAAGT
1 GGTAAAAATGCATAGAAAAGT
*
97927 GGTAAAAA-GTATAGAAAA
1 GGTAAAAATGCATAGAAAA
97945 ATAGCCATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.56, C:0.03, G:0.21, T:0.21
Consensus pattern (21 bp):
GGTAAAAATGCATAGAAAAGT
Found at i:98511 original size:26 final size:26
Alignment explanation
Indices: 98453--98635 Score: 189
Period size: 26 Copynumber: 6.9 Consensus size: 26
98443 TAAATTAGTA
98453 ATCAGTAAAAAAGAGTAAGAAAAGAGT
1 ATCAGT-AAAAAGAGTAAGAAAAGAGT
98480 CATCAGTAAAAAGAGTAAGAAACA-A-T
1 -ATCAGTAAAAAGAGTAAGAAA-AGAGT
*
98506 ATTCAGTAAAAAGAGTAAGAAAAGAGCC
1 A-TCAGTAAAAAGAGTAAGAAAAGAG-T
*
98534 ATCAGTAAGAAGAGTAAGAAACA-A-T
1 ATCAGTAAAAAGAGTAAGAAA-AGAGT
*
98559 ATTCAGTAAGAAGAGTAAGAAAAGAGT
1 A-TCAGTAAAAAGAGTAAGAAAAGAGT
*
98586 CATCAGTAAAAAGAGTAGGAAACA-A-T
1 -ATCAGTAAAAAGAGTAAGAAA-AGAGT
*
98612 ATTCACTAAAAAGAGTAAGAAAAG
1 A-TCAGTAAAAAGAGTAAGAAAAG
98636 CGCAATAGTA
Statistics
Matches: 135, Mismatches: 7, Indels: 28
0.79 0.04 0.16
Matches are distributed among these distances:
25 6 0.04
26 62 0.46
27 56 0.41
28 11 0.08
ACGTcount: A:0.56, C:0.08, G:0.20, T:0.16
Consensus pattern (26 bp):
ATCAGTAAAAAGAGTAAGAAAAGAGT
Found at i:98522 original size:53 final size:53
Alignment explanation
Indices: 98454--98635 Score: 310
Period size: 53 Copynumber: 3.4 Consensus size: 53
98444 AAATTAGTAA
98454 TCAGTAAAAAAGAGTAAGAAAAGAGTCATCAGTAAAAAGAGTAAGAAACAATAT
1 TCAGT-AAAAAGAGTAAGAAAAGAGTCATCAGTAAAAAGAGTAAGAAACAATAT
* *
98508 TCAGTAAAAAGAGTAAGAAAAGAGCCATCAGTAAGAAGAGTAAGAAACAATAT
1 TCAGTAAAAAGAGTAAGAAAAGAGTCATCAGTAAAAAGAGTAAGAAACAATAT
* *
98561 TCAGTAAGAAGAGTAAGAAAAGAGTCATCAGTAAAAAGAGTAGGAAACAATAT
1 TCAGTAAAAAGAGTAAGAAAAGAGTCATCAGTAAAAAGAGTAAGAAACAATAT
*
98614 TCACTAAAAAGAGTAAGAAAAG
1 TCAGTAAAAAGAGTAAGAAAAG
98636 CGCAATAGTA
Statistics
Matches: 120, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 115 0.96
54 5 0.04
ACGTcount: A:0.55, C:0.08, G:0.20, T:0.16
Consensus pattern (53 bp):
TCAGTAAAAAGAGTAAGAAAAGAGTCATCAGTAAAAAGAGTAAGAAACAATAT
Found at i:98671 original size:106 final size:105
Alignment explanation
Indices: 98444--98677 Score: 294
Period size: 106 Copynumber: 2.2 Consensus size: 105
98434 AATTCATAGT
*
98444 AAATTAGTAATCAGTAAAAAAGAGTAAGAAAAGAGTCATCAGTAAAAAGAGTAAGAAACAATATT
1 AAATT-GTAATCAGT-AAGAAGAGTAAGAAAAGAGTCATCAGTAAAAAGAGTAAGAAACAATATT
* * *
98509 CAGTAAAAAGAGTAAGAAAAGAGCCATCAGTAAGAAGAGTAAG
64 CACTAAAAAGAGTAAGAAAAGAGCAATCAGTAAGAACAG-AAG
