Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001372.1 Hibiscus syriacus cultivar Beakdansim tig00002684_pilon, whole genome shotgun sequence
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: 540953
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:11216 original size:197 final size:200
Alignment explanation
Indices: 10771--11253 Score: 535
Period size: 197 Copynumber: 2.4 Consensus size: 200
10761 TTTATACAAG
* * * *
10771 TATAAATATACCGG-TTAATTAGAAAACAGGTCAACATAATGTATCGACACTTGTGTAATTTGTG
1 TATAAATATACCGGTTTTATGAGAAAATAGGTCAA-ATAATGTATCGACACTTGTCTAATTTGTG
* ** * * *
10835 TCGATACTTATTATTCAGGATGAATGCACAAACGAGGTGCACACATAAAGTGTCGATATATTTAT
65 TCGATACTTATTATCCAAAATGAATACACAAAAGAGGTGCACACATAAAGTGTCGATACATTTAT
* * * *
10900 TAAAAGTATCGATCCCAAAAACATTGAAACCGATAATTATAATGTATTAGGTAAATTTAAAATGT
130 TAAAAGTATCGATCCCAAAAACATCGAAACCCATAAGTATAATGTAATAGGTAAATTTAAAATGT
10965 AACCGA
195 AACCGA
* * * *
10971 TATAAATAT--CGGTTTTATGATAAAATAGGTCAGCATCAA-GTGTCGACACTTG-CTAATTTTT
1 TATAAATATACCGGTTTTATGAGAAAATAGGTCA-AAT-AATGTATCGACACTTGTCTAA-TTTG
*
11032 TGTCGATACTT-TTGGTCCAAAATGAATAC-CAAAAG-GGTGCA-ACCATAAAGTGTCGATACAT
63 TGTCGATACTTATT-ATCCAAAATGAATACACAAAAGAGGTGCACA-CATAAAGTGTCGATACAT
** *
11093 TTA-TAAAAGTATCGAT-CCGGAAACATCGAAACCCATAAGTATAATGTAATAGGTAAATGTT-C
126 TTATTAAAAGTATCGATCCCAAAAACATCGAAACCCATAAGTATAATGTAATAGGTAAAT-TTAA
*
11155 AATGTAATCGA
190 AATGTAACCGA
* *
11166 TATAAATATACCGGTTTTATGAGATAATAGGTCTAAATAATGTATCGACACGTTGT-TAGTTTGT
1 TATAAATATACCGGTTTTATGAGAAAATAGGTC-AAATAATGTATCGACAC-TTGTCTAATTTGT
* * *
11230 GTCGATA-TTTTTTTCCAGAATGAA
64 GTCGATACTTATTATCCAAAATGAA
11254 ATATGAATGC
Statistics
Matches: 238, Mismatches: 31, Indels: 32
0.79 0.10 0.11
Matches are distributed among these distances:
195 55 0.23
196 30 0.13
197 70 0.29
198 19 0.08
199 53 0.22
200 11 0.05
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.32
Consensus pattern (200 bp):
TATAAATATACCGGTTTTATGAGAAAATAGGTCAAATAATGTATCGACACTTGTCTAATTTGTGT
CGATACTTATTATCCAAAATGAATACACAAAAGAGGTGCACACATAAAGTGTCGATACATTTATT
AAAAGTATCGATCCCAAAAACATCGAAACCCATAAGTATAATGTAATAGGTAAATTTAAAATGTA
ACCGA
Found at i:11471 original size:64 final size:64
Alignment explanation
Indices: 11403--11522 Score: 213
Period size: 64 Copynumber: 1.9 Consensus size: 64
11393 TACCTATTAC
*
11403 ATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTTCGGTTAAATGCCTATTTT
1 ATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATGCCTATTTT
* *
11467 ATTATATAAGTGTTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATG
1 ATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATG
11523 ATATAACATT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (64 bp):
ATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATGCCTATTTT
Found at i:12461 original size:35 final size:35
Alignment explanation
Indices: 12421--12488 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
12411 TATAATTAAG
*
12421 ACATTTCCTGTAGTCATTGAGACAAGTAATTAGCA
1 ACATTTCCTGTAGTAATTGAGACAAGTAATTAGCA
* *
12456 ACATTTCTTGTAGTAATTGAGACAATTAATTAG
1 ACATTTCCTGTAGTAATTGAGACAAGTAATTAG
12489 TAACTTGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (35 bp):
ACATTTCCTGTAGTAATTGAGACAAGTAATTAGCA
Found at i:13447 original size:6 final size:6
Alignment explanation
Indices: 13426--13489 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
13416 TACGGCCTTT
* * * * * *
13426 GTATGC GTATAC GTATGT GTATGT GTATGC ATATGC GTATAC GTATGT
1 GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC
*
13474 GTATAC GTATGC GTAT
1 GTATGC GTATGC GTAT
13490 ACATATGCAT
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.23, C:0.11, G:0.27, T:0.39
Consensus pattern (6 bp):
GTATGC
Found at i:13464 original size:24 final size:24
Alignment explanation
Indices: 13427--13496 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
13417 ACGGCCTTTG
* **
13427 TATGCGTATACGTATGTGTATGTG
1 TATGCGTATGCGTATACGTATGTG
*
13451 TATGCATATGCGTATACGTATGTG
1 TATGCGTATGCGTATACGTATGTG
* *
13475 TATACGTATGCGTATACATATG
1 TATGCGTATGCGTATACGTATG
13497 CATATATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (24 bp):
TATGCGTATGCGTATACGTATGTG
Found at i:13484 original size:30 final size:30
Alignment explanation
Indices: 13427--13485 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
13417 ACGGCCTTTG
**
13427 TATGCGTATACGTATGTGTATGTGTATGCA
1 TATGCGTATACGTATGTGTATACGTATGCA
13457 TATGCGTATACGTATGTGTATACGTATGC
1 TATGCGTATACGTATGTGTATACGTATGC
13486 GTATACATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.39
Consensus pattern (30 bp):
TATGCGTATACGTATGTGTATACGTATGCA
Found at i:13502 original size:24 final size:24
Alignment explanation
Indices: 13457--13502 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
13447 TGTGTATGCA
* **
13457 TATGCGTATACGTATGTGTATACG
1 TATGCGTATACATATGCATATACG
13481 TATGCGTATACATATGCATATA
1 TATGCGTATACATATGCATATA
13503 TATATATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (24 bp):
TATGCGTATACATATGCATATACG
Found at i:19113 original size:12 final size:12
Alignment explanation
Indices: 19093--19126 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
19083 AAAAAAAATA
*
19093 TTTAATTTTATT
1 TTTAATTTTAGT
*
19105 TTTAGTTTTAGT
1 TTTAATTTTAGT
19117 TTTAATTTTA
1 TTTAATTTTA
19127 ATATTATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (12 bp):
TTTAATTTTAGT
Found at i:20671 original size:22 final size:21
Alignment explanation
Indices: 20618--20671 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 21
20608 AAAGATCAAT
*
20618 AACATGTCA-AAAGACAAAAA
1 AACATGTCATAAAAACAAAAA
* * *
20638 AACGTATTATAAAAACAAAGAA
1 AACATGTCATAAAAACAAA-AA
20660 AACATGTCATAA
1 AACATGTCATAA
20672 GATAAAAGTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
20 6 0.24
21 8 0.32
22 11 0.44
ACGTcount: A:0.61, C:0.13, G:0.09, T:0.17
Consensus pattern (21 bp):
AACATGTCATAAAAACAAAAA
Found at i:22648 original size:2 final size:2
Alignment explanation
Indices: 22643--22667 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22633 TTATTTAAAT
22643 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
22668 GATTCACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27069 original size:6 final size:6
Alignment explanation
Indices: 27058--27512 Score: 892
Period size: 6 Copynumber: 75.5 Consensus size: 6
27048 TTACAGCCTT
27058 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
27106 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
27154 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
27202 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
27250 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
27298 TGTATG TGTATGTG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTA--TG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
27348 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
27396 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
27444 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
27492 TGTATG TGTATG TGTATG TGT
1 TGTATG TGTATG TGTATG TGT
27513 GGAAAGGGAA
Statistics
Matches: 447, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
6 441 0.99
8 6 0.01
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.50
Consensus pattern (6 bp):
TGTATG
Found at i:27776 original size:26 final size:29
Alignment explanation
Indices: 27739--27812 Score: 82
Period size: 31 Copynumber: 2.6 Consensus size: 29
27729 GCTCGACTAA
*
27739 ACTCTTTGCTCGTTAAAA-TT-TTGCTTG
1 ACTCGTTGCTCGTTAAAACTTGTTGCTTG
27766 ACTCG-TGCTCGTTAAGAAAACTTGTTGCTTG
1 ACTCGTTGCTCGTT---AAAACTTGTTGCTTG
*
27797 ACTCGTTGCTCATTAA
1 ACTCGTTGCTCGTTAA
27813 GCTCAATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
26 8 0.21
27 4 0.10
29 6 0.15
30 2 0.05
31 12 0.31
32 7 0.18
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.41
Consensus pattern (29 bp):
ACTCGTTGCTCGTTAAAACTTGTTGCTTG
Found at i:28830 original size:2 final size:2
Alignment explanation
Indices: 28825--28894 Score: 124
Period size: 2 Copynumber: 35.0 Consensus size: 2
28815 AAAATAAAAA
28825 AT AT AT GAT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28867 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
28895 GTATGATTCG
Statistics
Matches: 66, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 63 0.95
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33266 original size:33 final size:33
Alignment explanation
Indices: 33224--33286 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
33214 GGATTACACA
* *
33224 TTCTTTGTTTTTCATTTAATGGTATAAACTACT
1 TTCTATGTTTTTCATTTAATGGTACAAACTACT
*
33257 TTCTATGTTTTTTATTTAATGGTACAAACT
1 TTCTATGTTTTTCATTTAATGGTACAAACT
33287 TTTTAAGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.25, C:0.11, G:0.10, T:0.54
Consensus pattern (33 bp):
TTCTATGTTTTTCATTTAATGGTACAAACTACT
Found at i:38606 original size:22 final size:22
Alignment explanation
Indices: 38580--38636 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
38570 TAAAAAATAT
*
38580 TTTTAATTATTTTTAT-TTTTAA
1 TTTTAA-TATTTTTATAATTTAA
*
38602 TTTTAATATTCTTATAATTTAA
1 TTTTAATATTTTTATAATTTAA
*
38624 TTTAAATATTTTT
1 TTTTAATATTTTT
38637 TATTAAATAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 8 0.27
22 22 0.73
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTAATATTTTTATAATTTAA
Found at i:39517 original size:26 final size:26
Alignment explanation
Indices: 39476--39536 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
39466 TTAGGATTTT
39476 TAACTTTT-TTTTATAATCTTAAATA
1 TAACTTTTATTTTATAATCTTAAATA
39501 TAACTTTTATTTTATAATCTTAAATA
1 TAACTTTTATTTTATAATCTTAAATA
39527 TAACTTTTAT
1 TAACTTTTAT
39537 GATATAAGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 8 0.23
26 27 0.77
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (26 bp):
TAACTTTTATTTTATAATCTTAAATA
Found at i:39542 original size:26 final size:26
Alignment explanation
Indices: 39487--39543 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
