Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016423.1 Corchorus capsularis cultivar CVL-1 contig16444, 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: 67273
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:13278 original size:13 final size:13
Alignment explanation
Indices: 13257--13293 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
13247 ATGGTAAGAG
13257 TAAATAATAAATA
1 TAAATAATAAATA
* *
13270 TAAACAATATATA
1 TAAATAATAAATA
13283 TAAATAATAAA
1 TAAATAATAAA
13294 GAATTCTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (13 bp):
TAAATAATAAATA
Found at i:15121 original size:16 final size:15
Alignment explanation
Indices: 15072--15126 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
15062 TTTGAACCAT
*
15072 ATGACCCGAAACTAAAA
1 ATGACCC-AAAC-CAAA
*
15089 AAGACCCAAACCAAA
1 ATGACCCAAACCAAA
*
15104 ATTGACCCAAACCCAA
1 A-TGACCCAAACCAAA
15120 ATGACCC
1 ATGACCC
15127 GACATTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 10 0.30
16 17 0.52
17 6 0.18
ACGTcount: A:0.49, C:0.33, G:0.09, T:0.09
Consensus pattern (15 bp):
ATGACCCAAACCAAA
Found at i:15520 original size:11 final size:11
Alignment explanation
Indices: 15506--15533 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
15496 ATGGTAAAAA
15506 AAAATAATTAT
1 AAAATAATTAT
15517 AAAATAATTAT
1 AAAATAATTAT
15528 AAAATA
1 AAAATA
15534 TTGAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAATAATTAT
Found at i:16156 original size:13 final size:13
Alignment explanation
Indices: 16138--16162 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16128 TTTCCTTCTT
16138 CAGTCCATTTTTC
1 CAGTCCATTTTTC
16151 CAGTCCATTTTT
1 CAGTCCATTTTT
16163 GTTGGGTCCG
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:0.16, C:0.28, G:0.08, T:0.48
Consensus pattern (13 bp):
CAGTCCATTTTTC
Found at i:18808 original size:3 final size:3
Alignment explanation
Indices: 18802--18849 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
18792 ATATATTAAC
18802 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
18849 A
1 A
18850 ACATTAGATT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:26459 original size:45 final size:45
Alignment explanation
Indices: 26408--26497 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
26398 TAATAGAGTA
26408 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
*
26453 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
26498 AGAAGTAATC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
Found at i:26965 original size:48 final size:48
Alignment explanation
Indices: 26909--27005 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
26899 ACATGTCATA
26909 TTCCTTTATTTCCTTCTTTCCCCTCACCTTTTTGTTAATTACAAGATT
1 TTCCTTTATTTCCTTCTTTCCCCTCACCTTTTTGTTAATTACAAGATT
26957 TTCCTTTATTTCCTTCTTTCCCCTCACCTTTTTGTTAATTACAAGATT
1 TTCCTTTATTTCCTTCTTTCCCCTCACCTTTTTGTTAATTACAAGATT
27005 T
1 T
27006 CTAAAACCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.16, C:0.27, G:0.04, T:0.53
Consensus pattern (48 bp):
TTCCTTTATTTCCTTCTTTCCCCTCACCTTTTTGTTAATTACAAGATT
Found at i:32276 original size:11 final size:11
Alignment explanation
Indices: 32262--32299 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
32252 ATTCATAACA
32262 AATTTATAATT
1 AATTTATAATT
32273 AATTTATAATT
1 AATTTATAATT
32284 -ATTTGATAATT
1 AATTT-ATAATT
*
32295 TATTT
1 AATTT
32300 TATATAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:32359 original size:30 final size:30
Alignment explanation
Indices: 32324--32384 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
32314 ATGAATGTCT
32324 TTTGATTTTTCCAAACTAAATGAATACAAA
1 TTTGATTTTTCCAAACTAAATGAATACAAA
*
32354 TTTGATTTTTCTAAACTAAATGAATACAAA
1 TTTGATTTTTCCAAACTAAATGAATACAAA
32384 T
1 T
32385 ATAATAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTGATTTTTCCAAACTAAATGAATACAAA
Found at i:37753 original size:149 final size:149
