Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023458.1 Corchorus olitorius cultivar O-4 contig23491, 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: 4507
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Found at i:513 original size:154 final size:154
Alignment explanation
Indices: 1--1082 Score: 1607
Period size: 154 Copynumber: 7.0 Consensus size: 154
* * * *
1 GTTCGAAATGAGCTAAAAACTTCATAGTGGACTAATCTTACTAAAATGATTATAGTTAGGCCATA
1 GTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATAATTATAGTTAGGCCATA
* * * **
66 AACAATGGAAAGAAAAGCATTGTCGTTTGCCAAATCGAAGATGATTTTTAAAATGGAACTAATGG
66 AACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA-TTCT-AAACCGAACTAATGG
131 GCCCCGAATGGCCCAAAATAACAAGT
129 GCCCCGAATGGCCCAAAATAACAAGT
* *
157 GTTCAAAATGAGCTAAAAA-TGTTACAATGGACTAATCTTA-CAAATATAATTATAGTTAGGCCA
1 GTTCAAAATGAGCTAAAAACT-TCACAGTGGACTAATCTTACCAAA-ATAATTATAGTTAGGCCA
** * *
220 TAAACAATGGAAAGAAAAGCATTGTGGTTTTTCAAATCGAAGACGATTTTTAAAACGGAACTAAT
64 TAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA-TTCT-AAACCGAACTAAT
*
285 GGGCCCCGAATGGCCCGAAATAACAAGT
127 GGGCCCCGAATGGCCCAAAATAACAAGT
* * * *
313 GTTTAAAATAAGCTAAAAACTTCACAGTGGACTAATCTTACTAAAATGATTATAGTTAGGCCATA
1 GTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATAATTATAGTTAGGCCATA
* * *
378 AACAATGAAAAGAAAAACGTTGTGGTTTGCCAAATCGAAGACGATTCTAAACCGAACTAATGGGC
66 AACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTCTAAACCGAACTAATGGGC
* *
443 CCCGAAGGGCCCAAAAGAACAAGT
131 CCCGAATGGCCCAAAATAACAAGT
*
467 GTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATAATAATAGTTAGGCCATA
1 GTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATAATTATAGTTAGGCCATA
* *
532 AACAATGGAAAGAAAAGCCTTGTGGTTTGCCAAATCGAAGACGATTC-AACCCTGAACTAATGGG
66 AACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTCTAAACC-GAACTAATGGG
* * *
596 CCTCGAAAGGTCCAAAATAACAAGT
130 CCCCGAATGGCCCAAAATAACAAGT
*
621 GTTCAAAATGAGCTAAAAACTTAACAGTGGACTAATCTTACCAAAATAATTATAGTTAGGCCATA
1 GTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATAATTATAGTTAGGCCATA
* *
686 ATCAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTCAAAACCGAACTAATGGGC
66 AACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTCTAAACCGAACTAATGGGC
* * *
751 CTCGAAGGGCACAAAATAACAAGT
131 CCCGAATGGCCCAAAATAACAAGT
* * * *
775 GTTGAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACTAAAATGATTATAGTTAGGCCATT
1 GTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATAATTATAGTTAGGCCATA
*
840 AACAATGAAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTCTAAACCGAACTAATGGGC
66 AACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTCTAAACCGAACTAATGGGC
* * *
905 CCCGAA-GACCC-TAAGAACAAGT
131 CCCGAATGGCCCAAAATAACAAGT
* *
927 GTTCAAAATGAGCTAAAAACTTTACAGTGGACTAATCTTACCAAAATAATTATAGTTATGCCATA
1 GTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATAATTATAGTTAGGCCATA
* *
992 AACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTGTAAAACGGAACTAATGG
66 AACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA-TTCT-AAACCGAACTAATGG
1057 GCCCCGAATGGCCCAAAATAACAAGT
129 GCCCCGAATGGCCCAAAATAACAAGT
1083 TGATGTGCCA
Statistics
Matches: 842, Mismatches: 74, Indels: 20
0.90 0.08 0.02
Matches are distributed among these distances:
