Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009842.1 Corchorus capsularis cultivar CVL-1 contig09863, 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: 3265
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Found at i:1721 original size:324 final size:321
Alignment explanation
Indices: 1096--2958 Score: 2096
Period size: 324 Copynumber: 5.8 Consensus size: 321
1086 CGAAACGCGT
*** * * *
1096 TTTTCGACTAAAAAGTGACCC-ATTTTGTTTTTTCTGAATTTTTTTGCCATAATACACGGAAAAA
1 TTTT-GACTAAAAAGTGACCCGAAAAT-TTTTTTCTGAA-ATTTTTGCCACAATACTCGGAAAAA
* * * * * * **
1160 ATGTATAATTCAA-TGC-GAAAAAACTGAAGAGTTTTTCACGCATGC-AATATCGTTAATCCATT
63 ATATATAATTCAACT-CAAAAAAAATTGAAGGGTTTATCACGC-TTCTAATATCGTTTTTCCATT
* * * * *
1222 TTTTCCCGAATTTATTTCAAATTAAATGAAAACAAAATTCAGATGCTTGTAAGAACAAATCCTTA
126 TTTTTCCGAATTTATTTC-TATTAAAT-AAAACAAAAATCAGATGCTCGTAAAAACAAATCCTTA
* * * *
1287 GATCCATTGTGACTGAGATTTTGTTCTATGAATATAGACATTTGAAGGAGGGTTTCTGCCAAAAA
189 AATCCATTGTGGCTGAGATTTGGTTCTATGAATATAGATATTTGAAGGAGGGTTTCTGCCAAAAA
* * * * * *
1352 TCATGCAAGACTGA-ACTGGAACCCCGAAACGCGTTTTTTGCCCAAAAACCGTGATGGTTAGTAC
254 TCATGCAAAACTGAGTC-GGATCCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATTGTTAGTAT
1416 ACGA
318 ACGA
*
1420 TTTTGACTAAAAAGTGACCCGAAAATTTTTTTCTGAAATTTTTGCCACAATACCCGGAAAAAATA
1 TTTTGACTAAAAAGTGACCCGAAAATTTTTTTCTGAAATTTTTGCCACAATACTCGGAAAAAATA
*
1485 TATAATTCAACTCAAAAAAAAATTGAAGGGTTTATCACGCTTCTAATATCGTTTTTTTCATTTTT
66 TATAATTCAACTC-AAAAAAAATTGAAGGGTTTATCACGCTTCTAATATCG-TTTTTCCA-TTTT
* * * *
1550 TTTCCGAATTTATTTCTATTCAATAAAAAAAAAATCAGATGCTTGTAACAACAAATCCTTAAATC
128 TTTCCGAATTTATTTCTATTAAATAAAACAAAAATCAGATGCTCGTAAAAACAAATCCTTAAATC
*
1615 CATTGTGGCTGAGATTTGGTTCTATGAATATAGATATTTGAAGGAGGGTTTTTGCCAAAAATCAT
193 CATTGTGGCTGAGATTTGGTTCTATGAATATAGATATTTGAAGGAGGGTTTCTGCCAAAAATCAT
*
1680 GCAAAACTGAGTCAGATCCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATTGTTAGTATACGA
258 GCAAAACTGAGTCGGATCCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATTGTTAGTATACGA
* * * * *
1744 -TTTCAGCTAAAAAGTGACCCGAAAATTTTTTTTTTCAAATTTATGCCACAATAATCGGAAAAAA
1 TTTTGA-CTAAAAAGTGACCCGAAAA-TTTTTTTCTGAAATTTTTGCCACAATACTCGGAAAAAA
* * * * *
1808 TAAATCTTATTTAACGCAAAAAAGAAATTGAAGGGTTTTTCACGCTT-TCAATATCGTTTTTCCA
64 T--ATATAATTCAACTC-AAAAA-AAATTGAAGGGTTTATCACGCTTCT-AATATCGTTTTTCCA
* * *
1872 TTTTTTTCCGAATTTATTTCTAATTAAATCAAAACAAAATTAATATGCTCGTAAAAACAAATCCT
124 TTTTTTTCCGAATTTATTTCT-ATTAAAT-AAAACAAAAATCAGATGCTCGTAAAAACAAATCCT
* * * * * *
1937 TAAATCCATTGTGGCTGAGATTTAGTACGATGAATACAGATATTTTAAGGAGGCTTTCTGCCAAA
187 TAAATCCATTGTGGCTGAGATTTGGTTCTATGAATATAGATATTTGAAGGAGGGTTTCTGCCAAA
* * * * *
