Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006390.1 Corchorus capsularis cultivar CVL-1 contig06411, 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: 4993
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.33
Found at i:944 original size:106 final size:108
Alignment explanation
Indices: 737--1020 Score: 360
Period size: 106 Copynumber: 2.6 Consensus size: 108
727 AACCTTTATT
* * *
737 ACTGAAATCTT-TCTGAAATGACTGCACCGGATCTATTCGAGATCAACTCTGACCACCGAAAACT
1 ACTGAAAACTTCT-TGAAATGACCGCACCGGATCAATTCGAGATCAACTCTGACCACCGAAAACT
*
801 TCTTGAGACGACCACACCGTATCAATTGGAGATCAACTCTGACC
65 TCTTGAGACGACCACACCGGATCAATTGGAGATCAACTCTGACC
* * *
845 ACTGAAAACTTCTTGAAATGACCGCAACGG-TCCATTCGAGATCAACTCTGACCACTGAAAA-TT
1 ACTGAAAACTTCTTGAAATGACCGCACCGGATCAATTCGAGATCAACTCTGACCACCGAAAACTT
* * *
908 TTTTAGACGACCACACCGGATCAATTAGG-GGTCAACTCTGACC
66 CTTGAGACGACCACACCGGATCAATT-GGAGATCAACTCTGACC
* * * * * ***
951 ACCGAAAACTCCTTGGAATGACCGCACCGGATCAATTTGAGATCAACTCTGATCATTAAAAACTT
1 ACTGAAAACTTCTTGAAATGACCGCACCGGATCAATTCGAGATCAACTCTGACCACCGAAAACTT
1016 CTTGA
66 CTTGA
1021 AATGAGATCA
Statistics
Matches: 152, Mismatches: 20, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
106 64 0.42
107 57 0.38
108 30 0.20
109 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (108 bp):
ACTGAAAACTTCTTGAAATGACCGCACCGGATCAATTCGAGATCAACTCTGACCACCGAAAACTT
CTTGAGACGACCACACCGGATCAATTGGAGATCAACTCTGACC
Found at i:1025 original size:54 final size:54
Alignment explanation
Indices: 737--1025 Score: 314
Period size: 54 Copynumber: 5.4 Consensus size: 54
727 AACCTTTATT
* * *
737 ACTGAAATCTT-TCTGAAATGACTGCACCGGATCTATTCGAGATCAACTCTGACC
1 ACTGAAAACTTCT-TGAAATGACCGCACCGGATCAATTCGAGATCAACTCTGACC
* * * * * *
791 ACCGAAAACTTCTTGAGACGACCACACCGTATCAATTGGAGATCAACTCTGACC
1 ACTGAAAACTTCTTGAAATGACCGCACCGGATCAATTCGAGATCAACTCTGACC
* *
845 ACTGAAAACTTCTTGAAATGACCGCAACGG-TCCATTCGAGATCAACTCTGACC
1 ACTGAAAACTTCTTGAAATGACCGCACCGGATCAATTCGAGATCAACTCTGACC
* * * * * * * *
898 ACTGAAAA-TTTTTTAGACGACCACACCGGATCAATTAGGGGTCAACTCTGACC
1 ACTGAAAACTTCTTGAAATGACCGCACCGGATCAATTCGAGATCAACTCTGACC
* * * * *
951 ACCGAAAACTCCTTGGAATGACCGCACCGGATCAATTTGAGATCAACTCTGATC
1 ACTGAAAACTTCTTGAAATGACCGCACCGGATCAATTCGAGATCAACTCTGACC
* *
1005 ATTAAAAACTTCTTGAAATGA
1 ACTGAAAACTTCTTGAAATGA
1026 GATCAACTCT
Statistics
Matches: 188, Mismatches: 44, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
52 15 0.08
53 55 0.29
54 117 0.62
55 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (54 bp):
ACTGAAAACTTCTTGAAATGACCGCACCGGATCAATTCGAGATCAACTCTGACC
Found at i:1027 original size:35 final size:35
Alignment explanation
Indices: 988--1155 Score: 225
Period size: 35 Copynumber: 4.8 Consensus size: 35
978 CGGATCAATT
* *
988 TGAGATCAACTCTGATCATTAAAAACTTCTTGAAA
1 TGAGATCAACTCTGATCGTTGAAAACTTCTTGAAA
*
1023 TGAGATCAACTCTGATCGTTGAAAACTTCTTGGAA
1 TGAGATCAACTCTGATCGTTGAAAACTTCTTGAAA
*
1058 TGAGATCAACTCTGATC-TTCGAAAACTTCTTGGAA
1 TGAGATCAACTCTGATCGTT-GAAAACTTCTTGAAA
