Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019052.1 Corchorus olitorius cultivar O-4 contig19085, 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: 43573
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Found at i:456 original size:29 final size:29
Alignment explanation
Indices: 416--718 Score: 345
Period size: 29 Copynumber: 10.4 Consensus size: 29
406 ACCCAGAGTA
*
416 TGCAAAAATGACCAAAATGCCCCTAGATG
1 TGCAAAAATGACCAAAATGCCCCTGGATG
* * *
445 TGCAAAAGTGACCAAAATGCCCCTAGACG
1 TGCAAAAATGACCAAAATGCCCCTGGATG
*
474 TGCAAAAATGACCAAAATGCCCTTGGATG
1 TGCAAAAATGACCAAAATGCCCCTGGATG
*
503 TGCAAAAAATGACCAAAATGCCCTTGGATG
1 TGC-AAAAATGACCAAAATGCCCCTGGATG
* * ** *
533 TGCAAACATAATAAAAAATGCCCTTGGATG
1 TGCAAAAATGA-CCAAAATGCCCCTGGATG
** * * *
563 CACAAAAATGATCAAACTGCCCCTGGATA
1 TGCAAAAATGACCAAAATGCCCCTGGATG
* *
592 TGCAAAAATGACCATAATGCCCTTGGATG
1 TGCAAAAATGACCAAAATGCCCCTGGATG
* * *
621 GGCAAAAATGACCAAAATACCCCTAGATG
1 TGCAAAAATGACCAAAATGCCCCTGGATG
* *
650 TGCAAAAATGACCAAAATGCCCATGGACG
1 TGCAAAAATGACCAAAATGCCCCTGGATG
* * *
679 TGCAAATATGACCAAAATGCCCCTGGGTA
1 TGCAAAAATGACCAAAATGCCCCTGGATG
*
708 AGCAAAAATGA
1 TGCAAAAATGA
719 TCAATTAAGA
Statistics
Matches: 229, Mismatches: 43, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
29 177 0.77
30 52 0.23
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (29 bp):
TGCAAAAATGACCAAAATGCCCCTGGATG
Found at i:1254 original size:58 final size:58
Alignment explanation
Indices: 951--1476 Score: 685
Period size: 58 Copynumber: 8.9 Consensus size: 58
941 TAAAATATAG
* * *
951 ACTCTCAAACAGAGACCTCGACCAGGATTTTAAAACAAGATGAGATTTTGAATTGAAAAAAAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTG------AAA
* * *
1015 ACTCTCTAACAGAGACCTCGAACAAGATTTTTAAAGCAAGATAAGATTTTGAAATGAAAA
1 ACTCTCTAACAGAGACCTCGAACAGGA-TTTTAAAACAAGATAAGATTTTGAATTG-AAA
* *
1075 ACTCTCTAACAGAGACCTCGAACAGGATTTTTAAAATC-AGATAAGGATTTTTAAGATGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGA-TTTTAAAA-CAAGATAA-GATTTTGAA-TTGAAA
* * * * * *
1136 ACTCTCCAACAGAGACCTCGAACAGGGTTTTTAAAATAAGGTAGGATTTTGAATTGGAA
1 ACTCTCTAACAGAGACCTCGAACA-GGATTTTAAAACAAGATAAGATTTTGAATTGAAA
* * *
1195 ACTCTCTAACAGAGACCTCAAACAGGATTTTAAAACAAGATGAGATTTTGAATTGGAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
*
1253 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATGAGATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
* * *
1311 ACTCTCTAACAGAGTCCTCGAATAGGATTTTAAAACAAGATAAGATTTTAAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
* * *
1369 ACTCTCTAGCAGAGACCTCGAACAGGATTTTGAAACAAGATAAGATTTTAAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
* * *
1427 ACTCTCTAGCAGAGACCTCGAACAGGATTTTGAAATAAGATAAGATTTTG
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTG
1477 TTTTAAACTG
Statistics
Matches: 420, Mismatches: 36, Indels: 18
0.89 0.08 0.04
Matches are distributed among these distances:
58 241 0.57
59 26 0.06
