Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold901
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: 36362
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Found at i:2957 original size:14 final size:14
Alignment explanation
Indices: 2938--2978 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
2928 TTATTTATGA
2938 ATTTTAAAAATTAT
1 ATTTTAAAAATTAT
*
2952 ATTTTAAAAA-AAT
1 ATTTTAAAAATTAT
*
2965 A-ATTAAAAATTAT
1 ATTTTAAAAATTAT
2978 A
1 A
2979 CTTAAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
12 7 0.30
13 6 0.26
14 10 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTTTAAAAATTAT
Found at i:5152 original size:2 final size:2
Alignment explanation
Indices: 5145--5181 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
5135 ATAAGGGATC
* *
5145 TA TA TA TA TA TA TG TA TA TA TA TA TG TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5182 TTATTTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5164 original size:12 final size:12
Alignment explanation
Indices: 5147--5181 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
5137 AAGGGATCTA
5147 TATATATATATG
1 TATATATATATG
5159 TATATATATATG
1 TATATATATATG
5171 TATATATATAT
1 TATATATATAT
5182 TTATTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (12 bp):
TATATATATATG
Found at i:7707 original size:2 final size:2
Alignment explanation
Indices: 7700--7743 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
7690 TACTGAATGG
7700 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7742 AT
1 AT
7744 TTCATTATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7858 original size:3 final size:3
Alignment explanation
Indices: 7850--7884 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
7840 AATTTAGCAA
7850 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
7885 CTTAAAATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12971 original size:19 final size:20
Alignment explanation
Indices: 12947--12986 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
12937 AAACTTGATC
* *
12947 TTTTAAATATATTAAA-AAA
1 TTTTAAAAAAATTAAACAAA
12966 TTTTAAAAAAATTAAACAAA
1 TTTTAAAAAAATTAAACAAA
12986 T
1 T
12987 CCATGTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTTAAAAAAATTAAACAAA
Found at i:16048 original size:13 final size:13
Alignment explanation
Indices: 16030--16067 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
16020 TAGTCATGAG
16030 TTATAAATTATAT
1 TTATAAATTATAT
*
16043 TTATAAA-TATAA
1 TTATAAATTATAT
16055 TT-TAAATTATAT
1 TTATAAATTATAT
16067 T
1 T
16068 AAATATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 4 0.18
12 11 0.50
13 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTATAAATTATAT
Found at i:21598 original size:25 final size:26
Alignment explanation
Indices: 21545--21598 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
21535 ATAATAAATG
* *
21545 AATTTAAATTTTAAAGTATTTATATA
1 AATTTAAATTTTAAAGTATTTAAAAA
21571 AATTTAAA-TTTAAA-TATTATAAAAA
1 AATTTAAATTTTAAAGTATT-TAAAAA
21596 AAT
1 AAT
21599 AAAGATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 4 0.16
25 13 0.52
26 8 0.32
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
AATTTAAATTTTAAAGTATTTAAAAA
Found at i:22458 original size:2 final size:2
Alignment explanation
Indices: 22451--22487 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
22441 GGTTTTACAT
22451 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22488 GTTTGTGCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25978 original size:28 final size:28
Alignment explanation
Indices: 25946--26002 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
25936 CTGAAGAAAG
25946 AATATGTCACACAATAGCTCTACATCTT
1 AATATGTCACACAATAGCTCTACATCTT
25974 AATATGTCACACAATAGCTCTACATCTT
1 AATATGTCACACAATAGCTCTACATCTT
26002 A
1 A
26003 TTAACACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.25, G:0.07, T:0.32
Consensus pattern (28 bp):
