Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019674.1 Corchorus olitorius cultivar O-4 contig19707, 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: 40409
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3744 original size:17 final size:17
Alignment explanation
Indices: 3722--3756 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3712 CGGTGTATCG
3722 TATAATTTGCCTTTCTT
1 TATAATTTGCCTTTCTT
3739 TATAATTTGCCTTTCTT
1 TATAATTTGCCTTTCTT
3756 T
1 T
3757 TTTTTTTTCC
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:0.17, C:0.17, G:0.06, T:0.60
Consensus pattern (17 bp):
TATAATTTGCCTTTCTT
Found at i:4368 original size:18 final size:18
Alignment explanation
Indices: 4347--4387 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
4337 AAGAGGATCC
4347 TCTTCATATTCGACTTCG
1 TCTTCATATTCGACTTCG
* *
4365 TCTTCATTTTCGTCTTCG
1 TCTTCATATTCGACTTCG
4383 TCTTC
1 TCTTC
4388 GTCTTCGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.10, C:0.29, G:0.10, T:0.51
Consensus pattern (18 bp):
TCTTCATATTCGACTTCG
Found at i:4369 original size:6 final size:6
Alignment explanation
Indices: 4355--4395 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
4345 CCTCTTCATA
* * *
4355 TTCGAC TTCGTC TTCATT TTCGTC TTCGTC TTCGTC TTCGT
1 TTCGTC TTCGTC TTCGTC TTCGTC TTCGTC TTCGTC TTCGT
4396 ATTCTTCATC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.05, C:0.29, G:0.15, T:0.51
Consensus pattern (6 bp):
TTCGTC
Found at i:4394 original size:18 final size:18
Alignment explanation
Indices: 4347--4395 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
4337 AAGAGGATCC
* *
4347 TCTTCATATTCGACTTCG
1 TCTTCATCTTCGTCTTCG
*
4365 TCTTCATTTTCGTCTTCG
1 TCTTCATCTTCGTCTTCG
*
4383 TCTTCGTCTTCGT
1 TCTTCATCTTCGT
4396 ATTCTTCATC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.08, C:0.29, G:0.12, T:0.51
Consensus pattern (18 bp):
TCTTCATCTTCGTCTTCG
Found at i:6693 original size:34 final size:34
Alignment explanation
Indices: 6650--6745 Score: 192
Period size: 34 Copynumber: 2.8 Consensus size: 34
6640 GAGTTTAACT
6650 TGTAATTTGTTTGTTTATTTATTTGGTTACGGAA
1 TGTAATTTGTTTGTTTATTTATTTGGTTACGGAA
6684 TGTAATTTGTTTGTTTATTTATTTGGTTACGGAA
1 TGTAATTTGTTTGTTTATTTATTTGGTTACGGAA
6718 TGTAATTTGTTTGTTTATTTATTTGGTT
1 TGTAATTTGTTTGTTTATTTATTTGGTT
6746 TGTAGGTGGG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 62 1.00
ACGTcount: A:0.19, C:0.02, G:0.20, T:0.59
Consensus pattern (34 bp):
TGTAATTTGTTTGTTTATTTATTTGGTTACGGAA
Found at i:6891 original size:108 final size:108
Alignment explanation
Indices: 6723--6941 Score: 366
Period size: 108 Copynumber: 2.0 Consensus size: 108
6713 CGGAATGTAA
6723 TTTGTTTGTTTATTTATTTGGTTTGTAGGTGGGTATAATTTCTAATCTCTAGGTTCAAGAGCATG
1 TTTGTTTGTTTATTTATTTGGTTTGTAGGTGGGTATAATTTCTAATCTCTAGGTTCAAGAGCATG
*
6788 TGTTATGAGATTTCAATTGTATTTGTTGGCCCATAGATTAGCG
66 TGTTATGAGATTTCAATTGTATTTGTTGGCCCATAAATTAGCG
* * * *
6831 TTTGTTTGTTTATTTATTTGGTTTGTAGGTGGGTATAGTTTCTAGTTTCTAGGTTTAAGAGCATG
1 TTTGTTTGTTTATTTATTTGGTTTGTAGGTGGGTATAATTTCTAATCTCTAGGTTCAAGAGCATG
* * *
6896 TGTTATGAGATTTCAGTTGTATTTGTTGTCCCATAAATTAGTG
66 TGTTATGAGATTTCAATTGTATTTGTTGGCCCATAAATTAGCG
6939 TTT
1 TTT
6942 CGGTAATGTA
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
108 103 1.00
ACGTcount: A:0.20, C:0.08, G:0.23, T:0.49
Consensus pattern (108 bp):
TTTGTTTGTTTATTTATTTGGTTTGTAGGTGGGTATAATTTCTAATCTCTAGGTTCAAGAGCATG
TGTTATGAGATTTCAATTGTATTTGTTGGCCCATAAATTAGCG
Found at i:8001 original size:24 final size:25
Alignment explanation
Indices: 7955--8003 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
7945 TGCTCTGACT
*
7955 AATCCGGATCCGATCGGTGCACCTG
1 AATCCGGATCCGACCGGTGCACCTG
7980 AATCCGGAT-CGACCGGTGCACCTG
1 AATCCGGATCCGACCGGTGCACCTG
8004 GTTATGGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.20, C:0.33, G:0.29, T:0.18
Consensus pattern (25 bp):
AATCCGGATCCGACCGGTGCACCTG
Found at i:11334 original size:2 final size:2
Alignment explanation
Indices: 11327--11354 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11317 AATCACAAGT
11327 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11355 AATGTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13016 original size:44 final size:45
Alignment explanation
