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 56 of 297
Found at i:19939831 original size:20 final size:20
Alignment explanation
Indices: 19939779--19939832 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
19939769 TTGTATGGGA
19939779 TTGCACTTCGGTGCCTCTGT
1 TTGCACTTCGGTGCCTCTGT
* *
19939799 TTGTAC-TCTGGTGCCTTTGT
1 TTGCACTTC-GGTGCCTCTGT
19939819 TTGCACTTCGGTGC
1 TTGCACTTCGGTGC
19939833 TTATGTTACG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 2 0.07
20 25 0.86
21 2 0.07
ACGTcount: A:0.06, C:0.26, G:0.26, T:0.43
Consensus pattern (20 bp):
TTGCACTTCGGTGCCTCTGT
Found at i:19939839 original size:20 final size:19
Alignment explanation
Indices: 19939779--19939839 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
19939769 TTGTATGGGA
*
19939779 TTGCACTTCGGTGCCTCTGT
1 TTGCACTTCGGTG-CTTTGT
*
19939799 TTGTAC-TCTGGTGCCTTTGT
1 TTGCACTTC-GGTG-CTTTGT
19939819 TTGCACTTCGGTGCTTATGT
1 TTGCACTTCGGTGCTT-TGT
19939839 T
1 T
19939840 ACGCATCTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 5 0.14
20 28 0.80
21 2 0.06
ACGTcount: A:0.07, C:0.23, G:0.25, T:0.46
Consensus pattern (19 bp):
TTGCACTTCGGTGCTTTGT
Found at i:19941758 original size:39 final size:40
Alignment explanation
Indices: 19941644--19941828 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
19941634 GCTACTCGTT
* *
19941644 CAAATGCCTTCGGGACATAGCCCAG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
19941684 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
19941724 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
19941763 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
*
19941804 CAAA-GCCTTCGAGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
19941829 CATCATTCGA
Statistics
Matches: 125, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 33 0.26
40 78 0.62
41 12 0.10
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:19941812 original size:79 final size:80
Alignment explanation
Indices: 19941672--19941828 Score: 203
Period size: 79 Copynumber: 2.0 Consensus size: 80
19941662 AGCCCAGTTA
* * *
19941672 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCG-
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACCAAAGCCTTCGA
*
19941736 GGCTTAGCCCGGAAT
66 GACTTAGCCCGGAAT
** * *
19941751 TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA-CAAAGCCTTC
1 TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TAGCACCAAAGCCTTC
19941814 GAGACTTAGCCCGGA
64 GAGACTTAGCCCGGA
19941829 CATCATTCGA
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
78 3 0.04
79 48 0.72
80 16 0.24
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACCAAAGCCTTCGA
GACTTAGCCCGGAAT
Found at i:19943867 original size:48 final size:48
Alignment explanation
Indices: 19943750--19943920 Score: 188
Period size: 48 Copynumber: 3.6 Consensus size: 48
19943740 TATGTGTGCT
* * * * * *
19943750 AGTGTAAGACATGTCTGGGACAAGCATCAGCCACAGC-AT-GA-GAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTC-GCAATATACAAGCC
* **
19943796 AGTGTAAGACATGTCTGGGACATGCATTGGCCTCG-AGATATTTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGCA-ATATACAAGCC
*
19943844 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGCAATATACAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGCAATATACAAGCC
*
19943892 AGTGTAAGACCTGTCTGGGACATGGCATC
1 AGTGTAAGACATGTCTGGGACAT-GCATC
19943921 AGCTTGTTGT
Statistics
Matches: 106, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
45 1 0.01
46 32 0.30
48 67 0.63
49 6 0.06
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (48 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGCAATATACAAGCC
Found at i:19943993 original size:49 final size:49
Alignment explanation
Indices: 19943935--19944064 Score: 131
Period size: 49 Copynumber: 2.6 Consensus size: 49
19943925 TGTTGTGTGA
* *
19943935 CAGTGTAAGACCTGTCTGAGACATGACATTGAC-GC-CGATAGATGAGAGC
1 CAGTGTAAGACCTGTCTGAGACATGACATCGACAGCACGATA-A-GAAAGC
* * * * *
19943984 TAGTGTAAGACCTTTCT-AGGACATGGCATCGACATCACTATAAGAAAGC
1 CAGTGTAAGACCTGTCTGA-GACATGACATCGACAGCACGATAAGAAAGC
*
19944033 CAGTGTAAGACCATGTCTGGGACATGACATCG
1 CAGTGTAAGACC-TGTCTGAGACATGACATCG
19944065 GCATCTTAAC
Statistics
Matches: 65, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
48 1 0.02
49 43 0.66
50 17 0.26
51 4 0.06
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (49 bp):
CAGTGTAAGACCTGTCTGAGACATGACATCGACAGCACGATAAGAAAGC
Found at i:19945637 original size:5 final size:5
Alignment explanation
Indices: 19945623--19945684 Score: 72
Period size: 5 Copynumber: 11.6 Consensus size: 5
19945613 AACATGCAAG
19945623 AAAT- AAATA AAATA AAATAAA AAATA AAATA AAATA AAATAA AAATAA
1 AAATA AAATA AAATA AAAT--A AAATA AAATA AAATA AAAT-A AAAT-A
19945671 AAATAA AAATA AAA
1 AAAT-A AAATA AAA
19945685 ATTAAATTGG
Statistics
Matches: 54, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.07
5 28 0.52
6 17 0.31
7 5 0.09
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:19945648 original size:12 final size:11
Alignment explanation
Indices: 19945623--19945684 Score: 85
Period size: 12 Copynumber: 5.7 Consensus size: 11
19945613 AACATGCAAG
19945623 AAAT-AAAT-A
1 AAATAAAATAA
19945632 AAATAAAATAAA
1 AAATAAAAT-AA
19945644 AAATAAAAT-A
1 AAATAAAATAA
19945654 AAATAAAATAA
1 AAATAAAATAA
19945665 AAATAAAAATAA
1 AAAT-AAAATAA
19945677 AAATAAAA
1 AAATAAAA
19945685 ATTAAATTGG
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
9 4 0.08
10 14 0.29
11 9 0.19
12 21 0.44
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:19945649 original size:17 final size:17
Alignment explanation
Indices: 19945627--19945684 Score: 84
Period size: 17 Copynumber: 3.5 Consensus size: 17
19945617 TGCAAGAAAT
19945627 AAATAAAATAAAATAAA
1 AAATAAAATAAAATAAA
19945644 AAATAAAATAAAATAAA
1 AAATAAAATAAAATAAA
*
19945661 ATA-AAAATAAAA-ATAA
1 AAATAAAATAAAATA-AA
19945677 AAATAAAA
1 AAATAAAA
19945685 ATTAAATTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
15 1 0.03
16 13 0.35
17 23 0.62
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (17 bp):
AAATAAAATAAAATAAA
Found at i:19945651 original size:6 final size:6
Alignment explanation
Indices: 19945627--19945686 Score: 76
Period size: 6 Copynumber: 10.7 Consensus size: 6
19945617 TGCAAGAAAT
19945627 AAAT-A AAAT-A AAATAA AAA-ATA AAAT-A AAAT-A AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATA-A AAATAA AAATAA AAATAA AAATAA
19945671 AAATAA AAATAA AAAT
1 AAATAA AAATAA AAAT
19945687 TAAATTGGGT
Statistics
Matches: 51, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
5 20 0.39
6 31 0.61
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AAATAA
Found at i:19945655 original size:22 final size:21
Alignment explanation
Indices: 19945623--19945684 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 21
19945613 AACATGCAAG
19945623 AAAT-AAATAAAATAAAATAAA
1 AAATAAAATAAAATAAAAT-AA
19945644 AAATAAAATAAAATAAAATAA
1 AAATAAAATAAAATAAAATAA
19945665 AAATAAAAATAAAAATAAAA
1 AAAT-AAAAT-AAAATAAAA
19945685 ATTAAATTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.26
22 19 0.50
23 9 0.24
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (21 bp):
AAATAAAATAAAATAAAATAA
Found at i:19945691 original size:17 final size:17
Alignment explanation
Indices: 19945627--19945691 Score: 82
Period size: 17 Copynumber: 3.9 Consensus size: 17
19945617 TGCAAGAAAT
19945627 AAAT-AAAATAAAATAA
1 AAATAAAAATAAAATAA
19945643 AAA-ATAAAATAAAAT-A
1 AAATA-AAAATAAAATAA
19945659 AAATAAAAATAAAAATAA
1 AAATAAAAAT-AAAATAA
*
19945677 AAATAAAAATTAAAT
1 AAATAAAAATAAAAT
19945692 TGGGTTGTCT
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
16 12 0.28
17 20 0.47
18 11 0.26
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (17 bp):
AAATAAAAATAAAATAA
Found at i:19950847 original size:38 final size:38
Alignment explanation
Indices: 19950804--19950915 Score: 118
Period size: 39 Copynumber: 2.9 Consensus size: 38
19950794 AAAATTTATG
19950804 TGGTATTATATCCGGGTTAAATCCCGCAGGCTTAATAC
1 TGGTATTATATCCGGGTTAAATCCCGCAGGCTTAATAC
* * * * *
19950842 TGGTATTATATCCGGACTTATAGT-CCGCAGGCCTAGTGC
1 TGGTATTATATCCGG-GTTA-AATCCCGCAGGCTTAATAC
* *
19950881 TGGTAATAGATATCCGGGTTAAATCCTGCAGGCTT
1 TGGT-AT-TATATCCGGGTTAAATCCCGCAGGCTT
19950916 TGTGCTAGAA
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
38 15 0.25
39 21 0.36
40 15 0.25
41 8 0.14
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (38 bp):
TGGTATTATATCCGGGTTAAATCCCGCAGGCTTAATAC
Found at i:19954681 original size:49 final size:48
Alignment explanation
Indices: 19954509--19954681 Score: 170
Period size: 49 Copynumber: 3.6 Consensus size: 48
19954499 AAATGCTAAC
* * * *
19954509 GCCATGTTCCAGACATGGTCTTACACTGGCTAGCA-C-ATTGAAGTCGAT
1 GCCATGTCCCAGACA-GGTCTTACACTGGCTATCATCTATCG-GGTCGAT
* * ** * * * *
19954557 GCCGTGTCCTAGACAGGTCTTACACTAACTTTCATATATCGAGGCCAAT
1 GCCATGTCCCAGACAGGTCTTACACTGGCTATCATCTATCG-GGTCGAT
* *
19954606 GCCATGTCCCAGACAGGTCTCACACTGGCTCTCATCTATCGGTGTCGAT
1 GCCATGTCCCAGACAGGTCTTACACTGGCTATCATCTATCGG-GTCGAT
19954655 GCCATGTCCCAGACAGGTCTTACACTG
1 GCCATGTCCCAGACAGGTCTTACACTG
19954682 ACACACAAAA
Statistics
Matches: 100, Mismatches: 22, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
47 15 0.15
48 13 0.13
49 72 0.72
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (48 bp):
GCCATGTCCCAGACAGGTCTTACACTGGCTATCATCTATCGGGTCGAT
Found at i:19954758 original size:48 final size:46
Alignment explanation
Indices: 19954704--19954869 Score: 152
Period size: 46 Copynumber: 3.6 Consensus size: 46
19954694 CTGATGCCAC
* * * *
19954704 GTCCCAGACAAGTTTTACACTAGCTTGTATATCCCGAGGCCGATGCAT
1 GTCCCAGACATGTCTTACACTAGC-TCTA-ATCCCAAGGCCGATGCAT
* * * *
19954752 GTCCCAGATATGTCTTACACTAGCTCTAATCTCAATGTCGATGCAT
1 GTCCCAGACATGTCTTACACTAGCTCTAATCCCAAGGCCGATGCAT
* * * ***** *
19954798 GTCCCAGACATGTCTTACACTGGCACTCATGATGTGGCCAATGCAT
1 GTCCCAGACATGTCTTACACTAGCTCTAATCCCAAGGCCGATGCAT
*
19954844 GTCCCAGACATGTCTTACACTGGCTC
1 GTCCCAGACATGTCTTACACTAGCTC
19954870 ACATACCACC
Statistics
Matches: 97, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
46 73 0.75
47 3 0.03
48 21 0.22
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (46 bp):
GTCCCAGACATGTCTTACACTAGCTCTAATCCCAAGGCCGATGCAT
Found at i:19959476 original size:40 final size:40
Alignment explanation
Indices: 19959399--19959575 Score: 263
Period size: 40 Copynumber: 4.5 Consensus size: 40
19959389 AAACCAAGTA
* *
19959399 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
19959438 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
19959478 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
19959518 CCTTCGGG-CTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
19959557 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
19959576 TTATCATCCG
Statistics
Matches: 128, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
38 1 0.01
39 49 0.38
40 78 0.61
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:19959552 original size:79 final size:80
Alignment explanation
Indices: 19959399--19959575 Score: 263
Period size: 79 Copynumber: 2.2 Consensus size: 80
19959389 AAACCAAGTA
* * *
19959399 CCTTCGGGATTTAG-CCGGATATAGCTACTCGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAG
1 CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
*
19959463 TAACTCGCACAAATG
66 TAACTAGCACAAATG
19959478 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGG-CTTAGCCCGGA-ATT
1 CCTTCGGGACTTAGCCCGGATATAGCT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA-T
*
19959540 AGTCACTAGCACAAATG
64 AGTAACTAGCACAAATG
19959557 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
19959576 TTATCATCCG
Statistics
Matches: 90, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
TAACTAGCACAAATG
Found at i:19965522 original size:57 final size:57
Alignment explanation
Indices: 19965434--19965548 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
19965424 CCCAAGTTAC
19965434 TTGCTCTCGAGGCATAACAGAGATCAACGTATTCCACCAATAGTAGGCAGAATCACG
1 TTGCTCTCGAGGCATAACAGAGATCAACGTATTCCACCAATAGTAGGCAGAATCACG
19965491 TTGCTCTCGAGGCATAACAGAGATCAACGTATTCCACCAATAGTAGGCAGAATCACG
1 TTGCTCTCGAGGCATAACAGAGATCAACGTATTCCACCAATAGTAGGCAGAATCACG
