Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 160 of 204
Found at i:48004391 original size:13 final size:13
Alignment explanation
Indices: 48004373--48004401 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
48004363 GTTAAGAGTA
48004373 AAACTTTATTTGT
1 AAACTTTATTTGT
48004386 AAACTTTATTTGT
1 AAACTTTATTTGT
48004399 AAA
1 AAA
48004402 AAAGTCCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (13 bp):
AAACTTTATTTGT
Found at i:48017294 original size:7 final size:7
Alignment explanation
Indices: 48017282--48017344 Score: 92
Period size: 7 Copynumber: 8.9 Consensus size: 7
48017272 AATTGACATT
48017282 CCCTAAA
1 CCCTAAA
48017289 CCCTAAA
1 CCCTAAA
48017296 CCCTAAAA
1 CCCT-AAA
48017304 CCCT-AA
1 CCCTAAA
48017310 CCCTAAAA
1 CCCT-AAA
48017318 CCCTAAA
1 CCCTAAA
48017325 CCCTAAA
1 CCCTAAA
*
48017332 CCTTAAA
1 CCCTAAA
48017339 CCCTAA
1 CCCTAA
48017345 GCCTATCCCT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
6 6 0.12
7 32 0.63
8 13 0.25
ACGTcount: A:0.43, C:0.41, G:0.00, T:0.16
Consensus pattern (7 bp):
CCCTAAA
Found at i:48024716 original size:5 final size:5
Alignment explanation
Indices: 48024708--48024737 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
48024698 TAGAATAAAC
*
48024708 TTGGG TTGGG TTGGG TTGGG TTGGT TTGGG
1 TTGGG TTGGG TTGGG TTGGG TTGGG TTGGG
48024738 GTCAAGTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.57, T:0.43
Consensus pattern (5 bp):
TTGGG
Found at i:48035125 original size:40 final size:40
Alignment explanation
Indices: 48035079--48035169 Score: 114
Period size: 39 Copynumber: 2.3 Consensus size: 40
48035069 ATATTAAAAA
* *
48035079 TATATTATATTAAAAAAACTACCA-TAAATATAATAAATCT
1 TATATTATATTAAAAAAAC-ACAACTAAATATAATAAATAT
* *
48035119 TTTATTATATT-AAAAAACGCAACTAAATATAATAAATAT
1 TATATTATATTAAAAAAACACAACTAAATATAATAAATAT
*
48035158 TATATTGTATTA
1 TATATTATATTA
48035170 GATATAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.05
39 31 0.72
40 10 0.23
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (40 bp):
TATATTATATTAAAAAAACACAACTAAATATAATAAATAT
Found at i:48035886 original size:18 final size:20
Alignment explanation
Indices: 48035856--48035896 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
48035846 TATTATTAAA
48035856 TAAAATATTAAAAATATT-T
1 TAAAATATTAAAAATATTAT
*
48035875 TAAAAT-TTAAAATTATTAT
1 TAAAATATTAAAAATATTAT
48035894 TAA
1 TAA
48035897 TGCTAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAAATATTAAAAATATTAT
Found at i:48037875 original size:46 final size:46
Alignment explanation
Indices: 48037805--48037943 Score: 233
Period size: 46 Copynumber: 3.0 Consensus size: 46
48037795 CATGGCAAAG
* *
48037805 TGTGAAACGTAGGTATGGTATTTCAATGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
*
48037851 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
48037897 TGTAAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
48037943 T
1 T
48037944 ATAGCAATGT
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 87 1.00
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:48046764 original size:3 final size:3
Alignment explanation
Indices: 48046737--48046808 Score: 66
Period size: 3 Copynumber: 25.0 Consensus size: 3
48046727 TTGATAAATG
*
48046737 ATA A-A ATA A-A ATA A-A ATA CTA ATA ATA A-A ATA ATA ATA AGTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
48046779 A-A A-A ATAA ATAA ATA ATA ATA ATA ATA ATA
1 ATA ATA AT-A AT-A ATA ATA ATA ATA ATA ATA
48046809 GTAAACTAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
2 12 0.20
3 38 0.63
4 10 0.17
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (3 bp):
ATA
Found at i:48046765 original size:14 final size:14
Alignment explanation
Indices: 48046741--48046808 Score: 77
Period size: 14 Copynumber: 4.7 Consensus size: 14
48046731 TAAATGATAA
48046741 AATAA-AATAAAAT
1 AATAATAATAAAAT
*
48046754 ACTAATAATAAAAT
1 AATAATAATAAAAT
48046768 AATAATAAGTAAAA-
1 AATAATAA-TAAAAT
48046782 AATAAATAAATAATAAT
1 AAT-AAT-AATAA-AAT
48046799 AATAATAATA
1 AATAATAATA
48046809 GTAAACTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
13 4 0.09
14 18 0.38
15 15 0.32
16 7 0.15
17 3 0.06
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (14 bp):
AATAATAATAAAAT
Found at i:48047687 original size:20 final size:21
Alignment explanation
Indices: 48047658--48047716 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
48047648 ATGAAAAAAC
* * *
48047658 AATAGCAAAAAA-AGCAATAA
1 AATAGTAAAAAATAACAAGAA
48047678 AATAGTAAAAAATAACAAGAA
1 AATAGTAAAAAATAACAAGAA
* *
48047699 AACAGTAAAAAAGAACAA
1 AATAGTAAAAAATAACAA
48047717 CAATTTGTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
20 11 0.33
21 22 0.67
ACGTcount: A:0.71, C:0.08, G:0.10, T:0.10
Consensus pattern (21 bp):
AATAGTAAAAAATAACAAGAA
Found at i:48048022 original size:89 final size:89
Alignment explanation
Indices: 48047871--48048310 Score: 595
Period size: 89 Copynumber: 5.0 Consensus size: 89
48047861 TTTCACTTTT
* *
48047871 CAGACTGAAGATAACAGATATTGTCTTCCTGTATTGGCAACGAAGCAGATCGAAGACACCAGCCT
1 CAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCT
*
48047936 GGCCTCCCTGAGTTTGCAGCGAAG
66 GGCCTCCCTGAGTTTGCAGCGGAG
* *
48047960 CAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAACGAAGTAGATCGAAGACACCAGCCT
1 CAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCT
** *
48048025 GATCTCCC----TTAGC-GCGGAG
66 GGCCTCCCTGAGTTTGCAGCGGAG
* * * *
48048044 CATACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATTGAAGACACCAGTCT
1 CAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCT
* *
48048109 TGCCTCTCTGAGTTTGCAGCGGAG
66 GGCCTCCCTGAGTTTGCAGCGGAG
*
48048133 TAGACTGGAA-ATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCC
1 CAGACT-GAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCC
* *
48048197 TGACCTCCCTGAGTTTGCAGTGGAG
65 TGGCCTCCCTGAGTTTGCAGCGGAG
* * * *
48048222 CATACTGAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAAACACCAGCCT
1 CAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCT
* ** * *
48048287 TGCCTCTTTAAGTTTGCAGTGGAG
66 GGCCTCCCTGAGTTTGCAGCGGAG
48048311 TAGGTTGAAG
Statistics
Matches: 308, Mismatches: 36, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
84 68 0.22
85 4 0.01
88 7 0.02
89 226 0.73
90 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.24
Consensus pattern (89 bp):
CAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCT
GGCCTCCCTGAGTTTGCAGCGGAG
Found at i:48048163 original size:173 final size:175
Alignment explanation
Indices: 48047874--48048336 Score: 653
Period size: 173 Copynumber: 2.6 Consensus size: 175
48047864 CACTTTTCAG
* * * *
48047874 ACTGAAGATAACAGATATTGTCTTCCTGTATTGGCAACGAAGCAGATCGAAGACACCAGCCTGGC
1 ACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCTTGC
* * *
48047939 CTCCCTGAGTTTGCAGCGAAGCAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAACGAA
66 CTCTCTGAGTTTGCAGCGGAGTAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAACGAA
* *
48048004 GTAGATCGAAGACACCAGCCTGATCTCCC-TTAGC-GCGGAGCAT
131 GCAGATCGAAGACACCAGCCTGACCTCCCGTTAGCAGCGGAGCAT
* *
48048047 ACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATTGAAGACACCAGTCTTGC
1 ACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCTTGC
*
48048112 CTCTCTGAGTTTGCAGCGGAGTAGACTGGAA-ATAACAGATCTTGTCTTCCTGTATTGGCAGCGA
66 CTCTCTGAGTTTGCAGCGGAGTAGACT-GAAGATAACAGATCTTGTCTTCCTGTATTGGCAACGA
* *
48048176 AGCAGATCGAAGACACCAGCCTGACCTCCCTGAGTTTGCAGTGGAGCAT
130 AGCAGATCGAAGACACCAGCCTGACCTCCC---GTTAGCAGCGGAGCAT
* *
48048225 ACTGAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAAACACCAGCCTTGC
1 ACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCTTGC
* * * ** ***
48048290 CTCTTTAAGTTTGCAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCT
66 CTCTCTGAGTTTGCAGCGGAGTAGACTGAAGATAACAGATCTTGTCT
48048337 CCCTAAGTAG
Statistics
Matches: 257, Mismatches: 26, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
173 143 0.56
174 3 0.01
177 7 0.03
178 104 0.40
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (175 bp):
ACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCTTGC
CTCTCTGAGTTTGCAGCGGAGTAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAACGAA
GCAGATCGAAGACACCAGCCTGACCTCCCGTTAGCAGCGGAGCAT
Found at i:48048559 original size:51 final size:50
Alignment explanation
Indices: 48048492--48048851 Score: 291
Period size: 51 Copynumber: 7.4 Consensus size: 50
48048482 GGAGCAGATC
* *
48048492 GAAGACAGCGAATCTTATTTTCCTGGCGTTGCAGTGGAACAGATTAAAGCT
1 GAAGGCAGCGAATCTTATTTTCCTGGCGTTGCAGT-GAGCAGATTAAAGCT
* * * * *
48048543 AAAGGCAGCGAGTCTTATTTCCCTAGCG-T-C-G-CAGCAGATTAAAGCT
1 GAAGGCAGCGAATCTTATTTTCCTGGCGTTGCAGTGAGCAGATTAAAGCT
* * *
48048589 GAAGGCAGCGAGTCTTA-TTTCCTTGGCGTTACAGTAGAGCAGATTAAAGCA
1 GAAGGCAGCGAATCTTATTTTCC-TGGCGTTGCAGT-GAGCAGATTAAAGCT
* * * * * * *
48048640 AAAGACAGCAAATCTTATCTCCCTAGCG-T-C-GT-AGTAGATTAAAGCT
1 GAAGGCAGCGAATCTTATTTTCCTGGCGTTGCAGTGAGCAGATTAAAGCT
* * *
48048686 GAAGGCAGCGAATCTCA-TTTCCTTAGCATTGCAGTGGAGCAGATTAAAGCT
1 GAAGGCAGCGAATCTTATTTTCC-TGGCGTTGCAGT-GAGCAGATTAAAGCT
* * * *
48048737 GAAGGCAGCAAATCTTATCTCCCTGGCGTCGCAGT----AGATTAAAGCT
1 GAAGGCAGCGAATCTTATTTTCCTGGCGTTGCAGTGAGCAGATTAAAGCT
* * * *
48048783 GAAGGTAGCGAGTCTTA-TTTCCTTGGCATTGCAGTAGAGCAGATTAAAGTT
1 GAAGGCAGCGAATCTTATTTTCC-TGGCGTTGCAGT-GAGCAGATTAAAGCT
*
48048834 GAACGCAGCGAATCTTAT
1 GAAGGCAGCGAATCTTAT
48048852 CTCCCTGGAG
Statistics
Matches: 241, Mismatches: 47, Indels: 41
0.73 0.14 0.12
Matches are distributed among these distances:
45 10 0.04
46 97 0.40
47 2 0.01
48 5 0.02
49 5 0.02
50 2 0.01
51 114 0.47
52 6 0.02
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (50 bp):
GAAGGCAGCGAATCTTATTTTCCTGGCGTTGCAGTGAGCAGATTAAAGCT
Found at i:48048584 original size:46 final size:46
Alignment explanation
Indices: 48048531--48048857 Score: 251
Period size: 46 Copynumber: 6.8 Consensus size: 46
48048521 TGCAGTGGAA
* *
48048531 CAGATTAAAGCTAAAGGCAGCGAGTCTTATTTCCCTAGCGTCGCAG
1 CAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTCGCAG
* * * *
48048577 CAGATTAAAGCTGAAGGCAGCGAGTCTTATTTCCTTGGCGTTACAGTAGAG
1 CAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCG-T-C-G--CAG
** * * * *
48048628 CAGATTAAAGCAAAAGACAGCAAATCTTATCTCCCTAGCGTCGTAG
1 CAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTCGCAG
* * * * *
48048674 TAGATTAAAGCTGAAGGCAGCGAATCTCATTTCCTTAGCATTGCAGTGGAG
1 CAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGC-GT-C---GCAG
* * *
48048725 CAGATTAAAGCTGAAGGCAGCAAATCTTATCTCCCTGGCGTCGCAG
1 CAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTCGCAG
* * * * *
48048771 TAGATTAAAGCTGAAGGTAGCGAGTCTTATTTCCTTGGCATTGCAGTAG-AG
1 CAGATTAAAGCTGAAGGCAGCGAATCTTATTTCC----C-TAGC-GTCGCAG
* * *
48048822 CAGATTAAAGTTGAACGCAGCGAATCTTATCTCCCT
1 CAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCT
48048858 GGAGTTAAGA
Statistics
Matches: 221, Mismatches: 44, Indels: 32
0.74 0.15 0.11
Matches are distributed among these distances:
46 103 0.47
47 3 0.01
48 3 0.01
49 3 0.01
50 3 0.01
