Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019721.1 Corchorus olitorius cultivar O-4 contig19754, 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: 33276
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--34 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT 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
35 GGTCCAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1872 original size:107 final size:107
Alignment explanation
Indices: 1731--1947 Score: 353
Period size: 107 Copynumber: 2.0 Consensus size: 107
1721 CCGGTTTTTA
* * * * * * *
1731 TTATAGGGTTTTAGAAATAAAATACAAAATTAATTTCACTAAGTTTAGGTTCAAATTAAAATTTT
1 TTATAGAGTTTTAAAAATAAAATACAAAACTAATTTCACTAAATTTAGCTCCAAATCAAAATTTT
*
1796 ATTTTTATTTTAAAGGTAAATTCCATAATTAATAATTTATTG
66 ATTTTTATTTTAAAGGTAAATTCCATAATTAATAACTTATTG
1838 TTATAGAGTTTTAAAAATAAAATACAAAACTAATTTCACTAAATTTAGCTCCAAATCAAAATTTT
1 TTATAGAGTTTTAAAAATAAAATACAAAACTAATTTCACTAAATTTAGCTCCAAATCAAAATTTT
*
1903 ATTTTTATTTTAAGGGTAAATTCCATAATTAATAACTTATTG
66 ATTTTTATTTTAAAGGTAAATTCCATAATTAATAACTTATTG
1945 TTA
1 TTA
1948 GAAATAAAAT
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
107 101 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (107 bp):
TTATAGAGTTTTAAAAATAAAATACAAAACTAATTTCACTAAATTTAGCTCCAAATCAAAATTTT
ATTTTTATTTTAAAGGTAAATTCCATAATTAATAACTTATTG
Found at i:6010 original size:116 final size:118
Alignment explanation
Indices: 5796--6043 Score: 272
Period size: 116 Copynumber: 2.1 Consensus size: 118
5786 ACCTAGTCTG
* * * * *
5796 ATCATAAAGAGTTCGGTACTTGTTCTCGAGTTTGAGTTTTGTGAATGGAGAAAATCATGTTGCTG
1 ATCATAAAGAGTTCGGAACTTGTTCTCGACTTTGAATTTTGTGAATGGAGAAAATCATATTACTG
* * * **
5861 GAGACACTCAAACAAGATTAACTTGTAAGTTGTAAATAT-TTAAAA-AAAAAA
66 GAGACACTCAAACAAGATCAACGTGTAACTTGTAAATATACCAAAAGAAAAAA
*
5912 ATCATAAAGAGTTCGGAACTTGTTCTCGACTTTGAATTTTGTGAATGGAGAAAATCATATTACTT
1 ATCATAAAGAGTTCGGAACTTGTTCTCGACTTTGAATTTTGTGAATGGAGAAAATCATATTACTG
* * ** * *
5977 GAGGCTGACCTGATTCAA-A-CAAGGT-TAACTTGTAAATATACCAAAAGGAAAATA
66 GAGAC--A-CTCAAACAAGATCAACGTGTAACTTGTAAATATACCAAAA-GAAAAAA
6031 ATCATAAAGAGTT
1 ATCATAAAGAGTT
6044 AATTACCTGT
Statistics
Matches: 109, Mismatches: 17, Indels: 9
0.81 0.13 0.07
Matches are distributed among these distances:
116 76 0.70
117 7 0.06
118 2 0.02
119 24 0.22
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (118 bp):
ATCATAAAGAGTTCGGAACTTGTTCTCGACTTTGAATTTTGTGAATGGAGAAAATCATATTACTG
GAGACACTCAAACAAGATCAACGTGTAACTTGTAAATATACCAAAAGAAAAAA
Found at i:6748 original size:14 final size:14
Alignment explanation
Indices: 6731--6762 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
6721 GTTTTGTGAA
6731 ATAAATTCTATACT
1 ATAAATTCTATACT
6745 ATAAATTCTATACT
1 ATAAATTCTATACT
6759 ATAA
1 ATAA
6763 GTAACATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAAATTCTATACT
Found at i:9387 original size:21 final size:19
Alignment explanation
Indices: 9362--9419 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 19
9352 GCTGCTCTAA
9362 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
9383 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
*
9402 TAAACTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
9420 TGCTAAATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.48
21 17 0.52
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.34
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:9414 original size:19 final size:20
Alignment explanation
Indices: 9366--9419 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
9356 CTCTAATAAT
*
9366 CTCATCTGTACAGTACCTAAT
1 CTCATCTGTACAGTA-CTAAA
* *
9387 CTAATCTGTACAGT-GTAAA
1 CTCATCTGTACAGTACTAAA
9406 CTCATCTGTACAGT
1 CTCATCTGTACAGT
9420 TGCTAAATAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 16 0.55
21 13 0.45
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (20 bp):
CTCATCTGTACAGTACTAAA
Found at i:11907 original size:2 final size:2
Alignment explanation
Indices: 11900--11930 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11890 CATGATCAAC
11900 AT 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 AT A
11931 GTATGGAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13081 original size:2 final size:2
Alignment explanation
Indices: 13076--13114 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
13066 TTTTTGCAGA
13076 AT AT AT AT AT 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 AT AT AT AT AT A
13115 CTCACTGCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13714 original size:26 final size:26
Alignment explanation
Indices: 13685--13738 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
13675 ACGGTCTCAT
*
13685 GTTTTGTTGTCACCCAAGAGTTTTTG
1 GTTTTGTTGTCACCCAAAAGTTTTTG
* * *
13711 GTTTTGTTGTGATCCAAAATTTTTTG
1 GTTTTGTTGTCACCCAAAAGTTTTTG
13737 GT
1 GT
13739 ATATTTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.17, C:0.11, G:0.22, T:0.50
Consensus pattern (26 bp):
GTTTTGTTGTCACCCAAAAGTTTTTG
Found at i:13755 original size:26 final size:27
Alignment explanation
Indices: 13726--13780 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
13716 GTTGTGATCC
13726 AAAATTTT-TTGGTATATTTAAAAGTT
1 AAAATTTTATTGGTATATTTAAAAGTT
*
13752 AAAATTTTATTGGTATATTTAGAAGTT
1 AAAATTTTATTGGTATATTTAAAAGTT
13779 AA
1 AA
13781 TCTTGTTCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 8 0.30
27 19 0.70
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (27 bp):
AAAATTTTATTGGTATATTTAAAAGTT
Found at i:30921 original size:18 final size:18
Alignment explanation
Indices: 30898--30932 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
30888 GCGCTCTCGT
*
30898 TCTCTCTCCTTTTCCCGC
1 TCTCTCTCCTTCTCCCGC
30916 TCTCTCTCCTTCTCCCG
1 TCTCTCTCCTTCTCCCG
30933 TCGCTCCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.51, G:0.06, T:0.43
Consensus pattern (18 bp):
TCTCTCTCCTTCTCCCGC
Done.