Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 203 of 259
Found at i:64577816 original size:29 final size:28
Alignment explanation
Indices: 64577754--64577820 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
64577744 ATTATTTTTT
* *
64577754 TTATTATTACTACTCTTACTTTTATTAA
1 TTATTATTACTACTCTTACTTCTACTAA
*
64577782 TGTATTATTACTACTACTTTCTATCTACT-A
1 T-TATTATTACTACT-CTTACT-TCTACTAA
64577812 TTATTATTA
1 TTATTATTA
64577821 TCTTATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 1 0.03
29 21 0.64
30 7 0.21
31 4 0.12
ACGTcount: A:0.28, C:0.15, G:0.01, T:0.55
Consensus pattern (28 bp):
TTATTATTACTACTCTTACTTCTACTAA
Found at i:64577863 original size:29 final size:28
Alignment explanation
Indices: 64577811--64577883 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
64577801 TCTATCTACT
* *
64577811 ATTATTATTA-TCTTATTTAAAATATTA
1 ATTATTATTATTATTATTTAAAATAATA
*
64577838 A-TATTATTATTATTATTTCCATAATAATA
1 ATTATTATTATTATTATTT--AAAATAATA
64577867 ATTATTA-TATTATTATT
1 ATTATTATTATTATTATT
64577884 CTTATTAGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
26 8 0.21
27 8 0.21
29 18 0.46
30 5 0.13
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTATTATTATTATTATTTAAAATAATA
Found at i:64578195 original size:3 final size:3
Alignment explanation
Indices: 64578030--64578180 Score: 87
Period size: 3 Copynumber: 49.0 Consensus size: 3
64578020 TTTTACTTAC
* *
64578030 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
64578078 ACT ACTT A-T ATT CGTT AGT ATC ATT ATT AATT -TT ATCT -TT ATT -TT
1 ATT A-TT ATT ATT -ATT ATT ATT ATT ATT -ATT ATT AT-T ATT ATT ATT
* * * * *
64578123 CTTT ACT ATT ATT TTT ATT ATC ATT ATTT ATTT ATTT ATT CATT ACT
1 -ATT ATT ATT ATT ATT ATT ATT ATT A-TT A-TT A-TT ATT -ATT ATT
64578170 -TT ATT ATT ATT
1 ATT ATT ATT ATT
64578181 GTTCTCACTA
Statistics
Matches: 119, Mismatches: 17, Indels: 24
0.74 0.11 0.15
Matches are distributed among these distances:
2 8 0.07
3 87 0.73
4 24 0.20
ACGTcount: A:0.28, C:0.08, G:0.01, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:64578222 original size:14 final size:15
Alignment explanation
Indices: 64578192--64578224 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
64578182 TTCTCACTAT
*
64578192 TATTTATTTATTTCA
1 TATTTACTTATTTCA
64578207 TATTTACTTA-TTCA
1 TATTTACTTATTTCA
64578221 TATT
1 TATT
64578225 CATAAGTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTTACTTATTTCA
Found at i:64581881 original size:19 final size:20
Alignment explanation
Indices: 64581854--64581894 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
64581844 TTGCATTCTG
* *
64581854 TTCATTCATTTGCATTACAT
1 TTCATTCATATGCATTAAAT
64581874 TTCA-TCATATGCATTAAAT
1 TTCATTCATATGCATTAAAT
64581893 TT
1 TT
64581895 TGCAAAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (20 bp):
TTCATTCATATGCATTAAAT
Found at i:64590032 original size:44 final size:45
Alignment explanation
Indices: 64589984--64590256 Score: 124
Period size: 44 Copynumber: 6.2 Consensus size: 45
64589974 AATTCACAAC
64589984 CTTATCTCT-CTGAGGTAGCAAGAGAGCAGATTGAAGATTGAAGT
1 CTTATCTCTCCTGAGGTAGCAAGAGAGCAGATTGAAGATTGAAGT
* * * * *
64590028 CTTATCT-TCCTAAGGTAGCGAG-GAAGCATACTGAGGATTGAAGAT
1 CTTATCTCTCCTGAGGTAGCAAGAG-AGCAGATTGAAGATTGAAG-T
* * * * * * *
64590073 CTTA-CTC-CTTAAGCAGTAG--TG-GAGTAGATCGAAGATGGCGAA-A
1 CTTATCTCTCCTGAG--GTAGCAAGAGAGCAGATTGAAGAT--TGAAGT
* * * ** ***** *
64590116 CTTATCT-TCCTAAGGTAGCAGGAGAGTAGATTTTAGCCACCAGC
1 CTTATCTCTCCTGAGGTAGCAAGAGAGCAGATTGAAGATTGAAGT
* * *
64590160 CTTATCTCT-CTGAGGTAGCAAGAAAGCAGGTTGAAGATTGAATT
1 CTTATCTCTCCTGAGGTAGCAAGAGAGCAGATTGAAGATTGAAGT
*
64590204 CTTATCT-TCCTGAGGTAGCAAG-GAAGCAGACTG-AGAATTGAAGAT
1 CTTATCTCTCCTGAGGTAGCAAGAG-AGCAGATTGAAG-ATTGAAG-T
64590249 CTTATCTC
1 CTTATCTC
64590257 CCTAAGCAGT
Statistics
Matches: 166, Mismatches: 43, Indels: 38
0.67 0.17 0.15
Matches are distributed among these distances:
42 4 0.02
43 19 0.11
44 112 0.67
45 27 0.16
46 4 0.02
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (45 bp):
CTTATCTCTCCTGAGGTAGCAAGAGAGCAGATTGAAGATTGAAGT
Found at i:64590345 original size:88 final size:88
Alignment explanation
Indices: 64590071--64590363 Score: 258
Period size: 88 Copynumber: 3.3 Consensus size: 88
64590061 AGGATTGAAG
* * * *
64590071 ATCTTA-CTCCTTAAGCAGTAGTGGAGTAGATCGAAGATGGCGAAACTTATCTTCCTAAGGTAGC
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCTGAGGTAGC
* *
64590135 AGGAGAGTAGATTTTAGCCACCA
66 AGGGGAGCAGATTTTAGCCACCA
** * * * * * * *
64590158 GCCTTATCTCTCTGAG--GTAGCAAGAAAGCAGGTTGAAGAT--TGAATTCTTATCTTCCTGAGG
1 ATCTTATCTCCCTAAGCAGTAG--TG-GAGCAGATCGAAGATGGCGAA-TCTTATCTTCCTGAGG
* * * * * **
64590219 TAGCAAGGAAGCAGA-CTGAG-AATTGAA
62 TAGCAGGGGAGCAGATTTTAGCCA--CCA
64590246 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCTGAGGTAG
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCTGAGGTAG
*
64590311 CAGGGGAGCATATTTTAGCCACCA
65 CAGGGGAGCAGATTTTAGCCACCA
*
64590335 ATCTTGTCTCCCTAAGCAGTAGTGGAGCA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCA
64590364 AGCTAAAGAT
Statistics
Matches: 152, Mismatches: 40, Indels: 27
0.69 0.18 0.12
Matches are distributed among these distances:
86 5 0.03
87 10 0.07
88 73 0.48
89 53 0.35
90 6 0.04
91 5 0.03
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.26
Consensus pattern (88 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCTGAGGTAGC
AGGGGAGCAGATTTTAGCCACCA
Found at i:64590386 original size:177 final size:175
Alignment explanation
Indices: 64589980--64590410 Score: 480
Period size: 177 Copynumber: 2.4 Consensus size: 175
64589970 GGTGAATTCA
* * * * * *
64589980 CAACCTTATCTCTCTGAGGTAGCAAGAGAGC-AGATTGAAGATTGA-AGTCTTATCTTCCTAAGG
1 CAACCTTATCTCCCTAAGGTAG-AAGAAAGCAAG-CTAAAGATTGAGA-TCTTATCTTCCTGAGG
* * * * *
64590043 TAGCGAGGAAGCATACTGAGGATTGAAGATCTTACTCCTTAAGCAGTAGTGGAGTAGATCGAAGA
63 TAGCAAGGAAGCAGACTGAGAATTGAAGATCTTACTCCCTAAGCAGTAGTGGAGCAGATCGAAGA
*
64590108 TGGCGAAACTTATCTTCCTAAGGTAGCAGGAGAGTAGATTTTAGCCAC
128 TGGCGAAACTTATCTTCCTAAGGTAGCAGGAGAGCAGATTTTAGCCAC
* * * * * *
64590156 CAGCCTTATCTCTCTGAGGTAGCAAGAAAGCAGGTTGAAGATTGA-ATTCTTATCTTCCTGAGGT
1 CAACCTTATCTCCCTAAGGTAG-AAGAAAGCAAGCTAAAGATTGAGA-TCTTATCTTCCTGAGGT
64590220 AGCAAGGAAGCAGACTGAGAATTGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA
64 AGCAAGGAAGCAGACTGAGAATTGAAGATCTTA-CTCCCTAAGCAGTAGTGGAGCAGATCGAAGA
* * * *
64590285 TGGCGAATCTTATCTTCCTGAGGTAGCAGGGGAGCATATTTTAGCCAC
128 TGGCGAAACTTATCTTCCTAAGGTAGCAGGAGAGCAGATTTTAGCCAC
* * * *
64590333 CAATCTTGTCTCCCTAAGCAGTAG-TG-GAGCAAGCTAAAGATTGTAGATCTTATC-TCCATGAG
1 CAACCTTATCTCCCTAAG--GTAGAAGAAAGCAAGCTAAAGATTG-AGATCTTATCTTCC-TGAG
64590395 GTAGCAATGG-AGCAGA
62 GTAGCAA-GGAAGCAGA
64590411 TCGAAGACGG
Statistics
Matches: 222, Mismatches: 25, Indels: 15
0.85 0.10 0.06
Matches are distributed among these distances:
176 103 0.46
177 112 0.50
178 3 0.01
179 4 0.02
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (175 bp):
CAACCTTATCTCCCTAAGGTAGAAGAAAGCAAGCTAAAGATTGAGATCTTATCTTCCTGAGGTAG
CAAGGAAGCAGACTGAGAATTGAAGATCTTACTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
CGAAACTTATCTTCCTAAGGTAGCAGGAGAGCAGATTTTAGCCAC
Found at i:64590407 original size:88 final size:88
Alignment explanation
Indices: 64590071--64590408 Score: 219
Period size: 88 Copynumber: 3.8 Consensus size: 88
64590061 AGGATTGAAG
* * * * * *
64590071 ATCTTA-CTCCTTAAGCAGTAGTGGAGTAGATCGAAGATGGCGAAACTTATCTTCCTAAGGTAGC
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGAGAATCTTATCTTCCTGAGGTAGC
* *
64590135 -AGGAGAGTAGATTTTAGCCACCA
66 AAGG-GAGCATATTTTAGCCACCA
** * * * * * ** * *
64590158 GCCTTATCTCTCTGAG--GTAGCAAGAAAGCAGGTTGAAGATTGA-ATTCTTATCTTCCTGAGGT
1 ATCTTATCTCCCTAAGCAGTAG--TG-GAGCAGATCAAAGATGGAGAATCTTATCTTCCTGAGGT
* * * * * **
64590220 AGCAAGGAAGCAGA-CTGAG-AATTGAA
63 AGCAAGGGAGCATATTTTAGCCA--CCA
* *
64590246 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCTGAGGTAG
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGAGAATCTTATCTTCCTGAGGTAG
*
64590311 CAGGGGAGCATATTTTAGCCACCA
65 CAAGGGAGCATATTTTAGCCACCA
* * *
64590335 ATCTTGTCTCCCTAAGCAGTAGTGGAGCA-AGCTAAAGATTGTAG-ATCTTATC-TCCATGAGGT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-AAAGA-TGGAGAATCTTATCTTCC-TGAGGT
*
64590397 AGCAATGGAGCA
63 AGCAAGGGAGCA
64590409 GATCGAAGAC
Statistics
Matches: 187, Mismatches: 48, Indels: 31
0.70 0.18 0.12
Matches are distributed among these distances:
86 5 0.03
87 12 0.06
88 101 0.54
89 61 0.33
90 3 0.02
91 5 0.03
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (88 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGAGAATCTTATCTTCCTGAGGTAGC
AAGGGAGCATATTTTAGCCACCA
Found at i:64590428 original size:45 final size:43
Alignment explanation
Indices: 64590379--64590589 Score: 135
Period size: 45 Copynumber: 4.8 Consensus size: 43
64590369 AAGATTGTAG
64590379 ATCTTATCTCCATGAGGTAGCAATGGAGCAGATCGAAGACGGTGA
1 ATCTTATCTCCATGAGGTAGCAATGGAGCAGATCGAAGAC-GT-A
* * **
64590424 ATCTTATCTCCCTGATGTAGCAA-GGAAGCAGATTTAAGTCAC-TA
1 ATCTTATCTCCATGAGGTAGCAATGG-AGCAGATCGAAG--ACGTA
** * * * * * * *
64590468 GCCTTGTCTTCC-T-AAGCAGGAGTGGAGCAG-GCTGAAGATTGTA
1 ATCTTATC-TCCATGAGGTAGCAATGGAGCAGATC-GAAGA-CGTA
64590511 GATCTTATCTCCATGAGGTAGCAATGGAGCAGATCGAAGACGTCGA
1 -ATCTTATCTCCATGAGGTAGCAATGGAGCAGATCGAAGACGT--A
* * * *
64590557 ATCTTATCTCCCTGAGTTAACAAGGGAGCAGAT
1 ATCTTATCTCCATGAGGTAGCAATGGAGCAGAT
64590590 TTAAGCCATT
Statistics
Matches: 124, Mismatches: 28, Indels: 28
0.69 0.16 0.16
Matches are distributed among these distances:
41 1 0.01
43 18 0.15
44 19 0.15
45 82 0.66
46 2 0.02
47 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.25
Consensus pattern (43 bp):
ATCTTATCTCCATGAGGTAGCAATGGAGCAGATCGAAGACGTA
