Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold952
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: 47358
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:522 original size:13 final size:13
Alignment explanation
Indices: 504--528 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
494 TTATTTATAT
504 TTATTTTAAAAAA
1 TTATTTTAAAAAA
517 TTATTTTAAAAA
1 TTATTTTAAAAA
529 CTTTATATTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTATTTTAAAAAA
Found at i:1477 original size:18 final size:19
Alignment explanation
Indices: 1456--1493 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1446 TTTTTTAGAT
*
1456 AAAAAATAT-ATTTTTAAA
1 AAAAAATATCATATTTAAA
1474 AAAAAATATCATATTTAAA
1 AAAAAATATCATATTTAAA
1493 A
1 A
1494 TTAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAAATATCATATTTAAA
Found at i:3222 original size:22 final size:22
Alignment explanation
Indices: 3150--3223 Score: 59
Period size: 22 Copynumber: 3.6 Consensus size: 22
3140 ATATAAAAAT
*
3150 TTTAATTATTTAATATATTATA
1 TTTAAATATTTAATATATTATA
** *
3172 TTTTGATA--T-ATATTTTA-A
1 TTTAAATATTTAATATATTATA
* *
3190 ATAAAAT-TTTAATATATTATA
1 TTTAAATATTTAATATATTATA
3211 TTTAAATATTTAA
1 TTTAAATATTTAA
3224 AATTAAGAAT
Statistics
Matches: 36, Mismatches: 11, Indels: 10
0.63 0.19 0.18
Matches are distributed among these distances:
18 4 0.11
19 8 0.22
20 8 0.22
21 6 0.17
22 10 0.28
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (22 bp):
TTTAAATATTTAATATATTATA
Found at i:3308 original size:15 final size:16
Alignment explanation
Indices: 3280--3311 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3270 TATTTTTAAC
3280 AATAAATAATAAAATA
1 AATAAATAATAAAATA
3296 AATAAAT-ATAAAATA
1 AATAAATAATAAAATA
3311 A
1 A
3312 TGATATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
AATAAATAATAAAATA
Found at i:3383 original size:12 final size:12
Alignment explanation
Indices: 3360--3394 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
3350 ATGAATAATA
3360 AAATAATA-ATT
1 AAATAATATATT
3371 AAATAATATATT
1 AAATAATATATT
*
3383 AAAAAATATATT
1 AAATAATATATT
3395 TTATTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AAATAATATATT
Found at i:3395 original size:46 final size:46
Alignment explanation
Indices: 3307--3395 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 46
3297 ATAAATATAA
* * * * * *
3307 AATAATGATATAATATTTAAATATTATTTCAAAAATTTTATTTATG
1 AATAATAAAATAATAATTAAATAATATTTCAAAAAATATATTTATG
3353 AATAATAAAATAATAATTAAATAATATATT-AAAAAATATATTT
1 AATAATAAAATAATAATTAAATAATAT-TTCAAAAAATATATTT
3396 TATTTTATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
46 34 0.94
47 2 0.06
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (46 bp):
AATAATAAAATAATAATTAAATAATATTTCAAAAAATATATTTATG
Found at i:6213 original size:21 final size:19
Alignment explanation
Indices: 6187--6253 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 19
6177 ATAAAATTAC
6187 AAAATAATTAAAATATAATA
1 AAAATAA-TAAAATATAATA
*
6207 TAAAATAAATATAATAT-A-A
1 -AAAAT-AATAAAATATAATA
6226 AAAATAATATAAATATAATA
1 AAAATAATA-AAATATAATA
6246 ACAAATAA
1 A-AAATAA
6254 AAATTTATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 4 0.10
18 10 0.26
19 2 0.05
20 3 0.08
21 18 0.46
22 2 0.05
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAATAATAAAATATAATA
Found at i:6216 original size:16 final size:16
Alignment explanation
Indices: 6196--6243 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
6186 CAAAATAATT
6196 AAAATATAATATAAAA
1 AAAATATAATATAAAA
*
6212 TAAATATAATATAAAA
1 AAAATATAATATAAAA
6228 AATAATATAAATATAA
1 AA-AATAT-AATATAA
6244 TAACAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 16 0.57
17 5 0.18
18 7 0.25
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATATAATATAAAA
Found at i:6231 original size:18 final size:18
Alignment explanation
