Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015550.1 Corchorus olitorius cultivar O-4 contig15583, 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: 53259
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2864 original size:96 final size:96
Alignment explanation
Indices: 2700--2883 Score: 350
Period size: 96 Copynumber: 1.9 Consensus size: 96
2690 GAGTTTGTTT
*
2700 GTTTATTTTGGTAGGTATTTAGTTTATTTATGGTATAGTTTCTAGTTTGGGTTGAATTCTCATTT
1 GTTTATTTTGGTAGGTATGTAGTTTATTTATGGTATAGTTTCTAGTTTGGGTTGAATTCTCATTT
2765 AGATGTTTGGGTATAGAGATTTAGAATGTGA
66 AGATGTTTGGGTATAGAGATTTAGAATGTGA
*
2796 GTTTATTTTGGTAGGTATGTAGTTTATTTATGGTATAGTTTCTAGTTTGGGTTGAATTCTTATTT
1 GTTTATTTTGGTAGGTATGTAGTTTATTTATGGTATAGTTTCTAGTTTGGGTTGAATTCTCATTT
2861 AGATGTTTGGGTATAGAGATTTA
66 AGATGTTTGGGTATAGAGATTTA
2884 TTTGAATTGT
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 86 1.00
ACGTcount: A:0.22, C:0.03, G:0.25, T:0.50
Consensus pattern (96 bp):
GTTTATTTTGGTAGGTATGTAGTTTATTTATGGTATAGTTTCTAGTTTGGGTTGAATTCTCATTT
AGATGTTTGGGTATAGAGATTTAGAATGTGA
Found at i:3886 original size:103 final size:101
Alignment explanation
Indices: 3707--3910 Score: 356
Period size: 103 Copynumber: 2.0 Consensus size: 101
3697 AAAAATGTCT
* *
3707 AAAGATGTTACATTATTAATTTGGTTAAATTTGAGTTTGGTTTTTGTGTCATTTCCATTTTGGTT
1 AAAGATGTTACATTATTAATTCGGTTAAATTTGAGTTTGGTTTTTGTGTCATTTCCATCTTGGTT
3772 ATTTTGTTATTCTCATAAACTTCTAAGGGCATTTTTGA
66 ATTTTGTTA-T-TCATAAACTTCTAAGGGCATTTTTGA
3810 AAAGATGTTACATTATTAATTCGGTT-AATATTGAGTTTGGTTTTTGTGTCATTTCCATCTTGGT
1 AAAGATGTTACATTATTAATTCGGTTAAAT-TTGAGTTTGGTTTTTGTGTCATTTCCATCTTGGT
3874 TATTTTGTTATTCATAAACTTCTAAGGGCATTTTTGA
65 TATTTTGTTATTCATAAACTTCTAAGGGCATTTTTGA
3911 CTTTGTAGCA
Statistics
Matches: 98, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
101 26 0.27
102 4 0.04
103 68 0.69
ACGTcount: A:0.25, C:0.09, G:0.17, T:0.50
Consensus pattern (101 bp):
AAAGATGTTACATTATTAATTCGGTTAAATTTGAGTTTGGTTTTTGTGTCATTTCCATCTTGGTT
ATTTTGTTATTCATAAACTTCTAAGGGCATTTTTGA
Found at i:3938 original size:5 final size:5
Alignment explanation
Indices: 3928--3957 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
3918 GCATTTAAAT
3928 TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA
3958 CATATTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:4240 original size:31 final size:31
Alignment explanation
Indices: 4202--4279 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
4192 TTTTAGAATA
4202 AAGTCCCCAGATCTATTAATCTGTCAGGTTT
1 AAGTCCCCAGATCTATTAATCTGTCAGGTTT
* *
4233 AAGTCCCCAGATCTATTGATCTGTCGGGTTT
1 AAGTCCCCAGATCTATTAATCTGTCAGGTTT
*
4264 TAGT-CCCAGATCTATT
1 AAGTCCCCAGATCTATT
4280 GATTTGTCGG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 12 0.27
31 32 0.73
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (31 bp):
AAGTCCCCAGATCTATTAATCTGTCAGGTTT
Found at i:4274 original size:30 final size:30
Alignment explanation
Indices: 4207--4298 Score: 130
Period size: 30 Copynumber: 3.0 Consensus size: 30
4197 GAATAAAGTC
* * *
4207 CCCAGATCTATTAATCTGTCAGGTTTAAGT
1 CCCAGATCTATTGATCTGTCGGGTTTTAGT
4237 CCCCAGATCTATTGATCTGTCGGGTTTTAGT
1 -CCCAGATCTATTGATCTGTCGGGTTTTAGT
* *
4268 CCCAGATCTATTGATTTGTCGGATTTTAGT
1 CCCAGATCTATTGATCTGTCGGGTTTTAGT
4298 C
1 C
