Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012766.1 Kokia drynarioides strain JFW-HI SEQ_127778, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 264489
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 80 characters in sequence are not A, C, G, or T
Found at i:2002 original size:12 final size:12
Alignment explanation
Indices: 1981--2040 Score: 59
Period size: 12 Copynumber: 4.8 Consensus size: 12
1971 TCGCTACAAA
1981 TTCTTCTTCTTT
1 TTCTTCTTCTTT
*
1993 TTCTTTTTCTCTT
1 TTCTTCTTCT-TT
2006 GCTTCTTC-TCTCTT
1 --TTCTTCTTCT-TT
*
2020 TTCTTCTTCCTT
1 TTCTTCTTCTTT
2032 TTCTTCTTC
1 TTCTTCTTC
2041 AGCACCCACA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
12 26 0.63
13 4 0.10
14 6 0.15
15 5 0.12
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (12 bp):
TTCTTCTTCTTT
Found at i:2037 original size:27 final size:27
Alignment explanation
Indices: 1981--2040 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
1971 TCGCTACAAA
*
1981 TTCTTCTTCTTTTTCTTTTTCTCTTGC
1 TTCTTCTTCTTTTTCTTTTCCTCTTGC
*
2008 TTCTTC-TCTCTTTTCTTCTTCCT-TTTC
1 TTCTTCTTCT-TTTTCTT-TTCCTCTTGC
2035 TTCTTC
1 TTCTTC
2041 AGCACCCACA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 3 0.10
27 22 0.76
28 4 0.14
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (27 bp):
TTCTTCTTCTTTTTCTTTTCCTCTTGC
Found at i:3247 original size:21 final size:22
Alignment explanation
Indices: 3223--3273 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
3213 CAACTTCTAT
3223 CGATACATGC-ATACA-AACTAC
1 CGATACAT-CAATACATAACTAC
3244 CGATACATCAATATACATAACTAC
1 CGATACATC-A-ATACATAACTAC
3268 CGATAC
1 CGATAC
3274 TTGTAATCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 1 0.04
21 8 0.31
23 5 0.19
24 12 0.46
ACGTcount: A:0.43, C:0.27, G:0.08, T:0.22
Consensus pattern (22 bp):
CGATACATCAATACATAACTAC
Found at i:4997 original size:20 final size:20
Alignment explanation
Indices: 4959--5015 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
4949 CCATCATTAG
*
4959 TCTTAATTAATCATTTTTAA
1 TCTTAATTAATCATATTTAA
4979 TCTTAATTAAAT-ATATTTACA
1 TCTTAATT-AATCATATTTA-A
5000 -CTTAATATAAGTCATA
1 TCTTAAT-TAA-TCATA
5016 CTAAACCACT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
20 22 0.71
21 6 0.19
22 3 0.10
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (20 bp):
TCTTAATTAATCATATTTAA
Found at i:17777 original size:15 final size:15
Alignment explanation
Indices: 17736--17781 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
17726 TTAGTCACTT
*
17736 GAAAAAGAA-AAATGA
1 GAAAAAGAAGAAA-AA
17751 GAAAAAGAAAGAAAAA
1 GAAAAAG-AAGAAAAA
17767 GAAAAAGAAGAAAAA
1 GAAAAAGAAGAAAAA
17782 AATTTATGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 15 0.54
16 10 0.36
17 3 0.11
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (15 bp):
GAAAAAGAAGAAAAA
Found at i:22487 original size:23 final size:23
Alignment explanation
Indices: 22457--22502 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
22447 GGTAAGCTTC
22457 ATAGCTTAATAAGTTCGCAAGGT
1 ATAGCTTAATAAGTTCGCAAGGT
22480 ATAGCTTAATAAGTTCGCAAGGT
1 ATAGCTTAATAAGTTCGCAAGGT
22503 TCATCAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (23 bp):
ATAGCTTAATAAGTTCGCAAGGT
Found at i:23752 original size:20 final size:20
Alignment explanation
Indices: 23714--23752 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
23704 CAATCATTAG
*
23714 TCTTAATTAATCATTTTTAA
1 TCTTAATTAATCATATTTAA
23734 TCTTAATTAAAT-ATATTTA
1 TCTTAATT-AATCATATTTA
23753 CACTTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (20 bp):
TCTTAATTAATCATATTTAA
Found at i:38560 original size:51 final size:51
Alignment explanation
Indices: 38484--38587 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 51
38474 CCCCTTGTCT
*
38484 CTTTGTTAGATATTCCTCCACTCAAAGTGCTTATCTTTGTCATGATATCTC
1 CTTTGTTAGATATTCCTCCACTCAAAGTGCTTATCTTTATCATGATATCTC
* *
38535 CTTTGTTGGATATTCCTCCACTCAAAGTTCTTATCTTTATCATGATATCTC
1 CTTTGTTAGATATTCCTCCACTCAAAGTGCTTATCTTTATCATGATATCTC
38586 CT
1 CT
38588 CTAAATGTCT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.44
Consensus pattern (51 bp):
CTTTGTTAGATATTCCTCCACTCAAAGTGCTTATCTTTATCATGATATCTC
Found at i:43898 original size:112 final size:111
Alignment explanation
Indices: 43699--43923 Score: 423
Period size: 112 Copynumber: 2.0 Consensus size: 111
43689 AATTTGACAA
43699 AACAGACTGCAAATTCAGAATCAGGATGTCAAAAAATGGCTGGATAGGATTGGTGAAAAAAAGAC
1 AACAGACTGCAAATTCAGAATCAGGATGTCAAAAAATGGCTGGATAGGATTGGTGAAAAAAAGAC
43764 GACAGTCAAAGTCAAAGTTAACGGTCAATGATCAACATCAACGATC
66 GACAGTCAAAGTCAAAGTTAACGGTCAATGATCAACATCAACGATC
* *
43810 AANCAGACTGCAAATTCAGAATCAGGATGTCAAAAAATGGTTGGATAGGGTTGGTGAAAAAAAGA
1 AA-CAGACTGCAAATTCAGAATCAGGATGTCAAAAAATGGCTGGATAGGATTGGTGAAAAAAAGA
43875 CGACAGTCAAAGTCAAAGTTAACGGTCAATGATCAACATCAACGATC
65 CGACAGTCAAAGTCAAAGTTAACGGTCAATGATCAACATCAACGATC
43922 AA
1 AA
43924 TAGATCGGTC
Statistics
Matches: 111, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
111 2 0.02
112 109 0.98
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (111 bp):
AACAGACTGCAAATTCAGAATCAGGATGTCAAAAAATGGCTGGATAGGATTGGTGAAAAAAAGAC
GACAGTCAAAGTCAAAGTTAACGGTCAATGATCAACATCAACGATC
Found at i:47550 original size:45 final size:45
Alignment explanation
Indices: 47484--47715 Score: 281
Period size: 45 Copynumber: 5.1 Consensus size: 45
47474 GTCATTTGTC
* * *
47484 TTGAAGCAACCATCCAATCTTTTACCTCTAATCTAGAGGGACAGA
1 TTGAAGCAACCATCCAATCTTTTACCCCTAATCCAGAGGGGCAGA
* * * *
47529 TTGAAGCCATCATCCAGTCTTTTACCCCTAATCCAAAGGGGCAGA
1 TTGAAGCAACCATCCAATCTTTTACCCCTAATCCAGAGGGGCAGA
* **
47574 TTGAAGCCACCATCCAATCTTTTA-CCCTAATCCAGAATGGCAGA
1 TTGAAGCAACCATCCAATCTTTTACCCCTAATCCAGAGGGGCAGA
* *
47618 TTGAAGCAACCATCGAATCTTTTACCCCTAATCTAGAGGGGCAGA
1 TTGAAGCAACCATCCAATCTTTTACCCCTAATCCAGAGGGGCAGA
* *
47663 TTGAAG-ACACCAAATCCAATCTTTTATCCCTAAATTCAG-GGGGCAGA
1 TTGAAGCA-ACC--ATCCAATCTTTTACCCCT-AATCCAGAGGGGCAGA
47710 TTGAAG
1 TTGAAG
47716 TTACAACACC
Statistics
Matches: 161, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
44 40 0.25
45 86 0.53
47 30 0.19
48 5 0.03
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (45 bp):
TTGAAGCAACCATCCAATCTTTTACCCCTAATCCAGAGGGGCAGA
Found at i:47642 original size:89 final size:89
Alignment explanation
Indices: 47484--47715 Score: 288
Period size: 89 Copynumber: 2.6 Consensus size: 89
47474 GTCATTTGTC
* * * * *
47484 TTGAAGCAACCATCCAATCTTTTACCTCTAATCTAGAGGGACAGATTGAAGCCATCATCCAGTCT
1 TTGAAGCCACCATCCAATCTTTTACC-CTAATCCAGAGGGACAGATTGAAGCAACCATCCAATCT
47549 TTTACCCCTAATCCAAAGGGGCAGA
65 TTTACCCCTAATCCAAAGGGGCAGA
* *
47574 TTGAAGCCACCATCCAATCTTTTACCCTAATCCAGAATGG-CAGATTGAAGCAACCATCGAATCT
1 TTGAAGCCACCATCCAATCTTTTACCCTAATCCAG-AGGGACAGATTGAAGCAACCATCCAATCT
* *
47638 TTTACCCCTAATCTAGAGGGGCAGA
65 TTTACCCCTAATCCAAAGGGGCAGA
* * *
47663 TTGAAGACACCAAATCCAATCTTTTATCCCTAAATTCAG-GGGGCAGATTGAAG
1 TTGAAGCCACC--ATCCAATCTTTTA-CCCT-AATCCAGAGGGACAGATTGAAG
47716 TTACAACACC
Statistics
Matches: 124, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
89 61 0.49
90 28 0.23
91 15 0.12
92 14 0.11
93 6 0.05
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (89 bp):
TTGAAGCCACCATCCAATCTTTTACCCTAATCCAGAGGGACAGATTGAAGCAACCATCCAATCTT
TTACCCCTAATCCAAAGGGGCAGA
Found at i:55688 original size:57 final size:58
Alignment explanation
Indices: 55593--55743 Score: 162
Period size: 57 Copynumber: 2.6 Consensus size: 58
55583 TTTTAATAAG
* * * * *
55593 ATTATTGTTAAATATAATTTAATAAAAGAATAAATAATTTAATCATAAT-TTAACATT
1 ATTATTATTAAATATAATTTAATAAAATAATAAATAATTTAATAACAATCTTAACATA
* ** * *
55650 ATTATTATTAAATATAATTTAATAAAATAGTATTTAATTTAATAACATTCTTAATATA
1 ATTATTATTAAATATAATTTAATAAAATAATAAATAATTTAATAACAATCTTAACATA
*
55708 ATTATTATTAAAATATGAA-TTAATGAAAATTATAAA
1 ATTATTATT-AAATAT-AATTTAAT-AAAATAATAAA
55744 ATATAATATT
Statistics
Matches: 76, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
57 41 0.54
58 15 0.20
59 11 0.14
60 9 0.12
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (58 bp):
ATTATTATTAAATATAATTTAATAAAATAATAAATAATTTAATAACAATCTTAACATA
Found at i:55932 original size:14 final size:14
Alignment explanation
Indices: 55913--55939 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55903 TACATTCAAA
55913 CATAATCTATATGC
1 CATAATCTATATGC
55927 CATAATCTATATG
1 CATAATCTATATG
55940 TTAAATTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (14 bp):
CATAATCTATATGC
Found at i:74588 original size:23 final size:23
Alignment explanation
Indices: 74559--74639 Score: 85
Period size: 23 Copynumber: 3.5 Consensus size: 23
74549 ACATTGTTTG
74559 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATTAAGTTAAA
* **
74582 TAAACATGTTC-ATTTAATGTT-CG
1 TGAACATGTTCGA-TTAA-GTTAAA
*
74605 TGAACATATTCGATTAAGTTAAA
1 TGAACATGTTCGATTAAGTTAAA
*
74628 TGAGCATGTTCG
1 TGAACATGTTCG
74640 GGAACATTAA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
22 4 0.09
23 37 0.82
24 4 0.09
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (23 bp):
TGAACATGTTCGATTAAGTTAAA