19965548 T
1 T
19965549 AGCAAGGAGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (57 bp):
TTGCTCTCGAGGCATAACAGAGATCAACGTATTCCACCAATAGTAGGCAGAATCACG
Found at i:19971295 original size:57 final size:58
Alignment explanation
Indices: 19971197--19971338 Score: 164
Period size: 57 Copynumber: 2.5 Consensus size: 58
19971187 TACCATATTA
* * *
19971197 TAGGATTACCAGTCCAGGCTAAATCCTTTATGTAACGTATGC-TCAGAAGAGCTTA-AT
1 TAGGATTACCAGTCCAGGCTAAATCCTATATGTAACATATGCTTCAGAAGA-ATTATAT
* * * *
19971254 TAGGATTACAAGTCCAGGCTAAATCCTA-ATTGTATCATATGCTTGAGAGGAATTATAT
1 TAGGATTACCAGTCCAGGCTAAATCCTATA-TGTAACATATGCTTCAGAAGAATTATAT
* *
19971312 CAGGATTACCCGTCCAGGCTAAATCCT
1 TAGGATTACCAGTCCAGGCTAAATCCT
19971339 TTCTATAACG
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
56 1 0.01
57 39 0.54
58 32 0.44
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (58 bp):
TAGGATTACCAGTCCAGGCTAAATCCTATATGTAACATATGCTTCAGAAGAATTATAT
Found at i:19973341 original size:20 final size:20
Alignment explanation
Indices: 19973318--19973356 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19973308 AAAATGAATA
*
19973318 GTAATTATTATGAATTATCC
1 GTAAATATTATGAATTATCC
*
19973338 GTAAATGTTATGAATTATC
1 GTAAATATTATGAATTATC
19973357 TAGTAATGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.44
Consensus pattern (20 bp):
GTAAATATTATGAATTATCC
Found at i:19978550 original size:30 final size:30
Alignment explanation
Indices: 19978474--19978559 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
19978464 TTCAACTCAC
* *
19978474 GAGCTAAACCTTAGCTCAACTTCAGCTTAG
1 GAGCTAAACCTTAGCTCAACTTTAGCTAAG
* * *
19978504 GAGTTTAACCTCAGCTCAACTTTAGCTCAAG
1 GAGCTAAACCTTAGCTCAACTTTAGCT-AAG
* *
19978535 G-GCTAAAGCTTAGCTC-ATTTTAGCT
1 GAGCTAAACCTTAGCTCAACTTTAGCT
19978560 TAAACCCGAT
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
29 8 0.18
30 34 0.76
31 3 0.07
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (30 bp):
GAGCTAAACCTTAGCTCAACTTTAGCTAAG
Found at i:19981282 original size:47 final size:47
Alignment explanation
Indices: 19981204--19981402 Score: 272
Period size: 47 Copynumber: 4.2 Consensus size: 47
19981194 CCCTTCGGGA
* * * * * **
19981204 CTTATCACATTTATGCACTTTCACATCCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
* *
19981251 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
**
19981298 CTTATCACGCATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
*
19981345 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAAGC
19981394 CTTATCACA
1 CTTATCACA
19981403 ATTTAGAATT
Statistics
Matches: 134, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
47 90 0.67
49 44 0.33
ACGTcount: A:0.29, C:0.32, G:0.09, T:0.31
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
Found at i:19981398 original size:96 final size:94
Alignment explanation
Indices: 19981219--19981401 Score: 276
Period size: 96 Copynumber: 1.9 Consensus size: 94
19981209 CACATTTATG
* ** *
19981219 CACTTTCACATCCATCACATTGGCCACTCGGCCCTGTCACATATATACACTTTCACATTCATCAC
1 CACTTTCACATCCATCACATCGGCCACTAAGCCCTATCACATATATACACTTTCACATTCATCAC
19981284 ATCGGCCATTAAGCCTTATCACGCATATA
66 ATCGGCCATTAAGCCTTATCACGCATATA
* * *
19981313 CACTTTCACATTCATCACATCGGCCATTAAGCCTTATCACATATATATACACTTTCACATTCATC
1 CACTTTCACATCCATCACATCGGCCACTAAGCCCTATCAC--ATATATACACTTTCACATTCATC
*
19981378 ACATCGGCCATTAGGCCTTATCAC
64 ACATCGGCCATTAAGCCTTATCAC
19981402 AATTTAGAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
94 33 0.42
96 46 0.58
ACGTcount: A:0.28, C:0.33, G:0.09, T:0.30
Consensus pattern (94 bp):
CACTTTCACATCCATCACATCGGCCACTAAGCCCTATCACATATATACACTTTCACATTCATCAC
ATCGGCCATTAAGCCTTATCACGCATATA
Found at i:19983894 original size:16 final size:16
Alignment explanation
Indices: 19983873--19983907 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
19983863 TATCATATTA
19983873 TATCATATTGTAAATG
1 TATCATATTGTAAATG
19983889 TATCATATTGTAAATG
1 TATCATATTGTAAATG
19983905 TAT
1 TAT
19983908 TTATGACATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (16 bp):
TATCATATTGTAAATG
Found at i:19987183 original size:49 final size:48
Alignment explanation
Indices: 19987116--19987504 Score: 364
Period size: 49 Copynumber: 7.8 Consensus size: 48
19987106 GTAGACAGGG
* *
19987116 TTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
1 TTATC-GGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAA
* * *
19987165 TTATACGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCAAA
1 TTAT-CGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA
* * * ** *
19987215 GTTATCGGGTACGCATCGTAGCCAACACTTAGTACTACACATACGACCAA
1 -TTATC-GGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAA
* * * *
19987265 TTATCCGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCAAA
1 TTAT-CGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA
* * * ** *
19987315 GTTATCGGGTACGCATCGTAGCCAACACTTAGTACTACACATACGACCAA
1 -TTATC-GGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAA
* * * *
19987365 TTATCCGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCAAA
1 TTAT-CGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA
* * * ** *
19987415 GTTATCGGGTACGCATCGTAGCCAACACTTAGTACTACACATACGACCAA
1 -TTATC-GGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAA
*
19987465 TTATCCGATACACGTAGTAGCCTGCACTTAGTACTACACA
1 TTAT-CGGTACACGTAGTAGCCTGCACTTAGTACTACACA
19987505 CGTAACCTCA
Statistics
Matches: 267, Mismatches: 60, Indels: 26
0.76 0.17 0.07
Matches are distributed among these distances:
49 139 0.52
50 25 0.09
51 103 0.39
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (48 bp):
TTATCGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAA
Found at i:19987262 original size:100 final size:100
Alignment explanation
Indices: 19987115--19987507 Score: 723
Period size: 100 Copynumber: 3.9 Consensus size: 100
19987105 TGTAGACAGG
* * ** * * *
19987115 GTTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATACGGTACACGT
1 GTTATCGGGTACGCATCGTAGCCAACACTTAGTACTACACATACGACCAATTATCCGATACACGT
19987180 AGTAGCCTGCACTTAGTACTACACACGTGATCAAA
66 AGTAGCCTGCACTTAGTACTACACACGTGATCAAA
19987215 GTTATCGGGTACGCATCGTAGCCAACACTTAGTACTACACATACGACCAATTATCCGATACACGT
1 GTTATCGGGTACGCATCGTAGCCAACACTTAGTACTACACATACGACCAATTATCCGATACACGT
19987280 AGTAGCCTGCACTTAGTACTACACACGTGATCAAA
66 AGTAGCCTGCACTTAGTACTACACACGTGATCAAA
19987315 GTTATCGGGTACGCATCGTAGCCAACACTTAGTACTACACATACGACCAATTATCCGATACACGT
1 GTTATCGGGTACGCATCGTAGCCAACACTTAGTACTACACATACGACCAATTATCCGATACACGT
19987380 AGTAGCCTGCACTTAGTACTACACACGTGATCAAA
66 AGTAGCCTGCACTTAGTACTACACACGTGATCAAA
19987415 GTTATCGGGTACGCATCGTAGCCAACACTTAGTACTACACATACGACCAATTATCCGATACACGT
1 GTTATCGGGTACGCATCGTAGCCAACACTTAGTACTACACATACGACCAATTATCCGATACACGT
19987480 AGTAGCCTGCACTTAGTACTACACACGT
66 AGTAGCCTGCACTTAGTACTACACACGT
19987508 AACCTCACAA
Statistics
Matches: 286, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 286 1.00
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.25
Consensus pattern (100 bp):
GTTATCGGGTACGCATCGTAGCCAACACTTAGTACTACACATACGACCAATTATCCGATACACGT
AGTAGCCTGCACTTAGTACTACACACGTGATCAAA
Found at i:19987798 original size:27 final size:27
Alignment explanation
Indices: 19987758--19987811 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
19987748 TCATACATCC
* *
19987758 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
19987785 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
19987812 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:19990307 original size:29 final size:27
Alignment explanation
Indices: 19990289--19990358 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
19990279 ATATTAAGTC
19990289 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
19990316 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
19990344 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
19990359 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:19990352 original size:28 final size:28
Alignment explanation
Indices: 19990289--19990386 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
19990279 ATATTAAGTC
*
19990289 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
19990316 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
19990344 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
19990373 CGCACACTTAGTGC
1 CGCACACTTAGTGC
19990387 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:19994246 original size:19 final size:20
Alignment explanation
Indices: 19994193--19994249 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 20
19994183 AGCTGGCCTT
19994193 TATTATGTATAATTATAATATAA
1 TATTATG-A-AATTA-AATATAA
*
19994216 TATTTAT-TAATTAAATA-AA
1 TA-TTATGAAATTAAATATAA
19994235 TATTATGAAATTAAA
1 TATTATGAAATTAAA
19994250 CTCAATGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
18 4 0.13
19 11 0.37
20 4 0.13
21 5 0.17
23 2 0.07
24 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (20 bp):
TATTATGAAATTAAATATAA
Found at i:19994355 original size:11 final size:11
Alignment explanation
Indices: 19994327--19994369 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
19994317 GGAAGCATGC
* *
19994327 TCTTTTCTTTG
1 TCTTTTTTTTT
19994338 TCTTTTTTTTTT
1 TC-TTTTTTTTT
19994350 TCTTTTTTTTT
1 TCTTTTTTTTT
19994361 TCTCTTTTT
1 TCT-TTTTT
19994370 GTAACTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 14 0.50
12 14 0.50
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:19994356 original size:13 final size:13
Alignment explanation
Indices: 19994338--19994369 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
19994328 CTTTTCTTTG
19994338 TCTTTTTTTTTT-
1 TCTTTTTTTTTTC
19994350 TCTTTTTTTTTTC
1 TCTTTTTTTTTTC
19994363 TCTTTTT
1 TCTTTTT
19994370 GTAACTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TCTTTTTTTTTTC
Found at i:19995261 original size:28 final size:28
Alignment explanation
Indices: 19995224--19995281 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
19995214 AATATGTATA
19995224 AATATAATTATCTAAATGCAGTTAATAT
1 AATATAATTATCTAAATGCAGTTAATAT
19995252 AATATAATTATCTAAATGCAGTTAATAT
1 AATATAATTATCTAAATGCAGTTAATAT
19995280 AA
1 AA
19995282 CATGTTTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (28 bp):
AATATAATTATCTAAATGCAGTTAATAT
Found at i:19999356 original size:17 final size:18
Alignment explanation
Indices: 19999324--19999357 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19999314 TTGTCCTTTT
19999324 ATATAATGATTAATAAAG
1 ATATAATGATTAATAAAG
*
19999342 ATATGATGA-TAATAAA
1 ATATAATGATTAATAAA
19999358 ATTTGAACTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (18 bp):
ATATAATGATTAATAAAG
Found at i:19999451 original size:14 final size:14
Alignment explanation
Indices: 19999415--19999453 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
19999405 ATTTTATGTG
*
19999415 AATTTTTAATAAAT
1 AATTTTTATTAAAT
*
19999429 -ATATTTATTAAAT
1 AATTTTTATTAAAT
19999442 AATTTTTATTAA
1 AATTTTTATTAA
19999454 TATGTCATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AATTTTTATTAAAT
Found at i:20000000 original size:15 final size:15
Alignment explanation
Indices: 19999984--20000013 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
19999974 TAGTTATGTT
19999984 AATTAATTTTAATTTA
1 AATT-ATTTTAATTTA
20000000 AATTATTTTAATTT
1 AATTATTTTAATTT
20000014 GAACAGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
AATTATTTTAATTTA
Found at i:20005310 original size:33 final size:32
Alignment explanation
Indices: 20005239--20005317 Score: 106
Period size: 32 Copynumber: 2.4 Consensus size: 32
20005229 TTTTCCCGTT
*
20005239 GATTTCTTCATCGCCAAACCCCCTTCCCCATC
1 GATTTCTTCATCTCCAAACCCCCTTCCCCATC
* *
20005271 GATTTCTTCATCTTCAAACCCCTCTTCCCCGTC
1 GATTTCTTCATCTCCAAACCCC-CTTCCCCATC
20005304 -ATTTTCTTCATCTC
1 GA-TTTCTTCATCTC
20005318 TGAACACTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
32 21 0.51
33 20 0.49
ACGTcount: A:0.16, C:0.42, G:0.05, T:0.37
Consensus pattern (32 bp):
GATTTCTTCATCTCCAAACCCCCTTCCCCATC
Found at i:20013204 original size:45 final size:45
Alignment explanation
Indices: 20013140--20013359 Score: 322
Period size: 45 Copynumber: 5.0 Consensus size: 45
20013130 TATCGTACAG
* *
