Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019204.1 Corchorus olitorius cultivar O-4 contig19237, 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: 64194
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2705 original size:31 final size:31
Alignment explanation
Indices: 2639--2783 Score: 121
Period size: 31 Copynumber: 4.7 Consensus size: 31
2629 GCATGCCACG
* * *
2639 TGTCACTTTTTGGTACATGTGG-GATTACATG
1 TGTCACTTTTTGGTACACGTGGCG-TGACATA
* *
2670 TGTCACTTTTTGTTACACGTGGCGTGACAAA
1 TGTCACTTTTTGGTACACGTGGCGTGACATA
* * * * * **
2701 TGTCATTTTTTAGTGCACATGACGTGACACG
1 TGTCACTTTTTGGTACACGTGGCGTGACATA
* * *
2732 TGTCACTTTTTGGTAAACGTGGTGTGCCATA
1 TGTCACTTTTTGGTACACGTGGCGTGACATA
**
2763 TGTCACTTTTTAATACACGTG
1 TGTCACTTTTTGGTACACGTG
2784 ACATGTCATG
Statistics
Matches: 87, Mismatches: 26, Indels: 2
0.76 0.23 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (31 bp):
TGTCACTTTTTGGTACACGTGGCGTGACATA
Found at i:9467 original size:54 final size:54
Alignment explanation
Indices: 9381--9487 Score: 205
Period size: 54 Copynumber: 2.0 Consensus size: 54
9371 TTCCTTCAAA
*
9381 TTCAAATATACTTGCTTGTAAAGCAATGCACACCTTTGTCTAAATAATGATTTC
1 TTCAAATATACTTGCTTGTAAAGCAATACACACCTTTGTCTAAATAATGATTTC
9435 TTCAAATATACTTGCTTGTAAAGCAATACACACCTTTGTCTAAATAATGATTT
1 TTCAAATATACTTGCTTGTAAAGCAATACACACCTTTGTCTAAATAATGATTT
9488 TTTGTTCTTA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (54 bp):
TTCAAATATACTTGCTTGTAAAGCAATACACACCTTTGTCTAAATAATGATTTC
Found at i:25925 original size:115 final size:117
Alignment explanation
Indices: 25714--25948 Score: 420
Period size: 115 Copynumber: 2.0 Consensus size: 117
25704 TTATAATAGT
25714 GAAATCATAGATCCATTAACAGAATTTAAATGAACTTTAAGAAACATGAAAATGCAGTGAGATTG
1 GAAATCATAGATCCATTAACAGAATTTAAATGAACTTTAAGAAACATGAAAATGCAGTGAGATTG
25779 TATACCTTGAATTCGGCTATGTAAGCAAAAAAATGTTGCTTAATGTTACTAC
66 TATACCTTGAATTCGGCTATGTAAGCAAAAAAATGTTGCTTAATGTTACTAC
*
25831 GAAA-CATAGATCCATTAACAGAATTTAAATGAACTTTAA-AAACATGAAGATGCAGTGAGATTG
1 GAAATCATAGATCCATTAACAGAATTTAAATGAACTTTAAGAAACATGAAAATGCAGTGAGATTG
* **
25894 TATACCTTGAATTCGGCTATGTACGTGAAAAAATGTTGCTTAATGTTACTAC
66 TATACCTTGAATTCGGCTATGTAAGCAAAAAAATGTTGCTTAATGTTACTAC
25946 GAA
1 GAA
25949 CAGTCGAACA
Statistics
Matches: 114, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
115 75 0.66
116 35 0.31
117 4 0.04
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (117 bp):
GAAATCATAGATCCATTAACAGAATTTAAATGAACTTTAAGAAACATGAAAATGCAGTGAGATTG
TATACCTTGAATTCGGCTATGTAAGCAAAAAAATGTTGCTTAATGTTACTAC
Found at i:37717 original size:15 final size:15
Alignment explanation
Indices: 37697--37725 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
37687 GGGAATATCC
37697 TACTCTTCAGATGAG
1 TACTCTTCAGATGAG
37712 TACTCTTCAGATGA
1 TACTCTTCAGATGA
37726 AATAGGCGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (15 bp):
TACTCTTCAGATGAG
Found at i:46928 original size:2 final size:2
Alignment explanation
Indices: 46921--46956 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
