Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016646.1 Corchorus olitorius cultivar O-4 contig16679, 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: 31474
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Found at i:10690 original size:14 final size:14
Alignment explanation
Indices: 10671--10705 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
10661 GGGGCACAAG
10671 TGGGGCACCAAAAT
1 TGGGGCACCAAAAT
10685 TGGGGCACCAAAAT
1 TGGGGCACCAAAAT
10699 TGGGGCA
1 TGGGGCA
10706 GAGGATTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.20, G:0.34, T:0.14
Consensus pattern (14 bp):
TGGGGCACCAAAAT
Found at i:11890 original size:19 final size:17
Alignment explanation
Indices: 11834--11878 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
11824 TTGACCAACT
* *
11834 TATAT-ATATATATATA
1 TATATAATATACACATA
*
11850 TATATAATATACACATT
1 TATATAATATACACATA
11867 TATATAATATAC
1 TATATAATATAC
11879 CCTAATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (17 bp):
TATATAATATACACATA
Found at i:13885 original size:2 final size:2
Alignment explanation
Indices: 13878--13907 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
13868 TCAAATATGG
*
13878 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13908 TATTTTTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:14860 original size:42 final size:40
Alignment explanation
Indices: 14791--14878 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 40
14781 ACAATTAATG
* * *
14791 TTAGCTTTATTTTGATGAATTATCTAGAGATGGAGTAGAAT
1 TTAGATTTAATTTGATGAATTACCTAGAGAT-GAGTAGAAT
14832 ATTAGATTTAATTTGATGAATTACCTAGAGATGAGTAGAAT
1 -TTAGATTTAATTTGATGAATTACCTAGAGATGAGTAGAAT
14873 TTAGAT
1 TTAGAT
14879 AATGCACTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 6 0.14
41 9 0.21
42 28 0.65
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.40
Consensus pattern (40 bp):
TTAGATTTAATTTGATGAATTACCTAGAGATGAGTAGAAT
Found at i:18728 original size:21 final size:21
Alignment explanation
Indices: 18661--18818 Score: 97
Period size: 22 Copynumber: 7.2 Consensus size: 21
18651 TGAATATTTT
*
18661 TATGAAATTTTGATAACTATCC
1 TATGAAATTTTGATAATTA-CC
* *
18683 TATTAAATTTTGATAATCAACC
1 TATGAAATTTTGATAAT-TACC
*
18705 TATGGAATTTTGATAATTACC
1 TATGAAATTTTGATAATTACC
* * *
18726 TATGAAATTGTGGTAAACT-CC
1 TATGAAATTTTGAT-AATTACC
* * *
18747 ATATGAAACTTTGATAACCTAAC
1 -TATGAAATTTTGATAA-TTACC
* *
18770 TATAAAATTTTAATAAACCTT-CC
1 TATGAAATTTTGAT-AA--TTACC
*
18793 TATGAAATTTT-ATAATCTTCC
1 TATGAAATTTTGATAAT-TACC
18814 TATGA
1 TATGA
18819 TTTTTAATAA
Statistics
Matches: 107, Mismatches: 20, Indels: 19
0.73 0.14 0.13
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 27 0.25
22 61 0.57
23 15 0.14
24 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (21 bp):
TATGAAATTTTGATAATTACC
Found at i:22938 original size:30 final size:31
Alignment explanation
Indices: 22863--22939 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 31
22853 ATACCGTACA
* * **
22863 GGTCTCTCTACTTATAAAAAGGGATTGATTT
1 GGTCCCTCTACTTATAAAAACGGATCAATTT
*
22894 GGT-CCTCCTA-TTATAAAAACTG-TCAATTT
1 GGTCCCT-CTACTTATAAAAACGGATCAATTT
22923 GGTCCCTCTACTTATAA
1 GGTCCCTCTACTTATAA
22940 TTTGGTGTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
29 11 0.29
30 21 0.55
31 6 0.16
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (31 bp):
GGTCCCTCTACTTATAAAAACGGATCAATTT
Found at i:23291 original size:29 final size:30
Alignment explanation
Indices: 23204--23308 Score: 106
Period size: 31 Copynumber: 3.5 Consensus size: 30
23194 CAGATTTTGT
* ***
23204 TAAGTAGAGGGACCCAATTGATACCAAATTA
1 TAAGTAGAGGGACCAAATTGAT-CCTTTTTA
*
23235 TAAGTAGAGGGACCAAATTGA-CAGTTTTTA
1 TAAGTAGAGGGACCAAATTGATC-CTTTTTA
*
23265 T-AGTAGAGGGACCAAATTGATCCTTTTTTG
1 TAAGTAGAGGGACCAAATTGATCC-TTTTTA
*
23295 TAAATAGAGGGACC
1 TAAGTAGAGGGACC
23309 TGTACGGTAT
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
29 20 0.32
30 11 0.18
31 31 0.50
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (30 bp):
TAAGTAGAGGGACCAAATTGATCCTTTTTA
Found at i:23306 original size:31 final size:29
Alignment explanation
Indices: 23232--23308 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
23222 TGATACCAAA
23232 TTATAAGTAGAGGGACCAAATTGACAGTTT
1 TTATAA-TAGAGGGACCAAATTGACAGTTT
* **
23262 TTATAGTAGAGGGACCAAATTGATCCTTTT
1 TTATAATAGAGGGACCAAATTGA-CAGTTT
*
23292 TTGTAAATAGAGGGACC
1 TTAT-AATAGAGGGACC
23309 TGTACGGTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 17 0.43
30 12 0.30
31 11 0.28
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (29 bp):
TTATAATAGAGGGACCAAATTGACAGTTT
Found at i:23579 original size:46 final size:47
Alignment explanation
Indices: 23491--23586 Score: 185
Period size: 46 Copynumber: 2.1 Consensus size: 47
23481 TGAAATGAAA
23491 CTATTAAATCTCTATTTCCTAAAAAAAAACTATTAAATCTCTATGTG
1 CTATTAAATCTCTATTTCCTAAAAAAAAACTATTAAATCTCTATGTG
23538 CTATTAAATCTCTATTTCCT-AAAAAAAACTATTAAATCTCTATGTG
1 CTATTAAATCTCTATTTCCTAAAAAAAAACTATTAAATCTCTATGTG
23584 CTA
1 CTA
23587 AACATTTAGT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 29 0.59
47 20 0.41
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.39
Consensus pattern (47 bp):
CTATTAAATCTCTATTTCCTAAAAAAAAACTATTAAATCTCTATGTG
Done.