Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008824.1 Hibiscus syriacus cultivar Beakdansim tig00111996_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: 4603428
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 19
Found at i:1359826 original size:65 final size:64
Alignment explanation
Indices: 1359698--1359853 Score: 188
Period size: 65 Copynumber: 2.4 Consensus size: 64
1359688 ATACCCTATT
* * * * * *
1359698 TCGAATGCATTTTTTGTACCGATACACAACCGTACATCGATGTACTCCTGATTTTATTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAAACATACATCGATGCACTCCTGATCTTATTGAAACA
* *
1359762 TCGAATGCATTTTGTGTACCGATGCACAGAACATGCATCGATGCACTCCTAGCTCTT-TTGAAAC
1 TCGAATGCATTTTGTGTACCGATGCACA-AACATACATCGATGCACTCCT-GATCTTATTGAAAC
1359826 A
64 A
* * *
1359827 TCGAATGTAATTAGTGTACCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
1359854 CCCAAGTGTA
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 26 0.33
65 49 0.62
66 4 0.05
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Consensus pattern (64 bp):
TCGAATGCATTTTGTGTACCGATGCACAAACATACATCGATGCACTCCTGATCTTATTGAAACA
Found at i:1365721 original size:44 final size:43
Alignment explanation
Indices: 1365641--1365739 Score: 117
Period size: 44 Copynumber: 2.3 Consensus size: 43
1365631 GTGCACTATA
* * * * *
1365641 CATCAATACACTATAAAGTGTACCGATGCATCCCTTGAATATT
1 CATCGATACACTATAAAGTGCACCAATGCATCCCTTGAAGATG
* * *
1365684 CATCGATACACTATGAATGTGCACCAATGCATTCCTTGAAGGTG
1 CATCGATACACTAT-AAAGTGCACCAATGCATCCCTTGAAGATG
1365728 CATCGATACACT
1 CATCGATACACT
1365740 CTGCTGTGCA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 13 0.28
44 34 0.72
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.28
Consensus pattern (43 bp):
CATCGATACACTATAAAGTGCACCAATGCATCCCTTGAAGATG
Found at i:1367517 original size:16 final size:16
Alignment explanation
Indices: 1367493--1367531 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
1367483 TTCAATGGGC
1367493 GATGCGCGAACGTTTA
1 GATGCGCGAACGTTTA
*
1367509 GATGTGCGAACGTTTA
1 GATGCGCGAACGTTTA
1367525 GATGCGC
1 GATGCGC
1367532 TTAAACTCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (16 bp):
GATGCGCGAACGTTTA
Found at i:1368016 original size:13 final size:13
Alignment explanation
Indices: 1367994--1368027 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1367984 AGGGGGAGAA
*
1367994 ATTTTCAAAATTG
1 ATTTTCAAAAATG
1368007 A-TTTCAAAAATG
1 ATTTTCAAAAATG
1368019 ATTTTCAAA
1 ATTTTCAAA
1368028 GAAAATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:1368443 original size:64 final size:65
Alignment explanation
Indices: 1368369--1368504 Score: 222
Period size: 65 Copynumber: 2.1 Consensus size: 65
1368359 ACACCTTATT
*
1368369 TCGAATGCATTTTGTGTACCGATGCACAT-CCATGCATCAATGCACTCCT-GATTTTATTGAAAC
1 TCGAATGCATTTTGTGTACCGATGCACATACCATGCATCAATGCACTCCTGGATCTT-TTGAAAC
1368432 A
65 A
* *
1368433 TCGAATGCATTTTGTGTACCGATGCACATACCATGCATCGATGCACTCCTGGCTCTTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACATACCATGCATCAATGCACTCCTGGATCTTTTGAAACA
1368498 TCGAATG
1 TCGAATG
1368505 TAATTAGTGT
Statistics
Matches: 67, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
64 29 0.43
65 34 0.51
66 4 0.06
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACATACCATGCATCAATGCACTCCTGGATCTTTTGAAACA
Found at i:1368515 original size:65 final size:64
Alignment explanation
Indices: 1368369--1368521 Score: 200
Period size: 65 Copynumber: 2.4 Consensus size: 64
1368359 ACACCTTATT
* * *
1368369 TCGAATGCATTTTGTGTACCGATGCACATCCATGCATCAATGCACTCCTGATTTTATTGAAACA
1 TCGAATGCAATTAGTGTACCGATGCACATCCATGCATCAATGCACTCCTGATCTTATTGAAACA
* * * *
1368433 TCGAATGCATTTTGTGTACCGATGCACATACCATGCATCGATGCACTCCTGGCTCTT-TTGAAAC
1 TCGAATGCAATTAGTGTACCGATGCACAT-CCATGCATCAATGCACTCCT-GATCTTATTGAAAC
1368497 A
64 A
* *
1368498 TCGAATGTAATTAGTGTACGGATG
1 TCGAATGCAATTAGTGTACCGATG
1368522 TACCCCAAGT
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
64 29 0.36
65 47 0.59
66 4 0.05
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (64 bp):
TCGAATGCAATTAGTGTACCGATGCACATCCATGCATCAATGCACTCCTGATCTTATTGAAACA
Found at i:1371671 original size:44 final size:44
Alignment explanation
Indices: 1371580--1371676 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 44
1371570 ACCCGTATTT
* * * *
1371580 GTACTACTGTGTAATTTTACACACTAGTATCGATACATGTGTCG
1 GTACTACTATGTAATTTTACACACTAGTATCGATACATATATAG
* * *
1371624 GTACTACTATGTATTTTTACACA-TTGCTATCGATACCTATATAG
1 GTACTACTATGTAATTTTACACACTAG-TATCGATACATATATAG
*
1371668 GTACCACTA
1 GTACTACTA
1371677 GAACAATATC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 2 0.05
44 42 0.95
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (44 bp):
GTACTACTATGTAATTTTACACACTAGTATCGATACATATATAG
Found at i:1371922 original size:23 final size:24
Alignment explanation
Indices: 1371879--1371928 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
1371869 TGAATTGAAT
1371879 ATAAACTTAAAAATTGTTTTAAAA
1 ATAAACTTAAAAATTGTTTTAAAA
*
1371903 ATAATCTT-AAAATT-TCTTTAAAA
1 ATAAACTTAAAAATTGT-TTTAAAA
1371926 ATA
1 ATA
1371929 TGTATTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 1 0.04
23 16 0.67
24 7 0.29
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (24 bp):
ATAAACTTAAAAATTGTTTTAAAA
Found at i:1373875 original size:32 final size:32
Alignment explanation
Indices: 1373839--1373917 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 32
1373829 AACTGACATT
*
1373839 TTTCTAAAATGAATG-TATTTGTCAAT-AAAAAG
1 TTTCTAAAATGAATGATATAT-T-AATGAAAAAG
1373871 TTTCTAAAATGAAGTGATATATTAATGAAAAAG
1 TTTCTAAAATGAA-TGATATATTAATGAAAAAG
* *
1373904 TGTCTAAAGTGAAT
1 TTTCTAAAATGAAT
1373918 TAATTACTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
32 17 0.41
33 20 0.49
34 4 0.10
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.35
Consensus pattern (32 bp):
TTTCTAAAATGAATGATATATTAATGAAAAAG
Found at i:1373985 original size:104 final size:104
Alignment explanation
Indices: 1373798--1374025 Score: 314
Period size: 104 Copynumber: 2.2 Consensus size: 104
1373788 GCACTATAGT
** * *
1373798 TGTCTGAAGTGAATTAATTGTTGTATGAAAAAACTGACATTTTTCTAAAATGAATGTATTTGTCA
1 TGTCTGAAGTGAATTAATTACTGTATG-AAAAACTGACATTTCTCTAAAATGAATGTATTTATCA
*
1373863 ATAAAAAGTTTCTAAAATGAAGTGATATATTAATGAAAAAG
65 ATAAAAAGTTTCTAAAATGAAGTGATATATCAAT-AAAAAG
* * * * * *
1373904 TGTCTAAAGTGAATTAATTACTGTATG-AAAACTGACGTTTCTCTCAGATGAATTTATTTATCAC
1 TGTCTGAAGTGAATTAATTACTGTATGAAAAACTGACATTTCTCTAAAATGAATGTATTTATCAA
* *
1373968 TAAAAAGTTTCTGAAATGAAGTGATATATCAATTAAAAG
66 TAAAAAGTTTCTAAAATGAAGTGATATATCAATAAAAAG
1374007 TGTCTGAAGTGAATTAATT
1 TGTCTGAAGTGAATTAATT
1374026 GGCCACTGAA
Statistics
Matches: 108, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
103 23 0.21
104 61 0.56
106 24 0.22
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (104 bp):
TGTCTGAAGTGAATTAATTACTGTATGAAAAACTGACATTTCTCTAAAATGAATGTATTTATCAA
TAAAAAGTTTCTAAAATGAAGTGATATATCAATAAAAAG
Found at i:1374045 original size:23 final size:23
Alignment explanation
Indices: 1374013--1374062 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
1374003 AAAGTGTCTG
1374013 AAGTGAATTAATTGGCCACTGAA
1 AAGTGAATTAATTGGCCACTGAA
* *
1374036 AAGTGTATTAATTGGCCATTGAA
1 AAGTGAATTAATTGGCCACTGAA
1374059 AAGT
1 AAGT
1374063 TTTTGAATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (23 bp):
AAGTGAATTAATTGGCCACTGAA
Found at i:1388984 original size:35 final size:33
Alignment explanation
Indices: 1388937--1389036 Score: 127
Period size: 35 Copynumber: 3.1 Consensus size: 33
1388927 TGGTTGAGAT
* *
1388937 ACAACATCACCACCATCTCTATTTCAACATCAAC
1 ACAACACCACCACCA-CTCCATTTCAACATCAAC
1388971 ATCAACACCACCACCAACTCCATTTCAACATCAAC
1 A-CAACACCACCACC-ACTCCATTTCAACATCAAC
1389006 AC--CACCACCA--ACTCCATTTCAACATCAAC
1 ACAACACCACCACCACTCCATTTCAACATCAAC
1389035 AC
1 AC
1389037 CATCAACATC
Statistics
Matches: 62, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
29 21 0.34
32 8 0.13
34 2 0.03
35 30 0.48
36 1 0.02
ACGTcount: A:0.39, C:0.42, G:0.00, T:0.19
Consensus pattern (33 bp):
ACAACACCACCACCACTCCATTTCAACATCAAC
Found at i:1389036 original size:29 final size:29
Alignment explanation
Indices: 1388966--1389038 Score: 146
Period size: 29 Copynumber: 2.5 Consensus size: 29
1388956 TATTTCAACA
1388966 TCAACATCAACACCACCACCAACTCCATT
1 TCAACATCAACACCACCACCAACTCCATT
1388995 TCAACATCAACACCACCACCAACTCCATT
1 TCAACATCAACACCACCACCAACTCCATT
1389024 TCAACATCAACACCA
1 TCAACATCAACACCA
1389039 TCAACATCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.40, C:0.44, G:0.00, T:0.16
Consensus pattern (29 bp):
TCAACATCAACACCACCACCAACTCCATT
Found at i:1389054 original size:22 final size:22
Alignment explanation
Indices: 1389028--1389072 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1389018 TCCATTTCAA
1389028 CATCAACACCATCAACATCTTC
1 CATCAACACCATCAACATCTTC
**
1389050 CATCAAGGCCATCAACATCTTC
1 CATCAACACCATCAACATCTTC
1389072 C
1 C
1389073 TAATTCCGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.40, G:0.04, T:0.22
Consensus pattern (22 bp):
CATCAACACCATCAACATCTTC
Found at i:1393581 original size:17 final size:17
Alignment explanation
Indices: 1393559--1393613 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
1393549 ACACCATCAC
1393559 CAACACCATTTCAACAT
1 CAACACCATTTCAACAT
1393576 CAACACCA--TC-AC--
1 CAACACCATTTCAACAT
*
1393588 CAACTCCATTTCAACAT
1 CAACACCATTTCAACAT
1393605 CAACACCAT
1 CAACACCAT
1393614 CAACATCTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
12 7 0.23
14 4 0.13
15 4 0.13
17 16 0.52
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (17 bp):
CAACACCATTTCAACAT
Found at i:1393589 original size:29 final size:29
Alignment explanation
Indices: 1393547--1393615 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
1393537 GCTTGAGATA
1393547 CAACACCATCACCAACACCATTTCAACAT
1 CAACACCATCACCAACACCATTTCAACAT
*
1393576 CAACACCATCACCAACTCCATTTCAACAT
1 CAACACCATCACCAACACCATTTCAACAT
1393605 CAACACCATCA
1 CAACACCATCA
1393616 ACATCTTCCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.41, C:0.42, G:0.00, T:0.17
Consensus pattern (29 bp):
CAACACCATCACCAACACCATTTCAACAT
Found at i:1393628 original size:22 final size:22
Alignment explanation
Indices: 1393602--1393647 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
1393592 TCCATTTCAA
1393602 CATCAACACCATCAACATCTTC
1 CATCAACACCATCAACATCTTC
**
1393624 CATCAAGGCCATCAACATCTTC
1 CATCAACACCATCAACATCTTC
1393646 CA
1 CA
1393648 AATTTCATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.35, C:0.39, G:0.04, T:0.22
Consensus pattern (22 bp):
CATCAACACCATCAACATCTTC
Found at i:1401083 original size:15 final size:15
Alignment explanation
Indices: 1401063--1401091 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1401053 TTTTCATTTC
1401063 GTGGTAAAGGTCTCA
1 GTGGTAAAGGTCTCA
1401078 GTGGTAAAGGTCTC
1 GTGGTAAAGGTCTC
1401092 TTCAACACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.14, G:0.34, T:0.28
Consensus pattern (15 bp):
GTGGTAAAGGTCTCA
Found at i:1406069 original size:10 final size:10
Alignment explanation
Indices: 1406054--1406083 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
1406044 ACTTTAGTTT
1406054 TTTTTTTTTG
1 TTTTTTTTTG
1406064 TTTTTTTTTG
1 TTTTTTTTTG
1406074 TTTTGTTTTT
1 TTTT-TTTTT
1406084 TAAGTATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.74
11 5 0.26
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:1406071 original size:15 final size:15
