Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008242.1 Hibiscus syriacus cultivar Beakdansim tig00110890_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: 16962412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 73
Found at i:5660333 original size:33 final size:33
Alignment explanation
Indices: 5660269--5660369 Score: 80
Period size: 33 Copynumber: 3.0 Consensus size: 33
5660259 CTTGTTGATG
* * *
5660269 AATG-AAGGATGAT-TTAATGGTGATGAAATGGT
1 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
5660301 AATGAAAGGATGATGTTATTGGCGTGATATGGT
1 AATGAAAGGATGATGTTATTGGCGTGATATGGT
* * * * *
5660334 GATGGATTATGATGATGATATAGGCGTGATAATGGT
1 AAT-GA-AAGGATGATGTTATTGGCGTGAT-ATGGT
5660370 GATGGTCAGA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
32 4 0.07
33 19 0.34
34 9 0.16
35 19 0.34
36 5 0.09
ACGTcount: A:0.33, C:0.02, G:0.33, T:0.33
Consensus pattern (33 bp):
AATGAAAGGATGATGTTATTGGCGTGATATGGT
Found at i:5666000 original size:33 final size:32
Alignment explanation
Indices: 5665936--5666000 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
5665926 CTTGTTGATG
*
5665936 AATGAAGGATGATTTAATGGTGATGAAATGGT
1 AATGAAGGATGATTTAATGGCGATGAAATGGT
* *
5665968 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
1 AATG-AAGGATGAT-TTAATGGCGATGAAATGGT
5666001 GATGGATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 4 0.14
33 17 0.61
34 7 0.25
ACGTcount: A:0.34, C:0.02, G:0.32, T:0.32
Consensus pattern (32 bp):
AATGAAGGATGATTTAATGGCGATGAAATGGT
Found at i:5668142 original size:19 final size:20
Alignment explanation
Indices: 5668118--5668159 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
5668108 CGGCCAAGAG
*
5668118 CATGTATCTTCAT-TAAAAT
1 CATGTATCTTCATCAAAAAT
*
5668137 CATGTATTTTCATCAAAAAT
1 CATGTATCTTCATCAAAAAT
5668157 CAT
1 CAT
5668160 ATATTTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (20 bp):
CATGTATCTTCATCAAAAAT
Found at i:5668157 original size:20 final size:19
Alignment explanation
Indices: 5668118--5668168 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
5668108 CGGCCAAGAG
* *
5668118 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATAAAAAT
5668137 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCAT-AAAAAT
*
5668157 CATATATTTTCA
1 CATGTATTTTCA
5668169 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.43
Consensus pattern (19 bp):
CATGTATTTTCATAAAAAT
Found at i:5668895 original size:5 final size:5
Alignment explanation
Indices: 5668894--5668936 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
5668884 ATCAGAAAAG
*
5668894 AAGAA AAGAA GAA-AA GAAGAA AAGAA ATGAA AAGAA AAGAA AA
1 AAGAA AAGAA -AAGAA -AAGAA AAGAA AAGAA AAGAA AAGAA AA
5668937 AGAGAAGTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 30 0.88
6 4 0.12
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (5 bp):
AAGAA
Found at i:5668898 original size:8 final size:8
Alignment explanation
Indices: 5668887--5668929 Score: 68
Period size: 8 Copynumber: 5.1 Consensus size: 8
5668877 GAGAAAAATC
5668887 AGAAAAGA
1 AGAAAAGA
5668895 AGAAAAGA
1 AGAAAAGA
5668903 AGAAAAGA
1 AGAAAAGA
5668911 AGAAAAGAA
1 AGAAAAG-A
5668920 ATGAAAAGA
1 A-GAAAAGA
5668929 A
1 A
5668930 AAGAAAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
8 23 0.70
9 4 0.12
10 6 0.18
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (8 bp):
AGAAAAGA
Found at i:5671404 original size:30 final size:31
Alignment explanation
Indices: 5671352--5671411 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
5671342 CTTAGCTTTA
**
5671352 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
5671382 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
5671412 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:5672345 original size:19 final size:19
Alignment explanation
Indices: 5672321--5672368 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
5672311 CGGCCAAGAG
*
5672321 CATGTATCTTCAT-TAAAAT
1 CATGTAT-TTCATCAAAAAT
5672340 CATGTATTGTCATCAAAAAT
1 CATGTATT-TCATCAAAAAT
5672360 CATGTATTT
1 CATGTATTT
5672369 TCAAAGGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 1 0.04
19 12 0.46
20 13 0.50
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (19 bp):
CATGTATTTCATCAAAAAT
Found at i:5674559 original size:25 final size:26
Alignment explanation
Indices: 5674531--5674589 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 26
5674521 AAAATCAACA
*
5674531 AAGAAAAAGTCAAGCACTC-CAAAAG
1 AAGAAAAAGTCAAGCACTCAAAAAAG
* *
5674556 AAG-AAAAGTCAAGTATTCAAAAAAG
1 AAGAAAAAGTCAAGCACTCAAAAAAG
5674581 AAGAAAAAG
1 AAGAAAAAG
5674590 AAAAGAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.45
25 11 0.38
26 5 0.17
ACGTcount: A:0.61, C:0.12, G:0.17, T:0.10
Consensus pattern (26 bp):
AAGAAAAAGTCAAGCACTCAAAAAAG
Found at i:5677902 original size:23 final size:24
Alignment explanation
Indices: 5677860--5677912 Score: 90
Period size: 23 Copynumber: 2.2 Consensus size: 24
5677850 TTTCTTTCTT
5677860 TTTCTTCTTTTCGAGTGCTTTTAA
1 TTTCTTCTTTTCGAGTGCTTTTAA
*
5677884 TTTCTTCTTTT-GAGTGCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTTAA
5677907 TTTCTT
1 TTTCTT
5677913 TGCTGATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 17 0.61
24 11 0.39
ACGTcount: A:0.09, C:0.15, G:0.11, T:0.64
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTTAA
Found at i:5681227 original size:19 final size:19
Alignment explanation
Indices: 5681188--5681227 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
5681178 ATCAGAAAAG
**
5681188 AAGCACTCAAAAAGATTAA
1 AAGCACTCAAAAAGAAGAA
5681207 AAGCACTCAAAAAGAAGAA
1 AAGCACTCAAAAAGAAGAA
5681226 AA
1 AA
5681228 AGCAAAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.62, C:0.15, G:0.12, T:0.10
Consensus pattern (19 bp):
AAGCACTCAAAAAGAAGAA
Found at i:5684940 original size:20 final size:19
Alignment explanation
Indices: 5684897--5684935 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
5684887 ATCAGAAAAG
*
5684897 AAGCACTCAAAAAGATTGA
1 AAGCACTCAAAAAGATAGA
5684916 AAGCACTCAAAAAGA-AGA
1 AAGCACTCAAAAAGATAGA
5684934 AA
1 AA
5684936 AAGCAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.10
Consensus pattern (19 bp):
AAGCACTCAAAAAGATAGA
Found at i:5689860 original size:24 final size:24
Alignment explanation
Indices: 5689832--5689902 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 24
5689822 GATTCAAGAA
5689832 ACATGTCTTTTGAAGAACCAATAG
1 ACATGTCTTTTGAAGAACCAATAG
* * ** *
5689856 TCATGACTTTTGGTGATCCACA-AG
1 ACATGTCTTTTGAAGAACCA-ATAG
**
5689880 ACACATCTTTTGAAGAACCAATA
1 ACATGTCTTTTGAAGAACCAATA
5689903 ATTATGTCCC
Statistics
Matches: 33, Mismatches: 12, Indels: 4
0.67 0.24 0.08
Matches are distributed among these distances:
23 1 0.03
24 31 0.94
25 1 0.03
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (24 bp):
ACATGTCTTTTGAAGAACCAATAG
Found at i:5695691 original size:19 final size:21
Alignment explanation
Indices: 5695648--5695699 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
5695638 GAAACCCCTT
5695648 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
5695669 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
5695688 TGAAGATACATG
1 TGAAAATACATG
5695700 CTCTTGGATG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:5699017 original size:12 final size:11
Alignment explanation
Indices: 5699002--5699032 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
5698992 TTTTCTTTTC
5699002 TTTTTTTCTGA
1 TTTTTTTCTGA
5699013 TTTTTTTCTGA
1 TTTTTTTCTGA