152 111 0.13
153 10 0.01
154 463 0.55
155 15 0.02
156 239 0.28
157 4 0.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (154 bp):
GTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATAATTATAGTTAGGCCATA
AACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTCTAAACCGAACTAATGGGC
CCCGAATGGCCCAAAATAACAAGT
Found at i:2807 original size:21 final size:21
Alignment explanation
Indices: 2783--2835 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
2773 CATTGAACCT
2783 AATGGCATCTTCAATGGATCA
1 AATGGCATCTTCAATGGATCA
2804 AATGGCATCTTCAATGGATCA
1 AATGGCATCTTCAATGGATCA
2825 AATGGCATCTT
1 AATGGCATCTT
2836 TGGCATCTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (21 bp):
AATGGCATCTTCAATGGATCA
Found at i:3489 original size:154 final size:155
Alignment explanation
Indices: 2977--4503 Score: 2164
Period size: 154 Copynumber: 9.9 Consensus size: 155
2967 TTGGCACATC
* * *
2977 ACAAGTGTTGAAAATGAGCTAAAAACTTCACAGTGCACTAATCTTACCAAAATAATTATAGTTAG
1 ACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAG
* *
3042 GCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAATGGAAC
66 GCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA-TTTCAAAACGGAAC
* * **
3107 AAATGGGCCCTGAATCGCCCAAAATA
130 TAATGGGCCCCGAAAGGCCCAAAATA
* * * *
3133 ACAAGTGTT-TAAATGAGGTAAAAACTTCATAGTGGACTAATCTTACTAAAATGATTATAGTTAG
1 ACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAG
* * * *
3197 GCCATAAACAATGGAAAGAAAAGCATTGTCGTTTGCCAAATCGAAGATGATTTCTAAACCGAACT
66 GCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTCAAAACGGAACT
* *
3262 AATGGGCCCCGAAGGGCCCAAAAGA
131 AATGGGCCCCGAAAGGCCCAAAATA
*
3287 ACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATAATAGTTAG
1 ACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAG
* *
3352 GCCATAAACAATGGAAAGAAAAGCCTTGTGGTTTGCCAAATCGAAGACGA-TTCAAAACCGAACT
66 GCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTCAAAACGGAACT
* *
3416 AATGGGTCTCGAAAGGTCCC-AAATA
131 AATGGGCCCCGAAAGG-CCCAAAATA
* * * *
3441 ACAAGTGTTCAAAATGAGTTAAAAACTTAACAGTGGATTAATCTTACCAAAATAATTATAGTTAG
1 ACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAG
*
3506 GCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACGGAAC
66 GCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA-TTTCAAAACGGAAC
*
3571 TAATGGGCCCCGAATGGCCCAAAATA
130 TAATGGGCCCCGAAAGGCCCAAAATA
* * *
3597 ACAAGTGTTGAAAATGAGCTAAAAACCTCACAGTGGACTAATCTTACCAAAATAATTATAGTTAG
1 ACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAG
*
3662 GCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACGGAAC
66 GCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA-TTTCAAAACGGAAC
* **
3727 AAATGGGCCCCGAATCGCCCAAAATA
130 TAATGGGCCCCGAAAGGCCCAAAATA
* * *
3753 ACAAGTG-TCTAAATGAGCTAAAAACTTCATAGTGGACTAATCTTACTAAAATGATTATAGTTAG
1 ACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAG
*
3817 GCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACGGAAC
66 GCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA-TTTCAAAACGGAAC
* *
3882 TAATGGGCCCCGAATGGCCCAAAACA
130 TAATGGGCCCCGAAAGGCCCAAAATA
* * * *
3908 ACAAGTGTTTAAAATGAGCTAAAAACCTACACAGTGGACTAATCTTACCGAAATAATTATAGTTA
1 ACAAGTGTTCAAAATGAGCTAAAAA-CTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTA
3973 GGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA-TTCAAAACGGAAC
65 GGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTCAAAACGGAAC
* *
4037 TAATGGGCCCCGATAGGCCTAAAATA
130 TAATGGGCCCCGAAAGGCCCAAAATA
* * * * *
4063 ACAAGTGTTCAAAAT-ATTCTAAGAACATCACACTGGACTAATCTCACCAAAATGATTATAGTTA
1 ACAAGTGTTCAAAATGA-GCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTA
* *
4127 GGCCATAAACAATGGAAAGAAAAGCATT-TAGGGTTGCCAAATCGAAGACGA-TTCAAAACGGCA
65 GGCCATAAACAATGGAAAGAAAAGCATTGT-GGTTTGCCAAATCGAAGACGATTTCAAAACGGAA
* ** **
4190 CTAATGAGCCCCGTTAGGGACAAAATA
129 CTAATGGGCCCCGAAAGGCCCAAAATA
* * * *
4217 AAAAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTGATCTTACCAAAATGATTATCGTTAG
1 ACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAG
* * *
4282 GCCATAAACAATGGAAAGAAAAGCATCGAGGATTGCCAAATCGAAGACGA-TTCAAAACGGAACT
66 GCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTCAAAACGGAACT
* * *
4346 AATGGGCCCCGATAGGACTAAAATA
131 AATGGGCCCCGAAAGGCCCAAAATA
* * * *
4371 ACAAGTGTTCCAAAT-ATGCTAAGAACATCACTGTGGACTAAT-TTCACCAAAATGATTATAGTT
1 ACAAGTGTTCAAAATGA-GCTAAAAACTTCACAGTGGACTAATCTT-ACCAAAATGATTATAGTT
*
4434 AGGCCATAAACAATAGAAAGAAAAGCATATAG-GG-TTGCCAAATCGAAGACGA-TTCAAAACGG
64 AGGCCATAAACAATGGAAAGAAAAGCAT-T-GTGGTTTGCCAAATCGAAGACGATTTCAAAACGG
4496 AACTAATG
127 AACTAATG
4504 AGCC
Statistics
Matches: 1244, Mismatches: 112, Indels: 32
0.90 0.08 0.02
Matches are distributed among these distances:
153 4 0.00
154 541 0.43
155 403 0.32
156 211 0.17
157 85 0.07
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (155 bp):
ACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAG
GCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTCAAAACGGAACT
AATGGGCCCCGAAAGGCCCAAAATA
Found at i:4187 original size:620 final size:620
Alignment explanation
Indices: 2977--4503 Score: 2303
Period size: 620 Copynumber: 2.5 Consensus size: 620
2967 TTGGCACATC
*
2977 ACAAGTGTTGAAAATGAGCTAAAAACTTCACAGTGCACTAATCTTACCAAAATAATTATAGTTAG
1 ACAAGTGTTGAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATAATTATAGTTAG
*
3042 GCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAATGGAAC
66 GCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACGGAAC
* * *
3107 AAATGGGCCCTGAATCGCCCAAAATAACAAGTGTTTAAATGAGGTAAAAACTTCATAGTGGACTA
131 AAATGGGCCCCGAATCGCCCAAAATAACAAGTGTCTAAATGAGCTAAAAACTTCATAGTGGACTA
*
3172 ATCTTACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTCGTTTGCCAAA
196 ATCTTACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAA
* * * *
3237 TCGAAGATGATTTCT-AAACCGAACTAATGGGCCCCGAAGGGCCCAAAAGAACAAGTGTTCAAAA
261 TCGAAGACGATTTTTAAAACGGAACTAATGGGCCCCGAAGGGCCCAAAACAACAAGTGTTCAAAA
* *
3301 TGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATAATAGTTAGGCCATAAACAATGG
326 TGAGCTAAAAACTACACAGTGGACTAATCTTACCAAAATAATAATAGTTAGGCCATAAACAATGG
* * *
3366 AAAGAAAAGCCTTGTGGTTTGCCAAATCGAAGACGATTCAAAACCGAACTAATGGGTCTCGAAAG
391 AAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTCAAAACCGAACTAATGGGCCCCGAAAG
* * * * *
3431 GTCCCAAATAACAAGTGTTCAAAATGAGTTAAAAACTTAACAGTGGATTAATCTTACCAAAATAA
456 GTCCAAAATAACAAGTGTTCAAAATGAGTTAAAAACATAACACTGGACTAATCTCACCAAAATAA
* *
3496 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTT
521 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGGTTGCCAAATCGAAGACGA-TTTC
