Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold337
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1638316
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.28
Warning! 264207 characters in sequence are not A, C, G, or T
File 4 of 5
Found at i:624299 original size:35 final size:35
Alignment explanation
Indices: 624239--624328 Score: 112
Period size: 35 Copynumber: 2.6 Consensus size: 35
624229 ATATAGAAAC
*
624239 AGAGAAAAGAGAGACAGGA-AAAAGAGAGAAAGGA-
1 AGAGAAAAGAGAGAGA-GATAAAAGAGAGAAAGGAG
* *
624273 AGAGAAAAGTAGAGAGAGATAGAAGAGAGAGAGGAG
1 AGAGAAAAG-AGAGAGAGATAAAAGAGAGAAAGGAG
*
624309 AGAGAAAACAGAGAGAGATA
1 AGAGAAAAGAGAGAGAGATA
624329 TATAGATTCC
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
34 11 0.22
35 30 0.61
36 8 0.16
ACGTcount: A:0.58, C:0.02, G:0.37, T:0.03
Consensus pattern (35 bp):
AGAGAAAAGAGAGAGAGATAAAAGAGAGAAAGGAG
Found at i:624420 original size:2 final size:2
Alignment explanation
Indices: 624413--624438 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
624403 NNNNCAAACA
624413 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
624439 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:632684 original size:105 final size:105
Alignment explanation
Indices: 632502--632703 Score: 377
Period size: 105 Copynumber: 1.9 Consensus size: 105
632492 TAATTCCTTG
632502 GTTCTCAGGGCCTAGCATTGCAGTGATTTAAACTTAATTATAACAAAACGCAAATGGCTGCCGAA
1 GTTCTCAGGGCCTAGCATTGCAGTGATTTAAACTTAATTATAACAAAACGCAAATGGCTGCCGAA
632567 TCTAGTTACAAACGTCGTGATCAAGTTATGATCATTATTA
66 TCTAGTTACAAACGTCGTGATCAAGTTATGATCATTATTA
* * *
632607 GTTCTCGGGGCCTAGCATTGCAGTGATTTAAACTTTATTATAACAAAATGCAAATGGCTGCCGAA
1 GTTCTCAGGGCCTAGCATTGCAGTGATTTAAACTTAATTATAACAAAACGCAAATGGCTGCCGAA
632672 TCTAGTTACAAACGTCGTGATCAAGTTATGAT
66 TCTAGTTACAAACGTCGTGATCAAGTTATGAT
632704 TGCGACAGCA
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 94 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (105 bp):
GTTCTCAGGGCCTAGCATTGCAGTGATTTAAACTTAATTATAACAAAACGCAAATGGCTGCCGAA
TCTAGTTACAAACGTCGTGATCAAGTTATGATCATTATTA
Found at i:637695 original size:8 final size:8
Alignment explanation
Indices: 637674--637719 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 8
637664 GATCACATTT
637674 TGTCCGTC
1 TGTCCGTC
637682 -GTCCGTC
1 TGTCCGTC
637689 TGT-C--C
1 TGTCCGTC
637694 -GTCCGTC
1 TGTCCGTC
637701 TGTCCGTC
1 TGTCCGTC
637709 TGTCCGTC
1 TGTCCGTC
637717 TGT
1 TGT
637720 AAACTTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
4 2 0.06
5 2 0.06
7 9 0.27
8 20 0.61
ACGTcount: A:0.00, C:0.37, G:0.26, T:0.37
Consensus pattern (8 bp):
TGTCCGTC
Found at i:637697 original size:4 final size:4
Alignment explanation
Indices: 637675--637716 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
637665 ATCACATTTT
* * *
637675 GTCC GT-C GTCC GTCT GTCC GTCC GTCT GTCC GTCT GTCC GTC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTC
637717 TGTAAACTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.00, C:0.40, G:0.26, T:0.33
Consensus pattern (4 bp):
GTCC
Found at i:637698 original size:12 final size:12
Alignment explanation
Indices: 637681--637708 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
637671 TTTTGTCCGT
637681 CGTCCGTCTGTC
1 CGTCCGTCTGTC
637693 CGTCCGTCTGTC
1 CGTCCGTCTGTC
637705 CGTC
1 CGTC
637709 TGTCCGTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.43, G:0.25, T:0.32
Consensus pattern (12 bp):
CGTCCGTCTGTC
Found at i:649684 original size:2 final size:2
Alignment explanation
Indices: 649677--649713 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
649667 ATATCAAATT
649677 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
649714 TCTGCTTTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:653559 original size:2 final size:2
Alignment explanation
Indices: 653552--653577 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
653542 CTGATGTTTT
653552 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
653578 CCGACCGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:662687 original size:46 final size:46
Alignment explanation
Indices: 662497--662853 Score: 300
Period size: 46 Copynumber: 7.8 Consensus size: 46
662487 TGTTTTATAA
* ** *
662497 GTAAACAATGCATAGCT-ATAAAATATGTATACGTATAACATT-TTA-AA
1 GTAAACAATGCATAG-TAATGAAATATGTATAC--AT-ATTTTATTACAT
* ** * *
662544 GTAAACAGTGCATAGTAATG-AATATGTATACATAAATTATTAAAAA
1 GTAAACAATGCATAGTAATGAAATATGTATACATATTTTATT-ACAT
** * * *
662590 AAAAACAATGAATAGTAATGAAATATATATATACATATATTATTA-A-
1 GTAAACAATGCATAGTAATG-AA-ATATGTATACATATTTTATTACAT
* * *
662636 ATAAACATTGCATAGTAATGAAAAATGTA-AGCATATTTTATTACAT
1 GTAAACAATGCATAGTAATGAAATATGTATA-CATATTTTATTACAT
* * *
662682 GTAAACAATGCATAGGAATGAGA-ATGTATACATATTTTGTTACAT
1 GTAAACAATGCATAGTAATGAAATATGTATACATATTTTATTACAT
* * **
662727 GTAAATAATGCACAGTAATGAAATATGT-TCACATATTTGGTTACAT
1 GTAAACAATGCATAGTAATGAAATATGTAT-ACATATTTTATTACAT
* * * *
662773 GTAAACAATGCATAGTAATGTAATGTGTATAAATATTTTATCACAT
1 GTAAACAATGCATAGTAATGAAATATGTATACATATTTTATTACAT
* *
662819 GTTAACAATACATAGTAATGAAATATGTATACATA
1 GTAAACAATGCATAGTAATGAAATATGTATACATA
662854 ACAGTACATA
Statistics
Matches: 258, Mismatches: 38, Indels: 29
0.79 0.12 0.09
Matches are distributed among these distances:
43 5 0.02
44 20 0.08
45 43 0.17
46 152 0.59
47 18 0.07
48 2 0.01
49 18 0.07
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.33
Consensus pattern (46 bp):
GTAAACAATGCATAGTAATGAAATATGTATACATATTTTATTACAT
Found at i:662762 original size:91 final size:93
Alignment explanation
Indices: 662637--662846 Score: 257
Period size: 91 Copynumber: 2.3 Consensus size: 93
662627 TATTATTAAA
* * *
662637 TAAACATTGCATAGTAATGAAAAATG-TAAGCATATTTTATTACATGTAAACAATGCATAGGAAT
1 TAAACAATGCATAGTAATGAAATATGTTAAGCATATTTGATTACATGTAAACAATGCATAGGAAT
* * *
662701 G-AGA-ATGTATACATATTTTGTTACATG
66 GTA-ATATGTATAAATATTTTATCACATG
* * * * *
662728 TAAATAATGCACAGTAATGAAATATGTTCA-CATATTTGGTTACATGTAAACAATGCATAGTAAT
1 TAAACAATGCATAGTAATGAAATATGTTAAGCATATTTGATTACATGTAAACAATGCATAGGAAT
*
662792 GTAATGTGTATAAATATTTTATCACATG
66 GTAATATGTATAAATATTTTATCACATG
* *
662820 TTAACAATACATAGTAATGAAATATGT
1 TAAACAATGCATAGTAATGAAATATGT
662847 ATACATAACA
Statistics
Matches: 100, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
91 55 0.55
92 45 0.45
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (93 bp):
TAAACAATGCATAGTAATGAAATATGTTAAGCATATTTGATTACATGTAAACAATGCATAGGAAT
GTAATATGTATAAATATTTTATCACATG
Found at i:662862 original size:31 final size:31
Alignment explanation
Indices: 662821--662884 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
662811 TATCACATGT
662821 TAACAATACATAGTAATGAAATATGTATACA
1 TAACAATACATAGTAATGAAATATGTATACA
*
662852 TAACAGTACATAGTAATGAAATATGTATACA
1 TAACAATACATAGTAATGAAATATGTATACA
662883 TA
1 TA
662885 TTTTATTACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (31 bp):
TAACAATACATAGTAATGAAATATGTATACA
Found at i:662913 original size:46 final size:46
Alignment explanation
Indices: 662860--662949 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
662850 CATAACAGTA
*
662860 CATAGTAATGAAATATGTATACATATTTTATTACATGTAAACAATG
1 CATAGTAATGAAATATGTATACATATTTTACTACATGTAAACAATG
* * **
662906 CATAGTAATGAAATGTGTTTGTATATTTTACTACATGTAAACAA
1 CATAGTAATGAAATATGTATACATATTTTACTACATGTAAACAA
662950 GGTGAGCGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (46 bp):
CATAGTAATGAAATATGTATACATATTTTACTACATGTAAACAATG
Found at i:667706 original size:98 final size:98
Alignment explanation
Indices: 667553--667771 Score: 266
Period size: 98 Copynumber: 2.2 Consensus size: 98
667543 TAGACTCTCC
* * * *
667553 AATTGTATGAGGTCTTTACTAGAGACAGGAGTAGGCGAATAGGCGTCTAATTATGAAACATCAAT
1 AATTGTATGAGGTCTTTACTAGAGACAGGAGTAGGCGAAGAGACGTCTAAATATGAAACATCAAC
* *
667618 ACAAAGAGGTTAGGTCCATAT-AGATAAGACTCT
66 ACAAAGAGGTTAAGTCCATATGA-ATAAGACTAT
*
667651 AATTGTATGAGGTCTTTACTAGAGACA-GAGGTAGAG-GAAGAGACGTC-AAGATATGAAACATT
1 AATTGTATGAGGTCTTTACTAGAGACAGGA-GTAG-GCGAAGAGACGTCTAA-ATATGAAACATC
* *
667713 AACACAAAGTGGTTAAGTCCATATGAATAAGTCTAT
63 AACACAAAGAGGTTAAGTCCATATGAATAAGACTAT
* * *
667749 AATTGCATGAGTTGTTTACTAGA
1 AATTGTATGAGGTCTTTACTAGA
667772 CCAAATGGTT
Statistics
Matches: 105, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
97 4 0.04
98 99 0.94
99 2 0.02
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.27
