Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1265
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: 436287
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
File 1 of 3
Found at i:3332 original size:28 final size:28
Alignment explanation
Indices: 3291--3368 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
3281 GGATTCTTCA
*
3291 AAATCTTA-AAATTCTTAGAATTTGGTCC
1 AAAT-TTAGAAATTCTTAGAATTTGATCC
* * *
3319 AAATTTAGAGATTCTTAAAATTTGATCT
1 AAATTTAGAAATTCTTAGAATTTGATCC
*
3347 AAATTTAGAAATT-TTTGAATTT
1 AAATTTAGAAATTCTTAGAATTT
3369 TCAAACTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 10 0.24
28 32 0.76
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (28 bp):
AAATTTAGAAATTCTTAGAATTTGATCC
Found at i:3543 original size:17 final size:17
Alignment explanation
Indices: 3517--3588 Score: 65
Period size: 17 Copynumber: 4.1 Consensus size: 17
3507 AATAATATTT
3517 TAAAAAATTAAATTTGA
1 TAAAAAATTAAATTTGA
* *
3534 TAAAATATTAACA-GTGA
1 TAAAAAATTAA-ATTTGA
* *
3551 TATAAAATTGAAATTTTA
1 TAAAAAATT-AAATTTGA
3569 TAAAAAAATATAAATTTGA
1 T-AAAAAAT-TAAATTTGA
3588 T
1 T
3589 TTGTAATTCA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
17 21 0.50
18 6 0.14
19 14 0.33
20 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.36
Consensus pattern (17 bp):
TAAAAAATTAAATTTGA
Found at i:4586 original size:2 final size:2
Alignment explanation
Indices: 4579--4614 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4569 AGGTAATCAC
4579 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
4615 TATTGTATCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5121 original size:2 final size:2
Alignment explanation
Indices: 5114--5140 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5104 TTATGTTCCA
5114 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 A
5141 GATGCAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6032 original size:15 final size:14
Alignment explanation
Indices: 6008--6056 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
5998 AGTAAAAACG
6008 TATTTTAAATTTTA
1 TATTTTAAATTTTA
*
6022 TATTATTAAATTTAA
1 TATT-TTAAATTTTA
*
6037 TATTTTAATTTTTA
1 TATTTTAAATTTTA
6051 TATTTT
1 TATTTT
6057 TAAAATTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
14 18 0.58
15 13 0.42
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTTTAAATTTTA
Found at i:6057 original size:15 final size:15
Alignment explanation
Indices: 6010--6060 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
6000 TAAAAACGTA
6010 TTTTAAATTTTATAT
1 TTTTAAATTTTATAT
* *
6025 TATTAAATTTAATA-
1 TTTTAAATTTTATAT
*
6039 TTTTAATTTTTATAT
1 TTTTAAATTTTATAT
6054 TTTTAAA
1 TTTTAAA
6061 ATTATTAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTAAATTTTATAT
Found at i:27124 original size:27 final size:27
Alignment explanation
Indices: 27086--27138 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
27076 CTGTGCCGCC
*
27086 AATTTTGAAATTCAATTTGAAACAGTA
1 AATTATGAAATTCAATTTGAAACAGTA
27113 AATTATGAAATTCAATTTGAAACAGT
1 AATTATGAAATTCAATTTGAAACAGT
27139 GAAGGTTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (27 bp):
AATTATGAAATTCAATTTGAAACAGTA
Found at i:32593 original size:2 final size:2
Alignment explanation
Indices: 32588--32690 Score: 161
Period size: 2 Copynumber: 51.5 Consensus size: 2
32578 ACACACACAC
* *
32588 AT AT AT AT AC AT AT AT AT AT AT AT AT AC 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
* * *
32630 AT GT AT AT AT GT AT AT AT AT AT AT AT AT GT 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
32672 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
32691 AGGAAGAATA
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 91 1.00
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35909 original size:5 final size:5
Alignment explanation
Indices: 35899--35923 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
35889 CATCATCTAC
35899 AAGAA AAGAA AAGAA AAGAA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA
35924 TCTATAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:38078 original size:18 final size:18
Alignment explanation
Indices: 38055--38095 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
38045 TAAACTCAAT
38055 TATAGATTTTATATATAG
1 TATAGATTTTATATATAG
*
38073 TATAGATTTTATGTATAG
1 TATAGATTTTATATATAG
38091 TATAG
1 TATAG
38096 TTATATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.49
Consensus pattern (18 bp):
TATAGATTTTATATATAG
Found at i:39495 original size:18 final size:19
Alignment explanation
Indices: 39445--39497 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
39435 AGTCGGCACT
* *
39445 AAATTTCTTAATAGTTGAA
1 AAATTTTTTAATATTTGAA
39464 AAAGTTTATTTAATATTTG-A
1 AAA-TTT-TTTAATATTTGAA
39484 AAATTTTTTAATAT
1 AAATTTTTTAATAT
39498 AAATATTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 8 0.27
19 6 0.20
20 7 0.23
21 9 0.30
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.49
Consensus pattern (19 bp):
AAATTTTTTAATATTTGAA
Found at i:40052 original size:19 final size:18
Alignment explanation
Indices: 40011--40046 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
40001 GGCAAAATAT
*
40011 TTTGCACAAAAAATAGAA
1 TTTGCACAAAAAATAAAA
40029 TTTGC-CAAAAAATAAAA
1 TTTGCACAAAAAATAAAA
40046 T
1 T
40047 CTTTGCTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.56, C:0.11, G:0.08, T:0.25
Consensus pattern (18 bp):
TTTGCACAAAAAATAAAA
Found at i:40156 original size:21 final size:23
Alignment explanation
Indices: 40130--40173 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
40120 GTATTACATA
40130 ATATATT-ATTTATAT-ATATAT
1 ATATATTAATTTATATCATATAT
40151 ATATATTAAATTTATATCATATA
1 ATATATT-AATTTATATCATATA
40174 AAAATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATATTAATTTATATCATATAT
Found at i:40410 original size:79 final size:79
Alignment explanation
Indices: 40279--40436 Score: 316
Period size: 79 Copynumber: 2.0 Consensus size: 79
40269 TTTTTTAGAA
40279 AAATAATATTAGTGGGTCTAGATATTTAAGTTATCTATTTATAAATATGAATAAATTTAAATAAA
1 AAATAATATTAGTGGGTCTAGATATTTAAGTTATCTATTTATAAATATGAATAAATTTAAATAAA
40344 ATTTTAAGTGTTAT
66 ATTTTAAGTGTTAT
40358 AAATAATATTAGTGGGTCTAGATATTTAAGTTATCTATTTATAAATATGAATAAATTTAAATAAA
1 AAATAATATTAGTGGGTCTAGATATTTAAGTTATCTATTTATAAATATGAATAAATTTAAATAAA
40423 ATTTTAAGTGTTAT
66 ATTTTAAGTGTTAT
40437 TTCAAGTCAA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (79 bp):
AAATAATATTAGTGGGTCTAGATATTTAAGTTATCTATTTATAAATATGAATAAATTTAAATAAA
ATTTTAAGTGTTAT
Found at i:41132 original size:21 final size:21
Alignment explanation
Indices: 41108--41149 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
41098 TGTGGTGGAG
*
41108 TTTTGATTTAAAATTTAAATTT
1 TTTTGATTT-AAATCTAAATTT
*
41130 TTTTTATTTAAATCTAAATT
1 TTTTGATTTAAATCTAAATT
41150 AAGTGGGTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTTGATTTAAATCTAAATTT
Found at i:42613 original size:26 final size:28
Alignment explanation
Indices: 42545--42614 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 28
42535 AAGAATAGTT
42545 TAAATTAAATAAATTTAAATTATTAATTTTA
1 TAAA-TAAATAAAT-TAAATTA-TAATTTTA
42576 TAAATAAA-AAATTAAATTA-AATTTTA
1 TAAATAAATAAATTAAATTATAATTTTA
**
42602 -ATCTAAATAAATT
1 TAAATAAATAAATT
42615 GAACAAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
25 5 0.14
26 12 0.33
28 7 0.19
29 4 0.11
30 4 0.11
31 4 0.11
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (28 bp):
TAAATAAATAAATTAAATTATAATTTTA
Found at i:43093 original size:17 final size:17
Alignment explanation
Indices: 43071--43104 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
