Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005192.1 Corchorus capsularis cultivar CVL-1 contig05210, 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: 24211
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4662 original size:36 final size:36
Alignment explanation
Indices: 4615--4691 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 36
4605 TTTTGAGAAC
*
4615 GATCATTTCAGGATGTAACGTTACCCAATAGGATCA
1 GATCATTTCAGGATATAACGTTACCCAATAGGATCA
4651 GATCATTTCAGGATATAACGTTACCCAATAGGATCA
1 GATCATTTCAGGATATAACGTTACCCAATAGGATCA
*
4687 AATCA
1 GATCA
4692 GGATATTTCC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (36 bp):
GATCATTTCAGGATATAACGTTACCCAATAGGATCA
Found at i:6116 original size:1 final size:1
Alignment explanation
Indices: 6112--6136 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
6102 TTTTTTGAAA
6112 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
6137 AAGTTTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:10941 original size:328 final size:329
Alignment explanation
Indices: 10359--11381 Score: 835
Period size: 328 Copynumber: 3.2 Consensus size: 329
10349 AATTCAACTC
* ** *
10359 TTTCATATTTTTCTAAATTAATTTCTAATTAAATTGAAACTTGATTCAGATGCTTGTAAAAATAA
1 TTTCATATTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAATAA
* * * *
10424 ATTCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGATG
66 ATCCTTAAATGCAATGTGGCTGAGAATTGATTAGATAAATATAGATATTTCAAGGAGTCTCGACG
* ** ** * *
10489 CCAAAAATCATGTAAAATTGAGTCGGGACCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGGTT
131 CCAAAAATCATGCAAAACCGACCCGGGACCCCGAAACGCGTTTGTAGCAAAAAACCGTGATGATT
** * * *
10554 AGTACATGATTTCGGCTAAAATTTTGTAAAAAAGACCCGAAAAATTTTTCCTCAATTTTTGCCTA
196 AGTACACAATTTCGGCTAAAATTTTGCAAAAAAGACCCGAAAAATATTTCCTAAATTTTTGCCTA
*
10619 AAATAATCATGAAATATATATAATTTAATGCCAAAAATATTGGAGGACTTTTCACGCTTTTAATG
261 AAATAATCATAAAATATATATAATTTAATGCCAAAAATATTGGAGGACTTTTCACGCTTTTAATG
10684 TATT
326 TATT
*
10688 TTTCATATTTTTCTGAATTAATTTCTAATTAAATCG-AACAAGATTCAGATGCTCGTAAAAATAA
1 TTTCATATTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAATAA
* * * *
10752 ATCCTTAAATGCAATGTGGCTGAGAATTGATTAGATAAATATGGATATCTT-AAGGAGTTTTGGC
66 ATCCTTAAATGCAATGTGGCTGAGAATTGATTAGATAAATATAGATAT-TTCAAGGAGTCTCGAC
* * * **
10816 GCC-AAAATCATGCAAAACCGACCCGAGG-CTCTGGAACGCGTTTGTAGCCGAAAACCGTGATGA
130 GCCAAAAATCATGCAAAACCGACCCG-GGACCCCGAAACGCGTTTGTAGCAAAAAACCGTGATGA
* * * * * *
10879 TTATTACACAATTTCGGCTAAAATTTTGCAAAAATGGATCCGGAAGATATTTCCTAAATTTTTGG
194 TTAGTACACAATTTCGGCTAAAATTTTGCAAAAA-AGACCCGAAAAATATTTCCTAAATTTTTGC
* * * * ** ** *
10944 CTAAAATACTCATAAAATGT-TGA-AGGGTTT-TTG----ACGT-TTCTA--A--TAT--CG-TT
258 CTAAAATAATCATAAAATATAT-ATA--ATTTAATGCCAAAAATATTGGAGGACTTTTCACGCTT
*
10994 TT--TCCTACTT
320 TTAAT-GTA-TT
11004 TTTC-TGA---TT-T--A---ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAATA
1 TTTCAT-ATTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAATA
* * * * *
11059 AATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGTAGTCTCGAA
65 AATCCTTAAATGCAATGTGGCTGAGAATTGATTAGATAAATATAGATATTTCAAGGAGTCTCGAC
** ** ** * * *
11124 GCCAAAAATCATGCAAAATTGAGGCGGGTTCCCGGAACGCGTTTTTAGCCAAAAACCGTGATG--
130 GCCAAAAATCATGCAAAACCGACCCGGGACCCCGAAACGCGTTTGTAGCAAAAAACCGTGATGAT
* * * * *
11187 --G----------CGGCTAAAATTTTGCAAAAATTGACTCGAAAGATTTTTCTTCTTAATTTTTG
195 TAGTACACAATTTCGGCTAAAATTTTGCAAAAA-AGACCCGAAAAATATTTC--CTAAATTTTTG
* * * * * * * * * *
11240 GCTAAAATACTCATAAAA-ATATGTAATTGAATGCCAAAAACATTGAAGGGCGTTCCGCGCTTTT
257 CCTAAAATAATCATAAAATATATATAATTTAATGCCAAAAATATTGGAGGACTTTTCACGCTTTT
11304 AATATCGTATT
322 -A-AT-GTATT
* * * * *
11315 TCTAAT-TTTTTCTAAATTAATTTCTAATTAAATCGAAATAAGATTCAGACGCTATCGCAAAAAT
1 TTTCATATTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGC--TCGTAAAAAT
11379 AAA
64 AAA
11382 ATTTTAAATC
Statistics
Matches: 557, Mismatches: 91, Indels: 100
0.74 0.12 0.13
Matches are distributed among these distances:
295 36 0.06
296 3 0.01
297 30 0.05
300 1 0.00
301 3 0.01
305 1 0.00
307 20 0.04
308 89 0.16
309 47 0.08
310 1 0.00
311 4 0.01
312 6 0.01
313 4 0.01
314 2 0.00
315 3 0.01
316 12 0.02
317 2 0.00
319 33 0.06
321 13 0.02
323 3 0.01
324 2 0.00
327 77 0.14
328 126 0.23
329 39 0.07
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (329 bp):
TTTCATATTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAATAA
ATCCTTAAATGCAATGTGGCTGAGAATTGATTAGATAAATATAGATATTTCAAGGAGTCTCGACG
CCAAAAATCATGCAAAACCGACCCGGGACCCCGAAACGCGTTTGTAGCAAAAAACCGTGATGATT
AGTACACAATTTCGGCTAAAATTTTGCAAAAAAGACCCGAAAAATATTTCCTAAATTTTTGCCTA
AAATAATCATAAAATATATATAATTTAATGCCAAAAATATTGGAGGACTTTTCACGCTTTTAATG
TATT
Found at i:11103 original size:636 final size:637
Alignment explanation
Indices: 9692--11187 Score: 1604
Period size: 636 Copynumber: 2.3 Consensus size: 637
9682 CATAAAAAAG
* * * *
9692 ATTGAAGGGCTTTTAATGCTTCTAATATTGTTTTTCCTATTTTTATTCGAATTAATTTCTAATTA
1 ATTGAAGGG-TTTTTA-GATTCTAATATCGTTTTTCCTATTTTT-CT-GAATTAATTTCTAATTA
* ** * * * *
9757 AATCGAAACAAGATTCAGATGCTCGTGAAAGCAAATCCTTATATTCAATGTGGCTAAGATTTGGT
62 AATCGAAACAAGATTCAGATGCTCGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTTGAT
* * * ** ** *
9822 TAGTTGAGTATAAGATATTTCAAGGAGTTCTGGCACA-AAAAAAAAAATGCAAAACTGAGCCGGG
127 TAGATGAATAT-AGATATTTCAAGGAG-TCTCG-A-AGCCAAAAATCATGCAAAATTGAGCCGGG
* * * *
9886 TCCCGGAACTCGTTTTTAGCCGAAAACCGTAACGGGTAGTACACGATTTCGGCTAAAATTTTGCA
188 TCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGGTAGTACACGATTTCGGCTAAAATTTTGCA
* * *
9951 AAAATTGACTCCAAAGATTTTTCCTCAATTTCTAGTGAAAATACTCATAAAGAATATATAATTAA
253 AAAATAGACTCCAAAAATTTTTCCTCAATTTCTAGTGAAAATAATCATAAAGAATATATAATTAA
* * *
10016 ATGCCAAAAAATTGAAAGCCTTTTTCACGCTTCTAATATCGTTTTTCCTATTTTATTTCCAAATT
318 ATGCCAAAAAATTGAAAGACTTTTTCACGCTTCTAATATCATTTTTCCTATATTATTTCCAAATT
* *
10081 AATTACTGATTAAATCGAAAAAAGATTTAGATACTCGTAAAAAAAATCCTTAAATACAATGTGAC
383 AATTACTAATTAAATCGAAAAAAGATTCAGATACTCGTAAAAAAAATCCTTAAATACAATGTGAC
* * * *
10146 TGAGATTTAGTTAGATGAATATAGATATATTTTAAGGAGTCTTAGCGCTAAAAATCATGCAAAAC
