Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009001.1 Hibiscus syriacus cultivar Beakdansim tig00112383_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4740655
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 24
Found at i:1940936 original size:83 final size:83
Alignment explanation
Indices: 1940765--1940951 Score: 223
Period size: 83 Copynumber: 2.2 Consensus size: 83
1940755 CATAAATCTT
* * *
1940765 AGATGACACGCAATTGTGTGTCATAAATCTATGACGCGCATTTATGACGCGCATTGCGCGTCATT
1 AGATGACACAC-ATT-TGTGTCATAAATCTATGACACGCATTTATGACGCACATTGCGCGTCATT
* * * *
1940830 GAAGCCCCCGTCATAAATGA
64 GAAGCACACATCATAAATAA
* * ** *
1940850 AGATGACACATATTTGTGTCATAAATTTATGACACGCATTTATGACTTACATTGCGTGTCATTGA
1 AGATGACACACATTTGTGTCATAAATCTATGACACGCATTTATGACGCACATTGCGCGTCATTGA
1940915 AGCACACATCATTAAA-AA
66 AGCACACATCA-TAAATAA
*
1940933 AGATGACACACATTCGTGT
1 AGATGACACACATTTGTGT
1940952 TTCATGATTG
Statistics
Matches: 87, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
83 71 0.82
84 7 0.08
85 9 0.10
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (83 bp):
AGATGACACACATTTGTGTCATAAATCTATGACACGCATTTATGACGCACATTGCGCGTCATTGA
AGCACACATCATAAATAA
Found at i:1940981 original size:2 final size:2
Alignment explanation
Indices: 1940974--1941013 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1940964 TGTCGTAAAT
1940974 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1941014 TGTAGATTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1959883 original size:42 final size:42
Alignment explanation
Indices: 1959837--1959923 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
1959827 TACCCGTTTG
1959837 CAACCAATAGTCTTTTTACTTAAGGGTAAATCCACCAAGGGC
1 CAACCAATAGTCTTTTTACTTAAGGGTAAATCCACCAAGGGC
*
1959879 CAACCAATAGTCTTTTTACTTGAGGGTAAATCCACCAAGGGC
1 CAACCAATAGTCTTTTTACTTAAGGGTAAATCCACCAAGGGC
1959921 CAA
1 CAA
1959924 ATGATTCTCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.25
Consensus pattern (42 bp):
CAACCAATAGTCTTTTTACTTAAGGGTAAATCCACCAAGGGC
Found at i:1961119 original size:41 final size:43
Alignment explanation
Indices: 1960927--1961123 Score: 176
Period size: 44 Copynumber: 4.7 Consensus size: 43
1960917 AAGTTATGAA
* *
1960927 AAAAAACTTA-AGGCCTCAATTATAAAGTTAAAAAGTG-GATT
1 AAAAAACTTAGAGGCCTCAATTATAAAGGTAGAAAGTGAGATT
* * *
1960968 AAAAAA-TT-GGGTGCCTCAATTATAAAGGTAGATATTGAGATT
1 AAAAAACTTAGAG-GCCTCAATTATAAAGGTAGAAAGTGAGATT
* *
1961010 GAAAAAACTTA-AGGACTTCAATTGA-AAAGGTAGAAAGTGAGAATG
1 -AAAAAACTTAGAGG-CCTCAATT-ATAAAGGTAGAAAGTGAG-ATT
* * *
1961055 AAAAAACTTAAAAGCCTCAATTATAAAGTTA-AAAGTGAGATT
1 AAAAAACTTAGAGGCCTCAATTATAAAGGTAGAAAGTGAGATT
* * *
1961097 ACAAAA-TTAGGGGTCTCAATTATAAAG
1 AAAAAACTTAGAGGCCTCAATTATAAAG
1961124 ACAATAAAAG
Statistics
Matches: 126, Mismatches: 19, Indels: 22
0.75 0.11 0.13
Matches are distributed among these distances:
40 3 0.02
41 44 0.35
42 11 0.09
43 16 0.13
44 47 0.37
45 5 0.04
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (43 bp):
AAAAAACTTAGAGGCCTCAATTATAAAGGTAGAAAGTGAGATT
Found at i:1961157 original size:129 final size:128
Alignment explanation
Indices: 1960927--1961185 Score: 298
Period size: 129 Copynumber: 2.0 Consensus size: 128
1960917 AAGTTATGAA
*
1960927 AAAAAACTTAAGGCCTCAATTATAAAGTTAAAAAGTGGATTAAAAAATTGGGTGCCTCAATTATA
1 AAAAAACTTAAAGCCTCAATTATAAAGTTAAAAAGTGGATTAAAAAATTGGGTGCCTCAATTATA
** ** * * *
1960992 AAGGTAGATATTGAGATTGAAAAAACTTAAGGACTTCAATTGA-AAAGGTAGAAAGTGAGAATG
66 AAGACAGATAAGGAGATTGAAAAAACTTAAGAACTTCAATT-ATAAAGATAAAAAGTGAGAATG
* *
1961055 AAAAAACTTAAAAGCCTCAATTATAAAGTT-AAAAGTGAGATTACAAAATTAGGG-GTCTCAATT
1 AAAAAACTT-AAAGCCTCAATTATAAAGTTAAAAAGTG-GATTAAAAAATT-GGGTGCCTCAATT
1961118 ATAAAGACA-ATAAAAGGA-ATTGAAACAAA-TT-AGAAACTTCAATTATAAAGATAAAAAGTGA
63 ATAAAGACAGAT--AAGGAGATTGAAA-AAACTTAAG-AACTTCAATTATAAAGATAAAAAGTGA
*
1961179 GATTG
124 GAATG
1961184 AA
1 AA
1961186 TAATATTAGG
Statistics
Matches: 112, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
128 21 0.19
129 82 0.73
130 9 0.08
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.25
Consensus pattern (128 bp):
AAAAAACTTAAAGCCTCAATTATAAAGTTAAAAAGTGGATTAAAAAATTGGGTGCCTCAATTATA
AAGACAGATAAGGAGATTGAAAAAACTTAAGAACTTCAATTATAAAGATAAAAAGTGAGAATG
Found at i:1961184 original size:44 final size:43
Alignment explanation
Indices: 1960942--1961217 Score: 169
Period size: 44 Copynumber: 6.4 Consensus size: 43
1960932 ACTTAAGGCC
* * *** *
1960942 TCAATTATAAAGTTAAAAAGTG-GATT-AAAAAATTGGGTGCC
1 TCAATTATAAAGATAAAAAGTGAGATTGAAAAAATTAGAAACT
* * * * *
1960983 TCAATTATAAAGGTAGATATTGAGATTGAAAAAACTTA-AGGACT
1 TCAATTATAAAGATAAAAAGTGAGATTGAAAAAA-TTAGA-AACT
* * * *
1961027 TCAATTGA-AAAGGTAGAAAGTGAGAATGAAAAAACTTA-AAAGCC
1 TCAATT-ATAAAGATAAAAAGTGAGATTGAAAAAA-TTAGAAA-CT
* * ***
1961071 TCAATTATAAAG-TTAAAAGTGAGATT-ACAAAATTAG-GGGT
1 TCAATTATAAAGATAAAAAGTGAGATTGAAAAAATTAGAAACT
*
1961111 CTCAATTATAAAGACAATAAAAG-GA-ATTGAAACAAATTAGAAACT
1 -TCAATTATAAAGA-TA-AAAAGTGAGATTGAAA-AAATTAGAAACT
* * *
1961156 TCAATTATAAAGATAAAAAGTGAGATTGAATAATATTAGGACCT
1 TCAATTATAAAGATAAAAAGTGAGATTGAA-AAAATTAGAAACT
1961200 T-AATTATAAAGATAAAAA
1 TCAATTATAAAGATAAAAA
1961218 AATTAAGATT
Statistics
Matches: 185, Mismatches: 32, Indels: 34
0.74 0.13 0.14
Matches are distributed among these distances:
41 33 0.18
42 17 0.09
43 43 0.23
44 89 0.48
45 3 0.02
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (43 bp):
TCAATTATAAAGATAAAAAGTGAGATTGAAAAAATTAGAAACT
Found at i:1963406 original size:3 final size:3
Alignment explanation
Indices: 1963398--1963424 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1963388 AGGATAACAA
1963398 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1963425 TAACTCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1968753 original size:16 final size:18
Alignment explanation
Indices: 1968729--1968774 Score: 60
Period size: 16 Copynumber: 2.6 Consensus size: 18
1968719 CATAAAAATG
*
1968729 AACTCAAAAAAT-AAC-A
1 AACTAAAAAAATAAACTA
1968745 AACTAAAAAAATAAACTA
1 AACTAAAAAAATAAACTA
1968763 AACTAAGAAAAA
1 AACTAA-AAAAA
1968775 AAAATCTGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 11 0.42
17 3 0.12
18 7 0.27
19 5 0.19
ACGTcount: A:0.72, C:0.13, G:0.02, T:0.13
Consensus pattern (18 bp):
AACTAAAAAAATAAACTA
Found at i:1969844 original size:28 final size:28
Alignment explanation
Indices: 1969811--1969891 Score: 81
Period size: 28 Copynumber: 3.2 Consensus size: 28
1969801 GTATAACTTC
1969811 AATTTTCTTCTATTTTATATTAAAGATT
1 AATTTTCTTCTATTTTATATTAAAGATT
* *
1969839 AA-TTT-TTC-A---AAT-TTGAA-A-T
1 AATTTTCTTCTATTTTATATTAAAGATT
1969858 AATTTTCTTCTATTTTATATTAAAGATT
1 AATTTTCTTCTATTTTATATTAAAGATT
1969886 AATTTT
1 AATTTT
1969892 TCAAATTTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
19 3 0.08
20 4 0.10
21 7 0.17
22 3 0.08
25 3 0.08
26 7 0.17
27 4 0.10
28 9 0.22
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.56
Consensus pattern (28 bp):
AATTTTCTTCTATTTTATATTAAAGATT
Found at i:1969864 original size:47 final size:47
Alignment explanation
Indices: 1969811--1969904 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
1969801 GTATAACTTC
1969811 AATTTTCTTCTATTTTATATTAAAGATTAATTTTTCAAATTTGAAAT
1 AATTTTCTTCTATTTTATATTAAAGATTAATTTTTCAAATTTGAAAT
1969858 AATTTTCTTCTATTTTATATTAAAGATTAATTTTTCAAATTTGAAAT
1 AATTTTCTTCTATTTTATATTAAAGATTAATTTTTCAAATTTGAAAT
1969905 GATGAGAGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.53
Consensus pattern (47 bp):
AATTTTCTTCTATTTTATATTAAAGATTAATTTTTCAAATTTGAAAT
Found at i:1977946 original size:46 final size:46
Alignment explanation
Indices: 1977880--1978154 Score: 478
Period size: 46 Copynumber: 6.0 Consensus size: 46
1977870 ATTCTTAAAT
* *
1977880 TTTTAGTTATGACATCCTTTCATTCCTTAATGCATCCTTTCATGCA
1 TTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCA
*
1977926 TTTTAGTTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCA
1 TTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCA
* *
1977972 TTTTAGTTATGGCATCTTTTCATGCCTTAATGCATCCTTTCATTCA
1 TTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCA
*
1978018 TTTTAGTTATGGCATGCTTTCATGCCTTAATGCATCCTTTCATGCA
1 TTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCA
* *
1978064 TTTTAGTTATGGCATCCTTTCATGCCTTAATGCATTCTTTCATGTA
1 TTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCA
1978110 TTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 TTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1978155 CTTAATGCAT
Statistics
Matches: 217, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 217 1.00
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.45
Consensus pattern (46 bp):
TTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCA
Found at i:1978227 original size:18 final size:18
Alignment explanation
Indices: 1978204--1978265 Score: 115
Period size: 18 Copynumber: 3.4 Consensus size: 18
1978194 TTTAGAGCAG
*
1978204 TTCATACTCAGAAACTCA
1 TTCATAATCAGAAACTCA
1978222 TTCATAATCAGAAACTCA
1 TTCATAATCAGAAACTCA
1978240 TTCATAATCAGAAACTCA
1 TTCATAATCAGAAACTCA
1978258 TTCATAAT
1 TTCATAAT
1978266 ATCCTTTCCA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.31
Consensus pattern (18 bp):
TTCATAATCAGAAACTCA
Found at i:1981198 original size:15 final size:15
Alignment explanation
Indices: 1981180--1981211 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1981170 ATCCATCACC
1981180 GCTTCATCAACAACA
1 GCTTCATCAACAACA
*
1981195 GCTTCATCAGCAACA
1 GCTTCATCAACAACA
1981210 GC
1 GC
1981212 AACAGCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.34, G:0.12, T:0.19
Consensus pattern (15 bp):
GCTTCATCAACAACA
Found at i:1985754 original size:13 final size:13
Alignment explanation
Indices: 1985736--1985767 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
1985726 TAATAATAAA
1985736 ATAAATAAAATTG
1 ATAAATAAAATTG
1985749 ATAAATAAAATTG
1 ATAAATAAAATTG
1985762 AGTAAA
1 A-TAAA
1985768 AAGAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.28
Consensus pattern (13 bp):
