Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 125 of 203
Found at i:39656828 original size:43 final size:43
Alignment explanation
Indices: 39656766--39656894 Score: 118
Period size: 43 Copynumber: 3.0 Consensus size: 43
39656756 CATAGGATCT
* *
39656766 TCGATATGTGTTTTTGTGTAAGACCACGTTTGGGACTTTGGCA
1 TCGATATGTGTTTTCGTGTAAGACCACGTTTGGGACATTGGCA
* * * *
39656809 TCGATTTGTGTTTTCGTGTAAGACC-CTGTCTGGGGCAGTGGC-
1 TCGATATGTGTTTTCGTGTAAGACCAC-GTTTGGGACATTGGCA
* * ** * * *
39656851 TCGATCTATGAATACATGTAAGACCACGTTTGGGACGTTGGCA
1 TCGATATGTGTTTTCGTGTAAGACCACGTTTGGGACATTGGCA
39656894 T
1 T
39656895 TGTACGAGCC
Statistics
Matches: 67, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
42 31 0.46
43 36 0.54
ACGTcount: A:0.19, C:0.17, G:0.29, T:0.35
Consensus pattern (43 bp):
TCGATATGTGTTTTCGTGTAAGACCACGTTTGGGACATTGGCA
Found at i:39659556 original size:36 final size:36
Alignment explanation
Indices: 39659509--39659586 Score: 138
Period size: 36 Copynumber: 2.2 Consensus size: 36
39659499 TGTATTTTTT
*
39659509 ATATTGCTCTAAAATGAATTGAAACTTAATGGTTTG
1 ATATTGCTCTAAAATGAATTGAAACTTAATGGTATG
39659545 ATATTGCTCTAAAATGAATTGAAACTTAATGGTATG
1 ATATTGCTCTAAAATGAATTGAAACTTAATGGTATG
*
39659581 CTATTG
1 ATATTG
39659587 GAATGTTTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (36 bp):
ATATTGCTCTAAAATGAATTGAAACTTAATGGTATG
Found at i:39670093 original size:11 final size:11
Alignment explanation
Indices: 39670077--39670107 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
39670067 ATACCCATAC
39670077 CCCATACCTTG
1 CCCATACCTTG
*
39670088 CCCATACCTTT
1 CCCATACCTTG
39670099 CCCATACCT
1 CCCATACCT
39670108 ACCCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.03, T:0.29
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:39670680 original size:18 final size:18
Alignment explanation
Indices: 39670653--39670745 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
39670643 TACGACCGTT
39670653 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
39670671 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
39670689 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
39670707 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
39670725 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
39670743 TAC
1 TAC
39670746 AGTAGTTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:39674815 original size:11 final size:11
Alignment explanation
Indices: 39674799--39674829 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
39674789 ATACCCATAC
39674799 CCCATACCTTG
1 CCCATACCTTG
*
39674810 CCCATACCTTT
1 CCCATACCTTG
39674821 CCCATACCT
1 CCCATACCT
39674830 ACCCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.03, T:0.29
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:39676442 original size:14 final size:14
Alignment explanation
Indices: 39676425--39676452 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39676415 CTCACATTTC
39676425 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
39676439 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
39676453 GATTTCTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTCTTTTCTCCA
Found at i:39676527 original size:6 final size:6
Alignment explanation
Indices: 39676516--39676544 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
39676506 CTGTAAAATC
39676516 GATTTT GATTTT GATTTT GATTTT G-TTTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT
39676545 ACTTTTGCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.14, C:0.00, G:0.17, T:0.69
Consensus pattern (6 bp):
GATTTT
Found at i:39678147 original size:17 final size:17
Alignment explanation
Indices: 39678127--39678161 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
39678117 ATATTAAGAA
39678127 TTTTATTAAATTATATT
1 TTTTATTAAATTATATT
39678144 TTTTATTAAATTATATT
1 TTTTATTAAATTATATT
39678161 T
1 T
39678162 AATAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTATTAAATTATATT
Found at i:39678409 original size:45 final size:44
Alignment explanation
Indices: 39678318--39678413 Score: 113
Period size: 45 Copynumber: 2.2 Consensus size: 44
39678308 ATTACAACAT
* **
39678318 CATTCCATTCAACCAAACACAAGAATACTATTACGCCTCTGTTC
1 CATTACATTCAACCAAACACAAGAATACTATTACGCCTCTAATC
* * *
39678362 CATTACATTCAACCAAACA-ATTGAATTGCTATTATGCCTCTAATC
1 CATTACATTCAACCAAACACA-AGAA-TACTATTACGCCTCTAATC
39678407 CATTACA
1 CATTACA
39678414 GCGAACCAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
43 1 0.02
44 21 0.48
45 22 0.50
ACGTcount: A:0.35, C:0.28, G:0.06, T:0.30
Consensus pattern (44 bp):
CATTACATTCAACCAAACACAAGAATACTATTACGCCTCTAATC
Found at i:39678953 original size:38 final size:39
Alignment explanation
Indices: 39678901--39678974 Score: 132
Period size: 38 Copynumber: 1.9 Consensus size: 39
39678891 TAAAATTATC
39678901 TTTTTTTTTCTCTCTCATTTTATTTCCAAAGAGTTTTAG
1 TTTTTTTTTCTCTCTCATTTTATTTCCAAAGAGTTTTAG
*
39678940 TTTTTTTTT-TCTCTCATTTTATTTTCAAAGAGTTT
1 TTTTTTTTTCTCTCTCATTTTATTTCCAAAGAGTTT
39678975 CCAAATATGC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
38 25 0.74
39 9 0.26
ACGTcount: A:0.18, C:0.14, G:0.07, T:0.62
Consensus pattern (39 bp):
TTTTTTTTTCTCTCTCATTTTATTTCCAAAGAGTTTTAG
Found at i:39684708 original size:50 final size:50
Alignment explanation
Indices: 39684653--39684846 Score: 178
Period size: 50 Copynumber: 3.9 Consensus size: 50
39684643 CATTGAGGTT
* * *
39684653 ATGAGAGGTCCCATGTAAGACCATGTCTGAGACATGGCGTTGGCACCGAG
1 ATGAAAGGTCCCATGTAAGACCATGTCTGAGACATGGCATTGGCACCGAC
* ** * * *
39684703 ATGAGAGGTCCCCCGTAAGACCATGTCTGAGACATGTCATGGGCACCGAT
1 ATGAAAGGTCCCATGTAAGACCATGTCTGAGACATGGCATTGGCACCGAC
** * * *
39684753 ATGAAAACTCCCATGTAAGACCATATCT-AGGATATGACATTGGCA--GTAC
1 ATGAAAGGTCCCATGTAAGACCATGTCTGA-GACATGGCATTGGCACCG-AC
* ** * *
39684802 AAGAAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 ATGAAAGGTCCCATGTAAGACCATGTCTGAGACATGGCATTGGCA
39684847 TGTTATTATC
Statistics
Matches: 117, Mismatches: 24, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
48 1 0.01
49 38 0.32
50 78 0.67
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.22
Consensus pattern (50 bp):
ATGAAAGGTCCCATGTAAGACCATGTCTGAGACATGGCATTGGCACCGAC
Found at i:39693566 original size:23 final size:22
Alignment explanation
Indices: 39693514--39693566 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
39693504 TCCACGTCTT
*
39693514 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
39693536 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
39693559 TTTCTTTT
1 TTTCTTTT
39693567 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:39707310 original size:4 final size:4
Alignment explanation
Indices: 39707301--39707386 Score: 52
Period size: 4 Copynumber: 21.8 Consensus size: 4
39707291 TTTTCACTTG
* ** * * *
39707301 TTTA TTTA TTCA -TTA TTCC TTTTA TTTTA TTCA TTTA TTCA TTCA TTTA
1 TTTA TTTA TTTA TTTA TTTA TT-TA TT-TA TTTA TTTA TTTA TTTA TTTA
* * *
39707350 CTTG TTTA TATA -TTA TTTA TTTA TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
39707387 TAATTCTTCT
Statistics
Matches: 62, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
3 7 0.11
4 48 0.77
5 7 0.11
ACGTcount: A:0.23, C:0.08, G:0.01, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:39707331 original size:21 final size:21
Alignment explanation
Indices: 39707301--39707340 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
39707291 TTTTCACTTG
39707301 TTTATTTATTCA-TTATTCCT
1 TTTATTTATTCATTTATTCCT
39707321 TTTATTTTATTCATTTATTC
1 TTTA-TTTATTCATTTATTC
39707341 ATTCATTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 8 0.44
22 6 0.33
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTATTTATTCATTTATTCCT
Found at i:39707348 original size:21 final size:21
Alignment explanation
Indices: 39707305--39707348 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
39707295 CACTTGTTTA
* *
39707305 TTTATTCATTATTCCTTTTAT
1 TTTATTCATTATTCCATTCAT
39707326 TTTATTCATTTATT-CATTCAT
1 TTTATTCA-TTATTCCATTCAT
39707347 TT
1 TT
39707349 ACTTGTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.20, C:0.14, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTATTCATTATTCCATTCAT
Found at i:39710692 original size:10 final size:9
Alignment explanation
Indices: 39710672--39710723 Score: 54
Period size: 9 Copynumber: 5.6 Consensus size: 9
39710662 TTTTCTATTA
39710672 AAAACAAAAG
1 AAAA-AAAAG
39710682 AAACAAAAAG
1 AAA-AAAAAG
39710692 -AAAAAAAG
1 AAAAAAAAG
39710700 AAAAAAAA-
1 AAAAAAAAG
39710708 ATAAAAAGAAG
1 A-AAAAA-AAG
39710719 AAAAA
1 AAAAA
39710724 GAAGGCCAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
8 7 0.19
9 14 0.38
10 14 0.38
11 2 0.05
ACGTcount: A:0.85, C:0.04, G:0.10, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:39710700 original size:18 final size:18
Alignment explanation
Indices: 39710677--39710723 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
39710667 TATTAAAAAC
*
39710677 AAAAGAAACAAAAAGAAA
1 AAAAGAAAAAAAAAGAAA
*
39710695 AAAAGAAAAAAAAATAAA
1 AAAAGAAAAAAAAAGAAA
39710713 AAGAAGAAAAA
1 AA-AAGAAAAA
39710724 GAAGGCCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.85, C:0.02, G:0.11, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAAAAAAGAAA
Found at i:39710727 original size:9 final size:8
Alignment explanation
Indices: 39710686--39710726 Score: 57
Period size: 8 Copynumber: 5.0 Consensus size: 8
39710676 CAAAAGAAAC
39710686 AAAAAGAA
1 AAAAAGAA
39710694 AAAAAGAA
1 AAAAAGAA
39710702 AAAAA-AA
1 AAAAAGAA
39710709 TAAAAAGAA
1 -AAAAAGAA
39710718 GAAAAAGAA
1 -AAAAAGAA
39710727 GGCCAAGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
7 2 0.07
8 18 0.60
9 10 0.33
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.02
Consensus pattern (8 bp):
AAAAAGAA
Found at i:39711959 original size:137 final size:135
Alignment explanation
Indices: 39711507--39712002 Score: 428
Period size: 137 Copynumber: 3.6 Consensus size: 135
39711497 GATAGATTGA
* * * * *
39711507 AGATCATAGCAATCCTTATCTCCATGAAGCTGTAGTGGAGCAGACTAAAGATAGCGAATGTTATT
1 AGATCATAGCAAACCTTATCTCCCTGAAGTTATAGTGGAGCAGACTAAAGATAGCGAATCTTATT
* * * *
39711572 TCCCTGAAGTTGCAGTGGAACAGATTAAAGTTATAAATTACAGATCTTATCTTTCTGAAGTTGCA
66 TCCCTAAAGTTGCAGTGGAA-GGATTGAAG-TATAAATTACAGATCTTATCTCTCTGAAGTTGCA
*
39711637 GTAGAGC
129 GTAGAGT
* * * ** * * * * *
39711644 AAATCATATCAAAACTTATCTCTTTGAAGTTGA-AGTGGAACA-AGTTAAAAATAAACCAATCTT
1 AGATCATAGCAAACCTTATCTCCCTGAAGTT-ATAGTGGAGCAGA-CTAAAGAT-AGCGAATCTT
* ** * *** *
39711707 ATCTCCCTAAAGTTATAGTGGAGCAGG-TTGAAG-ACAGGCTACAAATCTTATCTC-CTTGAAGT
63 ATTTCCCTAAAGTTGCAGTGGA--AGGATTGAAGTATAAATTACAGATCTTATCTCTC-TGAAGT
* *
39711769 TGAAGTGGAGT
125 TGCAGTAGAGT
* * * * *
39711780 AGATTAAAGCCACAAACCTTATCCCCCTGAAGTTGTAGTGGAGCAGACTGAAGATAGCGAATCTT
1 AGATCATAG---CAAACCTTATCTCCCTGAAGTTATAGTGGAGCAGACTAAAGATAGCGAATCTT
* *
39711845 ATTTCCTTAAAGTTGCAGTGGAATGGATTGAAGCTATAAATTACAGATCTTATCTCTCTGAAGAT
63 ATTTCCCTAAAGTTGCAGTGGAA-GGATTGAAG-TATAAATTACAGATCTTATCTCTCTGAAGTT
39711910 GCAGTAGAGT
126 GCAGTAGAGT
* ** * * *
39711920 AGATCATAGCAAACCTTAGCTCCCTGAAGTTATAGTGGAGCAGGTTAAAGTTA-CGAGTCTTATC
1 AGATCATAGCAAACCTTATCTCCCTGAAGTTATAGTGGAGCAGACTAAAGATAGCGAATCTTATT
* *
39711984 TCCCTGAAGTTGCAATGGA
66 TCCCTAAAGTTGCAGTGGA
39712003 GCAGACTGAA
Statistics
Matches: 273, Mismatches: 70, Indels: 33
0.73 0.19 0.09
Matches are distributed among these distances:
135 1 0.00
136 61 0.22
137 77 0.28
138 62 0.23
139 32 0.12
140 39 0.14
141 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (135 bp):
AGATCATAGCAAACCTTATCTCCCTGAAGTTATAGTGGAGCAGACTAAAGATAGCGAATCTTATT
TCCCTAAAGTTGCAGTGGAAGGATTGAAGTATAAATTACAGATCTTATCTCTCTGAAGTTGCAGT
AGAGT
Found at i:39712047 original size:89 final size:88
Alignment explanation
Indices: 39711750--39712306 Score: 238
Period size: 96 Copynumber: 6.1 Consensus size: 88
39711740 ACAGGCTACA
* * * ** ** *
39711750 AATCTTATCTCCTTGAAGTTGAAGTGGAGTAGATTAAAGCCACAAACCTTATCCCCCTGAAGTTG
1 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGGTTAAAGTTAC-AGTCTTATCTCCCTGAAGTTG
*
39711815 TAGTGGAGCAGACTGAAGATAGCG
65 CAGTGGAGCAGACTGAAGATAGCG
* * * *
39711839 AATCTTATTTCCTTAAAGTTGCAGTGGAATGGATTGAAGCTATAAA-TTACAGATCTTATCTCTC
1 AATCTTATCTCCTTGAAGTTGCAGTGG-A-GCA--G--G-T-TAAAGTTACAG-TCTTATCTCCC
* * * * *
39711903 TGAAGATGCAGTAGAGTAGA-T---CATAGCA
