Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008425.1 Hibiscus syriacus cultivar Beakdansim tig00111208_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: 2340112
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 12
Found at i:1607573 original size:23 final size:23
Alignment explanation
Indices: 1607547--1607600 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
1607537 GAGATTTGTT
1607547 TCCATTGAAACACAAATTTTATC
1 TCCATTGAAACACAAATTTTATC
* *
1607570 TCCATTGAAACACATATTTTGTC
1 TCCATTGAAACACAAATTTTATC
1607593 TCCATTGA
1 TCCATTGA
1607601 GACCAGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (23 bp):
TCCATTGAAACACAAATTTTATC
Found at i:1608437 original size:54 final size:54
Alignment explanation
Indices: 1608364--1608579 Score: 236
Period size: 54 Copynumber: 4.0 Consensus size: 54
1608354 TCAAAAAAGT
* ** * * * *
1608364 AAATTTTCAAGACCGAGTAAGCTTTAGCGTTCCTTTATTACGTAGGAGTAGAGC
1 AAATTTCCAAGACTAAGTAAGCTCTAGCGTTCCTTTGTTATGGAGGAGTAGAGC
* * *
1608418 AAATTTCCAAGGCTAAGTAAACTCTAGCATTCCTTTGTTATGGAGGAGTAGAGC
1 AAATTTCCAAGACTAAGTAAGCTCTAGCGTTCCTTTGTTATGGAGGAGTAGAGC
* * * * *
1608472 AAATTCCCAAGACTGAA-TAAGTTCTAGTGTTCCTTTGTCATGGAGAAGTAGAGC
1 AAATTTCCAAGACT-AAGTAAGCTCTAGCGTTCCTTTGTTATGGAGGAGTAGAGC
* ** **
1608526 AAATTTTCAAGACCGAGCGAGCTCTAGCGTTCCTTTGTTATGGAGGAGTAGAGC
1 AAATTTCCAAGACTAAGTAAGCTCTAGCGTTCCTTTGTTATGGAGGAGTAGAGC
1608580 GGGTTATTCA
Statistics
Matches: 132, Mismatches: 28, Indels: 4
0.80 0.17 0.02
Matches are distributed among these distances:
53 1 0.01
54 129 0.98
55 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (54 bp):
AAATTTCCAAGACTAAGTAAGCTCTAGCGTTCCTTTGTTATGGAGGAGTAGAGC
Found at i:1610516 original size:51 final size:50
Alignment explanation
Indices: 1610408--1610504 Score: 113
Period size: 51 Copynumber: 1.9 Consensus size: 50
1610398 CTTAGCAGTA
* * * *
1610408 AAGCGCGCCCCCTGAACTGCGCTATATATTGATTTGGAGCCACGTGGGAT
1 AAGCGCGCCCCCTGAACCGCGCTATATACTGATTGGGAGACACGTGGGAT
* * *
1610458 AAGGCGCGCCCCCTGCACCGCGCTATATGCTGATATGGGATACACGT
1 AA-GCGCGCCCCCTGAACCGCGCTATATACTGAT-TGGGAGACACGT
1610505 AGGTATAGCG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
50 2 0.05
51 27 0.71
52 9 0.24
ACGTcount: A:0.22, C:0.29, G:0.28, T:0.22
Consensus pattern (50 bp):
AAGCGCGCCCCCTGAACCGCGCTATATACTGATTGGGAGACACGTGGGAT
Found at i:1610716 original size:20 final size:19
Alignment explanation
Indices: 1610671--1610718 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
1610661 CATCACACCA
* *
1610671 AATTCTCTCAATTTCTCTT
1 AATTCTCTCAAATACTCTT
1610690 AATTTCTCTCAAATACTCTT
1 AA-TTCTCTCAAATACTCTT
1610710 ATATTCTCT
1 A-ATTCTCT
1610719 GTTTAAGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 22 0.88
21 1 0.04
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (19 bp):
AATTCTCTCAAATACTCTT
Found at i:1610769 original size:23 final size:22
Alignment explanation
Indices: 1610743--1610787 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1610733 TTATTATATT
1610743 TTTAA-TATTTTATATTTAATTTA
1 TTTAAGTATTTTA-ATTT-ATTTA
1610766 TTTAAGTATTTTAATTTATTTA
1 TTTAAGTATTTTAATTTATTTA
1610788 ATATTTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.24
23 9 0.43
24 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTAAGTATTTTAATTTATTTA
Found at i:1610792 original size:17 final size:17
Alignment explanation
Indices: 1610748--1610795 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
1610738 ATATTTTTAA
*
1610748 TATTTTATA-TTTAATT
1 TATTTAATATTTTAATT
1610764 TATTTAAGTATTTTAATT
1 TATTTAA-TATTTTAATT
1610782 TATTTAATATTTTA
1 TATTTAATATTTTA
1610796 CTTATATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 6 0.21
17 9 0.31
18 14 0.48
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TATTTAATATTTTAATT
Found at i:1613161 original size:35 final size:35
Alignment explanation
Indices: 1613122--1613199 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 35
1613112 GTATTTCAGT
1613122 TAATTTTGTT-T-A-TTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATAATTTACCATTTAATA-C--TTATTG
*
1613157 TAATTTGGTTATAATTTACCATTTAATACTTATTG
1 TAATTTTGTTATAATTTACCATTTAATACTTATTG
1613192 TAAGTTTT
1 TAA-TTTT
1613200 TCGTATTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
35 18 0.49
36 4 0.11
37 2 0.05
38 13 0.35
ACGTcount: A:0.29, C:0.08, G:0.09, T:0.54
Consensus pattern (35 bp):
TAATTTTGTTATAATTTACCATTTAATACTTATTG
Found at i:1618043 original size:31 final size:32
Alignment explanation
Indices: 1618005--1618127 Score: 132
Period size: 31 Copynumber: 3.9 Consensus size: 32
1617995 GTCGAGGGTA
1618005 TACCTATGTT-TACGGAACATATGGACA-TAAT
1 TACCTATGTTCTACGGAACATATGGACAGT-AT
*
1618036 TACCTATG-TCTTTC-GAGACATATGGACAGTA-
1 TACCTATGTTC-TACGGA-ACATATGGACAGTAT
*
1618067 TACCTATGTTCTAAGGAACATATGGACAGT-T
1 TACCTATGTTCTACGGAACATATGGACAGTAT
* * *
1618098 TACCTAGGTTCTTCGGAACCTATGGACAGT
1 TACCTATGTTCTACGGAACATATGGACAGT
1618128 TACCGAGGAT
Statistics
Matches: 78, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
30 1 0.01
31 58 0.74
32 18 0.23
33 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Consensus pattern (32 bp):
TACCTATGTTCTACGGAACATATGGACAGTAT
Found at i:1618122 original size:62 final size:61
Alignment explanation
Indices: 1618002--1618131 Score: 160
Period size: 62 Copynumber: 2.1 Consensus size: 61
1617992 AGAGTCGAGG
* *
1618002 GTATACCTATGTTTACGGAACATATGGACATAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTTAAGGAACATATGGACAT-ATTACCTAGGTCTTTCGAGACATATGGACA
*
1618064 GTATACCTATGTTCTAAGGAACATATGGACAGT-TTACCTAGGT-TCTTCG-GAACCTATGGACA
1 GTATACCTATGTT-TAAGGAACATATGGACA-TATTACCTAGGTCT-TTCGAG-ACATATGGACA
1618126 GT-TACC
1 GTATACC
1618132 GAGGATCTTT
Statistics
Matches: 61, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
61 6 0.10
62 38 0.62
63 16 0.26
64 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (61 bp):
GTATACCTATGTTTAAGGAACATATGGACATATTACCTAGGTCTTTCGAGACATATGGACA
Found at i:1618159 original size:30 final size:30
Alignment explanation
Indices: 1618115--1618186 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
1618105 GTTCTTCGGA
* * *
1618115 ACCTATGGACAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTAACGAGGATCTTTATG
1618145 ACCTCTGGATAGTTAACGAGGATCTTTATG
1 ACCTCTGGATAGTTAACGAGGATCTTTATG
1618175 ACCTCTGGATAG
1 ACCTCTGGATAG
1618187 GTCATTCGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTAACGAGGATCTTTATG
Found at i:1619650 original size:51 final size:49
Alignment explanation
Indices: 1619533--1619659 Score: 139
Period size: 49 Copynumber: 2.6 Consensus size: 49
1619523 ATAATTATAC
** *
1619533 AAGGCGCGGTACCTGCACCGCGCCT-TATATAATTATATCAATTAAAGGT
1 AAGGCGCGGCCCCTGCCCCGCG-CTATATATAATTATATCAATTAAAGGT
* * * *
1619582 ATGGCTCGGCCCCTGCCCCGCGCTATATATAATTATGTCAGAGTTAAATGT
1 AAGGCGCGGCCCCTGCCCCGCGCTATATATAATTATATCA-A-TTAAAGGT
* *
1619633 AAGGCGCGGCCTCTGCCCCACGCTATA
1 AAGGCGCGGCCCCTGCCCCGCGCTATA
1619660 CCCCTACGTG
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
48 2 0.03
49 31 0.48
50 1 0.02
51 30 0.47
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (49 bp):
AAGGCGCGGCCCCTGCCCCGCGCTATATATAATTATATCAATTAAAGGT
Found at i:1623069 original size:20 final size:20
Alignment explanation
Indices: 1623044--1623084 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1623034 TTTCATCACA
1623044 TCAAATCCTCTCAAATTCTC
1 TCAAATCCTCTCAAATTCTC
* * *
1623064 TCAAATGCTCTTATATTCTC
1 TCAAATCCTCTCAAATTCTC
1623084 T
1 T
1623085 TATATCTGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.27, C:0.29, G:0.02, T:0.41
Consensus pattern (20 bp):
TCAAATCCTCTCAAATTCTC
Found at i:1623154 original size:24 final size:23
Alignment explanation
Indices: 1623103--1623170 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 23
1623093 TTTAAGGTAT
*
1623103 ATTTTATTATATTTAATATTTTA
1 ATTTTATTATATTTAATATTTAA
*
1623126 TTTTTAATT-TATTTAAGTATTTAA
1 ATTTT-ATTATATTTAA-TATTTAA
1623150 ATTTT-TTAATATTT--TATTTAA
1 ATTTTATT-ATATTTAATATTTAA
1623171 TTAATTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
21 7 0.18
22 2 0.05
23 11 0.29
24 18 0.47
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (23 bp):
ATTTTATTATATTTAATATTTAA
Found at i:1623164 original size:8 final size:8
Alignment explanation
Indices: 1623101--1623165 Score: 53
Period size: 8 Copynumber: 8.0 Consensus size: 8
1623091 TGTTTAAGGT
1623101 ATATTTTA
1 ATATTTTA
*
1623109 TTATATTTA
1 ATAT-TTTA
1623118 ATATTTT-
1 ATATTTTA
1623125 AT-TTTTA
1 ATATTTTA
*
1623132 ATTTATTTA
1 ATAT-TTTA
*
1623141 AGTATTTAA
1 A-TATTTTA
*
1623150 ATTTTTTA
1 ATATTTTA
1623158 ATATTTTA
1 ATATTTTA
1623166 TTTAATTAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
6 4 0.09
7 4 0.09
8 19 0.42
9 16 0.36
10 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (8 bp):
ATATTTTA
Found at i:1623165 original size:17 final size:19
Alignment explanation
Indices: 1623124--1623165 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
1623114 TTTAATATTT
*
1623124 TATTTTTAATTTATTTAAG
1 TATTTTAAATTTATTTAAG
1623143 TA-TTTAAATTT-TTTAA-
1 TATTTTAAATTTATTTAAG
1623159 TATTTTA
1 TATTTTA
1623166 TTTAATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.10
17 9 0.43
18 8 0.38
19 2 0.10
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TATTTTAAATTTATTTAAG
Found at i:1624225 original size:193 final size:193
Alignment explanation
Indices: 1623884--1624266 Score: 667
Period size: 193 Copynumber: 2.0 Consensus size: 193
1623874 GTCAGTTTTT
* *
1623884 ACTTTCCTATACAGGGAGATGTGTCGAGCCACTAACTACATGAAAAATACTATCGGCGGATGTCT
1 ACTTTCCTATACAGGGAGATGTGTCGAGCCACTAACTACAGGAAAAATACTATCGACGGATGTCT
* * *
1623949 CCTGCTGCTGTAGTCTTGGGCATGGTATCGATTGCTCTTTTTATGACCCGTTGTCAAGAACTCAT
66 CCTGCTGATGCAGTCTTAGGCATGGTATCGATTGCTCTTTTTATGACCCGTTGTCAAGAACTCAT
1624014 TCGTATTTCCGCTACTATTGAGGTAATTATAAAACTGATTTCGTATATTAATCATTTTATAAA
131 TCGTATTTCCGCTACTATTGAGGTAATTATAAAACTGATTTCGTATATTAATCATTTTATAAA
* * * *
1624077 ACTTTCTTATATAGGGAGATGTGTCGAGCCACTGACTACAGGAAAAATGCTATCGACGGATGTCT
1 ACTTTCCTATACAGGGAGATGTGTCGAGCCACTAACTACAGGAAAAATACTATCGACGGATGTCT
* *
1624142 CCTGCTGATGCAGTCTTAGGCATGGTATCGATTGTTCTTTTTATGTCCCGTTGTCAAGAACTCAT
66 CCTGCTGATGCAGTCTTAGGCATGGTATCGATTGCTCTTTTTATGACCCGTTGTCAAGAACTCAT
1624207 TCGTATTTCCGCTACTATTGAGGTAATTATAAAACTGATTTCGTATATTAATCATTTTAT
131 TCGTATTTCCGCTACTATTGAGGTAATTATAAAACTGATTTCGTATATTAATCATTTTAT
1624267 GCAGTGTATA
Statistics
Matches: 179, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
193 179 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (193 bp):
ACTTTCCTATACAGGGAGATGTGTCGAGCCACTAACTACAGGAAAAATACTATCGACGGATGTCT
CCTGCTGATGCAGTCTTAGGCATGGTATCGATTGCTCTTTTTATGACCCGTTGTCAAGAACTCAT
TCGTATTTCCGCTACTATTGAGGTAATTATAAAACTGATTTCGTATATTAATCATTTTATAAA
Found at i:1627760 original size:32 final size:32
Alignment explanation
Indices: 1627699--1627760 Score: 74
Period size: 32 Copynumber: 1.9 Consensus size: 32
1627689 TTAAATATAT
*
1627699 TAAACATATAAAAAATATCTAATCTTAATTAA
1 TAAACATATAAAAAATATCTAATCATAATTAA
*
1627731 TAAACATTAATAATAAATAT-TAA-CATAATT
1 TAAACA-T-ATAAAAAATATCTAATCATAATT
1627761 TAATTTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
32 12 0.46
33 4 0.15
34 10 0.38
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.35
Consensus pattern (32 bp):
TAAACATATAAAAAATATCTAATCATAATTAA
Found at i:1628357 original size:15 final size:15
Alignment explanation
