Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012430.1 Corchorus olitorius cultivar O-4 contig12463, 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: 14279
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:347 original size:42 final size:43
Alignment explanation
Indices: 292--386 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 43
282 AGTGCATTAT
*
292 CTAA-ATTATA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTATACCTCCATCTCTAGATAATTCATCAAAATAAAG
*
333 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTATA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
378 CTAATATTA
1 CTAATATTA
387 ATTGTTGCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
41 4 0.09
42 5 0.11
45 38 0.81
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTATACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:2411 original size:610 final size:610
Alignment explanation
Indices: 1252--2419 Score: 1883
Period size: 610 Copynumber: 1.9 Consensus size: 610
1242 ATATAATCAA
* *
1252 CAAATAAATCGAGATTTACCTCAAAATGTTATGGTGAGAAGTGAAAGCTCCCCACTTTAGGTTAT
1 CAAATAAATCCAGATTTACCTCAAAATGTTACGGTGAGAAGTGAAAGCTCCCCACTTTAGGTTAT
1317 GCCATCCTAAGGCGCTGCTAAATTAAATGGAAAGATCTTATCAACGTCCACCTGGAAATTTTAGG
66 GCCATCCTAAGGCGCTGCTAAATTAAATGGAAAGATCTTATCAACGTCCACCTGGAAATTTTAGG
* * *
1382 AAACAGAACGGAGTTCATGGAAAACCAATTCAGAGATATGTTAGGAAAGAAGAAACCCACCCAAA
131 AAACAGAACGGAGTGCATGGAAAACCAATTCAAAGAAATGTTAGGAAAGAAGAAACCCACCCAAA
* * * * * *
1447 TAGAAATGAAGACGAAAGGAAAACATAATTGGAATGTCAATAGTTTACTCACGAATCAACTATTA
196 TAGAAATGAAGACGAAAGGAAAACAGAACTGAAATGCCAATAGTTTACCCACGAATCAACCATTA
* * * * *
1512 TTGCATATACATTTATAGCACCAATCCTTTGGAATTCCGGCAGAGGAGTTGAATCGGTAAATTCT
261 TTGAAGATACATTTATAGCACCAATCCTTTGGAATTCCGGCAAAGGAGTTGAACCGGTAAATCCT
* * *
1577 AATATCCACACACAATTAATATGTAATTAAGACACACTTAATCATAAATATAAAAATAGTAAATT
326 AATATCCACACACAATTAATATGCAATTAAAACACACTTAATCATAAATATAAAAATAATAAATT
* *
1642 ACAAAAAAAGGGCAGCAGAAAAAGTAAGAGAGGAAATTCATCGAGGGCCTTTTTAGTCACCCGAA
391 ACAAAAAAAGGGCAGCAGAAAAAGTAAGAGAGGAAATTCATCAAAGGCCTTTTTAGTCACCCGAA
* * *
1707 AAGTGAAAAAAGACCAAAAAAAGTCAAAAGGAGGCACCACATTAATCCTCAATGTGGCCTTTAAG
456 AAGTGAAAAAAGACCAAAAAAAGTCAAAAGAAGCCACCACATTAATCCTCAATGTGACCTTTAAG
*
1772 TAATTTCCATAGTCACTAAAAATAATATATAGTATATACAATGCATCAGAAAATCATTGTACTTA
521 TAATTTCCATACTCACTAAAAATAATATATAGTATATACAATGCATCAGAAAATCATTGTACTTA
1837 GCATTGGCTAACTATAACATAAATC
586 GCATTGGCTAACTATAACATAAATC
* *
1862 CAAATAAATCCAGATTTACCTCAAAATGTTGCGGTGAGAAGTGAAAGCTCTCCACTTTAGGTTAT
1 CAAATAAATCCAGATTTACCTCAAAATGTTACGGTGAGAAGTGAAAGCTCCCCACTTTAGGTTAT
* * **
1927 GTCATCCTAAGGCGCTGCTAAATTAAATGGAAGGATCTTATCAACGTCCATTTGGAAATTTTAGG
66 GCCATCCTAAGGCGCTGCTAAATTAAATGGAAAGATCTTATCAACGTCCACCTGGAAATTTTAGG
*
1992 AAACAGAACGGAGTGCATGTG-AAACCAATTCAAAGAAATGTTAGGGAAGAAGAAACCCACCCAA
131 AAACAGAACGGAGTGCATG-GAAAACCAATTCAAAGAAATGTTAGGAAAGAAGAAACCCACCCAA
* *
2056 ATAGAAATGAAGACGAGAGGAAAACAGAACTGAAATGCCAATAGTTTACCCATGAATCAACCATT
195 ATAGAAATGAAGACGAAAGGAAAACAGAACTGAAATGCCAATAGTTTACCCACGAATCAACCATT
*
2121 ATTGAAGATACATTTATAGCACCAGTCCTTTGGAATTCCGGCAAAGGAGTTGAACCGGTAAATCC