57 TGAAGTTGCAGTGGAGCAGACTGAAGATAGCG
* * * **
39711931 AACCTTAGCTCCCTGAAGTTATAGTGGAGCAGGTTAAAGTTACGAGTCTTATCTCCCTGAAGTTG
1 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGGTTAAAGTTAC-AGTCTTATCTCCCTGAAGTTG
*
39711996 CAATGGAGCAGACTGAAGATAGCG
65 CAGTGGAGCAGACTGAAGATAGCG
* * * * *
39712020 AATCTTATTTCTTTGAAGTTGCAGTGGAATGGATTGAAGCTATAAA-TTACTGATCTTATCTCTC
1 AATCTTATCTCCTTGAAGTTGCAGTGG-A-GCA--G--G-T-TAAAGTTACAG-TCTTATCTCCC
* * * *
39712084 TGAAGTTGCAATAGAGCAGA-T---CATAGCA
57 TGAAGTTGCAGTGGAGCAGACTGAAGATAGCG
* * * * * * * * * *
39712112 AAACTTATCTCCCTAAAGTTGTAGTGGAACAGGTTAAAAATAAACTAATCTTATCTCCTTAAAGT
1 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGGTT-AAAGT-TAC-AGTCTTATCTCCCTGAAGT
* * * *
39712177 TACAGTAGAGCAGATTGAAGATAGGTTACA
63 TGCAGTGGAGCAGACTGAAGATA-G---CG
* * ** ** * *
39712207 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGAG-TAAAGCGACCAACCTTATCTCCTTTAAGTT
1 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAG-GTTAAAGTTA-CAGTCTTATCTCCCTGAAGTT
* ** *
39712271 GTAGTGGAGCAGGTTGAAGATA-CC
64 GCAGTGGAGCAGACTGAAGATAGCG
39712295 AATCTTATCTCC
1 AATCTTATCTCC
39712307 CTGAGCGGAG
Statistics
Matches: 355, Mismatches: 75, Indels: 77
0.70 0.15 0.15
Matches are distributed among these distances:
84 5 0.01
85 35 0.10
86 6 0.02
87 28 0.08
88 16 0.05
89 49 0.14
90 5 0.01
91 9 0.03
92 52 0.15
93 39 0.11
94 4 0.01
95 37 0.10
96 62 0.17
97 8 0.02
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (88 bp):
AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGGTTAAAGTTACAGTCTTATCTCCCTGAAGTTGC
AGTGGAGCAGACTGAAGATAGCG
Found at i:39712067 original size:181 final size:181
Alignment explanation
Indices: 39711797--39712149 Score: 580
Period size: 181 Copynumber: 2.0 Consensus size: 181
39711787 AGCCACAAAC
* *
39711797 CTTATCCCCCTGAAGTTGTAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCCTTAAAGTTGCA
1 CTTATCCCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCGAATCTTATTTCCTTAAAGTTGCA
* *
39711862 GTGGAATGGATTGAAGCTATAAATTACAGATCTTATCTCTCTGAAGATGCAGTAGAGTAGATCAT
66 GTGGAATGGATTGAAGCTATAAATTACAGATCTTATCTCTCTGAAGATGCAATAGAGCAGATCAT
* * *
39711927 AGCAAACCTTAGCTCCCTGAAGTTATAGTGGAGCAGGTTAAAGTTACGAGT
131 AGCAAAACTTAGCTCCCTAAAGTTATAGTGGAACAGGTTAAAGTTACGAGT
* * *
39711978 CTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCGAATCTTATTTCTTTGAAGTTGCA
1 CTTATCCCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCGAATCTTATTTCCTTAAAGTTGCA
* *
39712043 GTGGAATGGATTGAAGCTATAAATTACTGATCTTATCTCTCTGAAGTTGCAATAGAGCAGATCAT
66 GTGGAATGGATTGAAGCTATAAATTACAGATCTTATCTCTCTGAAGATGCAATAGAGCAGATCAT
* *
39712108 AGCAAAACTTATCTCCCTAAAGTTGTAGTGGAACAGGTTAAA
131 AGCAAAACTTAGCTCCCTAAAGTTATAGTGGAACAGGTTAAA
39712150 AATAAACTAA
Statistics
Matches: 158, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
181 158 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.30
Consensus pattern (181 bp):
CTTATCCCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCGAATCTTATTTCCTTAAAGTTGCA
GTGGAATGGATTGAAGCTATAAATTACAGATCTTATCTCTCTGAAGATGCAATAGAGCAGATCAT
AGCAAAACTTAGCTCCCTAAAGTTATAGTGGAACAGGTTAAAGTTACGAGT
Found at i:39712296 original size:44 final size:44
Alignment explanation
Indices: 39712115--39712308 Score: 156
Period size: 44 Copynumber: 4.2 Consensus size: 44
39712105 CATAGCAAAA
* * * *
39712115 CTTATCTCCCTAAAGTTGTAGTGGAACAGGTTAAAAATAAACTAAT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTAAAGAT--ACCAAT
* * * * * *
39712161 CTTATCTCCTTAAAGTTACAGTAGAGCAGATTGAAGATAGGTTACAAAT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGGTT--A-A-A-GATACCAAT
** *
39712210 CTTATCTCCCTAAAGTTGCAGTGGAGCAGAG-TAAAGCGACCAAC
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAG-GTTAAAGATACCAAT
* * * *
39712254 CTTATCTCCTTTAAGTTGTAGTGGAGCAGGTTGAAGATACCAAT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTAAAGATACCAAT
39712298 CTTATCTCCCT
1 CTTATCTCCCT
39712309 GAGCGGAGCA
Statistics
Matches: 116, Mismatches: 25, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
43 1 0.01
44 50 0.43
45 1 0.01
46 27 0.23
47 1 0.01
48 1 0.01
49 33 0.28
50 1 0.01
51 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (44 bp):
CTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTAAAGATACCAAT
Found at i:39712326 original size:37 final size:37
Alignment explanation
Indices: 39712276--39712347 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
39712266 AAGTTGTAGT
* * **
39712276 GGAGCAGGTTGAAGATACCAATCTTATCTCCCTGAGC
1 GGAGCAGATTGAAGATACAAATCCAATCTCCCTGAGC
*
39712313 GGAGCAGATTGAAGCTACAAATCCAATCTCCCTGA
1 GGAGCAGATTGAAGATACAAATCCAATCTCCCTGA
39712348 AGTTGTAGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (37 bp):
GGAGCAGATTGAAGATACAAATCCAATCTCCCTGAGC
Found at i:39714053 original size:12 final size:13
Alignment explanation
Indices: 39713999--39714053 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 13
39713989 TCATTGTTCC
39713999 TTTTATTTTATTCA
1 TTTTA-TTTATTCA
*
39714013 TTTTTATATATT-A
1 -TTTTATTTATTCA
39714026 -TTTATTTATTCA
1 TTTTATTTATTCA
39714038 -TTTATTTATT-A
1 TTTTATTTATTCA
39714049 TTTTA
1 TTTTA
39714054 ATCATTCTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
11 10 0.28
12 15 0.42
13 1 0.03
14 5 0.14
15 5 0.14
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTATTTATTCA
Found at i:39735955 original size:50 final size:50
Alignment explanation
Indices: 39735736--39735964 Score: 215
Period size: 50 Copynumber: 4.5 Consensus size: 50
39735726 AGAATGAGAC
* **
39735736 CTCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGGT
1 CTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCA---A-G--ATGAGAGGT
* * * * *
39735792 CCCACGTAAAACCATGTTTGGGACATGACGTTGGCACCAAGATGAGAGGT
1 CTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGT
* * *
39735842 CTCACGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGGT
1 CTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGT
* * * * * * **
39735892 CCCCTGTAAGACCATGTCTGGGACATGGCATGGGCATCAATATGAGAACT
1 CTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGT
* *
39735942 CTCATGTATGACCATATCTGGGA
1 CTCATGTAAGACCATGTCTGGGA
39735965 TAGTGCATTG
Statistics
Matches: 146, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
50 113 0.77
52 1 0.01
53 1 0.01
56 31 0.21
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (50 bp):
CTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGT
Found at i:39741384 original size:18 final size:18
Alignment explanation
Indices: 39741361--39741426 Score: 114
Period size: 18 Copynumber: 3.7 Consensus size: 18
39741351 AAAATGTGAG
*
39741361 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTC
39741379 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
*
39741397 CAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
39741415 AAATGATGTTCA
1 AAATGATGTTCA
39741427 AATTGATGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:39741952 original size:72 final size:72
Alignment explanation
Indices: 39741857--39742095 Score: 356
Period size: 72 Copynumber: 3.3 Consensus size: 72
39741847 CAATGCTAAA
* *
39741857 CTAGTTTTATCAATAGTTATTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATTAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
39741922 GTGCAAT
66 GTGCAAT
* *
39741929 CTAGTTTTATTAATGGCTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATTAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
*
39741994 GTGTAAT
66 GTGCAAT
* *
39742001 CTAGTTTTATTAATAGTTGTTTATGTTTGGTCTTTGGATATTGAATTTATGTTCTACTAATTTAT
1 CTAGTTTTATTAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
* *
39742066 ACT-AAAT
66 -GTGCAAT
* *
39742073 -TAGTTTGATCAATAGTTGTTTAT
1 CTAGTTTTATTAATAGTTGTTTAT
39742096 ATATGATTTT
Statistics
Matches: 153, Mismatches: 13, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
71 21 0.14
72 131 0.86
73 1 0.01
ACGTcount: A:0.24, C:0.06, G:0.16, T:0.54
Consensus pattern (72 bp):
CTAGTTTTATTAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
GTGCAAT
Found at i:39743410 original size:21 final size:20
Alignment explanation
Indices: 39743382--39743420 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
39743372 GCAGATTTTA
39743382 TGGAATATGA-AGATATTAAC
1 TGGAATATGAGA-ATATTAAC
39743402 TGGACATATGAGAATATTA
1 TGGA-ATATGAGAATATTA
39743421 TTGATTCAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 12 0.71
22 1 0.06
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.31
Consensus pattern (20 bp):
TGGAATATGAGAATATTAAC
Found at i:39744021 original size:13 final size:13
Alignment explanation
Indices: 39744005--39744036 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
39743995 ACTCTTTCAC
39744005 AGCATTTTCCAAA
1 AGCATTTTCCAAA
*
39744018 AGCACTTTCCAAA
1 AGCATTTTCCAAA
39744031 AGCATT
1 AGCATT
39744037 GCCAAAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.38, C:0.25, G:0.09, T:0.28
Consensus pattern (13 bp):
AGCATTTTCCAAA
Found at i:39744034 original size:26 final size:27
Alignment explanation
Indices: 39743983--39744036 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
39743973 GAACATTTTA
* *
39743983 TTTCTCAAAAGCACTCTTTCACAGCAT
1 TTTCTCAAAAGCACTCTTCCAAAGCAT
39744010 TTTC-CAAAAGCACT-TTCCAAAAGCAT
1 TTTCTCAAAAGCACTCTTCC-AAAGCAT
39744036 T
1 T
39744037 GCCAAAATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 3 0.12
26 17 0.71
27 4 0.17
ACGTcount: A:0.33, C:0.28, G:0.07, T:0.31
Consensus pattern (27 bp):
TTTCTCAAAAGCACTCTTCCAAAGCAT
Found at i:39744181 original size:14 final size:15
Alignment explanation
Indices: 39744156--39744187 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
39744146 AGAAGTGTTG
39744156 TATTCATTAATTTAA
1 TATTCATTAATTTAA
39744171 TATTC-TTAATTTAA
1 TATTCATTAATTTAA
39744185 TAT
1 TAT
39744188 ATATATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTCATTAATTTAA
Found at i:39744529 original size:22 final size:22
Alignment explanation
Indices: 39744484--39744531 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
39744474 GAGTCTTAAC
*
39744484 TTATTGCAATTTATTTTATCAA
1 TTATTGCAATATATTTTATCAA
*
39744506 TTATTGCAATAT-TTTTGTCAAA
1 TTATTGCAATATATTTTATC-AA
39744528 TTAT
1 TTAT
39744532 ATATATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.31, C:0.08, G:0.06, T:0.54
Consensus pattern (22 bp):
TTATTGCAATATATTTTATCAA
Found at i:39761090 original size:35 final size:35
Alignment explanation
Indices: 39761044--39761114 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
39761034 TAATGTAAGG
39761044 TGAGTTTGAAATGAGCATGATGGGAGAGCTCTCAT
1 TGAGTTTGAAATGAGCATGATGGGAGAGCTCTCAT
39761079 TGAGTTTGAAATGAGCATGATGGGAGAGCTCTCAT
1 TGAGTTTGAAATGAGCATGATGGGAGAGCTCTCAT
39761114 T
1 T
39761115 CTTTTTGGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.11, G:0.31, T:0.30
Consensus pattern (35 bp):
TGAGTTTGAAATGAGCATGATGGGAGAGCTCTCAT
Found at i:39766388 original size:55 final size:55
Alignment explanation
Indices: 39766321--39766428 Score: 173
Period size: 55 Copynumber: 2.0 Consensus size: 55
39766311 CTTAACTTGC
* *
39766321 AAACATTTTGATCTTGTAA-GAGTTATTTCGTTGTTTGCTTATTTGTATCTCTTTG
1 AAACATTCTGATCTTGTAAGGA-TTATTACGTTGTTTGCTTATTTGTATCTCTTTG
*
39766376 AAACATTCTGATCTTGTAAGGATTATTACTTTGTTTGCTTATTTGTATCTCTT
1 AAACATTCTGATCTTGTAAGGATTATTACGTTGTTTGCTTATTTGTATCTCTT
39766429 ATAGAGGGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
55 47 0.96
56 2 0.04
ACGTcount: A:0.21, C:0.12, G:0.15, T:0.52
Consensus pattern (55 bp):
AAACATTCTGATCTTGTAAGGATTATTACGTTGTTTGCTTATTTGTATCTCTTTG
Found at i:39768360 original size:5 final size:5
Alignment explanation
Indices: 39768350--39768374 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
39768340 TGAGCATTCG
39768350 ATCGA ATCGA ATCGA ATCGA ATCGA
1 ATCGA ATCGA ATCGA ATCGA ATCGA
39768375 TAATTTTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (5 bp):
ATCGA
Found at i:39768473 original size:5 final size:5
Alignment explanation
Indices: 39768465--39768490 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
39768455 GAGATGGAAC
39768465 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
39768491 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:39769421 original size:9 final size:9
Alignment explanation
Indices: 39769403--39769457 Score: 76
Period size: 9 Copynumber: 6.1 Consensus size: 9
39769393 TATAGTTTGA