Found at i:78295 original size:24 final size:24
Alignment explanation
Indices: 78188--78295 Score: 135
Period size: 24 Copynumber: 4.4 Consensus size: 24
78178 GTAAACTCGA
* * *
78188 GAATTCTATAGAAAGCATTTGTGGC
1 GAATTCTCT-GAAAGCCTTTGTGAC
78213 GAATTCTCTGGAAAGCCTTTGTGAC
1 GAATTCTCT-GAAAGCCTTTGTGAC
* *
78238 GAATTCTCTAAAAGCCTTTGTGGC
1 GAATTCTCTGAAAGCCTTTGTGAC
*
78262 AAATTCTCTGAAAGCCTTTGTGAC
1 GAATTCTCTGAAAGCCTTTGTGAC
*
78286 GAATTATCTG
1 GAATTCTCTG
78296 GAAAATCCGT
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
24 42 0.58
25 30 0.42
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (24 bp):
GAATTCTCTGAAAGCCTTTGTGAC
Found at i:95898 original size:6 final size:6
Alignment explanation
Indices: 95887--95931 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
95877 AGCCAAACAG
* *
95887 AATTTA AATTTA AATTT- ATTTTA AGTTTA AATTT- -ATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
95932 CTAATGTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.12
5 4 0.12
6 25 0.76
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (6 bp):
AATTTA
Found at i:95915 original size:17 final size:17
Alignment explanation
Indices: 95889--95931 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
95879 CCAAACAGAA
95889 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
95906 TTTAAGTTTAAATTTA-
1 TTTAAATTTAAATTTAT
95922 TTTAAATTTA
1 TTTAAATTTA
95932 CTAATGTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:97787 original size:28 final size:28
Alignment explanation
Indices: 97637--97842 Score: 132
Period size: 29 Copynumber: 7.1 Consensus size: 28
97627 CCCAAAAAGT
* *
97637 CCCTAAACTATCTAAAAATCATGTTTTGAC
1 CCCTAAACT-TCTAAAAATTATATTTT-AC
* * *
97667 CCCCAAACTT-TCCAACATT-TCATTTTGAC
1 CCCTAAACTTCT-AAAAATTAT-ATTTT-AC
*
97696 CCCTAAACTTCTCAAAAAATGCA-ATTTTA-
1 CCCTAAACTTCT--AAAAAT-TATATTTTAC
* * *
97725 CCCTCAAACTCCTTAAAATTTACAATTTTAC
1 CCCT-AAACTTC-TAAAAATTA-TATTTTAC
97756 CCCTAAACTTCTAAAAATTATATTTTAC
1 CCCTAAACTTCTAAAAATTATATTTTAC
* * *
97784 CCCTAAACTTTTAAAATTTCTATTTTTAC
1 CCCTAAACTTCTAAAAATTATA-TTTTAC
* * **
97813 CCCCAAACTTCTAAATATTACGTTTTAC
1 CCCTAAACTTCTAAAAATTATATTTTAC
97841 CC
1 CC
97843 TCGAATTTCT
Statistics
Matches: 138, Mismatches: 26, Indels: 26
0.73 0.14 0.14
Matches are distributed among these distances:
28 37 0.27
29 59 0.43
30 28 0.20
31 14 0.10
ACGTcount: A:0.34, C:0.27, G:0.02, T:0.36
Consensus pattern (28 bp):
CCCTAAACTTCTAAAAATTATATTTTAC
Found at i:97838 original size:29 final size:27
Alignment explanation
Indices: 97750--97842 Score: 98
Period size: 28 Copynumber: 3.3 Consensus size: 27
97740 AAATTTACAA
97750 TTTTACCCCTAAACTTCTAAAAATTA-T
1 TTTTACCCCTAAACTTCT-AAAATTACT
* *
97777 ATTTTACCCCTAAACTTTTAAAATTTCTAT
1 -TTTTACCCCTAAACTTCTAAAATTAC--T
* *
97807 TTTTACCCCCAAACTTCTAAATATTACG
1 TTTTACCCCTAAACTTCTAAA-ATTACT
97835 TTTTACCC
1 TTTTACCC
97843 TCGAATTTCT
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
27 6 0.11
28 25 0.45
29 19 0.35
30 5 0.09
ACGTcount: A:0.32, C:0.25, G:0.01, T:0.42
Consensus pattern (27 bp):
TTTTACCCCTAAACTTCTAAAATTACT
Found at i:97852 original size:28 final size:29
Alignment explanation
Indices: 97701--97930 Score: 123
Period size: 29 Copynumber: 7.9 Consensus size: 29
97691 TTGACCCCTA
* * * *
97701 AACTTCTCAAAAAATGCAATTTTACCCTCA
1 AACTTCT-AAAAATTACGATTTTACCCTCG
* * * *
97731 AACTCCTTAAAATTTACAATTTTACCC-CTA
1 AACTTC-TAAAAATTACGATTTTACCCTC-G
* *
97761 AACTTCTAAAAATTA-TATTTTACCC-CTA
1 AACTTCTAAAAATTACGATTTTACCCTC-G
* * * * *
97789 AACTT-TTAAAATTTCTATTTTTACCCCCA
1 AACTTCTAAAAATTACGA-TTTTACCCTCG
*
97818 AACTTCTAAATATTACG-TTTTACCCTCG
1 AACTTCTAAAAATTACGATTTTACCCTCG
* * *
97846 AATTTCTCAAAAATT-TGATTTTTCCCTCG
1 AACTTCT-AAAAATTACGATTTTACCCTCG
* * *
97875 AACTTCCAAAAATCAC-ATTTTTCCCCTCG
1 AACTTCTAAAAATTACGA-TTTTACCCTCG
* * *
97904 AACTTCAAAAAATTAAGTTTTTACCCT
1 AACTTCTAAAAATTACGATTTTACCCT
97931 GAATTTTCCT
Statistics
Matches: 160, Mismatches: 29, Indels: 23
0.75 0.14 0.11
Matches are distributed among these distances:
27 7 0.04
28 42 0.26
29 75 0.47
30 35 0.22
31 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (29 bp):
AACTTCTAAAAATTACGATTTTACCCTCG
Found at i:98456 original size:97 final size:97
Alignment explanation
Indices: 98263--98448 Score: 286
Period size: 97 Copynumber: 1.9 Consensus size: 97
98253 TTCAAATTTT
* * * *
98263 TTTAAATCTAGGCAGTATTCCTTTATTTCGGATTTTGAAAATTTGAGCCTTAACTTACTAGGCGC
1 TTTAAATCAAGGCAATATTCCTTTATTTCGGATTTTGAAAATCTGAGCCTTAACTTACTAGACGC
98328 GATTTTTCTTCAAACTGGGATAATCAAATACC
66 GATTTTTCTTCAAACTGGGATAATCAAATACC
* *
98360 TTTAAATCAAGGCAATATTCCTTTATCTT-GGGTTTTGAAAATCTGTGCCTTAACTTACTAGACG
1 TTTAAATCAAGGCAATATTCCTTTAT-TTCGGATTTTGAAAATCTGAGCCTTAACTTACTAGACG
98424 CGATTTTTCTTCAAA-TCGGGATAAT
65 CGATTTTTCTTCAAACT-GGGATAAT
98449 TGAATACCCT
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
96 1 0.01
97 78 0.96
98 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (97 bp):
TTTAAATCAAGGCAATATTCCTTTATTTCGGATTTTGAAAATCTGAGCCTTAACTTACTAGACGC
GATTTTTCTTCAAACTGGGATAATCAAATACC
Found at i:107277 original size:78 final size:78
Alignment explanation
Indices: 107185--107396 Score: 221
Period size: 78 Copynumber: 2.7 Consensus size: 78
107175 TCTTTCCCTA
* * * * **
107185 AACCTAGGGAAGATCATCATCAGCCAATCTCTTATCTCGAG-CTTGGAGCAGATTGTGGTCATTT
1 AACCTGGGGAAGATCATCATCAGCCAATCTCTTACCCCGAGCCTAGG-GCAGATTGCAGTCATTT
*
107249 GATCTTTTACCCCG
65 GATCTTCTACCCCG
* * * *
107263 AACCTGGGGCAGATCATCATCAACCAATCTCTCACCCCGAGCCTAGGGCAGATTGCAGTCGTTTG
1 AACCTGGGGAAGATCATCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGTCATTTG
**
107328 ATCTTCTACCTTG
66 ATCTTCTACCCCG
* * * * * * *
107341 AGCTTGGGGTAGATCACCATCAGCCAATCTCTT-GCCCAAGCCTGGGGCAGATTGCA
1 AACCTGGGGAAGATCATCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTGCA
107397 ACCATTCGAT
Statistics
Matches: 111, Mismatches: 22, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
77 20 0.18
78 87 0.78
79 4 0.04
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (78 bp):
AACCTGGGGAAGATCATCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGTCATTTG
ATCTTCTACCCCG
Found at i:107415 original size:18 final size:18
Alignment explanation
Indices: 107392--107429 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
107382 CTGGGGCAGA
*
107392 TTGCAACCATTCGATCTT
1 TTGCAACCATTCGAACTT
107410 TTGCAACCATTCGAACTT
1 TTGCAACCATTCGAACTT
107428 TT
1 TT
107430 ACCCCCAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (18 bp):
TTGCAACCATTCGAACTT
Found at i:107558 original size:78 final size:78
Alignment explanation
Indices: 107416--107724 Score: 348
Period size: 78 Copynumber: 3.9 Consensus size: 78
107406 TCTTTTGCAA
* * * * * * *
107416 CCATTCGAACTTTTACCCCCAAGCTTGGGGTAGATCACCATTAGCCAAATCTTTTACCCTGAGCC
1 CCATTCGATCTTTTA-CCCCGAGCCTGGGGCAGATCACCATCAG-CAAATCTCTTACCCCGAGCC
**
107481 TGGGGCAGATTGTAG
64 TGGGGCAGATTACAG
* * *
107496 CCATTCGATCTTTTATCTCGATCCTGGGGCAGATCACCATCAGCAAATCTCTTACCCCGAGCCTG
1 CCATTCGATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCAAATCTCTTACCCCGAGCCTG
* * *
107561 AGCCAGATTACAA
66 GGGCAGATTACAG
* * * * * *
107574 CTATTCAATCTTTTACCCCAAGCTTGGGGCAAATCACCATCAGCAAATCTCTTACCCCGAGCTTG
1 CCATTCGATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCAAATCTCTTACCCCGAGCCTG
*
107639 GGGTAGATTACAG
66 GGGCAGATTACAG
* * * * * *
107652 CCATTCGATCTCTCACCCCGAGCCTGGGGAAGATCATCATCAGCAAATCTCTTACCTCGAGCTTG
1 CCATTCGATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCAAATCTCTTACCCCGAGCCTG
107717 GGGCAGAT
66 GGGCAGAT
107725 CATTATCAGC
Statistics
Matches: 190, Mismatches: 39, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
78 155 0.82
79 21 0.11
80 14 0.07
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (78 bp):
CCATTCGATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCAAATCTCTTACCCCGAGCCTG
GGGCAGATTACAG
Found at i:107702 original size:39 final size:38
Alignment explanation
Indices: 107518--107762 Score: 188
Period size: 39 Copynumber: 6.3 Consensus size: 38
107508 TTATCTCGAT
107518 CCTGGGGCAGATCACCATCAGCAAATCTCTTACCCCGAG
1 CCTGGGGCAGATCA-CATCAGCAAATCTCTTACCCCGAG
* * * * * * *
107557 CCTGAGCCAGATTACAACTATTC-AATCTTTTACCCCAAG
1 CCTGGGGCAGATCACATC-A-GCAAATCTCTTACCCCGAG
* *
107596 CTTGGGGCAAATCACCATCAGCAAATCTCTTACCCCGAG
1 CCTGGGGCAGATCA-CATCAGCAAATCTCTTACCCCGAG
* * * * * * *
107635 CTTGGGGTAGATTACAGCCATTC-GATCTCTCACCCCGAG
1 CCTGGGGCAGATCACA-TCA-GCAAATCTCTTACCCCGAG
* *
107674 CCTGGGGAAGATCATCATCAGCAAATCTCTTACCTCGAG
1 CCTGGGGCAGATCA-CATCAGCAAATCTCTTACCCCGAG
* * * * *
107713 CTTGGGGCAGATCATTATCAGCCAATCTCTTACCCTGAT
1 CCTGGGGCAGATCA-CATCAGCAAATCTCTTACCCCGAG
*
107752 CATGGGGCAGA
1 CCTGGGGCAGA
107763 AGGCAGTCAT
Statistics
Matches: 159, Mismatches: 39, Indels: 16
0.74 0.18 0.07
Matches are distributed among these distances:
38 7 0.04
39 145 0.91
40 7 0.04
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.24
Consensus pattern (38 bp):
CCTGGGGCAGATCACATCAGCAAATCTCTTACCCCGAG
Found at i:107758 original size:78 final size:75
