Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold647
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: 27309
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Found at i:2648 original size:3 final size:3
Alignment explanation
Indices: 2640--2669 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2630 TTGATTACCT
2640 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2670 ATCAGCACTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:6390 original size:13 final size:13
Alignment explanation
Indices: 6359--6383 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6349 TAAAATTTAA
6359 AATTTATTTTTTT
1 AATTTATTTTTTT
6372 AATTTATTTTTT
1 AATTTATTTTTT
6384 ACTTTTAGGC
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
AATTTATTTTTTT
Found at i:6650 original size:21 final size:19
Alignment explanation
Indices: 6626--6683 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
6616 TCTTTGAAAA
6626 TAAATGATATTTATATATTTT
1 TAAAT-ATA-TTATATATTTT
* *
6647 TAAATATAATA-ATTATATT
1 TAAATATATTATA-TATTTT
6666 TAAA-ATATTATATATTTT
1 TAAATATATTATATATTTT
6684 ACATAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
18 11 0.35
19 12 0.39
20 3 0.10
21 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TAAATATATTATATATTTT
Found at i:6764 original size:8 final size:8
Alignment explanation
Indices: 6736--6775 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
6726 TATATGTATA
6736 TTTATA-T
1 TTTATATT
*
6743 TTTATTTAT
1 TTTATAT-T
6752 TTTATATT
1 TTTATATT
6760 TTTATATT
1 TTTATATT
6768 TTTATATT
1 TTTATATT
6776 ATATACATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 5 0.17
8 17 0.59
9 7 0.24
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTATATT
Found at i:6936 original size:27 final size:28
Alignment explanation
Indices: 6905--6977 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 28
6895 GTTGAGCTAA
6905 AATTTTTAAATATAAATATAAAAA-TAT
1 AATTTTTAAATATAAATATAAAAATTAT
*
6932 AATTTTTAAA-ATATAT-TAAAAATTAT
1 AATTTTTAAATATAAATATAAAAATTAT
* *
6958 ATATATTTATAT-TAAATATA
1 A-ATTTTTAAATATAAATATA
6978 TATTTAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 6 0.16
26 9 0.24
27 21 0.55
28 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
AATTTTTAAATATAAATATAAAAATTAT
Found at i:6942 original size:14 final size:14
Alignment explanation
Indices: 6905--6946 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
6895 GTTGAGCTAA
6905 AATTTTT-AAATAT
1 AATTTTTAAAATAT
* * *
6918 AAATATAAAAATAT
1 AATTTTTAAAATAT
6932 AATTTTTAAAATAT
1 AATTTTTAAAATAT
6946 A
1 A
6947 TTAAAAATTA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTTTTAAAATAT
Found at i:6978 original size:17 final size:17
Alignment explanation
Indices: 6956--6989 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6946 ATTAAAAATT
*
6956 ATATATATTTATATTAA
1 ATATATATTTAAATTAA
6973 ATATATATTTAAATTAA
1 ATATATATTTAAATTAA
6990 TCCTCACCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATATATTTAAATTAA
Found at i:7207 original size:15 final size:17
Alignment explanation
Indices: 7178--7209 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
7168 TCTAAGTACA
7178 AAAAAGAAAATTTAAAG
1 AAAAAGAAAATTTAAAG
7195 AAAAA-AAAA-TTAAAG
1 AAAAAGAAAATTTAAAG
7210 CCTACAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (17 bp):
AAAAAGAAAATTTAAAG
Found at i:9832 original size:15 final size:15
Alignment explanation
Indices: 9812--9840 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9802 TACAAAACAG
