Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020843.1 Corchorus olitorius cultivar O-4 contig20876, 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: 4880
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Found at i:3653 original size:17 final size:17
Alignment explanation
Indices: 3616--3657 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
3606 TACCCTTTTT
*
3616 TAATTTTTAATTGCTTA
1 TAATTTTTAATTGCTAA
3633 -AATTTTTAATT-CTGAA
1 TAATTTTTAATTGCT-AA
3649 TAATTTTTA
1 TAATTTTTA
3658 TTTACTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 2 0.09
16 12 0.55
17 8 0.36
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (17 bp):
TAATTTTTAATTGCTAA
Found at i:4807 original size:330 final size:330
Alignment explanation
Indices: 3896--4879 Score: 1540
Period size: 334 Copynumber: 3.0 Consensus size: 330
3886 TCATTTAGCC
* * * * *
3896 CAAGAAACCGTGATGGTTAGTACACGATTTCAGCTCAATTTTTGTAAAAACTGATCCGAAATTTT
1 CAAGAAATCGTGATGGTTAGTACACGATTTCAGCTGAAATTTTGCAAAAACTAATCCGAAATTTT
* * * *
3961 TTTTCTAAATTTTTGTG-CCCAATACTCATAAAAAAATATAATTCAACGCCAAAAAGATTTAAGG
66 TTTTCTAAA-TTTTG-GCCCCAATACTCATAAAAATATATAATCCAGCGCTAAAAAGATTTAAGG
* * *
4025 GCTTTTCATACTTCAAATATGGTTTTTCCTTTTTTTATCGAATTAATTTCTGACAAAACCGAATG
129 GCTTTTCATACTTCAAATATGGTTTTTCCTTTTTTTATCCAATTAATTTATGATAAAACCGAATG
* *
4090 AAGATTTAGATGCTCGTAAAAACGTATCCTTAAATCCATTGTAGCTGAGATTTGATTAGATTAAT
194 AAGATTTAGATGCTCGTAAAAACATATCCTTAAATCCATTGTAGCTGAGATTTGATTAGATTCAT
* * *
4155 ATAGATATTTCAAGGAGTTTTGATGCCAAAAATCTAGCAAAACTGAGCCGGGGCCCCGGAACGCG
259 ATAGATATTTCAAGGAGTCTCGACGCCAAAAATCTAGCAAAACTGAGCCGGGGCCCCGGAACGCG
4220 TTTTCAG
324 TTTTCAG
* * *
4227 CAAGAAATCGTGATGGTTAGTGCACGATTTCAGCTGAAATTTTGCAAAAACTTATCTGAAATTTT
1 CAAGAAATCGTGATGGTTAGTACACGATTTCAGCTGAAATTTTGCAAAAACTAATCCGAAATTTT
* * * *
4292 TTTTTTCAATTTTTGGCCACAATACTCATAAAAAATATATAATCTAGCGCTAAAAAGATTTAAGG
66 TTTTCT-AAATTTTGGCCCCAATACTCAT-AAAAATATATAATCCAGCGCTAAAAAGATTTAAGG
* * * *
4357 GCTTTTCATGCTTCAAATATGGTATTTCCTCTTTTTTTATCCAATTAATTTTTGATAAAACCGGA
129 GCTTTTCATACTTCAAATATGGT-TTTTC-CTTTTTTTATCCAATTAATTTATGATAAAACCGAA
* **
4422 TGAAGATTTCGATGCTCGTAAAAACATATCCTTAAATCCATTGTAAATGAGATTTGATTAGATTC
192 TGAAGATTTAGATGCTCGTAAAAACATATCCTTAAATCCATTGTAGCTGAGATTTGATTAGATTC
*
4487 ATATAGATATTTCAAGGAGTCTCGACGCAAAAAATCTAGCAAAACTGAGCCGGGGCCCCGGAACG
257 ATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCTAGCAAAACTGAGCCGGGGCCCCGGAACG
4552 CGTTTTCA-
322 CGTTTTCAG
* *
4560 CAAGAAATCGTGATAGTTAGTACACGATTTCAGTTGAAATTTTGCAAAAACTAATCCGAAATTTT
1 CAAGAAATCGTGATGGTTAGTACACGATTTCAGCTGAAATTTTGCAAAAACTAATCCGAAATTTT
*
4625 TTCTCTAAATTTTGGCCCCAATACTCATAGAAAATATATAATCCAGCGCTAAAAAGATTTAAGGG
66 TTTTCTAAATTTTGGCCCCAATACTCATA-AAAATATATAATCCAGCGCTAAAAAGATTTAAGGG
*
4690 CTTTTCATTCTTCAAATATGGTTTTTCCTTTTTTTATCCAATTAATTTATGATAAAACCGAATGA
130 CTTTTCATACTTCAAATATGGTTTTTCCTTTTTTTATCCAATTAATTTATGATAAAACCGAATGA
* *
4755 AGATTTGGATGCTCGTAAAAACATATCCTTAAATCCATTGTAGCTAAGATTTGATTAGATTCATA
195 AGATTTAGATGCTCGTAAAAACATATCCTTAAATCCATTGTAGCTGAGATTTGATTAGATTCATA
*
4820 TAGATATTTCAAGGAGTCTCGACGCCAAAAATCTAGCAAAACTGAGCCGGGGCCCTGGAA
260 TAGATATTTCAAGGAGTCTCGACGCCAAAAATCTAGCAAAACTGAGCCGGGGCCCCGGAA
4880 A
Statistics
Matches: 597, Mismatches: 50, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
330 156 0.26
331 84 0.14
332 129 0.22
333 68 0.11
334 160 0.27
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (330 bp):
CAAGAAATCGTGATGGTTAGTACACGATTTCAGCTGAAATTTTGCAAAAACTAATCCGAAATTTT
TTTTCTAAATTTTGGCCCCAATACTCATAAAAATATATAATCCAGCGCTAAAAAGATTTAAGGGC
TTTTCATACTTCAAATATGGTTTTTCCTTTTTTTATCCAATTAATTTATGATAAAACCGAATGAA
GATTTAGATGCTCGTAAAAACATATCCTTAAATCCATTGTAGCTGAGATTTGATTAGATTCATAT
AGATATTTCAAGGAGTCTCGACGCCAAAAATCTAGCAAAACTGAGCCGGGGCCCCGGAACGCGTT
TTCAG
Done.