Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009684.1 Corchorus olitorius cultivar O-4 contig09716, 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: 3101
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.36
Found at i:617 original size:307 final size:305
Alignment explanation
Indices: 127--1050 Score: 804
Period size: 332 Copynumber: 2.9 Consensus size: 305
117 ATCGTTTTCC
* * *
127 CTATTTTTTCTGAATAAATTTATACTTCAATCGAAATTGGTTTCTGAAGCTCGTAAAAACAAATC
1 CTATTTTTTCTAAATAAATTTATACTTCAATCGAAATCGGTTTCTGAAGCTCGTAAAAAAAAATC
* * * * * *
192 CTTAAATCCAATGTGGTTGAAATTCGGTTAGCTGAGTGGAGATATTTCATTGAGTCTTGTCGCCA
66 CTTAAATCCAATGTGGCTGAAATTCGCTTAGCTGAATAGAGATATTTCAATGAGTCTTGGCGCCA
* * * * *
257 AAAATCATGCGAAACTGAGTCGGGACCCCAGAACGCGTTTTCAGCTAAATACCGTGAT-TTTGGA
131 AAAATAATGCAAAACTGAGTCGGGACACCAGAACGCGTTTTCAGCTAAATACCGTGATGATTAG-
* * *
321 TAAACGATTTCAGCTTACTTTTTGCAGAAA-TTGACTCGAAATATTTTTCCTTAATTTTTTGCCA
195 TAAACGATTTCAGCTAACTTTTTG-AAAAATTTGACCCGAAATATTTTTCCTTAATTTTTTGCCA
385 AAATACTCCTGAAAATATATAATTCAATGCTAAAGATATTTTTCCTA
259 AAATACTCCTGAAAATATATAATTCAATGCTAAAGATATTTTTCCTA
* * * * *
432 CTATTTTTTCTAAATTTTAATTTCTAGTTCAATCGAAATCGGTTTCTGATGCTTG-AAGAAAAAA
1 CTATTTTTTCTAAA--TAAATTTATACTTCAATCGAAATCGGTTTCTGAAGCTCGTAA-AAAAAA
* ** * * * *
496 ATCCTTAAATCCAATGTGGCTGAGATTTTCTTAGTTGAATAGATATATTTCAATGAGTTTTGGGG
63 ATCCTTAAATCCAATGTGGCTGAAATTCGCTTAGCTGAATAGAGATATTTCAATGAGTCTTGGCG
* * **
561 CCAAAAATAATGCAAAACTGAGTC-GGAGCACCGGAACTCGTTTTTTGTCT-AATACCGTGATGA
128 CCAAAAATAATGCAAAACTGAGTCGGGA-CACCAGAACGCGTTTTCAG-CTAAATACCGTGATGA
* *
624 TTAGTACACGATTTCAGCTAATTTTTTGAAAAATTTGACCCGAAATATTTTTCCTTAATTTTTTG
191 TTAGTAAACGATTTCAGCTAACTTTTTGAAAAATTTGACCCGAAATATTTTTCCTTAATTTTTTG
** * *
689 CCAAAATACTCCTGAAAATATATAATTTCAACACCAAAAATATTGGAAGGCTTTTGACGTTTCTA
256 CCAAAATACTCCTGAAAATATATAA-TTCAATGCTAAAGATA-T-------TTTT--C----C--
754 ATATCA
304 ---T-A
* * * * *** *
760 TTTTCCTATTTTTTTCTGAATTAATTTGTAATTCAGGTGAAATCGGTTTCTGATGCTCGTAAAAA
1 -----CTA-TTTTTTCTAAATAAATTTATACTTCAATCGAAATCGGTTTCTGAAGCTCGTAAAAA
* * * * **
825 CAAATCCTTCAATCCATTGTGGCTGAGATTTTCTTAGCTGAATAGAGATATTTCAATGAGTGC-T