43061 GTAAATATTA
43071 TATTTAAAAAATAAGTT
1 TATTTAAAAAATAAGTT
*
43088 TATTTAAAATATAAGTT
1 TATTTAAAAAATAAGTT
43105 AAAAATTGAT
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:0.06, T:0.44
Consensus pattern (17 bp):
TATTTAAAAAATAAGTT
Found at i:43199 original size:23 final size:26
Alignment explanation
Indices: 43173--43233 Score: 65
Period size: 30 Copynumber: 2.3 Consensus size: 26
43163 TATATTATTT
43173 TATATTTATA-TAAA-A-TAAAAATA
1 TATATTTATAGTAAATATTAAAAATA
43196 TATAATATTATAGTGTAAATATTAAAAATA
1 TAT-AT-TTATA--GTAAATATTAAAAATA
43226 TATATTTA
1 TATATTTA
43234 AGATTATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
23 3 0.10
24 2 0.06
25 5 0.16
28 7 0.23
29 3 0.10
30 11 0.35
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (26 bp):
TATATTTATAGTAAATATTAAAAATA
Found at i:43547 original size:16 final size:17
Alignment explanation
Indices: 43529--43618 Score: 78
Period size: 18 Copynumber: 5.2 Consensus size: 17
43519 GTGATATAAT
43529 TAAATAATATAAAAAT-
1 TAAATAATATAAAAATA
43545 T-AA-AATATAAAAAATA
1 TAAATAATAT-AAAAATA
*
43561 TAATATTATATAAAAATAA
1 TAA-ATAATATAAAAAT-A
* *
43580 TATATAATATAAATATA
1 TAAATAATATAAAAATA
* *
43597 TAAATATTTTAAAAATTA
1 TAAATAATATAAAAA-TA
43615 TAAA
1 TAAA
43619 ATATAAATTA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
14 5 0.08
15 8 0.14
16 2 0.03
17 13 0.22
18 24 0.41
19 7 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAATAATATAAAAATA
Found at i:44102 original size:18 final size:19
Alignment explanation
Indices: 44064--44102 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
44054 TATTTAATTT
*
44064 TATATTTTAAAATTTTTAAA
1 TATATTTTAAAA-TTTAAAA
44084 TATATTTTAAAA-TTAAAA
1 TATATTTTAAAATTTAAAA
44102 T
1 T
44103 TAAAATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATATTTTAAAATTTAAAA
Found at i:44319 original size:23 final size:22
Alignment explanation
Indices: 44292--44344 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 22
44282 TAATCAACTC
44292 AAATTA-AAAATAACTTGAATTTA
1 AAATTACAAAATAA-TT-AATTTA
*
44315 AAATTATCCAAATAATTAATTTA
1 AAATTA-CAAAATAATTAATTTA
44338 AAATTAC
1 AAATTAC
44345 CTAACTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 1 0.04
23 18 0.67
24 2 0.07
25 6 0.22
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.36
Consensus pattern (22 bp):
AAATTACAAAATAATTAATTTA
Found at i:45251 original size:10 final size:10
Alignment explanation
Indices: 45232--45262 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
45222 TTAAAAATAA
45232 AATTTTATTT
1 AATTTTATTT
*
45242 AATTTAATTT
1 AATTTTATTT
45252 AATTTTATTT
1 AATTTTATTT
45262 A
1 A
45263 TGAATTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
AATTTTATTT
Found at i:46235 original size:2 final size:2
Alignment explanation
Indices: 46228--46253 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
46218 ACATTGTTTC
46228 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
46254 AAAAATTAAA
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46485 original size:27 final size:27
Alignment explanation
Indices: 46419--46488 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
46409 TATTTGATAA
*
46419 TATATAA-ATTTTAATATTAAATATTTT
1 TATATAATATTATAAT-TTAAATATTTT
* *
46446 TA-ATTATAATATAATTT-AATATTATT
1 TATATAATATTATAATTTAAATATT-TT
46472 TATATAATATTATAATT
1 TATATAATATTATAATT
46489 GAATTCAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
25 6 0.17
26 9 0.26
27 20 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TATATAATATTATAATTTAAATATTTT
Found at i:46487 original size:22 final size:23
Alignment explanation
Indices: 46425--46487 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 23
46415 ATAATATATA
*
46425 AATTTTAATATTA-AATATTTTT
1 AATTATAATATTATAATATTTTT
*
46447 AATTATAATATAATTTAATATTATTT
1 AATTATAATAT--TATAATATT-TTT
46473 -A-TATAATATTATAAT
1 AATTATAATATTATAAT
46488 TGAATTCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
22 15 0.44
24 9 0.26
25 7 0.21
26 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATTATAATATTATAATATTTTT
Found at i:48056 original size:58 final size:57
Alignment explanation
Indices: 47858--48166 Score: 175
Period size: 58 Copynumber: 5.4 Consensus size: 57
47848 CAAAATGGTC
* * * * * * *
47858 TTAAAATGTATGAAATCATAGAAAAGTCTCTAACT-ATGACAAATTACTAGAATA-A
1 TTAAAATGCATGAAATGATAAAAAAGTCTCTAAATCATGAAAAATGACTAAAATACA
** * * * * *
47913 TCTTAAAATGCATGAGAATGCATAAATGA-TC-ATAAATCATGAAAATTTAATAAAATGATA
1 --TTAAAATGCATGA-AATG-ATAAAAAAGTCTCTAAATCATGAAAAATGACTAAAAT-ACA
* * * * * * *
47973 TTAAAGTACATGAAGTGACATAAAAGTCTCTAAGTGATGAAAAATGACTAAAATACCA
1 TTAAAATGCATGAAATGATAAAAAAGTCTCTAAATCATGAAAAATGACTAAAATA-CA
* * * ** *
48031 TTAAAATGCATGAAATGATAAAAAAGTTTTCTATATCAT-AGAAAACGACTTCAATATCC
1 TTAAAATGCATGAAATGATAAAAAAG-TCTCTAAATCATGA-AAAATGACTAAAATA-CA
* * * *
48090 TTAAAATGCATGAAATGACTTAATAA-TTTCTAAATCATAAAAAATGACTAAAATGTACA
1 TTAAAATGCATGAAATGA-TAAAAAAGTCTCTAAATCATGAAAAATGACTAAAA--TACA
48149 -T-AAATGCATGAAATGATA
1 TTAAAATGCATGAAATGATA
48167 TAGTAATCTT
Statistics
Matches: 191, Mismatches: 47, Indels: 29
0.72 0.18 0.11
Matches are distributed among these distances:
56 5 0.03
57 37 0.19
58 94 0.49
59 47 0.25
60 8 0.04
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.29
Consensus pattern (57 bp):
TTAAAATGCATGAAATGATAAAAAAGTCTCTAAATCATGAAAAATGACTAAAATACA
Found at i:52024 original size:11 final size:11
Alignment explanation
Indices: 52008--52036 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
51998 AAGAAACTCA
52008 CTCTTTTTTTT
1 CTCTTTTTTTT
52019 CTCTTTTTTTT
1 CTCTTTTTTTT
52030 CT-TTTTT
1 CTCTTTTT
52037 ATTTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
CTCTTTTTTTT
Found at i:57187 original size:29 final size:29
Alignment explanation
Indices: 57136--57193 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
57126 TTTTACCCAG
**
57136 ATGTATCGATACATTCTTCAATGTATCGA
1 ATGTATCGATACATTCAACAATGTATCGA
* *
57165 ATGTATCGATACATTGAAGAATGTATCGA
1 ATGTATCGATACATTCAACAATGTATCGA
57194 TACATCTAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (29 bp):
ATGTATCGATACATTCAACAATGTATCGA
Found at i:64142 original size:14 final size:16
Alignment explanation
Indices: 64111--64157 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
64101 CAAAAAAGTC
64111 AAAA-GCAAAAGCACAA
1 AAAATGCAAAAGCA-AA
64127 AAAATG-AAAAG-AAA
1 AAAATGCAAAAGCAAA
*
64141 AAAGTGCAAAAGCAAA
1 AAAATGCAAAAGCAAA
64157 A
1 A
64158 CAAAAAGGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 7 0.26
15 6 0.22
16 13 0.48
17 1 0.04
ACGTcount: A:0.70, C:0.11, G:0.15, T:0.04
Consensus pattern (16 bp):
AAAATGCAAAAGCAAA
Found at i:64144 original size:23 final size:23
Alignment explanation
Indices: 64100--64142 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
64090 CTTCAAAATG
*
64100 ACAAAAAAGTCAAAAGCAAAAGC
1 ACAAAAAAGTCAAAAGAAAAAGC
*
64123 ACAAAAAA-TGAAAAGAAAAA
1 ACAAAAAAGTCAAAAGAAAAA
64143 AGTGCAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.72, C:0.12, G:0.12, T:0.05
Consensus pattern (23 bp):
ACAAAAAAGTCAAAAGAAAAAGC
Found at i:65265 original size:28 final size:29
Alignment explanation
Indices: 65226--65366 Score: 126
Period size: 32 Copynumber: 4.7 Consensus size: 29
65216 TCGTAATCCC
*
65226 CAAGTCTA-TGGCACCCTTTT-AAAGCCCA
1 CAAGTC-AGTGGCACTCTTTTCAAAGCCCA
*
65254 CAAGTCAGTGGCACTCTTTTCAAGGCCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
*
65283 CAAG-CTAGTGGTAACTCTTTTCAAAGCCCA
1 CAAGTC-AGTGG-CACTCTTTTCAAAGCCCA
* *
65313 CACGAGTCGGTGGTAACTCTTTTCAAAGCCCACA
1 CA--AGTCAGTGG-CACTCTTTTCAAAG-CC-CA