ATAAATAAAATTG
Found at i:1985787 original size:18 final size:18
Alignment explanation
Indices: 1985766--1985800 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1985756 AAATTGAGTA
1985766 AAAAGAAAAAATAAAAAT
1 AAAAGAAAAAATAAAAAT
*
1985784 AAAATAAAAAATAAAAA
1 AAAAGAAAAAATAAAAA
1985801 GGGTCAAATT
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:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (18 bp):
AAAAGAAAAAATAAAAAT
Found at i:1987016 original size:16 final size:17
Alignment explanation
Indices: 1986988--1987030 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1986978 AAACGTTAAT
1986988 AAAATAATAAAAAAAC-A
1 AAAATAAT-AAAAAACGA
1987005 AAAATAAT-AAAAACGA
1 AAAATAATAAAAAACGA
*
1987021 ATAATAATAA
1 AAAATAATAA
1987031 TATATTACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 6 0.26
16 8 0.35
17 9 0.39
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (17 bp):
AAAATAATAAAAAACGA
Found at i:1987052 original size:20 final size:21
Alignment explanation
Indices: 1987027--1987075 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
1987017 ACGAATAATA
* *
1987027 ATAATATATTACATATA-TAT
1 ATAATATATTACAAAAACTAT
*
1987047 ATAATAT-TTCCAAAAACTAT
1 ATAATATATTACAAAAACTAT
1987067 ATAATATAT
1 ATAATATAT
1987076 ATATTTTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 6 0.25
20 17 0.71
21 1 0.04
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAATATATTACAAAAACTAT
Found at i:1987068 original size:26 final size:26
Alignment explanation
Indices: 1987039--1987088 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
1987029 AATATATTAC
1987039 ATAT-ATATATAATATTTCCAAAAACT
1 ATATAATATAT-ATATTTCCAAAAACT
*
1987065 ATATAATATATATATTTTCAAAAA
1 ATATAATATATATATTTCCAAAAA
1987089 TATTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (26 bp):
ATATAATATATATATTTCCAAAAACT
Found at i:1987141 original size:23 final size:24
Alignment explanation
Indices: 1987115--1987160 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
1987105 ATTATATATA
* *
1987115 TATATTTTAAAT-GTTTTGAAAAC
1 TATATATTAAATAGTTTTCAAAAC
*
1987138 TATATATTATATAGTTTTCAAAA
1 TATATATTAAATAGTTTTCAAAA
1987161 ATGTTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (24 bp):
TATATATTAAATAGTTTTCAAAAC
Found at i:1987371 original size:37 final size:38
Alignment explanation
Indices: 1987057--1987550 Score: 379
Period size: 36 Copynumber: 13.3 Consensus size: 38
1987047 ATAATATTTC
* *
1987057 CAAAAACTATATAATATATATATTTTCAAAAATATTTT
1 CAAAAACTATATATTATATATATTTTCAAAAATGTTTT
**
1987095 --AAAACTATATATTATATATATATATT-TTAAATGTTTT
1 CAAAAACTATATATTATATATAT-T-TTCAAAAATGTTTT
* *
1987132 -GAAAACTATATATTATATA-GTTTTCAAAAATGTTTT
1 CAAAAACTATATATTATATATATTTTCAAAAATGTTTT
*
1987168 --AAAACTATATATTATATATGTTTTCAAAAATGTTTT
1 CAAAAACTATATATTATATATATTTTCAAAAATGTTTT
*
1987204 --AAAACTATATATTATATA-AGTTTTC-AAAATGATTT
1 CAAAAACTATATATTATATATA-TTTTCAAAAATGTTTT
* *
1987239 C-AAAACTATATATTATATA-AGTTTCTAAAATGTTTT
1 CAAAAACTATATATTATATATATTTTCAAAAATGTTTT
* ** *
1987275 CAAAAGCTATATATTATATATATTTTTTTAAAATATTTT
1 CAAAAACTATATATTATATATA-TTTTCAAAAATGTTTT
*
1987314 CAAACACTATATATTATATATATTTTC-AAAATGTTTT
1 CAAAAACTATATATTATATATATTTTCAAAAATGTTTT
* * * **
1987351 CAAAAATTGTATATTATATATATATTTTTAAAAATCATTT
1 CAAAAACTATATA-T-TATATATATTTTCAAAAATGTTTT
* * *
1987391 -GAAAACTATATAATATATATATTTTTTCAAAAATCATTTT
1 CAAAAACTATAT-AT-TATATATATTTTCAAAAAT-GTTTT
** * * *
1987431 C-AATGCTATATA--ATATATATTTTTAAAAACCGATTT
1 CAAAAACTATATATTATATATATTTTCAAAAA-TGTTTT
** * *
1987467 -GTAAACAATATA-T-TATATGTTTTCAAAAACTGTTTT
1 CAAAAACTATATATTATATATATTTTCAAAAA-TGTTTT
* *
1987503 CTAAAAAATTATATATTATA-AT-TTTT-AAAAATATTTT
1 C--AAAAACTATATATTATATATATTTTCAAAAATGTTTT
* *
1987540 TAAAAATTATA
1 CAAAAACTATA
1987551 CTATATTAAT
Statistics
Matches: 378, Mismatches: 53, Indels: 53
0.78 0.11 0.11
Matches are distributed among these distances:
35 43 0.11
36 143 0.38
37 51 0.13
38 31 0.08
39 85 0.22
40 23 0.06
41 2 0.01
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (38 bp):
CAAAAACTATATATTATATATATTTTCAAAAATGTTTT
Found at i:1987479 original size:38 final size:37
Alignment explanation
Indices: 1987368--1987533 Score: 108
Period size: 38 Copynumber: 4.5 Consensus size: 37
1987358 TGTATATTAT
* * *
1987368 ATATATATTTTTAAAAATCATTTGAAAACTATATA-A
1 ATATATATTTTTAAAAACCATTTGTAAACAATATATA
* * ***
1987404 TATATATATTTTTTCAAAAATCATTT-TCAATGCTATATA
1 -ATATATA-TTTTT-AAAAACCATTTGTAAACAATATATA
1987443 ATATATATTTTTAAAAACCGATTTGTAAACAATATAT-
1 ATATATATTTTTAAAAACC-ATTTGTAAACAATATATA
* * ** * *
1987480 -TATATGTTTTCAAAAACTGTTTTCTAAAAAATTATATA
1 ATATATATTTTTAAAAAC-CATTTGTAAACAA-TATATA
*
1987518 TTATA-ATTTTTAAAAA
1 ATATATATTTTTAAAAA
1987534 TATTTTTAAA
Statistics
Matches: 102, Mismatches: 18, Indels: 17
0.74 0.13 0.12
Matches are distributed among these distances:
36 30 0.29
37 21 0.21
38 35 0.34
39 16 0.16
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (37 bp):
ATATATATTTTTAAAAACCATTTGTAAACAATATATA
Found at i:1987558 original size:38 final size:39
Alignment explanation
Indices: 1987474--1987550 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
1987464 TTTGTAAACA
*
1987474 ATATATTATATGTTTTCAAAAACTGTTTTCTAAAAAATT
1 ATATATTATATGTTTTCAAAAACTATTTTCTAAAAAATT
1987513 ATATATTATAAT-TTTT-AAAAA-TATTTT-T-AAAAATT
1 ATATATTAT-ATGTTTTCAAAAACTATTTTCTAAAAAATT
1987548 ATA
1 ATA
1987551 CTATATTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
35 10 0.28
36 1 0.03
37 5 0.14
38 5 0.14
39 13 0.36
40 2 0.06
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (39 bp):
ATATATTATATGTTTTCAAAAACTATTTTCTAAAAAATT
Found at i:1988508 original size:84 final size:85
Alignment explanation
Indices: 1988167--1988574 Score: 581
Period size: 85 Copynumber: 4.8 Consensus size: 85
1988157 ATATGTCATC
* * * * * *
1988167 GAGCTAAATGAAATTGAACTCGACA-GTTTTTGTTAACAGATAGCCCTTCTCGCCTTGAGTTATG
1 GAGCTGAATGTAATCGAACTCGA-AGGTTTTGGTTGACAGATAGCCCTTCTCGCCTTGAGTTATA
*
1988231 CTGTAAATTTGATATG-CCTTT
65 CTGTAAATTTGATAGGTCC-TT
* *
1988252 GAGCTGAATGTAATCGAACTCGAAGGTTTTGGTTGACAGATAGCCTTTCTCGCCTTGAGTTATAT
1 GAGCTGAATGTAATCGAACTCGAAGGTTTTGGTTGACAGATAGCCCTTCTCGCCTTGAGTTATAC
*
1988317 TGTAAATTTAATAGGTCCTT
66 TGTAAATTTGATAGGTCCTT
* ** *
1988337 GAGCTGAATGTAATCGAACTCGAAGGTTTTGGTTGACAGATAACCCTTCTTTCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTTTTGGTTGACAGATAGCCCTTCTCGCCTTGAGTTATAC
**
1988402 TGTAAATTTGATAGGTTATT
66 TGTAAATTTGATAGGTCCTT
* * * *
1988422 GAGCTGAATATAATCGAACTCGAAGGTTTT-ATTGAAAAATAGCCCTTCTCGCCTTGAGTTATAC
1 GAGCTGAATGTAATCGAACTCGAAGGTTTTGGTTGACAGATAGCCCTTCTCGCCTTGAGTTATAC
1988486 TGTAAATTTGATAGGTCCTT
66 TGTAAATTTGATAGGTCCTT
*
1988506 GAGCTGAATGTAACCGAACTCGAAGGTTTT-GTTGACAGATAGCCCTTCTCGCCTTGAGTTATAC
1 GAGCTGAATGTAATCGAACTCGAAGGTTTTGGTTGACAGATAGCCCTTCTCGCCTTGAGTTATAC
1988570 TGTAA
66 TGTAA
1988575 TAGACTGGGA
Statistics
Matches: 287, Mismatches: 34, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
84 110 0.38
85 175 0.61
86 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (85 bp):
GAGCTGAATGTAATCGAACTCGAAGGTTTTGGTTGACAGATAGCCCTTCTCGCCTTGAGTTATAC
TGTAAATTTGATAGGTCCTT
Found at i:1990341 original size:99 final size:99
Alignment explanation
Indices: 1990167--1990368 Score: 305
Period size: 99 Copynumber: 2.0 Consensus size: 99
1990157 GGACAACTCA
* * * * *
1990167 ATATTATAATTACCTTTATCAGGCTAGCTGAATTTTATCCATAAAGTCGGGGTGTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGAGGCGTTTAACCAATT
* ** *
1990232 GCTCTAGAGGGATAGGTCAAGCTTTATTGTATAT
66 GCTCTAGAGGGACAACTCAAGCTTTATTGTATAC
1990266 ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGAGGCGTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGAGGCGTTTAACCAATT
* *
1990331 GCTCTGGAGGGACAACTCGAGCTTTATTGTATAC
66 GCTCTAGAGGGACAACTCAAGCTTTATTGTATAC
1990365 ATAT
1 ATAT
1990369 AATATTATAA
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
99 92 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (99 bp):
ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGAGGCGTTTAACCAATT
GCTCTAGAGGGACAACTCAAGCTTTATTGTATAC
Found at i:1995673 original size:30 final size:30
Alignment explanation
Indices: 1995613--1995674 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
1995603 TTGGACCTAA
* **
1995613 AAAATAATAAAAAAAAGAACAAATGTTAAT
1 AAAATAATAAAAAAAACAACAAATAATAAT
*
1995643 AAAATAATAATAAAAACAA-ATAATAATAAT
1 AAAATAATAAAAAAAACAACA-AATAATAAT
1995673 AA
1 AA
1995675 TATATTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (30 bp):
AAAATAATAAAAAAAACAACAAATAATAAT
Found at i:1995729 original size:38 final size:36
Alignment explanation
Indices: 1995687--1995781 Score: 118
Period size: 36 Copynumber: 2.6 Consensus size: 36
1995677 TATTATATAT
1995687 AAAATATTTCCATAAACTATATAATATATATATTTTCA
1 AAAATATTT-CA-AAACTATATAATATATATATTTTCA
* * * *
1995725 AAAATATTTTAAAACTATATATTATATATTTTTTTA
1 AAAATATTTCAAAACTATATAATATATATATTTTCA
* *
1995761 AAAAAAATTCAAAACTATATA
1 AAAATATTTCAAAACTATATA
1995782 GTTTTCAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
36 40 0.80
37 1 0.02
38 9 0.18
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (36 bp):
AAAATATTTCAAAACTATATAATATATATATTTTCA
Found at i:1995908 original size:37 final size:37
Alignment explanation
Indices: 1995821--1995912 Score: 150
Period size: 36 Copynumber: 2.5 Consensus size: 37
1995811 TATATATGTT
*
1995821 AAAAACTATATATTATATAAGTTTTCGAAATGATTTC
1 AAAAACTATATATTATATAAGTTTTCAAAATGATTTC
* *
1995858 -AAAACTATATATTATATAAGTTTTTAAAATGTTTTC
1 AAAAACTATATATTATATAAGTTTTCAAAATGATTTC
1995894 AAAAACTATATATTATATA
1 AAAAACTATATATTATATA
1995913 TATATTTTCA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
36 33 0.65
37 18 0.35
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (37 bp):
AAAAACTATATATTATATAAGTTTTCAAAATGATTTC
Found at i:1995934 original size:30 final size:29
Alignment explanation
Indices: 1995889--1995955 Score: 127
Period size: 28 Copynumber: 2.3 Consensus size: 29
1995879 TTTTAAAATG
