Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012461.1 Corchorus capsularis cultivar CVL-1 contig12482, 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: 35104
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:660 original size:120 final size:120
Alignment explanation
Indices: 447--666 Score: 345
Period size: 120 Copynumber: 1.8 Consensus size: 120
437 AATTAATTAA
447 GTTTTAAATATTTCAATCTAGTCTCTAGAGGACACATGTCACCCTTCAAGACCCGCTTGTGTAGT
1 GTTTTAAATATTTCAATCTAGTCTCTAGAGGACACATGTCACCCTTCAAGACCCGCTTGTGTAGT
* * * *
512 CTTCTAAACTCCACTGACGGTGTATTGTATGATTTGCCTATTACTTATTACTATT
66 CTGCTAAACTCCACTAACAGTGTATTGTATAATTTGCCTATTACTTATTACTATT
*
567 GTTTTAAATATTTCAATCTAGTC-CTTAGTA-GACACATGTCACCCTTCAGGACCCGCTTGTGTA
1 GTTTTAAATATTTCAATCTAGTCTC-TAG-AGGACACATGTCACCCTTCAAGACCCGCTTGTGTA
* *
630 GTCTGCTAAACTCCATTAACATTGTATTGTATAATTT
64 GTCTGCTAAACTCCACTAACAGTGTATTGTATAATTT
667 ACCTTAGTTT
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
119 1 0.01
120 89 0.98
121 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (120 bp):
GTTTTAAATATTTCAATCTAGTCTCTAGAGGACACATGTCACCCTTCAAGACCCGCTTGTGTAGT
CTGCTAAACTCCACTAACAGTGTATTGTATAATTTGCCTATTACTTATTACTATT
Found at i:4392 original size:25 final size:25
Alignment explanation
Indices: 4364--4436 Score: 66
Period size: 25 Copynumber: 3.1 Consensus size: 25
4354 TGATAAAGTT
4364 TCGGACTTGATGGTGGGTTTCAGAC
1 TCGGACTTGATGGTGGGTTTCAGAC
* * ** *
4389 TCGGCCTTGTTGAAGAG--TC---C
1 TCGGACTTGATGGTGGGTTTCAGAC
4409 TCGGACTTGATGGTGGGTTTCAGAC
1 TCGGACTTGATGGTGGGTTTCAGAC
4434 TCG
1 TCG
4437 AAATTGGCAA
Statistics
Matches: 33, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
20 13 0.39
22 2 0.06
23 2 0.06
25 16 0.48
ACGTcount: A:0.15, C:0.19, G:0.34, T:0.32
Consensus pattern (25 bp):
TCGGACTTGATGGTGGGTTTCAGAC
Found at i:14016 original size:48 final size:47
Alignment explanation
Indices: 13962--14185 Score: 125
Period size: 48 Copynumber: 4.9 Consensus size: 47
13952 ACCACCACCA
13962 CCACCACCTCCACGTTACAAATATAAATCACCACCACCGCCGTCTCCT
1 CCACCACCTCCACGTTACAAATATAAATCACCACC-CCGCCGTCTCCT
** ** * *
14010 CCACCACCTTTTA--TCTACAAATGCAAGTCACCA-CCC-CC-AC-CC-
1 CCACCACC-TCCACGT-TACAAATATAAATCACCACCCCGCCGTCTCCT
* * * *
14052 CCACCTCCACCACGTTACAAATATAGATCACCGCCGCCGCCGTCTCCT
1 CCACCACCTCCACGTTACAAATATAAATCACCACC-CCGCCGTCTCCT
** * * * * *
14100 CCACCACCTTTTA--TCTACAGATACAAGTCACCA-CCC-CC-ACT--A
1 CCACCACC-TCCACGT-TACAAATATAAATCACCACCCCGCCGTCTCCT
*
14142 CCACCACCTCCACGTTACAATTATAAATCACCACCACCGCCGTC
1 CCACCACCTCCACGTTACAAATATAAATCACCACC-CCGCCGTC
14186 GCCTGTAATT
Statistics
Matches: 124, Mismatches: 34, Indels: 38
0.63 0.17 0.19
Matches are distributed among these distances:
41 3 0.02
42 42 0.34
43 6 0.05
44 7 0.06
45 8 0.06
46 6 0.05
47 6 0.05
48 43 0.35
49 3 0.02
ACGTcount: A:0.28, C:0.46, G:0.07, T:0.19
Consensus pattern (47 bp):
CCACCACCTCCACGTTACAAATATAAATCACCACCCCGCCGTCTCCT
Found at i:14103 original size:90 final size:89