Alignment explanation
Indices: 107520--107760 Score: 216
Period size: 78 Copynumber: 3.1 Consensus size: 75
107510 ATCTCGATCC
* * * * * *
107520 TGGGGCAGATCACCATCAGCAAATCTCTTACCCCGAGCCTGAGCCAGATTACAACTATTCAATCT
1 TGGGGCAAATCACCATCAGCAAATCTCTTACCCCGAGCTTGGGGCAGATTACAGCCA-T--ATCT
* * * *
107585 TTTACCCCAAGCT
63 CTCACCCCGAGCA
*
107598 TGGGGCAAATCACCATCAGCAAATCTCTTACCCCGAGCTTGGGGTAGATTACAGCCATTCGATCT
1 TGGGGCAAATCACCATCAGCAAATCTCTTACCCCGAGCTTGGGGCAGATTACAGCCA-T--ATCT
*
107663 CTCACCCCGAGCC
63 CTCACCCCGAGCA
* *
107676 TGGGG-AAGATCATCATCAGCAAATCTCTTACCTCGAGCTTGGGGCAGATCATTATCAGCCA-AT
1 TGGGGCAA-ATCACCATCAGCAAATCTCTTACCCCGAGCTTGGGGCAG---ATTA-CAGCCATAT
* * *
107739 CTCTTACCCTGATCA
61 CTCTCACCCCGAGCA
107754 TGGGGCA
1 TGGGGCA
107761 GAAGGCAGTC
Statistics
Matches: 138, Mismatches: 19, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
77 2 0.01
78 125 0.91
79 1 0.01
81 4 0.03
82 6 0.04
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (75 bp):
TGGGGCAAATCACCATCAGCAAATCTCTTACCCCGAGCTTGGGGCAGATTACAGCCATATCTCTC
ACCCCGAGCA
Found at i:109949 original size:28 final size:29
Alignment explanation
Indices: 109739--110112 Score: 180
Period size: 30 Copynumber: 12.9 Consensus size: 29
109729 CCAAGAAAGT
109739 CCTTAAACTATCCAAAAA-T-CATGTTTTGAC
1 CCTTAAACT-TCCAAAAATTACAT-TTTTG-C
* *** **
109769 CCCTAAACTTTTTTAAAATTACATTTTAAC
1 CCTTAAAC-TTCCAAAAATTACATTTTTGC
* * *
109799 CCTTAAACTTCTTAAAAATTACAATTTTAC
1 CCTTAAACTTC-CAAAAATTACATTTTTGC
** * * *
109829 CCTCGAA-GTCCTTAAAATTACATTTTTAC
1 CCTTAAACTTCC-AAAAATTACATTTTTGC
* *
109858 CCTCAAACTTCTCAAAAATTACTTTTTTGC
1 CCTTAAACTTC-CAAAAATTACATTTTTGC
* *
109888 CCTTAAACTT---AAAAGTACTTTTTTGC
1 CCTTAAACTTCCAAAAATTACATTTTTGC
* *
109914 CC-CAAACTTCCAATAATTACATTTTT-C
1 CCTTAAACTTCCAAAAATTACATTTTTGC
* * **
109941 CCTTGAACTTCTAAAAATTATGTTTTTG-
1 CCTTAAACTTCCAAAAATTACATTTTTGC
*
109969 CCTTCAAAATTCTCAAAAATT-CTATTTTTGC
1 CCTT-AAACTTC-CAAAAATTAC-ATTTTTGC
*** *
110000 CCCCGAACTTCCAAAAATCACATTTTT-C
1 CCTTAAACTTCCAAAAATTACATTTTTGC
* * *
110028 CCTTGAACTTTCAAAAATTA-AGTTTTTAC
1 CCTTAAACTTCCAAAAATTACA-TTTTTGC
** ** * * *
110057 CCCGAATTTTCCTAAAATGACATTTTTACC
1 CCTTAAACTTCCAAAAATTACATTTTT-GC
*
110087 CCTAAAACTTTCC-AAAATTACATTTT
1 CCTTAAAC-TTCCAAAAATTACATTTT
110113 AACCTCAAAC
Statistics
Matches: 260, Mismatches: 62, Indels: 44
0.71 0.17 0.12
Matches are distributed among these distances:
25 6 0.02
26 17 0.07
27 4 0.02
28 55 0.21
29 61 0.23
30 102 0.39
31 12 0.05
32 3 0.01
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.39
Consensus pattern (29 bp):
CCTTAAACTTCCAAAAATTACATTTTTGC
Found at i:109956 original size:55 final size:56
Alignment explanation
Indices: 109781--110001 Score: 171
Period size: 59 Copynumber: 3.9 Consensus size: 56
109771 CTAAACTTTT
* * * * * * * *
109781 TTAAAATTACATTTTAACCCTTAAACTTCTTAAAAATTACAATTTTACCCTCGAAGTCC
1 TTAAAAGTACATTTTTACCCTCAAACTTCTCAAAAATTACATTTTTGCCCT-TAA--AC
* *
109840 TTAAAATTACATTTTTACCCTCAAACTTCTCAAAAATTACTTTTTTGCCCTTAAAC
1 TTAAAAGTACATTTTTACCCTCAAACTTCTCAAAAATTACATTTTTGCCCTTAAAC
* * * *
109896 TTAAAAGTACTTTTTTGCCC-CAAACTTC-CAATAATTACATTTTT-CCCTTGAAC
1 TTAAAAGTACATTTTTACCCTCAAACTTCTCAAAAATTACATTTTTGCCCTTAAAC
* ** * * *
109949 TTCTAAAAATTATGTTTTTGCCTTCAAAATTCTCAAAAATT-CTATTTTTGCCC
1 -T-T-AAAAGTACATTTTTACCCTCAAACTTCTCAAAAATTAC-ATTTTTGCCC
110002 CCGAACTTCC
Statistics
Matches: 135, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
53 8 0.06
54 15 0.11
55 9 0.07
56 32 0.24
57 8 0.06
58 15 0.11
59 48 0.36
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (56 bp):
TTAAAAGTACATTTTTACCCTCAAACTTCTCAAAAATTACATTTTTGCCCTTAAAC
Found at i:110096 original size:87 final size:87
Alignment explanation
Indices: 109842--110112 Score: 211
Period size: 87 Copynumber: 3.1 Consensus size: 87
109832 CGAAGTCCTT
** ** * ** * *
109842 AAAATTACATTTTTACCCTCAAACTTCTCAAAAATTACTTTTTTGCC-CTTAAA--CTTAAAAGT
1 AAAATTACATTTTT-CCCTTGAACTTCT-AAAAATTAAGTTTTTACCTCCAAAATTCTCAAAAAT
*
109904 ACT-TTTTTGCCCC-AAACTTCCA
64 ACTATTTTTACCCCAAAACTTCCA
* * * * *
109926 ATAATTACATTTTTCCCTTGAACTTCTAAAAATTATGTTTTTGCCTTCAAAATTCTCAAAAATTC
1 AAAATTACATTTTTCCCTTGAACTTCTAAAAATTAAGTTTTTACCTCCAAAATTCTCAAAAATAC
* **
109991 TATTTTTGCCCCCGAACTTCCA
66 TATTTTTACCCCAAAACTTCCA
* * * *
110013 AAAATCACATTTTTCCCTTGAACTT-TCAAAAATTAAGTTTTTACC-CC-GAATTTTCCTAAAAT
1 AAAATTACATTTTTCCCTTGAACTTCT-AAAAATTAAGTTTTTACCTCCAAAATTCT-CAAAAAT
110075 GAC-ATTTTTACCCCTAAAACTTTCC-
64 -ACTATTTTTACCCC-AAAAC-TTCCA
110100 AAAATTACATTTT
1 AAAATTACATTTT
110113 AACCTCAAAC
Statistics
Matches: 152, Mismatches: 25, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
82 16 0.11
83 14 0.09
84 13 0.09
85 14 0.09
86 28 0.18
87 63 0.41
88 4 0.03
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.39
Consensus pattern (87 bp):
AAAATTACATTTTTCCCTTGAACTTCTAAAAATTAAGTTTTTACCTCCAAAATTCTCAAAAATAC
TATTTTTACCCCAAAACTTCCA
Found at i:110123 original size:28 final size:29
Alignment explanation
Indices: 110033--110131 Score: 76
Period size: 28 Copynumber: 3.4 Consensus size: 29
110023 TTTTCCCTTG
* * * *
110033 AACTTTCAAAAATTA-AGTTTTTACCCCG
1 AACTTTCCAAAATTACAGTTTTAACCTCA
* * * * *
110061 AATTTTCCTAAAATGACATTTTTACCCCTAA
1 AACTTTCC-AAAATTACAGTTTTA-ACCTCA
110092 AACTTTCCAAAATTACA-TTTTAACCTCA
1 AACTTTCCAAAATTACAGTTTTAACCTCA
*
110120 AACTCTCCAAAA
1 AACTTTCCAAAA
110132 CTTCATTTTC
Statistics
Matches: 54, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
28 21 0.39
29 11 0.20
30 13 0.24
31 9 0.17
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.34
Consensus pattern (29 bp):
AACTTTCCAAAATTACAGTTTTAACCTCA
Found at i:110505 original size:97 final size:96
Alignment explanation
Indices: 110389--110578 Score: 256
Period size: 97 Copynumber: 2.0 Consensus size: 96
110379 AAAAATTTTA
* * * * **
110389 AAATCGAGGCAATATTCCTTTATTTCAGGTTTTGAAAATTTGTGT-CTTAACTTACTAGGCGTGA
1 AAATCAAGGCAATAATCCTTTATCTCAGGTTTTAAAAATTTGT-TCCTTAACTTACTAGGCACGA
**
110453 TTTTTCTTCAAACCTTGATAATCGAATACCCTT
65 TTTTT-TTCAAACCGGGATAATCGAATACCCTT
* *
110486 AAATCAAGGCAATAATCCTTTATCTCGGGTTTTAAAAATTTGTTCCTTAATTTACTAGGCACGAT
1 AAATCAAGGCAATAATCCTTTATCTCAGGTTTTAAAAATTTGTTCCTTAACTTACTAGGCACGAT
*
110551 TTTTTTCAAATCGGGATAATCGAATACC
66 TTTTTTCAAACCGGGATAATCGAATACC
110579 ATTTTTCAAG
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
96 22 0.27
97 59 0.73
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.38
Consensus pattern (96 bp):
AAATCAAGGCAATAATCCTTTATCTCAGGTTTTAAAAATTTGTTCCTTAACTTACTAGGCACGAT
TTTTTTCAAACCGGGATAATCGAATACCCTT
Found at i:124077 original size:11 final size:11
Alignment explanation
Indices: 124061--124085 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
124051 TGAATGTAAT
124061 ATTAAAGTTTA
1 ATTAAAGTTTA
124072 ATTAAAGTTTA
1 ATTAAAGTTTA
124083 ATT
1 ATT
124086 CATTAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (11 bp):
ATTAAAGTTTA
Found at i:129737 original size:24 final size:24
Alignment explanation
Indices: 129683--129739 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 24
129673 GGTGGCCAAT
129683 TGTTAAATTTTTATTTGAATTTTA
1 TGTTAAATTTTTATTTGAATTTTA
*
129707 TAATTAAATTTTTATTT-AATTTTAA
1 T-GTTAAATTTTTATTTGAATTTT-A
129732 TGTTAAAT
1 TGTTAAAT
129740 AGAATAGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 13 0.45
25 16 0.55
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (24 bp):
TGTTAAATTTTTATTTGAATTTTA
Found at i:138578 original size:12 final size:11
Alignment explanation
Indices: 138554--138593 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
138544 CAGGAAAAGG
138554 GAAG-GAAGAA
1 GAAGAGAAGAA
138564 GAAGAGAACGAA
1 GAAGAGAA-GAA
138576 GAA-A-AAGAA
1 GAAGAGAAGAA
138585 GAAGAGAAG
1 GAAGAGAAG
138594 GAAATTAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
9 6 0.23
10 7 0.27
11 7 0.27
12 6 0.23
ACGTcount: A:0.62, C:0.03, G:0.35, T:0.00
Consensus pattern (11 bp):
GAAGAGAAGAA
Found at i:139770 original size:23 final size:23
Alignment explanation
Indices: 139744--139787 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
139734 TCCAATCAGT
139744 AGCTTCTAGAAGGTCCAGTAAAC
1 AGCTTCTAGAAGGTCCAGTAAAC
*
139767 AGCTTCTAGAAGGTCTAGTAA
1 AGCTTCTAGAAGGTCCAGTAA
139788 GCAAGGATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (23 bp):
AGCTTCTAGAAGGTCCAGTAAAC
Found at i:146774 original size:19 final size:17
Alignment explanation
Indices: 146750--146799 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
146740 CAGTCACTTG
146750 AAAAGGAAAAAAAATGAGA
1 AAAAGGAAAAAAAA-GA-A
*
146769 AAAAGGAAGAAAAAGAA
1 AAAAGGAAAAAAAAGAA
*
146786 AAAGAAGAAAAAAA
1 AAA-AGGAAAAAAA
146800 CTTATGATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 4 0.15
18 10 0.37
19 13 0.48
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (17 bp):
AAAAGGAAAAAAAAGAA
Found at i:146798 original size:16 final size:16
Alignment explanation
Indices: 146766--146797 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
146756 AAAAAAAATG
146766 AGAAAAAGGAAGAAAA
