Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011596.1 Corchorus capsularis cultivar CVL-1 contig11617, 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: 61563
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:14922 original size:42 final size:42
Alignment explanation
Indices: 14876--14961 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 42
14866 GATTTTTGAA
* *
14876 AAAAAAAATTTAATTTTTCTTTTCCGTTTTTCCATTTTTTTT
1 AAAAAAAATTTAATTTTTATTTTCCGTTTTGCCATTTTTTTT
* ** * **
14918 AAAAAATATTTTTTTTTTATTTTCTGTTTTGCTTTTTTTTTT
1 AAAAAAAATTTAATTTTTATTTTCCGTTTTGCCATTTTTTTT
14960 AA
1 AA
14962 GAACTGTTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.64
Consensus pattern (42 bp):
AAAAAAAATTTAATTTTTATTTTCCGTTTTGCCATTTTTTTT
Found at i:20814 original size:840 final size:839
Alignment explanation
Indices: 18488--21000 Score: 4816
Period size: 841 Copynumber: 3.0 Consensus size: 839
18478 TTAATTTTTA
18488 TTTG-TTTTATTTTA-TTTTCTTTTCTTTTCTTTTTTAGGATTTTCCATACCAAAGGAGCAATAG
1 TTTGTTTTTATTTTATTTTTCTTTTCTTTTCTTTTTTAGGATTTTCCATACCAAAGGAGCAATAG
*
18551 GAGCTTACGTGTTGGACAATTGCAAAGCAAGAGAAATTAAATGGAGAATATGCCCCTTGCCGATT
66 GAGCTTACGTTTTGGACAATTGCAAAGCAAGAGAAATTAAATGGAGAATATGCCCCTTGCCGATT
* *
18616 CCAAATCCTTATTGGATCCAATTGGAGCTTATGCTTGGAGAATAGAGAAGCTTTATTTAACTCTA
131 CCAAATCCTCATTGGATCCAATTGGAGCTTATGCTTGGAGAATACAGAAGCTTTATTTAACTCTA
*
18681 TATTTTTCTTACAATGCTTTGATTGATTTTTCTTTGATATGCGATTCATATAGATATAGATATAG
196 TATTTTTCTTGCAATGCTTTGATTGATTTTTCTTTGATATGCGATTCATATAGATATAGATATAG
18746 GTTATATAGGTTAATTAGGATTTAAAGATGCATATATATTTTTGCTTTGATTTTCACGCTTGTTT
261 GTTATATAGGTTAATTAGGATTTAAAGATGCATATATATTTTTGCTTTGATTTTCACGCTTGTTT
18811 ATACATTGGGGACAATGTATCTTTTAAGTGTGGGGGAGTGAGTCTAATTGCATAGAAAATTGGCA
326 ATACATTGGGGACAATGTATCTTTTAAGTGTGGGGGAGTGAGTCTAATTGCATAGAAAATTGGCA
18876 TAATTTTTTCGAAAATTTTGATAAAATTTTGATTTTATATGCATCTATTGAGTTATTGATTTGAT
391 TAATTTTTTCGAAAATTTTGATAAAATTTTGATTTTATATGCATCTATTGAGTTATTGATTTGAT
18941 TTTTGATTGATGATTGCTTTGAATTTTTAAGAATGTTTGATTTATTGATTGATTTATAGTATGAT
456 TTTTGATTGATGATTGCTTTGAATTTTTAAGAATGTTTGATTTATTGATTGATTTATAGTATGAT
19006 ATCTTATTTCTTAGATTAGGTATAATTGAAGTTTGTGATATGAGCTTATTGCTTATTATTTCTAT
521 ATCTTATTTCTTAGATTAGGTATAATTGAAGTTTGTGATATGAGCTTATTGCTTATTATTTCTAT
19071 GATTGCCTATTTCTAGAACTTGTGTTTAATTTTTATTGAAACTACACTTATGAGAGTATTTTATG
586 GATTGCCTATTTCTAGAACTTGTGTTTAATTTTTATTGAAACTACACTTATGAGAGTATTTTATG
19136 AATATGTCAAAAATAAGTGTGGGGGACCATCTATATTAGAAGGGTAGTTTTAAAAAAAAATTCTT
651 AATATGTCAAAAATAAGTGTGGGGGACCATCTATATTAGAAGGGTAGTTTTAAAAAAAAATTCTT
19201 AAAAAGAGTGTTTTTCATGCAAGAGGAGAAGAGATATCTTTTGCCTTAAAAAATTTAAAAAAAAT
