Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009652.1 Corchorus olitorius cultivar O-4 contig09684, 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: 2394
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Found at i:1910 original size:610 final size:602
Alignment explanation
Indices: 475--1995 Score: 2250
Period size: 602 Copynumber: 2.5 Consensus size: 602
465 CAATACTCAT
* * * *
475 AAAAAAGATATATAATTCAAAGCCAAAAAGATTGACGAGATTTTT-ACGCTTCTAAATATC-GTT
1 AAAAAA-ATATATAATTCAACGCCAAAAAGATTAAAG-GTTTTTTCACGCTTCT-AATATCAGTT
** * *
538 TTCCCAC-TTTTTCCGAATTAAATTCTAATTAAATCGAAACAAGATTCAGATACTAGTAAAAACA
63 TTCAAACTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATTCTAGTAAAAACA
*
602 AATCCTTAAATCCAATGTGGCTGAGATTTGGTAAAATGAATATAGATATTTCAAGGGGTCTTTGC
128 AATCCTTAAATCCAATGTGTCTGAGATTTGGTAAAATGAATATAGATATTTCAAGGGGTCTTTGC
* **
667 ACCCAAAATCATATAAAATTGAGCCGGGCTCCAAAACGCGTTTTTAGCCAAAAACCGTGATGGTT
193 ACCCAAAATCATGTAAAATTGAGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTT
**
732 AGTACACGATTTTGGCTAAAAACTGACCCGAGGAGTTTTTACTCAGA-TTTTACCACAGCGTGGT
258 AGTACACGATTTTGGCTAAAAACTGACCCGAAAAGTTTTTACTCA-ATTTTTACCACAGCGTGGT
**** *
796 CGGTTCAAATCAGTCTTTGGAAAGCTATTATAATAGTAAAATCGATTTACGGTTTGAAAATTCAT
322 CGGTTCAAATCAGTCTCCAAAAAGCTATTATAATAGTAAAATCGATTTACGGTTTGAAAATGCAT
*
861 TTTTAAGTTGACCCACCTGCAGGAACTTCAGGACCAAAATCCAAAACGTTACACGCCATTTCGAA
387 TTTTAAGTTGACCCACCTGCAGGAACTTCAGGACCAAAATCCAAAACGTTACACGCAATTTCGAA
* * * * * * *
926 TGGAGTTCTGACGGTTCATACGATCCATATGTAATATATCTATCTCATCCGCATTTCACATTTTT
452 CGAACTTCTGACGGTCCATACGATCCATATGAAATATATCTATCCCATCCGCATCTCACATTTTT
* *
991 AGCCAAAAAAACGTGACACGATTTTGGCTAAAATTTTGCTAAAATTGTCCCGAAAAATTTTCCTC
517 AGCCAAAAAAACGTGAAACGATTTCGGCTAAAATTTTGCTAAAATTGTCCCGAAAAATTTT-CTC
*
1056 AATTTTTTTTGCCATACTACTC
581 AATTTTTTTTGCCACACTACTC
*
1078 AAAAAAATATATAATTCAACGCCAAAAAGATTAAAGGTTTTTTCACACTTCTAATATCAGTTTT-
1 AAAAAAATATATAATTCAACGCCAAAAAGATTAAAGGTTTTTTCACGCTTCTAATATCAGTTTTC
*
1142 GAACTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATTCTAGTAAAAACAAAT
66 AAACTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATTCTAGTAAAAACAAAT
* *
1207 CCTTAAATCCAATGTGTATGAGATTTGGTAAGATGAATATAGATATTTCAAGGGGTCTTTGCACC
131 CCTTAAATCCAATGTGTCTGAGATTTGGTAAAATGAATATAGATATTTCAAGGGGTCTTTGCACC
* * * *
1272 CTAAATCATGTAAAACTAAGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGATTAGT
196 CAAAATCATGTAAAATTGAGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGT
* *
