Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007923.1 Hibiscus syriacus cultivar Beakdansim tig00110328_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: 8415618
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 40
Found at i:1501100 original size:19 final size:20
Alignment explanation
Indices: 1501064--1501111 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
1501054 ATAATAATCT
*
1501064 TATTTTTAATATTGTAATAA
1 TATTTTAAATATTGTAATAA
* *
1501084 TATTTTAAAT-TTTTAATTA
1 TATTTTAAATATTGTAATAA
*
1501103 TATATTAAA
1 TATTTTAAA
1501112 ACTTAACTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TATTTTAAATATTGTAATAA
Found at i:1502606 original size:14 final size:14
Alignment explanation
Indices: 1502583--1502621 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
1502573 AAGTTATGAT
1502583 AATTTGTGAAAATA
1 AATTTGTGAAAATA
*
1502597 AATTTTTG-AAATA
1 AATTTGTGAAAATA
1502610 AATTTGTGAAAA
1 AATTTGTGAAAA
1502622 CAAAAGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (14 bp):
AATTTGTGAAAATA
Found at i:1506752 original size:15 final size:15
Alignment explanation
Indices: 1506729--1506801 Score: 60
Period size: 16 Copynumber: 4.7 Consensus size: 15
1506719 TAGCATAAGT
*
1506729 AAAACAAATAAAATG
1 AAAAAAAATAAAATG
*
1506744 AAAAAAAAT-AAATT
1 AAAAAAAATAAAATG
*
1506758 AACAGAAAATAAAATG
1 AA-AAAAAATAAAATG
*
1506774 AAAAAATAA-ATAAAGG
1 AAAAAA-AATA-AAATG
1506790 AAAAAAATATAA
1 AAAAAAA-ATAA
1506802 GAACATAGAG
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
14 6 0.13
15 19 0.41
16 20 0.43
17 1 0.02
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (15 bp):
AAAAAAAATAAAATG
Found at i:1506797 original size:30 final size:28
Alignment explanation
Indices: 1506729--1506798 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 28
1506719 TAGCATAAGT
**
1506729 AAAACAAATAAAATGAAAAAAAATAAATT
1 AAAA-AAATAAAATGAAAAAAAATAAAGG
1506758 AACAGAAAATAAAATGAAAAAATAAATAAAGG
1 AA-A-AAAATAAAATG-AAAAA-AAATAAAGG
1506790 AAAAAAATA
1 AAAAAAATA
1506799 TAAGAACATA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
29 2 0.06
30 17 0.49
31 7 0.20
32 9 0.26
ACGTcount: A:0.76, C:0.03, G:0.07, T:0.14
Consensus pattern (28 bp):
AAAAAAATAAAATGAAAAAAAATAAAGG
Found at i:1506911 original size:2 final size:2
Alignment explanation
Indices: 1506906--1506934 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1506896 AATATAAAGA
1506906 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1506935 AGTTATCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1507281 original size:4 final size:4
Alignment explanation
Indices: 1507272--1507406 Score: 53
Period size: 4 Copynumber: 32.5 Consensus size: 4
1507262 AACAAAATAC
* * * * * *
1507272 AAAT AAAT AAAT AATAT ATAT ATAT AAAT TAAG ATAT AAA- AAAT AAAA
1 AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * * * *
1507320 ATAAT AGTAA- AAAT AAAT AAAT AAAT AAAC CAA- AAAT AACT GAAT ATAGT
1 A-AAT A--AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT
*
1507370 AAAT AAAAT AGAA- AAAT ATAATT AAAT ATAT AAAT AA
1 AAAT -AAAT A-AAT AAAT A-AA-T AAAT AAAT AAAT AA
1507407 TAATACTAGA
Statistics
Matches: 98, Mismatches: 21, Indels: 24
0.69 0.15 0.17
Matches are distributed among these distances:
3 9 0.09
4 64 0.65
5 20 0.20
6 5 0.05
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:1509546 original size:95 final size:98
Alignment explanation
Indices: 1509380--1509784 Score: 397
Period size: 106 Copynumber: 4.0 Consensus size: 98
1509370 AAATTGTTTG
** * * *
1509380 TTGACAGTCAGCCGCACCTTCG-CTGTGAAGTTGAGCTTGTACTGTATCGAGTCTAATATCCTTC
1 TTGACAGTCAGCCGC-CCTTCGTC-GTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCCTTC
* ** *
1509444 GTTGTGAAGTAAAAATTGACTCTG-AA-T-GAAA-
64 GTCGTGAAGTTGAAATTGGCTCTGAAATTGGAAAT
* * *
1509475 CTGACAGTCAGCCGCTCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCCTTCA
1 TTGACAGTCAGCCGC-CCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCCTTCG
1509540 TCGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTT
65 TCGTGAAGTTGAAATTGGCTCTGAAATTGG-AAA-----T
* * * * *
1509580 GTTGACAATCAGCTGCCCCTTCATCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATGCTTC
1 -TTGACAGTCAGCCG-CCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCCTTC
* *
1509645 GTTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATTGTTT
64 GTCGTGAAGTTGAAATTGGCTCTGAAATT-GGAAA-----T
* * *
1509686 GTTGACAGTCAGCCGCCCATTCGTCGTGAAGTTGAGCTTGTGTTGTCTGGGGTCCAATATCTTTC
1 -TTGACAGTCAGCCGCCC-TTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCCTTC
1509751 GTCGTGAAGTTGAAATTGGCTCTGAAATTAGGAA
64 GTCGTGAAGTTGAAATTGGCTCTGAAATT-GGAA
1509785 GCCCCTTCGT
Statistics
Matches: 263, Mismatches: 32, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
95 74 0.28
96 2 0.01
97 1 0.00
98 1 0.00
99 3 0.01
105 3 0.01
106 176 0.67
107 3 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (98 bp):
TTGACAGTCAGCCGCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCCTTCGT
CGTGAAGTTGAAATTGGCTCTGAAATTGGAAAT
Found at i:1509583 original size:201 final size:205
Alignment explanation
Indices: 1509322--1509784 Score: 526
Period size: 201 Copynumber: 2.2 Consensus size: 205
1509312 ATACTGCTCC
* * **** *
1509322 GAGTCAAATATCC-TCATCCGTGAAGTTGAAATTGGTTCTGGCCCTGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCAT-CGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTGTTGACA
* * *
1509386 GTCAGCCGCACCTTC-GCTGTGAAGTTGAGCTTGTACTGTATCGAGTCTAATATCCTTCGTTGTG
65 ATCAGCCGCACCTTCATC-GTGAAGTTGAGCTTGTACTGTATCGAGTCCAATATCCTTCGTTGTG
* *
1509450 AAGTAAAAATTGACTCTG-AA-T-GAAA-CTGACAGTCAGCCGCTCC-TTCGTTGTGAAGTTGAG
129 AAGTAAAAATTGACTATGAAATTGGAAATCTGACAGTCAGCCGC-CCATTCGTCGTGAAGTTGAG
*
1509510 CTTGTGTTGTCTT
193 CTTGTGTTGTCTG
1509523 GAGTCCAATATCCTTCATCGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCATCGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTGTTGACAA
* * ** * * * *
1509588 TCAGCTGCCCCTTCATCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATGCTTCGTTGTGAA
66 TCAGCCGCACCTTCATCGTGAAGTTGAGCTTGTACTGTATCGAGTCCAATATCCTTCGTTGTGAA
** * *
1509653 GTTGAAATTGGCTATGAAATTGGGAAATTGTTTGTTGACAGTCAGCCGCCCATTCGTCGTGAAGT
131 GTAAAAATTGACTATGAAATT-GGAAA-----T-CTGACAGTCAGCCGCCCATTCGTCGTGAAGT
1509718 TGAGCTTGTGTTGTCTG
189 TGAGCTTGTGTTGTCTG
* * *
1509735 GGGTCCAATATCTTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTAGGAA
1 GAGTCCAATATCCTTCATCGTGAAGTTGAAATTGGCTCTGAAATT-GGAA
1509785 GCCCCTTCGT
Statistics
Matches: 219, Mismatches: 28, Indels: 18
0.83 0.11 0.07
Matches are distributed among these distances:
201 117 0.53
202 7 0.03
203 1 0.00
205 4 0.02
211 2 0.01
212 84 0.38
213 4 0.02
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (205 bp):
GAGTCCAATATCCTTCATCGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTGTTGACAA
TCAGCCGCACCTTCATCGTGAAGTTGAGCTTGTACTGTATCGAGTCCAATATCCTTCGTTGTGAA
GTAAAAATTGACTATGAAATTGGAAATCTGACAGTCAGCCGCCCATTCGTCGTGAAGTTGAGCTT
GTGTTGTCTG
Found at i:1509661 original size:106 final size:105
Alignment explanation
Indices: 1509476--1509784 Score: 474
Period size: 106 Copynumber: 2.9 Consensus size: 105
1509466 TGAATGAAAC
* * * *
1509476 TGACAGTCAGCCGCTCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCCTTCAT
1 TGACAGTCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATAT-CTTCGT
1509541 CGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTGT
65 CGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTGT
* * *
1509582 TGACAATCAGCTGCCCCTTCATCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATGCTTCGT
1 TGACAGTCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATAT-CTTCGT
* * *
1509647 TGTGAAGTTGAAATTGGCTATGAAATTGGGAAATTGTTTGT
65 CGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTGT
* *
1509688 TGACAGTCAGCCGCCCATTCGTCGTGAAGTTGAGCTTGTGTTGTCTGGGGTCCAATATCTTTCGT
1 TGACAGTCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATC-TTCGT
1509753 CGTGAAGTTGAAATTGGCTCTGAAATTAGGAA
65 CGTGAAGTTGAAATTGGCTCTGAAATT-GGAA
1509785 GCCCCTTCGT
Statistics
Matches: 182, Mismatches: 19, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
105 1 0.01
106 178 0.98
107 3 0.02
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (105 bp):
TGACAGTCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCTTCGTC
GTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTGT
Found at i:1510909 original size:8 final size:7
Alignment explanation
Indices: 1510894--1510942 Score: 64
Period size: 8 Copynumber: 6.7 Consensus size: 7
1510884 CTTATTTTTC
1510894 TTTTCTT
1 TTTTCTT
1510901 TTGTTCTT
1 TT-TTCTT
1510909 TTTCTCTT
1 TTT-TCTT
1510917 TTTTCTCT
1 TTTTCT-T
1510925 TTTTC-T
1 TTTTCTT
1510931 TTTTCTT
1 TTTTCTT
1510938 TTTTC
1 TTTTC
1510943 AATTTAGGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 6 0.16
7 12 0.32
8 20 0.53
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (7 bp):
TTTTCTT
Found at i:1510913 original size:6 final size:6
Alignment explanation
Indices: 1510888--1510940 Score: 56
Period size: 6 Copynumber: 8.8 Consensus size: 6
1510878 ACCCACCTTA
* *
1510888 TTTTTC -TTTTC TTTTGTTC TTTTTC TCTTT- TTTCTC TTTTTC TTTTTC
1 TTTTTC TTTTTC -TTT-TTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
1510936 TTTTT
1 TTTTT
1510941 TCAATTTAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 8 0.21
6 23 0.59
7 5 0.13
8 3 0.08
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:1510922 original size:23 final size:22
Alignment explanation
Indices: 1510894--1510941 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 22
1510884 CTTATTTTTC
1510894 TTTTCT-TTTGTTCTTTTTCTCTT
1 TTTTCTCTTT-TTCTTTTTCT-TT
1510917 TTTTCTCTTTTTCTTTTTCTTT
1 TTTTCTCTTTTTCTTTTTCTTT
1510939 TTT
1 TTT
1510942 CAATTTAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 5 0.21
23 16 0.67
24 3 0.12
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (22 bp):
TTTTCTCTTTTTCTTTTTCTTT
Found at i:1510995 original size:7 final size:7
Alignment explanation
Indices: 1510979--1511015 Score: 56
Period size: 7 Copynumber: 5.0 Consensus size: 7
1510969 ACCCTAAATG
1510979 TTTTTCTC
1 TTTTT-TC
1510987 TTTTTTC
1 TTTTTTC
1510994 TTTTTCTC
1 TTTTT-TC
1511002 TTTTTTC
1 TTTTTTC
1511009 TTTTTTC
1 TTTTTTC
1511016 AACTTAGGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 16 0.57
8 12 0.43
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTTC
Found at i:1510997 original size:15 final size:15
Alignment explanation
Indices: 1510979--1511013 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1510969 ACCCTAAATG
1510979 TTTTTCTCTTTTTTC
1 TTTTTCTCTTTTTTC
1510994 TTTTTCTCTTTTTTC
1 TTTTTCTCTTTTTTC
1511009 TTTTT
1 TTTTT
1511014 TCAACTTAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTCTCTTTTTTC
Found at i:1511032 original size:73 final size:72
Alignment explanation
Indices: 1510907--1511042 Score: 197
Period size: 73 Copynumber: 1.9 Consensus size: 72
1510897 TCTTTTGTTC
* *
1510907 TTTTTCTCTTTTTTCTCTTTTTCTTTTTCTTTTTTCAATTTAGGGAGTCCTTTC-AGGTTTTCAC
1 TTTTTCTCTTTTTTCTCTTTTTCTTTTTCTTTTTTCAACTTAGGGAGCCCTTTCGA-GTTTTCAC
1510971 CCTAAATG
65 CCTAAATG