716 AAAAAGAGTGTTTTTCATGCAAGAGGAGAAGAGATATCTTTTGCCTTAAAAAA-TTAAAAAAAAT
19266 TCCATTGTTGTCACTCTTCTCTTTAAACAAAAGGAGTTAGTAACCCTTGGGAAGAGTTTC
780 TCCATTGTTGTCACTCTTCTCTTTAAACAAAAGGAGTTAGTAACCCTTGGGAAGAGTTTC
19326 TTTGTTTTTATTTTATTTTTCTTTTCTTTTCTTTTTTAGGATTTTCCATACCAAAGGAGCAATAG
1 TTTGTTTTTATTTTATTTTTCTTTTCTTTTCTTTTTTAGGATTTTCCATACCAAAGGAGCAATAG
*
19391 GAGCTTACGTTTTGGACAATTGCAAAGCAAGAGAAATTAAATGGAGAATATGCACCTTGCCGATT
66 GAGCTTACGTTTTGGACAATTGCAAAGCAAGAGAAATTAAATGGAGAATATGCCCCTTGCCGATT
19456 CCAAATCCTCATTGGATCCAATTGGAGCTTATGCTTGGAGAATACAGAAGCTTTATTTAACTCTA
131 CCAAATCCTCATTGGATCCAATTGGAGCTTATGCTTGGAGAATACAGAAGCTTTATTTAACTCTA
19521 TATTTTTCTTGCAATGCTTTGATTGATTTTTCTTTGATATGCGATTCATATAGATATAGATATAG
196 TATTTTTCTTGCAATGCTTTGATTGATTTTTCTTTGATATGCGATTCATATAGATATAGATATAG
*
19586 GTTATATAGGTTAATTAGGATTTAAAGATGCATATATATTTTTGCTTTGATTTTCCACGCTTATT
261 GTTATATAGGTTAATTAGGATTTAAAGATGCATATATATTTTTGCTTTGATTTT-CACGCTTGTT
* * *
19651 TATACATTGGGGACAATGTATCTTTTAAGCGTAGGGGAGTAAGTCTAATTGCATAGAAAATTGGC
325 TATACATTGGGGACAATGTATCTTTTAAGTGTGGGGGAGTGAGTCTAATTGCATAGAAAATTGGC
19716 ATAATTTTTTCGAAAATTTTGATAAAATTTTGATTTTATATGCATCTATTGAGTTATTGATTTGA
390 ATAATTTTTTCGAAAATTTTGATAAAATTTTGATTTTATATGCATCTATTGAGTTATTGATTTGA
19781 TTTTTGATTGATGATTGCTTTGAATTTTTAAGAATGTTTGATTTATTGATTGATTTATAGTATGA
455 TTTTTGATTGATGATTGCTTTGAATTTTTAAGAATGTTTGATTTATTGATTGATTTATAGTATGA
19846 TATCTTATTTCTTAGATTAGGTATAATTGAAGTTTGTGATATGAGCTTATTGCTTATTATTTCTA
520 TATCTTATTTCTTAGATTAGGTATAATTGAAGTTTGTGATATGAGCTTATTGCTTATTATTTCTA
* * *
19911 TGATTGCCTATTTTTAGAACTTGTATTTAATTTTTATTGAAACTACACTTATGAGATTATTTTAT
585 TGATTGCCTATTTCTAGAACTTGTGTTTAATTTTTATTGAAACTACACTTATGAGAGTATTTTAT
19976 GAATATGTCAAAAATAAGTGTGGGGGACCATCTATATTAGAAGGGTAGTTTTAAAAAAAAATTCT
650 GAATATGTCAAAAATAAGTGTGGGGGACCATCTATATTAGAAGGGTAGTTTTAAAAAAAAATTCT
* * *
20041 TAAAAAGAGTGTTTTTCATGCAAGAGGAGAAGAGATATCTTTTTCCTTGACAAATTAAAAAAAAA
715 TAAAAAGAGTGTTTTTCATGCAAGAGGAGAAGAGATATCTTTTGCCTTAAAAAATT-AAAAAAAA
20106 TTCCATTGTTGTCACTCTTCTCTTTAAACAAAAGGAGTTAGTAACCCTTGGGAAGAGTTTC
779 TTCCATTGTTGTCACTCTTCTCTTTAAACAAAAGGAGTTAGTAACCCTTGGGAAGAGTTTC
20167 TTTGTTTTTATTTTATTTTTCTTTTCTTTTCTTTTTTAGGATTTTCCATACCAAAGGAGCAATAG
1 TTTGTTTTTATTTTATTTTTCTTTTCTTTTCTTTTTTAGGATTTTCCATACCAAAGGAGCAATAG
20232 GAGCTTACGTTTTGGACAATTGCAAAGCAAGAGAAATTAAATGGAGAATATGCCCCTTGCCGATT
66 GAGCTTACGTTTTGGACAATTGCAAAGCAAGAGAAATTAAATGGAGAATATGCCCCTTGCCGATT
20297 CCAAATCCTCATTGGATCCAATTGGAGCTTATGCTTGGAGAATACAGAAGCTTTATTTAACTCTA
131 CCAAATCCTCATTGGATCCAATTGGAGCTTATGCTTGGAGAATACAGAAGCTTTATTTAACTCTA
