Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009617.1 Hibiscus syriacus cultivar Beakdansim tig00117005_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: 3386631
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 16
Found at i:1664981 original size:14 final size:14
Alignment explanation
Indices: 1664962--1664988 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1664952 GTAATTTATT
1664962 ATTTTTTGTTGTTC
1 ATTTTTTGTTGTTC
1664976 ATTTTTTGTTGTT
1 ATTTTTTGTTGTT
1664989 TTGTATGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.04, G:0.15, T:0.74
Consensus pattern (14 bp):
ATTTTTTGTTGTTC
Found at i:1666625 original size:22 final size:23
Alignment explanation
Indices: 1666594--1666637 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1666584 CCATGGAACA
*
1666594 CTTGTTTGATTT-GTAATAATGC
1 CTTGTATGATTTAGTAATAATGC
1666616 CTTGTATGATTTAGTAATAATG
1 CTTGTATGATTTAGTAATAATG
1666638 AAATTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.48
Consensus pattern (23 bp):
CTTGTATGATTTAGTAATAATGC
Found at i:1666669 original size:18 final size:18
Alignment explanation
Indices: 1666621--1666699 Score: 54
Period size: 18 Copynumber: 4.4 Consensus size: 18
1666611 AATGCCTTGT
**
1666621 ATGATTTAGTAATAATGAA
1 ATGATTTAGTAAT-ATTTA
* *
1666640 ATTA-TTATTAATATTTA
1 ATGATTTAGTAATATTTA
* *
1666657 ATGATTTAGTAATAATGA
1 ATGATTTAGTAATATTTA
* *
1666675 TATTA-TTATTAATATTTA
1 -ATGATTTAGTAATATTTA
1666693 ATGATTT
1 ATGATTT
1666700 GATAGTAATG
Statistics
Matches: 44, Mismatches: 13, Indels: 7
0.69 0.20 0.11
Matches are distributed among these distances:
17 9 0.20
18 29 0.66
19 6 0.14
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (18 bp):
ATGATTTAGTAATATTTA
Found at i:1666695 original size:22 final size:22
Alignment explanation
Indices: 1666669--1666730 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 22
1666659 GATTTAGTAA
*
1666669 TAATGATATTATTATTAATATT
1 TAATGATATTATTACTAATATT
*
1666691 TAATGAT-TTGA-TAGTAATGATT
1 TAATGATATT-ATTACTAAT-ATT
1666713 TAAT-A-ATTATTACTAATA
1 TAATGATATTATTACTAATA
1666731 ATTATGGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
20 2 0.06
21 17 0.50
22 15 0.44
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (22 bp):
TAATGATATTATTACTAATATT
Found at i:1666711 original size:36 final size:36
Alignment explanation
Indices: 1666621--1666699 Score: 149
Period size: 36 Copynumber: 2.2 Consensus size: 36
1666611 AATGCCTTGT
*
1666621 ATGATTTAGTAATAATGAAATTATTATTAATATTTA
1 ATGATTTAGTAATAATGATATTATTATTAATATTTA
1666657 ATGATTTAGTAATAATGATATTATTATTAATATTTA
1 ATGATTTAGTAATAATGATATTATTATTAATATTTA
1666693 ATGATTT
1 ATGATTT
1666700 GATAGTAATG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (36 bp):
ATGATTTAGTAATAATGATATTATTATTAATATTTA
Found at i:1666931 original size:38 final size:36
Alignment explanation
Indices: 1666821--1666940 Score: 120
Period size: 38 Copynumber: 3.3 Consensus size: 36
1666811 TTTAAATATT
*
1666821 TAATGATTTAATACTAATGATTAGTAATT-ATTATTAA
1 TAATGATTTAATACT-ATTATTAGTAATTAATTA-TAA
* * *
1666858 TAATGATTTATTACTAATATT--TAATTATTTGATAA
1 TAATGATTTAATACTATTATTAGTAATTAATT-ATAA
* *
1666893 TAATGATTTACTAATGATTATTAGTAATTAAATTATAA
1 TAATGATTTAATACT-ATTATTAGTAATT-AATTATAA
1666931 TAATGATTTA
1 TAATGATTTA
1666941 GAAATAATCA
Statistics
Matches: 69, Mismatches: 8, Indels: 11
0.78 0.09 0.12
Matches are distributed among these distances:
34 5 0.07
35 18 0.26
36 10 0.14
37 14 0.20
38 19 0.28
39 3 0.04
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (36 bp):
TAATGATTTAATACTATTATTAGTAATTAATTATAA
Found at i:1666957 original size:26 final size:26
Alignment explanation
Indices: 1666845--1667194 Score: 237
Period size: 26 Copynumber: 14.2 Consensus size: 26
1666835 TAATGATTAG
* * *
1666845 TAATTATTATTAATAATGATTTATTAC
1 TAATCATTA-TAATAATGATTTAATAA
*
1666872 TAAT-ATT-TAAT--T-ATTTGATAA
1 TAATCATTATAATAATGATTTAATAA
* * *
1666893 TAATGATT-TACTAATGATTATTAGTAA
1 TAATCATTATAATAATGA-T-TTAATAA
1666920 TTAA--ATTATAATAATGATTTAGA-AA
1 -TAATCATTATAATAATGATTTA-ATAA
1666945 TAATCATTATAATAATGATTTAATAA
1 TAATCATTATAATAATGATTTAATAA
*
1666971 T-A--ATT-T--TAAT-ATTTAATGATT
1 TAATCATTATAATAATGATTTAAT-A-A
* * * *
1666992 TGATGATT-TAGTAATGATTTGATAA
1 TAATCATTATAATAATGATTTAATAA
*
1667017 TAATCATTATAATAATGATTTAGTAA
1 TAATCATTATAATAATGATTTAATAA
*
1667043 TAATCATTATAATAATTATTTAATAA
1 TAATCATTATAATAATGATTTAATAA
*
1667069 T-A--ATGATAATAATGATTTAATAA
1 TAATCATTATAATAATGATTTAATAA
* * *
1667092 TAATTATTATAATAATAATTTAATAC
1 TAATCATTATAATAATGATTTAATAA
*
1667118 TAATGATT-TAATAATGATTTAA-AA
1 TAATCATTATAATAATGATTTAATAA
* * *
1667142 TGAT-TTTATAATAATGATTTAATAC
1 TAATCATTATAATAATGATTTAATAA
* * *
1667167 TAATGATT-TAATAATTA-TTACTAA
1 TAATCATTATAATAATGATTTAATAA
1667191 TAAT
1 TAAT
1667195 TATGGAATAA
Statistics
Matches: 262, Mismatches: 34, Indels: 57
0.74 0.10 0.16
Matches are distributed among these distances:
19 7 0.03
20 5 0.02
21 11 0.04
22 9 0.03
23 25 0.10
24 40 0.15
25 40 0.15
26 99 0.38
27 23 0.09
28 3 0.01
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (26 bp):
TAATCATTATAATAATGATTTAATAA
Found at i:1667077 original size:20 final size:22
Alignment explanation
Indices: 1667040--1667173 Score: 72
Period size: 23 Copynumber: 5.6 Consensus size: 22
1667030 AATGATTTAG
* * *
1667040 TAATAATCATTATAATAATTATT
1 TAATAATAATGATAAT-ATGATT
1667063 TAATAATAATGATAATAATGATT
1 TAATAATAATGATAAT-ATGATT
* *
1667086 TAATAATAATTATTATAATAATAATT
1 TAATAAT-A--ATGATAAT-ATGATT
*
1667112 TAATACTAATGATTTAATAATGATT
1 TAATAATAATGA--TAAT-ATGATT
* *
1667137 TAA-AATGATTTTATAATAATGATT
1 TAATAAT-A-ATGATAAT-ATGATT
*
1667161 TAATACTAATGAT
1 TAATAATAATGAT
1667174 TTAATAATTA
Statistics
Matches: 89, Mismatches: 14, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
23 33 0.37
24 18 0.20
25 17 0.19
26 21 0.24
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
TAATAATAATGATAATATGATT
Found at i:1667145 original size:10 final size:11
Alignment explanation
Indices: 1666890--1667181 Score: 115
Period size: 12 Copynumber: 23.6 Consensus size: 11
1666880 AATTATTTGA
1666890 TAATAATGATT
1 TAATAATGATT
*
1666901 TACTAATGATTAT
1 TAATAATGA-T-T
* *
1666914 TAGTAATTAAATT
1 TAATAA-T-GATT
1666927 ATAATAATGATT
1 -TAATAATGATT
*
1666939 TAGAAATAATCATT
1 T---AATAATGATT
1666953 ATAATAATGATT
1 -TAATAATGATT
*
1666965 TAATAATAATT
1 TAATAATGATT
1666976 T--TAAT-ATT
1 TAATAATGATT
1666984 TAATGATTTGATGATT
1 TAAT-A----ATGATT
*
1667000 TAGTAATGATTT
1 TAATAATGA-TT
*
1667012 GATAATAATCATT
1 --TAATAATGATT
1667025 ATAATAATGATTT
1 -TAATAATGA-TT
*
1667038 AGTAATAATCATT
1 --TAATAATGATT
*
1667051 ATAATAATTATT
1 -TAATAATGATT
* *
1667063 TAATAATAATGA
1 TAATAATGAT-T
1667075 TAATAATGATTT
1 TAATAATGA-TT
*
1667087 AATAATAATTATT
1 --TAATAATGATT
*
1667100 ATAATAATAATT
1 -TAATAATGATT
1667112 TAATACTAATGATT
1 T-A-A-TAATGATT
1667126 TAATAATGATT
1 TAATAATGATT
1667137 TAA-AATGATTTT
1 TAATAATGA--TT
1667149 ATAATAATGATT
1 -TAATAATGATT
1667161 TAATACTAATGATT
1 T-A-A-TAATGATT
1667175 TAATAAT
1 TAATAAT
1667182 TATTACTAAT
Statistics
Matches: 222, Mismatches: 23, Indels: 72
0.70 0.07 0.23
Matches are distributed among these distances:
8 4 0.02
9 4 0.02
10 6 0.03
11 51 0.23
12 61 0.27
13 24 0.11
14 61 0.27
15 5 0.02
16 6 0.03
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (11 bp):
TAATAATGATT
Found at i:1667205 original size:49 final size:50
Alignment explanation
Indices: 1666845--1667197 Score: 277
Period size: 49 Copynumber: 7.1 Consensus size: 50
1666835 TAATGATTAG
* *
1666845 TAATTATTATTAATAATGATTTATTACTAAT-ATTTAAT--T-ATTTGATAA
1 TAATTATTA-TAATAATGATTTAATAATAATGATTTAATAATGATTT-ATAA
* * * *
1666893 TAATGATT-TACTAATGATTATTAGTAATTAA--ATTATAATAATGATTTAGAAA
1 TAATTATTATAATAATGA-T-TTAATAA-TAATGATT-TAATAATGATTTA-TAA
* * * * * *
1666945 TAATCATTATAATAATGATTTAATAATAAT--TTTAATATTTAATGAT-T
1 TAATTATTATAATAATGATTTAATAATAATGATTTAATAATGATTTATAA
* * * * *
1666992 TGATGATT-TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
1 TAATTATTATAATAATGATTTAATAATAATGATT-TAATAATGATTTA-TAA
* *
1667043 TAATCATTATAATAATTATTTAATAATAATGA--TAATAATGATTTAATAA
1 TAATTATTATAATAATGATTTAATAATAATGATTTAATAATGATTT-ATAA
* * *
1667092 TAATTATTATAATAATAATTTAATACTAATGATTTAATAATGATTTAAAA
1 TAATTATTATAATAATGATTTAATAATAATGATTTAATAATGATTTATAA
* * *
1667142 TGATT-TTATAATAATGATTTAATACTAATGATTTAATAATTA-TTACTAA
1 TAATTATTATAATAATGATTTAATAATAATGATTTAATAATGATTTA-TAA
1667191 TAATTAT
1 TAATTAT
1667198 GGAATAATAA
Statistics
Matches: 246, Mismatches: 38, Indels: 40
0.76 0.12 0.12
Matches are distributed among these distances:
46 27 0.11
47 7 0.03
48 20 0.08
49 110 0.45
50 15 0.06
51 26 0.11
52 33 0.13
53 8 0.03
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (50 bp):
TAATTATTATAATAATGATTTAATAATAATGATTTAATAATGATTTATAA
Found at i:1669372 original size:30 final size:29
Alignment explanation
Indices: 1669338--1669424 Score: 98
Period size: 30 Copynumber: 3.2 Consensus size: 29
1669328 TTCCTTAAAC
1669338 AACTATTAAACTATTCTTTAATATAACTTT
1 AACTA-TAAACTATTCTTTAATATAACTTT
1669368 AAC--T--A-T-TT-TTTAATATAACTTT
1 AACTATAAACTATTCTTTAATATAACTTT
*
1669390 AACTAATAAACTATTCTTTAATATAACTTA
1 AACT-ATAAACTATTCTTTAATATAACTTT
1669420 AACTA
1 AACTA
1669425 AAAAATAATT
Statistics
Matches: 48, Mismatches: 1, Indels: 17
0.73 0.02 0.26
Matches are distributed among these distances:
22 17 0.35
23 2 0.04
24 1 0.02
25 2 0.04
27 2 0.04
28 1 0.02
29 3 0.06
30 20 0.42
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.45
Consensus pattern (29 bp):
AACTATAAACTATTCTTTAATATAACTTT
Found at i:1669374 original size:22 final size:22
Alignment explanation
Indices: 1669346--1669394 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1669336 ACAACTATTA
1669346 AACTATTCTTTAATATAACTTT
1 AACTATTCTTTAATATAACTTT
*
1669368 AACTATTTTTTAATATAACTTT
1 AACTATTCTTTAATATAACTTT
1669390 AACTA
1 AACTA
1669395 ATAAACTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (22 bp):
AACTATTCTTTAATATAACTTT
Found at i:1669699 original size:18 final size:18
Alignment explanation
