Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011654.1 Corchorus olitorius cultivar O-4 contig11687, 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: 3849
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Found at i:285 original size:154 final size:153
Alignment explanation
Indices: 5--3610 Score: 5127
Period size: 154 Copynumber: 23.3 Consensus size: 153
1 GATC
* * * * *
5 AAAAGCATCGAAGG-TTGTCAAATAGAAGA-GATTCAATACGTCACTAATGGGCCCCGATAGGCG
1 AAAAGCATTG-AGGTTTGCCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGATAGGC-
* *
68 ACAAAATAACAAGTGTTACCAAATTAGCTAAAAAGC-TCACAGTGGACTAATCTCACCAAAATGA
63 CCAAAATAACAAGTGTT-CCAAATGAGCTAAAAA-CTTCACAGTGGACTAATCTCACCAAAATGA
* *
132 TTATAGTTAGACCATAAACAATGGAAAC
126 TTATAGTTAGGCCATAAACAATGGAAAG
* *
160 AAAAGCATTGAGGCTTGCCAAATCGAAGACAATTCAAAACAGAACTAATGGGCCCCGATAGGCCC
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGATAGGCCC
225 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
65 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
290 AGTTAGGCCATAAACAATGGAAAG
130 AGTTAGGCCATAAACAATGGAAAG
*
314 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAAGCCC
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGATAGGCCC
* * * * *
379 AAAATAACAAGTGTTCAAAATGAGCTAAAAACTTTAAAGTGGACTAATCTAAACAAAATGATTAT
65 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
* *
444 ACG-TAGGCAATAAACAATGGAAAC
130 A-GTTAGGCCATAAACAATGGAAAG
* * ** * *
468 AAAAGACATTGAGGCTTGCCAATTCGAAGAAAATTCAATACGTCACTAATGGGCCCCGATAGGCC
1 AAAAG-CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGATAGGCC
* * * * *
533 CAAAATAACAAGTGTTCCAAGTTAGCTAAAAAGTTAACAGTGGACTAATCTCACAAAAATGATTA
64 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
* * *
598 TAATTAGGCCATAAATAACGGAAAG
129 TAGTTAGGCCATAAACAATGGAAAG
* *
623 AAAAGCATTGAGGTTTTGCCAAATCGAAGACGATTGAAAAGGGAACTAATGGGCCCCGATAGGCC
1 AAAAGCATTGAGG-TTTGCCAAATCGAAGACGATTCAAAA-CGAACTAATGGGCCCCGATAGGCC
* * *
688 CAAAACAACAAGTATTCCAAATGAGCTAAAAACTTCACAGTGGACTATTCTCACCAAAATGATTA
64 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
*
753 TAGTTAGACCATAAACAATGGAAAG
129 TAGTTAGGCCATAAACAATGGAAAG
* * * * *
778 AAAAGCGTTGAGGTTTGCCAAATCCAAGACGATTCTAAACAAAACTAGTGGGCCCCGATAGGCCC
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGATAGGCCC
* *
843 AAAATAACAAGTGTTCCAACTGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGATTAT
65 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
**
908 AGTTAGGTGATAAACAATGGAAAG
130 AGTTAGGCCATAAACAATGGAAAG
932 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGATAGGCCC
*
997 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCATAGTGGACTAATCTCACCAAAATGATTAT
65 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
1062 AGTTAGGCCATAAACAATGGAAAG
130 AGTTAGGCCATAAACAATGGAAAG
* *
1086 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGAAACTAATGAGCTCCGATAGAG--
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGATAG-GCC
*
1149 AAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
64 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
* * *
1214 TAGTTAGGCCATACACAACGTAAAG
129 TAGTTAGGCCATAAACAATGGAAAG
* ** ** *
1239 AAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAAACTTCACTAATAATG-CCCGATAGACC
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAAT-GGGCCCCGATAGGCC
*
1303 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACTGTGGACTAATCTCACCAAAATGATTA
64 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
*
1368 TAGTTAGGGCATAAACAATGGAAAG
129 TAGTTAGGCCATAAACAATGGAAAG
* * * *
1393 AAAGGCATCGAAGG-TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCC
1 AAAAGCATTG-AGGTTTGCCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGATAGGCC
*
1457 CAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGATTA
64 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
1522 TAGTTAGGCCATAAACAATGGAAAG
129 TAGTTAGGCCATAAACAATGGAAAG