Alignment explanation
Indices: 1406051--1406084 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1406041 GTAACTTTAG
1406051 TTTTTTTT-TTTTGT
1 TTTTTTTTGTTTTGT
1406065 TTTTTTTTGTTTTGT
1 TTTTTTTTGTTTTGT
1406080 TTTTT
1 TTTTT
1406085 AAGTATACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (15 bp):
TTTTTTTTGTTTTGT
Found at i:1410377 original size:43 final size:42
Alignment explanation
Indices: 1410301--1410407 Score: 135
Period size: 43 Copynumber: 2.4 Consensus size: 42
1410291 ATAAATAAAT
1410301 AAATAAAATACACTAAAATTAAAAGAGAAAAAAATGAATAACTA
1 AAATAAAA-A-ACTAAAATTAAAAGAGAAAAAAATGAATAACTA
1410345 AAATAAAAAACTAAAATTAAAA-AGGAACAAAAATGAATAACTA
1 AAATAAAAAACTAAAATTAAAAGA-GAA-AAAAATGAATAACTA
* *
1410388 AATTGAAATAAATTAAAATT
1 AAAT-AAA-AAACTAAAATT
1410408 GATGGATTAA
Statistics
Matches: 57, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
41 1 0.02
42 16 0.28
43 19 0.33
44 11 0.19
45 10 0.18
ACGTcount: A:0.67, C:0.06, G:0.07, T:0.21
Consensus pattern (42 bp):
AAATAAAAAACTAAAATTAAAAGAGAAAAAAATGAATAACTA
Found at i:1412384 original size:84 final size:83
Alignment explanation
Indices: 1412154--1412440 Score: 301
Period size: 84 Copynumber: 3.4 Consensus size: 83
1412144 CTGAATGAAA
* * * * * * *
1412154 TCGAACTCGTCAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTTTAAATGATG
1 TCGAACTCG-AAGGTCTTTGG-TGACAAATAACCCTTCTAGACTTAAGCTATGCTGTAAATGATG
* * * *
1412219 TGCCCTCGAAGCTGAGTGTAA
64 TGCCTTAG-AGCTGAGCGTAG
* * * * * *
1412240 TCGAACTCGAGGGTCTTT-G-G-CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
1 TCGAACTCGAAGGTCTTTGGTGACAAATAACCCTTCTAGACTTAAGCTATGCTGTAAATGATGTG
1412302 CCTTAGAGCTGAGCGTAG
66 CCTTAGAGCTGAGCGTAG
* * * *
1412320 TCGAACTCAAAGGTCTTTTGGTGACATATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTTGGTGACAAATAACCCTTCTAGACTTAAGCTATGCTGTAAATGATGT
*
1412385 GCCTTGGAGCTGAGCGTAG
65 GCCTTAGAGCTGAGCGTAG
* *
1412404 TCGAACTCGAAGGTCTTTGTTGACAAATAATCCTTCT
1 TCGAACTCGAAGGTCTTTGGTGACAAATAACCCTTCT
1412441 TTGAGTTGGA
Statistics
Matches: 173, Mismatches: 24, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
80 23 0.13
81 45 0.26
82 2 0.01
83 20 0.12
84 67 0.39
85 7 0.04
86 9 0.05
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (83 bp):
TCGAACTCGAAGGTCTTTGGTGACAAATAACCCTTCTAGACTTAAGCTATGCTGTAAATGATGTG
CCTTAGAGCTGAGCGTAG
Found at i:1413237 original size:105 final size:105
Alignment explanation
Indices: 1412603--1414223 Score: 2562
Period size: 105 Copynumber: 15.4 Consensus size: 105
1412593 GCATTGTTCC
* ** * * * * *
1412603 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAA-CTGGGAAATTATTTGTTAACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATC-GAGAAA-TGTTTGTTGACA
1412667 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
1412709 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATCGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAA-TGTTTGTTGACAA
* *
1412774 CCAGCGGTCCCTTCGTCATGAAGTTGGACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
1412815 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATCGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAA-TGTTTGTTGACAA
1412880 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1412921 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAA-TGTTTGTTGACAA
* *
1412986 CCAGCGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTT
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
1413027 GAGTCCAATATCTTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAA-TGTTTGTTGACAA
* *
1413092 CCAGCGGTCCCTTCGCCGTGAAGTTGAACTTACGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1413133 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
*
1413198 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1413238 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTAACTCTGAAATCGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
* *
1413303 CAGCCGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1413343 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
1413408 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1413448 GAGTCCAATATTCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
1413513 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1413553 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
1413618 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1413658 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
*
1413723 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1413763 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
*
1413828 CAGCGGTCCCTTCGTCGTGAAGTTGAGCTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1413868 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAA-TGTTTGTTGACAA
* *
1413933 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGCCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1413974 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAA-TGTTTGTTGACAA
* *
1414039 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGCCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1414080 GAGTCCAATATCCTTCGTGGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
* * * * *
1414145 CAGCCGCCCCTTCGTCATGAAGTTGAGCTTGTGTTGTCTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * *
1414186 GA-TTCGAGATCCTTCGTTGAGAAGTTGAAATTTACTCT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCT
1414224 CGAGCAAATT
Statistics
Matches: 1447, Mismatches: 65, Indels: 7
0.95 0.04 0.00
Matches are distributed among these distances:
105 789 0.55
106 658 0.45
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1418006 original size:44 final size:44
Alignment explanation
Indices: 1417947--1418036 Score: 137
Period size: 44 Copynumber: 2.0 Consensus size: 44
1417937 ATAAATAAAT
*
1417947 AAATAAAATACACTAAAATT-AAAAGAGAAAAAAATGAATAACTA
1 AAATAAAAAACACTAAAATTAAAAAG-GAAAAAAATGAATAACTA
* *
1417991 AAATAAAAAATACTAAAATTAAAAAGGAACAAAATGAATAACTA
1 AAATAAAAAACACTAAAATTAAAAAGGAAAAAAATGAATAACTA
1418035 AA
1 AA
1418037 TTGAAATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
44 37 0.88
45 5 0.12
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.18
Consensus pattern (44 bp):
AAATAAAAAACACTAAAATTAAAAAGGAAAAAAATGAATAACTA
Found at i:1418052 original size:44 final size:43
Alignment explanation
Indices: 1417960--1418054 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 43
1417950 TAAAATACAC
1417960 TAAAATTAAAAGAGAAAAAAATGAATAACTAAAATAAAAAATA
1 TAAAATTAAAAGAGAAAAAAATGAATAACTAAAATAAAAAATA
* *
1418003 CTAAAATTAAAA-AGGAACAAAATGAATAACTAAATTGAAATAAAT-
1 -TAAAATTAAAAGA-GAAAAAAATGAATAACTAAAAT-AAA-AAATA
1418048 TAAAATT
1 TAAAATT
1418055 GATGGATTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
43 1 0.02
44 38 0.83
45 3 0.07
46 4 0.09
ACGTcount: A:0.66, C:0.04, G:0.07, T:0.22
Consensus pattern (43 bp):
TAAAATTAAAAGAGAAAAAAATGAATAACTAAAATAAAAAATA
Found at i:1441409 original size:39 final size:39
Alignment explanation
Indices: 1441352--1441441 Score: 128
Period size: 39 Copynumber: 2.3 Consensus size: 39
1441342 AGGACCTCAA
1441352 GTAAGGACTTACCATGTGCACAAAGAAGAGGAGCCTGAG
1 GTAAGGACTTACCATGTGCACAAAGAAGAGGAGCCTGAG
** *
1441391 GTAAGGACTTATCC-TGTGCACAAAGCCGAGGAGCCTGCG
1 GTAAGGACTTA-CCATGTGCACAAAGAAGAGGAGCCTGAG
*
1441430 GTAAGGTCTTAC
1 GTAAGGACTTAC
1441442 AGGTCATAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
38 1 0.02
39 43 0.93
40 2 0.04
ACGTcount: A:0.30, C:0.21, G:0.30, T:0.19
Consensus pattern (39 bp):
GTAAGGACTTACCATGTGCACAAAGAAGAGGAGCCTGAG
Found at i:1444009 original size:19 final size:20
Alignment explanation
Indices: 1443985--1444034 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
1443975 ATCAAGTTCT
1443985 TTTTTGAAGCCATGAAA-T-C
1 TTTTTGAAGCCAT-AAATTCC
*
1444004 TTTTTGAGGCCATAAATTCC
1 TTTTTGAAGCCATAAATTCC
1444024 TTTTGTGAAGC
1 TTTT-TGAAGC
1444035 TTAAAGAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 3 0.12
19 13 0.50
20 5 0.19
21 5 0.19
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (20 bp):
TTTTTGAAGCCATAAATTCC
Found at i:1451318 original size:18 final size:18
Alignment explanation
Indices: 1451273--1451320 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
1451263 TGCGTTTGGT
* *
1451273 TCACAGAATATAAGATTA
1 TCACGGAATAAAAGATTA
*
1451291 TCAGTGGGAATAAAAGATTA
1 TCA--CGGAATAAAAGATTA
1451311 TCACGGAATA
1 TCACGGAATA
1451321 GGATTACTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 9 0.38
20 15 0.62
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (18 bp):
TCACGGAATAAAAGATTA
Found at i:1451546 original size:37 final size:36
Alignment explanation
Indices: 1451466--1451546 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 36
1451456 AACAAATTGG
* *
1451466 AAAATATTTACATATTTTATTTAAAAAATTTAAATTT
1 AAAA-ATTTACATATTTTATTTAAAAAATTAAAATAT
* *
1451503 ATAAAATTTATATATTTTTTTTAAAAAATTGAAAATAT
1 A-AAAATTTACATATTTTATTTAAAAAATT-AAAATAT
1451541 AAAAAT
1 AAAAAT
1451547 GTTTAATGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
37 29 0.76
38 9 0.24
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (36 bp):
AAAAATTTACATATTTTATTTAAAAAATTAAAATAT
Found at i:1455687 original size:2 final size:2
Alignment explanation
Indices: 1455680--1455714 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1455670 TGGAAGCGAA
1455680 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1455715 AAGTTAGTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1462639 original size:12 final size:12
Alignment explanation
Indices: 1462622--1462651 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1462612 TCTCTAGGCA
1462622 TCTTCTCGCCAT
1 TCTTCTCGCCAT
*
1462634 TCTTCTCTCCAT
1 TCTTCTCGCCAT
1462646 TCTTCT
1 TCTTCT
1462652 GCTCCTTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.40, G:0.03, T:0.50
Consensus pattern (12 bp):
TCTTCTCGCCAT
Found at i:1470427 original size:3 final size:3
Alignment explanation
Indices: 1470419--1470449 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1470409 TATACTTCAT
*
1470419 TTC TTC TTC TTC TTC TTC TTC TTC TTT TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1470450 CTTTTCATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:1474320 original size:22 final size:22
Alignment explanation
Indices: 1474222--1474317 Score: 183
Period size: 22 Copynumber: 4.4 Consensus size: 22
1474212 CATTATGAAC
1474222 TTCTTCTCCTTTATCGGATGAG
1 TTCTTCTCCTTTATCGGATGAG
1474244 TTCTTCTCCTTTATCGGATGAG
1 TTCTTCTCCTTTATCGGATGAG
1474266 TTCTTCTCCTTTATCGGATGAG
1 TTCTTCTCCTTTATCGGATGAG
*
1474288 TTCTTCTCATTTATCGGATGAG
1 TTCTTCTCCTTTATCGGATGAG
1474310 TTCTTCTC
1 TTCTTCTC
1474318 ATTACGAACT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
22 73 1.00
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.47
Consensus pattern (22 bp):
TTCTTCTCCTTTATCGGATGAG
Found at i:1474548 original size:136 final size:135
Alignment explanation
Indices: 1474288--1474835 Score: 523
Period size: 136 Copynumber: 4.0 Consensus size: 135
1474278 ATCGGATGAG
* * * * * * * *
1474288 TTCTTCTCATTTATCGGATGAGTTCTTCTCATTACGAACTATCCACTAGAAATGTTAATCCCTCA
1 TTCTTCTCCTCTATCAGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTCATTCCCTCA
* * ** * * * ** * **
1474353 AGCAAGGTGTTGCTGACTCGAATTGTTGTGAATCGAGCAATAGGTCGAACAAGCTCTTCTCATTA
66 AGCGAGGCGTCACTGATTCAAAATGTCATGAATCAAGTGATAGGTCGAACAAGCTCTTCTCATTA
1474418 TGAAC
131 TGAAC
* *
1474423 TTCTTATACCTCTGTCAGATGAGTTCTTCTCATTATGAACTCTCCATCT-GAAATGTCATTCCCT
