Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006093.1 Hibiscus syriacus cultivar Beakdansim tig00014444_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: 3172561
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 13
Found at i:417464 original size:46 final size:46
Alignment explanation
Indices: 417374--417843 Score: 632
Period size: 46 Copynumber: 10.4 Consensus size: 46
417364 AGACATTAAT
* *
417374 GCATCCTTTCAGGCCTTAATGCGT-CTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
* * *
417419 GCATCCTTTAATGCCTTAATACATCCTTTCATGCATTTTATTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
* *
417465 ACATTCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
* *
417511 ACATCCTTTCATGCCTTAATGCATCCTTTCACGCATTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
* *
417557 TCATCCTTTCATGCCTTAATCCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
* * ** **
417603 ACATCCTTTCATGACTTAATGCATCCTTTCATGTGTTTTCCTTAAT-
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTT-ATG
*
417649 GCATCCTTTCATGCCTTAATGCATCCTTTCATGC--CTTA---AT-
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
*
417689 GCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
* * * * ** *
417735 CCATCCTATCATTCTTTAATGCATTTTTTCATGCATTTTAGTTTTG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
417781 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
*
417827 GCATCCTTTAATGCCTT
1 GCATCCTTTCATGCCTT
417844 TTAGTTATGA
Statistics
Matches: 372, Mismatches: 45, Indels: 15
0.86 0.10 0.03
Matches are distributed among these distances:
40 35 0.09
42 3 0.01
44 2 0.01
45 22 0.06
46 308 0.83
47 2 0.01
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.44
Consensus pattern (46 bp):
GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
Found at i:422599 original size:46 final size:46
Alignment explanation
Indices: 422532--423016 Score: 745
Period size: 46 Copynumber: 10.5 Consensus size: 46
422522 AATTATTCTT
* * *
422532 ATTTTAGTTATGGCATCCTTTCAGGCCTTAACGCATCCTTTAATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
422578 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCTTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
422624 ATTTTAGTTATGGCATCCTTTCATTCCTTAATGCATCATTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
422670 ATTTTAGCTATGGCATCCTTTCATCCCTTAATGCATCCTTTCATTC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
422716 ATTTTAGTTATGGCATCCTTTCAGGCCTTAATGCATCCTCTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
422762 ATTTTAGTTATGGCATCATTTCATGCCTTAATGCATCTTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * * *
422808 ATTTTATTTATGGCATCCTTTCATGCCTTAATACATCTTTTTATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
422854 ATTTTAGTTTTGGCATCATTTCATGCCTTAATGCATCATTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
422900 ATTTTAGTTATGGCATCCATTCAGGCCTTAATGCATCCTTTCATGT
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
422946 ATTTTAGTTATGGCATCCTTTCATGTCTTAATGCATCATTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
422992 ATTTTAGTTATGGCATCCTTTCATG
1 ATTTTAGTTATGGCATCCTTTCATG
423017 AATTGTAGTC
Statistics
Matches: 399, Mismatches: 40, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 399 1.00
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.44
Consensus pattern (46 bp):
ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:422876 original size:72 final size:72
Alignment explanation
Indices: 422532--423087 Score: 264
Period size: 72 Copynumber: 8.0 Consensus size: 72
422522 AATTATTCTT
* ** * *
422532 ATTTTAGTTATGGCATCCTTTCAGGCCTTAACGCATCCTTTAATGCATTTTAGTTATGGCATCCT
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATACATCTTTTCATGCATTTTAGTTATGGCATCCT
422597 TTCATGC
66 TTCATGC
* * * * * * *
422604 --CTTA---AT-GCATCTTTTCATGCATTTTAGTTATGGCATCCTTTCATTC--CTTA---AT-G
1 ATTTTAGTTATGGCATCCTTTCATGC--CTTA---AT-ACATCTTTTCATGCATTTTAGTTATGG
*
422657 CATCATTTCATGC
60 CATCCTTTCATGC
* * * * *
422670 ATTTTAGCTATGGCATCCTTTCATCCCTTAATGCATCCTTTCATTCATTTTAGTTATGGCATCCT
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATACATCTTTTCATGCATTTTAGTTATGGCATCCT
*
422735 TTCAGGC
66 TTCATGC
* * * * * *
422742 --CTTA---AT-GCATCCTCTCATGCATTTTAGTTATGGCATCATTTCATGC--CTTA---AT-G
1 ATTTTAGTTATGGCATCCTTTCATGC--CTTA---AT-ACATCTTTTCATGCATTTTAGTTATGG
*
422795 CATCTTTTCATGC
60 CATCCTTTCATGC
* * * *
422808 ATTTTATTTATGGCATCCTTTCATGCCTTAATACATCTTTTTATGCATTTTAGTTTTGGCATCAT
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATACATCTTTTCATGCATTTTAGTTATGGCATCCT
422873 TTCATGC
66 TTCATGC
* * * * * ** * *
422880 --CTTA---AT-GCATCATTTCATGCATT-TTA-GT-TATGGCATCCA-TTCAGGCCTTAAT-GC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATACATCT-TTTCATGCATTTTA-G--TT-ATGGC
*
422934 ATCCTTTCATGT
61 ATCCTTTCATGC
* * *
422946 ATTTTAGTTATGGCATCCTTTCATGTCTTAATGCATCATTTCATGCATTTTAGTTATGGCATCCT
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATACATCTTTTCATGCATTTTAGTTATGGCATCCT
*
423011 TTCATGA
66 TTCATGC
* * * * * *
423018 ATTGTAGTCATGGTATCCTTTCAGGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCATCCT
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATACATCTTTTCATGCATTTTAGTTATGGCATCCT
423083 TTCAT
66 TTCAT
423088 TTTTTTTAAT
Statistics
Matches: 366, Mismatches: 66, Indels: 104
0.68 0.12 0.19
Matches are distributed among these distances:
63 4 0.01
64 7 0.02
65 2 0.01
66 103 0.28
67 15 0.04
68 21 0.06
70 21 0.06
71 14 0.04
72 167 0.46
73 1 0.00
74 8 0.02
75 3 0.01
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.44
Consensus pattern (72 bp):
ATTTTAGTTATGGCATCCTTTCATGCCTTAATACATCTTTTCATGCATTTTAGTTATGGCATCCT
TTCATGC
Found at i:423054 original size:46 final size:46
Alignment explanation
Indices: 423004--423169 Score: 181
Period size: 46 Copynumber: 3.6 Consensus size: 46
422994 TTTAGTTATG
* * * *
423004 GCATCCTTTCATGAATTGTAGTCATGGTATCCTTTCAGGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGTATCCTTTCATGCCTTAAT
* ***
423050 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATTTTTTTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGTATCCTTTCA--TGCCTTAAT
* *
423098 GCATCTTTTCATGCATTTTAGTTATGGCT-TCCTTCCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGG-TATCCTTTCATGCCTTAAT
* * *
423144 GCGTCCTTTCATGCCTTTTAATTATG
1 GCATCCTTTCATGCATTTTAGTTATG
423170 AATTTGTTTT
Statistics
Matches: 99, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
46 61 0.62
48 38 0.38
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.46
Consensus pattern (46 bp):
GCATCCTTTCATGCATTTTAGTTATGGTATCCTTTCATGCCTTAAT
Found at i:423101 original size:22 final size:24
Alignment explanation
Indices: 423045--423121 Score: 70
Period size: 26 Copynumber: 3.1 Consensus size: 24
423035 CTTTCAGGCC
423045 TTAATGCATCCTTTCATGCATTTTAG
1 TTAATGCATCCTTTCAT--ATTTTAG
*
423071 TT-ATGGCATCCTTTCAT-TTTT-T
1 TTAAT-GCATCCTTTCATATTTTAG
*
423093 TTAATGCATCTTTTCATGCATTTTAG
1 TTAATGCATCCTTTCAT--ATTTTAG
423119 TTA
1 TTA
423122 TGGCTTCCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
22 13 0.31
23 6 0.14
25 6 0.14
26 17 0.40
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.52
Consensus pattern (24 bp):
TTAATGCATCCTTTCATATTTTAG
Found at i:428399 original size:46 final size:46
Alignment explanation
Indices: 428329--428902 Score: 715
Period size: 46 Copynumber: 12.6 Consensus size: 46
428319 TTATTCATAA
* *
428329 ATTTTAGTTATGGCATCCTCTCATGCATTAATGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * ** * *
428375 TTTTTAATTATGGGGTCCTTTCATGACTTAATGCATCCTTTCATGG
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
** * * *
428421 ATTTTAGTTATGGCGGCTTTTCATGCCTTAATGCATCTTTTCATGT
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
428467 ATTTTAGTTATGG-ATCCTTTCATGCCTTAATGTATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
428512 ATTTTAGTTATGGCATCCTTTTATGCCTTAATGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
428558 ATTTTAGTTATGGCATCCTTTAATGCCTTAATGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
428604 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * * *
428650 --CTCA---AT-GCATCCTTTCATACCTTAACGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
428690 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * * *
428736 --CTTA---AT-GCATCATTTCATTCAATTTAGTTATGGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC--CTTA---AT-GCATCCTTTCATGC
* * * *
428782 ATTTTTGTTATGGCATCCTTTCATACCTTAATGCATCATTTCATGA
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
428828 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
428874 ATTTTAGTTATGGTATCCTTTTATGCCTT
1 ATTTTAGTTATGGCATCCTTTCATGCCTT
428903 TTAGTTATGA
Statistics
Matches: 457, Mismatches: 52, Indels: 38
0.84 0.10 0.07
Matches are distributed among these distances:
40 44 0.10
41 4 0.01
42 5 0.01
44 5 0.01
45 43 0.09
46 335 0.73
47 2 0.00
48 2 0.00
50 3 0.01
51 2 0.00
52 12 0.03
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.44
Consensus pattern (46 bp):
ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:428537 original size:26 final size:26
Alignment explanation
Indices: 428329--428911 Score: 244
Period size: 20 Copynumber: 25.5 Consensus size: 26
428319 TTATTCATAA
*
428329 ATTTTAGTTATGGCATCCTCTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
428355 A--TTA---AT-GCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
* * **
428375 TTTTTAATTATGGGGTCCTTTCATG-
1 ATTTTAGTTATGGCATCCTTTCATGC
* *
428400 A-CTTA---AT-GCATCCTTTCATGG
1 ATTTTAGTTATGGCATCCTTTCATGC
** *
428421 ATTTTAGTTATGGCGGCTTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
* * *
428447 --CTTA---AT-GCATCTTTTCATGT
1 ATTTTAGTTATGGCATCCTTTCATGC
428467 ATTTTAGTTATGG-ATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
* *
428492 --CTTA---AT-GTATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
*
428512 ATTTTAGTTATGGCATCCTTTTATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
*
428538 --CTTA---AT-GCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
*
428558 ATTTTAGTTATGGCATCCTTTAATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
*
428584 --CTTA---AT-GCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
428604 ATTTTAGTTATGGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
*
428630 --CTTA---AT-GCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
* *
428650 --CTCA---AT-GCATCCTTTCAT--
1 ATTTTAGTTATGGCATCCTTTCATGC
** *
428668 ACCTTA---A-CGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
428690 ATTTTAGTTATGGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
* *
428716 --CTTA---AT-GCATCATTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
* * *
428736 --CTTA---AT-GCATCATTTCATTC
1 ATTTTAGTTATGGCATCCTTTCATGC
*
428756 AATTTAGTTATGGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
*
428782 ATTTTTGTTATGGCATCCTTTCAT--
1 ATTTTAGTTATGGCATCCTTTCATGC
** * *
428806 ACCTTA---AT-GCATCATTTCATGA
1 ATTTTAGTTATGGCATCCTTTCATGC
428828 ATTTTAGTTATGGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
* *
428854 --CTTA---AT-GCATCATTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
* *
428874 ATTTTAGTTATGGTATCCTTTTATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
*
428900 CTTTTAGTTATG
1 ATTTTAGTTATG
428912 AATTCATTTT
Statistics
Matches: 433, Mismatches: 60, Indels: 128
0.70 0.10 0.21
Matches are distributed among these distances:
19 1 0.00
20 178 0.41
21 19 0.04
22 32 0.07
23 3 0.01
24 27 0.06
25 29 0.07
26 144 0.33
