Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006880.1 Corchorus capsularis cultivar CVL-1 contig06901, 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: 55489
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:2407 original size:27 final size:26
Alignment explanation
Indices: 2350--2419 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 26
2340 GTGAACTTAG
* *
2350 AATGACCAAAATGCCCCTGAATGTGAC
1 AATGACCAAAATG-CCCTGAATGTAAA
* *
2377 AATGACCAAAATGCCCTTAGTGTAAAA
1 AATGACCAAAATGCCCTGAATGT-AAA
*
2404 AATGACTAAAATGCCC
1 AATGACCAAAATGCCC
2420 CTATGTGACC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 8 0.22
27 29 0.78
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (26 bp):
AATGACCAAAATGCCCTGAATGTAAA
Found at i:3070 original size:22 final size:22
Alignment explanation
Indices: 3028--3070 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3018 GAGTCATGAT
*
3028 ATGAAACACGACATCTCGAACG
1 ATGAAACACGACATATCGAACG
*
3050 ATGAAACACGACATATTGAAC
1 ATGAAACACGACATATCGAAC
3071 CAGAAGAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.23, G:0.16, T:0.16
Consensus pattern (22 bp):
ATGAAACACGACATATCGAACG
Found at i:12024 original size:18 final size:18
Alignment explanation
Indices: 12001--12039 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
11991 CACCACCGCT
*
12001 GCCATGACCCTCTCCATA
1 GCCATGACCCTCGCCATA
*
12019 GCCATGCCCCTCGCCATA
1 GCCATGACCCTCGCCATA
12037 GCC
1 GCC
12040 TTCACCATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.49, G:0.15, T:0.18
Consensus pattern (18 bp):
GCCATGACCCTCGCCATA
Found at i:15045 original size:66 final size:66
Alignment explanation
Indices: 14966--15094 Score: 208
Period size: 66 Copynumber: 2.0 Consensus size: 66
14956 CCAAAAGAAT
* *
14966 TACAAATAAAATATAG-CTTATGGCAATACTTAA-TATTTTTTTGTTTTATAATTAGAATATCTA
1 TACAAATAAAATATAGTC-TATGGCAATACTTAATTATTTTTATGTTTAAT-ATTAGAATATCTA
15029 ATA
64 ATA
15032 TACAAATAAAATATAGTCTATGGCAATACTTAATTATTTTTATGTTTAATATTAGAATATCTA
1 TACAAATAAAATATAGTCTATGGCAATACTTAATTATTTTTATGTTTAATATTAGAATATCTA
15095 TTTTTTTTGT
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
66 44 0.75
67 15 0.25
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (66 bp):
TACAAATAAAATATAGTCTATGGCAATACTTAATTATTTTTATGTTTAATATTAGAATATCTAAT
A
Found at i:15587 original size:21 final size:20
Alignment explanation
Indices: 15545--15588 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
15535 TCTTGTAATC
*
15545 TAAAATTACTAAAAAAGTTA
1 TAAAATTACTAAAAAAGCTA
* *
15565 TAAAAGTTATTAAAATAGCTA
1 TAAAA-TTACTAAAAAAGCTA
15586 TAA
1 TAA
15589 TGCTTTCCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
TAAAATTACTAAAAAAGCTA
Found at i:17437 original size:3 final size:3
Alignment explanation