* *
65347 CAAGTTAGTGGCACTTTTTT
1 CAAGTCAGTGGCACTCTTTT
65367 TTAAAAAAAA
Statistics
Matches: 95, Mismatches: 9, Indels: 15
0.80 0.08 0.13
Matches are distributed among these distances:
27 1 0.01
28 18 0.19
29 16 0.17
30 18 0.19
31 7 0.07
32 28 0.29
33 3 0.03
34 4 0.04
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (29 bp):
CAAGTCAGTGGCACTCTTTTCAAAGCCCA
Found at i:65347 original size:32 final size:30
Alignment explanation
Indices: 65241--65346 Score: 137
Period size: 32 Copynumber: 3.5 Consensus size: 30
65231 CTATGGCACC
*
65241 CTTTT-AAAGCCCACAAGTCAGTGG-CACT
1 CTTTTCAAAGCCCACAAGTCAGTGGTAACT
*
65269 CTTTTCAAGGCCCACAAG-CTAGTGGTAACT
1 CTTTTCAAAGCCCACAAGTC-AGTGGTAACT
*
65299 CTTTTCAAAGCCCACACGAGTCGGTGGTAACT
1 CTTTTCAAAGCCCACA--AGTCAGTGGTAACT
65331 CTTTTCAAAGCCCACA
1 CTTTTCAAAGCCCACA
65347 CAAGTTAGTG
Statistics
Matches: 68, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
28 6 0.09
29 16 0.24
30 18 0.26
32 27 0.40
33 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.25
Consensus pattern (30 bp):
CTTTTCAAAGCCCACAAGTCAGTGGTAACT
Found at i:69416 original size:3 final size:3
Alignment explanation
Indices: 69408--69445 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
69398 AGACTCTTTC
69408 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
69446 CAATCACAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:69664 original size:29 final size:29
Alignment explanation
Indices: 69622--69742 Score: 129
Period size: 29 Copynumber: 4.1 Consensus size: 29
69612 TTCACTTATT
*
69622 TAAGTTTTAATATTT-TTTTATATCTAAA
1 TAAGTTTTAATATTTAATTTATATCTAAA
*
69650 TAAGTCTTTGATATTTAATTTATATCTAAA
1 TAAGT-TTTAATATTTAATTTATATCTAAA
* * *
69680 TTAATTTTTAAAATTTTAATTTGTATCTAAA
1 -TAAGTTTTAATA-TTTAATTTATATCTAAA
* *
69711 TAATTTTTAA-ATTTTAATTTATACCTAAA
1 TAAGTTTTAATA-TTTAATTTATATCTAAA
69740 TAA
1 TAA
69743 ATTCTTAACA
Statistics
Matches: 81, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
28 5 0.06
29 29 0.36
30 27 0.33
31 20 0.25
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (29 bp):
TAAGTTTTAATATTTAATTTATATCTAAA
Found at i:69733 original size:60 final size:59
Alignment explanation
Indices: 69621--69750 Score: 147
Period size: 60 Copynumber: 2.2 Consensus size: 59
69611 TTTCACTTAT
* * * *
69621 TTAAGTTTTAATATTTTTTTATATCTAAATAAGTCTTTGATATTTAATTTATATCTAAA
1 TTAATTTTTAAAATTTTTTTATATCTAAATAAGTCTTTAATATTTAATTTATACCTAAA
* *
69680 TTAATTTTTAAAATTTTAATTTGTATCTAAATAA-TTTTTAA-ATTTTAATTTATACCTAAA
1 TTAATTTTTAAAATTTT--TTTATATCTAAATAAGTCTTTAATA-TTTAATTTATACCTAAA
* *
69740 TAAATTCTTAA
1 TTAATTTTTAA
69751 CATAATTTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
59 16 0.27
60 30 0.50
61 14 0.23
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.53
Consensus pattern (59 bp):
TTAATTTTTAAAATTTTTTTATATCTAAATAAGTCTTTAATATTTAATTTATACCTAAA
Found at i:70364 original size:19 final size:21
Alignment explanation
Indices: 70329--70367 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
70319 ACTAGTGAAC
70329 TAATACAATAGAAAATTAATT
1 TAATACAATAGAAAATTAATT
70350 TAAT-CAATA-AAAATTAAT
1 TAATACAATAGAAAATTAAT
70368 AAAAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 5 0.28
21 4 0.22
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (21 bp):
TAATACAATAGAAAATTAATT
Found at i:70487 original size:21 final size:21
Alignment explanation
Indices: 70461--70500 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
70451 GATTATATTA
70461 TTAAATTAAATAC-ATATTTTT
1 TTAAA-TAAATACTATATTTTT
*
70482 TTAAATAAGTACTATATTT
1 TTAAATAAATACTATATTT
70501 AAGATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (21 bp):
TTAAATAAATACTATATTTTT
Found at i:70899 original size:17 final size:17
Alignment explanation
Indices: 70873--70905 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
70863 GCTGTCTTTT
70873 AAGCCAGCAC-GAGTTA
1 AAGCCAGCACTGAGTTA
70889 AAGCACAGCACTGAGTT
1 AAGC-CAGCACTGAGTT
70906 TTTTTTTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.15
Consensus pattern (17 bp):
AAGCCAGCACTGAGTTA
Found at i:75812 original size:34 final size:34
Alignment explanation
Indices: 75774--75838 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
75764 AATTTCATTT
*
75774 GCTTTTAGTTTCTATAATCCACAAATTGATTCAG
1 GCTTTTAGTTTCTACAATCCACAAATTGATTCAG
*
75808 GCTTTTAGTTTCTACAATCCACTAATTGATT
1 GCTTTTAGTTTCTACAATCCACAAATTGATT
75839 TGGGTGGCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.43
Consensus pattern (34 bp):
GCTTTTAGTTTCTACAATCCACAAATTGATTCAG
Found at i:76982 original size:20 final size:20
Alignment explanation
Indices: 76942--76979 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
76932 AAAATTTTAA
76942 ATTAAATTGAAAAAAATAAT
1 ATTAAATTGAAAAAAATAAT
*
76962 ATTAAATT-AAAAATATAA
1 ATTAAATTGAAAAAAATAA
76980 ATAAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (20 bp):
ATTAAATTGAAAAAAATAAT
Found at i:77301 original size:15 final size:16
Alignment explanation
Indices: 77277--77310 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
77267 TCGAATTATT
77277 TTTTAATTT-AAATTA
1 TTTTAATTTAAAATTA
*
77292 TTTTATTTTAAAATTA
1 TTTTAATTTAAAATTA
77308 TTT
1 TTT
77311 GAAGTTAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTAATTTAAAATTA
Found at i:77486 original size:16 final size:15
Alignment explanation
Indices: 77465--77498 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
77455 TTTTTTAATT
77465 TTAAATTTAAATCAAA
1 TTAAATTTAAAT-AAA
77481 TTAAATTTAAATAAA
1 TTAAATTTAAATAAA
77496 TTA
1 TTA
77499 TTTGATCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAAATTTAAATAAA
Found at i:77576 original size:21 final size:21
Alignment explanation
Indices: 77540--77583 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
77530 TTGAAATATA
77540 AAAATAAAAAATAAAATTATTT
1 AAAATAAAAAATAAAATT-TTT
*
77562 AAAAT-AAATATAAAATTTTT
1 AAAATAAAAAATAAAATTTTT
77582 AA
1 AA
77584 TTTTTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 11 0.52
22 5 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAATAAAAAATAAAATTTTT
Found at i:78005 original size:30 final size:28
Alignment explanation
Indices: 77967--78023 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
77957 AATTTATCAT
*
77967 TTTAATATAATAATTATAATTTTTTTACA
1 TTTAATATAATAATTAT-ATTATTTTACA
*
77996 TTTATATATAATTATTATATTATTTTAC
1 TTTA-ATATAATAATTATATTATTTTAC
78024 GTAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.58
Consensus pattern (28 bp):
TTTAATATAATAATTATATTATTTTACA
Found at i:78296 original size:20 final size:19
Alignment explanation
Indices: 78273--78317 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
78263 TTATTAATTT
78273 TTTAAA-TAAATTAAATTAAA
1 TTTAAATTAAA-TAAATT-AA
78293 TTTAAATTTAAATAAATTAA
1 TTTAAA-TTAAATAAATTAA
78313 TTTAA
1 TTTAA
78318 TTTTTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 13 0.57
21 6 0.26
22 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTTAAATTAAATAAATTAA
Found at i:78305 original size:26 final size:27
Alignment explanation
Indices: 78273--78331 Score: 93
Period size: 26 Copynumber: 2.2 Consensus size: 27
78263 TTATTAATTT
78273 TTTAAATAAATTAAATTAA-ATTTAAA
1 TTTAAATAAATTAAATTAATATTTAAA
* *
78299 TTTAAATAAATTAATTTAATTTTTAAA
1 TTTAAATAAATTAAATTAATATTTAAA
78326 TTTAAA
1 TTTAAA
78332 ATTAAAATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 18 0.60
27 12 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TTTAAATAAATTAAATTAATATTTAAA
Found at i:78310 original size:21 final size:21
Alignment explanation
Indices: 78279--78326 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
