Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012617.1 Corchorus olitorius cultivar O-4 contig12650, 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: 42978
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Found at i:283 original size:32 final size:32
Alignment explanation
Indices: 242--379 Score: 258
Period size: 32 Copynumber: 4.3 Consensus size: 32
232 AAACAAGCCA
242 AAATAGCGGCGTTTCGGTACGGAAACGCCACT
1 AAATAGCGGCGTTTCGGTACGGAAACGCCACT
274 AAATAGCGGCGTTTCGGTACGGAAACGCCACT
1 AAATAGCGGCGTTTCGGTACGGAAACGCCACT
*
306 AAATAGCGGCGTTTCGGTACGGAAACACCACT
1 AAATAGCGGCGTTTCGGTACGGAAACGCCACT
*
338 AAATAGCGGCGTTTCGGTACGTAAACGCCACT
1 AAATAGCGGCGTTTCGGTACGGAAACGCCACT
370 AAATAGCGGC
1 AAATAGCGGC
380 TATTTTGAAA
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 103 1.00
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.19
Consensus pattern (32 bp):
AAATAGCGGCGTTTCGGTACGGAAACGCCACT
Found at i:3054 original size:22 final size:22
Alignment explanation
Indices: 3026--3074 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
3016 AGGCGATTGT
3026 TGACAGGAGCTGATTCTTTTTC
1 TGACAGGAGCTGATTCTTTTTC
3048 TGACAGGAGCTGATTCTTTTTC
1 TGACAGGAGCTGATTCTTTTTC
3070 TGACA
1 TGACA
3075 ACAGCTCGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.39
Consensus pattern (22 bp):
TGACAGGAGCTGATTCTTTTTC
Found at i:3080 original size:22 final size:22
Alignment explanation
Indices: 3033--3080 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
3023 TGTTGACAGG
**
3033 AGCTGATTCTTTTTCTGACAGG
1 AGCTGATTCTTTTTCTGACAAC
3055 AGCTGATTCTTTTTCTGACAAC
1 AGCTGATTCTTTTTCTGACAAC
3077 AGCT
1 AGCT
3081 CGCTTTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (22 bp):
AGCTGATTCTTTTTCTGACAAC
Found at i:5874 original size:12 final size:11
Alignment explanation
Indices: 5856--5885 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
5846 TTTCTGGTCG
5856 ATTTTTTTTTT
1 ATTTTTTTTTT
5867 ATTTTTTTTTT
1 ATTTTTTTTTT
5878 ATTTTTTT
1 ATTTTTTT
5886 CAATTAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (11 bp):
ATTTTTTTTTT
Found at i:6924 original size:21 final size:21
Alignment explanation
Indices: 6900--6963 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
6890 CCTTAGGCAA
6900 CTCCAATGAGCTTGAAACCTT
1 CTCCAATGAGCTTGAAACCTT
*
6921 CTCCAATGAGCTTGAAACTTT
1 CTCCAATGAGCTTGAAACCTT
*
6942 TTCCAATGAGCTTGAAA-CTT
1 CTCCAATGAGCTTGAAACCTT
6962 CT
1 CT
6964 TTATGTGAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 3 0.08
21 36 0.92
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (21 bp):
CTCCAATGAGCTTGAAACCTT
Found at i:7292 original size:15 final size:16
Alignment explanation
Indices: 7261--7316 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 16
7251 CGAAATTTAT
7261 TAATTATTTATT-A-AA
1 TAATTA-TTATTCAGAA
* *
7276 TAATAATTATTC-TAA
1 TAATTATTATTCAGAA
7291 TAATTATT-TTCAGAA
1 TAATTATTATTCAGAA
7306 TAATTATTATT
1 TAATTATTATT
7317 AAAATTCCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 8 0.24
15 24 0.71
16 2 0.06
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (16 bp):
TAATTATTATTCAGAA
Found at i:7725 original size:27 final size:27
Alignment explanation
Indices: 7686--7782 Score: 117
Period size: 27 Copynumber: 3.6 Consensus size: 27
7676 GGTCATCTGT
*
7686 GGGCATTTTAGTCATTTGCAC-GTCTAG
1 GGGCATTTTAGTCATTTGCACATTC-AG
*
7713 GGGCATTTCAGTCATTTGCACATTCAG
1 GGGCATTTTAGTCATTTGCACATTCAG
* * *
7740 GGGCATTTTGGTCATTTGTA-TTTCAG
1 GGGCATTTTAGTCATTTGCACATTCAG
*
7766 GGGCATTTTGGTCATTT
1 GGGCATTTTAGTCATTT
7783 TCTTTCTTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
26 22 0.35
27 39 0.62
28 2 0.03
ACGTcount: A:0.18, C:0.16, G:0.26, T:0.40
Consensus pattern (27 bp):
GGGCATTTTAGTCATTTGCACATTCAG
Found at i:8284 original size:16 final size:16
Alignment explanation
Indices: 8263--8306 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
8253 TATACATATT
8263 ATAATACAAGTATGGA
1 ATAATACAAGTATGGA
*
