Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006762.1 Kokia drynarioides strain JFW-HI SEQ_121360, 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: 23576
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Found at i:2581 original size:6 final size:6
Alignment explanation
Indices: 2570--2637 Score: 52
Period size: 6 Copynumber: 11.2 Consensus size: 6
2560 TTAAATTGGT
* **
2570 TTTAAA TTTAAA TTTATCTAT TTTAAA TTTAAA TTT-GC TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTA---AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
2620 TTT-AA -TTAAA TTTGAAA T
1 TTTAAA TTTAAA TTT-AAA T
2638 GATTTTAAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
4 2 0.04
5 7 0.14
6 31 0.63
7 4 0.08
9 5 0.10
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:2581 original size:17 final size:17
Alignment explanation
Indices: 2559--2622 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 17
2549 TTAAATTAGG
*
2559 TTTAAATTGGTTTTAAA
1 TTTAAATTTGTTTTAAA
*
2576 TTTAAATTTATCTATTTTAAA
1 TTTAAA--T-T-TGTTTTAAA
*
2597 TTTAAATTTGCTTTAAA
1 TTTAAATTTGTTTTAAA
2614 TTTAAATTT
1 TTTAAATTT
2623 AATTAAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 22 0.56
18 1 0.03
19 2 0.05
20 1 0.03
21 13 0.33
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (17 bp):
TTTAAATTTGTTTTAAA
Found at i:3359 original size:3 final size:3
Alignment explanation
Indices: 3351--3418 Score: 57
Period size: 3 Copynumber: 22.3 Consensus size: 3
3341 ACATTAATTT
* * * *
3351 ATA ATA ATA ATA ATA ATA ATA ACA GTA GTA ATA A-A TATA ACA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
* *
3396 ATGA TTA ATA ATA TTA ATA ATA A
1 AT-A ATA ATA ATA ATA ATA ATA A
3419 AAAAAGAAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
2 1 0.02
3 48 0.92
4 3 0.06
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:4099 original size:36 final size:36
Alignment explanation
Indices: 4040--4124 Score: 98
Period size: 36 Copynumber: 2.3 Consensus size: 36
4030 ACTTTATATA
* * *
4040 AACCCTCAAAATGGCGTAGTTTTGAGTGCTAAATTCC
1 AACCCT-AAAACGGCATAGTTTTGAGGGCTAAATTCC
* *
4077 AACCCTAAAACGGCATTGTTTTGAGGGCTGAATTCC
1 AACCCTAAAACGGCATAGTTTTGAGGGCTAAATTCC
* *
4113 AGCCCCAAAACG
1 AACCCTAAAACG
4125 ACGTCGTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 35 0.85
37 6 0.15
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (36 bp):
AACCCTAAAACGGCATAGTTTTGAGGGCTAAATTCC
Found at i:4134 original size:36 final size:36
Alignment explanation
Indices: 4058--4137 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
4048 AAATGGCGTA
* * * *
4058 GTTTTGAGTGCTAAATTCCAACCCTAAAACGGCATT
1 GTTTTGAGGGCTAAATTCCAACCCCAAAACGACATC
* * *
4094 GTTTTGAGGGCTGAATTCCAGCCCCAAAACGACGTC
