Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021863.1 Corchorus olitorius cultivar O-4 contig21896, 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: 41131
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Found at i:1108 original size:6 final size:6
Alignment explanation
Indices: 1091--1137 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
1081 GTACTTTTAT
1091 ATATAG -TATAG ATATAG ATATAG ATATAAG AT-TAG -TA-AG ATA-AG
1 ATATAG ATATAG ATATAG ATATAG ATAT-AG ATATAG ATATAG ATATAG
1135 ATA
1 ATA
1138 GTAAAATAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
4 3 0.08
5 14 0.38
6 16 0.43
7 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.17, T:0.32
Consensus pattern (6 bp):
ATATAG
Found at i:1146 original size:27 final size:29
Alignment explanation
Indices: 1094--1149 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
1084 CTTTTATATA
*
1094 TAGTATAGATATAGATATAGATATAAGAT
1 TAGTATAGATATAGATATAGAAATAAGAT
1123 TAGTA-AGATA-AGATAGTA-AAATAAGAT
1 TAGTATAGATATAGATA-TAGAAATAAGAT
1150 AAGATATATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 13 0.52
28 7 0.28
29 5 0.20
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (29 bp):
TAGTATAGATATAGATATAGAAATAAGAT
Found at i:5588 original size:13 final size:14
Alignment explanation
Indices: 5549--5585 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
5539 TTTGACGCGA
5549 AATTTTGAAATTCG
1 AATTTTGAAATTCG
*
5563 AAATTTGAAATTCG
1 AATTTTGAAATTCG
5577 AATTTTGAA
1 AATTTTGAA
5586 TTCTGGAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (14 bp):
AATTTTGAAATTCG
Found at i:9481 original size:76 final size:76
Alignment explanation
Indices: 9275--9584 Score: 460
Period size: 76 Copynumber: 4.1 Consensus size: 76
9265 TTAGACGTTA
* * * *
9275 AGCCGTTGAGTGAGTGGCGTCTGCGTGGACGCTCTTTCTCACTGGTAGACGAACGGGGGCGCCAG
1 AGCCGTTGAGTGAGCGGCGTCTGCATGGACGCTCTGTCTCACTGGTGGACGAACGGGGGCGCCAG
*
9340 TCTAGGCGCTC
66 TCTAGGCACTC
* * *
9351 AGCCGTT-AGTGATCGGCGTCTGCACGGACACTCTGTCTCACTGGTGGACGAACGGGGGCGCCAG
1 AGCCGTTGAGTGAGCGGCGTCTGCATGGACGCTCTGTCTCACTGGTGGACGAACGGGGGCGCCAG
9415 TCTAGGCACTC
66 TCTAGGCACTC
* *
9426 AGCCGTTGAGTGAGCGGCGTCTGCATGGACGCTCTGCCTCATTGGTGGACGAACGGGGGCGCCAG
1 AGCCGTTGAGTGAGCGGCGTCTGCATGGACGCTCTGTCTCACTGGTGGACGAACGGGGGCGCCAG
9491 TCTAGGCACTC
66 TCTAGGCACTC
** * *
9502 AGCCGTTGAGTGAGCGGCGTCTGTGTGGACGCTCTGTCTCACTGGTGGACGAACGGGGGCACCAT
1 AGCCGTTGAGTGAGCGGCGTCTGCATGGACGCTCTGTCTCACTGGTGGACGAACGGGGGCGCCAG
* **
9567 TTTAGGTGCTC
66 TCTAGGCACTC
9578 AGCCGTT
1 AGCCGTT
9585 ATTTGAAGAA
Statistics
Matches: 211, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
75 67 0.32
76 144 0.68
ACGTcount: A:0.15, C:0.27, G:0.36, T:0.22
Consensus pattern (76 bp):
AGCCGTTGAGTGAGCGGCGTCTGCATGGACGCTCTGTCTCACTGGTGGACGAACGGGGGCGCCAG
TCTAGGCACTC
Found at i:22213 original size:20 final size:21
Alignment explanation
Indices: 22175--22213 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
22165 GAGTTTCTAA
*
22175 AAAAGCTTATATAGTTTACTT
1 AAAACCTTATATAGTTTACTT
22196 AAAACCTTATAT-GTTTAC
1 AAAACCTTATATAGTTTAC