20013140 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAGTGCCGGTGAGA
1 TACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGA
* * * *
20013185 TACTATTCGGACCTTTGAGCCTAGCAGACTATAATGCCAGTGAGA
1 TACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGA
20013230 TACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGA
1 TACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGA
* *
20013275 TACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATACCGGTGAAA
1 TACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGA
*
20013320 TGA-TA-TCGGG-CTTCGAGCCTAGCAGGCGA-AATGCCGGTGA
1 T-ACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGA
20013360 ATGAATTCGG
Statistics
Matches: 162, Mismatches: 12, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
42 10 0.06
43 18 0.11
44 5 0.03
45 128 0.79
46 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (45 bp):
TACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGA
Found at i:20015081 original size:48 final size:48
Alignment explanation
Indices: 20015025--20015926 Score: 728
Period size: 48 Copynumber: 18.9 Consensus size: 48
20015015 GTGAATTACT
* * * *
20015025 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATGTCGAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCC
* * * *
20015073 AATGCCATGTCCCAGACATGGTCTTACACTAGCGCACATATCAATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCC
* * * *
20015121 GATGCCATGTCCCAGACATGGTCTTATACTGGCTCTCATAAT-GTGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-ATCGAGGCC
* * * * *
20015169 GATGCTATGTCCTAGACATTGTCTTACACTAG-TGCACATATCAATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCT-CACATATCGAGGCC
* * * * *
20015217 GAT-CCATGTCCCAGACATGGCCTTACACTGGCTCTCATAAT--ATTGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-ATCGA-GGCC
* * * *
20015264 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATGTCGAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCC
* * * * *
20015312 AATGCCATGTCCCAGACATGGTCTTATACTGGCTCTCATAAT-GTGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-ATCGAGGCC
* * * * *
20015360 GATGCTATGTCCTAGACATTGTCTTACACTAG-TGCACATATCAATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCT-CACATATCGAGGCC
* * * * *
20015408 GAT-CCATGTCCCAGACATGGCCTTACACTGGCTCTCATAAT--ATTGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-ATCGA-GGCC
* * * *
20015455 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATGTCGAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCC
* * * * *
20015503 AATGCCATGTCCCAGACATGGTCTTATACTGGCTCTCATAAT-GTGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-ATCGAGGCC
* * * * *
20015551 GATGCTATGTCCTAGACATTGTCTTACACTAG-TGCACATATCAATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCT-CACATATCGAGGCC
* * * * *
20015599 GAT-CCATGTCCCAGACATGGCCTTACACTGGCTCTCATAAT--ATTGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-ATCGA-GGCC
* * * *
20015646 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATGTCGAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCC
* * * * *
20015694 AATGCCATGTCCCAGACATGGTCTTATACTGGCTCTCATAAT-GTGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-ATCGAGGCC
* * * * *
20015742 GATGCTATGTCCTAGACATTGTCTTACACTAG-TGCACATATCAATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCT-CACATATCGAGGCC
* * * * *
20015790 GAT-CCATGTCCCAGACATGGCCTTACACTGGCTCTCATAAT--ATTGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-ATCGA-GGCC
* * * * * * *
20015837 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATTGTGACC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCC
* *
20015885 GATGCCTTGTCCCAGACATGGTCTTACACTAGCGCACATATC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATC
20015927 ACCTAAATGT
Statistics
Matches: 667, Mismatches: 151, Indels: 72
0.75 0.17 0.08
Matches are distributed among these distances:
46 4 0.01
47 149 0.22
48 506 0.76
49 8 0.01
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.29
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCC
Found at i:20015371 original size:191 final size:191
Alignment explanation
Indices: 20015074--20015910 Score: 1521
Period size: 191 Copynumber: 4.4 Consensus size: 191
20015064 GTCGAGGCTA
* * * * * * **
20015074 ATGCCATGTCCCAGACATGGTCTTACACTAGCGCACATATCAATGCCGATGCCATGTCCCAGACA
1 ATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATGTCGAGGCTAATGCCATGTCCCAGACA
20015139 TGGTCTTATACTGGCTCTCATAATGTGGCCGATGCTATGTCCTAGACATTGTCTTACACTAGTGC
66 TGGTCTTATACTGGCTCTCATAATGTGGCCGATGCTATGTCCTAGACATTGTCTTACACTAGTGC
20015204 ACATATCAATGCCGATCCATGTCCCAGACATGGCCTTACACTGGCTCTCATAATATTGTCG
131 ACATATCAATGCCGATCCATGTCCCAGACATGGCCTTACACTGGCTCTCATAATATTGTCG
20015265 ATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATGTCGAGGCTAATGCCATGTCCCAGACA
1 ATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATGTCGAGGCTAATGCCATGTCCCAGACA
20015330 TGGTCTTATACTGGCTCTCATAATGTGGCCGATGCTATGTCCTAGACATTGTCTTACACTAGTGC
66 TGGTCTTATACTGGCTCTCATAATGTGGCCGATGCTATGTCCTAGACATTGTCTTACACTAGTGC
20015395 ACATATCAATGCCGATCCATGTCCCAGACATGGCCTTACACTGGCTCTCATAATATTGTCG
131 ACATATCAATGCCGATCCATGTCCCAGACATGGCCTTACACTGGCTCTCATAATATTGTCG
20015456 ATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATGTCGAGGCTAATGCCATGTCCCAGACA
1 ATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATGTCGAGGCTAATGCCATGTCCCAGACA
20015521 TGGTCTTATACTGGCTCTCATAATGTGGCCGATGCTATGTCCTAGACATTGTCTTACACTAGTGC
66 TGGTCTTATACTGGCTCTCATAATGTGGCCGATGCTATGTCCTAGACATTGTCTTACACTAGTGC
20015586 ACATATCAATGCCGATCCATGTCCCAGACATGGCCTTACACTGGCTCTCATAATATTGTCG
131 ACATATCAATGCCGATCCATGTCCCAGACATGGCCTTACACTGGCTCTCATAATATTGTCG
20015647 ATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATGTCGAGGCTAATGCCATGTCCCAGACA
1 ATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATGTCGAGGCTAATGCCATGTCCCAGACA
20015712 TGGTCTTATACTGGCTCTCATAATGTGGCCGATGCTATGTCCTAGACATTGTCTTACACTAGTGC
66 TGGTCTTATACTGGCTCTCATAATGTGGCCGATGCTATGTCCTAGACATTGTCTTACACTAGTGC
20015777 ACATATCAATGCCGATCCATGTCCCAGACATGGCCTTACACTGGCTCTCATAATATTGTCG
131 ACATATCAATGCCGATCCATGTCCCAGACATGGCCTTACACTGGCTCTCATAATATTGTCG
* * * * * * ** *
20015838 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATTGTGACCGATGCCTTGTCCCAGACA
1 ATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATGTCGAGGCTAATGCCATGTCCCAGACA
20015903 TGGTCTTA
66 TGGTCTTA
20015911 CACTAGCGCA
Statistics
Matches: 629, Mismatches: 17, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
191 629 1.00
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.29
Consensus pattern (191 bp):
ATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATGTCGAGGCTAATGCCATGTCCCAGACA
TGGTCTTATACTGGCTCTCATAATGTGGCCGATGCTATGTCCTAGACATTGTCTTACACTAGTGC
ACATATCAATGCCGATCCATGTCCCAGACATGGCCTTACACTGGCTCTCATAATATTGTCG
Found at i:20015483 original size:239 final size:237
Alignment explanation
Indices: 20015025--20015927 Score: 763
Period size: 239 Copynumber: 3.8 Consensus size: 237
20015015 GTGAATTACT
20015025 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATGTCGAGGCTAATGCCATGTCCCAGAC
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATGTCGAGGCTAATGCCATGTCCCAGAC
* *
20015090 ATGGTCTTACACTAGCGCACATATCAATGCCGATGCCATGTCCCAGACATGGTCTTATACTGGCT
66 ATGGTCTTACACTAGCGCACATAT-AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCA
* * * *
20015155 CTCATAATGTGGCCGATGCTATGTCCTAGACATTGTCTTACACTAGTGCACATATCAATGCCGAT
130 CTCATAA-GTGGCCGATGCCATGTCCCAGACATGGCCTTACACTAGTGCACATATCAATGCCGAT
* *
20015220 CCATGTCCCAGACATGGCCTTACACTGGCTCTCATAATATTGTC
194 CCATGTCCCAAACATGGCCTTACACTAGCTCTCATAATATTGTC
20015264 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATGTCGAGGCTAATGCCATGTCCCAGAC
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATGTCGAGGCTAATGCCATGTCCCAGAC
* * * * * * * *
20015329 ATGGTCTTATACTGGCTCTCATA-ATGTGGCCGATGCTATGTCCTAGACATTGTCTTACACTAGT
66 ATGGTCTTACACTAGCGCACATATA-AT-GCCGATGCCATGTCCCAGACATGGTCTTACACT-G-
* * *
20015393 GCACAT-ATCAA-T-GCCGAT-CCATGTCCCAGACATGGCCTTACACTGGCT-CTCATAAT-ATT
127 GCAC-TCAT-AAGTGGCCGATGCCATGTCCCAGACATGGCCTTACACTAG-TGCACAT-ATCAAT
* * * * * *** *
20015452 GTCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACAT-GTCGAGGC
188 GCCGAT-CCATGTCCCAAACATGGCCTTACACTAGCTCTCATAATATTGTC
* * * * * * * * ** * *
20015502 TAATGCCATGTCCCAGACATGGTCTTATACTGGCTCTCATAAT-GTGGCCGATGCTATGTCCTAG
1 -GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACAT-GTCGAGGCTAATGCCATGTCCCAG
* * *
20015566 ACATTGTCTTACACTAGTGCACATATCAATGCCGAT-CCATGTCCCAGACATGGCCTTACACTGG
64 ACATGGTCTTACACTAGCGCACATAT-AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGG
* * * * * * * * * * *
20015630 CTCTCATAATATTGTCGATGCCATGTTCCAAACATGGTCTTACACTAGCT-CACATGTCGAGGCT
128 CACTCATAA-GTGGCCGATGCCATGTCCCAGACATGGCCTTACACTAG-TGCACATATCAATGCC
* * * * * * * *
20015694 AATGCCATGTCCCAGACATGGTCTTATACTGGCTCTCATAATGTGGCC
191 GAT-CCATGTCCCAAACATGGCCTTACACTAGCTCTCATAATATTGTC
* * * * * * **
20015742 GATGCTATG-TCCTAGACATTGTCTTACACTAG-TGCACATATCAATGCCGAT-CCATGTCCCAG
1 GATGCCATGTTCC-AAACATGGTCTTACACTAGCT-CACATGTCGAGGCTAATGCCATGTCCCAG
* * * * * * * *
20015804 ACATGGCCTTACACTGGCTCTCATAATATTGTCGATGCCATGTTCCAAACATGGTCTTACACTGG
64 ACATGGTCTTACACTAGCGCACAT-ATAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGG
* * * * * *
20015869 CTCTCATATTGTGACCGATGCCTTGTCCCAGACATGGTCTTACACTAGCGCACATATCA
128 CACTCATA-AGTGGCCGATGCCATGTCCCAGACATGGCCTTACACTAGTGCACATATCA
20015928 CCTAAATGTC
Statistics
Matches: 528, Mismatches: 109, Indels: 54
0.76 0.16 0.08
Matches are distributed among these distances:
235 3 0.01
236 5 0.01
237 3 0.01
238 105 0.20
239 396 0.75
240 7 0.01
241 6 0.01
242 3 0.01
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.29
Consensus pattern (237 bp):
GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATGTCGAGGCTAATGCCATGTCCCAGAC
ATGGTCTTACACTAGCGCACATATAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCAC
TCATAAGTGGCCGATGCCATGTCCCAGACATGGCCTTACACTAGTGCACATATCAATGCCGATCC
ATGTCCCAAACATGGCCTTACACTAGCTCTCATAATATTGTC
Found at i:20021199 original size:40 final size:40
Alignment explanation
Indices: 20021125--20021226 Score: 147
Period size: 40 Copynumber: 2.6 Consensus size: 40
20021115 AACCCAAGTA
*
20021125 CCTTCGGGAT-TTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGG-TCTTAGCCCGGATATAGCAACTAGCACAAATG
20021164 CCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATG
1 CCTTCGGGTCTTAGCCCGGATATAG-CAACTAGCACAAATG
*
20021204 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGTCTTAGCCCGGATAT
20021227 CATTCGAATA
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
38 1 0.02
39 12 0.21
40 44 0.76
41 1 0.02
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
CCTTCGGGTCTTAGCCCGGATATAGCAACTAGCACAAATG
Found at i:20025630 original size:27 final size:26
Alignment explanation
Indices: 20025575--20025630 Score: 60
Period size: 26 Copynumber: 2.1 Consensus size: 26
20025565 AACCTTAACA
* *
20025575 CTAGGGGTATATCAGTAATTTTACTC
1 CTAGGGGTAAATCAGTAATTTTACAC
*
20025601 CTAGGGGTAAATCTA-TAAATTTTCCAC
1 CTAGGGGTAAATC-AGT-AATTTTACAC
20025628 CTA
1 CTA
20025631 TAAAGGTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (26 bp):
CTAGGGGTAAATCAGTAATTTTACAC
Found at i:20040573 original size:129 final size:129
Alignment explanation
Indices: 20040343--20040601 Score: 500
Period size: 129 Copynumber: 2.0 Consensus size: 129
20040333 CAAAAAAAAA
*
20040343 TGGGTGTCATACTTGCCATCACCTAGCTGAAAAACCAAGAAAAAGAAGGGGAGAAAGGAACTTGG
1 TGGGTGTCATACTTGCCATCACCTAGCCGAAAAACCAAGAAAAAGAAGGGGAGAAAGGAACTTGG
20040408 GAGGGATTCAGCCATTGCTTGCCTAGGGAGAGTGTTTGATGTTGTGACATGAAAAATGAGGGAG
66 GAGGGATTCAGCCATTGCTTGCCTAGGGAGAGTGTTTGATGTTGTGACATGAAAAATGAGGGAG
20040472 TGGGTGTCATACTTGCCATCACCTAGCCGAAAAACCAAGAAAAAGAAGGGGAGAAAGGAACTTGG
1 TGGGTGTCATACTTGCCATCACCTAGCCGAAAAACCAAGAAAAAGAAGGGGAGAAAGGAACTTGG
*
20040537 GAGGGATTCGGCCATTGCTTGCCTAGGGAGAGTGTTTGATGTTGTGACATGAAAAATGAGGGAG
66 GAGGGATTCAGCCATTGCTTGCCTAGGGAGAGTGTTTGATGTTGTGACATGAAAAATGAGGGAG
20040601 T
1 T
20040602 TTGAATGCTT
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 128 1.00
ACGTcount: A:0.32, C:0.14, G:0.32, T:0.22
Consensus pattern (129 bp):
TGGGTGTCATACTTGCCATCACCTAGCCGAAAAACCAAGAAAAAGAAGGGGAGAAAGGAACTTGG