Found at i:64590740 original size:133 final size:134
Alignment explanation
Indices: 64590204--64590742 Score: 533
Period size: 133 Copynumber: 4.1 Consensus size: 134
64590194 AGATTGAATT
* * *
64590204 CTTATCTTCCTGAGGTAGCAAGGAAGCAGACTG-AGAATTGAAGATCTTATCTCCCT-AAGCAGT
1 CTTATCTTCCTGAGGTAACAAGGAAGCAGACTGAAG-ATTGAAGATCTTATCTCCATGAAGCAGC
* * * * * *
64590267 AGTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCTGAGGTAGCAGGGGAGCATATTTTAGCCA
65 AATGGAGCAGATCGAAGACGGCGAATCTTATCTCCCTGAGGTAGCAAGGGAGCAGATTTAAGCCA
* **
64590332 CCAAT
130 CTAGC
* * * ** * * * *
64590337 CTTGTCTCCCTAAGCAGT-A-GTGG-AGCA-AGCTAAAGATTGTAGATCTTATCTCCATGAGGTA
1 CTTATCTTCCTGAG--GTAACAAGGAAGCAGA-CTGAAGATTGAAGATCTTATCTCCATGAAGCA
* * * *
64590398 GCAATGGAGCAGATCGAAGACGGTGAATCTTATCTCCCTGATGTAGCAAGGAAGCAGATTTAAGT
63 GCAATGGAGCAGATCGAAGACGGCGAATCTTATCTCCCTGAGGTAGCAAGGGAGCAGATTTAAGC
64590463 CACTAGC
128 CACTAGC
* * * ** * * * * *
64590470 CTTGTCTTCCT-AAG-CAGGAGTGGAGCAGGCTGAAGATTGTAGATCTTATCTCCATGAGGTAGC
1 CTTATCTTCCTGAGGTAACAAG-GAAGCAGACTGAAGATTGAAGATCTTATCTCCATGAAGCAGC
* * *
64590533 AATGGAGCAGATCGAAGACGTCGAATCTTATCTCCCTGAGTTAACAAGGGAGCAGATTTAAGCCA
65 AATGGAGCAGATCGAAGACGGCGAATCTTATCTCCCTGAGGTAGCAAGGGAGCAGATTTAAGCCA
* *
64590598 TTAGT
130 CTAGC
* *
64590603 CTTATCTTCCTGAGGTAACAAGGAAGCAGACTGAAGATTGAAGATCTTATCTCCCT-AAGCAGTA
1 CTTATCTTCCTGAGGTAACAAGGAAGCAGACTGAAGATTGAAGATCTTATCTCCATGAAGCAGCA
* * *
64590667 GTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCC-GAGGTAGCAGGGGAGCAGATTTTAA-CC
66 ATGGAGCAGATCGAAGACGGCGAATCTTATC-TCCCTGAGGTAGCAAGGGAGCAGA-TTTAAGCC
64590730 ACTAGC
129 ACTAGC
64590736 CTTATCT
1 CTTATCT
64590743 AGTTGCAATA
Statistics
Matches: 333, Mismatches: 59, Indels: 28
0.79 0.14 0.07
Matches are distributed among these distances:
130 2 0.01
131 3 0.01
132 26 0.08
133 256 0.77
134 41 0.12
135 5 0.02
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (134 bp):
CTTATCTTCCTGAGGTAACAAGGAAGCAGACTGAAGATTGAAGATCTTATCTCCATGAAGCAGCA
ATGGAGCAGATCGAAGACGGCGAATCTTATCTCCCTGAGGTAGCAAGGGAGCAGATTTAAGCCAC
TAGC
Found at i:64590850 original size:127 final size:131
Alignment explanation
Indices: 64590683--64590976 Score: 301
Period size: 133 Copynumber: 2.3 Consensus size: 131
64590673 CAGATCGAAG
* * * ** *
64590683 ATGGCGAATCTTATCTTCCC-GAGGTAGCAGGGGAGCAGATTTTAACCACTAGCC-T-TA-TCT-
1 ATGGCGAATCTTATC-TCCCTGAAGTTGCAGTGGAGCAGATTACAACCACTAACCTTATACTCTA
* *
64590743 AGTTGCAATATAGCAGGTTGAAATCACAAGTCTTATCTCCCTGAATTTGCAACGGAGCAAACTAA
65 AGTTGCAATAGAGCAGGTTGAAATCACAAGTCTTATCTCCCTGAAGTTGCAACGGAGCAAACTAA
64590808 AA
130 AA
* ** *
64590810 ATGGCGAATCTTATCTCCCTGAAGTTGTAGTGGATTAGATTACAGCCACTAACCTTATATCTCTG
1 ATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTACAACCACTAACCTTATA-CTCT-
* * * * * ** * *
64590875 AAGTTGTAGTAGAGTAGGTTGAAATTACAAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTG
64 AAGTTGCAATAGAGCAGGTTGAAATCACAAGTCTTATCTCCCTGAAGTTGCAACGGAGCAAACTA
*
64590940 AAG
129 AAA
* * *
64590943 ATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGA
1 ATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGA
64590977 ACAAATTGAA
Statistics
Matches: 134, Mismatches: 26, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
126 4 0.03
127 39 0.29
128 1 0.01
129 2 0.01
131 3 0.02
133 85 0.63
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (131 bp):
ATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTACAACCACTAACCTTATACTCTAA
GTTGCAATAGAGCAGGTTGAAATCACAAGTCTTATCTCCCTGAAGTTGCAACGGAGCAAACTAAA
A
Found at i:64590964 original size:45 final size:44
Alignment explanation
Indices: 64590754--64591285 Score: 185
Period size: 45 Copynumber: 11.7 Consensus size: 44
64590744 GTTGCAATAT
* * * **
64590754 AGCAGGTTGAA-ATCACAAGTCTTATCTCCCTGAATTTGCAACGG
1 AGCAGATTGAAGAT-ACAAATCTTATCTCCCTGAAGTTGCAGTGG
* * * * * * *
64590798 AGCAAACTAAAAATGGCGAATCTTATCTCCCTGAAGTTGTAGTGG
1 AGCAGATTGAAGAT-ACAAATCTTATCTCCCTGAAGTTGCAGTGG
** ** * * * * * *
64590843 ATTAGATT-ACAGCCACTAACCTTATATCTCTGAAGTTGTAGTAG
1 AGCAGATTGA-AGATACAAATCTTATCTCCCTGAAGTTGCAGTGG
* * * *
64590887 AGTAGGTTGAA-ATTACAAGTCTTATCTCCCTGAAGTTGTAGTGG
1 AGCAGATTGAAGA-TACAAATCTTATCTCCCTGAAGTTGCAGTGG
* *
64590931 AGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGG
1 AGCAGATTGAAGATA-CAAATCTTATCTCCCTGAAGTTGCAGTGG
* * * * * * *
64590976 AACAAATTGAAGCTATAAATTACAAATCTTATCTCTC-GAAATTACAATAG
1 AGCAGATTGAAG------A-TACAAATCTTATCTCCCTGAAGTTGCAGTGG
* * * * *
64591026 AGAAGAATTAAAGCTAAAAACCTTATCTCCCTGAAGTTGCAGTGG
1 AGCAG-ATTGAAGATACAAATCTTATCTCCCTGAAGTTGCAGTGG
* ** *
64591071 AGCAGACTGAAGATAGTGAATCTTATTTCCCTGAAGTTGCAGTGG
1 AGCAGATTGAAGATA-CAAATCTTATCTCCCTGAAGTTGCAGTGG
** * * * * **
64591116 AATAGATTGAAGCTATAAATTACAAATCTTATCTCTC-GAAATTGAAATAA
1 AGCAGATTGAAG------A-TACAAATCTTATCTCCCTGAAGTTGCAGTGG
* * * * * * * *
64591166 AGTAGAATTAAAGCTAAAAAACCATATCTCCTTGAAGTTGCAGTGA
1 AGCAG-ATTGAAGAT-ACAAATCTTATCTCCCTGAAGTTGCAGTGG
* * * ** *
64591212 AGCAGACTGAAGACAATAAATCCCATCTCCCTGAAGTAGCAGTGG
1 AGCAGATTGAAGA-TACAAATCTTATCTCCCTGAAGTTGCAGTGG
* *
64591257 AGCAGATTGAAGTTGA-AGATCTTATCTCC
1 AGCAGATTGAAGAT-ACAAATCTTATCTCC
64591286 TTAAAGTGCA
Statistics
Matches: 348, Mismatches: 112, Indels: 56
0.67 0.22 0.11
Matches are distributed among these distances:
44 105 0.30
45 165 0.47
46 13 0.04
50 23 0.07
51 38 0.11
52 4 0.01
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.28
Consensus pattern (44 bp):
AGCAGATTGAAGATACAAATCTTATCTCCCTGAAGTTGCAGTGG
Found at i:64591070 original size:140 final size:141
Alignment explanation
Indices: 64590907--64591268 Score: 548
Period size: 140 Copynumber: 2.6 Consensus size: 141
64590897 AATTACAAGT
* *
64590907 CTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTAAATCTTATTTCCCTGAAGTTGCA
* *
64590972 GTGGAACAAATTGAAGCTATAAATTACAAATCTTATCTCTCGAAATT-ACAATAGAGAAGAATTA
66 GTGGAACAGATTGAAGCTATAAATTACAAATCTTATCTCTCGAAATTGA-AATAAAGAAGAATTA
64591036 AAGCT-AAAAAC
130 AAGCTAAAAAAC
*
64591047 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTGAATCTTATTTCCCTGAAGTTGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTAAATCTTATTTCCCTGAAGTTGCA
* *
64591112 GTGGAATAGATTGAAGCTATAAATTACAAATCTTATCTCTCGAAATTGAAATAAAGTAGAATTAA
66 GTGGAACAGATTGAAGCTATAAATTACAAATCTTATCTCTCGAAATTGAAATAAAGAAGAATTAA
64591177 AGCTAAAAAAC
131 AGCTAAAAAAC
* * * * * ** * *
64591188 CATATCTCCTTGAAGTTGCAGTGAAGCAGACTGAAGACAATAAATCCCATCTCCCTGAAGTAGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTAAATCTTATTTCCCTGAAGTTGCA
*
64591253 GTGGAGCAGATTGAAG
66 GTGGAACAGATTGAAG
64591269 TTGAAGATCT
Statistics
Matches: 201, Mismatches: 19, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
140 125 0.62
141 76 0.38
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (141 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTAAATCTTATTTCCCTGAAGTTGCA
GTGGAACAGATTGAAGCTATAAATTACAAATCTTATCTCTCGAAATTGAAATAAAGAAGAATTAA
AGCTAAAAAAC
Found at i:64592623 original size:9 final size:9
Alignment explanation
Indices: 64592610--64592671 Score: 72
Period size: 9 Copynumber: 6.9 Consensus size: 9
64592600 TTCAAATTAA
64592610 TTATT-TTT
1 TTATTATTT
*
64592618 ATTATTATAT
1 -TTATTATTT
*
64592628 TTATTATTA
1 TTATTATTT
*
64592637 TTATTATAT
1 TTATTATTT
*
64592646 TTACTATTT
1 TTATTATTT
64592655 TTATTATTT
1 TTATTATTT
64592664 TTATTATT
1 TTATTATT
64592672 ACTACTCTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
9 42 0.95
10 2 0.05
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (9 bp):
TTATTATTT
Found at i:64592624 original size:3 final size:3
Alignment explanation
Indices: 64592609--64592803 Score: 64
Period size: 3 Copynumber: 63.7 Consensus size: 3
64592599 TTTCAAATTA
* *
64592609 ATT ATT TTT ATT ATT A-T ATTT ATT ATT ATT ATT A-T ATTT ACT ATT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT A-TT ATT ATT
* * * * * * *
64592654 TTT ATT ATT TTT ATT ATT ACT ACT CTT ACTT -TT TTT AATGC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT -AT-T ATT ATT
* * * * *
64592701 ACT ACT ACTT -TCT ATCT ATT ATT ATT A-T CTT ATT -TT AAAT ATT AAT
1 ATT ATT A-TT AT-T AT-T ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT
* * * *
64592747 ATT ATT ATT -TCC ATA ATT ATT A-T ATT ATT ATT ATT CTT ATT AGT
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
64592791 ACGTT ATT ATT AT
1 A--TT ATT ATT AT
64592804 CTTTTCTACT
Statistics
Matches: 143, Mismatches: 30, Indels: 38
0.68 0.14 0.18
Matches are distributed among these distances:
2 13 0.09
3 111 0.78
4 17 0.12
5 2 0.01
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:64592637 original size:18 final size:18
Alignment explanation
Indices: 64592610--64592672 Score: 90
Period size: 18 Copynumber: 3.5 Consensus size: 18
64592600 TTCAAATTAA
*
64592610 TTATTTTTATTATTATAT
1 TTATTATTATTATTATAT
64592628 TTATTATTATTATTATAT
1 TTATTATTATTATTATAT
* * *
64592646 TTACTATTTTTATTATTT
1 TTATTATTATTATTATAT
64592664 TTATTATTA
1 TTATTATTA
64592673 CTACTCTTAC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
TTATTATTATTATTATAT
Found at i:64592786 original size:20 final size:22
Alignment explanation
Indices: 64592763--64592803 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
64592753 ATTTCCATAA
64592763 TTATTA-TA-TTATTATTATTC
1 TTATTAGTACTTATTATTATTC
64592783 TTATTAGTACGTTATTATTAT
1 TTATTAGTAC-TTATTATTAT
64592804 CTTTTCTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 2 0.11
23 10 0.56
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (22 bp):
TTATTAGTACTTATTATTATTC
Found at i:64592817 original size:20 final size:23
Alignment explanation
Indices: 64592771--64592824 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 23
64592761 AATTATTATA
*
64592771 TTATTATTATTCTTATTAGTACG
