Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017796.1 Corchorus olitorius cultivar O-4 contig17829, 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: 24780
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Found at i:661 original size:29 final size:30
Alignment explanation
Indices: 585--666 Score: 123
Period size: 31 Copynumber: 2.7 Consensus size: 30
575 GGGGCAGAGG
585 ATTTTCGTTCACTGTTTACCTATTTACAAACT
1 ATTTTCGTTCACTGTTTACCTATTTAC--ACT
617 -TTTTCGTTCACTGTTTACCTATTTAC-CT
1 ATTTTCGTTCACTGTTTACCTATTTACACT
*
645 ATTTTCGTTCACGGTTTACCTA
1 ATTTTCGTTCACTGTTTACCTA
667 AACCCTAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.04
29 20 0.42
31 26 0.54
ACGTcount: A:0.20, C:0.23, G:0.09, T:0.49
Consensus pattern (30 bp):
ATTTTCGTTCACTGTTTACCTATTTACACT
Found at i:979 original size:29 final size:30
Alignment explanation
Indices: 905--986 Score: 132
Period size: 31 Copynumber: 2.7 Consensus size: 30
895 GGGGCAGAGG
905 ATTTTCGTTCACTGTTTACCTATTTACAAACT
1 ATTTTCGTTCACTGTTTACCTATTTAC--ACT
937 -TTTTCGTTCACTGTTTACCTATTTAC-CT
1 ATTTTCGTTCACTGTTTACCTATTTACACT
965 ATTTTCGTTCACTGTTTACCTA
1 ATTTTCGTTCACTGTTTACCTA
987 AACCCTAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
28 2 0.04
29 21 0.43
31 26 0.53
ACGTcount: A:0.20, C:0.23, G:0.07, T:0.50
Consensus pattern (30 bp):
ATTTTCGTTCACTGTTTACCTATTTACACT
Found at i:1301 original size:29 final size:30
Alignment explanation
Indices: 1225--1308 Score: 109
Period size: 33 Copynumber: 2.7 Consensus size: 30
1215 GGGGCAGAGG
*
1225 ATTTTCATTCACTGTTTACCTATTTACAAAAACT
1 ATTTTCGTTCACTGTTTACCTATTTAC----ACT
1259 -TTTTCGTTCACTGTTTACCTATTTAC-CT
1 ATTTTCGTTCACTGTTTACCTATTTACACT
1287 ATTTTCGTTCACTGTTTACCTA
1 ATTTTCGTTCACTGTTTACCTA
1309 AATCCTAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
28 2 0.04
29 21 0.44
33 25 0.52
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.49
Consensus pattern (30 bp):
ATTTTCGTTCACTGTTTACCTATTTACACT
Found at i:1462 original size:322 final size:320
Alignment explanation
Indices: 354--1582 Score: 2228
Period size: 320 Copynumber: 3.8 Consensus size: 320
344 TTTATACAAG
* *
354 AAAATAAAATAAGAAACCCACATAAACATCAGGTTTAGCCCCAAATTAACAATAAATAATTATAT
1 AAAATAAAATAAGAAACTCACATAAATATCAGGTTTAGCCCCAAATTAACAATAAATAATTATAT
*
419 ATAAGGGTTAGTCCTAAATTTTAATACATT-CTCATAGGGTTTTAGAATGAAAATATAAAATTTA