8279 ATAATACAA-AATGGA
1 ATAATACAAGTATGGA
*
8294 ATAGTACAAGTAT
1 ATAATACAAGTAT
8307 AGGTTGCATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.52, C:0.07, G:0.16, T:0.25
Consensus pattern (16 bp):
ATAATACAAGTATGGA
Found at i:13159 original size:2 final size:2
Alignment explanation
Indices: 13152--13186 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
13142 TTTAAATTGA
13152 AT AT AT AT AT AT AT -T AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13187 AACATTGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13171 original size:13 final size:13
Alignment explanation
Indices: 13153--13186 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
13143 TTAAATTGAA
13153 TATATATATATAT
1 TATATATATATAT
13166 TATATATATATAT
1 TATATATATATAT
*
13179 AATATATA
1 TATATATA
13187 AACATTGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TATATATATATAT
Found at i:13172 original size:15 final size:15
Alignment explanation
Indices: 13152--13186 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
13142 TTTAAATTGA
*
13152 ATATATATATATATT
1 ATATATATATATAAT
13167 ATATATATATATAAT
1 ATATATATATATAAT
13182 ATATA
1 ATATA
13187 AACATTGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATATATATATAAT
Found at i:13404 original size:30 final size:30
Alignment explanation
Indices: 13368--13428 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
13358 TGGCTCGACC
*
13368 GAAGCCACAAGGAACTGCTGCCGCATCAAT
1 GAAGCCACAAGGAACTGCTACCGCATCAAT
13398 GAAGCCACAAGGAACTGCTACCGCATCAAT
1 GAAGCCACAAGGAACTGCTACCGCATCAAT
13428 G
1 G
13429 TCCCCAACAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.30, G:0.23, T:0.13
Consensus pattern (30 bp):
GAAGCCACAAGGAACTGCTACCGCATCAAT
Found at i:17049 original size:111 final size:111
Alignment explanation
Indices: 16670--17061 Score: 570
Period size: 112 Copynumber: 3.5 Consensus size: 111
16660 TCCCAAAAAT
* * *** * * *
16670 AAAAAATTAAATATTGCGGCGTTTCCAACATCAGAATTCCCCATTTATCGGCGTTTGGGATAGAA
1 AAAAAAATAAATATGGCGGCGTTTCCAACATCAGACGCCCCCATTTAGCGGCGTTTTGGATGGAA
*
16735 GCGTCGCTATATTTTTGCCTCATTTTTACCCAATTTATATTTTCCCA
66 GCGCCGCTATATTTTTGCCTCATTTTTACCCAATTTATA-TTTCCCA
* *
16782 AAAAAATTAAATATGGCGGCGTTTCCAACATCAGACGCCCCTATTTAGCGGCGTTTTGGATGGAA
1 AAAAAAATAAATATGGCGGCGTTTCCAACATCAGACGCCCCCATTTAGCGGCGTTTTGGATGGAA
*
16847 GCGCCGCTATA-TTTTGCCTCATGTTTACCCAATTTATATTTCCCCA
66 GCGCCGCTATATTTTTGCCTCATTTTTACCCAATTTATATTT-CCCA
* **
16893 AAAAAAATTAAATATGGCGGCGTTTCCAACATCAGACGCCCCCATTTGGCGGCGTTTTCAATGGA
1 AAAAAAA-TAAATATGGCGGCGTTTCCAACATCAGACGCCCCCATTTAGCGGCGTTTTGGATGGA
* * *
16958 AGTGCCGCTATATTTTTGCCTCATTTTTACTCAATTTATATTTCGCA
65 AGCGCCGCTATATTTTTGCCTCATTTTTACCCAATTTATATTTCCCA
* *
17005 AAAAAAAAAAATGTGGCGGCGTTTCCAACATCAGACGCCCCCATTTAGCGGCGTTTT
1 AAAAAAATAAATATGGCGGCGTTTCCAACATCAGACGCCCCCATTTAGCGGCGTTTT
17062 ACCCAGAAAC
Statistics
Matches: 255, Mismatches: 22, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
110 3 0.01
111 83 0.33
112 141 0.55
113 28 0.11
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (111 bp):
AAAAAAATAAATATGGCGGCGTTTCCAACATCAGACGCCCCCATTTAGCGGCGTTTTGGATGGAA
GCGCCGCTATATTTTTGCCTCATTTTTACCCAATTTATATTTCCCA
Found at i:25900 original size:26 final size:26
Alignment explanation
Indices: 25840--25891 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
25830 GCATTAGGGT
* **
25840 CACTTAGGGCATTTTGGTCATTTTTA
1 CACTAAGGGCATTTTGGTCATTTGCA
25866 CACTAAGGGCATTTTGGTCATTTGCA
1 CACTAAGGGCATTTTGGTCATTTGCA
25892 TATTCAGGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40
Consensus pattern (26 bp):
CACTAAGGGCATTTTGGTCATTTGCA
Found at i:34929 original size:19 final size:18
Alignment explanation
Indices: 34905--34940 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
34895 TGACGACTCA
34905 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
34924 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
34941 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.