5699024 TTTTTTTCT
1 TTTTTTTCT
5699033 CTTCTTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.06, C:0.10, G:0.06, T:0.77
Consensus pattern (11 bp):
TTTTTTTCTGA
Found at i:5699797 original size:19 final size:20
Alignment explanation
Indices: 5699752--5699800 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
5699742 ACCCCTTTGA
5699752 AAATACATGACTTTTAAATGG
1 AAATACATGACTTTTAAAT-G
5699773 AAATACATGA-TTTT-AATG
1 AAATACATGACTTTTAAATG
5699791 AAGATACATG
1 AA-ATACATG
5699801 CTCTTGGCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.11
19 10 0.37
20 4 0.15
21 10 0.37
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (20 bp):
AAATACATGACTTTTAAATG
Found at i:5701817 original size:25 final size:26
Alignment explanation
Indices: 5701789--5701845 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 26
5701779 AAAATCAGCA
* *
5701789 AAGAAAAAGTCAAGCATTC-TAAAAG
1 AAGAAAAAGTCAAGCACTCAAAAAAG
*
5701814 AAG-AAAAGTCAAGTACTCAAAAAAG
1 AAGAAAAAGTCAAGCACTCAAAAAAG
5701839 AAGAAAA
1 AAGAAAA
5701846 GTAAAGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 13 0.48
25 11 0.41
26 3 0.11
ACGTcount: A:0.61, C:0.11, G:0.16, T:0.12
Consensus pattern (26 bp):
AAGAAAAAGTCAAGCACTCAAAAAAG
Found at i:5701823 original size:24 final size:25
Alignment explanation
Indices: 5701793--5701847 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
5701783 TCAGCAAAGA
* *
5701793 AAAAGTCAAGCATTC-TAAAAGAAG
1 AAAAGTCAAGCACTCAAAAAAGAAG
*
5701817 AAAAGTCAAGTACTCAAAAAAGAAG
1 AAAAGTCAAGCACTCAAAAAAGAAG
5701842 AAAAGT
1 AAAAGT
5701848 AAAGAAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.58, C:0.11, G:0.16, T:0.15
Consensus pattern (25 bp):
AAAAGTCAAGCACTCAAAAAAGAAG
Found at i:5702894 original size:36 final size:35
Alignment explanation
Indices: 5702801--5702911 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
5702791 TTGGTGGTTA
* * * *
5702801 TATAGGCATGAAATGGTGATAGAAGATGGTAATGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
* *
5702836 TATAGGCGTGCAATGGTAATGGAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
5702871 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTG-AAATGGTGATGGAAGATGGTGATGT
5702907 T-TAGG
1 TATAGG
5702912 TAGTATCTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 43 0.64
36 24 0.36
ACGTcount: A:0.32, C:0.04, G:0.36, T:0.28
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
Found at i:5706067 original size:13 final size:14
Alignment explanation
Indices: 5706032--5706072 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
5706022 TTCTTTTATA
5706032 TTTTAT-TTATCTTG
1 TTTTATCTTAT-TTG
5706046 TTTTAATCTTATTT-
1 TTTT-ATCTTATTTG
5706060 TTTTATCTTATTT
1 TTTTATCTTATTT
5706073 CCAGCACCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 9 0.36
14 8 0.32
15 4 0.16
16 4 0.16
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.73
Consensus pattern (14 bp):
TTTTATCTTATTTG
Found at i:5708578 original size:10 final size:10
Alignment explanation
Indices: 5708565--5708603 Score: 60
Period size: 10 Copynumber: 3.7 Consensus size: 10
5708555 TGGACTAAAG
5708565 GTAGCTGGAA
1 GTAGCTGGAA
5708575 GTAGCTGGAA
1 GTAGCTGGAA
5708585 GTAGCTGGGAGA
1 GTAGCT-GGA-A
5708597 GTAGCTG
1 GTAGCTG
5708604 AGGAGCTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 16 0.59
11 4 0.15
12 7 0.26
ACGTcount: A:0.26, C:0.10, G:0.44, T:0.21
Consensus pattern (10 bp):
GTAGCTGGAA
Found at i:5709001 original size:19 final size:20
Alignment explanation
Indices: 5708977--5709027 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
5708967 CGGCCAAGAG
* *
5708977 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
5708996 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
5709016 CATGTATTTTCA
1 CATGTATTTTCA
5709028 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:5713198 original size:19 final size:20
Alignment explanation
Indices: 5713174--5713224 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
5713164 CGGCCAAGAG
* *
5713174 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
5713193 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
5713213 CATGTATTTTCA
1 CATGTATTTTCA
5713225 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:5721031 original size:19 final size:20
Alignment explanation
Indices: 5720984--5721034 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
5720974 GAAACCCCTC
**
5720984 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
5721004 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
5721023 TGAAGATACATG
1 TGAAAATACATG
5721035 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:5722574 original size:21 final size:21
Alignment explanation
Indices: 5722534--5722582 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
5722524 ATAGGAGTCT
*
5722534 TTTCTTTCTCTTTTTGTTTT-
1 TTTCTTTCTCTTTCTGTTTTG
5722554 TCTTCTTTCTTCTTTCT-TTTTG
1 T-TTCTTTC-TCTTTCTGTTTTG
5722576 TTTCTTT
1 TTTCTTT
5722583 TGTTGCAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 1 0.04
21 17 0.68
22 7 0.28
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (21 bp):
TTTCTTTCTCTTTCTGTTTTG
Found at i:5723001 original size:35 final size:35
Alignment explanation
Indices: 5722962--5723063 Score: 141
Period size: 35 Copynumber: 2.9 Consensus size: 35
5722952 ATTGGTGGTT
*
5722962 ATATAGGCGTGAAATGGTGATAGAAGATGGTAATG
1 ATATAGGCGTGAAATGGTGATGGAAGATGGTAATG
* * *
5722997 ATATAGGCGTGCAATGGTAATGGAAGATGGTGATG
1 ATATAGGCGTGAAATGGTGATGGAAGATGGTAATG
* *
5723032 TTATATGCGTGAAAATGGTGATGGAAGATGGT
1 ATATAGGCGTG-AAATGGTGATGGAAGATGGT
5723064 GATATTTAGG
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 40 0.69
36 18 0.31
ACGTcount: A:0.33, C:0.04, G:0.35, T:0.27
Consensus pattern (35 bp):
ATATAGGCGTGAAATGGTGATGGAAGATGGTAATG
Found at i:5725497 original size:24 final size:25
Alignment explanation
Indices: 5725454--5725506 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
5725444 TCATCAAATA
* * *
5725454 AAAAGTCAAGCATTC-CAAAATAAG
1 AAAAGTCAAGCACTCAAAAAAGAAG
*
5725478 AAAAGTCAAGTACTCAAAAAAGAAG
1 AAAAGTCAAGCACTCAAAAAAGAAG
5725503 AAAA
1 AAAA
5725507 AGCAAAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.60, C:0.13, G:0.13, T:0.13
Consensus pattern (25 bp):
AAAAGTCAAGCACTCAAAAAAGAAG
Found at i:5726727 original size:24 final size:23
Alignment explanation
Indices: 5726699--5726767 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 23
5726689 GATTCAAGAA
5726699 ACATGTCTTTTGAAGAACCAATAG
1 ACATGTCTTTTGAAGAACCAA-AG
* * ** * *
5726723 TCATGACTTTTGGTGATCCACACG
1 ACATGTCTTTTGAAGAACCA-AAG
5726747 ACATGTCTTTTGAAGAACCAA
1 ACATGTCTTTTGAAGAACCAA
5726768 CAATTATGTC
Statistics
Matches: 33, Mismatches: 11, Indels: 3
0.70 0.23 0.06
Matches are distributed among these distances:
23 1 0.03
24 31 0.94
25 1 0.03
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30
Consensus pattern (23 bp):
ACATGTCTTTTGAAGAACCAAAG
Found at i:5729396 original size:25 final size:26
Alignment explanation
Indices: 5729368--5729424 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 26
5729358 AAAATCAGCA
* *
5729368 AAGAAAAAGTCAAGCATTC-TAAAAG
1 AAGAAAAAGTCAAGCACTCAAAAAAG
*
5729393 AAG-AAAAGTCAAGTACTCAAAAAAG
1 AAGAAAAAGTCAAGCACTCAAAAAAG
5729418 AAGAAAA
1 AAGAAAA
5729425 GTAAAGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 13 0.48
25 11 0.41
26 3 0.11
ACGTcount: A:0.61, C:0.11, G:0.16, T:0.12
Consensus pattern (26 bp):
AAGAAAAAGTCAAGCACTCAAAAAAG
Found at i:5729402 original size:24 final size:25
