Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1274
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: 17518
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Found at i:9071 original size:23 final size:22
Alignment explanation
Indices: 9043--9086 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
9033 AATTAAATCA
9043 CTAAGATTACAAAATCATATCTT
1 CTAAGATTAC-AAATCATATCTT
* *
9066 CTAAGATTGCATATCATATCT
1 CTAAGATTACAAATCATATCT
9087 AAGATTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (22 bp):
CTAAGATTACAAATCATATCTT
Found at i:9078 original size:17 final size:19
Alignment explanation
Indices: 9065--9190 Score: 183
Period size: 19 Copynumber: 6.9 Consensus size: 19
9055 AATCATATCT
9065 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
9084 TCTAAGATTTCA-ATCATA
1 TCTAAGATTGCATATCATA
9102 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
9119 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
9138 TGTAAGATTTCA-ATCATA
1 TCTAAGATTGCATATCATA
9156 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
9173 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
9191 TGAAGATTAT
Statistics
Matches: 95, Mismatches: 6, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
17 32 0.34
18 29 0.31
19 34 0.36
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:9121 original size:35 final size:35
Alignment explanation
Indices: 9065--9182 Score: 143
Period size: 35 Copynumber: 3.3 Consensus size: 35
9055 AATCATATCT
9065 TCTAAGATTGCATATCATATCTAAGATTTCAATCATA
1 TCTAAGATTG--TATCATATCTAAGATTTCAATCATA
*
9102 TCTAAGATTGTATCATATCTAAGATTGCATATCATA
1 TCTAAGATTGTATCATATCTAAGATTTCA-ATCATA
*
9138 TGTAAGATT-TCAATCATATCTAAGATTGT--ATCATA
1 TCTAAGATTGT--ATCATATCTAAGATT-TCAATCATA
9173 TCTAAGATTG
1 TCTAAGATTG
9183 CATATCATTG
Statistics
Matches: 72, Mismatches: 4, Indels: 11
0.83 0.05 0.13
Matches are distributed among these distances:
35 33 0.46
36 14 0.19
37 25 0.35
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (35 bp):
TCTAAGATTGTATCATATCTAAGATTTCAATCATA
Found at i:9138 original size:54 final size:54
Alignment explanation
Indices: 9065--9190 Score: 243
Period size: 54 Copynumber: 2.3 Consensus size: 54
9055 AATCATATCT
9065 TCTAAGATTGCATATCATATCTAAGATTTCAATCATATCTAAGATTGTATCATA
1 TCTAAGATTGCATATCATATCTAAGATTTCAATCATATCTAAGATTGTATCATA
*
9119 TCTAAGATTGCATATCATATGTAAGATTTCAATCATATCTAAGATTGTATCATA
1 TCTAAGATTGCATATCATATCTAAGATTTCAATCATATCTAAGATTGTATCATA
9173 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
9191 TGAAGATTAT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 71 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (54 bp):
TCTAAGATTGCATATCATATCTAAGATTTCAATCATATCTAAGATTGTATCATA
Found at i:9196 original size:17 final size:19
Alignment explanation
Indices: 9068--9198 Score: 127
Period size: 17 Copynumber: 7.3 Consensus size: 19
9058 CATATCTTCT
*
9068 AAGATTGCATATCATATCT
1 AAGATTGCATATCATATCG
* *
9087 AAGATTTCA-ATCATATCT
1 AAGATTGCATATCATATCG
*
9105 AAGATTG--TATCATATCT
1 AAGATTGCATATCATATCG
9122 AAGATTGCATATCATAT-G
1 AAGATTGCATATCATATCG
* *
9140 TAAGATTTCA-ATCATATCT
1 -AAGATTGCATATCATATCG
*
9159 AAGATTG--TATCATATCT
1 AAGATTGCATATCATATCG
9176 AAGATTGCATATCAT-T-G
1 AAGATTGCATATCATATCG
9193 AAGATT
1 AAGATT
9199 ATATTTCCAT
Statistics
Matches: 97, Mismatches: 7, Indels: 18
0.80 0.06 0.15
Matches are distributed among these distances:
17 38 0.39
18 29 0.30
19 30 0.31
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.38
Consensus pattern (19 bp):
AAGATTGCATATCATATCG
Found at i:9346 original size:21 final size:20
Alignment explanation
Indices: 9309--9347 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
9299 TTGGACTTCG
**
9309 TTTTTTTTTGGGTTTATTAT
1 TTTTTTTTTGGACTTATTAT
9329 TTTTGTTTTTGGACTTATT
1 TTTT-TTTTTGGACTTATT
9348 TCTGGGCCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTGGACTTATTAT
Found at i:14427 original size:25 final size:25
Alignment explanation
Indices: 14394--14441 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
14384 TTATAATATG
* *
14394 AAAATGACCATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
14419 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
14442 GTTTATACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:14522 original size:11 final size:11
Alignment explanation
Indices: 14488--14544 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
14478 ACATGGTATG
14488 TATGATATGCA
1 TATGATATGCA
* *
14499 CATGACATG--
1 TATGATATGCA
14508 TATGATATGCA
1 TATGATATGCA
14519 TATGATATG--
1 TATGATATGCA
*
14528 TATGACATGCA
1 TATGATATGCA
*
14539 CATGAT
1 TATGAT
14545 GTATTTATGA
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (11 bp):
TATGATATGCA
Found at i:14544 original size:20 final size:20
Alignment explanation
Indices: 14478--14544 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
14468 ATTTTGATAA
*
14478 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
14498 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
* *
14518 ATATGATATGTATGACATGC
1 ACATGATATGTATGATATGC
14538 ACATGAT
1 ACATGAT
14545 GTATTTATGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:14633 original size:22 final size:23
Alignment explanation
Indices: 14595--14642 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
14585 AGGAAGTGCA
*
14595 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAATTATT
*
14618 AAAGGGCTT-TGCCCCAATTGTT
1 AAAGGGCTTATGCCCCAATTATT
14640 AAA
1 AAA
14643 AGAGGCTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAATTATT
Found at i:14644 original size:23 final size:24
Alignment explanation
Indices: 14594--14649 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
14584 GAGGAAGTGC
*
14594 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAATTATT
*
14618 -AAAGGGCTT-TGCCCCAATTGTT
1 AAAAGGGCTTATGCCCCAATTATT
14640 AAAAGAGGCT
1 AAAAG-GGCT
14650 AGGCCTCCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 11 0.39
23 13 0.46
24 4 0.14
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAATTATT
Found at i:14892 original size:31 final size:31
Alignment explanation
Indices: 14857--14917 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
14847 CGTTTATAGT
14857 AAAGGCTTCGGCCCAGTAATATGAAATATGG
1 AAAGGCTTCGGCCCAGTAATATGAAATATGG
* **
14888 AAAGGCTTTGGCCCAGTGTTATGAAATATG
1 AAAGGCTTCGGCCCAGTAATATGAAATATG
14918 AAATATGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGG
Found at i:16001 original size:25 final size:25
Alignment explanation
Indices: 15972--16022 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
15962 TGAATAGTAC
15972 TGAGACTCTACTATGATACTATAGA
1 TGAGACTCTACTATGATACTATAGA
15997 TGAGACTCTACTATGATACTATAGA
1 TGAGACTCTACTATGATACTATAGA
16022 T
1 T
16023 AGGGGAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (25 bp):
TGAGACTCTACTATGATACTATAGA
Done.