Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1714
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: 13048
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Found at i:189 original size:22 final size:24
Alignment explanation
Indices: 147--195 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
137 TATAATTTTC
* *
147 ATAATTTGATGAATTATTATATAT
1 ATAATATGATGAATTATTATAAAT
171 ATAATATGAT-AA-TATTATAAAT
1 ATAATATGATGAATTATTATAAAT
193 ATA
1 ATA
196 TTAAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 12 0.52
23 2 0.09
24 9 0.39
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
ATAATATGATGAATTATTATAAAT
Found at i:1116 original size:19 final size:19
Alignment explanation
Indices: 1088--1125 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1078 TTCATATTAA
*
1088 TTTAATTTTAAATAAATTT
1 TTTAAATTTAAATAAATTT
*
1107 TTTAAATTTAAATTAATTT
1 TTTAAATTTAAATAAATTT
1126 GACTCTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTAAATTTAAATAAATTT
Found at i:2800 original size:22 final size:23
Alignment explanation
Indices: 2764--2818 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
2754 GTATTATTTA
* *
2764 TTTAATTA-AATAATAT-TTAAT
1 TTTAATTATAAAAATATATAAAT
2785 TTTAATTATAAAAATATATAAAT
1 TTTAATTATAAAAATATATAAAT
*
2808 ATTAA-TATAAA
1 TTTAATTATAAA
2819 TATAAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.28
22 13 0.45
23 8 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTAATTATAAAAATATATAAAT
Found at i:4273 original size:2 final size:2
Alignment explanation
Indices: 4261--4298 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
4251 AAACTTATTA
4261 AT AT A- 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 AT AT AT A
4299 AAGCAAGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5058 original size:11 final size:10
Alignment explanation
Indices: 5042--5136 Score: 53
Period size: 11 Copynumber: 9.6 Consensus size: 10
5032 ATTTACGTGC
5042 TTATATTATGT
1 TTATATTAT-T
5053 TTATA-TA-T
1 TTATATTATT
*
5061 TT-TATTATA
1 TTATATTATT
5070 TTATAATTATGT
1 TTAT-ATTAT-T
5082 TT-TAATTATT
1 TTAT-ATTATT
5092 TTATATT-TAT
1 TTATATTAT-T
*
5102 TTA-AATATAT
1 TTATATTAT-T
5112 TTATA-TA-T
1 TTATATTATT
5120 TTATATTATAT
1 TTATATTAT-T
5131 TTATAT
1 TTATAT
5137 AATTATATTT
Statistics
Matches: 69, Mismatches: 3, Indels: 24
0.72 0.03 0.25
Matches are distributed among these distances:
7 2 0.03
8 11 0.16
9 7 0.10
10 21 0.30
11 26 0.38
12 2 0.03
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (10 bp):
TTATATTATT
Found at i:5112 original size:14 final size:15
Alignment explanation
Indices: 5093--5176 Score: 77
Period size: 14 Copynumber: 5.7 Consensus size: 15
5083 TTAATTATTT
*
5093 TATATT-TATTTAAA
1 TATATTATATTTATA
* *
5107 TATATT-TATATATT
1 TATATTATATTTATA
5121 TATATTATATTTATA
1 TATATTATATTTATA
5136 TA-ATTATATTTCATA
1 TATATTATATTT-ATA
*
5151 T-TATTAAATTATATA
1 TATATTATATT-TATA
5166 TATATATATAT
1 TATAT-TATAT
5177 ATGTAAATTG
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
14 26 0.46
15 23 0.40
16 4 0.07
17 4 0.07
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATTATATTTATA
Found at i:5118 original size:2 final size:2
Alignment explanation
Indices: 5106--5178 Score: 50
Period size: 2 Copynumber: 39.0 Consensus size: 2
5096 ATTTATTTAA
* * *
5106 AT AT AT TT AT AT AT TT AT AT -T AT AT TT AT AT A- AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
5145 TT CAT AT -T AT -T AA AT -T 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
5179 GTAAATTGTG
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
1 6 0.11
2 47 0.87
3 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:5131 original size:19 final size:19
Alignment explanation
Indices: 5042--5145 Score: 90
Period size: 19 Copynumber: 5.4 Consensus size: 19
5032 ATTTACGTGC
*
5042 TTATATTATGTTTATATAT
1 TTATATTATATTTATATAT
5061 TT-TATTATA-TTATAATTAT
1 TTATATTATATTTAT-A-TAT
*
5080 GTTTTAATTAT-TTTATATTTAT
1 -TTAT-ATTATATTTATA--TAT
*
5102 TTA-AATATATTTATATAT
1 TTATATTATATTTATATAT
*
5120 TTATATTATATTTATATAA
1 TTATATTATATTTATATAT
5139 TTATATT
1 TTATATT
5146 TCATATTATT
Statistics
Matches: 71, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
17 4 0.06
18 13 0.18
19 29 0.41
20 8 0.11
21 4 0.06
22 13 0.18
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TTATATTATATTTATATAT
Found at i:5733 original size:29 final size:32
Alignment explanation
Indices: 5701--5769 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 32
5691 TATTTATAAA
* *
5701 ATAATAAAATTT-TAT-AAAT-TTTATTTTTT
1 ATAATAAAATTTAAATAAAATATTTATTATTT
*
