Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 12862612
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 56
Found at i:5080164 original size:22 final size:22
Alignment explanation
Indices: 5080127--5080169 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5080117 TGCATCACGA
5080127 AAAACCTATAAAAAAAGAAAAT
1 AAAACCTATAAAAAAAGAAAAT
*
5080149 AAAACC-ATAAATAAAATAAAA
1 AAAACCTATAAA-AAAAGAAAA
5080170 ATACTAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.74, C:0.09, G:0.02, T:0.14
Consensus pattern (22 bp):
AAAACCTATAAAAAAAGAAAAT
Found at i:5081566 original size:41 final size:39
Alignment explanation
Indices: 5081539--5081648 Score: 114
Period size: 41 Copynumber: 2.7 Consensus size: 39
5081529 CTACATATAA
5081539 GTACTTTAGTGGCATTTTTATACAAACGCCGCCATAAAATC
1 GTACTTTAGTGGCATTTTTA-ACAAACGCCGCCATAAAA-C
* *
5081580 GTACTTTAGTGGCGTTTTTAATCAAACGCCG-CAAAAGAATC
1 GTACTTTAGTGGCATTTTTAA-CAAACGCCGCCATAA-AA-C
* *
5081621 ATTCTTTAGTGGCATTTTTGAAACAAAC
1 GTACTTTAGTGGCATTTTT--AACAAAC
5081649 ATTGCAATAG
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
40 5 0.08
41 48 0.80
42 5 0.08
43 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (39 bp):
GTACTTTAGTGGCATTTTTAACAAACGCCGCCATAAAAC
Found at i:5084312 original size:66 final size:63
Alignment explanation
Indices: 5084240--5084362 Score: 176
Period size: 66 Copynumber: 1.9 Consensus size: 63
5084230 AATGCATTTT
*
5084240 ATGCATCGATGCACTCAGGT-TTTTTATGAAAACACCGAATGCATTTTATGCATCGATGCATAGA
1 ATGCATCGATGCACTCA-GTCTTGTT-TG-AAACACCGAATGCA-TTTATGCATCGATGCATAGA
5084304 CC
62 CC
* *
5084306 ATGCATCGATGCACTCAGTCTTGTTTGAAACATCGAATGCATTTATGCATTGATGCA
1 ATGCATCGATGCACTCAGTCTTGTTTGAAACACCGAATGCATTTATGCATCGATGCA
5084363 CCCTTAGTGC
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
63 15 0.28
64 13 0.25
65 4 0.08
66 21 0.40
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (63 bp):
ATGCATCGATGCACTCAGTCTTGTTTGAAACACCGAATGCATTTATGCATCGATGCATAGACC
Found at i:5090181 original size:21 final size:21
Alignment explanation
Indices: 5090157--5090213 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 21
5090147 TTGTGCATAA
5090157 TGCATCGATACACTATGAATG
1 TGCATCGATACACTATGAATG
* *
5090178 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGAT--A-CACTATGAATG
5090202 TGCATCGATACA
1 TGCATCGATACA
5090214 TCATGAAGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 10 0.33
22 1 0.03
23 1 0.03
24 18 0.60
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (21 bp):
TGCATCGATACACTATGAATG
Found at i:5092957 original size:64 final size:64
Alignment explanation
Indices: 5092883--5093033 Score: 225
Period size: 64 Copynumber: 2.4 Consensus size: 64
5092873 ACACACCATT
* *
5092883 TCGAATGCATTTTATGCATCGATGCAC-TGCCATGCATCGATGCACTCAGG-TTTTTATAAAAAC
1 TCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTGTT-T-AAAAC
5092946 A
64 A
* * *
5092947 TCGAAAGCATTTTATGCATCGACGCACATACCATGCATCGATGCACTCAGGCTTGTTTGAAACA
1 TCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTGTTTAAAACA
5093011 TCGAATGCATTTTATGCATCGAT
1 TCGAATGCATTTTATGCATCGAT
5093034 TCATTAAGTG
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
64 51 0.65
65 23 0.29
66 4 0.05
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (64 bp):
TCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTGTTTAAAACA
Found at i:5094115 original size:31 final size:31
Alignment explanation
Indices: 5094075--5094181 Score: 110
Period size: 31 Copynumber: 3.4 Consensus size: 31
5094065 AGGTCCCGAA
*
5094075 GAACCTAGGTAAATTGTCCATATGTTCCTTG
1 GAACATAGGTAAATTGTCCATATGTTCCTTG
* *
5094106 GAACATAGGTATACTGTCCATATG-T-CTTG
1 GAACATAGGTAAATTGTCCATATGTTCCTTG
* * * *
5094135 AAAGACATAGGTAATTCTGTCCATATGTTCCGTA
1 -GA-ACATAGGTAAAT-TGTCCATATGTTCCTTG
5094169 GAACATAGGTAAA
1 GAACATAGGTAAA
5094182 CCCTCGACTC
Statistics
Matches: 60, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
29 4 0.07
30 2 0.03
31 30 0.50
32 20 0.33
33 2 0.03
34 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (31 bp):
GAACATAGGTAAATTGTCCATATGTTCCTTG
Found at i:5098432 original size:32 final size:31
Alignment explanation
Indices: 5098328--5098452 Score: 112
Period size: 31 Copynumber: 4.0 Consensus size: 31
5098318 AACCTCAGCA
* ** *
5098328 ACTGTCCATAGGTCCCGAAGAACCTAGGTAA-
1 ACTGTCCATATGTCCTTAA-AACATAGGTAAT
5098359 ACTGTCCATATGTCCCTTAAAACATAGGT-AT
1 ACTGTCCATATGT-CCTTAAAACATAGGTAAT
5098390 ACTGTCCATATGT-CTTGAAAGACATAGGTAAT
1 ACTGTCCATATGTCCTT-AAA-ACATAGGTAAT
* * * *
5098422 TCTGTCCATATGTTCCGTAGAACATAAGTAA
1 ACTGTCCATATG-TCCTTAAAACATAGGTAA
5098453 ACCCTCGACT
Statistics
Matches: 79, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
29 3 0.04
30 4 0.05
31 41 0.52
32 26 0.33
33 3 0.04
34 2 0.03
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.29
Consensus pattern (31 bp):
ACTGTCCATATGTCCTTAAAACATAGGTAAT
Found at i:5102397 original size:12 final size:14
Alignment explanation
Indices: 5102369--5102400 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
5102359 CACACATACA
5102369 TCATATCCTATAAC
1 TCATATCCTATAAC
5102383 TCATATCC-A-AAC
1 TCATATCCTATAAC
5102395 TCATAT
1 TCATAT
5102401 ATCAGTTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.50
13 1 0.06
14 8 0.44
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.34
Consensus pattern (14 bp):
TCATATCCTATAAC
Found at i:5102611 original size:30 final size:31
Alignment explanation
Indices: 5102572--5102638 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
5102562 GAATGACCTA
* * * *
5102572 TCCAGAGGTCATAAAGAACCTCGG-CAACTG
1 TCCATAGGTCACAAAAAACCTAGGTCAACTG
*
5102602 TCCATAGGTCCCAAAAAACCTAGGTCAACTG
1 TCCATAGGTCACAAAAAACCTAGGTCAACTG
5102633 TCCATA
1 TCCATA
5102639 TGTCCCTTAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 19 0.61
31 12 0.39
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.19
Consensus pattern (31 bp):
TCCATAGGTCACAAAAAACCTAGGTCAACTG
Found at i:5102668 original size:31 final size:31
Alignment explanation
Indices: 5102630--5102722 Score: 93
Period size: 31 Copynumber: 2.9 Consensus size: 31
5102620 CCTAGGTCAA
5102630 CTGTCCATATGTCCCTTAGAACATAGGTATATT
1 CTGTCCATATGT-CCTTAGAACATAGGTA-ATT
*
5102663 -T-TCCATATGT-CTTGAAAGACATAGGTAATT
1 CTGTCCATATGTCCTT-AGA-ACATAGGTAATT
* *
5102693 CTGCCCATATGTTCCGTAGAACATAGGTAA
1 CTGTCCATATG-TCCTTAGAACATAGGTAA
5102723 ACCCTCGACT
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
29 3 0.06
30 5 0.10
31 19 0.38
32 18 0.36
33 3 0.06
34 2 0.04
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (31 bp):
CTGTCCATATGTCCTTAGAACATAGGTAATT
Found at i:5107165 original size:19 final size:20
Alignment explanation
Indices: 5107141--5107191 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
5107131 AATGACCAAT
5107141 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* * *
5107160 AAAATCGCAAAGCGATTTAG
1 AAAATCGCAACGCGATATAC
5107180 AAAATCGCAACG
1 AAAATCGCAACG
5107192 TTAAAAAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.45, C:0.22, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:5107201 original size:20 final size:20
Alignment explanation
Indices: 5107178--5107231 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
5107168 AAAGCGATTT
*
5107178 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
* *
5107198 AGAAAATCGCAATGGTCAAA
1 AGAAAATCGCAACGGTAAAA
5107218 AGAAAATCGCAACG
1 AGAAAATCGCAACG
5107232 CGAGCTTCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.52, C:0.17, G:0.19, T:0.13
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:5107391 original size:6 final size:6
Alignment explanation
Indices: 5107380--5107436 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
5107370 TCTCGTCTCG
5107380 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
5107428 GGTCGT GGT
1 GGTCGT GGT
5107437 AATACGTGTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:5107539 original size:20 final size:20
Alignment explanation
Indices: 5107514--5107557 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
5107504 TTTTTAACTA
*
5107514 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
5107534 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
5107554 TTCT
1 TTCT
5107558 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:5107567 original size:20 final size:20
Alignment explanation
Indices: 5107546--5107775 Score: 248
Period size: 20 Copynumber: 11.3 Consensus size: 20
5107536 CTTTTTAACG
* *
5107546 TTGCGATTTTCTAAATCGCG
1 TTGCGATTCTCTAAATCGCA
*
5107566 TTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCA
*
5107586 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCA
* *
5107606 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCA
* *
5107626 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCA
5107646 TTGCGATTTTCTTCTAAATCG--
1 TTGCGA--TTC-TCTAAATCGCA
* * *
5107667 TTGCAACTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCA
*
5107687 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCA
*
5107707 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCA
* *
5107727 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTAAATCGCA
*
5107747 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TCTAAATCGCA
5107770 TTGCGA
1 TTGCGA
5107776 ACTTGGAAGC
Statistics
Matches: 181, Mismatches: 21, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
18 8 0.04
19 2 0.01
20 139 0.77
21 5 0.03
22 6 0.03
23 21 0.12
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (20 bp):
TTGCGATTCTCTAAATCGCA
Found at i:5107700 original size:101 final size:101
Alignment explanation
Indices: 5107554--5107767 Score: 347
Period size: 101 Copynumber: 2.1 Consensus size: 101
5107544 CGTTGCGATT
* * * *
5107554 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTC
1 TTCTAAAT--CGTTGCAACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATA
* * *
5107619 AGTCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTC
64 AATCGCATTGCGATTCTATCAATCGCATTGCGATTTTC
5107657 TTCTAAATCGTTGCAACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATAAA
1 TTCTAAATCGTTGCAACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATAAA
