Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007733.1 Hibiscus syriacus cultivar Beakdansim tig00109987_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: 1979160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1745084 original size:19 final size:19
Alignment explanation
Indices: 1745060--1745333 Score: 354
Period size: 19 Copynumber: 15.4 Consensus size: 19
1745050 GATTATCTCG
1745060 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1745079 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1745098 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
1745112 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1745131 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1745150 TTGCGATTTCCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1745169 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1745188 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1745207 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1745221 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1745240 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1745259 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1745273 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1745293 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
1745307 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1745326 TTGCGATT
1 TTGCGATT
1745334 GTATTTTCCG
Statistics
Matches: 226, Mismatches: 8, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 29 0.13
16 24 0.11
17 21 0.09
18 3 0.01
19 137 0.61
20 12 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1745100 original size:52 final size:52
Alignment explanation
Indices: 1745038--1745305 Score: 455
Period size: 52 Copynumber: 5.0 Consensus size: 52
1745028 TGCGTTTATA
*
1745038 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1745090 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1745142 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TT-C-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1745199 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1745251 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
1745304 AT
1 AT
1745306 GTTGGGATTT
Statistics
Matches: 207, Mismatches: 3, Indels: 11
0.94 0.01 0.05
Matches are distributed among these distances:
52 131 0.63
53 19 0.09
54 5 0.02
55 6 0.03
56 2 0.01
57 44 0.21
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1745189 original size:109 final size:105
Alignment explanation
Indices: 1745038--1745305 Score: 459
Period size: 109 Copynumber: 2.5 Consensus size: 105
1745028 TGCGTTTATA
1745038 ATTTCGCATTGCGATT-ATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
1 ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
*
1745102 GATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
66 GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1745142 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 ATTTCGCATTGCGA-TT-CATCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1745207 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
62 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1745251 ATTTCGCATTGCGATTC-TCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCAT
1745306 GTTGGGATTT
Statistics
Matches: 155, Mismatches: 3, Indels: 11
0.92 0.02 0.07
Matches are distributed among these distances:
104 29 0.19
105 19 0.12
106 4 0.03
107 6 0.04
108 2 0.01
109 95 0.61
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (105 bp):
ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1748557 original size:20 final size:20
Alignment explanation
Indices: 1748529--1748918 Score: 457
Period size: 20 Copynumber: 19.4 Consensus size: 20
1748519 AAATTTCAGT
* * * *
1748529 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1748549 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1748569 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1748589 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1748609 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1748629 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1748649 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1748669 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1748689 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1748709 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1748729 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
1748749 GTTGCGATTTTATGTATTA-TC
1 GTTGCGA-TTTACGGA-TACGC
1748770 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1748790 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
1748810 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
1748830 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1748850 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1748870 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
1748890 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
1748910 GTTGCGATT
1 GTTGCGATT
1748919 ATTGAAAATC
Statistics
Matches: 323, Mismatches: 36, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
19 7 0.02
20 295 0.91
21 19 0.06
22 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1749543 original size:6 final size:6
Alignment explanation
Indices: 1749532--1749564 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1749522 TGGGTTTATT
1749532 GGGAGG GGGAGG GGGAGG GGGAGG GGGAGG GGG
1 GGGAGG GGGAGG GGGAGG GGGAGG GGGAGG GGG
1749565 GAATTTAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.85, T:0.00
Consensus pattern (6 bp):
GGGAGG
Found at i:1752825 original size:19 final size:20
Alignment explanation
Indices: 1752803--1752842 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1752793 GTTTAGATTC
*
1752803 TTTTCAATTTTA-TTTATTA
1 TTTTAAATTTTATTTTATTA
1752822 TTTTAAATTTTATTTTATTA
1 TTTTAAATTTTATTTTATTA
1752842 T
1 T
1752843 AATCTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTAAATTTTATTTTATTA
Found at i:1756426 original size:17 final size:17
Alignment explanation
Indices: 1756404--1756441 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1756394 TACCCGATTA
1756404 CCGGGTACCCGCAAAAT
1 CCGGGTACCCGCAAAAT
* *
1756421 CCGGGTACCCGTAACAT
1 CCGGGTACCCGCAAAAT
1756438 CCGG
1 CCGG
1756442 ATCGAAACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.37, G:0.26, T:0.13
Consensus pattern (17 bp):
CCGGGTACCCGCAAAAT
Found at i:1756517 original size:16 final size:16
Alignment explanation
Indices: 1756479--1756521 Score: 79
Period size: 15 Copynumber: 2.8 Consensus size: 16
1756469 ACCTGGAAGT
1756479 TCCGGGTACCCGAAAA
1 TCCGGGTACCCGAAAA
1756495 TCC-GGTACCCGAAAA
1 TCCGGGTACCCGAAAA
1756510 TCCGGGTACCCG
1 TCCGGGTACCCG
1756522 GATTTGCACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.26, C:0.35, G:0.26, T:0.14
Consensus pattern (16 bp):
TCCGGGTACCCGAAAA
Found at i:1757271 original size:18 final size:17
Alignment explanation
Indices: 1757239--1757280 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
1757229 AAACTTATTG
1757239 AAAAATAAAAAATAA-A
1 AAAAATAAAAAATAATA
*
1757255 AGAAAATAAAAGGATAATA
1 A-AAAATAAAA-AATAATA
1757274 AAAAATA
1 AAAAATA
1757281 TCGATAATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 9 0.41
18 10 0.45
19 2 0.09
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (17 bp):
AAAAATAAAAAATAATA
Found at i:1767826 original size:30 final size:30
Alignment explanation
Indices: 1767790--1767850 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
1767780 AAACTGGAAG
1767790 GGGGCCAGTGATCATCAGCTGCCGTTTAAC
1 GGGGCCAGTGATCATCAGCTGCCGTTTAAC
1767820 GGGGCCAGTGATCATCAGCTGCCGTTTAAC
1 GGGGCCAGTGATCATCAGCTGCCGTTTAAC
1767850 G
1 G
1767851 AGTATGGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.20, C:0.26, G:0.31, T:0.23
Consensus pattern (30 bp):
GGGGCCAGTGATCATCAGCTGCCGTTTAAC
Found at i:1773151 original size:4 final size:4
Alignment explanation
Indices: 1773142--1773168 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1773132 GTTTTTGCTC
1773142 TTCT TTCT TTCT TTCT TTCT TTCT TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT TTC
1773169 AACGAAGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTCT
Found at i:1773463 original size:19 final size:19
Alignment explanation
Indices: 1773430--1773505 Score: 88
Period size: 19 Copynumber: 4.2 Consensus size: 19
1773420 AATTTATCAA
* *
1773430 TAAAATATA-TAAAAAACT
1 TAAATTATATTAAAAAAAT
1773448 TAAATTATATTAAAAAAAT
1 TAAATTATATTAAAAAAAT
* *
1773467 TAAA--A-AATAAAAAACT
1 TAAATTATATTAAAAAAAT
1773483 TAAATTATATTAAAAAAAT
1 TAAATTATATTAAAAAAAT
1773502 TAAA
1 TAAA
1773506 AAATTTAGGA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
16 13 0.27
17 1 0.02
18 9 0.19
19 25 0.52
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (19 bp):
TAAATTATATTAAAAAAAT
Found at i:1773468 original size:9 final size:9
Alignment explanation
Indices: 1773456--1773508 Score: 56
Period size: 9 Copynumber: 6.0 Consensus size: 9
1773446 CTTAAATTAT
1773456 ATTAAAAAA
1 ATTAAAAAA
1773465 ATT-AAAAA
1 ATTAAAAAA
1773473 A-TAAAAAA
1 ATTAAAAAA
* * *
1773481 CTTAAATTAT
1 ATTAAA-AAA
1773491 ATTAAAAAA
1 ATTAAAAAA
1773500 ATTAAAAAA
1 ATTAAAAAA
1773509 TTTAGGAAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
7 1 0.03
8 11 0.31
9 17 0.49
10 6 0.17
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (9 bp):
ATTAAAAAA
Found at i:1773477 original size:7 final size:8
Alignment explanation
Indices: 1773460--1773510 Score: 50
Period size: 8 Copynumber: 6.0 Consensus size: 8
1773450 AATTATATTA
