Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017834.1 Corchorus olitorius cultivar O-4 contig17867, 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: 12525
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:959 original size:22 final size:21
Alignment explanation
Indices: 922--1014 Score: 89
Period size: 22 Copynumber: 4.2 Consensus size: 21
912 TTAATTTTCT
* *
922 AATTTGGCCCCTTTTTTTTTG
1 AATTTGTCCCTTTTTTTTTTG
943 AATTTGTCCCTTGTTTTTTTTG
1 AATTTGTCCCTT-TTTTTTTTG
*
965 AATTTGTCCCCCTTTTTTTTTCTTT
1 AATTTGT--CCC-TTTTTTTT-TTG
* *
990 AATTTG-GCCTTTTTATTTTG
1 AATTTGTCCCTTTTTTTTTTG
1010 AATTT
1 AATTT
1015 TTCCTCCCCC
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
20 7 0.11
21 17 0.28
22 18 0.30
24 9 0.15
25 10 0.16
ACGTcount: A:0.12, C:0.16, G:0.11, T:0.61
Consensus pattern (21 bp):
AATTTGTCCCTTTTTTTTTTG
Found at i:1029 original size:47 final size:46
Alignment explanation
Indices: 929--1045 Score: 132
Period size: 47 Copynumber: 2.5 Consensus size: 46
919 TCTAATTTGG
* * *
929 CCCC-TTTTTTT-TTGAATTTGTCCCTTGTTTTTTTTGAATTTGTCC
1 CCCCTTTTTTTTCTTTAATTTG-GCCTTGTTTATTTTGAATTTGTCC
* *
974 CCCTTTTTTTTTCTTTAATTTGGCCTT-TTTATTTTGAATTTTTCCTC
1 CCCCTTTTTTTTCTTTAATTTGGCCTTGTTTATTTTGAATTTGT-C-C
*
1021 CCCCTTTTTCTTCTTTAATTTGGCC
1 CCCCTTTTTTTTCTTTAATTTGGCC
1046 CTTGATAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
45 17 0.28
46 12 0.20
47 32 0.52
ACGTcount: A:0.09, C:0.22, G:0.09, T:0.60
Consensus pattern (46 bp):
CCCCTTTTTTTTCTTTAATTTGGCCTTGTTTATTTTGAATTTGTCC
Found at i:4120 original size:27 final size:26
Alignment explanation
Indices: 4083--4167 Score: 89
Period size: 27 Copynumber: 3.0 Consensus size: 26
4073 CCAAACACCT
4083 TATTACTCCTTATATTTGTACAAGGTG
1 TATT-CTCCTTATATTTGTACAAGGTG
4110 TATTCTCCCTTATTATATTTGTACAAGGTG
1 TATTCT-CC---TTATATTTGTACAAGGTG
* * *
4140 CTATTCTCTTTCTATTTGTACAAAGTG
1 -TATTCTCCTTATATTTGTACAAGGTG
4167 T
1 T
4168 TATTTTTTAG
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
26 3 0.06
27 22 0.44
30 19 0.38
31 6 0.12
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (26 bp):
TATTCTCCTTATATTTGTACAAGGTG
Found at i:4399 original size:125 final size:125
Alignment explanation
Indices: 4177--4426 Score: 482
Period size: 125 Copynumber: 2.0 Consensus size: 125
4167 TTATTTTTTA
*
4177 GTATAGTTTTCAGTATGTGTAGTCTTCAGGCCTCTCGCTATTTGTTTCACGGTACAAAGTGTTCT
1 GTATAGTTTTCAGTATGTGTAGTCTTCAGGCCTCTCGCTATTTGTTTCACGGTACAAAGTGTTAT
4242 TTTTAGTATAGTTATTTTGTACATGTAGCTATATATGGAACACTACTAATACATATATTT
66 TTTTAGTATAGTTATTTTGTACATGTAGCTATATATGGAACACTACTAATACATATATTT
*