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (26 bp):
ATTTTAGTTATGGCATCCTTTCATGC
Found at i:428921 original size:26 final size:26
Alignment explanation
Indices: 428862--428922 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
428852 GCCTTAATGC
* *
428862 ATCATTTCATGCATTTTAGTTATGGT
1 ATCATTTTATGCATTTTAGTTATGAT
* *
428888 ATCCTTTTATGCCTTTTAGTTATGA-
1 ATCATTTTATGCATTTTAGTTATGAT
428913 ATTCATTTTA
1 A-TCATTTTA
428923 GAGCAGTTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 1 0.03
26 28 0.97
ACGTcount: A:0.23, C:0.13, G:0.11, T:0.52
Consensus pattern (26 bp):
ATCATTTTATGCATTTTAGTTATGAT
Found at i:434583 original size:19 final size:17
Alignment explanation
Indices: 434556--434598 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
434546 TCACGTCCAG
*
434556 ATTTTTTTAATATATATAT
1 ATTTATTTAA-ATA-ATAT
434575 ATTTATTTAAATAATAT
1 ATTTATTTAAATAATAT
434592 -TTTATTT
1 ATTTATTT
434599 TTTATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 7 0.30
17 4 0.17
18 3 0.13
19 9 0.39
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTATTTAAATAATAT
Found at i:434602 original size:19 final size:19
Alignment explanation
Indices: 434556--434602 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
434546 TCACGTCCAG
*
434556 ATTTTTTTAATATATATAT
1 ATTTTTTAAATATATATAT
*
434575 ATTTATTTAAATA-ATATTTT
1 ATTT-TTTAAATATATA-TAT
434595 ATTTTTTA
1 ATTTTTTA
434603 TAAAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTTTAAATATATATAT
Found at i:438757 original size:21 final size:22
Alignment explanation
Indices: 438722--438802 Score: 78
Period size: 21 Copynumber: 3.8 Consensus size: 22
438712 TTGGTGCAGA
*
438722 GGGAATCGA-TCCCCCCATGA-
1 GGGAACCGATTCCCCCCATGAG
**
438742 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCATG-AG
*
438765 GGGAACCGATTCCCCCTAT-AG
1 GGGAACCGATTCCCCCCATGAG
* *
438786 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
438803 TGGGGTTCTG
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
20 8 0.16
21 24 0.47
22 1 0.02
23 18 0.35
ACGTcount: A:0.23, C:0.35, G:0.25, T:0.17
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCATGAG
Found at i:442254 original size:24 final size:24
Alignment explanation
Indices: 442222--442274 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
442212 CTCAACAGAC
442222 CGGTTAGCGAACCGATCATATTAT
1 CGGTTAGCGAACCGATCATATTAT
* * * *
442246 CGGTTAGCGAATCGGTTATTTTAT
1 CGGTTAGCGAACCGATCATATTAT
442270 CGGTT
1 CGGTT
442275 CATTGGTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.36
Consensus pattern (24 bp):
CGGTTAGCGAACCGATCATATTAT
Found at i:443117 original size:24 final size:24
Alignment explanation
Indices: 443090--443145 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
443080 CGAACGGTTC
443090 AGCGGTTCTGGTCGGTTCACTAAT
1 AGCGGTTCTGGTCGGTTCACTAAT
443114 AGCGGTTCTGGTCGGTTCACTAAT
1 AGCGGTTCTGGTCGGTTCACTAAT
443138 AGCGGTTC
1 AGCGGTTC
443146 AACCGGTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.16, C:0.21, G:0.30, T:0.32
Consensus pattern (24 bp):
AGCGGTTCTGGTCGGTTCACTAAT
Found at i:444661 original size:14 final size:14
Alignment explanation
Indices: 444644--444678 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
444634 ATTATTTTCT
444644 AAAAATAAAAACAA
1 AAAAATAAAAACAA
* *
444658 AAAAATGAAAATAA
1 AAAAATAAAAACAA
444672 AAAAATA
1 AAAAATA
444679 TTTTCTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.83, C:0.03, G:0.03, T:0.11
Consensus pattern (14 bp):
AAAAATAAAAACAA
Found at i:445250 original size:17 final size:17
Alignment explanation
Indices: 445212--445250 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
445202 ATTAGCTCTA
*
445212 CAATTCTATTTTATTCT
1 CAATTCTATTTTATTAT
*
445229 TAATTCTATTTTATTAT
1 CAATTCTATTTTATTAT
445246 CAATT
1 CAATT
445251 TTGTCATTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.13, G:0.00, T:0.59
Consensus pattern (17 bp):
CAATTCTATTTTATTAT
Found at i:445275 original size:27 final size:27
Alignment explanation
Indices: 445234--445287 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
445224 ATTCTTAATT
*
445234 CTATTTTATTATCAATTTTGTCATTTC
1 CTATTTTATTATCAATTTGGTCATTTC
*
445261 CTATATTTATT-TCAATTTGGTTATTTC
1 CTAT-TTTATTATCAATTTGGTCATTTC
445288 AATATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.22, C:0.13, G:0.06, T:0.59
Consensus pattern (27 bp):
CTATTTTATTATCAATTTGGTCATTTC
Found at i:446926 original size:14 final size:13
Alignment explanation
Indices: 446904--446950 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
446894 ATTTTCTATA
446904 TTAATTATAATCC
1 TTAATTATAATCC
446917 TTATATTATAAAT-C
1 TTA-ATTAT-AATCC
*
446931 TTAATTATAATCA
1 TTAATTATAATCC
446944 TTAATTA
1 TTAATTA
446951 ATTTCATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 3 0.10
13 15 0.50
14 9 0.30
15 3 0.10
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (13 bp):
TTAATTATAATCC
Found at i:447548 original size:10 final size:10
Alignment explanation
Indices: 447534--447591 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
447524 CATGTTTAAT
*
447534 TATATACTTT
1 TATATACTTA
447544 TATATA-TATA
1 TATATACT-TA
*
447554 TATATAACATA
1 TATAT-ACTTA
447565 TATATACTTA
1 TATATACTTA
447575 TATATA-TATA
1 TATATACT-TA
447585 TATATAC
1 TATATAC
447592 ACACTTATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
9 2 0.05
10 30 0.75
11 8 0.20
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (10 bp):
TATATACTTA
Found at i:447549 original size:2 final size:2
Alignment explanation
Indices: 447544--447590 Score: 62
Period size: 2 Copynumber: 24.0 Consensus size: 2
447534 TATATACTTT
*
447544 TA TA TA TA TA TA TA TA -A CA TA TA TA TA CT- 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
447585 TA TA TA
1 TA TA TA
447591 CACACTTATG
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
1 2 0.05
2 38 0.93
3 1 0.02
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:449397 original size:2 final size:2
Alignment explanation
Indices: 449390--449460 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
449380 ACTACTTACT
449390 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
449432 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 T
449461 GTCAAAAAAA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:451627 original size:21 final size:21
Alignment explanation
Indices: 451602--451660 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
451592 TGCATTATGG
451602 CAAGGGGTTTTGAAACCAACT
1 CAAGGGGTTTTGAAACCAACT
451623 CAAGGGGTTTTGAAACCAACT
1 CAAGGGGTTTTGAAACCAACT
*
451644 CAGGGGGTTTTGAAACC
1 CAAGGGGTTTTGAAACC
451661 TCTATTGCTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (21 bp):
CAAGGGGTTTTGAAACCAACT
Found at i:461651 original size:16 final size:18
Alignment explanation
Indices: 461630--461663 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
461620 TGTAAGGTAA
461630 TTTTTT-TAA-TATATAT
1 TTTTTTATAATTATATAT
461646 TTTTTTATAATTATATAT
1 TTTTTTATAATTATATAT
461664 GATTAGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTTATAATTATATAT
Found at i:467410 original size:49 final size:49
Alignment explanation
Indices: 467338--467435 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 49
467328 AGAGTCATCC
*
467338 TGTGACTACATTCATTCACTCATATTCCTC-GACAACTCTTAGTTTTTTT
1 TGTGACTACATTCATTCACTCATATGCCTCAG-CAACTCTTAGTTTTTTT
*
467387 TGTGACTACTTTCATTCACTCATATGCCTCAGCAACTCTTAGTTTTTTT
1 TGTGACTACATTCATTCACTCATATGCCTCAGCAACTCTTAGTTTTTTT
467436 CATGGAGTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
49 45 0.98
50 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.09, T:0.45
Consensus pattern (49 bp):
TGTGACTACATTCATTCACTCATATGCCTCAGCAACTCTTAGTTTTTTT
Found at i:474231 original size:21 final size:20
Alignment explanation
Indices: 474205--474244 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
474195 CATCAAGTTT
*
474205 TTTTATTGAAGCCATGAAATC
1 TTTTATCGAAGCCAT-AAATC
*
474226 TTTTATCGATGCCATAAAT
1 TTTTATCGAAGCCATAAAT
474245 TCCTGCAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (20 bp):
TTTTATCGAAGCCATAAATC
Found at i:475078 original size:20 final size:20
Alignment explanation
Indices: 475050--475100 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
475040 TGCCCACGAT
*
475050 TCCATTGAGCCTGAAAGAAC
1 TCCACTGAGCCTGAAAGAAC
*
475070 TCCACTGAGCCTGAAGGAAC
1 TCCACTGAGCCTGAAAGAAC
*
475090 TCTACTGAGCC
1 TCCACTGAGCC
475101 AAGCTCTCAC
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:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (20 bp):
TCCACTGAGCCTGAAAGAAC
Found at i:479059 original size:13 final size:13
Alignment explanation
Indices: 479041--479095 Score: 67
Period size: 13 Copynumber: 4.2 Consensus size: 13
479031 ACTGCAAAAA
479041 AAATAAAATAATT
1 AAATAAAATAATT
*
479054 AAATAAAATACTT
1 AAATAAAATAATT
*
479067 AAAAAATAAATAATT
1 -AAATA-AAATAATT
479082 AAATAAAAT-ATT
1 AAATAAAATAATT
479094 AA
1 AA
479096 CAAAACATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
12 5 0.14
13 16 0.44
14 8 0.22
15 7 0.19
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAAAATAATT
Found at i:479070 original size:28 final size:27
Alignment explanation
Indices: 479038--479100 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 27
479028 ATAACTGCAA
479038 AAAAAATAAAATAATTAAATAAAATACTT
1 AAAAAAT-AAATAATTAAATAAAATA-TT
479067 AAAAAATAAATAATTAAATAAAATATT
1 AAAAAATAAATAATTAAATAAAATATT
479094 AACAAAA
1 AA-AAAA
479101 CATTAAATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
27 4 0.12
28 22 0.67
29 7 0.21
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.25
Consensus pattern (27 bp):
AAAAAATAAATAATTAAATAAAATATT
Found at i:479436 original size:51 final size:51
Alignment explanation
Indices: 479381--479485 Score: 138
Period size: 51 Copynumber: 2.1 Consensus size: 51
479371 TGCACCGTGT
** * *
479381 CTTACCCTGCATGGTGCCACATCAACATAAGGCATGGTGCATAGGTCGCGC
1 CTTACCCCACATGGCGCCACATCAACATAAGGCACGGTGCATAGGTCGCGC
* * * *
479432 CTTACCCCACGTGGCGCCACATCAGCATAAGGCGCGGTGCATGGGTCGCGC
1 CTTACCCCACATGGCGCCACATCAACATAAGGCACGGTGCATAGGTCGCGC
479483 CTT
1 CTT
479486 TCTGCAAAGG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.20, C:0.32, G:0.28, T:0.20
Consensus pattern (51 bp):
CTTACCCCACATGGCGCCACATCAACATAAGGCACGGTGCATAGGTCGCGC
Found at i:479922 original size:20 final size:20
Alignment explanation
Indices: 479894--479933 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
479884 AGTACCACGC
479894 CACCACCTGTAGCTATAAAG
1 CACCACCTGTAGCTATAAAG
*
479914 CACCTCCTGTAGCTATAAAG
1 CACCACCTGTAGCTATAAAG
479934 AAGGGTTAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (20 bp):
CACCACCTGTAGCTATAAAG
Found at i:483474 original size:131 final size:132
Alignment explanation
Indices: 483241--483522 Score: 319
Period size: 131 Copynumber: 2.1 Consensus size: 132
483231 ATGTGGGTCT
* *
483241 TCTCCACTACTCTTTAGGGGATATCAGACTCGTAAATTTTGATCCACTTTGCTGCTCTTCAAGGA
1 TCTCCACTACTCTTTAGGGGAGATCAGACTCGTAAATTTTGATCCACTTCGCTGCTCTTCAAGGA
* *
483306 AGATTGACTAAAACTTTATTTACTTCGCTGCTCTTCAGGAAGAACAAAT-TCGAAAGAAGAA-GA
66 AGATTGACGAAAAC-TGATTTACTTCGCTGCTCTTCAGGAAGAACAAATCT-GAAAGAAGAATGA
483369 -ATC
129 TATC
* * *
483372 TACTCCACTACTCTTTAGGGGAGATCAGACAT-GT-AATTTTGATCCACTTCGTTGCTCTTTAGG
1 T-CTCCACTACTCTTTAGGGGAGATCAGAC-TCGTAAATTTTGATCCACTTCGCTGCTCTTCAAG
* * * * *
483435 GAAGATTGAATCGGAAGC-GATTTGCTTCAG-TGCTCTTCAGGAGGACCAAATCTGAAAGAAGAA
64 GAAGATTG-A-CGAAAACTGATTTACTTC-GCTGCTCTTCAGGAAGAACAAATCTGAAAGAAGAA