GAGGGATTCAGCCATTGCTTGCCTAGGGAGAGTGTTTGATGTTGTGACATGAAAAATGAGGGAG
Found at i:20041951 original size:82 final size:81
Alignment explanation
Indices: 20041835--20041990 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
20041825 AAATTGTACA
* * * *
20041835 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
20041899 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
20041916 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
20041981 TGCGAGTTGA
65 TGCGAATTGA
20041991 TTGTATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 18 0.28
82 47 0.72
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:20041958 original size:55 final size:52
Alignment explanation
Indices: 20041834--20041987 Score: 175
Period size: 55 Copynumber: 2.9 Consensus size: 52
20041824 TAAATTGTAC
* *
20041834 AGCACTAAGTGTGCG-ATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG
1 AGCACTAAGTGTGCGAATT-GACTATGTGGCACTAAGTGTGCG-AGTGAATATG
* * *
20041887 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATG
1 A-GCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT-GAA-TATG
* * *
20041942 TAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGT
1 -AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT
20041988 TGATTGTATA
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
53 3 0.03
54 36 0.42
55 46 0.53
56 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (52 bp):
AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTGAATATG
Found at i:20041992 original size:27 final size:27
Alignment explanation
Indices: 20041835--20041990 Score: 163
Period size: 27 Copynumber: 5.7 Consensus size: 27
20041825 AAATTGTACA
*
20041835 GCACTAAGTGTGCG-ATTCGACTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
* *
20041862 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
20041889 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * *
20041916 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * *
20041944 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
20041971 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
20041991 TTGTATAGCA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
27 83 0.77
28 25 0.23
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:20042001 original size:27 final size:27
Alignment explanation
Indices: 20041827--20042011 Score: 101
Period size: 27 Copynumber: 6.8 Consensus size: 27
20041817 GCGGGATTAA
*
20041827 ATTGTACAGCACTAAGTGTGCG-ATTCG
1 ATTGTATAGCACTAAGTGTGCGAATT-G
*
20041854 ACTATGT-T-GCACTAAGTGTGCGAAATG
1 A-T-TGTATAGCACTAAGTGTGCGAATTG
20041881 AATATG-AT-GCACTAAGTGTGCGAATTG
1 -AT-TGTATAGCACTAAGTGTGCGAATTG
*** *** * *
20041908 ACCATGCGGCACTAAGTGTGCGAGTCTA
1 ATTGTATAGCACTAAGTGTGCGAAT-TG
* * * *
20041936 ACTATGTAGCACTAAGTGTGCGATTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*** * *
20041963 ATTACGTGGCACTAAGTGTGCGAGTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*
20041990 ATTGTATAGCACTGAGTGTGCG
1 ATTGTATAGCACTAAGTGTGCG
20042012 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 24, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.01
27 96 0.76
28 26 0.21
29 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
ATTGTATAGCACTAAGTGTGCGAATTG
Found at i:20042002 original size:82 final size:81
Alignment explanation
Indices: 20041827--20042011 Score: 210
Period size: 82 Copynumber: 2.3 Consensus size: 81
20041817 GCGGGATTAA
* * * *
20041827 ATTGTACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCA
1 ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
20041892 CTAAGTGTGCGAATTG
66 CTAAGTGTGCGAATTG
*** * * ** *
20041908 ACCATGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGG
1 ATTGTACAGCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-G
*
20041972 CACTAAGTGTGCGAGTTG
64 CACTAAGTGTGCGAATTG
* *
20041990 ATTGTATAGCACTGAGTGTGCG
1 ATTGTACAGCACTAAGTGTGCG
20042012 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
81 21 0.26
82 61 0.74
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
CTAAGTGTGCGAATTG
Found at i:20044426 original size:107 final size:107
Alignment explanation
Indices: 20044237--20044432 Score: 302
Period size: 107 Copynumber: 1.8 Consensus size: 107
20044227 GCCGCGTATC
* * *
20044237 GATGATTTGTTCGACCAACTGAAGGGAGCCTCAGTGTTCTCAAAAATAGATTTGAGATCGGGCTA
1 GATGATCTGTTCGACCAACTAAAGGGAGCATCAGTGTTCTCAAAAATAGATTTGAGATCGGGCTA
20044302 TTATCAGTTGCGAATTCGAGATTCAGATATTCCTAAAACTGT
66 TTATCAGTTGCGAATTCGAGATTCAGATATTCCTAAAACTGT
* * * * * *
20044344 GATGATCTGTTCGATCAATTAAAGGGAGCATCGGTGTTTTCAAAGATAGATTTGAGATCGGGTTA
1 GATGATCTGTTCGACCAACTAAAGGGAGCATCAGTGTTCTCAAAAATAGATTTGAGATCGGGCTA
*
20044409 TTATCAGTTGCGGATTCGAGATTC
66 TTATCAGTTGCGAATTCGAGATTC
20044433 GGACGTACCC
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
107 79 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (107 bp):
GATGATCTGTTCGACCAACTAAAGGGAGCATCAGTGTTCTCAAAAATAGATTTGAGATCGGGCTA
TTATCAGTTGCGAATTCGAGATTCAGATATTCCTAAAACTGT
Found at i:20045121 original size:55 final size:55
Alignment explanation
Indices: 20045055--20045162 Score: 216
Period size: 55 Copynumber: 2.0 Consensus size: 55
20045045 GGGTTGCGTA
20045055 TTGATGCAAGAAGGTCGAGTTGTGGCCTATGCGTCGAGACAATTGAAGCCACAAC
1 TTGATGCAAGAAGGTCGAGTTGTGGCCTATGCGTCGAGACAATTGAAGCCACAAC
20045110 TTGATGCAAGAAGGTCGAGTTGTGGCCTATGCGTCGAGACAATTGAAGCCACA
1 TTGATGCAAGAAGGTCGAGTTGTGGCCTATGCGTCGAGACAATTGAAGCCACA
20045163 CGAAAGAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.22
Consensus pattern (55 bp):
TTGATGCAAGAAGGTCGAGTTGTGGCCTATGCGTCGAGACAATTGAAGCCACAAC
Found at i:20046456 original size:56 final size:56
Alignment explanation
Indices: 20046370--20046480 Score: 204
Period size: 56 Copynumber: 2.0 Consensus size: 56
20046360 GACCGAGCTT
*
20046370 GGTGAAAGTAAAATTTTCGGAGTTGATTTGATTAAAGATGCTGAACAGAAAGTAAC
1 GGTGAAAGTAAAATTTTCGGAGTTGATTTGATTAAAGATGCCGAACAGAAAGTAAC
*
20046426 GGTGAAAGTAAAATTTTTGGAGTTGATTTGATTAAAGATGCCGAACAGAAAGTAA
1 GGTGAAAGTAAAATTTTCGGAGTTGATTTGATTAAAGATGCCGAACAGAAAGTAA
20046481 AGGTAATCCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.40, C:0.06, G:0.25, T:0.29
Consensus pattern (56 bp):
GGTGAAAGTAAAATTTTCGGAGTTGATTTGATTAAAGATGCCGAACAGAAAGTAAC
Found at i:20051333 original size:71 final size:71
Alignment explanation
Indices: 20051217--20051633 Score: 834
Period size: 71 Copynumber: 5.9 Consensus size: 71
20051207 TTTGTAATCT
20051217 GAGGTAAGTTGTTTGTAAATAATACAACTACATTGTTATTATATGTGTTTGAATTGATATAGTTC
1 GAGGTAAGTTGTTTGTAAATAATACAACTACATTGTTATTATATGTGTTTGAATTGATATAGTTC
20051282 TAATTC
66 TAATTC
20051288 GAGGTAAGTTGTTTGTAAATAATACAACTACATTGTTATTATATGTGTTTGAATTGATATAGTTC
1 GAGGTAAGTTGTTTGTAAATAATACAACTACATTGTTATTATATGTGTTTGAATTGATATAGTTC
20051353 TAATTC
66 TAATTC
20051359 GAGGTAAGTTGTTTGTAAATAATACAACTACATTGTTATTATATGTGTTTGAATTGATATAGTTC
1 GAGGTAAGTTGTTTGTAAATAATACAACTACATTGTTATTATATGTGTTTGAATTGATATAGTTC
20051424 TAATTC
66 TAATTC
20051430 GAGGTAAGTTGTTTGTAAATAATACAACTACATTGTTATTATATGTGTTTGAATTGATATAGTTC
1 GAGGTAAGTTGTTTGTAAATAATACAACTACATTGTTATTATATGTGTTTGAATTGATATAGTTC
20051495 TAATTC
66 TAATTC
20051501 GAGGTAAGTTGTTTGTAAATAATACAACTACATTGTTATTATATGTGTTTGAATTGATATAGTTC
1 GAGGTAAGTTGTTTGTAAATAATACAACTACATTGTTATTATATGTGTTTGAATTGATATAGTTC
20051566 TAATTC
66 TAATTC
20051572 GAGGTAAGTTGTTTGTAAATAATACAACTACATTGTTATTATATGTGTTTGAATTGATATAG
1 GAGGTAAGTTGTTTGTAAATAATACAACTACATTGTTATTATATGTGTTTGAATTGATATAG
20051634 CATAAATTGC
Statistics
Matches: 346, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 346 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (71 bp):
GAGGTAAGTTGTTTGTAAATAATACAACTACATTGTTATTATATGTGTTTGAATTGATATAGTTC
TAATTC
Found at i:20051824 original size:47 final size:45
Alignment explanation
Indices: 20051753--20051923 Score: 166
Period size: 47 Copynumber: 3.7 Consensus size: 45
20051743 TTATTTGTAC
* * * **
20051753 GCTAGTGTAGGACATCTCTGGGACATGCATCAGCTACATTATTAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCTACA-GACAAGA
**
20051799 GCTAGTGTAAGAACATGTCTGGGACATGGCATCAGCATTGAGACAAGA
1 GCTAGTGTAAG-ACATGTCTGGGACAT-GCATCAGC-TACAGACAAGA
* * * *
20051847 GCTAGTGTAAGACATGTCTGGGACATGCACCAGCTAC-GAGATGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCTACAGACAAGA
20051891 G-TCAGTGTAAGACCATGTCTGGGACATGGCATC
1 GCT-AGTGTAAGA-CATGTCTGGGACAT-GCATC
20051924 GGTGTGGATA
Statistics
Matches: 105, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
43 1 0.01
44 14 0.13
45 15 0.14
46 21 0.20
47 29 0.28
48 23 0.22
49 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (45 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCTACAGACAAGA
Found at i:20051942 original size:94 final size:94
Alignment explanation
Indices: 20051753--20051968 Score: 233
Period size: 94 Copynumber: 2.3 Consensus size: 94
20051743 TTATTTGTAC
* * * *
20051753 GCTAGTGTAGGACATCTCTGGGACATGCATCAGCTACATTATTAGAGCTAGTGTAAGAACATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCACCAGCTACATGATTAGAGCTAGTGTAAGAACATGTC
*
20051818 TGGGACATGGCATCAGCATTGAGACAAGA
66 TGGGACATGGCATCAGCATGGAGACAAGA
* *
20051847 GCTAGTGTAAGACATGTCTGGGACATGCACCAGCTACGA-GA-T-GTG-TCAGTGTAAGACCATG
1 GCTAGTGTAAGACATGTCTGGGACATGCACCAGCTAC-ATGATTAGAGCT-AGTGTAAGAACATG
* ** * **
20051908 TCTGGGACATGGCATCGGTGTGGATATGTGAGA
64 TCTGGGACATGGCATCAGCATGGAGA--CAAGA
*
20051941 GCTAGTGTAAGACTATGTTTGGGACATG
1 GCTAGTGTAAGAC-ATGTCTGGGACATG
20051969 GCGTCGGCCT
Statistics
Matches: 103, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
91 1 0.01
92 36 0.35
93 1 0.01
94 51 0.50
95 14 0.14
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (94 bp):
GCTAGTGTAAGACATGTCTGGGACATGCACCAGCTACATGATTAGAGCTAGTGTAAGAACATGTC
TGGGACATGGCATCAGCATGGAGACAAGA
Found at i:20051964 original size:50 final size:49
Alignment explanation
Indices: 20051893--20052070 Score: 166
Period size: 49 Copynumber: 3.7 Consensus size: 49
20051883 CGAGATGTGT
* ** *
20051893 CAGTGTAAGACCATGTCTGGGACATGGCATCGGTGTGGATATGT-GAGAGC
1 CAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGA-AT-TCGAGAGC
* * * *
20051943 TAGTGTAAGACTATGTTTGGGACATGGCGTCGGCCTCGAATTCGATAGC
1 CAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGAATTCGAGAGC
* * * * *
20051992 CAGTGTAAGACCATGTTTGAGACATGGCATC-GACTTG-A-TGGATAAGC
1 CAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGAATTCGA-GAGC
* *
20052039 CAGTGTAAGACCATGTCTGGGAAATGGCATCG
1 CAGTGTAAGACCATGTTTGGGACATGGCATCG
20052071 ACATTATACC
Statistics
Matches: 106, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
46 3 0.03
47 32 0.30
48 5 0.05
49 34 0.32
50 32 0.30
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.25
Consensus pattern (49 bp):
CAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGAATTCGAGAGC
Found at i:20052008 original size:49 final size:48
Alignment explanation
Indices: 20051802--20052070 Score: 180
Period size: 47 Copynumber: 5.6 Consensus size: 48
20051792 TATTAGAGCT
* * * ** * *
20051802 AGTGTAAGAACATGTCTGGGACATGGCATCAG-CATTGAGA-CAAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGAC-TCGA-ATTGATAGCC
* * *
20051850 AGTGTAAGA-CATGTCTGGGACAT-GCACCAG-CTACGAGA-TG-T-GTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGACT-CGA-ATTGATAGCC
** * * *
20051894 AGTGTAAGACCATGTCTGGGACATGGCATCGGTGTGGATATGTGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGACTCGA-AT-TGATAGCC
* * * *
20051944 AGTGTAAGACTATGTTTGGGACATGGCGTCGGCCTCGAATTCGATAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGACTCGAATT-GATAGCC
* * * *
20051993 AGTGTAAGACCATGTTTGAGACATGGCATC-GACTTG-ATGGATAAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGACTCGAATTGAT-AGCC
*
20052040 AGTGTAAGACCATGTCTGGGAAATGGCATCG
1 AGTGTAAGACCATGTCTGGGACATGGCATCG
20052071 ACATTATACC
Statistics
Matches: 178, Mismatches: 32, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
44 10 0.06
45 15 0.08
46 22 0.12
47 48 0.27
48 16 0.09
49 34 0.19
50 33 0.19
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGACTCGAATTGATAGCC
Found at i:20053240 original size:20 final size:21
Alignment explanation
Indices: 20053201--20053240 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
20053191 GTTATAATGA
20053201 CCACACGGGCGTGTTGCCCTT