78269 ATTTTTTAAA
78279 TAAATTAAATTAAATTTAA-ATT
1 TAAA-TAAATT-AATTTAATATT
*
78301 TAAATAAATTAATTTAATTTT
1 TAAATAAATTAATTTAATATT
78322 TAAAT
1 TAAAT
78327 TTAAAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 7 0.29
21 13 0.54
22 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TAAATAAATTAATTTAATATT
Found at i:79137 original size:17 final size:17
Alignment explanation
Indices: 79115--79160 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
79105 ATTCGTATTA
79115 TATTTTAATTTATC-GTT
1 TATTTTAATTTATCTG-T
*
79132 TATTTT-ATATAATCTGT
1 TATTTTAAT-TTATCTGT
79149 TATTTTAATTTA
1 TATTTTAATTTA
79161 ATTTAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
16 2 0.08
17 19 0.79
18 3 0.12
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.63
Consensus pattern (17 bp):
TATTTTAATTTATCTGT
Found at i:87100 original size:20 final size:22
Alignment explanation
Indices: 87049--87101 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
87039 AATAAATTTT
87049 ATTTTAATTATAAAAATATATAA
1 ATTTTAA-TATAAAAATATATAA
*
87072 ATATTAATATAAAAATA-A-AA
1 ATTTTAATATAAAAATATATAA
*
87092 TTTTTAATAT
1 ATTTTAATAT
87102 TTTTTTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.37
21 1 0.04
22 10 0.37
23 6 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTTAATATAAAAATATATAA
Found at i:88514 original size:26 final size:26
Alignment explanation
Indices: 88468--88528 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
88458 TTTAATAAGT
88468 TAAT-TAAA-TAAAAATTAAAAAATTA
1 TAATATAAATTAAAAATTAAAAAA-TA
88493 TAA-ATAAATTAAAAA-TATAAAAATA
1 TAATATAAATTAAAAATTA-AAAAATA
88518 TAATATAAATT
1 TAATATAAATT
88529 TTCATCATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
25 14 0.44
26 18 0.56
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (26 bp):
TAATATAAATTAAAAATTAAAAAATA
Found at i:88516 original size:19 final size:19
Alignment explanation
Indices: 88469--88517 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
88459 TTAATAAGTT
88469 AATTAAATAA-AAATTAAAA
1 AATTAAA-AATAAATTAAAA
*
88488 AATTATAAATAAATT-AAA
1 AATTAAAAATAAATTAAAA
88506 AATATAAAAATA
1 AAT-TAAAAATA
88518 TAATATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AATTAAAAATAAATTAAAA
Found at i:89185 original size:13 final size:12
Alignment explanation
Indices: 89149--89209 Score: 54
Period size: 13 Copynumber: 5.0 Consensus size: 12
89139 AATTTATGAT
*
89149 TTATTATAAAAA
1 TTATTATAAATA
89161 TTATTAATAAATA
1 TTATT-ATAAATA
89174 TTATTACT-AA-A
1 TTATTA-TAAATA
*
89185 TTATTATATATA
1 TTATTATAAATA
*
89197 TTTATAATAAATA
1 -TTATTATAAATA
89210 ATTAATTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
10 1 0.03
11 8 0.20
12 9 0.22
13 22 0.55
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (12 bp):
TTATTATAAATA
Found at i:89469 original size:28 final size:26
Alignment explanation
Indices: 89430--89531 Score: 91
Period size: 28 Copynumber: 3.8 Consensus size: 26
89420 ATACATTATC
*
89430 AATAAATCATATAATATTATTATATTAA
1 AATAAATTATATAAT-TTATTATA-TAA
*
89458 AATAAATTATATAATTTATTTTTAATAA
1 AATAAATTATATAATTTA-TTAT-ATAA
*
89486 AATAAAATAATATAATTTATTA-ATAA
1 AAT-AAATTATATAATTTATTATATAA
* * *
89512 GATATATT-TATAAATTATTA
1 AATAAATTATATAATTTATTA
89532 AGACATTTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
24 11 0.17
25 3 0.05
26 6 0.10
27 3 0.05
28 25 0.40
29 15 0.24
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (26 bp):
AATAAATTATATAATTTATTATATAA
Found at i:89500 original size:29 final size:28
Alignment explanation
Indices: 89430--89511 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
89420 ATACATTATC
* *
89430 AATAAATCATATAATATTA-TTATATTAA
1 AATAAATAATATAAT-TTATTTATAATAA
* *
89458 AATAAATTATATAATTTATTTTTAATAA
1 AATAAATAATATAATTTATTTATAATAA
*
89486 AATAAAATAATATAATTTATTAATAA
1 AAT-AAATAATATAATTTATTTATAA
89512 GATATATTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
27 3 0.07
28 24 0.52
29 19 0.41
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (28 bp):
AATAAATAATATAATTTATTTATAATAA
Found at i:90235 original size:15 final size:14
Alignment explanation
Indices: 90209--90257 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
90199 TTTTATATTT
90209 ATATAAAATTTAAA
1 ATATAAAATTTAAA
*
90223 ATATAATAATTTATA
1 ATATAA-AATTTAAA
* *
90238 TTATAAATTTTAAAA
1 ATATAAAATTT-AAA
90253 ATATA
1 ATATA
90258 TATCATATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 10 0.36
15 18 0.64
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATAAAATTTAAA
Found at i:90517 original size:28 final size:26
Alignment explanation
Indices: 90465--90512 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
90455 TTAAATCAAT
90465 TAAATAATTTATGTATTTATATTATG
1 TAAATAATTTATGTATTTATATTATG
90491 TAAAT-ATATT-T-TATTTATATTA
1 TAAATAAT-TTATGTATTTATATTA
90513 ATTATATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 3 0.14
26 7 0.33
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (26 bp):
TAAATAATTTATGTATTTATATTATG
Found at i:90642 original size:19 final size:18
Alignment explanation
Indices: 90595--90654 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
90585 CATATTAATG
*
90595 TTATATTATTTATCTAATA
1 TTATATTATTTAT-TTATA
*
90614 TTTTAATTATTTATTTATA
1 TTAT-ATTATTTATTTATA
* *
90633 TTATATTTATATAATTATA
1 TTATA-TTATTTATTTATA
90652 TTA
1 TTA
90655 AATATTATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
18 1 0.03
19 24 0.71
20 9 0.26
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATATTATTTATTTATA
Found at i:91109 original size:19 final size:17
Alignment explanation
Indices: 91085--91130 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 17
91075 TTAATTAAAT
91085 AAAAATTAAAAAATTATA
1 AAAAATTAAAAAA-TATA
91103 AATAAATT-AAAAATATA
1 AA-AAATTAAAAAATATA
91120 AAAAA-TAAAAA
1 AAAAATTAAAAA
91131 TTTTCATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.04
16 7 0.27
17 6 0.23
18 7 0.27
19 5 0.19
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAATTAAAAAATATA
Found at i:91114 original size:17 final size:16
Alignment explanation
Indices: 91083--91132 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
91073 AGTTAATTAA
*
91083 ATAAAAATTAAAAAATT
1 ATAAAAAAT-AAAAATT
91100 ATAAATAAATTAAAAA-T
1 ATAAA-AAA-TAAAAATT
91117 ATAAAAAATAAAAATT
1 ATAAAAAATAAAAATT
91133 TTCATCATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 6 0.21
16 4 0.14
17 11 0.38
18 7 0.24
19 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
ATAAAAAATAAAAATT
Found at i:91180 original size:3 final size:3
Alignment explanation
Indices: 91172--91196 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
91162 CTGCAAGAAA
91172 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
91197 CCCTACAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:92135 original size:22 final size:21
Alignment explanation
Indices: 92104--92161 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
92094 TTTAATAAAT
*
92104 AATATA-ATATAATTTATTAA
1 AATATATATATAAATTATTAA
*
92124 TGATATATATATAAATTATTAA
1 -AATATATATATAAATTATTAA
92146 AATATTATATATAAAT
1 AATA-TATATATAAAT
92162 AAAAAATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.25
22 24 0.75
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
AATATATATATAAATTATTAA
Found at i:92175 original size:22 final size:22
Alignment explanation
Indices: 92129--92177 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 22
92119 ATTAATGATA
*
92129 TATATATAAATTATTAAAATAT
1 TATATATAAATTATAAAAATAT
92151 TATATATAAA-TA-AAAAATAAT
1 TATATATAAATTATAAAAAT-AT
92172 T-TATAT
1 TATATAT
