Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011684.1 Corchorus capsularis cultivar CVL-1 contig11705, 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: 33801
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Found at i:328 original size:167 final size:166
Alignment explanation
Indices: 100--533 Score: 577
Period size: 167 Copynumber: 2.6 Consensus size: 166
90 AGAACTATTT
* * * *
100 TTTTTTTTGTCTTTTCCCACTTGGCAGATTACTTAAATGTCCCAACTTTTTATTCTTGAGGGGAT
1 TTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGAT
* * *
165 TAAATAACTAGACTTTTTGGTCATTTCTGAATTGACTTT-AATAGAGTATTGGAATTACTAAAAG
66 TAAATAACTA-ACTTTTTGGTCATTTCTGAATTGACTTTGAATAGAGTAGTGGAATTAATAAAAC
* * * ** * *
229 ATCCCTACCAAGGCTTGCTTTTGGAGTTAGAGAACTTA
130 ATCCCCACCAAGGATTGATGAT-GAGCTAGAGAACTAA
* *
267 TTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTCTGATTGTTGAGGGGAT
1 TTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGAT
* * * * *
332 TAAATAAGTAATGTTTTTGGTCATTTCTCAATGGA-TTTGAATAGAGTGGTGGAATTAATAAAAC
66 TAAATAACTAA-CTTTTTGGTCATTTCTGAATTGACTTTGAATAGAGTAGTGGAATTAATAAAAC
*
396 ATCCCCATCAAGGATTGATGATGAGCTAGAGAACTAA
130 ATCCCCACCAAGGATTGATGATGAGCTAGAGAACTAA
* * *
433 TCTTTTTCGTCTTTACTTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGAT
1 TTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGAT
498 TAAATAACTAAACTTTTTGGTCATTTCTCG-ATTGAC
66 TAAATAACT-AACTTTTTGGTCATTTCT-GAATTGAC
534 AAATGACTCA
Statistics
Matches: 231, Mismatches: 31, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
166 104 0.45
167 127 0.55
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (166 bp):
TTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGAT
TAAATAACTAACTTTTTGGTCATTTCTGAATTGACTTTGAATAGAGTAGTGGAATTAATAAAACA
TCCCCACCAAGGATTGATGATGAGCTAGAGAACTAA
Found at i:2952 original size:222 final size:222
Alignment explanation
Indices: 2563--2971 Score: 755
Period size: 222 Copynumber: 1.8 Consensus size: 222
2553 CAGTCCATCT
* * * *
2563 AGATGGTGGTATGTTTTAATCAATCTTTTAATGAGTACTTTTGTCTCCTGAACTTTACAGATTTA
1 AGATGGTGGTATGTTTTAATCAATCTTTTAATGAGTACTCTTATCCCCTAAACTTTACAGATTTA
*
2628 GATCAGTTTGCCCTTTCAATTAATTATTATGTCACATAGCCCTTTCAATTGTCAAAATCATGTCT
66 GATCAGTTTGCCCTCTCAATTAATTATTATGTCACATAGCCCTTTCAATTGTCAAAATCATGTCT
* *
2693 ATTGGATAGTAAGACTGCTCTTTATGCAAATTGAATTACAAGAGTAGTATTACTATTCAATTGGC
131 ATTGGATAGTAAGACTACTCTTTATGCAAACTGAATTACAAGAGTAGTATTACTATTCAATTGGC
2758 GCAATTTTAAAAATTGGATAAAAAATC
196 GCAATTTTAAAAATTGGATAAAAAATC
2785 AGATGGTGGTATGTTTTAATCAATCTTTTAATGAGTACTCTTATCCCCTAAACTTTACAGATTTA
1 AGATGGTGGTATGTTTTAATCAATCTTTTAATGAGTACTCTTATCCCCTAAACTTTACAGATTTA
2850 GATCAGTTTGCCCTCTCAATTAATTATTATGTCACATAGCCCTTTCAATTGTCAAAATCATGTCT
66 GATCAGTTTGCCCTCTCAATTAATTATTATGTCACATAGCCCTTTCAATTGTCAAAATCATGTCT
2915 ATTGGATAGTAAGACTACTCTTTATGCAAACTGAATTACAAGAGTAGTATTACTATT
131 ATTGGATAGTAAGACTACTCTTTATGCAAACTGAATTACAAGAGTAGTATTACTATT
2972 TTTTTTATGC
Statistics