Indices: 1669678--1669730 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 18
1669668 TTGTTTTACC
1669678 CTAATTTATAATAATAAA
1 CTAATTTATAATAATAAA
*
1669696 CTAATAATTTATAACAATAAA
1 C---TAATTTATAATAATAAA
1669717 CTAATTTA-AATAAT
1 CTAATTTATAATAAT
1669731 TATTCTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
17 5 0.17
18 8 0.27
21 17 0.57
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAATTTATAATAATAAA
Found at i:1669704 original size:21 final size:21
Alignment explanation
Indices: 1669679--1669721 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1669669 TGTTTTACCC
*
1669679 TAATTTATAATAATAAACTAA
1 TAATTTATAACAATAAACTAA
1669700 TAATTTATAACAATAAACTAA
1 TAATTTATAACAATAAACTAA
1669721 T
1 T
1669722 TTAAATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (21 bp):
TAATTTATAACAATAAACTAA
Found at i:1669883 original size:27 final size:29
Alignment explanation
Indices: 1669848--1669912 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
1669838 AAAATATAAC
*
1669848 TTAAGTATTTA-ACTAACT-ACAAACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
1669875 TTAAATA-TTAGACTAACTAACACACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
1669903 TTAATTATTT
1 TTAAATATTT
1669913 TTTTAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.09
27 13 0.41
28 14 0.44
29 2 0.06
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (29 bp):
TTAAATATTTAGACTAACTAACAAACTAA
Found at i:1670446 original size:29 final size:29
Alignment explanation
Indices: 1670413--1670469 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
1670403 CAAAGCATGC
*
1670413 ATGTCGTTGGGATGCCCTGGCGACCTACA
1 ATGTCGCTGGGATGCCCTGGCGACCTACA
1670442 ATGTCGCTGGGATGCCCTGGCGACCTAC
1 ATGTCGCTGGGATGCCCTGGCGACCTAC
1670470 CCAGAACCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.16, C:0.30, G:0.32, T:0.23
Consensus pattern (29 bp):
ATGTCGCTGGGATGCCCTGGCGACCTACA
Found at i:1672185 original size:4 final size:4
Alignment explanation
Indices: 1672176--1672201 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1672166 GTTCCCGTGT
1672176 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
1672202 TATCATGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:1676285 original size:35 final size:35
Alignment explanation
Indices: 1676246--1676352 Score: 84
Period size: 35 Copynumber: 3.2 Consensus size: 35
1676236 ATGTAACAAA
1676246 TGGAGCTATTCAAACAAGTAGTACTTCACATCTGG
1 TGGAGCTATTCAAACAAGTAGTACTTCACATCTGG
* * * ***
1676281 TGGAGCATACTCCAAAACAGGT-G-A----A-AACAAA
1 TGGAGC-TA-TTC-AAACAAGTAGTACTTCACATCTGG
1676312 TGGAGCTATTCAAACAAGTAGTACTTCACATCTGG
1 TGGAGCTATTCAAACAAGTAGTACTTCACATCTGG
1676347 TGGAGC
1 TGGAGC
1676353 ATACTCCAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 20
0.61 0.15 0.24
Matches are distributed among these distances:
28 7 0.14
29 3 0.06
30 3 0.06
31 8 0.16
32 1 0.02
34 1 0.02
35 14 0.28
36 3 0.06
37 3 0.06
38 7 0.14
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (35 bp):
TGGAGCTATTCAAACAAGTAGTACTTCACATCTGG
Found at i:1676346 original size:66 final size:66
Alignment explanation
Indices: 1676240--1676371 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
1676230 TAAAGAATGT
1676240 AACAAATGGAGCTATTCAAACAAGTAGTACTTCACATCTGGTGGAGCATACTCCAAAACAGGTGA
1 AACAAATGGAGCTATTCAAACAAGTAGTACTTCACATCTGGTGGAGCATACTCCAAAACAGGTGA
1676305 A
66 A
1676306 AACAAATGGAGCTATTCAAACAAGTAGTACTTCACATCTGGTGGAGCATACTCCAAAACAGGTGA
1 AACAAATGGAGCTATTCAAACAAGTAGTACTTCACATCTGGTGGAGCATACTCCAAAACAGGTGA
1676371 A
66 A
1676372 GTTTCAGTAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (66 bp):
AACAAATGGAGCTATTCAAACAAGTAGTACTTCACATCTGGTGGAGCATACTCCAAAACAGGTGA
A
Found at i:1681104 original size:28 final size:28
Alignment explanation
Indices: 1681064--1681117 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
1681054 AAACTACGTT
1681064 CATGTGGGAAATAACCTGGTTTCCTCAA
1 CATGTGGGAAATAACCTGGTTTCCTCAA
1681092 CATGTGGGAAATAACCTGGTTTCCTC
1 CATGTGGGAAATAACCTGGTTTCCTC
1681118 TCTGAAATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (28 bp):
CATGTGGGAAATAACCTGGTTTCCTCAA
Found at i:1683901 original size:13 final size:13
Alignment explanation
Indices: 1683883--1683915 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1683873 AAACAAAAGA
*
1683883 AAAATAAATAAAT
1 AAAATAAACAAAT
1683896 AAAATAAACAAAT
1 AAAATAAACAAAT
1683909 -AAATAAA
1 AAAATAAA
1683916 AAAAGTAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAATAAACAAAT
Found at i:1690096 original size:144 final size:145
Alignment explanation
Indices: 1689836--1690126 Score: 525
Period size: 144 Copynumber: 2.0 Consensus size: 145
1689826 AAGGTCCCAT
1689836 GGATGGAACGTTAACAACACCTTTTATTATTTATGCACAATAATTACTTCTAAAAATATATTAAA
1 GGATGGAACGTTAACAACACCTTTTATTATTTATGCACAATAATTACTTCTAAAAATATATTAAA
1689901 AAATATGTCAAAAGAATTAAAAAATAGGAAGAGTTCGTTGAGATATATACGTAC-ATACATC-TG
66 AAATATGTCAAAAGAATTAAAAAATAGGAAGAGTTCGTTGAGATATATACGTACAATACATCAT-
1689964 TGGGAGAAGAGAAGAA
130 TGGGAGAAGAGAAGAA
1689980 GGATGGAACGTTAACAACACCTTTTATTATTTATGCACAATAATTACTTCTAAAAATATATTAAA
1 GGATGGAACGTTAACAACACCTTTTATTATTTATGCACAATAATTACTTCTAAAAATATATTAAA
*
1690045 AAATATGTCAAAAGAATTAACAAA-AGGAAGAGTTCGTTTGAGATATATACGTACATATACATCA
66 AAATATGTCAAAAGAATTAAAAAATAGGAAGAGTTCG-TTGAGATATATACGTACA-ATACATCA
1690109 TTGGGAGAAGAGAAGAA
129 TTGGGAGAAGAGAAGAA
1690126 G
1 G
1690127 AAAGAAGAAT
Statistics
Matches: 142, Mismatches: 1, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
143 12 0.08
144 105 0.74
146 24 0.17
147 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (145 bp):
GGATGGAACGTTAACAACACCTTTTATTATTTATGCACAATAATTACTTCTAAAAATATATTAAA
AAATATGTCAAAAGAATTAAAAAATAGGAAGAGTTCGTTGAGATATATACGTACAATACATCATT
GGGAGAAGAGAAGAA
Found at i:1691421 original size:202 final size:200
Alignment explanation
Indices: 1691040--1691441 Score: 786
Period size: 202 Copynumber: 2.0 Consensus size: 200
1691030 GAACATATTC
1691040 ACCAACAATTTATGTTCGACAATCAAAGGAGTCACTTCACAGTGACACTCAAAATAAATTCAATA
1 ACCAACAATTTATGTTCGACAATCAAAGGAGTCACTTCACAGTGACACTCAAAATAAATTCAATA
1691105 TAGACATGTTTATAAACATGCTATATCTCAATTATTACAATTATGATCAATGTATTTTATCTACA
66 TAGACATGTTTATAAACATGCTATATCTCAATTATTACAATTATGATCAATGTATTTTATCTACA
1691170 TCAATCTACTAATGCAGATCACCTTTTTTGGGACATAGTGTAGAGTTCGATAACATCACATCAAG
131 TCAATCTACTAATGCAGATCACCTTTTTTGGGACATAGTGTAGAGTTCGATAACATCACATCAAG
1691235 AACTA
196 AACTA
1691240 ACCAACAATTTATGTTCGACAATCAAAGGAGTCACTTCACAGTGACACTCAAAATAAATTCAATA
1 ACCAACAATTTATGTTCGACAATCAAAGGAGTCACTTCACAGTGACACTCAAAATAAATTCAATA
1691305 TAGAACATGTTTATAAACATGCTATATCTCAATTATTACAATTATGACTCAATGTATTTTATCTA
66 TAG-ACATGTTTATAAACATGCTATATCTCAATTATTACAATTATGA-TCAATGTATTTTATCTA
1691370 CATCAATCTACTAATGCAGATCACCTTTTTTGGGACATAGTGTAGAGTTCGATAACATCACATCA
129 CATCAATCTACTAATGCAGATCACCTTTTTTGGGACATAGTGTAGAGTTCGATAACATCACATCA
1691435 AGAACTA
194 AGAACTA
1691442 CGAGGTTGCA
Statistics
Matches: 200, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
200 68 0.34
201 43 0.22
202 89 0.44
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (200 bp):
ACCAACAATTTATGTTCGACAATCAAAGGAGTCACTTCACAGTGACACTCAAAATAAATTCAATA
TAGACATGTTTATAAACATGCTATATCTCAATTATTACAATTATGATCAATGTATTTTATCTACA
TCAATCTACTAATGCAGATCACCTTTTTTGGGACATAGTGTAGAGTTCGATAACATCACATCAAG
AACTA
Found at i:1695704 original size:30 final size:30
Alignment explanation
Indices: 1695670--1695730 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
1695660 TTCCATAATT
1695670 TTTAAATAATTTTAATATCAGGGTAAAGTA
1 TTTAAATAATTTTAATATCAGGGTAAAGTA
1695700 TTTAAATAATTTTAATATCAGGGTAAAGTA
1 TTTAAATAATTTTAATATCAGGGTAAAGTA
1695730 T
1 T
1695731 ACCTATAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.43, C:0.03, G:0.13, T:0.41
Consensus pattern (30 bp):
TTTAAATAATTTTAATATCAGGGTAAAGTA
Found at i:1697325 original size:17 final size:17
Alignment explanation
Indices: 1697272--1697336 Score: 53
Period size: 21 Copynumber: 3.6 Consensus size: 17
1697262 TAAAAAATTA
*
1697272 AAATATAAT-TAA-AAT
1 AAATTTAATATAATAAT
*
1697287 AATATTTAATGTAATAAT
1 AA-ATTTAATATAATAAT
1697305 AAATTTAATATGAATAAAAAT
1 AAATTTAATAT-AAT---AAT
1697326 AAATTTAATAT
1 AAATTTAATAT
1697337 TTTTAAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
15 2 0.05
16 6 0.15
17 11 0.27
18 8 0.20
21 14 0.34
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
AAATTTAATATAATAAT
Found at i:1697824 original size:13 final size:14
Alignment explanation
Indices: 1697806--1697834 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1697796 ACCTAATTGG
1697806 AAATAATT-AAATT
1 AAATAATTAAAATT
1697819 AAATAATTAAAATT
1 AAATAATTAAAATT
1697833 AA
1 AA
1697835 TAACATATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AAATAATTAAAATT
Found at i:1700678 original size:14 final size:14
Alignment explanation
Indices: 1700659--1700685 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1700649 CTCAAGCTGG
1700659 GAGTATCGGTACTT
1 GAGTATCGGTACTT
1700673 GAGTATCGGTACT
1 GAGTATCGGTACT
1700686 GCTCTAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (14 bp):
GAGTATCGGTACTT
Found at i:1702237 original size:20 final size:20
Alignment explanation
Indices: 1702194--1702230 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1702184 TCTAAATCCT
*
1702194 TTTTCAAAATTTCATTTTGA
1 TTTTCAAAATTCCATTTTGA
1702214 TTTTCAAAA-TCCATTTT
1 TTTTCAAAATTCCATTTT
1702231 AGCTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.30, C:0.14, G:0.03, T:0.54
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTGA
Found at i:1715224 original size:15 final size:15
Alignment explanation
Indices: 1715206--1715250 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
1715196 GTAACCGGTT
1715206 TCGGTTTTAAAAAAA
1 TCGGTTTTAAAAAAA
**
1715221 TCGGTTTTTTTAAAAA
1 TCGG-TTTTAAAAAAA
*
1715237 TCGGTTATAAAAAA
1 TCGGTTTTAAAAAA
1715251 CCGATTTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (15 bp):
TCGGTTTTAAAAAAA
Found at i:1715435 original size:13 final size:13
Alignment explanation
Indices: 1715414--1715468 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1715404 AAGTTCGATA
