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 199 of 203
Found at i:63592055 original size:38 final size:40
Alignment explanation
Indices: 63591983--63592059 Score: 113
Period size: 38 Copynumber: 1.9 Consensus size: 40
63591973 AAATTAAATC
63591983 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTACAAAATCATA--TTCTAAGATTGCATATCATA
*
63592025 TCTAAGATTAC-ATATCATA-TCTAAGATTGCATATC
1 TCTAAGATTACAAAATCATATTCTAAGATTGCATATC
63592060 CTTGAAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 16 0.47
41 7 0.21
42 11 0.32
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (40 bp):
TCTAAGATTACAAAATCATATTCTAAGATTGCATATCATA
Found at i:63592666 original size:45 final size:45
Alignment explanation
Indices: 63592609--63593161 Score: 282
Period size: 45 Copynumber: 12.7 Consensus size: 45
63592599 TTGTTTATTT
* * * * *
63592609 AGTCTGCCCCACTGCAATTTTAGGGGGATAAGACTTGATTTCTTG
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
* *
63592654 AGTCTGCTCCACTGCACCTTCAGGGAGATAAGACTCGCTTTCTTG
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
* * *
63592699 GGTCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGA--T-GTG
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
* * ** *
63592741 A-TCTACT-CTCTGCAACTTCAAAGAGATAAGATCTGTGA-TT-TT-
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-CGATTTCTTG
* ** * * * *
63592783 AATCCACTCCACTGCAACTTAAGGGAGATAAGA-T-TATTGGCTTTC
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATT-TC-TTG
* * *** *
63592828 A-TCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCCATCTTC
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
* * * * *
63592872 AGTCTGC-CTCACTACAACTTCA-GGAGGATAAGGCTTGCTTACTT-
1 AGTCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTCGATTTCTTG
* * * *
63592916 AGTTTGCTCCACTGCAACTTTAGGGAGATAAGACTAGA-TGC--G
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
* * * *
63592958 A-TCTG-TTCTCTGCAACTTCAGAGAGATAAGATCTGTGA-TT-TT-
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-CGATTTCTTG
* * * * * * *
63593000 AATCCGCTCTACTGCGACTTCAGGGAGATAAGA-T-TATTGGCTTT
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATT-TCTTG
* * * *
63593044 AATCTGCTCCACTGCATCTTTAGGGAGATAAGACTCGCTTTCTTG
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
* * * * * *
63593089 GGTCTACTCCACTGCAACTTCATGGAGATAAAACCCGA-TGC--G
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
* *
63593131 A-TCTGCT-CTCTGCAACTTCAGAGAGATAAGA
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
63593162 TCTGTGATTT
Statistics
Matches: 387, Mismatches: 91, Indels: 65
0.71 0.17 0.12
Matches are distributed among these distances:
40 65 0.17
41 18 0.05
42 13 0.03
43 15 0.04
44 134 0.35
45 140 0.36
46 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.29
Consensus pattern (45 bp):
AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
Found at i:63592837 original size:44 final size:44
Alignment explanation
Indices: 63592606--63593248 Score: 184
Period size: 44 Copynumber: 14.8 Consensus size: 44
63592596 GGTTTGTTTA
* * * * * *
63592606 TTTAGTCTGCCCCACTGCAATTTTAGGGGGATAAGACTTGATT-TC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TT-ATTGGC
* * * ** *
63592651 TTGAGTCTGCTCCACTGCACCTTCAGGGAGATAAGACTCGCTT-TC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-T-TATTGGC
*** *** *
63592696 TTGGGTCTGCTCCACTGCAACTTCAGGGAGATAAG---ACCCGA
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATTGGC
* * * * ** * **
63592737 TGTGATCTACT-CTCTGCAACTTCAAAGAGATAAGATCT-GTGAT
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TATTGGC
** *
63592780 TTTAATCCACTCCACTGCAACTTAAGGGAGATAAGATTATTGGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATTGGC
* * * *
63592824 TTTCATCTGCTCCACTGCAACTTCAGGGAAATAAGA-T-TCGCC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATTGGC
* * * * *
63592866 ATCTTCAGTCTGC-CTCACTACAACTTCA-GGAGGATAAGGCTTGCTT-AC
1 -T-TT-AATCTGCTC-CACTGCAACTTCAGGGA-GATAA-GATT-ATTGGC
* * * * *
63592914 -TTAGTTTGCTCCACTGCAACTTTAGGGAGATAAGACTAGAT-GC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTA-TTGGC
* * * * * **
63592957 ---GATCTG-TTCTCTGCAACTTCAGAGAGATAAGATCT-GTGAT
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TATTGGC
* * *
63592997 TTTAATCCGCTCTACTGCGACTTCAGGGAGATAAGATTATTGGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATTGGC
* * ** *
63593041 TTTAATCTGCTCCACTGCATCTTTAGGGAGATAAGACTCGCTT-TC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-T-TATTGGC
*** * * *** *
63593086 TTGGGTCTACTCCACTGCAACTTCATGGAGATAA-A--ACCCGA
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATTGGC
*** * * * **
63593127 TGCGATCTGCT-CTCTGCAACTTCAGAGAGATAAGATCT-GTGAT
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TATTGGC
** * * **
63593170 TTTAATCCACTCCACTGCAACTTTAGGGAGATAGGATTATTAAC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATTGGC
* * *
63593214 TTTAATCTGTTCCATTGTAACTTCAGGGAGATAAG
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
63593249 GTTCGCCATC
Statistics
Matches: 431, Mismatches: 131, Indels: 73
0.68 0.21 0.11
Matches are distributed among these distances:
39 1 0.00
40 61 0.14
41 19 0.04
42 3 0.01
43 27 0.06
44 189 0.44
45 125 0.29
46 3 0.01
47 1 0.00
48 1 0.00
49 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (44 bp):
TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATTGGC
Found at i:63593025 original size:84 final size:84
Alignment explanation
Indices: 63592922--63593202 Score: 264
Period size: 84 Copynumber: 3.3 Consensus size: 84
63592912 ACTTAGTTTG
*
63592922 CTCCACTGCAACTTTAGGGAGATAAGACTAGATGCGATCTGTTCTCTGCAACTTCAGAGAGATAA
1 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGTTCTCTGCAACTTCAGAGAGATAA
*
63592987 GATCTGTGATTTTAATCCG
66 GATCTGTGATTTTAATCCA
* * * * * * * * * *
63593006 CTCTACTGCGACTTCAGGGAGATAAGATTA-TTGGCTTTAATCTGCTCCACTGCATCTTTAGGGA
1 CTCCACTGCAACTTCAGGGAGATAAGACTAGAT-GC---GATCTG-TTCTCTGCAACTTCAGAGA
** *
63593070 GATAAGA-CTCGCT--TTCTTGGGTCTA
61 GATAAGATCT-G-TGATT-TT-AATCCA
* * ** *
63593095 CTCCACTGCAACTTCATGGAGATAAAACCCGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
1 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGTTCTCTGCAACTTCAGAGAGATAA
63593160 GATCTGTGATTTTAATCCA
66 GATCTGTGATTTTAATCCA
*
63593179 CTCCACTGCAACTTTAGGGAGATA
1 CTCCACTGCAACTTCAGGGAGATA
63593203 GGATTATTAA
Statistics
Matches: 149, Mismatches: 35, Indels: 26
0.71 0.17 0.12
Matches are distributed among these distances:
83 1 0.01
84 54 0.36
85 23 0.15
86 9 0.06
87 9 0.06
88 24 0.16
89 28 0.19
90 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (84 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGTTCTCTGCAACTTCAGAGAGATAA
GATCTGTGATTTTAATCCA
Found at i:63593101 original size:173 final size:173
Alignment explanation
Indices: 63592833--63593248 Score: 496
Period size: 173 Copynumber: 2.4 Consensus size: 173
63592823 CTTTCATCTG
* *** * * * *
63592833 CTCCACTGCAACTTCAGGGAAATAAGATTCGCCATCTTCAGTCTGC-CTCACTACAACTTCA-GG
1 CTCCACTGCAACTTCAGGGAGATAAGATT-ATTAACTTTAATCTGCTC-CACTGCAACTTCAGGG
* * * * * * * * *
63592896 AGGATAAGGCTTGCTTACTT-AGTTTGCTCCACTGCAACTTTAGGGAGATAAGACTAGATGCGAT
64 A-GATAAGACTCGCTTTCTTGGGTCTACTCCACTGCAACTTCAGGGAGATAAAACCAGATGCGAT
* *
63592960 CTGTTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCG
128 CTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCA
* * ** * *
63593006 CTCTACTGCGACTTCAGGGAGATAAGATTATTGGCTTTAATCTGCTCCACTGCATCTTTAGGGAG
1 CTCCACTGCAACTTCAGGGAGATAAGATTATTAACTTTAATCTGCTCCACTGCAACTTCAGGGAG
* *
63593071 ATAAGACTCGCTTTCTTGGGTCTACTCCACTGCAACTTCATGGAGATAAAACCCGATGCGATCTG
66 ATAAGACTCGCTTTCTTGGGTCTACTCCACTGCAACTTCAGGGAGATAAAACCAGATGCGATCTG
63593136 CTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCA
131 CTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCA
* * * * *
63593179 CTCCACTGCAACTTTAGGGAGATAGGATTATTAACTTTAATCTGTTCCATTGTAACTTCAGGGAG
1 CTCCACTGCAACTTCAGGGAGATAAGATTATTAACTTTAATCTGCTCCACTGCAACTTCAGGGAG
63593244 ATAAG
66 ATAAG
63593249 GTTCGCCATC
Statistics
Matches: 203, Mismatches: 37, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
172 34 0.17
173 169 0.83
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (173 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTATTAACTTTAATCTGCTCCACTGCAACTTCAGGGAG
ATAAGACTCGCTTTCTTGGGTCTACTCCACTGCAACTTCAGGGAGATAAAACCAGATGCGATCTG
CTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCA
Found at i:63593109 original size:217 final size:218
Alignment explanation
Indices: 63592606--63593119 Score: 660
Period size: 217 Copynumber: 2.4 Consensus size: 218
63592596 GGTTTGTTTA
* * * * *
63592606 TTTAGTCTGCCCCACTGCAAT-TTTAGGGGGATAAGACTTGATTTCTTGAGTCTGCTCCACTGCA
1 TTTAATCTGCTCCACTGC-ATCTTTAGGGAGATAAGACTCGCTTTCTTGAGTCTGCTCCACTGCA
* * *
63592670 CCTTCAGG-GAGATAAGACTCGCTTTCTTGGGTCTGCTCCACTGCAACTTCAGGGAGATAAGACC
65 ACTTCAGGAG-GATAAGACTCGCTTACTTGAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACC
* *
63592734 CGATGTGATCTACTCTCTGCAACTTCAAAGAGATAAGATCTGTGATTTTAATCCACTCCACTGCA
129 AGATGCGATCTACTCTCTGCAACTTCAAAGAGATAAGATCTGTGATTTTAATCCACTCCACTGCA
63592799 ACTTAAGGGAGATAAGATTATTGGC
194 ACTTAAGGGAGATAAGATTATTGGC
* * * * * ** * *
63592824 TTTCATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCCATCTTCAGTCTGC-CTCACTACA
1 TTTAATCTGCTCCACTGCATCTTTAGGGAGATAAGACTCGCTTTCTTGAGTCTGCTC-CACTGCA
* * * * *
63592888 ACTTCAGGAGGATAAGGCTTGCTTACTT-AGTTTGCTCCACTGCAACTTTAGGGAGATAAGACTA
65 ACTTCAGGAGGATAAGACTCGCTTACTTGAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACCA
** * * * *
63592952 GATGCGATCTGTTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCTACTGCGA
130 GATGCGATCTACTCTCTGCAACTTCAAAGAGATAAGATCTGTGATTTTAATCCACTCCACTGCAA
*
63593017 CTTCAGGGAGATAAGATTATTGGC
195 CTTAAGGGAGATAAGATTATTGGC
* *
63593041 TTTAATCTGCTCCACTGCATCTTTAGGGAGATAAGACTCGCTTTCTTGGGTCTACTCCACTGCAA
1 TTTAATCTGCTCCACTGCATCTTTAGGGAGATAAGACTCGCTTTCTTGAGTCTGCTCCACTGCAA
63593106 CTTCATGGA-GATAA
66 CTTCA-GGAGGATAA
63593120 AACCCGATGC
Statistics
Matches: 249, Mismatches: 42, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
217 176 0.71
218 72 0.29
219 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (218 bp):
TTTAATCTGCTCCACTGCATCTTTAGGGAGATAAGACTCGCTTTCTTGAGTCTGCTCCACTGCAA
CTTCAGGAGGATAAGACTCGCTTACTTGAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACCAG
ATGCGATCTACTCTCTGCAACTTCAAAGAGATAAGATCTGTGATTTTAATCCACTCCACTGCAAC
TTAAGGGAGATAAGATTATTGGC
Found at i:63593450 original size:43 final size:42
Alignment explanation
Indices: 63593398--63593537 Score: 120
Period size: 43 Copynumber: 3.2 Consensus size: 42
