Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013601.1 Corchorus capsularis cultivar CVL-1 contig13622, 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: 41852
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:7465 original size:30 final size:30
Alignment explanation
Indices: 7427--7495 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
7417 GATCGGATCA
*
7427 CACCAAAGACATCAATGGATGGAGGAATCG
1 CACCAAAGACACCAATGGATGGAGGAATCG
* ** * *
7457 CGCCAAAGATGCCATTGGATGGAGGAATCT
1 CACCAAAGACACCAATGGATGGAGGAATCG
7487 CACCAAAGA
1 CACCAAAGA
7496 TGTGATCGGT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.38, C:0.22, G:0.26, T:0.14
Consensus pattern (30 bp):
CACCAAAGACACCAATGGATGGAGGAATCG
Found at i:8982 original size:11 final size:10
Alignment explanation
Indices: 8964--8997 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
8954 AATTGTCTTC
8964 AAATCTTCAA
1 AAATCTTCAA
8974 AATATCTTCAA
1 AA-ATCTTCAA
8985 GAAATCTTCAA
1 -AAATCTTCAA
8996 AA
1 AA
8998 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:16187 original size:30 final size:30
Alignment explanation
Indices: 16151--16213 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
16141 TGTCTTCAAG
*
16151 TCCATGATAAGTCCTT-GGTGCATCATTCCC
1 TCCATGATAAG-CCTTGGGCGCATCATTCCC
16181 TCCATGATAAGCCTTGGGCGCATCATTCCC
1 TCCATGATAAGCCTTGGGCGCATCATTCCC
16211 TCC
1 TCC
16214 CCCTTGAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.19, C:0.33, G:0.17, T:0.30
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGGCGCATCATTCCC
Found at i:17355 original size:21 final size:21
Alignment explanation
Indices: 17331--17376 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
17321 TCATGGTCCT
* *
17331 ATGCGATGGCGCGGCTACTCC
1 ATGCCATGGCACGGCTACTCC
* *
17352 ATGCCTTGGCACGGCTTCTCC
1 ATGCCATGGCACGGCTACTCC
17373 ATGC
1 ATGC
17377 TTTGGCCGGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.35, G:0.28, T:0.24
Consensus pattern (21 bp):
ATGCCATGGCACGGCTACTCC
Found at i:17381 original size:21 final size:21
Alignment explanation
Indices: 17337--17382 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
17327 TCCTATGCGA
*
17337 TGGCGCGGCTACTCCATGCCT
1 TGGCACGGCTACTCCATGCCT
* *
17358 TGGCACGGCTTCTCCATGCTT
1 TGGCACGGCTACTCCATGCCT
17379 TGGC
1 TGGC
17383 CGGTCATATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.35, G:0.28, T:0.28
Consensus pattern (21 bp):
TGGCACGGCTACTCCATGCCT
Found at i:18267 original size:6 final size:6
Alignment explanation
Indices: 18252--18282 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
18242 AAAGCAAAGA
18252 AAAT-T AAATCT AAATCT AAATCT AAATCT AA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AA
18283 GCAGATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATCT
Found at i:19652 original size:11 final size:10
Alignment explanation
Indices: 19634--19667 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
19624 AATTGTCTTC
19634 AAATCTTCAA
1 AAATCTTCAA
19644 AATATCTTCAA
1 AA-ATCTTCAA
19655 TAAATCTTCAA
1 -AAATCTTCAA
19666 AA
1 AA
19668 CACAAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:22132 original size:20 final size:21
Alignment explanation
Indices: 22083--22133 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
22073 CAAATTATGC
22083 ATGTTTTTATAGCTATTTTTAT
1 ATGTTTTT-TAGCTATTTTTAT
**
22105 ATACTTTTTA-CTATTTTTAT
1 ATGTTTTTTAGCTATTTTTAT
22125 ATGTTTTTT
1 ATGTTTTTT
22134 TACCCTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 17 0.68
21 2 0.08
22 6 0.24
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.67
Consensus pattern (21 bp):
ATGTTTTTTAGCTATTTTTAT
Found at i:25614 original size:2 final size:2
Alignment explanation
Indices: 25607--25635 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25597 TTGATATGTA
25607 AT 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 AT A
25636 AATAATGGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28009 original size:6 final size:6
Alignment explanation
Indices: 27998--28027 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
27988 TTTGGGAAGT
*
27998 GAAAAA GAAAAA AAAAAA GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
28028 CATTAAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:28097 original size:12 final size:12
Alignment explanation
Indices: 28080--28112 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
28070 AAATTGAAAT
*
28080 AAGAAATAAGAA
1 AAGAAAAAAGAA
28092 AAGAAAAAAGAA
1 AAGAAAAAAGAA
28104 AAGAAAAAA
1 AAGAAAAAA
28113 CTTGACAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (12 bp):
AAGAAAAAAGAA
Found at i:28536 original size:6 final size:6
Alignment explanation
Indices: 28525--28558 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
28515 AATTGCCATA
28525 ATTTAG ATTTAG ATTTAG ATTTAG ATTTA- ATTTA
1 ATTTAG ATTTAG ATTTAG ATTTAG ATTTAG ATTTA
28559 CTTTGCTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (6 bp):
ATTTAG
Found at i:29026 original size:40 final size:41
Alignment explanation
Indices: 28942--29027 Score: 95
Period size: 42 Copynumber: 2.1 Consensus size: 41
28932 GGGTTTCCGA
* *
28942 TTTTTGAAAAAAAAAAATTAATTTTTCTTTTTCCGTTTTTCT
1 TTTTTGAAAAAAAAAAA-TAATTTTTCATTTTCCGTTTTGCT
* * *
28984 TTTTTTAAAATAAAAAA-AATTTTT-ATTTTCTGTTTCTGCT
1 TTTTTGAAAAAAAAAAATAATTTTTCATTTTCCGTTT-TGCT
29024 TTTT
1 TTTT
29028 AATTTTTAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
39 9 0.24
40 14 0.37
42 15 0.39
ACGTcount: A:0.30, C:0.08, G:0.05, T:0.57
Consensus pattern (41 bp):
TTTTTGAAAAAAAAAAATAATTTTTCATTTTCCGTTTTGCT
Found at i:32958 original size:33 final size:34
Alignment explanation
Indices: 32913--32994 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 34
32903 GGTTGGTGCG
*
32913 CCAAG-CG-ATGGCCGGTTG-TGGCCGGACATGT
1 CCAAGTCGCATGGCCGGTTGATGGCCGGACATCT
* * * *
32944 CCATGTCGCGTGGCCGG-TGATGGCCGGGCTTCT
1 CCAAGTCGCATGGCCGGTTGATGGCCGGACATCT
32977 CCAAGTCGCATGGCCGGT
1 CCAAGTCGCATGGCCGGT
32995 CACTCGCGCC
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
31 4 0.10
32 4 0.10
33 32 0.80
ACGTcount: A:0.12, C:0.29, G:0.38, T:0.21
Consensus pattern (34 bp):
CCAAGTCGCATGGCCGGTTGATGGCCGGACATCT
Found at i:36067 original size:19 final size:18
Alignment explanation
Indices: 36043--36078 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
36033 TGAAGATTTC
36043 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
36062 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
36079 ATTATTTCAA
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:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.