Consensus pattern (98 bp):
AATTGTATGAGGTCTTTACTAGAGACAGGAGTAGGCGAAGAGACGTCTAAATATGAAACATCAAC
ACAAAGAGGTTAAGTCCATATGAATAAGACTAT
Found at i:673550 original size:1 final size:1
Alignment explanation
Indices: 673517--673541 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
673507 ATCACCTTGG
673517 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
673542 CAACAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:674061 original size:4 final size:4
Alignment explanation
Indices: 674054--674081 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
674044 GGGACAGACA
674054 GACG GACG GACG GACG GACG GACG GACG
1 GACG GACG GACG GACG GACG GACG GACG
674082 CAGAGGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.50, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:675368 original size:162 final size:161
Alignment explanation
Indices: 675134--675656 Score: 821
Period size: 162 Copynumber: 3.2 Consensus size: 161
675124 CTATGTTATC
* * * * *
675134 TCTTGGGATATAATTGGGGCTGTCCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATTTCATC
1 TCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAGTAAGGTTTTAAAAATTTAAATTTCATC
* *
675199 CAGGGAGTCAAATAGTAGCAGAAAATTGACGTTTATCACTAAAAAAGAATATAGATCCTAGAAAT
66 CAGGGAGTCAAATAGTAGCAGAAAATTGACGTTTATCACTAAAAAA-AACATAGATCCTAGAACT
675264 CCTCTTATGATTTAATGGATAGACACATCATA
130 CCTCTTATGATTTAATGGATAGACACATCATA
* * *
675296 TCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAGTAAAGTTGTAAAAATTTGAATTTCATC
1 TCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAGTAAGGTTTTAAAAATTTAAATTTCATC
* * * *
675361 CAGGGAGTCAAATAGTAGCAGAAAATGGACGTTTATCTCTAAAAAAACCCATAGATCCAAGAACT
66 CAGGGAGTCAAATAGTAGCAGAAAATTGACGTTTATCACTAAAAAAA-ACATAGATCCTAGAACT
*
675426 CCTCTTATGATTTAACGGATAGACACATCATA
130 CCTCTTATGATTTAATGGATAGACACATCATA
* *
675458 TCTTGAGATATGATAGGGACTGTTCTAAAGATGTGCAGTAAGGTTTTAAAAATTTAAATTTCATC
1 TCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAGTAAGGTTTTAAAAATTTAAATTTCATC
*
675523 CAGGGAGTCAAATAGTAGCAGAAAATTGACGTTTATCACTAAAAAAAACCATAAATCCTAGAACT
66 CAGGGAGTCAAATAGTAGCAGAAAATTGACGTTTATCACTAAAAAAAA-CATAGATCCTAGAACT
*
675588 CCTCTTATGATTTAATGGATGGACACATCATA
130 CCTCTTATGATTTAATGGATAGACACATCATA
* **
675620 TCTTGGGATATGATAGGAACTGTTCCCTAGATGTGCA
1 TCTTGGGATATGATAGGGACTGTTCTATAGATGTGCA
675657 ATACTGTTTT
Statistics
Matches: 327, Mismatches: 32, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
161 1 0.00
162 326 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (161 bp):
TCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAGTAAGGTTTTAAAAATTTAAATTTCATC
CAGGGAGTCAAATAGTAGCAGAAAATTGACGTTTATCACTAAAAAAAACATAGATCCTAGAACTC
CTCTTATGATTTAATGGATAGACACATCATA
Found at i:675982 original size:134 final size:135
Alignment explanation
Indices: 675750--676016 Score: 335
Period size: 134 Copynumber: 2.0 Consensus size: 135
675740 ATGGTTAAGG
*
675750 GGTGGGGATCTCAACTGTTTTCAAGATAATTGTGCACTTCCTGTTTGAGGAAGGTCACGACCACC
1 GGTGGGGATCTCAACTGTTTTCAAGATAATTGTGCACTTCCTGTTCGAGGAAGGTCACGACCACC
*** * * *
675815 CTTGGGGCCCATGACCTACATACCGTTTGATGCCCCTTGACA-CAAGGAACGAGAATAGATATGG
66 CACAGGGCCCATGACCTACATAACATTTGATGCCCCTTGACATC-AGAAACGAGAATAGATATGG
675879 TTTAAA
130 TTTAAA
* * * * * *
675885 GGTGTGGATCTCAACTGTTTTGAAGAT-ATTAAG-GGACTTGCTGTTCGAGG-GGGTCAGGACCA
1 GGTGGGGATCTCAACTGTTTTCAAGATAATT--GTGCACTTCCTGTTCGAGGAAGGTCACGACCA
** *
675947 CCCACAGGGCCCATGACCTACATAACATTTGATGCCCCTTGACATCAGAAACTTGAATATATATG
64 CCCACAGGGCCCATGACCTACATAACATTTGATGCCCCTTGACATCAGAAACGAGAATAGATATG
676012 GTTTA
129 GTTTA
676017 GGGGTCATGG
Statistics
Matches: 113, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
134 72 0.64
135 40 0.35
136 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (135 bp):
GGTGGGGATCTCAACTGTTTTCAAGATAATTGTGCACTTCCTGTTCGAGGAAGGTCACGACCACC
CACAGGGCCCATGACCTACATAACATTTGATGCCCCTTGACATCAGAAACGAGAATAGATATGGT
TTAAA
Found at i:695834 original size:2 final size:2
Alignment explanation
Indices: 695827--695865 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
695817 ATATTCATAT
695827 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
695866 TTGAAATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:713592 original size:2 final size:2
Alignment explanation
Indices: 713585--713615 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
713575 TGAAATGAAT
713585 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
713616 CACACAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:725052 original size:2 final size:2
Alignment explanation
Indices: 725047--725108 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
725037 TTTGTTTTAG
*
725047 CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
725089 CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT
725109 TATTCACTGT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:725864 original size:10 final size:10
Alignment explanation
Indices: 725849--725880 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
725839 AACATATCCT
725849 CTTGATATCA
1 CTTGATATCA
*
725859 CTTGATATCG
1 CTTGATATCA
725869 CTTGATATCA
1 CTTGATATCA
725879 CT
1 CT
725881 AACGTGACGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (10 bp):
CTTGATATCA
Found at i:726784 original size:17 final size:17
Alignment explanation
Indices: 726743--726787 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
726733 GTCTAATTAC
726743 TGCACGATATGCCAAAA
1 TGCACGATATGCCAAAA
* *
726760 TGCGCGATATG-CAAACT
1 TGCACGATATGCCAAA-A
726777 TGCACGATATG
1 TGCACGATATG
726788 AAGAACCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (17 bp):
TGCACGATATGCCAAAA
Found at i:735588 original size:12 final size:12
Alignment explanation
Indices: 735571--735610 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
735561 TGTAACCTTA
735571 CAACGTTGTAAT
1 CAACGTTGTAAT
735583 CAACGTTGTAATT
1 CAACGTTGTAA-T
*
735596 ACAAAGTTGTAAT
1 -CAACGTTGTAAT
735609 CA
1 CA
735611 GATCTTCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 13 0.52
13 2 0.08
14 10 0.40
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (12 bp):
CAACGTTGTAAT
Found at i:743009 original size:27 final size:27
Alignment explanation
Indices: 742978--743038 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
742968 TACTATTGTA
*
742978 ATAATTTAATATATTTAATAAATATAT
1 ATAATTTAATATATGTAATAAATATAT
* *
743005 ATAATTTAATATATGTATTTAATATAT
1 ATAATTTAATATATGTAATAAATATAT
743032 -TAATTTA
1 ATAATTTA
743039 TGTATGGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 7 0.23
27 24 0.77
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (27 bp):
ATAATTTAATATATGTAATAAATATAT
Found at i:743037 original size:13 final size:14
Alignment explanation
Indices: 742978--743038 Score: 74
Period size: 13 Copynumber: 4.6 Consensus size: 14
742968 TACTATTGTA
742978 ATAATTTAATATAT
1 ATAATTTAATATAT
* *
742992 TTAA-TAAATATAT
1 ATAATTTAATATAT
743005 ATAATTTAATATAT
1 ATAATTTAATATAT
*
743019 GT-ATTTAATATAT
1 ATAATTTAATATAT
743032 -TAATTTA
1 ATAATTTA
743039 TGTATGGAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
12 1 0.03
13 27 0.68
14 12 0.30
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
ATAATTTAATATAT
Found at i:744471 original size:15 final size:15
Alignment explanation
Indices: 744451--744479 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
744441 ATTGTTTTTG
744451 TAAAAAAAAAAAAAA
1 TAAAAAAAAAAAAAA
744466 TAAAAAAAAAAAAA
1 TAAAAAAAAAAAAA
744480 TCATTACCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (15 bp):
TAAAAAAAAAAAAAA
Found at i:744472 original size:13 final size:13
Alignment explanation
Indices: 744454--744478 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
744444 GTTTTTGTAA
744454 AAAAAAAAAAAAT
1 AAAAAAAAAAAAT
744467 AAAAAAAAAAAA
1 AAAAAAAAAAAA
744479 ATCATTACCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.96, C:0.00, G:0.00, T:0.04
Consensus pattern (13 bp):
AAAAAAAAAAAAT
Found at i:744472 original size:14 final size:14
Alignment explanation
Indices: 744453--744480 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
744443 TGTTTTTGTA
744453 AAAAAAAAAAAAAT
1 AAAAAAAAAAAAAT
744467 AAAAAAAAAAAAAT
1 AAAAAAAAAAAAAT
744481 CATTACCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (14 bp):
AAAAAAAAAAAAAT
Found at i:745890 original size:2 final size:2
Alignment explanation
