Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 142 of 210
Found at i:43199363 original size:5 final size:5
Alignment explanation
Indices: 43199353--43199397 Score: 76
Period size: 5 Copynumber: 9.4 Consensus size: 5
43199343 TGTATTAAGG
43199353 ATATA ATATA ATATA ATATA ATATA ATATA ATATA A-A-A ATATA AT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
43199398 TAAATTGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 2 0.05
4 2 0.05
5 34 0.89
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:43215017 original size:24 final size:23
Alignment explanation
Indices: 43214981--43215031 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
43214971 TTTAAGGGTT
* *
43214981 TTTTTTATCATTTTGTTTAAAAATA
1 TTTTTAATCA-TTT-TTTAAAAAAA
43215006 TTTTTAAT-ATTTTTTAAAAAAA
1 TTTTTAATCATTTTTTAAAAAAA
43215028 TTTT
1 TTTT
43215032 AGAAATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 13 0.54
23 3 0.12
24 1 0.04
25 7 0.29
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTTTAATCATTTTTTAAAAAAA
Found at i:43222748 original size:22 final size:22
Alignment explanation
Indices: 43222701--43222754 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
43222691 ATATGCTAGC
**
43222701 ATTTTAATTTAGTATTTCTATC
1 ATTTTAATTTAGTATTTCTAAA
*
43222723 ATTTTCAATTTGGT-TTTCTAAA
1 ATTTT-AATTTAGTATTTCTAAA
43222745 A-TTTAATTTA
1 ATTTTAATTTA
43222755 TCTTAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 5 0.19
21 3 0.11
22 12 0.44
23 7 0.26
ACGTcount: A:0.30, C:0.07, G:0.06, T:0.57
Consensus pattern (22 bp):
ATTTTAATTTAGTATTTCTAAA
Found at i:43225987 original size:22 final size:20
Alignment explanation
Indices: 43225958--43225998 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
43225948 GGTTATCCCG
*
43225958 GCCTTGTGGGTGGAGGCACAT
1 GCCTTGTGGAT-GAGGCACAT
43225979 GCCTCTGTGGATGAGGCACA
1 GCCT-TGTGGATGAGGCACA
43225999 CGCCCATGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.17, C:0.22, G:0.39, T:0.22
Consensus pattern (20 bp):
GCCTTGTGGATGAGGCACAT
Found at i:43225994 original size:21 final size:21
Alignment explanation
Indices: 43225970--43226015 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
43225960 CTTGTGGGTG
* *
43225970 GAGGCACATGCCTC-TGTGGAT
1 GAGGCACACGCC-CATGCGGAT
43225991 GAGGCACACGCCCATGCGGAT
1 GAGGCACACGCCCATGCGGAT
43226012 GAGG
1 GAGG
43226016 GATATGGTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.22, C:0.26, G:0.37, T:0.15
Consensus pattern (21 bp):
GAGGCACACGCCCATGCGGAT
Found at i:43233754 original size:16 final size:18
Alignment explanation
Indices: 43233721--43233754 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
43233711 TCAAGTTGTA
43233721 TCAGAACAAGAGCTTGAG
1 TCAGAACAAGAGCTTGAG
43233739 TCAGAAC-AGA-CTTGAG
1 TCAGAACAAGAGCTTGAG
43233755 CTTCTTGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (18 bp):
TCAGAACAAGAGCTTGAG
Found at i:43239050 original size:2 final size:2
Alignment explanation
Indices: 43239043--43239077 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
43239033 TGGAATGGGT
43239043 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43239078 TGTAAAATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:43243266 original size:55 final size:55
Alignment explanation
Indices: 43243182--43243312 Score: 181
Period size: 55 Copynumber: 2.4 Consensus size: 55
43243172 TTAATGAAAG
* *
43243182 CAAGTTAATGAGTTACACGGGCTAGTCACAAAGGCGTGTTGCTGGCCGTGTGACC
1 CAAGTCAATGAGTTACACGGGCTAGTCACAAAGGCGTGTGGCTGGCCGTGTGACC
* * * ** * *
43243237 CAAGTCAGTGAGTTACATGGGTTAGTCACACGGGGGTGTGGTTGGCCGTGTGACC
1 CAAGTCAATGAGTTACACGGGCTAGTCACAAAGGCGTGTGGCTGGCCGTGTGACC
43243292 CAAGTCAATGAGTTACACGGG
1 CAAGTCAATGAGTTACACGGG
43243313 GTCAGACATG
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 65 1.00
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.24
Consensus pattern (55 bp):
CAAGTCAATGAGTTACACGGGCTAGTCACAAAGGCGTGTGGCTGGCCGTGTGACC
Found at i:43246191 original size:34 final size:31
Alignment explanation
Indices: 43246135--43246202 Score: 82
Period size: 34 Copynumber: 2.1 Consensus size: 31
43246125 CAATTCAATA
* * *
43246135 ACAGTTCAGTTCAGTTGTGCCTTTGCTCATT
1 ACAGTTCAGTTCAGTTGGGCCTTAGCCCATT
43246166 ACAGTATCAGTATCAGTGTGGGCCTTAGCCCATT
1 ACAGT-TCAGT-TCAGT-TGGGCCTTAGCCCATT
43246200 ACA
1 ACA
43246203 CTGACAGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 5 0.16
32 5 0.16
33 5 0.16
34 16 0.52
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.34
Consensus pattern (31 bp):
ACAGTTCAGTTCAGTTGGGCCTTAGCCCATT
Found at i:43246525 original size:27 final size:27
Alignment explanation
Indices: 43246491--43246554 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
43246481 AATCATACAA
43246491 TCATTTTATAACATAGGGGCATAACAG
1 TCATTTTATAACATAGGGGCATAACAG
** ** *
43246518 TCATTTTACCATGTGGGGGCATAACAG
1 TCATTTTATAACATAGGGGCATAACAG
*
43246545 TCAGTTTATA
1 TCATTTTATA
43246555 TCAGTTTGGG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (27 bp):
TCATTTTATAACATAGGGGCATAACAG
Found at i:43247632 original size:44 final size:44
Alignment explanation
Indices: 43247569--43247657 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
43247559 TGCCACCAAT
*
43247569 CGGGATAACCTCTCCAATCCCATAATCTTCTCCTAAAATGACTC
1 CGGGATAACCTCTCCAATCCCATAATCTTCTCCTAAAATCACTC
43247613 CGGGATAACCTC-CCTAATCCCATAATCTTCTCCTAAAATCACTC
1 CGGGATAACCTCTCC-AATCCCATAATCTTCTCCTAAAATCACTC
43247657 C
1 C
43247658 AACCTTCCCA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
43 2 0.05
44 41 0.95
ACGTcount: A:0.29, C:0.36, G:0.08, T:0.27
Consensus pattern (44 bp):
CGGGATAACCTCTCCAATCCCATAATCTTCTCCTAAAATCACTC
Found at i:43255417 original size:23 final size:23
Alignment explanation
Indices: 43255391--43255443 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
43255381 AAGAAAGGTG
**
43255391 ACTGTAATATGCCGAAAATTACT
1 ACTGTAATACCCCGAAAATTACT
*
43255414 ACTGCAATACCCCGAAAATTACT
1 ACTGTAATACCCCGAAAATTACT
*
43255437 ACAGTAA
1 ACTGTAA
43255444 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.25
Consensus pattern (23 bp):
ACTGTAATACCCCGAAAATTACT
Found at i:43265412 original size:44 final size:44
Alignment explanation
Indices: 43265042--43265383 Score: 540
Period size: 44 Copynumber: 7.8 Consensus size: 44
43265032 TAAGTTCTAT
* * *
43265042 CTCCCTGAACAGTAGTGGAATAGGTGGAAGATTGTAAGTCCTAG
1 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCATGTCCTAG
43265086 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCATGTCCTAG
1 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCATGTCCTAG
* * *
43265130 CTCTCTGAACAGTAGTGGAATAGGTGGAAGACTGCATGTCCTAG
1 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCATGTCCTAG
* * *
43265174 CTCCCTGAACAGCAGTGGAATAGGTGGAAAATTGTATGTCCTAT
1 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCATGTCCTAG
** *
43265218 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTATAAGTCCTAG
1 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCATGTCCTAG
**
43265262 CTCCCTGAACAGCAGTGGAATAGGTCAAAGATTGCATGTCCTAG
1 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCATGTCCTAG
43265306 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCATGTCCTAG
1 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCATGTCCTAG
* *
43265350 CTCCCTGAATAGTAGTGGAATAGGTGGAAGATTG
1 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTG
43265384 TAGATCCTGT
Statistics
Matches: 273, Mismatches: 25, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 273 1.00
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.24
Consensus pattern (44 bp):
CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCATGTCCTAG
Found at i:43265861 original size:21 final size:21
Alignment explanation
Indices: 43265835--43265879 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
43265825 ATCGGGCAAA
43265835 ATTGGCCTTTTTTAGTCTTTG
1 ATTGGCCTTTTTTAGTCTTTG
43265856 ATTGGCCTTTTTTAGTCTTTG
1 ATTGGCCTTTTTTAGTCTTTG
43265877 ATT
1 ATT
43265880 CATTCCCGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.11, C:0.13, G:0.18, T:0.58
Consensus pattern (21 bp):
ATTGGCCTTTTTTAGTCTTTG
Found at i:43272889 original size:34 final size:34
Alignment explanation
Indices: 43272828--43272894 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
43272818 TCAGTTCAAT
*
43272828 TGGGCCTTTACCAATTACAGTATCAGTATCAGTG
1 TGGGCCTTTACCAATTACAGTATCAGTAACAGTG
*
43272862 TGGGCC-TTAGCCCATTACAGTGA-CAGTAACAGT
1 TGGGCCTTTA-CCAATTACAGT-ATCAGTAACAGT
43272895 TCAGACATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 3 0.10
34 25 0.86
35 1 0.03
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (34 bp):
TGGGCCTTTACCAATTACAGTATCAGTAACAGTG
Found at i:43273183 original size:27 final size:27
Alignment explanation
Indices: 43273131--43273212 Score: 96
Period size: 27 Copynumber: 3.1 Consensus size: 27
43273121 ACAGTCATAC
* *
43273131 ATAACATAA-AGCAT-ACAATCATTTT
1 ATAACATAAGGGCATAACAGTCATTTT
*
43273156 ATAACATAGGGGCATAACAGTCATTTT
1 ATAACATAAGGGCATAACAGTCATTTT
** *
43273183 ACCACGTAAGGGCATAACAGTCATTTT
1 ATAACATAAGGGCATAACAGTCATTTT
43273210 ATA
1 ATA
43273213 TCAGTTTCAG
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
25 8 0.17
26 4 0.09
27 34 0.74
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (27 bp):
ATAACATAAGGGCATAACAGTCATTTT
Found at i:43274299 original size:44 final size:44
Alignment explanation
Indices: 43274236--43274324 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
43274226 CCCACCAAAT
*
43274236 CGGGATAACCTCCCCAATCCCATAATCTTCT-CTTAAATGCACTC
1 CGGGATAACCTCCCCAATCCCATAATCTTCTCCTAAAAT-CACTC
43274280 CGGGATAACCTCCCCAATCCCATAATCTTCTCCTAAAATCACTC
1 CGGGATAACCTCCCCAATCCCATAATCTTCTCCTAAAATCACTC
43274324 C
1 C
43274325 AACCTTTCCA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
44 37 0.86
45 6 0.14
ACGTcount: A:0.28, C:0.38, G:0.08, T:0.26
Consensus pattern (44 bp):
CGGGATAACCTCCCCAATCCCATAATCTTCTCCTAAAATCACTC
Found at i:43276391 original size:16 final size:16
Alignment explanation
