Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007859.1 Hibiscus syriacus cultivar Beakdansim tig00110221_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: 3538007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 18
Found at i:2065996 original size:79 final size:80
Alignment explanation
Indices: 2065844--2065997 Score: 213
Period size: 79 Copynumber: 1.9 Consensus size: 80
2065834 TTTTTTAAAT
* ** *
2065844 ATTTTCGGTAAAACGTTACCTAAAACATTATTTTTTTTTCTACCGAAAATGTTAATATTAGGCAC
1 ATTTCCGGTAAAACACTACCTAAAACATTA--TTTTTTTATACCGAAAATGTTAATATTAGGCAC
2065909 TACATAAAATGTTTAAC
64 TACATAAAATGTTTAAC
*
2065926 ATTTCCGGTAAAACACTACCTAAAACATTA-TTTTTTATACC-AGAAATGTTAATATTGGGCACT
1 ATTTCCGGTAAAACACTACCTAAAACATTATTTTTTTATACCGA-AAATGTTAATATTAGGCACT
*
2065989 ACCTAAAAT
65 ACATAAAAT
2065998 ATTATTTTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
78 1 0.02
79 37 0.57
82 27 0.42
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (80 bp):
ATTTCCGGTAAAACACTACCTAAAACATTATTTTTTTATACCGAAAATGTTAATATTAGGCACTA
CATAAAATGTTTAAC
Found at i:2068238 original size:82 final size:83
Alignment explanation
Indices: 2068097--2068353 Score: 268
Period size: 82 Copynumber: 3.1 Consensus size: 83
2068087 TTAGCGGCGT
* * * * * * * * ** * * *
2068097 AAACGTCGCGACAGAGTAGTACTTTAGTGGCCTTTTTATACAAACGCCACAATA-AGTTCACCCA
1 AAACGCCGCAACAAAGTAGTACTTTAGCGGCGTTTATATAAAAACACCGTAATAGGGTTCATCTA
2068161 TAGTGACATTTTTTCAAC
66 TAGTGACATTTTTTCAAC
** * * ** *
2068179 AAACGCCGTGACAGATTAGTACTTTAGCGGCGTTTATA-AAAAATGCCGTAATAGGGTTCATTTA
1 AAACGCCGCAACAAAGTAGTACTTTAGCGGCGTTTATATAAAAACACCGTAATAGGGTTCATCTA
*
2068243 TAGTGGC-TTTTTTCAAC
66 TAGTGACATTTTTTCAAC
* * *
2068260 AAACGCCGCAATAAAGTAGTACTTTAGCGGCGTTTTTATACAAACACCGTAATAGGGTTCATCTA
1 AAACGCCGCAACAAAGTAGTACTTTAGCGGCGTTTATATAAAAACACCGTAATAGGGTTCATCTA
*
2068325 TAGTGAGATTTTTTCAAC
66 TAGTGACATTTTTTCAAC
2068343 AAACGCCGCAA
1 AAACGCCGCAA
2068354 TAGGGTTCAT
Statistics
Matches: 145, Mismatches: 27, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
81 53 0.37
82 71 0.49
83 21 0.14
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (83 bp):
AAACGCCGCAACAAAGTAGTACTTTAGCGGCGTTTATATAAAAACACCGTAATAGGGTTCATCTA
TAGTGACATTTTTTCAAC
Found at i:2068393 original size:39 final size:39
Alignment explanation
Indices: 2068292--2068405 Score: 117
Period size: 39 Copynumber: 2.8 Consensus size: 39
2068282 TTTAGCGGCG
*
2068292 TTTTTATACAAACA-CCGTAATAGGGTTCATCTATAGTGAGA
1 TTTTTATACAAA-AGCCGCAATAGGGTTCATC--TAGTGAGA
*
2068333 TTTTT-TCAACAAACGCCGCAATAGGGTTCATCTAGTG-GCA
1 TTTTTAT--ACAAAAGCCGCAATAGGGTTCATCTAGTGAG-A
* *
2068373 TTTTTATACAAAAGCTGCAATAGGGTTAATCTA
1 TTTTTATACAAAAGCCGCAATAGGGTTCATCTA
2068406 TAATGATATT
Statistics
Matches: 63, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
39 24 0.38
40 12 0.19
41 6 0.10
42 21 0.33
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (39 bp):
TTTTTATACAAAAGCCGCAATAGGGTTCATCTAGTGAGA
Found at i:2068405 original size:81 final size:82
Alignment explanation
Indices: 2068111--2068479 Score: 248
Period size: 81 Copynumber: 4.5 Consensus size: 82
2068101 GTCGCGACAG
* * * * * * * * *
2068111 AGTAGTACTTTAGTGGCCTTTTTATACAAACGCCACAATA-AGTTCACCCATAGTGACATTTTTT
1 AGTA-TACTCTAGCGGCATTTTTATACAAACACCGCAATAGGGTTCATCTATAGTGAGATTTTTT
** * *
2068175 CAACAAACGCCGTGACAG
65 CAACAAACGCCGCAATAA
* * * * * ** * * *
2068193 ATTAGTACTTTAGCGGCGTTTATA-AAAAATGCCGTAATAGGGTTCATTTATAGTG-GCTTTTTT
1 AGTA-TACTCTAGCGGCATTTTTATACAAACACCGCAATAGGGTTCATCTATAGTGAGATTTTTT
2068256 CAACAAACGCCGCAATAA
65 CAACAAACGCCGCAATAA
* * *
2068274 AGTAGTACTTTAGCGGCGTTTTTATACAAACACCGTAATAGGGTTCATCTATAGTGAGATTTTTT
1 AGTA-TACTCTAGCGGCATTTTTATACAAACACCGCAATAGGGTTCATCTATAGTGAGATTTTTT
*
2068339 CAACAAACGCCGCAATAG
65 CAACAAACGCCGCAATAA
* * * * * *
2068357 GGT-T-CATCTAGTGGCATTTTTATACAAA-AGCTGCAATAGGGTTAATCTATAATGATATTTTT