Indices: 745883--745957 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
745873 NNNNNNNNNN
745883 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
745925 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
745958 AGAGACCTCA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:747647 original size:2 final size:2
Alignment explanation
Indices: 747640--747676 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
747630 GTATACTTTA
* *
747640 CT CT CT CT CT CT CT CT CT CA CT CT TT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
747677 CAACCCAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.03, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:749346 original size:2 final size:2
Alignment explanation
Indices: 749339--749400 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
749329 ATTTAAGGAA
749339 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
749381 TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC
749401 ACATACGCAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:749901 original size:16 final size:16
Alignment explanation
Indices: 749865--749904 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
749855 CAGTTAATTG
*
749865 ATTAATCAATGAATCA
1 ATTATTCAATGAATCA
749881 ATTATTCAATGAATCA
1 ATTATTCAATGAATCA
749897 ATTATTCA
1 ATTATTCA
749905 TTGTTTGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTATTCAATGAATCA
Found at i:751941 original size:30 final size:30
Alignment explanation
Indices: 751905--752022 Score: 173
Period size: 30 Copynumber: 3.9 Consensus size: 30
751895 GGGGTTCAGG
* *
751905 CACAGCAGCTTGGCGCGGCCATTCCACAGA
1 CACAGCAGTTTGGAGCGGCCATTCCACAGA
751935 CACAGCAGTTTGGAGCGGCCATTCCACAGA
1 CACAGCAGTTTGGAGCGGCCATTCCACAGA
*
751965 CACAGCAGTTTGGAGCGGCTATTCCACAGA
1 CACAGCAGTTTGGAGCGGCCATTCCACAGA
* * * *
751995 CACAACAATTTGGCGCGGCCGTTCCACA
1 CACAGCAGTTTGGAGCGGCCATTCCACA
752023 ACAAACTTTT
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 80 1.00
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.17
Consensus pattern (30 bp):
CACAGCAGTTTGGAGCGGCCATTCCACAGA
Found at i:764987 original size:2 final size:2
Alignment explanation
Indices: 764982--765010 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
764972 GTGTACGAGC
764982 GA GA GA GA GA GA GA GA GA GA G- GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
765011 AAGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:769576 original size:2 final size:2
Alignment explanation
Indices: 769569--769599 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
769559 TTTCTCTTTT
769569 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
769600 GAGACACCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:769817 original size:2 final size:2
Alignment explanation
Indices: 769810--769862 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
769800 ACCTCCTGGT
769810 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
769851 TC TC TC TC TC TC
1 TC TC TC TC TC TC
769863 CAACCCAATC
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:781025 original size:4 final size:4
Alignment explanation
Indices: 781016--781053 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
781006 TGTTTACTCG
*
781016 CTGT CTGT CTGT CTGT ATGT CTGT CTGT CTGT CTGT CT
1 CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CT
781054 CTCTCTCTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.03, C:0.24, G:0.24, T:0.50
Consensus pattern (4 bp):
CTGT
Found at i:781084 original size:2 final size:2
Alignment explanation
Indices: 781051--781075 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
781041 TGTCTGTCTG
781051 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
781076 ATTTCTCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:785534 original size:166 final size:165
Alignment explanation
Indices: 785248--785745 Score: 818
Period size: 166 Copynumber: 3.0 Consensus size: 165
785238 NNNNNNNNNN
785248 AAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCCACCCTACCCCC
1 AAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCCACCCTACCCCC
* * *
785313 GGGGACCATGATTTGAACAAAATTGAATCTACACTACCTGAGGATGCTCCCATTTTAATTTGAGT
66 GGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAAGATGCTTCCATTTTAATTTGAG-
785378 CTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT
130 CTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT
*
785414 AAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCAAATTGTGGCCCCACCCTACCCCC
1 AAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCCACCCTACCCCC
* * *
785479 AGGGACCATGATTTGAACAAACTTGAATCTACACTTCCTGATGATGCTTCCATTTTAATTTGAGC
66 GGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAAGATGCTTCCATTTTAATTTGAGC
785544 TTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT
131 -TTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT
785580 AAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCCACCCTACCCCC
1 AAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCCACCCTACCCCC
* * *** *
785645 GGGGACCATGATTTGAAAAAACTTGAATCTACACTACCTGAAGATGCCTCCA-CACAAGTTTAAG
66 GGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAAGATGCTTCCATTTTAA-TTTGAG
* *
785709 CTTTACCGGCCTAATAGTTTTTGAGAAGAAGATTTTT
130 CTTT-CTGGCCTGATAGTTTTTGAGAAGAAGATTTTT
785746 GAAAAATACC
Statistics
Matches: 311, Mismatches: 18, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
165 6 0.02
166 305 0.98
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.33
Consensus pattern (165 bp):
AAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCCACCCTACCCCC
GGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAAGATGCTTCCATTTTAATTTGAGC
TTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT
Found at i:785926 original size:6 final size:6
Alignment explanation
Indices: 785915--785962 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
785905 TGAAAAGTTT
** *
785915 ACAACG ACAACG ACGGCG ACAACG ACAACG ACGACAG ACAACGG ACAA
1 ACAACG ACAACG ACAACG ACAACG ACAACG ACAAC-G ACAAC-G ACAA
785963 ATTGTGATCA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
6 24 0.71
7 10 0.29
ACGTcount: A:0.46, C:0.31, G:0.23, T:0.00
Consensus pattern (6 bp):
ACAACG
Found at i:785938 original size:18 final size:19
Alignment explanation
Indices: 785915--785962 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 19
785905 TGAAAAGTTT
*
785915 ACAACGACAACGACGGC-G
1 ACAACGACAACGACGACAG
785933 ACAACGACAACGACGACAG
1 ACAACGACAACGACGACAG
785952 ACAACGGACAA
1 ACAAC-GACAA
785963 ATTGTGATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 16 0.59
19 6 0.22
20 5 0.19
ACGTcount: A:0.46, C:0.31, G:0.23, T:0.00
Consensus pattern (19 bp):
ACAACGACAACGACGACAG
Found at i:786305 original size:2 final size:2
Alignment explanation
Indices: 786298--786357 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
786288 CCATCTTCAC
*
786298 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT AT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
786340 CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT
786358 GAATTTCGAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.02, C:0.48, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:786735 original size:1 final size:1
Alignment explanation
Indices: 786731--786757 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
786721 ATTAAAAAGC
786731 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
786758 GACATACACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:788154 original size:4 final size:4
Alignment explanation
Indices: 788147--788182 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
788137 TAAGTAATTC
*
788147 GTAA GTAA GTAA GTAA ATAA GTAA GTAA GTAA GTAA
1 GTAA GTAA GTAA GTAA GTAA GTAA GTAA GTAA GTAA
788183 TTGTTTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (4 bp):
GTAA
Found at i:788365 original size:2 final size:2
Alignment explanation
Indices: 788358--788416 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
788348 AACAGTCAAA
*
788358 AG AG AG AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
788400 AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG A
788417 ATAATTTTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:791110 original size:32 final size:33
Alignment explanation
