Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 133 of 427
Found at i:35737412 original size:14 final size:14
Alignment explanation
Indices: 35737393--35737426 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
35737383 TTAATATTTT
35737393 AATAATAAATTTAA
1 AATAATAAATTTAA
*
35737407 AATAAT-AATTTTA
1 AATAATAAATTTAA
35737420 AATAATA
1 AATAATA
35737427 TTATTCACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAATAAATTTAA
Found at i:35738193 original size:31 final size:28
Alignment explanation
Indices: 35738158--35738235 Score: 77
Period size: 31 Copynumber: 2.6 Consensus size: 28
35738148 AATAATTAGT
35738158 TAATTTTTTAATTTAAAAATATATATTTTTA
1 TAATTTTTTAATTTAAAAATA-A-A-TTTTA
*
35738189 TAATTATTTTTA-TTAAAAATAAATTTTA
1 TAATT-TTTTAATTTAAAAATAAATTTTA
* *
35738217 TCATTTTTAAAATTTAAAA
1 TAATTTTT-TAATTTAAAA
35738236 CATTAATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
27 3 0.08
28 10 0.25
29 7 0.17
30 1 0.03
31 14 0.35
32 5 0.12
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (28 bp):
TAATTTTTTAATTTAAAAATAAATTTTA
Found at i:35739098 original size:22 final size:22
Alignment explanation
Indices: 35739057--35739099 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
35739047 TATCTAAATA
*
35739057 ATAATAACAAAATAGTAACAAC
1 ATAATAACAAAATAGCAACAAC
* *
35739079 ATAATAATAAAATGGCAACAA
1 ATAATAACAAAATAGCAACAA
35739100 AACAATGGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.63, C:0.12, G:0.07, T:0.19
Consensus pattern (22 bp):
ATAATAACAAAATAGCAACAAC
Found at i:35740422 original size:27 final size:27
Alignment explanation
Indices: 35740391--35740495 Score: 133
Period size: 27 Copynumber: 3.9 Consensus size: 27
35740381 CTGCCAGAAT
* *
35740391 AGATAATGTGACAGAGGCACCAGATAC
1 AGATAATGTGGCAGAGCCACCAGATAC
35740418 AGATAATCGTGGCAGAGCCACCAGA-AC
1 AGATAAT-GTGGCAGAGCCACCAGATAC
*
35740445 AGAAATATGTGGCAGAGCCACCAGAT-C
1 AGATA-ATGTGGCAGAGCCACCAGATAC
*
35740472 AGATAATTGTGGCATAGCCACCAG
1 AGATAA-TGTGGCAGAGCCACCAG
35740496 GACGCTTCCT
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
26 1 0.01
27 51 0.74
28 17 0.25
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (27 bp):
AGATAATGTGGCAGAGCCACCAGATAC
Found at i:35741927 original size:24 final size:24
Alignment explanation
Indices: 35741900--35741969 Score: 115
Period size: 23 Copynumber: 3.0 Consensus size: 24
35741890 CTAGATTTCC
**
35741900 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
35741924 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
35741948 -CCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
35741970 TCCTGACAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
23 22 0.50
24 22 0.50
ACGTcount: A:0.26, C:0.39, G:0.01, T:0.34
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:35748248 original size:27 final size:26
Alignment explanation
Indices: 35748211--35748322 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
35748201 AGCATGGCTG
* *
35748211 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
35748237 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
35748265 CCAGAACAGAAATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
35748292 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
35748319 CCAG
1 CCAG
35748323 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 6 0.08
27 53 0.70
28 17 0.22
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:35748303 original size:54 final size:54
Alignment explanation
Indices: 35748211--35748322 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
35748201 AGCATGGCTG
* *
35748211 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* * *
35748265 CCAGAACAGAAATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGAAA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
35748319 CCAG
1 CCAG
35748323 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (54 bp):
CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:35749762 original size:24 final size:24
Alignment explanation
Indices: 35749735--35749809 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
35749725 CTAGATTTCC
**
35749735 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
35749759 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
*
35749783 CCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
35749807 TCC
1 TCC
35749810 TGACAGACTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.25, C:0.40, G:0.01, T:0.33
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:35762749 original size:79 final size:82
Alignment explanation
Indices: 35762609--35762793 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 82
35762599 TCGAATGATG
* * *
35762609 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
* *
35762673 CGTGTGAGTTAATA-AA
66 CGTGCGAGTCAATATAA
* **
35762689 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCAT
*
35762751 TCGTGCGAGTCACTATAA
65 TCGTGCGAGTCAATATAA
**
35762769 -CCGGGCTTCGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
35762794 AGCGAGTCGT
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 55 0.61
80 34 0.38
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (82 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTCAATATAA
Found at i:35762801 original size:40 final size:40
Alignment explanation
Indices: 35762610--35762801 Score: 142
Period size: 40 Copynumber: 4.8 Consensus size: 40
35762600 CGAATGATGT
* * * * *
35762610 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTCACTAAAC
** * * * * * *
35762650 CCGGACTAGGAT-CCGAAGGCATTCGTGTGAGTTAATAAAT
1 CCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTCACTAAAC
* * *
35762690 CCGGGCTAAG-CCCGAAGGCATTTGTGCAAGTTACTAAAC
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAAC
*
35762729 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCACTATAA-
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTA-AAC
* *
35762769 CCGGGCTT-CGTCCCGAAGGCATTTGAGCGAGTC
1 CCGGG-TTAAGTCCCGAAGGCATTTGTGCGAGTC
35762802 GTTATATCCG
Statistics
Matches: 124, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
39 32 0.26
40 82 0.66
41 10 0.08
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.23
Consensus pattern (40 bp):
CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAAC
Found at i:35762824 original size:79 final size:79
Alignment explanation
Indices: 35762609--35762826 Score: 174
Period size: 79 Copynumber: 2.7 Consensus size: 79
35762599 TCGAATGATG
* * * * ** *
35762609 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAGGA-TCCGAAGGCAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGAGC-AAGTCACTAAACCCGGGTTA-AATTCCGAAGGCAT
* *
35762672 TCGTGTGAGTTAATAAA
63 TCGTGCGAGTCAATAAA
* * * *
35762689 TCCGGGCTAAGCCCGAAGGCATTTGTGCAAGTTACTAAACCCGGGTTAAGTCCCGAAGGCATTCG
1 TCCGGGCTAAGCCCGAAGGCATTTGAGCAAGTCACTAAACCCGGGTTAAATTCCGAAGGCATTCG
*
35762754 TGCGAGTCACTATAA
66 TGCGAGTCAATA-AA
** * ** * *
35762769 -CCGGGCTTCGTCCCGAAGGCATTTGAGCGAGTCGTTATATCC-GGTTAAATTCCGAAGG
1 TCCGGGCTAAG-CCCGAAGGCATTTGAGCAAGTCACTAAACCCGGGTTAAATTCCGAAGG
35762827 TACGTGATTC
Statistics
Matches: 112, Mismatches: 22, Indels: 9
0.78 0.15 0.06
Matches are distributed among these distances:
79 68 0.61
80 44 0.39
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGCTAAGCCCGAAGGCATTTGAGCAAGTCACTAAACCCGGGTTAAATTCCGAAGGCATTCG
TGCGAGTCAATAAA
Found at i:35767736 original size:2 final size:2
Alignment explanation
Indices: 35767729--35767757 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35767719 TAAATGCAAA
35767729 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35767758 AAATAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35768421 original size:19 final size:19
Alignment explanation
Indices: 35768397--35768441 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
35768387 TTAAATTTAA
*
35768397 TTTAATTTTATATTAATTT
1 TTTAATTATATATTAATTT
35768416 TTTAATTATATATTAATTT
1 TTTAATTATATATTAATTT
*
35768435 ATTAATT
1 TTTAATT
35768442 GATTCATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTAATTATATATTAATTT
Found at i:35770326 original size:21 final size:21
Alignment explanation
Indices: 35770301--35770350 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
35770291 TGTAATCGAT
*
35770301 TATTTTTACA-TTATTTTTATA
1 TATTTTTA-ATTTACTTTTATA
35770322 TATTTTTTAATTTACTTTTATA
1 TA-TTTTTAATTTACTTTTATA
35770344 -ATTTTTA
1 TATTTTTA
35770351 TAATATTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.23
21 4 0.15
22 16 0.62
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTTTAATTTACTTTTATA
Found at i:35774194 original size:2 final size:2
Alignment explanation
Indices: 35774187--35774223 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
35774177 TTTAATTATT
35774187 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
35774224 TAGGGAAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35775125 original size:26 final size:25
Alignment explanation
Indices: 35775069--35775127 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
35775059 CTCAACTCTC
35775069 ATTTTTTTATTAAATTTGTATTAAGG
1 ATTTTTTTATTAAATTTGTATTAA-G
* * *
35775095 GTTTTTTAATT-AATATTGTATTATG
1 ATTTTTTTATTAAAT-TTGTATTAAG
35775120 ATTTTTTT
1 ATTTTTTT
35775128 GTATTTATTG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (25 bp):
ATTTTTTTATTAAATTTGTATTAAG
Found at i:35776089 original size:52 final size:52
Alignment explanation
Indices: 35776008--35776111 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
35775998 ATAGTTTGAG
* *
35776008 TTATTTGAGTTATTCAGATTAACTTGAATAAAAAAATCAAACTTTTCGGTTT
1 TTATTTAAGTTATTCAGATTAACTCGAATAAAAAAATCAAACTTTTCGGTTT
35776060 TTATTTAAGTTATTCAGATTAACTCGAATAAAAAAATCAAACTTTTCGGTTT