46911 TTCCATGTGA
46921 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
46957 ATTTCCTTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:58944 original size:17 final size:17
Alignment explanation
Indices: 58924--58959 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
58914 TTGTTTTCGT
58924 TTTTCTGTTTT-TTTTTG
1 TTTT-TGTTTTATTTTTG
58941 TTTTTGTTTTATTTTTG
1 TTTTTGTTTTATTTTTG
58958 TT
1 TT
58960 GTGTTGTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.03, C:0.03, G:0.11, T:0.83
Consensus pattern (17 bp):
TTTTTGTTTTATTTTTG
Found at i:63238 original size:238 final size:237
Alignment explanation
Indices: 62804--63274 Score: 651
Period size: 238 Copynumber: 2.0 Consensus size: 237
62794 CTCGTAAAAT
* *
62804 CAAATCGTTAAATTGAATGTGGGATGGATTTGGTTCAATGAATATAGTCATTTCAAGGAGTCTTT
1 CAAATCGTTAAATTGAATGTGGGATGGATTTGGTTCAATGAATACAGTCATATCAAGGAGTCTTT
* * *
62869 GCGTCAAAATTCATGCAAAATTGATCCGAGGCTCCGGAACGCGTTTTGAGCCAAAAACCGTGATA
66 GCGTCAAAAATCATGCAAAATTGATCCGAGGCTCCGGAACGCGTTTTAAGCAAAAAACCGTGATA
* * **
62934 GTTTATACACGATTTCGACGAAAATTTTGCAAAAACTGACTCAAAAGGTTTTTCCTCAATTTTTT
131 GGTTATACACGATTTCGACGAAAATTTTGCAAAAACTGACCCAAAAACTTTTTCCTCAATTTTTT
* * *
62999 GCCACAATACTTAGAATAAATACATAATTCAATGCCAAATAAA
196 GCCACAATACTCAGAA-AAATACATAAGTCAACGCCAAATAAA
* * *
63042 CAAATCGTTAAATTGAATTTGGGTTGGATTTGGTTCGATGAATACAGAT-ATATCAAGGAGTCTT
1 CAAATCGTTAAATTGAATGTGGGATGGATTTGGTTCAATGAATACAG-TCATATCAAGGAGTCTT
* * *
63106 TGCGTCAAAAATCATGTAAAATTGATCTGGGGCTCCGGAACGCGTTTTAAGCAAAAAACCGTGAT
65 TGCGTCAAAAATCATGCAAAATTGATCCGAGGCTCCGGAACGCGTTTTAAGCAAAAAACCGTGAT
* * * * * *
63171 -GGTTAGTACATGATTTCGGCTAATATTTTGCAAAAGCTGACCCAAAAACTTTTGTCCTGAA-TT
130 AGGTTA-TACACGATTTCGACGAAAATTTTGCAAAAACTGACCCAAAAACTTTT-TCCTCAATTT
* *
63234 TTTGCCACGATACTCAGAAAAATATATAAGTCAACGCCAAA
193 TTTGCCACAATACTCAGAAAAATACATAAGTCAACGCCAAA
63275 AAAATTGAAG
Statistics
Matches: 204, Mismatches: 26, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
237 23 0.11
238 174 0.85
239 7 0.03
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (237 bp):
CAAATCGTTAAATTGAATGTGGGATGGATTTGGTTCAATGAATACAGTCATATCAAGGAGTCTTT
GCGTCAAAAATCATGCAAAATTGATCCGAGGCTCCGGAACGCGTTTTAAGCAAAAAACCGTGATA
GGTTATACACGATTTCGACGAAAATTTTGCAAAAACTGACCCAAAAACTTTTTCCTCAATTTTTT
GCCACAATACTCAGAAAAATACATAAGTCAACGCCAAATAAA
Found at i:64151 original size:335 final size:322
Alignment explanation
Indices: 63068--64174 Score: 968
Period size: 335 Copynumber: 3.4 Consensus size: 322
63058 ATTTGGGTTG
* * * * * *
63068 GATTT-GGTTCGATGAATACAGATATATCAAGGAGTCTT-TGCGTCAAAAATCATGTAAAATTGA
1 GATTTAGGTTAGATGAATA-TGGTATTTCAAGGAGTCTTATGC--CAAAAATCATGCAAAACTGA
* * * * * *
63131 -TCTGGGGCTCCGGAACGCGTTTTAAGCAAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAT
63 GTC--GGACCCCGAAACTCGTTTTAAGCCAAAAACCGTGATGGTTAGTACA-GATTTCGACTAAT
* * * * *
63195 ATTTTGCAAAAGCTGACCCAAAAACTTTTGTCCTGAA-TTTTTGCCACGATACTCAGAA-AAATA
125 -TTTTGCAAAAACTGACCCGAAAAGTTTT-TCCTCAATTTTTTGCCACAATACTCAGAATAAATA
