Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012137.1 Corchorus olitorius cultivar O-4 contig12170, 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: 61444
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5975 original size:24 final size:24
Alignment explanation
Indices: 5943--5992 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 24
5933 TTGGTCTTTA
5943 TTTTTCT-ACTAACATTGTTATTT
1 TTTTTCTAACTAACATTGTTATTT
5966 TTTTTGCTACACTAACATTGTTATTT
1 TTTTT-CTA-ACTAACATTGTTATTT
5992 T
1 T
5993 AATGCTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 5 0.21
24 2 0.08
26 17 0.71
ACGTcount: A:0.22, C:0.14, G:0.06, T:0.58
Consensus pattern (24 bp):
TTTTTCTAACTAACATTGTTATTT
Found at i:12694 original size:27 final size:27
Alignment explanation
Indices: 12663--12717 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
12653 TAACACAGTC
12663 ACAATTATCATTGTTGTATAATCAACT
1 ACAATTATCATTGTTGTATAATCAACT
12690 ACAATTATCATTGTTGTATAATCAACT
1 ACAATTATCATTGTTGTATAATCAACT
12717 A
1 A
12718 TGTGTAGGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (27 bp):
ACAATTATCATTGTTGTATAATCAACT
Found at i:14343 original size:440 final size:441
Alignment explanation
Indices: 13423--14440 Score: 1145
Period size: 440 Copynumber: 2.3 Consensus size: 441
13413 TTTTTTAAAG
* * *
13423 TTTT-TTCAATTTATCCGATTAAGGTAATTCAAGTGTCTATTAAAAGATAATTTCATGATCTACA
1 TTTTGTTCTATTTGTCCGATTAAGGTAATTCAAGTGTCTATTAAAAGATAATTTCATGATATACA
* * * * * *
13487 ATTTTCATGAAGAACTCAAAAGCCAATTTTAATGTTTTGATTTAGAAAAATGCTTCCGAAATTTT
66 ACTTTCATGAAGAACTCAAAAGCAAATTTTAATGTTTTAATTCAAAAAAATGCTTCCGAAATTTG
* * ** * * *
13552 GTGGTTTTGATTGCCGGTCAATTTAATATCGTATATTTTTTTTGTATACATGTCCGATTGAAGTT
131 GTGGTTTCGATTGCCGGTCAATTTAATATCGCATATAATTTTCGTATACATGTCCAATTAAAGTT
* * * * *
13617 ATTGAAGTGTCAGTTAAAAGGTTATTGCATAATTTACAACTTTCATGAAGGACCCGAAAACTAAA
196 ATTCAAGTGTCAGTTAAAAGGTTACTGCATAATCTACAACTTTCATGAAGAAACCGAAAACTAAA
* * *
13682 TTTGATATACGAGTTTCATGAAGGGTTTAAAAGGAAATTTTTATGCTTCAAGATCTCCATTAACA
261 TTTGATATACGAGTTTCATGAAGGGTTAAAAAGGAAATTTTTATACTTCAAGATATCCATTAACA
* * * *
13747 AACATTTTCTCATTTGGATTATTTATCAAATGACCCTCATATTTTTCTACTTTATACTACTTAGT
326 AACAGTTTCTCATTTGAATTAGTTATCAAATGACCCTCATACTTTTCTACTTTATACTACTTAGT
* *
13812 CCTTTACAAATTCTATTTTAATCTAATGTTTAAGATTTATTTATTTTTTATT
391 CATTTACAAATTCTATCTTAATCTAATG-TTAAGATTTATTTATTTTTTATT
* * * * *
13864 TTTTGTTCTATCTGTCCGATTAAGTTGATTCATGTGTCTATTAAAAGGTAATTTCATGATATACA
1 TTTTGTTCTATTTGTCCGATTAAGGTAATTCAAGTGTCTATTAAAAGATAATTTCATGATATACA
* *
13929 ACTTTCATGAAGAACTCAAAAGCAAATTTTTATGTTTTAATTCAAAAAAATGCTTCCTAAATTTG
66 ACTTTCATGAAGAACTCAAAAGCAAATTTTAATGTTTTAATTCAAAAAAATGCTTCCGAAATTTG
* ** *
13994 GTTGTTTCGATTGTTGGTCTATTTAATA-C-CATATAATTTTCG-ATCCACATGTCCAATTAAAG
131 GTGGTTTCGATTGCCGGTCAATTTAATATCGCATATAATTTTCGTAT--ACATGTCCAATTAAAG
* * * * * *
14056 TTATTCAAGTGTCGGTTAAAAGGTTACTGTATGATCTACGACTTTCATGAAGAAACCG-AAAGTT
194 TTATTCAAGTGTCAGTTAAAAGGTTACTGCATAATCTACAACTTTCATGAAGAAACCGAAAACTA
* * * * *
14120 AATTTGATCTACGAGTTTCATTAAGGGTTCAAAAAGG-AATTTTTATATTTTAAGATATTCATTA
259 AATTTGATATACGAGTTTCATGAAGGGTT-AAAAAGGAAATTTTTATACTTCAAGATATCCATTA