Indices: 1628339--1628372 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1628329 AATTTTGAGT
1628339 TATTTGAAAATTTTA
1 TATTTGAAAATTTTA
*
1628354 TATTTTAAAATTTTA
1 TATTTGAAAATTTTA
1628369 -ATTT
1 TATTT
1628373 TATATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
TATTTGAAAATTTTA
Found at i:1629142 original size:17 final size:16
Alignment explanation
Indices: 1629120--1629158 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1629110 ATTCTTAATA
1629120 TTTAATTGAATAATTAT
1 TTTAATT-AATAATTAT
* *
1629137 TTTAATTTATAATTTT
1 TTTAATTAATAATTAT
1629153 TTTAAT
1 TTTAAT
1629159 ATTTAACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TTTAATTAATAATTAT
Found at i:1633699 original size:21 final size:21
Alignment explanation
Indices: 1633671--1633720 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1633661 TTCGTCGGAC
*
1633671 ATTTATTTATATTTTGTATTT
1 ATTTATTTATAATTTGTATTT
*
1633692 -TTATATTTGTAATTTGTATTT
1 ATT-TATTTATAATTTGTATTT
1633713 ATTTATTT
1 ATTTATTT
1633721 CATCACTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 2 0.08
21 21 0.84
22 2 0.08
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (21 bp):
ATTTATTTATAATTTGTATTT
Found at i:1647934 original size:6 final size:5
Alignment explanation
Indices: 1647900--1647930 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
1647890 TCTAGTCTCA
1647900 GGTCG GGTCG GGTCG GGTCG GGTCG TGGTCG
1 GGTCG GGTCG GGTCG GGTCG GGTCG -GGTCG
1647931 TGGTAATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
GGTCG
Found at i:1648043 original size:19 final size:19
Alignment explanation
Indices: 1648019--1648085 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
1648009 TCGTTGCGAT
1648019 TTTGGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
*
1648038 TTTGGAATAAATCGCAACGCGAA
1 TTTGGACT--ATCGCAA--CGAA
* * * *
1648061 CTTCGACTATCACACCGAA
1 TTTGGACTATCGCAACGAA
1648080 TTTGGA
1 TTTGGA
1648086 ATAAATCGCA
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
19 15 0.42
21 12 0.33
23 9 0.25
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (19 bp):
TTTGGACTATCGCAACGAA
Found at i:1648113 original size:23 final size:23
Alignment explanation
Indices: 1648027--1648181 Score: 178
Period size: 23 Copynumber: 6.8 Consensus size: 23
1648017 ATTTTGGACT
*
1648027 ATCGCAA--CGAATTTGGAATAA
1 ATCGCAACGCGAACTTGGAATAA
* *
1648048 ATCGCAACGCGAACTTCGACT--
1 ATCGCAACGCGAACTTGGAATAA
* *
1648069 ATCAC-AC-CGAATTTGGAATAA
1 ATCGCAACGCGAACTTGGAATAA
*
1648090 ATCGCAACGCGAACTTCGACTAAATAA
1 ATCGCAACGCGAACTT-G---GAATAA
1648117 ATCGCAACGCGAACTTGGAATAA
1 ATCGCAACGCGAACTTGGAATAA
1648140 ATCGCAACGCGAACTTGGAATAA
1 ATCGCAACGCGAACTTGGAATAA
1648163 ATCGCAACGCGAACTTGGA
1 ATCGCAACGCGAACTTGGA
1648182 CTATCGCAAT
Statistics
Matches: 113, Mismatches: 11, Indels: 18
0.80 0.08 0.13
Matches are distributed among these distances:
19 9 0.08
20 2 0.02
21 15 0.13
22 2 0.02
23 62 0.55
24 1 0.01
26 1 0.01
27 21 0.19
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.19
Consensus pattern (23 bp):
ATCGCAACGCGAACTTGGAATAA
Found at i:1648164 original size:50 final size:46
Alignment explanation
Indices: 1648027--1648181 Score: 187
Period size: 42 Copynumber: 3.4 Consensus size: 46
1648017 ATTTTGGACT
* *
1648027 ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTCGACT--
1 ATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTCGAATAA
* *
1648069 ATCAC-AC-CGAATTTGGAATAAATCGCAACGCGAACTTCGACTAAATAA
1 ATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTCG----AATAA
*
1648117 ATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTGGAATAA
1 ATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTCGAATAA
1648163 ATCGCAACGCGAACTTGGA
1 ATCGCAACGCGAACTTGGA
1648182 CTATCGCAAT
Statistics
Matches: 99, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
41 1 0.01
42 36 0.36
46 26 0.26
48 4 0.04
49 2 0.02
50 30 0.30
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.19
Consensus pattern (46 bp):
ATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTCGAATAA
Found at i:1648174 original size:73 final size:69
Alignment explanation
Indices: 1648043--1648184 Score: 203
Period size: 73 Copynumber: 2.0 Consensus size: 69
1648033 ACGAATTTGG
* *
1648043 AATAAATCGCAACGCGAACTTCGACTATCACACCGAATTTGGAATAAATCGCAACGCGAACTTCG
1 AATAAATCGCAACGCGAACTTCGAATATCACACCGAACTTGGAATAAATCGCAACGCGAACTTCG
1648108 ACTA
66 ACTA
* *
1648112 AATAAATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTGGAATAAATCGCAACGCGAAC
1 AATAAATCGCAACGCGAACTTCGAAT--ATCAC-AC-CGAACTTGGAATAAATCGCAACGCGAAC
*
1648177 TTGGACTA
62 TTCGACTA
1648185 TCGCAATGCG
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
69 24 0.38
71 4 0.06
72 2 0.03
73 34 0.53
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (69 bp):
AATAAATCGCAACGCGAACTTCGAATATCACACCGAACTTGGAATAAATCGCAACGCGAACTTCG
ACTA
Found at i:1652153 original size:292 final size:291
Alignment explanation
Indices: 1650984--1653028 Score: 3284
Period size: 292 Copynumber: 7.0 Consensus size: 291
1650974 TCGTCAGCCG
* * * *
1650984 CTTTTGCCCTATCGGTTGAACCAGCGTTTTCGACATTTTTAACCTC--T--ATCTCTCCAGCACG
1 CTTTTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTTCACCTCTTTCGATCTCTCCAGCATG
*
1651045 CTTCTTCTCCCTATTTTTATACCAGATTCTTTCGGGTCATTTTTAGGGATAAATCAACTTTTAAT
66 CTTATTCTCCCTATTTTTATACCAGATTCTTTCGGG-CATTTTTAGGGATAAATCAACTTTTAAT
* * *
1651110 CCCTAAAGTT-TACACTTTTTTAATTTATCTTTAAACTTAATTCGAATCTAGGGGTCAGCATTTT
130 CCCTAAAGTTAT-CACTTTTTTAATTTATCTTTAAACTTAATTCGAATTTAGGGGTGAGCATTCT
* * * * * *
1651174 AGATTAGGATCTAATCATATAAAATCATCGATGCAAGATTATTTATAAGGTTGTGATCTTAAAGA
194 AGATCAGGATCTAATCATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAGA
* *
1651239 TTACTTAGGATTGAAATATTTTAAGATATATTT
259 TTGCTTAGGATTGAAATCTTTTAAGATATATTT
* * * * * *
1651272 CTTTTGCCTTATCGGCTAAACCAACGTTTTCGACATTTTTCATCTCTCTCGATCTCTCCAACACG
1 CTTTTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTTCACCTCTTTCGATCTCTCCAGCATG
* * *
1651337 CTTCTTCTCCCTATTTTTATACTAGATTCTTTCGGGTCATTTTTAGGGATAAATTAACTTTTAAT
66 CTTATTCTCCCTATTTTTATACCAGATTCTTTCGGG-CATTTTTAGGGATAAATCAACTTTTAAT
** * *
1651402 CCCTAAAGTTATCACTTTTTTTAATTTATCTTTAAACTTAATTCGAATTTAGAAGTGAACTTTCT
130 CCCTAAAGTTATCAC-TTTTTTAATTTATCTTTAAACTTAATTCGAATTTAGGGGTGAGCATTCT
1651467 AGATCAGGATCTAATCATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAGA
194 AGATCAGGATCTAATCATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAGA
1651532 TTGCTTAGGATTGAAATCTTTTAAGATATATTT
259 TTGCTTAGGATTGAAATCTTTTAAGATATATTT
1651565 CTTTTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTTCACCTCTTTCGATCTCTCCAGCATG
1 CTTTTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTTCACCTCTTTCGATCTCTCCAGCATG
*
1651630 CTTATTCTCCCTATTTTTATACCAGATTCTTTCAGGTCA-TTTTAGGGATAAATCAACTTTTAAT
66 CTTATTCTCCCTATTTTTATACCAGATTCTTTC-GGGCATTTTTAGGGATAAATCAACTTTTAAT
* *
1651694 CCCTAAAGTTATCACTTTTTTAATTTATCTTTAAACTTAATTCAAATTTAGGGGTGAACATTCTA
130 CCCTAAAGTTATCACTTTTTTAATTTATCTTTAAACTTAATTCGAATTTAGGGGTGAGCATTCTA
*
1651759 GATCAGGATCTAATTATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAGAT
195 GATCAGGATCTAATCATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAGAT
1651824 TGCTTAGGATTGAAATCTTTTAAGATATATTT
260 TGCTTAGGATTGAAATCTTTTAAGATATATTT
1651856 CTTTTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTTCACCTCTTTCGATCTCTCCAGCATG
1 CTTTTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTTCACCTCTTTCGATCTCTCCAGCATG
1651921 CTTATTCTCCCTATTTTTATACCAGATTCTTTCAGGGCATTTTTAGGGATAAATCAACTTTTAAT
66 CTTATTCTCCCTATTTTTATACCAGATTCTTTC-GGGCATTTTTAGGGATAAATCAACTTTTAAT
*
1651986 CCCTAAAGTTATCACTTTTTTAATTTATCTTTAAACTTAATTCGAATCTAGGGGTGAGCATTCTA
130 CCCTAAAGTTATCACTTTTTTAATTTATCTTTAAACTTAATTCGAATTTAGGGGTGAGCATTCTA
* * *
1652051 GATCAGAATCTAATCATGTAAAATCATTGATGCAAGATTACTTAGAAGGTTGAGATCTTAAAGAT
195 GATCAGGATCTAATCATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAGAT
1652116 TGCTTAGGATTGAAATCTTTTAAGATATATTT
260 TGCTTAGGATTGAAATCTTTTAAGATATATTT
* * * * * *
1652148 CTTTTGCCTTATCGGCTAAACCAGCGTTTTCGACGTTTTTCACCTC--T--ATCCCTCCAACATG
1 CTTTTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTTCACCTCTTTCGATCTCTCCAGCATG
* *
1652209 CTTCTTCTCCCTATTTTTATACCAGATTCTTTCGGGTCATTTTTAGGGATAAATTAACTTTTAAT
66 CTTATTCTCCCTATTTTTATACCAGATTCTTTCGGG-CATTTTTAGGGATAAATCAACTTTTAAT
*
1652274 CCCTAAAGTTATCACTATTTTTAATTTACCTTTAAACTTAATTCGAATTTAGGGGTGAGCATTCT
130 CCCTAAAGTTATCACT-TTTTTAATTTATCTTTAAACTTAATTCGAATTTAGGGGTGAGCATTCT
*
1652339 AGATCAGGATCTAATTATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAGA
194 AGATCAGGATCTAATCATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAGA
1652404 TTGCTTAGGATTGAAATCTTTTAAGATATATTT
259 TTGCTTAGGATTGAAATCTTTTAAGATATATTT
* * * *
1652437 CTTTTGTCCTATCGGCTGAACCAACGTTTTCGACA-TTTTCACTTCTTTCTATCTCTCTAGCATG
1 CTTTTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTTCACCTCTTTCGATCTCTCCAGCATG
*
1652501 CTTATTCTCCCTATTTTTATACCAGATTATTTCGGGGCATTTTTAGGGATAAATCAACTTTTAAT
66 CTTATTCTCCCTATTTTTATACCAGATTCTTTC-GGGCATTTTTAGGGATAAATCAACTTTTAAT
* *
1652566 CCCTAAAGTTATCACTTTTTTTAATTTATCTTTAAACTTATTTCGAATTTAGGGGTGAGCAATCT
130 CCCTAAAGTTATCAC-TTTTTTAATTTATCTTTAAACTTAATTCGAATTTAGGGGTGAGCATTCT
1652631 AGATCAGGATCTAATCATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAGA
194 AGATCAGGATCTAATCATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAGA
*
1652696 TTGCTTAGGATTGAAATCTTTTAAGTTATATTT
259 TTGCTTAGGATTGAAATCTTTTAAGATATATTT
* * * * * *
1652729 CTTTTTCCCTATCGGCTGATCCAACGTTTTCAACATTTTTCACCTCTTTTGATCCCTCTAGCATG
1 CTTTTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTTCACCTCTTTCGATCTCTCCAGCATG
* *
1652794 ATTATTCTCCCTATTTTTATACCAGATTCTTTTGGGGCATTTTTAGGGATAAATCAACTTTTAAT
66 CTTATTCTCCCTATTTTTATACCAGATTC-TTTCGGGCATTTTTAGGGATAAATCAACTTTTAAT
** *
1652859 CCCTAAAGTTATCACTTTTTTTTAATTTATCTTTAAACTTAATTCGAATTTAGGGGTGAAAAATC
130 CCCTAAAGTTATCAC--TTTTTTAATTTATCTTTAAACTTAATTCGAATTTAGGGGTGAGCATTC
* *
1652924 TAGATGAGGATCTAATCATGTAAAATCATTGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAG
193 TAGATCAGGATCTAATCATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAG
1652989 ATTGCTTAGGATTGAAATCTTTTAAGATATATTT
258 ATTGCTTAGGATTGAAATCTTTTAAGATATATTT
1653023 CTTTTG
1 CTTTTG
1653029 AATATAAACT
Statistics
Matches: 1642, Mismatches: 96, Indels: 32
0.93 0.05 0.02
Matches are distributed among these distances:
287 3 0.00
288 136 0.08
289 170 0.10
290 3 0.00
291 245 0.15
292 606 0.37
293 327 0.20
294 152 0.09
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (291 bp):
CTTTTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTTCACCTCTTTCGATCTCTCCAGCATG
CTTATTCTCCCTATTTTTATACCAGATTCTTTCGGGCATTTTTAGGGATAAATCAACTTTTAATC
CCTAAAGTTATCACTTTTTTAATTTATCTTTAAACTTAATTCGAATTTAGGGGTGAGCATTCTAG
ATCAGGATCTAATCATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAGATT
GCTTAGGATTGAAATCTTTTAAGATATATTT
Found at i:1652422 original size:872 final size:874
Alignment explanation
Indices: 1650984--1653028 Score: 3451
Period size: 872 Copynumber: 2.3 Consensus size: 874
1650974 TCGTCAGCCG
* * * *
1650984 CTTTTGCCCTATCGGTTGAACCAGCGTTTTCGACATTTTTAACCTC--T-ATCTCTCCAGCACGC
1 CTTTTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTTCACCTCTTTGATCTCTCCAGCATGC
*
1651046 TTCTTCTCCCTATTTTTATACCAGATTCTTTCGGGTCATTTTTAGGGATAAATCAACTTTTAATC
66 TTATTCTCCCTATTTTTATACCAGATTCTTTCGGG-CATTTTTAGGGATAAATCAACTTTTAATC
* *
1651111 CCTAAAGTT-TACACTTTTTTAATTTATCTTTAAACTTAATTCGAATCTAGGGGTCAGCATTTTA
