Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010252.1 Corchorus olitorius cultivar O-4 contig10284, 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: 2057
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:576 original size:277 final size:278
Alignment explanation
Indices: 76--633 Score: 825
Period size: 277 Copynumber: 2.0 Consensus size: 278
66 TTTTTAAATC
* ** *
76 CAATTTGTCTGAGCATTCGCTAGATGAATATAGATATTTCAATGTGTCTTAAAGCCAAAAATCAT
1 CAATTTGTCTGAGCATTCGCTAGACGAATATAGATATTTCAATCAGTCTTAAAGCAAAAAATCAT
** *
141 GCAAAACTGAGCCGGGGCCCCGGAACGAATTTTTAGTTATAAACCGTGATGGTTAGTACATGATT
66 GCAAAACTGAGCCGGGGCCCCGGAACGAATTTTTAGGCATAAACCGTGATGGTTAATACATGATT
* * * ** *
206 TCGGCTAAAATTTTGCAAAAATTGACTTGAAACATTTCTCCTCAATTTTTGGCCAGAATACTCAT
131 TCGGCTAAAATTTTGCAAAAATTGACCTGAAACATTTATCATCAATTTTTGAACACAATACTCAT
* * * *
271 AAAGAATATATAACTCAATGCCAAAAAGATTGAAGGGCTTCCCACGCATCTAATATCGT-TTTCT
196 AAAAAATATATAACTCAACGACAAAAAGATTGAAGGGCTTCCCACGCATCCAATATCGTATTTC-
335 TTTTTTTTTCGAACTAATTT
260 TTTTTTTTT-GAACTAATTT
* * * *
355 CAATTTGTCTGAGCTTTCGCTAGACGAATATAGATATTTCAGTCAGTCTTGACGCAAAAAATCAT
1 CAATTTGTCTGAGCATTCGCTAGACGAATATAGATATTTCAATCAGTCTTAAAGCAAAAAATCAT
* **
420 GCAAAACTGAGCC-GGGTCCCGGAACGCGTTTTTAGGCA-AAACCGTGATGGTTAATACATGATT
66 GCAAAACTGAGCCGGGGCCCCGGAACGAATTTTTAGGCATAAACCGTGATGGTTAATACATGATT
*
483 TCGGCTAAAATTTTGCACAAATTGACCTGAAACATTTATCATCAATTTTTGAACACAATACTCAT
131 TCGGCTAAAATTTTGCAAAAATTGACCTGAAACATTTATCATCAATTTTTGAACACAATACTCAT
* *
548 AAAAAATATATAACTCAACGAGAAAAAGATTGAAGGGCTTCTCACGCATCCAATATCGTATTTCT
196 AAAAAATATATAACTCAACGACAAAAAGATTGAAGGGCTTCCCACGCATCCAATATCGTATTTCT
*
613 TTTTTTTTGAATTAATTT
261 TTTTTTTTGAACTAATTT
631 CAA
1 CAA
634 ATTAAATCGA
Statistics
Matches: 250, Mismatches: 28, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
276 12 0.05
277 144 0.58
278 24 0.10
279 70 0.28
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (278 bp):
CAATTTGTCTGAGCATTCGCTAGACGAATATAGATATTTCAATCAGTCTTAAAGCAAAAAATCAT
GCAAAACTGAGCCGGGGCCCCGGAACGAATTTTTAGGCATAAACCGTGATGGTTAATACATGATT
TCGGCTAAAATTTTGCAAAAATTGACCTGAAACATTTATCATCAATTTTTGAACACAATACTCAT
AAAAAATATATAACTCAACGACAAAAAGATTGAAGGGCTTCCCACGCATCCAATATCGTATTTCT
TTTTTTTTGAACTAATTT
Found at i:1736 original size:330 final size:330
Alignment explanation
Indices: 380--2057 Score: 1852
Period size: 329 Copynumber: 5.1 Consensus size: 330
370 TTCGCTAGAC
* * * * * *
380 GAATATAGATATTTCAGTCAGTCTTGACGCAAAAAATCATGCAAAACTGAGCCGGGTCCCGGAAC