5107722 TCGCATTGCGATTCTATCAATCGCATTGCGATTTTC
66 TCGCATTGCGATTCTATCAATCGCATTGCGATTTTC
5107758 TTCTAAATCG
1 TTCTAAATCG
5107768 CGTTGCGAAC
Statistics
Matches: 104, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
101 96 0.92
103 8 0.08
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (101 bp):
TTCTAAATCGTTGCAACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATAAA
TCGCATTGCGATTCTATCAATCGCATTGCGATTTTC
Found at i:5107814 original size:20 final size:20
Alignment explanation
Indices: 5107789--5107842 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
5107779 TGGAAGCTCG
*
5107789 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAA
*
5107809 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTTTTGAA
5107829 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
5107843 AAATCGCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.19, G:0.19, T:0.52
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAA
Found at i:5109818 original size:28 final size:28
Alignment explanation
Indices: 5109753--5109820 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
5109743 ATCACTGTTG
* *
5109753 ATTTCAAGCACTGGCTCGATGACATAAT
1 ATTTCAAGTACTGGCTCGATCACATAAT
* *
5109781 ATTTCTAGTATTGGCTCGATCACATAAT
1 ATTTCAAGTACTGGCTCGATCACATAAT
*
5109809 GTTTCAAGTACT
1 ATTTCAAGTACT
5109821 AGCTTGACGA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (28 bp):
ATTTCAAGTACTGGCTCGATCACATAAT
Found at i:5114891 original size:2 final size:2
Alignment explanation
Indices: 5114848--5114876 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5114838 GATGTGTAAG
5114848 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5114877 CATAAAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5118581 original size:24 final size:24
Alignment explanation
Indices: 5118533--5118579 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
5118523 TAGATTTAAA
*
5118533 AGACATGTTAGCCTCCTCGATTTT
1 AGACATGTTAACCTCCTCGATTTT
5118557 AGACA-GTTAACCTCCTCGATTTT
1 AGACATGTTAACCTCCTCGATTTT
5118580 TATATGGCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (24 bp):
AGACATGTTAACCTCCTCGATTTT
Found at i:5122384 original size:76 final size:76
Alignment explanation
Indices: 5122274--5122471 Score: 344
Period size: 76 Copynumber: 2.6 Consensus size: 76
5122264 ATTTTAAATA
*
5122274 TTATATTTTATCTTTGTTTTAGGTATTTTTGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
5122339 GGATATTATTT
66 GGATATTATTT
*
5122350 TTATATGTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
5122415 GGATATTATTT
66 GGATATTATTT
* *
5122426 TTATATTTTTATCTTTGTTTTAGATATTTTAATTTAAATA-GTTTTA
1 TTATA-TTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTA
5122472 ATTGTTTTAA
Statistics
Matches: 116, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
76 85 0.73
77 31 0.27
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (76 bp):
TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
GGATATTATTT
Found at i:5122484 original size:77 final size:77
Alignment explanation
Indices: 5122249--5122471 Score: 342
Period size: 76 Copynumber: 2.9 Consensus size: 77
5122239 AATTAAACGC
* *
5122249 AAGTTTTAGGATAATATTTTAAATATTATATTTTATCTTTGTTTTAGGTATTTTTGTTTAAATAG
1 AAGTTTTAGGATATTATTTT---TA-TAT-TTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAG
5122314 GTTTTAGTATTTTAATT
61 GTTTTAGTATTTTAATT
*
5122331 AAGTTTTAGGATATTATTTTTATA-TGTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT
1 AAGTTTTAGGATATTATTTTTATATTTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT
5122395 AGTATTTTAATT
66 AGTATTTTAATT
* *
5122407 AAGTTTTAGGATATTATTTTTATATTTTTATCTTTGTTTTAGATATTTTAATTTAAATA-GTTTT
1 AAGTTTTAGGATATTATTTTTATATTTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT
5122471 A
66 A
5122472 ATTGTTTTAA
Statistics
Matches: 134, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
76 80 0.60
77 31 0.23
78 2 0.01
79 2 0.01
82 19 0.14
ACGTcount: A:0.28, C:0.01, G:0.12, T:0.58
Consensus pattern (77 bp):
AAGTTTTAGGATATTATTTTTATATTTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT
AGTATTTTAATT
Found at i:5123136 original size:16 final size:16
Alignment explanation
Indices: 5123097--5123138 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
5123087 CCCAATTCAG
5123097 TTATTTTATTTATTTA
1 TTATTTTATTTATTTA
5123113 TT-TGTTTATTTAATTT-
1 TTAT-TTTATTT-ATTTA
5123129 TTATTTTATT
1 TTATTTTATT
5123139 ATACTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.04
16 17 0.74
17 5 0.22
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (16 bp):
TTATTTTATTTATTTA
Found at i:5123222 original size:19 final size:20
Alignment explanation
Indices: 5123198--5123243 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
5123188 TATTTATTAG
* *
5123198 TTTATTATTTTCTCTTTTA-
1 TTTATTATTATCTATTTTAT
5123217 TTTATTATTATCTATTTTAT
1 TTTATTATTATCTATTTTAT
5123237 TTTATTA
1 TTTATTA
5123244 AATCTTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTATTATTATCTATTTTAT
Found at i:5123306 original size:21 final size:22
Alignment explanation
Indices: 5123274--5123315 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
5123264 GAATTCTATC
5123274 TTTTTCTAAAATCA-AAAAACA
1 TTTTTCTAAAATCACAAAAACA
5123295 TTTTTACT-AAATCACAAAAAC
1 TTTTT-CTAAAATCACAAAAAC
5123316 CATAATCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (22 bp):
TTTTTCTAAAATCACAAAAACA
Found at i:5128651 original size:5 final size:5
Alignment explanation
Indices: 5128641--5128696 Score: 53
Period size: 5 Copynumber: 11.4 Consensus size: 5
5128631 TCGTTCTATT
* * **
5128641 TTTTA TTTTA TTTCA -TTT- TTTCA TTTTA TTTCG TTTTA TTTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA
5128690 TTTTA TT
1 TTTTA TT
5128697 AGAAAACTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
4 4 0.10
5 31 0.77
6 5 0.12
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:5128666 original size:18 final size:17
Alignment explanation
Indices: 5128638--5128693 Score: 69
Period size: 18 Copynumber: 3.3 Consensus size: 17
5128628 ATTTCGTTCT
5128638 ATTTTTTATTTTATTTC
1 ATTTTTTATTTTATTTC
5128655 ATTTTTTCATTTTATTTC
1 ATTTTTT-ATTTTATTTC
* * *
5128673 GTTTTAT-TTTTATTTT
1 ATTTTTTATTTTATTTC
5128689 ATTTT
1 ATTTT
5128694 ATTAGAAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
16 12 0.35
17 7 0.21
18 15 0.44
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (17 bp):
ATTTTTTATTTTATTTC
Found at i:5131292 original size:20 final size:20
Alignment explanation
Indices: 5131244--5131293 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
5131234 TTAATATTTA
* * *
5131244 TTATTTTCTTATTTTCTCTT
1 TTATTTTATTATTATCTATT
5131264 TTA-TTTATTATTATCTATT
1 TTATTTTATTATTATCTATT
5131283 TTATTTTATTA
1 TTATTTTATTA
5131294 AATCTTTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (20 bp):
TTATTTTATTATTATCTATT
Found at i:5140786 original size:22 final size:22
Alignment explanation
Indices: 5140731--5140786 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
5140721 AATCCAACCG
*
5140731 TTTGTAACTCATGTAATAAAGC
1 TTTGTAACTCTTGTAATAAAGC
* *
5140753 TTTGTAAGTCTTGTATTAAAGC
1 TTTGTAACTCTTGTAATAAAGC
5140775 TTTGTAACTCTT
1 TTTGTAACTCTT
5140787 ACATTGATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (22 bp):
TTTGTAACTCTTGTAATAAAGC
Found at i:5147185 original size:2 final size:2
Alignment explanation
Indices: 5147173--5147202 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5147163 ACTTATATGT
5147173 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5147203 GTTTTGTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5147280 original size:22 final size:21
Alignment explanation
Indices: 5147237--5147292 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
5147227 CCTTACTTTT
5147237 TTATTACTATATTTATT-T-TTA
1 TTATTA-TATATTT-TTCTATTA
5147258 TTATT-TA-ATTTTTCTATTA
1 TTATTATATATTTTTCTATTA
5147277 TTATTATATATTTTTC
1 TTATTATATATTTTTC
5147293 CCTCTCTCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 2 0.06
18 5 0.16
19 10 0.32
20 2 0.06
21 12 0.39
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (21 bp):
TTATTATATATTTTTCTATTA
Found at i:5158107 original size:44 final size:44
Alignment explanation
Indices: 5158044--5158131 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
5158034 ATAAATATTT
*
5158044 CGTTTAGGATAAAAACCCGAGAGGGCGCCCTAAATGGAAAAAAA
1 CGTTTAGGATAAAAACCCGAAAGGGCGCCCTAAATGGAAAAAAA
* * *
5158088 CGTTTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAA
1 CGTTTAGGATAAAAACCCGAAAGGGCGCCCTAAATGGAAAAAAA
5158132 AAATAGAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.42, C:0.18, G:0.25, T:0.15
Consensus pattern (44 bp):
CGTTTAGGATAAAAACCCGAAAGGGCGCCCTAAATGGAAAAAAA
Found at i:5159172 original size:98 final size:98
Alignment explanation
Indices: 5158910--5159688 Score: 1271
Period size: 98 Copynumber: 7.8 Consensus size: 98
5158900 TTACCCAGGT
*
5158910 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGGCGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
5158975 GGACCGCTGGTTGTCAACAGACATTTCTCAATTTCAGAGC
66 GGACCGCTGGTTGTCAATA-A-A-----CAATTTCAGAGC
5159015 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
5159080 GGACCGCTGGTTGTCAATAAACAATTTCAGGGC
66 GGACCGCTGGTTGTCAATAAACAATTTCAGAGC
5159113 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
5159178 GGACCGCTGGTTGTCAATAAACAATTTCAG-GAC
66 GGACCGCTGGTTGTCAATAAACAATTTCAGAG-C
* *
5159211 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTTAACTTCATGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
5159276 GGACCGCTGGTTGTCAATAAACAATTTCAGGGC
66 GGACCGCTGGTTGTCAATAAACAATTTCAGAGC
5159309 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
5159374 GGGCCGCTGGTTGTCAATAAACAATTTCAGAGC
66 GGACCGCTGGTTGTCAATAAACAATTTCAGAGC
5159407 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
5159472 GGACCGCTGGTTGTCAATAAACAATTTC----C
66 GGACCGCTGGTTGTCAATAAACAATTTCAGAGC
5159501 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
5159566 GGACCGCTGGTTGTCAATAAACAACTTCTTAATTTCAGAGC
66 GGACCGCTGGTTGTCAAT--A-AA---C--AATTTCAGAGC
* * * * *
5159607 CAATTTCAACTTCACAACGAAGGAGATTGGGCCCCAGACAACACAAGTTCAACTTCACAACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