63593388 ATTTTTAACT
63593398 TGCTTCGCTGCAACCTAGGGAGGCAAGGCTAGTGTCTTCGATC
1 TGCTTCGCTGCAACCTAGGGAGGCAAGGCT-GTGTCTTCGATC
* ** * * * * ** *
63593441 TGCTTCGCTG-TAGGTACAGGAGGCAAGATCTGCTATTTTTAACC
1 TGCTTCGCTGCAACCTA-GGGAGGCAAG-GCTG-TGTCTTCGATC
* *
63593485 TGCTTCGTTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATC
1 TGCTTCGCTGCAACCTAGGGAGGCAAGGCT-GTGTCTTCGATC
63593528 TGCTTCGCTG
1 TGCTTCGCTG
63593538 TCGGTGTAGG
Statistics
Matches: 69, Mismatches: 23, Indels: 10
0.68 0.23 0.10
Matches are distributed among these distances:
42 3 0.04
43 37 0.54
44 27 0.39
45 2 0.03
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (42 bp):
TGCTTCGCTGCAACCTAGGGAGGCAAGGCTGTGTCTTCGATC
Found at i:63593591 original size:88 final size:88
Alignment explanation
Indices: 63593336--63593638 Score: 482
Period size: 88 Copynumber: 3.5 Consensus size: 88
63593326 AGGGAGATAG
* * *
63593336 GGCTGGGGTCATCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACTTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* *
63593401 TTCGCTGCAACCTAGGGAGGCAA
66 TTCGTTGCAACCCAGGGAGGCAA
* * *
63593424 GGCTAGTGTCTTCGATCTGCTTCGCTGTAGGTACAGG-AGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
63593488 TTCGTTGCAACCCAGGGAGGCAA
66 TTCGTTGCAACCCAGGGAGGCAA
*
63593511 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* * *
63593576 TCCGTTACAACCCAGGTAGGCAA
66 TTCGTTGCAACCCAGGGAGGCAA
*
63593599 GGTTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAG
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAG
63593639 AATCTTTTCC
Statistics
Matches: 197, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
87 80 0.41
88 117 0.59
ACGTcount: A:0.18, C:0.23, G:0.30, T:0.29
Consensus pattern (88 bp):
GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
TTCGTTGCAACCCAGGGAGGCAA
Found at i:63595289 original size:14 final size:15
Alignment explanation
Indices: 63595266--63595298 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
63595256 ATCGACGCTT
63595266 TTCCAAATAAGG-CC
1 TTCCAAATAAGGACC
*
63595280 TTCCACATAAGGACC
1 TTCCAAATAAGGACC
63595295 TTCC
1 TTCC
63595299 CAGCTTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.30, C:0.33, G:0.12, T:0.24
Consensus pattern (15 bp):
TTCCAAATAAGGACC
Found at i:63600835 original size:19 final size:19
Alignment explanation
Indices: 63600811--63600883 Score: 128
Period size: 19 Copynumber: 3.8 Consensus size: 19
63600801 AATCATATAT
63600811 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
63600830 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
*
63600849 TCTAAGATTGCGTATCATA
1 TCTAAGATTGCATATCATA
63600868 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
63600884 CTTGAAGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:63600865 original size:38 final size:40
Alignment explanation
Indices: 63600788--63600883 Score: 133
Period size: 38 Copynumber: 2.4 Consensus size: 40
63600778 AAATTAAATC
*
63600788 TCTAAGATTACAAAATCATATATTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATCA-ATATTCTAAGATTGCATATCATA
*
63600830 TCTAAGATTACATATC-ATA-TCTAAGATTGCGTATCATA
1 TCTAAGATTACATATCAATATTCTAAGATTGCATATCATA
*
63600868 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
63600884 CTTGAAGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
38 33 0.65
39 3 0.06
41 4 0.08
42 11 0.22
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (40 bp):
TCTAAGATTACATATCAATATTCTAAGATTGCATATCATA
Found at i:63600867 original size:24 final size:19
Alignment explanation
Indices: 63600788--63600883 Score: 111
Period size: 19 Copynumber: 4.8 Consensus size: 19
63600778 AAATTAAATC
*
63600788 TCTAAGATTACAAAATCATATA
1 TCTAAGATTAC-ATATC--ATA
*
63600810 TTCTAAGATTGCATATCATA
1 -TCTAAGATTACATATCATA
63600830 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
* *
63600849 TCTAAGATTGCGTATCATA
1 TCTAAGATTACATATCATA
*
63600868 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
63600884 CTTGAAGATT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
19 50 0.75
20 3 0.04
22 4 0.06
23 10 0.15
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:63601337 original size:26 final size:26
Alignment explanation
Indices: 63601274--63601342 Score: 93
Period size: 26 Copynumber: 2.7 Consensus size: 26
63601264 ACATATACTG
* * *
63601274 TTACTGGCAACTTTGCTGCGTTATTG
1 TTACTGGCAGCTTTGCTGCGTCATTA
63601300 TTACTGGCAGCTTTGCTGCGTCATTA
1 TTACTGGCAGCTTTGCTGCGTCATTA
* *
63601326 TTATTGGTAGCTTTGCT
1 TTACTGGCAGCTTTGCT
63601343 ACGATATTGG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.14, C:0.19, G:0.23, T:0.43
Consensus pattern (26 bp):
TTACTGGCAGCTTTGCTGCGTCATTA
Found at i:63601496 original size:28 final size:28
Alignment explanation
Indices: 63601456--63601510 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
63601446 ATTGTATTGA
*
63601456 TTACTGTATTGGGCTAAGGCCCACACTG
1 TTACTGTAATGGGCTAAGGCCCACACTG
*
63601484 TTACTGTAATGGGCTAAGGCCTACACT
1 TTACTGTAATGGGCTAAGGCCCACACT
63601511 ATATTGATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (28 bp):
TTACTGTAATGGGCTAAGGCCCACACTG
Found at i:63605897 original size:9 final size:9
Alignment explanation
Indices: 63605869--63605936 Score: 57
Period size: 9 Copynumber: 7.3 Consensus size: 9
63605859 AATTTTTTTT
63605869 TAAATTAT-
1 TAAATTATG
63605877 TCAAAGTTATG
1 T-AAA-TTATG
63605888 TAAATTATG
1 TAAATTATG
*
63605897 TAAGTTATG
1 TAAATTATG
* *
63605906 CAAGTTATG
1 TAAATTATG
* *
63605915 TAAATTCTT
1 TAAATTATG
63605924 TAAAGTTATG
1 TAAA-TTATG
63605934 TAA
1 TAA
63605937 GTTTGGATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
8 1 0.02
9 33 0.69
10 13 0.27
11 1 0.02
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.43
Consensus pattern (9 bp):
TAAATTATG
Found at i:63605912 original size:27 final size:28
Alignment explanation
Indices: 63605880--63605939 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 28
63605870 AAATTATTCA
63605880 AAGTTATGTAAATTATGT-AAGTTATGC
1 AAGTTATGTAAATTATGTAAAGTTATGC
* * *
63605907 AAGTTATGTAAATTCTTTAAAGTTATGT
1 AAGTTATGTAAATTATGTAAAGTTATGC
63605935 AAGTT
1 AAGTT
63605940 TGGATTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 16 0.55
28 13 0.45
ACGTcount: A:0.37, C:0.03, G:0.17, T:0.43
Consensus pattern (28 bp):
AAGTTATGTAAATTATGTAAAGTTATGC
Found at i:63605938 original size:9 final size:9
Alignment explanation
Indices: 63605880--63605939 Score: 66
Period size: 9 Copynumber: 6.6 Consensus size: 9
63605870 AAATTATTCA
63605880 AAGTTATGT
1 AAGTTATGT
*
63605889 AAATTATGT
1 AAGTTATGT
*
63605898 AAGTTATGC
1 AAGTTATGT
63605907 AAGTTATGT
1 AAGTTATGT
* * *
63605916 AAATTCTTT
1 AAGTTATGT
63605925 AAAGTTATGT
1 -AAGTTATGT
63605935 AAGTT
1 AAGTT
63605940 TGGATTTTTA
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
9 34 0.85
10 6 0.15
ACGTcount: A:0.37, C:0.03, G:0.17, T:0.43
Consensus pattern (9 bp):
AAGTTATGT
Found at i:63606964 original size:41 final size:41
Alignment explanation
Indices: 63606904--63606989 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 41
63606894 TTTGTGGCGA
63606904 TTTTTTCAAAAACGCCACTA-TTGCTTACCTTTTGCGATGT
1 TTTTTTCAAAAACGCCACTATTTGCTTACCTTTTGCGATGT
* * *
63606944 TTTTTTCCAAAAATGTCACTATTTGCTTACCTTTTGCGGTGT
1 TTTTTT-CAAAAACGCCACTATTTGCTTACCTTTTGCGATGT
63606986 TTTT
1 TTTT
63606990 ATCATAAATG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 6 0.15
41 12 0.29
42 23 0.56
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.48
Consensus pattern (41 bp):
TTTTTTCAAAAACGCCACTATTTGCTTACCTTTTGCGATGT
Found at i:63607840 original size:14 final size:14
Alignment explanation
Indices: 63607798--63607855 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 14
63607788 AACCCAAACC
*
63607798 AAACACTAAAC-CAT
1 AAACTCTAAACAC-T
63607812 AAAC-CTACAAC-CT
1 AAACTCTA-AACACT
*
63607825 AAACTGTAAACACT
1 AAACTCTAAACACT
*
63607839 AAACTCTAAACATT
1 AAACTCTAAACACT
63607853 AAA
1 AAA
63607856 TTATTTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
13 11 0.29
14 27 0.71
ACGTcount: A:0.53, C:0.26, G:0.02, T:0.19
Consensus pattern (14 bp):
AAACTCTAAACACT
Found at i:63607848 original size:21 final size:20
Alignment explanation
Indices: 63607811--63607849 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
63607801 CACTAAACCA
63607811 TAAACCTACAACCTAAACTG
1 TAAACCTACAACCTAAACTG
63607831 TAAACACTA-AACTCTAAAC
1 TAAAC-CTACAAC-CTAAAC
63607850 ATTAAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.49, C:0.28, G:0.03, T:0.21
Consensus pattern (20 bp):
TAAACCTACAACCTAAACTG
Found at i:63608169 original size:39 final size:40
Alignment explanation
Indices: 63608126--63608205 Score: 117
Period size: 39 Copynumber: 2.0 Consensus size: 40
63608116 CGCTCTAAAT
*
63608126 CTCGATCTATAGCGGCGTTTTTCA-AAAGCCCCGCTAATG
1 CTCGATATATAGCGGCGTTTTTCAGAAAGCCCCGCTAATG
* * *
63608165 CTCGATATATAGCGGTGTTTTTCAGGAAGCGCCGCTAATG
1 CTCGATATATAGCGGCGTTTTTCAGAAAGCCCCGCTAATG
63608205 C
1 C
63608206 CACAAAAGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 22 0.61
40 14 0.39
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.29
Consensus pattern (40 bp):
CTCGATATATAGCGGCGTTTTTCAGAAAGCCCCGCTAATG
Found at i:63608334 original size:40 final size:39
Alignment explanation
Indices: 63608264--63608385 Score: 124
Period size: 40 Copynumber: 3.1 Consensus size: 39
63608254 ATGATTGATA
* *
63608264 TATAGCGGCGTTTTT-AAAGAAGTGCTGCTAATGGTCGACC
1 TATAGCGGCGTTTTTCAAATACGT-C-GCTAATGGTCGACC
* *
63608304 TATAGCGGCGTTTTTCAAATAGCGTCGCTAACGGTCAACC
1 TATAGCGGCGTTTTTCAAATA-CGTCGCTAATGGTCGACC
* * *
63608344 TATAGCGAC-TTTTTCAAATACCGCCGCTAATGCTCGA-C
1 TATAGCGGCGTTTTTCAAATA-CGTCGCTAATGGTCGACC
63608382 TATA
1 TATA
63608386 TCAACGTTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
38 5 0.07
39 23 0.33
40 35 0.50
41 5 0.07
42 2 0.03
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (39 bp):
TATAGCGGCGTTTTTCAAATACGTCGCTAATGGTCGACC
Found at i:63608710 original size:20 final size:20
Alignment explanation
Indices: 63608687--63608724 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
63608677 TTTATATATT
*
63608687 TTTTAGAATTTTTTTAATAA
1 TTTTAGAAGTTTTTTAATAA
*
63608707 TTTTTGAAGTTTTTTAAT
1 TTTTAGAAGTTTTTTAAT
63608725 TTTGCACTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (20 bp):
TTTTAGAAGTTTTTTAATAA
Found at i:63609451 original size:28 final size:27
Alignment explanation
Indices: 63609399--63609467 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 27
63609389 AAAAGTTAAT
*
63609399 AAAAAAAATTTTGGACCCCTTAAAAATTG
1 AAAAAAAA--TTGAACCCCTTAAAAATTG
*
63609428 AAAAACAATTGAACCCCTTAAAAAATTG
