Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021844.1 Corchorus olitorius cultivar O-4 contig21877, 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: 6780
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Found at i:579 original size:36 final size:37
Alignment explanation
Indices: 528--601 Score: 114
Period size: 36 Copynumber: 2.0 Consensus size: 37
518 TTTCATCAGG
* *
528 TTTAAGTTTTTAAATTGGGAAAGTTCCCA-CCAGTTT
1 TTTAAGTTTTCAAATTGGAAAAGTTCCCATCCAGTTT
*
564 TTTAAGTTTTCAAATTGGAAAAGTTCCCATTCAGTTT
1 TTTAAGTTTTCAAATTGGAAAAGTTCCCATCCAGTTT
601 T
1 T
602 CAAAGCATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 27 0.79
37 7 0.21
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (37 bp):
TTTAAGTTTTCAAATTGGAAAAGTTCCCATCCAGTTT
Found at i:613 original size:37 final size:36
Alignment explanation
Indices: 539--613 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 36
529 TTAAGTTTTT
* ** **
539 AAATTGGGAAAGTTCCCACCAGTTTTTTAAGTTTTC
1 AAATTGGAAAAGTTCCCACCAGTTTTCAAAGCATTC
*
575 AAATTGGAAAAGTTCCCATTCAGTTTTCAAAGCATTC
1 AAATTGGAAAAGTTCCCA-CCAGTTTTCAAAGCATTC
612 AA
1 AA
614 TCTATCTCTC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
36 17 0.53
37 15 0.47
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (36 bp):
AAATTGGAAAAGTTCCCACCAGTTTTCAAAGCATTC
Found at i:706 original size:52 final size:53
Alignment explanation
Indices: 570--802 Score: 273
Period size: 52 Copynumber: 4.4 Consensus size: 53
560 GTTTTTTAAG
* *
570 TTTTCAAA-TTGGAAAAGTTCCCATTCAGTTTTCAAAGCATTCAATCTATCTCTCTT
1 TTTTCAAATTTGG-AAAGTTCCCATCCAGTTTTCAAAGCATTCAATCTA--GCTC-T
*
626 TTTTCAAATTGGGAAAGTTCCCAT-CAGTTTTCAAAGCATTCAATCTAGCTCT
1 TTTTCAAATTTGGAAAGTTCCCATCCAGTTTTCAAAGCATTCAATCTAGCTCT
* *
678 TTTTCAAATTTGGAAAGTTCCCA-CCAGTTTTCAAAACAATCAATCTAGCT-T
1 TTTTCAAATTTGGAAAGTTCCCATCCAGTTTTCAAAGCATTCAATCTAGCTCT
* * * * *
729 TTTT-AAATTGGGAAAGTTCCCATCAAGTTTCCAAAGTATTCAATTTAGCTCT
1 TTTTCAAATTTGGAAAGTTCCCATCCAGTTTTCAAAGCATTCAATCTAGCTCT
781 TTTT--AATTTAGGGAAAGTTCCC
1 TTTTCAAATTT--GGAAAGTTCCC
803 GTCATTTTCG
Statistics
Matches: 158, Mismatches: 13, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
50 17 0.11
51 30 0.19
52 52 0.33
53 14 0.09
55 23 0.15
56 19 0.12
57 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (53 bp):
TTTTCAAATTTGGAAAGTTCCCATCCAGTTTTCAAAGCATTCAATCTAGCTCT
Found at i:770 original size:103 final size:106
Alignment explanation
Indices: 570--802 Score: 300
Period size: 103 Copynumber: 2.2 Consensus size: 106
560 GTTTTTTAAG
* * **
570 TTTTCAAA-TTGGAAAAGTTCCCATTCAGTTTTCAAAGCATTCAATCTATCTCTCTTTTTTCAAA
1 TTTTCAAATTTGG-AAAGTTCCCATCCAGTTTTCAAA-CA-TCAATCAATCTAGCTTTTTTCAAA
*
634 TTGGGAAAGTTCCCATCAGTTTTCAAAGCATTCAATCTAGCTCT
63 TTGGGAAAGTTCCCATCAGTTTCCAAAGCATTCAATCTAGCTCT
678 TTTTCAAATTTGGAAAGTTCCCA-CCAGTTTTCAAA-A-CAATCAATCTAGCTTTTTT-AAATTG
1 TTTTCAAATTTGGAAAGTTCCCATCCAGTTTTCAAACATCAATCAATCTAGCTTTTTTCAAATTG
* *
739 GGAAAGTTCCCATCAAGTTTCCAAAGTATTCAATTTAGCTCT
66 GGAAAGTTCCCATC-AGTTTCCAAAGCATTCAATCTAGCTCT
781 TTTT--AATTTAGGGAAAGTTCCC
1 TTTTCAAATTT--GGAAAGTTCCC
803 GTCATTTTCG
Statistics
Matches: 114, Mismatches: 7, Indels: 13
0.85 0.05 0.10
Matches are distributed among these distances:
101 5 0.04
102 20 0.18