1547 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGAAACTAATGGGCCCCGATAGGCCC
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGATAGGCCC
* * * * *
1612 AAAATAACAGGTGTTCCAAATGAGCTAAAAAGTTCAAAGTGGACTAATCTAAACAAAATGATTAC
65 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA-
* *
1677 TAGGTAGGCCATAAACAATTGGAAAC
129 TAGTTAGGCCATAAACAA-TGGAAAG
** * * *
1703 AAAAGCATTGAGCCTTGCCAATTCGAAGAAGATTCAAATACGTCACTAATCGGGCCCCGATAGGA
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA-ACG-AACTAAT-GGGCCCCGATAGG-
* **
1768 CCCAAAATAACAAGTGTTCCAAATGAGACT-AAAACTTTACAGTGGACTAATCT-AAAACAAATG
62 CCCAAAATAACAAGTGTTCCAAATGAG-CTAAAAACTTCACAGTGGACTAATCTCACCA-AAATG
* *
1831 ATTATAGGTAGGCCAATAAACAAAGGAAAG
125 ATTATAGTTAGGCC-ATAAACAATGGAAAG
* * * * *
1861 AAAAGCATTGAGGCTTGCCAATTCGAAGAAGATTCAATACGTCACTAATCGGGCCCCGATAGGAC
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG-AACTAAT-GGGCCCCGATAGG-C
*
1926 CCAAAATAACAAGTGTTCCAATTGAGACTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
63 CCAAAATAACAAGTGTTCCAAATGAG-CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
**
1991 TATAGTTAGGTGATAAACAATGGAAAG
127 TATAGTTAGGCCATAAACAATGGAAAG
* * * *
2018 AAAAGCATTGAGGTTTGCTAAATCGAAGGCGATTCAAAACGGAACTAATGAGCCCCGTTAGGCCC
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGATAGGCCC
** * *
2083 AAAATAACAAGTGTTCCGGATGAGTTAAAAACTTCATAGTGGACTAATCTCACCAAAATGATTAT
65 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
* *
2148 AGTTATGCCATAAACAATTGAAAG
130 AGTTAGGCCATAAACAATGGAAAG
* * *
2172 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAAGCCC
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGATAGGCCC
* *
2237 AAAATAACAAGTATTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGATTAT
65 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
**
2302 AGTTAAACCATAAACAATGGAAAG
130 AGTTAGGCCATAAACAATGGAAAG
* *
2326 CAAAGCGTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGATAGGCCC
* *
2391 AAAATAACAAGTATTCCAAATGAGCTAAAAACTTCACAGTGGATTAATCTCACCAAAATGATTAT
65 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
*
2456 AGTTAGGCCATAAACAATGGAAAC
130 AGTTAGGCCATAAACAATGGAAAG
* * * * * *
2480 AAAAGCATTGAGGCTTT-CCAATTCGAAGAAGATTCAATACGTCACCAATGGGCCCCGATTGGCC
1 AAAAGCATTGAGG-TTTGCCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGATAGGCC
* *
2544 CAAAATAACAAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTATTCTCACCAAAATGATTA
64 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
*
2609 TAGTTAGACCATAAACAATGGAAAG
129 TAGTTAGGCCATAAACAATGGAAAG
* * * * * *
2634 AAAAGCGTTGAGGTTTGCCAAATCCAAGACGATTCTAAACAAAACTAGTGGGCCTCGATAGGCCC
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGATAGGCCC
* *
2699 AAAATAACAAGTGTTCCAACTGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGATTAT
65 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
**
2764 AGTTAGGTGATAAACAATGGAAAG
130 AGTTAGGCCATAAACAATGGAAAG
* * * *
2788 AAAAGCATTGAGGTTTGCTAAATCGAAGGCGATTCAAAACGGAACTAATGAGCCCCGTTAGGCCC
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGATAGGCCC
* * * * *
2853 AAAATAACAAGTGTTCCGAATGAGTTAAAAACTTCATAGTGGACTAATCTCAGCAAAATAATTAT
65 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
* *
2918 AGTTATGCCATAAACAATTGAAAG
130 AGTTAGGCCATAAACAATGGAAAG
* *
2942 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCC
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGATAGGCCC
* *
3007 AAAATAACAAGTATTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGATTAT
65 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
* *
3072 AGTTAGACCATAAACAATTGAAAG
130 AGTTAGGCCATAAACAATGGAAAG
* * *
3096 AAAAGCGTTGAGGTTTGCCAAATCCAAGACGATTCTAAAGA-GAACTAGTGGGCCCCGATAGGCC
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC-AAA-ACGAACTAATGGGCCCCGATAGGCC
* *
3160 CAAAATAACAAGTATTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGATTA
64 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
*
3225 TAGTTAGACCATAAACAATGGAAAG
