Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013655.1 Kokia drynarioides strain JFW-HI SEQ_128683, 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: 28006
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.35
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:593 original size:17 final size:17
Alignment explanation
Indices: 568--675 Score: 128
Period size: 17 Copynumber: 6.3 Consensus size: 17
558 ATGGGACTTC
*
568 TTAAATTTAAAATAATT
1 TTAAATTTAAAATAAAT
*
585 TTAATTTTAAAAGTAAAT
1 TTAAATTTAAAA-TAAAT
* **
603 TTAAACTTAATTTAAAT
1 TTAAATTTAAAATAAAT
*
620 TTAAATTTAAAACAAAT
1 TTAAATTTAAAATAAAT
637 TTAAATTTAAAATAAA-
1 TTAAATTTAAAATAAAT
*
653 TTAAATCTTATAATAAAT
1 TTAAAT-TTAAAATAAAT
671 TTAAA
1 TTAAA
676 AAGGATTTTA
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
16 6 0.08
17 53 0.70
18 17 0.22
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.43
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:607 original size:6 final size:6
Alignment explanation
Indices: 568--675 Score: 68
Period size: 6 Copynumber: 18.8 Consensus size: 6
558 ATGGGACTTC
* * * * * *
568 TTAAAT TTAAA- ATAATT TTAATT TTAAAA GTAAAT TTAAAC TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
** *
614 TTAAAT TTAAAT TTAAA- ACAAAT TTAAAT TTAAA- ATAAA- TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
659 CTTATAA- -TAAAT TTAAA
1 -TTA-AAT TTAAAT TTAAA
676 AAGGATTTTA
Statistics
Matches: 78, Mismatches: 16, Indels: 16
0.71 0.15 0.15
Matches are distributed among these distances:
4 2 0.03
5 20 0.26
6 51 0.65
7 3 0.04
8 2 0.03
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.43
Consensus pattern (6 bp):
TTAAAT
Found at i:616 original size:11 final size:12
Alignment explanation
Indices: 598--675 Score: 53
Period size: 11 Copynumber: 6.8 Consensus size: 12
588 ATTTTAAAAG
598 TAAATTTAAACT
1 TAAATTTAAACT
*
610 T-AATTTAAATT
1 TAAATTTAAACT
621 TAAATTTAAAAC-
1 TAAATTT-AAACT
*
633 -AAATTTAAATT
1 TAAATTTAAACT
*
644 TAAA-ATAAA-T
1 TAAATTTAAACT
654 TAAATCTTATAA--
1 TAAAT-TTA-AACT
666 TAAATTTAAA
1 TAAATTTAAA
676 AAGGATTTTA
Statistics
Matches: 54, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
10 10 0.19
11 23 0.43
12 16 0.30
13 5 0.09
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAATTTAAACT
Found at i:616 original size:23 final size:24
Alignment explanation
Indices: 585--630 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
575 TAAAATAATT
585 TTAATTTTAAAAGTAAATTTAAAC
1 TTAATTTTAAAAGTAAATTTAAAC
**
609 TTAA-TTTAAATTTAAATTTAAA
1 TTAATTTTAAAAGTAAATTTAAA
631 ACAAATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
TTAATTTTAAAAGTAAATTTAAAC
Found at i:616 original size:29 final size:29
Alignment explanation
Indices: 569--624 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
559 TGGGACTTCT
*
569 TAAATTTAAAATAATTTTAATTTTAAAAG
1 TAAATTTAAAATAATTTTAAATTTAAAAG
*
598 TAAATTTAAACTTAA-TTTAAATTTAAA
1 TAAATTTAAA-ATAATTTTAAATTTAAA
625 TTTAAAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (29 bp):
TAAATTTAAAATAATTTTAAATTTAAAAG
Found at i:630 original size:29 final size:29
Alignment explanation
Indices: 568--630 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
558 ATGGGACTTC
*
568 TTAAATTTAAAATAATTTTAATTTTAAAA
1 TTAAATTTAAAATAATTTTAAATTTAAAA
* * *
597 GTAAATTTAAACTTAA-TTTAAATTTAAAT
1 TTAAATTTAAA-ATAATTTTAAATTTAAAA
626 TTAAA
1 TTAAA
631 ACAAATTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
