Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2523
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: 47638
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:7773 original size:25 final size:25
Alignment explanation
Indices: 7744--7793 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
7734 CAATTGCAAC
7744 AAGGGATTTATATAAACTATGATTT
1 AAGGGATTTATATAAACTATGATTT
7769 AAGGGATTTATATAAACTATGATTT
1 AAGGGATTTATATAAACTATGATTT
7794 TAACTCTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (25 bp):
AAGGGATTTATATAAACTATGATTT
Found at i:15094 original size:14 final size:14
Alignment explanation
Indices: 15074--15101 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
15064 TAAATATATA
15074 ATATTATTTTTATT
1 ATATTATTTTTATT
15088 ATATTATTTTTATT
1 ATATTATTTTTATT
15102 TTTATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
ATATTATTTTTATT
Found at i:15308 original size:13 final size:13
Alignment explanation
Indices: 15286--15318 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
15276 AATTTGAAAC
*
15286 TAAATATAGAATG
1 TAAATTTAGAATG
15299 TAAATTTAGAATG
1 TAAATTTAGAATG
15312 TAAATTT
1 TAAATTT
15319 GCACTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (13 bp):
TAAATTTAGAATG
Found at i:19686 original size:17 final size:17
Alignment explanation
Indices: 19666--19712 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
19656 ATATTTTATA
19666 AAAAATTAAAATATAAT
1 AAAAATTAAAATATAAT
19683 -AAAATTAAAA-ATAAT
1 AAAAATTAAAATATAAT
*
19698 ATAAA-TAAACATATA
1 AAAAATTAAA-ATATA
19713 TGTTAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 9 0.35
16 14 0.54
17 3 0.12
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAAATTAAAATATAAT
Found at i:19696 original size:15 final size:16
Alignment explanation
Indices: 19662--19712 Score: 63
Period size: 15 Copynumber: 3.2 Consensus size: 16
19652 AATTATATTT
19662 TATAA-AAAATTAAAA
1 TATAATAAAATTAAAA
19677 TATAATAAAATTAAAA
1 TATAATAAAATTAAAA
19693 -ATAATATAAA-TAAACA
1 TATAATA-AAATTAAA-A
19709 TATA
1 TATA
19713 TGTTAATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 15 0.47
16 14 0.44
17 3 0.09
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
TATAATAAAATTAAAA
Found at i:19759 original size:11 final size:11
Alignment explanation
Indices: 19722--19785 Score: 60
Period size: 11 Copynumber: 5.7 Consensus size: 11
19712 ATGTTAATTT
19722 ATATAAATAT-
1 ATATAAATATA
*
19732 ATA-AAATTTTAA
1 ATATAAA-TAT-A
*
19744 ATATAATTATA
1 ATATAAATATA
*
19755 ATATATAAAATA
1 ATATA-AATATA
19767 ATATAAATATA
1 ATATAAATATA
19778 ATATAAAT
1 ATATAAAT
19786 TTATAAATCA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
9 3 0.07
10 5 0.12
11 19 0.44
12 14 0.33
13 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATATAAATATA
Found at i:19773 original size:29 final size:27
Alignment explanation
Indices: 19722--19792 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 27
19712 ATGTTAATTT
*
19722 ATATAAATATATAAAATTTTAAATATA
1 ATATAAATATATAAAATTATAAATATA
19749 AT-TATAATATATAAAATAATATAAATATA
1 ATATA-AATATATAAAAT--TATAAATATA
*
19778 ATATAAATTTATAAA
1 ATATAAATATATAAA
19793 TCAATCCTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
26 2 0.05
27 14 0.37
29 20 0.53
30 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
ATATAAATATATAAAATTATAAATATA
Found at i:25168 original size:12 final size:11
Alignment explanation
Indices: 25153--25187 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
25143 AAGTTTTTTT
25153 ATATATTTAAA
1 ATATATTTAAA
25164 GATATATTTAAA
1 -ATATATTTAAA
*
25176 AGATATTTAAA
1 ATATATTTAAA
25187 A
1 A
25188 AATCATATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (11 bp):
ATATATTTAAA
Found at i:25179 original size:13 final size:12