130 CCTAAAGTTAT-CACTTTTTTAATTTATCTTTAAACTTAATTCGAATCTAGGGGTGAGCATTCTA
* * * * * *
1651175 GATTAGGATCTAATCATATAAAATCATCGATGCAAGATTATTTATAAGGTTGTGATCTTAAAGAT
194 GATCAGGATCTAATCATGTAAAATCATTGATGCAAGATTACTTAGAAGGTTGAGATCTTAAAGAT
* *
1651240 TACTTAGGATTGAAATATTTTAAGATATATTTCTTTTGCCTTATCGGCTAAACCAACGTTTTCGA
259 TGCTTAGGATTGAAATCTTTTAAGATATATTTCTTTTGCCTTATCGGCTAAACCAACGTTTTCGA
* *
1651305 CATTTTTCATCTCTCTCGATCTCTCCAACACGCTTCTTCTCCCTATTTTTATACTAGATTCTTTC
324 CATTTTTCATCTCTCTC-ATCCCTCCAACACGCTTCTTCTCCCTATTTTTATACCAGATTCTTTC
* *
1651370 GGGTCATTTTTAGGGATAAATTAACTTTTAATCCCTAAAGTTATCACTTTTTTTAATTTATCTTT
388 GGGTCATTTTTAGGGATAAATTAACTTTTAATCCCTAAAGTTATCACTATTTTTAATTTACCTTT
*
1651435 AAACTTAATTCGAATTTAGAAGTGAACTTTCTAGATCAGGATCTAATCATGTAAAATCATCGATG
453 AAACTTAATTCGAATTTAGAAGTGAACATTCTAGATCAGGATCTAATCATGTAAAATCATCGATG
1651500 CAAGATTACTTAGAAGGTTGAGATCTTGAAGATTGCTTAGGATTGAAATCTTTTAAGATATATTT
518 CAAGATTACTTAGAAGGTTGAGATCTTGAAGATTGCTTAGGATTGAAATCTTTTAAGATATATTT
1651565 CTTTTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTTCACCTCTTTCGATCTCTCCAGCATG
583 CTTTTGCCCTATCGGCTGAACCAACGTTTTCGACA-TTTTCACCTCTTTCGATCTCTCCAGCATG
* *
1651630 CTTATTCTCCCTATTTTTATACCAGATTCTTTCAGGTCA-TTTTAGGGATAAATCAACTTTTAAT
647 CTTATTCTCCCTATTTTTATACCAGATTATTTCAGGGCATTTTTAGGGATAAATCAACTTTTAAT
*
1651694 CCCTAAAGTTATCAC-TTTTTTAATTTATCTTTAAACTTAATTCAAATTTAGGGGTGAACATTCT
712 CCCTAAAGTTATCACTTTTTTTAATTTATCTTTAAACTTAATTCAAATTTAGGGGTGAACAATCT
*
1651758 AGATCAGGATCTAATTATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAGA
777 AGATCAGGATCTAATCATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAGA
1651823 TTGCTTAGGATTGAAATCTTTTAAGATATATTT
842 TTGCTTAGGATTGAAATCTTTTAAGATATATTT
1651856 CTTTTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTTCACCTCTTTCGATCTCTCCAGCATG
1 CTTTTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTTCACCTCTTT-GATCTCTCCAGCATG
1651921 CTTATTCTCCCTATTTTTATACCAGATTCTTTCAGGGCATTTTTAGGGATAAATCAACTTTTAAT
65 CTTATTCTCCCTATTTTTATACCAGATTCTTTC-GGGCATTTTTAGGGATAAATCAACTTTTAAT
1651986 CCCTAAAGTTATCACTTTTTTAATTTATCTTTAAACTTAATTCGAATCTAGGGGTGAGCATTCTA
129 CCCTAAAGTTATCACTTTTTTAATTTATCTTTAAACTTAATTCGAATCTAGGGGTGAGCATTCTA
*
1652051 GATCAGAATCTAATCATGTAAAATCATTGATGCAAGATTACTTAGAAGGTTGAGATCTTAAAGAT
194 GATCAGGATCTAATCATGTAAAATCATTGATGCAAGATTACTTAGAAGGTTGAGATCTTAAAGAT
*
1652116 TGCTTAGGATTGAAATCTTTTAAGATATATTTCTTTTGCCTTATCGGCTAAACCAGCGTTTTCGA
259 TGCTTAGGATTGAAATCTTTTAAGATATATTTCTTTTGCCTTATCGGCTAAACCAACGTTTTCGA
* *
1652181 CGTTTTTCA-C-CTCT-ATCCCTCCAACATGCTTCTTCTCCCTATTTTTATACCAGATTCTTTCG
324 CATTTTTCATCTCTCTCATCCCTCCAACACGCTTCTTCTCCCTATTTTTATACCAGATTCTTTCG
1652243 GGTCATTTTTAGGGATAAATTAACTTTTAATCCCTAAAGTTATCACTATTTTTAATTTACCTTTA
389 GGTCATTTTTAGGGATAAATTAACTTTTAATCCCTAAAGTTATCACTATTTTTAATTTACCTTTA
** * *
1652308 AACTTAATTCGAATTTAGGGGTGAGCATTCTAGATCAGGATCTAATTATGTAAAATCATCGATGC
454 AACTTAATTCGAATTTAGAAGTGAACATTCTAGATCAGGATCTAATCATGTAAAATCATCGATGC
1652373 AAGATTACTTAGAAGGTTGAGATCTTGAAGATTGCTTAGGATTGAAATCTTTTAAGATATATTTC
519 AAGATTACTTAGAAGGTTGAGATCTTGAAGATTGCTTAGGATTGAAATCTTTTAAGATATATTTC
* * * *
1652438 TTTTGTCCTATCGGCTGAACCAACGTTTTCGACATTTTCACTTCTTTCTATCTCTCTAGCATGCT
584 TTTTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTCACCTCTTTCGATCTCTCCAGCATGCT
*
1652503 TATTCTCCCTATTTTTATACCAGATTATTTCGGGGCATTTTTAGGGATAAATCAACTTTTAATCC
649 TATTCTCCCTATTTTTATACCAGATTATTTCAGGGCATTTTTAGGGATAAATCAACTTTTAATCC
* * *
1652568 CTAAAGTTATCACTTTTTTTAATTTATCTTTAAACTTATTTCGAATTTAGGGGTGAGCAATCTAG
714 CTAAAGTTATCACTTTTTTTAATTTATCTTTAAACTTAATTCAAATTTAGGGGTGAACAATCTAG
1652633 ATCAGGATCTAATCATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAGATT
779 ATCAGGATCTAATCATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAGATT
*
1652698 GCTTAGGATTGAAATCTTTTAAGTTATATTT
844 GCTTAGGATTGAAATCTTTTAAGATATATTT
* * * * *
1652729 CTTTTTCCCTATCGGCTGATCCAACGTTTTCAACATTTTTCACCTCTTTTGATCCCTCTAGCATG
1 CTTTTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTTCACCTC-TTTGATCTCTCCAGCATG
* *
1652794 ATTATTCTCCCTATTTTTATACCAGATTCTTTTGGGGCATTTTTAGGGATAAATCAACTTTTAAT
65 CTTATTCTCCCTATTTTTATACCAGATTC-TTTCGGGCATTTTTAGGGATAAATCAACTTTTAAT
* ** *
1652859 CCCTAAAGTTATCACTTTTTTTTAATTTATCTTTAAACTTAATTCGAATTTAGGGGTGAAAAATC
129 CCCTAAAGTTATCAC--TTTTTTAATTTATCTTTAAACTTAATTCGAATCTAGGGGTGAGCATTC
* *
1652924 TAGATGAGGATCTAATCATGTAAAATCATTGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAG
192 TAGATCAGGATCTAATCATGTAAAATCATTGATGCAAGATTACTTAGAAGGTTGAGATCTTAAAG
1652989 ATTGCTTAGGATTGAAATCTTTTAAGATATATTTCTTTTG
257 ATTGCTTAGGATTGAAATCTTTTAAGATATATTTCTTTTG
1653029 AATATAAACT
Statistics
Matches: 1106, Mismatches: 55, Indels: 21
0.94 0.05 0.02
Matches are distributed among these distances:
871 62 0.06
872 349 0.32
873 271 0.25
874 11 0.01
875 147 0.13
876 262 0.24
877 4 0.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (874 bp):
CTTTTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTTCACCTCTTTGATCTCTCCAGCATGC
TTATTCTCCCTATTTTTATACCAGATTCTTTCGGGCATTTTTAGGGATAAATCAACTTTTAATCC
CTAAAGTTATCACTTTTTTAATTTATCTTTAAACTTAATTCGAATCTAGGGGTGAGCATTCTAGA
TCAGGATCTAATCATGTAAAATCATTGATGCAAGATTACTTAGAAGGTTGAGATCTTAAAGATTG
CTTAGGATTGAAATCTTTTAAGATATATTTCTTTTGCCTTATCGGCTAAACCAACGTTTTCGACA
TTTTTCATCTCTCTCATCCCTCCAACACGCTTCTTCTCCCTATTTTTATACCAGATTCTTTCGGG
TCATTTTTAGGGATAAATTAACTTTTAATCCCTAAAGTTATCACTATTTTTAATTTACCTTTAAA
CTTAATTCGAATTTAGAAGTGAACATTCTAGATCAGGATCTAATCATGTAAAATCATCGATGCAA
GATTACTTAGAAGGTTGAGATCTTGAAGATTGCTTAGGATTGAAATCTTTTAAGATATATTTCTT
TTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTCACCTCTTTCGATCTCTCCAGCATGCTTA
TTCTCCCTATTTTTATACCAGATTATTTCAGGGCATTTTTAGGGATAAATCAACTTTTAATCCCT
AAAGTTATCACTTTTTTTAATTTATCTTTAAACTTAATTCAAATTTAGGGGTGAACAATCTAGAT
CAGGATCTAATCATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAGATTGC
TTAGGATTGAAATCTTTTAAGATATATTT
Found at i:1652463 original size:581 final size:581
Alignment explanation
Indices: 1650984--1653028 Score: 3314
Period size: 581 Copynumber: 3.5 Consensus size: 581
1650974 TCGTCAGCCG
* * * * *
1650984 CTTTTGCCCTATCGGTTGAACCAGCGTTTTCGACATTTTTAACCTC-T-ATCTCTCCAGCACGCT
1 CTTTTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTTCACCTCTTGATCCCTCCAGCATGCT
*
1651047 TCTTCTCCCTATTTTTATACCAGATTCTTTCGGGTCATTTTTAGGGATAAATCAACTTTTAATCC
66 TATTCTCCCTATTTTTATACCAGATTCTTTCGGGTCATTTTTAGGGATAAATCAACTTTTAATCC
* * * *
1651112 CTAAAGTT-TACACTTTTTTAATTTATCTTTAAACTTAATTCGAATCTAGGGGTCAGCATTTTAG
131 CTAAAGTTAT-CACTTTTTTAATTTATCTTTAAACTTAATTCGAATTTAGGGGTGAACATTCTAG
* * * * * *
1651176 ATTAGGATCTAATCATATAAAATCATCGATGCAAGATTATTTATAAGGTTGTGATCTTAAAGATT
195 ATCAGGATCTAATCATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAGATT
* * *
1651241 ACTTAGGATTGAAATATTTTAAGATATATTTCTTTTGCCTTATCGGCTAAACCAACGTTTTCGAC
260 GCTTAGGATTGAAATCTTTTAAGATATATTTCTTTTGCC-TATCGGCTGAACCAACGTTTTCGAC
* * * * * *
1651306 ATTTTTCATCTCTCTCGATCTCTCCAACACGCTTCTTCTCCCTATTTTTATACTAGATTCTTTCG
324 ATTTTTCACCTCTTTCGATCTCTCCAGCATGCTTATTCTCCCTATTTTTATACCAGATTCTTTCG
*
1651371 GGTCATTTTTAGGGATAAATTAACTTTTAATCCCTAAAGTTATCACTTTTTTTAATTTATCTTTA
389 GG-CATTTTTAGGGATAAATCAACTTTTAATCCCTAAAGTTATCACTTTTTTTAATTTATCTTTA
** * *
1651436 AACTTAATTCGAATTTAGAAGTGAACTTTCTAGATCAGGATCTAATCATGTAAAATCATCGATGC
453 AACTTAATTCGAATTTAGGGGTGAGCATTCTAGATCAGGATCTAATCATGTAAAATCATCGATGC
1651501 AAGATTACTTAGAAGGTTGAGATCTTGAAGATTGCTTAGGATTGAAATCTTTTAAGATATATTT
518 AAGATTACTTAGAAGGTTGAGATCTTGAAGATTGCTTAGGATTGAAATCTTTTAAGATATATTT
*
1651565 CTTTTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTTCACCTCTTTCGATCTCTCCAGCATG
1 CTTTTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTTCACCTC-TT-GATCCCTCCAGCATG
*
1651630 CTTATTCTCCCTATTTTTATACCAGATTCTTTCAGGTCA-TTTTAGGGATAAATCAACTTTTAAT
64 CTTATTCTCCCTATTTTTATACCAGATTCTTTCGGGTCATTTTTAGGGATAAATCAACTTTTAAT
*
1651694 CCCTAAAGTTATCACTTTTTTAATTTATCTTTAAACTTAATTCAAATTTAGGGGTGAACATTCTA
129 CCCTAAAGTTATCACTTTTTTAATTTATCTTTAAACTTAATTCGAATTTAGGGGTGAACATTCTA
*
1651759 GATCAGGATCTAATTATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAGAT
194 GATCAGGATCTAATCATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAGAT
1651824 TGCTTAGGATTGAAATCTTTTAAGATATATTTCTTTTGCCCTATCGGCTGAACCAACGTTTTCGA
259 TGCTTAGGATTGAAATCTTTTAAGATATATTTCTTTTG-CCTATCGGCTGAACCAACGTTTTCGA
1651889 CATTTTTCACCTCTTTCGATCTCTCCAGCATGCTTATTCTCCCTATTTTTATACCAGATTCTTTC
323 CATTTTTCACCTCTTTCGATCTCTCCAGCATGCTTATTCTCCCTATTTTTATACCAGATTCTTTC
1651954 AGGGCATTTTTAGGGATAAATCAACTTTTAATCCCTAAAGTTATCAC-TTTTTTAATTTATCTTT
388 -GGGCATTTTTAGGGATAAATCAACTTTTAATCCCTAAAGTTATCACTTTTTTTAATTTATCTTT
* * *
1652018 AAACTTAATTCGAATCTAGGGGTGAGCATTCTAGATCAGAATCTAATCATGTAAAATCATTGATG
452 AAACTTAATTCGAATTTAGGGGTGAGCATTCTAGATCAGGATCTAATCATGTAAAATCATCGATG
*
1652083 CAAGATTACTTAGAAGGTTGAGATCTTAAAGATTGCTTAGGATTGAAATCTTTTAAGATATATTT
517 CAAGATTACTTAGAAGGTTGAGATCTTGAAGATTGCTTAGGATTGAAATCTTTTAAGATATATTT
* * * * *
1652148 CTTTTGCCTTATCGGCTAAACCAGCGTTTTCGACGTTTTTCACCTC-T-ATCCCTCCAACATGCT
1 CTTTTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTTCACCTCTTGATCCCTCCAGCATGCT
* *
1652211 TCTTCTCCCTATTTTTATACCAGATTCTTTCGGGTCATTTTTAGGGATAAATTAACTTTTAATCC
66 TATTCTCCCTATTTTTATACCAGATTCTTTCGGGTCATTTTTAGGGATAAATCAACTTTTAATCC
* *
1652276 CTAAAGTTATCACTATTTTTAATTTACCTTTAAACTTAATTCGAATTTAGGGGTGAGCATTCTAG
131 CTAAAGTTATCACT-TTTTTAATTTATCTTTAAACTTAATTCGAATTTAGGGGTGAACATTCTAG
*
1652341 ATCAGGATCTAATTATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAGATT
195 ATCAGGATCTAATCATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAGATT
1652406 GCTTAGGATTGAAATCTTTTAAGATATATTTCTTTTGTCCTATCGGCTGAACCAACGTTTTCGAC
260 GCTTAGGATTGAAATCTTTTAAGATATATTTCTTTTG-CCTATCGGCTGAACCAACGTTTTCGAC
* * * *
1652471 A-TTTTCACTTCTTTCTATCTCTCTAGCATGCTTATTCTCCCTATTTTTATACCAGATTATTTCG
324 ATTTTTCACCTCTTTCGATCTCTCCAGCATGCTTATTCTCCCTATTTTTATACCAGATTCTTTC-
1652535 GGGCATTTTTAGGGATAAATCAACTTTTAATCCCTAAAGTTATCACTTTTTTTAATTTATCTTTA
388 GGGCATTTTTAGGGATAAATCAACTTTTAATCCCTAAAGTTATCACTTTTTTTAATTTATCTTTA
* *
1652600 AACTTATTTCGAATTTAGGGGTGAGCAATCTAGATCAGGATCTAATCATGTAAAATCATCGATGC
453 AACTTAATTCGAATTTAGGGGTGAGCATTCTAGATCAGGATCTAATCATGTAAAATCATCGATGC
*
1652665 AAGATTACTTAGAAGGTTGAGATCTTGAAGATTGCTTAGGATTGAAATCTTTTAAGTTATATTT
518 AAGATTACTTAGAAGGTTGAGATCTTGAAGATTGCTTAGGATTGAAATCTTTTAAGATATATTT
* * * *
1652729 CTTTTTCCCTATCGGCTGATCCAACGTTTTCAACATTTTTCACCTCTTTTGATCCCTCTAGCATG
1 CTTTTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTTCACCTC--TTGATCCCTCCAGCATG
* * *
1652794 ATTATTCTCCCTATTTTTATACCAGATTCTTTTGGGGCATTTTTAGGGATAAATCAACTTTTAAT
64 CTTATTCTCCCTATTTTTATACCAGATTCTTTCGGGTCATTTTTAGGGATAAATCAACTTTTAAT
* *
1652859 CCCTAAAGTTATCACTTTTTTTTAATTTATCTTTAAACTTAATTCGAATTTAGGGGTGAAAAATC
129 CCCTAAAGTTATCAC--TTTTTTAATTTATCTTTAAACTTAATTCGAATTTAGGGGTGAACATTC
* *
1652924 TAGATGAGGATCTAATCATGTAAAATCATTGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAG
192 TAGATCAGGATCTAATCATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAG
1652989 ATTGCTTAGGATTGAAATCTTTTAAGATATATTTCTTTTG
257 ATTGCTTAGGATTGAAATCTTTTAAGATATATTTCTTTTG
1653029 AATATAAACT
Statistics
Matches: 1366, Mismatches: 82, Indels: 27
0.93 0.06 0.02
Matches are distributed among these distances:
579 49 0.04
580 144 0.11
581 400 0.29
583 182 0.13
584 302 0.22
585 143 0.10
586 145 0.11
587 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (581 bp):
CTTTTGCCCTATCGGCTGAACCAACGTTTTCGACATTTTTCACCTCTTGATCCCTCCAGCATGCT