Indices: 43276372--43276402 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43276362 TTGAAAGAGT
43276372 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
43276388 TTTCAAATTTATATG
1 TTTCAAATATATATG
43276403 CTCCAAGATA
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:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:43276479 original size:23 final size:23
Alignment explanation
Indices: 43276436--43276482 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
43276426 GGTAAGAAAA
**
43276436 TTTTAATTTAACATGTTTAATTT
1 TTTTAATTTAACATGAATAATTT
*
43276459 TTTTAATTTAACTTGAATAATTT
1 TTTTAATTTAACATGAATAATTT
43276482 T
1 T
43276483 ATTCTATTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTAATTTAACATGAATAATTT
Found at i:43284648 original size:22 final size:22
Alignment explanation
Indices: 43284620--43284663 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
43284610 GCCTGTCGAT
43284620 ACAAATTTCAACAAAAGAAGAG
1 ACAAATTTCAACAAAAGAAGAG
43284642 ACAAATTTCAACAAAAGAAGAG
1 ACAAATTTCAACAAAAGAAGAG
43284664 TTAGGGAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (22 bp):
ACAAATTTCAACAAAAGAAGAG
Found at i:43284786 original size:23 final size:23
Alignment explanation
Indices: 43284724--43284788 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
43284714 ATAGGATTTA
*
43284724 CTTGTTTGGTAGTGGTGATGCGT
1 CTTGTTTGGTAGTGGTGATACGT
* * *
43284747 C-TGTTAT-TTATGGGGTGATACTT
1 CTTGTT-TGGTA-GTGGTGATACGT
43284770 CTTGTTTGGTAGTGGTGAT
1 CTTGTTTGGTAGTGGTGAT
43284789 GTGGCAAGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
22 6 0.19
23 20 0.62
24 6 0.19
ACGTcount: A:0.12, C:0.08, G:0.34, T:0.46
Consensus pattern (23 bp):
CTTGTTTGGTAGTGGTGATACGT
Found at i:43303791 original size:33 final size:30
Alignment explanation
Indices: 43303743--43303856 Score: 85
Period size: 33 Copynumber: 3.7 Consensus size: 30
43303733 TAACAACACA
*
43303743 TAATAACAATGAATAAGACATCAATAAATAACG
1 TAATAACAATAAATAA-A-A-CAATAAATAACG
*
43303776 TAATAACGATAAATAAAACAATAAATAAC-
1 TAATAACAATAAATAAAACAATAAATAACG
*
43303805 -AAT-A-AATAACA-ACAACAATAAATAACAACG
1 TAATAACAATAA-ATAAAACAATAAAT---AACG
*
43303835 ATAATAACAATAAATAATACAA
1 -TAATAACAATAAATAAAACAA
43303857 CACATAATAA
Statistics
Matches: 65, Mismatches: 6, Indels: 19
0.72 0.07 0.21
Matches are distributed among these distances:
26 15 0.23
27 2 0.03
28 3 0.05
29 3 0.05
30 11 0.17
31 1 0.02
32 4 0.06
33 16 0.25
34 10 0.15
ACGTcount: A:0.64, C:0.12, G:0.04, T:0.19
Consensus pattern (30 bp):
TAATAACAATAAATAAAACAATAAATAACG
Found at i:43303802 original size:22 final size:23
Alignment explanation
Indices: 43303777--43303851 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 23
43303767 TAAATAACGT
*
43303777 AATAACGATAAATAA-AACAATA
1 AATAACAATAAATAACAACAATA
43303799 AATAACAATAAATAACAACAACAATA
1 AATAACAATAAAT---AACAACAATA
** *
43303825 AATAACAA-CGATAATAACAATA
1 AATAACAATAAATAACAACAATA
43303847 AATAA
1 AATAA
43303852 TACAACACAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
22 26 0.58
25 4 0.09
26 15 0.33
ACGTcount: A:0.68, C:0.12, G:0.03, T:0.17
Consensus pattern (23 bp):
AATAACAATAAATAACAACAATA
Found at i:43303813 original size:26 final size:27
Alignment explanation
Indices: 43303764--43303832 Score: 79
Period size: 26 Copynumber: 2.5 Consensus size: 27
43303754 AATAAGACAT
43303764 CAATAAATAACGTAATAACGATAA-ATAAAA
1 CAATAAATAAC--AATAAC-ATAACA-AAAA
*
43303794 CAATAAATAACAATAA-ATAACAACAA
1 CAATAAATAACAATAACATAACAAAAA
43303820 CAATAAATAACAA
1 CAATAAATAACAA
43303833 CGATAATAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
26 20 0.54
27 1 0.03
28 5 0.14
30 11 0.30
ACGTcount: A:0.67, C:0.13, G:0.03, T:0.17
Consensus pattern (27 bp):
CAATAAATAACAATAACATAACAAAAA
Found at i:43303840 original size:12 final size:12
Alignment explanation
Indices: 43303787--43303866 Score: 65
Period size: 12 Copynumber: 6.4 Consensus size: 12
43303777 AATAACGATA
43303787 AATAA-AACAAT
1 AATAACAACAAT
*
43303798 AAATAACAATAAAT
1 -AATAACAA-CAAT
*
43303812 AACAACAACAAT
1 AATAACAACAAT
*
43303824 AAATAACAACGAT
1 -AATAACAACAAT
*
43303837 AATAACAATAAAT
1 AATAACAA-CAAT
43303850 AAT-ACAACACAT
1 AATAACAACA-AT
43303862 AATAA
1 AATAA
43303867 GACAATATTA
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
11 1 0.02
12 25 0.46
13 25 0.46
14 3 0.06
ACGTcount: A:0.68, C:0.14, G:0.01, T:0.17
Consensus pattern (12 bp):
AATAACAACAAT
Found at i:43303841 original size:16 final size:16
Alignment explanation
Indices: 43303802--43303833 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
43303792 AACAATAAAT
43303802 AACAATAAATAACAAC
1 AACAATAAATAACAAC
43303818 AACAATAAATAACAAC
1 AACAATAAATAACAAC
43303834 GATAATAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.19, G:0.00, T:0.12
Consensus pattern (16 bp):
AACAATAAATAACAAC
Found at i:43304008 original size:15 final size:15
Alignment explanation
Indices: 43303988--43304019 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
43303978 ACAAGGTTGT
*
43303988 AATAATAGTAATAAC
1 AATAATAATAATAAC
43304003 AATAATAATAATAAC
1 AATAATAATAATAAC
43304018 AA
1 AA
43304020 CAACAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.25
Consensus pattern (15 bp):
AATAATAATAATAAC
Found at i:43305730 original size:132 final size:132
Alignment explanation
Indices: 43305514--43305985 Score: 732
Period size: 132 Copynumber: 3.6 Consensus size: 132
43305504 GCTGCCTTCT
*
43305514 ATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAATCTTCAACCTATTCCACTACTG-CCTA
1 ATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAATCTTCAACCTATTCCACTGCTGTCC-A
* * *
43305578 GGGAGATAGGACTGGTGGCTTAAATCAGCTTCCTTACTACCTTGGGAAGATAAGATTCACCGTAT
65 GGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCT
43305643 TTG
130 TTG
* * *
43305646 ATCTGCTCCACTACTATTTAAGGAGACAAGATCTACAATCTTCAACCTATTCCACTGCTGTCCAG
1 ATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAATCTTCAACCTATTCCACTGCTGTCCAG
* * *
43305711 GGAGATAGGACCGGCGGCTTAAATCTGCTTCCCTACTA-CTTGGGAAGATAAGATTCACCATCTT
66 GGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTT
43305775 TG
131 TG
* * * * *
43305777 ATCTGCTCCACTAATGCTTAGGGAGACAGGATGTACAATCTTCAACCTAATCCACTGTTGTCCAG
1 ATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAATCTTCAACCTATTCCACTGCTGTCCAG
*
43305842 GGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTTACCGTCTT
66 GGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTT
43305907 TG
131 TG
* * * * *
43305909 ATCTACTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTATTCCACTGTTGTACAA
1 ATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAATCTTCAACCTATTCCACTGCTGTCCAG
43305974 GGAGATAGGACT
66 GGAGATAGGACT
43305986 TACAATCTTC
Statistics
Matches: 310, Mismatches: 28, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
131 119 0.38
132 189 0.61
133 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (132 bp):
ATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAATCTTCAACCTATTCCACTGCTGTCCAG
GGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTT
TG
Found at i:43305963 original size:44 final size:45
Alignment explanation
Indices: 43305915--43306028 Score: 144
Period size: 44 Copynumber: 2.6 Consensus size: 45
43305905 TTTGATCTAC
* * *
43305915 TCCACTACTGCTTAGGGAGACAGGATC-TACAATCTTCAACCTAT
1 TCCACTGCTGCTTAAGGAGATAGGATCTTACAATCTTCAACCTAT
* *
43305959 TCCACTGTTG-TACAAGGAGATAGGA-CTTACAATCTTCAACCTAT
1 TCCACTGCTGCT-TAAGGAGATAGGATCTTACAATCTTCAACCTAT
*
43306003 TCCACTGCTGCCTAAGGAGATAGGAT
1 TCCACTGCTGCTTAAGGAGATAGGAT
43306029 TTGCTATCTT
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
43 2 0.03
44 56 0.97
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (45 bp):
TCCACTGCTGCTTAAGGAGATAGGATCTTACAATCTTCAACCTAT
Found at i:43307330 original size:43 final size:44
Alignment explanation
Indices: 43307290--43307378 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 44
43307280 ATTTTTCATT
*
43307290 TTCATC-ATTTTTCGACTCAAAGCGCCCTTTGCGGGTTTTCACC
1 TTCATCTATTTTTCGACTCAAAGCGCCCTTTGCAGGTTTTCACC
* * *
43307333 TTGATCTTTTTTTTGACTCAAAGCGCCCTTTGCAGGTTTTCACC
1 TTCATCTATTTTTCGACTCAAAGCGCCCTTTGCAGGTTTTCACC
43307377 TT
1 TT
43307379 GGTCTCTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 5 0.12
44 36 0.88
ACGTcount: A:0.16, C:0.27, G:0.16, T:0.42
Consensus pattern (44 bp):
TTCATCTATTTTTCGACTCAAAGCGCCCTTTGCAGGTTTTCACC
Found at i:43318466 original size:15 final size:15
Alignment explanation
Indices: 43318446--43318477 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
43318436 ACAAGGCTGT
*
43318446 AATAATAGTAATAAC
1 AATAATAATAATAAC
43318461 AATAATAATAATAAC
1 AATAATAATAATAAC
43318476 AA
1 AA
43318478 CAACAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.25
Consensus pattern (15 bp):
AATAATAATAATAAC
Found at i:43321150 original size:26 final size:27
Alignment explanation
Indices: 43321088--43321150 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 27
43321078 GAAGCACGTT
*
43321088 AGGACAATCTAATGTAGGAAGTCCGCA
1 AGGACAATCTAATGTAGGAAGTCCACA
* * *
43321115 AGAACCATCTATTGT-GGAAGTCCACA
1 AGGACAATCTAATGTAGGAAGTCCACA
*
43321141 AGGACTATCT
1 AGGACAATCT
43321151 GATATATGGG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 18 0.60
27 12 0.40
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (27 bp):
AGGACAATCTAATGTAGGAAGTCCACA
Found at i:43329160 original size:16 final size:16
Alignment explanation
Indices: 43329139--43329179 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
43329129 TTCGCTGTAT
43329139 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
43329155 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
43329171 TGGAATAGA
1 TGGAATAGA
43329180 TGAGTAATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.39, C:0.02, G:0.37, T:0.22
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:43329186 original size:16 final size:16
Alignment explanation
Indices: 43329139--43329187 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
