Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 80 of 297
Found at i:28530115 original size:29 final size:29
Alignment explanation
Indices: 28530007--28530100 Score: 170
Period size: 29 Copynumber: 3.2 Consensus size: 29
28529997 CACACAACCA
*
28530007 AGCACACGGGTGTGTGGCATGGTTGACCT
1 AGCACACGGGTGTGTGGCATGGTTGGCCT
*
28530036 AGCACACGGGTGTGTGGCATGGTCGGCCT
1 AGCACACGGGTGTGTGGCATGGTTGGCCT
28530065 AGCACACGGGTGTGTGGCATGGTTGGCCT
1 AGCACACGGGTGTGTGGCATGGTTGGCCT
28530094 AGCACAC
1 AGCACAC
28530101 AAGCGTGCGG
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 62 1.00
ACGTcount: A:0.17, C:0.23, G:0.38, T:0.21
Consensus pattern (29 bp):
AGCACACGGGTGTGTGGCATGGTTGGCCT
Found at i:28570828 original size:47 final size:47
Alignment explanation
Indices: 28570753--28570870 Score: 166
Period size: 47 Copynumber: 2.5 Consensus size: 47
28570743 TTCGGGACTC
* * * *
28570753 ATCACATTTATACACTTTCACATCCATCACGTTGGCCACTT-GGCCCT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGGCCCT
* *
28570800 GTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCT
28570847 ATCACATATATACACTTTCACATT
1 ATCACATATATACACTTTCACATT
28570871 TATTCAAATA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
46 2 0.03
47 61 0.97
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (47 bp):
ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCT
Found at i:28572396 original size:48 final size:48
Alignment explanation
Indices: 28572319--28572414 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
28572309 TTTGCTTCTT
* *
28572319 CCCTTTTCTACTACAGCCTTTTCCCACCTTGTTAGATAAATACAATCA
1 CCCTTTTCTACTACAACCTTCTCCCACCTTGTTAGATAAATACAATCA
* *
28572367 CCCTTTTCTACTACAACCTTCTCCTACCTTGTTAGCTAAATACAATCA
1 CCCTTTTCTACTACAACCTTCTCCCACCTTGTTAGATAAATACAATCA
28572415 ACCCCAAAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.27, C:0.32, G:0.05, T:0.35
Consensus pattern (48 bp):
CCCTTTTCTACTACAACCTTCTCCCACCTTGTTAGATAAATACAATCA
Found at i:28579741 original size:24 final size:24
Alignment explanation
Indices: 28579675--28579750 Score: 82
Period size: 25 Copynumber: 3.1 Consensus size: 24
28579665 TGCTCTTTCA
* *
28579675 AGTTGTAAATCAGTATGCTC-TCACG
1 AGTTGT-AATCGGTAAGCTCAT-ACG
*
28579700 AATTGTAAGTCGGTAAGCTCATACG
1 AGTTGTAA-TCGGTAAGCTCATACG
*
28579725 AGTTGTAATCGGTAAGCTCACACG
1 AGTTGTAATCGGTAAGCTCATACG
28579749 AG
1 AG
28579751 CTGTGGAGCA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
24 19 0.43
25 24 0.55
26 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (24 bp):
AGTTGTAATCGGTAAGCTCATACG
Found at i:28584679 original size:23 final size:23
Alignment explanation
Indices: 28584649--28584698 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
28584639 CTCAAGGTTA
28584649 GGACGCAAGCACAATATCCGAAG
1 GGACGCAAGCACAATATCCGAAG
28584672 GGACGCAAGCACAATATCCGAAG
1 GGACGCAAGCACAATATCCGAAG
28584695 GGAC
1 GGAC
28584699 TCAGATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.38, C:0.26, G:0.28, T:0.08
Consensus pattern (23 bp):
GGACGCAAGCACAATATCCGAAG
Found at i:28589146 original size:21 final size:22
Alignment explanation
Indices: 28589079--28589149 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 22
28589069 ATAAGGTGTG
* * *
28589079 GATAAACCACT-TAATGGTGTA
1 GATAAACCACTCAAACGATGTA
* * *
28589100 GGTAAACTACTCAAACGATGTG
1 GATAAACCACTCAAACGATGTA
28589122 GATAAACCACT-AAAC-ACTGTA
1 GATAAACCACTCAAACGA-TGTA
28589143 GATAAAC
1 GATAAAC
28589150 TTCTCACACT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 1 0.03
21 23 0.59
22 15 0.38
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (22 bp):
GATAAACCACTCAAACGATGTA
Found at i:28589601 original size:28 final size:29
Alignment explanation
Indices: 28589553--28589631 Score: 97
Period size: 28 Copynumber: 2.7 Consensus size: 29
28589543 AAAATAGAGG
* *
28589553 AAAATTGTAAAATCTGAAAAAACTGTGGC
1 AAAACTGTAAAATCTGAAAAAACTATGGC
*
28589582 AAAACTGTAAAATCT-AAAAAATTATGGC
1 AAAACTGTAAAATCTGAAAAAACTATGGC
* *
28589610 AAAACTGAAAAATTTTGAAAAA
1 AAAACTGTAAAA-TCTGAAAAA
28589632 TAGTGGTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 22 0.51
29 16 0.37
30 5 0.12
ACGTcount: A:0.54, C:0.09, G:0.13, T:0.24
Consensus pattern (29 bp):
AAAACTGTAAAATCTGAAAAAACTATGGC
Found at i:28591066 original size:22 final size:21
Alignment explanation
Indices: 28591031--28591072 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
28591021 ACATTCACTA
* *
28591031 TTTTAATTATAAAATATTTAT
1 TTTTAATCATAAAAAATTTAT
28591052 TTTTACATCATAAAAAATTTA
1 TTTTA-ATCATAAAAAATTTA
28591073 AACTAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTTAATCATAAAAAATTTAT
Found at i:28594542 original size:22 final size:21
Alignment explanation
Indices: 28594516--28594564 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
28594506 TTTGTACTTA
28594516 AATTATTAACATAATGAATTTT
1 AATTATT-ACATAATGAATTTT
** *
28594538 AATTAATTTTATAATTAATTTT
1 AATT-ATTACATAATGAATTTT
28594560 AATTA
1 AATTA
28594565 ATTTTTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 19 0.83
23 3 0.13
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
AATTATTACATAATGAATTTT
Found at i:28594554 original size:12 final size:11
Alignment explanation
Indices: 28594534--28594579 Score: 62
Period size: 10 Copynumber: 4.4 Consensus size: 11
28594524 ACATAATGAA
28594534 TTTTAATTAAT
1 TTTTAATTAAT
28594545 TTTATAATTAA-
1 TTT-TAATTAAT
28594556 TTTTAATTAAT
1 TTTTAATTAAT
28594567 TTTT-ATT-AT
1 TTTTAATTAAT
28594576 TTTT
1 TTTT
28594580 GACAGATTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
9 6 0.18
10 10 0.30
11 10 0.30
12 7 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTTAATTAAT
Found at i:28594565 original size:22 final size:22
Alignment explanation
Indices: 28594526--28594569 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
28594516 AATTATTAAC
28594526 ATAATGAATTTTAATTAATTTT
1 ATAATGAATTTTAATTAATTTT
*
28594548 ATAATTAATTTTAATTAATTTT
1 ATAATGAATTTTAATTAATTTT
28594570 TATTATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
ATAATGAATTTTAATTAATTTT
Found at i:28594579 original size:10 final size:10
Alignment explanation
Indices: 28594527--28594578 Score: 61
Period size: 10 Copynumber: 5.1 Consensus size: 10
28594517 ATTATTAACA
*
28594527 TAATGAATTT
1 TAATTAATTT
28594537 TAATTAATTTT
1 TAATTAA-TTT
28594548 ATAATTAATTT
1 -TAATTAATTT
28594559 TAATTAATTT
1 TAATTAATTT
*
28594569 TTATT-ATTT
1 TAATTAATTT
28594578 T
1 T
28594579 TGACAGATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
9 5 0.13
10 20 0.53
11 6 0.16
12 7 0.18
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (10 bp):
TAATTAATTT
Found at i:28603782 original size:18 final size:18
Alignment explanation
Indices: 28603748--28603785 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
28603738 AACATTACAA
28603748 AAAAATTCAAAGTATTTAT
1 AAAAATTCAAAG-ATTTAT
28603767 AAAAATTCTAAA-ATTTAT
1 AAAAATTC-AAAGATTTAT
28603785 A
1 A
28603786 TTTTAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 8 0.44
20 3 0.17
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (18 bp):
AAAAATTCAAAGATTTAT
Found at i:28603806 original size:7 final size:7
Alignment explanation
Indices: 28603768--28603817 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
28603758 AGTATTTATA
28603768 AAAATTCT
1 AAAATT-T
28603776 AAAATTT
1 AAAATTT
* *
28603783 ATATTTT
1 AAAATTT
* *
28603790 AATATAT
1 AAAATTT
28603797 AAAATTT
1 AAAATTT
28603804 AAAATTT
1 AAAATTT
28603811 AAAATTT
1 AAAATTT
28603818 CTAAAGAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
7 28 0.82
8 6 0.18
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (7 bp):
AAAATTT
Found at i:28612589 original size:16 final size:16
Alignment explanation
Indices: 28612565--28612599 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
28612555 CCATGTCAAC
28612565 AAATATTAAAAATAAA
1 AAATATTAAAAATAAA
*
28612581 AAATCTTAAAAATAAA
1 AAATATTAAAAATAAA
28612597 AAA
1 AAA
28612600 AGCTTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATATTAAAAATAAA
Found at i:28613309 original size:22 final size:21
Alignment explanation
Indices: 28613270--28613310 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
28613260 TTTATTGGTA
**
28613270 ATTTTGTTATTATTTTAGAGG
1 ATTTTGTTATTAAGTTAGAGG
28613291 ATTTTGCTTATTAAGTTAGA
1 ATTTTG-TTATTAAGTTAGA
28613311 TCTACCTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.27, C:0.02, G:0.17, T:0.54
Consensus pattern (21 bp):
ATTTTGTTATTAAGTTAGAGG
Found at i:28619192 original size:40 final size:39
Alignment explanation
Indices: 28619148--28619234 Score: 93
Period size: 40 Copynumber: 2.2 Consensus size: 39
28619138 AAAAAGGAAG
* * *
28619148 AAATATTTGTGCTTAGAAGTAGGGGAGAAAACAGAAAAAA
1 AAATATTTATGCTCAGAAGAAGGGGAGAAAACA-AAAAAA
** * *
28619188 AAATATCAATGCTCAGTAGAATGGGAGAAAACAAAAAAA
1 AAATATTTATGCTCAGAAGAAGGGGAGAAAACAAAAAAA
*
28619227 AATTATTT
1 AAATATTT
28619235 TTTATGGGTG
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
39 11 0.30
40 26 0.70
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.22
Consensus pattern (39 bp):
AAATATTTATGCTCAGAAGAAGGGGAGAAAACAAAAAAA
Found at i:28621230 original size:40 final size:40
Alignment explanation
Indices: 28621175--28621471 Score: 297
Period size: 40 Copynumber: 7.4 Consensus size: 40
28621165 GATGATAACG
* *
28621175 GGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACTA-ATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATA-TCC
*
28621215 GGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCC
* *
28621255 GGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGTGTTACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGCTA---CTA-T-A-TCC
*
28621300 GGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCC
* *
28621340 GGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGTTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGCTA-CTATATCC
* * * * *
28621380 -GGTTAAATCCCGAAGGTACTTG-G-TA-CTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCC
* *
28621416 GGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGTTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGCTA-CTATATCC
* *
28621456 -GGTTAAATCCCGAAGG
1 GGGCTAAGTCCCGAAGG
28621472 TACTTGGTTT
Statistics
Matches: 216, Mismatches: 26, Indels: 31
0.79 0.10 0.11
Matches are distributed among these distances:
36 7 0.03
37 21 0.10
38 2 0.01
39 39 0.18
40 106 0.49
41 2 0.01
42 3 0.01
43 3 0.01
44 1 0.00
45 30 0.14