1773460 AAAAAATT
1 AAAAAATT
1773468 AAAAAA-T
1 AAAAAATT
1773475 AAAAAACTT
1 AAAAAA-TT
*
1773484 AAATTATATT
1 AAA--AAATT
1773494 AAAAAAATT
1 -AAAAAATT
1773503 AAAAAATT
1 AAAAAATT
1773511 TAGGAAACGA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
7 7 0.19
8 14 0.39
9 8 0.22
10 2 0.06
11 5 0.14
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (8 bp):
AAAAAATT
Found at i:1773478 original size:35 final size:35
Alignment explanation
Indices: 1773438--1773509 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
1773428 AATAAAATAT
1773438 ATAAAAAACTTAAATTATATTAAAAAAATTAAAAA
1 ATAAAAAACTTAAATTATATTAAAAAAATTAAAAA
1773473 ATAAAAAACTTAAATTATATTAAAAAAATTAAAAA
1 ATAAAAAACTTAAATTATATTAAAAAAATTAAAAA
1773508 AT
1 AT
1773510 TTAGGAAACG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (35 bp):
ATAAAAAACTTAAATTATATTAAAAAAATTAAAAA
Found at i:1774762 original size:29 final size:29
Alignment explanation
Indices: 1774729--1774813 Score: 143
Period size: 29 Copynumber: 2.9 Consensus size: 29
1774719 TCCCAACACA
*
1774729 TAGGTCGCCATGCCCTCAGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
*
1774758 TAGGTCGTCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
*
1774787 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCCCTCCGGGCGACCT
1774814 ACCCTCGCTC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.13, C:0.35, G:0.31, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCGGGCGACCTTG
Found at i:1774864 original size:33 final size:32
Alignment explanation
Indices: 1774817--1774910 Score: 107
Period size: 33 Copynumber: 2.8 Consensus size: 32
1774807 GCGACCTACC
* *
1774817 CTCGCTCGGCTGCCCTCGGATTCCCTCGCATAG
1 CTCGCTC-GATGCCCTCGGATGCCCTCGCATAG
*
1774850 CTCGCTCGATTGCCCTCCGATGCCCTCGCATAG
1 CTCGCTCGA-TGCCCTCGGATGCCCTCGCATAG
* * *
1774883 CTCGTTCGGATGGCCTCGGATGCTCTCG
1 CTCGCTC-GATGCCCTCGGATGCCCTCG
1774911 GATGACCTCG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
32 1 0.02
33 49 0.94
34 2 0.04
ACGTcount: A:0.10, C:0.39, G:0.26, T:0.26
Consensus pattern (32 bp):
CTCGCTCGATGCCCTCGGATGCCCTCGCATAG
Found at i:1774899 original size:23 final size:20
Alignment explanation
Indices: 1774868--1774925 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
1774858 ATTGCCCTCC
*
1774868 GATGCCCTCGCATAGCTCGTTCG
1 GATGACCTCGCAT-GCTC--TCG
* *
1774891 GATGGCCTCGGATGCTCTCG
1 GATGACCTCGCATGCTCTCG
*
1774911 GATGACCTCGGATGC
1 GATGACCTCGCATGC
1774926 CCAGCGTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.53
22 4 0.12
23 11 0.34
ACGTcount: A:0.14, C:0.31, G:0.31, T:0.24
Consensus pattern (20 bp):
GATGACCTCGCATGCTCTCG
Found at i:1774913 original size:20 final size:20
Alignment explanation
Indices: 1774888--1774925 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1774878 CATAGCTCGT
*
1774888 TCGGATGGCCTCGGATGCTC
1 TCGGATGACCTCGGATGCTC
1774908 TCGGATGACCTCGGATGC
1 TCGGATGACCTCGGATGC
1774926 CCAGCGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.29, G:0.34, T:0.24
Consensus pattern (20 bp):
TCGGATGACCTCGGATGCTC
Found at i:1775001 original size:29 final size:29
Alignment explanation
Indices: 1774964--1775021 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
1774954 GCAATCTCTT
*
1774964 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
* *
1774993 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
1775022 CGACCAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.28, G:0.36, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGGCGACCTA
Found at i:1775038 original size:22 final size:22
Alignment explanation
Indices: 1775010--1775052 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1775000 GCCCGGAAGG
1775010 CATGGCGACCTACGACCAACAC
1 CATGGCGACCTACGACCAACAC
1775032 CATGGCGACCTACGACCAACA
1 CATGGCGACCTACGACCAACA
1775053 TTGTGGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.40, G:0.19, T:0.09
Consensus pattern (22 bp):
CATGGCGACCTACGACCAACAC
Found at i:1779918 original size:31 final size:31
Alignment explanation
Indices: 1779880--1779956 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
1779870 GTTAACTTGG
*
1779880 AGTGACCACATCTTAATTAAATAAAAAAGAA
1 AGTGACCATATCTTAATTAAATAAAAAAGAA
*
1779911 AGTGACCATATCTTAATTAAATAAAAACGAA
1 AGTGACCATATCTTAATTAAATAAAAAAGAA
*
1779942 AGTGATCATATCTTA
1 AGTGACCATATCTTA
1779957 TGTTTATTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.27
Consensus pattern (31 bp):
AGTGACCATATCTTAATTAAATAAAAAAGAA
Found at i:1780890 original size:86 final size:85
Alignment explanation
Indices: 1780789--1780945 Score: 269
Period size: 86 Copynumber: 1.8 Consensus size: 85
1780779 TATTAAAAAC
* * *
1780789 ACTTCAAATGCAACTAAAACAATAAAAAATTGTATGAACAATTTTGAATTGTATGAGATATTAGA
1 ACTTCAAATGCAACTAAAACAATAAAAAATAGTATGAACAATATTGAATTGCATGAGATATTAGA
1780854 GTCCCTAGACGACTTCAACG
66 GTCCCTAGACGACTTCAACG
*
1780874 ACTTCAAAATGCAACTAAAACAATAAAAAATAGTATGAACAGTATTGAATTGCATGAGATATTAG
1 ACTTC-AAATGCAACTAAAACAATAAAAAATAGTATGAACAATATTGAATTGCATGAGATATTAG
1780939 AGTCCCT
65 AGTCCCT
1780946 CGACCACTAT
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
85 5 0.07
86 62 0.93
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (85 bp):
ACTTCAAATGCAACTAAAACAATAAAAAATAGTATGAACAATATTGAATTGCATGAGATATTAGA
GTCCCTAGACGACTTCAACG
Found at i:1781890 original size:31 final size:32
Alignment explanation
Indices: 1781848--1781909 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
1781838 ATGGGGTAAA
1781848 ATATGTGTTTAGTACATAAACTATT-AATTTTG
1 ATATGTGTTTAGTACATAAACT-TTCAATTTTG
*
1781880 ATATGT-TTTAGTACTTAAACTTTCAATTTT
1 ATATGTGTTTAGTACATAAACTTTCAATTTT
1781910 TTCAAAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 2 0.07
31 20 0.71
32 6 0.21
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.50
Consensus pattern (32 bp):
ATATGTGTTTAGTACATAAACTTTCAATTTTG
Found at i:1782140 original size:39 final size:39
Alignment explanation
Indices: 1782097--1782179 Score: 148
Period size: 39 Copynumber: 2.1 Consensus size: 39
1782087 CTCATGATTT
1782097 TATCAAAACCATGATAAACAATATCATACATAATAGTCA
1 TATCAAAACCATGATAAACAATATCATACATAATAGTCA
* *
1782136 TATCAAAGCCATGATAAACAATATTATACATAATAGTCA
1 TATCAAAACCATGATAAACAATATCATACATAATAGTCA
1782175 TATCA
1 TATCA
1782180 TATTCTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.28
Consensus pattern (39 bp):
TATCAAAACCATGATAAACAATATCATACATAATAGTCA
Found at i:1782248 original size:12 final size:12
Alignment explanation
Indices: 1782209--1782252 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
1782199 ACAATACAAA
1782209 ACTTTCATATCTC
1 ACTTTCATAT-TC
*
1782222 A-TTTGCATTTTC
1 ACTTT-CATATTC
1782234 ACTTTCATATTC
1 ACTTTCATATTC
1782246 ACTTTCA
1 ACTTTCA
1782253 CATTTTAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 19 0.70
13 8 0.30
ACGTcount: A:0.23, C:0.25, G:0.02, T:0.50
Consensus pattern (12 bp):
ACTTTCATATTC
Found at i:1784858 original size:30 final size:30
Alignment explanation
Indices: 1784797--1784863 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
1784787 TCAAAAACCT
*
1784797 AACTTTTAAAAAGTACACTTTTGGTCACTA
1 AACTTTTAAAAAGTACACTTTTAGTCACTA
* * *
1784827 AACTTTTGAAAATTAC-CTTTTTAGTCCCTA
1 AACTTTTAAAAAGTACAC-TTTTAGTCACTA
*
1784857 AATTTTT
1 AACTTTT
1784864 TTAAACTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.43
Consensus pattern (30 bp):
AACTTTTAAAAAGTACACTTTTAGTCACTA
Found at i:1786669 original size:12 final size:12
Alignment explanation
Indices: 1786652--1786687 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
1786642 ACCTAACTCC
1786652 TTATTCATACAT
1 TTATTCATACAT
1786664 TTATTCATACAT
1 TTATTCATACAT
1786676 TTATTCATACAT
1 TTATTCATACAT
1786688 GTGTAGTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (12 bp):
TTATTCATACAT
Found at i:1786732 original size:3 final size:3
Alignment explanation
Indices: 1786724--1786775 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
1786714 TTTTAACGTA
1786724 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1786772 TAT T
1 TAT T
1786776 TATAAACTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1786847 original size:13 final size:14
Alignment explanation
Indices: 1786814--1786849 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1786804 CAATTACATG
*
1786814 AAATCCTAAACCCT
1 AAATTCTAAACCCT
1786828 AAATTCTAAACCCT
1 AAATTCTAAACCCT
1786842 -AATTCTAA
1 AAATTCTAA
1786850 TGTGCTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (14 bp):
AAATTCTAAACCCT
Found at i:1787893 original size:10 final size:10
Alignment explanation
Indices: 1787870--1787905 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
1787860 TATCTTTTAT
*
1787870 ATTTAATTTTA
1 ATTT-ATTTCA
1787881 ATTTATTTCA
1 ATTTATTTCA
1787891 ATTTATTTCA
1 ATTTATTTCA
1787901 ATTTA
1 ATTTA
1787906 GTCACCGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 20 0.83
11 4 0.17
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (10 bp):
ATTTATTTCA
Found at i:1789813 original size:2 final size:2
Alignment explanation
Indices: 1789806--1789843 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1789796 TTAGGTGGAG
1789806 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
1789844 TCGGATCGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1807956 original size:20 final size:19
Alignment explanation
Indices: 1807927--1807964 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
1807917 CCACATCAGT
1807927 CAGAGGGTATCGATACCAG
1 CAGAGGGTATCGATACCAG
1807946 CAGATGGGTATCGATACCA
1 CAGA-GGGTATCGATACCA
1807965 AAGGTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.32, C:0.21, G:0.29, T:0.18