*** * *
98552 AAACAATATTCAGTAAGAAGAGTAAGAAAAGAGTCATCAGTAAAAAGAGTAGGAAACAATATTCA
1 AAATTGTAATCAGTAAGAAGAGTAAGAAAAGAGTCATCAGTAAAAAGAGTAAGAAACAATATTCA
*
98617 CTAAAAAGAGTAAGAAAAGCGCAAT-AGT-AGTCAACA-AAG
66 CTAAAAAGAGTAAGAAAAGAGCAATCAGTAAG--AACAGAAG
98656 AGTAATTGTAATCAGTAAGAAG
1 A--AATTGTAATCAGTAAGAAG
98678 TCAAGTGGTG
Statistics
Matches: 108, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
104 6 0.06
105 3 0.03
106 89 0.82
107 7 0.06
108 3 0.03
ACGTcount: A:0.54, C:0.09, G:0.20, T:0.18
Consensus pattern (105 bp):
AAATTGTAATCAGTAAGAAGAGTAAGAAAAGAGTCATCAGTAAAAAGAGTAAGAAACAATATTCA
CTAAAAAGAGTAAGAAAAGAGCAATCAGTAAGAACAGAAG
Found at i:98753 original size:7 final size:7
Alignment explanation
Indices: 98741--98775 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
98731 AAGAAAAATG
98741 GTAAAGA
1 GTAAAGA
98748 GTAAAGA
1 GTAAAGA
98755 GTAAAGA
1 GTAAAGA
**
98762 GTAATCA
1 GTAAAGA
98769 GTAAAGA
1 GTAAAGA
98776 AAAGAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.54, C:0.03, G:0.26, T:0.17
Consensus pattern (7 bp):
GTAAAGA
Found at i:98760 original size:14 final size:14
Alignment explanation
Indices: 98713--98775 Score: 56
Period size: 14 Copynumber: 4.6 Consensus size: 14
98703 AATGGCAATT
*
98713 AGTAAAGAGTAATC
1 AGTAAAGAGTAAAC
* * *
98727 AGTGAAGA-AAAAT
1 AGTAAAGAGTAAAC
* *
98740 GGTAAAGAGTAAAG
1 AGTAAAGAGTAAAC
*
98754 AGTAAAGAGTAATC
1 AGTAAAGAGTAAAC
98768 AGTAAAGA
1 AGTAAAGA
98776 AAAGAAAAAA
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
13 8 0.22
14 29 0.78
ACGTcount: A:0.54, C:0.03, G:0.25, T:0.17
Consensus pattern (14 bp):
AGTAAAGAGTAAAC
Found at i:98856 original size:40 final size:40
Alignment explanation
Indices: 98811--99121 Score: 170
Period size: 40 Copynumber: 7.4 Consensus size: 40
98801 AGTAATTAGT
*
98811 AAAATGGTAAAGAGTAAAGTAAAGAG-AGATCAGTAAA-AA
1 AAAATGGTAAAGAGTAAAGTAAAAAGTA-ATCAGTAAAGAA
98850 GAAAATGGTAAAGAGTAAAGTAAAAAGTAATCAGTAAAGAA
1 -AAAATGGTAAAGAGTAAAGTAAAAAGTAATCAGTAAAGAA
* * *
98891 AAAATGGTAATCG-GTAAAG-AGTAATAGTAATTAGT-AAGAA
1 AAAATGGTAA-AGAGTAAAGTA--AAAAGTAATCAGTAAAGAA
** ** * *
98931 GTAATGGTAATCAGTAAAAAGTAAAAAGGTAATCACTGAAA-AGT
1 AAAATGGTAAAGAGT--AAAGTAAAAA-GTAATCAGT-AAAGA-A
** * *
98975 AAAATGGTAATTAGTAAAAAGTAAAGAGTAATCAGCAAAG-A
1 AAAATGGTAAAGAGT--AAAGTAAAAAGTAATCAGTAAAGAA
* **
99016 AAAATAGTAAAGAGTAATTAGTAAAGAAAAAAT-AGTAAAGAATA
1 AAAATGGTAAAGAGTAA--AGTAAA-AAGTAATCAGTAAAG-A-A
*
99060 ATCAGTAAAGAGTAAAGAGTAAAGAGTAAAAAGTAATCAGTAAAGAA
