Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009950.1 Corchorus olitorius cultivar O-4 contig09982, 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: 10476
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Found at i:1231 original size:57 final size:56
Alignment explanation
Indices: 1119--1265 Score: 228
Period size: 57 Copynumber: 2.6 Consensus size: 56
1109 GCTGATATTG
* *
1119 TCATGTATAAAATATGGGGGATAG---AAAAAAAAAGAGAGTTATGGTCAGGAATC
1 TCATGTATAAAATATGGGAGATAGAAAAAAAAAAAAGAGAGTTATGGTAAGGAATC
1172 TCATGTATAAAATATGGGAGATAGAAAAAAAAAAAGAGAGAGTTATGGTAAGGAATC
1 TCATGTATAAAATATGGGAGATAGAAAAAAAAAAA-AGAGAGTTATGGTAAGGAATC
*
1229 TCATGTCTAAAATATGGGAGATAGAAAAAAAGAAAAA
1 TCATGTATAAAATATGGGAGATAGAAAAAAA-AAAAA
1266 AAAACAGTTT
Statistics
Matches: 86, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
53 23 0.27
56 8 0.09
57 51 0.59
58 4 0.05
ACGTcount: A:0.50, C:0.05, G:0.24, T:0.21
Consensus pattern (56 bp):
TCATGTATAAAATATGGGAGATAGAAAAAAAAAAAAGAGAGTTATGGTAAGGAATC
Found at i:2358 original size:16 final size:16
Alignment explanation
Indices: 2337--2367 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2327 CAGGAACATT
2337 ATTGATTTAATTAATG
1 ATTGATTTAATTAATG
2353 ATTGATTTAATTAAT
1 ATTGATTTAATTAAT
2368 TTCACTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (16 bp):
ATTGATTTAATTAATG
Found at i:3390 original size:2 final size:2
Alignment explanation
Indices: 3383--3410 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3373 GATTACCTTG
3383 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3411 CTAGAAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3438 original size:21 final size:21
Alignment explanation
Indices: 3412--3457 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
3402 TATATATATC
3412 TAGAAATGAAACTGGACAACA
1 TAGAAATGAAACTGGACAACA
3433 TAGAAATGAAACTGGACAACA
1 TAGAAATGAAACTGGACAACA
3454 TAGA
1 TAGA
3458 CTTATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.52, C:0.13, G:0.20, T:0.15
Consensus pattern (21 bp):
TAGAAATGAAACTGGACAACA
Found at i:5382 original size:3 final size:3
Alignment explanation
Indices: 5365--5459 Score: 106
Period size: 3 Copynumber: 32.0 Consensus size: 3
5355 GCATTGTTAC
*
5365 TAT TAT T-T TAC TAT TAT TAT TAT TAT TATT TAT TAT TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TA-T TAT TAT
* * * *
5411 TAT AAC TAT TAT TAT TA- TAA TAT TAT TAT TAT TA- TAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5457 TAT
1 TAT
5460 AGCCATAATA
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
2 6 0.08
3 67 0.85
4 6 0.08
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:5387 original size:17 final size:17
Alignment explanation
Indices: 5365--5459 Score: 93
Period size: 17 Copynumber: 5.4 Consensus size: 17
5355 GCATTGTTAC
*
5365 TATTATTTTACTATTAT
1 TATTATTTTAATATTAT
*
5382 TATTATTATTATTTATTAT
1 TATTATT-TTA-ATATTAT
*
5401 TATTTATTATT-ATAACTAT
1 TA-TTATT-TTAAT-ATTAT
*
5420 TATTATTATAATATTAT
1 TATTATTTTAATATTAT
*
5437 TATTATTATAATATTAT
1 TATTATTTTAATATTAT
5454 TATTAT
1 TATTAT
5460 AGCCATAATA
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
17 35 0.51
18 11 0.16
19 14 0.21
20 8 0.12
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTATTTTAATATTAT
Done.