1510979 TTTTTCTCTTTTTTCT-TTTTCTCTTTTTTCTTTTTTCAACTTA-GGACGCCCTTTCGAGTTTTC
1 TTTTTCTCTTTTTTCTCTTTT-TC-TTTTTCTTTTTTCAACTTAGGGA-GCCCTTTCGAGTTTTC
1511042 A
63 A
1511043 TTCTAAGCGA
Statistics
Matches: 58, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
71 4 0.07
72 21 0.36
73 32 0.55
74 1 0.02
ACGTcount: A:0.11, C:0.21, G:0.09, T:0.60
Consensus pattern (72 bp):
TTTTTCTCTTTTTTCTCTTTTTCTTTTTCTTTTTTCAACTTAGGGAGCCCTTTCGAGTTTTCACC
CTAAATG
Found at i:1521259 original size:16 final size:16
Alignment explanation
Indices: 1521212--1521274 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 16
1521202 AAGGAAAACA
1521212 AATAAAATGAAAAAA-
1 AATAAAATGAAAAAAT
*
1521227 AAT-AAAT-AAACAGAT
1 AATAAAATGAAA-AAAT
1521242 AATAAAATGAAAAAAT
1 AATAAAATGAAAAAAT
*
1521258 AA-ATAAAGGAAAAAAT
1 AATA-AAATGAAAAAAT
1521274 A
1 A
1521275 TAAGAACATA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
13 3 0.08
14 6 0.15
15 7 0.17
16 21 0.52
17 3 0.08
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.16
Consensus pattern (16 bp):
AATAAAATGAAAAAAT
Found at i:1522512 original size:10 final size:9
Alignment explanation
Indices: 1522477--1522556 Score: 70
Period size: 10 Copynumber: 8.3 Consensus size: 9
1522467 GCTGCTGGAA
*
1522477 ACCGGTTTA
1 ACCGGTTTG
*
1522486 ACCGGTTTTCA
1 ACCGG-TTT-G
1522497 ACCGGTTCTG
1 ACCGGTT-TG
1522507 ACCGGTTTG
1 ACCGGTTTG
*
1522516 ACCGGTTTCA
1 ACCGGTTT-G
*
1522526 ACCGGTTCG
1 ACCGGTTTG
1522535 AACCGGTTTG
1 -ACCGGTTTG
*
1522545 ACCGGTCTG
1 ACCGGTTTG
1522554 ACC
1 ACC
1522557 CGACCCGACC
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
9 26 0.43
10 27 0.45
11 7 0.12
ACGTcount: A:0.16, C:0.29, G:0.26, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:1522539 original size:29 final size:30
Alignment explanation
Indices: 1522476--1522550 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
1522466 GGCTGCTGGA
*
1522476 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
1522507 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
1522535 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
1522551 CTGACCCGAC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 13 0.31
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:1522575 original size:12 final size:12
Alignment explanation
Indices: 1522558--1522601 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
1522548 GGTCTGACCC
1522558 GACCCGACCGTT
1 GACCCGACCGTT
*
1522570 GACCCGACC--C
1 GACCCGACCGTT
1522580 GACCCGACCGTT
1 GACCCGACCGTT
1522592 GACCCGACCG
1 GACCCGACCG
1522602 ACCGTTGACT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.32
12 19 0.68
ACGTcount: A:0.18, C:0.48, G:0.25, T:0.09
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:1522579 original size:22 final size:22
Alignment explanation
Indices: 1522553--1522604 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1522543 TGACCGGTCT
1522553 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
1522575 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
1522597 GA-CCGACC
1 GACCCGACC
1522605 GTTGACTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 6 0.20
22 24 0.80
ACGTcount: A:0.19, C:0.50, G:0.23, T:0.08
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:1522604 original size:16 final size:17
Alignment explanation
Indices: 1522552--1522610 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 17
1522542 TTGACCGGTC
1522552 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
1522569 TGACCCGACCCGACCCGACCGT
1 T-----GACCCGACCCGACCGT
1522591 TGACCCGA-CCGACCGT
1 TGACCCGACCCGACCGT
1522607 TGAC
1 TGAC
1522611 TGTTGACTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
16 12 0.32
17 8 0.22
22 17 0.46
ACGTcount: A:0.19, C:0.46, G:0.24, T:0.12
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:1524222 original size:27 final size:28
Alignment explanation
Indices: 1524181--1524265 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 28
1524171 AAATAATAGT
1524181 AAAAATAAATAAATA-AATAAATAAACC
1 AAAAATAAATAAATATAATAAATAAACC
* * * **
1524208 AAAAATAACTGAATATAGTAAATAAAATAG
1 AAAAATAAATAAATATAATAAAT-AAA-CC
1524238 AAAAATATAATTAAATATATATAAATAA
1 AAAAATA-AA-TAAATATA-ATAAATAA
1524266 TAATACTAGA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
27 13 0.30
28 6 0.14
29 3 0.07
30 7 0.16
31 1 0.02
32 9 0.20
33 5 0.11
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (28 bp):
AAAAATAAATAAATATAATAAATAAACC
Found at i:1533221 original size:15 final size:14
Alignment explanation
Indices: 1533197--1533235 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
1533187 ATCCATTTTT
1533197 CATAACATATCACA
1 CATAACATATCACA
1533211 CATACACATATCACA
1 CATA-ACATATCACA
* *
1533226 TATAATATAT
1 CATAACATAT
1533236 ATATTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (14 bp):
CATAACATATCACA
Found at i:1533403 original size:31 final size:31
Alignment explanation
Indices: 1533355--1533476 Score: 192
Period size: 31 Copynumber: 4.0 Consensus size: 31
1533345 CCCGAATGAC
* *
1533355 CAGTCCATATGTTCCGAATAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
1533386 AAGTTCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1533417 CAGTCCATATGTCCC-AAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1533447 CAGTCCATATGTTCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
1533477 CCCTCGACTC
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
30 29 0.35
31 54 0.65
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1533456 original size:61 final size:62
Alignment explanation
Indices: 1533355--1533476 Score: 192
Period size: 61 Copynumber: 2.0 Consensus size: 62
1533345 CCCGAATGAC
* * *
1533355 CAGTCCATATGTTCCGAATAACATAGGTAAAAAGTTCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCCAAGAACATAGGTAAAAAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
1533417 CAGTCCATATG-TCCCAAGAACATAGGTAAACAGTCCATATGTTCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCCAAGAACATAGGTAAAAAGTCCATATGTCCCGAAGAACATAGGTAA
1533477 CCCTCGACTC
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
61 44 0.80
62 11 0.20
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (62 bp):
CAGTCCATATGTTCCCAAGAACATAGGTAAAAAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1534893 original size:196 final size:196
Alignment explanation
Indices: 1534559--1534956 Score: 778
Period size: 196 Copynumber: 2.0 Consensus size: 196
1534549 AATTTGATGC
1534559 TAATAACTTAAACGAATTTAATAGACCCATATTCACTTTTTCCTTTAGGAGTGTACCGATGCACT
1 TAATAACTTAAACGAATTTAATAGACCCATATTCACTTTTTCCTTTAGGAGTGTACCGATGCACT
1534624 ATGGGTACATCAGTACCCAAAATAGCTTCAAAATTTTCATGCATCGATGCCTGTCGGTGTGTATC
66 ATGGGTACATCAGTACCCAAAATAGCTTCAAAATTTTCATGCATCGATGCCTGTCGGTGTGTATC
1534689 GATGCACCTTCAAAATTGGTCTTAGTGCATCGGTACCCACTCATAGTGTATTGATGCACCTATCA
131 GATGCACCTTCAAAATTGGTCTTAGTGCATCGGTACCCACTCATAGTGTATTGATGCACCTATCA
1534754 A
196 A
*
1534755 TAATAACTTAAACGAATTTAATAGACTCATATTCACTTTTTCCTTTAGGAGTGTACCGATGCACT
1 TAATAACTTAAACGAATTTAATAGACCCATATTCACTTTTTCCTTTAGGAGTGTACCGATGCACT
*
1534820 ATGGGTACATCGGTACCCAAAATAGCTTCAAAATTTTCATGCATCGATGCCTGTCGGTGTGTATC
66 ATGGGTACATCAGTACCCAAAATAGCTTCAAAATTTTCATGCATCGATGCCTGTCGGTGTGTATC
1534885 GATGCACCTTCAAAATTGGTCTTAGTGCATCGGTACCCACTCATAGTGTATTGATGCACCTATCA
131 GATGCACCTTCAAAATTGGTCTTAGTGCATCGGTACCCACTCATAGTGTATTGATGCACCTATCA
1534950 A
196 A
1534951 TAATAA
1 TAATAA
1534957 ATTGGTTTCA
Statistics
Matches: 200, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
196 200 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32
Consensus pattern (196 bp):
TAATAACTTAAACGAATTTAATAGACCCATATTCACTTTTTCCTTTAGGAGTGTACCGATGCACT
ATGGGTACATCAGTACCCAAAATAGCTTCAAAATTTTCATGCATCGATGCCTGTCGGTGTGTATC
GATGCACCTTCAAAATTGGTCTTAGTGCATCGGTACCCACTCATAGTGTATTGATGCACCTATCA
A
Found at i:1540284 original size:22 final size:23
Alignment explanation
Indices: 1540231--1540285 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 23
1540221 ACTGTTTAAA
1540231 ATTTAGACCGGTTATGTTATATC
1 ATTTAGACCGGTTATGTTATATC
1540254 A-TTAGACCGGTTATGTTATATC
1 ATTTAGACCGGTTATGTTATATC
1540276 ATTTA-ACCGG
1 ATTTAGACCGG
1540286 AAATATTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 27 0.87
23 4 0.13
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (23 bp):
ATTTAGACCGGTTATGTTATATC
Found at i:1540294 original size:22 final size:22
Alignment explanation
Indices: 1540233--1540294 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
1540223 TGTTTAAAAT
** *
1540233 TTAGACCGGTTATGTTATATCA
1 TTAGACCGGAAATATTATATCA
** *
1540255 TTAGACCGGTTATGTTATATCA
1 TTAGACCGGAAATATTATATCA
1540277 TTTA-ACCGGAAATATTAT
1 -TTAGACCGGAAATATTAT
1540295 CAAGTACAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 33 0.92
23 3 0.08
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (22 bp):
TTAGACCGGAAATATTATATCA
Found at i:1540338 original size:23 final size:23
Alignment explanation
Indices: 1540303--1540350 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1540293 ATCAAGTACA
*
1540303 ATAATATATTAGGTAACGCTTAT
1 ATAATATAATAGGTAACGCTTAT
* *
1540326 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAACGCTTAT
1540349 AT
1 AT
1540351 TGACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAACGCTTAT
Found at i:1541097 original size:182 final size:182
Alignment explanation
Indices: 1540784--1541240 Score: 720
Period size: 182 Copynumber: 2.5 Consensus size: 182
1540774 ACTTTTTTAC
* * *
1540784 TACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACATGTCATATTATTATGGATCAA
1 TACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCAA
* *
1540849 TAAATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTTTTCTTTTTTAAATTCCAAAAG
66 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTTTTCTTTTTTAAATTCCAAAAG
* * *
1540914 TGTCGATACTTATAATAAAGTATTGACACTTTCAACATATTCGGTAGC-TCTT
131 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGT-TT
* *
1540966 TATCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCAA
*
1541031 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAA-TTTCTTCTTTTTTAAATTCTAAAA
66 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTT-TTCTTTTTTAAATTCCAAAA
*
1541095 GTGTCTATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGTTT
130 GTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGTTT
* ** * *
1541148 TACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCA
1 TACCGGTTTTGTCATTTCGAGACCGATTTTGTCA-TATTTTTACCTGTTATATTGTTATGGATCA
1541213 ATACATTTTTATAAAGTATCGACACTTT
65 ATACATTTTTATAAAGTATCGACACTTT
1541241 CAATATATCC
Statistics
Matches: 253, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
181 3 0.01
182 193 0.76
183 57 0.23
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (182 bp):
TACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCAA
TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTTTTCTTTTTTAAATTCCAAAAG
TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGTTT
Found at i:1541356 original size:112 final size:112
Alignment explanation
Indices: 1541110--1541460 Score: 578
Period size: 112 Copynumber: 3.1 Consensus size: 112
1541100 TATACTTATA
* * *