1337 ACACGATTTTGGATAAAAACTGACCTGAAAAGTTTTTACTCAATTTTTACCACAGCGTGGTCGGT
261 ACACGATTTTGGCTAAAAACTGACCCGAAAAGTTTTTACTCAATTTTTACCACAGCGTGGTCGGT
* *
1402 TCAAATCAGTCTCCAAAAAGGTATTCTAATAGTAAAA-CGAATTTACGGTTTGAAAGCTATGGCA
326 TCAAATCAGTCTCCAAAAAGCTATTATAATAGTAAAATCG-ATTTACGGTTTGAAA---AT-GCA
* *
1466 TTTTTAAGTTGACCCACCTGCAGGAACTTCAGGCCCAAAATTCAAAACGTTACACGCAATTTCGA
386 TTTTTAAGTTGACCCACCTGCAGGAACTTCAGGACCAAAATCCAAAACGTTACACGCAATTTCGA
* * **
1531 ACGAACTTCTGACGGTCCGTACGATCCATAT-AAGATATATCTATCCCATTCGCATCTCGTATTT
451 ACGAACTTCTGACGGTCCATACGATCCATATGAA-ATATATCTATCCCATCCGCATCTCACATTT
*
1595 TTAGCCAAAAAAATCGTGAAGAACGATTTCGGCTAAAATTTTGGTAAAATT-TACCCGAAAAATT
515 TTAGCCAAAAAAA-CGTG-A-AACGATTTCGGCTAAAATTTTGCTAAAATTGT-CCCGAAAAATT
*
1659 TT-TCACATTTTCTTTTGCCACACTACTT
576 TTCTCA-ATTTT-TTTTGCCACACTACTC
* * * *
1687 AGAAAAATATATAATTCAACGCCAAAACGATTAAAGGTTTTTTCACGCTACTAATATCATTTTTC
1 AAAAAAATATATAATTCAACGCCAAAAAGATTAAAGGTTTTTTCACGCTTCTAATATCAGTTTTC
*
1752 AAACTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATTCTAGTAAAAACAAAT
66 AAACTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATTCTAGTAAAAACAAAT
*
1817 CCTTAAATCCAATGTGTCTGAGATTTGATAAAATGAATATAGATATTTCAAGGGGTCTTTGCACC
131 CCTTAAATCCAATGTGTCTGAGATTTGGTAAAATGAATATAGATATTTCAAGGGGTCTTTGCACC
* * *
1882 CAAAATCATGTAAAATTGAGCTGGGCTCCGGAACGTGTTTTTAGCCAAAAATCGTGATGGTTAGT
196 CAAAATCATGTAAAATTGAGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGT
* ** *
1947 ATACGATTACGGCTAAAAACTGACCCGAAAAATTTTTACTTCAATTTTT
261 ACACGATTTTGGCTAAAAACTGACCCGAAAAGTTTTTAC-TCAATTTTT
1996 CTCAATACTC
Statistics
Matches: 828, Mismatches: 72, Indels: 28
0.89 0.08 0.03
Matches are distributed among these distances:
601 17 0.02
602 322 0.39
603 6 0.01
605 3 0.00
606 128 0.15
607 7 0.01
608 7 0.01
609 113 0.14
610 216 0.26
611 9 0.01
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (602 bp):
AAAAAAATATATAATTCAACGCCAAAAAGATTAAAGGTTTTTTCACGCTTCTAATATCAGTTTTC
AAACTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATTCTAGTAAAAACAAAT
CCTTAAATCCAATGTGTCTGAGATTTGGTAAAATGAATATAGATATTTCAAGGGGTCTTTGCACC
CAAAATCATGTAAAATTGAGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGT
ACACGATTTTGGCTAAAAACTGACCCGAAAAGTTTTTACTCAATTTTTACCACAGCGTGGTCGGT
TCAAATCAGTCTCCAAAAAGCTATTATAATAGTAAAATCGATTTACGGTTTGAAAATGCATTTTT
AAGTTGACCCACCTGCAGGAACTTCAGGACCAAAATCCAAAACGTTACACGCAATTTCGAACGAA
CTTCTGACGGTCCATACGATCCATATGAAATATATCTATCCCATCCGCATCTCACATTTTTAGCC
AAAAAAACGTGAAACGATTTCGGCTAAAATTTTGCTAAAATTGTCCCGAAAAATTTTCTCAATTT