TATTCTCCCTATTTTTATACCAGATTCTTTCGGGTCATTTTTAGGGATAAATCAACTTTTAATCC
CTAAAGTTATCACTTTTTTAATTTATCTTTAAACTTAATTCGAATTTAGGGGTGAACATTCTAGA
TCAGGATCTAATCATGTAAAATCATCGATGCAAGATTACTTAGAAGGTTGAGATCTTGAAGATTG
CTTAGGATTGAAATCTTTTAAGATATATTTCTTTTGCCTATCGGCTGAACCAACGTTTTCGACAT
TTTTCACCTCTTTCGATCTCTCCAGCATGCTTATTCTCCCTATTTTTATACCAGATTCTTTCGGG
CATTTTTAGGGATAAATCAACTTTTAATCCCTAAAGTTATCACTTTTTTTAATTTATCTTTAAAC
TTAATTCGAATTTAGGGGTGAGCATTCTAGATCAGGATCTAATCATGTAAAATCATCGATGCAAG
ATTACTTAGAAGGTTGAGATCTTGAAGATTGCTTAGGATTGAAATCTTTTAAGATATATTT
Found at i:1661899 original size:18 final size:18
Alignment explanation
Indices: 1661876--1661910 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1661866 AGAGTTGACC
* *
1661876 TATATATTTTTATTTAAT
1 TATATATATATATTTAAT
1661894 TATATATATATATTTAA
1 TATATATATATATTTAA
1661911 AAAAAAACGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATATATATATATTTAAT
Found at i:1662459 original size:14 final size:14
Alignment explanation
Indices: 1662413--1662450 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
1662403 CATTGGGCAT
*
1662413 CCGAAGCCATCCGA
1 CCGAGGCCATCCGA
*
1662427 CCGAGGGCATCCGA
1 CCGAGGCCATCCGA
1662441 CCGAGGCCAT
1 CCGAGGCCAT
1662451 TCGAGCGAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.39, G:0.29, T:0.08
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:1662559 original size:29 final size:29
Alignment explanation
Indices: 1662517--1662592 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
1662507 GGGAGTGCAT
*
1662517 GGAGTGCATGGCGACCTACAAGGTCGCGA
1 GGAGTGCATGGCGACCTACAAGGTCGCCA
*
1662546 GGAGTGCATGGCGACCTACAAGGTCGCCC
1 GGAGTGCATGGCGACCTACAAGGTCGCCA
*
1662575 GGAGGGCATGGCGACCTA
1 GGAGTGCATGGCGACCTA
1662593 TGCTTGGGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.22, C:0.26, G:0.38, T:0.13
Consensus pattern (29 bp):
GGAGTGCATGGCGACCTACAAGGTCGCCA
Found at i:1663158 original size:10 final size:10
Alignment explanation
Indices: 1663143--1663186 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
1663133 TAATTTTTTC
1663143 TATTTTCATT
1 TATTTTCATT
*
1663153 TATTTTCGTT
1 TATTTTCATT
1663163 TATATTT-ATT
1 TAT-TTTCATT
*
1663173 TATGTTCATT
1 TATTTTCATT
1663183 TATT
1 TATT
1663187 ATATTTGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 2 0.07
10 23 0.82
11 3 0.11
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (10 bp):
TATTTTCATT
Found at i:1663192 original size:23 final size:23
Alignment explanation
Indices: 1663162--1663254 Score: 89
Period size: 23 Copynumber: 4.0 Consensus size: 23
1663152 TTATTTTCGT
*
1663162 TTATATTTATTTATGTTCATTTA
1 TTATATTTGTTTATGTTCATTTA
* *
1663185 TTATATTTGTTTACGTTCATTCA
1 TTATATTTGTTTATGTTCATTTA
* *
1663208 TT-TGTGTTCGTTTATGTTCGTTTA
1 TTATAT-TT-GTTTATGTTCATTTA
* * *
1663232 TTGTGTTTGTTTATGTTCGTTTA
1 TTATATTTGTTTATGTTCATTTA
1663255 AATCCATTCG
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
22 2 0.03
23 39 0.65
24 16 0.27
25 3 0.05
ACGTcount: A:0.16, C:0.08, G:0.14, T:0.62
Consensus pattern (23 bp):
TTATATTTGTTTATGTTCATTTA
Found at i:1663227 original size:10 final size:10
Alignment explanation
Indices: 1663212--1663254 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
1663202 CATTCATTTG
1663212 TGTTCGTTTA
1 TGTTCGTTTA
1663222 TGTTCGTTTA
1 TGTTCGTTTA
*
1663232 TTGTGTTTGTTTA
1 ---TGTTCGTTTA
1663245 TGTTCGTTTA
1 TGTTCGTTTA
1663255 AATCCATTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 19 0.68
13 9 0.32
ACGTcount: A:0.09, C:0.07, G:0.21, T:0.63
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:1663291 original size:24 final size:24
Alignment explanation
Indices: 1663190--1663293 Score: 93
Period size: 24 Copynumber: 4.4 Consensus size: 24
1663180 ATTTATTATA
* *
1663190 TTTGTTTACGTTCATTCATTTGTG
1 TTTGTTTATGTTCGTTCATTTGTG
* *
1663214 TTCGTTTATGTTCGTTTA-TTGTG
1 TTTGTTTATGTTCGTTCATTTGTG
* ** ***
1663237 TTTGTTTATGTTCGTTTAAATCCA
1 TTTGTTTATGTTCGTTCATTTGTG
* *
1663261 TTCGTTTATATTCGTTCATTTGTG
1 TTTGTTTATGTTCGTTCATTTGTG
1663285 TTTGTTTAT
1 TTTGTTTAT
1663294 CATTTAAATG
Statistics
Matches: 61, Mismatches: 18, Indels: 2
0.75 0.22 0.02
Matches are distributed among these distances:
23 22 0.36
24 39 0.64
ACGTcount: A:0.13, C:0.11, G:0.16, T:0.60
Consensus pattern (24 bp):
TTTGTTTATGTTCGTTCATTTGTG
Found at i:1663770 original size:45 final size:45
Alignment explanation
Indices: 1663704--1663794 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
1663694 GTGTATATAT
* * *
1663704 TAATCTTATGTTTAATTACTCAATAAATACGTGTTTAAATAATTA
1 TAATCTTATGTTCAATCACTCAATAAATACGTGTTTAAAAAATTA
1663749 TAATCTTATGTTCAATCACTCAATAAATACGTGTTTAAAAAATTA
1 TAATCTTATGTTCAATCACTCAATAAATACGTGTTTAAAAAATTA
1663794 T
1 T
1663795 TTAAACACAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.42
Consensus pattern (45 bp):
TAATCTTATGTTCAATCACTCAATAAATACGTGTTTAAAAAATTA
Found at i:1664187 original size:28 final size:30
Alignment explanation
Indices: 1664154--1664214 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
1664144 TGTAAATTTA
1664154 AAAAATA-ATTTAATATA-AATATTAAAAT
1 AAAAATACATTTAATATATAATATTAAAAT
* *
1664182 AAAAATACTTTTTAATATATAATATTTAAAT
1 AAAAATAC-ATTTAATATATAATATTAAAAT
1664213 AA
1 AA
1664215 GAAAGCCAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.25
30 9 0.32
31 12 0.43
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (30 bp):
AAAAATACATTTAATATATAATATTAAAAT
Found at i:1664847 original size:26 final size:27
Alignment explanation
Indices: 1664816--1664869 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
1664806 ATTATTATTA
* *
1664816 TTATCTCT-TATTATTTTTTGAAATTT
1 TTATCTATATATTATTTTTGGAAATTT
1664842 TTATCTATGATATTATTTTTGGAAATTT
1 TTATCTAT-ATATTATTTTTGGAAATTT
1664870 AGAGAGAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.29
28 17 0.71
ACGTcount: A:0.26, C:0.06, G:0.07, T:0.61
Consensus pattern (27 bp):
TTATCTATATATTATTTTTGGAAATTT
Found at i:1670243 original size:15 final size:16
Alignment explanation
Indices: 1670225--1670254 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1670215 ATCTAATAAT
1670225 TTTTATAAA-AATATA
1 TTTTATAAACAATATA
1670240 TTTTATAAACAATAT
1 TTTTATAAACAATAT
1670255 TGAAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTTATAAACAATATA
Found at i:1672115 original size:16 final size:17
Alignment explanation
Indices: 1672085--1672117 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1672075 AATTTTTAAG
1672085 AAAATATATTAATTTAT
1 AAAATATATTAATTTAT
*
1672102 AAAA-ATATTTATTTAT
1 AAAATATATTAATTTAT
1672118 TTAGAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AAAATATATTAATTTAT
Found at i:1672270 original size:4 final size:4
Alignment explanation
Indices: 1672263--1672294 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
1672253 TTAATAAACG
1672263 AATA AATA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA
1672295 TTATATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:1672352 original size:12 final size:11
Alignment explanation
Indices: 1672323--1672398 Score: 50
Period size: 11 Copynumber: 6.5 Consensus size: 11
1672313 ATAACTTAAT
1672323 AATAATAATAA
1 AATAATAATAA
1672334 AATAATAATGAA
1 AATAATAAT-AA
*
1672346 GATAATAATTTAA
1 AATAATAA--TAA
1672359 ACAT-AT-ATCAA
1 A-ATAATAAT-AA
*
1672370 ACGTAATAATAA
1 A-ATAATAATAA
1672382 AATAA-AATAA
1 AATAATAATAA
1672392 TAATAAT
1 -AATAAT
1672399 TAAAATGAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 17
0.71 0.05 0.23
Matches are distributed among these distances:
10 6 0.12
11 22 0.42
12 15 0.29
13 6 0.12
14 3 0.06
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (11 bp):
AATAATAATAA
Found at i:1672404 original size:15 final size:14
Alignment explanation
Indices: 1672374--1672433 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 14
1672364 TATCAAACGT
1672374 AATAATAAAA-TAA
1 AATAATAAAATTAA
1672387 AATAATAATAATTAA
1 AATAATAA-AATTAA
1672402 AATGAA-AGAAATTAA
1 AAT-AATA-AAATTAA
*
1672417 AAGTAATAATATTAA
1 AA-TAATAAAATTAA
1672432 AA
1 AA
1672434 ACTAATGGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 8 0.20
14 2 0.05
15 25 0.62
16 5 0.12
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (14 bp):
AATAATAAAATTAA
Found at i:1673906 original size:2 final size:2
Alignment explanation
Indices: 1673899--1673949 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1673889 TTTTTATTTA
1673899 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1673941 AT AT AT AT A
1 AT AT AT AT A
1673950 ATAAAAAAGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1674034 original size:3 final size:3
Alignment explanation
Indices: 1674026--1674050 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1674016 AAGCATAAAG
1674026 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1674051 TTACTTTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1675578 original size:25 final size:23
Alignment explanation
Indices: 1675545--1675606 Score: 97
Period size: 23 Copynumber: 2.6 Consensus size: 23
1675535 TACAGATAAT
1675545 ACATAAAATATTATACACTCTCAAC
1 ACATAAAATATTATACA--CTCAAC
*
1675570 ACATCAAATATTATACACTCAAC
1 ACATAAAATATTATACACTCAAC
1675593 ACATAAAATATTAT
1 ACATAAAATATTAT
1675607 GTACAACTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 19 0.54
25 16 0.46
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (23 bp):
ACATAAAATATTATACACTCAAC
Found at i:1675611 original size:25 final size:24
Alignment explanation
Indices: 1675545--1675611 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 24
1675535 TACAGATAAT
1675545 ACATAAAATATTA-TACACTCTCAAC
1 ACATAAAATATTATTACA--CTCAAC
*
1675570 ACATCAAATATTA-TACACTCAAC
1 ACATAAAATATTATTACACTCAAC
1675593 ACATAAAATATTATGTACA
1 ACATAAAATATTAT-TACA
1675612 ACTAAAACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.47
25 20 0.53
ACGTcount: A:0.49, C:0.21, G:0.01, T:0.28
Consensus pattern (24 bp):
ACATAAAATATTATTACACTCAAC
Found at i:1682684 original size:18 final size:18
Alignment explanation
Indices: 1682661--1682697 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1682651 CGGTACTAAT
1682661 CTTAATATTGGTTGTCGA
1 CTTAATATTGGTTGTCGA
1682679 CTTAATATTGGTTGTCGA
1 CTTAATATTGGTTGTCGA
1682697 C
1 C
1682698 CGTCGATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.43
Consensus pattern (18 bp):
CTTAATATTGGTTGTCGA
Found at i:1682834 original size:24 final size:24
Alignment explanation
Indices: 1682800--1682845 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1682790 TTGTAACACG
1682800 TTTTTCCCTACTCTTGTGGCACAT
1 TTTTTCCCTACTCTTGTGGCACAT
* *
1682824 TTTTTCTCTACTTTTGTGGCAC
1 TTTTTCCCTACTCTTGTGGCAC
1682846 GTTACTTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.11, C:0.26, G:0.13, T:0.50
Consensus pattern (24 bp):
TTTTTCCCTACTCTTGTGGCACAT
Found at i:1684394 original size:39 final size:39
Alignment explanation
Indices: 1684351--1684478 Score: 205
Period size: 39 Copynumber: 3.4 Consensus size: 39
1684341 AGAGATGTAT
1684351 TCGATTCGTTTATGTTCACGAACAAACTGTTTTATTAAC
1 TCGATTCGTTTATGTTCACGAACAAACTGTTTTATTAAC
*
1684390 TCGATTCGTTTATGTTCACAAACAAACTGTTTTATTAAC
1 TCGATTCGTTTATGTTCACGAACAAACTGTTTTATTAAC
1684429 TCGA-TC----ATGTTCACGAACAAACTGTTTTATTAAC
1 TCGATTCGTTTATGTTCACGAACAAACTGTTTTATTAAC
1684463 TCGATT-GTTTATGTTC
1 TCGATTCGTTTATGTTC
1684479 GCTGACAAAC
Statistics
Matches: 82, Mismatches: 2, Indels: 11
0.86 0.02 0.12
Matches are distributed among these distances:
34 31 0.38
35 1 0.01
38 8 0.10
39 42 0.51
