Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024549.1 Corchorus olitorius cultivar O-4 contig24582, 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: 35151
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1599 original size:56 final size:57
Alignment explanation
Indices: 1512--1626 Score: 196
Period size: 56 Copynumber: 2.0 Consensus size: 57
1502 TTTGGTGATT
* * *
1512 AAAAATTTGATTAATTATTCTGTCTTTTTTACCGATATAAAGTGATTAATTTTGAAG
1 AAAAATTTGATTAATTATTCTGTCTATTTTACCAATATAAAGTGATTAATTTCGAAG
1569 AAAAA-TTGATTAATTATTCTGTCTATTTTACCAATATAAAGTGATTAATTTCGAAG
1 AAAAATTTGATTAATTATTCTGTCTATTTTACCAATATAAAGTGATTAATTTCGAAG
1625 AA
1 AA
1627 TGAAAATATA
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
56 50 0.91
57 5 0.09
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (57 bp):
AAAAATTTGATTAATTATTCTGTCTATTTTACCAATATAAAGTGATTAATTTCGAAG
Found at i:1859 original size:22 final size:20
Alignment explanation
Indices: 1826--1875 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
1816 ATTACTTTGT
1826 GAAAACAATTTTTTTGGTGAAA
1 GAAAA-AATTTTTTTGGTG-AA
**
1848 GAAAAAAGTTTTTTTTTTGAA
1 GAAAAAA-TTTTTTTGGTGAA
1869 GAAAAAA
1 GAAAAAA
1876 AGAAAGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.46, C:0.02, G:0.16, T:0.36
Consensus pattern (20 bp):
GAAAAAATTTTTTTGGTGAA
Found at i:3855 original size:23 final size:22
Alignment explanation
Indices: 3801--3856 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
3791 TTACGAAATG
*
3801 TTACTTATTTCTTTATAGCATTA
1 TTACTT-TTTCTTTATAACATTA
*
3824 TTA-TGTTTTCTTTATAAACTTTA
1 TTACT-TTTTCTTTAT-AACATTA
3847 TTACTTTTTC
1 TTACTTTTTC
3857 AGTAACCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 10 0.36
23 17 0.61
24 1 0.04
ACGTcount: A:0.23, C:0.12, G:0.04, T:0.61
Consensus pattern (22 bp):
TTACTTTTTCTTTATAACATTA
Found at i:4447 original size:18 final size:17
Alignment explanation
Indices: 4415--4448 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
4405 AATCCCTAAT
*
4415 AATATCATTTTAAAAAA
1 AATATCATTTAAAAAAA
4432 AATATCCATTTAAAAAA
1 AATAT-CATTTAAAAAA
4449 TTGTCACAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (17 bp):
AATATCATTTAAAAAAA
Found at i:8804 original size:11 final size:11
Alignment explanation
Indices: 8788--8812 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
8778 CCTTTGGAAA
8788 ATTGACAAAAT
1 ATTGACAAAAT
8799 ATTGACAAAAT
1 ATTGACAAAAT
8810 ATT
1 ATT
8813 TATCTGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (11 bp):
ATTGACAAAAT
Found at i:10631 original size:177 final size:177
Alignment explanation
Indices: 10263--10647 Score: 508
Period size: 177 Copynumber: 2.2 Consensus size: 177
10253 TTCCAGCATA
* * * * *
10263 AGCACAAATTATGTAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACTAACTCTTTGG
1 AGCAAAAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACTAAATCTTCGG
* * *
10328 AATCATTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTGCATGAAAGTTGTAGATCATG
66 AAGCATTTTTATACCTTGAACATTAAATTTAGCTTTCGAGTCCTGCATGAAAGTTGTAGATAATG
* * * * *
10393 GAACAACCTTTCAAGAGATACTTGAATCATCTCAATCAGACATCTGG
131 GAACAACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAACCGG
*
10440 AGCAAAAGTTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAAC-AAATCTTCGG
1 AGCAAAAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACTAAATCTTCGG
*
10504 AAGCATTTTTGATA-CTTGAAACATTAAATTTAGCTTTCGAGTCCTTCATGAAAGTTGTAGATAA
66 AAGCATTTTT-ATACCTTG-AACATTAAATTTAGCTTTCGAGTCCTGCATGAAAGTTGTAGATAA
* * * * *
10568 TGGAACAATCTTTTAATAGACACTTAAATCACCGT-AATCGGATAACCGG
129 TGGAACAACCTTTCAAGAGACACTTAAATCACC-TCAATCAGACAACCGG
* *
10617 AG-AGAAAATTATATAATGTTAAATAGACCGT
1 AGCA-AAAATTATATAATATTAAGTAGACCGT
10648 TTAGCCAAAC
Statistics
Matches: 181, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
176 22 0.12
177 158 0.87
178 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.31
Consensus pattern (177 bp):
AGCAAAAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACTAAATCTTCGG
AAGCATTTTTATACCTTGAACATTAAATTTAGCTTTCGAGTCCTGCATGAAAGTTGTAGATAATG
GAACAACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAACCGG
Found at i:10775 original size:21 final size:22
Alignment explanation
Indices: 10734--10775 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
10724 TGTGATAATA
10734 ACGAAAAAACCAATATCTAAATG
1 ACGAAAAAACCAATA-CTAAATG
10757 ACGAAAAAACCAATA-TAAA
1 ACGAAAAAACCAATACTAAA
10776 CAGTAATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
23 15 0.79
ACGTcount: A:0.62, C:0.17, G:0.07, T:0.14
Consensus pattern (22 bp):
ACGAAAAAACCAATACTAAATG
Found at i:11284 original size:14 final size:14
Alignment explanation
Indices: 11251--11292 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
11241 TTTATTACTG
11251 TTTTATTAAAT--T
1 TTTTATTAAATGAT
*
11263 GTTT-TTAAATGAT
1 TTTTATTAAATGAT
11276 TTTTATTAAATGAT
1 TTTTATTAAATGAT
11290 TTT
1 TTT
11293 GGGTGCATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 6 0.24
12 3 0.12
13 4 0.16
14 12 0.48
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (14 bp):
TTTTATTAAATGAT
Found at i:14450 original size:2 final size:2
Alignment explanation
Indices: 14443--14468 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14433 ATACTTAGAA
14443 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
14469 GATTATGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21588 original size:13 final size:13
Alignment explanation
Indices: 21570--21594 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21560 AAGTGTTTAG
21570 ATATATATATATT
1 ATATATATATATT
21583 ATATATATATAT
1 ATATATATATAT
21595 AAGTCTAAAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATATATATATT
Found at i:21801 original size:69 final size:71