Consensus pattern (19 bp):
CAGAGGGTATCGATACCAG
Found at i:1808666 original size:19 final size:19
Alignment explanation
Indices: 1808642--1808682 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1808632 TTCAGAGTAC
1808642 GACTTGAGTTATCTTAGAG
1 GACTTGAGTTATCTTAGAG
1808661 GACTTGAGTTATCTTAGAG
1 GACTTGAGTTATCTTAGAG
1808680 GAC
1 GAC
1808683 ATGTACTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (19 bp):
GACTTGAGTTATCTTAGAG
Found at i:1809785 original size:26 final size:25
Alignment explanation
Indices: 1809743--1809792 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
1809733 ATCAATTTTC
*
1809743 GCTCTCTCTAAATTTTTATAAGTTT
1 GCTCTCTCTAAAATTTTATAAGTTT
*
1809768 GCTCTCCTTTAAAATTTTATAAGTT
1 GCTCT-CTCTAAAATTTTATAAGTT
1809793 CACCCCCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.26, C:0.16, G:0.08, T:0.50
Consensus pattern (25 bp):
GCTCTCTCTAAAATTTTATAAGTTT
Found at i:1816902 original size:40 final size:37
Alignment explanation
Indices: 1816836--1816916 Score: 108
Period size: 40 Copynumber: 2.1 Consensus size: 37
1816826 AAACTAACAT
1816836 TAAATTTTGAACGGAGGTACTAAAATGAAACAAAAAC
1 TAAATTTTGAACGGAGGTACTAAAATGAAACAAAAAC
* * *
1816873 TAAAGTTTTTAACGGCAGGGTATTAAAATGGAACAAAAAC
1 TAAA-TTTTGAACGG-A-GGTACTAAAATGAAACAAAAAC
1816913 TAAA
1 TAAA
1816917 CTTTAGATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 4 0.11
38 9 0.24
39 1 0.03
40 24 0.63
ACGTcount: A:0.49, C:0.10, G:0.17, T:0.23
Consensus pattern (37 bp):
TAAATTTTGAACGGAGGTACTAAAATGAAACAAAAAC
Found at i:1828551 original size:2 final size:2
Alignment explanation
Indices: 1828544--1828585 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1828534 GATGTGTTGT
1828544 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1828586 ATTTCAAGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1831461 original size:61 final size:60
Alignment explanation
Indices: 1831345--1831513 Score: 137
Period size: 61 Copynumber: 2.8 Consensus size: 60
1831335 CGTATAGTTT
* * * * ** * * ** * *
1831345 GGGATAAAATTAGAATGTTCAGAAAGTTTGGAGATTAATTTAGAACGAATGTCATAGTTTG
1 GGGATGAAATTAGAATATTTA-AAAGTTTAGAGACCAATTTAAAATGAAAATCATAATTTA
* *
1831406 GGGAATGAAATT-GAA-ATGTTCAAAAGTTTTA-TGACTAATTTAAAATGAAAATCATAATTTA
1 GGG-ATGAAATTAGAATAT-TT-AAAAG-TTTAGAGACCAATTTAAAATGAAAATCATAATTTA
*
1831467 TGGATGAAATTAGAATATTTAAAAGTTTAGAGACCAATTTAAAATGA
1 GGGATGAAATTAGAATATTTAAAAGTTTAGAGACCAATTTAAAATGA
1831514 GAGTCGTACT
Statistics
Matches: 86, Mismatches: 15, Indels: 15
0.74 0.13 0.13
Matches are distributed among these distances:
59 4 0.05
60 29 0.34
61 40 0.47
62 13 0.15
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.33
Consensus pattern (60 bp):
GGGATGAAATTAGAATATTTAAAAGTTTAGAGACCAATTTAAAATGAAAATCATAATTTA
Found at i:1843971 original size:156 final size:149
Alignment explanation
Indices: 1843718--1843997 Score: 339
Period size: 156 Copynumber: 1.8 Consensus size: 149
1843708 AAATTGAAGG
*
1843718 AATAATGAGATTATGAAAAATTAAAGGACTAAATTGAAAAAAAATTATCAAAAAGAGGAATTGAA
1 AATAAAGAGATTATGAAAAATTAAAGGACTAAATTGAAAAAAAATTATCAAAAAGAGGAATTGAA
* * *
1843783 AATACATATTTATTCTACTATAGTTTAGGAGCA-TAACTCAAATTTGGTATAAAAAAATTAAAAT
66 AATACACATGTATTCTACTATAGTTTAGGAGCAGTAACTCAAATTTGATA-AAAAAAATTAAAAT
1843847 AAATGACGAATTGAAAAATA
130 AAATGACGAATTGAAAAATA
* * * **
1843867 AATAAAGAGATTATGAAAAATTGAAGGACTACATTGAAAAATAAAAAATTGCTGTCAAAAAGATT
1 AATAAAGAGATTATGAAAAATTAAAGGACTAAATTG---AA-AAAAAA-T--TATCAAAAAGAGG
* * * *
1843932 AATTGAAAGTATACATGTATTCTATTAT-GATTTAGGAGCATGTAATTCAAATTTGATAAAAAAA
59 AATTGAAAATACACATGTATTCTACTATAG-TTTAGGAGCA-GTAACTCAAATTTGATAAAAAAA
1843996 AT
122 AT
1843998 AGACTTAAAA
Statistics
Matches: 108, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
149 33 0.31
152 2 0.02
153 6 0.06
154 1 0.01
155 1 0.01
156 43 0.40
157 8 0.07
158 14 0.13
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (149 bp):
AATAAAGAGATTATGAAAAATTAAAGGACTAAATTGAAAAAAAATTATCAAAAAGAGGAATTGAA
AATACACATGTATTCTACTATAGTTTAGGAGCAGTAACTCAAATTTGATAAAAAAAATTAAAATA
AATGACGAATTGAAAAATA
Found at i:1844968 original size:55 final size:55
Alignment explanation
Indices: 1844815--1845211 Score: 392
Period size: 55 Copynumber: 7.2 Consensus size: 55
1844805 AGAGTAGTGA
* * * * *
1844815 AGCAAACCTGTTTATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAG
1 AGCAGACCCGTTTATTGAAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGG
** * * *
1844870 AGTGGACCCGTTTTATTGAAGATTGTTCGAGTTCTATAATCTCTGAAGGAATAGAG
1 AGCAGACCCG-TTTATTGAAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGG
* * * * * *
1844926 AGCAGACTCGTTTGTTGAAGATTGTTCGAGTTCCATACTCTCTGGTA-GAATAGAG
1 AGCAGACCCGTTTATTGAAGATTGTTCGAGTTCTATACTCCCT-GAAGGAATAGGG
* *
1844981 AGCGGACCCGTTT-TATGAAGATTGTTCGAGTTCTATACTCCCTGAACGAATAGGG
1 AGCAGACCCGTTTAT-TGAAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGG
** * *
1845036 AGTGGACCCGTTTATTGAAGATTGATT-GAG-TCTTATACTCCCTAAATGAATAGGG
1 AGCAGACCCGTTTATTGAAGATTG-TTCGAGTTC-TATACTCCCTGAAGGAATAGGG
* * * * * *
1845091 AGCAGACACGCTTGTTGAAGATTGATCGAG-TCTTATACTCCCTTAATGAATAGGG
1 AGCAGACCCGTTTATTGAAGATTGTTCGAGTTC-TATACTCCCTGAAGGAATAGGG
* ** * *
1845146 AGCAGACACGTTTGCTGAAGATTGGTCGAG-TCTTATACTCCCTGAAGGGATAGGG
1 AGCAGACCCGTTTATTGAAGATTGTTCGAGTTC-TATACTCCCTGAAGGAATAGGG
1845201 AGCAGACCCGT
1 AGCAGACCCGT
1845212 CATTCGAAGA
Statistics
Matches: 298, Mismatches: 36, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
54 6 0.02
55 237 0.80
56 55 0.18
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (55 bp):
AGCAGACCCGTTTATTGAAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGG
Found at i:1845167 original size:165 final size:164
Alignment explanation
Indices: 1844830--1845211 Score: 450
Period size: 165 Copynumber: 2.3 Consensus size: 164
1844820 ACCTGTTTAT
* * *
1844830 TGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGTGGACCCGTTTTATTGAAGATTG
1 TGAAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGGAGTGGACCCG-TTTATTGAAGATTG
* * * * *
1844895 TTCGAGTTCTATAATCTCTGAAGGAATAGAGAGCAGACTCGTTTGTTGAAGATTGTTCGAGTTCC
65 TTCGAGTTCTATAATCCCTAAAGGAATAGAGAGCAGACACGCTTGTTGAAGATTGATCGAGTTCC
* * * *
1844960 ATACTCTCTGGTAGAATAGAGAGCGGACCCGTTTTA
130 ATACTCCCT-GTAGAATAGAGAGCAGACACGTTTGA
*
1844996 TGAAGATTGTTCGAGTTCTATACTCCCTGAACGAATAGGGAGTGGACCCGTTTATTGAAGATTGA
1 TGAAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGGAGTGGACCCGTTTATTGAAGATTG-
* * *
1845061 TT-GAG-TCTTATACTCCCTAAATGAATAGGGAGCAGACACGCTTGTTGAAGATTGATCGAG-TC
65 TTCGAGTTC-TATAATCCCTAAAGGAATAGAGAGCAGACACGCTTGTTGAAGATTGATCGAGTTC
* * *
1845123 TTATACTCCCT-TAATGAATAGGGAGCAGACACGTTTGC
129 -CATACTCCCTGT-A-GAATAGAGAGCAGACACGTTTGA
* * **
1845161 TGAAGATTGGTCGAG-TCTTATACTCCCTGAAGGGATAGGGAGCAGACCCGT
1 TGAAGATTGTTCGAGTTC-TATACTCCCTGAAGGAATAGGGAGTGGACCCGT
1845212 CATTCGAAGA
Statistics
Matches: 186, Mismatches: 24, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
163 1 0.01
164 7 0.04
165 130 0.70
166 48 0.26
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (164 bp):
TGAAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGGAGTGGACCCGTTTATTGAAGATTGT
TCGAGTTCTATAATCCCTAAAGGAATAGAGAGCAGACACGCTTGTTGAAGATTGATCGAGTTCCA
TACTCCCTGTAGAATAGAGAGCAGACACGTTTGA
Found at i:1848987 original size:45 final size:47
Alignment explanation
Indices: 1848935--1849023 Score: 155
Period size: 45 Copynumber: 1.9 Consensus size: 47
1848925 TCAAATAAAT
1848935 GCATGCGAACTAGATATCATGCGGTTAGG-TTTATTTTT-TGAACAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
*
1848980 GCATGCGAATTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
1849024 TAACAAAGCA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 28 0.68
46 9 0.22
47 4 0.10
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (47 bp):
GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
Found at i:1851811 original size:75 final size:77
Alignment explanation
Indices: 1851697--1851895 Score: 289
Period size: 75 Copynumber: 2.6 Consensus size: 77
1851687 CCGTTGTACA
* * *
1851697 AGGGGGGAATCGGTACCCCCT-TGGGGGG-ATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
**
1851760 -CAAAACTGTTT
66 CCAAAACCATTT
* *
1851771 A-GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
1851835 CCAAAACCATTT
66 CCAAAACCATTT
*
1851847 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA
1 AGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCA
1851896 ATCTGTAATT
Statistics
Matches: 112, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
73 17 0.15
74 8 0.07
75 32 0.29
76 10 0.09
77 21 0.19
78 24 0.21
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.23
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
CCAAAACCATTT
Found at i:1852533 original size:17 final size:17
Alignment explanation
Indices: 1852511--1852554 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1852501 TTCATAAATC
1852511 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
*
1852528 CAAAATCAAACAATCCA
1 CAAAATCCAACAATCCA
1852545 -AAATATCCAA
1 CAAA-ATCCAA
1852555 AATGTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCCAACAATCCA
Found at i:1852546 original size:9 final size:8
Alignment explanation
Indices: 1852506--1852556 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
1852496 CACCATTCAT
1852506 AAATCC-A
1 AAATCCAA
1852513 AAATCCAA
1 AAATCCAA
*
1852521 CAATCCACA
1 AAATCCA-A
1852530 AAAT-CAA
1 AAATCCAA
1852537 ACAATCCAA
1 A-AATCCAA
1852546 AATATCCAA
1 AA-ATCCAA
1852555 AA
1 AA
1852557 TGTTGAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 8 0.22
