Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008645.1 Hibiscus syriacus cultivar Beakdansim tig00111621_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: 4138222
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 22
Found at i:3425088 original size:106 final size:106
Alignment explanation
Indices: 3424808--3425269 Score: 707
Period size: 106 Copynumber: 4.4 Consensus size: 106
3424798 ACGTTTTACC
*
3424808 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACG
* * *
3424873 ACGAAGGGACCGCTGGTTGTCAACGAA-CATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTT
3424913 CAGAGCCAATTTCAACTTCAC-ACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACG
3424977 ACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTT
* *
3425018 CGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACG
*
3425083 GCGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTT
* * * *
3425124 CGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCAC--AAGCTCAACTTCA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC-G-ACGTAAGTTCAACTTCA
* * ** * * *
3425187 CGACGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAGTTC
64 CGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTT
*
3425230 CAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
3425270 TGAACAATAC
Statistics
Matches: 333, Mismatches: 20, Indels: 7
0.93 0.06 0.02
Matches are distributed among these distances:
104 68 0.20
105 52 0.16
106 210 0.63
107 1 0.00
108 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (106 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTT
Found at i:3427067 original size:72 final size:76
Alignment explanation
Indices: 3426925--3427072 Score: 259
Period size: 72 Copynumber: 2.0 Consensus size: 76
3426915 GTAGATATAT
3426925 TATCGTTCGTACTTCTTTTCGTTTATTTTCATTTCATTTTGTATTTTTTTTATATACTAATATCT
1 TATCGTTCGTACTTCTTTTCGTTTATTTTCATTTCATTTTGTA-TTTTTTTATATACTAATATCT
3426990 TGTTTAAACGTA
65 TGTTTAAACGTA
3427002 TATCGTTCGTACTTC-TTTCGTTTA-TTTCATTTCATTTTGTA-TTTTTT-TATACTAATATCTT
1 TATCGTTCGTACTTCTTTTCGTTTATTTTCATTTCATTTTGTATTTTTTTATATACTAATATCTT
3427063 GTTTAAACGT
66 GTTTAAACGT
3427073 TATTATATAT
Statistics
Matches: 71, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
72 24 0.34
73 6 0.08
75 17 0.24
76 9 0.13
77 15 0.21
ACGTcount: A:0.20, C:0.14, G:0.08, T:0.58
Consensus pattern (76 bp):
TATCGTTCGTACTTCTTTTCGTTTATTTTCATTTCATTTTGTATTTTTTTATATACTAATATCTT
GTTTAAACGTA
Found at i:3429485 original size:15 final size:16
Alignment explanation
Indices: 3429465--3429506 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
3429455 TATTGATAAA
3429465 TTAATTTATAAAAG-T
1 TTAATTTATAAAAGAT
* *
3429480 TTAATTTTTAAATGAT
1 TTAATTTATAAAAGAT
*
3429496 TTAATGTATAA
1 TTAATTTATAA
3429507 TTATAGATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TTAATTTATAAAAGAT
Found at i:3429548 original size:21 final size:21
Alignment explanation
Indices: 3429524--3429563 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3429514 TTAGTTAAAA
3429524 AAAATTAAA-AGTAAATTATTT
1 AAAA-TAAAGAGTAAATTATTT
*
3429545 AAAATAAAGGGTAAATTAT
1 AAAATAAAGAGTAAATTAT
3429564 ACAAGTGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAATAAAGAGTAAATTATTT
Found at i:3431474 original size:22 final size:23
Alignment explanation
Indices: 3431440--3431484 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
3431430 ATAAAATAAT
3431440 AATAATATTTTTAA-AATATTAA
1 AATAATATTTTTAACAATATTAA
*
3431462 AATAAT-TTATTTAACATTATTAA
1 AATAATATT-TTTAACAATATTAA
3431485 TGTCAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 2 0.10
22 11 0.55
23 7 0.35
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
AATAATATTTTTAACAATATTAA
Found at i:3431606 original size:29 final size:27
Alignment explanation
Indices: 3431547--3431624 Score: 99
Period size: 29 Copynumber: 2.9 Consensus size: 27
3431537 TCGATTATTA
3431547 TATT-TTTATTAAAA-AATATAAT-TAT
1 TATTATTTATTAAAATAA-ATAATATAT
*
3431572 TATTATTTATTAAATTAGAATAATATAT
1 TATTATTTATTAAAATA-AATAATATAT
3431600 TAATTATTTATTAAAATAAATAATA
1 T-ATTATTTATTAAAATAAATAATA
3431625 AAATTAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
25 4 0.09
26 9 0.20
27 6 0.13
28 12 0.26
29 15 0.33
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (27 bp):
TATTATTTATTAAAATAAATAATATAT
Found at i:3431630 original size:29 final size:29
Alignment explanation
Indices: 3431573--3431631 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
3431563 TATAATTATT
* *
3431573 ATTATTTATTAAATTAGAATAATATATTA
1 ATTATTTATTAAAATAGAATAATAAATTA
3431602 ATTATTTATTAAAATA-AATAATAAAATTA
1 ATTATTTATTAAAATAGAATAAT-AAATTA
3431631 A
1 A
3431632 AATTTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (29 bp):
ATTATTTATTAAAATAGAATAATAAATTA
Found at i:3431630 original size:42 final size:41
Alignment explanation
Indices: 3431583--3431668 Score: 95
Period size: 42 Copynumber: 2.0 Consensus size: 41
3431573 ATTATTTATT
3431583 AAATTAGAATAATATATTAATTAT-TTATTAA-AATAAATAATA
1 AAATTA-AA-AATATATTAATTATATT-TTAAGAATAAATAATA
* * *
3431625 AAATTAAAATTTTATTAATTATATTTTAAGGAATAAATATTA
1 AAATTAAAAATATATTAATTATATTTTAA-GAATAAATAATA
3431667 AA
1 AA
3431669 TATTCTACAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
40 16 0.42
41 4 0.11
42 18 0.47
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (41 bp):
AAATTAAAAATATATTAATTATATTTTAAGAATAAATAATA
Found at i:3431847 original size:12 final size:12
Alignment explanation
Indices: 3431825--3431864 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
3431815 TTTTTATTAA
3431825 AATGATATTAAAT
1 AATG-TATTAAAT
3431838 AATGTATTAAAT
1 AATGTATTAAAT
* *
3431850 AATTTATAAAAT
1 AATGTATTAAAT
3431862 AAT
1 AAT
3431865 AATGTTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 21 0.84
13 4 0.16
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (12 bp):
AATGTATTAAAT
Found at i:3432813 original size:94 final size:93
Alignment explanation
Indices: 3432692--3432879 Score: 367
Period size: 94 Copynumber: 2.0 Consensus size: 93
3432682 TGGATTTGCC
3432692 AAAATGACAACAAAATCGCAACGCGAAATAAAAATCGCAACGCGATCCCCAGAATCGCAAATCCA
1 AAAATGACAACAAAATCGCAACGCGAAATAAAAATCGCAACGCGATCCCCAGAATCGCAAAT-CA
3432757 GTTTCCAAAATCGCAACGCGATTCTTGAA
65 GTTTCCAAAATCGCAACGCGATTCTTGAA
3432786 AAAATGACAACAAAATCGCAACGCGAAATAAAAATCGCAACGCGATCCCCAGAATCGCAAATCAG
1 AAAATGACAACAAAATCGCAACGCGAAATAAAAATCGCAACGCGATCCCCAGAATCGCAAATCAG
3432851 TTTCCAAAATCGCAACGCGATTCTTGAA
66 TTTCCAAAATCGCAACGCGATTCTTGAA
3432879 A
1 A
3432880 TCGCAATGCG
Statistics
Matches: 94, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
93 32 0.34
94 62 0.66
ACGTcount: A:0.43, C:0.26, G:0.15, T:0.16
Consensus pattern (93 bp):
AAAATGACAACAAAATCGCAACGCGAAATAAAAATCGCAACGCGATCCCCAGAATCGCAAATCAG
TTTCCAAAATCGCAACGCGATTCTTGAA
Found at i:3433008 original size:59 final size:58
Alignment explanation
Indices: 3432920--3433047 Score: 145
Period size: 59 Copynumber: 2.2 Consensus size: 58
3432910 GATTTTCCAA
* *
3432920 AATCGCAACGCGAATATGAAAATCGCAACGCGAA-CACATAAATCGCAACG-TGTATCCGT
1 AATCGCAACGCG-ATATGAAAATCGCAACGAGAATC-CATAAATCGCAACGAT-AATCCGT
* **
3432979 ATATCGCAACGCG-TATCGTAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 A-ATCGCAACGCGATAT-GAAAATCGCAACGAGAATCCATAAATCGCAACGATAATCCGT
3433038 AATCGCAACG
1 AATCGCAACG
3433048 AGAATCTATA
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
58 12 0.20
59 35 0.58
60 13 0.22
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (58 bp):
AATCGCAACGCGATATGAAAATCGCAACGAGAATCCATAAATCGCAACGATAATCCGT
Found at i:3433024 original size:39 final size:39
Alignment explanation
Indices: 3432919--3433066 Score: 138
Period size: 39 Copynumber: 3.8 Consensus size: 39
3432909 CGATTTTCCA
* * * * * *
3432919 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGCGTA-TCGT
* * * *
3432959 AAATCGCAACGTGTATCCGTATATCGCAACGCGTATCGT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGCGTATCGT
*
3432998 AAATCGCAACGAGAATCTGTAAATCGCAACG-ATAATCCGT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGCGT-AT-CGT
* *
3433038 -AATCGCAACGAGAATCTATAAATCACAAC
1 AAATCGCAACGAGAATCTGTAAATCGCAAC
3433067 ACTGAAATTT
Statistics
Matches: 90, Mismatches: 16, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
38 1 0.01
39 58 0.64
40 31 0.34
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (39 bp):
AAATCGCAACGAGAATCTGTAAATCGCAACGCGTATCGT
Found at i:3433029 original size:20 final size:20
Alignment explanation
Indices: 3432919--3433053 Score: 123
Period size: 20 Copynumber: 6.8 Consensus size: 20
3432909 CGATTTTCCA
* ** *
3432919 AAATCGCAACGCGAATATGA
1 AAATCGCAACGAGAATCCGT
* *
3432939 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGAGAATC-CGT
* *
3432959 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
3432979 ATATCGCAACGCGTAT-CGT
1 AAATCGCAACGAGAATCCGT
*
3432998 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
3433018 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
3433038 -AATCGCAACGAGAATC
1 AAATCGCAACGAGAATC
3433054 TATAAATCAC
Statistics
Matches: 96, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
19 31 0.32
20 64 0.67
21 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGAGAATCCGT
Found at i:3436599 original size:33 final size:33
Alignment explanation
Indices: 3436554--3436668 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
3436544 TCTTTTGGTT
3436554 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
3436587 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
3436620 GAAATGCAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3436653 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
3436669 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3436600 original size:19 final size:17
Alignment explanation
Indices: 3436562--3436660 Score: 81
Period size: 14 Copynumber: 6.1 Consensus size: 17
3436552 TTGAAATGAA
3436562 AATCGCAA--CGAGA-G
1 AATCGCAACGCGAGATG
3436576 AATCGCAACGCGAGATG
1 AATCGCAACGCGAGATG
3436593 ACAATCGCAA--CGAGA-G
1 --AATCGCAACGCGAGATG
*
3436609 AATCGCAACGCGAAATG
1 AATCGCAACGCGAGATG
3436626 CAAATCGCAA--CGAGA-G
1 --AATCGCAACGCGAGATG
*
3436642 AATCGCAACGCGAAATG
1 AATCGCAACGCGAGATG
3436659 AA
1 AA
3436661 AATCGCAATG
Statistics
Matches: 69, Mismatches: 3, Indels: 23
0.73 0.03 0.24
Matches are distributed among these distances:
14 24 0.35
16 15 0.22
17 14 0.20
19 16 0.23
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.09
Consensus pattern (17 bp):
AATCGCAACGCGAGATG
Found at i:3436666 original size:19 final size:18
Alignment explanation
Indices: 3436556--3436673 Score: 71
Period size: 19 Copynumber: 7.1 Consensus size: 18
3436546 TTTTGGTTGA
3436556 AATGAAAATCGCAA--CG
1 AATGAAAATCGCAACGCG
*
3436572 -A-GAGAATCGCAACGCG
1 AATGAAAATCGCAACGCG
*
3436588 AGATGACAATCGCAA--CG
1 A-ATGAAAATCGCAACGCG
*
3436605 -A-GAGAATCGCAACGCG
1 AATGAAAATCGCAACGCG
*
3436621 AAATGCAAATCGCAA--CG
1 -AATGAAAATCGCAACGCG
*
3436638 -A-GAGAATCGCAACGCG
1 AATGAAAATCGCAACGCG
*
3436654 AAATGAAAATCGCAATGCG
1 -AATGAAAATCGCAACGCG
3436673 A
1 A
3436674 TTTTGGTTTC
Statistics
Matches: 78, Mismatches: 9, Indels: 28
0.68 0.08 0.24
Matches are distributed among these distances:
14 29 0.37
15 3 0.04
16 6 0.08
17 4 0.05
18 4 0.05
19 32 0.41
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AATGAAAATCGCAACGCG
Found at i:3436702 original size:19 final size:19
Alignment explanation