9812 AAAATAAATAAATAA
1 AAAATAAATAAATAA
9827 AAAATAAATAAATA
1 AAAATAAATAAATA
9841 TGCTTATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAATAAATAAATAA
Found at i:10202 original size:20 final size:20
Alignment explanation
Indices: 10174--10211 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10164 AATCAAAATG
*
10174 ATATTAAATACAATATAATT
1 ATATAAAATACAATATAATT
*
10194 ATATAAAATATAATATAA
1 ATATAAAATACAATATAA
10212 AAATAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
ATATAAAATACAATATAATT
Found at i:10229 original size:11 final size:11
Alignment explanation
Indices: 10178--10310 Score: 62
Period size: 11 Copynumber: 12.4 Consensus size: 11
10168 AAAATGATAT
*
10178 TAAATACAATA
1 TAAATATAATA
*
10189 TAATTAT-ATA
1 TAAATATAATA
10199 -AAATATAATA
1 TAAATATAATA
*
10209 TAAAAATAATA
1 TAAATATAATA
* *
10220 TAAATTTAATT
1 TAAATATAATA
* * **
10231 TAAGTGTTTTA
1 TAAATATAATA
10242 -AAATAT-ATAA
1 TAAATATAAT-A
*
10252 TAAATTAAAATA
1 TAAA-TATAATA
*
10264 TAAATATAAAA
1 TAAATATAATA
*
10275 TATAT-TAAATA
1 TAAATAT-AATA
* *
10286 TTATTATAATA
1 TAAATATAATA
*
10297 T-AATAAAATA
1 TAAATATAATA
10307 TAAA
1 TAAA
10311 AATTAATATG
Statistics
Matches: 88, Mismatches: 25, Indels: 18
0.67 0.19 0.14
Matches are distributed among these distances:
9 6 0.07
10 20 0.23
11 52 0.59
12 8 0.09
13 2 0.02
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (11 bp):
TAAATATAATA
Found at i:10275 original size:13 final size:12
Alignment explanation
Indices: 10251--10310 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 12
10241 AAAATATATA
10251 ATAAATTAAAAT
1 ATAAATTAAAAT
10263 ATAAATATAAAAT
1 ATAAAT-TAAAAT
10276 AT--ATT-AAAT
1 ATAAATTAAAAT
* *
10285 AT-TATTATAAT
1 ATAAATTAAAAT
10296 AT-AA-TAAAAT
1 ATAAATTAAAAT
10306 ATAAA
1 ATAAA
10311 AATTAATATG
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
9 6 0.15
10 11 0.27
11 10 0.24
12 6 0.15
13 8 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATAAATTAAAAT
Found at i:10385 original size:21 final size:21
Alignment explanation
Indices: 10350--10411 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
10340 TTTTTAGTTT
10350 TAATATATTTATAAATATAAAAA
1 TAATA-ATTT-TAAATATAAAAA
* * **
10373 TAAT-ATTATTAAAAATTAATT
1 TAATAATT-TTAAATATAAAAA
10394 TAATAATTTTAAATATAA
1 TAATAATTTTAAATATAA
10412 TATAAAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
21 23 0.74
22 4 0.13
23 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATAATTTTAAATATAAAAA
Found at i:10417 original size:53 final size:58
Alignment explanation
Indices: 10292--10422 Score: 132
Period size: 53 Copynumber: 2.3 Consensus size: 58
10282 AATATTATTA
* ** *
10292 TAATATAATA-AAATATAAAAATTAATATGTAATTGTAAAAATTTTACTTTTTTAGTTT
1 TAATATAATATAAATATAAAAATTAATATGTAATTGTAAAAA-TTTAATTTAATAATTT
*
10350 TAATATATTTATAAATATAAAAA-TAATAT-T-A-T-TAAAAA-TTAATTTAATAATTT
1 TAATATA-ATATAAATATAAAAATTAATATGTAATTGTAAAAATTTAATTTAATAATTT
*
10403 TAAATATAATATAAAAATAA
1 T-AATATAATATAAATATAA
10423 TATGCTGATA
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
53 22 0.35
54 6 0.10
55 6 0.10
56 1 0.02
57 1 0.02
58 8 0.13
59 8 0.13
60 11 0.17
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (58 bp):
TAATATAATATAAATATAAAAATTAATATGTAATTGTAAAAATTTAATTTAATAATTT
Found at i:11180 original size:23 final size:23
Alignment explanation
Indices: 11154--11224 Score: 142
Period size: 23 Copynumber: 3.1 Consensus size: 23