*
1715414 AATTCAAATACTT
1 AATTGAAATACTT
1715427 AATTGAAATACTT
1 AATTGAAATACTT
* *
1715440 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
1715454 AATTGAAATACTT
1 AATTGAAATACTT
1715467 AA
1 AA
1715469 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:1715534 original size:32 final size:33
Alignment explanation
Indices: 1715454--1715551 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
1715444 AACTCAACAT
* * *
1715454 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1715487 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1715520 AATTC-AATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1715551 A
1 A
1715552 TTGAACAAAG
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
31 12 0.19
32 15 0.24
33 35 0.56
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:1721945 original size:63 final size:63
Alignment explanation
Indices: 1721869--1721994 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
1721859 TTCTTGTAGG
1721869 GTGCACTTAGATCCTTCAGGCTTCTGTGCAAGTGACGTGCAATTAAACATGATTATGTACTCC
1 GTGCACTTAGATCCTTCAGGCTTCTGTGCAAGTGACGTGCAATTAAACATGATTATGTACTCC
*
1721932 GTGCACTTAGATCCTTCAGGCTTCTGTGCAAGTGACGTGCAATTAAATATGATTATGTACTCC
1 GTGCACTTAGATCCTTCAGGCTTCTGTGCAAGTGACGTGCAATTAAACATGATTATGTACTCC
1721995 CTTGCGAGTC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (63 bp):
GTGCACTTAGATCCTTCAGGCTTCTGTGCAAGTGACGTGCAATTAAACATGATTATGTACTCC
Found at i:1722065 original size:70 final size:70
Alignment explanation
Indices: 1721972--1722507 Score: 357
Period size: 70 Copynumber: 7.8 Consensus size: 70
1721962 AGTGACGTGC
* * * * *
1721972 AATTAAATATGATTATGTACTCCCTTGCGAGTCACTCTAATCCTTCGGGGTTCCCATACGAGTCA
1 AATTAAATATGATTAGGTGCTCCCTTGCGAGTCACTCTAATCCTTCGGGGCTCCCGTGCGAGTCA
*
1722037 CCCAA
66 CCCGA
* * * * * *
1722042 AATTAAATATGATTAGGTGCTCCCGTGTGAGTCACTCTAATCCTTTGGGACTCTCGTGCGAATCA
1 AATTAAATATGATTAGGTGCTCCCTTGCGAGTCACTCTAATCCTTCGGGGCTCCCGTGCGAGTCA
1722107 CCC-A
66 CCCGA
* * * ** *
1722111 TAATTAAATATGACTAGGTACT-CCTCTGTGAGTCACTCTAATCCTTCAAGGCTCTCGTGCGAGT
1 -AATTAAATATGATTAGGTGCTCCCT-TGCGAGTCACTCTAATCCTTCGGGGCTCCCGTGCGAGT
*
1722175 AACCCGA
64 CACCCGA
* * * ** * * *
1722182 AATTAAATATGATTA-GTGCTCCGTAT--GAGTCACTCTAATCATTTGGAACTCCTGTACGAGTT
1 AATTAAATATGATTAGGTGCTCCCT-TGCGAGTCACTCTAATCCTTCGGGGCTCCCGTGCGAGTC
* * *
1722244 ATCTGG
65 ACCCGA
* * ** * * *
1722250 AATTAAATATGATTAGGAGCTCTCGTT-CGAGTCACAATAATCCTTCAGGGCTCCCATGCAAGTC
1 AATTAAATATGATTAGGTGCTC-CCTTGCGAGTCACTCTAATCCTTCGGGGCTCCCGTGCGAGTC
* *
1722314 ATCCGG
65 ACCCGA
* * *
1722320 AA-T-AATATGATTAGGTGCTCACGTGCGAGTCACTCTACTCCTTC-GGGCTCCCGTGCGAGTCG
1 AATTAAATATGATTAGGTGCTCCCTTGCGAGTCACTCTAATCCTTCGGGGCTCCCGTGCGAGTC-
* *
1722382 A-CTGT
65 ACCCGA
* * * * * * ** *
1722387 AA-T-AATATGATTATGTGAT-TCTGTGC-AGGTCAATCTAATCTTTTGGAACTCTCGTGCGAGT
1 AATTAAATATGATTAGGTGCTCCCT-TGCGA-GTCACTCTAATCCTTCGGGGCTCCCGTGCGAGT
*
1722448 CACCCGG
64 CACCCGA
* *** * *
1722455 AA-T-AATATGATTAAGTGCTCAGGTGCGAGTCACTCTACTCCTTCAGGGCTCCC
1 AATTAAATATGATTAGGTGCTCCCTTGCGAGTCACTCTAATCCTTCGGGGCTCCC
1722508 AAATTGAGGG
Statistics
Matches: 363, Mismatches: 88, Indels: 32
0.75 0.18 0.07
Matches are distributed among these distances:
66 2 0.01
67 51 0.14
68 130 0.36
69 15 0.04
70 164 0.45
71 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (70 bp):
AATTAAATATGATTAGGTGCTCCCTTGCGAGTCACTCTAATCCTTCGGGGCTCCCGTGCGAGTCA
CCCGA
Found at i:1722291 original size:138 final size:139
Alignment explanation
Indices: 1721972--1722356 Score: 372
Period size: 138 Copynumber: 2.8 Consensus size: 139
1721962 AGTGACGTGC
* * * ** ** * *
1721972 AATTAAATATGATTATGTACTCC-CTTGCGAGTCACTCTAATCCTTCGGGGTTCCCATACGAGTC
1 AATTAAATATGACTAGGTACTCCTC-TGTGAGTCACAATAATCCTTCAAGGCTCCCATGCGAGTC
* * * *
1722036 ACCCAAAATTAAATATGATTAGGTGCTCCCGTGTGAGTCACTCTAATCCTTTGGGACTCTCGTGC
65 ACCCGAAATTAAATATGATTAGGTGCT-CCGTGTGAGTCACTCTAATCATTTGGAACTCTCGTAC
*
1722101 GAATCACCCAT
129 GAATCACCCAG
** * * *
1722112 AATTAAATATGACTAGGTACTCCTCTGTGAGTCACTCTAATCCTTCAAGGCTCTCGTGCGAGTAA
1 AATTAAATATGACTAGGTACTCCTCTGTGAGTCACAATAATCCTTCAAGGCTCCCATGCGAGTCA
*
1722177 CCCGAAATTAAATATGATTA-GTGCTCCGTATGAGTCACTCTAATCATTTGGAACTC-CTGTACG
66 CCCGAAATTAAATATGATTAGGTGCTCCGTGTGAGTCACTCTAATCATTTGGAACTCTC-GTACG
* * * **
1722240 AGTTATCTGG
130 AATCACCCAG
* * *
1722250 AATTAAATATGATTAGG-AGCT-CTC-GTTCGAGTCACAATAATCCTTCAGGGCTCCCATGCAAG
1 AATTAAATATGACTAGGTA-CTCCTCTG-T-GAGTCACAATAATCCTTCAAGGCTCCCATGCGAG
* * *
1722312 TCATCCGGAA-T-AATATGATTAGGTGCTCACGTGCGAGTCACTCTA
63 TCACCCGAAATTAAATATGATTAGGTGCTC-CGTGTGAGTCACTCTA
1722357 CTCCTTCGGG
Statistics
Matches: 205, Mismatches: 33, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
136 11 0.05
137 13 0.06
138 103 0.50
139 5 0.02
140 72 0.35
141 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (139 bp):
AATTAAATATGACTAGGTACTCCTCTGTGAGTCACAATAATCCTTCAAGGCTCCCATGCGAGTCA
CCCGAAATTAAATATGATTAGGTGCTCCGTGTGAGTCACTCTAATCATTTGGAACTCTCGTACGA
ATCACCCAG
Found at i:1727360 original size:22 final size:21
Alignment explanation
Indices: 1727334--1727375 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1727324 AAAAAAGTTA
*
1727334 ATATGACCTTCGAATTATTTAT
1 ATATGA-CATCGAATTATTTAT
*
1727356 ATATGACATCTAATTATTTA
1 ATATGACATCGAATTATTTA
1727376 ATGGTACGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (21 bp):
ATATGACATCGAATTATTTAT
Found at i:1729684 original size:44 final size:43
Alignment explanation
Indices: 1729587--1729684 Score: 115
Period size: 43 Copynumber: 2.3 Consensus size: 43
1729577 TGATAACGAA
*
1729587 AAACGCCGCAATAGGTCACGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTCACGAGATTTAGCGGCGTTTTTCACAC
* *** * * *
1729630 AAACGTCGCAATAGGTGTTGAGATTTAGCGGCTTTTTTTGATAC
1 AAACGCCGCAATAGGTCACGAGATTTAGCGGC-GTTTTTCACAC
1729674 AAACGCCGCAA
1 AAACGCCGCAA
1729685 AATGTCATAT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 28 0.62
44 17 0.38
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (43 bp):
AAACGCCGCAATAGGTCACGAGATTTAGCGGCGTTTTTCACAC
Found at i:1729702 original size:43 final size:43
Alignment explanation
Indices: 1729655--1729811 Score: 215
Period size: 43 Copynumber: 3.7 Consensus size: 43
1729645 TGTTGAGATT
* * * *
1729655 TAGCGGCTTTTTTTGATACAAACGCCGCAAAATGTCATATCTA
1 TAGCGGCGTTTTTGGATACAAACGCCGCAAAAAGTCAGATCTA
* * * *
1729698 TAGCGACGTTTTTGGATACAAACACCGCAAAAGGTTAGATCTA
1 TAGCGGCGTTTTTGGATACAAACGCCGCAAAAAGTCAGATCTA
*
1729741 TAGCGGCGTTTCTGGATACAAACGCCGCAAAAAGTCAGATCTA
1 TAGCGGCGTTTTTGGATACAAACGCCGCAAAAAGTCAGATCTA
* *
1729784 TAGCGGCGTTTTTAGATACAAACTCCGC
1 TAGCGGCGTTTTTGGATACAAACGCCGC
1729812 TAATTACTAT
Statistics
Matches: 99, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 99 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (43 bp):
TAGCGGCGTTTTTGGATACAAACGCCGCAAAAAGTCAGATCTA
Found at i:1729709 original size:86 final size:86
Alignment explanation
Indices: 1729612--1729796 Score: 214
Period size: 86 Copynumber: 2.2 Consensus size: 86
1729602 TCACGAGATT
* ** * * * *
1729612 TAGCGGCGTTTTT-CCCACAAACGTCGCAATAGGTGTTGAGAT-T-TAGCGGCTTTTTTTGATAC
1 TAGCGGCGTTTTTGCACACAAACACCGCAA-AAG-GTT-AGATCTATAGCGGCGTTTCTGGATAC
* *
1729674 AAACGCCGCAAAATGTCATATCTA
63 AAACGCCGCAAAAAGTCAGATCTA
* * *
1729698 TAGCGACGTTTTTGGATACAAACACCGCAAAAGGTTAGATCTATAGCGGCGTTTCTGGATACAAA
1 TAGCGGCGTTTTTGCACACAAACACCGCAAAAGGTTAGATCTATAGCGGCGTTTCTGGATACAAA
1729763 CGCCGCAAAAAGTCAGATCTA
66 CGCCGCAAAAAGTCAGATCTA
1729784 TAGCGGCGTTTTT
1 TAGCGGCGTTTTT
1729797 AGATACAAAC
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
84 4 0.05
85 4 0.05
86 64 0.77
87 11 0.13
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (86 bp):
TAGCGGCGTTTTTGCACACAAACACCGCAAAAGGTTAGATCTATAGCGGCGTTTCTGGATACAAA
CGCCGCAAAAAGTCAGATCTA
Found at i:1733075 original size:41 final size:40
Alignment explanation
Indices: 1733012--1733308 Score: 218
Period size: 41 Copynumber: 7.2 Consensus size: 40
1733002 CGGCGTTTGT
* **
1733012 GCCACTAAAGTACTAGTCTATAGTGGCGTAAGTATATAAAC
1 GCCACTAAAGTACAAG-CTATAGTGGCGTTTGTATATAAAC
* *
1733053 GCCACTAAAGTACAAGCATATAGTGACGTTTGTATAAAAAC
1 GCCACTAAAGTACAAGC-TATAGTGGCGTTTGTATATAAAC
* * * *
1733094 GCCACTAAAGTATAAGTGTATAGCGGCGTTTGTATATAAAT
1 GCCACTAAAGTACAAG-CTATAGTGGCGTTTGTATATAAAC
* * * * * *
1733135 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTCTAAACACAAAC
1 GCCACTAAAGTACAAG-CTATAGTGGCGTTTGT--ATATAAAC
* * * *
1733178 GCCACTAAAGTACAAGTGTATAGCGGAGTTTGTATAAAAAC
1 GCCACTAAAGTACAAG-CTATAGTGGCGTTTGTATATAAAC
* * ** *
1733219 GCCACTAAAGTACGAGTCTTTAGCT-TTGTTTGTATAAAAAC
1 GCCACTAAAGTACAAG-CTATAG-TGGCGTTTGTATATAAAC
* * * * * *
1733260 ACCACTAAAGTACGAGTCTTTAGCGGCGTTTGTTTAAAAAAC
1 GCCACTAAAGTACAAG-CTATAGTGGCGTTTGTAT-ATAAAC
1733302 GCCACTA
1 GCCACTA
1733309 TGGCTGAACC
Statistics
Matches: 211, Mismatches: 38, Indels: 13
0.81 0.15 0.05
Matches are distributed among these distances:
40 1 0.00
41 165 0.78
42 12 0.06
43 33 0.16
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (40 bp):
GCCACTAAAGTACAAGCTATAGTGGCGTTTGTATATAAAC
Found at i:1733209 original size:84 final size:82
Alignment explanation
Indices: 1733012--1733308 Score: 317
Period size: 82 Copynumber: 3.6 Consensus size: 82
1733002 CGGCGTTTGT
* * * ** * *
1733012 GCCACTAAAGTACTAGTCTATAGTGGCGTAAGTATATAAACGCCACTAAAGTACAAG-CATATAG
1 GCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATATAAACGCCACTAAAGTACGAGTC-TTTAG
* * *
1733076 TGACGTTTGTATAAAAAC
65 CGACGTTTCTAAAAAAAC
* *
1733094 GCCACTAAAGTATAAGTGTATAGCGGCGTTTGTATATAAATGCCACTAAAGTACGAGTCTTTAGC
1 GCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATATAAACGCCACTAAAGTACGAGTCTTTAGC
*
1733159 GGCGTTTCTAAACACAAAC
66 GACGTTTCTAAA-A-AAAC
* *
1733178 GCCACTAAAGTACAAGTGTATAGCGGAGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGC
1 GCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATATAAACGCCACTAAAGTACGAGTCTTTAGC
*** * *
1733243 TTTGTTTGTATAAAAAC
66 GACGTTTCTAAAAAAAC
* * * * * *
1733260 ACCACTAAAGTACGAGTCTTTAGCGGCGTTTGTTTAAAAAACGCCACTA
1 GCCACTAAAGTACAAGTGTATAGCGGCGTTTGTAT-ATAAACGCCACTA
1733309 TGGCTGAACC
Statistics
