Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012855.1 Kokia drynarioides strain JFW-HI SEQ_127869, 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: 238010
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
Found at i:8283 original size:23 final size:20
Alignment explanation
Indices: 8237--8286 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
8227 ATGACATTAG
* *
8237 ACAATTAAATAAATTTATGC
1 ACAAATAAATAAATTTATGA
8257 ACAAATAAATAAATCTAATATGA
1 ACAAATAAATAAAT-T--TATGA
8280 ACAAATA
1 ACAAATA
8287 CTAAAAGACC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 13 0.52
21 1 0.04
23 11 0.44
ACGTcount: A:0.58, C:0.10, G:0.04, T:0.28
Consensus pattern (20 bp):
ACAAATAAATAAATTTATGA
Found at i:9585 original size:3 final size:3
Alignment explanation
Indices: 9577--9605 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
9567 AGACATTAGC
9577 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
9606 AACAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:10400 original size:49 final size:50
Alignment explanation
Indices: 10327--10537 Score: 125
Period size: 51 Copynumber: 4.2 Consensus size: 50
10317 AACTTTTTTT
* *
10327 TTAAAAAAACACTATTTTTCTTAAAAATCAAAACTTTTATTTTGAAATAG
1 TTAAAAAATCAATATTTTTCTTAAAAATCAAAACTTTTATTTTGAAATAG
* ** *
10377 TTAAAAAATCAAT-TTTTT-TT-TAAATTTAAACTTTT-TCTTTAAAAT-G
1 TTAAAAAATCAATATTTTTCTTAAAAATCAAAACTTTTAT-TTTGAAATAG
* * * * *
10423 ATTGAAAAAA--ATATTTTTATTTTTAAAAATCTAAACTTTCTTTTTTTTTAAA-A-
1 -TT-AAAAAATCA-ATATTT-TTCTTAAAAATCAAAAC--T-TTTATTTTGAAATAG
** * * * * *
10476 AAAAAAAATTAGTACTTTTCTTAAGAATCAAAACTTTTATTTCGAAATAG
1 TTAAAAAATCAATATTTTTCTTAAAAATCAAAACTTTTATTTTGAAATAG
10526 TTAAAAAATCAA
1 TTAAAAAATCAA
10538 ATCTTTGATT
Statistics
Matches: 120, Mismatches: 24, Indels: 34
0.67 0.13 0.19
Matches are distributed among these distances:
46 3 0.03
47 23 0.19
48 20 0.17
49 9 0.08
50 21 0.17
51 29 0.24
52 3 0.03
53 2 0.02
54 9 0.08
55 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.44
Consensus pattern (50 bp):
TTAAAAAATCAATATTTTTCTTAAAAATCAAAACTTTTATTTTGAAATAG
Found at i:12612 original size:69 final size:69
Alignment explanation
Indices: 12497--12760 Score: 316
Period size: 69 Copynumber: 3.8 Consensus size: 69
12487 TTTATTTTTT
* *
12497 ATATTAAGGCTCGCAGGTGAAGAA-TCGTAGCCTCCAACA-AAGTTAGCGAGAGCAAAGTTCCCA
1 ATATTAAGGCTCGCAGGTGAAGAACT-GCAGCCTCCAACACAA-TTAGCGAGAGCAAAGCTCCCA
12560 ACTATC
64 ACTATC
* * * * *
12566 ATATTAAGGCTCGCAGGTGAAGAATTGCAGCCTCTAACACAATTAGCAAGATCAAAGCTCCTAAC
1 ATATTAAGGCTCGCAGGTGAAGAACTGCAGCCTCCAACACAATTAGCGAGAGCAAAGCTCCCAAC
12631 TATC
66 TATC
* * * * ** *
12635 ATTTTAAGGCTCGCAGGTGAAGAACAGCAGCCTCCAACATAGTTAATGGGAGCAAAGCTCCCAAC
1 ATATTAAGGCTCGCAGGTGAAGAACTGCAGCCTCCAACACAATTAGCGAGAGCAAAGCTCCCAAC
**
12700 CGTC
66 TATC
* * * *
12704 ATATTAAGACTCGTAGGTGAAGAGCTGTAGCCTCCAACACAATTAGCGAGAGCAAAG
1 ATATTAAGGCTCGCAGGTGAAGAACTGCAGCCTCCAACACAATTAGCGAGAGCAAAG
12761 AGTTAAAAAC
Statistics
Matches: 162, Mismatches: 31, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
69 159 0.98
70 3 0.02
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (69 bp):
ATATTAAGGCTCGCAGGTGAAGAACTGCAGCCTCCAACACAATTAGCGAGAGCAAAGCTCCCAAC
TATC
Found at i:12748 original size:138 final size:138
Alignment explanation
Indices: 12500--12760 Score: 362
Period size: 138 Copynumber: 1.9 Consensus size: 138
12490 ATTTTTTATA
* * * *
12500 TTAAGGCTCGCAGGTGAAGAATCGTAGCCTCCAACAAAGTTAGCGAGAGCAAAGTTCCCAACTAT
1 TTAAGGCTCGCAGGTGAAGAATCGCAGCCTCCAACAAAGTTAACGAGAGCAAAGCTCCCAACCAT
* * * *
12565 CATATTAAGGCTCGCAGGTGAAGAATTGCAGCCTCTAACACAATTAGCAAGATCAAAGCTCCTAA
66 CATATTAAGACTCGCAGGTGAAGAACTGCAGCCTCCAACACAATTAGCAAGAGCAAAGCTCCTAA
12630 CTATCATT
131 CTATCATT
* * * *
12638 TTAAGGCTCGCAGGTGAAGAA-CAGCAGCCTCCAACATAGTTAATGGGAGCAAAGCTCCCAACCG
1 TTAAGGCTCGCAGGTGAAGAATC-GCAGCCTCCAACAAAGTTAACGAGAGCAAAGCTCCCAACCA
* * * *
12702 TCATATTAAGACTCGTAGGTGAAGAGCTGTAGCCTCCAACACAATTAGCGAGAGCAAAG
65 TCATATTAAGACTCGCAGGTGAAGAACTGCAGCCTCCAACACAATTAGCAAGAGCAAAG
12761 AGTTAAAAAC
Statistics
Matches: 106, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
137 1 0.01
138 105 0.99
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.20
Consensus pattern (138 bp):
TTAAGGCTCGCAGGTGAAGAATCGCAGCCTCCAACAAAGTTAACGAGAGCAAAGCTCCCAACCAT
CATATTAAGACTCGCAGGTGAAGAACTGCAGCCTCCAACACAATTAGCAAGAGCAAAGCTCCTAA
CTATCATT
Found at i:12900 original size:57 final size:56
Alignment explanation
Indices: 12788--12923 Score: 157
Period size: 57 Copynumber: 2.4 Consensus size: 56
12778 TTTTTTATTC
* * *
12788 TTTAAAATTTTCCCAAGTATAAAATAGCTTGCGGAATCACATTCCAAGCTCATTAT
1 TTTAAAATTTTCCCAAGTATAAAATAGCTCGCGGAATCACATTCCAAACTAATTAT
* * *
12844 TTTAGAAATTTTTCCAAGTATAAAATAGCTCGC-GAATTCGCATTTCAAACTAATTATT
1 TTTA-AAATTTTCCCAAGTATAAAATAGCTCGCGGAA-TCACATTCCAAACTAATTA-T
**
12902 TTTAACAATTTTCTTAAGTATA
1 TTTAA-AATTTTCCCAAGTATA
12924 CAACTACTAG
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
56 7 0.10
57 42 0.63
58 18 0.27
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (56 bp):
TTTAAAATTTTCCCAAGTATAAAATAGCTCGCGGAATCACATTCCAAACTAATTAT
Found at i:15657 original size:29 final size:28
Alignment explanation
Indices: 15601--15657 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
15591 GCTAGGCGAC
*
15601 AATGAGAGAAGAGATGAGAGAGTTGAGAG
1 AATGAGAGAAGAGATGAGAGAG-AGAGAG
15630 AATGAGAGAAGATTGATGAGAGA-AGAGA
1 AATGAGAGAAGA--GATGAGAGAGAGAGA
15658 TGATTTTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 16 0.64