43329129 TTCGCTGTAT
*
43329139 TGGAATAGAGGCGTAA
1 TGGAATAGAGGAGTAA
*
43329155 TGGAATAGAGGTGTAA
1 TGGAATAGAGGAGTAA
*
43329171 TGGAATAGATGAGTAA
1 TGGAATAGAGGAGTAA
43329187 T
1 T
43329188 AGCAAATCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.39, C:0.02, G:0.35, T:0.24
Consensus pattern (16 bp):
TGGAATAGAGGAGTAA
Found at i:43329217 original size:45 final size:44
Alignment explanation
Indices: 43329166--43329256 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 44
43329156 GGAATAGAGG
*
43329166 TGTAATGGAATAGATGAGTAATAGCAAATCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAGGAGTAATAG-AAATC-ATGTGTTTGGTTGAA
* * *
43329211 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGAGTAATAGAAATCATGTGTTTGGTTGAA
43329255 TG
1 TG
43329257 GAATAGAGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 18 0.44
45 22 0.54
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.35
Consensus pattern (44 bp):
TGTAATGGAATAGAGGAGTAATAGAAATCATGTGTTTGGTTGAA
Found at i:43329438 original size:16 final size:16
Alignment explanation
Indices: 43329401--43329442 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
43329391 TTAATCATAT
*
43329401 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
43329417 TT-AAATATATTATAA
1 TTAAAATATATTATAA
43329432 TTAAAATATAT
1 TTAAAATATAT
43329443 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:43329449 original size:14 final size:15
Alignment explanation
Indices: 43329410--43329451 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
43329400 TTTAAACATA
*
43329410 ATTATTATTAAATAT
1 ATTATAATTAAATAT
43329425 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
43329439 A-TATAATTTAATA
1 ATTATAATTAAATA
43329452 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:43329543 original size:120 final size:120
Alignment explanation
Indices: 43329399--43329696 Score: 551
Period size: 120 Copynumber: 2.5 Consensus size: 120
43329389 ATTTAATCAT
*
43329399 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
43329464 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
65 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
43329520 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
*
43329585 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
* *
43329640 AATTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
43329697 TAAAATAATT
Statistics
Matches: 173, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
120 169 0.98
121 4 0.02
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
Found at i:43329562 original size:18 final size:17
Alignment explanation
Indices: 43329541--43329575 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
43329531 TTATTATTAA
*
43329541 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
43329559 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
43329576 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:43329682 original size:18 final size:17
Alignment explanation
Indices: 43329659--43329695 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
43329649 AATTATTATT
43329659 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
43329675 AAATATATGATTTAATA
1 AAATATATGATTTAATA
43329692 AAAT
1 AAAT
43329696 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:43329744 original size:47 final size:46
Alignment explanation
Indices: 43329678--43329845 Score: 143
Period size: 47 Copynumber: 3.7 Consensus size: 46
43329668 TTAATTAAAA
*
43329678 TATATG-ATTTAATAAAATTTAAAATAATTATAACTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTATAA-TAATAAATTTTCT
* * **
43329725 TATATGAATTTGTATAATTTAAAATAATTATTATTACATATAA-TTTAA
1 TATATGAATTTATATAATTTAAAATAATTA-TAATA-ATA-AATTTTCT
* * *
43329773 TA-AT-AA--TATATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAATTTATATAATTT-AAAATAATT-ATAATAATAAATTTTCT
*
43329816 TATATGAATTTATACAATTTAAAATAATTA
1 TATATGAATTTATATAATTTAAAATAATTA
43329846 ATATTAAATA
Statistics
Matches: 94, Mismatches: 15, Indels: 25
0.70 0.11 0.19
Matches are distributed among these distances:
42 2 0.02
43 8 0.09
44 18 0.19
45 5 0.05
46 5 0.05
47 40 0.43
48 14 0.15
49 2 0.02
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTTTCT
Found at i:43329767 original size:26 final size:28
Alignment explanation
Indices: 43329737--43329797 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
43329727 TATGAATTTG
*
43329737 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
43329763 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
43329791 TAAAATT
1 TATAATT
43329798 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:43329807 original size:91 final size:91
Alignment explanation
Indices: 43329712--43329919 Score: 344
Period size: 91 Copynumber: 2.3 Consensus size: 91
43329702 TAATTATAAC
* * * *
43329712 TAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
43329777 AATATATAATTTCATAAAATTCTTGA
66 AATATATAATTTCATAAAATTCTTAA
43329803 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
43329868 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
*
43329894 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAATTTTCTTATATGAATTTA
43329920 CTAAAATCAA
Statistics
Matches: 109, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
91 89 0.82
92 20 0.18
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTAA
Found at i:43329879 original size:44 final size:43
Alignment explanation
Indices: 43329737--43329879 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 43
43329727 TATGAATTTG
* *
43329737 TATAATTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
** * * * *
43329781 TATAATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATGAATTTA
1 TATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATA
*
43329828 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
43329872 TATAATTT
1 TATAATTT
43329880 CATAAAATTC
Statistics
Matches: 74, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
43 3 0.04
44 32 0.43
45 7 0.09
46 7 0.09
47 22 0.30
48 3 0.04
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
Found at i:43329894 original size:47 final size:47
Alignment explanation
Indices: 43329762--43329900 Score: 137
Period size: 47 Copynumber: 3.0 Consensus size: 47
43329752 TTATTATTAC
* *
43329762 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
* * * ** *
43329809 AT-T--TTCTTAT-ATGAATTTATACAATT--TAAAATAATTAATATTAA
1 ATATAATT-TAATAATG-ATATATA-ATTTCATAAAATTCTTAATAATAA
43329853 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
43329900 A
1 A
43329901 ATGTTCTTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
44 20 0.29
45 13 0.19
46 13 0.19
47 23 0.33
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (47 bp):
ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
Found at i:43330971 original size:6 final size:6
Alignment explanation
Indices: 43330960--43330985 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
43330950 TAGTTTGAAC
43330960 ATTTAA ATTTAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA AT
43330986 AATTTCGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:43331444 original size:13 final size:13
Alignment explanation
Indices: 43331426--43331450 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43331416 ATCAAATTTG
43331426 TATGTACTCTTTA
1 TATGTACTCTTTA
43331439 TATGTACTCTTT
1 TATGTACTCTTT
43331451 CACTAATAAA
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:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (13 bp):
TATGTACTCTTTA
Found at i:43331605 original size:21 final size:21
Alignment explanation
Indices: 43331579--43331638 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
43331569 TTTCTATTAA
43331579 AAAAACATATAACCTATTAGT
1 AAAAACATATAACCTATTAGT
43331600 AAAAACATATAACCTATTAGT
1 AAAAACATATAACCTATTAGT
*
43331621 AAAAACATATAACATATT
1 AAAAACATATAACCTATT
43331639 TTAAATTCCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.55, C:0.13, G:0.03, T:0.28
Consensus pattern (21 bp):
AAAAACATATAACCTATTAGT
Found at i:43331991 original size:29 final size:29
Alignment explanation
Indices: 43331957--43332025 Score: 111
Period size: 29 Copynumber: 2.4 Consensus size: 29
43331947 AAACAAATGC
43331957 AACAATTTCCAGTTTCATTGAAAACAACA
1 AACAATTTCCAGTTTCATTGAAAACAACA
**
43331986 AACAATTTCCAGTTTCATTGAAAACTGCA
1 AACAATTTCCAGTTTCATTGAAAACAACA
*
43332015 GACAATTTCCA
1 AACAATTTCCA
43332026 TTGCAACAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.29
Consensus pattern (29 bp):
AACAATTTCCAGTTTCATTGAAAACAACA
Found at i:43341701 original size:2 final size:2
Alignment explanation
Indices: 43341694--43341720 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43341684 AAATATAGAA
43341694 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 A
43341721 AATTATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43342034 original size:11 final size:11
Alignment explanation
Indices: 43342013--43342049 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
43342003 TAAGTAGATT
43342013 AATAT-ATAAA
1 AATATAATAAA
43342023 AATATAATAAA
1 AATATAATAAA
43342034 AATATAATAAA
1 AATATAATAAA
43342045 AATAT
1 AATAT
43342050 TAAACTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 5 0.19
11 21 0.81
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AATATAATAAA
Found at i:43342046 original size:22 final size:23
Alignment explanation
Indices: 43342013--43342073 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
43342003 TAAGTAGATT
43342013 AATAT-ATAAAAATATAATAAA-
1 AATATAATAAAAATATAATAAAC
43342034 AATATAATAAAAATAT--TAAAC
1 AATATAATAAAAATATAATAAAC
43342055 TAAT-TAATAAAAAATATAA
1 -AATATAAT-AAAAATATAA
43342074 ACCGTAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
20 4 0.12
21 9 0.26
22 21 0.62
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
AATATAATAAAAATATAATAAAC
Found at i:43344589 original size:20 final size:18
Alignment explanation
Indices: 43344544--43344592 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
