Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009632.1 Corchorus olitorius cultivar O-4 contig09664, 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: 3303
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Found at i:2096 original size:330 final size:323
Alignment explanation
Indices: 277--2216 Score: 1649
Period size: 330 Copynumber: 5.9 Consensus size: 323
267 AAAACCGTTC
* * *
277 CGGCTAAAATTTTGCAAAAATTGACCCGAAAGATAATTCCTCAATTTTTTGCTAAAATACTCAT-
1 CGGCTAAAATTTTGCAAAAATTGA-CC-AAAGAT-TTTCCTCAATTTTTGGCAAAAATACTCATA
** ** *
341 AAAAATATA-AATTTGACATCAAAAAGATTGAAGGACTTTTAACGCTTCTAATAT-TGTTTTTCC
63 AAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCT-TTTTT--
* * * * *
404 TATTTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTCAGATGCTCATAAAAAGAAATCC
125 TA-CTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC
* * * *
469 TTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGTTATTTCGAGGAGTCTTGGCACAAA
189 TTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAA
* * ** *
534 AAATCATGCAAAACTGA-GCAGGGCTCTGGAACGGGTTTTTAGCC-GAAATCCGTGATGTA-T--
254 AAATCATGCAAAACTGACTCGGGGC-CTGGAACGCATTTTTAGCCAAAAAT-CGTGATGTAGTAC
594 ACGATTT
317 ACGATTT
* * * *
601 CGGCTAAAATTTTGCAAAAA-TGAGCCGAAAGATTTTTTTTCTCAAATTCTAGCAAAAATACTCA
1 CGGCTAAAATTTTGCAAAAATTGA-CC-AAAGA---TTTTCCTCAATTTTTGGCAAAAATACTCA
* * * *
665 CAAAAAATATATAATTCAACGCCACAAAA-ATTGAAAGTCTTTTTCACACTTCTAATATCGTTTT
61 TAAAAAATATATAATTCAACGCCA-AAAAGATTGAAGGAC-TTTTCACGCTTCTAATATC-TTTT
* * * * * ** *
729 TCCTACTTTATTTCCAAATTAATTGCTGATTAAATCGAAATAAGATTTAGATAATCTTAAAAACA
123 T-TTAC--T-TTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
* * *
794 AATCCTTAAATACAATGTGACTGAGATTTGATTAGATGAATATAGATATATTTTAAGGAGTCTTG
184 AATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAG--ATATTTCAAGGAGTCTTG
** * * * *
859 GCGCCGAAAATCATGCAAAACTGACCCGGGGCCTTGGAACGCGTTTTTAGCCAAAAA-AG-CATG
247 GCGCAAAAAATCATGCAAAACTGACTCGGGGCC-TGGAACGCATTTTTAGCCAAAAATCGTGATG
922 ATAGTACACGATTT
311 -TAGTACACGATTT
* ** * * * * *
936 CGGCTAAAATTTTGCAAAAA-TGTTCCGAATTATTTTTCT-AATTTTTAGCCACAATACTCACAA
1 CGGCTAAAATTTTGCAAAAATTG-ACC-AAAGATTTTCCTCAATTTTTGGCAAAAATACTCA-TA
* * * * * *
999 AAAAATATATAATTCAATGCCAAAAAGATTCAAGGGCTTCTCACGCTTCCAATATCGTTTTTCCT
63 AAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATC-TTTTT-TT
* * * * *
1064 ATTTTTTTCAAATTAATTTCTAATTAAATTGAAACATGATTCAAATGCTCGTAAAAA-AAATCCT
126 A-CTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT
* * **
1128 TAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGT-TT--CAAAATC
190 TAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGC-GCA--
* * * *
1190 AAAAACCATGCAAAACTGACCCGGCGCCTCGGAACGCGA--TTTAGCCAAAAAAACCGTGATG--
252 AAAAATCATGCAAAACTGACTCGGGGCCT-GGAACGC-ATTTTTAGCC--AAAAATCGTGATGTA
1251 GTACACGATTT
313 GTACACGATTT
* * ** * * * * *
1262 CGGCTAAACTTTTACAAACGTTGACC--CGATTTTCCTCAA-TTTTGAGCCACAATACTCACAAT
1 CGGCTAAAATTTTGCAAAAATTGACCAAAGATTTTCCTCAATTTTTG-GCAAAAATACTCATAAA
* * * * * *
1324 ATATATATAATTCAACTG-AAAAAAGATTGGAGGACTTCTCACGCTTTTAATATCGTTTTTCATA