Matches: 180, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
222 180 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (222 bp):
AGATGGTGGTATGTTTTAATCAATCTTTTAATGAGTACTCTTATCCCCTAAACTTTACAGATTTA
GATCAGTTTGCCCTCTCAATTAATTATTATGTCACATAGCCCTTTCAATTGTCAAAATCATGTCT
ATTGGATAGTAAGACTACTCTTTATGCAAACTGAATTACAAGAGTAGTATTACTATTCAATTGGC
GCAATTTTAAAAATTGGATAAAAAATC
Found at i:3645 original size:23 final size:25
Alignment explanation
Indices: 3619--3673 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
3609 ATATTATTAT
* *
3619 TATATATATATATA-T-TTTTGTTG
1 TATATATAAATATACTATTATGTTG
*
3642 TATATTTAAATATACTATTATGTTG
1 TATATATAAATATACTATTATGTTG
3667 TATATAT
1 TATATAT
3674 GTTCCTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 12 0.46
24 1 0.04
25 13 0.50
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (25 bp):
TATATATAAATATACTATTATGTTG
Found at i:4375 original size:2 final size:2
Alignment explanation
Indices: 4370--4430 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
4360 TATATATATA
4370 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
4412 TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG T
4431 ATGTTTAATC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:8606 original size:36 final size:33
Alignment explanation
Indices: 8559--8625 Score: 98
Period size: 36 Copynumber: 1.9 Consensus size: 33
8549 GCATCGAGTG
8559 CTCTTTTAGAAAGTGGGAATTTCTTTCTTAAGCTTT
1 CTCTTTTAGAAAGTGGG-ATTT-TTT-TTAAGCTTT
*
8595 CTCTTTTAGAAAGTGTGATTTTTTTTAAGCT
1 CTCTTTTAGAAAGTGGGATTTTTTTTAAGCT
8626 CTCCATGGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 7 0.23
34 3 0.10
35 4 0.13
36 16 0.53
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.49
Consensus pattern (33 bp):
CTCTTTTAGAAAGTGGGATTTTTTTTAAGCTTT
Found at i:12019 original size:23 final size:23
Alignment explanation
Indices: 11989--12040 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
11979 GCCCAAGCCC
11989 AACTCGGATTCGAGCATAAACCT
1 AACTCGGATTCGAGCATAAACCT
12012 AACTCGGATTCGAGCATAAACCT
1 AACTCGGATTCGAGCATAAACCT
12035 AACTCG
1 AACTCG
12041 AATTTGAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (23 bp):
AACTCGGATTCGAGCATAAACCT
Found at i:12287 original size:335 final size:336
Alignment explanation
Indices: 11676--12352 Score: 1015
Period size: 335 Copynumber: 2.0 Consensus size: 336
11666 GCCCAAGCCC
* *
11676 AACTCGGATTCGAGCATAAACCTAACTCGAATTTGAGATAATTTTAATCCATGCAATGGAAGATT
1 AACTCGGATTCGAGCATAAACCTAACTCGAATTTGAGATAATTTTAATCCATACAATGGAAAATT
11741 AATTAATTTTTTTTTCGCAAGAGAGAGAAATGTTCGAACCTGAGCTTAGCCTGATCTGCAAACCG
66 AATTAATTTTTTTTTCGCAAGAGAGAGAAATGTTCGAACCTGAGCTTAGCCTGATCTGCAAACCG
** * **
11806 GGCTTAAGCCAGAATTGGGGATATTTTGATCTAGACAAGCCCGAACTTGACTAAACCTATATTTT
131 GGCTTAAGCCAGAACCGGGGATAATTTGATCTAGACAAGCCCGAACTTGACTAAACCTATATTCG
* * *
11871 AATGAATTTTGAACCTAAATAAACTAGGAATCTTGATGAATCGCAGTCTGAATTCAGTCCAAACC
196 AATGAATTTTGAACCTAAATAAACTAGGAATCATAATGAATCGCAGTCTGAATTCAGCCCAAACC