66 ATAAGGGTTAGTCCTAAATTTTAATACATTCCCCATAGGGTTTTAGAATGAAAATATAAAATTTA
* * *
483 ATTTAATTACACAAACAAGGAATAACATTAAAAACTTAAAAGGGACACGTGTCATTATTTGATGG
131 ATTTAATTACGCAAATAAGGAATAACATTAAAAACTGAAAAGGGACACGTGTCATTATTTGATGG
548 ATGGGACACAAGTGGGGCACCAAAATTGGGGCAGAGGATTTTCGTTCACTGTTTACCTATTTACA
196 ATGGGACACAAGTGGGGCACCAAAATTGGGGCAGAGGATTTTCGTTCACTGTTTACCTATTTACA
*
613 AACTTTTTCGTTCACTGTTTACCTATTTACCTATTTTCGTTCACGGTTTACCTAAACCCT
261 AACTTTTTCGTTCACTGTTTACCTATTTACCTATTTTCGTTCACTGTTTACCTAAACCCT
* *
673 AAAATAAAATAAGAAACTCACATAAATACCAGGTTTAGCCCCAAATTAACAATAAATAATCATAT
1 AAAATAAAATAAGAAACTCACATAAATATCAGGTTTAGCCCCAAATTAACAATAAATAATTATAT
738 ATAAGGGTTAGTCCTAAATTTTAATACATTCCCCATAGGGTTTTAGAATGAAAATATAAAATTTA
66 ATAAGGGTTAGTCCTAAATTTTAATACATTCCCCATAGGGTTTTAGAATGAAAATATAAAATTTA
*
803 ATTTAATTACGCAAATAAGGAATAACATTAAAAACTGAAAAGGGACACGTGACATTATTTGATGG
131 ATTTAATTACGCAAATAAGGAATAACATTAAAAACTGAAAAGGGACACGTGTCATTATTTGATGG
*
868 ATGGGACACAAGTGGGGAACCAAAATTGGGGCAGAGGATTTTCGTTCACTGTTTACCTATTTACA
196 ATGGGACACAAGTGGGGCACCAAAATTGGGGCAGAGGATTTTCGTTCACTGTTTACCTATTTACA
933 AACTTTTTCGTTCACTGTTTACCTATTTACCTATTTTCGTTCACTGTTTACCTAAACCCT
261 AACTTTTTCGTTCACTGTTTACCTATTTACCTATTTTCGTTCACTGTTTACCTAAACCCT
993 AAAATAAAATAAGAAACTCACATAAATATCAGGTTTAGCCCCAAATTAACAATAAATAATCT-TA
1 AAAATAAAATAAGAAACTCACATAAATATCAGGTTTAGCCCCAAATTAACAATAAATAAT-TATA
1057 TATAAGGGTTAGTCCTAAATTTTAATACATTCCCCATAGGGTTTTAGAATGAAAATATAAAATTT
65 TATAAGGGTTAGTCCTAAATTTTAATACATTCCCCATAGGGTTTTAGAATGAAAATATAAAATTT
1122 AATTTAATTACGCAAATAAGGAATAACATTAAAAACTGAAAAGGGACACGTGTCATTATTTGATG
130 AATTTAATTACGCAAATAAGGAATAACATTAAAAACTGAAAAGGGACACGTGTCATTATTTGATG
* *
1187 GATGGGGCACAAGTGGGGCACCAAAATTGGGGCAGAGGATTTTCATTCACTGTTTACCTATTTAC
195 GATGGGACACAAGTGGGGCACCAAAATTGGGGCAGAGGATTTTCGTTCACTGTTTACCTATTTAC
*
1252 AAAAACTTTTTCGTTCACTGTTTACCTATTTACCTATTTTCGTTCACTGTTTACCTAAATCCT
260 --AAACTTTTTCGTTCACTGTTTACCTATTTACCTATTTTCGTTCACTGTTTACCTAAACCCT
* *
1315 AAAATAAAATAAGAAACTCACATGAATATCAGATTTAGCCCCAAATTAACAATAAATAATTATAT
1 AAAATAAAATAAGAAACTCACATAAATATCAGGTTTAGCCCCAAATTAACAATAAATAATTATAT
*
1380 ATAAGGGTTAGTCCTAAATTTTAATACATTCCCCATAGGGTTTTAGAATGAAAATATAAAATATA
66 ATAAGGGTTAGTCCTAAATTTTAATACATTCCCCATAGGGTTTTAGAATGAAAATATAAAATTTA
*
1445 ATTTAATTACGCAAATAAGGAATAACATTAAAAACTAAAAAGGGACACGTGTCATTATTTGATGG