Indices: 791073--791135 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
791063 CTGATTTTTT
*
791073 AAAATGCAATTAATTAC-TTTCAATTACTTTGA
1 AAAATGCAATTAAATACATTTCAATTACTTTGA
*
791105 AAAATGTAATTAAATACATTTCAATTACTTT
1 AAAATGCAATTAAATACATTTCAATTACTTT
791136 TTTTATATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (33 bp):
AAAATGCAATTAAATACATTTCAATTACTTTGA
Found at i:791938 original size:13 final size:13
Alignment explanation
Indices: 791920--791954 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
791910 TATGACACCT
791920 TTTTAACTTTAAC
1 TTTTAACTTTAAC
*
791933 TTTTAAATTTAAC
1 TTTTAACTTTAAC
791946 TTTTAACTT
1 TTTTAACTT
791955 GAAAAAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTAACTTTAAC
Found at i:791979 original size:11 final size:11
Alignment explanation
Indices: 791959--791995 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
791949 TAACTTGAAA
791959 AAAAGTAATTG
1 AAAAGTAATTG
*
791970 AAATGTAATTG
1 AAAAGTAATTG
791981 AAAAGTAATTG
1 AAAAGTAATTG
791992 AAAA
1 AAAA
791996 TACATGACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.16, T:0.27
Consensus pattern (11 bp):
AAAAGTAATTG
Found at i:796790 original size:15 final size:15
Alignment explanation
Indices: 796770--796799 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
796760 TGTGGATCGA
*
796770 CAAAACAACAGCAAC
1 CAAAACAACAACAAC
796785 CAAAACAACAACAAC
1 CAAAACAACAACAAC
796800 AACGAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.33, G:0.03, T:0.00
Consensus pattern (15 bp):
CAAAACAACAACAAC
Found at i:796796 original size:18 final size:17
Alignment explanation
Indices: 796773--796825 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
796763 GGATCGACAA
*
796773 AACAACAGCAACCAAAAC
1 AACAACA-CAACAAAAAC
796791 AACAACAACAACGAAAAA-
1 AACAAC-ACAAC-AAAAAC
796809 AACAA-ACAACAAAAAC
1 AACAACACAACAAAAAC
796825 A
1 A
796826 GCTTTAACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
15 5 0.16
16 6 0.19
18 15 0.48
19 5 0.16
ACGTcount: A:0.70, C:0.26, G:0.04, T:0.00
Consensus pattern (17 bp):
AACAACACAACAAAAAC
Found at i:802202 original size:11 final size:11
Alignment explanation
Indices: 802186--802218 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
802176 CCAGTGTTAA
802186 ACGATTTGTTT
1 ACGATTTGTTT
802197 ACGATTTGTTT
1 ACGATTTGTTT
*
802208 ACGATTCGTTT
1 ACGATTTGTTT
802219 TCACAACTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (11 bp):
ACGATTTGTTT
Found at i:807366 original size:8 final size:8
Alignment explanation
Indices: 807353--807453 Score: 100
Period size: 8 Copynumber: 12.6 Consensus size: 8
807343 GACATAAACT
807353 ATAAATAA
1 ATAAATAA
807361 ATAAATAA
1 ATAAATAA
807369 ATAAATACA
1 ATAAATA-A
*
807378 A-AGATAA
1 ATAAATAA
* *
807385 AAAAATAT
1 ATAAATAA
*
807393 TTAAATAA
1 ATAAATAA
807401 A-AAGATAA
1 ATAA-ATAA
* *
807409 ATAAACAG
1 ATAAATAA
807417 ATAAATAA
1 ATAAATAA
807425 A-AAGATAA
1 ATAA-ATAA
807433 ATAAATAA
1 ATAAATAA
807441 ATAAATAA
1 ATAAATAA
807449 ATAAA
1 ATAAA
807454 CAAAGTAACT
Statistics
Matches: 76, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
7 6 0.08
8 64 0.84
9 6 0.08
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.22
Consensus pattern (8 bp):
ATAAATAA
Found at i:807370 original size:12 final size:12
Alignment explanation
Indices: 807353--807453 Score: 100
Period size: 12 Copynumber: 8.4 Consensus size: 12
807343 GACATAAACT
807353 ATAAATAAATAA
1 ATAAATAAATAA
807365 ATAAATAAATACA
1 ATAAATAAATA-A
* *
807378 A-AGATAAAAAA
1 ATAAATAAATAA
**
807389 ATATTTAAATAA
1 ATAAATAAATAA
807401 A-AAGATAAATAA
1 ATAA-ATAAATAA
* *
807413 ACAGATAAATAA
1 ATAAATAAATAA
807425 A-AAGATAAATAA
1 ATAA-ATAAATAA
807437 ATAAATAAATAA
1 ATAAATAAATAA
807449 ATAAA
1 ATAAA
807454 CAAAGTAACT
Statistics
Matches: 74, Mismatches: 9, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
11 4 0.05
12 65 0.88
13 5 0.07
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.22
Consensus pattern (12 bp):
ATAAATAAATAA
Found at i:807390 original size:24 final size:24
Alignment explanation
Indices: 807357--807449 Score: 132
Period size: 24 Copynumber: 3.9 Consensus size: 24
807347 TAAACTATAA
*
807357 ATAAATAAATAAATAAATACAAAG
1 ATAAATAAATAAATAAATAAAAAG
* **
807381 ATAAAAAAATATTTAAATAAAAAG
1 ATAAATAAATAAATAAATAAAAAG
* *
807405 ATAAATAAACAGATAAATAAAAAG
1 ATAAATAAATAAATAAATAAAAAG
807429 ATAAATAAATAAATAAATAAA
1 ATAAATAAATAAATAAATAAA
807450 TAAACAAAGT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.22
Consensus pattern (24 bp):
ATAAATAAATAAATAAATAAAAAG
Found at i:816886 original size:17 final size:17
Alignment explanation
Indices: 816848--816886 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
816838 GATGATAAAG
* *
816848 AAAAACAAAAATAGGAA
1 AAAAACAAAAACAGAAA
*
816865 AAAAACAAGAACAGAAA
1 AAAAACAAAAACAGAAA
816882 AAAAA
1 AAAAA
816887 GTTATTTATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.79, C:0.08, G:0.10, T:0.03
Consensus pattern (17 bp):
AAAAACAAAAACAGAAA
Found at i:822950 original size:1 final size:1
Alignment explanation
Indices: 822944--822989 Score: 92
Period size: 1 Copynumber: 46.0 Consensus size: 1
822934 ATTATAAATA
822944 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
822990 ACAAAATCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:827214 original size:21 final size:21
Alignment explanation
Indices: 827169--827218 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
827159 AATCTTATAG
**
827169 CATATCATTAAAATTGCATAA
1 CATATCATTAAAAACGCATAA
* *
827190 CATATCATTAAAAACGCTTAC
1 CATATCATTAAAAACGCATAA
827211 CATATCAT
1 CATATCAT
827219 CGCATAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.32
Consensus pattern (21 bp):
CATATCATTAAAAACGCATAA
Found at i:828369 original size:56 final size:57
Alignment explanation
Indices: 828276--828384 Score: 193
Period size: 56 Copynumber: 1.9 Consensus size: 57
828266 ACTGAAGAAT
828276 AAGAAACCACACGATTTTGTAGTTAAAAATGACCCTTAAATATTGTAAAAAACAAAC
1 AAGAAACCACACGATTTTGTAGTTAAAAATGACCCTTAAATATTGTAAAAAACAAAC
* *
828333 AAGAAATCACACGA-TTTGTAGTTTAAAATGACCCTTAAATATTGTAAAAAAC
1 AAGAAACCACACGATTTTGTAGTTAAAAATGACCCTTAAATATTGTAAAAAAC
828385 CAAATTTACT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
56 37 0.74
57 13 0.26
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.27
Consensus pattern (57 bp):
AAGAAACCACACGATTTTGTAGTTAAAAATGACCCTTAAATATTGTAAAAAACAAAC
Found at i:829134 original size:2 final size:2
Alignment explanation
Indices: 829129--829177 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
829119 ATATATATAT
*
829129 AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
829171 AG AG AG A
1 AG AG AG A
829178 TTATCGACAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:839051 original size:2 final size:2
Alignment explanation
Indices: 839044--839076 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
839034 AAATATCGGA
839044 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
839077 CGAGGGTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:852530 original size:21 final size:21
Alignment explanation
Indices: 852506--852555 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
852496 ATTTTAACGA
852506 AATGCTATGAGATTTCAATGC
1 AATGCTATGAGATTTCAATGC
**
852527 AATGCTATGAGATTTGTATGC
1 AATGCTATGAGATTTCAATGC
*
852548 CATGCTAT
1 AATGCTAT
852556 CAGAAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (21 bp):
AATGCTATGAGATTTCAATGC
Found at i:856026 original size:8 final size:8
Alignment explanation
Indices: 856015--856063 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
856005 TAAAAAGTTT
856015 ACAGACGG
1 ACAGACGG
*
856023 ACAGACAG
1 ACAGACGG
* *
856031 ACGGACAG
1 ACAGACGG
*
856039 ACGGACGG
1 ACAGACGG
856047 ACAGACGG
1 ACAGACGG
856055 AC-GACGG
1 ACAGACGG
856062 AC
1 AC
856064 CAAATGTGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
7 7 0.19
8 30 0.81
ACGTcount: A:0.37, C:0.27, G:0.37, T:0.00
Consensus pattern (8 bp):
ACAGACGG
Found at i:856032 original size:12 final size:12
Alignment explanation
Indices: 856015--856057 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
856005 TAAAAAGTTT
856015 ACAGACGGACAG
1 ACAGACGGACAG
856027 ACAGACGGACAG
1 ACAGACGGACAG
*
856039 ACGGACGGACAG
1 ACAGACGGACAG
*
856051 ACGGACG
1 ACAGACG
856058 ACGGACCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.37, C:0.26, G:0.37, T:0.00