60 AAAATCCTTAAATCCAATGTGGCTGAAATTCGCTTAGCTGAATAGAGATATTTCAATGAGT-CTT
* * * * * * * **
889 GACGCTAAAAATCATGCAAAACTGAGTC-GAAGC-CCCGAAACACGTTTTTAGCTAAATACTATG
124 GGCGCCAAAAATAATGCAAAACTGAGTCGGGA-CACCAG-AACGCGTTTTCAGCTAAATACCGTG
* * * * * *
952 ATGGTTAGTACACGATTTCGGCTAAATATTTGCAAAAA-TTGACCCGAAATATATTTCCTTAATT
187 ATGATTAGTAAACGATTTCAGCTAACTTTTTG-AAAAATTTGACCCGAAATATTTTTCCTTAATT
* * *
1016 TTTAGCCAAAATACTCATAAAAATATATAATTCAA
251 TTTTGCCAAAATACTCCTGAAAATATATAATTCAA
1051 CACCAAAAAT
Statistics
Matches: 510, Mismatches: 70, Indels: 52
0.81 0.11 0.08
Matches are distributed among these distances:
305 13 0.03
306 9 0.02
307 213 0.42
308 17 0.03
309 1 0.00
316 4 0.01
318 1 0.00
322 1 0.00
327 1 0.00
328 1 0.00
331 10 0.02
332 219 0.43
333 10 0.02
334 10 0.02
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (305 bp):
CTATTTTTTCTAAATAAATTTATACTTCAATCGAAATCGGTTTCTGAAGCTCGTAAAAAAAAATC
CTTAAATCCAATGTGGCTGAAATTCGCTTAGCTGAATAGAGATATTTCAATGAGTCTTGGCGCCA
AAAATAATGCAAAACTGAGTCGGGACACCAGAACGCGTTTTCAGCTAAATACCGTGATGATTAGT
AAACGATTTCAGCTAACTTTTTGAAAAATTTGACCCGAAATATTTTTCCTTAATTTTTTGCCAAA
ATACTCCTGAAAATATATAATTCAATGCTAAAGATATTTTTCCTA
Found at i:1098 original size:332 final size:331
Alignment explanation
Indices: 432--3099 Score: 2707
Period size: 331 Copynumber: 8.1 Consensus size: 331
422 ATTTTTCCTA
* * * *
432 CTATTTTTTCTAAATTTTAATTTCTAGTTCAATCGAAATCGGTTTCTGATGCTTG-AAGAAAAAA
1 CTATTTTTTCTGAA--TTAATTTCTAATTCAATCGAAATCGGTTTCTGATGCTCGTAA-AAACAA
* * * * *
496 ATCCTTAAATCCAATGTGGCTGAGATTTTCTTAGTTGAATAGATATATTTCAATGAGTTTTGGGG
63 ATCCTTAAATCCATTGTGGCTGAGATTTTCTTAGCTGAATAGAGATATTTCAATGAGTCTTGGCG
* * * * * * *
561 CCAAAAATAATGCAAAACTGAGTCGGAGCACCGGAACTCGTTTTTTGTCT-AATACCGTGATGAT
128 CCAAAAATCATGCAAAACTGAGTCGGAGCCCCGAAACGCGTTTTTAG-CTAAATACCATGATGGT
* * *
625 TAGTACACGATTTCAGCTAATTTTTTG-AAAAATTTGACCCGAAATATTTTTCCTTAATTTTTTG
192 TAGTACACGATTTCGGCTAAATTTTTGCAAAAA-TTGACCCGAAATATTTTTCCTTAATTTTTAG
* * * *
689 CCAAAATACTCCTGAAAATATATAATTTCAACACCAAAAATATTGGAAGGCTTTTGACGTTTCTA
256 CCAAAATACTCATAAAAATATATAA-TTCAACACCAAAAATATTGAAAGGCTTTTGACGCTTCTA
754 ATATCA-TTTTC
320 ATATCATTTTTC
* *
765 CTATTTTTTTCTGAATTAATTTGTAATTCAGGT-GAAATCGGTTTCTGATGCTCGTAAAAACAAA