1 AGTATAC-TCTAGCGGCATTTTTATACAAACA-CCGCAATAGGGTTCATCTATAGTGAGATTTTT
*
2068419 ATCAACAAACGTCGCAA-AA
64 -TCAACAAACGCCGCAATAA
* * * * * * *
2068438 GACTCGTACTTTAGTGGCATTTGTATACAAACGCCGCTATAG
1 -AGT-ATACTCTAGCGGCATTTTTATACAAACACCGCAATAG
2068480 ACTCGTACTC
Statistics
Matches: 232, Mismatches: 44, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
80 2 0.01
81 101 0.44
82 74 0.32
83 26 0.11
84 28 0.12
85 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (82 bp):
AGTATACTCTAGCGGCATTTTTATACAAACACCGCAATAGGGTTCATCTATAGTGAGATTTTTTC
AACAAACGCCGCAATAA
Found at i:2073941 original size:42 final size:42
Alignment explanation
Indices: 2073884--2074065 Score: 138
Period size: 42 Copynumber: 4.3 Consensus size: 42
2073874 GTTTATTGCA
2073884 AAAAAAACCACTAAAGACAAGAGAATTAAC-AACGTTTGTGG-
1 AAAAAAACCACTAAAGACAAGAGAATTAACGAA-GTTTGTGGC
* ** * * *
2073925 AAAAAACGCCACTAAAGACATCATAATTAGCGGAGTTTGTGGC
1 AAAAAA-ACCACTAAAGACAAGAGAATTAACGAAGTTTGTGGC
* * * *
2073968 AAAAAAACCACTATAGACAAGAGAATTAGCGGTA-TTTGT-AC
1 AAAAAAACCACTAAAGACAAGAGAATTAAC-GAAGTTTGTGGC
** * * * *
2074009 TAAAAAGGCCACTAAAGACATGATAATTAAAGAAGTTTGTGAAC
1 -AAAAAAACCACTAAAGACAAGAGAATTAACGAAGTTTGTG-GC
*
2074053 AAAAACACCACTA
1 AAAAAAACCACTA
2074066 TAAATCAAAA
Statistics
Matches: 110, Mismatches: 23, Indels: 14
0.75 0.16 0.10
Matches are distributed among these distances:
41 9 0.08
42 79 0.72
43 20 0.18
44 2 0.02
ACGTcount: A:0.47, C:0.16, G:0.17, T:0.20
Consensus pattern (42 bp):
AAAAAAACCACTAAAGACAAGAGAATTAACGAAGTTTGTGGC
Found at i:2073994 original size:84 final size:85
Alignment explanation
Indices: 2073884--2074067 Score: 217
Period size: 84 Copynumber: 2.2 Consensus size: 85
2073874 GTTTATTGCA
* * **
2073884 AAAAAAACCACTAAAGACAAGAGAATTAACAACGTTTGTGGAAAAAACGCCACTAAAGACATCAT
1 AAAAAAACCACTATAGACAAGAGAATTAACAACATTTGTACAAAAAACGCCACTAAAGACATCAT
** * *
2073949 AATTAGCGGAGTTTGTG-GC
66 AATTAAAGAAGTTTGTGAAC
* *** * * *
2073968 AAAAAAACCACTATAGACAAGAGAATTAGCGGTATTTGTACTAAAAAGGCCACTAAAGACATGAT
1 AAAAAAACCACTATAGACAAGAGAATTAACAACATTTGTACAAAAAACGCCACTAAAGACATCAT
2074033 AATTAAAGAAGTTTGTGAAC
66 AATTAAAGAAGTTTGTGAAC
*
2074053 AAAAACACCACTATA
1 AAAAAAACCACTATA
2074068 AATCAAAACA
Statistics
Matches: 83, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
84 68 0.82
85 15 0.18
ACGTcount: A:0.47, C:0.16, G:0.17, T:0.20
Consensus pattern (85 bp):
AAAAAAACCACTATAGACAAGAGAATTAACAACATTTGTACAAAAAACGCCACTAAAGACATCAT
AATTAAAGAAGTTTGTGAAC
Found at i:2077040 original size:13 final size:14
Alignment explanation
Indices: 2077022--2077055 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
2077012 CAATTTCTCA
*
2077022 TTTTTTTCTTGTT-
1 TTTTTTTCTTCTTC
2077035 TTTTTTTCTTCTTC
1 TTTTTTTCTTCTTC
2077049 TTTTTTT
1 TTTTTTT
2077056 TTTCCTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (14 bp):
TTTTTTTCTTCTTC
Found at i:2077046 original size:16 final size:15
Alignment explanation
Indices: 2077022--2077058 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
2077012 CAATTTCTCA
*
2077022 TTTTTTTCTTGTTTT
1 TTTTTTTCTTCTTTT
2077037 TTTTTCTTCTTCTTTT
1 TTTTT-TTCTTCTTTT
2077053 TTTTTT
1 TTTTTT
2077059 CCTGATGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (15 bp):
TTTTTTTCTTCTTTT
Found at i:2080023 original size:82 final size:83
Alignment explanation
Indices: 2079882--2080256 Score: 334
Period size: 81 Copynumber: 4.6 Consensus size: 83
2079872 TTAGCGGCGT
* * * * *
2079882 AAACGCCGTGACAGAGTAGTACTTTAGTGGCCTTTTTATACAAACGCCACAATA-AGTTCACCCA
1 AAACGCCGTGACAGAGTAGTACTTTAGTGGCATTTTTATACAAACGCCATAATAGGGTTCATCTA
2079946 TAGTGACATTTTTTCAAC
66 TAGTGACATTTTTTCAAC
* * * * * * * *
2079964 AAACGCCGTGACAGATTAGTACTTTAGCGGCGTTTATA-AAAAATGCCGTAATAGGGTTCATTTA
1 AAACGCCGTGACAGAGTAGTACTTTAGTGGCATTTTTATACAAACGCCATAATAGGGTTCATCTA
* *
2080028 TAGTGGC-TTTTTTCAAA
66 TAGTGACATTTTTTCAAC
** * *
2080045 AAACGCCGCAATAAAGTAGTACTTTAGTGGCATTTTTATACAAACGCCATAATAGGGTTCATCTA
