Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008053.1 Hibiscus syriacus cultivar Beakdansim tig00110548_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: 6772376
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 32
Found at i:4374840 original size:22 final size:23
Alignment explanation
Indices: 4374793--4374856 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
4374783 TAATTATTAA
* *
4374793 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
4374814 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
4374837 -ATATTTTTAATATTATAATA
1 AATATTTATAATAATATAATA
4374857 AAATAATCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 11 0.30
22 22 0.59
23 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:4374954 original size:28 final size:28
Alignment explanation
Indices: 4374868--4374965 Score: 94
Period size: 28 Copynumber: 3.4 Consensus size: 28
4374858 AATAATCAAT
4374868 TATATTATAATAATATA-AGATATTATATT-
1 TATATT-TAATAATATATA-ATATTAT-TTA
* * *
4374897 TTTATTTTAATAAATATATAATGTTTTTTA
1 TATA-TTTAAT-AATATATAATATTATTTA
4374927 TATATTTAATAATGA-ATAATATTATTTA
1 TATATTTAATAAT-ATATAATATTATTTA
4374955 TATATTTAATA
1 TATATTTAATA
4374966 TTAATATACT
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
28 25 0.43
29 16 0.28
30 16 0.28
31 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (28 bp):
TATATTTAATAATATATAATATTATTTA
Found at i:4375017 original size:23 final size:22
Alignment explanation
Indices: 4374991--4375034 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4374981 AATAATATTT
4374991 TAATAAAGATATTTAAAATATAC
1 TAATAAAGAT-TTTAAAATATAC
* *
4375014 TAATTAATATTTTAAAATATA
1 TAATAAAGATTTTAAAATATA
4375035 ATATAACACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
TAATAAAGATTTTAAAATATAC
Found at i:4375153 original size:13 final size:13
Alignment explanation
Indices: 4375115--4375153 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
4375105 TATTAATATT
*
4375115 TTTATTAATAAAA
1 TTTAATAATAAAA
*
4375128 TTATAAAAATAAAA
1 TT-TAATAATAAAA
4375142 TTTAATAATAAA
1 TTTAATAATAAA
4375154 TAAATTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTAATAATAAAA
Found at i:4375420 original size:15 final size:15
Alignment explanation
Indices: 4375378--4375448 Score: 72
Period size: 15 Copynumber: 4.8 Consensus size: 15
4375368 TTCAAGAAAT
*
4375378 GTAATTCATTGTCCA
1 GTAATTCATTTTCCA
* **
4375393 G-ATTTCAAATTCCA
1 GTAATTCATTTTCCA
4375407 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
* **
4375422 ATAATTCAAATTCCA
1 GTAATTCATTTTCCA
4375437 GTAATTCATTTT
1 GTAATTCATTTT
4375449 TCAGAAAACC
Statistics
Matches: 42, Mismatches: 13, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
14 10 0.24
15 32 0.76
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.42
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:4375432 original size:30 final size:29
Alignment explanation
Indices: 4375378--4375453 Score: 109
Period size: 30 Copynumber: 2.6 Consensus size: 29
4375368 TTCAAGAAAT
*
4375378 GTAATTCATTGTCCAGATTTCAAATTCCA
1 GTAATTCATTTTCCAGATTTCAAATTCCA
4375407 GTAATTCATTTTCCA-ATAATTCAAATTCCA
1 GTAATTCATTTTCCAGAT--TTCAAATTCCA
*
4375437 GTAATTCATTTTTCAGA
1 GTAATTCATTTTCCAGA
4375454 AAACCAATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 2 0.05
29 14 0.33
30 25 0.60
31 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (29 bp):
GTAATTCATTTTCCAGATTTCAAATTCCA
Found at i:4377915 original size:16 final size:16
Alignment explanation
Indices: 4377894--4377927 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4377884 GATTCACATC
*
4377894 TTAAATTTATTAAAAA
1 TTAAATTAATTAAAAA
*
4377910 TTAAATTAATTTAAAA
1 TTAAATTAATTAAAAA
4377926 TT
1 TT
4377928 TATATTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAATTAATTAAAAA
Found at i:4379111 original size:16 final size:16
Alignment explanation
Indices: 4379073--4379103 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
4379063 TATACATTTC
4379073 AATAATCTTTTATTCT
1 AATAATCTTTTATTCT
4379089 AATAATCTTTTATTC
1 AATAATCTTTTATTC
4379104 CTTTAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (16 bp):
AATAATCTTTTATTCT
Found at i:4379230 original size:20 final size:20
Alignment explanation
Indices: 4379181--4379230 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
4379171 TAATACTATT
*
4379181 CACTGGTAATCTTTTATTTC
1 CACTGGTAATATTTTATTTC
**
4379201 CACTAATAATATTTTATTTC
1 CACTGGTAATATTTTATTTC
*
4379221 TACTGGTAAT
1 CACTGGTAAT
4379231 CTTACATTTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (20 bp):
CACTGGTAATATTTTATTTC
Found at i:4380108 original size:17 final size:17
Alignment explanation
Indices: 4380060--4380099 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
4380050 CGTAGATGGG
4380060 CACTCGGTAATTTATAA
1 CACTCGGTAATTTATAA
4380077 CACTCGGTAATTTATAA
1 CACTCGGTAATTTATAA
4380094 CACTCG
1 CACTCG
4380100 AACTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Consensus pattern (17 bp):
CACTCGGTAATTTATAA
Found at i:4380254 original size:30 final size:27
Alignment explanation
Indices: 4380214--4380319 Score: 76
Period size: 29 Copynumber: 3.9 Consensus size: 27
4380204 CAATATTCTA
*
4380214 AGCTTCGCTAAGCTTCACCTTTTCTCTCAT
1 AGCTTTGCTAAGCTT-A-C-TTTCTCTCAT
*
4380244 AGCTTTGCTAAG-TTA-TTTCTCGTCCT
1 AGCTTTGCTAAGCTTACTTTCTC-TCAT
* * * *
4380270 TGCTTTGCTAAGCTTTTTCATTCTCTAAT
1 AGCTTTGCTAAGC--TTACTTTCTCTCAT
4380299 AGCTTTGCTAAGC-TA-TTTCTC
1 AGCTTTGCTAAGCTTACTTTCTC
4380320 CTTTTGGCTT
Statistics
Matches: 61, Mismatches: 10, Indels: 15
0.71 0.12 0.17
Matches are distributed among these distances:
25 11 0.18
26 15 0.25
28 1 0.02
29 18 0.30
30 16 0.26
ACGTcount: A:0.17, C:0.25, G:0.12, T:0.45
Consensus pattern (27 bp):
AGCTTTGCTAAGCTTACTTTCTCTCAT
Found at i:4380330 original size:55 final size:57
Alignment explanation
Indices: 4380235--4380347 Score: 151
Period size: 55 Copynumber: 2.0 Consensus size: 57
4380225 GCTTCACCTT
* * *
4380235 TTCTCTCATAGCTTTGCTAAGTTATTTCTCGTCCTTGCTTTGCTAAG-CTTTT-TCA
1 TTCTCTAATAGCTTTGCTAAGCTATTTCTCCTCCTTGCTTTGCTAAGTCTTTTCTCA
* *
4380290 TTCTCTAATAGCTTTGCTAAGCTATTTCTCCT-TTTGGCTTTTCTAAGTCTTTTCTCA
1 TTCTCTAATAGCTTTGCTAAGCTATTTCTCCTCCTT-GCTTTGCTAAGTCTTTTCTCA
4380347 T
1 T
4380348 ATTACTTCTC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
54 2 0.04
55 39 0.78
56 5 0.10
57 4 0.08
ACGTcount: A:0.15, C:0.23, G:0.12, T:0.50
Consensus pattern (57 bp):
TTCTCTAATAGCTTTGCTAAGCTATTTCTCCTCCTTGCTTTGCTAAGTCTTTTCTCA
Found at i:4381577 original size:26 final size:26
Alignment explanation
Indices: 4381548--4381632 Score: 84
Period size: 26 Copynumber: 3.2 Consensus size: 26
4381538 TAAGCTTCAC
*
4381548 ATTTTCTCTCATAGCTTTACTAAGCT
1 ATTTTCTCTCATAGCTTTGCTAAGCT
* *
4381574 A-TTTCTCGTCCTTGCTTTGCTAAGCT
1 ATTTTCTC-TCATAGCTTTGCTAAGCT
4381600 -TTTTCATTCTCTAATAGCTTTGCTAAGCT
1 ATTTTC--TCTC--ATAGCTTTGCTAAGCT
4381629 ATTT
1 ATTT
4381633 CTCATTTTGG
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
25 6 0.13
26 20 0.43
27 2 0.04
28 2 0.04
29 14 0.30
30 3 0.06
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.48
Consensus pattern (26 bp):
ATTTTCTCTCATAGCTTTGCTAAGCT
Found at i:4385504 original size:5 final size:5
Alignment explanation
Indices: 4385490--4385519 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
4385480 TGATTCCTGG
4385490 AAAAT AAAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAA
4385520 CATGCTCGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:4400483 original size:55 final size:55
Alignment explanation
Indices: 4400417--4400838 Score: 398
Period size: 55 Copynumber: 7.8 Consensus size: 55
4400407 GTGAAGCAAA
* *
4400417 TGAAGATTGTTCGAGTCTTATACTCTCTGAACAAATAGAGAGCAGACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * * * * *
4400472 TGAAGATTGTTCAAGTCTCATACTCTCTTAAGCAATAGGGAGCAGACATGAATAT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * *
4400527 TGAAAATTGTTCGAGTCTAATACTCTCTGAAGAAATAGGGAGCAGACACGAATGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * * *
4400582 TGAAAATTATTTGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * * * *
4400637 TGAAGGTTGTTCAAGTCATATACTCTCTGAAAAAATAGGGAGCGGACACGTTTGAT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG-T
* * * *
4400693 TGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATGGGGAGCGGACAC-ATTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA-TTGT
* * * * ** *
4400744 TGAAGA-T-TT--AGTCCTATACTCTCTGAAGGAATAGAGAACAGACTTG-TTTT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * *
4400794 ATGAAGATTGTTTGAGTTTTATACTCCCTGAAGCAAA-AGGGAGCA
1 -TGAAGATTGTTCGAGTCTTATACTCTCTGAAG-AAATAGGGAGCA
4400839 AACCCAGTGG
Statistics
Matches: 306, Mismatches: 51, Indels: 20
0.81 0.14 0.05
Matches are distributed among these distances:
50 3 0.01
51 43 0.14
52 38 0.12
53 4 0.01
55 210 0.69
56 8 0.03
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (55 bp):
TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
Found at i:4416852 original size:51 final size:53
Alignment explanation
Indices: 4416735--4416853 Score: 134
Period size: 51 Copynumber: 2.2 Consensus size: 53
4416725 CATAATGAAG
* * * *
4416735 ATTGTTAAACATCTTGACATAGTTAGGTTGCTTGCACGAGGTTTGTGTTGTTTTA
1 ATTGTTATACATCTTAACATAGTTA-G-TGCTTACACGAGGTATGTGTTGTTTTA
* * * *
4416790 AGTATTGTACATCTTAACATAGTTA-TG-TTACATGAGGTATGTGTTGTTTTA
1 ATTGTTATACATCTTAACATAGTTAGTGCTTACACGAGGTATGTGTTGTTTTA
4416841 ATTGTTATACATC
1 ATTGTTATACATC
4416854 GTACTTTTAT
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
51 31 0.58
52 2 0.04
55 20 0.38
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (53 bp):
ATTGTTATACATCTTAACATAGTTAGTGCTTACACGAGGTATGTGTTGTTTTA
Found at i:4416950 original size:2 final size:2
Alignment explanation