260 ATTGAAGATACATTTATAGCACCAATCCTTTGGAATTCCGGCAAAGGAGTTGAACCGGTAAATCC
2186 TAATATCCACACACAATTAATATGCAATTAAAACACACTTAATCATAAATATAAAAATAATAAAT
325 TAATATCCACACACAATTAATATGCAATTAAAACACACTTAATCATAAATATAAAAATAATAAAT
* * * * *
2251 TAC-AAAAAAGGGCTGCAGGAACAGTAAGGGAGGAAATTCATCAAAGGCCTTTTTAGTCACCTGA
390 TACAAAAAAAGGGCAGCAGAAAAAGTAAGAGAGGAAATTCATCAAAGGCCTTTTTAGTCACCCGA
* * *
2315 AAAGTGAGAAAAAGACCAAAAAAAGTCAAAAGAAGCCATCACATTAATCCTCAATTTGACTTTTA
455 AAAGTGA-AAAAAGACCAAAAAAAGTCAAAAGAAGCCACCACATTAATCCTCAATGTGACCTTTA
**
2380 AGTAATTTTTATAACT-ACTAAAAATAATATATAGTATATA
519 AGTAATTTCCAT-ACTCACTAAAAATAATATATAGTATATA
2420 TAGTGTTAAA
Statistics
Matches: 510, Mismatches: 45, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
609 61 0.12
610 446 0.87
611 3 0.01
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (610 bp):
CAAATAAATCCAGATTTACCTCAAAATGTTACGGTGAGAAGTGAAAGCTCCCCACTTTAGGTTAT
GCCATCCTAAGGCGCTGCTAAATTAAATGGAAAGATCTTATCAACGTCCACCTGGAAATTTTAGG
AAACAGAACGGAGTGCATGGAAAACCAATTCAAAGAAATGTTAGGAAAGAAGAAACCCACCCAAA
TAGAAATGAAGACGAAAGGAAAACAGAACTGAAATGCCAATAGTTTACCCACGAATCAACCATTA
TTGAAGATACATTTATAGCACCAATCCTTTGGAATTCCGGCAAAGGAGTTGAACCGGTAAATCCT
AATATCCACACACAATTAATATGCAATTAAAACACACTTAATCATAAATATAAAAATAATAAATT
ACAAAAAAAGGGCAGCAGAAAAAGTAAGAGAGGAAATTCATCAAAGGCCTTTTTAGTCACCCGAA
AAGTGAAAAAAGACCAAAAAAAGTCAAAAGAAGCCACCACATTAATCCTCAATGTGACCTTTAAG
TAATTTCCATACTCACTAAAAATAATATATAGTATATACAATGCATCAGAAAATCATTGTACTTA
GCATTGGCTAACTATAACATAAATC
Found at i:5580 original size:21 final size:21
Alignment explanation
Indices: 5554--5603 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
5544 AGCCAGGCCA
5554 TGGCCTTTTATCATTTTTGTG
1 TGGCCTTTTATCATTTTTGTG
5575 TGGCCTTTTATCATTTTTGTG
1 TGGCCTTTTATCATTTTTGTG
5596 TGGCCTTT
1 TGGCCTTT
5604 CCTTAAAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.08, C:0.16, G:0.20, T:0.56
Consensus pattern (21 bp):
TGGCCTTTTATCATTTTTGTG
Found at i:5673 original size:6 final size:6
Alignment explanation
Indices: 5662--5689 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5652 CATACAATTA
5662 ATTTGC ATTTGC ATTTGC ATTTGC ATTT
1 ATTTGC ATTTGC ATTTGC ATTTGC ATTT
5690 ACATAGGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.14, T:0.54
Consensus pattern (6 bp):
ATTTGC
Found at i:13587 original size:14 final size:13
Alignment explanation
Indices: 13525--13589 Score: 78
Period size: 14 Copynumber: 4.8 Consensus size: 13
13515 AAGCATTTTT
13525 TTTTCAAAAATGA
1 TTTTCAAAAATGA
13538 TTTTCAAGAAACTG-
1 TTTTCAA-AAA-TGA
13552 TTTTCAAGAAATGA
1 TTTTCAA-AAATGA
*
13566 TATTCAAAAATGA
1 TTTTCAAAAATGA
13579 GTTTTCAAAAA
1 -TTTTCAAAAA
13590 GGTTTTGAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
13 15 0.33
14 29 0.63
15 2 0.04
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:14233 original size:2 final size:2
Alignment explanation
Indices: 14226--14272 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
14216 GTGAAGCCAA
14226 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
14268 AG AG A
1 AG AG A
14273 AGAAAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.