65 AAATATATAATTCAAC-GCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATC-TTTTT-TTA
* *
1388 TTTTTCAAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
127 CTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * * * * *
1453 AATGCAATGTGGCTGAGATTTTGATTAAATAAACAGAGATATTTCAAGGAGT-TTCGACGCAAAA
192 AATCCAATGTGGCTGAGA-TTTGATTAGATGAATATAGATATTTCAAGGAGTCTT-GGCGCAAAA
* * * * * ** *
1517 AATCATGCAAAACTGAGTCGGGGCCCCGAAATGCATTATTAGGAAAGCAAAACTGTGATGGTTAG
255 AATCATGCAAAACTGACTCGGGG-CCTGGAACGCATTTTTAGCCAA--AAATC-GTGAT-G-TAG
*
1582 TACACAATTT
314 TACACGATTT
* * * * * *
1592 TGGCTAAAATTTTACAAAAAATGACCTGAAA-ATTTTTTTCTTAATTTTTGGAAAAAATACTCAT
1 CGGCTAAAATTTTGCAAAAATTGACC--AAAGA--TTTTCCTCAATTTTTGGCAAAAATACTCAT
* * * * * * *
1656 GAAATATATATAATTTAATGCC-AAAAGATTGGAGGACTTTTCACGCTTTTCATA----TTTTT-
62 AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCTTTTTTTA
** * ** ** *
1715 C---T--GGATTAATGTCTAATTAAATCGAAACAAGATTTGGATTTTCGCAAAAACAAATCCTTA
127 CTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * **
1775 AATGCAATGTGCCTGAGATTTGATTAGATGAATAT-GAATATCACAAGGAGTCTTGGCGCAAAAA
192 AATCCAATGTGGCTGAGATTTGATTAGATGAATATAG-ATATTTCAAGGAGTCTTGGCGCAAAAA
* * * *
1839 ATTATGCAAAACCGACTCGGAGCTCTGGAACGCATTTTTAGCCAAAAATCGTGATGATTATTACA
256 ATCATGCAAAACTGACTCGGGGC-CTGGAACGCATTTTTAGCCAAAAATCGTGATG--TAGTACA
1904 CGATTT
318 CGATTT
** * *
1910 CAACTAAAATTTTGCAAAAATTGACCTAAAGGATATTACCTCAATTTTTGGCTAAAATACTCATA
1 CGGCTAAAATTTTGCAAAAATTGACC-AAA-GAT-TTTCCTCAATTTTTGGCAAAAATACTCATA
* ** *
1975 AAAAATATATAATTCAACGCCTAAAAATATTGAAGGGTTTTTTACGCTTCTAATAT-TTTTTATT
63 AAAAATATATAATTCAACGCC-AAAAAGATTGAAGGACTTTTCACGCTTCTAATATCTTTTT-TT
* * * *
2039 ACTTTTCCGAATTAATTTGTAATTAAATCGAAACAAGATTTATATGCTCGTAAAAACAAATCCTT
126 ACTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
* *
2104 AAATCCAATGTGGCTGAGATTTTATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAA
191 AAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAA
* * *
2169 ATCATACAAAACTGACTCGGGGCCCCGGAACGCTTTTTTAGCCAAAAA
256 ATCATGCAAAACTGACTCGGGG-CCTGGAACGCATTTTTAGCCAAAAA
2217 AACCGTGTTG
Statistics
Matches: 1313, Mismatches: 220, Indels: 160
0.78 0.13 0.09
Matches are distributed among these distances:
317 5 0.00
318 80 0.06
319 5 0.00
320 27 0.02
321 67 0.05
322 119 0.09
323 109 0.08
324 96 0.07
325 43 0.03
326 90 0.07
327 25 0.02
328 67 0.05
329 53 0.04
330 268 0.20
331 52 0.04
332 76 0.06
333 24 0.02
334 34 0.03
335 68 0.05
336 5 0.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (323 bp):
CGGCTAAAATTTTGCAAAAATTGACCAAAGATTTTCCTCAATTTTTGGCAAAAATACTCATAAAA
AATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCTTTTTTTACTTT
TCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATC
CAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCAT
GCAAAACTGACTCGGGGCCTGGAACGCATTTTTAGCCAAAAATCGTGATGTAGTACACGATTT
Found at i:2939 original size:331 final size:331
Alignment explanation
Indices: 2229--3240 Score: 1164
Period size: 331 Copynumber: 3.0 Consensus size: 331
2219 CCGTGTTGGT
** *
2229 AAAATTTTTCCTCAATTTTTGGCCACAACCCTCATAAAATATATATAATTCAAAGCCAAAAAGAT
