Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013575.1 Corchorus olitorius cultivar O-4 contig13608, 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: 19280
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:864 original size:12 final size:13
Alignment explanation
Indices: 835--866 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
825 TCTTTCTTTT
835 TTTTTTCATTTCA
1 TTTTTTCATTTCA
848 TTTTTTCATTTCA
1 TTTTTTCATTTCA
861 TTTTTT
1 TTTTTT
867 TTTCTTTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTTTCATTTCA
Found at i:2639 original size:12 final size:13
Alignment explanation
Indices: 2610--2643 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
2600 ATAATAACTC
*
2610 AAATTAATTTATT
1 AAATTAATTCATT
2623 AAATTAATTCA-T
1 AAATTAATTCATT
2635 AAATTAATT
1 AAATTAATT
2644 AAACCCTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
AAATTAATTCATT
Found at i:3379 original size:29 final size:29
Alignment explanation
Indices: 3323--3379 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
3313 TTAATTAATT
* ****
3323 AAATGTTTAATATTTTTTTTTGGCAAAAA
1 AAATATTTAATATTTTTTTTAAAAAAAAA
3352 AAATATTTAATATTTTTTTTAAAAAAAA
1 AAATATTTAATATTTTTTTTAAAAAAAA
3380 TTCCATGCCG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (29 bp):
AAATATTTAATATTTTTTTTAAAAAAAAA
Found at i:3573 original size:16 final size:16
Alignment explanation
Indices: 3552--3609 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
3542 TTGAGGATTT
3552 GTTGAAGAAATTGAAG
1 GTTGAAGAAATTGAAG
*
3568 GTTGAAGAAGTTTGAAG
1 GTTGAAGAA-ATTGAAG
*
3585 AAGTT--AGAAAATGAAG
1 --GTTGAAGAAATTGAAG
3601 GTTGAAGAA
1 GTTGAAGAA
3610 GTTTGAGAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 3 0.09
16 18 0.53
17 10 0.29
19 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.31, T:0.24
Consensus pattern (16 bp):
GTTGAAGAAATTGAAG
Found at i:3582 original size:10 final size:10
Alignment explanation
Indices: 3564--3627 Score: 51
Period size: 10 Copynumber: 6.3 Consensus size: 10
3554 TGAAGAAATT
*
3564 GAAGGTTGAA
1 GAAGTTTGAA
3574 GAAGTTTGAA
1 GAAGTTTGAA
*
3584 GAAGTTAGAAAA
1 GAAGTTTG--AA
*
3596 TGAAGGTTGAA
1 -GAAGTTTGAA
3607 GAAGTTTG-A
1 GAAGTTTGAA
*
3616 G-AGTTTTAA
1 GAAGTTTGAA
3625 GAA
1 GAA
3628 ATATGAACAA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
8 5 0.12
9 4 0.09
10 24 0.56
11 2 0.05
12 2 0.05
13 6 0.14
ACGTcount: A:0.42, C:0.00, G:0.31, T:0.27
Consensus pattern (10 bp):
GAAGTTTGAA
Found at i:3986 original size:38 final size:39
Alignment explanation
Indices: 3931--4005 Score: 134
Period size: 38 Copynumber: 1.9 Consensus size: 39
3921 TGCGCGGGGA
*
3931 TAATATCTAGTATATATAATCCTAACTACTTAATATACT
1 TAATATATAGTATATATAATCCTAACTACTTAATATACT
3970 TAATATATA-TATATATAATCCTAACTACTTAATATA
1 TAATATATAGTATATATAATCCTAACTACTTAATATA
4006 TATTTTCTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 27 0.77
39 8 0.23
ACGTcount: A:0.44, C:0.13, G:0.01, T:0.41
Consensus pattern (39 bp):
TAATATATAGTATATATAATCCTAACTACTTAATATACT
Found at i:8959 original size:14 final size:14
Alignment explanation
Indices: 8940--8970 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
8930 GTTTCGAGGA
8940 TCAAACTTGTATTC
1 TCAAACTTGTATTC
*
8954 TCAAACTTGTGTTC
1 TCAAACTTGTATTC
8968 TCA
1 TCA
8971 TCTTATCGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.42
Consensus pattern (14 bp):
TCAAACTTGTATTC
Found at i:13925 original size:22 final size:22
Alignment explanation
Indices: 13875--13974 Score: 89
Period size: 22 Copynumber: 4.5 Consensus size: 22
13865 TGAATATTTT
*
13875 TATGAAATTTTGAT-AATTACC-
1 TATGAAATTTTGATAAACT-CCA
* *
13896 TGTGAAATTGTGATAAACTCCA
1 TATGAAATTTTGATAAACTCCA
* **
13918 TATGAAATTTTGATAACCTAAA
1 TATGAAATTTTGATAAACTCCA
*
13940 TATGAAATTTTAATAAACCTTCCA
1 TATGAAATTTTGATAAA-C-TCCA
13964 -ATGAAATTTTG
1 TATGAAATTTTG
13975 TAACCTTCTT
Statistics
Matches: 62, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
21 14 0.23
22 35 0.56
23 11 0.18
24 2 0.03
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAAACTCCA
Found at i:13988 original size:21 final size:21
Alignment explanation
Indices: 13875--14017 Score: 76
Period size: 21 Copynumber: 6.6 Consensus size: 21
13865 TGAATATTTT
13875 TATGAAATTTTGATAA--TTACC
1 TATGAAATTTTG-TAACCTT-CC
* * *
13896 TGTGAAATTGTGATAAAC-TCC
1 TATGAAATTTTG-TAACCTTCC
***
13917 ATATGAAATTTTGATAACCTAAA
1 -TATGAAATTTTG-TAACCTTCC
*
13940 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTT-GT-AACCTTCC
* *
13963 AATGAAATTTTGTAACCTTCT
1 TATGAAATTTTGTAACCTTCC
** * *
13984 TATGATTTTTTATAACCTCCC
1 TATGAAATTTTGTAACCTTCC
*
14005 TATGAGATTTTGT
1 TATGAAATTTTGT
14018 TAATCTCCCT
Statistics
Matches: 92, Mismatches: 24, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
21 48 0.52
22 29 0.32
23 15 0.16
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.41
Consensus pattern (21 bp):
TATGAAATTTTGTAACCTTCC
Found at i:13988 original size:44 final size:44
Alignment explanation
Indices: 13875--13980 Score: 119
Period size: 44 Copynumber: 2.4 Consensus size: 44
13865 TGAATATTTT
* ** * *
13875 TATGAAATTTTGATAA-TTACCTGTGAAATTGTGATAAACTCCA
1 TATGAAATTTTGATAACCTAAATATGAAATTGTAATAAACTCCA
*
13918 TATGAAATTTTGATAACCTAAATATGAAATTTTAATAAACCTTCCA
1 TATGAAATTTTGATAACCTAAATATGAAATTGTAATAAA-C-TCCA
13964 -ATGAAATTTTG-TAACCT
1 TATGAAATTTTGATAACCT
13981 TCTTATGATT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
43 16 0.30
44 22 0.41
45 12 0.22
46 4 0.07
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTAAATATGAAATTGTAATAAACTCCA
Done.