*
483498 TGATATG
126 TGATATC
*
483505 T-TCCACTATTCTTTAGGG
1 TCTCCACTACTCTTTAGGG
483523 AAAACCAGAT
Statistics
Matches: 129, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
131 87 0.67
132 34 0.26
133 8 0.06
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (132 bp):
TCTCCACTACTCTTTAGGGGAGATCAGACTCGTAAATTTTGATCCACTTCGCTGCTCTTCAAGGA
AGATTGACGAAAACTGATTTACTTCGCTGCTCTTCAGGAAGAACAAATCTGAAAGAAGAATGATA
TC
Found at i:484188 original size:18 final size:19
Alignment explanation
Indices: 484156--484191 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
484146 GTTTTTTTTA
484156 TTTATTTTTTCTCTTTCTC
1 TTTATTTTTTCTCTTTCTC
484175 TTTATTTTTT-TCTTTCT
1 TTTATTTTTTCTCTTTCT
484192 ATTTTCTCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTATTTTTTCTCTTTCTC
Found at i:484607 original size:41 final size:42
Alignment explanation
Indices: 484557--484635 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
484547 AGGTCTTATA
* *
484557 GATGGCCCAAAGGACTT-ATCATCTTGCTCGAAAGACTGATG
1 GATGACCCAAAGGACTTAATCATCATGCTCGAAAGACTGATG
*
484598 GATGACCCAAAGGATTTAATCATCATGCTCGAAAGACT
1 GATGACCCAAAGGACTTAATCATCATGCTCGAAAGACT
484636 TAATGATGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
41 15 0.44
42 19 0.56
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (42 bp):
GATGACCCAAAGGACTTAATCATCATGCTCGAAAGACTGATG
Found at i:484653 original size:42 final size:41
Alignment explanation
Indices: 484557--484657 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 41
484547 AGGTCTTATA
* *
484557 GATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGATG
1 GATGGCCCAAAGGACTTATCATCATGCTCGAAAGACTAATG
* *
484598 GATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTAAT-
1 GATGGCCCAAAGGACTT-ATCATCATGCTCGAAAGAC-TAATG
* *
484640 GATGGCTCGAAGGACTTA
1 GATGGCCCAAAGGACTTA
484658 CTAATTTTGG
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
41 16 0.32
42 31 0.62
43 3 0.06
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (41 bp):
GATGGCCCAAAGGACTTATCATCATGCTCGAAAGACTAATG
Found at i:485036 original size:259 final size:257
Alignment explanation
Indices: 484218--485041 Score: 1168
Period size: 261 Copynumber: 3.2 Consensus size: 257
484208 AAAAATATTT
* * * *
484218 TAAATGAGAAACTTTGAAAATCGTCTTCTCATTTTCTTACAAATTCCATATGACAACATATTGCC
1 TAAATGAGAAACTTTGAAAATCGT-TTCTCATTTT-TTTCAAAAT-CATATGAAAACATCTTGCC
* * * *
484283 CAAAGGTCTTATAGATGGCTCGAAGGACTTATAATCTTGCTCGAAAGACTGAAAGATGGCTCAAA
63 CAAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGAAAGATGAC-CAAA
* *
484348 GGATTTAATCATCATGCTCGAAAGACTTACTGATTGCCCGAAGGACTTACCAATTTTGGAAATAG
127 GGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTACCAATTTTGGAAATAG
* *
484413 TTTACTTGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAGATTTCATTTTATGAAAATA
192 TTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAGATTTCATTTTCTGAAAATA
*
484478 T
257 A
* * ** ** *
484479 TAAGTGAGAACCTTTGAAAATTATTTTTCTCATTTTTCACAAACATCATATGAAAGCATCTTGCC
1 TAAATGAGAAACTTTGAAAA-T-CGTTTCTCATTTTTTTCAAA-ATCATATGAAAACATCTTGCC
**
484544 CAAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGATGGATGACCCAAA
63 CAAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGAAAGATGA-CCAAA
* *
484609 GGATTTAATCATCATGCTCGAAAGACTTAATGATGG-CTCGAAGGACTTACTAATTTTGGAAATA
127 GGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCT-GAAGGACTTACCAATTTTGGAAATA
*
484673 GTTTACTAGGTAAGAAACTTTGGAAAT-ATCTTTCTTACTTTTCAAATATTTCATTTTCTGAAAA
191 GTTTACTAGGTAAGAAACTTTGGAAATCA-CTTTCTTACTTTTCAAAGATTTCATTTTCTGAAAA
484737 TAA
255 TAA
* * * *
484740 TAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTTTGAAAATCATGTGAAAACATCCTGCCCA
1 TAAATGAGAAACTTTGAAAATCG-TTTCTCATTTTTTTCAAAATCATATGAAAACATCTTGCCCA
* *
484805 AAGGTCTTATAAATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGAACCGAAA-
65 AAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGAAAGATG-ACC-AAAG
*
484869 GATTTAATCATCATGCTCGAAAGACTTACTAATGGCCTGAAGGACTTACCAATTTTGGAAATAGT
128 GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTACCAATTTTGGAAATAGT
* * *
484934 TTACTAGGTAAGAAACTTTTGAAATCACTTTCTTACTTTTCAAAGATTTCATTTTCTAAAAATAC
193 TTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAGATTTCATTTTCTGAAAATAA
* *
484999 TAAATGAGAAACTTTGAAAATCGTTTCCCCGTTTTTTTCAAAA
1 TAAATGAGAAACTTTGAAAATCGTTT-CTCATTTTTTTCAAAA
485042 CAACTTAATG
Statistics
Matches: 503, Mismatches: 48, Indels: 26
0.87 0.08 0.05
Matches are distributed among these distances:
258 3 0.01
259 228 0.45
260 25 0.05
261 233 0.46
262 13 0.03
263 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (257 bp):
TAAATGAGAAACTTTGAAAATCGTTTCTCATTTTTTTCAAAATCATATGAAAACATCTTGCCCAA
AGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGAAAGATGACCAAAGGAT
TTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTACCAATTTTGGAAATAGTTTA
CTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAGATTTCATTTTCTGAAAATAA
Found at i:488033 original size:27 final size:27
Alignment explanation
Indices: 488002--488216 Score: 85
Period size: 27 Copynumber: 8.4 Consensus size: 27
487992 TATCATCATA
*
488002 GCATCTTTTCATGCATTTTTAGTTATG
1 GCATCCTTTCATGCATTTTTAGTTATG
*
488029 GCATCCTTTCATGC---CTTA--T-T-
1 GCATCCTTTCATGCATTTTTAGTTATG
*
488049 GCATCCGTTCATGCATTTTTAGTTATG
1 GCATCCTTTCATGCATTTTTAGTTATG
* *
488076 ACATCATTTCATGCCTTAATGCATTTTTAGTTATG
1 GCATC----C-T---TTCATGCATTTTTAGTTATG
**
488111 GCATCCTTTCAT--A-CCTTA---AT-
1 GCATCCTTTCATGCATTTTTAGTTATG
* *
488131 GCATACGTTCATGCATTTTTAGTTATG
1 GCATCCTTTCATGCATTTTTAGTTATG
* *
488158 GAATCCTTTCATGC---CTTA---AT-
1 GCATCCTTTCATGCATTTTTAGTTATG
* *
488178 GCATCCGTTCATGAATTTTTAGTTATG
1 GCATCCTTTCATGCATTTTTAGTTATG
*
488205 CCATCCTTTCAT
1 GCATCCTTTCAT
488217 ACCTTAATGC
Statistics
Matches: 134, Mismatches: 25, Indels: 58
0.62 0.12 0.27
Matches are distributed among these distances:
20 34 0.25
21 5 0.04
22 2 0.01
23 9 0.07
24 9 0.07
25 2 0.01
26 5 0.04
27 42 0.31
30 1 0.01
31 2 0.01
35 23 0.17
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (27 bp):
GCATCCTTTCATGCATTTTTAGTTATG
Found at i:488052 original size:20 final size:20
Alignment explanation
Indices: 488024--488062 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
488014 GCATTTTTAG
*
488024 TTATGGCATCCTTTCATGCC
1 TTATGGCATCCGTTCATGCC
*
488044 TTATTGCATCCGTTCATGC
1 TTATGGCATCCGTTCATGC
488063 ATTTTTAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.28, G:0.15, T:0.41
Consensus pattern (20 bp):
TTATGGCATCCGTTCATGCC
Found at i:488060 original size:47 final size:47
Alignment explanation
Indices: 488009--488099 Score: 155
Period size: 47 Copynumber: 1.9 Consensus size: 47
487999 ATAGCATCTT
* * *
488009 TTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTATTGCATCCG
1 TTCATGCATTTTTAGTTATGACATCATTTCATGCCTTAATGCATCCG
488056 TTCATGCATTTTTAGTTATGACATCATTTCATGCCTTAATGCAT
1 TTCATGCATTTTTAGTTATGACATCATTTCATGCCTTAATGCAT
488100 TTTTAGTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (47 bp):
TTCATGCATTTTTAGTTATGACATCATTTCATGCCTTAATGCATCCG
Found at i:488105 original size:35 final size:35
Alignment explanation
Indices: 488059--488134 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
488049 GCATCCGTTC
*
488059 ATGCATTTTTAGTTATGACATCATTTCATGCCTTA
1 ATGCATTTTTAGTTATGACATCATTTCATACCTTA
* *
488094 ATGCATTTTTAGTTATGGCATCCTTTCATACCTTA
1 ATGCATTTTTAGTTATGACATCATTTCATACCTTA
488129 ATGCAT
1 ATGCAT
488135 ACGTTCATGC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (35 bp):
ATGCATTTTTAGTTATGACATCATTTCATACCTTA
Found at i:488134 original size:82 final size:82
Alignment explanation
Indices: 488012--488181 Score: 288
Period size: 82 Copynumber: 2.1 Consensus size: 82
488002 GCATCTTTTC
* * *
488012 ATGCATTTTTAGTTATGGCATCCTTTCATGCCTTATTGCATCCGTTCATGCATTTTTAGTTAT-G
1 ATGCATTTTTAGTTATGGCATCCTTTCATACCTTAATGCATACGTTCATGCATTTTTAGTTATGG
488076 ACATCATTTCATGCCTTA
66 A-ATCATTTCATGCCTTA
488094 ATGCATTTTTAGTTATGGCATCCTTTCATACCTTAATGCATACGTTCATGCATTTTTAGTTATGG
1 ATGCATTTTTAGTTATGGCATCCTTTCATACCTTAATGCATACGTTCATGCATTTTTAGTTATGG
*
488159 AATCCTTTCATGCCTTA
66 AATCATTTCATGCCTTA
488176 ATGCAT
1 ATGCAT
488182 CCGTTCATGA
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
82 81 0.98
83 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.44
Consensus pattern (82 bp):
ATGCATTTTTAGTTATGGCATCCTTTCATACCTTAATGCATACGTTCATGCATTTTTAGTTATGG
AATCATTTCATGCCTTA
Found at i:488164 original size:47 final size:47
Alignment explanation
Indices: 488094--488244 Score: 239
Period size: 47 Copynumber: 3.2 Consensus size: 47
488084 TCATGCCTTA
488094 ATGCATTTTTAGTTATGGCATCCTTTCATACCTTAATGCATACGTTC
1 ATGCATTTTTAGTTATGGCATCCTTTCATACCTTAATGCATACGTTC
* * *
488141 ATGCATTTTTAGTTATGGAATCCTTTCATGCCTTAATGCATCCGTTC
1 ATGCATTTTTAGTTATGGCATCCTTTCATACCTTAATGCATACGTTC
* * **
488188 ATGAATTTTTAGTTATGCCATCCTTTCATACCTTAATGCATTTGTTC
1 ATGCATTTTTAGTTATGGCATCCTTTCATACCTTAATGCATACGTTC
488235 ATGCATTTTT
1 ATGCATTTTT
488245 TGGCATTGAT
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 94 1.00
ACGTcount: A:0.23, C:0.20, G:0.13, T:0.45
Consensus pattern (47 bp):
ATGCATTTTTAGTTATGGCATCCTTTCATACCTTAATGCATACGTTC
Found at i:494958 original size:47 final size:46
Alignment explanation
Indices: 494838--494960 Score: 165
Period size: 47 Copynumber: 2.6 Consensus size: 46
494828 TATCATCATA
* *
494838 GCATCTTTTCATGCATTTTTAATTATAGAATCCTTTCATGCCTTAAT
1 GCATC-TTTCATGCATTTTTAGTTATGGAATCCTTTCATGCCTTAAT
* * *
494885 GTATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGTCTTAAT
1 GCAT-CTTTCATGCATTTTTAGTTATGGAATCCTTTCATGCCTTAAT
*
494932 GCATCTGTTAATGCATTTTTAGTTATGGA
1 GCATCT-TTCATGCATTTTTAGTTATGGA
494961 TTAGGTTTAG
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
46 2 0.03
47 63 0.95
48 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.13, T:0.47
Consensus pattern (46 bp):
GCATCTTTCATGCATTTTTAGTTATGGAATCCTTTCATGCCTTAAT
Found at i:495474 original size:95 final size:95
Alignment explanation
Indices: 495338--495585 Score: 408
Period size: 95 Copynumber: 2.6 Consensus size: 95
495328 CAAGCTCATT
* * * * * *
495338 AGTATCGGTACTTCAATACTATGGTATCGAT-ACCCCTTTTCAATATCGATACCATTTCTATATT
1 AGTATCGATACTACTATACTATGGTATTGATAATCCC-TTTCAGTATCGATACCATTTCTATATT
*
495402 CTGTGTTTCATGGTATCGATACCCTTCTCTC
65 ATGTGTTTCATGGTATCGATACCCTTCTCTC
*
495433 AGTATTGATACTACTATACTATGGTATTGATAATCCCTTTCAGTATCGATACCATTTCTATATTA
1 AGTATCGATACTACTATACTATGGTATTGATAATCCCTTTCAGTATCGATACCATTTCTATATTA
495498 TGTGTTTCATGGTATCGATACCCTTCTCTC
66 TGTGTTTCATGGTATCGATACCCTTCTCTC
495528 AGTATCGATACTACTATACTATGGTATTGATAATCCCTTTCAGTATCGATACCATTTC
1 AGTATCGATACTACTATACTATGGTATTGATAATCCCTTTCAGTATCGATACCATTTC
495586 CCAGATTTAC
Statistics
Matches: 143, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
95 139 0.97
96 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.40
Consensus pattern (95 bp):
AGTATCGATACTACTATACTATGGTATTGATAATCCCTTTCAGTATCGATACCATTTCTATATTA
TGTGTTTCATGGTATCGATACCCTTCTCTC
Found at i:495478 original size:41 final size:41
Alignment explanation
Indices: 495431--495579 Score: 136
Period size: 41 Copynumber: 3.3 Consensus size: 41
495421 TACCCTTCTC
*
495431 TCAGTATTGATACTACTATACTATGGTATTGATAATCCCTT
1 TCAGTATCGATACTACTATACTATGGTATTGATAATCCCTT
* * * *
495472 TCAGTATCGATACCATTTCTATATTATGTGTTTCATGGTATCGATACCCTTCT
1 TCAGTATCGATA-C--TACTATACTATG-G--T-ATTG-AT-AAT-CCC-T-T
495525 CTCAGTATCGATACTACTATACTATGGTATTGATAATCCCTT
1 -TCAGTATCGATACTACTATACTATGGTATTGATAATCCCTT
495567 TCAGTATCGATAC