Alignment explanation
Indices: 5729372--5729426 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
5729362 TCAGCAAAGA
* *
5729372 AAAAGTCAAGCATTC-TAAAAGAAG
1 AAAAGTCAAGCACTCAAAAAAGAAG
*
5729396 AAAAGTCAAGTACTCAAAAAAGAAG
1 AAAAGTCAAGCACTCAAAAAAGAAG
5729421 AAAAGT
1 AAAAGT
5729427 AAAGAAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.58, C:0.11, G:0.16, T:0.15
Consensus pattern (25 bp):
AAAAGTCAAGCACTCAAAAAAGAAG
Found at i:5731073 original size:262 final size:259
Alignment explanation
Indices: 5730599--5731098 Score: 557
Period size: 262 Copynumber: 1.9 Consensus size: 259
5730589 TACCATGGAA
* * ** *
5730599 TTACCTTGTTTCCTTGCACATGTAGGTACATTGGAGCATGATGCATGTTGAGGTAGCTTGGTGAA
1 TTACATTGTTTCCTTGCACATATAGGTACATTGGAGCATGATGCATAATGAGGCAGCTTGGTGAA
* * * *
5730664 TGATTTGGACGTTATATGTAGCTCACAAACAACTTACAAAGTACAAGGCAGCTCATGGAACACTA
66 TGATTTGGACATCATATGCAGCTCACAAACAACTCACAAAGTACAAGGCAGCTCATGGAACACTA
* * * **
5730729 AGGGAAGCTCGATTCAGCTGGAGGAGCTTAAGGCTAGCTAAACTTAGCTAGTTGGACTATTTGGA
131 AGGAAAGCTCAATTCAGCTAGAGGAGCTTAAGGCTAGCTAAACTTAGCTAGAGGGAC-ATTTGGA
** * *
5730794 GCTGAGTTGCCAAAAGT-GATGTCAAAGGTAGCTGAATGTAGCTGAACATAATGTTAAGGAGCTA
195 GCAAAGTTG-CAAAAGTGGA-CT-AAAGGTAGCTGAAAGTAGCTGAACATAATGTTAAGGAGCTA
5730858 AAC
257 AAC
**
5730861 TTACATTGTTTCCTTGCACATATAGGTACATTGGAGTGTGATGCATAATGAGGCAGCTTGGTAGA
1 TTACATTGTTTCCTTGCACATATAGGTACATTGGAGCATGATGCATAATGAGGCAGCTTGGT-GA
* * * * * *
5730926 GT-ATTTGGACATCATATGCAGCTCACAAATAGCTCGCAAA-TATCATGGCAGCTCGTGGAACAC
65 ATGATTTGGACATCATATGCAGCTCACAAACAACTCACAAAGTA-CAAGGCAGCTCATGGAACAC
* * *
5730989 TAAGGAAAGCTCAACTT-AGCTAGAGGAGC-TAA-CCTGTAGCTGAACTTAGCTGGAGGAGAGC-
129 TAAGGAAAGCTCAA-TTCAGCTAGAGGAGCTTAAGGC--TAGCTAAACTTAGCTAGAGG-GA-CA
*
5731050 TTTGGATCAAAGTACTG-AAAAGTGGACTAAAGGTAGCTGAAAGTAGCTG
189 TTTGGAGCAAAGT--TGCAAAAGTGGACTAAAGGTAGCTGAAAGTAGCTG
5731099 GGAGAGTAGC
Statistics
Matches: 198, Mismatches: 30, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
260 1 0.01
261 25 0.13
262 160 0.81
263 9 0.05
264 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (259 bp):
TTACATTGTTTCCTTGCACATATAGGTACATTGGAGCATGATGCATAATGAGGCAGCTTGGTGAA
TGATTTGGACATCATATGCAGCTCACAAACAACTCACAAAGTACAAGGCAGCTCATGGAACACTA
AGGAAAGCTCAATTCAGCTAGAGGAGCTTAAGGCTAGCTAAACTTAGCTAGAGGGACATTTGGAG
CAAAGTTGCAAAAGTGGACTAAAGGTAGCTGAAAGTAGCTGAACATAATGTTAAGGAGCTAAAC
Found at i:5732203 original size:10 final size:10
Alignment explanation
Indices: 5732188--5732221 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
5732178 ACTCAAAAAG
5732188 AAGAAAAGGA
1 AAGAAAAGGA
5732198 AAGAAAAGGA
1 AAGAAAAGGA
5732208 AAG-AAA-GA
1 AAGAAAAGGA
5732216 AAGAAA
1 AAGAAA
5732222 GTTGAAGCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 5 0.22
9 5 0.22
10 13 0.57
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (10 bp):
AAGAAAAGGA
Found at i:5733138 original size:30 final size:31
Alignment explanation
Indices: 5733086--5733145 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
5733076 CTTAGCTTTA
**
5733086 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
5733116 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
5733146 GACAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:5734079 original size:19 final size:20
Alignment explanation
Indices: 5734055--5734096 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
5734045 CGGCCAAGAG
*
5734055 CATGTATCTTCAT-TAAAAT
1 CATGTATCTTCATAAAAAAT
*
5734074 CATGTATTTTCATAAAAAAT
1 CATGTATCTTCATAAAAAAT
5734094 CAT
1 CAT
5734097 ATATTTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.40
Consensus pattern (20 bp):
CATGTATCTTCATAAAAAAT
Found at i:5734094 original size:20 final size:19
Alignment explanation
Indices: 5734055--5734105 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
5734045 CGGCCAAGAG
* *
5734055 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATAAAAAT
5734074 CATGTATTTTCATAAAAAAT
1 CATGTATTTTCAT-AAAAAT
*
5734094 CATATATTTTCA
1 CATGTATTTTCA
5734106 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.39, C:0.14, G:0.04, T:0.43
Consensus pattern (19 bp):
CATGTATTTTCATAAAAAT
Found at i:5734865 original size:8 final size:8
Alignment explanation
Indices: 5734854--5734897 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
5734844 GAGAAAAATC
5734854 AGAAAAGA
1 AGAAAAGA
5734862 AGAAAAGA
1 AGAAAAGA
5734870 AGAAAAGAAA
1 AGAAAAG--A
5734880 AGAAAAGA
1 AGAAAAGA
5734888 A-AAAGAGA
1 AGAAA-AGA
5734896 AG
1 AG
5734898 TTCAAAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
7 3 0.09
8 21 0.66
10 8 0.25
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:5734867 original size:16 final size:16
Alignment explanation
Indices: 5734854--5734897 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
5734844 GAGAAAAATC
5734854 AGAAAAGAAGAAAAGA
1 AGAAAAGAAGAAAAGA
5734870 AGAAAAGAAAAGAAAAGA
1 AGAAAAG--AAGAAAAGA
5734888 A-AAAGAGAAG
1 AGAAA-AGAAG
5734898 TTCAAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 10 0.40
17 3 0.12
18 12 0.48
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (16 bp):
AGAAAAGAAGAAAAGA
Found at i:5734877 original size:13 final size:13
Alignment explanation
Indices: 5734854--5734888 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
5734844 GAGAAAAATC
5734854 AGAAAAGAAGAAA
1 AGAAAAGAAGAAA
5734867 AGAAGAA-AAGAAA
1 AGAA-AAGAAGAAA
5734880 AGAAAAGAA
1 AGAAAAGAA
5734889 AAAGAGAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.10
13 16 0.80
14 2 0.10
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAGAAA
Found at i:5738413 original size:35 final size:37
Alignment explanation
Indices: 5738344--5738423 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
5738334 ATACTATTTC
* *
5738344 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
*
5738381 CATCACCATAGTCCATC-ACCA-TATCACACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
5738416 CATCACCA
1 CATCACCA
5738424 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 3 0.08
37 16 0.40
ACGTcount: A:0.33, C:0.38, G:0.03, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACACCTATAT
Found at i:5738417 original size:11 final size:11
Alignment explanation
Indices: 5738377--5738423 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
5738367 TATCACGCCT
5738377 ATATCATCACC
1 ATATCATCACC
5738388 ATAGTCCATCACC
1 ATA-T-CATCACC
5738401 ATATCA-CACC
1 ATATCATCACC
5738411 TATATCATCACC
1 -ATATCATCACC
5738423 A
1 A
5738424 AATTCTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.12
11 12 0.38
12 6 0.19
13 10 0.31
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (11 bp):
ATATCATCACC
Found at i:5738421 original size:22 final size:24
Alignment explanation
Indices: 5738377--5738423 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
5738367 TATCACGCCT
5738377 ATATCATCACCATAGTCCATCACC
1 ATATCATCACCATAGTCCATCACC
5738401 ATATCA-CACCTATA-T-CATCACC
1 ATATCATCACC-ATAGTCCATCACC
5738423 A
1 A
5738424 AATTCTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 5 0.23
24 9 0.41
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (24 bp):
ATATCATCACCATAGTCCATCACC
Found at i:5738830 original size:12 final size:12
Alignment explanation
Indices: 5738801--5738843 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
5738791 AGTGCTACAA
5738801 AAAAAAGCAACAAG
1 AAAAAAG-AA-AAG
*
5738815 AAAAAAGAAAAC
1 AAAAAAGAAAAG
*
5738827 AAAAGAGAAAAG
1 AAAAAAGAAAAG
5738839 AAAAA
1 AAAAA
5738844 GACTCCTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 16 0.64