Indices: 17429--17465 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
17419 TCAACAAATT
17429 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
17466 ATTTTGATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:17764 original size:21 final size:21
Alignment explanation
Indices: 17740--17785 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
17730 CTCTACCAAA
*
17740 CTAATGAATGATCTATGTGAT
1 CTAATGAATGATCAATGTGAT
17761 CTAATGAATGATCAATGTGAT
1 CTAATGAATGATCAATGTGAT
17782 CTAA
1 CTAA
17786 AATGACATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (21 bp):
CTAATGAATGATCAATGTGAT
Found at i:18553 original size:793 final size:791
Alignment explanation
Indices: 17015--18557 Score: 2175
Period size: 793 Copynumber: 1.9 Consensus size: 791
17005 CTAATTTTTC
* * * *
17015 TTATTTAAGGTTACAAAAAAATTCTATAATAATGATTATACAAAAGGCATAATACTACTATCAAA
1 TTATTTAAGGTTACAAAAAAAATC-ATAATAATGATTAAAAAAAAGGCATAATACCACTATCAAA
*
17080 TAATCCAATAACCTTATAATATTAGTAATTTTAGTTATCAAATTTCTCATTTATGGGTTTCTAAT
65 TAATCCAATAACCTTACAATATTAGTAATTTTAGTTATCAAATTTCTCATTTATGGGTTTCTAAT
* * *
17145 TAGAAAGCTAACTCTATATTATCAAGAAATTTAACAACCTTACATGCTTAGTAGCTTTATCAATG
130 TAGAAAGCTAACTATAAATTATCAAGAAATTTAACAACCTTACATGCTTAGTAGATTTATCAATG
*
17210 GTGAATTGTTATTAACTTTTTAATCAAAGAATACTAAAAAAGTTGTAGTGAATAAAGAGATATTT
195 GTGAATTGTTATTAACTTTTTAATCAAAGAATACTAAAAAAGTTGTAGTGAATAAAGAGATATAT
* *
17275 AGGGTTAAAAAAAATAGAGAGGGTAATTTATTGATATATAGATTGATGGTTAGTTAAAGTTCTTA
260 AGGGTT-AAAAAAATAGAGAGGGTAATTTATTGATATATAGATTGATGGTCAGTTAAAGTCCTTA
* *
17340 TATATAGAATTAGGAGTTTAATTTTATTATTTTGTACTATGTGTATATGTTAATCAATCTTAGTG
324 TATATAGAATTAGGAGTTTAATTTTATTATCTTATACTATGTGTATATGTTAATCAATCTTAGTG
* * * * * * *
17405 TTTCATGAATATTTTCAACAAATTTTATTATTATTATTATTATTATTATTATTATTATTATATTT
389 TTACATAAATATTTTCAACAAATTTTATTATCATTATTATTATTATGATTATCATCACTATA---
* * * *
17470 TGATATCACTAATTTTACTATTTCAATCTCTCCAAAACAAATCTCACAATTCAACTAAACACATC
451 T-ATATCACTAATTTCACCATTTCAATCTCTACAAAACAAATCTCACAATTCAACCAAACACATC
* **
17535 CGTACCTGTAAGTCAAATTTGTATAAGGTTATTTTAAACTTAATGCAACATGAGGAAGAATAAAA
515 CGTACCTGGAAGTCAAATTTGTATAAGGTTATACTAAACTTAATGCAACATGAGGAAGAATAAAA
* **
17600 TTAGGTGTACAAAATTGGTTCCTAATTACTAATTCATATGTCCTTTCCTTTTTGGTGATAGAGAA
580 TTAGATGTACAAAATTAATTCCTAATTACTAATTCATATGTCCTTTCCTTTTTGGTGATAGAGAA
*
17665 ATTAAATTTATATATATGCGTATCTTTGGCAAGTTGAAGCAAAATTAAATGATATCTAGCTATTA
645 ATTAAATTTATATATATGCGTATCTTTAGCAAGTTGAAGCAAAATTAAATGATATCTAGCTATTA
*
17730 CTCTACCAAACTAATGAATGATCTATGTGATCTAATGAATGATCAATGTGATCTAAAATGACATA
710 CTCTACCAAACTAATGAATGATCAATGTGATCTAATGAATGATCAATGTGATCTAAAATGACATA
17795 GCAAAAAGGTAATAATT
775 GCAAAAAGGTAATAATT
* *
17812 TTATTTAAGGTTACAAAAAAAATC-T-ATAATGA-TAAAAAAAAGGCATAATACCACTATGAACT