Indices: 6197--6289 Score: 68
Period size: 18 Copynumber: 5.0 Consensus size: 18
6187 AAAATAATTA
6197 AAATATAATAT--AAAAT
1 AAATATAATATAAAAAAT
6213 AAATATAATATAAAAAAT
1 AAATATAATATAAAAAAT
6231 -AATATAAATATAATAACAAAT
1 AAATAT-AATAT-A-AA-AAAT
* * *
6252 AAAAAT-TTATAAAACAT
1 AAATATAATATAAAAAAT
6269 AAATTATTAATATAATAAAAT
1 AAA-TA-TAATATAA-AAAAT
6290 TTATATAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 17
0.72 0.07 0.20
Matches are distributed among these distances:
16 11 0.18
17 11 0.18
18 13 0.22
19 3 0.05
20 10 0.17
21 8 0.13
22 4 0.07
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATATAATATAAAAAAT
Found at i:6245 original size:28 final size:29
Alignment explanation
Indices: 6190--6302 Score: 92
Period size: 28 Copynumber: 3.9 Consensus size: 29
6180 AAATTACAAA
*
6190 ATAAT-TAAAATATAATATAAA-ATAAAT
1 ATAATATAAAAAATAATATAAATATAAAT
6217 ATAATATAAAAAATAATATAAATAT-AAT
1 ATAATATAAAAAATAATATAAATATAAAT
* * * *
6245 A-ACAAATAAAAATTTATA-AAACATAAATT
1 ATA-ATATAAAAAATAATATAAATATAAA-T
*
6274 ATTAATATAATAAAATTTATATAAATATA
1 A-TAATATAA-AAAA-TAATATAAATATA
6303 TAACATTTAA
Statistics
Matches: 68, Mismatches: 8, Indels: 14
0.76 0.09 0.16
Matches are distributed among these distances:
27 11 0.16
28 33 0.49
29 4 0.06
30 5 0.07
31 4 0.06
32 5 0.07
33 6 0.09
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (29 bp):
ATAATATAAAAAATAATATAAATATAAAT
Found at i:6460 original size:1 final size:1
Alignment explanation
Indices: 6454--6488 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
6444 ACTACAAATG
*
6454 AAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6489 GAACAGCACC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:6467 original size:9 final size:9
Alignment explanation
Indices: 6453--6491 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
6443 AACTACAAAT
6453 GAAAAAAAA
1 GAAAAAAAA
6462 GAAAAAAAA
1 GAAAAAAAA
*
6471 AAAAAAAAA
1 GAAAAAAAA
*
6480 AAAAAAAAA
1 GAAAAAAAA
6489 GAA
1 GAA
6492 CAGCACCCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:6864 original size:3 final size:3
Alignment explanation
Indices: 6856--6889 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
6846 CAAAAATCAG
6856 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
6890 CTTGGTCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:9412 original size:13 final size:13
Alignment explanation
Indices: 9394--9418 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9384 TTTTTTATAA
9394 AGTATTTATATTC
1 AGTATTTATATTC
9407 AGTATTTATATT
1 AGTATTTATATT
9419 TATTACTTAT
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:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (13 bp):
AGTATTTATATTC
Found at i:10431 original size:3 final size:3
Alignment explanation
Indices: 10423--10481 Score: 93
Period size: 3 Copynumber: 19.7 Consensus size: 3
10413 ACATAACACA
*
10423 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
10471 -AT AAT ATAT AA
1 AAT AAT A-AT AA
10482 ATTTAAATAA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:10487 original size:21 final size:21
Alignment explanation
Indices: 10443--10519 Score: 61
Period size: 21 Copynumber: 3.5 Consensus size: 21
10433 ATAATAATAA
10443 TAATAATAATAATA-AT-AATAT
1 TAATAAT-ATAATATATAAAT-T
10464 TAATAATATAATATATAAATT
1 TAATAATATAATATATAAATT
* *
10485 TAAATAA-AAAATATATTAAAATA
1 T-AATAATATAATATA-T-AAATT
10508 TATATAATATAA
1 TA-ATAATATAA
10520 ATCATTAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
20 6 0.13
21 18 0.39
22 10 0.22
23 9 0.20
24 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATAATATAATATATAAATT
Found at i:10552 original size:21 final size:22
Alignment explanation
Indices: 10503--10613 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 22
10493 AAATATATTA
* *
10503 AAATATATATAATA-TAAATCAT
1 AAATATATATAAAATTTAAT-AT