5159672 GGACCGCTGGTTGTCAA
66 GGACCGCTGGTTGTCAA
5159689 CAAGTAATTT
Statistics
Matches: 645, Mismatches: 15, Indels: 27
0.94 0.02 0.04
Matches are distributed among these distances:
94 84 0.13
96 1 0.00
97 3 0.00
98 387 0.60
99 1 0.00
100 1 0.00
102 6 0.01
103 1 0.00
104 1 0.00
105 82 0.13
106 78 0.12
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.22
Consensus pattern (98 bp):
CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
GGACCGCTGGTTGTCAATAAACAATTTCAGAGC
Found at i:5159685 original size:106 final size:106
Alignment explanation
Indices: 5159500--5159735 Score: 337
Period size: 106 Copynumber: 2.2 Consensus size: 106
5159490 AAACAATTTC
* * * *
5159500 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGAGATTGGACCCCAGACAACACAAGTTCAACTTCACAACGAA
* **
5159565 GGGACCGCTGGTTGTCAATAAACAACTTCTTAATTTCAGAG
66 GGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAG
*
5159606 CCAATTTCAACTTCACAACGAAGGAGATTGGGCCCCAGACAACACAAGTTCAACTTCACAACGAA
1 CCAATTTCAACTTCACAACGAAGGAGATTGGACCCCAGACAACACAAGTTCAACTTCACAACGAA
** * ** *
5159671 GGGACCGCTGGTTGTCAACAAGTAATTTCCCGGTTTTAGAG
66 GGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAG
*
5159712 CCAATTTCAACTTCACAGCGAAGG
1 CCAATTTCAACTTCACAACGAAGG
5159736 CCTCGAAACA
Statistics
Matches: 115, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
106 115 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.22
Consensus pattern (106 bp):
CCAATTTCAACTTCACAACGAAGGAGATTGGACCCCAGACAACACAAGTTCAACTTCACAACGAA
GGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAG
Found at i:5177967 original size:74 final size:75
Alignment explanation
Indices: 5177887--5178046 Score: 261
Period size: 74 Copynumber: 2.1 Consensus size: 75
5177877 TTAAATGACT
5177887 AGGGGTATCGGTA-CTCATTGGGCATTCTGTTTTTCTTGGAGCCAAAATTGGCATAGGGGTATCG
1 AGGGGTATCGGTATC-CATTGGGCATTCTGTTTTTCTTGGAGCCAAAATTGGCATAGGGGTATCG
5177951 GT-ACCCTATG
65 GTAACCCTATG
* * *
5177961 AGGGGTACCGGTATCCATTTGGCATTCTGTTTTTCTTGGAGCCAAAATTGGCATAGGGGTATCGT
1 AGGGGTATCGGTATCCATTGGGCATTCTGTTTTTCTTGGAGCCAAAATTGGCATAGGGGTATCGG
5178026 TACACCCTATG
66 TA-ACCCTATG
5178037 AGGGGTATCG
1 AGGGGTATCG
5178047 TTACCTCCGT
Statistics
Matches: 79, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
74 61 0.77
75 1 0.01
76 17 0.22
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (75 bp):
AGGGGTATCGGTATCCATTGGGCATTCTGTTTTTCTTGGAGCCAAAATTGGCATAGGGGTATCGG
TAACCCTATG
Found at i:5181501 original size:35 final size:34
Alignment explanation
Indices: 5181461--5181575 Score: 88
Period size: 35 Copynumber: 3.2 Consensus size: 34
5181451 TATTCAAATG
5181461 GTTTGGTAA-CCAACTTTGAAAAAATGGTTTTCAAA
1 GTTTGGTAATCCAACTTTG--AAAATGGTTTTCAAA
****
5181496 GTTTGGTAAATGTTTCTTTGAAAATGGTTTTCAAA
1 GTTTGGT-AATCCAACTTTGAAAATGGTTTTCAAA
**** *
5181531 GTTTGGTAAATGTTTCTTTGAAAAATAGTTTTTCAAA
1 GTTTGGT-AATCCAACTTTG-AAAAT-GGTTTTCAAA
5181568 GTTTGGTA
1 GTTTGGTA
5181576 GATGTTTGTT
Statistics
Matches: 71, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
35 42 0.59
36 8 0.11
37 21 0.30
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (34 bp):
GTTTGGTAATCCAACTTTGAAAATGGTTTTCAAA
Found at i:5181506 original size:21 final size:21
Alignment explanation
Indices: 5181482--5181542 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
5181472 AACTTTGAAA
5181482 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
5181503 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
5181517 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
5181538 AAATG
1 AAATG
5181543 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:5181515 original size:37 final size:36
Alignment explanation
Indices: 5181474--5181593 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
5181464 TGGTAACCAA
5181474 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
5181511 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
5181546 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
5181583 -GTTGAAAAATG
1 CTTTGAAAAATG
5181594 ATAATGGGAT
Statistics
Matches: 78, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
35 36 0.46
36 14 0.18
37 28 0.36
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:5186079 original size:21 final size:21
Alignment explanation
Indices: 5186055--5186115 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
5186045 AACTTTGAAA
5186055 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
5186076 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
5186090 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
5186111 AAATG
1 AAATG
5186116 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:5186146 original size:37 final size:37
Alignment explanation
Indices: 5186047--5186165 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 37
5186037 TGGTAACCAA
*
5186047 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATTGGTTTTCAAAGTTTGGTAAATGTTT
5186084 CTTTG-AAAA-TGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATTGGTTTTCAAAGTTTGGTAAATGTTT
* *
5186119 CTTTGAAAAATTGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATTGGTTTTCAAAGTTTGGTAAATGTTT
*
5186156 -GTTGAAAAAT
1 CTTTGAAAAAT
5186166 GATAATGGGA
Statistics
Matches: 77, Mismatches: 3, Indels: 5
0.91 0.04 0.06
Matches are distributed among these distances:
35 31 0.40
36 17 0.22
37 29 0.38
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (37 bp):
CTTTGAAAAATTGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:5186562 original size:38 final size:38
Alignment explanation
Indices: 5186504--5186683 Score: 148
Period size: 38 Copynumber: 4.7 Consensus size: 38
5186494 TTCCCAACAA
** * *
5186504 AACCAACTCAAACAATGGCAAATAATAAGCCAAAACGG
1 AACCAACTCACGCAAAGGCAAATAATAAGCCAAAGCGG
* ** * *
5186542 AACCAACTCAGGCAAAGGCAAATAAGT-TTCCAAATCGC
1 AACCAACTCACGCAAAGGCAAATAA-TAAGCCAAAGCGG
* * *
5186580 AACCAACTCACACAAAGGAAAATAATAGGCCAAAGCGG
1 AACCAACTCACGCAAAGGCAAATAATAAGCCAAAGCGG
** * * * * **
5186618 AA-CAAGAACATGTAAAGGAAAATAATAGGCCAAAGCAA
1 AACCAA-CTCACGCAAAGGCAAATAATAAGCCAAAGCGG
5186656 AACCAACTCACGCAAAGGCAAATAATAA
1 AACCAACTCACGCAAAGGCAAATAATAA
5186684 ATTTAATGTT
Statistics
Matches: 111, Mismatches: 27, Indels: 8
0.76 0.18 0.05
Matches are distributed among these distances:
37 4 0.04
38 103 0.93
39 4 0.04
ACGTcount: A:0.51, C:0.22, G:0.16, T:0.11
Consensus pattern (38 bp):
AACCAACTCACGCAAAGGCAAATAATAAGCCAAAGCGG
Found at i:5186635 original size:76 final size:76
Alignment explanation
Indices: 5186501--5186683 Score: 190
Period size: 76 Copynumber: 2.4 Consensus size: 76
5186491 TATTTCCCAA
* * ** *
5186501 CAAAACCAACTCAAACAATGGCAAATAATAAGCCAAAACGGAACCAACTCAGGCAAAGGCAAATA
1 CAAAACCAACTCACACAAAGGCAAATAATAAGCCAAAACGGAACCAAAACAGGCAAAGGAAAATA
** *
5186566 AGT-TTCCAAAT
66 A-TAGGCCAAAG
** * * * * *
5186577 CGCAACCAACTCACACAAAGGAAAATAATAGGCCAAAGCGGAA-CAAGAACATGTAAAGGAAAAT
1 CAAAACCAACTCACACAAAGGCAAATAATAAGCCAAAACGGAACCAA-AACAGGCAAAGGAAAAT
5186641 AATAGGCCAAAG
65 AATAGGCCAAAG
*
5186653 CAAAACCAACTCACGCAAAGGCAAATAATAA
1 CAAAACCAACTCACACAAAGGCAAATAATAA
5186684 ATTTAATGTT
Statistics
Matches: 85, Mismatches: 20, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
75 4 0.05
76 81 0.95
ACGTcount: A:0.51, C:0.22, G:0.15, T:0.11
Consensus pattern (76 bp):
CAAAACCAACTCACACAAAGGCAAATAATAAGCCAAAACGGAACCAAAACAGGCAAAGGAAAATA
ATAGGCCAAAG
Found at i:5186652 original size:18 final size:18
Alignment explanation
Indices: 5186592--5186657 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 18
5186582 CCAACTCACA
5186592 CAAAGGAAAATAATAGGC
1 CAAAGGAAAATAATAGGC
* * *
5186610 CAAAGCGGAACAAGAACATG-
1 CAAA--GGAA-AATAATAGGC
*
5186630 TAAAGGAAAATAATAGGC
1 CAAAGGAAAATAATAGGC
*
5186648 CAAAGCAAAA
1 CAAAGGAAAA
5186658 CCAACTCACG
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
17 6 0.17
18 16 0.46
20 7 0.20
21 6 0.17
ACGTcount: A:0.56, C:0.14, G:0.21, T:0.09
Consensus pattern (18 bp):
CAAAGGAAAATAATAGGC
Found at i:5190775 original size:38 final size:38
Alignment explanation
Indices: 5190729--5190983 Score: 235
Period size: 38 Copynumber: 6.7 Consensus size: 38
5190719 GATAGAATGG
*
5190729 AACCAACTCGCGCAAAGGAAAATAATAGGCCAAAGCAA
1 AACCAACTCACGCAAAGGAAAATAATAGGCCAAAGCAA
* ** * * * * **
5190767 AACGAACTCAAACAATGGCAAATAATAAGCCAAAACGG
1 AACCAACTCACGCAAAGGAAAATAATAGGCCAAAGCAA
* * * ** * **
5190805 AACCAACTCAGGCTAAGGCAAATAAGT-TTCCAAATCGG
1 AACCAACTCACGCAAAGGAAAATAA-TAGGCCAAAGCAA
* **
5190843 AACCAACTCACACAAAGGAAAATAATAGGCCAAAGCGG
1 AACCAACTCACGCAAAGGAAAATAATAGGCCAAAGCAA
* * *
5190881 AA-CAAGATCATGTAAAGGAAAATAATAGGCCAAAGCAA
1 AACCAA-CTCACGCAAAGGAAAATAATAGGCCAAAGCAA
* *
5190919 AACCAACTCACGCAAAGCATAATAATAGGCCAAAGCAA
1 AACCAACTCACGCAAAGGAAAATAATAGGCCAAAGCAA
*
5190957 AACCAACTCACGCAAAGGCAAATAATA
1 AACCAACTCACGCAAAGGAAAATAATA
5190984 AATTTAATGT
Statistics
Matches: 174, Mismatches: 39, Indels: 8
0.79 0.18 0.04
Matches are distributed among these distances:
37 4 0.02
38 166 0.95
39 4 0.02
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.11
Consensus pattern (38 bp):
AACCAACTCACGCAAAGGAAAATAATAGGCCAAAGCAA
Found at i:5190920 original size:18 final size:18
Alignment explanation
Indices: 5190894--5190958 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 18
5190884 AAGATCATGT
*
5190894 AAAGGAAAATAATAGGCC
1 AAAGCAAAATAATAGGCC
* *
5190912 AAAGCAAAACCAACTCACG-C
1 AAAGCAAAA-TAA-T-AGGCC
*
5190932 AAAGCATAATAATAGGCC
1 AAAGCAAAATAATAGGCC
5190950 AAAGCAAAA
1 AAAGCAAAA
5190959 CCAACTCACG
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
17 2 0.06
18 18 0.50
19 4 0.11
20 10 0.28
21 2 0.06
ACGTcount: A:0.55, C:0.20, G:0.15, T:0.09
Consensus pattern (18 bp):
AAAGCAAAATAATAGGCC
Found at i:5190936 original size:20 final size:20
Alignment explanation
Indices: 5190911--5190978 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
5190901 AATAATAGGC
5190911 CAAAGCAAAACCAACTCACG
1 CAAAGCAAAACCAACTCACG
* * *
5190931 CAAAGCATAA-TAA-T-AGG
1 CAAAGCAAAACCAACTCACG
5190948 CCAAAGCAAAACCAACTCACG
1 -CAAAGCAAAACCAACTCACG
5190969 CAAAGGCAAA
1 CAAA-GCAAA
5190979 TAATAAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