* * * * *
14184 AGAAATAGTTTCTTATTTGAATTAGTTATCAAATGACCCTCATACTTTTCTATTTTATGCTACTT
323 ACAAACAGTTTCTCATTTGAATTAGTTATCAAATGACCCTCATACTTTTCTACTTTATACTACTT
* * *
14249 AGTCATTTACAAATTCTATCTTATTC-GATG-TAACGCTTTATTT-TTTTTTAATTT
388 AGTCATTTACAAATTCTATCTTAATCTAATGTTAA-GATTTATTTATTTTTT-A-TT
* * * *
14303 TCTTTGTTTTATTTGTCCAATTAAGGTAATTCAGGTGTC---T---AG-TAATTTTATGATCA-A
1 T-TTTGTTCTATTTGTCCGATTAAGGTAATTCAAGTGTCTATTAAAAGATAATTTCATGAT-ATA
* * * * * * **
14360 GAAACTTTCATGAA-AGACTCAAAAGCTAATTTTCATGTTTCAATTCTAAAAAATACTTTTGAAA
64 -CAACTTTCATGAAGA-ACTCAAAAGCAAATTTTAATGTTTTAATTCAAAAAAATGCTTCCGAAA
* *
14424 TTTTGTGATTTCGATTG
127 TTTGGTGGTTTCGATTG
14441 ACAATCTATT
Statistics
Matches: 487, Mismatches: 79, Indels: 29
0.82 0.13 0.05
Matches are distributed among these distances:
433 13 0.03
434 69 0.14
437 10 0.02
438 9 0.02
439 8 0.02
440 172 0.35
441 74 0.15
442 132 0.27
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (441 bp):
TTTTGTTCTATTTGTCCGATTAAGGTAATTCAAGTGTCTATTAAAAGATAATTTCATGATATACA
ACTTTCATGAAGAACTCAAAAGCAAATTTTAATGTTTTAATTCAAAAAAATGCTTCCGAAATTTG
GTGGTTTCGATTGCCGGTCAATTTAATATCGCATATAATTTTCGTATACATGTCCAATTAAAGTT
ATTCAAGTGTCAGTTAAAAGGTTACTGCATAATCTACAACTTTCATGAAGAAACCGAAAACTAAA
TTTGATATACGAGTTTCATGAAGGGTTAAAAAGGAAATTTTTATACTTCAAGATATCCATTAACA
AACAGTTTCTCATTTGAATTAGTTATCAAATGACCCTCATACTTTTCTACTTTATACTACTTAGT
CATTTACAAATTCTATCTTAATCTAATGTTAAGATTTATTTATTTTTTATT
Found at i:29195 original size:10 final size:10
Alignment explanation
Indices: 29180--29208 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
29170 GGGGGGAGCA
29180 TCGGTCGGTT
1 TCGGTCGGTT
29190 TCGGTCGGTT
1 TCGGTCGGTT
29200 TCGGTCGGT
1 TCGGTCGGT
29209 GCGGTTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.21, G:0.41, T:0.38
Consensus pattern (10 bp):
TCGGTCGGTT
Found at i:36689 original size:35 final size:37
Alignment explanation
Indices: 36642--36711 Score: 94
Period size: 35 Copynumber: 1.9 Consensus size: 37
36632 AAAAGCAGAA
36642 AAATAAAGGAAAA-ATATATTTTTTT-TTG-AAAACGC
1 AAATAAAGGAAAATA-ATATTTTTTTATTGCAAAACGC
36677 AAATACAA-GAAAATAATATTTTTTTATTGCAAAAC
1 AAATA-AAGGAAAATAATATTTTTTTATTGCAAAAC
36712 CGAAATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
35 20 0.65
36 6 0.19
37 5 0.16
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.34
Consensus pattern (37 bp):
AAATAAAGGAAAATAATATTTTTTTATTGCAAAACGC
Found at i:43053 original size:33 final size:33
Alignment explanation
Indices: 43010--43076 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
43000 TGTTATATTT
* * *
43010 TTCAGTTTTAAGACTAGAAGTTGTGGTTTCATC
1 TTCAATTTTAACACTAGAAGTTGTGGTTTAATC
43043 TTCAATTTTAACACTAGAAGTTGTGGTTTAATC
1 TTCAATTTTAACACTAGAAGTTGTGGTTTAATC
43076 T
1 T
43077 GTGGACACCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (33 bp):
TTCAATTTTAACACTAGAAGTTGTGGTTTAATC
Found at i:44818 original size:2 final size:2
Alignment explanation
Indices: 44811--44840 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
44801 TGAAACATGC
44811 AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44841 AGTATGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46898 original size:22 final size:21