1 TTATTTAAGGTTACAAAAAAAATCATAATAATGATTAAAAAAAAGGCATAATACCACTATCAAAT
** * * *
17874 AATTTAATAACCTTACATTCTTAGTAATTTTGGTTATCAAATTTCTCATTTAT-GGTTTCTAATT
66 AATCCAATAACCTTACAATATTAGTAATTTTAGTTATCAAATTTCTCATTTATGGGTTTCTAATT
*
17938 AGAAAGCTAAACTATAGAATTATCAAGAAATTTAGCAACCTTACATGCTTAGTA-ATATTATCAA
131 AGAAAGCT-AACTATA-AATTATCAAGAAATTTAACAACCTTACATGCTTAGTAGAT-TTATCAA
* * *
18002 TGGTGAA-TGTTATTAA-TTTTTCAATCTAAGATTACTAAAAAAGTTGTAGTGGATAATTTAAGA
193 TGGTGAATTGTTATTAACTTTTT-AATCAAAGAATACTAAAAAAGTTGTAGT-G--AA-TAAAGA
* **
18065 GATATATAGGGTT-AAAAAATAGTGAGTTTAATTTATTGATATATAGATTGATGGTCAGTTAAAG
253 GATATATAGGGTTAAAAAAATAGAGAGGGTAATTTATTGATATATAGATTGATGGTCAGTTAAAG
* *
18129 TCCTTGTATATAGAATTAGGAGTTTAATTTTATTATCTTATTCTATGTGTATATGTTAATCAATC
318 TCCTTATATATAGAATTAGGAGTTTAATTTTATTATCTTATACTATGTGTATATGTTAATCAATC
* * * *
18194 TTAGTGTTACATAAATATTTTCAACAAATTTTATTCTCATTATTGTTATTCTGA-TGTCA-CACT
383 TTAGTGTTACATAAATATTTTCAACAAATTTTATTATCATTATTATTATTATGATTATCATCACT
* * * *
18257 GTA-ATA-C-CTAATTTCACCATTTCAATCTCTAC-AAACAAATTTCACAATTCAACCAATCATA
448 ATATATATCACTAATTTCACCATTTCAATCTCTACAAAACAAATCTCACAATTCAACCAAACACA
* * *
18318 TCGGT-CCTGGAAGTCAAGTTTGTATAAGGTTATAACTAAACTTAATGCAAACATGAGGAAGTAT
513 TCCGTACCTGGAAGTCAAATTTGTATAAGGTTAT-ACTAAACTTAATGC-AACATGAGGAAGAAT
18382 AAAATTAGATGTACAAAA-TAATTCCTAATTACTAATTCATATGTCC-TTCCTTTTTTTGGTGAT
576 AAAATTAGATGTACAAAATTAATTCCTAATTACTAATTCATATGTCCTTTCC--TTTTTGGTGAT
*
18445 AGAGAAATTAAATTTATATGCTATATATGCGTATCTTTAGCAAGTTGAAGTAAAATTAAAATTGA
639 AGAGAAATTAAA-TT-TA---TATATATGCGTATCTTTAGCAAGTTGAAGCAAAATT-AAA-TGA
* * *
18510 TATCTCGCTATTACTCTACCAAATTAATGAATTATCAATGTGATCTAA
697 TATCTAGCTATTACTCTACCAAACTAATGAATGATCAATGTGATCTAA
18558 AATAGCAAAA
Statistics
Matches: 664, Mismatches: 63, Indels: 42
0.86 0.08 0.05
Matches are distributed among these distances:
784 30 0.05
785 67 0.10
786 76 0.11
787 3 0.00
788 5 0.01
791 34 0.05
792 27 0.04
793 165 0.25
794 60 0.09
795 155 0.23
796 2 0.00
797 40 0.06
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.38
Consensus pattern (791 bp):
TTATTTAAGGTTACAAAAAAAATCATAATAATGATTAAAAAAAAGGCATAATACCACTATCAAAT
AATCCAATAACCTTACAATATTAGTAATTTTAGTTATCAAATTTCTCATTTATGGGTTTCTAATT
AGAAAGCTAACTATAAATTATCAAGAAATTTAACAACCTTACATGCTTAGTAGATTTATCAATGG
TGAATTGTTATTAACTTTTTAATCAAAGAATACTAAAAAAGTTGTAGTGAATAAAGAGATATATA
GGGTTAAAAAAATAGAGAGGGTAATTTATTGATATATAGATTGATGGTCAGTTAAAGTCCTTATA
TATAGAATTAGGAGTTTAATTTTATTATCTTATACTATGTGTATATGTTAATCAATCTTAGTGTT
ACATAAATATTTTCAACAAATTTTATTATCATTATTATTATTATGATTATCATCACTATATATAT
CACTAATTTCACCATTTCAATCTCTACAAAACAAATCTCACAATTCAACCAAACACATCCGTACC
TGGAAGTCAAATTTGTATAAGGTTATACTAAACTTAATGCAACATGAGGAAGAATAAAATTAGAT
GTACAAAATTAATTCCTAATTACTAATTCATATGTCCTTTCCTTTTTGGTGATAGAGAAATTAAA