*
39769403 TATTCAAAT
1 TATTCGAAT
39769412 TATTCGAAT
1 TATTCGAAT
39769421 TATGT-GAAT
1 TAT-TCGAAT
39769430 TATTCGAAT
1 TATTCGAAT
*
39769439 TATTCGAGT
1 TATTCGAAT
39769448 TATTCGAAT
1 TATTCGAAT
39769457 T
1 T
39769458 CGAAAACTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
8 1 0.02
9 39 0.95
10 1 0.02
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (9 bp):
TATTCGAAT
Found at i:39771708 original size:25 final size:24
Alignment explanation
Indices: 39771661--39771711 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
39771651 TAGTTTCCAC
39771661 TACTTTAGTTTTATTTTATTTTAT
1 TACTTTAGTTTTATTTTATTTTAT
*
39771685 TACTTTATGTTTTGTTATTA-TTTAT
1 TACTTTA-GTTTTATT-TTATTTTAT
39771710 TA
1 TA
39771712 ATTTTATTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 7 0.29
25 14 0.58
26 3 0.12
ACGTcount: A:0.22, C:0.04, G:0.06, T:0.69
Consensus pattern (24 bp):
TACTTTAGTTTTATTTTATTTTAT
Found at i:39791324 original size:12 final size:13
Alignment explanation
Indices: 39791301--39791365 Score: 60
Period size: 13 Copynumber: 4.7 Consensus size: 13
39791291 TTATGACTAC
*
39791301 ATTATAATATTTT
1 ATTATTATATTTT
39791314 ATT-TTATATTTT
1 ATTATTATATTTT
*
39791326 ATTATTATTGTTATTAAT
1 ATTATTA----TATT-TT
39791344 ATTATTATATTTT
1 ATTATTATATTTT
39791357 ATTATTATA
1 ATTATTATA
39791366 GTGATATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
12 11 0.26
13 16 0.37
14 4 0.09
17 4 0.09
18 8 0.19
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (13 bp):
ATTATTATATTTT
Found at i:39791332 original size:3 final size:3
Alignment explanation
Indices: 39791308--39791364 Score: 54
Period size: 3 Copynumber: 21.0 Consensus size: 3
39791298 TACATTATAA
* *
39791308 TAT T-T TAT T-T TA- TAT T-T TAT TAT TAT TGT TAT TAA TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39791351 TAT T-T TAT TAT TAT
1 TAT TAT TAT TAT TAT
39791365 AGTGATATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
2 12 0.27
3 32 0.73
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:39792456 original size:4 final size:4
Alignment explanation
Indices: 39792447--39792472 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
39792437 TCATGTTAAT
39792447 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
39792473 CATGAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:39795370 original size:52 final size:52
Alignment explanation
Indices: 39795306--39795420 Score: 178
Period size: 52 Copynumber: 2.2 Consensus size: 52
39795296 CAGATAAGGA
* *
39795306 TAAGG-TATGAAAGTTGATCATTCTCTTACTCTCCAAATTTGATTAACAACAT
1 TAAGGATA-GAAAGTTGATCATTCTCTTACTCTCCAAATTCGATCAACAACAT
* *
39795358 TAAGGATAGAAAGTTGATCCTTCTCTTACTCTCTAAATTCGATCAACAACAT
1 TAAGGATAGAAAGTTGATCATTCTCTTACTCTCCAAATTCGATCAACAACAT
39795410 TAAGGATAGAA
1 TAAGGATAGAA
39795421 TATAATTTGG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
52 56 0.97
53 2 0.03
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (52 bp):
TAAGGATAGAAAGTTGATCATTCTCTTACTCTCCAAATTCGATCAACAACAT
Found at i:39796295 original size:39 final size:38
Alignment explanation
Indices: 39796252--39796369 Score: 106
Period size: 36 Copynumber: 3.2 Consensus size: 38
39796242 TATAACATAA
39796252 TTTTAATATTATTATTTAATGTAAATATAATATAAGTA-
1 TTTTAATATTATTATTTAATGTAAATATAATATAA-TAT
*
39796290 TTTT--TATTATAATTTAATGTAAATATAA-AT-ATAT
1 TTTTAATATTATTATTTAATGTAAATATAATATAATAT
* * * *
39796324 TTTATCAT-TTATTATTTCAT-TTAATATATATAAAAATAT
1 TTT-TAATATTATTATTTAATGTAAATATA-AT-ATAATAT
39796363 TTTTAAT
1 TTTTAAT
39796370 GGGTCACTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
33 2 0.03
34 4 0.06
35 10 0.15
36 34 0.52
37 1 0.02
38 8 0.12
39 7 0.11
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (38 bp):
TTTTAATATTATTATTTAATGTAAATATAATATAATAT
Found at i:39796325 original size:33 final size:35
Alignment explanation
Indices: 39796240--39796328 Score: 112
Period size: 36 Copynumber: 2.5 Consensus size: 35
39796230 ATTATTATTT
*
39796240 AATATAACATA-ATTTTAATATTATTATTTAATGTA
1 AATATAACATATATTTT-ATATTATAATTTAATGTA
*
39796275 AATATAATATAAGTATTTT-TATTATAATTTAATGTA
1 AATATAACAT-A-TATTTTATATTATAATTTAATGTA
39796311 AATATAA-ATATATTTTAT
1 AATATAACATATATTTTAT
39796329 CATTTATTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
33 6 0.12
34 2 0.04
35 11 0.23
36 24 0.50
38 5 0.10
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (35 bp):
AATATAACATATATTTTATATTATAATTTAATGTA
Found at i:39797408 original size:34 final size:35
Alignment explanation
Indices: 39797364--39797430 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
39797354 CAGTAAAATA
*
39797364 TTTTCCGTAAAATGATTT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
*
39797398 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
39797431 TTGGTATTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:39813402 original size:17 final size:18
Alignment explanation
Indices: 39813382--39813416 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
39813372 TAGAATAGAA
*
39813382 AATAACTTAT-TGGGTTG
1 AATAAATTATATGGGTTG
39813399 AATAAATTATATGGGTTG
1 AATAAATTATATGGGTTG
39813417 GTTTCAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.34, C:0.03, G:0.23, T:0.40
Consensus pattern (18 bp):
AATAAATTATATGGGTTG
Found at i:39815760 original size:6 final size:6
Alignment explanation
Indices: 39815751--39815782 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
39815741 TAAGTCTAAG
39815751 AAAATA AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AA
39815783 TAAACTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:39817509 original size:23 final size:23
Alignment explanation
Indices: 39817482--39817544 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
39817472 TATATAGAAC
39817482 TAATAATAAAAATAAAAGATAATA
1 TAATAATAAAAATAAAA-ATAATA
39817506 -AATAATAAACTAAT-AAAATAATA
1 TAATAATAAA--AATAAAAATAATA
*
39817529 TAACTAATAAGAATAA
1 TAA-TAATAAAAATAA
39817545 TGGATAAGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
23 18 0.55
24 6 0.18
25 9 0.27
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.25
Consensus pattern (23 bp):
TAATAATAAAAATAAAAATAATA
Found at i:39817521 original size:8 final size:8
Alignment explanation
Indices: 39817501--39817538 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
39817491 AAATAAAAGA
39817501 TAATAAA-
1 TAATAAAC
39817508 TAATAAAC
1 TAATAAAC
*
39817516 TAATAAAA
1 TAATAAAC
39817524 TAATATAAC
1 TAATA-AAC
39817533 TAATAA
1 TAATAA
39817539 GAATAATGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
7 7 0.26
8 13 0.48
9 7 0.26
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (8 bp):
TAATAAAC
Found at i:39817531 original size:25 final size:23
Alignment explanation
Indices: 39817483--39817544 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 23
39817473 ATATAGAACT
*
39817483 AATAATAAAAATAAAAGATAATA
1 AATAATAAAAATAAAAAATAATA
39817506 AATAATAAACTAATAAAATAAT-ATA
1 AATAATAAA--AATAAAA-AATAATA
* *
39817531 ACTAATAAGAATAA
1 AATAATAAAAATAA
39817545 TGGATAAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 14 0.42
25 17 0.52
26 2 0.06
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.24
Consensus pattern (23 bp):
AATAATAAAAATAAAAAATAATA
Found at i:39818603 original size:115 final size:114
Alignment explanation
Indices: 39818394--39818605 Score: 275
Period size: 115 Copynumber: 1.8 Consensus size: 114
39818384 AAATTTTGGA
* * * *
39818394 AAAATTAAGTCTCAGGATCCACACGGCCAATGACATGCCTGTGTGTGCAAGCTAAGTGGGTCACA
1 AAAATTAAGTCTCAGGATCCACACGGCCAAGGACACGCCTGTGTGTCCAACCT-AGTGGGTCACA
** * *
39818459 TGGCCATGTCGCCAAGCCGTCTAACTCACTGTTGAATATTTTAAAATTTT
65 CAGCCATGTCGCCAAGCCATATAACTCACTGTTGAATATTTTAAAATTTT
*
39818509 AAAATTAAGTCTTAGGATCCACACGGCCAAGGACACGTCC-GTGTGTCCAGACCGT-GTGGGTCA
1 AAAATTAAGTCTCAGGATCCACACGGCCAAGGACACG-CCTGTGTGTCCA-ACC-TAGTGGGTCA
* *
39818572 CACAGCCATGTCGCCAGGCCATATAAGTCACTGT
63 CACAGCCATGTCGCCAAGCCATATAACTCACTGT
39818606 CAAAACCCTT
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
115 78 0.94
116 4 0.05
117 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (114 bp):
AAAATTAAGTCTCAGGATCCACACGGCCAAGGACACGCCTGTGTGTCCAACCTAGTGGGTCACAC
AGCCATGTCGCCAAGCCATATAACTCACTGTTGAATATTTTAAAATTTT
Found at i:39825517 original size:27 final size:29
Alignment explanation
Indices: 39825461--39825523 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 29
39825451 TTCAATTTAT
39825461 TTTAATAAATAATATAATTAATAATAAAAA
1 TTTAA-AAATAATATAATTAATAATAAAAA
* *
39825491 TTTAAAAA-AAT-TAATTAATTATTAAAA
1 TTTAAAAATAATATAATTAATAATAAAAA
*
39825518 GTTAAA
1 TTTAAA
39825524 TTTCTACAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 19 0.63
28 3 0.10
29 3 0.10
30 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (29 bp):
TTTAAAAATAATATAATTAATAATAAAAA
Found at i:39828715 original size:31 final size:30
Alignment explanation
Indices: 39828667--39828728 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
39828657 GTGAAATTTA
**
39828667 ATCATTTTATTGAAATAATATTTTAATTAAT
1 ATCATTTTATTGAAATAA-ATGATAATTAAT
**
39828698 ATCATTTTATTTTAATAAATGATAATTAAT
1 ATCATTTTATTGAAATAAATGATAATTAAT
39828728 A
1 A
39828729 GACTTGCTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (30 bp):
ATCATTTTATTGAAATAAATGATAATTAAT
Found at i:39832258 original size:465 final size:466
Alignment explanation
Indices: 39831280--39832272 Score: 1154
Period size: 467 Copynumber: 2.1 Consensus size: 466
39831270 AGTTTGCTAT
* * * * *
39831280 ACGAAACAACATTTTACTATTATCGACCTATAATTTAGGTTGCATGAAGCAAGAGTTTAGGCTAG
1 ACGAAATAACATTTCACTATTATGGACCTAGAATTTAGGTTGCATGAAGCAAGAGTTTGGGCTAG
* * ** * ** * *
39831345 GCAAACTAGAATCTCATTGTTATGTAGCAAGATTTTGGGATGTACAGAGCGATATTTCATTGCTA
66 ACAAACTAGAATCTCATTATTATAAAGCAAGAGTTAAGGATGTACAGAACGAGATTTCATTGCTA
* * * * * *
39831410 TGGAGCACATGATTGAGTTGCTCAAAGTAGGGATTTGCCATTATTAAGTAGGAGTTTGAATTACT
131 TAGAGCACATGATTGAGTTGCTCAAAGTAGAGATCTGCCATTATAAAGTAGAAGTTCGAATTACT
* **
39831475 CAAAAAAGGATTTCACTATTTGGGTGGGAGTAAGAGCTTGGGCTAGGTGGAGAAAGATTTTATTT
196 CAAAAAAGGATTTCACTATTTGGGAGGGAACAAGAGCTTGGGCTAGGTGGAGAAAGATTTTATTT
* * *
39831540 TATGGAGCAAGAGTTCGAATTTAGCAGAATAGGTGTTCAAACTATGTCATGTAAGATTTCATTCA
261 TATGGAGCAAGAGTTCGAATTTAGCAGAATAGGAGTTCAAACTATGTCATGTAAGATTTCACTAA
* * * ****
39831605 TATGGAGGAGTTTGGGTTATGAAGAGTAAGATTTTACCACTATGGAGTTGGAGTAGAAGATGCTT
326 TACGGAGGAGTTTGGG-TATGAAGAGTAAGATTTCACCACTATGAAGCACAAGTAGAAGATGCTT
* ** * *
39831670 GGAGTAAGATTTATTTGTTATGGAGTGGAAGTTTGCATTGCTCGAAGTAGGATTTATAGAGCAAG
390 GGAGTAAGATTTAATTGTTATGGAGCAGAAGTTTGCATTGCTCAAAGTAAGATTTATAGAGCAAG
39831735 AACTAAGGCTGC
455 AACTAAGGCTGC
* *** * *
39831747 AAGGTGTAAGATTTCACTATTATGGACCTAGAATTTAGGTTGCATGAAGTAAGAGTTTGGGCTAG
1 ACGAAATAACATTTCACTATTATGGACCTAGAATTTAGGTTGCATGAAGCAAGAGTTTGGGCTAG
* * *
39831812 ACGAAGTATG-ATCTCATTATTATAAAGCAAGAGTTAAGGATGTGTC-GAACGAGATTTCATTGC
66 ACAAACTA-GAATCTCATTATTATAAAGCAAGAGTTAAGGATGT-ACAGAACGAGATTTCATTGC
** ** ** *
39831875 TATAGAGCATGTGATTGAGTTGCTTGAAGTA-AGAGTCTGTTATTATAAAGTAGAAGTTCGCATT
129 TATAGAGCACATGATTGAGTTGCTCAAAGTAGAGA-TCTGCCATTATAAAGTAGAAGTTCGAATT
* * * * * *
39831939 ACTTAGAGAAGGATTTCACTGTTTGGGAGGGAACAAGAGCTTGGG-TTGTGTGGAGGAAGATTTT
193 ACTCAAAAAAGGATTTCACTATTTGGGAGGGAACAAGAGCTTGGGCTAG-GTGGAGAAAGATTTT
* ** ** *
39832003 ATTGTTATGGAGCAAGAGTTTGGGTTTAGCA-AAGTAGGAGTTTGATCTATGTCATGTAAGATTT
257 ATT-TTATGGAGCAAGAGTTCGAATTTAGCAGAA-TAGGAGTTCAAACTATGTCATGTAAGATTT
* * * * * *
39832067 CACTAATACGGAGGAGTTT-GG-ATTAAGAGTAGGATTTCACCATTGTGAAGCACAATTTGAAGA
320 CACTAATACGGAGGAGTTTGGGTATGAAGAGTAAGATTTCACCACTATGAAGCACAAGTAGAAGA
*
39832130 TGCTTGGAGTAAGATTTAATTGTTATGGAGCAGAAGTTTGCATTGCTCAAAGTAAGATTTATGGA
385 TGCTTGGAGTAAGATTTAATTGTTATGGAGCAGAAGTTTGCATTGCTCAAAGTAAGATTTATAGA
* ** *
39832195 TCAAGATTTTAGGCTGC
450 GCAAGAACTAAGGCTGC
* * *
39832212 ACGAAATAATATTTCACTATTATGGACCTCGAATTTGGGTTGCATGAAGCAAGAGTTTGGG
1 ACGAAATAACATTTCACTATTATGGACCTAGAATTTAGGTTGCATGAAGCAAGAGTTTGGG
39832273 ATGTGCGGAG
Statistics
Matches: 435, Mismatches: 85, Indels: 14
0.81 0.16 0.03
Matches are distributed among these distances:
465 155 0.36
466 4 0.01
467 208 0.48
468 68 0.16
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.32
Consensus pattern (466 bp):
ACGAAATAACATTTCACTATTATGGACCTAGAATTTAGGTTGCATGAAGCAAGAGTTTGGGCTAG