Indices: 3436669--3436713 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
3436659 AAAATCGCAA
**
3436669 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
3436688 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
3436707 TGCGATT
1 TGCGATT
3436714 CTCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.47
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:3436758 original size:20 final size:21
Alignment explanation
Indices: 3436711--3436788 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 21
3436701 TCGCGTTGCG
**
3436711 ATTCTCTCGTTGCG-CTTTTC
1 ATTCTCTCGTTGCGACTAGTC
3436731 ATTTCTCTCGTTGCGAC-AGTC
1 A-TTCTCTCGTTGCGACTAGTC
*
3436752 ATTCTCTCGTTGCGA-T-TTC
1 ATTCTCTCGTTGCGACTAGTC
*
3436771 ATTTATCTCGTTGCGACT
1 A-TTCTCTCGTTGCGACT
3436789 CTTCTGCAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
19 3 0.06
20 28 0.57
21 17 0.35
22 1 0.02
ACGTcount: A:0.12, C:0.27, G:0.17, T:0.45
Consensus pattern (21 bp):
ATTCTCTCGTTGCGACTAGTC
Found at i:3436781 original size:40 final size:41
Alignment explanation
Indices: 3436711--3436787 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 41
3436701 TCGCGTTGCG
* *
3436711 ATTCTCTCGTTGCGCTTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGCATTTCATTTATCTCGTTGCGACAGTC
3436752 ATTCTCTCGTTGCG-ATTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGCATTTCATTTATCTCGTTGCGAC
3436788 TCTTCTGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 20 0.59
41 14 0.41
ACGTcount: A:0.12, C:0.27, G:0.17, T:0.44
Consensus pattern (41 bp):
ATTCTCTCGTTGCGCATTTCATTTATCTCGTTGCGACAGTC
Found at i:3436912 original size:33 final size:33
Alignment explanation
Indices: 3436865--3436935 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3436855 AATACTAACT
*
3436865 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
3436898 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
3436931 TGAAA
1 TGAAA
3436936 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.15, G:0.25, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:3437169 original size:22 final size:22
Alignment explanation
Indices: 3437117--3437171 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
3437107 TGGTTGTGAG
**
3437117 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
3437139 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
3437161 GGATTTCTTCG
1 GGATTTCTTCG
3437172 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:3437340 original size:20 final size:20
Alignment explanation
Indices: 3437315--3437508 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
3437305 CTTTAAATAT
3437315 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3437335 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
3437357 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3437376 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
3437396 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
3437416 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3437436 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3437456 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
3437476 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
3437496 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3437509 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3437502 original size:60 final size:60
Alignment explanation
Indices: 3437315--3437508 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
3437305 CTTTAAATAT
**
3437315 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
3437376 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
3437436 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
3437496 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3437509 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:3437525 original size:21 final size:21
Alignment explanation
Indices: 3437495--3437577 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
3437485 ATTTTCATAT
*
3437495 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
3437516 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
3437537 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
3437558 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
3437578 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:3437568 original size:42 final size:43
Alignment explanation
Indices: 3437475--3437573 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
3437465 ATTTATGTGT
* *
3437475 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
3437516 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
3437558 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
3437574 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:3438281 original size:26 final size:26
Alignment explanation
Indices: 3438242--3438301 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 26
3438232 TTTTATAATA
**
3438242 ATAAATTTTTTATAATTTT-AAAAATT
1 ATAAATTTCATAT-ATTTTAAAAAATT
3438268 ATAAATTTCATATATTTTGAAAAAATT
1 ATAAATTTCATATATTTT-AAAAAATT
3438295 ATTAAAT
1 A-TAAAT
3438302 AATATTTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 5 0.17
26 11 0.38
27 8 0.28
28 5 0.17
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (26 bp):
ATAAATTTCATATATTTTAAAAAATT
Found at i:3439124 original size:343 final size:342
Alignment explanation
Indices: 3438288--3439127 Score: 1317
Period size: 346 Copynumber: 2.5 Consensus size: 342
3438278 TATATTTTGA
* * *
3438288 AAAAATTATTAAATAATATTTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTT
1 AAAAATTAATAAATAATAATTCATTTGATCCCTTAATTGTAATTAAAAGTTTATTTTAATA--TT
* *
3438353 TTTTATATTTTTAAACAATTAATTTTAAAAGGCAATA-ATTTTTTCAAAAATATATGAAATTTAT
64 TTTTATATTTTTAAACAATTAATTTTAAAAGGAAATATTTTTTTTCAAAAATATATGAAATTTAT
* *
3438417 AATTTTTTAAATTAT----AAA-TA-T-TTATCATCATCATCATCATTTTGTAAAAGAAATACTA
129 AATTTTTAAAATTATAAAAAAATTATTATTATCATCATCATCATCATTTTATAAAAGAAATACTA
*
3438475 GTTATAAAACTTTTATAAAAGTATTCATATTTTAAAATATTTACCCTCAAAGTTTTTATACTAGA
194 GTTATAAAACTTTTATAAAAGTATTCATATTTTAAAATACTTACCCTCAAAGTTTTTATACTAGA
** **
3438540 TTATATGTATTGTGTAATTTTAATGCAAAAATTTAAATAAATTTATTAAAAATGAATAAACATTA
259 TTATACATATTGTGTAATTTTAATGCAAAAATCAAAATAAATTTATTAAAAATGAATAAACATTA
*
3438605 TTAACTGTTGTTAAAAATT
324 TTAACTGTTGTTAAAAAAT
* *
3438624 AAAAATTAATAAATAATAATTCATTTGAT-CATTCAGTTGTAATTAAAAGTTTATTTTAATATTT
1 AAAAATTAATAAATAATAATTCATTTGATCCCTT-AATTGTAATTAAAAGTTTATTTTAATATTT
*
3438688 TTTATATTTTTAAACAATTAATTTTAAAAGGTAATATTTTTTTTTCAAAAATATATGAAATTTAT
65 TTTATATTTTTAAACAATTAATTTTAAAAGGAAATA-TTTTTTTTCAAAAATATATGAAATTTAT
* * *
3438753 AATTTTTAAAATTATAAAATATTTATTATTATTATCATCATCATCATTTTATAAAAGAAATACTA
129 AATTTTTAAAATTATAAAAAAATTATTATTATCATCATCATCATCATTTTATAAAAGAAATACTA
3438818 GTTATAAAACTTTTATAAAAGTATTCATATTTTAAAAATACTTACCCTCAAAGTTTTCCTATACT
194 GTTATAAAACTTTTATAAAAGTATTCATATTTT-AAAATACTTACCCTCAAAGTTTT--TATACT
*
3438883 AGATTATACATATTGTGTAATTTTAATG-ATAAAATCAAAATAATTTTATTAAAAATGAATAAAC
256 AGATTATACATATTGTGTAATTTTAATGCA-AAAATCAAAATAAATTTATTAAAAATGAATAAAC
3438947 ATTATTAACTGTTGTTAAAAAAT
320 ATTATTAACTGTTGTTAAAAAAT
* *
3438970 AAAAATTAATGAATAATAATTCATTTAATCCCTTAATTGTAATTAAAAGTTTATTTTAATA-TTT
1 AAAAATTAATAAATAATAATTCATTTGATCCCTTAATTGTAATTAAAAGTTTATTTTAATATTTT
*
3439034 TTATATTTTTAAACAATTAATTTTAAAAGAAAATATTTTTTTTC-AAAATATATGAAATTTATAA
66 TTATATTTTTAAACAATTAATTTTAAAAGGAAATATTTTTTTTCAAAAATATATGAAATTTATAA
3439098 TTTTTAAAATTATAAAAAAATTATTATTAT
131 TTTTTAAAATTATAAAAAAATTATTATTAT
3439128 AAAAAATAAA
Statistics
Matches: 462, Mismatches: 27, Indels: 23
0.90 0.05 0.04
Matches are distributed among these distances:
334 38 0.08
335 2 0.00
336 93 0.20
340 1 0.00
341 2 0.00
342 1 0.00
343 116 0.25
344 31 0.07
345 37 0.08
346 138 0.30
347 3 0.01
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (342 bp):
AAAAATTAATAAATAATAATTCATTTGATCCCTTAATTGTAATTAAAAGTTTATTTTAATATTTT
TTATATTTTTAAACAATTAATTTTAAAAGGAAATATTTTTTTTCAAAAATATATGAAATTTATAA
TTTTTAAAATTATAAAAAAATTATTATTATCATCATCATCATCATTTTATAAAAGAAATACTAGT
TATAAAACTTTTATAAAAGTATTCATATTTTAAAATACTTACCCTCAAAGTTTTTATACTAGATT
ATACATATTGTGTAATTTTAATGCAAAAATCAAAATAAATTTATTAAAAATGAATAAACATTATT
AACTGTTGTTAAAAAAT
Found at i:3446930 original size:22 final size:21
Alignment explanation
Indices: 3446881--3446959 Score: 113
Period size: 22 Copynumber: 3.7 Consensus size: 21
3446871 TCTGGGCTAG
*
3446881 GGGAATCGGTACCCATTCAAT
1 GGGAATCGGTACCCATTCAAA
*
3446902 GGGAATCGGTACCTATTCAAGA
1 GGGAATCGGTACCCATTCAA-A
3446924 GGGAATCGGTACCCATTCAAA
1 GGGAATCGGTACCCATTCAAA
*
3446945 GGGGAATCGATACCC
1 -GGGAATCGGTACCC
3446960 CCTCAACTGA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
21 20 0.38
22 32 0.62
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (21 bp):
GGGAATCGGTACCCATTCAAA
Found at i:3448618 original size:105 final size:104
Alignment explanation
Indices: 3448433--3448647 Score: 277
Period size: 105 Copynumber: 2.1 Consensus size: 104
3448423 GGTCTACGCA
* *
3448433 GTCCTTCGGGACATATAGGTATCCTATGGAACATCTATGAGGTCTTTTGAGACACATATTTGGTC
1 GTCCTTCGGGACATATAGGTATCCTATGGAACATCTATGAGGTCTTTTGAGACACATACTTGATC
* * *
3448498 CTTAGCATATGTATATGATTCTTAAGGAATTTTCTACGTG
66 CTTAGCATATCTATATGATTCTTAAGGAA-TTTATAAGTG
* * * * * * * *
3448538 GTCCTTCGGGACGTATATGTATTCTTTGGAGCATGTATGAGGTTTTTTGAGACACTTACTTGATC
1 GTCCTTCGGGACATATAGGTATCCTATGGAACATCTATGAGGTCTTTTGAGACACATACTTGATC
* * *
3448603 CTTGGTATATCTATATGGTTCTTAAGGAATTTATAAGTG
66 CTTAGCATATCTATATGATTCTTAAGGAATTTATAAGTG
3448642 GTCCTT
1 GTCCTT
3448648 ATGGACAATC
Statistics
Matches: 94, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
104 14 0.15
105 80 0.85
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.40
Consensus pattern (104 bp):
GTCCTTCGGGACATATAGGTATCCTATGGAACATCTATGAGGTCTTTTGAGACACATACTTGATC
CTTAGCATATCTATATGATTCTTAAGGAATTTATAAGTG
Found at i:3448709 original size:23 final size:24
Alignment explanation
Indices: 3448664--3448709 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3448654 AATCTTATAT
*
3448664 GGCACTACGGTGCAAATTCTACGC
1 GGCACTACGGTGCAAATTATACGC
*
3448688 GGCACTTCGGTGC-AATTATACG
1 GGCACTACGGTGCAAATTATACG
3448710 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (24 bp):
GGCACTACGGTGCAAATTATACGC
Found at i:3450365 original size:25 final size:25
Alignment explanation
Indices: 3450331--3450395 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
3450321 TGGATAAATG
*
3450331 AATGTGTGAATCAAAACTAAATGCA
1 AATGTTTGAATCAAAACTAAATGCA
3450356 AATGTTTGAATCAAAACTAAATGCA
1 AATGTTTGAATCAAAACTAAATGCA
3450381 AATGTTTGAATCAAA
1 AATGTTTGAATCAAA
3450396 TTAATTAGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.28
Consensus pattern (25 bp):
AATGTTTGAATCAAAACTAAATGCA
Found at i:3450419 original size:17 final size:17
Alignment explanation
Indices: 3450397--3450435 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
3450387 TGAATCAAAT
3450397 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
3450414 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
3450431 -AATTA
1 TAATTA
3450436 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:3454235 original size:3 final size:3
Alignment explanation
Indices: 3454220--3454297 Score: 111
Period size: 3 Copynumber: 26.0 Consensus size: 3
3454210 CATTTTTGAT
* * * *
3454220 TTA TTA CTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TAA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