1 CTA-TTTTTTCTGAATTAATTTCTAATTCA-ATCGAAATCGGTTTCTGATGCTCGTAAAAACAAA
* *
829 TCCTTCAATCCATTGTGGCTGAGATTTTCTTAGCTGAATAGAGATATTTCAATGAGTGC-TGACG
64 TCCTTAAATCCATTGTGGCTGAGATTTTCTTAGCTGAATAGAGATATTTCAATGAGT-CTTGGCG
* * * *
893 CTAAAAATCATGCAAAACTGAGTCGAAGCCCCGAAACACGTTTTTAGCTAAATACTATGATGGTT
128 CCAAAAATCATGCAAAACTGAGTCGGAGCCCCGAAACGCGTTTTTAGCTAAATACCATGATGGTT
* *
958 AGTACACGATTTCGGCTAAATATTTGCAAAAATTGACCCGAAATATATTTCCTTAATTTTTAGCC
193 AGTACACGATTTCGGCTAAATTTTTGCAAAAATTGACCCGAAATATTTTTCCTTAATTTTTAGCC
*
1023 AAAATACTCATAAAAATATATAATTCAACACCAAAAATATTTAAAGGCTTTTGACGCTTCTAATA
258 AAAATACTCATAAAAATATATAATTCAACACCAAAAATATTGAAAGGCTTTTGACGCTTCTAATA
1088 TCATTTTTC
323 TCATTTTTC
* * ** *
1097 CTATTTTTTTCTAAATTAATTTCTAATTC-ATGTGAAATTAGTTTCTAATGCTCGTAAAAACAAA
1 CTA-TTTTTTCTGAATTAATTTCTAATTCAAT-CGAAATCGGTTTCTGATGCTCGTAAAAACAAA
* *
1161 TCCTTCAATCCATTGTGGCTGAGATTTTCTTAGCTGAATAGAGATATTTCAATGAGACTTGGCGC
64 TCCTTAAATCCATTGTGGCTGAGATTTTCTTAGCTGAATAGAGATATTTCAATGAGTCTT-G-GC
** * * * * * * * * * * *
1226 GCCAAAAATCATGTGAAAGTTAGTCGGGGCCACAAAACACGTTTTCAGCCAAATACCGTAATTGT
127 GCCAAAAATCATGCAAAACTGAGTCGGAGCCCCGAAACGCGTTTTTAGCTAAATACCATGATGGT
* * * * *
1291 TAGTACACGATTTTGGCTTATTTTTTGCAGAAATTGACCCGAATTATTTTTCCTTAATTTTT-GA
192 TAGTACACGATTTCGGCTAAATTTTTGCAAAAATTGACCCGAAATATTTTTCCTTAATTTTTAG-
* ** * * * * *
1355 CCAAAATACTCATGAAAATATATAATTCAATGCTAAAAATATTGGACGGCTTTTCG-TGCTTCTG
256 CCAAAATACTCATAAAAATATATAATTCAACACCAAAAATATTGAAAGGCTTTT-GACGCTTCTA
** *
1419 ATATGGTTTTCC
320 ATATCATTTTTC
* * * * *
1431 CTCTTTTTTCTGAGTTAATTTCTAATTTCAATCGAATTCGGTTTATGATGGTCGTAAAAACAAAT
1 CTATTTTTTCTGAATTAATTTCTAA-TTCAATCGAAATCGGTTTCTGATGCTCGTAAAAACAAAT
** * * ** * * *
1496 CCTTATTTCCAATGTGTCTGAGATTTGGTTTGCTGAATAGAGATATTGCAATGAGTCTTGGCACC
65 CCTTAAATCCATTGTGGCTGAGATTTTCTTAGCTGAATAGAGATATTTCAATGAGTCTTGGCGCC
* * * * *
1561 AGAAATCATGCAAAACTGAGTCGG-GCCCCGAAACGCCTTTTTAGCCAAATACCGTGATGGTTAC
130 AAAAATCATGCAAAACTGAGTCGGAGCCCCGAAACGCGTTTTTAGCTAAATACCATGATGGTTAG
* * * *
1625 TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAATA-TTTTCCTAAATTTTTGGCCAA
195 TACACGATTTCGGCTAAATTTTTGCAAAAATTGACCCGAAATATTTTTCCTTAATTTTTAGCCAA
