Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020887.1 Corchorus olitorius cultivar O-4 contig20920, 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: 3519
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:26 original size:2 final size:2
Alignment explanation
Indices: 19--45 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9 GGGCAGATGA
19 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
46 GCTGAGCCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1112 original size:333 final size:332
Alignment explanation
Indices: 503--2489 Score: 2813
Period size: 333 Copynumber: 6.0 Consensus size: 332
493 CCGAATGAAT
**
503 ATATATAAATCATCGCCAAAAACTTTGAAGGGTTTTTAAAGCTTCGAATATCGTTTTTCCTATGC
1 ATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTAAAGCTTCGAATATCGTTTTTCCTATGC
* *
568 TTTTCCGAATTAATTTCCTATTAAATCGAAACTCGATTCTGATTCTCATAAAAACAAATCTTTAA
66 TTTTCCGAATTAATTTCCAATTAAATCGAAACTCGATTCTGATGCTCATAAAAACAAATCTTTAA
* *
633 ATCTTACGTGGCTAAGATTTGGGTAGATGAATATATATATTCCAAGGAGTCTCTGCGCCAAAAAT
131 ATCTTACGTGGCTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTCTGCGCCAAAAAT
* * * *
698 CACACAAAACTGAGCCGGGCCCTGGAACGCGTTTTTAGCCGAAAACTGTGATGGATAGCACACGA
196 CATACAAAAATGAGCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGATAGCACACGA
* *
763 TTTCAGTCAAGATTTTGCGAAAATTGACCCGAATGATTTTTCCTAAATTTTTGGCTAAAATGCTC
261 TTTCAGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTAAATTTTTGGCCAAAATGCTC
828 ATAAAAAA
326 AT-AAAAA
* * * * * * *
836 ATCTATAAATAATCGCCAAAAAGATTGAAGGCTTTTTCACGCTTCGAATACCGTTTTTCCTATGT
1 ATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTAAAGCTTCGAATATCGTTTTTCCTATGC
* * * * **
901 TTTTCCGAATTAATTTCCAATTAAATCGACACTGGATTTTGATGCGCATAAAAACATCTCTTTAA
66 TTTTCCGAATTAATTTCCAATTAAATCGAAACTCGATTCTGATGCTCATAAAAACAAATCTTTAA
*
966 ATCTTATGTGGCTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCT-TGACGCCAAAAA
131 ATCTTACGTGGCTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTCTG-CGCCAAAAA
* *
1030 T-ATACAAAAATGAGTCGGGGCCCCGGAATGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACAC
195 TCATACAAAAATGAG-CGGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGATAGCACAC
* * * * * **
1094 GATTTCGGTCAAGATTTTGCAAAAATTGACACTAATGATTTTTTCTCAATTTTTGGCCAAAATAA
259 GATTTCAGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTAAATTTTTGGCCAAAATGC
1159 TCATAATATATA
324 TCATAA-A-A-A
** * *
1171 TATATATAAATCATCGCCAAAAACTTTGAA-GGATTTTAAACGCTTCGATTATCGTTTTTCCTAT
1 -ATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTAAA-GCTTCGAATATCGTTTTTCCTAT
* * * *
1235 GCTTTTCCGAATTAATTTCCAATTAAATCGAAA-TTGTATTCTGATGCGCGTAAAAAGAAATCTT
64 GCTTTTCCGAATTAATTTCCAATTAAATCGAAACTCG-ATTCTGATGCTCATAAAAACAAATCTT
* * * *
1299 TAAATATTATGTGGCTGAGATTTGGGAAGATGAATATAGATATTACAAGGAGTCT-TGGCGCCAA
128 TAAATCTTACGTGGCTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTCT-GCGCCAA
* * * * *