1 TTCTTCT-CCTCTATCAGATGAGTTCTTCTCATTATGAACTCTCCA-CTGGAAATGTCATTCCCT
*
1474487 CAAGTGAGGCGTCACTGATTCAAAATGTCATGAATCAAGTGATAGGTCGAACAAGCTCTTCTCAT
64 CAAGCGAGGCGTCACTGATTCAAAATGTCATGAATCAAGTGATAGGTCGAACAAGCTCTTCTCAT
1474552 TATGAAC
129 TATGAAC
* * * * * * *
1474559 TTTTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACTCTTCACTGGAAATGTTGA-ACCCT
1 TTCTTCT-CCTCTATCAGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATG-TCATTCCCT
* * * *** * * *
1474623 CGAGTGAGGTGTTGTTGATTCAACTCCATATG-CGATGAATCGAGCT-A-AGGTTGAACAAGTTC
64 CAAGCGAGGCGTCACTGATTCAA----A-ATGTC-ATGAATCAAG-TGATAGGTCGAACAAGCTC
1474685 TTCTCATTATGAAC
122 TTCTCATTATGAAC
* * *
1474699 TTCTTCT-CTCTCATCAGATGAGTTCTTCTCATTATAAACTCTCCACTGGAAATGTCATTACCTT
1 TTCTTCTCCTCT-ATCAGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTCATTCCCTC
** * * *
1474763 AAGCGAGGCGTCACTGATTTGAAATGCCGTGAATCAAGTGATAGGTCGAACAAGTTCTTCTCATT
65 AAGCGAGGCGTCACTGATTCAAAATGTCATGAATCAAGTGATAGGTCGAACAAGCTCTTCTCATT
1474828 ATGAAC
130 ATGAAC
1474834 TT
1 TT
1474836 TCCACTAGAA
Statistics
Matches: 337, Mismatches: 60, Indels: 32
0.79 0.14 0.07
Matches are distributed among these distances:
133 1 0.00
134 12 0.04
135 40 0.12
136 171 0.51
137 4 0.01
138 5 0.01
139 55 0.16
140 35 0.10
141 13 0.04
142 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (135 bp):
TTCTTCTCCTCTATCAGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTCATTCCCTCA
AGCGAGGCGTCACTGATTCAAAATGTCATGAATCAAGTGATAGGTCGAACAAGCTCTTCTCATTA
TGAAC
Found at i:1475959 original size:109 final size:108
Alignment explanation
Indices: 1475763--1476346 Score: 608
Period size: 109 Copynumber: 5.4 Consensus size: 108
1475753 ATTCAAATAA
** * *
1475763 ATCAAGAAACCCCTGAAAACCAGACTTAATTTCTTTGAAAA-ATCATTTGAAAA-CATCAAGAAA
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTT-AAAACA-CATTTGAAAAGCATCAAGAAA
** * * * * * ***
1475826 CCCCTAAAAATTAGGCTTAATTTCTTTGAACGTTCATTTAAGAAAA-
64 CTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTT--GAAAAC
*
1475872 ATCAAGAAACTTCCGAAAATCAGACTTAGTTTCTTTAAAACACATTTGAAAAGCATCAAGAAACT
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAACACATTTGAAAAGCATCAAGAAACT
* * * *
1475937 TATAAAAATCATACTTAGTTTCTTTAAAAACTCATTTGAAATC
66 TCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAAAC
* * * * ** *
1475980 TTCATGAAACTTCTAAAAATCAGACTTAGTTTCGTTGAAAACTTATTTG-AAATCATCAAGAAAC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTC-TTTAAAACACATTTGAAAAGCATCAAGAAAC
* *
1476044 TTCTGAAAACCAGACTTAGTTTCTTTAAAAACTCACTTGAAAATC
65 TTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAAA-C
* * * ** *
1476089 ATCATGAAACTTCTGAAATTCAGACTTAGTTTCATTGAAAACTTATTTG-AAATCATCAAGAAAC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTC-TTTAAAACACATTTGAAAAGCATCAAGAAAC
* * *
1476153 TTCTGAAAACCAAACTTAGTTTCTTTAAAAACTCACTTGAAAATC
65 TTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAAA-C
* * * *
1476198 GTCAAGAAACTTCTAAAAATAAGACTTAGTTTCTTTAAAAAATTCATTT-AAAATG-ATCAAGAA
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAACA--CATTTGAAAA-GCATCAAGAA
* * *
1476261 ACTTCCGAAAATCAGAATTAGTTTC-TAAAAAACTCATTTGAAAATC
63 ACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAAA-C
1476307 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAA
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAA
1476347 ACTAATAAAA
Statistics
Matches: 411, Mismatches: 55, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
107 4 0.01
108 100 0.24
109 271 0.66
110 36 0.09
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (108 bp):
ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAACACATTTGAAAAGCATCAAGAAACT
TCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAAAC
Found at i:1476347 original size:109 final size:109
Alignment explanation
Indices: 1475872--1476347 Score: 609
Period size: 109 Copynumber: 4.4 Consensus size: 109
1475862 TTTAAGAAAA
* * * *
1475872 ATCAAGAAACTTCCGAAAATCAGACTTAGTTTCTTTAAAACA-CATTTGAAAAGCATCAAGAAAC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAAATTATTT-AAAATCATCAAGAAAC
* * * * * *
1475936 TTATAAAAATCATACTTAGTTTCTTTAAAAACTCATTTG-AAATC
65 TTCTGAAAACCAGAATTAGTTTCTTTAAAAACTCACTTGAAAATC
* * * * * * *
1475980 TTCATGAAACTTCTAAAAATCAGACTTAGTTTCGTTGAAAACTTATTTGAAATCATCAAGAAACT
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAAATTATTTAAAATCATCAAGAAACT
*
1476045 TCTGAAAACCAGACTTAGTTTCTTTAAAAACTCACTTGAAAATC
66 TCTGAAAACCAGAATTAGTTTCTTTAAAAACTCACTTGAAAATC
* * * * * *
1476089 ATCATGAAACTTCTGAAATTCAGACTTAGTTTCATTGAAAACTTATTTGAAATCATCAAGAAACT
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAAATTATTTAAAATCATCAAGAAACT
1476154 TCTGAAAACCA-AACTTAGTTTCTTTAAAAACTCACTTGAAAATC
66 TCTGAAAACCAGAA-TTAGTTTCTTTAAAAACTCACTTGAAAATC
* * * *
1476198 GTCAAGAAACTTCTAAAAATAAGACTTAGTTTCTTTAAAAAATTCATTTAAAATGATCAAGAAAC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAAATT-ATTTAAAATCATCAAGAAAC
* * * *
1476263 TTCCGAAAATCAGAATTAGTTTC-TAAAAAACTCATTTGAAAATC
65 TTCTGAAAACCAGAATTAGTTTCTTTAAAAACTCACTTGAAAATC
1476307 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAA
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAA
1476348 CTAATAAAAA
Statistics
Matches: 325, Mismatches: 38, Indels: 9
0.87 0.10 0.02
Matches are distributed among these distances:
108 83 0.26
109 204 0.63
110 36 0.11
111 2 0.01
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.32
Consensus pattern (109 bp):
ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAAATTATTTAAAATCATCAAGAAACT
TCTGAAAACCAGAATTAGTTTCTTTAAAAACTCACTTGAAAATC
Found at i:1476348 original size:55 final size:55
Alignment explanation
Indices: 1475763--1476349 Score: 672
Period size: 54 Copynumber: 10.8 Consensus size: 55
1475753 ATTCAAATAA
** * *
1475763 ATCAAGAAACCCCTGAAAACCAGACTTAATTTCTTTGAAAAA-TCATTTGAAAA-C
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTT-AAAAACTCATTTGAAAATC
** * * * * * ***
1475817 ATCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTTGAACGTTCATTTAAGAAAA--
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTT--GAAAATC
* * *
1475872 ATCAAGAAACTTCCGAAAATCAGACTTAGTTTCTTT-AAAACACATTTGAAAAGC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAAATC
* * *
1475926 ATCAAGAAACTTATAAAAATCATACTTAGTTTCTTTAAAAACTCATTTG-AAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAAATC
* * * * * *
1475980 TTCATGAAACTTCTAAAAATCAGACTTAGTTTCGTTGAAAACTTATTTG-AAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAAATC
* *
1476034 ATCAAGAAACTTCTGAAAACCAGACTTAGTTTCTTTAAAAACTCACTTGAAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAAATC
* * * * *
1476089 ATCATGAAACTTCTGAAATTCAGACTTAGTTTCATTGAAAACTTATTTG-AAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAAATC
* * *
1476143 ATCAAGAAACTTCTGAAAACCAAACTTAGTTTCTTTAAAAACTCACTTGAAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAAATC
* * * * *
1476198 GTCAAGAAACTTCTAAAAATAAGACTTAGTTTCTTTAAAAAATTCATTT-AAAATG
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTT-AAAAACTCATTTGAAAATC
* * *
1476253 ATCAAGAAACTTCCGAAAATCAGAATTAGTTTC-TAAAAAACTCATTTGAAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAAATC
1476307 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACT
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACT
1476350 AATAAAAAAT
Statistics
Matches: 449, Mismatches: 73, Indels: 21
0.83 0.13 0.04
Matches are distributed among these distances:
52 5 0.01
53 13 0.03
54 252 0.56
55 164 0.37
56 15 0.03
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (55 bp):
ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAAATC
Found at i:1478312 original size:7 final size:8
Alignment explanation
Indices: 1478300--1478378 Score: 55
Period size: 7 Copynumber: 10.4 Consensus size: 8
1478290 TATTTTCTTC
1478300 TTTATT-T
1 TTTATTCT
1478307 TTTATTCT
1 TTTATTCT
*
1478315 TTTCTTCT
1 TTTATTCT
*
1478323 CTCTTCCTTCT
1 -T-TT-ATTCT
1478334 TTT-TTCT
1 TTTATTCT
1478341 TTT-TTCT
1 TTTATTCT
1478348 TTT-TTCT
1 TTTATTCT
*
1478355 TTTTTTC-
1 TTTATTCT
1478362 TTT-TTCT
1 TTTATTCT
1478369 TTT-TTCT
1 TTTATTCT
1478376 TTT
1 TTT
1478379 GTTTTTCTCT
Statistics
Matches: 65, Mismatches: 1, Indels: 12
0.83 0.01 0.15
Matches are distributed among these distances:
6 3 0.05
7 40 0.62
8 11 0.17
9 3 0.05
10 3 0.05
11 5 0.08
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTATTCT
Found at i:1478341 original size:14 final size:14
Alignment explanation
Indices: 1478292--1478414 Score: 79
Period size: 14 Copynumber: 8.5 Consensus size: 14
1478282 GATCTGTCTA
*
1478292 TTTTCTTCTTTATT
1 TTTTCTTCTTTCTT
*
1478306 TTTTATTCTTTTCTT
1 TTTTCTTC-TTTCTT
* * *
1478321 CTCTCTTCCTTCTT
1 TTTTCTTCTTTCTT
*
1478335 TTTTCTTTTTTCTT
1 TTTTCTTCTTTCTT
*
1478349 TTTTCTT-TTTTTCT
1 TTTTCTTCTTTCT-T
*
1478363 TTTTCTTTTTTCTT
1 TTTTCTTCTTTCTT
* *
1478377 TTGTTTTTCTCTTTTT
1 TT-TTCTTCT-TTCTT
*
1478393 CTTTTGTT-TTTCTCT
1 -TTTTCTTCTTTCT-T
1478408 TTTTCTT
1 TTTTCTT
1478415 TTGTTTTTCT
Statistics
Matches: 84, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
13 4 0.05
14 49 0.58
15 21 0.25
16 8 0.10
17 2 0.02
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTTCTTCTTTCTT
Found at i:1478357 original size:13 final size:13
Alignment explanation
Indices: 1478334--1478455 Score: 94
Period size: 13 Copynumber: 9.2 Consensus size: 13
1478324 TCTTCCTTCT
1478334 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
1478347 TTTTTTCTTTTTTTC
1 -TTTTTC-TTTTTTC
1478362 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
*
1478375 TTTTGT-TTTTCTC
1 TTTT-TCTTTTTTC
*
1478388 TTTTTC--TTTTG
1 TTTTTCTTTTTTC
1478399 TTTTTCTCTTTTTC
1 TTTTTCT-TTTTTC
*
1478413 TTTTGT-TTTTCTC
1 TTTT-TCTTTTTTC
*
1478426 TTTTGT-TTGTTTC
1 TTTT-TCTTTTTTC
1478439 -TTTTCTGTTTTTAC
1 TTTTTCT-TTTTT-C
1478453 TTT
1 TTT
1478456 CTTTTTGTGT
Statistics
Matches: 89, Mismatches: 8, Indels: 21
0.75 0.07 0.18
Matches are distributed among these distances:
11 10 0.11
12 5 0.06
13 41 0.46
14 23 0.26
15 10 0.11
ACGTcount: A:0.01, C:0.14, G:0.05, T:0.80
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:1478371 original size:19 final size:19
Alignment explanation
Indices: 1478341--1478429 Score: 135
Period size: 19 Copynumber: 4.6 Consensus size: 19
1478331 TCTTTTTTCT
*
1478341 TTTTTCT-TTTTTCTTTTT
1 TTTTTCTCTTTTTCTTTTG
*
1478359 TTCTTTTTCTTTTTTCTTTTG
1 TT-TTTCTC-TTTTTCTTTTG
1478380 TTTTTCTCTTTTTCTTTTG
1 TTTTTCTCTTTTTCTTTTG
1478399 TTTTTCTCTTTTTCTTTTG
1 TTTTTCTCTTTTTCTTTTG
1478418 TTTTTCTCTTTT
1 TTTTTCTCTTTT
1478430 GTTTGTTTCT
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
18 2 0.03
19 46 0.71
20 5 0.08
21 12 0.18
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (19 bp):
TTTTTCTCTTTTTCTTTTG
Found at i:1478391 original size:7 final size:7
Alignment explanation
Indices: 1478330--1478429 Score: 79
Period size: 7 Copynumber: 15.3 Consensus size: 7
1478320 TCTCTCTTCC
*
1478330 TTCTTTT
1 TTCTCTT
*
1478337 TTCTTTT
1 TTCTCTT
*
1478344 TTCTTTT
1 TTCTCTT
1478351 TTCT-TT
1 TTCTCTT
*
1478357 TTTTCTT
1 TTCTCTT
1478364 TT-TCTT
1 TTCTCTT
*
1478370 TTTTCTT
1 TTCTCTT
*
1478377 TTGT-TT
1 TTCTCTT
1478383 TTCTCTT
1 TTCTCTT
1478390 TT-TCTT
1 TTCTCTT
*
1478396 TTGT-TT
1 TTCTCTT
1478402 TTCTCTT
1 TTCTCTT
1478409 TT-TCTT
1 TTCTCTT
*
1478415 TTGT-TT
1 TTCTCTT
1478421 TTCTCTT
1 TTCTCTT
1478428 TT
1 TT
1478430 GTTTGTTTCT
Statistics
Matches: 81, Mismatches: 5, Indels: 14
0.81 0.05 0.14
Matches are distributed among these distances:
6 38 0.47
7 43 0.53