Alignment explanation
Indices: 13916--14185 Score: 400
Period size: 90 Copynumber: 3.0 Consensus size: 89
13906 ATTCATACAA
* * *
13916 GTCTCCTCCTCCACCTTTTATCTACAAATACAAATCACCACCACCACCACCACCT--CCACGTTA
1 GTCTCCTCCACCACCTTTTATCTACAAATACAAGTCACCACCCCCACCACCACCTCCCCACGTTA
13979 CAAATATAAATCACCACCACCGCC
66 CAAATATAAATCACCACCACCGCC
* *
14003 GTCTCCTCCACCACCTTTTATCTACAAATGCAAGTCACCACCCCCACCCCCACCTCCACCACGTT
1 GTCTCCTCCACCACCTTTTATCTACAAATACAAGTCACCACCCCCACCACCACCTCC-CCACGTT
* * *
14068 ACAAATATAGATCACCGCCGCCGCC
65 ACAAATATAAATCACCACCACCGCC
* * *
14093 GTCTCCTCCACCACCTTTTATCTACAGATACAAGTCACCACCCCCACTACCACCACCTCCACGTT
1 GTCTCCTCCACCACCTTTTATCTACAAATACAAGTCACCACCCCCACCACCACCTCC-CCACGTT
*
14158 ACAATTATAAATCACCACCACCGCC
65 ACAAATATAAATCACCACCACCGCC
14183 GTC
1 GTC
14186 GCCTGTAATT
Statistics
Matches: 162, Mismatches: 18, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
87 50 0.31
90 112 0.69
ACGTcount: A:0.29, C:0.45, G:0.06, T:0.20
Consensus pattern (89 bp):
GTCTCCTCCACCACCTTTTATCTACAAATACAAGTCACCACCCCCACCACCACCTCCCCACGTTA
CAAATATAAATCACCACCACCGCC
Found at i:14795 original size:13 final size:13
Alignment explanation
Indices: 14777--14806 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
14767 TTTACCCAAC
14777 AAAAGAAAAAGAA
1 AAAAGAAAAAGAA
14790 AAAAGAAAAAGAA
1 AAAAGAAAAAGAA
14803 AAAA
1 AAAA
14807 AACCCTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAGAA
Found at i:21041 original size:17 final size:17
Alignment explanation
Indices: 21015--21056 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
21005 ATTGTCTCCC
* *
21015 AAATAGAAAAATACAAA
1 AAATAAAAAAATAAAAA
21032 AAATAAAAAAATAAAAA
1 AAATAAAAAAATAAAAA
21049 AAATAAAA
1 AAATAAAA
21057 GTAGTTTCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.12
Consensus pattern (17 bp):
AAATAAAAAAATAAAAA
Found at i:21050 original size:8 final size:8
Alignment explanation
Indices: 21015--21056 Score: 57
Period size: 8 Copynumber: 5.0 Consensus size: 8
21005 ATTGTCTCCC
*
21015 AAATAGAA
1 AAATAAAA
21023 AAATACAAA
1 AAATA-AAA
21032 AAATAAAA
1 AAATAAAA
21040 AAATAAAAA
1 AAAT-AAAA
21049 AAATAAAA
1 AAATAAAA
21057 GTAGTTTCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 16 0.52
9 15 0.48
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.12
Consensus pattern (8 bp):
AAATAAAA
Found at i:27997 original size:6 final size:6
Alignment explanation
Indices: 27986--28038 Score: 70
Period size: 6 Copynumber: 8.7 Consensus size: 6
27976 TTGATTGTTT
* * *
27986 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTTG TTGTTG TTGTTG TTGTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG -TTTTTG TTTTTG TTTTTG TTTTTG
28035 TTTT
1 TTTT
28039 CATTGGATGG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
6 38 0.86
7 6 0.14
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (6 bp):
TTTTTG
Found at i:28003 original size:12 final size:12
Alignment explanation
Indices: 27980--28038 Score: 73
