Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005474.1 Corchorus capsularis cultivar CVL-1 contig05492, 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: 6453
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.31
Found at i:811 original size:328 final size:318
Alignment explanation
Indices: 13--984 Score: 1022
Period size: 328 Copynumber: 3.0 Consensus size: 318
3 AAAAAACCGT
* * * *
13 GATGGTTAGTGCACGATTTTGGCTAAAAACTTACCCGAAAATTTTTTTCTCAATTTTTTGCCACA
1 GATGGTTAGTACACGATTTCGGCTAAAAACTAACCCGAAAATTTTTTACTCAATTTTTTGCCACA
* * * * *
78 ATACACA-AAAAAAAAACCTATTATTCAA-TGACAAAATGATTGACGGGTTCTTCACGTTTCAAA
66 ATACACAGAAAAAAATA--TATTATTCAACT-ACAAAAAGATTGACGGCTT-TTCACGCTTCTAA
* * * *
141 TATCGTTTTTCCATTTTTTTTCGAATTACTTTCTAATTAAATCCAAACAAGATTGAGATGCTCGA
127 TATCGTTTTT-CAATTTTTTCCGAATTAATTTCTAATTAAATGCAAACAAGATTGAGATGCTCGA
** * * *
206 AAAAAAACAATCCTTATATCCAATAAGGCTAAGATTTGGTTCTATGAATATAGATTTTTCAAGGA
191 AAAAAAA-AATCCTTATATCCAATGTGGCTGA-ATTTGGTTCGATGAATATAGATATTTCAAGGA
* * * *
271 GTTTTTGCGCCAAAAATCATGTAAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAGCGAAAAACT
254 GTCTTTGCGCC--AAATCATGCAAAATTAAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACT
*
336 AT
317 AC
* * * **
338 GATGGTTAGTACATGATTTCGGCTAAAAACTGATCAAAAGAATTTTTTACTCAATTTTTTGCCAC
1 GATGGTTAGTACACGATTTCGGCTAAAAACTAACCCGAA-AATTTTTTACTCAATTTTTTGCCAC
* * * * * *
403 AAAACACAG-AAAAAATCTATTATCCAACAACAAAAAGATTGACGGGTTTTTCTCGCTT-TAAAT
65 AATACACAGAAAAAAATATATTATTCAACTACAAAAAGATTGAC-GGCTTTTCACGCTTCT-AAT
* * * *
466 ATCATTTTTCCATTTTTTCCGAATTAATTTCTTATTAAATGCAAACGAGATTGAGATGCTCG-AA
128 ATCGTTTTTCAATTTTTTCCGAATTAATTTCTAATTAAATGCAAACAAGATTGAGATGCTCGAAA
** * *
530 AAAAAAATCCTTATATCCAATGTGGCTGACATTTGAATCGATGAATACAGATATTTGAAGGAGTC
193 AAAAAAATCCTTATATCCAATGTGGCTGA-ATTTGGTTCGATGAATATAGATATTTCAAGGAGTC
* *
595 TTTGCACC-AATCATGCAAAATTAAGTCGGGGCTCAGGAACGCGTTTTTAGCCAAAAACTGACCC
257 TTTGCGCCAAATCATGCAAAATTAAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACT-A--C
* * * *
659 GACGCGTGAGAATTAGTACACGATTTCAGCTAAAAACTAACCCGAAAAGTTTTTCCTAAATTTTT
1 GA----TG-G--TTAGTACACGATTTCGGCTAAAAACTAACCCGAAAATTTTTTACTCAATTTTT
** * * *
724 TGCCACAATACTTAGAAAAAAATATATAATTCAACTCCAAAAAGATTGACGTGCTTTTCACACTT
59 TGCCACAATACACAGAAAAAAATATATTATTCAACTACAAAAAGATTGACG-GCTTTTCACGCTT
* * * *
789 CTAACATCGTTTTTCAATTTTTTTCCGAATTAATTTATAATTAAATAG-AAATAAGATTCAGATG
123 CTAATATCGTTTTTCAA-TTTTTTCCGAATTAATTTCTAATTAAAT-GCAAACAAGATTGAGATG
* * * * * *
853 CTCGTACAAAAAAATCCTTATATCCAATGTGGCTGAGTTTGGTTCGAAGATTATAGATATTTCAG
186 CTCGAAAAAAAAAATCCTTATATCCAATGTGGCTGAATTTGGTTCGATGAATATAGATATTTCAA
* * * * * *
918 GGAGTCTTTGCGCCAAAAATCATACAAGATTAAGCCAGGGCTCCGGAATGCGTTTTTTGCCAAAA
251 GGAGTCTTTGCGCC--AAATCATGCAAAATTAAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAA
983 AC
314 AC
985 CGCGATTTCA
Statistics
Matches: 535, Mismatches: 88, Indels: 41
0.81 0.13 0.06
Matches are distributed among these distances:
318 47 0.09
319 1 0.00
321 58 0.11
322 7 0.01
323 46 0.09
324 40 0.07
325 38 0.07
326 38 0.07
327 29 0.05
328 79 0.15
329 78 0.15
330 31 0.06
332 43 0.08
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (318 bp):
GATGGTTAGTACACGATTTCGGCTAAAAACTAACCCGAAAATTTTTTACTCAATTTTTTGCCACA
ATACACAGAAAAAAATATATTATTCAACTACAAAAAGATTGACGGCTTTTCACGCTTCTAATATC
GTTTTTCAATTTTTTCCGAATTAATTTCTAATTAAATGCAAACAAGATTGAGATGCTCGAAAAAA
AAAATCCTTATATCCAATGTGGCTGAATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTG
CGCCAAATCATGCAAAATTAAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACTAC
Found at i:1609 original size:322 final size:322
Alignment explanation
Indices: 1078--3427 Score: 3170
Period size: 322 Copynumber: 7.4 Consensus size: 322
1068 TCACACTTCT
* * * *
1078 AATATCATTTTTCCA-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCT
1 AATATCGTTTTTCCATTTTTTTTCCGAATTACTTTCTAATTAAATCCAAACAAGATTGAGATGCT
** * * * **
1142 CGTACAAAAA-AAATCCTTATATCCAATGTGGCT-AGATTCGTTTCGAGGAATATAGTTATTTCA
66 CG-A-AAAAACAAATCCTTATATCCAATAAGGCTAAGATTTGGTTCGAAGAATATAAATATTTCA
* * * *
1205 AGGAGTCTTTGTGCCAAAAATCATGCAAAATTGATCCGGGGCTCCGGAACGAGTTTTTCGAAAAA
129 AGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAACGAGTTTTTAG-CAAA
* *
1270 AACCATGATGGTTAGTACACTATTTCGGCTAAAAACTTACCCGAAATTTTTTTTCTCAATTTTTT
193 AACCATGATGGTTAGTACACGATTTCGGCTAAAAACTTACCCGAAAATTTTTTTCTCAATTTTTT
* * * *
1335 GCCATAAGACACAGAAAAAACCTATTATTCAACGATAAAATGATTGACGGGTTGTTCACGTTTCA
258 GCCACAATACACAGAAAAAACCTATTATTCAACGACAAAATGATTGACGGGTTCTTCACGTTTCA
* *
1400 AATATCGTTTTTCCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCT
1 AATATCGTTTTTCCATTTTTTTTCCGAATTACTTTCTAATTAAATCCAAACAAGATTGAGATGCT
* * ** * *
1465 CGAAAAAA-AAGTCCTTACATCCAATATTGCTGAGATTTGGTTCGAAGAATATAGAA-ATTTCAT
66 CGAAAAAACAAATCCTTATATCCAATAAGGCTAAGATTTGGTTCGAAGAATATA-AATATTTCAA
* * ** * * * *
1528 GGAGTCTTTGCGCCAAAAATCTTGCAAAATTAATTCGGGGTTCAGGAACGCGTTTTTAGTCTAAA
130 GGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAACGAGTTTTTAG-CAAAA
* * * * * *
1593 ACCGTGAGGGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTG
194 ACCATGATGGTTAGTACACGATTTCGGCTAAAAACTTACCCGAAAATTTTTTTCTCAATTTTTTG
* ** * ** * * * ** *
1658 CCACAATACTCAGAAAAAATATATAATTCATTGCCAAAAAGATTGATGGGCTT-TTCACACTTCT
259 CCACAATACACAGAAAAAACCTATTATTCAACGACAAAATGATTGACGGG-TTCTTCACGTTTCA
* * ** * *
1722 AATATCATTTTTCCATTTTTTTTCCGAATTAATTTCTAATTAAATAGAAACAAGACTCAGATGCT
1 AATATCGTTTTTCCATTTTTTTTCCGAATTACTTTCTAATTAAATCCAAACAAGATTGAGATGCT
* * ** * * *
1787 CGTACATAA-AAATCCTTATATCCAATGTGGCT-AGATTCGGTTCGAGGAATATAGATATTTCAA