2002 AATCATGCACAACAGAGCCGGTTCCCCGAAACGCGTTTTTTGCCCAAAAA-C-TG--TG--ACGT
252 AATCATGCAAAACTGAGTCGGATCCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATTGTTA-GT
*
2061 ACACGA
316 ATACGA
* *
2067 TTTTG-CTTAAAAAGTGACCCGAAAA-TTTTTTCTGAAA-TTTTGCCACAATACTCAGAATAAAT
1 TTTTGAC-TAAAAAGTGACCCGAAAATTTTTTTCTGAAATTTTTGCCACAATACTCGGAAAAAAT
*
2129 ATATAATTCAACTCAAAAAAAATTGAAGGGTTTATCACGCATCTAATATCGTTTTTCCATTTTTT
65 ATATAATTCAACTCAAAAAAAATTGAAGGGTTTATCACGCTTCTAATATCGTTTTTCCATTTTTT
* * * *
2194 TCTGAATTTATTT-TAATCAAAT--AATAAAAA-CAGATGCTCGTAAAAACAAAACCTTAAATCC
130 TCCGAATTTATTTCT-ATTAAATAAAACAAAAATCAGATGCTCGTAAAAACAAATCCTTAAATCC
* *
2255 ATTGTGGCTGAGATTTGGTTCTATGAATATAGATATTTGAAGGAGTGTTTCTGCCAAAAATTATG
194 ATTGTGGCTGAGATTTGGTTCTATGAATATAGATATTTGAAGGAGGGTTTCTGCCAAAAATCATG
* * *
2320 CAAAACTGAGTCGGGTCCCCGAAACGCGTTTTTAGCCCAAAAATCGTGATTATTAGTATACGA
259 CAAAACTGAGTCGGATCCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATTGTTAGTATACGA
* * * * *
2383 TTTTG-GTAAAAAGTGACTCGAAATTTTTTTTTCTGAAATCTTTGCCACAATACTTGG-------
1 TTTTGACTAAAAAGTGACCCGAAA-ATTTTTTTCTGAAATTTTTGCCACAATACTCGGAAAAAAT
2440 A-A-AA---AA-T--AAAAAAATTGAAGGGTTTATCACGCTTCTAATATCGTTTTTCCATTTTTT
65 ATATAATTCAACTCAAAAAAAATTGAAGGGTTTATCACGCTTCTAATATCGTTTTTCCA-TTTTT
* * * * *
2497 TTCCCGAATTTATTTCTTATCAAATAATAGAAAAATCAGATACTAGTAAAAACAAATCCTTAAAT
129 TT-CCGAATTTATTTC-TATTAAATAAAACAAAAATCAGATGCTCGTAAAAACAAATCCTTAAAT
*
2562 CCATTGTGGCTGAGATTTGGTTCTATGAATATAGATATTTGAAGGAGGGTTTTTGCCAAAAATCA
192 CCATTGTGGCTGAGATTTGGTTCTATGAATATAGATATTTGAAGGAGGGTTTCTGCCAAAAATCA
** *
2627 TGCAAAACTGAGTCGGATCAACGAAACGCGTTTTTAGCCCAAAAACCGTGATTGTTAGTATACTA
257 TGCAAAACTGAGTCGGATCCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATTGTTAGTATACGA
* * * ** * * * *
2692 -TTTCAGCAAAAAAGTGACCTGGAATTTTTCTTTTCTCATATTTATT-CCACAATAATCAGAAAA
1 TTTTGA-CTAAAAAGTGACC-CGAAAATTT-TTTTCTGAAATTT-TTGCCACAATACTCGGAAAA
* * * * * *
2755 AA-ATCTTATTCAGCGCAAAAAATAAATTGAAGGGTTTTTCACGCTTAC-AATATCCTTTTTCCA
62 AATATATAATTCAACTC-AAAAA-AAATTGAAGGGTTTATCACGCTT-CTAATATCGTTTTTCCA
* * * * * *
2818 TTTTTTTGCGAATTTATTTCTAATTAAACCAAAATAAAATTCATATGCTCGTAAAAATAAATCCT
124 TTTTTTTCCGAATTTATTTCT-ATTAAA-TAAAACAAAAATCAGATGCTCGTAAAAACAAATCCT
* * **
2883 TAAATCCATTGTGGCTGAGATTTGGTTCTATGAATATAGACATTTGATGGAGGGTTTCTGAAAAA
187 TAAATCCATTGTGGCTGAGATTTGGTTCTATGAATATAGATATTTGAAGGAGGGTTTCTG-CCAA
2948 AAATCATGCAA
251 AAATCATGCAA
2959 TATCGTTTTT
Statistics
Matches: 1322, Mismatches: 156, Indels: 119
0.83 0.10 0.07
Matches are distributed among these distances:
303 43 0.03
304 7 0.01
305 12 0.01
306 9 0.01
307 1 0.00
308 9 0.01
309 149 0.11
310 15 0.01
311 147 0.11
312 9 0.01
313 2 0.00
315 25 0.02