1 TTATTTAAGTTATTCAGATTAACTCGAATAAAAAAATCAAACTTTTCGGTTT
35776112 AACTCGAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (52 bp):
TTATTTAAGTTATTCAGATTAACTCGAATAAAAAAATCAAACTTTTCGGTTT
Found at i:35780719 original size:39 final size:39
Alignment explanation
Indices: 35780676--35780751 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
35780666 CAGACTTATT
35780676 GTTACAAAATTTTGACATAAAATAGCCATTTTCTATGTG
1 GTTACAAAATTTTGACATAAAATAGCCATTTTCTATGTG
35780715 GTTACAAAATTTTGACATAAAATAGCCATTTTCTATG
1 GTTACAAAATTTTGACATAAAATAGCCATTTTCTATG
35780752 AAAACTCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (39 bp):
GTTACAAAATTTTGACATAAAATAGCCATTTTCTATGTG
Found at i:35781680 original size:87 final size:87
Alignment explanation
Indices: 35781574--35781746 Score: 274
Period size: 87 Copynumber: 2.0 Consensus size: 87
35781564 AAACTTCTAA
* * *
35781574 GTCAAATTATAAATAAGAAAAATATCTCTAGAAATTTATTAAAATAATTTCTTTAGAGAATTTTC
1 GTCAAATTAAAAATAAGAAAAATATCTCTAGAAATTTATTAAAATAATTTCTTCAAAGAATTTTC
*
35781639 TCTCTACAATTTTCTCTTGAAG
66 TCTCTACAACTTTCTCTTGAAG
* * *
35781661 GTCAAGTTAAAAATAAGAAAAGTATCTCTAGAAATTTTTTAAAATAATTTCTTCAAAGAATTTTC
1 GTCAAATTAAAAATAAGAAAAATATCTCTAGAAATTTATTAAAATAATTTCTTCAAAGAATTTTC
*
35781726 TCTCTATAACTTTCTCTTGAA
66 TCTCTACAACTTTCTCTTGAA
35781747 TTCAAGTGTA
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 78 1.00
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (87 bp):
GTCAAATTAAAAATAAGAAAAATATCTCTAGAAATTTATTAAAATAATTTCTTCAAAGAATTTTC
TCTCTACAACTTTCTCTTGAAG
Found at i:35781953 original size:68 final size:69
Alignment explanation
Indices: 35781828--35781958 Score: 201
Period size: 68 Copynumber: 1.9 Consensus size: 69
35781818 TAAACTTAAT
* * *
35781828 CACTTGAATATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAGA
1 CACTTGAATATTAAATTAAAAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAGA
35781893 CAAC
66 CAAC
* * *
35781897 CACTTTAATATTAAATTAAAAAAATAC-TATCAAGATAAGTATTAAATTTAATTTAATATTAA
1 CACTTGAATATTAAATTAAAAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAA
35781959 AACTATTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
68 32 0.57
69 24 0.43
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (69 bp):
CACTTGAATATTAAATTAAAAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAGA
CAAC
Found at i:35781974 original size:68 final size:69
Alignment explanation
Indices: 35781834--35781977 Score: 173
Period size: 68 Copynumber: 2.1 Consensus size: 69
35781824 TAATCACTTG
* * * *
35781834 AATATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAGACAACCA
1 AATATTAAATTAAAAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAAACAACCA
***
35781899 CTTT
66 AAAT
* * * **
35781903 AATATTAAATTAAAAAAATAC-TATCAAGATAAGTATTAAATTTAATTTAATATTAAAACTATTA
1 AATATTAAATTAAAAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAAACAACCA
35781967 AAAT
66 AAAT
35781971 AATATTA
1 AATATTA
35781978 TTTTTGAAAT
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
68 44 0.70
69 19 0.30
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (69 bp):
AATATTAAATTAAAAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAAACAACCA
AAAT
Found at i:35789906 original size:13 final size:14
Alignment explanation
Indices: 35789875--35789907 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
35789865 AATGCTTTTG
35789875 TAAAATTATAAACA
1 TAAAATTATAAACA
*
35789889 TAAAATTA-AAATA
1 TAAAATTATAAACA
35789902 TAAAAT
1 TAAAAT
35789908 AAGATTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAAATTATAAACA
Found at i:35789930 original size:6 final size:6
Alignment explanation
Indices: 35789916--35789948 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
35789906 ATAAGATTGA
*
35789916 ATAAGT ATAAAT ATAAAT ATAAAT ATAAAT ATA
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATA
35789949 TTAAATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (6 bp):
ATAAAT
Found at i:35801354 original size:18 final size:19
Alignment explanation
Indices: 35801331--35801373 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
35801321 CTAAAGAATC
*
35801331 TATATAACA-AAATTAAAA
1 TATATAAAATAAATTAAAA
35801349 TATATAAAATAAATTAAAA
1 TATATAAAATAAATTAAAA
35801368 TA-ATAA
1 TATATAA
35801374 GATTATTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
TATATAAAATAAATTAAAA
Found at i:35826209 original size:23 final size:23
Alignment explanation
Indices: 35826166--35826209 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
35826156 CATCATAATA
*
35826166 TCATCTATTTCATATCACAAAAC
1 TCATCTATATCATATCACAAAAC
*
35826189 TCATC-ATATCATCATCTCAAA
1 TCATCTATATCAT-ATCACAAA
35826210 CCAAACCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.34
Consensus pattern (23 bp):
TCATCTATATCATATCACAAAAC
Found at i:35830265 original size:8 final size:8
Alignment explanation
Indices: 35830254--35830278 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
35830244 GTGTTTTTGG
35830254 GGTTTTAA
1 GGTTTTAA
35830262 GGTTTTAA
1 GGTTTTAA
35830270 GGTTTTAA
1 GGTTTTAA
35830278 G
1 G
35830279 AGATTAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (8 bp):
GGTTTTAA
Found at i:35836142 original size:49 final size:49
Alignment explanation
Indices: 35836088--35836185 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
35836078 CTTCAAGAGA
35836088 TAGAAATGGAGAATAAATCAAATCTTGATTAGGGGTGATTAGCTCACTT
1 TAGAAATGGAGAATAAATCAAATCTTGATTAGGGGTGATTAGCTCACTT
*
35836137 TAGAAATGGAGAATAAATCAAATCTTGATTAGGGGTGATTAGCTTACTT
1 TAGAAATGGAGAATAAATCAAATCTTGATTAGGGGTGATTAGCTCACTT
35836186 CGGTAATCTC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (49 bp):
TAGAAATGGAGAATAAATCAAATCTTGATTAGGGGTGATTAGCTCACTT
Found at i:35844192 original size:48 final size:48
Alignment explanation
Indices: 35844118--35844491 Score: 392
Period size: 48 Copynumber: 7.8 Consensus size: 48
35844108 TAAATTTCCA
* * * * *
35844118 ATGCCATATCCCAGATATGGTCTTACACTGGCTCACATGTCGAGGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCAAGGCCG
* * * * * * * *
35844166 ATGCCATGTCCCAAACATGGTTTTACACTAGCTCTCTTCTTAATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCAAGGCCG
* * *
35844214 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATGTCGAGGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCAAGGCCG
* * *
35844262 ATGCCATATCCCAGACATGGTCTTACACTGGCTCACATGTCGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCAAGGCCG
* * * * * *
35844310 ATACCATGTCCCAGACATGGACTTACACTAGCTCTCGTCTCAATGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCAAGGCCG
* * * *
35844358 ATGCCATGTCCCAGGCATGGTCTTACACTAG-TGCACATATCAACGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCT-CACATGTCAAGGCCG
* * ** * *
35844406 ATGCCATGTCCCAAACATGGTCTTACACTAACTCTTATAAT-ATGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-GTCAAGGCCG
*
35844454 ATGCCATGTCCCAGACATGGTCTTACACTAGCACACAT
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT
35844492 ATCACTCAAT
Statistics
Matches: 267, Mismatches: 56, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
47 1 0.00
48 263 0.99
49 3 0.01
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCAAGGCCG
Found at i:35844378 original size:144 final size:144
Alignment explanation
Indices: 35844118--35844485 Score: 483
Period size: 144 Copynumber: 2.6 Consensus size: 144
35844108 TAAATTTCCA
* * *
35844118 ATGCCATATCCCAGATATGGTCTTACACTGGCTCACATGTCGAGGCTGATGCCATGTCCCAAACA
1 ATGCCATATCCCAGACATGGTCTTACACTGGCTCACATGTCGAGGCCGATGCCATGTCCCAGACA
* * * *
35844183 TGGTTTTACACTAGCTCTCTTCTTAATGCCAATGCCATGTCCCAGACATGGTCTTACACTGGCT-
66 TGGTCTTACACTAGCTCTCGTCTCAATGCCAATGCCATGTCCCAGACATGGTCTTACACTAG-TG
* * *
35844247 CACATGTCGA-GGTCG
130 CACATATCAACGCT-G
*
35844262 ATGCCATATCCCAGACATGGTCTTACACTGGCTCACATGTCGAGGCCGATACCATGTCCCAGACA
1 ATGCCATATCCCAGACATGGTCTTACACTGGCTCACATGTCGAGGCCGATGCCATGTCCCAGACA
* * *
35844327 TGGACTTACACTAGCTCTCGTCTCAATGCCGATGCCATGTCCCAGGCATGGTCTTACACTAGTGC
66 TGGTCTTACACTAGCTCTCGTCTCAATGCCAATGCCATGTCCCAGACATGGTCTTACACTAGTGC
35844392 ACATATCAACGCTG
131 ACATATCAACGCTG
* * ** ** *
35844406 ATGCCATGTCCCAAACATGGTCTTACACTAACTCTTATAAT--ATGGCCGATGCCATGTCCCAGA
1 ATGCCATATCCCAGACATGGTCTTACACTGGCTCACAT-GTCGA-GGCCGATGCCATGTCCCAGA
35844469 CATGGTCTTACACTAGC
64 CATGGTCTTACACTAGC
35844486 ACACATATCA
Statistics
Matches: 197, Mismatches: 23, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
143 2 0.01
144 192 0.97
145 3 0.02
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (144 bp):
ATGCCATATCCCAGACATGGTCTTACACTGGCTCACATGTCGAGGCCGATGCCATGTCCCAGACA
TGGTCTTACACTAGCTCTCGTCTCAATGCCAATGCCATGTCCCAGACATGGTCTTACACTAGTGC
ACATATCAACGCTG
Found at i:35846261 original size:22 final size:22
Alignment explanation
Indices: 35846228--35846270 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
35846218 TATATTGTTC
35846228 AATTCTAATTTGAATTCTTGGT
1 AATTCTAATTTGAATTCTTGGT
*
35846250 AATT-TAAGTTTGATTTCTTGG
1 AATTCTAA-TTTGAATTCTTGG
35846271 ACATAACTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.26, C:0.07, G:0.16, T:0.51
Consensus pattern (22 bp):
AATTCTAATTTGAATTCTTGGT
Found at i:35849419 original size:17 final size:18
Alignment explanation
Indices: 35849397--35849430 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
35849387 TTGGTTTTTT
35849397 TTTTTAAAATT-TTGTTC
1 TTTTTAAAATTATTGTTC
*
35849414 TTTTTAGAATTATTGTT
1 TTTTTAAAATTATTGTT
35849431 AAGATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.24, C:0.03, G:0.09, T:0.65
Consensus pattern (18 bp):
TTTTTAAAATTATTGTTC
Found at i:35850037 original size:29 final size:29
Alignment explanation
Indices: 35849968--35850038 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
