Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005531.1 Corchorus capsularis cultivar CVL-1 contig05549, 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: 34558
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3103 original size:334 final size:325
Alignment explanation
Indices: 1946--3174 Score: 1088
Period size: 334 Copynumber: 3.7 Consensus size: 325
1936 GGGTTCAACA
* * * * * *
1946 ACGATTTCAACTAAAATTTTGCAAAAATTAACACGAAATAATTCTCCTAAATTCTTGGCTAAAAT
1 ACGATTTCGACTAAAATTTTGCAAAAATTGACACGAAAGATTTCTCCTTAATTTTTGGCTAAAAT
* * *
2011 ACTCATAAAAATATATAATAT-AAAGCCAAAAAGATTGGAGGGCTTTTCATGCTTTT-ATATCGT
66 ACTCAT-AAAATATATAAT-TCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGT
* * *
2074 ATTTCTTATTTTTCTGAATTAAATTCTAATTAAATCCAAACAAAATTTAGATGCTCGTAAAAACA
129 ATTTCTTATTTTTCTGAATTAAATTCTAATTAAATCGAAACAAGATTTAGATGCTCATAAAAACA
** * * *
2139 AATTCTTAAATCCAATGTATTTGAGATTTTATTAGATGAATATGGATACCTTAAAGAGTATT-GG
194 AATTCTTAAATCCAATGTAGCTGAGATTTGATTAGATGAATATGGATA-TTTCAAGAGT-TTCGG
* * * * * *
2203 CGCCAAAAATCATGCAAAACTTAGTCAGGGCCCCAAAATGCGTTTTTAGCCAGAAACCATGATGA
257 -GCCAAAAATCATACAAAACTTAG-CCGGG-CCCAGAA--CGTTTTTAGCCAAAAACCGTGATGG
2268 TTG-T-TAC
317 TTGTTATAC
* * * * * * * *
2275 ACGATTTCGGCTAAAATTTTGCAAAAATTGACTCCAAAGTTTTTTCCTCT-ATTTTTAGCCACAA
1 ACGATTTCGACTAAAATTTTGCAAAAATTGACACGAAAGATTTCTCCT-TAATTTTTGGCTAAAA
* * * * * *
2339 TTCTCATAAAAATTATATAATTCAACGCCAAAAAAATTGAAGGACATTTCACTCTTTTAAAATCA
65 TACTCAT-AAAA-TATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATC-
* * * *
2404 TTTTTTCTATTATTTTTC-GAATTAAATTTCTAATTAAATCAAAACAAGATTTAGATACTCATAA
127 GTATTTC--TTATTTTTCTGAATTAAA-TTCTAATTAAATCGAAACAAGATTTAGATGCTCATAA
* * *
2468 AAACAAATTTTTAAATCCCATGTAGCTGAGATTTGATTAGATGAATATGGATATCTCAAG-GATT
189 AAACAAATTCTTAAATCCAATGTAGCTGAGATTTGATTAGATGAATATGGATATTTCAAGAG-TT
* * * * * * * *
2532 CCTGGCGTCAAAAATCATACAAAACTTAGTCGGAGCCCGGGAATGCCTTTTTAACCGAAAACTGT
253 TC-GG-GCCAAAAATCATACAAAACTTAGCCGG-GCCC-AGAA--CGTTTTTAGCCAAAAACCGT
2597 GAT-G--GTTACTAC
312 GATGGTTGTTA-TAC
* ** * * * * *
2609 ACGATTTCGGCTAAAATTTTATAAAAATTGACCCGAAAGTTATTAT-CTCAGTTTTTGGCTAAAA
1 ACGATTTCGACTAAAATTTTGCAAAAATTGACACGAAAGAT-TTCTCCTTAATTTTTGGCTAAAA
* * * * *
2673 TACTTATAAAAAATAATTAATTCAATGCC-AAAATATTGAAGGGCTTTTGACG-TTTCTAATATC
65 TACTCATAAAATAT-A-TAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTT-TAATATC
* * * * * * ** *
2736 GTTTTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTCAGATGCTTTTTAAAA
127 GTATTTCTTATTTTTCTGAATTAAATTCTAATTAAATCGAAACAAGATTTAGATGCTCATAAAAA
* * * *
2801 CAAATCCTTAAATCTAATGAAGCTGAAATTTGATTAGATGAATATGGATATTTCAAGTAGTTTCG
192 CAAATTCTTAAATCCAATGTAGCTGAGATTTGATTAGATGAATATGGATATTTCAAG-AGTTTCG
* * * *
2866 GAGCAAAAAAAAAACATTCAAAA-TTGAGCCGGGTCCCAGAACGTTTTTTAGTCAAAAACCGTGA
256 G-GC---CAAAAATCATACAAAACTT-AGCCGGG-CCCAGAACG-TTTTTAGCCAAAAACCGTGA
*
2930 TGGTTAGTTAGTAT
314 TGGTT-GTTA-TAC
2944 ACGATTTCGACT-AAATTTTGCAAAAATTGACACGAAAGATTTCTCCTTAATTTTTGGCTAAAAT
1 ACGATTTCGACTAAAATTTTGCAAAAATTGACACGAAAGATTTCTCCTTAATTTTTGGCTAAAAT
