Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011985.1 Corchorus capsularis cultivar CVL-1 contig12006, 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: 4218
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Found at i:3505 original size:333 final size:326
Alignment explanation
Indices: 2836--4209 Score: 1301
Period size: 332 Copynumber: 4.1 Consensus size: 326
2826 GGATTTAAGA
* * * *
2836 ATTTGTTTTTACGAGCATCTCAATCCGGTTTCGATTTAATTAGT-AATTAATTTGGAAAACAATA
1 ATTTGTTTTTACGAGCATCTCAATCAGGTTTCAATTTAATTA-TAAAGTAATTCGG-AAA-AATA
* * * * * * *
2900 GGAAAAACAATATTAG-AGATGTGAGAAGTCCTTCAATTTTTTTGGCATT-AAGTTATAT-A-TT
63 GGAAACA-AATATTAGAAG-CGTGAAAAGTCTTTCAA-TCTTTTGGCGTTGGA-TTATATAAGTT
** ** * * * * * *
2961 TTTTTGAGTAT-TGTGGCAAAAAATTGAGAAGAAATTTTTCGGGTCAATTTTTTGCAAATTTTAG
124 TTTAAGAGT-TCCATGGCCAAAAATT-AG-GGAAAATTTTCGGGT-AAATTTTTGTAAAATTTAG
* * * ** * * * *
3025 CTGAATTCGTGTACAAACCATCACAATTTTT-GACTAAAAACGCGTTCCGGAG-CCTCGGCTCTG
185 CAGAAATCGTGTACTAACCATCACGGTTTTTAG-CTAAAAATGCGTTTCGG-GTCC-CTGCTCAG
* * * *
3088 TTTTGCATGATTTTTGGCGCCATGTCTCATTGAAATATTTATATCCATCTAACCAAAACTCAACC
247 TTTTGCATGATTTTTAGCGCCAAGTCTCATTGAAATATCTATATCCATCTAAACAAAACTCAACC
* *
3153 ACATTGGATTTAAGG
312 ACATTGCATTTAGGG
* *
3168 ATTTGTTTTTACGAGCATCTGAATCATGTTTCAATTTAATTATAAAGTAATTCGGAAATAATAGG
1 ATTTGTTTTTACGAGCATCTCAATCAGGTTTCAATTTAATTATAAAGTAATTCGGAAA-AATAGG
3233 AAATCAAATATTAGAAGCGTGAAAAGTCTTTCAATCTTTTGGACGTTGGATTATATAAGTTTTTA
65 AAA-CAAATATTAGAAGCGTGAAAAGTCTTTCAATCTTTTGG-CGTTGGATTATATAAGTTTTTA
*
3298 TGAGTTCCATGGCCAAAAATTAGGGAAAATTCTTCCGGGTAAATTTTTGTAAAATTTAGCAGAAA
128 AGAGTTCCATGGCCAAAAATTAGGGAAAATT-TT-CGGGTAAATTTTTGTAAAATTTAGCAGAAA
* *
3363 TCGTGTACTAACCATCACGGTTTTTAGCTAAAAATTGCGTTTCGAGGTCCCTACTCAGTTTCGCA
191 TCGTGTACTAACCATCACGGTTTTTAGCTAAAAA-TGCGTTTCG-GGTCCCTGCTCAGTTTTGCA
* * * ** *
3428 TGATTTTTAGCGCCAAGAT-TTATTGAAATATCTATATTCATCTAAAGAAATTTCAGCCACATTG
254 TGATTTTTAGCGCCAAG-TCTCATTGAAATATCTATATCCATCTAAACAAAACTCAACCACATTG
3492 CATTTAGGG
318 CATTTAGGG
* * * *
3501 ATTTGTTTTTACGAGCAT-TCCAATCCGGTTTCGATTTAATTAGT-AATTAATTTGGAAAAAAAT
1 ATTTGTTTTTACGAGCATCT-CAATCAGGTTTCAATTTAATTA-TAAAGTAATTCGG--AAAAAT
