Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01008933.1 Corchorus olitorius cultivar O-4 contig08960, 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, 652
Length: 1087
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Found at i:281 original size:154 final size:154
Alignment explanation
Indices: 1--1081 Score: 1668
Period size: 154 Copynumber: 7.0 Consensus size: 154
* *
1 ATCTCACCAAAATGATTATAGTCAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
1 ATCTCACCAAAATGATTATAGTTAGACCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
66 TCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
66 TCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
*
131 AGCTAAAAACTTCACAGAGGATAA
131 AGCTAAAAACTTCACAGTGGATAA
* * *
155 ATCTCACCAAAATGATTATAGTTAGATCATAAATAATGGAAAGAAAAGCATTGAGGTTTTCCAAA
1 ATCTCACCAAAATGATTATAGTTAGACCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
* * *
220 TCGAGGACGATTCAAAACGTCACTAATGGTCCTCGATAGGCCCAAAATAACAAGTGGTCCAAATG
66 TCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
*
285 AGCTAAAAACTTCACAGAGGATAA
131 AGCTAAAAACTTCACAGTGGATAA
* * *
309 ATCTCACCAAAATGATTATAGTTAGATCATAAATAATGGAAAGAAAAGCATTGAGGTTTTCCAAA
1 ATCTCACCAAAATGATTATAGTTAGACCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
* *
374 TCGAGGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGGTCCAAATG
66 TCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
*
439 AGCTAAAAACTTCACAGTGGACT-C
131 AGCTAAAAACTTCACAGTGGA-TAA
* *
463 ATCTCACCAAAATGATTATAGTCAGGCCATAAACAATGGAAAGAAAAGCATTTGAGGTTTGCCAA
1 ATCTCACCAAAATGATTATAGTTAGACCATAAACAATGGAAAGAAAAGCA-TTGAGGTTTGCC-A
528 AATCGAAGACGATTTCAAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCA
64 AATCGAAGACGA-TTC-AAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCA
* * * * *
593 GATGAGTTAAAAACTTCTCAGTGCACAA
127 AATGAGCTAAAAACTTCACAGTGGATAA
* **
621 CTCTCACCAAAATGATTATAGTTAGGA-CATAAACAATGGAAAGAAAATAATTGAGGTTTGCCAA
1 ATCTCACCAAAATGATTATAGTTA-GACCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
* *
685 ATCGAAGACAATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAGAT
65 ATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAAT
* * *
750 GAGTTAAAAACTTCACAGTGCACAA
130 GAGCTAAAAACTTCACAGTGGATAA
**
775 ATCTCACCAAAATGATTATAGTTAGGA-CATAAACAATGGAAAGAAAATAATTGAGGTTTGCCAA
1 ATCTCACCAAAATGATTATAGTTA-GACCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
*
839 ATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCATAT
65 ATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAAT
904 GAGACTAAAAACTTCACAGTGGACT-A
130 GAG-CTAAAAACTTCACAGTGGA-TAA
* * * *
930 ATCTCACCAAAATGAATTATAGTTAGGCCGTAAACAATGGAAAGAAAGGCATCGAAGG-TTGCCA
1 ATCTCACCAAAATG-ATTATAGTTAGACCATAAACAATGGAAAGAAAAGCATTG-AGGTTTGCCA
* *
994 AATCGAAGACAATTCAAAACGTCACTAATGGTCCCCGATGGGCCCAAAATAACAAGTGTTCCAAA
64 AATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
1059 TGAGCTAAAAACTTCACAGTGGA
129 TGAGCTAAAAACTTCACAGTGGA
1082 CTAATC
Statistics
Matches: 869, Mismatches: 46, Indels: 23
0.93 0.05 0.02
Matches are distributed among these distances:
154 545 0.63
155 67 0.08
156 127 0.15
157 18 0.02
158 111 0.13
159 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (154 bp):
ATCTCACCAAAATGATTATAGTTAGACCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
TCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
AGCTAAAAACTTCACAGTGGATAA
Found at i:999 original size:466 final size:462