Matches: 183, Mismatches: 28, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
82 95 0.52
83 16 0.09
84 72 0.39
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (82 bp):
GCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATATAAACGCCACTAAAGTACGAGTCTTTAGC
GACGTTTCTAAAAAAAC
Found at i:1733250 original size:125 final size:125
Alignment explanation
Indices: 1733049--1733290 Score: 351
Period size: 125 Copynumber: 1.9 Consensus size: 125
1733039 GTAAGTATAT
* * *
1733049 AAACGCCACTAAAGTACAAGCATATAGTGACGTTTGTATAAAAACGCCACTAAAGTATAAGTGTA
1 AAACGCCACTAAAGTACAAGCATATAGGGACGTTTGTATAAAAACGCCACTAAAGTACAAGTCTA
* **
1733114 TAGCGGCGTTTGTATATAAATGCCACTAAAGTACGAGTCTTTAGCGGCGTTTCTAAACAC
66 TAGCGGCGTTTGTATAAAAACACCACTAAAGTACGAGTCTTTAGCGGCGTTTCTAAACAC
** *
1733174 AAACGCCACTAAAGTACAAGTGTATAGCGGA-GTTTGTATAAAAACGCCACTAAAGTACGAGTCT
1 AAACGCCACTAAAGTACAAGCATATAG-GGACGTTTGTATAAAAACGCCACTAAAGTACAAGTCT
* ***
1733238 TTAGCTTTGTTTGTATAAAAACACCACTAAAGTACGAGTCTTTAGCGGCGTTT
65 ATAGCGGCGTTTGTATAAAAACACCACTAAAGTACGAGTCTTTAGCGGCGTTT
1733291 GTTTAAAAAA
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
125 101 0.98
126 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (125 bp):
AAACGCCACTAAAGTACAAGCATATAGGGACGTTTGTATAAAAACGCCACTAAAGTACAAGTCTA
TAGCGGCGTTTGTATAAAAACACCACTAAAGTACGAGTCTTTAGCGGCGTTTCTAAACAC
Found at i:1736235 original size:32 final size:32
Alignment explanation
Indices: 1736169--1736228 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
1736159 ATGAGTTTCG
*
1736169 GTTTTCCAAAGATTAGGCTTCCAGTGTTTATA
1 GTTTTCCAAAGATTAGGCTTCCAGTATTTATA
1736201 GTTTTCCAAAGATTAGGCTTCCA-TATTT
1 GTTTTCCAAAGATTAGGCTTCCAGTATTT
1736229 GTTAGTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 4 0.15
32 23 0.85
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (32 bp):
GTTTTCCAAAGATTAGGCTTCCAGTATTTATA
Found at i:1744467 original size:3 final size:3
Alignment explanation
Indices: 1744461--1744534 Score: 139
Period size: 3 Copynumber: 24.7 Consensus size: 3
1744451 AAACAAAACC
1744461 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1744509 AAT AAC AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1744535 AGCAAGTGAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1746362 original size:15 final size:18
Alignment explanation
Indices: 1746344--1746379 Score: 51
Period size: 15 Copynumber: 2.2 Consensus size: 18
1746334 TGTGGCCAAA
1746344 TTTTTA-TTTT-AA-TTG
1 TTTTTAGTTTTGAATTTG
1746359 TTTTTAGTTTTGAATTTG
1 TTTTTAGTTTTGAATTTG
1746377 TTT
1 TTT
1746380 GGTTTTAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.33
16 4 0.22
17 2 0.11
18 6 0.33
ACGTcount: A:0.17, C:0.00, G:0.11, T:0.72
Consensus pattern (18 bp):
TTTTTAGTTTTGAATTTG
Found at i:1747506 original size:17 final size:18
Alignment explanation
Indices: 1747484--1747521 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1747474 TTTTGTTTTA
*
1747484 TTTTTATCTTTAAC-ATT
1 TTTTTATATTTAACTATT
*
1747501 TTTTTATATTTTACTATT
1 TTTTTATATTTAACTATT
1747519 TTT
1 TTT
1747522 CTTTTATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTATATTTAACTATT
Found at i:1749947 original size:30 final size:28
Alignment explanation
Indices: 1749911--1749971 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
1749901 TTTCGGTTGG
*
1749911 ATTTATTCTATTAAA-TATTAAATATATTAT
1 ATTTATT-AATTAAAGTA-TAAATAT-TTAT
1749941 ATTTATTAATTAAAGTATAAATATTTAT
1 ATTTATTAATTAAAGTATAAATATTTAT
1749969 ATT
1 ATT
1749972 AACTGAACCT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 7 0.24
29 13 0.45
30 9 0.31
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (28 bp):
ATTTATTAATTAAAGTATAAATATTTAT
Found at i:1763031 original size:31 final size:31
Alignment explanation
Indices: 1762974--1763068 Score: 138
Period size: 31 Copynumber: 3.1 Consensus size: 31
1762964 TCAAAAAAAA
1762974 TAAGATATTGTCACTTTCG-TTATATTTAAT
1 TAAGATATTGTCACTTTCGTTTATATTTAAT
*
1763004 TAAGGTATTGTCACTTTCGTTTATATTTAAT
1 TAAGATATTGTCACTTTCGTTTATATTTAAT
* * * *
1763035 TAAGATAGTATCATTTTCGTTTTTATTTAAT
1 TAAGATATTGTCACTTTCGTTTATATTTAAT
1763066 TAA
1 TAA
1763069 TATGTGGTCG
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 18 0.31
31 40 0.69
ACGTcount: A:0.29, C:0.08, G:0.11, T:0.52
Consensus pattern (31 bp):
TAAGATATTGTCACTTTCGTTTATATTTAAT
Found at i:1765361 original size:60 final size:62
Alignment explanation
Indices: 1765249--1765368 Score: 208
Period size: 60 Copynumber: 2.0 Consensus size: 62
1765239 GAAAGTGTTA
*
1765249 CATAACTTGTAGTTTTAATATATTTGATTGAGGGTTAATTTTCATAAGTATGGAAGATAATGT
1 CATAACTTGTAGTTTTAATATATTT-ATTGAGGGTTAATTTCCATAAGTATGGAAGATAATGT
1765312 CATAACTTGTAGTTTTAATATA-TT-TTGAGGGTTAATTTCCATAAGTATGGAAGATAA
1 CATAACTTGTAGTTTTAATATATTTATTGAGGGTTAATTTCCATAAGTATGGAAGATAA
1765369 AGACTTGCCA
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
60 32 0.57
62 2 0.04
63 22 0.39
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (62 bp):
CATAACTTGTAGTTTTAATATATTTATTGAGGGTTAATTTCCATAAGTATGGAAGATAATGT
Found at i:1779806 original size:3 final size:3
Alignment explanation
Indices: 1779798--1779838 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
1779788 CATACTAGGT
1779798 TAA TAA TAA TAA TAA TAA CT-A TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA
1779839 GAAAAAAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 1 0.03
3 34 0.94
4 1 0.03
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1781225 original size:2 final size:2
Alignment explanation
Indices: 1781218--1781255 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1781208 TACTCAATGA
1781218 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
1781256 TAAAATATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1781272 original size:14 final size:16
Alignment explanation
Indices: 1781226--1781273 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 16
1781216 GAATATATAT
*
1781226 ATATATATATATATATAT
1 ATATATATATAT-TA-AA
1781244 ATATATATATATTAAA
1 ATATATATATATTAAA
1781260 ATAT-TATAT-TTAAA
1 ATATATATATATTAAA
1781274 CACTTAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 5 0.17
15 5 0.17
16 5 0.17
17 2 0.07
18 12 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATATATATATTAAA
Found at i:1784454 original size:117 final size:117
Alignment explanation
Indices: 1784306--1784520 Score: 299
Period size: 117 Copynumber: 1.8 Consensus size: 117
1784296 TAAAAATGAT
* *
1784306 CTTCTTTTGAAAGCTAAAATAGACTTGGAAAATCAAAATAAAATTTTGTAA-AAGGAGTTAGAGC
1 CTTCTTTAGAAAGCTAAAATAGACTTGGAAAATCAAAATAAAATATTG-AAGAAGGAGTTAGAGC
* *
1784370 TTTCAAAAATGAAATCTGAAAACTTTGAAAAAGAAATTTTCGAATTAAACAAA
65 TCTCAAAAATAAAATCTGAAAACTTTGAAAAAGAAATTTTCGAATTAAACAAA
* * * * *
1784423 CTTCTTTAAGAAA-CTAAAATGGATTTTGAAAATCAAAATGAAATATTGAAGAAGGATTTAGAGC
1 CTTCTTT-AGAAAGCTAAAATAGACTTGGAAAATCAAAATAAAATATTGAAGAAGGAGTTAGAGC
* *
1784487 TCTCAAAAATAAAATTTGAAAGCTTTGAAAAAGA
65 TCTCAAAAATAAAATCTGAAAACTTTGAAAAAGA
1784521 GGATTTCAAT
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
116 2 0.02
117 79 0.93
118 4 0.05
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.29
Consensus pattern (117 bp):
CTTCTTTAGAAAGCTAAAATAGACTTGGAAAATCAAAATAAAATATTGAAGAAGGAGTTAGAGCT
CTCAAAAATAAAATCTGAAAACTTTGAAAAAGAAATTTTCGAATTAAACAAA
Found at i:1788438 original size:21 final size:20
Alignment explanation
Indices: 1788414--1788465 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 20
1788404 ACTTATGTAT
1788414 GATACACTATGAATGTGTACC
1 GATACACT-TGAATGTGTACC
*
1788435 GATACATTCCTTGAATGTGTATC
1 GATACA---CTTGAATGTGTACC
1788458 GATACACT
1 GATACACT
1788466 CAAGAGTGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 2 0.07
21 6 0.22
23 17 0.63
24 2 0.07
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (20 bp):
GATACACTTGAATGTGTACC
Found at i:1789891 original size:31 final size:31
Alignment explanation
Indices: 1789853--1789917 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
1789843 AGAGTCGAGG
*
1789853 GTTTACCTATG-TCTTTCGAGACATATGGACA
1 GTTTACCTAGGTTC-TTCGAGACATATGGACA
* *
1789884 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTTCGAGACATATGGACA
1789915 GTT
1 GTT
1789918 ACCGAGGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGAGACATATGGACA
Found at i:1789937 original size:30 final size:30
Alignment explanation
Indices: 1789876--1789999 Score: 128
Period size: 30 Copynumber: 4.2 Consensus size: 30
1789866 TTTCGAGACA
* * ***
1789876 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
1789907 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
1789937 TCTGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* * *
1789967 TCTGGATAGTTA-CG-GGGTCTTT-TGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
1789994 TTTGGA
1 TATGGA
1790000 TAGGTCCTTC
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
27 10 0.12
28 7 0.08
29 2 0.02
30 56 0.67
31 9 0.11
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:1790002 original size:27 final size:30
Alignment explanation
Indices: 1789903--1789999 Score: 137
Period size: 30 Copynumber: 3.3 Consensus size: 30
1789893 GGTTCTTCGG
*
1789903 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
1789933 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* *
1789963 GACCTCTGGATAGTTA-CG-GGGTCTTT-T
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
*
1789990 GACCTTTGGA
1 GACCTCTGGA
1790000 TAGGTCCTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
27 10 0.16
28 7 0.11
29 2 0.03
30 44 0.70
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.32
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:1790315 original size:2 final size:2
Alignment explanation
Indices: 1790272--1790307 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1790262 GTATGCGTGG
1790272 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
1790308 GAATATATGA
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:1793475 original size:20 final size:20
Alignment explanation
Indices: 1793430--1793487 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
1793420 GCATGGGTAG