Alignment explanation
Indices: 21723--21864 Score: 252
Period size: 69 Copynumber: 2.0 Consensus size: 71
21713 AAAAGTCTAA
*
21723 AATAATACTCATTATTTTTAAGTTAAAGTACATC-TTTTTTTT-AGATATTACGTTGAACAACAT
1 AATAATACTCATTATTTTTAAGTTAAAGTACATCTTTTTTTTTGAGATATTACGTTAAACAACAT
21786 ATTATT
66 ATTATT
21792 AATAATACTCATTATTTTTAAGTTAAAGTACATCTTTTTTTTTTGAGATATTACGTTAAACAACA
1 AATAATACTCATTATTTTTAAGTTAAAGTACATC-TTTTTTTTTGAGATATTACGTTAAACAACA
21857 TATTATT
65 TATTATT
21864 A
1 A
21865 TTATGATATA
Statistics
Matches: 69, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
69 34 0.49
71 8 0.12
72 27 0.39
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (71 bp):
AATAATACTCATTATTTTTAAGTTAAAGTACATCTTTTTTTTTGAGATATTACGTTAAACAACAT
ATTATT
Found at i:22355 original size:48 final size:48
Alignment explanation
Indices: 22291--22388 Score: 151
Period size: 48 Copynumber: 2.0 Consensus size: 48
22281 AAAAACTATT
* * * *
22291 TTGATTTATGAGTGTTATGATTTGCTCTAATCTCATAATATTTTTGTA
1 TTGATTCATAAGTGTTATGATTTGCTCTAATCTCATAAGATTTTGGTA
*
22339 TTGATTCATAAGTGTTATGATTTGCTTTAATCTCATAAGATTTTGGTA
1 TTGATTCATAAGTGTTATGATTTGCTCTAATCTCATAAGATTTTGGTA
22387 TT
1 TT
22389 AAATTAACGT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.26, C:0.08, G:0.15, T:0.51
Consensus pattern (48 bp):
TTGATTCATAAGTGTTATGATTTGCTCTAATCTCATAAGATTTTGGTA
Found at i:22374 original size:27 final size:27
Alignment explanation
Indices: 22301--22377 Score: 69
Period size: 27 Copynumber: 3.1 Consensus size: 27
22291 TTGATTTATG
*
22301 AGTGTTATGATTTGCTCTAATCTCATA
1 AGTGTTATGATTTGCTTTAATCTCATA
* *
22328 A----TAT-TTTTG-TATTGAT-TCATA
1 AGTGTTATGATTTGCT-TTAATCTCATA
22349 AGTGTTATGATTTGCTTTAATCTCATA
1 AGTGTTATGATTTGCTTTAATCTCATA
22376 AG
1 AG
22378 ATTTTGGTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 16
0.64 0.09 0.28
Matches are distributed among these distances:
21 7 0.19
22 7 0.19
23 3 0.08
25 3 0.08
26 8 0.22
27 9 0.24
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.48
Consensus pattern (27 bp):
AGTGTTATGATTTGCTTTAATCTCATA
Found at i:25561 original size:60 final size:59
Alignment explanation
Indices: 25489--25650 Score: 193
Period size: 60 Copynumber: 2.7 Consensus size: 59
25479 TAAGGCTACT
* * *
25489 CAAAGAAGGGCCTAACATTTGTCAAAATGCTCAAATAA-GGATCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAAC-TTTGTCAAAATGCTCAAATAAGGGCTC-GATCTTTTAATTTAGC
*
25549 CAAATAAGGGCCTAACGTTATG-GAAAATGCTCAAATAAGGGCTCGATCTTTTAATTTAGC
1 CAAATAAGGGCCTAAC-TT-TGTCAAAATGCTCAAATAAGGGCTCGATCTTTTAATTTAGC
* * * *
25609 CAAATAAGGACATAACGTTATCGAAAATGCTCAAATAAGGGC
1 CAAATAAGGGCCTAACTTTGTC-AAAATGCTCAAATAAGGGC
25651 ATGGCGTCAG
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
58 1 0.01
59 1 0.01
60 80 0.91
61 6 0.07
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (59 bp):