316 66 0.05
317 20 0.02
318 25 0.02
319 1 0.00
320 21 0.02
321 10 0.01
322 38 0.03
323 59 0.04
324 212 0.16
325 63 0.05
326 138 0.10
327 80 0.06
328 161 0.12
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (321 bp):
TTTTGACTAAAAAGTGACCCGAAAATTTTTTTCTGAAATTTTTGCCACAATACTCGGAAAAAATA
TATAATTCAACTCAAAAAAAATTGAAGGGTTTATCACGCTTCTAATATCGTTTTTCCATTTTTTT
CCGAATTTATTTCTATTAAATAAAACAAAAATCAGATGCTCGTAAAAACAAATCCTTAAATCCAT
TGTGGCTGAGATTTGGTTCTATGAATATAGATATTTGAAGGAGGGTTTCTGCCAAAAATCATGCA
AAACTGAGTCGGATCCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATTGTTAGTATACGA
Found at i:2676 original size:948 final size:956
Alignment explanation
Indices: 1123--2957 Score: 2621
Period size: 948 Copynumber: 1.9 Consensus size: 956
1113 ACCCATTTTG
* * * * *
1123 TTTTTTCTGAATTTTTTTGCCATAATACACGGAAAAAATGTATAATTCAATGCGAAAAAACTGAA
1 TTTTTTCTGAA-TATTTTGCCACAATACACAGAAAAAATATATAATTCAATGCAAAAAAACTGAA
* *
1188 GAGTTTTTCACGCATGCAATATCGTTAATCCATTTTTTCCCGAATTTATTTCAAATTAAATGAAA
65 GAGTTTATCACGCATGCAATATCGTTAATCCATTTTTTCCCGAATTTATTTCAAATCAAATGAAA
* * * * *
1253 ACAAAATTCAGATGCTTGTAAGAACAAATCCTTAGATCCATTGTGACTGAGATTTTGTTCTATGA
130 ACAAAA-TCAGATGCTCGTAAAAACAAAACCTTAAATCCATTGTGACTGAGATTTGGTTCTATGA
*
1318 ATATAGACATTTGAAGGAGGGTTTCTGCCAAAAATCATGCAAGACTGAACTGGAACCCCGAAACG
194 ATATAGACATTTGAAGGAGGGTTTCTGCCAAAAATCATGCAAAACTGAACTGGAACCCCGAAACG
* *
1383 CGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACGATTTTGACTAAAAAGTGACCCGAAAATTT
259 CGTTTTTAGCCCAAAAACCGTGATGATTAGTACACGATTTTGACTAAAAAGTGACCCGAAAATTT
*
1448 TTTTCTGAAATTTTTGCCACAATACCCGGAAAAAATATATAATTCAACTCAAAAAAAAATTGAAG
324 TTTTCTGAAATCTTTGCCACAATACCCGG-----A-ATATAA-T-AACT--AAAAAAAATTGAAG
*
1513 GGTTTATCACGCTTCTAATATCGTTTTTTTCATTTTTTTTCCGAATTTATTTCTATTCAATAAAA
379 GGTTTATCACGCTTCTAATATCGTTTTTTCCATTTTTTTTCCGAATTTATTTCTATTCAATAAAA
* * *
1578 AAAAAATCAGATGCTTGTAACAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCTATGAA
444 AAAAAATCAGATACTAGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCTATGAA
**
1643 TATAGATATTTGAAGGAGGGTTTTTGCCAAAAATCATGCAAAACTGAGTCAGATCCCCGAAACGC
509 TATAGATATTTGAAGGAGGGTTTTTGCCAAAAATCATGCAAAACTGAGTCAGATCAACGAAACGC
*
1708 GTTTTTAGCCCAAAAACCGTGATTGTTAGTATACGATTTCAGCTAAAAAGTGACCCGAAAATTTT
574 GTTTTTAGCCCAAAAACCGTGATTGTTAGTATACGATTTCAGCAAAAAAGTGACCCG-AAATTTT
*
1773 T-TTTT-TCAAATTTATGCCACAATAATCGGAAAAAATAAATCTTATTTAACGCAAAAAAGAAAT
638 TCTTTTCTCAAATTTATGCCACAATAATC--AAAAAA-AAATCTTATTCAACGCAAAAAAGAAAT
* * *
1836 TGAAGGGTTTTTCACGCTTTCAATATCGTTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAAT
700 TGAAGGGTTTTTCACGCTTACAATATCCTTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAAC
1901 CAAAACAAAATTAATATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTAGTACG
765 CAAAACAAAATTAATATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTAGTACG
* * **
1966 ATGAATACAGATATTTTAAGGAGGCTTTCTG-CCAAAAATCATGCACAACAGAGCCGGTTCCCCG
830 ATGAATACAGACATTTGAAGGAGGCTTTCTGAAAAAAAATCATGCACAACAGAGCCGGTTCCCCG
2030 AAACGCGTTTTTTGCCCAAAAACTGTGACGTACACGATTTTGCTTAAAAAGTGACCCGAAAA
895 AAACGCGTTTTTTGCCCAAAAACTGTGACGTACACGATTTTGCTTAAAAAGTGACCCGAAAA
* * *
2092 TTTTTTCTGAA-ATTTTGCCACAATACTCAGAATAAATATATAATTCAACT-CAAAAAAAATTGA
1 TTTTTTCTGAATATTTTGCCACAATACACAGAAAAAATATATAATTCAA-TGC-AAAAAAACTGA
* ** * * *
2155 AGGGTTTATCACGCAT-CTAATATCGTTTTTCCATTTTTTTCTGAATTTATTT-TAATCAAAT-A
64 AGAGTTTATCACGCATGC-AATATCGTTAATCCATTTTTTCCCGAATTTATTTCAAATCAAATGA
* *
2217 ATA-AAAA-CAGATGCTCGTAAAAACAAAACCTTAAATCCATTGTGGCTGAGATTTGGTTCTATG
128 AAACAAAATCAGATGCTCGTAAAAACAAAACCTTAAATCCATTGTGACTGAGATTTGGTTCTATG
* * * * **
2280 AATATAGATATTTGAAGGAGTGTTTCTGCCAAAAATTATGCAAAACTG-AGTCGGGTCCCCGAAA
193 AATATAGACATTTGAAGGAGGGTTTCTGCCAAAAATCATGCAAAACTGAACT-GGAACCCCGAAA
* * * * * *
2344 CGCGTTTTTAGCCCAAAAATCGTGATTATTAGTATACGATTTTG-GTAAAAAGTGACTCGAAATT
257 CGCGTTTTTAGCCCAAAAACCGTGATGATTAGTACACGATTTTGACTAAAAAGTGACCCGAAA-A
**
2408 TTTTTTTCTGAAATCTTTGCCACAATACTTGG-A-A-AA-AA-T-AAAAAAATTGAAGGGTTTAT
321 TTTTTTTCTGAAATCTTTGCCACAATACCCGGAATATAATAACTAAAAAAAATTGAAGGGTTTAT
* *
2467 CACGCTTCTAATATCG-TTTTTCCATTTTTTTTCCCGAATTTATTTCT-TATCAAATAATAGAAA
386 CACGCTTCTAATATCGTTTTTTCCATTTTTTTT-CCGAATTTATTTCTAT-TC-AATAAAAAAAA
2530 AATCAGATACTAGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCTATGAATATA
448 AATCAGATACTAGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCTATGAATATA
*
2595 GATATTTGAAGGAGGGTTTTTGCCAAAAATCATGCAAAACTGAGTCGGATCAACGAAACGCGTTT
513 GATATTTGAAGGAGGGTTTTTGCCAAAAATCATGCAAAACTGAGTCAGATCAACGAAACGCGTTT
* * *
2660 TTAGCCCAAAAACCGTGATTGTTAGTATACTATTTCAGCAAAAAAGTGACCTGGAATTTTTCTTT
578 TTAGCCCAAAAACCGTGATTGTTAGTATACGATTTCAGCAAAAAAGTGACCCGAAATTTTTCTTT
* * * * *
2725 TCTCATATTTATTCCACAATAATCAGAAAAAAATCTTATTCAGCGCAAAAAATAAATTGAAGGGT
643 TCTCAAATTTATGCCACAATAATCAAAAAAAAATCTTATTCAACGCAAAAAAGAAATTGAAGGGT
* *
2790 TTTTCACGCTTACAATATCCTTTTTCCATTTTTTTGCGAATTTATTTCTAATTAAACCAAAATAA
708 TTTTCACGCTTACAATATCCTTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAACCAAAACAA
* * * * * *
2855 AATTCATATGCTCGTAAAAATAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCTATGAATAT
773 AATTAATATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTAGTACGATGAATAC
* *
2920 AGACATTTGATGGAGGGTTTCTGAAAAAAAATCATGCA
838 AGACATTTGAAGGAGGCTTTCTGAAAAAAAATCATGCA
2958 ATATCGTTTT
Statistics
Matches: 778, Mismatches: 77, Indels: 44