* ** ** * *
1689 AATAATTTTTTAAATATATAATTCAACACCAAAAATATTTG-AAGGCTCTCGACGCTTCTAATAT
260 AATACTCATAAAAATATATAATTCAACACCAAAAATA-TTGAAAGGCTTTTGACGCTTCTAATAT
1753 CA-TTTTC
324 CATTTTTC
*
1760 CTATTTTTTTTCTAAATTAATTTCTAATTCAAGT-GAAATCGGTTTTCTGATGCTCGTAAAAACA
1 CTA--TTTTTTCTGAATTAATTTCTAATTCAA-TCGAAATCGG-TTTCTGATGCTCGTAAAAACA
* * * * **
1824 AATCCTTCATTCCATTGTGGCTAAGATTTTCTTAGCTGAATAGAGATATTTCAATGA-TATTTAA
62 AATCCTTAAATCCATTGTGGCTGAGATTTTCTTAGCTGAATAGAGATATTTCAATGAGT-CTTGG
* * ** * *
1888 CGCCAAAAATCATACAAAACTGAGTCGGAGCCCCAAAATACATTTTTAGCTAAATA-CAGTAATG
126 CGCCAAAAATCATGCAAAACTGAGTCGGAGCCCCGAAACGCGTTTTTAGCTAAATACCA-TGATG
*
1952 G-TAGTACACGATTTCGGC-AAATTTTTGCAAAAATTGACCCGAAATATTTTTTCTT-ATTTTTA
190 GTTAGTACACGATTTCGGCTAAATTTTTGCAAAAATTGACCCGAAATATTTTTCCTTAATTTTTA
* * * * *
2014 GGCCAAAATACTCATTAAAATATATAATTCCACACGAAAAATATTTAAAGGCTTTTGATGCTTCT
255 -GCCAAAATACTCATAAAAATATATAATTCAACACCAAAAATATTGAAAGGCTTTTGACGCTTCT
2079 AATATCATTTTTC
319 AATATCATTTTTC
* * * * * *
2092 CTAGTTTTTCTGAATTAATTTCTACTTCAGGT-GAAATTGGTTTCTAATGCTCGTCAAAAAAAAA
1 CTATTTTTTCTGAATTAATTTCTAATTCA-ATCGAAATCGGTTTCTGATGCTCGT---AAAAACA
* *
2156 AATCCTT-AATCAATTGTGGCTGAGATTTTCTTAGCTGAATAGAGATATTTCAATGAGTCTTGAC
62 AATCCTTAAATCCATTGTGGCTGAGATTTTCTTAGCTGAATAGAGATATTTCAATGAGTCTTGGC
* * *
2220 GCCAAAAATCATGCAAAACTGAGTTGGAGCCCAGGAACGCGTTTTTAGCTAAATACC--------
127 GCCAAAAATCATGCAAAACTGAGTCGGAGCCCCGAAACGCGTTTTTAGCTAAATACCATGATGGT
* * * **
2277 -AG-----GATTTCGACTAATTTTTTGCAAAAATTGACCCCAAATATTTTTCCTTAATTTTTTTC
192 TAGTACACGATTTCGGCTAAATTTTTGCAAAAATTGACCCGAAATATTTTTCCTTAATTTTTAGC
* * * * *
2336 CAAAATACTTAGAAAAATATATAATTCAACACCATAAATATT-AAACGGCTTTTCACGCTTTTAA
257 CAAAATACTCATAAAAATATATAATTCAACACCAAAAATATTGAAA-GGCTTTTGACGCTTCTAA
*
2400 TATCATTTTTTG
321 TATCA-TTTTTC
* * *
2412 CTA-TTTTTCTGAATTAATTTCTAATTCAATCGAAATAGGTTTCTAATGCTCGTAAAAAGAAATC
1 CTATTTTTTCTGAATTAATTTCTAATTCAATCGAAATCGGTTTCTGATGCTCGTAAAAACAAATC
* ** * *
2476 CTTAAATCCAATGTGGCTGAGATTTGGTTAGCCGAATAAAGATATTTCAATGAGTCTTGGCGCCA
66 CTTAAATCCATTGTGGCTGAGATTTTCTTAGCTGAATAGAGATATTTCAATGAGTCTTGGCGCCA
2541 AAAATCATGCAAAACTGAGTCGG-GCCCCCGAAACGCG---TTAG-T-AA-A-C--GA---TT--
