Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011931.1 Corchorus olitorius cultivar O-4 contig11964, 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, 984
Length: 1641
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Found at i:298 original size:154 final size:154
Alignment explanation
Indices: 1--1641 Score: 2410
Period size: 154 Copynumber: 10.7 Consensus size: 154
* * * * * *
1 AACTTCAAAGTGGACGTAATCTAAACAAAATGATTATAGGTAGGCCATAAACAATGGAAACAAAC
1 AACTTCACAGTGGAC-TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
* * *
66 GCATTGAGGCTTGCCAATTCGAAGAAGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAA
65 GCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAA
*
131 TAACAAGTGTTCCAAATTAGCTAAA
130 TAACAAGTGTTCCAAATGAGCTAAA
*
156 AAGTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * *
221 CCTTGAGGTTTGCCAAATCGAATACGAATCAATACGTCACTAATGGGCCCCGATAGGCCCAAAAT
66 CATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAAT
*
286 AACAAGTATTCCAAATGAGCTAAA
131 AACAAGTGTTCCAAATGAGCTAAA
* ** *
310 AACTTCACAGTGGACTAATTTCACCAAAATGATTATAGTTACACCATAAACAATGGAAAGAAACG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* **
375 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAAT
66 CATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAAT
* * *
440 AACAAGGGTTCCAACTGAGCTATA
131 AACAAGTGTTCCAAATGAGCTAAA
* * * *
464 AAGTTCACTGTGGACTAATCTCACCAAAATTATTATAGTTAGGCCATAAACAATGGAACGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* *
529 CCTTGAGGTTGGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAAT
66 CATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAAT
**
594 AACAAGTGTTCCAAATTTGCTAAA
131 AACAAGTGTTCCAAATGAGCTAAA
* * *
618 AAGTGCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAA
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * ** *
683 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAA-GGAGCCCCGATAGTCCCAAAA
66 CATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGG-GCCCCGATAGGCCCAAAA
*
747 TAACAAGTGTTCCAAATGAGCTACA
130 TAACAAGTGTTCCAAATGAGCTAAA
*
772 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGCAT-AACAATGGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * * *
836 CATTGAGGTTTGCCAAATCGAAGACTATTCAAAACAG-AACTAATGAGCCCCGATAGGCCCAAAA
66 CATTGAGGTTTGCCAAATCGAAGACGATTCAATAC-GTCACTAATGGGCCCCGATAGGCCCAAAA
900 TAACAAGTGTTCCAAATG-GCTAAA
130 TAACAAGTGTTCCAAATGAGCTAAA
*
924 AATTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * * * *
989 CGTTGAGGTTTGCCAAATCGAAGACGATTTAAAACG-GATTTAATGGGACCCCGATAGGCCCAAA
66 CATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCA-CTAATGGG-CCCCGATAGGCCCAAA
*
1053 ATAACAAGTGTTCCAACTGAGCTAAA
129 ATAACAAGTGTTCCAAATGAGCTAAA
* * * * *
1079 AAGTTCACAGTGGACTAATATCACCAACATGATTATAGTTAGGTCATAAATAATGGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* ** *
1144 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGAAACTAATGGGCCCCGATAGGCCTAAAAT
66 CATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAAT
*
1209 AACAGGTGTTCCAAATGAGCTAAA
131 AACAAGTGTTCCAAATGAGCTAAA
* * * * * *
1233 AACTTCAAAGTGGACTAATCTAAACAAAATGATTATAGGTAGGCCATAAACAATGGAAACAAACG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * *
1298 CATTGAGGCTTGCCAATTCGAAGAAGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAAT
66 CATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAAT
1363 AACAAGTGTTCCAAATGAGCTAAA
131 AACAAGTGTTCCAAATGAGCTAAA
* * *
1387 AATTTCACAGTGGACTAATCTCACCAAAATAATTATAGTTACGCCATAAACAATGGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * **
1452 CATTGAGGTTTGCAAAATCGAAGACGGTTCAATATATCACTAATGGGCCCCGATAGGCCCAAAAT
66 CATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAAT
1517 AACAAGTGTTCCAAATGAGCTAAA
131 AACAAGTGTTCCAAATGAGCTAAA
* * * * *
1541 AACTTCAAAGTGGACTAATCTAAACAAAATGATTATAGGTAGGCCATAAACAATGGAAACAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * *
1606 CATTGAGGCTTGCCAATTCGAAGAAGATTCAATACG
66 CATTGAGGTTTGCCAAATCGAAGACGATTCAATACG
Statistics
Matches: 1335, Mismatches: 143, Indels: 17
0.89 0.10 0.01
Matches are distributed among these distances:
152 52 0.04
153 147 0.11
154 1015 0.76
155 120 0.09
156 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (154 bp):
AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
CATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAAT
AACAAGTGTTCCAAATGAGCTAAA
Found at i:1527 original size:769 final size:770
Alignment explanation
Indices: 1--1637 Score: 2579
Period size: 769 Copynumber: 2.1 Consensus size: 770
*
1 AACTTCAAAGTGGACGTAATCTAAACAAAATGATTATAGGTAGGCCATAAACAATGGAAACAAAC
1 AACTTCAAAGTGGAC-TAATCTAAACAAAATGATTATAGGTAGGCCATAAACAATGGAAACAAAA
* * *
66 GCATTGAGGCTTGCCAATTCGAAGAAGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAA
65 GCATTGAGGCTTGCCAATTCGAAGAAGATTCAAAACGTAACTAATGAGCCCCGATAGGCCCAAAA
131 TAACAAGTGTTCCAAATTAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
130 TAACAAGTGTTCCAAATTAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* *
196 AGGCCATAAACAATGGAAAGAAAAGCCTTGAGGTTTGCCAAATCGAATACGAATCAATACGTCAC
195 AGGCCATAAACAATGGAAAGAAAAGCCTTGAGGTTTGCCAAATCGAAGACGAATCAAAACGTCAC
261 TAATGGGCCCCGATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTTCACAGTGGACT
260 TAATGGGCCCCGATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTTCACAGTGGACT
* *
326 AATTTCACCAAAATGATTATAGTTACACCATAAACAATGGAAAGAAACGCATTGAGGTTTGCCAA
325 AATATCACCAAAATGATTATAGTTACACCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
* *
391 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGGGTTCCAACT
390 ATCGAAGACGATTCAAAACGAAACTAATGGGCCCCGATAGGCCCAAAATAACAAGGGTTCCAAAT
* * ** * * * *
456 GAGCTATAAAGTTCACTGTGGACTAATCTCACCAAAATTATTATAGTTAGGCCATAAACAATGGA
455 GAGCTAAAAACTTCAAAGTGGACTAATCTAAACAAAATGATTATAGGTAGGCCATAAACAATGGA
* *
521 ACGAAAAGCCTTGAGGTTGGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGG
520 ACGAAAAGCATTGAGGTTGGCCAAATCGAAGAAGATTCAATACGTCACTAATGGGCCCCGATAGG
** *
586 CCCAAAATAACAAGTGTTCCAAATTTGCTAAAAAGTGCACAGTGGACTAATCTCACCAAAATGAT
585 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTGCACAGTGGACTAATCTCACCAAAATAAT
* *
651 TATAGTTAGGCCATAAACAATGGAAAGAAAAACATTGAGGTTTGCCAAATCGAAGACGATTCAAA
650 TATAGTTACGCCATAAACAATGGAAAGAAAAACATTGAGGTTTGCAAAATCGAAGACGATTCAAA
* * *
716 ATGGAACTAAGGAGCCCCGATAGTCCCAAAATAACAAGTGTTCCAAATGAGCTACA
715 ATAGAACTAAGGAGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
* * * * * *
772 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGCAT-AACAATGGAAAGAAAAG