11144 TTCGACTCTT
11154 CATTTTCTTTAAGTACTCATATC
1 CATTTTCTTTAAGTACTCATATC
11177 CATTTTCTTTAAGTACTCATATC
1 CATTTTCTTTAAGTACTCATATC
11200 CATTTTCTTTAAGTACTCATATC
1 CATTTTCTTTAAGTACTCATATC
11223 CA
1 CA
11225 ACGCATATTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.27, C:0.23, G:0.04, T:0.46
Consensus pattern (23 bp):
CATTTTCTTTAAGTACTCATATC
Found at i:13109 original size:30 final size:29
Alignment explanation
Indices: 13058--13114 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
13048 TTTATTTTAT
*
13058 TATTTTTTAAAATTAAATTAAAATAAAAA
1 TATTTTTTAAAAATAAATTAAAATAAAAA
* *
13087 TATTTTTTAAATAATAATTTAAATTAAA
1 TATTTTTTAAA-AATAAATTAAAATAAA
13115 TCGATTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TATTTTTTAAAAATAAATTAAAATAAAAA
Found at i:19099 original size:28 final size:29
Alignment explanation
Indices: 19047--19117 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 29
19037 ATATTTATTT
**
19047 TTTATTTAAAATATT-TTTATATTATA-A
1 TTTATTTAAAATATTATAAATATTATATA
19074 TTATATTTAAAATATTATAAAT-TTATATA
1 TT-TATTTAAAATATTATAAATATTATATA
*
19103 TTT-TTTAATATATTA
1 TTTATTTAAAATATTA
19118 ATATTTTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
27 13 0.34
28 19 0.50
29 6 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTATTTAAAATATTATAAATATTATATA
Found at i:19126 original size:20 final size:20
Alignment explanation
Indices: 19098--19136 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19088 TTATAAATTT
* *
19098 ATATATTTTTTAATATATTA
1 ATATATTTTATAAAATATTA
*
19118 ATATTTTTTATAAAATATT
1 ATATATTTTATAAAATATT
19137 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATATATTTTATAAAATATTA
Found at i:19154 original size:6 final size:6
Alignment explanation
Indices: 19133--19193 Score: 56
Period size: 6 Copynumber: 10.3 Consensus size: 6
19123 TTTTATAAAA
* * *
19133 TATTTT T-TTAT T-TTTT TATTTT TATTTT TATTTT TATTAT T-TTTA
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
19178 TATATTT TATATTT TA
1 TAT-TTT TAT-TTT TA
19194 ATCATTTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
5 11 0.24
6 24 0.52
7 11 0.24
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
TATTTT
Found at i:19154 original size:29 final size:30
Alignment explanation
Indices: 19104--19188 Score: 75
Period size: 29 Copynumber: 2.8 Consensus size: 30
19094 ATTTATATAT
* * *
19104 TTTTTAATATATTAATATTTTTTATAAAATA
1 TTTTTATTATTTTTATA-TTTTTATAAAATA
* ***
19135 TTTTT-TTATTTTTTTATTTTTAT-TTTTA
1 TTTTTATTATTTTTATATTTTTATAAAATA
19163 TTTTTATTATTTTTATATATTTTATA
1 TTTTTATTATTTTTATAT-TTTTATA
19189 TTTTAATCAT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
28 7 0.16
29 18 0.42
30 13 0.30
31 5 0.12
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (30 bp):
TTTTTATTATTTTTATATTTTTATAAAATA
Found at i:19175 original size:26 final size:26
Alignment explanation
Indices: 19137--19202 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
19127 ATAAAATATT
*
19137 TTTTTATT-TTTTTATTTTTATTTT-TA
1 TTTTTATTATTTTTA--TATATTTTATA
19163 TTTTTATTATTTTTATATATTTTATA
1 TTTTTATTATTTTTATATATTTTATA
* *
19189 TTTTAATCATTTTT
1 TTTTTATTATTTTT
19203 TATTATATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.20
26 22 0.63
27 6 0.17
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (26 bp):
TTTTTATTATTTTTATATATTTTATA
Found at i:19177 original size:9 final size:9
Alignment explanation
Indices: 19133--19208 Score: 63
Period size: 9 Copynumber: 8.7 Consensus size: 9