51 103 0.47
52 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.26
Consensus pattern (46 bp):
CAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTCGCAG
Found at i:48048859 original size:97 final size:97
Alignment explanation
Indices: 48048492--48048857 Score: 491
Period size: 97 Copynumber: 3.8 Consensus size: 97
48048482 GGAGCAGATC
* * * * * *
48048492 GAAGACAGCGAATCTTATTTTCC-TGGCGTTGCAGTGGAACAGATTAAAGCTAAAGGCAGCGAGT
1 GAAGGCAGCGAATCTTA-TTTCCTTGGCATTGCAGTAGAGCAGATTAAAGCTAAAGGCAGCAAAT
* *
48048556 CTTATTTCCCTAGCGTCGCAGCAGATTAAAGCT
65 CTTATCTCCCTAGCGTCGCAGTAGATTAAAGCT
* * * * *
48048589 GAAGGCAGCGAGTCTTATTTCCTTGGCGTTACAGTAGAGCAGATTAAAGCAAAAGACAGCAAATC
1 GAAGGCAGCGAATCTTATTTCCTTGGCATTGCAGTAGAGCAGATTAAAGCTAAAGGCAGCAAATC
*
48048654 TTATCTCCCTAGCGTCGTAGTAGATTAAAGCT
66 TTATCTCCCTAGCGTCGCAGTAGATTAAAGCT
* * * *
48048686 GAAGGCAGCGAATCTCATTTCCTTAGCATTGCAGTGGAGCAGATTAAAGCTGAAGGCAGCAAATC
1 GAAGGCAGCGAATCTTATTTCCTTGGCATTGCAGTAGAGCAGATTAAAGCTAAAGGCAGCAAATC
*
48048751 TTATCTCCCTGGCGTCGCAGTAGATTAAAGCT
66 TTATCTCCCTAGCGTCGCAGTAGATTAAAGCT
* * * * * *
48048783 GAAGGTAGCGAGTCTTATTTCCTTGGCATTGCAGTAGAGCAGATTAAAGTTGAACGCAGCGAATC
1 GAAGGCAGCGAATCTTATTTCCTTGGCATTGCAGTAGAGCAGATTAAAGCTAAAGGCAGCAAATC
48048848 TTATCTCCCT
66 TTATCTCCCT
48048858 GGAGTTAAGA
Statistics
Matches: 237, Mismatches: 31, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
96 5 0.02
97 232 0.98
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.26
Consensus pattern (97 bp):
GAAGGCAGCGAATCTTATTTCCTTGGCATTGCAGTAGAGCAGATTAAAGCTAAAGGCAGCAAATC
TTATCTCCCTAGCGTCGCAGTAGATTAAAGCT
Found at i:48051369 original size:22 final size:22
Alignment explanation
Indices: 48051328--48051416 Score: 78
Period size: 23 Copynumber: 4.0 Consensus size: 22
48051318 TTCAATGAAA
48051328 CTGGAAATTG--TTGCATTTGTT
1 CTGGAAATTGTTTTG-ATTTGTT
* *
48051349 -TTGATATTGTTCTTGATTTGTT
1 CTGGAAATTGTT-TTGATTTGTT
*
48051371 CTGGAAATTGTTTTGA-TAGTCT
1 CTGGAAATTGTTTTGATTTGT-T
48051393 GCTGGAAATTGTTCTTGATTTGTT
1 -CTGGAAATTGTT-TTGATTTGTT
48051417 AGTGAGTAGA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
20 7 0.13
21 3 0.06
22 12 0.22
23 24 0.44
24 5 0.09
25 3 0.06
ACGTcount: A:0.18, C:0.08, G:0.22, T:0.52
Consensus pattern (22 bp):
CTGGAAATTGTTTTGATTTGTT
Found at i:48052891 original size:6 final size:6
Alignment explanation
Indices: 48052880--48052905 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
48052870 ACGAAATTAT
48052880 ATTTAA ATTTAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA AT
48052906 GTTCAAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:48056275 original size:47 final size:47
Alignment explanation
Indices: 48056218--48056545 Score: 242
Period size: 47 Copynumber: 7.2 Consensus size: 47
48056208 ATATAAGAAC
* * *
48056218 ATTTATTATTAAGAATTTTATGAAATGATATATCATTATTAAATTAT
1 ATTTAATATTAAGAATTTTATGAAATTATATATAATTATTAAATTAT
** *
48056265 ATTTAATATTAATTA-TTT-T-AAATTATATA-AATTCATATAAGA--AA
1 ATTTAATATTAAGAATTTTATGAAATTATATATAATT-AT-TAA-ATTAT
* * *
48056309 ATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 ATTTAATATTAAGAATTTTATGAAATTATATATAATTATTAAATTAT
** *
48056356 ATTTAATATTAATTA-TTT-T-AAATTATATA-AATTCATATAAGA--AA
1 ATTTAATATTAAGAATTTTATGAAATTATATATAATT-AT-TAA-ATTAT
* * *
48056400 ATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 ATTTAATATTAAGAATTTTATGAAATTATATATAATTATTAAATTAT
** *
48056447 ATTTAATATTAATTA-TTT-T-AAATTATATA-AATTCATATAAGA--AA
1 ATTTAATATTAAGAATTTTATGAAATTATATATAATT-AT-TAA-ATTAT
* * ** *
48056491 ATTTATTATCAAGAATTTTATGAAATTATATATTTTTATTGAATTAT
1 ATTTAATATTAAGAATTTTATGAAATTATATATAATTATTAAATTAT
48056538 ATTTAATA
1 ATTTAATA
48056546 ATAATTATTT
Statistics
Matches: 215, Mismatches: 39, Indels: 54
0.70 0.13 0.18
Matches are distributed among these distances:
43 9 0.04
44 71 0.33
45 24 0.11
46 23 0.11
47 80 0.37
48 8 0.04
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (47 bp):
ATTTAATATTAAGAATTTTATGAAATTATATATAATTATTAAATTAT
Found at i:48056438 original size:101 final size:95
Alignment explanation
Indices: 48056201--48056666 Score: 581
Period size: 91 Copynumber: 5.0 Consensus size: 95
48056191 ATGATTTTAG
* * * *
48056201 TAAATTCATATAAGAACATTTATTATTAAGAATTTTATGAA-AT-GA-TATAT-CATTATTAAAT
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAATATATATTATATATATTATTAAAT
48056262 TATATTTAATATTAATTATTTTAAATTATA
66 TATATTTAATATTAATTATTTTAAATTATA
*
48056292 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAA-AT-TA-TATAT-CATTATTAAAT
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAATATATATTATATATATTATTAAAT
48056353 TATATTTAATATTAATTATTTTAAATTATA
66 TATATTTAATATTAATTATTTTAAATTATA
*
48056383 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAA-AT-TA-TATAT-CATTATTAAAT
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAATATATATTATATATATTATTAAAT
48056444 TATATTTAATATTAATTATTTTAAATTATA
66 TATATTTAATATTAATTATTTTAAATTATA
* *
48056474 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAA-AT-TA-TATAT-TTTTATTGAAT
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAATATATATTATATATATTATTAAAT
*
48056535 TATATTTAATAATAATTATTTTAAATTATA
66 TATATTTAATATTAATTATTTTAAATTATA
* * * * * *
48056565 CAAATTCATATAAGAAAATTTATTAGT-TATAATTATTTTAAAT-TTTATTAAATCATATATTTT
1 TAAATTCATATAAGAAAATTTATTA-TCAAGAATT-TTATGAATATATATT--AT-ATATA--TT
* *
48056628 AATTAAAATATATTTAATATTAATTATTTCAAATTATA
59 -ATTAAATTATATTTAATATTAATTATTTTAAATTATA
48056666 T
1 T
48056667 TTTTATAGTA
Statistics
Matches: 345, Mismatches: 18, Indels: 14
0.92 0.05 0.04
Matches are distributed among these distances:
91 295 0.86
92 7 0.02
93 2 0.01
94 1 0.00
96 2 0.01
97 2 0.01
98 1 0.00
100 2 0.01
101 33 0.10
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (95 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAATATATATTATATATATTATTAAAT
TATATTTAATATTAATTATTTTAAATTATA
Found at i:48056599 original size:47 final size:45
Alignment explanation
Indices: 48056274--48056608 Score: 214
Period size: 47 Copynumber: 7.3 Consensus size: 45
48056264 TATTTAATAT
48056274 TAATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCAA
1 TAATTATTTTAAATTATA-AAATTCATATAAGAAAATTTATTAT-AA
* * * ** *
48056321 GAATT-TTATGAAATTAT-ATA-TCAT-T-ATTAAATTATATTTAATAT
1 TAATTATT-TTAAATTATAAAATTCATATAAGAAAATT-TA-TT-ATAA
48056365 TAATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCAA
1 TAATTATTTTAAATTATA-AAATTCATATAAGAAAATTTATTAT-AA
* * * ** *
48056412 GAATT-TTATGAAATTAT-ATA-TCAT-T-ATTAAATTATATTTAATAT
1 TAATTATT-TTAAATTATAAAATTCATATAAGAAAATT-TA-TT-ATAA
48056456 TAATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCAA
1 TAATTATTTTAAATTATA-AAATTCATATAAGAAAATTTATTAT-AA
* * * ** *
48056503 GAATT-TTATGAAATTAT-ATATTTTTAT-TG--AATTATATTTAATAA
1 TAATTATT-TTAAATTATAAAATTCATATAAGAAAATT-TA-TT-ATAA
*
48056547 TAATTATTTTAAATTATACAAATTCATATAAGAAAATTTATTAGTTA
1 TAATTATTTTAAATTATA-AAATTCATATAAGAAAATTTATTA-TAA
48056594 TAATTATTTTAAATT
1 TAATTATTTTAAATT
48056609 TTATTAAATC
Statistics
Matches: 218, Mismatches: 37, Indels: 66
0.68 0.12 0.21
Matches are distributed among these distances:
42 16 0.07
43 8 0.04
44 55 0.25
45 23 0.11
46 22 0.10
47 70 0.32
48 8 0.04
49 16 0.07
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.48
Consensus pattern (45 bp):
TAATTATTTTAAATTATAAAATTCATATAAGAAAATTTATTATAA
Found at i:48056608 original size:91 final size:91
Alignment explanation
Indices: 48056201--48056589 Score: 706
Period size: 91 Copynumber: 4.3 Consensus size: 91
48056191 ATGATTTTAG
* * *
48056201 TAAATTCATATAAGAACATTTATTATTAAGAATTTTATGAAATGATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
48056266 TTTAATATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
48056292 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
48056357 TTTAATATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
48056383 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
48056448 TTTAATATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
** *
48056474 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTTTTATTGAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
*
48056539 TTTAATAATAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
*
48056565 CAAATTCATATAAGAAAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
48056590 GTTATAATTA
Statistics
Matches: 290, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 290 1.00
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TTTAATATTAATTATTTTAAATTATA
Found at i:48056846 original size:120 final size:121
Alignment explanation
Indices: 48056605--48056901 Score: 499
Period size: 120 Copynumber: 2.5 Consensus size: 121
48056595 AATTATTTTA
* *
48056605 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
* * *
48056669 TTATAGTATCATATATTATGGTTTTAGTAAATTCATATAAGAATATTGATTATTAAG
65 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
48056726 AATTTTATTAAATTATATTTTTTAATTAAAATATAGTTAATAATAATTATGTTAAATTATA-TTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
48056790 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
48056846 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAA
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
48056902 ATATGATTAA
Statistics
Matches: 165, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
120 109 0.66
121 54 0.33
122 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (121 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:48056886 original size:15 final size:15
Alignment explanation
Indices: 48056851--48056892 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
48056841 TTAAGAATTT
*
48056851 TATTAAATTAT-ATA
1 TATTTAATTATAATA
48056865 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
48056879 TATTTAATAATAAT
1 TATTTAATTATAAT
48056893 TATGTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:48057135 original size:16 final size:16
Alignment explanation
Indices: 48057114--48057162 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
48057104 TTGATTTGCT
48057114 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
48057130 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
48057146 ATTACACCTCTATTCC
1 ATTACGCCTCTATTCC
48057162 A
1 A
48057163 ATACAGCGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.22, C:0.37, G:0.04, T:0.37
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:48058375 original size:22 final size:23
Alignment explanation
Indices: 48058306--48058387 Score: 89
Period size: 22 Copynumber: 3.7 Consensus size: 23
48058296 CTTAACTATG
**
48058306 TTTTAAATTTATCATTAGCATTA
1 TTTTAAATTTATCATTAATATTA
* * *
48058329 TTTT-AATATATAATATACTATTA
1 TTTTAAATTTATCAT-TAATATTA
48058352 TTTTAAA-TTATCATTAATATTA
1 TTTTAAATTTATCATTAATATTA
48058374 -TTTAAATTTATCAT
1 TTTTAAATTTATCAT
48058388 ACATCATAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
21 6 0.12
22 22 0.45
23 19 0.39
24 2 0.04
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (23 bp):
TTTTAAATTTATCATTAATATTA
Found at i:48058405 original size:45 final size:45
Alignment explanation