60 52 0.12
61 47 0.11
62 5 0.01
64 24 0.06
65 25 0.06
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.26
Consensus pattern (58 bp):
ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
Found at i:2394 original size:40 final size:40
Alignment explanation
Indices: 2311--2392 Score: 116
Period size: 38 Copynumber: 2.1 Consensus size: 40
2301 TTTTTATTTA
*
2311 TTTTCTTTTTTCTGACCTCTCTCTGTTTTAGGCCAAGTTT
1 TTTTCTTTTTTCTGACCTCTCTCTATTTTAGGCCAAGTTT
*
2351 TTTTC-TTTTTC-GACCTCTTTCTATTTTAGGTCC-AGTTT
1 TTTTCTTTTTTCTGACCTCTCTCTATTTTAGG-CCAAGTTT
2389 TTTT
1 TTTT
2393 TTTAAAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
38 26 0.67
39 8 0.21
40 5 0.13
ACGTcount: A:0.10, C:0.21, G:0.11, T:0.59
Consensus pattern (40 bp):
TTTTCTTTTTTCTGACCTCTCTCTATTTTAGGCCAAGTTT
Found at i:2883 original size:29 final size:28
Alignment explanation
Indices: 2850--2929 Score: 99
Period size: 29 Copynumber: 2.8 Consensus size: 28
2840 TTAGGATCAC
*
2850 CTAGGGGCATTTTGGTCATTTTCAAGAAT
1 CTAGGGGCATTTTGGTCATTTTC-ACAAT
* *
2879 CTAGGGGCATTTTGGTCATTTGCACATT
1 CTAGGGGCATTTTGGTCATTTTCACAAT
2907 C-AGGGGGGCATTTTGGTCATTTT
1 CTA--GGGGCATTTTGGTCATTTT
2930 AAGTTCACAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
27 1 0.02
28 4 0.09
29 40 0.89
ACGTcount: A:0.19, C:0.15, G:0.28, T:0.39
Consensus pattern (28 bp):
CTAGGGGCATTTTGGTCATTTTCACAAT
Found at i:3546 original size:42 final size:42
Alignment explanation
Indices: 3487--3571 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
3477 CAATATATTT
3487 TACAAAATACAAAAAAAAAATGATTTTCATTTCACATTGGCA
1 TACAAAATACAAAAAAAAAATGATTTTCATTTCACATTGGCA
*
3529 TACAAAATACAAAAAAAAAATGATTTTCATTTCATATTGGCA
1 TACAAAATACAAAAAAAAAATGATTTTCATTTCACATTGGCA
3571 T
1 T
3572 TTTTTTTTGC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.31
Consensus pattern (42 bp):
TACAAAATACAAAAAAAAAATGATTTTCATTTCACATTGGCA
Found at i:19256 original size:12 final size:12
Alignment explanation
Indices: 19228--19269 Score: 57
Period size: 13 Copynumber: 3.3 Consensus size: 12
19218 TATTTACTGC
19228 TTTTATATAAATG
1 TTTTATA-AAATG
*
19241 TTTTATAAAATA
1 TTTTATAAAATG
19253 TTTTGATAAAATG
1 TTTT-ATAAAATG
19266 TTTT
1 TTTT
19270 GGGTGCATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (12 bp):
TTTTATAAAATG
Found at i:23606 original size:16 final size:15
Alignment explanation
Indices: 23572--23605 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
23562 AGGGGTAGGG
23572 TTTTCAGAATTAATT
1 TTTTCAGAATTAATT
*
23587 TTTTCAGAGTTAATT
1 TTTTCAGAATTAATT
23602 TTTT
1 TTTT
23606 TTTCTTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.59
Consensus pattern (15 bp):
TTTTCAGAATTAATT
Found at i:31317 original size:29 final size:29
Alignment explanation
Indices: 31263--31319 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
31253 CACATGATCC
***
31263 ATCGTGTTTAAATTTAATGGCTTTAAAAA
1 ATCGTGTTTAAATTTAATGAAATTAAAAA
31292 ATCGTGTTTAAA-TTAATGAAAATTAAAA
