Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015383.1 Corchorus capsularis cultivar CVL-1 contig15404, 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: 14609
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:563 original size:19 final size:19
Alignment explanation
Indices: 541--579 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
531 AGAAATTAAG
541 AAATAAAAAATAAATAAAA
1 AAATAAAAAATAAATAAAA
*
560 AAATAAGAAATAAATAAAA
1 AAATAAAAAATAAATAAAA
579 A
1 A
580 TTAATTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (19 bp):
AAATAAAAAATAAATAAAA
Found at i:703 original size:27 final size:27
Alignment explanation
Indices: 664--724 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
654 AAAATTAGAG
*
664 AAATGAAAGAAATTAAGAAATAAATAA
1 AAATTAAAGAAATTAAGAAATAAATAA
691 TAAATTAAA-AAATTAAGAAATAAATAA
1 -AAATTAAAGAAATTAAGAAATAAATAA
718 AAATTAA
1 AAATTAA
725 TTAATTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 7 0.22
27 18 0.56
28 7 0.22
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (27 bp):
AAATTAAAGAAATTAAGAAATAAATAA
Found at i:773 original size:141 final size:140
Alignment explanation
Indices: 503--775 Score: 483
Period size: 141 Copynumber: 1.9 Consensus size: 140
493 AAAACAAACT
*
503 AAAAAATATAAGAAATTAGAGAAATGAAAGAAATTAAGAAATAAAAAATAAATAAAAAAATAAGA
1 AAAAAATATAAAAAATTAGAGAAATGAAAGAAATTAAGAAATAAAAAATAAATAAAAAAATAAGA
568 AATAAATAAAAATTAATTAATTAAAATAAACATTATTTTTATGATCATAAAAACCTAAATTTTTT
66 AATAAATAAAAATTAATTAATTAAAATAAACATTATTTTTATGATCATAAAAACCTAAATTTTTT
633 TCCTTTCAGA
131 TCCTTTCAGA
* *
643 AAAAAATATAAAAAATTAGAGAAATGAAAGAAATTAAGAAATAAATAATAAATTAAAAAATTAAG
1 AAAAAATATAAAAAATTAGAGAAATGAAAGAAATTAAGAAATAAAAAATAAA-TAAAAAAATAAG
* *
708 AAATAAATAAAAATTAATTAATTAAAATTAACATTATTTTTATGAGTGATAAAAACCTAAATTTT
65 AAATAAATAAAAATTAATTAATTAAAATAAACATTATTTTTATGA-TCATAAAAACCTAAATTTT
773 TTT
129 TTT
776 TCTCTCTCTC
Statistics
Matches: 126, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
140 50 0.40
141 55 0.44
142 21 0.17
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (140 bp):
AAAAAATATAAAAAATTAGAGAAATGAAAGAAATTAAGAAATAAAAAATAAATAAAAAAATAAGA
AATAAATAAAAATTAATTAATTAAAATAAACATTATTTTTATGATCATAAAAACCTAAATTTTTT
TCCTTTCAGA
Found at i:984 original size:24 final size:24
Alignment explanation
Indices: 952--1000 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
942 AAAAAATATA
952 TATATTTATTATGCTTTATGCTTT
1 TATATTTATTATGCTTTATGCTTT
976 TATATTTATTATGCTTTATGCTTT
1 TATATTTATTATGCTTTATGCTTT
1000 T
1 T
1001 GTTTGGTTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.63
Consensus pattern (24 bp):
TATATTTATTATGCTTTATGCTTT
Found at i:2725 original size:91 final size:91
Alignment explanation
Indices: 2570--2750 Score: 292
Period size: 91 Copynumber: 2.0 Consensus size: 91
2560 TTTTTGCCTC
* * *