TTTATATATATGCGTATCTTTAGCAAGTTGAAGCAAAATTAAATGATATCTAGCTATTACTCTAC
CAAACTAATGAATGATCAATGTGATCTAATGAATGATCAATGTGATCTAAAATGACATAGCAAAA
AGGTAATAATT
Found at i:20780 original size:24 final size:24
Alignment explanation
Indices: 20730--20780 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
20720 AACCCCCAGA
* *
20730 TCCTGAACCAGAGCCAGCCCCAGC
1 TCCTGAACCAGAACCAGCCCCACC
*
20754 TCCTGATCCAGAACCA-CCTCCACC
1 TCCTGAACCAGAACCAGCC-CCACC
20778 TCC
1 TCC
20781 GAGGCCAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.24, C:0.49, G:0.14, T:0.14
Consensus pattern (24 bp):
TCCTGAACCAGAACCAGCCCCACC
Found at i:22821 original size:2 final size:2
Alignment explanation
Indices: 22814--22849 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
22804 GTTTGAACAA
22814 AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22850 TTAGAGGTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22959 original size:15 final size:15
Alignment explanation
Indices: 22939--22989 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
22929 GTCGAGTTAA
22939 ATTTGGGTCAGGTTG
1 ATTTGGGTCAGGTTG
*
22954 ATTTGGGTTC-GAGTTAA
1 ATTTGGG-TCAG-GTT-G
22971 ATTTGGGTCAGGTTG
1 ATTTGGGTCAGGTTG
22986 ATTT
1 ATTT
22990 TGATTCAGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 12 0.40
16 10 0.33
17 8 0.27
ACGTcount: A:0.18, C:0.06, G:0.33, T:0.43
Consensus pattern (15 bp):
ATTTGGGTCAGGTTG
Found at i:22968 original size:32 final size:32
Alignment explanation
Indices: 22930--23016 Score: 122
Period size: 32 Copynumber: 2.7 Consensus size: 32
22920 TTGAGTTAGG
*
22930 TCGAGTTAAATTTGGGTCAGGTTGATTTGGGT
1 TCGAGTTAAATTTGGGTCAGGTTGATTTGGAT
*
22962 TCGAGTTAAATTTGGGTCAGGTTGATTTTGAT
1 TCGAGTTAAATTTGGGTCAGGTTGATTTGGAT
* *
22994 TC-AGGTCAATTTTGGGTCAGGTT
1 TCGA-GTTAAATTTGGGTCAGGTT
23017 AATTCGGTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 1 0.02
32 49 0.98
ACGTcount: A:0.20, C:0.08, G:0.31, T:0.41
Consensus pattern (32 bp):
TCGAGTTAAATTTGGGTCAGGTTGATTTGGAT
Found at i:23013 original size:16 final size:16
Alignment explanation
Indices: 22934--23020 Score: 79
Period size: 16 Copynumber: 5.4 Consensus size: 16
22924 GTTAGGTCGA
*
22934 GTTAAATTTGGGTCAG
1 GTTAATTTTGGGTCAG
*
22950 GTTGA-TTTGGGTTC-G
1 GTTAATTTTGGG-TCAG
*
22965 AGTTAAATTTGGGTCAG
1 -GTTAATTTTGGGTCAG
* **
22982 GTTGATTTTGATTCAG
1 GTTAATTTTGGGTCAG
*
22998 GTCAATTTTGGGTCAG
1 GTTAATTTTGGGTCAG
23014 GTTAATT
1 GTTAATT
23021 CGGTTTCGGG
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
15 7 0.12
16 42 0.75
17 7 0.12
ACGTcount: A:0.21, C:0.07, G:0.30, T:0.43
Consensus pattern (16 bp):
GTTAATTTTGGGTCAG
Found at i:23574 original size:13 final size:13
Alignment explanation
Indices: 23556--23582 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