1793430 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
1793454 TGTATCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
1793474 TGCATCGATGCACT
1 TGCATCGATGCACT
1793488 TCAAGGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 2 0.06
24 12 0.38
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:1794000 original size:31 final size:31
Alignment explanation
Indices: 1793962--1794026 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
1793952 AGAGTCGAGG
1793962 GTTTACCTATG-TCTTTCGAGA-CATATGGACA
1 GTTTACCTATGTTC-TTCGAGATC-TATGGACA
*
1793993 GTTTACCTATGTTCTTCGGGATCTATGGACA
1 GTTTACCTATGTTCTTCGAGATCTATGGACA
1794024 GTT
1 GTT
1794027 ACCGAGGATC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGAGATCTATGGACA
Found at i:1794052 original size:30 final size:30
Alignment explanation
Indices: 1794018--1794110 Score: 134
Period size: 30 Copynumber: 3.1 Consensus size: 30
1794008 TCGGGATCTA
1794018 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1794048 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * * *
1794078 TGGATAGTTATCG-GGGTCTTTGTAACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1794107 TGGA
1 TGGA
1794111 TAGGTCCTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 17 0.29
30 41 0.71
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:1795301 original size:13 final size:13
Alignment explanation
Indices: 1795283--1795316 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1795273 CTACATATAA
* *
1795283 TTTTCAAACATTG
1 TTTTCAAAAATAG
1795296 TTTTCAAAAATAG
1 TTTTCAAAAATAG
1795309 TTTTCAAA
1 TTTTCAAA
1795317 TTTGCCCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (13 bp):
TTTTCAAAAATAG
Found at i:1797087 original size:13 final size:13
Alignment explanation
Indices: 1797065--1797098 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
1797055 AGGGGAAGTA
1797065 ATTTTCAAAAATG
1 ATTTTCAAAAATG
1797078 A-TTTCAAAAATG
1 ATTTTCAAAAATG
1797090 ATTTTCAAA
1 ATTTTCAAA
1797099 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:1802322 original size:2 final size:2
Alignment explanation
Indices: 1802315--1802339 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1802305 CTCCCAATAG
1802315 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1802340 GCTGTTTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1814339 original size:24 final size:23
Alignment explanation
Indices: 1814312--1814357 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
1814302 AAAATGTGAG
1814312 CCACAAGAATAGAGAAAATACATA
1 CCACAAGAATAGAGAAAA-ACATA
1814336 CCACAAGAATAGAGAAAAACAT
1 CCACAAGAATAGAGAAAAACAT
1814358 GTTATAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.59, C:0.17, G:0.13, T:0.11
Consensus pattern (23 bp):
CCACAAGAATAGAGAAAAACATA
Found at i:1815507 original size:39 final size:39
Alignment explanation
Indices: 1815464--1815547 Score: 96
Period size: 39 Copynumber: 2.2 Consensus size: 39
1815454 AGTTAAATAT
* *
1815464 GAAGACTCCACGACTGCATGGCGTCTTCAGAAAAATAAA
1 GAAGACTCCACGACTACATGGCATCTTCAGAAAAATAAA
* * * * **
1815503 GAAGATTTCACGACTACATGGTATCTTCAGACAAATTGA
1 GAAGACTCCACGACTACATGGCATCTTCAGAAAAATAAA
1815542 GAAGAC
1 GAAGAC
1815548 CCCAAAAGTA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.21
Consensus pattern (39 bp):
GAAGACTCCACGACTACATGGCATCTTCAGAAAAATAAA
Found at i:1818109 original size:211 final size:211
Alignment explanation
Indices: 1817703--1818126 Score: 773
Period size: 211 Copynumber: 2.0 Consensus size: 211
1817693 GCTCCCTTTT
1817703 AACTTCTGTTTGGATTTTAAATATGTAGTGCATTTCTTAACGCATGGGTCATTCTACATTAAGCC
1 AACTTCTGTTTGGATTTTAAATATGTAGTGCATTTCTTAACGCATGGGTCATTCTACATTAAGCC
1817768 ATTCTAGTTTTGAATGATGTTATTTTGGTCCTATTTCTGCCACCACTCTCACTTTGTCCCACACC
66 ATTCTAGTTTTGAATGATGTTATTTTGGTCCTATTTCTGCCACCACTCTCACTTTGTCCCACACC
* *
1817833 ATCACTTGGCTCTCATTGTTTTATTATTATGAAAAGATGGGCAATTTAAACTTCAACGTCAAAGC
131 ATCACTTGGCTCTCATTGTTTTACTATTATGAAAAGATGGGCAATTTAAACTTCAACGGCAAAGC
1817898 ATAAATTTGTGCTATA
196 ATAAATTTGTGCTATA
1817914 AACTTCTGTTTGGATTTTAAATATGTAGTGCATTTCTTAACGCATGGGTCATTTCTACATTAAGC
1 AACTTCTGTTTGGATTTTAAATATGTAGTGCATTTCTTAACGCATGGGTCA-TTCTACATTAAGC
1817979 CATTCTAGTTTTGAATGATGTTATTTTGGT-CTATTTCTGCCACCACTCTCACTTTGTCCCACAC
65 CATTCTAGTTTTGAATGATGTTATTTTGGTCCTATTTCTGCCACCACTCTCACTTTGTCCCACAC
*
1818043 CATCACTTGGCTCATCATTATTTTTACTA-TATGAAAAGATGGGCAATTTAAACTTC-ACGGCAA
130 CATCACTTGGCTC-TCATT-GTTTTACTATTATGAAAAGATGGGCAATTTAAACTTCAACGGCAA
1818106 AGCATAAATTTGTGCTATA
193 AGCATAAATTTGTGCTATA
1818125 AA
1 AA
1818127 GCATCAACAA
Statistics
Matches: 207, Mismatches: 3, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
211 125 0.60
212 75 0.36
213 7 0.03
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (211 bp):
AACTTCTGTTTGGATTTTAAATATGTAGTGCATTTCTTAACGCATGGGTCATTCTACATTAAGCC
ATTCTAGTTTTGAATGATGTTATTTTGGTCCTATTTCTGCCACCACTCTCACTTTGTCCCACACC
ATCACTTGGCTCTCATTGTTTTACTATTATGAAAAGATGGGCAATTTAAACTTCAACGGCAAAGC
ATAAATTTGTGCTATA
Found at i:1818344 original size:11 final size:11
Alignment explanation
Indices: 1818323--1818352 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
1818313 AATTTTTCAG
1818323 TTTACTTTTATT
1 TTTA-TTTTATT
1818335 TTTATTTTATT
1 TTTATTTTATT
1818346 TTTATTT
1 TTTATTT
1818353 ATTATTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:1823209 original size:73 final size:73
Alignment explanation
Indices: 1823122--1823271 Score: 228
Period size: 73 Copynumber: 2.1 Consensus size: 73
1823112 ATCCAATCAT
* * * * *
1823122 AACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTT
1 AACAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATTTTGCCTCTCTTGAGACAGTT
1823187 TCTCTTGA
66 TCTCTTGA
* * *
1823195 AACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATTTTGCCTCTCTTGAGATAGTT
1 AACAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATTTTGCCTCTCTTGAGACAGTT
1823260 TCTCTTGA
66 TCTCTTGA
1823268 AACA
1 AACA
1823272 CAAAAAAAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (73 bp):
AACAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATTTTGCCTCTCTTGAGACAGTT
TCTCTTGA
Found at i:1823212 original size:36 final size:36
Alignment explanation
Indices: 1823122--1823271 Score: 219
Period size: 37 Copynumber: 4.1 Consensus size: 36
1823112 ATCCAATCAT
* * * *
1823122 AACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGG
1 AACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGA
*
1823158 AACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGA
1 AAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGA
1823195 AACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGA
1 AACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGA
* *
1823231 AACAAAATTTTGCCTCTCTTGAGATAGTTTCTCTTGA
1 AAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGA
1823268 AACA
1 AACA
1823272 CAAAAAAAAA
Statistics
Matches: 104, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
36 39 0.38
37 65 0.62
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (36 bp):
AACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGA
Found at i:1824095 original size:15 final size:17
Alignment explanation
Indices: 1824075--1824108 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
1824065 TTATTTGTCT
1824075 TATACATT-TA-TAATA
1 TATACATTATACTAATA
1824090 TATACATTATACTAATA
1 TATACATTATACTAATA
1824107 TA
1 TA
1824109 GTTTTTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 2 0.12
17 7 0.41
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (17 bp):
TATACATTATACTAATA
Found at i:1825125 original size:18 final size:18
Alignment explanation
Indices: 1825102--1825144 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1825092 GTAGACACTA
1825102 ATTTTTCAGTTTGA-TTTT
1 ATTTTT-AGTTTGATTTTT
* *
1825120 ATTTTTATTTTTATTTTT
1 ATTTTTAGTTTGATTTTT
1825138 ATTTTTA
1 ATTTTTA
1825145 TTATTTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (18 bp):
ATTTTTAGTTTGATTTTT
Found at i:1825143 original size:19 final size:19
Alignment explanation
Indices: 1825116--1825187 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
1825106 TTCAGTTTGA
*
1825116 TTTTATTTTTATT-TTTAT
1 TTTTATTATTATTATTTAT
*
1825134 TTTTATTTTTATTATTTAT
1 TTTTATTATTATTATTTAT
*
1825153 TATTATTATTATTATTTAT
1 TTTTATTATTATTATTTAT
*
1825172 TATTATTATTATTATT
1 TTTTATTATTATTATT
1825188 ATTATTTAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
18 13 0.25
19 38 0.75
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTATTATTATTATTTAT
Found at i:1825155 original size:3 final size:3
Alignment explanation
Indices: 1825118--1825193 Score: 98
Period size: 3 Copynumber: 24.7 Consensus size: 3
1825108 CAGTTTGATT
* * * *
1825118 TTA TTT TTA TTT TTA TTT TTA TTT TTA TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
1825164 TTA TTTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT
1825194 TAAATAAATA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
3 57 0.90
4 6 0.10
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (3 bp):
TTA
Found at i:1826582 original size:29 final size:30
Alignment explanation
Indices: 1826534--1826592 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
1826524 AGGGCTATAC
1826534 ATTTTAATATTTTATATTTTAATC-CTATT
1 ATTTTAATATTTTATATTTTAATCACTATT
* *
1826563 ATTTTAAT-TTTATATGTTTTATTCACTATT
1 ATTTTAATATTT-TATATTTTAATCACTATT
1826593 TAATTGCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
29 18 0.69
30 5 0.19
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.63
Consensus pattern (30 bp):
ATTTTAATATTTTATATTTTAATCACTATT
Found at i:1826700 original size:10 final size:10
Alignment explanation
Indices: 1826687--1826716 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
1826677 AGTCATATAA
1826687 ATATATATTT
1 ATATATATTT
1826697 ATATATATTT
1 ATATATATTT
1826707 ATATATATTT
1 ATATATATTT
1826717 GTTTAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATATATATTT
Found at i:1827025 original size:26 final size:26
Alignment explanation
Indices: 1826962--1827027 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
1826952 ACTTTTATCA