46 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCC
Found at i:28621313 original size:85 final size:85
Alignment explanation
Indices: 28621175--28621448 Score: 387
Period size: 85 Copynumber: 3.4 Consensus size: 85
28621165 GATGATAACG
* *
28621175 GGGCTAAGTCCCGAAGGCATTTGTGC---TAGCG--ACTAATTCCGGGCTAAGTCCCGAAGGCAT
1 GGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGTGTTACTAATTCCGGGCTAAGTCCCGAAGGCAT
28621235 TTGTGCGAACTACTATATCC
66 TTGTGCGAACTACTATATCC
28621255 GGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGTGTTACTAATTCCGGGCTAAGTCCCGAAGGCAT
1 GGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGTGTTACTAATTCCGGGCTAAGTCCCGAAGGCAT
28621320 TTGTGCGAACTACTATATCC
66 TTGTGCGAACTACTATATCC
* * *
28621340 GGGCTAAGTCCCGAAGGCATTTGAGCGAGTA--GTTA-T-A-TCC-GGTTAAATCCCGAAGGTA-
1 GGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGTGTTACTAATTCCGGGCTAAGTCCCGAAGGCAT
* *
28621398 CT-TG-GTACTACTATATCC
66 TTGTGCGAACTACTATATCC
28621416 GGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGT
1 GGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGT
28621449 TATATCCGGT
Statistics
Matches: 180, Mismatches: 7, Indels: 16
0.89 0.03 0.08
Matches are distributed among these distances:
76 44 0.24
77 2 0.01
78 1 0.01
79 15 0.08
80 28 0.16
81 1 0.01
82 1 0.01
83 8 0.04
85 80 0.44
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (85 bp):
GGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGTGTTACTAATTCCGGGCTAAGTCCCGAAGGCAT
TTGTGCGAACTACTATATCC
Found at i:28621437 original size:76 final size:76
Alignment explanation
Indices: 28621243--28621479 Score: 348
Period size: 76 Copynumber: 3.0 Consensus size: 76
28621233 ATTTGTGCGA
* *
28621243 ACTACTATATCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGTGTTACTAATTCCGGGCTAAG
1 ACTACTATATCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTA--GTTA-T-A-TCC-GGTTAAA
* * *
28621308 TCCCGAAGGCATTTGTGCGA
60 TCCCGAAGGTA-CT-TG-GT
28621328 ACTACTATATCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGTTATATCCGGTTAAATCCCGA
1 ACTACTATATCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGTTATATCCGGTTAAATCCCGA
28621393 AGGTACTTGGT
66 AGGTACTTGGT
28621404 ACTACTATATCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGTTATATCCGGTTAAATCCCGA
1 ACTACTATATCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGTTATATCCGGTTAAATCCCGA
28621469 AGGTACTTGGT
66 AGGTACTTGGT
28621480 TTGGGAATGA
Statistics
Matches: 147, Mismatches: 5, Indels: 9
0.91 0.03 0.06
Matches are distributed among these distances:
76 77 0.52
77 2 0.01
78 1 0.01
79 15 0.10
80 3 0.02
81 1 0.01
82 1 0.01
83 4 0.03
85 43 0.29
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (76 bp):
ACTACTATATCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGTTATATCCGGTTAAATCCCGA
AGGTACTTGGT
Found at i:28625061 original size:45 final size:45
Alignment explanation
Indices: 28624953--28625079 Score: 147
Period size: 45 Copynumber: 2.9 Consensus size: 45
28624943 TTTTCTCAAA
*
28624953 TCACCGGCATT-TCGCCTGTTAGGCTCG-AGGCCCG-ATATCAGT
1 TCACCGGCATTATCGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
*
28624995 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGT-A-T
1 TCACCGGCATTATCGCCTGCTAGGCTCGAAGGCCCGAATA-TCAGT
** * *
28625039 CTCACCGGCATTATCGTTTGCTAAGCTCAAAGGCCCGAATA
1 -TCACCGGCATTATCGCCTGCTAGGCTCGAAGGCCCGAATA
28625080 ATCAAGTCAA
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
42 11 0.15
43 14 0.19
44 8 0.11
45 39 0.53
46 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (45 bp):
TCACCGGCATTATCGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
Found at i:28625457 original size:43 final size:43
Alignment explanation
Indices: 28625396--28625627 Score: 315
Period size: 43 Copynumber: 5.4 Consensus size: 43
28625386 ACATATCATT
* * *
28625396 TCACCGGCATTACGCCTGCTAGGCACGAAGGCTCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
* * *
28625439 TCACCAGCACGAAGCCTGCTAGGAACGAAGGCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
* *
28625482 TCATCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
* *
28625525 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCTCGAATACATA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
* * *
28625568 TCACCGGCACTAAGCCTACTAGGCATGAAGGCCCGAATATA-A
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
* *
28625610 T-ACCAGCACTAGGCCTGC
1 TCACCGGCACTAAGCCTGC
28625628 GGGATTTATC
Statistics
Matches: 169, Mismatches: 20, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
41 14 0.08
42 2 0.01
43 153 0.91
ACGTcount: A:0.31, C:0.32, G:0.23, T:0.14
Consensus pattern (43 bp):
TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
Found at i:28625647 original size:38 final size:38
Alignment explanation
Indices: 28625599--28625682 Score: 132
Period size: 38 Copynumber: 2.2 Consensus size: 38
28625589 GGCATGAAGG
* * *
28625599 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
28625637 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
28625675 CCCGAATA
1 CCCGAATA
28625683 CACATCAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (38 bp):
CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:28633726 original size:132 final size:132
Alignment explanation
Indices: 28633589--28633830 Score: 387
Period size: 132 Copynumber: 1.8 Consensus size: 132
28633579 AATCTCGAAG
* * *
28633589 GGATATTTGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTTCGCGA
1 GGATATTCGATTATTTCGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGA
*
28633654 ATTGCCAAATATCAAA-CTTTGCCTTCGTTTTAAAGAATTTTTAAAAGGCATGAGTGAAAGTTTG
66 ATTGCCAAATATCAAATC-TCGCCTTCGTTTTAAAGAATTTTTAAAAGGCATGAGTGAAAGTTTG
28633718 AAA
130 AAA
** *
28633721 GGATATTCGATTATTTCGAGCAAACTCGAAATTGCAACCCAACACGTTAGGGCACTATTCCGCGA
1 GGATATTCGATTATTTCGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGA
* *
28633786 ATTGCCAAATATCGAATCTCGTCTTCGTTTTAAAGAATTTTTAAA
66 ATTGCCAAATATCAAATCTCGCCTTCGTTTTAAAGAATTTTTAAA
28633831 TGAATACTTG
Statistics
Matches: 100, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
132 99 0.99
133 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (132 bp):
GGATATTCGATTATTTCGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGA
ATTGCCAAATATCAAATCTCGCCTTCGTTTTAAAGAATTTTTAAAAGGCATGAGTGAAAGTTTGA
AA
Found at i:28637161 original size:17 final size:17
Alignment explanation
Indices: 28637139--28637171 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
28637129 TAACTTTAAT
28637139 ATTAAATTTAATATTAG
1 ATTAAATTTAATATTAG
28637156 ATTAAATTTAATATTA
1 ATTAAATTTAATATTA
28637172 AATCTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
ATTAAATTTAATATTAG
Found at i:28644641 original size:23 final size:21
Alignment explanation
Indices: 28644615--28644657 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
28644605 GTTTTGTTCT
28644615 AAAAAATGACAAGTTTTTATAGG
1 AAAAAATG--AAGTTTTTATAGG
**
28644638 AAAACTTGAAGTTTTTATAG
1 AAAAAATGAAGTTTTTATAG
28644658 AGATTTGAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.67
23 6 0.33
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (21 bp):
AAAAAATGAAGTTTTTATAGG
Found at i:28648915 original size:15 final size:15
Alignment explanation
Indices: 28648895--28648923 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28648885 ACAGTCTTGT
28648895 TTGGGGGGGGGGGGG
1 TTGGGGGGGGGGGGG
28648910 TTGGGGGGGGGGGG
1 TTGGGGGGGGGGGG
28648924 TTTCTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.86, T:0.14
Consensus pattern (15 bp):
TTGGGGGGGGGGGGG
Found at i:28648917 original size:14 final size:14
Alignment explanation
Indices: 28648898--28648925 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28648888 GTCTTGTTTG
28648898 GGGGGGGGGGGGTT
1 GGGGGGGGGGGGTT
28648912 GGGGGGGGGGGGTT
1 GGGGGGGGGGGGTT
28648926 TCTAAATAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.86, T:0.14
Consensus pattern (14 bp):
GGGGGGGGGGGGTT
Found at i:28652923 original size:1 final size:1
Alignment explanation
Indices: 28652919--28652960 Score: 84
Period size: 1 Copynumber: 42.0 Consensus size: 1
28652909 GAGAAAAAGT
28652919 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
28652961 GGAGCGAAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:28654563 original size:16 final size:17
Alignment explanation
Indices: 28654532--28654564 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28654522 TTCATAAGTA
28654532 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
28654549 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
28654565 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:28654910 original size:46 final size:46
Alignment explanation
Indices: 28654845--28655072 Score: 312
Period size: 46 Copynumber: 5.0 Consensus size: 46
28654835 TTATCTTTGA
* * * * **
28654845 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* *
28654891 CATGTTGCCATGGTATCTTTCCACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * **
28654937 CACGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* *
28654983 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* *
28655029 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
28655073 ATCAGAGAGC
Statistics
Matches: 163, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 163 1.00
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
Found at i:28659601 original size:19 final size:20
Alignment explanation
Indices: 28659573--28659610 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
28659563 GAGTATTAGC
*
28659573 ATTGTGATATTGA-ATTGAT
1 ATTGTAATATTGATATTGAT
28659592 ATTGTAATATTGATATTGA
1 ATTGTAATATTGATATTGA
28659611 ATTAAGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.47
Consensus pattern (20 bp):
ATTGTAATATTGATATTGAT
Found at i:28661859 original size:46 final size:44
Alignment explanation
Indices: 28661806--28661980 Score: 174
Period size: 46 Copynumber: 3.8 Consensus size: 44
28661796 TTTTTGGGCA
*
28661806 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAA-G
*** * *
28661852 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GGAAG
*
28661899 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAA-G
* *
28661945 CCCGAGCTCGTTGAGTTGAG-CCTGAGTTCACTTATG
1 TCCGAACTCGTTGAGTTGAGTCC-GAGTTCACTTATG
28661981 AGCGGGTTAC
Statistics
Matches: 108, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 3 0.03
46 64 0.59
47 32 0.30
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (44 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAAG
Found at i:28661961 original size:93 final size:93
Alignment explanation
Indices: 28661802--28661973 Score: 274
Period size: 93 Copynumber: 1.8 Consensus size: 93
28661792 AGGATTTTTG
* *
28661802 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
28661867 TTGAGTCC-GAGTTCGAGAGATGTAACTA
66 TTGAG-CCTGAGTTCGAGAGATGTAACTA
* * * *
28661895 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
28661960 TTGAGCCTGAGTTC
66 TTGAGCCTGAGTTC
28661974 ACTTATGAGC
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGCCTGAGTTCGAGAGATGTAACTA
Found at i:28668292 original size:40 final size:40
Alignment explanation
Indices: 28668231--28668325 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 40
28668221 ATCTCTGTCT
* *
28668231 AACCCAACACACC-A-TGTGGGGATAAAATCAACCCACCC
1 AACCCTACACACCAAGTATGGGGATAAAATCAACCCACCC
* * * *
28668269 AGCCCTACACACGAAGTATGGGGATAGAATCAACCCATCC
1 AACCCTACACACCAAGTATGGGGATAAAATCAACCCACCC
28668309 AACCCTACACACCAAGT
1 AACCCTACACACCAAGT
28668326 GGTACTATAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 10 0.21
39 1 0.02
40 36 0.77
ACGTcount: A:0.38, C:0.35, G:0.15, T:0.13
Consensus pattern (40 bp):
AACCCTACACACCAAGTATGGGGATAAAATCAACCCACCC
Found at i:28674398 original size:40 final size:40
Alignment explanation
Indices: 28674333--28674427 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
28674323 CCATCTTCGT
* * *
28674333 CCAACCCAACACACC--ATGTGGGGATAAAATCGACCCAC
1 CCAACCCTACACACCAAATATGGGGATAAAATCAACCCAC
* * *
28674371 CCAGCCCTACACACCAAATATGGGGATAGAATCAACCCAT
1 CCAACCCTACACACCAAATATGGGGATAAAATCAACCCAC
*
28674411 CCAACCTTACACACCAA
1 CCAACCCTACACACCAA
28674428 GTGGTACCGT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 13 0.28
40 34 0.72
ACGTcount: A:0.38, C:0.37, G:0.13, T:0.13
Consensus pattern (40 bp):
CCAACCCTACACACCAAATATGGGGATAAAATCAACCCAC
Found at i:28677841 original size:22 final size:22
Alignment explanation
Indices: 28677799--28677841 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
28677789 ATTGAGAACA
* *
28677799 AATTAATTTTTTATTATTTTTG
1 AATTAATTTTTTATAAATTTTG
28677821 AATTAATTTTTT-TCAAATTTT
1 AATTAATTTTTTAT-AAATTTT
28677842 ATAGATTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
AATTAATTTTTTATAAATTTTG
Found at i:28702985 original size:25 final size:25
Alignment explanation
Indices: 28702951--28703002 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
28702941 ATTAAAGAAC
28702951 ATTGAAATTTATCTTTGCATCAATG
1 ATTGAAATTTATCTTTGCATCAATG
28702976 ATTGAAATTTATCTTTGCATCAATG
1 ATTGAAATTTATCTTTGCATCAATG
28703001 AT
1 AT
28703003 CAAACCCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (25 bp):
ATTGAAATTTATCTTTGCATCAATG
Found at i:28707503 original size:47 final size:47
Alignment explanation
Indices: 28707437--28707675 Score: 361
Period size: 47 Copynumber: 5.1 Consensus size: 47
28707427 GAAATGATAG
*
28707437 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * *
28707484 TAAGGCCTAATGGCCGATGTGATTAATGTGAAAGCGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
28707531 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
28707578 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * *
28707625 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
28707672 TAAG
1 TAAG
28707676 TCCCGAAGGG
Statistics
Matches: 173, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 173 1.00
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:28707850 original size:37 final size:37
Alignment explanation
Indices: 28707794--28707872 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
28707784 CTGAGCTCTA
* * *
28707794 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
28707831 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
28707868 AAGAC
1 AAGAC
28707873 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:28714213 original size:14 final size:14
Alignment explanation
Indices: 28714194--28714220 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28714184 GAGCGTTAGA
28714194 ATTATTTGACTAAG
1 ATTATTTGACTAAG
28714208 ATTATTTGACTAA
1 ATTATTTGACTAA
28714221 TATGATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.44
Consensus pattern (14 bp):
ATTATTTGACTAAG
Found at i:28719732 original size:13 final size:13
Alignment explanation
Indices: 28719716--28719760 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
28719706 AAAGAGAAGA
28719716 TATAATCAGAACT
1 TATAATCAGAACT
* **
28719729 TATAATGAGAAGA
1 TATAATCAGAACT
*
28719742 TATGATCAGAACT
1 TATAATCAGAACT
28719755 TATAAT
1 TATAAT
28719761 GAGATTATTA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (13 bp):
TATAATCAGAACT
Found at i:28719749 original size:26 final size:26
Alignment explanation
Indices: 28719709--28719764 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
28719699 ATCTCAAAAA
28719709 GAGAAGATATAATCAGAACTTATAAT
1 GAGAAGATATAATCAGAACTTATAAT
*
28719735 GAGAAGATATGATCAGAACTTATAAT
1 GAGAAGATATAATCAGAACTTATAAT
28719761 GAGA
1 GAGA
28719765 TTATTAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.25
Consensus pattern (26 bp):
GAGAAGATATAATCAGAACTTATAAT
Found at i:28719871 original size:68 final size:70
Alignment explanation
Indices: 28719746--28719884 Score: 237
Period size: 68 Copynumber: 2.0 Consensus size: 70
28719736 AGAAGATATG
28719746 ATCAGAACTTATAATGAGATTATTAAAAATAAAAAAACTTTACAAGTAATGTATGAAAAGGAAAT
1 ATCAGAACTTATAATGAGATTATT-AAAATAAAAAAACTTTACAAGTAATGTATGAAAAGGAAAT
28719811 TTTTTT
65 TTTTTT
* *
28719817 ATCAGAATTTATAATGAGATTATT-AAA-AAAAAAACTTTACAAGTAATGTATGAAAAGGAATTT
1 ATCAGAACTTATAATGAGATTATTAAAATAAAAAAACTTTACAAGTAATGTATGAAAAGGAAATT
28719880 TTTTT
66 TTTTT
28719885 GACAAAATGA
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
68 40 0.61
69 3 0.05
71 23 0.35
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.35
Consensus pattern (70 bp):
ATCAGAACTTATAATGAGATTATTAAAATAAAAAAACTTTACAAGTAATGTATGAAAAGGAAATT
TTTTT
Found at i:28720034 original size:2 final size:2
Alignment explanation
Indices: 28720027--28720051 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28720017 CACATTGTAT
28720027 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
28720052 GAGTAATTAG
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:28737280 original size:40 final size:40
Alignment explanation
Indices: 28737220--28737439 Score: 268
Period size: 40 Copynumber: 5.5 Consensus size: 40
28737210 TATTCGAATG
* *
28737220 ATATCCGGGCTAAGCCCCGAAGGCATTTATGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * *
28737260 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGACT
* *
28737300 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * *
28737340 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * **
28737380 ATATCCGGGCTAGGACCCGAAGGC-TTTGTGCGAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
28737419 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGA-CCCGAAG
28737440 ATACTTGGGT
Statistics
Matches: 156, Mismatches: 21, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
37 1 0.01
38 12 0.08
39 17 0.11
40 124 0.79
41 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
Found at i:28744661 original size:48 final size:48
Alignment explanation
Indices: 28744590--28744682 Score: 186
Period size: 48 Copynumber: 1.9 Consensus size: 48
28744580 TATGACGGGC
28744590 AGCCGAATGTGTATAGAGATCATGTTATAAAGCCAATCAAAATTGGGT
1 AGCCGAATGTGTATAGAGATCATGTTATAAAGCCAATCAAAATTGGGT
28744638 AGCCGAATGTGTATAGAGATCATGTTATAAAGCCAATCAAAATTG
1 AGCCGAATGTGTATAGAGATCATGTTATAAAGCCAATCAAAATTG
28744683 TGCTCTTTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.27
Consensus pattern (48 bp):
AGCCGAATGTGTATAGAGATCATGTTATAAAGCCAATCAAAATTGGGT
Found at i:28744873 original size:40 final size:40
Alignment explanation
Indices: 28744813--28745032 Score: 259
Period size: 40 Copynumber: 5.5 Consensus size: 40
28744803 TATTCGAATG
* *
28744813 ATATCCGGGCTAAGCCCCGAAGGCATTTATGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * **
28744853 ATATCCGGACTAAGATCCGAAGGCATTTGTGAGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGACT
* *
28744893 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * * *
28744933 ATATCCGGGCTAAGTCTCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* **
28744973 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCGAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
28745012 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGA-CCCGAAG
28745033 ATACTTGGGT
Statistics
Matches: 152, Mismatches: 25, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
37 1 0.01
38 13 0.09
39 17 0.11
40 119 0.78
41 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
Found at i:28745727 original size:46 final size:46
Alignment explanation
Indices: 28745672--28745765 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
28745662 TACTTTGTGC
* *
28745672 TATATATGCTAAAGGGTTAGTTGAATCATGGAAACTATGTAATAGG
1 TATATATGCTAAAGGGCTAGTTGAATCATGGAAACTATGAAATAGG
*
28745718 TATATATGCTAAAGGGCTAGTTGAATCATGGAGACTATGAAATAGG
1 TATATATGCTAAAGGGCTAGTTGAATCATGGAAACTATGAAATAGG
28745764 TA
1 TA
28745766 AAGTCTACCT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.31
Consensus pattern (46 bp):
TATATATGCTAAAGGGCTAGTTGAATCATGGAAACTATGAAATAGG
Found at i:28754307 original size:16 final size:16
Alignment explanation
Indices: 28754265--28754299 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
28754255 GTAGATCGGC
*
28754265 AAAAGCCGAAATGCCG
1 AAAAGCTGAAATGCCG
*
28754281 AAAAGCTGAAATGCTG
1 AAAAGCTGAAATGCCG
28754297 AAA
1 AAA
28754300 TGTTGAAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (16 bp):
AAAAGCTGAAATGCCG
Found at i:28763314 original size:14 final size:14
Alignment explanation
Indices: 28763295--28763355 Score: 70
Period size: 14 Copynumber: 4.4 Consensus size: 14
28763285 CTTCAGTTAT
28763295 TTAATTATAATTAA
1 TTAATTATAATTAA
*
28763309 TTAATTATATTTAA
1 TTAATTATAATTAA
* *
28763323 ATAATAAT-ATTAA
1 TTAATTATAATTAA
28763336 TTTAATTATAATTAA
1 -TTAATTATAATTAA
*
28763351 ATAAT
1 TTAAT
28763356 AATTCAAAGA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
13 4 0.11
14 29 0.76
15 5 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TTAATTATAATTAA
Found at i:28763340 original size:28 final size:27
Alignment explanation
Indices: 28763304--28763358 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 27
28763294 TTTAATTATA
*