43344534 TATAATTCTT
*
43344544 AAATTTTTAGTAAATTTA
1 AAATTTTTATTAAATTTA
*
43344562 AATTTTTTTATTAAAGTTTA
1 AA-ATTTTTATTAAA-TTTA
43344582 ATAATTTTTAT
1 A-AATTTTTAT
43344593 AATTTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 10 0.40
20 12 0.48
21 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (18 bp):
AAATTTTTATTAAATTTA
Found at i:43344596 original size:9 final size:9
Alignment explanation
Indices: 43344582--43344625 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
43344572 TTAAAGTTTA
43344582 ATAATTTTT
1 ATAATTTTT
43344591 ATAATTTTT
1 ATAATTTTT
*
43344600 ATTGATTTTT
1 A-TAATTTTT
43344610 AT--TTTTT
1 ATAATTTTT
43344617 ATAATTTTT
1 ATAATTTTT
43344626 TTGTCACATG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
7 7 0.23
9 16 0.52
10 8 0.26
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (9 bp):
ATAATTTTT
Found at i:43348642 original size:3 final size:3
Alignment explanation
Indices: 43348634--43348670 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
43348624 AGTATGGGTG
* *
43348634 TGA TGA TGA TGA TGA TGA TGA TGA CGA CGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
43348671 AGCGATGATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.30
Consensus pattern (3 bp):
TGA
Found at i:43359726 original size:28 final size:28
Alignment explanation
Indices: 43359656--43359728 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
43359646 CGACATACAT
* *
43359656 TAACAATCTGGGCCTGAGCTCTAAGCAG
1 TAACAGTCTGGGCCTTAGCTCTAAGCAG
**
43359684 TAACAGTCTAAGCCTTAGC-CTAAAGCAG
1 TAACAGTCTGGGCCTTAGCTCT-AAGCAG
*
43359712 TAACAGTGTGGGCCTTA
1 TAACAGTCTGGGCCTTA
43359729 ACCCAATACA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
27 2 0.05
28 35 0.95
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (28 bp):
TAACAGTCTGGGCCTTAGCTCTAAGCAG
Found at i:43360096 original size:27 final size:27
Alignment explanation
Indices: 43360067--43360299 Score: 290
Period size: 27 Copynumber: 8.6 Consensus size: 27
43360057 CAACTCCTAG
* * * * *
43360067 GGGTATTTCAATTATTTTACCTTTTGG
1 GGGTATTTCGATCATTTTACCCTTCGA
*
43360094 GGGTATCTC-AGTCATTTTACCCTTCGA
1 GGGTATTTCGA-TCATTTTACCCTTCGA
* *
43360121 GGGTATTTCGATCCTTTTACCCTTTGA
1 GGGTATTTCGATCATTTTACCCTTCGA
* *
43360148 GGGTATTTTGGTCATTTTACCCTTCGA
1 GGGTATTTCGATCATTTTACCCTTCGA
*
43360175 GGGAATTTCGATCATTTTACCCTTCGA
1 GGGTATTTCGATCATTTTACCCTTCGA
*
43360202 GGGTATTTCGATGATTTTACCCTTCGA
1 GGGTATTTCGATCATTTTACCCTTCGA
*
43360229 GGGTATTTCGGTCATTTTACCCTTCGA
1 GGGTATTTCGATCATTTTACCCTTCGA
* *
43360256 GGGCATTT-TAGTCATTTTACCCTTCGA
1 GGGTATTTCGA-TCATTTTACCCTTCGA
*
43360283 GGGCATTTCGATCATTT
1 GGGTATTTCGATCATTT
43360300 GAAGCCCATT
Statistics
Matches: 179, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
26 1 0.01
27 176 0.98
28 2 0.01
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (27 bp):
GGGTATTTCGATCATTTTACCCTTCGA
Found at i:43364214 original size:16 final size:17
Alignment explanation
Indices: 43364193--43364225 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
43364183 AAATTTGATC
43364193 GTATTT-TATTTAATAA
1 GTATTTATATTTAATAA
*
43364209 GTATTTATCTTTAATAA
1 GTATTTATATTTAATAA
43364226 ATTAATAGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (17 bp):
GTATTTATATTTAATAA
Found at i:43364841 original size:25 final size:25
Alignment explanation
Indices: 43364803--43364858 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 25
43364793 TTTCTCCTAA
43364803 ATTTTAATTGTATTGAATTAATTAAT
1 ATTTTAATTGTATTGAATT-ATTAAT
43364829 -TTTTCAATT-TATTGAATTATTAAT
1 ATTTT-AATTGTATTGAATTATTAAT
43364853 ATTTTA
1 ATTTTA
43364859 TACTGATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
24 7 0.25
25 17 0.61
26 4 0.14
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (25 bp):
ATTTTAATTGTATTGAATTATTAAT
Found at i:43366949 original size:27 final size:27
Alignment explanation
Indices: 43366911--43366964 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
43366901 TGTCCCAAAC
43366911 ACTAGATTCAGTACTATTCAAAATGTT
1 ACTAGATTCAGTACTATTCAAAATGTT
43366938 ACTAGATTCAGTACTATTCAAAATGTT
1 ACTAGATTCAGTACTATTCAAAATGTT
43366965 CCTTGAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (27 bp):
ACTAGATTCAGTACTATTCAAAATGTT
Found at i:43368352 original size:19 final size:20
Alignment explanation
Indices: 43368328--43368369 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
43368318 ATCTCAACCC
43368328 TTCTCATCTCT-TCACTTCA
1 TTCTCATCTCTCTCACTTCA
* *
43368347 TTCTCATTTCTCTCTCTTCA
1 TTCTCATCTCTCTCACTTCA
43368367 TTC
1 TTC
43368370 CCTTCCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.12, C:0.36, G:0.00, T:0.52
Consensus pattern (20 bp):
TTCTCATCTCTCTCACTTCA
Found at i:43374519 original size:53 final size:53
Alignment explanation
Indices: 43374439--43374543 Score: 156
Period size: 53 Copynumber: 2.0 Consensus size: 53
43374429 CACACTTCAC
* * *
43374439 CTTTATAAAGCATAAGTATTGACCTCACACGAAATATAAAATAGGAATATTAA
1 CTTTATAAAGCATAAGTACTGACCTCACACAAAATATAAAATAGAAATATTAA
* * *
43374492 CTTTATAAAGCATAATTACTGGCCTCACACAAAATATAAACTAGAAATATTA
1 CTTTATAAAGCATAAGTACTGACCTCACACAAAATATAAAATAGAAATATTA
43374544 CACACATAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.29
Consensus pattern (53 bp):
CTTTATAAAGCATAAGTACTGACCTCACACAAAATATAAAATAGAAATATTAA
Found at i:43379217 original size:20 final size:20
Alignment explanation
Indices: 43379194--43379259 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 20
43379184 AATTCCAAAA
43379194 AAAATATCAAAATTATTTTT
1 AAAATATCAAAATTATTTTT
* *
43379214 AAAAT-TTAAAA-TATTTAT
1 AAAATATCAAAATTATTTTT
43379232 AAAA-ATCCTAAAATTTATATTTT
1 AAAATAT-C-AAAA-TTAT-TTTT
43379255 AAAAT
1 AAAAT
43379260 TTTTTAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
18 11 0.31
19 5 0.14
20 9 0.26
22 3 0.09
23 7 0.20
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATATCAAAATTATTTTT
Found at i:43383400 original size:12 final size:12
Alignment explanation
Indices: 43383385--43383435 Score: 61
Period size: 12 Copynumber: 4.3 Consensus size: 12
43383375 AGATTATGTG
43383385 AAAAATTAAATA
1 AAAAATTAAATA
43383397 AAAAATTAAAT-
1 AAAAATTAAATA
43383408 -AAAATTAAATTA
1 AAAAATTAAA-TA
* *
43383420 AAAAAATAACTA
1 AAAAATTAAATA
43383432 AAAA
1 AAAA
43383436 CATGGTTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
12 17 0.50
13 7 0.21
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAATTAAATA
Found at i:43383411 original size:22 final size:23
Alignment explanation
Indices: 43383386--43383434 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
43383376 GATTATGTGA
*
43383386 AAAATTAAA-TAAAAAATTAAAT
1 AAAATTAAATTAAAAAAATAAAT
*
43383408 AAAATTAAATTAAAAAAATAACT
1 AAAATTAAATTAAAAAAATAAAT
43383431 AAAA
1 AAAA
43383435 ACATGGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (23 bp):
AAAATTAAATTAAAAAAATAAAT
Found at i:43386731 original size:17 final size:17
Alignment explanation
Indices: 43386685--43386734 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
43386675 TCTCAGATTT
* *
43386685 TGATACCCATATATTTC
1 TGATACCTATATCTTTC
*
43386702 TAATA-CTCATATCTTTC
1 TGATACCT-ATATCTTTC
43386719 TGATACCTATATCTTT
1 TGATACCTATATCTTT
43386735 GACTTTCTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 1 0.04
17 24 0.89
18 2 0.07
ACGTcount: A:0.28, C:0.22, G:0.04, T:0.46
Consensus pattern (17 bp):
TGATACCTATATCTTTC
Found at i:43391317 original size:17 final size:17
Alignment explanation
Indices: 43391295--43391327 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
43391285 TCTCAAATTT
43391295 TGATACCTATATCTTTC
1 TGATACCTATATCTTTC
43391312 TGATACCTATATCTTT
1 TGATACCTATATCTTT
43391328 GACTTTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.48
Consensus pattern (17 bp):
TGATACCTATATCTTTC
Found at i:43397859 original size:23 final size:22
Alignment explanation
Indices: 43397806--43397866 Score: 90
Period size: 21 Copynumber: 2.8 Consensus size: 22
43397796 CGACACATAA
43397806 GTGCCTAAA-ACAACACACGAG
1 GTGCCTAAATACAACACACGAG
43397827 GTGCCT-AATACAACACACGAG
1 GTGCCTAAATACAACACACGAG
*
43397848 GTGCCTGAAATACGACACA
1 GTGCCT-AAATACAACACA
43397867 TAAAGTGTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 2 0.06
21 24 0.67
23 10 0.28
ACGTcount: A:0.39, C:0.28, G:0.20, T:0.13
Consensus pattern (22 bp):
GTGCCTAAATACAACACACGAG
Found at i:43405736 original size:23 final size:23
Alignment explanation
Indices: 43405710--43405782 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
43405700 CACGAGGTGG
43405710 CTGAAATACGACACATAAAGTGC
1 CTGAAATACGACACATAAAGTGC
* *
43405733 CTGATATACGAAACATAAAGTGC
1 CTGAAATACGACACATAAAGTGC
*
43405756 CT-AATATACGTCACATAAAGTGC
1 CTGAA-ATACGACACATAAAGTGC
43405779 CTGA
1 CTGA
43405783 TCGGCAAGGC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
22 1 0.02
23 41 0.95
24 1 0.02
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (23 bp):
CTGAAATACGACACATAAAGTGC
Found at i:43410351 original size:22 final size:21
Alignment explanation
Indices: 43410326--43410366 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
43410316 TTATTCCTAT
*
43410326 AGAGAATTTGAGAGTTACAAAA
1 AGAGAA-TTCAGAGTTACAAAA
*
43410348 AGAGGATTCAGAGTTACAA
1 AGAGAATTCAGAGTTACAA
43410367 GCAAAATGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.46, C:0.07, G:0.24, T:0.22
Consensus pattern (21 bp):
AGAGAATTCAGAGTTACAAAA
Found at i:43413166 original size:23 final size:23
Alignment explanation
Indices: 43413128--43413178 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
43413118 ACTCAAACGG
* *
43413128 TGTAATATCCCTAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
43413151 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
43413174 AGTAA
1 TGTAA
43413179 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:43435645 original size:37 final size:37
Alignment explanation
Indices: 43435568--43435646 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
43435558 CTGATCTGGC