ACAAACTAGAATCTCATTATTATAAAGCAAGAGTTAAGGATGTACAGAACGAGATTTCATTGCTA
TAGAGCACATGATTGAGTTGCTCAAAGTAGAGATCTGCCATTATAAAGTAGAAGTTCGAATTACT
CAAAAAAGGATTTCACTATTTGGGAGGGAACAAGAGCTTGGGCTAGGTGGAGAAAGATTTTATTT
TATGGAGCAAGAGTTCGAATTTAGCAGAATAGGAGTTCAAACTATGTCATGTAAGATTTCACTAA
TACGGAGGAGTTTGGGTATGAAGAGTAAGATTTCACCACTATGAAGCACAAGTAGAAGATGCTTG
GAGTAAGATTTAATTGTTATGGAGCAGAAGTTTGCATTGCTCAAAGTAAGATTTATAGAGCAAGA
ACTAAGGCTGC
Found at i:39832494 original size:57 final size:57
Alignment explanation
Indices: 39832424--39832539 Score: 178
Period size: 57 Copynumber: 2.0 Consensus size: 57
39832414 GAAATGCAAA
* * * *
39832424 ATCTTAACTAATATATAATATTAGTATTTTAGGTAACTAATCTCCTAAGAATCAACT
1 ATCTTAACAAATATAGAATATCAATATTTTAGGTAACTAATCTCCTAAGAATCAACT
* *
39832481 ATCTTAACAAATATAGAATATCAATATTTTAGGTAACTAGTCTCCTAAGAATCAGCT
1 ATCTTAACAAATATAGAATATCAATATTTTAGGTAACTAATCTCCTAAGAATCAACT
39832538 AT
1 AT
39832540 ATAGTGTGAT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.36
Consensus pattern (57 bp):
ATCTTAACAAATATAGAATATCAATATTTTAGGTAACTAATCTCCTAAGAATCAACT
Found at i:39842485 original size:199 final size:199
Alignment explanation
Indices: 39842145--39842543 Score: 789
Period size: 199 Copynumber: 2.0 Consensus size: 199
39842135 TAACATTAGC
39842145 CGTAATACTAGAACGATTATAATGCTACAAACAATGAGTGGCATCTAGCAATGCATCATTGCTAC
1 CGTAATACTAGAACGATTATAATGCTACAAACAATGAGTGGCATCTAGCAATGCATCATTGCTAC
39842210 CTAAGTTAAAAGAAGTCATGATTCGACATAATTTTTTTGTGATTAACCTTTCATGCATTAATCCT
66 CTAAGTTAAAAGAAGTCATGATTCGACATAATTTTTTTGTGATTAACCTTTCATGCATTAATCCT
39842275 TAAGTCCTTTTATCTCTGGAATGGACATAAGTCATGGAATAGTCACACTTGCATAGTCCATCCCA
131 TAAGTCCTTTTATCTCTGGAATGGACATAAGTCATGGAATAGTCACACTTGCATAGTCCATCCCA
39842340 TGTT
196 TGTT
39842344 CGTAATACTAGAACGATTATAATGCTACAAACAATGAGTGGCATCTAGCAATGCATCATTGCTAC
1 CGTAATACTAGAACGATTATAATGCTACAAACAATGAGTGGCATCTAGCAATGCATCATTGCTAC
*
39842409 CTAAGTTAACAGAAGTCATGATTCGACATAATTTTTTTGTGATTAACCTTTCATGCATTAATCCT
66 CTAAGTTAAAAGAAGTCATGATTCGACATAATTTTTTTGTGATTAACCTTTCATGCATTAATCCT
39842474 TAAGTCCTTTTATCTCTGGAATGGACATAAGTCATGGAATAGTCACACTTGCATAGTCCATCCCA
131 TAAGTCCTTTTATCTCTGGAATGGACATAAGTCATGGAATAGTCACACTTGCATAGTCCATCCCA
39842539 TGTT
196 TGTT
39842543 C
1 C
39842544 CTTGATATCT
Statistics
Matches: 199, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
199 199 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.33
Consensus pattern (199 bp):
CGTAATACTAGAACGATTATAATGCTACAAACAATGAGTGGCATCTAGCAATGCATCATTGCTAC
CTAAGTTAAAAGAAGTCATGATTCGACATAATTTTTTTGTGATTAACCTTTCATGCATTAATCCT
TAAGTCCTTTTATCTCTGGAATGGACATAAGTCATGGAATAGTCACACTTGCATAGTCCATCCCA
TGTT
Found at i:39844971 original size:21 final size:21
Alignment explanation
Indices: 39844931--39844971 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
39844921 ATTTTTATTT
39844931 TTATTTTTTTATCCTTATGTGA
1 TTATTTTTTTAT-CTTATGTGA
39844953 TTATTATTTTTAT-TTATGT
1 TTATT-TTTTTATCTTATGT
39844972 TGGTATTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 5 0.28
23 7 0.39
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (21 bp):
TTATTTTTTTATCTTATGTGA
Found at i:39851390 original size:138 final size:138
Alignment explanation
Indices: 39851137--39851485 Score: 401
Period size: 138 Copynumber: 2.5 Consensus size: 138
39851127 TCTCAAATCC
* * * * * * *
39851137 TATACCCTTGAAGTAGTAGTGGGTCAGATTGAAACTAAAGTGACGAATCATCTTTCCCTGAAGTT
1 TATACCCCTGAAGTTGTAGTGGGTCGGAATGAAACTAAAGTGACGAATCATATCTCCCTAAAGTT
** ** **
39851202 GTAGTGGAGCAAGATGAAACAACAAATCATATATTTCTGAAGTTGTAGTGGATCGGATTGAAGAT
66 GTAGTGGAGCAAGATGAAACAACAAATCATATATCCCTGAAGTTACAGTGGATCAAATTGAAGAT
*
39851267 ATAATTCT
131 ACAATTCT
* * ** *
39851275 TATACCCCTGAAGTTGTAGTGGGTCGGAATGAAATTATAGTGGTGAATCTTATCTCCCTAAAGTT
1 TATACCCCTGAAGTTGTAGTGGGTCGGAATGAAACTAAAGTGACGAATCATATCTCCCTAAAGTT
* * * * *
39851340 GTAGTGTAGCAAGATGAAGCTACAAATCCTATATCCCTGAAGTTACAGTGGATCAAATTGAAGCT
66 GTAGTGGAGCAAGATGAAACAACAAATCATATATCCCTGAAGTTACAGTGGATCAAATTGAAGAT
39851405 ACAATTCT
131 ACAATTCT
* * * * * * * * *
39851413 TATACCTCTGAAGTTGCAGTGGGTCGAAATGAAACTACAGTGACAAATCCTATATCTCTGAAGTT
1 TATACCCCTGAAGTTGTAGTGGGTCGGAATGAAACTAAAGTGACGAATCATATCTCCCTAAAGTT
39851478 GTAGTGGA
66 GTAGTGGA
39851486 TCAAATTGAA
Statistics
Matches: 174, Mismatches: 37, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
138 174 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (138 bp):
TATACCCCTGAAGTTGTAGTGGGTCGGAATGAAACTAAAGTGACGAATCATATCTCCCTAAAGTT
GTAGTGGAGCAAGATGAAACAACAAATCATATATCCCTGAAGTTACAGTGGATCAAATTGAAGAT
ACAATTCT
Found at i:39851402 original size:44 final size:44
Alignment explanation
Indices: 39851354--39852009 Score: 159
Period size: 44 Copynumber: 14.1 Consensus size: 44
39851344 TGTAGCAAGA
*
39851354 TGAAGCTACAAATCCTATATCCCTGAAGTTACAGTGGATCAAAT
1 TGAAGCTACAAATCCTATATCCCTGAAGTTGCAGTGGATCAAAT
* * *
39851398 TGAAGCTACAATTCTTATA-CCTCTGAAGTTGCAGTGGGTCGAAA-
1 TGAAGCTACAAATCCTATATCC-CTGAAGTTGCAGTGGATC-AAAT
* * *
39851442 TGAAACTACAGTGACAAATCCTATATCTCTGAAGTTGTAGTGGATCAAAT
1 TG-AA--GC--T-ACAAATCCTATATCCCTGAAGTTGCAGTGGATCAAAT
** * * * * * **
39851492 TGAAGCTGTAATTCTTATAACCCTGAAGTTGCAATGGGTCGGAT
1 TGAAGCTACAAATCCTATATCCCTGAAGTTGCAGTGGATCAAAT
* * * * * *
39851536 TGAATCTACTATAGCAAGTCTTATCTCCCTGAAGCTGTAGTGGAGCAAGA-
1 TGAAGCTAC---A--AA-TCCTATATCCCTGAAGTTGCAGTGGATCAA-AT
* * * * *
39851586 TGGAGCTACAAATCCTATACCCCTGAAGTTGCAATGGGTCAGAT
1 TGAAGCTACAAATCCTATATCCCTGAAGTTGCAGTGGATCAAAT
* * * * * * * * *
39851630 TAAAGTTACCATAGCGAGTCTTATCTCCCTAAAGTTACAATGAAGCAAGA-
1 TGAAGCTA-CA-A---A-TCCTATATCCCTGAAGTTGCAGTGGATCAA-AT
* * * * * *
39851680 TGAAGTTACAAACCCTATA-CCCTTTAAGTTGTAGTAGG-TCAGAC
1 TGAAGCTACAAATCCTATATCCC-TGAAGTTGCAGT-GGATCAAAT
* * * **
39851724 TAAAGTTACCATAACGAATCTTATCCCCCTGAAGTT-CAGTGGAGT-AAGAT
1 TGAAG----C-T-ACAAATCCTATATCCCTGAAGTTGCAGTGGA-TCAA-AT
* ** *
39851774 TG-AGCTACAAATCCTATACCCCTGAAGTTATAGTGGGTCAAAT
1 TGAAGCTACAAATCCTATATCCCTGAAGTTGCAGTGGATCAAAT
* * * * ** *
39851817 TGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGTAGTAAAGCAAGA-
1 TGAAG----C-TA-CAAATCCTATATCCCTGAAGTTGCAGTGGATCAA-AT
* * * *
39851867 TGAAGCTACAAATCCTATACCCCTGAAGTTGTAGTGGGTCAGAT
1 TGAAGCTACAAATCCTATATCCCTGAAGTTGCAGTGGATCAAAT
* * * *
39851911 TGAAACTACAAATGGCGAATCT-TATCTCTCTAAAGTTACAGTGGAGCAAGA-
1 TGAAGCTACAAAT--C----CTATATC-C-CTGAAGTTGCAGTGGATCAA-AT
* * *
39851962 TGAAGCTACAAATCCTATACCCCTGAAGTTCCAGTAGG-TCAGAT
1 TGAAGCTACAAATCCTATATCCCTGAAGTTGCAGT-GGATCAAAT
39852006 TGAA
1 TGAA
39852010 ATTACCATAG
Statistics
Matches: 434, Mismatches: 117, Indels: 122
0.64 0.17 0.18
Matches are distributed among these distances:
43 34 0.08
44 175 0.40
45 20 0.05
46 6 0.01
47 4 0.01
48 4 0.01
49 23 0.05
50 134 0.31
51 33 0.08
52 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (44 bp):
TGAAGCTACAAATCCTATATCCCTGAAGTTGCAGTGGATCAAAT
Found at i:39851538 original size:138 final size:138
Alignment explanation
Indices: 39851137--39851544 Score: 388
Period size: 138 Copynumber: 3.0 Consensus size: 138
39851127 TCTCAAATCC
* * * * * * * * * *
39851137 TATACCCTTGAAGTAGTAGTGGGTC-AGATTGAAACTAAAGTGACGAATCATCTTTCCCTGAAGT
1 TATACCCCTGAAGTTGCAGTGGGTCGA-AATGAAACTACAGTGACAAATCCTATATCCCTAAAGT
* * * *** * *
39851201 TGTAGTGGAGCAAGATGAAACAACAAATCATATATTTCTGAAGTTGTAGTGGATCGGATTGAAGA
65 TGTAGTGGAGCAAGATGAAGCTACAAATCCTATAACCCTGAAGTTGCAGTGGATCGGATTGAAGC
*
39851266 TATAATTCT
130 TACAATTCT
* * * * *** * *
39851275 TATACCCCTGAAGTTGTAGTGGGTCGGAATGAAATTATAGTGGTGAATCTTATCTCCCTAAAGTT
1 TATACCCCTGAAGTTGCAGTGGGTCGAAATGAAACTACAGTGACAAATCCTATATCCCTAAAGTT
* * * **
39851340 GTAGTGTAGCAAGATGAAGCTACAAATCCTATATCCCTGAAGTTACAGTGGATCAAATTGAAGCT
66 GTAGTGGAGCAAGATGAAGCTACAAATCCTATAACCCTGAAGTTGCAGTGGATCGGATTGAAGCT
39851405 ACAATTCT
131 ACAATTCT
* * *
39851413 TATACCTCTGAAGTTGCAGTGGGTCGAAATGAAACTACAGTGACAAATCCTATATCTCTGAAGTT
1 TATACCCCTGAAGTTGCAGTGGGTCGAAATGAAACTACAGTGACAAATCCTATATCCCTAAAGTT
* ** * * * * *
39851478 GTAGTGGATCAA-ATTGAAGCTGTAATTCTTATAACCCTGAAGTTGCAATGGGTCGGATTGAATC
66 GTAGTGGAGCAAGA-TGAAGCTACAAATCCTATAACCCTGAAGTTGCAGTGGATCGGATTGAAGC
39851542 TAC
130 TAC
39851545 TATAGCAAGT
Statistics
Matches: 219, Mismatches: 49, Indels: 4
0.81 0.18 0.01
Matches are distributed among these distances:
137 1 0.00
138 218 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.30
Consensus pattern (138 bp):
TATACCCCTGAAGTTGCAGTGGGTCGAAATGAAACTACAGTGACAAATCCTATATCCCTAAAGTT
GTAGTGGAGCAAGATGAAGCTACAAATCCTATAACCCTGAAGTTGCAGTGGATCGGATTGAAGCT
ACAATTCT
Found at i:39851644 original size:94 final size:93
Alignment explanation
Indices: 39851364--39852042 Score: 616
Period size: 94 Copynumber: 7.2 Consensus size: 93
39851354 TGAAGCTACA
* * * * * * *
39851364 AATCCTATATCCCTGAAGTTACAGTGGATCAA-ATTGAAGCTACAATTCTTATACCTCTGAAGTT
1 AATCTTATCTCCCTGAAGTTATAGTGGAGCAAGA-TGAAGCTACAAATCCTATACCCCTGAAGTT
* * * *
39851428 GCAGTGGGTCGAAATGAAACTA-CAGT-GACA
65 GCAGTGGGTC-AGATTAAATTACCA-TAG-CG
* * * * * ** * * *
39851458 AATCCTATATCTCTGAAGTTGTAGTGGATCAA-ATTGAAGCTGTAATTCTTATAACCCTGAAGTT
1 AATCTTATCTCCCTGAAGTTATAGTGGAGCAAGA-TGAAGCTACAAATCCTATACCCCTGAAGTT
* * * *
39851522 GCAATGGGTCGGATTGAATCTACTATAGC-
65 GCAGTGGGTCAGATTAAAT-TACCATAGCG
* * *
39851551 AAGTCTTATCTCCCTGAAGCTGTAGTGGAGCAAGATGGAGCTACAAATCCTATACCCCTGAAGTT
1 AA-TCTTATCTCCCTGAAGTTATAGTGGAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTT
*
39851616 GCAATGGGTCAGATTAAAGTTACCATAGCG
65 GCAGTGGGTCAGATTAAA-TTACCATAGCG
* * * * * * * * *
39851646 AGTCTTATCTCCCTAAAGTTACAATGAAGCAAGATGAAGTTACAAACCCTATACCCTTTAAGTTG
1 AATCTTATCTCCCTGAAGTTATAGTGGAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTG
* * * *
39851711 TAGTAGGTCAGACTAAAGTTACCATAACG
66 CAGTGGGTCAGATTAAA-TTACCATAGCG
* * *
39851740 AATCTTATCCCCCTGAAGTT-CAGTGGAGTAAGATTG-AGCTACAAATCCTATACCCCTGAAGTT
1 AATCTTATCTCCCTGAAGTTATAGTGGAGCAAGA-TGAAGCTACAAATCCTATACCCCTGAAGTT
** * *
39851803 ATAGTGGGTCAAATTGAAGTTACCATAGCG
65 GCAGTGGGTCAGATT-AAATTACCATAGCG
* **
39851833 AATCTTATCTCCCTGAAGTTGTAGTAAAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTATAGTGGAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTG
* * * *
39851898 TAGTGGGTCAGATTGAAACTACAAATGGCG
66 CAGTGGGTCAGATT-AAATTAC-CATAGCG
* * * *
39851928 AATCTTATCTCTCTAAAGTTACAGTGGAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTC
1 AATCTTATCTCCCTGAAGTTATAGTGGAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTG
*
39851993 CAGTAGGTCAGATTGAAATTACCATAGCG
66 CAGTGGGTCAGATT-AAATTACCATAGCG
* *
39852022 AAACTTATCTCTCTGAAGTTA
1 AATCTTATCTCCCTGAAGTTA
39852043 CAGTAGGTCG
Statistics
Matches: 487, Mismatches: 86, Indels: 24
0.82 0.14 0.04
Matches are distributed among these distances:
93 81 0.17
94 319 0.66
95 87 0.18
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (93 bp):
AATCTTATCTCCCTGAAGTTATAGTGGAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTG
CAGTGGGTCAGATTAAATTACCATAGCG
Found at i:39851794 original size:187 final size:188
Alignment explanation
Indices: 39851554--39852044 Score: 623
Period size: 187 Copynumber: 2.6 Consensus size: 188
39851544 CTATAGCAAG
* *
39851554 TCTTATCTCCCTGAAGCTGT-AGTGGAGCAAGATGGAGCTACAAATCCTATACCCCTGAAGTTGC
1 TCTTATCTCCCTGAAG-T-TCAGTGGAGCAAGATTGAGCTACAAATCCTATACCCCTGAAGTTAC
* * * *
39851618 AATGGGTCAGATTAAAGTTACCATAGCGAGTCTTATCTCCCTAAAGTTACAATGAAGCAAGATGA
64 AGTGGGTCAGATTAAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTACAATAAAGCAAGATGA
* * * * *
39851683 AGTTACAAACCCTATACCCTTTAAGTTGTAGTAGGTCAGACT-AAAGTTAC-CATAACGAA
129 AGCTACAAACCCTATACCCCTGAAGTTGTAGTAGGTCAGACTGAAA-CTACAAATAACGAA
* * *
39851742 TCTTATCCCCCTGAAGTTCAGTGGAGTAAGATTGAGCTACAAATCCTATACCCCTGAAGTTATAG
1 TCTTATCTCCCTGAAGTTCAGTGGAGCAAGATTGAGCTACAAATCCTATACCCCTGAAGTTACAG
* * ** *
39851807 TGGGTCAAATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGTAGTAAAGCAAGATGAAG
66 TGGGTCAGATTAAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTACAATAAAGCAAGATGAAG
* * * **
39851872 CTACAAATCCTATACCCCTGAAGTTGTAGTGGGTCAGATTGAAACTACAAATGGCGAA
131 CTACAAACCCTATACCCCTGAAGTTGTAGTAGGTCAGACTGAAACTACAAATAACGAA
* * *
39851930 TCTTATCTCTCTAAAGTTACAGTGGAGCAAGA-TGAAGCTACAAATCCTATACCCCTGAAGTTCC
1 TCTTATCTCCCTGAAGTT-CAGTGGAGCAAGATTG-AGCTACAAATCCTATACCCCTGAAGTTAC
* * *
39851994 AGTAGGTCAGATTGAAA-TTACCATAGCGAAACTTATCTCTCTGAAGTTACA
64 AGTGGGTCAGATT-AAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTACA
39852045 GTAGGTCGGA
