Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013881.1 Corchorus capsularis cultivar CVL-1 contig13902, 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: 18725
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2044 original size:33 final size:33
Alignment explanation
Indices: 1974--2086 Score: 131
Period size: 33 Copynumber: 3.4 Consensus size: 33
1964 CGGAGACAAG
* *
1974 ACCGGCCACGCGATATGGACATGTCCGGCCATC-
1 ACCGGCCACGCGACATGGACATGCCCGGCCA-CA
* *
2007 ACCGGCCACGCGACATGGACATGGCCGGCTACA
1 ACCGGCCACGCGACATGGACATGCCCGGCCACA
** *
2040 ACCGGCCAAACGAC-TCGGCCATGCCCGGCCACA
1 ACCGGCCACGCGACAT-GGACATGCCCGGCCACA
2073 ACCGGCCACGCGAC
1 ACCGGCCACGCGAC
2087 CCTTTGTCTA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 2 0.03
33 66 0.97
ACGTcount: A:0.23, C:0.41, G:0.27, T:0.09
Consensus pattern (33 bp):
ACCGGCCACGCGACATGGACATGCCCGGCCACA
Found at i:3725 original size:33 final size:33
Alignment explanation
Indices: 3683--3748 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
3673 ACGTAAAGGG
* *
3683 CATGCAATTTCAAAAGGTGGGAGCACCATTAAT
1 CATGCAATTTAAAAAGGTGGGAACACCATTAAT
*
3716 CATGCAATTTAAAAAGGTGGGAACACTATTAAT
1 CATGCAATTTAAAAAGGTGGGAACACCATTAAT
3749 TGAAGTCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (33 bp):
CATGCAATTTAAAAAGGTGGGAACACCATTAAT
Found at i:7266 original size:92 final size:92
Alignment explanation
Indices: 7109--7294 Score: 363
Period size: 92 Copynumber: 2.0 Consensus size: 92
7099 TTTATTACAT
7109 TTGTATTAATTTAGTTTGGAAAAATCAAAAGACATTCATCCCCTTTTCCTATATAAAATAAATTA
1 TTGTATTAATTTAGTTTGGAAAAATCAAAAGACATTCATCCCCTTTTCCTATATAAAATAAATTA
7174 ATCAAATAATTATAAATTAATTATAAA
66 ATCAAATAATTATAAATTAATTATAAA
*
7201 TTGTATTCATTTAGTTTGGAAAAATCAAAAGACATTCATCCCCTTTTCCTATATAAAATAAATTA
1 TTGTATTAATTTAGTTTGGAAAAATCAAAAGACATTCATCCCCTTTTCCTATATAAAATAAATTA
7266 ATCAAATAATTATAAATTAATTATAAA
66 ATCAAATAATTATAAATTAATTATAAA
7293 TT
1 TT
7295 TTTTATGAAT
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 93 1.00
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (92 bp):
TTGTATTAATTTAGTTTGGAAAAATCAAAAGACATTCATCCCCTTTTCCTATATAAAATAAATTA
ATCAAATAATTATAAATTAATTATAAA
Found at i:14951 original size:369 final size:369
Alignment explanation
Indices: 14181--15106 Score: 1161
Period size: 369 Copynumber: 2.5 Consensus size: 369