22214 CTATAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (21 bp):
AAAACCTTATATAGTTTACTT
Found at i:23128 original size:32 final size:34
Alignment explanation
Indices: 23092--23159 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 34
23082 ATAATCTTAT
* *
23092 AAGATTAAT-TAAAAAGTTATTAAG-TAGTTCAA
1 AAGATTAATATAAAAAATTATCAAGCTAGTTCAA
* *
23124 AAGATTATTATAAAAAATTATCAGGCTAGTTCAA
1 AAGATTAATATAAAAAATTATCAAGCTAGTTCAA
23158 AA
1 AA
23160 TTGAAAATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 8 0.27
33 12 0.40
34 10 0.33
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.32
Consensus pattern (34 bp):
AAGATTAATATAAAAAATTATCAAGCTAGTTCAA
Found at i:24058 original size:15 final size:15
Alignment explanation
Indices: 24038--24067 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
24028 TATTATGAAT
24038 GTTGAAAAGTGTGTG
1 GTTGAAAAGTGTGTG
24053 GTTGAAAAGTGTGTG
1 GTTGAAAAGTGTGTG
24068 ATACTACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.40, T:0.33
Consensus pattern (15 bp):
GTTGAAAAGTGTGTG
Found at i:25696 original size:3 final size:3
Alignment explanation
Indices: 25690--25736 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
25680 CTTACTACTA
25690 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
25737 GTGGAATTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:25955 original size:21 final size:23
Alignment explanation
Indices: 25915--25999 Score: 87
Period size: 21 Copynumber: 4.0 Consensus size: 23
25905 GTGATTTTAT
25915 ATAGT-AG-TAAGAT-A-ATAAG
1 ATAGTAAGATAAGATAAGATAAG
25934 ATAGTAAGAT-AG-TAAGATAAG
1 ATAGTAAGATAAGATAAGATAAG
25955 ATAGTAAGATAAGATAAGAT-A-
1 ATAGTAAGATAAGATAAGATAAG
*
25976 ATAGTAAGATTAAGTATTAGATAA
1 ATAGTAAGA-TAAG-ATAAGATAA
26000 AACATAAATT
Statistics
Matches: 56, Mismatches: 1, Indels: 13
0.80 0.01 0.19
Matches are distributed among these distances:
19 6 0.11
20 5 0.09
21 25 0.45
22 7 0.12
23 12 0.21
24 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (23 bp):
ATAGTAAGATAAGATAAGATAAG
Found at i:25956 original size:13 final size:13
Alignment explanation
Indices: 25938--25970 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
25928 AATAAGATAG
25938 TAAGATAGTAAGA
1 TAAGATAGTAAGA
25951 TAAGATAGTAAGA
1 TAAGATAGTAAGA
25964 TAAGATA
1 TAAGATA
25971 AGATAATAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (13 bp):
TAAGATAGTAAGA
Found at i:40758 original size:27 final size:27
Alignment explanation
Indices: 40696--40818 Score: 162
Period size: 27 Copynumber: 4.7 Consensus size: 27
40686 AGGATCAACT
* *
40696 AGGGGCATTTTGGTCATTTTCA-A--A
1 AGGGGCATTTTGGTCATTTGCACATTC
*
40720 AGGGGCATTTTGGTCATTTACACATTC
1 AGGGGCATTTTGGTCATTTGCACATTC
40747 AGGGGCATTTTGGTCATTTGCACATTC
1 AGGGGCATTTTGGTCATTTGCACATTC
* *
40774 AGGGGCATTCTGGTCATTTGCACAGTC
1 AGGGGCATTTTGGTCATTTGCACATTC
* *
40801 AAGGGCATTGTGGTCATT
1 AGGGGCATTTTGGTCATT
40819 CGAACCCTTA
Statistics
Matches: 89, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
24 21 0.24
25 1 0.01
27 67 0.75
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTGCACATTC
Done.