1541110 ATAAAGTATCGACACTATCAACATATCCGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1541175 TTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
1541223 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
1541288 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACGTTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
* *
1541335 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTAACTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
** * * *
1541400 TTTGTCA-TTTTTTATTTGTTATATTATGATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
1541446 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
1541461 AAACCGACGA
Statistics
Matches: 224, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
111 47 0.21
112 108 0.48
113 69 0.31
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.45
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
Found at i:1548632 original size:15 final size:15
Alignment explanation
Indices: 1548614--1548664 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1548604 AAATGTCACG
*
1548614 AAATAAAAAGAAAAT
1 AAATAAAAATAAAAT
*
1548629 AAATACAAAATATAAAA
1 AAATA-AAAATA-AAAT
*
1548646 AAATAAAAATTAAAT
1 AAATAAAAATAAAAT
1548661 AAAT
1 AAAT
1548665 TAACTAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 12 0.40
16 10 0.33
17 8 0.27
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (15 bp):
AAATAAAAATAAAAT
Found at i:1548978 original size:2 final size:2
Alignment explanation
Indices: 1548971--1548998 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1548961 ATGTTAGGTA
1548971 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1548999 TAAATAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1549045 original size:2 final size:2
Alignment explanation
Indices: 1549040--1549066 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1549030 AAAAAATTAA
1549040 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1549067 ATGATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1549131 original size:52 final size:51
Alignment explanation
Indices: 1549048--1549145 Score: 128
Period size: 52 Copynumber: 1.9 Consensus size: 51
1549038 AAATATATAT
*
1549048 ATATATATATATATATATAATGATATTTAAAAAAAAGGAAAAAATAATGATA
1 ATATATATATATATATATAATAATATTTAAAAAAAA-GAAAAAATAATGATA
* *
1549100 ATATATATATATATAT-TAA-AATATTAGTAAAACAAATAAAAAATAA
1 ATATATATATATATATATAATAATATT--TAAAAAAAAGAAAAAATAA
1549146 CTAAATAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
50 5 0.12
51 12 0.29
52 24 0.59
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (51 bp):
ATATATATATATATATATAATAATATTTAAAAAAAAGAAAAAATAATGATA
Found at i:1549187 original size:3 final size:3
Alignment explanation
Indices: 1549179--1549221 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
1549169 CATAAAACAC
1549179 TAA TAA TAA TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1549222 AAAGAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1549237 original size:17 final size:18
Alignment explanation
Indices: 1549214--1549270 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 18
1549204 ATATAATAAT
1549214 AATAATAAAAAGAAAAAA
1 AATAATAAAAAGAAAAAA
1549232 AA-AATAAAAA-ATAAAAA
1 AATAATAAAAAGA-AAAAA
* *
1549249 AATAGTAAAATAGTAAAAA
1 AATAATAAAA-AGAAAAAA
1549268 AAT
1 AAT
1549271 GAAAATGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
16 1 0.03
17 15 0.45
18 8 0.24
19 9 0.27
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (18 bp):
AATAATAAAAAGAAAAAA
Found at i:1549249 original size:15 final size:14
Alignment explanation
Indices: 1549127--1549307 Score: 62
Period size: 14 Copynumber: 12.2 Consensus size: 14
1549117 AAAATATTAG
1549127 TAAAACAAATAAAAAA
1 TAAAA-AAAT-AAAAA
**
1549143 TAACTAAAT-AAAA
1 TAAAAAAATAAAAA
* * *
1549156 TAAAATATATATACA
1 TAAAA-AAATAAAAA
* * *
1549171 TAAAACACTAATAA
1 TAAAAAAATAAAAA
*
1549185 TAATAATAATAATAATA
1 TAA-AAAAATAA-AA-A
* * *
1549202 TAATATAATAATAA
1 TAAAAAAATAAAAA
* *
1549216 TAATAAAA-AGAAA
1 TAAAAAAATAAAAA
1549229 -AAAAAAATAAAAAA
1 TAAAAAAAT-AAAAA
1549243 TAAAAAAATAGTAAAATA
1 T-AAAAAA-A-TAAAA-A
*
1549261 GTAAAAAAATGAAAA
1 -TAAAAAAATAAAAA
*
1549276 TGAAAATAATAAAAA
1 T-AAAAAAATAAAAA
* *
1549291 TAAAAACATGAAAA
1 TAAAAAAATAAAAA
1549305 TAA
1 TAA
1549308 TATATATATA
Statistics
Matches: 122, Mismatches: 29, Indels: 30
0.67 0.16 0.17
Matches are distributed among these distances:
12 6 0.05
13 10 0.08
14 35 0.29
15 31 0.25
16 21 0.17
17 10 0.08
18 8 0.07
19 1 0.01
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (14 bp):
TAAAAAAATAAAAA
Found at i:1549275 original size:46 final size:47
Alignment explanation
Indices: 1549186--1549296 Score: 122
Period size: 46 Copynumber: 2.4 Consensus size: 47
1549176 CACTAATAAT
* * *
1549186 AATAATAATAATAATATAATATAATAATAATAATAAAAAGAAAA-AA
1 AATAATAAAAATAAAAAAATATAATAATAATAATAAAAAGAAAAGAA
*
1549232 AA-AATAAAAAATAAAAAAATAGTAA-AATAGTAA-AAAAATGAAAATGAA
1 AATAAT-AAAAATAAAAAAATA-TAATAATAATAATAAAAA-GAAAA-GAA
1549280 AATAATAAAAATAAAAA
1 AATAATAAAAATAAAAA
1549297 CATGAAAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
45 8 0.15
46 26 0.47
47 3 0.05
48 15 0.27
49 3 0.05
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.21
Consensus pattern (47 bp):
AATAATAAAAATAAAAAAATATAATAATAATAATAAAAAGAAAAGAA
Found at i:1549290 original size:9 final size:9
Alignment explanation
Indices: 1549179--1549293 Score: 74
Period size: 9 Copynumber: 12.3 Consensus size: 9
1549169 CATAAAACAC
*
1549179 TAATAATAA
1 TAATAAAAA
*
1549188 TAATAATAA
1 TAATAAAAA
*
1549197 TAATATAATA
1 TAATA-AAAA
*
1549207 TAATAATAA
1 TAATAAAAA
1549216 TAATAAAAA
1 TAATAAAAA
*
1549225 GAA-AAAAA
1 TAATAAAAA
*
1549233 AAATAAAAAA
1 TAAT-AAAAA
1549243 TAA-AAAAA
1 TAATAAAAA
*
1549251 TAGTAAAATA
1 TAATAAAA-A
1549261 GTAA-AAAAA
1 -TAATAAAAA
*
1549270 TGAAAATGAAAA
1 T---AATAAAAA
1549282 TAATAAAAA
1 TAATAAAAA
1549291 TAA
1 TAA
1549294 AAACATGAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 20
0.72 0.10 0.17
Matches are distributed among these distances:
8 15 0.18
9 41 0.49
10 19 0.23
11 4 0.05
12 5 0.06
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (9 bp):
TAATAAAAA
Found at i:1549292 original size:6 final size:6
Alignment explanation
Indices: 1549180--1549296 Score: 53
Period size: 6 Copynumber: 19.3 Consensus size: 6
1549170 ATAAAACACT
* * * * * * *
1549180 AATAAT AATAAT AATAAT AATATAA TATAAT AATAAT AATAAA AAGAAA
1 AATAAA AATAAA AATAAA AATA-AA AATAAA AATAAA AATAAA AATAAA
* * ** *
1549229 AA-AAA AATAAAA AATAAA AA-AAT AGT-AA AATAGT AA-AAA AATGAA
1 AATAAA AAT-AAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
1549274 AATGAAAA TAATAAA AATAAA AA
1 AAT--AAA -AATAAA AATAAA AA
1549297 CATGAAAATA
Statistics
Matches: 86, Mismatches: 16, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
5 14 0.16
6 54 0.63
7 13 0.15
8 2 0.02
9 3 0.03
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.21
Consensus pattern (6 bp):
AATAAA
Found at i:1551239 original size:85 final size:85
Alignment explanation
Indices: 1550929--1551422 Score: 559
Period size: 85 Copynumber: 5.8 Consensus size: 85
1550919 TGGTCCGCCA
* * * * * ** * *
1550929 TTGAGCTGAATGGAATTGAACTTGATA-GTTTTTGTTGATAGATAGCTTTTCTCGACTTAAGCTA
1 TTGAGCTGAATGTAATCGAACTCGA-AGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTA
* *
1550993 TGCTGTAAATTTGATATGCCC
65 TGCTGTAAATTTGATATGTCT
* * * * * ** * *
1551014 TTGAGCTGAGTGGAATCGAATTCAAAGG----TATTGACAGATAATCCTTCTCGACTTGAGTTAT
1 TTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTAT
* *
1551075 GTTGTAAATTTGATATGTCA
66 GCTGTAAATTTGATATGTCT
*
1551095 TTGAGCTGAATGTAAATCGAACTCGAAGGTCTTTG-TGAACAGATAGCCCTTCTCGCCTTGAGTT
1 TTGAGCTGAATGT-AATCGAACTCGAAGGTCTTTGTTG-ACAGATAGCCCTTCTCGCCTTGAGCT
1551159 ATGCTGTAAATTTGATATGTCT
64 ATGCTGTAAATTTGATATGTCT
*
1551181 TTGAGCTGAATGTAATCGAACTCAAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTAT
1 TTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTAT
* *
1551246 GTTGTAAATTTGATATGCCT
66 GCTGTAAATTTGATATGTCT
* * * ** * * * * *
1551266 TTGAGTTGAATGTAATCAAACTCGAGGGTCTTTACTGACATATAACACTTCTCGCATTGAGTTAT
1 TTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTAT
**
1551331 ATTGTAAATTTGATATGTCT
66 GCTGTAAATTTGATATGTCT
* *
1551351 TTGAGCTGAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCACCTTGAGCTAT
1 TTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTAT
1551416 GCTGTAA
66 GCTGTAA
1551423 TTGGATGGGA
Statistics
Matches: 344, Mismatches: 57, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
81 53 0.15
82 13 0.04
84 1 0.00
85 218 0.63
86 59 0.17
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (85 bp):
TTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTAT
GCTGTAAATTTGATATGTCT
Found at i:1556963 original size:15 final size:16
Alignment explanation
Indices: 1556913--1556963 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
1556903 AATAACTATA
* *
1556913 AAAATATAACGAAATAT
1 AAAATATAA-AAAATAC
*
1556930 AAAATA-AATAAATAC
1 AAAATATAAAAAATAC
1556945 AAAATATAAAAAATA-
1 AAAATATAAAAAATAC
1556960 AAAA
1 AAAA
1556964 CCAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 15 0.50
16 9 0.30
17 6 0.20
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.20
Consensus pattern (16 bp):
AAAATATAAAAAATAC
Found at i:1556969 original size:20 final size:22
Alignment explanation
Indices: 1556924--1556970 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
1556914 AAATATAACG
*
1556924 AAATATAAAATAAATAAATACA
1 AAATATAAAATAAATAAAAACA
*
1556946 AAATAT-AAA-AAATAAAAACC
1 AAATATAAAATAAATAAAAACA
1556966 AAATA
1 AAATA
1556971 AGTTAACTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 14 0.61
21 3 0.13
22 6 0.26
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (22 bp):
AAATATAAAATAAATAAAAACA
Found at i:1557157 original size:21 final size:21
Alignment explanation
Indices: 1557098--1557158 Score: 52
Period size: 21 Copynumber: 2.8 Consensus size: 21
1557088 ATTAGGTACA
1557098 AAAAAGAAAATAATA-ATAATAAT
1 AAAAA-AAAATAA-AGA-AATAAT
* * * *
1557121 AATAAATATTAGAGAAATAAT
1 AAAAAAAAATAAAGAAATAAT
1557142 AAAAAAAAATAAAGAAA
1 AAAAAAAAATAAAGAAA
1557159 CACACCTAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
21 20 0.69
22 5 0.17
23 4 0.14
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.20
Consensus pattern (21 bp):
AAAAAAAAATAAAGAAATAAT
Found at i:1558513 original size:3 final size:3
Alignment explanation
Indices: 1558505--1558562 Score: 89
Period size: 3 Copynumber: 18.7 Consensus size: 3
1558495 TATATATTTA
*
1558505 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TCT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
1558551 CTAT TAT TAT TA
1 -TAT TAT TAT TA
1558563 ATGCATAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
3 47 0.92
4 4 0.08
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1558695 original size:6 final size:6
Alignment explanation
Indices: 1558661--1558693 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1558651 AACATTTTTG
*
1558661 TTTATA TTTATA TTTATA TTTATA TTTTTA TTT
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTT
1558694 TTTCTTATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTATA
Found at i:1558830 original size:26 final size:25
Alignment explanation
Indices: 1558765--1558837 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 25
1558755 ATTTCTACTC
*
1558765 TTTTTTCACTATTTATTTATTTATTT
1 TTTTTTTACT-TTTATTTATTTATTT
* *
1558791 TCAATTTGTA-TTTTATTTATTTATTT
1 T--TTTTTTACTTTTATTTATTTATTT
*
1558817 ATTTTTTTACTTTTACTTATT
1 -TTTTTTTACTTTTATTTATT
1558838 AATTATTATA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
25 5 0.14
26 26 0.70
27 2 0.05
28 4 0.11
ACGTcount: A:0.21, C:0.07, G:0.01, T:0.71
Consensus pattern (25 bp):
TTTTTTTACTTTTATTTATTTATTT
Found at i:1559096 original size:27 final size:27
Alignment explanation
Indices: 1559013--1559140 Score: 77
Period size: 27 Copynumber: 4.7 Consensus size: 27
1559003 CATTTTTTAA
* * *
1559013 TTATTTTTTTATTATCACTATTATTATT
1 TTATTTATTTATTATTATTATTATT-TT
* *
1559041 TTACTTAACTTT-TTA-TA-TATGTATATT
1 TTA-TTTA-TTTATTATTATTAT-TATTTT
1559068 TTATTTATTTATTATTATTATTATTTT
1 TTATTTATTTATTATTATTATTATTTT
* * *
1559095 TTGTTGT-TGTGTTATTATTATTATTTT
1 TTATT-TATTTATTATTATTATTATTTT
* *
1559122 TTCCTTTTTTTATT-TTATT
1 TT-ATTTATTTATTATTATT
1559141 TGATTTGTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 19
0.72 0.11 0.17
Matches are distributed among these distances:
25 3 0.04
26 6 0.08
27 45 0.57
28 17 0.22
29 5 0.06
30 3 0.04
ACGTcount: A:0.22, C:0.05, G:0.04, T:0.70
Consensus pattern (27 bp):
TTATTTATTTATTATTATTATTATTTT
Found at i:1559358 original size:13 final size:13
Alignment explanation
Indices: 1559337--1559366 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1559327 TCAGATCGTT
*
1559337 ATTTTAACTTTCA
1 ATTTAAACTTTCA
1559350 ATTTAAACTTTCA
1 ATTTAAACTTTCA
1559363 ATTT
1 ATTT
1559367 TCTTAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTTAAACTTTCA
Found at i:1560100 original size:12 final size:12
Alignment explanation
Indices: 1560083--1560113 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1560073 TGCTTTGATA
1560083 TTATTTCTTGCT
1 TTATTTCTTGCT
1560095 TTATTTCTTGCT
1 TTATTTCTTGCT
1560107 TTATTTC
1 TTATTTC
1560114 CTGTTCAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.10, C:0.16, G:0.06, T:0.68
Consensus pattern (12 bp):
TTATTTCTTGCT
Found at i:1562009 original size:88 final size:88
Alignment explanation
Indices: 1561857--1562036 Score: 270
Period size: 88 Copynumber: 2.0 Consensus size: 88
1561847 ATATATATAC
* * ** * *
1561857 AATAAAGCTTGAGTTGTCCCTCTAAAGCAATTTTTTAAACTCCCCGGCTTTATGGATAAGATTCA
1 AATAAAACTTGAGTTGTCCCTCTAAAGAAATTGGTTAAACGCCCCGGCTTTACGGATAAGATTCA
*
1561922 GTTAGCCTGATAAAGGTAATTAT
66 GCTAGCCTGATAAAGGTAATTAT
* *
1561945 AATAAAACTTGAGTTGTCCCTCTAAGGAAATTGGTTAAACGCCCCGGCTTTACGGATAATATTCA
1 AATAAAACTTGAGTTGTCCCTCTAAAGAAATTGGTTAAACGCCCCGGCTTTACGGATAAGATTCA
*
1562010 GCTAGCCTGATAAAGGTGATTAT
66 GCTAGCCTGATAAAGGTAATTAT
1562033 AATA
1 AATA
1562037 TCTATACAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 82 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (88 bp):
AATAAAACTTGAGTTGTCCCTCTAAAGAAATTGGTTAAACGCCCCGGCTTTACGGATAAGATTCA
GCTAGCCTGATAAAGGTAATTAT
Found at i:1563390 original size:83 final size:84
Alignment explanation
Indices: 1563240--1563457 Score: 312
Period size: 83 Copynumber: 2.6 Consensus size: 84
1563230 TTGGCAGCAC
* *
1563240 AACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAAACATTCGAGTTCGACTACGCTCAGCTCTAA
1 AACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAAACCTTCGAGTTCGACTACGCTCAGCTCCAA
*
1563305 GGCACATCATTTGCAACAT
66 GGCACATCATTTACAACAT
* * * * * *
1563324 AGCTCAAGGCAAGAAGGGCTATTTGCCAA-AAAAAACCTTCGAGATCGAGTACGCTCAGCTCCAA
1 AACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAAACCTTCGAGTTCGACTACGCTCAGCTCCAA
*
1563388 GGCACATCATTTACAGCAT
66 GGCACATCATTTACAACAT
* * *
1563407 AACTCAAGGCTAGAAAGGTTATCTACCAACAAAAGACCTTCGAGTTCGACT
1 AACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAAACCTTCGAGTTCGACT
1563458 TACAACATAG
Statistics
Matches: 114, Mismatches: 19, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
83 71 0.62
84 43 0.38
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (84 bp):
AACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAAACCTTCGAGTTCGACTACGCTCAGCTCCAA
GGCACATCATTTACAACAT
Found at i:1563496 original size:59 final size:59
Alignment explanation
Indices: 1563398--1563516 Score: 175
Period size: 59 Copynumber: 2.0 Consensus size: 59
1563388 GGCACATCAT
* * *
1563398 TTACAGCATAACTCAAGGCTAGAAAGGTTATCTACCAACAAAAGACCTTCGAGTTCGAC
1 TTACAACATAACTCAAGGCAAGAAAGGCTATCTACCAACAAAAGACCTTCGAGTTCGAC
* * * *
1563457 TTACAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGAC
1 TTACAACATAACTCAAGGCAAGAAAGGCTATCTACCAACAAAAGACCTTCGAGTTCGAC
1563516 T
1 T
1563517 ACGCTCAGCT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (59 bp):
TTACAACATAACTCAAGGCAAGAAAGGCTATCTACCAACAAAAGACCTTCGAGTTCGAC
Found at i:1563585 original size:143 final size:142
Alignment explanation
Indices: 1563318--1563596 Score: 452
Period size: 143 Copynumber: 2.0 Consensus size: 142
1563308 ACATCATTTG
*
1563318 CAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAAAAAAAACCTTCGAGATCGAGTACGCTCAGC
1 CAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAAAAAAAACCTTCGAGATCGACTACGCTCAGC
*
1563383 TCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAAGGTTATCTACCAACAAAAGACCTTC
66 TCCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAAGGTTATCTACCAACAAAAGACCTTC
1563448 GAGTTCGACTTA
131 GAGTTCGACTTA
* *
1563460 CAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
1 CAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAA-AAAAAACCTTCGAGATCGACTACGCTCAG
* * ** *
1563525 CTCCAAGGCACATCATTTGCAACATAAGTCAAGGCTAG-AAGAGTTATCTGTCAACCAAAGACCT
65 CTCCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAAG-GTTATCTACCAACAAAAGACCT
1563589 TCGAGTTC
129 TCGAGTTC
1563597 TACTACGCTC
Statistics
Matches: 126, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
142 38 0.30
143 88 0.70
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (142 bp):
CAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAAAAAAAACCTTCGAGATCGACTACGCTCAGC
TCCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAAGGTTATCTACCAACAAAAGACCTTC
GAGTTCGACTTA
Found at i:1563602 original size:84 final size:84
Alignment explanation
Indices: 1563460--1563729 Score: 384
Period size: 84 Copynumber: 3.2 Consensus size: 84
1563450 GTTCGACTTA
* * * * * *
1563460 CAACAT-AGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
1 CAACATAAG-TCAAGGCTAGAAGAGTTATCTGCCAACCAAAGACCTTCGAGTTCTACTACGCTCA
1563524 GCTCCAAGGCACATCATTTG
65 GCTCCAAGGCACATCATTTG
*
1563544 CAACATAAGTCAAGGCTAGAAGAGTTATCTGTCAACCAAAGACCTTCGAGTTCTACTACGCTCAG
1 CAACATAAGTCAAGGCTAGAAGAGTTATCTGCCAACCAAAGACCTTCGAGTTCTACTACGCTCAG
1563609 CTCCAAGGCACATCATTTG
66 CTCCAAGGCACATCATTTG
* * * *
1563628 CAGCATAACTCAAGGCTAAAAGAGTTATCTGCCAACCAAATACCTTCGAGTT-TGACTACGCTCA
1 CAACATAAGTCAAGGCTAGAAGAGTTATCTGCCAACCAAAGACCTTCGAGTTCT-ACTACGCTCA
1563692 GCTCCAAGGCACATCATTTG
65 GCTCCAAGGCACATCATTTG
*
1563712 -AAGCATAAATCAAGGCTA
1 CAA-CATAAGTCAAGGCTA
1563730 AAAACCTTCA
Statistics
Matches: 169, Mismatches: 14, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
83 2 0.01
84 165 0.98
85 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (84 bp):
CAACATAAGTCAAGGCTAGAAGAGTTATCTGCCAACCAAAGACCTTCGAGTTCTACTACGCTCAG
CTCCAAGGCACATCATTTG
Found at i:1563772 original size:64 final size:64
Alignment explanation
Indices: 1563669--1563793 Score: 187
Period size: 64 Copynumber: 2.0 Consensus size: 64
1563659 CCAACCAAAT
*
1563669 ACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGAAGCATAAATCAAGGCTAAAA
1 ACCTTCAAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGAAGCATAAATCAAGGCTAAAA
* * * * **
1563733 ACCTTCAAGTTTGACTACGCTTAGCTCCAAGGCATATCATTTGCAGTATAGCTCAAGGCTA
1 ACCTTCAAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGAAGCATAAATCAAGGCTA
1563794 GAAGGGCTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (64 bp):
ACCTTCAAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGAAGCATAAATCAAGGCTAAAA
Found at i:1563836 original size:232 final size:231
Alignment explanation
Indices: 1563278--1564437 Score: 1030
Period size: 248 Copynumber: 4.9 Consensus size: 231
1563268 ACAAAAAACA
* * *
1563278 TTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGC
1 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCTAGAAGAGC
* * * * * *
1563343 TATTTGCCAA-AAAAAACCTTCGAGATCGAGTACGCTCAGCTCCAAGGCACATCATTTACAGCAT
66 TATCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCAT
* * * * *
1563407 AACTCAAGGCTAGAAA-GGTTATCTACCAACAAAAGACCTTCGAGTTCGACTTACAACAT-AGCT
130 AACTCAAGGCTA-AAAGGGTTATCTGCCAACCAAATACCTTCGAGTTTGAC-TAC-GC-TCAGCT
* * * **
1563470 -CAAGGCA-A-GA--AGGGC-TATTTGCCAA--C-AAAAGACC
191 CCAAGGCACATCATTTGAGCATAAAT--CAAGGCTAAAAGACC
1563504 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAAG-TCAAGGCTAGAAGAG
1 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACAT-AGCTCAAGGCTAGAAGAG
* *
1563568 TTATCTGTCAACCAAAGACCTTCGAGTTCTACTACGCTCAGCTCCAAGGCACATCATTTGCAGCA
65 CTATCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCA
*
1563633 TAACTCAAGGCTAAAAGAGTTATCTGCCAACCAAATACCTTCGAGTTTGACTACGCTCAGCTCCA
129 TAACTCAAGGCTAAAAGGGTTATCTGCCAACCAAATACCTTCGAGTTTGACTACGCTCAGCTCCA
1563698 AGGCACATCATTTGAAGCATAAATCAAGGCTAAAA-ACC
194 AGGCACATCATTTG-AGCATAAATCAAGGCTAAAAGACC
* * * * ** *
1563736 TTCAAGTTTGACTACGCTTAGCTCCAAGGCATATCATTTGCAGTATAGCTCAAGGCTAGAAGGGC
1 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCTAGAAGAGC
* *
1563801 TATCTGCCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCAT
66 TATCTGCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCAT
* * *
1563866 AACTCAAGGCTAGAAGGGTTATATGCCAACCAAATACCTTCGAATTTGACTACGCTCAGCTCCAA
130 AACTCAAGGCTAAAAGGGTTATCTGCCAACCAAATACCTTCGAGTTTGACTACGCTCAGCTCCAA
* **
1563931 GGCACATTATTTGCAGCATAGCTCAAGGCTAGAATATCTGCCACCAAAAGACC
195 GGCACATCATTTG-AGCATAAATCAA-G---G-----CT------AAAAGACC
* * * * * *
1563984 TTCGAGTTCGACTACGCTCAGCTCTAAGGCATATCATTTGCATCATAACTCAAGACTAGAAGAGT
1 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCTAGAAGAGC
* *
1564049 TATCTTCAAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCAT
66 TATCTGC-AACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCAT
* * ** * *
1564114 AACTCAAGGCTAGAAGGGTTATTTTTCAGCC-AATACCTTCGAGTTTAACTACGCTCAGCTCCAA
130 AACTCAAGGCTAAAAGGGTTATCTGCCAACCAAATACCTTCGAGTTTGACTACGCTCAGCTCCAA
* * *
1564178 GGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTTCCAACAAAAAACC
195 GGCACATCATTTG-AGCATA----AA-TC---AA-GGC-----T-----AAAAGACC
* * * * * ** * * * *
1564235 TTTGAGTTCGATTACACTCAACTCAAAGGCACATCATTTGCAGTATATCTCAAAGCTAGAAGGGT
1 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCTAGAAGAGC
* * * *
1564300 TATCTG---CCAAAGATCC-TCGAGTTCGATTACACTCAGCTTCAAGGGCACATTATTTGCAGCA
66 TATCTGCAACCAAAGA-CCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCA
* ** * * * *
1564361 TAACTCAAGGCTAGAAGGGTTATCTATCAA-CAAATACCTTTGAGTTCGATTACACTCAGCT-CA
129 TAACTCAAGGCTAAAAGGGTTATCTGCCAACCAAATACCTTCGAGTTTGACTACGCTCAGCTCCA
1564424 ATGGCACATCATTT
194 A-GGCACATCATTT
