Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013659.1 Corchorus capsularis cultivar CVL-1 contig13680, 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: 48154
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:295 original size:17 final size:17
Alignment explanation
Indices: 246--298 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
236 TTTTTACTTC
*
246 TAATTAATATTTATTAT
1 TAATTAATATTTGTTAT
* *
263 TATTTAAATATGTGTT-T
1 TAATT-AATATTTGTTAT
280 TAATTGAATATTTGTTAT
1 TAATT-AATATTTGTTAT
298 T
1 T
299 TCTTATTATT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 18 0.64
18 10 0.36
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (17 bp):
TAATTAATATTTGTTAT
Found at i:1722 original size:335 final size:330
Alignment explanation
Indices: 820--1771 Score: 972
Period size: 339 Copynumber: 2.8 Consensus size: 330
810 AAAATGACCT
* * *
820 GAAAGATTTTTCCTCAATTTTTGGTA-AAAATACTCATAAAAAATATATAATTCATGCCAAAAAT
1 GAAAGATTTTTCATCAATTTTTAG-AGAAAATACTCATAAAAAATATATAATTCACG-CAAAAAT
* * * * * * **
884 ATTGAAGGAC-TTTCATGCTTTTAAAATCATTTTT-C-ATATT-TTTCTGAATTAATTTCTAATT
64 ATTGAAAG-CTTTTCACGCTTCTAATATCGTTTTTCCTATTTTATTTCCAAATTAATTTCTAATT
* * * *
945 AAATCGAAATAAGATTCAGATGCACGTAAATACAAATCCTTAAATCCAATGTGGCTGAGATTTGA
128 AAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGA
* * *** ** * *
1010 TTAGATGAATA-AAAATATTTCAAGGAGTCTCAGCGTAAAAAATCATGCAAAACAAAACCGTGAC
193 TTAGATGAATATAGAATATTTCAAGGAGTCTTAGCACCAAAAATCATGCAAAACTGAACAG-GGC
* * *
1074 CTCGGAACGTGTTTTTAGCCAAAACCCGTGATGTCTATTACACGATTTCGGCTAAAATTTTGCAA
257 C-CGGAACGCGTTTTTAGCCAAAACCCGTGAAGTCTAGTACACGATTTCGGCTAAAATTTTGCAA
1139 AAATTAACCC
321 AAATTAACCC
* * * **
1149 AAAAGATATTTCATCAATTTTTTTTG-GCTAAAATACTCATAAAAAATATATAATTCGACATAAC
1 GAAAGATTTTTCATCAA--TTTTTAGAG--AAAATACTCATAAAAAATATATAATTC-ACGCAA-
* * * * **
1213 AAATATTGAAAGGTGTTTAACGCTTCTAATATTGTTTTTCCTATTTTTATCTGGATTAATTAATT
60 AAATATTGAAAGCT-TTTCACGCTTCTAATATCGTTTTTCCTA-TTTTATTTCCA--AATTAATT
* *
1278 TCTAATTAAATCG-AACAAGATTCAGATTCTCATAAAAACAAATCCTTAAATCCAATGTGGCTGA
121 TCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGA
* * *
1342 GATTTGGTTAGATGAATATAG-ATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAG
186 GATTTGATTAGATGAATATAGAATATTTCAAGGAGTCTTAGCACCAAAAATCATGCAAAACTGAA
* * *
1406 CAGGGCGCCAGAACGCGTTTTTAGCCGCAAA-CCGTGAAGAT-TAGTACACGATTTTGGCTAAAA
251 CAGGGC-CCGGAACGCGTTTTTAGCC-AAAACCCGTGAAG-TCTAGTACACGATTTCGGCTAAAA
*
1469 TTTTGCAAAAATTATCCC
313 TTTTGCAAAAATTAACCC
* * * * *
1487 GAAAGATTTTTCTTTAATTTCTAGAGAAAATACTCACAAAAAATATATAATTCAACGCAAAAAAA
1 GAAAGATTTTTCATCAATTTTTAGAGAAAATACTCATAAAAAATATATAATTC-ACGCAAAAATA
* * *
1552 TTGAAAGCCTTTTTCACGCTTCTAATATCGTTTTTCCTATTTTATTTCCAAATTAGTTGCTGATT
65 TTGAAAG-C-TTTTCACGCTTCTAATATCGTTTTTCCTATTTTATTTCCAAATTAATTTCTAATT
* * * * ** * *
1617 AAATCGAAACAAGATTTAGATACTCGTAAAAACAAATTCTTAAATACAATATGATTGAGATTCGC
128 AAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGA
* * * * * * *
1682 TTAGATGAATATAGATATATTTTAAGCAGTTTTAGCACCAAAAATTATGCAAGACTGATCCGGGG
193 TTAGATGAATATAGA-ATATTTCAAGGAGTCTTAGCACCAAAAATCATGCAAAACTGA-ACAGGG
*
1747 CCCCGGAACGCGTTTTTATCCAAAA
256 -CCCGGAACGCGTTTTTAGCCAAAA
1772 AATCTAAAAC
Statistics