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.41
Consensus pattern (39 bp):
TCGATTCGTTTATGTTCACGAACAAACTGTTTTATTAAC
Found at i:1684440 original size:34 final size:35
Alignment explanation
Indices: 1684361--1684467 Score: 162
Period size: 34 Copynumber: 3.0 Consensus size: 35
1684351 TCGATTCGTT
1684361 TATGTTCACGAACAAACTGTTTTATTAACTCGATTC
1 TATGTTCACGAACAAACTGTTTTATTAACTCGA-TC
*
1684397 GTTTATGTTCACAAACAAACTGTTTTATTAACTCGATC
1 ---TATGTTCACGAACAAACTGTTTTATTAACTCGATC
1684435 -ATGTTCACGAACAAACTGTTTTATTAACTCGAT
1 TATGTTCACGAACAAACTGTTTTATTAACTCGAT
1684468 TGTTTATGTT
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
34 32 0.48
38 2 0.03
39 32 0.48
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (35 bp):
TATGTTCACGAACAAACTGTTTTATTAACTCGATC
Found at i:1686640 original size:72 final size:71
Alignment explanation
Indices: 1686550--1686684 Score: 168
Period size: 72 Copynumber: 1.9 Consensus size: 71
1686540 GACGTTTTTC
* * * *
1686550 TAATAAACGCTACTATAGAT-AGATTTATTGCGACGT-TTTTTTAA-AAAACGCCACTATTATTG
1 TAATAAACGCCACTATAGATGA-ATTTATTGC--CGTGTTTGTCAAGAAAACGCCACTATCATTG
1686612 TGGTTTTAT
63 TGGTTTTAT
*
1686621 TAATAAAACGCCATTATAGATGAATTTATTGCCGTGTTTGTCAAGAAAACGCCACTATCATTGT
1 TAAT-AAACGCCACTATAGATGAATTTATTGCCGTGTTTGTCAAGAAAACGCCACTATCATTGT
1686685 CCCGAAATCG
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
70 3 0.05
71 10 0.18
72 41 0.75
73 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (71 bp):
TAATAAACGCCACTATAGATGAATTTATTGCCGTGTTTGTCAAGAAAACGCCACTATCATTGTGG
TTTTAT
Found at i:1703286 original size:29 final size:29
Alignment explanation
Indices: 1703253--1703357 Score: 165
Period size: 29 Copynumber: 3.6 Consensus size: 29
1703243 GGAGCAGGAG
*
1703253 GGAGTGCATGGCGACCTACAAGGTCGCCC
1 GGAGTGCATGGCAACCTACAAGGTCGCCC
1703282 GGAGTGCATGGCAACCTACAAGGTCGCCC
1 GGAGTGCATGGCAACCTACAAGGTCGCCC
* *
1703311 GGAGTGCATGGCAACCTACAAGGTCGTCT
1 GGAGTGCATGGCAACCTACAAGGTCGCCC
* *
1703340 GGAGGGCATGGCGACCTA
1 GGAGTGCATGGCAACCTA
1703358 TGCTTGGGAC
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 71 1.00
ACGTcount: A:0.23, C:0.28, G:0.34, T:0.15
Consensus pattern (29 bp):
GGAGTGCATGGCAACCTACAAGGTCGCCC
Found at i:1716061 original size:33 final size:33
Alignment explanation
Indices: 1716017--1716113 Score: 97
Period size: 33 Copynumber: 2.8 Consensus size: 33
1716007 TTAAAATAGT
*
1716017 TATTATATTTTATATTAATAATAATTATATAAA
1 TATTATTTTTTATATTAATAATAATTATATAAA
* * *
1716050 TATTATTTTTTAT-TAAAATAATATTTATATAAT
1 TATTATTTTTTATAT-TAATAATAATTATATAAA
* *
1716083 TATTATTTATTTAAATTTATTAATTAATTAT
1 TATTATTT-TTTATA-TTAATAA-TAATTAT
1716114 TTTTTGTGCT
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
32 1 0.02
33 35 0.69
34 4 0.08
35 4 0.08
36 7 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (33 bp):
TATTATTTTTTATATTAATAATAATTATATAAA
Found at i:1717919 original size:42 final size:41
Alignment explanation
Indices: 1717820--1717919 Score: 101
Period size: 42 Copynumber: 2.4 Consensus size: 41
1717810 ATGCCACAGT
* *
1717820 GGTACATGTCCAGCCCTCCACTTCAGATGCCATCTCCTCAGG
1 GGTACAT-TCCAGCCCACCACTTCAGATGCCATCTCCGCAGG
* * * * *
1717862 GGTATATGCCAAGCCCACCAGTTCATATGTCATCTCCGCAGG
1 GGTACATTCC-AGCCCACCACTTCAGATGCCATCTCCGCAGG
*
1717904 GTTACATTCCTAGCCC
1 GGTACATTCC-AGCCC
1717920 GCATGGTTAC
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
41 2 0.04
42 44 0.96
ACGTcount: A:0.21, C:0.35, G:0.19, T:0.25
Consensus pattern (41 bp):
GGTACATTCCAGCCCACCACTTCAGATGCCATCTCCGCAGG
Found at i:1717927 original size:21 final size:21
Alignment explanation
Indices: 1717897--1717969 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
1717887 TATGTCATCT
1717897 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
* *
1717918 CCGCATGGTTACATTTCTAGC
1 CCGCAGGGTTACATTCCTAGC
**
1717939 CCGCCA-GGTTACATAGCTAGC
1 CCG-CAGGGTTACATTCCTAGC
1717960 CCGCAGGGTT
1 CCGCAGGGTT
1717970 TTATACCATA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.04
21 42 0.91
22 2 0.04
ACGTcount: A:0.19, C:0.32, G:0.25, T:0.25
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:1718530 original size:34 final size:34
Alignment explanation
Indices: 1718491--1718597 Score: 133
Period size: 34 Copynumber: 3.1 Consensus size: 34
1718481 ATAAATTTTT
* *
1718491 TTAAAATACAAATTATAGAATTTGAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
* * * * *
1718525 TTAAAATTCAAATAATATTATTCCAAATTTAAAT
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
* *
1718559 TTAAAATATAAATTATAGTATTCGAAATTTAACA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
1718593 TTAAA
1 TTAAA
1718598 TTCAACTTAA
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 59 1.00
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCGAAATTTAAAA
Found at i:1721644 original size:21 final size:19
Alignment explanation
Indices: 1721620--1721658 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
1721610 ATTAAGTGAT
*
1721620 AAAATTAATAGATCAATAATC
1 AAAATAAATA-AT-AATAATC
1721641 AAAATAAATAATAATAAT
1 AAAATAAATAATAATAAT
1721659 ATAACCATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (19 bp):
AAAATAAATAATAATAATC
Found at i:1722782 original size:16 final size:15
Alignment explanation
Indices: 1722760--1722814 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
1722750 TATTAGAGTG
1722760 ATTAAATTAAAAATA
1 ATTAAATTAAAAATA
*
1722775 ATTTAAA-TATTAAATA
1 A-TTAAATTA-AAAATA
*
1722791 ATTAAATTTAAAAAAA
1 ATTAAA-TTAAAAATA
1722807 ATTAAATT
1 ATTAAATT
1722815 TTAATGACCA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
15 10 0.30
16 21 0.64
17 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTAAATTAAAAATA
Found at i:1722795 original size:31 final size:31
Alignment explanation
Indices: 1722760--1722818 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1722750 TATTAGAGTG
*
1722760 ATTAAA-TTAAAAATAATTTAAATATTAAATA
1 ATTAAATTTAAAAA-AAATTAAATATTAAATA
*
1722791 ATTAAATTTAAAAAAAATTAAATTTTAA
1 ATTAAATTTAAAAAAAATTAAATATTAA
1722819 TGACCAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (31 bp):
ATTAAATTTAAAAAAAATTAAATATTAAATA
Found at i:1725861 original size:12 final size:13
Alignment explanation
Indices: 1725833--1725861 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1725823 TTTGGTAATC
1725833 CCCGCCCCGATTA
1 CCCGCCCCGATTA
1725846 CCCGCCCCGA-TA
1 CCCGCCCCGATTA
1725858 CCCG
1 CCCG
1725862 ACTCGATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.14, C:0.59, G:0.17, T:0.10
Consensus pattern (13 bp):
CCCGCCCCGATTA
Found at i:1725935 original size:24 final size:26
Alignment explanation
Indices: 1725908--1725968 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 26
1725898 ATATATATAT
*
1725908 ATAATATTAATA-A-ATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
1725932 ATAA-A-AAATATATATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
*
1725956 AT-ATATATATATA
1 ATAATATAAATATA
1725969 CCCGACCCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
22 4 0.13
23 3 0.10
24 18 0.58
25 6 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATAATATAAATATATATTTAATTTAA
Found at i:1725950 original size:19 final size:19
Alignment explanation
Indices: 1725926--1725965 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1725916 AATAAATTTA
1725926 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
1725945 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
1725964 AT
1 AT
1725966 ATACCCGACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:1726010 original size:12 final size:12
Alignment explanation
Indices: 1725966--1726031 Score: 73
Period size: 12 Copynumber: 5.6 Consensus size: 12
1725956 ATATATATAT
*
1725966 ATACCCGACCCG
1 ATACCCGACCCA
*
1725978 ATTCCC-AGCCCA
1 ATACCCGA-CCCA
1725990 ATA-CCGACCCA
1 ATACCCGACCCA
1726001 ATACCCGACCCA
1 ATACCCGACCCA
* *
1726013 ATACCTGGCCCA
1 ATACCCGACCCA
1726025 ATACCCG
1 ATACCCG
1726032 TTTAAATAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
11 10 0.22
12 35 0.78
ACGTcount: A:0.29, C:0.47, G:0.12, T:0.12
Consensus pattern (12 bp):
ATACCCGACCCA
Found at i:1727872 original size:2 final size:2
Alignment explanation
Indices: 1727865--1727889 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1727855 ATTTTCAGCA
1727865 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 A
1727890 AAGGAACTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1728354 original size:14 final size:14
Alignment explanation
Indices: 1728337--1728383 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
1728327 TATTAGAATA
1728337 ATTTATTTAATATT
1 ATTTATTTAATATT
*
1728351 ATTTATGCTAATATT
1 ATTTAT-TTAATATT
*
1728366 A-TTATTAAAGTATT
1 ATTTATTTAA-TATT
1728380 ATTT
1 ATTT
1728384 CTATACTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 2 0.07
14 15 0.56
15 10 0.37
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (14 bp):
ATTTATTTAATATT
Found at i:1728499 original size:21 final size:22
Alignment explanation
Indices: 1728470--1728514 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
1728460 TATATAAAAA
*
1728470 TAAAATATT-A-TATTATATTT
1 TAAAATATTAATTAATATATTT
1728490 TAAAATTATTAATTAATATATTT
1 TAAAA-TATTAATTAATATATTT
1728513 TA
1 TA
1728515 TGGAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 4 0.19
22 1 0.05
23 11 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TAAAATATTAATTAATATATTT
Found at i:1728703 original size:26 final size:25
Alignment explanation
Indices: 1728643--1728703 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 25
1728633 ATTAATAATT
1728643 TATTATATATTAAGAATATAATAGTA
1 TATTAT-TATTAAGAATATAATAGTA
1728669 TCATATATTATTAA-AATATAATTGAGTA
1 T-AT-TATTATTAAGAATATAA-T-AGTA
1728697 TATTATT
1 TATTATT
1728704 GTAATAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
26 12 0.39
27 11 0.35
28 8 0.26
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (25 bp):
TATTATTATTAAGAATATAATAGTA
Found at i:1728709 original size:23 final size:25
Alignment explanation
Indices: 1728672--1728728 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 25
1728662 AATAGTATCA
1728672 TATATTATTAAAAT-ATAAT-TGAG
1 TATATTATTAAAATAATAATATGAG
** * *
1728695 TATATTATTGTAATAATAATATTAT
1 TATATTATTAAAATAATAATATGAG
1728720 TATATTATT
1 TATATTATT
1728729 TTGTTAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 12 0.43
24 5 0.18
25 11 0.39
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (25 bp):
TATATTATTAAAATAATAATATGAG
Found at i:1729225 original size:44 final size:44
Alignment explanation
Indices: 1729162--1729300 Score: 205
Period size: 44 Copynumber: 3.2 Consensus size: 44
1729152 TACCATGTTT
*
1729162 GGTATCAATACTACTATAAATAGTAGTATAGTTACTCCTTGGAC
1 GGTATCGATACTACTATAAATAGTAGTATAGTTACTCCTTGGAC
1729206 GGTATCGATACTACTATAAATAGTAGTATAGTTACTCCTTGGAC
1 GGTATCGATACTACTATAAATAGTAGTATAGTTACTCCTTGGAC
* * * *
1729250 GGTATCGATACTACTAT-AATA--A-TATCGATACTCCTTGAAG
1 GGTATCGATACTACTATAAATAGTAGTATAGTTACTCCTTGGAC
1729290 GGTATCGATAC
1 GGTATCGATAC
1729301 CGTTGGGTTG
Statistics
Matches: 90, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
40 25 0.28
41 1 0.01
43 4 0.04
44 60 0.67
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (44 bp):
GGTATCGATACTACTATAAATAGTAGTATAGTTACTCCTTGGAC
Found at i:1735646 original size:20 final size:20
Alignment explanation
Indices: 1735621--1735693 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
1735611 TGTGCACTTG
1735621 GTATCGATACTACTTACATA