1995889 TTTTCAAAAACTATATATTATATATATA-
1 TTTTCAAAAACTATATATTATATATATAT
1995917 TTTTCAAAAACTATATATTATATATATAT
1 TTTTCAAAAACTATATATTATATATATAT
1995946 TTTTCAAAAA
1 TTTTCAAAAA
1995956 TCATTTGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 28 0.74
29 10 0.26
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (29 bp):
TTTTCAAAAACTATATATTATATATATAT
Found at i:1995979 original size:105 final size:99
Alignment explanation
Indices: 1995806--1996030 Score: 249
Period size: 105 Copynumber: 2.2 Consensus size: 99
1995796 TTTAAAATTG
* * * *
1995806 TATAT-TATATATGTTAAAAACTATATATTATATAAGTTTTCGAAATGATTTCAAAACTATATAT
1 TATATATATATATTTTAAAAACTATATATTATATAAGTTTTCAAAATCATTTCAAAACTATATAA
*
1995870 TATATAAGTTTTTAAAAT-GTTTTCAAAAACTATA
66 TATATAAGTTTTTAAAATCATTTTC-AAAACTATA
* *
1995904 TATTATATATATATTTTCAAAAACTATATATTATATATATATTTTTCAAAAATCATTTGAAAACT
1 TA-TATATATATATTTT-AAAAACTATATA-T-TATATA-AGTTTTC-AAAATCATTTCAAAACT
*** *
1995969 ATATAATATATTTTTTTTTAAAATCATTTTCAAAGCTATA
60 ATATAATATATAAGTTTTTAAAATCATTTTCAAAACTATA
*
1996009 TA-ATATATATTTTTTTAAAAAC
1 TATATATATA-TATTTTAAAAAC
1996031 CGATTTTTAA
Statistics
Matches: 106, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
98 2 0.02
99 3 0.03
100 9 0.08
101 12 0.11
102 1 0.01
103 19 0.18
104 11 0.10
105 44 0.42
106 5 0.05
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.46
Consensus pattern (99 bp):
TATATATATATATTTTAAAAACTATATATTATATAAGTTTTCAAAATCATTTCAAAACTATATAA
TATATAAGTTTTTAAAATCATTTTCAAAACTATA
Found at i:1995985 original size:36 final size:38
Alignment explanation
Indices: 1995916--1996114 Score: 148
Period size: 38 Copynumber: 5.3 Consensus size: 38
1995906 TTATATATAT
*
1995916 ATTTTCAAAAACTATATATTATATATATATTTTTCAAAAATC
1 ATTTTC-AAAACTATATA--ATATATAT-TTTTTTAAAAATC
* *
1995958 A-TTTGAAAACTATATAATATAT-TTTTTTTTAAAATC
1 ATTTTCAAAACTATATAATATATATTTTTTTAAAAATC
* *
1995994 ATTTTCAAAGCTATATAATATATATTTTTTTAAAAACC
1 ATTTTCAAAACTATATAATATATATTTTTTTAAAAATC
* * *
1996032 GATTTT-TAAAC-AGTAT-AT-TATATGTTTTCAAAAATC
1 -ATTTTCAAAACTA-TATAATATATATTTTTTTAAAAATC
* * *
1996068 GTTTTCTAAAA--A-ATTATATATTATATTTTTCAAAAAT-
1 ATTTTC-AAAACTATATAATATA-TAT-TTTTTTAAAAATC
1996105 ATTTTCAAAA
1 ATTTTCAAAA
1996115 ATTATATTAT
Statistics
Matches: 131, Mismatches: 16, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
34 2 0.02
35 6 0.05
36 34 0.26
37 34 0.26
38 35 0.27
39 5 0.04
40 11 0.08
41 3 0.02
42 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (38 bp):
ATTTTCAAAACTATATAATATATATTTTTTTAAAAATC
Found at i:1996008 original size:37 final size:36
Alignment explanation
Indices: 1995918--1996028 Score: 132
Period size: 37 Copynumber: 2.9 Consensus size: 36
1995908 ATATATATAT
*
1995918 TTTCAAAAACTATATATTATATATATATTTTTCAAAAATCA
1 TTTC-AAAACTATATA--ATATATAT-TTTTT-TAAAATCA
* *
1995959 TTTGAAAACTATATAATATATTTTTTTTTAAAATCA
1 TTTCAAAACTATATAATATATATTTTTTTAAAATCA
*
1995995 TTTTCAAAGCTATATAATATATATTTTTTTAAAA
1 -TTTCAAAACTATATAATATATATTTTTTTAAAA
1996029 ACCGATTTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
36 7 0.11
37 35 0.56
38 7 0.11
40 11 0.17
41 3 0.05
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (36 bp):
TTTCAAAACTATATAATATATATTTTTTTAAAATCA
Found at i:1996054 original size:38 final size:36
Alignment explanation
Indices: 1995924--1996126 Score: 123
Period size: 36 Copynumber: 5.4 Consensus size: 36
1995914 ATATTTTCAA
**
1995924 AAACTATATATTATATATATATTTTTCAAAAATCATTTGA
1 AAAC-ATATATTATATAT-T-TTTTT-AAAAATCATTTTC
* *
1995964 AAAC-TATATAATATATTTTTTTTTAAAATCATTTTC
1 AAACATATATTATATA-TTTTTTTAAAAATCATTTTC
* * *
1996000 AAAGCTATATAATATATATTTTTTTAAAAACCGATTTTT
1 AAA-C-ATATATTATATATTTTTTTAAAAATC-ATTTTC
* * *
1996039 AAACAGTATA-T-TATATGTTTTCAAAAATCGTTTTC
1 AAACA-TATATTATATATTTTTTTAAAAATCATTTTC
1996074 TAAA-A-A-ATTATATATTATATTTTTCAAAAAT-ATTTTC
1 -AAACATATATTATATA-T-T-TTTTT-AAAAATCATTTTC
*
1996111 AAAAATTATATTATAT
1 AAACA-TATATTATAT
1996127 TAATATATAT
Statistics
Matches: 129, Mismatches: 17, Indels: 34
0.72 0.09 0.19
Matches are distributed among these distances:
32 1 0.01
33 2 0.02
34 4 0.03
35 6 0.05
36 34 0.26
37 18 0.14
38 34 0.26
39 19 0.15
40 11 0.09
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (36 bp):
AAACATATATTATATATTTTTTTAAAAATCATTTTC
Found at i:1996054 original size:75 final size:77
Alignment explanation
Indices: 1995916--1996103 Score: 187
Period size: 74 Copynumber: 2.5 Consensus size: 77
1995906 TTATATATAT
* *
1995916 ATTTTCAAAAACTATATATTATATATATATTTTTCAAAAATCATTTGAAAACTATATAATATATT
1 ATTTTCAAAAACTATATA-TATATATATATTTTTCAAAAACCATTTGAAAACTATATAATATATG
1995981 TTTTTTTAAAATC
65 TTTTTTTAAAATC
* * ** *
1995994 ATTTTC-AAAGCTATATA-ATATATAT-TTTTTTAAAAACCGATTTTTAAAC-AGTATATTATAT
1 ATTTTCAAAAACTATATATATATATATATTTTTCAAAAACC-ATTTGAAAACTA-TATAATATAT
**
1996055 G-TTTTCAAAAATC
64 GTTTTTTTAAAATC
*
1996068 GTTTTCTAAAAA--AT-TATATAT-TATATTTTTCAAAAA
1 ATTTTC-AAAAACTATATATATATATATATTTTTCAAAAA
1996104 TATTTTCAAA
Statistics
Matches: 92, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
73 5 0.05
74 43 0.47
75 25 0.27
76 3 0.03
77 10 0.11
78 6 0.07
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (77 bp):
ATTTTCAAAAACTATATATATATATATATTTTTCAAAAACCATTTGAAAACTATATAATATATGT
TTTTTTAAAATC
Found at i:1996090 original size:39 final size:35
Alignment explanation
Indices: 1996045--1996121 Score: 109
Period size: 35 Copynumber: 2.1 Consensus size: 35
1996035 TTTTAAACAG
*
1996045 TATATTATATGTTTTCAAAAATCGTTTTCTAAAAAATTA
1 TATATTATAT-TTTTCAAAAAT-ATTTTC--AAAAATTA
1996084 TATATTATATTTTTCAAAAATATTTTCAAAAATTA
1 TATATTATATTTTTCAAAAATATTTTCAAAAATTA
1996119 TAT
1 TAT
1996122 TATATTAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
35 11 0.30
37 5 0.14
38 11 0.30
39 10 0.27
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (35 bp):
TATATTATATTTTTCAAAAATATTTTCAAAAATTA
Found at i:2005125 original size:21 final size:21
Alignment explanation
Indices: 2005095--2005150 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
2005085 AAATTATTCA
*
2005095 AAAAATTAAATATCAAAATATC
1 AAAAA-TAAAAATCAAAATATC
* * *
2005117 AAAAATAAAAATTAAATTATT
1 AAAAATAAAAATCAAAATATC
2005138 AAAAATTAAAAAT
1 AAAAA-TAAAAAT
2005151 GTATTATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAATAAAAATCAAAATATC
Found at i:2005129 original size:28 final size:28
Alignment explanation
Indices: 2005095--2005150 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
2005085 AAATTATTCA
2005095 AAAAATTAAA-TATCAAAATATCAAAAAT
1 AAAAATTAAATTATCAAAA-ATCAAAAAT
* *
2005123 AAAAATTAAATTATTAAAAATTAAAAAT
1 AAAAATTAAATTATCAAAAATCAAAAAT
2005151 GTATTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.29
Consensus pattern (28 bp):
AAAAATTAAATTATCAAAAATCAAAAAT
Found at i:2005132 original size:7 final size:7
Alignment explanation
Indices: 2005095--2005150 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
2005085 AAATTATTCA
2005095 AAAAATT
1 AAAAATT
* *
2005102 AAATATC
1 AAAAATT
*
2005109 AAAATATC
1 AAAA-ATT
2005117 AAAAA-T
1 AAAAATT
2005123 AAAAATT
1 AAAAATT
*
2005130 AAATTATT
1 AAA-AATT
2005138 AAAAATT
1 AAAAATT
2005145 AAAAAT
1 AAAAAT
2005151 GTATTATTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
6 5 0.12
7 22 0.55
8 13 0.32
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.29
Consensus pattern (7 bp):
AAAAATT
Found at i:2006560 original size:36 final size:36
Alignment explanation
Indices: 2006516--2006589 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 36
2006506 ATGCAAACCA
*
2006516 TTTATATTTTAATTAATTTT-TATTGAATTGTGTAG
1 TTTATATTTTAATTAATTTTGTATTGAATCGTGTAG
*
2006551 TTTATTATTTTAATTAATTTTGTATTGGATCGTGTAG
1 TTTA-TATTTTAATTAATTTTGTATTGAATCGTGTAG
2006588 TT
1 TT
2006590 CAAAATGTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 4 0.11
36 16 0.46
37 15 0.43
ACGTcount: A:0.26, C:0.01, G:0.14, T:0.59
Consensus pattern (36 bp):
TTTATATTTTAATTAATTTTGTATTGAATCGTGTAG
Found at i:2008769 original size:29 final size:31
Alignment explanation
Indices: 2008701--2008766 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 31
2008691 TGTTCAAAGT
* *
2008701 TTGGCCACCAACCAAGATGAAATTTCTAATAAG
1 TTGGCCACCAACCAAGATGAAATTTC--ACAAC
2008734 TTGGCCACCAACCAAGATGAAATTTC-CAAC
1 TTGGCCACCAACCAAGATGAAATTTCACAAC
2008764 TTG
1 TTG
2008767 CCAACTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 5 0.16
33 26 0.84
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (31 bp):
TTGGCCACCAACCAAGATGAAATTTCACAAC
Found at i:2013532 original size:29 final size:31
Alignment explanation
Indices: 2013464--2013529 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 31
2013454 TGTTCAAAGT
* *
2013464 TTGGCCACCAACCAAGATGAAATTTCTAATAAG
1 TTGGCCACCAACCAAGATGAAATTTC--ACAAC
*
2013497 TTGGCCACCAATCAAGATGAAATTTC-CAAC
1 TTGGCCACCAACCAAGATGAAATTTCACAAC
2013527 TTG
1 TTG
2013530 CCAACTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 5 0.17
33 25 0.83
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (31 bp):
TTGGCCACCAACCAAGATGAAATTTCACAAC
Found at i:2020891 original size:2 final size:2
Alignment explanation
Indices: 2020884--2020918 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2020874 TTTGTATGTA
2020884 AT AT AT 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 AT AT AT A
2020919 GTACATATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2026978 original size:6 final size:6
Alignment explanation
Indices: 2026958--2026991 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
2026948 TACATACATA
2026958 AAAAAG -AAAAG -AAAAG AAAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
2026992 CAAGATATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.37
6 17 0.63
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:2030304 original size:16 final size:15
Alignment explanation
Indices: 2030245--2030309 Score: 60
Period size: 16 Copynumber: 4.1 Consensus size: 15
2030235 AAAATTTTTC
2030245 TAAAATATTAAATAAT
1 TAAAATATTAAA-AAT
* * *
2030261 TATAATATATATATAT
1 TAAAATAT-TAAAAAT