3454268 ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3454298 AAAATAATTA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:3455706 original size:19 final size:21
Alignment explanation
Indices: 3455684--3455724 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3455674 ATAGTTATAA
3455684 ATATATA-TAAT-AATTATTT
1 ATATATATTAATAAATTATTT
3455703 ATATATATTTAATAAATTATTT
1 ATATATA-TTAATAAATTATTT
3455725 TGATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATATATTAATAAATTATTT
Found at i:3455710 original size:21 final size:22
Alignment explanation
Indices: 3455684--3455724 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3455674 ATAGTTATAA
3455684 ATATATATAAT-AATTATTTAT
1 ATATATATAATAAATTATTTAT
*
3455705 ATATATTTAATAAATTATTT
1 ATATATATAATAAATTATTT
3455725 TGATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATATATATAATAAATTATTTAT
Found at i:3455920 original size:34 final size:34
Alignment explanation
Indices: 3455882--3455950 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
3455872 TGATATTTTT
* *
3455882 AAATAATAAATATTTTAAA-TAAATATAATTTTGA
1 AAATAAT-AAGATTATAAATTAAATATAATTTTGA
* *
3455916 AAATAATAGGATTATAAATTAAATATATTTTTGA
1 AAATAATAAGATTATAAATTAAATATAATTTTGA
3455950 A
1 A
3455951 TTTTAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 8 0.27
34 22 0.73
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.41
Consensus pattern (34 bp):
AAATAATAAGATTATAAATTAAATATAATTTTGA
Found at i:3456420 original size:16 final size:16
Alignment explanation
Indices: 3456399--3456457 Score: 68
Period size: 16 Copynumber: 3.6 Consensus size: 16
3456389 TTTCTTTTAA
3456399 ATTTTTAT-TACTTATT
1 ATTTTTATATA-TTATT
3456415 ATTTTTATATATTATT
1 ATTTTTATATATTATT
*
3456431 ATTTTT-TATTTTATTT
1 ATTTTTATATATTA-TT
3456447 ATTTATTATAT
1 ATTT-TTATAT
3456458 TCAAGAATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
15 6 0.16
16 25 0.66
17 4 0.11
18 3 0.08
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTTTATATATTATT
Found at i:3456452 original size:23 final size:24
Alignment explanation
Indices: 3456393--3456455 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
3456383 AATTCTTTTC
* * *
3456393 TTTTAAATTTTTATTACTTATTAT
1 TTTTATATATTTATTATTTATTAT
*
3456417 TTTTATATA-TTATTATTTTTTA-
1 TTTTATATATTTATTATTTATTAT
*
3456439 TTTTATTTATTTATTAT
1 TTTTATATATTTATTAT
3456456 ATTCAAGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 8 0.24
23 18 0.55
24 7 0.21
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTTATATATTTATTATTTATTAT
Found at i:3456458 original size:13 final size:13
Alignment explanation
Indices: 3456410--3456458 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
3456400 TTTTTATTAC
*
3456410 TTATTATTTTTAT
1 TTATTATATTTAT
*
3456423 ATATTATTATTT-T
1 TTATTA-TATTTAT
*
3456436 TTATTTTATTTAT
1 TTATTATATTTAT
3456449 TTATTATATT
1 TTATTATATT
3456459 CAAGAATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 5 0.17
13 20 0.69
14 4 0.14
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTATTATATTTAT
Found at i:3458079 original size:14 final size:14
Alignment explanation
Indices: 3458041--3458094 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
3458031 ATTTTAAATA
*
3458041 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
3458055 TTTTACATTTGCAT
1 ATTTACATTTGCAT
3458069 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
3458084 CTTTGCATTTG
1 ATTTACATTTG
3458095 TATTGCACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:3461378 original size:15 final size:16
Alignment explanation
Indices: 3461358--3461391 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
3461348 TCCAGCAAAG
3461358 AAAGAAGAAAAA-AAA
1 AAAGAAGAAAAAGAAA
3461373 AAAGAAGAAAAAGAAA
1 AAAGAAGAAAAAGAAA
3461389 AAA
1 AAA
3461392 ATTGAATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAGAAGAAAAAGAAA
Found at i:3461389 original size:18 final size:19
Alignment explanation
Indices: 3461354--3461392 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
3461344 CTCATCCAGC
3461354 AAAGAAAGAAGAAAAAAAA
1 AAAGAAAGAAGAAAAAAAA
3461373 AAAG-AAGAA-AAAGAAAAA
1 AAAGAAAGAAGAAA-AAAAA
3461391 AA
1 AA
3461393 TTGAATCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.16
18 12 0.63
19 4 0.21
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAGAAAGAAGAAAAAAAA
Found at i:3463720 original size:83 final size:83
Alignment explanation
Indices: 3463619--3463883 Score: 460
Period size: 83 Copynumber: 3.2 Consensus size: 83
3463609 AATGGAACAA
3463619 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
3463684 AATCATTGAATTTGGAAG
66 AATCATTGAATTTGGAAG
3463702 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
*
3463767 AATCATTGAATTTAGAAG
66 AATCATTGAATTTGGAAG
* * * *
3463785 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGG-TTGGACAGAAC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAAAAC
3463849 CAATCATTGAATTTGGAAG
65 CAATCATTGAATTTGGAAG
*
3463868 ATGAATTTGCTCATAG
1 ATGAATGTGCTCATAG
3463884 TAGAAATAAG
Statistics
Matches: 174, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
82 4 0.02
83 170 0.98
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (83 bp):
ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
AATCATTGAATTTGGAAG
Found at i:3466478 original size:22 final size:22
Alignment explanation
Indices: 3466452--3466506 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
3466442 ATCTACACTC
*
3466452 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
3466474 TTCAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
3466496 TTCAAAGATGA
1 TTCAAAGATGA
3466507 AAACTTTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:3467324 original size:20 final size:20
Alignment explanation
Indices: 3467262--3467325 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
3467252 TCCAGAGAAA
3467262 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
3467282 -ATC-TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
3467301 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
3467321 GTTCA
1 GTTCA
3467326 ACTTTTTGCT
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:3467886 original size:20 final size:20
Alignment explanation
Indices: 3467824--3467887 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
3467814 TCCAGAGAAA
3467824 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
3467844 -ATC-TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
3467863 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
3467883 GTTCA
1 GTTCA
3467888 ACTTTTGCTT
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:3468110 original size:20 final size:20
Alignment explanation
Indices: 3468048--3468111 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
3468038 TCCAGAGAAA
3468048 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
3468068 -ATC-TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
3468087 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
3468107 GTTCA
1 GTTCA
3468112 ACTTTTTGCT
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:3468421 original size:19 final size:19
Alignment explanation
Indices: 3468397--3468460 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
3468387 TTCATAATGA
3468397 GAAGAACTTATCTGAAGAG
1 GAAGAACTTATCTGAAGAG
**
3468416 GAAGAA-GAAGTTCAT-AATGA-
1 GAAGAACTTA--TC-TGAA-GAG
3468436 GAAGAACTTATCTGAAGAG
1 GAAGAACTTATCTGAAGAG
3468455 GAAGAA
1 GAAGAA
3468461 GAAGTTCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
18 4 0.12
19 16 0.47
20 10 0.29
21 4 0.12
ACGTcount: A:0.47, C:0.08, G:0.27, T:0.19
Consensus pattern (19 bp):
GAAGAACTTATCTGAAGAG
Found at i:3468423 original size:22 final size:22
Alignment explanation
Indices: 3468396--3468463 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
3468386 GTTCATAATG
3468396 AGAAGAACTTATCTGAAGAGGA
1 AGAAGAACTTATCTGAAGAGGA
* *
3468418 AGAAGAA-GT-TC--ATA-ATG-
1 AGAAGAACTTATCTGA-AGAGGA
3468435 AGAAGAACTTATCTGAAGAGGA
1 AGAAGAACTTATCTGAAGAGGA
3468457 AGAAGAA
1 AGAAGAA
3468464 GTTCATAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
17 7 0.20
18 4 0.11
19 3 0.09
20 3 0.09
21 4 0.11
22 14 0.40
ACGTcount: A:0.49, C:0.07, G:0.26, T:0.18
Consensus pattern (22 bp):
AGAAGAACTTATCTGAAGAGGA
Found at i:3468438 original size:39 final size:39
Alignment explanation
Indices: 3468379--3468483 Score: 201
Period size: 39 Copynumber: 2.7 Consensus size: 39
3468369 CAGCTTTTCC
*
3468379 AGAAAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGA
1 AGAAGAAGTTCATAATGAGAAGAACTTATCTGAAGAGGA
3468418 AGAAGAAGTTCATAATGAGAAGAACTTATCTGAAGAGGA
1 AGAAGAAGTTCATAATGAGAAGAACTTATCTGAAGAGGA
3468457 AGAAGAAGTTCATAATGAGAAGAACTT
1 AGAAGAAGTTCATAATGAGAAGAACTT
3468484 GTTCAACCTT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 65 1.00
ACGTcount: A:0.48, C:0.08, G:0.24, T:0.21
Consensus pattern (39 bp):
AGAAGAAGTTCATAATGAGAAGAACTTATCTGAAGAGGA
Found at i:3468469 original size:113 final size:112
Alignment explanation
Indices: 3466975--3468444 Score: 2147
Period size: 112 Copynumber: 13.1 Consensus size: 112
3466965 CATTTGAAGA
* *** * * ** *
3466975 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACCCGGTGGATCAGCAGTGT-CAGTTAGAG
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCA-TTTCCAGAGAAAG
* *
3467039 TTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATG
65 TTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATG
* * * * * * * * *** *
3467087 AGAAGAATTTGTTCAACCTTTTCCCTGAATTCATTACTTGATGAATTATTTTTTCCAGAGGAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
3467152 TCATAATGAGAAGAACTTATCTGAAGAGGAAG-AGAAAGTTCATAATG
66 TCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG-AAGTTCATAATG
* ** * * *
3467199 AGAAGAACTTGTTTAACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
3467264 TCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATG
66 TCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATG
*
3467311 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
* *
3467376 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
66 TCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATG
* * * *
3467424 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
*
3467489 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
66 TCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATG
* * *
3467537 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAGCTTTTCCAGAAAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
*
3467602 TCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATG
66 TCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATG
* * * * * * * * *** *
3467649 AGAAGAATTTGTTCAACCTTTTCCCTGAATTCATTACTTGATGAATTATTTTTTCCAGAGGAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
3467714 TCATAATGAGAAGAACTTATCTGAAGAGGAAG-AGAAAGTTCATAATG
66 TCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG-AAGTTCATAATG
* ** * * *
3467761 AGAAGAACTTGTTTAACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
3467826 TCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATG
66 TCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATG
3467873 AGAAGAACTTGTTCAA-CTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
* *
3467937 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
66 TCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATG
* * * * *
3467985 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATTAACATTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
