Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019886.1 Corchorus olitorius cultivar O-4 contig19919, 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: 59551
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:10866 original size:26 final size:24
Alignment explanation
Indices: 10837--10887 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
10827 GAGAATACTA
10837 TCAACAGAAGATATTATCAGAAGATT
1 TCAACAGAAG--ATTATCAGAAGATT
* *
10863 TCAACTGAAGATTATCTGAAGATT
1 TCAACAGAAGATTATCAGAAGATT
10887 T
1 T
10888 AAGTAGATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 14 0.61
26 9 0.39
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (24 bp):
TCAACAGAAGATTATCAGAAGATT
Found at i:15693 original size:9 final size:8
Alignment explanation
Indices: 15669--15698 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
15659 ATTTGAAGAT
15669 GATTTGAA
1 GATTTGAA
15677 GATTTGAA
1 GATTTGAA
15685 GACTTTGAA
1 GA-TTTGAA
15694 GATTT
1 GATTT
15699 ATTTCAAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.33, C:0.03, G:0.23, T:0.40
Consensus pattern (8 bp):
GATTTGAA
Found at i:17095 original size:15 final size:15
Alignment explanation
Indices: 17065--17106 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
17055 TTACTCTGTT
17065 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
17081 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
17096 TTGTTTTCTGT
1 TTGTTTTCTGT
17107 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:24458 original size:19 final size:19
Alignment explanation
Indices: 24436--24486 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
24426 GGGCTGAAAT
24436 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
24455 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
24474 TAATT-ATTATTAA
1 TAATTAATTATTAA
24487 AAATTCCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:26759 original size:47 final size:47
Alignment explanation
Indices: 26673--26764 Score: 123
Period size: 47 Copynumber: 2.0 Consensus size: 47
26663 GAGCGTGCCA
* * *
26673 ATCAATTTTGTCCAAAAATTGATAAAAAGTGCAATGAAAATTAAAAG
1 ATCAATTTTGTCCAAAAATTGAGAAAAAGTGCAAGGAAAAGTAAAAG
**
26720 ATCAATTTTGTAGTAAAAATTGAGAAAAAGTGC-AGGAAAAGTAAA
1 ATCAATTTTGT-CCAAAAATTGAGAAAAAGTGCAAGGAAAAGTAAA
26765 GGATTGCTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 21 0.54
48 18 0.46
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.26
Consensus pattern (47 bp):
ATCAATTTTGTCCAAAAATTGAGAAAAAGTGCAAGGAAAAGTAAAAG
Found at i:29401 original size:15 final size:14
Alignment explanation
Indices: 29367--29426 Score: 57
Period size: 15 Copynumber: 4.1 Consensus size: 14
29357 TAGTAAACAC
*
29367 TTTCGGTGCCATAAA
1 TTTCGGTGCCAT-CA
29382 TTTCGGTGCCATCA
1 TTTCGGTGCCATCA
* *
29396 TCTTCGGTGTCGTCGA
1 T-TTCGGTGCCATC-A
*
29412 TTTTGGTGCCATCA
1 TTTCGGTGCCATCA
29426 T
1 T
29427 CTTCTTCCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
14 4 0.11
15 31 0.84
16 2 0.05
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (14 bp):
TTTCGGTGCCATCA
Found at i:29404 original size:30 final size:30
Alignment explanation
Indices: 29368--29430 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
29358 AGTAAACACT
29368 TTCGGTGCCATAAATTTCGGTGCCATCATC
1 TTCGGTGCCATAAATTTCGGTGCCATCATC
* * ** *
29398 TTCGGTGTCGTCGATTTTGGTGCCATCATC
1 TTCGGTGCCATAAATTTCGGTGCCATCATC
29428 TTC
1 TTC
29431 TTCCATGACA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.14, C:0.25, G:0.22, T:0.38
Consensus pattern (30 bp):
TTCGGTGCCATAAATTTCGGTGCCATCATC
Found at i:30677 original size:18 final size:18
Alignment explanation
Indices: 30656--30725 Score: 95
Period size: 18 Copynumber: 3.9 Consensus size: 18
30646 AAGTGTGGCA
*
30656 ACTTGGTGCGGTGTGACC
1 ACTTGGTGCGGTGCGACC
*
30674 ACTTGGTGTGGTGCGACC
1 ACTTGGTGCGGTGCGACC
* **
30692 ATTTGGTGCGGTGCGAAT
1 ACTTGGTGCGGTGCGACC
30710 ACTTGGTGCGGTGCGA
1 ACTTGGTGCGGTGCGA
30726 TTTGTTGTTG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.13, C:0.19, G:0.40, T:0.29
Consensus pattern (18 bp):
ACTTGGTGCGGTGCGACC
Found at i:31361 original size:49 final size:47