1826962 ATTA-TATATATTAATATATATTTTT
1 ATTATTATATATTAATATATATTTTT
* * *
1826987 ATTATTTTTTATTAATATTTAGTTATTT
1 ATTATTATATATTAATATATA-TT-TTT
1827015 -TT-TTATATATTAA
1 ATTATTATATATTAA
1827028 GAAAAGAGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
25 4 0.12
26 22 0.67
27 4 0.12
28 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (26 bp):
ATTATTATATATTAATATATATTTTT
Found at i:1827580 original size:36 final size:37
Alignment explanation
Indices: 1827531--1827628 Score: 98
Period size: 35 Copynumber: 2.7 Consensus size: 37
1827521 AGTATATAAT
1827531 ATTTATTTATTTATTTATTTTTATTTTT-TCCTTT-TG
1 ATTTATTT-TTTATTTATTTTTATTTTTATCCTTTATG
**
1827567 ATTTATTATTTTA-TTA-TTTTATTTTTATTTTTTATG
1 ATTTATT-TTTTATTTATTTTTATTTTTATCCTTTATG
*
1827603 -TTTATTCTTTGATTTATTTTATATTT
1 ATTTATT-TTTTATTTATTTT-TATTT
1827629 ATTTAGTATT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
34 10 0.19
35 17 0.33
36 16 0.31
37 4 0.08
38 5 0.10
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.74
Consensus pattern (37 bp):
ATTTATTTTTTATTTATTTTTATTTTTATCCTTTATG
Found at i:1827606 original size:13 final size:12
Alignment explanation
Indices: 1827532--1827632 Score: 73
Period size: 13 Copynumber: 8.0 Consensus size: 12
1827522 GTATATAATA
1827532 TTTA-TTTATTT
1 TTTATTTTATTT
1827543 ATTTATTTTTATTT
1 -TTTA-TTTTATTT
*
1827557 TTTCCTTTTGATTT
1 TTT-ATTTT-ATTT
*
1827571 ATTATTTTATTAT
1 TTTATTTTATT-T
1827584 TTTATTTTTATTT
1 TTTA-TTTTATTT
1827597 TTTATGTTTATTCT
1 TTTAT-TTTATT-T
*
1827611 TTGA-TTTATTT
1 TTTATTTTATTT
*
1827622 TATA-TTTATTT
1 TTTATTTTATTT
1827633 AGTATTTTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
11 10 0.14
12 14 0.19
13 26 0.35
14 24 0.32
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:1827630 original size:36 final size:37
Alignment explanation
Indices: 1827531--1827632 Score: 108
Period size: 36 Copynumber: 2.8 Consensus size: 37
1827521 AGTATATAAT
1827531 ATTTATTTATTT-ATTTATTTT-TATTT-TTTCCTTTTG
1 ATTTA-TTATTTGATTTATTTTATATTTATTT-CTTTTG
* *
1827567 ATTTATTATTTTA-TTATTTTATTTTTATTT-TTTATG
1 ATTTATTATTTGATTTATTTTATATTTATTTCTTT-TG
*
1827603 -TTTATTCTTTGATTTATTTTATATTTATTT
1 ATTTATTATTTGATTTATTTTATATTTATTT
1827633 AGTATTTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
35 26 0.46
36 28 0.49
37 3 0.05
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.75
Consensus pattern (37 bp):
ATTTATTATTTGATTTATTTTATATTTATTTCTTTTG
Found at i:1827631 original size:47 final size:48
Alignment explanation
Indices: 1827529--1827644 Score: 127
Period size: 47 Copynumber: 2.4 Consensus size: 48
1827519 AAAGTATATA
1827529 ATATTTA-TTTATTTATTTATTTTTATTTTTTCCTTTTGATTTATTATT
1 ATATTTATTTTATTT-TTTATTTTTATTTTTTCCTTTTGATTTATTATT
*
1827577 TTA-TTATTTTA-TTTTTATTTTTTATGTTTATT-C-TTTGATTTATT-TT
1 ATATTTATTTTATTTTTTA-TTTTTAT-TTT-TTCCTTTTGATTTATTATT
1827623 ATATTTATTTAGTATTTTTTAT
1 ATATTTATTT--TATTTTTTAT
1827645 CTAACATTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
46 8 0.14
47 29 0.50
48 10 0.17
49 5 0.09
50 6 0.10
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.73
Consensus pattern (48 bp):
ATATTTATTTTATTTTTTATTTTTATTTTTTCCTTTTGATTTATTATT
Found at i:1827638 original size:11 final size:10
Alignment explanation
Indices: 1827529--1827644 Score: 56
Period size: 8 Copynumber: 12.2 Consensus size: 10
1827519 AAAGTATATA
1827529 ATATTTA-TT
1 ATATTTATTT
1827538 -TATTTATTT
1 ATATTTATTT
*
1827547 ATTTTTATTT
1 ATATTTATTT
**
1827557 -T-TTCCTTT
1 ATATTTATTT
1827565 -TGATTTA-TT
1 AT-ATTTATTT
1827574 AT-TTTA-TT
1 ATATTTATTT
1827582 AT-TTTATTT
1 ATATTTATTT
*
1827591 TTATTT-TTT
1 ATATTTATTT
*
1827600 ATGTTTATTCT
1 ATATTTATT-T
*
1827611 TTGATTTATTTT
1 AT-ATTTA-TTT
1827623 ATATTTATTT
1 ATATTTATTT
1827633 AGTATTT-TTT
1 A-TATTTATTT
1827643 AT
1 AT
1827645 CTAACATTTT
Statistics
Matches: 84, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
8 24 0.29
9 16 0.19
10 24 0.29
11 12 0.14
12 6 0.07
13 2 0.02
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.73
Consensus pattern (10 bp):
ATATTTATTT
Found at i:1829594 original size:21 final size:21
Alignment explanation
Indices: 1829568--1829612 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1829558 AATATGTAAA
*
1829568 TCGCGTTGTGATTTTCCGAAT
1 TCGCGTTGCGATTTTCCGAAT
1829589 TCGCGTTGCGATTTTCCGAAT
1 TCGCGTTGCGATTTTCCGAAT
1829610 TCG
1 TCG
1829613 AGATCGCGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.13, C:0.22, G:0.24, T:0.40
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCGAAT
Found at i:1833484 original size:81 final size:81
Alignment explanation
Indices: 1833393--1833547 Score: 283
Period size: 81 Copynumber: 1.9 Consensus size: 81
1833383 CACCTCCCCA
* *
1833393 AAAATATTTTATCATTAAAGAATAATGGGATAATTACCTATTTAGGCCTTTAAATTTTAATTTAT
1 AAAATATTTTATCATTAAAGAATAATGGGACAATTACCTATTTAGACCTTTAAATTTTAATTTAT
1833458 TTTGATTTTGCCTCCC
66 TTTGATTTTGCCTCCC
*
1833474 AAAATTTTTTATCATTAAAGAATAATGGGACAATTACCTATTTAGACCTTTAAATTTTAATTTAT
1 AAAATATTTTATCATTAAAGAATAATGGGACAATTACCTATTTAGACCTTTAAATTTTAATTTAT
1833539 TTTGATTTT
66 TTTGATTTT
1833548 ACCCCTCATT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 71 1.00
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.46
Consensus pattern (81 bp):
AAAATATTTTATCATTAAAGAATAATGGGACAATTACCTATTTAGACCTTTAAATTTTAATTTAT
TTTGATTTTGCCTCCC
Found at i:1840037 original size:14 final size:14
Alignment explanation
Indices: 1840010--1840056 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
1840000 TTTCGTCCCG
1840010 TTATTAT-T-TATA
1 TTATTATGTATATA
1840022 TTATTATGTATATA
1 TTATTATGTATATA
1840036 TTATTATTGTAT-TA
1 TTATTA-TGTATATA
*
1840050 ATATTAT
1 TTATTAT
1840057 AAATATTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
12 7 0.23
13 2 0.06
14 17 0.55
15 5 0.16
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (14 bp):
TTATTATGTATATA
Found at i:1840284 original size:16 final size:16
Alignment explanation
Indices: 1840260--1840298 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1840250 CAACAGAAAT
*
1840260 CCTAAGGTTCACCAAC
1 CCTAGGGTTCACCAAC
1840276 CCTAGGGTTCACCAAC
1 CCTAGGGTTCACCAAC
*
1840292 CTTAGGG
1 CCTAGGG
1840299 AGACTTTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.26, C:0.33, G:0.21, T:0.21
Consensus pattern (16 bp):
CCTAGGGTTCACCAAC
Found at i:1840346 original size:22 final size:22
Alignment explanation
Indices: 1840317--1840419 Score: 170
Period size: 22 Copynumber: 4.7 Consensus size: 22
1840307 GTGATGCCTA
*
1840317 CAACTGCTCCGCCGCCTATATC
1 CAACTGCTCCGCCGCCTACATC
* *
1840339 TAACTGCTCCGCCGCCTATATC
1 CAACTGCTCCGCCGCCTACATC
1840361 CAACTGCTCCGCCGCCTACATC
1 CAACTGCTCCGCCGCCTACATC
1840383 CAACTGCTCCGCCGCCTACATC
1 CAACTGCTCCGCCGCCTACATC
*
1840405 CAATTGCTCCGCCGC
1 CAACTGCTCCGCCGC
1840420 TAAATTTTGC
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 77 1.00
ACGTcount: A:0.17, C:0.47, G:0.15, T:0.21
Consensus pattern (22 bp):
CAACTGCTCCGCCGCCTACATC
Found at i:1841096 original size:22 final size:22
Alignment explanation
Indices: 1841070--1841120 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
1841060 AAATATTAAA
*
1841070 TTTAATTCCTAAAT-TTTGATAT
1 TTTAATTCCT-AATCTTTAATAT
*
1841092 TTTAATCCCTAATCTTTAATAT
1 TTTAATTCCTAATCTTTAATAT
1841114 TTTAATT
1 TTTAATT
1841121 TTAGTAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.31, C:0.12, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTAATTCCTAATCTTTAATAT
Found at i:1842374 original size:121 final size:118
Alignment explanation
Indices: 1842078--1842361 Score: 394
Period size: 118 Copynumber: 2.4 Consensus size: 118
1842068 AAGAAGTGGA
* * *
1842078 GATTAGTTGAAACTTTGACTAATCAATTAATTTTAAAATTTCCTTGGAGATTTGCAG-GGGATTC
1 GATTAGTTGAAACTTTGAATAATCAATTAATTTTAAAAGTTCCATGGAGATTTGC-GTGGGATTC
* *
1842142 TTTGCATGAATTTTAATTTTTATGGGTATTGCATGGGGTTTGAAAAATTAGCCT
65 TTTCCATGAATTTTAATTTTTATGGGTATTGCATGGGGTTTGAAAAATGAGCCT
*
1842196 GATTAGTTGAAACTTTGATTAATCAATTAATTTTAAAAGTTCCATGGAGATTTGCGTGGGATTCT
1 GATTAGTTGAAACTTTGAATAATCAATTAATTTTAAAAGTTCCATGGAGATTTGCGTGGGATTCT
* *
1842261 TTCCGTGAATTTTAAATTTTTCGTGGGTATTGCATGGGGTTTGAGAAAATGAGCTCT
66 TTCCATGAATTTT-AATTTTT-ATGGGTATTGCATGGGGTTTGA-AAAATGAGC-CT
* * *
1842318 -ATTAGTTGAAACTTTGAAAAAACAATTATTTTTAAATA-TTCCAT
1 GATTAGTTGAAACTTTGAATAATCAATTAATTTTAAA-AGTTCCAT
1842362 AGTGAATTGC
Statistics
Matches: 149, Mismatches: 11, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
117 1 0.01
118 71 0.48
119 7 0.05
120 21 0.14
121 46 0.31
122 3 0.02
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (118 bp):
GATTAGTTGAAACTTTGAATAATCAATTAATTTTAAAAGTTCCATGGAGATTTGCGTGGGATTCT
TTCCATGAATTTTAATTTTTATGGGTATTGCATGGGGTTTGAAAAATGAGCCT
Found at i:1851986 original size:137 final size:136
Alignment explanation
Indices: 1851735--1852387 Score: 907
Period size: 137 Copynumber: 4.8 Consensus size: 136
1851725 TATTTTAGGA
* *
1851735 AACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGAGTTATCTCAAATATCTTTA
1 AACATCATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
* ** *
1851800 AAGATGGCCAGACATT-CGCATCACGAAGGAACAATGTCATCCATTGATCATAACTCCTCATCAC
66 AAGATGG-CAGAC-TTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCAC
*
1851864 GAAGGAGC
129 GAAGAAGC
*
1851872 AACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
1 AACATCATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
* *
1851937 AAGATGGTCAGATTTCCTCATTACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACG
66 AAGATGG-CAGACTTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACG
*
1852002 AAGAAGT
130 AAGAAGC
* * *
1852009 AGCATCATCCTTAGATAACCAGATGTCCTCATCACGAAGGATCCGTGTTATCTCAAATATCTTTT
1 AACATCATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
* * * * *
1852074 AAGATGGTCAGGCGTCCTCATCATGAATGAACAATGTCATCCACCGATCAGAAATCCTCATCACG
66 AAGATGG-CAGACTTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACG
1852139 AAGAAGC
130 AAGAAGC
* * * *
1852146 ATCATCATCCTTAGATAACCAGATGTCCTCATCACGAATGAACTGTATTATCTCAAATATCTTTA
1 AACATCATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
* ** * * *