4299 AGTTTGTTGA
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 29 0.52
31 27 0.48
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.39
Consensus pattern (30 bp):
CCCAGATCTATTGATCTGTCGGGTTTTAGT
Found at i:4326 original size:14 final size:13
Alignment explanation
Indices: 4295--4340 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
4285 GTCGGATTTT
4295 AGTCAGTTTGTTG
1 AGTCAGTTTGTTG
*
4308 AGTCAGTTTTTTCG
1 AGTCAGTTTGTT-G
4322 AGTCAGTTAGTGTTG
1 AGTCAGTT--TGTTG
4337 AGTC
1 AGTC
4341 TGGCTTTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.39
14 9 0.32
15 5 0.18
16 3 0.11
ACGTcount: A:0.17, C:0.11, G:0.28, T:0.43
Consensus pattern (13 bp):
AGTCAGTTTGTTG
Found at i:4348 original size:29 final size:27
Alignment explanation
Indices: 4295--4348 Score: 63
Period size: 29 Copynumber: 1.9 Consensus size: 27
4285 GTCGGATTTT
**
4295 AGTCAGTTTGTTGAGTCAGTTTTTTCG
1 AGTCAGTTTGTTGAGTCAGGCTTTTCG
*
4322 AGTCAGTTAGTGTTGAGTCTGGCTTTT
1 AGTCAGTT--TGTTGAGTCAGGCTTTT
4349 GTCCAGTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 8 0.36
29 14 0.64
ACGTcount: A:0.15, C:0.11, G:0.28, T:0.46
Consensus pattern (27 bp):
AGTCAGTTTGTTGAGTCAGGCTTTTCG
Found at i:10809 original size:75 final size:75
Alignment explanation
Indices: 10685--10842 Score: 190
Period size: 75 Copynumber: 2.1 Consensus size: 75
10675 TAGGGATAGG
* * * * *
10685 GATAGGGATAGAGAAAGAGATCGAGAACGGGAGCGTGAACGACGCCGTTCCGAGAGAGAGAGGAG
1 GATAGGGATAGAGAAAGAGATCGAGAACGAGAACGAGAAAGACGCCGTTCCGAGAGAGAGAAGAG
10750 CAGTGACTCC
66 CAGTGACTCC
* * * * * * *
10760 GATAGGGATAGGGATAGGGATCGAGAACGAGAACGAGAAAGGCGTCGTTCTGAGAGGGAGAAGAG
1 GATAGGGATAGAGAAAGAGATCGAGAACGAGAACGAGAAAGACGCCGTTCCGAGAGAGAGAAGAG
* *
10825 CAGTGATTCG
66 CAGTGACTCC
10835 GATAGGGA
1 GATAGGGA
10843 AAAGGAAAGG
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.34, C:0.13, G:0.41, T:0.13
Consensus pattern (75 bp):
GATAGGGATAGAGAAAGAGATCGAGAACGAGAACGAGAAAGACGCCGTTCCGAGAGAGAGAAGAG
CAGTGACTCC
Found at i:10912 original size:6 final size:6
Alignment explanation
Indices: 10903--11043 Score: 52
Period size: 6 Copynumber: 22.5 Consensus size: 6
10893 AGAAAGAGAA
* ** *
10903 GGAAAG GGAAAG AGCTAG GGAGAA- GGAAAG AGAAAG GGAAAG GGAGAAG
1 GGAAAG GGAAAG GGAAAG GGA-AAG GGAAAG GGAAAG GGAAAG GGA-AAG
* * * * ** * *
10952 CGTGAACG TGAAAG GGAGAG GGAGCGAG AAAAGAG GGAAAG AGAAAG GGAGAG
1 -G-GAAAG GGAAAG GGAAAG GGA--AAG GGAA-AG GGAAAG GGAAAG GGAAAG
* * * *
11005 GGAGAG GGAGAG GGAGAG GGAAAA GGAGAA- GGAAAG GGA
1 GGAAAG GGAAAG GGAAAG GGAAAG GGA-AAG GGAAAG GGA
11044 GAGGAAGTCC
Statistics
Matches: 102, Mismatches: 23, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
5 4 0.04
6 79 0.77
7 10 0.10
8 7 0.07
9 2 0.02
ACGTcount: A:0.45, C:0.03, G:0.50, T:0.02
Consensus pattern (6 bp):
GGAAAG
Found at i:10940 original size:18 final size:17
Alignment explanation
Indices: 10894--10945 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
10884 GGGAACGCGA
10894 GAAAGAG-AA-GGAAAGG
1 GAAAGAGAAAGGGAAA-G
**
10910 GAAAGAGCTAGGGAGAAG
1 GAAAGAGAAAGGGA-AAG
10928 GAAAGAGAAAGGGAAAG
1 GAAAGAGAAAGGGAAAG
10945 G
1 G
10946 GAGAAGCGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 7 0.23
17 5 0.17
18 16 0.53
19 2 0.07
ACGTcount: A:0.52, C:0.02, G:0.44, T:0.02