8 13 0.35
9 16 0.43
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (8 bp):
AAATCCAA
Found at i:1854515 original size:21 final size:21
Alignment explanation
Indices: 1854489--1854528 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1854479 CAGAACCCCA
*
1854489 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1854510 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1854529 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1860461 original size:76 final size:77
Alignment explanation
Indices: 1860333--1860542 Score: 300
Period size: 76 Copynumber: 2.8 Consensus size: 77
1860323 CCGTTGTACA
* * *
1860333 AGGGGGGAATCGGTACCCCCT-TGGGGGG-ATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAG
**
1860396 -CAAAACTGTTT
66 CCAAAACCATTT
* *
1860407 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAG
1860472 CCAAAACCATTT
66 CCAAAACCATTT
* * *
1860484 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCAATCTGTAATT
1 AGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATT
1860543 TTTGGCTTTG
Statistics
Matches: 121, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
74 19 0.16
75 7 0.06
76 32 0.26
77 32 0.26
78 31 0.26
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.24
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAG
CCAAAACCATTT
Found at i:1868444 original size:10 final size:10
Alignment explanation
Indices: 1868369--1868452 Score: 54
Period size: 10 Copynumber: 8.6 Consensus size: 10
1868359 TTTCGATTGA
*
1868369 AGAAGAAATG
1 AGAAAAAATG
*
1868379 A-AAAAAAAG
1 AGAAAAAATG
**
1868388 AGAAAAAAAA
1 AGAAAAAATG
1868398 AGAAAAAATG
1 AGAAAAAATG
1868408 AGGAGGAAAAATG
1 A-GA--AAAAATG
1868421 A-AAGAAAAT-
1 AGAA-AAAATG
1868430 -G-AAAAATG
1 AGAAAAAATG
1868438 AGAAAAAATG
1 AGAAAAAATG
1868448 A-AAAA
1 AGAAAA
1868453 TGGTGGAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 19
0.71 0.06 0.23
Matches are distributed among these distances:
7 5 0.08
8 1 0.02
9 13 0.22
10 30 0.50
11 3 0.05
13 8 0.13
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (10 bp):
AGAAAAAATG
Found at i:1868471 original size:7 final size:7
Alignment explanation
Indices: 1868461--1868523 Score: 90
Period size: 7 Copynumber: 8.7 Consensus size: 7
1868451 AATGGTGGAA
*
1868461 AAAAAAG
1 AAAAATG
1868468 AAAAATG
1 AAAAATG
1868475 AAAAATG
1 AAAAATG
1868482 AAAAATG
1 AAAAATG
1868489 AAAAATG
1 AAAAATG
1868496 AAAAATG
1 AAAAATG
*
1868503 AAAAAAGAG
1 -AAAAA-TG
1868512 AAAAATG
1 AAAAATG
1868519 AAAAA
1 AAAAA
1868524 AAAGAGAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
7 40 0.78
8 10 0.20
9 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (7 bp):
AAAAATG
Found at i:1868485 original size:21 final size:22
Alignment explanation
Indices: 1868460--1868523 Score: 103
Period size: 21 Copynumber: 2.9 Consensus size: 22
1868450 AAATGGTGGA
1868460 AAAAAAAGAAAAATGAAAAATG
1 AAAAAAAGAAAAATGAAAAATG
*
1868482 -AAAAATGAAAAATGAAAAATG
1 AAAAAAAGAAAAATGAAAAATG
1868503 AAAAAAGAGAAAAATGAAAAA
1 AAAAAA-AGAAAAATGAAAAA
1868524 AAAGAGAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 20 0.53
22 5 0.13
23 13 0.34
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (22 bp):
AAAAAAAGAAAAATGAAAAATG
Found at i:1868506 original size:44 final size:48
Alignment explanation
Indices: 1868425--1868523 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 48
1868415 AAAATGAAAG
1868425 AAAATGAAAAATGAGAAAAAATGAAAAATGGTGGAAAAAAAAGAAAAATGA
1 AAAATGAAAAAT-AGAAAAAATGAAAAA--GTGGAAAAAAAAGAAAAATGA
*
1868476 AAAATGAAAAAT-G-AAAAATGAAAAA-T-GAAAAAAGAGAAAAATGA
1 AAAATGAAAAATAGAAAAAATGAAAAAGTGGAAAAAAAAGAAAAATGA
1868520 AAAA
1 AAAA
1868524 AAAGAGAAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
44 21 0.45
45 1 0.02
48 12 0.26
49 1 0.02
51 12 0.26
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.11
Consensus pattern (48 bp):
AAAATGAAAAATAGAAAAAATGAAAAAGTGGAAAAAAAAGAAAAATGA
Found at i:1868537 original size:14 final size:14
Alignment explanation
Indices: 1868460--1868537 Score: 75
Period size: 14 Copynumber: 5.3 Consensus size: 14
1868450 AAATGGTGGA
1868460 AAAAAAAGAAAAAT
1 AAAAAAAGAAAAAT
* *
1868474 GAAAAATGAAAAAT
1 AAAAAAAGAAAAAT
* *
1868488 GAAAAATGAAAAAT
1 AAAAAAAGAAAAAT
1868502 GAAAAAAGAGAAAAAT
1 -AAAAAA-AGAAAAAT
*
1868518 GAAAAAAAAGAGAAAT
1 --AAAAAAAGAAAAAT
1868534 AAAA
1 AAAA
1868538 GGAGGGTTCA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
14 30 0.55
15 5 0.09
16 14 0.25
17 6 0.11
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (14 bp):
AAAAAAAGAAAAAT
Found at i:1869958 original size:55 final size:55
Alignment explanation
Indices: 1869814--1870193 Score: 403
Period size: 55 Copynumber: 6.9 Consensus size: 55
1869804 AAGCAAACCT
* * * * *
1869814 GTTTATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGTGGACCC
1 GTTTATTGAAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACAC
* * * *
1869869 GTTTTATTGAAGATTGTTCGAGTTCTATAATCTCTGAAGGAATAGAGAGCGGACTC
1 G-TTTATTGAAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACAC
* * * * *
1869925 GTTTGTTGAAGATTGTTCGAGTTCCATACTCTCTGGTA-GAATAGAGAGCGGACAC
1 GTTTATTGAAGATTGTTCGAGTTCTATACTCCCT-GAAGGAATAGGGAGCGGACAC
* *
1869980 GTTT-TATGAAGATTGTTCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCC
1 GTTTAT-TGAAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACAC
* * *
1870035 GTTTATTGAAGATTGATT-GAG-TCTTATACTCCCTAAATGAATAGGGAGCAGACAC
1 GTTTATTGAAGATTG-TTCGAGTTC-TATACTCCCTGAAGGAATAGGGAGCGGACAC
* * * * *
1870090 GCTTGTTGAAGATTGATCGAG-TCTTATACTCCCTGAATGAATAGGGAGCAGACAC
1 GTTTATTGAAGATTGTTCGAGTTC-TATACTCCCTGAAGGAATAGGGAGCGGACAC
** * *
1870145 GTTTGCTGAAGATTGGTCGAG-TCTTATACTCCCTGAAGGGATAGGGAGC
1 GTTTATTGAAGATTGTTCGAGTTC-TATACTCCCTGAAGGAATAGGGAGC
1870194 AGACCCGTCA
Statistics
Matches: 290, Mismatches: 27, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
54 6 0.02
55 228 0.79
56 56 0.19
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (55 bp):
GTTTATTGAAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACAC
Found at i:1870146 original size:165 final size:165
Alignment explanation
Indices: 1869815--1870201 Score: 460
Period size: 165 Copynumber: 2.3 Consensus size: 165
1869805 AGCAAACCTG
* * * *
1869815 TTTATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGTGGACCCGTTTTATTGAA
1 TTTA-TGAAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACCCG-TTTATTGAA
* * * * * *
1869880 GATTGTTCGAGTTCTATAATCTCTGAAGGAATAGAGAGCGGACTCGTTTGTTGAAGATTGTTCGA
64 GATTGTTCGAGTTCTATAATCCCTAAAGGAATAGAGAGCAGACACGCTTGTTGAAGATTGATCGA
* * *
1869945 GTTCCATACTCTCTGGTAGAATAGAGAGCGGACACGT
129 GTTCCATACTCCCTGATAGAATAGAGAGCAGACACGT
*
1869982 TTTATGAAGATTGTTCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCGTTTATTGAAGA
1 TTTATGAAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACCCGTTTATTGAAGA
* * *
1870047 TTGATT-GAG-TCTTATACTCCCTAAATGAATAGGGAGCAGACACGCTTGTTGAAGATTGATCGA
66 TTG-TTCGAGTTC-TATAATCCCTAAAGGAATAGAGAGCAGACACGCTTGTTGAAGATTGATCGA
* *
1870110 G-TCTTATACTCCCTGA-ATGAATAGGGAGCAGACACGT
129 GTTC-CATACTCCCTGATA-GAATAGAGAGCAGACACGT
** * * *
1870147 TTGCTGAAGATTGGTCGAG-TCTTATACTCCCTGAAGGGATAGGGAGCAGACCCGT
1 TTTATGAAGATTGTTCGAGTTC-TATACTCCCTGAAGGAATAGGGAGCGGACCCGT
1870202 CATTCGAAGA
Statistics
Matches: 190, Mismatches: 25, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
164 7 0.04
165 132 0.69
166 47 0.25
167 4 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (165 bp):
TTTATGAAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACCCGTTTATTGAAGA
TTGTTCGAGTTCTATAATCCCTAAAGGAATAGAGAGCAGACACGCTTGTTGAAGATTGATCGAGT
TCCATACTCCCTGATAGAATAGAGAGCAGACACGT
Found at i:1870223 original size:110 final size:110
Alignment explanation
Indices: 1869987--1870224 Score: 300
Period size: 110 Copynumber: 2.2 Consensus size: 110
1869977 CACGTTTTAT
* * *
1869987 GAAGATTGTTCGAGT-TCTATACTCCCTGAACGAATAGGGAGCGGACCCGTTTATTGAAGATTGA
1 GAAGATTGTTCGAGTCT-TATACTCCCTGAACGAATAGGGAGCAGACACGTTTACTGAAGATTGA
* * * *
1870051 TTGAGTCTTATACTCCCTAAATGAATAGGGAGCAGACACGCTTGTT
65 TCGAGTCTTATACTCCCTAAAGGAATAGGGAGCAGACACGCATGTC
* * * *
1870097 GAAGATTGATCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGCTGAAGATTGGT
1 GAAGATTGTTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTACTGAAGATTGAT
* * *
1870162 CGAGTCTTATACTCCCTGAAGGGATAGGGAGCAGACCCGTCAT-TC
66 CGAGTCTTATACTCCCTAAAGGAATAGGGAGCAGACACG-CATGTC
* *
1870207 GAAGATTTTTCAAGTCTT
1 GAAGATTGTTCGAGTCTT
1870225 GTTTATCCTG
Statistics
Matches: 109, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
110 106 0.97
111 3 0.03
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (110 bp):
GAAGATTGTTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTACTGAAGATTGAT
CGAGTCTTATACTCCCTAAAGGAATAGGGAGCAGACACGCATGTC
Found at i:1873558 original size:2 final size:2
Alignment explanation
Indices: 1873551--1873681 Score: 255
Period size: 2 Copynumber: 66.0 Consensus size: 2
1873541 CAACATTTTG
1873551 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1873593 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A- AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1873634 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1873676 AC AC AC
1 AC AC AC
1873682 CCTAGATATG
Statistics
Matches: 128, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 127 0.99
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1874928 original size:26 final size:27
Alignment explanation
Indices: 1874878--1874931 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