131 ATTTAATTACGCAAATAAGGAATAACATTAAAAACTGAAAAGGGACACGTGTCATTATTTGATGG
* * *
1510 ATGGAACACAAGTGGGGCACCAATATTAGGGCAGAGGATTTTCGTTCACTGTTTACCTATTTACA
196 ATGGGACACAAGTGGGGCACCAAAATTGGGGCAGAGGATTTTCGTTCACTGTTTACCTATTTACA
1575 AACTTTTT
261 AACTTTTT
1583 TCTTTTAATT
Statistics
Matches: 878, Mismatches: 27, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
319 91 0.10
320 478 0.54
321 1 0.00
322 308 0.35
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (320 bp):
AAAATAAAATAAGAAACTCACATAAATATCAGGTTTAGCCCCAAATTAACAATAAATAATTATAT
ATAAGGGTTAGTCCTAAATTTTAATACATTCCCCATAGGGTTTTAGAATGAAAATATAAAATTTA
ATTTAATTACGCAAATAAGGAATAACATTAAAAACTGAAAAGGGACACGTGTCATTATTTGATGG
ATGGGACACAAGTGGGGCACCAAAATTGGGGCAGAGGATTTTCGTTCACTGTTTACCTATTTACA
AACTTTTTCGTTCACTGTTTACCTATTTACCTATTTTCGTTCACTGTTTACCTAAACCCT
Found at i:1574 original size:642 final size:639
Alignment explanation
Indices: 354--1582 Score: 2226
Period size: 642 Copynumber: 1.9 Consensus size: 639
344 TTTATACAAG
354 AAAATAAAATAAGAAACCCACATAAACATCAGGTTTAGCCCCAAATTAACAATAAATAATTATAT
1 AAAATAAAATAAGAAACCCACATAAACATCAGGTTTAGCCCCAAATTAACAATAAATAATTATAT
*
419 ATAAGGGTTAGTCCTAAATTTTAATACATTCTCATAGGGTTTTAGAATGAAAATATAAAATTTAA
66 ATAAGGGTTAGTCCTAAATTTTAATACATTCCCATAGGGTTTTAGAATGAAAATATAAAATTTAA
*
484 TTTAATTACACAAACAAGGAATAACATTAAAAACTTAAAAGGGACACGTGTCATTATTTGATGGA
131 TTTAATTACACAAACAAGGAATAACATTAAAAACTGAAAAGGGACACGTGTCATTATTTGATGGA
*
549 TGGGACACAAGTGGGGCACCAAAATTGGGGCAGAGGATTTTCGTTCACTGTTTACCTATTTACAA
196 TGGGACACAAGTGGGGCACCAAAATTGGGGCAGAGGATTTTCATTCACTGTTTACCTATTTACAA
614 ACTTTTTCGTTCACTGTTTACCTATTTACCTATTTTCGTTCACGGTTTACCTAAACCCTAAAATA
261 ACTTTTTCGTTCACTGTTTACCTATTTACCTATTTTCGTTCACGGTTTACCTAAACCCTAAAATA
*
679 AAATAAGAAACTCACATAAATACCAGGTTTAGCCCCAAATTAACAATAAATAATCATATATAAGG
326 AAATAAGAAACTCACATAAATACCAGATTTAGCCCCAAATTAACAATAAATAATCATATATAAGG
*
744 GTTAGTCCTAAATTTTAATACATTCCCCATAGGGTTTTAGAATGAAAATATAAAATTTAATTTAA
391 GTTAGTCCTAAATTTTAATACATTCCCCATAGGGTTTTAGAATGAAAATATAAAATATAATTTAA
* *
809 TTACGCAAATAAGGAATAACATTAAAAACTGAAAAGGGACACGTGACATTATTTGATGGATGGGA
456 TTACGCAAATAAGGAATAACATTAAAAACTAAAAAGGGACACGTGACATTATTTGATGGATGGAA
*
874 CACAAGTGGGGAACCAAAATTGGGGCAGAGGATTTTCGTTCACTGTTTACCTATTTACAAACTTT
521 CACAAGTGGGGAACCAAAATTAGGGCAGAGGATTTTCGTTCACTGTTTACCTATTTACAAACTTT