2570 TGAATTATGGGTCTAAAGACAATTTGCCTCTTAAATTAACATCGAGACAATTTACCCCATGAACT
1 TGAATTATGGGTCTAAAGACAATTTGCCCCCTAAATTAAAATCGAGACAATTTACCCCATGAACT
2635 CTCCAAATTCAAGACAATTTGCTCCT
66 CTCCAAATTCAAGACAATTTGCTCCT
*
2661 TGAATTATGGGTCTAAGGACAATTTGCCCCCTAAATTAAAATCGAGACAATTTACCCTC-TGAAC
1 TGAATTATGGGTCTAAAGACAATTTGCCCCCTAAATTAAAATCGAGACAATTTACCC-CATGAAC
* *
2725 TCTCTAAATTCAGGACAATTTGCTCC
65 TCTCCAAATTCAAGACAATTTGCTCC
2751 CTAAATTAAA
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
91 82 0.99
92 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.30
Consensus pattern (91 bp):
TGAATTATGGGTCTAAAGACAATTTGCCCCCTAAATTAAAATCGAGACAATTTACCCCATGAACT
CTCCAAATTCAAGACAATTTGCTCCT
Found at i:2744 original size:60 final size:60
Alignment explanation
Indices: 2676--2812 Score: 222
Period size: 60 Copynumber: 2.3 Consensus size: 60
2666 TATGGGTCTA
*
2676 AGGACAATTTGCCCCCTAAATTAAAATCGAGACAATTTACC-CTCTGAACTCTCTAAATTC
1 AGGACAATTTGCCCCCTAAATTAAAATCGAGACAATTTACCTC-CTGAACTCTCCAAATTC
* *
2736 AGGACAATTTGCTCCCTAAATTAAAATTGAGACAATTTACCTCCTGAACTCTCCAAATTC
1 AGGACAATTTGCCCCCTAAATTAAAATCGAGACAATTTACCTCCTGAACTCTCCAAATTC
*
2796 AAGACAATTTGCCCCCT
1 AGGACAATTTGCCCCCT
2813 GACTTATGGA
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
60 70 0.99
61 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.28
Consensus pattern (60 bp):
AGGACAATTTGCCCCCTAAATTAAAATCGAGACAATTTACCTCCTGAACTCTCCAAATTC
Found at i:2769 original size:28 final size:27
Alignment explanation
Indices: 2678--2773 Score: 84
Period size: 28 Copynumber: 3.3 Consensus size: 27
2668 TGGGTCTAAG
*
2678 GACAATTTGCCCCCTAAATTAAAATCGA
1 GACAATTTG-CCCCTAAATTAAAATTGA
* * * *
2706 GACAATTTACCCTCTGAACTCTCTAAATTCA
1 GACAATTTGCCC-CT-AAAT-T-AAAATTGA
2737 GGACAATTTGCTCCCTAAATTAAAATTGA
1 -GACAATTTGC-CCCTAAATTAAAATTGA
2766 GACAATTT
1 GACAATTT
2774 ACCTCCTGAA
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
27 3 0.06
28 18 0.34
29 9 0.17
30 2 0.04
31 8 0.15
32 11 0.21
33 2 0.04
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.30
Consensus pattern (27 bp):
GACAATTTGCCCCTAAATTAAAATTGA
Found at i:6200 original size:2 final size:2
Alignment explanation
Indices: 6157--6189 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6147 TACAATTCTC
6157 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6190 ATCACTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7383 original size:31 final size:29
Alignment explanation
Indices: 7348--7412 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 29
7338 GCTTAATGCC
*
7348 CAAATTGG-CCCTCTAACTATTGGTTTTGGGA
1 CAAATCGGCCCCT-TAACTATT--TTTTGGGA
*
7379 CAAATCGGCCCCTTATCTATTTTTTGGGA
1 CAAATCGGCCCCTTAACTATTTTTTGGGA
7408 CAAAT
1 CAAAT
7413 AAGCCCCACA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 13 0.42
31 14 0.45
32 4 0.13
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (29 bp):