Indices: 48058307--48058406 Score: 103
Period size: 45 Copynumber: 2.2 Consensus size: 45
48058297 TTAACTATGT
* * * * *
48058307 TTTAAATTTATCATTAGCATTATTTTAATATATAATATACTATTA
1 TTTAAAATTATCATTAACATTATTTAAATATATAATACACTATAA
* * * *
48058352 TTTTAAATTATCATTAATATTATTTAAATTTATCATACA-TCATAA
1 TTTAAAATTATCATTAACATTATTTAAATATATAATACACT-ATAA
48058397 TTTAAAATTA
1 TTTAAAATTA
48058407 ATATATTTTG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
44 1 0.02
45 43 0.98
ACGTcount: A:0.42, C:0.07, G:0.01, T:0.50
Consensus pattern (45 bp):
TTTAAAATTATCATTAACATTATTTAAATATATAATACACTATAA
Found at i:48061477 original size:19 final size:19
Alignment explanation
Indices: 48061453--48061489 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
48061443 CAATCAAGCA
48061453 ATAGTTATTCATGATTCAG
1 ATAGTTATTCATGATTCAG
48061472 ATAGTTATTCATGATTCA
1 ATAGTTATTCATGATTCA
48061490 CCCACTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (19 bp):
ATAGTTATTCATGATTCAG
Found at i:48061498 original size:19 final size:19
Alignment explanation
Indices: 48061457--48061499 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
48061447 CAAGCAATAG
* * *
48061457 TTATTCATGATTCAGATAG
1 TTATTCATGATTCACACAC
*
48061476 TTATTCATGATTCACCCAC
1 TTATTCATGATTCACACAC
48061495 TTATT
1 TTATT
48061500 TAAATAAACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (19 bp):
TTATTCATGATTCACACAC
Found at i:48068382 original size:18 final size:18
Alignment explanation
Indices: 48068356--48068390 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
48068346 AAAATTTTAA
48068356 AAATCAAATTTAAACTAG
1 AAATCAAATTTAAACTAG
*
48068374 AAATTAAATTTAAACTA
1 AAATCAAATTTAAACTA
48068391 ATTACAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.09, G:0.03, T:0.31
Consensus pattern (18 bp):
AAATCAAATTTAAACTAG
Found at i:48069928 original size:24 final size:24
Alignment explanation
Indices: 48069901--48069948 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
48069891 GTTCATGAAC
*
48069901 AAGCTCGTCCATTGGCTCATTTAT
1 AAGCTCGTCCATTGACTCATTTAT
* **
48069925 AAGCTCTTTTATTGACTCATTTAT
1 AAGCTCGTCCATTGACTCATTTAT
48069949 TTATTAATGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.44
Consensus pattern (24 bp):
AAGCTCGTCCATTGACTCATTTAT
Found at i:48074677 original size:61 final size:62
Alignment explanation
Indices: 48074499--48074677 Score: 143
Period size: 61 Copynumber: 2.9 Consensus size: 62
48074489 TTAGTCTAGT
* ** * *
48074499 AACAAAATTAGCCCTCTAATGTTTAC-ATATTCTATCAATTT-GATCTTAAATATAAAAAAATTT
1 AACAAATTTAGCCCTC-AACATTTACAAAATT-TATCAATTTAG-TCTTAAATCT-AAAAAATTT
48074562 C
62 C
* ** * * * *
48074563 AACAAATTTAGCTCTCAATGTTTACAAAATTTTTCATTTTAAT-TCTAATTCTAAAAAATTT-
1 AACAAATTTAGCCCTCAACATTTACAAAATTTATCAATTTAGTCT-TAAATCTAAAAAATTTC
* *
48074624 AATAAATTT-GACCCTCAACATTTACAAAATTTATCAATTTAGTCTTAACTCTAA
1 AACAAATTTAG-CCCTCAACATTTACAAAATTTATCAATTTAGTCTTAAATCTAA
48074678 TTTAAAAAAA
Statistics
Matches: 94, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
60 1 0.01
61 42 0.45
62 11 0.12
63 22 0.23
64 18 0.19
ACGTcount: A:0.41, C:0.16, G:0.04, T:0.40
Consensus pattern (62 bp):
AACAAATTTAGCCCTCAACATTTACAAAATTTATCAATTTAGTCTTAAATCTAAAAAATTTC
Found at i:48075160 original size:61 final size:62
Alignment explanation
Indices: 48075095--48075223 Score: 156
Period size: 61 Copynumber: 2.1 Consensus size: 62
48075085 AAGGGGAAAG
*
48075095 TTTATTGAATTTTTTAGAATTAGAACTAAAA-TGA-AAAATTTTGTAAACAAT-GAGGGCTAAA
1 TTTATTGAATTTTTTAGAATTAGAA-TAAAATTGATAAAA-TATGTAAACAATAGAGGGCTAAA
* * * * * *
48075156 TTTATTGAATTTTTTATATTTAGGATAAAATTGATAGAATATGTAAACATTAGAGGGCTAAT
1 TTTATTGAATTTTTTAGAATTAGAATAAAATTGATAAAATATGTAAACAATAGAGGGCTAAA
48075218 TTTATT
1 TTTATT
48075224 ACTAGACCAA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
60 5 0.09
61 35 0.60
62 18 0.31
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.41
Consensus pattern (62 bp):
TTTATTGAATTTTTTAGAATTAGAATAAAATTGATAAAATATGTAAACAATAGAGGGCTAAA
Found at i:48080236 original size:28 final size:28
Alignment explanation
Indices: 48080204--48080260 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
48080194 ATGGAAAGGA
48080204 AAGGATCGAGACCAAAATACCCCACGGT
1 AAGGATCGAGACCAAAATACCCCACGGT
48080232 AAGGATCGAGACCAAAATACCCCACGGT
1 AAGGATCGAGACCAAAATACCCCACGGT
48080260 A
1 A
48080261 TTACACTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.28, G:0.21, T:0.11
Consensus pattern (28 bp):
AAGGATCGAGACCAAAATACCCCACGGT
Found at i:48080385 original size:40 final size:40
Alignment explanation
Indices: 48080330--48080420 Score: 130
Period size: 40 Copynumber: 2.3 Consensus size: 40
48080320 TTCAAATTCT
*
48080330 TGAAAAGGTTGAAAAGGATACATCTGAAACGAATATCTAA
1 TGAAAAGGTTGAAAAGGATACATCCGAAACGAATATCTAA
* * *
48080370 TGAAAATGTTGAAAAGGATATATCCGAAATGAATATCT-A
1 TGAAAAGGTTGAAAAGGATACATCCGAAACGAATATCTAA
48080409 TCGAAAAGGTTG
1 T-GAAAAGGTTG
48080421 TTACCCTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
39 2 0.04
40 43 0.96
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.25
Consensus pattern (40 bp):
TGAAAAGGTTGAAAAGGATACATCCGAAACGAATATCTAA
Found at i:48081085 original size:22 final size:22
Alignment explanation
Indices: 48081025--48081082 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
48081015 AATCTTCAAG
48081025 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
48081044 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
48081066 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
48081083 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:48092507 original size:21 final size:22
Alignment explanation
Indices: 48092481--48092523 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
48092471 AGTAAATTAA
48092481 TATTTTTA-TTAAAAATTTATC
1 TATTTTTACTTAAAAATTTATC
48092502 TATTTTTACTGTTAAAAATTTA
1 TATTTTTAC--TTAAAAATTTA
48092524 CCCTTATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
24 11 0.58
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (22 bp):
TATTTTTACTTAAAAATTTATC
Found at i:48093987 original size:30 final size:30
Alignment explanation
Indices: 48093952--48094012 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
48093942 ACGTTGCAGG
*
48093952 TAAGTATTGAAAATTATATATTTAGGAACT
1 TAAGTATCGAAAATTATATATTTAGGAACT
48093982 TAAGTATCGAAAATTATATATTTAGGAACT
1 TAAGTATCGAAAATTATATATTTAGGAACT
48094012 T
1 T
48094013 GAGGAAATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.05, G:0.13, T:0.39
Consensus pattern (30 bp):
TAAGTATCGAAAATTATATATTTAGGAACT
Found at i:48096313 original size:44 final size:43
Alignment explanation
Indices: 48096203--48096327 Score: 139
Period size: 44 Copynumber: 2.9 Consensus size: 43
48096193 AGCTCATACA
* * * * *
48096203 ATGCCAACGTCCCAGACGTGGTCTTCCATGTAATTACATATTG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACAAATCG
48096246 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAAATCACAAATCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGT-AATCACAAATCG
*
48096290 ATGCCAACGTCCCAAACGTGGTCTTACACGATAA-CACA
1 ATGCCAACGTCCCAGACGTGGTCTTACACG-TAATCACA
48096328 CAACAGAATC
Statistics
Matches: 70, Mismatches: 6, Indels: 12
0.80 0.07 0.14
Matches are distributed among these distances:
42 2 0.03
43 29 0.41
44 36 0.51
45 3 0.04
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACAAATCG
Found at i:48096887 original size:28 final size:32
Alignment explanation
Indices: 48096830--48096889 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
48096820 CTAAGTCCAC
*
48096830 AAATTTTATTTATTTCACATTTTAGTCCCTAA
1 AAATATTATTTATTTCACATTTTAGTCCCTAA
48096862 AAATATTATTT-TTTCA-A-TTTAG-CCCTAA
1 AAATATTATTTATTTCACATTTTAGTCCCTAA
48096890 TTACTCAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 6 0.22
29 5 0.19
30 1 0.04
31 5 0.19
32 10 0.37
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.48
Consensus pattern (32 bp):
AAATATTATTTATTTCACATTTTAGTCCCTAA
Found at i:48100025 original size:3 final size:3
Alignment explanation
Indices: 48100017--48100043 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
48100007 TCCTATTAAT
48100017 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
48100044 CATTCTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:48104938 original size:17 final size:18
Alignment explanation
Indices: 48104905--48104938 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
48104895 TATGATTTGA
*
48104905 TAAATGATAATATAATTT
1 TAAATGATAATAAAATTT
48104923 TAAATGA-AATAAAATT
1 TAAATGATAATAAAATT
48104939 AAATAGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
TAAATGATAATAAAATTT
Found at i:48105891 original size:25 final size:25
Alignment explanation
Indices: 48105863--48105915 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
48105853 TATGAAAATA
*
48105863 AAATAATATCAAATAAAAATAAAAC
1 AAATAATAACAAATAAAAATAAAAC
* * *
48105888 AAATGATAACAAATAATAATGAAAC
1 AAATAATAACAAATAAAAATAAAAC
48105913 AAA
1 AAA
48105916 ACCTATTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.70, C:0.08, G:0.04, T:0.19
Consensus pattern (25 bp):
AAATAATAACAAATAAAAATAAAAC
Found at i:48109473 original size:21 final size:22
Alignment explanation
Indices: 48109422--48109473 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
48109412 TACGGCGAGG
*
48109422 GACGTGGCATGTACGGAGGCGC
1 GACGTGGCACGTACGGAGGCGC
*
48109444 GAACGTGGCACGTACGGAGGCGT
1 G-ACGTGGCACGTACGGAGGCGC
48109467 G-CGTGGC
1 GACGTGGC
48109474 TAGGGGAAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 6 0.22
22 1 0.04
23 20 0.74
ACGTcount: A:0.17, C:0.23, G:0.46, T:0.13
Consensus pattern (22 bp):
GACGTGGCACGTACGGAGGCGC
Found at i:48113338 original size:3 final size:3
Alignment explanation
Indices: 48113330--48113392 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
48113320 ATAGGTTTGA
48113330 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
48113378 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
48113393 ATTTCTATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:48123599 original size:42 final size:42
Alignment explanation
Indices: 48123538--48123623 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
48123528 AAAGAGAACC
* * *
48123538 AAGGTGAAAACCCATAAAGGGCGCTTTGAGTTCTAAAAA-AAT
1 AAGGTGAAAACCCACAAAGGGCGCTTGGAG-TCCAAAAATAAT
* *
48123580 AAGGTGAAAACCCGCAAAGGGTGCTTGGAGTCCAAAAATAAT
1 AAGGTGAAAACCCACAAAGGGCGCTTGGAGTCCAAAAATAAT
48123622 AA
1 AA
48123624 TAAAATGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
41 7 0.18
42 31 0.82
ACGTcount: A:0.43, C:0.15, G:0.23, T:0.19
Consensus pattern (42 bp):
AAGGTGAAAACCCACAAAGGGCGCTTGGAGTCCAAAAATAAT
Found at i:48124958 original size:44 final size:44
Alignment explanation
Indices: 48124905--48125037 Score: 110
Period size: 45 Copynumber: 3.0 Consensus size: 44
48124895 GCAGAGAAGT
48124905 AGATCGAAGACACCAACCTCGCCTCCCTGAGTTTGCAGCGGAGC
1 AGATCGAAGACACCAACCTCGCCTCCCTGAGTTTGCAGCGGAGC
* * * * * * * *
48124949 AGA-CTGAAGATAGCAGATCTTGTCTTCCTCT-A-TTGGCAGCGAAGT
1 AGATC-GAAGACACCA-ACCTCG-CCTCC-CTGAGTTTGCAGCGGAGC