448 TGAGATTGAGTTAGATAAATATAGAGATATCTTAAGGAGTCTTAGCGCTAAAAATCATGCAAAAC
* * * ** *
10211 TCACCCGGGGCCCCTGAATGCATTTAGCCAAAAACTGTGTGATTTCGACAAATGTACATGATTTT
513 TCACCCGAGGCCCCTGAACGCATTTAGCCAAAAACCGTGTGATTT-----AATGTACACAATTTC
* * * *
10276 GCCTAATATTTTACAAAAATTGACCAGAAATATCTTCCCTCATTTTTGTCTAAAATACTCATAAA
573 GCCTAAAATTTTACAAAAATGGACCAGAAATATCTTCCCTAATTTTTGGCTAAAATACTCATAAA
* * * * * *
10341 A-T--A---TATATA-ATTC--A-A-C-TCTTTCATATTTTTCTAAATTAATTTCTAATTAAATT
1 ATTGAAGGGTTTTTAGATTCTAATATCGTTTTTCCTATTTTTCTGAATTAATTTCTAATTAAATC
** * * *
10394 GAAACTTGATTCAGATGCTTGTAAAAATAAATTCTTAAATGCAATGTGGCTGAGATTTGATTAGA
66 GAAACAAGATTCAGATGCTCGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGA
* * * * *
10459 TGAATATAGATATTTCAAGGAGTCTCGATGCCAAAAATCATGTAAAATTGAGTCGGGACCCCGAA
131 TGAATATAGATATTTCAAGGAGTCTCGAAGCCAAAAATCATGCAAAATTGAGCCGGG-TCCCGGA
* * * *
10524 ACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGTAAAAA-AG
195 ACGCGTTTTTAGCCAAAAACCGTGATGGGTAGTACACGATTTCGGCTAAAATTTTGCAAAAATAG
* * *
10588 AC-CCGAAAAATTTTTCCTCAATTT-TTGCCT-AAAATAATCATGAAA-TATATATAATTTAATG
260 ACTCC-AAAAATTTTTCCTCAATTTCTAG--TGAAAATAATCAT-AAAGAATATATAATTAAATG
* * * * **
10649 CCAAAAATATTGGAGGAC-TTTTCACGCTTTTAATGT-ATTTTT-C-ATATT-TTTCTGAATTAA
321 CCAAAAA-ATTGAAAGACTTTTTCACGCTTCTAATATCATTTTTCCTATATTATTTCCAAATTAA
* * * * *
10709 TTTCTAATTAAATCG-AACAAGATTCAGATGCTCGTAAAAATAAATCCTTAAATGCAATGTGGCT
385 TTACTAATTAAATCGAAAAAAGATTCAGATACTCGTAAAAA-AAATCCTTAAATACAATGTGACT
* * *
10773 GAGAATTGA-TTAGATAAATAT-G-GATATCTTAAGGAGTTTTGGCGC-CAAAATCATGCAAAAC
449 GAG-ATTGAGTTAGATAAATATAGAGATATCTTAAGGAGTCTTAGCGCTAAAAATCATGCAAAAC
* * *
10834 -CGACCCGAGG-CTCTGGAACGCGTTTGTAGCCGAAAACCGTGATGA-TT-AT-TACACAATTTC
513 TC-ACCCGAGGCCCCT-GAACGC-ATT-TAGCCAAAAACCGTG-TGATTTAATGTACACAATTTC
* * *
10894 GGCTAAAATTTTGCAAAAATGGATCCGGAAGATAT-TT-CCTAAATTTTTGGCTAAAATACTCAT
573 GCCTAAAATTTTACAAAAATGGA-CCAGAA-ATATCTTCCCT-AATTTTTGGCTAAAATACTCAT
10957 AAA
635 AAA
* *
10960 ATGTTGAAGGGTTTTTGACGTTTCTAATATCGTTTTTCCTACTTTTTCTGATTTAATTTCTAATT
1 A--TTGAAGGGTTTTT-A-GATTCTAATATCGTTTTTCCTA-TTTTTCTGAATTAATTTCTAATT
11025 AAATCGAAACAAGATTCAGATGCTCGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTTGA
61 AAATCGAAACAAGATTCAGATGCTCGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTTGA
* *
11090 TTAGATGAATATAGATATTTCAAGTAGTCTCGAAGCCAAAAATCATGCAAAATTGAGGCGGGTTC
126 TTAGATGAATATAGATATTTCAAGGAGTCTCGAAGCCAAAAATCATGCAAAATTGAGCCGGG-TC
11155 CCGGAACGCGTTTTTAGCCAAAAACCGTGATGG
190 CCGGAACGCGTTTTTAGCCAAAAACCGTGATGG
11188 CGGCTAAAAT
Statistics
Matches: 705, Mismatches: 108, Indels: 81
0.79 0.12 0.09
Matches are distributed among these distances:
618 30 0.04
619 33 0.05
620 4 0.01
622 5 0.01
623 27 0.04
624 22 0.03
625 38 0.05
626 61 0.09
627 11 0.02
628 2 0.00
629 9 0.01
630 92 0.13
631 74 0.10
632 16 0.02
633 79 0.11
634 2 0.00
635 19 0.03
636 170 0.24
637 1 0.00
638 1 0.00
640 3 0.00
642 3 0.00
646 1 0.00
648 1 0.00
