Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013135.1 Corchorus olitorius cultivar O-4 contig13168, 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: 23714
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Found at i:1180 original size:33 final size:31
Alignment explanation
Indices: 1079--1219 Score: 120
Period size: 33 Copynumber: 4.3 Consensus size: 31
1069 TTGCAAAGAG
* * * *
1079 TGTTTTAGATGTTGTTTGCGATGATACTAAAAC
1 TGTTTT-GGTGTTGTTTGTGATGAAAC-AAATC
** *
1112 TAATTTGAGTGTTGTTTGTGATGACACTAAATC
1 TGTTTTG-GTGTTGTTTGTGATGAAAC-AAATC
1145 TGTTTTAGGTGTTGTTTGTGATGAAACAAATTC
1 TGTTTT-GGTGTTGTTTGTGATGAAACAAA-TC
* **
1178 TGTTTTGGATGCTAATTGTGATGAAAACAAATC
1 TGTTTTGG-TGTTGTTTGTGATG-AAACAAATC
1211 TGTTTTGGT
1 TGTTTTGGT
1220 TGATCATAGC
Statistics
Matches: 91, Mismatches: 12, Indels: 11
0.80 0.11 0.10
Matches are distributed among these distances:
32 7 0.08
33 76 0.84
34 8 0.09
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.43
Consensus pattern (31 bp):
TGTTTTGGTGTTGTTTGTGATGAAACAAATC
Found at i:2998 original size:21 final size:21
Alignment explanation
Indices: 2972--3063 Score: 150
Period size: 21 Copynumber: 4.4 Consensus size: 21
2962 TGCTAGGAGA
2972 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
2993 TCATTGGAGAAGGTTCTAAGC
1 TCATTGGAGAAGGTTCCAAGC
3014 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
3035 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
3056 TCATTGGA
1 TCATTGGA
3064 ATTGCCTAAG
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
20 2 0.03
21 65 0.97
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:4148 original size:35 final size:35
Alignment explanation
Indices: 4102--4622 Score: 537
Period size: 35 Copynumber: 14.9 Consensus size: 35
4092 GCTGGTCTTT
*
4102 AGTTGATCCAGGGCGATCTTTTTTCAGTTTATTTC
1 AGTTGATCCAGGGCGATCTTTCTTCAGTTTATTTC
* * * *
4137 AGTTGACCCAGGGTGGTCTTTCTTTAGTTTATTTC
1 AGTTGATCCAGGGCGATCTTTCTTCAGTTTATTTC
* *
4172 AGTTGACCCAAGGC-AGTCTTTCTTCAGTTTATTTC
1 AGTTGATCCAGGGCGA-TCTTTCTTCAGTTTATTTC
* * ** *
4207 AATTGACCCAGGGCGGCCTTTCTTCGGTTTATTTC
1 AGTTGATCCAGGGCGATCTTTCTTCAGTTTATTTC
* * * *
4242 AGTTGATCCAGGGTGATTTTTCTCCAGTTAATTTC
1 AGTTGATCCAGGGCGATCTTTCTTCAGTTTATTTC
* *
4277 AGTTGATCCAAGGCGATCTTTCTTCACTTTATTTC
1 AGTTGATCCAGGGCGATCTTTCTTCAGTTTATTTC
* * * *
4312 AGTTGATCCAAGGCGGTCTTTTCTTTAGTTTATTTT
1 AGTTGATCCAGGGCGATC-TTTCTTCAGTTTATTTC
* * *
4348 AGTTGATCCAGGGTGATCTTTCTCCAGTTAATTTC
1 AGTTGATCCAGGGCGATCTTTCTTCAGTTTATTTC
* * * *
4383 AGTTGACCCAAGGCGGTCTTTCTTTAGTTTATTTC
1 AGTTGATCCAGGGCGATCTTTCTTCAGTTTATTTC
* * *
4418 AGTTGATCTAGGGCGATCTTTCTTCAATTTATTTT
1 AGTTGATCCAGGGCGATCTTTCTTCAGTTTATTTC
* * *
4453 AATTGATCCA-GGTGAT-TCTTCTTCAGTTAATTTC
1 AGTTGATCCAGGGCGATCT-TTCTTCAGTTTATTTC
* *
4487 AATTGATCCAGGGCGATCTTTCCTCAG-TTATTTC
1 AGTTGATCCAGGGCGATCTTTCTTCAGTTTATTTC
* * * *
4521 AGTTGACCCAGGGCGGTCTTTCTTTAGTTAATTTC
1 AGTTGATCCAGGGCGATCTTTCTTCAGTTTATTTC
* * * *
4556 AATTGATCCAGGGTGGTCTTTCTTCGGTTTATTTC
1 AGTTGATCCAGGGCGATCTTTCTTCAGTTTATTTC
* * * * *
4591 AGTTGACCCAGAGTGGTCTTTCTCCAGTTTAT
1 AGTTGATCCAGGGCGATCTTTCTTCAGTTTAT
4623 GCCAGAACGA
Statistics
Matches: 399, Mismatches: 80, Indels: 14
0.81 0.16 0.03
Matches are distributed among these distances:
33 1 0.00
34 56 0.14
35 312 0.78
36 30 0.08
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.43
Consensus pattern (35 bp):
AGTTGATCCAGGGCGATCTTTCTTCAGTTTATTTC
Found at i:4297 original size:105 final size:105
Alignment explanation
Indices: 4102--4622 Score: 622
Period size: 105 Copynumber: 5.0 Consensus size: 105
4092 GCTGGTCTTT
* * * * * *
4102 AGTTGATCCAGGGCGATCTTTTTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTTAGTTT
1 AGTTGATCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTCTTCAGTTA
4167 ATTTCAGTTGACCCAAGGC-AGTCTTTCTTCAGTTTATTTC
66 ATTTCAGTTGACCCAAGGCGA-TCTTTCTTCAGTTTATTTC
* * * * * *
4207 AATTGACCCAGGGCGGCCTTTCTTCGGTTTATTTCAGTTGATCCAGGGTGATTTTTCTCCAGTTA
1 AGTTGATCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTCTTCAGTTA
* *
4272 ATTTCAGTTGATCCAAGGCGATCTTTCTTCACTTTATTTC
66 ATTTCAGTTGACCCAAGGCGATCTTTCTTCAGTTTATTTC
* * * *
4312 AGTTGATCCAAGGCGGTCTTTTCTTTAGTTTATTTTAGTTGATCCAGGGTGATCTTTCTCCAGTT
1 AGTTGATCCAGGGCGGTC-TTTCTTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTCTTCAGTT
* *
4377 AATTTCAGTTGACCCAAGGCGGTCTTTCTTTAGTTTATTTC
65 AATTTCAGTTGACCCAAGGCGATCTTTCTTCAGTTTATTTC
* * * * *
4418 AGTTGATCTAGGGCGATCTTTCTTCAATTTATTTTAATTGATCCA-GGTGAT-TCTTCTTCAGTT
1 AGTTGATCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGTGATCT-TTCTTCAGTT
* * * *
4481 AATTTCAATTGATCCAGGGCGATCTTTCCTCAG-TTATTTC
65 AATTTCAGTTGACCCAAGGCGATCTTTCTTCAGTTTATTTC
* * * * * * *
4521 AGTTGACCCAGGGCGGTCTTTCTTTAGTTAATTTCAATTGATCCAGGGTGGTCTTTCTTCGGTTT
1 AGTTGATCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTCTTCAGTTA
*
4586 ATTTCAGTTGACCCAGAGTG-G-TCTTTCTCCAGTTTAT
66 ATTTCAGTTGACCCA-AG-GCGATCTTTCTTCAGTTTAT
4623 GCCAGAACGA
Statistics
Matches: 354, Mismatches: 54, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
103 46 0.13
104 78 0.22
105 134 0.38
106 96 0.27
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.43
Consensus pattern (105 bp):
AGTTGATCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTCTTCAGTTA
ATTTCAGTTGACCCAAGGCGATCTTTCTTCAGTTTATTTC
Found at i:10722 original size:17 final size:16
Alignment explanation
Indices: 10700--10735 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
10690 CTCTGCTTTG
10700 TTTTCTAGTTTAATTGT
1 TTTTCT-GTTTAATTGT
10717 TTTTCTGTTTAATTGT
1 TTTTCTGTTTAATTGT
10733 TTT
1 TTT
10736 CCGTCAACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.14, C:0.06, G:0.11, T:0.69
Consensus pattern (16 bp):
TTTTCTGTTTAATTGT
Found at i:17038 original size:17 final size:16
Alignment explanation
Indices: 17016--17051 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
17006 CTCTGCTTTG
17016 TTTTCTAGTTTAATTGT
1 TTTTCT-GTTTAATTGT
17033 TTTTCTGTTTAATTGT
1 TTTTCTGTTTAATTGT
17049 TTT
1 TTT
17052 ATGTCAACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.14, C:0.06, G:0.11, T:0.69
Consensus pattern (16 bp):
TTTTCTGTTTAATTGT
Found at i:20316 original size:15 final size:16
Alignment explanation
Indices: 20288--20317 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
20278 ATTTATTGCC
20288 TTCTTTTGTAATTTAG
1 TTCTTTTGTAATTTAG
20304 TTCTTTT-TAATTTA
1 TTCTTTTGTAATTTA
20318 AATTTACTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (16 bp):
TTCTTTTGTAATTTAG
Done.