1852211 AAGATGGCTAGACGTT-CTCATCACGAAGGAACAATATCATCCATTGATCAAAATTCCTCATCAT
66 AAGATGGC-AGAC-TTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCAC
* *
1852275 AAAGGAGC
129 GAAGAAGC
* *
1852283 AGCATCATCCTTAGATAGA-CAGATGTCCTCATCACGAAGGAACCGAGTTATCTCAAATATCTTT
1 AACATCATCCTTAGATA-ACCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTT
*
1852347 AAAGATGGCTAGACATCCTCATCACGAAGGAACAATGTCAT
65 AAAGATGGC-AGACTTCCTCATCACGAAGGAACAATGTCAT
1852388 ACACTAGTTT
Statistics
Matches: 464, Mismatches: 47, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
136 4 0.01
137 458 0.99
138 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (136 bp):
AACATCATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
AAGATGGCAGACTTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACGA
AGAAGC
Found at i:1852272 original size:40 final size:43
Alignment explanation
Indices: 1852227--1852325 Score: 100
Period size: 40 Copynumber: 2.4 Consensus size: 43
1852217 GCTAGACGTT
*
1852227 CTCATCACGAAGGAACAATATCATCCATT-GATCA-A-A-AT-TC
1 CTCATCACGAAGGAACAACATCATCC-TTAGAT-AGACAGATGTC
** * *
1852267 CTCATCATAAAGGAGCAGCATCATCCTTAGATAGACAGATGTC
1 CTCATCACGAAGGAACAACATCATCCTTAGATAGACAGATGTC
1852310 CTCATCACGAAGGAAC
1 CTCATCACGAAGGAAC
1852326 CGAGTTATCT
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
39 3 0.07
40 25 0.54
41 1 0.02
42 2 0.04
43 15 0.33
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.22
Consensus pattern (43 bp):
CTCATCACGAAGGAACAACATCATCCTTAGATAGACAGATGTC
Found at i:1852566 original size:14 final size:14
Alignment explanation
Indices: 1852539--1852585 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
1852529 TTTCATCATG
1852539 TTATTA-TT-TATA
1 TTATTATTTATATA
1852551 TTATTATTTATATA
1 TTATTATTTATATA
1852565 TTATTATTGTAT-TA
1 TTATTATT-TATATA
1852579 TTATTAT
1 TTATTAT
1852586 AAATATTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 6 0.19
13 2 0.06
14 21 0.66
15 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
TTATTATTTATATA
Found at i:1852571 original size:26 final size:26
Alignment explanation
Indices: 1852539--1852596 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
1852529 TTTCATCATG
*
1852539 TTATTATTTATATTATTATT-TATATA
1 TTATTA-TTATATTATTATTATAAATA
*
1852565 TTATTATTGTATTATTATTATAAATA
1 TTATTATTATATTATTATTATAAATA
1852591 TTATTA
1 TTATTA
1852597 ATAGATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 12 0.41
26 17 0.59
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
TTATTATTATATTATTATTATAAATA
Found at i:1852915 original size:22 final size:22
Alignment explanation
Indices: 1852890--1852933 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1852880 TGCTACGCTA
* * *
1852890 CCTATATCCAACTGCTCTGCCG
1 CCTACATCCAACTCCTCCGCCG
1852912 CCTACATCCAACTCCTCCGCCG
1 CCTACATCCAACTCCTCCGCCG
1852934 TTATGTTCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.18, C:0.48, G:0.11, T:0.23
Consensus pattern (22 bp):
CCTACATCCAACTCCTCCGCCG
Found at i:1858577 original size:15 final size:17
Alignment explanation
Indices: 1858548--1858589 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 17
1858538 TTAAATTTAA
1858548 AAAATATTTTAAAAAAT
1 AAAATATTTTAAAAAAT
1858565 AAAAT-TTTTAAAAATATT
1 AAAATATTTTAAAAA-A-T
1858583 AAAATAT
1 AAAATAT
1858590 AAAACGTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 9 0.41
17 6 0.27
18 6 0.27
19 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAATATTTTAAAAAAT
Found at i:1863795 original size:37 final size:36
Alignment explanation
Indices: 1863754--1863947 Score: 101
Period size: 37 Copynumber: 5.6 Consensus size: 36
1863744 ATTATATTAG
*
1863754 ATAATATATAAGTAACCAAATAGGTAGTTTATCCTAA
1 ATAATATATAAGTGACCAAA-AGGTAGTTTATCCTAA
* * * **
1863791 ATAATA-ATCGAGTGATCAAAA--CA-TAAAT--TAA
1 ATAATATAT-AAGTGACCAAAAGGTAGTTTATCCTAA
1863822 ATAATATATAAGTGACCAAAGAGGTAGTTT-TCCCTAA
1 ATAATATATAAGTGACCAAA-AGGTAGTTTAT-CCTAA
* * ** *
1863859 ATAATA-ATCGAGTGACCAAAA--CA-TAAAT--TAG
1 ATAATATAT-AAGTGACCAAAAGGTAGTTTATCCTAA
* *
1863890 ATAATATATAAGTAACCAAATAGGTAGTTTACCCTAA
1 ATAATATATAAGTGACCAAA-AGGTAGTTTATCCTAA
*
1863927 ATAATA-ATCGAGTGACCAAAA
1 ATAATATAT-AAGTGACCAAAA
1863948 CATAAATTAG
Statistics
Matches: 113, Mismatches: 25, Indels: 39
0.64 0.14 0.22
Matches are distributed among these distances:
31 35 0.31
32 6 0.05
33 4 0.04
34 6 0.05
35 3 0.03
36 9 0.08
37 50 0.44
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (36 bp):
ATAATATATAAGTGACCAAAAGGTAGTTTATCCTAA
Found at i:1863840 original size:68 final size:68
Alignment explanation
Indices: 1863662--1863995 Score: 446
Period size: 68 Copynumber: 5.0 Consensus size: 68
1863652 AATTTAAAAA
* * *
1863662 AATAATCGAGTGACCAAAACATAAATTAGGTAATATATAAGTGACCAAAAATGTAGTTTACCCTA
1 AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
1863727 AAT
66 AAT
* * * * * * *
1863730 AAAAAT--A-T-A-TATGAA-TTATATTAGATAATATATAAGTAACCAAATAGGTAGTTTATCCT
1 AATAATCGAGTGACCA-AAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCT
1863789 AAAT
65 AAAT
* * * *
1863793 AATAATCGAGTGATCAAAACATAAATTAAATAATATATAAGTGACCAAAGAGGTAGTTTTCCCTA
1 AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
1863858 AAT
66 AAT
*
1863861 AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTAACCAAATAGGTAGTTTACCCTA
1 AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
1863926 AAT
66 AAT
* * * *
1863929 AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGATCAAATATGAAGTTTACTCTA
1 AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
1863994 AA
66 AA
1863996 AAATCCCGTA
Statistics
Matches: 229, Mismatches: 30, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
63 47 0.21
64 3 0.01
65 2 0.01
66 2 0.01
67 3 0.01
68 172 0.75
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.29
Consensus pattern (68 bp):
AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
AAT
Found at i:1863972 original size:31 final size:31
Alignment explanation
Indices: 1863869--1863977 Score: 83
Period size: 31 Copynumber: 3.3 Consensus size: 31
1863859 ATAATAATCG
1863869 AGTGACCAAAACATAAATTAGATAATATATA
1 AGTGACCAAAACATAAATTAGATAATATATA
* ** ** ** *
1863900 AGTAACCAAATAGGTAGTTTACCCTAAATAATAATCG
1 AGTGACCAAA-ACATAAATTA-GAT-AAT-AT-AT-A
1863937 AGTGACCAAAACATAAATTAGATAATATATA
1 AGTGACCAAAACATAAATTAGATAATATATA
*
1863968 AGTGATCAAA
1 AGTGACCAAA
1863978 TATGAAGTTT
Statistics
Matches: 55, Mismatches: 17, Indels: 12
0.65 0.20 0.14
Matches are distributed among these distances:
31 18 0.33
32 8 0.15
33 3 0.05
34 6 0.11
35 3 0.05
36 8 0.15
37 9 0.16
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (31 bp):
AGTGACCAAAACATAAATTAGATAATATATA
Found at i:1865267 original size:5 final size:5
Alignment explanation
Indices: 1865257--1865290 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1865247 TAAAGCAGAT
* *
1865257 GGATG GGATG GGATA GGATA GGATA GGATA GGAT
1 GGATA GGATA GGATA GGATA GGATA GGATA GGAT
1865291 TTACCTTGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.47, T:0.21
Consensus pattern (5 bp):
GGATA
Found at i:1867331 original size:36 final size:35
Alignment explanation
Indices: 1867290--1867357 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 35
1867280 ATACTTGTGG
* *
1867290 CGGTTGTTGTTGATGTGGCTGTTGTGGCAGCGGCGC
1 CGGTTGCTGCTGATGTGGCTGTTGTGG-AGCGGCGC
* *
1867326 CGGTTGCTGCTGCTGTTGCTGTTGTGGAGCGG
1 CGGTTGCTGCTGATGTGGCTGTTGTGGAGCGG
1867358 TGAAGTTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 5 0.18
36 23 0.82
ACGTcount: A:0.04, C:0.18, G:0.44, T:0.34
Consensus pattern (35 bp):
CGGTTGCTGCTGATGTGGCTGTTGTGGAGCGGCGC
Found at i:1873303 original size:22 final size:21
Alignment explanation
Indices: 1873223--1873303 Score: 65
Period size: 22 Copynumber: 3.7 Consensus size: 21
1873213 CAATACATGG
* *
1873223 AAGTGCGTTAGCACTGGTACTA
1 AAGTGCCTTAGCACT-GAACTA
* * *
1873245 AAGTGCCTCAGTACTGATACGA
1 AAGTGCCTTAGCACTGA-ACTA
*
1873267 AAGTGCATTCA-CACTGCAACTA
1 AAGTGCCTT-AGCACTG-AACTA
1873289 AAGTGCCTTAGCACT
1 AAGTGCCTTAGCACT
1873304 ATTGGCATAT
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
21 2 0.04
22 41 0.91
23 2 0.04
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (21 bp):
AAGTGCCTTAGCACTGAACTA
Found at i:1884695 original size:25 final size:26
Alignment explanation
Indices: 1884658--1884708 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1884648 ACATGATTTT
1884658 ATTTTAAAGGAG-ATGAATCTATAAA
1 ATTTTAAAGGAGAATGAATCTATAAA
*
1884683 ATTTT-AAGAGAGAATGAATTTATAAA
1 ATTTTAAAG-GAGAATGAATCTATAAA
1884709 CCTCAAAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 3 0.13
25 8 0.35
26 12 0.52
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.33
Consensus pattern (26 bp):
ATTTTAAAGGAGAATGAATCTATAAA
Found at i:1889024 original size:32 final size:32
Alignment explanation
Indices: 1888974--1889034 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
1888964 GAGGTGTGAA
* *
1888974 CGTTTAATGTCAAATGATTAAATTATCTTGAG
1 CGTTCAATATCAAATGATTAAATTATCTTGAG
1889006 CGTTCAATATCAAATGATTAAATTATCTT
1 CGTTCAATATCAAATGATTAAATTATCTT
1889035 TAAATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41
Consensus pattern (32 bp):
CGTTCAATATCAAATGATTAAATTATCTTGAG
Found at i:1894912 original size:35 final size:35
Alignment explanation
Indices: 1894859--1894932 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
1894849 CGTCACGAAC
*
1894859 AGTAAGACCCTGAACACAAAGCCGAGGAGCCTGCA
1 AGTAAGACCCTGAACACAAAGCCGAGGAGCCTCCA
*
1894894 AGTAAGGCCCT-AAGCACAAAGCCGAGGAGCCTCCA
1 AGTAAGACCCTGAA-CACAAAGCCGAGGAGCCTCCA
1894929 AGTA
1 AGTA
1894933 TTCTTCCTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 2 0.06
35 34 0.94
ACGTcount: A:0.36, C:0.28, G:0.26, T:0.09
Consensus pattern (35 bp):
AGTAAGACCCTGAACACAAAGCCGAGGAGCCTCCA
Found at i:1895041 original size:23 final size:22
Alignment explanation
Indices: 1895014--1895099 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 22
1895004 ATTCAAGTCA
1895014 AGTATCATATCAGAATCAGGTC
1 AGTATCATATCAGAATCAGGTC
* *
1895036 ATGTATCAAATCAGAATCCATGTC
1 A-GTATCATATCAGAAT-CAGGTC
*