3468050 TCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATG
66 TCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATG
*
3468097 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
* *
3468162 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
66 TCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATG
* * * *
3468210 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
*
3468275 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
66 TCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATG
* * *
3468323 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAGCTTTTCCAGAAAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
3468388 TCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATG
66 TCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATG
3468435 AGAAGAACTT
1 AGAAGAACTT
3468445 ATCTGAAGAG
Statistics
Matches: 1231, Mismatches: 118, Indels: 18
0.90 0.09 0.01
Matches are distributed among these distances:
111 74 0.06
112 664 0.54
113 493 0.40
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (112 bp):
AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
TCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATG
Found at i:3468474 original size:151 final size:152
Alignment explanation
Indices: 3468271--3468595 Score: 544
Period size: 151 Copynumber: 2.1 Consensus size: 152
3468261 TTTCCAGAGA
*
3468271 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * *
3468336 CAACTTTTTGCTTAAATTCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAG
66 CAACCTTTTCCCTAAATTCATCACTTGATGAATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAG
3468401 AACTTATCTGAAGAGGAAGAAG
131 AACTTATCTGAAGAGGAAGAAG
3468423 AAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * ** *
3468487 CAACCTTTTCCCTGAATTCATCACTTGATGAATTATTTTTTCCAGAGAAAGTTCATAATGAGAAG
66 CAACCTTTTCCCTAAATTCATCACTTGATGAATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAG
3468552 AACTTATCTGAAGAGGAAGAAG
131 AACTTATCTGAAGAGGAAGAAG
3468574 AAGTTCATAATGAGAAGAACTT
1 AAGTTCATAATGAGAAGAACTT
3468596 GTTTAACCTT
Statistics
Matches: 162, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
151 133 0.82
152 29 0.18
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (152 bp):
AAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACCTTTTCCCTAAATTCATCACTTGATGAATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAG
AACTTATCTGAAGAGGAAGAAG
Found at i:3468539 original size:112 final size:112
Alignment explanation
Indices: 3468423--3469495 Score: 1566
Period size: 113 Copynumber: 9.5 Consensus size: 112
3468413 GAGGAAGAAG
*
3468423 AAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* **
3468487 CAACCTTTTCCCTGAATTCATCACTTGATGAATTATTTTTTCCAGAGA
66 CAACCTTTT-CCTGAATTCATCACTTGATGGATTAGCTTTTCCAGAGA
*
3468535 AAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * *
3468599 TAACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGA
66 CAACCTTTTCCT-GAATTCATCACTTGATGGATTAGCTTTTCCAGAGA
*
3468647 AAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
** * * * *
3468711 CAAATTTTTGCTTAAATTCATCA-TTCGATGGATCAGCATTTCCAGAGA
66 CAACCTTTT-CCTGAATTCATCACTT-GATGGATTAGCTTTTCCAGAGA
* *
3468759 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * *
3468824 CAACCTTTTGCTCAAATCCATCA-TTCGATGGATCAGCATTTCCAGAGA
66 CAACCTTTTCCT-GAATTCATCACTT-GATGGATTAGCTTTTCCAGAGA
3468872 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * * *
3468937 CAACTTTTTGCTTAAATTCATCATTTGATGGATCAGCTTTTCCAGAAA
66 CAACCTTTT-CCTGAATTCATCACTTGATGGATTAGCTTTTCCAGAGA
*
3468985 AAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* **
3469049 CAACCTTTTCCCTGAATTCATCACTTGATGAATTATTTTTTCCAGAGA
66 CAACCTTTT-CCTGAATTCATCACTTGATGGATTAGCTTTTCCAGAGA
*
3469097 AAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * *
3469161 TAACCTTTTGCTCGAATTCATCACTTGATGGATTAGCTTTGCCAGGGA
66 CAACCTTTTCCT-GAATTCATCACTTGATGGATTAGCTTTTCCAGAGA
* *
3469209 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
3469274 CAACCTTTTGCCTGAATCCATCACTTGATGGATTAGCTTTGCCAGAGA
66 CAACCTTTT-CCTGAATTCATCACTTGATGGATTAGCTTTTCCAGAGA
*
3469322 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * *
3469387 CAACCTTTTACCTGAATTCATCAATTGATGGATCAGCCTTTCCAGAAA
66 CAACCTTTT-CCTGAATTCATCACTTGATGGATTAGCTTTTCCAGAGA
*
3469435 AAGTTCATAATGAAAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
3469496 CATCAAGAGC
Statistics
Matches: 886, Mismatches: 65, Indels: 19
0.91 0.07 0.02
Matches are distributed among these distances:
111 6 0.01
112 435 0.49
113 440 0.50
114 5 0.01
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (112 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACCTTTTCCTGAATTCATCACTTGATGGATTAGCTTTTCCAGAGA
Found at i:3468574 original size:601 final size:601
Alignment explanation
Indices: 3467822--3469045 Score: 2270
Period size: 601 Copynumber: 2.0 Consensus size: 601
3467812 TTTCCAGAGA
3467822 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * *
3467887 AACTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAA
66 AACTTTTCCCTAAATTCATCACTTGATGAATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAA
*
3467952 CTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCC
131 CTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCC
*
3468017 ATCATTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAG
196 ATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAG
* *
3468082 AAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAGC
261 AAGAAGTTCATAATGAGAAGAACTTGTTCAAATTTTTGCTTAAATTCATCATTCGATGGATCAGC
3468147 ATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAG
326 ATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAG
3468212 AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTC
391 AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTC
3468277 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTT
456 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTT
3468342 TTTGCTTAAATTCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTTA
521 TTTGCTTAAATTCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTTA
3468407 TCTGAAGAGGAAGAAG
586 TCTGAAGAGGAAGAAG
3468423 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * ***
3468488 AACCTTTTCCCTGAATTCATCACTTGATGAATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGA
66 AA-CTTTTCCCTAAATTCATCACTTGATGAATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGA
* * * * *
3468553 ACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATT
130 ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATC
3468617 CATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAA
195 CATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAA
3468682 GAAGAAGTTCATAATGAGAAGAACTTGTTCAAATTTTTGCTTAAATTCATCATTCGATGGATCAG
260 GAAGAAGTTCATAATGAGAAGAACTTGTTCAAATTTTTGCTTAAATTCATCATTCGATGGATCAG
3468747 CATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
325 CATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
3468812 GAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTT
390 GAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTT
3468877 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACT
455 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACT
3468942 TTTTGCTTAAATTCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTT
520 TTTTGCTTAAATTCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTT
3469007 ATCTGAAGAGGAAGAAG
585 ATCTGAAGAGGAAGAAG
3469024 AAGTTCATAATGAGAAGAACTT
1 AAGTTCATAATGAGAAGAACTT
3469046 GTTCAACCTT
Statistics
Matches: 604, Mismatches: 18, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
601 540 0.89
602 64 0.11
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (601 bp):
AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACTTTTCCCTAAATTCATCACTTGATGAATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAA
CTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCC
ATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAG
AAGAAGTTCATAATGAGAAGAACTTGTTCAAATTTTTGCTTAAATTCATCATTCGATGGATCAGC
ATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAG
AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTC
ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTT
TTTGCTTAAATTCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTTA
TCTGAAGAGGAAGAAG
Found at i:3468711 original size:20 final size:20
Alignment explanation
Indices: 3468649--3468712 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
3468639 TCCAGAGAAA
3468649 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
3468669 -ATC-TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
3468688 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
3468708 GTTCA
1 GTTCA
3468713 AATTTTTGCT
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:3469049 original size:20 final size:20
Alignment explanation
Indices: 3468987--3469050 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
3468977 TCCAGAAAAA
3468987 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
3469007 -ATC-TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
3469026 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
3469046 GTTCA
1 GTTCA
3469051 ACCTTTTCCC
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:3469223 original size:562 final size:561
Alignment explanation
Indices: 3466975--3469495 Score: 3050
Period size: 562 Copynumber: 4.4 Consensus size: 561
3466965 CATTTGAAGA
*** * * ** *
3466975 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACCCGGTGGATCAGCAGTGT-CAGTTAGAG
1 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAGCA-TTTCCAGAAAAAG
3467039 TTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
65 TTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
3467104 CTTTTCCCTGAATTCATTACTTGATGAATTATTTTTTCCAGAGGAAGTTCATAATGAGAAGAACT
130 CTTTTCCCTGAATTCATTACTTGATGAATTATTTTTTCCAGAGGAAGTTCATAATGAGAAGAACT
3467169 TATCTGAAGAGGAAGAGAAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATTCATC
195 TATCTGAAGAGGAAGAGAAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATTCATC
3467234 ACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
260 ACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
3467299 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAGCATT
325 AAGTTCATAATGAGAAGAACTTGTTCAAC-TTTTGCTTAAATTCATCATTTGATGGATCAGCATT
3467364 TCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAG
389 TCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAG
*
3467429 AATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATA
454 AATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAACATTTCCAGAGAAAGTTCATA
3467494 ATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
519 ATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
*
3467537 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAGCTTTTCCAGAAAAAGT
1 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAAAAAGT
*
3467602 TCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACC
66 TCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACC
3467667 TTTTCCCTGAATTCATTACTTGATGAATTATTTTTTCCAGAGGAAGTTCATAATGAGAAGAACTT
131 TTTTCCCTGAATTCATTACTTGATGAATTATTTTTTCCAGAGGAAGTTCATAATGAGAAGAACTT
3467732 ATCTGAAGAGGAAGAGAAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATTCATCA
196 ATCTGAAGAGGAAGAGAAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATTCATCA
3467797 CTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGA
261 CTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGA
3467862 AGTTCATAATGAGAAGAACTTGTTCAACTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTC
326 AGTTCATAATGAGAAGAACTTGTTCAACTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTC
3467927 CAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAA
391 CAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAA
* *
3467992 TTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATTAACATTTCCAGAGAAAGTTCATAAT
456 TTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAACATTTCCAGAGAAAGTTCATAAT
*
3468057 GAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATG
521 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
*
3468097 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAAAAAGT
3468162 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
66 TCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
* * * * * * *** *
3468227 CTTTT-GCTCAAATCCATCA-TTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAA
130 CTTTTCCCT-GAATTCATTACTT-GATGAATTATTTTTTCCAGAGGAAGTTCATAATGAGAAGAA
* * * **
3468290 CTCATCTGAAGAAGGAAGA-AGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATT
193 CTTATCTGAAG-AGGAAGAGA-AAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATT
* * * * *
3468354 CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAA
256 CATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAA
* * ***** *** * * ** *
3468419 GAAGAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
321 GAAGAAGTTCATAATGAGAAGAACTTGT-TCAA-CTTTTGCTTAAATTCATCAT---TTG-A-TG
* * * ** * ** ** * * *
3468484 GTTCAACCTTTTCC-CTG-AA-TTCATCACTTGATGAATTA-TTTTTTCCAGAGAAAGTTCATAA
379 GATC-AGCATTTCCAGAGAAAGTTCAT-A-ATGA-GAAGAACTCATCT-GA-AG-AAG-----GA
* * *** * * ***
3468545 TGAGAAGAACTT-ATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAAC-CTTTT
432 --AGAAGAAATTCA--T--A-ATG-AGAAGAA--T--T--T--GTTCAACCT-TTT-GCTCAAAT
* * * *
3468608 GC-TCGAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATC
479 CCATC--ATTC--GA--TG---GATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATC
3468672 TGAAG-AGGAAGAAGAAGTTCATAATG
535 TGAAGAAGGAAGAAGAAGTTCATAATG
* * *
3468698 AGAAGAACTTGTTCAAATTTTTGCTTAAATTCATCATTCGATGGATCAGCATTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAAAAAGT
3468763 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
66 TCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
* * * * * * *** *
3468828 CTTTT-GCTCAAATCCATCA-TTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAA
130 CTTTTCCCT-GAATTCATTACTT-GATGAATTATTTTTTCCAGAGGAAGTTCATAATGAGAAGAA
* * * **
3468891 CTCATCTGAAGAAGGAAGA-AGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATT
193 CTTATCTGAAG-AGGAAGAGA-AAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATT
* * * * *
3468955 CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAA
256 CATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAA
* * * * * * *
3469020 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCCCTGAATTCATCACTTGATGAATTAT
321 GAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTGCTTAAATTCATCATTTGATGGATCAG
** * *
3469085 TTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGA
385 CATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
* * * * * * *
3469149 GAAGAACTTGTTTAACCTTTTGCTCGAATTCATCACTT-GATGGATTAGC-TTTGCCAGGGAAAG
450 GAAGAATTTGTTCAACCTTTTGCTCAAATCCATCA-TTCGATGGATCAACATTT-CCAGAGAAAG
*
3469212 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
513 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * * * * * *
3469261 AGAAGAATTTGTTCAACCTTTTGCCTGAATCCATCACTTGATGGATTAGC-TTTGCCAGAGAAAG
1 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAGCATTT-CCAGAAAAAG
*
3469325 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
65 TTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAA
* * * * * *** ** *
3469390 CCTTTTACCTGAATTCATCAATTGATGGATCAGCCTTTCCAGAAAAAGTTCATAATGAAAAGAAC
129 CCTTTTCCCTGAATTCATTACTTGATGAATTATTTTTTCCAGAGGAAGTTCATAATGAGAAGAAC
*
3469455 TCATCTGAAGAAGGAAGA-AGAAGTTCATAATGAGAAGAACT
194 TTATCTGAAG-AGGAAGAGA-AAGTTCATAATGAGAAGAACT
3469496 CATCAAGAGC
Statistics
Matches: 1748, Mismatches: 146, Indels: 129
0.86 0.07 0.06
Matches are distributed among these distances:
560 113 0.06
561 283 0.16
562 517 0.30
563 232 0.13
564 14 0.01
565 2 0.00
567 7 0.00
568 4 0.00
569 13 0.01
570 20 0.01
571 9 0.01
572 3 0.00
573 1 0.00
575 1 0.00
577 1 0.00
578 1 0.00
579 16 0.01
580 3 0.00
581 1 0.00
582 1 0.00
583 3 0.00
584 16 0.01
585 1 0.00
586 2 0.00
588 1 0.00
590 1 0.00
591 2 0.00
592 7 0.00
593 8 0.00
594 16 0.01
595 10 0.01
596 5 0.00
597 6 0.00
598 2 0.00
600 10 0.01
601 416 0.24
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (561 bp):
AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAAAAAGT
TCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACC
TTTTCCCTGAATTCATTACTTGATGAATTATTTTTTCCAGAGGAAGTTCATAATGAGAAGAACTT
ATCTGAAGAGGAAGAGAAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATTCATCA
CTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAACTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTC
CAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAA
TTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAACATTTCCAGAGAAAGTTCATAAT
GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
Found at i:3469455 original size:450 final size:450
Alignment explanation
Indices: 3466975--3468444 Score: 2053
Period size: 450 Copynumber: 3.3 Consensus size: 450
3466965 CATTTGAAGA
* * * * ** * * ** *
3466975 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACCCGGTGGATCAGCAGTGT-CAGTTAGAG
1 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCA-TTTCCAGAGAAAG
* *
3467039 TTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAA
65 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
* * * * * ** **
3467103 CCTTTTCCCTGAATTCATTACTTGATGAATTATTTTTTCCAGAGGAAGTTCATAATGAGAAGAAC
130 CCTTTTACCTGAATTCATCAATTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAAC
* *
3467168 TTATCTGAAGAGGAAG-AGAAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATTCA
195 TTATCTGAAGAGGAAGAAG-AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCCTCGAATTCA
*
3467232 TCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGA
259 TCACTTGATGAATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGA
* *
3467297 AGAAGTTCATAATGAGAAGAACTTGTTC-AACTTTTTGCTTAAATTCATCATTTGATGGATCAGC
324 AGAAGTTCATAATGAGAAGAACTTGTTCAAAC-TTTTGCTCAAATTCATCATTCGATGGATCAGC
3467361 ATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
388 ATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
3467424 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGT
1 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGT
3467489 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
66 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
* * * * *
3467554 TTTTTGCTTAAATTCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACT
131 CTTTTACCTGAATTCATCAATTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACT
* *
3467619 TATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTCC-CTGAATTCAT
196 TATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCCTC-GAATTCAT
* *** *
3467683 TACTTGATGAATTATTTTTTCCAGAGGAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAG-A
260 CACTTGATGAATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAA
* * * * *
3467747 GAAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATTCATCACTT-GATGGATTAAC
325 G-AAGTTCATAATGAGAAGAACTTGTTCAAACTTTTGCTCAAATTCATCA-TTCGATGGATCAGC
* *
3467811 ATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATG
388 ATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* * * *
3467873 AGAAGAACTTGTTCAA-CTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
1 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGT
* *
3467937 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
66 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
* * * * * * * *
3468002 CTTTT-GCTCAAATCCATCATTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAAC
131 CTTTTACCT-GAATTCATCAATTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAAC
* * **
3468066 TTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCAT
195 TTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCCTCGAATTCAT
* * * * *
3468131 CATTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
260 CACTTGATGAATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGA
* * * *
3468196 AGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCA
324 AGAAGTTCATAATGAGAAGAACTTGTTCAAACTTTTGCTCAAATTCATCATTCGATGGATCAGCA
*
3468261 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
389 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* * * * * * *
3468323 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAGCTTTTCCAGAAAAAGT
1 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGT
*
3468388 TCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTT
66 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTT
3468445 ATCTGAAGAG
Statistics
Matches: 921, Mismatches: 86, Indels: 27
0.89 0.08 0.03
Matches are distributed among these distances:
447 1 0.00
448 272 0.30
449 213 0.23
450 359 0.39
451 76 0.08
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (450 bp):
AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGT
TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
CTTTTACCTGAATTCATCAATTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACT
TATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCCTCGAATTCATC
ACTTGATGAATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
AAGTTCATAATGAGAAGAACTTGTTCAAACTTTTGCTCAAATTCATCATTCGATGGATCAGCATT
TCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
Found at i:3469732 original size:3 final size:3
Alignment explanation
Indices: 3469717--3469797 Score: 117
Period size: 3 Copynumber: 27.0 Consensus size: 3
3469707 CATTTTTGAT
* * *
3469717 TTA TTA CTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
3469765 TAA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3469798 AAAATAATTA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:3472206 original size:2 final size:2
Alignment explanation
Indices: 3472201--3472225 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3472191 ATTTTTTTAT
3472201 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3472226 TAGTTTGCAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3472294 original size:26 final size:28
Alignment explanation
Indices: 3472248--3472303 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
3472238 GGTTTTTGGA
**
3472248 ATATATATAATATATGATTTTTGAAAAC
1 ATATATATAATATATGATTTTAAAAAAC
*
3472276 ATATATATTATATA-G-TTTTAAAAAAC
1 ATATATATAATATATGATTTTAAAAAAC
3472302 AT
1 AT
3472304 TTTGAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 11 0.44
27 1 0.04
28 13 0.52
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (28 bp):
ATATATATAATATATGATTTTAAAAAAC
Found at i:3472298 original size:24 final size:26
Alignment explanation
Indices: 3472250--3472299 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
3472240 TTTTTGGAAT
*
3472250 ATATATAATATATGATTTTTGAAAAC
1 ATATATAATATATGAGTTTTGAAAAC
* *
3472276 ATATATATTATAT-AGTTTTAAAAA
1 ATATATAATATATGAGTTTTGAAAA
3472300 ACATTTTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (26 bp):