* * *
48124994 AGATCGAAGACACCAACCTCGCCTCCTTGAGTTTTCAGTGGAGC
1 AGATCGAAGACACCAACCTCGCCTCCCTGAGTTTGCAGCGGAGC
48125038 TAACTAAAGA
Statistics
Matches: 63, Mismatches: 19, Indels: 14
0.66 0.20 0.15
Matches are distributed among these distances:
42 1 0.02
43 6 0.10
44 23 0.37
45 25 0.40
46 6 0.10
47 2 0.03
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.23
Consensus pattern (44 bp):
AGATCGAAGACACCAACCTCGCCTCCCTGAGTTTGCAGCGGAGC
Found at i:48125016 original size:89 final size:89
Alignment explanation
Indices: 48124865--48125037 Score: 301
Period size: 89 Copynumber: 1.9 Consensus size: 89
48124855 ATGGATTGAA
*
48124865 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGAGAAGTAGATCGAAGACACCAACCTCGCCTC
1 GAAGATAGCAGATCTTGTCTTCCTCTATTGGCAGAGAAGTAGATCGAAGACACCAACCTCGCCTC
48124930 CCTGAGTTTGCAGCGGAGCAGACT
66 CCTGAGTTTGCAGCGGAGCAGACT
*
48124954 GAAGATAGCAGATCTTGTCTTCCTCTATTGGCAGCGAAGTAGATCGAAGACACCAACCTCGCCTC
1 GAAGATAGCAGATCTTGTCTTCCTCTATTGGCAGAGAAGTAGATCGAAGACACCAACCTCGCCTC
* * *
48125019 CTTGAGTTTTCAGTGGAGC
66 CCTGAGTTTGCAGCGGAGC
48125038 TAACTAAAGA
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
89 79 1.00
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.24
Consensus pattern (89 bp):
GAAGATAGCAGATCTTGTCTTCCTCTATTGGCAGAGAAGTAGATCGAAGACACCAACCTCGCCTC
CCTGAGTTTGCAGCGGAGCAGACT
Found at i:48125079 original size:45 final size:44
Alignment explanation
Indices: 48125029--48125129 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 44
48125019 CTTGAGTTTT
48125029 CAGTGGAGCTA-ACTAAAGATAACCAA-CTTTATCTCCCTGAAGTTA
1 CAGTGGAGC-AGACTAAAG-TAACCAATC-TTATCTCCCTGAAGTTA
** * * *
48125074 CAGTGGAGCAGGTTGAAGTTACCAATCTTATCTCCCTGAAGTTG
1 CAGTGGAGCAGACTAAAGTAACCAATCTTATCTCCCTGAAGTTA
48125118 CAGTGGAGCAGA
1 CAGTGGAGCAGA
48125130 TTGAAGCTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
44 34 0.71
45 14 0.29
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (44 bp):
CAGTGGAGCAGACTAAAGTAACCAATCTTATCTCCCTGAAGTTA
Found at i:48125105 original size:44 final size:44
Alignment explanation
Indices: 48125057--48125531 Score: 218
Period size: 44 Copynumber: 10.6 Consensus size: 44
48125047 ATAACCAACT
*
48125057 TTATCTCCCTGAAGTTACAGTGGAGCAGGTTGAAGTTACCAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACCAATC
* * **
48125101 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTATTAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACCAATC
* * * * * *
48125145 CTATCTCCCTAAAGTTGTAGTGGAG-TGGATTAAAACGATA--AATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGG-TT-GAA-GTTACCAATC
* * * *
48125189 CTATAC-CCCTAAAGTTCCAGTGG-G-ATGGATTGAAGTCATCATGGCAAATC
1 TTAT-CTCCCTGAAGTTGCAGTGGAGCA-GG-TTGAAGT--T-A---CCAATC
* * ** * *
48125239 TTATCTCCCTGAAATTGCAGCGGAGCAGACTGAAGATAGCGAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTA-CCAATC
* * * *
48125284 TTATTTCTCTGAAGTTGCAGTGGAACAGATTGAAGCTATACACTACAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAG-T-T--AC--C-AATC
* * * * * * *
48125335 TTATCTCTCTGAAGTTGCAGTAGAACA-GAT-CA--TATCAAAC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACCAATC
* * * * * *
48125375 TTATCCCCCTAAAGTTGCAGTAGG-GCAGGTTGAAATTGCAAACC
1 TTATCTCCCTGAAGTTGCAGT-GGAGCAGGTTGAAGTTACCAATC
* * * * *
48125419 TTATCTTCCTGAAGTTGCAGTGAAGCAAGTTGAAGATA-CAATA
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACCAATC
* * * * **
48125462 TTATCTCCCTGAAGTTGCGGTGGATCAGATTGAAGCTATTAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACCAATC
* *
48125506 CTATCTCCCTGAAGTTACAGTGGAGC
1 TTATCTCCCTGAAGTTGCAGTGGAGC
48125532 GGATTAAAAC
Statistics
Matches: 325, Mismatches: 76, Indels: 60
0.70 0.16 0.13
Matches are distributed among these distances:
40 23 0.07
41 4 0.01
42 2 0.01
43 39 0.12
44 149 0.46
45 40 0.12
46 3 0.01
47 2 0.01
48 2 0.01
49 3 0.01
50 26 0.08
51 31 0.10
52 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACCAATC
Found at i:48125495 original size:43 final size:44
Alignment explanation
Indices: 48125419--48125527 Score: 114
Period size: 43 Copynumber: 2.5 Consensus size: 44
48125409 ATTGCAAACC
*
48125419 TTATCTTCCTGAAGTTGCAGTGAAGCAAGTTGAAGATA-CAATA
1 TTATCTCCCTGAAGTTGCAGTGAAGCAAGTTGAAGATATCAATA
* * * * * *
48125462 TTATCTCCCTGAAGTTGCGGTGGATC-AGATTGAAGCTATTAATC
1 TTATCTCCCTGAAGTTGCAGTGAAGCAAG-TTGAAGATATCAATA
* *
48125506 CTATCTCCCTGAAGTTACAGTG
1 TTATCTCCCTGAAGTTGCAGTG
48125528 GAGCGGATTA
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
42 2 0.04
43 30 0.56
44 22 0.41
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.32
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGAAGCAAGTTGAAGATATCAATA
Found at i:48125550 original size:44 final size:44
Alignment explanation
Indices: 48125463--48125553 Score: 110
Period size: 44 Copynumber: 2.1 Consensus size: 44
48125453 GATACAATAT
* * * * * * *
48125463 TATCTCCCTGAAGTTGCGGTGGATCAGATTGAAGCTATTAATCC
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACGATGAATCC
*
48125507 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACGATGAATCC
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACGATGAATCC
48125551 TAT
1 TAT
48125554 ACCTCTGAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.30
Consensus pattern (44 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACGATGAATCC
Found at i:48125924 original size:27 final size:27
Alignment explanation
Indices: 48125893--48125945 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
48125883 CAAGAATCTA
48125893 TGAGACCGGGCAAGATTGGTCTTTCTG
1 TGAGACCGGGCAAGATTGGTCTTTCTG
48125920 TGAGACCGGGCAAGATTGGTCTTTCT
1 TGAGACCGGGCAAGATTGGTCTTTCT
48125946 TAGTCTCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (27 bp):
TGAGACCGGGCAAGATTGGTCTTTCTG
Found at i:48127332 original size:3 final size:3
Alignment explanation
Indices: 48127324--48127362 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
48127314 ATAGGTTTGA
* * *
48127324 TAT TAT TAT TAT TAC TAT TGT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
48127363 ATTTCTATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:48127374 original size:15 final size:15
Alignment explanation
Indices: 48127324--48127371 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
48127314 ATAGGTTTGA
48127324 TATTATTATTATTAC
1 TATTATTATTATTAC
*
48127339 TATTGTTATTATTAC
1 TATTATTATTATTAC
*
48127354 TATTATTA-TATTTC
1 TATTATTATTATTAC
48127368 TATT
1 TATT
48127372 TATATTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 9 0.30
15 21 0.70
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.62
Consensus pattern (15 bp):
TATTATTATTATTAC
Found at i:48133559 original size:7 final size:7
Alignment explanation
Indices: 48133547--48133580 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
48133537 CTCTTACTTT
48133547 ATCCCTC
1 ATCCCTC
48133554 ATCCCTC
1 ATCCCTC
48133561 ATCCCTC
1 ATCCCTC
48133568 ATCCCTC
1 ATCCCTC
48133575 ATCCCT
1 ATCCCT
48133581 TTATTCCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.15, C:0.56, G:0.00, T:0.29
Consensus pattern (7 bp):
ATCCCTC
Found at i:48135739 original size:25 final size:24
Alignment explanation
Indices: 48135712--48135792 Score: 85
Period size: 25 Copynumber: 3.2 Consensus size: 24
48135702 GGACTCGCCA
48135712 CAGCTCGTATGAGCTTACCTATTT
1 CAGCTCGTATGAGCTTACCTATTT
*
48135736 ACAGCCCGTGA-GAGCTTA-CTGATTCT
1 -CAGCTCGT-ATGAGCTTACCT-ATT-T
*
48135762 CAGCTCGTATAAGCTTACCGTATTT
1 CAGCTCGTATGAGCTTACC-TATTT
48135787 CAGCTC
1 CAGCTC
48135793 AGAAAAGCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.06
25 37 0.79
26 6 0.13
27 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (24 bp):
CAGCTCGTATGAGCTTACCTATTT
Found at i:48150607 original size:17 final size:17
Alignment explanation
Indices: 48150585--48150631 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
48150575 TCGAAATTAT
48150585 AAAAATTAAAAAGTTT-A
1 AAAAATTAAAAA-TTTCA
*
48150602 AAAAATATAAGAATTTCA
1 AAAAAT-TAAAAATTTCA
48150620 AAAAATTAAAAA
1 AAAAATTAAAAA
48150632 ATAGTAACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (17 bp):
AAAAATTAAAAATTTCA
Found at i:48150607 original size:26 final size:27
Alignment explanation
Indices: 48150578--48150633 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
48150568 AAATTATTCG
*
48150578 AAATTATAA-AAATT-AAAAAGTTTAAA
1 AAATTATAAGAAATTCAAAAA-ATTAAA
*
48150604 AAA-TATAAGAATTTCAAAAAATTAAA
1 AAATTATAAGAAATTCAAAAAATTAAA
48150630 AAAT
1 AAAT
48150634 AGTAACCCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
25 5 0.20
26 15 0.60
27 5 0.20
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.29
Consensus pattern (27 bp):
AAATTATAAGAAATTCAAAAAATTAAA
Found at i:48151956 original size:29 final size:26
Alignment explanation
Indices: 48151920--48151977 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 26
48151910 TTGGTAAGTT
*
48151920 TTTATAATATTTTGAATTTTTATTATAA
1 TTTATAATATTTT-AACTTTT-TTATAA
*
48151948 TTTAGTAATATTTTTACTTTTTTATAA
1 TTTA-TAATATTTTAACTTTTTTATAA
48151975 TTT
1 TTT
48151978 TTAAACTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 9 0.33
28 9 0.33
29 9 0.33
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (26 bp):
TTTATAATATTTTAACTTTTTTATAA
Found at i:48153995 original size:40 final size:40
Alignment explanation
Indices: 48153871--48153999 Score: 136
Period size: 40 Copynumber: 3.2 Consensus size: 40
48153861 AAAACGCTGT
* * * * *
48153871 AAAAATTAAAATATTAATGGCGTTTTTGCATAAAGGCAAC
1 AAAAAATAAAATAATAATGGCGTTTTTCCATAAACGCCAC
* *
48153911 AAAAGATAAAGA-AGTAATGGCGTTTTTCCATAAACGCCAC
1 AAAAAATAAA-ATAATAATGGCGTTTTTCCATAAACGCCAC
* * *
48153951 AAAAAATAAAATAATAATAGCGTTTTT-CATAAATGCCGC
1 AAAAAATAAAATAATAATGGCGTTTTTCCATAAACGCCAC
*
48153990 TAAAAATAAA
1 AAAAAATAAA
48154000 GCAATAGCAG
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
39 20 0.27
40 54 0.72
41 1 0.01
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.26
Consensus pattern (40 bp):
AAAAAATAAAATAATAATGGCGTTTTTCCATAAACGCCAC
Found at i:48159999 original size:9 final size:9
Alignment explanation
Indices: 48159971--48160008 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
48159961 TGACTTTCAC
48159971 AATTCGAAT
1 AATTCGAAT
*
48159980 AACTTAG-AT
1 AA-TTCGAAT
48159989 AATTCGAAT
1 AATTCGAAT
48159998 AATTCGAAT
1 AATTCGAAT
48160007 AA
1 AA
48160009 CAGATTGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 3 0.12
9 19 0.76
10 3 0.12
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:48160130 original size:19 final size:19
Alignment explanation
Indices: 48160095--48160154 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
48160085 ACAAAAAGAA
* *
48160095 AAAATTCAAATTAATTTAT
1 AAAATTAAAAATAATTTAT
* *
48160114 AAGATTAAAAATAATTTTT
1 AAAATTAAAAATAATTTAT
*
48160133 AAAATTCAAAAT-ATTTAT
1 AAAATTAAAAATAATTTAT
48160151 AAAA
1 AAAA
48160155 AGTTTTTAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
18 9 0.26
19 25 0.74
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (19 bp):
AAAATTAAAAATAATTTAT
Found at i:48167038 original size:101 final size:101