1 AAACGCCGTGACAGAGTAGTACTTTAGTGGCATTTTTATACAAACGCCATAATAGGGTTCATCTA
*
2080110 TAGTGAGATTTTTTCAAC
66 TAGTGACATTTTTTCAAC
** * * * ** *
2080128 AAACGCCGCAATAG-GGA-T-CATCTAGTGGCATTTTTATACAAAAC-CTGTAATAGGGTTAATC
1 AAACGCCGTGACAGAGTAGTAC-TTTAGTGGCATTTTTATAC-AAACGCCATAATAGGGTTCATC
* *
2080189 TATAATGATATTTTTTCAAC
64 TATAGTGACATTTTTTCAAC
* ** * * * *
2080209 AAACGTCGCAAAAGACTCA-TACTTTAGTGGAATTTGTATACAAACGCC
1 AAACGCCGTGACAGAGT-AGTACTTTAGTGGCATTTTTATACAAACGCC
2080257 GCTATAGACT
Statistics
Matches: 239, Mismatches: 45, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
80 1 0.00
81 113 0.47
82 83 0.35
83 41 0.17
84 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (83 bp):
AAACGCCGTGACAGAGTAGTACTTTAGTGGCATTTTTATACAAACGCCATAATAGGGTTCATCTA
TAGTGACATTTTTTCAAC
Found at i:2080133 original size:42 final size:42
Alignment explanation
Indices: 2080008--2080213 Score: 139
Period size: 41 Copynumber: 5.0 Consensus size: 42
2079998 TATAAAAAAT
* * *
2080008 GCCGTAATAGGGTTCATTTATAGTG-GCTTTTTTCAAAAAAC
1 GCCGTAATAGGGTTCATCTATAGTGAGATTTTTTCAACAAAC
* ** *
2080049 GCCGCAATAAAG-T-AGTACTTTAGTG-GCA-TTTTT-ATACAAAC
1 GCCGTAATAGGGTTCA-T-CTATAGTGAG-ATTTTTTCA-ACAAAC
*
2080090 GCCATAATAGGGTTCATCTATAGTGAGATTTTTTCAACAAAC
1 GCCGTAATAGGGTTCATCTATAGTGAGATTTTTTCAACAAAC
* *
2080132 GCCGCAATAGGGATCATC--TAGTG-GCA-TTTTT-ATACAAAAC
1 GCCGTAATAGGGTTCATCTATAGTGAG-ATTTTTTCA-AC-AAAC
* * * *
2080172 -CTGTAATAGGGTTAATCTATAATGATATTTTTTCAACAAAC
1 GCCGTAATAGGGTTCATCTATAGTGAGATTTTTTCAACAAAC
2080213 G
1 G
2080214 TCGCAAAAGA
Statistics
Matches: 126, Mismatches: 21, Indels: 35
0.69 0.12 0.19
Matches are distributed among these distances:
38 1 0.01
39 22 0.17
40 13 0.10
41 51 0.40
42 36 0.29
43 3 0.02
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (42 bp):
GCCGTAATAGGGTTCATCTATAGTGAGATTTTTTCAACAAAC
Found at i:2080190 original size:39 final size:40
Alignment explanation
Indices: 2080069--2080190 Score: 119
Period size: 42 Copynumber: 3.0 Consensus size: 40
2080059 AGTAGTACTT
*
2080069 TAGTGGCATTTTTATAC-AAACGCCATAATAGGGTTCATC
1 TAGTGGCATTTTTATACAAAACGCCGTAATAGGGTTCATC
* *
2080108 TATAGTGAG-ATTTTT-T-CAACAAACGCCGCAATAGGGATCATC
1 --TAGTG-GCATTTTTATAC-A-AAACGCCGTAATAGGGTTCATC
* *
2080150 TAGTGGCATTTTTATACAAAAC-CTGTAATAGGGTTAATC
1 TAGTGGCATTTTTATACAAAACGCCGTAATAGGGTTCATC
2080189 TA
1 TA
2080191 TAATGATATT
Statistics
Matches: 67, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
39 17 0.25
40 16 0.24
41 13 0.19
42 21 0.31
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (40 bp):
TAGTGGCATTTTTATACAAAACGCCGTAATAGGGTTCATC
Found at i:2080236 original size:164 final size:161
Alignment explanation
Indices: 2079898--2080256 Score: 372
Period size: 164 Copynumber: 2.2 Consensus size: 161
2079888 CGTGACAGAG
*
2079898 TAGTACTTTAGTGGCCTTTTTATACAAACGCCACAATAAGTTCACCCATAGTGACATTTTTTCAA
1 TAGTACTTTAGTGGCATTTTTATACAAACGCCACAATAAGTTCACCCATAGTGACATTTTTTCAA
* * * *
2079963 CAAACGCCGTGACAGATTAGTACTTTAGCGGCGTTTATAAAAAATGCCGTAATAGGGTTCATTTA
66 CAAACGCCG-GACAGATTAGGACTCTAGCGGCGTTTATAAAAAA-GCCGTAATAGGGTTAATCTA
* * *
2080028 TAGTGGCTTTTTTCAAAAAACGCCGCAATAAAG
129 TAATGGATTTTTTCAAAAAACGCCGCAATAAAC
* * * * *
2080061 TAGTACTTTAGTGGCATTTTTATACAAACGCCATAATAGGGTTCATCTATAGTGAGATTTTTTCA
1 TAGTACTTTAGTGGCATTTTTATACAAACGCCACAATA-AGTTCACCCATAGTGACATTTTTTCA
* * *
2080126 ACAAACGCC-G-CA-A-TAGGGATCATCTAGTGGCATTTTTATACAAAA-CCTGTAATAGGGTTA
65 ACAAACGCCGGACAGATTA-GGA-C-TCTAGCGGC--GTTTATAAAAAAGCC-GTAATAGGGTTA
* * *
2080186 ATCTATAATGATATTTTTTCAACAAACGTCGCAA-AAGAC
124 ATCTATAATG-GATTTTTTCAAAAAACGCCGCAATAA-AC
* *
2080225 TCA-TACTTTAGTGGAATTTGTATACAAACGCC
1 T-AGTACTTTAGTGGCATTTTTATACAAACGCC
2080257 GCTATAGACT
Statistics
Matches: 165, Mismatches: 21, Indels: 19
0.80 0.10 0.09
Matches are distributed among these distances:
159 2 0.01
160 3 0.02
161 3 0.02