ATATATAATATATGAGTTTTGAAAAC
Found at i:3472331 original size:36 final size:35
Alignment explanation
Indices: 3472266--3472521 Score: 302
Period size: 36 Copynumber: 7.1 Consensus size: 35
3472256 AATATATGAT
* *
3472266 TTTTGAAAACATATATATTATATAGTTTTAAAAAACA
1 TTTTGAAAAC-TATATAATATATAGTTTT-TAAAACA
* *
3472303 TTTTG-AAA-TATATATATATATAGCTTTTAAAATA
1 TTTTGAAAACTATATA-ATATATAGTTTTTAAAACA
3472337 TTTTGAAAACTTATATAATATATAGTTTTTAAAACA
1 TTTTGAAAAC-TATATAATATATAGTTTTTAAAACA
*
3472373 ATTTGAAAACTTATATAATATATAGTTTTTAAAACA
1 TTTTGAAAAC-TATATAATATATAGTTTTTAAAACA
*
3472409 TTTTTGAAAACTTATATAATATATATTTTTTAAAACA
1 -TTTTGAAAAC-TATATAATATATAGTTTTTAAAACA
*
3472446 TTTTGAAAACTTATATAATATATAATTTTTAAAACA
1 TTTTGAAAAC-TATATAATATATAGTTTTTAAAACA
* * * *
3472482 GTTTGAAATATATATATAATATATA-ATTTTAAAATA
1 TTTTGAAA-A-CTATATAATATATAGTTTTTAAAACA
3472518 TTTT
1 TTTT
3472522 TTTAAAATAT
Statistics
Matches: 197, Mismatches: 15, Indels: 15
0.87 0.07 0.07
Matches are distributed among these distances:
34 16 0.08
35 13 0.07
36 109 0.55
37 59 0.30
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (35 bp):
TTTTGAAAACTATATAATATATAGTTTTTAAAACA
Found at i:3472423 original size:73 final size:72
Alignment explanation
Indices: 3472266--3472521 Score: 333
Period size: 73 Copynumber: 3.6 Consensus size: 72
3472256 AATATATGAT
* * * *
3472266 TTTTGAAAACATATATATTATATAGTTTTAAAAAACATTTTG-AAA--TATATATATATATAGCT
1 TTTTGAAAACTTATATAATATATAGTTTT-TAAAACATTTTGAAAACTTATATA-ATATATAGTT
*
3472328 TTTAAAATA
64 TTTAAAACA
*
3472337 TTTTGAAAACTTATATAATATATAGTTTTTAAAACAATTTGAAAACTTATATAATATATAGTTTT
1 TTTTGAAAACTTATATAATATATAGTTTTTAAAACATTTTGAAAACTTATATAATATATAGTTTT
3472402 TAAAACA
66 TAAAACA
* *
3472409 TTTTTGAAAACTTATATAATATATATTTTTTAAAACATTTTGAAAACTTATATAATATATAATTT
1 -TTTTGAAAACTTATATAATATATAGTTTTTAAAACATTTTGAAAACTTATATAATATATAGTTT
3472474 TTAAAACA
65 TTAAAACA
* * *
3472482 GTTTGAAATA-TATATATAATATATA-ATTTTAAAATATTTT
1 TTTTGAAA-ACT-TATATAATATATAGTTTTTAAAACATTTT
3472522 TTTAAAATAT
Statistics
Matches: 167, Mismatches: 12, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
70 10 0.06
71 30 0.18
72 38 0.23
73 89 0.53
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (72 bp):
TTTTGAAAACTTATATAATATATAGTTTTTAAAACATTTTGAAAACTTATATAATATATAGTTTT
TAAAACA
Found at i:3476896 original size:21 final size:21
Alignment explanation
Indices: 3476867--3476919 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
3476857 ATTCTGACTA
3476867 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
3476888 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
3476909 TCGCAATGCGA
1 TCGCATTGCGA
3476920 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:3476934 original size:20 final size:20
Alignment explanation
Indices: 3476909--3477001 Score: 168
Period size: 20 Copynumber: 4.7 Consensus size: 20
3476899 TTTTCCTAAT
3476909 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
3476929 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
3476949 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
3476969 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
3476989 TCGCAACGCGAAT
1 TCGCAATGCGAAT
3477002 CTGACTATCG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:3477012 original size:40 final size:40
Alignment explanation
Indices: 3476928--3477054 Score: 145
Period size: 40 Copynumber: 3.2 Consensus size: 40
3476918 GAATACGTAA
* * *
3476928 ATCGCAATGCGAATATGTAAATCGCAATGCGAATAC-GTA-A
1 ATCGCAATGCGAATACGTAAATCGCAACGCGAAT-CTG-ACT
3476968 ATCGCAATGCGAATACGTAAATCGCAACGCGAATCTGACT
1 ATCGCAATGCGAATACGTAAATCGCAACGCGAATCTGACT
* *
3477008 ATCGCAACGCGAAT-C-TGACTATCGCAACGCGAATCTGACT
1 ATCGCAATGCGAATACGT-A-AATCGCAACGCGAATCTGACT
3477048 ATCGCAA
1 ATCGCAA
3477055 CGAGATTCTG
Statistics
Matches: 78, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
38 1 0.01
39 4 0.05
40 73 0.94
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (40 bp):
ATCGCAATGCGAATACGTAAATCGCAACGCGAATCTGACT
Found at i:3477032 original size:60 final size:60
Alignment explanation
Indices: 3476909--3477099 Score: 194
Period size: 60 Copynumber: 3.2 Consensus size: 60
3476899 TTTTCCTAAT
* * * * * *
3476909 TCGCAATGCGAATACGTAAATCGCAATGCGAATATGTA-AATCGCAATGCGAATAC-GTA-AA
1 TCGCAACGCGAATACGTAAATCGCAACGCGAATCTG-ACTATCGCAACGCGAAT-CTG-ACTA
*
3476969 TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGACTATCGCAACGCGAATCTGACTA
1 TCGCAACGCGAATACGTAAATCGCAACGCGAATCTGACTATCGCAACGCGAATCTGACTA
* * * * *
3477029 TCGCAACGCGAAT-C-TGACTATCGCAACGAGATTCTGACTATCGCAACGAGATTCTGACTA
1 TCGCAACGCGAATACGT-A-AATCGCAACGCGAATCTGACTATCGCAACGCGAATCTGACTA
3477089 TCGCAACGCGA
1 TCGCAACGCGA
3477100 TTCTGACTAT
Statistics
Matches: 115, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
58 1 0.01
59 5 0.04
60 109 0.95
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (60 bp):
TCGCAACGCGAATACGTAAATCGCAACGCGAATCTGACTATCGCAACGCGAATCTGACTA
Found at i:3477135 original size:20 final size:20
Alignment explanation
Indices: 3476988--3477134 Score: 231
Period size: 20 Copynumber: 7.3 Consensus size: 20
3476978 GAATACGTAA
*
3476988 ATCGCAACGCGAATCTGACT
1 ATCGCAACGCGATTCTGACT
*
3477008 ATCGCAACGCGAATCTGACT
1 ATCGCAACGCGATTCTGACT
*
3477028 ATCGCAACGCGAATCTGACT
1 ATCGCAACGCGATTCTGACT
*
3477048 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
3477068 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
3477088 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
3477108 ATCGCAATGTGATTCTGACT
1 ATCGCAACGCGATTCTGACT
3477128 ATCGCAA
1 ATCGCAA
3477135 TACTGAATTT
Statistics
Matches: 122, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 122 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:3478003 original size:24 final size:24
Alignment explanation
Indices: 3477976--3478029 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3477966 GTATTCGAAA
3477976 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
3478000 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
3478024 TTTGAT
1 TTTGAT
3478030 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:3480498 original size:20 final size:20
Alignment explanation
Indices: 3480461--3480549 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
3480451 TAACGCGGAA
3480461 ATCGCAACGC-AAATATGACT
1 ATCGCAACGCGAAA-ATGACT
* *
3480481 ATCTCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
3480501 ATCGCAACGCGGAAATGAAT
1 ATCGCAACGCGAAAATGACT
3480521 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
3480541 ATCGCAACG
1 ATCGCAACG
3480550 AGAGAATCGT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 57 0.95
21 3 0.05
ACGTcount: A:0.40, C:0.25, G:0.18, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:3480609 original size:34 final size:34
Alignment explanation
Indices: 3480521--3480616 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
3480511 GGAAATGAAT
* **
3480521 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
*
3480555 ATCGTAATGCG-AAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
3480588 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCGAAAATGAAAATCGCAACG
3480617 CGAAACTAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.14
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:3480652 original size:20 final size:19
Alignment explanation
Indices: 3480627--3480693 Score: 81
Period size: 20 Copynumber: 3.7 Consensus size: 19
3480617 CGAAACTAAA
3480627 TTCGCATTGCGATTTTCATT
1 TTCGCATTGCGATTTTCA-T
3480647 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
3480663 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
3480680 TTCGCATTGCGATT
1 TTCGCATTGCGATT
3480694 CTCTCGTTGC
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
14 6 0.15
16 7 0.17
17 4 0.10
18 3 0.08
19 8 0.20
20 12 0.30
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:3480672 original size:14 final size:14
Alignment explanation
Indices: 3480653--3480706 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
3480643 CATTTTCGCA
3480653 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
3480667 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
3480684 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
3480700 TTGCGAT
1 TTGCGAT
3480707 AGTCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:3480676 original size:34 final size:34
Alignment explanation
Indices: 3480633--3480726 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 34
3480623 TAAATTCGCA
3480633 TTGCGATTTTCATTTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTTCGCATTGCGATTCTCTCG
3480667 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTTCGCATTGCGATTCTCTCG
** * *
3480700 TTGCGATAGTCATTTCCGCGTTGCGAT
1 TTGCGATTTTCATTTTCGCATTGCGAT
3480727 AGTCTGTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 31 0.56
34 24 0.44
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (34 bp):
TTGCGATTTTCATTTTCGCATTGCGATTCTCTCG
Found at i:3480851 original size:14 final size:14
Alignment explanation
Indices: 3480832--3480868 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3480822 TATCAATTAA
3480832 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3480846 ACAAATCATCTTTT
1 ACAAATCAACATTT
3480860 ACAAATCAA
1 ACAAATCAA
3480869 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3482314 original size:41 final size:42
Alignment explanation
Indices: 3482250--3482331 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 42
3482240 TCAAGAATGT
*
3482250 TGGGAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGGGACCTCTTCAACGATGACAGGGGCCTCTTGAACGG
* ** *
3482292 TGGGAGGGA-CTCTTGAGGGATGATAGGGGCCTCTTGAACG
1 TGGGAGGGACCTCTTCAACGATGACAGGGGCCTCTTGAACG
3482332 ATGACAGGTG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 26 0.74
42 9 0.26
ACGTcount: A:0.21, C:0.20, G:0.38, T:0.22
Consensus pattern (42 bp):
TGGGAGGGACCTCTTCAACGATGACAGGGGCCTCTTGAACGG
Found at i:3482334 original size:21 final size:21
Alignment explanation
Indices: 3482254--3482339 Score: 75
Period size: 21 Copynumber: 4.1 Consensus size: 21
3482244 GAATGTTGGG
* *
3482254 AGGGACCTCTTCAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
* * **
3482275 AGTGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTGAACGATGAC
* ** *
3482296 A-GGGACTCTTGAGGGATGAT
1 AGGGGCCTCTTGAACGATGAC
3482316 AGGGGCCTCTTGAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
3482337 AGG
1 AGG
3482340 TGAGTCGGGC
Statistics
Matches: 47, Mismatches: 17, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
20 13 0.28
21 34 0.72
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.21
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGATGAC
Found at i:3482841 original size:20 final size:20
Alignment explanation
Indices: 3482818--3482884 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
3482808 GAAACTTAAA
3482818 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
3482838 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
** **
3482858 ATCGCAATACGAATTTGACT
1 ATCGCAACGCGAAAATGACT
3482878 ATCGCAA
1 ATCGCAA
3482885 TGAGAATTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:3482885 original size:20 final size:20
Alignment explanation
Indices: 3482833--3482900 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
3482823 AACGCGAAAA
** **
3482833 TGACTATCGCAACGCGAAAA
1 TGACTATCGCAATACGAATT
3482853 TGACTATCGCAATACGAATT
1 TGACTATCGCAATACGAATT