1 GAATATAGATAATTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGCCCCGGAAC
* * * * * * *
445 GCGTTTTTAGGCAA-AACCGTGATGGTTAATACATGATTTCGGCTAAAATTTTGCACAAATTGAC
66 GCGTTTTCAGCCAAGAATCGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCAAAAATTGAC
* * * * * * **
509 CTGAAACATTTATCATCAATTTTTGAA-CACAATACTCATAAAAAATATATAACTCAACGAGAAA
131 CCGAAAGATTTTTCCTCAATTTTT-AACCGCAATACTCATAAAAAATATATAATTCAACGCCAAA
* * * **
573 AAGATTGAAGGGCTTCT-CACGCATCCAATATCGTATTTCTTTT-TTTTT--GAATTAATTTCAA
195 AAGATTGAAGGGCTT-TGCACGCTTCTAATATC--ATTTTTTTTATTTTTCCGAATTAATTTCCG
** * * * ** * **
634 ATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATTTGTCTGAGCCT
257 ATTAAATCGAAACATGATTCAAATGCTCGTAAAATCAAATCCTTAAATCCAACATGGCTGAGATT
* *
699 T-CACTAGAT
322 TGGAAT-GAT
* * *
708 GAATATAGATATTTGAATGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCCGGAGCCCCGGAA
1 GAATATAGATAATTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGG-GCCCCGGAA
* * *
773 CGCGTTTTCAGCCAAGAATCGTGATTGTTAAGTACACGGTTTCGGCAAAAATTTTGCAGAAATTG
65 CGCGTTTTCAGCCAAGAATCGTGATGGTT-AGTACACGATTTCGGCAAAAATTTTGCAAAAATTG
* * * * *
838 ACCCGAAAGATTTTTCCTCAATTTTTAACAGCAATACTCGTAAAAAATGTATTATTTAACGCCAA
129 ACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCATAAAAAATATATAATTCAACGCCAA
* * * * * *
903 AAATATTGCA-GGCTTTTCCACGCTTCTAATATCATTTTTTTAAATTTTCCGAATTAATTTTCGA
194 AAAGATTGAAGGGC-TTTGCACGCTTCTAATATCATTTTTTTTATTTTTCCGAATTAATTTCCGA
* * * *
967 TTGAATCGAAACATGATTTAAATGCTCGTAAAATCAAATCCTTTAATCCAACATGGTTGAGATTT
258 TTAAATCGAAACATGATTCAAATGCTCGTAAAATCAAATCCTTAAATCCAACATGGCTGAGATTT
1032 GGAATGAT
323 GGAATGAT
* * *
1040 GAATA-AGGATAATTCAATAAGTCTTGGCGCCTAAAATCGTGCAAAACTGAGCCGTGGCCCCGGA
1 GAATATA-GATAATTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCG-GGCCCCGGA
* * * *
1104 ACGCGTTTTCAGCAAAAAATTCGTGATGTTTAGTACACGAATTCGGCAAAAATTTTGC-AAAATT
64 ACGCGTTTTCAGCCAAGAA-TCGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCAAAAATT
* * * * * * *
1168 TACCCGAAGGATATTTCCTCAATTTTTATCCGCAATAGTCAT-AAAAATATATAACTCAACACCA
128 GACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCATAAAAAATATATAATTCAACGCCA
*
1232 AAAA-ATTGAAGGGCTTTGCACGCTTCTAATATCA-TTTTTTTATTTTTTCCGAATTAATTTCTG
193 AAAAGATTGAAGGGCTTTGCACGCTTCTAATATCATTTTTTTTA-TTTTTCCGAATTAATTTCCG
* * **
1295 ATTAAATCGAAAAATGATTTAAATGCTCGTAAAATCAAATCCTTAAATCCAAGGTGGCTGAGATT
257 ATTAAATCGAAACATGATTCAAATGCTCGTAAAATCAAATCCTTAAATCCAACATGGCTGAGA-T
*
1360 TTGG-ATAAT
321 TTGGAATGAT
* * * * *