14171 TCATGAATTT
* * *
14181 ATTCGAAAAAT-TCGAG-ATTTTCTTTAAATATGAGATTTTCTTTAGCAAAACCAACGACGCTCA
1 ATTCGAAAAATCT-G-GTATTTTCTTTAAATATGAGATTTTCTTTAACGAAACCAACAACGCTCA
* *
14244 TTGGTGTACATATACCGTCAAACTAATATGTGTGTGGGTTATCTCTTTTATCACTTTAAGTGAGT
64 TTGGTGTACATATACCGTCAAACTAATATGTGTGTGGATTA--TC---T-T---TTTAAGTGGGT
** * * * * *
14309 ACACTGATGATCTTTAAAGTTACCGAGTTAGGTCAATTGCTAGAGTGTTTTACTGATTCATTTAA
120 ACACCAATGACCTTTAAAGTTACCAAGCTAGGCCAATTGCTAGAGTGCTTTACTGATTCATTTAA
*
14374 AATTTGAAAAATATGATATTTTCTTTTAAACCTGAGATTTTCTTTAACGAAACCGACAACGCTCA
185 AATTTGAAAAATATGATATTTTCTTTTAAACCTGAGATTTTCTTGAACGAAACCGACAACGCTCA
* * * * * *
14439 TTAGTGTACATATACCACCAAACTAATGTGTGTGGATTTTCTTTTTAAGTTGGTATATCAATGAC
250 TTAGTGTACATAAACCACCAAACTAATGTATGTGGATTATCTTTTTAAGTGGGTACACCAATGAC
* *
14504 CTTTAAAGTTACCAAGCTTGACCAATTACTGGAGTGCTTTACTGATTCATTCAGA
315 CTGTAAAGTTACCAAGCTTGACCAATTACTGGAGTGCTTTACTAATTCATTCAGA
* * *
14559 ATTTGAAAAATCTGGTATTTTCTTTAAATATGAGATTTTCTCTAACGAAACCGACAACGCTCATT
1 ATTCGAAAAATCTGGTATTTTCTTTAAATATGAGATTTTCTTTAACGAAACCAACAACGCTCATT
* * *
14624 GGTATGCATATACTGTCAAACTAATATGTGTGTGGATTATCTTTTTAAGTGGGTACACCAATGAC
66 GGTGTACATATACCGTCAAACTAATATGTGTGTGGATTATCTTTTTAAGTGGGTACACCAATGAC
* * *
14689 CTTTAAAGTTACCAAGCT-GGACCAATTGCCTGGTGTGCTTTACTGATTCATTTAGAATTTGAAA
131 CTTTAAAGTTACCAAGCTAGG-CCAATTG-CTAGAGTGCTTTACTGATTCATTTAAAATTTGAAA
* *
14753 AATCTGATATTTTC-TTTAAACCTGAGATTTTCTTGAACGAAACCGACAACGGTCATT-GTTGTA
194 AATATGATATTTTCTTTTAAACCTGAGATTTTCTTGAACGAAACCGACAACGCTCATTAG-TGTA
** *
14816 CATAAACCATTAAACTAATGTATGTGGGTTAT-TTTTTAAGTGGGTACACCAATGACCTGTAAAG
258 CATAAACCACCAAACTAATGTATGTGGATTATCTTTTTAAGTGGGTACACCAATGACCTGTAAAG
* * ** *
14880 TTACCAAG-TTGGGCTAATTGTTGGAGTGCTTTACTAATTCATTTAGA
323 TTACCAAGCTT-GACCAATTACTGGAGTGCTTTACTAATTCATTCAGA
** * **
14927 ATTCGAAAAATCTGGTATTTTTCTTTAAACCTGAGATTTTCTTTAACGAAAACAACAATACTCAT
1 ATTCGAAAAATCTGGTA-TTTTCTTTAAATATGAGATTTTCTTTAACGAAACCAACAACGCTCAT
* *
14992 TAGTGTACATATACCGTCAAACTAATATGTGTGTGGATTATCTTTCTAAGTGGGTACACCAATGA
65 TGGTGTACATATACCGTCAAACTAATATGTGTGTGGATTATCTTTTTAAGTGGGTACACCAATGA
** * * *
15057 CC-TTAAAAATA-CACAGTTAGTCCAATTG-TTGAGTGCTTTACTGATTCATT
130 CCTTTAAAGTTACCA-AGCTAGGCCAATTGCTAGAGTGCTTTACTGATTCATT
15107 CATAAAGATA
Statistics
Matches: 480, Mismatches: 59, Indels: 30