162 10 0.06
163 57 0.35
164 89 0.54
165 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (161 bp):
TAGTACTTTAGTGGCATTTTTATACAAACGCCACAATAAGTTCACCCATAGTGACATTTTTTCAA
CAAACGCCGGACAGATTAGGACTCTAGCGGCGTTTATAAAAAAGCCGTAATAGGGTTAATCTATA
ATGGATTTTTTCAAAAAACGCCGCAATAAAC
Found at i:2085717 original size:42 final size:42
Alignment explanation
Indices: 2085660--2085841 Score: 138
Period size: 42 Copynumber: 4.3 Consensus size: 42
2085650 GTTTATTGCA
2085660 AAAAAAACCACTAAAGACAAGAGAATTAAC-AACGTTTGTGG-
1 AAAAAAACCACTAAAGACAAGAGAATTAACGAA-GTTTGTGGC
* ** * * *
2085701 AAAAAACGCCACTAAAGACATCATAATTAGCGGAGTTTGTGGC
1 AAAAAA-ACCACTAAAGACAAGAGAATTAACGAAGTTTGTGGC
* * * *
2085744 AAAAAAACCACTATAGACAAGAGAATTAGCGGTA-TTTGT-AC
1 AAAAAAACCACTAAAGACAAGAGAATTAAC-GAAGTTTGTGGC
** * * * *
2085785 TAAAAAGGCCACTAAAGACATGATAATTAAAGAAGTTTGTGAAC
1 -AAAAAAACCACTAAAGACAAGAGAATTAACGAAGTTTGTG-GC
*
2085829 AAAAACACCACTA
1 AAAAAAACCACTA
2085842 TAAATCAAAA
Statistics
Matches: 110, Mismatches: 23, Indels: 14
0.75 0.16 0.10
Matches are distributed among these distances:
41 9 0.08
42 79 0.72
43 20 0.18
44 2 0.02
ACGTcount: A:0.47, C:0.16, G:0.17, T:0.20
Consensus pattern (42 bp):
AAAAAAACCACTAAAGACAAGAGAATTAACGAAGTTTGTGGC
Found at i:2085770 original size:84 final size:85
Alignment explanation
Indices: 2085660--2085843 Score: 217
Period size: 84 Copynumber: 2.2 Consensus size: 85
2085650 GTTTATTGCA
* * **
2085660 AAAAAAACCACTAAAGACAAGAGAATTAACAACGTTTGTGGAAAAAACGCCACTAAAGACATCAT
1 AAAAAAACCACTATAGACAAGAGAATTAACAACATTTGTACAAAAAACGCCACTAAAGACATCAT
** * *
2085725 AATTAGCGGAGTTTGTG-GC
66 AATTAAAGAAGTTTGTGAAC
* *** * * *
2085744 AAAAAAACCACTATAGACAAGAGAATTAGCGGTATTTGTACTAAAAAGGCCACTAAAGACATGAT
1 AAAAAAACCACTATAGACAAGAGAATTAACAACATTTGTACAAAAAACGCCACTAAAGACATCAT
2085809 AATTAAAGAAGTTTGTGAAC
66 AATTAAAGAAGTTTGTGAAC
*
2085829 AAAAACACCACTATA
1 AAAAAAACCACTATA
2085844 AATCAAAACA
Statistics
Matches: 83, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
84 68 0.82
85 15 0.18
ACGTcount: A:0.47, C:0.16, G:0.17, T:0.20
Consensus pattern (85 bp):
AAAAAAACCACTATAGACAAGAGAATTAACAACATTTGTACAAAAAACGCCACTAAAGACATCAT
AATTAAAGAAGTTTGTGAAC
Found at i:2085910 original size:44 final size:44
Alignment explanation
Indices: 2085862--2085950 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
2085852 CATATAGCAA
* * *
2085862 CGTTTGAAAGAACAAACACTGCTATATAACTTGACCTTTTTCGG
1 CGTTTGAAAGAACAAACACCGCTATATAACTCGACCTTTTGCGG
2085906 CGTTTGAAAGAACAAACACCGCTATATAACTCGACCTTTTGCGG
1 CGTTTGAAAGAACAAACACCGCTATATAACTCGACCTTTTGCGG
2085950 C
1 C
2085951 ATTCAGGTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (44 bp):
CGTTTGAAAGAACAAACACCGCTATATAACTCGACCTTTTGCGG
Found at i:2088820 original size:15 final size:15
Alignment explanation
Indices: 2088797--2088831 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2088787 CAATTTCTCA
*
2088797 TTTTT-TTCTTGTTT
1 TTTTTCTTCTTCTTT
2088811 TTTTTCTTCTTCTTT
1 TTTTTCTTCTTCTTT
2088826 TTTTTC
1 TTTTTC
2088832 CTGATGAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (15 bp):
TTTTTCTTCTTCTTT
Found at i:2094938 original size:2 final size:2
Alignment explanation
Indices: 2094931--2094966 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2094921 TTTGTTGGAT
2094931 TC TC TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2094967 TCCTTGTATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2095991 original size:2 final size:2
Alignment explanation
Indices: 2095984--2096011 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2095974 CTAGCTCTTA
2095984 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
2096012 TTAAATTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2096930 original size:2 final size:2
Alignment explanation
Indices: 2096923--2096962 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2096913 CATTGAATTA