29 25 0.89
30 3 0.11
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (29 bp):
TTAAATTTAAAATAATTTTAAATTTAAAA
Found at i:637 original size:23 final size:23
Alignment explanation
Indices: 598--647 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
588 ATTTTAAAAG
*
598 TAAATTTAAACTTAATTTAAATT
1 TAAATTTAAACTAAATTTAAATT
621 TAAATTTAAAAC-AAATTTAAATT
1 TAAATTT-AAACTAAATTTAAATT
644 TAAA
1 TAAA
648 ATAAATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
TAAATTTAAACTAAATTTAAATT
Found at i:742 original size:3 final size:3
Alignment explanation
Indices: 736--773 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
726 ATTATTATTA
736 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
774 TTACACATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:1546 original size:29 final size:31
Alignment explanation
Indices: 1363--1546 Score: 107
Period size: 30 Copynumber: 6.2 Consensus size: 31
1353 ATAGTCCCTA
* * *
1363 CAAAAATTAAATTTTAA-CCCTCAAACTTTAT
1 CAAAAATCACATTTTAACCCCT-AAACTTTCT
* * * * *
1394 -AAAAATTACATTTTAATCCCTGAACCTT-A
1 CAAAAATCACATTTTAACCCCTAAACTTTCT
* * ** * *
1423 CAAAAA-CTAGATTTTGACCTATGAAC-TTCA
1 CAAAAATC-ACATTTTAACCCCTAAACTTTCT
* *
1453 CAAAAATCATATTTTAACCCCCAAAC-TTCT
1 CAAAAATCACATTTTAACCCCTAAACTTTCT
*
1483 CAAAAATCACATTTTAACCCCTGAACTTTCT
1 CAAAAATCACATTTTAACCCCTAAACTTTCT
* * *
1514 -AAAAAT-GCATTTTAA-CCTTAAACTTTTT
1 CAAAAATCACATTTTAACCCCTAAACTTTCT
1542 CAAAA
1 CAAAA
1547 TTACCATTTT
Statistics
Matches: 122, Mismatches: 24, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
28 10 0.08
29 14 0.11
30 89 0.73
31 9 0.07
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.33
Consensus pattern (31 bp):
CAAAAATCACATTTTAACCCCTAAACTTTCT
Found at i:1684 original size:30 final size:29
Alignment explanation
Indices: 1609--1684 Score: 71
Period size: 30 Copynumber: 2.6 Consensus size: 29
1599 CCAAAGTCAC
* * *
1609 ATTTTCGACCTCAAATTTTCCAAAAGTTTG
1 ATTTT-GACCCCAAATTTTCCAAAAATTTA
* * * *
1639 ATTTTAATCCTAAATTTTCTAAAAATTTCA
1 ATTTTGACCCCAAATTTTCCAAAAATTT-A
1669 ATTTTGACCCCAAATT
1 ATTTTGACCCCAAATT
1685 CCTCGAAAAT
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
29 17 0.49
30 18 0.51
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.42
Consensus pattern (29 bp):
ATTTTGACCCCAAATTTTCCAAAAATTTA
Found at i:4619 original size:18 final size:18
Alignment explanation
Indices: 4596--4643 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
4586 ACAATTCATA
4596 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* * *
4614 TCACTTTCACTTTCACTT
1 TCACTTTCAATTCCAATT
*
4632 TCTCTTTCAATT
1 TCACTTTCAATT
4644 TTGATCACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:4621 original size:6 final size:6
Alignment explanation
Indices: 4596--4640 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
4586 ACAATTCATA
* * * *
4596 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCTCTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
4641 ATTTTGATCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.20, C:0.31, G:0.00, T:0.49
Consensus pattern (6 bp):
TCACTT
Found at i:9683 original size:41 final size:38
Alignment explanation
Indices: 9580--9683 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
9570 TTCGAAGCAA
*
9580 TAAAGTGACACCCAGTGTCTCATCG-ACCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* * * ** * * *
9617 TAAAGTGATACCTAGTACCTCATCGAATCTATCTGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