Statistics
Matches: 260, Mismatches: 37, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
186 1 0.00
187 136 0.52
188 41 0.16
189 80 0.31
190 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (188 bp):
TCTTATCTCCCTGAAGTTCAGTGGAGCAAGATTGAGCTACAAATCCTATACCCCTGAAGTTACAG
TGGGTCAGATTAAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTACAATAAAGCAAGATGAAG
CTACAAACCCTATACCCCTGAAGTTGTAGTAGGTCAGACTGAAACTACAAATAACGAA
Found at i:39852059 original size:50 final size:50
Alignment explanation
Indices: 39851982--39852096 Score: 194
Period size: 50 Copynumber: 2.3 Consensus size: 50
39851972 AATCCTATAC
*
39851982 CCCTGAAGTTCCAGTAGGTCAGATTGAAATTACCATAGCGAAACTTATCT
1 CCCTGAAGTTACAGTAGGTCAGATTGAAATTACCATAGCGAAACTTATCT
* *
39852032 CTCTGAAGTTACAGTAGGTCGGATTGAAATTACCATAGCGAAACTTATCT
1 CCCTGAAGTTACAGTAGGTCAGATTGAAATTACCATAGCGAAACTTATCT
*
39852082 CCCTGAAGTTGCAGT
1 CCCTGAAGTTACAGT
39852097 GGAATAAAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (50 bp):
CCCTGAAGTTACAGTAGGTCAGATTGAAATTACCATAGCGAAACTTATCT
Found at i:39852185 original size:144 final size:144
Alignment explanation
Indices: 39851889--39852185 Score: 321
Period size: 144 Copynumber: 2.1 Consensus size: 144
39851879 TCCTATACCC
** * * * * * * *
39851889 CTGAAGTTGTAGTGGGTCAGATTGAAACTACAAATGGCGAATCTTATCTCTCTAAAGTTACAGTG
1 CTGAAGTTACAGTAGGTCGGATTGAAATTAC-CATAGCGAAACTTATCTCCCTAAAGTTACAGTG
* * * * * * *
39851954 GAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTCCAGTAGGTCAGATTGAAATTACCATA
65 GAACAAAATGAAACTACAAATCCTACACCCCTGAAGTTCCAGTAGGTCAGATTGAAACTACAACA
*
39852019 GCGAAACTTATCTCT
130 ACGAAACTTATCTCT
* *
39852034 CTGAAGTTACAGTAGGTCGGATTGAAATTACCATAGCGAAACTTATCTCCCTGAAGTTGCAGTGG
1 CTGAAGTTACAGTAGGTCGGATTGAAATTACCATAGCGAAACTTATCTCCCTAAAGTTACAGTGG
* ** * *
39852099 AATAAAATGAAACTACAAATCCTACACCCCTGAAGTTGTAGT-GAGTCGGGTTGAAACTACAACA
66 AACAAAATGAAACTACAAATCCTACACCCCTGAAGTTCCAGTAG-GTCAGATTGAAACTACAACA
39852163 AC-AAATCTTATCTC-
130 ACGAAA-CTTATCTCT
39852177 CTTGAAGTT
1 C-TGAAGTT
39852186 GCAATAGAGC
Statistics
Matches: 125, Mismatches: 24, Indels: 7
0.80 0.15 0.04
Matches are distributed among these distances:
143 5 0.04
144 94 0.75
145 26 0.21
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (144 bp):
CTGAAGTTACAGTAGGTCGGATTGAAATTACCATAGCGAAACTTATCTCCCTAAAGTTACAGTGG
AACAAAATGAAACTACAAATCCTACACCCCTGAAGTTCCAGTAGGTCAGATTGAAACTACAACAA
CGAAACTTATCTCT
Found at i:39869458 original size:9 final size:9
Alignment explanation
Indices: 39869444--39869468 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
39869434 AACATTTATG
39869444 TTTTTTTAA
1 TTTTTTTAA
39869453 TTTTTTTAA
1 TTTTTTTAA
39869462 TTTTTTT
1 TTTTTTT
39869469 TTCTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:39872194 original size:18 final size:18
Alignment explanation
Indices: 39872173--39872217 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
39872163 CATTCTTCTC
39872173 CCCTTTCCCCTTCTCCTT
1 CCCTTTCCCCTTCTCCTT
39872191 CCCTTTCCCCTTCTCCTT
1 CCCTTTCCCCTTCTCCTT
39872209 CCCTTTCCC
1 CCCTTTCCC
39872218 GTTTCGAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (18 bp):
CCCTTTCCCCTTCTCCTT
Found at i:39873394 original size:35 final size:34
Alignment explanation
Indices: 39873355--39873420 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
39873345 CAAACACCAG
*
39873355 AAAACATTTTCCAGTAAGTCATTTTACAGAAATGT
1 AAAACATTTTCCAG-AAATCATTTTACAGAAATGT
*
39873390 AAAACATTTTCCAGAAATCATTTTACGGAAA
1 AAAACATTTTCCAGAAATCATTTTACAGAAA
39873421 ATATTTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 15 0.52
35 14 0.48
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (34 bp):
AAAACATTTTCCAGAAATCATTTTACAGAAATGT
Found at i:39873525 original size:24 final size:24
Alignment explanation
Indices: 39873498--39873547 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
39873488 TCTACCAAAG
39873498 ATTTTAAAGCATGAAGTCAAAACA
1 ATTTTAAAGCATGAAGTCAAAACA
39873522 ATTTTAAAGCATGAAGTCAAAACA
1 ATTTTAAAGCATGAAGTCAAAACA
39873546 AT
1 AT
39873548 CACTTATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (24 bp):
ATTTTAAAGCATGAAGTCAAAACA
Found at i:39875979 original size:18 final size:18
Alignment explanation
Indices: 39875958--39876000 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
39875948 ATTTTACATA
*
39875958 TTTTAAATTATTCTAATT
1 TTTTAAATTATTATAATT
* *
39875976 TTTTAAGTTATTATTATT
1 TTTTAAATTATTATAATT
39875994 TTTTAAA
1 TTTTAAA
39876001 AATATATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTAAATTATTATAATT
Found at i:39876130 original size:25 final size:25
Alignment explanation
Indices: 39876102--39876150 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
39876092 AACTGTAATA
39876102 TATAATTTATAAATATATAAAAACG
1 TATAATTTATAAATATATAAAAACG
* * *
39876127 TATAGTTTATAAATTTATATAAAC
1 TATAATTTATAAATATATAAAAAC
39876151 ACATAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (25 bp):
TATAATTTATAAATATATAAAAACG
Found at i:39877625 original size:32 final size:32
Alignment explanation
Indices: 39877584--39877652 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
39877574 TAAATGCTAT
* *
39877584 TTAAATAATTGACTATAATGATACATAAAATA
1 TTAAATAATTGAATATAATGATACACAAAATA
* *
39877616 TTAAATAATTTAATATAATGATATACAAAATA
1 TTAAATAATTGAATATAATGATACACAAAATA
39877648 -TAAAT
1 TTAAAT
39877653 TAATCTAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
31 5 0.15
32 28 0.85
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.36
Consensus pattern (32 bp):
TTAAATAATTGAATATAATGATACACAAAATA
Found at i:39878249 original size:25 final size:27
Alignment explanation
Indices: 39878213--39878263 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
39878203 CAAGAAATGC
39878213 AATAAAATTA-TTAAAAAAT-TAAAAA
1 AATAAAATTATTTAAAAAATATAAAAA
*
39878238 AATATAAA-TATTTAGAAAATATAAAA
1 AATA-AAATTATTTAAAAAATATAAAA
39878264 CCAAGAGGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 6 0.27
26 11 0.50
27 5 0.23
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (27 bp):
AATAAAATTATTTAAAAAATATAAAAA
Found at i:39887058 original size:18 final size:18
Alignment explanation
Indices: 39887021--39887058 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
39887011 TAAATGATGA
39887021 ATTTAAAATATTAGTTGTT
1 ATTTAAAATATTA-TTGTT
39887040 ATTTAAAAGTATT-TTGTT
1 ATTTAAAA-TATTATTGTT
39887058 A
1 A
39887059 AGTGATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 8 0.44
20 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (18 bp):
ATTTAAAATATTATTGTT
Found at i:39887773 original size:25 final size:24
Alignment explanation
Indices: 39887745--39887804 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
39887735 AGCGTCCCGA
39887745 TATATGGCTCTCCAGAACTTCCTGT
1 TATATGGCTCTCC-GAACTTCCTGT
* * *
39887770 TATATGGTTCTTGCGAGCTTCCTGT
1 TATATGGCTC-TCCGAACTTCCTGT
39887795 T-TATGGCTCT
1 TATATGGCTCT
39887805 TATGAGCTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 1 0.03
24 7 0.23
25 20 0.67
26 2 0.07
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (24 bp):
TATATGGCTCTCCGAACTTCCTGT
Found at i:39887830 original size:25 final size:24
Alignment explanation
Indices: 39887797--39887938 Score: 126
Period size: 25 Copynumber: 5.8 Consensus size: 24
39887787 CTTCCTGTTT
39887797 ATGGCTCTTATGAGCTTCCCGATA
1 ATGGCTCTTATGAGCTTCCCGATA
**
39887821 ATTGGCTCTTCGGAGCTTCCCGATA
1 A-TGGCTCTTATGAGCTTCCCGATA
* *
39887846 ACTGACTCTTATGAGCTTCCTGATTA
1 A-TGGCTCTTATGAGCTTCCCGA-TA
**
39887872 ATGGCTCTTCA-GAGCTTCCTAATA
1 ATGGCTCTT-ATGAGCTTCCCGATA
* * * * *
39887896 TTGGCTCGCT-TGAACTTTCCGATT
1 ATGGCTC-TTATGAGCTTCCCGATA
39887920 ATGGCTCTTATGAGCTTCC
1 ATGGCTCTTATGAGCTTCC
39887939 TATTATACAG
Statistics
Matches: 92, Mismatches: 20, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
23 1 0.01
24 30 0.33
25 57 0.62
26 4 0.04
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.36
Consensus pattern (24 bp):
ATGGCTCTTATGAGCTTCCCGATA
Found at i:39887957 original size:25 final size:26
Alignment explanation
Indices: 39887929--39887988 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 26
39887919 TATGGCTCTT
*
39887929 ATGAGCTTCCT-ATTATACAGCTCGA
1 ATGAGCTTCCTCATTATACAGCTCAA
**
39887954 ATGAGCTT-CTCATTATATGGCTCAA
1 ATGAGCTTCCTCATTATACAGCTCAA
*
39887979 AAGAGCTTCC
1 ATGAGCTTCC
39887989 CGTTTACATG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 2 0.07
25 26 0.90
26 1 0.03
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (26 bp):
ATGAGCTTCCTCATTATACAGCTCAA
Found at i:39892076 original size:43 final size:44
Alignment explanation
Indices: 39892028--39892125 Score: 126
Period size: 43 Copynumber: 2.2 Consensus size: 44
39892018 GTGTTTTCCC
* * *
39892028 ACAAACGCCATTATAGAACATGATCTTTAGTAGCGATTTTA-CT
1 ACAAACGCCACTAAAGAACATGATCTTTAGTAGCGATTCTAGCT
* * *
39892071 ACAAACGCCGCTAAAGAACATGATCTTTTGTGGCGATTCTAGCT
1 ACAAACGCCACTAAAGAACATGATCTTTAGTAGCGATTCTAGCT
*
39892115 ACAAACACCAC
1 ACAAACGCCAC
39892126 AACATGCTCG
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
43 35 0.76
44 11 0.24
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (44 bp):
ACAAACGCCACTAAAGAACATGATCTTTAGTAGCGATTCTAGCT
Found at i:39893448 original size:19 final size:19
Alignment explanation
Indices: 39893420--39893464 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
39893410 CATATTTTTC
* *
39893420 AAAAAA-TATAAATATTAT
1 AAAAAATTATAAAGAATAT
39893438 AAAAAATTATAAAGAATAT
1 AAAAAATTATAAAGAATAT
39893457 ATAAAAAT
1 A-AAAAAT
39893465 GTTAAGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 6 0.26
19 11 0.48
20 6 0.26
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAAAATTATAAAGAATAT
Found at i:39897897 original size:60 final size:59
Alignment explanation
Indices: 39897787--39897900 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 59
39897777 TTTTAGGAAT
* * *
39897787 TAACTTTGATAAAAAAAAGTTAAACTCCCAATGAGAAAATATTTGCCAAGTTCAAGGCC
1 TAACTTGGATAAAAAAAAGTTAAACTCCCAATGAGAAAATAATTACCAAGTTCAAGGCC
*
39897846 TAACTTGGATAAAAGAAAAGTTTAAAC-CCCAAT-ATGAAAATAATTATCAAGTTCA
1 TAACTTGGATAAAA-AAAAG-TTAAACTCCCAATGA-GAAAATAATTACCAAGTTCA
39897901 GTGTTTAACT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
59 14 0.29
60 28 0.58
61 6 0.12
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.26
Consensus pattern (59 bp):
TAACTTGGATAAAAAAAAGTTAAACTCCCAATGAGAAAATAATTACCAAGTTCAAGGCC
Found at i:39897910 original size:60 final size:59
Alignment explanation
Indices: 39897786--39897948 Score: 149
Period size: 60 Copynumber: 2.8 Consensus size: 59
39897776 TTTTTAGGAA
* * *
39897786 TTAACTTTGATAAAAAAAAG-TTAAACTCCCAATGA-GAAAATATTTGCCAAGTTCAAGGC
1 TTAACTTGGATAAAAAAAAGTTTAAAC-CCCAAT-ATGAAAATAATTACCAAGTTCAAGGC
* * *
39897845 CTAACTTGGATAAAAGAAAAGTTTAAACCCCAATATGAAAATAATTATCAAGTTC-AGTGT
1 TTAACTTGGATAAAA-AAAAGTTTAAACCCCAATATGAAAATAATTACCAAGTTCAAG-GC
* * *
39897905 TTAACTTAGG-TTAAAAAAA-TTCAAGCCCCAATATGAGAAA-AATT
1 TTAACTT-GGATAAAAAAAAGTTTAAACCCCAATATGA-AAATAATT
39897949 GCCTTCGCAG
Statistics
Matches: 88, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
58 19 0.22
59 23 0.26
60 38 0.43
61 8 0.09
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.28
Consensus pattern (59 bp):
TTAACTTGGATAAAAAAAAGTTTAAACCCCAATATGAAAATAATTACCAAGTTCAAGGC
Found at i:39900418 original size:21 final size:21
Alignment explanation
Indices: 39900388--39900429 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39900378 TTTACATTAG
39900388 TGTCTAGAGA-CATCAAGAACA
1 TGTCTAGAGACCAT-AAGAACA
*
39900409 TGTCTTGAGACCATAAGAACA
1 TGTCTAGAGACCATAAGAACA
39900430 AATTTTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (21 bp):
TGTCTAGAGACCATAAGAACA
Found at i:39900665 original size:23 final size:22
Alignment explanation
Indices: 39900639--39900682 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39900629 ATACAAAAAC
*
39900639 AAGGGAACATTGCCTCGAGACAT
1 AAGGGAA-AATGCCTCGAGACAT
*
39900662 AAGGGAAAATGTCTCGAGACA
1 AAGGGAAAATGCCTCGAGACA
39900683 AAAATCCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.39, C:0.18, G:0.27, T:0.16
Consensus pattern (22 bp):
AAGGGAAAATGCCTCGAGACAT
Found at i:39902464 original size:11 final size:11
Alignment explanation
Indices: 39902448--39902535 Score: 71
Period size: 11 Copynumber: 8.4 Consensus size: 11
39902438 CTCTATTATT
39902448 CTCTCAATTTC