1 A--A--AATG-GTAAAGAGT-AA-AGTAAAAAGTAATCAGTAAAGAA
* *
99107 AAAATAGTAAGGAGT
1 AAAATGGTAAAGAGT
99122 GAGAAGAAAT
Statistics
Matches: 210, Mismatches: 34, Indels: 52
0.71 0.11 0.18
Matches are distributed among these distances:
39 3 0.01
40 65 0.31
41 42 0.20
42 26 0.12
43 11 0.05
44 27 0.13
45 1 0.00
46 1 0.00
47 2 0.01
48 8 0.04
49 22 0.10
50 2 0.01
ACGTcount: A:0.56, C:0.03, G:0.21, T:0.20
Consensus pattern (40 bp):
AAAATGGTAAAGAGTAAAGTAAAAAGTAATCAGTAAAGAA
Found at i:98927 original size:20 final size:20
Alignment explanation
Indices: 98875--98954 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
98865 TAAAGTAAAA
**
98875 AGTAATCAGTAAAGAAAAAAT
1 AGTAATCAGTAAAG-AGTAAT
* *
98896 GGTAATCGGTAAAGAGTAAT
1 AGTAATCAGTAAAGAGTAAT
*
98916 AGTAATTAGT-AAGAAGTAAT
1 AGTAATCAGTAAAG-AGTAAT
* *
98936 GGTAATCAGTAAAAAGTAA
1 AGTAATCAGTAAAGAGTAA
98955 AAAGGTAATC
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.06
20 30 0.64
21 14 0.30
ACGTcount: A:0.51, C:0.04, G:0.21, T:0.24
Consensus pattern (20 bp):
AGTAATCAGTAAAGAGTAAT
Found at i:99004 original size:14 final size:14
Alignment explanation
Indices: 98987--99095 Score: 89
Period size: 14 Copynumber: 7.9 Consensus size: 14
98977 AATGGTAATT
98987 AGTAAAAAGTAAAG
1 AGTAAAAAGTAAAG
** *
99001 AGTAATCAGCAAAG
1 AGTAAAAAGTAAAG
99015 A--AAAATAGTAAAG
1 AGTAAAA-AGTAAAG
**
99028 AGTAATTAGTAAAG
1 AGTAAAAAGTAAAG
*
99042 A-AAAAATAGTAAAG
1 AGTAAAA-AGTAAAG
* **
99056 AATAATCAGTAAAG
1 AGTAAAAAGTAAAG
*
99070 AGTAAAGAGTAAAG
1 AGTAAAAAGTAAAG
99084 AGTAAAAAGTAA
1 AGTAAAAAGTAA
99096 TCAGTAAAGA
Statistics
Matches: 72, Mismatches: 18, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
12 2 0.03
13 9 0.12
14 57 0.79
15 4 0.06
ACGTcount: A:0.61, C:0.03, G:0.19, T:0.17
Consensus pattern (14 bp):
AGTAAAAAGTAAAG
Found at i:99055 original size:28 final size:28
Alignment explanation
Indices: 98990--99121 Score: 133
Period size: 28 Copynumber: 4.5 Consensus size: 28
98980 GGTAATTAGT
*
98990 AAAA-AGTAAAGAGTAATCAGCAAAG-A
1 AAAATAGTAAAGAGTAATCAGTAAAGAA
*
99016 AAAATAGTAAAGAGTAATTAGTAAAGAA
1 AAAATAGTAAAGAGTAATCAGTAAAGAA
*
99044 AAAATAGTAAAGAATAATCAGTAAAGAGTAAA
1 AAAATAGTAAAGAGTAATCAGT-AA-AG--AA
* *
99076 GAGTAAAGAGTAAAAAGTAATCAGTAAAGAA
1 -A--AAATAGTAAAGAGTAATCAGTAAAGAA
*
99107 AAAATAGTAAGGAGT
1 AAAATAGTAAAGAGT
99122 GAGAAGAAAT
Statistics
Matches: 87, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
26 4 0.05
27 19 0.22
28 32 0.37
29 2 0.02
30 3 0.03