1 GTTTTGAGGGCTAAATTCCAACCCCAAAACGACATC
4130 GTTTTGAG
1 GTTTTGAG
4138 CTTGACCTAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (36 bp):
GTTTTGAGGGCTAAATTCCAACCCCAAAACGACATC
Found at i:4587 original size:29 final size:30
Alignment explanation
Indices: 4550--4757 Score: 159
Period size: 29 Copynumber: 7.1 Consensus size: 30
4540 CCCCAAAGGT
4550 CCCT-AAACTTTTCAAAAATTACA-TTTTA
1 CCCTCAAACTTTTCAAAAATTACATTTTTA
* * * *
4578 CCCCCAAAC-TATCCAAAATTCCATTTTTA
1 CCCTCAAACTTTTCAAAAATTACATTTTTA
* * **
4607 ACCTCGATTTTTTCCAAAAATTACATTTTTA
1 CCCTCAAACTTTT-CAAAAATTACATTTTTA
*
4638 CCCTCAAAC-TTTCAAAAATTCCATTTTTGA
1 CCCTCAAACTTTTCAAAAATTACATTTTT-A
* *
4668 -CCTC-GATTTTTCCAAAAATTAC-TATTTTA
1 CCCTCAAACTTTT-CAAAAATTACAT-TTTTA
*
4697 CCCTCAAAC-TTCCAAAAATTACATTTTTA
1 CCCTCAAACTTTTCAAAAATTACATTTTTA
* *
4726 CCC-C-GATTTTTCTAAAAATTATCA-TTTTA
1 CCCTCAAACTTTTC-AAAAATTA-CATTTTTA
4755 CCC
1 CCC
4758 CTGAATGTCT
Statistics
Matches: 140, Mismatches: 26, Indels: 27
0.73 0.13 0.14
Matches are distributed among these distances:
27 1 0.01
28 19 0.14
29 71 0.51
30 28 0.20
31 21 0.15
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (30 bp):
CCCTCAAACTTTTCAAAAATTACATTTTTA
Found at i:4654 original size:59 final size:57
Alignment explanation
Indices: 4558--4757 Score: 278
Period size: 59 Copynumber: 3.4 Consensus size: 57
4548 GTCCCTAAAC
*
4558 TTTT-CAAAAATTACATTTTACCCCCAAACTATCC-AAAATTCCATTTTTAACCTCGATT
1 TTTTCCAAAAATTACATTTTACCCTCAAACT-TCCAAAAATTCCATTTTT-ACCTCGA-T
*
4616 TTTTCCAAAAATTACATTTTTACCCTCAAACTTTCAAAAATTCCATTTTTGACCTCGAT
1 TTTTCCAAAAATTACA-TTTTACCCTCAAACTTCCAAAAATTCCATTTTT-ACCTCGAT
* *
4675 TTTTCCAAAAATTACTATTTTACCCTCAAACTTCCAAAAATTACATTTTTACCCCGAT
1 TTTTCCAAAAATTAC-ATTTTACCCTCAAACTTCCAAAAATTCCATTTTTACCTCGAT
*
4733 TTTTCTAAAAATTATCATTTTACCC
1 TTTTCCAAAAATTA-CATTTTACCC
4758 CTGAATGTCT
Statistics
Matches: 130, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
58 33 0.25
59 61 0.47
60 36 0.28
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (57 bp):
TTTTCCAAAAATTACATTTTACCCTCAAACTTCCAAAAATTCCATTTTTACCTCGAT
Found at i:4758 original size:29 final size:29
Alignment explanation
Indices: 4558--4804 Score: 150
Period size: 29 Copynumber: 8.4 Consensus size: 29
4548 GTCCCTAAAC
* *
4558 TTTT-CAAAAATTACA-TTTTACCCCCAAA
1 TTTTCCAAAAATTACATTTTTA-CCCCGAT
* * * *
4586 CTATCC-AAAATTCCATTTTTAACCTCGATT
1 TTTTCCAAAAATTACATTTTT-ACCCCGA-T
* *
4616 TTTTCCAAAAATTACATTTTTACCCTCAAA
1 TTTTCCAAAAATTACATTTTTACCC-CGAT
* * *
4646 CTTT-CAAAAATTCCATTTTTGACCTCGAT
1 TTTTCCAAAAATTACATTTTT-ACCCCGAT
*
4675 TTTTCCAAAAATTAC-TATTTTACCCTC-AA
1 TTTTCCAAAAATTACAT-TTTTACCC-CGAT
**
4704 ACTTCCAAAAATTACATTTTTACCCCGAT
1 TTTTCCAAAAATTACATTTTTACCCCGAT
*
4733 TTTTCTAAAAATTATCA-TTTTACCCCTGA-
