Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024487.1 Corchorus olitorius cultivar O-4 contig24520, 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: 60880
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:676 original size:31 final size:31
Alignment explanation
Indices: 616--706 Score: 96
Period size: 31 Copynumber: 3.0 Consensus size: 31
606 TTTTATTTTA
* ***
616 GACTGAAATCTCAAATAAGTCCCCCAACTTT
1 GACTAAAATCTCAAATAAGGGTCCCAACTTT
* *
647 GACTTAAATCTCAAATAAGGGTCCGAACTTT
1 GACTAAAATCTCAAATAAGGGTCCCAACTTT
* *
678 -A-AAAAATGTCAAATAAGGGTCCCAACTTT
1 GACTAAAATCTCAAATAAGGGTCCCAACTTT
707 TTGGGAAGGC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 24 0.47
30 1 0.02
31 26 0.51
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.26
Consensus pattern (31 bp):
GACTAAAATCTCAAATAAGGGTCCCAACTTT
Found at i:9346 original size:21 final size:21
Alignment explanation
Indices: 9321--9403 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 21
9311 TATCTTAGAT
9321 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
9342 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
* **
9363 ATAAATAATGA-GTTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
9385 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
9404 TTACTAAACG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
21 18 0.37
22 21 0.43
23 10 0.20
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:9354 original size:25 final size:25
Alignment explanation
Indices: 9323--9371 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
9313 TCTTAGATAT
*
9323 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
9348 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
9372 GAGTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:10836 original size:11 final size:11
Alignment explanation
Indices: 10822--10859 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
10812 ATTCATAACA
10822 AATTTATAATT
1 AATTTATAATT
10833 AATTTATAATT
1 AATTTATAATT
10844 -ATTTGATAATT
1 AATTT-ATAATT
*
10855 TATTT
1 AATTT
10860 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:22832 original size:16 final size:16
Alignment explanation
Indices: 22811--22844 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
22801 ATATCCATTT
22811 TTTTCTTCTTTAAATA
1 TTTTCTTCTTTAAATA
22827 TTTTCTTCTTTAAATA
1 TTTTCTTCTTTAAATA
22843 TT
1 TT
22845 CTGCTTGCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTCTTCTTTAAATA
Found at i:25919 original size:52 final size:52
Alignment explanation
Indices: 25836--25935 Score: 173
Period size: 52 Copynumber: 1.9 Consensus size: 52
25826 AGGTAATCAA
* *
25836 ATCTGACTTATATATTGCTTTTATTTCAAATTATATATTCTGAAATTGGATT
1 ATCTAACTTATATATTCCTTTTATTTCAAATTATATATTCTGAAATTGGATT
*
25888 ATCTAACTTATTTATTCCTTTTATTTCAAATTATATATTCTGAAATTG
1 ATCTAACTTATATATTCCTTTTATTTCAAATTATATATTCTGAAATTG
25936 ATCCCTACAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (52 bp):
ATCTAACTTATATATTCCTTTTATTTCAAATTATATATTCTGAAATTGGATT
Found at i:26651 original size:12 final size:12
Alignment explanation
Indices: 26636--26660 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
26626 AATATAGCTA
26636 TTTATATTCTGT
1 TTTATATTCTGT
26648 TTTATATTCTGT
1 TTTATATTCTGT
26660 T
1 T
26661 GCTCTTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (12 bp):
TTTATATTCTGT
Found at i:27749 original size:23 final size:21