Alignment explanation
Indices: 37483--37782 Score: 564
Period size: 149 Copynumber: 2.0 Consensus size: 149
37473 TCTGTATTAG
37483 GAATTGGACCGTTCAGGCTATCAACCCGTTGAAACCCGTGGAAAACCGCCTTAACCCGTTGAAAC
1 GAATTGGACCGTTCAGGCTATCAACCCGTTGAAACCCGTGGAAAACCGCCTTAACCCGTTGAAAC
* *
37548 CCGTAGATCCGGACGGATTTTGATGACCCGGACGAGTTAGATCTTAACTCTGAAATTTGGCTTGA
66 CCGTAGACCCGGACGGATTTTGATGACCCGGACGAGCTAGATCTTAACTCTGAAATTTGGCTTGA
37613 TAAACCTTTGCCGGTCGGT
131 TAAACCTTTGCCGGTCGGT
37632 GAATTGGACCGTTCAGGCTATCAACCCGTTGAAACCCGTGGAAAACCGCCTTAACCCGTTGAAAC
1 GAATTGGACCGTTCAGGCTATCAACCCGTTGAAACCCGTGGAAAACCGCCTTAACCCGTTGAAAC
*
37697 CCGTAGACCCGGACGGGTTTTGATGACCCGGACGAGCTAGATCTTAACTCTGAAATTTGGCTTGA
66 CCGTAGACCCGGACGGATTTTGATGACCCGGACGAGCTAGATCTTAACTCTGAAATTTGGCTTGA
*
37762 TAAACCTTTTCCGGTCGGT
131 TAAACCTTTGCCGGTCGGT
37781 GA
1 GA
37783 TTAGCTTGGC
Statistics
Matches: 147, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 147 1.00
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (149 bp):
GAATTGGACCGTTCAGGCTATCAACCCGTTGAAACCCGTGGAAAACCGCCTTAACCCGTTGAAAC
CCGTAGACCCGGACGGATTTTGATGACCCGGACGAGCTAGATCTTAACTCTGAAATTTGGCTTGA
TAAACCTTTGCCGGTCGGT
Found at i:39433 original size:33 final size:32
Alignment explanation
Indices: 39326--39465 Score: 145
Period size: 33 Copynumber: 4.2 Consensus size: 32
39316 AAGGATCATG
* ** *
39326 TGGCCGGTTGTGGCCTGGCATGGCCGAGTCGCA
1 TGGCCGG-TGTGGCCGGGCATCTCCAAGTCGCA
** * *
39359 TGGCCGGTTGTGGCCGGGCATGGCCATGTCGCG
1 TGGCCGG-TGTGGCCGGGCATCTCCAAGTCGCA
*
39392 TGGCCGGTGATGGCCGGACATCTCCAAGTCGCA
1 TGGCCGGTG-TGGCCGGGCATCTCCAAGTCGCA
* *
39425 TGGCCGGTGTTGCGCGGGCATCTCCAAGTCGCG
1 TGGCCGGTGTGGC-CGGGCATCTCCAAGTCGCA
39458 TGGCCGGT
1 TGGCCGGT
39466 CACAAGCGCT
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
32 5 0.05
33 88 0.95
ACGTcount: A:0.10, C:0.29, G:0.41, T:0.21
Consensus pattern (32 bp):
TGGCCGGTGTGGCCGGGCATCTCCAAGTCGCA
Found at i:44823 original size:10 final size:10
Alignment explanation
Indices: 44795--44824 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
44785 CGAATTTTTT
44795 TTTTTTGAT-
1 TTTTTTGATA
44804 TTTTTTGATA
1 TTTTTTGATA
44814 TTTTTTGATA
1 TTTTTTGATA
44824 T
1 T
44825 AACTACTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (10 bp):
TTTTTTGATA
Found at i:45909 original size:33 final size:33
Alignment explanation
Indices: 45853--45951 Score: 112
Period size: 33 Copynumber: 3.0 Consensus size: 33
45843 TGTGGCTGGT
** * *
45853 TGTGGC-CGGGCATGGCCATGTCGCGTGGCCGG
1 TGTGGCGCGGGCATCTCCAAGTCGCATGGCCGG
* *
45885 TGATGGC-CGGGCATCTTCAAGTCGCACGGCCGG
1 TG-TGGCGCGGGCATCTCCAAGTCGCATGGCCGG
*
45918 TGTTGCGCGGGCATCTCCAAGTCGCATGGCCGG
1 TGTGGCGCGGGCATCTCCAAGTCGCATGGCCGG
45951 T
1 T
45952 CACAAGTGCT
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
32 5 0.09
33 51 0.91
ACGTcount: A:0.11, C:0.29, G:0.39, T:0.20
Consensus pattern (33 bp):
TGTGGCGCGGGCATCTCCAAGTCGCATGGCCGG
Found at i:46378 original size:22 final size:21
Alignment explanation
Indices: 46353--46411 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
46343 TATATTTATA
46353 TTATTAGTAAATTAGTAAATAT
1 TTATTAGTAAATTA-TAAATAT
* * *
46375 TTATTAGTATATATATTATTAT
1 TTATTAGTAAAT-TATAAATAT
46397 TTATTAGTAAATTAT
1 TTATTAGTAAATTAT
46412 CAAAACATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 3 0.09
22 27 0.84
23 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.53
Consensus pattern (21 bp):
TTATTAGTAAATTATAAATAT
Found at i:46382 original size:14 final size:15
Alignment explanation
Indices: 46363--46395 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
46353 TTATTAGTAA
46363 ATTAGTAAATAT-TT
1 ATTAGTAAATATATT
*
46377 ATTAGTATATATATT
1 ATTAGTAAATATATT
46392 ATTA
1 ATTA
46396 TTTATTAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (15 bp):
ATTAGTAAATATATT
Found at i:46402 original size:44 final size:40
Alignment explanation