1 CCACACGGGCGTGTTGCCCTT
*
20053222 CCACACGGGTGTG-TGCCCT
1 CCACACGGGCGTGTTGCCCT
20053241 GTTTCAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.10, C:0.38, G:0.30, T:0.23
Consensus pattern (21 bp):
CCACACGGGCGTGTTGCCCTT
Found at i:20056293 original size:15 final size:15
Alignment explanation
Indices: 20056257--20056287 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20056247 AGGAAGAAAA
*
20056257 TACTGAGATAGAATC
1 TACTGAGACAGAATC
20056272 TACTGAGACAGAATC
1 TACTGAGACAGAATC
20056287 T
1 T
20056288 GTTGAGGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (15 bp):
TACTGAGACAGAATC
Found at i:20057792 original size:15 final size:16
Alignment explanation
Indices: 20057763--20057792 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20057753 AAGTTCAAGA
20057763 TTTCGGGACTTTTGGT
1 TTTCGGGACTTTTGGT
20057779 TTTCGGGA-TTTTGG
1 TTTCGGGACTTTTGG
20057793 GGCGTTACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.07, C:0.10, G:0.33, T:0.50
Consensus pattern (16 bp):
TTTCGGGACTTTTGGT
Found at i:20064370 original size:20 final size:20
Alignment explanation
Indices: 20064341--20064386 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
20064331 GGCACATATA
* * *
20064341 TTCATAAAATTTAAGAATTT
1 TTCATTAAATTTAACAACTT
*
20064361 TTCATTAAATTTTACAACTT
1 TTCATTAAATTTAACAACTT
20064381 TTCATT
1 TTCATT
20064387 TTAGTCCCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (20 bp):
TTCATTAAATTTAACAACTT
Found at i:20067180 original size:49 final size:51
Alignment explanation
Indices: 20067108--20067253 Score: 224
Period size: 52 Copynumber: 2.9 Consensus size: 51
20067098 ACTAGTGACT
*
20067108 CAAGTGTGGCACTATGTGAAGGCCACTTTGAGAAG-AGATAGCTT-GGTCA
1 CAAGTGTGGCACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTCGGTCA
*
20067157 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTCGGTCA
1 CAAGTGTGGCACTATGTGAAGGCCACTTTGTGAAG-AAGATAGCTTCGGTCA
* * *
20067209 CAAGTGTGACACTATGTTAAGGCCACTTTGTGAAGAAGGTAGCTT
1 CAAGTGTGGCACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTT
20067254 TGACTACAAG
Statistics
Matches: 88, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
49 33 0.38
51 18 0.20
52 37 0.42
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (51 bp):
CAAGTGTGGCACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTCGGTCA
Found at i:20067484 original size:49 final size:49
Alignment explanation
Indices: 20067412--20067509 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
20067402 TAAGATTGAT
20067412 ATGGAGTAAGTGTTACAATGAAAGTTACTACAAAGAAAACAGGAAAGAG
1 ATGGAGTAAGTGTTACAATGAAAGTTACTACAAAGAAAACAGGAAAGAG
*
20067461 ATGGAGTAAGTGTTACAATGAAAGTTACTACAAAGAAAACATGAAAGAG
1 ATGGAGTAAGTGTTACAATGAAAGTTACTACAAAGAAAACAGGAAAGAG
20067510 TGAAATTTAG
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:0.49, C:0.08, G:0.23, T:0.19
Consensus pattern (49 bp):
ATGGAGTAAGTGTTACAATGAAAGTTACTACAAAGAAAACAGGAAAGAG
Found at i:20072126 original size:79 final size:81
Alignment explanation
Indices: 20072017--20072199 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
20072007 TACTCGTTCA
* * *
20072017 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTC-GGATCTTAACCCGG
* *
20072080 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
20072097 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCACACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTCGGATCTTAACCCGGA
* *
20072160 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
20072176 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
20072200 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:20072199 original size:40 final size:40
Alignment explanation
Indices: 20072015--20072199 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
20072005 GCTACTCGTT
* * *
20072015 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
* * *
20072055 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
*
20072095 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCA-CA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACT-AGCA
* * *
20072134 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TAGCA
20072175 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
20072200 CATCATTCGA
Statistics
Matches: 124, Mismatches: 13, Indels: 16
0.81 0.08 0.10
Matches are distributed among these distances:
38 2 0.02
39 30 0.24
40 81 0.65
41 11 0.09
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
Found at i:20073488 original size:23 final size:24
Alignment explanation
Indices: 20073436--20073493 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
20073426 AAAGGATGGA
*
20073436 CACATTTT-TTTTTCTTTTGTTTT
1 CACATTTTCTTTCTCTTTTGTTTT
*
20073459 CATCATTTTCTTTCTCTTTTTTTTT
1 CA-CATTTTCTTTCTCTTTTGTTTT
20073484 C-CA-TTTCTTT
1 CACATTTTCTTT
20073494 ATTACTAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 7 0.23
23 4 0.13
24 6 0.19
25 14 0.45
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.71
Consensus pattern (24 bp):
CACATTTTCTTTCTCTTTTGTTTT
Found at i:20078148 original size:20 final size:20
Alignment explanation
Indices: 20078119--20078164 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
20078109 AGCACATGTA
* * *
20078119 TTCATAAAATTTAAGAATTT
1 TTCATTAAATTTAACAACTT
*
20078139 TTCATTAAATTTTACAACTT
1 TTCATTAAATTTAACAACTT
20078159 TTCATT
1 TTCATT
20078165 TTAGTCCTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (20 bp):
TTCATTAAATTTAACAACTT
Found at i:20078803 original size:20 final size:20
Alignment explanation
Indices: 20078762--20078803 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
20078752 AGCACATGTA
* *
20078762 TTCATAAAATTTAAGAATTT
1 TTCATAAAATTTAACAACTT
20078782 TTCATCAAAATTT-ACAACTT
1 TTCAT-AAAATTTAACAACTT
20078802 TT
1 TT
20078804 TATTTTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.45
Consensus pattern (20 bp):
TTCATAAAATTTAACAACTT
Found at i:20081583 original size:26 final size:26
Alignment explanation
Indices: 20081554--20081607 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
20081544 AGATATCGAA
*
20081554 GATGTTCCCGATACTAACTCGATAGC
1 GATGTTCCCGATACTAACTCAATAGC
20081580 GATGTTCCCGATACTAACTCAATAGC
1 GATGTTCCCGATACTAACTCAATAGC
20081606 GA
1 GA
20081608 ACTCGACCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (26 bp):
GATGTTCCCGATACTAACTCAATAGC
Found at i:20084775 original size:17 final size:19
Alignment explanation
Indices: 20084734--20084777 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
20084724 TGAAGTGTTT
*
20084734 TTTGAAAACCCTGTTTTCA
1 TTTGAAAACCCTGTCTTCA
20084753 -TTGAAAACCCT-TCTT-A
1 TTTGAAAACCCTGTCTTCA
20084769 TTTGAAAAC
1 TTTGAAAAC
20084778 TTGAGTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 1 0.04
17 11 0.48
18 11 0.48
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (19 bp):
TTTGAAAACCCTGTCTTCA
Found at i:20086069 original size:41 final size:41
Alignment explanation
Indices: 20086009--20086129 Score: 170
Period size: 41 Copynumber: 3.0 Consensus size: 41
20085999 AAAGCCAGCA
*
20086009 GTGGATCCACGGTCATCAAGCAACCATGCGATCCTTAATCG
1 GTGGATCCACGGTCATCAAGCAACCATGCGATCCTCAATCG
* * * *
20086050 GTGGATCCACGATCGTCAAGCAACTATGCAATCCTCAATCG
1 GTGGATCCACGGTCATCAAGCAACCATGCGATCCTCAATCG
* * *
20086091 GTGGATCTACGGTCATCAAGAAACCATGTGATCCTCAAT
1 GTGGATCCACGGTCATCAAGCAACCATGCGATCCTCAAT
20086130 TTCTTCCTCC
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (41 bp):
GTGGATCCACGGTCATCAAGCAACCATGCGATCCTCAATCG
Found at i:20086410 original size:27 final size:26
Alignment explanation
Indices: 20086367--20086431 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
20086357 TTTCACCCTA
*
20086367 CAAGGGTGTTTTCGTAAATGTACAAAC
1 CAAGGGT-ATTTCGTAAATGTACAAAC
* * *
20086394 CAAGGGTATTTCGGTAATTTTGCAAAC
1 CAAGGGTATTTC-GTAAATGTACAAAC
*
20086421 CAATGGTATTT
1 CAAGGGTATTT
20086432 TTGTAAGTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 4 0.12
27 28 0.88
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.34
Consensus pattern (26 bp):
CAAGGGTATTTCGTAAATGTACAAAC
Found at i:20086437 original size:27 final size:27
Alignment explanation
Indices: 20086389--20086593 Score: 153
Period size: 27 Copynumber: 7.6 Consensus size: 27
20086379 CGTAAATGTA
20086389 CAAACCAAGGGTATTTCGGTAATTTTG
1 CAAACCAAGGGTATTTCGGTAATTTTG
* **
20086416 CAAACCAATGGTATTTTTGTAAGTTTTG
1 CAAACCAAGGGTATTTCGGTAA-TTTTG
* * * *
20086444 -AAAGTCAATGGTACTTCTGTAATTTTG
1 CAAA-CCAAGGGTATTTCGGTAATTTTG
* ** * * *
20086471 TAAATTAGGGGTATTTCTGTAATTTTC
1 CAAACCAAGGGTATTTCGGTAATTTTG
* * *
20086498 CAAATCAAGGGTATTTTGGTAATTTTA
1 CAAACCAAGGGTATTTCGGTAATTTTG
* *** *
20086525 CTAATTGAGGGTATTTTGGTAATTTTG
1 CAAACCAAGGGTATTTCGGTAATTTTG
* * *
20086552 TAAACCAAGGGTA-TTCAGCAATTTTG
1 CAAACCAAGGGTATTTCGGTAATTTTG
*
20086578 TAAACCAAGGGTATTT
1 CAAACCAAGGGTATTT
20086594 TAGTAATTCT
Statistics
Matches: 145, Mismatches: 29, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
26 23 0.16
27 99 0.68
28 23 0.16
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (27 bp):
CAAACCAAGGGTATTTCGGTAATTTTG
Found at i:20086636 original size:27 final size:27
Alignment explanation
Indices: 20086590--20086665 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
20086580 AACCAAGGGT
* *
20086590 ATTTTAGTAATTCTACCCTATAGAGG-C
1 ATTTCAGTAATTCTACCCTACAG-GGAC
** *
20086617 ATTTCAGTAATTCTTTCCTACAGGGAT
1 ATTTCAGTAATTCTACCCTACAGGGAC
* *
20086644 ATTTCAGTAATACTAGCCTACA
1 ATTTCAGTAATTCTACCCTACA
20086666 AATATGAGAT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 2 0.05
27 38 0.95
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (27 bp):
ATTTCAGTAATTCTACCCTACAGGGAC
Found at i:20088670 original size:40 final size:40
Alignment explanation
Indices: 20088638--20089949 Score: 2056
Period size: 40 Copynumber: 32.8 Consensus size: 40
20088628 CCAGCATGAT
* * * * * *
20088638 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
*
20088678 TGCTCTTCGGAACTTAG-CACGGATATATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTC-CGGATACATCACTAGCACGAA
20088718 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* * * * *
20088758 TGCTCTTTGGGATTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* *
20088798 TGCTCTTCGAAACTTAGTCCGGACACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* * * * *
20088838 TACTATTTGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
20088878 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* * *
20088918 TGCTCTTTGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
20088958 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* * * * *
20088998 TGCTCTTCGGGATTTAGCCCGGATATATCACTAGCACAAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* * * *
20089038 TGATCTTTGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
20089078 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
20089118 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
20089158 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
20089198 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
20089238 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
20089278 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
20089318 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
20089358 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
20089398 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
20089438 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
20089478 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
20089518 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
20089558 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
20089598 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
20089638 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* * * *
20089678 TGCTCTTCGGGATTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* * *
20089718 TGCTCCTCTGG-ACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTC-GGAACTTAGTCCGGATACATCACTAGCACGAA
* * *
20089758 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* * * *
20089798 TGCTCCTCGGGACTTAG-CCGGGATATAACACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCC-GGATACATCACTAGCACGAA
* * * *
