Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011799.1 Corchorus olitorius cultivar O-4 contig11832, 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, 988
Length: 1647
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.20
Found at i:590 original size:155 final size:153
Alignment explanation
Indices: 1--1384 Score: 2019
Period size: 153 Copynumber: 9.0 Consensus size: 153
* * *
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GGTTACCAAATCGAAGACGATTCATA
* * *
66 ACGGA-ACTAAT-GGCCCCGAAAGGCCTAAAATAAACAAGTGTTCCAAATGAAGCTAAAAACTTC
65 AC-GACACTAATGGGCCCCGATAGGCCCAAAAT-AACAAGTGTTCCAAATG-ACCTAAAAACTTC
129 ACAGTGGACTAATCTCAACCAAAATGAT
127 ACAGTGGACTAATCTC-ACCAAAATGAT
* *
157 TTTAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTACCAAATCGAAGACGATTTATAA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTACCAAATCGAAGACGATTCATAA
* *
222 CGACACTAATGGGCCCCGATATGACCCAAAATAAGAAAGTGTTCCAAATGACCTAAAAACTTACA
66 CGACACTAATGGGCCCCGATA-GGCCCAAAATAA-CAAGTGTTCCAAATGACCTAAAAACTT-CA
287 CAGTGGACTAATCTCACCAAAATGAT
128 CAGTGGACTAATCTCACCAAAATGAT
* *
313 TATAGGTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTACCAAATCTAAGACGATTCATAA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTACCAAATCGAAGACGATTCATAA
*
378 CGACACTAATGGGCCCCGATAGGCACAAAATAACAAGTGTTCCAAATGACCTAAAAACTTCACAG
66 CGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGACCTAAAAACTTCACAG
443 TGGACTAATCTCACCGAAAATGAT
131 TGGACTAATCTCACC-AAAATGAT
* * *
467 TATAGGTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAGA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTACCAAATCGAAGACGATTCATA
*
532 ACGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAACGACCTAAAAACTTCACA
65 ACGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGACCTAAAAACTTCACA
*
597 GTGGACTAATCTTA-CAAAATGAT
130 GTGGACTAATCTCACCAAAATGAT
* * *
620 TATAGGTAGGCCATGAACAATGGAAAGAAAAGCATTGAGGTTACCAAATCTAAGACGATTCATAA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTACCAAATCGAAGACGATTCATAA
* **
685 CGACACTAATGGGCCCCGATAGGCACAAAATAACAAGTGTTCCATTTGACCTAAAAACTTCACAG
66 CGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGACCTAAAAACTTCACAG
* *
750 TGGACTAATCTTACAAAAATGAT
131 TGGACTAATCTCACCAAAATGAT
* * * * * *
773 TATAGGTCGGCCATAAACAATGGAAAGAAAAGCATTTAGGTTTCTAAATCGAAGACGATTCAGAA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTACCAAATCGAAGACGATTCATAA
* *
838 CGACACTAATGGGCCCCGATATGCCCAAAATAACAAGTGTTCCAAATGAACTAAAAACTTCACAG
66 CGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGACCTAAAAACTTCACAG
903 TGGACTAATCTCACCAAAATGAT
131 TGGACTAATCTCACCAAAATGAT
* *
926 TTTAGTTAGGCCATAAAGAATGGAAAGAAAAGCATTGAGGTTACCAAATCGAAGACGATTCATAA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTACCAAATCGAAGACGATTCATAA
*
991 CGACACTAATGGGCCCCGATACGGCACCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
66 CGACACTAATGGGCCCCGATA-GGC-CCAAAATAACAAGTGTTCCAAATGACCTAAAAACTTCAC
*
1056 AGTGGACTAATCTCACGAAAATGAT
129 AGTGGACTAATCTCACCAAAATGAT
* * * * *
1081 AAGAGTTAGGCCATAAACAATGGAAAGAAAAAGCATTGAGGTTTCTCAAATCAAAGACGATTCAA
1 TATAGTTAGGCCATAAACAATGGAAAG-AAAAGCATTGAGGTTAC-CAAATCGAAGACGATTCAT
* *
1146 AACGACAGTAATGGGCCCCGATAGGCCCAAAA-ATACAAGTGTTCCAAATGAGCTAAAAACTTCA
64 AACGACACTAATGGGCCCCGATAGGCCCAAAATA-ACAAGTGTTCCAAATGACCTAAAAACTTCA
* *
1210 CA-TAAGACTATTCTCACCAAAATGAT
128 CAGT-GGACTAATCTCACCAAAATGAT
** * * * * *
1236 TATAGTTAACCCATAAACAATGGAAACAAAAGC-TTCGAGGGTTGCCAAATCCAATACGATTCAA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT-GA-GGTTACCAAATCGAAGACGATTCAT