1564438 ACAGTGTAGC
Statistics
Matches: 791, Mismatches: 93, Indels: 78
0.82 0.10 0.08
Matches are distributed among these distances:
224 1 0.00
225 5 0.01
226 79 0.10
227 92 0.12
228 1 0.00
230 4 0.01
231 8 0.01
232 201 0.25
233 5 0.01
236 1 0.00
241 2 0.00
247 87 0.11
248 226 0.29
249 3 0.00
251 69 0.09
252 3 0.00
255 4 0.01
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (231 bp):
TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCTAGAAGAGC
TATCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATA
ACTCAAGGCTAAAAGGGTTATCTGCCAACCAAATACCTTCGAGTTTGACTACGCTCAGCTCCAAG
GCACATCATTTGAGCATAAATCAAGGCTAAAAGACC
Found at i:1563853 original size:148 final size:148
Alignment explanation
Indices: 1563585--1563877 Score: 437
Period size: 148 Copynumber: 2.0 Consensus size: 148
1563575 TCAACCAAAG
*
1563585 ACCTTCGAGTTCTACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAAAAG
1 ACCTTCAAGTTCTACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAAAAG
* * *
1563650 AGTTATCTGCCAACCAAATACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGAAG
66 AGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGAAG
1563715 CATAAATCAAGGCTAAAA
131 CATAAATCAAGGCTAAAA
* * * * *
1563733 ACCTTCAAGTT-TGACTACGCTTAGCTCCAAGGCATATCATTTGCAGTATAGCTCAAGGCTAGAA
1 ACCTTCAAGTTCT-ACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAAAA
* * *
1563797 GGGCTATCTGCC-ACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGC
65 GAGCTATCTGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGA
*
1563861 AGCATAACTCAAGGCTA
129 AGCATAAATCAAGGCTA
1563878 GAAGGGTTAT
Statistics
Matches: 130, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
147 4 0.03
148 126 0.97
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (148 bp):
ACCTTCAAGTTCTACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAAAAG
AGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGAAG
CATAAATCAAGGCTAAAA
Found at i:1563874 original size:84 final size:83
Alignment explanation
Indices: 1563733--1564573 Score: 848
Period size: 84 Copynumber: 10.2 Consensus size: 83
1563723 AAGGCTAAAA
* * * * * * *
1563733 ACCTTCAAGTTTGACTACGCTTAGCTCCAAGGCATATCATTTGCAGTATAGCTCAAGGCTAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAG
*
1563798 GGCTATCTGCCACCAAAAG
66 GGTTATCTGCCACC-AAAG
1563817 ACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAG
* *
1563882 GGTTATATGCCAACCAAAT
66 GGTTATCTGCC-ACCAAAG
* * * * *
1563901 ACCTTCGAATTTGACTACGCTCAGCTCCAAGGCACATTATTTGCAGCATAGCTCAAGGCTAGAA-
1 ACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAG
1563965 ---TATCTGCCACCAAAAG
66 GGTTATCTGCCACC-AAAG
* * *
1563981 ACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCATATCATTTGCATCATAACTCAAGACTAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAG
* * *
1564046 AGTTATCTTCAAACCAAAG
66 GGTTATCTGC-CACCAAAG
1564065 ACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAG
* ** *
1564130 GGTTATTTTTCAGCC-AAT
66 GGTTATCTGCCA-CCAAAG
** * * * *
1564148 ACCTTCGAGTTTAACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAG
* * * * *
1564213 GGCTATTTTCCAACAAAAA
66 GGTTATCTGCC-ACCAAAG
* * * * * * * *
1564232 ACCTTTGAGTTCGATTACACTCAACTCAAAGGCACATCATTTGCAGTATATCTCAAAGCTAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAG
1564297 GGTTATCTG---CCAAAG
66 GGTTATCTGCCACCAAAG
* * *
1564312 ATCC-TCGAGTTCGATTACACTCAGCT-TCAAGGGCACATTATTTGCAGCATAACTCAAGGCTAG
1 A-CCTTCGAGTTCGACTACGCTCAGCTCT-AA-GGCACATCATTTGCAGCATAACTCAAGGCTAG
** * *
1564375 AAGGGTTATCTATCAACAAAT
63 AAGGGTTATCTGCCACCAAAG
* * * * ** *
1564396 ACCTTTGAGTTCGATTACACTCAGCTC-AATGGCACATCATTTACAGTGTAGCTCAAGGCTAGAA
1 ACCTTCGAGTTCGACTACGCTCAGCTCTAA-GGCACATCATTTGCAGCATAACTCAAGGCTAGAA
*
1564460 GGGCTATCTG---CCAAAG
65 GGGTTATCTGCCACCAAAG
* * * * * *
1564476 ACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCCTTTGCAGCATAACTCAAGGCTAGAA
1 ACCTTCGAGTTCGACTACGCTCAGC-TCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAA
* ** *
1564541 GGGTTATTTTTCAGCC-AAT
65 GGGTTATCTGCCA-CCAAAG
1564560 ACCTTCGAGTTCGA
1 ACCTTCGAGTTCGA
1564574 TTCCATTCAG
Statistics
Matches: 637, Mismatches: 96, Indels: 48
0.82 0.12 0.06
Matches are distributed among these distances:
79 3 0.00
80 120 0.19
81 79 0.12
82 1 0.00
83 113 0.18
84 313 0.49
85 8 0.01
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.26
Consensus pattern (83 bp):
ACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAG
GGTTATCTGCCACCAAAG
Found at i:1564570 original size:248 final size:247
Alignment explanation
Indices: 1563729--1564590 Score: 926
Period size: 248 Copynumber: 3.5 Consensus size: 247
1563719 AATCAAGGCT
* * * * * * * * *
1563729 AAAA-ACCTTCAAGTTTGACTACGCTTAGCTCCAAGGCATATCATTTGCAGTATAGCTCAAGGCT
1 AAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCT
* ** *
1563793 AGAAGGGCTATCTGCCA-CCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCAT
66 AGAAGGGTTAT-TTTCAGCC-AAAGACCTTCGAGTTCGACTACACTCAGCTCTAAGGCACATCAT
** *
1563857 TTGCAGCATAACTCAAGGCTAGAAGGGTTATATGCCAACCAAATACCTTCGAATTTGACTACGCT
129 TTGCAGCATAACTCAAGGCTAGAAGGGTTATATATCAA-CAAATACCTTCGAGTTTGACTACGCT
*
1563922 CAGCTCCAAGGCACATTATTTGCAGCATAGCTCAAGGCTAGAA----TATCTGCCACC
193 CAGCTCCAAGGCACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTG---CC
* * * * * *
1563976 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCATATCATTTGCATCATAACTCAAGACT
1 AAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCT
* * * *
1564041 AGAAGAGTTATCTTCAAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATT
66 AGAAGGGTTATTTTC-AGCCAAAGACCTTCGAGTTCGACTACACTCAGCTCTAAGGCACATCATT
* * * * *
1564106 TGCAGCATAACTCAAGGCTAGAAGGGTTATTTTTCAGCCAATACCTTCGAGTTTAACTACGCTCA
130 TGCAGCATAACTCAAGGCTAGAAGGGTTATATATCAACAAATACCTTCGAGTTTGACTACGCTCA
* * * *
1564171 GCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTTCCAAC
195 GCTCCAAGGCACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTA-TCTGC--C
* * * * * *
1564227 AAAAAACCTTTGAGTTCGATTACACTCAACTCAAAGGCACATCATTTGCAGTATATCTCAAAGCT
1 AAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCT
* * *
1564292 AGAAGGGTTA---TCTGCCAAAGATCC-TCGAGTTCGATTACACTCAGCT-TCAAGGGCACATTA
66 AGAAGGGTTATTTTCAGCCAAAGA-CCTTCGAGTTCGACTACACTCAGCTCT-AA-GGCACATCA
* * * * *
1564352 TTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTATCAACAAATACCTTTGAGTTCGATTACACT
128 TTTGCAGCATAACTCAAGGCTAGAAGGGTTATATATCAACAAATACCTTCGAGTTTGACTACGCT
* **
1564417 CAGCT-CAATGGCACATCATTTACAGTGTAGCTCAAGGCTAGAAGGGCTATCTGCC
193 CAGCTCCAA-GGCACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTGCC
* * * *
1564472 -AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCCTTTGCAGCATAACTCAAGGC
1 AAAAGACCTTCGAGTTCGATTACACTCAGC-TCAAAGGCACATCATTTGCAGCATAACTCAAGGC
* * * *
1564536 TAGAAGGGTTATTTTTCAGCC-AATACCTTCGAGTTCGATTCCATTCAGCTC-AAGG
65 TAGAAGGGTTA-TTTTCAGCCAAAGACCTTCGAGTTCGACTACACTCAGCTCTAAGG
1564591 GTATGTCAAA
Statistics
Matches: 521, Mismatches: 73, Indels: 43
0.82 0.11 0.07
Matches are distributed among these distances:
244 25 0.05
245 40 0.08
246 3 0.01
247 107 0.21
248 271 0.52
249 8 0.02
251 65 0.12
252 2 0.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (247 bp):
AAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCT
AGAAGGGTTATTTTCAGCCAAAGACCTTCGAGTTCGACTACACTCAGCTCTAAGGCACATCATTT
GCAGCATAACTCAAGGCTAGAAGGGTTATATATCAACAAATACCTTCGAGTTTGACTACGCTCAG
CTCCAAGGCACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTGCC
Found at i:1564574 original size:164 final size:162
Alignment explanation
Indices: 1563755--1564590 Score: 887
Period size: 164 Copynumber: 5.1 Consensus size: 162
1563745 GACTACGCTT
*
1563755 AGCTCCAAGGCATATCATTTGCAGTATAGCTCAAGGCTAGAAGGGCTATCTGCCACCAAAAGACC
1 AGCT-CAAGGCACATCATTTGCAGTATAGCTCAAGGCTAGAAGGGCTATCTG---CC-AAAGACC
1563820 TTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGT
61 TTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGT
* ** * * * *
1563885 TATATGCCAACCAAATACCTTCGAATTTGACTACGCTC
126 TATTTTTCAACC-AATACCTTCGAGTTCGATTACACTC
* *
1563923 AGCTCCAAGGCACATTATTTGCAGCATAGCTCAAGGCTAGAA----TATCTGCCACCAAAAGACC
1 AGCT-CAAGGCACATCATTTGCAGTATAGCTCAAGGCTAGAAGGGCTATCTG---CC-AAAGACC
* * * *
1563984 TTCGAGTTCGACTACGCTCAGCTCTAAGGCATATCATTTGCATCATAACTCAAGACTAGAAGAGT
61 TTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGT
* * * *
1564049 TA-TCTTCAAACCAAAGACCTTCGAGTTCGACTACGCTC
126 TATTTTTC-AACC-AATACCTTCGAGTTCGATTACACTC
* * * * *
1564087 AGCTCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATTTTTCAGCC-AATACC
1 AGCTC-AAGGCACATCATTTGCAGTATAGCTCAAGGCTAGAAGGGCTA----TCTGCCAAAGACC
** * * * * *
1564151 TTCGAGTTTAACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGC
61 TTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGT
* * * *
1564216 TATTTTCCAACAAAAAACCTTTGAGTTCGATTACACTC
126 TATTTTTCAAC-CAATACCTTCGAGTTCGATTACACTC
* * * *
1564254 AACTCAAAGGCACATCATTTGCAGTATATCTCAAAGCTAGAAGGGTTATCTGCCAAAGATCC-TC
1 AGCTC-AAGGCACATCATTTGCAGTATAGCTCAAGGCTAGAAGGGCTATCTGCCAAAGA-CCTTC
* * *
1564318 GAGTTCGATTACACTCAGCT-TCAAGGGCACATTATTTGCAGCATAACTCAAGGCTAGAAGGGTT
64 GAGTTCGACTACGCTCAGCTCT-AA-GGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTT
* * * *
1564382 ATCTATCAACAAATACCTTTGAGTTCGATTACACTC
127 ATTTTTCAACCAATACCTTCGAGTTCGATTACACTC
* * *
1564418 AGCTCAATGGCACATCATTTACAGTGTAGCTCAAGGCTAGAAGGGCTATCTGCCAAAGACCCTCG
1 AGCTCAA-GGCACATCATTTGCAGTATAGCTCAAGGCTAGAAGGGCTATCTGCCAAAGACCTTCG
* * * * *
1564483 AGTTCGATTACACTCAGCTTCGAGGGCACATCCTTTGCAGCATAACTCAAGGCTAGAAGGGTTAT
65 AGTTCGACTACGCTCAGC-TCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTAT
* * *
1564548 TTTTCAGCCAATACCTTCGAGTTCGATTCCATTC
129 TTTTCAACCAATACCTTCGAGTTCGATTACACTC
1564582 AGCTCAAGG
1 AGCTCAAGG
1564591 GTATGTCAAA
Statistics
Matches: 575, Mismatches: 73, Indels: 45
0.83 0.11 0.06
Matches are distributed among these distances:
163 13 0.02
164 339 0.59
165 45 0.08
167 129 0.22
168 44 0.08
169 2 0.00
172 3 0.01
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.26
Consensus pattern (162 bp):
AGCTCAAGGCACATCATTTGCAGTATAGCTCAAGGCTAGAAGGGCTATCTGCCAAAGACCTTCGA
GTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATTT
TTCAACCAATACCTTCGAGTTCGATTACACTC
Found at i:1565248 original size:18 final size:17
Alignment explanation
Indices: 1565225--1565260 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
1565215 TCATACGATT
1565225 TATCATATATTATATTTA
1 TATCATATATT-TATTTA
1565243 TATCATATATTTATTTA
1 TATCATATATTTATTTA
1565260 T
1 T
1565261 CTTTTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
TATCATATATTTATTTA
Found at i:1566412 original size:3 final size:3
Alignment explanation
Indices: 1566368--1566489 Score: 70
Period size: 3 Copynumber: 38.0 Consensus size: 3
1566358 TTTATTTAAA
*
1566368 TAT TA- TAT TAT ATAT AAT TAT GTAT ATAT ATAT T-T ATAT TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT -TAT -TAT -TAT TAT -TAT TAT TAT
* *
1566413 TAT TAT TAT TAT TAT TAT TATT TCT CTAT TAT TAT TAAT GCAT ATAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT -TAT TAT TAT T-AT -TAT -TAT
* * *
1566460 TAT T-T TTT TCT TAT TAAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT
1566490 ATATATCTTT
Statistics
Matches: 96, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
2 5 0.05
3 64 0.67
4 27 0.28
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1566448 original size:32 final size:29
Alignment explanation
Indices: 1566406--1566489 Score: 87
Period size: 32 Copynumber: 2.7 Consensus size: 29
1566396 TATATTTATA
1566406 TTATTATTATTATTATTATTATTATTATTTC
1 TTATTATTATTATTATTATTATT-TT-TTTC
*
1566437 TCTATTATTATTAATGCATATATTATTTTTTTC
1 T-TATTATTATT-AT-TAT-TATTATTTTTTTC
*
1566470 TTATTAATTACTATTATTAT
1 TTATT-ATTATTATTATTAT
1566490 ATATATCTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
30 3 0.07
31 3 0.07
32 16 0.36
33 12 0.27
34 4 0.09
35 7 0.16
ACGTcount: A:0.30, C:0.06, G:0.01, T:0.63
Consensus pattern (29 bp):
TTATTATTATTATTATTATTATTTTTTTC
Found at i:1566491 original size:32 final size:32
Alignment explanation
Indices: 1566404--1566500 Score: 90
Period size: 33 Copynumber: 2.9 Consensus size: 32
1566394 TATATATTTA
1566404 TATTATTATTATTATTATTATTATTATTATTTCTC
1 TATTATTATTATTATTA-TATTATT-TT-TTTCTC
*
1566439 TATTATTATTAATGCA-TATATTATTTTTTTCT-
1 TATTATTATT-AT-TATTATATTATTTTTTTCTC
* *
1566471 TATTAATTACTATTATTATATATATCTTTT
1 TATT-ATTATTATTATTATAT-TATTTTTT
1566501 ATTTTACTTG
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
31 1 0.02
32 11 0.21
33 17 0.32
34 2 0.04
35 17 0.32
36 4 0.08
37 1 0.02
ACGTcount: A:0.30, C:0.06, G:0.01, T:0.63
Consensus pattern (32 bp):
TATTATTATTATTATTATATTATTTTTTTCTC
Found at i:1567092 original size:20 final size:19
Alignment explanation
Indices: 1567058--1567108 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
1567048 ATTTAGTTAC
* *
1567058 CTTATTTGGTCTTTACTTTT
1 CTTATTTTGTATTTA-TTTT
*
1567078 TTTATTTTGTATTTATTTT
1 CTTATTTTGTATTTATTTT
1567097 CTT-TTTT-TATTT
1 CTTATTTTGTATTT
1567109 CGGGACATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 5 0.19
18 4 0.15
19 6 0.22
20 12 0.44
ACGTcount: A:0.12, C:0.08, G:0.06, T:0.75
Consensus pattern (19 bp):
CTTATTTTGTATTTATTTT
Found at i:1567544 original size:24 final size:25
Alignment explanation
Indices: 1567502--1567548 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1567492 CGACAAATAT
*
1567502 AATATTAAATAAAAAAATAAAAAAA
1 AATAGTAAATAAAAAAATAAAAAAA
*
1567527 AATAGTAAA-AAAAGAATAAAAA
1 AATAGTAAATAAAAAAATAAAAA
1567549 CACTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (25 bp):
AATAGTAAATAAAAAAATAAAAAAA
Found at i:1567599 original size:63 final size:62
Alignment explanation
Indices: 1567506--1567623 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 62
1567496 AAATATAATA
*
1567506 TTAAATAAAAAAATAAAAAAAAATAGTAAAAAA-AGAATAAAAACACTATATATATAACGGTAT
1 TTAAATAAAAAAAGAAAAAAAAATAGTAAAAAATA-AATAAAAACA-TATATATATAACGGTAT
* * *
1567569 TTAAATAAAAAAAGAAAAAATAAT-GATAAAAAATAAATAAATATATATATATATA
1 TTAAATAAAAAAAGAAAAAAAAATAG-TAAAAAATAAATAAAAACATATATATATA
1567624 TTAGAATATT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
62 11 0.22
63 37 0.76
64 1 0.02
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.25
Consensus pattern (62 bp):
TTAAATAAAAAAAGAAAAAAAAATAGTAAAAAATAAATAAAAACATATATATATAACGGTAT
Found at i:1567700 original size:3 final size:3
Alignment explanation
Indices: 1567692--1567741 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
1567682 CATAAAACAC
*
1567692 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1567739 TAA
1 TAA
1567742 AAAGAAACAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1567786 original size:6 final size:6
Alignment explanation
Indices: 1567696--1567792 Score: 54
Period size: 6 Copynumber: 15.3 Consensus size: 6
1567686 AAACACTAAT
* * * *
1567696 AATAAT AATAAT AATAAT AATAATA ATATAAA AATAAT AATAATA AA-AAGA
1 AATAAA AATAAA AATAAA AATAA-A A-ATAAA AATAAA AATAA-A AATAA-A
* * *
1567747 AACAATA AATAAA AA-AAGA TAGTAAA AATGAA AATAAA AATAAA AA
1 AATAA-A AATAAA AATAA-A -AATAAA AATAAA AATAAA AATAAA AA
1567793 AACATGAATA
Statistics
Matches: 74, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
5 2 0.03
6 52 0.70
7 14 0.19
8 6 0.08
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.22
Consensus pattern (6 bp):
AATAAA
Found at i:1578950 original size:22 final size:23
Alignment explanation
Indices: 1578920--1578962 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1578910 ATAAATTATC
* *
1578920 TAAATAACTTATATTTAAACACT
1 TAAATAACTCATATATAAACACT
1578943 TAAA-AACTCATATATAAACA
1 TAAATAACTCATATATAAACA
1578963 ATATAGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (23 bp):
TAAATAACTCATATATAAACACT
Found at i:1593302 original size:7 final size:7
Alignment explanation
Indices: 1593285--1593338 Score: 90
Period size: 7 Copynumber: 7.6 Consensus size: 7
1593275 TCTATACATT
1593285 GCTCGCTG
1 GCTC-CTG
1593293 GCTCCTG
1 GCTCCTG
1593300 GCTCCTG
1 GCTCCTG
1593307 GCTCCTG
1 GCTCCTG
1593314 GCTCCTG
1 GCTCCTG
1593321 GCTCCTG
1 GCTCCTG
*
1593328 GCTCGTG
1 GCTCCTG
1593335 GCTC
1 GCTC
1593339 ATCCGAGAGT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
7 41 0.91
8 4 0.09
ACGTcount: A:0.00, C:0.41, G:0.31, T:0.28
Consensus pattern (7 bp):
GCTCCTG
Found at i:1594105 original size:32 final size:30
Alignment explanation
Indices: 1594065--1594132 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
1594055 TGAAAATTAG
* *
1594065 TTTTTAATATTTTTATAAATAATTATTTTAA
1 TTTTTAATACTTTAATAAATAA-TATTTTAA
**
1594096 TTTTATAATACTTTAATATTTAATATTTTAA
1 TTTT-TAATACTTTAATAAATAATATTTTAA
1594127 TTTTTA
1 TTTTTA
1594133 GTTAAAACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 2 0.06
31 16 0.50
32 14 0.44
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTTTAATACTTTAATAAATAATATTTTAA
Found at i:1594125 original size:8 final size:8
Alignment explanation
Indices: 1594066--1594132 Score: 52
Period size: 8 Copynumber: 8.6 Consensus size: 8
1594056 GAAAATTAGT
1594066 TTTTAATA
1 TTTTAATA
*
1594074 TTTTTATA
1 TTTTAATA
**
1594082 -AATAATTA
1 TTTTAA-TA
1594090 TTTTAAT-
1 TTTTAATA
1594097 TTTATAATA
1 TTT-TAATA
*
1594106 CTTTAATA
1 TTTTAATA
1594114 -TTTAATA
1 TTTTAATA
1594121 TTTTAAT-
1 TTTTAATA
1594128 TTTTA
1 TTTTA
1594133 GTTAAAACAA
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
7 17 0.36
8 25 0.53
9 5 0.11
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (8 bp):
TTTTAATA
Found at i:1594125 original size:15 final size:15
Alignment explanation
Indices: 1594067--1594132 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
1594057 AAAATTAGTT
*
1594067 TTTAATATTTTTATA
1 TTTAATATTTTAATA
** *
1594082 AATAATTATTTTAATT
1 TTTAA-TATTTTAATA
*
1594098 TTATAATACTTTAATA
1 TT-TAATATTTTAATA
*
1594114 TTTAATATTTTAATT
1 TTTAATATTTTAATA
1594129 TTTA
1 TTTA
1594133 GTTAAAACAA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
15 18 0.46
16 18 0.46
17 3 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTAATATTTTAATA
Found at i:1598743 original size:113 final size:115
Alignment explanation
Indices: 1598514--1598746 Score: 362
Period size: 113 Copynumber: 2.0 Consensus size: 115
1598504 TATGATTTCT
* * *
1598514 AAAATTTATAAAATTAAAAACAAAGGGGAAATTTTGGACTTTAATAATATATGATTCTAATGTTT
1 AAAATTTATAAAATGAAAAACAAAGGGGAAATTTTGGAATTTAATAATATACGATTCTAATGTTT
1598579 TGCTTGTGATATGGGATAGAATTTTGCTCATCAATCGTAGTCTGAACTAG
66 TGCTTGTGATATGGGATAGAATTTTGCTCATCAATCGTAGTCTGAACTAG
* * *
1598629 AAAATTTATAAAATGAAAAATAAAGGGG-AATTTTGGAATTTAATGATATACGATTTTAATGTTT
1 AAAATTTATAAAATGAAAAACAAAGGGGAAATTTTGGAATTTAATAATATACGATTCTAATGTTT
* * * *
1598693 TGCTTGTG-TATGGGGTAGAATTTTGCTCATCCATCGTAGTCTGGATTAG
66 TGCTTGTGATATGGGATAGAATTTTGCTCATCAATCGTAGTCTGAACTAG
1598742 AAAAT
1 AAAAT
1598747 CTTCTCACCC
Statistics
Matches: 108, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
113 42 0.39
114 40 0.37
115 26 0.24
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (115 bp):
AAAATTTATAAAATGAAAAACAAAGGGGAAATTTTGGAATTTAATAATATACGATTCTAATGTTT
TGCTTGTGATATGGGATAGAATTTTGCTCATCAATCGTAGTCTGAACTAG
Found at i:1601911 original size:19 final size:19
Alignment explanation
Indices: 1601887--1601932 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
1601877 TCCTTTATGA
1601887 GTGTATCGATACACTTATT
1 GTGTATCGATACACTTATT
1601906 GTGTATCGATACACTTATT
1 GTGTATCGATACACTTATT
1601925 GTGTATCG
1 GTGTATCG
1601933 GTACCTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (19 bp):
GTGTATCGATACACTTATT
Found at i:1614837 original size:21 final size:22
Alignment explanation
Indices: 1614811--1614851 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1614801 CCAGGACAGG
*
1614811 GAGTATTGGTA-CTCCTTTAAT
1 GAGTATCGGTATCTCCTTTAAT
*
1614832 GAGTATCGGTATTTCCTTTA
1 GAGTATCGGTATCTCCTTTA
1614852 TAATTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.44
Consensus pattern (22 bp):
GAGTATCGGTATCTCCTTTAAT
Found at i:1614942 original size:23 final size:24
Alignment explanation
Indices: 1614916--1614977 Score: 108
Period size: 23 Copynumber: 2.6 Consensus size: 24
1614906 CTATGCTCAT
1614916 AGTATCGATACTACTATGTAAAG-
1 AGTATCGATACTACTATGTAAAGC
1614939 AGTATCGATACTACTATGTAAAGC
1 AGTATCGATACTACTATGTAAAGC
*
1614963 AGTATCGGTACTACT
1 AGTATCGATACTACT
1614978 TTGAGTATCG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 23 0.62
24 14 0.38
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (24 bp):
AGTATCGATACTACTATGTAAAGC
Found at i:1620742 original size:27 final size:30
Alignment explanation
Indices: 1620682--1620743 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
1620672 TCTTAACTTA
*
1620682 AAAATATATTTCATTATTATTTTAGTTTTG
1 AAAATATATTTCATTATTATTATAGTTTTG
* *
1620712 AAAATATATTTTATTCTTA-TATA-TTTT-
1 AAAATATATTTCATTATTATTATAGTTTTG
1620739 AAAAT
1 AAAAT
1620744 TAAGATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 5 0.17
28 4 0.14
29 3 0.10
30 17 0.59
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (30 bp):
AAAATATATTTCATTATTATTATAGTTTTG
Found at i:1621033 original size:32 final size:32
Alignment explanation
Indices: 1620995--1621095 Score: 103
Period size: 32 Copynumber: 3.1 Consensus size: 32
1620985 GAGTTCAAAA
1620995 TTTTTTGTAGTTAAAATAAAAATAAAATATTT
1 TTTTTTGTAGTTAAAATAAAAATAAAATATTT
* * * * **
1621027 TTTTTTGTAGTTGAACTAAAAACATAATACTCC
1 TTTTTTGTAGTTAAAATAAAAATAAAATA-TTT
* *
1621060 ATTTTTGTAGTTAAGATAAAAATATAAAATATTT
1 TTTTTTGTAGTTAAAAT-AAAA-ATAAAATATTT
1621094 TT
1 TT
1621096 AAACTTAAAA
Statistics
Matches: 51, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
32 25 0.49
33 14 0.27
34 6 0.12
35 6 0.12
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.45
Consensus pattern (32 bp):
TTTTTTGTAGTTAAAATAAAAATAAAATATTT
Found at i:1621163 original size:53 final size:49
Alignment explanation
Indices: 1621106--1621247 Score: 131
Period size: 53 Copynumber: 2.7 Consensus size: 49
1621096 AAACTTAAAA
1621106 TAAGAATAATATATATATTTAAATAAAATAAAAATAAGATATACATTTTAAGT
1 TAAGAATAA-ATATATATTTAAATAAAATAAAAATAA-A-ATACATTTTAA-T
* * *
1621159 TAAGAATTAAATATATATTTCAAGTTAAAATAATAATAAAATATATTTTAAT
1 TAAGAA-TAAATATATATTT-AA-ATAAAATAAAAATAAAATACATTTTAAT
* * *
1621211 TAAAAATAAAAAACATATTTTTAAATGAAAATAAAAA
1 TAAGAAT---AAATATATATTTAAAT-AAAATAAAAA
1621248 ATATATTTTA
Statistics