CAAATAAGGGCCTAACTTTGTCAAAATGCTCAAATAAGGGCTCGATCTTTTAATTTAGC
Found at i:25587 original size:31 final size:30
Alignment explanation
Indices: 25549--25650 Score: 84
Period size: 31 Copynumber: 3.4 Consensus size: 30
25539 TTAATTTGGC
25549 CAAATAAGGGCCTAACGTTATGGAAAATGCT
1 CAAATAAGGGCCTAACGTTAT-GAAAATGCT
* * * **
25580 CAAATAAGGGCTCGATC-TT-TTAATTTAGC-
1 CAAATAAGGGC-CTAACGTTATGAAAAT-GCT
* *
25609 CAAATAAGGACATAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTAT-GAAAATGCT
25640 CAAATAAGGGC
1 CAAATAAGGGC
25651 ATGGCGTCAG
Statistics
Matches: 52, Mismatches: 13, Indels: 12
0.68 0.17 0.16
Matches are distributed among these distances:
28 2 0.04
29 15 0.29
30 6 0.12
31 26 0.50
32 3 0.06
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.25
Consensus pattern (30 bp):
CAAATAAGGGCCTAACGTTATGAAAATGCT
Found at i:25785 original size:60 final size:59
Alignment explanation
Indices: 25692--25854 Score: 238
Period size: 60 Copynumber: 2.7 Consensus size: 59
25682 TTCGATACCA
25692 GGCCCTTATTTGAGCATTTTCCATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTT-CATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
* * * *
25752 GGCCCTTATTTGAGTATTTTCAATAACATTAGGCCTTTATTTGGCCAAATTAAAATATCG
1 GGCCCTTATTTGAGCATTTTC-ATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
*
25812 AGCCCTTATTTGAGCATTTTGGCA-AACGTTAGGCCCTTATTTG
1 GGCCCTTATTTGAGCATTTT--CATAACGTTAGGCCCTTATTTG
25855 AACAATTTGC
Statistics
Matches: 92, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
59 1 0.01
60 89 0.97
61 1 0.01
62 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (59 bp):
GGCCCTTATTTGAGCATTTTCATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
Found at i:25823 original size:29 final size:29
Alignment explanation
Indices: 25724--25823 Score: 78
Period size: 29 Copynumber: 3.4 Consensus size: 29
25714 ATAACGTTAG
* *
25724 GCCCTTATTTGGCCAAATTAAAAGATCGG
1 GCCCTTATTTGGCCAAATTAAAACATCGA
* ** *
25753 GCCCTTATTTGAG-TATTTTCAATAACAT-TA
1 GCCCTTATTTG-GCCAAATT-AA-AACATCGA
* *
25783 GGCCTTTATTTGGCCAAATTAAAATATCGA
1 -GCCCTTATTTGGCCAAATTAAAACATCGA
25813 GCCCTTATTTG
1 GCCCTTATTTG
25824 AGCATTTTGG
Statistics
Matches: 52, Mismatches: 13, Indels: 12
0.68 0.17 0.16
Matches are distributed among these distances:
29 28 0.54
30 7 0.13
31 17 0.33
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (29 bp):
GCCCTTATTTGGCCAAATTAAAACATCGA
Found at i:26937 original size:52 final size:54
Alignment explanation
Indices: 26870--26998 Score: 181
Period size: 55 Copynumber: 2.4 Consensus size: 54
26860 TAGACGAAAA
26870 TTATATTATTTTTATG-TTAT-ATTACAAATTAATATGTGATTTATTATATTTAT
1 TTAT-TTATTTTTATGATTATGATTACAAATTAATATGTGATTTATTATATTTAT
* *
26923 TTTTTTATTTTTATGATTTATGATTACAAATTAGTATGTGATTTATTATATTTAT
1 TTATTTATTTTTATGA-TTATGATTACAAATTAATATGTGATTTATTATATTTAT
* *
26978 TTATTTGTTTTAATGAATTAT
1 TTATTTATTTTTATG-ATTAT