9655 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
9684 CTTAGGGTCA
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:9801 original size:6 final size:6
Alignment explanation
Indices: 9767--9822 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
9757 TAATAGGGAT
* * * *
9767 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTTCAA TTTCAC TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
9814 TTTCAA TTT
1 TTTCAA TTT
9823 TGATCACAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
4 1 0.02
5 3 0.07
6 34 0.83
7 3 0.07
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTCAA
Found at i:9809 original size:18 final size:18
Alignment explanation
Indices: 9786--9822 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
9776 ACAATTCATA
9786 TCACTTTCAATTTCAATT
1 TCACTTTCAATTTCAATT
*
9804 TCACTTTCACTTTCAATT
1 TCACTTTCAATTTCAATT
9822 T
1 T
9823 TGATCACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (18 bp):
TCACTTTCAATTTCAATT
Found at i:14199 original size:52 final size:52
Alignment explanation
Indices: 14076--14192 Score: 171
Period size: 52 Copynumber: 2.2 Consensus size: 52
14066 GTATAAATAC
* *
14076 GCGTTTACGCTCGCAAGCTTGCACACGTTTACGCTCGTCATCTTATACATAT
1 GCGTTTACGCTCGCAAGCTTGCACACGTTTACGCTCGTCAGCTTAAACATAT
* * * *
14128 GCGTTTATGCTTGCTAGCTTGCACACGTTTACGCTCGTCAGCTTAAACATTT
1 GCGTTTACGCTCGCAAGCTTGCACACGTTTACGCTCGTCAGCTTAAACATAT
*
14180 GCGTTTACACTCG
1 GCGTTTACGCTCG
14193 TCAGCTTATA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.34
Consensus pattern (52 bp):
GCGTTTACGCTCGCAAGCTTGCACACGTTTACGCTCGTCAGCTTAAACATAT
Found at i:14206 original size:80 final size:80
Alignment explanation
Indices: 14101--14282 Score: 247
Period size: 80 Copynumber: 2.3 Consensus size: 80
14091 AGCTTGCACA
* * * ** * *
14101 CGTTTACGCTCGTCATCTTATACATATGCGTTTATGCTTGCTAGCTTGCACACGTTTACGCTCGT
1 CGTTTACGCTCGTCAGCTTATACATATGCGTCTACGCTCACCAGCTTGCACACATTTACGCTCGT
*
14166 CAGCTTAAACATTTG
66 CAGCTTAAACATATG
* * *
14181 CGTTTACACTCGTCAGCTTATACATATGTGTCTACGCTCACCATCTTGCACACATTTACGCTCGT
1 CGTTTACGCTCGTCAGCTTATACATATGCGTCTACGCTCACCAGCTTGCACACATTTACGCTCGT
*
14246 CAGCTTATACATATG
66 CAGCTTAAACATATG
*
14261 CGTTTACGCTCGCCAGCTTATA
1 CGTTTACGCTCGTCAGCTTATA
14283 AACGTTTACA
Statistics
Matches: 88, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
80 88 1.00
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.35
Consensus pattern (80 bp):
CGTTTACGCTCGTCAGCTTATACATATGCGTCTACGCTCACCAGCTTGCACACATTTACGCTCGT
CAGCTTAAACATATG
Found at i:14277 original size:28 final size:28
Alignment explanation
Indices: 14101--14339 Score: 162
Period size: 28 Copynumber: 9.0 Consensus size: 28
14091 AGCTTGCACA
*
14101 CGTTTACGCTCGTCATCTTATACATATG
1 CGTTTACGCTCGTCAGCTTATACATATG
* * * *
14129 CGTTTATGCTTG-CTAGC-T-TGCACA--
1 CGTTTACGCTCGTC-AGCTTATACATATG
* *
14153 CGTTTACGCTCGTCAGCTTAAACATTTG
1 CGTTTACGCTCGTCAGCTTATACATATG
*
14181 CGTTTACACTCGTCAGCTTATACATATG
1 CGTTTACGCTCGTCAGCTTATACATATG
* * ** * * *
14209 TGTCTACGCTCACCATC-T-TGCACA--
1 CGTTTACGCTCGTCAGCTTATACATATG
*
14233 CATTTACGCTCGTCAGCTTATACATATG
1 CGTTTACGCTCGTCAGCTTATACATATG
*
14261 CGTTTACGCTCGCCAGCTTATA-A-A--
1 CGTTTACGCTCGTCAGCTTATACATATG
* * *
14285 CGTTTACACTCGTCAACTTATATATATG
1 CGTTTACGCTCGTCAGCTTATACATATG
* * * *
14313 TGTTTACGCTTGCCATCTTATACATAT
1 CGTTTACGCTCGTCAGCTTATACATAT
14340 ATACACACGC
Statistics
Matches: 156, Mismatches: 41, Indels: 28
0.69 0.18 0.12