AATATGTCACACAATAGCTCTACATCTT
Found at i:29221 original size:5 final size:5
Alignment explanation
Indices: 29208--29293 Score: 50
Period size: 5 Copynumber: 16.2 Consensus size: 5
29198 TGATTAAATT
*
29208 ATATAA ATATA ATATAA AAATA AT-TAA ATATA ATATA ATATTTA ATATA
1 ATAT-A ATATA ATAT-A ATATA ATAT-A ATATA ATATA ATA--TA ATATA
* * * *
29257 ATATTA ATACGA ATATA TTAAA ATTTA A-ATA ATATA A
1 ATA-TA ATA-TA ATATA ATATA ATATA ATATA ATATA A
29294 ATTATTATTA
Statistics
Matches: 62, Mismatches: 11, Indels: 15
0.70 0.12 0.17
Matches are distributed among these distances:
4 4 0.06
5 35 0.56
6 18 0.29
7 5 0.08
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:29256 original size:17 final size:17
Alignment explanation
Indices: 29208--29293 Score: 60
Period size: 17 Copynumber: 5.4 Consensus size: 17
29198 TGATTAAATT
*
29208 ATATAA-ATATAATATA
1 ATATAATATTTAATATA
*
29224 A-A-AATAATTAAATATA
1 ATATAAT-ATTTAATATA
29240 ATATAATATTTAATATA
1 ATATAATATTTAATATA
**
29257 ATATTAATA-CGAATAT-
1 ATA-TAATATTTAATATA
*
29273 AT-TAAAATTTAA-ATA
1 ATATAATATTTAATATA
29288 ATATAA
1 ATATAA
29294 ATTATTATTA
Statistics
Matches: 54, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
14 8 0.15
15 5 0.09
16 15 0.28
17 18 0.33
18 8 0.15
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (17 bp):
ATATAATATTTAATATA
Found at i:29265 original size:11 final size:10
Alignment explanation
Indices: 29202--29265 Score: 51
Period size: 11 Copynumber: 6.0 Consensus size: 10
29192 GAAATATGAT
29202 TAAATT-ATA
1 TAAATTAATA
29211 TAAATATAATA
1 TAAAT-TAATA
*
29222 TAAAAATAAT-
1 T-AAATTAATA
29232 TAAATATAATA
1 TAAAT-TAATA
29243 TAATATTTAATA
1 TAA-A-TTAATA
29255 TAATATTAATA
1 TAA-ATTAATA
29266 CGAATATATT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
9 8 0.17
10 6 0.13
11 17 0.37
12 14 0.30
13 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TAAATTAATA
Found at i:30736 original size:26 final size:26
Alignment explanation
Indices: 30687--30735 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
30677 ATACAATAAG
30687 TTTCTTTCTTTATAATATTCTTTTCT
1 TTTCTTTCTTTATAATATTCTTTTCT
30713 TTTCTTT-TTT-TAGATATTCTTTT
1 TTTCTTTCTTTATA-ATATTCTTTT
30736 TTAACTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 2 0.09
25 13 0.59
26 7 0.32
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.71
Consensus pattern (26 bp):
TTTCTTTCTTTATAATATTCTTTTCT
Found at i:30942 original size:22 final size:22
Alignment explanation
Indices: 30900--30952 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
30890 AAATTAATGA
30900 AAAT-TTTTTAAATTAATATTT
1 AAATATTTTTAAATTAATATTT
*
30921 ATATATTTTTATAATTAA-ATTT
1 AAATATTTTTA-AATTAATATTT
30943 AAATATTTTT
1 AAATATTTTT
30953 TTATTATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 3 0.11
22 19 0.68
23 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AAATATTTTTAAATTAATATTT
Found at i:30953 original size:24 final size:22
Alignment explanation
Indices: 30903--30964 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 22
30893 TTAATGAAAA
30903 TTTTTTA-AATTAATATTTATAT
1 TTTTTTATAATTAA-ATTTATAT
*
30925 ATTTTTATAATTAAATTTAAATAT
1 TTTTTTATAATTAAATTT--ATAT
*
30949 TTTTTTATTATTAAAT
1 TTTTTTATAATTAAAT
30965 AGTGATTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.29
23 6 0.18
24 18 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTTTTATAATTAAATTTATAT
Found at i:31220 original size:32 final size:33
Alignment explanation
Indices: 31184--31253 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
31174 AAGATTTTTA
* *
31184 TTTAAAT-TTAATTATAAA-ATTAATATAAATAT
1 TTTAAATATT-ATTATAAATAATAAAATAAATAT
* *
31216 TTTAAATATTATTTTAAATAATAAAATAAATTT
1 TTTAAATATTATTATAAATAATAAAATAAATAT
31249 TTTAA
1 TTTAA
31254 TCTATTTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (33 bp):
TTTAAATATTATTATAAATAATAAAATAAATAT
Found at i:31513 original size:31 final size:30
Alignment explanation