26999 TAACACACGT
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
52 11 0.16
53 3 0.04
54 4 0.06
55 48 0.72
56 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.60
Consensus pattern (54 bp):
TTATTTATTTTTATGATTATGATTACAAATTAATATGTGATTTATTATATTTAT
Found at i:28945 original size:26 final size:24
Alignment explanation
Indices: 28916--29037 Score: 70
Period size: 26 Copynumber: 4.8 Consensus size: 24
28906 CTAGCGTTGG
28916 GCCTGGCGCGCAGCCCAGGCTGCGCT
1 GCCTGGCGCGCAGCCCAGGCT-CG-T
* *
28942 GCCT-GCTGGGCAGCCCAGCGCTTGT
1 GCCTGGC-GCGCAGCCCAG-GCTCGT
* *
28967 GCCTGGCACGCGGCCCAGGCTACGTT
1 GCCTGGCGCGCAGCCCAGGCT-CG-T
* *
28993 GCCT-GCTAG-GCAGCCCAGCGCTTGG
1 GCCTGGC--GCGCAGCCCAG-GCTCGT
* *
29018 GCCTGGCGCACGGCCCAGGC
1 GCCTGGCGCGCAGCCCAGGC
29038 CGCTTGGCCT
Statistics
Matches: 74, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
24 6 0.08
25 29 0.39
26 33 0.45
27 6 0.08
ACGTcount: A:0.10, C:0.39, G:0.37, T:0.14
Consensus pattern (24 bp):
GCCTGGCGCGCAGCCCAGGCTCGT
Found at i:28982 original size:25 final size:25
Alignment explanation
Indices: 28954--29048 Score: 70
Period size: 26 Copynumber: 3.7 Consensus size: 25
28944 CTGCTGGGCA
28954 GCCCAGCGCTTGTGCCTGGCACGCG
1 GCCCAGCGCTTGTGCCTGGCACGCG
* * *
28979 GCCCAG-GCTACGTTGCCT-GCTAGGCA
1 GCCCAGCGCT-TG-TGCCTGGC-ACGCG
* * *
29005 GCCCAGCGCTTGGGCCTGGCGCACG
1 GCCCAGCGCTTGTGCCTGGCACGCG
29030 GCCCAGGCCGCTTG-GCCTG
1 GCCCA-G-CGCTTGTGCCTG
29049 CCTAGCAAGC
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
24 3 0.06
25 19 0.35
26 23 0.43
27 9 0.17
ACGTcount: A:0.09, C:0.39, G:0.36, T:0.16
Consensus pattern (25 bp):
GCCCAGCGCTTGTGCCTGGCACGCG
Found at i:28983 original size:51 final size:51
Alignment explanation
Indices: 28908--29037 Score: 190
Period size: 51 Copynumber: 2.6 Consensus size: 51
28898 AGCCAGGCCT
* * *
28908 AGCG-TTGGGCCTGGCGCGCAGCCCAGGCTGCGCTGCCTGCTGGGCAGCCC
1 AGCGCTTGGGCCTGGCGCGCGGCCCAGGCTACGCTGCCTGCTAGGCAGCCC
* * *
28958 AGCGCTTGTGCCTGGCACGCGGCCCAGGCTACGTTGCCTGCTAGGCAGCCC
1 AGCGCTTGGGCCTGGCGCGCGGCCCAGGCTACGCTGCCTGCTAGGCAGCCC
*
29009 AGCGCTTGGGCCTGGCGCACGGCCCAGGC
1 AGCGCTTGGGCCTGGCGCGCGGCCCAGGC
29038 CGCTTGGCCT
Statistics
Matches: 70, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
50 4 0.06
51 66 0.94
ACGTcount: A:0.10, C:0.38, G:0.38, T:0.15
Consensus pattern (51 bp):
AGCGCTTGGGCCTGGCGCGCGGCCCAGGCTACGCTGCCTGCTAGGCAGCCC
Found at i:29144 original size:26 final size:26
Alignment explanation
Indices: 29095--29162 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
29085 AACAAAAAAA
*
29095 AAAAGAAAAAGAAAGAAAAGAGAAGG
1 AAAAGAAAAAGAAAGAAAAGAGAAAG
* *
29121 AAAAGAAATATAAA-AAAAGAAGAAAG
1 AAAAGAAAAAGAAAGAAAAG-AGAAAG
29147 AAAAGAAAAAGGAAAG
1 AAAAGAAAAA-GAAAG
29163 GAATAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
25 5 0.15
26 26 0.76
27 3 0.09
