Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1419
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: 35275
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:1216 original size:82 final size:82
Alignment explanation
Indices: 1119--1286 Score: 336
Period size: 82 Copynumber: 2.0 Consensus size: 82
1109 AAACACATGA
1119 TTCCCCTCCTTGGTGCTCAGGTATGCATAAATTTATTCTGTTATCCATGGCTTTTGTTATCTTTA
1 TTCCCCTCCTTGGTGCTCAGGTATGCATAAATTTATTCTGTTATCCATGGCTTTTGTTATCTTTA
1184 TCTTTATAATGATTCTT
66 TCTTTATAATGATTCTT
1201 TTCCCCTCCTTGGTGCTCAGGTATGCATAAATTTATTCTGTTATCCATGGCTTTTGTTATCTTTA
1 TTCCCCTCCTTGGTGCTCAGGTATGCATAAATTTATTCTGTTATCCATGGCTTTTGTTATCTTTA
1266 TCTTTATAATGATTCTT
66 TCTTTATAATGATTCTT
1283 TTCC
1 TTCC
1287 TGCATATTTT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 86 1.00
ACGTcount: A:0.18, C:0.20, G:0.13, T:0.49
Consensus pattern (82 bp):
TTCCCCTCCTTGGTGCTCAGGTATGCATAAATTTATTCTGTTATCCATGGCTTTTGTTATCTTTA
TCTTTATAATGATTCTT
Found at i:20938 original size:102 final size:104
Alignment explanation
Indices: 20735--20939 Score: 378
Period size: 102 Copynumber: 2.0 Consensus size: 104
20725 ACTGTTCATT
*
20735 TTCATGTCTATTGAATGAAGTTTATTGCACTTCCCCGTGTGAGAGCAAAATTTTTTTTTATAATG
1 TTCATGTCTATTGAATGAAGTTTATTGCACTTCCCCATGTGAGAGCAAAA-TTTTTTTTATAATG
20800 TCATGAAAATTGCATGTTCGTGCCATCCAGGTTCCTAAAC
65 TCATGAAAATTGCATGTTCGTGCCATCCAGGTTCCTAAAC
20840 TTCAT-TCTATTGAATGAAGTTTATTGCACTTCCCCATGTGAGAGCAAAA-TTTTTTTATAATGT
1 TTCATGTCTATTGAATGAAGTTTATTGCACTTCCCCATGTGAGAGCAAAATTTTTTTTATAATGT
20903 CATGAAAATTGCATGTTCGTGCCATCCAGGTTCCTAA
66 CATGAAAATTGCATGTTCGTGCCATCCAGGTTCCTAA
20940 GCTTGCTTCA
Statistics
Matches: 99, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
102 51 0.52
104 43 0.43
105 5 0.05
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (104 bp):
TTCATGTCTATTGAATGAAGTTTATTGCACTTCCCCATGTGAGAGCAAAATTTTTTTTATAATGT
CATGAAAATTGCATGTTCGTGCCATCCAGGTTCCTAAAC
Found at i:24581 original size:3 final size:3
Alignment explanation
Indices: 24575--24603 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
24565 TTTTTTTTTC
24575 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
24604 TTTTTGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:25640 original size:3 final size:3
Alignment explanation
Indices: 25632--25671 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
25622 TGTAGCTCTT
25632 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
25672 CTTTCTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:26272 original size:16 final size:16
Alignment explanation
Indices: 26233--26265 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
26223 TTTTTAAAAA
26233 TTAATATTTAATAATT
1 TTAATATTTAATAATT
26249 TTAATATTT-ATAATT
1 TTAATATTTAATAATT
26264 TT
1 TT
26266 TTATATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAATATTTAATAATT
Found at i:33328 original size:2 final size:2
Alignment explanation
Indices: 33315--33353 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
33305 AGAAAACAGC
*
33315 AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
33354 CAAAACTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:33913 original size:3 final size:3
Alignment explanation
Indices: 33905--33937 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
33895 GAACTTGCAA
33905 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
33938 GATGGGAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.