2096923 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
2096963 CTGTGTGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2106055 original size:20 final size:21
Alignment explanation
Indices: 2106018--2106063 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
2106008 ATTCAATTGA
*
2106018 GTATCAATCCTTTTATGTAGG
1 GTATCAATCCTTTAATGTAGG
2106039 GTATCAAT-CTTTAATGTAGG
1 GTATCAATCCTTTAATGTAGG
2106059 GTATC
1 GTATC
2106064 GATATTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (21 bp):
GTATCAATCCTTTAATGTAGG
Found at i:2108543 original size:46 final size:46
Alignment explanation
Indices: 2108435--2108783 Score: 590
Period size: 46 Copynumber: 7.8 Consensus size: 46
2108425 AATAAAATCT
*
2108435 CTTACCATTT-ATTCCATAAGCCCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
2108480 CTTACCA--T--TT--ATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
2108520 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
2108566 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
2108612 CTTACCATTTAATTCCATAAGCTCGTAAGATTATTTTACCAATATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
2108658 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAGTATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
2108704 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
2108750 CTTGCCA-TT-ATTCCATAAGCACGTAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTT
2108784 GCATACTTAC
Statistics
Matches: 291, Mismatches: 7, Indels: 13
0.94 0.02 0.04
Matches are distributed among these distances:
40 36 0.12
42 3 0.01
43 1 0.00
44 26 0.09
45 9 0.03
46 216 0.74
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:2112570 original size:29 final size:28
Alignment explanation
Indices: 2112529--2112589 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
2112519 TGATTTCAAA
* *
2112529 TTTTATTTCTTAAATTTCCTAGTTTTCG
1 TTTTATTTCTTAAATTACCTAGTTTTCC
*
2112557 TTTTAATTTCTTAAATTACGTAGTTTTCC
1 TTTT-ATTTCTTAAATTACCTAGTTTTCC
2112586 TTTT
1 TTTT
2112590 TCTTAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 4 0.14
29 25 0.86
ACGTcount: A:0.20, C:0.13, G:0.07, T:0.61
Consensus pattern (28 bp):
TTTTATTTCTTAAATTACCTAGTTTTCC
Found at i:2115193 original size:11 final size:11
Alignment explanation
Indices: 2115179--2115220 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
2115169 ACTATATAGT
*
2115179 TTATATTTATA
1 TTATATATATA
2115190 TTAT-TATATA
1 TTATATATATA
*
2115200 TTATATATAAA
1 TTATATATATA
2115211 TTATATATAT
1 TTATATATAT
2115221 TATGTATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TTATATATATA
Found at i:2115219 original size:20 final size:20
Alignment explanation
Indices: 2115161--2115380 Score: 139
Period size: 20 Copynumber: 10.9 Consensus size: 20
2115151 TATAAAGTAG
* *
2115161 ATATAGAAACTATATAGT-TT
1 ATATATAAATTATATA-TATT
* *
2115181 ATATTTATATTATTATATATT
1 ATATATAAATTA-TATATATT
2115202 ATATATAAATTATATATATT
1 ATATATAAATTATATATATT
* * **
2115222 ATGTATAAACTATATATACC
1 ATATATAAATTATATATATT
* *
2115242 ATGTATAAACTATATAGT-TT
1 ATATATAAATTATATA-TATT
*
2115262 ATTTATAAATTATATATGAATT
1 ATATATAAATTATATAT--ATT
* *
2115284 ATATATAAACTATACA-ACTT
1 ATATATAAATTATATATA-TT
* * *
2115304 ATATTTATATTATGTATA--
1 ATATATAAATTATATATATT
*
2115322 AT-TATAAATAATATATATT
1 ATATATAAATTATATATATT
*
2115341 ATGTATAAATTATATACT-TT
1 ATATATAAATTATATA-TATT
*
2115361 ATTAATATAAACTATATATA
1 A-T-ATATAAATTATATATA
2115381 AACTCTATAG
Statistics
Matches: 156, Mismatches: 29, Indels: 28
0.73 0.14 0.13
Matches are distributed among these distances:
17 11 0.07
18 2 0.01
19 4 0.03
20 91 0.58
21 21 0.13
22 27 0.17
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (20 bp):
ATATATAAATTATATATATT
Found at i:2115257 original size:2 final size:2
Alignment explanation
Indices: 2115134--2115239 Score: 53
Period size: 2 Copynumber: 54.0 Consensus size: 2
2115124 TTGAAACAAC