Indices: 4416943--4416975 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4416933 TACATTTGAG
4416943 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
4416976 CATTATTCTT
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:4432771 original size:19 final size:19
Alignment explanation
Indices: 4432744--4432786 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
4432734 ATTATAAATA
* *
4432744 TATTAAAATTAATATATTC
1 TATTAAAATAAAAATATTC
* *
4432763 TATTGAAATAAAAATATTG
1 TATTAAAATAAAAATATTC
4432782 TATTA
1 TATTA
4432787 TGTTTTTTAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (19 bp):
TATTAAAATAAAAATATTC
Found at i:4432921 original size:30 final size:30
Alignment explanation
Indices: 4432885--4432941 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
4432875 ATTATTCATT
* *
4432885 ATTAATAATTAA-ATAACATTTTTTTATGAA
1 ATTAATAAATAATATAA-ATTTATTTATGAA
4432915 ATTAATAAATAATATAAATTTATTTAT
1 ATTAATAAATAATATAAATTTATTTAT
4432942 ACTTTATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (30 bp):
ATTAATAAATAATATAAATTTATTTATGAA
Found at i:4433198 original size:17 final size:16
Alignment explanation
Indices: 4433178--4433209 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
4433168 TAAAAAATAT
4433178 TAATTAATATATTTTAA
1 TAATTAATAT-TTTTAA
4433195 TAATTAATATTTTTA
1 TAATTAATATTTTTA
4433210 TTAAAATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAATTAATATTTTTAA
Found at i:4437639 original size:20 final size:20
Alignment explanation
Indices: 4437616--4437654 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4437606 AAATATAAAC
*
4437616 AAATAAAATTAAAACAATAA
1 AAATAAAACTAAAACAATAA
**
4437636 AAATACCACTAAAACAATA
1 AAATAAAACTAAAACAATA
4437655 TATTTTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.69, C:0.13, G:0.00, T:0.18
Consensus pattern (20 bp):
AAATAAAACTAAAACAATAA
Found at i:4439079 original size:3 final size:3
Alignment explanation
Indices: 4439071--4439146 Score: 136
Period size: 3 Copynumber: 25.7 Consensus size: 3
4439061 TTAATATATT
*
4439071 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4439119 TAA T-A TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
4439147 TGGTAAAAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 68 0.97
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4439877 original size:112 final size:112
Alignment explanation
Indices: 4439280--4439918 Score: 870
Period size: 114 Copynumber: 5.6 Consensus size: 112
4439270 ATTGAATAAA
* * ** *
4439280 TTCTTC-TCTTTCTTCAGATGAATTCTTCTCATTATGAACTTTCTGCTGGGGATGATGATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCT-CTGGAAAAGATGATCCATC
* * * *
4439344 AAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
64 AAATGATGAATTCAGGAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* * *
4439393 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAAC-TCTACCTGGCAATGTTGATCC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTTCT--CTGGAAAAGATGATCC
* * * * *
4439457 ATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTTATTATGAAC
61 ATCAAATGATGAATTCAGGAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
*
4439509 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTTCTCTGGAAAAGATGATCCATCA
* *
4439574 ATTTGATGAATTCAGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
65 A-ATGATGAATTCAGGAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* *
4439623 TTCTTCTTCCTTCTTCAGATGGGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTTCTCTGGAAAAGATGATCCATCA
* * *
4439688 ATTTGATGACTTCAGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
65 A-ATGATGAATTCAGGAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
*
4439737 TTCTTCTTCCTTCTTCAGATGACG-TCTTCTCATTATGAACTTCTCTGGAAAAGCTGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGA-GTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCA
* *
4439801 AATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
65 AATGATGAATTCAGGAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* **
4439849 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGCTGATCTTTCAA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCAA
4439914 ATGAT
66 ATGAT
4439919 AGATTTGAAT
Statistics
Matches: 486, Mismatches: 30, Indels: 21
0.91 0.06 0.04
Matches are distributed among these distances:
111 1 0.00
112 108 0.22
113 66 0.14
114 201 0.41
115 7 0.01
116 84 0.17
117 19 0.04
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (112 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCAA
ATGATGAATTCAGGAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
Found at i:4440755 original size:82 final size:83
Alignment explanation
Indices: 4440550--4441758 Score: 1973
Period size: 82 Copynumber: 14.7 Consensus size: 83
4440540 CCTACTGAAT
* * ** *
4440550 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATGTTCCGAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTCTAAACTCA
4440614 ATGATTGGTTCTG-CCAAAC
65 ATGATT-GTTCTGTCCAAAC
* * *
4440633 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATTGGCAAATTCATCTTCTAAACTCAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
4440698 TGATTGTTCTGTCC-AAC
66 TGATTGTTCTGTCCAAAC
* * *
4440715 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
4440780 TGATTGGTTCTG-CCAAAC
66 TGATT-GTTCTGTCCAAAC
*
4440798 TAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
4440863 TGATTGTTCTGTCC-AAC
66 TGATTGTTCTGTCCAAAC
* * *
4440880 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
4440945 TGATTGGTTCTG-CCAAAC
66 TGATT-GTTCTGTCCAAAC
* *
4440963 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAATTCAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
4441028 TGATTGTTCTGTCC-AAC
66 TGATTGTTCTGTCCAAAC
*
4441045 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTCTAAACTCA
4441109 ATGATTGTTCTG-CCAAAC
65 ATGATTGTTCTGTCCAAAC
4441127 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
4441192 TGATTGTTCTGTCC-AAC
66 TGATTGTTCTGTCCAAAC
* * *
4441209 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
4441274 TGATTGGTTCT-TCCAAAC
66 TGATT-GTTCTGTCCAAAC
4441292 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
4441357 TGATTGTTCTGTCC-AAC
66 TGATTGTTCTGTCCAAAC
* * *
4441374 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
4441439 TGATTGGTTCTG-CCAAAC
66 TGATT-GTTCTGTCCAAAC
4441457 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
4441522 TGATTGTTCTGTCC-AAC
66 TGATTGTTCTGTCCAAAC
* * *
4441539 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
4441604 TGATTGGTTCTG-CCAAAC
66 TGATT-GTTCTGTCCAAAC
*
4441622 CATATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
4441687 TGATTGTTCTGTCC-AAC
66 TGATTGTTCTGTCCAAAC
*
4441704 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTT
4441759 TCATTTAATT
Statistics
Matches: 1061, Mismatches: 44, Indels: 43
0.92 0.04 0.04
Matches are distributed among these distances:
81 4 0.00
82 600 0.57
83 455 0.43
84 2 0.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
TGATTGTTCTGTCCAAAC
Found at i:4440822 original size:165 final size:165
Alignment explanation
Indices: 4440550--4441758 Score: 2217
Period size: 165 Copynumber: 7.3 Consensus size: 165
4440540 CCTACTGAAT
* * * **
4440550 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATGTTCCGAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCTAAATTCA
* * *
4440614 ATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATTGGCAA
65 CTGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAA
*
4440679 ATTCATCTTCTAAACTCACTGATTGTTCTGTCCAAC
130 ATTCATCTTCTAAACTCAATGATTGTTCTGTCCAAC
4440715 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAC
*
4440780 TGATTGGTTCTGCCAAACTAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAA
66 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAA
4440845 TTCATCTTCTAAACTCAATGATTGTTCTGTCCAAC
131 TTCATCTTCTAAACTCAATGATTGTTCTGTCCAAC
4440880 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAC
4440945 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAA
66 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAA
* *
4441010 TTCATCTTCTAAATTCACTGATTGTTCTGTCCAAC
131 TTCATCTTCTAAACTCAATGATTGTTCTGTCCAAC
* * *
4441045 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCTAAATTCA
*
4441109 ATGATT-GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAA
65 CTGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAA
4441173 ATTCATCTTCTAAACTCAATGATTGTTCTGTCCAAC
130 ATTCATCTTCTAAACTCAATGATTGTTCTGTCCAAC
4441209 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAC
*
4441274 TGATTGGTTCTTCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAA
66 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAA
4441339 TTCATCTTCTAAACTCAATGATTGTTCTGTCCAAC
131 TTCATCTTCTAAACTCAATGATTGTTCTGTCCAAC
4441374 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAC
4441439 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAA
66 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAA
4441504 TTCATCTTCTAAACTCAATGATTGTTCTGTCCAAC
131 TTCATCTTCTAAACTCAATGATTGTTCTGTCCAAC
4441539 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAC
*
4441604 TGATTGGTTCTGCCAAACCATATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAA
66 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAA
4441669 TTCATCTTCTAAACTCAATGATTGTTCTGTCCAAC
131 TTCATCTTCTAAACTCAATGATTGTTCTGTCCAAC
4441704 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTT
4441759 TCATTTAATT
Statistics
Matches: 1014, Mismatches: 26, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
164 157 0.15
165 855 0.84
166 2 0.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (165 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAC
TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAA
TTCATCTTCTAAACTCAATGATTGTTCTGTCCAAC
Found at i:4442562 original size:16 final size:16
Alignment explanation
Indices: 4442541--4442580 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
4442531 GAATTTCCAA
4442541 AAATAAATTG-ACTCTC
1 AAATAAATTGAACT-TC
*
4442557 AAATAAATTGAACTTG
1 AAATAAATTGAACTTC
4442573 AAATAAAT
1 AAATAAAT
4442581 AGAATTGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (16 bp):
AAATAAATTGAACTTC
Found at i:4442938 original size:8 final size:8
Alignment explanation
Indices: 4442906--4442945 Score: 50
Period size: 7 Copynumber: 5.4 Consensus size: 8
4442896 CCTTTTCTTT
4442906 TTCTTTTC
1 TTCTTTTC
*
4442914 -TCTTTCC
1 TTCTTTTC
4442921 TT-TTTT-
1 TTCTTTTC
4442927 TTCTTTTC
1 TTCTTTTC
4442935 TTCTTTTC
1 TTCTTTTC
4442943 TTC
1 TTC
4442946 AAGCATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
6 2 0.07
7 13 0.48
8 12 0.44
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (8 bp):
TTCTTTTC
Found at i:4455614 original size:14 final size:15
Alignment explanation
Indices: 4455595--4455628 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4455585 GTCTGTAATT
4455595 ATTTATTT-ATATAG
1 ATTTATTTAATATAG
*
4455609 ATTTATTTAATATAT
1 ATTTATTTAATATAG
4455624 ATTTA
1 ATTTA
4455629 ATAATAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
ATTTATTTAATATAG
Found at i:4455635 original size:3 final size:3
Alignment explanation
Indices: 4455627--4455688 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
4455617 AATATATATT
*
4455627 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4455675 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
4455689 TGGGTGAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4456438 original size:10 final size:10
Alignment explanation
Indices: 4456423--4456456 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
4456413 AATAAAATTC
4456423 AAAAATTAAA
1 AAAAATTAAA
*
4456433 AAAAATTAAT
1 AAAAATTAAA
4456443 AAAAATATAAA
1 AAAAAT-TAAA
4456454 AAA
1 AAA
4456457 TATATTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 15 0.71
11 6 0.29
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:4457187 original size:16 final size:16
Alignment explanation
Indices: 4457166--4457197 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4457156 AAAGAGTGAT
4457166 GGTTTCATTTTTATCC
1 GGTTTCATTTTTATCC
4457182 GGTTTCATTTTTATCC
1 GGTTTCATTTTTATCC
4457198 TTTTATCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.19, G:0.12, T:0.56
Consensus pattern (16 bp):
GGTTTCATTTTTATCC
Found at i:4458014 original size:11 final size:11
Alignment explanation
Indices: 4457998--4458062 Score: 55
Period size: 11 Copynumber: 5.9 Consensus size: 11
4457988 TTTATATATT
4457998 TAATATTAATA
1 TAATATTAATA
4458009 TAATATT--T-
1 TAATATTAATA
4458017 TAATATTAATA
1 TAATATTAATA
4458028 TAATATTTTAATA
1 TAATA--TTAATA
* *
4458041 TTATTTTAATA
1 TAATATTAATA
*
4458052 CACATATTAAT
1 TA-ATATTAAT
4458063 TTTTAAAGTA
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
8 7 0.16
9 1 0.02
10 1 0.02
11 18 0.42
12 7 0.16
13 9 0.21
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (11 bp):
TAATATTAATA
Found at i:4458051 original size:19 final size:19
Alignment explanation
Indices: 4457991--4458043 Score: 97
Period size: 19 Copynumber: 2.7 Consensus size: 19
4457981 AAATTATTTT
4457991 ATATATTTAATATTAATATA
1 ATAT-TTTAATATTAATATA
4458011 ATATTTTAATATTAATATA
1 ATATTTTAATATTAATATA
4458030 ATATTTTAATATTA
1 ATATTTTAATATTA
4458044 TTTTAATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 29 0.88
20 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATTTTAATATTAATATA
Found at i:4458475 original size:33 final size:32
Alignment explanation
Indices: 4458404--4458485 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 32
4458394 TTATTTTAAT
*
4458404 AAATAATTTATAATATTTTTACTTCAATAGATA
1 AAATAATTT-TAATATTTTTACTTCAATAGAAA
* * *
4458437 TAATAATTTTAATATTTTTATTTACAATATAAA
1 AAATAATTTTAATATTTTTACTT-CAATAGAAA
4458470 AAATAATATTTTAATA
1 AAAT-A-ATTTTAATA
4458486 ATAATAATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 13 0.32
33 18 0.44
34 1 0.02
35 9 0.22
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.48
Consensus pattern (32 bp):
AAATAATTTTAATATTTTTACTTCAATAGAAA
Found at i:4467097 original size:2 final size:2
Alignment explanation
Indices: 4467087--4467126 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
4467077 ATATTTTTTC
4467087 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
4467127 TAAAGTTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4471344 original size:29 final size:28
Alignment explanation
Indices: 4471325--4471390 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 28
4471315 TTGAACCAGT
4471325 GAACCGGTAACATGGCCGGTTCGCTAACC
1 GAACCGGTAACATGGCCGGTTCGC-AACC
4471354 GAACCGGTAACATGGCCGGTTCGCTAACC
1 GAACCGGTAACATGGCCGGTTCGC-AACC
*
4471383 GATCCGGT
1 GAACCGGT
4471391 TCTAAAAACC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.23, C:0.30, G:0.29, T:0.18
Consensus pattern (28 bp):
GAACCGGTAACATGGCCGGTTCGCAACC
Found at i:4472826 original size:65 final size:65
Alignment explanation
Indices: 4472721--4472907 Score: 288
Period size: 65 Copynumber: 2.9 Consensus size: 65
4472711 TCATTTTCAC
* * * *
4472721 AATGTTCAAAATAAAAATATTAAACAAGAGTATCAAGTCTCAATAACACAATAAAATCAACACAA
1 AATGTTCAAAATAAAAATATCACACAAGAGTATCAAGTCTCAACAACATAATAAAATCAACACAA
*
4472786 GATGTTCAAAATAAAAATATCACACAA-ACGTATCAAGTCTCAACAACATAATAAAATCAACACA
1 AATGTTCAAAATAAAAATATCACACAAGA-GTATCAAGTCTCAACAACATAATAAAATCAACACA
4472850 A
65 A
*
4472851 AATGTTCAAAATAAAAATA-CTACACAAGAGTTTCAAGTCTCAACAACATAATAAAAT
1 AATGTTCAAAATAAAAATATC-ACACAAGAGTATCAAGTCTCAACAACATAATAAAAT
4472908 AGACAGTAGG
Statistics
Matches: 112, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
64 2 0.02
65 109 0.97
66 1 0.01
ACGTcount: A:0.55, C:0.17, G:0.06, T:0.22
Consensus pattern (65 bp):
AATGTTCAAAATAAAAATATCACACAAGAGTATCAAGTCTCAACAACATAATAAAATCAACACAA
Found at i:4475172 original size:19 final size:19
Alignment explanation
Indices: 4475132--4475173 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
4475122 AAATAATTAC
*
4475132 TTAAAATATTATTTTTTAT
1 TTAAAATATTATATTTTAT
4475151 TTAAAATATTAATATTTT-T
1 TTAAAATATT-ATATTTTAT
4475170 TTAA
1 TTAA
4475174 TATTTTCGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTAAAATATTATATTTTAT
Found at i:4475222 original size:27 final size:27
Alignment explanation
Indices: 4475170--4475222 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
4475160 TAATATTTTT
***
4475170 TTAATATTTTCGGTAAAATGTCTAATA
1 TTAATATTTTCGGTAAAATAAATAATA
4475197 TTAATATTTTCGGTAGAAA-AAATAAT
1 TTAATATTTTCGGTA-AAATAAATAAT
4475223 GTTTTAGGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 19 0.86
28 3 0.14
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.42
Consensus pattern (27 bp):
TTAATATTTTCGGTAAAATAAATAATA
Found at i:4475861 original size:37 final size:37
Alignment explanation
Indices: 4475787--4475861 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
4475777 CATTATAATT
* *
4475787 AATTTATATATTTTCTTTAAAAATTTTAAATTCATAA
1 AATTTATATATTTTCTTTAAAAATTTAAAAATCATAA
*
4475824 AATTTATATAATTTTTTTTACAAAA-TTAAAAAT-ATAA
1 AATTTATAT-ATTTTCTTTA-AAAATTTAAAAATCATAA
4475861 A
1 A
4475862 TAGGTTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 15 0.45
39 4 0.12
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (37 bp):
AATTTATATATTTTCTTTAAAAATTTAAAAATCATAA
Found at i:4477923 original size:22 final size:22
Alignment explanation
Indices: 4477897--4477940 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4477887 TAAAAGGTTT
* *
4477897 ATATATTTATAAATTTAACTTA
1 ATATAGTTACAAATTTAACTTA
*
4477919 ATATAGTTCCAAATTTAACTTA
1 ATATAGTTACAAATTTAACTTA
4477941 TAGTCCAACT
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:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (22 bp):
ATATAGTTACAAATTTAACTTA
Found at i:4480964 original size:31 final size:31
Alignment explanation
Indices: 4480887--4480978 Score: 132
Period size: 31 Copynumber: 3.0 Consensus size: 31
4480877 GGTCGAGGGT
* *
4480887 TTACCTATGTTCTTCAGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGA
4480918 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGA
* *
4480949 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
4480979 GTCCTTCGGG
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
31 55 0.98
32 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGA
Found at i:4481484 original size:21 final size:21
Alignment explanation
Indices: 4481459--4481501 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
4481449 AAAGAATATA
4481459 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
4481480 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
4481501 T
1 T
4481502 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:4482923 original size:2 final size:2
Alignment explanation
Indices: 4482916--4482947 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4482906 TAGCATTGCC
4482916 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
4482948 CATGCATGCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4489818 original size:18 final size:17
Alignment explanation
Indices: 4489765--4489822 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
4489755 GCAAACATTA
*
4489765 AATGAGCTAGTTTGATT-
1 AATGAACTAGTTT-ATTG
* *
4489782 AATAAACTAGTTTAATG
1 AATGAACTAGTTTATTG
4489799 AATGAACTAGCTTTATTG
1 AATGAACTAG-TTTATTG
4489817 AATGAA
1 AATGAA
4489823 GAACATACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
16 2 0.06
17 20 0.59
18 12 0.35
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (17 bp):
AATGAACTAGTTTATTG
Found at i:4491246 original size:80 final size:79