20089838 TGCTCTTCGGGACTTAGCCCGAATATATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* * * *
20089878 TGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* * *
20089918 TGCTCTGCAGG-ACTTAGCCCGGATATATCACT
1 TGCTCTTC-GGAACTTAGTCCGGATACATCACT
20089950 CTCAATTCTC
Statistics
Matches: 1200, Mismatches: 65, Indels: 14
0.94 0.05 0.01
Matches are distributed among these distances:
39 5 0.00
40 1188 0.99
41 7 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
Found at i:20091236 original size:153 final size:153
Alignment explanation
Indices: 20090958--20091267 Score: 593
Period size: 153 Copynumber: 2.0 Consensus size: 153
20090948 TTCCTTCGGG
20090958 CATACCATCCCTTTACCGAATATGCACATCTCATCATATACAATAGGCAGATAAACTTTCACATA
1 CATACCATCCCTTTACCGAATATGCACATCTCATCATATACAATAGGCAGATAAACTTTCACATA
20091023 AAAGTGAGCTCATGTGACATAGATAAATCATATGATTTCACATAACCTCTCACACTGATCCGATG
66 AAAGTGAGCTCATGTGACATAGATAAATCATATGATTTCACATAACCTCTCACACTGATCCGATG
20091088 TCACATAATCATAGGAATAGTCT
131 TCACATAATCATAGGAATAGTCT
*
20091111 CATACCATCCCTTTTCCGAATATGCACATCTCATCATATACAATAGGCAGATAAACTTTCACATA
1 CATACCATCCCTTTACCGAATATGCACATCTCATCATATACAATAGGCAGATAAACTTTCACATA
* *
20091176 AAAGTGAGCTCATGTGACATAGATATATCGTATGATTTCACATAACCTCTCACACTGATCCGATG
66 AAAGTGAGCTCATGTGACATAGATAAATCATATGATTTCACATAACCTCTCACACTGATCCGATG
20091241 TCACATAATCATAGGAATAGTCT
131 TCACATAATCATAGGAATAGTCT
20091264 CATA
1 CATA
20091268 GATTGCTCTC
Statistics
Matches: 154, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
153 154 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.29
Consensus pattern (153 bp):
CATACCATCCCTTTACCGAATATGCACATCTCATCATATACAATAGGCAGATAAACTTTCACATA
AAAGTGAGCTCATGTGACATAGATAAATCATATGATTTCACATAACCTCTCACACTGATCCGATG
TCACATAATCATAGGAATAGTCT
Found at i:20091544 original size:130 final size:130
Alignment explanation
Indices: 20091311--20091569 Score: 491
Period size: 130 Copynumber: 2.0 Consensus size: 130
20091301 TGATTTAGTT
* *
20091311 CAAATCAAGCTCACATATAAACTTGGAGTACATACTTTTTTAACCTTTCGCATTGAATATATTTA
1 CAAATCAAGCTCACATATAAACTTGGAGTACATACCTGTTTAACCTTTCGCATTGAATATATTTA
20091376 TAAGCAATTCTTATTACGAAGTCTTACCCGGACATAATCTCCACACGAAGTTATCGGGTCTTACG
66 TAAGCAATTCTTATTACGAAGTCTTACCCGGACATAATCTCCACACGAAGTTATCGGGTCTTACG
*
20091441 CAAATTAAGCTCACATATAAACTTGGAGTACATACCTGTTTAACCTTTCGCATTGAATATATTTA
1 CAAATCAAGCTCACATATAAACTTGGAGTACATACCTGTTTAACCTTTCGCATTGAATATATTTA
20091506 TAAGCAATTCTTATTACGAAGTCTTACCCGGACATAATCTCCACACGAAGTTATCGGGTCTTAC
66 TAAGCAATTCTTATTACGAAGTCTTACCCGGACATAATCTCCACACGAAGTTATCGGGTCTTAC
20091570 CCGGACAAAA
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 126 1.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (130 bp):
CAAATCAAGCTCACATATAAACTTGGAGTACATACCTGTTTAACCTTTCGCATTGAATATATTTA
TAAGCAATTCTTATTACGAAGTCTTACCCGGACATAATCTCCACACGAAGTTATCGGGTCTTACG
Found at i:20091576 original size:37 final size:37
Alignment explanation
Indices: 20091526--20091604 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
20091516 TTATTACGAA
* * *
20091526 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
**
20091563 GTCTTACCCGGACAAAATCCCCACACGTTGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
20091600 GTCTT
1 GTCTT
20091605 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:20091800 original size:47 final size:47
Alignment explanation
Indices: 20091722--20091941 Score: 314
Period size: 47 Copynumber: 4.6 Consensus size: 47
20091712 CCCTTCGGGA
* * * * * * * *
20091722 CTTATCACATTTATACACTTTCACATCCATCACGTTGGTCACTCGGC
1 CTTATCACATATATACACTTTCAAATTCATCACATCGGCCATTAGGC
* *
20091769 CATGTCACATATATACACTTTCAAATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCAAATTCATCACATCGGCCATTAGGC
*
20091816 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCAAATTCATCACATCGGCCATTAGGC
*
20091863 CTTATCACATATATACACTTTCATATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCAAATTCATCACATCGGCCATTAGGC
20091910 CTTATCACATATATATACACTTTCAAATTCAT
1 CTTATCAC--ATATATACACTTTCAAATTCAT
20091942 TCAAATATAC
Statistics
Matches: 156, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
47 135 0.87
49 21 0.13
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCAAATTCATCACATCGGCCATTAGGC
Found at i:20093162 original size:57 final size:57
Alignment explanation
Indices: 20093093--20093207 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
20093083 ACCAAAATCC
20093093 AATCATACATCTAACCTTTATCTCAATACCAAACCGAGTTATAAGATCATACATTAT
1 AATCATACATCTAACCTTTATCTCAATACCAAACCGAGTTATAAGATCATACATTAT
20093150 AATCATACATCTAACCTTTATCTCAATACCAAACCGAGTTATAAGATCATACATTAT
1 AATCATACATCTAACCTTTATCTCAATACCAAACCGAGTTATAAGATCATACATTAT
20093207 A
1 A
20093208 CTAAGCATAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.31
Consensus pattern (57 bp):
AATCATACATCTAACCTTTATCTCAATACCAAACCGAGTTATAAGATCATACATTAT
Found at i:20094092 original size:101 final size:101
Alignment explanation
Indices: 20093917--20094118 Score: 386
Period size: 101 Copynumber: 2.0 Consensus size: 101
20093907 TCAAAAATTA
*
20093917 ACACATGGGTCATGTTATGAGCACCAAAACAAACTCAACTTCACAAAAATTCCGAAAGAATCACA
1 ACACATGGGTCATGTTATGAGCACCAAAACAAACTCAAATTCACAAAAATTCCGAAAGAATCACA
20093982 TGATATCATACCTTAATTCCCCCCACACAAGATGGC
66 TGATATCATACCTTAATTCCCCCCACACAAGATGGC
*
20094018 ACACATGGGTCATGTTATGAGCACCAAAACAAACTCAAATTTACAAAAATTCCGAAAGAATCACA
1 ACACATGGGTCATGTTATGAGCACCAAAACAAACTCAAATTCACAAAAATTCCGAAAGAATCACA
20094083 TGATATCATACCTTAATTCCCCCCACACAAGATGGC
66 TGATATCATACCTTAATTCCCCCCACACAAGATGGC
20094119 CGAATGCCTT
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 99 1.00
ACGTcount: A:0.40, C:0.27, G:0.12, T:0.21
Consensus pattern (101 bp):
ACACATGGGTCATGTTATGAGCACCAAAACAAACTCAAATTCACAAAAATTCCGAAAGAATCACA
TGATATCATACCTTAATTCCCCCCACACAAGATGGC
Found at i:20096117 original size:40 final size:40
Alignment explanation
Indices: 20096085--20096356 Score: 391
Period size: 40 Copynumber: 6.8 Consensus size: 40
20096075 CCAGCATGAT
* * * *
20096085 TGCTCTTTGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
20096125 TGCTCTTCGGAACTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * * *
20096165 TACTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
20096205 TGCTCTTTGGGATTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * * *
20096245 TGCTCTTCGGAACTTAGTCTGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
*
20096285 TGCTCTTCGGGATTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
20096325 TGCTCTTCGGGACTTAGCCCGGATATATCACT
1 TGCTCTTCGGGACTTAGCCCGGATATATCACT
20096357 CTCAATTCTC
Statistics
Matches: 204, Mismatches: 28, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 204 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:20097684 original size:37 final size:37
Alignment explanation
Indices: 20097643--20097737 Score: 181
Period size: 37 Copynumber: 2.6 Consensus size: 37
20097633 ATATGAAGTT
*
20097643 ATCGGGTCTTACACGGACATAATCTCCACACGTAGTC
1 ATCGGGTCTTACCCGGACATAATCTCCACACGTAGTC
20097680 ATCGGGTCTTACCCGGACATAATCTCCACACGTAGTC
1 ATCGGGTCTTACCCGGACATAATCTCCACACGTAGTC
20097717 ATCGGGTCTTACCCGGACATA
1 ATCGGGTCTTACCCGGACATA
20097738 TTTCCAAGTT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (37 bp):
ATCGGGTCTTACCCGGACATAATCTCCACACGTAGTC
Found at i:20098003 original size:47 final size:47
Alignment explanation
Indices: 20097941--20098417 Score: 615
Period size: 47 Copynumber: 10.1 Consensus size: 47
20097931 ACACGTTTCG
* * * **
20097941 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* * * *
20097988 CATTGGCCATTCGGCCTTATCTCATATATGCATGGTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
20098035 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACA-T--T-A
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
20098078 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATT--TCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* * ** * *
20098123 CATTGACCATTCGGCCTTATCACGCATATATATATACAGGTTCACGTTCATCA
1 CATTGGCCATTCGGCCTTATCA--C----ACATACGCATGTTCACATTCATCA
* *
20098176 CATTGGCCATTCGGGCTTATCACACATACACATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
***
20098223 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCAT----GTTCACATTCATCA
*
20098274 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
*
20098321 CAGTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
*
20098368 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
20098415 CAT
1 CAT
20098418 AAAATCCTAA
Statistics
Matches: 384, Mismatches: 32, Indels: 28
0.86 0.07 0.06
Matches are distributed among these distances:
43 41 0.11
44 3 0.01
45 22 0.06
46 1 0.00
47 235 0.61
51 59 0.15
53 23 0.06
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.31
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
Found at i:20098195 original size:98 final size:95
Alignment explanation
Indices: 20097936--20098408 Score: 558
Period size: 98 Copynumber: 5.0 Consensus size: 95
20097926 CTCATACACG
* * * *
20097936 TTTCGCATTAGCCATTCGGCCTTACCAC-ATATAT-T-CATGTTCACATTCATCACATTGGCCAT
1 TTTCACATTGGCCATTCGGCCTTATCACAATATATATACAGGTTCACATTCATCACATTGGCCAT
* * * *
20097998 TCGGCCTTATCTCATATATGCATGGTCACA
66 TCGGCCTTATCACACATACGCATGTTCACA
* ** *
20098028 TTCATCACATTGGCCATTCGGCCTTATCAC---ACATACGCATGTTCACA-T--T-ACATTGGCC
1 TT--TCACATTGGCCATTCGGCCTTATCACAATATATATACAGGTTCACATTCATCACATTGGCC
20098086 ATTCGGCCTTATCACACATACGCATGTTCACA
64 ATTCGGCCTTATCACACATACGCATGTTCACA
* *
20098118 TTTCACATTGACCATTCGGCCTTATCACGCATATATATATACAGGTTCACGTTCATCACATTGGC
1 TTTCACATTGGCCATTCGGCCTTATCA--CA-ATATATATACAGGTTCACATTCATCACATTGGC
* *
20098183 CATTCGGGCTTATCACACATACACATGTTCACA
63 CATTCGGCCTTATCACACATACGCATGTTCACA
*
20098216 TTCATCACATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCACATTGGC
1 TT--TCACATTGGCCATTCGGCCTTATCACA-ATATATATACAGGTTCACATTCATCACATTGGC
20098281 CATTCGGCCTTATCACACATACGCATGTTCACA
63 CATTCGGCCTTATCACACATACGCATGTTCACA
* * * ** *
20098314 TCCATCACAGTGGCCATTCGGCCTTATCAC---ACATACGCATGTTCACATTCATCACATTGGCC
1 T--TTCACATTGGCCATTCGGCCTTATCACAATATATATACAGGTTCACATTCATCACATTGGCC
20098376 ATTCGGCCTTATCACACATACGCATGTTCACA
64 ATTCGGCCTTATCACACATACGCATGTTCACA
20098408 T
1 T
20098409 CCATCACATA
Statistics
Matches: 333, Mismatches: 30, Indels: 34
0.84 0.08 0.09
Matches are distributed among these distances:
88 24 0.07
90 40 0.12
91 1 0.00
92 5 0.02
93 1 0.00
94 105 0.32
95 1 0.00
97 1 0.00
98 131 0.39
100 24 0.07
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.31
Consensus pattern (95 bp):
TTTCACATTGGCCATTCGGCCTTATCACAATATATATACAGGTTCACATTCATCACATTGGCCAT
TCGGCCTTATCACACATACGCATGTTCACA
Found at i:20098328 original size:145 final size:142
Alignment explanation
Indices: 20097941--20098417 Score: 598
Period size: 145 Copynumber: 3.4 Consensus size: 142
20097931 ACACGTTTCG
*
20097941 CATTAGCCATTCGGCCTTA-C-CACATATAT-TCATGTTCACATTCATCACATTGGCCATTCGGC
1 CATTGGCCATTCGGCCTTATCACACATATATATC--GTTCACATTCATCACATTGGCCATTCGGC
* *
20098003 CTTATCTCATATATGCATGGTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCAT
64 CTTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCAT
20098068 GTTCACA-T--T-A
129 GTTCACATTCATCA
*** *
20098078 CATTGGCCATTCGGCCTTATCACACATACGCAT-GTTCACATT--TCACATTGACCATTCGGCCT
1 CATTGGCCATTCGGCCTTATCACACATATATATCGTTCACATTCATCACATTGGCCATTCGGCCT
* * * *
20098140 TATCACGCATATATATATACAGGTTCACGTTCATCACATTGGCCATTCGGGCTTATCACACATAC
66 TATCA--C----ATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATAC
*
20098205 ACATGTTCACATTCATCA
125 GCATGTTCACATTCATCA
20098223 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCACATTGGCCATTCGG
1 CATTGGCCATTCGGCCTTATCACACATATATAT-C--GTTCACATTCATCACATTGGCCATTCGG
* * * *
20098288 CCTTATCACACATACGCATGTTCACATCCATCACAGTGGCCATTCGGCCTTATCACACATACGCA
63 CCTTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCA
20098353 TGTTCACATTCATCA
128 TGTTCACATTCATCA
*** *
20098368 CATTGGCCATTCGGCCTTATCACACATACGCAT-GTTCACATCCATCACAT
1 CATTGGCCATTCGGCCTTATCACACATATATATCGTTCACATTCATCACAT
20098418 AAAATCCTAA
Statistics
Matches: 292, Mismatches: 29, Indels: 34
0.82 0.08 0.10
Matches are distributed among these distances:
135 23 0.08
137 28 0.10
138 1 0.00
139 6 0.02
140 1 0.00
141 74 0.25
