Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007894.1 Corchorus capsularis cultivar CVL-1 contig07915, 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: 49777
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:6316 original size:12 final size:12
Alignment explanation
Indices: 6270--6315 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
6260 ACTATTAACT
6270 ATATTAATTTAA
1 ATATTAATTTAA
*
6282 ATATTAATTGAA
1 ATATTAATTTAA
*
6294 ATATTAATTTTA
1 ATATTAATTTAA
6306 ATATTAATTT
1 ATATTAATTT
6316 TTATTTATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (12 bp):
ATATTAATTTAA
Found at i:6400 original size:11 final size:11
Alignment explanation
Indices: 6382--6420 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
6372 AGCCCGAAAT
6382 TCTCTTTTCTC
1 TCTCTTTTCTC
*
6393 TATCTTTTCTC
1 TCTCTTTTCTC
6404 TCTCTTTTCTC
1 TCTCTTTTCTC
6415 TCTCTT
1 TCTCTT
6421 CAAACTCGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (11 bp):
TCTCTTTTCTC
Found at i:8329 original size:17 final size:17
Alignment explanation
Indices: 8307--8341 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
8297 AAATAAAAGT
8307 TAAAAAATATTTAAAAA
1 TAAAAAATATTTAAAAA
8324 TAAAAAATATTTAAAAA
1 TAAAAAATATTTAAAAA
8341 T
1 T
8342 GCCACGTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAAAATATTTAAAAA
Found at i:9833 original size:19 final size:18
Alignment explanation
Indices: 9798--9833 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
9788 AAACTGGACA
*
9798 CTGCAACAATACCTACAG
1 CTGCAACAATACATACAG
9816 CTGCAACAAATACATACA
1 CTGCAAC-AATACATACA
9834 TAATGCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.44, C:0.31, G:0.08, T:0.17
Consensus pattern (18 bp):
CTGCAACAATACATACAG
Found at i:15168 original size:2 final size:2
Alignment explanation
Indices: 15161--15185 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15151 TTGTTTGTTA
15161 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
15186 ACCAGACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:15688 original size:100 final size:100
Alignment explanation
Indices: 15469--15739 Score: 456
Period size: 100 Copynumber: 2.7 Consensus size: 100
15459 TAATTCTACT
* * * *
15469 TTGCACTATTGACATAATTGGAGACAATTTTTGCAAAGATTCCT-TCATAATTGGGATAACTTTG
1 TTGCATTATTGACATAATTGGAGACAATTTTTGCAGAGATTCCTCT-ATGATAGGGATAACTTTG
15533 CAGACCATTTGCTTTATCTTCATCCAATGAGTTTGCC
65 CAGA-CATTTGCTTTATCTTCATCCAATGAGTTTGCC
15570 TTGCATTATTGACATAATTGGAGACAATTTTTGCAGAGATTCCTCTATGATAGGGATAACTTTGG
1 TTGCATTATTGACATAATTGGAGACAATTTTTGCAGAGATTCCTCTATGATAGGGATAACTTT-G
15635 CAGAC-TTTGCTTTATCTTCATCCAATGAGTTTGCC
65 CAGACATTTGCTTTATCTTCATCCAATGAGTTTGCC
15670 TTGCATTATTGACATAATTGGAGACAATTTTTGCAGAGATTCCTCTATGATAGGGATAACTTTTG
1 TTGCATTATTGACATAATTGGAGACAATTTTTGCAGAGATTCCTCTATGATAGGGATAAC-TTTG
15735 CAGAC
65 CAGAC
15740 CATTATTTCA
Statistics
Matches: 163, Mismatches: 4, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
100 96 0.59
101 61 0.37
102 6 0.04
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (100 bp):
TTGCATTATTGACATAATTGGAGACAATTTTTGCAGAGATTCCTCTATGATAGGGATAACTTTGC
AGACATTTGCTTTATCTTCATCCAATGAGTTTGCC
Found at i:20941 original size:18 final size:18
Alignment explanation
Indices: 20903--20937 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
20893 TAAAAATGTT
20903 TTTTGAAGATTTTTTGGA
1 TTTTGAAGATTTTTTGGA
20921 TTTTGAA-ATTTTTTGGA
1 TTTTGAAGATTTTTTGGA
20938 ATTTCATAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (18 bp):
TTTTGAAGATTTTTTGGA
Found at i:22978 original size:2 final size:2
Alignment explanation
Indices: 22971--22997 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22961 CCTGGCTCGG
22971 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
22998 AACTAGGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27247 original size:2 final size:2
Alignment explanation
Indices: 27240--27282 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
27230 TCATTCAATG
27240 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27279 TA TA
1 TA TA
27283 ATAATACTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:27949 original size:15 final size:15
Alignment explanation
Indices: 27929--27959 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27919 ATTAAATCTC
27929 TTCTTTATAGTGATT
1 TTCTTTATAGTGATT
*
27944 TTCTTTGTAGTGATT
1 TTCTTTATAGTGATT
27959 T
1 T
27960 ATAGGATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.06, G:0.16, T:0.61
Consensus pattern (15 bp):
TTCTTTATAGTGATT
Found at i:34309 original size:16 final size:16
Alignment explanation
Indices: 34290--34323 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
34280 TCCTCTTTCC
34290 TTCTCTACTTTTTTTT
1 TTCTCTACTTTTTTTT