Alignment explanation
Indices: 27718--27761 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
27708 AACCGATCAA
*
27718 TATTATTTTGCCTTTTTTATTTT
1 TATTATTTT-ACTTTTTT-TTTT
*
27741 TATTTTTTTACTTTTTTTTTT
1 TATTATTTTACTTTTTTTTTT
27762 ACTTAGGCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 7 0.37
23 8 0.42
ACGTcount: A:0.11, C:0.07, G:0.02, T:0.80
Consensus pattern (21 bp):
TATTATTTTACTTTTTTTTTT
Found at i:35925 original size:23 final size:23
Alignment explanation
Indices: 35876--35948 Score: 105
Period size: 23 Copynumber: 3.3 Consensus size: 23
35866 TTATCAACAA
*
35876 TCATAGGAAGG-TTA-CAAAATT
1 TCATAGGAAGGTTTATTAAAATT
35897 TCATAGGAAGGTTTATTAAAATT
1 TCATAGGAAGGTTTATTAAAATT
* *
35920 TTATAGAAAGGTTTATTAAAATT
1 TCATAGGAAGGTTTATTAAAATT
35943 TCATAG
1 TCATAG
35949 TTAGGTTATC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.24
22 3 0.07
23 32 0.70
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.37
Consensus pattern (23 bp):
TCATAGGAAGGTTTATTAAAATT
Found at i:36009 original size:22 final size:22
Alignment explanation
Indices: 35979--36039 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
35969 ATTTCATAGG
* * * *
35979 TATCGAAATTGCATAACGTGGT
1 TATCAAAATTTCATAAAGTAGT
*
36001 TATCAAAATTTAATAAAGTAGT
1 TATCAAAATTTCATAAAGTAGT
36023 TATCAAAATTTCATAAA
1 TATCAAAATTTCATAAA
36040 AATATTCAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.34
Consensus pattern (22 bp):
TATCAAAATTTCATAAAGTAGT
Found at i:50893 original size:26 final size:27
Alignment explanation
Indices: 50833--50884 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
50823 ACCAGCTGGC
* *
50833 ACCCCACACGTGACCTCCAAACGTACG
1 ACCCCACACATGACCTCCAAACGGACG
50860 ACCCCACACATGACCTCC-AACGGAC
1 ACCCCACACATGACCTCCAAACGGAC
50885 ACTTCCACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.31, C:0.46, G:0.13, T:0.10
Consensus pattern (27 bp):
ACCCCACACATGACCTCCAAACGGACG
Found at i:56045 original size:26 final size:26
Alignment explanation
Indices: 56016--56065 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
56006 TTGGCATCAT
56016 TTTCGTTTTTCTGTTT-TTTTTGTTTG
1 TTTCGTTTTTCT-TTTGTTTTTGTTTG
*
56042 TTTCGTTTTTGTTTTGTTTTTGTT
1 TTTCGTTTTTCTTTTGTTTTTGTT
56066 ACGTTGTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.00, C:0.06, G:0.16, T:0.78
Consensus pattern (26 bp):
TTTCGTTTTTCTTTTGTTTTTGTTTG
Found at i:57987 original size:22 final size:21
Alignment explanation
Indices: 57954--57997 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
57944 TATATTTACA
*
57954 TATTATATATATATATATTAG
1 TATTATATATATATATACTAG
57975 TATTAGTATATATATATACTAG
1 TATTA-TATATATATATACTAG
57997 T
1 T
57998 TAAAGCACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (21 bp):
TATTATATATATATATACTAG
Found at i:59586 original size:58 final size:58
Alignment explanation
Indices: 59487--59601 Score: 151
Period size: 58 Copynumber: 2.0 Consensus size: 58
59477 ATTAATCAAA
* *
59487 TATCAAGTGACATGTTCTTTATTAGGTGTATAAAAAAAGACGTTTTCGGACCAAGACT
1 TATCAAGTGACATGTTCTTTATTAGATGTATAAAAAAAGACGTTTTAGGACCAAGACT
* * * * *
59545 TATCGAGTGACATGTTTTTTTATTAGATGTCT-AAAACAGACGTTTTAGGACCGAGAC
1 TATCAAGTGACATG-TTCTTTATTAGATGTATAAAAAAAGACGTTTTAGGACCAAGAC
59602 ATGATGCTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
58 35 0.71
59 14 0.29
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGTATAAAAAAAGACGTTTTAGGACCAAGACT
Done.