142 1 0.00
144 1 0.00
145 123 0.42
149 10 0.03
151 24 0.08
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.31
Consensus pattern (142 bp):
CATTGGCCATTCGGCCTTATCACACATATATATCGTTCACATTCATCACATTGGCCATTCGGCCT
TATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGT
TCACATTCATCA
Found at i:20120920 original size:29 final size:28
Alignment explanation
Indices: 20120878--20120952 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 28
20120868 GTTACACATG
20120878 AGGCCCAAATCACATTTATATGGCCCATT
1 AGGCCCAAATCACATTTATATGG-CCATT
*
20120907 AGGCCCAAATCACATTCATATGGCCATT
1 AGGCCCAAATCACATTTATATGGCCATT
*
20120935 AGGCCCAAAACACATTTA
1 AGGCCCAAATCACATTTA
20120953 CAGTCATCCT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
28 21 0.49
29 22 0.51
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.24
Consensus pattern (28 bp):
AGGCCCAAATCACATTTATATGGCCATT
Found at i:20130267 original size:43 final size:42
Alignment explanation
Indices: 20130219--20130343 Score: 196
Period size: 43 Copynumber: 2.9 Consensus size: 42
20130209 GTTGGTATTA
20130219 TATTCGGGCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTA-TGCCGGTGATGTG
20130262 TATTCGGGCCTTCGTGCCTAGCAGGCTTCATGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTT-ATGCCGGTGATGTG
* * *
20130305 TATTCTGGCCTTCGTGCCTAGCAGGAGTAATGCCGGTGA
1 TATTCGGGCCTTCGTGCCTAGCAGG-CTTATGCCGGTGA
20130344 AATGATATGT
Statistics
Matches: 77, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
43 75 0.97
44 2 0.03
ACGTcount: A:0.14, C:0.24, G:0.33, T:0.30
Consensus pattern (42 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTATGCCGGTGATGTG
Found at i:20134564 original size:38 final size:38
Alignment explanation
Indices: 20134513--20134587 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
20134503 GTATTTGGCT
* *
20134513 TAAATCCCGCAGGCTTCGTGCTGGTATTATATTCGGGA
1 TAAATCCCGCAGGCCTAGTGCTGGTATTATATTCGGGA
*
20134551 TAAATCTCGCAGGCCTAGTGCTGGTATTATATTCGGG
1 TAAATCCCGCAGGCCTAGTGCTGGTATTATATTCGGG
20134588 CCTTCGTGCC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (38 bp):
TAAATCCCGCAGGCCTAGTGCTGGTATTATATTCGGGA
Found at i:20134638 original size:43 final size:43
Alignment explanation
Indices: 20134559--20134790 Score: 324
Period size: 43 Copynumber: 5.4 Consensus size: 43
20134549 GATAAATCTC
* * *
20134559 GCAGGCCTAGTGCTGGT-AT-TATATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
*
20134600 GCAGGCTTAGTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
*
20134643 ACAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* * ** *
20134686 GTAGGCTTCGTGCCGGTGATGTGTATTTAGGCCTTCCTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
20134729 GCAGGCTTCGTGCCGGTGATGTGTATTCGGACCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
20134772 GCAGGCGTAATGCCGGTGA
1 GCAGGCTTAGTGCCGGTGA
20134791 AATGATATGT
Statistics
Matches: 171, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
41 16 0.09
42 2 0.01
43 153 0.89
ACGTcount: A:0.13, C:0.23, G:0.33, T:0.31
Consensus pattern (43 bp):
GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
Found at i:20138333 original size:24 final size:23
Alignment explanation
Indices: 20138261--20138333 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 23
20138251 TCTGGTGCTC
20138261 CCTGATAATAACTCTTCA-GAGTTA
1 CCTGATAA-AACTCTT-ATGAGTTA
* * *
20138285 CCTG-TAAAGCTC-TATGAGCTC
1 CCTGATAAAACTCTTATGAGTTA
*
20138306 CCTGATTAAAACTCTTATGAGTTT
1 CCTGA-TAAAACTCTTATGAGTTA
20138330 CCTG
1 CCTG
20138334 TTTAGCCTGG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
20 1 0.03
21 9 0.23
22 4 0.10
23 10 0.26
24 15 0.38
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.34
Consensus pattern (23 bp):
CCTGATAAAACTCTTATGAGTTA
Found at i:20139950 original size:47 final size:44
Alignment explanation
Indices: 20139885--20140059 Score: 147
Period size: 46 Copynumber: 3.8 Consensus size: 44
20139875 GGGTTATTGT
*
20139885 GAGCTAGTGCAAGACATGTCTGGGACATGCATCGGCTACATT-ACGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATC-G--ACATTAACGA
*
20139931 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAAACGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGACATT--AACGA
* * *** * **
20139979 GAGCTAGTCTAAGACATGTCTAGGACATGCATTTTCCTCGA-GA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGACATTAACGA
*
20140022 TGTAAGCTAGTGTAAGACAGGTCTGGGACATGCATCGA
1 -G--AGCTAGTGTAAGACATGTCTGGGACATGCATCGA
20140060 TTACTAGTTG
Statistics
Matches: 104, Mismatches: 17, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
43 2 0.02
44 2 0.02
45 5 0.05
46 46 0.44
47 28 0.27
48 21 0.20
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (44 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGACATTAACGA
Found at i:20142352 original size:46 final size:46
Alignment explanation
Indices: 20142299--20142474 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
20142289 TGGTTGAGCA
*
20142299 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * * *
20142345 TCTGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
20142392 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
20142438 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
20142475 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 17, Indels: 14
0.77 0.12 0.10
Matches are distributed among these distances:
43 5 0.05
45 3 0.03
46 63 0.59
47 28 0.26
48 3 0.03
50 4 0.04
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:20142455 original size:93 final size:93
Alignment explanation
Indices: 20142296--20142466 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
20142286 GGATGGTTGA
* * *
20142296 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCTGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
20142361 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* * *
20142389 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
20142454 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
20142467 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:20149893 original size:102 final size:102
Alignment explanation
Indices: 20149717--20149902 Score: 336
Period size: 102 Copynumber: 1.8 Consensus size: 102
20149707 CAGACAAGTT
* *
20149717 TTCCATAGAAGACGAAAAATGTGAGATCGAGGGAAAAAGTCCGTTTGAACCTTAGGAATAGATTA
1 TTCCATAGAAGACGAAAAATGTGAGATCGAGGGAAAAAGCCCGTTTGAACCCTAGGAATAGATTA
20149782 GGATACAAGTGACATGTCACGAGTATCGGTTCCGATA
66 GGATACAAGTGACATGTCACGAGTATCGGTTCCGATA
**
20149819 TTCCATAGAAGACGGCAAATGTGAGATCGAGGGAAAAAGCCCGTTTGAACCCTAGGAATAGATTA
1 TTCCATAGAAGACGAAAAATGTGAGATCGAGGGAAAAAGCCCGTTTGAACCCTAGGAATAGATTA
20149884 GGATACAAGTGACATGTCA
66 GGATACAAGTGACATGTCA
20149903 ATAGGATGGT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 80 1.00
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.22
Consensus pattern (102 bp):
TTCCATAGAAGACGAAAAATGTGAGATCGAGGGAAAAAGCCCGTTTGAACCCTAGGAATAGATTA
GGATACAAGTGACATGTCACGAGTATCGGTTCCGATA
Found at i:20158165 original size:23 final size:23
Alignment explanation
Indices: 20158132--20158178 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
20158122 ATAGAAGCTG
*
20158132 TGACAGTCCTAATTTGACCCTAT
1 TGACAGCCCTAATTTGACCCTAT
20158155 TGACAGCCCTAATTTGACCCTAT
1 TGACAGCCCTAATTTGACCCTAT
20158178 T
1 T
20158179 CGGGAAGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.34
Consensus pattern (23 bp):
TGACAGCCCTAATTTGACCCTAT
Found at i:20160195 original size:40 final size:40
Alignment explanation
Indices: 20160150--20160245 Score: 140
Period size: 40 Copynumber: 2.4 Consensus size: 40
20160140 CTCGATATAT
* *
20160150 TGTATATCTGGGTTAAATTCTGCAGGCTT-AGTGCTGGTAA
1 TGTATATCTGGGTTAAATCCCGCAGGCTTCA-TGCTGGTAA
20160190 TGTATATCTGGGTTAAATCCCGCAGGCTTCATGCTGGTAA
1 TGTATATCTGGGTTAAATCCCGCAGGCTTCATGCTGGTAA
* *
20160230 AGTATATCCGGGTTAA
1 TGTATATCTGGGTTAA
20160246 GTTGTGACAG
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 50 0.98
41 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (40 bp):
TGTATATCTGGGTTAAATCCCGCAGGCTTCATGCTGGTAA
Found at i:20161947 original size:49 final size:49
Alignment explanation
Indices: 20161887--20162445 Score: 929
Period size: 49 Copynumber: 11.6 Consensus size: 49
20161877 GATAATTGTG
20161887 ATGTG-AA-TGTATATATATGTGATAAGGTCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGTCTAATGGCCGATGTGATGA
20161934 ATGTGAAAGTGTATATATATGTGATAAGGTCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGTCTAATGGCCGATGTGATGA
20161983 ATGTGAAAGTGTATATATATGTGATAAGGTCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGTCTAATGGCCGATGTGATGA
20162032 ATGTGAAAGTGTATATATATGTGATAAGGTCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGTCTAATGGCCGATGTGATGA
20162081 ATGTGAAAGTGTATATATATGTGATAAGGTCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGTCTAATGGCCGATGTGATGA
20162130 ATGTGAAAGTGTATATATATGTGATAAGGTCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGTCTAATGGCCGATGTGATGA
*
20162179 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGTCTAATGGCCGATGTGATGA
* * *
20162228 ATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGTCTAATGGCCGATGTGATGA
20162275 ATGTGAAAGTGTATATATATGTGATAAGGTCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGTCTAATGGCCGATGTGATGA
* *
20162324 ATGTGAAAGTGTATATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGTCTAATGGCCGATGTGATGA
* * * * * * *
20162373 ATGTGAAAGTG--TATATATGTGA-CAGAGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATATGTGATAAG-GTCTAATGGCCGATGTGATGA
20162420 ATGTGAAAGTGTATA-A-ATGTGATAAG
1 ATGTGAAAGTGTATATATATGTGATAAG
20162446 TCCCGAAGGG
Statistics
Matches: 489, Mismatches: 15, Indels: 15
0.94 0.03 0.03
Matches are distributed among these distances:
46 2 0.00
47 94 0.19
48 5 0.01
49 388 0.79
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.31
Consensus pattern (49 bp):
ATGTGAAAGTGTATATATATGTGATAAGGTCTAATGGCCGATGTGATGA
Found at i:20170194 original size:19 final size:21
Alignment explanation
Indices: 20170170--20170218 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
20170160 TGCTGAAACT
20170170 AAGAAA-GAA-AAGATTGAAA
1 AAGAAACGAAGAAGATTGAAA
*
20170189 AAGAAACTAAGGCAAGATTGAAA
1 AAGAAACGAA-G-AAGATTGAAA
20170212 AAGAAAC
1 AAGAAAC
20170219 TAAGGCATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 6 0.24
20 2 0.08
23 17 0.68
ACGTcount: A:0.63, C:0.06, G:0.20, T:0.10
Consensus pattern (21 bp):
AAGAAACGAAGAAGATTGAAA
Found at i:20170206 original size:23 final size:23
Alignment explanation
Indices: 20170179--20170225 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
20170169 TAAGAAAGAA
20170179 AAGATTGAAAAAGAAACTAAGGC
1 AAGATTGAAAAAGAAACTAAGGC
20170202 AAGATTGAAAAAGAAACTAAGGC
1 AAGATTGAAAAAGAAACTAAGGC
20170225 A
1 A
20170226 TTCGGCCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.57, C:0.09, G:0.21, T:0.13
Consensus pattern (23 bp):
AAGATTGAAAAAGAAACTAAGGC
Found at i:20171809 original size:40 final size:40
Alignment explanation
Indices: 20171764--20171923 Score: 198
Period size: 40 Copynumber: 4.0 Consensus size: 40
20171754 CTCGATATAT
*
20171764 TGTATATCCGGGTTAAATTCCGCAGGCTTAGTGCTGGTAA
1 TGTATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTAA
* *
20171804 TGTATATCCGGGTTAGATCCCGCAGGCTTCGTGCTGGTAA
1 TGTATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTAA
* *
20171844 AGTATATCCGGGTTAAATCCCGCAGGCTTAGTCCTGGT-A
1 TGTATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTAA
* * * * *
20171883 -CTATATCCGGGCCTAAAGTCCCACAGGCTTTGTGCTAGTAA
1 TGTATATCCGGG-TTAAA-TCCCGCAGGCTTAGTGCTGGTAA
20171924 CTGGATTCGG
Statistics
Matches: 104, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
38 10 0.10
39 5 0.05
40 88 0.85
41 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (40 bp):
TGTATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTAA
Found at i:20175827 original size:27 final size:27
Alignment explanation
Indices: 20175727--20175821 Score: 118
Period size: 27 Copynumber: 3.5 Consensus size: 27
20175717 CTCATATTTG
* * * * *
20175727 TAGGCTAGTATTACTGAAATACTCCTA
1 TAGGGTAGAATTACTAAAATGCCCCTA
*
20175754 TATGGTAGAATTACTAAAATGCCCCTA
1 TAGGGTAGAATTACTAAAATGCCCCTA
* *
20175781 TAGGATAGAATTACTAAAATGCCCCTG