Alignment explanation
Indices: 4491147--4491437 Score: 413
Period size: 80 Copynumber: 3.6 Consensus size: 79
4491137 CAGTAAAAAG
* * * * *
4491147 GGGAGCCAACCTAAGGATATACCTTGGGTCTGCCCAAGGACATCCTTAGATCCGTAGGGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGGGCCTACCCAA-GATATCCTTAGGTCCGTAGGGTTACCT
* * * *
4491212 TAAGCACAGAGCTAA
65 TATGCACACAACAAA
*
4491227 GGGAACCAACCTAGGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTCA-GGTTACC
1 GGGAACCAACCTAAGGATATACCTT-GGGCCTACCCAAGATATCCTTAGGTCCGT-AGGGTTACC
4491291 TTATGCACACAACAAA
64 TTATGCACACAACAAA
* * *
4491307 GGGAACCAACCTAAAGATATGCCTCGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
1 GGGAACCAACCTAAGGATATACCT-TGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
4491372 TATGCACACAACAAA
65 TATGCACACAACAAA
*
4491387 GGGAACCAACCTAAGGATATGCCTTGGGCCTACCCAAGATATCCTTAGGTC
1 GGGAACCAACCTAAGGATATACCTTGGGCCTACCCAAGATATCCTTAGGTC
4491438 TGTAAGGACT
Statistics
Matches: 191, Mismatches: 16, Indels: 9
0.88 0.07 0.04
Matches are distributed among these distances:
79 27 0.14
80 153 0.80
81 11 0.06
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.21
Consensus pattern (79 bp):
GGGAACCAACCTAAGGATATACCTTGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTT
ATGCACACAACAAA
Found at i:4493982 original size:249 final size:249
Alignment explanation
Indices: 4493544--4494045 Score: 977
Period size: 249 Copynumber: 2.0 Consensus size: 249
4493534 GAAATCAGTT
4493544 ATCGAGATTTCCTAAGCAAACTAGCATTTCTTATGTACATCTGTAATTTCATCAGATCAATATGT
1 ATCGAGATTTCCTAAGCAAACTAGCATTTCTTATGTACATCTGTAATTTCATCAGATCAATATGT
4493609 ATTTACAAACTTCTTATATAACTTTCAGGGTCAATTCTTGTCTTTTTACAACATAAGAGTATTTT
66 ATTTACAAACTTCTTATATAACTTTCAGGGTCAATTCTTGTCTTTTTACAACATAAGAGTATTTT
*
4493674 TGTAATTTATCACTTAAACTGTAGTATTTTCATACTTTATCAAATGAGATAATTTATACATTACA
131 TGTAATTTATCACTTAAACTGGAGTATTTTCATACTTTATCAAATGAGATAATTTATACATTACA
4493739 TATCCAATGCTGATTCTAATATCACTTAATCTAATAACTTGTAATTGAATTCAA
196 TATCCAATGCTGATTCTAATATCACTTAATCTAATAACTTGTAATTGAATTCAA
*
4493793 ATCGAGATTTCCTAAGCAAACTAGCATTTCTTATGTACATCTGTAGTTTCATCAGATCAATATGT
1 ATCGAGATTTCCTAAGCAAACTAGCATTTCTTATGTACATCTGTAATTTCATCAGATCAATATGT
*
4493858 ATTTACAAACTTCTTATATAACTTTCAGGGTCAATTCTTGTCTTTTTACAATATAAGAGTATTTT
66 ATTTACAAACTTCTTATATAACTTTCAGGGTCAATTCTTGTCTTTTTACAACATAAGAGTATTTT
4493923 TGTAATTTATCACTTAAACTGGAGTATTTTCATACTTTATCAAATGAGATAATTTATACATTACA
131 TGTAATTTATCACTTAAACTGGAGTATTTTCATACTTTATCAAATGAGATAATTTATACATTACA
4493988 TATCCAATGCTGATTCTAATATCACTTAATCTAATAACTTGTAATTGAATTCAA
196 TATCCAATGCTGATTCTAATATCACTTAATCTAATAACTTGTAATTGAATTCAA
4494042 ATCG
1 ATCG
4494046 TCTTTCAATT
Statistics
Matches: 250, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
249 250 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.41
Consensus pattern (249 bp):
ATCGAGATTTCCTAAGCAAACTAGCATTTCTTATGTACATCTGTAATTTCATCAGATCAATATGT
ATTTACAAACTTCTTATATAACTTTCAGGGTCAATTCTTGTCTTTTTACAACATAAGAGTATTTT
TGTAATTTATCACTTAAACTGGAGTATTTTCATACTTTATCAAATGAGATAATTTATACATTACA
TATCCAATGCTGATTCTAATATCACTTAATCTAATAACTTGTAATTGAATTCAA
Found at i:4494540 original size:17 final size:17
Alignment explanation
Indices: 4494518--4494555 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
4494508 TCAACAGTGA
*
4494518 TCAACGCCGGTCAACGG
1 TCAACGCAGGTCAACGG
*
4494535 TCAACGTAGGTCAACGG
1 TCAACGCAGGTCAACGG
4494552 TCAA
1 TCAA
4494556 TAGTCGACTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (17 bp):
TCAACGCAGGTCAACGG
Found at i:4500995 original size:17 final size:16
Alignment explanation
Indices: 4500975--4501032 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 16
4500965 AGTCCATGCA
*
4500975 AATGAGCTAGTTTGATT
1 AATGAACTAGTTT-ATT
4500992 AATGAACTAGTTTAATT
1 AATGAACTAGTTT-ATT
*
4501009 AGTGAACTAGCTTTATT
1 AATGAACTAG-TTTATT
4501026 GAATGAA
1 -AATGAA
4501033 GAACATACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
17 27 0.77
18 8 0.23
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.38
Consensus pattern (16 bp):
AATGAACTAGTTTATT
Found at i:4501863 original size:18 final size:18
Alignment explanation
Indices: 4501840--4501884 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
4501830 CACAACCCGG
4501840 CCCAACCCGACCCGTTGA
1 CCCAACCCGACCCGTTGA
* *
4501858 CCCAACCCAATCCGTTGA
1 CCCAACCCGACCCGTTGA
*
4501876 CCCGACCCG
1 CCCAACCCG
4501885 TTGACCGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.22, C:0.51, G:0.16, T:0.11
Consensus pattern (18 bp):
CCCAACCCGACCCGTTGA
Found at i:4504381 original size:24 final size:24
Alignment explanation
Indices: 4504354--4504468 Score: 144
Period size: 24 Copynumber: 4.8 Consensus size: 24
4504344 TTCGATTTAA
*
4504354 ATTCTGATATGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
4504378 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
*
4504402 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* * *
4504426 ATTTTGATCTGTTACTTGACCT-G
1 ATTCTGATCTGATACTTGACATGG
*
4504449 ATTTCTGATATGATACTTGA
1 A-TTCTGATCTGATACTTGA
4504469 TTTGAATTAT
Statistics
Matches: 80, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
23 3 0.04
24 76 0.95
25 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:4504593 original size:35 final size:35
Alignment explanation
Indices: 4504546--4504620 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
4504536 TGGAGGAAGA
*
4504546 TTACTTGGAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
* *
4504581 TTACTTGCAGGCTCTTTGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
4504616 TTACT
1 TTACT
4504621 GTTCGTGACG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.09, C:0.27, G:0.28, T:0.36
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
Found at i:4509115 original size:24 final size:24
Alignment explanation
Indices: 4509003--4509105 Score: 125
Period size: 24 Copynumber: 4.3 Consensus size: 24
4508993 GATTTTTTAT
*
4509003 TTGAATTCTGATTTGATACTTGAC
1 TTGAATTCTGATCTGATACTTGAC
* *
4509027 ATGGATTCTGATCTGATACTTGAC
1 TTGAATTCTGATCTGATACTTGAC
* * *
4509051 TTGGATTTTGATCTGTTACTTGAC
1 TTGAATTCTGATCTGATACTTGAC
* * *
4509075 CTGATTTCTGATATGATACTTGAC
1 TTGAATTCTGATCTGATACTTGAC
4509099 TTGAATT
1 TTGAATT
4509106 ATGTTTTGAT
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (24 bp):
TTGAATTCTGATCTGATACTTGAC
Found at i:4509222 original size:35 final size:35
Alignment explanation
Indices: 4509175--4509249 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
4509165 TGGAGGAAGA
*
4509175 TTACTTGGAGGCTCATCGGCTATGTGCTCAGGGCC
1 TTACTTGCAGGCTCATCGGCTATGTGCTCAGGGCC
* *
4509210 TTACTTGCAGGCTCATTGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCATCGGCTATGTGCTCAGGGCC
4509245 TTACT
1 TTACT
4509250 GTTCGGGACG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.13, C:0.25, G:0.28, T:0.33
Consensus pattern (35 bp):
TTACTTGCAGGCTCATCGGCTATGTGCTCAGGGCC
Found at i:4513254 original size:48 final size:48
Alignment explanation
Indices: 4513199--4513294 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
4513189 TTAATTTTTA
4513199 GAACCCATAAACTGTTGCAGAAATAGAAGAACATGTTTTCTTGGTTTC
1 GAACCCATAAACTGTTGCAGAAATAGAAGAACATGTTTTCTTGGTTTC
*
4513247 GAACCCATAAACTGTTGCAGAAATAGAAGAACATGTTTTCTTGTTTTC
1 GAACCCATAAACTGTTGCAGAAATAGAAGAACATGTTTTCTTGGTTTC
4513295 ATGATTTTCT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (48 bp):
GAACCCATAAACTGTTGCAGAAATAGAAGAACATGTTTTCTTGGTTTC
Found at i:4516263 original size:21 final size:23
Alignment explanation
Indices: 4516239--4516287 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
4516229 CAAGTCATGT
*
4516239 CATATAAAATCT-TAAGATT-TA
1 CATATAAAATCTATAAAATTATA
*
4516260 CATA-ATAATCTATAAAATTATA
1 CATATAAAATCTATAAAATTATA
4516282 CATATA
1 CATATA
4516288 TTCATAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 6 0.26
21 10 0.43
22 6 0.26
23 1 0.04
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (23 bp):
CATATAAAATCTATAAAATTATA
Found at i:4516432 original size:42 final size:42
Alignment explanation
Indices: 4516373--4516462 Score: 171
Period size: 42 Copynumber: 2.1 Consensus size: 42
4516363 AAGGTCTCAA
*
4516373 ACCCACAATGGGTATGACTTCTTACATCCACACCTGCCCACT
1 ACCCACAACGGGTATGACTTCTTACATCCACACCTGCCCACT
4516415 ACCCACAACGGGTATGACTTCTTACATCCACACCTGCCCACT
1 ACCCACAACGGGTATGACTTCTTACATCCACACCTGCCCACT
4516457 ACCCAC
1 ACCCAC
4516463 TAAAGTTATA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.27, C:0.41, G:0.11, T:0.21
Consensus pattern (42 bp):
ACCCACAACGGGTATGACTTCTTACATCCACACCTGCCCACT
Found at i:4517300 original size:16 final size:18
Alignment explanation
Indices: 4517279--4517316 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
4517269 TATGCTATTT
*
4517279 TTTTATTT-TTTGAAT-A
1 TTTTATTTATTTAAATAA
4517295 TTTTATTTATTTAAATAA
1 TTTTATTTATTTAAATAA
4517313 TTTT
1 TTTT
4517317 TTAAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTTATTTATTTAAATAA
Found at i:4518212 original size:32 final size:31
Alignment explanation
Indices: 4518176--4518252 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
4518166 CGGGGCCGTG
*
4518176 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
4518208 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
4518239 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
4518253 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:4518235 original size:63 final size:63
Alignment explanation
Indices: 4518129--4518252 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
4518119 CACTAAGGGA
* * ** *
4518129 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
4518192 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
4518253 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:4519381 original size:7 final size:7
Alignment explanation