31 2 0.02
32 2 0.02
33 3 0.03
34 2 0.02
35 18 0.21
ACGTcount: A:0.60, C:0.03, G:0.20, T:0.17
Consensus pattern (28 bp):
AAAATAGTAAAGAGTAATCAGTAAAGAA
Found at i:99075 original size:7 final size:7
Alignment explanation
Indices: 98987--99105 Score: 78
Period size: 7 Copynumber: 17.1 Consensus size: 7
98977 AATGGTAATT
*
98987 AGTAAAA
1 AGTAAAG
98994 AGTAAAG
1 AGTAAAG
**
99001 AGTAATC
1 AGTAAAG
*
99008 AGCAAAG
1 AGTAAAG
* *
99015 A-AAAAT
1 AGTAAAG
99021 AGTAAAG
1 AGTAAAG
**
99028 AGTAATT
1 AGTAAAG
99035 AGTAAAG
1 AGTAAAG
** *
99042 AAAAAAT
1 AGTAAAG
99049 AGTAAAG
1 AGTAAAG
* **
99056 AATAATC
1 AGTAAAG
99063 AGTAAAG
1 AGTAAAG
99070 AGTAAAG
1 AGTAAAG
99077 AGTAAAG
1 AGTAAAG
*
99084 AGTAAAA
1 AGTAAAG
**
99091 AGTAATC
1 AGTAAAG
99098 AGTAAAG
1 AGTAAAG
99105 A
1 A
99106 AAAAATAGTA
Statistics
Matches: 80, Mismatches: 31, Indels: 2
0.71 0.27 0.02
Matches are distributed among these distances:
6 4 0.05
7 76 0.95
ACGTcount: A:0.60, C:0.03, G:0.19, T:0.18
Consensus pattern (7 bp):
AGTAAAG
Found at i:99103 original size:35 final size:35
Alignment explanation
Indices: 99035--99208 Score: 107
Period size: 35 Copynumber: 5.1 Consensus size: 35
99025 AAGAGTAATT
** *
99035 AGTAAAGAAAAAATAGTAAAGAA-TAATCAGTAAAG
1 AGTAAAGAGTAAAGAGTAAA-AAGTAATCAGTAAAG
99070 AGTAAAGAGTAAAGAGTAAAAAGTAATCAGTAAAG
1 AGTAAAGAGTAAAGAGTAAAAAGTAATCAGTAAAG
** * * * * *
99105 AAAAAATAGTAAGGAGTGAGAAGAAATCAGTAAA-
1 AGTAAAGAGTAAAGAGTAAAAAGTAATCAGTAAAG
*
99139 A-T---G-GTAAAG-GATAAAGAGTAATCAGTAAAG
1 AGTAAAGAGTAAAGAG-TAAAAAGTAATCAGTAAAG
* ** *
99169 A-AAAATG-GTAAAGAGTAAAATCTTAATCAGTAAAA
1 AGTAAA-GAGTAAAGAGTAAAA-AGTAATCAGTAAAG
99204 AGTAA
1 AGTAA
99209 TGGCAATCAG
Statistics
Matches: 106, Mismatches: 23, Indels: 19
0.72 0.16 0.13
Matches are distributed among these distances:
28 1 0.01
29 19 0.18
30 1 0.01
34 14 0.13
35 69 0.65
36 2 0.02
ACGTcount: A:0.57, C:0.03, G:0.21, T:0.18
Consensus pattern (35 bp):
AGTAAAGAGTAAAGAGTAAAAAGTAATCAGTAAAG
Found at i:99115 original size:21 final size:21
Alignment explanation
Indices: 98839--99173 Score: 80
Period size: 21 Copynumber: 15.7 Consensus size: 21
98829 GTAAAGAGAG
*
98839 ATCAGTAAA-AAGAAAATGGTA
1 ATCAGTAAAGAA-AAAATAGTA
** *
98860 AAGAGTAAAG-TAAAA-AGTA
1 ATCAGTAAAGAAAAAATAGTA
*
98879 ATCAGTAAAGAAAAAATGGTA
1 ATCAGTAAAGAAAAAATAGTA
* **
98900 ATCGGTAAAG-AGTAATAGTA
1 ATCAGTAAAGAAAAAATAGTA
* ** *
98920 ATTAGT-AAGAAGTAATGGTA
1 ATCAGTAAAGAAAAAATAGTA
98940 ATCAGTAAA-AAGTAAAA-AGGTA