39477 AACTTTTTTT
**
39487 TATAATCTTAAATATAACTTTTATTT
1 TATAATCTTAAATATAACTTTTATGA
39513 TATAATCTTAAATATAACTTTTATGA
1 TATAATCTTAAATATAACTTTTATGA
39539 TATAA
1 TATAA
39544 GGTTATGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (26 bp):
TATAATCTTAAATATAACTTTTATGA
Found at i:42918 original size:22 final size:22
Alignment explanation
Indices: 42868--42930 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
42858 GAGTCGAGGG
42868 ATATACAGTGGTCCTTCGGG--
1 ATATACAGTGGTCCTTCGGGAC
*
42888 ATAT--TGTGGTCCTTCGGGAC
1 ATATACAGTGGTCCTTCGGGAC
*
42908 ATATACAGTGGTCATTCGGGAC
1 ATATACAGTGGTCCTTCGGGAC
42930 A
1 A
42931 AATATTCAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 13 0.36
20 8 0.22
22 15 0.42
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (22 bp):
ATATACAGTGGTCCTTCGGGAC
Found at i:50013 original size:18 final size:19
Alignment explanation
Indices: 49990--50038 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 19
49980 ACAATCGTCC
49990 TTCGGGACAT-AGTGGTCA
1 TTCGGGACATAAGTGGTCA
*
50008 TTCGGGATATATGAAGTGGTCA
1 TTCGGG--ACAT-AAGTGGTCA
50030 TTCGGGACA
1 TTCGGGACA
50039 AATATTCAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 6 0.24
20 5 0.20
22 14 0.56
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (19 bp):
TTCGGGACATAAGTGGTCA
Found at i:50694 original size:12 final size:12
Alignment explanation
Indices: 50661--50694 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
50651 TGTACTGTAG
* *
50661 CACTATTCACGA
1 CACTGTTCATGA
50673 CACTGTTCATGA
1 CACTGTTCATGA
50685 CACTGTTCAT
1 CACTGTTCAT
50695 ACGTATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.32
Consensus pattern (12 bp):
CACTGTTCATGA
Found at i:54246 original size:22 final size:23
Alignment explanation
Indices: 54215--54263 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
54205 ATAACATGTC
54215 AAAAGGCAAAAAAAACATATTAT
1 AAAAGGCAAAAAAAACATATTAT
* *
54238 AAAA-GCAAAGAAAACATGTTAT
1 AAAAGGCAAAAAAAACATATTAT
54260 AAAA
1 AAAA
54264 TAAAAGTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.65, C:0.08, G:0.10, T:0.16
Consensus pattern (23 bp):
AAAAGGCAAAAAAAACATATTAT
Found at i:54269 original size:22 final size:22
Alignment explanation
Indices: 54222--54269 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
54212 GTCAAAAGGC
54222 AAAA-AAAACATATTATAAAAG
1 AAAAGAAAACATATTATAAAAG
* * *
54243 CAAAGAAAACATGTTATAAAAT
1 AAAAGAAAACATATTATAAAAG
54265 AAAAG
1 AAAAG
54270 TTATTAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.19
Consensus pattern (22 bp):
AAAAGAAAACATATTATAAAAG
Found at i:55808 original size:2 final size:2
Alignment explanation
Indices: 55803--55846 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
55793 GACCATTTAA
55803 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55845 AT
1 AT
55847 GTATGCATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55978 original size:31 final size:30
Alignment explanation
Indices: 55908--55980 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
55898 AGCCATGTCT
** *
55908 CCCCAAAATTTAAAAAAATTATAATTTAGA
1 CCCCAAAATTTAAAAAAAAAATAATTTACA
* ** *
55938 CTCTTAAATTTAAAAAAAAAATTAATTTACC
1 CCCCAAAATTTAAAAAAAAAA-TAATTTACA
55969 CCCCAAAATTTA
1 CCCCAAAATTTA
55981 TAGAAATTCA
Statistics
Matches: 32, Mismatches: 10, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.51, C:0.16, G:0.01, T:0.32
Consensus pattern (30 bp):
CCCCAAAATTTAAAAAAAAAATAATTTACA
Found at i:56694 original size:20 final size:20
Alignment explanation
Indices: 56669--56709 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
56659 TAACAGATTG
*
56669 CCCAGAGGGTACCGATACCC
1 CCCAGAGGGCACCGATACCC
56689 CCCAGAGGGCACCGATACCC
1 CCCAGAGGGCACCGATACCC
56709 C
1 C
56710 TATATAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.44, G:0.24, T:0.07
Consensus pattern (20 bp):
CCCAGAGGGCACCGATACCC
Found at i:61363 original size:23 final size:22
Alignment explanation
Indices: 61332--61392 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 22
61322 TCTAGTGATA
*
61332 GGTATCGATACCCCCTTTGAATG
1 GGTACCGATACCCCC-TTGAATG
*
61355 GGTACCGATACCCTCCTTGAATT
1 GGTACCGATACCC-CCTTGAATG
61378 GGTACCGATACCCCC
1 GGTACCGATACCCCC
61393 CACGTGAGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
22 2 0.06
23 31 0.89
24 2 0.06
ACGTcount: A:0.21, C:0.33, G:0.20, T:0.26
Consensus pattern (22 bp):
GGTACCGATACCCCCTTGAATG
Found at i:64046 original size:20 final size:20
Alignment explanation
Indices: 64021--64058 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
64011 TAACATATTG
64021 CCCAGAGGGTACCGATACAC
1 CCCAGAGGGTACCGATACAC
64041 CCCAGAGGGTACCGATAC
1 CCCAGAGGGTACCGATAC
64059 CCCTATGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.34, G:0.26, T:0.11
Consensus pattern (20 bp):
CCCAGAGGGTACCGATACAC
Found at i:64426 original size:22 final size:22
Alignment explanation
Indices: 64401--64448 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
64391 TTTGAGCATT
64401 TTCAAGCCCATTTCATTCAATA
1 TTCAAGCCCATTTCATTCAATA
*
64423 TTCAAGCCTATTTCATTCAATA
1 TTCAAGCCCATTTCATTCAATA
64445 TTCA
1 TTCA
64449 TTTTTGCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (22 bp):
TTCAAGCCCATTTCATTCAATA
Found at i:65278 original size:6 final size:6
Alignment explanation
Indices: 65267--65305 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
65257 TTGAATTTTT
65267 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATA
65306 AATTGTTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
ATATTA
Found at i:66767 original size:22 final size:22
Alignment explanation
Indices: 66741--66791 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
66731 CCAGAATATT
66741 ACTTTAACTATTAAATAATTAC
1 ACTTTAACTATTAAATAATTAC
66763 ACTTTAACTATTAAATAATTAC
1 ACTTTAACTATTAAATAATTAC
66785 ACTTTAA
1 ACTTTAA
66792 TCCTCATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (22 bp):
ACTTTAACTATTAAATAATTAC
Found at i:74157 original size:13 final size:13
Alignment explanation
Indices: 74139--74164 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
74129 AGGAGGGGAA
74139 GCACAGATGAAGG
1 GCACAGATGAAGG
74152 GCACAGATGAAGG
1 GCACAGATGAAGG
74165 TGGGATGAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.38, T:0.08
Consensus pattern (13 bp):
GCACAGATGAAGG
Found at i:78750 original size:18 final size:19
Alignment explanation
Indices: 78727--78772 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
78717 AATTTTGTAC
*
78727 CGATACTCATGG-GAGTAT
1 CGATACTCAGGGAGAGTAT
*
78745 CGATACCCAGGGTAGAGTAT
1 CGATACTCAGGG-AGAGTAT
78765 CGATACTC
1 CGATACTC
78773 CCCATAGGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 10 0.43
20 13 0.57
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (19 bp):
CGATACTCAGGGAGAGTAT
Found at i:80922 original size:62 final size:65
Alignment explanation
Indices: 80851--81009 Score: 202
Period size: 62 Copynumber: 2.5 Consensus size: 65
80841 GTGCACTAAG
* * *
80851 AGTGCATCGATGCATGAAGTGCATTTGATG-TTTCA-AAATAGCC-TGAGTGCATCGATGCATGG
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAA-A-CCTTGAGTGCATCGATGCATGG
80913 -C
64 AC
* *
80914 A-TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCTTGAGTGCATCGATGCATGGAT
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTTGAGTGCATCGATGCATGGAC
* *
80978 AGTGCATCGATGCATAAACTGCATTCAATGTT
1 AGTGCATCGATGCATAAAATGCATTCGATGTT
81010 CAATTTATTC
Statistics
Matches: 84, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
62 27 0.32
63 26 0.31
64 4 0.05
65 27 0.32
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (65 bp):
AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTTGAGTGCATCGATGCATGGAC
Found at i:80934 original size:17 final size:17
Alignment explanation
Indices: 80898--80942 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
80888 ATAGCCTGAG
***
80898 TGCATCGATGCATGGCA
1 TGCATCGATGCATCAAA
80915 TGCATCGATGCATCAAA
1 TGCATCGATGCATCAAA
80932 TGCATTCGATG
1 TGCA-TCGATG
80943 TTTTCATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (17 bp):
TGCATCGATGCATCAAA
Found at i:84652 original size:17 final size:17
Alignment explanation
Indices: 84618--84653 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
84608 AGGTAAGCTC
* *
84618 TACAAGTGAGTATGCCT
1 TACAAGTGAGCATACCT
84635 TACAAGTGAGCATACCT
1 TACAAGTGAGCATACCT
84652 TA
1 TA
84654 GGTAACACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (17 bp):
TACAAGTGAGCATACCT
Found at i:95990 original size:55 final size:55
Alignment explanation
Indices: 95685--95998 Score: 427
Period size: 55 Copynumber: 5.7 Consensus size: 55
95675 TCGCTCCCTC
* * * * * *
95685 TTCTTTAGAGAGTAT-AGAACTCGGACAATCTTTAATAATCGTGTCTGCTCCCTAT
1 TTCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTAT
* *
95740 TTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTAT
1 TTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTAT
* * * *
95793 TTCTTCAGAGGGTATAAGACTCGAGCAATCTTCACCAATCGTGTCTGCCCCCTAT
1 TTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTAT
* **
95848 TTCTTCAGAGAGTATAAGACTCGAACAATTTTCAATGATCGCGTCTGCCCCCTAT
1 TTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTAT
* * *
95903 TTCTTCAGGGAGTATAAGACTCGAACAATCTTCAACGATCGCATCTGCCCCCTAT
1 TTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTAT
*
95958 TTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCG
1 TTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCG
95999 TTGGGAAACC
Statistics
Matches: 232, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
53 45 0.19
54 2 0.01
55 183 0.79
56 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.30
Consensus pattern (55 bp):
TTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTAT
Found at i:96933 original size:8 final size:7
Alignment explanation
Indices: 96920--96965 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
96910 TGAACCCTTC
96920 TTTTTTCA
1 TTTTTT-A
96928 TTTTTTA
1 TTTTTTA
96935 TTTTTT-
1 TTTTTTA
*
96941 TTATTT-
1 TTTTTTA
96947 TTTTTTA