1874868 TTCGTGAACC
1874878 AAACCCTAAACCCTGAAATCTAACTTA
1 AAACCCTAAACCCTGAAATCTAACTTA
* *
1874905 AAACCCTAAA-TCTTAAATCTAACTTA
1 AAACCCTAAACCCTGAAATCTAACTTA
1874931 A
1 A
1874932 CATATTACTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.46, C:0.26, G:0.02, T:0.26
Consensus pattern (27 bp):
AAACCCTAAACCCTGAAATCTAACTTA
Found at i:1875176 original size:36 final size:36
Alignment explanation
Indices: 1875104--1875176 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 36
1875094 TACTATACTT
* **
1875104 AATTTATATATTTTCTTTAAAAAATTAAATTCATAA
1 AATTTATATATTTTCTTGAAAAAATTAAAAACATAA
* *
1875140 AATTTATATAATTTT-TTGACAAAATTAAAAAGATAA
1 AATTTATAT-ATTTTCTTGAAAAAATTAAAAACATAA
1875176 A
1 A
1875177 TAGGTTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
36 26 0.84
37 5 0.16
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (36 bp):
AATTTATATATTTTCTTGAAAAAATTAAAAACATAA
Found at i:1881434 original size:21 final size:21
Alignment explanation
Indices: 1881395--1881434 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1881385 CCCCCTTTGA
* *
1881395 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACACCCCAC
*
1881416 AGGGGAATCGATACACCCC
1 AGGGGAACCGATACACCCC
1881435 TGGGGTTCTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.38, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACACCCCAC
Found at i:1885094 original size:17 final size:17
Alignment explanation
Indices: 1885072--1885107 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1885062 CCGGGGGTTG
1885072 GGAATAACTTATTACCA
1 GGAATAACTTATTACCA
*
1885089 GGAATAACTTATTCCCA
1 GGAATAACTTATTACCA
1885106 GG
1 GG
1885108 GGTTGGGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (17 bp):
GGAATAACTTATTACCA
Found at i:1885751 original size:3 final size:3
Alignment explanation
Indices: 1885658--1885734 Score: 75
Period size: 3 Copynumber: 24.3 Consensus size: 3
1885648 TAATACCGCA
* *
1885658 CTT CTT CTT CTC CTT CTT CCTT CTT CCTT CTT CCTT CCTT CTT -TT TTT
1 CTT CTT CTT CTT CTT CTT -CTT CTT -CTT CTT -CTT -CTT CTT CTT CTT
*
1885706 CTTT CTT CTT CTT CTT ATT CTT CTT CTT C
1 C-TT CTT CTT CTT CTT CTT CTT CTT CTT C
1885735 CACATTCTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
2 2 0.03
3 46 0.72
4 16 0.25
ACGTcount: A:0.01, C:0.35, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:1886851 original size:3 final size:3
Alignment explanation
Indices: 1886843--1886880 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
1886833 AAAGTGTGTG
1886843 AGA AGA AGA AGAA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA A
1886881 TTCTTTTTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1887007 original size:155 final size:155
Alignment explanation
Indices: 1886725--1887021 Score: 585
Period size: 155 Copynumber: 1.9 Consensus size: 155
1886715 TATTTTTTTT
1886725 ATTCTTTTTCCTTAGAAAGTAGAGAGAGAAACTGAATTTTATTGGGAAAATAGAGAGATAAAAAG
1 ATTCTTTTTCCTTAGAAAGTAGAGAGAGAAACTGAATTTTATTGGGAAAATAGAGAGATAAAAAG
1886790 AATTCAAGAAATGACAAGGTTTTGGATCTAGGATTTTATTGAGAAAGTGTGTGAGAAGAAGAAGA
66 AATTCAAGAAATGACAAGGTTTTGGATCTAGGATTTTATTGAGAAAGTGTGTGAGAAGAAGAAGA
1886855 AAGAAGAAGAAGAAGAAGAAGAAGA
131 AAGAAGAAGAAGAAGAAGAAGAAGA
1886880 ATTCTTTTTCCTTAGAAAGTAGAGAGAGAAACTGAATTTTATTGGGAAAATAGAGAGATAAAAAG
1 ATTCTTTTTCCTTAGAAAGTAGAGAGAGAAACTGAATTTTATTGGGAAAATAGAGAGATAAAAAG
*
1886945 AATTCAAGAAATGACAAGGTTTTGGATCTAGGATTTTATTGAGAAAGTGTGTGAGAAGAAGAAGG
66 AATTCAAGAAATGACAAGGTTTTGGATCTAGGATTTTATTGAGAAAGTGTGTGAGAAGAAGAAGA
1887010 AAGAAGAAGAAG
131 AAGAAGAAGAAG
1887022 GAGGAGGAGG
Statistics
Matches: 141, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
155 141 1.00
ACGTcount: A:0.44, C:0.05, G:0.26, T:0.25
Consensus pattern (155 bp):
ATTCTTTTTCCTTAGAAAGTAGAGAGAGAAACTGAATTTTATTGGGAAAATAGAGAGATAAAAAG
AATTCAAGAAATGACAAGGTTTTGGATCTAGGATTTTATTGAGAAAGTGTGTGAGAAGAAGAAGA
AAGAAGAAGAAGAAGAAGAAGAAGA
Found at i:1887016 original size:13 final size:13
Alignment explanation
Indices: 1886998--1887023 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1886988 AAAGTGTGTG
1886998 AGAAGAAGAAGGA
1 AGAAGAAGAAGGA
1887011 AGAAGAAGAAGGA
1 AGAAGAAGAAGGA
1887024 GGAGGAGGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (13 bp):
AGAAGAAGAAGGA
Found at i:1887026 original size:3 final size:3
Alignment explanation
Indices: 1887020--1887131 Score: 224
Period size: 3 Copynumber: 37.3 Consensus size: 3
1887010 AAGAAGAAGA
1887020 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
1887068 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
1887116 AGG AGG AGG AGG AGG A
1 AGG AGG AGG AGG AGG A
1887132 AGGAAGGAAG
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 109 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:1892584 original size:3 final size:3
Alignment explanation
Indices: 1892578--1892609 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1892568 ATTTTCGTTA
*
1892578 TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1892610 ATTTACATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1893821 original size:19 final size:19
Alignment explanation
Indices: 1893775--1893821 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1893765 CATTAATTTG
*
1893775 TATATTATGTTTGCTGATAT
1 TATATT-TGGTTGCTGATAT
1893795 TATAATTTGGTTG-TGATATT
1 TAT-ATTTGGTTGCTGATA-T
1893815 TATATTT
1 TATATTT
1893822 ATTTCGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (19 bp):
TATATTTGGTTGCTGATAT
Found at i:1898473 original size:16 final size:14
Alignment explanation
Indices: 1898451--1898529 Score: 79
Period size: 16 Copynumber: 5.1 Consensus size: 14
1898441 AGATCCAATT
1898451 AAAACAAAGAAAAA
1 AAAACAAAGAAAAA
1898465 GAGAAACAAAGAAAAA
1 -A-AAACAAAGAAAAA
1898481 AAAACAAAGCAAAAA
1 AAAACAAAG-AAAAA
1898496 AAAACAACA-ACAAAGA
1 AAAACAA-AGA-AAA-A
1898512 AAAAGCAAAGAACAAA
1 AAAA-CAAAGAA-AAA
1898528 AA
1 AA
1898530 GAGGACAAAG
Statistics
Matches: 56, Mismatches: 0, Indels: 15
0.79 0.00 0.21
Matches are distributed among these distances:
14 9 0.16
15 17 0.30
16 24 0.43
17 6 0.11
ACGTcount: A:0.78, C:0.11, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAACAAAGAAAAA
Found at i:1898509 original size:21 final size:19
Alignment explanation
Indices: 1898471--1898515 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
1898461 AAAAGAGAAA
*
1898471 CAAAGAAAAAAAAACAAAG
1 CAAAAAAAAAAAAACAAAG
1898490 CAAAAAAAAACAACAACAAAG
1 CAAAAAAAAA-AA-AACAAAG
1898511 -AAAAA
1 CAAAAA
1898516 GCAAAGAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 7 0.30
21 7 0.30
ACGTcount: A:0.80, C:0.13, G:0.07, T:0.00
Consensus pattern (19 bp):
CAAAAAAAAAAAAACAAAG
Found at i:1899576 original size:4 final size:4
Alignment explanation
Indices: 1899559--1899623 Score: 68
Period size: 4 Copynumber: 17.2 Consensus size: 4
1899549 AATCAAGAAA
*
1899559 ACAT ACAT -CAAT ACAT ACAT ACAT ACAA ACAT ACAT -CA- AC-T -CAT
1 ACAT ACAT AC-AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1899603 ACAT ACAT ACAT ATAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT A
1899624 ACACATGAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
2 1 0.02
3 5 0.10
4 44 0.86
5 1 0.02
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:1899597 original size:28 final size:28
Alignment explanation
Indices: 1899557--1899622 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
1899547 CAAATCAAGA
1899557 AAACATACATCAA-TACATACATACATAC
1 AAACATACATCAACT-CATACATACATAC
1899585 AAACATACATCAACTCATACATACATAC
1 AAACATACATCAACTCATACATACATAC
* *
1899613 ATATATACAT
1 AAACATACAT
1899623 AACACATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 34 0.97
29 1 0.03
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (28 bp):
AAACATACATCAACTCATACATACATAC
Found at i:1900334 original size:102 final size:102
Alignment explanation
Indices: 1900063--1900362 Score: 378
Period size: 103 Copynumber: 2.9 Consensus size: 102
1900053 TTTGAGAAAT
* *
1900063 TTAAAACAAA-TTGCGTCTCGCTTGAGACATTTTTTCCTTTGATATACAAATTTCGAATTTGCTT
1 TTAAAACAAACTT-CGTCTCGTTTGAGACA-TTTTTCCTTTGAGATACAAATTTCGAATTTGCTT
* *
1900127 CACTTGAAACAAAATTAATCTCACTTGAGATTGTTGTTTC
64 CACTT-AAACAAAATTAATCTCACTTGAGATTATTATTTC
* *
1900167 TTAAAACAAACTTCATCTCGCTTT-AGACATTTTTCCTTTGAGATACAAATTTTGAATTTGCTTC
1 TTAAAACAAACTTCGTCTCG-TTTGAGACATTTTTCCTTTGAGATACAAATTTCGAATTTGCTTC
1900231 ACTTAAAACAAAATT-ATCTCACTTGAGATTATTATTTC
65 ACTT-AAACAAAATTAATCTCACTTGAGATTATTATTTC
* **
1900269 TTTCAAAAC-AA-TTCTGTCTCGTTTGAGACATTTTTCCTTAGA-ATACAAATTTCGAATTTATT
1 -TT-AAAACAAACTTC-GTCTCGTTTGAGACATTTTTCCTTTGAGATACAAATTTCGAATTTGCT
* *
1900331 TCACATTAAACAAAGTTGATCTCACTTGAGAT
63 TCAC-TTAAACAAAATTAATCTCACTTGAGAT
1900363 CGTTTTCTCA
Statistics
Matches: 175, Mismatches: 13, Indels: 17
0.85 0.06 0.08
Matches are distributed among these distances:
102 57 0.33
103 88 0.50
104 26 0.15
105 4 0.02
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.40
Consensus pattern (102 bp):
TTAAAACAAACTTCGTCTCGTTTGAGACATTTTTCCTTTGAGATACAAATTTCGAATTTGCTTCA
CTTAAACAAAATTAATCTCACTTGAGATTATTATTTC
Found at i:1900397 original size:102 final size:102
Alignment explanation
Indices: 1900077--1900406 Score: 364
Period size: 103 Copynumber: 3.2 Consensus size: 102
1900067 AACAAATTGC
* *
1900077 GTCTCGCTTGAGACATTTTTTCCTTTGATATACAAATTTCGAATTTGCTTCACTTGAAACAAAAT
1 GTCTCGCTTGAGACA-TTTTTCCTTTGAGATACAAATTTCGAATTTGCTTCACTTAAAACAAAAT
* * *
1900142 TAATCTCACTTGAGATTGTTGTT-TCTTAAAACAAACTTC
65 T-ATCTCACTTGAGATAGTT-TTCTCTAAAAACAAACTTT
* * *
1900181 ATCTCGCTTTAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGCTTCACTTAAAACAAAATT
1 GTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTCGAATTTGCTTCACTTAAAACAAAATT
* * *
1900246 ATCTCACTTGAGATTATTATTTCTTTCAAAAC-AA-TTCT
66 ATCTCACTTGAGA-TAGT-TTTCTCTAAAAACAAACTT-T
* * ** *
1900284 GTCTCGTTTGAGACATTTTTCCTTAGA-ATACAAATTTCGAATTTATTTCACATT-AAACAAAGT
1 GTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTCGAATTTGCTTCAC-TTAAAACAAAAT
* *
1900347 TGATCTCACTTGAGATCGTTTTCTCAAAAAACAAACTTT
65 T-ATCTCACTTGAGATAGTTTTCTCTAAAAACAAACTTT
** *
1900386 GTCTTACTTGAGACAGTTTTC
1 GTCTCGCTTGAGACATTTTTC
1900407 TAAAAACAAA
Statistics
Matches: 191, Mismatches: 27, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
101 10 0.05
102 67 0.35
103 93 0.49
104 21 0.11
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.41
Consensus pattern (102 bp):
GTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTCGAATTTGCTTCACTTAAAACAAAATT
ATCTCACTTGAGATAGTTTTCTCTAAAAACAAACTTT
Found at i:1900422 original size:35 final size:36
Alignment explanation
Indices: 1900354--1900424 Score: 101
Period size: 35 Copynumber: 2.0 Consensus size: 36
1900344 AGTTGATCTC
1900354 ACTTGAGATCGTTTTCTCAAAAAACAAACTTTGTCTT
1 ACTTGAGATCGTTTTCT-AAAAAACAAACTTTGTCTT
*
1900391 ACTTGAGA-CAGTTTTCT-AAAAACAAATTTTGTCT
1 ACTTGAGATC-GTTTTCTAAAAAACAAACTTTGTCT
1900425 CGTTTAAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 16 0.50
36 1 0.03
37 15 0.47
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (36 bp):
ACTTGAGATCGTTTTCTAAAAAACAAACTTTGTCTT
Found at i:1900473 original size:36 final size:36
Alignment explanation
Indices: 1900338--1900474 Score: 118
Period size: 36 Copynumber: 3.8 Consensus size: 36
1900328 ATTTCACATT
** *
1900338 AAACAAA-GTTGATCTCACTTGAGATCGTTTTCTCAAA
1 AAACAAATGTTG-TCTCACTTGAGA-CAATTTCTCTAA
* *
1900375 AAACAAACT-TTGTCTTACTTGAGACAGTTT-TCTAA
1 AAACAAA-TGTTGTCTCACTTGAGACAATTTCTCTAA
* ** * * *
1900410 AAACAAATTTTGTCTCGTTTAAAACAATTTCTCTTA
1 AAACAAATGTTGTCTCACTTGAGACAATTTCTCTAA
*
1900446 AAACAAATGTTGTCTCAGTTGAGACAATT
1 AAACAAATGTTGTCTCACTTGAGACAATT
1900475 CTCCAAATTA
Statistics
Matches: 80, Mismatches: 16, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
34 1 0.01
35 26 0.32
36 32 0.40
37 18 0.22
38 3 0.04
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (36 bp):
AAACAAATGTTGTCTCACTTGAGACAATTTCTCTAA
Found at i:1900816 original size:32 final size:31
Alignment explanation
Indices: 1900702--1900826 Score: 92
Period size: 32 Copynumber: 3.9 Consensus size: 31
1900692 AAAAATCAAA
* *
1900702 ATCTTTGAGTTTGTTTCTCTTGAAATAAAACC
1 ATCTTTGAGTTTGTTTCTCTTGAAA-CAAATC
* * *
1900734 ATCTTTGAG-TCGTTTCCCTTGAAACAAATT
1 ATCTTTGAGTTTGTTTCTCTTGAAACAAATC
* ** *
1900764 TTGACTATTGAGACAT-TTTCTCTTAAAACAATATC
1 AT--CT-TTGAG-TTTGTTTCTCTTGAAACAA-ATC
*
1900799 ATCTTTGAGTTTGTTTCTCTGGAAACAA
1 ATCTTTGAGTTTGTTTCTCTTGAAACAA
1900827 GGTTTTATCC
Statistics
Matches: 70, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
30 4 0.06
31 14 0.20
32 29 0.41
33 7 0.10
34 13 0.19
35 3 0.04
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.42
Consensus pattern (31 bp):
ATCTTTGAGTTTGTTTCTCTTGAAACAAATC
Found at i:1900993 original size:64 final size:65
Alignment explanation
Indices: 1900923--1901062 Score: 176
Period size: 64 Copynumber: 2.2 Consensus size: 65
1900913 ATTTTTTGAA
* *
1900923 AAACAAAGTTTTGTTTATCTTGAGACAATAT-TTTTT-GAAAAATCATTGAATATGTTTCTTTGG
1 AAACAAAATTTTGTCTATCTTGAGACAATATCTTTTTAGAAAAATCATTGAATATGTTTCTTT-G
1900986 G
65 G
* * * * * * *
1900987 AAACAAAATTTTGTCTCTTTTGAGATAATTTCTTTTTAGAAAAATCTTTGAGTTTGTTTCTTTGG
1 AAACAAAATTTTGTCTATCTTGAGACAATATCTTTTTAGAAAAATCATTGAATATGTTTCTTTGG
1901052 AAACAAAATTT
1 AAACAAAATTT
1901063 ACCATCTTTG
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
64 25 0.38
65 18 0.28
66 22 0.34
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.45
Consensus pattern (65 bp):
AAACAAAATTTTGTCTATCTTGAGACAATATCTTTTTAGAAAAATCATTGAATATGTTTCTTTGG
Found at i:1901368 original size:33 final size:31
Alignment explanation
Indices: 1901283--1901375 Score: 97
Period size: 28 Copynumber: 3.0 Consensus size: 31
1901273 GAGACAGTTG
*
1901283 CTTTTGAA-ACACATTATCTTTGAGTTTGTTT
1 CTTTTGAACACA-ATTATCTTTGAGTCTGTTT
1901314 -TTCTTGAA-ACAA--ATCTTTGAGTCTGTTT
1 CTT-TTGAACACAATTATCTTTGAGTCTGTTT
*
1901342 CTTTTGAAGCACAACTTATCTTTGAGTCGGTTT
1 CTTTTGAA-CACAA-TTATCTTTGAGTCTGTTT
1901375 C
1 C
1901376 CCTTGAAACC
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
28 20 0.38
29 2 0.04
30 7 0.13
31 8 0.15
33 16 0.30
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.46
Consensus pattern (31 bp):
CTTTTGAACACAATTATCTTTGAGTCTGTTT
Found at i:1901457 original size:43 final size:43
Alignment explanation
Indices: 1901397--1901601 Score: 159
Period size: 43 Copynumber: 4.7 Consensus size: 43
1901387 TTATCCCTAA
* *
1901397 AGATGACCAGACCTCCTCATCACTTAGGAGCCGTGTCACCCCT
1 AGATAACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCT
* * *
1901440 AGATAACCAG-CCGTCCTCATCGCGTAGGAACCGAGTTATCATCCACCCCT
1 AGATAACCAGACC-TCCTCATCACGTAGGAGCC--G---T-GT-CACCCCT
** * * * * *
1901490 AGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCT
1 AGATAACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCT
* *
1901533 CG---ACCAGACCTCCTCATCACGTAAGAGCCGTGTCACCCCT
1 AGATAACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCT
*
1901573 AGATAACCA-ACCGTCCTCATCGCGTAGGA
1 AGATAACCAGACC-TCCTCATCACGTAGGA
1901602 ACCGAGTTAT
Statistics
Matches: 124, Mismatches: 25, Indels: 26
0.71 0.14 0.15
Matches are distributed among these distances:
40 33 0.27
42 5 0.04
43 50 0.40
44 1 0.01
45 2 0.02
48 2 0.02
49 1 0.01
50 29 0.23
51 1 0.01
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.21
Consensus pattern (43 bp):
AGATAACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCT
Found at i:1901551 original size:40 final size:40
Alignment explanation
Indices: 1901496--1901572 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
1901486 CCCTAGATGG
* * * *
1901496 CCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCTCGA
1 CCAGAACTCCTCATCACGTAAGAGCCGTGTCACCCCTCGA
*
1901536 CCAGACCTCCTCATCACGTAAGAGCCGTGTCACCCCT
1 CCAGAACTCCTCATCACGTAAGAGCCGTGTCACCCCT
1901573 AGATAACCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.23
Consensus pattern (40 bp):
CCAGAACTCCTCATCACGTAAGAGCCGTGTCACCCCTCGA
Found at i:1901714 original size:133 final size:133
Alignment explanation
Indices: 1901401--1901703 Score: 516
Period size: 133 Copynumber: 2.3 Consensus size: 133
1901391 CCCTAAAGAT
* *
1901401 GACCAGACCTCCTCATCACTTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTA
1 GACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAACCGTCCTCATCGCGTA
*
1901466 GGAACCGAGTTATCATCCACCCCTAGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCC
66 GGAACCGAGTTATCATCCACCCCTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCC
*
1901531 CTC
131 CCC
*
1901534 GACCAGACCTCCTCATCACGTAAGAGCCGTGTCACCCCTAGATAACCAACCGTCCTCATCGCGTA
1 GACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAACCGTCCTCATCGCGTA
* *
1901599 GGAACCGAGTTATCATCCACCCCTAGATGGCTAGAACTCTTCATCACGTATGAGCCGTGTTATCC
66 GGAACCGAGTTATCATCCACCCCTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCC
1901664 CCC
131 CCC
** *
1901667 GACCAGATTTCCTCATCACGTAGGAACCGTGTCACCC
1 GACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCC
1901704 TTAAACAACC
Statistics
Matches: 159, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
133 159 1.00
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.22
Consensus pattern (133 bp):
GACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAACCGTCCTCATCGCGTA
GGAACCGAGTTATCATCCACCCCTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCC
CCC
Found at i:1901908 original size:3 final size:3
Alignment explanation
Indices: 1901902--1901948 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
1901892 TATTTAATAT
* *
1901902 TTA TTA TTA TTG TTA -TA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1901949 ATTTACATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1903161 original size:19 final size:19
Alignment explanation
Indices: 1903115--1903161 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1903105 CATTAATTTG
*
1903115 TATATTATGTTTGATGATAT
1 TATATT-TGGTTGATGATAT
1903135 TATAATTTGGTTG-TGATATT
1 TAT-ATTTGGTTGATGATA-T
1903155 TATATTT
1 TATATTT
1903162 ATTTCGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (19 bp):
TATATTTGGTTGATGATAT
Found at i:1904253 original size:34 final size:34
Alignment explanation
Indices: 1904212--1904279 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
1904202 TTTAGTTAAT
1904212 CAATTTATTTTGTTGTATGCAAACGTCAATTTTA
1 CAATTTATTTTGTTGTATGCAAACGTCAATTTTA
1904246 CAATTTATTTTGTTGTATGCAAACGTCAATTTTA
1 CAATTTATTTTGTTGTATGCAAACGTCAATTTTA
1904280 TTTATATTCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (34 bp):
CAATTTATTTTGTTGTATGCAAACGTCAATTTTA
Found at i:1907030 original size:43 final size:43
Alignment explanation
Indices: 1906969--1907055 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
1906959 GCAAGCACAC
**
1906969 AAGAATACTTCTACCTTCTACACACAGAGGAGGATAGTACAAA
1 AAGAATACCACTACCTTCTACACACAGAGGAGGATAGTACAAA
1907012 AAGAATACCACTACCTTCTACACACAGAGGAGGATAGTACAAA
1 AAGAATACCACTACCTTCTACACACAGAGGAGGATAGTACAAA
1907055 A
1 A
1907056 GTGAAAATGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.44, C:0.22, G:0.16, T:0.18
Consensus pattern (43 bp):
AAGAATACCACTACCTTCTACACACAGAGGAGGATAGTACAAA
Found at i:1910912 original size:153 final size:153