4302 GTATAGTTTTCAGTATGTGTAGTCTTCAGGCCTCTCGCTGTTTGTTTCACGGTACAAAGTGTTAT
1 GTATAGTTTTCAGTATGTGTAGTCTTCAGGCCTCTCGCTATTTGTTTCACGGTACAAAGTGTTAT
4367 TTTTAGTATAGTTATTTTGTACATGTAGCTATATATGGAACACTACTAATACATATATTT
66 TTTTAGTATAGTTATTTTGTACATGTAGCTATATATGGAACACTACTAATACATATATTT
4427 TAGGCCTCCT
Statistics
Matches: 123, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 123 1.00
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (125 bp):
GTATAGTTTTCAGTATGTGTAGTCTTCAGGCCTCTCGCTATTTGTTTCACGGTACAAAGTGTTAT
TTTTAGTATAGTTATTTTGTACATGTAGCTATATATGGAACACTACTAATACATATATTT
Found at i:9151 original size:24 final size:24
Alignment explanation
Indices: 9117--9256 Score: 163
Period size: 24 Copynumber: 5.7 Consensus size: 24
9107 CCGCTAGAGC
* * *
9117 TAACGGTGGTGGACCTAATAGGGT
1 TAACGGCGGTGGAGCTAATGGGGT
9141 TAACGGCGGTGGAGCTAATGGGGT
1 TAACGGCGGTGGAGCTAATGGGGT
* *
9165 TAACGACGGTGGAGCTAATGGGGC
1 TAACGGCGGTGGAGCTAATGGGGT
* *
9189 TAACGGCGGCGGTGAAGCTAATGCGGT
1 TAA---CGGCGGTGGAGCTAATGGGGT
*
9216 TAACGGCGATGGAGCTAATGGGGT
1 TAACGGCGGTGGAGCTAATGGGGT
* *
9240 TCACGGTGGTGGAGCTA
1 TAACGGCGGTGGAGCTA
9257 TTGTAGGAGT
Statistics
Matches: 98, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
24 78 0.80
27 20 0.20
ACGTcount: A:0.23, C:0.15, G:0.41, T:0.21
Consensus pattern (24 bp):
TAACGGCGGTGGAGCTAATGGGGT
Found at i:9755 original size:55 final size:52
Alignment explanation
Indices: 9645--9776 Score: 185
Period size: 55 Copynumber: 2.5 Consensus size: 52
9635 ACCTTTCTCG
* * *
9645 TCTAATGTGATTAATGACTATTTTC-TATTAGTATCGATTTGGGATTTCTTT
1 TCTAATGTGATTGATGACTTTTTTCTTATTAGTATCGATCTGGGATTTCTTT
*
9696 TCTAATGTGATTGATGACTTTTTTCTATTAATTAGTATCTATCTGGGATTTCTTT
1 TCTAATGTGATTGATGACTTTTTTC--TT-ATTAGTATCGATCTGGGATTTCTTT
*
9751 TCTAATGTGATTGATTACTTTTTTCT
1 TCTAATGTGATTGATGACTTTTTTCT
9777 GGGATGTGTT
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
51 23 0.32
53 1 0.01
54 1 0.01
55 47 0.65
ACGTcount: A:0.22, C:0.11, G:0.14, T:0.53
Consensus pattern (52 bp):
TCTAATGTGATTGATGACTTTTTTCTTATTAGTATCGATCTGGGATTTCTTT
Found at i:10401 original size:60 final size:60
Alignment explanation
Indices: 10328--10440 Score: 226
Period size: 60 Copynumber: 1.9 Consensus size: 60
10318 CTGCTGCCAG
10328 TCATGAATTTTTACATTTGGCCCAACTTAAATTGTGTGAAAAAAGCTTGGTTCCTCCCAA
1 TCATGAATTTTTACATTTGGCCCAACTTAAATTGTGTGAAAAAAGCTTGGTTCCTCCCAA
10388 TCATGAATTTTTACATTTGGCCCAACTTAAATTGTGTGAAAAAAGCTTGGTTC
1 TCATGAATTTTTACATTTGGCCCAACTTAAATTGTGTGAAAAAAGCTTGGTTC
10441 TATTCTATGC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (60 bp):
TCATGAATTTTTACATTTGGCCCAACTTAAATTGTGTGAAAAAAGCTTGGTTCCTCCCAA
Done.