1 TTATTATTATTCTTATTACTACG
*
64592794 TTATTATTA-TCTT-TT-CTACT
1 TTATTATTATTCTTATTACTACG
*
64592814 TTATTACTATT
1 TTATTATTATT
64592825 ATTGTATTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 11 0.41
21 3 0.11
22 4 0.15
23 9 0.33
ACGTcount: A:0.24, C:0.11, G:0.04, T:0.61
Consensus pattern (23 bp):
TTATTATTATTCTTATTACTACG
Found at i:64592946 original size:3 final size:3
Alignment explanation
Indices: 64592940--64593085 Score: 77
Period size: 3 Copynumber: 47.7 Consensus size: 3
64592930 CATCATCATC
* *
64592940 ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT -TAT ATT CGTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT -ATT
* * * * *
64592986 AGT ATC ATT ATT AATT -TT ATCT -TT ATT -TT CTTT ACT ATT ATT TTT
1 ATT ATT ATT ATT -ATT ATT AT-T ATT ATT ATT -ATT ATT ATT ATT ATT
* * * * *
64593031 ATT ATC ATT ATTT ATTT ATTT ATT ACT ATT GTT ATT ATT ATT GTC A-T
1 ATT ATT ATT A-TT A-TT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
64593078 ATT ATT AT
1 ATT ATT AT
64593086 ATATGTTTTA
Statistics
Matches: 109, Mismatches: 23, Indels: 22
0.71 0.15 0.14
Matches are distributed among these distances:
2 7 0.06
3 82 0.75
4 20 0.18
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:64600432 original size:43 final size:41
Alignment explanation
Indices: 64600378--64600541 Score: 170
Period size: 43 Copynumber: 3.9 Consensus size: 41
64600368 TTTTGATATG
*
64600378 TGATTTCGTGTAAGACCACATCTGGGACATTGGCATCGATT
1 TGATTTCGTGTAAGACCACGTCTGGGACATTGGCATCGATT
* * * *
64600419 TGAGATTTTGTGTAAGACCATGTCTGGGACATCGGCATTGTATT
1 T--GATTTCGTGTAAGACCACGTCTGGGACATTGGCATCG-ATT
*
64600463 TGATTTCGTGTAAGACC-CTGTCTGGGACAATGGCATCGATATT
1 TGATTTCGTGTAAGACCAC-GTCTGGGACATTGGCATCG--ATT
* * *
64600506 TGATTACATGTAAGACCACGTCCT-GGACGTTGGCAT
1 TGATTTCGTGTAAGACCACGT-CTGGGACATTGGCAT
64600542 TGTTCGAGCT
Statistics
Matches: 102, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
41 1 0.01
42 31 0.30
43 63 0.62
44 7 0.07
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (41 bp):
TGATTTCGTGTAAGACCACGTCTGGGACATTGGCATCGATT
Found at i:64600541 original size:85 final size:85
Alignment explanation
Indices: 64600378--64600544 Score: 205
Period size: 85 Copynumber: 2.0 Consensus size: 85
64600368 TTTTGATATG
* *** *
64600378 TGATTTCGTGTAAGACCACATCTGGGACATTGGCATCGATTTGAGATTTTGTGTAAGACCATGTC
1 TGATTTCGTGTAAGACCACATCTGGGACAATGGCATCGATTTGAGATTACATGTAAGACCACGTC
64600443 TGGGACATCGGCATTGTATT
66 TGGGACATCGGCATTGTATT
* *
64600463 TGATTTCGTGTAAGACC-CTGTCTGGGACAATGGCATCGATATT-TGATTACATGTAAGACCACG
1 TGATTTCGTGTAAGACCAC-ATCTGGGACAATGGCATCGAT-TTGAGATTACATGTAAGACCACG
* *
64600526 TCCT-GGACGTTGGCATTGT
64 T-CTGGGACATCGGCATTGT
64600545 TCGAGCTTTC
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
84 1 0.01
85 65 0.93
86 4 0.06
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (85 bp):
TGATTTCGTGTAAGACCACATCTGGGACAATGGCATCGATTTGAGATTACATGTAAGACCACGTC
TGGGACATCGGCATTGTATT
Found at i:64602623 original size:23 final size:23
Alignment explanation
Indices: 64602593--64602645 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
64602583 GTGGTTAGTT
64602593 ATGTGTTAGTGTATCACTGGGAC
1 ATGTGTTAGTGTATCACTGGGAC
64602616 ATGTGTTAGTGTATCACTGGGAC
1 ATGTGTTAGTGTATCACTGGGAC
64602639 ATGTGTT
1 ATGTGTT
64602646 TGAATTCTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.21, C:0.11, G:0.30, T:0.38
Consensus pattern (23 bp):
ATGTGTTAGTGTATCACTGGGAC
Found at i:64604684 original size:43 final size:43
Alignment explanation
Indices: 64604623--64604709 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
64604613 AATTAAATGA
64604623 AATGTCAAATCAAGGACTAAAGGGTTAATAAGGTAAGGCTTGG
1 AATGTCAAATCAAGGACTAAAGGGTTAATAAGGTAAGGCTTGG
64604666 AATGTCAAATCAAGGACTAAAGGGTTAATAAGGTAAGGCTTGG
1 AATGTCAAATCAAGGACTAAAGGGTTAATAAGGTAAGGCTTGG
64604709 A
1 A
64604710 TAGCAATTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.40, C:0.09, G:0.28, T:0.23
Consensus pattern (43 bp):
AATGTCAAATCAAGGACTAAAGGGTTAATAAGGTAAGGCTTGG
Found at i:64606540 original size:13 final size:13
Alignment explanation
Indices: 64606508--64606542 Score: 56
Period size: 11 Copynumber: 2.8 Consensus size: 13
64606498 ACCCCACGAT
64606508 CATATACAGAACA
1 CATATACAGAACA
64606521 -A-ATACAGAACA
1 CATATACAGAACA
64606532 CATATACAGAA
1 CATATACAGAA
64606543 TTAACATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 10 0.50
12 2 0.10
13 8 0.40
ACGTcount: A:0.57, C:0.20, G:0.09, T:0.14
Consensus pattern (13 bp):
CATATACAGAACA
Found at i:64608048 original size:56 final size:56
Alignment explanation
Indices: 64607962--64608075 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
64607952 ATGGAACAAG
*
64607962 ATGCAAATATCATAATCGTACATCAATACTCTAACACGTGGCAAATGAAATCATTC
1 ATGCAAATACCATAATCGTACATCAATACTCTAACACGTGGCAAATGAAATCATTC
64608018 ATGCAAATACCATAATCGTACATCAATACTCTAACACGTGGCAAATGAAATCATTC
1 ATGCAAATACCATAATCGTACATCAATACTCTAACACGTGGCAAATGAAATCATTC
64608074 AT
1 AT
64608076 TGATATTGAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.26
Consensus pattern (56 bp):
ATGCAAATACCATAATCGTACATCAATACTCTAACACGTGGCAAATGAAATCATTC
Found at i:64609247 original size:29 final size:27
Alignment explanation
Indices: 64609176--64609260 Score: 71
Period size: 29 Copynumber: 2.9 Consensus size: 27
64609166 CTAAAGTATT
64609176 AGGTACTTTGTACTGGTGATTACATGATATC
1 AGGTACTTTGTAC-GGTGATT--AT-ATATC
* * *
64609207 AAGTAGTATGTATCGGTGATTATATCATC
1 AGGTACTTTGTA-CGGTGATTATAT-ATC
*
64609236 AGGTACTTTGTACCGGTGTTTATAT
1 AGGTACTTTGTA-CGGTGATTATAT
64609261 TTTATCAGGT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
28 2 0.05
29 25 0.57
31 16 0.36
32 1 0.02
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (27 bp):
AGGTACTTTGTACGGTGATTATATATC
Found at i:64609271 original size:31 final size:30
Alignment explanation
Indices: 64609176--64609273 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 30
64609166 CTAAAGTATT
* * *
64609176 AGGTACTTTGTACTGGTGATTACATGATATC
1 AGGTACTTTGTACCGGTGATTATAT-TTATC
* * * * *
64609207 AAGTAGTATGTATCGGTGATTATA-TCATC
1 AGGTACTTTGTACCGGTGATTATATTTATC
*
64609236 AGGTACTTTGTACCGGTGTTTATATTTTATC
1 AGGTACTTTGTACCGGTGATTATA-TTTATC
64609267 AGGTACT
1 AGGTACT
64609274 ACGTACCAGT
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
29 22 0.43
31 29 0.57
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (30 bp):
AGGTACTTTGTACCGGTGATTATATTTATC
Found at i:64613908 original size:22 final size:21
Alignment explanation
Indices: 64613873--64613913 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
64613863 TCTAAATGTG
* *
64613873 TTTTTTTATTAATTTTTATAA
1 TTTTTTTATAAATTATTATAA
64613894 TTTTTTATATAAATTATTAT
1 TTTTTT-TATAAATTATTAT
64613914 TTTTTTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTTTTATAAATTATTATAA
Found at i:64613919 original size:22 final size:20
Alignment explanation
Indices: 64613873--64613919 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
64613863 TCTAAATGTG
*
64613873 TTTTTTTATTAATTTTTATAA
1 TTTTTTTATTAATTATTAT-A
*
64613894 TTTTTTATATAAATTATTAT-
1 TTTTTT-TATTAATTATTATA
64613914 TTTTTT
1 TTTTTT
64613920 GTTTTTACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.26
21 6 0.26
22 11 0.48
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTTTATTAATTATTATA
Found at i:64617028 original size:67 final size:69
Alignment explanation
Indices: 64616956--64617089 Score: 184
Period size: 67 Copynumber: 2.0 Consensus size: 69
64616946 TTTAATAGAT
* * * * *
64616956 TTAATATTTAATTTAGTTTAATACTTATCTT-A-ACAGTATTTTATTAA-TTAATATTAAATTGA
1 TTAATATTAAATTTAATCTAATACTTATCTTGATA-AGTATTATATTAATTTAATATTAAAGTGA
64617018 TTATC
65 TTATC
*
64617023 TTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAATATTAAAGTGAT
1 TTAATATTAAATTTAATCTAATACTTATCTTGATAAGTATTATATTAATTTAATATTAAAGTGAT
64617088 TA
66 TA
64617090 AGTTTAATCA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
67 27 0.47
68 13 0.22
69 18 0.31
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (69 bp):
TTAATATTAAATTTAATCTAATACTTATCTTGATAAGTATTATATTAATTTAATATTAAAGTGAT
TATC
Found at i:64617046 original size:17 final size:17
Alignment explanation
Indices: 64616999--64617047 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 17
64616989 CAGTATTTTA
64616999 TTAAT-TAATATTAAAT
1 TTAATCTAATATTAAAT
*
64617015 TGATTATCTTAATATTAAAT
1 T--TAATC-TAATATTAAAT
64617035 TTAATCTAATATT
1 TTAATCTAATATT
64617048 TATCTTGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
16 1 0.04
17 7 0.26
18 7 0.26
20 12 0.44
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (17 bp):
TTAATCTAATATTAAAT
Found at i:64619882 original size:11 final size:11
Alignment explanation
Indices: 64619868--64619915 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
64619858 TAAAAAATAC
64619868 AAAAAATTTAA
1 AAAAAATTTAA
*
64619879 AAAAAATCTAA
1 AAAAAATTTAA
* * *
64619890 AGAATATATAA
1 AAAAAATTTAA
64619901 AAAAAAGTTTAA
1 AAAAAA-TTTAA
64619913 AAA
1 AAA
64619916 TTTTTGAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
11 22 0.76
12 7 0.24
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (11 bp):
AAAAAATTTAA
Found at i:64619902 original size:20 final size:20
Alignment explanation
Indices: 64619856--64619904 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
64619846 TTCAAATATT
*
64619856 TATAAAAAATACAAAAAATT
1 TATAAAAAATACAAAAAATA
* *
64619876 TAAAAAAAAT-CTAAAGAATA
1 TATAAAAAATAC-AAAAAATA
64619896 TATAAAAAA
1 TATAAAAAA
64619905 AAGTTTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (20 bp):
TATAAAAAATACAAAAAATA
Found at i:64621524 original size:30 final size:30
Alignment explanation
Indices: 64621490--64621549 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