Indices: 31447--31529 Score: 150
Period size: 29 Copynumber: 2.8 Consensus size: 30
31437 CACAAAATAA
31447 TAAAAAAAAAGTCAATTAATTACATTGTTT
1 TAAAAAAAAAGTCAATTAATTACATTGTTT
31477 T-AAAAAAAAGTCAATTAATTACATTGTTT
1 TAAAAAAAAAGTCAATTAATTACATTGTTT
31506 TAAAAAAAAGAGTCAATTAATTAC
1 TAAAAAAAA-AGTCAATTAATTAC
31530 GGTGAGCATA
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
29 29 0.57
30 8 0.16
31 14 0.27
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (30 bp):
TAAAAAAAAAGTCAATTAATTACATTGTTT
Found at i:32274 original size:23 final size:24
Alignment explanation
Indices: 32247--32312 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 24
32237 TATATTATCT
** *
32247 TTATATAATATAAATTATATAATA
1 TTATATAATATAAAAAATAAAATA
* *
32271 -TATAAAAAATAAAAAATAAAATA
1 TTATATAATATAAAAAATAAAATA
32294 TTATATAAT-TAAAAAATAA
1 TTATATAATATAAAAAATAA
32313 GTTAAATCGG
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
23 28 0.82
24 6 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
TTATATAATATAAAAAATAAAATA
Found at i:32757 original size:22 final size:22
Alignment explanation
Indices: 32712--32757 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
32702 TAAAATAATA
* *
32712 TATATTTTTATATTAATATTTT
1 TATACTTTTATATTAATATATT
32734 TATACTTTTATAATTAA-ATATT
1 TATACTTTTAT-ATTAATATATT
32756 TA
1 TA
32758 AATAAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TATACTTTTATATTAATATATT
Found at i:33498 original size:36 final size:33
Alignment explanation
Indices: 33451--33544 Score: 104
Period size: 32 Copynumber: 2.8 Consensus size: 33
33441 TTTAATTATA
*
33451 AAATATATATTAATATTATATTTATAAATAAACTTT
1 AAATA-ATATTAATATTATATTT-TAAATAAA-TAT
*
33487 AAATTAATATT-AT-TTA-AATTTAAATAAATAT
1 AAA-TAATATTAATATTATATTTTAAATAAATAT
*
33518 AAATAATTTTAATATTATATTTTAAAT
1 AAATAATATTAATATTATATTTTAAAT
33545 TTAATTTAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
30 6 0.12
31 7 0.14
32 11 0.22
33 11 0.22
34 3 0.06
35 2 0.04
36 8 0.16
37 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (33 bp):
AAATAATATTAATATTATATTTTAAATAAATAT
Found at i:33904 original size:30 final size:30
Alignment explanation
Indices: 33868--33929 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
33858 TATTTAAATT
* **
33868 TAAAAATTTAAATTATTATTTAAATATTAA
1 TAAAAATTAAAAAAATTATTTAAATATTAA
**
33898 TAAAAATTAAAAAAATTATTTTTATATTAA
1 TAAAAATTAAAAAAATTATTTAAATATTAA
33928 TA
1 TA
33930 TTAATATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
TAAAAATTAAAAAAATTATTTAAATATTAA
Found at i:34568 original size:22 final size:22
Alignment explanation
Indices: 34543--34585 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
34533 GAGAATGAAG
* *
34543 GAAGTAAATGGAAAGGGAAAGC
1 GAAGGAAAGGGAAAGGGAAAGC
34565 GAAGGAAAGGGAAAGGGAAAG
1 GAAGGAAAGGGAAAGGGAAAG
34586 AGAGTTAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.02, G:0.42, T:0.05
Consensus pattern (22 bp):
GAAGGAAAGGGAAAGGGAAAGC
Found at i:34959 original size:16 final size:17
Alignment explanation
Indices: 34935--34980 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
34925 GTAGCGATTC
*
34935 TTCATTTTTTTTTC-TT
1 TTCAATTTTTTTTCATT
*
34951 TTCAATTTTTTGTCATT
1 TTCAATTTTTTTTCATT
34968 TT-AATTTATTTTT
1 TTCAATTT-TTTTT
34981 ACGTATTTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 17 0.68
17 8 0.32
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (17 bp):
TTCAATTTTTTTTCATT
Found at i:36058 original size:19 final size:19
Alignment explanation
Indices: 36023--36069 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
36013 TTCTTATTAT
*
36023 TTATTTA-TTCTTCTCTTA
1 TTATTTACTTCTTATCTTA
*
36041 TTATTTACTTGTTATCTTA
1 TTATTTACTTCTTATCTTA
36060 TTATCTTACT
1 TTAT-TTACT
36070 CTTTTTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.28
19 13 0.52
20 5 0.20
ACGTcount: A:0.19, C:0.15, G:0.02, T:0.64
Consensus pattern (19 bp):
TTATTTACTTCTTATCTTA
Done.