1 AGAAAAAGGAAGAAAA
146782 AGAAAAA-GAAGAAAA
1 AGAAAAAGGAAGAAAA
146797 A
1 A
146798 AACTTATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (16 bp):
AGAAAAAGGAAGAAAA
Found at i:148770 original size:29 final size:29
Alignment explanation
Indices: 148724--148785 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
148714 GCAACATTTG
* * *
148724 TTTCTCAACACTTTTTTAGATTTTTTCCC
1 TTTCTAAACACATCTTTAGATTTTTTCCC
* *
148753 TTTCTAAACACATCTTTAGTTTTTTTCTC
1 TTTCTAAACACATCTTTAGATTTTTTCCC
148782 TTTC
1 TTTC
148786 CAGATTTTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.18, C:0.23, G:0.03, T:0.56
Consensus pattern (29 bp):
TTTCTAAACACATCTTTAGATTTTTTCCC
Found at i:155078 original size:35 final size:35
Alignment explanation
Indices: 155037--155106 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
155027 GGTTATTGAC
* *
155037 TGGTCCTTCAAAGCGACATCATGTAAATGATATAT
1 TGGTCCTTCAAAGCGACACCATGTAAACGATATAT
*
155072 TGGTCCTTCAAGGCGACACCATGTAAACGATATAT
1 TGGTCCTTCAAAGCGACACCATGTAAACGATATAT
155107 AGCATCTTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (35 bp):
TGGTCCTTCAAAGCGACACCATGTAAACGATATAT
Found at i:165723 original size:32 final size:32
Alignment explanation
Indices: 165681--165748 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
165671 TGAATCAATT
* *
165681 AATTTTAGATCTTTCCCACATAGTAACAGTTA
1 AATTTCAGATCTTTCCCAAATAGTAACAGTTA
*
165713 AATTTCAGATCTTTTCCAAATAGTAACAGTTA
1 AATTTCAGATCTTTCCCAAATAGTAACAGTTA
165745 AATT
1 AATT
165749 CAATTACTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (32 bp):
AATTTCAGATCTTTCCCAAATAGTAACAGTTA
Found at i:168469 original size:21 final size:19
Alignment explanation
Indices: 168445--168512 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 19
168435 TACAATTATG
168445 TTAATATCTAATTATAAATAT
1 TTAATAT-TAATT-TAAATAT
168466 TTAATGATTATATTTAAATAT
1 TTAAT-ATTA-ATTTAAATAT
* *
168487 TTAAAATATAATTTATATAT
1 TTAATAT-TAATTTAAATAT
168507 TCTAAT
1 T-TAAT
168513 TAAATTTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 12 0.30
21 23 0.57
22 5 0.12
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (19 bp):
TTAATATTAATTTAAATAT
Found at i:168501 original size:33 final size:32
Alignment explanation
Indices: 168464--168589 Score: 95
Period size: 33 Copynumber: 3.9 Consensus size: 32
168454 AATTATAAAT
168464 ATTTAATGATTATATTTAAATATTTAAAATATA
1 ATTTAAT-ATTATATTTAAATATTTAAAATATA
* * *
168497 ATTTATATATTCTAATTAAAT-TTTATAA-ATA
1 ATTTA-ATATTATATTTAAATATTTAAAATATA
168528 A-TTAATATTTATTACTTTAAAATATTT-AAA-AT-
1 ATTTAATA-TTA-TA-TTT-AAATATTTAAAATATA
*
168560 ATTTAAAATTTATATTTCAAATA-TTAAAAT
1 ATTTAATA-TTATATTT-AAATATTTAAAAT
168590 TTTATCAACA
Statistics
Matches: 76, Mismatches: 8, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
29 3 0.04
30 7 0.09
31 17 0.22
32 11 0.14
33 33 0.43
34 5 0.07
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (32 bp):
ATTTAATATTATATTTAAATATTTAAAATATA
Found at i:168557 original size:9 final size:9
Alignment explanation
Indices: 168543--168568 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
168533 TATTTATTAC
168543 TTTAAAATA
1 TTTAAAATA
168552 TTTAAAATA
1 TTTAAAATA
168561 TTTAAAAT
1 TTTAAAAT
168569 TTATATTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TTTAAAATA
Found at i:168594 original size:22 final size:22
Alignment explanation
Indices: 168549--168591 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
168539 TTACTTTAAA
168549 ATATTTAAAATATTTAAAATTT
1 ATATTTAAAATATTTAAAATTT
*
168571 ATATTTCAAATA-TTAAAATTT
1 ATATTTAAAATATTTAAAATTT
168592 TATCAACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATTTAAAATATTTAAAATTT
Found at i:175676 original size:23 final size:23
Alignment explanation
Indices: 175646--175695 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
175636 TCATCAATTG
175646 AATGTGTAAGTATTACTTAGGTA
1 AATGTGTAAGTATTACTTAGGTA
175669 AATGTGTAAGTATTACTTAGGTA
1 AATGTGTAAGTATTACTTAGGTA
175692 AATG
1 AATG
175696 ATTTTTCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (23 bp):
AATGTGTAAGTATTACTTAGGTA
Found at i:179429 original size:3 final size:3
Alignment explanation
Indices: 179364--179409 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
179354 TATTAATCAG
179364 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
179410 GTTAATGACA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:180549 original size:29 final size:28
Alignment explanation
Indices: 180517--180941 Score: 293
Period size: 29 Copynumber: 14.5 Consensus size: 28
180507 CCGAACTTCG
* *
180517 AAAAATCCCATTTTTGACCCTAAAATTTCA
1 AAAAATTCCATTTTT-ACCCTAAAA-TTCC
* *
180547 AAAAATTCCA-TTTTACCCCCAAACTTCC
1 AAAAATTCCATTTTTA-CCCTAAAATTCC
** *
180575 AAAAATTCCATTTTTATCCC-CGAACTCC
1 AAAAATTCCATTTTTA-CCCTAAAATTCC
* *
180603 AAAAATCCCATTTTTGACCCTGAAACTTCC
1 AAAAATTCCATTTTT-ACCCT-AAAATTCC
* *
180633 -AAAATTCCATTTTTACCCCTGAACTTCC
1 AAAAATTCCATTTTTA-CCCTAAAATTCC
*
180661 AAAAATCCCATTTTTAACACC-AAAACTTCC
1 AAAAATTCCATTTTT-AC-CCTAAAA-TTCC
* *
180691 AAAAATTCCATTTTTACCCCCAAACTTCC
1 AAAAATTCCATTTTTA-CCCTAAAATTCC
* * * *
180720 AAAGATCCCATTTTTGACCCCAAAACTTCA
1 AAAAATTCCATTTTT-ACCCTAAAA-TTCC
* * *
180750 AAAAATTCCATATTTACCCCCAAACTTCC
1 AAAAATTCCATTTTTA-CCCTAAAATTCC
* *
180779 AAAAATCCCATTTTTACCCTCAAACTTCC
1 AAAAATTCCATTTTTACCCT-AAAATTCC
* *
180808 AAAAATTCCATTTTTACCCTCGAACTTCC
1 AAAAATTCCATTTTTACCCT-AAAATTCC
** *
180837 AAAAACCCCATTTTTTGACCCTAAAACTTCT
1 AAAAATTCCA-TTTTT-ACCCTAAAA-TTCC
* * *
180868 AAAAATTACATTTTTACCCTCGAACTT-C
1 AAAAATTCCATTTTTACCCT-AAAATTCC
*
180896 ACAAAATTCCATTTTTAACCCCAAAATTTCCC
1 A-AAAATTCCATTTTT-ACCCTAAAA-TT-CC
*
180928 CAAAATTACCATTT
1 AAAAATT-CCATTT
180942 CACCCTCGAG
Statistics
Matches: 318, Mismatches: 51, Indels: 50
0.76 0.12 0.12
Matches are distributed among these distances:
28 47 0.15
29 162 0.51
30 81 0.25
31 21 0.07
32 7 0.02
ACGTcount: A:0.36, C:0.31, G:0.02, T:0.31
Consensus pattern (28 bp):
AAAAATTCCATTTTTACCCTAAAATTCC
Found at i:180629 original size:58 final size:58
Alignment explanation
Indices: 180510--180941 Score: 464
Period size: 59 Copynumber: 7.3 Consensus size: 58
180500 TTTACCCCCG
* * ** * * * **
180510 AACTTCGAAAAATCCCATTTTTGACCCTAAAATTTCAAAAAATTCCA-TTTT-ACCCCCA
1 AACTTCCAAAAATTCCATTTTT-ACCC-CGAACTTCCAAAAATCCCATTTTTGACCCTAA
*
180568 AACTTCCAAAAATTCCATTTTTATCCCCGAAC-TCCAAAAATCCCATTTTTGACCCTGA
1 AACTTCCAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCCTAA
*
180626 AACTTCC-AAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCCATTTTTAACACC-AA
1 AACTTCCAAAAATTCCATTTTTACCCC-GAACTTCCAAAAATCCCATTTTTGAC-CCTAA
* * *
180684 AACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAGATCCCATTTTTGACCCCAA
1 AACTTCCAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCCTAA
* * * *
180743 AACTTCAAAAAATTCCATATTTACCCCCAAACTTCCAAAAATCCCATTTTT-ACCCTCA
1 AACTTCCAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCCTAA
*
180801 AACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAACCCCATTTTTTGACCCTAA
1 AACTTCCAAAAATTCCATTTTTACCC-CGAACTTCCAAAAATCCCA-TTTTTGACCCTAA
* * * * *
180861 AACTTCTAAAAATTACATTTTTACCCTCGAACTT-CACAAAATTCCATTTTTAACCCCAA
1 AACTTCCAAAAATTCCATTTTTACCC-CGAACTTCCA-AAAATCCCATTTTTGACCCTAA
* *
180920 AATTTCCCCAAAATTACCATTT
1 AACTT-CCAAAAATT-CCATTT
180942 CACCCTCGAG
Statistics
Matches: 325, Mismatches: 34, Indels: 27
0.84 0.09 0.07
Matches are distributed among these distances:
56 15 0.05
57 29 0.09
58 108 0.33
59 112 0.34
60 56 0.17
61 5 0.02
ACGTcount: A:0.36, C:0.31, G:0.03, T:0.31
Consensus pattern (58 bp):
AACTTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATCCCATTTTTGACCCTAA
Found at i:184671 original size:32 final size:32
Alignment explanation
Indices: 184625--184691 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
184615 AATTTGTTCC
184625 TTTTATATCATATTTAGCATGCATTATTAGCA
1 TTTTATATCATATTTAGCATGCATTATTAGCA
*
184657 TTTTGTATCATATTTAGCATGCATTATTAGCA
1 TTTTATATCATATTTAGCATGCATTATTAGCA
184689 TTT
1 TTT
184692 CATACTTAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.49
Consensus pattern (32 bp):
TTTTATATCATATTTAGCATGCATTATTAGCA
Found at i:189053 original size:36 final size:36
Alignment explanation
Indices: 189004--189078 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
188994 GCCATTGCCA
*
189004 ACACACCTGAAATATGTTTTCCTAGGTGACAATGAT
1 ACACACCTAAAATATGTTTTCCTAGGTGACAATGAT
189040 ACACACCTAAAATATGTTTTCCTAGGTGACAATGAT
1 ACACACCTAAAATATGTTTTCCTAGGTGACAATGAT
189076 ACA
1 ACA
189079 TTGCCAATGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (36 bp):
ACACACCTAAAATATGTTTTCCTAGGTGACAATGAT
Found at i:199235 original size:41 final size:41
Alignment explanation
Indices: 199127--199235 Score: 114
Period size: 40 Copynumber: 2.7 Consensus size: 41
199117 ACATCTTCAA
* * * * *
199127 GGTTGGTCGCGACATAGACA-TGTTGTGCTGTGACATAGGG
1 GGTTGGTCGCAACATAGACATTCTTATGTTGCGACATAGGG
** *
199167 GGTT-GTCAAAACATAGACATTCCTATGTTGCGACATAGGG
1 GGTTGGTCGCAACATAGACATTCTTATGTTGCGACATAGGG