1 AAAAAAAATTGAACCCCTT-AAAAATTG
63609456 AAAAAAAATTGA
1 AAAAAAAATTGA
63609468 CCTCTTTCAG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 10 0.28
28 19 0.53
29 7 0.19
ACGTcount: A:0.55, C:0.13, G:0.09, T:0.23
Consensus pattern (27 bp):
AAAAAAAATTGAACCCCTTAAAAATTG
Found at i:63614427 original size:9 final size:10
Alignment explanation
Indices: 63614402--63614434 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
63614392 ATTTATAAAT
63614402 AATAGAAAAA
1 AATAGAAAAA
*
63614412 AATAGAAAAG
1 AATAGAAAAA
63614422 AA-AGAAAAA
1 AATAGAAAAA
63614431 AATA
1 AATA
63614435 CTCAGAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (10 bp):
AATAGAAAAA
Found at i:63616227 original size:18 final size:18
Alignment explanation
Indices: 63616172--63616227 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 18
63616162 AATTTTAATG
*
63616172 AAAAATT-TAAAAAATAT
1 AAAAATTATAAAAATTAT
63616189 AAAAATCGTA-AAAATATTAT
1 AAAAAT--TATAAAA-ATTAT
63616209 AAAAATTATAAAAATTAT
1 AAAAATTATAAAAATTAT
63616227 A
1 A
63616228 GAACTATAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
17 6 0.18
18 8 0.24
19 9 0.27
20 10 0.30
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAAATTATAAAAATTAT
Found at i:63616321 original size:20 final size:20
Alignment explanation
Indices: 63616265--63616324 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
63616255 TTTTATAAAG
*
63616265 TCGTAACAAAACTATAAAAAA
1 TCGTAAAAAAACTAT-AAAAA
* *
63616286 T-GTAAAGAAA-TATAAAAT
1 TCGTAAAAAAACTATAAAAA
63616304 TCGTAAAAAAACTATAAAAA
1 TCGTAAAAAAACTATAAAAA
63616324 T
1 T
63616325 TATCGTACCA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 5 0.16
19 11 0.34
20 15 0.47
21 1 0.03
ACGTcount: A:0.62, C:0.08, G:0.07, T:0.23
Consensus pattern (20 bp):
TCGTAAAAAAACTATAAAAA
Found at i:63616562 original size:30 final size:31
Alignment explanation
Indices: 63616526--63616589 Score: 85
Period size: 32 Copynumber: 2.1 Consensus size: 31
63616516 TTTTTTATGA
*
63616526 TTTTATAAAATTTTAC-AATTTTTATATTTT
1 TTTTATAAAATTTTACAAAATTTTATATTTT
**
63616556 TTTTATAACTTTTTACTAAAATTTTATATTTT
1 TTTTATAAAATTTTAC-AAAATTTTATATTTT
63616588 TT
1 TT
63616590 ATAATTTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 14 0.48
32 15 0.52
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (31 bp):
TTTTATAAAATTTTACAAAATTTTATATTTT
Found at i:63616598 original size:11 final size:10
Alignment explanation
Indices: 63616514--63616598 Score: 52
Period size: 10 Copynumber: 8.7 Consensus size: 10
63616504 TGCATTATAC
63616514 AATTTTTTAT
1 AATTTTTTAT
*
63616524 GA--TTTTAT
1 AATTTTTTAT
** *
63616532 AAAATTTTAC
1 AATTTTTTAT
63616542 AA-TTTTTAT
1 AATTTTTTAT
*
63616551 ATTTTTTTTAT
1 A-ATTTTTTAT
*
63616562 AACTTTTTACT
1 AATTTTTTA-T
**
63616573 AAAATTTTAT
1 AATTTTTTAT
63616583 -ATTTTTTAT
1 AATTTTTTAT
63616592 AATTTTT
1 AATTTTT
63616599 GTTACATGTC
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
8 7 0.12
9 13 0.23
10 21 0.37
11 16 0.28
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.64
Consensus pattern (10 bp):
AATTTTTTAT
Found at i:63616996 original size:21 final size:20
Alignment explanation
Indices: 63616954--63616996 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
63616944 AGCGTACCAA
*
63616954 AAATTTAGATTTATTAAATT
1 AAATTTAGATTAATTAAATT
63616974 AAATTTATGATGTAATT-AATT
1 AAATTTA-GAT-TAATTAAATT
63616995 AA
1 AA
63616997 TCAAATCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 7 0.35
21 9 0.45
22 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (20 bp):
AAATTTAGATTAATTAAATT
Found at i:63617282 original size:16 final size:16
Alignment explanation
Indices: 63617261--63617304 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
63617251 TAACTTAAAA
63617261 TTAATATTTAATTTTT
1 TTAATATTTAATTTTT
* *
63617277 TTAATAATTAA-ATTT
1 TTAATATTTAATTTTT
63617292 TTAAT-TTTAATTT
1 TTAATATTTAATTT
63617305 ATCAAACATC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 4 0.17
15 9 0.39
16 10 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTAATATTTAATTTTT
Found at i:63617298 original size:24 final size:22
Alignment explanation
Indices: 63617255--63617299 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
63617245 TATTTATAAC
63617255 TTAAAATTAATATTTAATTTTT
1 TTAAAATTAATATTTAATTTTT
*
63617277 TTAATAATTAAATTTTTAATTTT
1 TTAA-AATT-AATATTTAATTTT
63617300 AATTTATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 4 0.20
24 12 0.60
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTAAAATTAATATTTAATTTTT
Found at i:63622002 original size:31 final size:31
Alignment explanation
Indices: 63621967--63622029 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
63621957 CTTATACGAG
63621967 AAAATTCTTTGTTTACTTTAAGTGTTCTTTT
1 AAAATTCTTTGTTTACTTTAAGTGTTCTTTT
*
63621998 AAAATTCTTTGTTTATTTTAAGTGTTCTTTT
1 AAAATTCTTTGTTTACTTTAAGTGTTCTTTT
63622029 A
1 A
63622030 TTTAATTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.24, C:0.08, G:0.10, T:0.59
Consensus pattern (31 bp):
AAAATTCTTTGTTTACTTTAAGTGTTCTTTT
Found at i:63623686 original size:25 final size:23
Alignment explanation
Indices: 63623652--63623698 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
63623642 ATCTCATCTG
63623652 TTAAGCTATTTTTATATAAAAAAAA
1 TTAAGCTA-TTTTAT-TAAAAAAAA
63623677 TTAAGCTATTTTATTAAAAAAA
1 TTAAGCTATTTTATTAAAAAAA
63623699 TTTCTATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 8 0.36
24 6 0.27
25 8 0.36
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (23 bp):
TTAAGCTATTTTATTAAAAAAAA
Found at i:63627686 original size:17 final size:17
Alignment explanation
Indices: 63627666--63627699 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
63627656 CCCGAACCCA
*
63627666 TTTTCCCCCCAAATTTT
1 TTTTCACCCCAAATTTT
*
63627683 TTTTGACCCCAAATTTT
1 TTTTCACCCCAAATTTT
63627700 ACTCTCCCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.29, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTTCACCCCAAATTTT
Found at i:63629341 original size:43 final size:43
Alignment explanation
Indices: 63629280--63629502 Score: 251
Period size: 43 Copynumber: 5.3 Consensus size: 43
63629270 TTTATAAGAA
* * * *
63629280 AAAAACGCTGCTAAAGGTCATGTTCTATAGCGGCATTTTTGGG
1 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCATTTGTGGG
* *
63629323 AAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCATTTGTGGG
* *
63629366 AAAAGCGCTGCTAAAGGTCATGTTC-TTAGCGGCATTTTTGGG
1 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCATTTGTGGG
* * * * *
63629408 AAAAGCCCCACTAAAGGTCATATTCTTTAGCGGCGTTTGTAGG
1 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCATTTGTGGG
* * * *
63629451 AAAAGTGTCACTAAAGGTCATGTTCTTT--C-G--TTTGTAGG
1 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCATTTGTGGG
63629489 AAAAGCGCCGCTAA
1 AAAAGCGCCGCTAA
63629503 CTGTAGCAAA
Statistics
Matches: 155, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
38 19 0.12
40 1 0.01
41 1 0.01
42 36 0.23
43 98 0.63
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCATTTGTGGG
Found at i:63629435 original size:85 final size:85
Alignment explanation
Indices: 63629280--63629477 Score: 301
Period size: 85 Copynumber: 2.3 Consensus size: 85
63629270 TTTATAAGAA
* * *
63629280 AAAAACGCTGCTAAAGGTCATGTTCTATAGCGGCATTTTTGGGAAAAGCGCCGCTAAAGGTCATG
1 AAAAGCGCTGCTAAAGGTCATGTTCT-TAGCGGCATTTTTGGGAAAAGCCCCACTAAAGGTCATG
*
63629345 ATCTTTAGCGGCGTTTGTGGG
65 ATCTTTAGCGGCGTTTGTAGG
63629366 AAAAGCGCTGCTAAAGGTCATGTTCTTAGCGGCATTTTTGGGAAAAGCCCCACTAAAGGTCAT-A
1 AAAAGCGCTGCTAAAGGTCATGTTCTTAGCGGCATTTTTGGGAAAAGCCCCACTAAAGGTCATGA
63629430 TTCTTTAGCGGCGTTTGTAGG
66 -TCTTTAGCGGCGTTTGTAGG
* *
63629451 AAAAGTG-TCACTAAAGGTCATGTTCTT
1 AAAAGCGCT-GCTAAAGGTCATGTTCTT
63629478 TCGTTTGTAG
Statistics
Matches: 104, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
84 2 0.02
85 77 0.74
86 25 0.24
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (85 bp):
AAAAGCGCTGCTAAAGGTCATGTTCTTAGCGGCATTTTTGGGAAAAGCCCCACTAAAGGTCATGA
TCTTTAGCGGCGTTTGTAGG
Found at i:63635447 original size:59 final size:59
Alignment explanation
Indices: 63635381--63635729 Score: 511
Period size: 59 Copynumber: 5.9 Consensus size: 59
63635371 TACGATAATC
** *
63635381 ATTATTATGAAATATGATTATTTGTTTAGTTAATCAAAAATTAATTAATTATTCATAAA
1 ATTATTATGAAATATGATTATTTAATTAATTAATCAAAAATTAATTAATTATTCATAAA
* *
63635440 ATTATTATGAAATATGATTATTTAATTAATTAATCAAAAATTAAATAAATATTCATAAA
1 ATTATTATGAAATATGATTATTTAATTAATTAATCAAAAATTAATTAATTATTCATAAA
* * * *
63635499 GTTATTATGAAATACGATTATTTAATTAATTAATCAAAAATTAAATAAATATTCATAAA
1 ATTATTATGAAATATGATTATTTAATTAATTAATCAAAAATTAATTAATTATTCATAAA
* * * * *
63635558 ATTATTATGAAATATGATTATTTATTTAATTAATCGATAATTAATT-ACTATTCATAGA
1 ATTATTATGAAATATGATTATTTAATTAATTAATCAAAAATTAATTAATTATTCATAAA
*
63635616 ATTATTATGAAATATGATTATTTAATTAATTAATCAAAAATTAATTGATTAATTATTCATAGA
1 ATTATTATGAAATATGATTATTTAATTAATTAATCAAAAATT-A---ATTAATTATTCATAAA
*
63635679 ATTATTATGAATTATGATTATTTAATTAATTAATCAAAAATTAATTAATTA
1 ATTATTATGAAATATGATTATTTAATTAATTAATCAAAAATTAATTAATTA
63635730 GGGTTCCAAA
Statistics
Matches: 265, Mismatches: 20, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
58 49 0.18
59 160 0.60
62 4 0.02
63 52 0.20
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (59 bp):
ATTATTATGAAATATGATTATTTAATTAATTAATCAAAAATTAATTAATTATTCATAAA
Found at i:63635907 original size:20 final size:20
Alignment explanation
Indices: 63635844--63635907 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
63635834 CGGTCAGCCT
* *
63635844 AAATATAAAATAAATCAAAAA
1 AAATATAAATTATAT-AAAAA
* *
63635865 ATATATAAATTCTATAAAAA
1 AAATATAAATTATATAAAAA
63635885 AAATATAAATTATA-AAAATA
1 AAATATAAATTATATAAAA-A
63635905 AAA
1 AAA
63635908 AAATAGTTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
19 4 0.11
20 21 0.58
21 11 0.31
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (20 bp):
AAATATAAATTATATAAAAA
Found at i:63637328 original size:25 final size:25
Alignment explanation
Indices: 63637251--63637333 Score: 123
Period size: 25 Copynumber: 3.3 Consensus size: 25
63637241 CTTACACGGC
*
63637251 GATGCAGCAGAGGGCTGCTGACGGA-
1 GATGCAGCAGAGGGCTGCCGAC-GAT
* *
63637276 GAGGCAACAGAGGGCTGCCGACGAT
1 GATGCAGCAGAGGGCTGCCGACGAT
63637301 GATGCAGCAGAGGGCTGCCGACGAT
1 GATGCAGCAGAGGGCTGCCGACGAT
63637326 GATGCAGC
1 GATGCAGC
63637334 TGACGTTGGG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
24 2 0.04
25 50 0.96
ACGTcount: A:0.25, C:0.23, G:0.41, T:0.11
Consensus pattern (25 bp):
GATGCAGCAGAGGGCTGCCGACGAT
Found at i:63637440 original size:62 final size:62
Alignment explanation