Matches: 511, Mismatches: 85, Indels: 48
0.79 0.13 0.07
Matches are distributed among these distances:
329 14 0.03
331 6 0.01
332 47 0.09
333 74 0.14
334 37 0.07
335 96 0.19
336 28 0.05
337 5 0.01
338 77 0.15
339 105 0.21
340 22 0.04
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (330 bp):
GAAAGATTTTTCATCAATTTTTAGAGAAAATACTCATAAAAAATATATAATTCACGCAAAAATAT
TGAAAGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTATTTCCAAATTAATTTCTAATTAAA
TCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTA
GATGAATATAGAATATTTCAAGGAGTCTTAGCACCAAAAATCATGCAAAACTGAACAGGGCCCGG
AACGCGTTTTTAGCCAAAACCCGTGAAGTCTAGTACACGATTTCGGCTAAAATTTTGCAAAAATT
AACCC
Found at i:10160 original size:12 final size:12
Alignment explanation
Indices: 10143--10167 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10133 AGGGTTTGCA
10143 TTCTTCTCTGGT
1 TTCTTCTCTGGT
10155 TTCTTCTCTGGT
1 TTCTTCTCTGGT
10167 T
1 T
10168 CCGTATGAAG
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:0.00, C:0.24, G:0.16, T:0.60
Consensus pattern (12 bp):
TTCTTCTCTGGT
Found at i:23277 original size:3 final size:3
Alignment explanation
Indices: 23269--23305 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
23259 CCAACAAAAG
23269 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
23306 ACTTCCGTTC
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:24861 original size:17 final size:17
Alignment explanation
Indices: 24791--24918 Score: 163
Period size: 17 Copynumber: 7.7 Consensus size: 17
24781 TGGTGACCTC
*
24791 ACCAGGTGAATA-TTGT
1 ACCAGGTGAGTATTTGT
** * *
24807 ACTGGGTGAGTATCT-C
1 ACCAGGTGAGTATTTGT
*
24823 ACCAGGTGAGTA-TTGC
1 ACCAGGTGAGTATTTGT
24839 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTATTTGT
*
24856 ACCAGGTGAGTGTTTGT
1 ACCAGGTGAGTATTTGT
24873 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTATTTGT
*
24890 ACCAAGTGAGTATTTGT
1 ACCAGGTGAGTATTTGT
24907 ACCAGGTGAGTA
1 ACCAGGTGAGTA
24919 GGGTAGGAAC
Statistics
Matches: 96, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
15 1 0.01
16 32 0.33
17 63 0.66
ACGTcount: A:0.25, C:0.14, G:0.30, T:0.31
Consensus pattern (17 bp):
ACCAGGTGAGTATTTGT
Found at i:25372 original size:30 final size:28
Alignment explanation
Indices: 25337--25548 Score: 157
Period size: 30 Copynumber: 7.4 Consensus size: 28
25327 GGGAATTGGT
* *
25337 TCTCCCCTGGTGCGTGGCACTAGGGGAGTC
1 TCTCCCCTGGTGC--GGCACTTGGGGAGTG
* *
25367 CCTCCCTTGGTGC-GCAC-TGAGGGAGTG
1 TCTCCCCTGGTGCGGCACTTG-GGGAGTG
*
25394 TCTCCCCTGGTGCCACGCACTTGGGGAGTG
1 TCTCCCCTGGTG-C-GGCACTTGGGGAGTG
* **
25424 TCTCCCCTTGTGC-GCACTTGGGGAGCA
1 TCTCCCCTGGTGCGGCACTTGGGGAGTG
*
25451 TCTCCCCTGGTGGTGCGCACTTGGGGAGTG
1 TCTCCCCTGGT-GCG-GCACTTGGGGAGTG
* * * *
25481 TCTCCACTGGTGCGCCTCACCTGGGGGATTG
1 TCTCCCCTGGTGCG--GCA-CTTGGGGAGTG
* *
25512 ACTCCCTTGGTGC-GC-CTT-GGGAGTG
1 TCTCCCCTGGTGCGGCACTTGGGGAGTG
25537 TCTCCCCTGGTG
1 TCTCCCCTGGTG
25549 ACTTTTTTTT
Statistics
Matches: 146, Mismatches: 26, Indels: 25
0.74 0.13 0.13
Matches are distributed among these distances:
25 16 0.11
26 3 0.02
27 42 0.29
28 3 0.02
29 3 0.02
30 58 0.40
31 21 0.14
ACGTcount: A:0.09, C:0.31, G:0.34, T:0.25
Consensus pattern (28 bp):
TCTCCCCTGGTGCGGCACTTGGGGAGTG
Found at i:25429 original size:57 final size:57