CAAATCGGCCCCTTAACTATTTTTTGGGA
Found at i:8789 original size:31 final size:29
Alignment explanation
Indices: 8725--8789 Score: 69
Period size: 31 Copynumber: 2.2 Consensus size: 29
8715 TGTGGGGTTT
* *
8725 ATTTGTCCCAAAAAATAGATAAGGGGTCG
1 ATTTGTCCCAAAAAATAGATAAGGGGCCA
*
8754 ATTTGTCCCAAAATCAATAG-TTAGAGGGCCA
1 ATTTGTCCCAAAA--AATAGATAAG-GGGCCA
8785 ATTTG
1 ATTTG
8790 AGCATTAAGC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 13 0.43
30 3 0.10
31 14 0.47
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (29 bp):
ATTTGTCCCAAAAAATAGATAAGGGGCCA
Found at i:10091 original size:18 final size:19
Alignment explanation
Indices: 10068--10104 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
10058 CCTCTCTTCT
10068 CTCTCC-CCCACTAAGTCA
1 CTCTCCTCCCACTAAGTCA
*
10086 CTCTCCTCCCACTTAGTCA
1 CTCTCCTCCCACTAAGTCA
10105 AGATAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.19, C:0.49, G:0.05, T:0.27
Consensus pattern (19 bp):
CTCTCCTCCCACTAAGTCA
Found at i:11319 original size:31 final size:31
Alignment explanation
Indices: 11233--11380 Score: 112
Period size: 31 Copynumber: 5.0 Consensus size: 31
11223 ACGGTATCCG
* * ** *
11233 ACGTGGCATGCCATGTGGATTAAAAAGTAAC
1 ACGTGGCACGCCATGTGTACCAAAAAGTGAC
* * * * *
11264 ACATGGCAGGCCACGTGGATCAAAAAGTGAC
1 ACGTGGCACGCCATGTGTACCAAAAAGTGAC
* * *
11295 ATGTGGCACGCCATGTGTGCCAAAAAGTGGC
1 ACGTGGCACGCCATGTGTACCAAAAAGTGAC
* *
11326 ACGT--CA---CA--TGTACCAAAAAGTTAT
1 ACGTGGCACGCCATGTGTACCAAAAAGTGAC
11350 ACGTGGCACGCCATGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCATGTGTACCAAAAAGTGAC
11381 GCGGCATGCC
Statistics
Matches: 90, Mismatches: 20, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
24 16 0.18
26 4 0.04
29 4 0.04
31 66 0.73
ACGTcount: A:0.34, C:0.22, G:0.26, T:0.19
Consensus pattern (31 bp):
ACGTGGCACGCCATGTGTACCAAAAAGTGAC
Found at i:11324 original size:24 final size:24
Alignment explanation
Indices: 11297--11346 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
11287 AAAGTGACAT
** *
11297 GTGGCACGCCATGTGTGCCAAAAA
1 GTGGCACGCCACATGTACCAAAAA
*
11321 GTGGCACGTCACATGTACCAAAAA
1 GTGGCACGCCACATGTACCAAAAA
11345 GT
1 GT
11347 TATACGTGGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (24 bp):
GTGGCACGCCACATGTACCAAAAA
Found at i:12814 original size:29 final size:30
Alignment explanation
Indices: 12753--12823 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
12743 GTCTGAGACT
*
12753 AAAACGTCCAAAATTGAGAATTTAAGAAAC
1 AAAACGTTCAAAATTGAGAATTTAAGAAAC
* * **
12783 AAAACGTTCAATATTGA-AATTTAGGAGGC
1 AAAACGTTCAAAATTGAGAATTTAAGAAAC
*
12812 AAAATGTTCAAA
1 AAAACGTTCAAA
12824 CCGTACAATG
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 19 0.56
30 15 0.44
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.24
Consensus pattern (30 bp):
AAAACGTTCAAAATTGAGAATTTAAGAAAC
Done.