92178 TTTATTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 10 0.40
21 5 0.20
22 10 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TATATATAAATTATAAAAATAT
Found at i:92234 original size:27 final size:27
Alignment explanation
Indices: 92204--92298 Score: 70
Period size: 32 Copynumber: 3.3 Consensus size: 27
92194 TATATTTAAA
92204 ATATTTTATATTTATATAAATTTTGAT
1 ATATTTTATATTTATATAAATTTTGAT
*
92231 ATATTAATAATTAATATTATATAAATTTTAAGAT
1 ATATT--TTA-T-AT-TTATATAAATTTT--GAT
* *
92265 ATA-TTTATA-TTATATTATATTTTAAT
1 ATATTTTATATTTATA-TAAATTTTGAT
92291 -TATTTTAT
1 ATATTTTAT
92299 CGATATAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
25 2 0.04
26 7 0.13
27 10 0.18
28 7 0.13
29 3 0.05
30 2 0.04
31 4 0.07
32 13 0.24
33 1 0.02
34 6 0.11
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (27 bp):
ATATTTTATATTTATATAAATTTTGAT
Found at i:92240 original size:18 final size:17
Alignment explanation
Indices: 92193--92260 Score: 58
Period size: 16 Copynumber: 4.2 Consensus size: 17
92183 TATATTATAA
92193 TTATATTTA-A-AATATT
1 TTATATTTATATAA-ATT
92209 TTATATTTATATAAATT
1 TTATATTTATATAAATT
92226 TTGATATATTA-AT-AA-T
1 TT-ATAT-TTATATAAATT
*
92242 TAATA-TTATATAAATT
1 TTATATTTATATAAATT
92258 TTA
1 TTA
92261 AGATATATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
13 3 0.07
14 2 0.05
15 5 0.12
16 14 0.33
17 8 0.19
18 8 0.19
19 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (17 bp):
TTATATTTATATAAATT
Found at i:92254 original size:32 final size:31
Alignment explanation
Indices: 92209--92284 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 31
92199 TTAAAATATT
92209 TTATATTTATATAAATTTT-GATATATTAATAA
1 TTATA-TTATATAAATTTTAGATATATTAAT-A
*
92241 TTAATATTATATAAATTTTAAGATATATTTATA
1 TT-ATATTATATAAATTTT-AGATATATTAATA
92274 TTATATTATAT
1 TTATATTATAT
92285 TTTAATTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
32 24 0.60
33 6 0.15
34 10 0.25
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (31 bp):
TTATATTATATAAATTTTAGATATATTAATA
Found at i:92261 original size:17 final size:17
Alignment explanation
Indices: 92206--92261 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
92196 TATTTAAAAT
92206 ATTTT-ATATTTATATAA
1 ATTTTAATA-TTATATAA
92223 ATTTTGATATATTA-AT-A
1 ATTTT-A-ATATTATATAA
92240 A--TTAATATTATATAA
1 ATTTTAATATTATATAA
92255 ATTTTAA
1 ATTTTAA
92262 GATATATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
13 6 0.19
14 3 0.09
15 4 0.12
17 11 0.34
18 2 0.06
19 3 0.09
20 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
ATTTTAATATTATATAA
Found at i:92881 original size:17 final size:17
Alignment explanation
Indices: 92859--92939 Score: 57
Period size: 17 Copynumber: 4.9 Consensus size: 17
92849 TATTTAAAAT
92859 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
*
92876 ATTTTAAAATATTA-AT-A
1 ATTTT-ATAT-TTATATAA
92893 A-TTTATA-TTATA-AA
1 ATTTTATATTTATATAA
* *
92907 ATTTTTATATATATAAAA
1 A-TTTTATATTTATATAA
92925 ACTTTTAT-TTTATAT
1 A-TTTTATATTTATAT
92940 TTATATACAT
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
13 3 0.06
14 3 0.06
15 2 0.04
16 9 0.18
17 16 0.32
18 14 0.28
19 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:92898 original size:47 final size:47
Alignment explanation
Indices: 92821--92923 Score: 117
Period size: 47 Copynumber: 2.2 Consensus size: 47
92811 TAATTTGATA
**
92821 ATTTATAT--ATTTTATTATATTATAATTTTAT-TTA-AAATATTTTAT
1 ATTTATATAAATTTTAAAATATTATAATTTTATATTATAAA-ATTTT-T
92866 ATTTATATAAATTTTAAAATATTAATAA-TTTATATTATAAAATTTTT
1 ATTTATATAAATTTTAAAATATT-ATAATTTTATATTATAAAATTTTT
*
92913 ATATATATAAA
1 ATTTATATAAA
92924 AACTTTTATT
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
45 8 0.16
47 27 0.54
48 12 0.24
49 3 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (47 bp):
ATTTATATAAATTTTAAAATATTATAATTTTATATTATAAAATTTTT
Found at i:92925 original size:18 final size:18
Alignment explanation
Indices: 92854--92932 Score: 60
Period size: 18 Copynumber: 4.6 Consensus size: 18
92844 AATTTTATTT
*
92854 AAAATATTTTATATTTATA
1 AAAAT-TTTTATATATATA
* * *
92873 TAAATTTTAAAATAT-TA
1 AAAATTTTTATATATATA
*
92890 ATAA--TTTATAT-TAT-
1 AAAATTTTTATATATATA
92904 AAAATTTTTATATATATA
1 AAAATTTTTATATATATA
*
92922 AAAACTTTTAT
1 AAAATTTTTAT
92933 TTTATATTTA
Statistics
Matches: 45, Mismatches: 10, Indels: 11
0.68 0.15 0.17
Matches are distributed among these distances:
14 4 0.09
15 6 0.13
16 7 0.16
17 7 0.16
18 17 0.38
19 4 0.09
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (18 bp):
AAAATTTTTATATATATA
Found at i:92975 original size:15 final size:15
Alignment explanation
Indices: 92934--92973 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
92924 AACTTTTATT
*
92934 TTATATTTATATACA
1 TTATATTTAAATACA
92949 TTATATTTAAATA-A
1 TTATATTTAAATACA
92963 TTATATTTAAA
1 TTATATTTAAA
92974 ATTATCTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATATTTAAATACA
Found at i:93243 original size:5 final size:5
Alignment explanation
Indices: 93219--93339 Score: 60
Period size: 5 Copynumber: 25.2 Consensus size: 5
93209 ATTTATGTAT
* ** *
93219 TTATA TTA-A -TATA TTTTA TTATA TTATA TT-TA AAATA TTTTA TT-T-
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * * * *
93264 TTATA -TAAA TTTTA ATATA TTAATA CCTCATA TTATA -TATA TTTTA
1 TTATA TTATA TTATA TTATA TT-ATA --TTATA TTATA TTATA TTATA
**
93310 AAATA -TATA TTATA TTATA TTATA TTATA T
1 TTATA TTATA TTATA TTATA TTATA TTATA T
93340 AATTTTTAAT
Statistics
Matches: 85, Mismatches: 20, Indels: 22
0.67 0.16 0.17
Matches are distributed among these distances:
3 4 0.05
4 16 0.19
5 58 0.68
6 3 0.04
7 3 0.04
8 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (5 bp):
TTATA
Found at i:94000 original size:21 final size:22
Alignment explanation
Indices: 93974--94015 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
93964 GGATCCATAA
93974 AGACAAG-GATTGTATGACACC
1 AGACAAGTGATTGTATGACACC
* *
93995 AGACAAGTTATTGTTTGACAC
1 AGACAAGTGATTGTATGACAC
94016 ATTGGAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (22 bp):
AGACAAGTGATTGTATGACACC
Found at i:95923 original size:2 final size:2
Alignment explanation
Indices: 95916--95945 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
95906 TAAATTAGTT
95916 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
95946 AATTAAGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:96113 original size:3 final size:3
Alignment explanation
Indices: 96105--96147 Score: 68
Period size: 3 Copynumber: 13.7 Consensus size: 3
96095 TTGTTGAGTT
96105 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA TTA TT
96148 TTGCTTTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 32 0.84
4 6 0.16
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:106529 original size:26 final size:26
Alignment explanation
Indices: 106452--106531 Score: 135
Period size: 26 Copynumber: 3.1 Consensus size: 26
106442 GAGAATGTTC
106452 TTATTCCTAAAATATATGGAAAAT-A
1 TTATTCCTAAAATATATGGAAAATAA
106477 TTATTCCTAAAAATATATGGAAAATAA
1 TTATTCCT-AAAATATATGGAAAATAA
*
106504 TTATTCCTAAAGTATATGGAAAATAA
1 TTATTCCTAAAATATATGGAAAATAA
106530 TT
1 TT
106532 TAAGCTCGTT
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
25 8 0.15
26 35 0.67
27 9 0.17
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.36
Consensus pattern (26 bp):
TTATTCCTAAAATATATGGAAAATAA
Found at i:108868 original size:6 final size:6
Alignment explanation
Indices: 108853--108885 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
108843 TTTCCACCAT
*
108853 CATCAA CATCAC CATCAC CATCAC CATCAC CAT
1 CATCAC CATCAC CATCAC CATCAC CATCAC CAT