Indices: 12933--13025 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 45
12923 CTCTGGTATG
*
12933 GAAATCTCCTTCAATGAGTAAAGCAAAAACCAGAAAAAAAAA-AA
1 GAAATCTCCTTCAATGAGCAAAGCAAAAACCAGAAAAAAAAAGAA
* **
12977 GAAATCTCCTTCCATGAGCAAAGC-AAAACCAGGGGAAAAAAAGAA
1 GAAATCTCCTTCAATGAGCAAAGCAAAAACCA-GAAAAAAAAAGAA
13022 GAAA
1 GAAA
13026 AAAGAAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
43 7 0.16
44 30 0.70
45 6 0.14
ACGTcount: A:0.55, C:0.17, G:0.16, T:0.12
Consensus pattern (45 bp):
GAAATCTCCTTCAATGAGCAAAGCAAAAACCAGAAAAAAAAAGAA
Found at i:13039 original size:52 final size:52
Alignment explanation
Indices: 12971--13070 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 52
12961 ACCAGAAAAA
**
12971 AAAAAAGAAATCTCCTTCCATGAGCAAAGCAAAACCAGGGGAAAAAAAGAAG
1 AAAAAAGAAATCTCCTTCCATGAGCAAAGCAAAACCAGGAAAAAAAAAGAAG
* * **
13023 AAAAAAGAAATTTCCTTCGATGAGTGAAGCAAAACCAGGAAAAAAAAA
1 AAAAAAGAAATCTCCTTCCATGAGCAAAGCAAAACCAGGAAAAAAAAA
13071 AGGAAAGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.55, C:0.15, G:0.18, T:0.12
Consensus pattern (52 bp):
AAAAAAGAAATCTCCTTCCATGAGCAAAGCAAAACCAGGAAAAAAAAAGAAG
Found at i:21548 original size:24 final size:23
Alignment explanation
Indices: 21504--21548 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
21494 TTGACTAAGT
* *
21504 TTTGGTGTTGTTTGTTATTTTTG
1 TTTGGAGTTGTTTGGTATTTTTG
*
21527 TTTGGAGTCTGTTTGGTGTTTT
1 TTTGGAGT-TGTTTGGTATTTT
21549 GGTCTGTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.04, C:0.02, G:0.29, T:0.64
Consensus pattern (23 bp):
TTTGGAGTTGTTTGGTATTTTTG
Found at i:25980 original size:15 final size:15
Alignment explanation
Indices: 25960--26001 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
25950 CTTGGTTAAA
*
25960 TATCTATATCTATAG
1 TATCTATATCTATAC
25975 TATCTATATCTAT-C
1 TATCTATATCTATAC
25989 TATCTATA-CTATA
1 TATCTATATCTATA
26002 TATAAAAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.33, C:0.17, G:0.02, T:0.48
Consensus pattern (15 bp):
TATCTATATCTATAC
Found at i:30160 original size:13 final size:13
Alignment explanation
Indices: 30142--30167 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30132 TTATAATTCA
30142 ATTTCTAAATATT
1 ATTTCTAAATATT
30155 ATTTCTAAATATT
1 ATTTCTAAATATT
30168 GTATTTGGAA
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:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTTCTAAATATT
Found at i:32714 original size:16 final size:16
Alignment explanation
Indices: 32693--32723 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
32683 CAACTGTTGA
32693 ATATAGGTAGTGTAGG
1 ATATAGGTAGTGTAGG
32709 ATATAGGTAGTGTAG
1 ATATAGGTAGTGTAG
32724 CAAAGTAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (16 bp):
ATATAGGTAGTGTAGG
Found at i:36441 original size:79 final size:79
Alignment explanation
Indices: 36317--36468 Score: 295
Period size: 79 Copynumber: 1.9 Consensus size: 79
36307 ATTTTTACCT
*
36317 ACAAGAAATCTATCTAGAATTTTTCGTTTTAGAAATTCTCTGGGTTTCATGAATTAAATAAGTAA
1 ACAAGAAATCTATCTAGAATTTTTCGTTTTAGAAATTCTCTGGGTTTCATAAATTAAATAAGTAA
36382 ATATAGCTTTACTG
66 ATATAGCTTTACTG
36396 ACAAGAAATCTATCTAGAATTTTTCGTTTTAGAAATTCTCTGGGTTTCATAAATTAAATAAGTAA
1 ACAAGAAATCTATCTAGAATTTTTCGTTTTAGAAATTCTCTGGGTTTCATAAATTAAATAAGTAA
36461 ATATAGCT
66 ATATAGCT
36469 CCTGCTAAGC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 72 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (79 bp):
ACAAGAAATCTATCTAGAATTTTTCGTTTTAGAAATTCTCTGGGTTTCATAAATTAAATAAGTAA
ATATAGCTTTACTG
Found at i:36852 original size:20 final size:20
Alignment explanation
Indices: 36827--36867 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
36817 TTAATTATTG
*
36827 ATATGTTAAGTGGGTTTTTA
1 ATATGTTAAGTGAGTTTTTA
36847 ATATGTTAAGTGAGTTTTTA
1 ATATGTTAAGTGAGTTTTTA
36867 A
1 A
36868 GACATCTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (20 bp):
ATATGTTAAGTGAGTTTTTA
Found at i:39871 original size:3 final size:3
Alignment explanation
Indices: 39863--39939 Score: 154
Period size: 3 Copynumber: 25.7 Consensus size: 3
39853 TCTTGTTTTC
39863 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39911 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
39940 ATAAAATCGG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Done.