Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012441.1 Corchorus capsularis cultivar CVL-1 contig12462, 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: 9273
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:503 original size:8 final size:7
Alignment explanation
Indices: 493--534 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
483 TATTTATTAG
493 TATTATA
1 TATTATA
500 GTATT-TA
1 -TATTATA
507 T-TTATA
1 TATTATA
513 TATTATA
1 TATTATA
520 TA-TATA
1 TATTATA
526 TATTATA
1 TATTATA
533 TA
1 TA
535 ATAATAATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
5 2 0.06
6 10 0.32
7 15 0.48
8 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (7 bp):
TATTATA
Found at i:525 original size:13 final size:13
Alignment explanation
Indices: 477--534 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
467 ACTTGTTGGT
*
477 TTATA-ATATTTA
1 TTATATATATATA
489 TTAGTAT-TATAGTA
1 TTA-TATATATA-TA
*
503 TT-TATTTATATA
1 TTATATATATATA
515 TTATATATATATA
1 TTATATATATATA
528 TTATATA
1 TTATATA
535 ATAATAATAC
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
12 10 0.26
13 25 0.64
14 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (13 bp):
TTATATATATATA
Found at i:9185 original size:335 final size:328
Alignment explanation
Indices: 8187--9269 Score: 1446
Period size: 326 Copynumber: 3.3 Consensus size: 328
8177 TGAATACACA
* * *
8187 GCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGATTTTAGCAAAAAACC------
1 GCGCAAAAAATCATGAAAAACTGAGCCGGGG-CCCGGAACGCGATTTTAGTAAAAAACCGTAATA
*
8246 ----GT-CACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTAATG
65 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCTCAATTAATG
* * *
8306 GAAAAAATAATCATAAAAAATATATAATTCAATGCCAAAAATATTGAATGGCTTATCACGCTTCT
130 GCAAAAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGAATGGCTTTTCACGCTTCT
* ** * * *
8371 AATATCGTTTTTCCTTTTTTTTTTTCGAATTAATTTTTAATTAAATCGAAATAAGATTTAGATGT
195 AATATC-TTTTTCC---TTTTTTTTCAAATTAATTTCAAATCAAAACGAAACAAGATTTAGATGT
* * ** *
8436 TCGTAAAAACAAATCCTTAAA-GCCAATGTGGCTGAGATTTGGATAGATGAA-TACAAAAATTTA
256 TTGTAAAAACAAATCCTTAAATG-CAATTTGGCTGAGATTCAGATAGAT-AAGTACAAAAATTTC
*
8499 TAGGAGCCTT
319 TAGGAGTCTT
* * * * * ** *
8509 GGCGCAAAAAATCAGGGATAACTGAGCCGGGACCTCGGAACGCGATATTAGTAAAAAATTGAAAT
1 -GCGCAAAAAATCATGAAAAACTGAGCCGGGGCC-CGGAACGCGATTTTAGTAAAAAACCGTAAT
* * * * *
8574 AGTTAGTACACGATTTCGACTGAAATTTTGCAAAAATTTATCCGAAAGATTTTTTGCTCAATTTA
64 AGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTT-CTCAATTAA
8639 TGGCAAAAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGAATGGCTTTTCACGCTT
128 TGGCAAAAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGAATGGCTTTTCACGCTT
*
8704 CTAATATC---GT--TTTTTTTTCAAATTAATTTCAAATCAAAACGAAACAAGATTTAGATGTTT
193 CTAATATCTTTTTCCTTTTTTTTCAAATTAATTTCAAATCAAAACGAAACAAGATTTAGATGTTT
8764 GTAAAAACAAATCCTTAAATGCAATTTGGCTGAGATTCAGATAGATAAGTACAAAAATTTCTAGG
258 GTAAAAACAAATCCTTAAATGCAATTTGGCTGAGATTCAGATAGATAAGTACAAAAATTTCTAGG
8829 AGTCTCT
323 AGTCT-T
* * ** *
8836 GCGCAAAAAATCATGAAAAACTGAGCCGGGGTCCCGAAACACGATTTTAGCCAAAAACCGTGATA
1 GCGCAAAAAATCATGAAAAACTGAGCCGGGG-CCCGGAACGCGATTTTAGTAAAAAACCGTAATA
*
8901 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCTGAATTAATG
65 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCTCAATTAATG
*
8966 GCAAAAATAATCATAAAAAATATATAATTCAATGGCAAAAAGATTGAATGGCTTTTCACGCTTCT
130 GCAAAAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGAATGGCTTTTCACGCTTCT
9031 AATATCATTTTTCCTTTATTTTTCAAATTAATTTCAAATCAAAACGAAACAAGATTTAGATGTTT
195 AATATC-TTTTTCCTTT-TTTTTCAAATTAATTTCAAATCAAAACGAAACAAGATTTAGATGTTT
* *
9096 GTAAAAAAAAAAAATCCTTAAATGCAATTTGACTGAGATTCAGATAGATAAGTACAAAAATTTCT
258 GT---AAAAACAAATCCTTAAATGCAATTTGGCTGAGATTCAGATAGATAAGTACAAAAATTTCT
*
9161 AGGATTCTAT
320 AGGAGTCT-T
* * *
9171 GCGCAAAAAATCATGAAAAACTGAGTCGGGGCCCGGAACGCGATTTTAGTAAAAAACCTTCATAG
1 GCGCAAAAAATCATGAAAAACTGAGCCGGGGCCCGGAACGCGATTTTAGTAAAAAACCGTAATAG
* *
9236 CTAATACACGATTTCGGCTAAAATTTTGCAAAAA
66 TTAGTACACGATTTCGGCTAAAATTTTGCAAAAA
9270 ATGA
Statistics
Matches: 668, Mismatches: 65, Indels: 43
0.86 0.08 0.06
Matches are distributed among these distances:
322 2 0.00
323 47 0.07
325 81 0.12
326 202 0.30
327 4 0.01
329 1 0.00
331 4 0.01
332 49 0.07
333 2 0.00
334 102 0.15
335 174 0.26
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (328 bp):
GCGCAAAAAATCATGAAAAACTGAGCCGGGGCCCGGAACGCGATTTTAGTAAAAAACCGTAATAG
TTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCTCAATTAATGG
CAAAAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGAATGGCTTTTCACGCTTCTA
ATATCTTTTTCCTTTTTTTTCAAATTAATTTCAAATCAAAACGAAACAAGATTTAGATGTTTGTA
AAAACAAATCCTTAAATGCAATTTGGCTGAGATTCAGATAGATAAGTACAAAAATTTCTAGGAGT
CTT
Done.