Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013512.1 Corchorus olitorius cultivar O-4 contig13545, 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: 4853
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Found at i:1098 original size:19 final size:19
Alignment explanation
Indices: 1061--1099 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1051 CTCACTTCCA
*
1061 CTTCATCTTCTCCATCCTT
1 CTTCATCTTCTCCAACCTT
* *
1080 CTTCATCTTTTTCAACCTT
1 CTTCATCTTCTCCAACCTT
1099 C
1 C
1100 CACTCATCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.13, C:0.38, G:0.00, T:0.49
Consensus pattern (19 bp):
CTTCATCTTCTCCAACCTT
Found at i:1829 original size:19 final size:19
Alignment explanation
Indices: 1792--1830 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1782 CTCACTTCCA
*
1792 CTTCATCTTCTCCAGCCTT
1 CTTCATCTTCTCCAACCTT
* *
1811 CTTCATCTTTTTCAACCTT
1 CTTCATCTTCTCCAACCTT
1830 C
1 C
1831 CACTCATCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.13, C:0.38, G:0.03, T:0.46
Consensus pattern (19 bp):
CTTCATCTTCTCCAACCTT
Found at i:3498 original size:57 final size:57
Alignment explanation
Indices: 3421--3693 Score: 230
Period size: 56 Copynumber: 4.9 Consensus size: 57
3411 ACCCATTATC
** *
3421 TTACTATTGATTACCCTTTTACTTCTTGATTAACTTAATTACTCCGAATTAAGCTAA
1 TTACTATTGATTACTTTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAA
* * *
3478 TTACTATTGATTGCTTTTTTACTTCTTGATTAACTTAATTGCTCTGAATGAAGCTAA
1 TTACTATTGATTACTTTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAA
* * **
3535 TT-CTATTGATTACTTTTTTGACTTCTT--TTAAACTTAATAATTCTGAATTAAGCCCA
1 TTACTATTGATTACTTTTTT-ACTTCTTGATT-AACTTAATTACTCTGAATTAAGCTAA
* * * *
3591 -T--TATTGATCACCAATTTTTAC-TCTT-TTTAACTTAATTACTCTGAATTAA-ATCAA
1 TTACTATTGATTA-C-TTTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCT-AA
* * *
3645 TTACTGATT-ACCTT-TTTTTTTAC-TCTT-TTTAACTTAATTACTTTGAATT
1 TTACT-ATTGA--TTACTTTTTTACTTCTTGATTAACTTAATTACTCTGAATT
3694 GAGCCCATTA
Statistics
Matches: 180, Mismatches: 24, Indels: 25
0.79 0.10 0.11
Matches are distributed among these distances:
54 32 0.18
55 9 0.05
56 73 0.41
57 62 0.34
58 3 0.02
59 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (57 bp):
TTACTATTGATTACTTTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAA
Found at i:3623 original size:54 final size:53
Alignment explanation
Indices: 3541--3734 Score: 176
Period size: 56 Copynumber: 3.6 Consensus size: 53
3531 CTAATTCTAT
* * *
3541 TGATTA-CTTTTTTGACTTCTTTTAAACTTAATAATTCTGAATTAAGCCCATTAT
1 TGATTACCATTTTT-AC-TCTTTTTAACTTAATAATTCTGAATTAAGCCCATTAC
* * * ** *
3595 TGATCACCAATTTTTACTCTTTTTAACTTAATTACTCTGAATTAAATCAATTAC
1 TGATTACC-ATTTTTACTCTTTTTAACTTAATAATTCTGAATTAAGCCCATTAC
* * *
3649 TGATTACCTTTTTTTTTACTCTTTTTAACTTAATTACTT-TGAATTGAGCCCATTAC
1 TGATTACC---ATTTTTACTCTTTTTAACTTAA-TAATTCTGAATTAAGCCCATTAC
* * *
3705 TGATTACCATTTTTATTTTTTTTGACTTAA