Alignment explanation
Indices: 25337--25495 Score: 171
Period size: 57 Copynumber: 2.8 Consensus size: 57
25327 GGGAATTGGT
*** * ** **
25337 TCTCCCCTGGTGCGTGGCACTAGGGGAGTCCCTCCCTTGGTGCGCAC-TGAGGGAGTG
1 TCTCCCCTGGTGCCACGCACTTGGGGAGTGTCTCCCTTGGTGCGCACTTG-GGGAGCA
25394 TCTCCCCTGGTGCCACGCACTTGGGGAGTGTCTCCCCTT-GTGCGCACTTGGGGAGCA
1 TCTCCCCTGGTGCCACGCACTTGGGGAGTGTCT-CCCTTGGTGCGCACTTGGGGAGCA
***
25451 TCTCCCCTGGTGGTGCGCACTTGGGGAGTGTCTCCAC-TGGTGCGC
1 TCTCCCCTGGTGCCACGCACTTGGGGAGTGTCTCC-CTTGGTGCGC
25496 CTCACCTGGG
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
56 3 0.03
57 77 0.89
58 7 0.08
ACGTcount: A:0.09, C:0.31, G:0.35, T:0.25
Consensus pattern (57 bp):
TCTCCCCTGGTGCCACGCACTTGGGGAGTGTCTCCCTTGGTGCGCACTTGGGGAGCA
Found at i:25483 original size:87 final size:86
Alignment explanation
Indices: 25374--25548 Score: 214
Period size: 87 Copynumber: 2.0 Consensus size: 86
25364 GTCCCTCCCT
* * *
25374 TGGTGCGCACTGAGGGAGTGTCTCCCCTGGTGC-CACGCA-CTTGGGGAGTGTCTCCCCTT-GTG
1 TGGTGCGCACTGAGGGAGTGTCTCCACTGGTGCGC-CGCACCTGGGGGAGTGACT-CCCTTGGTG
25436 CGCACTTGGGGAGCATCTCCCCTGG
64 CGC-CTT-GGGAGCATCTCCCCTGG
* *
25461 TGGTGCGCACTTG-GGGAGTGTCTCCACTGGTGCGCCTCACCTGGGGGATTGACTCCCTTGGTGC
1 TGGTGCGCAC-TGAGGGAGTGTCTCCACTGGTGCGCCGCACCTGGGGGAGTGACTCCCTTGGTGC
**
25525 GCCTTGGGAGTGTCTCCCCTGG
65 GCCTTGGGAGCATCTCCCCTGG
25547 TG
1 TG
25549 ACTTTTTTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
86 17 0.22
87 40 0.52
88 20 0.26
ACGTcount: A:0.09, C:0.30, G:0.35, T:0.26
Consensus pattern (86 bp):
TGGTGCGCACTGAGGGAGTGTCTCCACTGGTGCGCCGCACCTGGGGGAGTGACTCCCTTGGTGCG
CCTTGGGAGCATCTCCCCTGG
Found at i:25632 original size:29 final size:31
Alignment explanation
Indices: 25584--25649 Score: 109
Period size: 29 Copynumber: 2.2 Consensus size: 31
25574 TCTCCCCTGG
*
25584 CACTTGGGGAGTCTCTCCCCTGGTGCGCGGA
1 CACTGGGGGAGTCTCTCCCCTGGTGCGCGGA
25615 CACTGGGGGAG-C-CTCCCCTGGTGCGCGGA
1 CACTGGGGGAGTCTCTCCCCTGGTGCGCGGA
25644 CACTGG
1 CACTGG
25650 AAATCTCCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 23 0.68
30 1 0.03
31 10 0.29
ACGTcount: A:0.11, C:0.33, G:0.38, T:0.18
Consensus pattern (31 bp):
CACTGGGGGAGTCTCTCCCCTGGTGCGCGGA
Found at i:25665 original size:27 final size:28
Alignment explanation
Indices: 25597--25667 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 28
25587 TTGGGGAGTC
* *
25597 TCTCCCCTGGTGCGCGGACACTGGGGGAG
1 TCTCCCCTGGTGCGCGGACACT-GGGAAA
*
25626 CCTCCCCTGGTGCGCGGACACT-GGAAA
1 TCTCCCCTGGTGCGCGGACACTGGGAAA
*
25653 TCTCCCTTGGTGCGC
1 TCTCCCCTGGTGCGC
25668 CCCTCTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 16 0.43
29 21 0.57
ACGTcount: A:0.11, C:0.35, G:0.34, T:0.20
Consensus pattern (28 bp):
TCTCCCCTGGTGCGCGGACACTGGGAAA
Found at i:27406 original size:12 final size:12
Alignment explanation
Indices: 27389--27426 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
27379 AAAGTGACCA
27389 CCCAAGAGAAAT
1 CCCAAGAGAAAT
27401 CCCAAGAGAAAT
1 CCCAAGAGAAAT
27413 CCC-AGAAGAAAT
1 CCCAAG-AGAAAT
27425 CC
1 CC
27427 AAAGGGAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 2 0.08
12 23 0.92
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.08
Consensus pattern (12 bp):
CCCAAGAGAAAT