Alignment explanation
Indices: 48166863--48167059 Score: 286
Period size: 101 Copynumber: 2.0 Consensus size: 101
48166853 AGGCCTATCA
* * * *
48166863 AACCTGGCTTGTTTCTTAGTCCTCTGAACAAAACTAGAGGGCTCTAAACCCCTCTTACTCTTACC
1 AACCTGGCTAGTTTCTTAGGCCTCTAAACAAAACTAGAGGGCTCAAAACCCCTCTTACTCTTACC
48166928 CCTCTCACGGTACCTATTTTCGCATTGAGAGCGCTT
66 CCTCTCACGGTACCTATTTTCGCATTGAGAGCGCTT
* * * * * *
48166964 AACCTGGCTAGTTTCTTAGGCCTTTAAATAGAATTAGATGGCTCAAAATCCCTCTTACTCTTACC
1 AACCTGGCTAGTTTCTTAGGCCTCTAAACAAAACTAGAGGGCTCAAAACCCCTCTTACTCTTACC
* *
48167029 CTTCTCACGGTACCTATTTTTGCATTGAGAG
66 CCTCTCACGGTACCTATTTTCGCATTGAGAG
48167060 TGCCTAACGT
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 84 1.00
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (101 bp):
AACCTGGCTAGTTTCTTAGGCCTCTAAACAAAACTAGAGGGCTCAAAACCCCTCTTACTCTTACC
CCTCTCACGGTACCTATTTTCGCATTGAGAGCGCTT
Found at i:48169373 original size:50 final size:50
Alignment explanation
Indices: 48169307--48169410 Score: 172
Period size: 50 Copynumber: 2.1 Consensus size: 50
48169297 GCTCACACAC
* * *
48169307 CCATGTAGCCTACACGACCCAAATGGCCCATATTGTGTGTGACACACAGT
1 CCATGTAGCCTACACGACCCAAATAGCCCATATTGTGTGTCACACACAAT
*
48169357 CCATGTAGCCTACACGACCCAAATAGCCCATATTGTGTGTCATACACAAT
1 CCATGTAGCCTACACGACCCAAATAGCCCATATTGTGTGTCACACACAAT
48169407 CCAT
1 CCAT
48169411 CACATAGCCG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (50 bp):
CCATGTAGCCTACACGACCCAAATAGCCCATATTGTGTGTCACACACAAT
Found at i:48171506 original size:14 final size:13
Alignment explanation
Indices: 48171469--48171515 Score: 55
Period size: 14 Copynumber: 3.8 Consensus size: 13
48171459 AAATTAAAAT
48171469 ATATTTATA-TTA
1 ATATTTATATTTA
48171481 AT-TTTA-ATTTA
1 ATATTTATATTTA
48171492 ATATTTAATATTTA
1 ATATTT-ATATTTA
*
48171506 ATAATTATAT
1 ATATTTATAT
48171516 ATTTTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
10 1 0.03
11 9 0.30
12 5 0.17
13 5 0.17
14 10 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATATTTATATTTA
Found at i:48172056 original size:22 final size:22
Alignment explanation
Indices: 48172009--48172056 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
48171999 CTTGAATTTT
*
48172009 TAAATTCAAAAATCATAAATAC
1 TAAATTCAAAAATCAAAAATAC
48172031 TAAATTCTTAAAAAT-AAAAATA-
1 TAAATTC--AAAAATCAAAAATAC
48172053 TAAA
1 TAAA
48172057 AATTAAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 11 0.48
23 6 0.26
24 6 0.26
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAATTCAAAAATCAAAAATAC
Found at i:48179890 original size:17 final size:17
Alignment explanation
Indices: 48179863--48179921 Score: 84
Period size: 17 Copynumber: 3.4 Consensus size: 17
48179853 AAGTTAATTC
48179863 TAAAATTATAAAAA-AT
1 TAAAATTATAAAAATAT
48179879 TAAAATTTATAAAAAATCAT
1 TAAAA-TTAT-AAAAAT-AT
48179899 TAAAATTATAAAAATAT
1 TAAAATTATAAAAATAT
48179916 TAAAAT
1 TAAAAT
48179922 ATTTAAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
16 5 0.13
17 12 0.31
18 11 0.28
19 4 0.10
20 7 0.18
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAATTATAAAAATAT
Found at i:48179902 original size:20 final size:18
Alignment explanation
Indices: 48179863--48179938 Score: 81
Period size: 18 Copynumber: 4.3 Consensus size: 18
48179853 AAGTTAATTC
48179863 TAAAA-TTATAAAAA-AT
1 TAAAATTTATAAAAATAT
48179879 TAAAATTTATAAAAAATCAT
1 TAAAATTTAT-AAAAAT-AT
48179899 TAAAA-TTATAAAAATAT
1 TAAAATTTATAAAAATAT
*
48179916 TAAAATATT-TAAAATTA-
1 TAAAAT-TTATAAAAATAT
48179933 TAAAAT
1 TAAAAT
48179939 ATCAAAGAAG
Statistics
Matches: 53, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
16 5 0.09
17 17 0.32
18 18 0.34
19 6 0.11
20 7 0.13
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAAATTTATAAAAATAT
Found at i:48179929 original size:17 final size:18
Alignment explanation
Indices: 48179863--48179940 Score: 83
Period size: 17 Copynumber: 4.4 Consensus size: 18
48179853 AAGTTAATTC
48179863 TAAAAT-TATAAAAA-AT
1 TAAAATATATAAAAATAT
*
48179879 TAAAATTTATAAAAAATCAT
1 TAAAATATAT-AAAAAT-AT
48179899 TAAAAT-TATAAAAATAT
1 TAAAATATATAAAAATAT
* *
48179916 TAAAATATTTAAAATTA-
1 TAAAATATATAAAAATAT
48179933 TAAAATAT
1 TAAAATAT
48179941 CAAAGAAGGT
Statistics
Matches: 55, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
16 6 0.11
17 19 0.35
18 19 0.35
19 3 0.05
20 8 0.15
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAAATATATAAAAATAT
Found at i:48182407 original size:40 final size:40
Alignment explanation
Indices: 48182362--48182441 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
48182352 ACAATGAGTG
48182362 CAAGCATATATTATACCACAAAGGCGTTGTCTACATGCCA
1 CAAGCATATATTATACCACAAAGGCGTTGTCTACATGCCA
48182402 CAAGCATATATTATACCACAAAGGCGTTGTCTACATGCCA
1 CAAGCATATATTATACCACAAAGGCGTTGTCTACATGCCA
48182442 TGCAAGCCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (40 bp):
CAAGCATATATTATACCACAAAGGCGTTGTCTACATGCCA
Found at i:48188206 original size:46 final size:46
Alignment explanation
Indices: 48188153--48188337 Score: 325
Period size: 46 Copynumber: 4.0 Consensus size: 46
48188143 ACATTGCTAT
* *
48188153 AACTCAGTATGGTTTTCTTCATTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
48188199 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
48188245 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
* *
48188291 AACTCAGTATGGTTTTCTTAATTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
48188337 A
1 A
48188338 TTTTGCCATG
Statistics
Matches: 133, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 133 1.00
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:48194321 original size:46 final size:46
Alignment explanation
Indices: 48194271--48194455 Score: 325
Period size: 46 Copynumber: 4.0 Consensus size: 46
48194261 ACATTGCTAT
* * *
48194271 AACTCAGTATGGTTTTCTTCATTGAAATATCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
48194317 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
48194363 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
48194409 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
48194455 A
1 A
48194456 TTTTGCCATG
Statistics
Matches: 133, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 133 1.00
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:48200097 original size:31 final size:31
Alignment explanation
Indices: 48200062--48200122 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
48200052 CTTTGTCATC
48200062 AATGGTTCT-AAAGATATAAGAAAATTTTGTG
1 AATGGTT-TGAAAGATATAAGAAAATTTTGTG
*
48200093 AATGGTTTGAAAGATATAAGAAATTTTTGT
1 AATGGTTTGAAAGATATAAGAAAATTTTGT
48200123 TTGTATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 1 0.04
31 27 0.96
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.38
Consensus pattern (31 bp):
AATGGTTTGAAAGATATAAGAAAATTTTGTG
Found at i:48200137 original size:31 final size:30
Alignment explanation
Indices: 48200070--48200139 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
48200060 TCAATGGTTC
48200070 TAAAGATATAAGAAAATTTTGTGAATGGTTT
1 TAAAGATATAAGAAAATTTTGTGAAT-GTTT
* * *
48200101 GAAAGATATAAGAAATTTTTGTTTGTAT-TTT
1 TAAAGATATAAGAAAATTTTG--TGAATGTTT
48200132 TAAAGATA
1 TAAAGATA
48200140 CTAGTGTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
31 29 0.88
33 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (30 bp):
TAAAGATATAAGAAAATTTTGTGAATGTTT
Found at i:48202578 original size:30 final size:30
Alignment explanation
Indices: 48202544--48202601 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
48202534 TTGTGGTTAT
*
48202544 ATGCACCTGAAGTTGCATGTTTTTTTTTAG
1 ATGCACCTGAAGTTGCAAGTTTTTTTTTAG
48202574 ATGCACCTGAAGTTGCAAGTTTTTTTTT
1 ATGCACCTGAAGTTGCAAGTTTTTTTTT
48202602 TGTTTAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.47
Consensus pattern (30 bp):
ATGCACCTGAAGTTGCAAGTTTTTTTTTAG
Found at i:48204518 original size:41 final size:41
Alignment explanation
Indices: 48204416--48204518 Score: 188
Period size: 43 Copynumber: 2.5 Consensus size: 41
48204406 AAACCGTAAT
48204416 TGTACTTTGAGTTAGCTTAAAAGCATTCATTCATTAGGTTC
1 TGTACTTTGAGTTAGCTTAAAAGCATTCATTCATTAGGTTC
48204457 TGTATACTTTGAGTTAGCTTAAAAGCATTCATTCATTAGGTTC
1 TG--TACTTTGAGTTAGCTTAAAAGCATTCATTCATTAGGTTC
48204500 TGTACTTTGAGTTAGCTTA
1 TGTACTTTGAGTTAGCTTA
48204519 GAGAAAAATC
Statistics
Matches: 60, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
41 19 0.32
43 41 0.68
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (41 bp):
TGTACTTTGAGTTAGCTTAAAAGCATTCATTCATTAGGTTC
Found at i:48220451 original size:26 final size:29
Alignment explanation
Indices: 48220422--48220487 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 29
48220412 GAAGAGAGGG
48220422 AATGAGAGAATGGAA-GAGAAATG-TT-A
1 AATGAGAGAATGGAATGAGAAATGATTAA
* *
48220448 AATGA-AGGAT-GAATGAGAGATGATTAA
1 AATGAGAGAATGGAATGAGAAATGATTAA
48220475 AATGAG-GAATGGA
1 AATGAGAGAATGGA
48220488 GGTGGGTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
24 3 0.09
25 11 0.34
26 7 0.22
27 9 0.28
28 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.20
Consensus pattern (29 bp):
AATGAGAGAATGGAATGAGAAATGATTAA
Found at i:48222066 original size:40 final size:40
Alignment explanation
Indices: 48222021--48222137 Score: 148
Period size: 40 Copynumber: 3.0 Consensus size: 40
48222011 GCGTTTGGAC
* *
48222021 AAAAAACGCCACGAAAAATCGAGCATTAGTGGCGCTTTTA
1 AAAAAACGCCACTAAAAATCGAGCATTAGCGGCGCTTTTA
* * *
48222061 AAAAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTTT
1 AAAAAACGCCACTAAAAATCGAGCATTAGCGGCGCTTTTA
** *
48222101 GGAAAACGCCACTAAAAAT-AAGCATTAGCGGCG-TTTT
1 AAAAAACGCCACTAAAAATCGAGCATTAGCGGCGCTTTT
48222138 CTGAAAAGCG
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
38 4 0.06
39 13 0.19
40 50 0.75
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (40 bp):
AAAAAACGCCACTAAAAATCGAGCATTAGCGGCGCTTTTA
Found at i:48222157 original size:39 final size:39
Alignment explanation
Indices: 48222023--48222157 Score: 112
Period size: 40 Copynumber: 3.4 Consensus size: 39
48222013 GTTTGGACAA
* * * ***
48222023 AAAACGCCACGAAAAATCGAGCATTAGTGGCGCTTTTAAA
1 AAAACGCCACAAAAAAT-AAGCATTAGCGGCGCTTTTTGG
* * * *
48222063 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTTTGG
1 AAAACGCCACAAAAAAT-AAGCATTAGCGGCGCTTTTTGG
*
48222103 AAAACGCCACTAAAAATAAGCATTAGCGGCG-TTTTCT-G
1 AAAACGCCACAAAAAATAAGCATTAGCGGCGCTTTT-TGG
*
48222141 AAAAGCGCCGCAAAAAA
1 AAAA-CGCCACAAAAAA
48222158 CCTAAGCCCA
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
38 9 0.11
39 24 0.30
40 48 0.59
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (39 bp):
AAAACGCCACAAAAAATAAGCATTAGCGGCGCTTTTTGG
Found at i:48223067 original size:15 final size:16
Alignment explanation
Indices: 48223047--48223078 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
48223037 GTTAAGATAG
48223047 TTATGGATTTAG-GGT
1 TTATGGATTTAGAGGT
48223062 TTATGGATTTAGAGGT
1 TTATGGATTTAGAGGT
48223078 T
1 T
48223079 AGAGGTTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (16 bp):
TTATGGATTTAGAGGT
Found at i:48223180 original size:125 final size:123