1 CTCTCAATTTC
39902459 CTCTCAATTTC
1 CTCTCAATTTC
39902470 CT-TCCAAATTT-
1 CTCT-C-AATTTC
*
39902481 CTCTCAA-ATC
1 CTCTCAATTTC
*
39902491 C-CT--ATTTA
1 CTCTCAATTTC
* *
39902499 ATCTCAATTTG
1 CTCTCAATTTC
*
39902510 ATCTCAATTTC
1 CTCTCAATTTC
39902521 CTCTCAATTTC
1 CTCTCAATTTC
39902532 CTCT
1 CTCT
39902536 TAAACCCCTA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 5 0.08
10 4 0.06
11 45 0.73
12 6 0.10
ACGTcount: A:0.23, C:0.32, G:0.01, T:0.44
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:39902517 original size:51 final size:51
Alignment explanation
Indices: 39902449--39902548 Score: 132
Period size: 51 Copynumber: 2.0 Consensus size: 51
39902439 TCTATTATTC
* *
39902449 TCTCAATTTCCTCTCAATTTCCT-TCCAAATTT-CTCTCAAATCCCTATTTAA
1 TCTCAATTTCATCTCAATTTCCTCT-C-AATTTCCTCTCAAACCCCTATTTAA
* *
39902500 TCTCAATTTGATCTCAATTTCCTCTCAATTTCCTCTTAAACCCCTATTT
1 TCTCAATTTCATCTCAATTTCCTCTCAATTTCCTCTCAAACCCCTATTT
39902549 TAAAATTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
50 5 0.12
51 37 0.86
52 1 0.02
ACGTcount: A:0.24, C:0.31, G:0.01, T:0.44
Consensus pattern (51 bp):
TCTCAATTTCATCTCAATTTCCTCTCAATTTCCTCTCAAACCCCTATTTAA
Found at i:39904153 original size:18 final size:18
Alignment explanation
Indices: 39904130--39904172 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
39904120 TGCCAGGTGC
* *
39904130 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
39904148 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
39904166 GTTTCCT
1 GTATCCT
39904173 TTTCTGAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:39904459 original size:21 final size:21
Alignment explanation
Indices: 39904413--39904460 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
39904403 CCAACACCGA
*
39904413 CAACCAGATACCCTACCAGAG
1 CAACCAGATACCCCACCAGAG
* *
39904434 GAACCAGA-ATCCCCACCGGAG
1 CAACCAGATA-CCCCACCAGAG
39904455 CAACCA
1 CAACCA
39904461 CAACCCCCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.38, C:0.40, G:0.17, T:0.06
Consensus pattern (21 bp):
CAACCAGATACCCCACCAGAG
Found at i:39913065 original size:15 final size:17
Alignment explanation
Indices: 39913045--39913081 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
39913035 ATAAATATGA
39913045 TATTTTT-ATTTCT-TT
1 TATTTTTAATTTCTGTT
*
39913060 TATTTTTAATTTTTGTT
1 TATTTTTAATTTCTGTT
39913077 TATTT
1 TATTT
39913082 ATTGTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 5 0.26
17 7 0.37
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (17 bp):
TATTTTTAATTTCTGTT
Found at i:39913109 original size:30 final size:26
Alignment explanation
Indices: 39913047--39913111 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 26
39913037 AAATATGATA
*
39913047 TTTTTATTTCTTTTATTTTTAATTTT
1 TTTTTATTTATTTTATTTTTAATTTT
*
39913073 TGTTTATTTATTGTTATTTGTTTAATTTCT
1 TTTTTATTTATT-TTA-TT-TTTAATTT-T
39913103 TTTTTATTT
1 TTTTTATTT
39913112 GTAAGTTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 10 0.31
27 3 0.09
28 2 0.06
29 8 0.25
30 9 0.28
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (26 bp):
TTTTTATTTATTTTATTTTTAATTTT
Found at i:39917100 original size:20 final size:20
Alignment explanation
Indices: 39917075--39917116 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
39917065 GAGGTTTGTG
39917075 TTCAAATCCCTTTCCTTGAA
1 TTCAAATCCCTTTCCTTGAA
39917095 TTCAAATCCCTTTCCTTGAA
1 TTCAAATCCCTTTCCTTGAA
39917115 TT
1 TT
39917117 TTTTGTAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.29, G:0.05, T:0.43
Consensus pattern (20 bp):
TTCAAATCCCTTTCCTTGAA
Found at i:39940722 original size:40 final size:40
Alignment explanation
Indices: 39940633--39940896 Score: 360
Period size: 40 Copynumber: 6.7 Consensus size: 40
39940623 TTGAATGATG
* *
39940633 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
* * *
39940672 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
39940712 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
39940751 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
39940791 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
39940831 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
39940872 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39940897 AACGAGGAGC
Statistics
Matches: 206, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
39 53 0.26
40 143 0.69
41 10 0.05
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:39940914 original size:120 final size:118
Alignment explanation
Indices: 39940633--39940929 Score: 338
Period size: 119 Copynumber: 2.5 Consensus size: 118
39940623 TTGAATGATG
* *
39940633 TCCGGGCTAAGTCCCGAAGGC-TTGTG--CTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
1 TCCGGGCTAAGTCCCGAAGGCATT-TGAAC-GAGTGACTAA-ATCCGG-TTAA-ATCCCGAAGGC
* *
39940693 ATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
61 ATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGTGCGAATTACTAAA
* ** * *
39940751 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCC-GGTTAAATCCCGAAGGCATTT
* *
39940816 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
65 GTGCGAGATACTAAATCCGGGCTAAG-CCCGAAGGCATTTGTGCGAATTACTA-AA
* * *
39940872 -CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCCGGTTAAATTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGTTAAATCCCGAAGG
39940930 TACGTGATTT
Statistics
Matches: 153, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
118 23 0.15
119 64 0.42
120 64 0.42
121 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (118 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCCGGTTAAATCCCGAAGGCATTTG
TGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGTGCGAATTACTAAA
Found at i:39947348 original size:40 final size:40
Alignment explanation
Indices: 39947292--39948243 Score: 1589
Period size: 40 Copynumber: 23.8 Consensus size: 40
39947282 AACATTGGAT
39947292 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
*
39947332 CATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
39947372 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
39947412 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
39947452 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
39947492 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
39947532 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
39947572 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
39947612 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
39947652 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
39947692 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
39947732 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
39947772 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
39947812 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
39947852 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
39947892 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
39947932 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
39947972 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
39948012 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
39948052 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
39948092 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
39948132 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
*
39948172 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTCA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
39948212 TATGTCCGGGTTAAGACCCGAAGGCAAATATG
1 TATATCCGGGCTAAGACCCGAAGGCAATTATG
39948244 TTTGTGGCTG
Statistics
Matches: 846, Mismatches: 66, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 846 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.22
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
Found at i:39947425 original size:80 final size:80
Alignment explanation
Indices: 39947292--39948243 Score: 1805
Period size: 80 Copynumber: 11.9 Consensus size: 80
39947282 AACATTGGAT
* * * *
39947292 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGACATATCCGGGCTAAGACCCGAAGGC
1 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
39947357 AATTATGCGAGTTGA
66 AATTATGCGAGTTGA
39947372 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
1 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
39947437 AATTATGCGAGTTGA
66 AATTATGCGAGTTGA
39947452 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
1 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
39947517 AATTATGCGAGTTGA
66 AATTATGCGAGTTGA
39947532 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
1 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
39947597 AATTATGCGAGTTGA
66 AATTATGCGAGTTGA
39947612 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
1 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
39947677 AATTATGCGAGTTGA
66 AATTATGCGAGTTGA
39947692 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
1 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
39947757 AATTATGCGAGTTGA
66 AATTATGCGAGTTGA
39947772 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
1 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
39947837 AATTATGCGAGTTGA
66 AATTATGCGAGTTGA
39947852 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
1 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
39947917 AATTATGCGAGTTGA
66 AATTATGCGAGTTGA
39947932 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
1 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
39947997 AATTATGCGAGTTGA
66 AATTATGCGAGTTGA
39948012 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
1 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
39948077 AATTATGCGAGTTGA
66 AATTATGCGAGTTGA
39948092 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
1 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
39948157 AATTATGCGAGTTGA
66 AATTATGCGAGTTGA
* * * * * *
39948172 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTCATATGTCCGGGTTAAGACCCGAAGGC
1 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
*
39948237 AAATATG
66 AATTATG
39948244 TTTGTGGCTG
Statistics
Matches: 861, Mismatches: 11, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 861 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.22
Consensus pattern (80 bp):
TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
AATTATGCGAGTTGA
Found at i:39955379 original size:68 final size:68
Alignment explanation
Indices: 39955230--39955387 Score: 153
Period size: 68 Copynumber: 2.3 Consensus size: 68
39955220 CTAGCCGATT
* * * *
39955230 TATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACTCATGCGACCTAGCTACA
1 TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAATCACACATGCGACCTAGCTACA
*
39955295 TTTA
65 TATA
* * *
39955299 TCTCTCACGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGTATCACACATGTGACCTAGCTA
1 TATCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGAATCACACATGCGACCTAGCTA
39955361 CTATATA
63 C-ATATA
39955368 GTATCTCGTAGC-CTTCTTGT
1 -TATCTCGTAGCTC-TCTTGT
39955388 ACACATGATG
Statistics
Matches: 74, Mismatches: 9, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
67 1 0.01
68 33 0.45
69 8 0.11
70 6 0.08
71 26 0.35
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.35
Consensus pattern (68 bp):
TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATCACACATGCGACCTAGCTACAT
ATA
Found at i:39956872 original size:37 final size:37
Alignment explanation
Indices: 39956822--39956896 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
39956812 GATGGAGGTA
* *
39956822 GTGGGTGTGATGGAGGTTGTGGACGGTTTAGTAGGGT
1 GTGGGGGTGATGGAGGTAGTGGACGGTTTAGTAGGGT
*
39956859 GTGGGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGT
1 GTGGGGGTGATGGAGGTAGTGGACGGTTTAGTAGGGT
39956896 G
1 G
39956897 ATGGAGTTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.15, C:0.01, G:0.53, T:0.31
Consensus pattern (37 bp):
GTGGGGGTGATGGAGGTAGTGGACGGTTTAGTAGGGT
Found at i:39956916 original size:29 final size:29
Alignment explanation
Indices: 39956863--39956925 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
39956853 TAGGGTGTGG
*
39956863 GGGTGATGGAGGTAGTGGATGGTTTAGTA
1 GGGTGATGGAGGTAGTGGATAGTTTAGTA
* *
39956892 GGGTGATGGAGTTAGTGG-TCAGTTTAGTG
1 GGGTGATGGAGGTAGTGGAT-AGTTTAGTA
39956921 GGGTG
1 GGGTG
39956926 TTTAATTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 1 0.03
29 29 0.97