Alignment explanation
Indices: 31260--31389 Score: 163
Period size: 49 Copynumber: 2.7 Consensus size: 47
31250 TAGCGTGCCA
* * * *
31260 ATCAATTTTGTCCAAAAATTTATAAAAAGTGCAATGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
31307 ATCAATTTTGTCTTAAAAATTGAGAAAAAGGTGCAA-GTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAA-GTGCAATG-AAAAATAAAAG
* *
31356 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCA
31390 GGAAAAGTAA
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
47 12 0.16
48 19 0.26
49 42 0.58
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.29
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
Found at i:34626 original size:15 final size:15
Alignment explanation
Indices: 34606--34636 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
34596 TATTTTTTTG
34606 TTACATGTGCTAGTT
1 TTACATGTGCTAGTT
34621 TTACATGTGCTAGTT
1 TTACATGTGCTAGTT
34636 T
1 T
34637 ATGTGGATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (15 bp):
TTACATGTGCTAGTT
Found at i:41534 original size:15 final size:15
Alignment explanation
Indices: 41514--41544 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41504 ACAGAGATTG
*
41514 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
41529 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
41544 A
1 A
41545 AACTAGAAAA
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:0.65, C:0.13, G:0.10, T:0.13
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:42333 original size:11 final size:11
Alignment explanation
Indices: 42317--42342 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42307 CCTTTGCCTA
42317 AAAACTAGAAG
1 AAAACTAGAAG
42328 AAAACTAGAAG
1 AAAACTAGAAG
42339 AAAA
1 AAAA
42343 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:44195 original size:29 final size:30
Alignment explanation
Indices: 44122--44206 Score: 111
Period size: 29 Copynumber: 2.8 Consensus size: 30
44112 AAGGCTAAAT
44122 GCTCAATTTGGTCCTAAACCTTTCACGGTCC
1 GCTCAATTTGGTCCTAAACCTTTCAC-GTCC
* * *
44153 GCTCGATTTGGTCCTAAACCTTCTGAC-T-G
1 GCTCAATTTGGTCCTAAACCTT-TCACGTCC
44182 GCTCAATTTGGTCCTAAACCTTTCA
1 GCTCAATTTGGTCCTAAACCTTTCA
44207 ATTTCTTAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
28 2 0.04
29 21 0.44
30 1 0.02
31 21 0.44
32 3 0.06
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.34
Consensus pattern (30 bp):
GCTCAATTTGGTCCTAAACCTTTCACGTCC
Found at i:44921 original size:69 final size:69
Alignment explanation
Indices: 44709--44929 Score: 219
Period size: 69 Copynumber: 3.2 Consensus size: 69
44699 TTGATTGTTA
44709 GGTTTTCTGGGTTTGTTTAAATTTGTTTGATA-TCTGAATGCTTGAAATGGTTTTGTGGGTTTGA
1 GGTTTTCTGGGTTTGTTTAAATTTGTTTGATATTC-GAATGCTTGAAATGGTTTTGTGGGTTTGA
44773 TTCTG
65 TTCTG
* * * *
44778 GGTTTTCTGGGTTTG-TAAGCATGGATTTAGGTTGAGGT-TTC-AATGGTCGAAATGGTTGTT-T
1 GGTTTTCTGGGTTTGTTTA--A---ATTT-GTTTGA--TATTCGAATGCTTGAAATGGTT-TTGT
* *
44839 --GATTG-TTAT-
57 GGGTTTGATTCTG
44848 -GTTTTCTGGGTTTGTTTAAATTTGTTTGATATTCGAATGCTTGAAATGGTTTTGTGGGTTTGAT
1 GGTTTTCTGGGTTTGTTTAAATTTGTTTGATATTCGAATGCTTGAAATGGTTTTGTGGGTTTGAT
44912 TCTG
66 TCTG
*
44916 GGTTTTCTAGGTTT
1 GGTTTTCTGGGTTT
44930 TCTGGGTTTG
Statistics
Matches: 120, Mismatches: 13, Indels: 38
0.70 0.08 0.22
Matches are distributed among these distances:
62 1 0.01
63 5 0.04
64 20 0.17
65 4 0.03
66 4 0.03
67 3 0.03
68 3 0.03
69 41 0.34
70 3 0.03
71 3 0.03
72 4 0.03
73 4 0.03
74 20 0.17
75 2 0.02
76 3 0.03
ACGTcount: A:0.16, C:0.06, G:0.29, T:0.49
Consensus pattern (69 bp):
GGTTTTCTGGGTTTGTTTAAATTTGTTTGATATTCGAATGCTTGAAATGGTTTTGTGGGTTTGAT
TCTG
Found at i:45640 original size:9 final size:9
Alignment explanation
Indices: 45623--45664 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
45613 GGATTGATAG
45623 ATGATGGAA
1 ATGATGGAA
*
45632 ATGAAGGAA
1 ATGATGGAA
45641 ATGATGGAA
1 ATGATGGAA
*
45650 ATGAGGGAA
1 ATGATGGAA
45659 ATGATG
1 ATGATG
45665 ACAACTTAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.19
Consensus pattern (9 bp):
ATGATGGAA
Found at i:45646 original size:18 final size:18
Alignment explanation
Indices: 45623--45664 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