0.84 0.10 0.05
Matches are distributed among these distances:
366 20 0.04
367 4 0.01
368 102 0.21
369 214 0.45
370 44 0.09
372 1 0.00
373 1 0.00
376 2 0.00
377 1 0.00
378 90 0.19
379 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (369 bp):
ATTCGAAAAATCTGGTATTTTCTTTAAATATGAGATTTTCTTTAACGAAACCAACAACGCTCATT
GGTGTACATATACCGTCAAACTAATATGTGTGTGGATTATCTTTTTAAGTGGGTACACCAATGAC
CTTTAAAGTTACCAAGCTAGGCCAATTGCTAGAGTGCTTTACTGATTCATTTAAAATTTGAAAAA
TATGATATTTTCTTTTAAACCTGAGATTTTCTTGAACGAAACCGACAACGCTCATTAGTGTACAT
AAACCACCAAACTAATGTATGTGGATTATCTTTTTAAGTGGGTACACCAATGACCTGTAAAGTTA
CCAAGCTTGACCAATTACTGGAGTGCTTTACTAATTCATTCAGA
Found at i:14953 original size:183 final size:185
Alignment explanation
Indices: 14197--15106 Score: 1048
Period size: 183 Copynumber: 4.9 Consensus size: 185
14187 AAAATTCGAG
** * * * * * *
14197 ATTTTCTTTAAATATGAGATTTTCTTTAGCAAAACCAACGACGCTCATTGGTGTACATATACCGT
1 ATTTTCTTTAAACCTGAGATTTTCTTTAACGAAACCGACAACGCTCATTAGTGTACATATACCAT
* * ** *
14262 CAAACTAATATGTGTGTGGGTTATCTCTTTTATCACTTTAAGTGAGTACACTGATGATCTTTAAA
66 CAAACTAATATGTGTGTGGATTA--TC---T-T---TTTAAGTGGGTACACCAATGACCTTTAAA
* ** * * * *
14327 GTTACCGAGTTAGGTCAATTGCTAGAGTGTTTTACTGATTCATTTAAAATTTGAAAAATATGAT
122 GTTACCAAGTTAGACCAATTGCTGGAGTGCTTTACTGATTCATTTAGAATTTGAAAAATCTGAT
14391 ATTTTCTTTTAAACCTGAGATTTTCTTTAACGAAACCGACAACGCTCATTAGTGTACATATACCA
1 ATTTTC-TTTAAACCTGAGATTTTCTTTAACGAAACCGACAACGCTCATTAGTGTACATATACCA
* * * * *
14456 CCAAACT-A-ATGTGTGTGGATTTTCTTTTTAAGTTGGTATATCAATGACCTTTAAAGTTACCAA
65 TCAAACTAATATGTGTGTGGATTATCTTTTTAAGTGGGTACACCAATGACCTTTAAAGTTACCAA
* * *
14519 GCTT-GACCAATTACTGGAGTGCTTTACTGATTCATTCAGAATTTGAAAAATCTGGT
130 G-TTAGACCAATTGCTGGAGTGCTTTACTGATTCATTTAGAATTTGAAAAATCTGAT
** * * * * **
14575 ATTTTCTTTAAATATGAGATTTTCTCTAACGAAACCGACAACGCTCATTGGTATGCATATACTGT
1 ATTTTCTTTAAACCTGAGATTTTCTTTAACGAAACCGACAACGCTCATTAGTGTACATATACCAT
14640 CAAACTAATATGTGTGTGGATTATCTTTTTAAGTGGGTACACCAATGACCTTTAAAGTTACCAAG
66 CAAACTAATATGTGTGTGGATTATCTTTTTAAGTGGGTACACCAATGACCTTTAAAGTTACCAAG
* * *
14705 CTGGACCAATTGCCTGGTGTGCTTTACTGATTCATTTAGAATTTGAAAAATCTGAT
131 TTAGACCAATTG-CTGGAGTGCTTTACTGATTCATTTAGAATTTGAAAAATCTGAT
* * *
14761 ATTTTCTTTAAACCTGAGATTTTCTTGAACGAAACCGACAACGGTCATT-GTTGTACATAAACCA
1 ATTTTCTTTAAACCTGAGATTTTCTTTAACGAAACCGACAACGCTCATTAG-TGTACATATACCA
