Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1188
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: 1075576
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 121203 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:502727 original size:147 final size:146
Alignment explanation
Indices: 502386--503096 Score: 996
Period size: 146 Copynumber: 4.9 Consensus size: 146
502376 TTTTTAACAA
* * * * * * * *
502386 TGACCTTGAACTT-CCTCAATTGACCTTTGGTCAAGGTCATGACATACTCTCAGGTTATAAGCAT
1 TGACCTTGACCTTGCC-CAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAA
* * * * * * *
502450 TC-TAGATGTGAATTAAGAACTTCCAATATTTGTCCATTAGAAAGATATGGACTGGACACGAGTT
65 TCTTTG-TGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATT
** *
502514 TTATAC-TTTTCTGCTAG
129 TTGCACTTTTTCTGCCAG
* * * *
502531 TGACCTTGGCCTTGCCCAAATGACCTTGGGTCAAGGTCATGACAAACCCTTAGCTTATAAGCAAT
1 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
* * * * *
502596 CTTTGTGTGAACTGAGAACTTCCAATGTTTCTTCATAAGAAAGATATGGACCGGACAAGTATTTT
66 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTT
*
502661 GCACTTTTTTCTGCCAT
131 GCAC-TTTTTCTGCCAG
* *
502678 TGACCTTGACCTTGTCCAAATGACCTTGGGTCAAGGTCATGACACACCCTAAGGTCATAAGCAAT
1 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
* *
502743 ATTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCTGACACGAATTTT
66 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTT
*
502808 GCACTTTTTCTTCCAG
131 GCACTTTTTCTGCCAG
* * * *
502824 TGACCTTGACCTTGCCCGAATGACCTTGGTTCAAGGTCATGACACACCCTTAAGTCATAAGCATT
1 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
*
502889 CTTTGTGTGAAGTAAGAACTTCTAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTT
66 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTT
*
502954 GCACTTTTTCTTCCAG
131 GCACTTTTTCTGCCAG
* *
502970 TGACCTTGACCTTGCCCGAATGACCTTGGTTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
1 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
*
503035 CTTTGTGTGAAGTAAGAACTTCTAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAAT
66 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAAT
503097 CGAACAGACA
Statistics
Matches: 512, Mismatches: 50, Indels: 7
0.90 0.09 0.01
Matches are distributed among these distances:
145 106 0.21
146 276 0.54
147 130 0.25
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (146 bp):
TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTT
GCACTTTTTCTGCCAG
Found at i:503116 original size:8 final size:8
Alignment explanation
Indices: 503103--503149 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
503093 GAATCGAACA
503103 GACAGACG
1 GACAGACG
503111 GACAGACG
1 GACAGACG
*
503119 GACGGACG
1 GACAGACG
* *
503127 GACGGACA
1 GACAGACG
*
503135 GACGGACG
1 GACAGACG
503143 GACAGAC
1 GACAGAC
503150 AAGGTGATTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.34, C:0.26, G:0.40, T:0.00
Consensus pattern (8 bp):
GACAGACG
Found at i:503117 original size:12 final size:12
Alignment explanation
Indices: 503100--503150 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
503090 CACGAATCGA
* *
503100 ACAGACAGACGG
1 ACAGACGGACAG
*
503112 ACAGACGGACGG
1 ACAGACGGACAG
*
503124 ACGGACGGACAG
1 ACAGACGGACAG
*
503136 ACGGACGGACAG
1 ACAGACGGACAG
503148 ACA
1 ACA
503151 AGGTGATTCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.37, C:0.25, G:0.37, T:0.00
Consensus pattern (12 bp):
ACAGACGGACAG
Found at i:503150 original size:4 final size:4
Alignment explanation
Indices: 503107--503145 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
503097 CGAACAGACA
* *
503107 GACG GACA GACG GACG GACG GACG GACA GACG GACG GAC
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GAC
503146 AGACAAGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.31, C:0.26, G:0.44, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:503912 original size:15 final size:15
Alignment explanation
Indices: 503892--503921 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
503882 AAATACATGT
*
503892 AAAATTATGATTAAA
1 AAAATTATGAATAAA
503907 AAAATTATGAATAAA
1 AAAATTATGAATAAA
503922 CACTTTGGCA
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:0.00, G:0.07, T:0.30
Consensus pattern (15 bp):
AAAATTATGAATAAA
Found at i:506300 original size:1 final size:1
Alignment explanation
Indices: 506294--506321 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
506284 TCCTATATAA
506294 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
506322 GAATATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:516707 original size:16 final size:16
Alignment explanation
Indices: 516686--516728 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
516676 AATGCCGGGC
516686 GTCCGTCCGTCCGTGT
1 GTCCGTCCGTCCGTGT
*
516702 GTCCGTGCGTCCGTGT
1 GTCCGTCCGTCCGTGT
*
516718 TTCCGTCCGTC
1 GTCCGTCCGTC
516729 ACACTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.00, C:0.37, G:0.30, T:0.33
Consensus pattern (16 bp):
GTCCGTCCGTCCGTGT
Found at i:517571 original size:4 final size:4
Alignment explanation
Indices: 517524--517556 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
517514 TTCTTCAAAA
517524 GATT GATT GATT GATT GATT GATT GATT GATT G
1 GATT GATT GATT GATT GATT GATT GATT GATT G
517557 CAATCAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (4 bp):
GATT
Found at i:518169 original size:10 final size:10
Alignment explanation
Indices: 518154--518191 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
518144 GCGTCGATTT
518154 ACCCAAATGG
1 ACCCAAATGG
*
518164 ACCCAAATGA
1 ACCCAAATGG
518174 ACCCAAATGG
1 ACCCAAATGG
518184 ACCCAAAT
1 ACCCAAAT
518192 TCAAGCGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.45, C:0.32, G:0.13, T:0.11
Consensus pattern (10 bp):
ACCCAAATGG
Found at i:518179 original size:20 final size:20
Alignment explanation
Indices: 518154--518191 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
518144 GCGTCGATTT
518154 ACCCAAATGGACCCAAATGA
1 ACCCAAATGGACCCAAATGA
518174 ACCCAAATGGACCCAAAT
1 ACCCAAATGGACCCAAAT
518192 TCAAGCGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.32, G:0.13, T:0.11
Consensus pattern (20 bp):
ACCCAAATGGACCCAAATGA
Found at i:518655 original size:10 final size:10
Alignment explanation
Indices: 518640--518679 Score: 71
Period size: 10 Copynumber: 4.0 Consensus size: 10
518630 ACTTTAATCG
518640 CCATTTGGGT
1 CCATTTGGGT
518650 CCATTTGGGT
1 CCATTTGGGT
*
518660 TCATTTGGGT
1 CCATTTGGGT
518670 CCATTTGGGT
1 CCATTTGGGT
518680 AAATCGACGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.10, C:0.17, G:0.30, T:0.42
Consensus pattern (10 bp):
CCATTTGGGT
Found at i:525865 original size:17 final size:16
Alignment explanation
Indices: 525845--525879 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
525835 CTGGCGTGCG
525845 ACCAGTTCTCGCCGAGT
1 ACCAGTTCTCGCC-AGT
*
525862 ACCATTTCTCGCCAGT
1 ACCAGTTCTCGCCAGT
525878 AC
1 AC
525880 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:525963 original size:17 final size:16
Alignment explanation
Indices: 525936--525970 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
525926 ACGTCACAAT
525936 GTACTGGCGAGAAATG
1 GTACTGGCGAGAAATG
*
525952 GTACTCGGCGAGAACTG
1 GTACT-GGCGAGAAATG
525969 GT
1 GT
525971 CGCACGCCAG
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:0.26, C:0.17, G:0.37, T:0.20
Consensus pattern (16 bp):
GTACTGGCGAGAAATG
Found at i:526566 original size:2 final size:2
Alignment explanation
Indices: 526520--526553 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
526510 AGACAGATTC
*
526520 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
526554 GGGTAGATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:532988 original size:4 final size:4
Alignment explanation
Indices: 532979--533263 Score: 273
Period size: 4 Copynumber: 71.2 Consensus size: 4
532969 TTTAACAAGA
* *
532979 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ACTG GTTG ATTG ATTG
1 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG
* * ** * *
533027 ACTG ATTG ATTG ATTG ATTG ACTG ATCA ATTG ACTG ATTG ATTG ACTG
1 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG
** * * ** *
533075 ATCA ATTG ACTG ATTG ATTG ACTG ATCA ATTG ATTG ACTG ATTG ATTG
1 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG
* * ** * *
533123 ATTG ACTG ATTG ATTG ACTG ATCA ATTG ATTG ATTG ATTG ATTA ACTG
1 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG
* * **
533171 ATTG ACTG ATTG ATTG ACTG ATCA ATTG ATTG ATTG ATTG ATTG ATTG
1 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG
* * * * * * * *
533219 ATTG ATTG GTTG GTTG GTTG GTTG GTTG GTTG GTTG GTTG ATTG A
1 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG A
533264 CTTATGATGA
Statistics
Matches: 229, Mismatches: 52, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 229 1.00
ACGTcount: A:0.24, C:0.06, G:0.26, T:0.44
Consensus pattern (4 bp):
ATTG
Found at i:538720 original size:17 final size:17
Alignment explanation
Indices: 538698--538731 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
538688 GCTACATATA
538698 TATTAGTATAACAATGT
1 TATTAGTATAACAATGT
538715 TATTAGTATAACAATGT
1 TATTAGTATAACAATGT
538732 GCATGTACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (17 bp):
TATTAGTATAACAATGT
Found at i:540861 original size:4 final size:4
Alignment explanation
Indices: 540852--540917 Score: 69
Period size: 4 Copynumber: 16.5 Consensus size: 4
540842 TAAAGATAAG
* * * *
540852 GTCT GTCT GTCT GTTT GTCT GTCT GTCT GTCT GTCT GTTT GTCC ATCT
1 GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT
* * *
540900 GTTT GTTT GTCT ATCT GT
1 GTCT GTCT GTCT GTCT GT
540918 GTTTCTCTGT
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.03, C:0.20, G:0.23, T:0.55
Consensus pattern (4 bp):
GTCT
Found at i:540872 original size:12 final size:12
Alignment explanation
Indices: 540855--540911 Score: 78
Period size: 12 Copynumber: 4.8 Consensus size: 12
540845 AGATAAGGTC
540855 TGTCTGTCTGTT
1 TGTCTGTCTGTT
*
540867 TGTCTGTCTGTC
1 TGTCTGTCTGTT
540879 TGTCTGTCTGTT
1 TGTCTGTCTGTT
**
540891 TGTCCATCTGTT
1 TGTCTGTCTGTT
*
540903 TGTTTGTCT
1 TGTCTGTCT
540912 ATCTGTGTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.02, C:0.19, G:0.23, T:0.56
Consensus pattern (12 bp):
TGTCTGTCTGTT
Found at i:540873 original size:16 final size:16
Alignment explanation
Indices: 540852--540930 Score: 72
Period size: 16 Copynumber: 5.1 Consensus size: 16
540842 TAAAGATAAG
* *
540852 GTCTGTCTGTCTGTTT
1 GTCTGTTTGTCTGTCT
*
540868 GTCTGTCTGTCTGTCT
1 GTCTGTTTGTCTGTCT
**
540884 GTCTGTTTGTCCATCT
1 GTCTGTTTGTCTGTCT
* *
540900 GTTTGTTTGTCTATCT
1 GTCTGTTTGTCTGTCT
*
540916 G--TGTTTCTCTGTCT
1 GTCTGTTTGTCTGTCT
540930 G
1 G
540931 CCCTTCTGTC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 12 0.22
16 43 0.78
ACGTcount: A:0.03, C:0.20, G:0.23, T:0.54
Consensus pattern (16 bp):
GTCTGTTTGTCTGTCT
Found at i:541016 original size:4 final size:4
Alignment explanation
Indices: 540993--541035 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
540983 AGTTGGTACA
* * *
540993 TCTG TCTG TTTG TTTT TCTG TCTG TCTG TCTG TCTG TCTG TCT
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCT
541036 ACCAAGGCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.00, C:0.21, G:0.21, T:0.58
Consensus pattern (4 bp):
TCTG
Found at i:544468 original size:44 final size:44
Alignment explanation
Indices: 544407--544557 Score: 168
Period size: 44 Copynumber: 3.5 Consensus size: 44
544397 ACTTCTTTTA
* * *
544407 TAATCGTAGCAGACCTGAAATATAAATATTACAGGGCTGAAATG
1 TAATCATAGCAGGCCTGAGATATAAATATTACAGGGCTGAAATG
* ** * *
544451 TAATCATAGCTGGCCTGAG--AT--AGGTTACAGGACT-AAGATA
1 TAATCATAGCAGGCCTGAGATATAAATATTACAGGGCTGAA-ATG
* *
544491 TTATCATAGCAGGCCTGAGATATAAATATTACAGGGCTGAGATG
1 TAATCATAGCAGGCCTGAGATATAAATATTACAGGGCTGAAATG
544535 TAATCATAGCAGGCCTGAGATAT
1 TAATCATAGCAGGCCTGAGATAT
544558 GTTACAGGAT
Statistics
Matches: 85, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
39 2 0.02
40 29 0.34
42 4 0.05
44 49 0.58
45 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (44 bp):
TAATCATAGCAGGCCTGAGATATAAATATTACAGGGCTGAAATG
Found at i:544511 original size:22 final size:22
Alignment explanation
Indices: 544405--544557 Score: 88
Period size: 22 Copynumber: 7.1 Consensus size: 22
544395 ATACTTCTTT
* * *
544405 TATAATCGTAGCAGACCTGAAA
1 TATAATCATAGCAGGCCTGAGA
* *
544427 TATAAAT-ATTA-CAGGGCTGAAA
1 TAT-AATCA-TAGCAGGCCTGAGA
* *
544449 TGTAATCATAGCTGGCCTGAGA
1 TATAATCATAGCAGGCCTGAGA
** * *
544471 TA-GGT--TA-CAGGACTAAGA
1 TATAATCATAGCAGGCCTGAGA
*
544489 TATTATCATAGCAGGCCTGAGA
1 TATAATCATAGCAGGCCTGAGA
*
544511 TATAAAT-ATTA-CAGGGCTGAGA
1 TAT-AATCA-TAGCAGGCCTGAGA
*
544533 TGTAATCATAGCAGGCCTGAGA
1 TATAATCATAGCAGGCCTGAGA
544555 TAT
1 TAT
544558 GTTACAGGAT
Statistics
Matches: 97, Mismatches: 22, Indels: 24
0.68 0.15 0.17
Matches are distributed among these distances:
18 10 0.10
19 3 0.03
21 13 0.13
22 62 0.64
23 9 0.09
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (22 bp):
TATAATCATAGCAGGCCTGAGA
Found at i:544554 original size:84 final size:84
Alignment explanation
Indices: 544413--544566 Score: 263
Period size: 84 Copynumber: 1.8 Consensus size: 84
544403 TTTATAATCG
*
544413 TAGCAGACCTGAAATATAAATATTACAGGGCTGAAATGTAATCATAGCTGGCCTGAGATAGGTTA
1 TAGCAGACCTGAAATATAAATATTACAGGGCTGAAATGTAATCATAGCAGGCCTGAGATAGGTTA
