Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015188.1 Corchorus capsularis cultivar CVL-1 contig15209, 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: 45796
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:8432 original size:4 final size:4
Alignment explanation
Indices: 8423--8456 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
8413 TAAATATTAC
*
8423 TTTA TTTA TTTA GTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
8457 CGTAAGTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:8665 original size:6 final size:6
Alignment explanation
Indices: 8648--8686 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
8638 CTAAAAGCAA
* * *
8648 AAAAAA AAAAAG AAAAAG GAAAAG AAAAAG AAAAGG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
8687 GCTAATAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:8675 original size:17 final size:17
Alignment explanation
Indices: 8649--8686 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
8639 TAAAAGCAAA
8649 AAAAAAAAAAGAAAAAGG
1 AAAAAAAAAAG-AAAAGG
*
8667 AAAAGAAAAAGAAAAGG
1 AAAAAAAAAAGAAAAGG
8684 AAA
1 AAA
8687 GCTAATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGAAAAGG
Found at i:8970 original size:14 final size:12
Alignment explanation
Indices: 8953--8989 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
8943 AAAAAAAGTA
8953 ATATA-ATATAT
1 ATATATATATAT
8964 AT-TATAT-TAT
1 ATATATATATAT
8974 ATATATATATAT
1 ATATATATATAT
8986 ATAT
1 ATAT
8990 GGAATATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
10 7 0.30
11 9 0.39
12 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
ATATATATATAT
Found at i:8996 original size:19 final size:19
Alignment explanation
Indices: 8952--8998 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
8942 GAAAAAAAGT
8952 AATATAATATATATTATAT-
1 AATAT-ATATATATTATATG
*
8971 TATATATATATATATATATGG
1 AATATATATATAT-TATAT-G
8992 AATATAT
1 AATATAT
8999 TGTTGGAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 8 0.35
19 9 0.39
21 6 0.26
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (19 bp):
AATATATATATATTATATG
Found at i:8998 original size:2 final size:2
Alignment explanation
Indices: 8953--8989 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
8943 AAAAAAAGTA
8953 AT AT A- AT AT AT AT -T AT AT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8990 GGAATATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:9155 original size:10 final size:10
Alignment explanation
Indices: 9140--9165 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
9130 CGAAATTTGA
9140 AATTCGTCCG
1 AATTCGTCCG
9150 AATTCGTCCG
1 AATTCGTCCG
9160 AATTCG
1 AATTCG
9166 AACCCGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (10 bp):
AATTCGTCCG
Found at i:9238 original size:16 final size:16
Alignment explanation
Indices: 9217--9257 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
9207 GAACTCGTCT
* *
9217 CGAACCCGAAATTACC
1 CGAACCCGAAAATACA
9233 CGAACCCGAAAATACA
1 CGAACCCGAAAATACA
9249 CGAACCCGA
1 CGAACCCGA
9258 GACAACTCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.41, C:0.37, G:0.15, T:0.07
Consensus pattern (16 bp):
CGAACCCGAAAATACA
Found at i:10070 original size:16 final size:16
Alignment explanation
Indices: 10030--10072 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
10020 ACCCGACCCG
*
10030 ACCCGAACCCGAAAAA
