Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013743.1 Corchorus capsularis cultivar CVL-1 contig13764, 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: 9807
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:111 original size:31 final size:29
Alignment explanation
Indices: 45--124 Score: 115
Period size: 29 Copynumber: 2.7 Consensus size: 29
35 CTCATTTTTG
* *
45 AAACGTAAGGGATTAATTTGTCCCAAAAA
1 AAACATAAGGGATTATTTTGTCCCAAAAA
74 AAACATAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTATTTTGTCCCAAAA--A
*
105 AAACATAAGGGATTTTTTTG
1 AAACATAAGGGATTATTTTG
125 GGTATTTAGC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 26 0.57
31 20 0.43
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (29 bp):
AAACATAAGGGATTATTTTGTCCCAAAAA
Found at i:1515 original size:9 final size:9
Alignment explanation
Indices: 1501--1527 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1491 TTAAGCTTTA
1501 AGTGTTCTT
1 AGTGTTCTT
1510 AGTGTTCTT
1 AGTGTTCTT
1519 AGTGTTCTT
1 AGTGTTCTT
1528 CATTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.22, T:0.56
Consensus pattern (9 bp):
AGTGTTCTT
Found at i:1977 original size:31 final size:31
Alignment explanation
Indices: 1919--1977 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
1909 TTGGACGAAA
* * *
1919 TAAAAGGTTTGATACTAAGTTGTGATTTTCT
1 TAAAAGGTTTGATACCAAATTGAGATTTTCT
*
1950 TAAAAGGTTTGGTACCAAATTGAGATTT
1 TAAAAGGTTTGATACCAAATTGAGATTT
1978 CAGCCTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (31 bp):
TAAAAGGTTTGATACCAAATTGAGATTTTCT
Found at i:4869 original size:3 final size:3
Alignment explanation
Indices: 4861--4898 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
4851 CATATAGTTT
4861 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4899 CGGTATTCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5101 original size:29 final size:29
Alignment explanation
Indices: 5055--5111 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
5045 CCGACCCATA
*
5055 TTAGTGAGCTCATATAGTCACGTATGTTG
1 TTAGTGAGCTCATATAGTCACATATGTTG
*
5084 TTAGTGAGCTCATGTAGTCACATATGTT
1 TTAGTGAGCTCATATAGTCACATATGTT
5112 CTGAGTGGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.39
Consensus pattern (29 bp):
TTAGTGAGCTCATATAGTCACATATGTTG
Found at i:5118 original size:29 final size:29
Alignment explanation
Indices: 5057--5118 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
5047 GACCCATATT
* * *
5057 AGTGAGCTCATATAGTCACGTATGTTGTT
1 AGTGAGCTCATATAGTCACATATGTTCTG
*
5086 AGTGAGCTCATGTAGTCACATATGTTCTG
1 AGTGAGCTCATATAGTCACATATGTTCTG
5115 AGTG
1 AGTG
5119 GATTAAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (29 bp):
AGTGAGCTCATATAGTCACATATGTTCTG
Found at i:7396 original size:125 final size:125
Alignment explanation
Indices: 7147--7403 Score: 315
Period size: 127 Copynumber: 2.0 Consensus size: 125
7137 ACTTGGTTAA
*
7147 TTACTAACAAGGCCCTCAATTAGTTTCTCATCATTCCCTTTTCCTCCAGTCCTTTTTTGTAATTC
1 TTACTAACAAGGCCCTCAATTAGTTTCTCACCATTCCCTTTTCCTCCAGTCCTTTTTTGTAATTC
* * * *
7212 AAGGGTTTTTAACCAGTTGAATGTGAAAGTATTTATTGATCATAAAATCATGTATTATTTAT
66 AAGGGTCTTTAACCAGTTCAA-GT-AAAGTATTTATTGACCATAAAATCATATATTATTTAT
* * * * * *
7274 TTACTAAGAAGGTCCT-AACTTAGTTTCTCACCATTGCTTTTTCCTCTAGTCTTTTTTTTTGTAA
1 TTACTAACAAGGCCCTCAA-TTAGTTTCTCACCATTCCCTTTTCCTCCAGTC--CTTTTTTGTAA
* *
7338 TTACAAGGGTCTTTAACCAGTTCAA-T-CA-TGTTTATTGACCATAAAATCATATATTATTTAT
63 TT-CAAGGGTCTTTAACCAGTTCAAGTAAAGTATTTATTGACCATAAAATCATATATTATTTAT
7399 TTACT
1 TTACT
7404 TCATCAAACC
Statistics
Matches: 113, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
125 35 0.31
126 3 0.03
127 42 0.37
128 1 0.01
129 12 0.11
130 20 0.18
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.44
Consensus pattern (125 bp):
TTACTAACAAGGCCCTCAATTAGTTTCTCACCATTCCCTTTTCCTCCAGTCCTTTTTTGTAATTC
AAGGGTCTTTAACCAGTTCAAGTAAAGTATTTATTGACCATAAAATCATATATTATTTAT
Found at i:9378 original size:2 final size:2
Alignment explanation
Indices: 9371--9408 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
9361 TTCAAAGGCA
9371 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9409 ACTTTCTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9396 original size:17 final size:17
Alignment explanation
Indices: 9374--9407 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
9364 AAAGGCAATA
9374 TATATATATATATATAT
1 TATATATATATATATAT
9391 TATATATATATATATAT
1 TATATATATATATATAT
9408 AACTTTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATAT
Done.