Consensus pattern (17 bp):
GAAAGAGAAAGGGAAAG
Found at i:10946 original size:24 final size:24
Alignment explanation
Indices: 10898--11043 Score: 78
Period size: 24 Copynumber: 5.8 Consensus size: 24
10888 ACGCGAGAAA
* * **
10898 GAGAAGGAAAGGGAAAGAGCTAGG
1 GAGAAGGAAAGAGAAAGGGAAAGG
10922 GAGAAGGAAAGAGAAAGGGAAAGG
1 GAGAAGGAAAGAGAAAGGGAAAGG
* * *
10946 GAGAAGCGTGAACGTGAAAGGGAGAGG
1 GAGAA--G-GAAAGAGAAAGGGAAAGG
* * *
10973 GAGCGAGAAAAGAGGGAAAGAGAAAGG
1 GAG-AAGGAAAGA--GAAAGGGAAAGG
* * * * *
11000 GAGAGGGAGAGGGAGAGGGAGAGG
1 GAGAAGGAAAGAGAAAGGGAAAGG
*
11024 GAAAAGGAGAAG-GAAAGGGA
1 GAGAAGGA-AAGAGAAAGGGA
11044 GAGGAAGTCC
Statistics
Matches: 90, Mismatches: 25, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
24 47 0.52
25 5 0.06
26 6 0.07
27 31 0.34
28 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.49, T:0.02
Consensus pattern (24 bp):
GAGAAGGAAAGAGAAAGGGAAAGG
Found at i:10974 original size:33 final size:33
Alignment explanation
Indices: 10928--11015 Score: 86
Period size: 33 Copynumber: 2.7 Consensus size: 33
10918 TAGGGAGAAG
* * * * * * *
10928 GAAAGAGAAAGGGAAAGGGAGAAGCGTGAACGT
1 GAAAGGGAGAGGGAGAGGGAGAAGAGGGAAAGA
* * *
10961 GAAAGGGAGAGGGAGCGAGAAAAGAGGGAAAGA
1 GAAAGGGAGAGGGAGAGGGAGAAGAGGGAAAGA
10994 GAAAGGGAGAGGGAGAGGGAGA
1 GAAAGGGAGAGGGAGAGGGAGA
11016 GGGAGAGGGA
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.45, C:0.03, G:0.49, T:0.02
Consensus pattern (33 bp):
GAAAGGGAGAGGGAGAGGGAGAAGAGGGAAAGA
Found at i:11006 original size:18 final size:18
Alignment explanation
Indices: 10961--11027 Score: 68
Period size: 18 Copynumber: 3.9 Consensus size: 18
10951 GCGTGAACGT
**
10961 GAAAGGGAGAGGGAGCGA
1 GAAAGGGAGAGGGAAAGA
10979 GAAA---AGAGGGAAAGA
1 GAAAGGGAGAGGGAAAGA
* *
10994 GAAAGGGAGAGGGAGAGG
1 GAAAGGGAGAGGGAAAGA
*
11012 GAGAGGGAGAGGGAAA
1 GAAAGGGAGAGGGAAA
11028 AGGAGAAGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
15 13 0.32
18 27 0.68
ACGTcount: A:0.45, C:0.01, G:0.54, T:0.00
Consensus pattern (18 bp):
GAAAGGGAGAGGGAAAGA
Found at i:11012 original size:12 final size:12
Alignment explanation
Indices: 10983--11047 Score: 76
Period size: 12 Copynumber: 5.4 Consensus size: 12
10973 GAGCGAGAAA
*
10983 AGAGGGAAAGAG
1 AGAGGGAAAGGG
* *
10995 AAAGGGAGAGGG
1 AGAGGGAAAGGG
*
11007 AGAGGGAGAGGG
1 AGAGGGAAAGGG
*
11019 AGAGGGAAAAGG
1 AGAGGGAAAGGG
*
11031 AGAAGGAAAGGG
1 AGAGGGAAAGGG
11043 AGAGG
1 AGAGG
11048 AAGTCCAGGG
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 44 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (12 bp):
AGAGGGAAAGGG
Found at i:11032 original size:18 final size:18
Alignment explanation
Indices: 10983--11043 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
10973 GAGCGAGAAA
*
10983 AGAGGG-AAAGAGAAAGGG
1 AGAGGGAAAAG-GAGAGGG
* *
11001 AGAGGGAGAGGGAGAGGG
1 AGAGGGAAAAGGAGAGGG
*
11019 AGAGGGAAAAGGAGAAGG
1 AGAGGGAAAAGGAGAGGG
*
11037 AAAGGGA
1 AGAGGGA
11044 GAGGAAGTCC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
18 33 0.94
19 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (18 bp):
AGAGGGAAAAGGAGAGGG
Found at i:11058 original size:45 final size:45
Alignment explanation
Indices: 10964--11050 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
10954 TGAACGTGAA