Matches are distributed among these distances:
24 43 0.28
25 4 0.03
26 16 0.10
27 4 0.03
28 89 0.57
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (28 bp):
CGTTTACGCTCGTCAGCTTATACATATG
Found at i:14296 original size:24 final size:24
Alignment explanation
Indices: 14261--14306 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
14251 TATACATATG
* *
14261 CGTTTACGCTCGCCAGCTTATAAA
1 CGTTTACACTCGCCAACTTATAAA
*
14285 CGTTTACACTCGTCAACTTATA
1 CGTTTACACTCGCCAACTTATA
14307 TATATGTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.33
Consensus pattern (24 bp):
CGTTTACACTCGCCAACTTATAAA
Found at i:14318 original size:132 final size:132
Alignment explanation
Indices: 14093--14339 Score: 332
Period size: 132 Copynumber: 1.9 Consensus size: 132
14083 CGCTCGCAAG
* * * * * * *
14093 CTTGCACACGTTTACGCTCGTCATCTTATACATATGCGTTTATGCTTGCTAGCTTGCACACGTTT
1 CTTGCACACATTTACGCTCGTCAGCTTATACATATGCGTTTACGCTCGCCAGCTTACAAACGTTT
* * * *
14158 ACGCTCGTCAGCTTAAACATTTGCGTTTACACTCGTCAGCTTATACATATGTGTCTACGCTCACC
66 ACACTCGTCAACTTAAACATATGCGTTTACACTCGCCAGCTTATACATATGTGTCTACGCTCACC
14223 AT
131 AT
*
14225 CTTGCACACATTTACGCTCGTCAGCTTATACATATGCGTTTACGCTCGCCAGCTTATAAACGTTT
1 CTTGCACACATTTACGCTCGTCAGCTTATACATATGCGTTTACGCTCGCCAGCTTACAAACGTTT
* * * * * *
14290 ACACTCGTCAACTTATATATATGTGTTTACGCTTGCCATCTTATACATAT
66 ACACTCGTCAACTTAAACATATGCGTTTACACTCGCCAGCTTATACATAT
14340 ATACACACGC
Statistics
Matches: 97, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
132 97 1.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (132 bp):
CTTGCACACATTTACGCTCGTCAGCTTATACATATGCGTTTACGCTCGCCAGCTTACAAACGTTT
ACACTCGTCAACTTAAACATATGCGTTTACACTCGCCAGCTTATACATATGTGTCTACGCTCACC
AT
Found at i:14333 original size:52 final size:52
Alignment explanation
Indices: 14181--14334 Score: 200
Period size: 52 Copynumber: 3.0 Consensus size: 52
14171 TAAACATTTG
* * ** *
14181 CGTTTACACTCGTCAGCTTATACATATGTGTCTACGCTCACCATCTTGCACA
1 CGTTTACACTCGTCAGCTTATACATATGTGTTTACGCTCGCCATCTTATAAA
* * * *
14233 CATTTACGCTCGTCAGCTTATACATATGCGTTTACGCTCGCCAGCTTATAAA
1 CGTTTACACTCGTCAGCTTATACATATGTGTTTACGCTCGCCATCTTATAAA
* * *
14285 CGTTTACACTCGTCAACTTATATATATGTGTTTACGCTTGCCATCTTATA
1 CGTTTACACTCGTCAGCTTATACATATGTGTTTACGCTCGCCATCTTATA
14335 CATATATACA
Statistics
Matches: 86, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 86 1.00
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.36
Consensus pattern (52 bp):
CGTTTACACTCGTCAGCTTATACATATGTGTTTACGCTCGCCATCTTATAAA
Found at i:14345 original size:52 final size:52
Alignment explanation
Indices: 14183--14353 Score: 191
Period size: 52 Copynumber: 3.3 Consensus size: 52
14173 AACATTTGCG
* * * **
14183 TTTACACTCGTCAGCTTATACATATGTGTCTACGCTCACCATCTTGCACACA
1 TTTACACTCGTCAACTTATACATATGTGTTTACGCTCGCCATCTTATACACA
* * * * * *
14235 TTTACGCTCGTCAGCTTATACATATGCGTTTACGCTCGCCAGCTTATAAACG
1 TTTACACTCGTCAACTTATACATATGTGTTTACGCTCGCCATCTTATACACA
* * *
14287 TTTACACTCGTCAACTTATATATATGTGTTTACGCTTGCCATCTTATACATA
1 TTTACACTCGTCAACTTATACATATGTGTTTACGCTCGCCATCTTATACACA
* *
14339 TATACACACG-CAACT
1 TTTACACTCGTCAACT
14354 ATTTAATTTA
Statistics
Matches: 99, Mismatches: 20, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
51 5 0.05
52 94 0.95
ACGTcount: A:0.26, C:0.27, G:0.12, T:0.35
Consensus pattern (52 bp):
TTTACACTCGTCAACTTATACATATGTGTTTACGCTCGCCATCTTATACACA
Found at i:20102 original size:21 final size:21
Alignment explanation
