Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3790
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: 49897
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Found at i:4210 original size:23 final size:22
Alignment explanation
Indices: 4138--4225 Score: 92
Period size: 21 Copynumber: 4.1 Consensus size: 22
4128 TACCTGATCA
*
4138 GAATACGACACATAA-GTGCCT
1 GAATACGACACACAAGGTGCCT
*
4159 GAA-ACGACACACGAGGTGCCT
1 GAATACGACACACAAGGTGCCT
* *
4180 G-CTGCGACACACAAGGTGCCT
1 GAATACGACACACAAGGTGCCT
* *
4201 GAAATACGACACATAAAGTGCCT
1 G-AATACGACACACAAGGTGCCT
4224 GA
1 GA
4226 TCAGTAAAGC
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
20 9 0.17
21 27 0.50
22 1 0.02
23 17 0.31
ACGTcount: A:0.35, C:0.26, G:0.24, T:0.15
Consensus pattern (22 bp):
GAATACGACACACAAGGTGCCT
Found at i:4222 original size:44 final size:41
Alignment explanation
Indices: 4143--4224 Score: 101
Period size: 44 Copynumber: 1.9 Consensus size: 41
4133 GATCAGAATA
* * *
4143 CGACACATAAGTGCCTGAAACGACACACGAGGTGCCTGCTG
1 CGACACACAAGTGCCTGAAACGACACACAAAGTGCCTGCTG
*
4184 CGACACACAAGGTGCCTGAAATACGACACATAAAGTGCCTG
1 CGACACACAA-GTGCCTG-AA-ACGACACACAAAGTGCCTG
4225 ATCAGTAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 9 0.26
42 7 0.21
43 2 0.06
44 16 0.47
ACGTcount: A:0.33, C:0.28, G:0.24, T:0.15
Consensus pattern (41 bp):
CGACACACAAGTGCCTGAAACGACACACAAAGTGCCTGCTG
Found at i:4462 original size:28 final size:28
Alignment explanation
Indices: 4430--4512 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
4420 AACACACCAG
* *
4430 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
4458 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
4486 TATAATCCATCCAAAACACA-CAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
4513 GCACAAAGTG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 40 0.80
29 10 0.20
ACGTcount: A:0.47, C:0.30, G:0.04, T:0.19
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:4485 original size:23 final size:23
Alignment explanation
Indices: 4416--4486 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 23
4406 AAATGTCCAA
*
4416 CCAAAACACACCAGTATAATCCT
1 CCAAAACACACCAGAATAATCCT
4439 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG----A-ATAATCCT
*
4467 CCCAAACACACCAGAATAAT
1 CCAAAACACACCAGAATAAT
4487 ATAATCCATC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
23 19 0.46
24 1 0.02
28 21 0.51
ACGTcount: A:0.45, C:0.34, G:0.04, T:0.17
Consensus pattern (23 bp):
CCAAAACACACCAGAATAATCCT
Found at i:15488 original size:13 final size:14
Alignment explanation
Indices: 15472--15513 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
15462 TTTTGATTTT
15472 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
15485 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
15500 ATTTTAAATAATAT
1 ATTTT-AATAATAT
15514 TATTAGCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:15498 original size:16 final size:16
Alignment explanation
Indices: 15476--15512 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
15466 GATTTTATTT
15476 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
15493 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
15508 TAATA
1 TAATA
15513 TTATTAGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:15565 original size:15 final size:15
Alignment explanation
Indices: 15545--15601 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
15535 ATTCAATGTT
15545 AATATTTTAATAATA
1 AATATTTTAATAATA
*
15560 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
15579 AATATATTAATAATA
1 AATATTTTAATAATA
*
15594 AATGTTTT
1 AATATTTT
15602 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:21977 original size:19 final size:19
Alignment explanation
Indices: 21955--22001 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
21945 GAAATAAAAT
* *
21955 AAAAATAAAAATAAAAAGG
1 AAAAATAAAAACAAAAAGA
*
21974 AAAAATAATAACAAAAAGA
1 AAAAATAAAAACAAAAAGA
21993 AAGAAATAA
1 AA-AAATAA
22002 CAAAAGGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.79, C:0.02, G:0.09, T:0.11
Consensus pattern (19 bp):
AAAAATAAAAACAAAAAGA
Found at i:22002 original size:17 final size:17
Alignment explanation
Indices: 21935--22006 Score: 60
Period size: 17 Copynumber: 4.2 Consensus size: 17
21925 GTTGAGAATA
21935 AAAAAGAAAAGAAATAA-
1 AAAAAG-AAAGAAATAAC
* * *
21952 AATAA-AAATAAA-AAT
1 AAAAAGAAAGAAATAAC
*
21967 AAAAAGGAAAAATAATAAC
1 AAAAA-GAAAGA-AATAAC
21986 AAAAAGAAAGAAATAAC
1 AAAAAGAAAGAAATAAC
22003 AAAA
1 AAAA
22007 GGAGAACGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
14 2 0.05
15 10 0.23
17 18 0.41
18 7 0.16
19 7 0.16
ACGTcount: A:0.79, C:0.03, G:0.08, T:0.10
Consensus pattern (17 bp):
AAAAAGAAAGAAATAAC