1363 AAATCATACAAAAATGAGCTGGGGCCCCGGTACGCGTTTTTAGCCAAAAACTGTGACGGTTAACA
192 AAATCATACAAAAATGAGC-GGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGATAGCA
* * *** *
1428 CGCGATTTCGGTCAAGATTTTGCAAAAATTGAAAAGAAATGATTTTTCCTCAATTTTTGGCCAAA
256 CACGATTTCAGTCAAGATTTTGCAAAAATTGACCCG-AATGATTTTTCCTAAATTTTTGGCCAAA
*
1493 ATACTCAT-AAAA
320 ATGCTCATAAAAA
*
1505 ATATATAAATCATGGCCAAAAAGATTGAAGGGTTTTTAAAGCTTCGAATATCGTTTTTCCTATGC
1 ATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTAAAGCTTCGAATATCGTTTTTCCTATGC
* * * *
1570 TTTTCCGAATTAATTTCCTATTAACTCGAAACTCGATTCTGATTCTCATAAAAGCAAATCTTTAA
66 TTTTCCGAATTAATTTCCAATTAAATCGAAACTCGATTCTGATGCTCATAAAAACAAATCTTTAA
* *
1635 ATCTTACATGGCTGAGATTTGGGTAGATGAATATAGATATTCCAAGAAGTCTCTGCGCCAAAAAA
131 ATCTTACGTGGCTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTCTGCGCC-AAAAA
* * * *
1700 TCACACAAAACTGAGCCGGACCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGATAGCACACG
195 TCATACAAAAATGAGCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGATAGCACACG
* *
1765 ATTTCAGTCAAGATTTTGCGAAAATTGACCCGAATGATTTTTCCTAAATTTTTGGCTAAAATGCT
260 ATTTCAGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTAAATTTTTGGCCAAAATGCT
1830 CATAAAAA
325 CATAAAAA
* * *
1838 ATATATAAATCTTGGCCAATAAGATTGAAGGGTTTTTAAAGCTTCGAATATCGTTTTTCCTATGC
1 ATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTAAAGCTTCGAATATCGTTTTTCCTATGC
* * * *
1903 TTCTCCGAATTAATTTCCTATTAAATCGAAACTCGATTCTGATTCTCATAAAAACAAATTTTTAA
66 TTTTCCGAATTAATTTCCAATTAAATCGAAACTCGATTCTGATGCTCATAAAAACAAATCTTTAA
*
1968 ATCTTACGTGGCTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTCTACGCCAAAAAT
131 ATCTTACGTGGCTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTCTGCGCCAAAAAT
* * *
2033 CACACAAAACTGAGTC-GGGCTCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGATAGCACACG
196 CATACAAAAATGAG-CGGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGATAGCACACG
* *
2097 ATTTCAGTCAAGATTTTGCGAAAATTGACCCGAATGATTTTTCCTAAATTTTTGGCTAAAATGCT
260 ATTTCAGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTAAATTTTTGGCCAAAATGCT
2162 CAT-AAAA
325 CATAAAAA
* * * * * *
2169 ATATATAAATCATCGCCTAAAAGATTGAAGGCTTTTTCACGCTTCGAATACCGTTTTTCCTATGT
1 ATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTAAAGCTTCGAATATCGTTTTTCCTATGC
* * * * *
2234 TTTTCCGAATTAATTTCAAATTAAATCGAAACTGGATTTTGATGCTCGTAAAAGCAAATCTTTAA
66 TTTTCCGAATTAATTTCCAATTAAATCGAAACTCGATTCTGATGCTCATAAAAACAAATCTTTAA
* *
2299 ATCTTATGTGGCTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGT-TTTGGCGCCAAAAA
131 ATCTTACGTGGCTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTCT-GCGCCAAAAA
* * *
2363 TCATACAATAATGAGCAGGGGCCTCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACAC
195 TCATACAAAAATGAGC-GGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGATAGCACAC
* * * * *
2428 GATTTCAGTCAAGATTTTGCAAAAATTAACGCAAATGATTTTTCCTCAATATTTGGCCAAAA
259 GATTTCAGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTAAATTTTTGGCCAAAA
2490 ATATTGAAGG
Statistics
Matches: 1484, Mismatches: 149, Indels: 43
0.89 0.09 0.03
Matches are distributed among these distances:
330 3 0.00
331 186 0.13
332 281 0.19
333 686 0.46
334 33 0.02
335 10 0.01
336 164 0.11
337 87 0.06
338 34 0.02
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (332 bp):
ATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTAAAGCTTCGAATATCGTTTTTCCTATGC
TTTTCCGAATTAATTTCCAATTAAATCGAAACTCGATTCTGATGCTCATAAAAACAAATCTTTAA
ATCTTACGTGGCTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTCTGCGCCAAAAAT
CATACAAAAATGAGCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGATAGCACACGA
TTTCAGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTAAATTTTTGGCCAAAATGCTC
ATAAAAA
Found at i:3103 original size:331 final size:333
Alignment explanation
Indices: 2518--3132 Score: 874
Period size: 331 Copynumber: 1.9 Consensus size: 333
2508 AGCTTCGAAA
* * * *
2518 ATCGTTTTTCCTATGCTTCTCAGAATTAATTTACAATTAAAATCGAAACTGGATTCTGATGCTCG
1 ATCGTTTCTCCTATGATTCTCAGAATTAATTTACAATTAAAATCGAAACTAGATTCGGATGCTCG
* * *
2583 TAATAACAAATCTTTAAAAATCATGGGGCTGAGATTTGGGCAGATGAATATAGATATTCAAAAGA
66 TAAAAAAAAATCTTTAAAAATCATGGGGCCGAGATTTGGGCAGATGAATATAGATATTCAAAAGA
* * *
2648 ATATCTGCGCCAAAAATAACACAAAACTGAGCCAGGGCCCTGGAACGCGTTTTTAGCCGAAAACT
131 ACATCTGCGCCAAAAATAACACAAAACAGAGCCAGGGCCCCGGAACGCGTTTTTAGCCGAAAACT
*
2713 GTGATAGTTAGCACAAGATTTCGGTCAAGAATTTGCAAAAATTGACCCGAATGATTTTTCATCAA
196 GTGATAGTTAGCACAAGATTTCGGTCAAGAATTTGCAAAAATTGACCCAAATGATTTTTCATCAA
*
2778 TTTTTGGCCAAAATACACATAAAAATATATAAATCATCGCCAAAAGTATTGTAGGGTTTTCCATG
261 TTTTTGGCCAAAATACACACAAAAATATATAAATCATCGCCAAAAGTATTGTAGGGTTTTCCATG
2843 TTTCGATT
326 TTTCGATT
* * *
2851 ATCGTTTCTCCTATGATTTTCCGAATTAATTTCCAATT-AAATCGAAACTAGATTCGGATGCTCG
1 ATCGTTTCTCCTATGATTCTCAGAATTAATTTACAATTAAAATCGAAACTAGATTCGGATGCTCG
** * * * * * * *
2915 TAAAAAAAAATCTTTAAATCTTATGTGGCCGAGATTTTGGTAGATTAATATAGATATTCCAAGGA
66 TAAAAAAAAATCTTTAAAAATCATGGGGCCGAGATTTGGGCAGATGAATATAGATATTCAAAAGA
* * * * ** *
2980 GCCTCTGCGCCAAAAATCACACAAAACAGTG-TTGGGCCCCGGAACGCGTTTTTAGCCGAAACCT
131 ACATCTGCGCCAAAAATAACACAAAACAGAGCCAGGGCCCCGGAACGCGTTTTTAGCCGAAAACT
* * * ** *
3044 GTGATGGTTAGCACACGATTTCGGTCAAGATTTTGCAAAAATTGATGCAAATGATTTTTCCTCAA
196 GTGATAGTTAGCACAAGATTTCGGTCAAGAATTTGCAAAAATTGACCCAAATGATTTTTCATCAA
*
3109 TTTTTGGCCAAAATTCACACAAAA
261 TTTTTGGCCAAAATACACACAAAA
3133 CTAAGTTGAA
Statistics
Matches: 244, Mismatches: 38, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
331 109 0.45
332 102 0.42
333 33 0.14
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (333 bp):
ATCGTTTCTCCTATGATTCTCAGAATTAATTTACAATTAAAATCGAAACTAGATTCGGATGCTCG
TAAAAAAAAATCTTTAAAAATCATGGGGCCGAGATTTGGGCAGATGAATATAGATATTCAAAAGA
ACATCTGCGCCAAAAATAACACAAAACAGAGCCAGGGCCCCGGAACGCGTTTTTAGCCGAAAACT
GTGATAGTTAGCACAAGATTTCGGTCAAGAATTTGCAAAAATTGACCCAAATGATTTTTCATCAA
TTTTTGGCCAAAATACACACAAAAATATATAAATCATCGCCAAAAGTATTGTAGGGTTTTCCATG
TTTCGATT
Done.