66 CG-AAAAAACAAATCCTTATATCCAATAAGGCTAAGATTTGGTTCGAAGAATATAAATATTTCAA
* * * *
1850 TGAGTCTTTGCGACAAAAATCATGCAAAATTGAGTCGGGGCTCCGGAACGAGTTTCTAGCAAAAA
130 GGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAACGAGTTTTTAGCAAAAA
* *
1915 TCCATAATGGTTAGTACACGATTTCGGCTAAAAACTTA-CCTAAAATTTTTTTCTCAATTTTTTG
195 -CCATGATGGTTAGTACACGATTTCGGCTAAAAACTTACCCGAAAATTTTTTTCTCAATTTTTTG
*
1979 CCACAATATACAGAAAAAACCTATTATTCAACGACAAAATGATTGACGGGTTCTTCACGTTTCA
259 CCACAATACACAGAAAAAACCTATTATTCAACGACAAAATGATTGACGGGTTCTTCACGTTTCA
*
2043 AATATCGTTTTTCCATTTTTTTT-CGAATTACTTTCTAATTAAATCCAAACAAGATTGAGATGTT
1 AATATCGTTTTTCCATTTTTTTTCCGAATTACTTTCTAATTAAATCCAAACAAGATTGAGATGCT
* * *
2107 CGAACAAACAAATCCTCATATCCAATAAGGCTAAGATTTGGTTCGATGAATATAAATATTTCAAG
66 CGAAAAAACAAATCCTTATATCCAATAAGGCTAAGATTTGGTTCGAAGAATATAAATATTTCAAG
*
2172 GAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTCCGGAACGAGTTTTTAGCAAAAAA
131 GAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAACGAGTTTTTAGC-AAAAA
*
2237 CC----------GTACACGATTTCGGCTAAAAACTTACCCGAAAGTTTTTTTCTCAATTTTTTGC
195 CCATGATGGTTAGTACACGATTTCGGCTAAAAACTTACCCGAAAATTTTTTTCTCAATTTTTTGC
*
2292 CACAATACACAGAAAAAACCTATTATTCAACGACAAAATGATTGACGGGTTGTTCACGTTTCA
260 CACAATACACAGAAAAAACCTATTATTCAACGACAAAATGATTGACGGGTTCTTCACGTTTCA
* *
2355 AATATCGTTTTTCCA-TTTTTTTGCGAATTACTTTATAATTAAATCCAAACAAGATTGAGATGCT
1 AATATCGTTTTTCCATTTTTTTTCCGAATTACTTTCTAATTAAATCCAAACAAGATTGAGATGCT
* * *
2419 TGAAAAACACAAATCCTTATATCCAATAAGGCTAAGATTTGGTTTGATGAATATAAATATTTCAA
66 CGAAAAA-ACAAATCCTTATATCCAATAAGGCTAAGATTTGGTTCGAAGAATATAAATATTTCAA
2484 GGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAACGAGTTTTTAGC----A
130 GGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAACGAGTTTTTAGCAAAAA
* * *
2545 -C----------GTACATGATTTCAGCTAAAAACTTA-CCGAAATTTTTTTTCT-AATTTTTTGC
195 CCATGATGGTTAGTACACGATTTCGGCTAAAAACTTACCCGAAAATTTTTTTCTCAATTTTTTGC
* * *
2597 CACAATACACAGAAAAAACCTATTATTCGATGACAAAATTATTGACGGGTTCTTCACGTTTCA
260 CACAATACACAGAAAAAACCTATTATTCAACGACAAAATGATTGACGGGTTCTTCACGTTTCA
*
2660 AATATCGTTTTTCC-TTTTTTTTCCAAATTACTTTCTAATTAAATCCAAACAAGATTGAGATGCT
1 AATATCGTTTTTCCATTTTTTTTCCGAATTACTTTCTAATTAAATCCAAACAAGATTGAGATGCT
*
2724 CGAAAAAACAAATCCTTATATCCAATAAGGCTAAGATTTGTTTCGATA-AATATAAATATTTCAA
66 CGAAAAAACAAATCCTTATATCCAATAAGGCTAAGATTTGGTTCGA-AGAATATAAATATTTCAA
* **
2788 GGAGTCTTTGCGCAAAAAATCATGCAAAATTGAGCCGGGGCTTAGGAACGAGTTTTTAGCAAAAA
130 GGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAACGAGTTTTTAGCAAAAA
* *
2853 GCTATGATGGTTAGTACACGATTTCGGCTAAAAACTTACTCGAAAATTTTTTTCTCAATTTTTTG
195 -CCATGATGGTTAGTACACGATTTCGGCTAAAAACTTACCCGAAAATTTTTTTCTCAATTTTTTG
* *
2918 CCACAATACATAGAAAAAACCTATTATTCAACGACAAAATGATTGACGGGTTCTTCACGTTGCA
259 CCACAATACACAGAAAAAACCTATTATTCAACGACAAAATGATTGACGGGTTCTTCACGTTTCA