544478 CAGGACTAAGATATTATCA
66 CAGGACTAAGATATTATCA
* * * *
544497 TAGCAGGCCTGAGATATAAATATTACAGGGCTGAGATGTAATCATAGCAGGCCTGAGATATGTTA
1 TAGCAGACCTGAAATATAAATATTACAGGGCTGAAATGTAATCATAGCAGGCCTGAGATAGGTTA
544562 CAGGA
66 CAGGA
544567 TTAATGTAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 65 1.00
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.25
Consensus pattern (84 bp):
TAGCAGACCTGAAATATAAATATTACAGGGCTGAAATGTAATCATAGCAGGCCTGAGATAGGTTA
CAGGACTAAGATATTATCA
Found at i:544829 original size:39 final size:39
Alignment explanation
Indices: 544769--544861 Score: 154
Period size: 39 Copynumber: 2.4 Consensus size: 39
544759 TATCAAACAT
544769 TGTAATTCATACAATACATAAATTACTGCACACCTC-TG
1 TGTAATTCATACAATACATAAATTACTGCACACCTCTTG
544807 ATGT-ATATCATACAATACATAAATTACTGCACACCTCTTG
1 -TGTAAT-TCATACAATACATAAATTACTGCACACCTCTTG
544847 TGTAATTCATACAAT
1 TGTAATTCATACAAT
544862 GTATAACCCA
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
38 2 0.04
39 45 0.88
40 4 0.08
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.33
Consensus pattern (39 bp):
TGTAATTCATACAATACATAAATTACTGCACACCTCTTG
Found at i:545911 original size:44 final size:44
Alignment explanation
Indices: 545861--546306 Score: 892
Period size: 44 Copynumber: 10.1 Consensus size: 44
545851 CCTCTACAGT
545861 TTCTATTGATAAGAACAAAAGTTCTTGGACTCTCTAGATCACCA
1 TTCTATTGATAAGAACAAAAGTTCTTGGACTCTCTAGATCACCA
545905 TTCTATTGATAAGAACAAAAGTTCTTGGACTCTCTAGATCACCA
1 TTCTATTGATAAGAACAAAAGTTCTTGGACTCTCTAGATCACCA
545949 TTCTATTGATAAGAACAAAAGTTCTTGGACTCTCTAGATCACCA
1 TTCTATTGATAAGAACAAAAGTTCTTGGACTCTCTAGATCACCA
545993 TTCTATTGATAAGAACAAAAGTTCTTGGACTCTCTAGATCACCA
1 TTCTATTGATAAGAACAAAAGTTCTTGGACTCTCTAGATCACCA
546037 TTCTATTGATAAGAACAAAAGTTCTTGGACTCTCTAGATCACCA
1 TTCTATTGATAAGAACAAAAGTTCTTGGACTCTCTAGATCACCA
546081 TTCTATTGATAAGAACAAAAGTTCTTGGACTCTCTAGATCACCA
1 TTCTATTGATAAGAACAAAAGTTCTTGGACTCTCTAGATCACCA
546125 TTCTATTGATAAGAACAAAAGTTCTTGGACTCTCTAGATCACCA
1 TTCTATTGATAAGAACAAAAGTTCTTGGACTCTCTAGATCACCA
546169 TTCTATTGATAAGAACAAAAGTTCTTGGACTCTCTAGATCACCA
1 TTCTATTGATAAGAACAAAAGTTCTTGGACTCTCTAGATCACCA
546213 TTCTATTGATAAGAACAAAAGTTCTTGGACTCTCTAGATCACCA
1 TTCTATTGATAAGAACAAAAGTTCTTGGACTCTCTAGATCACCA
546257 TTCTATTGATAAGAACAAAAGTTCTTGGACTCTCTAGATCACCA
1 TTCTATTGATAAGAACAAAAGTTCTTGGACTCTCTAGATCACCA
546301 TTCTAT
1 TTCTAT
546307 ACACCGTGTC
Statistics
Matches: 402, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 402 1.00
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.32
Consensus pattern (44 bp):
TTCTATTGATAAGAACAAAAGTTCTTGGACTCTCTAGATCACCA
Found at i:546868 original size:18 final size:18
Alignment explanation
Indices: 546832--546987 Score: 179
Period size: 18 Copynumber: 8.7 Consensus size: 18
546822 ATTCACATAC
*
546832 TAGACCATGTACA-TATA
1 TAGAACATGTACATTATA
* *
546849 TAGACCACGTACATTATA
1 TAGAACATGTACATTATA
**
546867 TAGAAGGTGTACATTATA
1 TAGAACATGTACATTATA
* *
546885 TAGACCATGTAAATTATA
1 TAGAACATGTACATTATA
**
546903 TAGAAGGTGTACATTATA
1 TAGAACATGTACATTATA
**
546921 TAGAAGGTGTACATTATA
1 TAGAACATGTACATTATA
*
546939 TAGACCATGTACATTATA
1 TAGAACATGTACATTATA
*
546957 TAGAACGTGTACATTATA
1 TAGAACATGTACATTATA
*
546975 TAGAACTTGTACA
1 TAGAACATGTACA
546988 GAGAACAGTA
Statistics
Matches: 119, Mismatches: 19, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
17 12 0.10
18 107 0.90
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (18 bp):
TAGAACATGTACATTATA
Found at i:546987 original size:54 final size:54
Alignment explanation
Indices: 546832--546979 Score: 244
Period size: 54 Copynumber: 2.8 Consensus size: 54
546822 ATTCACATAC
* **
546832 TAGACCATGTACA-TATATAGACCACGTACATTATATAGAAGGTGTACATTATA
1 TAGACCATGTACATTATATAGAACGTGTACATTATATAGAAGGTGTACATTATA
* *
546885 TAGACCATGTAAATTATATAGAAGGTGTACATTATATAGAAGGTGTACATTATA
1 TAGACCATGTACATTATATAGAACGTGTACATTATATAGAAGGTGTACATTATA
546939 TAGACCATGTACATTATATAGAACGTGTACATTATATAGAA
1 TAGACCATGTACATTATATAGAACGTGTACATTATATAGAA
546980 CTTGTACAGA
Statistics
Matches: 87, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
53 12 0.14
54 75 0.86
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (54 bp):
TAGACCATGTACATTATATAGAACGTGTACATTATATAGAAGGTGTACATTATA
Found at i:547284 original size:30 final size:30
Alignment explanation
Indices: 547248--547427 Score: 281
Period size: 30 Copynumber: 5.9 Consensus size: 30
547238 GTGCAGTGTT
* * *
547248 TGTATAAGTCATTCAAGTTATCGAGCACAG
1 TGTATAAGTCATTCAAGTCATCTAGTACAG
547278 TGTATAAGTCATTCAAGTCATCTAGTACAG
1 TGTATAAGTCATTCAAGTCATCTAGTACAG
547308 TGTATAAGTCATTCAAGTCATCTAGTACAG
1 TGTATAAGTCATTCAAGTCATCTAGTACAG
547338 TGTATAAGTCATTCAAGTCATCTAGTACAG
1 TGTATAAGTCATTCAAGTCATCTAGTACAG
*
547368 TGTATAAGTCGA-TCAAGTCACCTAGTACAG
1 TGTATAAGTC-ATTCAAGTCATCTAGTACAG
*
547398 TGTATTTAAGTCATTCAAGTCACCTAGTAC
1 TGTA--TAAGTCATTCAAGTCATCTAGTAC
547428 TGCATATATG
Statistics
Matches: 142, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
30 118 0.83
31 2 0.01
32 22 0.15
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (30 bp):
TGTATAAGTCATTCAAGTCATCTAGTACAG
Found at i:547449 original size:62 final size:61
Alignment explanation
Indices: 547250--547486 Score: 218
Period size: 60 Copynumber: 3.9 Consensus size: 61
547240 GCAGTGTTTG
* * * * **
547250 TATAAGTC-ATTCAAGTTATCGAGCACAGTGTA-TAAGTCATTCAAGTCATCTAGTACAGTG
1 TATAAGTCGA-TCAAGTCATCTAGTACAGTGTATTAAGTCATTCAAGTCACCTAGTACAGCA
* **
547310 TATAAGTC-ATTCAAGTCATCTAGTACAGTGTA-TAAGTCATTCAAGTCATCTAGTACAGTG
1 TATAAGTCGA-TCAAGTCATCTAGTACAGTGTATTAAGTCATTCAAGTCACCTAGTACAGCA
* *
547370 TATAAGTCGATCAAGTCACCTAGTACAGTGTATTTAAGTCATTCAAGTCACCTAGTACTGCA
1 TATAAGTCGATCAAGTCATCTAGTACAGTGTA-TTAAGTCATTCAAGTCACCTAGTACAGCA
* * * * *
547432 TATATGAT-G-TTAGAGTCATCTTGTACAGTGTATAAAGTTGA-TCAAGTCATCCTAG
1 TATAAG-TCGATCA-AGTCATCTAGTACAGTGTATTAAG-TCATTCAAGTCA-CCTAG
547487 CTTAGTGTGT
Statistics
Matches: 156, Mismatches: 14, Indels: 12
0.86 0.08 0.07
Matches are distributed among these distances:
60 86 0.55
61 15 0.10
62 54 0.35
63 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (61 bp):
TATAAGTCGATCAAGTCATCTAGTACAGTGTATTAAGTCATTCAAGTCACCTAGTACAGCA
Found at i:558548 original size:39 final size:39
Alignment explanation
Indices: 558201--558523 Score: 555
Period size: 39 Copynumber: 8.3 Consensus size: 39
558191 TATCAAACAT
558201 TGTAATTCATACAATACATAAATTACTGCACACCTCTGA
1 TGTAATTCATACAATACATAAATTACTGCACACCTCTGA
558240 TGT-ATATCATACAATACATAAATTACTGCACACCTCTGA
1 TGTAAT-TCATACAATACATAAATTACTGCACACCTCTGA
*
558279 TGTAATTCAT---ATACATAAATTACTGCGCACCTCTGA
1 TGTAATTCATACAATACATAAATTACTGCACACCTCTGA
558315 TGTAATTCATACAATACATAAATTACTGCACACCTCTGA
1 TGTAATTCATACAATACATAAATTACTGCACACCTCTGA
*
558354 TGTAATTCATATATTATACATAAATTACTGCACACCTCTGA
1 TGTAATTCATACA--ATACATAAATTACTGCACACCTCTGA
558395 TGTAATTCATACAATACATAAATTACTGCACACCTCTGA
1 TGTAATTCATACAATACATAAATTACTGCACACCTCTGA
*
558434 TATAATTCATACAATACATAAATTACTGCACACCTCTGA
1 TGTAATTCATACAATACATAAATTACTGCACACCTCTGA
*
558473 TGTAATTCATACAATGCATAAATTACTGCACACCTCTGA
1 TGTAATTCATACAATACATAAATTACTGCACACCTCTGA
558512 TGTAATTCATAC
1 TGTAATTCATAC
558524 CAGGTATAAC
Statistics
Matches: 270, Mismatches: 7, Indels: 14
0.93 0.02 0.05
Matches are distributed among these distances:
36 35 0.13
38 2 0.01
39 193 0.71
40 2 0.01
41 38 0.14
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.32
Consensus pattern (39 bp):
TGTAATTCATACAATACATAAATTACTGCACACCTCTGA
Found at i:560136 original size:16 final size:16
Alignment explanation
Indices: 560115--560190 Score: 80
Period size: 18 Copynumber: 4.5 Consensus size: 16
560105 GCCAGTATTC
*
560115 ACATTATAGAACATGT
1 ACATTATAGACCATGT
**
560131 ACATTATAGACCATAA
1 ACATTATAGACCATGT
560147 ACATTATATAGACCATGT
1 ACA-T-TATAGACCATGT
*
560165 ACATTATATAGACCATGA
1 ACA-T-TATAGACCATGT
560183 ACATTATA
1 ACATTATA
560191 TAGAACGTGT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
16 20 0.38
17 2 0.04
18 30 0.58
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (16 bp):
ACATTATAGACCATGT
Found at i:560158 original size:18 final size:18
Alignment explanation
Indices: 560135--560194 Score: 102
Period size: 18 Copynumber: 3.3 Consensus size: 18
560125 ACATGTACAT
*
560135 TATAGACCATAAACATTA
1 TATAGACCATGAACATTA
*
560153 TATAGACCATGTACATTA
1 TATAGACCATGAACATTA
560171 TATAGACCATGAACATTA
1 TATAGACCATGAACATTA
560189 TATAGA
1 TATAGA
560195 ACGTGTACAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (18 bp):
TATAGACCATGAACATTA
Found at i:560164 original size:34 final size:36
Alignment explanation
Indices: 560119--560203 Score: 129
Period size: 36 Copynumber: 2.4 Consensus size: 36
560109 GTATTCACAT
560119 TATAGAACATGTACA-T-TATAGACCATAAACATTA
1 TATAGAACATGTACATTATATAGACCATAAACATTA
* *
560153 TATAGACCATGTACATTATATAGACCATGAACATTA
1 TATAGAACATGTACATTATATAGACCATAAACATTA
*
560189 TATAGAACGTGTACA
1 TATAGAACATGTACA
560204 GAGAACAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 14 0.31
35 1 0.02
36 30 0.67
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (36 bp):
TATAGAACATGTACATTATATAGACCATAAACATTA
Found at i:560527 original size:64 final size:63
Alignment explanation
Indices: 560442--560587 Score: 177
Period size: 64 Copynumber: 2.3 Consensus size: 63
560432 TTGCATTGCT
* * * * *
560442 TTCAGGTTATCCTAGTGCAGTGTGTGTATAAGTCATTGAAGTCATCTAGTATAGTGTA-TAAGTC
1 TTCAAGTTA-CCTAGTACAGTGTAT-T-TAAGTCATTCAAGTCATCTAGTACAGTGTATTAAGTC
560506 A
63 A
* *
560507 TTCAAGTTACCTAGTACAGTGTATTTGAGTCATTCAAGTTATCTAGTACAGTGTATTTAAGTCA
1 TTCAAGTTACCTAGTACAGTGTATTTAAGTCATTCAAGTCATCTAGTACAGTGTA-TTAAGTCA
*
560571 TTCAAGTCACCTAGTAC
1 TTCAAGTTACCTAGTAC
560588 TGCATATATG
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
62 26 0.37
63 1 0.01
64 36 0.51
65 8 0.11
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (63 bp):
TTCAAGTTACCTAGTACAGTGTATTTAAGTCATTCAAGTCATCTAGTACAGTGTATTAAGTCA
Found at i:560543 original size:32 final size:32
Alignment explanation
Indices: 560470--560587 Score: 159
Period size: 32 Copynumber: 3.8 Consensus size: 32
560460 AGTGTGTGTA
* * *
560470 TAAGTCATTGAAGTCATCTAGTATAGTGTA--
1 TAAGTCATTCAAGTCACCTAGTACAGTGTATT
*
560500 TAAGTCATTCAAGTTACCTAGTACAGTGTATT
1 TAAGTCATTCAAGTCACCTAGTACAGTGTATT
* * *
560532 TGAGTCATTCAAGTTATCTAGTACAGTGTATT
1 TAAGTCATTCAAGTCACCTAGTACAGTGTATT
560564 TAAGTCATTCAAGTCACCTAGTAC
1 TAAGTCATTCAAGTCACCTAGTAC
560588 TGCATATATG
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
30 26 0.34
32 51 0.66
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.36
Consensus pattern (32 bp):
TAAGTCATTCAAGTCACCTAGTACAGTGTATT
Found at i:568115 original size:13 final size:13
Alignment explanation
Indices: 568097--568121 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
568087 TATTTCCGAA
568097 TTTTTTGTTTAAT
1 TTTTTTGTTTAAT
568110 TTTTTTGTTTAA
1 TTTTTTGTTTAA
568122 ATCAAAATGT
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:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (13 bp):
TTTTTTGTTTAAT
Found at i:569679 original size:20 final size:20
Alignment explanation
Indices: 569654--569694 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
569644 GCTCCTCCGA
569654 GTCCTAGACCGTGAATCTTG
1 GTCCTAGACCGTGAATCTTG
569674 GTCCTAGACCGTGAATCTTG
1 GTCCTAGACCGTGAATCTTG
569694 G
1 G
569695 CCCCGAGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (20 bp):
GTCCTAGACCGTGAATCTTG
Found at i:570512 original size:21 final size:21
Alignment explanation
Indices: 570488--570579 Score: 116
Period size: 21 Copynumber: 4.4 Consensus size: 21
570478 ATCTGCCACC
570488 ACTTGTCAGATAATTATGTCG
1 ACTTGTCAGATAATTATGTCG
570509 ACTTGTCAGATGAA-TATGTCG
1 ACTTGTCAGAT-AATTATGTCG
* *
570530 ACTTGTCAGATATTTATGTCA
1 ACTTGTCAGATAATTATGTCG
* *
570551 ACTTGTCAGAT-CTTAATGTTG
1 ACTTGTCAGATAATT-ATGTCG
570572 ACTTGTCA
1 ACTTGTCA
570580 AAAAAAAACC
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
20 3 0.05
21 58 0.92
22 2 0.03
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.39
Consensus pattern (21 bp):
ACTTGTCAGATAATTATGTCG
Found at i:570801 original size:21 final size:21
Alignment explanation
Indices: 570775--570933 Score: 151
Period size: 21 Copynumber: 7.7 Consensus size: 21
570765 TAAGTCGAGG
* *
570775 TGTCAGATAATGATGTTGACT
1 TGTCAGATAATTATGTCGACT
*
570796 TGTCAGAT-ATTATGTCGTCT
1 TGTCAGATAATTATGTCGACT
* *
570816 TGTCAAATAATTATGTCGAAT
1 TGTCAGATAATTATGTCGACT
*
570837 TGTCTGATAATTATGTCGACT
1 TGTCAGATAATTATGTCGACT
* * *
570858 TGTCAAATGATTATGTCCACT
1 TGTCAGATAATTATGTCGACT
*** **
570879 TAAAAGATGCTTATGTCGACT
1 TGTCAGATAATTATGTCGACT
** *
570900 TGTCAGATTCTTATGTCAACT
1 TGTCAGATAATTATGTCGACT
570921 TGTCAGA-AATTAT
1 TGTCAGATAATTAT
570934 TATTTCAACT
Statistics
Matches: 111, Mismatches: 26, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
20 20 0.18
21 91 0.82
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.40
Consensus pattern (21 bp):
TGTCAGATAATTATGTCGACT
Found at i:571057 original size:42 final size:43
Alignment explanation
Indices: 570988--571078 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 43
570978 GTGGATAAGT
*
570988 GACAAGTCGACTTAAAGAACTGACAAGTCAACATAATTATC-G
1 GACAAGTCGACATAAAGAACTGACAAGTCAACATAATTATCTG
* * * *
571030 GACAAGTCGACATCAAGATCTGTCAAGTCGACATAATTATCTG
1 GACAAGTCGACATAAAGAACTGACAAGTCAACATAATTATCTG
571073 G-CAAGT
1 GACAAGT