* * * *
14825 TTAAACT-A-ATGTATGTGGGTTAT-TTTTTAAGTGGGTACACCAATGACCTGTAAAGTTACCAA
65 TCAAACTAATATGTGTGTGGATTATCTTTTTAAGTGGGTACACCAATGACCTTTAAAGTTACCAA
* * * * * * *
14887 GTTGGGCTAATTGTTGGAGTGCTTTACTAATTCATTTAGAATTCGAAAAATCTGGT
130 GTTAGACCAATTGCTGGAGTGCTTTACTGATTCATTTAGAATTTGAAAAATCTGAT
* * ** *
14943 ATTTTTCTTTAAACCTGAGATTTTCTTTAACGAAAACAACAATACTCATTAGTGTACATATACCG
1 A-TTTTCTTTAAACCTGAGATTTTCTTTAACGAAACCGACAACGCTCATTAGTGTACATATACCA
* **
15008 TCAAACTAATATGTGTGTGGATTATCTTTCTAAGTGGGTACACCAATGACC-TTAAAAATA-CAC
65 TCAAACTAATATGTGTGTGGATTATCTTTTTAAGTGGGTACACCAATGACCTTTAAAGTTACCA-
* *
15071 AGTTAGTCCAATTG-TTGAGTGCTTTACTGATTCATT
129 AGTTAGACCAATTGCTGGAGTGCTTTACTGATTCATT
15107 CATAAAGATA
Statistics
Matches: 615, Mismatches: 88, Indels: 36
0.83 0.12 0.05
Matches are distributed among these distances:
182 39 0.06
183 163 0.27
184 118 0.19
185 94 0.15
186 122 0.20
187 1 0.00
188 1 0.00
191 2 0.00
193 12 0.02
194 7 0.01
195 56 0.09
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (185 bp):
ATTTTCTTTAAACCTGAGATTTTCTTTAACGAAACCGACAACGCTCATTAGTGTACATATACCAT
CAAACTAATATGTGTGTGGATTATCTTTTTAAGTGGGTACACCAATGACCTTTAAAGTTACCAAG
TTAGACCAATTGCTGGAGTGCTTTACTGATTCATTTAGAATTTGAAAAATCTGAT
Found at i:15733 original size:108 final size:107
Alignment explanation
Indices: 15541--15754 Score: 329
Period size: 108 Copynumber: 2.0 Consensus size: 107
15531 CATTTGATTA
* * * * *
15541 TACAACTTTTGTGAAAGGAAATTTTAATGCGTACAACGCACAGTCCCCTTGATTAATTAAACCGA
1 TACAACTTTTGTGAAAGAAAACTATAATGCGCACAACACACAGTCCCCTTGATTAATTAAACCGA
*
15606 AATATTATTATTTCGTAGTATATAGTACAGTCCTACTACGAAG
66 AATATTATTATTTCATAGTATATAGTA-AGTCCTACTACGAAG
* * *
15649 TACAACTTTTGTGAAAGAAAACTATAATGCGCACAACACACAGTTCCCTTGATTAATTAGACTGA
1 TACAACTTTTGTGAAAGAAAACTATAATGCGCACAACACACAGTCCCCTTGATTAATTAAACCGA
*
15714 AATATTATTATTTCATAGTATATAGTAAGTTCTACTACGAA
66 AATATTATTATTTCATAGTATATAGTAAGTCCTACTACGAA
15755 TGCTAGTGAT
Statistics
Matches: 96, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
107 13 0.14
108 83 0.86
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.33
Consensus pattern (107 bp):
TACAACTTTTGTGAAAGAAAACTATAATGCGCACAACACACAGTCCCCTTGATTAATTAAACCGA
AATATTATTATTTCATAGTATATAGTAAGTCCTACTACGAAG
Found at i:16130 original size:129 final size:130
Alignment explanation