0.87 0.09 0.05
Matches are distributed among these distances:
946 186 0.24
947 76 0.10
948 187 0.24
949 20 0.03
950 1 0.00
951 2 0.00
954 2 0.00
955 1 0.00
956 1 0.00
962 18 0.02
963 172 0.22
965 4 0.01
966 3 0.00
967 40 0.05
968 54 0.07
969 11 0.01
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (956 bp):
TTTTTTCTGAATATTTTGCCACAATACACAGAAAAAATATATAATTCAATGCAAAAAAACTGAAG
AGTTTATCACGCATGCAATATCGTTAATCCATTTTTTCCCGAATTTATTTCAAATCAAATGAAAA
CAAAATCAGATGCTCGTAAAAACAAAACCTTAAATCCATTGTGACTGAGATTTGGTTCTATGAAT
ATAGACATTTGAAGGAGGGTTTCTGCCAAAAATCATGCAAAACTGAACTGGAACCCCGAAACGCG
TTTTTAGCCCAAAAACCGTGATGATTAGTACACGATTTTGACTAAAAAGTGACCCGAAAATTTTT
TTCTGAAATCTTTGCCACAATACCCGGAATATAATAACTAAAAAAAATTGAAGGGTTTATCACGC
TTCTAATATCGTTTTTTCCATTTTTTTTCCGAATTTATTTCTATTCAATAAAAAAAAAATCAGAT
ACTAGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCTATGAATATAGATATTTG
AAGGAGGGTTTTTGCCAAAAATCATGCAAAACTGAGTCAGATCAACGAAACGCGTTTTTAGCCCA
AAAACCGTGATTGTTAGTATACGATTTCAGCAAAAAAGTGACCCGAAATTTTTCTTTTCTCAAAT
TTATGCCACAATAATCAAAAAAAAATCTTATTCAACGCAAAAAAGAAATTGAAGGGTTTTTCACG
CTTACAATATCCTTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAACCAAAACAAAATTAATA
TGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTAGTACGATGAATACAGACATTT
GAAGGAGGCTTTCTGAAAAAAAATCATGCACAACAGAGCCGGTTCCCCGAAACGCGTTTTTTGCC
CAAAAACTGTGACGTACACGATTTTGCTTAAAAAGTGACCCGAAAA
Found at i:3053 original size:148 final size:152
Alignment explanation
Indices: 2802--3075 Score: 448
Period size: 148 Copynumber: 1.8 Consensus size: 152
2792 TTCACGCTTA
*
2802 CAATATCCTTTTTCCATTTTTTTGCGAATTTATTTCTAATTAAACCAAAATAAAATTCATATGCT
1 CAATATCCTTTTTCCATTTTTTT-CGAATTTATTTCTAATTAAA-CAAAATAAAATTCAGATGCT
* *
2867 CGTAAAAATAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCTATGAATATAGACATTTGATG
64 CGTAAAAATAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATACAGACATTTGATG
2932 GAGGGTTTCTGAAAAAAAATCATG
129 GAGGGTTTCTGAAAAAAAATCATG
* *
2956 CAATATCGTTTTTCCATTTTTTT-GAATTTATTTCTAATTAAA-TAAA-AAAA-TCAGATGCTCG
1 CAATATCCTTTTTCCATTTTTTTCGAATTTATTTCTAATTAAACAAAATAAAATTCAGATGCTCG
*
3017 TAAAAATAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATACAGATATTT
66 TAAAAATAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATACAGACATTT
3076 CAATGTGGCT
Statistics
Matches: 114, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
148 66 0.58
149 4 0.04
150 3 0.03
152 19 0.17
154 22 0.19
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (152 bp):
CAATATCCTTTTTCCATTTTTTTCGAATTTATTTCTAATTAAACAAAATAAAATTCAGATGCTCG
TAAAAATAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATACAGACATTTGATGGA
GGGTTTCTGAAAAAAAATCATG
Done.