Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011404.1 Corchorus olitorius cultivar O-4 contig11437, 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: 1732
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.27
Found at i:1104 original size:154 final size:152
Alignment explanation
Indices: 698--1729 Score: 1451
Period size: 154 Copynumber: 6.7 Consensus size: 152
688 ATTCGTATCA
* * *
698 ACTAATCTCACCAAAATGATTATAGTTAGGGCATAAACAATTGAAAGAAAAGCATCGAGGGTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGA-GGTTTC
** *
763 CAAATCGAAGACGATTCAAAACAAAACTAATGGGCCCCGA-ATGGCACAAAATAACAAGTGTTCG
65 CAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGATA-GGC-CAAAATAACAAGTGTTCC
*
827 AAATGAGC-AAAATCTTCACAGTGG
128 AAATGAGCTAAAAACTTCACAGTGG
* * * *
851 ACTAATCTCACTAAAAGGATTATAGTTAGGCCATAAACAAT-GAAAGAAACGCATGGAGGTTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGTTT-C
** * *
915 CAAATCGAAGACGATTCAAAACAAAACTAAAGGGCCCTGATAGGTCCAAAATAACAAGTGTTCCA
65 CAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGATAGG-CCAAAATAACAAGTGTTCCA
*
980 AATGAGTTAAAAACTTCACAGTGG
129 AATGAGCTAAAAACTTCACAGTGG
* ** * *
1004 ACTAACCTCTGCAAAATGATTATAGATAGGCCATAAACAATGGAAAGAAAGGCATCGAGGGTTTC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGA-GGTTTC
* *
1069 CAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCA
65 CAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGATAGGC-CAAAATAACAAGTGTTCCA
1134 AATGAGCTAAAAACTTCACAGTGG
129 AATGAGCTAAAAACTTCACAGTGG
* * * * *
1158 ACTAATCTCACTAAAATGATTATAGTTAGGCCATGAAGAATGGAAAGAAAAGCATTGAGGTATGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGT-TTC
* *
1223 CAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCA
65 CAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGATAGG-CCAAAATAACAAGTGTTCCA
1288 AATGAGCTAAAAACTTCACAGTGG
129 AATGAGCTAAAAACTTCACAGTGG
* * *
1312 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAATGAAAAGAATCGAGGTTGCC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGTTTCC
* *
1377 AAATCGAAGACGATTCAAAACGTCACTAATGCGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
66 AAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGATAGG-CCAAAATAACAAGTGTTCCAA
*
1442 ATGAGCTAAAAACTTCACGGTGG
130 ATGAGCTAAAAACTTCACAGTGG
* * * **
1465 ACAAATCTCACCAAAATGATTATAGTTAGGCGATAAACAATGGAATGAAAAGCATTAAGGTTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGTTT-C
* **
1530 CAAATCGAAGACAATTCAAAACAG-AACTAATGGGCCTTGATAGGCACAAAATAACAAGTGTTCC
65 CAAATCGAAGACGATTCAAAAC-GTAACTAATGGGCCCCGATAGGC-CAAAATAACAAGTGTTCC
*
1594 AAAAGAGCTAAAAACTTCACAGTGG
128 AAATGAGCTAAAAACTTCACAGTGG
* * *
1619 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAATGAAAAGAATTGAGGTTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGTTT-C
* * *
1684 CAAACCGAAGACGATTCAAAATGTCACTAATGGGCCCCGATAGGCC
65 CAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGATAGGCC
1730 CAA
Statistics
Matches: 795, Mismatches: 71, Indels: 26
0.89 0.08 0.03
Matches are distributed among these distances:
151 4 0.01
152 79 0.10
153 243 0.31
154 462 0.58
155 7 0.01
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.20
Consensus pattern (152 bp):
ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGTTTCC
AAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGATAGGCCAAAATAACAAGTGTTCCAAA
TGAGCTAAAAACTTCACAGTGG
Found at i:1438 original size:307 final size:307
Alignment explanation
Indices: 698--1728 Score: 1575
Period size: 307 Copynumber: 3.4 Consensus size: 307
688 ATTCGTATCA
* * *
698 ACTAATCTCACCAAAATGATTATAGTTAGGGCATAAACAATTGAAAGAAAAGCATCGAGGGTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGAATCGAGGGTTGC
** *
763 CAAATCGAAGACGATTCAAAACAAAACTAATGGGCCCCGA-ATGGCACAAAATAACAAGTGTTCG
66 CAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGATA-GGCACAAAATAACAAGTGTTCC
* *
827 AAATGAGC-AAAATCTTCACAGTGGACTAATCTCACTAAAAGGATTATAGTTAGGCCATAAACAA
130 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAA
* * * *
891 T-GAAAGAAACGCATGGAGGTTTGCCAAATCGAAGACGATTCAAAACAAAACTAAAGGGCCCTGA
195 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCTGA
* *
955 TAGGTCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGG
259 TAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
* ** * * * *
1004 ACTAACCTCTGCAAAATGATTATAGATAGGCCATAAACAATGGAAAGAAAGGCATCGAGGGTTTC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGAATCGAGGGTTGC
* *
1069 CAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCA
66 CAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGATAGGCACAAAATAACAAGTGTTCCA
* *
1134 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATGAAGAAT
131 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAAT
* *
1199 GGAAAGAAAAGCATTGAGGTATGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCTGAT
196 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCTGAT
1264 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
260 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