1 AACTTCAAAGTGGACTAATCTAAACAAAATGATTATAGGTAGGCCATAAACAATGGAAACAAAAG
* * **
836 CATTGAGGTTTGCCAAATCGAAGACTATTCAAAACAG-AACTAATGAGCCCCGATAGGCCCAAAA
66 CATTGAGGCTTGCCAATTCGAAGAAGATTCAAAAC-GTAACTAATGAGCCCCGATAGGCCCAAAA
* *
900 TAACAAGTGTTCCAAA-TGGCTAAAAATTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
130 TAACAAGTGTTCCAAATTAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * * *
964 AGGCCATAAACAATGGAAAGAAAAGCGTTGAGGTTTGCCAAATCGAAGACGATTTAAAACG-GAT
195 AGGCCATAAACAATGGAAAGAAAAGCCTTGAGGTTTGCCAAATCGAAGACGAATCAAAACGTCA-
* * * *
1028 TTAATGGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAACTGAGCTAAAAAGTTCACAGTGGA
259 CTAATGGG-CCCCGATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTTCACAGTGGA
* *** *
1093 CTAATATCACCAACATGATTATAGTTAGGTCATAAATAATGGAAAGAAAAGCATTGAGGTTTGCC
323 CTAATATCACCAAAATGATTATAGTTACACCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCC
*
1158 AAATCGAAGACGATTCAAAACGAAACTAATGGGCCCCGATAGGCCTAAAATAAC-AGGTGTTCCA
388 AAATCGAAGACGATTCAAAACGAAACTAATGGGCCCCGATAGGCCCAAAATAACAAGG-GTTCCA
1222 AATGAGCTAAAAACTTCAAAGTGGACTAATCTAAACAAAATGATTATAGGTAGGCCATAAACAAT
452 AATGAGCTAAAAACTTCAAAGTGGACTAATCTAAACAAAATGATTATAGGTAGGCCATAAACAAT
* *
1287 GGAAAC-AAACGCATTGAGGCTT-GCCAATTCGAAGAAGATTCAATACGTCACTAATGGGCCCCG
517 GG-AACGAAAAGCATTGAGG-TTGGCCAAATCGAAGAAGATTCAATACGTCACTAATGGGCCCCG
* *
1350 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGACTAATCTCACCAAA
580 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTGCACAGTGGACTAATCTCACCAAA
* *
1415 ATAATTATAGTTACGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCAAAATCGAAGACGGT
645 ATAATTATAGTTACGCCATAAACAATGGAAAGAAAAACATTGAGGTTTGCAAAATCGAAGACGAT
* **
1480 TCAATATATCACTAATGG-GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
710 TCAAAATAGAACTAA-GGAGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
1541 AACTTCAAAGTGGACTAATCTAAACAAAATGATTATAGGTAGGCCATAAACAATGGAAACAAAAG
1 AACTTCAAAGTGGACTAATCTAAACAAAATGATTATAGGTAGGCCATAAACAATGGAAACAAAAG
1606 CATTGAGGCTTGCCAATTCGAAGAAGATTCAA
66 CATTGAGGCTTGCCAATTCGAAGAAGATTCAA
1638 TACG
Statistics
Matches: 785, Mismatches: 73, Indels: 17
0.90 0.08 0.02
Matches are distributed among these distances:
767 1 0.00
768 112 0.14
769 578 0.74
770 80 0.10
771 14 0.02
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (770 bp):
AACTTCAAAGTGGACTAATCTAAACAAAATGATTATAGGTAGGCCATAAACAATGGAAACAAAAG
CATTGAGGCTTGCCAATTCGAAGAAGATTCAAAACGTAACTAATGAGCCCCGATAGGCCCAAAAT
AACAAGTGTTCCAAATTAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
GGCCATAAACAATGGAAAGAAAAGCCTTGAGGTTTGCCAAATCGAAGACGAATCAAAACGTCACT
AATGGGCCCCGATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTTCACAGTGGACTA
ATATCACCAAAATGATTATAGTTACACCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
TCGAAGACGATTCAAAACGAAACTAATGGGCCCCGATAGGCCCAAAATAACAAGGGTTCCAAATG
AGCTAAAAACTTCAAAGTGGACTAATCTAAACAAAATGATTATAGGTAGGCCATAAACAATGGAA
CGAAAAGCATTGAGGTTGGCCAAATCGAAGAAGATTCAATACGTCACTAATGGGCCCCGATAGGC
CCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTGCACAGTGGACTAATCTCACCAAAATAATT
ATAGTTACGCCATAAACAATGGAAAGAAAAACATTGAGGTTTGCAAAATCGAAGACGATTCAAAA
TAGAACTAAGGAGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
Done.