Indices: 63637339--63637458 Score: 170
Period size: 62 Copynumber: 1.9 Consensus size: 62
63637329 GCAGCTGACG
* * *
63637339 TTGGGGAAAAGAGTCAGGGATTTCGGGGAAGGGGGGAACTAATTTGGGGAAAAATAAAAGGAA
1 TTGGGAAAAAAAGTCAGGGATTTCGGGGAAGGGGAGAACTAATTTGGGG-AAAATAAAAGGAA
* * *
63637402 TTGGGAAAAAAAGTTAGGGATTT-TGGGAAGGGGAGAACTGATTTGGGGAAAATAAAA
1 TTGGGAAAAAAAGTCAGGGATTTCGGGGAAGGGGAGAACTAATTTGGGGAAAATAAAA
63637459 CGGGAAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
61 9 0.18
62 22 0.43
63 20 0.39
ACGTcount: A:0.39, C:0.03, G:0.38, T:0.20
Consensus pattern (62 bp):
TTGGGAAAAAAAGTCAGGGATTTCGGGGAAGGGGAGAACTAATTTGGGGAAAATAAAAGGAA
Found at i:63637595 original size:75 final size:74
Alignment explanation
Indices: 63637402--63637603 Score: 183
Period size: 75 Copynumber: 2.6 Consensus size: 74
63637392 ATAAAAGGAA
*
63637402 TTGGGAAAAAAAGTTAGGGATTTTGGGAAGGGGAGAACTGATTTGGGGAAAATAAAACGGGAAAA
1 TTGGG-AAAAAA-TTAGGGATTTTGGGAA-GGG-GAACTAATTTGGGGAAAATAAAACGGGAAAA
*
63637467 AAATAAAGGGATT
62 AAAGAAAGGGATT
* * * * * * ** *
63637480 TCT-GGATAAAATTAGGGATTTCGTGGAGGGGGAATTAATTTGGGGGAAATGAATTGGGGAAAAA
1 T-TGGGAAAAAATTAGGGATTTTG-GGAAGGGGAACTAATTTGGGGAAAATAAAACGGGAAAAAA
* *
63637544 GGGAAGGG-TT
64 AGAAAGGGATT
* *
63637554 TTGGGAAAAATACTTAGGGATTTTGGGAAGGGGAACAAATTTAGGGAAAA
1 TTGGGAAAAA-A-TTAGGGATTTTGGGAAGGGGAACTAATTTGGGGAAAA
63637604 CGACCAAGGC
Statistics
Matches: 99, Mismatches: 20, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
73 1 0.01
74 9 0.09
75 52 0.53
76 25 0.25
77 8 0.08
78 3 0.03
79 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.35, T:0.23
Consensus pattern (74 bp):
TTGGGAAAAAATTAGGGATTTTGGGAAGGGGAACTAATTTGGGGAAAATAAAACGGGAAAAAAAG
AAAGGGATT
Found at i:63644103 original size:12 final size:13
Alignment explanation
Indices: 63644086--63644114 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
63644076 CTCATACATG
63644086 AATAAATAAA-GC
1 AATAAATAAATGC
63644098 AATAAATAAATGC
1 AATAAATAAATGC
63644111 AATA
1 AATA
63644115 GTTATAGCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:63653586 original size:18 final size:16
Alignment explanation
Indices: 63653563--63653598 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
63653553 AAATGGCTTT
63653563 TAAAAGTATATTATAAAA
1 TAAAAGT-TATTA-AAAA
63653581 TAAAAGTTATTAAAAA
1 TAAAAGTTATTAAAAA
63653597 TA
1 TA
63653599 TATTATATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
TAAAAGTTATTAAAAA
Found at i:63658277 original size:18 final size:16
Alignment explanation
Indices: 63658254--63658289 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
63658244 AAATGGCTTT
63658254 TAAAAGTATATTATAAAA
1 TAAAAGT-TATTA-AAAA
63658272 TAAAAGTTATTAAAAA
1 TAAAAGTTATTAAAAA
63658288 TA
1 TA
63658290 TATTATATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
TAAAAGTTATTAAAAA
Found at i:63665387 original size:44 final size:41
Alignment explanation
Indices: 63665311--63665417 Score: 130
Period size: 44 Copynumber: 2.6 Consensus size: 41
63665301 TGTGACTTGG
* *
63665311 GTTGGTTT-GGGTTAGAAATTGATTCAGGAATCGATTAACAAA
1 GTTGGTTTAGGGTTAGAAATCGATTCAAGAATCGATTAAC--A
*
63665353 GTTGGTTTAGGGTTAGAATATCGATTCAATAATCGATTAACA
1 GTTGGTTTAGGGTTAGAA-ATCGATTCAAGAATCGATTAACA
*
63665395 --TGGTATAGGGTTAGAAATCGATT
1 GTTGGTTTAGGGTTAGAAATCGATT
63665418 GATCTTTTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
39 7 0.12
40 15 0.25
42 9 0.15
43 9 0.15
44 19 0.32
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.35
Consensus pattern (41 bp):
GTTGGTTTAGGGTTAGAAATCGATTCAAGAATCGATTAACA
Found at i:63665819 original size:48 final size:48
Alignment explanation
Indices: 63665744--63665867 Score: 203
Period size: 48 Copynumber: 2.6 Consensus size: 48
63665734 TTATTGTTTG
*** *
63665744 TATCAAACTGATGTTTATTGTTTGTATCTGTCATTGTATGAATGGCAT
1 TATCAAACTGATGTTTATTGTTTGTATCAACCATTGTATGAATGACAT
*
63665792 TATGAAACTGATGTTTATTGTTTGTATCAACCATTGTATGAATGACAT
1 TATCAAACTGATGTTTATTGTTTGTATCAACCATTGTATGAATGACAT
63665840 TATCAAACTGATGTTTATTGTTTGTATC
1 TATCAAACTGATGTTTATTGTTTGTATC
63665868 CTAGCTACTA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.45
Consensus pattern (48 bp):
TATCAAACTGATGTTTATTGTTTGTATCAACCATTGTATGAATGACAT
Found at i:63666105 original size:26 final size:26
Alignment explanation
Indices: 63666073--63666125 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
63666063 TTTGCCTATG
63666073 TTGTATTAAATGGTTTGGTTATTGTC
1 TTGTATTAAATGGTTTGGTTATTGTC
*
63666099 TTGTATTAAATGGTTTGGTTTTTGTC
1 TTGTATTAAATGGTTTGGTTATTGTC
63666125 T
1 T
63666126 ACCTTTATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.17, C:0.04, G:0.23, T:0.57
Consensus pattern (26 bp):
TTGTATTAAATGGTTTGGTTATTGTC
Found at i:63677306 original size:5 final size:5
Alignment explanation
Indices: 63677296--63677350 Score: 110
Period size: 5 Copynumber: 11.0 Consensus size: 5
63677286 TCATTATCAC
63677296 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
63677346 ATTAT
1 ATTAT
63677351 TATAACATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 50 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:63681954 original size:22 final size:22
Alignment explanation
Indices: 63681926--63681968 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
63681916 ATAAAATAAA
63681926 AGTAAAATTCC-CATAGAATTAT
1 AGTAAAA-TCCTCATAGAATTAT
*
63681948 AGTAAAATCCTTATAGAATTA
1 AGTAAAATCCTCATAGAATTA
63681969 AATTTCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.33
Consensus pattern (22 bp):
AGTAAAATCCTCATAGAATTAT
Found at i:63682229 original size:11 final size:12
Alignment explanation
Indices: 63682200--63682229 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
63682190 GTGTGTTCTT
63682200 TATTTTTATTTC
1 TATTTTTATTTC
63682212 TATTTTTATTTC
1 TATTTTTATTTC
63682224 TATTTT
1 TATTTT
63682230 CTTTGTGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.77
Consensus pattern (12 bp):
TATTTTTATTTC
Found at i:63684139 original size:68 final size:67
Alignment explanation
Indices: 63684065--63684263 Score: 209
Period size: 68 Copynumber: 3.0 Consensus size: 67
63684055 ATTTTAATAG
* * *
63684065 ATTTAATATTTAATTTAATTTAATAATTATCTTAATATTATTTTATTAATTTAATATTAAAGTGA
1 ATTTAATATTTAATTTAATTTAATATTTATCTTAATAATATTATATTAATTTAATATTAAAGTGA
63684130 TT
66 TT
* *
63684132 ATCTTAATATTTAATTTAATTTAATGTTTATCTTGTAGATTAATATTCTATTAATTT-A-A-T-A
1 AT-TTAATATTTAATTTAATTTAATATTTATC-T-TA-A-TAATATTATATTAATTTAATATTAA
63684193 A--G---
61 AGTGATT
* * *
63684195 ATTTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAATATTAAAGTG
1 ATTTAATATTTAATTTAATTTAATATTTATCTTAATAA-TATTATATTAATTTAATATTAAAGTG
63684260 ATT
65 ATT
63684263 A
1 A
63684264 AGTTTAATCA
Statistics
Matches: 108, Mismatches: 9, Indels: 29
0.74 0.06 0.20
Matches are distributed among these distances:
58 3 0.03
59 14 0.13
60 2 0.02
61 2 0.02
62 27 0.25
63 4 0.04
65 1 0.01
66 1 0.01
67 2 0.02
68 30 0.28
69 2 0.02
70 3 0.03
71 2 0.02
72 15 0.14
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (67 bp):
ATTTAATATTTAATTTAATTTAATATTTATCTTAATAATATTATATTAATTTAATATTAAAGTGA
TT
Found at i:63684210 original size:62 final size:59
Alignment explanation
Indices: 63684135--63684251 Score: 155
Period size: 62 Copynumber: 1.9 Consensus size: 59
63684125 AGTGATTATC
* * * *
63684135 TTAATATTTAATTTAATTTAATGTTTATCTTGTAGATTAA-TATTCTATTAATTTAATAAGAT
1 TTAATATTAAATTTAATCTAATATTTATC-T-T-GA-TAAGTATTATATTAATTTAATAAGAT
63684197 TTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAATA
63684252 TTAAAGTGAT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
58 3 0.06
59 19 0.38
60 1 0.02
61 1 0.02
62 26 0.52
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.52
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAATAAGAT
Found at i:63686371 original size:14 final size:13
Alignment explanation
Indices: 63686348--63686389 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
63686338 TAATATTTGA
63686348 TTTATTATTTTAT
1 TTTATTATTTTAT
63686361 TTTAGTTA-TTTAT
1 TTTA-TTATTTTAT
*
63686374 TTTAATTGTTTTAT
1 TTT-ATTATTTTAT
63686388 TT
1 TT
63686390 GACTTGGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (13 bp):
TTTATTATTTTAT
Found at i:63687973 original size:7 final size:7
Alignment explanation
Indices: 63687961--63688014 Score: 81
Period size: 7 Copynumber: 7.4 Consensus size: 7
63687951 TAACTTACCC
63687961 TAGGGTT
1 TAGGGTT
63687968 TAGGGTTT
1 TAGGG-TT
63687976 TAGGGTT
1 TAGGGTT
63687983 TAGGGTT
1 TAGGGTT
*
63687990 TAAGGTTT
1 T-AGGGTT
63687998 TAGGGTT
1 TAGGGTT
63688005 TAGGGTT
1 TAGGGTT
63688012 TAG
1 TAG
63688015 TGGTGTTTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
7 30 0.70
8 13 0.30
ACGTcount: A:0.17, C:0.00, G:0.39, T:0.44
Consensus pattern (7 bp):
TAGGGTT
Found at i:63687981 original size:15 final size:15
Alignment explanation
Indices: 63687961--63688014 Score: 83
Period size: 15 Copynumber: 3.7 Consensus size: 15
63687951 TAACTTACCC
63687961 TAGGGTTTAGGGTTT
1 TAGGGTTTAGGGTTT
63687976 TAGGGTTTAGGGTTT
1 TAGGGTTTAGGGTTT
* *
63687991 AAGGTTTTAGGG-TT
1 TAGGGTTTAGGGTTT
63688005 TAGGGTTTAG
1 TAGGGTTTAG
63688015 TGGTGTTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
14 10 0.29
15 25 0.71
ACGTcount: A:0.17, C:0.00, G:0.39, T:0.44
Consensus pattern (15 bp):
TAGGGTTTAGGGTTT
Found at i:63687988 original size:22 final size:22
Alignment explanation
Indices: 63687961--63688014 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
63687951 TAACTTACCC
63687961 TAGGGTTTAGGGTTTTAGGGTT
1 TAGGGTTTAGGGTTTTAGGGTT
*
63687983 TAGGGTTTAAGGTTTTAGGGTT
1 TAGGGTTTAGGGTTTTAGGGTT
63688005 TAGGGTTTAG
1 TAGGGTTTAG
63688015 TGGTGTTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.17, C:0.00, G:0.39, T:0.44
Consensus pattern (22 bp):
TAGGGTTTAGGGTTTTAGGGTT
Found at i:63688555 original size:160 final size:160
Alignment explanation
Indices: 63688362--63688681 Score: 541
Period size: 160 Copynumber: 2.0 Consensus size: 160
63688352 TGTTGCATTA
** ** * *
63688362 AATAAGTTTTTTTAAAGTATTTTACATATTTTCTCTTGCAACAAAATTTTCTATCTTGACCTTTA
1 AATAAGTTTCCTTAAACCATTTTAAACATTTTCTCTTGCAACAAAATTTTCTATCTTGACCTTTA
*
63688427 ACGATGAATTTTTACATAATAAGATTAAACTTCTTGATTTTTATAATTATGTGAAATTCTTAACT
66 ACGATGAATTTTTACATAACAAGATTAAACTTCTTGATTTTTATAATTATGTGAAATTCTTAACT
*
63688492 CATCGTTGGAAATTCTTATGGATGACCGTG
131 CATCATTGGAAATTCTTATGGATGACCGTG
*
63688522 AATAAGTTTCCTTAAACCATTTTAAACATTTTCTCTTGCAACAAAATTTTTTATCTTGACCTTTA
1 AATAAGTTTCCTTAAACCATTTTAAACATTTTCTCTTGCAACAAAATTTTCTATCTTGACCTTTA
* *
63688587 ACGATGAATTTTTACATAACAATATTAAACTTCTTTATTTTTATAATTATGTGAAATTCTTAACT
66 ACGATGAATTTTTACATAACAAGATTAAACTTCTTGATTTTTATAATTATGTGAAATTCTTAACT