23546 ACTAAGTAAC
23556 TAACAAATAAGGT
1 TAACAAATAAGGT
23569 TAACAAATAAGGT
1 TAACAAATAAGGT
23582 T
1 T
23583 GAGATCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (13 bp):
TAACAAATAAGGT
Found at i:31952 original size:8 final size:8
Alignment explanation
Indices: 31939--31964 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
31929 GACATGATAC
31939 TATTATTA
1 TATTATTA
31947 TATTATTA
1 TATTATTA
31955 TATTATTA
1 TATTATTA
31963 TA
1 TA
31965 GTCAAAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATTATTA
Found at i:36977 original size:39 final size:39
Alignment explanation
Indices: 36923--37006 Score: 159
Period size: 39 Copynumber: 2.1 Consensus size: 39
36913 GGGGAAAGAA
36923 TTTTCCTTATTCTTTTTTTTCTTGAAATTAATTAAGATG
1 TTTTCCTTATTCTTTTTTTTCTTGAAATTAATTAAGATG
36962 TTTTCCTTATTCTTTTTTTTCTTGAAATTAATTAAGATG
1 TTTTCCTTATTCTTTTTTTTCTTGAAATTAATTAAGATG
37001 TATTTC
1 T-TTTC
37007 TCTCTAAAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 40 0.91
40 4 0.09
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.60
Consensus pattern (39 bp):
TTTTCCTTATTCTTTTTTTTCTTGAAATTAATTAAGATG
Found at i:37516 original size:50 final size:50
Alignment explanation
Indices: 37407--37518 Score: 145
Period size: 50 Copynumber: 2.2 Consensus size: 50
37397 AACCAGCAAT
** *
37407 ACCAGCAATACATAGTTTGAAAATAAACAACATTACTGGGAAGAAGATAA
1 ACCAGCAATACATAGTTCCAAAATAAACAACATTACTGGAAAGAAGATAA
* * *
37457 ACTC-GCAATACATAGTTCCACAATAAACAACATTACTGTAAAGGAGATAA
1 AC-CAGCAATACATAGTTCCAAAATAAACAACATTACTGGAAAGAAGATAA
*
37507 ACCAACAATACA
1 ACCAGCAATACA
37519 ATCACAAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
49 1 0.02
50 51 0.96
51 1 0.02
ACGTcount: A:0.49, C:0.19, G:0.12, T:0.20
Consensus pattern (50 bp):
ACCAGCAATACATAGTTCCAAAATAAACAACATTACTGGAAAGAAGATAA
Found at i:39558 original size:34 final size:34
Alignment explanation
Indices: 39507--39571 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
39497 ACAAATTGCG
* *
39507 ATATAGAGGAATCAAAACATTAGGAATTAAAGCA
1 ATATAGAGGAATCAAAACATAACGAATTAAAGCA
* *
39541 ATATAGAGTAATGAAAACATAACGAATTAAA
1 ATATAGAGGAATCAAAACATAACGAATTAAA
39572 AGGAAATAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.55, C:0.08, G:0.15, T:0.22
Consensus pattern (34 bp):
ATATAGAGGAATCAAAACATAACGAATTAAAGCA
Found at i:44053 original size:20 final size:20
Alignment explanation
Indices: 44014--44053 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
44004 TATTTTTATA
*
44014 GCTATTTTTATATGTTTTTT
1 GCTATTTTTATATGTATTTT
*
44034 GCTATTTTTATGTGTATTTT
1 GCTATTTTTATATGTATTTT
44054 ACCCCTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.05, G:0.12, T:0.68
Consensus pattern (20 bp):
GCTATTTTTATATGTATTTT
Found at i:46708 original size:12 final size:12