Alignment explanation
Indices: 1--1079 Score: 1750
Period size: 466 Copynumber: 2.3 Consensus size: 462
1 ATCTCACCAAAATGATTATAGTCAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
1 ATCTCACCAAAATGATTATAGTCAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
66 TCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
66 TCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
* * * *
131 AGCTAAAAACTTCACAGAGGATAAATCTCACCAAAATGATTATAGTTAGATCATAAATAATGGAA
131 AGCTAAAAACTTCACAGTGCACAAATCTCACCAAAATGATTATAGTTAGATCATAAACAATGGAA
* * * * *
196 AGAAAAGCATTGAGGTTTTCCAAATCGAGGACGATTCAAAACGTCACTAATGGTCCTCGATAGGC
196 AGAAAAGAATTGAGGTTTGCCAAATCGAAGACAATTCAAAACGTCACTAATGGTCCCCGATAGGC
* *
261 CCAAAATAACAAGTGGTCCAAATGAGCTAAAAACTTCACAGAGGATAAATCTCACCAAAATGATT
261 CCAAAATAACAAGTGGTCCAAATGAGCTAAAAACTTCACAGAGCACAAATCTCACCAAAATGATT
* * * *
326 ATAGTTAGATCATAAATAATGGAAAGAAAAGCATTGAGGTTTTCCAAATCGAGGACGATTCAAAA
326 ATAGTTAGATCATAAACAATGGAAAGAAAAGAATTGAGGTTTGCCAAATCGAAGACGATTCAAAA
391 CGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGGTCCAAATGAGCTAAAAACTTCACAG
391 CGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGGTCCAAATGAGCTAAAAACTTCACAG
*
456 TGGACTC
456 TGGACTA
463 ATCTCACCAAAATGATTATAGTCAGGCCATAAACAATGGAAAGAAAAGCATTTGAGGTTTGCCAA
1 ATCTCACCAAAATGATTATAGTCAGGCCATAAACAATGGAAAGAAAAGCA-TTGAGGTTTGCC-A
528 AATCGAAGACGATTTCAAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCA
64 AATCGAAGACGA-TTC-AAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCA
* * * *
593 GATGAGTTAAAAACTTCTCAGTGCACAACTCTCACCAAAATGATTATAGTTAGGA-CATAAACAA
127 AATGAGCTAAAAACTTCACAGTGCACAAATCTCACCAAAATGATTATAGTTA-GATCATAAACAA
*
657 TGGAAAGAAAATAATTGAGGTTTGCCAAATCGAAGACAATTCAAAACGTCACTAATGGTCCCCGA
191 TGGAAAGAAAAGAATTGAGGTTTGCCAAATCGAAGACAATTCAAAACGTCACTAATGGTCCCCGA
* * * *
722 TAGGCCCAAAATAACAAGTGTTCCAGATGAGTTAAAAACTTCACAGTGCACAAATCTCACCAAAA
256 TAGGCCCAAAATAACAAGTGGTCCAAATGAGCTAAAAACTTCACAGAGCACAAATCTCACCAAAA
*
787 TGATTATAGTTAGGA-CATAAACAATGGAAAGAAAATAATTGAGGTTTGCCAAATCGAAGACGAT
321 TGATTATAGTTA-GATCATAAACAATGGAAAGAAAAGAATTGAGGTTTGCCAAATCGAAGACGAT
* *
851 TCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCATATGAGACTAAAAAC
385 TCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGGTCCAAATGAG-CTAAAAAC
916 TTCACAGTGGACTA
449 TTCACAGTGGACTA
* * * *
930 ATCTCACCAAAATGAATTATAGTTAGGCCGTAAACAATGGAAAGAAAGGCATCGAAGG-TTGCCA
1 ATCTCACCAAAATG-ATTATAGTCAGGCCATAAACAATGGAAAGAAAAGCATTG-AGGTTTGCCA
* *
994 AATCGAAGACAATTCAAAACGTCACTAATGGTCCCCGATGGGCCCAAAATAACAAGTGTTCCAAA
64 AATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
1059 TGAGCTAAAAACTTCACAGTG
129 TGAGCTAAAAACTTCACAGTG
1080 GACTAATC
Statistics
Matches: 571, Mismatches: 37, Indels: 16
0.92 0.06 0.03
Matches are distributed among these distances:
462 50 0.09
463 12 0.02
464 80 0.14
465 6 0.01
466 341 0.60
467 46 0.08
468 36 0.06
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (462 bp):
ATCTCACCAAAATGATTATAGTCAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
TCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
AGCTAAAAACTTCACAGTGCACAAATCTCACCAAAATGATTATAGTTAGATCATAAACAATGGAA
AGAAAAGAATTGAGGTTTGCCAAATCGAAGACAATTCAAAACGTCACTAATGGTCCCCGATAGGC
CCAAAATAACAAGTGGTCCAAATGAGCTAAAAACTTCACAGAGCACAAATCTCACCAAAATGATT
ATAGTTAGATCATAAACAATGGAAAGAAAAGAATTGAGGTTTGCCAAATCGAAGACGATTCAAAA
CGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGGTCCAAATGAGCTAAAAACTTCACAG
TGGACTA
Done.