3482873 TGACTATCGCAATGA-GAATT
1 TGACTATCGCAAT-ACGAATT
3482893 TGACTATC
1 TGACTATC
3482901 ACAACGAGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 42 0.98
21 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (20 bp):
TGACTATCGCAATACGAATT
Found at i:3482909 original size:20 final size:20
Alignment explanation
Indices: 3482868--3482909 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3482858 ATCGCAATAC
* *
3482868 GAATTTGACTATCGCAATGA
1 GAATTTGACTATCACAACGA
3482888 GAATTTGACTATCACAACGA
1 GAATTTGACTATCACAACGA
3482908 GA
1 GA
3482910 GAATCGCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (20 bp):
GAATTTGACTATCACAACGA
Found at i:3483061 original size:20 final size:20
Alignment explanation
Indices: 3483036--3483087 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
3483026 GCGATTCTCT
3483036 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
3483056 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
3483076 CATTGCGATAGT
1 CGTTGCGATAGT
3483088 AAACTATTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:3483075 original size:87 final size:87
Alignment explanation
Indices: 3482919--3483084 Score: 242
Period size: 87 Copynumber: 1.9 Consensus size: 87
3482909 AGAATCGCAA
* * *
3482919 TGCGATTTTCATTTCGCATTGAGATTCTTTCGTTGCGATAGTCAAATTCGTATTGTGATAGTCAT
1 TGCGATTTTCATTTCGCATTGAGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
*
3482984 TTTCGCGTTGCGATTTTGTTGT
66 TTTCGCATTGCGATTTTGTTGT
* * * ** *
3483006 TGCGGTTTTTATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCAT
1 TGCGATTTTCATTTCGCATTGAGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
3483071 TTTCGCATTGCGAT
66 TTTCGCATTGCGAT
3483085 AGTAAACTAT
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.16, C:0.17, G:0.22, T:0.45
Consensus pattern (87 bp):
TGCGATTTTCATTTCGCATTGAGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
TTTCGCATTGCGATTTTGTTGT
Found at i:3483660 original size:18 final size:18
Alignment explanation
Indices: 3483614--3483660 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
3483604 TATATTCGGG
*
3483614 TCGATCAGGTGATGGCTC
1 TCGATGAGGTGATGGCTC
* *
3483632 TGGGTGAGGTGATGGCTC
1 TCGATGAGGTGATGGCTC
*
3483650 TCGATGTGGTG
1 TCGATGAGGTG
3483661 GATGCTCATC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.13, C:0.15, G:0.43, T:0.30
Consensus pattern (18 bp):
TCGATGAGGTGATGGCTC
Found at i:3485004 original size:20 final size:20
Alignment explanation
Indices: 3484981--3485109 Score: 110
Period size: 20 Copynumber: 6.8 Consensus size: 20
3484971 TCTGAAACTT
3484981 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
3485001 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
3485021 ACTATCGTAACACGAATTTG
1 AAAATCGCAACACGAAAATG
** *
3485041 ATTATCGC-A-ACG-CAA-G
1 AAAATCGCAACACGAAAATG
*
3485057 --AATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
3485074 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
* *
3485094 ACAATCGCAACGCGAA
1 AAAATCGCAACACGAA
3485110 TTTGACTATC
Statistics
Matches: 87, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
14 5 0.06
15 1 0.01
16 5 0.06
17 1 0.01
18 3 0.03
19 12 0.14
20 60 0.69
ACGTcount: A:0.47, C:0.22, G:0.17, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:3485101 original size:53 final size:54
Alignment explanation
Indices: 3485003--3485106 Score: 129
Period size: 53 Copynumber: 1.9 Consensus size: 54
3484993 CGAAAATGAA
** * ** **
3485003 AATCGCAACACGAAAATGACTATCGTAACACGAATTTGATTATCGCAACGCAAG
1 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACAATCGCAACGCAAG
*
3485057 AATCGCAACGCG-AAATGAAAATCGCAACACGAAAATGACAATCGCAACGC
1 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACAATCGCAACGC
3485107 GAATTTGACT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
53 31 0.74
54 11 0.26
ACGTcount: A:0.43, C:0.24, G:0.17, T:0.15
Consensus pattern (54 bp):
AATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACAATCGCAACGCAAG
Found at i:3485110 original size:73 final size:73
Alignment explanation
Indices: 3484983--3485157 Score: 278
Period size: 73 Copynumber: 2.4 Consensus size: 73
3484973 TGAAACTTAA
* * * *
3484983 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGTAACACGAATTTGATTATCG
1 AATCGCAACGCG-AAATGAAAATCGCAACACGAAAATGACAATCGCAACACGAATTTGACTATCG
*
3485048 CAACGCAAG
65 CAACACAAG
*
3485057 AATCGCAACGCGAAATGAAAATCGCAACACGAAAATGACAATCGCAACGCGAATTTGACTATCGC
1 AATCGCAACGCGAAATGAAAATCGCAACACGAAAATGACAATCGCAACACGAATTTGACTATCGC
3485122 AACACAAG
66 AACACAAG
*
3485130 AATCGCAACGCGAAATGAAAATCACAAC
1 AATCGCAACGCGAAATGAAAATCGCAAC
3485158 GACAGAATCG
Statistics
Matches: 94, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
73 83 0.88
74 11 0.12
ACGTcount: A:0.45, C:0.23, G:0.17, T:0.15
Consensus pattern (73 bp):
AATCGCAACGCGAAATGAAAATCGCAACACGAAAATGACAATCGCAACACGAATTTGACTATCGC
AACACAAG
Found at i:3485115 original size:20 final size:19
Alignment explanation
Indices: 3484983--3485158 Score: 93
Period size: 20 Copynumber: 9.5 Consensus size: 19
3484973 TGAAACTTAA
* *
3484983 AATCGCAACACGAAAATGAA
1 AATCGCAACGCG-AAATGAC
*
3485003 AATCGCAACACGAAAATGAC
1 AATCGCAACGCG-AAATGAC
* * * * *
3485023 TATCGTAACACGAATTTGAT
1 AATCGCAACGCGAA-ATGAC
*
3485043 TATCGCAACGC--AA-G--
1 AATCGCAACGCGAAATGAC
*
3485057 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAC
*
3485076 AATCGCAACACGAAAATGAC
1 AATCGCAACGCG-AAATGAC
*
3485096 AATCGCAACGCGAATTTGAC
1 AATCGCAACGCGAA-ATGAC
* *
3485116 TATCGCAACAC--AA-G--
1 AATCGCAACGCGAAATGAC
*
3485130 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAC
*
3485149 AATCACAACG
1 AATCGCAACG
3485159 ACAGAATCGC
Statistics
Matches: 124, Mismatches: 19, Indels: 27
0.73 0.11 0.16
Matches are distributed among these distances:
14 19 0.15
16 6 0.05
17 2 0.02
18 2 0.02
19 24 0.19
20 71 0.57
ACGTcount: A:0.45, C:0.23, G:0.17, T:0.15
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAC
Found at i:3485518 original size:22 final size:21
Alignment explanation
Indices: 3485493--3485567 Score: 87
Period size: 22 Copynumber: 3.5 Consensus size: 21
3485483 TGACCGTGAA
3485493 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGCCGGAGATGG-GAC
* *
3485515 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGCCGGAGAT-GGGAC
*
3485537 TGATTTCGTCGGAGATGGGAC
1 TGATTTCGCCGGAGATGGGAC
* *
3485558 GGATGTCGCC
1 TGATTTCGCC
3485568 TTACAGAGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 12 0.26
22 32 0.70
23 2 0.04
ACGTcount: A:0.20, C:0.17, G:0.39, T:0.24
Consensus pattern (21 bp):
TGATTTCGCCGGAGATGGGAC
Found at i:3485779 original size:20 final size:20
Alignment explanation
Indices: 3485756--3485808 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
3485746 CGATAGTCAG
*
3485756 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
3485776 ATTCGCATTGCAATTTACGT
1 ATTCGCATTGCGATTTACGT
3485796 ATTCGCATTGCGA
1 ATTCGCATTGCGA
3485809 ATTAGGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:3485822 original size:21 final size:20
Alignment explanation
Indices: 3485798--3485849 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
3485788 ATTTACGTAT
3485798 TCGCATTGCGAATTAGGAAAA
1 TCGCA-TGCGAATTAGGAAAA
* *
3485819 TCGCACGCGAATTTGGAAAA
1 TCGCATGCGAATTAGGAAAA
3485839 TCGCAATGCGA
1 TCGC-ATGCGA
3485850 TAGTCAGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (20 bp):
TCGCATGCGAATTAGGAAAA
Found at i:3485830 original size:20 final size:20
Alignment explanation
Indices: 3485805--3485843 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3485795 TATTCGCATT
3485805 GCGAATTAGGAAAATCGCAC
1 GCGAATTAGGAAAATCGCAC
*
3485825 GCGAATTTGGAAAATCGCA
1 GCGAATTAGGAAAATCGCA
3485844 ATGCGATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (20 bp):
GCGAATTAGGAAAATCGCAC
Found at i:3493217 original size:25 final size:25
Alignment explanation
Indices: 3493188--3493236 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3493178 ACTAAAACTA
3493188 ATAAAAAATATT-TAAAAAACAATAC
1 ATAAAAAAT-TTGTAAAAAACAATAC
*
3493213 ATAAAAAATTTGTAAAAAATAATA
1 ATAAAAAATTTGTAAAAAACAATA
3493237 GTTTTAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (25 bp):
ATAAAAAATTTGTAAAAAACAATAC
Found at i:3502098 original size:27 final size:28
Alignment explanation
Indices: 3502042--3502099 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
3502032 AGAGGTGAAC
*
3502042 AAAAAATCCGAATATCCGATTTTGCGCA
1 AAAAAATCCGAATATCCGATTTTGCCCA
* *
3502070 AAAAATATCCGAA-A-CCGGTTTTTCCCA
1 AAAAA-ATCCGAATATCCGATTTTGCCCA
3502097 AAA
1 AAA
3502100 CCGGTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 13 0.50
28 6 0.23
29 7 0.27
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.24
Consensus pattern (28 bp):
AAAAAATCCGAATATCCGATTTTGCCCA
Found at i:3504532 original size:21 final size:21
Alignment explanation
Indices: 3504508--3504549 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3504498 AGTTTATTTT
3504508 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
3504529 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
3504550 AACTTGGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:3504586 original size:33 final size:33
Alignment explanation
Indices: 3504544--3504646 Score: 174
Period size: 33 Copynumber: 3.2 Consensus size: 33
3504534 TTTGTTTCAA
3504544 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
3504577 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* *
3504610 TTATCGAACTTGGAAGTATTT-AGTATTTCAA-
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
3504641 TTATCG
1 TTATCG
3504647 TAAACTTTGT
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 6 0.09
32 9 0.13
33 53 0.78
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:3508224 original size:58 final size:58
Alignment explanation
Indices: 3508121--3508236 Score: 178
Period size: 58 Copynumber: 2.0 Consensus size: 58
3508111 CTTTGGAGTG
* * * *
3508121 GTTCTTCTTGAGCTGGTGACTGGTGAGAAACTTACACACGTATCCAAAGCTCCTGAGA
1 GTTCATCTTGAGCTGGTGACTGGTGAGAAACCTACACACGAATCCAAACCTCCTGAGA
* *
3508179 GTTCATCTTGAGTTGGTGACTGGTGAGAAACCTACGCACGAATCCAAACCTCCTGAGA
1 GTTCATCTTGAGCTGGTGACTGGTGAGAAACCTACACACGAATCCAAACCTCCTGAGA
3508237 TCTTCAAAGG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (58 bp):
GTTCATCTTGAGCTGGTGACTGGTGAGAAACCTACACACGAATCCAAACCTCCTGAGA
Found at i:3508559 original size:28 final size:28
Alignment explanation
Indices: 3508527--3508610 Score: 159
Period size: 28 Copynumber: 3.0 Consensus size: 28
3508517 TATAGTTGCT
*
3508527 CGAGAAATCAACGAGAGTCAGTGAAGCA
1 CGAGAAATCAAGGAGAGTCAGTGAAGCA
3508555 CGAGAAATCAAGGAGAGTCAGTGAAGCA
1 CGAGAAATCAAGGAGAGTCAGTGAAGCA
3508583 CGAGAAATCAAGGAGAGTCAGTGAAGCA
1 CGAGAAATCAAGGAGAGTCAGTGAAGCA
3508611 ATATGGAATA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.43, C:0.15, G:0.31, T:0.11
Consensus pattern (28 bp):
CGAGAAATCAAGGAGAGTCAGTGAAGCA
Found at i:3516214 original size:32 final size:32
Alignment explanation
Indices: 3516178--3516239 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
3516168 GATTACTCAA
* * *
3516178 TTGTTACTTGTTAAATTTGTTACTCATTAAGC
1 TTGTTACCTGGTAAATTTGATACTCATTAAGC
*
3516210 TTGTTACCTGGTAAATTTGATGCTCATTAA
1 TTGTTACCTGGTAAATTTGATACTCATTAA
3516240 TCTCCTCCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.47
Consensus pattern (32 bp):
TTGTTACCTGGTAAATTTGATACTCATTAAGC
Found at i:3516873 original size:2 final size:2
Alignment explanation