571079 GGTGGCATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 41 0.95
43 2 0.05
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (43 bp):
GACAAGTCGACATAAAGAACTGACAAGTCAACATAATTATCTG
Found at i:571071 original size:21 final size:21
Alignment explanation
Indices: 570987--571078 Score: 87
Period size: 21 Copynumber: 4.4 Consensus size: 21
570977 CGTGGATAAG
* ** *
570987 TGACAAGTCGACTTAAAGAAC
1 TGACAAGTCGACATAATTATC
*
571008 TGACAAGTCAACATAATTATC
1 TGACAAGTCGACATAATTATC
* *
571029 GGACAAGTCGACATCAA-GATC
1 TGACAAGTCGACAT-AATTATC
*
571050 TGTCAAGTCGACATAATTATC
1 TGACAAGTCGACATAATTATC
*
571071 TGGCAAGT
1 TGACAAGT
571079 GGTGGCATAT
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
20 2 0.04
21 53 0.93
22 2 0.04
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (21 bp):
TGACAAGTCGACATAATTATC
Found at i:577519 original size:53 final size:55
Alignment explanation
Indices: 577404--577680 Score: 447
Period size: 55 Copynumber: 5.1 Consensus size: 55
577394 CAATACTGCA
* *
577404 TGTGATTCTAGTAATCAAGCAGTGATATCTGAATATTCAAACAGCCTTTCAATAC
1 TGTGATTCTAGTAATCATGCAGCGATATCTGAATATTCAAACAGCCTTTCAATAC
*
577459 TGTGATTCAAGTAATCATGCAGCGATATCTG-A-ATTCAAACAGCCTTTCAATAC
1 TGTGATTCTAGTAATCATGCAGCGATATCTGAATATTCAAACAGCCTTTCAATAC
*
577512 TGCGATTCTAGTAATCATGCAGCGATATCTGAATATTCAAACAGCCTTTCAATAC
1 TGTGATTCTAGTAATCATGCAGCGATATCTGAATATTCAAACAGCCTTTCAATAC
* *
577567 TGTGATTCAAGTAATCATGCAGCGATATCTG-A-ATTCAAACAGCCTTTCAATTC
1 TGTGATTCTAGTAATCATGCAGCGATATCTGAATATTCAAACAGCCTTTCAATAC
*
577620 TGTGATTCTAGTAATCACGCAGCGATATCTGAATATTCAAACAGCCTTTCAATGA-
1 TGTGATTCTAGTAATCATGCAGCGATATCTGAATATTCAAACAGCCTTTCAAT-AC
577675 TGTGAT
1 TGTGAT
577681 ATCCTGATCT
Statistics
Matches: 206, Mismatches: 11, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
53 99 0.48
54 4 0.02
55 103 0.50
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Consensus pattern (55 bp):
TGTGATTCTAGTAATCATGCAGCGATATCTGAATATTCAAACAGCCTTTCAATAC
Found at i:577563 original size:108 final size:108
Alignment explanation
Indices: 577370--577680 Score: 489
Period size: 108 Copynumber: 2.8 Consensus size: 108
577360 GCAGCGATAT
** * * *
577370 GATATCTGAATTCAAGTATCCATTCAATACTGCATGTGATTCTAGTAATCAAGCAGTGATATCTG
1 GATATCTGAATTCAAACAGCCTTTCAATACTGC----GATTCTAGTAATCAAGCAGCGATATCTG
577435 AATATTCAAACAGCCTTTCAATACTGTGATTCAAGTAATCATGCAGC
62 AATATTCAAACAGCCTTTCAATACTGTGATTCAAGTAATCATGCAGC
*
577482 GATATCTGAATTCAAACAGCCTTTCAATACTGCGATTCTAGTAATCATGCAGCGATATCTGAATA
1 GATATCTGAATTCAAACAGCCTTTCAATACTGCGATTCTAGTAATCAAGCAGCGATATCTGAATA
577547 TTCAAACAGCCTTTCAATACTGTGATTCAAGTAATCATGCAGC
66 TTCAAACAGCCTTTCAATACTGTGATTCAAGTAATCATGCAGC
* * *
577590 GATATCTGAATTCAAACAGCCTTTCAATTCTGTGATTCTAGTAATCACGCAGCGATATCTGAATA
1 GATATCTGAATTCAAACAGCCTTTCAATACTGCGATTCTAGTAATCAAGCAGCGATATCTGAATA
577655 TTCAAACAGCCTTTCAATGA-TGTGAT
66 TTCAAACAGCCTTTCAAT-ACTGTGAT
577681 ATCCTGATCT
Statistics
Matches: 189, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
108 159 0.84
109 1 0.01
112 29 0.15
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (108 bp):
GATATCTGAATTCAAACAGCCTTTCAATACTGCGATTCTAGTAATCAAGCAGCGATATCTGAATA
TTCAAACAGCCTTTCAATACTGTGATTCAAGTAATCATGCAGC
Found at i:581350 original size:13 final size:13
Alignment explanation
Indices: 581332--581364 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
581322 TGATAAAAAG
581332 GAATTAAATGATA
1 GAATTAAATGATA
581345 GAATTAAATGATA
1 GAATTAAATGATA
581358 GAATTAA
1 GAATTAA
581365 TCATTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.15, T:0.30
Consensus pattern (13 bp):
GAATTAAATGATA
Found at i:584856 original size:20 final size:20
Alignment explanation
Indices: 584827--585044 Score: 296
Period size: 20 Copynumber: 11.0 Consensus size: 20
584817 CATAACACTG
584827 TATGTTAAGGTAAGTCACAC
1 TATGTTAAGGTAAGTCACAC
***
584847 TGCATTAAGGT--GTCACAC
1 TATGTTAAGGTAAGTCACAC
584865 TATGTTAAGGTAAGTCACAC
1 TATGTTAAGGTAAGTCACAC
584885 TATGTTAAGGTAAGTCACAC
1 TATGTTAAGGTAAGTCACAC
*
584905 TACGTTAAGGTAAGTCACAC
1 TATGTTAAGGTAAGTCACAC
* *
584925 TATGTAAAGGTGAGTCACAC
1 TATGTTAAGGTAAGTCACAC
** *
584945 TACATTAAAGTAAGTCACAC
1 TATGTTAAGGTAAGTCACAC
* *
584965 TTTGATAAGGTAAGTCACAC
1 TATGTTAAGGTAAGTCACAC
* *
584985 TATGTTAAGGTTAGTCACAT
1 TATGTTAAGGTAAGTCACAC
*
585005 TATGTTAAGGTAAGTCACAT
1 TATGTTAAGGTAAGTCACAC
585025 TATGTTAAGGTAAGTCACAC
1 TATGTTAAGGTAAGTCACAC
585045 CAATGTTTAA
Statistics
Matches: 170, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
18 15 0.09
20 155 0.91
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.30
Consensus pattern (20 bp):
TATGTTAAGGTAAGTCACAC
Found at i:586005 original size:16 final size:16
Alignment explanation
Indices: 585984--586016 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
585974 AGGAAAATTT
*
585984 ACTCTTGATTTCTCGA
1 ACTCTTGATCTCTCGA
586000 ACTCTTGATCTCTCGA
1 ACTCTTGATCTCTCGA
586016 A
1 A
586017 GCCTTTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.27, G:0.12, T:0.39
Consensus pattern (16 bp):
ACTCTTGATCTCTCGA
Found at i:588562 original size:17 final size:17
Alignment explanation
Indices: 588540--588604 Score: 58
Period size: 17 Copynumber: 3.5 Consensus size: 17
588530 GATAGTAGAC
588540 CTAGATATCAGACAGAT
1 CTAGATATCAGACAGAT
* *
588557 CTAGATATTGTAGGATAGTAGAT
1 CTAGATA-T-CA-GACA---GAT
588580 CTAGATATCAGACAGAT
1 CTAGATATCAGACAGAT
588597 CTAGATAT
1 CTAGATAT
588605 TGTAGGATAG
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
17 18 0.47
18 1 0.03
19 1 0.03
20 6 0.16
21 1 0.03
22 1 0.03
23 10 0.26
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.29
Consensus pattern (17 bp):
CTAGATATCAGACAGAT
Found at i:588579 original size:23 final size:23
Alignment explanation
Indices: 588553--588667 Score: 110
Period size: 23 Copynumber: 5.5 Consensus size: 23
588543 GATATCAGAC
588553 AGATCTAGATATTGTAGGATAGT
1 AGATCTAGATATTGTAGGATAGT
* *
588576 AGATCTAGATA-T-CA-G--A-C
1 AGATCTAGATATTGTAGGATAGT
588593 AGATCTAGATATTGTAGGATAGT
1 AGATCTAGATATTGTAGGATAGT
*
588616 AGATCTAGATA-T-CA-GA-A--
1 AGATCTAGATATTGTAGGATAGT
588633 AGATCTAGATATTGTAGGATAGT
1 AGATCTAGATATTGTAGGATAGT
*
588656 AAATCTAGATAT
1 AGATCTAGATAT
588668 CAGAAAGATC
Statistics
Matches: 73, Mismatches: 7, Indels: 24
0.70 0.07 0.23
Matches are distributed among these distances:
17 22 0.30
18 3 0.04
19 3 0.04
20 6 0.08
21 3 0.04
22 3 0.04
23 33 0.45
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (23 bp):
AGATCTAGATATTGTAGGATAGT
Found at i:588584 original size:40 final size:40
Alignment explanation
Indices: 588527--588862 Score: 399
Period size: 40 Copynumber: 8.0 Consensus size: 40
588517 ATTGAAGATC
* *
588527 TAGGATAGTAGACCTAGATATCAGACAGATCTAGATATTG
1 TAGGATAGTAGATCTAGATATCAGAAAGATCTAGATATTG
*
588567 TAGGATAGTAGATCTAGATATCAGACAGATCTAGATATTG
1 TAGGATAGTAGATCTAGATATCAGAAAGATCTAGATATTG
588607 TAGGATAGTAGATCTAGATATCAGAAAGATCTAGATATTG
1 TAGGATAGTAGATCTAGATATCAGAAAGATCTAGATATTG
* *
588647 TAGGATAGTAAATCTAGATATCAGAAAGATCTAAATATTG
1 TAGGATAGTAGATCTAGATATCAGAAAGATCTAGATATTG
588687 TAGATCTATGATAGTAGATCTAGATATCAGAAAGATCTAGATATTAAG
1 TAG------GATAGTAGATCTAGATATCAGAAAGATCTAGATATT--G
* * *
588735 ATATAGGATAGTAGAGT-GAGGTATCAGAAAGATGTAGATATTG
1 ---TAGGATAGTAGA-TCTAGATATCAGAAAGATCTAGATATTG
588778 TAGGATA-TAAGATCTAGATATCAGAAAGATCTAGATATTG
1 TAGGATAGT-AGATCTAGATATCAGAAAGATCTAGATATTG
588818 TAGATCTATGATAGTAGATCTAGATATCA-AACAGATCTAGATATT
1 TAG------GATAGTAGATCTAGATATCAGAA-AGATCTAGATATT
588863 AAGATATAGG
Statistics
Matches: 262, Mismatches: 12, Indels: 38
0.84 0.04 0.12
Matches are distributed among these distances:
39 2 0.01
40 155 0.59
43 1 0.00
45 33 0.13
46 66 0.25
47 1 0.00
48 1 0.00
51 3 0.01
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.30
Consensus pattern (40 bp):
TAGGATAGTAGATCTAGATATCAGAAAGATCTAGATATTG
Found at i:588636 original size:17 final size:17
Alignment explanation
Indices: 588576--588730 Score: 79
Period size: 17 Copynumber: 8.7 Consensus size: 17
588566 GTAGGATAGT
*
588576 AGATCTAGATATCAGAC
1 AGATCTAGATATCAGAA
*
588593 AGATCTAGATATTGTAGGATA
1 AGATCTAGATA-T-CA-GA-A
588614 GTAGATCTAGATATCAGAA
1 --AGATCTAGATATCAGAA
*
588633 AGATCTAGATATTGTAGGATA
1 AGATCTAGATA-T-CA-GA-A
*
588654 GTAAATCTAGATATCAGAA
1 --AGATCTAGATATCAGAA
* * *
588673 AGATCTAAATAT-TG-T
1 AGATCTAGATATCAGAA
*
588688 AGATCT--ATGAT-AG-T
1 AGATCTAGAT-ATCAGAA
588702 AGATCTAGATATCAGAA
1 AGATCTAGATATCAGAA
588719 AGATCTAGATAT
1 AGATCTAGATAT
588731 TAAGATATAG
Statistics
Matches: 109, Mismatches: 12, Indels: 34
0.70 0.08 0.22
Matches are distributed among these distances:
13 2 0.02
14 10 0.09
15 8 0.07
16 5 0.05
17 44 0.40
18 2 0.02
19 4 0.04
20 8 0.07
21 3 0.03
22 2 0.02
23 21 0.19
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.30
Consensus pattern (17 bp):
AGATCTAGATATCAGAA
Found at i:588779 original size:131 final size:131
Alignment explanation
Indices: 588527--588876 Score: 503
Period size: 131 Copynumber: 2.8 Consensus size: 131
588517 ATTGAAGATC
* * *
588527 TAGGATAGTAGACCTAGATATCAGACAGATCTAGATATTGTAG------GATAGTAGATCTAGAT
1 TAGGATAGTAAATCTAGATATCAGAAAGATCTAGATATTGTAGATCTATGATAGTAGATCTAGAT
* *
588586 ATCAGACAGATCTAGATATT--G---TAGGATAGTAGATCTAGATATCAGAAAGATCTAGATATT
66 ATCAGAAAGATCTAGATATTAAGATATAGGATAGTAGATCGAGATATCAGAAAGATCTAGATATT
588646 G
131 G
*
588647 TAGGATAGTAAATCTAGATATCAGAAAGATCTAAATATTGTAGATCTATGATAGTAGATCTAGAT
1 TAGGATAGTAAATCTAGATATCAGAAAGATCTAGATATTGTAGATCTATGATAGTAGATCTAGAT
* *
588712 ATCAGAAAGATCTAGATATTAAGATATAGGATAGTAGAGT-GAGGTATCAGAAAGATGTAGATAT
66 ATCAGAAAGATCTAGATATTAAGATATAGGATAGTAGA-TCGAGATATCAGAAAGATCTAGATAT
588776 TG
130 TG
588778 TAGGATA-TAAGATCTAGATATCAGAAAGATCTAGATATTGTAGATCTATGATAGTAGATCTAGA
1 TAGGATAGTAA-ATCTAGATATCAGAAAGATCTAGATATTGTAGATCTATGATAGTAGATCTAGA
588842 TATCA-AACAGATCTAGATATTAAGATATAGGATAG
65 TATCAGAA-AGATCTAGATATTAAGATATAGGATAG
588877 CAAAGCTGTA
Statistics
Matches: 207, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
120 39 0.19
126 35 0.17
128 1 0.00
130 5 0.02
131 126 0.61
132 1 0.00
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.30
Consensus pattern (131 bp):
TAGGATAGTAAATCTAGATATCAGAAAGATCTAGATATTGTAGATCTATGATAGTAGATCTAGAT
ATCAGAAAGATCTAGATATTAAGATATAGGATAGTAGATCGAGATATCAGAAAGATCTAGATATT
G
Found at i:588836 original size:14 final size:14
Alignment explanation
Indices: 588804--588844 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
588794 GATATCAGAA
588804 AGATCTAGATATTGT
1 AGATCTAGATA-TGT
588819 AGATCTATGATA-GT
1 AGATCTA-GATATGT
588833 AGATCTAGATAT
1 AGATCTAGATAT
588845 CAAACAGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.17
14 9 0.38
15 7 0.29
16 4 0.17
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.37
Consensus pattern (14 bp):
AGATCTAGATATGT
Found at i:588933 original size:16 final size:16
Alignment explanation
Indices: 588914--589078 Score: 127
Period size: 16 Copynumber: 10.4 Consensus size: 16
588904 AATAACTTTC
588914 CTGTACAATAGTCTAG
1 CTGTACAATAGTCTAG
* ** *
588930 CTGTA-AAAAACCTAC
1 CTGTACAATAGTCTAG
* *
588945 CTGTACTATAGTCTAA
1 CTGTACAATAGTCTAG
588961 CTGTACAATTA-TCTAG
1 CTGTACAA-TAGTCTAG
* * **
588977 CTTTACAATAGCCTTC
1 CTGTACAATAGTCTAG
* * *
588993 CTGTATAATATTATAG
1 CTGTACAATAGTCTAG
* *
589009 CTGTACAAGAGTCAAG
1 CTGTACAATAGTCTAG
* * *
589025 GTGTACACTAGCCTAG
1 CTGTACAATAGTCTAG
*
589041 ATGTACAATAGTCTAG
1 CTGTACAATAGTCTAG
*
589057 ATGTACAATAGTCTAG
1 CTGTACAATAGTCTAG
589073 CTGTAC
1 CTGTAC
589079 TCATAGTATT
Statistics
Matches: 110, Mismatches: 36, Indels: 6
0.72 0.24 0.04
Matches are distributed among these distances:
15 13 0.12
16 95 0.86
17 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (16 bp):
CTGTACAATAGTCTAG
Found at i:591479 original size:41 final size:42
Alignment explanation
Indices: 591328--591577 Score: 353
Period size: 42 Copynumber: 6.0 Consensus size: 42
591318 GTAAGAGAGG
* **
591328 GAGGATGGTAAGTCAGAGTAAAGAAAGGTAACCTAGTGGTAA
1 GAGGAGGGTAAGTCAGAGTGGAGAAAGGTAACCTAGTGGTAA
** *
591370 GAGGAGGGTAAGTCAGAGTAAAGAAAGGTAACCTAGTGATAA
1 GAGGAGGGTAAGTCAGAGTGGAGAAAGGTAACCTAGTGGTAA
* *
591412 GTGGAGGGTAAGTCAGAGTGGAGAAAGGTAACTTAGTGGTAA
1 GAGGAGGGTAAGTCAGAGTGGAGAAAGGTAACCTAGTGGTAA
591454 GAGGAGGGT-AGTCAGAGTGGAGAAAGGTAACCTAGTGGTAA
1 GAGGAGGGTAAGTCAGAGTGGAGAAAGGTAACCTAGTGGTAA
591495 GAGGAGGGT-AGTCAGAGTGGAGAAAGGTAACCTAGTGGTAA
1 GAGGAGGGTAAGTCAGAGTGGAGAAAGGTAACCTAGTGGTAA
** * * *
591536 GAGGTA-AATAAGTCAGTGTGGAGAAAGGCAACCCAGTGGTAA
1 GAGG-AGGGTAAGTCAGAGTGGAGAAAGGTAACCTAGTGGTAA
591578 ATGGTAAATA
Statistics
Matches: 192, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
41 77 0.40
42 115 0.60
ACGTcount: A:0.37, C:0.08, G:0.37, T:0.18
Consensus pattern (42 bp):
GAGGAGGGTAAGTCAGAGTGGAGAAAGGTAACCTAGTGGTAA
Found at i:591550 original size:83 final size:84
Alignment explanation
Indices: 591328--591577 Score: 353
Period size: 83 Copynumber: 3.0 Consensus size: 84
591318 GTAAGAGAGG
* ** **
591328 GAGGATGGTAAGTCAGAGTAAAGAAAGGTAACCTAGTGGTAAGAGGAGGGTAAGTCAGAGTAAAG
1 GAGGAGGGTAAGTCAGAGTGGAGAAAGGTAACCTAGTGGTAAGAGGAGGGTAAGTCAGAGTGGAG
*
591393 AAAGGTAACCTAGTGATAA
66 AAAGGTAACCTAGTGGTAA
* *
591412 GTGGAGGGTAAGTCAGAGTGGAGAAAGGTAACTTAGTGGTAAGAGGAGGGT-AGTCAGAGTGGAG
1 GAGGAGGGTAAGTCAGAGTGGAGAAAGGTAACCTAGTGGTAAGAGGAGGGTAAGTCAGAGTGGAG
591476 AAAGGTAACCTAGTGGTAA
66 AAAGGTAACCTAGTGGTAA
** *
591495 GAGGAGGGT-AGTCAGAGTGGAGAAAGGTAACCTAGTGGTAAGAGGTA-AATAAGTCAGTGTGGA