* * * *
2115134 TA TA -A TA TA TA TA TA TA TA TA AA GTA GA TA TA GA AA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA
* * *
2115177 GTT TA TA TT TA TA T- TA T- TA TA TA T- TA TA TA TA AA T- TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
2115216 TA TA T- TA TG TA TA AA CTA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA
2115240 CCATGTATAA
Statistics
Matches: 77, Mismatches: 17, Indels: 20
0.68 0.15 0.18
Matches are distributed among these distances:
1 6 0.08
2 67 0.87
3 4 0.05
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2115395 original size:33 final size:33
Alignment explanation
Indices: 2115330--2115395 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
2115320 TAATTATAAA
* * * *
2115330 TAATATATATTATGTATAAATTATATACTTTAT
1 TAATATAAACTATATATAAACTATATACTTTAT
* *
2115363 TAATATAAACTATATATAAACTCTATAGTTTAT
1 TAATATAAACTATATATAAACTATATACTTTAT
2115396 ATATATAGTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (33 bp):
TAATATAAACTATATATAAACTATATACTTTAT
Found at i:2115525 original size:20 final size:20
Alignment explanation
Indices: 2115500--2115565 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 20
2115490 TATACTAACT
2115500 TATACTATATGTTAACTATA
1 TATACTATATGTTAACTATA
*
2115520 TATACTATATAGTTTAC-ATA
1 TATACTATAT-GTTAACTATA
2115540 TGA-ACTATATGTATAAACTATA
1 T-ATACTATATGT-T-AACTATA
2115562 TATA
1 TATA
2115566 TAAACTATGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
19 2 0.05
20 22 0.58
21 9 0.24
22 5 0.13
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (20 bp):
TATACTATATGTTAACTATA
Found at i:2115560 original size:13 final size:13
Alignment explanation
Indices: 2115434--2115573 Score: 63
Period size: 13 Copynumber: 10.1 Consensus size: 13
2115424 TTTATGGAAT
2115434 TATATATAAACTA
1 TATATATAAACTA
*
2115447 TATAGTTTATAGA-TA
1 TATA---TATAAACTA
2115462 GTAGTATATAAAC--
1 -TA-TATATAAACTA
*
2115475 TATATATAAACAA
1 TATATATAAACTA
2115488 TATATACT-AACTTA
1 TATATA-TAAAC-TA
*
2115502 TACTATATGTTAACTA
1 TA-TATA--TAAACTA
* *
2115518 TATATACTATATAGTT
1 TATATA-TA-A-ACTA
* *
2115534 TACATATGAACTA
1 TATATATAAACTA
*
2115547 TATGTATAAACTA
1 TATATATAAACTA
2115560 TATATATAAACTA
1 TATATATAAACTA
2115573 T
1 T
2115574 GTAAACTATA
Statistics
Matches: 96, Mismatches: 16, Indels: 30
0.68 0.11 0.21
Matches are distributed among these distances:
11 9 0.09
12 2 0.02
13 38 0.40
14 11 0.11
15 12 0.12
16 19 0.20
17 5 0.05
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:2115639 original size:50 final size:50
Alignment explanation
Indices: 2115575--2115685 Score: 204
Period size: 50 Copynumber: 2.2 Consensus size: 50
2115565 ATAAACTATG
2115575 TAAACTATATAATATATATAGTTTAGTAGTTTACATAAGAACTATATATA
1 TAAACTATATAATATATATAGTTTAGTAGTTTACATAAGAACTATATATA
* *
2115625 TAAACTATGTAATATATATAGTTTAGTAGTTTACATATGAACTATATATA
1 TAAACTATATAATATATATAGTTTAGTAGTTTACATAAGAACTATATATA
2115675 TAAACTATATA
1 TAAACTATATA
2115686 GTTTACGTAT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 58 1.00
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (50 bp):
TAAACTATATAATATATATAGTTTAGTAGTTTACATAAGAACTATATATA
Found at i:2115709 original size:24 final size:24
Alignment explanation
Indices: 2115680--2115729 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2115670 ATATATAAAC
2115680 TATATAGTTTACGT-ATGAACTATA
1 TATATAGTTTA-GTAATGAACTATA
*
2115704 TATATAGTTTATTAATGAACTATA
1 TATATAGTTTAGTAATGAACTATA
2115728 TA
1 TA
2115730 AACTATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (24 bp):
TATATAGTTTAGTAATGAACTATA
Found at i:2115738 original size:24 final size:24
Alignment explanation
Indices: 2115694--2115739 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2115684 TAGTTTACGT
*
2115694 ATGAACTATATATATAGTTTATTA
1 ATGAACTATATAAATAGTTTATTA
2115718 ATGAACTATATAAACTA-TTTAT
1 ATGAACTATATAAA-TAGTTTAT