Alignment explanation
Indices: 1910580--1910991 Score: 572
Period size: 153 Copynumber: 2.7 Consensus size: 153
1910570 CCACGACCTG
*
1910580 TTTATCCTCAGCCTTCTTTTCCTCTACATTTTCATCAACTTTCTTCTCCTCAATTCGATCAACAA
1 TTTATCCTCAGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCTCCTCAATTCGATCAACAA
* * * * *
1910645 CCTTATCAGCTTGAGCTTCACTGATTTTCTTCTTCTTCTTGGTTTTCGCTTTGACAACTTTCGAT
66 CCTTGTCATCTTGAGCTTCACT-A-----ATCTTCTTCTTGGATTTCGCTTCGACAACTTTCGAT
*
1910710 GTTTGGGAAGCACTTGGTGGTTCAACATA
125 GTTTGGGAAGCACTTGGCGGTTCAACATA
* ** *
1910739 TTTATCCTCAGCCCTCTTTTCCTCTACATTTTCATCAACCTTCTTCTCCTTGATTCGATCAACAG
1 TTTATCCTCAGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCTCCTCAATTCGATCAACAA
* *
1910804 CCTTGTCATCTTGAGGTTCACTAATCTTCTTCTTGGATTTCTCTTCGACAACTTTCGATGTTTGG
66 CCTTGTCATCTTGAGCTTCACTAATCTTCTTCTTGGATTTCGCTTCGACAACTTTCGATGTTTGG
*
1910869 GAAGCACTTGGCGTTTCAACATA
131 GAAGCACTTGGCGGTTCAACATA
* * * *
1910892 TTTTTCTTCAGCCTTCTTTTCCTCTACATTTTCGTCAACCTTCTTCTCCTCAATTCGATCCACAA
1 TTTATCCTCAGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCTCCTCAATTCGATCAACAA
* * * *
1910957 CCTTGTTATCTTGAGCTTCATTGATCCTCTTCTTG
66 CCTTGTCATCTTGAGCTTCACTAATCTTCTTCTTG
1910992 TTCTTGGTTT
Statistics
Matches: 226, Mismatches: 27, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
153 146 0.65
158 1 0.00
159 79 0.35
ACGTcount: A:0.18, C:0.28, G:0.12, T:0.43
Consensus pattern (153 bp):
TTTATCCTCAGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCTCCTCAATTCGATCAACAA
CCTTGTCATCTTGAGCTTCACTAATCTTCTTCTTGGATTTCGCTTCGACAACTTTCGATGTTTGG
GAAGCACTTGGCGGTTCAACATA
Found at i:1918705 original size:9 final size:8
Alignment explanation
Indices: 1918693--1918770 Score: 52
Period size: 9 Copynumber: 9.2 Consensus size: 8
1918683 AATATTTTAT
1918693 ATATAATTA
1 ATATAA-TA
*
1918702 ATATAAAA
1 ATATAATA
1918710 ATATAA-A
1 ATATAATA
*
1918717 ATATTATA
1 ATATAATA
1918725 TATATAATTA
1 -ATATAA-TA
*
1918735 ATATAAAAA
1 ATAT-AATA
1918744 ATATAA-A
1 ATATAATA
*
1918751 ATATTATA
1 ATATAATA
1918759 TATATATATA
1 -ATATA-ATA
1918769 AT
1 AT
1918771 CGGGGCGGGG
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
7 12 0.21
8 11 0.20
9 26 0.46
10 7 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATATAATA
Found at i:1918727 original size:33 final size:34
Alignment explanation
Indices: 1918681--1918764 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
1918671 CCCGAACCCG
*
1918681 AAAATATTTTATATATAATTAATAT-AAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
1918714 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
1918748 AAAATATTATATATATA
1 AAAATATTATATATATA
1918765 TATAATCGGG
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 24 0.49
34 25 0.51
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:1921723 original size:36 final size:36
Alignment explanation
Indices: 1921684--1921837 Score: 169
Period size: 36 Copynumber: 4.4 Consensus size: 36
1921674 ATGAAGATGA
* *
1921684 AACATGCATTTATGTAGATGCATAAACCATGCAT-C
1 AACATACATTTATGCAGATGCATAAACCATGCATGC
*
1921719 AAACATACATTTATGCAGATACA-AATACCATGCATGC
1 -AACATACATTTATGCAGATGCATAA-ACCATGCATGC
*
1921756 AACATACATGTATGCAGATGC-T--ACCATGCATGC
1 AACATACATTTATGCAGATGCATAAACCATGCATGC
* *
1921789 AACATACATTTATGCAGATACA-AATGCCATGCA-GC
1 AACATACATTTATGCAGATGCATAA-ACCATGCATGC
1921824 TAACATACATTTAT
1 -AACATACATTTAT
1921838 ACATACAAAT
Statistics
Matches: 102, Mismatches: 8, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
33 30 0.29
35 4 0.04
36 67 0.66
37 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (36 bp):
AACATACATTTATGCAGATGCATAAACCATGCATGC
Found at i:1921770 original size:15 final size:15
Alignment explanation
Indices: 1921747--1921797 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
1921737 ATACAAATAC
1921747 CATGCATGCAACATA
1 CATGCATGCAACATA
*
1921762 CATGTATGCAGATGC-TA
1 CATGCATGCA-A--CATA
1921779 CCATGCATGCAACATA
1 -CATGCATGCAACATA
1921795 CAT
1 CAT
1921798 TTATGCAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
15 13 0.45
16 3 0.10
17 3 0.10
18 10 0.34
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (15 bp):
CATGCATGCAACATA
Found at i:1921786 original size:33 final size:34
Alignment explanation
Indices: 1921684--1921855 Score: 161
Period size: 36 Copynumber: 4.9 Consensus size: 34
1921674 ATGAAGATGA
* * *
1921684 AACATGCATTTATGTAGATGCATAAACCATGCAT-C
1 AACATACATTTATGCAGATACAT--ACCATGCATGC
1921719 AAACATACATTTATGCAGATACAAATACCATGCATGC
1 -AACATACATTTATGCAGATAC--ATACCATGCATGC
* *
1921756 AACATACATGTATGCAGATGC-TACCATGCATGC
1 AACATACATTTATGCAGATACATACCATGCATGC
*
1921789 AACATACATTTATGCAGATACAAATGCCATGCA-GC
1 AACATACATTTATGCAGATAC--ATACCATGCATGC
* * * *
1921824 TAACATACATTTATACATACAAATACCATGCA
1 -AACATACATTTATGCAGATACATACCATGCA
1921856 GCCAACACAT
Statistics
Matches: 116, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
33 31 0.27
34 9 0.08
35 2 0.02
36 71 0.61
37 1 0.01
38 2 0.02
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (34 bp):
AACATACATTTATGCAGATACATACCATGCATGC
Found at i:1926227 original size:21 final size:21
Alignment explanation
Indices: 1926185--1926227 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1926175 TTTTCGGGCT
* * *
1926185 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1926206 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1926227 A
1 A
1926228 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1926279 original size:20 final size:20
Alignment explanation
Indices: 1926254--1926291 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1926244 GAATGCTAGA
*
1926254 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
1926274 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
1926292 TGAGAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:1926954 original size:149 final size:150
Alignment explanation
Indices: 1926766--1927081 Score: 555
Period size: 150 Copynumber: 2.1 Consensus size: 150
1926756 GGGTAGAGGG
* *
1926766 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
* * *
1926830 TGCTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
1926895 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
*
1926915 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1926980 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
1927045 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
1927065 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
1927082 TGCATTTATA
Statistics
Matches: 159, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
149 52 0.33
150 107 0.67
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.34
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:1927093 original size:23 final size:23
Alignment explanation
Indices: 1927049--1927093 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1927039 ATCATTATAT
*
1927049 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
1927072 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1927094 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1935127 original size:6 final size:6
Alignment explanation
Indices: 1935116--1935170 Score: 101
Period size: 6 Copynumber: 9.2 Consensus size: 6
1935106 TCGGCTCGGC
*
1935116 TCGTGG TCGTGG TCGTGG TCGTGG TCATGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1935164 TCGTGG T
1 TCGTGG T
1935171 TTTTAGAGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.02, C:0.16, G:0.47, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:1935433 original size:22 final size:22
Alignment explanation
Indices: 1935408--1935462 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1935398 TCAGGAGTTA
* *
1935408 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1935430 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
1935452 CGGGAGTTATA
1 CAGGAGTTATA
1935463 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1940775 original size:21 final size:21
Alignment explanation
Indices: 1940749--1940792 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1940739 ATTCTGGGCT
* *
1940749 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
1940770 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
1940791 AG
1 AG
1940793 CGAATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:1941924 original size:31 final size:31
Alignment explanation
Indices: 1941836--1941943 Score: 94
Period size: 31 Copynumber: 3.5 Consensus size: 31
1941826 AGTCGAGGGT
* * *
1941836 TTTACCTATG-TCTTTCGAGACATATGGACAA
1 TTTACCTAGGTTCTTT-GGGACATATGGACAG
* * ** *
1941867 TATACCTATGTTCTAAGGAACATATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
*
1941898 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
* *
1941929 -TTGCCGAGGTTCTTT
1 TTTACCTAGGTTCTTT
1941944 ATGACCTCTG
Statistics
Matches: 62, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
30 13 0.21
31 46 0.74
32 3 0.05
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (31 bp):
TTTACCTAGGTTCTTTGGGACATATGGACAG
Found at i:1941941 original size:30 final size:30
Alignment explanation
Indices: 1941889--1941984 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
1941879 CTAAGGAACA
* *
1941889 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTGTGACC
* *
1941920 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTGTGACC
* * *
1941950 TCTGGATAGTTACCG-GGGTCTTTGTGACC
1 TATGGACAGTTACCGAGGTTCTTTGTGACC
*
1941979 TCTGGA
1 TATGGA
1941985 TATGTCCTTC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 18 0.32
30 29 0.52
31 9 0.16
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.34