1 GAGGAGGGTAAGTCAGAGTGGAGAAAGGTAACCTAGTGGTAAGAGG-AGGGTAAGTCAGAGTGGA
* *
591558 GAAAGGCAACCCAGTGGTAA
65 GAAAGGTAACCTAGTGGTAA
591578 ATGGTAAATA
Statistics
Matches: 149, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
82 36 0.24
83 67 0.45
84 46 0.31
ACGTcount: A:0.37, C:0.08, G:0.37, T:0.18
Consensus pattern (84 bp):
GAGGAGGGTAAGTCAGAGTGGAGAAAGGTAACCTAGTGGTAAGAGGAGGGTAAGTCAGAGTGGAG
AAAGGTAACCTAGTGGTAA
Found at i:591584 original size:42 final size:42
Alignment explanation
Indices: 591336--591604 Score: 194
Period size: 42 Copynumber: 6.5 Consensus size: 42
591326 GGGAGGATGG
** * * **
591336 TAAGTCAGAGTAAAGAAAGGTAACCTAGTGGTAAGAGG-AGGG
1 TAAGTCAGAGTGGAGAAAGGCAACCCAGTGGTAAGAGGTA-AA
** * * * * **
591378 TAAGTCAGAGTAAAGAAAGGTAACCTAGTGATAAGTGG-AGGG
1 TAAGTCAGAGTGGAGAAAGGCAACCCAGTGGTAAGAGGTA-AA
* ** **
591420 TAAGTCAGAGTGGAGAAAGGTAACTTAGTGGTAAGAGG-AGGG
1 TAAGTCAGAGTGGAGAAAGGCAACCCAGTGGTAAGAGGTA-AA
* * **
591462 T-AGTCAGAGTGGAGAAAGGTAACCTAGTGGTAAGAGG-AGGG
1 TAAGTCAGAGTGGAGAAAGGCAACCCAGTGGTAAGAGGTA-AA
* *
591503 T-AGTCAGAGTGGAGAAAGGTAACCTAGTGGTAAGAGGTAAA
1 TAAGTCAGAGTGGAGAAAGGCAACCCAGTGGTAAGAGGTAAA
*
591544 TAAGTCAGTGTGGAGAAAGGCAACCCAGTGGTAA-ATGGTAAA
1 TAAGTCAGAGTGGAGAAAGGCAACCCAGTGGTAAGA-GGTAAA
591586 TAAGTCAGAG-GGAAGAAAG
1 TAAGTCAGAGTGG-AGAAAG
591605 ACGAAAATAC
Statistics
Matches: 209, Mismatches: 14, Indels: 8
0.90 0.06 0.03
Matches are distributed among these distances:
41 80 0.38
42 129 0.62
ACGTcount: A:0.39, C:0.07, G:0.36, T:0.18
Consensus pattern (42 bp):
TAAGTCAGAGTGGAGAAAGGCAACCCAGTGGTAAGAGGTAAA
Found at i:592703 original size:19 final size:19
Alignment explanation
Indices: 592679--592721 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
592669 CACACAGATA
592679 TTTGTTTGTTTTGTGTTCC
1 TTTGTTTGTTTTGTGTTCC
592698 TTTGTTTGTTTTGTGTTCC
1 TTTGTTTGTTTTGTGTTCC
592717 TTTGT
1 TTTGT
592722 GTTCAGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.00, C:0.09, G:0.21, T:0.70
Consensus pattern (19 bp):
TTTGTTTGTTTTGTGTTCC
Found at i:592720 original size:10 final size:10
Alignment explanation
Indices: 592688--592725 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
592678 ATTTGTTTGT
592688 TTTGTGTTCC
1 TTTGTGTTCC
**
592698 TTTGT-TTGT
1 TTTGTGTTCC
592707 TTTGTGTTCC
1 TTTGTGTTCC
592717 TTTGTGTTC
1 TTTGTGTTC
592726 AGTTTAATCC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
9 7 0.30
10 16 0.70
ACGTcount: A:0.00, C:0.13, G:0.21, T:0.66
Consensus pattern (10 bp):
TTTGTGTTCC
Found at i:594920 original size:138 final size:138
Alignment explanation
Indices: 594657--594958 Score: 410
Period size: 138 Copynumber: 2.2 Consensus size: 138
594647 GTGGGGTTGT
* * ** * * **
594657 CTGTGTATTTATAGGTAATGCTGTTGTCTGTGTTTTTACAGGTAACACTGTTGTCTGTGTGTTTA
1 CTGTGTGTTTACAGGTAACACTGTTGTCTGTGTATTAACAGGTAACACTGTTGTCTGTACGTTTA
* * *
594722 CAGGTAACATTGATGTGTGTGTGTTTACAGGTAACACTGCTGTCTGTGTGTTTAAAAGGTAACAC
66 CAGGTAACACTGATGTCTGTGTGTTTACAGGTAACACTGCTGACTGTGTGTTTAAAAGGTAACAC
* *
594787 TGTTGATA
131 TATTGACA
* *
594795 CTGTGTGTTTACAGGTAACACTTTTGTCTGTGTATTAACAGGTAACATTGTTGTCTGTACGTTTA
1 CTGTGTGTTTACAGGTAACACTGTTGTCTGTGTATTAACAGGTAACACTGTTGTCTGTACGTTTA
* * *
594860 -AGGTAACACTGCTGTCTGTGTGTTTACAGGTAACACTGTTGACACTGTGTGTTT-ACAGGTAAC
66 CAGGTAACACTGATGTCTGTGTGTTTACAGGTAACACTGCTG--ACTGTGTGTTTAAAAGGTAAC
594923 ACTATTGACA
129 ACTATTGACA
594933 CTGTGTGTTTACAGGTAACACTGTTG
1 CTGTGTGTTTACAGGTAACACTGTTG
594959 ACACTGTTTG
Statistics
Matches: 143, Mismatches: 19, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
137 37 0.26
138 96 0.67
139 10 0.07
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.39
Consensus pattern (138 bp):
CTGTGTGTTTACAGGTAACACTGTTGTCTGTGTATTAACAGGTAACACTGTTGTCTGTACGTTTA
CAGGTAACACTGATGTCTGTGTGTTTACAGGTAACACTGCTGACTGTGTGTTTAAAAGGTAACAC
TATTGACA
Found at i:594924 original size:29 final size:27
Alignment explanation
Indices: 594652--594984 Score: 380
Period size: 27 Copynumber: 12.0 Consensus size: 27
594642 TCAGTGTGGG
* * **
594652 GTTGTCTGTGTATTTATAGGTAATGCT
1 GTTGTCTGTGTGTTTACAGGTAACACT
*
594679 GTTGTCTGTGTTTTTACAGGTAACACT
1 GTTGTCTGTGTGTTTACAGGTAACACT
*
594706 GTTGTCTGTGTGTTTACAGGTAACATT
1 GTTGTCTGTGTGTTTACAGGTAACACT
* *
594733 GATGTGTGTGTGTTTACAGGTAACACT
1 GTTGTCTGTGTGTTTACAGGTAACACT
* *
594760 GCTGTCTGTGTGTTTAAAAGGTAACACT
1 GTTGTCTGTGTGTTT-ACAGGTAACACT
594788 GTTGATACTGTGTGTTTACAGGTAACACT
1 GTTG-T-CTGTGTGTTTACAGGTAACACT
* * * *
594817 TTTGTCTGTGTATTAACAGGTAACATT
1 GTTGTCTGTGTGTTTACAGGTAACACT
**
594844 GTTGTCTGTACGTTTA-AGGTAACACT
1 GTTGTCTGTGTGTTTACAGGTAACACT
*
594870 GCTGTCTGTGTGTTTACAGGTAACACT
1 GTTGTCTGTGTGTTTACAGGTAACACT
*
594897 GTTGACACTGTGTGTTTACAGGTAACACT
1 GTTG--TCTGTGTGTTTACAGGTAACACT
* *
594926 ATTGACACTGTGTGTTTACAGGTAACACT
1 GTTG--TCTGTGTGTTTACAGGTAACACT
* *
594955 GTTGACACTGTTTGTTTACAGGTAACACT
1 GTTG--TCTGTGTGTTTACAGGTAACACT
594984 G
1 G
594985 AAAAAAGTTG
Statistics
Matches: 268, Mismatches: 32, Indels: 10
0.86 0.10 0.03
Matches are distributed among these distances:
26 22 0.08
27 128 0.48
28 15 0.06
29 93 0.35
30 10 0.04
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.39
Consensus pattern (27 bp):
GTTGTCTGTGTGTTTACAGGTAACACT
Found at i:597416 original size:50 final size:50
Alignment explanation
Indices: 597341--597440 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
597331 ACTGTACAAC
597341 TGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTCAAGAAT
1 TGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTCAAGAAT
*
597391 TGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTCAGGAAT
1 TGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTCAAGAAT
597441 ACCAGGTAAG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (50 bp):
TGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTCAAGAAT
Found at i:597432 original size:37 final size:37
Alignment explanation
Indices: 597391--597470 Score: 142
Period size: 37 Copynumber: 2.2 Consensus size: 37
597381 ACTCAAGAAT
*
597391 TGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAAC
1 TGGACTCAGGAATACCAGGTAAGGGAAGCTCAATAAC
*
597428 TGGACTCAGGAATACCAGGTAAGGGAAGCTCAATGAC
1 TGGACTCAGGAATACCAGGTAAGGGAAGCTCAATAAC
597465 TGGACT
1 TGGACT
597471 AAAAAACTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.34, C:0.19, G:0.30, T:0.17
Consensus pattern (37 bp):
TGGACTCAGGAATACCAGGTAAGGGAAGCTCAATAAC
Found at i:597484 original size:87 final size:87
Alignment explanation
Indices: 597338--597520 Score: 321
Period size: 87 Copynumber: 2.1 Consensus size: 87
597328 ACCACTGTAC
* * * *
597338 AACTGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTCAAGAATTGGACTCAGGAA
1 AACTGGACTCAGGAATACCAGGTAAGGGAAGCTCAATAACTGGACTAAAAAACTGGACTCAGGAA
597403 TACCAGGTGAGGGAAGCTCAAT
66 TACCAGGTGAGGGAAGCTCAAT
*
597425 AACTGGACTCAGGAATACCAGGTAAGGGAAGCTCAATGACTGGACTAAAAAACTGGACTCAGGAA
1 AACTGGACTCAGGAATACCAGGTAAGGGAAGCTCAATAACTGGACTAAAAAACTGGACTCAGGAA
597490 TACCAGGTGAGGGAAGCTCAAT
66 TACCAGGTGAGGGAAGCTCAAT
597512 AACTGGACT
1 AACTGGACT
597521 AAAAAACTGG
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 91 1.00
ACGTcount: A:0.37, C:0.19, G:0.28, T:0.17
Consensus pattern (87 bp):
AACTGGACTCAGGAATACCAGGTAAGGGAAGCTCAATAACTGGACTAAAAAACTGGACTCAGGAA
TACCAGGTGAGGGAAGCTCAAT
Found at i:597582 original size:50 final size:50
Alignment explanation
Indices: 597425--597570 Score: 274
Period size: 50 Copynumber: 2.9 Consensus size: 50
597415 GAAGCTCAAT
* *
597425 AACTGGACTCAGGAATACCAGGTAAGGGAAGCTCAATGACTGGACTAAAA
1 AACTGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTAAAA
597475 AACTGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTAAAA
1 AACTGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTAAAA
597525 AACTGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACT
1 AACTGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACT
597571 CAAGAATTGG
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 94 1.00
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.16
Consensus pattern (50 bp):
AACTGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTAAAA
Found at i:598668 original size:20 final size:21
Alignment explanation
Indices: 598637--598692 Score: 89
Period size: 20 Copynumber: 2.8 Consensus size: 21
598627 GCTCACACAC
598637 ACACACATGTATATCATATAT
1 ACACACATGTATATCATATAT
*
598658 ACA-ATATGTATAT-ATATAT
1 ACACACATGTATATCATATAT
598677 ACACACATGTATATCA
1 ACACACATGTATATCA
598693 ATGTTTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 9 0.29
20 18 0.58
21 4 0.13
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (21 bp):
ACACACATGTATATCATATAT
Found at i:600626 original size:15 final size:14
Alignment explanation
Indices: 600607--600640 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
600597 TTGATATCTC
*
600607 AAATTTTTTTATCA
1 AAATTTGTTTATCA
600621 ATAATTTGTTTATCA
1 A-AATTTGTTTATCA
600636 AAATT
1 AAATT
600641 CGAATTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (14 bp):
AAATTTGTTTATCA
Found at i:602751 original size:29 final size:29
Alignment explanation
Indices: 602702--602905 Score: 214
Period size: 29 Copynumber: 6.8 Consensus size: 29
602692 TATGTGATGG
*
602702 ACATAAAACCCTAT-TTAAAGGTAAGCCAC
1 ACATAACACCCTATGTT-AAGGTAAGCCAC
* ** *
602731 ACATAAAACATTATGTTAAGGTAAGTCAC
1 ACATAACACCCTATGTTAAGGTAAGCCAC
602760 ACATAACACCCTATGTTACACGTAAGATAAGCCAC
1 ACATAACACCCTATGTTA-A-G---G-TAAGCCAC
*
602795 ACATAACACCCTATGTTAAGGTAAGTCAC
1 ACATAACACCCTATGTTAAGGTAAGCCAC
602824 ACATAACACCCTATGTTAAGGTAA-CTCAC
1 ACATAACACCCTATGTTAAGGTAAGC-CAC
* * *
602853 ACATAACACCCTATCTTAAGGTAGGTCAC
1 ACATAACACCCTATGTTAAGGTAAGCCAC
* * *
602882 ACATAACAGCTTTTGTTAAGGTAA
1 ACATAACACCCTATGTTAAGGTAA
602906 ATCCCACCAT
Statistics
Matches: 149, Mismatches: 17, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
29 116 0.78
30 4 0.03
31 1 0.01
33 1 0.01
34 2 0.01
35 25 0.17
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.25
Consensus pattern (29 bp):
ACATAACACCCTATGTTAAGGTAAGCCAC
Found at i:602924 original size:20 final size:20
Alignment explanation
Indices: 602895--602942 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
602885 TAACAGCTTT
*
602895 TGTTAAGGTAAATCCCACCA
1 TGTTAAGGTAAATCACACCA
* *
602915 TGTTATGGTAAGTCACACCA
1 TGTTAAGGTAAATCACACCA
602935 TGTTAAGG
1 TGTTAAGG
602943 AGTGTTCTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (20 bp):
TGTTAAGGTAAATCACACCA
Found at i:604063 original size:96 final size:96
Alignment explanation
Indices: 603963--604142 Score: 247
Period size: 96 Copynumber: 1.9 Consensus size: 96
603953 TGTAGGATAG
*
603963 TAGATCTAGATATT-AAGATATAGGATAGTAGATCTAAAT-TTACAGAAAGATCTAGACATTGTA
1 TAGATCTAGATATTGAAGATATAGGATAGAAGATCTAAATATT--AGAAAGATCTAGACATTGTA
*
604026 GATCTAGGATAGTAGATCTAGATAATTATCAGA
64 GATATAGGATAGTAGATCTAGATAATTATCAGA
* * * * * *
604059 TAGATCTAGATATTGTAGATCTATGATAGAAGATTTAGATATTAGAAAGATCTAGATATTGTAGA
1 TAGATCTAGATATTGAAGATATAGGATAGAAGATCTAAATATTAGAAAGATCTAGACATTGTAGA
*
604124 TATAGGCTAGTAGATCTAG
66 TATAGGATAGTAGATCTAG
604143 GCATTAGAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
96 52 0.71
97 19 0.26
98 2 0.03
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (96 bp):
TAGATCTAGATATTGAAGATATAGGATAGAAGATCTAAATATTAGAAAGATCTAGACATTGTAGA
TATAGGATAGTAGATCTAGATAATTATCAGA
Found at i:604183 original size:46 final size:46
Alignment explanation
Indices: 603964--604175 Score: 239
Period size: 46 Copynumber: 4.5 Consensus size: 46
603954 GTAGGATAGT
* * *
603964 AGATCTAGATATT-AAGATATAGGATAGTAGATCTA-AATTTACAGAA
1 AGATCTAGATATTGTAGATCTAGGATAGTAGATCTAGAAATT--AGAA
* *
604010 AGATCTAGACATTGTAGATCTAGGATAGTAGATCTAGATAATTATCAGAT
1 AGATCTAGATATTGTAGATCTAGGATAGTAGATCTAGA-AA-T-T-AGAA
* * * *
604060 AGATCTAGATATTGTAGATCTATGATAGAAGATTTAGATATTAGAA
1 AGATCTAGATATTGTAGATCTAGGATAGTAGATCTAGAAATTAGAA
* * **
604106 AGATCTAGATATTGTAGATATAGGCTAGTAGATCTAGGCATTAGAA
1 AGATCTAGATATTGTAGATCTAGGATAGTAGATCTAGAAATTAGAA
604152 AGATCTAGATATTGTAGATCTAGG
1 AGATCTAGATATTGTAGATCTAGG
604176 TTGGTAGAGC
Statistics
Matches: 142, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
46 77 0.54
47 21 0.15
48 2 0.01
49 2 0.01
50 39 0.27
51 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.32
Consensus pattern (46 bp):
AGATCTAGATATTGTAGATCTAGGATAGTAGATCTAGAAATTAGAA
Found at i:606573 original size:39 final size:39
Alignment explanation
Indices: 606486--608206 Score: 2008
Period size: 39 Copynumber: 43.8 Consensus size: 39
606476 GAGGAGAGAT
* *
606486 AGGTAGGTCAGTTGGG-GGTGGGGTAAGTCAGTGGGGGGTG
1 AGGTAAGTCAG-TGGGAGGTGAGGTAAGTCAGT-GGGGGTG
606526 AGGTAAGTCA-TAGGGAGGTGAGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGT-GGGAGGTGAGGTAAGTCAGTGGGGGTG
* *
606565 AGGTAAGTCAGTGGG-GATGAGTTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTG
* * *
606603 AGGTAAGTCAGAGGGAGGTGAGGTAAGTCGGGGGGGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTG
*
606642 AGGTAGGTCAGTGGGAGGTGAGGTAAGTCA-TAGGGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGT-GGG-GGTG
* *
606682 AGGTAAGTCAGTGGG-GATGAGGTAAGTCAGTGGGGTTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTG
606720 AGGTAAGTCA-TAGGGAGGTGAGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGT-GGGAGGTGAGGTAAGTCAGTGGGGGTG
*
606759 AGGTAAGTCGGTGGG-GGTGAGGTAAGTCA-TAGGGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGT-GGG-GGTG
* *