1 TTTTTTA
96954 TTTTTTCA
1 TTTTTT-A
96962 TTTT
1 TTTT
96966 CACTCATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 10 0.29
7 13 0.38
8 11 0.32
ACGTcount: A:0.11, C:0.04, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTA
Found at i:96940 original size:9 final size:9
Alignment explanation
Indices: 96928--96959 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
96918 TCTTTTTTCA
96928 TTTTTTATT
1 TTTTTTATT
96937 TTTTTTATTT
1 TTTTTTA-TT
96947 TTTTTTATT
1 TTTTTTATT
96956 TTTT
1 TTTT
96960 CATTTTCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTATT
Found at i:96941 original size:10 final size:10
Alignment explanation
Indices: 96928--96959 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
96918 TCTTTTTTCA
96928 TTTTTTA-TT
1 TTTTTTATTT
96937 TTTTTTATTT
1 TTTTTTATTT
96947 TTTTTTATTT
1 TTTTTTATTT
96957 TTT
1 TTT
96960 CATTTTCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 7 0.32
10 15 0.68
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:100490 original size:8 final size:8
Alignment explanation
Indices: 100477--100504 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
100467 AAAAGAAGAT
100477 ATATATAC
1 ATATATAC
100485 ATATATAC
1 ATATATAC
100493 ATATATAC
1 ATATATAC
100501 ATAT
1 ATAT
100505 GGGAGAATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:113028 original size:36 final size:36
Alignment explanation
Indices: 112981--113053 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
112971 TACTCCACTA
112981 ATGTCCCCGGATTAGTCCTGGTCATAAATCAAAAAC
1 ATGTCCCCGGATTAGTCCTGGTCATAAATCAAAAAC
113017 ATGTCCCCGGATTAGTCCTGGTCATAAATCAAAAAC
1 ATGTCCCCGGATTAGTCCTGGTCATAAATCAAAAAC
113053 A
1 A
113054 AACAAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (36 bp):
ATGTCCCCGGATTAGTCCTGGTCATAAATCAAAAAC
Found at i:114886 original size:22 final size:22
Alignment explanation
Indices: 114861--114908 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
114851 TGACAATATT
*
114861 GTAATTTTAGGAAAGTACAAGG
1 GTAATTTTAGAAAAGTACAAGG
114883 GTAATTTTAGAAAAGTACAAGG
1 GTAATTTTAGAAAAGTACAAGG
114905 GTAA
1 GTAA
114909 AATTGGAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.25, T:0.27
Consensus pattern (22 bp):
GTAATTTTAGAAAAGTACAAGG
Found at i:116192 original size:2 final size:2
Alignment explanation
Indices: 116185--116223 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
116175 CATTTTACCT
* *
116185 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
116224 GTATGTATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:116228 original size:4 final size:4
Alignment explanation
Indices: 116201--116990 Score: 1443
Period size: 4 Copynumber: 199.0 Consensus size: 4
116191 TATATATATA
* * *
116201 TATG TATA TATA TATG TATA TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
116249 TATG TATG TATG TATG CATG CATG CATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
116297 TATG TATG TATG CATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
116345 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
116393 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
116441 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
116489 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
116537 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
116585 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
116633 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
116681 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
116729 --TG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
116775 TATG TATG TATG TATG TATG TATG TATG TATG TA-- TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
116821 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
116869 TA-- TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
116915 TA-- TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
116961 TATG TATG TATG TATG TATG ATATG ATATG
1 TATG TATG TATG TATG TATG -TATG -TATG
116991 AGGAAGACTT
Statistics
Matches: 769, Mismatches: 8, Indels: 17
0.97 0.01 0.02
Matches are distributed among these distances:
2 8 0.01
4 752 0.98
5 9 0.01
ACGTcount: A:0.26, C:0.01, G:0.24, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:119198 original size:2 final size:2
Alignment explanation
Indices: 119191--119251 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
119181 CCAAACAAAG
119191 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
119233 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
119252 AAGTATGCCT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:119762 original size:29 final size:29
Alignment explanation
Indices: 119725--119782 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
119715 AACTATTCAC
*
119725 AAGCGTAAAATTGTGAATTCAAATTCGAT
1 AAGCATAAAATTGTGAATTCAAATTCGAT
*
119754 AAGCATAAAATTGTGTATTCAAATTCGAT
1 AAGCATAAAATTGTGAATTCAAATTCGAT
119783 CTGGGGGTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (29 bp):
AAGCATAAAATTGTGAATTCAAATTCGAT
Found at i:120420 original size:2 final size:2
Alignment explanation
Indices: 120413--120443 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
120403 TAAAAATACA
120413 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 A
120444 ATTTAAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:133042 original size:48 final size:50
Alignment explanation
Indices: 132990--133106 Score: 150
Period size: 48 Copynumber: 2.4 Consensus size: 50
132980 TTTACATCAA
*
132990 TGTAAGTATGTGTTAAGTGCTACA-CTTTT-TTTTATTCACTTACACCGT
1 TGTAAGTATGTGTTAAGTGCTACATCTTTTATTTTATTCACTTACACCGG
* * * *
133038 TGTAAGTGTGTATTAAGTGCTATATTTTTTTATTTTATTCACTTACACCGG
1 TGTAAGTATGTGTTAAGTGCTACA-TCTTTTATTTTATTCACTTACACCGG
*
133089 TGT-TGTATGTGTTAAGTG
1 TGTAAGTATGTGTTAAGTG
133107 TTACTGTCGA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
48 21 0.36
50 16 0.28
51 21 0.36
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (50 bp):
TGTAAGTATGTGTTAAGTGCTACATCTTTTATTTTATTCACTTACACCGG
Found at i:133288 original size:15 final size:16
Alignment explanation
Indices: 133268--133300 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
133258 TACCTTTTAA
133268 AATAA-TTTAAAAAAT
1 AATAATTTTAAAAAAT
*
133283 AATAATTTTAAAAGAT
1 AATAATTTTAAAAAAT
133299 AA
1 AA
133301 AAAAATGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
AATAATTTTAAAAAAT
Found at i:135315 original size:3 final size:3
Alignment explanation
Indices: 135301--135351 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
135291 CAAAAACAAA
135301 AAT AAT AA- AAT AAT -AT AA- AAT AAT AAT AAT AATT AA- AATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AA-T AAT
135344 AAT AAT AA
1 AAT AAT AA
135352 AATTAGCAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
2 8 0.19
3 29 0.69
4 5 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:135331 original size:19 final size:18
Alignment explanation
Indices: 135299--135351 Score: 81
Period size: 19 Copynumber: 2.9 Consensus size: 18
135289 TACAAAAACA
135299 AAAATAATAA-AATAATAT
1 AAAATAATAATAATAAT-T
135317 AAAATAATAATAATAATT
1 AAAATAATAATAATAATT
135335 AAAATTAATAATAATAA
1 AAAA-TAATAATAATAA
135352 AATTAGCAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAATAATAATAATAATT
Found at i:138650 original size:13 final size:14
Alignment explanation
Indices: 138632--138662 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
138622 AATTTTGGAA
138632 AAAAGG-AAATTTG
1 AAAAGGAAAATTTG
138645 AAAAGGAAAATTTG
1 AAAAGGAAAATTTG
138659 AAAA
1 AAAA
138663 ATTATGGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.19, T:0.19
Consensus pattern (14 bp):
AAAAGGAAAATTTG
Found at i:138733 original size:27 final size:28
Alignment explanation
Indices: 138701--138800 Score: 96
Period size: 29 Copynumber: 3.6 Consensus size: 28
138691 CGGGGAAAAA
* *
138701 GAAATTTTACACAA-TAATTCTGAAACAT
1 GAAATTTTA-AAAATTAATTCTGAAACAG
*
138729 G-AATTTTAAAAATTAATTCTTAAACAG
1 GAAATTTTAAAAATTAATTCTGAAACAG
* * ** *
138756 GAAATTTTAAAAGCTAAATTCCAAAATAG
1 GAAATTTTAAAA-ATTAATTCTGAAACAG
138785 GAAATTTTAAAAATTA
1 GAAATTTTAAAAATTA
138801 GTTTTTACTG
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
26 3 0.05
27 20 0.34
28 13 0.22
29 23 0.39
ACGTcount: A:0.50, C:0.09, G:0.08, T:0.33
Consensus pattern (28 bp):
GAAATTTTAAAAATTAATTCTGAAACAG
Found at i:138979 original size:28 final size:28
Alignment explanation
Indices: 138882--138979 Score: 107
Period size: 27 Copynumber: 3.6 Consensus size: 28
138872 AAACTGAATA
*
138882 AAAAATTAATTCCGAAACATGA-ATTCTT
1 AAAAATTAATTCCGAAACAGGATA-TCTT
138910 -AAAATTAACTT-CGAAACAGGCAT-T-TT
1 AAAAATTAA-TTCCGAAACAGG-ATATCTT
*
138936 AAAAATTAATTACGAAACAGGATATCTT
1 AAAAATTAATTCCGAAACAGGATATCTT
*
138964 AAAAATTATTTCCGAA
1 AAAAATTAATTCCGAA
138980 GTAGGACGTT
Statistics
Matches: 60, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
26 6 0.10
27 35 0.58
28 19 0.32
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.31
Consensus pattern (28 bp):
AAAAATTAATTCCGAAACAGGATATCTT
Found at i:141731 original size:24 final size:24
Alignment explanation
Indices: 141704--141763 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
141694 TTTCACTTAA
*
141704 TGGAGCAGGCGTTGCACGCATTGT
1 TGGAGCATGCGTTGCACGCATTGT
* * *
141728 TGGAGCATGTGTTGTATGCATTGT
1 TGGAGCATGCGTTGCACGCATTGT
141752 TGGAGCATGCGT
1 TGGAGCATGCGT
141764 CGTTGGAGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.17, C:0.15, G:0.37, T:0.32
Consensus pattern (24 bp):
TGGAGCATGCGTTGCACGCATTGT
Found at i:144121 original size:12 final size:13
Alignment explanation
Indices: 144104--144133 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
144094 CATCAAAACA
144104 ATATAACAT-TAT
1 ATATAACATATAT
144116 ATATAACATATAT
1 ATATAACATATAT
144129 ATATA
1 ATATA
144134 TCACACATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATAACATATAT
Found at i:144214 original size:16 final size:14
Alignment explanation
Indices: 144178--144206 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