* *
199207 GGTTGGTTGCAACATAGACATTTTTATGT
1 GGTTGGTCGCAACATAGACATTCTTATGT
199236 CACGAAGAAG
Statistics
Matches: 54, Mismatches: 13, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
39 12 0.22
40 23 0.43
41 19 0.35
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (41 bp):
GGTTGGTCGCAACATAGACATTCTTATGTTGCGACATAGGG
Found at i:204356 original size:46 final size:46
Alignment explanation
Indices: 204289--204379 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
204279 AGAAAAGGTA
204289 TGTAAAACCCTAGTGCTAAAGGCCCTATTTATAGCCATGGATAGTT
1 TGTAAAACCCTAGTGCTAAAGGCCCTATTTATAGCCATGGATAGTT
* *
204335 TGTAAACCCCTAGTGCTAAAGGCCCTATTTATAGCCTTGGATAGT
1 TGTAAAACCCTAGTGCTAAAGGCCCTATTTATAGCCATGGATAGT
204380 CATTTTCCTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (46 bp):
TGTAAAACCCTAGTGCTAAAGGCCCTATTTATAGCCATGGATAGTT
Found at i:204634 original size:41 final size:40
Alignment explanation
Indices: 204548--204659 Score: 118
Period size: 41 Copynumber: 2.8 Consensus size: 40
204538 AATCATCTTC
* * *
204548 AGGGTTGGTCGTGACATAGACA-TGCTGTGTTGCGACATA
1 AGGGTTGGTCGCGACATAGACATTCCTATGTTGCGACATA
* *
204587 AGGGGTTTGTCGCGACATAGACATTCCTATGTTGTGACATA
1 A-GGGTTGGTCGCGACATAGACATTCCTATGTTGCGACATA
* * * *
204628 GAGGGTTGGTTGCAATATAGACATTTCTATGT
1 -AGGGTTGGTCGCGACATAGACATTCCTATGT
204660 CACGATAAAG
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
39 1 0.02
40 19 0.32
41 39 0.65
42 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.32
Consensus pattern (40 bp):
AGGGTTGGTCGCGACATAGACATTCCTATGTTGCGACATA
Found at i:207974 original size:18 final size:18
Alignment explanation
Indices: 207951--207988 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
207941 TCTTGTCCTC
207951 AAGCAAACAAAACAAGAA
1 AAGCAAACAAAACAAGAA
* *
207969 AAGCAAATAAAGCAAGAA
1 AAGCAAACAAAACAAGAA
207987 AA
1 AA
207989 ATAAAGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.71, C:0.13, G:0.13, T:0.03
Consensus pattern (18 bp):
AAGCAAACAAAACAAGAA
Found at i:214779 original size:30 final size:31
Alignment explanation
Indices: 214720--214780 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
214710 ATTATGTCAA
* *
214720 AAATAAAATATAAAAATTAAATGTCAAATTT
1 AAATAAAATATAAAAATAAAATGTAAAATTT
214751 AAAT-AAATATAAAAATCAAAAT-TAAAATTT
1 AAATAAAATATAAAAAT-AAAATGTAAAATTT
214781 CACCATTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (31 bp):
AAATAAAATATAAAAATAAAATGTAAAATTT
Found at i:221297 original size:27 final size:29
Alignment explanation
Indices: 221259--221312 Score: 69
Period size: 27 Copynumber: 1.9 Consensus size: 29
221249 ACTAAGTTTT
*
221259 AATTTTTCTTTA-CTTTTC-TTTTTTTCA
1 AATTTTTCTTTATATTTTCATTTTTTTCA
221286 AATTTATT-TTTATATTTTCATTTTTTT
1 AATTT-TTCTTTATATTTTCATTTTTTT
221313 ATATTTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 9 0.39
28 7 0.30
29 7 0.30
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (29 bp):
AATTTTTCTTTATATTTTCATTTTTTTCA
Found at i:228301 original size:16 final size:16
Alignment explanation
Indices: 228280--228314 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
228270 ATTCCTTGTA
228280 ATTTTA-TCACTTTAAC
1 ATTTTAGTC-CTTTAAC
228296 ATTTTAGTCCTTTAAC
1 ATTTTAGTCCTTTAAC
228312 ATT
1 ATT
228315 AAAATTACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.29, C:0.17, G:0.03, T:0.51
Consensus pattern (16 bp):
ATTTTAGTCCTTTAAC
Found at i:229258 original size:21 final size:21
Alignment explanation
Indices: 229232--229272 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
229222 ATATAGTACA
229232 TGGGCTTAGGTACTGATACCG
1 TGGGCTTAGGTACTGATACCG
*
229253 TGGGCTTAGGTATTGATACC
1 TGGGCTTAGGTACTGATACC
229273 TAGTCCCCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.17, G:0.32, T:0.32
Consensus pattern (21 bp):
TGGGCTTAGGTACTGATACCG
Found at i:229834 original size:13 final size:13
Alignment explanation
Indices: 229810--229842 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
229800 TATCATAATT
229810 TTTTCTTT-TAAA
1 TTTTCTTTATAAA
229822 TTTTCTTTATAAA
1 TTTTCTTTATAAA
229835 TTTT-TTTA
1 TTTTCTTTA
229843 CTAAGATCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTCTTTATAAA
Found at i:230912 original size:59 final size:59
Alignment explanation
Indices: 230849--231043 Score: 191
Period size: 58 Copynumber: 3.3 Consensus size: 59
230839 ATCCTAGGGT
**
230849 AAAATGGTAATTTTTAGAAAAAATCAGGATAAAAAATGGAATTTTTTTACATTTGGGGC
1 AAAATGGTAATTTTTAGAAAAAATCAGGATAAAAAATGGAATTTTTGAACATTTGGGGC
* * * * *
230908 AAAATGGTGATTTTTAG-AAAAATC-GAGATCAAAAATGGAATTTTCGAACATCTGGGGG
1 AAAATGGTAATTTTTAGAAAAAATCAG-GATAAAAAATGGAATTTTTGAACATTTGGGGC
* *** * * * * *
230966 TAAATGGTAATTTTTA-AAAGTTTTAGGGTTAAAAATGGAATTTTTGGAA-GTTTAGGGGT
1 AAAATGGTAATTTTTAGAAAAAATCAGGATAAAAAATGGAATTTTT-GAACATTT-GGGGC
231025 AAAATGGTAATTTTTAGAA
1 AAAATGGTAATTTTTAGAA
231044 GTTTCAGAGT
Statistics
Matches: 110, Mismatches: 20, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
57 1 0.01
58 68 0.62
59 39 0.35
60 2 0.02
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTAGAAAAAATCAGGATAAAAAATGGAATTTTTGAACATTTGGGGC
Found at i:231010 original size:30 final size:31
Alignment explanation
Indices: 230967--231058 Score: 118
Period size: 29 Copynumber: 3.1 Consensus size: 31
230957 ATCTGGGGGT
*
230967 AAATGGTAATTTTTAAAAGTTTTAGGGTTAA
1 AAATGGTAATTTTTAGAAGTTTTAGGGTTAA
* *
230998 AAATGG-AATTTTTGGAAG-TTTAGGGGT-A
1 AAATGGTAATTTTTAGAAGTTTTAGGGTTAA
* *
231026 AAATGGTAATTTTTAGAAGTTTCAGAGTTAA
1 AAATGGTAATTTTTAGAAGTTTTAGGGTTAA
231057 AA
1 AA
231059 TAAGAATTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
28 7 0.14
29 19 0.37
30 16 0.31
31 9 0.18
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.38
Consensus pattern (31 bp):
AAATGGTAATTTTTAGAAGTTTTAGGGTTAA
Found at i:231056 original size:59 final size:59
Alignment explanation
Indices: 230845--231216 Score: 209
Period size: 59 Copynumber: 6.3 Consensus size: 59
230835 AGACATCCTA
* **
230845 GGGTAAAATGGTAATTTTTAGAAAAAATCAG-GATAAAAAATGGAATTTTTTTACA-TTTG
1 GGGTAAAATGGTAATTTTTAG-AAAAATCAGAGATTAAAAATGGAATTTTTGGA-AGTTTG
* * * * * *
230904 GGGCAAAATGGTGATTTTTAGAAAAATC-GAGATCAAAAATGGAA-TTTTCGAACATCTGG
1 GGGTAAAATGGTAATTTTTAGAAAAATCAGAGATTAAAAATGGAATTTTTGGAA-GT-TTG
** * *
230963 GGGT-AAATGGTAATTTTTA-AAAGTTTTAG-GGTTAAAAATGGAATTTTTGGAAGTTTAG
1 GGGTAAAATGGTAATTTTTAGAAA-AATCAGAGATTAAAAATGGAATTTTTGGAAGTTT-G
*** * *
231021 GGGTAAAATGGTAATTTTTAGAAGTTTCAGAG-TT-AAAATAAGAATTTTTGGAAGTTCG
1 GGGTAAAATGGTAATTTTTAGAAAAATCAGAGATTAAAAAT-GGAATTTTTGGAAGTTTG
* * * * * * * **
231079 AGTGTAAAAAT-GTCATTTTTAGGAAAATCA-AGGTCAAAAATAGAATTTTGGGAAGTTCCA
1 -GGGT-AAAATGGTAATTTTTAGAAAAATCAGAGATTAAAAATGGAATTTTTGGAAGTT-TG
* * * * *
231139 GGGTAAAAAT-GTCATTTTTAGGAAAATCA-AGGTCAAAAAT--AATATTTTGGGAAGTTCG
1 GGGT-AAAATGGTAATTTTTAGAAAAATCAGAGATTAAAAATGGAAT-TTTT-GGAAGTTTG
231197 AGGGTAAAAAT-GTAATTTTT
1 -GGGT-AAAATGGTAATTTTT
231217 TAAAGTTTAG
Statistics
Matches: 260, Mismatches: 33, Indels: 40
0.78 0.10 0.12
Matches are distributed among these distances:
56 1 0.00
57 13 0.05
58 66 0.25
59 166 0.64
60 14 0.05
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTAGAAAAATCAGAGATTAAAAATGGAATTTTTGGAAGTTTG
Found at i:231067 original size:30 final size:29
Alignment explanation
Indices: 230974--231076 Score: 102
Period size: 30 Copynumber: 3.5 Consensus size: 29
230964 GGTAAATGGT
*
230974 AATTTTTAAAAGTTTTAGGGTTAAAA-ATGG
1 AATTTTTAGAAG-TTTAGGGTTAAAATA-GG
* *
231004 AATTTTTGGAAGTTTAGGGGTAAAAT-GG
1 AATTTTTAGAAGTTTAGGGTTAAAATAGG
* *
231032 TAATTTTTAGAAGTTTCAGAGTTAAAATAAG
1 -AATTTTTAGAAGTTT-AGGGTTAAAATAGG
*
231063 AATTTTTGGAAGTT
1 AATTTTTAGAAGTT
231077 CGAGTGTAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
28 2 0.03
29 26 0.43
30 32 0.52
31 1 0.02
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.40
Consensus pattern (29 bp):
AATTTTTAGAAGTTTAGGGTTAAAATAGG
Found at i:231089 original size:30 final size:28
Alignment explanation
Indices: 230995--231216 Score: 105
Period size: 30 Copynumber: 7.6 Consensus size: 28
230985 GTTTTAGGGT
* * *
230995 TAAAAATGGAATTTTTGGAAGTTTAGGGG
1 TAAAAATAGAATTTTTGGAAG-TTCGAGG
* *
231024 T-AAAATGGTAATTTTTAGAAGTTTC-AGAG
1 TAAAAATAG-AATTTTTGGAAG-TTCGAG-G
*
231053 TTAAAATAAGAATTTTTGGAAGTTCGAGTG
1 TAAAAAT-AGAATTTTTGGAAGTTCGAG-G
* ** *
231083 TAAAAAT-GTCATTTTTAGGAAAATCAAGG
1 TAAAAATAG-AATTTTT-GGAAGTTCGAGG
* *
231112 TCAAAAATAGAATTTTGGGAAGTTCCAGGG
1 T-AAAAATAGAATTTTTGGAAGTTCGA-GG
* ** *
231142 TAAAAAT-GTCATTTTTAGGAAAATCAAGG
1 TAAAAATAG-AATTTTT-GGAAGTTCGAGG
*
231171 TCAAAAATA-ATATTTTGGGAAGTTCGAGGG
1 T-AAAAATAGA-ATTTTTGGAAGTTCGA-GG
231201 TAAAAAT-GTAATTTTT
1 TAAAAATAG-AATTTTT
231217 TAAAGTTTAG
Statistics
Matches: 148, Mismatches: 27, Indels: 36
0.70 0.13 0.17
Matches are distributed among these distances:
28 10 0.07
29 67 0.45
30 69 0.47
31 2 0.01
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (28 bp):
TAAAAATAGAATTTTTGGAAGTTCGAGG
Found at i:231096 original size:29 final size:28
Alignment explanation