64621480 ACTTAACAAG
*
64621490 CAAATACCTCTAAAATAATAATAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
* *
64621520 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
64621550 TAATAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:64626911 original size:28 final size:28
Alignment explanation
Indices: 64626879--64626935 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
64626869 GAGACGTAAA
**
64626879 CTTCAAAATTGGGAAGCCAGGAAACTTT
1 CTTCAAAATTAAGAAGCCAGGAAACTTT
*
64626907 CTTCAGAATTAAGAAGCCAGGAAACTTT
1 CTTCAAAATTAAGAAGCCAGGAAACTTT
64626935 C
1 C
64626936 CTTTGTAGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (28 bp):
CTTCAAAATTAAGAAGCCAGGAAACTTT
Found at i:64628869 original size:3 final size:3
Alignment explanation
Indices: 64628861--64628892 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
64628851 TGAATGTACT
64628861 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
64628893 CAAAATAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:64630190 original size:29 final size:29
Alignment explanation
Indices: 64630148--64630204 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
64630138 TGTTATATCA
64630148 TATTTTAAAAATGGAAGGACTTAACGAGC
1 TATTTTAAAAATGGAAGGACTTAACGAGC
*
64630177 TATTTTGAAAATGGAAGGACTTAACGAG
1 TATTTTAAAAATGGAAGGACTTAACGAG
64630205 TTTAACATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (29 bp):
TATTTTAAAAATGGAAGGACTTAACGAGC
Found at i:64633659 original size:24 final size:24
Alignment explanation
Indices: 64633627--64633674 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
64633617 CTCTAAGAAT
*
64633627 GTGAAGCATATTATGAGAGAGAGA
1 GTGAAGCATATTATCAGAGAGAGA
64633651 GTGAAGCATATTATCAGAGAGAGA
1 GTGAAGCATATTATCAGAGAGAGA
64633675 CTTCTATCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.31, T:0.21
Consensus pattern (24 bp):
GTGAAGCATATTATCAGAGAGAGA
Found at i:64640696 original size:15 final size:16
Alignment explanation
Indices: 64640670--64640699 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
64640660 GACTCGGTTG
64640670 TTTCTCAGGAAAACAT
1 TTTCTCAGGAAAACAT
64640686 TTTCT-AGGAAAACA
1 TTTCTCAGGAAAACA
64640700 CTCTTTCAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (16 bp):
TTTCTCAGGAAAACAT
Found at i:64642778 original size:31 final size:31
Alignment explanation
Indices: 64642710--64642778 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
64642700 TCGGTAACTG
* **
64642710 AACTATTCGAAAGTTTTCATTTAAATCATTA
1 AACTATTCAAAAGTTTTCATTTAAATCACCA
* *
64642741 AACTATTCAAAAGTTTTTATTTAAGTCACCA
1 AACTATTCAAAAGTTTTCATTTAAATCACCA
*
64642772 AGCTATT
1 AACTATT
64642779 AAGTTTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (31 bp):
AACTATTCAAAAGTTTTCATTTAAATCACCA
Found at i:64644103 original size:17 final size:17
Alignment explanation
Indices: 64644083--64644117 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
64644073 AACAAAAAAA
*
64644083 AAACCAAAAATAAAATT
1 AAACCAAAAACAAAATT
*
64644100 AAACCCAAAACAAAATT
1 AAACCAAAAACAAAATT
64644117 A
1 A
64644118 GACAGTCCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14
Consensus pattern (17 bp):
AAACCAAAAACAAAATT
Found at i:64646689 original size:256 final size:256
Alignment explanation
Indices: 64646225--64646699 Score: 736
Period size: 256 Copynumber: 1.9 Consensus size: 256
64646215 CGTTTTATTC
* * **
64646225 AAAATAAGGCAACATTTCGTGTTTGGAAATTTCGAGAAAATCGTGCCCTACGTGCTGGGTTTCGA
1 AAAACAAGGCAAAATTTCGTGTTCAGAAATTTCGAGAAAATCGTGCCCTACGTGCTGGGTTTCGA
* * * *
64646290 TTTATTATTTAACCGAACAATCGAATATCCTTTTTAAAATTTCAATGCATAAGTTTTGGAAATCC
66 TTTATCATTTAACCGAACAACCGAATATCCTTTTTAAAATTTCAATACATAAGTTTTGGAAATCA
*
64646355 TGAGATGATTTTGGTATCGAAGGTTTGAAATATCATGTCCTACGTATTGGATGTGATATTTTATT
131 TGAGATAATTTTGGTATCGAAGGTTTGAAATATCATGTCCTACGTATTGGATGTGATATTTTATT
* *
64646420 TCTTCGAAACAAGAGAATCTTAATTGCTTCATACTATGGCATTTTTATTCAAGACTTTTTT
196 TCTCCGAAACAAGAAAATCTTAATTGCTTCATACTATGGCATTTTTATTCAAGACTTTTTT
* *
64646481 AAAACAAGGCAAAATTTCGTGTTCAGAAATTTCGAG-AAATTGTGCCCTACGTGTTGGGTTTCGA
1 AAAACAAGGCAAAATTTCGTGTTCAGAAATTTCGAGAAAATCGTGCCCTACGTGCTGGGTTTCGA
* * * *
64646545 TTTATCGTTTGACTGAACAACCGAATATCCTTTTTTAAAATTTCAATACATGAGTTTTGGAAATC
66 TTTATCATTTAACCGAACAACCGAATATCC-TTTTTAAAATTTCAATACATAAGTTTTGGAAATC
* * * *
64646610 ATGAGATAATTTTGGTATCGGAGGTTTGAAATGTCGTGTCCTACGTGTTGGATGTGATATTTTAT
130 ATGAGATAATTTTGGTATCGAAGGTTTGAAATATCATGTCCTACGTATTGGATGTGATATTTTAT
*
64646675 TTCTCCGGAACAAGAAAATCTTAAT
195 TTCTCCGAAACAAGAAAATCTTAAT
64646700 ATCCACTTCA
Statistics
Matches: 196, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
255 51 0.26
256 145 0.74
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (256 bp):
AAAACAAGGCAAAATTTCGTGTTCAGAAATTTCGAGAAAATCGTGCCCTACGTGCTGGGTTTCGA
TTTATCATTTAACCGAACAACCGAATATCCTTTTTAAAATTTCAATACATAAGTTTTGGAAATCA
TGAGATAATTTTGGTATCGAAGGTTTGAAATATCATGTCCTACGTATTGGATGTGATATTTTATT
TCTCCGAAACAAGAAAATCTTAATTGCTTCATACTATGGCATTTTTATTCAAGACTTTTTT
Found at i:64658603 original size:227 final size:227
Alignment explanation
Indices: 64658188--64658615 Score: 588
Period size: 227 Copynumber: 1.9 Consensus size: 227
64658178 CTGAATTTGC
* * * *
64658188 AGTGGAGCAGACCGAAAATAGCAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATTAAAGCTA
1 AGTGGACCAGACCGAAAATAACAGATCTTATCTCTCTGAAGTTGCAGCAGAGCAGATTAAAGCTA
* * * *
64658253 TAAATCCTATACCTCTGAAGTTGCAGCAGGTCAGATCAAATCTACCATGGTGAATCCTATTTCCC
66 TAAATCCTATACCTCTGAAGTTACAACAGGTCAGATCAAATCTACCATGGCGAATCCTACTTCCC
*** * * * * *
64658318 TGAAGTTGCAGTGGAGCAGATCGAAGCCACTAACCTTATTTCCCTGAAATTACAGTGGAGCAGGT
131 TGAAGTTGCAGCAAAACAGATCGAAGCCACCAACCTTATCTCACTGAAATTACAGTGGAGCAGAT
64658383 TGAAGTTACGAGTCTTATCTTACTGAAGTTAT
196 TGAAGTTACGAGTCTTATCTTACTGAAGTTAT
* * *
64658415 AGTGGACCAGACTGAAAATAACGGATCTTATCTCTTTGAAGTTGCAGCAGAGCAGATTAAAGCTA
1 AGTGGACCAGACCGAAAATAACAGATCTTATCTCTCTGAAGTTGCAGCAGAGCAGATTAAAGCTA
* *
64658480 TAAATCCTATACCTCTGAAGTTACAACAGGTCGGATCAAATCTACCATGGCGAATCTTACCTT-C
66 TAAATCCTATACCTCTGAAGTTACAACAGGTCAGATCAAATCTACCATGGCGAATCCTA-CTTCC
* * * ** * *
64658544 TTGAAGTTGCAGCAAAACAGATTGGAGCCACCAGTCTTATCTCACTGAAGTTGCAGTGGAGCAGA
130 CTGAAGTTGCAGCAAAACAGATCGAAGCCACCAACCTTATCTCACTGAAATTACAGTGGAGCAGA
64658609 TTGAAGT
195 TTGAAGT
64658616 CACAAACTTT
Statistics
Matches: 172, Mismatches: 28, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
227 170 0.99
228 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (227 bp):
AGTGGACCAGACCGAAAATAACAGATCTTATCTCTCTGAAGTTGCAGCAGAGCAGATTAAAGCTA
TAAATCCTATACCTCTGAAGTTACAACAGGTCAGATCAAATCTACCATGGCGAATCCTACTTCCC
TGAAGTTGCAGCAAAACAGATCGAAGCCACCAACCTTATCTCACTGAAATTACAGTGGAGCAGAT
TGAAGTTACGAGTCTTATCTTACTGAAGTTAT
Found at i:64661435 original size:253 final size:253
Alignment explanation
Indices: 64660987--64661443 Score: 700
Period size: 253 Copynumber: 1.8 Consensus size: 253
64660977 AAGGCAACAT
* *
64660987 TTCGTGTTTGGAAATTTCGAGAAAATCGTGCCCTACGTGCTGGGTTTCGATTTATCATTTAACCG
1 TTCGTGTTCGAAAATTTCGAGAAAATCGTGCCCTACGTGCTGGGTTTCGATTTATCATTTAACCG
* * * * *
64661052 AACAACCGAATATCCTTTTTAAAATTTCAATGCGTAAGTTTTGGAAATCCTGAGATGATTTTGGA
66 AACAACCAAATATCCTTTTTAAAATTTCAATACATAAGTTTTGGAAATCATGAGATAATTTTGGA
** *
64661117 ATCGAAGGTTTGAAATATTGTGTCCTACGTGCTGGATGTGATATTTTATTTCTTCGAAACAAGAG
131 ATCGAAGGTTTGAAATACCGTGTCCTACGTGCTGGATGTGATATTTTATTTCTCCGAAACAAGAG
64661182 AATCTTAATCGCTTCATACTATGACATTTTTATTCAAGACATTTTTAAAACAAGGCAA
196 AATCTTAATCGCTTCATACTATGACATTTTTATTCAAGACATTTTTAAAACAAGGCAA
* * * * *
64661240 TTCGTGTTCGAAAATTTTGAG-AAATTGTGCCCTACGTGTTGGGTTTCGATTTATCATTTGACTG
1 TTCGTGTTCGAAAATTTCGAGAAAATCGTGCCCTACGTGCTGGGTTTCGATTTATCATTTAACCG
*
64661304 AACAACCAAATATCCTTTTTTAAAATTTCAATACATGAGTTTTGGAAATCATGAGATAATTTTGG
66 AACAACCAAATATCC-TTTTTAAAATTTCAATACATAAGTTTTGGAAATCATGAGATAATTTTGG
* * * * * *
64661369 TATTGGAGGTTTGAAATGCCGTGTCCTACGTGTTGGATGTGATATTTTATTTCTCCGGAACAAGA
130 AATCGAAGGTTTGAAATACCGTGTCCTACGTGCTGGATGTGATATTTTATTTCTCCGAAACAAGA
64661434 GAATCTTAAT
195 GAATCTTAAT
64661444 ATCCACTTCA
Statistics
Matches: 181, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
252 53 0.29
253 128 0.71
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.37
Consensus pattern (253 bp):
TTCGTGTTCGAAAATTTCGAGAAAATCGTGCCCTACGTGCTGGGTTTCGATTTATCATTTAACCG
AACAACCAAATATCCTTTTTAAAATTTCAATACATAAGTTTTGGAAATCATGAGATAATTTTGGA
ATCGAAGGTTTGAAATACCGTGTCCTACGTGCTGGATGTGATATTTTATTTCTCCGAAACAAGAG
AATCTTAATCGCTTCATACTATGACATTTTTATTCAAGACATTTTTAAAACAAGGCAA
Found at i:64662461 original size:2 final size:2
Alignment explanation
Indices: 64662454--64662482 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
64662444 TTGCACCAAG
64662454 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
64662483 GGATCTATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:64666785 original size:21 final size:21
Alignment explanation
Indices: 64666759--64666800 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
64666749 AAATAAAAAA
64666759 TTATTT-TTAACTAAAAAATAC
1 TTATTTATTAA-TAAAAAATAC
64666780 TTATTTAATTAATAAAAAATA
1 TTATTT-ATTAATAAAAAATA
64666801 ATTTTATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 9 0.47
23 4 0.21
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (21 bp):
TTATTTATTAATAAAAAATAC
Found at i:64672715 original size:30 final size:31
Alignment explanation
Indices: 64672664--64672736 Score: 130
Period size: 30 Copynumber: 2.4 Consensus size: 31
64672654 TCTCCCTTTC
*
64672664 TTCTTTCTCTTTTCTTTTTTTTTTCTTTCTT
1 TTCTTTCTGTTTTCTTTTTTTTTTCTTTCTT
64672695 TTCTTTCTGTTTTC-TTTTTTTTTCTTTCTT
1 TTCTTTCTGTTTTCTTTTTTTTTTCTTTCTT
64672725 TTCTTTCTGTTT
1 TTCTTTCTGTTT
64672737 CATATGGCTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 28 0.68
31 13 0.32