* *
3561 AAAACGGAACTAATGGGCCCCGA-ATGGCCCAAAATA
585 AAAACGGAACTAATGAGCCCCGATA-GGCACAAAATA
*
3597 ACAAGTGTTGAAAATGAGCTAAAAACCTCACAGTGGACTAATCTTACCAAAATAATTATAGTTAG
1 ACAAGTGTTGAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATAATTATAGTTAG
3662 GCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACGGAAC
66 GCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACGGAAC
3727 AAATGGGCCCCGAATCGCCCAAAATAACAAGTGTCTAAATGAGCTAAAAACTTCATAGTGGACTA
131 AAATGGGCCCCGAATCGCCCAAAATAACAAGTGTCTAAATGAGCTAAAAACTTCATAGTGGACTA
3792 ATCTTACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAA
196 ATCTTACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAA
* *
3857 TCGAAGACGATTTTTAAAACGGAACTAATGGGCCCCGAATGGCCCAAAACAACAAGTGTTTAAAA
261 TCGAAGACGATTTTTAAAACGGAACTAATGGGCCCCGAAGGGCCCAAAACAACAAGTGTTCAAAA
* *
3922 TGAGCTAAAAACCTACACAGTGGACTAATCTTACCGAAATAATTATAGTTAGGCCATAAACAATG
326 TGAGCTAAAAA-CTACACAGTGGACTAATCTTACCAAAATAATAATAGTTAGGCCATAAACAATG
* *
3987 GAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATA
390 GAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTCAAAACCGAACTAATGGGCCCCGAAA
* * *
4052 GG-CCTAAAATAACAAGTGTTCAAAAT-ATTCTAAGAACATCACACTGGACTAATCTCACCAAAA
455 GGTCC-AAAATAACAAGTGTTCAAAATGAGT-TAAAAACATAACACTGGACTAATCTCACCAAAA
*
4115 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT-TAGGGTTGCCAAATCGAAGACGA-
518 TAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGT-GGGTTGCCAAATCGAAGACGAT
* * *
4178 TTCAAAACGGCACTAATGAGCCCCGTTAGGGACAAAATA
582 TTCAAAACGGAACTAATGAGCCCCGATAGGCACAAAATA
* ** * * *
4217 AAAAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTGATCTTACCAAAATGATTATCGTTAG
1 ACAAGTGTTGAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATAATTATAGTTAG
* * * *
4282 GCCATAAACAATGGAAAGAAAAGCATCGAGGATTGCCAAATCGAAGACGA--TTCAAAACGGAAC
66 GCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACGGAAC
* * * * * * *
4345 TAATGGGCCCCG-ATAGGACTAAAATAACAAGTGTTCCAAAT-ATGCTAAGAACATCACT-GTGG
131 AAATGGGCCCCGAAT-CGCCCAAAATAACAAGTG-TCTAAATGA-GCTAAAAACTTCA-TAGTGG
* *
4407 ACTAAT-TTCACCAAAATGATTATAGTTAGGCCATAAACAATAGAAAGAAAAGCATATAG-GG-T
192 ACTAATCTT-ACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT-T-GTGGTT
*
4469 TGCCAAATCGAAGACGA--TTCAAAACGGAACTAATG
254 TGCCAAATCGAAGACGATTTTTAAAACGGAACTAATG
4504 AGCC
Statistics
Matches: 835, Mismatches: 59, Indels: 29
0.90 0.06 0.03
Matches are distributed among these distances:
617 19 0.02
618 41 0.05
619 89 0.11
620 406 0.49
621 63 0.08
622 217 0.26
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (620 bp):
ACAAGTGTTGAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATAATTATAGTTAG
GCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACGGAAC
AAATGGGCCCCGAATCGCCCAAAATAACAAGTGTCTAAATGAGCTAAAAACTTCATAGTGGACTA
ATCTTACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAA
TCGAAGACGATTTTTAAAACGGAACTAATGGGCCCCGAAGGGCCCAAAACAACAAGTGTTCAAAA
TGAGCTAAAAACTACACAGTGGACTAATCTTACCAAAATAATAATAGTTAGGCCATAAACAATGG
AAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTCAAAACCGAACTAATGGGCCCCGAAAG
GTCCAAAATAACAAGTGTTCAAAATGAGTTAAAAACATAACACTGGACTAATCTCACCAAAATAA
TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGGTTGCCAAATCGAAGACGATTTCA
AAACGGAACTAATGAGCCCCGATAGGCACAAAATA
Done.