Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015824.1 Corchorus olitorius cultivar O-4 contig15857, 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: 58706
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:7669 original size:29 final size:30
Alignment explanation
Indices: 7599--7670 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 30
7589 ATACCATACA
7599 GGTCCCTCTACTTACAAATAATGATCAATTT
1 GGTCCCTCTAC-TACAAATAATGATCAATTT
* *
7630 GGT-CTTCCTACTACAAA-AACTG-TTAATTT
1 GGTCCCT-CTACTACAAATAA-TGATCAATTT
7659 GGTCCCTCTACT
1 GGTCCCTCTACT
7671 TATAATTTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
29 16 0.46
30 12 0.34
31 7 0.20
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (30 bp):
GGTCCCTCTACTACAAATAATGATCAATTT
Found at i:8025 original size:29 final size:29
Alignment explanation
Indices: 7970--8040 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
7960 CCAAATTGTA
**
7970 AGTAGAGGGACCAAATTGACAGTTTTTAT
1 AGTAGAGGGACCAAATTGACACCTTTTAT
* *
7999 AGTAGGGGGACCAAATTGATC-CCTTTTTGT
1 AGTAGAGGGACCAAATTGA-CACC-TTTTAT
8029 CAGTAGAGGGAC
1 -AGTAGAGGGAC
8041 TTCTACGGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
29 18 0.53
30 6 0.18
31 10 0.29
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (29 bp):
AGTAGAGGGACCAAATTGACACCTTTTAT
Found at i:12591 original size:13 final size:13
Alignment explanation
Indices: 12566--12610 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
12556 GCATGGCCGC
12566 CTTTTGTTT-TTTT
1 CTTTT-TTTGTTTT
*
12579 GTTTTTTTGTTTT
1 CTTTTTTTGTTTT
*
12592 TTTTTTTTGTTTT
1 CTTTTTTTGTTTT
12605 CTTTTT
1 CTTTTT
12611 CGAATGAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 3 0.11
13 25 0.89
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (13 bp):
CTTTTTTTGTTTT
Found at i:12604 original size:8 final size:8
Alignment explanation
Indices: 12567--12599 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
12557 CATGGCCGCC
12567 TTTTGTTT
1 TTTTGTTT
12575 TTTTGTTT
1 TTTTGTTT
12583 TTTTGTTT
1 TTTTGTTT
12591 TTTT-TTT
1 TTTTGTTT
12598 TT
1 TT
12600 GTTTTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.20
8 20 0.80
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (8 bp):
TTTTGTTT
Found at i:19895 original size:11 final size:11
Alignment explanation
Indices: 19879--19903 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19869 TCCCAATATA
19879 TAAATCCTTTT
1 TAAATCCTTTT
19890 TAAATCCTTTT
1 TAAATCCTTTT
19901 TAA
1 TAA
19904 CTATATCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (11 bp):
TAAATCCTTTT
Found at i:24559 original size:18 final size:18
Alignment explanation
Indices: 24533--24577 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
24523 TTTCGGAGTT
* *
24533 TCGGCTTCGATTTACGAG
1 TCGGGTTCGAGTTACGAG
* *
24551 TCGGGTTCGGGTTACGGG
1 TCGGGTTCGAGTTACGAG
24569 TCGGGTTCG
1 TCGGGTTCG
24578 TCGAGATCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.09, C:0.20, G:0.40, T:0.31
Consensus pattern (18 bp):
TCGGGTTCGAGTTACGAG
Found at i:30717 original size:2 final size:2
Alignment explanation
Indices: 30710--30740 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
30700 TAATTACCCT
*
30710 TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30741 TGATTGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:36188 original size:13 final size:13
Alignment explanation
Indices: 36148--36190 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
36138 TTAATGTTTC
36148 AAGTAGTAACAAA
1 AAGTAGTAACAAA
* * *
36161 AAGAAGGAAAAAAA
1 AAGTA-GTAACAAA
36175 AAGTAGTAACAAA
1 AAGTAGTAACAAA
36188 AAG
1 AAG
36191 AAAAGAAAAG
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
13 13 0.57
14 10 0.43
ACGTcount: A:0.67, C:0.05, G:0.19, T:0.09
Consensus pattern (13 bp):
AAGTAGTAACAAA
Found at i:36204 original size:13 final size:13
Alignment explanation
Indices: 36188--36215 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
36178 TAGTAACAAA
36188 AAGAAAAGAAAAG
1 AAGAAAAGAAAAG
36201 AAGAAAAGAAAAG
1 AAGAAAAGAAAAG
36214 AA
1 AA
36216 ATCCCAACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAGAAAAGAAAAG
Found at i:41718 original size:54 final size:54
Alignment explanation
Indices: 41643--41753 Score: 152
Period size: 54 Copynumber: 2.1 Consensus size: 54
41633 GGTGATTTTT
* * * *
41643 GATCACTTCTGGTGATTTTGGGTGGTAATTTCATATCACCCCATTTGGTTTGCA
1 GATCACTTCTGGTGATCTTGGGTGGTAATCTCAGATCACCCCATTTGATTTGCA
* *
41697 GATCAC-TCGTGGTGATCTTGGGTGGTAATCTCAGATCACCGCGTTTGATTTGCA
1 GATCACTTC-TGGTGATCTTGGGTGGTAATCTCAGATCACCCCATTTGATTTGCA
41751 GAT
1 GAT
41754 GTTACACTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
53 2 0.04
54 48 0.96
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (54 bp):
GATCACTTCTGGTGATCTTGGGTGGTAATCTCAGATCACCCCATTTGATTTGCA
Found at i:45351 original size:17 final size:17
Alignment explanation
Indices: 45329--45383 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
45319 AATTATCCCC
*
45329 AGATCACTAGTGATCTA
1 AGATCACCAGTGATCTA
*
45346 AGATCACCAGTGATGTA
1 AGATCACCAGTGATCTA
* * *
45363 AGATTACCGGTGATCAA
1 AGATCACCAGTGATCTA
45380 AGAT
1 AGAT
45384 TACATGAGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (17 bp):
AGATCACCAGTGATCTA
Found at i:52573 original size:6 final size:6
Alignment explanation
Indices: 52562--52606 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
52552 CTTTGAATCT
*
52562 TACCTA TACCTA TACCTA TGCCTA TACCTATA TACCT- TACCTA TA
1 TACCTA TACCTA TACCTA TACCTA TACC--TA TACCTA TACCTA TA
52607 TATTAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 5 0.15
6 23 0.68
8 6 0.18
ACGTcount: A:0.31, C:0.31, G:0.02, T:0.36
Consensus pattern (6 bp):
TACCTA
Found at i:54738 original size:2 final size:2
Alignment explanation
Indices: 54731--54756 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54721 ACTAGTCTCT
54731 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
54757 AAAGCTAGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.