17 2 0.05
18 10 0.27
19 4 0.11
20 14 0.38
21 7 0.19
ACGTcount: A:0.51, C:0.28, G:0.13, T:0.07
Consensus pattern (20 bp):
CAAAGCAAAACCAACTCACG
Found at i:5190943 original size:114 final size:114
Alignment explanation
Indices: 5190727--5190983 Score: 268
Period size: 114 Copynumber: 2.3 Consensus size: 114
5190717 AGGATAGAAT
* * * *
5190727 GGAACCAACTCGCGCAAAGGAAAATAATAGGCCAAAGCAAAACGAACTCAAACAATGGCAAATAA
1 GGAACCAACTCACGCAAAGGAAAATAATAGGCCAAAGCAAAACGAAATCAAACAAAGGAAAATAA
** * * ** *
5190792 TAAGCCAAAACGGAACCAACTCAGGCTAAGGCAAATAAGT-TTCCAAATC
66 TAAGCCAAAACAAAACCAACTCACGCTAAAGCAAATAA-TAGGCCAAAGC
* ** ***
5190841 GGAACCAACTCACACAAAGGAAAATAATAGGCCAAAGCGGAAC-AAGATCATGTAAAGGAAAATA
1 GGAACCAACTCACGCAAAGGAAAATAATAGGCCAAAGCAAAACGAA-ATCAAACAAAGGAAAATA
* *
5190905 ATAGGCCAAAGCAAAACCAACTCACGC-AAAGCATAATAATAGGCCAAAGC
65 ATAAGCCAAAACAAAACCAACTCACGCTAAAGCA-AATAATAGGCCAAAGC
** *
5190955 AAAACCAACTCACGCAAAGGCAAATAATA
1 GGAACCAACTCACGCAAAGGAAAATAATA
5190984 AATTTAATGT
Statistics
Matches: 117, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
113 8 0.07
114 109 0.93
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.11
Consensus pattern (114 bp):
GGAACCAACTCACGCAAAGGAAAATAATAGGCCAAAGCAAAACGAAATCAAACAAAGGAAAATAA
TAAGCCAAAACAAAACCAACTCACGCTAAAGCAAATAATAGGCCAAAGC
Found at i:5193187 original size:2 final size:2
Alignment explanation
Indices: 5193180--5193249 Score: 133
Period size: 2 Copynumber: 35.5 Consensus size: 2
5193170 ATTGTGTATT
5193180 TA TA TA TA TA TA TA 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 TA TA TA TA
5193222 TA TA TA TA TA TA TA TA -A TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5193250 CTGTGTGTGT
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 66 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5197768 original size:137 final size:138
Alignment explanation
Indices: 5197530--5197787 Score: 380
Period size: 137 Copynumber: 1.9 Consensus size: 138
5197520 AAATTCTATG
* * *
5197530 TAAAAGTTATCGATCGATTTTGTTTAATTCATAATGGTGCATTTTTTGTATCAGTACTATGTGTA
1 TAAAAGTTATCGATCGATTTTGTTTAATGCATAATGGTGCATTTTTCGTATCAGTACAATGTGTA
*
5197595 CTTTCGGCACTAAATGTGCAATCATGGTATTCATAATGAGTTTGTG-ATTACCATTTCAATATAC
66 CTTTCGGCACTAAATGTGCAATCATGGAATTCATAATGAG-TTGTGAATTACCATTTCAATATAC
5197659 AATTATGTA
130 AATTATGTA
*
5197668 TAAAAGTTATCGATCGATTTTGTTTAATGCATAATGGTGCA-TTTTCGTATCCGTACAATGTGTA
1 TAAAAGTTATCGATCGATTTTGTTTAATGCATAATGGTGCATTTTTCGTATCAGTACAATGTGTA
* ** *
5197732 CTTTCGGCATTATGTGTGC-ATCCATGGAATAT-ATAATGAGTTGTGAATTTCCATTT
66 CTTTCGGCACTAAATGTGCAAT-CATGGAAT-TCATAATGAGTTGTGAATTACCATTT
5197788 TGACACTTTG
Statistics
Matches: 108, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
136 7 0.06
137 60 0.56
138 41 0.38
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.41
Consensus pattern (138 bp):
TAAAAGTTATCGATCGATTTTGTTTAATGCATAATGGTGCATTTTTCGTATCAGTACAATGTGTA
CTTTCGGCACTAAATGTGCAATCATGGAATTCATAATGAGTTGTGAATTACCATTTCAATATACA
ATTATGTA
Found at i:5204227 original size:27 final size:27
Alignment explanation
Indices: 5204189--5204271 Score: 166
Period size: 27 Copynumber: 3.1 Consensus size: 27
5204179 GCATTTTTGA
5204189 ATCAGTACTATGTGTACTTTCAGCGCT
1 ATCAGTACTATGTGTACTTTCAGCGCT
5204216 ATCAGTACTATGTGTACTTTCAGCGCT
1 ATCAGTACTATGTGTACTTTCAGCGCT
5204243 ATCAGTACTATGTGTACTTTCAGCGCT
1 ATCAGTACTATGTGTACTTTCAGCGCT
5204270 AT
1 AT
5204272 GTATGCATCC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (27 bp):
ATCAGTACTATGTGTACTTTCAGCGCT
Found at i:5214689 original size:21 final size:20
Alignment explanation
Indices: 5214664--5214702 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5214654 TATCAAGGTC
*
5214664 TTTGTTGAAGCCATGAAATCT
1 TTTGTCGAAGCCAT-AAATCT
*
5214685 TTTGTCGATGCCATAAAT
1 TTTGTCGAAGCCATAAAT
5214703 TCCTACAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (20 bp):
TTTGTCGAAGCCATAAATCT
Found at i:5221086 original size:2 final size:2
Alignment explanation
Indices: 5221079--5221143 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
5221069 TTTAATATTA
5221079 AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5221120 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
5221144 GTGTGTGTGT
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5221148 original size:2 final size:2
Alignment explanation
Indices: 5221143--5221184 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5221133 TATATATATA
5221143 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
5221185 AGTAATTATA
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:5222431 original size:20 final size:20
Alignment explanation
Indices: 5222408--5222458 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
5222398 AAAAAGAGGT
* *
5222408 AGTATCGATACTGACTTATC
1 AGTATCGATACTGACTCAGC
*
5222428 AGTATCGATACTGACTCAGG
1 AGTATCGATACTGACTCAGC
5222448 AGTATCGATAC
1 AGTATCGATAC
5222459 CAAAAGCTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (20 bp):
AGTATCGATACTGACTCAGC
Found at i:5226674 original size:130 final size:128
Alignment explanation
Indices: 5226396--5226690 Score: 326
Period size: 130 Copynumber: 2.3 Consensus size: 128
5226386 TCTAAGGAGC
* * * * **
5226396 AGTGAAGCATATCATTTTTTTCAAATTTGGTCTTCTTGCAGAGCAGTGAAGCAAATAATGTTCGA
1 AGTGAAGCATATC-TTTTTTTCATATTTGGTCTTCTTGAAGAGCAATGAAGCAAATAATGATAAA
* * *
5226461 TTCAATTTCCCCTAAAGAGTAGTCGAGTGAATCAAAAAAATTTAGATATAGTCTTCTTGAAGAGA
65 TTCAATTTCACCTAAAGAGCAGTCGAGTGAAT-AAAAAAATTTAGATATAGTCTTCCTGAAGAGA
** * * *
5226526 AGTGAAGCGGATCATTTTTCTCATACTTGGTCTTCTTGAAGAGCAATGAAGCAAATTA-GCATAA
1 AGTGAAGCATATC-TTTTTTTCATATTTGGTCTTCTTGAAGAGCAATGAAGCAAATAATG-ATAA
* * *
5226590 ATTCAACTTT-ACCTAAAGAGCAGTGGAGTGAAT-AAAAAATTTAGATCTGGTCTTCCTGAAGAG
64 ATTCAA-TTTCACCTAAAGAGCAGTCGAGTGAATAAAAAAATTTAGATATAGTCTTCCTGAAGAG
*
5226653 T
128 A
*
5226654 AGTGAAGCATATTCTTTTTTTTTCATATTTGATCTTC
1 AGTGAAGCATA-TC--TTTTTTTCATATTTGGTCTTC
5226691 CTAAAGAATA
Statistics
Matches: 137, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
128 36 0.26
129 3 0.02
130 95 0.69
131 3 0.02
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (128 bp):
AGTGAAGCATATCTTTTTTTCATATTTGGTCTTCTTGAAGAGCAATGAAGCAAATAATGATAAAT
TCAATTTCACCTAAAGAGCAGTCGAGTGAATAAAAAAATTTAGATATAGTCTTCCTGAAGAGA
Found at i:5226708 original size:130 final size:129
Alignment explanation
Indices: 5226471--5226729 Score: 286
Period size: 130 Copynumber: 2.0 Consensus size: 129
5226461 TTCAATTTCC
* * *
5226471 CCTAAAGAGTAGTCGAGTGAATCAAAAAAATTTAGATATAGTCTTCTTGAAGAGAAGTGAAGCGG
1 CCTAAAGAGCAGTCGAGTGAAT-AAAAAAATTTAGATATAGTCTTCCTGAAGAGAAGTGAAGCAG
* * * * * * *
5226536 ATCATTTTTCTCATACTTGGTCTTCTTGAAGAGCAATGAAGCAAATTAGCATAAATTCAACTTTA
65 ATCATTTTTCTCATACTTGATCTTCCTAAAGAACAATAAAGCAAATCAACATAAATTCAACTTTA
* * * * *
5226601 CCTAAAGAGCAGTGGAGTGAAT-AAAAAATTTAGATCTGGTCTTCCTGAAGAGTAGTGAAGCATA
1 CCTAAAGAGCAGTCGAGTGAATAAAAAAATTTAGATATAGTCTTCCTGAAGAGAAGTGAAGCAGA
* * * * * * *
5226665 TTCTTTTTTTTTCATATTTGATCTTCCTAAAGAATAGTAAAGCAAATCAACCTCAATTCAACTTT
66 -TC-ATTTTTCTCATACTTGATCTTCCTAAAGAACAATAAAGCAAATCAACATAAATTCAACTTT
5226730 CCCAAAAGTC
Statistics
Matches: 105, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
128 36 0.34
129 2 0.02
130 67 0.64
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (129 bp):
CCTAAAGAGCAGTCGAGTGAATAAAAAAATTTAGATATAGTCTTCCTGAAGAGAAGTGAAGCAGA
TCATTTTTCTCATACTTGATCTTCCTAAAGAACAATAAAGCAAATCAACATAAATTCAACTTTA
Found at i:5227783 original size:2 final size:2
Alignment explanation
Indices: 5227778--5227816 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5227768 TGTGAGTAAT
5227778 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5227817 TAGAAGTACA
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:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5230469 original size:60 final size:60
Alignment explanation
Indices: 5230294--5230472 Score: 155
Period size: 60 Copynumber: 3.0 Consensus size: 60
5230284 TGAATTTAGG
* * * * * * ** **
5230294 GATGACATTGAAAGATCTAAAAGTTTAGGGAACAATTTATAATGAGATTCATAGTTTGGG
1 GATGAAATTGAAATATTTAAAAGTTTAAGGAATAATTTAAAATGAGGGTCATAGTTTGAA
* * * * * *
5230354 GATGAAATTTG-AATGTTCAAAAGTTTAAGGACTAATTTAGAAGGGGGGAT-ATAGTTTGAA
1 GATGAAA-TTGAAATATTTAAAAGTTTAAGGAATAATTTAAAATGAGGG-TCATAGTTTGAA
* * *
5230414 GATGAAATTGAAATATTTAAAAGTTTAAGGATTAATTTAAAATAAGGGTCGTAGTTTGA
1 GATGAAATTGAAATATTTAAAAGTTTAAGGAATAATTTAAAATGAGGGTCATAGTTTGA
5230473 GAATATATGA
Statistics
Matches: 92, Mismatches: 23, Indels: 8
0.75 0.19 0.07
Matches are distributed among these distances:
59 4 0.04
60 84 0.91
61 4 0.04
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (60 bp):
GATGAAATTGAAATATTTAAAAGTTTAAGGAATAATTTAAAATGAGGGTCATAGTTTGAA
Found at i:5231725 original size:6 final size:6
Alignment explanation
Indices: 5231714--5231738 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5231704 GGATATATAT
5231714 TATGCA TATGCA TATGCA TATGCA T
1 TATGCA TATGCA TATGCA TATGCA T
5231739 GCATGTACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (6 bp):
TATGCA
Found at i:5233945 original size:60 final size:60
Alignment explanation
Indices: 5233877--5234007 Score: 151
Period size: 60 Copynumber: 2.2 Consensus size: 60
5233867 AGGATAAATT
* *
5233877 TTAC-AAATGGTACTCCAACTATA-AAGTATTATTTTATTAAGTCTCTCGACTATTAA-AA
1 TTACAAAATGGTACTCCAACTATATAA-CATTACTTTATTAAGTCTCTCGACTATTAACAA
* * * * *
5233935 CTTACAAAATGGTCCTCCGATTATATAACATTACTTTATTAAGTCTCTTGATTATTAACAA
1 -TTACAAAATGGTACTCCAACTATATAACATTACTTTATTAAGTCTCTCGACTATTAACAA
*
5233996 TTGCAAAATGGT
1 TTACAAAATGGT
5234008 CACAATACTA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
59 4 0.07
60 53 0.87
61 4 0.07
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (60 bp):
TTACAAAATGGTACTCCAACTATATAACATTACTTTATTAAGTCTCTCGACTATTAACAA
Found at i:5245144 original size:21 final size:21
Alignment explanation
Indices: 5245118--5245157 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
5245108 TAAATTGTAT
5245118 ATCGATGCACTGCTACAGTGC
1 ATCGATGCACTGCTACAGTGC
5245139 ATCGATGCACTGCTACAGT
1 ATCGATGCACTGCTACAGT
5245158 AACTTCGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (21 bp):