1 ATCGTGTTTAAATTTAATG-AAATTAAAA
31320 TAATAATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.39
Consensus pattern (29 bp):
ATCGTGTTTAAATTTAATGAAATTAAAAA
Found at i:33867 original size:22 final size:22
Alignment explanation
Indices: 33833--33875 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
33823 GAATTTCAAA
* *
33833 ACAAGTCCTGCCCAAGACTTGG
1 ACAACTCCAGCCCAAGACTTGG
*
33855 ACAACTCCAGCCCAGGACTTG
1 ACAACTCCAGCCCAAGACTTG
33876 TTGCGGGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.35, G:0.21, T:0.16
Consensus pattern (22 bp):
ACAACTCCAGCCCAAGACTTGG
Found at i:33872 original size:71 final size:71
Alignment explanation
Indices: 33692--33862 Score: 326
Period size: 71 Copynumber: 2.4 Consensus size: 71
33682 AAAAAATAGG
*
33692 ACAAGTCCTGCCCAGGACTT-GACAACTCCTGGGCAGGACGTGGTCTGTTGAAAGAAGCAAGAAT
1 ACAAGTCCTGCCCAAGACTTGGACAACTCCTGGGCAGGACGTGGTCTGTTGAAAGAAGCAAGAAT
33756 TTCAAA
66 TTCAAA
33762 ACAAGTCCTGCCCAAGACTTGGACAACTCCTGGGCAGGACGTGGTCTGTTGAAAGAAGCAAGAAT
1 ACAAGTCCTGCCCAAGACTTGGACAACTCCTGGGCAGGACGTGGTCTGTTGAAAGAAGCAAGAAT
33827 TTCAAA
66 TTCAAA
33833 ACAAGTCCTGCCCAAGACTTGGACAACTCC
1 ACAAGTCCTGCCCAAGACTTGGACAACTCC
33863 AGCCCAGGAC
Statistics
Matches: 99, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
70 19 0.19
71 80 0.81
ACGTcount: A:0.32, C:0.25, G:0.24, T:0.19
Consensus pattern (71 bp):
ACAAGTCCTGCCCAAGACTTGGACAACTCCTGGGCAGGACGTGGTCTGTTGAAAGAAGCAAGAAT
TTCAAA
Found at i:34534 original size:15 final size:15
Alignment explanation
Indices: 34511--34541 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
34501 GGATATATCG
*
34511 AAAATATAAAAAATA
1 AAAAAATAAAAAATA
34526 AAAAAATAAAAAATA
1 AAAAAATAAAAAATA
34541 A
1 A
34542 TTCGACCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAAAATAAAAAATA
Found at i:35034 original size:21 final size:21
Alignment explanation
Indices: 35008--35049 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
34998 TAGGGCTATA
35008 AAACCTTACCCAGGCGCGGCC
1 AAACCTTACCCAGGCGCGGCC
*
35029 AAACCTTGCCCAGGCGCGGCC
1 AAACCTTACCCAGGCGCGGCC
35050 TACCCCATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.43, G:0.26, T:0.10
Consensus pattern (21 bp):
AAACCTTACCCAGGCGCGGCC
Found at i:35108 original size:21 final size:21
Alignment explanation
Indices: 35082--35122 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
35072 TTTGTTTCGA
*
35082 AACCTTGCCCAGGCGCAGCCC
1 AACCTTGCCCAAGCGCAGCCC
35103 AACCTTGCCCAAGCGCAGCC
1 AACCTTGCCCAAGCGCAGCC
35123 TACCTCAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.46, G:0.22, T:0.10
Consensus pattern (21 bp):
AACCTTGCCCAAGCGCAGCCC
Found at i:38557 original size:2 final size:2
Alignment explanation
Indices: 38550--38578 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38540 TCTTTTACAC
38550 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38579 TAACCGATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.