20362 TATTTTTCTTGCAATGCTTTGATTGATTTTTCTTTGATATGCGATTCATATAGATATAGATATAG
196 TATTTTTCTTGCAATGCTTTGATTGATTTTTCTTTGATATGCGATTCATATAGATATAGATATAG
20427 GTTATATAGGTTAATTAGGATTTAAAGATGCATATATATTTTTGCTTTGATTTTCACGCTTGTTT
261 GTTATATAGGTTAATTAGGATTTAAAGATGCATATATATTTTTGCTTTGATTTTCACGCTTGTTT
*
20492 ATACATTGTGGACAATGTATCTTTTAAGTGTGGGGGAGTGAGTCTAATTGCATAGAAAATTGGCA
326 ATACATTGGGGACAATGTATCTTTTAAGTGTGGGGGAGTGAGTCTAATTGCATAGAAAATTGGCA
20557 TAATTTTTTCGAAAATTTTGATAAAATTTTGATTTTATATGCATCTATTGAGTTATTGATTTGAT
391 TAATTTTTTCGAAAATTTTGATAAAATTTTGATTTTATATGCATCTATTGAGTTATTGATTTGAT
20622 TTTTGATTGATGATTGCTTTGAATTTTTAAGAATGTTTGATTTATTGATTGATTTATAGTATGAT
456 TTTTGATTGATGATTGCTTTGAATTTTTAAGAATGTTTGATTTATTGATTGATTTATAGTATGAT
*
20687 ATCTTATTTCTTAGATTAGGTATAATTGAAGTTTGTGATATGAGCATATTGCTTATTATTTCTAT
521 ATCTTATTTCTTAGATTAGGTATAATTGAAGTTTGTGATATGAGCTTATTGCTTATTATTTCTAT
20752 GATTGCCTATTTCTAGAACTTGTGTTTAATTTTTATTGAAACTACACTTATGAGAGTATTTTATG
586 GATTGCCTATTTCTAGAACTTGTGTTTAATTTTTATTGAAACTACACTTATGAGAGTATTTTATG
20817 AATATGTCAAAAATAAGTGTGGGGGACCATCTATATTAGAAGGGTAGTTTTAAAAAAAAA-TCTT
651 AATATGTCAAAAATAAGTGTGGGGGACCATCTATATTAGAAGGGTAGTTTTAAAAAAAAATTCTT
*
20881 AAAAAGAGTGTTTTTCATGCAAGAGGAGAAGAGATATCTTTTGCCTTAAAAAATTTAAAAAAATT
716 AAAAAGAGTGTTTTTCATGCAAGAGGAGAAGAGATATCTTTTGCCTTAAAAAATTAAAAAAAATT
20946 CCATTGTTGTCACTCTTCTCTTTAAACAAAAGGAGTTAGTAACCCTTGGGAAGAG
781 CCATTGTTGTCACTCTTCTCTTTAAACAAAAGGAGTTAGTAACCCTTGGGAAGAG
21001 GATAAGAGGC
Statistics
Matches: 1642, Mismatches: 29, Indels: 8
0.98 0.02 0.00
Matches are distributed among these distances:
838 68 0.04
839 66 0.04
840 682 0.42
841 826 0.50
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (839 bp):
TTTGTTTTTATTTTATTTTTCTTTTCTTTTCTTTTTTAGGATTTTCCATACCAAAGGAGCAATAG
GAGCTTACGTTTTGGACAATTGCAAAGCAAGAGAAATTAAATGGAGAATATGCCCCTTGCCGATT
CCAAATCCTCATTGGATCCAATTGGAGCTTATGCTTGGAGAATACAGAAGCTTTATTTAACTCTA
TATTTTTCTTGCAATGCTTTGATTGATTTTTCTTTGATATGCGATTCATATAGATATAGATATAG
GTTATATAGGTTAATTAGGATTTAAAGATGCATATATATTTTTGCTTTGATTTTCACGCTTGTTT
ATACATTGGGGACAATGTATCTTTTAAGTGTGGGGGAGTGAGTCTAATTGCATAGAAAATTGGCA
TAATTTTTTCGAAAATTTTGATAAAATTTTGATTTTATATGCATCTATTGAGTTATTGATTTGAT
TTTTGATTGATGATTGCTTTGAATTTTTAAGAATGTTTGATTTATTGATTGATTTATAGTATGAT
ATCTTATTTCTTAGATTAGGTATAATTGAAGTTTGTGATATGAGCTTATTGCTTATTATTTCTAT
GATTGCCTATTTCTAGAACTTGTGTTTAATTTTTATTGAAACTACACTTATGAGAGTATTTTATG
AATATGTCAAAAATAAGTGTGGGGGACCATCTATATTAGAAGGGTAGTTTTAAAAAAAAATTCTT
AAAAAGAGTGTTTTTCATGCAAGAGGAGAAGAGATATCTTTTGCCTTAAAAAATTAAAAAAAATT
CCATTGTTGTCACTCTTCTCTTTAAACAAAAGGAGTTAGTAACCCTTGGGAAGAGTTTC
Found at i:39306 original size:33 final size:33
Alignment explanation