ATCGATGCACTGCTACAGTGC
Found at i:5245522 original size:2 final size:2
Alignment explanation
Indices: 5245482--5245509 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5245472 ACATATAAGA
5245482 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5245510 CCATTTCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5245926 original size:21 final size:21
Alignment explanation
Indices: 5245902--5245953 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
5245892 AAAATTATCT
5245902 TAGTGCATCGGTACACACTCA
1 TAGTGCATCGGTACACACTCA
5245923 TAGTGCATCGGTACACACTCA
1 TAGTGCATCGGTACACACTCA
5245944 TAGTGCATCG
1 TAGTGCATCG
5245954 ATGCACTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (21 bp):
TAGTGCATCGGTACACACTCA
Found at i:5268899 original size:31 final size:32
Alignment explanation
Indices: 5268843--5268913 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
5268833 AAAAATAGTT
*
5268843 AATTTATCTTTTTTTCTAAACAATTTTAACTA
1 AATTTATCTTTTTTTCTAAACAATTTCAACTA
*
5268875 AATTTATCTTTTTTT-TAAATAATTTCAACTA
1 AATTTATCTTTTTTTCTAAACAATTTCAACTA
5268906 AACTTTAT
1 AA-TTTAT
5268914 AATTAAGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 16 0.44
32 20 0.56
ACGTcount: A:0.35, C:0.11, G:0.00, T:0.54
Consensus pattern (32 bp):
AATTTATCTTTTTTTCTAAACAATTTCAACTA
Found at i:5270479 original size:25 final size:25
Alignment explanation
Indices: 5270425--5270480 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
5270415 AAACTTCAAG
*
5270425 CTTTTGGATGAGGACATCTCAATGAT
1 CTTTTGGATGAGGACATCTAAAT-AT
*
5270451 -TTTTGGGTGAGGACATCTAACAT-T
1 CTTTTGGATGAGGACATCTAA-ATAT
5270475 CTTTTG
1 CTTTTG
5270481 ATCGTGGGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 1 0.04
25 23 0.88
26 2 0.08
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.39
Consensus pattern (25 bp):
CTTTTGGATGAGGACATCTAAATAT
Found at i:5271411 original size:20 final size:20
Alignment explanation
Indices: 5271388--5271427 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5271378 CTATCGCTTA
5271388 TCGCTTGCTTCTCTCACTTC
1 TCGCTTGCTTCTCTCACTTC
5271408 TCGCTTGCTTCTCTCACTTC
1 TCGCTTGCTTCTCTCACTTC
5271428 AGCTTCGACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.05, C:0.40, G:0.10, T:0.45
Consensus pattern (20 bp):
TCGCTTGCTTCTCTCACTTC
Found at i:5275351 original size:61 final size:62
Alignment explanation
Indices: 5275270--5275435 Score: 190
Period size: 62 Copynumber: 2.7 Consensus size: 62
5275260 GGGCTTGAGA
* * * * * * * *
5275270 GCCTACCCAAGAAAGTTCTCAGGGCCAC-GGGCCTATCTAAGAAAGATCTCAAATCTGCAGG
1 GCCTACCCAAGAATGATCTCAGGGCCACGGGGCCTACCCAAGAAAAATCCCAAAGCCGCAGG
* * **
5275331 GCCTATCCAAGAATGATCTCAGGGCCACGGGGCCTACCCCAGAAAAATCCCAGGGCCGCAGG
1 GCCTACCCAAGAATGATCTCAGGGCCACGGGGCCTACCCAAGAAAAATCCCAAAGCCGCAGG
* * *
5275393 GCCTACCCAAGAATGATCTCAGGGCCGCAGAGCCTACCCAAGA
1 GCCTACCCAAGAATGATCTCAGGGCCACGGGGCCTACCCAAGA
5275436 GTCACATTAG
Statistics
Matches: 87, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
61 25 0.29
62 62 0.71
ACGTcount: A:0.30, C:0.32, G:0.25, T:0.14
Consensus pattern (62 bp):
GCCTACCCAAGAATGATCTCAGGGCCACGGGGCCTACCCAAGAAAAATCCCAAAGCCGCAGG
Found at i:5275364 original size:31 final size:31
Alignment explanation
Indices: 5275270--5275435 Score: 163
Period size: 31 Copynumber: 5.4 Consensus size: 31
5275260 GGGCTTGAGA
*
5275270 GCCTACCCAAGAAAGTTCTCAGGGCCAC-GG
1 GCCTACCCAAGAAAGATCTCAGGGCCACAGG
* * *** **
5275300 GCCTATCTAAGAAAGATCTCAAATCTGCAGG
1 GCCTACCCAAGAAAGATCTCAGGGCCACAGG
* * *
5275331 GCCTATCCAAGAATGATCTCAGGGCCACGGG
1 GCCTACCCAAGAAAGATCTCAGGGCCACAGG
* * * *
5275362 GCCTACCCCAGAAAAATCCCAGGGCCGCAGG
1 GCCTACCCAAGAAAGATCTCAGGGCCACAGG
* * *
5275393 GCCTACCCAAGAATGATCTCAGGGCCGCAGA
1 GCCTACCCAAGAAAGATCTCAGGGCCACAGG
5275424 GCCTACCCAAGA
1 GCCTACCCAAGA
5275436 GTCACATTAG
Statistics
Matches: 107, Mismatches: 28, Indels: 1
0.79 0.21 0.01
Matches are distributed among these distances:
30 20 0.19
31 87 0.81
ACGTcount: A:0.30, C:0.32, G:0.25, T:0.14
Consensus pattern (31 bp):
GCCTACCCAAGAAAGATCTCAGGGCCACAGG
Found at i:5279980 original size:20 final size:21
Alignment explanation
Indices: 5279940--5279978 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
5279930 AAATTTCTAA
5279940 AAATTTATTAATTTTTTAAAT
1 AAATTTATTAATTTTTTAAAT
5279961 AAATTT-TT-ATTTTTTAAA
1 AAATTTATTAATTTTTTAAA
5279979 ATTATTGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 2 0.11
21 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
AAATTTATTAATTTTTTAAAT
Found at i:5280304 original size:3 final size:3
Alignment explanation
Indices: 5280296--5280323 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5280286 GCTTAACATC
5280296 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5280324 TGATCAAATT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5281001 original size:27 final size:26
Alignment explanation
Indices: 5280933--5281010 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 26
5280923 GGAAATTAGA
5280933 AGGGATTAATAAAGAATATTTAAAAATTT
1 AGGGATTAATAAA-AAT-TTT-AAAATTT
* *
5280962 -GGGTCTTAATAAAAATTCTAAAATTT
1 AGGG-ATTAATAAAAATTTTAAAATTT
5280988 AGGGATTAATTAAAAATTTTAAA
1 AGGGATTAA-TAAAAATTTTAAA
5281011 TGGTTAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
26 11 0.26
27 17 0.40
28 6 0.14
29 8 0.19
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.36
Consensus pattern (26 bp):
AGGGATTAATAAAAATTTTAAAATTT
Found at i:5281011 original size:26 final size:25
Alignment explanation
Indices: 5280933--5281011 Score: 70
Period size: 26 Copynumber: 2.9 Consensus size: 25
5280923 GGAAATTAGA
5280933 AGGGATTAATAAAGAATATTTAAAAATTT
1 AGGGATTAATAAA-AAT-TTT--AAATTT
* *
5280962 -GGGTCTTAATAAAAATTCTAAAATTT
1 AGGG-ATTAATAAAAATT-TTAAATTT
5280988 AGGGATTAATTAAAAATTTTAAAT
1 AGGGATTAA-TAAAAATTTTAAAT
5281012 GGTTAATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
26 15 0.36
27 12 0.29
28 7 0.17
29 8 0.19
ACGTcount: A:0.48, C:0.03, G:0.13, T:0.37
Consensus pattern (25 bp):
AGGGATTAATAAAAATTTTAAATTT
Found at i:5282809 original size:32 final size:32
Alignment explanation
Indices: 5282758--5282849 Score: 107
Period size: 32 Copynumber: 2.9 Consensus size: 32
5282748 ATTGTAAAAG
* *
5282758 TTTGATCAAA-TTAATGATCATTTTCT-ATCTA
1 TTTGATAAAATTTAATGATCATTTTATAAT-TA
*
5282789 TTTGATAAAATTTAATGATCATTTTATAATTT
1 TTTGATAAAATTTAATGATCATTTTATAATTA
* * *
5282821 TTTGATATATTTTAATAATCATTTTATAA
1 TTTGATAAAATTTAATGATCATTTTATAA
5282850 CTTTTGAAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
31 9 0.17
32 42 0.79
33 2 0.04
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (32 bp):
TTTGATAAAATTTAATGATCATTTTATAATTA
Found at i:5282945 original size:2 final size:2
Alignment explanation
Indices: 5282938--5283027 Score: 162
Period size: 2 Copynumber: 45.0 Consensus size: 2
5282928 TTTGAAAATC
* *
5282938 AT AT AT AT AG AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5282980 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5283022 AT AT AT
1 AT AT AT
5283028 TAGTTTTCCA
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5284536 original size:33 final size:31
Alignment explanation
Indices: 5284479--5284544 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 31
5284469 AAGCTAATTT
*
5284479 TTTTATTTTATTATAATCATTTAATAGTTTTTA
1 TTTTATTATATTATAATCATTTAAT--TTTTTA
*
5284512 TTTTATTATATTTTAAT-ATATTAATTTTTTA
1 TTTTATTATATTATAATCAT-TTAATTTTTTA
5284543 TT
1 TT
5284545 ACCTTTTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 8 0.27
32 2 0.07
33 20 0.67
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (31 bp):
TTTTATTATATTATAATCATTTAATTTTTTA
Found at i:5285880 original size:21 final size:21
Alignment explanation
Indices: 5285820--5285897 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
5285810 TCTGCAGTAG
* * * *
5285820 TTTCAAATGCCACTATAGCCA
1 TTTCAGATGCCACCACAACCA
* * * *
5285841 TTTCAGATGGCATCGCAACCGT
1 TTTCAGATGCCACCACAACC-A
5285863 TTTC-GATGCCACCACAACCA
1 TTTCAGATGCCACCACAACCA
5285883 TTTCAGATGCCACCA
1 TTTCAGATGCCACCA
5285898 TCGTAGGGTT
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
20 4 0.09
21 35 0.81
22 4 0.09
ACGTcount: A:0.28, C:0.32, G:0.14, T:0.26
Consensus pattern (21 bp):
TTTCAGATGCCACCACAACCA
Found at i:5286326 original size:25 final size:25
Alignment explanation
Indices: 5286292--5286416 Score: 89
Period size: 25 Copynumber: 5.5 Consensus size: 25
5286282 TCGATAGACT
*
5286292 TGTTTTTATTTATTTTGTTTCTTAA
1 TGTTTTTATTTATTATGTTTCTTAA
5286317 TGTTTTTATTTAATTATG------AA
1 TGTTTTTATTT-ATTATGTTTCTTAA
* *
5286337 -CTTTTTATTTATTTTGTTTCTTAA
1 TGTTTTTATTTATTATGTTTCTTAA
5286361 TGTTTTTATTTAGTTATG------AA
1 TGTTTTTATTTA-TTATGTTTCTTAA
*
5286381 -CTTTTTATTTATTATGTTTCTTAA
1 TGTTTTTATTTATTATGTTTCTTAA
*
5286405 TGTTTTTCTTTA
1 TGTTTTTATTTA
5286417 ATTACAGACT
Statistics
Matches: 76, Mismatches: 8, Indels: 32
0.66 0.07 0.28
Matches are distributed among these distances:
18 10 0.13
19 19 0.25
20 4 0.05
24 4 0.05
25 30 0.39
26 9 0.12
ACGTcount: A:0.20, C:0.05, G:0.08, T:0.67
Consensus pattern (25 bp):
TGTTTTTATTTATTATGTTTCTTAA
Found at i:5286357 original size:44 final size:44
Alignment explanation
Indices: 5286294--5286505 Score: 318
Period size: 44 Copynumber: 4.8 Consensus size: 44
5286284 GATAGACTTG
5286294 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGAAC
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGAAC
*
5286338 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAGTTATGAAC
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGAAC
* * *
5286382 TTTTTATTTATTATGTTTCTTAATGTTTTTCTTTAATTA-CAGAC
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGA-AC
* *
5286426 TTTTTATTTAGTTTGTTTCTTAATTTTTTTATTATTTAATTATGAAC
1 TTTTTATTTATTTTGTTTCTTAA--TGTTT-TTATTTAATTATGAAC
*
5286473 TTTTTATTTATTTTGTTTCTAAATGTTTTTATT
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATT
5286506 ATTTAATTGT
Statistics
Matches: 150, Mismatches: 13, Indels: 10
0.87 0.08 0.06
Matches are distributed among these distances:
43 1 0.01
44 107 0.71
45 4 0.03
46 4 0.03
47 33 0.22
48 1 0.01
ACGTcount: A:0.22, C:0.05, G:0.07, T:0.66