* *
43435568 GTGTTATCGGTTGGATTAGCTCTTATGAGAGTTTGGT
1 GTGTTATCGGATGGATTAGCTCTTATGAGAGATTGGT
*
43435605 GTGTTATCGGATGGATTAGCTCTTATGAGCA-ATTGTT
1 GTGTTATCGGATGGATTAGCTCTTATGAG-AGATTGGT
43435642 GTGTT
1 GTGTT
43435647 CGGTTGGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.18, C:0.09, G:0.30, T:0.43
Consensus pattern (37 bp):
GTGTTATCGGATGGATTAGCTCTTATGAGAGATTGGT
Found at i:43441018 original size:26 final size:25
Alignment explanation
Indices: 43440984--43441064 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 25
43440974 AATATGTGAT
*
43440984 TTAATTTGGTCTTAGTTTAGAACAAA
1 TTAAATTGGTCTTAGTTTAG-ACAAA
* *
43441010 TTAAATTGGTCTTA-TTTCGGACACA
1 TTAAATTGGTCTTAGTTT-AGACAAA
43441035 TT-AATTGTGT-TTATTGTTTAGACAAA
1 TTAAATTG-GTCTTA--GTTTAGACAAA
43441061 TTAA
1 TTAA
43441065 TTGTGTCCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
24 8 0.18
25 11 0.25
26 21 0.48
27 4 0.09
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (25 bp):
TTAAATTGGTCTTAGTTTAGACAAA
Found at i:43449895 original size:64 final size:64
Alignment explanation
Indices: 43449817--43449947 Score: 253
Period size: 64 Copynumber: 2.0 Consensus size: 64
43449807 GCAATATGCC
*
43449817 AAATTAGTGGACAGTCCACATCATTAACATTGCATATTGTTTTAAGATGAACAAGAATGGAACT
1 AAATTAGTGGACAGTCCACATCATTAACATTGCATACTGTTTTAAGATGAACAAGAATGGAACT
43449881 AAATTAGTGGACAGTCCACATCATTAACATTGCATACTGTTTTAAGATGAACAAGAATGGAACT
1 AAATTAGTGGACAGTCCACATCATTAACATTGCATACTGTTTTAAGATGAACAAGAATGGAACT
43449945 AAA
1 AAA
43449948 GTGTCTACCG
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (64 bp):
AAATTAGTGGACAGTCCACATCATTAACATTGCATACTGTTTTAAGATGAACAAGAATGGAACT
Found at i:43455892 original size:37 final size:37
Alignment explanation
Indices: 43455851--43455925 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
43455841 TGCATGTACT
43455851 TAACCGCTTCAGCGATCTTCGCCTTATCTACCAGAAC
1 TAACCGCTTCAGCGATCTTCGCCTTATCTACCAGAAC
* *
43455888 TAACCTCTTCAGCGGTCTTCGCCTTATCTACCAGAAC
1 TAACCGCTTCAGCGATCTTCGCCTTATCTACCAGAAC
43455925 T
1 T
43455926 GCGAACTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.23, C:0.35, G:0.13, T:0.29
Consensus pattern (37 bp):
TAACCGCTTCAGCGATCTTCGCCTTATCTACCAGAAC
Found at i:43467371 original size:19 final size:18
Alignment explanation
Indices: 43467349--43467390 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
43467339 ATAATTTCAG
43467349 ATAATATAA-ATTATTTTAA
1 ATAATATAAGA-TATTTT-A
*
43467368 ATAAAATAAGATATTTTA
1 ATAATATAAGATATTTTA
43467386 ATAAT
1 ATAAT
43467391 TTTCCTAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 5 0.25
19 14 0.70
20 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
ATAATATAAGATATTTTA
Found at i:43470681 original size:22 final size:22
Alignment explanation
Indices: 43470647--43470710 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
43470637 AGAACTTTGA
43470647 ATCTATATCTGATATGCTCTGC
1 ATCTATATCTGATATGCTCTGC
* *
43470669 ATCTGTATTTGATATGCTCTGC
1 ATCTATATCTGATATGCTCTGC
43470691 ATCTATATCT-ATGATGCTCT
1 ATCTATATCTGAT-ATGCTCT
43470711 ATTTCTGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 2 0.05
22 35 0.95
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.44
Consensus pattern (22 bp):
ATCTATATCTGATATGCTCTGC
Found at i:43480389 original size:71 final size:66
Alignment explanation
Indices: 43480312--43480459 Score: 188
Period size: 66 Copynumber: 2.2 Consensus size: 66
43480302 CAAATAGCAA
* * * * *
43480312 AATCTTACATTCTAACCAAATGAAATAAATAAATAAAAAGGTAATGTAATATACTTAGTAATGTG
1 AATCTTACATTCCAACCAAATG----AAACAAA-AAAAAGGTAATATAAAATACCTAGTAATGTG
*
43480377 CTAAGT
61 CTAAAT
*
43480383 AATCTTATATTCCAACCAAATGAAACAAAAAAAAGGTAATATAAAATACCTAGTAATGTGCTAAA
1 AATCTTACATTCCAACCAAATGAAACAAAAAAAAGGTAATATAAAATACCTAGTAATGTGCTAAA
43480448 T
66 T
43480449 AATCTTACATT
1 AATCTTACATT
43480460 TTGACAATCA
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
66 43 0.62
67 6 0.09
71 20 0.29
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.30
Consensus pattern (66 bp):
AATCTTACATTCCAACCAAATGAAACAAAAAAAAGGTAATATAAAATACCTAGTAATGTGCTAAA
T
Found at i:43484064 original size:21 final size:22
Alignment explanation
Indices: 43484028--43484069 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
43484018 CTCCAAAACA
*
43484028 AGGGAAAATAGGTTA-CATTTT
1 AGGGAAAATAGCTTACCATTTT
*
43484049 AGGGAAAATATCTTACCATTT
1 AGGGAAAATAGCTTACCATTT
43484070 CAATTTCCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (22 bp):
AGGGAAAATAGCTTACCATTTT
Found at i:43484470 original size:34 final size:35
Alignment explanation
Indices: 43484412--43484478 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
43484402 CAAACAGCAG
*
43484412 AAAATATTTTCTAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
*
43484447 AAAATATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
43484479 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.34
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:43485645 original size:11 final size:13
Alignment explanation
Indices: 43485629--43485661 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
43485619 ATTTCATGAA
43485629 AAAATTTCG-T-G
1 AAAATTTCGTTCG
43485640 AAAATTTCGTTCG
1 AAAATTTCGTTCG
43485653 AAAATTTCG
1 AAAATTTCG
43485662 ACGTTTGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 1 0.05
13 10 0.50
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (13 bp):
AAAATTTCGTTCG
Found at i:43486930 original size:51 final size:50
Alignment explanation
Indices: 43486861--43487385 Score: 478
Period size: 51 Copynumber: 10.4 Consensus size: 50
43486851 GTAGCATTGT
*
43486861 GTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTGA
1 GTGAAGGCTACTACGTGTACCGATAAAT-ATGGTCACATGTGTAGTACTGA
* * * * * * *
43486912 GTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGTACTGT
1 GTGAAGGCTACTACGTGTACCGATAA-ATATGGTCACATGTGTAGTACTGA
* * *
43486963 GTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAA
1 GTGAAGGCTACTACGTGTACCGATAAAT-ATGGTCACATGTGTAGTACTGA
* * * * * * *
43487014 GTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGTACTGT
1 GTGAAGGCTACTACGTGTACCGATAA-ATATGGTCACATGTGTAGTACTGA
*
43487065 GTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTGA
1 GTGAAGGCTACTACGTGTACCGATAAAT-ATGGTCACATGTGTAGTACTGA
* * * * * *
43487116 GTGAAGGTTACAATGTGTACCGAGAAGCTTTGGTCAC--GTGTAGTACT-A
1 GTGAAGGCTACTACGTGTACCGATAA-ATATGGTCACATGTGTAGTACTGA
* * *
43487164 TGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAA
1 -GTGAAGGCTACTACGTGTACCGATAAAT-ATGGTCACATGTGTAGTACTGA
* * *
43487216 GTGAAGGCTACTATGTGTACCGA-AAAGCTTTGGTCACGTGTGTAGTACT-A
1 GTGAAGGCTACTACGTGTACCGATAAA--TATGGTCACATGTGTAGTACTGA
* * *
43487266 TGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGATCACGTGTGTAGTACT-A
1 -GTGAAGGCTACTACGTGTACCGATAAATA--TGGTCACATGTGTAGTACTGA
* * *
43487316 TGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGATCACGTGTGTAGTACT-A
1 -GTGAAGGCTACTACGTGTACCGATAAATA--TGGTCACATGTGTAGTACTGA
*
43487366 TGTGAAGGCTATTACGTGTA
1 -GTGAAGGCTACTACGTGTA
43487386 TCGAATGATA
Statistics
Matches: 396, Mismatches: 62, Indels: 33
0.81 0.13 0.07
Matches are distributed among these distances:
48 2 0.01
49 37 0.09
50 93 0.23
51 259 0.65
52 5 0.01
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (50 bp):
GTGAAGGCTACTACGTGTACCGATAAATATGGTCACATGTGTAGTACTGA
Found at i:43487020 original size:102 final size:102
Alignment explanation
Indices: 43486844--43487389 Score: 798
Period size: 102 Copynumber: 5.4 Consensus size: 102
43486834 TATCGATGAA
* * * *
43486844 CACGTGTGTAGCATTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
*
43486909 TGAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
* *
43486946 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
43487011 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
* *
43487048 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
* *
43487113 TGAGTGAAGGTTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
*
43487150 CAC--GTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
* *
43487213 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
* * * *
43487250 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGATCACGTGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATA-ATGGTCACATGTGTAGTA
* * * * * *
43487313 CTATGTGAAGGCTACTACGTGAACCGTA-AAAC-TTGAT
65 CTAAGTGAAGGCTACAATGTGTACCG-AGAAGCTTTGGT
* *
43487350 CACGTGTGTAGTACTATGTGAAGGCTATTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
43487390 ATGATAAAAG
Statistics
Matches: 410, Mismatches: 29, Indels: 11
0.91 0.06 0.02
Matches are distributed among these distances:
100 133 0.32
101 45 0.11
102 232 0.57
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.29
Consensus pattern (102 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
Found at i:43487412 original size:151 final size:150
Alignment explanation
Indices: 43486860--43487422 Score: 496
Period size: 151 Copynumber: 3.7 Consensus size: 150
43486850 TGTAGCATTG
* * * *
43486860 TGTGAAGGCTACTACGTGTATCGATAAATA-ATGGTCACATGTGTAGTACTGA-GTGAAGGCTAC
1 TGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGGTCACGTGTGTAGTACT-ATGTGAAGGCTAC
* * * * * * * * *
43486923 AATGTGTACCGAGAAGCT-TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGAT
63 TACGTGTATCGA-ATGATAATGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-T
***
43486987 AAATGATGGTCACATGTGTAGTACTA
126 AAAACTTGGTCAC-TGTGTAGTACTA
* * * * * *
43487013 AGTGAAGGCTACAATGTGTACCG-AGAAGCTTTGGTCACGTGTGTAGTACTGTGTGAAGGCTACT
1 TGTGAAGGCTACTACGTGAACCGTA-AAAC-TTGGTCACGTGTGTAGTACTATGTGAAGGCTACT
* * * * *
43487077 ACGTGTATCG-ATAAATAATGGTCACATGTGTAGTACTGA-GTGAAGGTTACAATGTGTACCG-A
64 ACGTGTATCGAAT-GATAATGGTCACATGTGTAGTACT-ATGTGAAGGCTACTACGTGAACCGTA
*
43487139 GAAGCTTTGGTCAC-GTGTAGTACTA
127 -AAAC-TTGGTCACTGTGTAGTACTA
* *** * *
43487164 TGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAGTGAAGGCTACTA
1 TGTGAAGGCTACTACGTGAACCG-TAAAACTTGGTCACGTGTGTAGTACTATGTGAAGGCTACTA