* * *
10964 AGGGAGAGGGAGCGAGAAAAGAGGGAAAGAGAAAGGGAGAGGGAG
1 AGGGAGAGGGAGAGAGAAAAGAGAGAAAGAGAAAGGGAGAGGAAG
*
11009 AGGGAGAGGGAGAGGGAAAAG-GAG-AAG-GAAAGGGAGAGGAAG
1 AGGGAGAGGGAGAGAGAAAAGAGAGAAAGAGAAAGGGAGAGGAAG
11051 TCCAGGGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 14 0.37
43 3 0.08
44 2 0.05
45 19 0.50
ACGTcount: A:0.45, C:0.01, G:0.54, T:0.00
Consensus pattern (45 bp):
AGGGAGAGGGAGAGAGAAAAGAGAGAAAGAGAAAGGGAGAGGAAG
Found at i:22964 original size:23 final size:23
Alignment explanation
Indices: 22932--22976 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
22922 CAATCGAACG
*
22932 TATTCGTGTCAGACACATATTCA
1 TATTCATGTCAGACACATATTCA
**
22955 TATTCATGTCAGATGCATATTC
1 TATTCATGTCAGACACATATTC
22977 TTATCCCGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (23 bp):
TATTCATGTCAGACACATATTCA
Found at i:29361 original size:6 final size:6
Alignment explanation
Indices: 29350--29385 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
29340 GGGATATGGC
* *
29350 GGTGGA GGTGGA GGCGGA GGTGGA GGTGGT GGTGGA
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA
29386 TATGGGAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.14, C:0.03, G:0.67, T:0.17
Consensus pattern (6 bp):
GGTGGA
Found at i:36547 original size:2 final size:2
Alignment explanation
Indices: 36540--36571 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
36530 CTCGATACAA
36540 AT AT AT AT AT AT AT AT AT AT A- AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36572 TTAATTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36576 original size:14 final size:15
Alignment explanation
Indices: 36540--36576 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
36530 CTCGATACAA
36540 ATATAT-ATATATAT
1 ATATATAATATATAT
36554 ATATATAATAT-TAT
1 ATATATAATATATAT
*
36568 ATATTTAAT
1 ATATATAAT
36577 TAAAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATATAATATATAT
Found at i:36751 original size:38 final size:37
Alignment explanation
Indices: 36696--36768 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
36686 TCGAACTTGT
*
36696 CGAGTCGAGCTCGAGTAGCTCGA-TACTCGATTCGAGC
1 CGAGTCGAGCTCGAGTAGCTC-ACTACTCGACTCGAGC
*
36733 CGAGCTCGAGCTGGAGTAGCTCACTACTCGACTCGA
1 CGAG-TCGAGCTCGAGTAGCTCACTACTCGACTCGA
36769 CTCAATTACA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
37 5 0.16
38 27 0.84
ACGTcount: A:0.22, C:0.29, G:0.29, T:0.21
Consensus pattern (37 bp):
CGAGTCGAGCTCGAGTAGCTCACTACTCGACTCGAGC
Found at i:37731 original size:2 final size:2
Alignment explanation
Indices: 37724--37758 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
37714 GTCTCCAGCT
37724 TA TA TA 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 TA TA TA T
37759 CCACCTGCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:51779 original size:31 final size:33
Alignment explanation
Indices: 51743--51807 Score: 112
Period size: 35 Copynumber: 1.9 Consensus size: 33
51733 TTTCCGTTGT
51743 TTATTTAAAAACCAAAACAATTAACCAACACATA
1 TTATTTAAAAACCAAAACAATTAACCAACACA-A
51777 TTTATTTAAAAACCAAAACAATTAACCAACA
1 -TTATTTAAAAACCAAAACAATTAACCAACA
51808 GTAGTATATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25
Consensus pattern (33 bp):
TTATTTAAAAACCAAAACAATTAACCAACACAA
Done.