13 2 0.08
14 7 0.28
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:5738832 original size:17 final size:18
Alignment explanation
Indices: 5738799--5738842 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
5738789 AAAGTGCTAC
*
5738799 AAAAA-AAAGCAACAAGA
1 AAAAAGAAAACAACAAGA
5738816 AAAAAGAAAACAA-AAGA
1 AAAAAGAAAACAACAAGA
*
5738833 GAAAAGAAAA
1 AAAAAGAAAA
5738843 AGACTCCTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.80, C:0.07, G:0.14, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAACAACAAGA
Found at i:5742351 original size:35 final size:37
Alignment explanation
Indices: 5742282--5742361 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
5742272 ATACTATTTC
* *
5742282 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
*
5742319 CATCACCATAGTCCATC-ACCA-TATCACACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
5742354 CATCACCA
1 CATCACCA
5742362 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 3 0.08
37 16 0.40
ACGTcount: A:0.33, C:0.38, G:0.03, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACACCTATAT
Found at i:5742355 original size:11 final size:11
Alignment explanation
Indices: 5742315--5742361 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
5742305 TATCACGCCT
5742315 ATATCATCACC
1 ATATCATCACC
5742326 ATAGTCCATCACC
1 ATA-T-CATCACC
5742339 ATATCA-CACC
1 ATATCATCACC
5742349 TATATCATCACC
1 -ATATCATCACC
5742361 A
1 A
5742362 AATTCTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.12
11 12 0.38
12 6 0.19
13 10 0.31
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (11 bp):
ATATCATCACC
Found at i:5742359 original size:22 final size:24
Alignment explanation
Indices: 5742315--5742361 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
5742305 TATCACGCCT
5742315 ATATCATCACCATAGTCCATCACC
1 ATATCATCACCATAGTCCATCACC
5742339 ATATCA-CACCTATA-T-CATCACC
1 ATATCATCACC-ATAGTCCATCACC
5742361 A
1 A
5742362 AATTCTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 5 0.23
24 9 0.41
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (24 bp):
ATATCATCACCATAGTCCATCACC
Found at i:5744103 original size:24 final size:24
Alignment explanation
Indices: 5744076--5744133 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
5744066 TCAAAACATC
5744076 AAGAGACATGTCTTGTGAATCACA
1 AAGAGACATGTCTTGTGAATCACA
* *
5744100 AAGAGATATGTCTTGTGGATCACA
1 AAGAGACATGTCTTGTGAATCACA
*
5744124 AAGAGTCATG
1 AAGAGACATG
5744134 CCTATTGGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (24 bp):
AAGAGACATGTCTTGTGAATCACA
Found at i:5748664 original size:24 final size:25
Alignment explanation
Indices: 5748618--5748672 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
5748608 ATAGTTATGC
*
5748618 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
5748642 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
5748667 CA-TTGA
1 CACTTGA
5748673 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:5753737 original size:2 final size:2
Alignment explanation
Indices: 5753730--5753781 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
5753720 TATAATTATC
5753730 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
5753772 AT AT AT AT AT
1 AT AT AT AT AT
5753782 TATCTATAGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5758323 original size:11 final size:12
Alignment explanation
Indices: 5758283--5758325 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
5758273 AAATTTTAAC
* *
5758283 TTTTTTGGCTTT
1 TTTTTTTGCCTT
5758295 TTTTTTTGCCTT
1 TTTTTTTGCCTT
*
5758307 TGTTTTT-CCTT
1 TTTTTTTGCCTT
5758318 TTTTTTTG
1 TTTTTTTG
5758326 TTTTTTTCTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.77
Consensus pattern (12 bp):
TTTTTTTGCCTT
Found at i:5763989 original size:18 final size:18
Alignment explanation
Indices: 5763963--5763999 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5763953 TGACTACAAG
5763963 ACATACTTTACCATTTAC
1 ACATACTTTACCATTTAC
*
5763981 ACATTCTTTACCATTTAC
1 ACATACTTTACCATTTAC
5763999 A
1 A
5764000 TGGCAATGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.27, G:0.00, T:0.41
Consensus pattern (18 bp):
ACATACTTTACCATTTAC
Found at i:5764563 original size:13 final size:15
Alignment explanation
Indices: 5764540--5764571 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5764530 CTTCTTTGCA
5764540 TTTTGCTTTCTTT-G
1 TTTTGCTTTCTTTAG
5764554 TTTT-CTTTCTTTAG
1 TTTTGCTTTCTTTAG
5764568 TTTT
1 TTTT
5764572 TCTTCACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.03, C:0.12, G:0.09, T:0.75
Consensus pattern (15 bp):
TTTTGCTTTCTTTAG
Found at i:5766005 original size:25 final size:25
Alignment explanation
Indices: 5765977--5766056 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
5765967 CTACCATCCC
5765977 TTATAGCATTTGTTCCTTCTTAGTT
1 TTATAGCATTTGTTCCTTCTTAGTT
* * * * * **
5766002 TTATAAGAAATGGGTCTTTGC-T-CCT
1 TTAT-AGCATTTGTTCCTT-CTTAGTT
5766027 TTATAGCATTTGTTCCTTCTTAGTT
1 TTATAGCATTTGTTCCTTCTTAGTT
5766052 TTATA
1 TTATA
5766057 AGATACTACC
Statistics
Matches: 37, Mismatches: 14, Indels: 8
0.63 0.24 0.14
Matches are distributed among these distances:
23 1 0.03
24 10 0.27
25 15 0.41
26 10 0.27
27 1 0.03
ACGTcount: A:0.20, C:0.15, G:0.14, T:0.51
Consensus pattern (25 bp):
TTATAGCATTTGTTCCTTCTTAGTT
Found at i:5766568 original size:7 final size:6
Alignment explanation
Indices: 5766537--5766589 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
5766527 GTGCTGCAAC
* * * *
5766537 AAAAGTA AAAAAA AAAAGA AAAAGA AAGAAGA AATACA AAAAGA TAAAGA
1 AAAAG-A AAAAGA AAAAGA AAAAGA AA-AAGA AAAAGA AAAAGA AAAAGA
5766587 AAA
1 AAA
5766590 GACTCCTACA
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
6 27 0.73
7 10 0.27
ACGTcount: A:0.79, C:0.02, G:0.13, T:0.06
Consensus pattern (6 bp):
AAAAGA
Found at i:5766883 original size:17 final size:17
Alignment explanation
Indices: 5766861--5766894 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5766851 TATCCTACCC
5766861 CTATACCATAACCATTT
1 CTATACCATAACCATTT
* *
5766878 CTATACCCTATCCATTT
1 CTATACCATAACCATTT
5766895 TTTTAAGCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.38
Consensus pattern (17 bp):
CTATACCATAACCATTT
Found at i:5775886 original size:39 final size:41
Alignment explanation
Indices: 5775838--5775915 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 41
5775828 AAAGTGAAAG
**
5775838 AAAGCAAGAAAAA-TCAGCAAAGAAAA-TTGAAAGCACTCGA
1 AAAGCAAGAAAAAGAAAG-AAAGAAAAGTTGAAAGCACTCGA
*
5775878 AAAG-AAGAAAAAGAAAGAAAGAAAAGTTGGAAGCACTC
1 AAAGCAAGAAAAAGAAAGAAAGAAAAGTTGAAAGCACTC
5775916 ATCAACAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 16 0.48
40 17 0.52
ACGTcount: A:0.59, C:0.12, G:0.21, T:0.09
Consensus pattern (41 bp):
AAAGCAAGAAAAAGAAAGAAAGAAAAGTTGAAAGCACTCGA
Found at i:5787481 original size:19 final size:19
Alignment explanation
Indices: 5787461--5787534 Score: 89
Period size: 19 Copynumber: 4.0 Consensus size: 19
5787451 TTTTTGAATT
*
5787461 TCTTTTTCTTTTCTTTTTT
1 TCTTTTTCTTTTCTTTTTG
** *
5787480 TC-TGAT-TATTCTTTTTG
1 TCTTTTTCTTTTCTTTTTG
*
5787497 TCTTTTTCTCTTCTTTTTG
1 TCTTTTTCTTTTCTTTTTG
5787516 TCTTTTTCTTTTCTTTTTG
1 TCTTTTTCTTTTCTTTTTG
5787535 CACTCCAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
17 11 0.24
18 4 0.09
19 30 0.67
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.76
Consensus pattern (19 bp):
TCTTTTTCTTTTCTTTTTG
Found at i:5788303 original size:19 final size:21
Alignment explanation