28763304 ATTAATTAATTATATTTAAATAATAAT
1 ATTAATTAATTATAATTAAATAATAAT
28763331 ATTAATTTAATTATAATTAAATAATAAT
1 ATTAA-TTAATTATAATTAAATAATAAT
28763359 TCAAAGAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTAATTAATTATAATTAAATAATAAT
Found at i:28765046 original size:18 final size:18
Alignment explanation
Indices: 28765023--28765058 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28765013 CCATACTGAT
28765023 TTGTGAAACGTAGGTATG
1 TTGTGAAACGTAGGTATG
28765041 TTGTGAAACGTAGGTATG
1 TTGTGAAACGTAGGTATG
28765059 GTATTATCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.33, T:0.33
Consensus pattern (18 bp):
TTGTGAAACGTAGGTATG
Found at i:28765068 original size:53 final size:53
Alignment explanation
Indices: 28764988--28765093 Score: 167
Period size: 53 Copynumber: 2.0 Consensus size: 53
28764978 CATGGAAAAA
* **
28764988 TTGTGAAACGTAGGTATGGTATCATCCATACTGATTTGTGAAACGTAGGTATG
1 TTGTGAAACGTAGGTATGGTATCATCCATACTGAGTTAAGAAACGTAGGTATG
* *
28765041 TTGTGAAACGTAGGTATGGTATTATCCATACTGAGTTAAGAAATGTAGGTATG
1 TTGTGAAACGTAGGTATGGTATCATCCATACTGAGTTAAGAAACGTAGGTATG
28765094 GCATTCCCAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.34
Consensus pattern (53 bp):
TTGTGAAACGTAGGTATGGTATCATCCATACTGAGTTAAGAAACGTAGGTATG
Found at i:28765111 original size:34 final size:36
Alignment explanation
Indices: 28765045--28765128 Score: 102
Period size: 34 Copynumber: 2.4 Consensus size: 36
28765035 GGTATGTTGT
* * * *
28765045 GAAACGTAGGTATGGTATTATCCATACTGAGTT-AA
1 GAAATGTAGGTATGGCATTACCCATACCGAGTTGAA
*
28765080 GAAATGTAGGTATGGCATT-CCCATACCGAGTTGTA
1 GAAATGTAGGTATGGCATTACCCATACCGAGTTGAA
28765115 -AAATGTAGGTATGG
1 GAAATGTAGGTATGG
28765129 TTTTTTATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
34 25 0.58
35 18 0.42
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (36 bp):
GAAATGTAGGTATGGCATTACCCATACCGAGTTGAA
Found at i:28772476 original size:35 final size:35
Alignment explanation
Indices: 28772437--28772602 Score: 197
Period size: 35 Copynumber: 4.7 Consensus size: 35
28772427 ATCCATGGCG
* * *
28772437 GAGTTGTGAAACGTATGTATGGTATCATCCATACT
1 GAGTTGTGAAATGTAGGTATGGTATTATCCATACT
* *
28772472 GAGTTGAGAAATGTAGGTATGGTATTAACCATACT
1 GAGTTGTGAAATGTAGGTATGGTATTATCCATACT
*
28772507 AAGTTGTGAAATGTAGGTATGGTATTATCCATACT
1 GAGTTGTGAAATGTAGGTATGGTATTATCCATACT
** * * * * * *
28772542 GAGTTAAGAAACGTAAGTACGGCATTTTCCATACC
1 GAGTTGTGAAATGTAGGTATGGTATTATCCATACT
*
28772577 GAGTTGTAAAATGTAGGTATGGTATT
1 GAGTTGTGAAATGTAGGTATGGTATT
28772603 TCAATGAGGA
Statistics
Matches: 107, Mismatches: 24, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 107 1.00
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (35 bp):
GAGTTGTGAAATGTAGGTATGGTATTATCCATACT
Found at i:28784104 original size:13 final size:13
Alignment explanation
Indices: 28784086--28784110 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28784076 ATAAAGAATA
28784086 AAATTAACTAACT
1 AAATTAACTAACT
28784099 AAATTAACTAAC
1 AAATTAACTAAC
28784111 GAATGCGTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATTAACTAACT
Found at i:28786139 original size:42 final size:43
Alignment explanation
Indices: 28786062--28786182 Score: 140
Period size: 43 Copynumber: 2.8 Consensus size: 43
28786052 CATCGACTTA
* *
28786062 TGATTTACGTGTAAGACCACGTTTGGGACGTTGGCA-TCATATT
1 TGATTT-CGTGTAAGACCACGTCTGGCACGTTGGCATTCATATT
*
28786105 TGATTTCGTGTAAGACC-CTGTCTGGCACAG-TGGCATTGATATT
1 TGATTTCGTGTAAGACCAC-GTCTGGCAC-GTTGGCATTCATATT
* * *
28786148 TGATTACATGTAAGACCACGTCTGGGACGTTGGCA
1 TGATTTCGTGTAAGACCACGTCTGGCACGTTGGCA
28786183 CTGTACGAGC
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
41 1 0.01
42 24 0.36
43 41 0.61
44 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.32
Consensus pattern (43 bp):
TGATTTCGTGTAAGACCACGTCTGGCACGTTGGCATTCATATT
Found at i:28786147 original size:43 final size:42
Alignment explanation
Indices: 28786022--28786182 Score: 139
Period size: 43 Copynumber: 3.8 Consensus size: 42
28786012 CGAGATGTGT
* * * * * *
28786022 TTTCATGTAAGACCATGTCTGGGATGTTGACATCGACT-TATGA
1 TTTCGTGTAAGACCACGTCTGGCACGTTGGCATC-A-TATTTGA
* *
28786065 TTTACGTGTAAGACCACGTTTGGGACGTTGGCATCATATTTGA
1 TTT-CGTGTAAGACCACGTCTGGCACGTTGGCATCATATTTGA
*
28786108 TTTCGTGTAAGACC-CTGTCTGGCACAG-TGGCATTGATATTTGA
1 TTTCGTGTAAGACCAC-GTCTGGCAC-GTTGGCA-TCATATTTGA
* * *
28786151 TTACATGTAAGACCACGTCTGGGACGTTGGCA
1 TTTCGTGTAAGACCACGTCTGGCACGTTGGCA
28786183 CTGTACGAGC
Statistics
Matches: 99, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
41 1 0.01
42 25 0.25
43 46 0.46
44 27 0.27
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (42 bp):
TTTCGTGTAAGACCACGTCTGGCACGTTGGCATCATATTTGA
Found at i:28795599 original size:55 final size:55
Alignment explanation
Indices: 28795467--28795601 Score: 128
Period size: 55 Copynumber: 2.5 Consensus size: 55
28795457 GCCATTGGTG
* * **
28795467 AACCTGCCAAAAC-AACACAGGCATGCGACACGCCCGTGCCTTGAAACCGTGGCCA
1 AACCTGTC-AAACTAACACAGGCGTGCGACACGCCCGTGCCAAGAAACCGTGGCCA
* * * * * * * *
28795522 AACCTGTCAAATTATCATAGGCGTGTGACACGTCCGTGCCAAGCAACCGTGGTCG
1 AACCTGTCAAACTAACACAGGCGTGCGACACGCCCGTGCCAAGAAACCGTGGCCA
* *
28795577 AACCTGTTAGACTAACACAGGCGTG
1 AACCTGTCAAACTAACACAGGCGTG
28795602 GGACTACATA
Statistics
Matches: 62, Mismatches: 17, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
54 3 0.05
55 59 0.95
ACGTcount: A:0.29, C:0.30, G:0.24, T:0.17
Consensus pattern (55 bp):
AACCTGTCAAACTAACACAGGCGTGCGACACGCCCGTGCCAAGAAACCGTGGCCA
Found at i:28796138 original size:23 final size:23
Alignment explanation
Indices: 28796093--28796139 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
28796083 CATTCTATTG
* *
28796093 TCATACCCATGCCATTACTATGC
1 TCATACCCATGCCACTACCATGC
* *
28796116 TCATTCCCATGCTACTACCATGC
1 TCATACCCATGCCACTACCATGC
28796139 T
1 T
28796140 AATGTCAGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.36, G:0.09, T:0.32
Consensus pattern (23 bp):
TCATACCCATGCCACTACCATGC
Found at i:28797541 original size:17 final size:16
Alignment explanation
Indices: 28797501--28797544 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
28797491 AATTTTTTAA
28797501 ATTTTAATTTTATTTT
1 ATTTTAATTTTATTTT
28797517 CATTTTAATTTTATGTTT
1 -ATTTTAATTTTAT-TTT
28797535 -TTATTAATTT
1 ATT-TTAATTT
28797545 CACCTTTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.08
17 20 0.80
18 3 0.12
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (16 bp):
ATTTTAATTTTATTTT
Found at i:28807901 original size:22 final size:22
Alignment explanation
Indices: 28807866--28807907 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
28807856 TAAATATGTA
*
28807866 TAAATGATCTTTTGGTATGTCG
1 TAAATGATCTTTTGATATGTCG
28807888 TAAAGTGATC-TTTGATATGT
1 TAAA-TGATCTTTTGATATGT
28807908 TTTTATGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.26, C:0.07, G:0.21, T:0.45
Consensus pattern (22 bp):
TAAATGATCTTTTGATATGTCG
Found at i:28819548 original size:40 final size:40
Alignment explanation
Indices: 28819450--28819752 Score: 380
Period size: 40 Copynumber: 7.6 Consensus size: 40
28819440 TCCTCGTTCA
* * * ** *
28819450 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
28819489 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
28819529 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
28819569 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
28819609 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
28819649 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
28819689 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
28819729 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
28819753 CAGCATTCAA
Statistics
Matches: 239, Mismatches: 20, Indels: 9
0.89 0.07 0.03
Matches are distributed among these distances:
39 37 0.15
40 194 0.81
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:28827481 original size:40 final size:40
Alignment explanation
Indices: 28827433--28827820 Score: 722
Period size: 40 Copynumber: 9.7 Consensus size: 40
28827423 GCAAACACAT
* *
28827433 TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
28827473 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
28827513 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
28827553 TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
28827593 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
28827633 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
28827673 TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
28827713 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
28827753 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
28827793 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
28827821 TCCAATGCTC
Statistics
Matches: 338, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 338 1.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:28833033 original size:2 final size:2
Alignment explanation
Indices: 28833028--28833072 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
28833018 TCCTTTGATT
*
28833028 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
28833070 TC T
1 TC T
28833073 TGTTTTTATC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:28836436 original size:21 final size:21
Alignment explanation
Indices: 28836379--28836428 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
28836369 GCACGGTTTG
*
28836379 CTCACATGGCCATTTGACCCA
1 CTCACATGGCCATGTGACCCA
*
28836400 CTCACACGGCCATGTGACCCA
1 CTCACATGGCCATGTGACCCA
28836421 CTCACATG
1 CTCACATG
28836429 AACATGTGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.24, C:0.40, G:0.16, T:0.20
Consensus pattern (21 bp):
CTCACATGGCCATGTGACCCA
Found at i:28839293 original size:46 final size:46
Alignment explanation
Indices: 28839191--28839296 Score: 176
Period size: 46 Copynumber: 2.3 Consensus size: 46
28839181 TGTTTGGGCA
* * *
28839191 TCCGAACTCGCTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
*
28839237 TTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
28839283 TCCGAACTCGTTGA
1 TCCGAACTCGTTGA
28839297 ACATATGTGG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 55 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:28841832 original size:15 final size:15
Alignment explanation
Indices: 28841812--28841880 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
28841802 GTATCTTGGG
28841812 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
28841827 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