606798 AGGTAAGTCAGTGGG-GGTGAGGTAAGTCAGCGGGGGGG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTG
* * *
606836 AGGGAAGTCA-TAGGGAGGGGAGGTAAGTCAGTGGGGGGG
1 AGGTAAGTCAGT-GGGAGGTGAGGTAAGTCAGTGGGGGTG
* * * *
606875 AGGGAAGTCAGTGGG-GGGGAGGGAAGTCA-TAGGGGGGGG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGT--GGGGGTG
* * * *
606914 AGGTAAGTCAGTGGG-GGGGGGGGAAGTCAGTGGGGGGG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTG
* * * *
606952 AGGGAAGTCA-TAGGGGGGGGAGGTAAGTCAGTGGGGGGG
1 AGGTAAGTCAGT-GGGAGGTGAGGTAAGTCAGTGGGGGTG
* * * *
606991 GGGGAAGTCAGTGGG-GGGGAGGGAAGTCA-TAGGGAGG-G
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGT-GGG-GGTG
* *
607029 AGGGAAGTCA-TAGGGAGGGGAGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGT-GGGAGGTGAGGTAAGTCAGTGGGGGTG
*
607068 AGGTAAGTCA-TAGGGAGGTGAGGTAAGTCAGTCGGAGGTG
1 AGGTAAGTCAGT-GGGAGGTGAGGTAAGTCAGT-GGGGGTG
* * *
607108 AGATAAGTCAGTGTGAGGTGAGGTAAGTAAGTGGGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGG-GGTG
* *
607148 AGATAAGTCAGTGTGAGGTGAGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTG
*
607187 AGGTAAGTCAGTGTGAGGTGAGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTG
*
607226 AGGTAAGTCAGTGTGAGGTGAGGTAAGTCAGTGGGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGG-GGTG
* * * * *
607266 GGGTAAGTCAGTGTGAGGTGAGATATGTCAGTGTGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTG-GGGGTG
* *
607306 AGGTAAGTCAGTGTGAGGTGAGGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTG-GGGGTG
*
607346 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGAAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGG-GGGTG
* *
607386 AGATAAGTCAGTGTGAGGTGAGGTAAGTCAGTGGGGGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGT-GGGGGTG
* * * * * *
607426 AGATAAGTCAGTGTGTGGTGAGGTAGGTTA--GGGGGTA
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTG
* *
607463 AGGTAAGTCAGTGTGAGGTGAGGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTG-GGGGTG
* *
607503 AGGTAAGTCAGTGTGAGGTGAGGTTAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTG
*
607542 AGGTAAGTCAGTGTGAGGTGAGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTG
* *
607581 AGGTAAGTCAGTGTGAGGTGAGGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTG-GGGGTG
* **
607621 TGGTAAGTCAGTGGG-GGTGAGGTAAGTCAGTGTGATGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTG-GGGGTG
* *
607660 AGGTAAGTCAGTGTGAGGTGAGGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTG-GGGGTG
607700 AGGTAAGTCAGTGGG-GGTGAGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTG
* * *
607738 AGATAAGTCAGTGTGAGGTGGGGTAAGTCAGTGGGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGG-GGTG
*
607778 AGATAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGG-GGTG
* ** *
607818 AGGTCAGTCAGTGGG-GGTGAAATAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTG-GGGGTG
* *
607857 GGGTAAGTCAGTGGGAGGTGAGATAAGTCAGTGGGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGG-GGTG
*
607897 AGGTTAGTCAGTGGG-GGTGAGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTG
607935 AGGTAAGTCAGTGGG-GGTGAGGTAAGTCA-TAGGGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGT-GGG-GGTG
**
607974 AGGTAAGTCAGTGGG-GGTGACATAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTG
608012 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTG
* * *
608051 ATGTAAGTCAGTGTGAGGTGAGGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTG-GGGGTG
* *
608091 AGGTTAGTCAGTGTGAGGTGAGGTAAGTCAGTGGGTAGGTTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGG--GG-TG
* * *
608133 -GTTAAGTCATTAGGAGAGGTGAGGTAAGTCAGTTGGAGCAGT-
1 AGGTAAGTCAGT-GG-GAGGTGAGGTAAGTCAG-TGG-G-GGTG
* *
608175 TGGTAAGTAAGTGGGTAGGTGAGGTAAGTCAG
1 AGGTAAGTCAGTGGG-AGGTGAGGTAAGTCAG
608207 AGGAGTGGTA
Statistics
Matches: 1508, Mismatches: 114, Indels: 116
0.87 0.07 0.07
Matches are distributed among these distances:
37 40 0.03
38 219 0.15
39 672 0.45
40 510 0.34
41 15 0.01
42 21 0.01
43 26 0.02
44 4 0.00
45 1 0.00
ACGTcount: A:0.24, C:0.05, G:0.49, T:0.21
Consensus pattern (39 bp):
AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTG
Found at i:606626 original size:58 final size:58
Alignment explanation
Indices: 606486--608206 Score: 2024
Period size: 58 Copynumber: 29.2 Consensus size: 58
606476 GAGGAGAGAT
* *
606486 AGGTAGGTCAGTTGGG-GGTGGGGTAAGTCAGTGGGGGGTGAGGTAAGTCA-TAGGGAGGTG
1 AGGTAAGTCAG-TGGGAGGTGAGGTAAGTCAGT-GGGGGTGAGGTAAGTCAGT-GGG-GGTG
* *
606546 AGGTAAGTCAGTGGG-GGTGAGGTAAGTCAGTGGGGATGAGTTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTGAGGTAAGTCAGTGGGGGTG
* * * *
606603 AGGTAAGTCAGAGGGAGGTGAGGTAAGTCGGGGGGGGTGAGGTAGGTCAGTGGGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTGAGGTAAGTCAGTGGG-GGTG
* *
606662 AGGTAAGTCA-TAGGGAGGTGAGGTAAGTCAGTGGGGATGAGGTAAGTCAGTGGGGTTG
1 AGGTAAGTCAGT-GGGAGGTGAGGTAAGTCAGTGGGGGTGAGGTAAGTCAGTGGGGGTG
*
606720 AGGTAAGTCA-TAGGGAGGTGAGGTAAGTCAGTGGGGGTGAGGTAAGTCGGTGGGGGTG
1 AGGTAAGTCAGT-GGGAGGTGAGGTAAGTCAGTGGGGGTGAGGTAAGTCAGTGGGGGTG
* *
606778 AGGTAAGTCA-TAGGGAGGTGAGGTAAGTCAGTGGGGGTGAGGTAAGTCAGCGGGGGGG
1 AGGTAAGTCAGT-GGGAGGTGAGGTAAGTCAGTGGGGGTGAGGTAAGTCAGTGGGGGTG
* * * * *
606836 AGGGAAGTCA-TAGGGAGGGGAGGTAAGTCAGTGGGGGGGAGGGAAGTCAGTGGGGGGG
1 AGGTAAGTCAGT-GGGAGGTGAGGTAAGTCAGTGGGGGTGAGGTAAGTCAGTGGGGGTG
* * * * * * *
606894 AGGGAAGTCA-TAGGGGGGGGAGGTAAGTCAGTGGGGGGGGGGGAAGTCAGTGGGGGGG
1 AGGTAAGTCAGT-GGGAGGTGAGGTAAGTCAGTGGGGGTGAGGTAAGTCAGTGGGGGTG
* * * * * * *
606952 AGGGAAGTCA-TAGGGGGGGGAGGTAAGTCAGTGGGGGGGGGGGAAGTCAGTGGGGGGG
1 AGGTAAGTCAGT-GGGAGGTGAGGTAAGTCAGTGGGGGTGAGGTAAGTCAGTGGGGGTG
* * *
607010 AGGGAAGTCA-TAGGGAGG-GAGGGAAGTCA-TAGGGAGGGGAGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGT-GGGAGGTGAGGTAAGTCAGT-GGG-GGTGAGGTAAGTCAGTGGGGGTG
* * *
607068 AGGTAAGTCA-TAGGGAGGTGAGGTAAGTCAGTCGGAGGTGAGATAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGT-GGGAGGTGAGGTAAGTCAGT-GGGGGTGAGGTAAGTCAGTG-GGGGTG
* * *
607128 AGGTAAGTAAGTGGGAGGTGAGATAAGTCAGTGTGAGGTGAGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTG-GGGGTGAGGTAAGTCAGTGGGGGTG
* *
607187 AGGTAAGTCAGTGTGAGGTGAGGTAAGTCAGTGGGGGTGAGGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTGAGGTAAGTCAGTG-GGGGTG
* * * * *
607246 AGGTAAGTCAGTGGGAGGTGGGGTAAGTCAGTGTGAGGTGAGATATGTCAGTGTGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTG-GGGGTGAGGTAAGTCAGTG-GGGGTG
* *
607306 AGGTAAGTCAGTGTGAGGTGAGGTAAGTCAGTGTGAGGTGAGGTAAGTCAGTGGGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTG-GGGGTGAGGTAAGTCAGTGGG-GGTG
* * *
607366 AGGTAAGTCAGTGGAAGGTGAGATAAGTCAGTGTGAGGTGAGGTAAGTCAGTGGGGGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTG-GGGGTGAGGTAAGTCAGT-GGGGGTG
* * * * * * *
607426 AGATAAGTCAGTGTGTGGTGAGGTAGGTTA--GGGGGTAAGGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTGAGGTAAGTCAGTG-GGGGTG
* * *
607483 AGGTAAGTCAGTGTGAGGTGAGGTAAGTCAGTGTGAGGTGAGGTTAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTG-GGGGTGAGGTAAGTCAGTGGGGGTG
* *
607542 AGGTAAGTCAGTGTGAGGTGAGGTAAGTCAGTGGGGGTGAGGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTGAGGTAAGTCAGTG-GGGGTG
* * **
607601 AGGTAAGTCAGTGTGAGGTGTGGTAAGTCAGTGGGGGTGAGGTAAGTCAGTGTGATGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTGAGGTAAGTCAGTG-GGGGTG
* *
607660 AGGTAAGTCAGTGTGAGGTGAGGTAAGTCAGTGTGAGGTGAGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTG-GGGGTGAGGTAAGTCAGTGGGGGTG
* * *
607719 AGGTAAGTCAGTGGG-GGTGAGATAAGTCAGTGTGAGGTGGGGTAAGTCAGTGGGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTG-GGGGTGAGGTAAGTCAGTGGG-GGTG
* *
607778 AGATAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGAGGTGAGGTCAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGG-GGTGAGGTAAGTCAGTGGGGGTG
** * * *
607837 AAATAAGTCAGTGTGAGGTGGGGTAAGTCAGTGGGAGGTGAGATAAGTCAGTGGGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGG-GGTGAGGTAAGTCAGTGGG-GGTG
*
607897 AGGTTAGTCAGTGGG-GGTGAGGTAAGTCAGTGGGGGTGAGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTGAGGTAAGTCAGTGGGGGTG
**
607954 AGGTAAGTCA-TAGGGAGGTGAGGTAAGTCAGTGGGGGTGACATAAGTCAGTGGGGGTG
1 AGGTAAGTCAGT-GGGAGGTGAGGTAAGTCAGTGGGGGTGAGGTAAGTCAGTGGGGGTG
* *
608012 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTGATGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTGAGGTAAGTCAGTG-GGGGTG
* * *
608071 AGGTAAGTCAGTGTGAGGTGAGGTTAGTCAGTGTGAGGTGAGGTAAGTCAGTGGGTAGGTTG
1 AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTG-GGGGTGAGGTAAGTCAGTGGG--GG-TG
* * * * *
608133 -GTTAAGTCATTAGGAGAGGTGAGGTAAGTCAGTTGGAGCAGT-TGGTAAGTAAGTGGGTAGGTG
1 AGGTAAGTCAGT-GG-GAGGTGAGGTAAGTCAG-TGG-G-GGTGAGGTAAGTCAGTGGG--GGTG
608196 AGGTAAGTCAG
1 AGGTAAGTCAG
608207 AGGAGTGGTA
Statistics
Matches: 1492, Mismatches: 130, Indels: 74
0.88 0.08 0.04
Matches are distributed among these distances:
56 3 0.00
57 94 0.06
58 564 0.38
59 450 0.30
60 315 0.21
61 15 0.01
62 3 0.00
63 19 0.01
64 27 0.02
65 2 0.00
ACGTcount: A:0.24, C:0.05, G:0.49, T:0.21
Consensus pattern (58 bp):
AGGTAAGTCAGTGGGAGGTGAGGTAAGTCAGTGGGGGTGAGGTAAGTCAGTGGGGGTG
Found at i:607104 original size:20 final size:19
Alignment explanation
Indices: 606486--608233 Score: 1772
Period size: 20 Copynumber: 88.8 Consensus size: 19
606476 GAGGAGAGAT
* *
606486 AGGTAGGTCAGTTGGGGGTG
1 AGGTAAGTCAG-TGGAGGTG
* *
606506 GGGTAAGTCAGTGGGGGGTG
1 AGGTAAGTCAGT-GGAGGTG
606526 AGGTAAGTCA-TAGGGAGGTG
1 AGGTAAGTCAGT--GGAGGTG
*
606546 AGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGAGGTG
606565 AGGTAAGTCAGTGG-GGATG
1 AGGTAAGTCAGTGGAGG-TG
* *
606584 AGTTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGAGGTG
*
606603 AGGTAAGTCAGAGGGAGGTG
1 AGGTAAGTCAG-TGGAGGTG
* * *
606623 AGGTAAGTCGGGGGGGGTG
1 AGGTAAGTCAGTGGAGGTG
*
606642 AGGTAGGTCAGTGGGAGGTG
1 AGGTAAGTCAGT-GGAGGTG
606662 AGGTAAGTCA-TAGGGAGGTG
1 AGGTAAGTCAGT--GGAGGTG
606682 AGGTAAGTCAGTGG-GGATG
1 AGGTAAGTCAGTGGAGG-TG
606701 AGGTAAGTCAGTGG-GGTTG
1 AGGTAAGTCAGTGGAGG-TG
606720 AGGTAAGTCA-TAGGGAGGTG
1 AGGTAAGTCAGT--GGAGGTG
*
606740 AGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGAGGTG
* *
606759 AGGTAAGTCGGTGGGGGTG
1 AGGTAAGTCAGTGGAGGTG
606778 AGGTAAGTCA-TAGGGAGGTG
1 AGGTAAGTCAGT--GGAGGTG
*
606798 AGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGAGGTG
* * *
606817 AGGTAAGTCAGCGGGGGGG
1 AGGTAAGTCAGTGGAGGTG
* *
606836 AGGGAAGTCA-TAGGGAGGGG
1 AGGTAAGTCAGT--GGAGGTG
* *
606856 AGGTAAGTCAGTGGGGGGG
1 AGGTAAGTCAGTGGAGGTG
* * *
606875 AGGGAAGTCAGTGGGGGGG
1 AGGTAAGTCAGTGGAGGTG
* * *
606894 AGGGAAGTCA-TAGGGGGGGG
1 AGGTAAGTCAGT--GGAGGTG
* *
606914 AGGTAAGTCAGTGGGGGGG
1 AGGTAAGTCAGTGGAGGTG
* * * *
606933 GGGGAAGTCAGTGGGGGGG
1 AGGTAAGTCAGTGGAGGTG
* * *
606952 AGGGAAGTCA-TAGGGGGGGG
1 AGGTAAGTCAGT--GGAGGTG
* *
606972 AGGTAAGTCAGTGGGGGGG
1 AGGTAAGTCAGTGGAGGTG
* * * *
606991 GGGGAAGTCAGTGGGGGGG
1 AGGTAAGTCAGTGGAGGTG
*
607010 AGGGAAGTCA-TAGGGAGG-G
1 AGGTAAGTCAGT--GGAGGTG
* *
607029 AGGGAAGTCA-TAGGGAGGGG
1 AGGTAAGTCAGT--GGAGGTG
*
607049 AGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGAGGTG
607068 AGGTAAGTCA-TAGGGAGGTG
1 AGGTAAGTCAGT--GGAGGTG
607088 AGGTAAGTCAGTCGGAGGTG
1 AGGTAAGTCAGT-GGAGGTG
*
607108 AGATAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTG-GAGGTG
*
607128 AGGTAAGTAAGTGGGAGGTG
1 AGGTAAGTCAGT-GGAGGTG
*
607148 AGATAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTG-GAGGTG
*
607168 AGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGAGGTG
607187 AGGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTG-GAGGTG
*
607207 AGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGAGGTG
607226 AGGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTG-GAGGTG
607246 AGGTAAGTCAGTGGGAGGTG
1 AGGTAAGTCAGT-GGAGGTG
*
607266 GGGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTG-GAGGTG
* *
607286 AGATATGTCAGTGTGAGGTG
1 AGGTAAGTCAGTG-GAGGTG
607306 AGGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTG-GAGGTG
607326 AGGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTG-GAGGTG
607346 AGGTAAGTCAGTGGGAGGTG
1 AGGTAAGTCAGT-GGAGGTG
607366 AGGTAAGTCAGTGGAAGGTG
1 AGGTAAGTCAGTGG-AGGTG
*
607386 AGATAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTG-GAGGTG
*
607406 AGGTAAGTCAGTGGGGGGTG
1 AGGTAAGTCAGT-GGAGGTG
* *
607426 AGATAAGTCAGTGTGTGGTG
1 AGGTAAGTCAGTG-GAGGTG
* * *
607446 AGGTAGGTTAG-GG-GGTA
1 AGGTAAGTCAGTGGAGGTG
607463 AGGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTG-GAGGTG
607483 AGGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTG-GAGGTG
607503 AGGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTG-GAGGTG
* *
607523 AGGTTAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGAGGTG
607542 AGGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTG-GAGGTG
*
607562 AGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGAGGTG
607581 AGGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTG-GAGGTG
607601 AGGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTG-GAGGTG
* *
607621 TGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGAGGTG
*
607640 AGGTAAGTCAGTGTGATGTG
1 AGGTAAGTCAGTG-GAGGTG
607660 AGGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTG-GAGGTG
607680 AGGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTG-GAGGTG
*
607700 AGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGAGGTG
*
607719 AGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGAGGTG
*
607738 AGATAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTG-GAGGTG