103 55 0.48
105 1 0.01
107 11 0.10
108 18 0.16
109 4 0.04
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (106 bp):
TTTTCAAATTTGGAAAGTTCCCATCCAGTTTTCAAACATCAATCAATCTAGCTTTTTTCAAATTG
GGAAAGTTCCCATCAGTTTCCAAAGCATTCAATCTAGCTCT
Found at i:4055 original size:76 final size:73
Alignment explanation
Indices: 3926--4068 Score: 180
Period size: 76 Copynumber: 1.9 Consensus size: 73
3916 GGACTATGAG
*
3926 CAAAAGAATGATGAGTTTTAATCAAAGTTTTCAAAAAATCAGTCTTAATCAAAACTATGATTTCG
1 CAAAAGAATGATGAGTTTTAATCAAAGTTTTC-AAAAATCAGTCTTAATCAAAACAATGATTTCG
3991 AGTTGTGAA
65 AGTTGTGAA
* * * **
4000 CAAAGGAATGATGGTGTTTTAATCAAAAGATGTTTC-AAAATCAGTTTTGGTCAAAACAATGATT
1 CAAAAGAATGAT-GAGTTTTAATC-AAAG-T-TTTCAAAAATCAGTCTTAATCAAAACAATGATT
4064 TCGAG
62 TCGAG
4069 GTAACCGAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
74 11 0.19
75 10 0.17
76 33 0.56
77 1 0.02
78 4 0.07
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.32
Consensus pattern (73 bp):
CAAAAGAATGATGAGTTTTAATCAAAGTTTTCAAAAATCAGTCTTAATCAAAACAATGATTTCGA
GTTGTGAA
Found at i:4907 original size:18 final size:17
Alignment explanation
Indices: 4880--4940 Score: 88
Period size: 17 Copynumber: 3.6 Consensus size: 17
4870 TTCAAAAAAA
4880 AAATAAAAAAATCAATC
1 AAATAAAAAAATCAATC
4897 AAATAAAAAAAATCAATC
1 AAAT-AAAAAAATCAATC
* *
4915 AAATCAAAAAATCAAAC
1 AAATAAAAAAATCAATC
4932 AAA-AAAAAA
1 AAATAAAAAA
4941 CAAAAAAACA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
16 5 0.12
17 18 0.45
18 17 0.43
ACGTcount: A:0.75, C:0.11, G:0.00, T:0.13
Consensus pattern (17 bp):
AAATAAAAAAATCAATC
Found at i:4918 original size:9 final size:9
Alignment explanation
Indices: 4888--4967 Score: 65
Period size: 9 Copynumber: 8.9 Consensus size: 9
4878 AAAAATAAAA
*
4888 AAATCAATC
1 AAATCAAAC
* *
4897 AAATAAAAA
1 AAATCAAAC
*
4906 AAATCAATC
1 AAATCAAAC
4915 AAATCAAA-
1 AAATCAAAC
4923 AAATCAAAC
1 AAATCAAAC
**
4932 AAAAAAAAAC
1 -AAATCAAAC
*
4942 AAA-AAAAC
1 AAATCAAAC
4950 AAATCAAATC
1 AAATCAAA-C
4960 AAATCAAA
1 AAATCAAA
4968 ATCAAAATCA
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
8 16 0.28
9 25 0.44
10 16 0.28
ACGTcount: A:0.72, C:0.15, G:0.00, T:0.12
Consensus pattern (9 bp):
AAATCAAAC
Found at i:4921 original size:5 final size:5
Alignment explanation
Indices: 4888--4979 Score: 56
Period size: 5 Copynumber: 19.6 Consensus size: 5
4878 AAAAATAAAA
**
4888 AAATC -AATC AAAT- AAAAA AAATC -AATC AAATC AAA-- AAATC AAA-C
1 AAATC AAATC AAATC AAATC AAATC AAATC AAATC AAATC AAATC AAATC
** * *
4932 AAAAA AAAAC AAA-- AAAAC AAATC AAATC AAATC AAAATC AAAATC AAA
1 AAATC AAATC AAATC AAATC AAATC AAATC AAATC -AAATC -AAATC AAA
4980 AGAGAATGGA
Statistics
Matches: 72, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
3 6 0.08
4 15 0.21
5 40 0.56
6 11 0.15
ACGTcount: A:0.72, C:0.15, G:0.00, T:0.13
Consensus pattern (5 bp):
AAATC
Found at i:4975 original size:22 final size:22
Alignment explanation
Indices: 4887--4979 Score: 65
Period size: 22 Copynumber: 4.4 Consensus size: 22
4877 AAAAAATAAA
4887 AAAATC-AATCAAAT-AAAA--
1 AAAATCAAATCAAATCAAAATC
4905 AAAATC-AATCAAATCAAAAAATC
1 AAAATCAAATCAAATC--AAAATC
** * **
4928 -AAA-CAAAAAAAAACAAAAAA
1 AAAATCAAATCAAATCAAAATC
4948 ACAAATCAAATCAAATCAAAATC
