Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009931.1 Corchorus capsularis cultivar CVL-1 contig09952, 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: 6005
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30
Found at i:4421 original size:2 final size:2
Alignment explanation
Indices: 4416--4444 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4406 TGTGTGTGTG
4416 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4445 GTAGTTGTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5961 original size:333 final size:333
Alignment explanation
Indices: 4600--6005 Score: 1841
Period size: 322 Copynumber: 4.3 Consensus size: 333
4590 ATCTAACAGT
* * *
4600 TCACGGTTTTTGGCTAAAAACGCGTTTTGGGGCCCCGGCTCAATTTCGAATGATTTTTGGCACCG
1 TCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAATTTTGCATGATTTTTGGCACCG
* *
4665 AGACTCCTTGAATTATCTATATTCATCTAACCAA-ATCTCAGTCACATTGGATTT-AGGCATTTC
66 AGACACCTTCAATTATCTATATTCATCTAACCAATA-CTCAGTCACATTGGATTTAAGG-ATTTC
* *
4728 TTTTTACGAGCTTCTGAATCTTATTTTGATTTAATTAAAAATTAATTC--ATAAAAATAAGAAAA
129 TTTTTACGAGCTTCTGAATCTTATTTCGATTTAATTAAAAATTAATTCAGAAAAAAATAAG-AAA
*
4791 ACGATATTAGAAGCGTGAAAAACTCTTCAATATTTTTGGTGTTAAATTATAGATTTATTATGAGT
193 ACGATATTAGAAGCGTGAAAAACTCTTCAATATTTTTGGTGTTAAATTATAGATTTTTTATGAGT
* *
4856 GTTGTGGCCAAAAATTCAGGACAAA-ATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATT
258 GTTGTGGCCAAAAATTCA-GAAAAATATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATC
4920 ATGTACTAACCA
322 ATGTACTAACCA
** * * * *
4932 TCACCTTTTTTTGGCTAAAAACGCGTTTACAGGGTCCCGGCTCAATTTTGCATGATTCTTGGCGC
1 TCA-CGGTTTTTGGCTAAAAACGCGTTT-CGGGGCCCCGGCTCAATTTTGCATGATTTTTGGCAC
* * * ** *
4997 CCAG--A-C-TCGAAATATCTATATTCATCTAACCAATTCTTGGTCACATTGGATTTAAGAATTT
64 CGAGACACCTTC-AATTATCTATATTCATCTAACCAATACTCAGTCACATTGGATTTAAGGATTT
* * **
5058 CTTGTTACGAGCTTCTGGATCTTATTTTTATTTAATTAAAAATTAATTCAG----AAA-AA-AAA
128 CTTTTTACGAGCTTCTGAATCTTATTTCGATTTAATTAAAAATTAATTCAGAAAAAAATAAGAAA
* * * *
5117 ACGATATTAGTAGCGTAAAAAACTCTTCAA-ATTTTTTTGTGTTAAATTATAGAGTTTTTATGAG
193 ACGATATTAGAAGCGTGAAAAACTCTTCAATA-TTTTTGGTGTTAAATTATAGATTTTTTATGAG
* * * * *
5181 TGTTGTGGCCAAACATTCAGGAAAATA-TTTTCGAGTCAATTTTTTCAAAATTTAAGCCGAAATC
257 TGTTGTGGCCAAAAATTCAGAAAAATATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATC
*
5245 ATGTACTAACTA
322 ATGTACTAACCA
* * * * * *
5257 TCACGATTTTTGGCTAAAAATGCATTTTGGGGCCCTGGCTCAATTTTGCATGATTTTTGGCGCCG
1 TCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAATTTTGCATGATTTTTGGCACCG
* * * *
5322 AGACACCTTCAATTATCTATATTCATCTAAGCAACT-CTCAGTCACATTGCATTGAATGATTTCT
66 AGACACCTTCAATTATCTATATTCATCTAACCAA-TACTCAGTCACATTGGATTTAAGGATTTCT
*
5386 TTTTACGAGCTTCTGAATCTTATTTCG------------ATTAATTCAGAAAAAAATAAGAAAAT
130 TTTTACGAGCTTCTGAATCTTATTTCGATTTAATTAAAAATTAATTCAGAAAAAAATAAGAAAAC
* * *
5439 GATATTAGAAGCTTGAATAACTCTTCAATATTTTTGGTGTTAAATTATAGATATTTTATGAGTGT
195 GATATTAGAAGCGTGAAAAACTCTTCAATATTTTTGGTGTTAAATTATAGATTTTTTATGAGTGT
* * * *
5504 TGTGGCCAAAAAATTGAGAAAAATATTGTTCGGGTCAATATTTGCAAAATTTTAGCCGAAATCTT
260 TGTGGCC-AAAAATTCAGAAAAATATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCAT
5569 GTACTAACCA
324 GTACTAACCA
* * *
5579 TCACGGCTTTTGGCTAAAAACGCGTTTTGGGG-CCCGGCTCACCTTTTGCATGATTTTTGGCACC
1 TCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCA-ATTTTGCATGATTTTTGGCACC
5643 GAGACACCTTCAATTATCTATATTCATCTAACCAATACTCAGTCACATTGGATTTAAGGATTTCT
65 GAGACACCTTCAATTATCTATATTCATCTAACCAATACTCAGTCACATTGGATTTAAGGATTTCT
* * *
5708 TTTTACGAGCTTCTGAATCTTATTTCGATTTAATTAAAACTTAATTCAGAAAAAAATAAGGAAAT
130 TTTTACGAGCTTCTGAATCTTATTTCGATTTAATTAAAAATTAATTCAGAAAAAAATAAGAAAAC
* *
5773 GATATTAGAAG-GTTGAAAAACTTTTCGATATTTTTGGTGTTAAATTATAGATTTTTTATGAGTG
195 GATATTAGAAGCG-TGAAAAACTCTTCAATATTTTTGGTGTTAAATTATAGATTTTTTATGAGTG
* *
5837 TTGTGGCCAAAAATTGAGAAAAATATTTTTCGGGTCAATTTTTGCAAACTTTTAGCCGAAATCAT
259 TTGTGGCCAAAAATTCAGAAAAATATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCAT
5902 GTACTAACCA
324 GTACTAACCA
* * *
5912 TCACGGTTTTTGGCTAAAAACGGGTTTCCGGGCCCCGGCTTAATTTTGCATGATTTTTGGCACCG
1 TCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAATTTTGCATGATTTTTGGCACCG
* * * *
5977 AGCCATCTTGAATTATCGATATTCATCTA
66 AGACACCTTCAATTATCTATATTCATCTA
Statistics
Matches: 930, Mismatches: 105, Indels: 77
0.84 0.09 0.07
Matches are distributed among these distances:
314 10 0.01
318 3 0.00
319 2 0.00
320 67 0.07
321 24 0.03
322 176 0.19
323 34 0.04
324 20 0.02
325 53 0.06
326 147 0.16
327 3 0.00
328 2 0.00
329 3 0.00
330 1 0.00
331 90 0.10
332 5 0.01
333 160 0.17
334 130 0.14
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (333 bp):
TCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAATTTTGCATGATTTTTGGCACCG
AGACACCTTCAATTATCTATATTCATCTAACCAATACTCAGTCACATTGGATTTAAGGATTTCTT
TTTACGAGCTTCTGAATCTTATTTCGATTTAATTAAAAATTAATTCAGAAAAAAATAAGAAAACG
ATATTAGAAGCGTGAAAAACTCTTCAATATTTTTGGTGTTAAATTATAGATTTTTTATGAGTGTT
GTGGCCAAAAATTCAGAAAAATATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGT
ACTAACCA
Done.