* *
11936 TTAAATTATCCAAATCCCACAGTAT-TCACTTCTAAAAACTTAAGCCCAAGCCCAACTCGGA-TT
261 TTAAATTATCCAAATCCCAAAGTATCT-ACTTCTAAAAACTTAAGCCCAAGCCCAACTCGGACAT
11999 CGAGCATAAACCT
325 -GAGCATAAACCT
*
12012 AACTCGGATTCGAGCATAAACCTAACTCGAATTTGAGATAATTTTAATCCATACAATTGAAAATT
1 AACTCGGATTCGAGCATAAACCTAACTCGAATTTGAGATAATTTTAATCCATACAATGGAAAATT
* * * *
12077 AATTAA-TTTTTTTTCGCAAGAGAGAGAAATGTTTGAACCTGAGCTTAGTCTTATCTGTAAACCG
66 AATTAATTTTTTTTTCGCAAGAGAGAGAAATGTTCGAACCTGAGCTTAGCCTGATCTGCAAACCG
* * * *
12141 GGCTTAGGCC-GTAACCGGGGATAATTTGATCTA-ACCAAGCCTGACCTTGACTTAACCTATATT
131 GGCTTAAGCCAG-AACCGGGGATAATTTGATCTAGA-CAAGCCCGAACTTGACTAAACCTATATT
* *
12204 CGAATGAATTTTGAACCTAAATAAGCTCGGAATCATAATGAA-CTGCAGTCTGAATTCAGCCCAA
194 CGAATGAATTTTGAACCTAAATAAACTAGGAATCATAATGAATC-GCAGTCTGAATTCAGCCCAA
* * ** *
12268 ACCTTAAATTATCCAAATCCCAAATTATCTGCTTCTACCAACTTAAGCCCATGCCCAACTCGGAC
258 ACCTTAAATTATCCAAATCCCAAAGTATCTACTTCTAAAAACTTAAGCCCAAGCCCAACTCGGAC
12333 ATGAGCATAAACCT
323 ATGAGCATAAACCT
12347 AACTCG
1 AACTCG
12353 AATTTGAGAT
Statistics
Matches: 308, Mismatches: 28, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
334 3 0.01
335 235 0.76
336 70 0.23
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (336 bp):
AACTCGGATTCGAGCATAAACCTAACTCGAATTTGAGATAATTTTAATCCATACAATGGAAAATT
AATTAATTTTTTTTTCGCAAGAGAGAGAAATGTTCGAACCTGAGCTTAGCCTGATCTGCAAACCG
GGCTTAAGCCAGAACCGGGGATAATTTGATCTAGACAAGCCCGAACTTGACTAAACCTATATTCG
AATGAATTTTGAACCTAAATAAACTAGGAATCATAATGAATCGCAGTCTGAATTCAGCCCAAACC
TTAAATTATCCAAATCCCAAAGTATCTACTTCTAAAAACTTAAGCCCAAGCCCAACTCGGACATG
AGCATAAACCT
Found at i:14629 original size:62 final size:64
Alignment explanation
Indices: 14547--14713 Score: 257
Period size: 62 Copynumber: 2.6 Consensus size: 64
14537 TAATTTATAA
*
14547 TACTTTATAATATATAATATATATAATTTAAATAAAAATAATAT-AA-AATTTTGCTCAAATTT
1 TACTTTATAATATATAATATATATAATTTAAATAAAAATAATATAAATAATTTTGCTCAAATAT
* *
14609 TACTTTATAATATATAATATATATAATTTAAATAAAAATAATATAAATAATTTTGCTTAGATAT
1 TACTTTATAATATATAATATATATAATTTAAATAAAAATAATATAAATAATTTTGCTCAAATAT
* *
14673 TACTTTATATAATATATAATATATAGAATTTAAATCAAAAT
1 TAC-TT-TATAATATATAATATATATAATTTAAATAAAAAT
14714 CAAAATCAAA
Statistics
Matches: 96, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
62 44 0.46
63 2 0.02
64 16 0.17
65 2 0.02
66 32 0.33
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (64 bp):
TACTTTATAATATATAATATATATAATTTAAATAAAAATAATATAAATAATTTTGCTCAAATAT
Found at i:18088 original size:4 final size:4
Alignment explanation
Indices: 18081--18144 Score: 119
Period size: 4 Copynumber: 16.0 Consensus size: 4
18071 TATATATATA
*
18081 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TTTG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
18129 TATG TATG TATG TATG
1 TATG TATG TATG TATG
18145 AATATAGAGT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 58 1.00
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:18314 original size:2 final size:2