1 TTTTCCAAAAATTA-CATTTTTACCCC-GAT
* * * * *
4762 ATGTCTAAAAATTTCATTTTTAACCCCGAA
1 TTTTCCAAAAATTACATTTTT-ACCCCGAT
* *
4792 CTTTCCCAAAATT
1 TTTTCCAAAAATT
4805 TCCATTTTCC
Statistics
Matches: 168, Mismatches: 34, Indels: 32
0.72 0.15 0.14
Matches are distributed among these distances:
28 13 0.08
29 93 0.55
30 47 0.28
31 15 0.09
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (29 bp):
TTTTCCAAAAATTACATTTTTACCCCGAT
Found at i:4772 original size:58 final size:57
Alignment explanation
Indices: 4558--4804 Score: 268
Period size: 59 Copynumber: 4.2 Consensus size: 57
4548 GTCCCTAAAC
* * *
4558 TTTT-CAAAAATTACATTTTACCCCCAAACTATCCAAAATTCCATTTTTAACCTCGATT
1 TTTTCCAAAAATTACATTTTACCCTCAAACT-TCAAAAATTCCATTTTTAACCCCGA-T
* *
4616 TTTTCCAAAAATTACATTTTTACCCTCAAACTTTCAAAAATTCCATTTTTGACCTCGAT
1 TTTTCCAAAAATTACA-TTTTACCCTCAAAC-TTCAAAAATTCCATTTTTAACCCCGAT
*
4675 TTTTCCAAAAATTACTATTTTACCCTCAAACTTCCAAAAATTACATTTTT-ACCCCGAT
1 TTTTCCAAAAATTAC-ATTTTACCCTCAAACTT-CAAAAATTCCATTTTTAACCCCGAT
* * * *
4733 TTTTCTAAAAATTATCATTTTACCC-CTGAA-TGTCTAAAAATTTCATTTTTAACCCCGAA
1 TTTTCCAAAAATTA-CATTTTACCCTC-AAACT-TC-AAAAATTCCATTTTTAACCCCGAT
* *
4792 CTTTCCCAAAATT
1 TTTTCCAAAAATT
4805 TCCATTTTCC
Statistics
Matches: 167, Mismatches: 12, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
57 3 0.02
58 52 0.31
59 74 0.44
60 37 0.22
61 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (57 bp):
TTTTCCAAAAATTACATTTTACCCTCAAACTTCAAAAATTCCATTTTTAACCCCGAT
Found at i:16627 original size:49 final size:48
Alignment explanation
Indices: 16568--16990 Score: 331
Period size: 49 Copynumber: 8.7 Consensus size: 48
16558 GTACCATGAA
* * *
16568 ACATGAAGGGAAAAATTTAAGCCGCAACGACGAATCCAGTAGCACGAAG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAC-AAG
* * *
16617 ATATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCTAGTACCACAAAG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAC-AAG
** ** * * * *
16666 ACACAAAGGGAAATG-TTTAAGTTGCAATGACGAA-CCTAGTATCTCAGAG
1 ACATGAAGGGAAA-GATTTAAGCCGCAACGGCGAATCC-AGTACCACA-AG
*
16715 ACATGAAGGGAAAGATTTAAGCCGCAACGGGGAATCCAGTACCACAAAG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAC-AAG
** * * * * * *
16764 ACACCAAGGAAAAGGTTTAAGTCGCAATGGCGAA-CCTAGAACCTCAGAG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCACA-AG
* * * *
16813 ACATAAAGGGAAAGATGTAAGCCACAACGGCGAATCCAATACCACGAA-
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAC-AAG
* * * * *
16861 A-A-CAAGGGAAAGGTTTAAGTCGCAATGGCGAA-CCTAGTACCTCAGAG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCACA-AG
* *
16908 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCGCGAAA
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAC-AAG
* * * *
16957 ATACGAAGGGAAAGGA-TTAAGTCGCAACAGCGAA