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (7 bp):
TTCTCTT
Found at i:1478462 original size:32 final size:31
Alignment explanation
Indices: 1478330--1478463 Score: 104
Period size: 32 Copynumber: 4.4 Consensus size: 31
1478320 TCTCTCTTCC
* *
1478330 TTCTTTTTTCTTTTTTCTTTT-T-TCTTTT-T
1 TTCTCTTTTGTTTTTTCTTTTCTGT-TTTTCT
* *
1478359 TTCT-TTTTCTTTTTTCTTTTGT-TTTTCTCT
1 TTCTCTTTTGTTTTTTCTTTTCTGTTTT-TCT
*
1478389 TTTTCTTTTGTTTTTCTCTTTTTCT-TTTGTT-T
1 TTCTCTTTTGTTTTT-TC-TTTTCTGTTT-TTCT
1478421 TTCTCTTTTGTTTGTTTCTTTTCTGTTTTTACT
1 TTCTCTTTTGTTT-TTTCTTTTCTGTTTTT-CT
1478454 TTCT-TTTTGT
1 TTCTCTTTTGT
1478464 GTGTGTTTTT
Statistics
Matches: 90, Mismatches: 4, Indels: 19
0.80 0.04 0.17
Matches are distributed among these distances:
28 19 0.21
29 7 0.08
30 4 0.04
31 17 0.19
32 26 0.29
33 16 0.18
34 1 0.01
ACGTcount: A:0.01, C:0.14, G:0.05, T:0.80
Consensus pattern (31 bp):
TTCTCTTTTGTTTTTTCTTTTCTGTTTTTCT
Found at i:1480130 original size:250 final size:252
Alignment explanation
Indices: 1479689--1480190 Score: 990
Period size: 250 Copynumber: 2.0 Consensus size: 252
1479679 ATTCTTTTCG
1479689 AAGTACGAAGGGGTGACTTCAATTTACCTCAAAAGATTCCGCGGGTTACTCCCAAGATCCGTGAT
1 AAGTACGAAGGGGTGACTTCAATTTACCTCAAAAGATTCCGCGGGTTACTCCCAAGATCCGTGAT
1479754 TAATGCACGTTGAGATGTAATGTATATCATGTAATGTACGATGTATAGATGCTAATGTAAAGATG
66 TAATGCACGTTGAGATGTAATGTATATCATGTAATGTACGATGTATAGATGCTAATGTAAAGATG
1479819 CAAATATGCTTATGCAAATGCAAAATGCAAAATGTGAATACAAAATAAAAAATTTAAATGCAACA
131 CAAATATGCTTATGCAAATGCAAAATGCAAAATGTGAATACAAAATAAAAAATTTAAATGCAACA
1479884 AAAGAATTGATCCCAAAGTAATTTTCATAAAACAACTT-CAAAG-ACACACAATGTC
196 AAAGAATTGATCCCAAAGTAATTTTCATAAAACAACTTCCAAAGAACACACAATGTC
1479939 AAGTACGAAGGGGTGACTTCAATTTACCTCAAAAGATTCCGCGGGTTACTCCCAAGATCCGTGAT
1 AAGTACGAAGGGGTGACTTCAATTTACCTCAAAAGATTCCGCGGGTTACTCCCAAGATCCGTGAT
1480004 TAATGCACGTTGAGATGTAATGTATATCATGTAATGTACGATGTATAGATGCTAATGTAAAGATG
66 TAATGCACGTTGAGATGTAATGTATATCATGTAATGTACGATGTATAGATGCTAATGTAAAGATG
1480069 CAAATATGCTTATGCAAATGCAAAATGCAAAATGTGAATACAAAATAAAAAATTTAAATGCAACA
131 CAAATATGCTTATGCAAATGCAAAATGCAAAATGTGAATACAAAATAAAAAATTTAAATGCAACA
1480134 AAAGAATTGATCCCAAAGTAATTTTCATAAAACAACTTCCAAAGAACACACAATGTC
196 AAAGAATTGATCCCAAAGTAATTTTCATAAAACAACTTCCAAAGAACACACAATGTC
1480191 TCAATCCACC
Statistics
Matches: 250, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
250 233 0.93
251 5 0.02
252 12 0.05
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (252 bp):
AAGTACGAAGGGGTGACTTCAATTTACCTCAAAAGATTCCGCGGGTTACTCCCAAGATCCGTGAT
TAATGCACGTTGAGATGTAATGTATATCATGTAATGTACGATGTATAGATGCTAATGTAAAGATG
CAAATATGCTTATGCAAATGCAAAATGCAAAATGTGAATACAAAATAAAAAATTTAAATGCAACA
AAAGAATTGATCCCAAAGTAATTTTCATAAAACAACTTCCAAAGAACACACAATGTC
Found at i:1482758 original size:24 final size:24
Alignment explanation
Indices: 1482731--1482801 Score: 60
Period size: 23 Copynumber: 3.0 Consensus size: 24
1482721 GTACTTAAGT
1482731 TAAAAAACATAAAATTGTACGTTC
1 TAAAAAACATAAAATTGTACGTTC
* * *
1482755 TAAAGAA-ATTAAA--GTAC-TTAAGT
1 TAAAAAACATAAAATTGTACGTT---C
1482778 TAAAAAACATAAAATTGTACGTTC
1 TAAAAAACATAAAATTGTACGTTC
1482802 ACCTAAATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
20 2 0.06
21 4 0.12
23 11 0.32
24 11 0.32
26 4 0.12
27 2 0.06
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.30
Consensus pattern (24 bp):
TAAAAAACATAAAATTGTACGTTC
Found at i:1482759 original size:47 final size:47
Alignment explanation
Indices: 1482708--1482801 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
1482698 CAAATGTAAA
1482708 TAAAGAAATTAAAGTACTTAAGTTAAAAAACATAAAATTGTACGTTC
1 TAAAGAAATTAAAGTACTTAAGTTAAAAAACATAAAATTGTACGTTC
1482755 TAAAGAAATTAAAGTACTTAAGTTAAAAAACATAAAATTGTACGTTC
1 TAAAGAAATTAAAGTACTTAAGTTAAAAAACATAAAATTGTACGTTC
1482802 ACCTAAATTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.30
Consensus pattern (47 bp):
TAAAGAAATTAAAGTACTTAAGTTAAAAAACATAAAATTGTACGTTC
Found at i:1489493 original size:53 final size:53
Alignment explanation
Indices: 1489413--1489518 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
1489403 AGTCCTCATC
1489413 CCACCAAAGTACCCTCCACACGGAGATGTATGGCAATGAAATAAGATCTCCTT
1 CCACCAAAGTACCCTCCACACGGAGATGTATGGCAATGAAATAAGATCTCCTT
1489466 CCACCAAAGTACCCTCCACACGGAGATGTATGGCAATGAAATAAGATCTCCTT
1 CCACCAAAGTACCCTCCACACGGAGATGTATGGCAATGAAATAAGATCTCCTT
1489519 ATGTTATTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (53 bp):
CCACCAAAGTACCCTCCACACGGAGATGTATGGCAATGAAATAAGATCTCCTT
Found at i:1497664 original size:23 final size:22
Alignment explanation
Indices: 1497638--1497692 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
1497628 CACCACAGCT
1497638 TGTATAAATGCACCGAAGTGCCA
1 TGTA-AAATGCACCGAAGTGCCA
* *
1497661 TGTAGAATTACACCGAAGTGCCA
1 TGTA-AAATGCACCGAAGTGCCA
*
1497684 TATAAAATG
1 TGTAAAATG
1497693 TCCCTAAAGA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 3 0.12
23 23 0.88
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (22 bp):
TGTAAAATGCACCGAAGTGCCA
Found at i:1498186 original size:2 final size:2
Alignment explanation
Indices: 1498181--1498235 Score: 89
Period size: 2 Copynumber: 29.0 Consensus size: 2
1498171 ATATCTTATC
1498181 AT AT AT AT A- AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1498221 AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT
1498236 CTGCAAATAC
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 47 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1499122 original size:20 final size:20
Alignment explanation
Indices: 1499094--1499131 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1499084 CTTCCCTTGA
1499094 AGTGCATCGATACATTCTAT
1 AGTGCATCGATACATTCTAT
* *
1499114 AGTGTATCGATGCATTCT
1 AGTGCATCGATACATTCT
1499132 TTAACATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAT
Found at i:1499290 original size:64 final size:63
Alignment explanation
Indices: 1499139--1499297 Score: 176
Period size: 63 Copynumber: 2.5 Consensus size: 63
1499129 TCTTTAACAT
* * * * *
1499139 GTGCATCGATACACTGCCCATGCATCGATACAAAAATTACCTTCGATGTTTTAATTTTAAGGG
1 GTGCATCGATGCACTTCCTATGCATCGATACAAAAATTACATTCGATGTTTCAATTTTAAGGG
* ** * * **
1499202 GTGCATCGATGCAC-TCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAATTG
1 GTGCATCGATGCACTTCC-TATGCATCGATACAAAAATTACATTCGATGTTT-CAATTTTAAGGG
*
1499266 GTGCATCGATGCACTTCCTGTGCATCGATACA
1 GTGCATCGATGCACTTCCTATGCATCGATACA
1499298 CACTGAACAA
Statistics
Matches: 79, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
62 2 0.03
63 40 0.51
64 34 0.43
65 3 0.04
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (63 bp):
GTGCATCGATGCACTTCCTATGCATCGATACAAAAATTACATTCGATGTTTCAATTTTAAGGG
Found at i:1502696 original size:23 final size:23
Alignment explanation
Indices: 1502678--1502761 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 23
1502668 CTCGTATAAA
1502678 TGCACTGAAGTGCCACGTAGAAT
1 TGCACTGAAGTGCCACGTAGAAT
*
1502701 TGCAAC-GAAGTGCCGCGTAGAAT
1 TGC-ACTGAAGTGCCACGTAGAAT
* * * * *
1502724 TACACCGAACTACCGCGTAGAAT
1 TGCACTGAAGTGCCACGTAGAAT
1502747 TGCACTGAAGTGCCA
1 TGCACTGAAGTGCCA
1502762 TATAAAACGT
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
22 2 0.04
23 46 0.92
24 2 0.04
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
TGCACTGAAGTGCCACGTAGAAT
Found at i:1503240 original size:2 final size:2
Alignment explanation
Indices: 1503233--1503287 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
1503223 ATGGTTTTAC
1503233 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1503274 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1503288 CTGCAAATAC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1507581 original size:154 final size:155
Alignment explanation
Indices: 1507300--1507606 Score: 607
Period size: 154 Copynumber: 2.0 Consensus size: 155
1507290 AATCCCTGTC
1507300 TGCCTCTAGCCCAACACCATAACAACAACCTCAATTGACTATTCATTAACCAAAGAAGCATCATA
1 TGCCTCTAGCCCAACACCATAACAACAACCTCAATTGACTATTCATTAACCAAAGAAGCATCATA
1507365 ATGGTCAGAATCATTAGGAACATCAACTGACACAACAACCTCTTTCATATTTCAGGCTTGATTAG
66 ATGGTCAGAATCATTAGGAACATCAACTGACACAACAACCTCTTTCATATTTCAGGCTTGATTAG
1507430 GCTTGCACACTTAAGCCTTCAATGT
131 GCTTGCACACTTAAGCCTTCAATGT
1507455 TGCCTCTAGCCCAACACCATAAC-ACAACCTCAATTGACTATTCATTAACCAAAGAAGCATCATA
1 TGCCTCTAGCCCAACACCATAACAACAACCTCAATTGACTATTCATTAACCAAAGAAGCATCATA
1507519 ATGGTCAGAATCATTAGGAACATCAACTGACACAACAACCTCTTTCATATTTCAGGCTTGATTAG
66 ATGGTCAGAATCATTAGGAACATCAACTGACACAACAACCTCTTTCATATTTCAGGCTTGATTAG
1507584 GCTTGCACACTTAAGCCTTCAAT
131 GCTTGCACACTTAAGCCTTCAAT
1507607 TGAACTTTGC
Statistics
Matches: 152, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
154 129 0.85
155 23 0.15
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.26
Consensus pattern (155 bp):
TGCCTCTAGCCCAACACCATAACAACAACCTCAATTGACTATTCATTAACCAAAGAAGCATCATA
ATGGTCAGAATCATTAGGAACATCAACTGACACAACAACCTCTTTCATATTTCAGGCTTGATTAG
GCTTGCACACTTAAGCCTTCAATGT
Found at i:1513390 original size:30 final size:30
Alignment explanation
Indices: 1513356--1513426 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
1513346 TTTGTAATTC
*
1513356 CAAATTAATTAAAATATAATTTAATTATTT
1 CAAATTAAATAAAATATAATTTAATTATTT
* * *
1513386 CAAATTAAATAAATTCTTATTTAATTATTT
1 CAAATTAAATAAAATATAATTTAATTATTT
**
1513416 TGAATTAAATA
1 CAAATTAAATA
1513427 TTCATTAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (30 bp):
CAAATTAAATAAAATATAATTTAATTATTT
Found at i:1515420 original size:21 final size:23
Alignment explanation
Indices: 1515391--1515439 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
1515381 GTACCGATAC
*
1515391 TCCTACTTG-GGTATCGGTA-TT
1 TCCTACTTGTGGTATCGATACTT
*
1515412 TCCTTCTTGTGGTATCGATACTT
1 TCCTACTTGTGGTATCGATACTT
1515435 TCCTA
1 TCCTA
1515440 AGCATCGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 8 0.35
22 9 0.39
23 6 0.26
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.45
Consensus pattern (23 bp):
TCCTACTTGTGGTATCGATACTT
Found at i:1517150 original size:76 final size:81
Alignment explanation
Indices: 1517013--1517163 Score: 190
Period size: 76 Copynumber: 1.9 Consensus size: 81
1517003 AATAAGTAAG
1517013 CATTAAAAGAATGTAATTTAGATTACAACTCTTTTAATTGATATATATAATTCAGAATAATTAAA
1 CATTAAAAGAATGTAATTTAGATTACAACTCTTTTAATTGATATATATAATTCAGAATAATTAAA
1517078 TAAT-TTTTAAATAAA
66 TAATATTTTAAATAAA
* * * * *
1517093 CATTAAAA-ATTGTAA-TTATGATTATAAGTC-TTTAA-TG-TATATTTAATT-TGAATTAATTA
1 CATTAAAAGAATGTAATTTA-GATTACAACTCTTTTAATTGATATATATAATTCAGAA-TAATTA
1517152 AATAATATTTTA
64 AATAATATTTTA
1517164 TTTATTAATT
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
75 3 0.05
76 22 0.35
77 7 0.11
78 8 0.13
79 15 0.24
80 8 0.13
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.44
Consensus pattern (81 bp):
CATTAAAAGAATGTAATTTAGATTACAACTCTTTTAATTGATATATATAATTCAGAATAATTAAA
TAATATTTTAAATAAA
Found at i:1524041 original size:25 final size:24
Alignment explanation
Indices: 1523986--1524033 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1523976 ATAAGTCTTT
1523986 AATATATATTTAATTTGAATTAATTA
1 AATA-ATATTTAATTT-AATTAATTA
*
1524012 AATAATATTTTATTT-ATTAATT
1 AATAATATTTAATTTAATTAATT
1524034 CGAAATAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
25 10 0.48
26 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
AATAATATTTAATTTAATTAATTA
Found at i:1545311 original size:21 final size:20
Alignment explanation
Indices: 1545270--1545329 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