63688652 CATCATTGGAAATTCTTATGGATGACCGTG
131 CATCATTGGAAATTCTTATGGATGACCGTG
63688682 TATATTAAAA
Statistics
Matches: 149, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
160 149 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.44
Consensus pattern (160 bp):
AATAAGTTTCCTTAAACCATTTTAAACATTTTCTCTTGCAACAAAATTTTCTATCTTGACCTTTA
ACGATGAATTTTTACATAACAAGATTAAACTTCTTGATTTTTATAATTATGTGAAATTCTTAACT
CATCATTGGAAATTCTTATGGATGACCGTG
Found at i:63690500 original size:22 final size:22
Alignment explanation
Indices: 63690475--63690803 Score: 408
Period size: 22 Copynumber: 15.0 Consensus size: 22
63690465 CCAGCATTCA
63690475 GACAACATTTAATCAACAATTG
1 GACAACATTTAATCAACAATTG
* * * * *
63690497 GACATCAATCAATCAACATTTA
1 GACAACATTTAATCAACAATTG
63690519 GACAACATTTAATCAACAATTG
1 GACAACATTTAATCAACAATTG
* * *
63690541 GACAGCATTAAATCAACATTTG
1 GACAACATTTAATCAACAATTG
**
63690563 GACAGTATTTAATCAACAATTG
1 GACAACATTTAATCAACAATTG
* * *
63690585 GACAACATTCAATCAATATTTG
1 GACAACATTTAATCAACAATTG
63690607 GACAACATTTAATCAACAATTG
1 GACAACATTTAATCAACAATTG
* *
63690629 TACAACA-TTAATTCAACATTTG
1 GACAACATTTAA-TCAACAATTG
63690651 GACAACATTTAATCAACAATTG
1 GACAACATTTAATCAACAATTG
* * * *
63690673 GACAGCATTCAATCAATATTTG
1 GACAACATTTAATCAACAATTG
63690695 GACAACATTTAATCAACAATTG
1 GACAACATTTAATCAACAATTG
* *
63690717 GACAACATTCAATCAACATTTG
1 GACAACATTTAATCAACAATTG
63690739 GACAACATTTAATCAACAATTG
1 GACAACATTTAATCAACAATTG
* * * *
63690761 GACAACATTCAATCCATATTTG
1 GACAACATTTAATCAACAATTG
*
63690783 GACAGCATTTAATCAACAATT
1 GACAACATTTAATCAACAATT
63690804 TTTACATCAA
Statistics
Matches: 256, Mismatches: 49, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
21 4 0.02
22 248 0.97
23 4 0.02
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.29
Consensus pattern (22 bp):
GACAACATTTAATCAACAATTG
Found at i:63690530 original size:44 final size:44
Alignment explanation
Indices: 63690475--63690803 Score: 516
Period size: 44 Copynumber: 7.5 Consensus size: 44
63690465 CCAGCATTCA
* * *
63690475 GACAACATTTAATCAACAATTGGACATCAATCAATCAACATTTA
1 GACAACATTTAATCAACAATTGGACAACATTCAATCAACATTTG
* *
63690519 GACAACATTTAATCAACAATTGGACAGCATTAAATCAACATTTG
1 GACAACATTTAATCAACAATTGGACAACATTCAATCAACATTTG
** *
63690563 GACAGTATTTAATCAACAATTGGACAACATTCAATCAATATTTG
1 GACAACATTTAATCAACAATTGGACAACATTCAATCAACATTTG
*
63690607 GACAACATTTAATCAACAATTGTACAACATT-AATTCAACATTTG
1 GACAACATTTAATCAACAATTGGACAACATTCAA-TCAACATTTG
* *
63690651 GACAACATTTAATCAACAATTGGACAGCATTCAATCAATATTTG
1 GACAACATTTAATCAACAATTGGACAACATTCAATCAACATTTG
63690695 GACAACATTTAATCAACAATTGGACAACATTCAATCAACATTTG
1 GACAACATTTAATCAACAATTGGACAACATTCAATCAACATTTG
* *
63690739 GACAACATTTAATCAACAATTGGACAACATTCAATCCATATTTG
1 GACAACATTTAATCAACAATTGGACAACATTCAATCAACATTTG
*
63690783 GACAGCATTTAATCAACAATT
1 GACAACATTTAATCAACAATT
63690804 TTTACATCAA
Statistics
Matches: 262, Mismatches: 21, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
43 2 0.01
44 258 0.98
45 2 0.01
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.29
Consensus pattern (44 bp):
GACAACATTTAATCAACAATTGGACAACATTCAATCAACATTTG
Found at i:63696800 original size:13 final size:13
Alignment explanation
Indices: 63696784--63696849 Score: 53
Period size: 13 Copynumber: 5.1 Consensus size: 13
63696774 TTTAAATTAA
*
63696784 ATTTTTTAAAAGC
1 ATTTTTCAAAAGC
* *
63696797 ATTTCTCAAAAGT
1 ATTTTTCAAAAGC
*
63696810 ATTTTTTC-ACAGC
1 A-TTTTTCAAAAGC
* *
63696823 AGTTCTCAAAAGC
1 ATTTTTCAAAAGC
*
63696836 ACTTTTCAAAAGC
1 ATTTTTCAAAAGC
63696849 A
1 A
63696850 ATGAAGAACT
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
12 4 0.10
13 31 0.77
14 5 0.12
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (13 bp):
ATTTTTCAAAAGC
Found at i:63696813 original size:26 final size:26
Alignment explanation
Indices: 63696784--63696849 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
63696774 TTTAAATTAA
* *
63696784 ATTTTTTAAAAGCATTTCTCAAAAGT
1 ATTTTTTAAAAGCAGTTCTCAAAAGC
* *
63696810 ATTTTTTCACAGCAGTTCTCAAAAGC
1 ATTTTTTAAAAGCAGTTCTCAAAAGC
* *
63696836 ACTTTTCAAAAGCA
1 ATTTTTTAAAAGCA
63696850 ATGAAGAACT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (26 bp):
ATTTTTTAAAAGCAGTTCTCAAAAGC
Found at i:63698371 original size:29 final size:30
Alignment explanation
Indices: 63698310--63698371 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 30
63698300 AAATTTATAT
* *
63698310 ATGAATTTTGATTTAATGTGTAATTTGATAC
1 ATGAATTTTGATTT-AGGTGTAATTTGACAC
63698341 ATGAATTTTGATTT-GGTGT-ATTTGTACAC
1 ATGAATTTTGATTTAGGTGTAATTTG-ACAC
63698370 AT
1 AT
63698372 TAAACTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.18
29 9 0.32
31 14 0.50
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.48
Consensus pattern (30 bp):
ATGAATTTTGATTTAGGTGTAATTTGACAC
Found at i:63706398 original size:27 final size:27
Alignment explanation
Indices: 63706367--63706544 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
63706357 TAAATTGTAC
63706367 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
63706394 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
63706420 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
63706448 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
63706476 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
63706503 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
63706530 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
63706545 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:63706481 original size:82 final size:81
Alignment explanation
Indices: 63706368--63706523 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
63706358 AAATTGTACA
* *
63706368 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
63706432 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
63706449 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
63706514 TGCGAGTTGA
65 TGCGAATTGA
63706524 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:63706535 original size:82 final size:81
Alignment explanation
Indices: 63706364--63706544 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
63706354 GATTAAATTG
* *
63706364 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
63706429 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
63706445 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
63706509 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
63706527 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
63706545 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:63707937 original size:15 final size:16
Alignment explanation
Indices: 63707917--63707946 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
63707907 AAATACAACA
63707917 GAAAATA-AATTTAAG
1 GAAAATAGAATTTAAG
63707932 GAAAATAGAATTTAA
1 GAAAATAGAATTTAA
63707947 ATTTTTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (16 bp):
GAAAATAGAATTTAAG
Found at i:63708960 original size:20 final size:19
Alignment explanation
Indices: 63708923--63708965 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
63708913 TACTCCCCCA
63708923 TTTATTTCCCCCCAAAACCT
1 TTTATTTCCCCCCAAAA-CT
* * *
63708943 TTTATTTTCCTCCTAAACT
1 TTTATTTCCCCCCAAAACT
63708962 TTTA
1 TTTA
63708966 CTTCTCACCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTATTTCCCCCCAAAACT
Found at i:63713732 original size:3 final size:3
Alignment explanation
Indices: 63713724--63713752 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
63713714 AAGAGGGTGC
63713724 TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
63713753 GTTAACATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:63714938 original size:15 final size:14
Alignment explanation
Indices: 63714899--63714938 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
63714889 GAAGAAATTC
63714899 AATAATAAAAAATA
1 AATAATAAAAAATA
*
63714913 AATATTTAAAAAATA
1 AATA-ATAAAAAATA
*
63714928 AATAATGAAAA
1 AATAATAAAAA
63714939 TGAAAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (14 bp):
AATAATAAAAAATA
Found at i:63716499 original size:20 final size:18
Alignment explanation
Indices: 63716453--63716509 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 18
63716443 ATTAATAAAA
63716453 AAATATTAATATAATTATT
1 AAATATTAATATAA-TATT
*
63716472 AAAT-TTAATTTAATATT
1 AAATATTAATATAATATT
*
63716489 AAATCTATTAAAATAATATT
1 AAA--TATTAATATAATATT
63716509 A
1 A
63716510 TTTTTGGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
17 7 0.22
18 8 0.25
19 5 0.16
20 12 0.38
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATATTAATATAATATT
Found at i:63718067 original size:56 final size:54
Alignment explanation
Indices: 63717944--63718104 Score: 232
Period size: 56 Copynumber: 2.9 Consensus size: 54
63717934 GCCATGGCAA
* * * * *
63717944 GAAGACCATATAGTGTAATACTTAGTCTGGGACTATTACACCATATGGGGAAGT
1 GAAGACCATATAGTGTAAGACCTAGTCTGGGACTATGACATCATATGGGGAAAT
*
63717998 GAAGACCATATAGTGTAAGACCTAGTCATGGTGGCTATGACATCATATGGGGAAAT
1 GAAGACCATATAGTGTAAGACCTAGTC-TGG-GACTATGACATCATATGGGGAAAT
* *
63718054 GAAGACCACATAGTGTAAGACCTAGTCTGGGACTATGACGTCATATGGGGA
1 GAAGACCATATAGTGTAAGACCTAGTCTGGGACTATGACATCATATGGGGA
63718105 TAAAAGTAAA
Statistics
Matches: 96, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
54 44 0.46
55 6 0.06
56 46 0.48
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.25
Consensus pattern (54 bp):
GAAGACCATATAGTGTAAGACCTAGTCTGGGACTATGACATCATATGGGGAAAT
Found at i:63722455 original size:21 final size:21
Alignment explanation
Indices: 63722425--63722464 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
63722415 TTACACTCCA
63722425 ACTCCATCCAACCCTACACGG
1 ACTCCATCCAACCCTACACGG
*
63722446 ACTCCGTCCAACCCTACAC
1 ACTCCATCCAACCCTACAC
63722465 TCCATGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.50, G:0.07, T:0.15
Consensus pattern (21 bp):
ACTCCATCCAACCCTACACGG
Found at i:63726912 original size:47 final size:49
Alignment explanation
Indices: 63726745--63726926 Score: 169
Period size: 50 Copynumber: 3.7 Consensus size: 49
63726735 GTGAGTGTGC
* ** * *
63726745 CAGTGTAAGACCATGTTTGGGACATGATATCGGCA-C--AGTCCGAGGAGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAAG--AGAAGAGT
*
63726793 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATGGATAGAGAAGAGT
1 -C-AGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGA-AGAGAAGAGT
* *
63726845 CAGTGTAAGACCATGTCTGGGACATGGCATCTGC-TCG-AGATG-AGTGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAAGA-GAAGAGT
** *
63726892 CAGTGTAAGACCACATCTGGGGCATGGCATCGGCA
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
63726927 CCAATATGTG