144168 CTATCAATAT
144178 TCTTATAATTTATA
1 TCTTATAATTTATA
144192 TCTTATAA-TTATA
1 TCTTATAATTTATA
144205 TC
1 TC
144207 CTCTTATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (14 bp):
TCTTATAATTTATA
Found at i:156702 original size:22 final size:22
Alignment explanation
Indices: 156674--156737 Score: 119
Period size: 22 Copynumber: 2.9 Consensus size: 22
156664 TCGAGGGTTA
*
156674 CATAGGTCATTCGGGACATATG
1 CATAGGTCCTTCGGGACATATG
156696 CATAGGTCCTTCGGGACATATG
1 CATAGGTCCTTCGGGACATATG
156718 CATAGGTCCTTCGGGACATA
1 CATAGGTCCTTCGGGACATA
156738 GATTTTACAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (22 bp):
CATAGGTCCTTCGGGACATATG
Found at i:162411 original size:45 final size:45
Alignment explanation
Indices: 162346--162661 Score: 314
Period size: 45 Copynumber: 7.0 Consensus size: 45
162336 CACTTTAAAT
* * * * * *
162346 TATAACAT-CTTTTCTATTGATAATGCATCCATTTGCATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
* *
162390 TATAGAATACTTTTTTGTTGATAATGTACCCATATACATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
* * * * *
162435 CATAGTATA-TCGTTATGTTAATAATGTACCCATATACATTTCAAC
1 TATAGCATACT-TTTCTGTTGATAATGTACCCATATACATTTCAAC
* * * * * * *
162480 TCTAGCATGCTCTTCTGCTGATAATGCACCCATTTGCATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
* * * * * * *
162525 TCTAGCATACATTTATGTTGATAATGCATCAATATGCATTTCAAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC-AAC
* *
162571 -CTAGCATACTTTTCTGTTGATAATGTATCCATATACATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
* *
162615 CATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
162660 TA
1 TA
162662 CGATATCTTT
Statistics
Matches: 226, Mismatches: 41, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
44 10 0.04
45 212 0.94
46 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (45 bp):
TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
Found at i:162546 original size:135 final size:135
Alignment explanation
Indices: 162363--162661 Score: 361
Period size: 135 Copynumber: 2.2 Consensus size: 135
162353 TCTTTTCTAT
* * * * *
162363 TGATAATGCATCCATTTGCATTTCAACTATAGAATACTTTTTTGTTGATAATGTACCCATATACA
1 TGATAATGCACCCATTTGCATTTCAACTATAGAATACATTTATGTTGATAATGCACCAATATACA
* *
162428 TTTC-AACCATAGTATA-TCGTTATGTTAATAATGTACCCATATACATTTCAACTC-TAGCATGC
66 TTTCAAACC-TAGCATACT-GTTATGTTAATAATGTACCCATATACATTTCAAC-CATAGCATAC
162490 TCTTCTGC
128 TCTTCTGC
* * * *
162498 TGATAATGCACCCATTTGCATTTCAACTCTAGCATACATTTATGTTGATAATGCATCAATATGCA
1 TGATAATGCACCCATTTGCATTTCAACTATAGAATACATTTATGTTGATAATGCACCAATATACA
* * * * * *
162563 TTTCAAACCTAGCATACTTTTCTGTTGATAATGTATCCATATACATTTCAACCATAGTATACTTT
66 TTTCAAACCTAGCATACTGTTATGTTAATAATGTACCCATATACATTTCAACCATAGCATACTCT
*
162628 TCTGT
131 TCTGC
* * *
162633 TGATAATGTACCCATATACATTTCAACTA
1 TGATAATGCACCCATTTGCATTTCAACTA
162662 CGATATCTTT
Statistics
Matches: 139, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
134 1 0.01
135 133 0.96
136 5 0.04
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (135 bp):
TGATAATGCACCCATTTGCATTTCAACTATAGAATACATTTATGTTGATAATGCACCAATATACA
TTTCAAACCTAGCATACTGTTATGTTAATAATGTACCCATATACATTTCAACCATAGCATACTCT
TCTGC
Found at i:162684 original size:45 final size:44
Alignment explanation
Indices: 162381--162698 Score: 146
Period size: 45 Copynumber: 7.1 Consensus size: 44
162371 CATCCATTTG
* * * ***
162381 CATTTCAACTATAGAATACTTTTTTGTTGATAATGTACCCATATA
1 CATTTCAACCATAGTATACTTTTCTGCCAATAATGTA-CCATATA
* * **
162426 CATTTCAACCATAGTATA-TCGTTATGTTAATAATGTACCCATATA
1 CATTTCAACCATAGTATACT-TTTCTGCCAATAATGTA-CCATATA
* * * ** * * *
162471 CATTTCAACTC-TAGCATGCTCTTCTGCTGATAATGCACCCATTTG
1 CATTTCAAC-CATAGTATACTTTTCTGCCAATAATGTA-CCATATA
* * * *** * * *
162516 CATTTCAACTC-TAGCATACATTTATGTTGATAATGCATCAATATG
1 CATTTCAAC-CATAGTATACTTTTCTGCCAATAATGTA-CCATATA
* ***
162561 CATTTCAAACC-TAGCATACTTTTCTGTTGATAATGTATCCATATA
1 CATTTC-AACCATAGTATACTTTTCTGCCAATAATGTA-CCATATA
***
162606 CATTTCAACCATAGTATACTTTTCTGTTGATAATGTACCCATATA
1 CATTTCAACCATAGTATACTTTTCTGCCAATAATGTA-CCATATA
* *
162651 CATTTCAA-C-TACG-ATATCTTTTCATGCCAATAATGCACCATATG
1 CATTTCAACCATA-GTATA-CTTTTC-TGCCAATAATGTACCATATA
162695 CATT
1 CATT
162699 AGTATTTTCA
Statistics
Matches: 231, Mismatches: 34, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
43 5 0.02
44 23 0.10
45 198 0.86
46 5 0.02
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (44 bp):
CATTTCAACCATAGTATACTTTTCTGCCAATAATGTACCATATA
Found at i:162684 original size:90 final size:89
Alignment explanation
Indices: 162362--162698 Score: 283
Period size: 90 Copynumber: 3.8 Consensus size: 89
162352 ATCTTTTCTA
* * * * * * * *
162362 TTGATAATGCATCCATTTGCATTTCAACTATAGA-ATACTTTTTTGTTGATAATGTACCCATATA
1 TTGATAATGTACCCATATACATTTCAACTA-CGATAT-CTTTTCTGCTGATAATGCACCCATATA
*
162426 CATTTCAACCATAGTATA-TCGTTATG
64 CATTTCAACCATAGTATACT-TTTATG
* * * * * *
162452 TTAATAATGTACCCATATACATTTCAACT-CTAGCATGCTCTTCTGCTGATAATGCACCCATTTG
1 TTGATAATGTACCCATATACATTTCAACTACGA-TAT-CTTTTCTGCTGATAATGCACCCATATA
* *
162516 CATTTCAACTC-TAGCATACATTTATG
64 CATTTCAAC-CATAGTATACTTTTATG
* * * * * * *
162542 TTGATAATGCATCAATATGCATTTCAAACCTA-GCATA-CTTTTCTGTTGATAATGTATCCATAT
1 TTGATAATGTACCCATATACATTTC-AA-CTACG-ATATCTTTTCTGCTGATAATGCACCCATAT
*
162605 ACATTTCAACCATAGTATACTTTTCTG
63 ACATTTCAACCATAGTATACTTTTATG
** *
162632 TTGATAATGTACCCATATACATTTCAACTACGATATCTTTTCATGCCAATAATGCA-CCATATGC
1 TTGATAATGTACCCATATACATTTCAACTACGATATCTTTTC-TGCTGATAATGCACCCATATAC
162696 ATT
65 ATT
162699 AGTATTTTCA
Statistics
Matches: 193, Mismatches: 42, Indels: 25
0.74 0.16 0.10
Matches are distributed among these distances:
88 7 0.04
89 20 0.10
90 159 0.82
91 3 0.02
92 3 0.02
93 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (89 bp):
TTGATAATGTACCCATATACATTTCAACTACGATATCTTTTCTGCTGATAATGCACCCATATACA
TTTCAACCATAGTATACTTTTATG
Found at i:162684 original size:135 final size:133
Alignment explanation
Indices: 162450--162698 Score: 297
Period size: 135 Copynumber: 1.8 Consensus size: 133
162440 TATATCGTTA
* *
162450 TGTTAATAATGTACCCATATACATTTCAACTCTAGCATGCTCTTCTGCTGATAATGCACCCATTT
1 TGTTAATAATGTACCCATATACATTTCAACTCTAGCATACTCTTCTGCTGATAATGCACCCATAT
* ***
162515 GCATTTCAACTCTAGCATACATTTATGTTGATAATGCATCAATATGCATTTCAAACCTAGCATAC
66 ACATTTCAACTC-AGCATACATTTATGCCAATAATGCA-CAATATGCATTTCAAACCTAGCATAC
162580 TTTTC
129 TTTTC
* * * * * *
162585 TGTTGATAATGTATCCATATACATTTCAAC-CATAGTATACTTTTCTGTTGATAATGTACCCATA
1 TGTTAATAATGTACCCATATACATTTCAACTC-TAGCATACTCTTCTGCTGATAATGCACCCATA
* *
162649 TACATTTCAACT-A-CGATATCTTTTCATGCCAATAATGCACCATATGCATT
65 TACATTTCAACTCAGC-ATA-CATTT-ATGCCAATAATGCACAATATGCATT
162699 AGTATTTTCA
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
132 1 0.01
133 4 0.04
134 15 0.16
135 76 0.79
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.38
Consensus pattern (133 bp):
TGTTAATAATGTACCCATATACATTTCAACTCTAGCATACTCTTCTGCTGATAATGCACCCATAT
ACATTTCAACTCAGCATACATTTATGCCAATAATGCACAATATGCATTTCAAACCTAGCATACTT
TTC
Found at i:167926 original size:45 final size:45
Alignment explanation
Indices: 167861--168214 Score: 356
Period size: 45 Copynumber: 7.9 Consensus size: 45
167851 CACTTTACAT
* **
167861 TATAACAT-CTTTTCTGTTGATAATGCACCCATATGGATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAAC
** * *
167905 TATAATATACTTTTCTTTTGATAATGTACCCATATACATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAAC
* * *
167950 CATAGTATA-TCATTCTGTTGATAATGCACCCATATACATTTCAAC
1 TATAGCATACT-TTTCTGTTGATAATGCACCCATATACATTTCAAC
* * * *
167995 TCTAGCATGCTCTTCTGTTGATAATGCACCCATATGCATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAAC
* * *
168040 TCTAGCATACATTTCTGTTGATAATGCACCCATATGCATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAAC
* * *
168085 TCTAGCATACTTTTCTATTGATAATGTACCCATATACATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAAC
** * * * * *
168130 TATAATATACATTTT-TGTTGATAATGTACTCATATAAATTACAAT
1 TATAGCATAC-TTTTCTGTTGATAATGCACCCATATACATTTCAAC
** * * * *
168175 TACGGCAT-CCTTTCATGCTAATAATGCACCCATATGCATT
1 TATAGCATACTTTTC-TGTTGATAATGCACCCATATACATT
168215 AGTATTTTCA
Statistics
Matches: 262, Mismatches: 42, Indels: 11
0.83 0.13 0.03
Matches are distributed among these distances:
43 3 0.01
44 9 0.03
45 245 0.94
46 5 0.02
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.38
Consensus pattern (45 bp):
TATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAAC
Found at i:168026 original size:90 final size:90
Alignment explanation
Indices: 167871--168165 Score: 396
Period size: 90 Copynumber: 3.3 Consensus size: 90
167861 TATAACATCT
** * ** *
167871 TTTCTGTTGATAATGCACCCATATGGATTTCAACTATAATATACTTTTCTTTTGATAATGTACCC
1 TTTCTGTTGATAATGCACCCATATACATTTCAACTCTAGCATACTTTTCTATTGATAATGTACCC
167936 ATATACATTTCAACCATAGTATATCA
66 ATATACATTTCAACCATAGTATA-CA
* * * *
167962 -TTCTGTTGATAATGCACCCATATACATTTCAACTCTAGCATGCTCTTCTGTTGATAATGCACCC
1 TTTCTGTTGATAATGCACCCATATACATTTCAACTCTAGCATACTTTTCTATTGATAATGTACCC
* *
168026 ATATGCATTTCAACTC-TAGCATACA
66 ATATACATTTCAAC-CATAGTATACA
*
168051 TTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCATACTTTTCTATTGATAATGTACCC
1 TTTCTGTTGATAATGCACCCATATACATTTCAACTCTAGCATACTTTTCTATTGATAATGTACCC
* *
168116 ATATACATTTCAACTATAATATACA
66 ATATACATTTCAACCATAGTATACA
* * *
168141 TTTTTGTTGATAATGTACTCATATA
1 TTTCTGTTGATAATGCACCCATATA
168166 AATTACAATT
Statistics
Matches: 177, Mismatches: 24, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
89 2 0.01
90 174 0.98
91 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.39
Consensus pattern (90 bp):
TTTCTGTTGATAATGCACCCATATACATTTCAACTCTAGCATACTTTTCTATTGATAATGTACCC
ATATACATTTCAACCATAGTATACA
Found at i:168774 original size:96 final size:95
Alignment explanation
Indices: 168643--168835 Score: 239
Period size: 96 Copynumber: 2.0 Consensus size: 95
168633 ACCGATACTT
* * * *
168643 CTATACTACGGTACCAATACCCCCTTCAGGTATCGATACCAAAAATAGGTTCGATGTT-GCATGG
1 CTATACTACGATACCAATACCCCCTTCAGGTATCGATACCAAAAATAGATTCAATGTTAGCA-AG