1 ATCAGTAAAGAA--AAAATA-GTA
* * *
98962 ATCACTGAAA-AGTAAAATGGTA
1 ATCAGT-AAAGA-AAAAATAGTA
* * *
98984 ATTAGTAAA-AAGTAAAGAGTA
1 ATCAGTAAAGAA-AAAATAGTA
*
99005 ATCAGCAAAGAAAAATAGTAAAGAGTA
1 ATCAGTAAAGAAAAA-A-T----AGTA
*
99032 ATTAGTAAAGAAAAAATAGTA
1 ATCAGTAAAGAAAAAATAGTA
** * ** ** *
99053 AAGAATAATCAGTAAAGAGTA
1 ATCAGTAAAGAAAAAATAGTA
** ** *
99074 AAGAGTAAAGAGTAAAAAGTA
1 ATCAGTAAAGAAAAAATAGTA
99095 ATCAGTAAAGAAAAAATAGTA
1 ATCAGTAAAGAAAAAATAGTA
** * *
99116 AGGAGT-GAGAAGAAATCAGTAAA
1 ATCAGTAAAGAAAAAAT-AGT--A
* * * *
99139 AT-GGTAAAGGATAAAGAGTA
1 ATCAGTAAAGAAAAAATAGTA
99159 ATCAGTAAAGAAAAA
1 ATCAGTAAAGAAAAA
99174 TGGTAAAGAG
Statistics
Matches: 226, Mismatches: 64, Indels: 48
0.67 0.19 0.14
Matches are distributed among these distances:
19 14 0.06
20 46 0.20
21 106 0.47
22 29 0.13
23 12 0.05
25 1 0.00
26 1 0.00
27 17 0.08
ACGTcount: A:0.56, C:0.04, G:0.21, T:0.19
Consensus pattern (21 bp):
ATCAGTAAAGAAAAAATAGTA
Found at i:99250 original size:42 final size:43
Alignment explanation
Indices: 99176--99265 Score: 103
Period size: 42 Copynumber: 2.1 Consensus size: 43
99166 AAGAAAAATG
* * *
99176 GTAAAGAGTAAAATCTTAATCAGTAAAAAGTAATG-GCAATCA
1 GTAAAGAATAAAATATTAATCAGTAAAAAGTAAAGAGCAATCA
** *
99218 GTAAAGAATAAAATATTAA-CTAGTAATCAGTAAAGAGTAATCA
1 GTAAAGAATAAAATATTAATC-AGTAAAAAGTAAAGAGCAATCA
99261 GTAAA
1 GTAAA
99266 AAGTGAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
41 1 0.03
42 28 0.70
43 11 0.28
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (43 bp):
GTAAAGAATAAAATATTAATCAGTAAAAAGTAAAGAGCAATCA
Found at i:99258 original size:14 final size:14
Alignment explanation
Indices: 99239--99265 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
99229 AATATTAACT
99239 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
99253 AGTAATCAGTAAA
1 AGTAATCAGTAAA
99266 AAGTGAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (14 bp):
AGTAATCAGTAAAG
Found at i:101954 original size:14 final size:13
Alignment explanation
Indices: 101914--101957 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 13
101904 GTACTAAAAA
101914 TAATATAATATAT
1 TAATATAATATAT
101927 ATATATATATATATAT
1 -TA-ATATA-ATATAT
101943 TAATAGTAATATAT
1 TAATA-TAATATAT
101957 T
1 T
101958 TTTACCACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 12 0.44
15 9 0.33
16 6 0.22
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (13 bp):
TAATATAATATAT
Found at i:104522 original size:17 final size:17