31 9 0.36
ACGTcount: A:0.47, C:0.00, G:0.39, T:0.14
Consensus pattern (28 bp):
AATGAGAGAAGAGATGAGAGAGAGAGAG
Found at i:21643 original size:16 final size:16
Alignment explanation
Indices: 21622--21664 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 16
21612 GACAAGGATG
*
21622 GTAACGGTGTGCGATA
1 GTAACGGCGTGCGATA
21638 GTAACGGCAGCGTGCGATA
1 GTAAC-G--GCGTGCGATA
21657 GTAACGGC
1 GTAACGGC
21665 AGCATGCGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
16 7 0.30
17 1 0.04
18 1 0.04
19 14 0.61
ACGTcount: A:0.26, C:0.19, G:0.37, T:0.19
Consensus pattern (16 bp):
GTAACGGCGTGCGATA
Found at i:21654 original size:19 final size:19
Alignment explanation
Indices: 21630--21673 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
21620 TGGTAACGGT
21630 GTGCGATAGTAACGGCAGC
1 GTGCGATAGTAACGGCAGC
21649 GTGCGATAGTAACGGCAGC
1 GTGCGATAGTAACGGCAGC
*
21668 ATGCGA
1 GTGCGA
21674 CAATGATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.27, C:0.20, G:0.36, T:0.16
Consensus pattern (19 bp):
GTGCGATAGTAACGGCAGC
Found at i:28356 original size:17 final size:17
Alignment explanation
Indices: 28310--28367 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
28300 ATATATATGG
**
28310 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
* **
28327 AGATGCAGCGACAATAA
1 AAATGCAATGACAATAA
*
28344 AAATGCAATGACATTAA
1 AAATGCAATGACAATAA
*
28361 TAATGCA
1 AAATGCA
28368 TGGACAATTA
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.21
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:28367 original size:34 final size:34
Alignment explanation
Indices: 28310--28375 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
28300 ATATATATGG
*
28310 AAATGCAATGACAATGTAGATGCA-GCGACAATAA
1 AAATGCAATGACAATATAGATGCATG-GACAATAA
*
28344 AAATGCAATGACATTAATA-ATGCATGGACAAT
1 AAATGCAATGACAAT-ATAGATGCATGGACAAT
28376 TATACTACAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 25 0.89
35 3 0.11
ACGTcount: A:0.47, C:0.14, G:0.18, T:0.21
Consensus pattern (34 bp):
AAATGCAATGACAATATAGATGCATGGACAATAA
Found at i:31149 original size:69 final size:69
Alignment explanation
Indices: 31031--31168 Score: 258
Period size: 69 Copynumber: 2.0 Consensus size: 69
31021 GTCTCACAAG
31031 GTGCAATCCATGAGAAGGATCCAATCTATACCGTCTCAGCATCGAAACATGAAATATATTATGAA
1 GTGCAATCCATGAGAAGGATCCAATCTATACCGTCTCAGCATCGAAACATGAAATATATTATGAA
31096 TCTT
66 TCTT
* *
31100 GTGCAATCCATGAGAAGGATCCAATCTATACCGTCTCAGCATTGGAACATGAAATATATTATGAA
1 GTGCAATCCATGAGAAGGATCCAATCTATACCGTCTCAGCATCGAAACATGAAATATATTATGAA
31165 TCTT
66 TCTT
31169 CTCCAATTTT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (69 bp):
GTGCAATCCATGAGAAGGATCCAATCTATACCGTCTCAGCATCGAAACATGAAATATATTATGAA
TCTT
Found at i:54444 original size:89 final size:90
Alignment explanation
Indices: 54292--54466 Score: 264
Period size: 89 Copynumber: 2.0 Consensus size: 90
54282 AATCTGGCAT
* *
54292 ATATTTACTGCCTTATAAAAACATGGAGCCAAGTTGAGAGTGCCAAATCAATTCGTGACAATAAT
1 ATATTTACTGCCGTATAAAAACATGGAGCCAAGTTGAGAGTGCCAAACCAATTCGTGACAATAAT
* * *
54357 AAAATTATCTTCTCGATTTTACCAC
66 AAAATAATCCTCTCAATTTTACCAC
* *
54382 ATATTTACTGCCGTAT-AAAACATGGAGCCAAG-TGAAGAGTGCCAAACCGATTCGTGATAATAA
1 ATATTTACTGCCGTATAAAAACATGGAGCCAAGTTG-AGAGTGCCAAACCAATTCGTGACAATAA
54445 TAAAATAATCCTCTCAATTTTA
65 TAAAATAATCCTCTCAATTTTA
54467 ACAACTGTTC
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
88 2 0.03
89 60 0.78
90 15 0.19
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (90 bp):
ATATTTACTGCCGTATAAAAACATGGAGCCAAGTTGAGAGTGCCAAACCAATTCGTGACAATAAT
AAAATAATCCTCTCAATTTTACCAC
Found at i:55127 original size:19 final size:19
Alignment explanation
Indices: 55087--55148 Score: 65
Period size: 18 Copynumber: 3.2 Consensus size: 19
55077 TAAATACAAA
*
55087 ATTTAGAATTTTTATAAA-T
1 ATTTAGAA-TTTTAAAAATT
55106 ATTTAGAATTTTAAAAATT
1 ATTTAGAATTTTAAAAATT
*
55125 ATTT-GCATTTTATGAAAATT
1 ATTTAGAATTTTA--AAAATT
55145 ATTT
1 ATTT
55149 TGATTATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
18 15 0.39
19 13 0.34
20 10 0.26
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (19 bp):
ATTTAGAATTTTAAAAATT
Found at i:58451 original size:21 final size:21
Alignment explanation
Indices: 58427--58469 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
58417 CACTTATACA
58427 ATTTAATCCTCATACCTAATT
1 ATTTAATCCTCATACCTAATT
58448 ATTTAATCCTCATACCTAATT
1 ATTTAATCCTCATACCTAATT
58469 A
1 A
58470 AACACTACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTTAATCCTCATACCTAATT
Found at i:62831 original size:24 final size:24
Alignment explanation
Indices: 62776--62822 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
62766 TTCAGAGAAT
*
62776 TTTGTGTTTGCGTTTTAAGGGTTC
1 TTTGTTTTTGCGTTTTAAGGGTTC
* *
62800 TTTGTTTTTGGGTTTTCAGGGTT
1 TTTGTTTTTGCGTTTTAAGGGTT
62823 TTATTTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.06, C:0.06, G:0.30, T:0.57
Consensus pattern (24 bp):
TTTGTTTTTGCGTTTTAAGGGTTC
Found at i:66586 original size:29 final size:29
Alignment explanation
Indices: 66544--66606 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
66534 AGCGCGCTCA
* *
66544 TTGTTTTGTTAATGCACTTTGGTGCCACT
1 TTGTTCTGTTAATGCACTTTGGCGCCACT
66573 TTGTTCTGTTAATGCACTTTGGCGCCACT
1 TTGTTCTGTTAATGCACTTTGGCGCCACT
*
66602 ATGTT
1 TTGTT
66607 ATGCTAAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.46
Consensus pattern (29 bp):
TTGTTCTGTTAATGCACTTTGGCGCCACT