Indices: 4519369--4519406 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
4519359 ATAAAAGAAA
4519369 GTCAACG
1 GTCAACG
4519376 GTCAACG
1 GTCAACG
4519383 GTCAACG
1 GTCAACG
4519390 GTCAACG
1 GTCAACG
4519397 GTCAACG
1 GTCAACG
4519404 GTC
1 GTC
4519407 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:4519413 original size:5 final size:5
Alignment explanation
Indices: 4519403--4519443 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
4519393 AACGGTCAAC
*
4519403 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC
4519444 AACAGTCGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:4519424 original size:22 final size:22
Alignment explanation
Indices: 4519396--4519460 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
4519386 AACGGTCAAC
4519396 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
4519418 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
* *
4519440 GGTCAACAGTCGGGTCAGGTC
1 GGTCAACGGTCGGGTCGGGTC
4519461 AGACCGGTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.12, C:0.23, G:0.46, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:4519483 original size:19 final size:18
Alignment explanation
Indices: 4519457--4519554 Score: 117
Period size: 19 Copynumber: 5.2 Consensus size: 18
4519447 AGTCGGGTCA
4519457 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
4519475 GGCTCAGACCGGTCAAACC
1 GG-TCAGACCGGTCAAACC
4519494 GAGTCAGACCGGTCAAACC
1 G-GTCAGACCGGTCAAACC
*
4519513 GGTTC-GAACCGGTTGAAACC
1 GG-TCAG-ACCGG-TCAAACC
*
4519533 GGTCAAACCGGTCAGAACC
1 GGTCAGACCGGTCA-AACC
4519552 GGT
1 GGT
4519555 TGAAAACCGG
Statistics
Matches: 70, Mismatches: 3, Indels: 13
0.81 0.03 0.15
Matches are distributed among these distances:
18 6 0.09
19 55 0.79
20 9 0.13
ACGTcount: A:0.28, C:0.31, G:0.29, T:0.13
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:4519500 original size:38 final size:38
Alignment explanation
Indices: 4519457--4519574 Score: 127
Period size: 38 Copynumber: 3.1 Consensus size: 38
4519447 AGTCGGGTCA
4519457 GGTCAGACCGGTCAAACCGGCTC-AGACCGG-TCAAACC
1 GGTCAGACCGGTCAAACCGGCTCGA-ACCGGTTCAAACC
* *
4519494 GAGTCAGACCGGTCAAACCGGTTCGAACCGGTTGAAACC
1 G-GTCAGACCGGTCAAACCGGCTCGAACCGGTTCAAACC
* *
4519533 GGTCAAACCGGTCAGAACCGG-TTGAAAACCGGTT-AAACC
1 GGTCAGACCGGTCA-AACCGGCTCG--AACCGGTTCAAACC
4519572 GGT
1 GGT
4519575 TTCCAGCAGC
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
37 1 0.01
38 40 0.56
39 22 0.31
40 8 0.11
ACGTcount: A:0.29, C:0.29, G:0.28, T:0.14
Consensus pattern (38 bp):
GGTCAGACCGGTCAAACCGGCTCGAACCGGTTCAAACC
Found at i:4519555 original size:29 final size:28
Alignment explanation
Indices: 4519457--4519574 Score: 116
Period size: 29 Copynumber: 4.1 Consensus size: 28
4519447 AGTCGGGTCA
*
4519457 GGTCAG-ACCGGTCAAACCGGCTCAGACC
1 GGTCAGAACCGGTCAAACCGG-TCAAACC
*
4519485 GGTCA-AACCGAGTCAGACCGGTCAAACC
1 GGTCAGAACCG-GTCAAACCGGTCAAACC
*
4519513 GGTTC-GAACCGGTTGAAACCGGTCAAACC
1 GG-TCAGAACCGG-TCAAACCGGTCAAACC
* *
4519542 GGTCAGAACCGGTTGAAAACCGGTTAAACC
1 GGTCAGAACCGG-T-CAAACCGGTCAAACC
4519572 GGT
1 GGT
4519575 TTCCAGCAGC
Statistics
Matches: 77, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
28 20 0.26
29 41 0.53
30 16 0.21
ACGTcount: A:0.29, C:0.29, G:0.28, T:0.14
Consensus pattern (28 bp):
GGTCAGAACCGGTCAAACCGGTCAAACC
Found at i:4519575 original size:9 final size:9
Alignment explanation
Indices: 4519457--4519574 Score: 110
Period size: 9 Copynumber: 12.3 Consensus size: 9
4519447 AGTCGGGTCA
*
4519457 GGTCAGACC
1 GGTCAAACC
4519466 GGTCAAACC
1 GGTCAAACC
*
4519475 GGCTCAGACC
1 GG-TCAAACC
4519485 GGTCAAACC
1 GGTCAAACC
*
4519494 GAGTCAGACC
1 G-GTCAAACC
4519504 GGTCAAACC
1 GGTCAAACC
*
4519513 GGTTCGAACC
1 GG-TCAAACC
*
4519523 GGTTGAAACC
1 GG-TCAAACC
4519533 GGTCAAACC
1 GGTCAAACC
4519542 GGTCAGAACC
1 GGTCA-AACC
*
4519552 GGTTGAAAACC
1 GG-T-CAAACC
*
4519563 GGTTAAACC
1 GGTCAAACC
4519572 GGT
1 GGT
4519575 TTCCAGCAGC
Statistics
Matches: 92, Mismatches: 11, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
9 45 0.49
10 39 0.42
11 7 0.08
12 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.28, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:4525822 original size:32 final size:31
Alignment explanation
Indices: 4525786--4525861 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
4525776 CGGGGCCGTG
*
4525786 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
* **
4525818 GGGCCTACC-GAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
4525848 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
4525862 GTCACATTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 21 0.57
31 7 0.19
32 9 0.24
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:4526739 original size:7 final size:7
Alignment explanation
Indices: 4526727--4526757 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
4526717 ATAAAAGAAA
4526727 GTCAACG
1 GTCAACG
4526734 GTCAACG
1 GTCAACG
4526741 GTCAACG
1 GTCAACG
4526748 GTCAACG
1 GTCAACG
4526755 GTC
1 GTC
4526758 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:4526775 original size:22 final size:22
Alignment explanation
Indices: 4526747--4526811 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
4526737 AACGGTCAAC
4526747 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
4526769 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
4526791 GGTCAACAGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
4526812 AGACCGGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:4526811 original size:5 final size:5
Alignment explanation
Indices: 4526754--4526794 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
4526744 AACGGTCAAC
*
4526754 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC
4526795 AACAGTCGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:4526834 original size:19 final size:18
Alignment explanation
Indices: 4526808--4526905 Score: 117
Period size: 19 Copynumber: 5.2 Consensus size: 18
4526798 AGTCGGGTCG
4526808 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
4526826 GGCTCAGACCGGTCAAACC
1 GG-TCAGACCGGTCAAACC
4526845 GAGTCAGACCGGTCAAACC
1 G-GTCAGACCGGTCAAACC
*
4526864 GGTTC-GAACCGGTTGAAACC
1 GG-TCAG-ACCGG-TCAAACC
*
4526884 GGTCAAACCGGTCAGAACC
1 GGTCAGACCGGTCA-AACC
4526903 GGT
1 GGT
4526906 TGAAAACCGG
Statistics
Matches: 70, Mismatches: 3, Indels: 13
0.81 0.03 0.15
Matches are distributed among these distances:
18 6 0.09
19 55 0.79
20 9 0.13
ACGTcount: A:0.28, C:0.31, G:0.29, T:0.13
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:4526851 original size:38 final size:38
Alignment explanation
Indices: 4526808--4526925 Score: 127
Period size: 38 Copynumber: 3.1 Consensus size: 38
4526798 AGTCGGGTCG
4526808 GGTCAGACCGGTCAAACCGGCTC-AGACCGG-TCAAACC
1 GGTCAGACCGGTCAAACCGGCTCGA-ACCGGTTCAAACC
* *
4526845 GAGTCAGACCGGTCAAACCGGTTCGAACCGGTTGAAACC
1 G-GTCAGACCGGTCAAACCGGCTCGAACCGGTTCAAACC
* *
4526884 GGTCAAACCGGTCAGAACCGG-TTGAAAACCGGTT-AAACC
1 GGTCAGACCGGTCA-AACCGGCTCG--AACCGGTTCAAACC
4526923 GGT
1 GGT
4526926 TTCCAGCAGC
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
37 1 0.01
38 40 0.56
39 22 0.31
40 8 0.11
ACGTcount: A:0.29, C:0.29, G:0.28, T:0.14
Consensus pattern (38 bp):
GGTCAGACCGGTCAAACCGGCTCGAACCGGTTCAAACC
Found at i:4526906 original size:29 final size:28
Alignment explanation
Indices: 4526808--4526925 Score: 116
Period size: 29 Copynumber: 4.1 Consensus size: 28
4526798 AGTCGGGTCG
*
4526808 GGTCAG-ACCGGTCAAACCGGCTCAGACC
1 GGTCAGAACCGGTCAAACCGG-TCAAACC
*
4526836 GGTCA-AACCGAGTCAGACCGGTCAAACC
1 GGTCAGAACCG-GTCAAACCGGTCAAACC
*
4526864 GGTTC-GAACCGGTTGAAACCGGTCAAACC
1 GG-TCAGAACCGG-TCAAACCGGTCAAACC
* *
4526893 GGTCAGAACCGGTTGAAAACCGGTTAAACC
1 GGTCAGAACCGG-T-CAAACCGGTCAAACC
4526923 GGT
1 GGT
4526926 TTCCAGCAGC
Statistics
Matches: 77, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
28 20 0.26
29 41 0.53
30 16 0.21
ACGTcount: A:0.29, C:0.29, G:0.28, T:0.14
Consensus pattern (28 bp):
GGTCAGAACCGGTCAAACCGGTCAAACC
Found at i:4526926 original size:9 final size:9
Alignment explanation
Indices: 4526808--4526925 Score: 110
Period size: 9 Copynumber: 12.3 Consensus size: 9
4526798 AGTCGGGTCG
*
4526808 GGTCAGACC
1 GGTCAAACC
4526817 GGTCAAACC
1 GGTCAAACC
*
4526826 GGCTCAGACC
1 GG-TCAAACC
4526836 GGTCAAACC
1 GGTCAAACC
*
4526845 GAGTCAGACC
1 G-GTCAAACC
4526855 GGTCAAACC
1 GGTCAAACC
*
4526864 GGTTCGAACC
1 GG-TCAAACC
*
4526874 GGTTGAAACC
1 GG-TCAAACC
4526884 GGTCAAACC
1 GGTCAAACC
4526893 GGTCAGAACC
1 GGTCA-AACC
*
4526903 GGTTGAAAACC
1 GG-T-CAAACC
*
4526914 GGTTAAACC
1 GGTCAAACC
4526923 GGT
1 GGT
4526926 TTCCAGCAGC
Statistics
Matches: 92, Mismatches: 11, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
9 45 0.49
10 39 0.42
11 7 0.08
12 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.28, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:4528309 original size:2 final size:2
Alignment explanation
Indices: 4528302--4528348 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
4528292 TATTCAAAGC
4528302 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
4528344 AT AT A
1 AT AT A
4528349 ACACTCTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4528680 original size:27 final size:27
Alignment explanation
Indices: 4528628--4528683 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
4528618 CCGCCATCAC
* *
4528628 CACTTTGAACTTGAAACTCTATAGCAT
1 CACTTTGAACTTGAAACTCCACAGCAT
*
4528655 CACTTTGAACTTGAAAGTCCACAGCAT
1 CACTTTGAACTTGAAACTCCACAGCAT
4528682 CA
1 CA
4528684 AGATCTTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.29
Consensus pattern (27 bp):
CACTTTGAACTTGAAACTCCACAGCAT
Found at i:4528982 original size:30 final size:30
Alignment explanation
Indices: 4528934--4529036 Score: 147