45613 GGATTGATAG
45623 ATGATGGAAATGAAGGAA
1 ATGATGGAAATGAAGGAA
*
45641 ATGATGGAAATGAGGGAA
1 ATGATGGAAATGAAGGAA
45659 ATGATG
1 ATGATG
45665 ACAACTTAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.19
Consensus pattern (18 bp):
ATGATGGAAATGAAGGAA
Found at i:45700 original size:24 final size:24
Alignment explanation
Indices: 45651--45716 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
45641 ATGATGGAAA
** *
45651 TGAGGGAAATGATGACAACTTAGG
1 TGAGGGAAATGATGGTAACATAGG
45675 TGAGGGAAATGATGGTAACA-ATGG
1 TGAGGGAAATGATGGTAACATA-GG
*
45699 TGA-GGATAATGGTGGTAA
1 TGAGGGA-AATGATGGTAA
45717 TCAGAATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 4 0.11
24 32 0.89
ACGTcount: A:0.36, C:0.05, G:0.36, T:0.23
Consensus pattern (24 bp):
TGAGGGAAATGATGGTAACATAGG
Found at i:54982 original size:2 final size:2
Alignment explanation
Indices: 54975--55043 Score: 64
Period size: 2 Copynumber: 38.5 Consensus size: 2
54965 GTTTAATAAT
*
54975 TA TA TA TA TA -A T- TA TA TA TA TC TA -A TA T- TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
55012 TA TA -A TA TA TA TA TA TA TT TA -A T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55044 TAATAAACGG
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
1 8 0.15
2 47 0.85
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55007 original size:19 final size:18
Alignment explanation
Indices: 54980--55048 Score: 71
Period size: 19 Copynumber: 4.2 Consensus size: 18
54970 ATAATTATAT
*
54980 ATATAATTATATATATCTA
1 ATATTATTATATATAT-TA
54999 ATATTATTATATATA-TA
1 ATATTATTATATATATTA
55016 ATA-TA-TATATATATT-
1 ATATTATTATATATATTA
55031 -TA--ATTATATATATTA
1 ATATTATTATATATATTA
55046 ATA
1 ATA
55049 AACGGTCGGT
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
13 1 0.02
14 12 0.27
15 8 0.18
16 5 0.11
17 5 0.11
19 14 0.31
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATTATTATATATATTA
Found at i:55034 original size:17 final size:17
Alignment explanation
Indices: 54975--55043 Score: 76
Period size: 17 Copynumber: 4.3 Consensus size: 17
54965 GTTTAATAAT
54975 TATATATAT-A-AT-TA
1 TATATATATAATATATA
*
54989 TATATATCTAATAT-TA
1 TATATATATAATATATA
55005 TTATATATATAATATATA
1 -TATATATATAATATATA
*
55023 TATATATTTAAT-TATA
1 TATATATATAATATATA
55039 TATAT
1 TATAT
55044 TAATAAACGG
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
14 8 0.17
15 1 0.02
16 13 0.27
17 24 0.50
18 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATATATAATATATA
Found at i:57502 original size:130 final size:131
Alignment explanation
Indices: 57254--57520 Score: 360
Period size: 130 Copynumber: 2.0 Consensus size: 131
57244 CATTGTTTAA
* * * *
57254 ACTTTTATAATTGTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAAC
1 ACTTTTATAATTGTACTCAACTAAAAACTATATTTTTATGTAACTAAATCTAATATCTCTATAAC
* * * *
57319 TATTTAATTTTTGCCATTTTACTATTTTAATTAAACAACTTATATATACTAGAATTTTTTAAATA
66 TATTTAATTTTTACCATTTTACTATTTTAATTAAACAACTTAGATATACTAGAACTTTTAAAATA
57384 T
131 T
* * * *
57385 ACTTTTATAGTTTTATTCAACTAAAAACTATATTTTTATGTAACTAAATCTAATATC-CTATACC
1 ACTTTTATAATTGTACTCAACTAAAAACTATATTTTTATGTAACTAAATCTAATATCTCTATAAC
* *
57449 TATTTTATTTTTACCATTTTACTGA-TTTAATTGAAA-AACTTAGATATATTAGAACTTTTAAAA
66 TATTTAATTTTTACCATTTTACT-ATTTTAATT-AAACAACTTAGATATACTAGAACTTTTAAAA
57512 TAT
129 TAT
*
57515 ATTTTT
1 ACTTTT
57521 TAAATGAAAT
Statistics
Matches: 119, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
130 64 0.54
131 55 0.46
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.48
Consensus pattern (131 bp):
ACTTTTATAATTGTACTCAACTAAAAACTATATTTTTATGTAACTAAATCTAATATCTCTATAAC
TATTTAATTTTTACCATTTTACTATTTTAATTAAACAACTTAGATATACTAGAACTTTTAAAATA
T
Found at i:59483 original size:21 final size:22
Alignment explanation
Indices: 59450--59491 Score: 68
Period size: 21 Copynumber: 1.9 Consensus size: 22
59440 TATTAAAAGA
59450 TAAAAAGAAATTAAAAAAAAATC
1 TAAAAAG-AATTAAAAAAAAATC
59473 TAAAAAG-ATTAAAAAAAAA
1 TAAAAAGAATTAAAAAAAAA
59492 ACCAGACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (22 bp):
TAAAAAGAATTAAAAAAAAATC
Done.