* * *
63258 TATAAGTCAACGCCAAAAAAATTGAAGGGTTTCTCACGCTTCTAATATAGTTTTTCTATTATTTT
188 TAT-ATTC-ACGCC-AAAAAATTGAAGGGTTTTTCACGATTCTAATATAGTTTTTCTA-T-TTTT
* * * *
63323 TCGTATTTATTTCTAATTAAATCCAAACAAGATTCAGATGATTGTAAAAACAAATCCTTAAATCC
248 TCG-AATTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC
63388 AATGTGGCTGA
312 AATGTGGCTGA
* * ** *
63399 GA-TTAGGTTAGATGATTATAGGTATTTTAAGGAGTCTCGGTGCCAAAAATCATGCAAAACTAAG
1 GATTTAGGTTAGATGAATAT-GGTATTTCAAGGAGTCT-TATGCCAAAAATCATGCAAAACTGAG
* * * * * * *
63463 CCGGAGCCCCTAAACGCGCTTTGAGCCAAAAACCGTGATGGTTAGT----ATAT-GA-T--TTTC
64 TCGGA-CCCCGAAACTCGTTTTAAGCCAAAAACCGTGATGGTTAGTACAGATTTCGACTAATTTT
* * *
63520 AGCTAAAAACTGACCCGAATAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAATATATATAT
128 TGC-AAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAG-AATA-A-ATAT
* * * * * *
63585 ATATAT-ATG-CAAAAAAGTTTGACGGGCTTTTCACGATTCTAATATCGTTTTCTCCACTTTTTC
189 ATAT-TCACGCCAAAAAA--TTGAAGGGTTTTTCACGATTCTAATATAGTTTT-TCTATTTTTTC
* *
63648 GAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCCCGTAAAAACAAATCCTTAAATCCAA
250 GAATT-ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
*
63713 TTTGGCTGA
314 TGTGGCTGA
* * * *
63722 GATTT-GGTTCAG-TGAATAAAGGTATTTCAAAGGAGT-TTTTGCACCAAAAATAATGCAAAATT
1 GATTTAGGTT-AGATGAAT-ATGGTATTTC-AAGGAGTCTTATG--CCAAAAATCATGCAAAACT
* * * * *
63784 GA-TCCCGGGCTCCGGAACGT-GTTTTGAGCCAAAAAACCGTGATAGTTAGTACACGATTTCGAC
61 GAGT--CGGACCCCGAAAC-TCGTTTTAAGCC-AAAAACCGTGATGGTTAGTACA-GATTTCGAC
*
63847 TAAATTTTTGCAAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAAAACTCAGAATAA
121 T-AATTTTTGCAAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAATAA
* * * *
63912 ATACATGATTCAGGGCCAGAAAAATTGAAGGGTTTTTCACGTTTCTAATATTGTTTTTCATATTT
185 ATATAT-ATTCA-CGCCA-AAAAATTGAAGGGTTTTTCACGATTCTAATATAGTTTTTC-TATTT
* *
63977 CTTTACGAACTTATTTCTAATTAAATCGAAATAAG-TCTAAGATGCTCGTAAAAACAAATCCTTA
246 -TTT-CGAA-TTATTTCTAATTAAATCGAAACAAGAT-TCAGATGCTCGTAAAAACAAATCCTTA
*
64041 TATCCAATGTGGCTGA
307 AATCCAATGTGGCTGA
* * * *
64057 GATTTAGGTTAGATGAATATGGATATTTCATGGAGTCTATATGTCGAAAACCATGCAAAACTGAG
1 GATTTAGGTTAGATGAATATGG-TATTTCAAGGAGTCT-TATGCCAAAAATCATGCAAAACTGAG
*
64122 TCGAGACCCCGAAACTACGTTTT-AGCCAAAAACCGTGATGGGTAG-AC-GATTTC
64 TCG-GACCCCGAAACT-CGTTTTAAGCCAAAAACCGTGATGGTTAGTACAGATTTC
64175 AGCTAAAAAC
Statistics
Matches: 626, Mismatches: 94, Indels: 112
0.75 0.11 0.13
Matches are distributed among these distances:
321 9 0.01
322 48 0.08
323 90 0.14
324 77 0.12
325 27 0.04
326 10 0.02
330 7 0.01
331 92 0.15
332 8 0.01
333 42 0.07
334 71 0.11
335 118 0.19
336 24 0.04
337 3 0.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (322 bp):
GATTTAGGTTAGATGAATATGGTATTTCAAGGAGTCTTATGCCAAAAATCATGCAAAACTGAGTC
GGACCCCGAAACTCGTTTTAAGCCAAAAACCGTGATGGTTAGTACAGATTTCGACTAATTTTTGC
AAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAATAAATATATATTCA
CGCCAAAAAATTGAAGGGTTTTTCACGATTCTAATATAGTTTTTCTATTTTTTCGAATTATTTCT
AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGA
Done.