Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011061.1 Corchorus capsularis cultivar CVL-1 contig11082, 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: 2095
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Found at i:660 original size:323 final size:319
Alignment explanation
Indices: 1--1827 Score: 2229
Period size: 323 Copynumber: 5.6 Consensus size: 319
* * * * *
1 GCATTCTATTTAACGATTTGGTTCTACGAGAATCTGAATCTTCTTTCGATTTAATTAGAAATAAA
1 GCATTCAATTTAACGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * * * *
66 TTCAGAAAAAAAAAACTTGAAAAACGATATTAAAAGCGTGAAAAAACCCTTCTATCTTTTTTGTG
66 TTCAG----AAAAAACTGGAAAAACGATATTAGAAGCGTG-AAAAACCCTTCAATCTTTTTGGCG
* * * * * *
131 TTGAATTACATATTTTATCTGAGTATTCCTGCAAAAAATTGAGAAAAAAAATTTCCGATCAGATT
126 TTGAATTATATATTTTTTCTGAGTATTCTTGCAAAAAATTGAG-AAAAAAATTTTCGGTCAGTTT
*
196 TTAGCAGAAATCGTG---T-A-CATCACGGTTTTTTTGCTAAAAACGCGTTCCGGGGCTCAGCTC
190 TTAGCAGAAATCGTGTACTAACCATCACGG-TTTTTTGCTAAAAACGCGTTCCGGGGCCCAGCTC
* * * *
256 AGTTTTGCTTGATTTTTTGCGTAAAAACTGTTTGAAATATCTATATAGATCCAACAAAATCCCAA
254 AGTTTTGCTTGATTTTTTGCGTAAAGACTGTTTGAAATATTTAT-TAAATCCAACCAAATCCCAA
321 CC
318 CC
* *
323 GCTTTCAATTTAACGATTTGTTTTTACGAGAATCTTAATCTTGTTTCGATTTAATTAGAAATTAA
1 GCATTCAATTTAACGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* *
388 TTCAGAAAAAACTGGAAAAACGATATTAGAATCTTGAAAAACCCTTCAATCTTTTTGGCGTTGAA
66 TTCAGAAAAAACTGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAA
453 TTATATATTTTTTCTGAGTATTCTTGCAAAAAATTGAGGAAAAAAATTTTACGGTCAGTTTTTAG
131 TTATATATTTTTTCTGAGTATTCTTGCAAAAAATTGA-GAAAAAAATTTT-CGGTCAGTTTTTAG
*
518 CAGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAATGCGTTCCGGGGTCCCAGCTCAGTT
194 CAGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGG-CCCAGCTCAGTT
*
583 TTGCTTGATTTTTTGTGTAAAGACTGTTTGAAATATTTATGTAAATCCAACCAAATCCCAACC
258 TTGCTTGATTTTTTGCGTAAAGACTGTTTGAAATATTTAT-TAAATCCAACCAAATCCCAACC
* * * *
646 GCATTCGATTTAACGAATTGTTTTTACAAGAGTCTGAATCTTGTTTCGATTTAATTAGAAATTAA
1 GCATTCAATTTAACGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
** *
711 TTTCAGAAAAAACTGGAAAAACGATATTAGAAGAATGAAAAAAACCCTTAAATCTTTTTGGCGTT
66 -TTCAGAAAAAACTGGAAAAACGATATTAGAAGCGTG--AAAAACCCTTCAATCTTTTTGGCGTT
* * *
776 GAATTATATATTTTTTCTGAGTATTCTTGCAAAAGATTGAGAAAAAAGTTTTCGGGTCAATTTTT
128 GAATTATATATTTTTTCTGAGTATTCTTGCAAAAAATTGAGAAAAAAATTTTC-GGTC-AGTTTT
* * * * * *
841 TAACAGAAAATCGTGTACTAACCATCAC-GTTTTTGGCTAAAAACGCGTTCTGAGGCCTTAACTC
191 TAGCAG-AAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCC-CAGCTC
* * * *
905 TA-ATTTGCTTGATTTTTTGCGTAAAGACTGTGTGAAATATCTATATTATATTCCTGAACAAAAT
254 -AGTTTTGCTTGATTTTTTGCGTAAAGACTGTTTGAAATAT-T-TATTA-AATCC--AACCAAAT
969 CCCAACC
313 CCCAACC
** * *
976 ATATTCAATTAAACGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAAATAGAAATTAA
1 GCATTCAATTTAACGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * * *
1041 TTCAAAAAAAAACTGGAAAAACGATATTAAAAGCGTGAAAAACCCTTGAATCTTTTTCGCGTTGA
66 TTC-AGAAAAAACTGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTG-
* * * * *
1106 AATTACATATTTTAATCTGAGTATTCCTGCAAAAAATTGAAAAAAAAAATTTTCCGGTCTGTTTT
129 AATTATATATTTT-TTCTGAGTATTCTTGCAAAAAATTG-AGAAAAAAATTTT-CGGTCAGTTTT
* * * * *
1171 TAGCAAAAATCGTGTAC-AATCATCACGGTTTTTGGCTAAAAACGCGTTCCAGGGCCTCGGCTCA
191 TAGCAGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCC-CAGCTCA
* ** * * * *
1235 GTTTTGCTTAATTTTTTGCGTAAAGACTGTTTGAAATATTTATATTGATCAAACCATATCCTAGC
255 GTTTTGCTTGATTTTTTGCGTAAAGACTGTTTGAAATATTTAT-TAAATCCAACCAAATCCCAAC
1300 C
319 C
* * *
1301 GCATTCATTTTAACGATTTGCTTTTACGAGATTTCT-AATCTTGTTTCGATTTAATTAGAAATTA
1 GCATTCAATTTAACGATTTGTTTTTACGAGA-ATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* *
1365 ATTCAGAAAAACACTGGAAAAACGATATTAGAAGCATGAAAAACCCTTCAATCTTTTTGGTGTTG
65 ATTCAGAAAAA-ACTGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTG
* ** * * *
1430 AATTATATATTTGTTCTGAGTATTCTTGCAAAAAATCAATAAAAAAAATTTCGGGTCAATTTTTA
129 AATTATATATTTTTTCTGAGTATTCTTGCAAAAAATTGAGAAAAAAATTTTC-GGTCAGTTTTTA
* * * ** *
1495 GCAGAAATCTTGTACTAACCATTACGGTTTTTTGCTAAAAACGCTTTCCGAGACCCCGGCTCAGT
193 GCAGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTCCG-GGGCCCAGCTCAGT
* * * * * *
1560 TTTGCTTGATTTTTGGCGTAAAGACTCTTTGAAATACTATATT-CATCGAACCAAAATCCCAGCC
257 TTTGCTTGATTTTTTGCGTAAAGACTGTTTGAAATA-TTTATTAAATCCAACC-AAATCCCAACC
** * * * *
1624 AAATTCGATTAAACGATTTTTTTTTTACGAGAA-CTTGAATCTTGTTTCGACTTAATTAGAAATT
1 GCATTCAATTTAACGA-TTTGTTTTTACGAGAATC-TGAATCTTGTTTCGATTTAATTAGAAATT
*
1688 AATTCAGAAAAAACTGGAAAAACGATATTAGAAGCGTGAAAATCCCGTT-AATCTTTTTGGCGTT
64 AATTCAGAAAAAACTGGAAAAACGATATTAGAAGCGTGAAAAACCC-TTCAATCTTTTTGGCGTT
* * * * *
1752 GAATTATAAATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGACAAGTTTTT
128 GAATTATATATTTTTTCTGAGTATTCTTGCAAAAAATTGAGAAAAAAATTTTCGGTC-AGTTTTT
1817 AGCAGAAATCG
192 AGCAGAAATCG
1828 CACAGTTTTT
Statistics
Matches: 1305, Mismatches: 159, Indels: 81
0.84 0.10 0.05
Matches are distributed among these distances:
317 70 0.05
318 51 0.04
321 2 0.00
322 134 0.10
323 355 0.27
324 111 0.09
325 133 0.10
326 139 0.11
327 30 0.02
328 43 0.03
329 91 0.07
330 130 0.10
331 15 0.01
332 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Consensus pattern (319 bp):
GCATTCAATTTAACGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
TTCAGAAAAAACTGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAA
TTATATATTTTTTCTGAGTATTCTTGCAAAAAATTGAGAAAAAAATTTTCGGTCAGTTTTTAGCA
GAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCAGCTCAGTTTTG
CTTGATTTTTTGCGTAAAGACTGTTTGAAATATTTATTAAATCCAACCAAATCCCAACC
Done.