Matches: 74, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
51 1 0.01
52 7 0.09
53 37 0.50
54 16 0.22
55 13 0.18
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (49 bp):
TAAGAATAAATATATATTTAAATAAAATAAAAATAAAATACATTTTAAT
Found at i:1621203 original size:30 final size:29
Alignment explanation
Indices: 1621068--1621316 Score: 108
Period size: 30 Copynumber: 9.0 Consensus size: 29
1621058 CCATTTTTGT
* *
1621068 AGTTAAGATAAAAATATAAA-ATATTTTTAA
1 AGTTAAAATAAAAATA-AAATATATATTT-A
* * *
1621098 ACTTAAAATAAGAATAATATATATATTTA
1 AGTTAAAATAAAAATAAAATATATATTTA
* * *
1621127 A-ATAAAATAAAAATAAGATATACATTTTA
1 AGTTAAAATAAAAATAAAATATATA-TTTA
1621156 AGTTAAGAAT-----T-AAATATATATTTCA
1 AGTTAA-AATAAAAATAAAATATATATTT-A
*
1621181 AGTTAAAATAATAATAAAATATAT-TTTA
1 AGTTAAAATAAAAATAAAATATATATTTA
*
1621209 A-TTAAAA-ATAAAA-AACATAT-T-TTTA
1 AGTTAAAATA-AAAATAAAATATATATTTA
* *
1621234 AATGAAAAT---AA-AAAATATAT-TTTA
1 AGTTAAAATAAAAATAAAATATATATTTA
*
1621258 TA-TTAAAATTAAAATAAAATATAT-TTAATA
1 -AGTTAAAATAAAAATAAAATATATATT--TA
* * ** *
1621288 AGTTAATACAAAGTTAAAATATATTTTTA
1 AGTTAAAATAAAAATAAAATATATATTTA
1621317 GAAGTTAAGA
Statistics
Matches: 173, Mismatches: 22, Indels: 49
0.71 0.09 0.20
Matches are distributed among these distances:
23 8 0.05
24 17 0.10
25 21 0.12
26 13 0.08
27 11 0.06
28 32 0.18
29 16 0.09
30 50 0.29
31 5 0.03
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (29 bp):
AGTTAAAATAAAAATAAAATATATATTTA
Found at i:1621218 original size:25 final size:25
Alignment explanation
Indices: 1621076--1621283 Score: 113
Period size: 28 Copynumber: 7.8 Consensus size: 25
1621066 GTAGTTAAGA
1621076 TAAAAAT-ATAAAATAT-TTTTAAACT
1 TAAAAATAATAAAATATATTTT-AA-T
* *
1621101 TAAAATAAGAATAATATATATATTTAAAT
1 T-AAA-AATAATAA-A-ATATATTTTAAT
* * *
1621130 AAAATAAAAATAAGATATACATTTTAAGT
1 TAAA-AATAATAA-A-ATATATTTTAA-T
* *
1621159 TAAGAAT--TAAATATATATTTCAAGT
1 TAAAAATAATAAA-ATATATTTTAA-T
1621184 TAAAATAATAATAAAATATATTTTAAT
1 T-AAA-AATAATAAAATATATTTTAAT
* *
1621211 TAAAAATAA-AAAACATATTTTTAAA
1 TAAAAATAATAAAATATA-TTTTAAT
*
1621236 TGAAAATAA-AAAATATATTTTATAT
1 TAAAAATAATAAAATATATTTTA-AT
*
1621261 TAAAATTAAAATAAAATATATTT
1 TAAAA--ATAATAAAATATATTT
1621284 AATAAGTTAA
Statistics
Matches: 146, Mismatches: 21, Indels: 29
0.74 0.11 0.15
Matches are distributed among these distances:
24 12 0.08
25 46 0.32
26 11 0.08
27 10 0.07
28 49 0.34
29 9 0.06
30 6 0.04
31 3 0.02
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (25 bp):
TAAAAATAATAAAATATATTTTAAT
Found at i:1621228 original size:24 final size:24
Alignment explanation
Indices: 1621134--1621286 Score: 117
Period size: 25 Copynumber: 6.0 Consensus size: 24
1621124 TTAAATAAAA
* * *
1621134 TAAAAATAAGATATACATTTTAAGT
1 TAAAAATAAAAAATATATTTTAA-T
* * * *
1621159 TAAGAATTAAATATATATTTCAAGT
1 TAAAAATAAAAAATATATTTTAA-T
1621184 TAAAATAATAATAAAATATATTTTAAT
1 T-AAA-AATAA-AAAATATATTTTAAT
* *
1621211 TAAAAATAAAAAACATATTTTTAAA
1 TAAAAATAAAAAATATA-TTTTAAT
*
1621236 TGAAAATAAAAAATATATTTTATAT
1 TAAAAATAAAAAATATATTTTA-AT
* *
1621261 TAAAATTAAAATAAAATATATTTAAT
1 TAAAAATAAAA-AATATAT-TTTAAT
1621287 AAGTTAATAC
Statistics
Matches: 104, Mismatches: 17, Indels: 13
0.78 0.13 0.10
Matches are distributed among these distances:
24 12 0.12
25 57 0.55
26 13 0.12
27 10 0.10
28 12 0.12
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (24 bp):
TAAAAATAAAAAATATATTTTAAT
Found at i:1621253 original size:77 final size:77
Alignment explanation
Indices: 1621078--1621283 Score: 193
Period size: 77 Copynumber: 2.6 Consensus size: 77
1621068 AGTTAAGATA
* * *
1621078 AAAATATAAAATATTTTTAAACTTAAAATAAGAATAATATATATATTTAAATAAAATAAAAATAA
1 AAAATAAAAAATATATTTAAA-TTAAAATAA-AATAAAATATAT-TTTAAATAAAATAAAAATAA
* * *
1621143 GATATACATTTTAAGTT
63 CATAT--ATTTTAAATG
* * * *
1621160 AAGAATTAAATATATATTTCAAGTTAAAATAATAATAAAATATATTTTAATTAAAA-ATAAAA-A
1 AA-AATAAAAAATATATTT-AAATTAAAATAA-AATAAAATATATTTTAAATAAAATA-AAAATA
1621223 ACATAT-TTTTAAATG
62 ACATATATTTTAAATG
*
1621238 AAAATAAAAAATATATTTTATATTAAAATTAAAATAAAATATATTT
1 AAAATAAAAAATATA-TTTAAATTAAAA-TAAAATAAAATATATTT
1621284 AATAAGTTAA
Statistics
Matches: 104, Mismatches: 15, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
77 32 0.31
78 15 0.14
81 7 0.07
82 16 0.15
83 32 0.31
84 2 0.02
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (77 bp):
AAAATAAAAAATATATTTAAATTAAAATAAAATAAAATATATTTTAAATAAAATAAAAATAACAT
ATATTTTAAATG
Found at i:1621356 original size:25 final size:25
Alignment explanation
Indices: 1621326--1621406 Score: 89
Period size: 25 Copynumber: 3.3 Consensus size: 25
1621316 AGAAGTTAAG
1621326 ATATATTTTAAGTATTTATACAAAT
1 ATATATTTTAAGTATTTATACAAAT
* *
1621351 ATATATTAT-A-TA-TTAGA-AGTTAAT
1 ATATATTTTAAGTATTTATACA---AAT
1621375 ATATATTTTAAGTATTTATACAAAT
1 ATATATTTTAAGTATTTATACAAAT
1621400 ATATATT
1 ATATATT
1621407 ATATTTTGTC
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
21 1 0.02
22 4 0.09
23 2 0.04
24 12 0.27
25 19 0.42
26 2 0.04
27 4 0.09
28 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.48
Consensus pattern (25 bp):
ATATATTTTAAGTATTTATACAAAT
Found at i:1621383 original size:49 final size:49
Alignment explanation
Indices: 1621314--1621410 Score: 185
Period size: 49 Copynumber: 2.0 Consensus size: 49
1621304 AAATATATTT
1621314 TTAGAAGTTAAGATATATTTTAAGTATTTATACAAATATATATTATATA
1 TTAGAAGTTAAGATATATTTTAAGTATTTATACAAATATATATTATATA
*
1621363 TTAGAAGTTAATATATATTTTAAGTATTTATACAAATATATATTATAT
1 TTAGAAGTTAAGATATATTTTAAGTATTTATACAAATATATATTATAT
1621411 TTTGTCAATA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (49 bp):
TTAGAAGTTAAGATATATTTTAAGTATTTATACAAATATATATTATATA
Found at i:1644122 original size:15 final size:15
Alignment explanation
Indices: 1644102--1644130 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1644092 CTTAGTAGTG
1644102 TAACCCCCTAGACCA
1 TAACCCCCTAGACCA
1644117 TAACCCCCTAGACC
1 TAACCCCCTAGACC
1644131 CGGCCTATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.48, G:0.07, T:0.14
Consensus pattern (15 bp):
TAACCCCCTAGACCA
Found at i:1644749 original size:32 final size:31
Alignment explanation
Indices: 1644713--1644788 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
1644703 GGGGCCGTGA
*
1644713 GGCCTACCTAAGAACACATCTTAGGGCCGCAG
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCAG
** **
1644745 GGCCTACCCGAGAATGATCTCAGGGCCGCAG
1 GGCCTACCTAAGAAACATCTCAGGGCCGCAG
*
1644776 AGCCTACCTAAGA
1 GGCCTACCTAAGA
1644789 GTCACATTAG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 24 0.67
32 12 0.33
ACGTcount: A:0.28, C:0.32, G:0.26, T:0.14
Consensus pattern (31 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCAG
Found at i:1644771 original size:63 final size:63
Alignment explanation
Indices: 1644665--1644788 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
1644655 CCCTAAGGGA
* * *
1644665 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCG-TGAGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGA-GCCTACCTAAGAAC
* *
1644728 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
1644789 GTCACATTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 2 0.04
63 49 0.92
64 2 0.04
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:1645670 original size:7 final size:7
Alignment explanation
Indices: 1645658--1645696 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
1645648 GTCAAAGAAA
1645658 GTCAACG
1 GTCAACG
1645665 GTCAACG
1 GTCAACG
1645672 GTC-ACG
1 GTCAACG
1645678 GTCAACG
1 GTCAACG
1645685 GTC-ACG
1 GTCAACG
1645691 GTCAAC
1 GTCAAC
1645697 AGTCGGGTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 12 0.40
7 18 0.60
ACGTcount: A:0.26, C:0.31, G:0.28, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:1645680 original size:13 final size:13
Alignment explanation
Indices: 1645662--1645696 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
1645652 AAGAAAGTCA
1645662 ACGGTCAACGGTC
1 ACGGTCAACGGTC
1645675 ACGGTCAACGGTC
1 ACGGTCAACGGTC
1645688 ACGGTCAAC
1 ACGGTCAAC
1645697 AGTCGGGTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.26, C:0.31, G:0.29, T:0.14
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:1645712 original size:17 final size:17
Alignment explanation
Indices: 1645690--1645747 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
1645680 CAACGGTCAC
1645690 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
*
1645707 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1645724 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1645741 GGTCAAC
1 GGTCAAC
1645748 CCGGTTCAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:1645765 original size:19 final size:20
Alignment explanation
Indices: 1645741--1645811 Score: 101
Period size: 19 Copynumber: 3.6 Consensus size: 20
1645731 AGTCGGGTCG
*
1645741 GGTCAACCCGGTTCAG-ACC
1 GGTCAAACCGGTTCAGAACC
1645760 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAGAACC
* *
1645779 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTCAGAACC
1645799 GGTCAAACCGGTT
1 GGTCAAACCGGTT
1645812 TTCCAGCAGC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
18 1 0.02
19 30 0.64
20 16 0.34
ACGTcount: A:0.27, C:0.30, G:0.25, T:0.18
Consensus pattern (20 bp):
GGTCAAACCGGTTCAGAACC
Found at i:1645778 original size:10 final size:10
Alignment explanation
Indices: 1645743--1645811 Score: 72
Period size: 9 Copynumber: 7.1 Consensus size: 10
1645733 TCGGGTCGGG
*
1645743 TCAACCCGGT
1 TCAAACCGGT
*
1645753 TCAGACCGG-
1 TCAAACCGGT
1645762 TCAAACCGGT
1 TCAAACCGGT
*
1645772 TCGAACCGG-
1 TCAAACCGGT
1645781 TCAAACCGGT
1 TCAAACCGGT
*
1645791 TCAAAACTGG-
1 TC-AAACCGGT
1645801 TCAAACCGGT
1 TCAAACCGGT
1645811 T
1 T
1645812 TTCCAGCAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 22 0.46
10 20 0.42
11 6 0.12
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:1653069 original size:15 final size:15
Alignment explanation
Indices: 1653049--1653077 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1653039 CTTAGTAGTG
1653049 TAACCCCCTAGACCA
1 TAACCCCCTAGACCA
1653064 TAACCCCCTAGACC
1 TAACCCCCTAGACC
1653078 CGGCCTATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.48, G:0.07, T:0.14
Consensus pattern (15 bp):
TAACCCCCTAGACCA
Found at i:1653696 original size:32 final size:31
Alignment explanation
Indices: 1653660--1653735 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
1653650 GGGGCCGTGA
*
1653660 GGCCTACCTAAGAACACATCTTAGGGCCGCAG
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCAG
** **
1653692 GGCCTACCCGAGAATGATCTCAGGGCCGCAG
1 GGCCTACCTAAGAAACATCTCAGGGCCGCAG
*
1653723 AGCCTACCTAAGA
1 GGCCTACCTAAGA
1653736 GTCACATTAG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 24 0.67
32 12 0.33
ACGTcount: A:0.28, C:0.32, G:0.26, T:0.14
Consensus pattern (31 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCAG
Found at i:1653718 original size:63 final size:63
Alignment explanation
Indices: 1653612--1653735 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
1653602 CCCTAAGGGA
* * *
1653612 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCG-TGAGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGA-GCCTACCTAAGAAC
