Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2470
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: 12782
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:378 original size:17 final size:17
Alignment explanation
Indices: 345--382 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
335 AAGAAAATAA
*
345 AATTTTATAATTAAAATT
1 AATTTTATAAATAAAA-T
363 AATTTT-TAAATAAAAT
1 AATTTTATAAATAAAAT
379 AATT
1 AATT
383 AATTATCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 8 0.42
18 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTTTATAAATAAAAT
Found at i:1789 original size:20 final size:22
Alignment explanation
Indices: 1764--1804 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
1754 GTTAATGATG
1764 TTATTTA-ATTAAAA-TAAAAC
1 TTATTTATATTAAAATTAAAAC
1784 TTATTTATATTAAAATTAAAA
1 TTATTTATATTAAAATTAAAA
1805 AAAATTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
21 7 0.37
22 5 0.26
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TTATTTATATTAAAATTAAAAC
Found at i:2295 original size:16 final size:16
Alignment explanation
Indices: 2269--2315 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
2259 CTACACTTAT
2269 ATATAAATTATTTTAAA
1 ATAT-AATTATTTTAAA
*
2286 TTATAATTATATTTAAA
1 ATATAATTAT-TTTAAA
*
2303 ATAT-TTTATTTTA
1 ATATAATTATTTTA
2316 TATTTACAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 4 0.15
16 10 0.38
17 12 0.46
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATAATTATTTTAAA
Found at i:4913 original size:27 final size:27
Alignment explanation
Indices: 4884--4939 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
4874 TATATTTAAA
* *
4884 TTTTATTATTTTAAAAATAAATATTTAT
1 TTTTA-TATTATAAAAATAAAAATTTAT
4912 TTTTATATTATAAAAATAAAAATTTAT
1 TTTTATATTATAAAAATAAAAATTTAT
4939 T
1 T
4940 AAAAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTTATATTATAAAAATAAAAATTTAT
Found at i:7766 original size:1 final size:1
Alignment explanation
Indices: 7760--7784 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
7750 ACTCAAACCC
7760 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
7785 CTCAACATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:8152 original size:2 final size:2
Alignment explanation
Indices: 8145--8183 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
8135 TAATGAAAGC
* *
8145 GA GA GA GA GA GA GA GA GA GA G- GA GA GA GG GA GG GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
8184 TTGGACCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (2 bp):
GA
Found at i:8171 original size:19 final size:19
Alignment explanation
Indices: 8147--8183 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
8137 ATGAAAGCGA
8147 GAGAGAGAGAGAGAGAGAG
1 GAGAGAGAGAGAGAGAGAG
* *
8166 GAGAGAGGGAGGGAGAGA
1 GAGAGAGAGAGAGAGAGA
8184 TTGGACCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (19 bp):
GAGAGAGAGAGAGAGAGAG
Found at i:8409 original size:20 final size:19
Alignment explanation
Indices: 8386--8433 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
8376 TTTAATAGAC
8386 ATTTTTATTTTTTATTATTA
1 ATTTTTATTTTTTATT-TTA
* *
8406 ATTTTGAGTTTTTATTTTA
1 ATTTTTATTTTTTATTTTA
*
8425 AATTTTATT
1 ATTTTTATT
8434 AAAGAATAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (19 bp):
ATTTTTATTTTTTATTTTA
Found at i:11743 original size:26 final size:26
Alignment explanation
Indices: 11713--11762 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
11703 TATAGATTTT
11713 TATTATA-TTTATATTATATTTAAATA
1 TATTATATTTTA-ATTATATTTAAATA
*
11739 TATTATATTTTAATTATTTTTAAA
1 TATTATATTTTAATTATATTTAAA
11763 ATTTTGTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TATTATATTTTAATTATATTTAAATA
Found at i:12086 original size:19 final size:19
Alignment explanation
Indices: 12046--12181 Score: 63
Period size: 19 Copynumber: 7.2 Consensus size: 19
12036 ATTATTTTTT
**
12046 AAATTTAAAAA-AATTATGA
1 AAATTTAAAAATAAAAAT-A
12065 AAATTTAAAAATAAAAATA
1 AAATTTAAAAATAAAAATA
* *
12084 AAA--TAAAAA-AAATTATC
1 AAATTTAAAAATAAA-AATA
12101 AAA--TAAAAATAAAAAATA
1 AAATTTAAAAAT-AAAAATA
*
12119 TTAATATTCATAAAAT-AAAATA
1 --AA-ATTTA-AAAATAAAAATA
* * *
12141 AAATTCAAAAA-ATATATA
1 AAATTTAAAAATAAAAATA
*
12159 AAATTCAAAAAATAAAAATA
1 AAATT-TAAAAATAAAAATA
12179 AAA
1 AAA
12182 AATTATAAAA
Statistics
Matches: 92, Mismatches: 12, Indels: 25
0.71 0.09 0.19
