Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2986
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: 31260
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3182 original size:20 final size:20
Alignment explanation
Indices: 3159--3205 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
3149 CCAGTTCCCC
* *
3159 GAGCTCTTTTTAGCTCACTT
1 GAGCTCATTTAAGCTCACTT
**
3179 GAGCTCATTTAAGCTCGTTT
1 GAGCTCATTTAAGCTCACTT
3199 GAGCTCA
1 GAGCTCA
3206 ATCGAGCTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (20 bp):
GAGCTCATTTAAGCTCACTT
Found at i:3183 original size:10 final size:10
Alignment explanation
Indices: 3159--3228 Score: 50
Period size: 10 Copynumber: 6.9 Consensus size: 10
3149 CCAGTTCCCC
*
3159 GAGCTCTTTT
1 GAGCTCATTT
* *
3169 TAGCTCACTT
1 GAGCTCATTT
3179 GAGCTCATTT
1 GAGCTCATTT
* *
3189 AAGCTCGTTT
1 GAGCTCATTT
* *
3199 GAGCTCAATC
1 GAGCTCATTT
*
3209 GAGCTTAGTTT
1 GAGCTCA-TTT
*
3220 CAGCTCATT
1 GAGCTCATT
3229 CCTTTAACTT
Statistics
Matches: 43, Mismatches: 16, Indels: 2
0.70 0.26 0.03
Matches are distributed among these distances:
10 37 0.86
11 6 0.14
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.39
Consensus pattern (10 bp):
GAGCTCATTT
Found at i:8692 original size:30 final size:30
Alignment explanation
Indices: 8658--8754 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
8648 TAAACTAAAA
8658 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
8688 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
8718 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
8747 ATGAGCTA
1 -TGAGCTA
8755 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:10945 original size:12 final size:12
Alignment explanation
Indices: 10930--10960 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
10920 TTCTTTTTGC
10930 TTTTCAAAGGCT
1 TTTTCAAAGGCT
10942 TTTTCAAAGGCT
1 TTTTCAAAGGCT
10954 TTTTCAA
1 TTTTCAA
10961 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:11037 original size:6 final size:6
Alignment explanation
Indices: 11021--11070 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
11011 TTTCTTTTTA
*
11021 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
11070 T
1 T
11071 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:11053 original size:37 final size:37
Alignment explanation
Indices: 11010--11080 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
11000 CTTGCCTCTC
11010 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
11047 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
11081 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:11081 original size:16 final size:16
Alignment explanation
Indices: 11006--11066 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
10996 GCCTCTTGCC
*
11006 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
11022 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
11038 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
11054 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
11067 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:12040 original size:13 final size:13
Alignment explanation
Indices: 12014--12051 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
12004 TTTTTTTTCC
12014 TTTTTTTC-G-AT
1 TTTTTTTCTGAAT
12025 TTTTTTT-TGAAT
1 TTTTTTTCTGAAT
12037 TTTTTTTCTGAAT
1 TTTTTTTCTGAAT
12050 TT
1 TT
12052 CTTCTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.33
12 9 0.38
13 7 0.29
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (13 bp):
TTTTTTTCTGAAT
Found at i:13805 original size:30 final size:30
Alignment explanation
Indices: 13771--13867 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
13761 TAAACTAAAA
13771 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
13801 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
13831 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
13860 ATGAGCTA
1 -TGAGCTA
13868 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:14650 original size:34 final size:34
Alignment explanation
Indices: 14612--14708 Score: 88
Period size: 34 Copynumber: 3.1 Consensus size: 34
14602 TAAAGTCATG
14612 CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
1 CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
** **
14646 CATTAAATAA-AGTCA---T-GTT-AGTTT--A-
1 CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
14671 -ATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
1 CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
14704 CATTA
1 CATTA
14709 AATTAAGTCA
Statistics
Matches: 45, Mismatches: 8, Indels: 20
0.62 0.11 0.27
Matches are distributed among these distances:
24 7 0.16
25 3 0.07
26 1 0.02
28 6 0.13
29 6 0.13
30 6 0.13
32 1 0.02
33 3 0.07
34 12 0.27
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (34 bp):
CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
Found at i:15361 original size:20 final size:20
Alignment explanation
Indices: 15329--15366 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
15319 TTAAGGACTT
15329 TTTAAATTTAATATAGTTTTA
1 TTTAAATTTAATA-AGTTTTA
15350 TTTAAA-TTAATAAGTTT
1 TTTAAATTTAATAAGTTT
15367 GCATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTAAATTTAATAAGTTTTA
Found at i:21911 original size:10 final size:9
Alignment explanation
Indices: 21898--21932 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
21888 CTTTTCACTT
21898 TTTTTTGTTC
1 TTTTTT-TTC
*
21908 TTTTTTTAC
1 TTTTTTTTC
21917 TTTTTTTTC
1 TTTTTTTTC
21926 TTTTTTT
1 TTTTTTT
21933 GCTCACTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.74