35849958 TCTACTTTGA
* * * *
35849968 AAATGTCCAACGTGGTACTTGTAATTTGG
1 AAATGTCCAATGTAGTACTCGTAATTTAG
**
35849997 AAATGTAAAATGTAGTACTCGTAATTTAG
1 AAATGTCCAATGTAGTACTCGTAATTTAG
35850026 AAATGTCCAATGT
1 AAATGTCCAATGT
35850039 GATAACTGAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (29 bp):
AAATGTCCAATGTAGTACTCGTAATTTAG
Found at i:35850377 original size:19 final size:19
Alignment explanation
Indices: 35850323--35850377 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
35850313 AAAAATAGAT
35850323 TTTTTATATATTTTAA-TAA
1 TTTTTATAT-TTTTAATTAA
* * **
35850342 TTTTAAAATTTAAAATTAA
1 TTTTTATATTTTTAATTAA
35850361 TTTTTATATTTTTAATT
1 TTTTTATATTTTTAATT
35850378 TTAAATATTT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTATATTTTTAATTAA
Found at i:35871480 original size:20 final size:22
Alignment explanation
Indices: 35871431--35871499 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 22
35871421 AGAGTAGTAT
*
35871431 AGTCTTGAGACTTACTAGTCTA
1 AGTCTCGAGACTTACTAGTCTA
* *
35871453 AGTATCGAGACTTAC-CGT-TA
1 AGTCTCGAGACTTACTAGTCTA
* * *
35871473 AGTCTCGAGCCTTATTTGTCT-
1 AGTCTCGAGACTTACTAGTCTA
35871494 AGTCTC
1 AGTCTC
35871500 AACACTTCAA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
20 14 0.37
21 10 0.26
22 14 0.37
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (22 bp):
AGTCTCGAGACTTACTAGTCTA
Found at i:35881145 original size:29 final size:29
Alignment explanation
Indices: 35881103--35881163 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
35881093 TCGTGAATAC
35881103 TTAGAATATAAATGACATGCCATTAGGGA
1 TTAGAATATAAATGACATGCCATTAGGGA
*
35881132 TTAGAATATAAATGACATGTCATTAGGGA
1 TTAGAATATAAATGACATGCCATTAGGGA
35881161 TTA
1 TTA
35881164 ACAGTTTTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (29 bp):
TTAGAATATAAATGACATGCCATTAGGGA
Found at i:35884584 original size:30 final size:30
Alignment explanation
Indices: 35884550--35884609 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
35884540 ACTTAACATG
*
35884550 CAAATACCTCTAAAATAATAATAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
* *
35884580 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
35884610 TAATAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:35885159 original size:10 final size:10
Alignment explanation
Indices: 35885144--35885170 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
35885134 AATCACCCTA
35885144 GGCCCATATT
1 GGCCCATATT
35885154 GGCCCATATT
1 GGCCCATATT
35885164 GGCCCAT
1 GGCCCAT
35885171 TAGGCCATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.33, G:0.22, T:0.26
Consensus pattern (10 bp):
GGCCCATATT
Found at i:35890838 original size:12 final size:12
Alignment explanation
Indices: 35890821--35890845 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35890811 TTGCTTATAG
35890821 TTTTTTATTTTA
1 TTTTTTATTTTA
35890833 TTTTTTATTTTA
1 TTTTTTATTTTA
35890845 T
1 T
35890846 ATACTTTAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTATTTTA
Found at i:35892928 original size:144 final size:144
Alignment explanation
Indices: 35892668--35892962 Score: 563
Period size: 144 Copynumber: 2.0 Consensus size: 144
35892658 TGTCTTAGTA
35892668 ATATTGAACACGATACAAACATGGCATATAAAAAATAAATATAACATATGACATGAAAAAATGAC
1 ATATTGAACACGATACAAACATGGCATATAAAAAATAAATATAACATATGACATGAAAAAATGAC
*
35892733 TCGAATATATGGACTGTCAGATCTAATGCTGCATTCATGTGGAACTCACTAACATATGCTTCTTT
66 TCGAATATATGGACTGTCAGATCTAATACTGCATTCATGTGGAACTCACTAACATATGCTTCTTT
35892798 ACTCTTGAGCAGGT
131 ACTCTTGAGCAGGT
*
35892812 ATATTGAACACGATACAAACATGGCATATAAAAAATAAATATATCATATGACATGAAAAAATGAC
1 ATATTGAACACGATACAAACATGGCATATAAAAAATAAATATAACATATGACATGAAAAAATGAC
35892877 TCGAATATATGGACTGTCAGATCTAATACTGCATTCATGTGGAACTCACTAACATATGCTTCTTT
66 TCGAATATATGGACTGTCAGATCTAATACTGCATTCATGTGGAACTCACTAACATATGCTTCTTT
35892942 ACTCTTGAGCAGGT
131 ACTCTTGAGCAGGT
35892956 ATCATTG
1 AT-ATTG
35892963 GCCTTCAATC
Statistics
Matches: 148, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
144 144 0.97
145 4 0.03
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (144 bp):
ATATTGAACACGATACAAACATGGCATATAAAAAATAAATATAACATATGACATGAAAAAATGAC
TCGAATATATGGACTGTCAGATCTAATACTGCATTCATGTGGAACTCACTAACATATGCTTCTTT
ACTCTTGAGCAGGT
Found at i:35893880 original size:14 final size:14
Alignment explanation
Indices: 35893861--35893890 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
35893851 GATAATGTCT
35893861 ATGAAGGCAAAGAA
1 ATGAAGGCAAAGAA
35893875 ATGAAGGCAAAGAA
1 ATGAAGGCAAAGAA
35893889 AT
1 AT
35893891 AGGAGGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.57, C:0.07, G:0.27, T:0.10
Consensus pattern (14 bp):
ATGAAGGCAAAGAA
Found at i:35895313 original size:23 final size:23
Alignment explanation
Indices: 35895285--35895330 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
35895275 AGATATGATA
35895285 TGTAATCTTAGAAGATATAATTT
1 TGTAATCTTAGAAGATATAATTT
*
35895308 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
35895331 GTAGATATCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.43
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:35903376 original size:31 final size:31
Alignment explanation
Indices: 35903341--35903400 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
35903331 TAATGGACTG
*
35903341 CTAGGGACTTAAGGAGAAATCGGCCTAACTA
1 CTAGGGACTTAAGGAGAAATCAGCCTAACTA
35903372 CTAGGGACTTAAGGAGAAATCAGCCTAAC
1 CTAGGGACTTAAGGAGAAATCAGCCTAAC
35903401 ATGAGTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.18
Consensus pattern (31 bp):
CTAGGGACTTAAGGAGAAATCAGCCTAACTA
Found at i:35903981 original size:41 final size:43
Alignment explanation
Indices: 35903871--35904013 Score: 132
Period size: 43 Copynumber: 3.4 Consensus size: 43
35903861 GTGTGATTCG
* * * * * *
35903871 TGTAAGACCATGTCTGGGACATTGGCATC-AAAGTGA-GAAAACG
1 TGTAAGACCATGTCTGAGACAGTGGCATCGATA-T-ATGATAGCA
* * *
35903914 TGTAAGACTATGTCTGGGACATTGGCATC-ATATATGATA-CA
1 TGTAAGACCATGTCTGAGACAGTGGCATCGATATATGATAGCA
* *
35903955 TGTAAGACCCTGTCTGAGACAGTGGCATCGATATGTGATAGCA
1 TGTAAGACCATGTCTGAGACAGTGGCATCGATATATGATAGCA
*
35903998 TGTAAGACCATATCTG
1 TGTAAGACCATGTCTG
35904014 GGATATGACA
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
41 27 0.31
42 13 0.15
43 46 0.53
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (43 bp):
TGTAAGACCATGTCTGAGACAGTGGCATCGATATATGATAGCA
Found at i:35907658 original size:77 final size:77
Alignment explanation
Indices: 35907570--35907868 Score: 474
Period size: 77 Copynumber: 3.9 Consensus size: 77
35907560 AATTCAAATC
* *
35907570 TTATCATTCTTTAAAATTTAAATTGAATTAAAATTCCATCATCTTTTTAACTTCTTATCCTAATT
1 TTATCATTCTTTAAAATTTAAATAGAATTAAAATTCCATCATCTTTTTATCTTCTTATCCTAATT
35907635 TGAAATCATATA
66 TGAAATCATATA
* * * *
35907647 TTATCCTTCTTTAAAATTTAAATAAAATTAAAATTTCATCATCTTTTTATCTTATTATCCTAATT
1 TTATCATTCTTTAAAATTTAAATAGAATTAAAATTCCATCATCTTTTTATCTTCTTATCCTAATT
*
35907712 TAAAATCATATA
66 TGAAATCATATA
* *
35907724 TTATCATTCTTTAAAATTTAAATAGAAATAAAATTTCATCATCTTTTTATCTTCTTATCCTAATT
1 TTATCATTCTTTAAAATTTAAATAGAATTAAAATTCCATCATCTTTTTATCTTCTTATCCTAATT
* *
35907789 TGAAATCACATC
66 TGAAATCATATA
* *
35907801 TTATCCTTCTTTAAAATTTAAATAGAATTAAAATTCCAT-ATCTTTTTACCTTCTTATCCTAATT
1 TTATCATTCTTTAAAATTTAAATAGAATTAAAATTCCATCATCTTTTTATCTTCTTATCCTAATT
35907865 TGAA
66 TGAA
35907869 TTTCAAATTA
Statistics
Matches: 204, Mismatches: 18, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
76 28 0.14
77 176 0.86
ACGTcount: A:0.36, C:0.15, G:0.02, T:0.47
Consensus pattern (77 bp):
TTATCATTCTTTAAAATTTAAATAGAATTAAAATTCCATCATCTTTTTATCTTCTTATCCTAATT
TGAAATCATATA
Found at i:35908008 original size:15 final size:15
Alignment explanation
Indices: 35907988--35908021 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
35907978 TCACATCCCA
*
35907988 AAAATTGGGTTAGCG
1 AAAATTGGATTAGCG
*
35908003 AAAATTGGATTAGTG
1 AAAATTGGATTAGCG
35908018 AAAA
1 AAAA
35908022 ATGAGAGTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.26, T:0.26
Consensus pattern (15 bp):
AAAATTGGATTAGCG
Found at i:35915038 original size:15 final size:15
Alignment explanation
Indices: 35915018--35915050 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
35915008 TCATATCCCA
*
35915018 AAAATTGGGTTAGTG
1 AAAATTGGATTAGTG
35915033 AAAATTGGATTAGTG
1 AAAATTGGATTAGTG
35915048 AAA
1 AAA
35915051 CGTGAGAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.30
Consensus pattern (15 bp):
AAAATTGGATTAGTG
Found at i:35917163 original size:28 final size:28
Alignment explanation
Indices: 35917124--35917187 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
35917114 AAGAATAATT
*
35917124 TTTTTCTATTTTTAATAAAATTTAA-ATA
1 TTTTTATATTTTTAATAAAATTTAATA-A
*
35917152 TTTTTATATTTTTATTAAAATTTAATAA
1 TTTTTATATTTTTAATAAAATTTAATAA
35917180 TTTTTATA
1 TTTTTATA
35917188 ACTTTTATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 32 0.97
29 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTTATATTTTTAATAAAATTTAATAA
Found at i:35917215 original size:9 final size:9
Alignment explanation
Indices: 35917151--35917219 Score: 54
Period size: 9 Copynumber: 7.7 Consensus size: 9
35917141 AAATTTAAAT
35917151 ATTTTTAT-
1 ATTTTTATA
35917159 ATTTTTATTAA
1 ATTTTTA-T-A
* *
35917170 AATTTAATA
1 ATTTTTATA
35917179 ATTTTTATA
1 ATTTTTATA
* *
35917188 ACTTTTATTG
1 ATTTTTA-TA
35917198 A-TTTT-TA
1 ATTTTTATA
35917205 ATTTTTATA
1 ATTTTTATA
35917214 ATTTTT
1 ATTTTT
35917220 TGCCATATGT
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
7 2 0.04
8 11 0.23
9 27 0.56
10 3 0.06
11 5 0.10
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (9 bp):
ATTTTTATA
Found at i:35917513 original size:87 final size:86