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (31 bp):
TTCTTTCTGTTTTCTTTTTTTTTTCTTTCTT
Found at i:64672749 original size:30 final size:30
Alignment explanation
Indices: 64672685--64672756 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
64672675 TTCTTTTTTT
* ***
64672685 TTTCTTTCTTTTCTTTCTGTTTTCTTTTTT
1 TTTCTTTCTTTTCTTTCTGTTTTCTATGGC
64672715 TTTCTTTCTTTTCTTTCTG-TTTCATATGGC
1 TTTCTTTCTTTTCTTTCTGTTTTC-TATGGC
64672745 TTTCTTTCTTTT
1 TTTCTTTCTTTT
64672757 AATACTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 4 0.11
30 33 0.89
ACGTcount: A:0.03, C:0.18, G:0.06, T:0.74
Consensus pattern (30 bp):
TTTCTTTCTTTTCTTTCTGTTTTCTATGGC
Found at i:64672751 original size:4 final size:4
Alignment explanation
Indices: 64672649--64672732 Score: 63
Period size: 4 Copynumber: 22.0 Consensus size: 4
64672639 GCGTTGAACC
** * *
64672649 TTCT TTCT CCCT TTC- TTCT TTCT CT-T TTCT TT-T TTTT TTCT TTCTT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC-T
*
64672695 TTCT TTCT GT-T TTCT TT-T TT-T TTCT TTCTT TTCT TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC-T TTCT TTCT
64672733 GTTTCATATG
Statistics
Matches: 64, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
3 16 0.25
4 40 0.62
5 8 0.12
ACGTcount: A:0.00, C:0.23, G:0.01, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:64676234 original size:34 final size:34
Alignment explanation
Indices: 64676196--64676268 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 34
64676186 GAATAATCCC
*
64676196 TTGAATATTAGCAATAAAACACCTAATTGCCCCA
1 TTGAATATTAGCAATAAAACACCCAATTGCCCCA
*
64676230 TTGAATATTAGCAATAAAACACCCAATTGCCCCC
1 TTGAATATTAGCAATAAAACACCCAATTGCCCCA
64676264 TTGAA
1 TTGAA
64676269 CTCTCTAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.26
Consensus pattern (34 bp):
TTGAATATTAGCAATAAAACACCCAATTGCCCCA
Found at i:64677465 original size:24 final size:24
Alignment explanation
Indices: 64677438--64677486 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
64677428 TTAAGATAGA
64677438 GCTAAGGTTTTTGAGTTAACCAGT
1 GCTAAGGTTTTTGAGTTAACCAGT
64677462 GCTAAGGTTTTTGAGTTAACCAGT
1 GCTAAGGTTTTTGAGTTAACCAGT
64677486 G
1 G
64677487 GACGTTTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (24 bp):
GCTAAGGTTTTTGAGTTAACCAGT
Found at i:64679463 original size:21 final size:20
Alignment explanation
Indices: 64679429--64679475 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
64679419 ATATATGTAC
64679429 AAATATACACAAAACAATAT
1 AAATATACACAAAACAATAT
*
64679449 AAATGATATACAAAACAATAT
1 AAAT-ATACACAAAACAATAT
*
64679470 ATATAT
1 AAATAT
64679476 GAACAGATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.62, C:0.11, G:0.02, T:0.26
Consensus pattern (20 bp):
AAATATACACAAAACAATAT
Found at i:64679472 original size:23 final size:21
Alignment explanation
Indices: 64679429--64679470 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
64679419 ATATATGTAC
64679429 AAAT-ATACACAAAACAATAT
1 AAATGATACACAAAACAATAT
*
64679449 AAATGATATACAAAACAATAT
1 AAATGATACACAAAACAATAT
64679470 A
1 A
64679471 TATATGAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.64, C:0.12, G:0.02, T:0.21
Consensus pattern (21 bp):
AAATGATACACAAAACAATAT
Found at i:64680184 original size:21 final size:21
Alignment explanation
Indices: 64680160--64680199 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
64680150 TCTCATTTGG
*
64680160 CAAACCCTAGATCC-CCTCCTT
1 CAAACACT-GATCCGCCTCCTT
64680181 CAAACACTGATCCGCCTCC
1 CAAACACTGATCCGCCTCC
64680200 CTAAACAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.25, C:0.47, G:0.07, T:0.20
Consensus pattern (21 bp):
CAAACACTGATCCGCCTCCTT
Found at i:64680205 original size:20 final size:20
Alignment explanation
Indices: 64680169--64680206 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
64680159 GCAAACCCTA
*
64680169 GATCCCCTCCTTCAAACACT
1 GATCCCCTCCCTCAAACACT
64680189 GATCCGCCTCCCT-AAACA
1 GATCC-CCTCCCTCAAACA
64680207 GCAACCAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.26, C:0.45, G:0.08, T:0.21
Consensus pattern (20 bp):
GATCCCCTCCCTCAAACACT
Found at i:64682684 original size:15 final size:14
Alignment explanation
Indices: 64682664--64682697 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
64682654 TACATCTCCC
*
64682664 TTTTTATTATTTTTA
1 TTTTTATT-TATTTA
64682679 TTTTTATTTATTTA
1 TTTTTATTTATTTA
64682693 TTTTT
1 TTTTT
64682698 GCTTAAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTATTTATTTA
Found at i:64682853 original size:96 final size:97
Alignment explanation
Indices: 64682689--64682872 Score: 282
Period size: 96 Copynumber: 1.9 Consensus size: 97
64682679 TTTTTATTTA
* * * * *
64682689 TTTATTTTTGCTTAAGAATATATCGAACCTTTTGACGTGAAGAGAGATGACAGCCAATCATATCA
1 TTTATTTTTGCTTAAGAACATATCGAACCTTTTGACGCGAAAAGAGATGACAGCCAAGCACATCA
*
64682754 CCCTGGTTACTCAGCCT-ACACACTCCTAATT
66 CCCTAGTTACTCAGCCTAACACACTCCTAATT
*
64682785 TTTATTTTTGCTTAAGAACATATCGAA-CTTATTGACGCGAAAAGAGATGACAGCCAAGCACCTC
1 TTTATTTTTGCTTAAGAACATATCGAACCTT-TTGACGCGAAAAGAGATGACAGCCAAGCACATC
64682849 ACCCTAGTTACTCAGCCTAACACA
65 ACCCTAGTTACTCAGCCTAACACA
64682873 TTCTTAAAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
95 3 0.04
96 71 0.90
97 5 0.06
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (97 bp):
TTTATTTTTGCTTAAGAACATATCGAACCTTTTGACGCGAAAAGAGATGACAGCCAAGCACATCA
CCCTAGTTACTCAGCCTAACACACTCCTAATT
Found at i:64689749 original size:22 final size:22
Alignment explanation
Indices: 64689724--64689766 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
64689714 GAATTTTCCC
64689724 AAAAGATTTTCTCCAATTTCTA
1 AAAAGATTTTCTCCAATTTCTA
64689746 AAAAGATTTTCTCCAATTTCT
1 AAAAGATTTTCTCCAATTTCT
64689767 CTCTGTGCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.42
Consensus pattern (22 bp):
AAAAGATTTTCTCCAATTTCTA
Found at i:64691265 original size:4 final size:4
Alignment explanation
Indices: 64691252--64691294 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
64691242 TATCAACATC
64691252 TAAA -AAA TAAA TAAA T-AA TATAA TATAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TA-AA TA-AA TAAA TAAA TAAA TAA
64691295 GAAAGAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 6 0.17
4 21 0.58
5 9 0.25
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:64691306 original size:25 final size:25
Alignment explanation
Indices: 64691256--64691308 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
64691246 AACATCTAAA
* * *
64691256 AAATAAATAAATAATATAATATAAT
1 AAATAAATAAATAAGATAAAAAAAT
64691281 AAATAAATAAATAAGA-AAGAAAAAT
1 AAATAAATAAATAAGATAA-AAAAAT
64691306 AAA
1 AAA
64691309 AATAAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (25 bp):
AAATAAATAAATAAGATAAAAAAAT
Found at i:64695904 original size:92 final size:93
Alignment explanation
Indices: 64695793--64695962 Score: 288
Period size: 92 Copynumber: 1.8 Consensus size: 93
64695783 GCCCATAAGT
* *
64695793 GAACTCGGACTCAACTCAACGAGCTCGAGCGTTCGCATCCATAAGTGAACTCGGACTCAACTC-A
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
64695857 CGAGCTCGAATGCCTAGTTACATCTCAC
66 CGAGCTCGAATGCCTAGTTACATCTCAC
*
64695885 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
* *
64695950 CGAGTTCGGATGC
66 CGAGCTCGAATGC
64695963 TAAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
92 60 0.83
93 12 0.17
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGAATGCCTAGTTACATCTCAC
Found at i:64695957 original size:46 final size:46
Alignment explanation
Indices: 64695785--64695953 Score: 204
Period size: 46 Copynumber: 3.7 Consensus size: 46
64695775 TGTAACCCGC
* *
64695785 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCAT
*
64695831 CCATAAGTGAACTCGGACTCAACTC-ACGAGCTCGAATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAA---C-A-TTCGCAT
* * *
64695880 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCAT
64695923 CCATAAGTGAACTCGGACTCAACTCAACGAG
1 CCATAAGTGAACTCGGACTCAACTCAACGAG
64695954 TTCGGATGCT
Statistics
Matches: 104, Mismatches: 9, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 12 0.12
46 65 0.62
47 12 0.12
48 2 0.02
49 3 0.03
50 2 0.02
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCAT
Found at i:64700064 original size:93 final size:93
Alignment explanation
Indices: 64699905--64700076 Score: 254
Period size: 93 Copynumber: 1.8 Consensus size: 93
64699895 GCCCATAAGT
* * * *
64699905 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCATCCATAAGTGAACTTGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
64699970 CGAGCTCAGATGCCTAGTTACATCTCTC
66 CGAGCTCAGATGCCTAGTTACATCTCTC
* * * *
64699998 GAACTCGGACTTAACTTAACGAGTTCGGACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
* *
64700063 CGAGTTCGGATGCC
66 CGAGCTCAGATGCC
64700077 CAAACATCCT
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCAGATGCCTAGTTACATCTCTC
Found at i:64702502 original size:14 final size:15
Alignment explanation
Indices: 64702466--64702505 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
64702456 ATAGAAAACC
64702466 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
*
64702481 GAATAAAGAGATCCA
1 GAATAAAGAAATCCA
64702496 G-ATAAAGAAA
1 GAATAAAGAAA
64702506 CCCAAGATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.60, C:0.10, G:0.17, T:0.12
Consensus pattern (15 bp):
GAATAAAGAAATCCA
Found at i:64705503 original size:93 final size:93
Alignment explanation
Indices: 64705391--64705562 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
64705381 GCCCATAAGT
* * **
64705391 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTTGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
64705456 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
64705484 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