28841842 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
28841857 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
28841872 TTTCTTTAT
1 TTTCTTTAT
28841881 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:28841881 original size:30 final size:30
Alignment explanation
Indices: 28841803--28841890 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
28841793 CATAGTATCG
* * * *
28841803 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
28841833 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
28841863 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
28841891 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:28856930 original size:16 final size:16
Alignment explanation
Indices: 28856906--28856936 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28856896 ACAGCTATAC
*
28856906 CATGGCCCATACCATT
1 CATGACCCATACCATT
28856922 CATGACCCATACCAT
1 CATGACCCATACCAT
28856937 GGCCGGCCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.39, G:0.10, T:0.23
Consensus pattern (16 bp):
CATGACCCATACCATT
Found at i:28859369 original size:5 final size:5
Alignment explanation
Indices: 28859359--28859388 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
28859349 TCTACTTTTA
28859359 TTAAT TTAAT TTAAT TTAAT TTAAT ATTAA
1 TTAAT TTAAT TTAAT TTAAT TTAAT -TTAA
28859389 ACCTTGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TTAAT
Found at i:28880923 original size:68 final size:68
Alignment explanation
Indices: 28880850--28881001 Score: 177
Period size: 67 Copynumber: 2.2 Consensus size: 68
28880840 CATCATGTGT
* * * * *
28880850 ACAAGAGAGCTACGAGACATTATGATGTAGCTAGGTTGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTACGAGACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
28880913 TGTAG
64 TGTAG
* * *
28880918 ACAAGAGAGCTAC-AG-GATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCAT
1 ACAAGAGAGCTACGAGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCAT
28880981 GTAG
65 GTAG
28880985 ACAAGAGAGCTACGAGA
1 ACAAGAGAGCTACGAGA
28881002 TAAACTGGCT
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
64 23 0.32
65 3 0.04
66 3 0.04
67 27 0.38
68 15 0.21
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.22
Consensus pattern (68 bp):
ACAAGAGAGCTACGAGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATG
TAG
Found at i:28885086 original size:50 final size:50
Alignment explanation
Indices: 28884771--28885905 Score: 1997
Period size: 50 Copynumber: 22.9 Consensus size: 50
28884761 GAAATTGATG
* * *
28884771 TATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA-ATATG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
* * * *
28884819 TATGAGATAAGTATATGTGGTAAAGCCGACTGGCTAATGTG-AA-ATATG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
* *
28884867 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA-ATATG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
* * * *
28884915 TATGAGATAAGTATATGTGGTAAAGCCGACTGGCTAATGTG-AA-ATATG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
* **
28884963 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA-ATAGG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
*
28885011 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATA
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
28885061 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
28885111 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
28885161 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
28885211 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
28885261 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
28885311 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
28885361 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
28885411 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
28885461 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
28885511 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
28885561 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
28885611 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
28885661 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
28885711 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
28885761 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
* *
28885811 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA-ATATG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
* *
28885859 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATAT
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATAT
28885906 GTAGGCGATG
Statistics
Matches: 1069, Mismatches: 14, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
48 269 0.25
49 6 0.01
50 794 0.74
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (50 bp):
TATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATA
Found at i:28886105 original size:37 final size:38
Alignment explanation
Indices: 28886055--28886162 Score: 184
Period size: 37 Copynumber: 2.9 Consensus size: 38
28886045 GGAAATATAT
28886055 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTA-TG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATTG
28886092 TCCGGGTAAGACCCGATGACTACGTGTGGAGA-TATTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATTG
* *
28886129 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT
28886163 TCATCTGAGC
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
36 2 0.03
37 64 0.96
38 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.25
Consensus pattern (38 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATTG
Found at i:28889334 original size:40 final size:40
Alignment explanation
Indices: 28889279--28889358 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
28889269 GAAATCACTG
*
28889279 TTTGCTTTACGAGCGATGAATTTACGCTTGTCTGTTCTAC
1 TTTGCTTTACGAGCGATGAATTTACACTTGTCTGTTCTAC
28889319 TTTGCTTTACGAGCGATGAATTTACACTTGTCTGTTCTAC
1 TTTGCTTTACGAGCGATGAATTTACACTTGTCTGTTCTAC
28889359 CCGACAATGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.42
Consensus pattern (40 bp):
TTTGCTTTACGAGCGATGAATTTACACTTGTCTGTTCTAC
Found at i:28889669 original size:21 final size:21
Alignment explanation
Indices: 28889643--28889682 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
28889633 GAAACGTTAA
28889643 TTTTGGTGGCATGGTATGAGG
1 TTTTGGTGGCATGGTATGAGG
28889664 TTTTGGTGGCATGGTATGA
1 TTTTGGTGGCATGGTATGA
28889683 AACGAGACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.05, G:0.40, T:0.40
Consensus pattern (21 bp):
TTTTGGTGGCATGGTATGAGG
Found at i:28892577 original size:40 final size:40
Alignment explanation
Indices: 28892493--28892677 Score: 218
Period size: 40 Copynumber: 4.7 Consensus size: 40
28892483 TCGAATGATG
* *
28892493 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
*
28892532 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
28892573 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTCACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
28892612 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
28892651 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
28892678 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
39 35 0.28
40 80 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:28892629 original size:79 final size:81
Alignment explanation
Indices: 28892493--28892675 Score: 241
Period size: 79 Copynumber: 2.3 Consensus size: 81
28892483 TCGAATGATG
* * *
28892493 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTCACTAAATCCGGACTAAGATCCGAAGGCATT
28892557 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* **
28892572 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTCACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTCACTAAATCCGGACTAAGAT-CCGAAGGCA
28892634 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
28892652 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
28892676 TGAACGAGTA
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 1 0.01
79 60 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTCACTAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:28892699 original size:79 final size:78
Alignment explanation
Indices: 28892494--28892710 Score: 237
Period size: 79 Copynumber: 2.7 Consensus size: 78
28892484 CGAATGATGT
* *
28892494 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGT-GACTATATCCGGACTAAGATCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTAG-CTATATCCGG-TTAAG-TCCGAAGGCATT
*
28892557 TGTGCGAGTTACTAATT
62 TGTGCGAGTTACTAATA
* *
28892574 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTCA-CTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-AGCTATATCC-GGTTAAGT-CCGAAGGCATTT
28892637 GTGCGAGTTACT-ATAA
63 GTGCGAGTTACTAAT-A
* ** *
28892653 CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCCGGTTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTT-AAGTCCGAAGG
28892711 TACGTGATTC
Statistics
Matches: 117, Mismatches: 11, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
78 3 0.03
79 68 0.58
80 46 0.39
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (78 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTTAAGTCCGAAGGCATTTGTG
CGAGTTACTAATA
Found at i:28899113 original size:78 final size:81
Alignment explanation
Indices: 28898979--28899161 Score: 232
Period size: 78 Copynumber: 2.3 Consensus size: 81
28898969 TGAATGATGT
*
28898979 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
*
28899043 GTGCGAGATACTA-AT
66 GTGCGAGATACTATAA
* * * * **
28899058 TCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCATT
*
28899120 TGTGCGAGTTACTATAA
65 TGTGCGAGATACTATAA
*
28899137 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
28899162 AACGAGGAGC
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
77 1 0.01
78 49 0.55
79 25 0.28
80 14 0.16
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTATAA
Found at i:28899123 original size:40 final size:40
Alignment explanation
Indices: 28898978--28899161 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
28898968 TTGAATGATG
* * * *
28898978 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
28899018 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACT-AA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28899057 TTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28899096 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
28899137 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28899162 AACGAGGAGC
Statistics