2030277 TAAAAT-TCTAAAACAT
1 TAAAATAT-TAAAA-AT
2030293 TAAAATATTAAAAAT
1 TAAAATATTAAAAAT
2030308 TA
1 TA
2030310 TATAATTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
15 8 0.21
16 27 0.69
17 4 0.10
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAATATTAAAAAT
Found at i:2030455 original size:18 final size:18
Alignment explanation
Indices: 2030432--2030485 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
2030422 AGACTGCCTA
*
2030432 AAAATATTGTTAAGACA-T
1 AAAATATTGTTAA-AAATT
*
2030450 AAAATATTATTAAAAATT
1 AAAATATTGTTAAAAATT
2030468 AAAATA-TGTT-AAAATT
1 AAAATATTGTTAAAAATT
2030484 AA
1 AA
2030486 TTGTATGAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 8 0.25
17 5 0.16
18 19 0.59
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (18 bp):
AAAATATTGTTAAAAATT
Found at i:2030581 original size:21 final size:22
Alignment explanation
Indices: 2030556--2030597 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2030546 CTTGAATCAT
2030556 AAATTTTACT-AAAATATGTTA
1 AAATTTTACTAAAAATATGTTA
*
2030577 AAATTTTATTAAAAATATGTT
1 AAATTTTACTAAAAATATGTT
2030598 TCAACACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (22 bp):
AAATTTTACTAAAAATATGTTA
Found at i:2038048 original size:18 final size:18
Alignment explanation
Indices: 2038014--2038051 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2038004 GGTTTTTTTA
*
2038014 TTTTATGTTGTTTTTGTT
1 TTTTATGTTATTTTTGTT
2038032 TTTTAT-TTATTTATTGTT
1 TTTTATGTTATTT-TTGTT
2038050 TT
1 TT
2038052 AATATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.79
Consensus pattern (18 bp):
TTTTATGTTATTTTTGTT
Found at i:2038051 original size:23 final size:23
Alignment explanation
Indices: 2038007--2038051 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2037997 TATTTTAGGT
*
2038007 TTTTTTATTTTATGTTGTTTTTG
1 TTTTTTATTTTATATTGTTTTTG
*
2038030 TTTTTTATTTATTTATTGTTTT
1 TTTTTTATTT-TATATTGTTTT
2038052 AATATTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.11, C:0.00, G:0.09, T:0.80
Consensus pattern (23 bp):
TTTTTTATTTTATATTGTTTTTG
Found at i:2044940 original size:29 final size:29
Alignment explanation
Indices: 2044907--2044977 Score: 117
Period size: 29 Copynumber: 2.4 Consensus size: 29
2044897 CATTATTGAG
*
2044907 TCCATTGACTATTAAATGTTACAAAATGA
1 TCCATCGACTATTAAATGTTACAAAATGA
2044936 TCCATCGACTATTAAATGTTACAAAATGA
1 TCCATCGACTATTAAATGTTACAAAATGA
2044965 T-CACTCGACTATT
1 TCCA-TCGACTATT
2044978 CATTATATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 2 0.05
29 38 0.95
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (29 bp):
TCCATCGACTATTAAATGTTACAAAATGA
Found at i:2045304 original size:60 final size:60
Alignment explanation
Indices: 2045174--2045316 Score: 137
Period size: 60 Copynumber: 2.4 Consensus size: 60
2045164 AACATAATGA
* * * * * *
2045174 ATAGTCGAGTGACCATTTTATAACTCTTAATAGTTAAGGGACTCAACAAAACAACTTCTT
1 ATAGTCAAGGGACCATTTTGTAACTCTTAATAATCAAGGGACTCAACAAAACAACTTCCT
* * * * *
2045234 ATAATTAAGGGACCATTTTGTAACAT-TTATTAATCAAGGGACTCAATAAAAC-ATTATCCT
1 ATAGTCAAGGGACCATTTTGTAAC-TCTTAATAATCAAGGGACTCAACAAAACAACT-TCCT
*
2045294 ATAGTCAAGGGATCGATTTTGTA
1 ATAGTCAAGGGA-CCATTTTGTA
2045317 CTTTACCCTT
Statistics
Matches: 66, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
59 2 0.03
60 54 0.82
61 10 0.15
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (60 bp):
ATAGTCAAGGGACCATTTTGTAACTCTTAATAATCAAGGGACTCAACAAAACAACTTCCT
Found at i:2049136 original size:27 final size:28
Alignment explanation
Indices: 2049099--2049156 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
2049089 TGTGACAGAT
*
2049099 AAGTTAAATTG-ATTTTTTTAAA-TTTG
1 AAGTTAAATTGAATTTTTTAAAAGTTTG
2049125 AAGTCTAAATTGAATTTTTTAAAAGTTTG
1 AAGT-TAAATTGAATTTTTTAAAAGTTTG
2049154 AAG
1 AAG
2049157 GTTTATTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 4 0.14
27 7 0.25
28 10 0.36
29 7 0.25
ACGTcount: A:0.38, C:0.02, G:0.14, T:0.47
Consensus pattern (28 bp):
AAGTTAAATTGAATTTTTTAAAAGTTTG
Found at i:2049278 original size:14 final size:16
Alignment explanation
Indices: 2049261--2049292 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2049251 AAATAAATTT
2049261 TATT-AAAAT-ATAAA
1 TATTAAAAATAATAAA
2049275 TATTAAAAATAATAAA
1 TATTAAAAATAATAAA
2049291 TA
1 TA
2049293 CTTATTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 5 0.31
16 7 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TATTAAAAATAATAAA
Found at i:2049325 original size:16 final size:17
Alignment explanation
Indices: 2049306--2049338 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2049296 ATTATAAAAT
*
2049306 TAAG-AAAAATTAAACA
1 TAAGTAAAAAGTAAACA
2049322 TAAGTAAAAAGTAAACA
1 TAAGTAAAAAGTAAACA
2049339 AATAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.67, C:0.06, G:0.09, T:0.18
Consensus pattern (17 bp):
TAAGTAAAAAGTAAACA
Found at i:2049508 original size:16 final size:16
Alignment explanation
Indices: 2049483--2049574 Score: 53
Period size: 16 Copynumber: 5.1 Consensus size: 16
2049473 TTATATTATT
2049483 TTAA-TCATAAATTTA
1 TTAATTCATAAATTTA
2049498 TTAATTCATAAATATATA
1 TTAATTCATAAAT-T-TA
2049516 TTTTTAATATCATAACATACTAATA
1 ---TTAAT-TCATAA-AT--T--TA
2049541 TTTAA-TCATAAATTTA
1 -TTAATTCATAAATTTA
*
2049557 TTAATTCATAAATATA
1 TTAATTCATAAATTTA
2049573 TT
1 TT
2049575 TTTTAATATC
Statistics
Matches: 64, Mismatches: 2, Indels: 21
0.74 0.02 0.24
Matches are distributed among these distances:
15 8 0.12
16 22 0.34
17 1 0.02
18 3 0.05
20 2 0.03
21 11 0.17
22 6 0.09
23 7 0.11
24 1 0.02
25 3 0.05
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAATTCATAAATTTA
Found at i:2049545 original size:59 final size:58
Alignment explanation
Indices: 2049482--2049598 Score: 225
Period size: 59 Copynumber: 2.0 Consensus size: 58
2049472 TTTATATTAT
2049482 TTTAATCATAAATTTATTAATTCATAAATATATATTTTTAATATCATAACATACTAATA
1 TTTAATCATAAATTTATTAATTCATAAATATAT-TTTTTAATATCATAACATACTAATA
2049541 TTTAATCATAAATTTATTAATTCATAAATATATTTTTTAATATCATAACATACTAATA
1 TTTAATCATAAATTTATTAATTCATAAATATATTTTTTAATATCATAACATACTAATA
2049599 CCAAAATTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 25 0.43
59 33 0.57
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.46
Consensus pattern (58 bp):
TTTAATCATAAATTTATTAATTCATAAATATATTTTTTAATATCATAACATACTAATA
Found at i:2049546 original size:23 final size:21
Alignment explanation
Indices: 2049498--2049588 Score: 72
Period size: 21 Copynumber: 4.5 Consensus size: 21
2049488 CATAAATTTA
*
2049498 TTAATTCATAAATATATATTT
1 TTAATTCATAAATATATATAT
2049519 TTAATATCATAACATACTA-ATAT
1 TTAAT-TCATAA-ATA-TATATAT
2049542 TTAA-TCAT-AA-AT-T-TA-
1 TTAATTCATAAATATATATAT
*
2049557 TTAATTCATAAATATAT-TTT
1 TTAATTCATAAATATATATAT
2049577 TTAATATCATAA
1 TTAAT-TCATAA
2049589 CATACTAATA
Statistics
Matches: 58, Mismatches: 2, Indels: 20
0.73 0.03 0.25
Matches are distributed among these distances:
15 4 0.07
16 6 0.10
17 3 0.05
18 3 0.05
19 3 0.05
20 6 0.10
21 15 0.26
22 6 0.10
23 10 0.17
24 2 0.03
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAATTCATAAATATATATAT
Found at i:2051166 original size:15 final size:15
Alignment explanation
Indices: 2051146--2051179 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
2051136 AAAAAATATT
2051146 TTTTGAAGTTTTTTA
1 TTTTGAAGTTTTTTA
2051161 TTTTGAAGTTTTTTA
1 TTTTGAAGTTTTTTA
2051176 TTTT
1 TTTT
2051180 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.71
Consensus pattern (15 bp):
TTTTGAAGTTTTTTA
Found at i:2060074 original size:13 final size:13
Alignment explanation
Indices: 2060052--2060086 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2060042 AGGTAAATAG
2060052 TTAA-TATATTAT
1 TTAATTATATTAT
*
2060064 TTACTTATATTAT
1 TTAATTATATTAT
2060077 TTAATTATAT
1 TTAATTATAT
2060087 GTACATTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 3 0.15
13 17 0.85
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (13 bp):
TTAATTATATTAT
Found at i:2061418 original size:51 final size:53
Alignment explanation
Indices: 2061305--2061422 Score: 150
Period size: 51 Copynumber: 2.2 Consensus size: 53
2061295 CATAATGAAG
* * *
2061305 ATTATTGAACATCTTGACATAGTTAGGTTGGTTGCACGAGATATGTGTTGTTTTA
1 ATTATTGTACATCTTAACATAGTTA-G-TGGTTACACGAGATATGTGTTGTTTTA
* * *
2061360 AGTATTGTACATCTTAACATAGTTA-T-GTTACATGAGGTATGTGTTGTTTTA
1 ATTATTGTACATCTTAACATAGTTAGTGGTTACACGAGATATGTGTTGTTTTA
2061411 ATTATTGTACAT
1 ATTATTGTACAT
2061423 TGTACTTTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
51 33 0.59
52 1 0.02
55 22 0.39
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.44
Consensus pattern (53 bp):
ATTATTGTACATCTTAACATAGTTAGTGGTTACACGAGATATGTGTTGTTTTA
Found at i:2064372 original size:50 final size:51
Alignment explanation
Indices: 2064285--2064382 Score: 173
Period size: 50 Copynumber: 1.9 Consensus size: 51
2064275 CCTTCCCCCA
2064285 TCTTGTCTTCTTCTCTCTTCCTGCTTTTCTTTCTCTGTATGTAGGAACCAT
1 TCTTGTCTTCTTCTCTCTTCCTGCTTTTCTTTCTCTGTATGTAGGAACCAT
2064336 TCTTGTCTTCTTC-CTCTCTCC-GCTTTTCTTTCTCTGTATGTAGGAAC
1 TCTTGTCTTCTTCTCTCT-TCCTGCTTTTCTTTCTCTGTATGTAGGAAC
2064383 GGAAATATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
50 30 0.65
51 16 0.35
ACGTcount: A:0.09, C:0.29, G:0.12, T:0.50
Consensus pattern (51 bp):
TCTTGTCTTCTTCTCTCTTCCTGCTTTTCTTTCTCTGTATGTAGGAACCAT
Found at i:2065375 original size:234 final size:233
Alignment explanation
Indices: 2064913--2065383 Score: 897
Period size: 234 Copynumber: 2.0 Consensus size: 233
2064903 AGTGATTAGG
2064913 AACATAAACCTTTGTGTTTTACCTTGTTCATTTGATGATTGCAGGTGGATTTGCAATGAAAAAAA
1 AACATAAACCTTTGTGTTTTACCTTGTTCATTTGATGATTGCAGGTGGATTTGCAATGAAAAAAA
2064978 AGCTGAAATAAAGCACAGTAATGAGATTCCTCTCAGCTCCATATCAGTTTCTCTCAAGATTTTTC
66 AGCTGAAATAAAGCACAGTAATGAGATTCCTCTCAGCTCCATATCAGTTTCTCTCAAGATTTTTC
2065043 CTTTTTAACATTGAGCGCAGCTTTCTAATTTTCTGACCATGGAGTTGATTTTATATAGAGAGAAA
131 CTTTTTAACATTGAGCGCAGCTTTCTAATTTTCTGACCATGGAGTTGATTTTATATAGAGAGAAA
2065108 CCCCATTTACAAAGAGGAAAGAGAAAGAGAAGAAGAAGA