1 ACATGAAGGGAAA-GATTTAAGCCGCAACGGCGAA
16991 CCCTATACCT
Statistics
Matches: 291, Mismatches: 65, Indels: 36
0.74 0.17 0.09
Matches are distributed among these distances:
45 3 0.01
46 31 0.11
47 2 0.01
48 8 0.03
49 235 0.81
50 12 0.04
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.15
Consensus pattern (48 bp):
ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAG
Found at i:17012 original size:98 final size:97
Alignment explanation
Indices: 16619--17002 Score: 524
Period size: 98 Copynumber: 3.9 Consensus size: 97
16609 GCACGAAGAT
* * *
16619 ATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCTAGTACCACAAAGACACAAAGGGAAATGTTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAAGACAC-AAGGGAAAGGTTT
* * *
16684 AAGTTGCAATGACGAACCTAGTATCTCAGAGAC
65 AAGTCGCAATGGCGAACCTAGTACCTCAGAGAC
* *
16717 ATGAAGGGAAAGATTTAAGCCGCAACGGGGAATCCAGTACCACAAAGACACCAAGGAAAAGGTTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAAGACA-CAAGGGAAAGGTTT
*
16782 AAGTCGCAATGGCGAACCTAGAACCTCAGAGAC
65 AAGTCGCAATGGCGAACCTAGTACCTCAGAGAC
* * * * *
16815 ATAAAGGGAAAGATGTAAGCCACAACGGCGAATCCAATACCACGAA-A-ACAAGGGAAAGGTTTA
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAAGACACAAGGGAAAGGTTTA
16878 AGTCGCAATGGCGAACCTAGTACCTCAGAGAC
66 AGTCGCAATGGCGAACCTAGTACCTCAGAGAC
* * *
16910 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCGCGAAA-ATACGAAGGGAAAGGAT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAC-AAAGACAC-AAGGGAAAGGTT
**
16974 TAAGTCGCAACAGCGAACCCTA-TACCTCA
64 TAAGTCGCAATGGCGAA-CCTAGTACCTCA
17003 AAAGCATGAA
Statistics
Matches: 256, Mismatches: 25, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
95 83 0.32
96 4 0.02
97 3 0.01
98 161 0.63
99 5 0.02
ACGTcount: A:0.40, C:0.21, G:0.24, T:0.15
Consensus pattern (97 bp):
ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAAGACACAAGGGAAAGGTTTA
AGTCGCAATGGCGAACCTAGTACCTCAGAGAC
Found at i:17491 original size:6 final size:6
Alignment explanation
Indices: 17470--17549 Score: 58
Period size: 6 Copynumber: 13.2 Consensus size: 6
17460 TTAAATTGGT
** * **
17470 TTTAAA TTTATT TTTAAA TTTAAA TTTATCTAT TTTAAA TTTAAA TTT-GC
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA---AA TTTAAA TTTAAA TTTAAA
17520 TTTAAA TTTAAA TTT-AA -TTAAA TTTGAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA T
17550 GATTTTAAAC
Statistics
Matches: 57, Mismatches: 10, Indels: 13
0.71 0.12 0.16
Matches are distributed among these distances:
4 2 0.04
5 7 0.12
6 39 0.68
7 4 0.07
9 5 0.09
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:17507 original size:21 final size:18
Alignment explanation
Indices: 17470--17535 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 18
17460 TTAAATTGGT
