Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011508.1 Corchorus olitorius cultivar O-4 contig11541, 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: 2831
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.22
Found at i:769 original size:21 final size:21
Alignment explanation
Indices: 740--787 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
730 TCCCATGTCA
*
740 CAATAAGCTTAGAACCTT-CTC
1 CAATGAGCTTAGAA-CTTGCTC
*
761 CAATGAGCTTGGAACTTGCTC
1 CAATGAGCTTAGAACTTGCTC
782 CAATGA
1 CAATGA
788 TCTCCTAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (21 bp):
CAATGAGCTTAGAACTTGCTC
Found at i:847 original size:40 final size:40
Alignment explanation
Indices: 792--870 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
782 CAATGATCTC
792 CTAGCATCTTCAAGACCATGATGAGTCCGTGGCGCATCAG
1 CTAGCATCTTCAAGACCATGATGAGTCCGTGGCGCATCAG
*
832 CTAGCATCTTCAAGACCATGATGAGTCCTTGGCGCATCA
1 CTAGCATCTTCAAGACCATGATGAGTCCGTGGCGCATCA
871 ATCAGGTCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CTAGCATCTTCAAGACCATGATGAGTCCGTGGCGCATCAG
Found at i:1777 original size:153 final size:154
Alignment explanation
Indices: 878--2831 Score: 2981
Period size: 154 Copynumber: 12.8 Consensus size: 154
868 TCAATCAGGT
* * *
878 CATAAACATTGGAAAGTAAAGCATTGAGGGTTGCCAGATCGAAGACGATTCAAAACGGAACTAAT
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
** * *
943 GGGTGTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGATAAAAACTTCACAGTGGATTAATC
66 GGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
1008 TCACCAAAATGATTATAGTTAGGC
131 TCACCAAAATGATTATAGTTAGGC
* *
1032 CATAAACAATGGAAGGAAAAG-AGTTGAGGGTTGCCAGATCGAAGACGATTCAAAACGGAACTAA
1 CATAAACAATGGAAAGAAAAGCA-TTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
** *
1096 TGGGTGTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGATAAAAACTTCACAGTGGACTAAT
65 TGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
1161 CTCACCAAAATGATTATAG-TAGGC
130 CTCACCAAAATGATTATAGTTAGGC
* * ** *
1185 CATAAACAATGGAAAGAAAAGCATTGAGCGTTG-CAAGTCGAAGACGATTCAAAACGTCATTAAT
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
* *
1249 GGGCCCCGATAGGCCCAAAATGAA-AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAA
66 GGGCCTCGATAGGCCCAAAAT-AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
*
1313 CTCACCAAAATTATTATAGTTAGGC
130 CTCACCAAAATGATTATAGTTAGGC
* * * * * *
1338 CATAAACAATGGAAAGAAAAGCATCGAGGTTTCCCAAATTGAAGACGATTTAGAAC-GACACTAA
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA-ACTAA
* * * * * ***
1402 TGGTCCCCGATATGCCCAAAATAACAATTGTTCCAAATGAGTTAAAAACTTCAGTTTGGACTAAT
65 TGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
*
1467 CTCACGAAAATGA-TATTAGTTAGGC
130 CTCACCAAAATGATTA-TAGTTAGGC
*
1492 CATAAACAATGGAAAGAAAACCATTGA-GGTTGCCAAATCGAAGACGATTCAAAAC-GAACTAAT
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
*
1555 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
66 GGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
1620 TCACCAAAATGATTATAGTTAGGC
131 TCACCAAAATGATTATAGTTAGGC
***
1644 CATAAACGAATGGAAAGAAAAGCATTGAGGGTTG-CAAATCGAAGACGATTCAAAACATCACTAA
1 CATAAAC-AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
* *
1708 TGGACC-CTGATAGG-CCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
65 TGGGCCTC-GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
*
1771 TATCACCAAAATGATTATAGTTAGGC
129 TCTCACCAAAATGATTATAGTTAGGC
1797 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
*
1862 GGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATA
66 GGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
1927 TCACCAAAATGATTATAGTTAGGC
131 TCACCAAAATGATTATAGTTAGGC
*
1951 CATAAAC-ATGGAAAGAGAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
* *
2015 GGGCCTCGATAGGTCCAAAATAACACGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