TTTTTGCCACACTACTC
Found at i:2231 original size:320 final size:317
Alignment explanation
Indices: 1689--2394 Score: 1134
Period size: 320 Copynumber: 2.2 Consensus size: 317
1679 CACTACTTAG
* * * * * *
1689 AAAA-ATATATAATTCAACGCCAAAACGATTAAAG-GTTTTTTCACGCTACT-AATATCATTTTT
1 AAAAGATATATAATTCAACGCCAAAAAGATTGACGAGATTTTT-ACGCTTCTAAATATC-GTTTT
* *
1751 CAAACTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATTCTAGTAAAAACAAA
64 C--CCATTTTTCCGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATTCTAGTAAAAACAAA
1816 TCCTTAAATCCAATGTGTCTGAGATTTGATAAAATGAATATAGATATTTCAAGGGGTCTTTGCAC
127 TCCTTAAATCCAATGTGTCTGAGATTTGATAAAATGAATATAGATATTTCAAGGGGTCTTTGCAC
* * *
1881 CCAAAATCATGTAAAATTGAGCTGGGCTCCGGAACGTGTTTTTAGCCAAAAATCGTGATGGTTA-
192 CCAAAATCATGTAAAATTGAGCCGGGCTCCGGAACGTATTTTTAGCCAAAAACCGTGA----TAC
1945 GTATACGATTACGGCTAAAAACTGACCCGAAAAATTTTTACTTC-AATTTTTCTCAATACTCATA
253 GTATACGATTACGGCTAAAAACTGACCCGAAAAATTTTTAC-TCAAATTTTTCTCAATACTCATA
2009 A
317 A
2010 AAAAGATATATAATTCAACGCCAAAAAGATTGACGAGATTTTTACGCTTCTAAATATCGTTTTCC
1 AAAAGATATATAATTCAACGCCAAAAAGATTGACGAGATTTTTACGCTTCTAAATATCGTTTTCC
* * *
2075 CATTTTTCCGGATTAATTTCTAATTAAATCGAAACAAGATTCAGATTTTAGTAAAAACAAATCCT
66 CATTTTTCCGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATTCTAGTAAAAACAAATCCT
*
2140 TAAATCCAATGTGTCTGAGATTTGGTAAAATGAATATAGATATTTCAAGGGGTCTTTGCACCCAA
131 TAAATCCAATGTGTCTGAGATTTGATAAAATGAATATAGATATTTCAAGGGGTCTTTGCACCCAA
2205 AATCATGTAAAATTGAGCCGGGCTCCGGAACGTATTTTTAGCCAAAAACCGTGATACGTATACGA
196 AATCATGTAAAATTGAGCCGGGCTCCGGAACGTATTTTTAGCCAAAAACCGTGATACGTATACGA
* *
2270 TTACGGCTAAAAACTGACCCGAAAAATTTTTTCTCAAATTTTTCTCAATACTCATGA
261 TTACGGCTAAAAACTGACCCGAAAAATTTTTACTCAAATTTTTCTCAATACTCATAA
*
2327 AAAAGATATATAATTCAACGCCAAAAAGATTGACGAGATTTTTACGCTTCTAAATATCGCTTTCC
1 AAAAGATATATAATTCAACGCCAAAAAGATTGACGAGATTTTTACGCTTCTAAATATCGTTTTCC
2392 CAT
66 CAT
Statistics
Matches: 362, Mismatches: 18, Indels: 14
0.92 0.05 0.04
Matches are distributed among these distances:
316 4 0.01
317 127 0.35
320 176 0.49
321 4 0.01
322 39 0.11
323 12 0.03
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (317 bp):
AAAAGATATATAATTCAACGCCAAAAAGATTGACGAGATTTTTACGCTTCTAAATATCGTTTTCC
CATTTTTCCGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATTCTAGTAAAAACAAATCCT
TAAATCCAATGTGTCTGAGATTTGATAAAATGAATATAGATATTTCAAGGGGTCTTTGCACCCAA
AATCATGTAAAATTGAGCCGGGCTCCGGAACGTATTTTTAGCCAAAAACCGTGATACGTATACGA
TTACGGCTAAAAACTGACCCGAAAAATTTTTACTCAAATTTTTCTCAATACTCATAA
Done.