Indices: 230995--231216 Score: 130
Period size: 29 Copynumber: 7.6 Consensus size: 28
230985 GTTTTAGGGT
* * *
230995 TAAAAATGGAATTTTTGGAAGTTTAGGGG
1 TAAAAATGTAATTTTTGGAAGTTCA-AGG
* *
231024 T-AAAATGGTAATTTTTAGAAGTTTCAGAGT
1 TAAAAAT-GTAATTTTTGGAAG-TTCA-AGG
* *
231054 TAAAATAAG-AATTTTTGGAAGTTCGAGTG
1 TAAAA-ATGTAATTTTTGGAAGTTCAAG-G
* **
231083 TAAAAATGTCATTTTTAGGAAAATCAAGG
1 TAAAAATGTAATTTTT-GGAAGTTCAAGG
* *
231112 TCAAAAATAG-AATTTTGGGAAGTTCCAGGG
1 T-AAAAAT-GTAATTTTTGGAAGTT-CAAGG
* **
231142 TAAAAATGTCATTTTTAGGAAAATCAAGG
1 TAAAAATGTAATTTTT-GGAAGTTCAAGG
*
231171 TCAAAAA--TAATATTTTGGGAAGTTCGAGGG
1 T-AAAAATGTAAT-TTTT-GGAAGTTC-AAGG
231201 TAAAAATGTAATTTTT
1 TAAAAATGTAATTTTT
231217 TAAAGTTTAG
Statistics
Matches: 147, Mismatches: 29, Indels: 33
0.70 0.14 0.16
Matches are distributed among these distances:
28 13 0.09
29 65 0.44
30 59 0.40
31 9 0.06
32 1 0.01
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (28 bp):
TAAAAATGTAATTTTTGGAAGTTCAAGG
Found at i:231232 original size:59 final size:58
Alignment explanation
Indices: 230967--231253 Score: 233
Period size: 59 Copynumber: 4.8 Consensus size: 58
230957 ATCTGGGGGT
* * ** * *
230967 AAATGGTAATTTTTAAAAGTTTTAGGGTTAAAAATGGAATTTTTGGAAGTT-TAGGGGT-A
1 AAAT-GTAATTTTTAGAAG-TTTAGGGTCAAAAATAAAATTTTGGGAAGTTCGA-GGGTAA
* * * *
231026 AAATGGTAATTTTTAGAAGTTTCAGAGT-TAAAATAAGAATTTTTGGAAGTTCGAGTGTAA
1 AAAT-GTAATTTTTAGAAGTTT-AGGGTCAAAAATAA-AATTTTGGGAAGTTCGAGGGTAA
* ** * * * *
231086 AAATGTCATTTTTAGGAAAATCAAGGTCAAAAATAGAATTTTGGGAAGTTCCAGGGTAA
1 AAATGTAATTTTTA-GAAGTTTAGGGTCAAAAATAAAATTTTGGGAAGTTCGAGGGTAA
* ** * * *
231145 AAATGTCATTTTTAGGAAAATCAAGGTCAAAAATAATATTTTGGGAAGTTCGAGGGTAA
1 AAATGTAATTTTTA-GAAGTTTAGGGTCAAAAATAAAATTTTGGGAAGTTCGAGGGTAA
231204 AAATGTAATTTTTTA-AAGTTTAGGGGTC-AAAATAAAATTTTGGAGAAGTT
1 AAATGTAA-TTTTTAGAAGTTTA-GGGTCAAAAATAAAATTTTGG-GAAGTT
231254 TAGGGGTCAA
Statistics
Matches: 192, Mismatches: 27, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
58 26 0.14
59 144 0.75
60 22 0.11
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.34
Consensus pattern (58 bp):
AAATGTAATTTTTAGAAGTTTAGGGTCAAAAATAAAATTTTGGGAAGTTCGAGGGTAA
Found at i:231255 original size:30 final size:29
Alignment explanation
Indices: 231198--231348 Score: 169
Period size: 30 Copynumber: 5.1 Consensus size: 29
231188 GGAAGTTCGA
* * **
231198 GGGTAAAAATGTAATTTTTTAAAGTTTAG
1 GGGTCAAAATATAATTTTGGAAAGTTTAG
*
231227 GGGTCAAAATAAAATTTTGGAGAAGTTTAG
1 GGGTCAAAATATAATTTTGGA-AAGTTTAG
231257 GGGTCAAAATATAATTTTGGAAATGTTTAG
1 GGGTCAAAATATAATTTTGGAAA-GTTTAG
*
231287 GGGTCAAAATGTAATTTTGGAAAAGTTT-G
1 GGGTCAAAATATAATTTTGG-AAAGTTTAG
* * *
231316 GCGATCAAAATATGATTTTTGGATAGTTTAG
1 G-GGTCAAAATAT-AATTTTGGAAAGTTTAG
231347 GG
1 GG
231349 ACCTCCAGGG
Statistics
Matches: 105, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
29 20 0.19
30 73 0.70
31 12 0.11
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (29 bp):
GGGTCAAAATATAATTTTGGAAAGTTTAG
Found at i:231303 original size:60 final size:58
Alignment explanation
Indices: 231169--231348 Score: 191
Period size: 60 Copynumber: 3.0 Consensus size: 58
231159 GGAAAATCAA
* * * * **
231169 GGTCAAAAATAATATTTTGG-GAAGTTCGAGGGTAAAAATGTAATTTTTTAAAGTTTAGG
1 GGTC-AAAATAAAATTTTGGAGAAGTTTG-GGGTCAAAATATAATTTTGGAAAGTTTAGG
231228 GGTCAAAATAAAATTTTGGAGAAGTTTAGGGGTCAAAATATAATTTTGGAAATGTTTAGG
1 GGTCAAAATAAAATTTTGGAGAAGTTT-GGGGTCAAAATATAATTTTGGAAA-GTTTAGG
** * * * *
231288 GGTCAAAATGTAATTTTGGAAAAGTTTGGCGATCAAAATATGATTTTTGGATAGTTTAGG
1 GGTCAAAATAAAATTTTGGAGAAGTTTGG-GGTCAAAATAT-AATTTTGGAAAGTTTAGG
231348 G
1 G
231349 ACCTCCAGGG
Statistics
Matches: 104, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
58 14 0.13
59 31 0.30
60 50 0.48
61 9 0.09
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (58 bp):
GGTCAAAATAAAATTTTGGAGAAGTTTGGGGTCAAAATATAATTTTGGAAAGTTTAGG
Found at i:232143 original size:20 final size:20
Alignment explanation
Indices: 232118--232173 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
232108 AAACCCAAAA
232118 CAAGATCCGATTTTGCTTGT
1 CAAGATCCGATTTTGCTTGT
232138 CAAGATCCGATTTTGCTTGT
1 CAAGATCCGATTTTGCTTGT
*
232158 CAAAATCCCGATTTTG
1 CAAGAT-CCGATTTTG
232174 GTTCTTTAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 25 0.74
21 9 0.26
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (20 bp):
CAAGATCCGATTTTGCTTGT
Found at i:233295 original size:13 final size:13
Alignment explanation
Indices: 233274--233304 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
233264 CTCACAATGG
*
233274 TTATTGGCCCCTA
1 TTATCGGCCCCTA
233287 TTATCGGCCCCTA
1 TTATCGGCCCCTA
233300 TTATC
1 TTATC
233305 ATACTCTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.32, G:0.13, T:0.39
Consensus pattern (13 bp):
TTATCGGCCCCTA
Found at i:235981 original size:99 final size:99
Alignment explanation
Indices: 235871--236071 Score: 366
Period size: 99 Copynumber: 2.0 Consensus size: 99
235861 CAGTTTTTCT
235871 ATCATTTTTTCCATCTCAGCATTCTTCCTCTCGAAATCTTGTTTAATTATTTCTAGTTCAGACGG
1 ATCATTTTTTCCATCTCAGCATTCTTCCTCTCGAAATCTTGTTTAATTATTTCTAGTTCAGACGG
*
235936 GACAACCTGCAAGTGTTCTTCAATTGGGCGGATA
66 GACAACCTGCAAGTGTTCTTCAATTGGGCGGACA
* * *
235970 ATCATTTTTTCCATCTCAGCATTCTTCCTTTCGAAATCTTGTTTAATTATTTGTAGTTCAGTCGG
1 ATCATTTTTTCCATCTCAGCATTCTTCCTCTCGAAATCTTGTTTAATTATTTCTAGTTCAGACGG
236035 GACAACCTGCAAGTGTTCTTCAATTGGGCGGACA
66 GACAACCTGCAAGTGTTCTTCAATTGGGCGGACA
236069 ATC
1 ATC
236072 TCCAGGTTTG
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 98 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (99 bp):
ATCATTTTTTCCATCTCAGCATTCTTCCTCTCGAAATCTTGTTTAATTATTTCTAGTTCAGACGG
GACAACCTGCAAGTGTTCTTCAATTGGGCGGACA
Found at i:238689 original size:28 final size:28
Alignment explanation
Indices: 238588--238692 Score: 79
Period size: 29 Copynumber: 3.6 Consensus size: 28
238578 AATAACCGAC
**
238588 GGTAAAATGGTAATTTTTGACATTCGTGG
1 GGTAAAATGGTAATTTTAAACATTCG-GG
* * * *
238617 AGCAAAATGGTAATTTTGGGAAA-GTTCGAG
1 GGTAAAATGGTAATTTT---AAACATTCGGG
* *
238647 GTTAAAA-AGTGAATTTTAAACATTCGGG
1 GGTAAAATGGT-AATTTTAAACATTCGGG
238675 GGTAAAATGGTAATTTTA
1 GGTAAAATGGTAATTTTA
238693 GAAAAAAATT
Statistics
Matches: 56, Mismatches: 14, Indels: 13
0.67 0.17 0.16
Matches are distributed among these distances:
27 3 0.05
28 18 0.32
29 19 0.34
30 11 0.20
31 4 0.07
32 1 0.02
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.33
Consensus pattern (28 bp):
GGTAAAATGGTAATTTTAAACATTCGGG
Found at i:238712 original size:58 final size:59
Alignment explanation
Indices: 238602--238814 Score: 193
Period size: 59 Copynumber: 3.6 Consensus size: 59
238592 AAATGGTAAT
* ** ** * *
238602 TTTTG-ACATTCGTGGAGCAAAATGGTAATTTT-GGGAAAGTTCGAGGTTAAAAAGTGAA
1 TTTTGAACATTCG-GGGGCAAAATGGTAATTTTAGAAAAAAATCGAGATCAAAAAGTGAA
* * * *
238660 TTTTAAACATTCGGGGGTAAAATGGTAATTTTAGAAAAAAAT-TAGATCAAAAATTGAA
1 TTTTGAACATTCGGGGGCAAAATGGTAATTTTAGAAAAAAATCGAGATCAAAAAGTGAA
* * **
238718 TTTTTGGACATTCGAGGGCAAAATGGTAATTTTTAG--AAAAATCGAGATCAAAAACGAAAA
1 -TTTTGAACATTCGGGGGCAAAATGGTAA-TTTTAGAAAAAAATCGAGATCAAAAA-GTGAA
* * *
238778 TTTTGAACATCCAGGGGCAAAATGGTAATTTTTGAAA
1 TTTTGAACATTCGGGGGCAAAATGGTAATTTTAGAAA
238815 GTTTCGAGGT
Statistics
Matches: 123, Mismatches: 24, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
58 44 0.36
59 70 0.57
60 9 0.07
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (59 bp):
TTTTGAACATTCGGGGGCAAAATGGTAATTTTAGAAAAAAATCGAGATCAAAAAGTGAA
Found at i:238805 original size:118 final size:117
Alignment explanation
Indices: 238599--238814 Score: 281
Period size: 118 Copynumber: 1.8 Consensus size: 117
238589 GTAAAATGGT
* * ** * * **
238599 AATTTTTGACATTCGTGGAGCAAAATGGTAATTTTGGGAAAGTTCGAGGTTAAAAAGTGAATTTT
1 AATTTTTGACATTCGAGGAGCAAAATGGTAATTTTGAGAAAAATCGAGATCAAAAAGAAAATTTT
* * *
238664 AAACATTCGGGGGTAAAATGGTAATTTTAGAAAAAAATTAGATCAAAAATTG
66 AAACATCCAGGGGCAAAATGGTAATTTTAGAAAAAAATTAGATCAAAAATTG
*
238716 AATTTTTGGACATTCGAGG-GCAAAATGGTAATTTTTAGAAAAATCGAGATCAAAAACGAAAATT
1 AATTTTT-GACATTCGAGGAGCAAAATGGTAATTTTGAGAAAAATCGAGATCAAAAA-GAAAATT
* *
238780 TTGAACATCCAGGGGCAAAATGGTAATTTTTGAAA
64 TTAAACATCCAGGGGCAAAATGGTAATTTTAGAAA
238815 GTTTCGAGGT
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
117 38 0.46
118 45 0.54
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.30
Consensus pattern (117 bp):
AATTTTTGACATTCGAGGAGCAAAATGGTAATTTTGAGAAAAATCGAGATCAAAAAGAAAATTTT
AAACATCCAGGGGCAAAATGGTAATTTTAGAAAAAAATTAGATCAAAAATTG
Found at i:238828 original size:118 final size:117
Alignment explanation
Indices: 238591--238843 Score: 264
Period size: 118 Copynumber: 2.2 Consensus size: 117
238581 AACCGACGGT
* * ** * *
238591 AAAA-TGGTAATTTTT-GACATTCGTGGAGCAAAATGGTAATTTTGGGAAAGTTCGAGGTTAAAA
1 AAAATTGG-AATTTTTGGACATTCGAGGAGCAAAATGGTAATTTTGAGAAAAATCGAGATCAAAA
** * * *
238654 AGTGAATTTTAAACATTCGGGGGTAAAATGGTAATTTTAGAAAAAAATTAGATC
65 AGAAAATTTTAAACATCCAGGGGCAAAATGGTAATTTTAG-AAAAAATTAGATC
*
238708 AAAAATT-GAATTTTTGGACATTCGAGG-GCAAAATGGTAATTTTTAGAAAAATCGAGATCAAAA