* * * * * *
43487229 TGTGTACCGAAAAGCT-TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAA
65 CGTGTATCG-AATGATAATGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAA
*
43487293 ACTTGATCACGTGTGTAGTACTA
129 ACTTGGTCAC-TGTGTAGTACTA
* *
43487316 TGTGAAGGCTACTACGTGAACCGTAAAACTTGATCACGTGTGTAGTACTATGTGAAGGCTATTAC
1 TGTGAAGGCTACTACGTGAACCGTAAAACTTGGTCACGTGTGTAGTACTATGTGAAGGCTACTAC
** * * *
43487381 GTGTATCGAATGATAAAAGTAACATGGGTAGTACTGTGTGAA
66 GTGTATCGAATGATAATGGTCACATGTGTAGTACTATGTGAA
43487423 AAACCCCAAA
Statistics
Matches: 324, Mismatches: 68, Indels: 38
0.75 0.16 0.09
Matches are distributed among these distances:
150 12 0.04
151 170 0.52
152 42 0.13
153 100 0.31
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (150 bp):
TGTGAAGGCTACTACGTGAACCGTAAAACTTGGTCACGTGTGTAGTACTATGTGAAGGCTACTAC
GTGTATCGAATGATAATGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAAC
TTGGTCACTGTGTAGTACTA
Found at i:43487415 original size:202 final size:204
Alignment explanation
Indices: 43486844--43487389 Score: 845
Period size: 202 Copynumber: 2.7 Consensus size: 204
43486834 TATCGATGAA
* *
43486844 CACGTGTGTAGCATTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTAC
*
43486909 TGAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGTACTGTGTGAAGGCTAC
66 TGAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGTACTATGTGAAGGCTAC
*
43486974 TACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGA
131 TACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAAA
43487039 AGCTTTGGT
196 AGCTTTGGT
43487048 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTAC
*
43487113 TGAGTGAAGGTTACAATGTGTACCGAGAAGCTTTGGTCAC--GTGTAGTACTATGTGAAGGCTAC
66 TGAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGTACTATGTGAAGGCTAC
*
43487176 TACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAAA
131 TACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAAA
43487241 AGCTTTGGT
196 AGCTTTGGT
* * * * * *
43487250 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGATCACGTGTGTAGTA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATA-ATGGTCACATGTGTAGTA
* * * * *
43487313 CT-ATGTGAAGGCTACTACGTGAACCGTA-AAAC-TTGATCACGTGTGTAGTACTATGTGAAGGC
65 CTGA-GTGAAGGCTACAATGTGTACCG-AGAAGCTTTGGTCACGTGTGTAGTACTATGTGAAGGC
* *
43487375 TATTACGTGTATCGA
128 TACTACGTGAATCGA
43487390 ATGATAAAAG
Statistics
Matches: 317, Mismatches: 20, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
200 9 0.03
201 42 0.13
202 164 0.52
204 102 0.32
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.29
Consensus pattern (204 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTAC
TGAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGTACTATGTGAAGGCTAC
TACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAAA
AGCTTTGGT
Found at i:43494635 original size:22 final size:22
Alignment explanation
Indices: 43494573--43494662 Score: 119
Period size: 22 Copynumber: 4.1 Consensus size: 22
43494563 ATTGTTCAAA
* **
43494573 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
43494595 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
43494617 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
* * *
43494639 CATGAGGGTTTAGTTCGTTA-C
1 CATGAGAGCTTAGTACGTTAGC
43494660 CAT
1 CAT
43494663 ATAAAGACCT
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
21 4 0.06
22 58 0.94
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.29
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:43495604 original size:219 final size:219
Alignment explanation
Indices: 43495225--43495663 Score: 817
Period size: 219 Copynumber: 2.0 Consensus size: 219
43495215 GAGGCAGCTC
43495225 ATTTGTTCCTTAGACATGTGGTGAAATATTGGGGAGTGTCACAGTCTATCATTAATGATCGAGGG
1 ATTTGTTCCTTAGACATGTGGTGAAATATTGGGGAGTGTCACAGTCTATCATTAATGATCGAGGG
* *
43495290 GTGATTCACGAGCTGGTTCTGGACGGAGTTGTTCAAGTTAATGGGCTTAGACTTGATCTTTTCCA
66 GTGATTCACGAGCTGGTTCTGGACGGAGTTGTTCAAGTTAATAGGCTCAGACTTGATCTTTTCCA
*
43495355 CTAGTATACATCCACAAACAGATGGTCAAACATAGTAAGTGAATGCGTTGTCGGGGACGTATCTT
131 CTAGTATACATCCACAAACAGATGGTCAAACATAGCAAGTGAATGCGTTGTCGGGGACGTATCTT
43495420 CGGTACTATGTGAGTGCCACACAA
196 CGGTACTATGTGAGTGCCACACAA
*
43495444 ATTTGTTCCTTAGACATGTGGTGAAATATTGGGGAGTGTTACAGTCTATCATTAATGATCGAGGG
1 ATTTGTTCCTTAGACATGTGGTGAAATATTGGGGAGTGTCACAGTCTATCATTAATGATCGAGGG
43495509 GTGATTCACGAGCTGGTTCTGGACGGAGTTGTTCAAGTTAATAGGCTCAGACTTGATCTTTTCCA
66 GTGATTCACGAGCTGGTTCTGGACGGAGTTGTTCAAGTTAATAGGCTCAGACTTGATCTTTTCCA
*
43495574 CTAGTATACATCCACAAATC-GATGGTCAAACATAGCAAGTGAATGTGTTGTCGGGGACGTATCT
131 CTAGTATACATCCACAAA-CAGATGGTCAAACATAGCAAGTGAATGCGTTGTCGGGGACGTATCT
43495638 TCGGTACTATGTGAGTGCCACACAA
195 TCGGTACTATGTGAGTGCCACACAA
43495663 A
1 A
43495664 AGGACTGGCC
Statistics
Matches: 214, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
219 213 1.00
220 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (219 bp):
ATTTGTTCCTTAGACATGTGGTGAAATATTGGGGAGTGTCACAGTCTATCATTAATGATCGAGGG
GTGATTCACGAGCTGGTTCTGGACGGAGTTGTTCAAGTTAATAGGCTCAGACTTGATCTTTTCCA
CTAGTATACATCCACAAACAGATGGTCAAACATAGCAAGTGAATGCGTTGTCGGGGACGTATCTT
CGGTACTATGTGAGTGCCACACAA
Found at i:43496591 original size:20 final size:19
Alignment explanation
Indices: 43496538--43496594 Score: 64
Period size: 17 Copynumber: 3.1 Consensus size: 19
43496528 AGCTTGGCAC
* *
43496538 ATATGGAATGTAATCTTTG
1 ATATGAAATGTAATCTTAG
*
43496557 A-A-GAAATGCAATCTTAG
1 ATATGAAATGTAATCTTAG
43496574 ATATGAAATGTAAATCTTAG
1 ATATGAAATGT-AATCTTAG
43496594 A
1 A
43496595 AGATATGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 13 0.42
18 2 0.06
19 7 0.23
20 9 0.29
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (19 bp):
ATATGAAATGTAATCTTAG
Found at i:43498512 original size:14 final size:14
Alignment explanation
Indices: 43498493--43498521 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
43498483 CAATATATAT
43498493 ATAAGAATTATACG
1 ATAAGAATTATACG
43498507 ATAAGAATTATACG
1 ATAAGAATTATACG
43498521 A
1 A
43498522 ATCCATCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (14 bp):
ATAAGAATTATACG
Found at i:43500966 original size:18 final size:18
Alignment explanation
Indices: 43500940--43500974 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
43500930 GTGTGAGTTT
*
43500940 GTGTTTGTGTGGGTGTGG
1 GTGTGTGTGTGGGTGTGG
43500958 GTGTGTGTGTGGGTGTG
1 GTGTGTGTGTGGGTGTG
43500975 TGAGAGAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.57, T:0.43
Consensus pattern (18 bp):
GTGTGTGTGTGGGTGTGG
Found at i:43500975 original size:12 final size:12
Alignment explanation
Indices: 43500946--43500976 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
43500936 GTTTGTGTTT
*
43500946 GTGTGGGTGTGG
1 GTGTGTGTGTGG
43500958 GTGTGTGTGTGG
1 GTGTGTGTGTGG
43500970 GTGTGTG
1 GTGTGTG
43500977 AGAGAGAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.61, T:0.39
Consensus pattern (12 bp):
GTGTGTGTGTGG
Found at i:43512423 original size:38 final size:41
Alignment explanation
Indices: 43512345--43512425 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 41
43512335 TAAAAAGTAT
* * *
43512345 TTATATTAAAAAACATTATCATAAATATAATGAATGTTTTA
1 TTATATTAAAAAACATCATAATAAATATAATGAATATTTTA
* *
43512386 TTATATTAAAAAACA-CA-AATTAATAT-ATTAATATTTTA
1 TTATATTAAAAAACATCATAATAAATATAATGAATATTTTA
43512424 TT
1 TT
43512426 GTATATAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
38 12 0.34
39 7 0.20
40 1 0.03
41 15 0.43
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.43
Consensus pattern (41 bp):
TTATATTAAAAAACATCATAATAAATATAATGAATATTTTA
Found at i:43514705 original size:22 final size:23
Alignment explanation
Indices: 43514656--43514705 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
43514646 ACACGCATAG
*
43514656 TTTT-TAATATATATGCATATTT
1 TTTTATAATATATATGCATATTA
*
43514678 TCTTTATAATATATATGTATA-TA
1 T-TTTATAATATATATGCATATTA
43514701 TTTTA
1 TTTTA
43514706 AACTTTTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 5 0.21
23 5 0.21
24 14 0.58
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (23 bp):
TTTTATAATATATATGCATATTA
Found at i:43519673 original size:15 final size:15
Alignment explanation
Indices: 43519655--43519695 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
43519645 AAAAAAAATC
43519655 AAAATCAAAATCTAA
1 AAAATCAAAATCTAA
43519670 AAAATCAAAATCTAA
1 AAAATCAAAATCTAA
*
43519685 AAAATGAAAAT
1 AAAATCAAAAT
43519696 GATGAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.68, C:0.10, G:0.02, T:0.20
Consensus pattern (15 bp):
AAAATCAAAATCTAA
Found at i:43519733 original size:11 final size:11
Alignment explanation
Indices: 43519699--43519731 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
43519689 TGAAAATGAT
43519699 GAAAAAGGAAAA
1 GAAAAA-GAAAA
43519711 GAAAAAGAAAA
1 GAAAAAGAAAA
43519722 G-AAAAGAAAA
1 GAAAAAGAAAA
43519732 AGGAGAGGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 9 0.43
11 6 0.29
12 6 0.29
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
GAAAAAGAAAA
Found at i:43521366 original size:36 final size:36
Alignment explanation
Indices: 43521319--43521394 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
43521309 CTCTTTGGCA
*
43521319 TTACAGTGGAATAGATTGAAACCACAATGGCGAATC
1 TTACAGTGGAATAGATTGAAACCACAACGGCGAATC
43521355 TTACAGTGGAATAGATTGAAACCACAACGGCGAATC
1 TTACAGTGGAATAGATTGAAACCACAACGGCGAATC
43521391 TTAC
1 TTAC
43521395 TTCCTTAGTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.22
Consensus pattern (36 bp):
TTACAGTGGAATAGATTGAAACCACAACGGCGAATC
Found at i:43521805 original size:44 final size:45
Alignment explanation
Indices: 43521756--43521949 Score: 170
Period size: 44 Copynumber: 4.4 Consensus size: 45
43521746 CATCCAATCC
* *
43521756 TATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAATCAT-AGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCATCAGATCT
* ***
43521800 TATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCATC--CAG-TCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCATCAGATCT
* ** ** *
43521840 TATCTCTCTAAAGTTGCAGTGGAGCAGACAGAAAAAAAATCA-ATCC
1 TATCTCTCTGAAGTTGCAGTGGAGCAG--ATTAAAATCATCAGATCT
* * *
43521886 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAA-CTTCAGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCATCAGATCT
*
43521930 TATCTCTCTGAAATTGCAGT
1 TATCTCTCTGAAGTTGCAGT
43521950 AGAATAGATC
Statistics
Matches: 116, Mismatches: 25, Indels: 18
0.73 0.16 0.11
Matches are distributed among these distances:
40 21 0.18
41 8 0.07
42 4 0.03
43 11 0.09
44 44 0.38
46 28 0.24
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (45 bp):
TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCATCAGATCT
Found at i:43526099 original size:25 final size:25
Alignment explanation
Indices: 43526071--43526124 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
43526061 AAATGTGGAC
*
43526071 AAAATAAAACCATAAAATTGTAGAT
1 AAAATAAAACCACAAAATTGTAGAT
*
43526096 AAAATAAAACCACAAAATTGTGGAT
1 AAAATAAAACCACAAAATTGTAGAT
43526121 AAAA
1 AAAA
43526125 CCATGATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.20
Consensus pattern (25 bp):
AAAATAAAACCACAAAATTGTAGAT
Found at i:43529019 original size:50 final size:52
Alignment explanation
Indices: 43528894--43529024 Score: 151
Period size: 50 Copynumber: 2.6 Consensus size: 52
43528884 TGAACAAATG
* * *
43528894 AGTTACTTAATGCA-AGACTTAATTTAATGATGCAGACTTAAACTAACATGGG
1 AGTTACATAATGCATA-ACTTTATTTAATGATGCAGACTTAAACTAACATGGA
** * * *
43528946 AGTTACATAATGCATGTCATTATTT-ATGATGCATACTT-AACTAGCATGGA
1 AGTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGGA
*
43528996 AGTTACATAATGCATAACTTTATTAAATG
1 AGTTACATAATGCATAACTTTATTTAATG
43529025 CAGAACACAC
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
50 31 0.48
51 15 0.23
52 19 0.29
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.34
Consensus pattern (52 bp):
AGTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGGA
Found at i:43533537 original size:2 final size:2
Alignment explanation
Indices: 43533530--43533558 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43533520 TTAGAAGGGG
43533530 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 G
43533559 GGGGGTATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:43552552 original size:22 final size:22
Alignment explanation
Indices: 43552473--43552544 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
43552463 AAGCGGCAAA
* **
43552473 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
43552495 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
43552517 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
43552539 CATGAG
1 CATGAG
43552545 GGTTTAGTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:43562508 original size:35 final size:36
Alignment explanation
Indices: 43562461--43562533 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 36
43562451 CCTAAAGTTT
*
43562461 TACATTTCTTAACCCCGTAGTGCCATCATATTCATA
1 TACATTTCTTAACCCCGTAATGCCATCATATTCATA
*
43562497 TACA-TTCTTAACCCTGTAATGCCATCATATTCATA
1 TACATTTCTTAACCCCGTAATGCCATCATATTCATA
43562532 TA
1 TA
43562534 ATCCATCTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 31 0.89
36 4 0.11
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.37
Consensus pattern (36 bp):
TACATTTCTTAACCCCGTAATGCCATCATATTCATA
Found at i:43562890 original size:457 final size:457
Alignment explanation
Indices: 43562036--43562924 Score: 1679
Period size: 457 Copynumber: 1.9 Consensus size: 457
43562026 AATAACAATC
43562036 CATATACATTCTTAACCCCGTAATGCCACCATATTCATATAATCCATCTATATATACATTTCAAT
1 CATATACATTCTTAACCCCGTAATGCCACCATATTCATATAATCCATCTATATATACATTTCAAT
43562101 TCCATTAAATACATCATACCTATTTGTGGTAATTATATCATTCATTCTTTACGATTTAGTCCTTT
66 TCCATTAAATACATCATACCTATTTGTGGTAATTATATCATTCATTCTTTACGATTTAGTCCTTT
* *
43562166 AGATGCCGATTTCACCAAAATTACATAACAATTTAAACTAATAAGTAAACAATATAATACAAAAA
131 AGATGCCGATTTCACCAAAATTACATAACAATCTAAACTAATAAGTAAAAAATATAATACAAAAA
43562231 TATCATGAATTAAATAAGTAAGTCTCATATGTACTTACCTAGCAAAAACAACAATTGATAAGGTG
196 TATCATGAATTAAATAAGTAAGTCTCATATGTACTTACCTAGCAAAAACAACAATTGATAAGGTG
*
43562296 TTAGGAACTAATCCGTAATTTTACATTTTCCTCGATTATTATACGATTGATTCAATTCTTGGTGT
261 TCAGGAACTAATCCGTAATTTTACATTTTCCTCGATTATTATACGATTGATTCAATTCTTGGTGT
43562361 ATAATAATTTATTTCAATTTATCAATTCAAAATCTCTTATAAAATTCAATTATAAGCATATATCA
326 ATAATAATTTATTTCAATTTATCAATTCAAAATCTCTTATAAAATTCAATTATAAGCATATATCA
43562426 ATTCAATTTCATTTAAAAAAAGTTCCCTAAAGTTTTACATTTCTTAACCCCGTAGTGCCATCATA
391 ATTCAATTTCATTTAAAAAAAGTTCCCTAAAGTTTTACATTTCTTAACCCCGTAGTGCCATCATA
43562491 TT
456 TT
* *
43562493 CATATACATTCTTAACCCTGTAATGCCATCATATTCATATAATCCATCTATATATACATTTCAAT
1 CATATACATTCTTAACCCCGTAATGCCACCATATTCATATAATCCATCTATATATACATTTCAAT
43562558 TCCATTAAATACATCATACCTATTTGTGGTAATTATATCATTCATTCTTTACGATTTAGTCCTTT
66 TCCATTAAATACATCATACCTATTTGTGGTAATTATATCATTCATTCTTTACGATTTAGTCCTTT
43562623 AGATGCCGATTTCACCAAAATTACATAACAATCTAAACTAATAAGTAAAAAATATAATACAAAAA
131 AGATGCCGATTTCACCAAAATTACATAACAATCTAAACTAATAAGTAAAAAATATAATACAAAAA
43562688 TATCATGAATTAAATAAGTAAGTCTCATATGTACTTACCTAGCAAAAACAACAATTGATAAGGTG
196 TATCATGAATTAAATAAGTAAGTCTCATATGTACTTACCTAGCAAAAACAACAATTGATAAGGTG
* * *
43562753 TCAGGAACTAATCTGTAATTTTACATTTTCCTCGATTATTATACGATTGGTTCAATTCTTTGTGT
261 TCAGGAACTAATCCGTAATTTTACATTTTCCTCGATTATTATACGATTGATTCAATTCTTGGTGT
* *
43562818 ATAATAATTTATTTCAATTTATCAATTCAAAATCTTTTATAAAATTCTATTATAAGCATATATCA
326 ATAATAATTTATTTCAATTTATCAATTCAAAATCTCTTATAAAATTCAATTATAAGCATATATCA
*
43562883 ATTCAATTTCATTTTAAAAAAGTTCCCTAAAGTTTTACATTT
391 ATTCAATTTCATTTAAAAAAAGTTCCCTAAAGTTTTACATTT
43562925 TCTTCAATTT
Statistics
Matches: 421, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
457 421 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (457 bp):
CATATACATTCTTAACCCCGTAATGCCACCATATTCATATAATCCATCTATATATACATTTCAAT
TCCATTAAATACATCATACCTATTTGTGGTAATTATATCATTCATTCTTTACGATTTAGTCCTTT
AGATGCCGATTTCACCAAAATTACATAACAATCTAAACTAATAAGTAAAAAATATAATACAAAAA
TATCATGAATTAAATAAGTAAGTCTCATATGTACTTACCTAGCAAAAACAACAATTGATAAGGTG
TCAGGAACTAATCCGTAATTTTACATTTTCCTCGATTATTATACGATTGATTCAATTCTTGGTGT
ATAATAATTTATTTCAATTTATCAATTCAAAATCTCTTATAAAATTCAATTATAAGCATATATCA
ATTCAATTTCATTTAAAAAAAGTTCCCTAAAGTTTTACATTTCTTAACCCCGTAGTGCCATCATA
TT
Found at i:43564804 original size:33 final size:29
Alignment explanation
Indices: 43564689--43564823 Score: 107
Period size: 29 Copynumber: 4.5 Consensus size: 29
43564679 AAGTACTGTA
*
43564689 ATATAT-ACATATATGAGTTTT-GTTATT-T
1 ATATATAATATATATG-GTTTTGGTT-TTAT
* *
43564717 AAATATAATATATATGGGTTTTGGTGTTAT
1 ATATATAATATATAT-GGTTTTGGTTTTAT
* *
43564747 ATATATAATATATAT-GTGTGGGTTTTATT
1 ATATATAATATATATGGTTTTGGTTTTA-T
*
43564776 ATATATAATATATATGCGTTTATAGGTTTTGT
1 ATATATAATATATATG-GTTT-T-GGTTTTAT
*
43564808 ATCATCTAATATATAT
1 AT-ATATAATATATAT
43564824 AAATGTATAT
Statistics
Matches: 86, Mismatches: 11, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
28 14 0.16
29 30 0.35
30 18 0.21
31 3 0.03
32 3 0.03
33 18 0.21
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.50
Consensus pattern (29 bp):
ATATATAATATATATGGTTTTGGTTTTAT
Found at i:43565188 original size:36 final size:36
Alignment explanation
Indices: 43565146--43565221 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
43565136 GTTATATTAT
* *
43565146 GAACCATGTTAACTTGGTGAAT-TATATTATTATGGC
1 GAACCATGTTAACTTGGTG-ATGTATATTAATATGAC
*
43565182 GAACCATGTTAATTTGGTGATGTATATTAATATGAC
1 GAACCATGTTAACTTGGTGATGTATATTAATATGAC
43565218 GAAC
1 GAAC
43565222 TATATTAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 2 0.06
36 34 0.94
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.37
Consensus pattern (36 bp):
GAACCATGTTAACTTGGTGATGTATATTAATATGAC
Found at i:43565230 original size:36 final size:36
Alignment explanation
Indices: 43565146--43565232 Score: 104
Period size: 36 Copynumber: 2.4 Consensus size: 36
43565136 GTTATATTAT
* * * *
43565146 GAACCATGTTAACTTGGTGAATTATATTATTATGGC
1 GAACCATATTAATTTGGTGAATTATATTAATATGAC
*
43565182 GAACCATGTTAATTTGGTG-ATGTATATTAATATGAC
1 GAACCATATTAATTTGGTGAAT-TATATTAATATGAC
*
43565218 GAACTATATTAATTT
1 GAACCATATTAATTT
43565233 TCCAAACTGT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
35 2 0.04
36 43 0.96
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.40
Consensus pattern (36 bp):
GAACCATATTAATTTGGTGAATTATATTAATATGAC
Found at i:43565864 original size:17 final size:17
Alignment explanation
Indices: 43565844--43565922 Score: 68
Period size: 17 Copynumber: 4.6 Consensus size: 17
43565834 TTATGATGGA
43565844 GCATGAACTGTTATTTT
1 GCATGAACTGTTATTTT
* **
43565861 GCATGAATTGTTATTCG
1 GCATGAACTGTTATTTT
* * *
43565878 GTATGAATTGGTATTTT
1 GCATGAACTGTTATTTT
** *
43565895 ATATGAACTATTATTTT
1 GCATGAACTGTTATTTT
*
43565912 GCATGAGCTGT
1 GCATGAACTGT
43565923 CCTTTGGCAA
Statistics
Matches: 47, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 47 1.00
ACGTcount: A:0.25, C:0.09, G:0.20, T:0.46
Consensus pattern (17 bp):
GCATGAACTGTTATTTT
Found at i:43567647 original size:14 final size:14
Alignment explanation
Indices: 43567625--43567658 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
43567615 TTTAAAAAAA
* *
43567625 ATATGTATATGTGT
1 ATATATATATGTAT
43567639 ATATATATATGTAT
1 ATATATATATGTAT
43567653 ATATAT
1 ATATAT
43567659 GTATATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (14 bp):
ATATATATATGTAT
Found at i:43567742 original size:2 final size:2
Alignment explanation
Indices: 43567693--43567723 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
43567683 ATAGTAAGAA
43567693 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
43567724 AAAGTGTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43567889 original size:3 final size:3
Alignment explanation
Indices: 43567875--43567972 Score: 67
Period size: 3 Copynumber: 31.7 Consensus size: 3
43567865 TAAATGGGTA
* *
43567875 AAT AAA AAT AAT AAT AAGGT AAGT AAT AAT AAT AA- ATAC AAT AAT AAT
