Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010479.1 Corchorus olitorius cultivar O-4 contig10511, 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: 3789
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Found at i:1754 original size:18 final size:18
Alignment explanation
Indices: 1731--1767 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1721 TCCCCTCACA
1731 GTCCAGTGTATTTCTTCT
1 GTCCAGTGTATTTCTTCT
1749 GTCCAGTGTATTTCTTCT
1 GTCCAGTGTATTTCTTCT
1767 G
1 G
1768 CATTTGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.22, G:0.19, T:0.49
Consensus pattern (18 bp):
GTCCAGTGTATTTCTTCT
Found at i:3655 original size:577 final size:570
Alignment explanation
Indices: 2712--3787 Score: 1836
Period size: 577 Copynumber: 1.9 Consensus size: 570
2702 TTCAAGTGTC
* *
2712 CATTTTAAAGACAAAGATCATCATTGCTTTGCTTTCTAATTCTATTTTTCTTTTGCTATAGAGTG
1 CATTTTAAAGACAAAGATCATCATTACTTGGCTTTCTAATTCTATTTTTCTTTTGCTATAGAGTG
*
2777 AATGAAAAAAAAAAGTGCAAAAAAGAGTGAATGAAAATGGAGCTAAATGCCCTATTCCTAAAGAG
66 AATGAAAAAAAAAAGTGCAAAAAAGAGTGAATGAAAATGGAGCTAAATACCCTATTCCTAAAGAG
*
2842 TAGAGGACTTTAAATCCCACATCGCCCCTTTACCCATCCCAGCCCACTTTACCTATATATATATA
131 TAGAGGACTTAAAATCCCACATCGCCCCTTTACCCATCCCAGCCCACTTTACCTATATATATATA
* *
2907 AAATATAAACAGGTCAAGTTGCTCTTACATCTACAGTGATCTACTTGATAGGAAAAGCAAAAGTC
196 AAAAATAAACAGGTCAAGTTGCGCTTACATCTACAGTGATCTACTTGATAGGAAAAGCAAAAGTC
*
2972 AGGTGCTTTTCTTTTTCTTTTCTATTGATTTATTTACTGATTTGCATGCAATTTTAATTGTTTAG
261 AGGTGCCTTTCTTTTTCTTTTCTATTGATTTATTTACTGATTTGCATGCAATTTTAATTGTTTAG
*
3037 TGAATTTACTTTTAGTAAACCCTAATTTCTTTGAATACCAAAAAGAAACCCTAAGCTTCTCGAG-
326 TGAATTTACTCTTAGTAAACCCTAATTTCTTTGAATACCAAAAAGAAACCCTAAGCTTCTCGAGA
*
3101 AAAAAATGAAAAAGAATGAAGTAGGAGAAACAAAGATGAGGAAAATTTCAAATTTAACAAAGAAA
391 AAAAAATGAAAAAGAATGAAGTAGGAGAAACAAAGATGAGG-AAA-TTCAAATTAAACAAAGAAA
*
3166 AAAAGCAGTCATTTTGTTCTACTCCA-TCCTATAAGCTTTAGCCTTTAGTCCTTATTTACTTAAA
454 AAAAACAGTCATTTTGTTCTACTCCATTCC-ATAAGCTTTAGCCTTTAGTCCTTATTTACTTAAA
3230 TAAAAGTTCTTCCCATTATTTCTATTGCAAGATATCATTACATTGGATCGGAT
518 TAAAAGTTCTTCCCATTATTTCTATTGCAAGATATCATTACATTGGATCGGAT
3283 CATTTTAAAGACAAAGATCATCATTACTTGGCTTTCTAATTCTATTTTTCTTTTGCTATAGAGTG
1 CATTTTAAAGACAAAGATCATCATTACTTGGCTTTCTAATTCTATTTTTCTTTTGCTATAGAGTG
**
3348 AATGAAAAAAAAAAGTAGCAAAAAAGAGTGAATGAAAATGGAGCTAAATACCCTATTTTTAAAGA
66 AATGAAAAAAAAAAGT-GCAAAAAAGAGTGAATGAAAATGGAGCTAAATACCCTATTCCTAAAGA
3413 GTAGAGGACTTAAAATCCCACATCGCCCCTTTACCCATCCCAGCCCACTTTACCTACATATATAT
130 GTAGAGGACTTAAAATCCCACATCGCCCCTTTACCCATCCCAGCCCACTTTACCT--ATATATAT
*
3478 ATATATATAAATAAATAGGTCAAGTTGCGCTTACATCTACAGTGATCTACTTGATAGGAAAAGCA
193 ATA-A-A-AAATAAACAGGTCAAGTTGCGCTTACATCTACAGTGATCTACTTGATAGGAAAAGCA
* *
3543 TAAA-TCAGGTGCCTTTC-TTTTCTTTTCTATTGATTTATTTACTGATTTAGCGTGCAGTTTTAA
255 -AAAGTCAGGTGCCTTTCTTTTTCTTTTCTATTGATTTATTTACTGATTT-GCATGCAATTTTAA
* *
3606 TTGTTTAGTGAATTTACTCTTAGTAAACCCTGATTTCTTTGAATACCAAAGAGAAACCCTAAGCT
318 TTGTTTAGTGAATTTACTCTTAGTAAACCCTAATTTCTTTGAATACCAAAAAGAAACCCTAAGCT
* *
3671 TCTTGAGAAAAAAATGAAAAAGAATGAAGTAGGAGAAACAAAGATGAGGAAATTCAAGTTAAACA
383 TCTCGAGAAAAAAATGAAAAAGAATGAAGTAGGAGAAACAAAGATGAGGAAATTCAAATTAAACA
* *
3736 GAGAAAAAAAACAGTCATTTTGTTCTACTCCATTCCATAAGCTTTATCCTTT
448 AAGAAAAAAAACAGTCATTTTGTTCTACTCCATTCCATAAGCTTTAGCCTTT
3788 TG
Statistics
Matches: 474, Mismatches: 21, Indels: 15
0.93 0.04 0.03
Matches are distributed among these distances:
571 79 0.17
572 99 0.21
574 11 0.02
575 1 0.00
576 88 0.19
577 152 0.32
578 44 0.09
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (570 bp):
CATTTTAAAGACAAAGATCATCATTACTTGGCTTTCTAATTCTATTTTTCTTTTGCTATAGAGTG
AATGAAAAAAAAAAGTGCAAAAAAGAGTGAATGAAAATGGAGCTAAATACCCTATTCCTAAAGAG
TAGAGGACTTAAAATCCCACATCGCCCCTTTACCCATCCCAGCCCACTTTACCTATATATATATA
AAAAATAAACAGGTCAAGTTGCGCTTACATCTACAGTGATCTACTTGATAGGAAAAGCAAAAGTC
AGGTGCCTTTCTTTTTCTTTTCTATTGATTTATTTACTGATTTGCATGCAATTTTAATTGTTTAG
TGAATTTACTCTTAGTAAACCCTAATTTCTTTGAATACCAAAAAGAAACCCTAAGCTTCTCGAGA
AAAAAATGAAAAAGAATGAAGTAGGAGAAACAAAGATGAGGAAATTCAAATTAAACAAAGAAAAA
AAACAGTCATTTTGTTCTACTCCATTCCATAAGCTTTAGCCTTTAGTCCTTATTTACTTAAATAA
AAGTTCTTCCCATTATTTCTATTGCAAGATATCATTACATTGGATCGGAT
Done.