64705549 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
64705563 CAAACATCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:64705558 original size:46 final size:46
Alignment explanation
Indices: 64705383--64705558 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
64705373 TGTAACCCGC
* *
64705383 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
64705429 CCATAAGTGAACTTGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
64705475 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
64705522 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
64705559 TGCCCAAACA
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 68 0.63
47 31 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:64707368 original size:16 final size:17
Alignment explanation
Indices: 64707337--64707369 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
64707327 TTCATAAGTA
64707337 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
64707354 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
64707370 GCACCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:64707697 original size:46 final size:46
Alignment explanation
Indices: 64707632--64707905 Score: 361
Period size: 46 Copynumber: 6.0 Consensus size: 46
64707622 TTATCTTTGA
* * * *
64707632 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGT
*
64707678 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * * **
64707724 CACGCTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * *
64707770 CATGTTGCCATGGTATCTTTCAACCATAGTCTTATTCATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * *
64707816 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * *
64707862 CAGGTTGCCATGGTATCTTTCAACTATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
64707906 ATCAAAGAGC
Statistics
Matches: 207, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 4 0.02
46 203 0.98
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
Found at i:64713651 original size:38 final size:38
Alignment explanation
Indices: 64713559--64713637 Score: 135
Period size: 38 Copynumber: 2.1 Consensus size: 38
64713549 GCGTACCTGG
64713559 GAAAAGAATAAAA-AAAACAGAATTAAAAGTTTTGATCT
1 GAAAA-AATAAAATAAAACAGAATTAAAAGTTTTGATCT
64713597 GAAAAAATAAAATAAAACAGAATTAAAAGTTTTGAT-T
1 GAAAAAATAAAATAAAACAGAATTAAAAGTTTTGATCT
64713634 GAAA
1 GAAA
64713638 TTTCAAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
37 12 0.30
38 28 0.70
ACGTcount: A:0.59, C:0.04, G:0.13, T:0.24
Consensus pattern (38 bp):
GAAAAAATAAAATAAAACAGAATTAAAAGTTTTGATCT
Found at i:64714382 original size:10 final size:10
Alignment explanation
Indices: 64714366--64714414 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
64714356 TAAATTCTAG
64714366 AAGATAAATA
1 AAGATAAATA
*
64714376 TAGATAAATA
1 AAGATAAATA
*
64714386 AAGATAATTA
1 AAGATAAATA
64714396 AAGATAAATGA
1 AAGATAAAT-A
64714407 AA-ATAAAT
1 AAGATAAAT
64714415 CCTAAAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 31 0.91
11 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.24
Consensus pattern (10 bp):
AAGATAAATA
Found at i:64715053 original size:107 final size:105
Alignment explanation
Indices: 64714859--64715092 Score: 263
Period size: 107 Copynumber: 2.2 Consensus size: 105
64714849 AAATGCAAGA
* * * * * * *
64714859 CCATATAGTTGAGATCCATGGCATTGTGTGATACGAAACTACTCACGGTGTTGCTTCTATAAGAT
1 CCATATGGCTGAGA-CCATGGCATTGTGTAATACAAAACCACTCACGGTATTGCTTCCATAAGAT
* * ** *
64714924 GAAGTTTGGATTGGCAGATCACGACATGATTAGGTGTAAGC
65 GAAGTCTAGATTGGCAGATCACGACATGAGAAGGTATAAGC
* * *
64714965 CCTTGTGGCTGAGACCAATGGCTTTGTGTAATACAAAACCACTCACGGTATTGGC-TCCAGTAAG
1 CCATATGGCTGAGACC-ATGGCATTGTGTAATACAAAACCACTCACGGTATT-GCTTCCA-TAAG
* *
64715029 ATGAAGTCTAGATTGGCATATCACGACATGAGAAGGTATAAGT
63 ATGAAGTCTAGATTGGCAGATCACGACATGAGAAGGTATAAGC
64715072 CCATATGGCTGAGACTCATGG
1 CCATATGGCTGAGAC-CATGG
64715093 TATAATATGA
Statistics
Matches: 105, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
105 2 0.02
106 43 0.41
107 59 0.56
108 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (105 bp):
CCATATGGCTGAGACCATGGCATTGTGTAATACAAAACCACTCACGGTATTGCTTCCATAAGATG
AAGTCTAGATTGGCAGATCACGACATGAGAAGGTATAAGC
Found at i:64725996 original size:11 final size:11
Alignment explanation
Indices: 64725980--64726004 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
64725970 AGTTGAGGCG
64725980 ATGACAAATAT
1 ATGACAAATAT
64725991 ATGACAAATAT
1 ATGACAAATAT
64726002 ATG
1 ATG
64726005 TAGGGTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (11 bp):
ATGACAAATAT
Found at i:64736418 original size:29 final size:30
Alignment explanation
Indices: 64736359--64736416 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
64736349 TCCGAGCCTT
*
64736359 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
64736389 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
64736417 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:64736647 original size:13 final size:13
Alignment explanation
Indices: 64736629--64736659 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
64736619 TTTCAGCAAC
64736629 TATGAATTTATTT
1 TATGAATTTATTT
64736642 TATGAATTTATTT
1 TATGAATTTATTT
*
64736655 GATGA
1 TATGA
64736660 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:64736829 original size:50 final size:50
Alignment explanation
Indices: 64736754--64736895 Score: 248
Period size: 50 Copynumber: 2.8 Consensus size: 50
64736744 ATTTGGGTAA
64736754 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
64736804 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
64736854 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
64736896 TGTTATTATC
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 88 1.00
ACGTcount: A:0.25, C:0.23, G:0.32, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:64743902 original size:29 final size:30
Alignment explanation
Indices: 64743843--64743900 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
64743833 TCCGAGCCTT
*
64743843 GGGGAAAAAATGTAATTATGTAAAAGTTTA
1 GGGGAAAAAATGTAATTATGAAAAAGTTTA
* * *
64743873 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGAAAAAATGTAATTATGAAAAAGTT
64743901 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.43, C:0.02, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGAAAAAATGTAATTATGAAAAAGTTTA
Found at i:64744131 original size:13 final size:13
Alignment explanation
Indices: 64744113--64744143 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
64744103 TTCCAGCAAC
64744113 TATGAATTTATTT
1 TATGAATTTATTT
64744126 TATGAATTTATTT
1 TATGAATTTATTT
*
64744139 GATGA
1 TATGA
64744144 TGATCTAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:64744315 original size:50 final size:50
Alignment explanation
Indices: 64744238--64744429 Score: 278
Period size: 50 Copynumber: 3.8 Consensus size: 50
64744228 ATTTGGGTAA
* *
64744238 AGAGGT-CCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
*
64744287 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
* * * *
64744337 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
** *
64744387 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
64744430 TGTTATTATC
Statistics
Matches: 127, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
49 6 0.05
50 87 0.69
51 34 0.27
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
Found at i:64744429 original size:101 final size:100
Alignment explanation
Indices: 64744249--64744429 Score: 290
Period size: 101 Copynumber: 1.8 Consensus size: 100
64744239 GAGGTCCATG
* * * * **
64744249 TAAGACCATGTTTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGG
1 TAAGACCATGTCTGGGACATGGCATGGGCACCAACATGAGACATCCCATGTAAGACCATGTCTGG
64744314 GACATGGCGTTGGCACCAAGATGAGAGGTCCCCTA
66 GACATGGCGTTGGCACCAAGATGAGAGGTCCCCTA
64744349 TAAGACCATGTCTGGGACATGGCATGGGCACCAACATGAGAACATCCCATGTAAGACCATGTCTG
1 TAAGACCATGTCTGGGACATGGCATGGGCACCAACATGAG-ACATCCCATGTAAGACCATGTCTG
*
64744414 GGACATGGCTTTGGCA
65 GGACATGGCGTTGGCA
64744430 TGTTATTATC
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
100 36 0.49
101 37 0.51
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (100 bp):
TAAGACCATGTCTGGGACATGGCATGGGCACCAACATGAGACATCCCATGTAAGACCATGTCTGG
GACATGGCGTTGGCACCAAGATGAGAGGTCCCCTA
Found at i:64756574 original size:18 final size:18
Alignment explanation
Indices: 64756548--64756582 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
64756538 ATCAAAATTT
64756548 TAAAAATCAAATTTAAAC
1 TAAAAATCAAATTTAAAC
*
64756566 TAAAGATCAAATTTAAA
1 TAAAAATCAAATTTAAA
64756583 TTAATTATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.09, G:0.03, T:0.29
Consensus pattern (18 bp):
TAAAAATCAAATTTAAAC
Found at i:64756656 original size:29 final size:29
Alignment explanation
Indices: 64756623--64756714 Score: 121
Period size: 29 Copynumber: 3.1 Consensus size: 29
64756613 TAATTTGATC
* *
64756623 TTTATCCAGCCAATTTCAATTCTTCAATT
1 TTTATCCAGCCAACTTCAAATCTTCAATT
* * *
64756652 TTTATCCAGCCTACTTCAAATCTTTAATC
1 TTTATCCAGCCAACTTCAAATCTTCAATT
*
64756681 TTTATCCAGCCAACTTCAAATATTCAATCT
1 TTTATCCAGCCAACTTCAAATCTTCAAT-T
64756711 TTTA
1 TTTA
64756715 ATATAGAGTA
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 49 0.92
30 4 0.08
ACGTcount: A:0.29, C:0.25, G:0.03, T:0.42
Consensus pattern (29 bp):
TTTATCCAGCCAACTTCAAATCTTCAATT
Found at i:64774259 original size:26 final size:25
Alignment explanation
Indices: 64774204--64774259 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
64774194 GGATATGTAT
*
64774204 ATTTTTATTTTAACATATTTTTCTA
1 ATTTTTATTTTAACATAGTTTTCTA
* *
64774229 TTTTTCTATTTTATATATAGTTTT-TA
1 ATTTT-TATTTTA-ACATAGTTTTCTA
64774255 ATTTT
1 ATTTT
64774260 AAAATAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
