Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011626.1 Corchorus olitorius cultivar O-4 contig11659, 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: 1897
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Found at i:287 original size:154 final size:154
Alignment explanation
Indices: 1--1897 Score: 2666
Period size: 154 Copynumber: 12.3 Consensus size: 154
* * * * *
1 GGGCTCCGATAGGCCCAAACGTAACAAGTGTACCAAATGAGTTAAAAACTTCAAAGTAGGACTAA
1 GGGCCCCGATAGGCCCAAA-ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT-GGACTAA
* * * * * * *
66 TCTCGACCATAATGATTACAGTTAGGCAATAAACAATGG--AGGAAAGAATTGAGGTTTGCCAAG
64 TCTC-ACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
**
129 TCGAAGACGATTCAAAACGGAACTTGT
128 TCGAAGACGATTCAAAACGGAACTAAT
*
156 GGG-CCCGATAGGCCCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTATT
1 GGGCCCCGATAGGCCC-AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
* * * *
220 CTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAATACAAGCATTGAGGTTT-CCAAAAT
65 CTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCC-AAAT
*
284 CGAAGACAATTCAAAACGGAACTAAT
129 CGAAGACGATTCAAAACGGAACTAAT
* * * * *
310 TGG-CCCGTTTGGCCCAAAATAACAAGTGTTCCAAGTGAGCTAAAAACTTCACAGTGGACTAACC
1 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* * *
374 TCACCAAAATGATTATAGTTAGGCCATAATCAATGGAAAGAAAAGTATTGAGGTTTGCCAAATCG
66 TCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
* * * **
439 AAGAGGATTCAATATGTCACTAAT
131 AAGACGATTCAAAACGGAACTAAT
* *
463 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCGAATGAGCTAAAAACTTCATAGTGGACTAATC
1 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* * * * *
528 TTACCAAAATGATTATATTTAGTCCATAAA-ATATGGAAAGAGAAGCTTTGAGGTTTGACAAATC
66 TCACCAAAATGATTATAGTTAGTCCATAAACA-ATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
*
592 GAAGAC-ATTTCAAAATGGAACTAAT
130 GAAGACGA-TTCAAAACGGAACTAAT
* *
617 GGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAGTC
1 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* *
682 TCACCAATATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGCTTTGCCAAATCG
66 TCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
**
747 AAGACGATTCAAAACGTCACTAAT
131 AAGACGATTCAAAACGGAACTAAT
*
771 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCATAGTGGACTAATC
1 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* * * *
836 TCTCTAAAATGATTATATTTAGTCCATAAA-ATATGGAAAGAAAAGCTTTGAGGTTTGCCAAATC
66 TCACCAAAATGATTATAGTTAGTCCATAAACA-ATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
*
900 GAAGACGATTCAAAACAGAACTAAT
130 GAAGACGATTCAAAACGGAACTAAT
* * *
925 GGG-CCCGATAAGCCCAAAATAACAAGTGTTGCGAATGAGCTAAAAACTTCACAGTGGACTAATC
1 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* * *
989 TCACCCAACTGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGTATTGAGGTTTGCCAAATCG
66 TCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
* * * **
1054 AAGAGGATTCAATATGTCACTAAT
131 AAGACGATTCAAAACGGAACTAAT
* * *
1078 GGGCCCCGATAGACCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATG
1 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* * *
1143 TCACCAAAATGATTATATTTAGTCCCTAAA-ATATGGAAAGAAAAGCTTTGAGGTTTGCCAAATC
66 TCACCAAAATGATTATAGTTAGTCCATAAACA-ATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
**
1207 GAAGACGATTCAAAACGTCACTAAT
130 GAAGACGATTCAAAACGGAACTAAT
* * * * * *
1232 GGGCCTCGATAGGCCCAAAGTAACATGTGTTCTAAATGAGCTAAAATCTTTACAGTGGACTAATC
1 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* * *
1297 AT-ACCAAAATGATTATAGTTAGTCCCTAACCAATGGAAAGAAAAGCATTGAGATTTGCCAAATC