Found at i:70772 original size:21 final size:22
Alignment explanation
Indices: 70722--70781 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
70712 ATAAAAAACC
* *
70722 CAAAATATAAAAGTCCAAATATA
1 CAAAATA-AAAAGCCCAAATACA
*
70745 CATAATAAAAAGCCCAAATACA
1 CAAAATAAAAAGCCCAAATACA
*
70767 -AAAATAATAA-CCCAA
1 CAAAATAAAAAGCCCAA
70782 GGCCCAAACT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 5 0.16
21 8 0.25
22 13 0.41
23 6 0.19
ACGTcount: A:0.62, C:0.18, G:0.03, T:0.17
Consensus pattern (22 bp):
CAAAATAAAAAGCCCAAATACA
Found at i:71165 original size:3 final size:3
Alignment explanation
Indices: 71159--71193 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
71149 CTTCGAAAGA
*
71159 AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
71194 GTAAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:71751 original size:12 final size:11
Alignment explanation
Indices: 71730--71801 Score: 65
Period size: 12 Copynumber: 6.1 Consensus size: 11
71720 CCTTTGCATA
71730 TTTTTATTTAT
1 TTTTTATTTAT
71741 TTTTGTATTTAT
1 TTTT-TATTTAT
*
71753 TTTATATTTTAAT
1 TTTTTA-TTT-AT
*
71766 TTTTATATTCAT
1 TTTT-TATTTAT
71778 TTTATTATTT-T
1 TTT-TTATTTAT
71789 ATTTTTATTTAT
1 -TTTTTATTTAT
71801 T
1 T
71802 AATTATTTAC
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
11 14 0.28
12 26 0.52
13 8 0.16
14 2 0.04
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.75
Consensus pattern (11 bp):
TTTTTATTTAT
Found at i:71770 original size:19 final size:19
Alignment explanation
Indices: 71727--71798 Score: 60
Period size: 19 Copynumber: 3.9 Consensus size: 19
71717 AGTCCTTTGC
* *
71727 ATATTTT-TATTTATTTTT
1 ATATTTTATTTTTATTTTA
*
71745 GTA-TTTATTTTATATTTTA
1 ATATTTTATTTT-TATTTTA
* *
71764 AT-TTTTATATTCATTTTA
1 ATATTTTATTTTTATTTTA
*
71782 TTATTTTATTTTTATTT
1 ATATTTTATTTTTATTT
71799 ATTAATTATT
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
17 3 0.07
18 12 0.29
19 26 0.63
ACGTcount: A:0.24, C:0.01, G:0.01, T:0.74
Consensus pattern (19 bp):
ATATTTTATTTTTATTTTA
Found at i:71771 original size:14 final size:14
Alignment explanation
Indices: 71752--71830 Score: 51
Period size: 14 Copynumber: 5.8 Consensus size: 14
71742 TTTGTATTTA
71752 TTTTATATTTTAAT
1 TTTTATATTTTAAT
*
71766 TTTTATA--TTCA-
1 TTTTATATTTTAAT
71777 TTTTATTATTTT-AT
1 TTTTA-TATTTTAAT
71791 TTTTAT-TTATTAAT
1 TTTTATATT-TTAAT
* * *
71805 TATTTACATTGTGAT
1 T-TTTATATTTTAAT
*
71820 ATTTATATTTT
1 TTTTATATTTT
71831 TTGCCCCTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
11 5 0.10
12 7 0.14
13 4 0.08
14 25 0.50
15 7 0.14
16 2 0.04
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.68
Consensus pattern (14 bp):
TTTTATATTTTAAT
Found at i:71774 original size:25 final size:24
Alignment explanation
Indices: 71728--71796 Score: 88
Period size: 25 Copynumber: 2.9 Consensus size: 24
71718 GTCCTTTGCA
*
71728 TATTTT-TA-TTTATTTTTGTATT
1 TATTTTATATTTTATTTTTATATT
71750 TATTTTATATTTTAATTTTTATATT
1 TATTTTATATTTT-ATTTTTATATT
*
71775 CATTTTATTATTTTATTTTTAT
1 TATTTTA-TATTTTATTTTTAT
71797 TTATTAATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
22 6 0.15
23 2 0.05
24 3 0.07
25 24 0.59
26 6 0.15
ACGTcount: A:0.23, C:0.01, G:0.01, T:0.74
Consensus pattern (24 bp):
TATTTTATATTTTATTTTTATATT
Found at i:71787 original size:37 final size:35
Alignment explanation
Indices: 71729--71798 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 35
71719 TCCTTTGCAT
71729 ATTTTTATTTATTTTTGTA-TTTATTTTATATTTTA
1 ATTTTTATTTATTTTTGTATTTTATTTT-TATTTTA
71764 ATTTTTATATTCATTTTAT-TATTTTATTTTTATTT
1 ATTTTTAT-TT-ATTTT-TGTATTTTATTTTTATTT
71799 ATTAATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
35 8 0.26
36 2 0.06
37 12 0.39
38 9 0.29
ACGTcount: A:0.23, C:0.01, G:0.01, T:0.74
Consensus pattern (35 bp):
ATTTTTATTTATTTTTGTATTTTATTTTTATTTTA
Found at i:72109 original size:17 final size:17
Alignment explanation
Indices: 72087--72127 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
72077 ATGCACCCCT
72087 TTTATTTTTATAATTTA
1 TTTATTTTTATAATTTA
* **
72104 TTTATTTTTCTTTTTTA
1 TTTATTTTTATAATTTA
72121 TTTATTT
1 TTTATTT
72128 CATGCTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTATTTTTATAATTTA
Found at i:95309 original size:79 final size:80
Alignment explanation
Indices: 95129--95332 Score: 229
Period size: 79 Copynumber: 2.6 Consensus size: 80
95119 ATAAACTGAT
** *
95129 AATCCTAGCACCCAGTGCCTAG-AAATTAAACCGCAAAAGTGAG--CAGATCTAATTGGATTAAC
1 AATCCTAGCACCCAGTGCCTAGCGGA-TAAACCGCAAATGTGAGCCCAGATCTAATTGGATTAAC
* *
95191 TAATGAATAACTGTCA
65 TAATCAATAACCGTCA
* * * * *
95207 AGTCCTAGCACCTAGTGCCTAGCGGATAAACCGCAATTGTGAGCCCAGCTCTAGTTGGATTAAC-
1 AATCCTAGCACCCAGTGCCTAGCGGATAAACCGCAAATGTGAGCCCAGATCTAATTGGATTAACT
* *
95271 CATCAATATCCGTCA
66 AATCAATAACCGTCA
* *
95286 AATCCT-GACACCCAGTGCCTAGCGGACAAACCGCAAATGTGTGCCCA
1 AATCCTAG-CACCCAGTGCCTAGCGGATAAACCGCAAATGTGAGCCCA
95333 TCACTAGTCA
Statistics
Matches: 105, Mismatches: 17, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
78 36 0.34
79 52 0.50
80 17 0.16
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (80 bp):
AATCCTAGCACCCAGTGCCTAGCGGATAAACCGCAAATGTGAGCCCAGATCTAATTGGATTAACT
AATCAATAACCGTCA
Found at i:98080 original size:17 final size:18
Alignment explanation
Indices: 98058--98146 Score: 112
Period size: 17 Copynumber: 5.1 Consensus size: 18
98048 CCCAATTTTA
*
98058 AATTTTAAATTTTAA-TT
1 AATTTTAAATTTAAATTT
*
98075 AATTTTAAGTTT-AATTT
1 AATTTTAAATTTAAATTT
*
98092 TATTTTAAATTTAAATTT