* *
10525 TAATATAT-TAAAATTTTATAT
1 AAATATATATAAAATTTAATAT
10546 AAATATATAATAAAATTTAATAT
1 AAATATAT-ATAAAATTTAATAT
* *
10569 AAATATA-ATAACA-TAAATTAT
1 AAATATATATAAAATTTAA-TAT
* *
10590 TAATATATAAAAAATTTATATAT
1 AAATATATATAAAATTTA-ATAT
10613 A
1 A
10614 TCACGGTCGG
Statistics
Matches: 69, Mismatches: 13, Indels: 13
0.73 0.14 0.14
Matches are distributed among these distances:
20 3 0.04
21 27 0.39
22 14 0.20
23 24 0.35
24 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AAATATATATAAAATTTAATAT
Found at i:10559 original size:23 final size:23
Alignment explanation
Indices: 10527--10613 Score: 85
Period size: 23 Copynumber: 3.9 Consensus size: 23
10517 TAAATCATTA
*
10527 ATATATTAAAATTTTATATAAAT
1 ATATAATAAAATTTTATATAAAT
*
10550 ATATAATAAAATTTAATATAAAT
1 ATATAATAAAATTTTATATAAAT
*
10573 ATAATAACATAAA--TTAT-T-AAT
1 AT-ATAATA-AAATTTTATATAAAT
10594 ATATAA-AAAATTTATATATA
1 ATATAATAAAATTT-TATATA
10614 TCACGGTCGG
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
18 3 0.06
19 1 0.02
20 5 0.09
21 8 0.15
22 2 0.04
23 26 0.49
24 5 0.09
25 3 0.06
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (23 bp):
ATATAATAAAATTTTATATAAAT
Found at i:10561 original size:12 final size:12
Alignment explanation
Indices: 10422--10609 Score: 70
Period size: 12 Copynumber: 16.8 Consensus size: 12
10412 CACATAACAC
10422 AAATA-ATAATA
1 AAATATATAATA
10433 ATAATA-ATAATA
1 A-AATATATAATA
10445 ATAATA-ATAATA
1 A-AATATATAATA
10457 ATAATAT-TAATA
1 A-AATATATAATA
*
10469 ATATA-AT-ATA
1 AAATATATAATA
*
10479 TAAATTTA-AATA
1 -AAATATATAATA
* *
10491 AAAAATATATTA
1 AAATATATAATA
10503 AAATATAT-ATA
1 AAATATATAATA
* * *
10514 ATATAAATCAT-
1 AAATATATAATA
*
10525 TAATATAT--TA
1 AAATATATAATA
*
10535 AAAT-T-TTATA
1 AAATATATAATA
10545 TAAATATATAATA
1 -AAATATATAATA
10558 AAAT-T-TAATA
1 AAATATATAATA
*
10568 TAA-ATATAATA
1 AAATATATAATA
* * *
10579 ACATAAATTAT-
1 AAATATATAATA
*
10590 TAATATATAA-A
1 AAATATATAATA
*
10601 AAATTTATA
1 AAATATATA
10610 TATATCACGG
Statistics
Matches: 133, Mismatches: 26, Indels: 36
0.68 0.13 0.18
Matches are distributed among these distances:
8 1 0.01
9 2 0.02
10 16 0.12
11 50 0.38
12 60 0.45
13 4 0.03
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATATATAATA
Found at i:17121 original size:20 final size:21
Alignment explanation
Indices: 17098--17149 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
17088 ATTTAAGTTT
17098 ATTTATATTATAAATA-AATA
1 ATTTATATTATAAATATAATA
* ** *
17118 ATTTAAATT-TATTTATATTA
1 ATTTATATTATAAATATAATA
17138 ATTTATATTATA
1 ATTTATATTATA
17150 TATTTTTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 4 0.16
20 19 0.76
21 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTATATTATAAATATAATA
Found at i:17239 original size:63 final size:65
Alignment explanation
Indices: 17095--17245 Score: 156
Period size: 65 Copynumber: 2.3 Consensus size: 65
17085 AATATTTAAG
*
17095 TTTATTTATATTATAA-ATAAATAATTTAAATTTATTTATATTAATTTATATTATATATTTTTAA
1 TTTATTT-TA-TATAATATAAATAATTTAAATTTATTTATATTAATTTATATTATATATTTATAA
17159 AA
64 AA
17161 TTTAATTTT-TGATAATATAAATAATTTATCATATTT-TTTA-A-T-ATTTATATTATAT-TATT
1 TTT-ATTTTAT-ATAATATAAATAATTTA--A-ATTTATTTATATTAATTTATATTATATAT-TT
*
17220 AT-ATA
60 ATAAAA
17225 TTTATTTTATATAATATAAAT
1 TTTATTTTATATAATATAAAT
17246 TTACATAATA
Statistics
Matches: 75, Mismatches: 2, Indels: 19
0.78 0.02 0.20
Matches are distributed among these distances:
63 16 0.21
64 8 0.11
65 20 0.27
66 17 0.23
67 5 0.07
68 5 0.07
69 4 0.05
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.57
Consensus pattern (65 bp):
TTTATTTTATATAATATAAATAATTTAAATTTATTTATATTAATTTATATTATATATTTATAAAA
Found at i:17321 original size:24 final size:24
Alignment explanation
Indices: 17294--17343 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
17284 GTTGTATTAC
*
17294 TAAAAAAT-AAATTAAGTTTTAATT