Indices: 3516866--3516897 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3516856 GATTTGTACC
*
3516866 AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3516898 TTTGAATATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3518139 original size:20 final size:20
Alignment explanation
Indices: 3518101--3518184 Score: 65
Period size: 19 Copynumber: 4.5 Consensus size: 20
3518091 TATTCTCTTA
*
3518101 TAATTGTTTAAGGTATTTTTAT
1 TAATTATTTAA-GTATTTTT-T
3518123 T-A-TATTTAA-TATTTTTT
1 TAATTATTTAAGTATTTTTT
3518140 TAATTATTTAAGTA---TTT
1 TAATTATTTAAGTATTTTTT
* * *
3518157 AAATTTTTTAA-TATTTATT
1 TAATTATTTAAGTATTTTTT
3518176 TAATTATTT
1 TAATTATTT
3518185 TTTTTGCATA
Statistics
Matches: 50, Mismatches: 6, Indels: 15
0.70 0.08 0.21
Matches are distributed among these distances:
16 2 0.04
17 14 0.28
18 8 0.16
19 16 0.32
20 8 0.16
21 1 0.02
22 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (20 bp):
TAATTATTTAAGTATTTTTT
Found at i:3518171 original size:16 final size:17
Alignment explanation
Indices: 3518141--3518173 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3518131 ATATTTTTTT
3518141 AATTATTTAAGTATTTA
1 AATTATTTAAGTATTTA
*
3518158 AATTTTTTAA-TATTTA
1 AATTATTTAAGTATTTA
3518174 TTTAATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
AATTATTTAAGTATTTA
Found at i:3527163 original size:12 final size:12
Alignment explanation
Indices: 3527146--3527170 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3527136 AGTTTCCAGA
3527146 TTTTCTTCTTCT
1 TTTTCTTCTTCT
3527158 TTTTCTTCTTCT
1 TTTTCTTCTTCT
3527170 T
1 T
3527171 CACCGTGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCTTCTTCT
Found at i:3527672 original size:20 final size:21
Alignment explanation
Indices: 3527629--3527681 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
3527619 CTAGGCTATG
*
3527629 TGCATCGATGCACATTCAATA
1 TGCACCGATGCACATTCAATA
3527650 TGCACCGATGCACATTC-ATA
1 TGCACCGATGCACATTCAATA
3527670 TGCACCGATGCA
1 TGCACCGATGCA
3527682 TCAAGGATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (21 bp):
TGCACCGATGCACATTCAATA
Found at i:3527748 original size:18 final size:18
Alignment explanation
Indices: 3527714--3527763 Score: 91
Period size: 18 Copynumber: 2.7 Consensus size: 18
3527704 TTCAAGGTGT
3527714 ATCGATGCACATAAAGTGC
1 ATCGATGCAC-TAAAGTGC
3527733 ATCGATGCACTAAAGTGC
1 ATCGATGCACTAAAGTGC
3527751 ATCGATGCACTAA
1 ATCGATGCACTAA
3527764 TTTAAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 21 0.68
19 10 0.32
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (18 bp):
ATCGATGCACTAAAGTGC
Found at i:3527842 original size:63 final size:63
Alignment explanation
Indices: 3527728--3527887 Score: 161
Period size: 63 Copynumber: 2.5 Consensus size: 63
3527718 ATGCACATAA
*
3527728 AGTGCATCGATGCACTAAAGTGCATCGATGCACTAATTTAAAATAAAAACATCGAATGCCATC
1 AGTGCATCGATGCACTAAAGTGCATCGATGCACCAATTTAAAATAAAAACATCGAATGCCATC
* * * *
3527791 AGTGTATCGATGCAC-AAGTAGTGCATCGATGCACCCCA-TT-AAATACAAACATCGAATG-GAT
1 AGTGCATCGATGCACTAA--AGTGCATCGATGCA-CCAATTTAAAATAAAAACATCGAATGCCA-
*
3527852 TT
62 TC
*
3527854 A-TGCACCGATGCA-TAGATAGTGCATCGATGCACC
1 AGTGCATCGATGCACTA-A-AGTGCATCGATGCACC
3527888 CATCAAGGGA
Statistics
Matches: 83, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
61 2 0.02
62 29 0.35
63 34 0.41
64 16 0.19
65 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.24
Consensus pattern (63 bp):
AGTGCATCGATGCACTAAAGTGCATCGATGCACCAATTTAAAATAAAAACATCGAATGCCATC
Found at i:3528573 original size:23 final size:23
Alignment explanation
Indices: 3528522--3528583 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
3528512 ACAATCTTAT
*
3528522 ATGGCACTACGGTGCAATTCTAC
1 ATGGCACTTCGGTGCAATTCTAC
**
3528545 GCGGCACTTCGGTGCAATTCTAC
1 ATGGCACTTCGGTGCAATTCTAC
*
3528568 ATGGCACTTTGGTGCA
1 ATGGCACTTCGGTGCA
3528584 TTTATACGAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.27
Consensus pattern (23 bp):
ATGGCACTTCGGTGCAATTCTAC
Found at i:3529703 original size:35 final size:32
Alignment explanation
Indices: 3529668--3529749 Score: 85
Period size: 35 Copynumber: 2.4 Consensus size: 32
3529658 TTTGGTTAAT
3529668 TTTGTT-TATTACCATTTAATATCAGTTATTGTAA
1 TTTGTTATATTACCATTTAATA-C--TTATTGTAA
3529702 TTTGTTTATCATTTACCATTTAATACTTATTGTAA
1 TTTG-TTAT-A-TTACCATTTAATACTTATTGTAA
*
3529737 GTTTGTTGTATTA
1 -TTTGTTATATTA
3529750 AAATTATTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
33 3 0.07
34 5 0.12
35 14 0.33
36 5 0.12
37 2 0.05
38 13 0.31
ACGTcount: A:0.27, C:0.09, G:0.10, T:0.55
Consensus pattern (32 bp):
TTTGTTATATTACCATTTAATACTTATTGTAA
Found at i:3535127 original size:38 final size:38
Alignment explanation
Indices: 3535076--3535163 Score: 158
Period size: 38 Copynumber: 2.3 Consensus size: 38
3535066 GTAACTAGAC
3535076 TGTTCTTTTTTTAAAGGATTTTATTATCTAAATTGTCT
1 TGTTCTTTTTTTAAAGGATTTTATTATCTAAATTGTCT
3535114 TGTTCTTTTTTTAAAGGATTTTATTATCTAAATTGTCT
1 TGTTCTTTTTTTAAAGGATTTTATTATCTAAATTGTCT
*
3535152 TGTGTATTTTTT
1 TGT-TCTTTTTT
3535164 ATACTAAGGA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 41 0.85
39 7 0.15
ACGTcount: A:0.22, C:0.07, G:0.11, T:0.60
Consensus pattern (38 bp):
TGTTCTTTTTTTAAAGGATTTTATTATCTAAATTGTCT
Found at i:3535312 original size:31 final size:30
Alignment explanation
Indices: 3535266--3535369 Score: 115
Period size: 31 Copynumber: 3.5 Consensus size: 30
3535256 AAGTTGAAGG
3535266 TTAAATT-A-ATTTTATCTAAGTTTAAAGA
1 TTAAATTAATATTTTATCTAAGTTTAAAGA
** *
3535294 TTAAATTGAGAT-TTTTATCTAAAATTAAAGG
1 TTAAATT-A-ATATTTTATCTAAGTTTAAAGA
3535325 TTAAATTAATATTTTATCTAAAGTTTAAAGA
1 TTAAATTAATATTTTATCT-AAGTTTAAAGA
* *
3535356 TCAAATTAAAATTT
1 TTAAATTAATATTT
3535370 AAGTTTTTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
28 7 0.11
29 2 0.03
30 9 0.15
31 44 0.71
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (30 bp):
TTAAATTAATATTTTATCTAAGTTTAAAGA
Found at i:3535328 original size:59 final size:62
Alignment explanation
Indices: 3535248--3535362 Score: 173
Period size: 59 Copynumber: 1.9 Consensus size: 62
3535238 CAGGTAGGTA
* * * *
3535248 TTTATTTAAAGTTGAAGGTTAAATT-A-ATTTTATCT-AAGTTTAAAGATTAAATTGAGATT
1 TTTATCTAAAATTAAAGGTTAAATTAATATTTTATCTAAAGTTTAAAGATCAAATTGAGATT
3535307 TTTATCTAAAATTAAAGGTTAAATTAATATTTTATCTAAAGTTTAAAGATCAAATT
1 TTTATCTAAAATTAAAGGTTAAATTAATATTTTATCTAAAGTTTAAAGATCAAATT
3535363 AAAATTTAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 22 0.45
60 1 0.02
61 9 0.18
62 17 0.35
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.44
Consensus pattern (62 bp):
TTTATCTAAAATTAAAGGTTAAATTAATATTTTATCTAAAGTTTAAAGATCAAATTGAGATT
Found at i:3540676 original size:55 final size:55
Alignment explanation
Indices: 3540592--3540701 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
3540582 TATATTTGAT
* *
3540592 ATTTAAATTTTATGAAAAGACCATAGTATTAATTTCTCAAGAAGCCAATTTAATA
1 ATTTAAATTTTATGAAAAGACCATAGTATTAAATTCTCAAGAAGCCAATTGAATA
3540647 ATTTAAATTTTATGAAAAGACCATAGTATTAAATTCTCAAGAAGCCAATTGAATA
1 ATTTAAATTTTATGAAAAGACCATAGTATTAAATTCTCAAGAAGCCAATTGAATA
3540702 GCATATTCCA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.35
Consensus pattern (55 bp):
ATTTAAATTTTATGAAAAGACCATAGTATTAAATTCTCAAGAAGCCAATTGAATA
Found at i:3545928 original size:13 final size:13
Alignment explanation
Indices: 3545910--3545936 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3545900 ACATGTTAAT
3545910 ACTTGGTCAAATA
1 ACTTGGTCAAATA
3545923 ACTTGGTCAAATA
1 ACTTGGTCAAATA
3545936 A
1 A
3545937 GCAAAAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ACTTGGTCAAATA
Found at i:3550910 original size:21 final size:21
Alignment explanation
Indices: 3550881--3550933 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
3550871 ATTCTCACTA
3550881 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
3550902 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
3550923 TCGCAATGCGA
1 TCGCATTGCGA
3550934 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:3550948 original size:20 final size:20
Alignment explanation
Indices: 3550923--3551053 Score: 158
Period size: 20 Copynumber: 6.7 Consensus size: 20
3550913 TTTTCCTAAT
3550923 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
3550943 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
3550963 TCGCAATGCAAATAC-T-AT
1 TCGCAATGCGAATACGTAAA
* *
3550981 TCGCATTACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
** *
3551001 TCGCAATATGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
* **
3551021 TCGCAATACGAATATATAAA
1 TCGCAATGCGAATACGTAAA
3551041 TCGCAATGCGAAT
1 TCGCAATGCGAAT
3551054 CTGACTATTG
Statistics
Matches: 97, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
18 13 0.13
19 2 0.02
20 82 0.85
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:3551066 original size:20 final size:20
Alignment explanation
Indices: 3551043--3551126 Score: 69
Period size: 20 Copynumber: 4.2 Consensus size: 20
3551033 TATATAAATC
*
3551043 GCAATGCGAATCTGACTATT
1 GCAACGCGAATCTGACTATT
* *
3551063 GCAACGCTAATCTGACTATC
1 GCAACGCGAATCTGACTATT
* * * *
3551083 ACAACGAGATTCTGACTATC
1 GCAACGCGAATCTGACTATT
* * * *
3551103 GTAACGAGATTCTGACTATC
1 GCAACGCGAATCTGACTATT
3551123 GCAA
1 GCAA
3551127 TACTGAATTT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (20 bp):
GCAACGCGAATCTGACTATT
Found at i:3552014 original size:24 final size:24
Alignment explanation
Indices: 3551956--3552002 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
3551946 AGTCAGTATT
*
3551956 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
3551980 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
3552003 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:3554479 original size:20 final size:19
Alignment explanation
Indices: 3554456--3554529 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 19
3554446 TAACGCGAAT
3554456 ATGACTATCGCAACATGGAA
1 ATGACTATCGCAACA-GGAA
3554476 ATGACTATCGCAAC-GCGAA
1 ATGACTATCGCAACAG-GAA
*
3554495 ATTCACTATCGCAACACGGAA
1 A-TGACTATCGCAACA-GGAA
3554516 ATGACTATCGCAAC
1 ATGACTATCGCAAC
3554530 GAAAGAATCG
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.02
19 4 0.08
20 38 0.79
21 4 0.08
22 1 0.02
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.19
Consensus pattern (19 bp):
ATGACTATCGCAACAGGAA
Found at i:3554503 original size:40 final size:40
Alignment explanation
Indices: 3554442--3554530 Score: 135
Period size: 40 Copynumber: 2.2 Consensus size: 40
3554432 CAACGCGGAA
* * *
3554442 ATCGTAACGCGAATATGACTATCGCAACATGGAAATGACT
1 ATCGCAACGCGAATATCACTATCGCAACACGGAAATGACT
3554482 ATCGCAACGCGAA-ATTCACTATCGCAACACGGAAATGACT
1 ATCGCAACGCGAATA-TCACTATCGCAACACGGAAATGACT
3554522 ATCGCAACG
1 ATCGCAACG
3554531 AAAGAATCGC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 1 0.02
40 44 0.98
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (40 bp):
ATCGCAACGCGAATATCACTATCGCAACACGGAAATGACT
Found at i:3554541 original size:14 final size:14
Alignment explanation
Indices: 3554522--3554575 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
3554512 GGAAATGACT
3554522 ATCGCAACGAAAGA
1 ATCGCAACGAAAGA
3554536 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CGAAA-G--A
*
3554555 ATCGCAACGAGAGA
1 ATCGCAACGAAAGA
3554569 ATCGCAA
1 ATCGCAA
3554576 TGCGAAAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 15 0.44
16 6 0.18
17 5 0.15
19 8 0.24
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAAAGA
Done.