Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023679.1 Corchorus olitorius cultivar O-4 contig23712, 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: 5197
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Found at i:1002 original size:18 final size:17
Alignment explanation
Indices: 979--1013 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
969 AAATTAGTTT
979 TGGAAATTAGGGAAATTA
1 TGGAAATTA-GGAAATTA
997 TGGAAATTAGGAAATTA
1 TGGAAATTAGGAAATTA
1014 AATGAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.29
Consensus pattern (17 bp):
TGGAAATTAGGAAATTA
Found at i:1011 original size:8 final size:9
Alignment explanation
Indices: 980--1013 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
970 AATTAGTTTT
980 GGAAATTAG
1 GGAAATTAG
*
989 GGAAATTAT
1 GGAAATTAG
998 GGAAATTA-
1 GGAAATTAG
1006 GGAAATTA
1 GGAAATTA
1014 AATGAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26
Consensus pattern (9 bp):
GGAAATTAG
Found at i:2366 original size:49 final size:47
Alignment explanation
Indices: 2291--2431 Score: 171
Period size: 49 Copynumber: 2.9 Consensus size: 47
2281 CAAGCAATCC
2291 TTTACTTTTTAC-TGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
1 TTTA-TTTTTACTTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACT
* *
2339 TTTATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTATTTTTACTTGCA-CTTTTTCTCAATTTTT-ATACAAAATTGAACT
* *
2388 TTTAATTTT-CATTGCACTTTTTATCAATTTTT-TGACAAAATTGA
1 TTTATTTTTAC-TTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA
2432 TTGGCACGCT
Statistics
Matches: 83, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
47 17 0.20
48 24 0.29
49 41 0.49
50 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.52
Consensus pattern (47 bp):
TTTATTTTTACTTGCACTTTTTCTCAATTTTTATACAAAATTGAACT
Found at i:3456 original size:330 final size:330
Alignment explanation
Indices: 2849--3482 Score: 1214
Period size: 330 Copynumber: 1.9 Consensus size: 330
2839 AGGATATTAG
* *
2849 TTAATGATTTGGTGAATGCACTTTTTCCATATCCCAAGTTGTTGCTTGAGTTTCAGGTTGCTTAG
1 TTAATCATTTGGTGAATGCACTTTTTCCATATCCCAAGTTGTTGCTTGAGTTTCAGGTTGCTCAG
2914 TATTCATCCATCAAATCCCATCAAATCCCACTTTTGAATGCTCCCTGCAAGTTAGAAGTATTTAG
66 TATTCATCCATCAAATCCCATCAAATCCCACTTTTGAATGCTCCCTGCAAGTTAGAAGTATTTAG
*
2979 TAAATTGGGGTATTTTAGAATTGCTTAAATGTTTTGTTTTGCAACTAATCTTACTGGCTGTCTTT
131 TAAATTGGGGTATTTTAGAATTGCTTAAATGTTTTGTTTTGCAACTAATCTTACTGACTGTCTTT
* *
3044 TAATCTTATTGTTTATTACTTATATAGTTTTTGACTGATTACTTTGATTAATAATTTTAGATAAT
196 TAATCTTACTGTCTATTACTTATATAGTTTTTGACTGATTACTTTGATTAATAATTTTAGATAAT
3109 GGGAAAATGCAAGAGAATCATTTGCTTCAACTGCTATCTGTAATTTTAGATAATATTACTTATAT
261 GGGAAAATGCAAGAGAATCATTTGCTTCAACTGCTATCTGTAATTTTAGATAATATTACTTATAT
3174 AGTTT
326 AGTTT
3179 TTAATCATTTGGTGAATGCACTTTTTCCATATCCCAAGTTGTTGCTTGAGTTTCAGGTTGCTCAG
1 TTAATCATTTGGTGAATGCACTTTTTCCATATCCCAAGTTGTTGCTTGAGTTTCAGGTTGCTCAG
3244 TATTCATCCATCAAATCCCATCAAATCCCACTTTTGAATGCTCCCTGCAAGTTAGAAGTATTTAG
66 TATTCATCCATCAAATCCCATCAAATCCCACTTTTGAATGCTCCCTGCAAGTTAGAAGTATTTAG
3309 TAAATTGGGGTATTTTAGAATTGCTTAAATGTTTTGTTTTGCAACTAATCTTACTGACTGTCTTT
131 TAAATTGGGGTATTTTAGAATTGCTTAAATGTTTTGTTTTGCAACTAATCTTACTGACTGTCTTT
3374 TAATCTTACTGTCTATTACTTATATAGTTTTTGACTGATTACTTTGATTAATAATTTTAGATAAT
196 TAATCTTACTGTCTATTACTTATATAGTTTTTGACTGATTACTTTGATTAATAATTTTAGATAAT
*
3439 GGGAAAATGCAAGAGAATCATTTGCTTCAGCTGCTATCTGTAAT
261 GGGAAAATGCAAGAGAATCATTTGCTTCAACTGCTATCTGTAAT
3483 ATTACAGTGG
Statistics
Matches: 298, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
330 298 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (330 bp):
TTAATCATTTGGTGAATGCACTTTTTCCATATCCCAAGTTGTTGCTTGAGTTTCAGGTTGCTCAG
TATTCATCCATCAAATCCCATCAAATCCCACTTTTGAATGCTCCCTGCAAGTTAGAAGTATTTAG
TAAATTGGGGTATTTTAGAATTGCTTAAATGTTTTGTTTTGCAACTAATCTTACTGACTGTCTTT
TAATCTTACTGTCTATTACTTATATAGTTTTTGACTGATTACTTTGATTAATAATTTTAGATAAT
GGGAAAATGCAAGAGAATCATTTGCTTCAACTGCTATCTGTAATTTTAGATAATATTACTTATAT
AGTTT
Done.