2115740 ATATTGTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (24 bp):
ATGAACTATATAAATAGTTTATTA
Found at i:2116318 original size:2 final size:2
Alignment explanation
Indices: 2116313--2116408 Score: 54
Period size: 2 Copynumber: 46.0 Consensus size: 2
2116303 ATATAAAAAC
* * *
2116313 TA TA TA TA TA TA TA TA TA TA TA TA AA CTA TA TA AA CTA TA -A TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA
* * *
2116356 TA TA TA TA AA CTA TA TA CTA TA GT- TGA TA TT TA TA CA CTA TA TA
1 TA TA TA TA TA -TA TA TA -TA TA -TA T-A TA TA TA TA TA -TA TA TA
2116400 -A TA TA TA TA
1 TA TA TA TA TA
2116409 GTTTACATTA
Statistics
Matches: 72, Mismatches: 12, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
1 3 0.04
2 61 0.85
3 8 0.11
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:2116330 original size:27 final size:26
Alignment explanation
Indices: 2116300--2116449 Score: 107
Period size: 27 Copynumber: 5.7 Consensus size: 26
2116290 ACATATGAAC
*
2116300 TATATATAAAAACTATATATATATATA
1 TATATATATAAACTATATATATATA-A
*
2116327 TATATATATAAACTATATAAACTATAA
1 TATATATATAAACTATATATA-TATAA
*
2116354 TTTATATATAAACTATATACTATAGT--
1 TATATATATAAACTATATA-TATA-TAA
* *
2116380 TGATATTTATACACTATATA-ATAT-A
1 T-ATATATATAAACTATATATATATAA
* * *
2116405 TATAGT-T-TACATTAT-TACATATGAA
1 TATA-TATATAAACTATATATATAT-AA
2116430 CTATATATATAAACTATATA
1 -TATATATATAAACTATATA
2116450 GTTTACATAT
Statistics
Matches: 100, Mismatches: 10, Indels: 25
0.74 0.07 0.19
Matches are distributed among these distances:
22 2 0.02
23 11 0.11
24 5 0.05
25 7 0.07
26 6 0.06
27 61 0.61
28 8 0.08
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (26 bp):
TATATATATAAACTATATATATATAA
Found at i:2116413 original size:25 final size:24
Alignment explanation
Indices: 2116300--2116543 Score: 93
Period size: 27 Copynumber: 10.0 Consensus size: 24
2116290 ACATATGAAC
*
2116300 TATATATAAAAACTATATATATATATA
1 TATATATATAAAC--TATATA-ATATA
2116327 TATATATATAAACTATATAAACTATAA
1 TATATATATAAACTATAT-AA-TAT-A
* *
2116354 TTTATATATAAACTATATACTATA
1 TATATATATAAACTATATAATATA
* *
2116378 GTTGATATTTATACACTATATAATATA
1 --T-ATATATATAAACTATATAATATA
* *
2116405 TATAGT-T-TACATTAT-TACATATGAA
1 TATA-TATATAAACTATATA-ATAT--A
*
2116430 CTATATATATAAACTATAT-A-GT-
1 -TATATATATAAACTATATAATATA
* * *
2116452 T-TACATATGAACTA-ACT-ATTTA
1 TATATATATAAACTATA-TAATATA
2116474 TATA-ATATAAACTATAT--T-T-
1 TATATATATAAACTATATAATATA
* * *
2116493 TATATTTATATACTATATACTATA
1 TATATATATAAACTATATAATATA
*
2116517 GTTGATATTTATAAACTATATAATATA
1 --T-ATATATATAAACTATATAATATA
2116544 ATTTATACTT
Statistics
Matches: 171, Mismatches: 19, Indels: 54
0.70 0.08 0.22
Matches are distributed among these distances:
19 5 0.03
20 25 0.15
21 3 0.02
22 14 0.08
23 15 0.09
24 5 0.03
25 14 0.08
26 13 0.08
27 76 0.44
28 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.43
Consensus pattern (24 bp):
TATATATATAAACTATATAATATA
Found at i:2116500 original size:27 final size:27
Alignment explanation
Indices: 2116468--2116571 Score: 104
Period size: 27 Copynumber: 3.9 Consensus size: 27
2116458 ATGAACTAAC
2116468 TATTTATATAATATAAACTATATTTTA
1 TATTTATATAATATAAACTATATTTTA
* * * *
2116495 TATTTATATACTATATACTATAGTTGA
1 TATTTATATAATATAAACTATATTTTA
*
2116522 TATTTATA-AACTATATAA-TATAATTTA
1 TATTTATATAA-TATA-AACTATATTTTA
* * *
2116549 TACTTATATAATTTATACTATAT
1 TATTTATATAATATAAACTATAT
2116572 CAATTCAAAG
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
26 2 0.03
27 56 0.92
28 3 0.05
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (27 bp):
TATTTATATAATATAAACTATATTTTA
Found at i:2116529 original size:139 final size:131
Alignment explanation
Indices: 2116288--2116543 Score: 352
Period size: 139 Copynumber: 1.9 Consensus size: 131
2116278 ACTATATCGT
*
2116288 TTACATATGAACTATATATAAAAACTATATATATATATATATATATATAAACTATATAAACTATA