1545260 GCATAACTAA
*
1545270 ATATAATAAACAATAATTAAC
1 ATAT-ATAAATAATAATTAAC
* *
1545291 CTATATAATTAATAATATAAC
1 ATATATAAATAATAAT-TAAC
1545312 ATATATAAATAACTAATT
1 ATATATAAATAA-TAATT
1545330 GTAATAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 10 0.31
21 18 0.56
22 4 0.12
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (20 bp):
ATATATAAATAATAATTAAC
Found at i:1547234 original size:42 final size:42
Alignment explanation
Indices: 1547179--1547386 Score: 328
Period size: 42 Copynumber: 5.0 Consensus size: 42
1547169 GAGCCTAGGA
*
1547179 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGG
* *
1547221 AAATTGTAAGGCTTACCCTTGCACACAGCAAAGAAACCTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGG
* * *
1547263 AAACTATAAGGCTTA-CCTTGAACACAGCAAAGGAACATGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGG
*
1547304 AAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAACCTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGG
* *
1547346 AAACTGTAAGGTTTACCCTTGCACACAACAAAGGAACCTGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGG
1547387 AATACTTCCT
Statistics
Matches: 150, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
41 37 0.25
42 113 0.75
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (42 bp):
AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGG
Found at i:1547295 original size:83 final size:84
Alignment explanation
Indices: 1547179--1547386 Score: 339
Period size: 83 Copynumber: 2.5 Consensus size: 84
1547169 GAGCCTAGGA
*
1547179 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGAAATTGTAAGGCTTACCCTTGCA
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGAAACTGTAAGGCTTACCCTTGCA
1547244 CACAGC-AAAGAAACCTGGG
66 CACAGCAAAAG-AACCTGGG
* * * *
1547263 AAACTATAAGGCTTA-CCTTGAACACAGCAAAGGAACATGGGAAACTGTAAGGCTTACCCTTGCA
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGAAACTGTAAGGCTTACCCTTGCA
1547327 CACAGCAAAAGAACCTGGG
66 CACAGCAAAAGAACCTGGG
*
1547346 AAACTGTAAGGTTTACCCTTGCACACAACAAAGGAACCTGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
1547387 AATACTTCCT
Statistics
Matches: 112, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
83 72 0.64
84 40 0.36
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (84 bp):
AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGAAACTGTAAGGCTTACCCTTGCA
CACAGCAAAAGAACCTGGG
Found at i:1554590 original size:42 final size:42
Alignment explanation
Indices: 1554449--1554820 Score: 602
Period size: 42 Copynumber: 8.8 Consensus size: 42
1554439 CTATACATCG
* * * * *
1554449 GTAAGGCTTATCCTATGCACAAAGCAGAGGAGCCTAGGAAAACT
1 GTAAGGCTTACCCT-TGCACACAGCAAAGGAACCT-GGGAAACT
1554493 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCT-GGAAACT
1 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACT
* *
1554534 GTAAGGCTTGCCCTTGCACAGAGCAAAGGAACCTGGGAAACT
1 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACT
**
1554576 GTAAGGCTTACCCTTAAACACAGCAAAGGAACCTGGGAAACT
1 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACT
* *
1554618 GTAAGGCTTACCCTTGCACACAGCAAAGTAACCAGGGAAACT
1 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACT
1554660 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACT
1 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACT
* *
1554702 GTAAGGTTTACCCTTGCACACAACAAAGGAACCTGGGAAACT
1 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACT
1554744 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACT
1 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACT
1554786 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTG
1554821 AAATATTTCC
Statistics
Matches: 306, Mismatches: 21, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
41 38 0.12
42 238 0.78
43 17 0.06
44 13 0.04
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.17
Consensus pattern (42 bp):
GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACT
Found at i:1569360 original size:15 final size:15
Alignment explanation
Indices: 1569342--1569381 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1569332 AGTTAAAAAT
1569342 AATAAATAAAGAT-AA
1 AATAAA-AAAGATAAA
*
1569357 AATAAAATAGATAAA
1 AATAAAAAAGATAAA
1569372 AATAAAAAAG
1 AATAAAAAAG
1569382 GAATATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.17
Consensus pattern (15 bp):
AATAAAAAAGATAAA
Found at i:1569365 original size:20 final size:19
Alignment explanation
Indices: 1569313--1569380 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
1569303 GGGTTCCCTT
*
1569313 TAAAAAAAAGTTAAATTAAAGT
1 TAAAAAAAA--TAAA-TAAAGA
*
1569335 TAAAAATAATAAATAAAGA
1 TAAAAAAAATAAATAAAGA
* *
1569354 TAAAATAAAATAGATAAAAA
1 TAAAA-AAAATAAATAAAGA
1569374 TAAAAAA
1 TAAAAAA
1569381 GGAATATATT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 12 0.30
20 20 0.50
22 8 0.20
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (19 bp):
TAAAAAAAATAAATAAAGA
Found at i:1570569 original size:2 final size:2
Alignment explanation
Indices: 1570520--1570549 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1570510 TTTCAGAAAC
1570520 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1570550 CTTTAAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1576689 original size:2 final size:2
Alignment explanation
Indices: 1576682--1576708 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1576672 GTGGAGGGAA
1576682 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1576709 AGAAAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1590607 original size:14 final size:13
Alignment explanation
Indices: 1590588--1590639 Score: 51
Period size: 10 Copynumber: 4.3 Consensus size: 13
1590578 AAAAAATGAA
1590588 AAAAGAAATTAAAG
1 AAAAGAAA-TAAAG
1590602 AAAAGAAATAAAG
1 AAAAGAAATAAAG
1590615 ---AGAAATAAAG
1 AAAAGAAATAAAG
*
1590625 AGAA-AAA-AAAG
1 AAAAGAAATAAAG
1590636 AAAA
1 AAAA
1590640 AAAGGGATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
10 10 0.29
11 7 0.21
12 3 0.09
13 6 0.18
14 8 0.24
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (13 bp):
AAAAGAAATAAAG
Found at i:1590620 original size:10 final size:10
Alignment explanation
Indices: 1590605--1590643 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
1590595 ATTAAAGAAA
1590605 AGAAATAAAG
1 AGAAATAAAG
1590615 AGAAATAAAG
1 AGAAATAAAG
*
1590625 AGAAA-AAAA
1 AGAAATAAAG
*
1590634 AGAAAAAAAG
1 AGAAATAAAG
1590644 GGATGATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (10 bp):
AGAAATAAAG
Found at i:1591747 original size:32 final size:32
Alignment explanation
Indices: 1591673--1591748 Score: 107
Period size: 32 Copynumber: 2.4 Consensus size: 32
1591663 GCATTGTTAA
* * *
1591673 AGATTCAACAACAAATGTTGGGGCATATTTGG
1 AGATTCAACATCAAATATTGAGGCATATTTGG
*
1591705 AGATTCAACATCGAATATTGAGGCATATTTGG
1 AGATTCAACATCAAATATTGAGGCATATTTGG
*
1591737 GGATTCAACATC
1 AGATTCAACATC
1591749 CTGATGCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (32 bp):
AGATTCAACATCAAATATTGAGGCATATTTGG
Found at i:1592072 original size:43 final size:43
Alignment explanation
Indices: 1592023--1592146 Score: 151
Period size: 43 Copynumber: 2.9 Consensus size: 43
1592013 ACGAAGGGGC
*
1592023 CATCCATGATTTCAACTCCATGACGGAGGATATCGTACCAACG
1 CATCCATGATTTCAACTCCATGACGGAGGATATCGTACCAACA
* * * *
1592066 GATCCATGATTTCAACTCCACGACGGAGGATATCGTGCCCACA
1 CATCCATGATTTCAACTCCATGACGGAGGATATCGTACCAACA
* * * *
1592109 CATCCACGGTTTCAACTTCATGACGAAGAGA-ATCGTAC
1 CATCCATGATTTCAACTCCATGACGGAG-GATATCGTAC
1592147 ACACAAGCAG
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
43 66 0.97
44 2 0.03
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (43 bp):
CATCCATGATTTCAACTCCATGACGGAGGATATCGTACCAACA
Found at i:1592407 original size:43 final size:43
Alignment explanation
Indices: 1592358--1592481 Score: 144
Period size: 43 Copynumber: 2.9 Consensus size: 43
1592348 ACGAAGGGGC
* *
1592358 CATCCACGATTTCAACTCCACGACGGATGATATCGTACCAACG
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* * * *
1592401 GATCCACGATTTCAACCCCACGACGGAGGATATCGTGCCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* *
1592444 CATCCAC-AGTTTCAACTTCACGACGAAGGGA-ATCGTAC
1 CATCCACGA-TTTCAACTCCACGACGGA-GGATATCGTAC
1592482 ACACAAGCAT
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
42 1 0.01
43 64 0.94
44 3 0.04
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.19
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
Found at i:1592523 original size:335 final size:335
Alignment explanation
Indices: 1591908--1592665 Score: 1295
Period size: 335 Copynumber: 2.3 Consensus size: 335
1591898 TGCAGCTTTT
* *
1591908 AGAGTCAATTTCAACTTCA-GAACGAAGGATATTGGACTCAAAATAGCACAAGCTTGGATTTCAA
1 AGAGCCAATTTCAACTTCACG-ACGAAGGATATTGGACTCAAAACAGCACAAGCTTGGATTTCAA
* *
1591972 CTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCATGATTTCA
65 CTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCAAGACGAAGGGGCCATCCACGATTTCA
* * *
1592037 ACTCCATGACGGAGGATATCGTACCAACGGATCCATGATTTCAACTCCACGACGGAGGATATCGT
130 ACTCCACGACGGAGGATATCGTACCAACGGATCCACGATTTCAACCCCACGACGGAGGATATCGT
* *
1592102 GCCCACACATCCACGGTTTCAACTTCATGACGAAGAGAATCGTACACACAAGCAGCATCAATCTC
195 GCCCACACATCCACAGTTTCAACTTCACGACGAAGAGAATCGTACACACAAGCAGCATCAATCTC
* *
1592167 TAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAAGAGTGTTTGTCAATAAAC
260 TAGATTGGATTTCAACTTCACGACAAAGGATATCCAACTCAAAGAAAGAGTGTCTGTCAATAAAC
1592232 TTTCCAGTTTC
325 TTTCCAGTTTC
1592243 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCAAAACAGCACAAGCTTGGATTTCAAC
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCAAAACAGCACAAGCTTGGATTTCAAC
*
1592308 TTCACGACGAATGATATTCAAGTCAAGGCTCAACTTCAAGACGAAGGGGCCATCCACGATTTCAA
66 TTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCAAGACGAAGGGGCCATCCACGATTTCAA
*
1592373 CTCCACGACGGATGATATCGTACCAACGGATCCACGATTTCAACCCCACGACGGAGGATATCGTG
131 CTCCACGACGGAGGATATCGTACCAACGGATCCACGATTTCAACCCCACGACGGAGGATATCGTG
* *
1592438 CCCACACATCCACAGTTTCAACTTCACGACGAAGGGAATCGTACACACAAGCATCATCAATCTCT
196 CCCACACATCCACAGTTTCAACTTCACGACGAAGAGAATCGTACACACAAGCAGCATCAATCTCT
*
1592503 AGATTGGATTTCAACTTCACGACAAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACT
261 AGATTGGATTTCAACTTCACGACAAAGGATATCCAACTCAAAGAAAGAGTGTCTGTCAATAAACT
*
1592568 TTCCAGTTTT
326 TTCCAGTTTC
* * *
1592578 AGAGCCAATTTCAACTTCACGACGAAGAATATTGTACT-AGAAACAACACAAGCTTGGATTTCAA
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCA-AAACAGCACAAGCTTGGATTTCAA
*
1592642 CTTCACGATGAAGGATATTCAAGT
65 CTTCACGACGAAGGATATTCAAGT
1592666 TAAGCCTTCA
Statistics
Matches: 399, Mismatches: 22, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
334 1 0.00
335 397 0.99
336 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (335 bp):
AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCAAAACAGCACAAGCTTGGATTTCAAC
TTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCAAGACGAAGGGGCCATCCACGATTTCAA
CTCCACGACGGAGGATATCGTACCAACGGATCCACGATTTCAACCCCACGACGGAGGATATCGTG
CCCACACATCCACAGTTTCAACTTCACGACGAAGAGAATCGTACACACAAGCAGCATCAATCTCT
AGATTGGATTTCAACTTCACGACAAAGGATATCCAACTCAAAGAAAGAGTGTCTGTCAATAAACT
TTCCAGTTTC
Found at i:1592755 original size:42 final size:42
Alignment explanation
Indices: 1592693--1592901 Score: 258
Period size: 42 Copynumber: 5.0 Consensus size: 42
1592683 GAAGCAAGTC
1592693 CATCAGTAAGTC-TTCTGAGCATGATGCTTAAATCCTTCGGGT
1 CATCAGTAAGTCTTTC-GAGCATGATGCTTAAATCCTTCGGGT
* *
1592735 CATCAATAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGT
** * * * * *
1592777 TGTCTGTAAGCCTTTCGAGCATGAGGCTTAAATCATTCGGGC
1 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGT
*
1592819 CATCAGTAAGTCTTCCGAGCATGATGCTTAAATCCTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGT
* * * * * *
1592861 CATCAGTAAGCCTTTCAAGTATGATGATTAAGTCATTCGGG
1 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGG
1592902 CAATCTAAAG
Statistics
Matches: 140, Mismatches: 26, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
42 137 0.98
43 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.33
Consensus pattern (42 bp):
CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGT
Found at i:1592953 original size:37 final size:37
Alignment explanation
Indices: 1592902--1592978 Score: 129
Period size: 37 Copynumber: 2.1 Consensus size: 37
1592892 GTCATTCGGG
*
1592902 CAATCTAAAGCCTTCATCAAAGAGTAGTGAAGCAAAT
1 CAATCTAAAGCCTTCACCAAAGAGTAGTGAAGCAAAT
1592939 CAATCTTAAA-CCTTCACCAAAGAGTAGTGAAGCAAAT
1 CAATC-TAAAGCCTTCACCAAAGAGTAGTGAAGCAAAT
1592976 CAA
1 CAA
1592979 ATCTGATATT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
37 34 0.89
38 4 0.11
ACGTcount: A:0.44, C:0.21, G:0.14, T:0.21
Consensus pattern (37 bp):
CAATCTAAAGCCTTCACCAAAGAGTAGTGAAGCAAAT
Found at i:1593180 original size:112 final size:112
Alignment explanation
Indices: 1592979--1593397 Score: 705
Period size: 112 Copynumber: 3.7 Consensus size: 112
1592969 AGCAAATCAA
1592979 ATCTGATATTCCCTCAGAAGAAGCGGAACAGATCTCTCTTTTTCAAGATTTGATATTCCCTGAGT
1 ATCTGATATTCCCTCAGAAGAAGCGGAACAGATCTCTCTTTTTCAAGATTTGATATTCCCTGAGT
* *
1593044 GACAGCGGAACACGTCTTTCCACGATTCAATTGATTAACTCTCACAG
66 GACAGCGGAACAAGTCTTTTCACGATTCAATTGATTAACTCTCACAG
* *
1593091 ATCTGATATTCTCTCAGAATAAGCGGAACAGATCTCTCTTTTTCAAGATTTGATATTCCCTGAGT
1 ATCTGATATTCCCTCAGAAGAAGCGGAACAGATCTCTCTTTTTCAAGATTTGATATTCCCTGAGT
*
1593156 GACAGCGGAACAAGTCTTTTCACGATTCAATTGATCAACTCTCACAG
66 GACAGCGGAACAAGTCTTTTCACGATTCAATTGATTAACTCTCACAG
* **
1593203 ATCTGATATTCCCTCAAAAGAAGCATAACAGATCTCTCTTTTTCAAGATTTGATATTCCCTGAGT
1 ATCTGATATTCCCTCAGAAGAAGCGGAACAGATCTCTCTTTTTCAAGATTTGATATTCCCTGAGT
*
1593268 GACAGCGGAACAAGT-TTTTCCACGATTCAATTGATTAACTTTCACAG
66 GACAGCGGAACAAGTCTTTT-CACGATTCAATTGATTAACTCTCACAG
* * *
1593315 ATCTGATATTCCCTCAGAAGAAGTGGAACATATCCCTCTTTTTCAAGATTTGATATTCCCTGAGT
1 ATCTGATATTCCCTCAGAAGAAGCGGAACAGATCTCTCTTTTTCAAGATTTGATATTCCCTGAGT
*
1593380 GATAGCGGAACAAGTCTT
66 GACAGCGGAACAAGTCTT
1593398 GCCAATTCCT
Statistics
Matches: 286, Mismatches: 19, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
111 4 0.01
112 280 0.98
113 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (112 bp):
ATCTGATATTCCCTCAGAAGAAGCGGAACAGATCTCTCTTTTTCAAGATTTGATATTCCCTGAGT
GACAGCGGAACAAGTCTTTTCACGATTCAATTGATTAACTCTCACAG
Found at i:1597082 original size:12 final size:14
Alignment explanation
Indices: 1597048--1597074 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1597038 AAGTAATCAA
1597048 AGATAAAAAAATAT
1 AGATAAAAAAATAT
1597062 AGATAAAAAAATA
1 AGATAAAAAAATA
1597075 AATTAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (14 bp):
AGATAAAAAAATAT
Found at i:1597520 original size:3 final size:3
Alignment explanation
Indices: 1597512--1597568 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
1597502 TAAATTTAAA
* *
1597512 AAT AAT AAT AAT -AT GAA- AAT TA- AAT AAT AAT TAT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1597555 AAT AAT AAT GAT AA
1 AAT AAT AAT AAT AA
1597569 ATAAATAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 5 0.11
3 38 0.86
4 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1599315 original size:18 final size:19
Alignment explanation
Indices: 1599292--1599335 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1599282 ACAGTAATTC
*
1599292 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTA
1599310 TATTCCCACTGGTAATCTTA
1 TATT-CCACTGGTAATCTTA
1599330 TATTCC
1 TATTCC
1599336 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.20, C:0.25, G:0.09, T:0.45
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTA
Found at i:1599323 original size:20 final size:20
Alignment explanation
Indices: 1599298--1599335 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1599288 ATTCTATTCC
*
1599298 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTATATTCCCA
1599318 CTGGTAATCTTATATTCC
1 CTGGTAATCTTATATTCC
1599336 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Found at i:1599587 original size:2 final size:2
Alignment explanation
Indices: 1599580--1599605 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1599570 GATTAGAAAT
1599580 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
1599606 ATGTAAGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1599775 original size:21 final size:21
Alignment explanation
Indices: 1599751--1599792 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1599741 TTACAATAGA
*
1599751 TTTCAACACAACTTTTGAGAT
1 TTTCAACACAACTTTTAAGAT
1599772 TTTCAACACAACTTTTAAGAT
1 TTTCAACACAACTTTTAAGAT
1599793 AGACTCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (21 bp):
TTTCAACACAACTTTTAAGAT
Found at i:1601047 original size:19 final size:19
Alignment explanation
Indices: 1601020--1601057 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1601010 ACTGAACCTC
* *
1601020 AACTGATTCAAACTTAAAA
1 AACTAATTCAAAATTAAAA
1601039 AACTAATTCAAAATTAAAA
1 AACTAATTCAAAATTAAAA
1601058 TAATTGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (19 bp):
AACTAATTCAAAATTAAAA
Found at i:1612061 original size:45 final size:46
Alignment explanation
Indices: 1612012--1612102 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
1612002 AAACATCGAA
* * *
1612012 TGCATTTTATGCATTGATGCAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1612057 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1612103 ATTTTTCAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 20 0.48
46 22 0.52
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
Found at i:1619504 original size:21 final size:21
Alignment explanation
Indices: 1619462--1619505 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1619452 ACTCTGGGAG
* *
1619462 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
1619483 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
1619504 CT
1 CT
1619506 CCTCCTCCGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:1620720 original size:45 final size:46
Alignment explanation
Indices: 1620671--1620758 Score: 151
Period size: 45 Copynumber: 1.9 Consensus size: 46
1620661 AAACATCGAA
* *
1620671 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1620716 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACT
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACT
1620759 AAGATTTTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 21 0.52
46 19 0.47
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.27
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
Found at i:1620749 original size:20 final size:21
Alignment explanation
Indices: 1620724--1620762 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1620714 AGTGCATTTG
1620724 ATGCATCGATGCAC-AAGACC
1 ATGCATCGATGCACTAAGACC
1620744 ATGCATCGATGCACTAAGA
1 ATGCATCGATGCACTAAGA
1620763 TTTTTCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.18
Consensus pattern (21 bp):
ATGCATCGATGCACTAAGACC
Found at i:1622691 original size:30 final size:30
Alignment explanation
Indices: 1622655--1622719 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
1622645 CTTATTCATT
1622655 CACATCTTTACTTAGCTCAATTCATGCATA
1 CACATCTTTACTTAGCTCAATTCATGCATA
* *
1622685 CACATCTTTACTTAGCTTAGTTCATGCATA
1 CACATCTTTACTTAGCTCAATTCATGCATA
1622715 CACAT
1 CACAT
1622720 TCATAGTTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.29, C:0.26, G:0.08, T:0.37
Consensus pattern (30 bp):
CACATCTTTACTTAGCTCAATTCATGCATA
Found at i:1631858 original size:12 final size:12
Alignment explanation
Indices: 1631843--1631916 Score: 51
Period size: 13 Copynumber: 5.9 Consensus size: 12
1631833 ATGTCATCGT
**
1631843 TAAAATTTTTAA
1 TAAAATTTAAAA
1631855 TAAAATATTAAAA
1 TAAAAT-TTAAAA
*
1631868 TAAAATTCAAAA
1 TAAAATTTAAAA
* *
1631880 TAAATATTCAATA
1 TAAA-ATTTAAAA
*
1631893 T-AATTTTAAAATA
1 TAAAATTT-AAA-A
1631906 TAAAATTTAAA
1 TAAAATTTAAA
1631917 TACCAAAACA
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
11 2 0.04
12 19 0.39
13 23 0.47
14 5 0.10
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (12 bp):
TAAAATTTAAAA
Found at i:1632696 original size:12 final size:13
Alignment explanation
Indices: 1632676--1632704 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1632666 GCTCTTCGTG
1632676 TTTCTTCACTTGT
1 TTTCTTCACTTGT
1632689 TTTC-TCACTTGT
1 TTTCTTCACTTGT
1632701 TTTC
1 TTTC
1632705 AAACCCTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.07, C:0.24, G:0.07, T:0.62
Consensus pattern (13 bp):
TTTCTTCACTTGT
Found at i:1633490 original size:17 final size:17
Alignment explanation
Indices: 1633463--1633501 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1633453 AATTTACAAT
*
1633463 TAATT-TAAATAATATC
1 TAATTATAAATAATAAC
1633479 TAATTATAAATAATAAC
1 TAATTATAAATAATAAC
1633496 TAATTA
1 TAATTA
1633502 ATTTGATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATTATAAATAATAAC
Found at i:1633581 original size:11 final size:11
Alignment explanation
Indices: 1633565--1633589 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1633555 TTGATTTGAG
1633565 TTTTAAATGGA
1 TTTTAAATGGA
1633576 TTTTAAATGGA
1 TTTTAAATGGA
1633587 TTT
1 TTT
1633590 GACCTCTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (11 bp):
TTTTAAATGGA
Found at i:1640852 original size:21 final size:20
Alignment explanation
Indices: 1640766--1640923 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1640756 AAATGACCAA
**
1640766 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1640785 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1640805 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1640825 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1640846 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1640867 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1640887 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1640908 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1640924 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1640939 original size:40 final size:40
Alignment explanation
Indices: 1640890--1641044 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
1640880 CGATTTTCCA
* ** *
1640890 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * *
1640930 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
* ** *
1640970 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
1641010 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1641045 TATTTAAAGC
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 62 0.65
41 33 0.34
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Found at i:1640952 original size:20 final size:20
Alignment explanation
Indices: 1640890--1641043 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
1640880 CGATTTTCCA
* ** *
1640890 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1640910 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1640930 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1640950 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1640970 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1640990 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1641010 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1641031 AAATCGCAACGCG