131 AAAATCATGCAAAACTGAGTCGGAG-CCCCGAAACGCGTTTTTAGCTAAATACCATGATGGTTAG
* * * * *
2591 T---C-A-----GCTAAAATTTTGCAAAAATTGACCCGAAATATTTATTTCTCAATTTTTGGACA
195 TACACGATTTCGGCTAAATTTTTGCAAAAATTGACCCGAAATATTT-TTCCTTAATTTTTAGCCA
* ** * * * ** *
2647 AAATACCCCA-AAAAATATATAATTCAACTGCAAAAATATTGGACA-GATTTTCACAATTTTAAT
259 AAATA-CTCATAAAAATATATAATTCAACACCAAAAATATT-GAAAGGCTTTTGACGCTTCTAAT
** * *
2710 ATTGTTATCC
322 ATCATTTTTC
* * * *
2720 CTATTTTTTCTGAATAAATTTGTACTTCAATCGAAATTGGTTTCTGATGCTCGTAAAAACAAATC
1 CTATTTTTTCTGAATTAATTTCTAATTCAATCGAAATCGGTTTCTGATGCTCGTAAAAACAAATC
** * *
2785 CTTAAATCCGA-TGTGGCTGAGATTTGGTTAGCTGAGTAGAAATATTTCAATGAGTCTTGGCGCC
66 CTTAAATCC-ATTGTGGCTGAGATTTTCTTAGCTGAATAGAGATATTTCAATGAGTCTTGGCGCC
* ** * * * *
2849 AAAAATCATGTAAAACTGAGTCGGTTCCACG-AACGCGTTTTCAGCCAAATACCATGATTGTTTA
130 AAAAATCATGCAAAACTGAGTCGGAGCCCCGAAACGCGTTTTTAGCTAAATACCATGA-TGGTTA
* * * * *
2913 GTACACGATTTCGGCTTAATTTTTGTAGAAATTGACCCGAAATATTTTTCCTTAATTTTTCGACA
194 GTACACGATTTCGGCTAAATTTTTGCAAAAATTGACCCGAAATATTTTTCCTTAATTTTTAGCCA
* * ** * * * *
2978 AAATTCTCATGAAAATATATAATTCAATGCTAAAGATATTGGACGGC-TTT-ACGTGCTTCTAAT
259 AAATACTCATAAAAATATATAATTCAACACCAAAAATATTGAAAGGCTTTTGAC--GCTTCTAAT
* *
3041 ATCGTTTTCC
322 ATCATTTTTC
* * * *
3051 CCATTTTTTCTGAATTAATTTCTGATTTCAATCGAATTCGGTTTATGAT
1 CTATTTTTTCTGAATTAATTTCT-AATTCAATCGAAATCGGTTTCTGAT
3100 AC
Statistics
Matches: 1954, Mismatches: 296, Indels: 171
0.81 0.12 0.07
Matches are distributed among these distances:
308 42 0.02
309 202 0.10
310 4 0.00
311 6 0.00
312 2 0.00
313 4 0.00
314 5 0.00
315 1 0.00
316 14 0.01
317 88 0.05
318 12 0.01
319 136 0.07
320 14 0.01
321 2 0.00
323 3 0.00
326 1 0.00
327 1 0.00
329 22 0.01
330 149 0.08
331 488 0.25
332 463 0.24
333 34 0.02
334 258 0.13
335 3 0.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (331 bp):
CTATTTTTTCTGAATTAATTTCTAATTCAATCGAAATCGGTTTCTGATGCTCGTAAAAACAAATC
CTTAAATCCATTGTGGCTGAGATTTTCTTAGCTGAATAGAGATATTTCAATGAGTCTTGGCGCCA
AAAATCATGCAAAACTGAGTCGGAGCCCCGAAACGCGTTTTTAGCTAAATACCATGATGGTTAGT
ACACGATTTCGGCTAAATTTTTGCAAAAATTGACCCGAAATATTTTTCCTTAATTTTTAGCCAAA
ATACTCATAAAAATATATAATTCAACACCAAAAATATTGAAAGGCTTTTGACGCTTCTAATATCA
TTTTTC
Done.