* * * *
1300 AACGGA-ACTAAT-GGCCCCGAAAGGCCTAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCA
64 AAC-GACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGACCTAAAAACTTCA
1363 CAGTGGACTAATCTCACCAAAA
128 CAGTGGACTAATCTCACCAAAA
1385 CAATGGAAAG
Statistics
Matches: 1127, Mismatches: 82, Indels: 41
0.90 0.07 0.03
Matches are distributed among these distances:
152 96 0.09
153 358 0.32
154 116 0.10
155 309 0.27
156 170 0.15
157 78 0.07
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (153 bp):
TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTACCAAATCGAAGACGATTCATAA
CGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGACCTAAAAACTTCACAG
TGGACTAATCTCACCAAAATGAT
Found at i:1333 original size:463 final size:458
Alignment explanation
Indices: 3--1647 Score: 2306
Period size: 463 Copynumber: 3.6 Consensus size: 458
1 TA
* * * *
3 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAAC
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAGAAC
* *
68 GGA-ACTAAT-GGCCCCGAAAGGCCTAAAATAAACAAGTGTTCCAAATGAAGCTAAAAACTTCAC
66 -GACACTAATGGGCCCCGATAGGCCCAAAAT-AACAAGTGTTCCAAATG-AGCTAAAAACTTCAC
* ***
131 AGTGGACTAATCTCAACCAAAATGATTTTAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAG
128 AGTGGACTAATCTC-ACGAAAATGATAAGAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAG
* * * * *
196 GTTACCAAATCGAAGACGATTTATAACGACACTAATGGGCCCCGATATGACCCAAAATAAGAAAG
192 GTTACCAAATCAAAGACGATTCAAAACGACACTAATGGGCCCCGATA-GGCCCAAAATAA-CAAG
261 TGTTCCAAATGACCTAAAAACTTACACAGTGGACTAATCTCACCAAAATGATTATAGGTAGGCCA
255 TGTTCCAAATGACCTAAAAACTT-CACAGTGGACTAATCTCACCAAAATGATTATAGGTAGGCCA
* *
326 TAAACAATGGAAAGAAAAGCATTGAGGTTACCAAATCTAAGACGATTCATAACGACACTAATGGG
319 TAAACAATGGAAAGAAAAGCATTGAGGTTACCAAATCCAAGACGATTCAAAACGACACTAATGGG
*
391 CCCCGATAGGCACAAAATAACAAGTGTTCCAAATGACCTAAAAACTTCACAGTGGACTAATCTCA
384 CCCCGATAGGC-CAAAATAACAAGTGTTCCAAATGAACTAAAAACTTCACAGTGGACTAATCTCA
456 CCGAAAATGATT
448 CC-AAAATGATT
*
468 ATAGGTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAGAA
1 -TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAGAA
* *
533 CGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAACGACCTAAAAACTTCACAG
65 CGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
* * * * *
598 TGGACTAATCTTAC-AAAATGATTATAGGTAGGCCATGAACAATGGAAAGAAAAGCATTGAGGTT
130 TGGACTAATCTCACGAAAATGATAAGAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTT
* * *
662 ACCAAATCTAAGACGATTCATAACGACACTAATGGGCCCCGATAGGCACAAAATAACAAGTGTTC
195 ACCAAATCAAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTC
** * * *
727 CATTTGACCTAAAAACTTCACAGTGGACTAATCTTACAAAAATGATTATAGGTCGGCCATAAACA
260 CAAATGACCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGGTAGGCCATAAACA
* * * * *
792 ATGGAAAGAAAAGCATTTAGGTTTCTAAATCGAAGACGATTCAGAACGACACTAATGGGCCCCGA
325 ATGGAAAGAAAAGCATTGAGGTTACCAAATCCAAGACGATTCAAAACGACACTAATGGGCCCCGA
*
857 TATGCCCAAAATAACAAGTGTTCCAAATGAACTAAAAACTTCACAGTGGACTAATCTCACCAAAA
390 TA-GGCCAAAATAACAAGTGTTCCAAATGAACTAAAAACTTCACAGTGGACTAATCTCACCAAAA
922 TGATTT
454 TGA-TT
* * *
928 TAGTTAGGCCATAAAGAATGGAAAGAAAAGCATTGAGG-TTACCAAATCGAAGACGATTCATAAC
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAGAAC
992 GACACTAATGGGCCCCGATACGGCACCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
66 GACACTAATGGGCCCCGATA-GGC-CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
1057 GTGGACTAATCTCACGAAAATGATAAGAGTTAGGCCATAAACAATGGAAAGAAAAAGCATTGAGG