Alignment explanation
Indices: 18307--18367 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
18297 ATGTTTTATA
18307 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
18349 TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG T
18368 ACGGTAGTGC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:19982 original size:10 final size:8
Alignment explanation
Indices: 19941--19998 Score: 62
Period size: 8 Copynumber: 6.8 Consensus size: 8
19931 ATATATTGTA
19941 CAATATATT
1 CAATATA-T
*
19950 TAATATATT
1 CAATATA-T
*
19959 GAATATAT
1 CAATATAT
19967 CAATATAT
1 CAATATAT
19975 CAATATAT
1 CAATATAT
19983 CAAAATATAT
1 C--AATATAT
19993 CAATAT
1 CAATAT
19999 TGTGCTTTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
8 22 0.50
9 14 0.32
10 8 0.18
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.40
Consensus pattern (8 bp):
CAATATAT
Found at i:19982 original size:18 final size:17
Alignment explanation
Indices: 19941--19998 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 17
19931 ATATATTGTA
**
19941 CAATATATTTAATATATT
1 CAATATATCAAATATA-T
*
19959 GAATATATC-AATATAT
1 CAATATATCAAATATAT
19975 CAATATATCAAAATATAT
1 CAATATATC-AAATATAT
19993 CAATAT
1 CAATAT
19999 TGTGCTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 9 0.26
17 6 0.17
18 20 0.57
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.40
Consensus pattern (17 bp):
CAATATATCAAATATAT
Found at i:21559 original size:2 final size:2
Alignment explanation
Indices: 21552--21587 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
21542 TTATTTAGTA
21552 AT AT AT AT AT 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 AT AT AT AT AT
21588 TCATTGAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24683 original size:26 final size:26
Alignment explanation
Indices: 24654--24709 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
24644 CCATGTAGTT
24654 ATAAATATAGCAAGTGGCAAGTGATA
1 ATAAATATAGCAAGTGGCAAGTGATA
*
24680 ATAAATATAGCAAGTGGCAAGTGATG
1 ATAAATATAGCAAGTGGCAAGTGATA
24706 ATAA
1 ATAA
24710 GTGTTAGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.46, C:0.07, G:0.23, T:0.23
Consensus pattern (26 bp):
ATAAATATAGCAAGTGGCAAGTGATA
Found at i:25123 original size:26 final size:26
Alignment explanation
Indices: 25084--25139 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
25074 GAAACAGAAA
*
25084 CTTTAACTATAATATATCGTGTTGCC
1 CTTTAACTAGAATATATCGTGTTGCC
25110 CTTTAACTAGAATATATCGTGTTGCC
1 CTTTAACTAGAATATATCGTGTTGCC
25136 CTTT
1 CTTT
25140 TTTTTCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (26 bp):
CTTTAACTAGAATATATCGTGTTGCC
Found at i:27517 original size:4 final size:4
Alignment explanation
Indices: 27508--27536 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
27498 GTAAATTCTC
27508 TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT T
27537 CTCCCTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Done.