Consensus pattern (12 bp):
ACAGACGGACAG
Found at i:856798 original size:31 final size:31
Alignment explanation
Indices: 856760--856903 Score: 225
Period size: 31 Copynumber: 4.6 Consensus size: 31
856750 AATTTAGGAA
856760 AATAAATTCAAAATGTAAATTTAATAAAGAT
1 AATAAATTCAAAATGTAAATTTAATAAAGAT
**
856791 AATAAATTCAAAATGTATAATTTAACCAAGAT
1 AATAAATTCAAAATGTA-AATTTAATAAAGAT
* *
856823 AATAAATTCAAAATGAAAATTCAATAAAGAT
1 AATAAATTCAAAATGTAAATTTAATAAAGAT
* *
856854 AATAAACTCAAAATGTAAATTTAATAAACAT
1 AATAAATTCAAAATGTAAATTTAATAAAGAT
856885 AATAAATTCAAAATGTAAA
1 AATAAATTCAAAATGTAAA
856904 GAACTAACAA
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
31 73 0.72
32 28 0.28
ACGTcount: A:0.58, C:0.07, G:0.06, T:0.29
Consensus pattern (31 bp):
AATAAATTCAAAATGTAAATTTAATAAAGAT
Found at i:856859 original size:63 final size:62
Alignment explanation
Indices: 856760--856899 Score: 217
Period size: 63 Copynumber: 2.2 Consensus size: 62
856750 AATTTAGGAA
* * * * *
856760 AATAAATTCAAAATGTAAATTTAATAAAGATAATAAATTCAAAATGTATAATTTAACCAAGAT
1 AATAAATTCAAAATGAAAATTCAATAAAGATAATAAACTCAAAATGTA-AATTTAACAAACAT
*
856823 AATAAATTCAAAATGAAAATTCAATAAAGATAATAAACTCAAAATGTAAATTTAATAAACAT
1 AATAAATTCAAAATGAAAATTCAATAAAGATAATAAACTCAAAATGTAAATTTAACAAACAT
856885 AATAAATTCAAAATG
1 AATAAATTCAAAATG
856900 TAAAGAACTA
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
62 26 0.37
63 45 0.63
ACGTcount: A:0.58, C:0.07, G:0.06, T:0.29
Consensus pattern (62 bp):
AATAAATTCAAAATGAAAATTCAATAAAGATAATAAACTCAAAATGTAAATTTAACAAACAT
Found at i:857795 original size:43 final size:43
Alignment explanation
Indices: 857735--857818 Score: 150
Period size: 43 Copynumber: 2.0 Consensus size: 43
857725 ACTCTAATTT
857735 AAAATAATTCCAAAAGGCAACTACTCTAAATATTTTAAGAATA
1 AAAATAATTCCAAAAGGCAACTACTCTAAATATTTTAAGAATA
* *
857778 AAAATAATTCCAGAAGGCAACTTCTCTAAATATTTTAAGAA
1 AAAATAATTCCAAAAGGCAACTACTCTAAATATTTTAAGAA
857819 CTTACGGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.29
Consensus pattern (43 bp):
AAAATAATTCCAAAAGGCAACTACTCTAAATATTTTAAGAATA
Found at i:859089 original size:4 final size:4
Alignment explanation
Indices: 859082--859122 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
859072 ACAGACAGAC
859082 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT A
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT A
859123 AATAAAAGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
AGAT
Found at i:859138 original size:15 final size:15
Alignment explanation
Indices: 859114--859143 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
859104 ATAGATAGAT
*
859114 AGATAGATAAATAAA
1 AGATAAATAAATAAA
859129 AGATAAATAAATAAA
1 AGATAAATAAATAAA
859144 TAAATGAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (15 bp):
AGATAAATAAATAAA
Found at i:859142 original size:19 final size:19
Alignment explanation
Indices: 859110--859147 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
859100 ATAGATAGAT
* *
859110 AGATAGATAGATAAATAAA
1 AGATAAATAAATAAATAAA
859129 AGATAAATAAATAAATAAA
1 AGATAAATAAATAAATAAA
859148 TGAAAACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (19 bp):
AGATAAATAAATAAATAAA
Found at i:862807 original size:18 final size:18
Alignment explanation
Indices: 862775--862810 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
862765 TGAAGTGCAT
**
862775 TTATTTATTTTTTTAGAA
1 TTATTTATTGATTTAGAA
862793 TTATTTATTGATTTAGAA
1 TTATTTATTGATTTAGAA
862811 AACCAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (18 bp):
TTATTTATTGATTTAGAA
Found at i:863074 original size:22 final size:22
Alignment explanation
Indices: 863049--863119 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
863039 TGAGTTTACT
863049 AAAGTGGAACCAGAGTAAACCC
1 AAAGTGGAACCAGAGTAAACCC
* *
863071 AAAGT-AAATCCAAAGTAAACCC
1 AAAGTGGAA-CCAGAGTAAACCC
* *
863093 AGAGTGGACACAGAGAGTAAACACC
1 AAAGTGGA-AC-CAGAGTAAAC-CC
863118 AA
1 AA
863120 TCAGAAGTAC
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
21 2 0.05
22 21 0.57
23 2 0.05
24 9 0.24
25 3 0.08
ACGTcount: A:0.49, C:0.21, G:0.20, T:0.10
Consensus pattern (22 bp):
AAAGTGGAACCAGAGTAAACCC
Found at i:863078 original size:11 final size:11
Alignment explanation
Indices: 863062--863093 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
863052 GTGGAACCAG
863062 AGTAAACCCAA
1 AGTAAACCCAA
*
863073 AGTAAATCCAA
1 AGTAAACCCAA
863084 AGTAAACCCA
1 AGTAAACCCA
863094 GAGTGGACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.53, C:0.25, G:0.09, T:0.12
Consensus pattern (11 bp):
AGTAAACCCAA
Found at i:868011 original size:2 final size:2
Alignment explanation
Indices: 868004--868068 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
867994 TTTGCCCATA
868004 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
868046 AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG A
868069 AAGGGGAGGG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:870649 original size:8 final size:8
Alignment explanation
Indices: 870599--870655 Score: 62
Period size: 8 Copynumber: 7.2 Consensus size: 8
870589 GATCACCTTT
870599 TGTCCGTC
1 TGTCCGTC
*
870607 -GTTCGTC
1 TGTCCGTC
870614 TGTCCGTC
1 TGTCCGTC
*
870622 CGTCCGTC
1 TGTCCGTC
* *
870630 CGTCCGTT
1 TGTCCGTC
*
870638 TGTCTGTC
1 TGTCCGTC
870646 TGTCCGTC
1 TGTCCGTC
870654 TG
1 TG
870656 AAAACTTTCC
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
7 6 0.15
8 34 0.85
ACGTcount: A:0.00, C:0.35, G:0.26, T:0.39
Consensus pattern (8 bp):
TGTCCGTC
Found at i:876921 original size:2 final size:2
Alignment explanation
Indices: 876914--876999 Score: 172
Period size: 2 Copynumber: 43.0 Consensus size: 2
876904 NNNNNNNNNN
876914 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
876956 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
876998 CT
1 CT
877000 GGGCGAGTTA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:877638 original size:3 final size:3
Alignment explanation
Indices: 877630--877669 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
877620 AAATTCCAAG
877630 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA G
1 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA G
877670 AAGCTTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.33
Consensus pattern (3 bp):
GTA
Found at i:882047 original size:22 final size:22
Alignment explanation
Indices: 882019--882061 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
882009 TTATTTAATA
882019 TAAATCAAAATTGAAATCATTT
1 TAAATCAAAATTGAAATCATTT
* *
882041 TAAATCAACATTTAAATCATT
1 TAAATCAAAATTGAAATCATT
882062 AGAAGGATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (22 bp):
TAAATCAAAATTGAAATCATTT
Found at i:882752 original size:21 final size:21
Alignment explanation
Indices: 882704--882757 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
882694 GCTTGCTGAT
**
882704 TTCCATTTGGGCTCAATTTGGG
1 TTCCATTTGGG-TCAATTTACG
*
882726 TT-CATTTGGGTCATTTTACG
1 TTCCATTTGGGTCAATTTACG
882746 TTCCATTTGGGT
1 TTCCATTTGGGT
882758 AAATCGACGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.32
21 17 0.61
22 2 0.07
ACGTcount: A:0.13, C:0.17, G:0.24, T:0.46
Consensus pattern (21 bp):
TTCCATTTGGGTCAATTTACG
Found at i:883041 original size:14 final size:14
Alignment explanation
Indices: 883022--883059 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
883012 TTGAATGTTG
883022 TAAATTCCAAGAAA
1 TAAATTCCAAGAAA
883036 TAAATTCCAAGAAA
1 TAAATTCCAAGAAA
883050 TAAATTCCAA
1 TAAATTCCAA
883060 TGTAAAGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.55, C:0.16, G:0.05, T:0.24
Consensus pattern (14 bp):
TAAATTCCAAGAAA
Found at i:898757 original size:58 final size:58
Alignment explanation
Indices: 898639--898750 Score: 197
Period size: 58 Copynumber: 1.9 Consensus size: 58
898629 GATTAAAATT
* *
898639 TTTGGCTGAAAGGTCTTTGCAGTCTCAGAAAGGTTTGTTATGATGAATTTGACTAATA
1 TTTGGCTGAAAGGTCTTTGCAGTCTCAAAAAGGTTTGTTATGATGAATTGGACTAATA
*
898697 TTTGGCTGAAAGGTCTTTGCAGTCTCAAAAAGGTTTGTTGTGATGAATTGGACT
1 TTTGGCTGAAAGGTCTTTGCAGTCTCAAAAAGGTTTGTTATGATGAATTGGACT
898751 GTTATTTTCA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.38
Consensus pattern (58 bp):
TTTGGCTGAAAGGTCTTTGCAGTCTCAAAAAGGTTTGTTATGATGAATTGGACTAATA
Found at i:902072 original size:17 final size:18
Alignment explanation
Indices: 902037--902073 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