10 6 0.26
ACGTcount: A:0.03, C:0.09, G:0.03, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:21918 original size:21 final size:20
Alignment explanation
Indices: 21889--21947 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
21879 CTCGCAAGAC
*
21889 TTTTCACTTTTTTTTGTTCTT
1 TTTTCACTTTTTTTTCTT-TT
*
21910 TTTTTACTTTTTTTTCTTTT
1 TTTTCACTTTTTTTTCTTTT
21930 TTTGCTCACTTCTTTTTT
1 TTT--TCACTT-TTTTTT
21948 TTTATGCTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 5 0.16
21 16 0.50
22 5 0.16
23 6 0.19
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.76
Consensus pattern (20 bp):
TTTTCACTTTTTTTTCTTTT
Found at i:25024 original size:30 final size:30
Alignment explanation
Indices: 24990--25085 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
24980 TAAACTAAAA
24990 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
25020 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
25050 TGAGCTAAG-TTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
25078 ATGAGCTA
1 -TGAGCTA
25086 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
28 1 0.02
29 21 0.41
30 26 0.51
31 3 0.06
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:27240 original size:12 final size:12
Alignment explanation
Indices: 27202--27233 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
27192 CACTCTCAAA
27202 TTTC-TTTTCAT
1 TTTCTTTTTCAT
27213 TTTCTTTTTCAT
1 TTTCTTTTTCAT
27225 TTTCTTTTT
1 TTTCTTTTT
27234 GCTTTTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTCTTTTTCAT
Found at i:27251 original size:12 final size:12
Alignment explanation
Indices: 27236--27266 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
27226 TTCTTTTTGC
27236 TTTTCAAAGGCT
1 TTTTCAAAGGCT
27248 TTTTCAAAGGCT
1 TTTTCAAAGGCT
27260 TTTTCAA
1 TTTTCAA
27267 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:27342 original size:6 final size:6
Alignment explanation
Indices: 27326--27375 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
27316 TTTCTTTTTA
*
27326 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
27375 T
1 T
27376 ATTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:27372 original size:37 final size:37
Alignment explanation
Indices: 27315--27385 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
27305 CTTGCCTCTC
27315 TTTTCTTTTTATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTATTTCATTTTCTTTATT-TTCTCTTGCT
*
27352 TTTTCTTTTTCTTTTC-TTTTCTTTATTTTCTCTT
1 TTTTCTTTTT-ATTTCATTTTCTTTATTTTCTCTT
27386 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.04, C:0.18, G:0.01, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTATTTCATTTTCTTTATTTTCTCTTGCT
Found at i:28260 original size:10 final size:10
Alignment explanation
Indices: 28245--28285 Score: 64
Period size: 10 Copynumber: 3.9 Consensus size: 10
28235 ATATACTTCG
28245 ATTTTTTTTA
1 ATTTTTTTTA
28255 ATTTTTTTTCA
1 ATTTTTTTT-A
28266 ATTTTTTTTTA
1 A-TTTTTTTTA
28277 ATTTTTTTT
1 ATTTTTTTT
28286 CGAATTTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 17 0.59
11 4 0.14
12 8 0.28
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (10 bp):
ATTTTTTTTA
Found at i:28262 original size:11 final size:11
Alignment explanation
Indices: 28246--28285 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
28236 TATACTTCGA
28246 TTTTTTTTAAT
1 TTTTTTTTAAT
*
28257 TTTTTTTCAAT
1 TTTTTTTTAAT
28268 TTTTTTTTAAT
1 TTTTTTTTAAT
28279 TTTTTTT
1 TTTTTTT
28286 CGAATTTCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTTTAAT
Found at i:28271 original size:22 final size:23
Alignment explanation
Indices: 28246--28292 Score: 87
Period size: 22 Copynumber: 2.1 Consensus size: 23
28236 TATACTTCGA
28246 TTTTTTTTAATTTTTTTTC-AAT
1 TTTTTTTTAATTTTTTTTCGAAT
28268 TTTTTTTTAATTTTTTTTCGAAT
1 TTTTTTTTAATTTTTTTTCGAAT
28291 TT
1 TT
28293 CCTCTTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (23 bp):
TTTTTTTTAATTTTTTTTCGAAT
Found at i:30025 original size:30 final size:30
Alignment explanation
Indices: 29991--30147 Score: 149
Period size: 30 Copynumber: 5.2 Consensus size: 30
29981 AAAACTAAAA
29991 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
30021 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
30051 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
30081 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
30111 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
30140 ATGAGCTA
1 -TGAGCTA
30148 GGAGTGAGCT
Statistics
Matches: 97, Mismatches: 25, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
29 6 0.06
30 85 0.88
31 6 0.06
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:30084 original size:60 final size:60
Alignment explanation
Indices: 29991--30146 Score: 287
Period size: 60 Copynumber: 2.6 Consensus size: 60
29981 AAAACTAAAA
29991 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGTTGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGTTGAGCTGAGGCTAAACTCCTAAGCTGAAGT
30051 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGTTGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGTTGAGCTGAGGCTAAACTCCTAAGCTGAAGT
*
30111 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-TATGAGCT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT-TGAGCT
30147 AGGAGTGAGC
Statistics
Matches: 94, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
59 1 0.01
60 93 0.99
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (60 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGTTGAGCTGAGGCTAAACTCCTAAGCTGAAGT
Done.