Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2696
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: 4726
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.36
Found at i:2278 original size:15 final size:16
Alignment explanation
Indices: 2242--2281 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
2232 TGTAATATTT
*
2242 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATTAA
2259 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
2274 ATAAAATT
1 ATAAAATT
2282 TATTTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:2284 original size:16 final size:17
Alignment explanation
Indices: 2242--2284 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
2232 TGTAATATTT
*
2242 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
2259 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
2274 ATAAAATTTAT
1 ATAAAATTTAT
2285 TTAAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:2715 original size:15 final size:14
Alignment explanation
Indices: 2688--2745 Score: 55
Period size: 15 Copynumber: 4.0 Consensus size: 14
2678 ATACATAAAT
*
2688 TTTTTTCTCTTTTT
1 TTTTTTCTCTTTTC
*
2702 TTTCTTTCTTTTTTCC
1 TTT-TTTCTCTTTT-C
*
2718 CTTTTTCTCTTTTC
1 TTTTTTCTCTTTTC
2732 TTTCTTTCT-TTTTC
1 TTT-TTTCTCTTTTC
2746 CAACCTTGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
14 11 0.31
15 23 0.64
16 2 0.06
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTTCTCTTTTC
Found at i:2716 original size:22 final size:23
Alignment explanation
Indices: 2688--2744 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
2678 ATACATAAAT
*
2688 TTTTTTCTCTTTTTTTTC-TTTC
1 TTTTTTCTCTTTTTTCTCTTTTC
*
2710 TTTTTTC-CCTTTTTCTCTTTTC
1 TTTTTTCTCTTTTTTCTCTTTTC
*
2732 TTTCTT-TCTTTTT
1 TTTTTTCTCTTTTT
2745 CCAACCTTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 8 0.28
22 21 0.72
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTTTCTCTTTTTTCTCTTTTC
Found at i:2739 original size:8 final size:7
Alignment explanation
Indices: 2688--2744 Score: 53
Period size: 8 Copynumber: 7.7 Consensus size: 7
2678 ATACATAAAT
2688 TTTTTTC
1 TTTTTTC
2695 TCTTTTT-
1 T-TTTTTC
2702 TTTCTTTC
1 TTT-TTTC
2710 TTTTTTCC
1 TTTTTT-C
*
2718 CTTTTTC
1 TTTTTTC
*
2725 TCTTTTC
1 TTTTTTC
2732 TTTCTTTC
1 TTT-TTTC
2740 TTTTT
1 TTTTT
2745 CCAACCTTGC
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
6 2 0.05
7 18 0.44
8 21 0.51
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTTC
Found at i:3120 original size:15 final size:16
Alignment explanation
Indices: 3081--3122 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
3071 ATATGTAAAT
3081 AATAAGAATATACATAC
1 AATAA-AATATACATAC
*
3098 ATATAAAATATACAT-G
1 A-ATAAAATATACATAC
3114 AATAAAATA
1 AATAAAATA
3123 AATTTTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 8 0.35
16 1 0.04
17 10 0.43
18 4 0.17
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.26
Consensus pattern (16 bp):
AATAAAATATACATAC
Found at i:3216 original size:9 final size:8
Alignment explanation
Indices: 3197--3251 Score: 56
Period size: 8 Copynumber: 6.6 Consensus size: 8
3187 AATACAGAAG
3197 TTTTTTCT
1 TTTTTTCT
3205 TTTTTTCT
1 TTTTTTCT
3213 TTTTTTCT
1 TTTTTTCT
*
3221 TATTCTTTAT
1 T-TT-TTTCT
* *
3231 TTATTTAT
1 TTTTTTCT
*
3239 TTCTTTCT
1 TTTTTTCT
3247 TTTTT
1 TTTTT
3252 GACAAAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
8 32 0.80
9 3 0.08
10 5 0.12
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTCT
Found at i:3241 original size:22 final size:22
Alignment explanation
Indices: 3201--3243 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3191 CAGAAGTTTT
* * *
3201 TTCTTTTTTTCTTTTTTTCTTA
1 TTCTTTATTTATTTATTTCTTA
3223 TTCTTTATTTATTTATTTCTT
1 TTCTTTATTTATTTATTTCTT
3244 TCTTTTTTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (22 bp):
TTCTTTATTTATTTATTTCTTA
Found at i:3923 original size:22 final size:24
Alignment explanation
Indices: 3898--3942 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
3888 ACAAACTTAG
3898 CATAT-ATATAAAAA-AAT-TAAAA
1 CATATCATA-AAAAATAATATAAAA
3920 CATATCATAAAAAATAATATAAA
1 CATATCATAAAAAATAATATAAA
3943 TACGATACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 10 0.50
23 6 0.30
24 4 0.20
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (24 bp):
CATATCATAAAAAATAATATAAAA
Found at i:4198 original size:22 final size:24
Alignment explanation
Indices: 4150--4200 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
4140 TTCAAATTTT
* *
4150 AAAAAATATAATATTTGACATATA
1 AAAAAATATAATATATGACATAAA
4174 AAAAAATATAA-ATATGA-ATAAA
1 AAAAAATATAATATATGACATAAA
4196 AAAAA
1 AAAAA
4201 TTTCTCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.36
23 5 0.20
24 11 0.44
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (24 bp):
AAAAAATATAATATATGACATAAA
Found at i:4216 original size:4 final size:4
Alignment explanation
Indices: 4209--4269 Score: 72
Period size: 4 Copynumber: 15.5 Consensus size: 4
4199 AATTTCTCTT
* * *
4209 TTTC TTTC TTTC CTT- TTTC TTTT TTTC TCT- TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
4255 TTTTC TTTC TTTC TT
1 -TTTC TTTC TTTC TT
4270 CCTTCTATCT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
3 4 0.08
4 40 0.83
5 4 0.08
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:4258 original size:17 final size:17
Alignment explanation
Indices: 4209--4269 Score: 81
Period size: 17 Copynumber: 3.6 Consensus size: 17
4199 AATTTCTCTT
4209 TTTCTTTCTTTCCTTTTTC
1 TTTCTTTCTTT-C-TTTTC
*
4228 TTT-TTT-TCTCTTTTC
1 TTTCTTTCTTTCTTTTC
4243 TTTCTTTCTTTCTTTTC
1 TTTCTTTCTTTCTTTTC
4260 TTTCTTTCTT
1 TTTCTTTCTT
4270 CCTTCTATCT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.21
16 4 0.11
17 20 0.53
18 3 0.08
19 3 0.08
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTCTTTCTTTCTTTTC
Done.