Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1301
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: 22223
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Found at i:1134 original size:14 final size:15
Alignment explanation
Indices: 1105--1141 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1095 ATAATATTAA
1105 ATAATTTTAAATTTT
1 ATAATTTTAAATTTT
1120 A-AATTTT-AATATTT
1 ATAATTTTAAAT-TTT
1134 ATAATTTT
1 ATAATTTT
1142 TTTCTATCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.15
14 10 0.50
15 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATAATTTTAAATTTT
Found at i:1796 original size:13 final size:13
Alignment explanation
Indices: 1780--1804 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1770 AAATTTTTTT
1780 ATTAATATTTATA
1 ATTAATATTTATA
1793 ATTAATATTTAT
1 ATTAATATTTAT
1805 CATAATTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTAATATTTATA
Found at i:1833 original size:20 final size:20
Alignment explanation
Indices: 1777--1833 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
1767 TTTAAATTTT
1777 TTTATTAATATTTATAATTAATA
1 TTTATT-ATA-TT-TAATTAATA
* * *
1800 TTTATCATAATTAATTATTA
1 TTTATTATATTTAATTAATA
1820 TTTATTATATTTAA
1 TTTATTATATTTAA
1834 AATTATAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 20 0.69
21 1 0.03
22 3 0.10
23 5 0.17
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTATTATATTTAATTAATA
Found at i:2696 original size:16 final size:16
Alignment explanation
Indices: 2671--2704 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2661 TTATATTTTT
*
2671 TTTATTTTTTTAAATA
1 TTTATATTTTTAAATA
*
2687 TTTATATTTTTACATA
1 TTTATATTTTTAAATA
2703 TT
1 TT
2705 CGTAAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATATTTTTAAATA
Found at i:4156 original size:19 final size:18
Alignment explanation
Indices: 4112--4159 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
4102 ACATAAATAT
* *
4112 AAAAATATAAATTTTAAA
1 AAAAATTTAAATTATAAA
**
4130 AACTATTTAAATATATAAA
1 AAAAATTTAAAT-TATAAA
4149 AAAAATTTAAA
1 AAAAATTTAAA
4160 AATTAAATAT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAATTTAAATTATAAA
Found at i:4723 original size:2 final size:2
Alignment explanation
Indices: 4674--4706 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4664 TTCACTAATG
4674 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4707 CACACACACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5921 original size:21 final size:21
Alignment explanation
Indices: 5880--5921 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5870 ACAGATAATT
*
5880 ATTTTAAAAAGTAAAATTTTA
1 ATTTTAAAAAGTAAAAGTTTA
*
5901 ATTTTAATAA-TAATAAGTTTA
1 ATTTTAAAAAGTAA-AAGTTTA
5922 CTGCTTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (21 bp):
ATTTTAAAAAGTAAAAGTTTA
Found at i:12379 original size:19 final size:19
Alignment explanation
Indices: 12355--12394 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
12345 ACCTGCGTTT
*
12355 GAGTGACAAAACATTTAAA
1 GAGTGACAAAACATCTAAA
*
12374 GAGTGATAAAACATCTAAA
1 GAGTGACAAAACATCTAAA
12393 GA
1 GA
12395 AGATACGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.10, G:0.17, T:0.20
Consensus pattern (19 bp):
GAGTGACAAAACATCTAAA
Found at i:17204 original size:9 final size:10
Alignment explanation
Indices: 17174--17251 Score: 56
Period size: 10 Copynumber: 8.0 Consensus size: 10
17164 GCCATAACTG
17174 TATTTATATTA
1 TATTTAT-TTA
*
17185 TATTAATTTA
1 TATTTATTTA
17195 T-TTTATTTA
1 TATTTATTTA
*
17204 TGTTT-TTTA
1 TATTTATTTA
*
17213 TA--TATATA
1 TATTTATTTA
* *
17221 TATATATATA
1 TATTTATTTA
*
17231 TTTTTATATTA
1 TATTTAT-TTA
17242 TATTTATTTA
1 TATTTATTTA
17252 AATTATTTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
7 1 0.02
8 5 0.09
9 13 0.24
10 21 0.39
11 14 0.26
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (10 bp):
TATTTATTTA
Found at i:17328 original size:18 final size:19
Alignment explanation
Indices: 17296--17331 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17286 ATATCATAAT
*
17296 TTTTTATATATTTATATTG
1 TTTTAATATATTTATATTG
17315 TTTTAATATA-TTATATT
1 TTTTAATATATTTATATT
17332 AATATATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTTAATATATTTATATTG
Found at i:18469 original size:6 final size:6
Alignment explanation
Indices: 18450--18489 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
18440 GTTATATATA
18450 AAAATT AAAA-- AAAATT AAAATT AAAAATT AAAATT AAAAT
1 AAAATT AAAATT AAAATT AAAATT -AAAATT AAAATT AAAAT
18490 GTTTTGGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 4 0.13
6 21 0.68
7 6 0.19
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (6 bp):
AAAATT
Found at i:18477 original size:13 final size:13