Consensus pattern (44 bp):
TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGAAC
Found at i:5286540 original size:91 final size:91
Alignment explanation
Indices: 5286294--5286549 Score: 231
Period size: 88 Copynumber: 2.8 Consensus size: 91
5286284 GATAGACTTG
* * * ** * *
5286294 TTTTTATTTATTTTGTTTCTTAATGTTTTT-ATTTAATTA-TGAACTTTTTATTTATTTTGTTTC
1 TTTTTATTTATTATGTTTCTAAATGTTTTTCA-TTAATTACAG-ACTTTGAATTTAGTTTGTATC
*
5286357 TTAATG-TT-T-TTATTTAGTTATGAAC
64 TTAATGTTTGTATTATTTAATTATGAAC
* * ** *
5286382 TTTTTATTTATTATGTTTCTTAATGTTTTTCTTTAATTACAGACTTTTTATTTAGTTTGTTTCTT
1 TTTTTATTTATTATGTTTCTAAATGTTTTTCATTAATTACAGACTTTGAATTTAGTTTGTATCTT
* *
5286447 AATTTTTTTATTATTTAATTATGAAC
66 AATGTTTGTATTATTTAATTATGAAC
* * ***
5286473 TTTTTATTTATTTTGTTTCTAAATGTTTTT-ATTATTTA-ATTGTTTGAATTATAACGTTTGTAT
1 TTTTTATTTATTATGTTTCTAAATGTTTTTCATTAATTACAGACTTTGAATT-T-A-GTTTGTAT
5286536 -TTAATGTTTGTATT
63 CTTAATGTTTGTATT
5286550 TAATTGTTTT
Statistics
Matches: 142, Mismatches: 18, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
88 61 0.43
89 10 0.07
90 8 0.06
91 56 0.39
92 7 0.05
ACGTcount: A:0.23, C:0.05, G:0.08, T:0.64
Consensus pattern (91 bp):
TTTTTATTTATTATGTTTCTAAATGTTTTTCATTAATTACAGACTTTGAATTTAGTTTGTATCTT
AATGTTTGTATTATTTAATTATGAAC
Found at i:5286540 original size:135 final size:132
Alignment explanation
Indices: 5286294--5286554 Score: 334
Period size: 135 Copynumber: 2.0 Consensus size: 132
5286284 GATAGACTTG
* *
5286294 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGAACTTTTTATTTATTTTGTTTCTT
1 TTTTTATTTAGTTTGTTTCTTAATGTTTTTATTTAATTATGAACTTTTTATTTATTTTGTTTCTA
* * * * *
5286359 AATGTTTTTATTTAGTTATGAACTTTTTATTTATTATGTTTCTTAATGTTTTTCTTTAATTACAG
66 AATGTTTTTATTTAGTTATGAACTTTTTAATTATAACGTTTCTTAATGTTTGTATTTAATTACAG
5286424 AC
131 AC
*
5286426 TTTTTATTTAGTTTGTTTCTTAATTTTTTTATTATTTAATTATGAACTTTTTATTTATTTTGTTT
1 TTTTTATTTAGTTTGTTTCTTAA--TGTTT-TTATTTAATTATGAACTTTTTATTTATTTTGTTT
*
5286491 CTAAATGTTTTTA-TTA-TT-T-AA-TTGTTTGAATTATAACGTTTGTATTTAATGTTTGTATTT
63 CTAAATGTTTTTATTTAGTTATGAACTT-TTT-AATTATAACG-TT-T-CTTAATGTTTGTATTT
5286551 AATT
123 AATT
5286555 GTTTTTATTG
Statistics
Matches: 112, Mismatches: 9, Indels: 13
0.84 0.07 0.10
Matches are distributed among these distances:
130 2 0.02
131 5 0.04
132 30 0.27
133 4 0.04
134 8 0.07
135 63 0.56
ACGTcount: A:0.23, C:0.05, G:0.08, T:0.64
Consensus pattern (132 bp):
TTTTTATTTAGTTTGTTTCTTAATGTTTTTATTTAATTATGAACTTTTTATTTATTTTGTTTCTA
AATGTTTTTATTTAGTTATGAACTTTTTAATTATAACGTTTCTTAATGTTTGTATTTAATTACAG
AC
Found at i:5286546 original size:13 final size:14
Alignment explanation
Indices: 5286505--5286563 Score: 68
Period size: 14 Copynumber: 4.3 Consensus size: 14
5286495 ATGTTTTTAT
5286505 TATTTAATTGTTTG
1 TATTTAATTGTTTG
* *
5286519 AATTATAA-CGTTTG
1 TATT-TAATTGTTTG
5286533 TATTTAA-TGTTTG
1 TATTTAATTGTTTG
*
5286546 TATTTAATTGTTTT
1 TATTTAATTGTTTG
5286560 TATT
1 TATT
5286564 GTTTTTATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
13 15 0.39
14 20 0.53
15 3 0.08
ACGTcount: A:0.25, C:0.02, G:0.12, T:0.61
Consensus pattern (14 bp):
TATTTAATTGTTTG
Found at i:5286561 original size:23 final size:23
Alignment explanation
Indices: 5286530--5286600 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
5286520 ATTATAACGT
* *
5286530 TTGTATTTAATGTTTGTATTTAA
1 TTGTTTTTAATGTTTTTATTTAA
*
5286553 TTGTTTTTATTGTTTTTA-TTAA
1 TTGTTTTTAATGTTTTTATTTAA
*
5286575 TTAGTTTGTAATGTTTTTATTTAA
1 TT-GTTTTTAATGTTTTTATTTAA
5286599 TT
1 TT
5286601 TTCACTTCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
22 6 0.15
23 29 0.71
24 6 0.15
ACGTcount: A:0.23, C:0.00, G:0.11, T:0.66
Consensus pattern (23 bp):
TTGTTTTTAATGTTTTTATTTAA
Found at i:5289673 original size:18 final size:17
Alignment explanation
Indices: 5289649--5289697 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
5289639 CCGACCCGAC
*
5289649 CCGACCCGTTGACATGA
1 CCGACCCGTTGACACGA
*
5289666 CTCGACCCGTTGACCCGA
1 C-CGACCCGTTGACACGA
5289684 CCTGACCCGTTGAC
1 CC-GACCCGTTGAC
5289698 TATTGACCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 2 0.07
18 26 0.93
ACGTcount: A:0.18, C:0.41, G:0.22, T:0.18
Consensus pattern (17 bp):
CCGACCCGTTGACACGA
Found at i:5290574 original size:22 final size:21
Alignment explanation
Indices: 5290549--5290593 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5290539 ATATGATAAA
5290549 ACTACATATGTGCTTAAGAAAT
1 ACTACAT-TGTGCTTAAGAAAT
* * *
5290571 ACTAGATTTTGCTTACGAAAT
1 ACTACATTGTGCTTAAGAAAT
5290592 AC
1 AC
5290594 GGATAATCGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (21 bp):
ACTACATTGTGCTTAAGAAAT
Found at i:5292177 original size:24 final size:24
Alignment explanation
Indices: 5292150--5292281 Score: 133
Period size: 24 Copynumber: 5.5 Consensus size: 24
5292140 TCGATTTGAT
5292150 TTATGATCTGATACTTGACATGGA
1 TTATGATCTGATACTTGACATGGA
5292174 TTATGATCTGATA-TCTGACATGGA
1 TTATGATCTGATACT-TGACATGGA
*
5292198 TT-TCGATCTGATACTTGACTTGGA
1 TTAT-GATCTGATACTTGACATGGA
* * *
5292222 TTCTGATATGATACTTGACCTGGA
1 TTATGATCTGATACTTGACATGGA
* * * ** *
5292246 TTTTAATATGATACTTGATGTGAA
1 TTATGATCTGATACTTGACATGGA
*
5292270 TTATGATTTGAT
1 TTATGATCTGAT
5292282 TTTTGATATA
Statistics
Matches: 93, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.02
24 89 0.96
25 2 0.02
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (24 bp):
TTATGATCTGATACTTGACATGGA
Found at i:5298911 original size:27 final size:27
Alignment explanation
Indices: 5298844--5298902 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
5298834 CCTAATATTA
*
5298844 AAATAAACAATGATGAGATAATTACGC
1 AAATAAACAATTATGAGATAATTACGC
*
5298871 AAATAAACAATTATGAGATAATTACTC
1 AAATAAACAATTATGAGATAATTACGC
5298898 AAATA
1 AAATA
5298903 CCTCATTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.25
Consensus pattern (27 bp):
AAATAAACAATTATGAGATAATTACGC
Found at i:5305722 original size:20 final size:20
Alignment explanation
Indices: 5305685--5305722 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5305675 GCCTATGCTT
*
5305685 TATCGATACTAAAGGTAGAG
1 TATCGATACCAAAGGTAGAG
*
5305705 TATCGATACCAAATGTAG
1 TATCGATACCAAAGGTAG
5305723 GTCTTATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (20 bp):
TATCGATACCAAAGGTAGAG
Found at i:5306001 original size:20 final size:19
Alignment explanation
Indices: 5305960--5306002 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
5305950 TTTTGGTATT
** *
5305960 GATACCCAGGGTGGGTGTC
1 GATACCCAGGGTCAGTGGC
5305979 GATACCCAAGGGTCAGTGGC
1 GATACCC-AGGGTCAGTGGC
5305999 GATA
1 GATA
5306003 TCGCAAGGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.23, C:0.21, G:0.37, T:0.19
Consensus pattern (19 bp):
GATACCCAGGGTCAGTGGC
Found at i:5309315 original size:19 final size:20
Alignment explanation
Indices: 5309269--5309315 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
5309259 AGTTTCCAAA
* *
5309269 TTCGAAACGCGAATTTCTTT
1 TTCGCAACGCAAATTTCTTT
*
5309289 TTCACAACGCAAATTTC-TT
1 TTCGCAACGCAAATTTCTTT
5309308 TTCGCAAC
1 TTCGCAAC
5309316 AAGATTTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.36
Consensus pattern (20 bp):
TTCGCAACGCAAATTTCTTT
Found at i:5309362 original size:40 final size:40
Alignment explanation
Indices: 5309289--5309401 Score: 104
Period size: 40 Copynumber: 2.9 Consensus size: 40
5309279 GAATTTCTTT
* * * * *
5309289 TTCACAACGC-AAATTTCTTTTCGCAACAAGATTTTCTAA
1 TTCACAACACGAATTTTATTTTCGCAACAAGATTTCCGAA
* * * **
5309328 TTCACAACAGGGATTTTGTTTTCGCAACGCGATTTCCGAA
1 TTCACAACACGAATTTTATTTTCGCAACAAGATTTCCGAA
* *
5309368 TTCGCAACACGAATTTTAATTTCGCAACAA-ATTT
1 TTCACAACACGAATTTTATTTTCGCAACAAGATTT
5309402 TATTTTCGCA
Statistics
Matches: 57, Mismatches: 16, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
39 12 0.21
40 45 0.79
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (40 bp):
TTCACAACACGAATTTTATTTTCGCAACAAGATTTCCGAA
Found at i:5309402 original size:18 final size:19
Alignment explanation
Indices: 5309368--5309417 Score: 75
Period size: 18 Copynumber: 2.6 Consensus size: 19
5309358 GATTTCCGAA
5309368 TTCGCAACACGAATTTTAAT
1 TTCGCAACAC-AATTTTAAT
*
5309388 TTCGCAACA-AATTTTATT
1 TTCGCAACACAATTTTAAT
5309406 TTCGCAACACAA
1 TTCGCAACACAA
5309418 CCTAAATCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 17 0.61
19 2 0.07
20 9 0.32
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (19 bp):
TTCGCAACACAATTTTAAT
Found at i:5309492 original size:16 final size:15
Alignment explanation
Indices: 5309457--5309495 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
5309447 TCCCCATCTC
*
5309457 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
5309472 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
5309488 TAATTTTT
1 TAATTTTT
5309496 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:5310106 original size:12 final size:12
Alignment explanation
Indices: 5310085--5310118 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5310075 ACCACATTTC
*
5310085 CAATACCAAACA
1 CAATATCAAACA
5310097 CAATATCAAACA
1 CAATATCAAACA
*
5310109 CAATCTCAAA
1 CAATATCAAA
5310119 ACCATAACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:5310959 original size:3 final size:3
Alignment explanation
Indices: 5310951--5311049 Score: 134
Period size: 3 Copynumber: 34.0 Consensus size: 3
5310941 AGTTCGCATT
**
5310951 TTA TTA TTA TTA TTA TTA TTA -TA TTA -TA TTA TTA TTA TTA AGA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
5310997 TTA TTA TTA TTA TTA TATA TTA TTA TTA TTA ATA TTA TTA TT- TT-
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5311041 TTA TTA TTA
1 TTA TTA TTA
5311050 AATAAATATA
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
2 8 0.09
3 75 0.87
4 3 0.03
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:5311006 original size:37 final size:37
Alignment explanation
Indices: 5310956--5311049 Score: 145
Period size: 37 Copynumber: 2.5 Consensus size: 37
5310946 GCATTTTATT
5310956 ATTATTATTATTATTA-TATTATATTATTATTATTAAG
1 ATTATTATTATTATTATTA-TATATTATTATTATTAAG
*
5310993 ATTATTATTATTATTATTATATATTATTATTATTAAT
1 ATTATTATTATTATTATTATATATTATTATTATTAAG
*
5311030 ATTATTATTTTTTATTATTA
1 ATTATTA-TTATTATTATTA