66 GGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
2080 TCACCAAAATGATTATAGTTAGGC
131 TCACCAAAATGATTATAGTTAGGC
*
2104 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGAAACTAAT
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
* * * * *
2169 GGGCCTCGATAGGCCCAAAATAACAAGTGTTCCGAATGAGTTAAAAACCTCAAACTGGACTAATC
66 GGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* *
2234 TTACCAAAATGATTATAGTTAGGT
131 TCACCAAAATGATTATAGTTAGGC
**
2258 CATAAACTTTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA-GAGAACTAA
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACG-GAACTAA
*
2322 TGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTAAT
65 TGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
2387 CTCACCAAAATGATTATAGTTAGGC
130 CTCACCAAAATGATTATAGTTAGGC
* * * **
2412 CATAAACAATGGGAAGAAAGGCATTGAGGGTTG-CAAATCGAAGAGGATTCAAAACGTCACTAAT
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
* * *
2476 GGGCCCCGATAGG-CCAAAATAAAAAGTGTTCCAAATGAGCTAAAAAC-TCACAGTGGACTAATA
66 GGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* * *
2539 TCAACAAAATAATTATAGTTAAGC
131 TCACCAAAATGATTATAGTTAGGC
* **
2563 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAGTCGAAGACGATTCAAAACGTCACTAAT
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
* * * *
2628 GGGCCCCGATAGGCTCAAAATAATAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATT
66 GGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* *
2693 TTACCAAAATGATTATAGTTAGAC
131 TCACCAAAATGATTATAGTTAGGC
* *
2717 CATAAACCATGGAAAGAAAAGCATTGAGGGTCT-CCAAATCGAAGACGATTTAAAACGGAACTAA
1 CATAAACAATGGAAAGAAAAGCATTGAGGGT-TGCCAAATCGAAGACGATTCAAAACGGAACTAA
*
2781 TGGGCCTCGATATGCCCAAAAT-ACAAGTGTTCCAAATGAGCTAAAAACTTC
65 TGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
Statistics
Matches: 1654, Mismatches: 123, Indels: 47
0.91 0.07 0.03
Matches are distributed among these distances:
151 67 0.04
152 292 0.18
153 510 0.31
154 784 0.47
155 1 0.00
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (154 bp):
CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
GGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
TCACCAAAATGATTATAGTTAGGC
Found at i:1862 original size:459 final size:462
Alignment explanation
Indices: 878--2831 Score: 3026
Period size: 459 Copynumber: 4.3 Consensus size: 462
868 TCAATCAGGT
* * *
878 CATAAACATTGGAAAGTAAAGCATTGAGGGTTGCCAGATCGAAGACGATTCAAAACGGAACTAAT
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
** * *
943 GGGTGTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGATAAAAACTTCACAGTGGATTAATC
66 GGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* *
1008 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAGGAAAAG-AGTTGAGGGTTGCCAGATC
131 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA-TTGAGGGTTGCCAAATC
***
1072 GAAGACGATTCAAAACGGAACTAATGGGTGTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAG
195 GAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAG
*
1137 ATAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAG-TAGGCCATAAACAATGGAAAG
260 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* * * *
1201 AAAAGCATTGAGCGTTG-CAAGTCGAAGACGATTCAAAACGTCATTAATGGGCCCCGATAGGCCC
325 AAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACATCACTAATGGGCCCCGATAGGCCC
* *
1265 AAAATGAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA-ACTCACCAAAATTATTA
390 AAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATA-TCACCAAAATGATTA
1329 TAGTTAGGC
454 TAGTTAGGC
* * * * * *
1338 CATAAACAATGGAAAGAAAAGCATCGAGGTTTCCCAAATTGAAGACGATTTAGAAC-GACACTAA
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA-ACTAA
* * * * * ***
1402 TGGTCCCCGATATGCCCAAAATAACAATTGTTCCAAATGAGTTAAAAACTTCAGTTTGGACTAAT