1 AATTTTAAATTTAAATTT
*
98110 ATTTTTAAATTTAAATTT
1 AATTTTAAATTTAAATTT
*
98128 -ATTTTAAGTTTAAATTT
1 AATTTTAAATTTAAATTT
98145 AA
1 AA
98147 AATTTAAATG
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
16 2 0.03
17 38 0.61
18 22 0.35
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
AATTTTAAATTTAAATTT
Found at i:98099 original size:23 final size:22
Alignment explanation
Indices: 98051--98117 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 22
98041 CATTAAACCC
98051 AATTTTAAATTTTAAATTTTAATT
1 AATTTTAAA-TTT-AATTTTAATT
* *
98075 AATTTTAAGTTTAATTTTATTTT
1 AATTTTAAATTTAATTTTA-ATT
* *
98098 AAATTTAAATTTATTTTTAA
1 AATTTTAAATTTAATTTTAA
98118 ATTTAAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
22 7 0.19
23 21 0.58
24 8 0.22
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (22 bp):
AATTTTAAATTTAATTTTAATT
Found at i:98123 original size:35 final size:35
Alignment explanation
Indices: 98059--98155 Score: 124
Period size: 35 Copynumber: 2.8 Consensus size: 35
98049 CCAATTTTAA
* * *
98059 ATTTTAAATTTTAA-TTAATTTTAAGTTTAATTTT
1 ATTTTAAATTTAAATTTAATTTTAAATTTAAATTT
*
98093 ATTTTAAATTTAAATTTATTTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTTAATTTTAAATTTAAATTT
* *
98128 ATTTTAAGTTTAAATTTAAAATTTAAAT
1 ATTTTAAATTTAAATTT-AATTTTAAAT
98156 GTCCAAAATG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
34 13 0.24
35 33 0.61
36 8 0.15
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (35 bp):
ATTTTAAATTTAAATTTAATTTTAAATTTAAATTT
Found at i:98147 original size:6 final size:6
Alignment explanation
Indices: 98054--98155 Score: 84
Period size: 6 Copynumber: 17.2 Consensus size: 6
98044 TAAACCCAAT
* * * * *
98054 TTTAAA TTTTAAA TTTTAA -TTAAT TTTAAG TTT-AA TTTTAT TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** * *
98101 TTTAAA TTTATT TTTAAA TTTAAA TTT-AT TTTAAG TTTAAA TTTAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA
98149 TTTAAA T
1 TTTAAA T
98156 GTCCAAAATG
Statistics
Matches: 76, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
5 11 0.14
6 53 0.70
7 12 0.16
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:98802 original size:13 final size:13
Alignment explanation
Indices: 98774--98815 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
98764 CTAAGGGTTT
98774 TAATAAATAAAT-A
1 TAAT-AATAAATAA
* *
98787 TAATATTAATTAA
1 TAATAATAAATAA
98800 TAATAATAAATAA
1 TAATAATAAATAA
98813 TAA
1 TAA
98816 AAAGAAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 5 0.21
13 19 0.79
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATAATAAATAA
Found at i:99411 original size:5 final size:5
Alignment explanation
Indices: 99401--99442 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
99391 TTGACCCTAT
* * *
99401 CCGAC CCGAC CCGAC CCTAT CCGAC CCGAC CCGAT CCGAC CC
1 CCGAC CCGAC CCGAC CCGAC CCGAC CCGAC CCGAC CCGAC CC
99443 AGCCTCAGGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.19, C:0.57, G:0.17, T:0.07
Consensus pattern (5 bp):
CCGAC
Found at i:99416 original size:20 final size:20
Alignment explanation
Indices: 99393--99434 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
99383 GACATCGTTT
99393 GACCCTATCCGACCCGACCC
1 GACCCTATCCGACCCGACCC
99413 GACCCTATCCGACCCGACCC
1 GACCCTATCCGACCCGACCC
99433 GA
1 GA
99435 TCCGACCCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.52, G:0.17, T:0.10
Consensus pattern (20 bp):
GACCCTATCCGACCCGACCC
Found at i:99424 original size:15 final size:15
Alignment explanation
Indices: 99401--99442 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
99391 TTGACCCTAT
*
99401 CCGACCCGACCCGAC
1 CCGATCCGACCCGAC
*
99416 CCTATCCGACCCGAC
1 CCGATCCGACCCGAC
99431 CCGATCCGACCC
1 CCGATCCGACCC
99443 AGCCTCAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.19, C:0.57, G:0.17, T:0.07
Consensus pattern (15 bp):
CCGATCCGACCCGAC
Found at i:99865 original size:29 final size:29
Alignment explanation
Indices: 99821--100019 Score: 133
Period size: 29 Copynumber: 6.9 Consensus size: 29
99811 AAAAGGTCCC
*
99821 TAAACTATC-CAAAAATCATATTTTAACCCT
1 TAAACT-TCTCAAAAATCACATTTT-ACCCT
* *
99851 TGAACTTCTC-AAAATTACATTTTTACCCT
1 TAAACTTCTCAAAAATCACA-TTTTACCCT
* * * * *
99880 CAAACATCTCAAAAATTATATTTTTCCCT
1 TAAACTTCTCAAAAATCACATTTTACCCT
*
99909 TAAACTTC-CAAAAATCACATTTTACCCC
1 TAAACTTCTCAAAAATCACATTTTACCCT
* * *
99937 TAAATTTCTCAAAAATTACATTTTTCCCCT
1 TAAACTTCTCAAAAATCACA-TTTTACCCT
* * *
99967 CT-AACTTC-CCAAAATGAC-TTCTTACCCC
1 -TAAACTTCTCAAAAATCACATT-TTACCCT
* *
99995 TAAAGCTT-TCCAAAATTACATTTTA
1 TAAA-CTTCTCAAAAATCACATTTTA
100020 ACCCCAAAAC
Statistics
Matches: 134, Mismatches: 24, Indels: 23
0.74 0.13 0.13
Matches are distributed among these distances:
27 3 0.02
28 30 0.22
29 68 0.51
30 32 0.24
31 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (29 bp):
TAAACTTCTCAAAAATCACATTTTACCCT
Found at i:99980 original size:87 final size:87
Alignment explanation
Indices: 99817--100032 Score: 226
Period size: 87 Copynumber: 2.5 Consensus size: 87
99807 GCCCAAAAGG
* * *
99817 TCCCTAAACTATCCAAAAATCATATTTTAACCCTTGAACTTCTCAAAATTACATTTTTACCCTCA
1 TCCCTAAACTATCCAAAAATCACATTTTAACCCCTAAACTTCTCAAAATTACATTTTTACCCTCA
*
99882 AACATCTCAAAAATTATATTTT
66 AACATCCCAAAAATTATATTTT
* *
99904 TCCCTTAAACT-TCCAAAAATCACATTTT-ACCCCTAAATTTCTCAAAAATTACATTTTTCCCCT
1 TCCC-TAAACTATCCAAAAATCACATTTTAACCCCTAAACTTCTC-AAAATTACATTTTTACCCT
* * * *
99967 CTAACTTCCC-AAAATGACT-TCTTA
64 CAAACATCCCAAAAATTA-TAT-TTT
* * * *