939 TTCGTTCACTGTTTACCTATTTACCTATTTTCGTTCACTGTTTACCTAAACCCT
586 TTCGTTCACTGTTTACCTATTTACCTATTTTCGTTCACTGTTTACCTAAACCCT
* *
993 AAAATAAAATAAGAAACTCACATAAATATCAGGTTTAGCCCCAAATTAACAATAAATAATCT-TA
1 AAAATAAAATAAGAAACCCACATAAACATCAGGTTTAGCCCCAAATTAACAATAAATAAT-TATA
1057 TATAAGGGTTAGTCCTAAATTTTAATACATTCCCCATAGGGTTTTAGAATGAAAATATAAAATTT
65 TATAAGGGTTAGTCCTAAATTTTAATACATT-CCCATAGGGTTTTAGAATGAAAATATAAAATTT
* *
1122 AATTTAATTACGCAAATAAGGAATAACATTAAAAACTGAAAAGGGACACGTGTCATTATTTGATG
129 AATTTAATTACACAAACAAGGAATAACATTAAAAACTGAAAAGGGACACGTGTCATTATTTGATG
*
1187 GATGGGGCACAAGTGGGGCACCAAAATTGGGGCAGAGGATTTTCATTCACTGTTTACCTATTTAC
194 GATGGGACACAAGTGGGGCACCAAAATTGGGGCAGAGGATTTTCATTCACTGTTTACCTATTTAC
* *
1252 AAAAACTTTTTCGTTCACTGTTTACCTATTTACCTATTTTCGTTCACTGTTTACCTAAATCCTAA
259 --AAACTTTTTCGTTCACTGTTTACCTATTTACCTATTTTCGTTCACGGTTTACCTAAACCCTAA
* * *
1317 AATAAAATAAGAAACTCACATGAATATCAGATTTAGCCCCAAATTAACAATAAATAATTATATAT
322 AATAAAATAAGAAACTCACATAAATACCAGATTTAGCCCCAAATTAACAATAAATAATCATATAT
1382 AAGGGTTAGTCCTAAATTTTAATACATTCCCCATAGGGTTTTAGAATGAAAATATAAAATATAAT
387 AAGGGTTAGTCCTAAATTTTAATACATTCCCCATAGGGTTTTAGAATGAAAATATAAAATATAAT
*
1447 TTAATTACGCAAATAAGGAATAACATTAAAAACTAAAAAGGGACACGTGTCATTATTTGATGGAT
452 TTAATTACGCAAATAAGGAATAACATTAAAAACTAAAAAGGGACACGTGACATTATTTGATGGAT
* *
1512 GGAACACAAGTGGGGCACCAATATTAGGGCAGAGGATTTTCGTTCACTGTTTACCTATTTACAAA
517 GGAACACAAGTGGGGAACCAAAATTAGGGCAGAGGATTTTCGTTCACTGTTTACCTATTTACAAA
1577 CTTTTT
582 CTTTTT
1583 TCTTTTAATT
Statistics
Matches: 565, Mismatches: 21, Indels: 5
0.96 0.04 0.01
Matches are distributed among these distances:
639 91 0.16
640 158 0.28
642 316 0.56
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (639 bp):
AAAATAAAATAAGAAACCCACATAAACATCAGGTTTAGCCCCAAATTAACAATAAATAATTATAT
ATAAGGGTTAGTCCTAAATTTTAATACATTCCCATAGGGTTTTAGAATGAAAATATAAAATTTAA
TTTAATTACACAAACAAGGAATAACATTAAAAACTGAAAAGGGACACGTGTCATTATTTGATGGA
TGGGACACAAGTGGGGCACCAAAATTGGGGCAGAGGATTTTCATTCACTGTTTACCTATTTACAA
ACTTTTTCGTTCACTGTTTACCTATTTACCTATTTTCGTTCACGGTTTACCTAAACCCTAAAATA
AAATAAGAAACTCACATAAATACCAGATTTAGCCCCAAATTAACAATAAATAATCATATATAAGG
GTTAGTCCTAAATTTTAATACATTCCCCATAGGGTTTTAGAATGAAAATATAAAATATAATTTAA
TTACGCAAATAAGGAATAACATTAAAAACTAAAAAGGGACACGTGACATTATTTGATGGATGGAA
CACAAGTGGGGAACCAAAATTAGGGCAGAGGATTTTCGTTCACTGTTTACCTATTTACAAACTTT
TTCGTTCACTGTTTACCTATTTACCTATTTTCGTTCACTGTTTACCTAAACCCT