65 TGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
* *
1467 CTCACGAAAATGA-TATTAGTTAGGCCATAAACAATGGAAAGAAAACCATTGA-GGTTGCCAAAT
130 CTCACCAAAATGATTA-TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAAT
1530 CGAAGACGATTCAAAAC-GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGA
194 CGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGA
1594 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACGAATGGAA
259 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC-AATGGAA
* *
1659 AGAAAAGCATTGAGGGTTG-CAAATCGAAGACGATTCAAAACATCACTAATGGACCCTGATAGG-
323 AGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACATCACTAATGGGCCCCGATAGGC
1722 CCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATATCACCAAAATGATT
388 CCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATATCACCAAAATGATT
1787 ATAGTTAGGC
453 ATAGTTAGGC
1797 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
*
1862 GGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATA
66 GGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
*
1927 TCACCAAAATGATTATAGTTAGGCCATAAAC-ATGGAAAGAGAAGCATTGAGGGTTGCCAAATCG
131 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCG
* * *
1991 AAGACGATTCAAAACGGAACTAATGGGCCTCGATAGGTCCAAAATAACACGTGTTCCAAATGAGC
196 AAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
2056 TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
261 TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
* *
2121 AAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGA-AACTAATGGGCCTCGATAGGCCC
326 AAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAC-ATCACTAATGGGCCCCGATAGGCCC
* * * * * * * *
2185 AAAATAACAAGTGTTCCGAATGAGTTAAAAACCTCAAACTGGACTAATCTTACCAAAATGATTAT
390 AAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATATCACCAAAATGATTAT
*
2250 AGTTAGGT
455 AGTTAGGC
**
2258 CATAAACTTTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA-GAGAACTAA
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACG-GAACTAA
*
2322 TGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTAAT
65 TGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
* *
2387 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGGAAGAAAGGCATTGAGGGTTG-CAAATC
130 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATC
* ** *
2451 GAAGAGGATTCAAAACGTCACTAATGGGCCCCGATAGG-CCAAAATAAAAAGTGTTCCAAATGAG
195 GAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAG
* * * *
2515 CTAAAAAC-TCACAGTGGACTAATATCAACAAAATAATTATAGTTAAGCCATAAACAATGGAAAG
260 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* * *
2579 AAAAGCATTGAGGGTTGCCAAGTCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCTC
325 AAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACATCACTAATGGGCCCCGATAGGCCC
* * *
2644 AAAATAATAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATTTTACCAAAATGATTAT
390 AAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATATCACCAAAATGATTAT
*
2709 AGTTAGAC
455 AGTTAGGC
* *
2717 CATAAACCATGGAAAGAAAAGCATTGAGGGTCT-CCAAATCGAAGACGATTTAAAACGGAACTAA
1 CATAAACAATGGAAAGAAAAGCATTGAGGGT-TGCCAAATCGAAGACGATTCAAAACGGAACTAA
*
2781 TGGGCCTCGATATGCCCAAAAT-ACAAGTGTTCCAAATGAGCTAAAAACTTC
65 TGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
Statistics
Matches: 1370, Mismatches: 106, Indels: 38
0.90 0.07 0.03
Matches are distributed among these distances:
458 132 0.10
459 560 0.41
460 393 0.29
461 263 0.19
462 22 0.02
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (462 bp):
CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
GGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCG
AAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
AAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACATCACTAATGGGCCCCGATAGGCCCA
AAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATATCACCAAAATGATTATA
GTTAGGC
Done.