902027 GTAAAAAGAG
902037 AAAATGACATCAACAATA
1 AAAATGACATCAACAATA
902055 AAAAT-ACAGTCAAC-ATA
1 AAAATGACA-TCAACAATA
902072 AA
1 AA
902074 TTACATCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.62, C:0.16, G:0.05, T:0.16
Consensus pattern (18 bp):
AAAATGACATCAACAATA
Found at i:919872 original size:21 final size:21
Alignment explanation
Indices: 919838--919917 Score: 117
Period size: 21 Copynumber: 3.8 Consensus size: 21
919828 AATTTAATGC
* *
919838 TATGCTATGGTATGCGATTT-
1 TATGCTATGCTATGAGATTTG
*
919858 TAATGATATGCTATGAGATTTG
1 T-ATGCTATGCTATGAGATTTG
919880 TATGCTATGCTATGAGATTTG
1 TATGCTATGCTATGAGATTTG
919901 TATGCTATGCTATGAGA
1 TATGCTATGCTATGAGA
919918 AATTGAAATG
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
20 1 0.02
21 52 0.96
22 1 0.02
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (21 bp):
TATGCTATGCTATGAGATTTG
Found at i:919945 original size:5 final size:5
Alignment explanation
Indices: 919941--919974 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
919931 GGCTTAATGG
* *
919941 TATGG TATGC TATGC TATGC TATGG TATGC TATG
1 TATGC TATGC TATGC TATGC TATGC TATGC TATG
919975 AGATTTGAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.41
Consensus pattern (5 bp):
TATGC
Found at i:919959 original size:10 final size:10
Alignment explanation
Indices: 919941--919974 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
919931 GGCTTAATGG
919941 TATGGTATGC
1 TATGGTATGC
*
919951 TATGCTATGC
1 TATGGTATGC
919961 TATGGTATGC
1 TATGGTATGC
919971 TATG
1 TATG
919975 AGATTTGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.41
Consensus pattern (10 bp):
TATGGTATGC
Found at i:920140 original size:10 final size:10
Alignment explanation
Indices: 920122--920155 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
920112 AATAACGTTG
*
920122 TATGCTATGC
1 TATGGTATGC
920132 TATGGTATGC
1 TATGGTATGC
*
920142 TATGGTATGA
1 TATGGTATGC
920152 TATG
1 TATG
920156 ATGAATGCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (10 bp):
TATGGTATGC
Found at i:920141 original size:15 final size:15
Alignment explanation
Indices: 920121--920155 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
920111 AAATAACGTT
920121 GTATGCTATGCTATG
1 GTATGCTATGCTATG
*
920136 GTATGCTATGGTATG
1 GTATGCTATGCTATG
*
920151 ATATG
1 GTATG
920156 ATGAATGCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.09, G:0.29, T:0.40
Consensus pattern (15 bp):
GTATGCTATGCTATG
Found at i:920206 original size:21 final size:21
Alignment explanation
Indices: 920168--920255 Score: 126
Period size: 21 Copynumber: 4.2 Consensus size: 21
920158 GAATGCGATT
*
920168 CTATGAGATTGT-ATGCTATG
1 CTATGAGATTCTAATGCTATG
*
920188 GTATGAGATTCTAATGCTATG
1 CTATGAGATTCTAATGCTATG
*
920209 CTATGAGATTCCAATGCTATG
1 CTATGAGATTCTAATGCTATG
920230 CTATGAGATT-TCAATGCTATG
1 CTATGAGATTCT-AATGCTATG
920251 CTATG
1 CTATG
920256 CAATGGTGTA
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
20 10 0.16
21 51 0.84
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.38
Consensus pattern (21 bp):
CTATGAGATTCTAATGCTATG
Found at i:920226 original size:42 final size:41
Alignment explanation
Indices: 920138--920255 Score: 130
Period size: 42 Copynumber: 2.8 Consensus size: 41
920128 ATGCTATGGT
* * * * * **
920138 ATGCTATGGTATGATATGATGAATGCGATTCTATGAGATTGT
1 ATGCTATGGTATGAGAT-TTCAATGCTATGCTATGAGATTCA
920180 ATGCTATGGTATGAGA-TTCTAATGCTATGCTATGAGATTCCA
1 ATGCTATGGTATGAGATTTC-AATGCTATGCTATGAGATT-CA
*
920222 ATGCTATGCTATGAGATTTCAATGCTATGCTATG
1 ATGCTATGGTATGAGATTTCAATGCTATGCTATG
920256 CAATGGTGTA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
40 1 0.02
41 17 0.26
42 44 0.68
43 3 0.05
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (41 bp):
ATGCTATGGTATGAGATTTCAATGCTATGCTATGAGATTCA
Found at i:931055 original size:4 final size:4
Alignment explanation
Indices: 931046--931107 Score: 124
Period size: 4 Copynumber: 15.5 Consensus size: 4
931036 ACTGCTGAGT
931046 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
931094 GATA GATA GATA GA
1 GATA GATA GATA GA
931108 ATTTTGCTAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.26, T:0.24
Consensus pattern (4 bp):
GATA
Found at i:931901 original size:2 final size:2
Alignment explanation
Indices: 931888--931919 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
931878 TTGGATCATT
*
931888 TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
931920 GATTGATCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:935110 original size:1 final size:1
Alignment explanation
Indices: 935106--935186 Score: 108
Period size: 1 Copynumber: 81.0 Consensus size: 1
935096 CCCCCCCCCC
* * * *
935106 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACACAAAAAAACAAAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
935171 AAACAAAACAAAAAAA
1 AAAAAAAAAAAAAAAA
935187 CCCAATGTGA
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 68 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:940808 original size:12 final size:12
Alignment explanation
Indices: 940791--940836 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
940781 TCTGTCATCC
940791 GTCTGTCCGTCT
1 GTCTGTCCGTCT
* *
940803 GTCTGTCTGTTT
1 GTCTGTCCGTCT
*
940815 GTCTGTCCGTCC
1 GTCTGTCCGTCT
*
940827 GTCAGTCCGT
1 GTCTGTCCGT
940837 AAACTTTTCA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.02, C:0.30, G:0.26, T:0.41
Consensus pattern (12 bp):
GTCTGTCCGTCT
Found at i:942347 original size:17 final size:16
Alignment explanation
Indices: 942322--942356 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
942312 CTGGCGTGCG
942322 ACCAGTTCTCGCCGAGT
1 ACCAGTTCTCGCC-AGT
*
942339 ACCATTTCTCGCCAGT
1 ACCAGTTCTCGCCAGT
942355 AC
1 AC
942357 ATTGTGACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.20, C:0.37, G:0.17, T:0.26
Consensus pattern (16 bp):
ACCAGTTCTCGCCAGT
Found at i:945093 original size:18 final size:17
Alignment explanation
Indices: 945072--945117 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
945062 ATTCAAAATG
945072 TAAATTTAATAAAGGTAA
1 TAAATTTAATAAAGGT-A
*
945090 TAAATTT-A-AAATGTA
1 TAAATTTAATAAAGGTA
945105 T-AATTTAATAAAG
1 TAAATTTAATAAAG
945118 ATCATAGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
14 5 0.21
15 3 0.12
16 8 0.33
17 1 0.04
18 7 0.29
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (17 bp):
TAAATTTAATAAAGGTA
Found at i:945104 original size:31 final size:31
Alignment explanation
Indices: 945061--945232 Score: 245
Period size: 31 Copynumber: 5.5 Consensus size: 31
945051 TAAGAAAATT
*
945061 AATTCAAAATGTAAATTTAATAAAGGTAATA
1 AATTCAAAATGTAAATTTAATAAAGATAATA
* *
945092 AATTTAAAATGTATAATTTAATAAAGATCATA
1 AATTCAAAATGTA-AATTTAATAAAGATAATA
*
945124 GATTCAAAATGTAAATTTAATAAAGATAATA
1 AATTCAAAATGTAAATTTAATAAAGATAATA
* * *
945155 AATTCAAAATGTAAATTTAAAAAAATATAATG
1 AATTCAAAATGTAAATTT-AATAAAGATAATA
*
945187 AATTCAAAATGTAAATTTAATAAAGATAACA
1 AATTCAAAATGTAAATTTAATAAAGATAATA
*
945218 AATTCATAATGTAAA
1 AATTCAAAATGTAAA
945233 GAACTAACAA
Statistics
Matches: 124, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
31 69 0.56
32 55 0.44
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.33
Consensus pattern (31 bp):
AATTCAAAATGTAAATTTAATAAAGATAATA
Found at i:945141 original size:63 final size:63
Alignment explanation
Indices: 945061--945232 Score: 251
Period size: 63 Copynumber: 2.7 Consensus size: 63
945051 TAAGAAAATT
* * *
945061 AATTCAAAATGTAAATTTAATAAAGGTAATAAATTTAAAATGTATAATTTAATAAAGATCAT-A-
1 AATTCAAAATGTAAATTTAATAAAGATAATAAATTCAAAATGTA-AATTTAA-AAAAAT-ATAAT
945124 G
63 G
945125 -ATTCAAAATGTAAATTTAATAAAGATAATAAATTCAAAATGTAAATTTAAAAAAATATAATG
1 AATTCAAAATGTAAATTTAATAAAGATAATAAATTCAAAATGTAAATTTAAAAAAATATAATG
* *
945187 AATTCAAAATGTAAATTTAATAAAGATAACAAATTCATAATGTAAA
1 AATTCAAAATGTAAATTTAATAAAGATAATAAATTCAAAATGTAAA
945233 GAACTAACAA
Statistics
Matches: 100, Mismatches: 5, Indels: 7
0.89 0.04 0.06
Matches are distributed among these distances:
60 2 0.02
61 6 0.06
62 8 0.08
63 84 0.84
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.33
Consensus pattern (63 bp):
AATTCAAAATGTAAATTTAATAAAGATAATAAATTCAAAATGTAAATTTAAAAAAATATAATG
Found at i:947099 original size:16 final size:16
Alignment explanation
Indices: 947080--947110 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