** * * * * * * *
3564 AGGAAA-AATGATATTAGAAATGAGAGAAGCCCTTCAATTTTTTTGGCATT-GAGTTATATATAT
62 AGGAAACAA--ATATTAGAAGCGTGAAAAGTCTTTCAA-TCTTTTGGCGTTGGA-TTATATA-AG
** * * * * *
3627 TTTTTGGGAGTAT--AGTGGCAAAAAATTGATGAGAAAATTTTCAGGTCAATTTTTTGCAAAATT
122 TTTTTAAGAGT-TCCA-TGGCCAAAAATT-A-GGGAAAATTTTCGGGT-AAATTTTTGTAAAA-T
* * * * * *
3690 TTAGCTGAAATCGTGTAC-AACCATCACGATTTTT-GACTAAAAACGCGTTCCGGGGCCCTGGTT
181 TTAGCAGAAATCGTGTACTAACCATCACGGTTTTTAG-CTAAAAATGCGTTTCGGGTCCCT-GCT
* * * * *
3753 CTGTTTTGCATGATTTTTGGCGCCATGTCTCATTGAAATATCTATATCCATATAACCAAAACTCA
244 CAGTTTTGCATGATTTTTAGCGCCAAGTCTCATTGAAATATCTATATCCATCTAAACAAAACTCA
*
3818 ACCACATTGGATTT-GAGG
309 ACCACATTGCATTTAG-GG
* * * * *
3836 ATTTGTTTCTACGAGCATCTGAATCATGTTTCAATTTAAGTATAAAGTAATTCAGAAAAATAGGA
1 ATTTGTTTTTACGAGCATCTCAATCAGGTTTCAATTTAATTATAAAGTAATTCGGAAAAATAGGA
* * * *
3901 GAACAGATATTAGAAGCGTGAAAATTCTTTCAATCTTTTTGGCGTTGAATTATATAGGTTTTTAA
66 -AACAAATATTAGAAGCGTGAAAAGTCTTTCAATC-TTTTGGCGTTGGATTATATAAGTTTTTAA
*
3966 GAGTTCCATGGCCAAAAATTAGGGAAAATGATTTCGGGTAAATTTTTGTAAAAATTTAGCAGAGA
129 GAGTTCCATGGCCAAAAATTAGGGAAAAT--TTTCGGGTAAATTTTTGT-AAAATTTAGCAGAAA
* *
4031 TCGTGTACTAACCATCACGGTTTTTAGTTAAAAATGCGTTTCGGGGTCCCGGCTCAGTTTTGCAT
191 TCGTGTACTAACCATCACGGTTTTTAGCTAAAAATGCGTTTC-GGGTCCCTGCTCAGTTTTGCAT
* * ** *
4096 GATTTTTAGCGCCAAGATC-CATTGAAATATCTATATTCATCTAAAGAAATTTCAACCACATTTC
255 GATTTTTAGCGCCAAG-TCTCATTGAAATATCTATATCCATCTAAACAAAACTCAACCACATTGC
4160 ATTTAGGG
319 ATTTAGGG
* * *
4168 ATTTGTTTTTACGAGCATTTCAATCCGGTTTCGATTTAATTA
1 ATTTGTTTTTACGAGCATCTCAATCAGGTTTCAATTTAATTA
4210 GTAATTAAT
Statistics
Matches: 848, Mismatches: 144, Indels: 100
0.78 0.13 0.09
Matches are distributed among these distances:
330 14 0.02
331 77 0.09
332 272 0.32
333 209 0.25
334 58 0.07
335 153 0.18
336 39 0.05
337 26 0.03
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (326 bp):
ATTTGTTTTTACGAGCATCTCAATCAGGTTTCAATTTAATTATAAAGTAATTCGGAAAAATAGGA
AACAAATATTAGAAGCGTGAAAAGTCTTTCAATCTTTTGGCGTTGGATTATATAAGTTTTTAAGA
GTTCCATGGCCAAAAATTAGGGAAAATTTTCGGGTAAATTTTTGTAAAATTTAGCAGAAATCGTG
TACTAACCATCACGGTTTTTAGCTAAAAATGCGTTTCGGGTCCCTGCTCAGTTTTGCATGATTTT
TAGCGCCAAGTCTCATTGAAATATCTATATCCATCTAAACAAAACTCAACCACATTGCATTTAGG