1 TCAGTATCGATAC
495580 CATTTCCCAG
Statistics
Matches: 86, Mismatches: 9, Indels: 26
0.71 0.07 0.21
Matches are distributed among these distances:
41 24 0.28
42 2 0.02
43 1 0.01
44 13 0.15
45 3 0.03
46 2 0.02
47 4 0.05
48 4 0.05
49 2 0.02
50 3 0.03
51 13 0.15
52 1 0.01
53 2 0.02
54 12 0.14
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (41 bp):
TCAGTATCGATACTACTATACTATGGTATTGATAATCCCTT
Found at i:499504 original size:46 final size:46
Alignment explanation
Indices: 499436--499523 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
499426 ACCGCTATGT
* * *
499436 ATTTTCATTTGTGGCATCCTTTCATGCCAATTATGCTTTGTTATAC
1 ATTTTCATATATGGCATCCTTTCATGCCAATTATGCATTGTTATAC
*
499482 ATTTTCATATATGGCATTCTTTCATGCCAATTATGCATTGTT
1 ATTTTCATATATGGCATCCTTTCATGCCAATTATGCATTGTT
499524 CTTCATCTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.22, C:0.18, G:0.12, T:0.48
Consensus pattern (46 bp):
ATTTTCATATATGGCATCCTTTCATGCCAATTATGCATTGTTATAC
Found at i:499858 original size:54 final size:54
Alignment explanation
Indices: 499745--500190 Score: 511
Period size: 54 Copynumber: 8.3 Consensus size: 54
499735 ACTCTGTAGT
* * * * * * **
499745 TTGCACACGTAGTGCC-AATACGGTCATTCATAAACATATTATGAATTTCGTGGG
1 TTGCACACTTAGTGCCGAA-ACGGTTATTCATCAACATATGATGAATTCCATGAA
* * * * *
499799 GTGCACACATAGTGCCGAAATGGTTATTCATCAACATATGATGCATTCCGTGAA
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCATGAA
* * * *
499853 TTGCACACTTAGTGCAGAAACTGATAATCATCAACATATGATGAATT-CATGAA
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCATGAA
*
499906 TTGCACACTTAGTGCCAAAACGGTTA-TCATCAACATATGATGAATTCCATGAA
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCATGAA
* **
499959 TTGCACACTTAGTGCCGAAACAGTTATTCATCAACATATGATGAATTCTTTGAA
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCATGAA
* ** * * *
500013 TTGCACACTTAGTGTCGAAACAATTATTCATCAACATATGATGAGTTCTATAAA
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCATGAA
* * *
500067 TTGCACACTTAGTGCTGAAACGGTTATTCATCAACATATGATGAAATCCGTGAA
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCATGAA
* * * * ** *
500121 ATGCATACATAGTGACGAAACGGTTATTTGTCAATATATGATGAATTCCATGAA
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCATGAA
* *
500175 CTACACACTTAGTGCC
1 TTGCACACTTAGTGCC
500191 TATATGGTAA
Statistics
Matches: 333, Mismatches: 56, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
52 20 0.06
53 57 0.17
54 254 0.76
55 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (54 bp):
TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCATGAA
Found at i:500550 original size:20 final size:20
Alignment explanation
Indices: 500512--500550 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
500502 TTCTGGCTCA
* *
500512 ATAGTATCGATACCCCTACC
1 ATAGTATCAATACCACTACC
*
500532 ATAGTATCAATACTACTAC
1 ATAGTATCAATACCACTAC
500551 ACTATGGTAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (20 bp):
ATAGTATCAATACCACTACC
Found at i:505456 original size:46 final size:46
Alignment explanation
Indices: 505361--505448 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
505351 ACCGCTTTGT
* * * *
505361 ATTTTCATTTGTGGCATCCTTTCATGCCAATTATGCATTGTTATAC
1 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGAACTATTATAC
505407 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGAACTATT
1 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGAACTATT
505449 CTTCATTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.11, T:0.45
Consensus pattern (46 bp):
ATTTTCATTTATGGCATCCTTTCATGCCAATTATGAACTATTATAC
Found at i:505724 original size:54 final size:54
Alignment explanation
Indices: 505666--505786 Score: 145
Period size: 54 Copynumber: 2.2 Consensus size: 54
505656 CAACACAATC
* * * * * *
505666 ATTCATAAACATATTATGAATTTCGT-AGGGTGCACACATAGTGCCGAAACGGTT
1 ATTCATCAACATATGATGAATTCCGTGA-AGTGCACACATACTGCCGAAACGATT
* * *
505720 ATTCACCAACATATGATGAATTCCGTGAATTGCACACTTACTGCCGAAACGATT
1 ATTCATCAACATATGATGAATTCCGTGAAGTGCACACATACTGCCGAAACGATT
505774 ATTCATCAACATA
1 ATTCATCAACATA
505787 ACCTATAGAC
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 55 0.98
55 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.29
Consensus pattern (54 bp):
ATTCATCAACATATGATGAATTCCGTGAAGTGCACACATACTGCCGAAACGATT
Found at i:506170 original size:16 final size:16
Alignment explanation
Indices: 506149--506186 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
506139 AATTAGACTA
506149 TATATTTATACAATAT
1 TATATTTATACAATAT
506165 TATATTTATACAATAT
1 TATATTTATACAATAT
506181 TATATT
1 TATATT
506187 GAACAATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATTTATACAATAT
Found at i:507399 original size:55 final size:54
Alignment explanation
Indices: 507267--507491 Score: 321
Period size: 54 Copynumber: 4.2 Consensus size: 54
507257 GTCCCTTAAC
*
507267 CACTTAG-GTCGAAACGG-TATTTCATCAATATATGATGAATT-TCGTGAATTGCA
1 CACTTAGTGTCGAAACGGTTA-TTCATCAACATATGATGAATTCT-GTGAATTGCA
* * *
507320 CACTTAATGCCGAAACGATTATTCATCAACATATGATGAATTCTGTGAATTTGCA
1 CACTTAGTGTCGAAACGGTTATTCATCAACATATGATGAATTCTGTGAA-TTGCA
* *
507375 CACTTGGTGTCGAAACGGTTATTCATCAACATATAATGAATTCTGTGAATTGCA
1 CACTTAGTGTCGAAACGGTTATTCATCAACATATGATGAATTCTGTGAATTGCA
* * *
507429 CACTTAGTGTCGAAACGGTTATTCATCAACATATGTTGAATTCCGTGAATTACA
1 CACTTAGTGTCGAAACGGTTATTCATCAACATATGATGAATTCTGTGAATTGCA
507483 CACTTAGTG
1 CACTTAGTG
507492 CCTATTTGGC
Statistics
Matches: 154, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
53 6 0.04
54 96 0.62
55 52 0.34
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (54 bp):
CACTTAGTGTCGAAACGGTTATTCATCAACATATGATGAATTCTGTGAATTGCA
Found at i:507469 original size:109 final size:108
Alignment explanation
Indices: 507274--507487 Score: 315
Period size: 109 Copynumber: 2.0 Consensus size: 108
507264 AACCACTTAG
* *
507274 GTCGAAACGGTATTTCATCAATATATGATGAATTTCGTGAATTGCACACTTAATGCCGAAACGAT
1 GTCGAAACGGTATTTCATCAACATATAATGAATTTCGTGAATTGCACACTTAATGCCGAAACGAT
* *
507339 TATTCATCAACATATGATGAATTCTGTGAATTTGCACACTTGGT
66 TATTCATCAACATATGATGAATTCCGTGAA-TTACACACTTGGT
* *
507383 GTCGAAACGGT-TATTCATCAACATATAATGAA-TTCTGTGAATTGCACACTTAGTGTCGAAACG
1 GTCGAAACGGTAT-TTCATCAACATATAATGAATTTC-GTGAATTGCACACTTAATGCCGAAACG
* *
507446 GTTATTCATCAACATATGTTGAATTCCGTGAATTACACACTT
64 ATTATTCATCAACATATGATGAATTCCGTGAATTACACACTT
507488 AGTGCCTATT
Statistics
Matches: 95, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
108 13 0.14
109 82 0.86
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (108 bp):
GTCGAAACGGTATTTCATCAACATATAATGAATTTCGTGAATTGCACACTTAATGCCGAAACGAT
TATTCATCAACATATGATGAATTCCGTGAATTACACACTTGGT
Found at i:507962 original size:21 final size:21
Alignment explanation
Indices: 507936--508031 Score: 183
Period size: 21 Copynumber: 4.6 Consensus size: 21
507926 CCACCTATCG
507936 GTATCGATACTTCTTGCATCA
1 GTATCGATACTTCTTGCATCA
507957 GTATCGATACTTCTTGCATCA
1 GTATCGATACTTCTTGCATCA
507978 GTATCGATACTTCTTGCATCA
1 GTATCGATACTTCTTGCATCA
*
507999 GTATCGATACTTCTTACATCA
1 GTATCGATACTTCTTGCATCA
508020 GTATCGATACTT
1 GTATCGATACTT
508032 ACTAGCAGTT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
21 74 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.39
Consensus pattern (21 bp):
GTATCGATACTTCTTGCATCA
Found at i:517506 original size:2 final size:2
Alignment explanation
Indices: 517501--517537 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
517491 TAATACATTT
517501 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 T
517538 GCTCACTCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:519316 original size:131 final size:131
Alignment explanation
Indices: 518987--519352 Score: 450
Period size: 131 Copynumber: 2.8 Consensus size: 131
518977 ATAATTTTAA
* * * * *
518987 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAAAATAAATGACCTTTCACGCCTTAAA-AA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGATCTCTCATGCCTTAAAGCA
* * ** * *
519051 ATCATTCATTAC-CCTAATTGAAATGAAGAGATATAACTATTTTGTCTTAAAATTCAATATTGGT
66 GTCATTTATTACTCC-AATTGAAATGAAGAGATATAACTATTCCGTCTTAAAAATCAATATTGAT
519115 TC
130 TC
* * * * *
519117 GAG-TAAATCAATAATATCTAATGATTTCTAATCGAGAATAAATGATCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGATCTCTCATGCCTTAAAGCA
* * *
519181 GTCATTTATTACTCCAATTGAAATGAAGATATATCACTATTCCGTCTTAAAAATCAATATTTATT
66 GTCATTTATTACTCCAATTGAAATGAAGAGATATAACTATTCCGTCTTAAAAATCAATATTGATT
519246 C
131 C
* * * * *
519247 GAGAGAAAACGGTAATATCGAATTATTTCCAATAGAGAATGAATGATCTCTCTTGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGATCTCTCATGCCTTAAAGCA
** * *
519312 GTCATTTATTACTCCAACCGAAATGAAAAGATATTACTATT
66 GTCATTTATTACTCCAATTGAAATGAAGAGATATAACTATT
519353 ATTAATATTG
Statistics
Matches: 199, Mismatches: 34, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
129 49 0.25
130 61 0.31
131 89 0.45
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (131 bp):
GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGATCTCTCATGCCTTAAAGCA
GTCATTTATTACTCCAATTGAAATGAAGAGATATAACTATTCCGTCTTAAAAATCAATATTGATT
C
Found at i:521460 original size:14 final size:14
Alignment explanation
Indices: 521443--521471 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
521433 AAGCCTGCAG
521443 AAATAAAAATATAT
1 AAATAAAAATATAT
521457 AAATAAAAATATAT
1 AAATAAAAATATAT
521471 A
1 A
521472 TTAATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAATAAAAATATAT
Found at i:521488 original size:12 final size:12
Alignment explanation
Indices: 521473--521501 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
521463 AAATATATAT
521473 TAATATTAATAA
1 TAATATTAATAA
521485 TAATATTAATAA
1 TAATATTAATAA
521497 TAATA
1 TAATA
521502 ATGATAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAATATTAATAA
Found at i:521922 original size:133 final size:134
Alignment explanation
Indices: 521674--522326 Score: 706
Period size: 133 Copynumber: 4.9 Consensus size: 134
521664 CTCTATTGTT
* * * * * * * * **
521674 TTGATTTATTCCACTGTTCTTCAGGAAAGATTGAATCGAGACATACGTGTTCCACTACTACTCAG
1 TTGATTCATTCCACTATTCTTTAGGGAAGATTGAAACGAGGCAGACTTGTTCCACTGTTACTCAG
* * * * * *
521739 GGAAGATCAAATCTTGAAAGATATGGATCTGTTCCGCTGCTTTTTGAGGGAAAATTAGATCT-AG
66 GGAAGATCAAATCTTGAAAGAGATGGATTTATTCCGCTTCTTCTTGAGGGAAAATCAGATCTGAG
* *
521803 AAACA
131 -GACG
* * * * *
521808 TTGATTCATTCCACTATTC-TTAGGGAATATTTAAACGAGGCAAACTTGTTCAACTGTTACTCAT
1 TTGATTCATTCCACTATTCTTTAGGGAAGATTGAAACGAGGCAGACTTGTTCCACTGTTACTCAG
* ** *
521872 GGAAGATCAAATCTTGAAAGAGATGGATTTGTTCCGCTTCTTCTCAAGGGAAAATCAGATCTGGG
66 GGAAGATCAAATCTTGAAAGAGATGGATTTATTCCGCTTCTTCTTGAGGGAAAATCAGATCTGAG
521937 GACG
131 GACG
* ** *
521941 TTGATTTATTCCACTGCTCTTTACGGAAGATT-AAATCGAGGCAGACTTGTTCCA-TGTTACTCA
1 TTGATTCATTCCACTATTCTTTAGGGAAGATTGAAA-CGAGGCAGACTTGTTCCACTGTTACTCA
* * * * *
522004 GGGAAGATCAAATATTAAAAGAAATGGATTT-TCTCCGCTTGTTCTTGAGGGAAAATCATATCTG
65 GGGAAGATCAAATCTTGAAAGAGATGGATTTAT-TCCGCTTCTTCTTGAGGGAAAATCAGATCTG
522068 AGGACG
129 AGGACG
* * * * * * *
522074 TTGATTCATTCCATTGTTCTTTAGGGAAGATTGAATCGAGGCATACTTGTTCCACTATTATTCAT
1 TTGATTCATTCCACTATTCTTTAGGGAAGATTGAAACGAGGCAGACTTGTTCCACTGTTACTCAG
* * * * * *
522139 GAAAGATCAAATATTGAAAGAGAAGGATTCATTCCGCTTCTTCTTGAGGGGAAATCAGATTTGAG
66 GGAAGATCAAATCTTGAAAGAGATGGATTTATTCCGCTTCTTCTTGAGGGAAAATCAGATCTGAG
*
522204 GATG
131 GACG
* * * * * *
522208 TTGATTCATTCCATTATTCTTCAGGGAAGATTGAATCGAAGTAGACTTGTTCTACTGTTACTCAG
1 TTGATTCATTCCACTATTCTTTAGGGAAGATTGAAACGAGGCAGACTTGTTCCACTGTTACTCAG
* *
522273 GGAAGAAT-AAATCTTGAAAGAGAGGGATTTATTTCGCTTCTTCTTGAGGGAAAA