25 4 0.16
26 13 0.52
27 8 0.32
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (25 bp):
ATTTTTATTTTAACATAGTTTTCTA
Found at i:64775896 original size:45 final size:45
Alignment explanation
Indices: 64775846--64775967 Score: 199
Period size: 45 Copynumber: 2.7 Consensus size: 45
64775836 ATACGCTTAC
64775846 AATGAGTAAGACCATAGCTAAAAGATGCTATGACATTGTGACAAA
1 AATGAGTAAGACCATAGCTAAAAGATGCTATGACATTGTGACAAA
* * *
64775891 AATGAGTAAGACCATAGCTCAAAGATGCTATAACATTGTGACAAG
1 AATGAGTAAGACCATAGCTAAAAGATGCTATGACATTGTGACAAA
* *
64775936 AATGAGTAAGACCATAGCTGAAAGATGTTATG
1 AATGAGTAAGACCATAGCTAAAAGATGCTATG
64775968 GCGTGTTGGT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 71 1.00
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (45 bp):
AATGAGTAAGACCATAGCTAAAAGATGCTATGACATTGTGACAAA
Found at i:64775913 original size:23 final size:23
Alignment explanation
Indices: 64775846--64775913 Score: 54
Period size: 23 Copynumber: 3.0 Consensus size: 23
64775836 ATACGCTTAC
64775846 AATGAGTAAGACCATAGCT-AAA
1 AATGAGTAAGACCATAGCTCAAA
* * *
64775868 AGATG-CTATGA-CATTG-TGACAAA
1 A-ATGAGTAAGACCATAGCT--CAAA
64775891 AATGAGTAAGACCATAGCTCAAA
1 AATGAGTAAGACCATAGCTCAAA
64775914 GATGCTATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 13
0.63 0.12 0.25
Matches are distributed among these distances:
20 1 0.03
21 4 0.12
22 8 0.24
23 15 0.45
24 4 0.12
25 1 0.03
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.21
Consensus pattern (23 bp):
AATGAGTAAGACCATAGCTCAAA
Found at i:64780309 original size:23 final size:23
Alignment explanation
Indices: 64780279--64780324 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
64780269 TTAAAAGTAA
64780279 GATTTTCTCAAGATTTTTATGTT
1 GATTTTCTCAAGATTTTTATGTT
64780302 GATTTTCTCAAGATTTTTATGTT
1 GATTTTCTCAAGATTTTTATGTT
64780325 CTTTAGAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.09, G:0.13, T:0.57
Consensus pattern (23 bp):
GATTTTCTCAAGATTTTTATGTT
Found at i:64782024 original size:19 final size:19
Alignment explanation
Indices: 64781981--64782040 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 19
64781971 ATTTTAAATA
64781981 AGTTTTTATTAATTTATAAT
1 AGTTTTTA-TAATTTATAAT
* *
64782001 A-TTTTTATAATTTCTCAT
1 AGTTTTTATAATTTATAAT
*
64782019 AGTTTTTTAATAATTTTTAAT
1 AG-TTTTT-ATAATTTATAAT
64782040 A
1 A
64782041 ATTATTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 10 0.30
19 6 0.18
20 6 0.18
21 11 0.33
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (19 bp):
AGTTTTTATAATTTATAAT
Found at i:64782037 original size:10 final size:10
Alignment explanation
Indices: 64781969--64782043 Score: 64
Period size: 10 Copynumber: 7.5 Consensus size: 10
64781959 ATATTTGTTG
*
64781969 TAATTTTAAA
1 TAATTTTTAA
*
64781979 TAAGTTTTTAT
1 TAA-TTTTTAA
*
64781990 TAATTTATAA
1 TAATTTTTAA
64782000 T-ATTTTT-A
1 TAATTTTTAA
* *
64782008 TAATTTCTCA
1 TAATTTTTAA
*
64782018 TAGTTTTTTAA
1 TA-ATTTTTAA
64782029 TAATTTTTAA
1 TAATTTTTAA
64782039 TAATT
1 TAATT
64782044 ATTTGAAAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
8 2 0.04
9 10 0.20
10 24 0.47
11 15 0.29
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:64784779 original size:18 final size:18
Alignment explanation
Indices: 64784747--64784784 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
64784737 ACAATTTTGA
*
64784747 TTAAATTATAATTAT-TT
1 TTAAATTACAATTATCTT
64784764 TTAAATATACAATTATCTT
1 TTAAAT-TACAATTATCTT
64784783 TT
1 TT
64784785 TAACTTCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 8 0.44
19 4 0.22
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAAATTACAATTATCTT
Found at i:64797061 original size:31 final size:31
Alignment explanation
Indices: 64797026--64797087 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
64797016 AATAATAACC
64797026 CAATGACTTAAAT-AATAACTTTCAAATAGTT
1 CAATGACTTAAATGAA-AACTTTCAAATAGTT
* *
64797057 CAATGATTTAAATGAAAGCTTTCAAATAGTT
1 CAATGACTTAAATGAAAACTTTCAAATAGTT
64797088 TAGTGGCTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (31 bp):
CAATGACTTAAATGAAAACTTTCAAATAGTT
Found at i:64798523 original size:20 final size:20
Alignment explanation
Indices: 64798487--64798526 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
64798477 CTTACAACTT
64798487 GAAAAATAAAATTTTTCATAA
1 GAAAAATAAAA-TTTTCATAA
64798508 GAAAATATAAAA-TTTCATA
1 GAAAA-ATAAAATTTTCATA
64798527 TTTCGATCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (20 bp):
GAAAAATAAAATTTTCATAA
Found at i:64809169 original size:38 final size:38
Alignment explanation
Indices: 64809118--64809194 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
64809108 ATTTAAACCT
64809118 AAGCTTAAAAGTAAAAATAAATATCTACTCATAATTAG
1 AAGCTTAAAAGTAAAAATAAATATCTACTCATAATTAG
64809156 AAGCTTAAAAGTAAAAATAAATATCTACTCATAATTAG
1 AAGCTTAAAAGTAAAAATAAATATCTACTCATAATTAG
64809194 A
1 A
64809195 TTATGCTCTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.29
Consensus pattern (38 bp):
AAGCTTAAAAGTAAAAATAAATATCTACTCATAATTAG
Found at i:64812545 original size:12 final size:11
Alignment explanation
Indices: 64812519--64812544 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
64812509 TCATCTGCCC
64812519 TTTTCTTTTTT
1 TTTTCTTTTTT
64812530 TTTTCTTTTTT
1 TTTTCTTTTTT
64812541 TTTT
1 TTTT
64812545 TTGCAATCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:64818389 original size:12 final size:12
Alignment explanation
Indices: 64818368--64818408 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
64818358 TCAACAAAAA
* *
64818368 AAACATGCAAGC
1 AAACAAGCAAAC
64818380 AAACAAGCAAAC
1 AAACAAGCAAAC
*
64818392 AAACAAACAAAC
1 AAACAAGCAAAC
64818404 AAACA
1 AAACA
64818409 TCAAATCTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.66, C:0.24, G:0.07, T:0.02
Consensus pattern (12 bp):
AAACAAGCAAAC
Found at i:64818394 original size:4 final size:4
Alignment explanation
Indices: 64818379--64818408 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
64818369 AACATGCAAG
*
64818379 CAAA CAAG CAAA CAAA CAAA CAAA CAAA CA
1 CAAA CAAA CAAA CAAA CAAA CAAA CAAA CA
64818409 TCAAATCTTC
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:0.70, C:0.27, G:0.03, T:0.00
Consensus pattern (4 bp):
CAAA
Found at i:64824617 original size:18 final size:18
Alignment explanation
Indices: 64824583--64824616 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
64824573 CTTTTATTAA
64824583 ATGATTATTATTATTTTG
1 ATGATTATTATTATTTTG
*
64824601 ATGATT-TTTTTATTTT
1 ATGATTATTATTATTTT
64824617 TTTCATACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (18 bp):
ATGATTATTATTATTTTG
Found at i:64824852 original size:29 final size:29
Alignment explanation
Indices: 64824793--64824852 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 29
64824783 TTTAATCTAA
* * * *
64824793 TGTGTAATTCTATACATGTACTTTGATTT
1 TGTGGAATTCTATACATGAAATTTGAATT
* *
64824822 TGTGGAATTTTATACATGAAATTTTAATT
1 TGTGGAATTCTATACATGAAATTTGAATT
64824851 TG
1 TG
64824853 ATCAGATTCT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (29 bp):
TGTGGAATTCTATACATGAAATTTGAATT
Found at i:64827054 original size:25 final size:26
Alignment explanation
Indices: 64827028--64827078 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
64827018 TAAAAAAATA
64827028 AAAATAAA-AA-TTCTAAAATTATAT
1 AAAATAAATAATTTCTAAAATTATAT
*
64827052 AAAATAAATAATTTTCTTAAATTATAT
1 AAAATAAATAA-TTTCTAAAATTATAT
64827079 TTTTACTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 8 0.35
25 2 0.09
27 13 0.57
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (26 bp):
AAAATAAATAATTTCTAAAATTATAT
Found at i:64827118 original size:21 final size:21
Alignment explanation
Indices: 64827093--64827133 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
64827083 ACTTTTGAAA
64827093 TTATAAAAAAATATAAAATTG
1 TTATAAAAAAATATAAAATTG
* *
64827114 TTATAAAAATATTTAAAATT
1 TTATAAAAAAATATAAAATT
64827134 AACATGAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
TTATAAAAAAATATAAAATTG
Found at i:64830187 original size:15 final size:16
Alignment explanation
Indices: 64830167--64830197 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
64830157 TAATGCAAAG
64830167 TGAATTG-AAATATAT
1 TGAATTGAAAATATAT
64830182 TGAATTGAAAATATAT
1 TGAATTGAAAATATAT
64830198 ATGATTAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (16 bp):
TGAATTGAAAATATAT
Found at i:64830422 original size:12 final size:12
Alignment explanation
Indices: 64830405--64830434 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
64830395 GTACCGCTAC
64830405 TGTTACTGTTAT
1 TGTTACTGTTAT
64830417 TGTTACTGTTAT
1 TGTTACTGTTAT
*
64830429 CGTTAC
1 TGTTAC
64830435 GGTGTATTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.13, G:0.17, T:0.53
Consensus pattern (12 bp):
TGTTACTGTTAT
Found at i:64834592 original size:46 final size:46
Alignment explanation
Indices: 64834534--64834855 Score: 511
Period size: 46 Copynumber: 7.0 Consensus size: 46
64834524 GTGTGCTCTT
64834534 TGATAT-AGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGA-AATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
64834580 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
*
64834626 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
*
64834672 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
**
64834718 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
* * *
64834764 TGATATGAAATGAGTAAGACCATGGTTGAAGGATACCATGGCAACA
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
*** **
64834810 TGACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 TGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
64834856 ATGACAGAAA
Statistics
Matches: 262, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