108886 AATCACGACC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.36, C:0.45, G:0.00, T:0.18
Consensus pattern (6 bp):
CATCAC
Found at i:109804 original size:15 final size:15
Alignment explanation
Indices: 109780--109828 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
109770 AATTATTAAT
*
109780 TAAAATATTTAATAA
1 TAAAAAATTTAATAA
*
109795 TAAAAAATTTAAAAA
1 TAAAAAATTTAATAA
* *
109810 AAAAAAATTAAATAA
1 TAAAAAATTTAATAA
109825 TAAA
1 TAAA
109829 TAATAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAAAAATTTAATAA
Found at i:113548 original size:17 final size:17
Alignment explanation
Indices: 113526--113558 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
113516 CTTGAGAGAT
113526 AAATTGCGAATACTATC
1 AAATTGCGAATACTATC
*
113543 AAATTGTGAATACTAT
1 AAATTGCGAATACTAT
113559 TAAGCACTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (17 bp):
AAATTGCGAATACTATC
Found at i:120773 original size:21 final size:21
Alignment explanation
Indices: 120716--120780 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
120706 TAAAATAAAA
* *
120716 TATATTTATTAAATTAAATTAT
1 TATATTT-TTAAAATAATTTAT
* *
120738 TA-AATTTAAATAATAATTTAT
1 TATATTTTTAA-AATAATTTAT
*
120759 TATATTTTTAAAATATTTTAT
1 TATATTTTTAAAATAATTTAT
120780 T
1 T
120781 TTAAATAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
20 3 0.09
21 23 0.68
22 8 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATATTTTTAAAATAATTTAT
Found at i:120784 original size:15 final size:15
Alignment explanation
Indices: 120764--120805 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
120754 TTTATTATAT
*
120764 TTTTAAAATATTTTA
1 TTTTAAAATAATTTA
120779 TTTT-AAATAATTTA
1 TTTTAAAATAATTTA
*
120793 TTATAAAAATAAT
1 TT-TTAAAATAAT
120806 AATTTATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 11 0.48
15 5 0.22
16 7 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTTAAAATAATTTA
Found at i:120826 original size:19 final size:19
Alignment explanation
Indices: 120784--120829 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
120774 TTTTATTTTA
*
120784 AATAATTTATTATAAAAAT
1 AATAATTTATAATAAAAAT
*
120803 AATAATTTATAATTATAAAT
1 AATAATTTATAA-TAAAAAT
120823 -ATAATTT
1 AATAATTT
120830 TATTTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATAATTTATAATAAAAAT
Found at i:120831 original size:20 final size:21
Alignment explanation
Indices: 120792--120832 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
120782 TAAATAATTT
120792 ATTATAAAAATAATAATTTATA
1 ATTATAAAAATAAT-ATTTATA
*
120814 ATTATAAATATAAT-TTTAT
1 ATTATAAAAATAATATTTAT
120833 TTTTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
22 13 0.72
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTATAAAAATAATATTTATA
Found at i:122989 original size:30 final size:31
Alignment explanation
Indices: 122950--123012 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
122940 ATATCTGATT
*
122950 TAAATAA-TTTAAATTATTATTTATAAATTAA
1 TAAATAATTTTAAA-AATTATTTATAAATTAA
* *
122981 TAAA-AATTTTAAAAATTATTTTTATATTAA
1 TAAATAATTTTAAAAATTATTTATAAATTAA
123011 TA
1 TA
123013 TTTATATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 18 0.64
31 10 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
TAAATAATTTTAAAAATTATTTATAAATTAA
Found at i:123025 original size:22 final size:21
Alignment explanation
Indices: 123000--123051 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 21
122990 TAAAAATTAT
*
123000 TTTTATATTAATATTTATATAA
1 TTTTATATTAA-ATTTAAATAA
123022 TTTTATAATTAAATTTAAATAA
1 TTTTAT-ATTAAATTTAAATAA
123044 TTATTATA
1 TT-TTATA
123052 GACCTTTGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTATATTAAATTTAAATAA
Found at i:124925 original size:24 final size:25
Alignment explanation
Indices: 124898--124945 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
124888 TGTCGGACAA
124898 AAGTGTT-AAACATGAGTACCACAC
1 AAGTGTTAAAACATGAGTACCACAC
124922 AAGTGTTAAAACATGAGTACCACA
1 AAGTGTTAAAACATGAGTACCACA
124946 AGAAAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.21
Consensus pattern (25 bp):
AAGTGTTAAAACATGAGTACCACAC
Found at i:127083 original size:16 final size:16
Alignment explanation
Indices: 127026--127082 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
127016 TAATTATATG
*
127026 AATTCAAAATGATCTAA
1 AATTCAAAATAATCT-A
*
127043 AATT-AAAACAATCTA
1 AATTCAAAATAATCTA
* *
127058 AACTCGAAATAATCTA
1 AATTCAAAATAATCTA
127074 CAATTCAAA
1 -AATTCAAA
127083 TGATAAGAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
15 4 0.13
16 17 0.55
17 10 0.32
ACGTcount: A:0.54, C:0.16, G:0.04, T:0.26
Consensus pattern (16 bp):
AATTCAAAATAATCTA
Found at i:134129 original size:12 final size:13
Alignment explanation
Indices: 134097--134130 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
134087 AATTTAAGCT
134097 AAAGCAAAGACAG
1 AAAGCAAAGACAG
134110 -AAGCAAAGACAG
1 AAAGCAAAGACAG
134122 AAAG-AAAGA
1 AAAGCAAAGA
134131 AAGATGGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 17 0.85
13 3 0.15
ACGTcount: A:0.65, C:0.12, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAGCAAAGACAG
Found at i:134599 original size:136 final size:135
Alignment explanation
Indices: 134354--134599 Score: 339
Period size: 136 Copynumber: 1.8 Consensus size: 135
134344 ATGGGGCCCG
* * ** *
134354 ATATGACACGTGGCAGAGACCTTCCATCGCGTAAGGCTTTGTGTTTTGTGCTTCATGTTTAGAAC
1 ATATGACACGCGGCAGAGACCTTCCATAGCGTAAGGCTTAATGTTTTGTGCTTCATGTTGAGAAC
* *
134419 CAGTTAGAGACCGGGGTGAGAGAGAAAGAGAGGGAGGCAAAGGTCAAAGACTCAAACAAAAAAGG
66 CAGTTAGAGACCGGAGTGAGAGAGAAAGAGAGAGAGGCAAAGGTCAAAGACTCAAACAAAAAAGG
134484 CTTCA
131 CTTCA
* * * * *
134489 ATATGACACGCGGCAGTGACCTTCTATAGCGTGAGGCTTAATGTTTTGTGCTTTCATGTTGGGGA
1 ATATGACACGCGGCAGAGACCTTCCATAGCGTAAGGCTTAATGTTTTGTGC-TTCATGTTGAGAA
* * * *
134554 TCAGTTAGAGACCTGAGTGAGAGAGACAGAGAGAGAGGCAGAGGTC
65 CCAGTTAGAGACCGGAGTGAGAGAGAAAGAGAGAGAGGCAAAGGTC
134600 CCGAAGGCAC
Statistics
Matches: 94, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
135 44 0.47
136 50 0.53
ACGTcount: A:0.30, C:0.16, G:0.31, T:0.23
Consensus pattern (135 bp):
ATATGACACGCGGCAGAGACCTTCCATAGCGTAAGGCTTAATGTTTTGTGCTTCATGTTGAGAAC
CAGTTAGAGACCGGAGTGAGAGAGAAAGAGAGAGAGGCAAAGGTCAAAGACTCAAACAAAAAAGG
CTTCA
Found at i:136204 original size:16 final size:16
Alignment explanation
Indices: 136168--136200 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
136158 TTTTTTATAT
*
136168 TATATAAATCATATAA
1 TATATAAATCATAAAA
136184 TATATAAAT-ATAAAA
1 TATATAAATCATAAAA
136199 TA
1 TA
136201 ATATTTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
TATATAAATCATAAAA
Found at i:136651 original size:25 final size:28
Alignment explanation
Indices: 136623--136678 Score: 73
Period size: 25 Copynumber: 2.1 Consensus size: 28
136613 ATTAAATATA
*
136623 TTTATTCGAAT-ATT-TATATT-ATAAT
1 TTTATTCAAATAATTATATATTAATAAT
*
136648 TTTATTTAAATAATTATATATTAATAAT
1 TTTATTCAAATAATTATATATTAATAAT
136676 TTT
1 TTT
136679 TATATATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 9 0.35
26 3 0.12
27 6 0.23
28 8 0.31
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (28 bp):
TTTATTCAAATAATTATATATTAATAAT
Found at i:136660 original size:14 final size:14
Alignment explanation
Indices: 136635--136683 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
136625 TATTCGAATA
136635 TTTATATT-ATAAT
1 TTTATATTAATAAT
136648 TTTAT-TTAAATAAT
1 TTTATATT-AATAAT
*
136662 TATATATTAATAATT
1 TTTATATTAATAA-T
136677 TTTATAT
1 TTTATAT
136684 ATTTAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 2 0.07
13 5 0.17
14 14 0.47