1 TGATTACCATTTTTACTCTTTTTAACTTAA
3735 CTACAAATTA
Statistics
Matches: 112, Mismatches: 23, Indels: 11
0.77 0.16 0.08
Matches are distributed among these distances:
53 18 0.16
54 42 0.38
55 3 0.03
56 47 0.42
57 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50
Consensus pattern (53 bp):
TGATTACCATTTTTACTCTTTTTAACTTAATAATTCTGAATTAAGCCCATTAC
Found at i:3851 original size:32 final size:32
Alignment explanation
Indices: 3700--4361 Score: 523
Period size: 32 Copynumber: 20.8 Consensus size: 32
3690 AATTGAGCCC
* *
3700 ATTACTGATTACCATTTTTATTTTTTTTG-ACTTA
1 ATTACTGATTACCA-TTTTA--CTTTTTGAATTTA
* ** * * *
3734 ACTACAAATTATCATTTTTACTCTTTTTAACTTA
1 ATTACTGATTACCA-TTTTACT-TTTTGAATTTA
* * * * * *
3768 CTTACTGATTTCCATTTTCCTTATAGAACTTA
1 ATTACTGATTACCATTTTACTTTTTGAATTTA
* *
3800 ATTTGCTGATTATCA--TTACTTTTTGAATTTA
1 A-TTACTGATTACCATTTTACTTTTTGAATTTA
* * * *
3831 CTTACGGATTTCCATTTTACTCTTTGAATTTA
1 ATTACTGATTACCATTTTACTTTTTGAATTTA
* * *
3863 ATTACTGATTCCCATTTTACTCTTCGAA---A
1 ATTACTGATTACCATTTTACTTTTTGAATTTA
* *
3892 ATTACTGATTACCA-TTCA-TTTTTGAATTGA
1 ATTACTGATTACCATTTTACTTTTTGAATTTA
** * *
3922 ATTACTGATTTTCATTTTCCTTATTGAATTTA
1 ATTACTGATTACCATTTTACTTTTTGAATTTA
* * * *
3954 ATTATTGAGTACCATTTTAGTCTTTGAATTTA
1 ATTACTGATTACCATTTTACTTTTTGAATTTA
* *
3986 ATTACTGAATACCATTTTACTTTTTGAACTTGA
1 ATTACTGATTACCATTTTACTTTTTGAA-TTTA
*
4019 ATTACTGATTACCATTTTACTTTTTGAATTGA
1 ATTACTGATTACCATTTTACTTTTTGAATTTA
* * *
4051 ATTACTGATTTCCA----CCTTATTGAATTTA
1 ATTACTGATTACCATTTTACTTTTTGAATTTA
* *
4079 ATTACTGATTACCATTTCACTCTTTGAATTTA
1 ATTACTGATTACCATTTTACTTTTTGAATTTA
*
4111 ATTACTGATTACCATTTTACTTTTTGAACTTGA
1 ATTACTGATTACCATTTTACTTTTTGAA-TTTA
* * **
4144 ATTACTGATTACCATTTTACTCTCTGAATAAA
1 ATTACTGATTACCATTTTACTTTTTGAATTTA
* * *
4176 ATTATTGATTACCATTTTACTCTTTGAATTGA
1 ATTACTGATTACCATTTTACTTTTTGAATTTA
* *
4208 ATTACTGATTTCCATTTTACTCTTAT-AATTTA
1 ATTACTGATTACCATTTTACT-TTTTGAATTTA
* ** *
4240 ATTACTAATTACCATTTTACTCATTGAATTTG
1 ATTACTGATTACCATTTTACTTTTTGAATTTA
4272 ATTACTGATTACCA--TTACATTTTACTG-ATTTCCA
1 ATTACTGATTACCATTTTAC-TTTT--TGAATTT--A
* * * * *
4306 TTTTACTGATTATCATTTTACTCTTTGAACTTG
1 -ATTACTGATTACCATTTTACTTTTTGAATTTA
4339 ATTACTGATTACCA--TTACTTTTT
1 ATTACTGATTACCATTTTACTTTTT
4362 ACTGATTATC
Statistics
Matches: 501, Mismatches: 100, Indels: 58
0.76 0.15 0.09
Matches are distributed among these distances:
27 6 0.01
28 27 0.05
29 14 0.03
30 34 0.07
31 17 0.03
32 267 0.53
33 83 0.17
34 31 0.06
35 15 0.03
36 3 0.01
37 4 0.01
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (32 bp):
ATTACTGATTACCATTTTACTTTTTGAATTTA
Found at i:4309 original size:15 final size:15
Alignment explanation
Indices: 4285--4327 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
4275 ACTGATTACC
4285 ATTA-CATTTTACTG
1 ATTATCATTTTACTG
4299 ATT-TCCATTTTACTG
1 ATTAT-CATTTTACTG
4314 ATTATCATTTTACT
1 ATTATCATTTTACT