Matches: 125, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 23 0.18
39 21 0.17
40 71 0.57
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28910603 original size:39 final size:40
Alignment explanation
Indices: 28910502--28910704 Score: 220
Period size: 40 Copynumber: 5.1 Consensus size: 40
28910492 TCGAATGATG
* *
28910502 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATA
*
28910542 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-A
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA
* * *
28910581 TTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTCACTAAA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
*
28910621 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
* * * **
28910661 ACCAGGCTATGT-CCGAAGGCATTTGAACGAG-TAGCTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATA
28910700 TCCGG
1 TCCGG
28910705 TTAAATTCCG
Statistics
Matches: 138, Mismatches: 18, Indels: 15
0.81 0.11 0.09
Matches are distributed among these distances:
38 2 0.01
39 59 0.43
40 69 0.50
41 8 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
Found at i:28910638 original size:79 final size:80
Alignment explanation
Indices: 28910502--28910658 Score: 221
Period size: 79 Copynumber: 2.0 Consensus size: 80
28910492 TCGAATGATG
* * *
28910502 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTGGTGCTAAGTCACTAAATCCGGACTAAGATCCGAAGGCATTT
28910567 GTGCGAGTTACTAAT
66 GTGCGAGTTACTAAT
* **
28910582 TCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTCACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTGGTGCTAAGTCACTAAATCCGGACTAAGAT-CCGAAGGCAT
28910644 TTGTGCGAGTTACTA
64 TTGTGCGAGTTACTA
28910659 TAACCAGGCT
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
78 1 0.01
79 51 0.74
80 17 0.25
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTGGTGCTAAGTCACTAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGTTACTAAT
Found at i:28910669 original size:79 final size:80
Alignment explanation
Indices: 28910506--28910683 Score: 211
Period size: 79 Copynumber: 2.2 Consensus size: 80
28910496 ATGATGTCCG
* * *
28910506 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTTGTG
1 GGCTAAG-CCCGAAGGCATTGGTGCTAAGTCACTAAATCCGGACTAAGATCCGAAGGCATTTGTG
* *
28910570 CGAGTTACTAATTCCG
65 CGAGTTACTAATACCA
* **
28910586 GGCTAAGCCCGAAGGCATTGGTGC-GAGTCACTAAATCCGGGTTAAG-TCCCGAAGGCATTTGTG
1 GGCTAAGCCCGAAGGCATTGGTGCTAAGTCACTAAATCCGGACTAAGAT-CCGAAGGCATTTGTG
28910649 CGAGTTACT-ATAACCA
65 CGAGTTACTAAT-ACCA
* *
28910665 GGCTATGTCCGAAGGCATT
1 GGCTAAGCCCGAAGGCATT
28910684 TGAACGAGTA
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
78 3 0.04
79 69 0.81
80 13 0.15
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
GGCTAAGCCCGAAGGCATTGGTGCTAAGTCACTAAATCCGGACTAAGATCCGAAGGCATTTGTGC
GAGTTACTAATACCA
Found at i:28910692 original size:79 final size:78
Alignment explanation
Indices: 28910555--28910718 Score: 197
Period size: 79 Copynumber: 2.1 Consensus size: 78
28910545 GGACTAAGAT
* * **
28910555 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTCA-CTA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCAGGCTAAGCCCGAAGGCATTGGAACGAGT-AGCTA
*
28910619 AATCCGGGTTAAGTC
65 AATCC-GGTTAAATC
* * *
28910634 CCGAAGGCATTTGTGCGAGTTACT-ATAACCAGGCTATGTCCGAAGGCATTTGAACGAGTAGCTA
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCAGGCTAAGCCCGAAGGCATTGGAACGAGTAGCTA
* *
28910698 TATCCGGTTAAATT
65 AATCCGGTTAAATC
28910712 CCGAAGG
1 CCGAAGG
28910719 TACGTGATTC
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
78 17 0.23
79 56 0.77
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCAGGCTAAGCCCGAAGGCATTGGAACGAGTAGCTAA
ATCCGGTTAAATC
Found at i:28915835 original size:40 final size:40
Alignment explanation
Indices: 28915773--28915935 Score: 240
Period size: 40 Copynumber: 4.1 Consensus size: 40
28915763 AAACCAAGTA
* * *
28915773 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
**
28915812 CCTTCGGGACTTAGCCCGGATATAGTAGTTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
28915852 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
28915892 CCTTCGGGACTTAGCTCGGAAATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
28915932 CCTT
1 CCTT
28915936 NNNNNNNNNN
Statistics
Matches: 113, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
39 13 0.12
40 100 0.88
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:28923012 original size:174 final size:174
Alignment explanation
Indices: 28922722--28923071 Score: 682
Period size: 174 Copynumber: 2.0 Consensus size: 174
28922712 TCTCAATAAC
*
28922722 CATATACATACAAAATGATTATATCACTATGCTCAAAATATATAAGCCATTTTCGCATGGCTATC
1 CATATACATACAAAATAATTATATCACTATGCTCAAAATATATAAGCCATTTTCGCATGGCTATC
28922787 CAAATATATACAACACCAAAGTACTTGACTATTAAAAAAAGGGCAGTCCTATACATGCCATTAGC
66 CAAATATATACAACACCAAAGTACTTGACTATTAAAAAAAGGGCAGTCCTATACATGCCATTAGC
28922852 AGAGTTCAACTAAAAGAGTACCAAAAGGGCTTTGATAGTGTGGA
131 AGAGTTCAACTAAAAGAGTACCAAAAGGGCTTTGATAGTGTGGA
28922896 CATATACATACAAAATAATTATATCACTATGCTCAAAATATATAAGCCATTTTCGCATGGCTATC
1 CATATACATACAAAATAATTATATCACTATGCTCAAAATATATAAGCCATTTTCGCATGGCTATC
28922961 CAAATATATACAACACCAAAGTACTTGACTATTAAAAAAAGGGCAGTCCTATACATGCCATTAGC
66 CAAATATATACAACACCAAAGTACTTGACTATTAAAAAAAGGGCAGTCCTATACATGCCATTAGC
*
28923026 AGAGTTCAACTAAAAGAGTACGAAAAGGGCTTTGATAGTGTGGA
131 AGAGTTCAACTAAAAGAGTACCAAAAGGGCTTTGATAGTGTGGA
28923070 CA
1 CA
28923072 ACTTCGACTT
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
174 174 1.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (174 bp):
CATATACATACAAAATAATTATATCACTATGCTCAAAATATATAAGCCATTTTCGCATGGCTATC
CAAATATATACAACACCAAAGTACTTGACTATTAAAAAAAGGGCAGTCCTATACATGCCATTAGC
AGAGTTCAACTAAAAGAGTACCAAAAGGGCTTTGATAGTGTGGA
Found at i:28933043 original size:43 final size:43
Alignment explanation
Indices: 28932981--28933207 Score: 247
Period size: 43 Copynumber: 5.3 Consensus size: 43
28932971 NNNNNNNNNN
* * * *
28932981 TTAGCGGCGTTTTTAGGAAAAGCGTCGCTAAAAGTCATGACCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGACCT
* * *
28933024 TTAGCGGGGTTTGTGGGAAAAGTGCCGCTACAGGTCATGACCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGACCT
* * * *
28933067 TTAGCGGCGTTTGTGGAAAAAGCGCCGTTACAGGTCATGATCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGACCT
* * **
28933110 TTAGCGGCGTCTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGACCT
* *** ** * *
28933153 TTAGCGGCGTTTTTTCAAAAAAAGCCGCTAAAGGTCCTGATCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGACCT
28933196 TTAGCGGCGTTT
1 TTAGCGGCGTTT
28933208 TTTTCTAAAA
Statistics
Matches: 158, Mismatches: 26, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 158 1.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.28
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGACCT
Found at i:28933126 original size:86 final size:86
Alignment explanation
Indices: 28932981--28933205 Score: 272
Period size: 86 Copynumber: 2.6 Consensus size: 86
28932971 NNNNNNNNNN
* * * * *
28932981 TTAGCGGCGTTTTTAGG-AAAAGCGTCGCTAAAAGTCATGACCTTTAGCGGGGTTTGTGGGAAAA
1 TTAGCGGCGTTTTT-GGAAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTCTGTGGGAAAA
* *
28933045 GTGCCGCTACAGGTCATGACCT
65 GCGCCGCTAAAGGTCATGACCT
* * *
28933067 TTAGCGGCGTTTGTGGAAAAAGCGCCGTTACAGGTCATGATCTTTAGCGGCGTCTGTGGGAAAAG
1 TTAGCGGCGTTTTTGGAAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTCTGTGGGAAAAG
* **
28933132 CGCCGCTAAAGGTCCTGGTCT
66 CGCCGCTAAAGGTCATGACCT
** ** *
28933153 TTAGCGGCGTTTTTTCAAAAAAAGCCGCTAAAGGTCCTGATCTTTAGCGGCGT
1 TTAGCGGCGTTTTTGGAAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGT
28933206 TTTTTTCTAA
Statistics
Matches: 117, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
85 2 0.02
86 115 0.98
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (86 bp):
TTAGCGGCGTTTTTGGAAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTCTGTGGGAAAAG
CGCCGCTAAAGGTCATGACCT
Found at i:28939797 original size:13 final size:14
Alignment explanation
Indices: 28939781--28939816 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
28939771 CAATCTCATA
28939781 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
28939794 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
28939807 TCTC-ATTTCA
1 TCTCAATTTCA
28939817 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:28939806 original size:18 final size:19
Alignment explanation
Indices: 28939768--28939808 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
28939758 TGGTTCATGT
28939768 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
28939787 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
28939805 TTTC
1 TTTC
28939809 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:28939998 original size:39 final size:38
Alignment explanation
Indices: 28939931--28940065 Score: 110
Period size: 39 Copynumber: 3.4 Consensus size: 38
28939921 ACCAATATGG
* * *
28939931 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTA-TCCGAAGAAATATTTGA
* * * *
28939970 CACCCAGTGTCTCATCGGCCTATCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTATCCGAAGAAATATTTGA
* * * *
28940008 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTATCCGAAGAAATAT-TTGA
*
28940049 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
28940066 ACTCGAGGTC
Statistics
Matches: 74, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
38 18 0.24
39 37 0.50
40 3 0.04
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTATCCGAAGAAATATTTGA
Found at i:28940063 original size:41 final size:41
Alignment explanation
Indices: 28939967--28940066 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 41
28939957 AAGCAATATT
*
28939967 TGACACCCAGTGTCTCATCG-GCCTATCCGAAGTAAAGTTG
1 TGACACCCAGTGTCTCATCGAACCTATCCGAAGTAAAGTTG
* ** *
28940007 -G-TACCCAGTACCTCATCGAATCTATCCGAAG-AAA-TATAG
1 TGACACCCAGTGTCTCATCGAACCTATCCGAAGTAAAGT-T-G
28940046 TGACACCCAGTGTCTCATCGA
1 TGACACCCAGTGTCTCATCGA
28940067 CTCGAGGTCG
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
37 1 0.02
38 18 0.38
39 12 0.26
40 1 0.02
41 15 0.32
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (41 bp):
TGACACCCAGTGTCTCATCGAACCTATCCGAAGTAAAGTTG
Found at i:28940331 original size:18 final size:19
Alignment explanation
Indices: 28940305--28940343 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
28940295 TTTCAATTCA
28940305 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
28940324 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