Statistics
Matches: 113, Mismatches: 13, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
47 37 0.33
48 1 0.01
49 3 0.03
50 63 0.56
51 1 0.01
52 6 0.05
54 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.22
Consensus pattern (49 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAAGAGAAGAGT
Found at i:63742792 original size:64 final size:63
Alignment explanation
Indices: 63742697--63742918 Score: 241
Period size: 64 Copynumber: 3.4 Consensus size: 63
63742687 ATTTAAAAAG
* * *
63742697 TAAAAAAATAGATAAAA-ATATATACATAATATTAAATTTAAGTATTTAAGAAGTAAAAGAATAA
1 TAAATAAATAGATAAAATAAATATA-AAAATATTAAATTTAAGTATTTAA-AAGTAAAAGAATAA
*
63742761 TAAATAAATTGATAAAATAAATATAAAAATATTAAATTTAAGTATTTAAAAGTAAAATAATATGA
1 TAAATAAATAGATAAAATAAATATAAAAATATTAAATTTAAGTATTTAAAAGT---A-AA-A-G-
*
63742826 AACAAA
59 AA-TAA
* * *
63742832 TAAATAAATAGATATAACAAATATAAATAATATTAAATTTAGGTATTTAAAAAGTAAAAGAATAA
1 TAAATAAATAGATAAAATAAATATAAA-AATATTAAATTTAAGTATTT-AAAAGTAAAAGAATAA
*
63742897 TAAATAAATAAAT-AAATAAATA
1 TAAATAAATAGATAAAATAAATA
63742919 GATAAAACGA
Statistics
Matches: 134, Mismatches: 13, Indels: 22
0.79 0.08 0.13
Matches are distributed among these distances:
63 4 0.03
64 45 0.34
65 20 0.15
66 3 0.02
67 3 0.02
68 2 0.01
69 3 0.02
70 3 0.02
71 26 0.19
72 19 0.14
73 6 0.04
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.30
Consensus pattern (63 bp):
TAAATAAATAGATAAAATAAATATAAAAATATTAAATTTAAGTATTTAAAAGTAAAAGAATAA
Found at i:63742904 original size:4 final size:4
Alignment explanation
Indices: 63742895--63742924 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
63742885 GTAAAAGAAT
*
63742895 AATA AATA AATA AATA AATA AATA GATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
63742925 ACGAATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:63742914 original size:73 final size:71
Alignment explanation
Indices: 63742759--63742936 Score: 230
Period size: 77 Copynumber: 2.4 Consensus size: 71
63742749 GTAAAAGAAT
* * *
63742759 AATAAATAAATTGATAAAATAAATATAAAAATATTAAATTTAAGTATTTAAAAGTAAAATAATAT
1 AATAAATAAATAGATAAAACAAATATAAAAATATTAAATTTAAGTATTTAAAAGTAAAAGAATAT
63742824 GAAACA
66 GAAACA
* *
63742830 AATAAATAAATAGATATAACAAATATAAATAATATTAAATTTAGGTATTTAAAAAGTAAAAGAAT
1 AATAAATAAATAGATAAAACAAATATAAA-AATATTAAATTTAAGTATTT-AAAAGTAAAAGAAT
* *
63742895 AATAAATAAATA
64 -AT---GAAACA
*
63742907 AATAAATAAATAGATAAAACGAATATAAAA
1 AATAAATAAATAGATAAAACAAATATAAAA
63742937 GGATGAAATT
Statistics
Matches: 92, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
71 26 0.28
72 19 0.21
73 13 0.14
74 2 0.02
76 1 0.01
77 31 0.34
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (71 bp):
AATAAATAAATAGATAAAACAAATATAAAAATATTAAATTTAAGTATTTAAAAGTAAAAGAATAT
GAAACA
Found at i:63751070 original size:15 final size:13
Alignment explanation
Indices: 63751044--63751069 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
63751034 TCAGGTTAGG
63751044 AGTGAGAGATATA
1 AGTGAGAGATATA
63751057 AGTGAGAGATATA
1 AGTGAGAGATATA
63751070 TGAATAATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (13 bp):
AGTGAGAGATATA
Found at i:63753561 original size:32 final size:32
Alignment explanation
Indices: 63753525--63753613 Score: 110
Period size: 33 Copynumber: 2.8 Consensus size: 32
63753515 ATAACTTTTT
*
63753525 CAGAAAATATTTTCAGGAAATC-TGCCAAACAA
1 CAGAAAATATTTTCAGCAAATCAT-CCAAACAA
*
63753557 CAGAAAATATTTTACA-CAAATTCATCCAAACAC
1 CAGAAAATATTTT-CAGCAAA-TCATCCAAACAA
*
63753590 CAGAAAATATTTTCAGTAAATCAT
1 CAGAAAATATTTTCAGCAAATCAT
63753614 TTTCCAGAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
32 22 0.44
33 27 0.54
34 1 0.02
ACGTcount: A:0.47, C:0.19, G:0.08, T:0.26
Consensus pattern (32 bp):
CAGAAAATATTTTCAGCAAATCATCCAAACAA
Found at i:63753863 original size:16 final size:15
Alignment explanation
Indices: 63753835--63753866 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
63753825 TTAATAGTAA
63753835 AAATTAATCTAAATT
1 AAATTAATCTAAATT
63753850 AAATTAACTCTAAATT
1 AAATTAA-TCTAAATT
63753866 A
1 A
63753867 TTATCCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATTAATCTAAATT
Found at i:63754123 original size:31 final size:33
Alignment explanation
Indices: 63754071--63754132 Score: 101
Period size: 31 Copynumber: 1.9 Consensus size: 33
63754061 TCATTAAAAT
63754071 TTAATTAAATAAAAAATTATATTAATATTAATA
1 TTAATTAAATAAAAAATTATATTAATATTAATA
*
63754104 TTAATT-AA-AAATAATTATATTAATATTAA
1 TTAATTAAATAAAAAATTATATTAATATTAA
63754133 AAAAGTGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 20 0.71
32 2 0.07
33 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
TTAATTAAATAAAAAATTATATTAATATTAATA
Found at i:63763879 original size:11 final size:13
Alignment explanation
Indices: 63763859--63763890 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
63763849 AATAAATTAA
63763859 TAAAATATCAT-T
1 TAAAATATCATAT
63763871 TAAAA-ATCATAT
1 TAAAATATCATAT
63763883 TAAAATAT
1 TAAAATAT
63763891 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:63765720 original size:3 final size:3
Alignment explanation
Indices: 63765712--63765741 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
63765702 AACAACCAAA
63765712 ATC ATC ATC ATC ATC ATC ATC ATC AT- ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
63765742 AACTTAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:63769852 original size:19 final size:20
Alignment explanation
Indices: 63769818--63769856 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
63769808 CTCACATGCC
*
63769818 AAAGTGAAAAATTGATTTTT
1 AAAGTGAAAAAGTGATTTTT
63769838 AAAGTG-AAAAGTGATTTTT
1 AAAGTGAAAAAGTGATTTTT
63769857 GTGGCCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.44, C:0.00, G:0.18, T:0.38
Consensus pattern (20 bp):
AAAGTGAAAAAGTGATTTTT
Found at i:63769981 original size:47 final size:47
Alignment explanation
Indices: 63769902--63770061 Score: 184
Period size: 47 Copynumber: 3.4 Consensus size: 47
63769892 AAGGAGGAAA
* * *
63769902 AAGTGACAG-TTTATCTGCAAAAATGGTTGCTTGTCCACAATATTAT
1 AAGTGGCAGATTTATCTGCAAAAGTGGTGGCTTGTCCACAATATTAT
* * * *
63769948 AATGTGGCA-ATTTATCTACAAAAGTGGTGGCTTGTCTATAATTTTATT
1 AA-GTGGCAGATTTATCTGCAAAAGTGGTGGCTTGTCCACAATATTA-T
63769996 AAGTGGCAGA-TTATCTGCAAAAGTGGTGGCTTGTCCACAATATTATT
1 AAGTGGCAGATTTATCTGCAAAAGTGGTGGCTTGTCCACAATATTA-T
* *
63770043 AACTGGAAG-TTTATCTGCA
1 AAGTGGCAGATTTATCTGCA
63770062 TTACTGTGAC
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
46 2 0.02
47 90 0.94
48 4 0.04
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.36
Consensus pattern (47 bp):
AAGTGGCAGATTTATCTGCAAAAGTGGTGGCTTGTCCACAATATTAT
Found at i:63776164 original size:43 final size:42
Alignment explanation
Indices: 63776110--63776280 Score: 193
Period size: 43 Copynumber: 4.0 Consensus size: 42
63776100 ACATAGGATT
* * **
63776110 TCGATATGTGTTTTCGTGTAAGACCATGTCTGGGATGTTGGCA
1 TCGAT-TGTGATTACGTGTAAGACCATGTCTGGGACATTGGCA
*
63776153 TCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACATTGGCA
1 TCGA-TTGTGATTACGTGTAAGACCATGTCTGGGACATTGGCA
* * *
63776196 TCGTATT-TGATT-TGTGTAAGACCCTGTCTGGGACAGTGGCA
1 TCG-ATTGTGATTACGTGTAAGACCATGTCTGGGACATTGGCA
* * *
63776237 TCGATATGTGATTACATGTAAGACAACGTCTGGGACATTGGCA
1 TCGAT-TGTGATTACGTGTAAGACCATGTCTGGGACATTGGCA
63776280 T
1 T
63776281 TGTACGAGTC
Statistics
Matches: 110, Mismatches: 13, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
40 2 0.02
41 30 0.27
42 9 0.08
43 67 0.61
44 2 0.02
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.33
Consensus pattern (42 bp):
TCGATTGTGATTACGTGTAAGACCATGTCTGGGACATTGGCA
Found at i:63776268 original size:84 final size:84
Alignment explanation
Indices: 63776125--63776280 Score: 226
Period size: 84 Copynumber: 1.9 Consensus size: 84
63776115 ATGTGTTTTC
* * * * *
63776125 GTGTAAGACCATGTCTGGGATGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACA
1 GTGTAAGACCATGTCTGGGAAGTTGGCATCGACTTGTGATTACATGTAAGACAACGTCTGGGACA
63776190 TTGGCATCGTATTTGATTT
66 TTGGCATCGTATTTGATTT
*
63776209 GTGTAAGACCCTGTCTGGGACAG-TGGCATCGA-TATGTGATTACATGTAAGACAACGTCTGGGA
1 GTGTAAGACCATGTCTGGGA-AGTTGGCATCGACT-TGTGATTACATGTAAGACAACGTCTGGGA
63776272 CATTGGCAT
64 CATTGGCAT
63776281 TGTACGAGTC
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
83 1 0.02
84 62 0.97
85 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (84 bp):
GTGTAAGACCATGTCTGGGAAGTTGGCATCGACTTGTGATTACATGTAAGACAACGTCTGGGACA
TTGGCATCGTATTTGATTT
Found at i:63776470 original size:16 final size:17
Alignment explanation
Indices: 63776441--63776472 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
63776431 TGAATTGATG
63776441 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
63776458 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
63776473 TTGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:63783579 original size:63 final size:62
Alignment explanation
Indices: 63783505--63783627 Score: 158
Period size: 63 Copynumber: 2.0 Consensus size: 62
63783495 AGGCATACGG
* * *
63783505 GCTAGGGACACGGGCGTGTGTCC-AAGCCGTATAACTTACTGTTTTGGATTTAAGGTCACACGA
1 GCTAGAGACACGGGCATGTG-CCGAAGCCGTATAACTCACTG-TTTGGATTTAAGGTCACACGA
* * * *
63783568 GCTAGAGACACGGGCATGTGCCGAGGCCGTGTAACTCATTGTTTGGCTTTAAGGTCACAC
1 GCTAGAGACACGGGCATGTGCCGAAGCCGTATAACTCACTGTTTGGATTTAAGGTCACAC
63783628 AGGCTTAGGA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
62 20 0.38
63 32 0.62
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (62 bp):
GCTAGAGACACGGGCATGTGCCGAAGCCGTATAACTCACTGTTTGGATTTAAGGTCACACGA
Found at i:63783657 original size:62 final size:63
Alignment explanation
Indices: 63783519--63783663 Score: 145
Period size: 62 Copynumber: 2.3 Consensus size: 63
63783509 GGGACACGGG
* * * * **
63783519 CGTGTGTCCAAGCCGTATAACTTACTGTTTTGGATTTAAGGTCACACGAGCTAGAGACACGGG
1 CGTGTGTCCAGGCCGTGTAACTCACTGTTTTGGATTTAAGGTCACACGAGCTAGAGACAAGAA
* * *
63783582 CATGTG-CCGAGGCCGTGTAACTCATTG-TTTGGCTTTAAGGTCACAC-AGGCTTAG-GACAAGA
1 CGTGTGTCC-AGGCCGTGTAACTCACTGTTTTGGATTTAAGGTCACACGA-GC-TAGAGACAAGA
63783643 A
63 A
*
63783644 CGTGTGTCCAGGCCATGTAA
1 CGTGTGTCCAGGCCGTGTAA
63783664 GGGGTTGTGA
Statistics
Matches: 67, Mismatches: 11, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
61 1 0.01
62 42 0.63
63 24 0.36
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (63 bp):
CGTGTGTCCAGGCCGTGTAACTCACTGTTTTGGATTTAAGGTCACACGAGCTAGAGACAAGAA
Found at i:63784293 original size:22 final size:23
Alignment explanation
Indices: 63784244--63784299 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
63784234 GGAATTTGCA
*
63784244 TCTGTATTTGATATGTTCTACAT
1 TCTGTATATGATATGTTCTACAT