1 TAAAAAATAAAATTAA-ATTTAATT
* *
17318 TAAATATTAAAATTAAATTTAATT
1 TAAAAAATAAAATTAAATTTAATT
17342 TA
1 TA
17344 TTTTTAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TAAAAAATAAAATTAAATTTAATT
Found at i:17352 original size:17 final size:16
Alignment explanation
Indices: 17338--17391 Score: 65
Period size: 15 Copynumber: 3.3 Consensus size: 16
17328 AATTAAATTT
17338 AATTTATTTTTAAATA
1 AATTTATTTTTAAATA
* *
17354 AATTT-TATTTATATA
1 AATTTATTTTTAAATA
17369 AATTTATTTTTTAAATTA
1 AATTTA-TTTTTAAA-TA
17387 AATTT
1 AATTT
17392 TTTAAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 13 0.42
16 5 0.16
17 6 0.19
18 7 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AATTTATTTTTAAATA
Found at i:17822 original size:14 final size:14
Alignment explanation
Indices: 17803--17835 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
17793 AATAAGAGAT
17803 ATTTTATTT-TATTA
1 ATTTTATTTATA-TA
17817 ATTTTATTTATATA
1 ATTTTATTTATATA
17831 ATTTT
1 ATTTT
17836 TTACTGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.89
15 2 0.11
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTTTATTTATATA
Found at i:17910 original size:29 final size:28
Alignment explanation
Indices: 17865--17920 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
17855 AATTATTTAA
*
17865 TAAAAATATAATAAAAAATTATAAATAT
1 TAAAAATAAAATAAAAAATTATAAATAT
* * *
17893 TAAAAATTAAAATTAAAATTTATTAATA
1 TAAAAA-TAAAATAAAAAATTATAAATA
17921 CCAATTAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
TAAAAATAAAATAAAAAATTATAAATAT
Found at i:21213 original size:28 final size:29
Alignment explanation
Indices: 21181--21243 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
21171 TAATTTAAAA
21181 AATTTATGT-ATTTATATTATATTTATAT
1 AATTTATGTAATTTATATTATATTTATAT
* * * *
21209 TATTT-TTTAATTTATTTTATTTTTATAT
1 AATTTATGTAATTTATATTATATTTATAT
21237 AATTTAT
1 AATTTAT
21244 TATAATGATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 2 0.07
28 25 0.89
29 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (29 bp):
AATTTATGTAATTTATATTATATTTATAT
Found at i:21229 original size:20 final size:21
Alignment explanation
Indices: 21200--21244 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
21190 ATTTATATTA
*
21200 TATTTATATTATTT-TTTAATT
1 TATTTATATT-TTTATATAATT
21221 TATTT-TATTTTTATATAATT
1 TATTTATATTTTTATATAATT
21241 TATT
1 TATT
21245 ATAATGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 14 0.64
21 5 0.23
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TATTTATATTTTTATATAATT
Found at i:22226 original size:16 final size:17
Alignment explanation
Indices: 22196--22227 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
22186 TTCAGCTTAA
22196 AAAAATAAAATATTTTT
1 AAAAATAAAATATTTTT
22213 AAAAATAAAA-ATTTT
1 AAAAATAAAATATTTT
22228 ATTTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAAATAAAATATTTTT
Found at i:22897 original size:14 final size:14
Alignment explanation
Indices: 22878--22929 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
22868 GTATTCGAAT
22878 TATTTTTTATATTA
1 TATTTTTTATATTA
22892 TATTTTATGTCATATTA
1 TATTTT-T-T-ATATTA
*
22909 TTAATTTTTTATATCA
1 -T-ATTTTTTATATTA
22925 TATTT
1 TATTT
22930 ATATTATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
14 10 0.31
15 2 0.06
16 6 0.19
17 7 0.22
18 2 0.06
19 5 0.16
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (14 bp):
TATTTTTTATATTA
Found at i:22939 original size:21 final size:21
Alignment explanation
Indices: 22883--22939 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 21
22873 CGAATTATTT
*
22883 TTTATATTATATTTTATGTCATA
1 TTTATA-T-TATTTTATATCATA
22906 -TTATTAATT-TTTTATATCATA
1 TTTA-T-ATTATTTTATATCATA
22927 TTTATATTATTTT
1 TTTATATTATTTT
22940 TAAAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
20 3 0.10
21 16 0.55
22 7 0.24
23 2 0.07
