Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011072.1 Corchorus olitorius cultivar O-4 contig11105, 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: 1806
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:494 original size:154 final size:154
Alignment explanation
Indices: 1--1801 Score: 2594
Period size: 154 Copynumber: 11.6 Consensus size: 154
*
1 CATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAAT
1 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
*
66 AACAAGTATTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
66 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
131 GGCCATACAACAATAGGAAAGAAAAG
131 GGCCATA-AACAAT-GGAAAGAAAAG
* * * *
157 CATTGAGGTTTGCCAAATCGAAGACGATTTAATACGTCAGTAATGGGCCCCGATAGGCGCAAAAT
1 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
* *
222 AACAAGTGTTCCAACTGAGCTAAAAAGTTCACAGTGGACTAATCTCACC-AAATGATTATAGTTA
66 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
*
286 GGTCATAAACAATGGAAAGAAAAG
131 GGCCATAAACAATGGAAAGAAAAG
* ** * * *
310 CATTGAGGTTTGCCAAATCGAAAACGATTCAAAACGGAACTAATGAGCCCCGTTAGACCCAAAAT
1 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
* * * *
375 AACAAGTGTTCCGAATGAGCTAAAAACTTCACGGTGGACAAATCTCACCAAAATTATTATAGTTA
66 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
440 GGCCATAAACAATGGAAAGAAAAG
131 GGCCATAAACAATGGAAAGAAAAG
* * **
464 CATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCATTAATGGGCCCCGATAGGCTGAAAAT
1 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
* * * * * *
529 AACAAGTGTTCAAAATAAGCTAAAAACTTCAAAGTGGACTAATCTAAACAAAATGATTANAG-TA
66 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
*
593 GGCCATAAACAATGGAAA-CAAAG
131 GGCCATAAACAATGGAAAGAAAAG
* * * *
616 CATTGAGGCTTGCCAAATTCGAAGA-AATTCAATACGTCACTAATGGGCCACGATAGGCCCAAAA
1 CATTGAGGTTTGCCAAA-TCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAA
*
680 TAACAAGTATTCCAAATGAGCTAAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTACTAG
65 TAACAAGTGTTCCAAATGAGCT-AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA-TAG
*
745 TTAGACCATAAACGAATGGAAAGAAAAG
128 TTAGGCCATAAAC-AATGGAAAGAAAAG
* ** *
773 CGTTGAGGTTTGCCAAAATCGAAGACGATTACAAAACGGAACTAATGGGCCCCGATAAGCCCAAA
1 CATTGAGGTTTGCC-AAATCGAAGACGATT-CAAAACGTCACTAATGGGCCCCGATAGGCCCAAA
*
838 ATAACAAGTGTTCCAAATGAGCTAAAAAGTTCACAGTGGTACTAATCTCACCAAAATGATTATAG
64 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG-ACTAATCTCACCAAAATGATTATAG
903 TTAGGCCATAAACAATGGAAAGAAAAG
128 TTAGGCCATAAACAATGGAAAGAAAAG
* ** *
930 CATTGAGGTTTGCCAAATCGAAGGCGATTC-AAACGGAACTAATGGGCCCCGATAGGTCCGAAAA
1 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGG-CCCAAAA
* *
994 TAACAAGTGTTCCAAATGAGCTAAAACCTTCACAGTAGACTAATCTCACCAAAATGATTATACGT
65 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA-GT
1059 TAGGCCCCATAAACAATGGAAAGAAAAG
129 TAGG--CCATAAACAATGGAAAGAAAAG
** **
1087 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCTTGATAGGCCCAAAAT
1 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
* ** *
1152 AACAAGTGTTCCAAATGAGCCAAAAACTTCACAGTGTTCTAATCTCACCGAAATGATTATAGTTA
66 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
1217 GGCCATAAACAATGGAAAGAAAAG
131 GGCCATAAACAATGGAAAGAAAAG
** **
1241 CATCAAAGG-TTGCCAAATC-AATGACGATTCAAAACGTCACTAATGGGCCTTGATAGGCCCAAA
1 CAT-TGAGGTTTGCCAAATCGAA-GACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAA
* *** *
1304 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATTTTCTAATCTCACCGAAATGATTATAGT
64 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
1369 TAGGCCATAAA-AATGGAAAGAAAAG
129 TAGGCCATAAACAATGGAAAGAAAAG
** * ** * **
1394 CATCAAGGGTTGCCAAATCGATTACGATTCAAAACGTCATTAATGGGCCTTGATAGGCCCAAAAT
1 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
1459 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
66 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
*
1524 GGCCATAAACAATGGAAAGAAAAA
131 GGCCATAAACAATGGAAAGAAAAG
* * * ** * *
1548 TATTGAGGTTTACCAAATCGAAGACGATTTAAAACGTCACTAATGGGCCTTGATGGGCACAAAAT
1 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
* * **
1613 AACAAGTGTTCTAAATGAGCTAAAAACTTCACAGCGGACTAATCTCACCAAAAAAATTATAGTTA
66 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
1678 GGCCATAAACAATGGAAAGAAAA-
131 GGCCATAAACAATGGAAAGAAAAG
* ***
1701 CATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCTTTGATAGGCCCAAAAT
1 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
*
1766 AACAAGTGTTCCAAATGAGCGAAAAAACTTCACAGT
66 AACAAGTGTTCCAAATGAGC-TAAAAACTTCACAGT
1802 TTTCT
Statistics
Matches: 1494, Mismatches: 129, Indels: 46
0.90 0.08 0.03
Matches are distributed among these distances:
152 77 0.05
153 389 0.26
154 513 0.34
155 83 0.06
156 136 0.09
157 163 0.11
158 60 0.04
159 73 0.05
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (154 bp):
CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