Alignment explanation
Indices: 25153--25186 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
25143 AAGTTTTTTT
25153 ATATATTTAAAG
1 ATATATTTAAAG
25165 ATATATTTAAA-
1 ATATATTTAAAG
*
25176 AGATATTTAAA
1 ATATATTTAAA
25187 AAATCATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (12 bp):
ATATATTTAAAG
Found at i:26388 original size:21 final size:21
Alignment explanation
Indices: 26363--26442 Score: 64
Period size: 18 Copynumber: 4.0 Consensus size: 21
26353 TGACTCAATC
26363 TATTTATAAATCT-AAATTTAT
1 TATTTATAAAT-TAAAATTTAT
*
26384 TATTTATTATATTAAAATTTAT
1 TATTTA-TAAATTAAAATTTAT
*
26406 T-TTTAT--ATTAATATTTA-
1 TATTTATAAATTAAAATTTAT
*
26423 TATTTTTATAATT-AAATTTA
1 TATTTATA-AATTAAAATTTA
26443 AATAAAATAC
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
17 1 0.02
18 14 0.29
20 7 0.14
21 14 0.29
22 13 0.27
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTATAAATTAAAATTTAT
Found at i:26413 original size:18 final size:18
Alignment explanation
Indices: 26383--26442 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 18
26373 TCTAAATTTA
26383 TTATTTATTATATTAAAAT
1 TTATTT-TTATATTAAAAT
*
26402 TTATTTTTATATTAATATT
1 TTATTTTTATATTAA-AAT
26421 TATATTTTTATAATT-AAAT
1 T-TATTTTTAT-ATTAAAAT
26440 TTA
1 TTA
26443 AATAAAATAC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
18 11 0.31
19 12 0.33
20 10 0.28
21 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATTTTTATATTAAAAT
Found at i:26475 original size:17 final size:19
Alignment explanation
Indices: 26439--26481 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
26429 TATAATTAAA
26439 TTTAAATAAAATACATTAT
1 TTTAAATAAAATACATTAT
*
26458 TTTAATTAAAA-A-ATTAT
1 TTTAAATAAAATACATTAT
*
26475 TTCAAAT
1 TTTAAAT
26482 CACATCAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 10 0.48
18 1 0.05
19 10 0.48
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
TTTAAATAAAATACATTAT
Found at i:26895 original size:24 final size:25
Alignment explanation
Indices: 26868--26921 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
26858 TTCATAATAT
* *
26868 ATATTTTTTAAAAT-TTAATTTTTA
1 ATATTTTTTAAAATATAAATATTTA
26892 ATA-TTTTTAAAATATAAATATTTA
1 ATATTTTTTAAAATATAAATATTTA
26916 ATATTT
1 ATATTT
26922 ACATTAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 10 0.38
24 14 0.54
25 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
ATATTTTTTAAAATATAAATATTTA
Found at i:27211 original size:18 final size:17
Alignment explanation
Indices: 27170--27224 Score: 62
Period size: 18 Copynumber: 3.3 Consensus size: 17
27160 CTATACGATG
*
27170 ATATAT-TAAATATGAA
1 ATATATATAAATATTAA
27186 CATA-ATATAAATTATTAA
1 -ATATATATAAA-TATTAA
27204 ATATATATAAAT-TTAA
1 ATATATATAAATATTAA
27220 ATATA
1 ATATA
27225 AATTTACTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
16 11 0.32
17 11 0.32
18 12 0.35
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
ATATATATAAATATTAA
Found at i:27223 original size:30 final size:30
Alignment explanation
Indices: 27189--27245 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
27179 ATATGAACAT
*
27189 AATATAAA-TTATTAAATATATATAAATTTA
1 AATATAAATTTACTAAATATAT-TAAATTTA
*
27219 AATATAAATTTACTATATATATTAAAT
1 AATATAAATTTACTAAATATATTAAAT
27246 ATATTATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (30 bp):
AATATAAATTTACTAAATATATTAAATTTA
Found at i:37934 original size:25 final size:25
Alignment explanation
Indices: 37902--37951 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
37892 GTAAGAGTTA
37902 AAATCATAGTTTATATAAATCCCTT
1 AAATCATAGTTTATATAAATCCCTT
37927 AAATCATAGTTTATATAAATCCCTT
1 AAATCATAGTTTATATAAATCCCTT
37952 GTTGCAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (25 bp):
AAATCATAGTTTATATAAATCCCTT
Done.