G
Found at i:4211 original size:667 final size:665
Alignment explanation
Indices: 2836--4218 Score: 2276
Period size: 668 Copynumber: 2.1 Consensus size: 665
2826 GGATTTAAGA
* *
2836 ATTTGTTTTTACGAGCATCTCAATCCGGTTTCGATTTAATTAGTAATTAATTTGGAAAACAATAG
1 ATTTGTTTTTACGAGCATTTCAATCCGGTTTCGATTTAATTAGTAATTAATTTGGAAAAAAATAG
* * *
2901 GAAAAACAATATTAGAGATGTGAGAAGTCCTTCAATTTTTTTGGCATTAAGTTATATATTTTTTT
66 GAAAAACAATATTAGAAATGAGAGAAGCCCTTCAATTTTTTTGGCATTAAGTTATATATTTTTTT
* * * *
2966 GAGTATTGTGGCAAAAAATTGAGAAGAAATTTTTCGGGTCAATTTTTTGCAAATTTTAGCTGAAT
131 GAGTATAGTGGCAAAAAATTGAGAAGAAAATTTTCAGGTCAATTTTTTGCAAATTTTAGCTGAAA
3031 TCGTGTACAAACCATCACAATTTTTGACTAAAAACGCGTTCCGGAGCCTCGGCTCTGTTTTGCAT
196 TCGTGTACAAACCATCACAATTTTTGACTAAAAACGCGTTCCGGAGCCTCGGCTCTGTTTTGCAT
* *
3096 GATTTTTGGCGCCATGTCTCATTGAAATATTTATATCCATCTAACCAAAACTCAACCACATTGGA
261 GATTTTTGGCGCCATGTCTCATTGAAATATCTATATCCATATAACCAAAACTCAACCACATTGGA
* * *
3161 TTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCAATTTAATTATAAAGTAATTCGGAAA
326 TTTAAGGATTTGTTTCTACGAGCATCTGAATCATGTTTCAATTTAAGTATAAAGTAATTCAGAAA
*
3226 TAATAGGAAATCAAATATTAGAAGCGTGAAAAGTCTTTCAATCTTTTGGACGTTGGATTATATAA
391 TAATAGGAAATCAAATATTAGAAGCGTGAAAAGTCTTTCAATCTTTTGGACGTTGAATTATATAA
* **
3291 GTTTTTATGAGTTCCATGGCCAAAAATTAGGGAAAATTCTTCCGGGTAAATTTTTGTAAAATTTA
456 GTTTTTAAGAGTTCCATGGCCAAAAATTAGGGAAAATGATTCCGGGTAAATTTTTGTAAAATTTA
*
3356 GCAGAAATCGTGTACTAACCATCACGGTTTTTAGCTAAAAATTGCGTTTCGAGGTCCCTACTCAG
521 GCAGAAATCGTGTACTAACCATCACGGTTTTTAGCTAAAAATTGCGTTTCGAGGTCCCGACTCAG
** *
3421 TTTCGCATGATTTTTAGCGCCAAGATTTATTGAAATATCTATATTCATCTAAAGAAATTTCAGCC
586 TTTCGCATGATTTTTAGCGCCAAGATCCATTGAAATATCTATATTCATCTAAAGAAATTTCAACC
3486 ACATTGCATTTAGGG
651 ACATTGCATTTAGGG
*
3501 ATTTGTTTTTACGAGCATTCCAATCCGGTTTCGATTTAATTAGTAATTAATTTGGAAAAAAATAG
1 ATTTGTTTTTACGAGCATTTCAATCCGGTTTCGATTTAATTAGTAATTAATTTGGAAAAAAATAG
** *
3566 GAAAAATGATATTAGAAATGAGAGAAGCCCTTCAATTTTTTTGGCATTGAGTTATATATATTTTT
66 GAAAAACAATATTAGAAATGAGAGAAGCCCTTCAATTTTTTTGGCATTAAGTTATATAT-TTTTT
3631 TGGGAGTATAGTGGCAAAAAATTGATG-AGAAAATTTTCAGGTCAATTTTTTGCAAAATTTTAGC
130 T--GAGTATAGTGGCAAAAAATTGA-GAAGAAAATTTTCAGGTCAATTTTTTGC-AAATTTTAGC
* * *