1369 GAATATAGATAAATC-ATCGAGTCTTGGGGCCAAAAATCATGCAAAATTGAACCGGCGTCCCGGA
1 GAATATAGATAATTCAAT-GAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGG-GCCCCGGA
* * *
1433 ACGCGTTTTCAGCCAAGAATCGAGATGGTTTGTACACGATTTCTGCAAAAATTTTGCAAAAATTG
64 ACGCGTTTTCAGCCAAGAATCGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCAAAAATTG
* * * * *
1498 ACCCGAAATATTTTTCATCAATTTTTAACCGCAATACTCTTAAAAAATACATAATTCAATGCCAA
129 ACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCATAAAAAATATATAATTCAACGCCAA
* * *
1563 AAAGATTGAAGGGCTTTGCACACTTCTAATATAATTTTTTTTATTTTTCTGAATTAATTTCCGAT
194 AAAGATTGAAGGGCTTTGCACGCTTCTAATATCATTTTTTTTATTTTTCCGAATTAATTTCCGAT
* **
1628 TAAATCGAAACATGATTCAAATG-TCGGAAAATCAAATCCTTAAATCCAATGTGGCTGAGATTTG
259 TAAATCGAAACATGATTCAAATGCTCGTAAAATCAAATCCTTAAATCCAACATGGCTGAGATTTG
*
1692 GGATGAT
324 GAATGAT
* * * * **
1699 GAATATAAATATTTCAATGAGTTTTGGCGCAAAAAATCATGCAAAACTGAGCCGGGGCCTTGGAA
1 GAATATAGATAATTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCC-GGGCCCCGGAA
* * * *
1764 CGCGTTTTCAACCAAGAATCGCGATGGTTAGTTCACGA-TACGGCAAAAA--TTG--------G-
65 CGCGTTTTCAGCCAAGAATCGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCAAAAATTGA
* * * *
1817 CCCGAAAGATTATTCCTCAATTTTTAACCGAAATAGTCTTAAAAAATATATAATTCAACGCCAAA
130 CCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCATAAAAAATATATAATTCAACGCCAAA
** * * *
1882 AAGATTGAAGTTCTTTGCACGCCTCTAATATCTATTTTTTTAATTTTT-CGAATTAATTTCCGAA
195 AAGATTGAAGGGCTTTGCACGCTTCTAATATC-ATTTTTTTTATTTTTCCGAATTAATTTCCGAT
* * * *
1946 TAAATTGAAATATGATTCAAATACTCGTAAAATC-AATCATTAAATCCAACATGGCTGAGATTTG
259 TAAATCGAAACATGATTCAAATGCTCGTAAAATCAAATCCTTAAATCCAACATGGCTGAGATTTG
2010 GAATGAT
324 GAATGAT
* *
2017 GAATATAGATAAATCAATGAGTCCTAGG-GACCAAAAATCAT
1 GAATATAGATAATTCAATGAGT-CTTGGCG-CCAAAAATCAT
Statistics
Matches: 1148, Mismatches: 172, Indels: 69
0.83 0.12 0.05
Matches are distributed among these distances:
318 172 0.15
319 37 0.03
327 3 0.00
328 94 0.08
329 250 0.22
330 194 0.17
331 216 0.19
332 170 0.15
333 12 0.01
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (330 bp):
GAATATAGATAATTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGCCCCGGAAC
GCGTTTTCAGCCAAGAATCGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCAAAAATTGAC
CCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCATAAAAAATATATAATTCAACGCCAAAA
AGATTGAAGGGCTTTGCACGCTTCTAATATCATTTTTTTTATTTTTCCGAATTAATTTCCGATTA
AATCGAAACATGATTCAAATGCTCGTAAAATCAAATCCTTAAATCCAACATGGCTGAGATTTGGA
ATGAT
Done.