1 A-AAATCAAATCAAATCAAAATC
4971 AAAATCAAA
1 AAAATCAAA
4980 AGAGAATGGA
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
18 14 0.25
20 4 0.07
21 5 0.09
22 20 0.36
23 13 0.23
ACGTcount: A:0.72, C:0.15, G:0.00, T:0.13
Consensus pattern (22 bp):
AAAATCAAATCAAATCAAAATC
Found at i:4980 original size:35 final size:33
Alignment explanation
Indices: 4871--4980 Score: 101
Period size: 31 Copynumber: 3.5 Consensus size: 33
4861 ATCAAGAATT
*
4871 TCAAAAAAAA--AATAAAA-AAATC-AATCAAA
1 TCAAAAAAAATCAAAAAAACAAATCAAATCAAA
* *
4900 T-AAAAAAAATCAATCAAATCAAA--AAATCAAA
1 TCAAAAAAAATCAA-AAAAACAAATCAAATCAAA
*
4931 -CAAAAAAAAACAAAAAAACAAATCAAATCAAA
1 TCAAAAAAAATCAAAAAAACAAATCAAATCAAA
4963 TCAAAATCAAAATCAAAA
1 TCAAAA--AAAATCAAAA
4981 GAGAATGGAT
Statistics
Matches: 64, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
28 8 0.12
29 1 0.02
30 9 0.14
31 21 0.33
32 11 0.17
33 5 0.08
35 9 0.14
ACGTcount: A:0.74, C:0.14, G:0.00, T:0.13
Consensus pattern (33 bp):
TCAAAAAAAATCAAAAAAACAAATCAAATCAAA
Found at i:6210 original size:79 final size:79
Alignment explanation
Indices: 6111--6451 Score: 549
Period size: 79 Copynumber: 4.3 Consensus size: 79
6101 AGTTTCAATC
6111 ACAACATCAGACTCAGAGTTATTTTTCAAGTTGACCGCACCTTGGTCATCTTTCATCATCGATCA
1 ACAACATCAGACTCAGAGTTATTTTTCAAGTTGACCGCACCTTGGTCATCTTTCATCATCGATCA
**
6176 AGAAGTTTTTGGTT
66 AGAAGTTTTCAGTT
* *
6190 ACAATATCAGACTCAAAGTTATTTTTCAAGTTGACCGCACCTTGGTCATCTTTCATCATCGATCA
1 ACAACATCAGACTCAGAGTTATTTTTCAAGTTGACCGCACCTTGGTCATCTTTCATCATCGATCA
6255 AGAAGTTTTCAGTT
66 AGAAGTTTTCAGTT
* *
6269 ACAACATCAGACTCAGAGTTATTTTTCAAGTTGATCGCACCTTGGTCCTCTTTCATCATCGATCA
1 ACAACATCAGACTCAGAGTTATTTTTCAAGTTGACCGCACCTTGGTCATCTTTCATCATCGATCA
6334 AGAAGTTTTCAGTT
66 AGAAGTTTTCAGTT
* * * *
6348 ACAACATCAGACTCAGAGTTATTTTTCAAGTTGACCACACATTGGTCCTTTTTCATCATC-AGTC
1 ACAACATCAGACTCAGAGTTATTTTTCAAGTTGACCGCACCTTGGTCATCTTTCATCATCGA-TC
*
6412 AAGGAGTTTTCAGTT
65 AAGAAGTTTTCAGTT
* *
6427 ACAACATCAGATTCATAGTTATTTT
1 ACAACATCAGACTCAGAGTTATTTT
6452 CCAAAGGTAA
Statistics
Matches: 246, Mismatches: 15, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
78 1 0.00
79 245 1.00
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (79 bp):
ACAACATCAGACTCAGAGTTATTTTTCAAGTTGACCGCACCTTGGTCATCTTTCATCATCGATCA
AGAAGTTTTCAGTT
Found at i:6614 original size:50 final size:50
Alignment explanation
Indices: 6539--6780 Score: 457
Period size: 50 Copynumber: 4.8 Consensus size: 50
6529 AATACTTTGA
*
6539 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATGGG
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATGGG
6589 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATGGG
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATGGG
*
6639 CTTTTCCACAAGCCAAACTCGTTTCCATGCGAGTCAATTATCAACATGGG
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATGGG
*
6689 CTTTTCCACAAGCCAAACTTGTTTCCATACGAGTCAATTATCAACATGGG
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATGGG
6739 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATC
Statistics
Matches: 187, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 187 1.00
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (50 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATGGG
Done.