* * *
168707 TATCGATACCCTTACCGTAGGTATCGATACCA
65 TATCGATACCCTCACCAT-GGTATCAATACCA
* * *
168739 CTATACTATGATACCAATA-CCCCTAT-ATGGTATCGATACCAAAATTAGATTCAATGTTATCAA
1 CTATACTACGATACCAATACCCCCT-TCA-GGTATCGATACCAAAAATAGATTCAATGTTAGCAA
168802 GTATCGATACCCTCACCATGGTATCAATACCA
64 GTATCGATACCCTCACCATGGTATCAATACCA
168834 CT
1 CT
168836 TCATTAGGTA
Statistics
Matches: 84, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
95 20 0.24
96 62 0.74
97 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.28
Consensus pattern (95 bp):
CTATACTACGATACCAATACCCCCTTCAGGTATCGATACCAAAAATAGATTCAATGTTAGCAAGT
ATCGATACCCTCACCATGGTATCAATACCA
Found at i:173191 original size:81 final size:82
Alignment explanation
Indices: 173035--173200 Score: 181
Period size: 81 Copynumber: 2.0 Consensus size: 82
173025 ATTTATTGTC
* * * * *
173035 TTACTCAACAGTATTTAACCCTTTATCTAGCTGGCATAATTGACACCTTTCTGCCAATTGCACAG
1 TTACTCAACAGTACTTAACCCTTCATCTAACTAGCATAATTGACACCTTTCTGCCAATTGCACAA
* *
173100 TTAGACCATTA-TTCTT
66 CTAGACCATTACATCTT
* ** * * * *
173116 TTACTCAACGGTACTTAACTGTTCATCTAACTAGCATAATTTACACCTTTTTGTCAATTGGACAA
1 TTACTCAACAGTACTTAACCCTTCATCTAACTAGCATAATTGACACCTTTCTGCCAATTGCACAA
**
173181 CTAGGTCATTACATCTT
66 CTAGACCATTACATCTT
173198 TTA
1 TTA
173201 TTTTGAAATA
Statistics
Matches: 68, Mismatches: 16, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
81 61 0.90
82 7 0.10
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (82 bp):
TTACTCAACAGTACTTAACCCTTCATCTAACTAGCATAATTGACACCTTTCTGCCAATTGCACAA
CTAGACCATTACATCTT
Found at i:173858 original size:45 final size:45
Alignment explanation
Indices: 173641--173896 Score: 334
Period size: 45 Copynumber: 5.7 Consensus size: 45
173631 AATTTAACAT
* * *
173641 CTTTTCTGTTGATAATACACCCATATGCATTTCAAATATAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* * * *
173686 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAATATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* * **
173731 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAACATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
173776 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* * *
173821 CTTTTTTGTTGATAATGCACCCATATGCATTTCAACTCTGGCAT-
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* ***
173865 CCTTTCATGCCAATAATGCACCCATATGCATT
1 CTTTTC-TGTTGATAATGCACCCATATGCATT
173897 ATTCTATTAT
Statistics
Matches: 191, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
44 4 0.02
45 187 0.98
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.39
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
Found at i:173909 original size:34 final size:34
Alignment explanation
Indices: 173866--174004 Score: 98
Period size: 34 Copynumber: 3.8 Consensus size: 34
173856 CTCTGGCATC
*
173866 CTTTCATGCCAATAATGCACCCATATGCATTATT
1 CTTTTATGCCAATAATGCACCCATATGCATTATT
* * * * *
173900 CTATTATGCCGATAATGTACCTATATACATATCATCT
1 CTTTTATGCCAATAATGCACCCATATGCAT-T-AT-T
*
173937 AAGGCATCCTTTCATGCCACTAATGCACCCATATGCATTATT
1 ----C-T--TTT-ATGCCAATAATGCACCCATATGCATTATT
* *
173979 CTTTTATGCCGATAATGTACCCATAT
1 CTTTTATGCCAATAATGCACCCATAT
174005 ACATATCAGC
Statistics
Matches: 79, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
34 42 0.53
35 4 0.05
36 2 0.03
37 2 0.03
38 1 0.01
41 1 0.01
42 2 0.03
43 2 0.03
44 3 0.04
45 20 0.25
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.35
Consensus pattern (34 bp):
CTTTTATGCCAATAATGCACCCATATGCATTATT
Found at i:173962 original size:79 final size:79
Alignment explanation
Indices: 173831--174064 Score: 351
Period size: 79 Copynumber: 3.0 Consensus size: 79
173821 CTTTTTTGTT
* * * * ** *
173831 GATAATGCACCCATATGCATTTCAACTCTGGCATCCTTTCATGCCAATAATGCACCCATATGCAT
1 GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGCACCCATATGCAT
*
173896 TATTCTATTATGCC
66 TATTCTTTTATGCC
* *
173910 GATAATGTACCTATATACATATCATCTAAGGCATCCTTTCATGCCACTAATGCACCCATATGCAT
1 GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGCACCCATATGCAT
173975 TATTCTTTTATGCC
66 TATTCTTTTATGCC
* **
173989 GATAATGTACCCATATACATATCAGCTAAAGCATAATTTCATGCCACTAATGCACCCATATGCAT
1 GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGCACCCATATGCAT
174054 TATTCTTTTAT
66 TATTCTTTTAT
174065 TCATTAGTTT
Statistics
Matches: 141, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 141 1.00
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.34
Consensus pattern (79 bp):
GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGCACCCATATGCAT
TATTCTTTTATGCC
Found at i:174517 original size:19 final size:21
Alignment explanation
Indices: 174466--174521 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 21
174456 TTCCCTCACC
174466 ATGGTATCGATA-CCCCTATGTT
1 ATGGTATCGATACCCCCTA--TT
*
174488 ATGGTACCGATACCCCCTA-T
1 ATGGTATCGATACCCCCTATT
174508 A-GGTATCGATACCC
1 ATGGTATCGATACCC
174522 AAATTAGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 12 0.39
20 2 0.06
22 11 0.35
23 6 0.19
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGGTATCGATACCCCCTATT
Found at i:179886 original size:22 final size:22
Alignment explanation
Indices: 179860--179908 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
179850 TATATTTTCA
179860 TATTTTTCTCACCTTAGATTAT
1 TATTTTTCTCACCTTAGATTAT
179882 TATTTTTCTCACCTTAGATTAT
1 TATTTTTCTCACCTTAGATTAT
179904 TATTT
1 TATTT
179909 CCTCACTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.16, G:0.04, T:0.57
Consensus pattern (22 bp):
TATTTTTCTCACCTTAGATTAT
Found at i:179904 original size:19 final size:20
Alignment explanation
Indices: 179860--179914 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 20
179850 TATATTTTCA
179860 TATTTTTCTCACCTTAGATTAT
1 TATTTTTCTCACCTTAG--TAT
179882 TATTTTTCTCACCTTAG-AT
1 TATTTTTCTCACCTTAGTAT
179901 TATTATTTCCTCAC
1 TATT-TTT-CTCAC
179915 TAAGTTATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.19
20 3 0.10
21 5 0.16
22 17 0.55
ACGTcount: A:0.22, C:0.22, G:0.04, T:0.53
Consensus pattern (20 bp):
TATTTTTCTCACCTTAGTAT
Found at i:180149 original size:29 final size:28
Alignment explanation
Indices: 180115--180482 Score: 217
Period size: 29 Copynumber: 12.8 Consensus size: 28
180105 ATTTCTATAG
180115 AGATATTTTAATAATTAATTCTAAACGCT
1 AGATATTTTAATAATTAATTCT-AACGCT
** * *
180144 AGATATCCTAATAATTAATTTCTATCG-G
1 AGATATTTTAATAATTAA-TTCTAACGCT
* *
180172 AGAAATTTTAATAATTAATTCTAAAAGCT
1 AGATATTTTAATAATTAATTCT-AACGCT
* ** ** *
180201 GGATATCCTAATAATTAATTTCTATTGCA
1 AGATATTTTAATAATTAA-TTCTAACGCT
* *
180230 AGATATTTTACTAATTAATTCTAAATGCT
1 AGATATTTTAATAATTAATTCT-AACGCT
* **
180259 GGATATCCTAATAATTAATTTCTAACTG-T
1 AGATATTTTAATAATTAA-TTCTAAC-GCT
*
180288 TGATATTTTAATAATTAATTCTAAACGCT
1 AGATATTTTAATAATTAATTCT-AACGCT
*
180317 GGATGATATTTTACTAATTAATTCTAAACGCT
1 --A-GATATTTTAATAATTAATTCT-AACGCT
* ** * *
180349 -GCATATTCTAATAATTTTTTCTATCTC-
1 AG-ATATTTTAATAATTAATTCTAACGCT
* *
180376 GGATATTTTAATAATTAATTTCTATCG-T
1 AGATATTTTAATAATTAA-TTCTAACGCT
* * *
180404 GGAATATTTTACTAATTAATTTTAATCGCT
1 AG-ATATTTTAATAATTAATTCTAA-CGCT
* * * * *
180434 GGATATTCTATTAATCAATTTCTATCGC-
1 AGATATTTTAATAATTAA-TTCTAACGCT
* *
180462 AAATATTTCAATAATTAATTC
1 AGATATTTTAATAATTAATTC
180483 CAAATGCTTG
Statistics
Matches: 262, Mismatches: 57, Indels: 42
0.73 0.16 0.12
Matches are distributed among these distances:
27 20 0.08
28 56 0.21
29 139 0.53
30 20 0.08
32 27 0.10
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.43
Consensus pattern (28 bp):
AGATATTTTAATAATTAATTCTAACGCT
Found at i:180189 original size:57 final size:57
Alignment explanation
Indices: 180098--180482 Score: 348
Period size: 58 Copynumber: 6.7 Consensus size: 57
180088 TAAACACTGG
* * *
180098 ATAATTCATTTCTAT-AGAGATATTTTAATAATTAATTCTAAACGCTAGATATCCTA
1 ATAATTAATTTCTATCGGAGATATTTTAATAATTAATTCTAAACGCTGGATATCCTA
* *
180154 ATAATTAATTTCTATCGGAGAAATTTTAATAATTAATTCTAAAAGCTGGATATCCTA
1 ATAATTAATTTCTATCGGAGATATTTTAATAATTAATTCTAAACGCTGGATATCCTA
* * * *
180211 ATAATTAATTTCTATTGCAAGATATTTTACTAATTAATTCTAAATGCTGGATATCCTA
1 ATAATTAATTTCTATCG-GAGATATTTTAATAATTAATTCTAAACGCTGGATATCCTA
* ** **
180269 ATAATTAATTTCTAACTGTTGATATTTTAATAATTAATTCTAAACGCTGGATGATATTTTA
1 ATAATTAATTTCTATC-GGAGATATTTTAATAATTAATTCTAAACGCT-G--GATATCCTA
* * ** * ** * * **
180330 CTAATTAA-TTCTAAACGCTGCATATTCTAATAATTTTTTCT-ATCTC-GGATATTTTA
1 ATAATTAATTTCT-ATCGGAG-ATATTTTAATAATTAATTCTAAACGCTGGATATCCTA
* * * *
180386 ATAATTAATTTCTATCGTG-GAATATTTTACTAATTAATTTTAATCGCTGGATATTCTA
1 ATAATTAATTTCTATCG-GAG-ATATTTTAATAATTAATTCTAAACGCTGGATATCCTA
* * * * *
180444 TTAATCAATTTCTATCGCAAATATTTCAATAATTAATTC
1 ATAATTAATTTCTATCGGAGATATTTTAATAATTAATTC
180483 CAAATGCTTG
Statistics
Matches: 273, Mismatches: 43, Indels: 25
0.80 0.13 0.07
Matches are distributed among these distances:
56 49 0.18
57 77 0.28
58 101 0.37
59 2 0.01
60 10 0.04
61 34 0.12
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (57 bp):
ATAATTAATTTCTATCGGAGATATTTTAATAATTAATTCTAAACGCTGGATATCCTA
Found at i:181096 original size:58 final size:58
Alignment explanation
Indices: 181012--181227 Score: 249
Period size: 58 Copynumber: 3.8 Consensus size: 58
181002 TGGATATCCG
* * **
181012 ATAATTAATTTTTATCGCA-GATATTTTACTAATTAATTCTAAAAGCTGGATATGGTA
1 ATAATTAATTTCTATCGCAGGATATTTTAATAATTAATTCTAAAAGCTGGATATACTA
* * * * * *
181069 ATAACTAATTTCTATAGAAGGATATTTTAATAAATAGTTCTAAAAACTGGATATACTA
1 ATAATTAATTTCTATCGCAGGATATTTTAATAATTAATTCTAAAAGCTGGATATACTA
* * * * *
181127 ATAATTAATTTCTATCGCTGG-T-TTTTACTAATTAATTCTAAACGCGGGATATCCTA
1 ATAATTAATTTCTATCGCAGGATATTTTAATAATTAATTCTAAAAGCTGGATATACTA
* * *
181183 ATCATTAATTTCTACCGCAGGATATTTTAATAATTAATTCCAAAA
1 ATAATTAATTTCTATCGCAGGATATTTTAATAATTAATTCTAAAA
181228 CGAGACATTT
Statistics
Matches: 129, Mismatches: 27, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
56 45 0.35
57 17 0.13
58 67 0.52
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (58 bp):
ATAATTAATTTCTATCGCAGGATATTTTAATAATTAATTCTAAAAGCTGGATATACTA