Indices: 20078--20127 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
20068 AGTTTGTTGC
20078 ATCGGTAGAAGTAATAATTGT
1 ATCGGTAGAAGTAATAATTGT
* * *
20099 ATCGGTAGTAGTCATACTTGT
1 ATCGGTAGAAGTAATAATTGT
*
20120 ATAGGTAG
1 ATCGGTAG
20128 GACCTTCCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (21 bp):
ATCGGTAGAAGTAATAATTGT
Found at i:21009 original size:17 final size:18
Alignment explanation
Indices: 20982--21016 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
20972 TAAGTAAATA
*
20982 TCATCATCAAACTAAACT
1 TCATCATCAAACAAAACT
21000 TCAT-ATCAAACAAAACT
1 TCATCATCAAACAAAACT
21017 CATTTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (18 bp):
TCATCATCAAACAAAACT
Found at i:21674 original size:31 final size:27
Alignment explanation
Indices: 21602--21682 Score: 74
Period size: 31 Copynumber: 2.8 Consensus size: 27
21592 AAAAGAGTAA
* *
21602 AATTTTACTTACTGTTTAAAAATGTTTT
1 AATTTTA-TTACTATTTTAAAATGTTTT
21630 AATTTT-TTAACTATTTTAAAATGCATTTAT
1 AATTTTATT-ACTATTTTAAAATG--TTT-T
21660 GAATTTTATTACTATTTTGAAAA
1 -AATTTTATTACTATTTT-AAAA
21683 AAATAAATAG
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
26 2 0.05
27 12 0.27
28 6 0.14
29 3 0.07
30 1 0.02
31 14 0.32
32 6 0.14
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (27 bp):
AATTTTATTACTATTTTAAAATGTTTT
Found at i:22042 original size:60 final size:60
Alignment explanation
Indices: 21868--22073 Score: 312
Period size: 60 Copynumber: 3.5 Consensus size: 60
21858 TTTAAGCCTT
* * *
21868 TATCATTTAATAAAATAGAAGTTTACTTTGAATTTTTTTGTACACATTATTTTTATATTG
1 TATCATTTAAAAAAATAGAAGTTTACTTTGAATATTTTTGTACACATTATTTTTATATTC
*
21928 TATCATTTAAAAAAATAAAAG-TT-CTTTTGAATA-TTTTGTACACATTATTTTTATATTC
1 TATCATTTAAAAAAATAGAAGTTTAC-TTTGAATATTTTTGTACACATTATTTTTATATTC
* *
21986 TATCATTTAATAAAATAGAAGTTTACTTTGAATATTTTTGTACACATTCTTTTTATATTGC
1 TATCATTTAAAAAAATAGAAGTTTACTTTGAATATTTTTGTACACATTATTTTTATATT-C
22047 -ATCATTTAAAAAAATAGAAGTTTACTT
1 TATCATTTAAAAAAATAGAAGTTTACTT
22074 CTTCATTTAG
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
58 44 0.33
59 19 0.14
60 69 0.52
61 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.48
Consensus pattern (60 bp):
TATCATTTAAAAAAATAGAAGTTTACTTTGAATATTTTTGTACACATTATTTTTATATTC
Found at i:27694 original size:12 final size:12
Alignment explanation
Indices: 27677--27758 Score: 55
Period size: 12 Copynumber: 6.9 Consensus size: 12
27667 CGTTTGTTTA
27677 ATGTTCATGAAC
1 ATGTTCATGAAC
*
27689 ATGTTCATTTAAC
1 ATGTTCA-TGAAC
*
27702 ---TTAATCGAAC
1 ATGTTCAT-GAAC
*
27712 ATGTTCACGAAC
1 ATGTTCATGAAC
**
27724 AT-TAAATGAAC
1 ATGTTCATGAAC
27735 ATGTTCATGAAC
1 ATGTTCATGAAC
*
27747 AATGTTAATGAA
1 -ATGTTCATGAA
27759 TAATAAACAA
Statistics
Matches: 52, Mismatches: 11, Indels: 13
0.68 0.14 0.17
Matches are distributed among these distances:
9 1 0.02
10 6 0.12
11 8 0.15
12 20 0.38
13 17 0.33
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (12 bp):
ATGTTCATGAAC
Found at i:27728 original size:23 final size:23
Alignment explanation
Indices: 27683--27747 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 23
27673 TTTAATGTTC
*
27683 ATGAACATGTTCATTTAAC-TT-A
1 ATGAACATGTTCA-TGAACATTAA
*
27705 ATCGAACATGTTCACGAACATTAA
1 AT-GAACATGTTCATGAACATTAA
27729 ATGAACATGTTCATGAACA
1 ATGAACATGTTCATGAACA
27748 ATGTTAATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.14
23 29 0.78
24 3 0.08
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (23 bp):
ATGAACATGTTCATGAACATTAA
Done.