Indices: 46331--46410 Score: 115
Period size: 44 Copynumber: 1.9 Consensus size: 40
46321 AAAAAAATAT
46331 ATATTTTTAATATATATTTATATTATTAGTAAATTAGTAA
1 ATATTTTTAATATATATTTATATTATTAGTAAATTAGTAA
*
46371 ATATTTATTAGTATATATATTATTATTTATTAGTAAATTA
1 ATATTT-TTAATATATAT-TTA-TA-TTATTAGTAAATTA
46411 TCAAAACATA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
40 6 0.17
41 10 0.29
42 3 0.09
43 2 0.06
44 14 0.40
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (40 bp):
ATATTTTTAATATATATTTATATTATTAGTAAATTAGTAA
Found at i:46454 original size:2 final size:2
Alignment explanation
Indices: 46449--46489 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
46439 TTTATTGAAC
*
46449 AT AT AT AT AT GA- AT AC AT A- 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 AT AT AT
46490 TTCGGGGCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 31 0.91
3 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:47695 original size:30 final size:31
Alignment explanation
Indices: 47654--47718 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
47644 TGGCTATTTA
* ** *
47654 GAAATATATTTTTTAAAAAAG-GTATAATCG
1 GAAATACATTTTAGAAAAAAGAGTACAATCG
*
47684 GAAATACATTTTAGAAAAATGAGTACAATCG
1 GAAATACATTTTAGAAAAAAGAGTACAATCG
47715 GAAA
1 GAAA
47719 ATATAAAGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 17 0.59
31 12 0.41
ACGTcount: A:0.49, C:0.06, G:0.15, T:0.29
Consensus pattern (31 bp):
GAAATACATTTTAGAAAAAAGAGTACAATCG
Found at i:47754 original size:2 final size:2
Alignment explanation
Indices: 47747--47810 Score: 52
Period size: 2 Copynumber: 34.5 Consensus size: 2
47737 TTCGTACTTT
*
47747 TA TA TA TA GTA TA TA GA TA TA TA TA TA TA TA TA T- TA -A TA T-
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47787 TA T- TA T- TA T- TA TGA TA TA -A TA TA T
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA T
47811 TTTATTATTG
Statistics
Matches: 51, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
1 7 0.14
2 40 0.78
3 4 0.08
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55252 original size:18 final size:18
Alignment explanation
Indices: 55231--55271 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
55221 AATGGGGTTG
55231 AAGGATAAAAT-GTCTAAA
1 AAGGATAAAATAGT-TAAA
*
55249 AAGGATAAATTAGTTAAA
1 AAGGATAAAATAGTTAAA
55267 AAGGA
1 AAGGA
55272 AAGAGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.56, C:0.02, G:0.20, T:0.22
Consensus pattern (18 bp):
AAGGATAAAATAGTTAAA
Found at i:62847 original size:22 final size:23
Alignment explanation
Indices: 62758--62864 Score: 90
Period size: 23 Copynumber: 4.4 Consensus size: 23
62748 AACCCTAAAC
* *
62758 ATAACGTTAAGAACTTAATATAT
1 ATAACATTAAGAATTTAATATAT
* *
62781 ATAACCTTAAGAATTAAATATAACGTTAT
1 ATAACATTAAGAATT-TA-AT-A---TAT
62810 ATAACATTAAGAATTTAATATAT
1 ATAACATTAAGAATTTAATATAT
* * *
62833 ATAACGTT-AGAATTTAATTTAC
1 ATAACATTAAGAATTTAATATAT
62855 ATAACATTAA
1 ATAACATTAA
62865 AAATAAATAA
Statistics
Matches: 68, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
22 19 0.28
23 24 0.35
24 1 0.01
25 2 0.03
26 2 0.03
27 2 0.03
28 1 0.01
29 17 0.25
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (23 bp):
ATAACATTAAGAATTTAATATAT
Found at i:62895 original size:53 final size:53
Alignment explanation
Indices: 62824--62936 Score: 172
Period size: 53 Copynumber: 2.1 Consensus size: 53
62814 CATTAAGAAT
62824 TTAATATATATAACGTTAGAATTTAATTTACATAACATTAAAAATAAATAACAA
1 TTAA-ATATATAACGTTAGAATTTAATTTACATAACATTAAAAATAAATAACAA
* * * *
62878 TTAAATATATAATGTTAGAATTTAATTTGCATAACGTTAAAAATAAATGACAA
1 TTAAATATATAACGTTAGAATTTAATTTACATAACATTAAAAATAAATAACAA
*
62931 CTAAAT
1 TTAAAT
62937 TTGTGATCCA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 50 0.93
54 4 0.07
ACGTcount: A:0.51, C:0.07, G:0.06, T:0.35
Consensus pattern (53 bp):
TTAAATATATAACGTTAGAATTTAATTTACATAACATTAAAAATAAATAACAA
Done.