*
1312 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAATGAAAAGAATCGA-GGTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGAATCGAGGGTTGC
* * *
1376 CAAATCGAAGACGATTCAAAACGTCACTAATGCGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
66 CAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGATAGGCACAAAATAACAAGTGTTCCA
* * * *
1441 AATGAGCTAAAAACTTCACGGTGGACAAATCTCACCAAAATGATTATAGTTAGGCGATAAACAAT
131 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAAT
* * * *
1506 GGAATGAAAAGCATTAAGGTTTGCCAAATCGAAGACAATTCAAAACAGAACTAATGGGCCTTGAT
196 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCTGAT
* *
1571 AGGCACAAAATAACAAGTGTTCCAAAAGAGCTAAAAACTTCACAGTGG
260 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
* * *
1619 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAATGAAAAGAATTGAGGTTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGAATCGAGGGTTGC
* * *
1684 CAAACCGAAGACGATTCAAAATGTCACTAATGGGCCCCGATAGGC
66 CAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGATAGGC
1729 CCAA
Statistics
Matches: 664, Mismatches: 55, Indels: 10
0.91 0.08 0.01
Matches are distributed among these distances:
306 124 0.19
307 338 0.51
308 202 0.30
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (307 bp):
ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGAATCGAGGGTTGC
CAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGATAGGCACAAAATAACAAGTGTTCCA
AATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAAT
GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGAACTAATGGGCCCTGATA
GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
Found at i:1559 original size:461 final size:459
Alignment explanation
Indices: 698--1732 Score: 1554
Period size: 461 Copynumber: 2.2 Consensus size: 459
688 ATTCGTATCA
* * *
698 ACTAATCTCACCAAAATGATTATAGTTAGGGCATAAACAATTGAAAGAAAAGCATCGAGGGTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GGTTGC
*** * *
763 CAAATCGAAGACGATTCAAAACAAAACTAATGGGCCCCGA-ATGGCACAAAATAACAAGTGTTCG
65 CAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATA-GGCCCAAAATAACAAGTGTTCC
* *
827 AAATGAGCAAAATCTTCACAGTGGACTAATCTCACTAAAAGGATTATAGTTAGGCCATAAACAAT
129 AAATGAGCAAAAACTTCACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAAT
* * * * *
892 GAAAGAAACGCATGGAGGTTTGCCAAATCGAAGACGATTCAAAACAAAACTAAAGGGCCCTGATA
194 GAAAGAAAAGAATCGAGGTTTGCCAAATCGAAGACGATTCAAAACAAAACTAAAGCGCCCCGATA
* * * **
957 GGTCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAACCTCTGCAAAATG
259 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACAAACCTCACCAAAATG
* * *
1022 ATTATAGATAGGCCATAAACAATGGAAAGAAAGGCATCGAGGGTTTCCAAATCGAAGACGATTCA
324 ATTATAGATAGGCCATAAACAATGGAAAGAAAAGCATCGAAGGTTTCCAAATCGAAGACAATTCA
* *
1087 AAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
389 AAACAGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAAAGAGCTAAAAACTTCA
1152 CAGTGG
454 CAGTGG
* * *
1158 ACTAATCTCACTAAAATGATTATAGTTAGGCCATGAAGAATGGAAAGAAAAGCATTGAGGTATGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGT-TGC
*
1223 CAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCA
65 CAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
*
1288 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
130 AATGAGC-AAAAACTTCACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAAT
* *** *
1353 GGAATGAAAAGAATCGAGG-TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGCGCCCCGAT
194 -GAAAGAAAAGAATCGAGGTTTGCCAAATCGAAGACGATTCAAAACAAAACTAAAGCGCCCCGAT
* *
1417 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACGGTGGACAAATCTCACCAAAAT
258 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACAAACCTCACCAAAAT
* * * *
1482 GATTATAGTTAGGCGATAAACAATGGAATGAAAAGCAT-TAAGGTTTGCCAAATCGAAGACAATT
323 GATTATAGATAGGCCATAAACAATGGAAAGAAAAGCATCGAAGGTTT-CCAAATCGAAGACAATT
** *
1546 CAAAACAGAACTAATGGGCCTTGATAGGCACAAAATAACAAGTGTTCCAAAAGAGCTAAAAACTT
387 CAAAACAGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAAAGAGCTAAAAACTT
1611 CACAGTGG
452 CACAGTGG
* *
1619 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAATGAAAAGAATTGAGGTTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTGC
* *
1684 CAAACCGAAGACGATTCAAAATGTCACTAATGGGCCCCGATAGGCCCAA
65 CAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAA
Statistics
Matches: 517, Mismatches: 52, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
459 3 0.01
460 125 0.24
461 374 0.72
462 15 0.03
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (459 bp):
ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTGCC
AAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
ATGAGCAAAAACTTCACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGA
AAGAAAAGAATCGAGGTTTGCCAAATCGAAGACGATTCAAAACAAAACTAAAGCGCCCCGATAGG
CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACAAACCTCACCAAAATGAT
TATAGATAGGCCATAAACAATGGAAAGAAAAGCATCGAAGGTTTCCAAATCGAAGACAATTCAAA
ACAGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAAAGAGCTAAAAACTTCACA
GTGG
Done.