Period size: 30 Copynumber: 3.5 Consensus size: 30
4528924 ACAGAATCGT
*
4528934 CGGTTCACATCG-TTTTGTCGGTTCTCAAC
1 CGGTTCACACCGATTTTGTCGGTTCTCAAC
4528963 CGGTTCACACCGATTTTGTCGGTTCTCAAC
1 CGGTTCACACCGATTTTGTCGGTTCTCAAC
* * *
4528993 CGGTTCACACCGATTTTGGCAGTTCCCAAC
1 CGGTTCACACCGATTTTGTCGGTTCTCAAC
*
4529023 CGGTTC-TACCGATT
1 CGGTTCACACCGATT
4529037 CTTTAGTGGT
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
29 18 0.26
30 50 0.74
ACGTcount: A:0.17, C:0.30, G:0.20, T:0.33
Consensus pattern (30 bp):
CGGTTCACACCGATTTTGTCGGTTCTCAAC
Found at i:4532256 original size:2 final size:2
Alignment explanation
Indices: 4532249--4532280 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4532239 TACATTTTCA
4532249 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
4532281 TAAATCAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4534782 original size:17 final size:17
Alignment explanation
Indices: 4534738--4534771 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4534728 CTAAGGTTAA
4534738 AACTCTAATTATTAAAC
1 AACTCTAATTATTAAAC
4534755 AACTCTAATTATTAAAC
1 AACTCTAATTATTAAAC
4534772 CTAATTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (17 bp):
AACTCTAATTATTAAAC
Found at i:4536482 original size:6 final size:6
Alignment explanation
Indices: 4536459--4536483 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4536449 TGTTGGGCTA
4536459 GGGTTT GGGTTT GGGTTT GGGTTT G
1 GGGTTT GGGTTT GGGTTT GGGTTT G
4536484 AATGTTAGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (6 bp):
GGGTTT
Found at i:4546790 original size:25 final size:25
Alignment explanation
Indices: 4546762--4546823 Score: 58
Period size: 25 Copynumber: 2.6 Consensus size: 25
4546752 AATATTTTAT
4546762 ATATAAT-TAATATAAAAAATATAAA
1 ATATAATATAA-ATAAAAAATATAAA
* * **
4546787 ATATTATATAAATGATTAATATAAA
1 ATATAATATAAATAAAAAATATAAA
4546812 ATAT-ATA-AAATA
1 ATATAATATAAATA
4546824 TTATATATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
23 4 0.13
24 3 0.10
25 21 0.68
26 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
ATATAATATAAATAAAAAATATAAA
Found at i:4546790 original size:34 final size:34
Alignment explanation
Indices: 4546750--4546834 Score: 134
Period size: 34 Copynumber: 2.5 Consensus size: 34
4546740 CTTGAACCTG
*
4546750 AAAATATTTTATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
* * *
4546784 AAAATATTATATAAATGATTAATATAAAATATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
4546818 AAAATATTATATATATA
1 AAAATATTATATATATA
4546835 TATATATATA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:4546797 original size:12 final size:12
Alignment explanation
Indices: 4546780--4546844 Score: 57
Period size: 12 Copynumber: 5.4 Consensus size: 12
4546770 AATATAAAAA
4546780 ATATAAAATATT
1 ATATAAAATATT
4546792 ATAT-AAATGATT
1 ATATAAAAT-ATT
4546804 A-ATATAAA-A-T
1 ATATA-AAATATT
4546814 ATATAAAATATT
1 ATATAAAATATT
*
4546826 ATATATATATATAT
1 ATATA-AAATAT-T
4546840 ATATA
1 ATATA
4546845 TAATCGGGGT
Statistics
Matches: 44, Mismatches: 1, Indels: 14
0.75 0.02 0.24
Matches are distributed among these distances:
10 5 0.11
11 11 0.25
12 14 0.32
13 8 0.18
14 6 0.14
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (12 bp):
ATATAAAATATT
Found at i:4546819 original size:22 final size:23
Alignment explanation
Indices: 4546751--4546842 Score: 66
Period size: 22 Copynumber: 4.0 Consensus size: 23
4546741 TTGAACCTGA
* *
4546751 AAATATTTTATATATAATTAATAT
1 AAATATTATATATATAAAT-ATAT
* * * *
4546775 AAAAAATATA-AAAT-ATTATAT
1 AAATATTATATATATAAATATAT
4546796 AAATGATTA-ATATA-AAATATAT
1 AAAT-ATTATATATATAAATATAT
*
4546818 AAAATATTATATATATATATATAT
1 -AAATATTATATATATAAATATAT
4546842 A
1 A
4546843 TATAATCGGG
Statistics
Matches: 53, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
21 8 0.15
22 18 0.34
23 13 0.25
24 14 0.26
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (23 bp):
AAATATTATATATATAAATATAT
Found at i:4552888 original size:26 final size:26
Alignment explanation
Indices: 4552859--4552910 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
4552849 GACTCGGTAA
*
4552859 AAGCTTGACTCGAGTTGACTTAACTC
1 AAGCTTGACTCGAGTTGACTCAACTC
*
4552885 AAGCTTGACTCGAGTTTACTCAACTC
1 AAGCTTGACTCGAGTTGACTCAACTC
4552911 GAACTCGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (26 bp):
AAGCTTGACTCGAGTTGACTCAACTC
Found at i:4558844 original size:29 final size:29
Alignment explanation
Indices: 4558802--4558860 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
4558792 CGGTCTGCTT
4558802 AACAGTTGTTAGGGCTTGAAGTTTTGTTG
1 AACAGTTGTTAGGGCTTGAAGTTTTGTTG
4558831 AACAGTTGTTAGGGCTTGAAGTTTTGTTG
1 AACAGTTGTTAGGGCTTGAAGTTTTGTTG
4558860 A
1 A
4558861 TGTCAATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.22, C:0.07, G:0.31, T:0.41
Consensus pattern (29 bp):
AACAGTTGTTAGGGCTTGAAGTTTTGTTG
Found at i:4560993 original size:370 final size:370
Alignment explanation
Indices: 4560312--4561037 Score: 1407
Period size: 370 Copynumber: 2.0 Consensus size: 370
4560302 GGAAAAAAAA
4560312 CATTCATCAGGGATCATAATGCATCAATGAACTTAACATGTCATCTTAGCTTTCTATATGTTTTT
1 CATTCATCAGGGATCATAATGCATCAATGAACTTAACATGTCATCTTAGCTTTCTATATGTTTTT
*
4560377 ATATGGTAGGAGCATGACAGCATGCATGTCTTTCTATTTATGCCTCCTCATCTCTGTGCATGAAA
66 ATATGGTAGGAGCATGACAGCATGCATGTCTTTCTATATATGCCTCCTCATCTCTGTGCATGAAA
4560442 TTCATAAAACCTTCATGGTGATTATTGTGATGAACACATTTGGGAGCATTGGCCGGAAGCTGCAG
131 TTCATAAAACCTTCATGGTGATTATTGTGATGAACACATTTGGGAGCATTGGCCGGAAGCTGCAG
*
4560507 ATAGGTCCAAGGTGGTGCCTCTGAGTGTCGGAGTAGGAGAAGATTCTAGTTTGGAGCAACTGATC
196 ATAGGTCCAAGGCGGTGCCTCTGAGTGTCGGAGTAGGAGAAGATTCTAGTTTGGAGCAACTGATC
*
4560572 ATCCGAGTAATAAATCCCAGGGACAAAGATAGAAGGACAGAAGGCTAACTGCTCGTTCTCAGCAA
261 ATCCGAGTAATAAATCCCAGGGACAAAGATAGAAGGACAGAAGGCTAACTGCTCATTCTCAGCAA
4560637 AGAAGTTATCAATGTTTTTGTTCAAAACCATGATGCATCAATGAC
326 AGAAGTTATCAATGTTTTTGTTCAAAACCATGATGCATCAATGAC
*
4560682 CATTCATCAGGGATCATAATGCATCGATGAACTTAACATGTCATCTTAGCTTTCTATATGTTTTT
1 CATTCATCAGGGATCATAATGCATCAATGAACTTAACATGTCATCTTAGCTTTCTATATGTTTTT
4560747 ATATGGTAGGAGCATGACAGCATGCATGTCTTTCTATATATGCCTCCTCATCTCTGTGCATGAAA
66 ATATGGTAGGAGCATGACAGCATGCATGTCTTTCTATATATGCCTCCTCATCTCTGTGCATGAAA
*
4560812 TTCATAAAACCTTCATGGTGATTATTGTGATGAACACATTTGGGAGCATTGGCCGGACGCTGCAG
131 TTCATAAAACCTTCATGGTGATTATTGTGATGAACACATTTGGGAGCATTGGCCGGAAGCTGCAG
4560877 ATAGGTCCAAGGCGGTGCCTCTGAGTGTCGGAGTAGGAGAAGATTCTAGTTTGGAGCAACTGATC
196 ATAGGTCCAAGGCGGTGCCTCTGAGTGTCGGAGTAGGAGAAGATTCTAGTTTGGAGCAACTGATC
4560942 ATCCGAGTAATAAATCCCAGGGACAAAGATAGAAGGACAGAAGGCTAACTGCTCATTCTCAGCAA
261 ATCCGAGTAATAAATCCCAGGGACAAAGATAGAAGGACAGAAGGCTAACTGCTCATTCTCAGCAA
4561007 AGAAGTTATCAATGTTTTTGTTCAAAACCAT
326 AGAAGTTATCAATGTTTTTGTTCAAAACCAT
4561038 TCGACCCACC
Statistics
Matches: 351, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
370 351 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (370 bp):
CATTCATCAGGGATCATAATGCATCAATGAACTTAACATGTCATCTTAGCTTTCTATATGTTTTT
ATATGGTAGGAGCATGACAGCATGCATGTCTTTCTATATATGCCTCCTCATCTCTGTGCATGAAA
TTCATAAAACCTTCATGGTGATTATTGTGATGAACACATTTGGGAGCATTGGCCGGAAGCTGCAG
ATAGGTCCAAGGCGGTGCCTCTGAGTGTCGGAGTAGGAGAAGATTCTAGTTTGGAGCAACTGATC
ATCCGAGTAATAAATCCCAGGGACAAAGATAGAAGGACAGAAGGCTAACTGCTCATTCTCAGCAA
AGAAGTTATCAATGTTTTTGTTCAAAACCATGATGCATCAATGAC
Found at i:4564863 original size:2 final size:2
Alignment explanation
Indices: 4564757--4564854 Score: 178
Period size: 2 Copynumber: 48.0 Consensus size: 2
4564747 CCCTATTGTC
4564757 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
4564799 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
4564841 AT AT CAT AT CAT AT
1 AT AT -AT AT -AT AT
4564855 CACATATATT
Statistics
Matches: 94, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
2 90 0.96
3 4 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4570486 original size:14 final size:13
Alignment explanation
Indices: 4570451--4570506 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
4570441 TATAAATAAA
4570451 TTTATTTT-TATT
1 TTTATTTTATATT
*
4570463 TTATAATTTATACTT
1 TT-TATTTTATA-TT
*
4570478 TTTATTTTATTTT
1 TTTATTTTATATT
* *
4570491 TTTAATTTAAATT
1 TTTATTTTATATT
4570504 TTT
1 TTT
4570507 TTAAAAACTC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
12 2 0.06
13 20 0.57
14 9 0.26
15 4 0.11
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTATTTTATATT
Found at i:4570505 original size:26 final size:24
Alignment explanation
Indices: 4570447--4570508 Score: 70
Period size: 26 Copynumber: 2.5 Consensus size: 24
4570437 AAAATATAAA
*
4570447 TAAATTTATTTTTATTTTATAATT
1 TAAATTTTTTTTTATTTTATAATT
* *
4570471 TATACTTTTTATTTTATTTTTTTAATT
1 TA-AATTTTT-TTTTA-TTTTATAATT
4570498 TAAATTTTTTT
1 TAAATTTTTTT
4570509 AAAAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
24 2 0.06
25 7 0.23
26 11 0.35
27 11 0.35
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (24 bp):
TAAATTTTTTTTTATTTTATAATT
Found at i:4570506 original size:27 final size:27
Alignment explanation
Indices: 4570451--4570507 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
4570441 TATAAATAAA
*
4570451 TTTATTTTTATTTTATAATTTATACTT
1 TTTATTTTTATTTTATAATTTAAACTT
* *
4570478 TTTA-TTTTATTTTTTTAATTTAAATTT
1 TTTATTTTTA-TTTTATAATTTAAACTT
4570505 TTT
1 TTT
4570508 TAAAAACTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (27 bp):
TTTATTTTTATTTTATAATTTAAACTT
Found at i:4579485 original size:15 final size:15
Alignment explanation
Indices: 4579463--4579502 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
4579453 CACTTTTATC
4579463 ACGACGATGACGACG
1 ACGACGATGACGACG
* *
4579478 ATGACGATGGCGACG
1 ACGACGATGACGACG
4579493 ACGACGATGA
1 ACGACGATGA
4579503 TGACAGCGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.23, G:0.35, T:0.10