196 CCCCATTTACAAAGAGGAAAGAG-AAGAGAAGAAGAAGA
2065147 AACATAAACCTTTGTGTTTTACCTTGTTCATTTGATGATTGCAGGTGGATTTGCAATGAAAAAAA
1 AACATAAACCTTTGTGTTTTACCTTGTTCATTTGATGATTGCAGGTGGATTTGCAATGAAAAAAA
2065212 AGCTGAAATAAAGCACAGTAATGAAGATTCCTCTCAGCTCCATATCAGTTTTCTCTCAAGATTTT
66 AGCTGAAATAAAGCACAGTAATG-AGATTCCTCTCAGCTCCATATCAG-TTTCTCTCAAGATTTT
2065277 TCCTTTTTAACATTGAGCGCAGCTTTCTAATTTTCTGACCATGGAGTTGATTTTATATAGAAGAG
129 TCCTTTTTAACATTGAGCGCAGCTTTCTAATTTTCTGACCATGGAGTTGATTTTATATAG-AGAG
2065342 AAACCCCATTTACAAAGAGGAAAGAGAAGAAGAAGAAGAAGA
193 AAACCCCATTTACAAAGAGGAAAGAGAAG-AGAAGAAGAAGA
2065384 GCAGACACGA
Statistics
Matches: 233, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
234 88 0.38
235 24 0.10
236 79 0.34
237 42 0.18
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (233 bp):
AACATAAACCTTTGTGTTTTACCTTGTTCATTTGATGATTGCAGGTGGATTTGCAATGAAAAAAA
AGCTGAAATAAAGCACAGTAATGAGATTCCTCTCAGCTCCATATCAGTTTCTCTCAAGATTTTTC
CTTTTTAACATTGAGCGCAGCTTTCTAATTTTCTGACCATGGAGTTGATTTTATATAGAGAGAAA
CCCCATTTACAAAGAGGAAAGAGAAGAGAAGAAGAAGA
Found at i:2069822 original size:22 final size:21
Alignment explanation
Indices: 2069783--2069823 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2069773 GCTTCCATAA
* *
2069783 ATTTTAAACCCCTTTAAACCG
1 ATTTTAAAACCCTATAAACCG
2069804 ATTTTAAAACCCTAATAAAC
1 ATTTTAAAACCCT-ATAAAC
2069824 GAACCATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.41, C:0.24, G:0.02, T:0.32
Consensus pattern (21 bp):
ATTTTAAAACCCTATAAACCG
Found at i:2071526 original size:32 final size:32
Alignment explanation
Indices: 2071485--2071553 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
2071475 AACCGGGTAT
*
2071485 CGGGTACCCGATTCCCGGATACCCGCAAAATC
1 CGGGTACCCGATTACCGGATACCCGCAAAATC
* * *
2071517 CGGGTACCCGATTACCGGGTACCCGTAACATC
1 CGGGTACCCGATTACCGGATACCCGCAAAATC
2071549 CGGGT
1 CGGGT
2071554 CGAGACACGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.22, C:0.35, G:0.26, T:0.17
Consensus pattern (32 bp):
CGGGTACCCGATTACCGGATACCCGCAAAATC
Found at i:2071536 original size:15 final size:15
Alignment explanation
Indices: 2071485--2071541 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
2071475 AACCGGGTAT
*
2071485 CGGGTACCCGATTCC
1 CGGGTACCCGATTAC
* **
2071500 CGGATACCCGCAAAATC
1 CGGGTACCCG-ATTA-C
2071517 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
2071532 CGGGTACCCG
1 CGGGTACCCG
2071542 TAACATCCGG
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
15 20 0.61
16 3 0.09
17 10 0.30
ACGTcount: A:0.21, C:0.37, G:0.26, T:0.16
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:2074207 original size:27 final size:27
Alignment explanation
Indices: 2074169--2074222 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
2074159 AGCCTTCATT
2074169 GCTTGTTCCTTGGTAGCATGTGAATAG
1 GCTTGTTCCTTGGTAGCATGTGAATAG
2074196 GCTTGTTCCTTGGTAGCATGTGAATAG
1 GCTTGTTCCTTGGTAGCATGTGAATAG
2074223 CCTTCAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.30, T:0.37
Consensus pattern (27 bp):
GCTTGTTCCTTGGTAGCATGTGAATAG
Found at i:2074986 original size:14 final size:14
Alignment explanation
Indices: 2074963--2074999 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2074953 CGAATTATAG
*
2074963 TATTCTTCCCTTAT
1 TATTCCTCCCTTAT
2074977 TATTCCTCCCTTAT
1 TATTCCTCCCTTAT
2074991 TATTCCTCC
1 TATTCCTCC
2075000 TTCCTCACGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.14, C:0.35, G:0.00, T:0.51
Consensus pattern (14 bp):
TATTCCTCCCTTAT
Found at i:2077816 original size:23 final size:22
Alignment explanation
Indices: 2077772--2077816 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2077762 AATGTCATGG
* *
2077772 GGGAACTGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
2077794 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
2077817 AAATTGTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.31, C:0.31, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:2079264 original size:119 final size:121
Alignment explanation
Indices: 2079027--2079388 Score: 620
Period size: 119 Copynumber: 3.0 Consensus size: 121
2079017 CGAGGGTCTA
* *
2079027 TGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGACTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
2079092 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
*
2079148 TGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* * **
2079213 GAT-CATTG-GCATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
*
2079267 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
**
2079332 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
2079388 T
1 T
2079389 ATTATATGGC
Statistics
Matches: 224, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
119 110 0.49
120 6 0.03
121 108 0.48
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:2079272 original size:18 final size:18
Alignment explanation
Indices: 2079249--2079284 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2079239 AGGAATGATA
2079249 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
2079267 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
2079285 ATATGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:2079445 original size:23 final size:23
Alignment explanation
Indices: 2079391--2079463 Score: 96
Period size: 23 Copynumber: 3.3 Consensus size: 23
2079381 TGGACATTAT
2079391 TATATGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAATTC
***
2079414 TACGCGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAATTC
*
2079437 TATATGGCACTTCGGTGC-ATT-
1 TATATGGCACTACGGTGCAATTC
2079458 TATATG
1 TATATG
2079464 AGTTGTGGTG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.14
22 3 0.07
23 34 0.79
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (23 bp):
TATATGGCACTACGGTGCAATTC
Found at i:2083309 original size:23 final size:22
Alignment explanation
Indices: 2083265--2083309 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2083255 AATGTCATGG
*
2083265 GGGAACCAATACCCCCACAGGA
1 GGGAACCAATACCCCCAAAGGA
* *
2083287 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCAATACCCCC-AAAGGA
2083310 AAATTGTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.33, C:0.33, G:0.24, T:0.09
Consensus pattern (22 bp):
GGGAACCAATACCCCCAAAGGA
Found at i:2084633 original size:18 final size:18
Alignment explanation
Indices: 2084610--2084645 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2084600 AGGAATGATA
2084610 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
2084628 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
2084646 ATATGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:2084666 original size:121 final size:120
Alignment explanation
Indices: 2084507--2084868 Score: 636
Period size: 121 Copynumber: 3.0 Consensus size: 120
2084497 CGAGGGTCTA
2084507 TGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
2084572 GATCCCTAGTATATGTATATGATTTTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAG-ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
*
2084628 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* *
2084693 GATCCTTGGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAG-ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
*
2084749 TGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
**
2084814 GATCCCTAG-TATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACAT
66 GATCCCTAGATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
2084868 T
1 T
2084869 ATTATATGGC
Statistics
Matches: 230, Mismatches: 11, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
119 44 0.19
121 186 0.81
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (120 bp):
TGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:2084754 original size:18 final size:18
Alignment explanation
Indices: 2084731--2084766 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2084721 AGGAATGATA
*
2084731 TGTGGTCCTTCGGGACAT
1 TGTGGTCATTCGGGACAT
2084749 TGTGGTCATTCGGGACAT
1 TGTGGTCATTCGGGACAT
2084767 ATATGTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.19, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCATTCGGGACAT
Found at i:2084768 original size:62 final size:62
Alignment explanation
Indices: 2084582--2084768 Score: 153
Period size: 62 Copynumber: 3.1 Consensus size: 62
2084572 GATCCCTAGT
*
2084582 ATATGTATATGATTTTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGAC
1 ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGAC
* * * * * *
2084644 ATA--TATGT-ATTCTT-TGGAA-CATGTGTGAAGT-CTGGT-GAGACACATACT-TGATCCTT-
1 ATATGTATATGATTCTTAAGGAATGATATGTG--GTCCT--TCG-G-GACAT--TGTGGTCCTTC
2084700 -GG-C
58 GGGAC
*
2084703 ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCATTCGGGAC
1 ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGAC
2084765 ATAT
1 ATAT
2084769 ATGTATTCTT
Statistics
Matches: 92, Mismatches: 14, Indels: 38
0.64 0.10 0.26
Matches are distributed among these distances:
57 6 0.07
58 7 0.08
59 18 0.20
60 12 0.13
61 12 0.13
62 24 0.26
63 7 0.08
64 6 0.07
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.36
Consensus pattern (62 bp):
ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGAC
Found at i:2084943 original size:23 final size:23
Alignment explanation
Indices: 2084875--2084935 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
2084865 CATTATTATA
*
2084875 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
*
2084898 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
2084921 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
2084936 TTTATATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:2086175 original size:2 final size:2
Alignment explanation
Indices: 2086168--2086237 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
2086158 TAGAAGGTAA
2086168 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2086210 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2086238 GTGTGTGTGT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2086242 original size:2 final size:2
Alignment explanation