Indices: 5788253--5788304 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
5788243 GAAATCCCTT
5788253 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
*
5788274 TAAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
5788293 TGAAGATACATG
1 TGAAAATACATG
5788305 CTCTTGGCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:5789601 original size:2 final size:2
Alignment explanation
Indices: 5789594--5789629 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5789584 TATCACCAAC
5789594 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
5789630 CCGCTTCCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5791811 original size:11 final size:11
Alignment explanation
Indices: 5791771--5791817 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
5791761 TATTACGCTT
5791771 ATATCATCACC
1 ATATCATCACC
5791782 ATAGTCCATCACC
1 ATA-T-CATCACC
5791795 ATATCA-CACC
1 ATATCATCACC
5791805 TATATCATCACC
1 -ATATCATCACC
5791817 A
1 A
5791818 AATTCTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.12
11 12 0.38
12 6 0.19
13 10 0.31
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (11 bp):
ATATCATCACC
Found at i:5791815 original size:22 final size:24
Alignment explanation
Indices: 5791771--5791817 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
5791761 TATTACGCTT
5791771 ATATCATCACCATAGTCCATCACC
1 ATATCATCACCATAGTCCATCACC
5791795 ATATCA-CACCTATA-T-CATCACC
1 ATATCATCACC-ATAGTCCATCACC
5791817 A
1 A
5791818 AATTCTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 5 0.23
24 9 0.41
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (24 bp):
ATATCATCACCATAGTCCATCACC
Found at i:5791816 original size:35 final size:37
Alignment explanation
Indices: 5791738--5791817 Score: 101
Period size: 35 Copynumber: 2.2 Consensus size: 37
5791728 ATACTATTTC
* * * *
5791738 CATCACCATAATCCATCTTCCATTATTACGCTTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
*
5791775 CATCACCATAGTCCATC-ACCA-TATCACACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
5791810 CATCACCA
1 CATCACCA
5791818 AATTCTCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
35 19 0.50
36 3 0.08
37 16 0.42
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.30
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACACCTATAT
Found at i:5792291 original size:14 final size:15
Alignment explanation
Indices: 5792257--5792303 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
5792247 AATTTGGAGT
5792257 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
5792272 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
5792286 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
5792303 G
1 G
5792304 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:5795744 original size:35 final size:36
Alignment explanation
Indices: 5795675--5795754 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 36
5795665 ATACTATTTC
*
5795675 CATCACCATAATCCATATTCCATTATCACGCCTATAT
1 CATCACCATAATCCATA-TCCATTATCACACCTATAT
*
5795712 CATCACCATAGTCCATCA-CCA-TATCACACCTATAT
1 CATCACCATAATCCAT-ATCCATTATCACACCTATAT
5795747 CATCACCA
1 CATCACCA
5795755 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
35 21 0.52
36 3 0.08
37 15 0.38
38 1 0.03
ACGTcount: A:0.34, C:0.36, G:0.03, T:0.28
Consensus pattern (36 bp):
CATCACCATAATCCATATCCATTATCACACCTATAT
Found at i:5795748 original size:11 final size:11
Alignment explanation
Indices: 5795708--5795754 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
5795698 TATCACGCCT
5795708 ATATCATCACC
1 ATATCATCACC
5795719 ATAGTCCATCACC
1 ATA-T-CATCACC
5795732 ATATCA-CACC
1 ATATCATCACC
5795742 TATATCATCACC
1 -ATATCATCACC
5795754 A
1 A
5795755 AATTCTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.12
11 12 0.38
12 6 0.19
13 10 0.31
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (11 bp):
ATATCATCACC
Found at i:5795752 original size:22 final size:24
Alignment explanation
Indices: 5795708--5795754 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
5795698 TATCACGCCT
5795708 ATATCATCACCATAGTCCATCACC
1 ATATCATCACCATAGTCCATCACC
5795732 ATATCA-CACCTATA-T-CATCACC
1 ATATCATCACC-ATAGTCCATCACC
5795754 A
1 A
5795755 AATTCTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 5 0.23
24 9 0.41
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (24 bp):
ATATCATCACCATAGTCCATCACC
Found at i:5796228 original size:14 final size:15
Alignment explanation
Indices: 5796194--5796240 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
5796184 AATTTGGAGT
5796194 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
5796209 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
5796223 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
5796240 G
1 G
5796241 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:5799681 original size:35 final size:37
Alignment explanation
Indices: 5799612--5799691 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
5799602 ATACTATTTC
* *
5799612 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
*
5799649 CATCACCATAGTCCATC-ACCA-TATCACACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
5799684 CATCACCA
1 CATCACCA
5799692 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 3 0.08
37 16 0.40
ACGTcount: A:0.33, C:0.38, G:0.03, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACACCTATAT
Found at i:5799685 original size:11 final size:11
Alignment explanation
Indices: 5799645--5799691 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
5799635 TATCACGCCT
5799645 ATATCATCACC
1 ATATCATCACC
5799656 ATAGTCCATCACC
1 ATA-T-CATCACC
5799669 ATATCA-CACC
1 ATATCATCACC
5799679 TATATCATCACC
1 -ATATCATCACC
5799691 A
1 A
5799692 AATTCTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.12
11 12 0.38
12 6 0.19
13 10 0.31
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (11 bp):
ATATCATCACC
Found at i:5799689 original size:22 final size:24
Alignment explanation
Indices: 5799645--5799691 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
5799635 TATCACGCCT
5799645 ATATCATCACCATAGTCCATCACC
1 ATATCATCACCATAGTCCATCACC
5799669 ATATCA-CACCTATA-T-CATCACC
1 ATATCATCACC-ATAGTCCATCACC
5799691 A
1 A
5799692 AATTCTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 5 0.23
24 9 0.41
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (24 bp):
ATATCATCACCATAGTCCATCACC
Found at i:5803620 original size:35 final size:37
Alignment explanation
Indices: 5803551--5803630 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
5803541 ATACTATTTC
* *
5803551 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
*
5803588 CATCACCATAGTCCATC-ACCA-TATCACACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
5803623 CATCACCA
1 CATCACCA
5803631 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 3 0.08
37 16 0.40
ACGTcount: A:0.33, C:0.38, G:0.03, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACACCTATAT
Found at i:5803624 original size:11 final size:11
Alignment explanation
Indices: 5803584--5803630 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
5803574 TATCACGCCT
5803584 ATATCATCACC
1 ATATCATCACC
5803595 ATAGTCCATCACC
1 ATA-T-CATCACC
5803608 ATATCA-CACC
1 ATATCATCACC
5803618 TATATCATCACC
1 -ATATCATCACC
5803630 A
1 A
5803631 AATTCTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.12
11 12 0.38
12 6 0.19
13 10 0.31
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (11 bp):
ATATCATCACC
Found at i:5803628 original size:22 final size:24
Alignment explanation