99991 CCCCTAAAGCTTTCC-AAAATTACATTTTAACCCCAAAACTTC
1 TCCCTAAA-CTATCCAAAAATCACATTTTAACCCCTAAACTTC
100033 ATTTTTGACC
Statistics
Matches: 108, Mismatches: 14, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
86 23 0.21
87 65 0.60
88 20 0.19
ACGTcount: A:0.36, C:0.28, G:0.01, T:0.35
Consensus pattern (87 bp):
TCCCTAAACTATCCAAAAATCACATTTTAACCCCTAAACTTCTCAAAATTACATTTTTACCCTCA
AACATCCCAAAAATTATATTTT
Found at i:99996 original size:58 final size:58
Alignment explanation
Indices: 99818--100018 Score: 177
Period size: 58 Copynumber: 3.5 Consensus size: 58
99808 CCCAAAAGGT
* * * * * *
99818 CCCTAAACTATC-CAAAAATCATATTTTAACCCTTGAACTTCTC-AAAATTACATTTTTA-
1 CCCTAAACTTTCTCAAAAATTACATTTT-TCCCTTAAACTTC-CAAAAATCACA-TTTTAC
* *
99876 CCCTCAAAC-ATCTCAAAAATTATATTTTTCCCTTAAACTTCCAAAAATCACATTTTAC
1 CCCT-AAACTTTCTCAAAAATTACATTTTTCCCTTAAACTTCCAAAAATCACATTTTAC
* *
99934 CCCTAAA-TTTCTCAAAAATTACATTTTTCCCCTCT-AACTTCCCAAAATGAC-TTCTTAC
1 CCCTAAACTTTCTCAAAAATTACATTTTT-CCCT-TAAACTTCCAAAAATCACATT-TTAC
99992 CCCTAAAGCTTTC-C-AAAATTACATTTT
1 CCCTAAA-CTTTCTCAAAAATTACATTTT
100019 AACCCCAAAA
Statistics
Matches: 125, Mismatches: 8, Indels: 20
0.82 0.05 0.13
Matches are distributed among these distances:
57 29 0.23
58 72 0.58
59 20 0.16
60 4 0.03
ACGTcount: A:0.35, C:0.27, G:0.01, T:0.36
Consensus pattern (58 bp):
CCCTAAACTTTCTCAAAAATTACATTTTTCCCTTAAACTTCCAAAAATCACATTTTAC
Found at i:101127 original size:15 final size:16
Alignment explanation
Indices: 101107--101144 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
101097 GTGTTCTTCC
101107 TTTTTTTTC-CTTCTT
1 TTTTTTTTCTCTTCTT
*
101122 TTTTTTTTCTTTTCTT
1 TTTTTTTTCTCTTCTT
*
101138 TCTTTTT
1 TTTTTTT
101145 GGTGGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTTTCTCTTCTT
Found at i:101131 original size:11 final size:12
Alignment explanation
Indices: 101100--101141 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
101090 TCCAATGGTG
101100 TTCTTCCTTTTTT
1 TTCTT-CTTTTTT
101113 TTCCTTCTTTTTT
1 TT-CTTCTTTTTT
*
101126 TT-TTCTTTTCT
1 TTCTTCTTTTTT
101137 TTCTT
1 TTCTT
101142 TTTGGTGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 10 0.38
12 2 0.08
13 11 0.42
14 3 0.12
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTCTTCTTTTTT
Found at i:101140 original size:20 final size:19
Alignment explanation
Indices: 101107--101144 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
101097 GTGTTCTTCC
101107 TTTTTTTTCCTTCTTTTTT
1 TTTTTTTTCCTTCTTTTTT
*
101126 TTTTCTTTTCTTTCTTTTT
1 TTTT-TTTTCCTTCTTTTT
101145 GGTGGAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTTTTCCTTCTTTTTT
Found at i:110197 original size:11 final size:11
Alignment explanation
Indices: 110181--110237 Score: 82
Period size: 11 Copynumber: 5.3 Consensus size: 11
110171 GGTGTTCTTC
110181 CTTCTTTTTTT
1 CTTCTTTTTTT
110192 CTTCTTTTTTT
1 CTTCTTTTTTT
*
110203 CTTTTTTTTTT
1 CTTCTTTTTTT
110214 CTT-TTTTTTT
1 CTTCTTTTTTT
110224 -TTCTTTTCTTT
1 CTTCTTTT-TTT
110235 CTT
1 CTT
110238 TTTGGTGGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
9 2 0.05
10 11 0.26
11 27 0.64
12 2 0.05
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
CTTCTTTTTTT
Found at i:110206 original size:19 final size:19
Alignment explanation
Indices: 110182--110240 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
110172 GTGTTCTTCC
110182 TTCTTTTTTTCTTCTTTTT
1 TTCTTTTTTTCTTCTTTTT
*
110201 TTCTTTTTTTTTTCTTTTT
1 TTCTTTTTTTCTTCTTTTT
*
110220 TTTTTTCTTTTCTTTCTTTTT
1 TTCTTT-TTTTC-TTCTTTTT
110241 GGTGGAATTC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
19 23 0.66
20 4 0.11
21 8 0.23
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (19 bp):
TTCTTTTTTTCTTCTTTTT
Found at i:110213 original size:22 final size:21
Alignment explanation
Indices: 110185--110240 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 21
110175 TTCTTCCTTC
110185 TTTTTTTCTTCTTTTTTTCTT-T
1 TTTTTTTCTT-TTTTTTT-TTCT
110207 TTTTTTTCTTTTTTTTTTTCT
1 TTTTTTTCTTTTTTTTTTTCT
*
110228 TTTCTTTCTTTTT
1 TTTTTTTCTTTTT
110241 GGTGGAATTC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 2 0.06
21 20 0.62
22 10 0.31
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (21 bp):
TTTTTTTCTTTTTTTTTTTCT
Found at i:111160 original size:8 final size:8
Alignment explanation
Indices: 111147--111175 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
111137 CTTGTCCATG
111147 ATGTGACT
1 ATGTGACT
111155 ATGTGACT
1 ATGTGACT
111163 ATGTGACT
1 ATGTGACT
111171 ATGTG
1 ATGTG
111176 GTCATTTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.28, T:0.38
Consensus pattern (8 bp):
ATGTGACT
Found at i:112988 original size:45 final size:45
Alignment explanation
Indices: 112905--112991 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
112895 ACTTGAGGGG
* * *
112905 AAATGATAGAAATCAAGGAGTTGATTAAGACAATTTTGATGAAAT
1 AAATGATAGAAATCAAGAAGTTAATTAAGACAAATTTGATGAAAT
* * *
112950 AAATGATAGAAATTAAGAAGTTAATTGAGATAAATTTGATGA
1 AAATGATAGAAATCAAGAAGTTAATTAAGACAAATTTGATGA
112992 TATTTTATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.48, C:0.02, G:0.20, T:0.30
Consensus pattern (45 bp):
AAATGATAGAAATCAAGAAGTTAATTAAGACAAATTTGATGAAAT
Found at i:113089 original size:55 final size:56
Alignment explanation
Indices: 112982--113094 Score: 174
Period size: 55 Copynumber: 2.0 Consensus size: 56
112972 AATTGAGATA
* * *
112982 AATTTGATGATATTTTATTTATTTCTTTGTTTAGGATTGAGTCAATCATTGATTAT
1 AATTTGATGAGATTTTATTTATTTCTTTCTTTAAGATTGAGTCAATCATTGATTAT