129 TAGTTAGGCCATAAACAATGGAAAG
* *
3250 -AAAGCGTTGAGGTTTACCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGATAGGCCC
* *
3314 AAAATAACAAGTATTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGATTAT
65 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
*
3379 AGTTAGACCATAAACAATGGAAAG
130 AGTTAGGCCATAAACAATGGAAAG
* * * *
3403 AAAAGCGTTGAGGTTTGCCAAATCCAAGACGATTCTAAACAGAACTAGTGGGCCCCGATAGGCCC
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGATAGGCCC
* * * *
3468 AAAATAACAAGTGTTCCAACTGACCTAAAAAGTTAACAGTGGACTAATCT-ATCCAAAATGGATT
65 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA-CCAAAAT-GATT
3532 ATAGTTAGGCCATAAACAATGGAAAG
128 ATAGTTAGGCCATAAACAATGGAAAG
*
3558 AAAAGCATTGA-GTTTGCCAAATCGAAGACGATTCAAAACGGAGCTAATGGGCC
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCC
3611 ATAAACAATT
Statistics
Matches: 3113, Mismatches: 292, Indels: 93
0.89 0.08 0.03
Matches are distributed among these distances:
151 1 0.00
152 3 0.00
153 293 0.09
154 2052 0.66
155 391 0.13
156 81 0.03
157 119 0.04
158 106 0.03
159 65 0.02
160 2 0.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (153 bp):
AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGAACTAATGGGCCCCGATAGGCCCA
AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
GTTAGGCCATAAACAATGGAAAG
Found at i:3619 original size:68 final size:69
Alignment explanation
Indices: 3539--3679 Score: 248
Period size: 69 Copynumber: 2.1 Consensus size: 69
3529 ATTATAGTTA
*
3539 GGCCATAAACAATGGAAAGAAAAGCATTGA-GTTTGCCAAATCGAAGACGATTCAAAACGGAGCT
1 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACT
3603 AATG
66 AATG
* *
3607 GGCCATAAACAATTGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGGTTCAAAACGGAACT
1 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACT
3672 AATG
66 AATG
3676 GGCC
1 GGCC
3680 CCGATAGGCC
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
68 29 0.42
69 40 0.58
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (69 bp):
GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACT
AATG
Found at i:3827 original size:220 final size:223
Alignment explanation
Indices: 3386--3849 Score: 799
Period size: 220 Copynumber: 2.1 Consensus size: 223
3376 TATAGTTAGA
* * * *
3386 CCATAAACAATGGAAAGAAAAGCGTTGAGGTTTGCCAAATCCAAGACGATTCTAAACAGAACTAG
1 CCATAAACAATTGAAAGAAAAGCATTGAGGTTTGCCAAATCCAAGACGATTCAAAACAGAACTAA
* *
3451 TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAACTGACCTAAAAAGTTAACAGTGGACTAAT
66 TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGACCTAAAAACTTAACAGTGGACTAAT
3516 CTATCCAAAATGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGTTTGCCAAATC
131 CTATCCAAAATGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGTTTGCCAAATC
*
3581 GAAGACGATTCAAAACGGAGCTAATGGG
196 GAAGACGATTCAAAACGGAACTAATGGG
* * *
3609 CCATAAACAATTGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGGTTCAAAACGGAACTAA
1 CCATAAACAATTGAAAGAAAAGCATTGAGGTTTGCCAAATCCAAGACGATTCAAAACAGAACTAA
* *
3674 TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT-AAAACTTCACAGTGGACTAAT
66 TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGACCTAAAAACTTAACAGTGGACTAAT
3738 CTATCC-AAAT-GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGTTTGCCAAATC
131 CTATCCAAAATGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGTTTGCCAAATC
3801 GAAGACGATTCAAAACGGAACTAATGGG
196 GAAGACGATTCAAAACGGAACTAATGGG
3829 CCATAAACAATTGAAAGAAAA
1 CCATAAACAATTGAAAGAAAA
Statistics
Matches: 229, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
220 101 0.44
221 4 0.02
222 25 0.11
223 99 0.43
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20
Consensus pattern (223 bp):
CCATAAACAATTGAAAGAAAAGCATTGAGGTTTGCCAAATCCAAGACGATTCAAAACAGAACTAA
TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGACCTAAAAACTTAACAGTGGACTAAT
CTATCCAAAATGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGTTTGCCAAATC
GAAGACGATTCAAAACGGAACTAATGGG
Done.