Alignment explanation
Indices: 46844--46924 Score: 92
Period size: 22 Copynumber: 3.8 Consensus size: 21
46834 TTATAGGGAG
* * *
46844 ATTAACAAAATCTCATAGGTA
1 ATTATCAAAATTTCATAGATA
46865 ATTAT-AAAATTTCATAGCATA
1 ATTATCAAAATTTCATAG-ATA
*
46886 ATTATCAAAATTTAATAGGATA
1 ATTATCAAAATTTCATA-GATA
*
46908 GTTATCAAAATTTCATA
1 ATTATCAAAATTTCATA
46925 AAAAAATTCA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
20 11 0.22
21 11 0.22
22 28 0.55
23 1 0.02
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (21 bp):
ATTATCAAAATTTCATAGATA
Found at i:48764 original size:60 final size:60
Alignment explanation
Indices: 48671--48787 Score: 234
Period size: 60 Copynumber: 1.9 Consensus size: 60
48661 GATTCTTATC
48671 TTTTACAGTTTGTGAATACATTAGCAGCTTCCTGCTTCTTTTTGGAAGAAAATGAACCTT
1 TTTTACAGTTTGTGAATACATTAGCAGCTTCCTGCTTCTTTTTGGAAGAAAATGAACCTT
48731 TTTTACAGTTTGTGAATACATTAGCAGCTTCCTGCTTCTTTTTGGAAGAAAATGAAC
1 TTTTACAGTTTGTGAATACATTAGCAGCTTCCTGCTTCTTTTTGGAAGAAAATGAAC
48788 TTTAACAGTC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.39
Consensus pattern (60 bp):
TTTTACAGTTTGTGAATACATTAGCAGCTTCCTGCTTCTTTTTGGAAGAAAATGAACCTT
Found at i:53002 original size:21 final size:23
Alignment explanation
Indices: 52977--53021 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
52967 ATTATAAATT
52977 AATTAAAACATATA-ATAT-TAA
1 AATTAAAACATATATATATATAA
* *
52998 AATTAATATATATATATATATAA
1 AATTAAAACATATATATATATAA
53021 A
1 A
53022 TTGTGTGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 4 0.20
23 4 0.20
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
AATTAAAACATATATATATATAA
Found at i:56687 original size:72 final size:73
Alignment explanation
Indices: 56582--56856 Score: 329
Period size: 74 Copynumber: 3.7 Consensus size: 73
56572 TTCCATAAAG
*
56582 AAAAGGCTAATTTGCTCCCTTTTTACAAGTCTATGCATGCAATTGGTAATTTTGGAATTTAACCA
1 AAAAGGCTAATTTGCT-CCTTTTTACAAGTCTAGGCATGCAATTGGTAATTTTGGAATTTAACCA
*
56647 -CTCATCCA
65 GTTCATCCA
* * *
56655 AAAAGGCTAATTTGCTTCTTTTTACAAGTCTATGCATGCAATTGGTAAATTTGGAATTTAACCAG
1 AAAAGGCTAATTTGCTCCTTTTTACAAGTCTAGGCATGCAATTGGTAATTTTGGAATTTAACCAG
*
56720 TTCTATTCA
66 TTC-ATCCA
* ** * *
56729 AAAAGGCTAATTTGCTCCTTTTTACAAGTTTAGGTGTGCAATAGGTAATTTTGAAATTTAACCAA
1 AAAAGGCTAATTTGCTCCTTTTTACAAGTCTAGGCATGCAATTGGTAATTTTGGAATTTAACC-A
* *
56794 TTTCCATCTA
65 GTT-CATCCA
* ** * *
56804 AAAAAGCTAATTTATTCATTTTTACAAGTAC-AGGCGTGCAATTGGTAATTTTG
1 AAAAGGCTAATTTGCTCCTTTTTACAAGT-CTAGGCATGCAATTGGTAATTTTG
56857 TATTTTTTTT
Statistics
Matches: 175, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
72 46 0.26
73 18 0.10
74 59 0.34
75 51 0.29
76 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.38
Consensus pattern (73 bp):
AAAAGGCTAATTTGCTCCTTTTTACAAGTCTAGGCATGCAATTGGTAATTTTGGAATTTAACCAG
TTCATCCA
Found at i:57903 original size:2 final size:2
Alignment explanation
Indices: 57896--57924 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
57886 TTTCCATTAA
57896 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
57925 CACTAAATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.