1 -AAAATTGGAATTTTTGGACATTCGAGGAGCAAAATGGTAATTTTGAGAAAAATCGAGATCAAAA
* * ** *
238771 ACGAAAATTTTGAACATCCAGGGGCAAAATGGTAATTTTTG-AAAGTTTCGAGGTC
65 A-GAAAATTTTAAACATCCAGGGGCAAAATGGTAATTTTAGAAAAAATT--AGATC
238826 AAAATTGGAATTTTTGGA
1 AAAATTGGAATTTTTGGA
238844 AGTTTCGAGG
Statistics
Matches: 112, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
116 5 0.04
117 44 0.39
118 62 0.55
119 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.31
Consensus pattern (117 bp):
AAAATTGGAATTTTTGGACATTCGAGGAGCAAAATGGTAATTTTGAGAAAAATCGAGATCAAAAA
GAAAATTTTAAACATCCAGGGGCAAAATGGTAATTTTAGAAAAAATTAGATC
Found at i:238841 original size:59 final size:58
Alignment explanation
Indices: 238591--238841 Score: 178
Period size: 59 Copynumber: 4.3 Consensus size: 58
238581 AACCGACGGT
* * *
238591 AAAA-TGGTAATTTTTG-ACATTCGTGGAGCAAAATGGTAATTTTGGGAAAG-TTCGAGGTT
1 AAAATTGG-AATTTTTGAACATTCG-GG-GCAAAATGGTAATTTT-TGAAAGATTCGAGATC
* * * * *
238650 AAAA-AGTGAA-TTTTAAACATTCGGGGGTAAAATGGTAATTTTAGAAAAAAATT--AGATC
1 AAAATTG-GAATTTTTGAACATTC-GGGGCAAAATGGTAATTTTTG--AAAGATTCGAGATC
* *
238708 AAAAATT-GAATTTTTGGACATTCGAGGGCAAAATGGTAATTTTTAGAAA-AATCGAGATC
1 -AAAATTGGAATTTTTGAACATTCG-GGGCAAAATGGTAATTTTT-GAAAGATTCGAGATC
** * * * * *
238767 AAAAACGAAAATTTTGAACATCCAGGGGCAAAATGGTAATTTTTGAAAGTTTCGAGGTC
1 AAAATTGGAATTTTTGAACATTC-GGGGCAAAATGGTAATTTTTGAAAGATTCGAGATC
238826 AAAATTGGAATTTTTG
1 AAAATTGGAATTTTTG
238842 GAAGTTTCGA
Statistics
Matches: 150, Mismatches: 26, Indels: 32
0.72 0.12 0.15
Matches are distributed among these distances:
57 3 0.02
58 37 0.25
59 104 0.69
60 6 0.04
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (58 bp):
AAAATTGGAATTTTTGAACATTCGGGGCAAAATGGTAATTTTTGAAAGATTCGAGATC
Found at i:238895 original size:28 final size:29
Alignment explanation
Indices: 238832--238897 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
238822 GGTCAAAATT
* * **
238832 GGAATTTTTGGAAGTTTCGAGGTTAAAATT
1 GGAA-TTTTGGAAGTTTAGAGGGTAAAAAA
238862 GGAATTTTGGAAGTTTAG-GGGTAAAAAA
1 GGAATTTTGGAAGTTTAGAGGGTAAAAAA
*
238890 GTAATTTT
1 GGAATTTT
238898 TTGGAAAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 14 0.45
29 13 0.42
30 4 0.13
ACGTcount: A:0.33, C:0.02, G:0.27, T:0.38
Consensus pattern (29 bp):
GGAATTTTGGAAGTTTAGAGGGTAAAAAA
Found at i:238898 original size:29 final size:30
Alignment explanation
Indices: 238790--239030 Score: 131
Period size: 30 Copynumber: 8.1 Consensus size: 30
238780 TTGAACATCC
* *
238790 AGGGG-CAAAATGGTAATTTTTGAAAGTTT
1 AGGGGTCAAAATAGTAATTTTTGGAAGTTT
* * * *
238819 CGAGGTCAAAATTGGAATTTTTGGAAGTTT
1 AGGGGTCAAAATAGTAATTTTTGGAAGTTT
* * * * *
238849 CGAGGTTAAAATTGGAA-TTTTGGAAGTTT
1 AGGGGTCAAAATAGTAATTTTTGGAAGTTT
* ** *
238878 AGGGGT-AAAAAAGTAATTTTTTGGAAAATC
1 AGGGGTCAAAATAGTAA-TTTTTGGAAGTTT
* * *
238908 A-TGGTCAAAAATAG-AATTTTGGGAAGTTC
1 AGGGGTC-AAAATAGTAATTTTTGGAAGTTT
* * * *** *
238937 GGGGGTAAAAAT-GCAATTTTCAAAAAATTT
1 AGGGGTCAAAATAGTAATTTT-TGGAAGTTT
238967 AGGGGTCAAAATA-TAA-TTTTGGAAAAGTTT
1 AGGGGTCAAAATAGTAATTTTTGG--AAGTTT
*
238997 AGGGGTCAAAATA-TGATTTTTGGATAGTTT
1 AGGGGTCAAAATAGTAATTTTTGGA-AGTTT
239027 AGGG
1 AGGG
239031 ACCTCTCGGA
Statistics
Matches: 164, Mismatches: 35, Indels: 25
0.73 0.16 0.11
Matches are distributed among these distances:
28 8 0.05
29 47 0.29
30 97 0.59
31 12 0.07
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.34
Consensus pattern (30 bp):
AGGGGTCAAAATAGTAATTTTTGGAAGTTT
Found at i:246285 original size:18 final size:17
Alignment explanation
Indices: 246246--246292 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
246236 CTATAGTTAG
246246 ATTG-CATT-CATTTTT
1 ATTGTCATTGCATTTTT
246261 ATTGTCATTGCATTTTAT
1 ATTGTCATTGCATTTT-T
*
246279 TTTGTCATTGCATT
1 ATTGTCATTGCATT
246293 CCTTTTGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 4 0.14
16 4 0.14
17 6 0.21
18 14 0.50
ACGTcount: A:0.19, C:0.13, G:0.11, T:0.57
Consensus pattern (17 bp):
ATTGTCATTGCATTTTT
Found at i:246907 original size:6 final size:6
Alignment explanation
Indices: 246896--246938 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
246886 TTGTTGAATG
*
246896 AGAAAA AGAAAA GGAAAA GAGAAAA AGAGAAA AGAAAA AGAAA
1 AGAAAA AGAAAA AGAAAA -AGAAAA AGA-AAA AGAAAA AGAAA
246939 TATTGCTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 22 0.67
7 11 0.33
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:246917 original size:19 final size:20
Alignment explanation
Indices: 246895--246938 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
246885 ATTGTTGAAT
*
246895 GAGAAAAAGA-AAAGGAAAA
1 GAGAAAAAGAGAAAAGAAAA
246914 GAGAAAAAGAGAAAAGAAAA
1 GAGAAAAAGAGAAAAGAAAA
246934 -AGAAA
1 GAGAAA
246939 TATTGCTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (20 bp):
GAGAAAAAGAGAAAAGAAAA
Found at i:246920 original size:13 final size:14
Alignment explanation
Indices: 246895--246936 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
246885 ATTGTTGAAT
246895 GAGAAAA-AGAAAA
1 GAGAAAAGAGAAAA
246908 G-GAAAAGAGAAAAA
1 GAGAAAAGAG-AAAA
246922 GAGAAAAGA-AAAA
1 GAGAAAAGAGAAAA
246935 GA
1 GA
246937 AATATTGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 5 0.19
13 9 0.35
14 5 0.19
15 7 0.27
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
GAGAAAAGAGAAAA
Found at i:246928 original size:21 final size:20
Alignment explanation
Indices: 246898--246936 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
246888 GTTGAATGAG
*
246898 AAAAAGAAAAGGAAAAGAGA
1 AAAAAGAAAAGAAAAAGAGA
246918 AAAAGAGAAAAGAAAAAGA
1 AAAA-AGAAAAGAAAAAGA
246937 AATATTGCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAGAAAAAGAGA
Found at i:252310 original size:29 final size:28
Alignment explanation
Indices: 252277--252665 Score: 151
Period size: 29 Copynumber: 13.3 Consensus size: 28
252267 CTAAACTGTT
252277 CAAAAATTACATTTTACCCCCGAACTTC
1 CAAAAATTACATTTTACCCCCGAACTTC
* * *
252305 CAAAAATTCCATTTTTGA-CCTCGAAACTTT
1 CAAAAATTACA-TTTT-ACCCCCG-AACTTC
* * *
252335 CAAAAATTACTTTTTTACCCACAAACTTC
1 CAAAAATTAC-ATTTTACCCCCGAACTTC
* * ** *
252364 CAAAAATTCCATTTTGACCTCAAAACTTT
1 CAAAAATTACATTTT-ACCCCCGAACTTC
* * *
252393 CAGAAATTATATTTTTACCACCGAACTTC
1 CAAAAATTACA-TTTTACCCCCGAACTTC
* ** ** *
252422 CAAAAATTTCATTTTGACTTCAAAACTTT
1 CAAAAATTACATTTT-ACCCCCGAACTTC
** * * *
252451 TTAAAATTACATTTTTATCCCCAAAATTC
1 CAAAAATTACA-TTTTACCCCCGAACTTC
*
252480 CAAAAATTCCATTTTTTGA-CCCCGAAACTTC
1 CAAAAATTACA--TTTT-ACCCCCG-AACTTC
* * * *
252511 CAGAAATTCCATTTTTACCCTCGAACCTC
1 CAAAAATTACA-TTTTACCCCCGAACTTC
* ***
252540 TAAAAATT-CTATTTTTAACCCTAAAACTTC
1 CAAAAATTAC-A-TTTT-ACCCCCGAACTTC
* *
252570 TAAAAATTACATTTTTACCCTCGAA-TGTC
1 CAAAAATTACA-TTTTACCCCCGAACT-TC
* * * * **
252599 TAAAAACTCCTTTTTTGACCCCAAAAC-TC
1 CAAAAATTAC-ATTTT-ACCCCCGAACTTC
252628 TCAAAAATTACCATTTTACCCCCGAA-TGTC
1 -CAAAAATTA-CATTTTACCCCCGAACT-TC
252658 CAAAAATT
1 CAAAAATT
252666 CCGTTTTTAT
Statistics
Matches: 272, Mismatches: 65, Indels: 47
0.71 0.17 0.12
Matches are distributed among these distances:
28 20 0.07
29 144 0.53
30 90 0.33
31 18 0.07
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (28 bp):
CAAAAATTACATTTTACCCCCGAACTTC
Found at i:252362 original size:59 final size:59
Alignment explanation
Indices: 252269--252673 Score: 389
Period size: 59 Copynumber: 6.9 Consensus size: 59
252259 GGAGGTCCCT
* *
252269 AAACTGTTCAAAAATTACA-TTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCTCG
1 AAACT-TTCAAAAATTACATTTTTACCCACGAACTTCCAAAAATTCCATTTTTGACCTCA
* *
252328 AAACTTTCAAAAATTACTTTTTTACCCACAAACTTCCAAAAATTCCA-TTTTGACCTCA
1 AAACTTTCAAAAATTACATTTTTACCCACGAACTTCCAAAAATTCCATTTTTGACCTCA
* * * *
252386 AAACTTTCAGAAATTATATTTTTA-CCACCGAACTTCCAAAAATTTCA-TTTTGACTTCA
1 AAACTTTCAAAAATTACATTTTTACCCA-CGAACTTCCAAAAATTCCATTTTTGACCTCA
** * * * *
252444 AAACTTTTTAAAATTACATTTTTATCCC-CAAAATTCCAAAAATTCCATTTTTTGACCCCG
1 AAACTTTCAAAAATTACATTTTTA-CCCACGAACTTCCAAAAATTCCA-TTTTTGACCTCA
* * * * * * * *
252504 AAACTTCCAGAAATTCCATTTTTACCCTCGAACCTCTAAAAATTCTATTTTTAACC-CTA
1 AAACTTTCAAAAATTACATTTTTACCCACGAACTTCCAAAAATTCCATTTTTGACCTC-A
* * * * *
252563 AAAC-TTCTAAAAATTACATTTTTACCCTCGAA-TGTCTAAAAACTCCTTTTTTGACCCCA
1 AAACTTTC-AAAAATTACATTTTTACCCACGAACT-TCCAAAAATTCCATTTTTGACCTCA
* * *
252622 AAACTCTCAAAAATTACCA-TTTTACCCCCGAA-TGTCCAAAAATTCCGTTTTT
1 AAACTTTCAAAAATTA-CATTTTTACCCACGAACT-TCCAAAAATTCCATTTTT
252674 ATCCCGATTT
Statistics
Matches: 288, Mismatches: 45, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
57 3 0.01
58 109 0.38
59 128 0.44
60 48 0.17
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.35
Consensus pattern (59 bp):
AAACTTTCAAAAATTACATTTTTACCCACGAACTTCCAAAAATTCCATTTTTGACCTCA
Found at i:252719 original size:29 final size:28
Alignment explanation
Indices: 252630--252719 Score: 67
Period size: 29 Copynumber: 3.1 Consensus size: 28
252620 CAAAACTCTC
* * **
252630 AAAAATTACCATTTTACCCCCGAATGTCC
1 AAAAATTACCGTTTTA-CCCCGGATGTTT
* *
252659 AAAAATT-CCGTTTTTATCCC-GATTTTTCT
1 AAAAATTACCG-TTTTACCCCGGA-TGTT-T