Alignment explanation
Indices: 35917320--35917630 Score: 331
Period size: 86 Copynumber: 3.6 Consensus size: 86
35917310 GGTTAAAGAG
* * * ** * *
35917320 CCTTTTTAATGCATTTT-ACAGTTCAAATACCTAATTGAGTGTAAAAAAAAAAGGGGCTTAATTT
1 CCTTTTTAATGCATTTTGAAAGTTCAAATACCCAATTGAGTGCAAAAAAAGTAGGGACTTAATTG
** * *
35917384 TTCTTTTTTTTAA-TTTGAGGG
66 TT-TTTTTTGAAAGTTTGATGA
* *
35917405 CTTTTTTAATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAGTAGGGACTTAATTG
1 CCTTTTTAATGCATTTTGAAAGTTCAAATACCCAATTGAGTGCAAAAAAAGTAGGGACTTAATTG
35917470 TTTTTTCTTGAAAGTTTGATGA
66 TTTTTT-TTGAAAGTTTGATGA
* * * * * *
35917492 TCTTTTTGATGCATTTTGAAAGTTCCAATACCTAATTGAATGCAAAAAAAAGGTAAGGACTTAAT
1 CCTTTTTAATGCATTTTGAAAGTTCAAATACCCAATTGAGTGC-AAAAAAA-GTAGGGACTTAAT
*
35917557 TGCTTTTTTTGAAAAAGTTTGATGA
64 TGTTTTTTTTG--AAAGTTTGATGA
* * * *
35917582 CCTTTTTGATACATTTTGAAAGTTCAAATA-TCAATTGAGTGTAAAAAAA
1 CCTTTTTAATGCATTTTGAAAGTTCAAATACCCAATTGAGTGCAAAAAAA
35917631 AAAGTATTTA
Statistics
Matches: 190, Mismatches: 29, Indels: 11
0.83 0.13 0.05
Matches are distributed among these distances:
85 20 0.11
86 45 0.24
87 42 0.22
88 17 0.09
89 27 0.14
90 39 0.21
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (86 bp):
CCTTTTTAATGCATTTTGAAAGTTCAAATACCCAATTGAGTGCAAAAAAAGTAGGGACTTAATTG
TTTTTTTTGAAAGTTTGATGA
Found at i:35917632 original size:90 final size:86
Alignment explanation
Indices: 35917320--35917631 Score: 305
Period size: 87 Copynumber: 3.6 Consensus size: 86
35917310 GGTTAAAGAG
* * *
35917320 CCTTTTTAATGCATTTT-ACAGTTCAAATACCTAATTGAGTGTAAAAAAAA--AAGGGGCTTAAT
1 CCTTTTTGATGCATTTTGAAAGTTCAAATACC-AATTGAGTG-AAAAAAAAGTAA-GGACTTAA-
* * * *
35917382 TTTTCTTTTT-TT-TAA-TTTGAGGG
62 -TTGCTTTTTCTTGAAAGTTTGATGA
* * * * *
35917405 CTTTTTTAATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAGTAGGGACTTAATTG
1 CCTTTTTGATGCATTTTGAAAGTTCAAATA-CCAATTGAGTGAAAAAAAAGTAAGGACTTAATTG
*
35917470 TTTTTTCTTGAAAGTTTGATGA
65 CTTTTTCTTGAAAGTTTGATGA
* * *
35917492 TCTTTTTGATGCATTTTGAAAGTTCCAATACCTAATTGAATGCAAAAAAAAGGTAAGGACTTAAT
1 CCTTTTTGATGCATTTTGAAAGTTCAAATACC-AATTGAGTG-AAAAAAAA-GTAAGGACTTAAT
35917557 TGCTTTTT-TTGAAAAAGTTTGATGA
63 TGCTTTTTCTTG--AAAGTTTGATGA
* *
35917582 CCTTTTTGATACATTTTGAAAGTTCAAATATCAATTGAGTGTAAAAAAAA
1 CCTTTTTGATGCATTTTGAAAGTTCAAATACCAATTGAGTG-AAAAAAAA
35917632 AAGTATTTAA
Statistics
Matches: 189, Mismatches: 26, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
84 7 0.04
85 25 0.13
86 30 0.16
87 42 0.22
88 10 0.05
89 35 0.19
90 40 0.21
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (86 bp):
CCTTTTTGATGCATTTTGAAAGTTCAAATACCAATTGAGTGAAAAAAAAGTAAGGACTTAATTGC
TTTTTCTTGAAAGTTTGATGA
Found at i:35919812 original size:121 final size:121
Alignment explanation
Indices: 35919598--35919841 Score: 488
Period size: 121 Copynumber: 2.0 Consensus size: 121
35919588 AATTAGGTGA
35919598 TAACCTATTAGATTCATGCATTATCCTTAAAATGTGACATTCAACAAGTTAATACTTAAAAATAG
1 TAACCTATTAGATTCATGCATTATCCTTAAAATGTGACATTCAACAAGTTAATACTTAAAAATAG
35919663 AAAAAGAGATTATAATTAATGAAATTAGAACTCAAACCTACTTAAATGTCACCTCT
66 AAAAAGAGATTATAATTAATGAAATTAGAACTCAAACCTACTTAAATGTCACCTCT
35919719 TAACCTATTAGATTCATGCATTATCCTTAAAATGTGACATTCAACAAGTTAATACTTAAAAATAG
1 TAACCTATTAGATTCATGCATTATCCTTAAAATGTGACATTCAACAAGTTAATACTTAAAAATAG
35919784 AAAAAGAGATTATAATTAATGAAATTAGAACTCAAACCTACTTAAATGTCACCTCT
66 AAAAAGAGATTATAATTAATGAAATTAGAACTCAAACCTACTTAAATGTCACCTCT
35919840 TA
1 TA
35919842 CAGCTAACTT
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 123 1.00
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.32
Consensus pattern (121 bp):
TAACCTATTAGATTCATGCATTATCCTTAAAATGTGACATTCAACAAGTTAATACTTAAAAATAG
AAAAAGAGATTATAATTAATGAAATTAGAACTCAAACCTACTTAAATGTCACCTCT
Found at i:35931259 original size:68 final size:70
Alignment explanation
Indices: 35931187--35931384 Score: 294
Period size: 71 Copynumber: 2.8 Consensus size: 70
35931177 ACACCCTGTA
* * * *
35931187 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
35931249 ATAAAT
65 ATAAAT
*
35931255 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
35931320 ATAAAT
65 ATAAAT
*
35931326 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
35931385 AGACAAATCG
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 24 0.20
69 3 0.02
70 1 0.01
71 93 0.77
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (70 bp):
GTAGCTAGGTCGCATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:35931298 original size:41 final size:41
Alignment explanation
Indices: 35931253--35931370 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
35931243 TGAAAGATAA
35931253 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
35931294 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
35931324 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
35931365 ATGTAG
1 ATGTAG
35931371 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:35931310 original size:71 final size:71
Alignment explanation
Indices: 35931221--35931384 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
35931211 GAGATGTATC
35931221 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
35931286 AGGACA
66 AGGACA
35931292 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
35931357 AGGACA
66 AGGACA
35931363 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
35931385 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:35933451 original size:65 final size:65
Alignment explanation
Indices: 35933341--35933508 Score: 218
Period size: 65 Copynumber: 2.6 Consensus size: 65
35933331 AGCCACATCA
* * * *
35933341 GGACGCACACAAAGAGCTACGTTTGTGTCGCAACATATGCAGGATCACAACTGATCGCATAAC-T
1 GGACGCTCACAAAGAGCTGCGTTTGTGTCACAACATATGCAGGATCACAACGGATCGCATAACAT
*
35933405 GGACGCTCACACAA-AGCTGCGTTTGTGTCTACAACATATGCAGGATCATAACGGATCGCATAAC
1 GGACGCTCACA-AAGAGCTGCGTTTGTGTC-ACAACATATGCAGGATCACAACGGATCGCATAAC
35933469 AT
64 AT
* * *
35933471 -GACGCTCACAAAGAGCTGCGGTAGTG-CACAACACATGC
1 GGACGCTCACAAAGAGCTGCGTTTGTGTCACAACATATGC
35933509 CAAATCACTA
Statistics
Matches: 92, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
63 10 0.11
64 27 0.29
65 54 0.59
66 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.20
Consensus pattern (65 bp):
GGACGCTCACAAAGAGCTGCGTTTGTGTCACAACATATGCAGGATCACAACGGATCGCATAACAT
Found at i:35935171 original size:15 final size:15
Alignment explanation
Indices: 35935151--35935179 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
35935141 TAATCTTTTA
35935151 AGCTTGAAAATTGAT
1 AGCTTGAAAATTGAT
35935166 AGCTTGAAAATTGA
1 AGCTTGAAAATTGA
35935180 CTTTAATACA
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:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (15 bp):
AGCTTGAAAATTGAT
Found at i:35939472 original size:46 final size:46
Alignment explanation
Indices: 35939405--35939533 Score: 222
Period size: 46 Copynumber: 2.8 Consensus size: 46
35939395 TGTAACCCGC
* * * *
35939405 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
35939451 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
35939497 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
35939534 TGCTCAACCA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:35939552 original size:46 final size:45
Alignment explanation
Indices: 35939413--35939552 Score: 140
Period size: 46 Copynumber: 3.0 Consensus size: 45
35939403 GCCCATAAGC
* ** * *
35939413 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTC-GCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-T-AGT
*** *
35939459 GAACTCGGACTCAACTCAACGAGTTCGGACATTC-GCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-T-AGT
35939505 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTC-ACCATCCTAGT
35939551 GA
1 GA
35939553 CATGTCACTT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
46 79 0.93
47 1 0.01
48 5 0.06
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCCTAGT
Found at i:35942764 original size:7 final size:7
Alignment explanation
Indices: 35942754--35942782 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
35942744 AAAAAAAAGT
35942754 AGAAATA
1 AGAAATA
35942761 AGAAATA
1 AGAAATA
35942768 AGAAATA
1 AGAAATA
35942775 AGAAATA
1 AGAAATA
35942782 A
1 A
35942783 AATTAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
AGAAATA
Found at i:35949845 original size:29 final size:29
Alignment explanation
Indices: 35949783--35949885 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
35949773 GTGACGAGAT
* * *
35949783 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* * *
35949812 CGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* *
35949841 TGGCACTATGTGTGCGGGCTT-GAATCATA
1 TGGCACTAAGTGTGCGAGCTTGGAAT-ATA
35949870 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
35949886 TGATTGAGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 3 0.05
29 58 0.95
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGGAATATA
Found at i:35957857 original size:29 final size:29
Alignment explanation
Indices: 35957795--35957897 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
35957785 GTGACGAGAT
* * *
35957795 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* * *
35957824 CGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* *
35957853 TGGCACTATGTGTGCGGGCTT-GAATCATA
1 TGGCACTAAGTGTGCGAGCTTGGAAT-ATA
35957882 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
35957898 TGATTGAGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 3 0.05
29 58 0.95
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGGAATATA
Found at i:35959705 original size:14 final size:14
Alignment explanation
Indices: 35959667--35959710 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
35959657 CAAAATGTAC
35959667 AATATAATTAAA-T