66 -TCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
1361 GAAGACGATTCAAAACGGAACTAAT
130 GAAGACGATTCAAAACGGAACTAAT
* * * *
1386 GGGCCCCGAAAGACCCAAAATAACAAGTGTTCCAAATGAGCTACAAACTTTACAGTGGACTAATC
1 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* ** *
1451 TCATCAAAATGATTATAGTTAAACCATAAACAATGGAAGGAAAAGCATTGAGGTTTGCCAAATCG
66 TCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
*
1516 AAGACGATTCAAAACAGAACTAAT
131 AAGACGATTCAAAACGGAACTAAT
* *
1540 GGGCCCCGATAGGCCCAAAATAACAAGTGTTGCAAATGAGCTAAAAACTTCACAGTGAACTAATC
1 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
*
1605 TCACCAAAATGATTATAGTTACTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
66 TCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
*
1670 AAGACGATTCAAAACAGAACTAAT
131 AAGACGATTCAAAACGGAACTAAT
* *
1694 GGGCCCCGATAGGCCCAAAATAACAAGTGTTACAAATGAGCAAAAAACTTCACAGTGGACTAATC
1 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
1759 TCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
66 TCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
* ** * **
1824 AAGAGGATTCAGTATGTCACTAAT
131 AAGACGATTCAAAACGGAACTAAT
* * *
1848 GGGCCCCGACAGGTCCAAAAT-ACAAGTGTTCCAAACGAGCTAAAGAACTT
1 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA-AACTT
Statistics
Matches: 1555, Mismatches: 169, Indels: 37
0.88 0.10 0.02
Matches are distributed among these distances:
152 30 0.02
153 294 0.19
154 1221 0.79
155 10 0.01
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (154 bp):
GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
TCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
AAGACGATTCAAAACGGAACTAAT
Found at i:1192 original size:615 final size:614
Alignment explanation
Indices: 1--1897 Score: 2799
Period size: 615 Copynumber: 3.1 Consensus size: 614
* * * * *
1 GGGCTCCGATAGGCCCAAACGTAACAAGTGTACCAAATGAGTTAAAAACTTCAAAGTAGGACTAA
1 GGGCCCCGATAGGCCCAAA-ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT-GGACTAA
* * * * * *
66 TCTCGACC-ATAATGATTACAGTTAGGCAATAAACAATGG--AGGAAAGAATTGAGGTTTGCCAA
64 TCTC-ACCAAT-ATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGATTTGCCAA
* **
128 GTCGAAGACGATTCAAAACGGAACTTGTGGG-CCCGATAGGCCCAAAAATAACAAGTGTTCCAAA
127 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC-AAAATAACAAGTGTTCCAAA
* * *
192 TGAGCTAAAAACTTCACAGTGGACTATTCTCACTAAAATGATTATAGTTAGGCCATAAACAATGG
191 TGAGCTAAAAACTTCACAGTGGACTAATCTCTCTAAAATGATTATAGTTAGACCATAAACAATGG
* * * * * * *
257 AAATACAAGCATTGAGGTTT-CCAAAATCGAAGACAATTCAAAACGGAACTAATTGGCCCGTTTG
256 AAAGAAAAGCATTGAGGTTTGCC-AAATCGAAGACGATTCAAAACAGAACTAATGGGCCCGATAG
* * *
321 GCCCAAAATAACAAGTGTTCCAAGTGAGCTAAAAACTTCACAGTGGACTAACCTCACCAAAATGA
320 GCCCAAAATAACAAGTGTTGCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* *
386 TTATAGTTAGGCCATAATCAATGGAAAGAAAAGTATTGAGGTTTGCCAAATCGAAGAGGATTCAA
385 TTATAGTTAGTCCATAAACAATGGAAAGAAAAGTATTGAGGTTTGCCAAATCGAAGAGGATTCAA
* *
451 TATGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCGAATGAGCTAAAAACTTCAT
450 TATGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
* *
516 AGTGGACTAATCTTACCAAAATGATTATATTTAGTCCATAAAATATGGAAAGAGAAGCTTTGAGG
515 AGTGGACTAATCTCACCAAAATGATTATATTTAGTCCATAAAATATGGAAAGAAAAGCTTTGAGG
* **
581 TTTGACAAATCGAAGACATTTCAAAATGGAACTAAT
580 TTTGCCAAATCGAAGACA-TTCAAAATGTCACTAAT
* *
617 GGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAGTC
1 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
*
682 TCACCAATATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGCTTTGCCAAATCG
66 TCACCAATATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGATTTGCCAAATCG
**
747 AAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
131 AAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
* * *
812 TAAAAACTTCATAGTGGACTAATCTCTCTAAAATGATTATATTTAGTCCATAAA-ATATGGAAAG
196 TAAAAACTTCACAGTGGACTAATCTCTCTAAAATGATTATAGTTAGACCATAAACA-ATGGAAAG
* *
876 AAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCGATAAGCCCA
260 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCGATAGGCCCA
* * *
941 AAATAACAAGTGTTGCGAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCCAACTGATTATA
325 AAATAACAAGTGTTGCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
1006 GTTAGTCCATAAACAATGGAAAGAAAAGTATTGAGGTTTGCCAAATCGAAGAGGATTCAATATGT
390 GTTAGTCCATAAACAATGGAAAGAAAAGTATTGAGGTTTGCCAAATCGAAGAGGATTCAATATGT
* *
1071 CACTAATGGGCCCCGATAGACCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGG
455 CACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
* *
1136 ACTAATGTCACCAAAATGATTATATTTAGTCCCTAAAATATGGAAAGAAAAGCTTTGAGGTTTGC
520 ACTAATCTCACCAAAATGATTATATTTAGTCCATAAAATATGGAAAGAAAAGCTTTGAGGTTTGC
*
1201 CAAATCGAAGACGATTCAAAACGTCACTAAT
585 CAAATCGAAGAC-ATTCAAAATGTCACTAAT
* * * * * *
1232 GGGCCTCGATAGGCCCAAAGTAACATGTGTTCTAAATGAGCTAAAATCTTTACAGTGGACTAATC
1 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* * *
1297 AT-ACCAAAATGATTATAGTTAGTCCCTAACCAATGGAAAGAAAAGCATTGAGATTTGCCAAATC
66 -TCACCAATATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGATTTGCCAAATC
* *
1361 GAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGACCCAAAATAACAAGTGTTCCAAATGAG
130 GAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAG
* * * *
1426 CTACAAACTTTACAGTGGACTAATCTCATC-AAAATGATTATAGTTAAACCATAAACAATGGAAG
195 CTAAAAACTTCACAGTGGACTAATCTC-TCTAAAATGATTATAGTTAGACCATAAACAATGGAAA
1490 GAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGATAGGCC
259 GAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGG-CCCGATAGGCC
*
1555 CAAAATAACAAGTGTTGCAAATGAGCTAAAAACTTCACAGTGAACTAATCTCACCAAAATGATTA
323 CAAAATAACAAGTGTTGCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
* * * *
1620 TAGTTACTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
388 TAGTTAGTCCATAAACAATGGAAAGAAAAGTATTGAGGTTTGCCAAATCGAAGAGGATTCAATA-
* * * *
1685 AG-AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTACAAATGAGCAAAAAACTTCACAG
452 TGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
* *
1749 TGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACA-ATGGAAAGAAAAGCATTGAGGT
517 TGGACTAATCTCACCAAAATGATTATATTTAGTCCATAAA-ATATGGAAAGAAAAGCTTTGAGGT
* **
1813 TTGCCAAATCGAAGAGGATTCAGTATGTCACTAAT
581 TTGCCAAATCGAAGA-CATTCAAAATGTCACTAAT
* * *
1848 GGGCCCCGACAGGTCCAAAAT-ACAAGTGTTCCAAACGAGCTAAAGAACTT
1 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA-AACTT
Statistics
Matches: 1159, Mismatches: 107, Indels: 30
0.89 0.08 0.02
Matches are distributed among these distances:
613 28 0.02
614 13 0.01
615 783 0.68
616 333 0.29
617 2 0.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (614 bp):
GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
TCACCAATATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGATTTGCCAAATCG
AAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
TAAAAACTTCACAGTGGACTAATCTCTCTAAAATGATTATAGTTAGACCATAAACAATGGAAAGA
AAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCGATAGGCCCAA
AATAACAAGTGTTGCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAG
TTAGTCCATAAACAATGGAAAGAAAAGTATTGAGGTTTGCCAAATCGAAGAGGATTCAATATGTC
ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
CTAATCTCACCAAAATGATTATATTTAGTCCATAAAATATGGAAAGAAAAGCTTTGAGGTTTGCC
AAATCGAAGACATTCAAAATGTCACTAAT
Done.