1 AAATCGCAACGCG
1641044 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.82
21 17 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1641466 original size:33 final size:33
Alignment explanation
Indices: 1641427--1641497 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1641417 TTCACTTAGA
*
1641427 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1641460 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1641493 TTTCA
1 TTTCA
1641498 ATTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1641621 original size:20 final size:20
Alignment explanation
Indices: 1641577--1641686 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
1641567 TGCAGAAGAG
*
1641577 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
1641598 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
1641618 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
1641639 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
1641653 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
1641672 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
1641687 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:1641634 original size:41 final size:38
Alignment explanation
Indices: 1641570--1641686 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
1641560 TTCAATTTGC
* *
1641570 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1641608 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
1641649 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1641682 AGAAT
1 AGAAT
1641687 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:1641656 original size:14 final size:14
Alignment explanation
Indices: 1641637--1641693 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1641627 GAGAAATGAA
1641637 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1641651 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1641670 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1641684 AATCGCAACG
1 AATCGCAACG
1641694 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1641669 original size:33 final size:33
Alignment explanation
Indices: 1641629--1641709 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
1641619 CGCAACGAGA
1641629 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1641662 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
1641695 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
1641710 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1641727 original size:19 final size:19
Alignment explanation
Indices: 1641705--1641802 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
1641695 GAAACCAAAA
*
1641705 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1641724 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1641738 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1641757 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
**
1641771 TCTAGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1641790 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1641803 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
16 6 0.10
17 6 0.10
19 31 0.50
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1641746 original size:14 final size:14
Alignment explanation
Indices: 1641727--1641816 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
1641717 TTTCATTTCG
1641727 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1641741 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1641760 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
1641774 AGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1641793 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1641807 CGTTGCGATT
1 CGTTGCGATT
1641817 TTCATTTCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 29 0.48
16 6 0.10
17 6 0.10
19 19 0.32
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1641752 original size:33 final size:33
Alignment explanation
Indices: 1641710--1641824 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
1641700 CAAAATCGCA
1641710 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1641743 TTGCGATTTTCATTTCGCGTTGCGATTCTCTAG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1641776 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1641809 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1641825 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1643682 original size:93 final size:93
Alignment explanation
Indices: 1643523--1643990 Score: 904
Period size: 93 Copynumber: 5.1 Consensus size: 93
1643513 TAGATTGCTT
*
1643523 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1643588 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1643616 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1643681 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1643709 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1643774 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1643801 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1643866 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1643894 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
1643959 TTTGTCTTTGTTTTATCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1643986 AGTAA
1 AGTAA
1643991 TGCAATCCAT
Statistics
Matches: 372, Mismatches: 2, Indels: 3
0.99 0.01 0.01
Matches are distributed among these distances:
92 98 0.26
93 274 0.74
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1643839 original size:185 final size:186
Alignment explanation
Indices: 1643523--1643990 Score: 904
Period size: 185 Copynumber: 2.5 Consensus size: 186
1643513 TAGATTGCTT
*
1643523 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1643588 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1643653 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1643709 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1643774 -TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1643838 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1643894 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
1643959 TTTGTCTTTGTTTTATCTTTTGGTTG-AAGTAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAA
1643991 TGCAATCCAT
Statistics
Matches: 279, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
185 191 0.68
186 88 0.32
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1644078 original size:19 final size:19
Alignment explanation
Indices: 1644038--1644166 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1644028 TAGTTTACTT
* *
1644038 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1644058 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1644077 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1644096 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1644110 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1644129 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
*
1644143 TCGCAACGCGAAAACAAAA
1 TCGCAACGCGAAACCAAAA
1644162 TCGCA
1 TCGCA
1644167 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1644117 original size:33 final size:32
Alignment explanation
Indices: 1644074--1644166 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
1644064 CGCGAAACCA
**
1644074 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAAACAAAATCGCAACGAC
*
1644106 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAAACAAAATCGCAACGAC
1644139 AAGATCGCAACGCGAAAACAAAATCGCA
1 AA-ATCGCAACGCGAAAACAAAATCGCA
1644167 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.04
33 54 0.96
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAAACAAAATCGCAACGAC
Found at i:1644184 original size:19 final size:19
Alignment explanation
Indices: 1644162--1644473 Score: 323
Period size: 19 Copynumber: 17.7 Consensus size: 19
1644152 GAAAACAAAA
1644162 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1644181 TCGCGTTGCGA--TTC-TT
1 TCGCATTGCGATTTTCATT
1644197 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1644214 TCGCATTGCGA--TTC-TG
1 TCGCATTGCGATTTTCATT
1644230 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* **
1644247 TCGCGTTGCGATTTTGGTT
1 TCGCATTGCGATTTTCATT
* **
1644266 TCGCGTTGCGATTTTGGTT
1 TCGCATTGCGATTTTCATT
* *
1644285 TCGCGTTGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
1644304 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1644320 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1644337 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1644356 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1644372 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1644389 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1644408 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1644427 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
1644445 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
1644461 TCGCATTGCGATT
1 TCGCATTGCGATT
1644474 CTCTCGTTGC
Statistics
Matches: 252, Mismatches: 15, Indels: 52
0.79 0.05 0.16
Matches are distributed among these distances:
14 35 0.14
16 31 0.12
17 29 0.12
18 1 0.00
19 140 0.56
20 16 0.06
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1644203 original size:14 final size:14
Alignment explanation
Indices: 1644184--1644240 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1644174 TTTCATTTCG
1644184 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1644198 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1644215 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1644231 CGTTGCGATT
1 CGTTGCGATT
1644241 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1644209 original size:33 final size:33
Alignment explanation
Indices: 1644167--1644487 Score: 278
Period size: 33 Copynumber: 9.2 Consensus size: 33
1644157 CAAAATCGCA
*
1644167 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
*
1644200 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
* *
1644233 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCGCG
1 TTGCGATTTTCATTTCGCATTGCGA--TT-CTTT--CG
** * *
1644271 TTGCGATTTTGGTTTCGCGTTGCGATTTTAATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG
*
1644307 CATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG
*
1644340 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1644375 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG
1644411 CATTGCGATTTTCATTTCCGCATTGCGA-T-TTTCATG
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTTTC--G
* *
1644447 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1644480 TTGCGATT
1 TTGCGATT
1644488 GTAATTTCCG
Statistics
Matches: 247, Mismatches: 18, Indels: 46
0.79 0.06 0.15
Matches are distributed among these distances:
33 121 0.49
34 19 0.08
35 19 0.08
36 19 0.08
38 59 0.24
39 10 0.04
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
Found at i:1644254 original size:52 final size:50
Alignment explanation
Indices: 1644200--1644473 Score: 195
Period size: 52 Copynumber: 5.2 Consensus size: 50
1644190 GATTCTTTCG
*
1644200 TTGCGATTTTCATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCG
1 TTGCGATTTTC-TTTCGC-TTGCGATTCTGTCGTTGCGATTTTCATTTCGCA
* * *
1644252 TTGCGATTTTGGTTTCGCGTTGCGATTTTGGTTTCGCGTTGCGATTTTAATTTCGCA
1 TTGCGATTTT-CTTTCGC-TTGCGATTCT-G--T--CGTTGCGATTTTCATTTCGCA
* *
1644309 TTGCGA--TTCTCTCG-TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCTTTCGCTTGCGA--TTC-TGTCG--TTGCGATTTTCATTTCGCA