17470 TTTAAATTTATTTTTAAA
1 TTTAAATTTATTTTTAAA
17488 TTTAAATTTATCTATTTTAAA
1 TTTAAATTTA--T-TTTTAAA
**
17509 TTTAAATTT-GCTTTAAA
1 TTTAAATTTATTTTTAAA
17526 TTTAAATTTA
1 TTTAAATTTA
17536 ATTAAATTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
17 15 0.36
18 10 0.24
20 1 0.02
21 16 0.38
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTAAATTTATTTTTAAA
Found at i:18349 original size:3 final size:3
Alignment explanation
Indices: 18341--18408 Score: 66
Period size: 3 Copynumber: 22.3 Consensus size: 3
18331 ACATTAATTT
* * *
18341 ATA ATA ATA ATA ATA ATA ATA ACA GTA GTA ATA A-A TATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
* *
18386 ATGA TTA ATA ATA TTA ATA ATA A
1 AT-A ATA ATA ATA ATA ATA ATA A
18409 AAAAAATGGA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
2 1 0.02
3 50 0.93
4 3 0.06
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:19663 original size:59 final size:59
Alignment explanation
Indices: 19540--19882 Score: 324
Period size: 58 Copynumber: 5.8 Consensus size: 59
19530 CGAACTCTCT
* * * **
19540 AAAATTTCATTTTTGACCTTATTTTTTTCCAAAAATTA-CATTTTTACCCCCGAACATTCC-
1 AAAATTCCATTTTTGACCATA-ATTTTTCCAAAAATTACCA-TTTTACCCCTAAAC-TTCCA
* * *
19600 AAAATTCCATTTTTGACCATGATTTTTCCAAAAATTACTATTTTGCCCCTAAACTTCCA
1 AAAATTCCATTTTTGACCATAATTTTTCCAAAAATTACCATTTTACCCCTAAACTTCCA
* * *** ***
19659 AAAATTCCATTTTTAACCTTAATTTTTTTGAAAATTACCATTTTACCCCCGGACTTCCA
1 AAAATTCCATTTTTGACCATAATTTTTCCAAAAATTACCATTTTACCCCTAAACTTCCA
* * * *
19718 AAAATTCCA-TTTTGACCCTTATTTTTCCAAAAATTACCATTTTACCTCTAGACTTCCA
1 AAAATTCCATTTTTGACCATAATTTTTCCAAAAATTACCATTTTACCCCTAAACTTCCA
* * *
19776 AAAATTCCA-TTTTGACC-TCAATTTTTCCAAAAATTATCATTTTACCCTTAAA-TGTCTA
1 AAAATTCCATTTTTGACCAT-AATTTTTCCAAAAATTACCATTTTACCCCTAAACT-TCCA
* * * * *
19834 AAAATTTCATTTTTAACCCA-AA-CTTTCCTAAAATTACCATTTTCCCCCT
1 AAAATTCCATTTTTGA-CCATAATTTTTCCAAAAATTACCATTTTACCCCT
19883 GAGTGTCCAA
Statistics
Matches: 235, Mismatches: 41, Indels: 16
0.80 0.14 0.05
Matches are distributed among these distances:
57 2 0.01
58 122 0.52
59 90 0.38
60 21 0.09
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (59 bp):
AAAATTCCATTTTTGACCATAATTTTTCCAAAAATTACCATTTTACCCCTAAACTTCCA
Found at i:19672 original size:29 final size:29
Alignment explanation
Indices: 19566--19876 Score: 127
Period size: 29 Copynumber: 10.6 Consensus size: 29
19556 CCTTATTTTT
* **
19566 TTCCAAAAATTACATTTTTACCCCCGAAC
1 TTCCAAAAATTCCATTTTTACCCCTAAAC
* ***
19595 ATTCC-AAAATTCCATTTTTGA-CCATGATTT
1 -TTCCAAAAATTCCATTTTT-ACCCCT-AAAC
* *
19625 TTCCAAAAATTAC-TATTTTGCCCCTAAAC
1 TTCCAAAAATTCCAT-TTTTACCCCTAAAC
* * **
19654 TTCCAAAAATTCCATTTTTAACCTTAATTT
1 TTCCAAAAATTCCATTTTTACCCCTAA-AC
*** ***
19684 TTTTGAAAATTACCA-TTTTACCCCCGGAC