* *
34306 TTCTTTTCTTTTTTTT
1 TTCTCTACTTTTTTTT
34322 TT
1 TT
34324 TAAAAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (16 bp):
TTCTCTACTTTTTTTT
Found at i:39480 original size:20 final size:20
Alignment explanation
Indices: 39455--39492 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
39445 TGGAGTAACA
39455 GTGAAATCCTTCAAAAAAGG
1 GTGAAATCCTTCAAAAAAGG
*
39475 GTGAAATCCTTTAAAAAA
1 GTGAAATCCTTCAAAAAA
39493 TGGATCTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (20 bp):
GTGAAATCCTTCAAAAAAGG
Found at i:40086 original size:16 final size:13
Alignment explanation
Indices: 40054--40079 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40044 GGTTTTAATT
40054 TTATTTTTTTTTA
1 TTATTTTTTTTTA
40067 TTATTTTTTTTTA
1 TTATTTTTTTTTA
40080 ACATTATGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTATTTTTTTTTA
Found at i:45790 original size:20 final size:20
Alignment explanation
Indices: 45765--45899 Score: 82
Period size: 20 Copynumber: 6.7 Consensus size: 20
45755 AGATATTTTT
45765 ATATATAATATATATTTAAA
1 ATATATAATATATATTTAAA
* *
45785 ATATATTATATATA-TT-AT
1 ATATATAATATATATTTAAA
* * **
45803 AT-TAT-ATATGTTTTTATT
1 ATATATAATATATATTTAAA
*
45821 ATATATAA-ATAAAATTTAAA
1 ATATATAATAT-ATATTTAAA
*
45841 ATATATTATATATATTATAAA
1 ATATATAATATATATT-TAAA
*
45862 TATATTTTATATAAATATATTTAAA
1 -ATA---TATA-ATATATATTTAAA
*
45887 ATATATTATATAT
1 ATATATAATATAT
45900 GTTTTTATTA
Statistics
Matches: 87, Mismatches: 16, Indels: 24
0.69 0.13 0.19
Matches are distributed among these distances:
16 5 0.06
17 5 0.06
18 6 0.07
19 7 0.08
20 34 0.39
21 9 0.10
22 3 0.03
24 3 0.03
25 7 0.08
26 8 0.09
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (20 bp):
ATATATAATATATATTTAAA
Found at i:45904 original size:88 final size:92
Alignment explanation
Indices: 45766--45937 Score: 248
Period size: 88 Copynumber: 1.9 Consensus size: 92
45756 GATATTTTTA
*
45766 TATATAATATATATTTAAAATATATTATATATATTATATTATATATGTTTTTATTATATAT-A-A
1 TATATAATATATATTTAAAATATATTATATATAATATATTATATATGTTTTTATTATATATAATA
45829 ATAAAATTTAAAATATATTATATATAT
66 ATAAAATTTAAAATATATTATATATAT
*
45856 TATA-AATATATTTTATATAAATATATT-TA-A-AATATATTATATATGTTTTTATTATATATAA
1 TATATAATATATATT-TA-AAATATATTATATATAATATATTATATATGTTTTTATTATATAT-A
45917 ATTAATAAAATTTAAAATATA
63 A-TAATAAAATTTAAAATATA
45938 GTTTAAATAT
Statistics
Matches: 74, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
88 28 0.38
89 10 0.14
90 9 0.12
91 9 0.12
92 18 0.24
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (92 bp):
TATATAATATATATTTAAAATATATTATATATAATATATTATATATGTTTTTATTATATATAATA
ATAAAATTTAAAATATATTATATATAT
Found at i:45915 original size:2 final size:2
Alignment explanation
Indices: 45764--45899 Score: 55
Period size: 2 Copynumber: 74.5 Consensus size: 2
45754 TAGATATTTT
* *
45764 TA TA TA TA -A TA TA TA TT TA -A AA TA TA T- TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
45802 TA T- TA TA TA TG TT TT TA T- TA TA TA TA AA TA -A AA TT TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
45840 AA TA TA T- TA TA TA TA T- TA TA AA TA TA T- TT TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
45879 TA TT TA -A AA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
45900 GTTTTTATTA
Statistics
Matches: 101, Mismatches: 20, Indels: 26
0.69 0.14 0.18
Matches are distributed among these distances:
1 13 0.13
2 88 0.87
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45930 original size:46 final size:44
Alignment explanation
Indices: 45800--45937 Score: 156
Period size: 46 Copynumber: 3.1 Consensus size: 44
45790 TTATATATAT
45800 TATATTATATATGTTTTTATTATATAT-A-AATAAAATTTAAAA
1 TATATTATATATGTTTTTATTATATATAATAATAAAATTTAAAA
* * * * * *
45842 TATATTATATATATTATAAATATATTTTATATAA-ATATATTTAAAA
1 TATATTATATATGTTTTTATTATA-TATA-ATAATA-AAATTTAAAA
45888 TATATTATATATGTTTTTATTATATATAAATTAATAAAATTTAAAA
1 TATATTATATATGTTTTTATTATATAT-AA-TAATAAAATTTAAAA
45934 TATA
1 TATA
45938 GTTTAAATAT
Statistics
Matches: 76, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
42 20 0.26
43 2 0.03
45 5 0.07
46 48 0.63
47 1 0.01
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (44 bp):
TATATTATATATGTTTTTATTATATATAATAATAAAATTTAAAA
Found at i:46835 original size:25 final size:22
Alignment explanation
Indices: 46801--46852 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 22
46791 AATGAAACCT
46801 GAAAAAAATAGAAAAAGAACGAA
1 GAAAAAAATAGAAAAAGAA-GAA
* *
46824 GGAAAAAGAATAGGAATAGAAGAA
1 -GAAAAA-AATAGAAAAAGAAGAA
46848 GAAAA
1 GAAAA
46853 GACAACAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 5 0.20
24 9 0.36
25 11 0.44
ACGTcount: A:0.69, C:0.02, G:0.23, T:0.06
Consensus pattern (22 bp):
GAAAAAAATAGAAAAAGAAGAA
Done.