Indices: 5803584--5803630 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
5803574 TATCACGCCT
5803584 ATATCATCACCATAGTCCATCACC
1 ATATCATCACCATAGTCCATCACC
5803608 ATATCA-CACCTATA-T-CATCACC
1 ATATCATCACC-ATAGTCCATCACC
5803630 A
1 A
5803631 AATTCTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 5 0.23
24 9 0.41
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (24 bp):
ATATCATCACCATAGTCCATCACC
Found at i:5809367 original size:24 final size:24
Alignment explanation
Indices: 5809340--5809385 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
5809330 TCTTTTCTTT
5809340 GTTTTTC-TTCTTTTTGAGTGCTGG
1 GTTTTTCTTTC-TTTTGAGTGCTGG
5809364 GTTTTTCTTTCTTTTGAGTGCT
1 GTTTTTCTTTCTTTTGAGTGCT
5809386 TCACTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.04, C:0.13, G:0.22, T:0.61
Consensus pattern (24 bp):
GTTTTTCTTTCTTTTGAGTGCTGG
Found at i:5811985 original size:33 final size:33
Alignment explanation
Indices: 5811943--5812011 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
5811933 GTTGATGAAT
*
5811943 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
5811976 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
5812009 GAA
1 GAA
5812012 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:5812016 original size:13 final size:12
Alignment explanation
Indices: 5811997--5812093 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
5811987 TTATTGGCGT
5811997 GATATGGTGATG
1 GATATGGTGATG
5812009 GAATATGGTGAT-
1 G-ATATGGTGATG
*
5812021 GATATAGGCG-T-
1 GATAT-GGTGATG
5812032 GATAATGGTGATG
1 GAT-ATGGTGATG
5812045 GACTATGGTGAT-
1 GA-TATGGTGATG
*
5812057 GATATAGGCG-T-
1 GATAT-GGTGATG
*
5812068 GATAATGGAGATG
1 GAT-ATGGTGATG
5812081 GATTATGGTGATG
1 GA-TATGGTGATG
5812094 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:5812052 original size:36 final size:36
Alignment explanation
Indices: 5811982--5812094 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
5811972 AATGGAAGGA
* *
5811982 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
5812017 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
5812053 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
5812089 TGATGA
1 TGATGA
5812095 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:5817703 original size:33 final size:33
Alignment explanation
Indices: 5817661--5817729 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
5817651 GTTGATGAAT
*
5817661 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
5817694 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
5817727 GAA
1 GAA
5817730 TATGGTAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:5817759 original size:36 final size:36
Alignment explanation
Indices: 5817700--5817812 Score: 147
Period size: 36 Copynumber: 3.2 Consensus size: 36
5817690 AATGGAAGGA
* * *
5817700 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCATGATAATGGTGATGGAATATGG
* *
5817735 TAATGATATAGGCATGATAATGGTGATGGACTATGG
1 TGATGATATAGGCATGATAATGGTGATGGAATATGG
* * *
5817771 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCATGATAATGGTGATGGAATATGG
5817807 TGATGA
1 TGATGA
5817813 AAATAGTATC
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 14 0.21
36 54 0.79
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCATGATAATGGTGATGGAATATGG
Found at i:5820574 original size:2 final size:2
Alignment explanation
Indices: 5820567--5820602 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5820557 TATCACCAAC
5820567 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
5820603 TCTGCTTCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5826470 original size:35 final size:37
Alignment explanation
Indices: 5826402--5826481 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
5826392 ATACTATTTC
* *
5826402 CATCCCCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCATCCATTATCACGCCTATAT
*
5826439 CATCACCATAGTCCATCAT-CA-TATCACGCCTATAT
1 CATCACCATAATCCATCATCCATTATCACGCCTATAT
5826474 CATCACCA
1 CATCACCA
5826482 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 22 0.55
36 2 0.05
37 16 0.40
ACGTcount: A:0.30, C:0.38, G:0.04, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCATCCATTATCACGCCTATAT
Found at i:5827019 original size:11 final size:11
Alignment explanation
Indices: 5827003--5827055 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
5826993 TTTGAACTTC
*
5827003 TCTTTTTCTTT
1 TCTTTTTCTCT
*
5827014 TCTTTTCTTCTTT
1 TC-TTT-TTCTCT
5827027 TCTTCTTT-TCT
1 TCTT-TTTCTCT
5827038 TCTTTTTCTCT
1 TCTTTTTCTCT
5827049 TCTTTTT
1 TCTTTTT
5827056 GCACTCCAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 3 0.08
11 18 0.49
12 7 0.19
13 9 0.24
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TCTTTTTCTCT
Found at i:5827024 original size:8 final size:8
Alignment explanation
Indices: 5827013--5827043 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
5827003 TCTTTTTCTT
5827013 TTCTTTTC
1 TTCTTTTC
5827021 TTCTTTTC
1 TTCTTTTC
5827029 TTCTTTTC
1 TTCTTTTC
5827037 TTCTTTT
1 TTCTTTT
5827044 TCTCTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTCTTTTC
Found at i:5831338 original size:2 final size:2
Alignment explanation
Indices: 5831331--5831384 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
5831321 TGTCACCAAC
5831331 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
5831373 AT AT AT AT AT AT
1 AT AT AT AT AT AT
5831385 CGCTTCCATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5833986 original size:2 final size:2
Alignment explanation
Indices: 5833979--5834006 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5833969 TATCACCAAC
5833979 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
5834007 TCCGCTTCCG
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:5835947 original size:24 final size:24
Alignment explanation
Indices: 5835920--5835993 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
5835910 AATGTCAAGG
*
5835920 GACATAACTGTTGGTTCTTCAAAA
1 GACATGACTGTTGGTTCTTCAAAA
* * **
5835944 GACATGTCT-TGTGGATCACCAAAA
1 GACATGACTGT-TGGTTCTTCAAAA
* *
5835968 GTCATGACTGTTGATTCTTCAAAA
1 GACATGACTGTTGGTTCTTCAAAA
5835992 GA
1 GA
5835994 TATGTTTCTT
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
23 1 0.03
24 34 0.94
25 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (24 bp):
GACATGACTGTTGGTTCTTCAAAA
Found at i:5837244 original size:25 final size:26
Alignment explanation
Indices: 5837189--5837247 Score: 95
Period size: 24 Copynumber: 2.3 Consensus size: 26
5837179 CTTTTCTTTG
*
5837189 CTTTTTCTTCTTTTTTGAGTGCTTGA
1 CTTTTTCTTCTTTTTGGAGTGCTTGA
5837215 C-TTTTCTTC-TTTTGGAGTGCTTGA
1 CTTTTTCTTCTTTTTGGAGTGCTTGA
5837239 CTTTTTCTT
1 CTTTTTCTT
5837248 TGCTGATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
24 15 0.48
25 15 0.48
26 1 0.03
ACGTcount: A:0.07, C:0.17, G:0.15, T:0.61
Consensus pattern (26 bp):
CTTTTTCTTCTTTTTGGAGTGCTTGA
Found at i:5839345 original size:18 final size:18
Alignment explanation
Indices: 5839324--5839358 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5839314 AAATGATTTT
5839324 TTTAAAGAAAATACATGA
1 TTTAAAGAAAATACATGA
* *
5839342 TTTAATGAAAGTACATG
1 TTTAAAGAAAATACATG
5839359 CTTTTGGCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (18 bp):
TTTAAAGAAAATACATGA
Found at i:5839352 original size:22 final size:22
Alignment explanation
Indices: 5839308--5839352 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
5839298 AAACCCCTTT
** *
5839308 GAAAATAAATGATTTTTTTAAA
1 GAAAATAAATGATTTAATGAAA
*
5839330 GAAAATACATGATTTAATGAAA