Indices: 39263--39386 Score: 142
Period size: 33 Copynumber: 3.7 Consensus size: 33
39253 TAGACAAAGG
* * * *
39263 GTCGCATGGCCGGTTGTGGCCGGGCATGGCCAA
1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT
** * *
39296 GTCGTTTGGCCGGTTGTAGCCGGCCATGTCCAT
1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT
39329 GTCGCGTGGCCGG-TGATGGCCGGACATGTCCAT
1 GTCGCGTGGCCGGTTG-TGGCCGGACATGTCCAT
39362 GTCGCGTGGCCGGTCTTGTGGCCGG
1 GTCGCGTGGCCGG--TTGTGGCCGG
39387 TGTTGCGCGG
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
32 2 0.03
33 66 0.86
35 7 0.09
36 2 0.03
ACGTcount: A:0.09, C:0.27, G:0.40, T:0.23
Consensus pattern (33 bp):
GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT
Found at i:46533 original size:95 final size:95
Alignment explanation
Indices: 46369--46544 Score: 309
Period size: 95 Copynumber: 1.9 Consensus size: 95
46359 CCCAACAGTA
46369 AAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATATCAAAGTCCCC
1 AAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATATCAAAGTCCCC
46434 AAACACATATAACACATGGGCAACTCTCTC
66 AAACACATATAACACATGGGCAACTCTCTC
* *
46464 AAAGTCCTCAAGCACAAGGGCATTCATAAGTTCCTAAACACAGAGGCATCTATA-CGAAAGTCCC
1 AAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATATC-AAAGTCCC
*
46528 TAAACACATATAACACA
65 CAAACACATATAACACA
46545 AGGTCCCAAA
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
94 1 0.01
95 76 0.99
ACGTcount: A:0.40, C:0.28, G:0.13, T:0.19
Consensus pattern (95 bp):
AAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATATCAAAGTCCCC
AAACACATATAACACATGGGCAACTCTCTC
Found at i:61111 original size:26 final size:28
Alignment explanation
Indices: 61068--61146 Score: 92
Period size: 26 Copynumber: 2.9 Consensus size: 28
61058 GCGTTAGGGT
* *
61068 CATCTAG-GGGCATATTGGTCATTTTTA
1 CATCTAGAGGGCATTTTGGTCATTTTCA
*
61095 TA-CTA-AGGGCATTTTGGTCATTTTCA
1 CATCTAGAGGGCATTTTGGTCATTTTCA
* *
61121 CATTTAGGGGGCATTTTGGTCATTTT
1 CATCTAGAGGGCATTTTGGTCATTTT
61147 AAGGTCACTT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
26 22 0.51
27 3 0.07
28 18 0.42
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.43
Consensus pattern (28 bp):
CATCTAGAGGGCATTTTGGTCATTTTCA
Found at i:61353 original size:18 final size:18
Alignment explanation
Indices: 61330--61367 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
61320 TAGCTTTGTG
61330 GTAGTTTAATCCGGTTTA
1 GTAGTTTAATCCGGTTTA
61348 GTAGTTTAATCCGGTTTA
1 GTAGTTTAATCCGGTTTA
61366 GT
1 GT
61368 TCATCGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.11, G:0.24, T:0.45
Consensus pattern (18 bp):
GTAGTTTAATCCGGTTTA
Done.