1 GTATCGATACTACTTACATA
*
1735641 GTATCGATACTACTCTTGC-TA
1 GTATCGATACTA--CTTACATA
*
1735662 GGTATTGATACTAC-TAGCATA
1 -GTATCGATACTACTTA-CATA
*
1735683 TTATCGATACT
1 GTATCGATACT
1735694 TCTATCATCG
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
19 1 0.02
20 23 0.53
21 4 0.09
22 15 0.35
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (20 bp):
GTATCGATACTACTTACATA
Found at i:1737623 original size:16 final size:16
Alignment explanation
Indices: 1737599--1737633 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1737589 TGATGAATGA
* *
1737599 TTTGGATATTTGGTTG
1 TTTGAATATTTGGATG
1737615 TTTGAATATTTGGATG
1 TTTGAATATTTGGATG
1737631 TTT
1 TTT
1737634 TGGTTATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.26, T:0.57
Consensus pattern (16 bp):
TTTGAATATTTGGATG
Found at i:1737635 original size:25 final size:25
Alignment explanation
Indices: 1737592--1737643 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1737582 ACCATTTTGA
*
1737592 TGAATGATTTGGATATTTGGTTGTT
1 TGAATGATTTGGATATTTGGTTATT
*
1737617 TGAAT-ATTTGGATGTTTTGGTTATT
1 TGAATGATTTGGAT-ATTTGGTTATT
1737642 TG
1 TG
1737644 TGTCTTTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.19, C:0.00, G:0.27, T:0.54
Consensus pattern (25 bp):
TGAATGATTTGGATATTTGGTTATT
Found at i:1739346 original size:20 final size:21
Alignment explanation
Indices: 1739307--1739347 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1739297 CTTACAGAAA
1739307 ATTAAACCATAAAATGATTTT
1 ATTAAACCATAAAATGATTTT
* *
1739328 ATTAAATCAT-AAGTGATTTT
1 ATTAAACCATAAAATGATTTT
1739348 CCATAAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (21 bp):
ATTAAACCATAAAATGATTTT
Found at i:1741429 original size:2 final size:2
Alignment explanation
Indices: 1741422--1741455 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1741412 AACCTACATA
1741422 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1741456 TAATTGAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1741663 original size:43 final size:42
Alignment explanation
Indices: 1741573--1741665 Score: 102
Period size: 43 Copynumber: 2.2 Consensus size: 42
1741563 AAATACAAAG
1741573 AATTTTTTTGTATCTTAAAATAAAAAATAACAAAGAAAAATA
1 AATTTTTTTGTATCTTAAAATAAAAAATAACAAAGAAAAATA
* * *
1741615 TATTTTTATT-TAT-TTAAAAATAAAATAATAATAATA-ATAAATA
1 AATTTTT-TTGTATCTT-AAAATAAAA-AATAACAA-AGAAAAATA
1741658 AATTTTTT
1 AATTTTTT
1741666 AGATAGAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
41 2 0.05
42 19 0.44
43 21 0.49
44 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (42 bp):
AATTTTTTTGTATCTTAAAATAAAAAATAACAAAGAAAAATA
Found at i:1742190 original size:24 final size:24
Alignment explanation
Indices: 1742162--1742222 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
1742152 TGGAGTAACC
1742162 AAATTTAATAATTTTTATAAAATT
1 AAATTTAATAATTTTTATAAAATT
1742186 AAATTTAATAATTTTTATAAAATT
1 AAATTTAATAATTTTTATAAAATT
1742210 AAATTTAATAATT
1 AAATTTAATAATT
1742223 AAATATATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AAATTTAATAATTTTTATAAAATT
Found at i:1745270 original size:55 final size:56
Alignment explanation
Indices: 1745161--1745276 Score: 173
Period size: 56 Copynumber: 2.1 Consensus size: 56
1745151 CAACGAGTTA
*
1745161 AGCAACAAAATTTCTTAATGAGCATGAGTCAGAGAAAAATTTTAATGAGGTTAACG
1 AGCAACAAAATTTCTTAATGAGCACGAGTCAGAGAAAAATTTTAATGAGGTTAACG
* * *
1745217 AGCAACAAATTTTCTTAATGAGCACGAGTC-GAGCAAAATTTTAACT-AGTTTAACG
1 AGCAACAAAATTTCTTAATGAGCACGAGTCAGAGAAAAATTTTAA-TGAGGTTAACG
1745272 AGCAA
1 AGCAA
1745277 TGAGTCGAGT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
55 26 0.47
56 29 0.53
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (56 bp):
AGCAACAAAATTTCTTAATGAGCACGAGTCAGAGAAAAATTTTAATGAGGTTAACG
Found at i:1746647 original size:15 final size:15
Alignment explanation
Indices: 1746629--1746670 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
1746619 TTCCGGAAAA
1746629 TGAATTACTGGAATT
1 TGAATTACTGGAATT
1746644 TGAATTACTGGAATT
1 TGAATTACTGGAATT
1746659 TGAATT-CTGGAA
1 TGAATTACTGGAA
1746671 AATGAATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 6 0.22
15 21 0.78
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.38
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:1746704 original size:14 final size:14
Alignment explanation
Indices: 1746682--1746720 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1746672 ATGAATTATA
*
1746682 TTTCTGGAAAACAT
1 TTTCCGGAAAACAT
1746696 TTTCCGGAAAACAT
1 TTTCCGGAAAACAT
*
1746710 TTTCCGTAAAA
1 TTTCCGGAAAA
1746721 TGAATTACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (14 bp):
TTTCCGGAAAACAT
Found at i:1747015 original size:23 final size:23
Alignment explanation
Indices: 1746966--1747028 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
1746956 GTGTTATATT
* **
1746966 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
*
1746989 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTAATTAAA
1747012 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
1747029 AAATAATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 22 0.65
24 1 0.03
25 11 0.32
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:1747022 original size:12 final size:12
Alignment explanation
Indices: 1746988--1747028 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
1746978 TATTAATTAG
1746988 TATA-TTTTAAA
1 TATATTTTTAAA
1746999 TATATTTATTAAA
1 TATATTT-TTAAA
1747012 -ATATTATTTAAA
1 TATATT-TTTAAA
1747024 TATAT
1 TATAT
1747029 AAATAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 4 0.15
12 12 0.46
13 10 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TATATTTTTAAA
Found at i:1747056 original size:19 final size:20
Alignment explanation
Indices: 1747004--1747056 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
1746994 TTAAATATAT
1747004 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
1747023 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
1747044 TTATTAAATATAT
1 TTATTAAATATAT
1747057 AAATTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 6 0.21
22 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:1747069 original size:30 final size:29
Alignment explanation
Indices: 1747012--1747123 Score: 101
Period size: 28 Copynumber: 3.9 Consensus size: 29
1747002 ATTTATTAAA
1747012 ATATTATTTAAATATATAAA-TAATATTAT
1 ATATTA-TTAAATATATAAATTAATATTAT
**
1747041 -TCATTATTAAATATATAAATTTTTTATTAT
1 AT-ATTATTAAATATATAAA-TTAATATTAT
*
1747071 ATATTATTAAA-ATAAAAATATAATATTAT
1 ATATTATTAAATATATAAAT-TAATATTAT
* *
1747100 A-AATATT-AATAAATAAA-TAATATT
1 ATATTATTAAATATATAAATTAATATT
1747124 TTGATGAAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
26 7 0.10
27 2 0.03
28 25 0.36
29 18 0.26
30 16 0.23
31 1 0.01
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (29 bp):
ATATTATTAAATATATAAATTAATATTAT
Found at i:1747351 original size:42 final size:42
Alignment explanation
Indices: 1747288--1747403 Score: 207
Period size: 42 Copynumber: 2.8 Consensus size: 42
1747278 ATGAATTACA
*
1747288 TTCCGGAAAAC-AATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACATT
1747329 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACATT
*
1747371 TTCCGGAAAACGAATTACGTAAAACAAACACGG
1 TTCCGGAAAACGAATTACGTGAAACAAACACGG
1747404 TAATTCGGGG
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
41 11 0.15
42 61 0.85
ACGTcount: A:0.47, C:0.20, G:0.17, T:0.16
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACATT
Found at i:1747771 original size:42 final size:42
Alignment explanation
Indices: 1747712--1747827 Score: 214
Period size: 42 Copynumber: 2.8 Consensus size: 42
1747702 CCCGAATTCT
*
1747712 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
*
1747754 CGTGTTTGTTTCACGTAATTCGTTTTCTGGAAAACGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
1747796 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1747828 TGTAATTCAT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.16, C:0.19, G:0.20, T:0.45
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
Found at i:1748051 original size:12 final size:12
Alignment explanation
Indices: 1748016--1748087 Score: 53
Period size: 12 Copynumber: 6.2 Consensus size: 12
1748006 TAATTATTAA
*
1748016 AATATTTAAAAT
1 AATATTTATAAT
1748028 -ATATTTAT--T
1 AATATTTATAAT
1748037 AATATTTATAAT
1 AATATTTATAAT
*
1748049 AATATATA-ATAT
1 AATATTTATA-AT
*
1748061 AATATTTTTAAT
1 AATATTTATAAT
* * *
1748073 ATTATATAAAAT
1 AATATTTATAAT
1748085 AAT
1 AAT
1748088 CAATTATATT
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
9 1 0.02
10 8 0.17
11 8 0.17
12 28 0.61
13 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
AATATTTATAAT
Found at i:1748052 original size:24 final size:23
Alignment explanation
Indices: 1748009--1748079 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 23
1747999 AAAATATTAA
*
1748009 TTATTAAAATATTTAA-AATATAT
1 TTATTAATAT-TTTAATAATATAT
1748032 TTATTAATATTTATAATAATATA-
1 TTATTAATATTT-TAATAATATAT
* *
1748055 TAATATAATATTTTTAATATTATAT
1 TTAT-TAATA-TTTTAATAATATAT
1748080 AAAATAATCA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 2 0.05
23 15 0.38
24 20 0.50
25 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTATTAATATTTTAATAATATAT
Found at i:1748080 original size:24 final size:24
Alignment explanation
Indices: 1748036--1748087 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1748026 ATATATTTAT
*
1748036 TAATATTTATAATAATATATAATA
1 TAATATTTATAATAATATATAAAA
* *
1748060 TAATATTTTTAATATTATATAAAA
1 TAATATTTATAATAATATATAAAA
1748084 TAAT
1 TAAT
1748088 CAATTATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TAATATTTATAATAATATATAAAA
Found at i:1748138 original size:24 final size:23
Alignment explanation
Indices: 1748106--1748152 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1748096 TTATAATAAT
* *
1748106 ATAAGATATTATATTTTTATTTTA
1 ATAAGATATAATAATTTT-TTTTA
*
1748130 ATAATATATAATAATTTTTTTTA
1 ATAAGATATAATAATTTTTTTTA
1748153 TATATTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
ATAAGATATAATAATTTTTTTTA
Found at i:1748141 original size:54 final size:53
Alignment explanation
Indices: 1748042--1748145 Score: 133
Period size: 54 Copynumber: 1.9 Consensus size: 53
1748032 TTATTAATAT
1748042 TTATAATAATATATAATATAATATTTTTAATATTATATAAAATAATCAATTATA
1 TTATAATAATATATAATATAATATTTTTAATATTATATAAAATAAT-AATTATA
* *
1748096 TTATAATAATATA-AGATATTATATTTTT-ATTTTA-ATAATATATAATAATT
1 TTATAATAATATATA-ATATAATATTTTTAATATTATATAA-A-ATAATAATT
1748146 TTTTTTATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
52 4 0.09
53 11 0.24
54 30 0.67
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (53 bp):
TTATAATAATATATAATATAATATTTTTAATATTATATAAAATAATAATTATA
Found at i:1748159 original size:32 final size:29
Alignment explanation
Indices: 1748025--1748197 Score: 112
Period size: 29 Copynumber: 5.9 Consensus size: 29
1748015 AAATATTTAA
1748025 AATA-TATTTATTAATATTTATAATAATATAT
1 AATATTATTTA-T-ATATTT-TAATAATATAT
*
1748056 AATA-TA---ATAT-TTTTAATATTATAT
1 AATATTATTTATATATTTTAATAATATAT
* * ** *
1748080 AAAATAATCAATTATATTATAATAATATA-
1 AATATTATTTA-TATATTTTAATAATATAT
*
1748109 AGATATTATATT-TTTATTTTAATAATATAT
1 A-ATATTAT-TTATATATTTTAATAATATAT
*
1748139 AATAATTTTTTTTATATATTTTAATAATGA-AT
1 AAT-A--TTATTTATATATTTTAATAAT-ATAT
*
1748171 AATATTATTTATATATTTCAATAATAT
1 AATATTATTTATATATTTTAATAATAT
1748198 TTTAGTAATG
Statistics
Matches: 112, Mismatches: 15, Indels: 32
0.70 0.09 0.20