66 GGAAG-ATCAAATCTTGAAAGAGATGGATTTATTCCGCTTCTTCTTGAGGGAAAA
522327 AGGGGATGTT
Statistics
Matches: 437, Mismatches: 74, Indels: 16
0.83 0.14 0.03
Matches are distributed among these distances:
132 1 0.00
133 222 0.51
134 211 0.48
135 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (134 bp):
TTGATTCATTCCACTATTCTTTAGGGAAGATTGAAACGAGGCAGACTTGTTCCACTGTTACTCAG
GGAAGATCAAATCTTGAAAGAGATGGATTTATTCCGCTTCTTCTTGAGGGAAAATCAGATCTGAG
GACG
Found at i:522149 original size:267 final size:265
Alignment explanation
Indices: 521674--522326 Score: 765
Period size: 267 Copynumber: 2.4 Consensus size: 265
521664 CTCTATTGTT
* * * **
521674 TTGATTTATTCCACTGTTCTTCAGGAAAGATTGAATCGAGACATACGTGTTCCACTACTACTCAG
1 TTGATTTATTCCACTGTTCTTCAGG-AAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAG
* * * *
521739 GGAAGATCAAATCTTGAAAGATATGGATCTGTTCCGC-TGCTTTTTGAGGGAAAATTAGATCTAG
65 GGAAGATCAAATCTTGAAAGAAATGGAT-TTTTCCGCTTG-TTCTTGAGGGAAAATCAGATCTAG
* * *
521803 AAACATTGATTCATTCCACTATTCTTAGGGAATATTTAAACGAGGCAAACTTGTTCAACTGTTAC
128 AAACATTGATTCATTCCACTATTCTTAGGGAAGATTGAAACGAGGCAAACTTGTTCAACTATTAC
* * * **
521868 TCATGGAAGATCAAATCTTGAAAGAGATGGATTTGTTCCGCTTCTTCTCAAGGGAAAATCAGATC
193 TCATGAAAGATCAAATATTGAAAGAGAAGGATTCATTCCGCTTCTTCTCAAGGGAAAATCAGATC
*
521933 TGGGGACG
258 TGAGGACG
* * *
521941 TTGATTTATTCCACTGCTCTTTACGGAAGATTAAATCGAGGCAGACTTGTTCCA-TGTTACTCAG
1 TTGATTTATTCCACTGTTCTTCA-GGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAG
* * *
522005 GGAAGATCAAATATTAAAAGAAATGGATTTTCTCCGCTTGTTCTTGAGGGAAAATCATATCT-GA
65 GGAAGATCAAATCTTGAAAGAAATGGATTTT-TCCGCTTGTTCTTGAGGGAAAATCAGATCTAGA
* * * * * * *
522069 GGACGTTGATTCATTCCATTGTTCTTTAGGGAAGATTGAATCGAGGCATACTTGTTCCACTATTA
129 -AACATTGATTCATTCCACTATTC-TTAGGGAAGATTGAAACGAGGCAAACTTGTTCAACTATTA
* ** *
522134 TTCATGAAAGATCAAATATTGAAAGAGAAGGATTCATTCCGCTTCTTCTTGAGGGGAAATCAGAT
192 CTCATGAAAGATCAAATATTGAAAGAGAAGGATTCATTCCGCTTCTTCTCAAGGGAAAATCAGAT
* *
522199 TTGAGGATG
257 CTGAGGACG
* * * * * *
522208 TTGATTCATTCCATTATTCTTCAGGGAAGATTGAATCGAAGTAGACTTGTTCTACTGTTACTCAG
1 TTGATTTATTCCACTGTTCTTCA-GGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAG
* * * *
522273 GGAAGAAT-AAATCTTGAAAGAGAGGGATTTATTTCGCTTCTTCTTGAGGGAAAA
65 GGAAG-ATCAAATCTTGAAAGAAATGGATTT-TTCCGCTTGTTCTTGAGGGAAAA
522327 AGGGGATGTT
Statistics
Matches: 325, Mismatches: 53, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
265 4 0.01
266 76 0.23
267 187 0.58
268 55 0.17
269 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (265 bp):
TTGATTTATTCCACTGTTCTTCAGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGG
GAAGATCAAATCTTGAAAGAAATGGATTTTTCCGCTTGTTCTTGAGGGAAAATCAGATCTAGAAA
CATTGATTCATTCCACTATTCTTAGGGAAGATTGAAACGAGGCAAACTTGTTCAACTATTACTCA
TGAAAGATCAAATATTGAAAGAGAAGGATTCATTCCGCTTCTTCTCAAGGGAAAATCAGATCTGA
GGACG
Found at i:523656 original size:17 final size:17
Alignment explanation
Indices: 523617--523756 Score: 112
Period size: 17 Copynumber: 8.0 Consensus size: 17
523607 CTTTTATTTG
523617 TTCTCTTTTTCTTT-TT
1 TTCTCTTTTTCTTTCTT
523633 TTC-CTTTTTCTTTCTT
1 TTCTCTTTTTCTTTCTT
523649 TTCTCTTTCTT-TTTCTT
1 TTCTCTTT-TTCTTTCTT
* *
523666 TTTTCATTTTTTTTCTCATT
1 TTCTC-TTTTTCTT-TC-TT
* *
523686 TTCATTTTATTTCTTTATT
1 TTC-TCTT-TTTCTTTCTT
523705 TTCT-TTCTTTCTTTTCTT
1 TTCTCTT-TTTC-TTTCTT
523723 TT-TCTTTTTTCTTTCTT
1 TTCTC-TTTTTCTTTCTT
523740 TT-TCATTTTTCTTTCTT
1 TTCTC-TTTTTCTTTCTT
523757 CATGCGAAGT
Statistics
Matches: 104, Mismatches: 8, Indels: 23
0.77 0.06 0.17
Matches are distributed among these distances:
15 10 0.10
16 8 0.08
17 45 0.43
18 19 0.18
19 9 0.09
20 7 0.07
21 6 0.06
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (17 bp):
TTCTCTTTTTCTTTCTT
Found at i:523675 original size:13 final size:13
Alignment explanation
Indices: 523654--523759 Score: 59
Period size: 13 Copynumber: 8.5 Consensus size: 13
523644 TTCTTTTCTC
*
523654 TTTCTTTTTCTTT
1 TTTCATTTTCTTT
523667 TTTCATTTT-TTT
1 TTTCATTTTCTTT
* *
523679 TCTCATTTTC-AT
1 TTTCATTTTCTTT
523691 TTT-A-TTTCTTT
1 TTTCATTTTCTTT
523702 ATTT--TCTTTCTTTCT
1 -TTTCAT-TTTC-TT-T
*
523717 TTTCTTTTTCTTT
1 TTTCATTTTCTTT
523730 TTTC--TTTC-TT
1 TTTCATTTTCTTT
523740 TTTCATTTTTCTTT
1 TTTCA-TTTTCTTT
*
523754 CTTCAT
1 TTTCAT
523760 GCGAAGTACT
Statistics
Matches: 74, Mismatches: 6, Indels: 26
0.70 0.06 0.25
Matches are distributed among these distances:
10 10 0.14
11 6 0.08
12 17 0.23
13 22 0.30
14 13 0.18
15 5 0.07
16 1 0.01
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTCATTTTCTTT
Found at i:523748 original size:7 final size:6
Alignment explanation
Indices: 523620--523753 Score: 75
Period size: 6 Copynumber: 21.8 Consensus size: 6
523610 TTATTTGTTC
*
523620 TCTTTT TCTTTT T-TTCCTT T-TTCTT TC-TTT TCTCTT TCTTTT TCTTTTT
1 TCTTTT TCTTTT TCTT--TT TCTT-TT TCTTTT TCTTTT TCTTTT TC-TTTT
* * * *
523669 TCATTTT T-TTTC TCATTT TCATTT TATTTCT T-TATTT TCTTTCT T-TCTTT
1 TC-TTTT TCTTTT TCTTTT TCTTTT TCTTT-T TCT-TTT TCTTT-T TCT-TTT
*
523719 TCTTTT TCTTTT T-TCTT TCTTTT TCATTTT TCTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TC-TTTT TCTTT
523754 CTTCATGCGA
Statistics
Matches: 104, Mismatches: 10, Indels: 28
0.73 0.07 0.20
Matches are distributed among these distances:
5 14 0.13
6 58 0.56
7 32 0.31
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (6 bp):
TCTTTT
Found at i:530204 original size:14 final size:15
Alignment explanation
Indices: 530164--530206 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
530154 CTTCCTTTAT
530164 ATTTTTCTTT-TTCC
1 ATTTTTCTTTATTCC
530178 ATTTATCTCTTTATT-C
1 ATTT-T-TCTTTATTCC
530194 ATTTTTCTTTATT
1 ATTTTTCTTTATT
530207 TTCATTGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 12 0.46
15 2 0.08
16 10 0.38
17 2 0.08
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTTCTTTATTCC
Found at i:530343 original size:45 final size:45
Alignment explanation
Indices: 530217--530436 Score: 253
Period size: 45 Copynumber: 4.8 Consensus size: 45
530207 TTCATTGAAA
* * * * * *
530217 GCATCCATTCATG-CTTGTAATGCACCATTTTTCATTTTCACTTATG
1 GCATCCTTTCATGCCTT-TTATACACCATTATACATTTT-ATTTATG
* * * *
530263 GCAACCGTTCATGCCTTTTTATATACTATTATACATTTTATTTATG
1 GCATCCTTTCATGCC-TTTTATACACCATTATACATTTTATTTATG
*
530309 GCATCCTTTCATGCCTTTTATACACCATTATACATTTCATTTATG
1 GCATCCTTTCATGCCTTTTATACACCATTATACATTTTATTTATG
* *
530354 GCATCTTTTCATGCCTTTTATACACCATTATACATTTCATTTATG
1 GCATCCTTTCATGCCTTTTATACACCATTATACATTTTATTTATG
* * * *
530399 GCATCTTTTGATGTCTTTTATACACCATTATATATTTT
1 GCATCCTTTCATGCCTTTTATACACCATTATACATTTT
530437 TATACATCTA
Statistics
Matches: 153, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
45 105 0.69
46 30 0.20
47 16 0.10
48 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.08, T:0.47
Consensus pattern (45 bp):
GCATCCTTTCATGCCTTTTATACACCATTATACATTTTATTTATG
Found at i:530894 original size:58 final size:59
Alignment explanation
Indices: 530802--530967 Score: 271
Period size: 59 Copynumber: 2.8 Consensus size: 59
530792 CACATTTCCC
* * *
530802 ATATGGAAATTCATACATTTAGTATGAATCTCTTAACAATTT-GCACACAAAGTGCCCA
1 ATATGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCA
*
530860 ATATGGAAATTTATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCA
1 ATATGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCA
**
530919 ATACAGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACAC
1 ATATGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACAC
530968 TTAGTGCAAT
Statistics
Matches: 100, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
58 38 0.38
59 62 0.62
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (59 bp):
ATATGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCA
Found at i:533657 original size:22 final size:22
Alignment explanation
Indices: 533578--533657 Score: 124
Period size: 22 Copynumber: 3.6 Consensus size: 22
533568 TGTTTGAGCC
*
533578 TTCATAGGGGTATAGATACCCA
1 TTCATAGGGGTATTGATACCCA
* * *
533600 TTCATAGAGGTATCGGTACCCA
1 TTCATAGGGGTATTGATACCCA
533622 TTCATAGGGGTATTGATACCCA
1 TTCATAGGGGTATTGATACCCA
533644 TTCATAGGGGTATT
1 TTCATAGGGGTATT
533658 CGTACCTCTT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (22 bp):
TTCATAGGGGTATTGATACCCA
Found at i:535013 original size:19 final size:20
Alignment explanation
Indices: 534984--535021 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
534974 CAAAATTTCA
534984 TTTTGATTTTCAAAATCGAC
1 TTTTGATTTTCAAAATCGAC
535004 TTTT-ATTTTCAAAATCGA
1 TTTTGATTTTCAAAATCGA
535022 TTTATCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (20 bp):
TTTTGATTTTCAAAATCGAC
Found at i:541725 original size:55 final size:55
Alignment explanation
Indices: 541676--541781 Score: 142
Period size: 55 Copynumber: 1.9 Consensus size: 55
541666 GATGCACTCT
* **
541676 CCATGCATCGATGCACTTGAAATATTTTCAAACATCGAATGCA-TTGATGCACAAG
1 CCATGCATCAATGCACAGGAAAT-TTTTCAAACATCGAATGCACTTGATGCACAAG
** *
541731 CCATGCATCAATGCACAGGCTATTTTTCAAACATCGAATGCACTTCATGCA
1 CCATGCATCAATGCACAGGAAATTTTTCAAACATCGAATGCACTTGATGCA
541782 TCGATGCACT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
54 19 0.43
55 25 0.57
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (55 bp):
CCATGCATCAATGCACAGGAAATTTTTCAAACATCGAATGCACTTGATGCACAAG
Found at i:541790 original size:17 final size:19
Alignment explanation
Indices: 541762--541810 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
541752 ATTTTTCAAA
541762 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
541780 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
541799 CACCGATGCACT
1 CATCGATGCACT
541811 AGGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:547638 original size:24 final size:22
Alignment explanation
Indices: 547610--547690 Score: 85
Period size: 24 Copynumber: 3.6 Consensus size: 22
547600 CACTTAACAA
547610 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCAT-CC-TTGAATG
*
547634 TGCATCGATGCAT-C-TGCATG
1 TGCATCGATGCATCCTTGAATG
* *
547654 ATGCACCGATGCATGCCTTGAATA
1 -TGCATCGATGCAT-CCTTGAATG
547678 TGCATCGATGCAT
1 TGCATCGATGCAT
547691 AAGACCATGC
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
20 5 0.10
21 12 0.25
22 1 0.02
23 13 0.27
24 17 0.35
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATG
Found at i:550403 original size:64 final size:64
Alignment explanation
Indices: 550335--550496 Score: 220
Period size: 64 Copynumber: 2.5 Consensus size: 64
550325 GCTTTAATTG
*
550335 AACATCGAATGCATTTCATGCACCGATGCACTCTCCATGCATCGATGCACTC-GAA-ATATTTTC
1 AACATCGAATGCATTTCATGCATCGATGCACTCTCCATGCATCGATGCAC-CAGAATAT-TTTTC
550398 A
64 A
* *** **
550399 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACCAGGCTATTTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACTCTCCATGCATCGATGCACCAGAATATTTTTCA
*
550463 AACATCGAATGCACTTCATGCATCGATGCACTCT
1 AACATCGAATGCATTTCATGCATCGATGCACTCT
550497 TAGTGCACCG
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 1 0.01
64 81 0.96
65 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACTCTCCATGCATCGATGCACCAGAATATTTTTCA
Found at i:551490 original size:131 final size:131
Alignment explanation
Indices: 551247--551606 Score: 522
Period size: 131 Copynumber: 2.7 Consensus size: 131
551237 TAATTTTAAG
* * *
551247 AGAGAAAACGATAATATCTAATTATTTCCAATTGAGAATAAATGACCTTTCACGCCTTAAAACAA
1 AGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCACGCCTTAAAGCAA
* * * ** *
551312 TCATTTATTACCCCAATTGAAATGAAGAGATATCACTATTTTGTCTTAAAATTCAATATTGATTC
66 TCATTTATTACTCCAATCGAAATGAAGAGATATCAATATTTCATCTTAAAAATCAATATTGATTC