* *
1093 TGAGATCAACTCTGATCGTTGGAAACCTCTT-AGAA
1 TGAGATCAACTCTGATCGTTGAAAACTTCTTGA-AA
*
1128 TGAGATCAACTCTGCTC-TTCGAAAACTT
1 TGAGATCAACTCTGATCGTT-GAAAACTT
1156 TGAAAGATCA
Statistics
Matches: 120, Mismatches: 9, Indels: 8
0.88 0.07 0.06
Matches are distributed among these distances:
34 4 0.03
35 114 0.95
36 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (35 bp):
TGAGATCAACTCTGATCGTTGAAAACTTCTTGAAA
Found at i:1071 original size:70 final size:70
Alignment explanation
Indices: 988--1155 Score: 257
Period size: 70 Copynumber: 2.4 Consensus size: 70
978 CGGATCAATT
*
988 TGAGATCAACTCTGATCATT-AAAAACTTCTTGAAATGAGATCAACTCTGATCGTTGAAAACTTC
1 TGAGATCAACTCTGATC-TTCAAAAACTTCTTGAAATGAGATCAACTCTGATCGTTGAAAACCTC
*
1052 TTGGAA
65 TTAGAA
* * *
1058 TGAGATCAACTCTGATCTTCGAAAACTTCTTGGAATGAGATCAACTCTGATCGTTGGAAACCTCT
1 TGAGATCAACTCTGATCTTCAAAAACTTCTTGAAATGAGATCAACTCTGATCGTTGAAAACCTCT
1123 TAGAA
66 TAGAA
* *
1128 TGAGATCAACTCTGCTCTTCGAAAACTT
1 TGAGATCAACTCTGATCTTCAAAAACTT
1156 TGAAAGATCA
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
69 2 0.02
70 89 0.98
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (70 bp):
TGAGATCAACTCTGATCTTCAAAAACTTCTTGAAATGAGATCAACTCTGATCGTTGAAAACCTCT
TAGAA
Found at i:2055 original size:12 final size:12
Alignment explanation
Indices: 2040--2103 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 12
2030 TTCCTTTCTT
2040 TTTTTCTTTTTC
1 TTTTTCTTTTTC
2052 TTTTTC-TTTTC
1 TTTTTCTTTTTC
2063 TTTTT-TTTGTT-
1 TTTTTCTTT-TTC
*
2074 TGTTTTGTTTTTC
1 T-TTTTCTTTTTC
*
2087 -TTTTCTCTCTTC
1 TTTTTCT-TTTTC
2099 TTTTT
1 TTTTT
2104 TTGTTTTGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
11 18 0.42
12 18 0.42
13 7 0.16
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (12 bp):
TTTTTCTTTTTC
Found at i:2085 original size:35 final size:35
Alignment explanation
Indices: 2041--2120 Score: 110
Period size: 36 Copynumber: 2.3 Consensus size: 35
2031 TCCTTTCTTT
*
2041 TTTTCTTTTTCTTTT-TCTTTTCTTTTTTT-TGTTTG
1 TTTT-TTTTTCTTTTCTCTCTTCTTTTTTTGT-TTTG
2076 TTTTGTTTTTCTTTTCTCTCTTCTTTTTTTGTTTTG
1 TTTT-TTTTTCTTTTCTCTCTTCTTTTTTTGTTTTG
2112 TTTTTTTTT
1 TTTTTTTTT
2121 GGAACCTTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
35 19 0.46
36 21 0.51
37 1 0.02
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.82
Consensus pattern (35 bp):
TTTTTTTTTCTTTTCTCTCTTCTTTTTTTGTTTTG
Found at i:2112 original size:36 final size:34
Alignment explanation
Indices: 2041--2120 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 34
2031 TCCTTTCTTT
*
2041 TTTTCTTTTTCTTTTTCTTTTCTTTTTTTTGTTTG
1 TTTT-TTTTTCTTTTTCTCTTCTTTTTTTTGTTTG
2076 TTTTGTTTTTCTTTTCTCTCTTC-TTTTTTTGTTTTG
1 TTTT-TTTTTCTTTT-TCTCTTCTTTTTTTTG-TTTG
2112 TTTTTTTTT
1 TTTTTTTTT
2121 GGAACCTTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
35 27 0.66
36 14 0.34
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.82
Consensus pattern (34 bp):
TTTTTTTTTCTTTTTCTCTTCTTTTTTTTGTTTG
Done.