Found at i:181147 original size:29 final size:29
Alignment explanation
Indices: 181012--181221 Score: 101
Period size: 29 Copynumber: 7.3 Consensus size: 29
181002 TGGATATCCG
* * * *
181012 ATAATTAATTTTTATCGC-AGATATTTTA
1 ATAATTAATTTCTAACGCTGGATATTCTA
* * **
181040 CTAATTAA-TTCTAAAAGCTGGATATGGTA
1 ATAATTAATTTCT-AACGCTGGATATTCTA
* ** *
181069 ATAACTAATTTCTATA-GAAGGATATTTTA
1 ATAATTAATTTCTA-ACGCTGGATATTCTA
* * ** *
181098 ATAAAT-AGTTCTAAAAACTGGATATACTA
1 ATAATTAATTTCT-AACGCTGGATATTCTA
* *
181127 ATAATTAATTTCTATCGCTGG-T-TTTTA
1 ATAATTAATTTCTAACGCTGGATATTCTA
* * *
181154 CTAATTAA-TTCTAAACGCGGGATATCCTA
1 ATAATTAATTTCT-AACGCTGGATATTCTA
* * * *
181183 ATCATTAATTTCTACCGCAGGATATTTTA
1 ATAATTAATTTCTAACGCTGGATATTCTA
181212 ATAATTAATT
1 ATAATTAATT
181222 CCAAAACGAG
Statistics
Matches: 132, Mismatches: 39, Indels: 21
0.69 0.20 0.11
Matches are distributed among these distances:
26 4 0.03
27 19 0.14
28 18 0.14
29 77 0.58
30 14 0.11
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.40
Consensus pattern (29 bp):
ATAATTAATTTCTAACGCTGGATATTCTA
Found at i:181596 original size:28 final size:29
Alignment explanation
Indices: 181550--181616 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
181540 GATGTTTCAA
* *
181550 CAATTAATTCCGAGAGCT-GATATGTTAG
1 CAATTAATTCAGACAGCTGGATATGTTAG
* *
181578 CAATTAATTCAGACCGCTGGATATTTTAG
1 CAATTAATTCAGACAGCTGGATATGTTAG
* *
181607 TAGTTAATTC
1 CAATTAATTC
181617 GGGTCAGATA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 15 0.47
29 17 0.53
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (29 bp):
CAATTAATTCAGACAGCTGGATATGTTAG
Found at i:181761 original size:28 final size:27
Alignment explanation
Indices: 181712--181784 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 27
181702 AGCACTGGAT
* *
181712 ATTGTAATAATTAATTACAAAACAGGAC
1 ATTGTAAAAATTAATT-CAAAACAGAAC
*
181740 ATTTTAAAAATTAATTCTAAAACAGAAC
1 ATTGTAAAAATTAATTC-AAAACAGAAC
*
181768 ATTGTAATAATTAATTC
1 ATTGTAAAAATTAATTC
181785 CCAAATATGA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.03
28 38 0.97
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (27 bp):
ATTGTAAAAATTAATTCAAAACAGAAC
Found at i:181778 original size:85 final size:86
Alignment explanation
Indices: 181623--181783 Score: 211
Period size: 85 Copynumber: 1.9 Consensus size: 86
181613 ATTCGGGTCA
* * * * *
181623 GATATTATAATTATTAATTACGAACACAGGACAGTTTAATAATTAATTCCTAACATAGAAATTAA
1 GATATTATAATAATTAATTACGAAAACAGGACAGTTTAAAAATTAATTCCTAAAACAGAAATTAA
181688 TATAATTAATTTTGAGCACTG
66 TATAATTAATTTTGAGCACTG
* *
181709 GATATTGTAATAATTAATTAC-AAAACAGGACATTTTAAAAATTAATT-CTAAAACAGAACATT-
1 GATATTATAATAATTAATTACGAAAACAGGACAGTTTAAAAATTAATTCCTAAAACAGAA-ATTA
*
181771 GTAATAATTAATT
65 AT-ATAATTAATT
181784 CCCAAATATG
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
84 10 0.15
85 36 0.55
86 19 0.29
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.35
Consensus pattern (86 bp):
GATATTATAATAATTAATTACGAAAACAGGACAGTTTAAAAATTAATTCCTAAAACAGAAATTAA
TATAATTAATTTTGAGCACTG
Found at i:182023 original size:28 final size:29
Alignment explanation
Indices: 181983--182097 Score: 100
Period size: 28 Copynumber: 4.2 Consensus size: 29
181973 GATATATTTT
181983 AAACAGGACATTTTAGAAATGAATTTCC-
1 AAACAGGACATTTTAGAAATGAATTTCCA
* * **
182011 AAATAGGAAATTTTA-AAATTTATTTCCA
1 AAACAGGACATTTTAGAAATGAATTTCCA
* *
182039 AAACAGGACATTTT-GAAATTTAA-TTCCG
1 AAACAGGACATTTTAGAAA-TGAATTTCCA
* *
182067 AAACAGGAC-TTTT-GAAATTAA-TTCCG
1 AAACAGGACATTTTAGAAATGAATTTCCA
182093 AAACA
1 AAACA
182098 AGATCTTTGA
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
26 14 0.18
27 18 0.24
28 41 0.54
29 3 0.04
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.31
Consensus pattern (29 bp):
AAACAGGACATTTTAGAAATGAATTTCCA
Found at i:182144 original size:81 final size:80
Alignment explanation
Indices: 182019--182260 Score: 258
Period size: 81 Copynumber: 3.0 Consensus size: 80
182009 CCAAATAGGA
* * * * *
182019 AATTTT-AAAATTTATTTCCAAAACAGGACATTTTGAAATTTAATTCCGAAACAGGACTTTTGAA
1 AATTTTGAAAATTTAATTCCGAAACAAGA-ATTTTGAAAATTAATTCCGAAACAAGACTTTTGAA
182083 ATTAATTCCGAAACA-
65 ATTAATTCCGAAACAG
* * * *
182098 AGATCTTTGAAAA-TTAATTCCGAAACATGATATTTTAAAAATTAATTCCGAAACATGATATTTT
1 A-AT-TTTGAAAATTTAATTCCGAAACAAGA-ATTTTGAAAATTAATTCCGAAACAAGA-CTTTT
* *
182162 AAAAATTAATTCCGAGACAG
62 -GAAATTAATTCCGAAACAG
* * *
182182 AATTTTTAAAATTTAATTCCGAAA-AAGACTTTTGAAAATTAATTCTGAAACAAGACATTTTGAA
1 AATTTTGAAAATTTAATTCCGAAACAAGAATTTTGAAAATTAATTCCGAAACAAGAC-TTTTG-A
182246 AATTAATTCCGAAAC
64 AATTAATTCCGAAAC
182261 GGAAAATTTT
Statistics
Matches: 135, Mismatches: 19, Indels: 16
0.79 0.11 0.09
Matches are distributed among these distances:
79 1 0.01
80 2 0.01
81 83 0.61
82 18 0.13
83 30 0.22
84 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (80 bp):
AATTTTGAAAATTTAATTCCGAAACAAGAATTTTGAAAATTAATTCCGAAACAAGACTTTTGAAA
TTAATTCCGAAACAG
Found at i:182147 original size:28 final size:27
Alignment explanation
Indices: 182019--182276 Score: 247
Period size: 28 Copynumber: 9.4 Consensus size: 27
182009 CCAAATAGGA
* * * *
182019 AATTTTAAAATTTATTTCCAAAACAGG
1 AATTTTAAAAATTAATTCCGAAACAAG
* * *
182046 ACATTTTGAAATTTAATTCCGAAACAGG
1 A-ATTTTAAAAATTAATTCCGAAACAAG
* *
182074 ACTTTT-GAAATTAATTCCGAAACAAG
1 AATTTTAAAAATTAATTCCGAAACAAG
* *
182100 -ATCTTTGAAAATTAATTCCGAAACATG
1 AAT-TTTAAAAATTAATTCCGAAACAAG
*
182127 ATATTTTAAAAATTAATTCCGAAACATG
1 A-ATTTTAAAAATTAATTCCGAAACAAG
*
182155 ATATTTTAAAAATTAATTCCGAGAC-AG
1 A-ATTTTAAAAATTAATTCCGAAACAAG
*
182182 AATTTTTAAAATTTAATTCCGAAA-AAG
1 AA-TTTTAAAAATTAATTCCGAAACAAG
* * *
182209 ACTTTTGAAAATTAATTCTGAAACAAG
1 AATTTTAAAAATTAATTCCGAAACAAG
*
182236 ACATTTTGAAAATTAATTCCGAAACGGAA-
1 A-ATTTTAAAAATTAATTCCGAAAC--AAG
182265 AATTTTAAAAAT
1 AATTTTAAAAAT
182277 CTTATTCCCA
Statistics
Matches: 198, Mismatches: 22, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
25 1 0.01
26 39 0.20
27 51 0.26
28 102 0.52
29 3 0.02
30 2 0.01
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.34
Consensus pattern (27 bp):
AATTTTAAAAATTAATTCCGAAACAAG
Found at i:182175 original size:109 final size:109
Alignment explanation
Indices: 182020--182276 Score: 322
Period size: 109 Copynumber: 2.4 Consensus size: 109
182010 CAAATAGGAA
* * * * * * *
182020 ATTTTAAAATTTATTTCCAAAACAGGACATTTTGAAATTTAATTCCGAAACAGGACTTTTGAAA-
1 ATTTTAAAAATTAATTCCGAAACAGGACATTTTAAAAATTAATTCCGAAACAGAACTTTTAAAAT
* *
182084 TTAATTCCGAAACAAGA-TCTTTGAAAATTAATTCCGAAACATGAT
66 TTAATTCCGAAA-AAGACT-TTTGAAAATTAATTCCGAAACAAGAC
* * * *
182129 ATTTTAAAAATTAATTCCGAAACATGATATTTTAAAAATTAATTCCGAGACAGAATTTTTAAAAT
1 ATTTTAAAAATTAATTCCGAAACAGGACATTTTAAAAATTAATTCCGAAACAGAACTTTTAAAAT
*
182194 TTAATTCCGAAAAAGACTTTTGAAAATTAATTCTGAAACAAGAC
66 TTAATTCCGAAAAAGACTTTTGAAAATTAATTCCGAAACAAGAC
* *
182238 ATTTTGAAAATTAATTCCGAAAC-GGAAAATTTTAAAAAT
1 ATTTTAAAAATTAATTCCGAAACAGG-ACATTTTAAAAAT
182277 CTTATTCCCA
Statistics
Matches: 128, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
108 1 0.01
109 114 0.89
110 13 0.10
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (109 bp):
ATTTTAAAAATTAATTCCGAAACAGGACATTTTAAAAATTAATTCCGAAACAGAACTTTTAAAAT
TTAATTCCGAAAAAGACTTTTGAAAATTAATTCCGAAACAAGAC
Found at i:185444 original size:5 final size:5
Alignment explanation
Indices: 185390--185454 Score: 62
Period size: 5 Copynumber: 13.0 Consensus size: 5
185380 TGTCAACACT
* * * *
185390 TAAAT TAAAA TAGAA TAGAAG TAAAA T-AAA TAAAA T-AAA TAACA TAAAAA
1 TAAAA TAAAA TAAAA TA-AAA TAAAA TAAAA TAAAA TAAAA TAAAA T-AAAA
185440 TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA
185455 ATTACTATCA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
4 8 0.16
5 34 0.69
6 7 0.14
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:185881 original size:15 final size:15
Alignment explanation
Indices: 185851--185892 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
185841 GTACAGAAAA
185851 AGTATATAAATAAAT
1 AGTATATAAATAAAT
185866 AGTA-ATAAATATAAT
1 AGTATATAAATA-AAT
*
185881 A-TATATACATAA
1 AGTATATAAATAA
185893 TAATTCCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (15 bp):
AGTATATAAATAAAT
Found at i:190614 original size:120 final size:120
Alignment explanation
Indices: 190438--190752 Score: 508
Period size: 120 Copynumber: 2.6 Consensus size: 120
190428 TGAAGGGATT
* * * * * *
190438 AAGGATAAGATTACCGGTGACAAAGATGACGACGACAAACATCATAA-AAAAGGTAAAGACGATA
1 AAGGACAAGATCACCGGCGACAAAGACGACGACGACAAGCATCACAAGAAAA-GTAAAGACGATA
190502 AACATCACAAGGATCACAAACATCATGATAAAGATGAAGGGATAATAGATAAGATC
65 AACATCACAAGGATCACAAACATCATGATAAAGATGAAGGGATAATAGATAAGATC
190558 AAGGACAAGATCACCGGCGACAAAGACGACGACGACAAGCATCACAAGAAAAGTAAAGACGATAA
1 AAGGACAAGATCACCGGCGACAAAGACGACGACGACAAGCATCACAAGAAAAGTAAAGACGATAA
190623 ACATCACAAGGATCACAAACATCATGATAAAGATGAAGGGATAATAGATAAGATC
66 ACATCACAAGGATCACAAACATCATGATAAAGATGAAGGGATAATAGATAAGATC
* * *
190678 AAAGACAAGATCACCGGCGACAAAGACGACGACGACAAGCACCACAAG-AAAGACAAAGACGATA
1 AAGGACAAGATCACCGGCGACAAAGACGACGACGACAAGCATCACAAGAAAAG-TAAAGACGATA
*
190742 AGCATCACAAG
65 AACATCACAAG
190753 AAGGACAAGG
Statistics
Matches: 183, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
119 4 0.02
120 175 0.96
121 4 0.02
ACGTcount: A:0.50, C:0.18, G:0.21, T:0.11
Consensus pattern (120 bp):
AAGGACAAGATCACCGGCGACAAAGACGACGACGACAAGCATCACAAGAAAAGTAAAGACGATAA
ACATCACAAGGATCACAAACATCATGATAAAGATGAAGGGATAATAGATAAGATC
Found at i:190731 original size:27 final size:27
Alignment explanation
Indices: 190699--190765 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
190689 CACCGGCGAC
* *
190699 AAAGACGACGACGACAAGCACCACAAG
1 AAAGACAAAGACGACAAGCACCACAAG
* *
190726 AAAGACAAAGACGATAAGCATCACAAG
1 AAAGACAAAGACGACAAGCACCACAAG
* *
190753 AAGGACAAGGACG
1 AAAGACAAAGACG
190766 GTCATGGCAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.51, C:0.22, G:0.24, T:0.03
Consensus pattern (27 bp):
AAAGACAAAGACGACAAGCACCACAAG
Found at i:193479 original size:85 final size:83