4328 CTTTGAACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 3 0.12
15 22 0.85
16 1 0.04
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (15 bp):
ATTATCATTTTACTG
Found at i:4323 original size:67 final size:67
Alignment explanation
Indices: 4241--4376 Score: 211
Period size: 67 Copynumber: 2.0 Consensus size: 67
4231 TATAATTTAA
*
4241 TTACTAATTACCATTTTACTCATTGAATTTGATTACTGATTACCATTACATTTTACTGATT-TCC
1 TTACTAATTACCATTTTACTCATTGAACTTGATTACTGATTACCATTACATTTTACTGATTATCC
4305 ATT
66 -TT
* * * *
4308 TTACTGATTATCATTTTACTCTTTGAACTTGATTACTGATTACCATTACTTTTTACTGATTATCC
1 TTACTAATTACCATTTTACTCATTGAACTTGATTACTGATTACCATTACATTTTACTGATTATCC
4373 TT
66 TT
4375 TT
1 TT
4377 CTTCTTGACC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
67 60 0.95
68 3 0.05
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.50
Consensus pattern (67 bp):
TTACTAATTACCATTTTACTCATTGAACTTGATTACTGATTACCATTACATTTTACTGATTATCC
TT
Found at i:4357 original size:129 final size:127
Alignment explanation
Indices: 3815--4354 Score: 435
Period size: 125 Copynumber: 4.2 Consensus size: 127
3805 CTGATTATCA
* * * * * *
3815 TTACTTTTTGAATTTACTTACGGATTTCCATTTTACTCTTTGAATTTAATTACTGATTCCCATTT
1 TTACTCTTTGAATTGA-TTACTGATTACCA-TTTACTCTTTGAATTTAATTACTAATTACCATTT
* * ** **
3880 TACTC-TTCGAA----AATTACTGATTACCATT-CA-TTTTTGAATTGAATTACTGATTTTCATT
64 TACTCATT-GAACTTGAATTACTGATTACCATTACACTCTCTGAATAAAATTACTGATTACCATT
* * * * *
3938 TTCCT-TATTGAATTTAATTATTGAGTACCATTTTAGTCTTTGAATTTAATTACTGAA-TACCAT
1 TTACTCT-TTGAA-TTGATTACTGATTACCA-TTTACTCTTTGAATTTAATTACT-AATTACCAT
** ** * * ** * *
4001 TTTACTTTTTGAACTTGAATTACTGATTACCATTTTACTTTTTGAATTGAATTACTGATTTCCAC
62 TTTACTCATTGAACTTGAATTACTGATTACCATTACACTCTCTGAATAAAATTACTGATTACCAT
*
4066 C
127 T
* *
4067 TTA----TTGAATTTAATTACTGATTACCATTTCACTCTTTGAATTTAATTACTGATTACCATTT
1 TTACTCTTTGAA-TTGATTACTGATTACCATTT-ACTCTTTGAATTTAATTACTAATTACCATTT
** ** *
4128 TACTTTTTGAACTTGAATTACTGATTACCATTTTACTCTCTGAATAAAATTATTGATTACCATT
64 TACTCATTGAACTTGAATTACTGATTACCATTACACTCTCTGAATAAAATTACTGATTACCATT
*
4192 TTACTCTTTGAATTGAATTACTGATTTCCATTTTACTCTTAT-AATTTAATTACTAATTACCATT
1 TTACTCTTTGAATTG-ATTACTGATTACCA-TTTACTCTT-TGAATTTAATTACTAATTACCATT
* * * * * ** *
4256 TTACTCATTGAATTTG-ATTACTGATTACCATTACATTTTACTGATTTCCATTTTACTGATTATC
63 TTACTCATTGAACTTGAATTACTGATTACCATTACACTCT-CTGA-AT-AAAATTACTGATTACC
4320 ATT
125 ATT
4323 TTACTCTTTGAACTTGATTACTGATTACCATT
1 TTACTCTTTGAA-TTGATTACTGATTACCATT
4355 ACTTTTTACT
Statistics
Matches: 350, Mismatches: 44, Indels: 39
0.81 0.10 0.09
Matches are distributed among these distances:
122 1 0.00
123 55 0.16
124 10 0.03
125 107 0.31
127 17 0.05
128 22 0.06
129 89 0.25
130 7 0.02
131 39 0.11
132 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.49
Consensus pattern (127 bp):
TTACTCTTTGAATTGATTACTGATTACCATTTACTCTTTGAATTTAATTACTAATTACCATTTTA
CTCATTGAACTTGAATTACTGATTACCATTACACTCTCTGAATAAAATTACTGATTACCATT
Done.