Alignment explanation
Indices: 46688--46725 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
46678 CCGAACCGTT
46688 TAATAATATATA
1 TAATAATATATA
46700 TAAT--TATATA
1 TAATAATATATA
46710 TAATAATATATA
1 TAATAATATATA
46722 TAAT
1 TAAT
46726 TATTAAACGG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.42
12 14 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAATAATATATA
Found at i:46709 original size:10 final size:10
Alignment explanation
Indices: 46690--46728 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
46680 GAACCGTTTA
46690 ATAA-TATAT
1 ATAATTATAT
46699 ATAATTATAT
1 ATAATTATAT
46709 ATAATAATATAT
1 ATAAT--TATAT
46721 ATAATTAT
1 ATAATTAT
46729 TAAACGGTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 4 0.15
10 13 0.48
12 10 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
ATAATTATAT
Found at i:48589 original size:48 final size:48
Alignment explanation
Indices: 48526--48763 Score: 302
Period size: 48 Copynumber: 4.9 Consensus size: 48
48516 AAGATGTAAC
48526 CTTTGAGTAAAAGATTGAACTTTAAAGTAATTTGTAAATAAAGTATAAT
1 CTTTGAG-AAAAGATTGAACTTTAAAGTAATTTGTAAATAAAGTATAAT
*
48575 CTTTGAGAAAAGATTGAACTTTAAAGTAATTTGTAAATAAAGTGTAAT
1 CTTTGAGAAAAGATTGAACTTTAAAGTAATTTGTAAATAAAGTATAAT
*
48623 CTTTGAGAAAAGATTGAACTTTAAAGTAATTTGTAAATAAAGTGTAAT
1 CTTTGAGAAAAGATTGAACTTTAAAGTAATTTGTAAATAAAGTATAAT
* ** * *
48671 CTTTGAGAAAAGATAGAACCTTATTGATTAATTTGTAAATAAAAGTGA-GAT
1 CTTTGAGAAAAGATTGAA-CTT-TAAAGTAATTTGTAAAT-AAAGT-ATAAT
* *
48722 CTTTAAGTAAAAGATT-AACCTTTTAAA-TAGTTTGTAAATAAA
1 CTTTGAG-AAAAGATTGAA-C-TTTAAAGTAATTTGTAAATAAA
48764 AATGAGAAGA
Statistics
Matches: 171, Mismatches: 12, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
48 105 0.61
49 13 0.08
50 25 0.15
51 19 0.11
52 9 0.05
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (48 bp):
CTTTGAGAAAAGATTGAACTTTAAAGTAATTTGTAAATAAAGTATAAT
Found at i:48646 original size:96 final size:99
Alignment explanation
Indices: 48514--48763 Score: 341
Period size: 96 Copynumber: 2.5 Consensus size: 99
48504 TGATTTATGT
*
48514 TAAAGATGTAACCTTTGAGTAAAAGATTGAACTTTAAAGTAATTTGTAAATAAAGTATAATCTTT
1 TAAAG-TGTAATCTTTGAGTAAAAGATTGAACTTTAAAGTAATTTGTAAATAAAGTATAATCTTT
*
48579 GAGAAAAGATTGAA-CTT-TAAAGTAATTTGTAAA
65 GAGAAAAGATAGAACCTTATAAAGTAATTTGTAAA
*
48612 TAAAGTGTAATCTTTGAG-AAAAGATTGAACTTTAAAGTAATTTGTAAATAAAGTGTAATCTTTG
1 TAAAGTGTAATCTTTGAGTAAAAGATTGAACTTTAAAGTAATTTGTAAATAAAGTATAATCTTTG
** *
48676 AGAAAAGATAGAACCTTATTGATTAATTTGTAAA
66 AGAAAAGATAGAACCTTATAAAGTAATTTGTAAA
* *
48710 TAAAAGTG-AGATCTTTAAGTAAAAGATT-AACCTTTTAAA-TAGTTTGTAAATAAA
1 T-AAAGTGTA-ATCTTTGAGTAAAAGATTGAA-C-TTTAAAGTAATTTGTAAATAAA
48764 AATGAGAAGA
Statistics
Matches: 137, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