1 AATATAATTAAATT
35959680 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
35959695 AA-ATAATTTAATT
1 AATATAATTAAATT
35959708 AAT
1 AAT
35959711 TGTTTACCCG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:35963405 original size:17 final size:17
Alignment explanation
Indices: 35963383--35963418 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
35963373 CAAGACATGC
35963383 AAGCAAGAAGCCAAG-CA
1 AAGCAAGAA-CCAAGACA
35963400 AAGCAAGAACCAAGACA
1 AAGCAAGAACCAAGACA
35963417 AA
1 AA
35963419 ATTTCAGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.58, C:0.22, G:0.19, T:0.00
Consensus pattern (17 bp):
AAGCAAGAACCAAGACA
Found at i:35968335 original size:40 final size:40
Alignment explanation
Indices: 35968290--35968419 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
35968280 CGGAATACAA
35968290 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* * *
35968330 CCGGATAGAACGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * * *
35968370 CCGGATGTAGCCGCTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
35968410 CCGGATATAA
1 CCGGATATAA
35968420 TTTCCAGCAA
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 3 0.04
40 74 0.96
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.22
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:35976451 original size:40 final size:40
Alignment explanation
Indices: 35976406--35976535 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
35976396 CGGAATACAA
35976406 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* * *
35976446 CCGGATAGAACGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * * *
35976486 CCGGATGTAGCCGCTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
35976526 CCGGATATAA
1 CCGGATATAA
35976536 TTTCCAGCAA
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 3 0.04
40 74 0.96
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.22
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:35978836 original size:18 final size:18
Alignment explanation
Indices: 35978793--35978839 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
35978783 AATAATAGGG
*
35978793 AAAAA-TGTAATTTTTTC
1 AAAAAGTGTAAATTTTTC
35978810 AAAAAGTGTAAATTTTTC
1 AAAAAGTGTAAATTTTTC
*
35978828 AAAAGGTGTAAA
1 AAAAAGTGTAAA
35978840 CTGTGTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.47, C:0.04, G:0.13, T:0.36
Consensus pattern (18 bp):
AAAAAGTGTAAATTTTTC
Found at i:35979124 original size:40 final size:40
Alignment explanation
Indices: 35979080--35979171 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 40
35979070 GAACGACATA
*
35979080 TCGGCTAAGA-ATGACACTTAGTGTGCGGTTTGAAATAGCT
1 TCGGCTAA-ATATGACACTTAGTGTGCGATTTGAAATAGCT
* * *
35979120 TCGGCTAAATGTGACACTTGGTGTGCGATTTGAGATAGCT
1 TCGGCTAAATATGACACTTAGTGTGCGATTTGAAATAGCT
*
35979160 TCGGCTATATAT
1 TCGGCTAAATAT
35979172 ATATGTGACA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 1 0.02
40 44 0.98
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (40 bp):
TCGGCTAAATATGACACTTAGTGTGCGATTTGAAATAGCT
Found at i:35983299 original size:29 final size:29
Alignment explanation
Indices: 35983267--35983338 Score: 126
Period size: 29 Copynumber: 2.5 Consensus size: 29
35983257 TTCGAGCTCT
* *
35983267 CACACCTAGTGCCGTATATTTCCAGCATG
1 CACACTTAGTGCCATATATTTCCAGCATG
35983296 CACACTTAGTGCCATATATTTCCAGCATG
1 CACACTTAGTGCCATATATTTCCAGCATG
35983325 CACACTTAGTGCCA
1 CACACTTAGTGCCA
35983339 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (29 bp):
CACACTTAGTGCCATATATTTCCAGCATG
Found at i:35991186 original size:2 final size:2
Alignment explanation
Indices: 35991179--35991207 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35991169 TCGATCGGAG
35991179 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35991208 GAGTACGCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35991332 original size:29 final size:29
Alignment explanation
Indices: 35991300--35991372 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
35991290 CTTCGAGCTC
*
35991300 GCACACCCAGTGCCGTATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
35991329 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
35991358 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
35991373 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:35999360 original size:18 final size:17
Alignment explanation
Indices: 35999337--35999370 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
35999327 TAGCTGTGCC
35999337 GTTTTCTCTTCTGTATTA
1 GTTTTCTCTTCT-TATTA
35999355 GTTTTCTCTTCTTATT
1 GTTTTCTCTTCTTATT
35999371 TTCTTCCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.09, C:0.18, G:0.09, T:0.65
Consensus pattern (17 bp):
GTTTTCTCTTCTTATTA
Found at i:36000525 original size:25 final size:24
Alignment explanation
Indices: 36000492--36000539 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
36000482 TTATAACATG
* * *
36000492 AAAATGACCGTTTTGCCCCTAGGT
1 AAAATGACCATTATACCCCTAGGT
36000516 AAAAGTGACCATTATACCCCTAGG
1 AAAA-TGACCATTATACCCCTAGG
36000540 GTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (24 bp):
AAAATGACCATTATACCCCTAGGT
Found at i:36000590 original size:9 final size:9
Alignment explanation
Indices: 36000578--36000634 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
36000568 TTTGATAAAC
36000578 ATGATATGT
1 ATGATATGT
*
36000587 ATGATATGCAC
1 ATGATATG--T
*
36000598 ATGACATGT
1 ATGATATGT
*
36000607 ATGATATGCAC
1 ATGATATG--T
36000618 ATGATATGT
1 ATGATATGT
36000627 ATGATATG
1 ATGATATG
36000635 CACATGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:36000601 original size:20 final size:20
Alignment explanation
Indices: 36000576--36000646 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
36000566 ATTTTGATAA
36000576 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
36000596 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
36000616 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
36000636 ACATGAGATGT
1 ACATGATATGT
36000647 TCATAAATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:36000623 original size:11 final size:11
Alignment explanation
Indices: 36000587--36000641 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
36000577 CATGATATGT
36000587 ATGATATGCAC
1 ATGATATGCAC
* *
36000598 ATGACATG--T
1 ATGATATGCAC
36000607 ATGATATGCAC
1 ATGATATGCAC
*
36000618 ATGATATG--T
1 ATGATATGCAC
36000627 ATGATATGCAC
1 ATGATATGCAC
36000638 ATGA
1 ATGA
36000642 GATGTTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:36000771 original size:24 final size:24
Alignment explanation
Indices: 36000691--36000928 Score: 322
Period size: 24 Copynumber: 10.0 Consensus size: 24
36000681 GGAGGAAGTG
36000691 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
36000715 -TAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
36000738 -TAAAGGGCTTATGCCCCAGTTAG
1 CAAAAGGGCTTATGCCCCAGTTAT
*
36000761 CAAAAGGGCTTATGCCCTAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
36000785 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
36000809 TAAAAGGGCTTTTGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* * *
36000833 TAAAAGGGCTTTTGCCCTAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
36000857 CAAAAGGGCTTATGCCCTAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
36000881 CAAAAGGGCTT-TGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
36000904 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 CAAAAG-GGCTTATGCC-CCAGTTAT
36000929 ATGATAAAGC
Statistics
Matches: 196, Mismatches: 14, Indels: 7
0.90 0.06 0.03
Matches are distributed among these distances:
23 61 0.31
24 127 0.65
25 8 0.04
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
CAAAAGGGCTTATGCCCCAGTTAT
Found at i:36001157 original size:31 final size:31
Alignment explanation
Indices: 36001122--36001185 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
36001112 CGTTTACAGT
36001122 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
36001153 AAAGGCTTCGGCCCAGTGTTATGAATTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
36001184 AA
1 AA
36001186 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:36008550 original size:44 final size:44
Alignment explanation
Indices: 36008347--36008557 Score: 165
Period size: 46 Copynumber: 4.6 Consensus size: 44
36008337 TATGTGGACC
* * * *
36008347 AGTGTTAGACATGTCTGGGACATGCATCGGCCACATA-ATGAGATCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCA-AGATGTG--CT
* * * * * * *
36008393 ATTGTAAGACCATGTCTAGGACATGGCATCTGCATTGAGACAAGTGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CTCA-AGATGTGCT
* * *
36008441 AGTGTAAGACATGTCTGGGACATGCATTGGCCTCGAGATGTTAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATG-T-GCT
* *
36008487 AGTGTCAGACATGTCTGGGACATGCGTCGG-CTACAAGATGTGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CAAGATGTGCT
*
36008531 AGTGTAAGACATGTTTGGGACATGCAT
1 AGTGTAAGACATGTCTGGGACATGCAT
36008558 TAGTATGATT
Statistics
Matches: 129, Mismatches: 29, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
44 29 0.22
45 5 0.04
46 48 0.37
47 26 0.20
48 16 0.12
49 2 0.02
50 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATGTGCT
Found at i:36012841 original size:18 final size:17
Alignment explanation
Indices: 36012813--36012846 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
36012803 GGTCTTAGCC
*
36012813 CATTACAGAATGAGAAA
1 CATTACAGAATCAGAAA
36012830 CATTATCAGAATCAGAA
1 CATTA-CAGAATCAGAA
36012847 TCAAAATTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.21
Consensus pattern (17 bp):
CATTACAGAATCAGAAA
Found at i:36013050 original size:27 final size:26
Alignment explanation
Indices: 36012996--36013060 Score: 85