24 1 0.03
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTATATTATTTTATATCATA
Found at i:26755 original size:2 final size:2
Alignment explanation
Indices: 26748--26780 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
26738 ACATGTTTGA
*
26748 AT AT AT AT AT AT AT AT AG 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
26781 CATTTTTCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:28487 original size:16 final size:16
Alignment explanation
Indices: 28468--28506 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
28458 ACTGCTCAAA
28468 TCTGATATACATGTAC
1 TCTGATATACATGTAC
28484 TCTGATATACATGTAC
1 TCTGATATACATGTAC
28500 TCTGATA
1 TCTGATA
28507 ATAATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (16 bp):
TCTGATATACATGTAC
Found at i:32365 original size:2 final size:2
Alignment explanation
Indices: 32358--32390 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
32348 CCTTTTGAGG
32358 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
32391 GAGAGAGAGA
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:32395 original size:2 final size:2
Alignment explanation
Indices: 32390--32415 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
32380 ATATATATAT
32390 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
32416 TTTGCTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:33092 original size:6 final size:6
Alignment explanation
Indices: 33081--33138 Score: 50
Period size: 6 Copynumber: 9.7 Consensus size: 6
33071 TTTATTAATC
*
33081 ATATAA ATATAA ATAT-A ATATAA ATTATTAA ATAT-A TTA-AA ATATTAA
1 ATATAA ATATAA ATATAA ATATAA A-TA-TAA ATATAA ATATAA ATA-TAA
*
33129 ATATGA ATAT
1 ATATAA ATAT
33139 GATACATGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
5 11 0.26
6 19 0.44
7 9 0.21
8 4 0.09
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (6 bp):
ATATAA
Found at i:33103 original size:17 final size:18
Alignment explanation
Indices: 33081--33175 Score: 77
Period size: 17 Copynumber: 4.9 Consensus size: 18
33071 TTTATTAATC
33081 ATATAAATA-TAAATATA
1 ATATAAATATTAAATATA
33098 ATATAAATTATTAAATATA
1 ATATAAA-TATTAAATATA
*
33117 TTA-AAATATTAAATATGA
1 ATATAAATATTAAATAT-A
33135 ATATGATACATGTATTAAATATCA
1 ATAT-A-A-A--TATTAAATAT-A
*
33159 ATTTAAATATCTAAATA
1 ATATAAATAT-TAAATA
33176 AAAGAATTGC
Statistics
Matches: 64, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
17 17 0.27
18 8 0.12
19 13 0.20
20 7 0.11
21 2 0.03
22 2 0.03
23 1 0.02
24 14 0.22
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (18 bp):
ATATAAATATTAAATATA
Found at i:33132 original size:36 final size:42
Alignment explanation
Indices: 33085--33175 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 42
33075 TTAATCATAT
33085 AAATA-TAAATAT-AATAT-A-A-AT-TATTAAATAT-ATTA
1 AAATATTAAATATGAATATGATACATGTATTAAATATAATTA
*
33120 AAATATTAAATATGAATATGATACATGTATTAAATATCAATTT
1 AAATATTAAATATGAATATGATACATGTATTAAATAT-AATTA
33163 AAATATCTAAATA
1 AAATAT-TAAATA
33176 AAAGAATTGC
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
35 5 0.11
36 7 0.15
37 5 0.11
38 1 0.02
39 1 0.02
40 2 0.04
41 10 0.22
43 9 0.20
44 6 0.13
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (42 bp):
AAATATTAAATATGAATATGATACATGTATTAAATATAATTA
Found at i:35872 original size:30 final size:30
Alignment explanation
Indices: 35787--35885 Score: 94
Period size: 30 Copynumber: 3.3 Consensus size: 30
35777 TTAAGATATA
* *
35787 AAAAAGTAAAAA-TTATTTAATAATAAAATT
1 AAAAATTAAAAATTTATTTAATTAT-AAATT
* * ** * *
35817 ATAAGTTAAACGTTTGTTTTA-TATAAATT
1 AAAAATTAAAAATTTATTTAATTATAAATT
35846 AAAAATTAAAAATTTATTTAATTATAAATT
1 AAAAATTAAAAATTTATTTAATTATAAATT
*
35876 AAAATTTAAA
1 AAAAATTAAA
35886 CATATCTAAG
Statistics
Matches: 52, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
29 20 0.38
30 26 0.50
31 6 0.12