*
607758 GGGTAAGTCAGTGGGAGGTG
1 AGGTAAGTCAGT-GGAGGTG
*
607778 AGATAAGTCAGTGGGAGGTG
1 AGGTAAGTCAGT-GGAGGTG
607798 AGGTAAGTCAGTGGGAGGTG
1 AGGTAAGTCAGT-GGAGGTG
* *
607818 AGGTCAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGAGGTG
**
607837 AAATAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTG-GAGGTG
*
607857 GGGTAAGTCAGTGGGAGGTG
1 AGGTAAGTCAGT-GGAGGTG
*
607877 AGATAAGTCAGTGGGAGGTG
1 AGGTAAGTCAGT-GGAGGTG
* *
607897 AGGTTAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGAGGTG
*
607916 AGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGAGGTG
*
607935 AGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGAGGTG
607954 AGGTAAGTCA-TAGGGAGGTG
1 AGGTAAGTCAGT--GGAGGTG
*
607974 AGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGAGGTG
** *
607993 ACATAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGAGGTG
608012 AGGTAAGTCAGTGGGAGGTG
1 AGGTAAGTCAGT-GGAGGTG
*
608032 AGGTAAGTCAGTGGGGGTG
1 AGGTAAGTCAGTGGAGGTG
*
608051 ATGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTG-GAGGTG
608071 AGGTAAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTG-GAGGTG
*
608091 AGGTTAGTCAGTGTGAGGTG
1 AGGTAAGTCAGTG-GAGGTG
608111 AGGTAAGTCAGTGGGTAGGTTG
1 AGGTAAGTCAGT-GG-AGG-TG
* *
608133 -GTTAAGTCATTAGGAGAGGTG
1 AGGTAAGTCAGT--G-GAGGTG
608154 AGGTAAGTCAGTTGGAGCAGT-
1 AGGTAAGTCAG-TGGAG--GTG
* *
608175 TGGTAAGTAAGTGGGTAGGTG
1 AGGTAAGTCAGT-GG-AGGTG
*
608196 AGGTAAGTCAGAGGA-GTGG
1 AGGTAAGTCAGTGGAGGT-G
608215 TAGGTTAAGTCAGATGGAG
1 -AGG-TAAGTCAG-TGGAG
608234 ATGGGGAAGG
Statistics
Matches: 1521, Mismatches: 130, Indels: 151
0.84 0.07 0.08
Matches are distributed among these distances:
17 12 0.01
18 15 0.01
19 551 0.36
20 856 0.56
21 63 0.04
22 22 0.01
23 2 0.00
ACGTcount: A:0.24, C:0.05, G:0.49, T:0.21
Consensus pattern (19 bp):
AGGTAAGTCAGTGGAGGTG
Found at i:608402 original size:19 final size:20
Alignment explanation
Indices: 608358--608402 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
608348 ATGTTAGTTA
608358 GGAGGTGGGGTATATCAGTG
1 GGAGGTGGGGTATATCAGTG
608378 GGAGGTGGGGTATATCAGT-
1 GGAGGTGGGGTATATCAGTG
608397 GGAGGT
1 GGAGGT
608403 TAGGTAAGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.20, C:0.04, G:0.51, T:0.24
Consensus pattern (20 bp):
GGAGGTGGGGTATATCAGTG
Found at i:608408 original size:19 final size:20
Alignment explanation
Indices: 608358--608408 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
608348 ATGTTAGTTA
*
608358 GGAGGTGGGGTATATCAGTG
1 GGAGGTGAGGTATATCAGTG
*
608378 GGAGGTGGGGTATATCAGT-
1 GGAGGTGAGGTATATCAGTG
*
608397 GGAGGTTAGGTA
1 GGAGGTGAGGTA
608409 AGTCAAATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 10 0.34
20 19 0.66
ACGTcount: A:0.22, C:0.04, G:0.49, T:0.25
Consensus pattern (20 bp):
GGAGGTGAGGTATATCAGTG
Found at i:610907 original size:68 final size:68
Alignment explanation
Indices: 610787--610962 Score: 246
Period size: 68 Copynumber: 2.6 Consensus size: 68
610777 ATATGACCCT
* * * * ** * *
610787 TTATTACAGTACACAATTACCATTACTTGGA-CTATTCTTTATCTTGATGTAATTCAACCAATGG
1 TTATTACAGTACACGACTACCGTTACATGGACCCGTTCTTTATCTTAATGTAATACAACCAATGG
*
610851 TAA
66 CAA
*
610854 TTATTATAGTACACGACTACCGTTACATGGACCCGTTCTTTATCTTAATGTAATACAACCAATGG
1 TTATTACAGTACACGACTACCGTTACATGGACCCGTTCTTTATCTTAATGTAATACAACCAATGG
*
610919 CAT
66 CAA
610922 TTATTACAGTACACGACTACCGTTACATGGACCCGTTCTTT
1 TTATTACAGTACACGACTACCGTTACATGGACCCGTTCTTT
610963 GACCCGAGTG
Statistics
Matches: 96, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 26 0.27
68 70 0.73
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (68 bp):
TTATTACAGTACACGACTACCGTTACATGGACCCGTTCTTTATCTTAATGTAATACAACCAATGG
CAA
Found at i:611359 original size:27 final size:27
Alignment explanation
Indices: 611329--612327 Score: 1005
Period size: 27 Copynumber: 36.5 Consensus size: 27
611319 AGGTGTTAAG
*
611329 AGGTAACACTGTTGACTGTGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
* *
611356 AGGTGACACTGTTGTATGTGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
*
611383 AGGTAATACTGTTGTCTGTGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
* *
611410 AGGTGACACTGTTGTATGTGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
* * * *
611437 AGGTGACACTGTTGTATGTGTGTTAAG
1 AGGTAACACTGTTGTCTGTGTGTTTAC
* * ** *
611464 AGATCACACTGTTGAATGTGTCTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
** * *
611491 AGGTAACACAATTTTCTGTGTTTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
611518 AGGTATA-ACTGTTGTCTGTGTGTTAACAGCTAC
1 AGGTA-ACACTGTTGTCTGTGTGTT------TAC
* *
611551 ATGTAGCACTGTTGTCTGTGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
*
611578 AGGAAACACTGTTGTCTGTGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
* ** ** *
611605 AGGTAATAAAGTTAACTGTGTGTTTTC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
** *
611632 AGGTAACACTAATGAC--TGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
* *
611657 AGGTAACACTGTTGACAGTGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
*
611684 AAGTAACACTGTTGTCTGTGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
* *
611711 GGGTAACACTGTTGTCAGTGTGTCTACAGGTAC
1 AGGTAACACTGTTGTCTGTGTGT-T-----TAC
* * ** *
611744 TGGTAATACTGTTAACTGTGTGTATAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
* *
611771 AGGAAACACTGTTGACTGTGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
* * *
611798 AGGTACTGGTAATACAGTTAAT-TGTGTGTTTAC
1 ----A--GGTAACACTGTT-GTCTGTGTGTTTAC
*
611831 AGGTAACACTGTTGTC--TGTGTTTAT
1 AGGTAACACTGTTGTCTGTGTGTTTAC
*
611856 TGGTAACACTGTTGTCTGTGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
* * * *
611883 AGGTTATACTGTCGACTGTGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
*
611910 AGGTAACACTGCTGTCTGTGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
* * *
611937 AGGTAACACTGTTGACTTTGTGTTTAT
1 AGGTAACACTGTTGTCTGTGTGTTTAC
* *
611964 GGGTAATACTGTTGTCTGTGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
* *
611991 AGGTAAAACTGTTTTCTGTGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
612018 AGGTAACACTGTTGTC--TGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
* *
612043 CGGTAACATTGTTGTCTGTGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
*
612070 AGGTAACACTATTGTC--TGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
* *
612095 GGGTAACATTGTTGTCTGTGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
612122 AGGTAACACTGTTGTC--TGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
* *
612147 GGGTAACATTGTTGTCTGTGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
612174 AGGTAACACTGTTGTCTGTGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
*
612201 AGGTAACACTGTTGTCTGGGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
** *
612228 AGGTAACACTACTGACTGTGTGTTTGCAGCTGC
1 AGGTAACACTGTTGTCTGTGTGTTT--A----C
*
612261 AGGTAACATTGTTGTCTGTGTGTTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
* * *
612288 AGGTAACATTGTTGACTGTGTATTTAC
1 AGGTAACACTGTTGTCTGTGTGTTTAC
612315 AGGTAACACTGTT
1 AGGTAACACTGTT
612328 AATCATTTGT
Statistics
Matches: 806, Mismatches: 128, Indels: 76
0.80 0.13 0.08
Matches are distributed among these distances:
25 113 0.14
26 1 0.00
27 599 0.74
28 2 0.00
29 2 0.00
31 2 0.00
33 87 0.11
ACGTcount: A:0.21, C:0.14, G:0.25, T:0.40
Consensus pattern (27 bp):
AGGTAACACTGTTGTCTGTGTGTTTAC
Found at i:611749 original size:33 final size:33
Alignment explanation
Indices: 611712--611835 Score: 107
Period size: 33 Copynumber: 3.9 Consensus size: 33
611702 TGTGTTTACG
* * *
611712 GGTAACACTGTTGTCAGTGTGTCTACAGGTACT
1 GGTAACACTGTTGACTGTGTGTATACAGGTACT
* *
611745 GGTAATACTGTTAACTGTGTGTATACAGG-A--
1 GGTAACACTGTTGACTGTGTGTATACAGGTACT
*
611775 ---AACACTGTTGACTGTGTGTTTACAGGTACT
1 GGTAACACTGTTGACTGTGTGTATACAGGTACT
* * * * *
611805 GGTAATACAGTTAATTGTGTGTTTACAGGTA
1 GGTAACACTGTTGACTGTGTGTATACAGGTA
611836 ACACTGTTGT
Statistics
Matches: 73, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
27 23 0.32
28 1 0.01
32 1 0.01
33 48 0.66
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (33 bp):
GGTAACACTGTTGACTGTGTGTATACAGGTACT
Found at i:611784 original size:60 final size:60
Alignment explanation
Indices: 611699--611851 Score: 234
Period size: 60 Copynumber: 2.5 Consensus size: 60
611689 ACACTGTTGT
* * *
611699 CTGTGTGTTTACGGGTAACACTGTTGTCAGTGTGTCTACAGGTACTGGTAATACTGTTAA
1 CTGTGTGTTTACAGGTAACACTGTTGTCTGTGTGTCTACAGGTACTGGTAATACAGTTAA
* * * *
611759 CTGTGTGTATACAGGAAACACTGTTGACTGTGTGTTTACAGGTACTGGTAATACAGTTAA
1 CTGTGTGTTTACAGGTAACACTGTTGTCTGTGTGTCTACAGGTACTGGTAATACAGTTAA
*
611819 TTGTGTGTTTACAGGTAACACTGTTGTCTGTGT
1 CTGTGTGTTTACAGGTAACACTGTTGTCTGTGT
611852 TTATTGGTAA
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 82 1.00
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.37
Consensus pattern (60 bp):
CTGTGTGTTTACAGGTAACACTGTTGTCTGTGTGTCTACAGGTACTGGTAATACAGTTAA
Found at i:614081 original size:50 final size:50
Alignment explanation
Indices: 613651--614056 Score: 751
Period size: 50 Copynumber: 8.1 Consensus size: 50
613641 ACTGTACAAC
613651 TGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTCAAGAAT
1 TGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTCAAGAAT
*
613701 TGGACTCGGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTCAAGAAT
1 TGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTCAAGAAT
*
613751 TGGACTCAGGAATACCAGGTG-GGGAAGCTCAGTAACTGGACTCAAGAAT
1 TGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTCAAGAAT
*
613800 TGGACTCAGGAATACCAGATGAGGGAAGCTCAATAACTGGACTCAAGAAT
1 TGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTCAAGAAT
613850 TGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTCAAGAAT
1 TGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTCAAGAAT
*
613900 TGGAATCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTCAAGAAT
1 TGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTCAAGAAT
613950 TGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTCAAGAAT
1 TGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTCAAGAAT
* *
614000 TGGACTCGGGAATACCAGGTGAGGGAAGCTCAATGACTGGACTCAAGAAT
1 TGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTCAAGAAT
614050 TGGACTC
1 TGGACTC
614057 GGGTGTTTCA
Statistics
Matches: 345, Mismatches: 10, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
49 47 0.14
50 298 0.86
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (50 bp):
TGGACTCAGGAATACCAGGTGAGGGAAGCTCAATAACTGGACTCAAGAAT
Found at i:623524 original size:2 final size:2
Alignment explanation
Indices: 623517--623558 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
623507 TTATCTGAAT
623517 GA GA GA GA GA GA GA GA 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 GA GA GA GA GA GA GA GA
623559 ATAACAACGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:627465 original size:26 final size:26
Alignment explanation
Indices: 627436--627490 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
627426 GTGCTTTTCA
* * *
627436 ATCACTGCCTACCACAGCGCCACTCG
1 ATCACCGCCTACCACAGCACCACACG
* *
627462 ATCACCGTCTACCACGGCACCACACG
1 ATCACCGCCTACCACAGCACCACACG
627488 ATC
1 ATC
627491 GAGACAACGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.25, C:0.45, G:0.15, T:0.15
Consensus pattern (26 bp):
ATCACCGCCTACCACAGCACCACACG
Found at i:627520 original size:57 final size:59
Alignment explanation
Indices: 627459--627574 Score: 164
Period size: 57 Copynumber: 2.0 Consensus size: 59
627449 ACAGCGCCAC
* * *
627459 TCGATCACCGTCTACCACGGCACCACA-CG-ATCGAGACAACGCCTACCCCACAGCGAA
1 TCGATCACCGTCTACCACAGCACCACACCGTATCAAGACAACACCTACCCCACAGCGAA
* *
627516 TCGATCACCGTCTACCACAGCGCCACACTCGTGTCAAGACAACACCTACCCCACAGCGA
1 TCGATCACCGTCTACCACAGCACCACAC-CGTATCAAGACAACACCTACCCCACAGCGA
627575 TATTCAATCA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
57 25 0.49
59 2 0.04
60 24 0.47
ACGTcount: A:0.29, C:0.42, G:0.16, T:0.12
Consensus pattern (59 bp):
TCGATCACCGTCTACCACAGCACCACACCGTATCAAGACAACACCTACCCCACAGCGAA
Found at i:627821 original size:15 final size:15
Alignment explanation
Indices: 627801--627834 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
627791 ATAATGAGAC
627801 TGAGATCGAAAGTGG
1 TGAGATCGAAAGTGG
627816 TGAGATCGAAAGTGG
1 TGAGATCGAAAGTGG
627831 TGAG
1 TGAG
627835 TTCGTCTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.06, G:0.41, T:0.21
Consensus pattern (15 bp):
TGAGATCGAAAGTGG
Found at i:635434 original size:14 final size:14
Alignment explanation
Indices: 635417--635449 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
635407 GGTAAAGTTA
635417 GCTACTAGTAACTG
1 GCTACTAGTAACTG
635431 GCTACTAGTAACTG
1 GCTACTAGTAACTG
635445 GCTAC
1 GCTAC
635450 GAGAAGTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (14 bp):
GCTACTAGTAACTG
Found at i:640972 original size:14 final size:14
Alignment explanation
Indices: 640953--640987 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
640943 CTTACTTCTC
640953 GTAGCCAGTTACTA
1 GTAGCCAGTTACTA
640967 GTAGCCAGTTACTA
1 GTAGCCAGTTACTA
640981 GTAGCCA
1 GTAGCCA
640988 ACTTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (14 bp):
GTAGCCAGTTACTA
Found at i:640993 original size:51 final size:51
Alignment explanation
Indices: 640916--641020 Score: 158
Period size: 51 Copynumber: 2.1 Consensus size: 51
640906 NNNNNNTCTC
* * *
640916 GTAGCCAGTTACTAGTAGCTAGCTTTT-CTTACTTCTCGTAGCCAGTTACTA