15 9 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTATATTAATAAT
Found at i:136701 original size:6 final size:6
Alignment explanation
Indices: 136690--136740 Score: 59
Period size: 6 Copynumber: 8.3 Consensus size: 6
136680 ATATATTTAA
* *
136690 TATATT TATA-T TATATT TATATT TATATT ATATAAT TATTAGT TATATT
1 TATATT TATATT TATATT TATATT TATATT -TATATT TA-TATT TATATT
136739 TA
1 TA
136741 AAATTAACAC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
5 5 0.13
6 24 0.62
7 10 0.26
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (6 bp):
TATATT
Found at i:136720 original size:11 final size:11
Alignment explanation
Indices: 136632--136738 Score: 61
Period size: 9 Copynumber: 10.0 Consensus size: 11
136622 ATTTATTCGA
136632 ATATTTATATT
1 ATATTTATATT
136643 ATAATTT-TATT
1 AT-ATTTATATT
**
136654 -TAAATA-ATT
1 ATATTTATATT
136663 ATATATTA-A-T
1 ATAT-TTATATT
*
136673 A-ATTTTTA-T
1 ATATTTATATT
136682 ATATTTA-A-T
1 ATATTTATATT
136691 ATATTTATATT
1 ATATTTATATT
136702 ATATTTATATTT
1 ATATTTATA-TT
136714 ATATTATATAATT
1 ATATT-TAT-ATT
*
136727 ATTAGTTATATT
1 A-TATTTATATT
136739 TAAAATTAAC
Statistics
Matches: 77, Mismatches: 7, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
8 2 0.03
9 19 0.25
10 10 0.13
11 19 0.25
12 14 0.18
13 9 0.12
14 4 0.05
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (11 bp):
ATATTTATATT
Found at i:136729 original size:17 final size:17
Alignment explanation
Indices: 136633--136729 Score: 72
Period size: 17 Copynumber: 6.2 Consensus size: 17
136623 TTTATTCGAA
136633 TATTTATA-T-TATAA-
1 TATTTATATTATATAAT
*
136647 T-TTTAT-TTAAATAAT
1 TATTTATATTATATAAT
136662 TA--TATATTA-ATAAT
1 TATTTATATTATATAAT
*
136676 T-TTTATA-TATTTAAT
1 TATTTATATTATATAAT
*
136691 ATATTTATATTATAT-TT
1 -TATTTATATTATATAAT
136708 ATATTTATATTATATAAT
1 -TATTTATATTATATAAT
136726 TATT
1 TATT
136730 AGTTATATTT
Statistics
Matches: 66, Mismatches: 5, Indels: 21
0.72 0.05 0.23
Matches are distributed among these distances:
13 6 0.09
14 16 0.24
15 12 0.18
16 1 0.02
17 26 0.39
18 5 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTTATATTATATAAT
Found at i:138932 original size:21 final size:22
Alignment explanation
Indices: 138890--138937 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
138880 TTAATTTTTA
*
138890 AAAATTGAATTGAATTAAATTT
1 AAAATTAAATTGAATTAAATTT
**
138912 AAAATTAAATT-AATTTTATTT
1 AAAATTAAATTGAATTAAATTT
138933 AAAAT
1 AAAAT
138938 CTTTATTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (22 bp):
AAAATTAAATTGAATTAAATTT
Found at i:140697 original size:32 final size:32
Alignment explanation
Indices: 140661--140727 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
140651 GGAATTATTT
*
140661 ACTCTCTTTTTATTTCCTGGGTCTGAAATCTG
1 ACTCTCTGTTTATTTCCTGGGTCTGAAATCTG
*
140693 ACTCTCTGTTTATTTTCTGGGTCTGAAATCTG
1 ACTCTCTGTTTATTTCCTGGGTCTGAAATCTG
140725 ACT
1 ACT
140728 GAGCAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.46
Consensus pattern (32 bp):
ACTCTCTGTTTATTTCCTGGGTCTGAAATCTG
Found at i:146671 original size:19 final size:18
Alignment explanation
Indices: 146647--146701 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 18
146637 TTATTTGATA
146647 ATTTATATATTCCTATTAT
1 ATTTATATATT-CTATTAT
*
146666 ATTTATATATTTTATTAT
1 ATTTATATATTCTATTAT
146684 A-TTATA-A-T-TATTAT
1 ATTTATATATTCTATTAT
146698 ATTT
1 ATTT
146702 TAATTATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
14 7 0.21
15 3 0.09
16 1 0.03
17 5 0.15
18 7 0.21
19 11 0.32
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTATATATTCTATTAT
Found at i:146687 original size:23 final size:25
Alignment explanation
Indices: 146660--146708 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
146650 TATATATTCC
*
146660 TATTATATTTA-TATATTTT-ATTA
1 TATTATAATTATTATATTTTAATTA
146683 TATTATAATTATTATATTTTAATTA
1 TATTATAATTATTATATTTTAATTA
146708 T
1 T
146709 TTTTTTATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.43
24 8 0.35
25 5 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TATTATAATTATTATATTTTAATTA
Found at i:146696 original size:14 final size:14
Alignment explanation
Indices: 146677--146709 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
146667 TTTATATATT
146677 TTATTATATTATAA
1 TTATTATATTATAA
*
146691 TTATTATATTTTAA
1 TTATTATATTATAA
146705 TTATT
1 TTATT
146710 TTTTTATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATTATATTATAA
Found at i:146701 original size:32 final size:34
Alignment explanation
Indices: 146660--146723 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
146650 TATATATTCC
146660 TATTATA-TTT-ATATATTTTATTAT-ATTATAAT
1 TATTATATTTTAAT-TATTTTATTATGATTATAAT
*
146692 TATTATATTTTAATTATTTTTTTATGATTATA
1 TATTATATTTTAATTATTTTATTATGATTATA
146724 TTCGTATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 7 0.25
33 13 0.46
34 8 0.29
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (34 bp):
TATTATATTTTAATTATTTTATTATGATTATAAT
Found at i:146721 original size:25 final size:24
Alignment explanation
Indices: 146671--146725 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
146661 ATTATATTTA
*
146671 TATATTTTATTATATTATAATTAT
1 TATATTTTATTATATTATAATGAT
* * *
146695 TATATTTTAATTATTTTTTTATGAT
1 TATATTTT-ATTATATTATAATGAT
146720 TATATT
1 TATATT
146726 CGTATAATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (24 bp):
TATATTTTATTATATTATAATGAT
Found at i:149847 original size:24 final size:24
Alignment explanation
Indices: 149810--149866 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 24
149800 ATAATGATAA
149810 AATATTTTAATAAATTATACCTAAAAAT
1 AATA-TTTAA-AAA-TAT-CCTAAAAAT
*
149838 AATATTTAAAAATATGCTAAAAAT
1 AATATTTAAAAATATCCTAAAAAT
149862 AATAT
1 AATAT
149867 AAAATATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 13 0.46
25 3 0.11
26 3 0.11
27 5 0.18
28 4 0.14
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (24 bp):
AATATTTAAAAATATCCTAAAAAT
Found at i:149885 original size:48 final size:48
Alignment explanation
Indices: 149833--149991 Score: 133
Period size: 50 Copynumber: 3.2 Consensus size: 48
149823 ATTATACCTA
* *
149833 AAAATAATATTTAAAAATATGCTAAAAATAATATAAAATATTTTTAAC
1 AAAATAATATTTAAAAATATGTTAAAAATAATATAAAATATTATTAAC
* * * **** * *
149881 AAAATAATAATTATTAATATATTTTTTCTAT-ATATATATATATTAAATATA-
1 AAAATAAT-ATT-TAAAAATATGTTAAAAATAATATA-AAATATT-ATTA-AC
* * *
149932 AAAATAATATTTAAAATTATGTTGAAAATAATATAAAATATCATTAAC
1 AAAATAATATTTAAAAATATGTTAAAAATAATATAAAATATTATTAAC
149980 AAAATAATATTT
1 AAAATAATATTT
149992 TTAATATATT
Statistics
Matches: 82, Mismatches: 22, Indels: 14
0.69 0.19 0.12
Matches are distributed among these distances:
47 1 0.01
48 23 0.28
49 23 0.28
50 24 0.29
51 10 0.12
52 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (48 bp):
AAAATAATATTTAAAAATATGTTAAAAATAATATAAAATATTATTAAC
Found at i:154161 original size:33 final size:32
Alignment explanation
Indices: 154083--154161 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 32
154073 TTAGATTTTT
*
154083 TAATTT-ATTATTTAAATATGCTTTATTCATA
1 TAATTTAATTATTTAAATATGATTTATTCATA
*
154114 TGAATTTAGA-TATTTAAATATGATATTTATTTATA
1 T-AATTTA-ATTATTTAAATATG--ATTTATTCATA
154149 T-ATTTAATTATTT
1 TAATTTAATTATTT
154162 TTAAACTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
31 1 0.03
32 6 0.15
33 22 0.55
34 1 0.03
35 10 0.25
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.56
Consensus pattern (32 bp):
TAATTTAATTATTTAAATATGATTTATTCATA
Found at i:154775 original size:23 final size:23
Alignment explanation
Indices: 154734--154800 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 23