551377 A
131 A
* * * * *
551378 AGTGAAAACGATAATATCTAATGATTTCCAATCAAGAATAAATGACCTCTCATGCCTTAAAGCAT
1 AGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCACGCCTTAAAGCAA
551443 TCATTTATTACTCCAATCGAAATGAAGAGATATCAATATTTCATCTTAAAAATCAATATTGATTC
66 TCATTTATTACTCCAATCGAAATGAAGAGATATCAATATTTCATCTTAAAAATCAATATTGATTC
*
551508 G
131 A
* * * * *
551509 AGAGAAAATGGTAATATCGAATTATTTCCAATCGAGAATAAATGACATCTCACACCTTAAAGCAA
1 AGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCACGCCTTAAAGCAA
* *
551574 TCATTTATTACTCCAACCGAAATGAAAAGATAT
66 TCATTTATTACTCCAATCGAAATGAAGAGATAT
551607 TACTATTCTC
Statistics
Matches: 202, Mismatches: 27, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
131 202 1.00
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (131 bp):
AGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCACGCCTTAAAGCAA
TCATTTATTACTCCAATCGAAATGAAGAGATATCAATATTTCATCTTAAAAATCAATATTGATTC
A
Found at i:554934 original size:23 final size:23
Alignment explanation
Indices: 554906--554966 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
554896 ATCAAGTACA
* *
554906 ATAATATATTAGGTAATGCTTAT
1 ATAATATAATAGGTAACGCTTAT
554929 ATAATATAATAGGTAACGCTTAT
1 ATAATATAATAGGTAACGCTTAT
*
554952 ATAATAAAATAGGTA
1 ATAATATAATAGGTA
554967 TTTAACCAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.46, C:0.05, G:0.13, T:0.36
Consensus pattern (23 bp):
ATAATATAATAGGTAACGCTTAT
Found at i:555218 original size:21 final size:21
Alignment explanation
Indices: 555194--555234 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
555184 TCATTCTGGA
555194 AAAAAGTATCGACACATTATT
1 AAAAAGTATCGACACATTATT
*
555215 AAAAAGTGTCGACACATTAT
1 AAAAAGTATCGACACATTAT
555235 GTAGATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (21 bp):
AAAAAGTATCGACACATTATT
Found at i:555519 original size:20 final size:18
Alignment explanation
Indices: 555475--555519 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 18
555465 CTGGTATCTC
555475 TTTACCGGTTTTATCTTT
1 TTTACCGGTTTTATCTTT
555493 TCCTTACCGGTTTTATCATATT
1 T--TTACCGGTTTTATC-T-TT
555515 TTTAC
1 TTTAC
555520 ATGTTATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 1 0.04
20 18 0.78
21 1 0.04
22 3 0.13
ACGTcount: A:0.16, C:0.20, G:0.09, T:0.56
Consensus pattern (18 bp):
TTTACCGGTTTTATCTTT
Found at i:555845 original size:182 final size:181
Alignment explanation
Indices: 555378--555927 Score: 756
Period size: 181 Copynumber: 3.0 Consensus size: 181
555368 TACCCGTCTT
*
555378 ATCGACACTTTT-TAAGCGCTAAAACTG-ATTCTCCTTTAAATTTA-T-TGTGTCGATACTTATA
1 ATCGACA-TTTTAT-AGCGCTAAAACTGCA-TCTCCTTTAAATTCACTATGTGTCGATACTTATA
* *
555439 TTAAAGTATCGACACTTGAAATATATCTGGTATCTCTTTACCGGTTTTATCTTTTCCTTACCGGT
63 TTAAAGTATCGACACTTGAAATATATCTGGTATCTCTTTACCGGTTTTATCTTTTCCTGACCGAT
* *
555504 TTTATCATATTTTTACATGTTATATCTTTGTGGATCGATACATATTTATAAAGA
128 TTTATCATATTTTTACTTGTTATATCATTGTGGATCGATACATATTTATAAAGA
* * *
555558 ATCGACACTTTATAGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTATATTA
1 ATCGACATTTTATAGCGCTAAAACTGCATCTCCTTTAAATTCACTATGTGTCGATACTTATATTA
* *
555623 AAGTATCGACACTTGCAATATATCTGGTATCTCTTTACCGGTATTATCTTTTCCTGACCGATTTT
66 AAGTATCGACACTTGAAATATATCTGGTATCTCTTTACCGGTTTTATCTTTTCCTGACCGATTTT
* * *
555688 GTCATATTTTTACTTGTTATATCATTGTGAATCAATACATATTTATAAAGA
131 ATCATATTTTTACTTGTTATATCATTGTGGATCGATACATATTTATAAAGA
*
555739 ATCGACATTTTATAG-GCATTAAAACTGCATCACCTTTAAATTCACTATGTGTCGATACTTATAT
1 ATCGACATTTTATAGCGC--TAAAACTGCATCTCCTTTAAATTCACTATGTGTCGATACTTATAT
** * * * *
555803 TAAAGTATCGACAAGTGTAATATATCTAGTAGTGT-TTTACCGGTTTTATCTTTTCGTGACCGAT
64 TAAAGTATCGACACTTGAAATATATCTGGTA-TCTCTTTACCGGTTTTATCTTTTCCTGACCGAT
* * * * *
555867 TTTATCATATATTTT-TTTGTTATATTAATGTGGATCGATATAT-TTTATAAAGT
128 TTTATCATAT-TTTTACTTGTTATATCATTGTGGATCGATACATATTTATAAAGA
555920 ATCGACAT
1 ATCGACAT
555928 AAACCGACAA
Statistics
Matches: 330, Mismatches: 32, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
179 30 0.09
180 10 0.03
181 157 0.48
182 127 0.38
183 6 0.02
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.43
Consensus pattern (181 bp):
ATCGACATTTTATAGCGCTAAAACTGCATCTCCTTTAAATTCACTATGTGTCGATACTTATATTA
AAGTATCGACACTTGAAATATATCTGGTATCTCTTTACCGGTTTTATCTTTTCCTGACCGATTTT
ATCATATTTTTACTTGTTATATCATTGTGGATCGATACATATTTATAAAGA
Found at i:561831 original size:39 final size:39
Alignment explanation
Indices: 561788--561866 Score: 88
Period size: 39 Copynumber: 2.0 Consensus size: 39
561778 TAGAATGTAA
*
561788 TATTATACTATATTATAATAAATT-ATTATTTTATTATTT
1 TATTAAACTATATTATAATAAATTAATTA-TTTATTATTT
* * * * *
561827 TATTAAATTGTATTGTATTATATTAATTATTTATTATTT
1 TATTAAACTATATTATAATAAATTAATTATTTATTATTT
561866 T
1 T
561867 TTGTAGTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
39 29 0.88
40 4 0.12
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (39 bp):
TATTAAACTATATTATAATAAATTAATTATTTATTATTT
Found at i:563937 original size:3 final size:3
Alignment explanation
Indices: 563929--563953 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
563919 GTCGACGATA
563929 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
563954 GAGTAAGGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:567387 original size:21 final size:22
Alignment explanation
Indices: 567371--567468 Score: 81
Period size: 23 Copynumber: 4.4 Consensus size: 22
567361 CACCGAATTT
567371 CCACATA-TTTCTCCCGAATGA
1 CCACATAGTTTCTCCCGAATGA
*
567392 CCACATAGTTTTGTCCCGAATGA
1 CCACATAG-TTTCTCCCGAATGA
* ** * *
567415 CAACATAGGTTAGTCCCAAAGGA
1 CCACATA-GTTTCTCCCGAATGA
* * *
567438 CCACATAGGTTTGTCCTGAAGGA
1 CCACATA-GTTTCTCCCGAATGA
567461 CCACATAG
1 CCACATAG
567469 AACCCTTGAC
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
21 7 0.11
22 1 0.02
23 56 0.86
24 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (22 bp):
CCACATAGTTTCTCCCGAATGA
Found at i:567411 original size:23 final size:23
Alignment explanation
Indices: 567382--567468 Score: 111
Period size: 23 Copynumber: 3.8 Consensus size: 23
567372 CACATATTTC
* *
567382 TCCCGAATGACCACATAGTTTTG
1 TCCCGAAGGACCACATAGGTTTG
* * *
567405 TCCCGAATGACAACATAGGTTAG
1 TCCCGAAGGACCACATAGGTTTG
*
567428 TCCCAAAGGACCACATAGGTTTG
1 TCCCGAAGGACCACATAGGTTTG
*
567451 TCCTGAAGGACCACATAG
1 TCCCGAAGGACCACATAG
567469 AACCCTTGAC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (23 bp):
TCCCGAAGGACCACATAGGTTTG
Found at i:573270 original size:59 final size:59
Alignment explanation
Indices: 573166--573281 Score: 137
Period size: 59 Copynumber: 2.0 Consensus size: 59
573156 ATATGAAACA
* * * *
573166 AATGTTTACACATACATATGGTATGTGATAGAAGAAAAGAAATATGTGA-TTATAAGATC
1 AATGATTACACATACATATGATACGTGACAGAAGAAAAGAAATATGT-ATTTATAAGATC
* * *
573225 AATGATTACACGTACATGTGATACGTGACAGAA-AAGAAGAGATATGTATTTATAAGA
1 AATGATTACACATACATATGATACGTGACAGAAGAA-AAGAAATATGTATTTATAAGA
573282 GAAATGATAT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
58 3 0.06
59 45 0.94
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.28
Consensus pattern (59 bp):
AATGATTACACATACATATGATACGTGACAGAAGAAAAGAAATATGTATTTATAAGATC
Found at i:573486 original size:31 final size:32
Alignment explanation
Indices: 573397--573487 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 32
573387 AGTCGAGGGT
*
573397 TTACCTATGTTCTACGGAACATATGGACAGAA
1 TTACCTATGTTCTAAGGAACATATGGACAGAA
*** *
573429 TTACCTATG-TCTTTCGAGACAAATGGAC--AA
1 TTACCTATGTTCTAAGGA-ACATATGGACAGAA
573459 TATACCTATGTTCTAAGGAACATATGGAC
1 T-TACCTATGTTCTAAGGAACATATGGAC
573488 TGTTTACCTA
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
30 3 0.06
31 22 0.46
32 23 0.48
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (32 bp):
TTACCTATGTTCTAAGGAACATATGGACAGAA
Found at i:573496 original size:31 final size:31
Alignment explanation
Indices: 573395--573522 Score: 105
Period size: 31 Copynumber: 4.1 Consensus size: 31
573385 AGAGTCGAGG
*
573395 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
* *** *
573426 GAATTACCTATG-TCTTTCGAGACAAATGGACA
1 G-TTTACCTATGTTCTAAGGA-ACATATGGACA
* * *
573458 ATATACCTATGTTCTAAGGAACATATGGACT
1 GTTTACCTATGTTCTAAGGAACATATGGACA
* ** * *
573489 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
573520 GTT
1 GTT
573523 GTCGAGGTTC
Statistics
Matches: 73, Mismatches: 21, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
31 49 0.67
32 24 0.33
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (31 bp):
GTTTACCTATGTTCTAAGGAACATATGGACA
Found at i:579710 original size:21 final size:21
Alignment explanation
Indices: 579684--579747 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
579674 CTCAGATTGT
*
579684 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGAACAGATTCCCCC
579705 CCAGGGGGAACAGATTCCCCCC
1 CCAGGGGGAACAGATT-CCCCC
*
579727 CCAGGGGGAACAAATTCCCCC
1 CCAGGGGGAACAGATTCCCCC
579748 TGTCTAACGG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
21 20 0.50
22 20 0.50
ACGTcount: A:0.23, C:0.39, G:0.27, T:0.11
Consensus pattern (21 bp):
CCAGGGGGAACAGATTCCCCC
Found at i:579725 original size:22 final size:22
Alignment explanation
Indices: 579684--579747 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
579674 CTCAGATTGT
*
579684 CCAGGGGGTACAGATT-CCCCC
1 CCAGGGGGAACAGATTCCCCCC
579705 CCAGGGGGAACAGATTCCCCCC
1 CCAGGGGGAACAGATTCCCCCC
*
579727 CCAGGGGGAACAAATTCCCCC
1 CCAGGGGGAACAGATTCCCCC
579748 TGTCTAACGG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 15 0.38
22 25 0.62
ACGTcount: A:0.23, C:0.39, G:0.27, T:0.11
Consensus pattern (22 bp):
CCAGGGGGAACAGATTCCCCCC
Found at i:580135 original size:34 final size:32
Alignment explanation
Indices: 580096--580165 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
580086 TTTTGTAAAG
* *
580096 GGGAAAGGTTCTAGTTTAGCTCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGTTTAGCCCG-G-AAAAACTA
580130 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
580162 GGGA
1 GGGA
580166 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
Found at i:581040 original size:19 final size:20
Alignment explanation
Indices: 581016--581063 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
581006 AACGATTTTC
*
581016 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
581035 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
581055 TTTTGAAAA
1 TTTTGAAAA
581064 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:582565 original size:20 final size:19
Alignment explanation
Indices: 582512--582569 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 19
582502 GATTGTCCAA
582512 GGGGTACATATTCTCCCCCAG
1 GGGGTAC-TATTC-CCCCCAG
* *
582533 GGGGAACAAATTCCCCCCAG
1 GGGGTAC-TATTCCCCCCAG
582553 GGGGTACTGATTCCCCC
1 GGGGTACT-ATTCCCCC
582570 TGTCTAACGG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 21 0.66
21 11 0.34
ACGTcount: A:0.21, C:0.34, G:0.26, T:0.19
Consensus pattern (19 bp):
GGGGTACTATTCCCCCCAG
Found at i:582957 original size:34 final size:32
Alignment explanation
Indices: 582918--582987 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
582908 TTTTGTAAAG
*
582918 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
582952 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
582984 GGGA
1 GGGA
582988 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:583328 original size:166 final size:166
Alignment explanation
Indices: 583048--583377 Score: 597
Period size: 166 Copynumber: 2.0 Consensus size: 166
583038 TATTGGAAAA
* *
583048 TCCTTTGTGAGGAGCTAAGGTAGTGGACGTAGACTTTGGTTGAGAAAGTCGAACCACTATAAATT