Consensus pattern (15 bp):
ACGACGATGACGACG
Found at i:4579759 original size:35 final size:33
Alignment explanation
Indices: 4579720--4579804 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
4579710 ATATTTCAGT
4579720 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
4579755 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
4579790 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
4579805 TAAATACCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:4582107 original size:62 final size:63
Alignment explanation
Indices: 4582039--4582199 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 63
4582029 CGGTGCACCA
*
4582039 AGTGTGCATCGATGCATGAAATGCA-TCGATGTTTGAAAAATAGTC-TGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGTCAAGTGCATCGATGCATGG
** * *
4582101 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGTCA-AGTGCATCGATGCATGG
* * *
4582166 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
4582200 CAATTAATTC
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
62 22 0.26
63 14 0.17
64 6 0.07
65 42 0.50
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (63 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGTCAAGTGCATCGATGCATGG
Found at i:4582171 original size:19 final size:19
Alignment explanation
Indices: 4582147--4582197 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
4582137 GAAAATATTC
4582147 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
4582166 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
4582185 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
4582198 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:4582565 original size:18 final size:19
Alignment explanation
Indices: 4582544--4582580 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
4582534 TCCCAAATAT
4582544 CATAAACATCCAAA-CAAA
1 CATAAACATCCAAATCAAA
4582562 CATAAACATCCAAATCAAA
1 CATAAACATCCAAATCAAA
4582581 AAGTTTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (19 bp):
CATAAACATCCAAATCAAA
Found at i:4583247 original size:64 final size:64
Alignment explanation
Indices: 4583194--4583356 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 64
4583184 CGGTGCACCA
*
4583194 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * * **
4583258 CTTGTGCATCGATACATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
4583323 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
4583357 CAATTAATTC
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
64 38 0.46
65 45 0.54
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:4583328 original size:19 final size:19
Alignment explanation
Indices: 4583304--4583354 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
4583294 GAAAATATTC
4583304 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
4583323 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
4583342 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
4583355 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:4585785 original size:51 final size:51
Alignment explanation
Indices: 4585730--4585871 Score: 214
Period size: 51 Copynumber: 2.8 Consensus size: 51
4585720 CCCCTACGTG
*
4585730 GCGTATAGCGCGGAGCAGGGGGCGCGCTATACCCCACGTGTAACTCAGTCA
1 GCGTATAGCGCGGAGCAGGGGGCGCGCTATACCCCACGTGTAACCCAGTCA
* *
4585781 GCGTATAGCGCAGAGCAGGGGGCGCGTTATACCCCACGTGTAACCCAGTCA
1 GCGTATAGCGCGGAGCAGGGGGCGCGCTATACCCCACGTGTAACCCAGTCA
* * *
4585832 GCGTATAGCGTGGTA-CATGGGGCGCGCTATACTCCACGTG
1 GCGTATAGCGCGG-AGCAGGGGGCGCGCTATACCCCACGTG
4585872 ACGCCAAATC
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
51 81 0.99
52 1 0.01
ACGTcount: A:0.21, C:0.28, G:0.33, T:0.18
Consensus pattern (51 bp):
GCGTATAGCGCGGAGCAGGGGGCGCGCTATACCCCACGTGTAACCCAGTCA
Found at i:4588072 original size:17 final size:15
Alignment explanation
Indices: 4588032--4588074 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
4588022 CTTAAAGTTA
4588032 AATATTATTTTAAAT
1 AATATTATTTTAAAT
4588047 AAT-TATATTTGTACAAT
1 AATAT-TATTT-TA-AAT
4588064 AATATTATTTT
1 AATATTATTTT
4588075 TCACCTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 1 0.04
15 8 0.33
16 3 0.12
17 11 0.46
18 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (15 bp):
AATATTATTTTAAAT
Found at i:4599780 original size:29 final size:30
Alignment explanation
Indices: 4599709--4599781 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
4599699 AAAAAAAATC
* **
4599709 CTTTAGTTACTTGTTTTGACAAAAATATAA
1 CTTTAGATACTTAATTTGACAAAAATATAA
4599739 CTTTAGATACTTAATTTGACTAAAAA-AT-A
1 CTTTAGATACTTAATTTGAC-AAAAATATAA
* *
4599768 TTTTAGGTACTTAA
1 CTTTAGATACTTAA
4599782 ATGGAAAAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 13 0.35
30 19 0.51
31 5 0.14
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (30 bp):
CTTTAGATACTTAATTTGACAAAAATATAA
Found at i:4600288 original size:60 final size:60
Alignment explanation
Indices: 4600223--4600356 Score: 184
Period size: 60 Copynumber: 2.2 Consensus size: 60
4600213 TAGAATGAGG
* *
4600223 GTCATAGTTTGGGGATGACATTGGAAT-TCTCAAAAGCTTAAGGACTAATTTTAGATG-GAA
1 GTCATAGTTTGGGGATGAAATTGGAATATC-CAAAAGCTTAAGGACTAA-TTTAAATGAGAA
* *
4600283 GTCATAGTTTGGGGATTAAATTGGAATATCCAAAAGTTTAAGGACTAATTTAAATGAGAA
1 GTCATAGTTTGGGGATGAAATTGGAATATCCAAAAGCTTAAGGACTAATTTAAATGAGAA
*
4600343 -TAATAGTTTGGGGA
1 GTCATAGTTTGGGGA
4600357 CATATGATGC
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
59 20 0.30
60 45 0.67
61 2 0.03
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.32
Consensus pattern (60 bp):
GTCATAGTTTGGGGATGAAATTGGAATATCCAAAAGCTTAAGGACTAATTTAAATGAGAA
Found at i:4603478 original size:25 final size:25
Alignment explanation
Indices: 4603444--4603497 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
4603434 TACCCATCTC
4603444 GTTTTCCCATATCTTCGTTGTCATT
1 GTTTTCCCATATCTTCGTTGTCATT
4603469 GTTTTCCCATATCTTCGTTGTCATT
1 GTTTTCCCATATCTTCGTTGTCATT
4603494 GTTT
1 GTTT
4603498 GGAGATTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.11, C:0.22, G:0.13, T:0.54
Consensus pattern (25 bp):
GTTTTCCCATATCTTCGTTGTCATT
Found at i:4603599 original size:18 final size:19
Alignment explanation
Indices: 4603576--4603611 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4603566 ATCTGCCATC
4603576 TTAACC-TTCTTCTTTGCA
1 TTAACCTTTCTTCTTTGCA
4603594 TTAACCTTTCTTCTTTGC
1 TTAACCTTTCTTCTTTGC
4603612 TTTTTTCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.14, C:0.28, G:0.06, T:0.53
Consensus pattern (19 bp):
TTAACCTTTCTTCTTTGCA
Found at i:4604152 original size:9 final size:8
Alignment explanation
Indices: 4604136--4604205 Score: 52
Period size: 9 Copynumber: 8.1 Consensus size: 8
4604126 GTCAAAAAAG
4604136 ATAAAATA
1 ATAAAATA
4604144 ATAATAATA
1 ATAA-AATA
4604153 AT-AAATAA
1 ATAAAAT-A
*
4604161 ATCAAATCA
1 ATAAAAT-A
* *
4604170 AGGAAAAAA
1 A-TAAAATA
4604179 CATAAAATA
1 -ATAAAATA
4604188 ATAATAATA
1 ATAA-AATA
4604197 ATAAAATA
1 ATAAAATA
4604205 A
1 A
4604206 ATCAAAGGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
7 3 0.06
8 17 0.34
9 26 0.52
10 4 0.08
ACGTcount: A:0.70, C:0.04, G:0.03, T:0.23
Consensus pattern (8 bp):
ATAAAATA
Found at i:4604195 original size:6 final size:5
Alignment explanation
Indices: 4604136--4604232 Score: 58
Period size: 5 Copynumber: 19.2 Consensus size: 5
4604126 GTCAAAAAAG
* * ** *
4604136 ATAAA ATAATA ATAATA AT-AA AT-AA ATCAA ATCAA GGAAA A-AAC ATAAA
1 ATAAA ATAA-A ATAA-A ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
**
4604185 ATAATA ATAATA ATAAA AT-AA ATCAAA GGAAA ATAAA ATAAA ATAAA
1 ATAA-A ATAA-A ATAAA ATAAA AT-AAA ATAAA ATAAA ATAAA ATAAA
4604232 A
1 A
4604233 AAGGAAAATA
Statistics
Matches: 76, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
4 14 0.18
5 40 0.53
6 22 0.29
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:4604231 original size:47 final size:45
Alignment explanation
Indices: 4604129--4604264 Score: 143
Period size: 47 Copynumber: 3.0 Consensus size: 45
4604119 CTAAAAAGTC
* ** *
4604129 AAAAAAGATAAAATAATAATAATAATAAATAAATCAAA-TCAAGG
1 AAAAAAAATAAAATAATAATAATAATAAATAAATCAAAGGAAAAG
* *
4604173 AAAAAACATAAAATAATAATAATAATAAAATAAATCAAAGGAAAAT
1 AAAAAAAATAAAATAATAATAATAAT-AAATAAATCAAAGGAAAAG
*
4604219 AAAATAAAATAAAA-AAGGAA-AATATATCAAATAAATCAAAGGAAAA
1 AAAA-AAAATAAAATAA-TAATAATA-AT-AAATAAATCAAAGGAAAA
4604265 AATGTAAAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
44 25 0.32
45 12 0.15
46 12 0.15
47 30 0.38
ACGTcount: A:0.71, C:0.04, G:0.07, T:0.18
Consensus pattern (45 bp):
AAAAAAAATAAAATAATAATAATAATAAATAAATCAAAGGAAAAG
Found at i:4604235 original size:23 final size:24
Alignment explanation
Indices: 4604190--4604264 Score: 91
Period size: 25 Copynumber: 3.1 Consensus size: 24
4604180 ATAAAATAAT
4604190 AATAATAATAAAATAAATCAAAGGAA
1 AATAA-AATAAAATAAA-CAAAGGAA
4604216 AATAAAATAAAATAAA-AAAGGAA
1 AATAAAATAAAATAAACAAAGGAA
* *
4604239 AAT-ATATCAAATAAATCAAAGGAA
1 AATAAAATAAAATAAA-CAAAGGAA
4604263 AA
1 AA
4604265 AATGTAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
22 10 0.22
23 10 0.22
24 9 0.20
25 11 0.24
26 5 0.11
ACGTcount: A:0.71, C:0.04, G:0.08, T:0.17
Consensus pattern (24 bp):
AATAAAATAAAATAAACAAAGGAA
Found at i:4604371 original size:11 final size:11
Alignment explanation
Indices: 4604343--4604379 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
4604333 AGAAACATGA
*
4604343 AATAAAATAAAA
1 AATAAAAT-AAT
4604355 AATAAAATAAT
1 AATAAAATAAT
4604366 AATAAAATAAT
1 AATAAAATAAT
4604377 AAT
1 AAT
4604380 GAATCAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:4606097 original size:494 final size:494
Alignment explanation
Indices: 4605166--4606158 Score: 1961
Period size: 494 Copynumber: 2.0 Consensus size: 494
4605156 ATGCATGCTT
4605166 GTTT-TTAGTCCAATTTCAGTTCTAATCAAACTCTACTACCCCTATTTGTTTGACATCCACGGTT