Alignment explanation
Indices: 104502--104538 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
104492 AACAGAGGAT
*
104502 TTTGGGCAAAAGTACCA
1 TTTGGGAAAAAGTACCA
*
104519 TTTGGGAAAAAGTATCA
1 TTTGGGAAAAAGTACCA
104536 TTT
1 TTT
104539 TTTCCCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (17 bp):
TTTGGGAAAAAGTACCA
Found at i:104892 original size:29 final size:30
Alignment explanation
Indices: 104836--104893 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
104826 TTTAGGAGGC
* *
104836 AAAATGTCTAAAATTGAGAATTCGAGGGGA
1 AAAATGTCCAAAATTGAGAATTCAAGGGGA
*
104866 AAAATGTCCAAAATTGA-AATTTAAGGGG
1 AAAATGTCCAAAATTGAGAATTCAAGGGG
104894 CAACGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.45, C:0.07, G:0.24, T:0.24
Consensus pattern (30 bp):
AAAATGTCCAAAATTGAGAATTCAAGGGGA
Found at i:110980 original size:5 final size:5
Alignment explanation
Indices: 110958--111008 Score: 77
Period size: 5 Copynumber: 10.2 Consensus size: 5
110948 TCACACACAC
*
110958 ACAAA A-AAA ACAAC ACAAA ACAAA ACAAAA ACAAA ACAAA ACAAA ACAAA
1 ACAAA ACAAA ACAAA ACAAA ACAAA AC-AAA ACAAA ACAAA ACAAA ACAAA
111008 A
1 A
111009 ACATATGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
4 4 0.10
5 33 0.79
6 5 0.12
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (5 bp):
ACAAA
Found at i:110989 original size:21 final size:21
Alignment explanation
Indices: 110963--111011 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
110953 CACACACAAA
*
110963 AAAAACAACACAAAACAAAAC
1 AAAAACAAAACAAAACAAAAC
110984 AAAAACAAAACAAAACAAAAC
1 AAAAACAAAACAAAACAAAAC
111005 AAAAACA
1 AAAAACA
111012 TATGTTTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (21 bp):
AAAAACAAAACAAAACAAAAC
Found at i:111064 original size:39 final size:40
Alignment explanation
Indices: 111019--111095 Score: 138
Period size: 39 Copynumber: 1.9 Consensus size: 40
111009 ACATATGTTT
111019 ACATATACAACAAAAATGGCCTATGTCG-CCATATATACA
1 ACATATACAACAAAAATGGCCTATGTCGCCCATATATACA
*
111058 ACATATACAACAACAATGGCCTATGTCGCCCATATATA
1 ACATATACAACAAAAATGGCCTATGTCGCCCATATATA
111096 TTAAATGGCC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 27 0.75
40 9 0.25
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.23
Consensus pattern (40 bp):
ACATATACAACAAAAATGGCCTATGTCGCCCATATATACA
Found at i:111177 original size:32 final size:29
Alignment explanation
Indices: 111136--111219 Score: 105
Period size: 29 Copynumber: 2.8 Consensus size: 29