Matches are distributed among these distances:
16 3 0.03
17 17 0.18
18 15 0.16
19 28 0.30
20 16 0.17
21 1 0.01
22 6 0.07
23 1 0.01
24 5 0.05
ACGTcount: A:0.71, C:0.03, G:0.01, T:0.26
Consensus pattern (19 bp):
AAATTTAAAAATAAAAATA
Found at i:12087 original size:28 final size:29
Alignment explanation
Indices: 12055--12192 Score: 99
Period size: 28 Copynumber: 4.8 Consensus size: 29
12045 TAAATTTAAA
*
12055 AAAATTATGAAAATTTA-AAAATAAAAAT
1 AAAATTATAAAAATTTATAAAATAAAAAT
* * *
12083 AAAA-TAAAAAAAATTATCAAATAAAAAT
1 AAAATTATAAAAATTTATAAAATAAAAAT
* * * *
12111 AAAAAATATTAATATTCATAAAAT-AAAAT
1 -AAAATTATAAAAATTTATAAAATAAAAAT
*
12140 AAAATTCA-AAAAATATATAAAATTCAAAAAAT
1 AAAATT-ATAAAAATTTATAAAA-T--AAAAAT
*
12172 AAAA--ATAAAAAATTATAAAAT
1 AAAATTATAAAAATTTATAAAAT
12193 TTTGTAAAAT
Statistics
Matches: 84, Mismatches: 17, Indels: 17
0.71 0.14 0.14
Matches are distributed among these distances:
27 9 0.11
28 29 0.35
29 13 0.15
30 24 0.29
32 9 0.11
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.26
Consensus pattern (29 bp):
AAAATTATAAAAATTTATAAAATAAAAAT
Found at i:12107 original size:22 final size:23
Alignment explanation
Indices: 12079--12121 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
12069 TTAAAAATAA
12079 AAAT-AAAATAAAAAAAATTATC
1 AAATAAAAATAAAAAAAATTATC
*
12101 AAATAAAAATAAAAAATATTA
1 AAATAAAAATAAAAAAAATTA
12122 ATATTCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (23 bp):
AAATAAAAATAAAAAAAATTATC
Found at i:12200 original size:26 final size:26
Alignment explanation
Indices: 12171--12243 Score: 71
Period size: 25 Copynumber: 2.9 Consensus size: 26
12161 ATTCAAAAAA
12171 TAAAAATA-AAAAATTATAAAATTTTG
1 TAAAAATATAAAAA-TATAAAATTTTG
* * *
12197 TAAAATTATTAAAATATAAAA-TTTA
1 TAAAAATATAAAAATATAAAATTTTG
* *
12222 AAAAAAGATAAAAATA-AAAATT
1 TAAAAATATAAAAATATAAAATT
12244 AAATTAAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
24 4 0.11
25 16 0.42
26 14 0.37
27 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (26 bp):
TAAAAATATAAAAATATAAAATTTTG
Found at i:12266 original size:28 final size:28
Alignment explanation
Indices: 12235--12294 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
12225 AAAGATAAAA
*
12235 ATAAAAATTAAATTAAATTCAAAAAATT
1 ATAAAAAATAAATTAAATTCAAAAAATT
** *
12263 ATAAAAAATCCATTAAATTTAAAAAATT
1 ATAAAAAATAAATTAAATTCAAAAAATT
12291 ATAA
1 ATAA
12295 TTTTCAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAAAAAATAAATTAAATTCAAAAAATT
Found at i:12324 original size:14 final size:13
Alignment explanation
Indices: 12287--12325 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
12277 AAATTTAAAA
12287 AATTATAATTTTC
1 AATTATAATTTTC
12300 AATTATAATTTTC
1 AATTATAATTTTC
*
12313 TATTATTAATTTT
1 AATTA-TAATTTT
12326 TTGAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 17 0.71
14 7 0.29
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (13 bp):
AATTATAATTTTC
Found at i:12332 original size:29 final size:27
Alignment explanation
Indices: 12295--12348 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
12285 AAAATTATAA
*
12295 TTTTCAATTATAATTTTCTATTATTAATT
1 TTTTCAATT-TAATTTT-TATAATTAATT
* *
12324 TTTTGAATTTTATTTTTATAATTAA
1 TTTTCAATTTAATTTTTATAATTAA
12349 AACTTATGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 8 0.36
28 6 0.27
29 8 0.36
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (27 bp):
TTTTCAATTTAATTTTTATAATTAATT
Found at i:12396 original size:10 final size:9
Alignment explanation
Indices: 12363--12400 Score: 53
Period size: 8 Copynumber: 4.3 Consensus size: 9
12353 TATGAATTTT
12363 ATTTTTA-A
1 ATTTTTATA
12371 ATTTTTATA
1 ATTTTTATA
12380 A-TTTTATA
1 ATTTTTATA
12388 GATTTTTATA
1 -ATTTTTATA
12398 ATT
1 ATT
12401 CTGAATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 14 0.52
9 6 0.22
10 7 0.26
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (9 bp):
ATTTTTATA
Found at i:12410 original size:16 final size:17
Alignment explanation
Indices: 12370--12412 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
12360 TTTATTTTTA
* *
12370 AATTTTTATAATTTTAT
1 AATTTTTATAATTCTAG
12387 AGATTTTTATAATTCT-G
1 A-ATTTTTATAATTCTAG
12404 AATTTTTAT
1 AATTTTTAT
12413 TTTTGTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 8 0.35
17 2 0.09
18 13 0.57
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (17 bp):
AATTTTTATAATTCTAG
Done.