96 57 0.42
97 15 0.11
98 20 0.15
99 16 0.12
100 23 0.17
101 6 0.04
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.35
Consensus pattern (99 bp):
TAAAGTGTAATCTTTGAGTAAAAGATTGAACTTTAAAGTAATTTGTAAATAAAGTATAATCTTTG
AGAAAAGATAGAACCTTATAAAGTAATTTGTAAA
Found at i:48742 original size:51 final size:50
Alignment explanation
Indices: 48526--49017 Score: 309
Period size: 51 Copynumber: 9.9 Consensus size: 50
48516 AAGATGTAAC
* ** * *
48526 CTTTGAGTAAAAGATTGAA-CTTTAAAGTAATTTGTAAAT-AAAGT-ATAAT
1 CTTTAAGTAAAAGATT-AACCTTTTGATTAATTTGTAAATAAAAGTGA-GAT
* ** *
48575 CTTTGAG-AAAAGATTGAA-CTTTAAAGTAATTTGTAAAT-AAAGTGTA-AT
1 CTTTAAGTAAAAGATT-AACCTTTTGATTAATTTGTAAATAAAAGTG-AGAT
* ** *
48623 CTTTGAG-AAAAGATTGAA-CTTTAAAGTAATTTGTAAAT-AAAGTGTA-AT
1 CTTTAAGTAAAAGATT-AACCTTTTGATTAATTTGTAAATAAAAGTG-AGAT
* *
48671 CTTTGAG-AAAAGATAGAACCTTATTGATTAATTTGTAAATAAAAGTGAGAT
1 CTTTAAGTAAAAGAT-TAACCTT-TTGATTAATTTGTAAATAAAAGTGAGAT
* * * * *
48722 CTTTAAGTAAAAGATTAACCTTTTAAATAGTTTGTAAATAAAAATGAGAA
1 CTTTAAGTAAAAGATTAACCTTTTGATTAATTTGTAAATAAAAGTGAGAT
**
48772 GATTAAGTAAAAGATTGAACCTTTTGATTAATTTGTAAATAAAAGTGAGAT
1 CTTTAAGTAAAAGATT-AACCTTTTGATTAATTTGTAAATAAAAGTGAGAT
* * * * * * * *
48823 CTTTAGGCT-AAAGATTGACCTTTTAAGTAATTTAT-GATAAAAATAAGA-
1 CTTTAAG-TAAAAGATTAACCTTTTGATTAATTTGTAAATAAAAGTGAGAT
* * * * * *
48871 CATTTGAACTAAAGAGATTAAACTTTTGATCAATTTGTAAATAAAGGTGAAAC
1 C-TTT-AAGTAAA-AGATTAACCTTTTGATTAATTTGTAAATAAAAGTGAGAT
* * * * * *
48924 CTTTGGACTAAAAGATTAA-ATTTTAGATTAATTCGTAAATAAAAATGAAAT
1 CTTT-AAGTAAAAGATTAACCTTTT-GATTAATTTGTAAATAAAAGTGAGAT
* *
48975 CTTTGAACTAAAAGATTGAA--TTTTGATTGATTTGTAAATAAAA
1 CTTT-AAGTAAAAGATT-AACCTTTTGATTAATTTGTAAATAAAA
49018 AATGAGACCT
Statistics
Matches: 374, Mismatches: 51, Indels: 35
0.81 0.11 0.08
Matches are distributed among these distances:
48 103 0.28
49 24 0.06
50 92 0.25
51 126 0.34
52 28 0.07
53 1 0.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (50 bp):
CTTTAAGTAAAAGATTAACCTTTTGATTAATTTGTAAATAAAAGTGAGAT
Found at i:48808 original size:101 final size:99
Alignment explanation
Indices: 48526--49017 Score: 404
Period size: 101 Copynumber: 4.9 Consensus size: 99
48516 AAGATGTAAC
* * * *
48526 CTTTGAGTAAAAGATTGAAC-TTTAAAGTAATTTGTAAATAAAGTAT-AATCTTTG-A-GAAAAG
1 CTTTAAGTAAAAGATT-AACTTTTAAA-TAATTTGTAAATAAA-AATGAAACTTTGAACTAAAAG
** *
48587 ATTGAACTTTAAAGTAATTTGTAAAT-AAAGTGTA-AT
63 ATTGAACTTTTGATTAATTTGTAAATAAAAGTG-AGAT
* * * *
48623 CTTTGAG-AAAAGATTGAAC-TTTAAAGTAATTTGTAAAT-AAAGTGTAATCTTTG-A-GAAAAG
1 CTTTAAGTAAAAGATT-AACTTTTAAA-TAATTTGTAAATAAAAATG-AAACTTTGAACTAAAAG
*
48683 ATAGAACCTTATTGATTAATTTGTAAATAAAAGTGAGAT
63 ATTGAA-CTT-TTGATTAATTTGTAAATAAAAGTGAGAT
* ** *
48722 CTTTAAGTAAAAGATTAACCTTTTAAATAGTTTGTAAATAAAAATGAGAAGATT-AAGTAAAAGA