Indices: 15806--16198 Score: 659
Period size: 128 Copynumber: 3.0 Consensus size: 130
15796 ATATTTCGTA
*
15806 GATTTAATTAAATGCTATTAGTCTATTAGAAACTTTGGTTCAAGAAGTTGAAATCTATAAAAACT
1 GATTTAATTAAATGCTATTAGTCTATTAGAAAC----GTT--TGAAGTTGAAATCTATAAAAACT
**
15871 AAATCAGATATATATATTTCGTAGATTTAATTAAATGCAAATTAACAAAATTAAAAAATAATTAT
60 AAATTTGATATATATATTTCGTAGATTTAATTAAATGCAAATTAACAAAATTAAAAAATAATTAT
15936 ATAATG
125 ATAATG
15942 GA--TAATTAAATGCTATTAGTCTATTAGAAACGTTTGAAGTTGAAATCTATAAAAACTAAATTT
1 GATTTAATTAAATGCTATTAGTCTATTAGAAACGTTTGAAGTTGAAATCTATAAAAACTAAATTT
16005 GATATATATATTTCGTAGATTTAATTAAATGCAAATTAACAAAATT-AAAAATAATTATATAATG
66 GATATATATATTTCGTAGATTTAATTAAATGCAAATTAACAAAATTAAAAAATAATTATATAATG
16069 GATTTAATTAAATGCTATTAGTCTATTAGAAACGTTTGAAGTTGAAATCTATAAAAACTAAATTT
1 GATTTAATTAAATGCTATTAGTCTATTAGAAACGTTTGAAGTTGAAATCTATAAAAACTAAATTT
* *
16134 GAGATATATA-TTCGTAGATTTAATTAAATGTAAATTAACAAAATTAAAAAATAATTATATAATG
66 GATATATATATTTCGTAGATTTAATTAAATGCAAATTAACAAAATTAAAAAATAATTATATAATG
16198 G
1 G
16199 CAATTTAGAA
Statistics
Matches: 249, Mismatches: 5, Indels: 13
0.93 0.02 0.05
Matches are distributed among these distances:
127 20 0.08
128 106 0.43
129 89 0.36
130 3 0.01
134 29 0.12
136 2 0.01
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (130 bp):
GATTTAATTAAATGCTATTAGTCTATTAGAAACGTTTGAAGTTGAAATCTATAAAAACTAAATTT
GATATATATATTTCGTAGATTTAATTAAATGCAAATTAACAAAATTAAAAAATAATTATATAATG
Found at i:16261 original size:23 final size:23
Alignment explanation
Indices: 16230--16280 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
16220 AAATAAGGAT
* * *
16230 ATAATAGGCTTTTGAAAAGTTAA
1 ATAAGAGGCGTTTCAAAAGTTAA
16253 ATAAGAGGCGTTTCAAAAGTTAA
1 ATAAGAGGCGTTTCAAAAGTTAA
16276 ATAAG
1 ATAAG
16281 GGTACAATAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.29
Consensus pattern (23 bp):
ATAAGAGGCGTTTCAAAAGTTAA
Found at i:16296 original size:31 final size:31
Alignment explanation
Indices: 16258--16321 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
16248 GTTAAATAAG
16258 AGGCGTTTCAAAAGTTAAATAAGGGTACAAT
1 AGGCGTTTCAAAAGTTAAATAAGGGTACAAT
*
16289 AGGCGTTTTAAAAGTTAAATAAGGGTACAAT
1 AGGCGTTTCAAAAGTTAAATAAGGGTACAAT
16320 AG
1 AG
16322 ACATTTATAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (31 bp):
AGGCGTTTCAAAAGTTAAATAAGGGTACAAT
Done.