Period size: 12 Copynumber: 4.8 Consensus size: 12
27970 AAATTGTTGA
*
27980 TTGTTTTTTTTG
1 TTGTTGTTTTTG
*
27992 TTTTTGTTTTTG
1 TTGTTGTTTTTG
*
28004 TTTTTGTTTTTTG
1 TTGTTG-TTTTTG
*
28017 TTGTTGTTGTTG
1 TTGTTGTTTTTG
28029 TTGTTGTTTT
1 TTGTTGTTTT
28039 CATTGGATGG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
12 30 0.73
13 11 0.27
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (12 bp):
TTGTTGTTTTTG
Found at i:28014 original size:19 final size:19
Alignment explanation
Indices: 27980--28030 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
27970 AAATTGTTGA
*
27980 TTGTTTTTTTTG-TTTTTG
1 TTGTTGTTTTTGTTTTTTG
*
27998 TTTTTGTTTTTGTTTTTTG
1 TTGTTGTTTTTGTTTTTTG
*
28017 TTGTTGTTGTTGTT
1 TTGTTGTTTTTGTT
28031 GTTGTTTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 10 0.36
19 18 0.64
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (19 bp):
TTGTTGTTTTTGTTTTTTG
Found at i:28022 original size:3 final size:3
Alignment explanation
Indices: 27973--28036 Score: 60
Period size: 3 Copynumber: 21.7 Consensus size: 3
27963 TTCATACAAA
* * * * *
27973 TTG TTG ATTG TTT TTT TTG TTT TTG TTT TTG TTT TTG TT- TT- TTG
1 TTG TTG -TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
28017 TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TT
28037 TTCATTGGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
2 4 0.08
3 44 0.86
4 3 0.06
ACGTcount: A:0.02, C:0.00, G:0.22, T:0.77
Consensus pattern (3 bp):
TTG
Found at i:28023 original size:25 final size:25
Alignment explanation
Indices: 27973--28038 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
27963 TTCATACAAA
*
27973 TTGTTGATTGTT-TTTTTTGTTTTTG
1 TTGTTG-TTGTTGTTTTTTGTTGTTG
* *
27998 TTTTTGTTTTTGTTTTTTGTTGTTG
1 TTGTTGTTGTTGTTTTTTGTTGTTG
28023 TTGTTGTTGTTGTTTT
1 TTGTTGTTGTTGTTTT
28039 CATTGGATGG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 4 0.11
25 31 0.89
ACGTcount: A:0.02, C:0.00, G:0.21, T:0.77
Consensus pattern (25 bp):
TTGTTGTTGTTGTTTTTTGTTGTTG
Found at i:28596 original size:42 final size:41
Alignment explanation
Indices: 28550--28640 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 41
28540 GGTCGTATTG
*
28550 CTTCTGTCCAGACCCAAAATCAGCCTCAACAAGGTCCTA-GCA
1 CTTCTGTCCAGA-CAAAAATCAGCCTCAACAAGGTCCTACG-A
* *
28592 CTTCTGTTTCAGACAAAAATCAGCCTCAACCAGGTCCTACGA
1 CTTCTG-TCCAGACAAAAATCAGCCTCAACAAGGTCCTACGA
28634 CTTCTGT
1 CTTCTGT
28641 TCCAACTACT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
41 1 0.02
42 37 0.84
43 6 0.14
ACGTcount: A:0.29, C:0.33, G:0.14, T:0.24
Consensus pattern (41 bp):
CTTCTGTCCAGACAAAAATCAGCCTCAACAAGGTCCTACGA
Found at i:34383 original size:2 final size:2
Alignment explanation
Indices: 34371--34404 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
34361 TTACTATTAT
* *
34371 TA TA TA CA TA TA TA CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34405 AATGACGAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Done.