252688 AAAAATTACCGTTTTACCCTCGGATGTTT
1 AAAAATTACCGTTTTACCC-CGGATGTTT
252717 AAA
1 AAA
252720 TTTCCATTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
27 1 0.02
28 7 0.15
29 30 0.64
30 7 0.15
31 2 0.04
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.37
Consensus pattern (28 bp):
AAAAATTACCGTTTTACCCCGGATGTTT
Found at i:252808 original size:29 final size:29
Alignment explanation
Indices: 252747--252807 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 29
252737 AAATTTTTCC
252747 AAAATTACCATTTTTGCCCCCGAGAATAT
1 AAAATTACCATTTTTGCCCCCGAGAATAT
* *
252776 AAAATTACCA-TTTTGCCCCCGAGTATCT
1 AAAATTACCATTTTTGCCCCCGAGAATAT
252804 AAAA
1 AAAA
252808 AGTCTCATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 20 0.67
29 10 0.33
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.30
Consensus pattern (29 bp):
AAAATTACCATTTTTGCCCCCGAGAATAT
Found at i:256840 original size:63 final size:63
Alignment explanation
Indices: 256762--256887 Score: 225
Period size: 63 Copynumber: 2.0 Consensus size: 63
256752 AATTGAGAAA
256762 GAGTCAAGTGAAGAATGGAACATATTGAAAGTTCGTCCCCACACCCTCGGAAGTGTTTTGGAC
1 GAGTCAAGTGAAGAATGGAACATATTGAAAGTTCGTCCCCACACCCTCGGAAGTGTTTTGGAC
* * *
256825 GAGTCAAGTGAAGAATGGAACCTATTGAGAGTTTGTCCCCACACCCTCGGAAGTGTTTTGGAC
1 GAGTCAAGTGAAGAATGGAACATATTGAAAGTTCGTCCCCACACCCTCGGAAGTGTTTTGGAC
256888 AACTAGACTG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.25
Consensus pattern (63 bp):
GAGTCAAGTGAAGAATGGAACATATTGAAAGTTCGTCCCCACACCCTCGGAAGTGTTTTGGAC
Found at i:258503 original size:5 final size:6
Alignment explanation
Indices: 258435--258502 Score: 52
Period size: 6 Copynumber: 11.5 Consensus size: 6
258425 ATAAATAAAT
* * * *
258435 AAAACA AAAAGA AAAAGA AAAA-A ACAA-A AAAATA AATAATA ATAAA-A
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AA-AAGA A-AAAGA
*
258482 AAGAGA AAAAGA AAAAGA AAA
1 AAAAGA AAAAGA AAAAGA AAA
258503 GGAGAGGTCG
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
5 10 0.19
6 35 0.66
7 7 0.13
8 1 0.02
ACGTcount: A:0.82, C:0.03, G:0.09, T:0.06
Consensus pattern (6 bp):
AAAAGA
Found at i:259838 original size:48 final size:50
Alignment explanation
Indices: 259713--259852 Score: 176
Period size: 50 Copynumber: 2.8 Consensus size: 50
259703 GTTTAACAGG
* * * * *
259713 GAAAGATCTAAGACCGCAACGGTAGATCCAGTACCACAAAAACACGACGG
1 GAAAGATCTAAGACCGCAACGGTGGATCCAGTACCACGAAGACACGAAGA
** *
259763 GAAAGATCTAAGACCGCAACAATGGATCCAGTATCACGAAGACAC-AAGA
1 GAAAGATCTAAGACCGCAACGGTGGATCCAGTACCACGAAGACACGAAGA
* *
259812 GAAAGATCTAAG-CCGCAACGGCGGATCCAATACCACGAAGA
1 GAAAGATCTAAGACCGCAACGGTGGATCCAGTACCACGAAGA
259853 TTCGAAGGGA
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
48 24 0.31
49 14 0.18
50 39 0.51
ACGTcount: A:0.42, C:0.25, G:0.22, T:0.11
Consensus pattern (50 bp):
GAAAGATCTAAGACCGCAACGGTGGATCCAGTACCACGAAGACACGAAGA
Found at i:260716 original size:206 final size:206
Alignment explanation
Indices: 260364--261219 Score: 1165
Period size: 206 Copynumber: 4.2 Consensus size: 206
260354 TGAGGCGGTT
* * * *
260364 ATCTTCCTGATGAGATACTGAGAAGTATACCAACTC--A---GCGCTCGATGTGAGCAAATCTTC
1 ATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTC
*
260424 GAATC-CAGCTTCCTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAATGGCTAGCTTCCTGA
66 GAATCACAGCTTCCTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAATGGTTAGCTTCCTGA
* * *
260488 TGAGATACTGATAAGTGGACCAAATTCGTCTTCCTGATAAGATACAGAGAAGCA-GATTGAAACA
131 TGAGATACTGAGAAGCGAACCAAATTCGTCTTCCTGATAAGATACAGAGAAG-AGGATTGAAACA
**
260552 AACGACGTGATC
195 AACGACACGATC
*
260564 ATCTTCCTGATGAGATACTGAGAAGAAGACCAAA-CCAACTCCACGCTCGATGTGAGCAAATCTT
1 ATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAAC-CCACGCTCGATGTGAGCAAATCTT
*
260628 CGAATCACAACTTCCTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAATGGTTAGCTTCCTG
65 CGAATCACAGCTTCCTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAATGGTTAGCTTCCTG
* * * * *
260693 ATGAGATACTGAGAAGCGGACCAAAGTCGTCTTCTTAATGAGATACAGAGAAGAGGATTGAAACA
130 ATGAGATACTGAGAAGCGAACCAAATTCGTCTTCCTGATAAGATACAGAGAAGAGGATTGAAACA
*
260758 AACGACACGGTC
195 AACGACACGATC
* **
260770 ATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACCCATACTCGATGTGAGCAAATCTTC
1 ATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTC
* * *
260835 GGATAACAGCTTCCTGATGAGATACTGAGAAACGGGTCGAAGCAATAAAATGGTTAGCTTCCTGA
66 GAATCACAGCTTCCTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAATGGTTAGCTTCCTGA
** * *
260900 TGAGATACTGAGAAGCGAATTAAATTTGTCTTCCTGATGAGATACAGAGAAGAGGATTGAAACAA
131 TGAGATACTGAGAAGCGAACCAAATTCGTCTTCCTGATAAGATACAGAGAAGAGGATTGAAACAA
260965 ACGACACGATC
196 ACGACACGATC
260976 ATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTC
1 ATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTC
* * * * * *
261041 GAA-CCCTAGCTTCTTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAGTGGTTAGCTCCCTG
66 GAATCAC-AGCTTCCTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAATGGTTAGCTTCCTG
* * * * * * **
261105 ATGAGATACGGAGAAGTGAACTAAATCCGTCTTCCTGATGAA-ACACAGAGAAGTGGATCAAAAC
130 ATGAGATACTGAGAAGCGAACCAAATTCGTCTTCCTGAT-AAGATACAGAGAAGAGGATTGAAAC
** **
261169 AAGTGATGCGATC
194 AAACGACACGATC
* * *
261182 ACCTTCCTGATGAGATACTGAGAAGAAGGCCAAGTCAA
1 ATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
261220 TGAAACCAGA
Statistics
Matches: 585, Mismatches: 60, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
199 1 0.00
200 31 0.05
201 1 0.00
205 29 0.05
206 518 0.89
207 5 0.01
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (206 bp):
ATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTC
GAATCACAGCTTCCTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAATGGTTAGCTTCCTGA
TGAGATACTGAGAAGCGAACCAAATTCGTCTTCCTGATAAGATACAGAGAAGAGGATTGAAACAA
ACGACACGATC
Found at i:262338 original size:13 final size:13
Alignment explanation
Indices: 262310--262347 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
262300 TTATTGATAT
*
262310 TAATAAT-AATAT
1 TAATAATAAATAG
262322 TAATAATAAATAG
1 TAATAATAAATAG
*
262335 TAATATTAAATAG
1 TAATAATAAATAG
262348 CATTAATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (13 bp):
TAATAATAAATAG
Found at i:263985 original size:29 final size:29
Alignment explanation
Indices: 263704--264061 Score: 303
Period size: 29 Copynumber: 12.2 Consensus size: 29
263694 AAACTGTTCG
*
263704 AAAATTACA-TTTTACCCCCGAACTTCCA
1 AAAATTACATTTTTACCCCCAAACTTCCA
* *
263732 AAAATT-CTATTTTTGACCTCGAAACTTCCA
1 AAAATTAC-ATTTTT-ACCCCCAAACTTCCA
* *
263762 AAAATTACTTTTTTACCCCCAAACTTCTA
1 AAAATTACATTTTTACCCCCAAACTTCCA
* * * * *
263791 AAAATTCCATTTTGACCTCGAAACTTTCA
1 AAAATTACATTTTTACCCCCAAACTTCCA
* *
263820 AAAATTATATTTTTACCCCCGAACTTCCA
1 AAAATTACATTTTTACCCCCAAACTTCCA
* * ** * ***
263849 AAAATTTCATTTTGACTTCAAAACTTTTT
1 AAAATTACATTTTTACCCCCAAACTTCCA
* *
263878 AAAATTACATTTTTACCCTCGAACTTCCA
1 AAAATTACATTTTTACCCCCAAACTTCCA
* *
263907 AAAATTCCATTTTTTGACCCCGAAACTTCCA
1 AAAATTACA-TTTTT-ACCCCCAAACTTCCA
* * *
263938 AAAATTTCATTTTTAACCCCAAAACTTCTA
1 AAAATTACATTTTT-ACCCCCAAACTTCCA
263968 AAAATTACATTTTTACCCCCAAA-TATCCA
1 AAAATTACATTTTTACCCCCAAACT-TCCA
* * * *
263997 AAAACTCCATTTTTTACCCCAAAAC-TCGTA
1 AAAATTACA-TTTTTACCCCCAAACTTC-CA
* *
264027 AAAATTACCA-TTTTACCCCCGAACATCCA
1 AAAATTA-CATTTTTACCCCCAAACTTCCA
264056 AAAATT
1 AAAATT
264062 CCGTTTTTTA
Statistics
Matches: 257, Mismatches: 61, Indels: 23
0.75 0.18 0.07
Matches are distributed among these distances:
27 1 0.00
28 8 0.03
29 145 0.56
30 80 0.31
31 23 0.09
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAATTACATTTTTACCCCCAAACTTCCA
Found at i:264029 original size:59 final size:59
Alignment explanation
Indices: 263713--264071 Score: 220
Period size: 59 Copynumber: 6.1 Consensus size: 59
263703 GAAAATTACA
** * * * *
263713 TTTTACCCCCGAACTTCCAAAAATT-CTATTTTTGACCTCGAAACT-TCCAAAAATTAC-TT
1 TTTTACCCCAAAACTTCTAAAAATTAC-ATTTTT-ACCCCCAAA-TATCCAAAAATTCCATT
* * * * * *
263772 TTTTACCCCCAAACTTCTAAAAATTCCATTTTGACCTCGAAACT-TTCAAAAATT--ATAT
1 TTTTACCCCAAAACTTCTAAAAATTACATTTTTACCCCCAAA-TATCCAAAAATTCCAT-T
** * * * ** * *** *
263830 TTTTACCCCCGAACTTCCAAAAATTTCATTTTGACTTCAAAACT-TTTTAAAATTACA-T
1 TTTTACCCCAAAACTTCTAAAAATTACATTTTTACCCCCAAA-TATCCAAAAATTCCATT
* * * * *
263888 TTTTACCCTC-GAACTTCCAAAAATTCCATTTTTTGACCCCGAAACT-TCCAAAAATTTCATT
1 TTTTACCC-CAAAACTTCTAAAAATTACA-TTTTT-ACCCCCAAA-TATCCAAAAATTCCATT
* *
263949 TTTAACCCCAAAACTTCTAAAAATTACATTTTTACCCCCAAATATCCAAAAACTCCATT
1 TTTTACCCCAAAACTTCTAAAAATTACATTTTTACCCCCAAATATCCAAAAATTCCATT
* * *
264008 TTTTACCCCAAAAC-TCGTAAAAATTACCA-TTTTACCCCCGAACATCCAAAAATTCCGTT
1 TTTTACCCCAAAACTTC-TAAAAATTA-CATTTTTACCCCCAAATATCCAAAAATTCCATT
264067 TTTTA
1 TTTTA
264072 TCCTATTTTC
Statistics
Matches: 255, Mismatches: 32, Indels: 26
0.81 0.10 0.08
Matches are distributed among these distances:
57 1 0.00
58 97 0.38
59 107 0.42
60 27 0.11
61 23 0.09
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (59 bp):
TTTTACCCCAAAACTTCTAAAAATTACATTTTTACCCCCAAATATCCAAAAATTCCATT
Done.