1 GTTTGTTAGTCCAATTTCAGTTCTAATCAAACTCTACTACCCCTATTTGTTTGACATCCACGGTT
*
4605230 ATTGCTCATGGCCGAGAGAATCGGGCTTTGTTGAGTAGTTGGTGTCTCACATATTCACGTCGGTT
66 ATTGCTCATGGCCGAGAGAATCGGGCTTTGTTGAGCAGTTGGTGTCTCACATATTCACGTCGGTT
4605295 GGAGGCCGAGAAGAGTGGGGGTCGTTGCGTGAGAAGTGGCGTGCCAAGGGAGGGAACCTCGATCA
131 GGAGGCCGAGAAGAGTGGGGGTCGTTGCGTGAGAAGTGGCGTGCCAAGGGAGGGAACCTCGATCA
4605360 AGAACATGACATGAGGCGCTAGGGTTCTGAAAACCCTAGCTGATGCGGATGGAACGCGTTTTGGA
196 AGAACATGACATGAGGCGCTAGGGTTCTGAAAACCCTAGCTGATGCGGATGGAACGCGTTTTGGA
4605425 TCTTGGCTGGGCCATACGTGGACTAATTTCATTTGATGTAACAGGTCTGCACAAATGTAAAGAAT
261 TCTTGGCTGGGCCATACGTGGACTAATTTCATTTGATGTAACAGGTCTGCACAAATGTAAAGAAT
4605490 AAAATTACTAATATAATAATATTAATAAATAAAAGACAAAATTAAGTGTCTTCAGCTGCCCCTCT
326 AAAATTACTAATATAATAATATTAATAAATAAAAGACAAAATTAAGTGTCTTCAGCTGCCCCTCT
4605555 TTGCTCATTATCGTGTAACGACAATAGAGCAAAGATTAAAAGACACAGATTTTGTCCATATCGAA
391 TTGCTCATTATCGTGTAACGACAATAGAGCAAAGATTAAAAGACACAGATTTTGTCCATATCGAA
4605620 TATCCTCCGTCGTAGAGTTGAAATCCGATATTGAAACTG
456 TATCCTCCGTCGTAGAGTTGAAATCCGATATTGAAACTG
4605659 GTTTGTTAGTCCAATTTCAGTTCTAATCAAACTCTACTACCCCTATTTGTTTGACATCCACGGTT
1 GTTTGTTAGTCCAATTTCAGTTCTAATCAAACTCTACTACCCCTATTTGTTTGACATCCACGGTT
4605724 ATTGCTCATGGCCGAGAGAATCGGGCTTTGTTGAGCAGTTGGTGTCTCACATATTCACGTCGGTT
66 ATTGCTCATGGCCGAGAGAATCGGGCTTTGTTGAGCAGTTGGTGTCTCACATATTCACGTCGGTT
4605789 GGAGGCCGAGAAGAGTGGGGGTCGTTGCGTGAGAAGTGGCGTGCCAAGGGAGGGAACCTCGATCA
131 GGAGGCCGAGAAGAGTGGGGGTCGTTGCGTGAGAAGTGGCGTGCCAAGGGAGGGAACCTCGATCA
4605854 AGAACATGACATGAGGCGCTAGGGTTCTGAAAACCCTAGCTGATGCGGATGGAACGCGTTTTGGA
196 AGAACATGACATGAGGCGCTAGGGTTCTGAAAACCCTAGCTGATGCGGATGGAACGCGTTTTGGA
4605919 TCTTGGCTGGGCCATACGTGGACTAATTTCATTTGATGTAACAGGTCTGCACAAATGTAAAGAAT
261 TCTTGGCTGGGCCATACGTGGACTAATTTCATTTGATGTAACAGGTCTGCACAAATGTAAAGAAT
4605984 AAAATTACTAATATAATAATATTAATAAATAAAAGACAAAATTAAGTGTCTTCAGCTGCCCCTCT
326 AAAATTACTAATATAATAATATTAATAAATAAAAGACAAAATTAAGTGTCTTCAGCTGCCCCTCT
*
4606049 TTGCTCATTGTCGTGTAACGACAATAGAGCAAAGATTAAAAGACACAGATTTTGTCCATATCGAA
391 TTGCTCATTATCGTGTAACGACAATAGAGCAAAGATTAAAAGACACAGATTTTGTCCATATCGAA
4606114 TATCCTCCGTCGTAGAGTTGAAATCCGATATTGAAACTG
456 TATCCTCCGTCGTAGAGTTGAAATCCGATATTGAAACTG
4606153 GTTTGT
1 GTTTGT
4606159 CAATTGACCA
Statistics
Matches: 497, Mismatches: 2, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
493 4 0.01
494 493 0.99
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (494 bp):
GTTTGTTAGTCCAATTTCAGTTCTAATCAAACTCTACTACCCCTATTTGTTTGACATCCACGGTT
ATTGCTCATGGCCGAGAGAATCGGGCTTTGTTGAGCAGTTGGTGTCTCACATATTCACGTCGGTT
GGAGGCCGAGAAGAGTGGGGGTCGTTGCGTGAGAAGTGGCGTGCCAAGGGAGGGAACCTCGATCA
AGAACATGACATGAGGCGCTAGGGTTCTGAAAACCCTAGCTGATGCGGATGGAACGCGTTTTGGA
TCTTGGCTGGGCCATACGTGGACTAATTTCATTTGATGTAACAGGTCTGCACAAATGTAAAGAAT
AAAATTACTAATATAATAATATTAATAAATAAAAGACAAAATTAAGTGTCTTCAGCTGCCCCTCT
TTGCTCATTATCGTGTAACGACAATAGAGCAAAGATTAAAAGACACAGATTTTGTCCATATCGAA
TATCCTCCGTCGTAGAGTTGAAATCCGATATTGAAACTG
Found at i:4606540 original size:106 final size:106
Alignment explanation
Indices: 4606359--4607210 Score: 1420
Period size: 106 Copynumber: 8.0 Consensus size: 106
4606349 GTATTGCTCC
* ** *
4606359 GAGTCCAATATCCTTCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * ** * *
4606423 ATCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTATTATCTC
65 ACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
4606465 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
4606530 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
4606571 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
4606636 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
4606677 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGCCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
4606742 CCAGCGGTCCCTTCTTCGTGAAGTTAAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
4606783 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
4606848 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
4606889 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
4606954 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
4606995 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
4607060 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
4607101 GAGTCTAATATCCTTCTCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
4607166 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
4607207 GAGT
1 GAGT
4607211 GGCACAATAT
Statistics
Matches: 707, Mismatches: 37, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
105 1 0.00
106 705 1.00
107 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:4608904 original size:27 final size:25
Alignment explanation
Indices: 4608879--4608934 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 25
4608869 ATCCCTTTTT
4608879 CTTTTTGATCTT-TGTTCTTTCTTTTTT
1 CTTTTTGATCTTAT-TTC--TCTTTTTT
* *
4608906 CCTTTTGTTCTTATTTCTCTTTTTT
1 CTTTTTGATCTTATTTCTCTTTTTT
4608931 CTTT
1 CTTT
4608935 GTTTTTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
25 11 0.44
27 13 0.52
28 1 0.04
ACGTcount: A:0.04, C:0.18, G:0.05, T:0.73
Consensus pattern (25 bp):
CTTTTTGATCTTATTTCTCTTTTTT
Found at i:4608916 original size:16 final size:15
Alignment explanation
Indices: 4608896--4608967 Score: 67
Period size: 16 Copynumber: 4.7 Consensus size: 15
4608886 ATCTTTGTTC
4608896 TTTCTTTTTTCCTTT
1 TTTCTTTTTTCCTTT
*
4608911 TGTTCTTATTTCTCTTT
1 T-TTCTTTTTTC-CTTT
4608928 TTTCTTTGTTT--TTT
1 TTTCTTT-TTTCCTTT
* *
4608942 TTGCTTTTTTTCTTCT
1 TTTCTTTTTTCCTT-T
4608958 TTTCTTTTTT
1 TTTCTTTTTT
4608968 GTTCTTGATT
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
13 3 0.06
14 9 0.19
15 3 0.06
16 24 0.51
17 8 0.17
ACGTcount: A:0.01, C:0.15, G:0.04, T:0.79
Consensus pattern (15 bp):
TTTCTTTTTTCCTTT
Found at i:4608935 original size:23 final size:23
Alignment explanation
Indices: 4608898--4608955 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 23
4608888 CTTTGTTCTT
4608898 TCTTTTTTCCTTTTGTTCTTATTT-C
1 TCTTTTTT-C-TTTGTT-TTATTTGC
*
4608923 TCTTTTTTCTTTGTTTTTTTTGC
1 TCTTTTTTCTTTGTTTTATTTGC
4608946 T-TTTTTTCTT
1 TCTTTTTTCTT
4608956 CTTTTCTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 14 0.45
23 8 0.26
24 1 0.03
25 8 0.26
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.78
Consensus pattern (23 bp):
TCTTTTTTCTTTGTTTTATTTGC
Found at i:4611963 original size:20 final size:20
Alignment explanation
Indices: 4611938--4612002 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
4611928 AAATAATAAT
4611938 AATAAATCAAAAGGAGAAAA
1 AATAAATCAAAAGGAGAAAA
** *
4611958 AATAAAAT-AAAATAAG-ATA
1 AAT-AAATCAAAAGGAGAAAA
*
4611977 AATAAATC-AAAGGAAAATAA
1 AATAAATCAAAAGGAGAA-AA
4611997 AATAAA
1 AATAAA
4612003 ATAAAAATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
18 8 0.24
19 6 0.18
20 16 0.47
21 4 0.12
ACGTcount: A:0.72, C:0.03, G:0.09, T:0.15
Consensus pattern (20 bp):
AATAAATCAAAAGGAGAAAA
Found at i:4611981 original size:39 final size:37
Alignment explanation
Indices: 4611905--4612179 Score: 151
Period size: 34 Copynumber: 7.5 Consensus size: 37
4611895 CATAAATTTG
4611905 AAATAAATC-AAGGAAAAAACATAAAAT--AAT-A-AT
1 AAATAAATCAAAGGAAAAAA-ATAAAATAAAATAATAT
*
4611938 -AATAAATCAAAAGGAGAAAAAATAAAATAAAATAAGAT
1 AAATAAATC-AAAGGA-AAAAAATAAAATAAAATAATAT
4611976 AAATAAATCAAAGGAAAATAAAATAAAATAAAA-ATATAT
1 AAATAAATCAAAGG-AAA-AAAATAAAATAAAATA-ATAT
* *
4612015 CAAATAAATCAAAGGAAAAAATGTAAAAAAATATATATATAT
1 -AAATAAATCAAAGGAAAAAA-ATAAAATAA-A-ATA-ATAT
* *
4612057 AAGATAAA--AATA-GTAAAAAAT-ATATATAAAT-A-A-
1 AA-ATAAATCAA-AGGAAAAAAATAAAATA-AAATAATAT
* * *
4612090 AAATAAATCAAA-GAGAAAACATGAAATAAAATAA-AA
1 AAATAAATCAAAGGA-AAAAAATAAAATAAAATAATAT
* *
4612126 AAATAAA--ATAA-TAATAAAATAATAATAAAAT-A-AT
1 AAATAAATCA-AAGGAAAAAAATAA-AATAAAATAATAT
*
4612160 AAATGAATCAAAGGAAAAAA
1 AAATAAATCAAAGGAAAAAA
4612180 TGAATAGTTG
Statistics
Matches: 194, Mismatches: 18, Indels: 57
0.72 0.07 0.21
Matches are distributed among these distances:
32 13 0.07
33 4 0.02
34 40 0.21
35 25 0.13
36 16 0.08
37 3 0.02
38 17 0.09
39 38 0.20
40 23 0.12
41 4 0.02
42 11 0.06
ACGTcount: A:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (37 bp):
AAATAAATCAAAGGAAAAAAATAAAATAAAATAATAT
Found at i:4612011 original size:6 final size:5
Alignment explanation
Indices: 4611956--4612008 Score: 56
Period size: 5 Copynumber: 10.8 Consensus size: 5
4611946 AAAAGGAGAA
* **
4611956 AAAAT AAAAT AAAAT AAGAT -AAAT -AAAT CAAAGG AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT
4612005 AAAA
1 AAAA
4612009 ATATATCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
4 7 0.17
5 31 0.77
6 2 0.05
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:4612057 original size:44 final size:40
Alignment explanation
Indices: 4611938--4612033 Score: 135
Period size: 40 Copynumber: 2.4 Consensus size: 40
4611928 AAATAATAAT
* *
4611938 AATAAATCAAAAGGAGAA-AAAATAAAAT-AAAATAAGAT-A
1 AATAAATC-AAAGGAAAATAAAATAAAATAAAAAT-ATATCA
4611977 AATAAATCAAAGGAAAATAAAATAAAATAAAAATATATCA
1 AATAAATCAAAGGAAAATAAAATAAAATAAAAATATATCA
4612017 AATAAATCAAAGGAAAA
1 AATAAATCAAAGGAAAA
4612034 AATGTAAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
38 8 0.15
39 21 0.40
40 23 0.44
ACGTcount: A:0.71, C:0.04, G:0.08, T:0.17
Consensus pattern (40 bp):
AATAAATCAAAGGAAAATAAAATAAAATAAAAATATATCA
Found at i:4612075 original size:31 final size:31
Alignment explanation
Indices: 4612031--4612089 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
4612021 AATCAAAGGA
*
4612031 AAAAATGTAAAAAAATATATATATATAAGAT
1 AAAAATGTAAAAAAATATATATAAATAAGAT
4612062 AAAAATAGT-AAAAAATATATATAAATAA
1 AAAAAT-GTAAAAAAATATATATAAATAA
4612090 AAATAAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (31 bp):
AAAAATGTAAAAAAATATATATAAATAAGAT
Done.