19123 TTTTATAAAA
19133 TATT-TTTT
1 TATTATTTT
19141 TATT-TTTT
1 TATTATTTT
19149 TATT-TTTAT
1 TATTATTT-T
*
19158 TTTTATTTT
1 TATTATTTT
19167 TATTATTTT
1 TATTATTTT
19176 TA-TATATTT
1 TATTAT-TTT
19185 TA-TATTTT
1 TATTATTTT
* *
19193 AATCATTTTT
1 TATTA-TTTT
19203 TATTAT
1 TATTAT
19209 ATAATAATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
8 22 0.39
9 25 0.44
10 10 0.18
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.76
Consensus pattern (9 bp):
TATTATTTT
Found at i:19203 original size:18 final size:17
Alignment explanation
Indices: 19095--19205 Score: 71
Period size: 15 Copynumber: 6.9 Consensus size: 17
19085 ATATTATAAA
19095 TTTATATATTTTTTAATAT
1 TTTA-ATATTTTTT-ATAT
*
19114 ATTAATATTTTTTATA-
1 TTTAATATTTTTTATAT
*
19130 --AAATATTTTTT-TAT
1 TTTAATATTTTTTATAT
**
19144 TTTTTTA-TTTTTAT-T
1 TTTAATATTTTTTATAT
19159 TTT-AT-TTTTATTAT-T
1 TTTAATATTTT-TTATAT
*
19174 TTT-ATATATTTTATAT
1 TTTAATATTTTTTATAT
19190 TTTAATCATTTTTTAT
1 TTTAAT-ATTTTTTAT
19206 TATATAATAA
Statistics
Matches: 74, Mismatches: 8, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
13 2 0.03
14 14 0.19
15 23 0.31
16 10 0.14
17 5 0.07
18 17 0.23
19 3 0.04
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTAATATTTTTTATAT
Found at i:19208 original size:36 final size:29
Alignment explanation
Indices: 19133--19193 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
19123 TTTTATAAAA
19133 TATTTTT-TTATTTTTTTATTTTTATTTT
1 TATTTTTATTATTTTTTTATTTTTATTTT
*
19161 TATTTTTATTATTTTTATATATTTTATATTT
1 TATTTTTATTATTTTTTTAT-TTTTAT-TTT
19192 TA
1 TA
19194 ATCATTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 7 0.24
29 11 0.38
30 6 0.21
31 5 0.17
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (29 bp):
TATTTTTATTATTTTTTTATTTTTATTTT
Found at i:19403 original size:20 final size:21
Alignment explanation
Indices: 19332--19407 Score: 61
Period size: 20 Copynumber: 3.7 Consensus size: 21
19322 TGAGTGTTGT
19332 TAAAATATTATTTAAAGT-TAA
1 TAAAATATTATTTAAA-TATAA
*
19353 GTAATATATTATTTATAATAT--
1 -TAAAATATTATTTA-AATATAA
** *
19374 TATTATTTTATTTAAATATAA
1 TAAAATATTATTTAAATATAA
19395 TAAAAT-TTATTTA
1 TAAAATATTATTTA
19408 TTATTTACAT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
19 5 0.11
20 19 0.42
21 4 0.09
22 14 0.31
23 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (21 bp):
TAAAATATTATTTAAATATAA
Found at i:19424 original size:27 final size:30
Alignment explanation
Indices: 19369--19444 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 30
19359 TATTATTTAT
*
19369 AATATTATTATTTTATTTAAATATAAT-AA
1 AATATTATTATATTATTTAAATATAATAAA
*
19398 AAT-TTATT-TATTATTTACAT-TACATAAA
1 AATATTATTATATTATTTAAATATA-ATAAA
19426 AATATTATTATATATATTT
1 AATATTATTATAT-TATTT
19445 TTTAAGTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 2 0.05
27 12 0.30
28 10 0.25
29 8 0.20
30 3 0.08
31 5 0.12
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (30 bp):
AATATTATTATATTATTTAAATATAATAAA
Found at i:19569 original size:6 final size:6
Alignment explanation
Indices: 19558--19615 Score: 100
Period size: 6 Copynumber: 9.7 Consensus size: 6
19548 AAATATGAAC
19558 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTATAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT-TAT
19607 TTTT-T TTTT
1 TTTTAT TTTT
19616 GAAGAAGAGT
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.10
6 40 0.78
7 6 0.12
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Done.