Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012969.1 Corchorus olitorius cultivar O-4 contig13002, 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: 16841
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:877 original size:18 final size:18
Alignment explanation
Indices: 849--885 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
839 GCCTATAATT
849 AATTAAAACTAATGTAGAA
1 AATTAAAACTAATGT-GAA
868 AATT-AAACTAATGTGAA
1 AATTAAAACTAATGTGAA
885 A
1 A
886 GCATGCATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 10 0.56
19 4 0.22
ACGTcount: A:0.57, C:0.05, G:0.11, T:0.27
Consensus pattern (18 bp):
AATTAAAACTAATGTGAA
Found at i:4399 original size:21 final size:21
Alignment explanation
Indices: 4375--4414 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4365 AAATGGCAAA
*
4375 ATCCATAATTTCTCCAAATTG
1 ATCCATAATTGCTCCAAATTG
4396 ATCCATAATTGCTCCAAAT
1 ATCCATAATTGCTCCAAAT
4415 CTTCATAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (21 bp):
ATCCATAATTGCTCCAAATTG
Found at i:5185 original size:30 final size:30
Alignment explanation
Indices: 5133--5215 Score: 132
Period size: 30 Copynumber: 2.8 Consensus size: 30
5123 CGTTTGGATG
5133 TTTTGCCCCTTGAACT-TCAATTTTAGACA
1 TTTTGCCCCTTGAACTCTCAATTTTAGACA
* * *
5162 TTTTGCCTCATGAACTCTCAATTTTGGACA
1 TTTTGCCCCTTGAACTCTCAATTTTAGACA
5192 TTTTGCCCCTTGAACTCTCAATTT
1 TTTTGCCCCTTGAACTCTCAATTT
5216 GAGCCTCTGT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 14 0.29
30 34 0.71
ACGTcount: A:0.22, C:0.25, G:0.11, T:0.42
Consensus pattern (30 bp):
TTTTGCCCCTTGAACTCTCAATTTTAGACA
Found at i:5356 original size:30 final size:30
Alignment explanation
Indices: 5295--5403 Score: 123
Period size: 31 Copynumber: 3.6 Consensus size: 30
5285 CGTGGACAGA
* * * *
5295 GTTTTGGACGTTTTGTTCTCTAAAATTGTAC
1 GTTTTGGACGTTTTG-CCCCTGAACTTGTAC
*
5326 GTTTTGGACATTTTGCCCCTGAACTTGTAC
1 GTTTTGGACGTTTTGCCCCTGAACTTGTAC
*
5356 GTTTTGAACGTTTTGCCCCCTGAACTTGTAC
1 GTTTTGGACGTTTTG-CCCCTGAACTTGTAC
*
5387 --TTTGGATGTTTTGCCCC
1 GTTTTGGACGTTTTGCCCC
5404 CTAAACAACT
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
28 4 0.06
29 11 0.16
30 24 0.35
31 29 0.43
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.43
Consensus pattern (30 bp):
GTTTTGGACGTTTTGCCCCTGAACTTGTAC
Found at i:5400 original size:29 final size:30
Alignment explanation
Indices: 5320--5405 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
5310 TTCTCTAAAA
* *
5320 TTGTACGTTTTGGACATTTTG-CCCCTGAAC
1 TTGTACG-TTTGAACGTTTTGCCCCCTGAAC
5350 TTGTACGTTTTGAACGTTTTGCCCCCTGAAC
1 TTGTACG-TTTGAACGTTTTGCCCCCTGAAC
* *
5381 TTGTAC-TTTGGATGTTTTGCCCCCT
1 TTGTACGTTTGAACGTTTTGCCCCCT
5406 AAACAACTAG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
29 17 0.33
30 19 0.37
31 15 0.29
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (30 bp):
TTGTACGTTTGAACGTTTTGCCCCCTGAAC
Found at i:5511 original size:29 final size:30
Alignment explanation
Indices: 5470--5530 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
5460 ACGGAGGCTC
*
5470 AAATTGAAAGTTCAGGGGGCAAAATGTCCA
1 AAATTGAAAGTTCAGGGGGCAAAACGTCCA
*
5500 AAATTG-AAGTTCAGGGTGCAAAACGTCCA
1 AAATTGAAAGTTCAGGGGGCAAAACGTCCA
5529 AA
1 AA
5531 CACTACAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 23 0.79
30 6 0.21
ACGTcount: A:0.41, C:0.15, G:0.25, T:0.20
Consensus pattern (30 bp):
AAATTGAAAGTTCAGGGGGCAAAACGTCCA
Found at i:6102 original size:10 final size:10
Alignment explanation
Indices: 6087--6114 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
6077 CGTTTTAGTC
6087 AAATATCCGT
1 AAATATCCGT
6097 AAATATCCGT
1 AAATATCCGT
6107 AAATATCC
1 AAATATCC
6115 ATATTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (10 bp):
AAATATCCGT
Found at i:7271 original size:13 final size:13
Alignment explanation
Indices: 7240--7277 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
7230 CATTGATACC
*
7240 TCGATAAATCCG-
1 TCGATATATCCGT
*
7252 CCGATATATCCGT
1 TCGATATATCCGT
7265 TCGATATATCCGT
1 TCGATATATCCGT
7278 GGATATCTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (13 bp):
TCGATATATCCGT
Found at i:9128 original size:22 final size:21
Alignment explanation
Indices: 9076--9129 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
9066 TGCTTCTTGA
9076 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
9097 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
9116 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
9130 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Done.