Indices: 2086237--2086267 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2086227 TATATATATA
2086237 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2086268 ATGAAAGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2087443 original size:18 final size:18
Alignment explanation
Indices: 2087420--2087460 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2087410 TTGATTAATA
2087420 AACTAACATTATTCAAAG
1 AACTAACATTATTCAAAG
* *
2087438 AACTAACTTTATTCAATG
1 AACTAACATTATTCAAAG
2087456 AACTA
1 AACTA
2087461 GATGCATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.17, G:0.05, T:0.32
Consensus pattern (18 bp):
AACTAACATTATTCAAAG
Found at i:2087609 original size:18 final size:18
Alignment explanation
Indices: 2087586--2087621 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2087576 AAATGCAATG
2087586 AATTCT-ATGCAAACTTCA
1 AATTCTCATGCAAA-TTCA
2087604 AATTCTCATGCAAATTCA
1 AATTCTCATGCAAATTCA
2087622 TGCACAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (18 bp):
AATTCTCATGCAAATTCA
Found at i:2099130 original size:8 final size:8
Alignment explanation
Indices: 2099117--2099148 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
2099107 CTAACAAAAT
2099117 ACTAATAA
1 ACTAATAA
2099125 ACTAATAA
1 ACTAATAA
*
2099133 ACTGATAA
1 ACTAATAA
2099141 ACTAATAA
1 ACTAATAA
2099149 CATAATTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.59, C:0.12, G:0.03, T:0.25
Consensus pattern (8 bp):
ACTAATAA
Found at i:2102180 original size:84 final size:83
Alignment explanation
Indices: 2102051--2102217 Score: 309
Period size: 84 Copynumber: 2.0 Consensus size: 83
2102041 ACATTTTGCA
2102051 GAGACACAACCTGTTTCTACCCATCTTCTCCCAATCAGAACCTAATACTCCTCAAACTCCCCAAC
1 GAGACACAACCTGTTTCTACCCATCTTCTCCCAATCAGAACCTAATACTCCTCAAACTCCCCAAC
2102116 CAAAC-CTAATACACCAC
66 CAAACACTAATACACCAC
2102133 GAGACACAACCTGTTTCTACCCCATCTTCTCCCCAATCAGAACCTAATACTCCTCAAACTCCCCA
1 GAGACACAACCTGTTTCTA-CCCATCTTCT-CCCAATCAGAACCTAATACTCCTCAAACTCCCCA
2102198 ACCAAACACTAATACACCAC
64 ACCAAACACTAATACACCAC
2102218 ATCCCAATAT
Statistics
Matches: 82, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
82 19 0.23
83 10 0.12
84 41 0.50
85 12 0.15
ACGTcount: A:0.34, C:0.41, G:0.05, T:0.20
Consensus pattern (83 bp):
GAGACACAACCTGTTTCTACCCATCTTCTCCCAATCAGAACCTAATACTCCTCAAACTCCCCAAC
CAAACACTAATACACCAC
Found at i:2103749 original size:27 final size:24
Alignment explanation
Indices: 2103699--2103744 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2103689 GAAGGTCTGA
*
2103699 TGCTTCCAGAATCCCAGCCGCCTC
1 TGCTTCAAGAATCCCAGCCGCCTC
2103723 TGCTTCAAGAATCCCAGCCGCC
1 TGCTTCAAGAATCCCAGCCGCC
2103745 GCCTCACTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.43, G:0.17, T:0.20
Consensus pattern (24 bp):
TGCTTCAAGAATCCCAGCCGCCTC
Found at i:2104020 original size:14 final size:12
Alignment explanation
Indices: 2103983--2104007 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2103973 ACGACAATAA
2103983 AAAAAAAAACAG
1 AAAAAAAAACAG
2103995 AAAAAAAAACAG
1 AAAAAAAAACAG
2104007 A
1 A
2104008 GAAAGAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAACAG
Found at i:2104845 original size:31 final size:31
Alignment explanation
Indices: 2104788--2104846 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
2104778 TAGATTTTTA
** *
2104788 ATTTTATTTTTTTAGTTATTTATGTTTTCAT
1 ATTTTATTTTTTTAAATATATATGTTTTCAT
2104819 ATTTTATTGTTTTTAAATATAT-TGTTTT
1 ATTTTATT-TTTTTAAATATATATGTTTT
2104847 AGTAATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 14 0.58
32 10 0.42
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (31 bp):
ATTTTATTTTTTTAAATATATATGTTTTCAT
Found at i:2107138 original size:8 final size:7
Alignment explanation
Indices: 2107114--2107155 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
2107104 TTTTCATACA
2107114 TGCA-TT
1 TGCATTT
2107120 TGCATTT
1 TGCATTT
2107127 TGCATCTT
1 TGCAT-TT
2107135 TGCATTT
1 TGCATTT
* *
2107142 TTCATTG
1 TGCATTT
2107149 TGCATTT
1 TGCATTT
2107156 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:2107138 original size:15 final size:14
Alignment explanation
Indices: 2107114--2107155 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
2107104 TTTTCATACA
2107114 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
2107127 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
2107142 TTCATTGTGCATTT
1 TGCATTTTGCATTT
2107156 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:2107244 original size:26 final size:26
Alignment explanation
Indices: 2107215--2107273 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
2107205 CATTCACATA
*
2107215 TTTACATTTGAATTTGCATTTGCATT
1 TTTACATTTGAATTTACATTTGCATT
* * *
2107241 TTTACGTTTGTATTTACATTTTCATT
1 TTTACATTTGAATTTACATTTGCATT
2107267 TTTACAT
1 TTTACAT
2107274 AATTACATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.58
Consensus pattern (26 bp):
TTTACATTTGAATTTACATTTGCATT
Found at i:2109263 original size:16 final size:16
Alignment explanation
Indices: 2109222--2109280 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
2109212 TCCAGCAAAG
*
2109222 AAAGAAAAAAAATAGAA
1 AAAGAAAAAAAA-ACAA
2109239 ATAA-AAAAAAACAACAA
1 A-AAGAAAAAAA-AACAA
*
2109256 AAAGAAAAAAAAAGAA
1 AAAGAAAAAAAAACAA
*
2109272 AAAGGAAAA
1 AAAGAAAAA
2109281 TTGAATCAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
16 14 0.39
17 19 0.53
18 3 0.08
ACGTcount: A:0.83, C:0.03, G:0.10, T:0.03
Consensus pattern (16 bp):
AAAGAAAAAAAAACAA
Found at i:2109263 original size:19 final size:18
Alignment explanation
Indices: 2109218--2109268 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
2109208 CTCATCCAGC
* *
2109218 AAAGAAAGAAAAAAAATAG
1 AAAGAAA-AAAAAAAACAA
*
2109237 AAATAAAAAAAAACAACAA
1 AAAGAAAAAAAAA-AACAA
2109256 AAAGAAAAAAAAA
1 AAAGAAAAAAAAA
2109269 GAAAAAGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.84, C:0.04, G:0.08, T:0.04
Consensus pattern (18 bp):
AAAGAAAAAAAAAAACAA
Found at i:2111913 original size:84 final size:81
Alignment explanation
Indices: 2111518--2111985 Score: 785
Period size: 81 Copynumber: 5.7 Consensus size: 81
2111508 ACTGGAACAA
2111518 ATATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 ATATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
2111583 CCAATCATTGAATTGG
66 CCAATCATTGAATTGG
2111599 ATATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 ATATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
2111664 CCAATCATTGAATTGG
66 CCAATCATTGAATTGG
2111680 ATATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 ATATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
2111745 CCAATCATTGAATTGG
66 CCAATCATTGAATTGG
2111761 ATATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 ATATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
*
2111826 CTAATCATTGAATTTGG
66 CCAATCATTGAA-TTGG
* *
2111843 AAGAATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACA-
1 -A-TATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
*
2111907 AGACTAATCATTGAATTTGG
64 A-ACCAATCATTGAA-TTGG
* * * * *
2111927 AAGAATAATGTGTTCAATAGCATCTTTTGGAAATGTTCTTTGAGTTATCTAATCTGGTT
1 -A-TATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
2111986 TGGTATGAAC
Statistics
Matches: 376, Mismatches: 7, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
81 238 0.63
82 4 0.01
83 2 0.01
84 132 0.35
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (81 bp):
ATATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
CCAATCATTGAATTGG
Found at i:2112132 original size:104 final size:104
Alignment explanation
Indices: 2112005--2112204 Score: 303
Period size: 104 Copynumber: 1.9 Consensus size: 104
2111995 CCCCAAAAAC
* * * *
2112005 CAATCATTGGATTTTAAAGATGAATTTGC-CTATAGTAGAAATAAGGAGGCTCAATAGCATCTTC
1 CAATCATTGAATTTGAAAGATGAATTTGCTC-ATAGTAAAAATAAGGAGACTCAATAGCATCTTC
* *
2112069 TGGAAGTGTTCTTTGAGTTATCTGATTTGGTTGGACAGAA
65 TGGAAGTATTCTTTGAGTTATCTGATCTGGTTGGACAGAA
* * *
2112109 CAATCATTGAATTTGGAAGATGAATTTGCTCATAGTAAAAATAAGGATACTCAATAGCATTTTCT
1 CAATCATTGAATTTGAAAGATGAATTTGCTCATAGTAAAAATAAGGAGACTCAATAGCATCTTCT
2112174 GGAAGTATTCTTTGAGTTATCTGATCTGGTT
66 GGAAGTATTCTTTGAGTTATCTGATCTGGTT
2112205 CGGTAGGAAT
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
104 85 0.99
105 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.36
Consensus pattern (104 bp):
CAATCATTGAATTTGAAAGATGAATTTGCTCATAGTAAAAATAAGGAGACTCAATAGCATCTTCT
GGAAGTATTCTTTGAGTTATCTGATCTGGTTGGACAGAA
Found at i:2114861 original size:22 final size:22
Alignment explanation
Indices: 2114832--2114886 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
2114822 ATCTACACTC
*
2114832 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
2114854 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
2114876 TTCAAAGATGA
1 TTCAAAGATGA
2114887 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:2115998 original size:118 final size:115
Alignment explanation
Indices: 2115356--2116465 Score: 1546
Period size: 118 Copynumber: 9.7 Consensus size: 115
2115346 TTTCCAGTTC
*
2115356 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
** * * *
2115421 CAA-CTTTTCGCTTGAATTCATCA-TTCGAT-GATTCAGTATTT-CC--AGTTC
66 CAACCTTTTTTC-TGAATTCATCACTT-GATGGATT-A-TTTTTGCCAGAGGTA
2115469 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * * * * **
2115534 CAACC-TTTTACTTGAATCCATCATTTGCTGGATCAGCCTTT-CC--AGGTA
66 CAACCTTTTTTC-TGAATTCATCACTTGATGGATTA-TTTTTGCCAGAGGTA
*
2115582 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* *
2115647 CAACCTTTTTGTTTGAATTCATCACTTGATGGATTATTGTTGCCAGAGGTA
66 CAACCTTTTT-TCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGGTA
2115698 GAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
1 GAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
* * * * * *
2115763 GTTCAACC-TTTTGCTCAAATCCATCACTTGATGAATCAACTTTT-CCAGA-G-A
63 GTTCAACCTTTTTTCT-GAATTCATCACTTGATGGAT-TATTTTTGCCAGAGGTA
2115814 -AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