Found at i:27798 original size:18 final size:18
Alignment explanation
Indices: 27770--27824 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
27760 TAGTGAGGAA
* *
27770 AATGGAGAACCTGACGGT
1 AATGAAGAACCTGACAGT
*
27788 GATGAAGAACCTGACAGT
1 AATGAAGAACCTGACAGT
*
27806 AATGAAGAACTTGACAGT
1 AATGAAGAACCTGACAGT
27824 A
1 A
27825 GTAGTGATGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.40, C:0.15, G:0.27, T:0.18
Consensus pattern (18 bp):
AATGAAGAACCTGACAGT
Found at i:29079 original size:26 final size:26
Alignment explanation
Indices: 28951--29082 Score: 151
Period size: 26 Copynumber: 5.0 Consensus size: 26
28941 TGCGTCCCTA
* *
28951 GGGAGACCTCCCCTGGCTCGCTACT-G
1 GGGAG-CCTCCCCTGGCGCGCTGCTGG
*
28977 GGGAGCCTCCCTTGGCGCGCT-CTGCCG
1 GGGAGCCTCCCCTGGCGCGCTGCTG--G
* * *
29004 GGGAGTCTCCCGTGGCGCGCTGCCGG
1 GGGAGCCTCCCCTGGCGCGCTGCTGG
*
29030 GGGAGTCTCCCCTGGCGCGCTGCTGG
1 GGGAGCCTCCCCTGGCGCGCTGCTGG
*
29056 GGGAGCCTCCCCTGGCACGCTGCTGG
1 GGGAGCCTCCCCTGGCGCGCTGCTGG
29082 G
1 G
29083 CCTCCTCTAG
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
24 2 0.02
25 14 0.15
26 55 0.59
27 20 0.22
28 2 0.02
ACGTcount: A:0.06, C:0.37, G:0.39, T:0.17
Consensus pattern (26 bp):
GGGAGCCTCCCCTGGCGCGCTGCTGG
Found at i:29629 original size:17 final size:17
Alignment explanation
Indices: 29575--29686 Score: 165
Period size: 17 Copynumber: 6.7 Consensus size: 17
29565 TGGTGACCTC
*
29575 ACCAGGTGAATA-TTGT
1 ACCAGGTGAGTATTTGT
** *
29591 ACTGGGTGAGTA-TTGC
1 ACCAGGTGAGTATTTGT
29607 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTATTTGT
*
29624 ACCAGGTGAGTGTTTGT
1 ACCAGGTGAGTATTTGT
29641 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTATTTGT
29658 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTATTTGT
29675 ACCAGGTGAGTA
1 ACCAGGTGAGTA
29687 GGGTAGGAAC
Statistics
Matches: 86, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
16 22 0.26
17 64 0.74
ACGTcount: A:0.24, C:0.12, G:0.31, T:0.32
Consensus pattern (17 bp):
ACCAGGTGAGTATTTGT
Found at i:31216 original size:2 final size:2
Alignment explanation
Indices: 31209--31233 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31199 GACTAGCTAA
31209 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 A
31234 CTCCTATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32908 original size:18 final size:20
Alignment explanation
Indices: 32873--32909 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
32863 TAGTCAGTTC
32873 TTTGAGTTCAGTTTAGTTTT
1 TTTGAGTTCAGTTTAGTTTT
32893 TTTGAG-TCAG-TTAGTTT
1 TTTGAGTTCAGTTTAGTTT
32910 GAGTCTGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 4 0.24
20 6 0.35
ACGTcount: A:0.16, C:0.05, G:0.22, T:0.57
Consensus pattern (20 bp):
TTTGAGTTCAGTTTAGTTTT
Found at i:36985 original size:32 final size:32
Alignment explanation
Indices: 36944--37009 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
36934 ACTAAACTAC
36944 AATCTTTTGGGTTTATTCCATAATAATAAGAT
1 AATCTTTTGGGTTTATTCCATAATAATAAGAT
36976 AATCTTTTGGGTTTATTCCATAATAATAAGAT
1 AATCTTTTGGGTTTATTCCATAATAATAAGAT
37008 AA
1 AA
37010 AGATTATTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.42
Consensus pattern (32 bp):
AATCTTTTGGGTTTATTCCATAATAATAAGAT
Done.