947070 ACAAACAGAC
947080 AGATAGATAGATAAAA
1 AGATAGATAGATAAAA
*
947096 AGATATATAGATAAA
1 AGATAGATAGATAAA
947111 TACAAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AGATAGATAGATAAAA
Found at i:951305 original size:20 final size:18
Alignment explanation
Indices: 951282--951326 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
951272 TCTCTCACCC
951282 TCTCTCTGTCTCTATCTTGG
1 TCTCTCTGTCTCTATC-T-G
* *
951302 TCTCACTGTCTCTGTCTG
1 TCTCTCTGTCTCTATCTG
951320 TCTCTCT
1 TCTCTCT
951327 CGATCGATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 1 0.05
20 14 0.64
ACGTcount: A:0.04, C:0.33, G:0.13, T:0.49
Consensus pattern (18 bp):
TCTCTCTGTCTCTATCTG
Found at i:951876 original size:22 final size:22
Alignment explanation
Indices: 951851--951921 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 22
951841 TGAGTTTACT
951851 AAAGTGGAACAAGAGTAAACCC
1 AAAGTGGAACAAGAGTAAACCC
*
951873 AAAGT-AAATCCAA-AGTAAACCC
1 AAAGTGGAA--CAAGAGTAAACCC
*
951895 AGAGTGGACACAGAGAGTAAACACC
1 AAAGTGGA-ACA-AGAGTAAAC-CC
951920 AA
1 AA
951922 TCAGAAGTAC
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
21 2 0.05
22 20 0.53
23 5 0.13
24 8 0.21
25 3 0.08
ACGTcount: A:0.51, C:0.20, G:0.20, T:0.10
Consensus pattern (22 bp):
AAAGTGGAACAAGAGTAAACCC
Found at i:951880 original size:11 final size:11
Alignment explanation
Indices: 951864--951895 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
951854 GTGGAACAAG
951864 AGTAAACCCAA
1 AGTAAACCCAA
*
951875 AGTAAATCCAA
1 AGTAAACCCAA
951886 AGTAAACCCA
1 AGTAAACCCA
951896 GAGTGGACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.53, C:0.25, G:0.09, T:0.12
Consensus pattern (11 bp):
AGTAAACCCAA
Found at i:961436 original size:4 final size:4
Alignment explanation
Indices: 961427--961492 Score: 132
Period size: 4 Copynumber: 16.5 Consensus size: 4
961417 ACTGCTGAGT
961427 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
961475 GATA GATA GATA GATA GA
1 GATA GATA GATA GATA GA
961493 CTTAATTTTG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.26, T:0.24
Consensus pattern (4 bp):
GATA
Found at i:962877 original size:18 final size:18
Alignment explanation
Indices: 962854--962889 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
962844 TATTTGGATC
962854 ATCTCTCTCTCTTTCTAT
1 ATCTCTCTCTCTTTCTAT
*
962872 ATCTCTTTCTCTTTCTAT
1 ATCTCTCTCTCTTTCTAT
962890 CGATCAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.31, G:0.00, T:0.58
Consensus pattern (18 bp):
ATCTCTCTCTCTTTCTAT
Found at i:967522 original size:10 final size:10
Alignment explanation
Indices: 967504--967558 Score: 65
Period size: 10 Copynumber: 5.3 Consensus size: 10
967494 GATTCTGATA
967504 CACGAACGAT
1 CACGAACGAT
*
967514 CACGCACGAT
1 CACGAACGAT
967524 ACACGAACGAT
1 -CACGAACGAT
*
967535 CACGCACGAT
1 CACGAACGAT
*
967545 ACACGGACGAT
1 -CACGAACGAT
967556 CAC
1 CAC
967559 TAACTTACTG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 21 0.54
11 18 0.46
ACGTcount: A:0.36, C:0.35, G:0.20, T:0.09
Consensus pattern (10 bp):
CACGAACGAT
Found at i:967524 original size:21 final size:21
Alignment explanation
Indices: 967500--967558 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
967490 GCACGATTCT
967500 GATACACGAACGATCACGCAC
1 GATACACGAACGATCACGCAC
967521 GATACACGAACGATCACGCAC
1 GATACACGAACGATCACGCAC
*
967542 GATACACGGACGATCAC
1 GATACACGAACGATCAC
967559 TAACTTACTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.37, C:0.32, G:0.20, T:0.10
Consensus pattern (21 bp):
GATACACGAACGATCACGCAC
Found at i:967533 original size:11 final size:11
Alignment explanation
Indices: 967500--967555 Score: 71
Period size: 11 Copynumber: 5.3 Consensus size: 11
967490 GCACGATTCT
967500 GATACACGAAC
1 GATACACGAAC
*
967511 GAT-CACGCAC
1 GATACACGAAC
967521 GATACACGAAC
1 GATACACGAAC
*
967532 GAT-CACGCAC
1 GATACACGAAC
*
967542 GATACACGGAC
1 GATACACGAAC
967553 GAT
1 GAT
967556 CACTAACTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 18 0.46
11 21 0.54
ACGTcount: A:0.38, C:0.30, G:0.21, T:0.11
Consensus pattern (11 bp):
GATACACGAAC
Found at i:973725 original size:26 final size:26
Alignment explanation
Indices: 973696--973775 Score: 133
Period size: 26 Copynumber: 3.1 Consensus size: 26
973686 ACTACAGTTG
*
973696 ACTAAGTTCATTTTGATTAGTCGATT
1 ACTAAGTTCATTTTGATTGGTCGATT
*
973722 ACTAAGTTTATTTTGATTGGTCGATT
1 ACTAAGTTCATTTTGATTGGTCGATT
*
973748 TCTAAGTTCATTTTGATTGGTCGATT
1 ACTAAGTTCATTTTGATTGGTCGATT
973774 AC
1 AC
973776 CGGTGTTGTA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.47
Consensus pattern (26 bp):
ACTAAGTTCATTTTGATTGGTCGATT
Found at i:977492 original size:2 final size:2
Alignment explanation
Indices: 977485--977524 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
977475 AGATCAATAG
* * *
977485 GA GA GA GA GA GA AA GA AA GA TA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
977525 CTATGTTGCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.55, C:0.00, G:0.42, T:0.03
Consensus pattern (2 bp):
GA
Found at i:978384 original size:22 final size:22
Alignment explanation
Indices: 978343--978384 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
978333 TAAAATGGAT
* *
978343 CCGAAAGCAAACCCCGAGTAAA
1 CCGAAAGAAAACCCCAAGTAAA
*
978365 CCGAAAGAAAATCCCAAGTA
1 CCGAAAGAAAACCCCAAGTA
978385 GAGTTTTTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.29, G:0.17, T:0.07
Consensus pattern (22 bp):
CCGAAAGAAAACCCCAAGTAAA
Found at i:979168 original size:2 final size:2
Alignment explanation
Indices: 979161--979206 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
979151 CGTGTCTTAG
979161 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
979203 TC TC
1 TC TC
979207 CATACATTAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:980563 original size:51 final size:51
Alignment explanation
Indices: 980508--980654 Score: 160
Period size: 51 Copynumber: 2.9 Consensus size: 51
980498 AACGACAACT
* *
980508 ACAACAAGACCTGCAACAACGACATCGGCAACAACTACGACTTCACTGACA
1 ACAACAAGACCTGCAACAACGACACCGGCAACAACTACGACTACACTGACA
* * *
980559 ACAAC--GACGCTGGCATCAACGACACCGACAACAACTACGACTACAGTGACA
1 ACAACAAGAC-CT-GCAACAACGACACCGGCAACAACTACGACTACACTGACA
* * * *
980610 CCAACAACAACT---ACAACGACACCTGCAACAACTACGACTACACTG
1 ACAACAAGACCTGCAACAACGACACCGGCAACAACTACGACTACACTG
980655 TCACCAACGA
Statistics
Matches: 80, Mismatches: 12, Indels: 11
0.78 0.12 0.11
Matches are distributed among these distances:
48 29 0.36
49 3 0.04
50 2 0.03
51 43 0.54
52 2 0.03
53 1 0.01
ACGTcount: A:0.41, C:0.35, G:0.14, T:0.11
Consensus pattern (51 bp):
ACAACAAGACCTGCAACAACGACACCGGCAACAACTACGACTACACTGACA
Found at i:980573 original size:114 final size:114
Alignment explanation
Indices: 980422--980641 Score: 253
Period size: 114 Copynumber: 1.9 Consensus size: 114
980412 ATGACACCAA
* * * * * * **
980422 CAACAACTACGACTACACTGACAATAACAATCTTGGCAACACCCACATCAACAACGATTTTAACT
1 CAACAACTACGACTACACTGACAACAACAATCCTGGCAACAACCACACCAACAACAACTACAACT
* * *
980487 TCACTGACACCAACGACAACTACAACAAGACCTGCAACAACGACATCGG
66 ACACTGACACCAACAACAACTACAACAACACCTGCAACAACGACATCGG
* * * * * *
980536 CAACAACTACGACTTCACTGACAACAACGA-CGCTGGCATCAACGACACCGACAACAACTACGAC
1 CAACAACTACGACTACACTGACAACAACAATC-CTGGCAACAACCACACCAACAACAACTACAAC
* *
980600 TACAGTGACACCAACAACAACTACAACGACACCTGCAACAAC
65 TACACTGACACCAACAACAACTACAACAACACCTGCAACAAC
980642 TACGACTACA
Statistics
Matches: 86, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
113 1 0.01
114 85 0.99
ACGTcount: A:0.41, C:0.34, G:0.11, T:0.13
Consensus pattern (114 bp):
CAACAACTACGACTACACTGACAACAACAATCCTGGCAACAACCACACCAACAACAACTACAACT
ACACTGACACCAACAACAACTACAACAACACCTGCAACAACGACATCGG
Found at i:980609 original size:27 final size:26
Alignment explanation
Indices: 980579--980671 Score: 88
Period size: 27 Copynumber: 3.7 Consensus size: 26
980569 TGGCATCAAC
*
980579 GACACCGACAACAACTACGACTACAGT
1 GACACCAACAACAACTACGACTACA-T
980606 GACACCAACAACAACTAC-A--AC--
1 GACACCAACAACAACTACGACTACAT
**
980627 GACACCTGCAACAACTACGACTACACT
1 GACACCAACAACAACTACGACTACA-T
* *
980654 GTCACCAACGACAACTAC
1 GACACCAACAACAACTAC
980672 AACAACACCG
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
21 16 0.30
22 1 0.02
24 4 0.08
26 1 0.02
27 31 0.58
ACGTcount: A:0.42, C:0.37, G:0.11, T:0.11
Consensus pattern (26 bp):
GACACCAACAACAACTACGACTACAT