1 CTTTAAGTAAAAGATTAA-CTTTTAAATAATTTGTAAATAAAAATGA-AACTTTGAACTAAAAGA
48786 TTGAACCTTTTGATTAATTTGTAAATAAAAGTGAGAT
64 TTGAA-CTTTTGATTAATTTGTAAATAAAAGTGAGAT
* * * * *
48823 CTTTAGGCT-AAAGATTGACCTTTTAAGTAATTTAT-GATAAAAAT-AAGACATTTGAACTAAAG
1 CTTTAAG-TAAAAGATT-AACTTTTAAATAATTTGTAAATAAAAATGAA-AC-TTTGAACTAAA-
* * * * *
48885 AGATTAAACTTTTGATCAATTTGTAAATAAAGGTGAAAC
61 AGATTGAACTTTTGATTAATTTGTAAATAAAAGTGAGAT
* * * * *
48924 CTTTGGACTAAAAGATTAAATTTTAGATTAATTCGTAAATAAAAATGAAATCTTTGAACTAAAAG
1 CTTT-AAGTAAAAGATTAACTTTTA-AATAATTTGTAAATAAAAATGAAA-CTTTGAACTAAAAG
*
48989 ATTGAA-TTTTGATTGATTTGTAAATAAAA
63 ATTGAACTTTTGATTAATTTGTAAATAAAA
49018 AATGAGACCT
Statistics
Matches: 329, Mismatches: 41, Indels: 46
0.79 0.10 0.11
Matches are distributed among these distances:
94 1 0.00
95 2 0.01
96 51 0.16
97 10 0.03
98 16 0.05
99 18 0.05
100 31 0.09
101 133 0.40
102 44 0.13
103 20 0.06
104 3 0.01
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (99 bp):
CTTTAAGTAAAAGATTAACTTTTAAATAATTTGTAAATAAAAATGAAACTTTGAACTAAAAGATT
GAACTTTTGATTAATTTGTAAATAAAAGTGAGAT
Found at i:50800 original size:17 final size:18
Alignment explanation
Indices: 50768--50802 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
50758 GCTGTGCAAG
50768 AACCGACCGAAACCAAAT
1 AACCGACCGAAACCAAAT
*
50786 AACCGGCCG-AACCAAAT
1 AACCGACCGAAACCAAAT
50803 CATAAACGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.46, C:0.34, G:0.14, T:0.06
Consensus pattern (18 bp):
AACCGACCGAAACCAAAT
Found at i:51193 original size:12 final size:12
Alignment explanation
Indices: 51162--51186 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51152 ATAAACCCTA
51162 AACCAAAAACCG
1 AACCAAAAACCG
51174 AACCAAAAACCG
1 AACCAAAAACCG
51186 A
1 A
51187 CCGAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.32, G:0.08, T:0.00
Consensus pattern (12 bp):
AACCAAAAACCG
Found at i:52659 original size:15 final size:15
Alignment explanation
Indices: 52639--52668 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52629 TCATGGTCCC
52639 GACAAATAAGATTTT
1 GACAAATAAGATTTT
*
52654 GACAAATCAGATTTT
1 GACAAATAAGATTTT
52669 TTCCTACAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (15 bp):
GACAAATAAGATTTT
Found at i:52814 original size:49 final size:49
Alignment explanation
Indices: 52742--52843 Score: 195
Period size: 49 Copynumber: 2.1 Consensus size: 49
52732 CTCATCTGGT
*
52742 GAAACTAGAGGTTAAACCTGGTGCTAAATTAGTGTCTAGATTTTAGGAA
1 GAAACTAGAGGTTAAACCTGGTGCTAAATTAGTGCCTAGATTTTAGGAA
52791 GAAACTAGAGGTTAAACCTGGTGCTAAATTAGTGCCTAGATTTTAGGAA
1 GAAACTAGAGGTTAAACCTGGTGCTAAATTAGTGCCTAGATTTTAGGAA
52840 GAAA
1 GAAA
52844 TATGACTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (49 bp):
GAAACTAGAGGTTAAACCTGGTGCTAAATTAGTGCCTAGATTTTAGGAA
Done.