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (26 bp):
AAAAGAAAAAGAAAGAAAAGAGAAAG
Found at i:29162 original size:11 final size:10
Alignment explanation
Indices: 29090--29162 Score: 60
Period size: 10 Copynumber: 7.0 Consensus size: 10
29080 GCCCAAACAA
*
29090 AAAAAAAAAG
1 AAAAAGAAAG
29100 AAAAAGAAAG
1 AAAAAGAAAG
29110 -AAAAGAGAAG
1 AAAAAGA-AAG
* *
29120 GAAAAGAAAT
1 AAAAAGAAAG
29130 ATAAAA-AAAG
1 A-AAAAGAAAG
29140 AAGAAAGAAAAG
1 AA-AAAG-AAAG
29152 AAAAAGGAAAG
1 AAAAA-GAAAG
29163 GAATAAAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
9 7 0.13
10 21 0.40
11 17 0.33
12 7 0.13
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:31525 original size:78 final size:80
Alignment explanation
Indices: 31394--31543 Score: 223
Period size: 78 Copynumber: 1.9 Consensus size: 80
31384 TTTTTTCTAC
* * * * *
31394 AAAACTCTATTTTTATATAATTAATCTAATAGTATCTTTATAATTATTTTATTTTACCATTTTAC
1 AAAACTCTATTTTTATATAACTAATATAATAATATCCTTATAACTATTTTATTTTACCATTTTAC
31459 TATTTTACTCAACTA
66 TATTTTACTCAACTA
*
31474 AAAACTCTATTTTTATTTAACTAA-AT-ATAATATCCTTATAACTATTTTATTTTACCATTTTAC
1 AAAACTCTATTTTTATATAACTAATATAATAATATCCTTATAACTATTTTATTTTACCATTTTAC
*
31537 TGTTTTA
66 TATTTTA
31544 ATTAAAAAAC
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
78 40 0.63
79 1 0.02
80 22 0.35
ACGTcount: A:0.35, C:0.13, G:0.01, T:0.51
Consensus pattern (80 bp):
AAAACTCTATTTTTATATAACTAATATAATAATATCCTTATAACTATTTTATTTTACCATTTTAC
TATTTTACTCAACTA
Found at i:31718 original size:75 final size:77
Alignment explanation
Indices: 31631--31795 Score: 246
Period size: 77 Copynumber: 2.2 Consensus size: 77
31621 ATAAATAAAC
* * * * *
31631 TTTTAC-AGTTTTATTCCACTAAAAACTCTA-TTT-TTTAATTAAATCTAATATCTTTATAACTA
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTGTTTAATTAAATATAATAACCTTATAACTA
31693 TTTTATTTTACCA
65 TTTTATTTTACCA
*
31706 TTTTACTATTTTACTCAACTAAAAACTCTATTTTGTTTAATTAAGTATAATAACCTTATAACTAT
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTGTTTAATTAAATATAATAACCTTATAACTAT
31771 TTTATTTTACCA
66 TTTATTTTACCA
31783 TTTTACTATTTTA
1 TTTTACTATTTTA
31796 ATTAAAAAAA
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
75 26 0.32
76 4 0.05
77 51 0.63
ACGTcount: A:0.33, C:0.14, G:0.02, T:0.51
Consensus pattern (77 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTGTTTAATTAAATATAATAACCTTATAACTAT
TTTATTTTACCA
Found at i:32304 original size:29 final size:29
Alignment explanation
Indices: 32268--32345 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
32258 AGGATCACCT
*
32268 AGGGGCATTTTGGTCATTTTTTCACATTC
1 AGGGGCATTTTGGTCATTTTTGCACATTC
* * *
32297 AGGGGCATTATGGTCATTTCTGCATATTC
1 AGGGGCATTTTGGTCATTTTTGCACATTC
*
32326 AGGGGCATTTTGATCATTTT
1 AGGGGCATTTTGGTCATTTT
32346 AAGTTCATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.42
Consensus pattern (29 bp):
AGGGGCATTTTGGTCATTTTTGCACATTC
Done.