1 AAAATTTTTCCTCAATTTTTGGCCACAATTCTCATAAAA-ATATATAATTCAAAGACAAAAAGAT
* * * *
2294 TGAAGGGTTTTTCACG-CTTCTAATATCGTTTTTCCAATTTTTTCTGAATTAATTTCAAATAAAA
65 TGAAGGGTTTTTTACGACTTCTAATATCATTTTTCCAATTTTTTCTGAATTAATTTCGAATTAAA
* * * * *
2358 TCGAAACATGATTCAAATGGTCGTAAGAAC-AAATCCTTAAATCCAATGTGGCTGAGATTTGGTT
130 TAGAAACATGATTCAAATGCTCGTAAAAACTAAATCCTTAAATCCAAAGTGGCTGAGATTTGGTC
* *
2422 AGAT-ATATATAAATATTTCAAGAAGTCTTCTTGCTAAAAAATCATACAAAACTGAATCGGGGCC
195 AGATGA-ATATAAATATTTCAAG-AGTCTTCGTGC-AAAAAATCATGCAAAACTGAA-CGGGGCC
* * * *
2486 CCGAAACGCTTTTTTAGCTTAAAA-CTGTGATGGAAAGTACACGATTTCGGCTAAAATTTTGC-T
256 CAGAAACGCGTTTTTAGCTTAAAATC-ATGATGGAAAGTACACGATTTCGGCTAAAATTTTGCAA
2549 AAATTGATCC-G
320 AAATTGATCCAG
** ** *
2560 AAAGATTTTTCCAAAATTTTTTTCCACAATTCTCATAAAAAAATATAATTCAAAGACAAAAAGAT
1 AAA-ATTTTTCCTCAATTTTTGGCCACAATTCTCATAAAAATATATAATTCAAAGACAAAAAGAT
* * *
2625 TGAAGGGTTTTTTA-GACTTCTAATATCATTTTTCCAACTTTTTCAGAATTAGTTTCGAATTAAA
65 TGAAGGGTTTTTTACGACTTCTAATATCATTTTTCCAATTTTTTCTGAATTAATTTCGAATTAAA
* * * *
2689 TGGAAACATGATTCAAATGCTCATAAAAACTAAATCCCTAAATCCAAAGTGGCAGAGATTTGGTC
130 TAGAAACATGATTCAAATGCTCGTAAAAACTAAATCCTTAAATCCAAAGTGGCTGAGATTTGGTC
* * * * *
2754 AGATGAATATAGATAGTTCAATGAGTCTTCGTGCCAAAAATCATGCAAAACTGAACGGGGACTAG
195 AGATGAATATAAATATTTCAA-GAGTCTTCGTGCAAAAAATCATGCAAAACTGAACGGGGCCCAG
* * *
2819 AAATGCGTTTTTAGC-TAAAATCATGATGGATAGTGCACGATTTCGGCTAAAATTTTGCAAAAAT
259 AAACGCGTTTTTAGCTTAAAATCATGATGGAAAGTACACGATTTCGGCTAAAATTTTGCAAAAAT
2883 TGATCCAG
324 TGATCCAG
* * * * **
2891 AAAATTTTTCCTCAATTTTTGGCCATAATTCTCATAAACAATATATAATTCAAGGATAGAAATCT
1 AAAATTTTTCCTCAATTTTTGGCCACAATTCTCATAAA-AATATATAATTCAAAGACAAAAAGAT
* * * * *
2956 TGAAGGGTTTTTTTCAGGA-TTTTAATATCTTTTTTCCAATTTTTTTCTTAATTAATTTTGAATT
65 TGAAGGG-TTTTTT-ACGACTTCTAATATCATTTTTCCAA-TTTTTTCTGAATTAATTTCGAATT
** * *
3020 AAATAGAAACATGAAACAAATGCTCGTAAAAAGTAAAAACAAAACATTAAATCCAAAGTGGCTGA
127 AAATAGAAACATGATTCAAATGCTCGTAAAAACT-AAATC----C-TTAAATCCAAAGTGGCTGA
* *
3085 GATTTGGTCAGATGAATATAAATATTTCAAGGATTCTTCGTGCAAAAAATCATG-AAAACTGAGT
186 GATTTGGTCAGATGAATATAAATATTTCAA-GAGTCTTCGTGCAAAAAATCATGCAAAACTGA-A
* * * * * * * * *
3149 CTGTGTCCCA-AAACGCGTTTTTAGCTTAAAGTCTTTATGAAAAGTATACGATTTCAGCTAACAT
249 C-GGGGCCCAGAAACGCGTTTTTAGCTTAAAATCATGATGGAAAGTACACGATTTCGGCTAAAAT
* *
3213 TCTACAAAAATTGATCCAG
313 TTTGCAAAAATTGATCCAG
3232 AAAATTTTT
1 AAAATTTTT
3241 GGCACAAATC
Statistics
Matches: 574, Mismatches: 85, Indels: 34
0.83 0.12 0.05
Matches are distributed among these distances:
329 38 0.07
330 62 0.11
331 157 0.27
332 93 0.16
333 21 0.04
334 50 0.09
335 4 0.01
339 9 0.02
340 81 0.14
341 59 0.10
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (331 bp):
AAAATTTTTCCTCAATTTTTGGCCACAATTCTCATAAAAATATATAATTCAAAGACAAAAAGATT
GAAGGGTTTTTTACGACTTCTAATATCATTTTTCCAATTTTTTCTGAATTAATTTCGAATTAAAT
AGAAACATGATTCAAATGCTCGTAAAAACTAAATCCTTAAATCCAAAGTGGCTGAGATTTGGTCA
GATGAATATAAATATTTCAAGAGTCTTCGTGCAAAAAATCATGCAAAACTGAACGGGGCCCAGAA
ACGCGTTTTTAGCTTAAAATCATGATGGAAAGTACACGATTTCGGCTAAAATTTTGCAAAAATTG
ATCCAG
Done.