Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011653.1 Corchorus olitorius cultivar O-4 contig11686, 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, 859
Length: 1432
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Found at i:360 original size:154 final size:154
Alignment explanation
Indices: 1--1432 Score: 2047
Period size: 154 Copynumber: 9.3 Consensus size: 154
* * * * *
1 TAGGCCATAAACAATGGAAAGAAAAACATTGAGGTTTGCCAAATCAAAGATGATTCAAAACGGAA
1 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTAA
*
66 CTAATGGGCCCCGATAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAAGTGGA
66 CTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC-AGTGGA
131 CTAATCTCACCAAAATGATTATAGT
130 CTAATCTCACCAAAATGATTATAGT
* * ** * * * *
156 TAGTCCATATAA-AATGGAAAGAAAAGCTTTGAGTTTTGCCAAATCAAAGACGATTCAATACATC
1 TAGGCCATA-AACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTA
* *
220 ACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAAAGAGCTAAAAACTTCATC-GTGG
65 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA-CAGTGG
284 ACTAATCTCACCAAAATGATTATAGT
129 ACTAATCTCACCAAAATGATTATAGT
* * * *
310 TAGGCCATAAACAATAGAAAGAAAAACATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAA
1 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTAA
* * * *
375 CTAATGGGCCCCGATAGGCCCAAAATATCAATTGTTCCAAATGTGCTAAAAACTTCATAGTGGAC
66 CTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
440 TAATCTCACCAAAATGATTATAGT
131 TAATCTCACCAAAATGATTATAGT
* *
464 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTG-TAAATCGAAGACGATTCAAAACGTCA
1 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTAA
** * * * *
528 CTAATGATCCCCAATAGGACCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAT
66 CTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
593 TAATCTCACCAAAATGATTATAGT
131 TAATCTCACCAAAATGATTATAGT
* * * * * *
617 TAGGGCATATACAATGGAAATAAAAGCTTTGAGGGTTGCAAAATCGAAGACGATTCAAAAC-AAT
1 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTA-
* ** *
681 ACTAATGGACCCTAATAGGCCCAAAATAACAGGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
65 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
746 CTAATCTCACCAAAATGATTATAGT
130 CTAATCTCACCAAAATGATTATAGT
* * * **
771 TAGGGCATAAACAAAGGAAAGAAAAGACATTGAGGGTTGCCAAATCGAAGACAATTCAAAACAAA
1 TAGGCCATAAACAATGGAAAGAAAAG-CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTA
*
836 ACTAATTGGCCCCGATAGGCCCCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
65 ACTAATGGGCCCCGATAGG-CCC-AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
901 GACTAATCTCACCAAAATGATTATAGT
128 GACTAATCTCACCAAAATGATTATAGT
* *
928 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATTGAAGACGATTCAAAACGGAA
1 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTAA
* **
993 CTAATGGGCCCCGATAGGCCCAAAATATCAAGTGTTCCAAATTTGCTAAAAACTTCACAGTGGAC
66 CTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
1058 TAATCTCACCAAAATGATTATAGT
131 TAATCTCACCAAAATGATTATAGT
*
1082 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTG-CAAATCGAAGACGATTCAAAACGTCA
1 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTAA
* * * * * *
1146 CTAATGAGCCCCAATAGGACCAAAATAAAAAGTGTTCCAAATGAGCT-AAAATTTCACAGTGGAT