1 GTAGCCAGTTACTAGTAGCCAACTTTTACTTA-ATCTCGTAGCCAGTTACTA
*
640967 GTAGCCAGTTACTAGTAGCCAACTTTTATTTAATCTCGTAGCCAGTTACTA
1 GTAGCCAGTTACTAGTAGCCAACTTTTACTTAATCTCGTAGCCAGTTACTA
641018 GTA
1 GTA
641021 ACTAGCTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
51 46 0.94
52 3 0.06
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (51 bp):
GTAGCCAGTTACTAGTAGCCAACTTTTACTTAATCTCGTAGCCAGTTACTA
Found at i:641017 original size:37 final size:37
Alignment explanation
Indices: 640967--641061 Score: 120
Period size: 37 Copynumber: 2.6 Consensus size: 37
640957 CCAGTTACTA
*
640967 GTAGCCAGTTACTAGTAGCCAACTTTTATTTA-ATCTC
1 GTAGCCAGTTACTAGTAGCCAACTTTT-CTTACATCTC
* * * *
641004 GTAGCCAGTTACTAGTAACTAGCTTTTCTTACTTCTC
1 GTAGCCAGTTACTAGTAGCCAACTTTTCTTACATCTC
*
641041 GTAGCCAGTTATTAGTAGCCA
1 GTAGCCAGTTACTAGTAGCCA
641062 GTTACTAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
36 3 0.06
37 46 0.94
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
GTAGCCAGTTACTAGTAGCCAACTTTTCTTACATCTC
Found at i:641061 original size:88 final size:88
Alignment explanation
Indices: 640912--641080 Score: 302
Period size: 88 Copynumber: 1.9 Consensus size: 88
640902 NNNNNNNNNN
*
640912 TCTCGTAGCCAGTTACTAGTAGCTAGCTTTTCTTACTTCTCGTAGCCAGTTACTAGTAGCCAGTT
1 TCTCGTAGCCAGTTACTAGTAACTAGCTTTTCTTACTTCTCGTAGCCAGTTACTAGTAGCCAGTT
*
640977 ACTAGTAGCCAACTTTTATTTAA
66 ACTAATAGCCAACTTTTATTTAA
*
641000 TCTCGTAGCCAGTTACTAGTAACTAGCTTTTCTTACTTCTCGTAGCCAGTTATTAGTAGCCAGTT
1 TCTCGTAGCCAGTTACTAGTAACTAGCTTTTCTTACTTCTCGTAGCCAGTTACTAGTAGCCAGTT
*
641065 ACTAATAGCTAACTTT
66 ACTAATAGCCAACTTT
641081 ACCTATCTAC
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 77 1.00
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.38
Consensus pattern (88 bp):
TCTCGTAGCCAGTTACTAGTAACTAGCTTTTCTTACTTCTCGTAGCCAGTTACTAGTAGCCAGTT
ACTAATAGCCAACTTTTATTTAA
Found at i:644737 original size:449 final size:448
Alignment explanation
Indices: 643900--644766 Score: 1653
Period size: 449 Copynumber: 1.9 Consensus size: 448
643890 GAATATACTC
*
643900 TACTCACGACAATGGATAACTAAAGACATACTAGTAATGAACTATATAACGAACATAACAAACGA
1 TACTCACGACAATGGATAACTAAAGAAATACTAGTAATGAACTATATAACGAACATAACAAACGA
643965 ATAACTGACGAAAGGGAATTCAAACAATACAAATTACAAATAAAACACATTGAAACAACAAAGTT
66 ATAACTGACGAAAGGGAATTCAAACAATACAAATTACAAATAAAACACATTGAAACAACAAAGTT
644030 ATCCCAGGACCATTTAATAAAAAATAGAATGAGAATGAATAAGTAAATTGGTTTACTCACCTCAG
131 ATCCCAGGACCATTTAATAAAAAATAGAATGAGAATGAATAAGTAAATTGGTTTACTCACCTCAG
* *
644095 AAGCCGTGTCTGTTTTATAAAATTAGAGAATTGATCTACAGAAACTGATAATATCAGGAAGAACG
196 AAGCCGTGTCTGTTTTATAAAATTAGAGAATTGAACGACAGAAACTGATAATATCAGGAAGAACG
*
644160 TGCAGGTGATTTTACCCGGTCCAAAGAGGCCCAAAAACCTAAACTCAGGTGGATATAAACAGGTA
261 TGCAGGTGATTTTACCCCGTCCAAAGAGGCCCAAAAACCTAAACTCAGGTGGATATAAACAGGTA
644225 TCGAAGGGTACCAGAAAGGGTAATAAAATTAGAGGTCCAGTACAGGATAACTATAAATAAAAGAC
326 TCGAAGGGTACCAGAAAGGGTAATAAAATTAGAGGTCCAGTACAGGATAACTATAAATAAAAGAC
644290 AAATTAAAACAGCATCGTAAATATAACACTCTCAACTAATATGTTTTCCAATATAATA
391 AAATTAAAACAGCATCGTAAATATAACACTCTCAACTAATATGTTTTCCAATATAATA
644348 TACTCACGACAATGGATAACTAAAGAAATACTAGTAATGAACTATATAACGAACATAACAAACGA
1 TACTCACGACAATGGATAACTAAAGAAATACTAGTAATGAACTATATAACGAACATAACAAACGA
644413 ATAACTGACGAAAGGGATATTCAAACAATACAAATTACAAATAAAACACATTGAAACAACAAAGT
66 ATAACTGACGAAAGGGA-ATTCAAACAATACAAATTACAAATAAAACACATTGAAACAACAAAGT
*
644478 TATCCCAGGACCATTTAATAAACAATAGAATGAGAATGAATAAGTAAATTGGTTTACTCACCTCA
130 TATCCCAGGACCATTTAATAAAAAATAGAATGAGAATGAATAAGTAAATTGGTTTACTCACCTCA
644543 GAAGCCGTGTCTGTTTTATAAAATTAGAGAATTGAACGACAGAAACTGATAATATCAGGAAGAAC
195 GAAGCCGTGTCTGTTTTATAAAATTAGAGAATTGAACGACAGAAACTGATAATATCAGGAAGAAC
644608 GTGCAGGTGATTTTACCCCGTCCAAAGAGGCCCAAAAACCTAAACTCAGGTGGATATAAACAGGT
260 GTGCAGGTGATTTTACCCCGTCCAAAGAGGCCCAAAAACCTAAACTCAGGTGGATATAAACAGGT
* *
644673 ATTGAGGGGTACCAGAAAGGGTAATAAAATTAGAGGTCCAGTACAGGATAACTATAAATAAAAGA
325 ATCGAAGGGTACCAGAAAGGGTAATAAAATTAGAGGTCCAGTACAGGATAACTATAAATAAAAGA
*
644738 CAAATTAAAACAGCATCGTAAATGTAACA
390 CAAATTAAAACAGCATCGTAAATATAACA
644767 ATACCTCCCC
Statistics
Matches: 410, Mismatches: 8, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
448 81 0.20
449 329 0.80
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.22
Consensus pattern (448 bp):
TACTCACGACAATGGATAACTAAAGAAATACTAGTAATGAACTATATAACGAACATAACAAACGA
ATAACTGACGAAAGGGAATTCAAACAATACAAATTACAAATAAAACACATTGAAACAACAAAGTT
ATCCCAGGACCATTTAATAAAAAATAGAATGAGAATGAATAAGTAAATTGGTTTACTCACCTCAG
AAGCCGTGTCTGTTTTATAAAATTAGAGAATTGAACGACAGAAACTGATAATATCAGGAAGAACG
TGCAGGTGATTTTACCCCGTCCAAAGAGGCCCAAAAACCTAAACTCAGGTGGATATAAACAGGTA
TCGAAGGGTACCAGAAAGGGTAATAAAATTAGAGGTCCAGTACAGGATAACTATAAATAAAAGAC
AAATTAAAACAGCATCGTAAATATAACACTCTCAACTAATATGTTTTCCAATATAATA
Found at i:658093 original size:55 final size:58
Alignment explanation
Indices: 657959--658100 Score: 184
Period size: 55 Copynumber: 2.4 Consensus size: 58
657949 ACATTAAGAG
*
657959 TGAATTGTTAAATTCAGTTATACATACTTAGTATTTTAAAGATATGGTTAATATGTATAAC
1 TGAATTGTTAAATTCAGTTATACATAC-TAGTA--TTAAAGATATGGTAAATATGTATAAC
* * *
658020 TGAATT-TAACAATGCAGTTATACATAC-A-TA-TACAGATATGGTAAATATGTATAAC
1 TGAATTGTTA-AATTCAGTTATACATACTAGTATTAAAGATATGGTAAATATGTATAAC
658075 TGAATTGTTAAATTCAGTTATACATA
1 TGAATTGTTAAATTCAGTTATACATA
658101 TTTACCATAT
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
55 44 0.60
56 2 0.03
58 2 0.03
59 1 0.01
60 2 0.03
61 22 0.30
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (58 bp):
TGAATTGTTAAATTCAGTTATACATACTAGTATTAAAGATATGGTAAATATGTATAAC
Found at i:670197 original size:321 final size:321
Alignment explanation
Indices: 669615--670253 Score: 1181
Period size: 321 Copynumber: 2.0 Consensus size: 321
669605 GGTTTTAGAG
669615 AAGAAGTTCAAAATGTGAAAAGTTTACAGACGGACAGACAGAAAAACGAACAGACGGACGGACGA
1 AAGAAGTTCAAAATGTGAAAAGTTTACAGACGGACAGACAGAAAAACGAACAGACGGACGGACGA
*
669680 GGACAAAATGTGATCAGAAAAGCTCACTTGAGCTTTCAGCTCAGGTGAACTAAAACCCATTAAAT
66 GGACAAAATGTGATCAGAAAAGCTCACTTGAGCTTTCAGCTCAGGTGAACTAAAACCCATTAAAC
669745 AATCATTTATAGTCTGTATCAATTTTAGAGTAATGGTGAAAACAAAATTGCCATAACAATGCAAA
131 AATCATTTATAGTCTGTATCAATTTTAGAGTAATGGTGAAAACAAAATTGCCATAACAATGCAAA
669810 TTGATACACTCCAATACTTTTTGCTATACAATGTTTCATATATAACATAGAATAACGATTCATTC
196 TTGATACACTCCAATACTTTTTGCTATACAATGTTTCATATATAACATAGAATAACGATTCATTC
669875 AACAAAACATTCATACAAGTAACTTGACAGTTTGTGCATACCAAATCATATCAATATGTTC
261 AACAAAACATTCATACAAGTAACTTGACAGTTTGTGCATACCAAATCATATCAATATGTTC
*
669936 AAGAAGTTCAAAATGTGAAAAGTTTAGAGACGGACAGACAGAAAAACGAACAGACGGACGGACGA
1 AAGAAGTTCAAAATGTGAAAAGTTTACAGACGGACAGACAGAAAAACGAACAGACGGACGGACGA
*
670001 GGACAAAATGTGATCAGAAAAGCTCACTTGAGCTTTCAGCTCAGGTGAGCTAAAACCCATTAAAC
66 GGACAAAATGTGATCAGAAAAGCTCACTTGAGCTTTCAGCTCAGGTGAACTAAAACCCATTAAAC
* *
670066 AATCATTTATAGTCTGTATCAATTTTAGAGTAATGGTTAGAACAAAATTGCCATAACAATGCAAA
131 AATCATTTATAGTCTGTATCAATTTTAGAGTAATGGTGAAAACAAAATTGCCATAACAATGCAAA
*
670131 TTGATACTCTCCAATA-TTGTTTGCTATACAATGTTTCATATATAACATAGAATAACGATTCATT
196 TTGATACACTCCAATACTT-TTTGCTATACAATGTTTCATATATAACATAGAATAACGATTCATT
** *
670195 CAACAAAACATTCATACTGGTATCTTGACAGTTTGTGCATACCAAATCATATCAATATG
260 CAACAAAACATTCATACAAGTAACTTGACAGTTTGTGCATACCAAATCATATCAATATG
670254 CAATTTACAA
Statistics
Matches: 308, Mismatches: 9, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
320 2 0.01
321 306 0.99
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (321 bp):
AAGAAGTTCAAAATGTGAAAAGTTTACAGACGGACAGACAGAAAAACGAACAGACGGACGGACGA
GGACAAAATGTGATCAGAAAAGCTCACTTGAGCTTTCAGCTCAGGTGAACTAAAACCCATTAAAC
AATCATTTATAGTCTGTATCAATTTTAGAGTAATGGTGAAAACAAAATTGCCATAACAATGCAAA
TTGATACACTCCAATACTTTTTGCTATACAATGTTTCATATATAACATAGAATAACGATTCATTC
AACAAAACATTCATACAAGTAACTTGACAGTTTGTGCATACCAAATCATATCAATATGTTC
Found at i:673238 original size:2 final size:2
Alignment explanation
Indices: 673231--673301 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
673221 TCGAACATTA
673231 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
673273 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
673302 CGCTAATTTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:676437 original size:3 final size:3
Alignment explanation
Indices: 676429--676456 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
676419 TTCATTTAGA
676429 TAG TAG TAG TAG TAG TAG TAG TAG TAG T
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG T
676457 GTGTAGGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TAG
Found at i:682220 original size:4 final size:4
Alignment explanation
Indices: 682211--682236 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
682201 GTTACCCTGT
682211 TCCG TCCG TCCG TCCG TCCG TCCG TC
1 TCCG TCCG TCCG TCCG TCCG TCCG TC
682237 TGTCNCTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.50, G:0.23, T:0.27
Consensus pattern (4 bp):
TCCG
Found at i:682859 original size:15 final size:15
Alignment explanation
Indices: 682831--682865 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
682821 CATATGATAC
682831 AATA-TGTATAATAT
1 AATATTGTATAATAT
*
682845 AATATTGTATTATAT
1 AATATTGTATAATAT
682860 AATATT
1 AATATT
682866 TTTCTTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (15 bp):
AATATTGTATAATAT
Found at i:682984 original size:10 final size:10
Alignment explanation
Indices: 682965--683003 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
682955 ATCAAAAATG
*
682965 ATACAGTATC
1 ATACAATATC
682975 ATACAATATC
1 ATACAATATC
* *
682985 ATACTATATT
1 ATACAATATC
682995 ATACAATAT
1 ATACAATAT
683004 AATATCATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.36
Consensus pattern (10 bp):
ATACAATATC
Found at i:683387 original size:13 final size:14
Alignment explanation
Indices: 683369--683410 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
683359 TAATATGATA
683369 AAGGTG-GTCTCAT
1 AAGGTGAGTCTCAT
683382 AAGGTGAAGTCTCAT
1 AAGGTG-AGTCTCAT
683397 AAGGGTGATGTCTC
1 AA-GGTGA-GTCTC
683411 GTCTCGGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 6 0.24
15 10 0.40
16 9 0.36
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (14 bp):
AAGGTGAGTCTCAT
Found at i:683395 original size:15 final size:16
Alignment explanation
Indices: 683375--683410 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
683365 GATAAAGGTG
683375 GTCTCATAA-GGTGAA
1 GTCTCATAAGGGTGAA
*
683390 GTCTCATAAGGGTGAT
1 GTCTCATAAGGGTGAA
683406 GTCTC
1 GTCTC
683411 GTCTCGGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.31
Consensus pattern (16 bp):
GTCTCATAAGGGTGAA
Found at i:685667 original size:25 final size:25
Alignment explanation
Indices: 685637--685698 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
685627 AAACTACTAG
*
685637 TATCACTATTATTACTATCCCAAAA-
1 TATCACTATTATTACTAT-ACAAAAC
*
685662 TTTCACTATTATTACTATACAAAAC
1 TATCACTATTATTACTATACAAAAC
685687 TATCACTATTAT
1 TATCACTATTAT
685699 AACTCCCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 5 0.15
25 28 0.85
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.40
Consensus pattern (25 bp):
TATCACTATTATTACTATACAAAAC
Found at i:690919 original size:34 final size:34
Alignment explanation
Indices: 690871--690938 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
690861 TTCAAATCTA
* *
690871 TAACTCGTATTCACTTTGTTTCATTTATATATTG
1 TAACTCGTAATCACTTTGTTTCATTAATATATTG
690905 TAACTCGTAATCACTTTGTTTCATTAATATATTG
1 TAACTCGTAATCACTTTGTTTCATTAATATATTG
690939 AACGTCTCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (34 bp):
TAACTCGTAATCACTTTGTTTCATTAATATATTG
Found at i:693211 original size:62 final size:62
Alignment explanation
Indices: 693052--693836 Score: 1196
Period size: 62 Copynumber: 12.7 Consensus size: 62
693042 AACCATACAG
*
693052 ATCAGACCCAGGCATTCCACGGCTTGTGTAAGGCGAAACCACCCTGTAAAATAGAAC-AAGC
1 ATCAGACCCAGGCATTCCACGGCTTGTGTAAGGCGAAACCACCCTGTAAAATAGAACAAAAC
*
693113 ATCAGACCCAGGCATTCCACGGCTTGTGTAAGGCGAAACCACCCTCTAAAATAGAACAAAAC
1 ATCAGACCCAGGCATTCCACGGCTTGTGTAAGGCGAAACCACCCTGTAAAATAGAACAAAAC
* *
693175 GTCAGACCCAGGCATTCCACGGCTTGTGTAAGGCGAAACCATCCTGTAAAATAGAACAAAAC
1 ATCAGACCCAGGCATTCCACGGCTTGTGTAAGGCGAAACCACCCTGTAAAATAGAACAAAAC
**
693237 ATTGGACCCAGGCATTCCACGGCTTGTGTAAGGCGAAACCACCCTGTAAAATAGAACAAAAC
1 ATCAGACCCAGGCATTCCACGGCTTGTGTAAGGCGAAACCACCCTGTAAAATAGAACAAAAC
* * *
693299 ATCAGACCCAGGCATTCCGCGGCTTGTGTAAGGCGAAACCACCCTGTACAATAGAAC-AAGC
1 ATCAGACCCAGGCATTCCACGGCTTGTGTAAGGCGAAACCACCCTGTAAAATAGAACAAAAC
*
693360 ATCAGACCCAGGCATTCCGCGGCTTGTGTAAGGCGAAACCACCCTGTAAAATAGAACAAAAC
1 ATCAGACCCAGGCATTCCACGGCTTGTGTAAGGCGAAACCACCCTGTAAAATAGAACAAAAC
* * *
693422 ATCAGACCCAGACATTCCGCGGCTTGTGTAAGGCGAAACCACCCTGTAAATTAGAACAAAAC
1 ATCAGACCCAGGCATTCCACGGCTTGTGTAAGGCGAAACCACCCTGTAAAATAGAACAAAAC
* * ** *
693484 ACCAGACCCACGCATTCCACGGCTTAAGTAAGGCGAAACCACCCTGTAAGATAGAACAAAAC
1 ATCAGACCCAGGCATTCCACGGCTTGTGTAAGGCGAAACCACCCTGTAAAATAGAACAAAAC
* * ** * *
693546 ACCAGACCCACGCATTCCACGGCTTAAGTAAGGCGAAACCACCCTGTAAGATAGAACAAAGC
1 ATCAGACCCAGGCATTCCACGGCTTGTGTAAGGCGAAACCACCCTGTAAAATAGAACAAAAC
**
693608 ATTGGACCCAGGCATTCCACGGCTTGTGTAAGGCGAAACCACCCTGTAAAATAGAACAAAAC
1 ATCAGACCCAGGCATTCCACGGCTTGTGTAAGGCGAAACCACCCTGTAAAATAGAACAAAAC
* * ** *
693670 ACCAGACCCACGCATTCCACGGCTTAAGTAAGGCGAAACCACCCTGTAAATTAGAACAAAAC
1 ATCAGACCCAGGCATTCCACGGCTTGTGTAAGGCGAAACCACCCTGTAAAATAGAACAAAAC
* * * ** * *
693732 ACCAGACCCACGCATTCCACGGCATAAGTAAGGCGAAACCACCCTATAAGATAGAACAAAAC