* * * *
3008 ACTCATAAAAGTATATAATTCAACGCTAAAAAGATTGGAGGGCTTTTAACGCATTT-ATATCGTA
66 ACTCATAAAA-TATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTA
* * * * * **
3072 TTTCTTATTTTTTATAAAGTAAATTCTAATTAAATCGGAACAAGATTTAGATGCTCGTAAAAATT
130 TTTCTTA-TTTTTCTGAATTAAATTCTAATTAAATCGAAACAAGATTTAGATGCTCATAAAAACA
* * * * *
3137 AATTATTAAATTCAATGTTGCTAAGATTTGGTTAGATG
194 AATTCTTAAATCCAATGTAGCTGAGATTTGATTAGATG
3175 GTGTAAAGTA
Statistics
Matches: 718, Mismatches: 143, Indels: 73
0.77 0.15 0.08
Matches are distributed among these distances:
329 61 0.08
330 131 0.18
331 32 0.04
332 27 0.04
333 94 0.13
334 349 0.49
335 24 0.03
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.35
Consensus pattern (325 bp):
ACGATTTCGACTAAAATTTTGCAAAAATTGACACGAAAGATTTCTCCTTAATTTTTGGCTAAAAT
ACTCATAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTAT
TTCTTATTTTTCTGAATTAAATTCTAATTAAATCGAAACAAGATTTAGATGCTCATAAAAACAAA
TTCTTAAATCCAATGTAGCTGAGATTTGATTAGATGAATATGGATATTTCAAGAGTTTCGGGCCA
AAAATCATACAAAACTTAGCCGGGCCCAGAACGTTTTTAGCCAAAAACCGTGATGGTTGTTATAC
Found at i:3418 original size:41 final size:41
Alignment explanation
Indices: 3365--3442 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
3355 TTTATAACCA
*
3365 GGGGCTAAACCTGGATTTAATTTCTTACCTTAATTATCAGG
1 GGGGCTAAACCTGAATTTAATTTCTTACCTTAATTATCAGG
* * *
3406 GGGGTTAAACCTGAATTTAATTTGTTTCCTTAATTAT
1 GGGGCTAAACCTGAATTTAATTTCTTACCTTAATTAT
3443 TAAGAGGGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (41 bp):
GGGGCTAAACCTGAATTTAATTTCTTACCTTAATTATCAGG
Found at i:3464 original size:13 final size:13
Alignment explanation
Indices: 3446--3482 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
3436 TAATTATTAA
*
3446 GAGGGACAATTTT
1 GAGGGACAAATTT
3459 GAGGGACAAATTT
1 GAGGGACAAATTT
*
3472 GAGGGTCAAAT
1 GAGGGACAAAT
3483 AGAATTATCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.32, T:0.24
Consensus pattern (13 bp):
GAGGGACAAATTT
Found at i:4135 original size:5 final size:5
Alignment explanation
Indices: 4118--4154 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
4108 CAAATAGTAG
*
4118 TAAGA TAAAA TAAGA TAAGA TAAGA T-AG- TAAGA TAAG
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAG
4155 GAATAAGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
3 1 0.04
4 4 0.14
5 23 0.82
ACGTcount: A:0.59, C:0.00, G:0.19, T:0.22
Consensus pattern (5 bp):
TAAGA
Found at i:11586 original size:107 final size:107
Alignment explanation
Indices: 11403--11773 Score: 656
Period size: 107 Copynumber: 3.5 Consensus size: 107
11393 AATTTTTCTA
* ** * *
11403 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAGTTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
11466 TTTCTAAAACCCTATAACAATAAATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATAAATTATTAATTATGGAATTT
11508 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
11573 TTTCTAAAACCCTATAACAATAAATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATAAATTATTAATTATGGAATTT
11615 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