Period size: 27 Copynumber: 2.5 Consensus size: 26
36012986 AGCATGGCTG
*
36012996 CCAGAACAGATATTGTGACAGAGTCA
1 CCAGAACAGATATTGTGACAGAGCCA
* *
36013022 CCAGATACAGATATTGTGGCGGAGCCA
1 CCAGA-ACAGATATTGTGACAGAGCCA
*
36013049 CCAAAACAGATA
1 CCAGAACAGATA
36013061 ATATGGTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 12 0.35
27 22 0.65
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATATTGTGACAGAGCCA
Found at i:36013427 original size:27 final size:26
Alignment explanation
Indices: 36013397--36013474 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 26
36013387 GTGACAGAGT
36013397 CACCAGATACAGATATTGTGGCAGAAC
1 CACCAGA-ACAGATATTGTGGCAGAAC
* * *
36013424 CACCAGAACAGATCTTTGTGGCATAGC
1 CACCAGAACAGAT-ATTGTGGCAGAAC
* *
36013451 CACCAAAAATAGATATTTGTGGCA
1 CACC-AGAACAGATA-TTGTGGCA
36013475 TAGCCACTAG
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
26 6 0.14
27 21 0.50
28 15 0.36
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (26 bp):
CACCAGAACAGATATTGTGGCAGAAC
Found at i:36013473 original size:28 final size:27
Alignment explanation
Indices: 36013405--36013481 Score: 93
Period size: 28 Copynumber: 2.9 Consensus size: 27
36013395 GTCACCAGAT
* * *
36013405 ACAGATA-TTGTGGCAGAACCACCAGA
1 ACAGATATTTGTGGCATAGCCACCAAA
*
36013431 ACAGATCTTTGTGGCATAGCCACCAAAA
1 ACAGATATTTGTGGCATAGCCACC-AAA
*
36013459 ATAGATATTTGTGGCATAGCCAC
1 ACAGATATTTGTGGCATAGCCAC
36013482 TAGAACGCTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.14
27 14 0.33
28 23 0.53
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (27 bp):
ACAGATATTTGTGGCATAGCCACCAAA
Found at i:36013718 original size:27 final size:27
Alignment explanation
Indices: 36013683--36013800 Score: 182
Period size: 27 Copynumber: 4.4 Consensus size: 27
36013673 AAGGGCAAAA
* *
36013683 CAGTCATTCTACCCCACAGGGGTATTT
1 CAGTAATTCTACCCTACAGGGGTATTT
*
36013710 TAGTAATTCTACCCTACAGGGGTATTT
1 CAGTAATTCTACCCTACAGGGGTATTT
36013737 CAGTAATTCTACCCTACAGGGGTATTT
1 CAGTAATTCTACCCTACAGGGGTATTT
* * *
36013764 CAGTCATTCTAACCTATAGGGGTATTT
1 CAGTAATTCTACCCTACAGGGGTATTT
36013791 CAGTAATTCT
1 CAGTAATTCT
36013801 GTAAATCGAG
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 83 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (27 bp):
CAGTAATTCTACCCTACAGGGGTATTT
Found at i:36013813 original size:27 final size:27
Alignment explanation
Indices: 36013793--36014137 Score: 410
Period size: 27 Copynumber: 12.8 Consensus size: 27
36013783 GGGTATTTCA
*
36013793 GTAATTCTGTAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
36013820 GTAATTCTGTAAATTGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * *
36013847 GTAATTTTATAAATTGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
36013874 GTAATTCTGTAAATCGAGGGTGAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * *
36013901 ATAATTCTGTAAATTGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
36013928 ATAATTCTGTAAA-CTGAGGTTAAAACG
1 GTAATTCTGTAAATC-GAGGGTAAAACG
* *
36013955 GTAATTCTATAAACCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* **
36013982 GTAATTCTGTAAA-CTGAGGTTAAAATA
1 GTAATTCTGTAAATC-GAGGGTAAAACG
* *
36014009 GTAATTCTGTAACT-GAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
36014035 ATAATTCTGTAAATTGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
36014062 GTAATTTTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
36014089 GTAATTCTATAAA-CTGAGGGTAAAATG
1 GTAATTCTGTAAATC-GAGGGTAAAACG
* *
36014116 GTAATTTTGTAAATCGGGGGTA
1 GTAATTCTGTAAATCGAGGGTA
36014138 CTTTGGTCAT
Statistics
Matches: 274, Mismatches: 37, Indels: 14
0.84 0.11 0.04
Matches are distributed among these distances:
26 24 0.09
27 248 0.91
28 2 0.01
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.30
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACG
Found at i:36014164 original size:81 final size:81
Alignment explanation
Indices: 36013793--36014137 Score: 467
Period size: 81 Copynumber: 4.3 Consensus size: 81
36013783 GGGTATTTCA
* *
36013793 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATTGAGGGTAAAACGGTAATTTTATA
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAACGGTAATTCTATA
*
36013858 AATTGAGGGTAAAACG
66 AACTGAGGGTAAAACG
* * * * *
36013874 GTAATTCTGTAAATCGAGGGTGAAACGATAATTCTGTAAATTGAGGGTAAAATGATAATTCTGTA
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAACGGTAATTCTATA
*
36013939 AACTGAGGTTAAAACG
66 AACTGAGGGTAAAACG
* * * * ** *
36013955 GTAATTCTATAAACCGAGGGTAAAACGGTAATTCTGTAAACTGAGGTTAAAATAGTAATTCTGT-
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAACGGTAATTCTATA
*
36014019 AACTGAGGGTAAAATG
66 AACTGAGGGTAAAACG
* * * *
36014035 ATAATTCTGTAAATTGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTATA
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAACGGTAATTCTATA
*
36014100 AACTGAGGGTAAAATG
66 AACTGAGGGTAAAACG
* *
36014116 GTAATTTTGTAAATCGGGGGTA
1 GTAATTCTGTAAATCGAGGGTA
36014138 CTTTGGTCAT
Statistics
Matches: 229, Mismatches: 34, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
80 67 0.29
81 162 0.71
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.30
Consensus pattern (81 bp):
GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAACGGTAATTCTATA
AACTGAGGGTAAAACG
Found at i:36016160 original size:18 final size:17
Alignment explanation
Indices: 36016132--36016165 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
36016122 AGTCTTAGCC
*
36016132 CATTACAGAATGAGAAA
1 CATTACAGAATCAGAAA
36016149 CATTATCAGAATCAGAA
1 CATTA-CAGAATCAGAA
36016166 TCAAAATTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.21
Consensus pattern (17 bp):
CATTACAGAATCAGAAA
Found at i:36016369 original size:27 final size:26
Alignment explanation
Indices: 36016315--36016379 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 26
36016305 AGCATGGCTG
**
36016315 CCAGAACAGATATTGTGACAGAGTCA
1 CCAGAACAGATATTGTGACAGACCCA
* *
36016341 CCAGATACAGATATTGTGGCCGACCCA
1 CCAGA-ACAGATATTGTGACAGACCCA
*
36016368 CCAAAACAGATA
1 CCAGAACAGATA
36016380 ATATGGCAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 12 0.36
27 21 0.64
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATATTGTGACAGACCCA
Found at i:36016814 original size:28 final size:27
Alignment explanation
Indices: 36016746--36016822 Score: 93
Period size: 28 Copynumber: 2.9 Consensus size: 27
36016736 GTCACTAGAT
* * *
36016746 ACAGATA-TTGTGGCAGAACCACCAGA
1 ACAGATATTTGTGGCATAGCCACCAAA
*
36016772 ACAGATCTTTGTGGCATAGCCACCAAAA
1 ACAGATATTTGTGGCATAGCCACC-AAA
*
36016800 ATAGATATTTGTGGCATAGCCAC
1 ACAGATATTTGTGGCATAGCCAC
36016823 TAGAACGCTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.14
27 14 0.33
28 23 0.53
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (27 bp):
ACAGATATTTGTGGCATAGCCACCAAA
Found at i:36017083 original size:27 final size:27
Alignment explanation
Indices: 36017053--36017195 Score: 187
Period size: 27 Copynumber: 5.3 Consensus size: 27
36017043 GGGTAAAATG
* * * *
36017053 GTAATTTTACCCCACAAGGGTATCTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* * *
36017080 GTAATTCTACCCCACAGGGGTGTTTTA
1 GTAATTCTACCCTACAGGGGTATTTCA
36017107 GTAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
36017134 GTAATTCTAACCTATAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
36017161 GTAATTCTAACCTATAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
36017188 GTAATTCT
1 GTAATTCT
36017196 GTAAATCGAG
Statistics
Matches: 106, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 106 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTCA
Found at i:36017208 original size:27 final size:27
Alignment explanation
Indices: 36017188--36017523 Score: 442
Period size: 27 Copynumber: 12.5 Consensus size: 27
36017178 GGGTATTTCA
* *
36017188 GTAATTCTGTAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATTGAGGGTAAAACG
36017215 GTAATTCTGTAAATTGAGGGTAAAACG
1 GTAATTCTGTAAATTGAGGGTAAAACG
* * *
36017242 ATAATTTTATAAATTGAGGGTAAAACG
1 GTAATTCTGTAAATTGAGGGTAAAACG
* *
36017269 GTAATTCTGTAAATCGAGGGTGAAACG
1 GTAATTCTGTAAATTGAGGGTAAAACG
*
36017296 GTAATTCTGTAAATTGAGGGTAAAATG
1 GTAATTCTGTAAATTGAGGGTAAAACG
* * *
36017323 ATAATTCTGTAAACTGAGGTTAAAACG
1 GTAATTCTGTAAATTGAGGGTAAAACG
* **
36017350 GTAATTCTAT-AACCGAGGGTAAAACG
1 GTAATTCTGTAAATTGAGGGTAAAACG
* ** *
36017376 GTAATTCTGTAAACTGAGATTAAAACA
1 GTAATTCTGTAAATTGAGGGTAAAACG
*
36017403 GTAATTCTGT-AACTGAGGGTAAAACG
1 GTAATTCTGTAAATTGAGGGTAAAACG
36017429 GTAATTCTGTAAATTGAGGGTAAAACG
1 GTAATTCTGTAAATTGAGGGTAAAACG
*
36017456 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATTGAGGGTAAAACG
* * *
36017483 GTAATTCTATAAACTGAGGGTAAAATG
1 GTAATTCTGTAAATTGAGGGTAAAACG
*
36017510 GTAATTTTGTAAAT
1 GTAATTCTGTAAAT
36017524 CGGGGGTACT
Statistics
Matches: 269, Mismatches: 38, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
26 46 0.17
27 223 0.83
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (27 bp):
GTAATTCTGTAAATTGAGGGTAAAACG
Found at i:36017558 original size:81 final size:81
Alignment explanation
Indices: 36017188--36017531 Score: 487
Period size: 81 Copynumber: 4.3 Consensus size: 81
36017178 GGGTATTTCA
* *
36017188 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATTGAGGGTAAAACGATAATTTTATA
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAACGATAATTCTATA
*
36017253 AATTGAGGGTAAAACG
66 AACTGAGGGTAAAACG
* * *
36017269 GTAATTCTGTAAATCGAGGGTGAAACGGTAATTCTGTAAATTGAGGGTAAAATGATAATTCTGTA
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAACGATAATTCTATA
*
36017334 AACTGAGGTTAAAACG
66 AACTGAGGGTAAAACG
* * * ** *
36017350 GTAATTCTAT-AACCGAGGGTAAAACGGTAATTCTGTAAACTGAGATTAAAAC-AGTAATTCTGT
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAACGA-TAATTCTAT