111126 ACTATTACCT
*
111136 TGGCCTATGACGCCACTCCATATATACAAAAA
1 TGGCCTATGACGCCAC-ACATATAT--AAAAA
* *
111168 TGGCCTATGATGCCACACATATATAACAA
1 TGGCCTATGACGCCACACATATATAAAAA
*
111197 TGGCCTATGGCGCCACACATATA
1 TGGCCTATGACGCCACACATATA
111220 ACAATGGCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
29 25 0.53
31 7 0.15
32 15 0.32
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (29 bp):
TGGCCTATGACGCCACACATATATAAAAA
Found at i:111199 original size:29 final size:29
Alignment explanation
Indices: 111069--111238 Score: 114
Period size: 27 Copynumber: 5.7 Consensus size: 29
111059 CATATACAAC
* *
111069 AACAATGGCCTATGTCGCC-CATATATAT
1 AACAATGGCCTATGACGCCACACATATAT
* *
111097 TA-AATGGCCTATGTCGCCACATATCATGAACTAT
1 AACAATGGCCTATGACGCCAC--A-CAT--A-TAT
* ** *
111131 TACCTTGGCCTATGACGCCACTCCATATAT
1 AACAATGGCCTATGACGCCAC-ACATATAT
* *
111161 ACAAAAATGGCCTATGATGCCACACATATAT
1 --AACAATGGCCTATGACGCCACACATATAT
*
111192 AACAATGGCCTATGGCGCCACAC--ATAT
1 AACAATGGCCTATGACGCCACACATATAT
* *
111219 AACAATGGCTTATGTCGCCA
1 AACAATGGCCTATGACGCCA
111239 AATACTTAAG
Statistics
Matches: 115, Mismatches: 17, Indels: 21
0.75 0.11 0.14
Matches are distributed among these distances:
27 38 0.33
28 2 0.02
29 20 0.17
30 4 0.03
31 10 0.09
32 16 0.14
33 4 0.03
34 6 0.05
35 15 0.13
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (29 bp):
AACAATGGCCTATGACGCCACACATATAT
Found at i:111426 original size:88 final size:87
Alignment explanation
Indices: 111308--111708 Score: 491
Period size: 88 Copynumber: 4.5 Consensus size: 87
111298 AAAAATATTT
* * * *
111308 TCATTGCCGCTAATCAAAGCGAGCTAAATATCTAAATGTTCCCTCCAAGTAGCAGAATCTTTTCT
1 TCATTGCCGCTAA-CAAAGCAAGCTCAATATCTAAATGCTCCCTCCAAGTAGTAGAATCTTTTCT
*
111373 CCTTGTAGAGGTCGAAAGCATTC
65 CCTTGTAGAGGTCGAAAGCACTC
* *
111396 TCATTGCTGCTAACAAAGGCAAGCTCAATATCTAAATGCTCCATCCAAGTAGTAGAATCTTTTCT
1 TCATTGCCGCTAACAAA-GCAAGCTCAATATCTAAATGCTCCCTCCAAGTAGTAGAATCTTTTCT
111461 CCTTGTAGAGGTCGAAAGCACTC
65 CCTTGTAGAGGTCGAAAGCACTC
* *** * *
111484 TTATTATTGCTAACAAAAGCAAGCTCAATATTTAAATGCTCCCTCCAAGTAGTAGAATATTTTCT
1 TCATTGCCGCTAAC-AAAGCAAGCTCAATATCTAAATGCTCCCTCCAAGTAGTAGAATCTTTTCT
*
111549 CCTTGTAGAGGTTGAAAGCACTC
65 CCTTGTAGAGGTCGAAAGCACTC
* * * * * *
111572 TTATTGCCGGTAATCAAAGCGAGCTTAATATCTATATGCTCCCTCCAAGTAGTTGAATCTTTTTT
1 TCATTGCCGCTAA-CAAAGCAAGCTCAATATCTAAATGCTCCCTCCAAGTAGTAGAATC--TTTT
* *
111637 CTCCTTGTAGAGGTTGAAAGCACTT
63 CTCCTTGTAGAGGTCGAAAGCACTC
* * *