2115878 CAACCTTTTTTCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGGTA
66 CAACCTTTTTTCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGGTA
2115928 GAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
1 GAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
2115993 GTTCAACCTTTTTTCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGGTA
63 GTTCAACCTTTTTTCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGGTA
2116046 GAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
1 GAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
2116111 GTTCAACCTTTTTTCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGGTA
63 GTTCAACCTTTTTTCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGGTA
2116164 GAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
1 GAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
* **
2116229 GTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGCCAGA-AAA
63 GTTCAACCTTTTTTCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGGTA
* *
2116281 G-GTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * * ** *
2116345 CAACC-TTTTGCTCAAATCCATCACTTGATGGAGCAGCTTTT-CCAGA-G-A
66 CAACCTTTTTTCT-GAATTCATCACTTGATGGATTA-TTTTTGCCAGAGGTA
*
2116393 -AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
2116457 CAA-CTTTTT
66 CAACCTTTTT
2116466 GCATAATTCT
Statistics
Matches: 923, Mismatches: 49, Indels: 51
0.90 0.05 0.05
Matches are distributed among these distances:
111 6 0.01
112 147 0.16
113 245 0.27
114 37 0.04
115 36 0.04
116 41 0.04
117 5 0.01
118 353 0.38
119 53 0.06
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (115 bp):
GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
CAACCTTTTTTCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGGTA
Found at i:2116998 original size:76 final size:76
Alignment explanation
Indices: 2116872--2117209 Score: 563
Period size: 76 Copynumber: 4.5 Consensus size: 76
2116862 CTATTTCCCA
* * * **
2116872 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAACCCTACGGGAGCTTTTTGATGTTTTCAA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAAAGCTTTTTGATGTTTTCAA
2116937 AGCCTTCGGGT
66 AGCCTTCGGGT
2116948 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAAAGCTTTTTGATGTTTTCAA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAAAGCTTTTTGATGTTTTCAA
2117013 AGCCTTCGGGT
66 AGCCTTCGGGT
2117024 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAAAGCTTTTTGATG-TTTCAA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAAAGCTTTTTGATGTTTTCAA
2117088 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
2117099 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC-AGGAGCTTTTTAATGTTTTCA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGA-AAGCTTTTTGATGTTTTCA
*
2117163 AAACCTTCGGGT
65 AAGCCTTCGGGT
* *
2117175 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAA
2117210 CATTTCTATC
Statistics
Matches: 250, Mismatches: 10, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
74 1 0.00
75 71 0.28
76 178 0.71
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (76 bp):
CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAAAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:2117149 original size:151 final size:152
Alignment explanation
Indices: 2116872--2117209 Score: 572
Period size: 151 Copynumber: 2.2 Consensus size: 152
2116862 CTATTTCCCA
**
2116872 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAACCCTACGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAACCCTACGAAAGCTTTTTGATGTTTTCAA
2116937 AGCCTTCGGGTCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAAAGCTTTTT
66 AGCCTTCGGGTCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAAAGCTTTTT
* *
2117002 GATGTTTTCAAAGCCTTCGGGT
131 AATGTTTTCAAAACCTTCGGGT
* * *
2117024 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAAAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAACCCTACGAAAGCTTTTTGATGTTTTCAA
*
2117088 AGCCTTCGGGTCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC-AGGAGCTTTT
66 AGCCTTCGGGTCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGA-AAGCTTTT
2117152 TAATGTTTTCAAAACCTTCGGGT
130 TAATGTTTTCAAAACCTTCGGGT
*
2117175 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
2117210 CATTTCTATC
Statistics
Matches: 175, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
150 1 0.01
151 121 0.69
152 53 0.30
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (152 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAACCCTACGAAAGCTTTTTGATGTTTTCAA
AGCCTTCGGGTCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAAAGCTTTTT
AATGTTTTCAAAACCTTCGGGT
Found at i:2117342 original size:3 final size:3
Alignment explanation
Indices: 2117336--2117444 Score: 146
Period size: 3 Copynumber: 35.7 Consensus size: 3
2117326 TCATTTAAAT
** *
2117336 TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
2117384 TTA TTA TTA TTA TTA TCA TTA TTTA TTA TTA TTA TTA TCA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
2117430 TATA TTA TTA TTA TT
1 T-TA TTA TTA TTA TT
2117445 TAATAAATAA
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
3 86 0.93
4 6 0.07
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2117630 original size:30 final size:27
Alignment explanation
Indices: 2117562--2117625 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
2117552 CCTAGCCACC
*
2117562 CCCAGCCGCCTCTGATGCTTCCAGAAT
1 CCCAGCCGCCTCTGATGCTTCAAGAAT
2117589 CCCAGCCGCCTCTGATGCTTCAAGAAT
1 CCCAGCCGCCTCTGATGCTTCAAGAAT
2117616 CCCAGCCGCC
1 CCCAGCCGCC
2117626 GCCTCACTGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.19, C:0.44, G:0.19, T:0.19
Consensus pattern (27 bp):
CCCAGCCGCCTCTGATGCTTCAAGAAT
Found at i:2117888 original size:14 final size:15
Alignment explanation
Indices: 2117869--2117898 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2117859 CGACAATAAA
2117869 AAAAAACAGA-AAAG
1 AAAAAACAGAGAAAG
2117883 AAAAAACAGAGAAAG
1 AAAAAACAGAGAAAG
2117898 A
1 A
2117899 GAACACAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.77, C:0.07, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAACAGAGAAAG
Found at i:2118747 original size:19 final size:18
Alignment explanation
Indices: 2118698--2118748 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
2118688 TAGATTTTTA
2118698 ATTTTATT-TTTTTAGTT
1 ATTTTATTGTTTTTAGTT
* *
2118715 ATTTTATATGTTTTCATTT
1 ATTTTAT-TGTTTTTAGTT
2118734 ATTTTATTGTTTTTA
1 ATTTTATTGTTTTTA
2118749 AATATATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 7 0.24
18 8 0.28
19 14 0.48
ACGTcount: A:0.20, C:0.02, G:0.06, T:0.73
Consensus pattern (18 bp):
ATTTTATTGTTTTTAGTT
Found at i:2122900 original size:21 final size:21
Alignment explanation
Indices: 2122874--2122915 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2122864 TGCAAGGAGT
*
2122874 CTTCACTTGAAGA-CTCCAAGA
1 CTTCACTT-AAAACCTCCAAGA
2122895 CTTCACTTAAAACCTCCAAGA
1 CTTCACTTAAAACCTCCAAGA
2122916 TTACTATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.36, C:0.31, G:0.10, T:0.24
Consensus pattern (21 bp):
CTTCACTTAAAACCTCCAAGA
Found at i:2123847 original size:41 final size:44
Alignment explanation
Indices: 2123775--2123859 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 44
2123765 GCATATTTAA
* * *
2123775 TATTAACATACTATTTTAGTATCATTTTAATAA-A-AATATAAT
1 TATTAACATAATATTTTAGTATAATTGTAATAATATAATATAAT
2123817 TATTAAC-TAATATTTATAG-ATAATTGTAATAATATAATATAAT
1 TATTAACATAATATTT-TAGTATAATTGTAATAATATAATATAAT
2123860 ATTTTAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
41 18 0.49
42 11 0.30
43 8 0.22
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.45
Consensus pattern (44 bp):
TATTAACATAATATTTTAGTATAATTGTAATAATATAATATAAT
Found at i:2124034 original size:14 final size:14
Alignment explanation
Indices: 2124015--2124054 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
2124005 AAATATAATA
2124015 TAATATTCTT-ATTT
1 TAATATT-TTAATTT
2124029 TAATATTTTAATTT
1 TAATATTTTAATTT
2124043 TAATATTTTAAT
1 TAATATTTTAAT
2124055 AATATATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 2 0.08
14 23 0.92
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TAATATTTTAATTT
Found at i:2124037 original size:8 final size:8
Alignment explanation
Indices: 2124024--2124071 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
2124014 ATAATATTCT
2124024 TATTTTAA
1 TATTTTAA
2124032 TATTTT-A
1 TATTTTAA
2124039 -ATTTTAA
1 TATTTTAA
2124046 TATTTTAA
1 TATTTTAA
* * *
2124054 TAATATAT
1 TATTTTAA
2124062 TATTTTAA
1 TATTTTAA
2124070 TA
1 TA
2124072 AATAATTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
6 5 0.16
7 2 0.06
8 25 0.78
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TATTTTAA
Found at i:2124077 original size:20 final size:19
Alignment explanation
Indices: 2124052--2124112 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
2124042 TTAATATTTT
2124052 AATAATATATTATTTTAATA
1 AATAAT-TATTATTTTAATA
* *
2124072 AATAA-T-TTAATATAATTA
1 AATAATTATTATTTTAA-TA
2124090 TAATAATT-TTATTTTAATA
1 -AATAATTATTATTTTAATA
2124109 AATA
1 AATA
2124113 TAATAATCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 7 0.21
18 7 0.21
19 7 0.21
20 13 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AATAATTATTATTTTAATA
Found at i:2126876 original size:3 final size:3
Alignment explanation
Indices: 2126868--2126922 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
2126858 GTAAAAGTTG
2126868 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2126916 TAA TAA T
1 TAA TAA T
2126923 TTTTTGAGAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2127089 original size:40 final size:40
Alignment explanation
Indices: 2127045--2127211 Score: 210
Period size: 40 Copynumber: 4.2 Consensus size: 40
2127035 TCTAAAGGAT
** * *
2127045 GATGACACAGTTCCTATGTGATGATGAGACCTAGTCGAGG
1 GATGACATGGTTCCTACGTGATGAGGAGACCTAGTCGAGG
* *
2127085 GATGACATGGTTCCTACGTGATAAGGAGACCTAGTTGAGG
1 GATGACATGGTTCCTACGTGATGAGGAGACCTAGTCGAGG
* *
2127125 GATGACATGGTTCCTACATAATGAGGAGACCTAGTCGAGG