46 225 0.86
47 37 0.14
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (46 bp):
TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
Found at i:64834885 original size:46 final size:46
Alignment explanation
Indices: 64834534--64834892 Score: 506
Period size: 46 Copynumber: 7.8 Consensus size: 46
64834524 GTGTGCTCTT
*
64834534 TGATAT-AGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGA-AATGAGTAAGACCATGGTTGAAAGATACCATGGCAACC
*
64834580 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACC
* *
64834626 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACC
* *
64834672 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACC
*
64834718 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACC
* *
64834764 TGATATGAAATGAGTAAGACCATGGTTGAAGGATACCATGGCAACA
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACC
*** * *
64834810 TGACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACC
* ** * *
64834857 TGACA-GAAAACAAGTAAAACCATAGTTGAAAGATAC
1 TGATATG-AAATGAGTAAGACCATGGTTGAAAGATAC
64834893 TATGACATCA
Statistics
Matches: 293, Mismatches: 18, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
46 251 0.86
47 42 0.14
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACC
Found at i:64840177 original size:4 final size:4
Alignment explanation
Indices: 64840168--64840194 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
64840158 CTACTCAAAG
64840168 ATTT ATTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATT
64840195 CATATAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:64850350 original size:21 final size:21
Alignment explanation
Indices: 64850325--64850366 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
64850315 ATTAGAAAAC
64850325 ATGTAAAAGTACAAGATAAAT
1 ATGTAAAAGTACAAGATAAAT
64850346 ATGTAAAAGTACAAGATAAAT
1 ATGTAAAAGTACAAGATAAAT
64850367 TACATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.24
Consensus pattern (21 bp):
ATGTAAAAGTACAAGATAAAT
Found at i:64854379 original size:27 final size:27
Alignment explanation
Indices: 64854342--64854411 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
64854332 CAAGCAAATG
64854342 AATAAAA-AAAATAAATAAAAGAAGG-
1 AATAAAATAAAATAAATAAAAGAAGGT
*
64854367 AATTAAAATAAAACAAATAAAAGAAGGT
1 AA-TAAAATAAAATAAATAAAAGAAGGT
64854395 AATAATAATAATAATAA
1 AATAA-AATAA-AATAA
64854412 TAATAATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
25 2 0.05
26 5 0.13
27 20 0.53
28 7 0.18
29 4 0.11
ACGTcount: A:0.71, C:0.01, G:0.09, T:0.19
Consensus pattern (27 bp):
AATAAAATAAAATAAATAAAAGAAGGT
Found at i:64854402 original size:3 final size:3
Alignment explanation
Indices: 64854394--64854418 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
64854384 TAAAAGAAGG
64854394 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
64854419 TTAAACTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:64856332 original size:12 final size:12
Alignment explanation
Indices: 64856315--64856346 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
64856305 TAGTTAGAAA
64856315 AAGAAATTATTG
1 AAGAAATTATTG
64856327 AAGAAATTATTG
1 AAGAAATTATTG
64856339 AAGAAATT
1 AAGAAATT
64856347 GGGTAAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (12 bp):
AAGAAATTATTG
Found at i:64867241 original size:13 final size:13
Alignment explanation
Indices: 64867219--64867248 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
64867209 CAAAGGGGTT
64867219 GAGAAAAAAAATA
1 GAGAAAAAAAATA
*
64867232 GAGAAGAAAAATA
1 GAGAAAAAAAATA
64867245 GAGA
1 GAGA
64867249 TAGGGAGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (13 bp):
GAGAAAAAAAATA
Found at i:64868372 original size:19 final size:19
Alignment explanation
Indices: 64868328--64868366 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
64868318 TAGTGTATAG
* *
64868328 ATGAATTGAAATTTGGATG
1 ATGAATTGAAATTTGAATA
64868347 ATGAATTGAAATTTGAATA
1 ATGAATTGAAATTTGAATA
64868366 A
1 A
64868367 GTAATTTAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.36
Consensus pattern (19 bp):
ATGAATTGAAATTTGAATA
Found at i:64872506 original size:46 final size:46
Alignment explanation
Indices: 64872456--64872631 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
64872446 TGGTTGAGCA
64872456 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
64872502 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * *
64872547 CATTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTGTGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
64872595 CCCGAGCTCGTTGTGTTGAGTCTGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
64872632 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 16, Indels: 18
0.76 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 59 0.56
47 28 0.27
48 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:64872622 original size:93 final size:93
Alignment explanation
Indices: 64872453--64872624 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
64872443 GGATGGTTGA
* *
64872453 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
64872518 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
64872546 GCATTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTGTGGATGCGAACGCCCGAGCTCGTTGTGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
64872611 TGAGTCTGAGTTCG
66 TGAGTCCGAGTTCG
64872625 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:64876588 original size:29 final size:30
Alignment explanation
Indices: 64876539--64876602 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
64876529 TGTTTTATTA
* * *
64876539 TGGTA-TTTTACTTTTATAAATGTCCAATG
1 TGGTACTTGTACTTTGATAAATGTACAATG
*
64876568 TGGTACTTGTACTTTGA-AAATGTATAATG
1 TGGTACTTGTACTTTGATAAATGTACAATG
64876597 TGGTAC
1 TGGTAC
64876603 CTAAATTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (30 bp):
TGGTACTTGTACTTTGATAAATGTACAATG
Found at i:64877785 original size:15 final size:14
Alignment explanation
Indices: 64877742--64877782 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
64877732 TTGGACTTAT
64877742 TTTTTATATTTTAA
1 TTTTTATATTTTAA
64877756 TTTAATTA-ATTTTAA
1 TTT--TTATATTTTAA
64877771 TTTTTATATTTT
1 TTTTTATATTTT
64877783 TAAAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 3 0.12
14 8 0.33
15 10 0.42
16 3 0.12
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTATATTTTAA
Found at i:64878423 original size:64 final size:64
Alignment explanation
Indices: 64878322--64878451 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
64878312 TTTCTTTAGC
64878322 TTTTTAAAGCCTTAAGATAACTTTATTAGATAGTGATCTCATATCTTTTTTAATACTATTGAAT
1 TTTTTAAAGCCTTAAGATAACTTTATTAGATAGTGATCTCATATCTTTTTTAATACTATTGAAT
64878386 TTTTTAAAGCCTTAAGATAACTTTATTAGATAGTGATCTCATATCTTTTTTAATACTATTGAAT
1 TTTTTAAAGCCTTAAGATAACTTTATTAGATAGTGATCTCATATCTTTTTTAATACTATTGAAT
64878450 TT
1 TT
64878452 GATTACTCTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (64 bp):
TTTTTAAAGCCTTAAGATAACTTTATTAGATAGTGATCTCATATCTTTTTTAATACTATTGAAT
Found at i:64888834 original size:27 final size:27
Alignment explanation
Indices: 64888804--64888858 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
64888794 TAGGGAATTT
64888804 TTTGAAACCATTGAATTCAAATTATGG
1 TTTGAAACCATTGAATTCAAATTATGG
64888831 TTTGAAACCATTGAATTCAAATTATGG
1 TTTGAAACCATTGAATTCAAATTATGG
64888858 T
1 T
64888859 AAGGTAGCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (27 bp):
TTTGAAACCATTGAATTCAAATTATGG
Found at i:64893812 original size:30 final size:30
Alignment explanation
Indices: 64893773--64893835 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
64893763 ACTTGTTTTA
64893773 TTGTCAATTTTGTTATTATTTTAAAGACAT
1 TTGTCAATTTTGTTATTATTTTAAAGACAT
* * *
64893803 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTCAATTTTGTTATTATTTTAAAGACAT
64893833 TTG
1 TTG
64893836 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.05, G:0.14, T:0.56
Consensus pattern (30 bp):
TTGTCAATTTTGTTATTATTTTAAAGACAT
Found at i:64899903 original size:24 final size:24
Alignment explanation
Indices: 64899833--64899930 Score: 135
Period size: 24 Copynumber: 4.1 Consensus size: 24
64899823 GTCGCTGTCC
*
64899833 CCCTTGCCCTTACCATTGCTGTCG
1 CCCTTGCCCTTACCATTGCTGTTG
64899857 CCCTTGCCCTTACCATTGCTGTTG
1 CCCTTGCCCTTACCATTGCTGTTG
*
64899881 CCCTTGCTCTTACCATTGCTGTTG
1 CCCTTGCCCTTACCATTGCTGTTG
* * *
64899905 CCATAT-CCATTACCATTGTTGTTG
1 CCCT-TGCCCTTACCATTGCTGTTG
64899929 CC
1 CC
64899931 ATTCCCATTG
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
24 66 0.99
25 1 0.01
ACGTcount: A:0.11, C:0.36, G:0.15, T:0.38
Consensus pattern (24 bp):
CCCTTGCCCTTACCATTGCTGTTG
Found at i:64899908 original size:12 final size:12
Alignment explanation
Indices: 64899845--64899908 Score: 56
Period size: 12 Copynumber: 5.3 Consensus size: 12
64899835 CTTGCCCTTA
*
64899845 CCATTGCTGTCG
1 CCATTGCTGTTG
* ** *
64899857 CCCTTGCCCTTA
1 CCATTGCTGTTG
64899869 CCATTGCTGTTG
1 CCATTGCTGTTG
* * *
64899881 CCCTTGCTCTTA
1 CCATTGCTGTTG
64899893 CCATTGCTGTTG
1 CCATTGCTGTTG
64899905 CCAT
1 CCAT
64899909 ATCCATTACC
Statistics
Matches: 37, Mismatches: 15, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.09, C:0.36, G:0.17, T:0.38
Consensus pattern (12 bp):
CCATTGCTGTTG
Found at i:64903741 original size:17 final size:18
Alignment explanation
Indices: 64903721--64903764 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
64903711 ATTTTTTATG
64903721 AAATTTTTAT-ATATTTT
1 AAATTTTTATAATATTTT
*
64903738 AAATTTTTTTGAATATTTT
1 AAATTTTTAT-AATATTTT
64903757 ATAATTTT
1 A-AATTTT
64903765 AAATTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 9 0.39
19 8 0.35
20 6 0.26
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
AAATTTTTATAATATTTT
Done.