1 ATCAGACCCAGGCATTCCACGGCTTGTGTAAGGCGAAACCACCCTGTAAAATAGAACAAAAC
**
693794 ATTGGACCCAGGCATTCCACGGCTTGTGTAAGGCGAAACCACC
1 ATCAGACCCAGGCATTCCACGGCTTGTGTAAGGCGAAACCACC
693837 GTTCTACGGC
Statistics
Matches: 669, Mismatches: 53, Indels: 3
0.92 0.07 0.00
Matches are distributed among these distances:
61 115 0.17
62 554 0.83
ACGTcount: A:0.36, C:0.29, G:0.20, T:0.16
Consensus pattern (62 bp):
ATCAGACCCAGGCATTCCACGGCTTGTGTAAGGCGAAACCACCCTGTAAAATAGAACAAAAC
Found at i:695205 original size:2 final size:2
Alignment explanation
Indices: 695198--695236 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
695188 AACGACGTAT
695198 GA 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 GA G
695237 CTTGATTGGT
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:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:701473 original size:13 final size:13
Alignment explanation
Indices: 701455--701482 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
701445 TAAATTTACG
701455 TACAACGCTGTGT
1 TACAACGCTGTGT
701468 TACAACGCTGTGT
1 TACAACGCTGTGT
701481 TA
1 TA
701483 ATTTTTGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (13 bp):
TACAACGCTGTGT
Found at i:707307 original size:15 final size:16
Alignment explanation
Indices: 707276--707313 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
707266 AGAGGTATCC
*
707276 GGAGAAATCGTACCCT
1 GGAGAAATCGTAACCT
707292 GGAGAAA-CGTAACCT
1 GGAGAAATCGTAACCT
*
707307 GAAGAAA
1 GGAGAAA
707314 ACGTTGTAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.42, C:0.18, G:0.26, T:0.13
Consensus pattern (16 bp):
GGAGAAATCGTAACCT
Found at i:711898 original size:33 final size:33
Alignment explanation
Indices: 711856--711921 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
711846 TTACAACGTT
711856 CTATAACTTTTCTCTGATGTAAACATCCGGGGG
1 CTATAACTTTTCTCTGATGTAAACATCCGGGGG
711889 CTATAACTTTTCTCTGATGTAAACATCCGGGGG
1 CTATAACTTTTCTCTGATGTAAACATCCGGGGG
711922 TTTGTTACTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.33
Consensus pattern (33 bp):
CTATAACTTTTCTCTGATGTAAACATCCGGGGG
Found at i:712266 original size:43 final size:43
Alignment explanation
Indices: 712219--712333 Score: 142
Period size: 43 Copynumber: 2.7 Consensus size: 43
712209 TAAAAATATT
* *
712219 TTTATCTCGTAATTACGAGAAAAGATCTCGTTA-AATCGAGTTA
1 TTTATCTCGTTATTATGAGAAAAGATCTCGTTATAAT-GAGTTA
* * * *
712262 TTTATTTTGTTATTTTGAGAAAAGATCTCGTTATTATGAGTTA
1 TTTATCTCGTTATTATGAGAAAAGATCTCGTTATAATGAGTTA
* *
712305 ATTATCTCGTTATTATAAGAAAAGATCTC
1 TTTATCTCGTTATTATGAGAAAAGATCTC
712334 CTAATAACGA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 58 0.97
44 2 0.03
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (43 bp):
TTTATCTCGTTATTATGAGAAAAGATCTCGTTATAATGAGTTA
Found at i:712294 original size:21 final size:21
Alignment explanation
Indices: 712270--712333 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
712260 TATTTATTTT
*
712270 GTTATTTTGAGAAAAGATCTC
1 GTTATTATGAGAAAAGATCTC
* **
712291 GTTATTATGAGTTAATTATCTC
1 GTTATTATGAG-AAAAGATCTC
*
712313 GTTATTATAAGAAAAGATCTC
1 GTTATTATGAGAAAAGATCTC
712334 CTAATAACGA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (21 bp):
GTTATTATGAGAAAAGATCTC
Found at i:723910 original size:13 final size:13
Alignment explanation
Indices: 723892--723918 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
723882 TGTACAACAT
723892 ACATATTCACTAG
1 ACATATTCACTAG
723905 ACATATTCACTAG
1 ACATATTCACTAG
723918 A
1 A
723919 AATTTATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (13 bp):
ACATATTCACTAG
Found at i:724414 original size:70 final size:70
Alignment explanation
Indices: 724331--724546 Score: 405
Period size: 70 Copynumber: 3.1 Consensus size: 70
724321 TGTAGAGATG
724331 TTTTATCGTTATCGTTAATAATGAAGCCTTGGTCAGGACGCCCTATATTTCATCAGAGGCCAGTG
1 TTTTATCGTTATCGTTAATAATGAAGCCTTGGTCAGGACGCCCTATATTTCATCAGAGGCCAGTG
724396 TGGTT
66 TGGTT
*
724401 TTTTATCGTTATCGTTAATAATGAAGCCTTGGCCAGGACGCCCTATATTTCATCAGAGGCCAGTG
1 TTTTATCGTTATCGTTAATAATGAAGCCTTGGTCAGGACGCCCTATATTTCATCAGAGGCCAGTG
724466 TGGTT
66 TGGTT
*
724471 TTTTATCGTTATCGTTAATAATGAAGTCTTGGTCAGGACGCCCTATATTTCATCAGAGGCCAGTG
1 TTTTATCGTTATCGTTAATAATGAAGCCTTGGTCAGGACGCCCTATATTTCATCAGAGGCCAGTG
724536 TGGTT
66 TGGTT
724541 CTTTTA
1 -TTTTA
724547 GGTATAATCA
Statistics
Matches: 142, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
70 137 0.96
71 5 0.04
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.37
Consensus pattern (70 bp):
TTTTATCGTTATCGTTAATAATGAAGCCTTGGTCAGGACGCCCTATATTTCATCAGAGGCCAGTG
TGGTT
Found at i:726268 original size:31 final size:29
Alignment explanation
Indices: 726230--726337 Score: 102
Period size: 31 Copynumber: 3.8 Consensus size: 29
726220 CGCGCTAACA
726230 CACAACACGCCGTCGCGCTAACGCAACTTT
1 CACAACACGCCGTCGCGCTAAC-CAACTTT
726260 CCACAACACGCCGTCGCGCTAA-C-A----
1 -CACAACACGCCGTCGCGCTAACCAACTTT
*
726284 CACAACACGCCGTCGCACTAACACAACTTT
1 CACAACACGCCGTCGCGCTAAC-CAACTTT
* *
726314 GCACAAACATGCCATCGCGCTAAC
1 -CAC-AACACGCCGTCGCGCTAAC
726338 ACACAATGCA
Statistics
Matches: 64, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
23 20 0.31
25 1 0.02
26 1 0.02
28 1 0.02
29 1 0.02
31 24 0.38
32 16 0.25
ACGTcount: A:0.31, C:0.41, G:0.15, T:0.14
Consensus pattern (29 bp):
CACAACACGCCGTCGCGCTAACCAACTTT
Found at i:726305 original size:54 final size:55
Alignment explanation
Indices: 726217--726343 Score: 202
Period size: 54 Copynumber: 2.3 Consensus size: 55
726207 ATAAACGAGA
* *
726217 CATCGCGCTAACACACAACACGCCGTCGCGCTAACGCAACTTTCCAC-AACACGC
1 CATCGCGCTAACACACAACACGCCGTCGCACTAACACAACTTTCCACAAACACGC
* * *
726271 CGTCGCGCTAACACACAACACGCCGTCGCACTAACACAACTTTGCACAAACATGC
1 CATCGCGCTAACACACAACACGCCGTCGCACTAACACAACTTTCCACAAACACGC
726326 CATCGCGCTAACACACAA
1 CATCGCGCTAACACACAA
726344 TGCACTATCG
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
54 43 0.65
55 23 0.35
ACGTcount: A:0.32, C:0.40, G:0.14, T:0.13
Consensus pattern (55 bp):
CATCGCGCTAACACACAACACGCCGTCGCACTAACACAACTTTCCACAAACACGC
Found at i:726310 original size:21 final size:23
Alignment explanation
Indices: 726261--726308 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
726251 CGCAACTTTC
*
726261 CACAACACGCCGTCGCGCTAACA
1 CACAACACGCCGTCGCACTAACA
726284 CACAACACGCCGTCGCACTAACA
1 CACAACACGCCGTCGCACTAACA
726307 CA
1 CA
726309 ACTTTGCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.44, G:0.15, T:0.08
Consensus pattern (23 bp):
CACAACACGCCGTCGCACTAACA
Found at i:726377 original size:23 final size:23
Alignment explanation
Indices: 726315--726383 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
726305 CACAACTTTG
*
726315 CACA-AACATGCCATCGCGCTAA
1 CACACAACACGCCATCGCGCTAA
** * *
726337 CACACAATGCACTATCGCGCTAA
1 CACACAACACGCCATCGCGCTAA
*
726360 CACACAACACGCCGTCGCGCTAA
1 CACACAACACGCCATCGCGCTAA
726383 C
1 C
726384 GCAACTTTGC
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
22 4 0.11
23 32 0.89
ACGTcount: A:0.33, C:0.39, G:0.14, T:0.13
Consensus pattern (23 bp):
CACACAACACGCCATCGCGCTAA
Found at i:726403 original size:31 final size:31
Alignment explanation
Indices: 726362--726487 Score: 207
Period size: 31 Copynumber: 4.1 Consensus size: 31
726352 CGCGCTAACA
*
726362 CACAACACGCCGTCGCGCTAACGCAACTTTG
1 CACAACACGCCGTCGCGCTAACACAACTTTG
*
726393 CATAACACGCCGTCGCGCTAACACAACTTTG
1 CACAACACGCCGTCGCGCTAACACAACTTTG
*
726424 CACAACACGCCGTCGTGCTAACACAACTTTG
1 CACAACACGCCGTCGCGCTAACACAACTTTG
* *
726455 CACAACACGCCGTCGCGCCAACGCAACTTTG
1 CACAACACGCCGTCGCGCTAACACAACTTTG
726486 CA
1 CA
726488 AGTTTCACAG
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 88 1.00
ACGTcount: A:0.28, C:0.38, G:0.17, T:0.17
Consensus pattern (31 bp):
CACAACACGCCGTCGCGCTAACACAACTTTG
Found at i:726426 original size:78 final size:78
Alignment explanation
Indices: 726273--726417 Score: 238
Period size: 78 Copynumber: 1.9 Consensus size: 78
726263 CAACACGCCG
*
726273 TCGCGCTAACACACAACACGCCGTCGCACTAACACAACTTTGCACAAACATGCCATCGCGCTAAC
1 TCGCGCTAACACACAACACGCCGTCGCACTAACACAACTTTGCACAAACACGCCATCGCGCTAAC
726338 ACACAATGCACTA
66 ACACAATGCACTA
* * * *
726351 TCGCGCTAACACACAACACGCCGTCGCGCTAACGCAACTTTGCA-TAACACGCCGTCGCGCTAAC
1 TCGCGCTAACACACAACACGCCGTCGCACTAACACAACTTTGCACAAACACGCCATCGCGCTAAC
726415 ACA
66 ACA
726418 ACTTTGCACA
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
77 20 0.32
78 42 0.68
ACGTcount: A:0.32, C:0.38, G:0.15, T:0.15
Consensus pattern (78 bp):
TCGCGCTAACACACAACACGCCGTCGCACTAACACAACTTTGCACAAACACGCCATCGCGCTAAC
ACACAATGCACTA
Found at i:737233 original size:31 final size:31
Alignment explanation
Indices: 737195--737695 Score: 560
Period size: 31 Copynumber: 17.7 Consensus size: 31
737185 NNNNNNNTGT
737195 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
**
737226 GTTAGCGCGACGGCGTGTTGTGCAAAGTTTT
1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
737257 GTTAGCGCGACGGCGTGTTGT-----G-T--
1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
737280 GTTAGCGCGACGGCGTGTTGT-----G-T--
1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
737303 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
737334 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
737365 GTTAGCGCGACGGCGTGTTGT-----G-T--
1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
737388 GTTAGCGCGGA-GGCGTGTTGTGCAAAGTTGC
1 GTTAGCGC-GACGGCGTGTTGTGCAAAGTTGC
*
737419 GTTAGCGCGACGGCGTGTTGTGCAAAATTGC
1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
*
737450 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGT
1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
*
737481 GTTAGCGCGACGGCGTGTTATGCAAAGTTGC
1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
*
737512 GTTAGTGCGACGGCGTGTTGT-----G-T--
1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
737535 GTTAGCGCGACGGCGTGTTGT-----G-T--
1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
737558 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
*
737589 GTTAGCGCGACGGCGTATTGTGCAAAGTTGC
1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
737620 GTTAGCGCGACGGCGTGTTGT-----G-T--
1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
* *
737643 GTTAGCACGACGGCGTGTTATGCAAAGTTGC
1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
*
737674 GTTAGAGCGACGGCGTGTTGTG
1 GTTAGCGCGACGGCGTGTTGTG
737696 TGTTAGCGCG
Statistics
Matches: 419, Mismatches: 17, Indels: 68
0.83 0.03 0.13
Matches are distributed among these distances:
23 124 0.30
24 2 0.00
25 4 0.01
26 4 0.01
28 4 0.01
29 4 0.01
30 2 0.00
31 275 0.66
ACGTcount: A:0.15, C:0.18, G:0.39, T:0.28
Consensus pattern (31 bp):
GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
Found at i:737286 original size:23 final size:23
Alignment explanation
Indices: 737256--737324 Score: 138
Period size: 23 Copynumber: 3.0 Consensus size: 23
737246 TGCAAAGTTT
737256 TGTTAGCGCGACGGCGTGTTGTG
1 TGTTAGCGCGACGGCGTGTTGTG
737279 TGTTAGCGCGACGGCGTGTTGTG
1 TGTTAGCGCGACGGCGTGTTGTG
737302 TGTTAGCGCGACGGCGTGTTGTG
1 TGTTAGCGCGACGGCGTGTTGTG
737325 CAAAGTTGCG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.09, C:0.17, G:0.43, T:0.30
Consensus pattern (23 bp):
TGTTAGCGCGACGGCGTGTTGTG
Found at i:737370 original size:85 final size:85
Alignment explanation
Indices: 737280--737695 Score: 625
Period size: 85 Copynumber: 4.9 Consensus size: 85
737270 CGTGTTGTGT
737280 GTTAGCGCGACGGCGTGTTGTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGCGTTAGCGCGAC
1 GTTAGCGCGACGGCGTGTTGTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGCGTTAGCGCGAC
737345 GGCGTGTTGTGCAAAGTTGC
66 GGCGTGTTGTGCAAAGTTGC
737365 GTTAGCGCGACGGCGTGTTGTGTGTTAGCGCGGA-GGCGTGTTGTGCAAAGTTGCGTTAGCGCGA
1 GTTAGCGCGACGGCGTGTTGTGTGTTAGCGC-GACGGCGTGTTGTGCAAAGTTGCGTTAGCGCGA
*
737429 CGGCGTGTTGTGCAAAATTGC
65 CGGCGTGTTGTGCAAAGTTGC
*
737450 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTATGCAAAGTTGCGTT
1 GTTAGCGCGACGGCGTG-T-T-----G-TGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGCGTT
*
737515 AGTGCGACGGCGTGTTGT-----G-T--
58 AGCGCGACGGCGTGTTGTGCAAAGTTGC
737535 GTTAGCGCGACGGCGTGTTGTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGCGTTAGCGCGAC
1 GTTAGCGCGACGGCGTGTTGTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGCGTTAGCGCGAC
*
737600 GGCGTATTGTGCAAAGTTGC
66 GGCGTGTTGTGCAAAGTTGC
* * *
737620 GTTAGCGCGACGGCGTGTTGTGTGTTAGCACGACGGCGTGTTATGCAAAGTTGCGTTAGAGCGAC
1 GTTAGCGCGACGGCGTGTTGTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGCGTTAGCGCGAC
737685 GGCGTGTTGTG
66 GGCGTGTTGTG
737696 TGTTAGCGCG
Statistics
Matches: 302, Mismatches: 11, Indels: 36
0.87 0.03 0.10
Matches are distributed among these distances:
77 52 0.17
78 1 0.00
82 1 0.00
83 2 0.01
84 1 0.00
85 187 0.62
86 3 0.01
87 2 0.01
92 3 0.01
93 50 0.17
ACGTcount: A:0.15, C:0.18, G:0.39, T:0.28
Consensus pattern (85 bp):
GTTAGCGCGACGGCGTGTTGTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGCGTTAGCGCGAC
GGCGTGTTGTGCAAAGTTGC
Found at i:737391 original size:23 final size:23
Alignment explanation
Indices: 737365--737409 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
737355 GCAAAGTTGC
737365 GTTAGCGC-GACGGCGTGTTGTGT
1 GTTAGCGCGGA-GGCGTGTTGTGT
737388 GTTAGCGCGGAGGCGTGTTGTG
1 GTTAGCGCGGAGGCGTGTTGTG
737410 CAAAGTTGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.09, C:0.16, G:0.47, T:0.29
Consensus pattern (23 bp):
GTTAGCGCGGAGGCGTGTTGTGT
Done.