129 GTGGACTAATCTCACGAAAATGATAAGAGTTAGGCCATAAACAATGGAAAG-AAAAGCATTGAGG
* *
1122 TTTCTCAAATCAAAGACGATTCAAAACGACAGTAATGGGCCCCGATAGGCCCAAAA-ATACAAGT
193 TTAC-CAAATCAAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCCCAAAATA-ACAAGT
* * * * **
1186 GTTCCAAATGAGCTAAAAACTTCACA-TAAGACTATTCTCACCAAAATGATTATAGTTAACCCAT
256 GTTCCAAATGACCTAAAAACTTCACAGT-GGACTAATCTCACCAAAATGATTATAGGTAGGCCAT
* * *
1250 AAACAATGGAAACAAAAGC-TTCGAGGGTTGCCAAATCCAATACGATTCAAAACGGA-ACTAAT-
320 AAACAATGGAAAGAAAAGCATT-GA-GGTTACCAAATCCAAGACGATTCAAAAC-GACACTAATG
* * *
1312 GGCCCCGAAAGGCCTAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCT
382 GGCCCCGATAGGCC-AAAATAACAAGTGTTCCAAATGAACTAAAAACTTCACAGTGGACTAATCT
1377 ---C---------
446 CACCAAAATGATT
*
1378 -----A--CCA-AAACAATGGAAAGAAAAGCTTTGAGGTTTCCCAAATCGAAGACGATTCAGAAC
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAGAAC
*
1435 GACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCGCAGT
66 GACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
*
1500 GGACTAATCTCACGAAAATGATAAGAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT
131 GGACTAATCTCACGAAAATGATAAGAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTA
*
1565 CTCAAATCAAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCCTAAAA-ATACAAGTGTT
196 C-CAAATCAAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCCCAAAATA-ACAAGTGTT
*
1629 CCAAATGAGCTAAAAACTT
259 CCAAATGACCTAAAAACTT
Statistics
Matches: 1088, Mismatches: 75, Indels: 58
0.89 0.06 0.05
Matches are distributed among these distances:
440 97 0.09
441 90 0.08
442 27 0.02
443 47 0.04
445 1 0.00
458 44 0.04
459 46 0.04
460 215 0.20
461 57 0.05
462 33 0.03
463 269 0.25
464 31 0.03
465 31 0.03
466 82 0.08
467 18 0.02
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.20
Consensus pattern (458 bp):
TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAGAAC
GACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
GGACTAATCTCACGAAAATGATAAGAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTA
CCAAATCAAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
AAATGACCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGGTAGGCCATAAACAA
TGGAAAGAAAAGCATTGAGGTTACCAAATCCAAGACGATTCAAAACGACACTAATGGGCCCCGAT
AGGCCAAAATAACAAGTGTTCCAAATGAACTAAAAACTTCACAGTGGACTAATCTCACCAAAATG
ATT
Found at i:1490 original size:133 final size:132
Alignment explanation
Indices: 1250--1517 Score: 403
Period size: 133 Copynumber: 2.0 Consensus size: 132
1240 GTTAACCCAT
* *
1250 AAACAATGGAAACAAAAGCTTCGAGGGTTGCCAAATCCAATACGATTCAAAACGGAACTAATGGC
1 AAACAATGGAAACAAAAGCTTCGAGGGTTCCCAAATCCAAGACGATTCAAAACGGAACTAATGGC
*
1315 CCCGAAAGGCCTAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAC
66 CCCGAAAGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAC
1380 CA
131 CA
* * * * *
1382 AAACAATGGAAAGAAAAGCTTTGAGGTTTCCCAAATCGAAGACGATTCAGAAC-GACACTAATGG
1 AAACAATGGAAACAAAAGCTTCGAGGGTTCCCAAATCCAAGACGATTCAAAACGGA-ACTAAT-G
* * *
1446 GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCGCAGTGGACTAATCTC
64 GCCCCGAAAGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
*
1511 ACGA
129 ACCA
1515 AAA
1 AAA
1518 TGATAAGAGT
Statistics
Matches: 122, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
131 2 0.02
132 52 0.43
133 68 0.56
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (132 bp):
AAACAATGGAAACAAAAGCTTCGAGGGTTCCCAAATCCAAGACGATTCAAAACGGAACTAATGGC
CCCGAAAGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAC
CA
Done.