36017413 -AACTGAGGGTAAAACG
65 AAACTGAGGGTAAAACG
* * *
36017429 GTAATTCTGTAAATTGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATA
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAACGATAATTCTATA
*
36017494 AACTGAGGGTAAAATG
66 AACTGAGGGTAAAACG
* *
36017510 GTAATTTTGTAAATCGGGGGTA
1 GTAATTCTGTAAATCGAGGGTA
36017532 CTTTGGTAAT
Statistics
Matches: 231, Mismatches: 28, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
79 25 0.11
80 89 0.39
81 117 0.51
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (81 bp):
GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAACGATAATTCTATA
AACTGAGGGTAAAACG
Found at i:36019555 original size:18 final size:17
Alignment explanation
Indices: 36019527--36019560 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
36019517 GGTCTTAACC
*
36019527 CATTACAGAATGAGAAA
1 CATTACAGAATCAGAAA
36019544 CATTATCAGAATCAGAA
1 CATTA-CAGAATCAGAA
36019561 TCAGAATTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.21
Consensus pattern (17 bp):
CATTACAGAATCAGAAA
Found at i:36019994 original size:22 final size:22
Alignment explanation
Indices: 36019946--36020004 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
36019936 GTAAATACGT
*
36019946 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
36019968 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
36019990 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
36020005 CAACAACGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:36020186 original size:27 final size:29
Alignment explanation
Indices: 36020156--36020221 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 29
36020146 ATTATGACAG
*
36020156 AGCCACCAGAATA-A-ATATTTGTGGCAT
1 AGCCACCAGAAAACAGATATTTGTGGCAT
36020183 AGCCACCA-AAAACAGATATTTGTGGCAT
1 AGCCACCAGAAAACAGATATTTGTGGCAT
*
36020211 AGCCACAAGAA
1 AGCCACCAGAA
36020222 CACTTCCTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 3 0.09
27 9 0.26
28 20 0.59
29 2 0.06
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (29 bp):
AGCCACCAGAAAACAGATATTTGTGGCAT
Found at i:36020474 original size:27 final size:28
Alignment explanation
Indices: 36020412--36020474 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 28
36020402 CAGTCACTTG
*
36020412 CCCATAAGGGCAAAACAGTCATTTAACA
1 CCCATAAGGGCAAAACAGTAATTTAACA
** *
36020440 CCC-T-AGGGCAAAATGGTAATTTTAC-
1 CCCATAAGGGCAAAACAGTAATTTAACA
36020465 CCCATAAGGG
1 CCCATAAGGG
36020475 TATCTCGGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
25 3 0.10
26 18 0.62
27 5 0.17
28 3 0.10
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.21
Consensus pattern (28 bp):
CCCATAAGGGCAAAACAGTAATTTAACA
Found at i:36020512 original size:27 final size:27
Alignment explanation
Indices: 36020455--36020571 Score: 153
Period size: 27 Copynumber: 4.3 Consensus size: 27
36020445 GGGCAAAATG
* * * * *
36020455 GTAATTTTACCCCATAAGGGTATCTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
*
36020482 GTAATTCTACCCTACAAGGGTATTTTA
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
36020509 GTAATTCTACCCTACAGGGGTTTTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
*
36020536 GTAATTCTAACCTACAAGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
36020563 GTAATTCTA
1 GTAATTCTA
36020572 TAAATCGAGG
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 78 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (27 bp):
GTAATTCTACCCTACAAGGGTATTTCA
Found at i:36020582 original size:27 final size:27
Alignment explanation
Indices: 36020561--36020907 Score: 300
Period size: 27 Copynumber: 12.9 Consensus size: 27
36020551 AAGGGTATTT
36020561 CAGTAATTCTATAAATCGAGGGTAAAA
1 CAGTAATTCTATAAATCGAGGGTAAAA
** *
36020588 TGGTAATTCTATAAATTGAGGGTAAAA
1 CAGTAATTCTATAAATCGAGGGTAAAA
*
36020615 CAGTAATTCTGTAAA-CTGAGGGTAAAA
1 CAGTAATTCTATAAATC-GAGGGTAAAA
* * *
36020642 CGGTAATTCTGTAAATCGAGGGTGAAA
1 CAGTAATTCTATAAATCGAGGGTAAAA
* *
36020669 CAGTAACTCTGTAAATCGAGGGTAAAA
1 CAGTAATTCTATAAATCGAGGGTAAAA
* *
36020696 C-GATAATTCTATAAA-CTGAAGGTGAAA
1 CAG-TAATTCTATAAATC-GAGGGTAAAA
* * * *
36020723 CGGTAATTTTGTAAACCGAGGGTAAAA
1 CAGTAATTCTATAAATCGAGGGTAAAA
* *
36020750 C-GATAATTTTGTAAA-CTGAGGGTAAAA
1 CAG-TAATTCTATAAATC-GAGGGTAAAA
*
36020777 C-GATAATTCTATAAATTGAGGGTAAAA
1 CAG-TAATTCTATAAATCGAGGGTAAAA
* *
36020804 CGGTAATTCTGTAAATCGAGGGT-AAA
1 CAGTAATTCTATAAATCGAGGGTAAAA
* * *
36020830 C-GATAATTTTGTAAATCGAGCGTAAAA
1 CAG-TAATTCTATAAATCGAGGGTAAAA
** * *
36020857 TGGTAATTTTGTAAA-CTGAGGGTAAAA
1 CAGTAATTCTATAAATC-GAGGGTAAAA
36020884 C-GATAATTCTATAAATCGAGGGTA
1 CAG-TAATTCTATAAATCGAGGGTA
36020908 CTTTGGTAAT
Statistics
Matches: 272, Mismatches: 32, Indels: 32
0.81 0.10 0.10
Matches are distributed among these distances:
25 1 0.00
26 28 0.10
27 237 0.87
28 6 0.02
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (27 bp):
CAGTAATTCTATAAATCGAGGGTAAAA
Found at i:36020637 original size:81 final size:81
Alignment explanation
Indices: 36020563--36020907 Score: 437
Period size: 81 Copynumber: 4.3 Consensus size: 81
36020553 GGGTATTTCA
* * * * * *
36020563 GTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAAC-AGTAATTCTGT
1 GTAATTCTGTAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAACGA-TAATTCTAT
36020627 AAACTGAGGGTAAAACG
65 AAACTGAGGGTAAAACG
* *
36020644 GTAATTCTGTAAATCGAGGGTGAAAC-AGTAACTCTGTAAATCGAGGGTAAAACGATAATTCTAT
1 GTAATTCTGTAAATCGAGGGTAAAACGA-TAATTCTGTAAATCGAGGGTAAAACGATAATTCTAT
* *
36020708 AAACTGAAGGTGAAACG
65 AAACTGAGGGTAAAACG
* * *
36020725 GTAATTTTGTAAACCGAGGGTAAAACGATAATTTTGTAAA-CTGAGGGTAAAACGATAATTCTAT
1 GTAATTCTGTAAATCGAGGGTAAAACGATAATTCTGTAAATC-GAGGGTAAAACGATAATTCTAT
*
36020789 AAATTGAGGGTAAAACG
65 AAACTGAGGGTAAAACG
* * * * * *
36020806 GTAATTCTGTAAATCGAGGGT-AAACGATAATTTTGTAAATCGAGCGTAAAATGGTAATTTTGTA
1 GTAATTCTGTAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAACGATAATTCTATA
36020870 AACTGAGGGTAAAACG
66 AACTGAGGGTAAAACG
* *
36020886 ATAATTCTATAAATCGAGGGTA
1 GTAATTCTGTAAATCGAGGGTA
36020908 CTTTGGTAAT
Statistics
Matches: 230, Mismatches: 28, Indels: 12
0.85 0.10 0.04
Matches are distributed among these distances:
80 71 0.31
81 157 0.68
82 2 0.01
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.28
Consensus pattern (81 bp):
GTAATTCTGTAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAACGATAATTCTATA
AACTGAGGGTAAAACG
Found at i:36020920 original size:54 final size:54
Alignment explanation
Indices: 36020564--36020907 Score: 403
Period size: 54 Copynumber: 6.4 Consensus size: 54
36020554 GGTATTTCAG
* * * *
36020564 TAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAAC-A
1 TAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAACTGAGGGTAAAACGA
*
36020617 GTAATTCTGTAAA-CTGAGGGTAAAACGGTAATTCTGTAAA-TCGAGGGTGAAAC-A
1 -TAATTCTGTAAATC-GAGGGTAAAACGGTAATTCTGTAAACT-GAGGGTAAAACGA
* * * * * *
36020671 GTAACTCTGTAAATCGAGGGTAAAACGATAATTCTATAAACTGAAGGTGAAACGG
1 -TAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAACTGAGGGTAAAACGA
* * * *
36020726 TAATTTTGTAAACCGAGGGTAAAACGATAATTTTGTAAACTGAGGGTAAAACGA
1 TAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAACTGAGGGTAAAACGA
* *
36020780 TAATTCTATAAATTGAGGGTAAAACGGTAATTCTGTAAA-TCGAGGGT-AAACGA
1 TAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAACT-GAGGGTAAAACGA
* * * *
36020833 TAATTTTGTAAATCGAGCGTAAAATGGTAATTTTGTAAACTGAGGGTAAAACGA
1 TAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAACTGAGGGTAAAACGA
*
36020887 TAATTCTATAAATCGAGGGTA
1 TAATTCTGTAAATCGAGGGTA
36020908 CTTTGGTAAT
Statistics
Matches: 250, Mismatches: 32, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
53 48 0.19
54 200 0.80
55 2 0.01
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (54 bp):
TAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAACTGAGGGTAAAACGA
Found at i:36027201 original size:25 final size:25
Alignment explanation
Indices: 36027172--36027219 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
36027162 TTATAATATG
* * *
36027172 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
36027197 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
36027220 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:36027322 original size:20 final size:20
Alignment explanation
Indices: 36027262--36027322 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
36027252 ATAAATATGG
*
36027262 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
36027282 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
36027302 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
36027322 T
1 T
36027323 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:36027399 original size:24 final size:24
Alignment explanation
Indices: 36027372--36027490 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
36027362 GAGGAAGTGA
*
36027372 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
36027396 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
36027419 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
36027443 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
36027467 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
36027491 ATGATAAAGC
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
23 22 0.26
24 53 0.62
25 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:36027441 original size:47 final size:48
Alignment explanation
Indices: 36027372--36027490 Score: 170
Period size: 47 Copynumber: 2.5 Consensus size: 48
36027362 GAGGAAGTGA
36027372 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
** *
36027419 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
*
36027467 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