1 TTCCAAAAATT-CCATTTTTACCCCTAAAC
* * ***
19713 TTCCAAAAATTCCATTTTGACCCTTATTT
1 TTCCAAAAATTCCATTTTTACCCCTAAAC
* *
19742 TTCCAAAAATTACCA-TTTTACCTCTAGAC
1 TTCCAAAAATT-CCATTTTTACCCCTAAAC
* * **
19771 TTCCAAAAATTCCATTTTGACCTC-AATTT
1 TTCCAAAAATTCCATTTTTACCCCTAA-AC
* *
19800 TTCCAAAAATTATCA-TTTTACCCTTAAA-
1 TTCCAAAAATT-CCATTTTTACCCCTAAAC
* * *
19828 TGTCTAAAAATTTCATTTTTAACCC-AAAC
1 T-TCCAAAAATTCCATTTTTACCCCTAAAC
*
19857 TTTCCTAAAATTACCATTTT
1 -TTCCAAAAATT-CCATTTT
19877 CCCCCTGAGT
Statistics
Matches: 202, Mismatches: 60, Indels: 38
0.67 0.20 0.13
Matches are distributed among these distances:
28 14 0.07
29 136 0.67
30 49 0.24
31 3 0.01
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.40
Consensus pattern (29 bp):
TTCCAAAAATTCCATTTTTACCCCTAAAC
Found at i:19772 original size:58 final size:57
Alignment explanation
Indices: 19540--19822 Score: 302
Period size: 59 Copynumber: 4.8 Consensus size: 57
19530 CGAACTCTCT
*
19540 AAAATTTCATTTTTGACCTTATTTTTTTCCAAAAATTA-CATTTTTACCCCC-GAACATTCC-
1 AAAATTCCA-TTTTGACCTTA--TTTTTCCAAAAATTACCA-TTTTACCCCCAG-AC-TTCCA
* * * * *
19600 AAAATTCCATTTTTGACCATGATTTTTCCAAAAATTACTATTTTGCCCCTAAACTTCCA
1 AAAATTCCA-TTTTGACC-TTATTTTTCCAAAAATTACCATTTTACCCCCAGACTTCCA
* *** *
19659 AAAATTCCATTTTTAACCTTAATTTTTTTGAAAATTACCATTTTACCCCCGGACTTCCA
1 AAAATTCCA-TTTTGACCTT-ATTTTTCCAAAAATTACCATTTTACCCCCAGACTTCCA
* *
19718 AAAATTCCATTTTGACCCTTATTTTTCCAAAAATTACCATTTTACCTCTAGACTTCCA
1 AAAATTCCATTTTGA-CCTTATTTTTCCAAAAATTACCATTTTACCCCCAGACTTCCA
* *
19776 AAAATTCCATTTTGACCTCAATTTTTCCAAAAATTATCATTTTACCC
1 AAAATTCCATTTTGACCT-TATTTTTCCAAAAATTACCATTTTACCC
19823 TTAAATGTCT
Statistics
Matches: 190, Mismatches: 26, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
57 3 0.02
58 82 0.43
59 85 0.45
60 18 0.09
61 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (57 bp):
AAAATTCCATTTTGACCTTATTTTTCCAAAAATTACCATTTTACCCCCAGACTTCCA
Found at i:19919 original size:28 final size:28
Alignment explanation
Indices: 19863--19922 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
19853 AAACTTTCCT
* *
19863 AAAATTACCATTTTCCCCCTGAGTGTCC
1 AAAATTACCATCTTCCCCCTGAGTATCC
* * *
19891 AAAATTACCATCTTGCCCTTGGGTATCC
1 AAAATTACCATCTTCCCCCTGAGTATCC
19919 AAAA
1 AAAA
19923 ATCTCATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (28 bp):
AAAATTACCATCTTCCCCCTGAGTATCC
Found at i:22399 original size:16 final size:18
Alignment explanation
Indices: 22359--22400 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
22349 GATTCACTTT
22359 TAAAAAATATTTTTGAGA
1 TAAAAAATATTTTTGAGA
*
22377 TAAAAAATATTTTTGAAA
1 TAAAAAATATTTTTGAGA
22395 TAAAAA
1 TAAAAA
22401 CATTCTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (18 bp):
TAAAAAATATTTTTGAGA
Done.