28940342 AT
1 AT
28940344 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:28941625 original size:5 final size:5
Alignment explanation
Indices: 28941615--28941665 Score: 84
Period size: 5 Copynumber: 10.0 Consensus size: 5
28941605 TTACTTATTT
*
28941615 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATAATA ATTTA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA ATATA
28941666 TATTTTAACA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
5 38 0.88
6 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:28946636 original size:74 final size:74
Alignment explanation
Indices: 28946515--28946660 Score: 274
Period size: 74 Copynumber: 2.0 Consensus size: 74
28946505 TATTCTTCTT
*
28946515 TTTTCTATTTCTCTTCTTCAAAACCATTCATCAATTCTGCTGTTCATCAATACTTTTGCTGAAGT
1 TTTTCTATTTCTCTTCTTCAAAACCATTCATCAATTCTGCTGTTCATCAATACTTTTGCCGAAGT
28946580 CACAAAAGC
66 CACAAAAGC
28946589 TTTTCTATTTCTCTTCTTCAAAACCATTCATCAATTCTGCTGTTCATCAATACTTTTGCCGAAGT
1 TTTTCTATTTCTCTTCTTCAAAACCATTCATCAATTCTGCTGTTCATCAATACTTTTGCCGAAGT
*
28946654 CGCAAAA
66 CACAAAA
28946661 CCCGAAATCC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.40
Consensus pattern (74 bp):
TTTTCTATTTCTCTTCTTCAAAACCATTCATCAATTCTGCTGTTCATCAATACTTTTGCCGAAGT
CACAAAAGC
Found at i:28964227 original size:40 final size:40
Alignment explanation
Indices: 28964172--28964272 Score: 168
Period size: 40 Copynumber: 2.5 Consensus size: 40
28964162 TATTCGGATG
28964172 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
28964212 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
28964252 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
28964273 ATACTTGGGT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
39 14 0.24
40 44 0.76
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:28968447 original size:46 final size:45
Alignment explanation
Indices: 28968282--28968458 Score: 153
Period size: 44 Copynumber: 3.8 Consensus size: 45
28968272 TGGGATAAGT
* * *
28968282 TGCCGATGCCATGTCCCAGACATGGTCTTATACTAGCTCTCATAAATACG
1 TGCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCACTCAT--AT-TG
* * *
28968332 TGCTGATGCATGTCCC-GAACATGTCTTACACTAGCAC-GACTCTT-
1 TGCCGATGCATGTCCCAG-ACATGTCTTACACTAGCACTCA-TATTG
* * * * * *
28968376 AGCCAATGCATATCTCATACATGTCTTACACTGGCACTCATATTG
1 TGCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCATATTG
28968421 TGGCCGATGCATGTCCCAGACATGTCTTACACTAGCAC
1 T-GCCGATGCATGTCCCAGACATGTCTTACACTAGCAC
28968459 ACAAGAAATC
Statistics
Matches: 100, Mismatches: 21, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
44 32 0.32
45 1 0.01
46 32 0.32
47 1 0.01
48 15 0.15
49 12 0.12
50 7 0.07
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (45 bp):
TGCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCATATTG
Found at i:28973462 original size:19 final size:20
Alignment explanation
Indices: 28973438--28973477 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
28973428 GATAACTCAG
28973438 GAAAA-TTTTACAAAACATA
1 GAAAATTTTTACAAAACATA
*
28973457 GAAAATTTTTACAAAATATA
1 GAAAATTTTTACAAAACATA
28973477 G
1 G
28973478 GGGACACACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (20 bp):
GAAAATTTTTACAAAACATA
Found at i:28987873 original size:30 final size:30
Alignment explanation
Indices: 28987837--28987895 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
28987827 TGTACTAACC
*
28987837 TCATTTTAACTTATATAT-ATATATCACAAA
1 TCATTTTAAC-TATATATCATACATCACAAA
* *
28987867 TCATTTTCACTATATTTCATACATCACAA
1 TCATTTTAACTATATATCATACATCACAA
28987896 GTATAGGCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.42
Consensus pattern (30 bp):
TCATTTTAACTATATATCATACATCACAAA
Found at i:29001046 original size:42 final size:42
Alignment explanation
Indices: 29000945--29001274 Score: 394
Period size: 42 Copynumber: 7.8 Consensus size: 42
29000935 AACGGGTACA
* * * *
29000945 ATGCCGACGTCCCAGACGTGGTCTTACATGTAATTCA-ATATCG
1 ATGCCGATGTCCCAGACATGGTCTTACACG-AAATCAGATA-CG
** * * * *
29000988 ATGCCTCTGTCCCAGACAGGGTCTTACATGAAATTAGATATG
1 ATGCCGATGTCCCAGACATGGTCTTACACGAAATCAGATACG
* * *
29001030 ATGCCAATGTCCCAGACATGGTCTTACACAAAAGCAGATACG
1 ATGCCGATGTCCCAGACATGGTCTTACACGAAATCAGATACG
*
29001072 ATGCCGATGTCCCAGACATGGTCTTACACAAAATCAGATACG
1 ATGCCGATGTCCCAGACATGGTCTTACACGAAATCAGATACG
* * *
29001114 ATGTCGATGTCCCAGACATGGTTTTACACAAAATCAGATACG
1 ATGCCGATGTCCCAGACATGGTCTTACACGAAATCAGATACG
* *
29001156 ATGCCAATGTCCCAGACAT-ATCTTACACGAAATCAGATACG
1 ATGCCGATGTCCCAGACATGGTCTTACACGAAATCAGATACG
** * * *
29001197 AAACTGATGTCCCAGACATGGTCTTACATGAAATTAGATACG
1 ATGCCGATGTCCCAGACATGGTCTTACACGAAATCAGATACG
*
29001239 ATGCCGATGTCCCAAACATGGTCTTACACGTAAATC
1 ATGCCGATGTCCCAGACATGGTCTTACACG-AAATC
29001275 TCAAATCGAG
Statistics
Matches: 246, Mismatches: 38, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
41 34 0.14
42 180 0.73
43 32 0.13
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (42 bp):
ATGCCGATGTCCCAGACATGGTCTTACACGAAATCAGATACG
Found at i:29001237 original size:125 final size:126
Alignment explanation
Indices: 29000948--29001267 Score: 410
Period size: 125 Copynumber: 2.5 Consensus size: 126
29000938 GGGTACAATG
* * * ** *
29000948 CCGACGTCCCAGACGTGGTCTTACATGTAATTCA-ATATCGATGCCTCTGTCCCAGACAGGGTCT
1 CCGATGTCCCAGACATGGTCTTACATGAAATT-AGATA-CGATGCCGATGTCCCAGACATGGTCT
** * * * **
29001012 TACATGAAATTAGATATGATGCCAATGTCCCAGACATGGTCTTACACAAAAGCAGATACGATG
64 TACACAAAATCAGATACGATGCCAATGTCCCAGACATGATCTTACACAAAAGCAGATACGAAA
** * * *
29001075 CCGATGTCCCAGACATGGTCTTACACAAAATCAGATACGATGTCGATGTCCCAGACATGGTTTTA
1 CCGATGTCCCAGACATGGTCTTACATGAAATTAGATACGATGCCGATGTCCCAGACATGGTCTTA
* *
29001140 CACAAAATCAGATACGATGCCAATGTCCCAGACAT-ATCTTACACGAAATCAGATACGAAA
66 CACAAAATCAGATACGATGCCAATGTCCCAGACATGATCTTACACAAAAGCAGATACGAAA
* *
29001200 CTGATGTCCCAGACATGGTCTTACATGAAATTAGATACGATGCCGATGTCCCAAACATGGTCTTA
1 CCGATGTCCCAGACATGGTCTTACATGAAATTAGATACGATGCCGATGTCCCAGACATGGTCTTA
29001265 CAC
66 CAC
29001268 GTAAATCTCA
Statistics
Matches: 165, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
125 81 0.49
126 55 0.33
127 29 0.18
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (126 bp):
CCGATGTCCCAGACATGGTCTTACATGAAATTAGATACGATGCCGATGTCCCAGACATGGTCTTA
CACAAAATCAGATACGATGCCAATGTCCCAGACATGATCTTACACAAAAGCAGATACGAAA
Found at i:29007927 original size:42 final size:42
Alignment explanation
Indices: 29007877--29008064 Score: 268
Period size: 42 Copynumber: 4.5 Consensus size: 42
29007867 AATGCCTCTA
* * * *
29007877 TCCCAGACAGGGTCTTGCACGAAATCAGATATGATGCTGATG
1 TCCCAGACATGGTCTTACACGAAATCAGATACGATGCCGATG
* * *
29007919 TCCCAGACATGGTCTTACACAAAATCAAATACGATGCCAATG
1 TCCCAGACATGGTCTTACACGAAATCAGATACGATGCCGATG
*
29007961 TCCCAGACATGGTCTTACACGAAATCGGATACGATGCCGATG
1 TCCCAGACATGGTCTTACACGAAATCAGATACGATGCCGATG
* *
29008003 TCCCAGACATGGTCTTACATGAAATCAGATACGATGTCGATG
1 TCCCAGACATGGTCTTACACGAAATCAGATACGATGCCGATG
* *
29008045 TCCCAGACATCGACTTACAC
1 TCCCAGACATGGTCTTACAC
29008065 TTAAATCTCA
Statistics
Matches: 129, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 129 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (42 bp):
TCCCAGACATGGTCTTACACGAAATCAGATACGATGCCGATG
Found at i:29014158 original size:46 final size:46
Alignment explanation
Indices: 29013984--29014255 Score: 227
Period size: 46 Copynumber: 5.8 Consensus size: 46
29013974 CATTGGTGTG
* * * *
29013984 AGCCAGTGTAGGACCATG-CTTGGGACATGGCATCGACATTGAGACAAGT
1 AGCCAGTGTAAGACCATGTC-TGGGACATGGCATCGGC-TCGAG--ATGT
* * * *
29014033 -GCTAGTGTAAGA-CATGTCTAGGACAT-GCATCAGCCTCGAGACGT
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATC-GGCTCGAGATGT
29014077 AAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACGAGATGT
1 -AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCT-CGAGATGT
* * * *
29014123 -GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGATATGCGAG
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTC-GAGAT--G-T
* *
29014172 AGCTAGTGTAA-ACCATGTCTGGGACATGGCATTGGCCTCGATGATGAT
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG-CTCGA-GATG-T
*
29014220 AGCCAGTGTAAGACCATGTCCGGGACATGGCATCGG
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG
29014256 TAACTTACCC
Statistics
Matches: 185, Mismatches: 23, Indels: 30
0.78 0.10 0.13
Matches are distributed among these distances:
44 14 0.08
45 18 0.10
46 57 0.31
47 13 0.07
48 24 0.13
49 47 0.25
50 12 0.06
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (46 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGT
Found at i:29014247 original size:98 final size:94
Alignment explanation
Indices: 29014082--29014255 Score: 253
Period size: 98 Copynumber: 1.8 Consensus size: 94
29014072 GACGTAAGCC
* *
29014082 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGTGTCAGTGTAAGACCATGTCTGGGA
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGTGCCAGTGTAAGACCATGTCCGGGA
29014147 CATGGCATCGGCACGGATATGCGAGAGCT
66 CATGGCATCGGCACGGATATGCGAGAGCT
*
29014176 AGTGTAA-ACCATGTCTGGGACATGGCATTGGCCT-CGATGATGATAGCCAGTGTAAGACCATGT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGG-CTACGA-GATG-T-GCCAGTGTAAGACCATGT
29014239 CCGGGACATGGCATCGG
60 CCGGGACATGGCATCGG
29014256 TAACTTACCC
Statistics
Matches: 71, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
93 1 0.01
94 21 0.30
95 9 0.13
96 6 0.08
97 1 0.01
98 33 0.46
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.22
Consensus pattern (94 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGTGCCAGTGTAAGACCATGTCCGGGA
CATGGCATCGGCACGGATATGCGAGAGCT
Found at i:29020335 original size:39 final size:39
Alignment explanation
Indices: 29020277--29020431 Score: 247
Period size: 39 Copynumber: 4.0 Consensus size: 39
29020267 AGTGATGAAG
* *
29020277 TATATCCAGACTTAGGGTCCGCAGGCTATGTGCTGGAAC
1 TATATCCAGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* *
29020316 TATATCCGGACTTAAGGTCCGCAGGCTATGTGATGGAAT
1 TATATCCAGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
29020355 TATATCCAGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCAGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* * *
29020394 TATAACCAGACTTAAGGTCCGCAGACTACGTGCTGGAA
1 TATATCCAGACTTAAGGTCCGCAGGCTATGTGCTGGAA
29020432 ATATGTCCGG
Statistics
Matches: 107, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 107 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (39 bp):
TATATCCAGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