5311050 AATAAATATA
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
37 40 0.75
38 13 0.25
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (37 bp):
ATTATTATTATTATTATTATATATTATTATTATTAAG
Found at i:5311063 original size:25 final size:23
Alignment explanation
Indices: 5310950--5311063 Score: 89
Period size: 25 Copynumber: 5.1 Consensus size: 23
5310940 TAGTTCGCAT
* *
5310950 TTTATTATTATTATTATTATTATA
1 TTTATTATTATTAATAATA-TATA
* *
5310974 TTATATTATTATTATTAAGAT-TA
1 TT-TATTATTATTAATAATATATA
5310997 -TTATTATTATT-AT--TATATA
1 TTTATTATTATTAATAATATATA
*
5311016 -TTATTATTATTAATATTAT-TA
1 TTTATTATTATTAATAATATATA
*
5311037 TTTTTTATTATTAAATAAATATATA
1 TTTATTATTATT-AAT-AATATATA
5311062 TT
1 TT
5311064 ACAAATTACA
Statistics
Matches: 75, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
18 2 0.03
19 13 0.17
20 3 0.04
21 12 0.16
22 14 0.19
23 5 0.07
24 7 0.09
25 19 0.25
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (23 bp):
TTTATTATTATTAATAATATATA
Found at i:5311064 original size:37 final size:36
Alignment explanation
Indices: 5310955--5311064 Score: 109
Period size: 37 Copynumber: 3.0 Consensus size: 36
5310945 CGCATTTTAT
5310955 TATTATTATTATTATTA-TATTATATTATTAT-TATTAA
1 TATTATTATT-TT-TTATTATTATA-TATTATATATTAA
* *
5310992 GATTATTA-TTATTATTATTATATATTATTATTATTAA
1 TATTATTATTTTTTATTATTATATATTA-TA-TATTAA
* *
5311029 TATTATTATTTTTTATTATTAAATAAATATATATTA
1 TATTATTATTTTTTATTATTATAT-ATTATATATTA
5311065 CAAATTACAA
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
34 8 0.13
35 9 0.15
36 1 0.02
37 25 0.41
38 15 0.25
39 3 0.05
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (36 bp):
TATTATTATTTTTTATTATTATATATTATATATTAA
Found at i:5311118 original size:22 final size:22
Alignment explanation
Indices: 5311073--5311126 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 22
5311063 TACAAATTAC
5311073 AATAAGACCCAGAAGGCCCAAAT
1 AATAA-ACCCAGAAGGCCCAAAT
*
5311096 -ATCAAACCCAGACCGGCCC-AAT
1 AAT-AAACCCAGA-AGGCCCAAAT
5311118 AATAAACCC
1 AATAAACCC
5311127 TAAACCCATC
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.44, C:0.33, G:0.13, T:0.09
Consensus pattern (22 bp):
AATAAACCCAGAAGGCCCAAAT
Found at i:5313139 original size:11 final size:13
Alignment explanation
Indices: 5313102--5313141 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
5313092 TGTTTAATAA
5313102 AATATA-TATATT
1 AATATATTATATT
*
5313114 AATATATTATCTT
1 AATATATTATATT
5313127 AA-A-ATTATATT
1 AATATATTATATT
5313138 AATA
1 AATA
5313142 AACTTTGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 8 0.33
13 7 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATTATATT
Found at i:5321154 original size:20 final size:22
Alignment explanation
Indices: 5321108--5321165 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
5321098 TACATCTACA
*
5321108 CTCTTCAAGGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
5321130 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
* *
5321152 CTTTTCGAAGATGA
1 CTCTTCAAAGATGA
5321166 AAGCTTTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:5321951 original size:164 final size:166
Alignment explanation
Indices: 5321679--5322007 Score: 590
Period size: 164 Copynumber: 2.0 Consensus size: 166
5321669 TAAAAATGAA
5321679 CATTATCTTGAGATTGGGGCAATATTACCCAATCAACATGTTATTTTGAAAAATAATGAGAAAAC
1 CATTATCTTGAGATTGGGGCAATATTACCCAATCAACATGTTATTTTGAAAAATAATGAGAAAAC
* *
5321744 GATTTCCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAATGATTT
66 GATTTCCATAGTTTCTCATTTAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
5321809 CCTTAG-TTTTTTACTTAGTAAACTATTTCCAACAG
131 CCTTAGTTTTTTTACTTAGTAAACTATTTCCAACAG
* *
5321844 CATTATCTTGAGATTGGGGC-ATGTTACCCAATTAACATGTTATTTTGAAAAATAATGAGAAAAC
1 CATTATCTTGAGATTGGGGCAATATTACCCAATCAACATGTTATTTTGAAAAATAATGAGAAAAC
* *
5321908 GATTTTCATAGTTTCTCATTTAATCTTTTTTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
66 GATTTCCATAGTTTCTCATTTAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
5321973 CCTTAGTTTTTTTACTTAGTAAACTATTTCCAACA
131 CCTTAGTTTTTTTACTTAGTAAACTATTTCCAACA
5322008 TCCGTAAGCC
Statistics
Matches: 157, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
164 109 0.69
165 48 0.31
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.39
Consensus pattern (166 bp):
CATTATCTTGAGATTGGGGCAATATTACCCAATCAACATGTTATTTTGAAAAATAATGAGAAAAC
GATTTCCATAGTTTCTCATTTAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
CCTTAGTTTTTTTACTTAGTAAACTATTTCCAACAG
Found at i:5322626 original size:73 final size:73
Alignment explanation
Indices: 5322006--5322599 Score: 902
Period size: 73 Copynumber: 8.0 Consensus size: 73
5321996 CTATTTCCAA
* * * * * *
5322006 CATCCGTAAGCCCTGCAGTGCAGGATCTTTTCAAAAAGCCTTCGGGAGCATTTTGATCTTAAACC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
*
5322071 CTCAGGGC
66 CTCAGGGT
*
5322079 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAATC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
5322144 CTCAGGGT
66 CTCAGGGT
*
5322152 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAATC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
*
5322217 CTTAGGGT
66 CTCAGGGT
5322225 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
5322290 CTCAGGGT
66 CTCAGGGT
* * *
5322298 CATCTGTAAGACCTACAGTGCATGATGTTTCCAAAAATCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGA---TCTTAA
5322363 ACCCTCAGGGT
63 ACCCTCAGGGT
*
5322374 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGA--TCTT-AA
* *
5322439 AGCCTTAGGGT
63 ACCCTCAGGGT
* * *
5322450 CATCTGTAAGACCTATAGTGCATGATATTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
5322515 CTC-GTGGT
66 CTCAG-GGT
* * * *
5322523 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGATTTTTTATTTTAAAAG
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTT-AAAC
5322588 CCTCAGGGT
65 CCTCAGGGT
5322597 CAT
1 CAT
5322600 TCATAAGACC
Statistics
Matches: 485, Mismatches: 29, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
72 1 0.00
73 327 0.67
74 17 0.04
75 5 0.01
76 135 0.28
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (73 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
CTCAGGGT
Found at i:5322767 original size:3 final size:3
Alignment explanation
Indices: 5322752--5322848 Score: 117
Period size: 3 Copynumber: 32.3 Consensus size: 3
5322742 TTTAGTTCGC
* * **
5322752 ATT ATT TTT ATT ATT ATT ATT ATT -CT ATT A-T ATT ATT ATT ATT AAG
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
5322798 ATT ATT ATT ATT ATAT ATT ATT ATT ATT AAT ATT ATT ATT ATTT ATT
1 ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT
5322845 ATT A
1 ATT A
5322849 AATAAATATA
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
2 3 0.04
3 71 0.89
4 6 0.08
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:5322794 original size:31 final size:29
Alignment explanation
Indices: 5322752--5322848 Score: 126
Period size: 28 Copynumber: 3.3 Consensus size: 29
5322742 TTTAGTTCGC
*
5322752 ATTATTTTTATTATTATTATTATTCTATTAT
1 ATTATTATTATTATTATTATTA-T-TATTAT
**
5322783 ATTATTATTATTAAGATTATTATTATTAT
1 ATTATTATTATTATTATTATTATTATTAT
*
5322812 A-TATTATTATTATTAATATTATTATTAT
1 ATTATTATTATTATTATTATTATTATTAT
5322840 -TTATTATTA
1 ATTATTATTA
5322849 AATAAATATA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
28 32 0.54
29 7 0.12
30 1 0.02
31 19 0.32
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (29 bp):
ATTATTATTATTATTATTATTATTATTAT
Found at i:5324940 original size:11 final size:13
Alignment explanation
Indices: 5324903--5324942 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
5324893 TGTTTAATAA
5324903 AATATA-TATATT
1 AATATATTATATT
*
5324915 AATATATTATCTT
1 AATATATTATATT
5324928 AA-A-ATTATATT
1 AATATATTATATT
5324939 AATA
1 AATA
5324943 ATCTTAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 8 0.33
13 7 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATTATATT
Found at i:5326914 original size:16 final size:16
Alignment explanation
Indices: 5326893--5326928 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5326883 TGCAGATTGA
* *
5326893 AATTAAACAACAAATC
1 AATTAAACAAAAAAAC
5326909 AATTAAACAAAAAAAC
1 AATTAAACAAAAAAAC
5326925 AATT
1 AATT
5326929 TTTATTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.67, C:0.14, G:0.00, T:0.19
Consensus pattern (16 bp):
AATTAAACAAAAAAAC
Found at i:5328357 original size:21 final size:21
Alignment explanation
Indices: 5328331--5328440 Score: 89
Period size: 21 Copynumber: 5.3 Consensus size: 21
5328321 GTATACCATA
* *
5328331 TGGATCCTGAATGGTGGGAGG
1 TGGATCCTGAACGATGGGAGG
*
5328352 TGGATCTTGAACGATGGGAGG
1 TGGATCCTGAACGATGGGAGG
* * ** *
5328373 -GGCCTCTTGAACGATGACAAG
1 TGG-ATCCTGAACGATGGGAGG
* *
5328394 T-AATCCTGAACAATGGGAGG
1 TGGATCCTGAACGATGGGAGG
* *
5328414 TGGATCCTGAACAATGGTAGG
1 TGGATCCTGAACGATGGGAGG
5328435 TGGATC
1 TGGATC
5328441 GAGCTTCTTC
Statistics
Matches: 70, Mismatches: 16, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
20 15 0.21
21 55 0.79
ACGTcount: A:0.26, C:0.15, G:0.36, T:0.23
Consensus pattern (21 bp):
TGGATCCTGAACGATGGGAGG
Found at i:5328594 original size:4 final size:4
Alignment explanation
Indices: 5328573--5328606 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
5328563 GGTTCGCTAA
* *
5328573 AAAT AAAT TAAT ACAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
5328607 TGCCGAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:5328739 original size:21 final size:21
Alignment explanation
Indices: 5328715--5328766 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
5328705 TGAAACAATC
* * *
5328715 TCACGTAGAGTAGCTACCTCA
1 TCACGTAAAGAAGATACCTCA
5328736 TCACGTAAAGAAGATACCTCA
1 TCACGTAAAGAAGATACCTCA
*
5328757 CCACGTAAAG
1 TCACGTAAAG
5328767 CACCATTGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.19
Consensus pattern (21 bp):
TCACGTAAAGAAGATACCTCA
Found at i:5328900 original size:3 final size:3
Alignment explanation
Indices: 5328888--5328967 Score: 76
Period size: 3 Copynumber: 27.3 Consensus size: 3
5328878 TTATATTAAA
* * *
5328888 ATT A-T ATT ATT ATT CTT ATT A-T ATT ATT ATT ATT ATA ACT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