ACGTcount: A:0.17, C:0.02, G:0.49, T:0.32
Consensus pattern (29 bp):
GGGTGATGGAGGTAGTGGATAGTTTAGTA
Found at i:39957367 original size:133 final size:133
Alignment explanation
Indices: 39957137--39958732 Score: 2236
Period size: 133 Copynumber: 12.3 Consensus size: 133
39957127 GATCTGCTGT
* * * * * * *
39957137 AATTTGATCTGTTTTACACCTGCTCAG-AAAGATAAGATCTGGTATGTTTAGCCTGCTCCACTCC
1 AATTTGATCTGCTCTGCTCCTGCTCAGCGAAGATAAGATCTAGTA--TTTAGCTTGCTCCACTCC
** * * *
39957201 TGCTCAGTGAAGATAAGGCTAATGATTGGAATCTGCTCCATTGCCGATACATGGAGATAAGATAC
64 TGCTCAGTGAAGATAAGGCTGGTGGTTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTC
*
39957266 ATCAA
129 ACCAA
* * * * *
39957271 AATTTGATCTGCTTTGCTCCTGCTCAGCGAAGATAAGATATAGTATATAGCCTGTTCCACTCCTG
1 AATTTGATCTGCTCTGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCTTGCTCCACTCCTG
* * *
39957336 CTAAGTGAAGATAAGGCTGGTGGTTGAAATCTACTCCATTGCCGATACATAGAGATAAGATTCAC
66 CTCAGTGAAGATAAGGCTGGTGGTTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCAC
39957401 CAA
131 CAA
39957404 AATTTGA-----TCTG---CTG---A--G-AGATAAGATCTAGTATTTAGCTTGCTCCACTCCTG
1 AATTTGATCTGCTCTGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCTTGCTCCACTCCTG
*
39957455 CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCAC
66 CTCAGTGAAGATAAGGCTGGTGGTTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCAC
39957520 CAA
131 CAA
39957523 AATTTGA-----TCTG---CTG---A--G-AGATAAGATCTAGTATTTAGCTTGCTCCACTCCTG
1 AATTTGATCTGCTCTGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCTTGCTCCACTCCTG
*
39957574 CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCAC
66 CTCAGTGAAGATAAGGCTGGTGGTTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCAC
39957639 CAA
131 CAA
39957642 AATTTGA-----TCTG---CTG---A--G-AGATAAGATCTAGTATTTAGCTTGCTCCACTCCTG
1 AATTTGATCTGCTCTGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCTTGCTCCACTCCTG
** * * * *
39957693 CTCAGTGAAGATAAGGCTAATGATTGGAATCTGCTCCATTGCCGATACATGGAGATAAGATACAT
66 CTCAGTGAAGATAAGGCTGGTGGTTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCAC
39957758 CAA
131 CAA
* * * * *
39957761 AATTTGATCTGCTTTGCTCCTGCTCAGCGAAGATAAGATATAGTATATAGCCTGTTCCACTCCTG
1 AATTTGATCTGCTCTGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCTTGCTCCACTCCTG
* * *
39957826 CTAAGTGAAGATAAGGCTGGTGGTTGAAATCTACTCCATTGCCGATACATAGAGATAAGATTCAC
66 CTCAGTGAAGATAAGGCTGGTGGTTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCAC
39957891 CAA
131 CAA
**
39957894 AATTTGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCTTGCTCCACTCCTG
1 AATTTGATCTGCTCTGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCTTGCTCCACTCCTG
** * * * *
39957959 CTCAGTGAAGATAAGGCTAATGATTGGAATCTGCTCCATTGCCGATACATGGAGATAAGATACAT
66 CTCAGTGAAGATAAGGCTGGTGGTTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCAC
39958024 CAA
131 CAA
* * * * *
39958027 AATTTGATCTGCTTTGCTCCTGCTCAGCGAAGATAAGATATAGTATATAGCCTGTTCCACTCCTG
1 AATTTGATCTGCTCTGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCTTGCTCCACTCCTG
* * *
39958092 CTAAGTGAAGATAAGGCTGGTGGTTGAAATCTACTCCATTGCCGATACATAGAGATAAGATTCAC
66 CTCAGTGAAGATAAGGCTGGTGGTTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCAC
39958157 CAA
131 CAA
**
39958160 AATTTGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCTTGCTCCACTCCTG
1 AATTTGATCTGCTCTGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCTTGCTCCACTCCTG
*
39958225 CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCAC
66 CTCAGTGAAGATAAGGCTGGTGGTTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCAC
39958290 CAA
131 CAA
**
39958293 AATTTGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCTTGCTCCACTCCTG
1 AATTTGATCTGCTCTGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCTTGCTCCACTCCTG
*
39958358 CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCAC
66 CTCAGTGAAGATAAGGCTGGTGGTTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCAC
39958423 CAA
131 CAA
*
39958426 AATTTGATCTGCT-TCACTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCTTGCTCCACTCCT
1 AATTTGATCTGCTCT-GCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCTTGCTCCACTCCT
* *
39958490 GCTCAGTGAAGATAAGGCTGGTGGTTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCG
65 GCTCAGTGAAGATAAGGCTGGTGGTTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCA
*
39958555 TCAA
130 CCAA
* *
39958559 AATTTGATCTGCTCCGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCTTGCTCCACTCCTA
1 AATTTGATCTGCTCTGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCTTGCTCCACTCCTG
* **
39958624 CTCAGTGAAGATAAGGCTGGTGGTTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGT
66 CTCAGTGAAGATAAGGCTGGTGGTTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCAC
39958689 CAA
131 CAA
*
39958692 AATTTGATCTGCTCCGCTCCTGCTCAGCGAAGATAAGATCT
1 AATTTGATCTGCTCTGCTCCTGCTCAGCGAAGATAAGATCT
39958733 GTCGAAATTT
Statistics
Matches: 1347, Mismatches: 98, Indels: 35
0.91 0.07 0.02
Matches are distributed among these distances:
119 333 0.25
120 1 0.00
122 1 0.00
124 3 0.00
125 3 0.00
127 3 0.00
128 3 0.00
130 1 0.00
132 1 0.00
133 960 0.71
134 24 0.02
135 14 0.01
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (133 bp):
AATTTGATCTGCTCTGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCTTGCTCCACTCCTG
CTCAGTGAAGATAAGGCTGGTGGTTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCAC
CAA
Found at i:39958221 original size:43 final size:44
Alignment explanation
Indices: 39957895--39958732 Score: 310
Period size: 43 Copynumber: 18.9 Consensus size: 44
39957885 ATTCACCAAA
39957895 ATTT-GATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGT
1 ATTTAGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGT
* * * *
39957938 ATTTAGCT-TGCTCCACTCCTGCTCAGTGAAGATAAG-GCTAAT
1 ATTTAGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGT
* * * **
39957980 GA-TTGGAATCTGCTCCATTGCC-GATACATG-G-AGATAAGATACATCAAA
1 -ATTTAG-ATCTGCTCCACT-CCTGCT-CA-GCGAAGATAAGAT-C-T-AGT
*** *
39958028 ATTT-GATCTGCTTTGCTCCTGCTCAGCGAAGATAAGATATAGT
1 ATTTAGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGT
* * * * * * *
39958071 ATATAG-CCTGTTCCACTCCTGCTAAGTGAAGATAAG-GCTGGT
1 ATTTAGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGT
* * * * * * ** * **
39958113 GGTTGAAATCTACTCCATTGCC-GATACATAG-AGATAAGATTCACCAAA
1 -ATTTAGATCTGCTCCACT-CCTGCT-CAGCGAAGATAAGA-T--CTAGT
39958161 ATTT-GATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGT
1 ATTTAGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGT
* * * *
39958204 ATTTAGCT-TGCTCCACTCCTGCTCAGTGAAGATAAG-GCTGGT
1 ATTTAGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGT
** * * * * * **
39958246 GGCTGAAATCTGCTCCATTGCC-GATACATG-G-AGATAAGATTCACCAAA
1 -ATTTAGATCTGCTCCACT-CCTGCT-CA-GCGAAGATAAGA-T--CTAGT
39958294 ATTT-GATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGT
1 ATTTAGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGT
* * * *
39958337 ATTTAGCT-TGCTCCACTCCTGCTCAGTGAAGATAAG-GCTGGT
1 ATTTAGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGT
** * * * * * **
39958379 GGCTGAAATCTGCTCCATTGCC-GATACATG-G-AGATAAGATTCACCAAA
1 -ATTTAGATCTGCTCCACT-CCTGCT-CA-GCGAAGATAAGA-T--CTAGT
*
39958427 ATTT-GATCTGCTTCACTCCTGCTCAGCGAAGATAAGATCTAGT
1 ATTTAGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGT
* * * *
39958470 ATTTAGCT-TGCTCCACTCCTGCTCAGTGAAGATAAG-GCTGGT
1 ATTTAGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGT
* * * * **
39958512 GGTTTAAATCTGCTCCATTGCC-GATACATG-G-AGATAAGATTCGTCAAA
1 -ATTTAGATCTGCTCCACT-CCTGCT-CA-GCGAAGATAAGA-TC-T-AGT
*
39958560 ATTT-GATCTGCTCCGCTCCTGCTCAGCGAAGATAAGATCTAGT
1 ATTTAGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGT
* * * * *
39958603 ATTTAGCT-TGCTCCACTCCTACTCAGTGAAGATAAG-GCTGGT
1 ATTTAGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGT
* * * * **
39958645 GGTTTAAATCTGCTCCATTGCC-GATACATG-G-AGATAAGATTCGTCAAA
1 -ATTTAGATCTGCTCCACT-CCTGCT-CA-GCGAAGATAAGA-TC-T-AGT
*
39958693 ATTT-GATCTGCTCCGCTCCTGCTCAGCGAAGATAAGATCT
1 ATTTAGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCT
39958733 GTCGAAATTT
Statistics
Matches: 567, Mismatches: 150, Indels: 155
0.65 0.17 0.18
Matches are distributed among these distances:
42 26 0.05
43 206 0.36
44 119 0.21
45 66 0.12
46 128 0.23
47 15 0.03
48 7 0.01
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (44 bp):
ATTTAGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGT
Found at i:39960964 original size:19 final size:20
Alignment explanation
Indices: 39960940--39960986 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
39960930 TTTTTTGAAT
* *
39960940 TAATGCACATG-ATGTGATG
1 TAATGCAAATGCATGGGATG
39960959 TAATGCAAATGCATGGGATG
1 TAATGCAAATGCATGGGATG
39960979 -AATGCAAA
1 TAATGCAAA
39960987 AGAAAATGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.26
Consensus pattern (20 bp):
TAATGCAAATGCATGGGATG
Found at i:39962173 original size:18 final size:18
Alignment explanation
Indices: 39962135--39962173 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
39962125 AAATATATTA
* * *
39962135 ATATTATTATATTATATT
1 ATATTATTAAATTAAAAT
39962153 ATATTATTAAATTAAAAT
1 ATATTATTAAATTAAAAT
39962171 ATA
1 ATA
39962174 AAGTAAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATTATTAAATTAAAAT
Found at i:39962235 original size:18 final size:19
Alignment explanation
Indices: 39962191--39962236 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
39962181 TAAAAGAAGT
39962191 GAAATA-AAAGAAACAAAA
1 GAAATAGAAAGAAACAAAA
*
39962209 GAAAAAGAAAG-AACAAACA
1 GAAATAGAAAGAAACAAA-A
39962228 -AAATAGAAA
1 GAAATAGAAA
39962237 ATGAAATAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.76, C:0.07, G:0.13, T:0.04
Consensus pattern (19 bp):
GAAATAGAAAGAAACAAAA
Found at i:39962273 original size:14 final size:14
Alignment explanation
Indices: 39962249--39962292 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
39962239 GAAATAGGGG
39962249 AGAAAAAAGGAGAA
1 AGAAAAAAGGAGAA
* * *
39962263 AGGATAAAGGATAA
1 AGAAAAAAGGAGAA
39962277 AGAAAAGAAGGAGAA
1 AGAAAA-AAGGAGAA
39962292 A
1 A
39962293 ATTAGGGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.66, C:0.00, G:0.30, T:0.05
Consensus pattern (14 bp):
AGAAAAAAGGAGAA
Found at i:39965770 original size:48 final size:47
Alignment explanation
Indices: 39965699--39965971 Score: 237
Period size: 48 Copynumber: 5.7 Consensus size: 47
39965689 AGGGTAAACT
* * *
39965699 GCCGAGGCCATGTCCTAGACATGGTCTTACACTTGCTTACATGTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTT-CATGTCGAG
*
39965747 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATGTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TCATGTCGAG
* * * * *
39965795 GCTGATGCCATGTGCCAGACATGGTCTTACACTGGC-TCTTGTCTCAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTCATG--TCGAG
* * * * * * ** *
39965843 ACCAATGCCATGTTCCAAACATGGTCTTACTCTTGCTTTCATAAC-ATT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGC-TTCATGTCGA-G
* * * * * *
39965891 GCCGATGCCATGTTCTAAACATGGTCTTACACTGGCTCTC-TTTATGTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TCATGT-CGAG
39965939 GCCGATGCCATGTCCCAGACATGGTCTTACACT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT
39965972 AGTATACATA
Statistics
Matches: 183, Mismatches: 33, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
46 3 0.02
47 3 0.02
48 174 0.95
50 3 0.02
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTCATGTCGAG
Found at i:39970924 original size:40 final size:40
Alignment explanation
Indices: 39970851--39971940 Score: 1905
Period size: 40 Copynumber: 27.3 Consensus size: 40
39970841 CTGCTCGCTC
* * * * *
39970851 AAATGTCTTCGGGAC-TAGCCCGGTTATAGTAACTCGCAC
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
* * * * *
39970890 AAATGCCTTCGGGACTTAACCCGGTTATAGTAACTCGCAC
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
* * * * * * *
39970930 AAATGTCTTTGGGACTTAACCCGGTTATAGTAACTCGCAC
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
* * *
39970970 AAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCAC
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
39971010 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
39971050 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
39971090 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