649 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (637 bp):
ATTGAAGGGTTTTTAGATTCTAATATCGTTTTTCCTATTTTTCTGAATTAATTTCTAATTAAATC
GAAACAAGATTCAGATGCTCGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGA
TGAATATAGATATTTCAAGGAGTCTCGAAGCCAAAAATCATGCAAAATTGAGCCGGGTCCCGGAA
CGCGTTTTTAGCCAAAAACCGTGATGGGTAGTACACGATTTCGGCTAAAATTTTGCAAAAATAGA
CTCCAAAAATTTTTCCTCAATTTCTAGTGAAAATAATCATAAAGAATATATAATTAAATGCCAAA
AAATTGAAAGACTTTTTCACGCTTCTAATATCATTTTTCCTATATTATTTCCAAATTAATTACTA
ATTAAATCGAAAAAAGATTCAGATACTCGTAAAAAAAATCCTTAAATACAATGTGACTGAGATTG
AGTTAGATAAATATAGAGATATCTTAAGGAGTCTTAGCGCTAAAAATCATGCAAAACTCACCCGA
GGCCCCTGAACGCATTTAGCCAAAAACCGTGTGATTTAATGTACACAATTTCGCCTAAAATTTTA
CAAAAATGGACCAGAAATATCTTCCCTAATTTTTGGCTAAAATACTCATAAA
Found at i:12091 original size:13 final size:13
Alignment explanation
Indices: 12073--12097 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12063 TATATAGTAG
12073 TAAGATAAGATAC
1 TAAGATAAGATAC
12086 TAAGATAAGATA
1 TAAGATAAGATA
12098 AGATAATAAG
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:0.56, C:0.04, G:0.16, T:0.24
Consensus pattern (13 bp):
TAAGATAAGATAC
Found at i:12096 original size:18 final size:18
Alignment explanation
Indices: 12073--12109 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
12063 TATATAGTAG
*
12073 TAAGATAAGATACTAAGA
1 TAAGATAAGATAATAAGA
12091 TAAGATAAGATAATAAGA
1 TAAGATAAGATAATAAGA
12109 T
1 T
12110 GTGCGGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.57, C:0.03, G:0.16, T:0.24
Consensus pattern (18 bp):
TAAGATAAGATAATAAGA
Found at i:16730 original size:26 final size:28
Alignment explanation
Indices: 16699--16767 Score: 92
Period size: 26 Copynumber: 2.6 Consensus size: 28
16689 AAAAAATCCT
16699 AAGCAACT-TTTTTTT-TGCCAAAAAAA
1 AAGCAACTATTTTTTTGTGCCAAAAAAA
16725 AAGCAACTAATTTTTTTGTGCC--AAAAA
1 AAGCAACT-ATTTTTTTGTGCCAAAAAAA
*
16752 AAGCAACTAATTTTTT
1 AAGCAACTATTTTTTT
16768 AAATTATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
26 15 0.38
27 13 0.33
28 7 0.18
29 4 0.10
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (28 bp):
AAGCAACTATTTTTTTGTGCCAAAAAAA
Found at i:16738 original size:27 final size:26
Alignment explanation
Indices: 16699--16767 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 26
16689 AAAAAATCCT
*
16699 AAGCAACT--TTTTTTTTGCCAAAAAAA
1 AAGCAACTAATTTTTTGTGCC--AAAAA
16725 AAGCAACTAATTTTTTTGTGCCAAAAA
1 AAGCAACTAA-TTTTTTGTGCCAAAAA
16752 AAGCAACTAATTTTTT
1 AAGCAACTAATTTTTT
16768 AAATTATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
26 14 0.36
27 15 0.38
29 10 0.26
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (26 bp):
AAGCAACTAATTTTTTGTGCCAAAAA
Found at i:22909 original size:6 final size:6
Alignment explanation
Indices: 22899--22929 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
22889 GTTTTCATGA
*
22899 AAAAAA AAAAAC AAAAAC AAAAAC AAAAAC A
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC A
22930 CTTTACTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Done.