1 GAAAATAAATGATTTAATGAAA
5839352 G
1 G
5839353 TACATGCTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.02, G:0.13, T:0.33
Consensus pattern (22 bp):
GAAAATAAATGATTTAATGAAA
Found at i:5846480 original size:11 final size:11
Alignment explanation
Indices: 5846464--5846490 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5846454 ATGCCTTGAT
5846464 GATGATTGAAG
1 GATGATTGAAG
5846475 GATGATTGAAG
1 GATGATTGAAG
5846486 GATGA
1 GATGA
5846491 ATAGATGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.26
Consensus pattern (11 bp):
GATGATTGAAG
Found at i:5846615 original size:36 final size:35
Alignment explanation
Indices: 5846518--5846627 Score: 150
Period size: 35 Copynumber: 3.1 Consensus size: 35
5846508 GGTGGTTATT
* * *
5846518 TAGGCGTGAAATGGAGATAGAAGATGGTAATGATA
1 TAGGCGTGAAATGGAGATGGAAGATGGTGATGTTA
* *
5846553 TAGGCGTGCAATGTTA-ATGGAAGATGGTGATGTTA
1 TAGGCGTGAAATG-GAGATGGAAGATGGTGATGTTA
5846588 TAGGCGTGAAAATGGAGATGGAAGATGGTGATGTTA
1 TAGGCGTG-AAATGGAGATGGAAGATGGTGATGTTA
5846624 TAGG
1 TAGG
5846628 TAGTATCTTA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
35 37 0.57
36 28 0.43
ACGTcount: A:0.34, C:0.04, G:0.36, T:0.26
Consensus pattern (35 bp):
TAGGCGTGAAATGGAGATGGAAGATGGTGATGTTA
Found at i:5848218 original size:21 final size:21
Alignment explanation
Indices: 5848192--5848238 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
5848182 GATTTGTCCT
*
5848192 CAAATCGAAAGGTGACTTCCC
1 CAAATCAAAAGGTGACTTCCC
*
5848213 CAAATCAAAAGGTGACTTCTC
1 CAAATCAAAAGGTGACTTCCC
5848234 CAAAT
1 CAAAT
5848239 TGTACGCCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.21
Consensus pattern (21 bp):
CAAATCAAAAGGTGACTTCCC
Found at i:5855645 original size:15 final size:15
Alignment explanation
Indices: 5855627--5855669 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
5855617 TTTCTTCACT
5855627 TTTTTTTTCTTTGAA
1 TTTTTTTTCTTTGAA
* **
5855642 TTTTTCTTCTTTTTA
1 TTTTTTTTCTTTGAA
*
5855657 TTTTCTTTCTTTG
1 TTTTTTTTCTTTG
5855670 GCACTCCAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.07, C:0.12, G:0.05, T:0.77
Consensus pattern (15 bp):
TTTTTTTTCTTTGAA
Found at i:5855737 original size:22 final size:22
Alignment explanation
Indices: 5855695--5855737 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
5855685 TATAGGAGTA
*
5855695 TTCTTCTTTTCTTTTTGTTTTT
1 TTCTTCTTTTCTTGTTGTTTTT
*
5855717 TTCTTC-TTTCTTGTTGCTTTT
1 TTCTTCTTTTCTTGTTGTTTTT
5855738 GTTGCAGCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (22 bp):
TTCTTCTTTTCTTGTTGTTTTT
Found at i:5856219 original size:36 final size:35
Alignment explanation
Indices: 5856128--5856237 Score: 150
Period size: 35 Copynumber: 3.1 Consensus size: 35
5856118 GGTGGTTATT
* * *
5856128 TAGGCGTGAAATGGAGATAGAAGATGGTAATGATA
1 TAGGCGTGAAATGGAGATGGAAGATGGTGATGTTA
*
5856163 TAGGCGTGCAATGGTA-ATGGAAGATGGTGATGTTA
1 TAGGCGTGAAATGG-AGATGGAAGATGGTGATGTTA
*
5856198 TAGGCATGAAAATGGAGATGGAAGATGGTGATGTTA
1 TAGGCGTG-AAATGGAGATGGAAGATGGTGATGTTA
5856234 TAGG
1 TAGG
5856238 TAGTATCTTA
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
35 37 0.56
36 29 0.44
ACGTcount: A:0.35, C:0.04, G:0.36, T:0.25
Consensus pattern (35 bp):
TAGGCGTGAAATGGAGATGGAAGATGGTGATGTTA
Found at i:5856612 original size:19 final size:20
Alignment explanation
Indices: 5856574--5856616 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
5856564 GAAACCCCTT
*
5856574 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
5856594 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
5856613 TGAA
1 TGAA
5856617 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:5859177 original size:25 final size:27
Alignment explanation
Indices: 5859130--5859186 Score: 73
Period size: 25 Copynumber: 2.1 Consensus size: 27
5859120 CTTTCTTTTC
*
5859130 TTTTCTTCTATTTTGTTTGAGTGCTTGAA
1 TTTTCTTCTATTTTG--TGAGTGCTTCAA
5859159 TTTTCTTCT-TTTTG-GAGTGCTTCAA
1 TTTTCTTCTATTTTGTGAGTGCTTCAA
5859184 TTT
1 TTT
5859187 CTTTGCTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 13 0.48
28 5 0.19
29 9 0.33
ACGTcount: A:0.12, C:0.12, G:0.16, T:0.60
Consensus pattern (27 bp):
TTTTCTTCTATTTTGTGAGTGCTTCAA
Found at i:5861961 original size:25 final size:25
Alignment explanation
Indices: 5861914--5861960 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
5861904 AAAGGAATTG
*
5861914 AAGCACTCCAAAAGAAAGAAAAATC
1 AAGCACTCAAAAAGAAAGAAAAATC
5861939 AAGCACTCAAAAAG-AAGAAAAA
1 AAGCACTCAAAAAGAAAGAAAAA
5861961 AATAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.64, C:0.17, G:0.13, T:0.06
Consensus pattern (25 bp):
AAGCACTCAAAAAGAAAGAAAAATC
Found at i:5865943 original size:15 final size:15
Alignment explanation
Indices: 5865932--5865960 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5865922 ACTCAAAAAG
5865932 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
5865947 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
5865961 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:5878866 original size:11 final size:11
Alignment explanation
Indices: 5878844--5878890 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
5878834 TTTGAGAATT
5878844 TGGTGATGATA
1 TGGTGATGATA
5878855 TAGGTG-TGATA
1 T-GGTGATGATA
5878866 TGGTGATGGACTA
1 TGGTGAT-GA-TA
5878879 TGGTGATGATA
1 TGGTGATGATA
5878890 T
1 T
5878891 AGGCGTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.12
11 11 0.34
12 8 0.25
13 9 0.28
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (11 bp):
TGGTGATGATA
Found at i:5878872 original size:22 final size:24
Alignment explanation
Indices: 5878844--5878890 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
5878834 TTTGAGAATT
5878844 TGGTGAT-GA-TATAGGTG-TGATA
1 TGGTGATGGACTAT-GGTGATGATA
5878866 TGGTGATGGACTATGGTGATGATA
1 TGGTGATGGACTATGGTGATGATA
5878890 T
1 T
5878891 AGGCGTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
23 6 0.27
24 9 0.41
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (24 bp):
TGGTGATGGACTATGGTGATGATA
Found at i:5878890 original size:35 final size:37
Alignment explanation
Indices: 5878844--5878923 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
5878834 TTTGAGAATT
* *
5878844 TGGTGATGATATAGGTGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
5878879 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
5878916 TGGTGATG
1 TGGTGATG
5878924 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 20 0.50
36 4 0.10
37 16 0.40
ACGTcount: A:0.28, C:0.03, G:0.38, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:5882931 original size:11 final size:11
Alignment explanation
Indices: 5882909--5882955 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
5882899 TTTGAGAATT
5882909 TGGTGATGATA
1 TGGTGATGATA
5882920 TAGGTG-TGATA
1 T-GGTGATGATA
5882931 TGGTGATGGACTA
1 TGGTGAT-GA-TA
5882944 TGGTGATGATA
1 TGGTGATGATA
5882955 T
1 T
5882956 AGGCGTGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.12
11 11 0.34
12 8 0.25
13 9 0.28
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (11 bp):
TGGTGATGATA
Found at i:5882937 original size:22 final size:24
Alignment explanation
Indices: 5882909--5882955 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
5882899 TTTGAGAATT
5882909 TGGTGAT-GA-TATAGGTG-TGATA
1 TGGTGATGGACTAT-GGTGATGATA
5882931 TGGTGATGGACTATGGTGATGATA
1 TGGTGATGGACTATGGTGATGATA
5882955 T
1 T
5882956 AGGCGTGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
23 6 0.27
24 9 0.41
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (24 bp):