66 CTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
1210 TAATCTCACCAAAATGATTATAGT
131 TAATCTCACCAAAATGATTATAGT
* *
1234 TAGGGCATATACAATGGAAAGAAAAGCATTGA-GGTTG-CAAATCGAAGACGATTCAAAACGTCA
1 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGT-A
** * * *
1297 ACTAAT-GATCCCAATAGG-CTAAATATAAAAAAGTGTTCCAAAATGAAGCTAAAAAACTTCACA
65 ACTAATGGGCCCCGATAGGCCCAAA-AT-AACAAGTGTTCC-AAATG-AGCT-AAAAACTTCACA
1360 GTGGACTAATCTACACCAAAAATGATTATAGT
125 GTGGACTAATCT-CACC-AAAATGATTATAGT
*
1392 TAGGGCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCA
1 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCA
Statistics
Matches: 1155, Mismatches: 101, Indels: 37
0.89 0.08 0.03
Matches are distributed among these distances:
150 4 0.00
151 40 0.03
152 87 0.08
153 206 0.18
154 433 0.37
155 157 0.14
156 81 0.07
157 95 0.08
158 45 0.04
159 5 0.00
160 2 0.00
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (154 bp):
TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTAA
CTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
TAATCTCACCAAAATGATTATAGT
Found at i:663 original size:307 final size:308
Alignment explanation
Indices: 1--1432 Score: 2085
Period size: 307 Copynumber: 4.6 Consensus size: 308
* * * *
1 TAGGCCATAAACAATGGAAAGAAAAACATTGAGGTTTGCCAAATCAAAGATGATTCAAAACGGAA
1 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAA
*
66 CTAATGGGCCCCGATAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAAGTGGA
66 CTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC-AGTGGA
* * **
131 CTAATCTCACCAAAATGATTATAGTTAGTCCATATAA-AATGGAAAGAAAAGCTTTGAGTTTTGC
130 CTAATCTCACCAAAATGATTATAGTTAGGCCATA-AACAATGGAAAGAAAAGCATTGAGGGTTGC
* * * ** * *
195 CAAATCAAAGACGATTCAATACATCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCA
194 CAAATCGAAGACGATTCAAAACATCACTAATGAGCCCCAATAGGACCAAAATAAAAAGTGTTCCA
*
260 AAAGAGCTAAAAACTTCATC-GTGGACTAATCTCACCAAAATGATTATAGT
259 AATGAGCTAAAAACTTCA-CAGTGGACTAATCTCACCAAAATGATTATAGT
* * *
310 TAGGCCATAAACAATAGAAAGAAAAACATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAA
1 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAA
* * * *
375 CTAATGGGCCCCGATAGGCCCAAAATATCAATTGTTCCAAATGTGCTAAAAACTTCATAGTGGAC
66 CTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
*
440 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTG-TA
131 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCA
* *
504 AATCGAAGACGATTCAAAACGTCACTAATGATCCCCAATAGGACCAAAATAAAAAGTGTTCCAAA
196 AATCGAAGACGATTCAAAACATCACTAATGAGCCCCAATAGGACCAAAATAAAAAGTGTTCCAAA
*
569 TGAGCTAAAAACTTCACAGTGGATTAATCTCACCAAAATGATTATAGT
261 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
* * * * * *
617 TAGGGCATATACAATGGAAATAAAAGCTTTGAGGGTTGCAAAATCGAAGACGATTCAAAAC-AAT
1 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA-
* ** *
681 ACTAATGGACCCTAATAGGCCCAAAATAACAGGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
65 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
* *
746 CTAATCTCACCAAAATGATTATAGTTAGGGCATAAACAAAGGAAAGAAAAGACATTGAGGGTTGC
130 CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG-CATTGAGGGTTGC
* ** * * *
811 CAAATCGAAGACAATTCAAAACAAAACTAATTG-GCCCCGATAGGCCCCAAAAATAACAAGTGTT
194 CAAATCGAAGACGATTCAAAACATCACTAA-TGAGCCCCAATAGG-ACC-AAAATAAAAAGTGTT