1 AAT AAT AAT AAT AAT AA--T AA-T AAT AAT AAT AAT A-AT AAT AAT AAT
* * * *
43567923 GAT AAT AAT AAT AAT AAGT -TT AAT AAGT -TT AAT AAT AAT AAA AAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AA-T AAT AAT AAT AAT AAT AAT
43567968 AAT AA
1 AAT AA
43567973 CGGGACTAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 16
0.74 0.11 0.16
Matches are distributed among these distances:
2 3 0.04
3 63 0.83
4 7 0.09
5 3 0.04
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:43569315 original size:43 final size:43
Alignment explanation
Indices: 43569268--43569369 Score: 150
Period size: 43 Copynumber: 2.4 Consensus size: 43
43569258 TCCACTGCGT
* * *
43569268 CTTGTCGCTTCGATCTACTCCACTGCACTTCAGAGAGATATGA
1 CTTGTAGCTTCAATCTACTCCACTGCACTTCAGAAAGATATGA
* * *
43569311 CTTGTAGCTTCAATCCACTCCACTGCACTTCAGAAAGGTCTGA
1 CTTGTAGCTTCAATCTACTCCACTGCACTTCAGAAAGATATGA
43569354 CTTGTAGCTTCAATCT
1 CTTGTAGCTTCAATCT
43569370 TCTTCGCAGC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (43 bp):
CTTGTAGCTTCAATCTACTCCACTGCACTTCAGAAAGATATGA
Found at i:43569577 original size:44 final size:44
Alignment explanation
Indices: 43569529--43569953 Score: 165
Period size: 44 Copynumber: 9.4 Consensus size: 44
43569519 AGTCTACTCC
*
43569529 ACTGCAACTTCAGGGAGATAAGGTTTGCTACTTCAACCTGCTCT
1 ACTGCAACTTCAGGGAGATAAGGTTTGCTACTTCAATCTGCTCT
* ** * * *
43569573 ACTGCAACTTTAAAGAGATAAGGTTTGATA--T-GATCTGTTCT
1 ACTGCAACTTCAGGGAGATAAGGTTTGCTACTTCAATCTGCTCT
* * * * * * * *
43569614 ACTGTAACTTCATAGAGATGAGATCA-GTTATGGTAGATTTAATTTGTTCC
1 ACTGCAACTTC--AG-G--GAGATAAGGTT-TGCTA-CTTCAATCTGCTCT
* * *
43569664 ACTGCAACTTCAGGGAAATAAGATTTGCTATCTTTAATCTGCTCT
1 ACTGCAACTTCAGGGAGATAAGGTTTGCTA-CTTCAATCTGCTCT
* ** * *
43569709 ACTACAACTTCAGGGAGAT-AGGATCCATCATTTTAAC-CCACTCTACTGCTCT
1 ACTGCAACTTCAGGGAGATAAGG-T---T--TGCT-ACTTCA--AT-CTGCTCT
* * * * *
43569761 ACTGCAAATTCAAGGAGGT-AGGATTAG-TAACTTCAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGG-TTTGCT-ACTTCAATCTGCTCT
* * * * * *
43569805 ACTGCATCTTCAGGGAGATAAGACTTAG-TACGATCAATCTGCCCC
1 ACTGCAACTTCAGGGAGATAAG-GTTTGCTAC-TTCAATCTGCTCT
* * *
43569850 ACTGCAACTTCA-GGAGGATAAGATTTGCTATTTCAACCTGCTCT
1 ACTGCAACTTCAGGGA-GATAAGGTTTGCTACTTCAATCTGCTCT
* * * *
43569894 ACTGCAACTTCAGAGAGATAAAGTTTGATA--T-GATCTGCTCT
1 ACTGCAACTTCAGGGAGATAAGGTTTGCTACTTCAATCTGCTCT
* *
43569935 ACTACAACTTCAGAGAGAT
1 ACTGCAACTTCAGGGAGAT
43569954 GAGATCTGTG
Statistics
Matches: 288, Mismatches: 65, Indels: 59
0.70 0.16 0.14
Matches are distributed among these distances:
41 42 0.15
42 2 0.01
43 1 0.00
44 89 0.31
45 80 0.28
46 16 0.06
47 3 0.01
48 3 0.01
49 3 0.01
50 20 0.07
51 2 0.01
52 27 0.09
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (44 bp):
ACTGCAACTTCAGGGAGATAAGGTTTGCTACTTCAATCTGCTCT
Found at i:43570034 original size:44 final size:44
Alignment explanation
Indices: 43569985--43570182 Score: 175
Period size: 44 Copynumber: 4.5 Consensus size: 44
43569975 AAACATTTGC
* *
43569985 TATCTTCAGTCTGCTACACTGCAACATCAGTGAGATAAGACTTG
1 TATCTTCAGTCTGCTACACTGCAACTTCAGGGAGATAAGACTTG
* * * **
43570029 TATCTTCAATCTG-TCCCACTGCAACTTCAGGGGGATAAGGTTTG
1 TATCTTCAGTCTGCT-ACACTGCAACTTCAGGGAGATAAGACTTG
* * * *
43570073 ACATCCTCAGTCTGCTTCACTGCAACTTTAGGGAGATAAGACTTG
1 -TATCTTCAGTCTGCTACACTGCAACTTCAGGGAGATAAGACTTG
** ** **
43570118 TATCTTCAACCTGCCCCACTGCAACTTCAAGGG-GATAAGGTTTG
1 TATCTTCAGTCTGCTACACTGCAACTTC-AGGGAGATAAGACTTG
* *
43570162 CTATCCTCAGTCTGCTCCACT
1 -TATCTTCAGTCTGCTACACT
43570183 ACTGCTTAGG
Statistics
Matches: 121, Mismatches: 28, Indels: 9
0.77 0.18 0.06
Matches are distributed among these distances:
43 1 0.01
44 65 0.54
45 54 0.45
46 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (44 bp):
TATCTTCAGTCTGCTACACTGCAACTTCAGGGAGATAAGACTTG
Found at i:43570141 original size:89 final size:89
Alignment explanation
Indices: 43569980--43570182 Score: 309
Period size: 89 Copynumber: 2.3 Consensus size: 89
43569970 CAAGGAAACA
* * * *
43569980 TTTGCTATCTTCAGTCTGCTACACTGCAACATCAGTGAGATAAGACTTGTATCTTCAATCTGTCC
1 TTTGCTATCCTCAGTCTGCTACACTGCAACATCAGGGAGATAAGACTTGTATCTTCAACCTGCCC
*
43570045 CACTGCAACTTCAGGGGGATAAGG
66 CACTGCAACTTCAAGGGGATAAGG
* * *
43570069 TTTGAC-ATCCTCAGTCTGCTTCACTGCAACTTTAGGGAGATAAGACTTGTATCTTCAACCTGCC
1 TTTG-CTATCCTCAGTCTGCTACACTGCAACATCAGGGAGATAAGACTTGTATCTTCAACCTGCC
43570133 CCACTGCAACTTCAAGGGGATAAGG
65 CCACTGCAACTTCAAGGGGATAAGG
*
43570158 TTTGCTATCCTCAGTCTGCTCCACT
1 TTTGCTATCCTCAGTCTGCTACACT
43570183 ACTGCTTAGG
Statistics
Matches: 103, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
88 1 0.01
89 101 0.98
90 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (89 bp):
TTTGCTATCCTCAGTCTGCTACACTGCAACATCAGGGAGATAAGACTTGTATCTTCAACCTGCCC
CACTGCAACTTCAAGGGGATAAGG
Found at i:43570347 original size:90 final size:90
Alignment explanation
Indices: 43570213--43570663 Score: 654
Period size: 90 Copynumber: 5.0 Consensus size: 90
43570203 CTGCAATATC
* * * * *
43570213 CGATCTACTTTGTTGCCAATACAGAAAGACAAGATCTGTTATCTTC-GACCTACTTCACTGCCAA
1 CGATCTACTTTGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAG-TCTACTTCGCTGCCAA
*
43570277 TACAGGAAGACAAGATCTG-TCATCTT
65 TACAGGAAGACAAGACCTGCT-ATCTT
* * *
43570303 CGATCTACTTCGCTGCCAATACAGGAAGATAAGATCTGCTATCTTCAGTCTACTTCGCTACCAAT
1 CGATCTACTTTGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCTGCCAAT
43570368 ACAGGAAGACAAGACCTGCTATCTT
66 ACAGGAAGACAAGACCTGCTATCTT
* * *
43570393 CGATCTACTTCGCTGCCGATACAGGAAGACAAGATCTGCTATCTTCAGTTTACTTCGCTGCCAAT
1 CGATCTACTTTGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCTGCCAAT
*
43570458 ACAGGAAGACAAAACCTGCTATCTT
66 ACAGGAAGACAAGACCTGCTATCTT
* * * * *
43570483 TGATCTACTTTGCTGCAAATACAGGAAAATAAGTTCTGCTATCTTCAGTCTACTTCGCTGCCAAT
1 CGATCTACTTTGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCTGCCAAT
*
43570548 ACAGGAAGACAAGACCAGCTATCTT
66 ACAGGAAGACAAGACCTGCTATCTT
* * * * *
43570573 TGATCTACTTTGTTGCCGATACAGGAAGACAAAATCTGCTATCTTCAGTCTACTTCGCTACCAAT
1 CGATCTACTTTGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCTGCCAAT
43570638 ACAGGAAGACAAGACCTGCTATCTT
66 ACAGGAAGACAAGACCTGCTATCTT
43570663 C
1 C
43570664 ACTGATCTGT
Statistics
Matches: 325, Mismatches: 34, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
90 323 0.99
91 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (90 bp):
CGATCTACTTTGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCTGCCAAT
ACAGGAAGACAAGACCTGCTATCTT
Found at i:43570664 original size:45 final size:46
Alignment explanation
Indices: 43570214--43570664 Score: 571
Period size: 45 Copynumber: 10.0 Consensus size: 46
43570204 TGCAATATCC
* * * *
43570214 GATCTACTTTGTTGCCAATACAGAAAGACAAGATCTGTTATCTTC-
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
* *
43570259 GACCTACTTCACTGCCAATACAGGAAGACAAGATCTG-TCATCTTC-
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCT-ATCTTCA
*
43570304 GATCTACTTCGCTGCCAATACAGGAAGATAAGATCTGCTATCTTCA
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
* *
43570350 G-TCTACTTCGCTACCAATACAGGAAGACAAGACCTGCTATCTTC-
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
*
43570394 GATCTACTTCGCTGCCGATACAGGAAGACAAGATCTGCTATCTTCA
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
* * * *
43570440 G-TTTACTTCGCTGCCAATACAGGAAGACAAAACCTGCTATCTT-T
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
* * * * *
43570484 GATCTACTTTGCTGCAAATACAGGAAAATAAGTTCTGCTATCTTCA
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
* * *
43570530 G-TCTACTTCGCTGCCAATACAGGAAGACAAGACCAGCTATCTT-T
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
* * * *
43570574 GATCTACTTTGTTGCCGATACAGGAAGACAAAATCTGCTATCTTCA
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
* *
43570620 G-TCTACTTCGCTACCAATACAGGAAGACAAGACCTGCTATCTTCA
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
43570665 CTGATCTGTT
Statistics
Matches: 348, Mismatches: 49, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
44 4 0.01
45 339 0.97
46 5 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (46 bp):
GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
Found at i:43572393 original size:22 final size:22
Alignment explanation
Indices: 43572368--43572410 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
43572358 TCTCCCTATT
43572368 TTGCTACAATTTTACTATTATG
1 TTGCTACAATTTTACTATTATG
* *
43572390 TTGCTACTATTTTATTATTAT
1 TTGCTACAATTTTACTATTAT
43572411 TGTTTGGATA
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:0.26, C:0.12, G:0.07, T:0.56
Consensus pattern (22 bp):
TTGCTACAATTTTACTATTATG
Found at i:43572474 original size:30 final size:30
Alignment explanation
Indices: 43572440--43572502 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
43572430 ACTTATTTTA
43572440 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
43572470 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
43572500 TTG
1 TTG
43572503 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:43572655 original size:12 final size:12
Alignment explanation
Indices: 43572625--43572657 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
43572615 TATATATTTT
43572625 AAAATT-ATATA
1 AAAATTAATATA
43572636 AAAA-TAATATA
1 AAAATTAATATA
43572647 AAAATTAATAT
1 AAAATTAATAT
43572658 GGCGGGTCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:43576948 original size:61 final size:58
Alignment explanation
Indices: 43576845--43576960 Score: 169
Period size: 61 Copynumber: 1.9 Consensus size: 58
43576835 ATCACTTCAA
* * *
43576845 TATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAATC
1 TATTAAATCAATAGAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATC
*
43576903 TATTAAATCAATAGAATATTTATCTGTAAGATAAATATTAAATTAAATTTAATATTAA
1 TATTAAATCAATAGAATACTTATC---AAGATAAATATTAAATTAAATTTAATATTAA
43576961 GATAATTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 21 0.41
61 30 0.59
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (58 bp):
TATTAAATCAATAGAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATC
Done.