Alignment explanation
Indices: 193333--193489 Score: 217
Period size: 85 Copynumber: 1.9 Consensus size: 83
193323 AAAAATGATT
* * *
193333 AAATTAGGGACCTAAATTATAAAAGTAAAAGTGTGTTGAAGAAAGTAAGGGTCTCAATTATAAAG
1 AAATTAGGGACATAAATTATAAAAGTAAAAGTGAGTTGAAAAAAGTAAGGGTCTCAATTATAAAG
193398 GTAAAAATGAGATTAAAA
66 GTAAAAATGAGATTAAAA
* * * *
193416 AAATTAGGGA-ATTAATTATAAAGGTAGAAAGTGAGATTGAAAAAAATTAAGGGTCTCTATTATA
1 AAATTAGGGACATAAATTATAAAAGTA-AAAGTGAG-TTG-AAAAAAGTAAGGGTCTCAATTATA
193480 AAGGTAAAAA
63 AAGGTAAAAA
193490 GTGGGACTAA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
82 13 0.20
83 17 0.27
84 3 0.05
85 31 0.48
ACGTcount: A:0.50, C:0.04, G:0.20, T:0.26
Consensus pattern (83 bp):
AAATTAGGGACATAAATTATAAAAGTAAAAGTGAGTTGAAAAAAGTAAGGGTCTCAATTATAAAG
GTAAAAATGAGATTAAAA
Found at i:193491 original size:44 final size:44
Alignment explanation
Indices: 193348--193492 Score: 160
Period size: 41 Copynumber: 3.4 Consensus size: 44
193338 AGGGACCTAA
* * * * *
193348 ATTATAAAAGT-AAAAGTGTG-TTG-AAGAAAGTAAGGGTCTCA
1 ATTATAAAGGTAAAAAGTGAGATTGAAAAAAATTAAGGGTCTCT
**
193389 ATTATAAAGGTAAAAA-TGAGATT-AAAAAAATT-AGGGAAT-T
1 ATTATAAAGGTAAAAAGTGAGATTGAAAAAAATTAAGGGTCTCT
*
193429 AATTATAAAGGTAGAAAGTGAGATTGAAAAAAATTAAGGGTCTCT
1 -ATTATAAAGGTAAAAAGTGAGATTGAAAAAAATTAAGGGTCTCT
193474 ATTATAAAGGTAAAAAGTG
1 ATTATAAAGGTAAAAAGTG
193493 GGACTAAAAA
Statistics
Matches: 85, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
41 33 0.39
42 19 0.22
43 9 0.11
44 23 0.27
45 1 0.01
ACGTcount: A:0.49, C:0.03, G:0.21, T:0.27
Consensus pattern (44 bp):
ATTATAAAGGTAAAAAGTGAGATTGAAAAAAATTAAGGGTCTCT
Found at i:193518 original size:85 final size:81
Alignment explanation
Indices: 193333--193519 Score: 216
Period size: 85 Copynumber: 2.2 Consensus size: 81
193323 AAAAATGATT
* * *
193333 AAATTAGGGACCTAAATTATAAAAGTAAAAGTGTGTTGAAGAAAGTAAGGGTCTCAATTATAAAG
1 AAATTAGGGATCT-AATTATAAAAGTAAAAGTGAGTTGAAAAAAGTAAGGGTCTCAATTATAAAG
*
193398 GTAAAAATGAGATTAAAA
65 GTAAAAATGAGACT-AAA
* * *
193416 AAATTAGGGAAT-TAATTATAAAGGTAGAAAGTGAGATTGAAAAAAATTAAGGGTCTCTATTATA
1 AAATTAGGG-ATCTAATTATAAAAGTA-AAAGTGAG-TTG-AAAAAAGTAAGGGTCTCAATTATA
*
193480 AAGGTAAAAAGTGGGACT-AA
62 AAGGTAAAAA-TGAGACTAAA
193500 AAATTAGGGATCTCAATTAT
1 AAATTAGGGATCT-AATTAT
193520 TTTTTTGACC
Statistics
Matches: 89, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
82 12 0.13
83 19 0.21
84 16 0.18
85 37 0.42
86 5 0.06
ACGTcount: A:0.48, C:0.05, G:0.21, T:0.27
Consensus pattern (81 bp):
AAATTAGGGATCTAATTATAAAAGTAAAAGTGAGTTGAAAAAAGTAAGGGTCTCAATTATAAAGG
TAAAAATGAGACTAAA
Found at i:193519 original size:41 final size:41
Alignment explanation
Indices: 193380--193519 Score: 158
Period size: 41 Copynumber: 3.3 Consensus size: 41
193370 GAAGAAAGTA
193380 AGGGTCTCAATTATAAAGGTAAAAA-TGAGATTAAAAAAATT
1 AGGGTCTCAATTATAAAGGTAAAAAGTGAGATT-AAAAAATT
** * *
193421 AGGGAATTAATTATAAAGGTAGAAAGTGAGATTGAAAAAAATT
1 AGGGTCTCAATTATAAAGGTAAAAAGTGAGATT--AAAAAATT
* * *
193464 AAGGGTCTCTATTATAAAGGTAAAAAGTGGGACT-AAAAATT
1 -AGGGTCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAATT
193505 AGGGATCTCAATTAT
1 AGGG-TCTCAATTAT
193520 TTTTTTGACC
Statistics
Matches: 83, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
40 4 0.05
41 37 0.45
42 7 0.08
43 9 0.11
44 26 0.31
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.27
Consensus pattern (41 bp):
AGGGTCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAATT
Found at i:196163 original size:45 final size:45
Alignment explanation
Indices: 196114--196213 Score: 141
Period size: 45 Copynumber: 2.2 Consensus size: 45
196104 TGCACTCTCA
196114 ATGCATCGATACACTC-GGA-ATATTTTCAAACATCGAATGCATTTG
1 ATGCATCGATACAC-CAGGATAT-TTTTCAAACATCGAATGCATTTG
* * *
196159 ATGCATCGATGCACCAGGCTATTTTTCAAACATCGAATGCATTTT
1 ATGCATCGATACACCAGGATATTTTTCAAACATCGAATGCATTTG
196204 ATGCATCGAT
1 ATGCATCGAT
196214 GCATCCTTAG
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
44 1 0.02
45 47 0.94
46 2 0.04
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (45 bp):
ATGCATCGATACACCAGGATATTTTTCAAACATCGAATGCATTTG
Found at i:203621 original size:21 final size:21
Alignment explanation
Indices: 203579--203622 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
203569 ACCCCGGGAG
*
203579 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
203600 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
203621 CT
1 CT
203623 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:204277 original size:31 final size:31
Alignment explanation
Indices: 204206--204285 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
204196 ATTTAACAAA
* * **
204206 AAGGGGGAGAAAATTTAAGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
204237 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
*
204268 AAGGGGGAGTAAGATTTT
1 AAGGGGGAGTAAGTTTTT
204286 CAAAATAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.33, C:0.03, G:0.35, T:0.30
Consensus pattern (31 bp):
AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
Found at i:204750 original size:27 final size:27
Alignment explanation
Indices: 204708--204776 Score: 120
Period size: 27 Copynumber: 2.5 Consensus size: 27
204698 TTAAACATCG
*
204708 AATGCATTTGATGCATTGATGCACAAGC
1 AATGCA-TCGATGCATTGATGCACAAGC
204736 AATGCATCGATGCATTGATGCACAAGC
1 AATGCATCGATGCATTGATGCACAAGC
204763 AATGCATCGATGCA
1 AATGCATCGATGCA
204777 CCAGGCTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 34 0.85
28 6 0.15
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (27 bp):
AATGCATCGATGCATTGATGCACAAGC
Found at i:208172 original size:20 final size:19
Alignment explanation
Indices: 208126--208174 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
208116 ATAAACGTGA
208126 AAGATGAAAATATGTTCTC
1 AAGATGAAAATATGTTCTC
* *
208145 AAGTTGAAGAAT-TGTTTGTC
1 AAGATGAA-AATATG-TTCTC
208165 AAGATGAAAA
1 AAGATGAAAA
208175 GTTGATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (19 bp):
AAGATGAAAATATGTTCTC
Found at i:208944 original size:16 final size:16
Alignment explanation
Indices: 208923--208954 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
208913 TAAGCCTAAA
208923 TATTATAATAATCCTT
1 TATTATAATAATCCTT
208939 TATTATAATAATCCTT
1 TATTATAATAATCCTT
208955 GGTTTAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTATAATAATCCTT
Found at i:220780 original size:39 final size:36
Alignment explanation
Indices: 220719--220822 Score: 154
Period size: 36 Copynumber: 2.9 Consensus size: 36
220709 AGGCGGCGCT
* * * *
220719 TGTTGTTGAACTTGATCTGCAGTAGTTACAACTGTA
1 TGTTGTTGCATTTGATCTGCAGCAGTTTCAACTGTA
*
220755 TGTTGTTGCATTTGATCTGCAGCAGTTTCAACTGTG
1 TGTTGTTGCATTTGATCTGCAGCAGTTTCAACTGTA
*
220791 TGTTGTTGCATTTGATTTGCAGCAGTTTCAAC
1 TGTTGTTGCATTTGATCTGCAGCAGTTTCAAC
220823 CTCCTCCTCA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.41
Consensus pattern (36 bp):
TGTTGTTGCATTTGATCTGCAGCAGTTTCAACTGTA
Found at i:224816 original size:36 final size:36
Alignment explanation
Indices: 224769--224840 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
224759 CCGTTAATTT
*
224769 GATGATGTATTAGCAGATGGAGAGATGAATAATAGA
1 GATGATGTATTAGCAGATGGAGAGATGAAAAATAGA
224805 GATGATGTATTAGCAGATGGAGAGATGAAAAATAGA
1 GATGATGTATTAGCAGATGGAGAGATGAAAAATAGA
224841 CTGCCCATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.43, C:0.03, G:0.31, T:0.24
Consensus pattern (36 bp):
GATGATGTATTAGCAGATGGAGAGATGAAAAATAGA
Found at i:231396 original size:29 final size:28
Alignment explanation
Indices: 231316--231396 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 28
231306 TTTAGTTGAA
* *
231316 TCAAATTGATATTTTATCTAATATTTAAGGT
1 TCAAATT-ATA-TTTATCTAA-AGTTAAGCT
*
231347 TCAAATTATATTTCATATAAAGTTAAGCT
1 TCAAATTATATTT-ATCTAAAGTTAAGCT
231376 T-AAATTAGTATTATATCTAAA
1 TCAAATTA-TATT-TATCTAAA
231397 ATTCAAGAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
28 6 0.14
29 21 0.49
30 9 0.21
31 7 0.16
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (28 bp):
TCAAATTATATTTATCTAAAGTTAAGCT
Found at i:232328 original size:24 final size:24
Alignment explanation
Indices: 232300--232354 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
232290 AATAGTGGTT
232300 ATTATAAAATATATTTTTATTATA
1 ATTATAAAATATATTTTTATTATA
*** *
232324 ATTATATTTTTTATTTTTATTATA
1 ATTATAAAATATATTTTTATTATA
232348 ATT-TAAA
1 ATTATAAA
232355 TTGATATATT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTATAAAATATATTTTTATTATA
Found at i:232338 original size:18 final size:18
Alignment explanation
Indices: 232298--232334 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
232288 TTAATAGTGG
232298 TTATTATAAAATATATTT
1 TTATTATAAAATATATTT
*
232316 TTATTAT-AATTATATTT
1 TTATTATAAAATATATTT
232333 TT
1 TT
232335 TATTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATTATAAAATATATTT
Found at i:232345 original size:18 final size:19
Alignment explanation
Indices: 232298--232351 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 19
232288 TTAATAGTGG
*
232298 TTATTATAA-AATATATTT
1 TTATTATAATTATATATTT
232316 TTATTATAATTATAT-TTT
1 TTATTATAATTATATATTT
* *
232334 TTATTTTTATTATA-ATTT
1 TTATTATAATTATATATTT
232352 AAATTGATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 27 0.87
19 4 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTATAATTATATATTT
Found at i:233348 original size:45 final size:45
Alignment explanation
Indices: 233297--233415 Score: 179
Period size: 45 Copynumber: 2.6 Consensus size: 45
233287 GGTGCACTAA
*
233297 GAGTGCATCGATGCAGAAAATGCATTCGATG-TTTCA-AACAAGCCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AA-CCT
*
233342 GAGTGCATCGATGCATAAAATGCATTTGATGTTTTCATAAAACCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCT
*
233387 GAGTGCATCGATACATAAAATGCATTCGA
1 GAGTGCATCGATGCATAAAATGCATTCGA
233416 AATGGTGTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
45 59 0.87
46 7 0.10
47 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (45 bp):
GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCT
Found at i:236075 original size:23 final size:23
Alignment explanation
Indices: 236045--236121 Score: 63
Period size: 23 Copynumber: 3.4 Consensus size: 23
236035 GCATGGCTTT
236045 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* *
236068 GTGCATCGGTGCATC-TTC-ATGA
1 GTGCATCGATGCA-CATTCAAGGA
* *
236090 -TGTATCGATGCATATTCAAAGG-
1 GTGCATCGATGCACATTC-AAGGA
236112 GATGCATCGA
1 G-TGCATCGA
236122 GGCATTATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
21 13 0.32
22 3 0.07
23 17 0.41
24 8 0.20
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.27
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:242017 original size:64 final size:63
Alignment explanation
Indices: 241903--242088 Score: 313
Period size: 64 Copynumber: 2.9 Consensus size: 63
241893 TTCACTAAAA
*
241903 GTGCATCAATGCATAAAATGCATT-GATGTTTCAAATAAGCCTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAA-AAGCCTGAGTGCATCGATGCATGGTAT
241966 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAGCCTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAA-AAGCCTGAGTGCATCGATGCATGGTAT
242030 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAA-CCTGAGTGCATCGATGCAT
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AAAAGCCTGAGTGCATCGATGCAT
242089 AAAATGCATT
Statistics
Matches: 118, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
63 23 0.19
64 86 0.73
65 7 0.06
66 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.30
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAAAGCCTGAGTGCATCGATGCATGGTAT
Found at i:242629 original size:13 final size:13
Alignment explanation
Indices: 242586--242636 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
242576 TTTTAAATTA
*
242586 CACTTTTAAAA-C
1 CACTTTTAAAAGT
*
242598 CACTTATAAAAGTT
1 CACTTTTAAAAG-T
242612 CACTTTTAAAAGT
1 CACTTTTAAAAGT
242625 CACTTTTTAAAA
1 CAC-TTTTAAAA
242637 TTAATGTCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 10 0.30
13 4 0.12
14 19 0.58
ACGTcount: A:0.41, C:0.18, G:0.04, T:0.37
Consensus pattern (13 bp):
CACTTTTAAAAGT
Found at i:246463 original size:3 final size:3
Alignment explanation
Indices: 246443--246485 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
246433 ATCTAAAAAA
246443 TAT TAT TAAT TAT T-T TAT TAT TAT TAT TAT TAT T-T TAT ATAT T
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT T
246486 CTACATTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 4 0.11
3 26 0.72
4 6 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:247956 original size:30 final size:30
Alignment explanation
Indices: 247922--248015 Score: 118
Period size: 30 Copynumber: 3.2 Consensus size: 30
247912 GTTTAGCCTC
* **
247922 TAAATTTCTATTTTCACTATTTTGGTCCTT
1 TAAATTTATATTTTTGCTATTTTGGTCCTT
* *
247952 TAAATTTATGTTTTTGCTA-TTTAGTCCTT
1 TAAATTTATATTTTTGCTATTTTGGTCCTT
* *
247981 TAAGTTTATATTTTTGCTATTTTGATCCTT
1 TAAATTTATATTTTTGCTATTTTGGTCCTT
248011 TAAAT
1 TAAAT
248016 AGAATATGAT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 26 0.49
30 27 0.51
ACGTcount: A:0.22, C:0.12, G:0.09, T:0.57
Consensus pattern (30 bp):
TAAATTTATATTTTTGCTATTTTGGTCCTT
Found at i:247988 original size:29 final size:29
Alignment explanation
Indices: 247913--248015 Score: 109
Period size: 29 Copynumber: 3.5 Consensus size: 29
247903 ATATTTATGG
* * **
247913 TTTAG-CCTCTAAATTTCTATTTTCACTA
1 TTTAGTCCTTTAAATTTATATTTTTGCTA
* *
247941 TTTTGGTCCTTTAAATTTATGTTTTTGCTA
1 -TTTAGTCCTTTAAATTTATATTTTTGCTA
*
247971 TTTAGTCCTTTAAGTTTATATTTTTGCTA
1 TTTAGTCCTTTAAATTTATATTTTTGCTA
*
248000 TTTTGATCCTTTAAAT
1 TTTAG-TCCTTTAAAT
248016 AGAATATGAT
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
29 34 0.56
30 27 0.44
ACGTcount: A:0.21, C:0.14, G:0.09, T:0.56
Consensus pattern (29 bp):
TTTAGTCCTTTAAATTTATATTTTTGCTA
Found at i:248802 original size:17 final size:17
Alignment explanation
Indices: 248780--248818 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
248770 TGAATCAAAT
248780 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
248797 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
248814 -AATTA
1 TAATTA
248819 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:251020 original size:21 final size:20
Alignment explanation
Indices: 250982--251021 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
250972 ATCAATATTT
*
250982 TTTGCATATGCATTTGCATC
1 TTTGCATATGCATCTGCATC
*
251002 TTTGCATTTTGCATCTGCAT
1 TTTGCA-TATGCATCTGCAT
251022 TTCATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.17, C:0.20, G:0.15, T:0.47
Consensus pattern (20 bp):
TTTGCATATGCATCTGCATC
Found at i:252368 original size:10 final size:10
Alignment explanation
Indices: 252355--252383 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
252345 AAATAATAAG
252355 AAAAAGG-AA
1 AAAAAGGAAA
252364 AAAAAGGAAA
1 AAAAAGGAAA
252374 AAAAAGGAAA
1 AAAAAGGAAA
252384 GAAACACATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.37
10 12 0.63
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAAAGGAAA
Found at i:253459 original size:31 final size:32
Alignment explanation
Indices: 253413--253475 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
253403 AAGAAATGAT
253413 GAATGTTGGGGCATCTTTGGAGATTCAACATC
1 GAATGTTGGGGCATCTTTGGAGATTCAACATC
253445 GAATGTT-GGGCATCTTTGGAGATTCAACATC
1 GAATGTTGGGGCATCTTTGGAGATTCAACATC
253476 TTGAAGTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 24 0.77
32 7 0.23
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (32 bp):
GAATGTTGGGGCATCTTTGGAGATTCAACATC
Found at i:253696 original size:36 final size:33
Alignment explanation
Indices: 253611--253696 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 33
253601 AAAAACACAT
* * *
253611 TTTGTCTCGCTTAAGACAGTTTTCTCTAAAAAAA
1 TTTGTCTCGCTTGAGATA-ATTTCTCTAAAAAAA
*
253645 TTTGTCTCTCTTGAGATAATTTCTCTCAAAACAAA
1 TTTGTCTCGCTTGAGATAATTTCTCT-AAAA-AAA
*
253680 TTTCGTTTCGCTTGAGA
1 TTT-GTCTCGCTTGAGA
253697 CATTTTCCCT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
33 7 0.16
34 19 0.44
35 6 0.14
36 11 0.26
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.41
Consensus pattern (33 bp):
TTTGTCTCGCTTGAGATAATTTCTCTAAAAAAA
Found at i:253897 original size:66 final size:67
Alignment explanation
Indices: 253827--254204 Score: 396
Period size: 67 Copynumber: 5.7 Consensus size: 67
253817 ACTTTGAAAT
* * *
253827 TATTTATCTTGAAACAAAGTTTTGTCTCCCTTGAGACAATTTCTTTTGAAA-AAAAATCTTTGAG
1 TATTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAAATCTTTGAG
253891 TC
66 TC
* * **
253893 TATTT-TCTTTGAAACAAAGTTTTATCTCTCTTGAGACAAGTTCTCTTGAAACAAAGGTCTTTGA
1 TATTTCTC-TTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAAATCTTTGA
253957 GTC
65 GTC
* * * * *
253960 TGTTTCTCTTAAAACAAAGTTTTGTCTCTCTTGAGACAGTTTTTCTTG-AA-AAAAGTCTTTGAG
1 TATTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAAATCTTTGAG
254023 TC
66 TC
* * * ***
254025 TATTTCTCTTGAAACAAAGTTTTGTCTCCCTTGAGTCAGTTTCTCTTGAAACACCCATCTTTGAG
1 TATTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAAATCTTTGAG
254090 AT-
66 -TC
** * * * * ***
254092 GGTTTCCCTTGAAACGAA-TTTTG--TCGCTTGAGACAGTTTCTCTTGAAACACCCATCTTTGAG
1 TATTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAAATCTTTGAG
254154 TC
66 TC
* * * *
254156 TATTTCCCTTGAAACAAA-TCTTGTCTCTCTTGAGAGAATTTCTGTTGAA
1 TATTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAA
254205 TTATATTTTG
Statistics
Matches: 267, Mismatches: 36, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
63 1 0.00
64 56 0.21
65 59 0.22
66 73 0.27
67 75 0.28
68 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (67 bp):
TATTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAAATCTTTGAG
TC
Found at i:254058 original size:132 final size:131
Alignment explanation
Indices: 253833--254204 Score: 409
Period size: 132 Copynumber: 2.8 Consensus size: 131
253823 AAATTATTTA
*
253833 TCTTGAAACAAAGTTTTGTCTCCCTTGAGACAATTTCTT-TTGAAAAAAAATCTTTGAGTCTATT
1 TCTTGAAACAAAGTTTTGTCTCCCTTGAGACAGTTT-TTCTTG--AAAAAATCTTTGAGTCTATT
* **
253897 T-TCTTTGAAACAAAGTTTTATCTCTCTTGAGACAAGTTCTCTTGAAACAAAGGTCTTTGAG-TC
63 TCTC-TTGAAACAAAGTTTTGTCTCTCTTGAGACAAGTTCTCTTGAAACAAACATCTTTGAGAT-
*
253960 TGTTTC
126 GGTTTC
* *
253966 TCTTAAAACAAAGTTTTGTCTCTCTTGAGACAGTTTTTCTTGAAAAAAGTCTTTGAGTCTATTTC
1 TCTTGAAACAAAGTTTTGTCTCCCTTGAGACAGTTTTTCTTGAAAAAA-TCTTTGAGTCTATTTC
* * **
254031 TCTTGAAACAAAGTTTTGTCTCCCTTGAGTC-AGTTTCTCTTGAAACACCCATCTTTGAGATGGT
65 TCTTGAAACAAAGTTTTGTCTCTCTTGAGACAAG-TTCTCTTGAAACAAACATCTTTGAGATGGT
254095 TTC
129 TTC
* * * * *
254098 CCTTGAAACGAA-TTTTG--TCGCTTGAGACAGTTTCTCTTGAAACACCCATCTTTGAGTCTATT
1 TCTTGAAACAAAGTTTTGTCTCCCTTGAGACAGTTTTTCTTGAAA-A--AATCTTTGAGTCTATT
* * * * *
254160 TCCCTTGAAACAAA-TCTTGTCTCTCTTGAGAGAATTTCTGTTGAA
63 TCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAAGTTCTCTTGAA
254205 TTATATTTTG
Statistics
Matches: 206, Mismatches: 24, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
129 23 0.11
130 24 0.12
131 41 0.20
132 79 0.38
133 39 0.19
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (131 bp):
TCTTGAAACAAAGTTTTGTCTCCCTTGAGACAGTTTTTCTTGAAAAAATCTTTGAGTCTATTTCT
CTTGAAACAAAGTTTTGTCTCTCTTGAGACAAGTTCTCTTGAAACAAACATCTTTGAGATGGTTT
C
Found at i:254513 original size:17 final size:18
Alignment explanation
Indices: 254482--254515 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
254472 TTCCATAATG
254482 TAAAATGGTACCGATACC
1 TAAAATGGTACCGATACC
*
254500 TAAAA-GGTATCGATAC
1 TAAAATGGTACCGATAC
254516 AACTACGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (18 bp):
TAAAATGGTACCGATACC
Found at i:257913 original size:20 final size:20
Alignment explanation
Indices: 257888--257937 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
257878 TCATGAACAA
257888 GTACCGATACTATTCATATG
1 GTACCGATACTATTCATATG
* *
257908 GTACCGATATTGTTCATATG
1 GTACCGATACTATTCATATG
257928 GTACCGATAC
1 GTACCGATAC
257938 CAAGGTAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (20 bp):
GTACCGATACTATTCATATG
Done.