39971130 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
39971170 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
39971210 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
39971250 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
39971290 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
39971330 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
39971370 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
39971410 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
39971450 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
39971490 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
39971530 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
39971570 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
39971610 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
39971650 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
39971690 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
39971730 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
* *
39971770 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTCGCAC
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
39971810 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
* * *
39971850 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTCGTAC
1 AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
* * *
39971890 AAATGCCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCAC
1 AAATGCCTTCGGGACTTAGCTCGGATA-TAGTAACTAGCAA
39971930 AAATGCCTTCG
1 AAATGCCTTCG
39971941 TTATCATCCG
Statistics
Matches: 1027, Mismatches: 22, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
39 15 0.01
40 1012 0.99
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.25
Consensus pattern (40 bp):
AAATGCCTTCGGGACTTAGCTCGGATATAGTAACTAGCAA
Found at i:39991178 original size:40 final size:40
Alignment explanation
Indices: 39991123--39991593 Score: 888
Period size: 40 Copynumber: 11.8 Consensus size: 40
39991113 ACATTGGATT
39991123 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAC
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAC
39991163 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAC
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAC
39991203 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAC
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAC
39991243 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAC
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAC
39991283 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAC
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAC
39991323 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAC
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAC
39991363 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAC
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAC
39991403 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAC
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAC
39991443 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAC
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAC
*
39991483 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAC
* *
39991523 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTCAT
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAC
* * *
39991563 ATGTCCGGGTTAAGACCCGAAGGCAAATATG
1 ATATCCGGGCTAAGACCCGAAGGCAATTATG
39991594 TTTGCGGCTG
Statistics
Matches: 426, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 426 1.00
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.20
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAC
Found at i:39996422 original size:39 final size:40
Alignment explanation
Indices: 39996327--39996510 Score: 186
Period size: 40 Copynumber: 4.7 Consensus size: 40
39996317 TTGAATGCTG
*
39996327 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* *
39996365 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
* *
39996406 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
39996445 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
39996484 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
39996511 AACGAGGAGC
Statistics
Matches: 123, Mismatches: 13, Indels: 17
0.80 0.08 0.11
Matches are distributed among these distances:
39 52 0.42
40 59 0.48
41 11 0.09
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:39996462 original size:79 final size:81
Alignment explanation
Indices: 39996327--39996510 Score: 213
Period size: 79 Copynumber: 2.3 Consensus size: 81
39996317 TTGAATGCTG
*
39996327 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
39996390 TGTGCGAGA-TACTA-A
66 TGTGCGA-ATTACTATA
* * **
39996405 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAA-ATCCGGGTTAAG-TCCCGAAGGC
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
39996466 ATTTGTGCGAATTACTATA
63 ATTTGTGCGAATTACTATA
* *
39996485 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39996511 AACGAGGAGC
Statistics
Matches: 91, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
78 11 0.12
79 57 0.63
80 23 0.25
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
TGTGCGAATTACTATA
Found at i:39996532 original size:79 final size:79
Alignment explanation
Indices: 39996379--39996543 Score: 185
Period size: 79 Copynumber: 2.1 Consensus size: 79
39996369 GGACTAAGAT
* * ** *
39996379 CCGAAGGTATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
*
39996444 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
*
39996458 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-
* *
39996520 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAATC
39996537 CCGAAGG
1 CCGAAGG
39996544 TACGTGATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
78 3 0.04
79 45 0.62
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAATC
Found at i:39998036 original size:20 final size:19
Alignment explanation
Indices: 39998011--39998051 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
39998001 CCAATATAGT
*
39998011 GGTCAATGCTCTTAGTTGAA
1 GGTCAATGCTC-GAGTTGAA
*
39998031 GGTCAATGTTCGAGTTGAA
1 GGTCAATGCTCGAGTTGAA
39998050 GG
1 GG
39998052 CGATTTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.24, C:0.12, G:0.32, T:0.32
Consensus pattern (19 bp):
GGTCAATGCTCGAGTTGAA
Found at i:40008657 original size:14 final size:14
Alignment explanation
Indices: 40008639--40008668 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
40008629 AATATTCTTC
40008639 TAAAAATAGTT-AT
1 TAAAAATAGTTAAT
40008652 TAAAAATAGTTAAT
1 TAAAAATAGTTAAT
40008666 TAA
1 TAA
40008669 TTTTAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (14 bp):
TAAAAATAGTTAAT
Found at i:40008777 original size:18 final size:18
Alignment explanation
Indices: 40008743--40008777 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40008733 TTAGAGTTTA
* *
40008743 TATCTAAATTTATTTAAT
1 TATCTAAATTAAATTAAT
40008761 TATCTAAATTAAATTAA
1 TATCTAAATTAAATTAA
40008778 ACTACGATGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (18 bp):
TATCTAAATTAAATTAAT
Found at i:40011617 original size:22 final size:21
Alignment explanation
Indices: 40011592--40011634 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
40011582 GAGACTAATT
40011592 TAAAACAATTCAAAAA-TTTTGA
1 TAAAA-AATT-AAAAACTTTTGA
*
40011614 TAAAAAGTTAAAAACTTTTGA
1 TAAAAAATTAAAAACTTTTGA
40011635 AAACATGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (21 bp):
TAAAAAATTAAAAACTTTTGA
Found at i:40016354 original size:91 final size:92
Alignment explanation
Indices: 40016239--40016467 Score: 302
Period size: 92 Copynumber: 2.5 Consensus size: 92
40016229 TAATATTAGT
* *
40016239 TGTGATATTAAATTAGCGAGCTATTTGGAGTAACGATAGTAAATCAGCTAACTCA-AAGATT-TT
1 TGTGATCTTAAATTAGCGAGCTATTTGGAGTAACGATAGAAAATCAGCTAACTCAGAAGATTATT
40016302 TCATGATAGTAAATCAATGAACTTAGGC
66 T-ATGATAGTAAATCAATGAACTTAGGC
* * * * *
40016330 TGTGATCTTAAATCAGCGAGCTATTCGGAGTAACGGA-AGAAAATCAGTTGACTTAGAAGATTAT
1 TGTGATCTTAAATTAGCGAGCTATTTGGAGTAAC-GATAGAAAATCAGCTAACTCAGAAGATTAT
*
40016394 TTATGATAGTAAATCAATGAACTTAGGT
65 TTATGATAGTAAATCAATGAACTTAGGC
* * * * *
40016422 TGTGATCTTAAATTAGTGAACTGTTTGGAGTAGCGATACAAAATCA
1 TGTGATCTTAAATTAGCGAGCTATTTGGAGTAACGATAGAAAATCA
40016468 ATTGTTAGAT
Statistics
Matches: 119, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
91 47 0.39
92 69 0.58
93 3 0.03
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (92 bp):
TGTGATCTTAAATTAGCGAGCTATTTGGAGTAACGATAGAAAATCAGCTAACTCAGAAGATTATT
TATGATAGTAAATCAATGAACTTAGGC
Found at i:40024029 original size:13 final size:15
Alignment explanation
Indices: 40024011--40024042 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
40024001 GAAAGGGAAG
40024011 GAGAAGAA-AAGAA-
1 GAGAAGAAGAAGAAT
40024024 GAGAAGAAGAAGAAT
1 GAGAAGAAGAAGAAT
40024039 GAGA
1 GAGA
40024043 GGGTGGGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 5 0.29
15 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.34, T:0.03
Consensus pattern (15 bp):
GAGAAGAAGAAGAAT
Found at i:40024057 original size:5 final size:5
Alignment explanation
Indices: 40024047--40024076 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
40024037 ATGAGAGGGT
40024047 GGGAA GGGAA GGGAA GGGAA GGGAA GGGAA
1 GGGAA GGGAA GGGAA GGGAA GGGAA GGGAA
40024077 AAAGAAAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (5 bp):
GGGAA
Found at i:40024460 original size:16 final size:17
Alignment explanation
Indices: 40024439--40024473 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
40024429 GTTATTTTGA
40024439 TTATTTTAATATT-TTT
1 TTATTTTAATATTGTTT
40024455 TTATTTTAATATTGTTT
1 TTATTTTAATATTGTTT
40024472 TT
1 TT
40024474 TATAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TTATTTTAATATTGTTT
Found at i:40027222 original size:64 final size:62
Alignment explanation
Indices: 40027153--40027322 Score: 159
Period size: 62 Copynumber: 2.7 Consensus size: 62
40027143 ATTAATTGCA
* *
40027153 ACATTAGAACATTAAAACACT-AAAACAACA-T-TAATATAAATTTTATTTGTAATATAAATTAA
1 ACATTACAACATTAAAA-ACTGAAAACAACATTGTAATATAAA---T-TGTGTAATATAAATTAA
40027215 AT
61 AT
* * * * * *
40027217 ACATTACATCACTAAAAATTGGAACCAACATTGTAATATAAATTGTGTTATATAAATTAAAT
1 ACATTACAACATTAAAAACTGAAAACAACATTGTAATATAAATTGTGTAATATAAATTAAAT
* * *
40027279 ACATTACAACATTAAAAATTG-GAACAAACTTTGTAATATAAATT
1 ACATTACAACATTAAAAACTGAAAAC-AACATTGTAATATAAATT
40027323 AGGTACATTG
Statistics
Matches: 89, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
61 2 0.02
62 53 0.60
63 3 0.03
64 21 0.24
65 1 0.01
66 9 0.10
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.34
Consensus pattern (62 bp):
ACATTACAACATTAAAAACTGAAAACAACATTGTAATATAAATTGTGTAATATAAATTAAAT
Found at i:40027283 original size:62 final size:62
Alignment explanation
Indices: 40027204--40027322 Score: 202
Period size: 62 Copynumber: 1.9 Consensus size: 62
40027194 TTTATTTGTA
* *
40027204 ATATAAATTAAATACATTACATCACTAAAAATTGGAACCAACATTGTAATATAAATTGTGTT
1 ATATAAATTAAATACATTACAACACTAAAAATTGGAACAAACATTGTAATATAAATTGTGTT
* *
40027266 ATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATT
1 ATATAAATTAAATACATTACAACACTAAAAATTGGAACAAACATTGTAATATAAATT
40027323 AGGTACATTG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.34
Consensus pattern (62 bp):
ATATAAATTAAATACATTACAACACTAAAAATTGGAACAAACATTGTAATATAAATTGTGTT
Found at i:40030585 original size:27 final size:27
Alignment explanation
Indices: 40030554--40030628 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 27
40030544 CTAGGTGTGT
40030554 CGCCTATCAAATAGGCACCACTAGTGC
1 CGCCTATCAAATAGGCACCACTAGTGC
* *** *
40030581 CGCCTATCAGATAGGGGTCACTGGTGC
1 CGCCTATCAAATAGGCACCACTAGTGC
* * *
40030608 CACCTATCAAGTAGACACCAC
1 CGCCTATCAAATAGGCACCAC
40030629 ACCCCCTTCG
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.28, C:0.32, G:0.21, T:0.19
Consensus pattern (27 bp):
CGCCTATCAAATAGGCACCACTAGTGC
Found at i:40031799 original size:17 final size:17
Alignment explanation
Indices: 40031772--40031806 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40031762 ATAAAATAAG
40031772 ATTTTTATTATT-TTTA
1 ATTTTTATTATTATTTA
40031788 ATTTTATATTATTATTTA
1 ATTTT-TATTATTATTTA
40031806 A
1 A
40031807 AGACTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 7 0.41
18 5 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTATTATTATTTA
Done.