GGCCATAAACAATGGAAAGAAAAG
Found at i:571 original size:307 final size:308
Alignment explanation
Indices: 1--1801 Score: 2594
Period size: 307 Copynumber: 5.8 Consensus size: 308
*
1 CATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAAT
1 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
*
66 AACAAGTATTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
66 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
* *
131 GGCCATACAACAATAGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTTAATACGTCA
131 GGCCATA-AACAAT-GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCA
* * * *
196 GTAATGGGCCCCGATAGGCGCAAAATAACAAGTGTTCCAACTGAGCTAAAAAGTTCACAGTGGAC
194 CTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
*
261 TAATCTCACC-AAATGATTATAGTTAGGTCATAAACAATGGAAAGAAAAG
259 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* ** * * *
310 CATTGAGGTTTGCCAAATCGAAAACGATTCAAAACGGAACTAATGAGCCCCGTTAGACCCAAAAT
1 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
* * * *
375 AACAAGTGTTCCGAATGAGCTAAAAACTTCACGGTGGACAAATCTCACCAAAATTATTATAGTTA
66 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
* *
440 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCATT
131 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACT
** * * *
505 AATGGGCCCCGATAGGCTGAAAATAACAAGTGTTCAAAATAAGCTAAAAACTTCAAAGTGGACTA
196 AATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
* * * *
570 ATCTAAACAAAATGATTANAG-TAGGCCATAAACAATGGAAA-CAAAG
261 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * * *
616 CATTGAGGCTTGCCAAATTCGAAGA-AATTCAATACGTCACTAATGGGCCACGATAGGCCCAAAA
1 CATTGAGGTTTGCCAAA-TCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAA
*
680 TAACAAGTATTCCAAATGAGCTAAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTACTAG
65 TAACAAGTGTTCCAAATGAGCT-AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA-TAG
* *
745 TTAGACCATAAACGAATGGAAAGAAAAGCGTTGAGGTTTGCCAAAATCGAAGACGATTACAAAAC
128 TTAGGCCATAAAC-AATGGAAAGAAAAGCATTGAGGTTTGCC-AAATCGAAGACGATT-CAAAAC
** * *
810 GGAACTAATGGGCCCCGATAAGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTTCACAGT
190 GTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
875 GGTACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
255 GG-ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* ** *
930 CATTGAGGTTTGCCAAATCGAAGGCGATTC-AAACGGAACTAATGGGCCCCGATAGGTCCGAAAA
1 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGG-CCCAAAA
* *
994 TAACAAGTGTTCCAAATGAGCTAAAACCTTCACAGTAGACTAATCTCACCAAAATGATTATACGT
65 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA-GT
*
1059 TAGGCCCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGG
129 TAGG--CCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGT
* ** * *
1124 AACTAATGGGCCTTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCCAAAAACTTCACAGTGT
192 CACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
* *
1189 TCTAATCTCACCGAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
257 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
** **
1241 CATCAAAGG-TTGCCAAATC-AATGACGATTCAAAACGTCACTAATGGGCCTTGATAGGCCCAAA
1 CAT-TGAGGTTTGCCAAATCGAA-GACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAA
* *** *
1304 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATTTTCTAATCTCACCGAAATGATTATAGT
64 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
** * **
1369 TAGGCCATAAA-AATGGAAAGAAAAGCATCAAGGGTTGCCAAATCGATTACGATTCAAAACGTCA
129 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCA
* **
1433 TTAATGGGCCTTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
194 CTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
*
1498 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAA
259 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * * ** * *
1548 TATTGAGGTTTACCAAATCGAAGACGATTTAAAACGTCACTAATGGGCCTTGATGGGCACAAAAT
1 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
* * **
1613 AACAAGTGTTCTAAATGAGCTAAAAACTTCACAGCGGACTAATCTCACCAAAAAAATTATAGTTA
66 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
*
1678 GGCCATAAACAATGGAAAGAAAA-CATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGTCACT
131 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACT
*** *
1742 AATGGGCTTTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCGAAAAAACTTCACAGT
196 AATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC-TAAAAACTTCACAGT
1802 TTTCT
Statistics
Matches: 1339, Mismatches: 131, Indels: 45
0.88 0.09 0.03
Matches are distributed among these distances:
306 74 0.06
307 522 0.39
308 68 0.05
309 152 0.11
310 23 0.02
311 194 0.14
312 116 0.09
313 104 0.08
314 78 0.06
315 8 0.01
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (308 bp):
CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACT
AATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
Done.