1 TCCTTGGTGAGGAGCTAAGGTAGTGGACGTAGACTTTGGTTGAGAAAGTCGAACCACTATAAATC
* * *
583113 GTTGTGCAATTCTCTATCTTTCAATCTCCTTACTCCCTAAACACAAAACCGTTCCGACCCCTTTT
66 GCTGTGCAATTCTCTATATTTCAATCTCCTTACTCCCTAAACACAAAACCGTTCCGACCCCTCTT
*
583178 TGCAAACCGTTCCAGTTGTCGATTCGAGCTTCCGCT
131 TGCAAACCGTTACAGTTGTCGATTCGAGCTTCCGCT
583214 TCCTTGGTGAGGAGCTAAGGTAGTGGACGTAGACTTTGGTTGAGAAAGTCGAACCACTATAAATC
1 TCCTTGGTGAGGAGCTAAGGTAGTGGACGTAGACTTTGGTTGAGAAAGTCGAACCACTATAAATC
583279 GCTGTGCAATTCTCTATATTTCAATCTCCTTACTCCCTAAACACAAAACCGTTCCGACCCCTCTT
66 GCTGTGCAATTCTCTATATTTCAATCTCCTTACTCCCTAAACACAAAACCGTTCCGACCCCTCTT
*
583344 TGCAAACCGTTACGGTTGTCGATTCGAGCTTCCG
131 TGCAAACCGTTACAGTTGTCGATTCGAGCTTCCG
583378 AAAATCCTAA
Statistics
Matches: 157, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
166 157 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (166 bp):
TCCTTGGTGAGGAGCTAAGGTAGTGGACGTAGACTTTGGTTGAGAAAGTCGAACCACTATAAATC
GCTGTGCAATTCTCTATATTTCAATCTCCTTACTCCCTAAACACAAAACCGTTCCGACCCCTCTT
TGCAAACCGTTACAGTTGTCGATTCGAGCTTCCGCT
Found at i:583618 original size:2 final size:2
Alignment explanation
Indices: 583571--583599 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
583561 TTCATTAATT
583571 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 T
583600 GGAAGAGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:584092 original size:18 final size:19
Alignment explanation
Indices: 584051--584092 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
584041 TTGGTTCACG
*
584051 GAATGTAAGATTACCAGTGA
1 GAATGTAAAATTACCAG-GA
584071 GAATGTAAAATTACCA-GA
1 GAATGTAAAATTACCAGGA
584089 GAAT
1 GAAT
584093 AAGATTATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24
Consensus pattern (19 bp):
GAATGTAAAATTACCAGGA
Found at i:585594 original size:47 final size:48
Alignment explanation
Indices: 585501--585618 Score: 161
Period size: 47 Copynumber: 2.5 Consensus size: 48
585491 GTTTTCATGC
* * *
585501 AATTTAACTATTCAAAA-TAAAACACAAATAGGGGAGTTTGTTAATGT
1 AATTTTACCATTCAAAATTAAAACACAAATAGGGGAGTTTGTGAATGT
*
585548 AATTTTACCATTCAAAATTAAAACATAAATAGGGG-GTTT-TGGAATGT
1 AATTTTACCATTCAAAATTAAAACACAAATAGGGGAGTTTGT-GAATGT
*
585595 AACTTTACCATTCAAAATTAAAAC
1 AATTTTACCATTCAAAATTAAAAC
585619 TTACCTTTCA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
46 1 0.02
47 47 0.73
48 16 0.25
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (48 bp):
AATTTTACCATTCAAAATTAAAACACAAATAGGGGAGTTTGTGAATGT
Found at i:585716 original size:11 final size:11
Alignment explanation
Indices: 585700--585730 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
585690 GTTCAAGTGC
585700 TGGGTGATTGT
1 TGGGTGATTGT
585711 TGGGTGATTGT
1 TGGGTGATTGT
585722 TGGGTGATT
1 TGGGTGATT
585731 ATTAGGCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.10, C:0.00, G:0.45, T:0.45
Consensus pattern (11 bp):
TGGGTGATTGT
Found at i:589213 original size:21 final size:21
Alignment explanation
Indices: 589187--589227 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
589177 GGAGAGTTTG
589187 ATTTTT-TTATTTAAAAATAAT
1 ATTTTTATTA-TTAAAAATAAT
589208 ATTTTTATTATTAAAAATAA
1 ATTTTTATTATTAAAAATAA
589228 AAAAATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTTTATTATTAAAAATAAT
Found at i:589260 original size:21 final size:21
Alignment explanation
Indices: 589236--589280 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
589226 AAAAAAATTA
589236 TAAAA-TATAACAGTAGAAACC
1 TAAAAGTATAAC-GTAGAAACC
589257 TAAAAGTATAACGTAGAAACC
1 TAAAAGTATAACGTAGAAACC
589278 TAA
1 TAA
589281 TTTTATCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.56, C:0.13, G:0.11, T:0.20
Consensus pattern (21 bp):
TAAAAGTATAACGTAGAAACC
Found at i:589414 original size:21 final size:20
Alignment explanation
Indices: 589390--589428 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
589380 TTCGTTAAAT
*
589390 GATTTTATTTATTTTTATTAA
1 GATTTTATTT-TTCTTATTAA
589411 GATTTTATTTTTCTTATT
1 GATTTTATTTTTCTTATT
589429 TTTACCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (20 bp):
GATTTTATTTTTCTTATTAA
Found at i:592914 original size:3 final size:3
Alignment explanation
Indices: 592900--592937 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
592890 ATGTAAACAA
592900 AAT AATT AAT AAT AAT AAT AAT -AT AATT AAT AAT AAT A
1 AAT AA-T AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT A
592938 TTTTTTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.06
3 24 0.75
4 6 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:593492 original size:131 final size:131
Alignment explanation
Indices: 593111--593493 Score: 424
Period size: 131 Copynumber: 2.9 Consensus size: 131
593101 ACACTGCTCA
* * * * * *
593111 TACGTGATGAAGAAGTCTGGTCATCTAAGGGTGACATGACTCCTACGTGATGAGGAGATCTAGTA
1 TACGTGATGAGGAAGGCTGGTTATCTAGGGGTGACATGACTCCTACGTGATGAGGAGGTCTAGTC
* * * * * *
593176 AGTGGATGACATGGTTCCTACGCGATGAGGATGACATGCCATCTTTAGGGAGTGTGATAACACGG
66 GGGGGATGACAAGGTTCCTACGCGATGAGGATGATAAGCCATCTTTAGGGA---TGATAACACAG
*
593241 TTTC
128 TTCC
* * * * * * *
593245 TATGCGATGAGGACGGCTGATTATCTAGGGGTGACACGACTCCTCCGTGATGGGGAGGTCTAGTC
1 TACGTGATGAGGAAGGCTGGTTATCTAGGGGTGACATGACTCCTACGTGATGAGGAGGTCTAGTC
* * * * *
593310 GGGGGATGACACGGTTCCTATGTGATGAAGATGATAAGTCATCTTTAGGGATGATAACACAGTTC
66 GGGGGATGACAAGGTTCCTACGCGATGAGGATGATAAGCCATCTTTAGGGATGATAACACAGTTC
593375 C
131 C
* * * * *
593376 TACGTGATGAGGATGGCTGGTTATCTAGGGGTGACATGGCTCTTACGTGATGAGGAGGTTTGGTC
1 TACGTGATGAGGAAGGCTGGTTATCTAGGGGTGACATGACTCCTACGTGATGAGGAGGTCTAGTC
* * * * *
593441 GGGGGATGAAAAGGTTCCTGCACGATGAGGATGGTAAACCATCTTTAGGGATG
66 GGGGGATGACAAGGTTCCTACGCGATGAGGATGATAAGCCATCTTTAGGGATG
593494 GTAGACCATC
Statistics
Matches: 204, Mismatches: 45, Indels: 3
0.81 0.18 0.01
Matches are distributed among these distances:
131 110 0.54
134 94 0.46
ACGTcount: A:0.25, C:0.16, G:0.33, T:0.27
Consensus pattern (131 bp):
TACGTGATGAGGAAGGCTGGTTATCTAGGGGTGACATGACTCCTACGTGATGAGGAGGTCTAGTC
GGGGGATGACAAGGTTCCTACGCGATGAGGATGATAAGCCATCTTTAGGGATGATAACACAGTTC
C
Found at i:593494 original size:20 final size:20
Alignment explanation
Indices: 593469--593513 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
593459 TGCACGATGA
593469 GGATGGTAAACCATCTTTAG
1 GGATGGTAAACCATCTTTAG
*
593489 GGATGGTAGACCATCTTTAG
1 GGATGGTAAACCATCTTTAG
593509 GGATG
1 GGATG
593514 ATGTCTCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.13, G:0.31, T:0.29
Consensus pattern (20 bp):
GGATGGTAAACCATCTTTAG
Found at i:593650 original size:30 final size:29
Alignment explanation
Indices: 593615--593802 Score: 108
Period size: 30 Copynumber: 5.8 Consensus size: 29
593605 GAGACAAAAC
*
593615 TTGTTTCAAGGGAAACTGACTCAAAGATT
1 TTGTTTCAAGAGAAACTGACTCAAAGATT
* * *
593644 TGTGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAAAT
1 T-TGTTTCAAGAGAAACTGACTCAA---AG-----ATT
*
593682 TTGTTTCAAGGGAAACAT-ACTCAAAGATT
1 TTGTTTCAAGAGAAAC-TGACTCAAAGATT
*
593711 TGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 T-TGTTTCAAGAGAAACTGACTCAA---AG-----ATT
* *
593749 TTGTTTCAAGGGAAACAGACTCAAAGACTT
1 TTGTTTCAAGAGAAACTGACTCAAAGA-TT
*
593779 TTGTTTCAAGAGAAACTGTCTCAA
1 TTGTTTCAAGAGAAACTGACTCAA
593803 GAGAGACAAA
Statistics
Matches: 122, Mismatches: 16, Indels: 41
0.68 0.09 0.23
Matches are distributed among these distances:
29 6 0.05
30 62 0.51
33 4 0.03
34 4 0.03
37 38 0.31
38 8 0.07
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (29 bp):
TTGTTTCAAGAGAAACTGACTCAAAGATT
Found at i:593671 original size:66 final size:66
Alignment explanation
Indices: 593519--593887 Score: 478
Period size: 67 Copynumber: 5.6 Consensus size: 66
593509 GGATGATGTC
* * *
593519 TCAAGAGAGACTATCTCAAGAGAGACAAAATTCGTTTCAAGGGAAAC-GACTCAAAGATGATTGT
1 TCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAGACTCAAAGAT--TTGT
593583 -TT
64 GTT
* * * *
593585 T-AAGAGAAACTATCAT-AAGGGAGACAAAACTTGTTTCAAGGGAAACTGACTCAAAGATTTGTG
1 TCAAGAGAAACTGTC-TCAAGAGAGACAAAATTTGTTTCAAGGGAAACAGACTCAAAGATTTGTG
593648 TT
65 TT
* * *
593650 TCAAGAGAAATTGTCTCAAGGGAGACAAAAATTTGTTTCAAGGGAAACATACTCAAAGATTTGTG
1 TCAAGAGAAACTGTCTCAAGAGAGAC-AAAATTTGTTTCAAGGGAAACAGACTCAAAGATTTGTG
593715 TT
65 TT
*
593717 TCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACAGACTCAAAGACTTT-T
1 TCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACAGACTCAAAGA-TTTGT
593781 GTT
64 GTT
* * * *
593784 TCAAGAGAAACTGTCTCAAGAGAGACAAAACTGTGTTTCAAGAGAAACAAACTCAAAGACTTGTG
1 TCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACAGACTCAAAGATTTGTG
*
593849 CT
65 TT
* *
593851 TCAAGAGAAACTATCTCAAGAGAGAAAAAATTTGTTT
1 TCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT
593888 TGAGAAAAAT
Statistics
Matches: 273, Mismatches: 21, Indels: 18
0.88 0.07 0.06
Matches are distributed among these distances:
64 4 0.01
65 43 0.16
66 45 0.16
67 178 0.65
68 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.25
Consensus pattern (66 bp):
TCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAGACTCAAAGATTTGTGT
T
Found at i:593705 original size:37 final size:37
Alignment explanation
Indices: 593664--593839 Score: 107
Period size: 37 Copynumber: 5.1 Consensus size: 37
593654 GAGAAATTGT
*
593664 CTCAAGGGAGACAAAAATTTGTTTCAAGGGAAACATA
1 CTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACATA
* *
593701 CTCAA---AG-----ATTTGTGTTTCAAGAGAAAC-TGT
1 CTCAAGGGAGACAAAATTT-TGTTTCAAGGGAAACAT-A
*
593731 CTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACAGA
1 CTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACATA
* *
593768 CTCAA---AGAC----TTTTGTTTCAAGAGAAAC-TGT
1 CTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACAT-A
* * * * *
593798 CTCAAGAGAGACAAAACTGTGTTTCAAGAGAAACAAA
1 CTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACATA
593835 CTCAA
1 CTCAA
593840 AGACTTGTGC
Statistics
Matches: 106, Mismatches: 13, Indels: 40
0.67 0.08 0.25
Matches are distributed among these distances:
29 4 0.04
30 41 0.39
33 6 0.06
34 6 0.06
37 45 0.42
38 4 0.04
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.24
Consensus pattern (37 bp):
CTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACATA
Found at i:593905 original size:36 final size:37
Alignment explanation
Indices: 593864--593985 Score: 149
Period size: 37 Copynumber: 3.3 Consensus size: 37
593854 AGAGAAACTA
*
593864 TCTCAAGAGAGAAAAAATTTG-TTTTGAGAAAAATTG
1 TCTCAAGCGAGAAAAAATTTGTTTTTGAGAAAAATTG
* * *
593900 TCTCAAGCGAGACACAATTTGTTTTTAGAGAAAAA-CG
1 TCTCAAGCGAGAAAAAATTTGTTTTT-GAGAAAAATTG
* * *
593937 TCTCAAGCGAGATAAAATTTGTTTTTAAGAAAACTTG
1 TCTCAAGCGAGAAAAAATTTGTTTTTGAGAAAAATTG
*
593974 TCTCAAACGAGA
1 TCTCAAGCGAGA
593986 TGACCATTTG
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
36 24 0.33
37 41 0.56
38 8 0.11
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (37 bp):
TCTCAAGCGAGAAAAAATTTGTTTTTGAGAAAAATTG
Found at i:594015 original size:74 final size:72
Alignment explanation
Indices: 593854--594015 Score: 200
Period size: 74 Copynumber: 2.2 Consensus size: 72
593844 TTGTGCTTCA
* * *
593854 AGAGAAACTATCTCAAGAGAGAAAAAATTTGTTTTGAGAAAAATTGTCTCAAGCGAGACACAATT
1 AGAGAAACAATCTCAAGAGAGAAAAAATTTGTTTTAAGAAAAATTGTCTCAAACGAGACACAATT
*
593919 TGTTTTT
66 TGTTTTG
* * * *
593926 AGAGAAA-AACGTCTCAAGCGAGATAAAATTTGTTTTTAAGAAAACTTGTCTCAAACGAGATGAC
1 AGAGAAACAA--TCTCAAGAGAGAAAAAATTTG-TTTTAAGAAAAATTGTCTCAAACGAGA-CAC
*
593990 CATTTGTTTTG
62 AATTTGTTTTG
594001 AGAGAAACAATCTCA
1 AGAGAAACAATCTCA
594016 GAGGTGATCG