* * *
11680 TTTCTAAAACCCTATAACAATGAATTATTAATTTTGAAATTT
66 TTTCTAAAACCCTATAACAATAAATTATTAATTATGGAATTT
11722 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
11774 AGGCTATATT
Statistics
Matches: 256, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
105 27 0.11
106 15 0.06
107 214 0.84
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.40
Consensus pattern (107 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
TTTCTAAAACCCTATAACAATAAATTATTAATTATGGAATTT
Found at i:14505 original size:12 final size:13
Alignment explanation
Indices: 14480--14508 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
14470 TTACTGCATG
14480 CCATCTTCACTCT
1 CCATCTTCACTCT
14493 CCATCTT-ACTCT
1 CCATCTTCACTCT
14505 CCAT
1 CCAT
14509 TATTTCTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.17, C:0.45, G:0.00, T:0.38
Consensus pattern (13 bp):
CCATCTTCACTCT
Found at i:20737 original size:27 final size:28
Alignment explanation
Indices: 20691--20744 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
20681 CTATAAAATC
20691 AGCCATGGTCTCAACCGGCCAAAAAAAAA
1 AGCCATGGTCTCAA-CGGCCAAAAAAAAA
*
20720 AGCCATGGTCTCAA-GGCCATAAAAA
1 AGCCATGGTCTCAACGGCCAAAAAAA
20745 CCAGTTCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 10 0.42
29 14 0.58
ACGTcount: A:0.43, C:0.26, G:0.19, T:0.13
Consensus pattern (28 bp):
AGCCATGGTCTCAACGGCCAAAAAAAAA
Found at i:22545 original size:42 final size:43
Alignment explanation
Indices: 22489--22571 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
22479 CGTATTTGGC
* *
22489 TTATCGTGTCTCGTGTC-TGAATCGTGTC-GGACACGATTAAGA
1 TTATCATGTCTCGTGTCGT-AATCGTGTCAAGACACGATTAAGA
*
22531 TTATCATGTTTCGTGTCGTAATCGTGTCAAGACACGATTAA
1 TTATCATGTCTCGTGTCGTAATCGTGTCAAGACACGATTAA
22572 CACGTTTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 24 0.67
43 12 0.33
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (43 bp):
TTATCATGTCTCGTGTCGTAATCGTGTCAAGACACGATTAAGA
Found at i:22584 original size:20 final size:21
Alignment explanation
Indices: 22559--22601 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
22549 TAATCGTGTC
*
22559 AAGACACGATTAACACG-TTT
1 AAGACACGAGTAACACGCTTT
*
22579 AAGACACGAGTGACACGCTTT
1 AAGACACGAGTAACACGCTTT
22600 AA
1 AA
22602 TTAACGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (21 bp):
AAGACACGAGTAACACGCTTT
Found at i:28552 original size:24 final size:24
Alignment explanation
Indices: 28520--28638 Score: 150
Period size: 24 Copynumber: 5.0 Consensus size: 24
28510 TTCATGCTCC
* *
28520 GAATCATCTCCAATGTCATCATCT
1 GAATTATCTCCAATATCATCATCT
* *
28544 AAATTATCTTCAATATCATCATCT
1 GAATTATCTCCAATATCATCATCT
** *
28568 GAGCTGTCTCCAATATCATCATCT
1 GAATTATCTCCAATATCATCATCT
28592 GAATTATCTCCAATATCATCATCT
1 GAATTATCTCCAATATCATCATCT
*
28616 GAATTATCTTCAATAAT-ATCATC
1 GAATTATCTCCAAT-ATCATCATC
28639 CTTGCTCCAA
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
24 79 0.98
25 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.37
Consensus pattern (24 bp):
GAATTATCTCCAATATCATCATCT
Done.