111662 TCCTTGCAGCTATCAAAGCAAGCTC-ATCATCTAAATG-TCTCCTCCAA
1 TCATTGCCGCTAACAAAGCAAGCTCAAT-ATCTAAATGCTC-CCTCCAA
111709 AATTAACTTC
Statistics
Matches: 273, Mismatches: 33, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
87 4 0.01
88 204 0.75
89 29 0.11
90 36 0.13
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (87 bp):
TCATTGCCGCTAACAAAGCAAGCTCAATATCTAAATGCTCCCTCCAAGTAGTAGAATCTTTTCTC
CTTGTAGAGGTCGAAAGCACTC
Found at i:112823 original size:16 final size:15
Alignment explanation
Indices: 112784--112826 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
112774 TTCGAGCGGG
*
112784 TTTGGATTCGGATAT
1 TTTGGGTTCGGATAT
* *
112799 TTCGGGTTCGGGTATT
1 TTTGGGTTCGGATA-T
112815 TTTGGGTTCGGA
1 TTTGGGTTCGGA
112827 CTCGGATCGG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.12, C:0.09, G:0.35, T:0.44
Consensus pattern (15 bp):
TTTGGGTTCGGATAT
Found at i:120100 original size:31 final size:31
Alignment explanation
Indices: 120045--120119 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
120035 ACACCCCTGC
*
120045 TACAGGTAATA-ACCACGTGGTTACACACGT
1 TACAGGTAATACCCCACGTGGTTACACACGT
*
120075 TACAGGTAATACCCCACTTGGTTACACACGT
1 TACAGGTAATACCCCACGTGGTTACACACGT
* *
120106 TATAGGTAACACCC
1 TACAGGTAATACCC
120120 TGTAACTGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 11 0.28
31 29 0.73
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (31 bp):
TACAGGTAATACCCCACGTGGTTACACACGT
Found at i:120147 original size:16 final size:16
Alignment explanation
Indices: 120126--120183 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
120116 ACCCTGTAAC
120126 TGGTAATACATGTTGT
1 TGGTAATACATGTTGT
* *
120142 TGGTAATACCT-TATGAC
1 TGGTAATACATGT-TG-T
120159 TGGTAATACATGTTGT
1 TGGTAATACATGTTGT
120175 TGGTAATAC
1 TGGTAATAC
120184 CATATAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 1 0.03
16 21 0.60
17 12 0.34
18 1 0.03
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (16 bp):
TGGTAATACATGTTGT
Found at i:124770 original size:24 final size:22
Alignment explanation
Indices: 124723--124775 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
124713 TTCCATTTCT
124723 TTTTTTCTCTTTTCTCTTTCCC
1 TTTTTTCTCTTTTCTCTTTCCC
* *
124745 TTTTTTCTTTTTTTTCTCTTCTCC
1 TTTTTTCTCTTTTCTCT-TTC-CC
*
124769 TTCTTTC
1 TTTTTTC
124776 CTGAAACCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 15 0.58
23 3 0.12
24 8 0.31
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTTTCTCTTTTCTCTTTCCC
Done.