36027491 ATGATAAAGC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
47 43 0.66
48 11 0.17
49 11 0.17
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
Found at i:36027717 original size:31 final size:31
Alignment explanation
Indices: 36027682--36027776 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
36027672 CGTTTACAGT
36027682 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
36027713 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
36027744 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
36027775 AA
1 AA
36027777 TATGAAAAGG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:36034273 original size:25 final size:25
Alignment explanation
Indices: 36034244--36034291 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
36034234 TTATAATATG
* * *
36034244 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
36034269 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
36034292 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:36034394 original size:20 final size:20
Alignment explanation
Indices: 36034334--36034394 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
36034324 ATAAATATGG
*
36034334 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
36034354 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
36034374 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
36034394 T
1 T
36034395 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:36034488 original size:23 final size:24
Alignment explanation
Indices: 36034444--36034585 Score: 200
Period size: 24 Copynumber: 6.0 Consensus size: 24
36034434 GAGGAAGTGA
36034444 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
36034468 AAAAGGGCTTATG-CCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
36034491 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
36034514 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
36034538 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
36034562 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
36034586 ATGATAAAGC
Statistics
Matches: 109, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
23 46 0.42
24 52 0.48
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:36034513 original size:47 final size:47
Alignment explanation
Indices: 36034444--36034585 Score: 198
Period size: 47 Copynumber: 3.0 Consensus size: 47
36034434 GAGGAAGTGA
36034444 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATG-CCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
36034491 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
36034538 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
36034586 ATGATAAAGC
Statistics
Matches: 87, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
46 13 0.15
47 52 0.60
48 11 0.13
49 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:36034850 original size:30 final size:31
Alignment explanation
Indices: 36034777--36034870 Score: 172
Period size: 31 Copynumber: 3.1 Consensus size: 31
36034767 CGTTTACAGT
36034777 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
36034808 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
36034839 AAAGG-TTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
36034869 AA
1 AA
36034871 TATGAAAAGG
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
30 26 0.42
31 36 0.58
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:36035726 original size:22 final size:23
Alignment explanation
Indices: 36035701--36035756 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
36035691 TATAAAATCT
36035701 AATAAAAA-TAAGCTTAAAGA-AA
1 AATAAAAAGTAAGCTTAAA-ATAA
**
36035723 AATAAAAAGTATTCTTAAAATAA
1 AATAAAAAGTAAGCTTAAAATAA
36035746 AAT-AAAAGTAA
1 AATAAAAAGTAA
36035757 AAACATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 16 0.55
23 13 0.45
ACGTcount: A:0.66, C:0.04, G:0.07, T:0.23
Consensus pattern (23 bp):
AATAAAAAGTAAGCTTAAAATAA
Found at i:36063877 original size:18 final size:17
Alignment explanation
Indices: 36063854--36063887 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
36063844 TAGCTGTGCC
36063854 GTTTTCTCTTCTGTATTA
1 GTTTTCTCTTCT-TATTA
36063872 GTTTTCTCTTCTTATT
1 GTTTTCTCTTCTTATT
36063888 TTCTTCCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.09, C:0.18, G:0.09, T:0.65
Consensus pattern (17 bp):
GTTTTCTCTTCTTATTA
Found at i:36065041 original size:25 final size:24
Alignment explanation
Indices: 36065008--36065055 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
36064998 TTATAACATG
* * *
36065008 AAAATGACCGTTTTGCCCCTAGGT
1 AAAATGACCATTATACCCCTAGGT
36065032 AAAAGTGACCATTATACCCCTAGG
1 AAAA-TGACCATTATACCCCTAGG
36065056 GTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (24 bp):
AAAATGACCATTATACCCCTAGGT
Found at i:36065143 original size:19 final size:20
Alignment explanation
Indices: 36065092--36065161 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
36065082 ATTTTGATAA
*
36065092 ACATGATATGTATGATATGC
1 ACATGACATGTATGATATGC
36065112 ACATGACATGTATGATATGC
1 ACATGACATGTATGATATGC
36065132 ACATGA-ATGTATGATATGC
1 ACATGACATGTATGATATGC
*
36065151 ACATGAGATGT
1 ACATGACATGT
36065162 TCATAAATGC
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 19 0.40
20 29 0.60
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (20 bp):
ACATGACATGTATGATATGC
Found at i:36065287 original size:24 final size:24
Alignment explanation
Indices: 36065206--36065443 Score: 349
Period size: 24 Copynumber: 10.0 Consensus size: 24
36065196 GGCGGAAGTG
36065206 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
36065230 -TAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
36065253 -TAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
36065276 CAAAAGGCCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
36065300 CAATAGGGCTTATGCCCTAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
36065324 TAAAAGGGCTTTTGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
36065348 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
36065372 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
36065396 CAAAAGGGCTT-TGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
36065419 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 CAAAAG-GGCTTATGCC-CCAGTTAT
36065444 ATGATAAAGC
Statistics
Matches: 196, Mismatches: 14, Indels: 7
0.90 0.06 0.03
Matches are distributed among these distances:
23 63 0.32
24 125 0.64
25 8 0.04
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (24 bp):
CAAAAGGGCTTATGCCCCAGTTAT
Found at i:36065672 original size:31 final size:31
Alignment explanation
Indices: 36065637--36065700 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
36065627 CGTTTACAGT
36065637 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
36065668 AAAGGCTTCGGCCCAGTGTTATGAATTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
36065699 AA
1 AA
36065701 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:36073267 original size:27 final size:28
Alignment explanation
Indices: 36073210--36073279 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
36073200 AAATTTGTAC
**
36073210 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
*
36073238 AGCACTATGTGTGCG-AGCTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
36073265 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
36073280 GACTCACTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 24 0.63
28 14 0.37
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:36081235 original size:27 final size:28
Alignment explanation
Indices: 36081178--36081247 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
36081168 AAATTTGTAC
**
36081178 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
*
36081206 AGCACTATGTGTGCG-AGCTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
36081233 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
36081248 GACTCACTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 24 0.63
28 14 0.37
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:36086619 original size:27 final size:28
Alignment explanation
Indices: 36086556--36086664 Score: 107
Period size: 28 Copynumber: 3.9 Consensus size: 28
36086546 CATGAGATTG
* ** *
36086556 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGAGTT-TGATTATATA
36086585 GCACTAAGTGTG-GAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
* *
36086612 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCGAGTTTGATTATAT-A
* *
36086640 GCACTAAGTGTGTGAGCTT-ATTATA
1 GCACTAAGTGTGCGAGTTTGATTATA
36086665 CATTCTCTAA
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
27 24 0.36
28 31 0.46
29 12 0.18
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:36086642 original size:28 final size:29
Alignment explanation
Indices: 36086556--36086651 Score: 110
Period size: 28 Copynumber: 3.4 Consensus size: 29
36086546 CATGAGATTG
* *
36086556 GCACTAAGTGTGCGGGTTCAAAT-TGTATA
1 GCACTAAGTGTGCGAGTTCGAATAT-TATA
* *
36086585 GCACTAAGTGTG-GAGTTTGATTA-TATA
1 GCACTAAGTGTGCGAGTTCGAATATTATA
*
36086612 GCACTAAGTGTGCGAGTTCGACTATTA-A
1 GCACTAAGTGTGCGAGTTCGAATATTATA
36086640 GCACTAAGTGTG
1 GCACTAAGTGTG
36086652 TGAGCTTATT
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
27 16 0.28
28 28 0.48
29 14 0.24
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGTTCGAATATTATA
Found at i:36091095 original size:13 final size:13
Alignment explanation
Indices: 36091077--36091105 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
36091067 TAACATATTA
36091077 TTTCATTTACTAT
1 TTTCATTTACTAT
36091090 TTTCATTTACTAT
1 TTTCATTTACTAT
36091103 TTT
1 TTT
36091106 AACCTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTCATTTACTAT
Done.