* *
113038 AATTTGATGAGATTTTA-TTCTTTCTTTCTTTAAGATTGAGTCAATCCTTGATTAT
1 AATTTGATGAGATTTTATTTATTTCTTTCTTTAAGATTGAGTCAATCATTGATTAT
113093 AA
1 AA
113095 AGATTCTTCA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
55 36 0.69
56 16 0.31
ACGTcount: A:0.27, C:0.08, G:0.13, T:0.51
Consensus pattern (56 bp):
AATTTGATGAGATTTTATTTATTTCTTTCTTTAAGATTGAGTCAATCATTGATTAT
Found at i:116466 original size:22 final size:22
Alignment explanation
Indices: 116434--116527 Score: 92
Period size: 21 Copynumber: 4.5 Consensus size: 22
116424 TCATATCCCT
116434 TAATTTAAAATACCCTAAACCC
1 TAATTTAAAATACCCTAAACCC
* * *
116456 TTATATAAAATA-CCAAAACCC
1 TAATTTAAAATACCCTAAACCC
* * *
116477 TAATTT-TAATAACCTAAAACC
1 TAATTTAAAATACCCTAAACCC
116498 TAATTTAAAA-ACCCTAAA--C
1 TAATTTAAAATACCCTAAACCC
116517 TAA-TTAAAATA
1 TAATTTAAAATA
116528 AAAATACTCT
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
18 6 0.10
19 5 0.08
20 4 0.07
21 32 0.54
22 12 0.20
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (22 bp):
TAATTTAAAATACCCTAAACCC
Found at i:116699 original size:31 final size:31
Alignment explanation
Indices: 116641--116700 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
116631 AAAAAAGGGG
* *
116641 AAAAATGCATCCACATGGGCACTTTTTTGGA
1 AAAAAAGCATCCACATGGGCACATTTTTGGA
* **
116672 AAAAAAGCTTCCACATGGGTGCATTTTTG
1 AAAAAAGCATCCACATGGGCACATTTTTG
116701 TTGCACAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (31 bp):
AAAAAAGCATCCACATGGGCACATTTTTGGA
Found at i:116753 original size:72 final size:73
Alignment explanation
Indices: 116664--116799 Score: 177
Period size: 72 Copynumber: 1.9 Consensus size: 73
116654 CATGGGCACT
* * * *
116664 TTTTTGGAAAAAAAGCTTCCACATGGGT-GCATTTTTGTTGCACAAAAGGAAAAGCGCTTCCACA
1 TTTTTGGAAAAAAAGCTTCCACAT-GATCGCACTTTTGTTGCACAAAAGGAAAAACACTTCCACA
116728 CGTGGGCAG
65 CGTGGGCAG
* * * *
116737 TTTTTGG-AAAAAAGCTTTCACGTGATCGCGCTTTTGTTGCACAGAAGGAAAAACACTTCCACA
1 TTTTTGGAAAAAAAGCTTCCACATGATCGCACTTTTGTTGCACAAAAGGAAAAACACTTCCACA
116800 TGGAAGATCT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
71 2 0.04
72 45 0.83
73 7 0.13
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (73 bp):
TTTTTGGAAAAAAAGCTTCCACATGATCGCACTTTTGTTGCACAAAAGGAAAAACACTTCCACAC
GTGGGCAG
Found at i:119884 original size:49 final size:50
Alignment explanation
Indices: 119801--119899 Score: 132
Period size: 49 Copynumber: 2.0 Consensus size: 50
119791 ATCTGCAAGA
*
119801 CAAGTCCACATTATTCTGTATCAGGTAGTAAATCTGA-AAATATCTGGTGG
1 CAAGTCCACATTATTCTGTATCAGGCAGTAAATCT-ACAAATATCTGGTGG
* *
119851 CAAGTCCACA-TATTCTGTATCTA-GCAGTCAATCTACAAATATTTGGTGG
1 CAAGTCCACATTATTCTGTATC-AGGCAGTAAATCTACAAATATCTGGTGG
119900 TTAAACCAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
48 1 0.02
49 32 0.73
50 11 0.25
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (50 bp):
CAAGTCCACATTATTCTGTATCAGGCAGTAAATCTACAAATATCTGGTGG
Found at i:120892 original size:40 final size:40
Alignment explanation
Indices: 120837--120926 Score: 180
Period size: 40 Copynumber: 2.2 Consensus size: 40
120827 TTAACGGTGA
120837 TGCTGACATGATTGTTAGTTGACTAACAGTCAACATAAAC
1 TGCTGACATGATTGTTAGTTGACTAACAGTCAACATAAAC
120877 TGCTGACATGATTGTTAGTTGACTAACAGTCAACATAAAC
1 TGCTGACATGATTGTTAGTTGACTAACAGTCAACATAAAC
120917 TGCTGACATG
1 TGCTGACATG
120927 GCTGTCCAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (40 bp):
TGCTGACATGATTGTTAGTTGACTAACAGTCAACATAAAC
Found at i:121055 original size:38 final size:39
Alignment explanation
Indices: 120990--121069 Score: 135
Period size: 38 Copynumber: 2.1 Consensus size: 39
120980 ACAAATTATT
120990 TTAAAATTATTAAAATTATTTTTTTGAAATATAAAATTA
1 TTAAAATTATTAAAATTATTTTTTTGAAATATAAAATTA
* *
121029 TTAAAATTATT-ATATTATTTTTTTGAAGTATAAAATTA
1 TTAAAATTATTAAAATTATTTTTTTGAAATATAAAATTA
121067 TTA
1 TTA
121070 TATGATTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 28 0.72
39 11 0.28
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (39 bp):
TTAAAATTATTAAAATTATTTTTTTGAAATATAAAATTA
Found at i:124031 original size:23 final size:22
Alignment explanation
Indices: 123990--124032 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
123980 CTAGTTGTGC
*
123990 ACCACCAATACCTCACCACTGA
1 ACCACCAAAACCTCACCACTGA
*
124012 ACCACCACAAACCTCCCCACT
1 ACCACCA-AAACCTCACCACT
124033 CCTTTTCTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.35, C:0.51, G:0.02, T:0.12
Consensus pattern (22 bp):
ACCACCAAAACCTCACCACTGA
Found at i:131420 original size:29 final size:29
Alignment explanation
Indices: 131378--131434 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
131368 ACAAACATGA
*
131378 TAAAACAAGTAAAACATTTTTCGGAAAAG
1 TAAAACAAGTAAAACATTTTTCGAAAAAG
*
131407 TAAAATAAGTAAAACATTTTTCGAAAAA
1 TAAAACAAGTAAAACATTTTTCGAAAAA
131435 TTAATTACGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.54, C:0.09, G:0.11, T:0.26
Consensus pattern (29 bp):
TAAAACAAGTAAAACATTTTTCGAAAAAG
Found at i:135048 original size:17 final size:17
Alignment explanation
Indices: 135004--135059 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
134994 AAAATAAGTA
*
135004 TAAAAAATTATCCGAAT
1 TAAAAAATTAACCGAAT
** *
135021 TATTCAAATTACCCGAAT
1 TA-AAAAATTAACCGAAT
135039 TAAAAAATTAACCGAAT
1 TAAAAAATTAACCGAAT
135056 TAAA
1 TAAA
135060 GATTGAATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
17 18 0.56
18 14 0.44
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (17 bp):
TAAAAAATTAACCGAAT