875 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
256 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
*
928 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATTGAAGACGATTCAAAACGGAA
1 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAA
* **
993 CTAATGGGCCCCGATAGGCCCAAAATATCAAGTGTTCCAAATTTGCTAAAAACTTCACAGTGGAC
66 CTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
1058 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTG-CA
131 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCA
*
1122 AATCGAAGACGATTCAAAACGTCACTAATGAGCCCCAATAGGACCAAAATAAAAAGTGTTCCAAA
196 AATCGAAGACGATTCAAAACATCACTAATGAGCCCCAATAGGACCAAAATAAAAAGTGTTCCAAA
* *
1187 TGAGCT-AAAATTTCACAGTGGATTAATCTCACCAAAATGATTATAGT
261 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
* * *
1234 TAGGGCATATACAATGGAAAGAAAAGCATTGA-GGTTG-CAAATCGAAGACGATTCAAAACGTCA
1 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACG-GA
** * * *
1297 ACTAAT-GATCCCAATAGG-CTAAATATAAAAAAGTGTTCCAAAATGAAGCTAAAAAACTTCACA
65 ACTAATGGGCCCCGATAGGCCCAAA-AT-AACAAGTGTTCC-AAATG-AGCT-AAAAACTTCACA
*
1360 GTGGACTAATCTACACCAAAAATGATTATAGTTAGGGCATAAACAATGGAAAGAAAAGCATTGAG
125 GTGGACTAATCT-CACC-AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAG
1425 GGTTGCCA
188 GGTTGCCA
Statistics
Matches: 1013, Mismatches: 91, Indels: 36
0.89 0.08 0.03
Matches are distributed among these distances:
303 4 0.00
304 33 0.03
305 22 0.02
306 75 0.07
307 290 0.29
308 102 0.10
309 189 0.19
310 67 0.07
311 230 0.23
312 1 0.00
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (308 bp):
TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAA
CTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCA
AATCGAAGACGATTCAAAACATCACTAATGAGCCCCAATAGGACCAAAATAAAAAGTGTTCCAAA
TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
Found at i:1185 original size:618 final size:611
Alignment explanation
Indices: 1--1432 Score: 2264
Period size: 618 Copynumber: 2.3 Consensus size: 611
* * * * * *
1 TAGGCCATAAACAATGGAAAGAAAAACATTGAGGTTTGCCAAATCAAAGATGATTCAAAACGGA-
1 TAGGGCATATACAATGGAAAGAAAAGCATTGAGGGTTG-CAAATCGAAGACGATTCAAAAC--AT
* *
65 ACTAATGGGCCCCGATAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAAGTGG
63 ACTAAT-GGACCCAATAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC-AGTGG
** * **
130 ACTAATCTCACCAAAATGATTATAGTTAGTCCATATAA-AATGGAAAGAAAAGCTTTGAGTTTTG
126 ACTAATCTCACCAAAATGATTATAGTTAGGGCATA-AACAATGGAAAGAAAAGCATTGAGGGTTG
* * ** *
194 CCAAATCAAAGACGATTCAATACATCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCC
190 CCAAATCAAAGACAATTCAAAACAAAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
259 AAAAGAGCTAAAAACTTCATCGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
255 AAAAGAGCTAAAAACTTCATCGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
*
324 TAGAAAGAAAAACATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA
320 TAGAAAGAAAAACATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA
* *
389 TAGGCCCAAAATATCAATTGTTCCAAATGTGCTAAAAACTTCATAGTGGACTAATCTCACCAAAA
385 TAGGCCCAAAATATCAAGTGTTCCAAATGTGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA
*
454 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGTAAATCGAAGACGATTC
450 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCAAATCGAAGACGATTC
*
519 AAAACGTCACTAATGATCCCCAATAGGACCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTC
515 AAAACGTCACTAATGAGCCCCAATAGGACCAAAATAAAAAGTGTTCCAAATGAGCT-AAAACTTC
584 ACAGTGGATTAATCTCACCAAAATGATTATAGT
579 ACAGTGGATTAATCTCACCAAAATGATTATAGT
* *
617 TAGGGCATATACAATGGAAATAAAAGCTTTGAGGGTTGCAAAATCGAAGACGATTCAAAACAATA
1 TAGGGCATATACAATGGAAAGAAAAGCATTGAGGGTTGC-AAATCGAAGACGATTCAAAAC-ATA
* *
682 CTAATGGACCCTAATAGGCCCAAAATAACAGGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
64 CTAATGGACCC-AATAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
*
747 TAATCTCACCAAAATGATTATAGTTAGGGCATAAACAAAGGAAAGAAAAGACATTGAGGGTTGCC
128 TAATCTCACCAAAATGATTATAGTTAGGGCATAAACAATGGAAAGAAAAG-CATTGAGGGTTGCC
* *
812 AAATCGAAGACAATTCAAAACAAAACTAATTGGCCCCGATAGGCCCCAAAAATAACAAGTGTTCC
192 AAATCAAAGACAATTCAAAACAAAACTAATGGGCCCCGATAGG-CCC-AAAATAACAAGTGTTCC
*
877 AAATGAGCTAAAAACTTCA-CAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
255 AAAAGAGCTAAAAACTTCATC-GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
* * *
941 ATGGAAAGAAAAGCATTGAGGGTTGCCAAATTGAAGACGATTCAAAACGGAACTAATGGGCCCCG
319 ATAGAAAGAAAAACATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCG
*
1006 ATAGGCCCAAAATATCAAGTGTTCCAAATTTGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
384 ATAGGCCCAAAATATCAAGTGTTCCAAATGTGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
1071 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCAAATCGAAGACGATT
449 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCAAATCGAAGACGATT
*
1136 CAAAACGTCACTAATGAGCCCCAATAGGACCAAAATAAAAAGTGTTCCAAATGAGCTAAAATTTC
514 CAAAACGTCACTAATGAGCCCCAATAGGACCAAAATAAAAAGTGTTCCAAATGAGCTAAAACTTC
1201 ACAGTGGATTAATCTCACCAAAATGATTATAGT
579 ACAGTGGATTAATCTCACCAAAATGATTATAGT
*
1234 TAGGGCATATACAATGGAAAGAAAAGCATTGA-GGTTGCAAATCGAAGACGATTCAAAACGTCAA
1 TAGGGCATATACAATGGAAAGAAAAGCATTGAGGGTTGCAAATCGAAGACGATTCAAAACAT--A
*
1298 CTAAT-GATCCCAATAGG-CTAAATATAAAAAAGTGTTCCAAAATGAAGCTAAAAAACTTCACAG
64 CTAATGGA-CCCAATAGGCCTAAA-AT-AACAAGTGTTCC-AAATG-AGCT-AAAAACTTCACAG
1361 TGGACTAATCTACACCAAAAATGATTATAGTTAGGGCATAAACAATGGAAAGAAAAGCATTGAGG
123 TGGACTAATCT-CACC-AAAATGATTATAGTTAGGGCATAAACAATGGAAAGAAAAGCATTGAGG
1426 GTTGCCA
186 GTTGCCA
Statistics
Matches: 754, Mismatches: 44, Indels: 32
0.91 0.05 0.04
Matches are distributed among these distances:
614 7 0.01
615 89 0.12
616 172 0.23
617 79 0.10
618 325 0.43
619 24 0.03
620 19 0.03
621 39 0.05
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (611 bp):
TAGGGCATATACAATGGAAAGAAAAGCATTGAGGGTTGCAAATCGAAGACGATTCAAAACATACT
AATGGACCCAATAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
TCTCACCAAAATGATTATAGTTAGGGCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAAT
CAAAGACAATTCAAAACAAAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAAAGA
GCTAAAAACTTCATCGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATAGAAA
GAAAAACATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
CAAAATATCAAGTGTTCCAAATGTGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCAAATCGAAGACGATTCAAAACG
TCACTAATGAGCCCCAATAGGACCAAAATAAAAAGTGTTCCAAATGAGCTAAAACTTCACAGTGG
ATTAATCTCACCAAAATGATTATAGT
Done.