Found at i:29020458 original size:78 final size:78
Alignment explanation
Indices: 29020268--29020459 Score: 199
Period size: 78 Copynumber: 2.5 Consensus size: 78
29020258 ATGACACTCA
* * ** * * *
29020268 GTGAT-GAAGTATATCCAGACTTAGGGTCCGCAGGCTATGTGCTGGAACTATATCCGGACTTAAG
1 GTGATGGAAATATATCCAGACTAAAAGTCCACAGGCTATGTGCTGGAACTATAACCAGACTTAAG
* *
29020332 GTCCGCAGGCTAT
66 GTCCGCAGACTAC
* * * * *
29020345 GTGATGGAATTATATCCAGACTTAAGGTCCGCAGGCTATGTGCTGGAATTATAACCAGACTTAAG
1 GTGATGGAAATATATCCAGACTAAAAGTCCACAGGCTATGTGCTGGAACTATAACCAGACTTAAG
29020410 GTCCGCAGACTAC
66 GTCCGCAGACTAC
* * * *
29020423 GTGCTGGAAATATGTCCGGGC-AAAAGTCCCACAGGCT
1 GTGATGGAAATATATCCAGACTAAAAGT-CCACAGGCT
29020460 TCAAGCTGGT
Statistics
Matches: 98, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
77 9 0.09
78 89 0.91
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.24
Consensus pattern (78 bp):
GTGATGGAAATATATCCAGACTAAAAGTCCACAGGCTATGTGCTGGAACTATAACCAGACTTAAG
GTCCGCAGACTAC
Found at i:29036910 original size:6 final size:6
Alignment explanation
Indices: 29036892--29037004 Score: 63
Period size: 6 Copynumber: 18.3 Consensus size: 6
29036882 AAGAAACATT
* * *
29036892 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATTAG- GTGACAGA ATCAAA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* * * *
29036941 ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA ATCGGT ATCAGGTA A-CAGA
1 ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA
*
29036991 ATCAAA ATCAGA AT
1 ATCAGA ATCAGA AT
29037005 GTGAATGCAA
Statistics
Matches: 80, Mismatches: 16, Indels: 22
0.68 0.14 0.19
Matches are distributed among these distances:
5 6 0.08
6 62 0.77
7 9 0.11
8 3 0.04
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:29036937 original size:25 final size:25
Alignment explanation
Indices: 29036906--29037004 Score: 108
Period size: 25 Copynumber: 3.7 Consensus size: 25
29036896 GAACTAGAAT
* * *
29036906 CAGAATCAGAATCAGAATTAGGTGA
1 CAGAATCAAAATCAGAATCAGGTAA
*
29036931 CAGAATCAAAATCAGTATCAGGTAA
1 CAGAATCAAAATCAGAATCAGGTAA
29036956 CAGAATCAAAATCAGAATCGGTATCAGGTAA
1 CAGAATCAAAATCAG-A-----ATCAGGTAA
29036987 CAGAATCAAAATCAGAAT
1 CAGAATCAAAATCAGAAT
29037005 GTGAATGCAA
Statistics
Matches: 63, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
25 38 0.60
30 1 0.02
31 24 0.38
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.19
Consensus pattern (25 bp):
CAGAATCAAAATCAGAATCAGGTAA
Found at i:29036937 original size:31 final size:31
Alignment explanation
Indices: 29036934--29037004 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
29036924 TAGGTGACAG
*
29036934 AATCAAAATCAGTATCAGGTAACAGAATCAA
1 AATCAGAATCAGTATCAGGTAACAGAATCAA
*
29036965 AATCAGAATCGGTATCAGGTAACAGAATCAA
1 AATCAGAATCAGTATCAGGTAACAGAATCAA
29036996 AATCAGAAT
1 AATCAGAAT
29037005 GTGAATGCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.20
Consensus pattern (31 bp):
AATCAGAATCAGTATCAGGTAACAGAATCAA
Found at i:29037436 original size:27 final size:27
Alignment explanation
Indices: 29037406--29037709 Score: 455
Period size: 27 Copynumber: 11.3 Consensus size: 27
29037396 GGGGCAAAAT
* * *
29037406 GGTAATTTTACCCTACAAGGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
29037433 GGTAATTCTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
29037460 GGTATTTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
29037487 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
29037514 GATCATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
29037541 GGTTATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
29037568 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
29037595 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
29037622 GGTAATTCTATCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
29037649 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
29037676 CGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
29037703 GGTAATT
1 GGTAATT
29037710 ACACAAAGTA
Statistics
Matches: 254, Mismatches: 23, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 254 1.00
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:29037764 original size:27 final size:27
Alignment explanation
Indices: 29037695--29037792 Score: 92
Period size: 27 Copynumber: 3.6 Consensus size: 27
29037685 ACCCTACAAG
* ** *
29037695 GGTATTTCGGTAATTACACAAAGTAGA
1 GGTATTTTGGTAATTTTACAAACTAGA
29037722 GGTATTTTGGTAATTTTACAAACTA-A
1 GGTATTTTGGTAATTTTACAAACTAGA
*** *
29037748 TGGTATTTTGGTAATTTTATTGA-TCGA
1 -GGTATTTTGGTAATTTTACAAACTAGA
29037775 GGGTATTTTGGTAATTTT
1 -GGTATTTTGGTAATTTT
29037793 GTAAACCAAG
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
26 2 0.03
27 58 0.97
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (27 bp):
GGTATTTTGGTAATTTTACAAACTAGA
Found at i:29037804 original size:27 final size:27
Alignment explanation
Indices: 29037722--29037819 Score: 106
Period size: 27 Copynumber: 3.6 Consensus size: 27
29037712 ACAAAGTAGA
* * *
29037722 GGTATTTTGGTAATTTTACAAACTAAT
1 GGTATTTTGGTAATTTTATAAACCAAG
** * *
29037749 GGTATTTTGGTAATTTTATTGATCGAG
1 GGTATTTTGGTAATTTTATAAACCAAG
*
29037776 GGTATTTTGGTAATTTTGTAAACCAAG
1 GGTATTTTGGTAATTTTATAAACCAAG
**
29037803 GGTATTTCAGTAATTTT
1 GGTATTTTGGTAATTTT
29037820 TTACATTGAG
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.28, C:0.06, G:0.20, T:0.46
Consensus pattern (27 bp):
GGTATTTTGGTAATTTTATAAACCAAG
Found at i:29037831 original size:54 final size:54
Alignment explanation
Indices: 29037722--29037833 Score: 136
Period size: 54 Copynumber: 2.1 Consensus size: 54
29037712 ACAAAGTAGA
* * ** *
29037722 GGTATTTTGGTAATTTTACAAACTAATGGTATTTTGGTAATTTTATTGATCGAG
1 GGTATTTTGGTAATTTTACAAACCAAGGGTATTTCAGTAATTTTATTCATCGAG
** *
29037776 GGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTTT-TTACATTGAG
1 GGTATTTTGGTAATTTTACAAACCAAGGGTATTTCAGTAATTTTATT-CATCGAG
29037830 GGTA
1 GGTA
29037834 AAATGGTAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
53 2 0.04
54 47 0.96
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.45
Consensus pattern (54 bp):
GGTATTTTGGTAATTTTACAAACCAAGGGTATTTCAGTAATTTTATTCATCGAG
Found at i:29037842 original size:27 final size:27
Alignment explanation
Indices: 29037827--29038173 Score: 505
Period size: 27 Copynumber: 12.8 Consensus size: 27
29037817 TTTTTACATT
29037827 GAGGGTAAAATGGTAATTCTATAAATC
1 GAGGGTAAAATGGTAATTCTATAAATC
* * *
29037854 GAGGGTAAGACGGTAATTCTGTAAATC
1 GAGGGTAAAATGGTAATTCTATAAATC
*
29037881 GAGGGTAAAATAGTAATTCTATAAATC
1 GAGGGTAAAATGGTAATTCTATAAATC
* *
29037908 AAGGGTAAAATGGTAATTCTGTAAATC
1 GAGGGTAAAATGGTAATTCTATAAATC
*
29037935 GAGGGTAAAATAGTAATTCTATAAATC
1 GAGGGTAAAATGGTAATTCTATAAATC
* *
29037962 TAGGGTAAAATGGTAATTCTGTAAATC
1 GAGGGTAAAATGGTAATTCTATAAATC
*
29037989 GAGGGTAAAATAGTAATTCTATAAATC
1 GAGGGTAAAATGGTAATTCTATAAATC
* * *
29038016 GAGGGTAAAACGGTAATTTTGTAAATC
1 GAGGGTAAAATGGTAATTCTATAAATC
*
29038043 GAGGGTAAAATAGTAATTCTATAAATC
1 GAGGGTAAAATGGTAATTCTATAAATC
*
29038070 GAGGGTAAAATGGTAATTCTGTAAATC
1 GAGGGTAAAATGGTAATTCTATAAATC
*
29038097 GAGGGTAAAAATAGTAATTCTATAAATC
1 GAGGGT-AAAATGGTAATTCTATAAATC
* * * *
29038125 GAGGGTAAAACGATAATTCTGTAAATT
1 GAGGGTAAAATGGTAATTCTATAAATC
29038152 GAGGGTAAAATGGTAATTCTAT
1 GAGGGTAAAATGGTAATTCTAT
29038174 CTTACAGGAG
Statistics
Matches: 280, Mismatches: 39, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
27 255 0.91
28 25 0.09
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (27 bp):
GAGGGTAAAATGGTAATTCTATAAATC
Found at i:29038213 original size:27 final size:27
Alignment explanation
Indices: 29038183--29038338 Score: 145
Period size: 27 Copynumber: 5.8 Consensus size: 27
29038173 TCTTACAGGA
29038183 GTATTTCAGTAATTTTACAAATCGAGG
1 GTATTTCAGTAATTTTACAAATCGAGG
*
29038210 GTATTTCAGTAATTTTGCAAA-CTGAGG
1 GTATTTCAGTAATTTTACAAATC-GAGG
**
29038237 GTATTTTTGTAATTTTACAAATCGAGG
1 GTATTTCAGTAATTTTACAAATCGAGG
* ** * * *
29038264 ATATTTGGGTAATTTTATATATCGGGG
1 GTATTTCAGTAATTTTACAAATCGAGG
* * *
29038291 GTACTTT-GGTAATTTTACAAGTTGAGG
1 GTA-TTTCAGTAATTTTACAAATCGAGG
** *
29038318 GTATTTTTGTAATTTTGCAAA
1 GTATTTCAGTAATTTTACAAA
29038339 CAGGGATAAC
Statistics
Matches: 106, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
26 4 0.04
27 98 0.92
28 4 0.04
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (27 bp):
GTATTTCAGTAATTTTACAAATCGAGG
Found at i:29038249 original size:81 final size:81
Alignment explanation
Indices: 29038179--29038331 Score: 191
Period size: 81 Copynumber: 1.9 Consensus size: 81
29038169 TCTATCTTAC
*
29038179 AGGAGTATTTCAGTAATTTTACAAATCGAGGGTA-TTTCAGTAATTTTGCAAACTGAGGGTATTT
1 AGGA-TATTTCAGTAATTTTACAAATCGAGGGTACTTT-AGTAATTTTACAAACTGAGGGTATTT
*
29038243 TTGTAATTTTACAAATCG
64 TTGTAATTCTACAAATCG
** * * * * **
29038261 AGGATATTTGGGTAATTTTATATATCGGGGGTACTTTGGTAATTTTACAAGTTGAGGGTATTTTT
1 AGGATATTTCAGTAATTTTACAAATCGAGGGTACTTTAGTAATTTTACAAACTGAGGGTATTTTT
29038326 GTAATT
66 GTAATT
29038332 TTGCAAACAG
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
81 54 0.89
82 7 0.11
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42
Consensus pattern (81 bp):
AGGATATTTCAGTAATTTTACAAATCGAGGGTACTTTAGTAATTTTACAAACTGAGGGTATTTTT
GTAATTCTACAAATCG
Found at i:29040430 original size:57 final size:57
Alignment explanation
Indices: 29040342--29040454 Score: 217
Period size: 57 Copynumber: 2.0 Consensus size: 57
29040332 CTCTTCCGAC
*
29040342 GTCCTACAATTGATTAGCACAGTTCTTATTTACAAACCATAATCACTAAACTCCAAT
1 GTCCTACAATTGATTAGCACAATTCTTATTTACAAACCATAATCACTAAACTCCAAT
29040399 GTCCTACAATTGATTAGCACAATTCTTATTTACAAACCATAATCACTAAACTCCAA
1 GTCCTACAATTGATTAGCACAATTCTTATTTACAAACCATAATCACTAAACTCCAA
29040455 AACTTACGCA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (57 bp):
GTCCTACAATTGATTAGCACAATTCTTATTTACAAACCATAATCACTAAACTCCAAT
Found at i:29041190 original size:48 final size:49
Alignment explanation
Indices: 29041116--29041215 Score: 193
Period size: 48 Copynumber: 2.1 Consensus size: 49
29041106 GGTTTCAGCT
29041116 AGAGAGGAAAAAAAAAGAGAAAAGAACAACCCTAAGGTGTTTAAGCAGA
1 AGAGAGGAAAAAAAAAGAGAAAAGAACAACCCTAAGGTGTTTAAGCAGA
29041165 AGAGAGG-AAAAAAAAGAGAAAAGAACAACCCTAAGGTGTTTAAGCAGA
1 AGAGAGGAAAAAAAAAGAGAAAAGAACAACCCTAAGGTGTTTAAGCAGA
29041213 AGA
1 AGA
29041216 AAACGGCACC
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 44 0.86
49 7 0.14
ACGTcount: A:0.55, C:0.10, G:0.25, T:0.10
Consensus pattern (49 bp):
AGAGAGGAAAAAAAAAGAGAAAAGAACAACCCTAAGGTGTTTAAGCAGA
Done.