TGGTGATGGACTATGGTGATGATA
Found at i:5882985 original size:37 final size:35
Alignment explanation
Indices: 5882909--5882988 Score: 97
Period size: 35 Copynumber: 2.2 Consensus size: 35
5882899 TTTGAGAATT
* * **
5882909 TGGTGATGATATAGGTGTGATATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGAAATGAAGATGGACTA
*
5882944 TGGTGATGATATAGGCGTGACAATTGAAGATGGATTA
1 TGGTGATGATATAGGCGTGA-AA-TGAAGATGGACTA
5882981 TGGTGATG
1 TGGTGATG
5882989 GAAATAGTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
35 19 0.50
36 1 0.03
37 18 0.47
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.33
Consensus pattern (35 bp):
TGGTGATGATATAGGCGTGAAATGAAGATGGACTA
Found at i:5890100 original size:30 final size:30
Alignment explanation
Indices: 5890064--5890120 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
5890054 GTGCTGGCAC
5890064 GCACATGGGTGCTGTTTTGTTCCAAATCAT
1 GCACATGGGTGCTGTTTTGTTCCAAATCAT
*
5890094 GCACATGGGTGTTGTTTTGTTCCAAAT
1 GCACATGGGTGCTGTTTTGTTCCAAAT
5890121 GGTGAGTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (30 bp):
GCACATGGGTGCTGTTTTGTTCCAAATCAT
Found at i:5895857 original size:25 final size:25
Alignment explanation
Indices: 5895800--5895862 Score: 101
Period size: 24 Copynumber: 2.6 Consensus size: 25
5895790 CCAGAACTTT
*
5895800 TTCTTTTTTTTTTTAATTTTCGGAA
1 TTCTCTTTTTTTTTAATTTTCGGAA
*
5895825 TT-TGTTTTTTTTTAATTTTCGGAA
1 TTCTCTTTTTTTTTAATTTTCGGAA
5895849 TTCTCTTTTTTTTT
1 TTCTCTTTTTTTTT
5895863 TCAAGATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 23 0.66
25 12 0.34
ACGTcount: A:0.13, C:0.08, G:0.08, T:0.71
Consensus pattern (25 bp):
TTCTCTTTTTTTTTAATTTTCGGAA
Found at i:5897567 original size:24 final size:25
Alignment explanation
Indices: 5897535--5897582 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
5897525 GCCTATTTTG
* *
5897535 GATGAAGAACCTGAA-ACAATGCAA
1 GATGAAGAAACTGAAGAAAATGCAA
5897559 GATGAAGAAACTGAAGAAAATGCA
1 GATGAAGAAACTGAAGAAAATGCA
5897583 GATCATGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.52, C:0.12, G:0.23, T:0.12
Consensus pattern (25 bp):
GATGAAGAAACTGAAGAAAATGCAA
Found at i:5898471 original size:19 final size:19
Alignment explanation
Indices: 5898440--5898481 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
5898430 AGGGGATAAT
5898440 AATATAAGTAATGAAATGA
1 AATATAAGTAATGAAATGA
5898459 AATATTAAG-AATGAAATGA
1 AATA-TAAGTAATGAAATGA
5898478 AATA
1 AATA
5898482 AAGAAAGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (19 bp):
AATATAAGTAATGAAATGA
Found at i:5898936 original size:19 final size:20
Alignment explanation
Indices: 5898894--5898945 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
5898884 AAAACCCCTT
*
5898894 TGAAAATACATGATTTTTTGA
1 TGAAAATACATGA-TTTTTAA
5898915 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
5898934 TGAAGATACATG
1 TGAAAATACATG
5898946 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 16 0.55
21 13 0.45
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:5899879 original size:30 final size:31
Alignment explanation
Indices: 5899840--5899899 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
5899830 ACATGCTGCC
**
5899840 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
5899871 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
5899900 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:5907988 original size:7 final size:7
Alignment explanation
Indices: 5907978--5908010 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
5907968 TTTTTAATTT
5907978 TTTTTCC
1 TTTTTCC
5907985 TTTTTCC
1 TTTTTCC
5907992 TTTTTCC
1 TTTTTCC
5907999 TTTTTCC
1 TTTTTCC
5908006 TTTTT
1 TTTTT
5908011 TCTTGCTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCC
Found at i:5911294 original size:6 final size:6
Alignment explanation
Indices: 5911253--5911296 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
5911243 AAAAGCAACA
*
5911253 AAAAGAG AAAAAG AAAGAAG AAAAAC AAAAAG -AAAAG AAAAAG A
1 AAAA-AG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
5911297 CTCCTACATC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:5920595 original size:15 final size:17
Alignment explanation
Indices: 5920559--5920592 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
5920549 TTTGATAACA
5920559 TTTC-TATCTATTTCCT
1 TTTCTTATCTATTTCCT
5920575 TTTCTTATC-ATTTCCT
1 TTTCTTATCTATTTCCT
5920591 TT
1 TT
5920593 CTTCTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTCTTATCTATTTCCT
Found at i:5925638 original size:30 final size:27
Alignment explanation
Indices: 5925604--5925658 Score: 74
Period size: 30 Copynumber: 1.9 Consensus size: 27
5925594 GAATTGTTGA
5925604 TGAGTGCTTCCAAATTTTCTTTCTTTTTTT
1 TGAGTGCTTCC-AA-TTTC-TTCTTTTTTT
*
5925634 TGAGTGCTTTCAATTTCTTCTTTTT
1 TGAGTGCTTCCAATTTCTTCTTTTT
5925659 GAGTGCTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 8 0.33
28 4 0.17
29 2 0.08
30 10 0.42
ACGTcount: A:0.13, C:0.16, G:0.11, T:0.60
Consensus pattern (27 bp):
TGAGTGCTTCCAATTTCTTCTTTTTTT
Found at i:5934501 original size:23 final size:25
Alignment explanation
Indices: 5934474--5934525 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
5934464 TATCCATCCT
*
5934474 TTATTTA-TTTCATTTCAT-TATTA
1 TTATTTATTTTCATTACATATATTA
*
5934497 TTATTTATTTTCATTACTTATATTA
1 TTATTTATTTTCATTACATATATTA
5934522 TTAT
1 TTAT
5934526 CCCCTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.28
24 9 0.36
25 9 0.36
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (25 bp):
TTATTTATTTTCATTACATATATTA
Found at i:5934811 original size:13 final size:12
Alignment explanation
Indices: 5934775--5934822 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 12
5934765 ATTGGAGTGC
5934775 AAAAAGAAGAGA
1 AAAAAGAAGAGA
5934787 AAAATCAGAAGAGA
1 AAAA--AGAAGAGA
*
5934801 AGAAAAGAAGAAA
1 A-AAAAGAAGAGA
5934814 ATAAAAGAA
1 A-AAAAGAA
5934823 AAAGAGAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 4 0.13
13 15 0.48
14 9 0.29
15 3 0.10
ACGTcount: A:0.73, C:0.02, G:0.21, T:0.04
Consensus pattern (12 bp):
AAAAAGAAGAGA
Found at i:5938343 original size:23 final size:25
Alignment explanation
Indices: 5938316--5938367 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
5938306 TCTCTATCCT
*
5938316 TTATTTA-TTTCATTTCAT-TATTA
1 TTATTTATTTTCATTACATATATTA
*
5938339 TTATTTATTTTCATTACTTATATTA
1 TTATTTATTTTCATTACATATATTA
5938364 TTAT
1 TTAT
5938368 CCACTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.28
24 9 0.36
25 9 0.36
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (25 bp):
TTATTTATTTTCATTACATATATTA
Found at i:5943956 original size:21 final size:22
Alignment explanation
Indices: 5943918--5943960 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
5943908 CCATCTCTAT
5943918 CTTTTCTTTATTTCATTTCATTC
1 CTTTTCTTTA-TTCATTTCATTC
5943941 CTTTTCTTTA-TCATTTCATT
1 CTTTTCTTTATTCATTTCATT
5943961 AATCTTCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 10 0.50
23 10 0.50
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.65
Consensus pattern (22 bp):
CTTTTCTTTATTCATTTCATTC
Found at i:5946922 original size:24 final size:24
Alignment explanation
Indices: 5946873--5946922 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
5946863 GTACAGAAGT
* *
5946873 GCCTTACATCAAGTGGCATCAGAA
1 GCCTTACATCAAGCGGAATCAGAA
*
5946897 GCCTTGCATCAAGCGGTAATCA-AA
1 GCCTTACATCAAGCGG-AATCAGAA
5946921 GC
1 GC
5946923 TTTGGTGGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (24 bp):
GCCTTACATCAAGCGGAATCAGAA
Done.