* *
63784267 T-TGTATATGATATTTTCTA-TT
1 TCTGTATATGATATGTTCTACAT
*
63784288 TCTGTATCTGAT
1 TCTGTATATGAT
63784300 TTTGAGAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.07
22 25 0.89
23 1 0.04
ACGTcount: A:0.21, C:0.11, G:0.12, T:0.55
Consensus pattern (23 bp):
TCTGTATATGATATGTTCTACAT
Found at i:63787424 original size:22 final size:22
Alignment explanation
Indices: 63787380--63787437 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
63787370 TAGGAATTTG
* *
63787380 CATCTATATCTAATATGTCCTA
1 CATCTGTATCTGATATGTCCTA
* *
63787402 CATCTGTATCTGATATTTTCTA
1 CATCTGTATCTGATATGTCCTA
* *
63787424 CTTTTGTATCTGAT
1 CATCTGTATCTGAT
63787438 TCGAAGAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.24, C:0.19, G:0.09, T:0.48
Consensus pattern (22 bp):
CATCTGTATCTGATATGTCCTA
Found at i:63790543 original size:16 final size:16
Alignment explanation
Indices: 63790519--63790549 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
63790509 CTCATGTATG
*
63790519 TTCATAATTTCACAAC
1 TTCACAATTTCACAAC
63790535 TTCACAATTTCACAA
1 TTCACAATTTCACAA
63790550 GCGTACATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
TTCACAATTTCACAAC
Found at i:63800989 original size:39 final size:39
Alignment explanation
Indices: 63800945--63801075 Score: 145
Period size: 39 Copynumber: 3.4 Consensus size: 39
63800935 CACGGACATA
*
63800945 CCACACGAGCATGTAGGTGTTGGGCCAGTCCGTGTGGGC
1 CCACACGAGCATGTAGGTGTTGGGCCAGGCCGTGTGGGC
* * * *
63800984 CCACACAAGCATGTTGGTGTTGGGTCAGGCCGTGTTGGC
1 CCACACGAGCATGTAGGTGTTGGGCCAGGCCGTGTGGGC
* * * * * *
63801023 CCACACGGGGATTTAGGTGTTGGGCTAGGCTGTGTGCGC
1 CCACACGAGCATGTAGGTGTTGGGCCAGGCCGTGTGGGC
* *
63801062 GCACACGGGCATGT
1 CCACACGAGCATGT
63801076 GAGCCCATAA
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 74 1.00
ACGTcount: A:0.15, C:0.24, G:0.38, T:0.23
Consensus pattern (39 bp):
CCACACGAGCATGTAGGTGTTGGGCCAGGCCGTGTGGGC
Found at i:63811850 original size:8 final size:8
Alignment explanation
Indices: 63811837--63811862 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
63811827 GTATGTTGTT
63811837 AATTTCAC
1 AATTTCAC
63811845 AATTTCAC
1 AATTTCAC
63811853 AATTTCAC
1 AATTTCAC
63811861 AA
1 AA
63811863 GCATCCGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (8 bp):
AATTTCAC
Found at i:63814408 original size:5 final size:6
Alignment explanation
Indices: 63814392--63814417 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
63814382 AATTTTAAAG
63814392 ATTTTT ATTTTT ATTTTT ATTTTT AT
1 ATTTTT ATTTTT ATTTTT ATTTTT AT
63814418 AGAATTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:63817096 original size:16 final size:15
Alignment explanation
Indices: 63817075--63817139 Score: 51
Period size: 16 Copynumber: 4.0 Consensus size: 15
63817065 AGTTTCATGA
63817075 TCCATTTCAATTCAAT
1 TCCATTTCAATTC-AT
63817091 TCCATTTTC-ATATCAT
1 TCCA-TTTCAAT-TCAT
63817107 TCTCATTTCAATTTCAT
1 TC-CATTTCAA-TTCAT
* *
63817124 TTCATGTTCAAATCAT
1 TCCAT-TTCAATTCAT
63817140 ATATTGCCTA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
16 21 0.51
17 19 0.46
18 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.02, T:0.48
Consensus pattern (15 bp):
TCCATTTCAATTCAT
Found at i:63817118 original size:28 final size:29
Alignment explanation
Indices: 63817067--63817129 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
63817057 AAAAACCAAG
63817067 TTTCATGATCCATTTCAATTCAATTCCAT
1 TTTCATGATCCATTTCAATTCAATTCCAT
* *
63817096 TTTCAT-AT-CATTCTCATTTCAATTTCA-
1 TTTCATGATCCATT-TCAATTCAATTCCAT
63817123 TTTCATG
1 TTTCATG
63817130 TTCAAATCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 10 0.33
28 14 0.47
29 6 0.20
ACGTcount: A:0.25, C:0.22, G:0.03, T:0.49
Consensus pattern (29 bp):
TTTCATGATCCATTTCAATTCAATTCCAT
Found at i:63817123 original size:17 final size:17
Alignment explanation
Indices: 63817077--63817134 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
63817067 TTTCATGATC
63817077 CATTTCAA-TTCAATTC-
1 CATTTCAATTTC-ATTCT
*
63817093 CATTTTC-ATATCATTCT
1 CA-TTTCAATTTCATTCT
63817110 CATTTCAATTTCATT-T
1 CATTTCAATTTCATTCT
63817126 CATGTTCAA
1 CAT-TTCAA
63817135 ATCATATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 15 0.43
17 20 0.57
ACGTcount: A:0.28, C:0.22, G:0.02, T:0.48
Consensus pattern (17 bp):
CATTTCAATTTCATTCT
Found at i:63817139 original size:33 final size:33
Alignment explanation
Indices: 63817077--63817139 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
63817067 TTTCATGATC
* *
63817077 CATTTCAATTCAATTCCATTTTCATATCATTCT
1 CATTTCAATTCAATTCCATGTTCAAATCATTCT
*
63817110 CATTTCAATTTC-ATTTCATGTTCAAATCAT
1 CATTTCAA-TTCAATTCCATGTTCAAATCAT
63817140 ATATTGCCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 23 0.88
34 3 0.12
ACGTcount: A:0.29, C:0.22, G:0.02, T:0.48
Consensus pattern (33 bp):
CATTTCAATTCAATTCCATGTTCAAATCATTCT
Found at i:63827081 original size:17 final size:17
Alignment explanation
Indices: 63827055--63827095 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
63827045 GTGGAGGGAG
63827055 GTCACCGTTCAAGTTTA
1 GTCACCGTTCAAGTTTA
*
63827072 GTCACTGTTCAAGTTTA
1 GTCACCGTTCAAGTTTA
*
63827089 GCCACCG
1 GTCACCG
63827096 CTCTTGGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (17 bp):
GTCACCGTTCAAGTTTA
Found at i:63830341 original size:88 final size:88
Alignment explanation
Indices: 63830166--63830387 Score: 250
Period size: 88 Copynumber: 2.5 Consensus size: 88
63830156 CAATGAAGAC
* **
63830166 AGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCCCTGGG
1 AGCAGATCTTGCCTTCCTGTACCGACAGCAAAGCAGATCAAAGACACCAGCCTTGCCTCCCTGAA
*
63830231 CTACAGCGGAGCGGGTTAAAAAT
66 CTACAGCGGAGCAGGTTAAAAAT
* ** * * *
63830254 AGCAGATTTTGCCTTCCTGTACCGGTAGCAAAGCAGATCGAAA-ACTCCAGCCTTGTCTCCTTGA
1 AGCAGATCTTGCCTTCCTGTACCGACAGCAAAGCAGATC-AAAGACACCAGCCTTGCCTCCCTGA
* * *
63830318 AC-AGCAGTGGAGTAGGTTGAAAAT
65 ACTA-CAGCGGAGCAGGTTAAAAAT
* * * **
63830342 AGCAGACCTTGCCTTCCTGTACTGGCAGTGAAGCAGATCAAAGACA
1 AGCAGATCTTGCCTTCCTGTACCGACAGCAAAGCAGATCAAAGACA
63830388 TCAGTTTTAT
Statistics
Matches: 111, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
87 4 0.04
88 104 0.94
89 3 0.03
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.21
Consensus pattern (88 bp):
AGCAGATCTTGCCTTCCTGTACCGACAGCAAAGCAGATCAAAGACACCAGCCTTGCCTCCCTGAA
CTACAGCGGAGCAGGTTAAAAAT
Found at i:63830973 original size:44 final size:43
Alignment explanation
Indices: 63830906--63831240 Score: 197
Period size: 44 Copynumber: 7.7 Consensus size: 43
63830896 AATGGCGAAC
*
63830906 CTTATCTCTCTAAAGTTGCAGTGGAGCAGATTAAAGCCAATAAT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAG-CAATAAT
* * * * * ** *
63830950 CCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAACTTTGGAT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCAAT-AAT
** * * * * *
63830994 CTTATCTTTCTAAAGTTGTAG-AGAGCAGA-T--CGCATCTAGT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCA-ATAAT
* * *
63831034 CTTATCTCCCTAAAGTTGCAGTGGAGCAGACT-AAGTAAGCAAGT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCAA-TAA-T
* *
63831078 CTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGC-A-AAT
1 CTTATCTC-CCTAAAGTTGCAGTGGA-GCAGA-TTAA-A--GCAATAAT
*
63831123 CTTATCTCCCTAAAGTGGCAGTGGAGCAGATTAAAGCCAATAAT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAG-CAATAAT
* * * *
63831167 CCTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACCACAT-AT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATT-AAAGCA-ATAAT
* * * *
63831211 TTTATCTCTCTAAAGTTACAG-AGAGCAGAT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGAT
63831241 CGCATCCAGT
Statistics
Matches: 221, Mismatches: 49, Indels: 43
0.71 0.16 0.14
Matches are distributed among these distances:
40 20 0.09
41 9 0.04
42 3 0.01
43 24 0.11
44 127 0.57
45 29 0.13
46 6 0.03
47 1 0.00
48 1 0.00
49 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (43 bp):
CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCAATAAT
Found at i:63831303 original size:128 final size:128
Alignment explanation
Indices: 63831122--63831370 Score: 286
Period size: 128 Copynumber: 1.9 Consensus size: 128
63831112 AGATGGCAAA
* * * * *
63831122 TCTTATCTCCCTAAAGTGGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCC-CTGAAGTTGT
1 TCTTATCTCCCTAAAGTGGCAGTGAAGCAGATCAAAGACAACAATCCTATCTCCTC-GAAGTTGC
* * * * *
63831186 AGTGGAGCAGATTAAAACCACATATTTTATCTCTCTAAAGTTACAGAGAGCAGATCGCATCCAG
65 AGTGGAGCAGATTAAAACCACAAATCTTAACTCTCTAAAGCTACAGAGAACAGATCGCATCCAG
* * * *
63831250 TCTTATCTCCCTGAAGTTGCAGTGAAGCAGA-CAGAAGACACCAATCCTATCTCCTCGAGGTTGC
1 TCTTATCTCCCTAAAGTGGCAGTGAAGCAGATCA-AAGACAACAATCCTATCTCCTCGAAGTTGC
** * * * *
63831314 AGTGGAGTGGATTGAAACCGCAAATCTTAACTCTCTGAAGCTGCAGAGAACAGATCG
65 AGTGGAGCAGATTAAAACCACAAATCTTAACTCTCTAAAGCTACAGAGAACAGATCG
63831371 TATCAAATTC
Statistics
Matches: 99, Mismatches: 20, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
127 1 0.01
128 97 0.98
129 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (128 bp):
TCTTATCTCCCTAAAGTGGCAGTGAAGCAGATCAAAGACAACAATCCTATCTCCTCGAAGTTGCA
GTGGAGCAGATTAAAACCACAAATCTTAACTCTCTAAAGCTACAGAGAACAGATCGCATCCAG
Found at i:63831315 original size:217 final size:217
Alignment explanation
Indices: 63830897--63831317 Score: 605
Period size: 217 Copynumber: 1.9 Consensus size: 217
63830887 CAACATTGCA
* * *
63830897 ATGGCGAACCTTATCTCTCTAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTG
1 ATGGCAAACCTTATCTCCCTAAAGTGGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTG
* **** * **
63830962 AAGTTGTAGTGGAGCGGATTAAAACTTTGGATCTTATCTTTCTAAAGTTGTAGAGAGCAGATCGC
66 AAGTTGTAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTTACAGAGAGCAGATCGC
* * * * *
63831027 ATCTAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAA
131 ATCCAGTCTTATCTCCCTAAAGTTGCAGTGAAGCAGACGAAGTAACCAAGTCCTATCCTCCTGAA
63831092 GTTGCAGTGAGGCAGACTGAAG
196 GTTGCAGTGAGGCAGACTGAAG
*
63831114 ATGGCAAATCTTATCTCCCTAAAGTGGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTG
1 ATGGCAAACCTTATCTCCCTAAAGTGGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTG
* *
63831179 AAGTTGTAGTGGAGCAGATTAAAACCACATATTTTATCTCTCTAAAGTTACAGAGAGCAGATCGC
66 AAGTTGTAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTTACAGAGAGCAGATCGC
*
63831244 ATCCAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGACAGAAG-ACACCAA-TCCTAT-CTCCTC
131 ATCCAGTCTTATCTCCCTAAAGTTGCAGTGAAGCAGAC-GAAGTA-ACCAAGTCCTATCCTCCT-
*
63831306 GAGGTTGCAGTG
193 GAAGTTGCAGTG
63831318 GAGTGGATTG
Statistics
Matches: 180, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
216 5 0.03
217 168 0.93
218 7 0.04