Found at i:2644 original size:32 final size:32
Alignment explanation
Indices: 2603--2666 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
2593 CGAAACGCGG
*
2603 GCCAAATTCTAGTGGAATTTAGTGTTTGAAAA
1 GCCAAATTCTAGTAGAATTTAGTGTTTGAAAA
2635 GCCAAATTCTAGTAGAATTTAGTGTTTGAAAA
1 GCCAAATTCTAGTAGAATTTAGTGTTTGAAAA
2667 TAGGCATTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.34
Consensus pattern (32 bp):
GCCAAATTCTAGTAGAATTTAGTGTTTGAAAA
Found at i:8449 original size:7 final size:7
Alignment explanation
Indices: 8437--8490 Score: 72
Period size: 7 Copynumber: 7.6 Consensus size: 7
8427 TATATGAAAT
8437 GGAAAAA
1 GGAAAAA
*
8444 GGAAAAGG
1 GGAAAA-A
8452 GGAAAAA
1 GGAAAAA
8459 GGAAAAA
1 GGAAAAA
8466 GGAAAAA
1 GGAAAAA
8473 GGAAAAA
1 GGAAAAA
* *
8480 TGAGAAA
1 GGAAAAA
8487 GGAA
1 GGAA
8491 GACTGTGTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
7 34 0.85
8 6 0.15
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (7 bp):
GGAAAAA
Found at i:11784 original size:25 final size:23
Alignment explanation
Indices: 11750--11799 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
11740 AGTTTCAAAC
11750 AAGAAAAACCATAATACCAACTTAA
1 AAGAAAAACC-TAATACCAA-TTAA
* *
11775 AAGAACAACCTTATACCAATTAA
1 AAGAAAAACCTAATACCAATTAA
11798 AA
1 AA
11800 ATATTTGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 6 0.26
24 8 0.35
25 9 0.39
ACGTcount: A:0.58, C:0.20, G:0.04, T:0.18
Consensus pattern (23 bp):
AAGAAAAACCTAATACCAATTAA
Found at i:17628 original size:43 final size:43
Alignment explanation
Indices: 17580--17663 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
17570 TTTACTTACG
*
17580 TAAAAGAATGTATTTAATTAGCATATAGATACGGCGTCATCGA
1 TAAAAGAATGTATATAATTAGCATATAGATACGGCGTCATCGA
* *
17623 TAAAAGAATGTATATAATTAGTATATAGATATGGCGTCATC
1 TAAAAGAATGTATATAATTAGCATATAGATACGGCGTCATC
17664 AAGAAGAGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (43 bp):
TAAAAGAATGTATATAATTAGCATATAGATACGGCGTCATCGA
Found at i:18828 original size:6 final size:6
Alignment explanation
Indices: 18813--18846 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
18803 AAAACCCAGG
* *
18813 AAAAAA AAAAAC AAAAAC AAAAAA AAAAAC AAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAA
18847 TTTCCATACC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Done.