154724 AAGAAGATAT
154734 TATTAAAAATAT--TTAATTTTTA
1 TATTAAAAATATAATT-ATTTTTA
*
154756 TATTAAAAATATAATTATTTTAA
1 TATTAAAAATATAATTATTTTTA
*
154779 TA-TAAATATATTAA-TATTTTTA
1 TATTAAAAATA-TAATTATTTTTA
154801 AATAAATAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
22 26 0.67
23 11 0.28
24 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTAAAAATATAATTATTTTTA
Found at i:154801 original size:23 final size:23
Alignment explanation
Indices: 154749--154829 Score: 73
Period size: 23 Copynumber: 3.6 Consensus size: 23
154739 AAAATATTTA
*
154749 ATTTTT-ATATTAAAAATA-TAAT
1 ATTTTTAATA-TAAATATATTAAT
154771 -TATTTTAATATAAATATATTAAT
1 AT-TTTTAATATAAATATATTAAT
154794 ATTTTTAA-ATAAATA-ATTACTAT
1 ATTTTTAATATAAATATATTA--AT
*
154817 ATATTTAATATAA
1 ATTTTTAATATAA
154830 TTAAAATCAT
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
21 5 0.10
22 18 0.36
23 22 0.44
24 5 0.10
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTTTAATATAAATATATTAAT
Found at i:155724 original size:15 final size:16
Alignment explanation
Indices: 155704--155741 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
155694 TTAATTTTAG
*
155704 ATTATTTCGAA-TCAA
1 ATTATTTCAAATTCAA
*
155719 ATTATTTCAAATTCGA
1 ATTATTTCAAATTCAA
155735 ATTATTT
1 ATTATTT
155742 TAGTTTTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (16 bp):
ATTATTTCAAATTCAA
Found at i:156035 original size:20 final size:19
Alignment explanation
Indices: 156010--156070 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
156000 TTTTAAAAAA
156010 TTAATTAAATTTTTTAAAT
1 TTAATTAAATTTTTTAAAT
* *
156029 TTAAATTAAAATTTTAAAAT
1 TT-AATTAAATTTTTTAAAT
* * *
156049 ATATTTAAATTATTTTTAAT
1 TTAATTAAATT-TTTTAAAT
156069 TT
1 TT
156071 CAATATAATT
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
19 9 0.28
20 23 0.72
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTAATTAAATTTTTTAAAT
Found at i:156069 original size:28 final size:28
Alignment explanation
Indices: 156038--156099 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
156028 TTTAAATTAA
*
156038 AATTTTAAAATATATTTAAATT-ATTTTT
1 AATTTTAAAATA-ATTTAAATTAATTATT
* * *
156066 AATTTCAATATAATTTAATTTAATTATT
1 AATTTTAAAATAATTTAAATTAATTATT
156094 AATTTT
1 AATTTT
156100 TTAATCACAC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 8 0.29
28 20 0.71
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (28 bp):
AATTTTAAAATAATTTAAATTAATTATT
Found at i:169324 original size:14 final size:14
Alignment explanation
Indices: 169290--169333 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
169280 TTATCCGAAT
*
169290 ATATGTATATATTATA
1 ATATTTATAT-TTA-A
*
169306 ATATTTATTTTTAA
1 ATATTTATATTTAA
169320 ATATTTATATTTAA
1 ATATTTATATTTAA
169334 TGGTTGTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 14 0.56
15 3 0.12
16 8 0.32
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
ATATTTATATTTAA
Found at i:172372 original size:22 final size:23
Alignment explanation
Indices: 172347--172390 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
172337 GAATCATTCT
172347 AAATTTAAATCAAT-TAGATTTA
1 AAATTTAAATCAATCTAGATTTA
* *
172369 AAATTTAAGTTAATCTAGATTT
1 AAATTTAAATCAATCTAGATTT
172391 GGTTAAACGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (23 bp):
AAATTTAAATCAATCTAGATTTA
Found at i:172618 original size:20 final size:20
Alignment explanation
Indices: 172595--172657 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
172585 TTAAAAAATT
172595 AATTAAATTTTTTAAATTTA
1 AATTAAATTTTTTAAATTTA
* ** *
172615 AATTAAAATTTAAAAATAT-
1 AATTAAATTTTTTAAATTTA
* *
172634 ATTTAAATTATTTTTAATTTA
1 AATTAAATT-TTTTAAATTTA
172655 AAT
1 AAT
172658 ATAATTTAAT
Statistics
Matches: 30, Mismatches: 11, Indels: 3
0.68 0.25 0.07
Matches are distributed among these distances:
19 7 0.23
20 21 0.70
21 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTAAATTTTTTAAATTTA
Found at i:172640 original size:39 final size:38
Alignment explanation
Indices: 172588--172666 Score: 106
Period size: 39 Copynumber: 2.1 Consensus size: 38
172578 TCAGATTTTA
172588 AAAAATTAATTAAATT-TTTTAAATTTAAATTAAAATTT
1 AAAAATTAATTAAATTATTTTAAATTTAAA-TAAAATTT
* * *
172626 AAAAATATATTTAAATTATTTTTAATTTAAATATAATTT
1 AAAAAT-TAATTAAATTATTTTAAATTTAAATAAAATTT
172665 AA
1 AA
172667 TTTAATTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
38 6 0.17
39 18 0.50
40 12 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (38 bp):
AAAAATTAATTAAATTATTTTAAATTTAAATAAAATTT
Found at i:172655 original size:16 final size:16
Alignment explanation
Indices: 172634--172676 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
172624 TTAAAAATAT
172634 ATTTAAATTATTTTTA
1 ATTTAAATTATTTTTA
*
172650 ATTTAAA-TATAATTTA
1 ATTTAAATTAT-TTTTA
172666 ATTT-AATTATT
1 ATTTAAATTATT
172677 AATTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTAAATTATTTTTA
Found at i:172656 original size:28 final size:28
Alignment explanation
Indices: 172621--172681 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
172611 TTTAAATTAA
*
172621 AATTTAAAAATATATTTAAATT-ATTTTT
1 AATTTAAAAATA-ATTTAAATTAATTATT
* *
172649 AATTTAAATATAATTTAATTTAATTATT
1 AATTTAAAAATAATTTAAATTAATTATT
172677 AATTT
1 AATTT
172682 TTTTAATCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 8 0.28
28 21 0.72
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
AATTTAAAAATAATTTAAATTAATTATT
Found at i:175107 original size:2 final size:2
Alignment explanation
Indices: 175100--175145 Score: 83
Period size: 2 Copynumber: 22.5 Consensus size: 2
175090 TGAAGATTCT
175100 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
175143 TA T
1 TA T
175146 TTGTGTGTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:181126 original size:15 final size:15
Alignment explanation
Indices: 181106--181147 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
181096 AGCAACTACT
*
181106 GCAACAACAGCAGCA
1 GCAACAACAACAGCA
*
181121 GCAACAACAACAGCG
1 GCAACAACAACAGCA
*
181136 GCAGCAACAACA
1 GCAACAACAACA
181148 ACAGTTGCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.48, C:0.33, G:0.19, T:0.00
Consensus pattern (15 bp):
GCAACAACAACAGCA
Found at i:181128 original size:18 final size:18
Alignment explanation
Indices: 181107--181151 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
181097 GCAACTACTG
181107 CAACAACAGCAGCAGCAA
1 CAACAACAGCAGCAGCAA
*
181125 CAACAACAGCGGCAGCAA
1 CAACAACAGCAGCAGCAA
181143 CAACAACAG
1 CAACAACAG
181152 TTGCACCAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.49, C:0.33, G:0.18, T:0.00
Consensus pattern (18 bp):
CAACAACAGCAGCAGCAA
Found at i:188638 original size:19 final size:17
Alignment explanation
Indices: 188610--188648 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
188600 ATGAAGGATA
188610 TATATATATAACTTAATTT
1 TATATATATAA--TAATTT
*
188629 TATATTTATAATAATTT
1 TATATATATAATAATTT
188646 TAT
1 TAT
188649 TTATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
19 10 0.53
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATATATAATAATTT
Found at i:191165 original size:18 final size:18
Alignment explanation
Indices: 191144--191207 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
191134 ATTTAAATAG
191144 ATAATAAAATTAATTTTA
1 ATAATAAAATTAATTTTA
* **
191162 ATAAAATCAAAAATAATAATA
1 AT--AAT-AAAATTAATTTTA
*
191183 ATAATAAAATTAATTTTT
1 ATAATAAAATTAATTTTA
191201 ATAATAA
1 ATAATAA
191208 TAAAATTAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
18 18 0.50
19 3 0.08
20 3 0.08
21 12 0.33
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAATAAAATTAATTTTA
Done.