* *
1653675 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
1653736 GTCACATTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 2 0.04
63 49 0.92
64 2 0.04
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:1654617 original size:7 final size:7
Alignment explanation
Indices: 1654605--1654643 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
1654595 GTCAAAGAAA
1654605 GTCAACG
1 GTCAACG
1654612 GTCAACG
1 GTCAACG
1654619 GTC-ACG
1 GTCAACG
1654625 GTCAACG
1 GTCAACG
1654632 GTC-ACG
1 GTCAACG
1654638 GTCAAC
1 GTCAAC
1654644 AGTCGGGTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 12 0.40
7 18 0.60
ACGTcount: A:0.26, C:0.31, G:0.28, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:1654627 original size:13 final size:13
Alignment explanation
Indices: 1654609--1654643 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
1654599 AAGAAAGTCA
1654609 ACGGTCAACGGTC
1 ACGGTCAACGGTC
1654622 ACGGTCAACGGTC
1 ACGGTCAACGGTC
1654635 ACGGTCAAC
1 ACGGTCAAC
1654644 AGTCGGGTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.26, C:0.31, G:0.29, T:0.14
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:1654659 original size:17 final size:17
Alignment explanation
Indices: 1654637--1654694 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
1654627 CAACGGTCAC
1654637 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
*
1654654 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1654671 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1654688 GGTCAAC
1 GGTCAAC
1654695 CCGGTTCAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:1654712 original size:19 final size:20
Alignment explanation
Indices: 1654688--1654758 Score: 101
Period size: 19 Copynumber: 3.6 Consensus size: 20
1654678 AGTCGGGTCG
*
1654688 GGTCAACCCGGTTCAG-ACC
1 GGTCAAACCGGTTCAGAACC
1654707 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAGAACC
* *
1654726 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTCAGAACC
1654746 GGTCAAACCGGTT
1 GGTCAAACCGGTT
1654759 TTCCAGCTGC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
18 1 0.02
19 30 0.64
20 16 0.34
ACGTcount: A:0.27, C:0.30, G:0.25, T:0.18
Consensus pattern (20 bp):
GGTCAAACCGGTTCAGAACC
Found at i:1654725 original size:10 final size:10
Alignment explanation
Indices: 1654690--1654758 Score: 72
Period size: 9 Copynumber: 7.1 Consensus size: 10
1654680 TCGGGTCGGG
*
1654690 TCAACCCGGT
1 TCAAACCGGT
*
1654700 TCAGACCGG-
1 TCAAACCGGT
1654709 TCAAACCGGT
1 TCAAACCGGT
*
1654719 TCGAACCGG-
1 TCAAACCGGT
1654728 TCAAACCGGT
1 TCAAACCGGT
*
1654738 TCAAAACTGG-
1 TC-AAACCGGT
1654748 TCAAACCGGT
1 TCAAACCGGT
1654758 T
1 T
1654759 TTCCAGCTGC
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 22 0.46
10 20 0.42
11 6 0.12
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:1655798 original size:19 final size:20
Alignment explanation
Indices: 1655756--1655803 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1655746 GAGAGAAGCG
1655756 AAAAAGGAAATTCGAGACCA
1 AAAAAGGAAATTCGAGACCA
1655776 AAAAAGGAAATTCGAGACC-
1 AAAAAGGAAATTCGAGACCA
1655795 AAAAAGGAA
1 AAAAAGGAA
1655804 TTTGGGGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 9 0.32
20 19 0.68
ACGTcount: A:0.58, C:0.12, G:0.21, T:0.08
Consensus pattern (20 bp):
AAAAAGGAAATTCGAGACCA
Found at i:1656897 original size:42 final size:41
Alignment explanation
Indices: 1656864--1656953 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 41
1656854 ATATTTATCA
*
1656864 ATAATTTTAATAATATAATATTATATTTTATTATTATAATTAT
1 ATAATTATAAT-ATATAATATTATATTTTATTATTAT-ATTAT
* *
1656907 ATTATTATAATATATAATATTATATTTTAATT-TTAATAATAT
1 ATAATTATAATATATAATATTATATTTT-ATTATT-ATATTAT
1656949 ATAAT
1 ATAAT
1656954 AAATTATTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
42 27 0.66
43 14 0.34
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (41 bp):
ATAATTATAATATATAATATTATATTTTATTATTATATTAT
Found at i:1656927 original size:29 final size:29
Alignment explanation
Indices: 1656895--1656954 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
1656885 TATATTTTAT
1656895 TATTATAATTAT-ATTATT-ATAATATATAA
1 TATTAT-ATTATAATT-TTAATAATATATAA
*
1656924 TATTATATTTTAATTTTAATAATATATAA
1 TATTATATTATAATTTTAATAATATATAA
1656953 TA
1 TA
1656955 AATTATTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TATTATATTATAATTTTAATAATATATAA
Found at i:1656963 original size:21 final size:20
Alignment explanation
Indices: 1656935--1656975 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1656925 ATTATATTTT
*
1656935 AATTTTAATAATATATAATA
1 AATTTTAATAAAATATAATA
*
1656955 AATTATTAATAAAATTTAATA
1 AATT-TTAATAAAATATAATA
1656976 TTATTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTTTAATAAAATATAATA
Found at i:1656975 original size:50 final size:48
Alignment explanation
Indices: 1656873--1656994 Score: 124
Period size: 50 Copynumber: 2.5 Consensus size: 48
1656863 AATAATTTTA
* * * * *
1656873 ATAATATAATATTAT-ATTTTATTATTATAATTATATTATTATAATAT
1 ATAATATTATATTTTAATTTTATAATTATAATTAAATTATTATAAAAT
1656920 ATAATATTATATTTTAATTTTAATAATATATAA-TAAATTATTAATAAAAT
1 ATAATATTATATTTTAATTTT-ATAAT-TATAATTAAATTATT-ATAAAAT
* *
1656970 TTAATATTAT-TTATTAATTTCATAA
1 ATAATATTATATT-TTAATTTTATAA
1656995 AAATAATATT
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
47 13 0.21
48 5 0.08
49 18 0.29
50 27 0.43
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (48 bp):
ATAATATTATATTTTAATTTTATAATTATAATTAAATTATTATAAAAT
Found at i:1657077 original size:51 final size:51
Alignment explanation
Indices: 1657017--1657144 Score: 127
Period size: 42 Copynumber: 2.7 Consensus size: 51
1657007 TGAATTATTG
* * *
1657017 AATATTTAATATATACTCTTTAAAATGTAATATAATATTATTATTTTAATT
1 AATAATTAATATATACTCTTTAAAATGTAATATAATATTATTATTATAATA
* *
1657068 AATAATTAATATA-A--C--T--AAT-T-ATATATTATTTTTATTATAATA
1 AATAATTAATATATACTCTTTAAAATGTAATATAATATTATTATTATAATA
1657110 AATAATT-A-ATATACTCTTTAAAA-GTAATATAATAT
1 AATAATTAATATATACTCTTTAAAATGTAATATAATAT
1657145 AATCAGTAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 21
0.70 0.07 0.24
Matches are distributed among these distances:
40 3 0.05
41 2 0.03
42 25 0.40
43 2 0.03
44 3 0.05
45 1 0.02
46 1 0.02
47 3 0.05
48 9 0.15
50 1 0.02
51 12 0.19
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.48
Consensus pattern (51 bp):
AATAATTAATATATACTCTTTAAAATGTAATATAATATTATTATTATAATA
Found at i:1658697 original size:22 final size:21
Alignment explanation
Indices: 1658668--1658709 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1658658 TGATCAAATG
1658668 ATATTATTTTAGT-ATTTTTAT
1 ATATTATTTT-GTGATTTTTAT
1658689 ATATATATTTTGTGATTTTTA
1 ATAT-TATTTTGTGATTTTTA
1658710 GGTAGAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (21 bp):
ATATTATTTTGTGATTTTTAT
Found at i:1661260 original size:15 final size:15
Alignment explanation
Indices: 1661236--1661283 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
1661226 GAGAAATGAA
*
1661236 ATAAGGTATGTGATT
1 ATAAGATATGTGATT
*
1661251 ATAAGATATGTGATA
1 ATAAGATATGTGATT
* *
1661266 ATAAGTTATATGATT
1 ATAAGATATGTGATT
1661281 ATA
1 ATA
1661284 TGATCATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.40
Consensus pattern (15 bp):
ATAAGATATGTGATT
Found at i:1661753 original size:23 final size:23
Alignment explanation
Indices: 1661719--1661778 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
1661709 CATCTTATAT
*
1661719 GGCACTAT-AGTGCAATTCTACGA
1 GGCACT-TCAGTGCAATCCTACGA
*
1661742 GGCACTTCAGTGCAATCCTACGT
1 GGCACTTCAGTGCAATCCTACGA
* *
1661765 GACACTTCGGTGCA
1 GGCACTTCAGTGCA
1661779 TTTATAAGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (23 bp):
GGCACTTCAGTGCAATCCTACGA
Found at i:1665432 original size:63 final size:64
Alignment explanation
Indices: 1665293--1665413 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 64
1665283 ATTGTTCAAG
* * * * *
1665293 GTGTATCGATGCACATGAAGTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCAATACACCCCCTTAAAATAAAAACATCGAATGCCATCA
* *
1665357 GTGTATCGATGCACAAGTAGTGCATCAATACACCCCCTT-AAATACAAACATCGAATG
1 GTGTATCGATGCACAAGAAGTGCATCAATACACCCCCTTAAAATAAAAACATCGAATG
1665414 GGATTTATGT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
63 17 0.34
64 33 0.66
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (64 bp):
GTGTATCGATGCACAAGAAGTGCATCAATACACCCCCTTAAAATAAAAACATCGAATGCCATCA
Found at i:1665454 original size:63 final size:64
Alignment explanation
Indices: 1665293--1665454 Score: 179
Period size: 63 Copynumber: 2.5 Consensus size: 64
1665283 ATTGTTCAAG
* *
1665293 GTGTATCGATGCACATGA-AGTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACA-GATAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCA
* * * ** *
1665357 GTGTATCGATGCACA-AGTAGTGCATCAATACACCCCCTT-AAATACAAACATCGAATGGGATTT
1 GTGTATCGATGCACAGA-TAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCA-TC
1665420 A
64 A
* *
1665421 -TGTATCGATGCATAGATAGTCCATCGATGCACCC
1 GTGTATCGATGCACAGATAGTGCATCGATGCACCC
1665455 GTCAAGGGAT
Statistics
Matches: 82, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
62 1 0.01
63 46 0.56
64 35 0.43
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (64 bp):
GTGTATCGATGCACAGATAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCA
Found at i:1666524 original size:15 final size:15
Alignment explanation
Indices: 1666500--1666547 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
1666490 GAAAAATGAA
*
1666500 ATAAGGTATGTGATT
1 ATAAGATATGTGATT
*
1666515 ATAAGATATGTGATA
1 ATAAGATATGTGATT
* *
1666530 ATAAGTTATATGATT
1 ATAAGATATGTGATT
1666545 ATA
1 ATA
1666548 TGATCATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.40
Consensus pattern (15 bp):
ATAAGATATGTGATT
Found at i:1667016 original size:23 final size:23
Alignment explanation
Indices: 1666985--1667065 Score: 135
Period size: 23 Copynumber: 3.5 Consensus size: 23
1666975 TCTTATATGA
* *
1666985 CACTACGGTGCAATTCTACGTGG
1 CACTTCGGTGCAATCCTACGTGG
*
1667008 CACTTCGGTGCAATCCTATGTGG
1 CACTTCGGTGCAATCCTACGTGG
1667031 CACTTCGGTGCAATCCTACGTGG
1 CACTTCGGTGCAATCCTACGTGG
1667054 CACTTCGGTGCA
1 CACTTCGGTGCA
1667066 TTTATATGAG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.27
Consensus pattern (23 bp):
CACTTCGGTGCAATCCTACGTGG
Found at i:1668921 original size:2 final size:2
Alignment explanation
Indices: 1668914--1668972 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
1668904 AATAAACATC
1668914 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1668956 AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1668973 CAATAGCCTT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1671075 original size:31 final size:31
Alignment explanation
Indices: 1671003--1671066 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
1670993 AGTTACATCG
* *
1671003 GGGACCATATTGCAAACAGACTAAATGTTGA
1 GGGACCATATTACAAACAAACTAAATGTTGA
1671034 GGGACCATATTACAAACAAACTAAATGTT-A
1 GGGACCATATTACAAACAAACTAAATGTTGA
1671064 GGG
1 GGG
1671067 GATTATATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.22
Consensus pattern (31 bp):
GGGACCATATTACAAACAAACTAAATGTTGA
Done.