Alignment explanation
Indices: 48223045--48223376 Score: 312
Period size: 125 Copynumber: 2.7 Consensus size: 123
48223035 AGGTTAAGAT
* * *
48223045 AGTTATGGATTTAGGGTTTATGGATTTAGAGGTTAGAGGTTAGGGGTTAGGTTTAGATTAATTAA
1 AGTTAGGGATTTAGGGTTTA-GGATTTAGAGG-T-GAGGTTAGGGTTTAGGTTTAGATTAATTAG
* * **
48223110 TGTGTTTTAATTTATATATTAAATAATGTTTAGGGGTTAG-GGATTTTGGG-TC------A-
63 TGTTTTTTAATTTATATATTAAATAAGGTTTAGGGGTTAGTGG-TTAGGGGTTCAAGTTAAG
* * *
48223163 AGTTAGGG-TTTAGGGATTAGGGATTCAG-GGTCG-GGTTAGGGTTTAGAATTTAGATTAATTAG
1 AGTTAGGGATTTAGGGTTTA-GGATTTAGAGGT-GAGGTTAGGGTTTAG-GTTTAGATTAATTAG
* ***
48223225 TGTTTTTTAATTTATTTATTAAATAAGGTTTAGGGGTTAGTGGTTAGGGGTTTGGGGTTAAG
63 TGTTTTTTAATTTATATATTAAATAAGGTTTAGGGGTTAGTGGTTAGGGG-TTCAAGTTAAG
* * *
48223287 AGTTAGTGATTTAGGGTTTAGAGA-TTCGAGGTCAGGTTAGGGTTTAAGGTTTAGATTAATTAGT
1 AGTTAGGGATTTAGGGTTTAG-GATTTAGAGGTGAGGTTAGGGTTT-AGGTTTAGATTAATTAGT
* *
48223351 ATTTTTTAATTTATATACTAAATAAG
64 GTTTTTTAATTTATATATTAAATAAG
48223377 TTCTTATATA
Statistics
Matches: 175, Mismatches: 23, Indels: 25
0.78 0.10 0.11
Matches are distributed among these distances:
114 12 0.07
115 57 0.33
116 4 0.02
117 18 0.10
118 7 0.04
123 1 0.01
124 10 0.06
125 64 0.37
126 2 0.01
ACGTcount: A:0.27, C:0.02, G:0.29, T:0.42
Consensus pattern (123 bp):
AGTTAGGGATTTAGGGTTTAGGATTTAGAGGTGAGGTTAGGGTTTAGGTTTAGATTAATTAGTGT
TTTTTAATTTATATATTAAATAAGGTTTAGGGGTTAGTGGTTAGGGGTTCAAGTTAAG
Found at i:48223183 original size:33 final size:33
Alignment explanation
Indices: 48223137--48223208 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
48223127 ATTAAATAAT
* **
48223137 GTTTAGGGGTTAGGGATTTTGGGTCAAGTTAGG
1 GTTTAGGGATTAGGGATTCAGGGTCAAGTTAGG
**
48223170 GTTTAGGGATTAGGGATTCAGGGTCGGGTTAGG
1 GTTTAGGGATTAGGGATTCAGGGTCAAGTTAGG
48223203 GTTTAG
1 GTTTAG
48223209 AATTTAGATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.18, C:0.04, G:0.43, T:0.35
Consensus pattern (33 bp):
GTTTAGGGATTAGGGATTCAGGGTCAAGTTAGG
Found at i:48228957 original size:43 final size:43
Alignment explanation
Indices: 48228897--48228987 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
48228887 CTTTGAGTTC
* *
48228897 ATTA-CAAGATTTCCTTGATTAA-ATAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGA-AAATGCATTATATCTTTT
* *
48228939 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATGTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
48228982 ATTACC
1 ATTACC
48228988 TTGCATATGT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
42 4 0.09
43 38 0.88
44 1 0.02
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
Found at i:48229363 original size:43 final size:43
Alignment explanation
Indices: 48229285--48229640 Score: 457
Period size: 43 Copynumber: 8.3 Consensus size: 43
48229275 AGGTTATGTT
* * * * *
48229285 TTTAGCGGCGTTTTTGCGAGAAGCGCCACTAAAGGT-TTGATC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* **
48229327 TATAGCGGCGTTTGTGACAAAAAGCGCCGCTAAAGGT-TATGGTC
1 TTTAGCGGCGTTTGTG-GGAAAAGCGCCGCTAAAGGTCT-TGGTC
* * *
48229371 TTTAGCGGCGTTTGTGGGGAAAGCGCCGCCAAAGGTCTTTGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* *
48229414 TTTAGCGGTGTTTGTGGG-AAAGCGCCGCTAATGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
** * *
48229456 TTTAGCGGCGTTTGTTAGAAAAGCGCCGCTAATGATCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * *
48229499 TTTAGCGGTGTTTGTGGGAAAAGCGCCACTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
48229542 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAATGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * *
48229585 TTTGGCGGCATTTGTGGGAAAAGCGCCGCTAAAGGTCTTGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
48229628 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
48229641 TTAGAAAAAA
Statistics
Matches: 273, Mismatches: 37, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
42 50 0.18
43 203 0.74
44 20 0.07
ACGTcount: A:0.19, C:0.18, G:0.32, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:48229570 original size:171 final size:171
Alignment explanation
Indices: 48229285--48229648 Score: 498
Period size: 171 Copynumber: 2.1 Consensus size: 171
48229275 AGGTTATGTT
* * *
48229285 TTTAGCGGCGTTTTTGCGAGAAGCGCCACTAAAGGTTTGATCTATAGCGGCGTTTGTGACAAAAA
1 TTTAGCGGCGTTTTT-AGAAAAGCGCCACTAAAGATTTGATCTATAGCGGCGTTTGTGACAAAAA
* * * *
48229350 GCGCCGCTAAAGGTTATGGTCTTTAGCGGCGTTTGTGGGGAAAGCGCCGCCAAAGGTCTTTGTCT
65 GCGCCACTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCCAAAGGTCTTGGTCT
** *
48229415 TTAGCGGTGTTTGTGGG-AAAGCGCCGCTAATGGTCTTGGTC
130 TTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * * * **
48229456 TTTAGCGGCGTTTGTTAGAAAAGCGCCGCTAATGATCTTGGTCTTTAGCGGTGTTTGTG-GGAAA
1 TTTAGCGGCGTTT-TTAGAAAAGCGCCACTAAAGAT-TTGATCTATAGCGGCGTTTGTGACAAAA
* *
48229520 AGCGCCACTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAATGGTCTTGGTC
64 AGCGCCACTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCCAAAGGTCTTGGTC
* *
48229585 TTTGGCGGCATTTGTGGGAAAAGCGCCGCTAAAGGTCTTGTTC
129 TTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
48229628 TTTAGCGGCGTTTTTAGAAAA
1 TTTAGCGGCGTTTTTAGAAAA
48229649 AAAACGCCGC
Statistics
Matches: 169, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
171 113 0.67
172 56 0.33
ACGTcount: A:0.20, C:0.18, G:0.32, T:0.30
Consensus pattern (171 bp):
TTTAGCGGCGTTTTTAGAAAAGCGCCACTAAAGATTTGATCTATAGCGGCGTTTGTGACAAAAAG
CGCCACTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCCAAAGGTCTTGGTCTT
TAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:48232964 original size:63 final size:64
Alignment explanation
Indices: 48232865--48232986 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 64
48232855 TATCGATAAT
* ** * *
48232865 TTTAAATATTTTTCATATATATATTTGTAGTCTAATTTTTAATTCCTCGATAAATTATAATATA
1 TTTAAATATTTTTCACATATATATTTACAATCTAATTTTTAATTCCTCAATAAATTATAATATA
* * * * *
48232929 TTTAAATA-TTTTCACATGTATATTTACAATTTAATTTTTAGTTTCTTAATAAATTATA
1 TTTAAATATTTTTCACATATATATTTACAATCTAATTTTTAATTCCTCAATAAATTATA
48232987 TGTTATATAT
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
63 40 0.83
64 8 0.17
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.52
Consensus pattern (64 bp):
TTTAAATATTTTTCACATATATATTTACAATCTAATTTTTAATTCCTCAATAAATTATAATATA
Found at i:48235853 original size:3 final size:3
Alignment explanation
Indices: 48235845--48235884 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
48235835 AGTAATTCCT
48235845 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
48235885 CATATAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:48237782 original size:44 final size:44
Alignment explanation
Indices: 48237556--48238164 Score: 273
Period size: 44 Copynumber: 13.6 Consensus size: 44
48237546 GCTTCTCTGT
* * * * *
48237556 CAGTATAGGAAGGCAAGATCTGTTTTTCCTCGATCTACTTCGCCAC
1 CAGTATAGGAAGACAAGATCTG-CTATCCTTGATCTACTTC-ACAC
* * * * * *
48237602 CAGTATGGGAAGATAAAATCTG-TAT-ATTCGATCCACTTCGCTAC
1 CAGTATAGGAAGACAAGATCTGCTATCCTT-GATCTACTTCAC-AC
* * * * ** *
48237646 C-GATATAGGAAGACAGGACCTACTATCTTTGATCTGTTTCACGC
1 CAG-TATAGGAAGACAAGATCTGCTATCCTTGATCTACTTCACAC
* * * * * * * *
48237690 CGGTACATGAAAACGAA-ATCTGCTTTCTTTAATCTGCTTTGC-CAC
1 CAGTATAGGAAGAC-AAGATCTGCTATCCTTGATCTAC-TT-CACAC
* * *
48237735 CAGTATGGGAAGGCAAGATCTGGTATCCTTGATCTACTTCACAC
1 CAGTATAGGAAGACAAGATCTGCTATCCTTGATCTACTTCACAC
* * * * *
48237779 CAGTACATGAAGACAAGATCTGCT-TTCTTCGATCTGCTTCGCCAC
1 CAGTATAGGAAGACAAGATCTGCTATCCTT-GATCTACTTC-ACAC
* * * * * *
48237824 CAGTATGGGAAGGCAAAATCTG-TAT-GTTCGATCCACTTCGCTAC
1 CAGTATAGGAAGACAAGATCTGCTATCCTT-GATCTACTTCAC-AC
* * * * *
48237868 CAATATAGGAAGACATGACCTGCTATCTTTGATCTACTTCACGC
1 CAGTATAGGAAGACAAGATCTGCTATCCTTGATCTACTTCACAC
* * * * * *
48237912 CAGTACATGAAGATAAGATCTGCT-TTCTTCGATCTGCTTCGCCAC
1 CAGTATAGGAAGACAAGATCTGCTATCCTT-GATCTACTTC-ACAC
* * * * * *
48237957 TAGTATGGGAAGACAAGATCTGTTATCTTTAATCTACTTCACGC
1 CAGTATAGGAAGACAAGATCTGCTATCCTTGATCTACTTCACAC
* * * * * * *
48238001 CAGTACATGAAGATAAGATCTGCTTTCTTCTTCGACCTGCTTCGCCAC
1 CAGTATAGGAAGACAAGATCTGCTATC--CTT-GATCTACTTC-ACAC
* * * *
48238049 CAGTATGGGAAGGCAAGATCTGCTATCTTTGATCTACTTCACGC
1 CAGTATAGGAAGACAAGATCTGCTATCCTTGATCTACTTCACAC
* * * * * * * *
48238093 CAGTACATGAAGACAAGACCTGCTTTCTTTGATTTGCTTCGCCAC
1 CAGTATAGGAAGACAAGATCTGCTATCCTTGATCTACTTC-ACAC
* * *
48238138 CAGTATGGGAAGGCAAGATCTGTTATC
1 CAGTATAGGAAGACAAGATCTGCTATC
48238165 TCTTCAACCT
Statistics
Matches: 405, Mismatches: 133, Indels: 51
0.69 0.23 0.09
Matches are distributed among these distances:
43 12 0.03
44 201 0.50
45 132 0.33
46 30 0.07
47 7 0.02
48 23 0.06
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (44 bp):
CAGTATAGGAAGACAAGATCTGCTATCCTTGATCTACTTCACAC
Found at i:48237804 original size:89 final size:89
Alignment explanation
Indices: 48237669--48237845 Score: 248
Period size: 89 Copynumber: 2.0 Consensus size: 89
48237659 CAGGACCTAC
* ** * * * *
48237669 TATCTTTGATCTGTTTCACGCCGGTACATGAAAACGAAATCTGCTTTCTTTAATCTGCTTTGCCA
1 TATCCTTGATCTACTTCACACCAGTACATGAAAACGAAATCTGCTTTCTTCAATCTGCTTCGCCA
*
48237734 CCAGTATGGGAAGGCAAGATCTGG
66 CCAGTATGGGAAGGCAAAATCTGG
* *
48237758 TATCCTTGATCTACTTCACACCAGTACATGAAGAC-AAGATCTGCTTTCTTCGATCTGCTTCGCC
1 TATCCTTGATCTACTTCACACCAGTACATGAAAACGAA-ATCTGCTTTCTTCAATCTGCTTCGCC
48237822 ACCAGTATGGGAAGGCAAAATCTG
65 ACCAGTATGGGAAGGCAAAATCTG
48237846 TATGTTCGAT
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
88 2 0.03
89 75 0.97
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.31
Consensus pattern (89 bp):
TATCCTTGATCTACTTCACACCAGTACATGAAAACGAAATCTGCTTTCTTCAATCTGCTTCGCCA
CCAGTATGGGAAGGCAAAATCTGG
Found at i:48237813 original size:133 final size:133
Alignment explanation
Indices: 48237692--48237996 Score: 304
Period size: 133 Copynumber: 2.3 Consensus size: 133
48237682 TTTCACGCCG
* * * * ** * * * * *
48237692 GTACATGAAAACGAAATCTGCTTTCTTTAATCTGCTTTGCCACCAGTATGGGAAGGCAAGATCTG
1 GTACAGGAAAACAAAATCTG-TATCTTCAATCCACTTCGCCACCAATATAGGAAGACAAGACCTG
* *
48237757 GTATCCTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCC
65 CTATCCTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGAC
48237822 ACCA
130 ACCA
** ** * * * *
48237826 GTATGGGAAGGCAAAATCTGTATGTTCGATCCACTTCGCTACCAATATAGGAAGACATGACCTGC
1 GTACAGGAAAACAAAATCTGTATCTTCAATCCACTTCGCCACCAATATAGGAAGACAAGACCTGC
* * * *
48237891 TATCTTTGATCTACTTCACGCCAGTACATGAAGATAAGATCTGCTTTCTTCGATCTGCTTCGCCA
66 TATCCTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGACA
*
48237956 CTA
131 CCA
** * * * *
48237959 GTATGGGAAGACAAGATCTGTTATCTTTAATCTACTTC
1 GTACAGGAAAACAAAATCTG-TATCTTCAATCCACTTC
48237997 ACGCCAGTAC
Statistics
Matches: 140, Mismatches: 30, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
133 113 0.81
134 27 0.19
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (133 bp):
GTACAGGAAAACAAAATCTGTATCTTCAATCCACTTCGCCACCAATATAGGAAGACAAGACCTGC
TATCCTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGACA
CCA
Found at i:48237833 original size:222 final size:222
Alignment explanation
Indices: 48237564--48238088 Score: 710