Matches are distributed among these distances:
24 13 0.12
25 4 0.04
26 2 0.02
27 1 0.01
28 3 0.03
29 40 0.36
30 18 0.16
31 9 0.08
32 21 0.19
33 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (29 bp):
AATATTATTTATATATTTTAATAATATAT
Found at i:1748388 original size:20 final size:20
Alignment explanation
Indices: 1748363--1748432 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
1748353 TTTCCAGATG
1748363 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
1748383 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
* *
1748403 TTTTACAGAAATGTAATTTA
1 TTTTCCAGAAATGTAATTCA
1748423 TTTTCCAGAA
1 TTTTCCAGAA
1748433 TTCAAATTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:1748441 original size:40 final size:40
Alignment explanation
Indices: 1748363--1748441 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
1748353 TTTCCAGATG
* **
1748363 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
* *
1748403 TTTTACAGAAATGTAATTTATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
1748442 CAGTAATTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:1748451 original size:15 final size:15
Alignment explanation
Indices: 1748425--1748496 Score: 119
Period size: 15 Copynumber: 4.9 Consensus size: 15
1748415 GTAATTTATT
1748425 TTCCAG-AATTCAAA
1 TTCCAGTAATTCAAA
**
1748439 TTCCAGTAATTCATT
1 TTCCAGTAATTCAAA
1748454 TTCCAGTAATTCAAA
1 TTCCAGTAATTCAAA
1748469 TTCCAGTAATTCAAA
1 TTCCAGTAATTCAAA
1748484 TTCCAGTAATTCA
1 TTCCAGTAATTCA
1748497 TTTTCTGGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
14 6 0.11
15 47 0.89
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (15 bp):
TTCCAGTAATTCAAA
Found at i:1748467 original size:30 final size:30
Alignment explanation
Indices: 1748415--1748496 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
1748405 TTACAGAAAT
*
1748415 GTAATTTATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
1748444 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
1748474 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
1748497 TTTTCTGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 15 0.31
30 34 0.69
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:1753589 original size:44 final size:42
Alignment explanation
Indices: 1753541--1753873 Score: 237
Period size: 44 Copynumber: 7.6 Consensus size: 42
1753531 GCAAAAATGA
*
1753541 TAAGGTCTTATCCTTGCACATAGCAAAAGAGCCTGAGGAAACTG
1 TAAGG-CTTA-CCTTGCACACAGCAAAAGAGCCTGAGGAAACTG
* * *
1753585 TAAGGCTATCCCTTGCACACAGCAAAGGAACCTGTAGGAAACTG
1 TAAGGCT-TACCTTGCACACAGCAAAAGAGCCTG-AGGAAACTG
*
1753629 TAAGGCTTACCTTTGCACACAACAAAAG-GACCT-AGGGAAACTG
1 TAAGGCTTACC-TTGCACACAGCAAAAGAG-CCTGA-GGAAACTG
* * * * *
1753672 TAAGGCTTACCTTTGTACACAAC-AAAGGGACATGGGGGAAACTG
1 TAAGGCTTACC-TTGCACACAGCAAAAGAG-CCT-GAGGAAACTG
* * * *
1753716 TAAGACTTACCTTTGCACACAAC-AAAGGGACATGGAGGAAACTG
1 TAAGGCTTACC-TTGCACACAGCAAAAGAG-CCT-GAGGAAACTG
* * *
1753760 TAAGGCTTACCTTTGCACACAAC-AAAGGGACCTGGGGGAAACTG
1 TAAGGCTTACC-TTGCACACAGCAAAAGAG-CCT-GAGGAAACTG
* * * * *
1753804 TAAGGCTTACCTTTGTATACAAC-AAAGGGACCTGGGGGAAACTG
1 TAAGGCTTACC-TTGCACACAGCAAAAGAG-CCT-GAGGAAACTG
*
1753848 TAAGGCTTACCTTTGCACACAACAAA
1 TAAGGCTTACC-TTGCACACAGCAAA
1753874 TGGACCTGCT
Statistics
Matches: 259, Mismatches: 21, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
42 5 0.02
43 60 0.23
44 192 0.74
45 2 0.01
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (42 bp):
TAAGGCTTACCTTGCACACAGCAAAAGAGCCTGAGGAAACTG
Found at i:1753879 original size:44 final size:44
Alignment explanation
Indices: 1753577--1753881 Score: 452
Period size: 44 Copynumber: 7.0 Consensus size: 44
1753567 AAGAGCCTGA
* * * **
1753577 GGAAACTGTAAGGC-TATCCCTTGCACACAGCAAAGGAACCTGTA
1 GGAAACTGTAAGGCTTA-CCTTTGCACACAACAAAGGGACCTGGG
* *
1753621 GGAAACTGTAAGGCTTACCTTTGCACACAACAAAAGGACCT-AG
1 GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGG
* *
1753664 GGAAACTGTAAGGCTTACCTTTGTACACAACAAAGGGACATGGG
1 GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGG
* * *
1753708 GGAAACTGTAAGACTTACCTTTGCACACAACAAAGGGACATGGA
1 GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGG
1753752 GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGG
1 GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGG
* *
1753796 GGAAACTGTAAGGCTTACCTTTGTATACAACAAAGGGACCTGGG
1 GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGG
*
1753840 GGAAACTGTAAGGCTTACCTTTGCACACAACAAATGGACCTG
1 GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTG
1753882 CTGTAACAAT
Statistics
Matches: 238, Mismatches: 21, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
43 38 0.16
44 198 0.83
45 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (44 bp):
GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGG
Found at i:1756725 original size:13 final size:13
Alignment explanation
Indices: 1756707--1756738 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1756697 TATGGTCAAC
1756707 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1756720 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1756733 GGTCAA
1 GGTCAA
1756739 GTTAATGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.19, C:0.22, G:0.44, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1758844 original size:87 final size:87
Alignment explanation
Indices: 1758711--1758973 Score: 427
Period size: 87 Copynumber: 3.0 Consensus size: 87
1758701 AGCAAAAGAG
* * * * *
1758711 CCTGAGGAAACTGTAAGGCTTACCCTTGAACACAACAAAGGAACCTGTGGGAAACTGTAAGGCTT
1 CCTGGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGGGGAAACTGTAAGGCTT
1758776 ACCTTTGCACACAACAAAGGGA
66 ACCTTTGCACACAACAAAGGGA
1758798 CCTGGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGGGGAAACTGTAAGGCTT
1 CCTGGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGGGGAAACTGTAAGGCTT
*
1758863 ACTTTTGCACACAACAAAGGGA
66 ACCTTTGCACACAACAAAGGGA
* * *
1758885 CCTGGGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACATGGGGGAAACTTTAAGTCT
1 CCT-GGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGGGGAAACTGTAAGGCT
*
1758950 TACCTTTGCACACAACAAATGGA
65 TACCTTTGCACACAACAAAGGGA
1758973 C
1 C
1758974 ATGCTGTAAC
Statistics
Matches: 164, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
87 84 0.51
88 80 0.49
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.20
Consensus pattern (87 bp):
CCTGGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGGGGAAACTGTAAGGCTT
ACCTTTGCACACAACAAAGGGA
Found at i:1758914 original size:131 final size:132
Alignment explanation
Indices: 1758716--1758973 Score: 428
Period size: 131 Copynumber: 2.0 Consensus size: 132
1758706 AAGAGCCTGA
*
1758716 GGAAACTGTAAGGCTTACCCTTGAACACAACAAAGGAACCTGTGGGAAACTGTAAGGCTTACCTT
1 GGAAACTGTAAGGCTTACCCTTGAACACAACAAAGGAACCTGGGGGAAACTGTAAGGCTTACCTT
*
1758781 TGCACACAACAAAGGGACCT-GGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTG
66 TGCACACAACAAAGGGACATGGGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTG
1758845 GG
131 GG
** * *
1758847 GGAAACTGTAAGGCTTACTTTTGCACACAACAAAGGGACCTGGGGGAAACTGTAAGGCTTACCTT
1 GGAAACTGTAAGGCTTACCCTTGAACACAACAAAGGAACCTGGGGGAAACTGTAAGGCTTACCTT
* * *
1758912 TGCACACAACAAAGGGACATGGGGGAAACTTTAAGTCTTACCTTTGCACACAACAAATGGAC
66 TGCACACAACAAAGGGACATGGGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGAC
1758974 ATGCTGTAAC
Statistics
Matches: 117, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
131 79 0.68
132 38 0.32
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (132 bp):
GGAAACTGTAAGGCTTACCCTTGAACACAACAAAGGAACCTGGGGGAAACTGTAAGGCTTACCTT
TGCACACAACAAAGGGACATGGGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTG
GG
Found at i:1758976 original size:44 final size:44
Alignment explanation
Indices: 1758716--1758973 Score: 428
Period size: 44 Copynumber: 5.9 Consensus size: 44
1758706 AAGAGCCTGA
* * * *
1758716 GGAAACTGTAAGGCTTACCCTTGAACACAACAAAGGAACCTGTG
1 GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGG
1758760 GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCT-GG
1 GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGG
1758803 GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGG
1 GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGG
*
1758847 GGAAACTGTAAGGCTTACTTTTGCACACAACAAAGGGACCTGGG
1 GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGG
*
1758891 GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACATGGG
1 GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGG
* * *
1758935 GGAAACTTTAAGTCTTACCTTTGCACACAACAAATGGAC
1 GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGAC
1758974 ATGCTGTAAC
Statistics
Matches: 203, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
43 42 0.21
44 161 0.79
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (44 bp):
GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGG
Found at i:1763793 original size:44 final size:43
Alignment explanation
Indices: 1763738--1764046 Score: 483
Period size: 44 Copynumber: 7.1 Consensus size: 43
1763728 AGCAAAAGAG
* * * *
1763738 CCTGAGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAA
1 CCTGGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGA
1763781 CCTGTGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGA
1 CCTG-GGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGA
1763825 CCTGGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGA
1 CCTGGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGA
* *
1763868 CCTGGGGAAACTGTAAGGCTTACCTTTGCATACAATAAAGGGA
1 CCTGGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGA
*
1763911 CCTGGGGGAAACTGTAAGGCTTACCTTTGCACACATCAAAGGGA
1 CCT-GGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGA
1763955 CCTGGGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGA
1 CCT-GGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGA
* * * *
1763999 CATGGGGGAAATTGTAAGGCTTACCTTTGCACACAGCAAATGGA
1 CCT-GGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGA
1764043 CCTG
1 CCTG
1764047 CTGTAACGGT
Statistics
Matches: 249, Mismatches: 15, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
43 88 0.35
44 161 0.65
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (43 bp):
CCTGGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGA
Found at i:1763838 original size:87 final size:87
Alignment explanation
Indices: 1763743--1764046 Score: 502
Period size: 87 Copynumber: 3.5 Consensus size: 87
1763733 AAGAGCCTGA
* *
1763743 GGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGTGGGAAACTGTAAGGCTTACCTT
1 GGAAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTG-GGGAAACTGTAAGGCTTACCTT
1763808 TGCACACAACAAAGGGACCT-GG
65 TGCACACAACAAAGGGACCTGGG
*
1763830 GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGGGAAACTGTAAGGCTTACCTTT
1 GGAAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCTTT
* *
1763895 GCATACAATAAAGGGACCTGGG
66 GCACACAACAAAGGGACCTGGG
*
1763917 GGAAACTGTAAGGCTTACCTTTGCACACATCAAAGGGACCTGGGGGAAACTGTAAGGCTTACCTT
1 GGAAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCT-GGGGAAACTGTAAGGCTTACCTT
*
1763982 TGCACACAACAAAGGGACATGGG
65 TGCACACAACAAAGGGACCTGGG
* *
1764005 GGAAATTGTAAGGCTTACCTTTGCACACAGCAAATGGACCTG
1 GGAAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTG
1764047 CTGTAACGGT
Statistics
Matches: 203, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
86 40 0.20
87 82 0.40
88 81 0.40
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (87 bp):
GGAAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCTTT
GCACACAACAAAGGGACCTGGG
Found at i:1768145 original size:29 final size:30
Alignment explanation
Indices: 1768075--1768134 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1768065 CAATTTAAGG
*
1768075 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTAAATTTA
1768106 CAAAATGTTTTTGGACTT-AATTAAATTTA
1 CAAAATGTTTTTGGACTTGAATTAAATTTA
1768135 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 12 0.43
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTAAATTTA
Found at i:1768256 original size:21 final size:21
Alignment explanation
Indices: 1768214--1768353 Score: 69
Period size: 21 Copynumber: 6.8 Consensus size: 21
1768204 AGGGTGTCAA
*
1768214 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCATGC
*
1768235 AGTGCATCCATGCATCGATGC
1 AGTGCATCCATGCATCCATGC
* *
1768256 A-T-CAGGCAATGCATCCATGC
1 AGTGCA-TCCATGCATCCATGC
* ** * * *
1768276 A-TCCAAACATCGAATACAAT-T
1 AGTGCATCCAT-GCAT-CCATGC
* *
1768297 AGTGCATCGATGCATCCTTGCC
1 AGTGCATCCATGCATCCATG-C
*
1768319 A-TGCATCGATGCATCC-TGCC
1 AGTGCATCCATGCATCCATG-C
1768339 A-TGCATCCATGCATC
1 AGTGCATCCATGCATC
1768354 AAGGCTGCAA
Statistics
Matches: 92, Mismatches: 20, Indels: 15
0.72 0.16 0.12
Matches are distributed among these distances:
19 2 0.02
20 37 0.40
21 44 0.48
22 9 0.10
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATGCATCCATGC
Found at i:1768340 original size:20 final size:21
Alignment explanation
Indices: 1768299--1768353 Score: 94
Period size: 20 Copynumber: 2.7 Consensus size: 21
1768289 ATACAATTAG
1768299 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
1768320 TGCATCGATGCATCC-TGCCA
1 TGCATCGATGCATCCTTGCCA
*
1768340 TGCATCCATGCATC
1 TGCATCGATGCATC
1768354 AAGGCTGCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 18 0.55
21 15 0.45
ACGTcount: A:0.20, C:0.35, G:0.18, T:0.27
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCCA
Found at i:1768757 original size:34 final size:32
Alignment explanation
Indices: 1768718--1768787 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1768708 TTTTGTAAAG
* *
1768718 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1768752 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1768784 GGGA
1 GGGA
1768788 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1769672 original size:19 final size:20
Alignment explanation
Indices: 1769648--1769695 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1769638 AATGATTTTC
*
1769648 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
1769667 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
1769687 TTTTGAAAA
1 TTTTGAAAA
1769696 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:1770868 original size:21 final size:21
Alignment explanation
Indices: 1770842--1770881 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1770832 CAACAATTGG
1770842 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
*
1770863 TAACAATTGATATCTTTTT
1 TAACAATTGATATCATTTT
1770882 CATTAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:1771021 original size:34 final size:30
Alignment explanation
Indices: 1770983--1771051 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
1770973 TTGATATAAC
1770983 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
1771017 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
1771046 AATTTA
1 AATTTA
1771052 TTCAATGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:1771062 original size:29 final size:30
Alignment explanation
Indices: 1770992--1771051 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1770982 CAATTTAAGG
1770992 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1771023 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1771052 TTCAATGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1771176 original size:21 final size:21
Alignment explanation
Indices: 1771131--1771184 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1771121 AGGGTGTCAA
*
1771131 AGTGCATCTATGCATCCCTAC
1 AGTGCATCCATGCATCCCTAC
* **
1771152 AGTGCATCCATGCATCCTTGT
1 AGTGCATCCATGCATCCCTAC
1771173 AGTGCATCCATG
1 AGTGCATCCATG
1771185 TATCTGCACT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.30
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTAC
Found at i:1771292 original size:20 final size:20
Alignment explanation
Indices: 1771251--1771325 Score: 123
Period size: 20 Copynumber: 3.7 Consensus size: 20
1771241 ATGCAATTAG
1771251 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCC-TGCCA
1771272 TGCATCGATGCATCCTGCCA
1 TGCATCGATGCATCCTGCCA
*
1771292 TGTATCGATGCATCCTGCCA
1 TGCATCGATGCATCCTGCCA
*
1771312 TGCATCCATGCATC
1 TGCATCGATGCATC
1771326 AAGTCTGCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 36 0.71
21 15 0.29
ACGTcount: A:0.20, C:0.33, G:0.19, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCATCCTGCCA
Found at i:1771729 original size:34 final size:32
Alignment explanation
Indices: 1771690--1771759 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1771680 TTTTGTAAAG
* *
1771690 GGGAAATGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTATCCCG-G-AAAAACTA
*
1771724 GGGAAAGGTTCTAGTTTATCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTATCCCGGAAAAACTA
1771756 GGGA
1 GGGA
1771760 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTATCCCGGAAAAACTA
Found at i:1772645 original size:87 final size:87
Alignment explanation
Indices: 1772507--1772801 Score: 416
Period size: 87 Copynumber: 3.4 Consensus size: 87
1772497 GCAAAAACGA
* * * *
1772507 TAAGGTCTTATCC-TTGCACATAGCAAA-AGAGCCTGAGGAAACTGTAAGGCTTACAC-TTGTAC
1 TAAGG-CTTA-CCTTTGCACACAGCAAAGGGA-CCTGGGGAAACTGTAAGGCTTAC-CTTTGCAC
* *
1772569 ACAACAAAGGAACCTGTGGGAAACTG
62 ACAACAAAGGGACCTGGGGGAAACTG
* *
1772595 TAAGGCTTACCTTTTCACACAACAAAGGGACCTGGGGAAACTGTAAGGCTTACCTTTGCACACAA
1 TAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCTTTGCACACAA
*
1772660 CAAAGGGACCTGGGGGAAATTG
66 CAAAGGGACCTGGGGGAAACTG
* *
1772682 TAAGGCTTACCTTTGCACACAGCAAAGGTACCTGGGGAAACTGTAAGGCATACCTTTGCACACAA
1 TAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCTTTGCACACAA
*
1772747 CAAAGGGACATGGGGGAAACTG
66 CAAAGGGACCTGGGGGAAACTG
*
1772769 TAAGGCTTACCTTTGCACACAGCAAATGGACCT
1 TAAGGCTTACCTTTGCACACAGCAAAGGGACCT
1772802 ACTGTAACGG
Statistics
Matches: 187, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
86 3 0.02
87 177 0.95
88 7 0.04
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (87 bp):
TAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCTTTGCACACAA
CAAAGGGACCTGGGGGAAACTG
Found at i:1772647 original size:43 final size:43
Alignment explanation
Indices: 1772538--1772801 Score: 386
Period size: 44 Copynumber: 6.1 Consensus size: 43
1772528 AGCAAAAGAG
* * *
1772538 CCTGAGGAAACTGTAAGGCTTACAC-TTGTACACAACAAAGGAA
1 CCTGGGGAAACTGTAAGGCTTAC-CTTTGCACACAACAAAGGGA
*
1772581 CCTGTGGGAAACTGTAAGGCTTACCTTTTCACACAACAAAGGGA
1 CCTG-GGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGA
1772625 CCTGGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGA
1 CCTGGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGA
* * *
1772668 CCTGGGGGAAATTGTAAGGCTTACCTTTGCACACAGCAAAGGTA
1 CCT-GGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGA
*
1772712 CCTGGGGAAACTGTAAGGCATACCTTTGCACACAACAAAGGGA
1 CCTGGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGA
* * *
1772755 CATGGGGGAAACTGTAAGGCTTACCTTTGCACACAGCAAATGGA
1 CCT-GGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGA
1772799 CCT
1 CCT
1772802 ACTGTAACGG
Statistics
Matches: 200, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
43 84 0.42
44 116 0.58
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (43 bp):
CCTGGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGA
Found at i:1777675 original size:44 final size:43
Alignment explanation
Indices: 1777627--1777872 Score: 357
Period size: 44 Copynumber: 5.6 Consensus size: 43
1777617 AAGAGCTTGA
* *
1777627 GGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGTG
1 GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTG-G
*
1777671 GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACTTGG
1 GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGG
* * *
1777714 GGAAACTGTAAGGCTTATCTTTGTACACAACAAATGGACCTGG
1 GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGG
** *
1777757 GGAAAACTGTAAGGCTTACCTTTTTACACAGCAAAGGGACCTGGG
1 GG-AAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCT-GG
* *
1777802 GGAAACTGTAAGGCTTACTTTTGCACACAACAAAGGGACATGGG
1 GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCT-GG
1777846 GGAAACTGTAAGGCTTACCTTTGCACA
1 GGAAACTGTAAGGCTTACCTTTGCACA
1777873 TAGCAAATGG
Statistics
Matches: 183, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
43 42 0.23
44 137 0.75
45 4 0.02
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.22
Consensus pattern (43 bp):
GGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGG
Found at i:1777695 original size:87 final size:85
Alignment explanation
Indices: 1777591--1777879 Score: 339
Period size: 87 Copynumber: 3.3 Consensus size: 85
1777581 GCAAAAACGA
* * *
1777591 TAAGGTCTTATCC-TTGCACATAGCAAAAGAGCTTGAGGAAACTGTAAGGCTTACCCTTGCACAC
1 TAAGG-CTTA-CCTTTGCACACAGCAAAAGAGCTTGGGGAAACTGTAAGGCTTACCTTTGCACAC
1777655 AACAAAGGAACCTGTGGGAAACTG
64 AACAAAGG-ACCTG-GGGAAACTG
* * * *
1777679 TAAGGCTTACCTTTGCACACAAC-AAAGGGACTTGGGGAAACTGTAAGGCTTATCTTTGTACACA
1 TAAGGCTTACCTTTGCACACAGCAAAAGAG-CTTGGGGAAACTGTAAGGCTTACCTTTGCACACA
1777743 ACAAATGGACCTGGGGAAAACTG
65 ACAAA-GGACCTGGGG-AAACTG
** * * * *
1777766 TAAGGCTTACCTTTTTACACAGCAAAGGGACCTGGGGGAAACTGTAAGGCTTACTTTTGCACACA
1 TAAGGCTTACCTTTGCACACAGCAAA-AGAGCTTGGGGAAACTGTAAGGCTTACCTTTGCACACA
*
1777831 ACAAAGGGACATGGGGGAAACTG
65 ACAAA-GGACCT-GGGGAAACTG
*
1777854 TAAGGCTTACCTTTGCACATAGCAAA
1 TAAGGCTTACCTTTGCACACAGCAAA
1777880 TGGACCCGCA
Statistics
Matches: 172, Mismatches: 22, Indels: 14
0.83 0.11 0.07
Matches are distributed among these distances:
86 10 0.06
87 79 0.46
88 78 0.45
89 5 0.03
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.22
Consensus pattern (85 bp):
TAAGGCTTACCTTTGCACACAGCAAAAGAGCTTGGGGAAACTGTAAGGCTTACCTTTGCACACAA
CAAAGGACCTGGGGAAACTG
Found at i:1777799 original size:131 final size:132
Alignment explanation
Indices: 1777629--1777885 Score: 399
Period size: 131 Copynumber: 2.0 Consensus size: 132
1777619 GAGCTTGAGG
*
1777629 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGTGGGAAACTGTAAGGCTTACCTTTG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGGAAACTGTAAGGCTTACCTTTG
* * *
1777694 CACACAACAAAGGGAC-TTGGGGAAACTGTAAGGCTTATCTTTGTACACAACAAATGGACCTGGG
66 CACACAACAAAGGGACATGGGGGAAACTGTAAGGCTTACCTTTGCACACAACAAATGGACCTGGG
1777758 GA
131 GA
* ** * * *
1777760 AAACTGTAAGGCTTACCTTTTTACACAGCAAAGGGACCTGGGGGAAACTGTAAGGCTTACTTTTG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGGAAACTGTAAGGCTTACCTTTG
* *
1777825 CACACAACAAAGGGACATGGGGGAAACTGTAAGGCTTACCTTTGCACATAGCAAATGGACC
66 CACACAACAAAGGGACATGGGGGAAACTGTAAGGCTTACCTTTGCACACAACAAATGGACC
1777886 CGCAGTAACG
Statistics
Matches: 113, Mismatches: 12, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
131 74 0.65
132 39 0.35
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (132 bp):
AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGGAAACTGTAAGGCTTACCTTTG
CACACAACAAAGGGACATGGGGGAAACTGTAAGGCTTACCTTTGCACACAACAAATGGACCTGGG
GA
Done.