* *
1644361 TTGCGA--TTCTCTCG-TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCTTTCGCTTGCGA--TTC-TGTCG--TTGCGATTTTCATTTCGCA
*
1644413 TTGCGATTTTCATTTCCGCATTGCGATT-T-TCATGTTGGGATTTTCATTTCGCA
1 TTGCGATTTTC-TTT-CGC-TTGCGATTCTGTC--GTTGCGATTTTCATTTCGCA
1644466 TTGCGATT
1 TTGCGATT
1644474 CTCTCGTTGC
Statistics
Matches: 191, Mismatches: 12, Indels: 37
0.80 0.05 0.15
Matches are distributed among these distances:
50 2 0.01
52 108 0.57
53 29 0.15
54 10 0.05
55 7 0.04
56 4 0.02
57 25 0.13
58 6 0.03
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (50 bp):
TTGCGATTTTCTTTCGCTTGCGATTCTGTCGTTGCGATTTTCATTTCGCA
Found at i:1646948 original size:24 final size:24
Alignment explanation
Indices: 1646914--1646960 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1646904 CTGAAACATC
1646914 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1646938 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1646961 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1647671 original size:20 final size:20
Alignment explanation
Indices: 1647643--1647952 Score: 343
Period size: 20 Copynumber: 15.5 Consensus size: 20
1647633 AAATTTCAGT
* *
1647643 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
1647663 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
1647683 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
1647703 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
1647723 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
1647743 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
1647763 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
1647783 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* * *
1647803 GTTGCGATTTACAGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
1647823 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
1647843 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
1647863 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
1647883 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* *
1647903 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
1647923 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
1647943 GTTGCGATTT
1 GTTGCGATTT
1647953 TGGAAAATCG
Statistics
Matches: 254, Mismatches: 34, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
20 253 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:1647703 original size:40 final size:40
Alignment explanation
Indices: 1647643--1647952 Score: 394
Period size: 40 Copynumber: 7.8 Consensus size: 40
1647633 AAATTTCAGT
* *
1647643 GTTGTGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
*
1647683 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
*
1647723 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
*
1647763 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
* *
1647803 GTTGCGATTTACAGATACGCGTTGCGATATACGGA-TA-C
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
* * * *
1647841 GCATTGCGATTTACGGATACGCGTTGCGATATACGGA-TACAC
1 G--TTGCGATTTACAGATTCGCGTTGCGATTTACGGATTA-TC
* * * **
1647883 GTTGCGATTTACGGATACGCGTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACG-GATTATC
* *
1647923 GTTGCGATTTTCATATTCGCGTTGCGATTT
1 GTTGCGATTTACAGATTCGCGTTGCGATTT
1647953 TGGAAAATCG
Statistics
Matches: 251, Mismatches: 13, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
38 2 0.01
39 2 0.01
40 243 0.97
41 2 0.01
42 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (40 bp):
GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
Found at i:1647969 original size:21 final size:21
Alignment explanation
Indices: 1647939--1648021 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1647929 ATTTTCATAT
*
1647939 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1647960 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1647981 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1648002 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1648022 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1648012 original size:42 final size:43
Alignment explanation
Indices: 1647919--1648017 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1647909 ATTTATGTGT
* *
1647919 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1647960 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1648002 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1648018 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1653392 original size:21 final size:20
Alignment explanation
Indices: 1653366--1653422 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
1653356 ACTAAAATAT
1653366 AAGGGATCGATCCTTTAGTCA
1 AAGGGATCGATCCTTTAG-CA
* * *
1653387 AAGGGATCAAT-CTTTTGCT
1 AAGGGATCGATCCTTTAGCA
*
1653406 AAGGGATCGATCATTTA
1 AAGGGATCGATCCTTTA
1653423 AGCCAAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 11 0.38
20 8 0.28
21 10 0.34
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (20 bp):
AAGGGATCGATCCTTTAGCA
Found at i:1670514 original size:90 final size:90
Alignment explanation
Indices: 1670407--1670584 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 90
1670397 TAATCTCGAA
* * * * *
1670407 TATTTAATTTCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAATATCCCTAATATGAT
1 TATTAAATTCCAATTAATGAAATATAAATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
*
1670472 TAGTGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
*
1670497 TATTAAATTCCAATTAATGAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
1 TATTAAATTCCAATTAATGAAATATAAATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
*
1670562 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
1670585 GTGTGTTAGA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.38
Consensus pattern (90 bp):
TATTAAATTCCAATTAATGAAATATAAATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
TAGGGTAACTTGGATATAAAAGGAT
Found at i:1677794 original size:3 final size:3
Alignment explanation
Indices: 1677786--1677827 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1677776 TATATGACTA
1677786 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1677828 TAAATATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1679596 original size:123 final size:123
Alignment explanation
Indices: 1679461--1680360 Score: 930
Period size: 123 Copynumber: 7.6 Consensus size: 123
1679451 GAATTGAACT
* *
1679461 AAGGTTGAACAAGTTCTTCTCATTTTGAACTTCTTCTTCTTCTTCAAATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
* *
1679526 GAACTCCT-TCTGGAAATGCTGATATTGATCTATCTCCTTCTGCGATAGAGTCGAGCAA
66 GAACT-CTATCTGGAAATGTTGATATTGATCTATCTCCTTCTGTGATAGAGTCGAGCAA
* * *
1679584 AAGGTTGAACAAGTTCTTCTCATTGTGAACTTTTTCTTCTTCTTCAAATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
* ** *
1679649 GAACTCCT-TCTGGAAATGTTGATACTGATCTATCTCCTTCTACGATATAGTCGAGCAA
66 GAACT-CTATCTGGAAATGTTGATATTGATCTATCTCCTTCTGTGATAGAGTCGAGCAA
* *
1679707 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
* *
1679772 GAACACT-TCTGGAAATGTTAATGA-TGATCTATCTCCTTCTGTGATAGAGTC-ATGCAA
66 GAACTCTATCTGGAAATGTTGAT-ATTGATCTATCTCCTTCTGTGATAGAGTCGA-GCAA
* * * * *
1679829 AAGGTTGAACAAGCTATTCTCATTATAAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
* * * ** *
1679894 GAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTATGATAGAGTC-ATGCAA
66 GAACTCTATCTGGAAATGTTGATATTGATCTATCTCCTTCTGTGATAGAGTCGA-GCAA
* *
1679952 AAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
* * * ** * *
1680017 GAACTTTCTCTGG-AA-----ATATTGATCCA--T-C--GAGTGAT-GAATTCAAGCAA
66 GAACTCTATCTGGAAATGTTGATATTGATCTATCTCCTTCTGTGATAG-AGTCGAGCAA
* * *
1680064 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAATTATTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTA
* * * * ** *
1680129 TGAACTCTACCTGGCAA---TG---CTGATCCA--T-C--GAGTGAT-GAATTCGAGCAA
65 TGAACTCTATCTGGAAATGTTGATATTGATCTATCTCCTTCTGTGATAG-AGTCGAGCAA
1680177 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTA
* * * ** *
1680242 TGAACTCTACCTGGCAA---TG---TTGATCCA--T-C--GAGTGAT-GAATTCGAGCAA
65 TGAACTCTATCTGGAAATGTTGATATTGATCTATCTCCTTCTGTGATAG-AGTCGAGCAA
* *
1680290 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATAAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTA
1680355 TGAACT
65 TGAACT
1680361 ATTTTTGGAA
Statistics
Matches: 714, Mismatches: 53, Indels: 30
0.90 0.07 0.04
Matches are distributed among these distances:
111 1 0.00
112 47 0.07
113 240 0.34
114 3 0.00
115 1 0.00
117 8 0.01
121 1 0.00
122 111 0.16
123 302 0.42
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (123 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
GAACTCTATCTGGAAATGTTGATATTGATCTATCTCCTTCTGTGATAGAGTCGAGCAA
Found at i:1679892 original size:245 final size:236
Alignment explanation
Indices: 1679461--1680360 Score: 1000
Period size: 245 Copynumber: 3.8 Consensus size: 236
1679451 GAATTGAACT
* * *
1679461 AAGGTTGAACAAGTTCTTCTCATTTTGAACTTCTTCTTCTTCTTCAAATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * *
1679526 GAACTCCT-TCTGGAAATGCTGATATTGATCTATCTCCTTCTGCGAT-AGAGTCGAGCAAAAGGT
66 GAACT-CTATCTGGAAA---TG-TATTGATCCA--T-C--CAGTGATGA-AGTCGAGCAAAAGGT
* * * *
1679589 TGAACAAGTTCTTCTCATTGTGAACTTTTTCTT-CTTCTTCAAATGAGTTCTTCTCATTATGAAC
120 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAAC
*
1679653 TCCT-TCTGGAAATGTTGATACTGATCTATCTCCTTCTACGATATAGTCGAGCAA
185 T-CTATCTGGAAA-GTTGAT-CTGATCTATCTCCTTCTATGATATAGTCGAGCAA
*
1679707 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * *
1679772 GAACACT-TCTGGAAATGTTAATGATGATCTATCTCCTTCTGTGAT-AGAGTC-ATGCAAAAGGT
66 GAACTCTATCTGGAAATG-T-AT--TGATCCA--T-C--CAGTGATGA-AGTCGA-GCAAAAGGT
* * *
1679834 TGAACAAGCTATTCTCATTATAAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAAC
120 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAAC
* * *
1679898 TTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTATGATAGAGTC-ATGCAA
185 TCTATCTGG-AAAGTTGAT-CTGATCTATCTCCTTCTATGATATAGTCGA-GCAA
*
1679952 AAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * * *
1680017 GAACTTTCTCTGGAAA--TATTGATCCATCGAGTGATGAATTCAAGCAAAAGGTTGAACAAGTTC
66 GAACTCTATCTGGAAATGTATTGATCCATCCAGTGATGAAGTCGAGCAAAAGGTTGAACAAGTTC
* * * *
1680080 TTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAA-TTATTCTCATTATGAACTCTACCTGGC
131 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-AAGTTCTTCTCATTATGAACTCTATCTGGA
* *** *
1680144 AA--TG--CTGATCCATC-GAGT-GATGA-AT--TCGAGCAA
195 AAGTTGATCTGATCTATCTCCTTCTATGATATAGTCGAGCAA
1680177 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTA
* * * *
1680242 TGAACTCTACCTGGCAATG--TTGATCCATCGAGTGATGAATTCGAGCAAAAGGTTGAACAAGTT
65 TGAACTCTATCTGGAAATGTATTGATCCATCCAGTGATGAAGTCGAGCAAAAGGTTGAACAAGTT
*
1680305 CTTCTCATTATGAACTTCTTATTCCTTCTTCAGATAAGTTCTTCTCATTATGAACT
130 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACT
1680361 ATTTTTGGAA
Statistics
Matches: 587, Mismatches: 49, Indels: 56
0.85 0.07 0.08
Matches are distributed among these distances:
225 47 0.08
226 132 0.22
227 1 0.00
228 4 0.01
229 1 0.00
230 9 0.02
233 2 0.00
235 50 0.09
236 33 0.06
237 3 0.01
238 1 0.00
240 6 0.01
242 5 0.01
243 3 0.01
244 3 0.01
245 210 0.36
246 77 0.13
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (236 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
GAACTCTATCTGGAAATGTATTGATCCATCCAGTGATGAAGTCGAGCAAAAGGTTGAACAAGTTC
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTATCTGGAA
AGTTGATCTGATCTATCTCCTTCTATGATATAGTCGAGCAA
Done.