Found at i:980614 original size:21 final size:21
Alignment explanation
Indices: 980585--980624 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
980575 CAACGACACC
* *
980585 GACAACAACTACGACTACAGT
1 GACAACAACAACAACTACAGT
*
980606 GACACCAACAACAACTACA
1 GACAACAACAACAACTACA
980625 ACGACACCTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.33, G:0.10, T:0.10
Consensus pattern (21 bp):
GACAACAACAACAACTACAGT
Found at i:980631 original size:48 final size:47
Alignment explanation
Indices: 980523--980689 Score: 174
Period size: 48 Copynumber: 3.4 Consensus size: 47
980513 AAGACCTGCA
* * * * *
980523 ACAACGACATCGGCAACAACTACGACTTCACTGACAACAACGAC-GCT
1 ACAACGACA-CCGCAACAACTACGACTACACTGACACCAACAACAACT
*
980570 GGCATCAACGACACCGACAACAACTACGACTACAGTGACACCAACAACAACT
1 ---A-CAACGACACCG-CAACAACTACGACTACACTGACACCAACAACAACT
* *
980622 ACAACGACACCTGCAACAACTACGACTACACTGTCACCAACGACAACT
1 ACAACGACACC-GCAACAACTACGACTACACTGACACCAACAACAACT
*
980670 ACAACAACACCGGCAACAAC
1 ACAACGACACC-GCAACAAC
980690 GACATTGAAA
Statistics
Matches: 102, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
48 60 0.59
49 2 0.02
50 3 0.03
51 35 0.34
52 2 0.02
ACGTcount: A:0.41, C:0.36, G:0.13, T:0.10
Consensus pattern (47 bp):
ACAACGACACCGCAACAACTACGACTACACTGACACCAACAACAACT
Found at i:980688 original size:162 final size:162
Alignment explanation
Indices: 980488--981655 Score: 630
Period size: 165 Copynumber: 7.0 Consensus size: 162
980478 ATTTTAACTT
* * ** **
980488 CACTGACACCAACGACAACTACAACAAGACCTGCAACAACGACATCGGCAACAACTACGACTTCA
1 CACTGACACCAACGACAACTACAACAACACCGGCAACAACGACATCGAAAACAACTACGACTAAA
* * * * *
980553 CTGACAACAACGACGCTGGCATCAACGA-CACCGACAACAACTACGACTACAGTGACACCAACAA
66 CTGACAACAACGACACCGGCAACAAC-ACCACCGACAACAACTACAACTACACTGACACCAACAA
* *
980617 CAACTACAACGACACCTGCAACAACTACGACTA
130 CAACTACAACAACACCGGCAACAACTACGACTA
* *
980650 CACTGTCACCAACGACAACTACAACAACACCGGCAACAACGACATTGAAAACAACTACGACTAAA
1 CACTGACACCAACGACAACTACAACAACACCGGCAACAACGACATCGAAAACAACTACGACTAAA
* * * * *
980715 TTGACACCAACGATACCGGCAACAACACCATCGACAACAACTACAACTACACTGACACCAACGAC
66 CTGACAACAACGACACCGGCAACAACACCACCGACAACAACTACAACTACACTGACACCAACAAC
*
980780 AACTACAACAACACCGGCAACAACGAC-ACTGA
131 AACTACAACAACACCGGCAACAACTACGACT-A
* * * * * * *
980812 -A--AACAACTACGACTAAACTGTCACCAACGATACCGGCAACAAAGACACCGGCAACAACTAAG
1 CACTGACACCAACGAC--AAC--T-A-CAACAACACCGGCAACAACGACATC-G-AA-AAC--A-
* ** *
980874 ACTAC-ACTGTCACCAAC-GACAACTACAACGACACCGGCAACAATGA-CATTGAAAACAACTAC
54 ACTACGAC--T-A--AACTGAC-A--ACAACGACACCGGCAACAA-CACCACCGACAACAACTAC
* * * *
980936 GACTACACTGTCACCAACGAC-ACTGGCAACAAGGACACCGGCAACAACTACGACTA
110 AACTACACTGACACCAACAACAACT-ACAAC-A--ACACCGGCAACAACTACGACTA
* * * * * * *
980992 CTCTGTCACCATCGACAACTACAACGACACCGGCAACAAAGACATTGAAAACAACTACGACTACA
1 CACTGACACCAACGACAACTACAACAACACCGGCAACAACGACATCGAAAACAACTACGACTAAA
* * * * * * *
981057 CTGTCACCAACGACACTGGCAACAAGGA-CACCGGCAACAACTACGACTACACTGACACCAACTA
66 CTGACAACAACGACACCGGCAACAA-CACCACCGACAACAACTACAACTACACTGACACCAACAA
* * * *
981121 C-ACTGGCAACAACGACACCGGCAACAACGACACCGGCAA
130 CAACT----ACAACAACACCGGCAACAAC--TA-CGACTA
* * * * * * * *
981160 CAACT-ACGACTACACTGTCACCAACGACAACTACAACGACACCGGCAACAACGACATTGAAAAC
1 C-ACTGAC-ACCA-AC-G--A-CAACTACAACAACACCGGCA---ACAACGAC---ATCGAAAAC
* * * * * * * *
981224 AACTACGACTACACTGTCACCAACGACACTGGCAACAAGGA-CACCGGCAACAACTACGACTACT
53 AACTACGACTAAACTGACAACAACGACACCGGCAACAA-CACCACCGACAACAACTACAACTACA
* * * * *
981288 CTGTCACCAACGACAACTACAACGACACCGGCAACAACGAC-ATTGA
117 CTGACACCAACAACAACTACAACAACACCGGCAACAACTACGACT-A
* * * * * * * **
981334 -A--AACAACTACGACTACACTGTCACCAACGACACTGGCAACAAGGACACCGGCAACAACTACG
1 CACTGACACCAACGAC-A-AC--T-A-CAACAACACCGGCAACAACGACATCGAAAACAACTACG
* * * * * * * *
981396 ACTACACTGTCACCAACGACACTGGCAACAAGGA-CACCGGCAACAACTACGACTACACTGTCAC
60 ACTAAACTGACAACAACGACACCGGCAACAA-CACCACCGACAACAACTACAACTACACTGACAC
* *
981460 CAACGAC-ACTAGCAACAAGGACACCGGCAACAACTAAGACTA
124 CAACAACAACTA-CAAC-A--ACACCGGCAACAACTACGACTA
* * * * * *
981502 CATTGTCACCAACGACAACTACAACGACACCGGCAACAGCGACATTGAAAACAACTACGACTACA
1 CACTGACACCAACGACAACTACAACAACACCGGCAACAACGACATCGAAAACAACTACGACTAAA
* * * * * * * * * *
981567 CTGTCACCAACGACACTGGCAACAAGGA-CACCGGCAACAACTACGACTACTCTGTCACCATCGA
66 CTGACAACAACGACACCGGCAACAA-CACCACCGACAACAACTACAACTACACTGACACCAACAA
* *
981631 CAACTACAACGACACCAGCAACAAC
130 CAACTACAACAACACCGGCAACAAC
981656 GACATTGAAA
Statistics
Matches: 817, Mismatches: 119, Indels: 140
0.76 0.11 0.13
Matches are distributed among these distances:
159 8 0.01
161 8 0.01
162 148 0.18
163 1 0.00
164 5 0.01
165 278 0.34
166 8 0.01
167 9 0.01
168 37 0.05
169 13 0.02
170 8 0.01
171 31 0.04
172 5 0.01
173 2 0.00
174 24 0.03
175 6 0.01
176 4 0.00
177 101 0.12
178 3 0.00
179 1 0.00
180 101 0.12
181 9 0.01
183 7 0.01
ACGTcount: A:0.41, C:0.34, G:0.14, T:0.11
Consensus pattern (162 bp):
CACTGACACCAACGACAACTACAACAACACCGGCAACAACGACATCGAAAACAACTACGACTAAA
CTGACAACAACGACACCGGCAACAACACCACCGACAACAACTACAACTACACTGACACCAACAAC
AACTACAACAACACCGGCAACAACTACGACTA
Found at i:980689 original size:63 final size:63
Alignment explanation
Indices: 980622--980841 Score: 225
Period size: 63 Copynumber: 3.7 Consensus size: 63
980612 AACAACAACT
*
980622 ACAACGACACCTG-CAACAACTACGACTACACTGTCACCAACGACAACTACAACAACACCGGCA
1 ACAACGACA-CTGAAAACAACTACGACTACACTGTCACCAACGACAACTACAACAACACCGGCA
* * * *
980685 ACAACGACATTGAAAACAACTACGACTA-AAT-T-------GAC-AC--CAACGATACCGGCA
1 ACAACGACACTGAAAACAACTACGACTACACTGTCACCAACGACAACTACAACAACACCGGCA
** * * *
980736 ACAACACCATC-GACAACAACTACAACTACACTGACACCAACGACAACTACAACAACACCGGCA
1 ACAACGACA-CTGAAAACAACTACGACTACACTGTCACCAACGACAACTACAACAACACCGGCA
*
980799 ACAACGACACTGAAAACAACTACGACTAAACTGTCACCAACGA
1 ACAACGACACTGAAAACAACTACGACTACACTGTCACCAACGA
980842 TACCGGCAAC
Statistics
Matches: 122, Mismatches: 20, Indels: 30
0.71 0.12 0.17
Matches are distributed among these distances:
51 34 0.28
52 2 0.02
53 2 0.02
54 3 0.02
60 3 0.02
61 3 0.02
62 5 0.04
63 70 0.57
ACGTcount: A:0.45, C:0.34, G:0.11, T:0.10
Consensus pattern (63 bp):
ACAACGACACTGAAAACAACTACGACTACACTGTCACCAACGACAACTACAACAACACCGGCA
Found at i:980736 original size:51 final size:51
Alignment explanation
Indices: 980678--980778 Score: 141
Period size: 51 Copynumber: 2.0 Consensus size: 51
980668 CTACAACAAC
* * *
980678 ACCGGCAACAACGA-CATTGAAAACAACTACGACTAAATTGACACCAACGAT
1 ACCGGCAACAAC-ACCATCGAAAACAACTACAACTAAACTGACACCAACGAT
* *
980729 ACCGGCAACAACACCATCGACAACAACTACAACTACACTGACACCAACGA
1 ACCGGCAACAACACCATCGAAAACAACTACAACTAAACTGACACCAACGA
980779 CAACTACAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 1 0.02
51 43 0.98
ACGTcount: A:0.45, C:0.33, G:0.12, T:0.11
Consensus pattern (51 bp):
ACCGGCAACAACACCATCGAAAACAACTACAACTAAACTGACACCAACGAT
Found at i:980771 original size:21 final size:21
Alignment explanation
Indices: 980747--980786 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
980737 CAACACCATC
*
980747 GACAACAACTACAACTACACT
1 GACAACAACGACAACTACACT
*
980768 GACACCAACGACAACTACA
1 GACAACAACGACAACTACA
980787 ACAACACCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.35, G:0.07, T:0.10
Consensus pattern (21 bp):
GACAACAACGACAACTACACT
Found at i:980793 original size:27 final size:27
Alignment explanation
Indices: 980751--980807 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
980741 ACCATCGACA
* * *
980751 ACAACTACAACTACACTGACACCAACG
1 ACAACTACAACAACACCGACAACAACG
*
980778 ACAACTACAACAACACCGGCAACAACG
1 ACAACTACAACAACACCGACAACAACG
980805 ACA
1 ACA
980808 CTGAAAACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.47, C:0.37, G:0.09, T:0.07
Consensus pattern (27 bp):
ACAACTACAACAACACCGACAACAACG
Found at i:980803 original size:51 final size:51
Alignment explanation
Indices: 980699--980803 Score: 120
Period size: 51 Copynumber: 2.1 Consensus size: 51
980689 CGACATTGAA
* * * * * * *
980699 AACAACTACGACTAAATTGACACCAACGATACCGGCAACAACACCATCGAC
1 AACAACTACAACTAAACTGACACCAACGACAACGACAACAACACCAGCAAC
* * *
980750 AACAACTACAACTACACTGACACCAACGACAACTACAACAACACCGGCAAC
1 AACAACTACAACTAAACTGACACCAACGACAACGACAACAACACCAGCAAC
980801 AAC
1 AAC
980804 GACACTGAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.46, C:0.35, G:0.10, T:0.10
Consensus pattern (51 bp):
AACAACTACAACTAAACTGACACCAACGACAACGACAACAACACCAGCAAC
Done.