Found at i:135800 original size:31 final size:32
Alignment explanation
Indices: 135765--135831 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
135755 GTACAATTTT
*
135765 GTCATTGAATTATT-AAAAAATTTTCATTTAA
1 GTCATTGAAGTATTCAAAAAATTTTCATTTAA
** *
135796 GTCATTGAAGTATTCAAAAGTTTTTTATTTAA
1 GTCATTGAAGTATTCAAAAAATTTTCATTTAA
135828 GTCA
1 GTCA
135832 CTGGGTTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 13 0.42
32 18 0.58
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.45
Consensus pattern (32 bp):
GTCATTGAAGTATTCAAAAAATTTTCATTTAA
Found at i:139173 original size:29 final size:29
Alignment explanation
Indices: 139103--139174 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 29
139093 ATTAAAAAAT
139103 TACAAGGACTAAAATTGATCAATTGGAAAAG
1 TACAAGGACTAAAATTGATCAATT-G-AAAG
* *
139134 TATAAGAACTAAAATTGATCAAATT-AAAG
1 TACAAGGACTAAAATTGATC-AATTGAAAG
139163 TACAAGGACTAA
1 TACAAGGACTAA
139175 GAGCTGAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 14 0.39
31 18 0.50
32 4 0.11
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.24
Consensus pattern (29 bp):
TACAAGGACTAAAATTGATCAATTGAAAG
Found at i:151896 original size:16 final size:18
Alignment explanation
Indices: 151863--151897 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
151853 ATTTTACTAT
151863 AATAGCAAAAGAATGAAG
1 AATAGCAAAAGAATGAAG
151881 AATA-CAAAAG-ATGAAG
1 AATAGCAAAAGAATGAAG
151897 A
1 A
151898 TAAAATCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 6 0.35
18 4 0.24
ACGTcount: A:0.63, C:0.06, G:0.20, T:0.11
Consensus pattern (18 bp):
AATAGCAAAAGAATGAAG
Found at i:152100 original size:24 final size:24
Alignment explanation
Indices: 152072--152130 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
152062 TAGACTAATA
*
152072 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAT
* *
152096 AGAGTTTAATTGAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAT
152120 AGAGTTTAACT
1 AGAGTTTAACT
152131 AAAAGATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAT
Found at i:154097 original size:24 final size:24
Alignment explanation
Indices: 154036--154098 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
154026 TAGACTAATA
* * *
154036 AGAGTTTGACTCAAATAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
154060 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
154084 ATAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
154099 GATTATTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.51, C:0.10, G:0.13, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:162941 original size:22 final size:22
Alignment explanation
Indices: 162916--162965 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
162906 GATAAGTTTG
162916 TAAATTTATGTTATGAATGAAT
1 TAAATTTATGTTATGAATGAAT
162938 TAAATTTATGTTATGAATGAAT
1 TAAATTTATGTTATGAATGAAT
162960 TAAATT
1 TAAATT
162966 GAATTATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (22 bp):
TAAATTTATGTTATGAATGAAT
Found at i:172812 original size:19 final size:17
Alignment explanation
Indices: 172788--172824 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
172778 AAAGTCGAGA
172788 AAAAAAATAAGAGAAAAAT
1 AAAAAAATAA-A-AAAAAT
172807 AAAAAAATAAAAAAAAT
1 AAAAAAATAAAAAAAAT
172824 A
1 A
172825 TTTTGTGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 1 0.06
19 10 0.56
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (17 bp):
AAAAAAATAAAAAAAAT
Found at i:184440 original size:30 final size:30
Alignment explanation
Indices: 184401--184478 Score: 95
Period size: 31 Copynumber: 2.6 Consensus size: 30
184391 AATTGATAAA
* *
184401 TAAATTTTTATTTTG-TGAAATTATATATAT
1 TAAACTTTTATTTTGATCAAATT-TATATAT
184431 TAAACTTTTATTTTGGATCAAATTTATATAT
1 TAAACTTTTATTTT-GATCAAATTTATATAT
* *
184462 AAAACTTTAATTTTGAT
1 TAAACTTTTATTTTGAT
184479 TTAATTTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 16 0.38
31 20 0.48
32 6 0.14
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (30 bp):
TAAACTTTTATTTTGATCAAATTTATATAT
Found at i:184488 original size:31 final size:31
Alignment explanation
Indices: 184419--184489 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
184409 TATTTTGTGA
* * *
184419 AATTATATATATTAAACTTTTATTTTGGATC
1 AATTTTATATATAAAACTTTAATTTTGGATC
* *
184450 AAATTTATATATAAAACTTTAATTTT-GATTT
1 AATTTTATATATAAAACTTTAATTTTGGA-TC
184481 AATTTTATA
1 AATTTTATA
184490 CATTTAAAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (31 bp):
AATTTTATATATAAAACTTTAATTTTGGATC
Found at i:194878 original size:15 final size:15
Alignment explanation
Indices: 194858--194887 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
194848 ATGTGAATTG
194858 TGCTTGAAAGGTAAA
1 TGCTTGAAAGGTAAA
194873 TGCTTGAAAGGTAAA
1 TGCTTGAAAGGTAAA
194888 ATGACTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.27, T:0.27
Consensus pattern (15 bp):
TGCTTGAAAGGTAAA
Found at i:197869 original size:11 final size:12
Alignment explanation
Indices: 197853--197885 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
197843 GGACCCAAGA
197853 TGAATTAATTT-
1 TGAATTAATTTG
*
197864 TGAATTCATTTG
1 TGAATTAATTTG
197876 TGAATTAATT
1 TGAATTAATT
197886 CACTTGTGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.52
Consensus pattern (12 bp):
TGAATTAATTTG
Found at i:200295 original size:14 final size:14
Alignment explanation
Indices: 200273--200335 Score: 60
Period size: 13 Copynumber: 4.6 Consensus size: 14
200263 CATATATCAC
200273 TTCATATAATTATT
1 TTCATATAATTATT
*