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTGTGACC
Found at i:1945435 original size:5 final size:5
Alignment explanation
Indices: 1945425--1945450 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1945415 TATTATTATT
1945425 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
1945451 GAAACCTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:1946303 original size:21 final size:21
Alignment explanation
Indices: 1946268--1946311 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1946258 ATTCTGGGCT
* *
1946268 AGGGGAATCGGTACC-CATTCA
1 AGGGGAACCGATACCTC-TTCA
1946289 AGGGGAACCGATACCTCTTCA
1 AGGGGAACCGATACCTCTTCA
1946310 AG
1 AG
1946312 CGAATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (21 bp):
AGGGGAACCGATACCTCTTCA
Found at i:1947449 original size:31 final size:31
Alignment explanation
Indices: 1947355--1947462 Score: 94
Period size: 31 Copynumber: 3.5 Consensus size: 31
1947345 AGTCGAGGGT
* * *
1947355 TTTACCTATG-TCTTTCGAGACATGTGGACAG
1 TTTACCTAGGTTCTTTGGA-ACATATGGACAG
* * **
1947386 TATACCTATGTTCTAAGGAACATATGGACAG
1 TTTACCTAGGTTCTTTGGAACATATGGACAG
* *
1947417 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTTACCTAGGTTCTTTGGAACATATGGACAG
* *
1947448 -TTGCCGAGGTTCTTT
1 TTTACCTAGGTTCTTT
1947463 ATGACCTCTG
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
30 13 0.21
31 45 0.71
32 5 0.08
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (31 bp):
TTTACCTAGGTTCTTTGGAACATATGGACAG
Found at i:1947460 original size:30 final size:30
Alignment explanation
Indices: 1947408--1947503 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
1947398 CTAAGGAACA
* *
1947408 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTGTGACC
* *
1947439 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTGTGACC
* * *
1947469 TCTGGATAGTTACCG-GGGTCTTTGTGACC
1 TATGGACAGTTACCGAGGTTCTTTGTGACC
*
1947498 TCTGGA
1 TATGGA
1947504 TATGTCCTTC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 18 0.32
30 29 0.52
31 9 0.16
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.34
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTGTGACC
Found at i:1949276 original size:5 final size:5
Alignment explanation
Indices: 1949252--1949305 Score: 63
Period size: 5 Copynumber: 10.8 Consensus size: 5
1949242 GTCCGTCCGT
* * * * *
1949252 CTCGG CTCGT CTCGG CTCGG CTCGG CACGG CACGG CACGG CTCGG CTTGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
1949302 CTCG
1 CTCG
1949306 TGGTCGTGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.06, C:0.39, G:0.37, T:0.19
Consensus pattern (5 bp):
CTCGG
Found at i:1949314 original size:6 final size:6
Alignment explanation
Indices: 1949303--1949339 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
1949293 TCGGCTTGGC
*
1949303 TCGTGG TCGTGG TCGAGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1949340 AATACGTGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.03, C:0.16, G:0.49, T:0.32
Consensus pattern (6 bp):
TCGTGG
Found at i:1949639 original size:22 final size:22
Alignment explanation
Indices: 1949614--1949668 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1949604 TCAGGAGTTA
* *
1949614 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1949636 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
1949658 CGGGAGTTATA
1 CAGGAGTTATA
1949669 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1950695 original size:2 final size:2
Alignment explanation
Indices: 1950688--1950750 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
1950678 GCAACTCGTT
1950688 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1950730 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
1950751 TAAAAATTAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1951317 original size:2 final size:2
Alignment explanation
Indices: 1951310--1951349 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1951300 AAGTAGAAAC
1951310 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
1951350 CATTGTATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1951719 original size:39 final size:38
Alignment explanation
Indices: 1951653--1951739 Score: 111
Period size: 39 Copynumber: 2.3 Consensus size: 38
1951643 ATAAATGAAC
* * *
1951653 GAATAAATATTTTGTTCGTGTTAATTTATTTAATTAAAT
1 GAATAAATATTTTATTCATATTAATTTATTT-ATTAAAT
* *
1951692 GAATAAATTTTTTATTCATATTCATTTATTTATTAAAT
1 GAATAAATATTTTATTCATATTAATTTATTTATTAAAT
*
1951730 AAATAAATAT
1 GAATAAATAT
1951740 AAATGAATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
38 15 0.37
39 26 0.63
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (38 bp):
GAATAAATATTTTATTCATATTAATTTATTTATTAAAT
Found at i:1952959 original size:20 final size:20
Alignment explanation
Indices: 1952936--1952996 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 20
1952926 AAAGATTATC
1952936 TTTAAAAGACGATTGATATA
1 TTTAAAAGACGATTGATATA
* *
1952956 TTTATAA-A--A-T--TATC
1 TTTAAAAGACGATTGATATA
*
1952970 CTTAAAAGACGATTGATATA
1 TTTAAAAGACGATTGATATA
1952990 TTTAAAA
1 TTTAAAA
1952997 AATTTATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 12
0.62 0.13 0.26
Matches are distributed among these distances:
14 8 0.28
15 1 0.03
16 1 0.03
17 2 0.07
18 1 0.03
19 1 0.03
20 15 0.52
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.38
Consensus pattern (20 bp):
TTTAAAAGACGATTGATATA
Found at i:1952975 original size:34 final size:34
Alignment explanation
Indices: 1952930--1953000 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
1952920 GAAGACAAAG
* *
1952930 ATTATCTTTAAAAGACGATTGATATATTTATAAA
1 ATTATCCTTAAAAGACGATTGATATATTTAAAAA
1952964 ATTATCCTTAAAAGACGATTGATATATTTAAAAA
1 ATTATCCTTAAAAGACGATTGATATATTTAAAAA
1952998 ATT
1 ATT
1953001 TATTTTAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.39
Consensus pattern (34 bp):
ATTATCCTTAAAAGACGATTGATATATTTAAAAA
Found at i:1953106 original size:13 final size:13
Alignment explanation
Indices: 1953090--1953117 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1953080 AAGACACTTT
1953090 AAATGAAACATTA
1 AAATGAAACATTA
1953103 AAATGAAACATTA
1 AAATGAAACATTA
1953116 AA
1 AA
1953118 GAGACACGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AAATGAAACATTA
Found at i:1954775 original size:20 final size:20
Alignment explanation
Indices: 1954750--1954842 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
1954740 TTTTCCCAAT
1954750 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1954770 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
1954790 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* * *
1954811 TCGCAACGCGAATTGAGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1954832 TCGCAATGCGA
1 TCGCAATGCGA
1954843 TACTGACTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 27 0.46
21 32 0.54
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1954792 original size:41 final size:41
Alignment explanation
Indices: 1954747--1954842 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
1954737 CGATTTTCCC
*
1954747 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
1954788 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
*
1954829 AAATCGCAATGCGA
1 AATTCGCAATGCGA
1954843 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
Found at i:1954855 original size:41 final size:41
Alignment explanation
Indices: 1954769--1954900 Score: 117
Period size: 41 Copynumber: 3.2 Consensus size: 41
1954759 GAATAAGTAA
* * * *
1954769 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCG-ATACTG-ACT
1954810 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
* * * * * *
1954851 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGAGAAAATCGCAATGCGATACTGACT
*
1954892 TTCGCAACG
1 ATCGCAACG
1954901 AGATACTGAC
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
40 4 0.05
41 70 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
Found at i:1954856 original size:20 final size:20
Alignment explanation
Indices: 1954831--1954925 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
1954821 AATTGAGAAA
*
1954831 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1954851 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1954872 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
1954892 TTCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1954912 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1954926 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1955141 original size:22 final size:22
Alignment explanation
Indices: 1955113--1955156 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1955103 CACTCTCTCA
1955113 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1955135 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1955157 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1955445 original size:20 final size:20
Alignment explanation
Indices: 1955420--1955457 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1955410 CGATTCTCTC
1955420 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
1955440 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1955458 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:1956795 original size:18 final size:18
Alignment explanation
Indices: 1956774--1956818 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1956764 TCCACTTCGG
*
1956774 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
1956792 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
1956810 GAGCCATCA
1 GAGCCATCA
1956819 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Done.