Found at i:22042 original size:17 final size:18
Alignment explanation
Indices: 22016--22059 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
22006 AGGAGAACGT
*
22016 AGAAAAGAAGGAAAGA-A
1 AGAAAGGAAGGAAAGACA
*
22033 AGAAAGGAAGGAATGACA
1 AGAAAGGAAGGAAAGACA
*
22051 AAAAAGGAA
1 AGAAAGGAA
22060 ATTTGTGGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.66, C:0.02, G:0.30, T:0.02
Consensus pattern (18 bp):
AGAAAGGAAGGAAAGACA
Found at i:23141 original size:23 final size:23
Alignment explanation
Indices: 23072--23142 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 23
23062 AAATGTCCAA
*
23072 CCAAAACACACCAGTATAATCCT
1 CCAAAACACACCAGAATAATCCT
23095 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG----A-ATAATCCT
*
23123 CCCAAACACACCAGAATAAT
1 CCAAAACACACCAGAATAAT
23143 ATGATCCATC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
23 19 0.46
24 1 0.02
28 21 0.51
ACGTcount: A:0.45, C:0.34, G:0.04, T:0.17
Consensus pattern (23 bp):
CCAAAACACACCAGAATAATCCT
Found at i:23168 original size:29 final size:28
Alignment explanation
Indices: 23086--23169 Score: 114
Period size: 28 Copynumber: 3.0 Consensus size: 28
23076 AACACACCAG
* *
23086 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
23114 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
* *
23142 TATGATCCATCCAAAACACACTAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
23170 GCACAAAGTG
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
28 32 0.65
29 17 0.35
ACGTcount: A:0.45, C:0.30, G:0.05, T:0.20
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:34163 original size:13 final size:14
Alignment explanation
Indices: 34147--34188 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
34137 TTTTGATTTT
34147 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
34160 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
34175 ATTTTAAATAATAT
1 ATTTT-AATAATAT
34189 TATTAGCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:34173 original size:16 final size:16
Alignment explanation
Indices: 34151--34187 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
34141 GATTTTATTT
34151 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
34168 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
34183 TAATA
1 TAATA
34188 TTATTAGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:34240 original size:15 final size:15
Alignment explanation
Indices: 34220--34276 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
34210 ATTCAATGTT
34220 AATATTTTAATAATA
1 AATATTTTAATAATA
*
34235 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
34254 AATATATTAATAATA
1 AATATTTTAATAATA
*
34269 AATGTTTT
1 AATATTTT
34277 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:40498 original size:19 final size:19
Alignment explanation
Indices: 40474--40514 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
40464 GACTTATAAG
40474 AGATTTGAATCGTAGAAGT
1 AGATTTGAATCGTAGAAGT
40493 AGATTTGAATCGTAGAAGT
1 AGATTTGAATCGTAGAAGT
40512 AGA
1 AGA
40515 GGAGAAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.39, C:0.05, G:0.27, T:0.29
Consensus pattern (19 bp):
AGATTTGAATCGTAGAAGT
Found at i:40639 original size:16 final size:15
Alignment explanation
Indices: 40618--40693 Score: 64
Period size: 16 Copynumber: 4.7 Consensus size: 15
40608 TTGAGTTGAG
40618 AATAAAAAAGAAAAGA
1 AATAAAAAAGAAAA-A
40634 AATAAAATAA-AATAAA
1 AATAAAA-AAGAA-AAA
*
40650 AATAAAAAGGAAAAA
1 AATAAAAAAGAAAAA
*
40665 TAATAACAAAAAGAAAGA
1 -AAT-A-AAAAAGAAAAA
40683 AATAACAAAAG
1 AATAA-AAAAG
40694 GAGAACGTGG
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
15 5 0.10
16 28 0.56
17 8 0.16
18 9 0.18
ACGTcount: A:0.78, C:0.03, G:0.09, T:0.11
Consensus pattern (15 bp):
AATAAAAAAGAAAAA
Found at i:40664 original size:19 final size:19
Alignment explanation
Indices: 40642--40687 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
40632 GAAATAAAAT
* *
40642 AAAATAAAAATAAAAAGGA
1 AAAATAAAAACAAAAAGAA
*
40661 AAAATAATAACAAAAAGAA
1 AAAATAAAAACAAAAAGAA
40680 AGAAATAA
1 A-AAATAA
40688 CAAAAGGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.78, C:0.02, G:0.09, T:0.11
Consensus pattern (19 bp):
AAAATAAAAACAAAAAGAA
Found at i:40727 original size:16 final size:18
Alignment explanation
Indices: 40703--40744 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
40693 GGAGAACGTG
*
40703 GAAAAGAAGGAA-GA-AA
1 GAAAGGAAGGAATGACAA
40719 GAAAGGAAGGAATGACAA
1 GAAAGGAAGGAATGACAA
*
40737 AAAAGGAA
1 GAAAGGAA
40745 ATTTGTGGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 11 0.50
17 2 0.09
18 9 0.41
ACGTcount: A:0.64, C:0.02, G:0.31, T:0.02
Consensus pattern (18 bp):
GAAAGGAAGGAATGACAA
Done.