1895060 AATATCATATCAGAATCTAGGTC
1 AGTATCATATCAGAATC-AGGTC
* *
1895083 AGTTACCATAACAGAAT
1 AG-TATCATATCAGAAT
1895100 TCAAATCAGA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
22 2 0.04
23 32 0.62
24 18 0.35
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (22 bp):
AGTATCATATCAGAATCAGGTC
Found at i:1900024 original size:18 final size:18
Alignment explanation
Indices: 1900001--1900046 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
1899991 AACATTCTCA
*
1900001 GTAATCTTATTCCCGCTG
1 GTAATCTTATTCCCACTG
* *
1900019 GTAATCATATTCCCATTG
1 GTAATCTTATTCCCACTG
*
1900037 ATAATCTTAT
1 GTAATCTTAT
1900047 ATTTTGTTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (18 bp):
GTAATCTTATTCCCACTG
Found at i:1901804 original size:31 final size:31
Alignment explanation
Indices: 1901768--1901827 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1901758 AACTTAAAAG
* *
1901768 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
1901799 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
1901828 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:1902366 original size:16 final size:15
Alignment explanation
Indices: 1902338--1902388 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1902328 TATAAAATTT
1902338 TAATAATATATAAAA
1 TAATAATATATAAAA
*
1902353 TAATTATATGATAAAA
1 TAATAATAT-ATAAAA
* *
1902369 TTAAT-ATCTATAATA
1 -TAATAATATATAAAA
1902384 TAATA
1 TAATA
1902389 TTAAAAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 4 0.13
15 13 0.43
16 9 0.30
17 4 0.13
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (15 bp):
TAATAATATATAAAA
Found at i:1902432 original size:28 final size:27
Alignment explanation
Indices: 1902400--1902488 Score: 83
Period size: 26 Copynumber: 3.1 Consensus size: 27
1902390 TAAAAATTAT
1902400 TTAATTTATTTAAAAATTAATATTAAAA
1 TTAA-TTATTTAAAAATTAATATTAAAA
* *
1902428 TTAA-TATCT-ATAATATAATATTAATAAA
1 TTAATTATTTAAAAAT-TAATATT-A-AAA
*
1902456 TTTAATTATATAAAAAATTAATATTAAAA
1 -TTAATTAT-TTAAAAATTAATATTAAAA
1902485 TTAA
1 TTAA
1902489 AATCAAATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
25 4 0.08
26 11 0.22
27 1 0.02
28 11 0.22
29 7 0.14
30 4 0.08
31 7 0.14
32 4 0.08
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (27 bp):
TTAATTATTTAAAAATTAATATTAAAA
Found at i:1902448 original size:14 final size:12
Alignment explanation
Indices: 1902364--1902511 Score: 76
Period size: 12 Copynumber: 11.8 Consensus size: 12
1902354 AATTATATGA
1902364 TAAAATTAATAT
1 TAAAATTAATAT
*
1902376 CTATAATATAATAT
1 -TAAAAT-TAATAT
1902390 TAAAAATT-AT-T
1 T-AAAATTAATAT
*
1902401 T--AATTTAT-T
1 TAAAATTAATAT
1902410 TAAAAATTAATAT
1 T-AAAATTAATAT
1902423 TAAAATTAATAT
1 TAAAATTAATAT
*
1902435 CTATAATATAATAT
1 -TAAAAT-TAATAT
1902449 TAATAAATTTAATTAT
1 T-A-AAA-TTAA-TAT
1902465 ATAAAAAATTAATAT
1 -T--AAAATTAATAT
*
1902480 TAAAATTAA-AA
1 TAAAATTAATAT
*
1902491 TCAAATATAATA-
1 TAAAAT-TAATAT
1902503 TAAAATTAA
1 TAAAATTAA
1902512 ATATAAAACC
Statistics
Matches: 110, Mismatches: 8, Indels: 36
0.71 0.05 0.23
Matches are distributed among these distances:
8 4 0.04
9 4 0.04
11 11 0.10
12 35 0.32
13 16 0.15
14 18 0.16
15 8 0.07
16 8 0.07
17 4 0.04
18 2 0.02
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAATTAATAT
Found at i:1902452 original size:20 final size:20
Alignment explanation
Indices: 1902363--1902453 Score: 57
Period size: 20 Copynumber: 4.6 Consensus size: 20
1902353 TAATTATATG
*
1902363 ATAAAATTAATATCTATAAT
1 ATAATATTAATATCTATAAT
*
1902383 ATAATATTAAAAAT-TATTTAAT
1 ATAATATT-AATATCTA--TAAT
* **
1902405 -TTAT-TTAA-AAAT-TAAT
1 ATAATATTAATATCTATAAT
*
1902421 ATTAAAATTAATATCTATAAT
1 A-TAATATTAATATCTATAAT
1902442 ATAATATTAATA
1 ATAATATTAATA
1902454 AATTTAATTA
Statistics
Matches: 53, Mismatches: 9, Indels: 18
0.66 0.11 0.22
Matches are distributed among these distances:
16 4 0.08
18 3 0.06
19 7 0.13
20 23 0.43
21 12 0.23
22 4 0.08
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAATATTAATATCTATAAT
Found at i:1902486 original size:57 final size:58
Alignment explanation
Indices: 1902331--1902507 Score: 215
Period size: 57 Copynumber: 3.1 Consensus size: 58
1902321 TAAAAAATAT
1902331 AAAAT-TTTAATAATATATAAAATAATT-ATATGATAAAATTAATATCTATAATATAATATTA
1 AAAATATTTAAT--TATATAAAA-AATTAATAT--TAAAATTAATATCTATAATATAATATTA
*
1902392 AAAATTATTTAATT-TATTTAAAAATTAATATTAAAATTAATATCTATAATATAATATTA
1 AAAA-TATTTAATTATA-TAAAAAATTAATATTAAAATTAATATCTATAATATAATATTA
* *
1902451 ATAA-ATTTAATTATATAAAAAATTAATATTAAAATTAAAATC-A-AATATAATA-TA
1 AAAATATTTAATTATATAAAAAATTAATATTAAAATTAATATCTATAATATAATATTA
1902505 AAA
1 AAA
1902508 TTAAATATAA
Statistics
Matches: 106, Mismatches: 5, Indels: 17
0.83 0.04 0.13
Matches are distributed among these distances:
54 4 0.04
55 9 0.08
56 1 0.01
57 33 0.31
58 2 0.02
59 31 0.29
60 6 0.06
61 13 0.12
62 1 0.01
63 6 0.06
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.41
Consensus pattern (58 bp):
AAAATATTTAATTATATAAAAAATTAATATTAAAATTAATATCTATAATATAATATTA
Found at i:1902513 original size:57 final size:58
Alignment explanation
Indices: 1902289--1902513 Score: 184
Period size: 57 Copynumber: 3.8 Consensus size: 58
1902279 ACAAATCCAA
* * *
1902289 AAAAAATTATATTTAACTT-AAATC-A-AA-ATAATTAAAAAATATAAAATTTTAATAATATAT
1 AAAAAATTATATTAAAATTAAAATCTATAATATAA-TATAAAAT-T-AAA-TTTAAT--TATAT
*
1902349 AAAATAATTATATGATAAAATTAATATCTATAATATAATATTAAAAATT--ATTTAATT-TATT
1 AAAA-AATTATAT--TAAAATTAAAATCTATAATATAATA-T-AAAATTAAATTTAATTATA-T
* * *
1902410 TAAAAATTAATATTAAAATTAATATCTATAATATAATAT-TAA-TAAATTTAATTATAT
1 AAAAAATT-ATATTAAAATTAAAATCTATAATATAATATAAAATTAAATTTAATTATAT
1902467 AAAAAATTAATATTAAAATTAAAATC-A-AATATAATATAAAATTAAAT
1 AAAAAATT-ATATTAAAATTAAAATCTATAATATAATATAAAATTAAAT
1902514 ATAAAACCCC
Statistics
Matches: 140, Mismatches: 9, Indels: 35
0.76 0.05 0.19
Matches are distributed among these distances:
55 11 0.08
56 5 0.04
57 38 0.27
58 3 0.02
59 25 0.18
60 10 0.07
61 17 0.12
63 11 0.08
64 5 0.04
65 1 0.01
66 4 0.03
67 5 0.04
68 5 0.04
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (58 bp):
AAAAAATTATATTAAAATTAAAATCTATAATATAATATAAAATTAAATTTAATTATAT
Found at i:1902514 original size:12 final size:12
Alignment explanation
Indices: 1902459--1902519 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
1902449 TAATAAATTT
* *
1902459 AATTATATAAAA
1 AATTAAATATAA
1902471 AATT-AATATTAA
1 AATTAAATA-TAA
*
1902483 AATTAAA-ATCA
1 AATTAAATATAA
1902494 AA-TATAATATAA
1 AATTA-AATATAA
1902506 AATTAAATATAA
1 AATTAAATATAA
1902518 AA
1 AA
1902520 CCCCATGTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
10 2 0.05
11 9 0.22
12 25 0.62
13 4 0.10
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (12 bp):
AATTAAATATAA
Found at i:1906615 original size:25 final size:25
Alignment explanation
Indices: 1906579--1906630 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1906569 GTATTGGTCC
*
1906579 CCCGTCCTCGTCCCCGTTTAAAAAA
1 CCCGTCCTCGTCCCCGCTTAAAAAA
1906604 CCCGTACC-CGTCCCCGCTTAAAAAA
1 CCCGT-CCTCGTCCCCGCTTAAAAAA
1906629 CC
1 CC
1906631 GCGGGGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.25, C:0.44, G:0.12, T:0.19
Consensus pattern (25 bp):
CCCGTCCTCGTCCCCGCTTAAAAAA
Found at i:1906928 original size:30 final size:30
Alignment explanation
Indices: 1906889--1906961 Score: 121
Period size: 30 Copynumber: 2.4 Consensus size: 30
1906879 TTACTAAACT
1906889 CGTCCCCGTTTAACATAAACAGTTTT-TCC
1 CGTCCCCGTTTAACATAAACAGTTTTCTCC
*
1906918 CGTCCCCCGTTTAGCATAAACAGTTTTCTCC
1 CGT-CCCCGTTTAACATAAACAGTTTTCTCC
1906949 CGTCCCCGTTTAA
1 CGTCCCCGTTTAA
1906962 TTCGATTTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
29 3 0.08
30 31 0.77
31 6 0.15
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.33
Consensus pattern (30 bp):
CGTCCCCGTTTAACATAAACAGTTTTCTCC
Found at i:1907535 original size:2 final size:2
Alignment explanation
Indices: 1907528--1907560 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1907518 GTACGTGACA
1907528 AT AT 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 AT AT A
1907561 CATGATCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1914329 original size:17 final size:18
Alignment explanation
Indices: 1914292--1914332 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1914282 ATATTATGTA
*
1914292 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
1914310 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
1914327 TTTACT
1 TTTACT
1914333 AATATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:1920380 original size:51 final size:50
Alignment explanation
Indices: 1920278--1920385 Score: 112
Period size: 51 Copynumber: 2.1 Consensus size: 50
1920268 CCCTACGTGG
* **
1920278 CGTATAGCGCGGATCAGGGGGCGCGCTATACACATGTATAACCCATGTCAA
1 CGTATAGCGCGGATCAGGGGGCGCGCTATACACACGTAT-ACCCAAATCAA
* *
1920329 CGTATAGCGCGG-TACAGGGGGCGCGCTATACCCCACGTAGT-GCCAAATCAA
1 CGTATAGCGCGGAT-CAGGGGGCGCGCTATA-CACACGTA-TACCCAAATCAA
*
1920380 CATATA
1 CGTATA
1920386 ACACGGGGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
50 1 0.02
51 40 0.83
52 6 0.12
53 1 0.02
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.19
Consensus pattern (50 bp):
CGTATAGCGCGGATCAGGGGGCGCGCTATACACACGTATACCCAAATCAA
Found at i:1924382 original size:21 final size:18
Alignment explanation
Indices: 1924342--1924382 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 18
1924332 CAAAAAGAAT
1924342 ATTAAAAAAACATTAGTA
1 ATTAAAAAAACATTAGTA
1924360 ATTAAAATAAACTATTAAGTA
1 ATTAAAA-AAAC-ATT-AGTA
1924381 AT
1 AT
1924383 AAGTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 4 0.20
20 3 0.15
21 6 0.30
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTAAAAAAACATTAGTA
Found at i:1932188 original size:20 final size:21
Alignment explanation
Indices: 1932165--1932204 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1932155 TATATTTTAA
1932165 ATTTT-TATTAAAAATTTATT
1 ATTTTCTATTAAAAATTTATT
* *
1932185 ATTTTCTTTTAAAAGTTTAT
1 ATTTTCTATTAAAAATTTAT
1932205 AAGTTCATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (21 bp):
ATTTTCTATTAAAAATTTATT
Done.