200287 TTCAAATAATTGA--
1 TTCATATAATT-ATT
200300 TTCATATAATTA-T
1 TTCATATAATTATT
* * *
200313 TTCATTTATTTGTT
1 TTCATATAATTATT
200327 TTCATATAA
1 TTCATATAA
200336 CTGATTCATA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
12 1 0.03
13 19 0.49
14 18 0.46
15 1 0.03
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.54
Consensus pattern (14 bp):
TTCATATAATTATT
Found at i:200308 original size:13 final size:13
Alignment explanation
Indices: 200273--200348 Score: 57
Period size: 13 Copynumber: 5.7 Consensus size: 13
200263 CATATATCAC
200273 TTCATATAATT-A
1 TTCATATAATTGA
*
200285 TTTTCAAATAATTGA
1 --TTCATATAATTGA
200300 TTCATATAATT-A
1 TTCATATAATTGA
* * *
200312 TTTCATTTATTTGTT
1 -TTCATATAATTG-A
*
200327 TTCATATAACTGA
1 TTCATATAATTGA
200340 TTCATATAA
1 TTCATATAA
200349 CCATCCCATA
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
12 1 0.02
13 28 0.57
14 19 0.39
15 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (13 bp):
TTCATATAATTGA
Found at i:213669 original size:41 final size:41
Alignment explanation
Indices: 213545--213662 Score: 184
Period size: 41 Copynumber: 2.9 Consensus size: 41
213535 TTCATCATTA
**
213545 CACCAGCTCAAAAGCCTGCTAAGTTGTAGCTTGAATAGTTT
1 CACCAGCTCAAAAGCCTGCTAAGCCGTAGCTTGAATAGTTT
*
213586 CA-CAGGCTCAAAATCCTGCTAAGCCGTAGCTTGAATAGTTT
1 CACCA-GCTCAAAAGCCTGCTAAGCCGTAGCTTGAATAGTTT
*
213627 CACCAGCTCAATAGCCTGCTAAGCCGTAGCTTGAAT
1 CACCAGCTCAAAAGCCTGCTAAGCCGTAGCTTGAAT
213663 TATTTCATGC
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
40 2 0.03
41 66 0.94
42 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.26
Consensus pattern (41 bp):
CACCAGCTCAAAAGCCTGCTAAGCCGTAGCTTGAATAGTTT
Found at i:220319 original size:41 final size:39
Alignment explanation
Indices: 220192--220312 Score: 134
Period size: 41 Copynumber: 2.9 Consensus size: 39
220182 CATATCACCC
* *
220192 TTTCACCGGCTCAAAAGCTTGCTAAGTCGTAGCTTGAATAG
1 TTTCACCGGCTC-AAAGC-TACTAAGCCGTAGCTTGAATAG
** * *
220233 TTTCACTAGCTCTAAAGCCTACTAAACCGTAGCTTAAATAG
1 TTTCACCGGCTC-AAAG-CTACTAAGCCGTAGCTTGAATAG
220274 TTTCACCGGCTCAATAGTCTACTAAGCCGTAGCTTGAAT
1 TTTCACCGGCTCAA-AG-CTACTAAGCCGTAGCTTGAAT
220313 TATTTCATGC
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
40 2 0.03
41 63 0.95
42 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (39 bp):
TTTCACCGGCTCAAAGCTACTAAGCCGTAGCTTGAATAG
Found at i:222669 original size:101 final size:103
Alignment explanation
Indices: 222484--222670 Score: 324
Period size: 101 Copynumber: 1.8 Consensus size: 103
222474 GAATTATAAA
* * *
222484 AAAATAAATTAGGAGTGTGTTGGGCTGAGTAACTGGGATGGAGTCCTTGGGTTGTCATTCCATTT
1 AAAATAAATTAGGAGTGTGTTGGGCTAAGTAACCGGGATGGAGTCCTTGGGCTGTCATTCCATTT
222549 CACGTCAAAAGGGCCAATACATTCTTAAGTAAAAAATG
66 CACGTCAAAAGGGCCAATACATTCTTAAGTAAAAAATG
222587 AAAATAAATTAGGAGTGTGTTGGGCTAAGTAACCGGGAT-GAGT-CTTGGGCTGTCATTCCATTT
1 AAAATAAATTAGGAGTGTGTTGGGCTAAGTAACCGGGATGGAGTCCTTGGGCTGTCATTCCATTT
*
222650 CGCGTCAAAAGGGCCAATACA
66 CACGTCAAAAGGGCCAATACA
222671 ATTTCCTTAA
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
101 39 0.49
102 4 0.05
103 37 0.46
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (103 bp):
AAAATAAATTAGGAGTGTGTTGGGCTAAGTAACCGGGATGGAGTCCTTGGGCTGTCATTCCATTT
CACGTCAAAAGGGCCAATACATTCTTAAGTAAAAAATG
Found at i:222684 original size:101 final size:102
Alignment explanation
Indices: 222484--222691 Score: 307
Period size: 101 Copynumber: 2.0 Consensus size: 102
222474 GAATTATAAA
* * *
222484 AAAATAAATTAGGAGTGTGTTGGGCTGAGTAACTGGGATGGAGTCCTTGGGTTGTCATTCCATTT
1 AAAATAAATTAGGAGTGTGTTGGGCTAAGTAACCGGGATGGAGTCCTTGGGCTGTCATTCCATTT
*
222549 CACGTCAAAAGGGCCAATACATTCTTAAGTAAAAAATG
66 CACGTCAAAAGGGCCAATACATTCTTAAG-AAAAAAAG
222587 AAAATAAATTAGGAGTGTGTTGGGCTAAGTAACCGGGAT-GAGT-CTTGGGCTGTCATTCCATTT
1 AAAATAAATTAGGAGTGTGTTGGGCTAAGTAACCGGGATGGAGTCCTTGGGCTGTCATTCCATTT
*
222650 CGCGTCAAAAGGGCCAATACAATTTCCTT-A-AAAAAAAG
66 CACGTCAAAAGGGCCAATAC-A-TT-CTTAAGAAAAAAAG
222688 AAAA
1 AAAA
222692 AAAGAAAATC
Statistics
Matches: 97, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
101 49 0.51
102 5 0.05
103 40 0.41
104 3 0.03
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.27
Consensus pattern (102 bp):
AAAATAAATTAGGAGTGTGTTGGGCTAAGTAACCGGGATGGAGTCCTTGGGCTGTCATTCCATTT
CACGTCAAAAGGGCCAATACATTCTTAAGAAAAAAAG
Found at i:223277 original size:13 final size:13
Alignment explanation
Indices: 223259--223283 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
223249 TAAATTCTAT
223259 TTTAGGATTATTA
1 TTTAGGATTATTA
223272 TTTAGGATTATT
1 TTTAGGATTATT
223284 TTGATATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (13 bp):
TTTAGGATTATTA
Found at i:224325 original size:13 final size:14
Alignment explanation
Indices: 224300--224329 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
224290 TCCTAACAGT
224300 ATGTAATATGTAAA
1 ATGTAATATGTAAA
224314 ATGTAA-ATGTAAA
1 ATGTAATATGTAAA
224327 ATG
1 ATG
224330 GTGTTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (14 bp):
ATGTAATATGTAAA
Found at i:229755 original size:25 final size:25
Alignment explanation
Indices: 229727--229774 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
229717 AAACAACTTC
229727 TGAAAAAAAACTC-AAGAGCAATTCT
1 TGAAAAAAAACTCAAAGAG-AATTCT
*
229752 TGAAGAAAAACTCAAAGAGAATT
1 TGAAAAAAAACTCAAAGAGAATT
229775 ATTATTAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.54, C:0.12, G:0.15, T:0.19
Consensus pattern (25 bp):
TGAAAAAAAACTCAAAGAGAATTCT
Done.