* * *
2982 AATATCGTTTTTCTATTGTTTTT-CGAATTACTTTATAATTAAATCCAAACAAGATTGAGATGCT
1 AATATCGTTTTTCCATTTTTTTTCCGAATTACTTTCTAATTAAATCCAAACAAGATTGAGATGCT
* * *
3046 TGAAAAAACACAAATCCTTATATCCAATAAGGCTAAGATTCGGTTCGATGAATATAAATATTTCA
66 CG-AAAAA-ACAAATCCTTATATCCAATAAGGCTAAGATTTGGTTCGAAGAATATAAATATTTCA
* * * * *
3111 AGGAGTTTTTACGCCAAAAATCATGCAAAATTGAGACAGGGCTCCGGAACGAGTTTTTAGGAAAA
129 AGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAACGAGTTTTTA-GCAAA
* *
3176 AACCGTGATGGTTAGTACACGA-TTCGGCTAAAAACTTACCCGAAAATTTTTCTCTCAATTTTTT
193 AACCATGATGGTTAGTACACGATTTCGGCTAAAAACTTACCCGAAAATTTTTTTCTCAATTTTTT
3240 GCCACAATACACAGAAAAAACCTATTATTCAACGACAAAATGATTGACGGGTTCTTCACGTTTCA
258 GCCACAATACACAGAAAAAACCTATTATTCAACGACAAAATGATTGACGGGTTCTTCACGTTTCA
* *
3305 AATATCGTTTTTCCA-TTTTTTT-CAAATTACTTTCTAATTAAATCCAAACAAGATTTAGATGCT
1 AATATCGTTTTTCCATTTTTTTTCCGAATTACTTTCTAATTAAATCCAAACAAGATTGAGATGCT
* *
3368 CGAAAAAACAAATCCTTATATCCAATAAGACTAAGATTTGGTTCGATA-AATATAGATATT
66 CGAAAAAACAAATCCTTATATCCAATAAGGCTAAGATTTGGTTCGA-AGAATATAAATATT
3428 GAATCCATAA
Statistics
Matches: 1808, Mismatches: 180, Indels: 82
0.87 0.09 0.04
Matches are distributed among these distances:
304 110 0.06
305 135 0.07
306 15 0.01
307 24 0.01
308 2 0.00
311 32 0.02
312 145 0.08
313 114 0.06
319 3 0.00
320 130 0.07
321 229 0.13
322 537 0.30
323 204 0.11
324 122 0.07
325 6 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (322 bp):
AATATCGTTTTTCCATTTTTTTTCCGAATTACTTTCTAATTAAATCCAAACAAGATTGAGATGCT
CGAAAAAACAAATCCTTATATCCAATAAGGCTAAGATTTGGTTCGAAGAATATAAATATTTCAAG
GAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAACGAGTTTTTAGCAAAAAC
CATGATGGTTAGTACACGATTTCGGCTAAAAACTTACCCGAAAATTTTTTTCTCAATTTTTTGCC
ACAATACACAGAAAAAACCTATTATTCAACGACAAAATGATTGACGGGTTCTTCACGTTTCA
Found at i:4565 original size:44 final size:44
Alignment explanation
Indices: 4502--4591 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
4492 TATTACATTG
4502 GATCCGACTAATTCAGAGTCTGAGTCGTGTTGAATCATCGTGTT
1 GATCCGACTAATTCAGAGTCTGAGTCGTGTTGAATCATCGTGTT
4546 GATCCGACTAATTCAGAGTCTGAGTCGTGTTGAATCATCGTGTT
1 GATCCGACTAATTCAGAGTCTGAGTCGTGTTGAATCATCGTGTT
4590 GA
1 GA
4592 ACCATTATGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (44 bp):
GATCCGACTAATTCAGAGTCTGAGTCGTGTTGAATCATCGTGTT
Found at i:4643 original size:39 final size:39
Alignment explanation
Indices: 4600--4678 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
4590 GAACCATTAT
4600 GTGGAGTCAAGTCAAGCCGTATTGGATCAATATGTGAAA
1 GTGGAGTCAAGTCAAGCCGTATTGGATCAATATGTGAAA
*
4639 GTGGAGTCAAGTCAAGTCGTATTGGATCAATATGTGAAA
1 GTGGAGTCAAGTCAAGCCGTATTGGATCAATATGTGAAA
4678 G
1 G
4679 CTTTCACAGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (39 bp):
GTGGAGTCAAGTCAAGCCGTATTGGATCAATATGTGAAA
Done.