Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6649.1
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: 10584
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Found at i:812 original size:21 final size:18
Alignment explanation
Indices: 770--814 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
760 TTTTTCAAAC
770 TCTTTTTCAAATCCTCTT
1 TCTTTTTCAAATCCTCTT
*
788 TCTTTTATCACATCACTCATT
1 TCTTTT-TCAAATC-CTC-TT
809 TCTTTT
1 TCTTTT
815 GTACTCTCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
19 6 0.26
20 3 0.13
21 8 0.35
ACGTcount: A:0.18, C:0.27, G:0.00, T:0.56
Consensus pattern (18 bp):
TCTTTTTCAAATCCTCTT
Found at i:948 original size:15 final size:16
Alignment explanation
Indices: 923--954 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
913 TATCTCACAC
923 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
939 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
954 T
1 T
955 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:3134 original size:90 final size:90
Alignment explanation
Indices: 3017--3215 Score: 389
Period size: 90 Copynumber: 2.2 Consensus size: 90
3007 CAAGATTTAA
*
3017 AATCTTGATTTTCTTGATTCTTGAAATCGCTCCGAACAGCAAAATTGGGCCAAGATTCGATTTCT
1 AATCTTGATTTTCTTGATTCTTAAAATCGCTCCGAACAGCAAAATTGGGCCAAGATTCGATTTCT
3082 TGATTTTCTTGAAAACAAGAAAGTG
66 TGATTTTCTTGAAAACAAGAAAGTG
3107 AATCTTGATTTTCTTGATTCTTAAAATCGCTCCGAACAGCAAAATTGGGCCAAGATTCGATTTCT
1 AATCTTGATTTTCTTGATTCTTAAAATCGCTCCGAACAGCAAAATTGGGCCAAGATTCGATTTCT
3172 TGATTTTCTTGAAAACAAGAAAGTG
66 TGATTTTCTTGAAAACAAGAAAGTG
3197 AATCTTGATTTTCTTGATT
1 AATCTTGATTTTCTTGATT
3216 TGAGCCCATC
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 108 1.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.37
Consensus pattern (90 bp):
AATCTTGATTTTCTTGATTCTTAAAATCGCTCCGAACAGCAAAATTGGGCCAAGATTCGATTTCT
TGATTTTCTTGAAAACAAGAAAGTG
Found at i:4730 original size:21 final size:23
Alignment explanation
Indices: 4685--4731 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
4675 TCACCTGCAA
* *
4685 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
4708 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
4729 TAA
1 TAA
4732 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:10089 original size:15 final size:16
Alignment explanation
Indices: 10069--10109 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
10059 CTTCTTCTTC
10069 TTTTTTTCACGAAAATT
1 TTTTTTTCACGAAAA-T
*
10086 TTTTTTTCACG-AATT
1 TTTTTTTCACGAAAAT
10101 TTTTTTTCA
1 TTTTTTTCA
10110 ACTTGATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.43
16 2 0.09
17 11 0.48
ACGTcount: A:0.22, C:0.12, G:0.05, T:0.61
Consensus pattern (16 bp):
TTTTTTTCACGAAAAT
Found at i:10091 original size:17 final size:15
Alignment explanation
Indices: 10069--10109 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 15
10059 CTTCTTCTTC
10069 TTTTTTTCACGAAAATT
1 TTTTTTTCACG--AATT
10086 TTTTTTTCACGAATT
1 TTTTTTTCACGAATT
10101 TTTTTTTCA
1 TTTTTTTCA
10110 ACTTGATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 13 0.54
17 11 0.46
ACGTcount: A:0.22, C:0.12, G:0.05, T:0.61
Consensus pattern (15 bp):
TTTTTTTCACGAATT
Found at i:10166 original size:12 final size:12
Alignment explanation
Indices: 10149--10204 Score: 87
Period size: 12 Copynumber: 4.7 Consensus size: 12
10139 GAAACCAAAT
10149 TTTTTTTTTCAA
1 TTTTTTTTTCAA
10161 TTTTTTTTTCAA
1 TTTTTTTTTCAA
*
10173 TTTTTTTTTGAA
1 TTTTTTTTTCAA
10185 -TTTTTTTTCGAA
1 TTTTTTTTTC-AA
10197 TTTTTTTT
1 TTTTTTTT
10205 GAAGAAACTA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
11 8 0.20
12 25 0.62
13 7 0.17
ACGTcount: A:0.14, C:0.05, G:0.04, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTCAA
Done.