3695 TGAAATCGTGTAC-AACCATCACGATTTTTGACTAAAAACGCGTTCCGGGGCC-CTGGTTCTGTT
191 TGAAATCGTGTACAAACCATCACAATTTTTGACTAAAAACGCGTTCCGGAGCCTC-GGCTCTGTT
3758 TTGCATGATTTTTGGCGCCATGTCTCATTGAAATATCTATATCCATATAACCAAAACTCAACCAC
255 TTGCATGATTTTTGGCGCCATGTCTCATTGAAATATCTATATCCATATAACCAAAACTCAACCAC
*
3823 ATTGGATTTGAGGATTTGTTTCTACGAGCATCTGAATCATGTTTCAATTTAAGTATAAAGTAATT
320 ATTGGATTTAAGGATTTGTTTCTACGAGCATCTGAATCATGTTTCAATTTAAGTATAAAGTAATT
* *
3888 CAGAAA-AATAGGAGAA-CAGATATTAGAAGCGTGAAAATTCTTTCAATCTTTTTGG-CGTTGAA
385 CAGAAATAATAGGA-AATCAAATATTAGAAGCGTGAAAAGTCTTTCAATC-TTTTGGACGTTGAA
* *
3950 TTATATAGGTTTTTAAGAGTTCCATGGCCAAAAATTAGGGAAAATGATTTCGGGTAAATTTTTGT
448 TTATATAAGTTTTTAAGAGTTCCATGGCCAAAAATTAGGGAAAATGATTCCGGGTAAATTTTTGT
* * *
4015 AAAAATTTAGCAGAGATCGTGTACTAACCATCACGGTTTTTAGTTAAAAA-TGCGTTTCGGGGTC
513 -AAAATTTAGCAGAAATCGTGTACTAACCATCACGGTTTTTAGCTAAAAATTGCGTTTCGAGGTC
* *
4079 CCGGCTCAGTTTTGCATGATTTTTAGCGCCAAGATCCATTGAAATATCTATATTCATCTAAAGAA
577 CCGACTCAGTTTCGCATGATTTTTAGCGCCAAGATCCATTGAAATATCTATATTCATCTAAAGAA
*
4144 ATTTCAACCACATTTCATTTAGGG
642 ATTTCAACCACATTGCATTTAGGG
4168 ATTTGTTTTTACGAGCATTTCAATCCGGTTTCGATTTAATTAGTAATTAAT
1 ATTTGTTTTTACGAGCATTTCAATCCGGTTTCGATTTAATTAGTAATTAAT
Statistics
Matches: 668, Mismatches: 41, Indels: 16
0.92 0.06 0.02
Matches are distributed among these distances:
665 115 0.17
666 6 0.01
667 249 0.37
668 275 0.41
669 23 0.03
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.36
Consensus pattern (665 bp):
ATTTGTTTTTACGAGCATTTCAATCCGGTTTCGATTTAATTAGTAATTAATTTGGAAAAAAATAG
GAAAAACAATATTAGAAATGAGAGAAGCCCTTCAATTTTTTTGGCATTAAGTTATATATTTTTTT
GAGTATAGTGGCAAAAAATTGAGAAGAAAATTTTCAGGTCAATTTTTTGCAAATTTTAGCTGAAA
TCGTGTACAAACCATCACAATTTTTGACTAAAAACGCGTTCCGGAGCCTCGGCTCTGTTTTGCAT
GATTTTTGGCGCCATGTCTCATTGAAATATCTATATCCATATAACCAAAACTCAACCACATTGGA
TTTAAGGATTTGTTTCTACGAGCATCTGAATCATGTTTCAATTTAAGTATAAAGTAATTCAGAAA
TAATAGGAAATCAAATATTAGAAGCGTGAAAAGTCTTTCAATCTTTTGGACGTTGAATTATATAA
GTTTTTAAGAGTTCCATGGCCAAAAATTAGGGAAAATGATTCCGGGTAAATTTTTGTAAAATTTA
GCAGAAATCGTGTACTAACCATCACGGTTTTTAGCTAAAAATTGCGTTTCGAGGTCCCGACTCAG
TTTCGCATGATTTTTAGCGCCAAGATCCATTGAAATATCTATATTCATCTAAAGAAATTTCAACC
ACATTGCATTTAGGG
Done.