5328933 ATT ATA ATAC ATT ATT ATT ATT ATT ACT ATT ATT A
1 ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT A
5328968 ATGTTACATA
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
2 6 0.10
3 54 0.87
4 2 0.03
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:5332210 original size:21 final size:21
Alignment explanation
Indices: 5332186--5332246 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
5332176 CAAAATCGGG
5332186 AGACATGAAGACCATTCATAA
1 AGACATGAAGACCATTCATAA
* *
5332207 AGACAAGAAGACCCTTCATAA
1 AGACATGAAGACCATTCATAA
* *
5332228 AGATATAAAGACCACTTCA
1 AGACATGAAGACCA-TTCA
5332247 CATTGGAGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 29 0.88
22 4 0.12
ACGTcount: A:0.48, C:0.21, G:0.13, T:0.18
Consensus pattern (21 bp):
AGACATGAAGACCATTCATAA
Found at i:5335441 original size:23 final size:23
Alignment explanation
Indices: 5335381--5335435 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
5335371 AAGCTTGAAC
5335381 AAATGGAAGATTTCAGAGAACTG
1 AAATGGAAGATTTCAGAGAACTG
5335404 AAATGGAAGATTTCAGAGAACTG
1 AAATGGAAGATTTCAGAGAACTG
5335427 AAATGGAAG
1 AAATGGAAG
5335436 TGTTCAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.45, C:0.07, G:0.27, T:0.20
Consensus pattern (23 bp):
AAATGGAAGATTTCAGAGAACTG
Found at i:5336397 original size:125 final size:124
Alignment explanation
Indices: 5336154--5336525 Score: 435
Period size: 125 Copynumber: 3.0 Consensus size: 124
5336144 AAGTTAGGAT
* * *
5336154 ATATTGGGGCACGACTG-AGCC-CATCATGTTGAGATGATAAGATTCAGACCAAGGAGGCATGAA
1 ATATTGGGGCACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAGGAGGCTTGAA
* * * *
5336217 GAATGAGCTTTACAATTTGAAGTGATGGGACATTTTGAAGGCCCTTACCGGTATAAGTTA
66 GAATGAGCCTTACAATTTGAGGTGATGGG-CATTTTGAAGGCCCATACCAGTATAAGTTA
* *
5336277 ATGTTGGGGTACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAGGAGGCTTGAA
1 ATATTGGGGCACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAGGAGGCTTGAA
* * *
5336342 GAACGAGCCTTACAATTTGAGGTGATAGGGCATTTTGAAGGCACATACCAGTATAAGGTA
66 GAATGAGCCTTACAATTTGAGGTGAT-GGGCATTTTGAAGGCCCATACCAGTATAAGTTA
** * * * * * * * *
5336402 ATATTGGGGCGTGACTAAACCCATATTATGTTGAGATGACAAGATACAGTCCAAGAAGACCTTG-
1 ATATTGGGGCACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAGGAG-GCTTGA
* * * ** *
5336466 ATAATAAGCCTTACAATTAGAGGTCTTGTGGCATTTTGAAGGCCCGTACCAGTATAAGTT
65 AGAATGAGCCTTACAATTTGAGGTGATG-GGCATTTTGAAGGCCCATACCAGTATAAGTT
5336526 GACGTTGCGG
Statistics
Matches: 211, Mismatches: 33, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
123 15 0.07
124 4 0.02
125 185 0.88
126 7 0.03
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (124 bp):
ATATTGGGGCACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAGGAGGCTTGAA
GAATGAGCCTTACAATTTGAGGTGATGGGCATTTTGAAGGCCCATACCAGTATAAGTTA
Found at i:5337909 original size:36 final size:37
Alignment explanation
Indices: 5337839--5337933 Score: 140
Period size: 36 Copynumber: 2.6 Consensus size: 37
5337829 GCCTTTACTG
* *
5337839 AAGAGTAGTGAATCAAATCCATCTTAATCCTTCACCA
1 AAGAGTAGTGAAGCAAATCCATCTTAATCATTCACCA
*
5337876 AAGAGTAGTGAAGCAAA-CCATCTTAAGT-ATTCACCG
1 AAGAGTAGTGAAGCAAATCCATCTTAA-TCATTCACCA
5337912 AAGAGTAGTGAAGCAAATCCAT
1 AAGAGTAGTGAAGCAAATCCAT
5337934 TTTATGCCTT
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
36 32 0.60
37 21 0.40
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (37 bp):
AAGAGTAGTGAAGCAAATCCATCTTAATCATTCACCA
Found at i:5338497 original size:56 final size:56
Alignment explanation
Indices: 5338435--5338565 Score: 181
Period size: 56 Copynumber: 2.3 Consensus size: 56
5338425 TACTCTCTAG
* *
5338435 AGAAAGAGAGAACTAACCCGTTTGTAGAAAATTATTCGAGTTCTATAATTCCTGAA
1 AGAAAGAGAGAACGAACCCGTTTGCAGAAAATTATTCGAGTTCTATAATTCCTGAA
* * * *
5338491 AGAAAGAGGGAGCGAACCCGTTTGCAGAACATTATTCGAGTTCTATACTTCCTGAA
1 AGAAAGAGAGAACGAACCCGTTTGCAGAAAATTATTCGAGTTCTATAATTCCTGAA
* * *
5338547 AGAAATAGGGAGCGAACCC
1 AGAAAGAGAGAACGAACCC
5338566 ATTCGTGGAA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 68 1.00
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.24
Consensus pattern (56 bp):
AGAAAGAGAGAACGAACCCGTTTGCAGAAAATTATTCGAGTTCTATAATTCCTGAA
Found at i:5338585 original size:56 final size:56
Alignment explanation
Indices: 5338460--5338614 Score: 190
Period size: 56 Copynumber: 2.8 Consensus size: 56
5338450 ACCCGTTTGT
* * * * *
5338460 AGAAAATTATTCGAGTTCTATAATTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGC
1 AGAACATTATTCGAGTTCTATACTTCCTGAAAGAAATAGGGAGCGAACCCATTCGC
*
5338516 AGAACATTATTCGAGTTCTATACTTCCTGAAAGAAATAGGGAGCGAACCCATTCGT
1 AGAACATTATTCGAGTTCTATACTTCCTGAAAGAAATAGGGAGCGAACCCATTCGC
* * *
5338572 GGAAGATTGTTCGAG-TCTTATAC-TCTCTG-AAGAAATAGGGAGC
1 AGAACATTATTCGAGTTC-TATACTTC-CTGAAAGAAATAGGGAGC
5338615 AGACATGATT
Statistics
Matches: 88, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
55 18 0.20
56 70 0.80
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (56 bp):
AGAACATTATTCGAGTTCTATACTTCCTGAAAGAAATAGGGAGCGAACCCATTCGC
Found at i:5338644 original size:55 final size:52
Alignment explanation
Indices: 5338581--5338927 Score: 384
Period size: 55 Copynumber: 6.6 Consensus size: 52
5338571 TGGAAGATTG
* * *
5338581 TTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACATGATTGTTGAAAA
1 TTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGA
* * *
5338633 TTTTTCTAGTCTTATACTCTCTGAAAGAATAGGGAGCAGACACGATTGTTCAAGA
1 ---TTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGA
*
5338688 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAAACACGATTGTT---G-
1 ---TTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGA
* * * *
5338739 TTTGAGTCTTATACTCTCTCAAGGAATAGGGAGGAGACACGTTTGTTGAAGA
1 TTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGA
* * * * *
5338791 TT-GAGTCCTATACTCTCTGAAGAAATAGGGAGCGGACACGTTTGTTGAAGGTTG
1 TTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAA-G--A
* *
5338845 TTCAAGTCTTATACTCTCTGAAGGAATAGGGAGC-GAACACGTTTGTTGAAGA
1 TTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAG-ACACGATTGTTGAAGA
*
5338897 -TCGAGTCCTATACTCTCTGAAGGAATAGGGA
1 TTCGAGTCTTATACTCTCTGAAGGAATAGGGA
5338928 ACAAACCTGT
Statistics
Matches: 256, Mismatches: 27, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
48 42 0.16
51 72 0.28
52 4 0.02
54 4 0.02
55 134 0.52
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (52 bp):
TTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGA
Found at i:5338862 original size:154 final size:156
Alignment explanation
Indices: 5338578--5338927 Score: 463
Period size: 154 Copynumber: 2.2 Consensus size: 156
5338568 TCGTGGAAGA
* * *
5338578 TTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACATGATTGTTGAAAATTTTTCTAGT
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAAA--TTTCGAGT
* *
5338643 CTTATACTCTCTGAAAGAATAGGGAGCAGACACGATTGTTCAAGATTGTTCGAGTCTTATACTCT
64 CCTATACTCTCTGAAAGAATAGGGAGCAGACACGATTGTTCAAGATTGTTCAAGTCTTATACTCT
5338708 CTGAAGGAATAGGGAGCAAACACGATTG
129 CTGAAGGAATAGGGAGCAAACACGATTG
* * * * *
5338736 TTGTTTGAGTCTTATACTCTCTCAAGGAATAGGGAGGAGACACGTTTGTTGAAGA-TT-GAGTCC
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAAATTTCGAGTCC
* * * *
5338799 TATACTCTCTG-AAGAAATAGGGAGCGGACACGTTTGTTGAAGGTTGTTCAAGTCTTATACTCTC
66 TATACTCTCTGAAAG-AATAGGGAGCAGACACGATTGTTCAAGATTGTTCAAGTCTTATACTCTC
* *
5338863 TGAAGGAATAGGGAGCGAACACGTTTG
130 TGAAGGAATAGGGAGCAAACACGATTG
* *
5338890 TTGAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGA
1 TT---GTTCGAGTCTTATACTCTCTGAAGGAATAGGGA
5338928 ACAAACCTGT
Statistics
Matches: 168, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
153 3 0.02
154 86 0.51
155 2 0.01
157 29 0.17
158 48 0.29
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.30
Consensus pattern (156 bp):
TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAAATTTCGAGTCC
TATACTCTCTGAAAGAATAGGGAGCAGACACGATTGTTCAAGATTGTTCAAGTCTTATACTCTCT
GAAGGAATAGGGAGCAAACACGATTG
Found at i:5338946 original size:106 final size:106
Alignment explanation
Indices: 5338582--5338986 Score: 416
Period size: 106 Copynumber: 3.8 Consensus size: 106
5338572 GGAAGATTGT
* * * * * * *
5338582 TCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACATGATTGTTGAAAATTTTTCTAGTCTTA
1 TCGAGTCCTATACTCTCTGAAGAAATAGGGAGCAAACACG-TTTTTGAAGATTGTTCGAGTCTTA
* * *
5338647 TACTCTCTGAAAGAATAGGGAGC-AGACACGATTGTTCAAGA
65 TACTCTCTGAAGGAATAGGGAGCGAGACACGTTTGTTGAAGA
* * * *
5338688 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAAACACG--ATT---G-TTGTTTGAGTC
1 ----TCGAGTCCTATACTCTCTGAAGAAATAGGGAGCAAACACGTTTTTGAAGATTGTTCGAGTC
*
5338747 TTATACTCTCTCAAGGAATAGGGAG-GAGACACGTTTGTTGAAGA
62 TTATACTCTCTGAAGGAATAGGGAGCGAGACACGTTTGTTGAAGA
* ** * *
5338791 TTGAGTCCTATACTCTCTGAAGAAATAGGGAGCGGACACGTTTGTTGAAGGTTGTTCAAGTCTTA
1 TCGAGTCCTATACTCTCTGAAGAAATAGGGAGCAAACACGTTT-TTGAAGATTGTTCGAGTCTTA
5338856 TACTCTCTGAAGGAATAGGGAGCGA-ACACGTTTGTTGAAGA
65 TACTCTCTGAAGGAATAGGGAGCGAGACACGTTTGTTGAAGA
* * * *
5338897 TCGAGTCCTATACTCTCTGAAGGAATAGGGAACAAAC-CTGTTTTATGAAGATTGTTTGAGTTTT
1 TCGAGTCCTATACTCTCTGAAGAAATAGGGAGCAAACAC-GTTTT-TGAAGATTGTTCGAGTCTT
* * * *
5338961 ACACTCCCTGAAGCAAGAGGGAGCGA
64 ATACTCTCTGAAGGAATAGGGAGCGA
5338987 ACCCGCTGGT
Statistics
Matches: 250, Mismatches: 34, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
99 35 0.14
102 2 0.01
103 47 0.19
105 3 0.01
106 122 0.49
107 4 0.02
110 37 0.15
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (106 bp):
TCGAGTCCTATACTCTCTGAAGAAATAGGGAGCAAACACGTTTTTGAAGATTGTTCGAGTCTTAT
ACTCTCTGAAGGAATAGGGAGCGAGACACGTTTGTTGAAGA
Found at i:5339188 original size:3 final size:3
Alignment explanation
Indices: 5339176--5339270 Score: 115
Period size: 3 Copynumber: 32.3 Consensus size: 3
5339166 TTAATTTAAA
5339176 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
5339222 ATT ATT ATA ACT ATT A-T ATT ATA ATAC ATT ATT ATT ATT ACT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT
5339267 ATT A
1 ATT A
5339271 ATGTTACATA
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
2 6 0.08
3 71 0.90
4 2 0.03
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Done.