Alignment explanation
Indices: 18448--18488 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
18438 TTGTTATATA
18448 TAAAAATT-AAA-
1 TAAAAATTAAAAT
18459 -AAAAATTAAAAT
1 TAAAAATTAAAAT
18471 TAAAAATTAAAAT
1 TAAAAATTAAAAT
18484 TAAAA
1 TAAAA
18489 TGTTTTGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.26
11 3 0.11
13 17 0.63
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
TAAAAATTAAAAT
Found at i:19028 original size:19 final size:20
Alignment explanation
Indices: 18995--19037 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
18985 TTTTTAGTAA
*
18995 AAAAATATTAGAATTTATT-T
1 AAAAATAATAGAA-TTATTAT
19015 AAAAATAATA-AATTATTAT
1 AAAAATAATAGAATTATTAT
19034 AAAA
1 AAAA
19038 TTACTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 7 0.33
20 9 0.43
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAAATAATAGAATTATTAT
Found at i:19515 original size:20 final size:19
Alignment explanation
Indices: 19487--19526 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
19477 ATAAAGTTTA
19487 AATTTTTTTAATTTAAATT
1 AATTTTTTTAATTTAAATT
19506 AATTTATTTTAATTTAAATT
1 AATTT-TTTTAATTTAAATT
19526 A
1 A
19527 TTATTGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTTTTTTAATTTAAATT
Found at i:19835 original size:20 final size:21
Alignment explanation
Indices: 19810--19848 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
19800 TCAAATTTAT
19810 TAAAT-ATAATATT-ATTAATA
1 TAAATAAT-ATATTAATTAATA
19830 TAAATAATATATTAATTAA
1 TAAATAATATATTAATTAA
19849 ACTTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAATAATATATTAATTAATA
Found at i:19838 original size:18 final size:16
Alignment explanation
Indices: 19815--19849 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
19805 TTTATTAAAT
19815 ATAATATTATTAATATAA
1 ATAATA-TATTAAT-TAA
19833 ATAATATATTAATTAA
1 ATAATATATTAATTAA
19849 A
1 A
19850 CTTTAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 7 0.41
18 6 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAATATATTAATTAA
Found at i:20003 original size:13 final size:13
Alignment explanation
Indices: 19981--20019 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
19971 TTATTTCATA
*
19981 ATATTTTAAATAT
1 ATATTATAAATAT
19994 ATATTATAAATAT
1 ATATTATAAATAT
*
20007 ATA-TATATATAT
1 ATATTATAAATAT
20019 A
1 A
20020 GAGAGAGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATATTATAAATAT
Found at i:20943 original size:15 final size:15
Alignment explanation
Indices: 20925--20955 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20915 TAATTTTTTA
*
20925 TTAATTTATATTGAT
1 TTAATTTAAATTGAT
20940 TTAATTTAAATTGAT
1 TTAATTTAAATTGAT
20955 T
1 T
20956 AATAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (15 bp):
TTAATTTAAATTGAT
Found at i:20997 original size:13 final size:12
Alignment explanation
Indices: 20978--21013 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
20968 ATATTTTATT
20978 TAAAATTAATTA
1 TAAAATTAATTA
*
20990 TAAAAATTAAATA
1 T-AAAATTAATTA
21003 TAAAATTAATT
1 TAAAATTAATT
21014 TTTATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
TAAAATTAATTA
Found at i:21075 original size:16 final size:17
Alignment explanation
Indices: 21054--21090 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
21044 TGAATAATAT
*
21054 AAATAAA-TTAAATCAA
1 AAATAAATTTAAATAAA
21070 AAATAAATTTAAATAAA
1 AAATAAATTTAAATAAA
21087 AAAT
1 AAAT
21091 TTAAAATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATAAATTTAAATAAA
Found at i:21245 original size:3 final size:3
Alignment explanation
Indices: 21237--21278 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
21227 AACAAATGTA
*
21237 AAT AAT AAT AAT AAT AAT TAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
21279 TAATTGTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:21583 original size:14 final size:14
Alignment explanation
Indices: 21549--21607 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
21539 TTAGTAATGT
*
21549 AATTTATTAA-TAA
1 AATTTAATAATTAA
21562 AATATTAATAATTAA
1 AAT-TTAATAATTAA
**
21577 AATTTAATTTTTAA
1 AATTTAATAATTAA
21591 TAATTTAA-AATTTAA
1 -AATTTAATAA-TTAA
21606 AA
1 AA
21608 GAATTTTGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
13 3 0.08
14 17 0.46
15 17 0.46
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AATTTAATAATTAA
Found at i:21604 original size:15 final size:15
Alignment explanation
Indices: 21559--21607 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
21549 AATTTATTAA
21559 TAAAATATTAATAA-T
1 TAAAAT-TTAATAATT
*
21574 TAAAATTTAAT-TTT
1 TAAAATTTAATAATT
21588 TAATAATTTAA-AATT
1 TAA-AATTTAATAATT
21603 TAAAA
1 TAAAA
21608 GAATTTTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAAATTTAATAATT
Done.