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (30 bp):
AAAAATTAAAAATTTATTTAATTATAAATT
Found at i:35879 original size:29 final size:29
Alignment explanation
Indices: 35788--35881 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
35778 TAAGATATAA
* *
35788 AAAAGTAAAAA-TTATTTAATAATAAAATT
1 AAAATTAAAAATTTATTTAATTAT-AAATT
* ** * *
35817 ATAAGTTAAACGTTTGTTTTA-TATAAATT
1 A-AAATTAAAAATTTATTTAATTATAAATT
35846 AAAAATTAAAAATTTATTTAATTATAAATT
1 -AAAATTAAAAATTTATTTAATTATAAATT
35876 AAAATT
1 AAAATT
35882 TAAACATATC
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
29 26 0.53
30 17 0.35
31 6 0.12
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.41
Consensus pattern (29 bp):
AAAATTAAAAATTTATTTAATTATAAATT
Found at i:36570 original size:2 final size:2
Alignment explanation
Indices: 36563--36605 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
36553 GTACTTGCTT
36563 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36605 T
1 T
36606 TCTTCATTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36898 original size:3 final size:3
Alignment explanation
Indices: 36890--36921 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
36880 CCACAAGGCT
36890 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
36922 CTTTGTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:39876 original size:13 final size:14
Alignment explanation
Indices: 39858--39894 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
39848 TTATTAAAAT
*
39858 AATATTATT-TTAA
1 AATATTATTATCAA
39871 AATATT-TTATCAA
1 AATATTATTATCAA
39884 AATATTATTAT
1 AATATTATTAT
39895 TTTATCACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 2 0.10
13 15 0.71
14 4 0.19
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (14 bp):
AATATTATTATCAA
Found at i:39898 original size:29 final size:28
Alignment explanation
Indices: 39832--39898 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
39822 TTAAAGTACC
*
39832 TTATT-TTTTAAAAAACTTATTAAAATA
1 TTATTATTTTAAAAAACTTATCAAAATA
* **
39859 ATATTATTTTAAAATATTTTATCAAAATA
1 TTATTATTTTAAAA-AACTTATCAAAATA
39888 TTATTATTTTA
1 TTATTATTTTA
39899 TCACGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
27 4 0.12
28 8 0.24
29 21 0.64
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (28 bp):
TTATTATTTTAAAAAACTTATCAAAATA
Found at i:40082 original size:14 final size:15
Alignment explanation
Indices: 40063--40092 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40053 TTAATTAATT
40063 ATATTAA-TAAATAA
1 ATATTAATTAAATAA
40077 ATATTAATTAAATAA
1 ATATTAATTAAATAA
40092 A
1 A
40093 AAATATGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATATTAATTAAATAA
Found at i:40096 original size:18 final size:19
Alignment explanation
Indices: 40068--40103 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
40058 TAATTATATT
*
40068 AATAAATAAATATTAATTA
1 AATAAATAAATATGAATTA
40087 AATAAA-AAATATGAATT
1 AATAAATAAATATGAATT
40104 TTTTAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
AATAAATAAATATGAATTA
Found at i:40322 original size:15 final size:15
Alignment explanation
Indices: 40297--40338 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
40287 TTATTTTAAA
*
40297 ATTATAATTTTTATTT
1 ATTAT-ATTTTTAGTT
40313 ATTA-ATTTTTAGTT
1 ATTATATTTTTAGTT
40327 ATTATATTTTTA
1 ATTATATTTTTA
40339 AAAAATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 13 0.54
15 7 0.29
16 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
ATTATATTTTTAGTT
Found at i:44097 original size:24 final size:24
Alignment explanation
Indices: 44070--44116 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
44060 ATTATAAATT
* *
44070 CAACATGTTCCTAGAATTTTAATC
1 CAACATGATACTAGAATTTTAATC
44094 CAACATGATACTAGAATTTTAAT
1 CAACATGATACTAGAATTTTAAT
44117 AGAAGTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (24 bp):
CAACATGATACTAGAATTTTAATC
Done.