5730 ATAATTAAATTTAAATAAAATATTTATTATTT
1 ATAATAAAATTTAAATAAAATATTTATTATTT
5762 AGTAATAA
1 A-TAATAA
5770 TTTAAACTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 11 0.34
30 2 0.06
31 4 0.12
32 10 0.31
33 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (32 bp):
ATAATAAAATTTAAATAAAATATTTATTATTT
Found at i:5775 original size:31 final size:31
Alignment explanation
Indices: 5716--5775 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
5706 AAAATTTTAT
*
5716 AAATTTTATTTTTTATAATTAAATTTAAATA
1 AAATTTTATTATTTATAATTAAATTTAAATA
5747 AAATATTTATTATTTAGTAA-T-AATTTAAA
1 AAAT-TTTATTATTTA-TAATTAAATTTAAA
5776 CTTGATCATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 12 0.46
32 11 0.42
33 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (31 bp):
AAATTTTATTATTTATAATTAAATTTAAATA
Found at i:11007 original size:17 final size:17
Alignment explanation
Indices: 10985--11039 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 17
10975 TCTTTATCAG
10985 TATATTTTATTAT-TTCA
1 TATATTTTATTATATT-A
11002 TATATTTATATTATAGTTA
1 TATATTT-TATTATA-TTA
*
11021 TATTTTTTATTATATTA
1 TATATTTTATTATATTA
11038 TA
1 TA
11040 ATTATAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
17 12 0.35
18 13 0.38
19 7 0.21
20 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (17 bp):
TATATTTTATTATATTA
Found at i:11091 original size:11 final size:11
Alignment explanation
Indices: 11060--11143 Score: 83
Period size: 10 Copynumber: 8.1 Consensus size: 11
11050 AATTATTTTA
11060 ATTTATATAA-
1 ATTTATATAAT
*
11070 ATTT-TAAAAT
1 ATTTATATAAT
11080 ATTTATATAAT
1 ATTTATATAAT
11091 A-TTA-AT-AT
1 ATTTATATAAT
11099 ATTTATATAAGT
1 ATTTATATAA-T
11111 -TTTATATAAT
1 ATTTATATAAT
*
11121 A-TTATATATCT
1 ATTTATATA-AT
11132 ATTTATATAAT
1 ATTTATATAAT
11143 A
1 A
11144 CTTGACATAC
Statistics
Matches: 61, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
8 3 0.05
9 9 0.15
10 21 0.34
11 20 0.33
12 8 0.13
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (11 bp):
ATTTATATAAT
Found at i:11117 original size:19 final size:18
Alignment explanation
Indices: 10985--11128 Score: 71
Period size: 19 Copynumber: 7.7 Consensus size: 18
10975 TCTTTATCAG
* *
10985 TATATTT-TATTATTTCA
1 TATATTTATATAATTTTA
* *
11002 TATATTTATATTATAGTTA
1 TATATTTATATAAT-TTTA
* * *
11021 TAT-TTTTTATTATATTA
1 TATATTTATATAATTTTA
* *
11038 TA-ATTATAAATAAATTATTT
1 TATATT-TATAT-AATT-TTA
11058 TA-ATTTATATAAATTTTAA
1 TATATTTATAT-AATTTT-A
* *
11077 AATATTTATATAATATTAA
1 TATATTTATATAAT-TTTA
11096 TATATTTATATAAGTTTTA
1 TATATTTATATAA-TTTTA
11115 TATAATATTATATA
1 TAT-AT-TTATATA
11129 TCTATTTATA
Statistics
Matches: 100, Mismatches: 15, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
17 14 0.14
18 20 0.20
19 39 0.39
20 20 0.20
21 7 0.07
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (18 bp):
TATATTTATATAATTTTA
Found at i:11139 original size:39 final size:37
Alignment explanation
Indices: 11056--11139 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 37
11046 AATAAATTAT
11056 TTTA-ATTTATATAAATTTTAAAATATTTATATAATA
1 TTTATATTTATATAAATTTTAAAATATTTATATAATA
* *
11092 TTAATATATTTATATAAGTTTTATATAATA-TTATATATCTA
1 TT--TATATTTATATAAATTTTA-A-AATATTTATATA-ATA
11133 TTTATAT
1 TTTATAT
11140 AATACTTGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
36 2 0.05
38 2 0.05
39 20 0.50
40 8 0.20
41 8 0.20
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (37 bp):
TTTATATTTATATAAATTTTAAAATATTTATATAATA
Found at i:11140 original size:33 final size:30
Alignment explanation
Indices: 11081--11141 Score: 95
Period size: 30 Copynumber: 1.9 Consensus size: 30
11071 TTTTAAAATA
11081 TTTATATAATATTAATATATTTATATAAGT
1 TTTATATAATATTAATATATTTATATAAGT
11111 TTTATATAATATTATATATCTATTTATATAA
1 TTTATATAATATTA-ATA--TATTTATATAA
11142 TACTTGACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 14 0.50
31 3 0.11
33 11 0.39
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (30 bp):
TTTATATAATATTAATATATTTATATAAGT
Found at i:12057 original size:23 final size:23
Alignment explanation
Indices: 12029--12100 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 23
12019 TATTTTATTT
*
12029 TATATTAATAAATTTTAAAAATA
1 TATATTAATAAATTTTAAATATA
*
12052 TATATTTAT-AA--TT-AATATA
1 TATATTAATAAATTTTAAATATA
*
12071 TATATTTAATACATATTTAAATATA
1 TATA-TTAATAAAT-TTTAAATATA
12096 TATAT
1 TATAT
12101 ATATATATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
19 9 0.23
20 6 0.15
21 1 0.03
22 2 0.05
23 8 0.21
24 3 0.08
25 10 0.26
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (23 bp):
TATATTAATAAATTTTAAATATA
Done.