1 ACCCGAACCCAAAAAA
* *
10046 ACTCAAACCCAAAAAA
1 ACCCGAACCCAAAAAA
10062 ACCCGAACCCA
1 ACCCGAACCCA
10073 CCCAAACCCG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.51, C:0.40, G:0.07, T:0.02
Consensus pattern (16 bp):
ACCCGAACCCAAAAAA
Found at i:21864 original size:31 final size:31
Alignment explanation
Indices: 21826--21887 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
21816 CAATGCTGAC
21826 TTAAATTTAAAATATAAATAATACAGACAAT
1 TTAAATTTAAAATATAAATAATACAGACAAT
21857 TTAAATTTAAAATATAAATAATACAGACAAT
1 TTAAATTTAAAATATAAATAATACAGACAAT
21888 CGTCAGAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.32
Consensus pattern (31 bp):
TTAAATTTAAAATATAAATAATACAGACAAT
Found at i:26215 original size:7 final size:7
Alignment explanation
Indices: 26203--26242 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
26193 GATAATATGA
26203 AAAAAAC
1 AAAAAAC
26210 AAAAAAC
1 AAAAAAC
26217 AAAAAAC
1 AAAAAAC
*
26224 AAAAAGC
1 AAAAAAC
*
26231 AAAAAGC
1 AAAAAAC
26238 AAAAA
1 AAAAA
26243 CCTCATGGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.82, C:0.12, G:0.05, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:29621 original size:2 final size:2
Alignment explanation
Indices: 29616--29658 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
29606 TTCAAAAAAA
29616 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
29658 A
1 A
29659 TTCCATATCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:37031 original size:120 final size:120
Alignment explanation
Indices: 36813--37121 Score: 503
Period size: 120 Copynumber: 2.6 Consensus size: 120
36803 TCATAAGTTC
* *
36813 CCTTGGCAGATTCTAAAGTCTCTTCACCTTTGCTTTTGGCTGCGTCATAGCCTTGTTTGGCTTTG
1 CCTTGGCAGATTCTAAAGTCTCTTCACCTTTTCCTTTGGCTGCGTCATAGCCTTGTTTGGCTTTG
*
36878 TCCTTGGCCCACCTAAGATTCTCCTCTGCTTCCGCTGTCTTCTTCTTTGTTTCAT
66 TCCTTGGCCCACCTAAGATTCTCCTCTGCTTCCGCCGTCTTCTTCTTTGTTTCAT
* *
36933 CCTTGGCAGACTCTAAAGTCTCTTCACCTTTTCCTTTGGCTGCGTTATAGCCTTGTTTGGCTTTG
1 CCTTGGCAGATTCTAAAGTCTCTTCACCTTTTCCTTTGGCTGCGTCATAGCCTTGTTTGGCTTTG
* * *
36998 TCCTTGGCCCACCTCAGGTTCTCCTCTGTTTCCGCCGTCTTCTTCTTTGTTTCAT
66 TCCTTGGCCCACCTAAGATTCTCCTCTGCTTCCGCCGTCTTCTTCTTTGTTTCAT
* *
37053 CCTTGGCAGATTCTAAAGTCTCTTCACC-TTTGCTTCTGGCTGCCTCATAGCCTTGTTTGGCTTT
1 CCTTGGCAGATTCTAAAGTCTCTTCACCTTTTCCTT-TGGCTGCGTCATAGCCTTGTTTGGCTTT
*
37117 CTCCT
65 GTCCT
37122 CTGTTTCCGC
Statistics
Matches: 175, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
119 6 0.03
120 169 0.97
ACGTcount: A:0.10, C:0.30, G:0.17, T:0.42
Consensus pattern (120 bp):
CCTTGGCAGATTCTAAAGTCTCTTCACCTTTTCCTTTGGCTGCGTCATAGCCTTGTTTGGCTTTG
TCCTTGGCCCACCTAAGATTCTCCTCTGCTTCCGCCGTCTTCTTCTTTGTTTCAT
Found at i:41727 original size:13 final size:12
Alignment explanation
Indices: 41705--41737 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 12
41695 TTCGTTTGAC
41705 TTTTTTTTTCTT
1 TTTTTTTTTCTT
41717 TTTTCTTTTTCTT
1 TTTT-TTTTTCTT
41730 TTTTTTTT
1 TTTTTTTT
41738 GGTCAAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:45546 original size:13 final size:14
Alignment explanation
Indices: 45528--45556 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
45518 CCACCAAGCC
45528 AAAAAAAAAT-AAT
1 AAAAAAAAATCAAT
45541 AAAAAAAAATCAAT
1 AAAAAAAAATCAAT
45555 AA
1 AA
45557 TGTATCCGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAAAAAAATCAAT
Done.