1 TAGGGTAGAATTACTAAAATGCCCCTA
20175808 TAGGGTAGAATTAC
1 TAGGGTAGAATTAC
20175822 AGAAATACTC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (27 bp):
TAGGGTAGAATTACTAAAATGCCCCTA
Found at i:20175846 original size:27 final size:26
Alignment explanation
Indices: 20175816--20175884 Score: 86
Period size: 25 Copynumber: 2.6 Consensus size: 26
20175806 TGTAGGGTAG
*
20175816 AATTACAGAAATACTCTTGGTTTAAAA
1 AATTACA-AAATACCCTTGGTTTAAAA
* *
20175843 AATTACTAAA-ACCCTTGGTTTACAA
1 AATTACAAAATACCCTTGGTTTAAAA
20175868 AATTACCAAAATACCCT
1 AATTA-CAAAATACCCT
20175885 CGATTAGCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 18 0.50
26 7 0.19
27 11 0.31
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.30
Consensus pattern (26 bp):
AATTACAAAATACCCTTGGTTTAAAA
Found at i:20176032 original size:81 final size:81
Alignment explanation
Indices: 20175894--20176089 Score: 216
Period size: 81 Copynumber: 2.4 Consensus size: 81
20175884 TCGATTAGCA
* * * * * **
20175894 AAATACCCTTAAATTGTGAAATTACCAAAATACCCTTGACCTGTTAAATTACTGAAATACCCTTG
1 AAATACCCTTAATTTATAAAATTACCAAAATACCCCTAACCTGGAAAATTACTGAAATACCCTTG
* *
20175959 ACTT-GTCAAATTATCG
66 ACTTAG-AAAATTATAG
**
20175975 AAATACCCTTAATTTATAAAATTACCAAAATACCCCTAATTTGGAAAATTA-TCGAAATACCCTT
1 AAATACCCTTAATTTATAAAATTACCAAAATACCCCTAACCTGGAAAATTACT-GAAATACCCTT
*
20176039 GATTTAGAAAATTATAG
65 GACTTAGAAAATTATAG
* * * *
20176056 AAATACCCCTGATTTACAAAATTACCGAAATACC
1 AAATACCCTTAATTTATAAAATTACCAAAATACC
20176090 TTTAGTTTGT
Statistics
Matches: 97, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
80 1 0.01
81 95 0.98
82 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (81 bp):
AAATACCCTTAATTTATAAAATTACCAAAATACCCCTAACCTGGAAAATTACTGAAATACCCTTG
ACTTAGAAAATTATAG
Found at i:20176043 original size:27 final size:27
Alignment explanation
Indices: 20175894--20176089 Score: 151
Period size: 27 Copynumber: 7.3 Consensus size: 27
20175884 TCGATTAGCA
* * *
20175894 AAATACCCTTAAATTGTG-AAATTACCA
1 AAATACCCTTGATTTG-GAAAATTACCG
** ** *
20175921 AAATACCCTTGACCTGTTAAATTACTG
1 AAATACCCTTGATTTGGAAAATTACCG
* ** *
20175948 AAATACCCTTGACTTGTCAAATTATCG
1 AAATACCCTTGATTTGGAAAATTACCG
* ** *
20175975 AAATACCCTTAATTTATAAAATTACCA
1 AAATACCCTTGATTTGGAAAATTACCG
* * *
20176002 AAATACCCCTAATTTGGAAAATTATCG
1 AAATACCCTTGATTTGGAAAATTACCG
* **
20176029 AAATACCCTTGATTTAGAAAATTATAG
1 AAATACCCTTGATTTGGAAAATTACCG
* **
20176056 AAATACCCCTGATTTACAAAATTACCG
1 AAATACCCTTGATTTGGAAAATTACCG
20176083 AAATACC
1 AAATACC
20176090 TTTAGTTTGT
Statistics
Matches: 139, Mismatches: 29, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
27 139 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
AAATACCCTTGATTTGGAAAATTACCG
Found at i:20176385 original size:41 final size:41
Alignment explanation
Indices: 20176338--20176460 Score: 158
Period size: 41 Copynumber: 3.0 Consensus size: 41
20176328 AGAGGAAGAA
* * *
20176338 ATTGAGGATCACATGGTTGCTTAAAGACTGTGGATCTACCG
1 ATTGAGGATCGCATGGTTGCTTAACGACTGTGGATCCACCG
*
20176379 ATTGAGGATCGCATGGTTGCTTAACGA-TCGTGGATCCACTG
1 ATTGAGGATCGCATGGTTGCTTAACGACT-GTGGATCCACCG
* * * *
20176420 ATTAAGGATCGCATGCTTGCTTGACGACCGTGGATCCACCG
1 ATTGAGGATCGCATGGTTGCTTAACGACTGTGGATCCACCG
20176461 GTGGATTTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
40 1 0.01
41 70 0.99
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (41 bp):
ATTGAGGATCGCATGGTTGCTTAACGACTGTGGATCCACCG
Found at i:20176635 original size:22 final size:22
Alignment explanation
Indices: 20176605--20176666 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
20176595 AATTATTCTG
* *
20176605 ATTATGGCTTTGCGCCAACCTA
1 ATTATGGCTCTGTGCCAACCTA
20176627 CA-TATGGCTCTGTGCCAACCTA
1 -ATTATGGCTCTGTGCCAACCTA
*
20176649 ATTATGGCTGTGTGCCAA
1 ATTATGGCTCTGTGCCAA
20176667 ACGTATTTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31
Consensus pattern (22 bp):
ATTATGGCTCTGTGCCAACCTA
Found at i:20179630 original size:27 final size:27
Alignment explanation
Indices: 20179600--20179707 Score: 137
Period size: 27 Copynumber: 4.0 Consensus size: 27
20179590 AATCTCAAAT
* *
20179600 CTGTAGGCTAGTATTACTGAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
*
20179627 CTGTAGGGTAGAATTACTGAAATGCCC
1 CTGTAGGGTAGAATTACTGAAATACCC
* * * *
20179654 CTATAGGATAGAATTATTGAAATGCCC
1 CTGTAGGGTAGAATTACTGAAATACCC
20179681 CTGTAGGGTAGAATTTA-TGAAATACCC
1 CTGTAGGGTAGAA-TTACTGAAATACCC
20179708 TTGGTTTACA
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
27 68 0.96
28 3 0.04
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (27 bp):
CTGTAGGGTAGAATTACTGAAATACCC
Found at i:20179730 original size:25 final size:27
Alignment explanation
Indices: 20179700--20179761 Score: 92
Period size: 25 Copynumber: 2.4 Consensus size: 27
20179690 AGAATTTATG
* *
20179700 AAATACCCTTGGTTTACAAAA-TA-CT
1 AAATACCCTTGATTTACAAAATTACCA
20179725 AAATACCCTTGATTTACAAAATTACCA
1 AAATACCCTTGATTTACAAAATTACCA
20179752 AAATACCCTT
1 AAATACCCTT
20179762 AATTAGCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 20 0.61
26 2 0.06
27 11 0.33
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.31
Consensus pattern (27 bp):
AAATACCCTTGATTTACAAAATTACCA
Found at i:20179791 original size:18 final size:18
Alignment explanation
Indices: 20179744--20179783 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
20179734 TGATTTACAA
*
20179744 AATTACCAAAATACCCTT
1 AATTAGCAAAATACCCTT
20179762 AATTAGCAAAATACCCTT
1 AATTAGCAAAATACCCTT
20179780 AATT
1 AATT
20179784 TGTGAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.23, G:0.03, T:0.30
Consensus pattern (18 bp):
AATTAGCAAAATACCCTT
Found at i:20179792 original size:27 final size:27
Alignment explanation
Indices: 20179770--20180031 Score: 192
Period size: 27 Copynumber: 9.7 Consensus size: 27
20179760 TTAATTAGCA
* * * *
20179770 AAATACCCTTAATTTGTGAAATTACCT
1 AAATACCCTTGATTTGTAAAATTATCG
**
20179797 AAATACCCTTGACCTGTAAAATTATCG
1 AAATACCCTTGATTTGTAAAATTATCG
* * * * *
20179824 AAACACCCTCGACTTGTTAAATTACCG
1 AAATACCCTTGATTTGTAAAATTATCG
* *
20179851 AAATACCCTCGATTTGTAAAATTATCA
1 AAATACCCTTGATTTGTAAAATTATCG
* * *
20179878 AAATAACCC-TAATTTGGAAAAATATCG
1 AAAT-ACCCTTGATTTGTAAAATTATCG
*
20179905 AAATACCCTTGATTTG-AAAATT-TACAA
1 AAATACCCTTGATTTGTAAAATTAT-C-G
* * * *
20179932 AAATACCCCTGACTTGCAAAATTATAG
1 AAATACCCTTGATTTGTAAAATTATCG
* **
20179959 AAATACCCTTAACTTTCAAAAATTA-CAG
1 AAATACCCTTGA-TTTGTAAAATTATC-G
* *
20179987 AAATACCATT-AGTTTGCAAAATTATCG
1 AAATACCCTTGA-TTTGTAAAATTATCG
*
20180014 AAATACCCTTGGTTTGTA
1 AAATACCCTTGATTTGTA
20180032 GATTTACCAA
Statistics
Matches: 184, Mismatches: 41, Indels: 20
0.75 0.17 0.08
Matches are distributed among these distances:
25 1 0.01
26 10 0.05
27 142 0.77
28 30 0.16
29 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATACCCTTGATTTGTAAAATTATCG
Found at i:20180410 original size:41 final size:41
Alignment explanation
Indices: 20180292--20180410 Score: 175
Period size: 41 Copynumber: 2.9 Consensus size: 41
20180282 GAAGAAATTG
** * ** *
20180292 AGGATCGCATGGTTGCTTGGTGACCGTGAATCCACTAATTG
1 AGGATCGCATGGTTGCTTGACGACCGTGGATCCACCGATTA
20180333 AGGATCGCATGGTTGCTTGACGACCGTGGATCCACCGATTA
1 AGGATCGCATGGTTGCTTGACGACCGTGGATCCACCGATTA
*
20180374 AGGATCGCATGGTTGCTTGACGACCTTGGATCCACCG
1 AGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
20180411 GCGACTTTTA
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (41 bp):
AGGATCGCATGGTTGCTTGACGACCGTGGATCCACCGATTA
Found at i:20183597 original size:27 final size:27
Alignment explanation
Indices: 20183568--20183675 Score: 135
Period size: 27 Copynumber: 4.0 Consensus size: 27
20183558 AATCTCATAT
* * *
20183568 CTGTAGGCTAGTATTACTGAAATACCT
1 CTGTAGGATAGAATTACTGAAATACCC
* * *
20183595 CTGTAGGGTCGAATTACTGAAATGCCC
1 CTGTAGGATAGAATTACTGAAATACCC
* *
20183622 CTGTAAGATAGAATTACTGAAATGCCC
1 CTGTAGGATAGAATTACTGAAATACCC
*
20183649 CTGTAGGATAGAATTTCTGAAATACCC
1 CTGTAGGATAGAATTACTGAAATACCC
20183676 TTGGTTTACA
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 70 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (27 bp):
CTGTAGGATAGAATTACTGAAATACCC
Found at i:20183697 original size:26 final size:27
Alignment explanation
Indices: 20183668--20183729 Score: 108
Period size: 26 Copynumber: 2.3 Consensus size: 27
20183658 AGAATTTCTG
*
20183668 AAATACCCTTGGTTTACAAAATTA-CT
1 AAATACCCTTGGTTTACAAAATTACCA
20183694 AAATACCCTTGGTTTACAAAATTACCA
1 AAATACCCTTGGTTTACAAAATTACCA
20183721 AAATACCCT
1 AAATACCCT
20183730 CAATTAGCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 24 0.71
27 10 0.29
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (27 bp):
AAATACCCTTGGTTTACAAAATTACCA
Found at i:20183734 original size:18 final size:19
Alignment explanation
Indices: 20183713--20183748 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20183703 TGGTTTACAA
20183713 AATTACCAAAA-TACCCTC
1 AATTACCAAAATTACCCTC
*
20183731 AATTAGCAAAATTACCCT
1 AATTACCAAAATTACCCT
20183749 GATTTGTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.44, C:0.28, G:0.03, T:0.25
Consensus pattern (19 bp):
AATTACCAAAATTACCCTC
Found at i:20183804 original size:27 final size:27
Alignment explanation
Indices: 20183774--20183825 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
20183764 AGAAATATCC
* *
20183774 TTGACCTGTAAAATTCCCTAAATACTG
1 TTGACCTGTAAAATTACCGAAATACTG
* *
20183801 TTGACTTGTTAAATTACCGAAATAC
1 TTGACCTGTAAAATTACCGAAATAC
20183826 CCTCGATTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (27 bp):
TTGACCTGTAAAATTACCGAAATACTG
Found at i:20183888 original size:27 final size:27
Alignment explanation
Indices: 20183811--20183897 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 27
20183801 TTGACTTGTT
* * *
20183811 AAATTACCGAAATACCCTCGATTTGTA
1 AAATTACCGATATACCCTTGATTTGGA
* * *
20183838 AAATTACCAATATACCCCTAATTTGGA
1 AAATTACCGATATACCCTTGATTTGGA
* * *
20183865 AAATTACTGATATACCTTTGATTTAGA
1 AAATTACCGATATACCCTTGATTTGGA
20183892 AAATTA
1 AAATTA
20183898 TAGAAATACC
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.33
Consensus pattern (27 bp):
AAATTACCGATATACCCTTGATTTGGA
Found at i:20183980 original size:27 final size:27
Alignment explanation
Indices: 20183811--20183993 Score: 81
Period size: 27 Copynumber: 6.7 Consensus size: 27
20183801 TTGACTTGTT
* * * *
20183811 AAATTACCGAAATACCCTCGATTTGTA
1 AAATTATCGAAATACCCTTGGTTTGCA
* * ** *
20183838 AAATTA-CCAATATACCCCTAATTTGGA
1 AAATTATCGAA-ATACCCTTGGTTTGCA
* * *
20183865 AAATTA-CTGATATACCTTTGATTTAG-A
1 AAATTATC-GAAATACCCTTGGTTT-GCA
*
20183892 AAATTATAGAAATACCC-TGGACTTT-CA
1 AAATTATCGAAATACCCTTGG--TTTGCA
* *
20183919 AAAGTTA-CAAAAATACCATTGGTTTGCA
1 AAA-TTATC-GAAATACCCTTGGTTTGCA
* *
20183947 AAATTATTGAAATACCCTTGGTTTGTA
1 AAATTATCGAAATACCCTTGGTTTGCA
* * *
20183974 GATTTATCGAAACACCCTTG
1 AAATTATCGAAATACCCTTG
20183994 TAGGGTGAAA
Statistics
Matches: 119, Mismatches: 25, Indels: 24
0.71 0.15 0.14
Matches are distributed among these distances:
26 5 0.04
27 91 0.76
28 20 0.17
29 3 0.03
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (27 bp):
AAATTATCGAAATACCCTTGGTTTGCA
Found at i:20184286 original size:41 final size:41
Alignment explanation
Indices: 20184231--20184353 Score: 147
Period size: 41 Copynumber: 3.0 Consensus size: 41
20184221 AGAGGAAGAA
* * *
20184231 ATTAAGGATCGCATGGTTGCTTGACGACCGTGGATCAACTG
1 ATTAAGAATTGCATGGTTGCTTGACGACCGTGGATCAACCG
* * * *
20184272 ATTGAGAATTGCATGGTTGCTTGACTACTGTGGATCCACCG
1 ATTAAGAATTGCATGGTTGCTTGACGACCGTGGATCAACCG
* * * *
20184313 ATTAAGGATTCCATGGTTGCTTGACGATCGTGGATCCACCG
1 ATTAAGAATTGCATGGTTGCTTGACGACCGTGGATCAACCG
20184354 GTAGCTTTTA
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (41 bp):
ATTAAGAATTGCATGGTTGCTTGACGACCGTGGATCAACCG
Found at i:20184547 original size:22 final size:22
Alignment explanation
Indices: 20184495--20184548 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
20184485 GCCAATTATT
* *
20184495 CTGATTATGGCTTTGCGCCAAC
1 CTGATTATGGCTCTACGCCAAC
* *
20184517 CT-ACATATGGCTCTATGCCAAC
1 CTGA-TTATGGCTCTACGCCAAC
20184539 CTGATTATGG
1 CTGATTATGG
20184549 TTGTGTGCCA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.31
Consensus pattern (22 bp):
CTGATTATGGCTCTACGCCAAC
Done.