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (217 bp):
ATGGCAAACCTTATCTCCCTAAAGTGGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTG
AAGTTGTAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTTACAGAGAGCAGATCGC
ATCCAGTCTTATCTCCCTAAAGTTGCAGTGAAGCAGACGAAGTAACCAAGTCCTATCCTCCTGAA
GTTGCAGTGAGGCAGACTGAAG
Found at i:63837342 original size:35 final size:35
Alignment explanation
Indices: 63837302--63837371 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
63837292 AAAAGTAAGT
63837302 ACTTCAAGAATCTGATTATGCTTAAGTAATGTTAA
1 ACTTCAAGAATCTGATTATGCTTAAGTAATGTTAA
63837337 ACTTCAAGAATCTGATTATGCTTAAGTAATGTTAA
1 ACTTCAAGAATCTGATTATGCTTAAGTAATGTTAA
63837372 TTAGAAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.37
Consensus pattern (35 bp):
ACTTCAAGAATCTGATTATGCTTAAGTAATGTTAA
Found at i:63837957 original size:21 final size:21
Alignment explanation
Indices: 63837933--63837998 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
63837923 AAATTATCTG
63837933 CACCATTGAGTGGTTTATCCA
1 CACCATTGAGTGGTTTATCCA
** *
63837954 CACCATTTGAGCAGTTTATCTA
1 CACCA-TTGAGTGGTTTATCCA
* *
63837976 CATCGTTGAGTGGTTTATCCA
1 CACCATTGAGTGGTTTATCCA
63837997 CA
1 CA
63837999 TAGTGTAGTA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
21 20 0.56
22 16 0.44
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (21 bp):
CACCATTGAGTGGTTTATCCA
Found at i:63838012 original size:21 final size:21
Alignment explanation
Indices: 63837938--63838012 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
63837928 ATCTGCACCA
* * *
63837938 TTGAGTGGTTTATCCACACCAT
1 TTGAGTAGTTTATCCACA-TAG
* * *
63837960 TTGAGCAGTTTATCTACATCG
1 TTGAGTAGTTTATCCACATAG
*
63837981 TTGAGTGGTTTATCCACATAG
1 TTGAGTAGTTTATCCACATAG
63838002 -TGTAGTAGTTT
1 TTG-AGTAGTTT
63838013 TTATCTACAC
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
20 2 0.05
21 24 0.59
22 15 0.37
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (21 bp):
TTGAGTAGTTTATCCACATAG
Found at i:63839291 original size:33 final size:33
Alignment explanation
Indices: 63839225--63839292 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
63839215 TTATTTCTTA
*
63839225 TTATTTAGTTTTATTTATTTCTTGTTTTATTTT
1 TTATTTAGTTTTATTTATTTCTTGTTTCATTTT
*
63839258 TTATTCTA-TTTTATTT-TATTCTTGTTTCCTTTT
1 TTATT-TAGTTTTATTTAT-TTCTTGTTTCATTTT
63839291 TT
1 TT
63839293 TCTTTATGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 1 0.03
33 28 0.90
34 2 0.06
ACGTcount: A:0.13, C:0.07, G:0.04, T:0.75
Consensus pattern (33 bp):
TTATTTAGTTTTATTTATTTCTTGTTTCATTTT
Found at i:63856142 original size:50 final size:52
Alignment explanation
Indices: 63856087--63856195 Score: 136
Period size: 50 Copynumber: 2.1 Consensus size: 52
63856077 GCATTTACCA
*
63856087 TCACACACCACAACCAAC-CAAATACT-AGTTAGGAT-T-TGGGAGGGTAATGT
1 TCACACACCACAACCAACTCAAAT--TGACTTAGGATATATGGGAGGGTAATGT
* * *
63856137 TCACACACCACAATCAACTCAAATTGACTTCGGATATATGGGAGTGTAATGT
1 TCACACACCACAACCAACTCAAATTGACTTAGGATATATGGGAGGGTAATGT
63856189 TCACACA
1 TCACACA
63856196 AGCTAACAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
49 1 0.02
50 24 0.47
51 6 0.12
52 20 0.39
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (52 bp):
TCACACACCACAACCAACTCAAATTGACTTAGGATATATGGGAGGGTAATGT
Found at i:63860828 original size:14 final size:14
Alignment explanation
Indices: 63860811--63860845 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
63860801 ATACAATATA
*
63860811 AATTTATATTTAAT
1 AATTCATATTTAAT
*
63860825 AATTCATTTTTAAT
1 AATTCATATTTAAT
63860839 AATTCAT
1 AATTCAT
63860846 TAATAAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (14 bp):
AATTCATATTTAAT
Found at i:63860846 original size:14 final size:14
Alignment explanation
Indices: 63860819--63860846 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
63860809 TAAATTTATA
63860819 TTTAATAATTCATT
1 TTTAATAATTCATT
63860833 TTTAATAATTCATT
1 TTTAATAATTCATT
63860847 AATAAATTGG
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:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAATAATTCATT
Found at i:63861316 original size:19 final size:19
Alignment explanation
Indices: 63861294--63861331 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
63861284 TCAACCATCC
63861294 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
63861313 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
63861332 ACTCTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:63866940 original size:15 final size:15
Alignment explanation
Indices: 63866920--63866954 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
63866910 TGGGACTCTG
*
63866920 TTTTAAAAAAAGTTT
1 TTTTAAAAAAAGTAT
*
63866935 TTTTAAATAAAGTAT
1 TTTTAAAAAAAGTAT
63866950 TTTTA
1 TTTTA
63866955 TATCATGAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (15 bp):
TTTTAAAAAAAGTAT
Found at i:63883741 original size:21 final size:21
Alignment explanation
Indices: 63883717--63883758 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
63883707 ACTTGTTAAT
63883717 ATTTT-AATATATGAAATATAA
1 ATTTTAAATAT-TGAAATATAA
*
63883738 ATTTTAAATATTTAAATATAA
1 ATTTTAAATATTGAAATATAA
63883759 CCATTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
ATTTTAAATATTGAAATATAA
Found at i:63885192 original size:156 final size:156
Alignment explanation
Indices: 63884908--63885200 Score: 507
Period size: 156 Copynumber: 1.9 Consensus size: 156
63884898 GTATTGACTT
* *
63884908 ACTTTGTTCACTGTAAGAAATATCTAGTCTGGTAAGACAAACATATCGTAGGGTACCAACCACTT
1 ACTTTGTTCACTGTAAGAAATATCTAGTCTGGTAAGACAAACATATCATAGGGTACCAACAACTT
63884973 TTCCATACAGATGCAATCTAAAAATGGTTGACCATCAATAGCATAGAGTTTAGGCCATAAAAGGC
66 TTCCATACAGATGCAATCTAAAAATGGTTGACCATCAATAGCATAGAGTTTAGGCCATAAAAGGC
63885038 CTCAAGTAAGTGAATAGCATGTATTG
131 CTCAAGTAAGTGAATAGCATGTATTG
*
63885064 ACTTTGTTCACTGTAAGAAATATCTAGTCTGGTAAGACAAACATATCATATGGTACCAACAACTT
1 ACTTTGTTCACTGTAAGAAATATCTAGTCTGGTAAGACAAACATATCATAGGGTACCAACAACTT
* * *
63885129 TTCCATACAGATGCAATCTGAAAATTGTTGACCATCAATAGCAGT-GTGTTTAGGCCATAAAAGG
66 TTCCATACAGATGCAATCTAAAAATGGTTGACCATCAATAGCA-TAGAGTTTAGGCCATAAAAGG
*
63885193 CTTCAAGT
130 CCTCAAGT
63885201 GTGAAAAACA
Statistics
Matches: 129, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
156 128 0.99
157 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (156 bp):
ACTTTGTTCACTGTAAGAAATATCTAGTCTGGTAAGACAAACATATCATAGGGTACCAACAACTT
TTCCATACAGATGCAATCTAAAAATGGTTGACCATCAATAGCATAGAGTTTAGGCCATAAAAGGC
CTCAAGTAAGTGAATAGCATGTATTG
Found at i:63889196 original size:12 final size:11
Alignment explanation
Indices: 63889140--63889202 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
63889130 TTTAGGATAA
63889140 TTTTAAA-TA-
1 TTTTAAATTAT
63889149 TTTTAAATTTAT
1 TTTTAAA-TTAT
**
63889161 TTTTCCA-TAT
1 TTTTAAATTAT
*
63889171 TTTT-AATGGAT
1 TTTTAAAT-TAT
63889182 TTTTAAATTAT
1 TTTTAAATTAT
63889193 TTTTAAATTA
1 TTTTAAATTA
63889203 GCCTCGAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
9 8 0.19
10 7 0.16
11 20 0.47
12 8 0.19
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (11 bp):
TTTTAAATTAT
Found at i:63894977 original size:26 final size:25
Alignment explanation
Indices: 63894946--63895004 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 25
63894936 TTATATGCAT
* *
63894946 TTTTGTTTAGTTTATTATAATTATA
1 TTTTGTTTAGTTTATTAAAATAATA
63894971 TGTTTGTTTAGTTTATTAAAATAATA
1 T-TTTGTTTAGTTTATTAAAATAATA
63894997 TTTT-TTTA
1 TTTTGTTTA
63895005 ATTAAGATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 4 0.13
25 4 0.13
26 23 0.74
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (25 bp):
TTTTGTTTAGTTTATTAAAATAATA
Found at i:63906530 original size:322 final size:322
Alignment explanation
Indices: 63905945--63906590 Score: 1292
Period size: 322 Copynumber: 2.0 Consensus size: 322
63905935 TCATGCATTA
63905945 ATCCTTAAGTCCTTTATCTCTAGAATGGACACAAGTCATGGAATAGTCACACTTGCATAGTCCAT
1 ATCCTTAAGTCCTTTATCTCTAGAATGGACACAAGTCATGGAATAGTCACACTTGCATAGTCCAT
63906010 CCATTGTTCCTTGATATCTTGAGTAAACTATGATATATAAATAAGTATGACATCTCATATCAACT
66 CCATTGTTCCTTGATATCTTGAGTAAACTATGATATATAAATAAGTATGACATCTCATATCAACT
63906075 TATTTGAGCATGACCATGCATTTCTAGTCTCACTCAATCAAGTGGCCTAGGTTATTACTCCCATT
131 TATTTGAGCATGACCATGCATTTCTAGTCTCACTCAATCAAGTGGCCTAGGTTATTACTCCCATT
63906140 ATGTAGGAGGGACTTATCCTCTATTGATCAACCATATCTCTCTACATAGGTTGTGGTATATATAA
196 ATGTAGGAGGGACTTATCCTCTATTGATCAACCATATCTCTCTACATAGGTTGTGGTATATATAA
63906205 CATCAGCCTTTATAGAACAACCAGTTATGGTGTACGTTTGACTGTATCAAAATAATCAACTC
261 CATCAGCCTTTATAGAACAACCAGTTATGGTGTACGTTTGACTGTATCAAAATAATCAACTC
63906267 ATCCTTAAGTCCTTTATCTCTAGAATGGACACAAGTCATGGAATAGTCACACTTGCATAGTCCAT
1 ATCCTTAAGTCCTTTATCTCTAGAATGGACACAAGTCATGGAATAGTCACACTTGCATAGTCCAT
63906332 CCATTGTTCCTTGATATCTTGAGTAAACTATGATATATAAATAAGTATGACATCTCATATCAACT
66 CCATTGTTCCTTGATATCTTGAGTAAACTATGATATATAAATAAGTATGACATCTCATATCAACT
63906397 TATTTGAGCATGACCATGCATTTCTAGTCTCACTCAATCAAGTGGCCTAGGTTATTACTCCCATT
131 TATTTGAGCATGACCATGCATTTCTAGTCTCACTCAATCAAGTGGCCTAGGTTATTACTCCCATT
63906462 ATGTAGGAGGGACTTATCCTCTATTGATCAACCATATCTCTCTACATAGGTTGTGGTATATATAA
196 ATGTAGGAGGGACTTATCCTCTATTGATCAACCATATCTCTCTACATAGGTTGTGGTATATATAA
63906527 CATCAGCCTTTATAGAACAACCAGTTATGGTGTACGTTTGACTGTATCAAAATAATCAACTC
261 CATCAGCCTTTATAGAACAACCAGTTATGGTGTACGTTTGACTGTATCAAAATAATCAACTC
63906589 AT
1 AT
63906591 GATGTTGGGA
Statistics
Matches: 324, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
322 324 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (322 bp):
ATCCTTAAGTCCTTTATCTCTAGAATGGACACAAGTCATGGAATAGTCACACTTGCATAGTCCAT
CCATTGTTCCTTGATATCTTGAGTAAACTATGATATATAAATAAGTATGACATCTCATATCAACT
TATTTGAGCATGACCATGCATTTCTAGTCTCACTCAATCAAGTGGCCTAGGTTATTACTCCCATT
ATGTAGGAGGGACTTATCCTCTATTGATCAACCATATCTCTCTACATAGGTTGTGGTATATATAA
CATCAGCCTTTATAGAACAACCAGTTATGGTGTACGTTTGACTGTATCAAAATAATCAACTC
Found at i:63913830 original size:93 final size:92
Alignment explanation
Indices: 63913698--63913892 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
63913688 TTGATTTTAG
* *
63913698 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATTA
1 TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATTA
* *
63913762 TATTTAAT-ATTAATTATTTTAAATTGTA
65 TATGTAATAATT-ATTATTTTAAATTATA
* *
63913790 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAA-TTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
63913855 TATGTAATAATTATTATTTTAAATTATA
65 TATGTAATAATTATTATTTTAAATTATA
*
63913883 CAAATTCATA
1 TAAATTCATA
63913893 AACTATAATC
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 17 0.18
93 71 0.76
94 5 0.05
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Done.