Period size: 222 Copynumber: 2.3 Consensus size: 222
48237554 GTCAGTATAG
* * * * *
48237564 GAAGGCAAGATCTGTTTTTCCTCGATCTACTTCGCCACCAGTATGGGAAGATAAAATCTGTATAT
1 GAAGACAAGATCTG-CTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAAATCTGTATAT
* ** *
48237629 TCGATCCACTTCGCTACCGATATAGGAAGACAGGACCTACTATCTTTGATCTGTTTCACGCCGGT
65 TCGATCCACTTCGCTACCAATATAGGAAGACAGGACCTACTATCTTTGATCTACTTCACGCCAGT
* * *
48237694 ACATGAAAACGAA-ATCTGCTTTCTTTAATCTGCTTTGCCACCAGTATGGGAAGGCAAGATCTGG
130 ACATGAAAA-GAAGATCTGCTTTCTTCAATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGG
*
48237758 TATCCTTGATCTACTTCACACCAGTACAT
194 TATCCTTAATCTACTTCACACCAGTACAT
* *
48237787 GAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAAATCTGTATGTT
1 GAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAAATCTGTATATT
* *
48237852 CGATCCACTTCGCTACCAATATAGGAAGACATGACCTGCTATCTTTGATCTACTTCACGCCAGTA
66 CGATCCACTTCGCTACCAATATAGGAAGACAGGACCTACTATCTTTGATCTACTTCACGCCAGTA
* * * * *
48237917 CATGAAGATAAGATCTGCTTTCTTCGATCTGCTTCGCCACTAGTATGGGAAGACAAGATCTGTTA
131 CATGAAAAGAAGATCTGCTTTCTTCAATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGGTA
* *
48237982 TCTTTAATCTACTTCACGCCAGTACAT
196 TCCTTAATCTACTTCACACCAGTACAT
* * * *
48238009 GAAGATAAGATCTGCTTTCTTCTTCGACCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGCTA
1 GAAGACAAGATCTGC--T-TTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAAATCTG-TA
* * *
48238074 TCTTTGATCTACTTC
62 TATTCGATCCACTTC
48238089 ACGCCAGTAC
Statistics
Matches: 267, Mismatches: 30, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
221 2 0.01
222 196 0.73
223 13 0.05
224 1 0.00
225 41 0.15
226 14 0.05
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.30
Consensus pattern (222 bp):
GAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAAATCTGTATATT
CGATCCACTTCGCTACCAATATAGGAAGACAGGACCTACTATCTTTGATCTACTTCACGCCAGTA
CATGAAAAGAAGATCTGCTTTCTTCAATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGGTA
TCCTTAATCTACTTCACACCAGTACAT
Found at i:48237880 original size:89 final size:89
Alignment explanation
Indices: 48237707--48237907 Score: 244
Period size: 89 Copynumber: 2.3 Consensus size: 89
48237697 TGAAAACGAA
* * * *
48237707 ATCTGCTTTCTTTAATCTGCTTTGCCACCAGTATGGGAAGGCAAGATCTGGTATCCTTGATCTAC
1 ATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAAATCTGGTATCCTTGATCCAC
* *
48237772 TTCACACCAGTACATGAAGACAAG
66 TTCACACCAATACAGGAAGACAAG
* *
48237796 ATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAAATCT-GTAT-GTTCGATCCA
1 ATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAAATCTGGTATCCTT-GATCCA
* * *
48237859 CTTCGCTACCAATATAGGAAGACATG
65 CTTCAC-ACCAATACAGGAAGACAAG
* * *
48237885 ACCTGCTATCTTTGATCTACTTC
1 ATCTGCTTTCTTTGATCTGCTTC
48237908 ACGCCAGTAC
Statistics
Matches: 95, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
87 2 0.02
88 14 0.15
89 79 0.83
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (89 bp):
ATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAAATCTGGTATCCTTGATCCAC
TTCACACCAATACAGGAAGACAAG
Found at i:48238024 original size:133 final size:133
Alignment explanation
Indices: 48237742--48238029 Score: 371
Period size: 133 Copynumber: 2.2 Consensus size: 133
48237732 CACCAGTATG
* * *
48237742 GGAAGGCAAGATCTGGTATCCTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTCT
1 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTCT
* * * *
48237807 TCGATCTGCTTCGCCACCAGTATGGGAAGGCAAAATCTGTATGTTCGATCCACTTCGCTACCAAT
66 TCGATCTGCTTCGCCACCAGTATGGGAAGACAAAATCTGTATCTTCAATCCACTTCACTACCAAT
*
48237872 ATA
131 ACA
* * * *
48237875 GGAAGACATGACCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGATAAGATCTGCTTTCT
1 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTCT
* * * * * *
48237940 TCGATCTGCTTCGCCACTAGTATGGGAAGACAAGATCTGTTATCTTTAATCTACTTCAC-GCCAG
66 TCGATCTGCTTCGCCACCAGTATGGGAAGACAAAATCTG-TATCTTCAATCCACTTCACTACCAA
48238004 TACA
130 TACA
* * *
48238008 TGAAGATAAGATCTGCTTTCTT
1 GGAAGACAAGATCTGCTATCTT
48238030 CTTCGACCTG
Statistics
Matches: 131, Mismatches: 23, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
133 117 0.89
134 14 0.11
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (133 bp):
GGAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTCT
TCGATCTGCTTCGCCACCAGTATGGGAAGACAAAATCTGTATCTTCAATCCACTTCACTACCAAT
ACA
Found at i:48238076 original size:92 final size:92
Alignment explanation
Indices: 48237850--48238165 Score: 437
Period size: 89 Copynumber: 3.5 Consensus size: 92
48237840 AATCTGTATG
** * * * * *
48237850 TTCGATCCACTTCGCTACCAATATAGGAAGACATGACCTGCTATCTTTGATCTACTTCACGCCAG
1 TTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAG
48237915 TACATGAAGATAAGATCTGC--T-TTC
66 TACATGAAGATAAGATCTGCTTTCTTC
* * *
48237939 TTCGATCTGCTTCGCCACTAGTATGGGAAGACAAGATCTGTTATCTTTAATCTACTTCACGCCAG
1 TTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAG
48238004 TACATGAAGATAAGATCTGCTTTCTTC
66 TACATGAAGATAAGATCTGCTTTCTTC
* *
48238031 TTCGACCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGCTATCTTTGATCTACTTCACGCCAG
1 TTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAG
* *
48238096 TACATGAAGACAAGACCTGCTTTC-T-
66 TACATGAAGATAAGATCTGCTTTCTTC
* * *
48238121 TT-GATTTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTATCT
1 TTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCT
48238166 CTTCAACCTG
Statistics
Matches: 204, Mismatches: 20, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
89 115 0.56
90 2 0.01
91 2 0.01
92 85 0.42
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.31
Consensus pattern (92 bp):
TTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAG
TACATGAAGATAAGATCTGCTTTCTTC
Found at i:48246198 original size:20 final size:20
Alignment explanation
Indices: 48246173--48246212 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
48246163 TAAAGGTCTT
48246173 TAATGCATATAATGCAATGC
1 TAATGCATATAATGCAATGC
* *
48246193 TAATGCATATGATGCGATGC
1 TAATGCATATAATGCAATGC
48246213 ATGAGATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (20 bp):
TAATGCATATAATGCAATGC
Found at i:48260526 original size:22 final size:25
Alignment explanation
Indices: 48260501--48260553 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
48260491 TTATAAATTC
*
48260501 AATTTAAAAG-ATA-TGAT-ACAAT
1 AATTTAAAAGCATATTAATAACAAT
*
48260523 AATTT-CAAGCATATTAATAACAAT
1 AATTTAAAAGCATATTAATAACAAT
48260547 AATTTAA
1 AATTTAA
48260554 TCATAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 3 0.12
22 8 0.33
23 3 0.12
24 10 0.42
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.34
Consensus pattern (25 bp):
AATTTAAAAGCATATTAATAACAAT
Found at i:48261547 original size:32 final size:32
Alignment explanation
Indices: 48261511--48261581 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 32
48261501 TTCATTCTGG
* *
48261511 GTGACCAAAAATAAAAGCGTCCGA-AAAATTGA
1 GTGACCAAAAATAAAAGC-ACCCATAAAATTGA
*
48261543 GTGACC-AAAATAAAAGCACCCATAAAATTGG
1 GTGACCAAAAATAAAAGCACCCATAAAATTGA
48261574 GTGACCAA
1 GTGACCAA
48261582 GTAAATAGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 3 0.09
31 24 0.71
32 7 0.21
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.15
Consensus pattern (32 bp):
GTGACCAAAAATAAAAGCACCCATAAAATTGA
Found at i:48262729 original size:6 final size:6
Alignment explanation
Indices: 48262705--48262743 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
48262695 TGTTTAGATC
**
48262705 TTATAT TTAATAT AAATAT TTATAT TTATAT TTATAT TT
1 TTATAT TT-ATAT TTATAT TTATAT TTATAT TTATAT TT
48262744 GTTCGCTAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 24 0.86
7 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TTATAT
Found at i:48271267 original size:26 final size:24
Alignment explanation
Indices: 48271238--48271304 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 24
48271228 TGATCTTTCC
48271238 AATGTGCAAGCTGCAAGCTCAGCAAA
1 AATGT-CAAGCTGCAAGCTCAGC-AA
* *
48271264 AATGTACAAGCTACAAGCTTAGCAA
1 AATGT-CAAGCTGCAAGCTCAGCAA
*
48271289 GATGTCAAAGCTGCAA
1 AATGTC-AAGCTGCAA
48271305 ACTTAGCGAG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 1 0.03
25 14 0.40
26 20 0.57
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.18
Consensus pattern (24 bp):
AATGTCAAGCTGCAAGCTCAGCAA
Found at i:48271299 original size:25 final size:26
Alignment explanation
Indices: 48271238--48271311 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 26
48271228 TGATCTTTCC
* *
48271238 AATGTGCAAGCTGCAAGCTCAGCAAA
1 AATGTACAAGCTGCAAGCTTAGCAAA
*
48271264 AATGTACAAGCTACAAGCTTAGC-AA
1 AATGTACAAGCTGCAAGCTTAGCAAA
* *
48271289 GATGT-CAAAGCTGCAAACTTAGC
1 AATGTAC-AAGCTGCAAGCTTAGC
48271312 GAGAAGTGCG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
24 1 0.02
25 20 0.49
26 20 0.49
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (26 bp):
AATGTACAAGCTGCAAGCTTAGCAAA
Found at i:48272070 original size:25 final size:26
Alignment explanation
Indices: 48272025--48272086 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
48272015 ACATTTCTCA
*
48272025 CTAATCTTGCAGCTTTGACA-TCTTG
1 CTAAGCTTGCAGCTTTGACATTCTTG
*
48272050 CTAAGCTTGCAGC-TTGCACATTTTTG
1 CTAAGCTTGCAGCTTTG-ACATTCTTG
*
48272076 CTGAGCTTGCA
1 CTAAGCTTGCA
48272087 CATTGGAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.09
25 15 0.47
26 14 0.44
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.37
Consensus pattern (26 bp):
CTAAGCTTGCAGCTTTGACATTCTTG
Found at i:48275138 original size:6 final size:6
Alignment explanation
Indices: 48275123--48275155 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
48275113 TTTTGGAAAG
48275123 AAAAAT -AAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
48275156 GATTTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:48287453 original size:18 final size:18
Alignment explanation
Indices: 48287432--48287473 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
48287422 CAGTAGTATA
48287432 CAAAGCAACTGTAGTTTG
1 CAAAGCAACTGTAGTTTG
48287450 CAAAGCAACTGTAGTTTG
1 CAAAGCAACTGTAGTTTG
48287468 CAAAGC
1 CAAAGC
48287474 GGCTTTCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (18 bp):
CAAAGCAACTGTAGTTTG
Found at i:48291281 original size:24 final size:24
Alignment explanation
Indices: 48291254--48291306 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
48291244 CTAATTCTAG
*
48291254 TAAATG-TAAAATATATTATGCTAA
1 TAAATGCT-AAATATATTATACTAA
*
48291278 TAAATGCTAAATATATTATACTAC
1 TAAATGCTAAATATATTATACTAA
48291302 TAAAT
1 TAAAT
48291307 ATTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.38
Consensus pattern (24 bp):
TAAATGCTAAATATATTATACTAA
Found at i:48291609 original size:21 final size:21
Alignment explanation
Indices: 48291576--48291615 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
48291566 TCTCTTAATG
* *
48291576 AAAACACTTTCAAATATCTTT
1 AAAACACTCTCAAACATCTTT
*
48291597 AAAATACTCTCAAACATCT
1 AAAACACTCTCAAACATCT
48291616 ACTAATGACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAACACTCTCAAACATCTTT
Found at i:48292359 original size:13 final size:13
Alignment explanation
Indices: 48292322--48292370 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
48292312 CATGGGTTTG
*
48292322 ATATTTTGATT-T
1 ATATATTGATTAT
*
48292334 GATATTTTGATTAT
1 -ATATATTGATTAT
48292348 ATATATTGATTAT
1 ATATATTGATTAT
48292361 ATATATTGAT
1 ATATATTGAT
48292371 GTTTGAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
13 33 0.97
14 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (13 bp):
ATATATTGATTAT
Found at i:48299975 original size:58 final size:58
Alignment explanation
Indices: 48299913--48300040 Score: 177
Period size: 58 Copynumber: 2.2 Consensus size: 58
48299903 ATTTAATAAG
* * * *
48299913 ATTATTATTAAATATATTTTAATAAAAATAATAAACAATTTAATCACATT-TTAACATA
1 ATTATTATTAAATACAATTTAAT-AAAATAACAAACAATTTAATAACATTCTTAACATA
* * *
48299971 ATTATTATTAAATACAATTTAATAAAATAACATATAATTTAATAACATTCTTAATATA
1 ATTATTATTAAATACAATTTAATAAAATAACAAACAATTTAATAACATTCTTAACATA
48300029 ATTATTATTAAA
1 ATTATTATTAAA
48300041 ATGTGAATTA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 22 0.35
58 40 0.65
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (58 bp):
ATTATTATTAAATACAATTTAATAAAATAACAAACAATTTAATAACATTCTTAACATA
Found at i:48301070 original size:21 final size:21
Alignment explanation
Indices: 48301045--48301085 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
48301035 AATTTGGTCA
48301045 AAACAAGATAATAAAGACAAT
1 AAACAAGATAATAAAGACAAT
48301066 AAACAAGATAATAAAGACAA
1 AAACAAGATAATAAAGACAA
48301086 CAACCATCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.68, C:0.10, G:0.10, T:0.12
Consensus pattern (21 bp):
AAACAAGATAATAAAGACAAT
Found at i:48319441 original size:17 final size:18
Alignment explanation
Indices: 48319412--48319448 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
48319402 TTTTTTTATT
48319412 TTATATAGATATAAATAC
1 TTATATAGATATAAATAC
*
48319430 TTATAT-GATATATATAC
1 TTATATAGATATAAATAC
48319447 TT
1 TT
48319449 TACACTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (18 bp):
TTATATAGATATAAATAC
Found at i:48323973 original size:13 final size:13
Alignment explanation
Indices: 48323955--48323980 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48323945 GTAAAAAAGG
48323955 AGAAAAAGAAAAA
1 AGAAAAAGAAAAA
48323968 AGAAAAAGAAAAA
1 AGAAAAAGAAAAA
48323981 GGAGAGGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AGAAAAAGAAAAA
Found at i:48324794 original size:7 final size:7
Alignment explanation
Indices: 48324795--48324832 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
48324785 AATGAAAAAT
48324795 AATGAAA
1 AATGAAA
48324802 AAT-AAA
1 AATGAAA
48324808 AATGAAA
1 AATGAAA
48324815 AATGAAA
1 AATGAAA
48324822 AA-GTAAA
1 AATG-AAA
48324829 AATG
1 AATG
48324833 GAGAGGCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
6 7 0.25
7 20 0.71
8 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (7 bp):
AATGAAA
Found at i:48324829 original size:13 final size:13
Alignment explanation
Indices: 48324782--48324823 Score: 54
Period size: 10 Copynumber: 3.4 Consensus size: 13
48324772 GAGTCAAACA
48324782 AAAAATGAAAAAT
1 AAAAATGAAAAAT
48324795 ---AATGAAAAAT
1 AAAAATGAAAAAT
48324805 AAAAATGAAAAAT
1 AAAAATGAAAAAT
48324818 GAAAAA
1 -AAAAA
48324824 GTAAAAATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
10 10 0.40
13 10 0.40
14 5 0.20
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (13 bp):
AAAAATGAAAAAT
Found at i:48326261 original size:100 final size:99
Alignment explanation
Indices: 48326088--48326611 Score: 660
Period size: 100 Copynumber: 5.3 Consensus size: 99
48326078 AAACCATAGT
*
48326088 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGGTGCAGCGGAACAGA
** *
48326153 TTGAAGCTACAACGGCGAATCTCACTTCCTCGACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCC-CAACA
* * * *
48326188 TTGCAATTTAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGAGGTGCAGCGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGGTGCAGCGGAACAGA
* *
48326253 TTGAAGCTACAACGGTGAATTTTGCTTCCCCAACA
66 TTGAAGCTACAACGGCGAATCTTGCTT-CCCAACA
* * * *
48326288 TTGCAATT-AAAA-ATTGAAGCTACAATGGTGAATCTTACATT-CCAGGCGGTGCAGCGAAATAG
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTAC-TTCCCAGGCGGTGCAGCGGAACAG
*
48326350 ATTGAAGCTACAACGGAG-ATCTTGCTTCCCTAACA
65 ATTGAAGCTACAACGGCGAATCTTGCTTCCC-AACA
* * *
48326385 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACGATGTAGCGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGGTGCAGCGGAACAGA
* * ** * **
48326450 TTGAAGCTACGATGGCGAATCTCACATCCTTGACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCC-CAACA
* * * * * * *
48326485 TTACAATTTAAAATATTAAAGCCACAATGGCGAATCTTACTTCCCAGGCGGTGCAACGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGGTGCAGCGGAACAGA
*
48326550 TTGAAGCTACAACGGTGAATCTTGCTTCCCTAACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCC-AACA
*
48326585 TTGCAATTAAAAAGATTAAAGCTACAA
1 TTGCAATTAAAAAGATTGAAGCTACAA
48326612 GTCAGAACTC
Statistics
Matches: 361, Mismatches: 54, Indels: 18
0.83 0.12 0.04
Matches are distributed among these distances:
96 3 0.01
97 20 0.06
98 65 0.18
99 61 0.17
100 210 0.58
101 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (99 bp):
TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGGTGCAGCGGAACAGA
TTGAAGCTACAACGGCGAATCTTGCTTCCCAACA
Found at i:48326601 original size:50 final size:49
Alignment explanation
Indices: 48326088--48326611 Score: 340
Period size: 50 Copynumber: 10.6 Consensus size: 49
48326078 AAACCATAGT
*
48326088 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCA-AC-A
**** * * *
48326139 -TGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTCACTTCCTCGACA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCC-CAACA
* * * **
48326188 TTGCAATTTAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAACA
* **** * * * *
48326237 GGTGCAGCGGAACAGATTGAAGCTACAACGGTGAATTTTGCTTCCCCAACA
1 -TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTT-CCCAACA
* * * *
48326288 TTGCAATT-AAAA-ATTGAAGCTACAATGGTGAATCTTACATT-CCAGGCG
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTAC-TTCCCA-ACA
* *** * * *
48326336 GTGCAGCGAAATAGATTGAAGCTACAACGGAG-ATCTTGCTTCCCTAACA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCC-AACA
48326385 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCA-AC-A
* **** * * * * * **
48326436 -TGTAGCGGAACAGATTGAAGCTACGATGGCGAATCTCACATCCTTGACA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCC-CAACA
* * * * * * * *
48326485 TTACAATTTAAAATATTAAAGCCACAATGGCGAATCTTACTTCCCAGGCG
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCA-ACA
* *** * * *
48326535 GTGCAACGGAACAGATTGAAGCTACAACGGTGAATCTTGCTTCCCTAACA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCC-AACA
*
48326585 TTGCAATTAAAAAGATTAAAGCTACAA
1 TTGCAATTAAAAAGATTGAAGCTACAA
48326612 GTCAGAACTC
Statistics
Matches: 350, Mismatches: 106, Indels: 35
0.71 0.22 0.07
Matches are distributed among these distances:
47 3 0.01
48 30 0.09
49 48 0.14
50 261 0.75
51 8 0.02
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (49 bp):
TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAACA
Found at i:48327166 original size:12 final size:12
Alignment explanation
Indices: 48327151--48327176 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
48327141 TAACGGGAAC
48327151 TCTCTCTTTTTT
1 TCTCTCTTTTTT
48327163 TCTCTCTTTTTT
1 TCTCTCTTTTTT
48327175 TC
1 TC
48327177 AATTCTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
TCTCTCTTTTTT
Found at i:48328292 original size:17 final size:16
Alignment explanation
Indices: 48328266--48328299 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
48328256 TTTTATTTTA
48328266 TATAGATATAAATACT
1 TATAGATATAAATACT
*
48328282 TATAGGATATATATACT
1 TATA-GATATAAATACT
48328299 T
1 T
48328300 TACACTTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (16 bp):
TATAGATATAAATACT
Found at i:48332085 original size:11 final size:11
Alignment explanation
Indices: 48332071--48332103 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
48332061 TTTCTCTAAT
48332071 ATATTAAATTA
1 ATATTAAATTA
48332082 ATATT-AATTA
1 ATATTAAATTA
*
48332092 ATATTATATTA
1 ATATTAAATTA
48332103 A
1 A
48332104 CAAAACTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATATTAAATTA
Found at i:48332543 original size:17 final size:16
Alignment explanation
Indices: 48332513--48332555 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
48332503 GAAAAATAAA
48332513 TAAAAGAAATAAAAGT
1 TAAAAGAAATAAAAGT
48332529 TAAAAGAACATAAAAG-
1 TAAAAGAA-ATAAAAGT
48332545 -AAAA-AAATAAA
1 TAAAAGAAATAAA
48332556 CTGCTCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 5 0.19
14 2 0.08
15 4 0.15
16 8 0.31
17 7 0.27
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.14
Consensus pattern (16 bp):
TAAAAGAAATAAAAGT
Found at i:48332754 original size:29 final size:28
Alignment explanation
Indices: 48332678--48332756 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 28
48332668 TGAAAGGCTC
48332678 AGTGACTAAAATGTTGCAACATGTTAACATA
1 AGTGACTAAAATG-T--AACATGTTAACATA
**
48332709 AGTGACTAAAACATAACAT-TTCAAACATA
1 AGTGACTAAAATGTAACATGTT--AACATA
48332738 AGTGACTAAAATGTAACAT
1 AGTGACTAAAATGTAACAT
48332757 AAGAAAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
27 2 0.05
28 5 0.12
29 23 0.55
30 1 0.02
31 11 0.26
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.27
Consensus pattern (28 bp):
AGTGACTAAAATGTAACATGTTAACATA
Found at i:48332767 original size:29 final size:29
Alignment explanation
Indices: 48332706--48332767 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
48332696 ACATGTTAAC
** *
48332706 ATAAGTGACTAAAACATAACATTTCAAAC
1 ATAAGTGACTAAAACATAACATAACAAAA
** *
48332735 ATAAGTGACTAAAATGTAACATAAGAAAA
1 ATAAGTGACTAAAACATAACATAACAAAA
48332764 ATAA
1 ATAA
48332768 AATTGACTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.56, C:0.11, G:0.10, T:0.23
Consensus pattern (29 bp):
ATAAGTGACTAAAACATAACATAACAAAA
Found at i:48333500 original size:43 final size:43
Alignment explanation
Indices: 48333422--48333642 Score: 189
Period size: 43 Copynumber: 5.2 Consensus size: 43
48333412 CGTTATAGGC
* * *
48333422 GATGATGCACT-TATGTG-CAAGTATATTTGCTTTGGTTTATTC
1 GATGATGCACTATGTGTGCCAA-TATAATTGCTTTGGTTTATTT
* * * *
48333464 GATGATGCATTACGGGTGCCAATATAATTGCTTTGGTTCATTT
1 GATGATGCACTATGTGTGCCAATATAATTGCTTTGGTTTATTT
* * * *
48333507 GATGATGCACTATGTGCGCCAGTATAATTG-TTCTGGCTTGTTT
1 GATGATGCACTATGTGTGCCAATATAATTGCTT-TGGTTTATTT
* * * * **
48333550 GATGATGCACTATGTATGCCAATATAATTGCTTCGGCTTGTCC
1 GATGATGCACTATGTGTGCCAATATAATTGCTTTGGTTTATTT
* * * *
48333593 AATGATGCACTATGTGTGCCACTAT-ATTTCTTTTGGTTTATCT
1 GATGATGCACTATGTGTGCCAATATAATTGC-TTTGGTTTATTT
*
48333636 GGTGATG
1 GATGATG
48333643 TATTGCGGTG
Statistics
Matches: 143, Mismatches: 31, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
42 16 0.11
43 122 0.85
44 5 0.03
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (43 bp):
GATGATGCACTATGTGTGCCAATATAATTGCTTTGGTTTATTT
Done.