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
71 1 0.01
72 7 0.09
73 19 0.25
74 29 0.38
75 18 0.24
76 2 0.03
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (72 bp):
AGAGAAACAATCTCAAGAGAGAAAAAATTTGTTTTAAGAAAAATTGTCTCAAACGAGACACAATT
TGTTTTG
Found at i:599219 original size:65 final size:64
Alignment explanation
Indices: 599090--599244 Score: 179
Period size: 65 Copynumber: 2.4 Consensus size: 64
599080 ACACCCCATT
* * * *
599090 TCGAATGCATTTTATGCATCGATGCACTGCCATGCATCGACGCACTCAGGATTTTATGGAAACA
1 TCGAATGCATTTTATGCATCGATGCAATACCATGCATCGACGCACTCAAGATTGTATGGAAACA
* * *
599154 TTGAATGCATTTTATGCATCGATGCATATACCATGCATCGATGCACTCCAAGCTTGGT-T-GAAA
1 TCGAATGCATTTTATGCATCGATGCA-ATACCATGCATCGACGCACT-CAAGATT-GTATGGAAA
599217 CA
63 CA
* * *
599219 TCAAATTCATTTTATGCATCTATGCA
1 TCGAATGCATTTTATGCATCGATGCA
599245 CCCTTAGTGC
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 25 0.32
65 45 0.58
66 6 0.08
67 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (64 bp):
TCGAATGCATTTTATGCATCGATGCAATACCATGCATCGACGCACTCAAGATTGTATGGAAACA
Found at i:599330 original size:21 final size:21
Alignment explanation
Indices: 599305--599359 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
599295 TTTACACTTG
599305 ATGCATCGATGCATCTTGACT
1 ATGCATCGATGCATCTTGACT
*
599326 ATGCATTGATGCATCTTGACT
1 ATGCATCGATGCATCTTGACT
599347 ATGCATCGATGCA
1 ATGCATCGATGCA
599360 CACACGCTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGACT
Found at i:605115 original size:23 final size:23
Alignment explanation
Indices: 605087--605166 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 23
605077 ACACTATCCA
605087 GTGCATCGATGCATCCTATGAAT
1 GTGCATCGATGCATCCTATGAAT
* * *
605110 GTGCATCAATACAT-C-ATGAAG
1 GTGCATCGATGCATCCTATGAAT
*
605131 GTGCACCGATGCACTCCT-TGAAT
1 GTGCATCGATGCA-TCCTATGAAT
*
605154 GTGCATTGATGCA
1 GTGCATCGATGCA
605167 CTCAGTAGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
21 15 0.33
22 2 0.04
23 28 0.62
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.28
Consensus pattern (23 bp):
GTGCATCGATGCATCCTATGAAT
Found at i:608294 original size:27 final size:27
Alignment explanation
Indices: 608247--608303 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
608237 CTTTGAATGC
* * *
608247 TTGAACTTATATTTATATATTTGGTTT
1 TTGAACTTATATTGATATATTAGATTT
* *
608274 TTGAACTTATATTGGTTTATTAGATTT
1 TTGAACTTATATTGATATATTAGATTT
608301 TTG
1 TTG
608304 CATCATTTAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.04, G:0.14, T:0.58
Consensus pattern (27 bp):
TTGAACTTATATTGATATATTAGATTT
Found at i:608549 original size:12 final size:12
Alignment explanation
Indices: 608532--608567 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
608522 AGTAAGGGAG
608532 AGTAATAAAATT
1 AGTAATAAAATT
608544 AGTAATAAAATT
1 AGTAATAAAATT
608556 AGTAATAAAATT
1 AGTAATAAAATT
608568 GATTTCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (12 bp):
AGTAATAAAATT
Found at i:609018 original size:65 final size:65
Alignment explanation
Indices: 608942--609066 Score: 209
Period size: 65 Copynumber: 1.9 Consensus size: 65
608932 AATGCATTTT
608942 ATGCATCGATGCACT-CAGGATT-TTATGGAAACATCGAATGCATTTTATGCATCGATGCACAAA
1 ATGCATCGATGCACTCCAGGATTGTT-T-GAAACATCGAATGCATTTTATGCATCGATGCACAAA
609005 CC
64 CC
*
609007 ATGCATCGATGCACTCCAGGCTTGTTTGAAACATCGAATGCATTTTATGCATCGATGCAC
1 ATGCATCGATGCACTCCAGGATTGTTTGAAACATCGAATGCATTTTATGCATCGATGCAC
609067 CCTTAGTGCA
Statistics
Matches: 57, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
65 48 0.84
66 7 0.12
67 2 0.04
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (65 bp):
ATGCATCGATGCACTCCAGGATTGTTTGAAACATCGAATGCATTTTATGCATCGATGCACAAACC
Found at i:610367 original size:107 final size:110
Alignment explanation
Indices: 610253--610461 Score: 259
Period size: 107 Copynumber: 1.9 Consensus size: 110
610243 CCTAAACGTA
* * * *
610253 AAAACATGCTAAACA-TACAGGGACTAAATTGA-AAATAACCCTAAAATATATAACA-GTCAT-A
1 AAAACATGCTAAA-AGTAAAGGGACTAAACT-ACAAATAAACCAAAAATATATAACATG-CATAA
610314 AAAATAGG-AAAATCACAAAAA-AGTCCCTACAGGTGACTAACATGCT
63 AAAATAGGAAAAATCACAAAAACAGTCCCTACAGGTGACTAACATGCT
*
610360 AAAACATGCTAAAAGTAAAGGGACTAAACTACAATTAAACCAAAAATATATAACATGCATAAAAA
1 AAAACATGCTAAAAGTAAAGGGACTAAACTACAAATAAACCAAAAATATATAACATGCATAAAAA
* * * *
610425 ATGGGTAAAAATTACAAAAACATTCCCTTCAGGTGAC
66 ATAGG-AAAAATCACAAAAACAGTCCCTACAGGTGAC
610462 CGTTTTGCAA
Statistics
Matches: 86, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
106 2 0.02
107 49 0.57
108 9 0.10
110 12 0.14
111 14 0.16
ACGTcount: A:0.51, C:0.17, G:0.12, T:0.20
Consensus pattern (110 bp):
AAAACATGCTAAAAGTAAAGGGACTAAACTACAAATAAACCAAAAATATATAACATGCATAAAAA
ATAGGAAAAATCACAAAAACAGTCCCTACAGGTGACTAACATGCT
Found at i:612102 original size:6 final size:6
Alignment explanation
Indices: 612093--612127 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
612083 ATGGCTGCTG
612093 CTGCAA CTGCAA CTGCAA CTGCAA CTGCAA CTGCA
1 CTGCAA CTGCAA CTGCAA CTGCAA CTGCAA CTGCA
612128 TCTGGTGGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.31, C:0.34, G:0.17, T:0.17
Consensus pattern (6 bp):
CTGCAA
Found at i:624189 original size:23 final size:24
Alignment explanation
Indices: 624146--624194 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
624136 TGATAAGTTA
624146 TATATTATAAAAAATTAAAAATATT
1 TATATTATAAAAAATTAAAAAT-TT
*
624171 TATATTA-AAAAAGTT-AAAATTT
1 TATATTATAAAAAATTAAAAATTT
624193 TA
1 TA
624195 ATCCATAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 5 0.22
24 7 0.30
25 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
TATATTATAAAAAATTAAAAATTT
Found at i:629039 original size:81 final size:82
Alignment explanation
Indices: 628954--629103 Score: 185
Period size: 81 Copynumber: 1.8 Consensus size: 82
628944 CGTTTTTCCA
* * * * * *
628954 ATAAACGCAACTAAAGACTCGTACTTTAGTGGCATTTTTATACAAACGCC-CTATAGACTCATAT
1 ATAAACACAACTAAAGACTCATACTTTAGTGACATTTTTATACAAACGCCGCTAAAGACTAATAC
629018 TTTAATGGTATTTCTAT
66 TTTAATGGTATTTCTAT
** * * **
629035 ATAAACACCGCTATAGACTCATACTTTATTGATGTTTTTATACAAACGCCGCTAAAGACTAATAC
1 ATAAACACAACTAAAGACTCATACTTTAGTGACATTTTTATACAAACGCCGCTAAAGACTAATAC
629100 TTTA
66 TTTA
629104 GTGGCGTTTG
Statistics
Matches: 56, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
81 41 0.73
82 15 0.27
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (82 bp):
ATAAACACAACTAAAGACTCATACTTTAGTGACATTTTTATACAAACGCCGCTAAAGACTAATAC
TTTAATGGTATTTCTAT
Found at i:629050 original size:41 final size:41
Alignment explanation
Indices: 628968--629103 Score: 157
Period size: 41 Copynumber: 3.3 Consensus size: 41
628958 ACGCAACTAA
* * *
628968 AGACTCGTACTTTAGTGGCATTTTTATACAAACGCC-CTAT
1 AGACTCATACTTTAATGGTATTTTTATACAAACGCCGCTAT
* * * *
629008 AGACTCATATTTTAATGGTATTTCTATATAAACACCGCTAT
1 AGACTCATACTTTAATGGTATTTTTATACAAACGCCGCTAT
* * * *
629049 AGACTCATACTTTATTGATGTTTTTATACAAACGCCGCTAA
1 AGACTCATACTTTAATGGTATTTTTATACAAACGCCGCTAT
*
629090 AGACTAATACTTTA
1 AGACTCATACTTTA
629104 GTGGCGTTTG
Statistics
Matches: 79, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
40 29 0.37
41 50 0.63
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (41 bp):
AGACTCATACTTTAATGGTATTTTTATACAAACGCCGCTAT
Found at i:629621 original size:23 final size:23
Alignment explanation
Indices: 629572--629621 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
629562 AACTTTGAGG
* *
629572 GGTTAAGGTTTTTGCGAGTTTAT
1 GGTTAAGGTTTTTGCGAGGTTAA
*
629595 GGTTAGGGTTTTTG-GAGGGTTAA
1 GGTTAAGGTTTTTGCGA-GGTTAA
629618 GGTT
1 GGTT
629622 TTTGGGTCTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.16, C:0.02, G:0.38, T:0.44
Consensus pattern (23 bp):
GGTTAAGGTTTTTGCGAGGTTAA
Found at i:633264 original size:43 final size:42
Alignment explanation
Indices: 633203--633522 Score: 320
Period size: 43 Copynumber: 7.5 Consensus size: 42
633193 AATTAGCAGT
* * *
633203 GTTTGTATTCAAAAACGCCACTATAGATTTGACATTTTGCGGC
1 GTTTGT-TCCAAAAACGCCGCTATAGATTTGACCTTTTGCGGC
* * * *
633246 GTTTGTTCCAAAAAACGCCGCTATATATCTGATCTTTTACGGC
1 GTTTGTTCC-AAAAACGCCGCTATAGATTTGACCTTTTGCGGC
* * * *
633289 GTTTGTTCCAAAAACGCCACTATATATCTGACCTTTTGCGAC
1 GTTTGTTCCAAAAACGCCGCTATAGATTTGACCTTTTGCGGC
* *
633331 GTTTGTTCCAAAAAACGCCGCTATAGATCTGACCTCTTGCGGC
1 GTTTGTTCC-AAAAACGCCGCTATAGATTTGACCTTTTGCGGC
* * ** * * *
633374 GTTTGTTCCAAAAATGCCAC--TAGATATCAACCTTTCGTGGT
1 GTTTGTTCCAAAAACGCCGCTATAGAT-TTGACCTTTTGCGGC
* *
633415 GTTTGTTCCAAAAACGTCGCTATAGATCTTAACCTTTTGCGGC
1 GTTTGTTCCAAAAACGCCGCTATAGAT-TTGACCTTTTGCGGC
* ** * * *
633458 GTTTATTCCAAAATTGCCGCTATAAATATCGACCTTTTGCGTC
1 GTTTGTTCCAAAAACGCCGCTATAGAT-TTGACCTTTTGCGGC
633501 GTTTGTTCCAAAAACGCCGCTA
1 GTTTGTTCCAAAAACGCCGCTA
633523 CCTTTAACGA
Statistics
Matches: 228, Mismatches: 44, Indels: 10
0.81 0.16 0.04
Matches are distributed among these distances:
40 5 0.02
41 25 0.11
42 49 0.21
43 149 0.65
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (42 bp):
GTTTGTTCCAAAAACGCCGCTATAGATTTGACCTTTTGCGGC
Found at i:633347 original size:85 final size:83
Alignment explanation
Indices: 633203--633522 Score: 370
Period size: 85 Copynumber: 3.8 Consensus size: 83
633193 AATTAGCAGT
* * * *
633203 GTTTGTATTCAAAAACGCCACTATAGATTTGACATTTTGCGGCGTTTGTTCCAAAAAACGCCGCT
1 GTTTGT-TCCAAAAACGCCACTATATA-TCGACCTTTTGCGGCGTTTGTTCC-AAAAACGCCGCT
* * *
633268 ATATATCTGATCTTTTACGGC
63 ATAGATCTGACCTTTTGCGGC
*
633289 GTTTGTTCCAAAAACGCCACTATATATCTGACCTTTTGCGACGTTTGTTCCAAAAAACGCCGCTA
1 GTTTGTTCCAAAAACGCCACTATATATC-GACCTTTTGCGGCGTTTGTTCC-AAAAACGCCGCTA
*
633354 TAGATCTGACCTCTTGCGGC
64 TAGATCTGACCTTTTGCGGC
* * * * * * *
633374 GTTTGTTCCAAAAATGCCACTAGATATCAACCTTTCGTGGTGTTTGTTCCAAAAACGTCGCTATA
1 GTTTGTTCCAAAAACGCCACTATATATCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATA
*
633439 GATCTTAACCTTTTGCGGC
66 GATC-TGACCTTTTGCGGC
* ** * *
633458 GTTTATTCCAAAATTGCCGCTATAAATATCGACCTTTTGCGTCGTTTGTTCCAAAAACGCCGCTA
1 GTTTGTTCCAAAAACGCCACTAT--ATATCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTA
633523 CCTTTAACGA
Statistics
Matches: 201, Mismatches: 29, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
83 18 0.09
84 49 0.24
85 94 0.47
86 40 0.20
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (83 bp):
GTTTGTTCCAAAAACGCCACTATATATCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATA
GATCTGACCTTTTGCGGC
Found at i:634017 original size:12 final size:12
Alignment explanation
Indices: 633997--634044 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
633987 CACTTATGTT
* *
633997 TAATAATATAAA
1 TAATTATATATA
634009 TAATTATATATA
1 TAATTATATATA
634021 T-A-TATATATA
1 TAATTATATATA
*
634031 TAATTATGTATA
1 TAATTATATATA
634043 TA
1 TA
634045 TTCTTATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 9 0.29
11 2 0.06
12 20 0.65
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (12 bp):
TAATTATATATA
Found at i:634020 original size:2 final size:2
Alignment explanation
Indices: 634013--634099 Score: 60
Period size: 2 Copynumber: 45.0 Consensus size: 2
634003 TATAAATAAT
* *
634013 TA TA TA TA TA TA TA TA TA TA -A T- TA TG TA TA TA T- TC T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
634051 TA TA TA CA TA TA CT- TA TA TA TA CTT TA TA CT- TA TA TA TA TT
1 TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA
634092 TA TA TA TA
1 TA TA TA TA
634100 CTTATTTATA
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
1 6 0.09
2 59 0.87
3 3 0.04
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.52
Consensus pattern (2 bp):
TA
Done.