1 GATGACATGGTTCCTACGTGATGAGGAGACCTAGTCGAGG
* * * *
2127165 GACGACATGGTTCCTACGTGATGAGAAAATCTAGTCG-GTG
1 GATGACATGGTTCCTACGTGATGAGGAGACCTAGTCGAG-G
2127205 GATGACA
1 GATGACA
2127212 ATGTTTGTTG
Statistics
Matches: 109, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
39 1 0.01
40 108 0.99
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.24
Consensus pattern (40 bp):
GATGACATGGTTCCTACGTGATGAGGAGACCTAGTCGAGG
Found at i:2127965 original size:43 final size:43
Alignment explanation
Indices: 2127871--2127972 Score: 141
Period size: 43 Copynumber: 2.4 Consensus size: 43
2127861 TTCATCGTGA
* *** *
2127871 AGTTGAAACCGTGGATGTGTGGGCACGATATCCTCCGTCGTGG
1 AGTTGAAATCGTGGATCCATGGGCACGATATCCTCCGTAGTGG
*
2127914 AGTTGAAATCGTGGATCCATGGGTACGATATCCTCCGTAGTGG
1 AGTTGAAATCGTGGATCCATGGGCACGATATCCTCCGTAGTGG
*
2127957 AGTTGAAATCATGGAT
1 AGTTGAAATCGTGGAT
2127973 AGCCCCTTCG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (43 bp):
AGTTGAAATCGTGGATCCATGGGCACGATATCCTCCGTAGTGG
Found at i:2128171 original size:43 final size:43
Alignment explanation
Indices: 2128069--2128178 Score: 157
Period size: 43 Copynumber: 2.6 Consensus size: 43
2128059 TGATTCCCTT
* * * *
2128069 CGTCGTGAAGTTGAAACCATGGTTGTGTGGGCACGATATCCTC
1 CGTCGTGGAGTTGAAATCATGGATCTGTGGGCACGATATCCTC
*
2128112 CGTCGTGGAGTTGAAATCATGGATCTGTGGGTACGATATCCTC
1 CGTCGTGGAGTTGAAATCATGGATCTGTGGGCACGATATCCTC
* *
2128155 CGTCTTGGAGTTGAAATCGTGGAT
1 CGTCGTGGAGTTGAAATCATGGAT
2128179 GGCCCCTTCG
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (43 bp):
CGTCGTGGAGTTGAAATCATGGATCTGTGGGCACGATATCCTC
Found at i:2128213 original size:206 final size:206
Alignment explanation
Indices: 2127852--2128292 Score: 702
Period size: 206 Copynumber: 2.1 Consensus size: 206
2127842 ACTTGTGTGT
*
2127852 ACGATTCCCTTCATCGTGAAGTTGAAACCGTGGATGTGTGGGCACGATATCCTCCGTCGTGGAGT
1 ACGATTCCCTTCATCGTGAAGTTGAAACCATGGATGTGTGGGCACGATATCCTCCGTCGTGGAGT
*
2127917 TGAAATCGTGGATCCATGGGTACGATATCCTCCGTAGTGGAGTTGAAATCATGGATAGCCCCTTC
66 TGAAATCATGGATCCATGGGTACGATATCCTCCGTAGTGGAGTTGAAATCATGGATAGCCCCTTC
* *
2127982 GTCGTTAAGTTGAGCCTTAACTTGAATATCCTTCATCGTGAAGTTAAAATCCACGTATTGTATGT
131 GTCGTGAAGTTGAGCCTTAACTTGAATATCCTTCATCGTGAAGTTAAAATCCAAGTATTGTATGT
** *
2128047 TGTGGGTGGAC
196 TGCAGGTGAAC
* * *
2128058 ATGATTCCCTTCGTCGTGAAGTTGAAACCATGGTTGTGTGGGCACGATATCCTCCGTCGTGGAGT
1 ACGATTCCCTTCATCGTGAAGTTGAAACCATGGATGTGTGGGCACGATATCCTCCGTCGTGGAGT
** ** * *
2128123 TGAAATCATGGATCTGTGGGTACGATATCCTCCGTCTTGGAGTTGAAATCGTGGATGGCCCCTTC
66 TGAAATCATGGATCCATGGGTACGATATCCTCCGTAGTGGAGTTGAAATCATGGATAGCCCCTTC
* * * *
2128188 GTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGCAGTTGAAATCCAAGTATTGTATGT
131 GTCGTGAAGTTGAGCCTTAACTTGAATATCCTTCATCGTGAAGTTAAAATCCAAGTATTGTATGT
2128253 TGCAGGTGAAC
196 TGCAGGTGAAC
2128264 ACGATTCCCTTCATCGTGAAGTTGAAACC
1 ACGATTCCCTTCATCGTGAAGTTGAAACC
2128293 GTAGATGACC
Statistics
Matches: 213, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
206 213 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (206 bp):
ACGATTCCCTTCATCGTGAAGTTGAAACCATGGATGTGTGGGCACGATATCCTCCGTCGTGGAGT
TGAAATCATGGATCCATGGGTACGATATCCTCCGTAGTGGAGTTGAAATCATGGATAGCCCCTTC
GTCGTGAAGTTGAGCCTTAACTTGAATATCCTTCATCGTGAAGTTAAAATCCAAGTATTGTATGT
TGCAGGTGAAC
Found at i:2128472 original size:64 final size:64
Alignment explanation
Indices: 2128390--2128512 Score: 185
Period size: 64 Copynumber: 1.9 Consensus size: 64
2128380 GTTTCGAGTT
* * *
2128390 CAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGGAAA-TTTTTTGTTTAGTA
1 CAATATCCTTCATTGTGAAGTTAAAATTGACTCTGAATGAAA-TGGGAAAGTTGTTTGTTTAGTA
* *
2128454 CAATATCCTTCATTGTGAAGTTAAAATTGACTTTGAATGAAATTGGAAAGTTGTTTGTT
1 CAATATCCTTCATTGTGAAGTTAAAATTGACTCTGAATGAAATGGGAAAGTTGTTTGTT
2128513 GACAGACGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
63 6 0.11
64 47 0.89
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.40
Consensus pattern (64 bp):
CAATATCCTTCATTGTGAAGTTAAAATTGACTCTGAATGAAATGGGAAAGTTGTTTGTTTAGTA
Found at i:2129921 original size:18 final size:17
Alignment explanation
Indices: 2129898--2129954 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
2129888 TTCTTGTTCA
2129898 TTTTTCTTTGCTTTCTTT
1 TTTTTCTTT-CTTTCTTT
*
2129916 TTTTTCTTTTTCTTTGTTT
1 TTTTTC--TTTCTTTCTTT
*
2129935 TTTGTT-TTTATTTCTTT
1 TTT-TTCTTTCTTTCTTT
2129952 TTT
1 TTT
2129955 CTTTTTACTC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 12 0.36
18 6 0.18
19 10 0.30
20 5 0.15
ACGTcount: A:0.02, C:0.11, G:0.05, T:0.82
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTT
Found at i:2129926 original size:24 final size:22
Alignment explanation
Indices: 2129898--2129960 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
2129888 TTCTTGTTCA
2129898 TTTTTCTTTGCTTTCTTTTTTTT
1 TTTTTCTTTG-TTTCTTTTTTTT
*
2129921 CTTTTTCTTTGTTT-TTTGTTTT
1 -TTTTTCTTTGTTTCTTTTTTTT
*
2129943 TATTTCTTT-TTTCTTTTT
1 TTTTTCTTTGTTTCTTTTT
2129961 ACTCTTTGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 3 0.09
21 12 0.34
22 7 0.20
23 3 0.09
24 10 0.29
ACGTcount: A:0.02, C:0.11, G:0.05, T:0.83
Consensus pattern (22 bp):
TTTTTCTTTGTTTCTTTTTTTT
Found at i:2129935 original size:17 final size:17
Alignment explanation
Indices: 2129915--2129961 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
2129905 TTGCTTTCTT
* *
2129915 TTTTTTCTTTTTCTTTG
1 TTTTTTCTTTTTATTTC
*
2129932 TTTTTTGTTTTTATTTC
1 TTTTTTCTTTTTATTTC
2129949 TTTTTTCTTTTTA
1 TTTTTTCTTTTTA
2129962 CTCTTTGTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.04, C:0.09, G:0.04, T:0.83
Consensus pattern (17 bp):
TTTTTTCTTTTTATTTC
Found at i:2129966 original size:16 final size:17
Alignment explanation
Indices: 2129915--2129972 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
2129905 TTGCTTTCTT
* * *
2129915 TTTTTTCTTTTTCTTTG
1 TTTTTTCTTTTTATCTC
* *
2129932 TTTTTTGTTTTTATTTC
1 TTTTTTCTTTTTATCTC
2129949 TTTTTTCTTTTTA-CTC
1 TTTTTTCTTTTTATCTC
*
2129965 TTTGTTCT
1 TTTTTTCT
2129973 GATTGGATCT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
16 9 0.26
17 26 0.74
ACGTcount: A:0.03, C:0.12, G:0.05, T:0.79
Consensus pattern (17 bp):
TTTTTTCTTTTTATCTC
Found at i:2135215 original size:12 final size:12
Alignment explanation
Indices: 2135198--2135222 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2135188 TAATTTATGG
2135198 TATTTTAATATT
1 TATTTTAATATT
2135210 TATTTTAATATT
1 TATTTTAATATT
2135222 T
1 T
2135223 TAAATTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTTTAATATT
Found at i:2135248 original size:15 final size:14
Alignment explanation
Indices: 2135198--2135247 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
2135188 TAATTTATGG
2135198 TATTTTAATA-TT-
1 TATTTTAATATTTA
2135210 TATTTTAATATTTTA
1 TATTTTAATA-TTTA
*
2135225 AATTTTAAATATTTA
1 TATTTT-AATATTTA
2135240 TATTTTAA
1 TATTTTAA
2135248 AAATATAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 10 0.31
14 4 0.12
15 14 0.44
16 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTTTAATATTTA
Found at i:2137629 original size:21 final size:20
Alignment explanation
Indices: 2137601--2137639 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2137591 GAGTTTTAAA
*
2137601 GCATGAGTATCGATACTCAT
1 GCATGAGTATCAATACTCAT
2137621 GCATAGAGTATCAATACTC
1 GCAT-GAGTATCAATACTC
2137640 TAGGCTCGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (20 bp):
GCATGAGTATCAATACTCAT
Found at i:2140111 original size:20 final size:20
Alignment explanation
Indices: 2140041--2140098 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
2140031 TGATTCAATT
2140041 AGTATCGATACCGAAGGGGG
1 AGTATCGATACCGAAGGGGG
2140061 AGTATCGATACCGAAGGGGG
1 AGTATCGATACCGAAGGGGG
*
2140081 TGTATCGATACCGAAGGG
1 AGTATCGATACCGAAGGG
2140099 AAGGCATCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.29, C:0.16, G:0.38, T:0.17
Consensus pattern (20 bp):
AGTATCGATACCGAAGGGGG
Found at i:2140182 original size:21 final size:21
Alignment explanation
Indices: 2140137--2140206 Score: 101
Period size: 21 Copynumber: 3.5 Consensus size: 21
2140127 TGCAAAAATG
2140137 GTATCGATACCATAG--TAGA
1 GTATCGATACCATAGTATAGA
*
2140156 GTATCGATACCATAGTATAGT
1 GTATCGATACCATAGTATAGA
*
2140177 GTATCGATACCATAGTA-AGG
1 GTATCGATACCATAGTATAGA
2140197 GTATCGATAC
1 GTATCGATAC
2140207 TATGGAGCCA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
19 15 0.32
20 12 0.26
21 20 0.43
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (21 bp):
GTATCGATACCATAGTATAGA
Found at i:2140673 original size:55 final size:55
Alignment explanation
Indices: 2140531--2140967 Score: 534
Period size: 55 Copynumber: 7.9 Consensus size: 55
2140521 ACTAAGTGTA
* * * * * *
2140531 GTACATGCACTATGTGTACAAATCCACGGAATTCATCATGGGTTGATGAATAGTC
1 GTACAGGCACTATGTGTGCAAAACCACGAAATTCATCATGAGTTGATGAATAGCC
* * *
2140586 GTACAAGGCACTATGTGTGTAAAACCACGAAATTCATCATGGGTTAATGAATAGCC
1 GTAC-AGGCACTATGTGTGCAAAACCACGAAATTCATCATGAGTTGATGAATAGCC
* * * *
2140642 ATACATGAACTATGTGTGCAAAACCACGAAATTCATCATGAGTTGATGAATAGTC
1 GTACAGGCACTATGTGTGCAAAACCACGAAATTCATCATGAGTTGATGAATAGCC
* * * * * * *
2140697 ATATAGACACTATGTGTGCAAAACTAAGGAATTCATCATGAGTTGATGAATAGTC
1 GTACAGGCACTATGTGTGCAAAACCACGAAATTCATCATGAGTTGATGAATAGCC
* * * *
2140752 GTATAGACACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCC
1 GTACAGGCACTATGTGTGCAAAACCACGAAATTCATCATGAGTTGATGAATAGCC
* * * * *
2140807 GTACAGGCACTAGGTGTGCAAATCCACGGAATTTATCATGGGTTGATGAATAGCC
1 GTACAGGCACTATGTGTGCAAAACCACGAAATTCATCATGAGTTGATGAATAGCC
* * *
2140862 TTACAGGCACTATGTGTACAAAACCAC-ATAATTCATCATGAGTGGATGAATAGCC
1 GTACAGGCACTATGTGTGCAAAACCACGA-AATTCATCATGAGTTGATGAATAGCC
* * *
2140917 GTACAGGCACTGTGTGTACAAAACCACGAAATTCATCATAAGTTGATGAAT
1 GTACAGGCACTATGTGTGCAAAACCACGAAATTCATCATGAGTTGATGAAT
2140968 TACCATATAG
Statistics
Matches: 336, Mismatches: 43, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
55 288 0.86
56 48 0.14
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (55 bp):
GTACAGGCACTATGTGTGCAAAACCACGAAATTCATCATGAGTTGATGAATAGCC
Done.