1 TTACATATGAACTATATATAAAAACTATATATATACATATATATATATAAACTATATAAACTATA
*
2116353 ATTTATATATAAACTATATACTATAGTTGATATTTATACACTATATAATATATATAGTTTACATT
66 ATTTATATATAAACTATATACTATAGTTGATATTTATAAACTATATAATATATATAGTTTACATT
2116418 A
131 A
* * * *
2116419 TTACATATGAACTATATATATAAACTATATAGTTTACATATGAACTAACTATTTATA-TAATATA
1 TTACATATGAACTATATATAAAAACTATATA-TATACATAT--A-T-A-TATATAAACT-ATATA
* *
2116483 AACTATATTTTATATTTATATACTATATACTATAGTTGATATTTATAAACTATATAATATA
59 AACTATAATTTATA--TATAAACTATATACTATAGTTGATATTTATAAACTATATAATATA
2116544 ATTTATACTT
Statistics
Matches: 108, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
131 30 0.28
132 7 0.06
134 1 0.01
135 1 0.01
136 2 0.02
137 24 0.22
139 43 0.40
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.43
Consensus pattern (131 bp):
TTACATATGAACTATATATAAAAACTATATATATACATATATATATATAAACTATATAAACTATA
ATTTATATATAAACTATATACTATAGTTGATATTTATAAACTATATAATATATATAGTTTACATT
A
Found at i:2116549 original size:54 final size:54
Alignment explanation
Indices: 2116468--2116570 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
2116458 ATGAACTAAC
* * *
2116468 TATTTATATAATATAAACTATATTTTATATTTATATACTATATACTATAGTTGA
1 TATTTATATAATATAAACTATAATTTATACTTATATAATATATACTATAGTTGA
*
2116522 TATTTATA-AACTATATAA-TATAATTTATACTTATATAATTTATACTATA
1 TATTTATATAA-TATA-AACTATAATTTATACTTATATAATATATACTATA
2116571 TCAATTCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
53 2 0.05
54 39 0.91
55 2 0.05
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.50
Consensus pattern (54 bp):
TATTTATATAATATAAACTATAATTTATACTTATATAATATATACTATAGTTGA
Found at i:2116559 original size:15 final size:14
Alignment explanation
Indices: 2116539--2116576 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
2116529 AAACTATATA
2116539 ATATAATTTATACTT
1 ATATAATTTATAC-T
2116554 ATATAATTTATACT
1 ATATAATTTATACT
2116568 ATATCAATT
1 ATAT-AATT
2116577 CAAAGTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATAATTTATACT
Found at i:2116615 original size:15 final size:15
Alignment explanation
Indices: 2116597--2116633 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
2116587 ATTATATGTA
2116597 TGAATACTATATAGT
1 TGAATACTATATAGT
2116612 TGAATACTATATAGT
1 TGAATACTATATAGT
2116627 TGAATAC
1 TGAATAC
2116634 ATTAATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.38
Consensus pattern (15 bp):
TGAATACTATATAGT
Found at i:2116746 original size:33 final size:33
Alignment explanation
Indices: 2116728--2116814 Score: 156
Period size: 33 Copynumber: 2.6 Consensus size: 33
2116718 AAAGTATATG
2116728 GTATATATAAACTATATATTATATAGTTCATTA
1 GTATATATAAACTATATATTATATAGTTCATTA
*
2116761 GTATATATCAACTATATATTATATAGTTCATTA
1 GTATATATAAACTATATATTATATAGTTCATTA
*
2116794 GTATATATAACCTATATATTA
1 GTATATATAAACTATATATTA
2116815 ATTTATTAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (33 bp):
GTATATATAAACTATATATTATATAGTTCATTA
Found at i:2116750 original size:18 final size:18
Alignment explanation
Indices: 2116711--2116785 Score: 59
Period size: 18 Copynumber: 4.3 Consensus size: 18
2116701 ATATGAACTA
* *
2116711 TATATATAAAGTATATGG
1 TATATATAAACTATATAG
2116729 TATATATAAACTATATA-
1 TATATATAAACTATATAG
**
2116746 T-TATAT-AGTTCAT-TAG
1 TATATATAAACT-ATATAG
* *
2116762 TATATATCAACTATATAT
1 TATATATAAACTATATAG
2116780 TATATA
1 TATATA
2116786 GTTCATTAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
15 4 0.09
16 8 0.18
17 8 0.18
18 25 0.56
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (18 bp):
TATATATAAACTATATAG
Found at i:2116765 original size:20 final size:20
Alignment explanation
Indices: 2116742--2116799 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
2116732 ATATAAACTA
2116742 TATATTATATAGTTCATTAG
1 TATATTATATAGTTCATTAG
2116762 TATA-TATCA-A---C--TA-
1 TATATTAT-ATAGTTCATTAG
2116775 TATATTATATAGTTCATTAG
1 TATATTATATAGTTCATTAG
2116795 TATAT
1 TATAT
2116800 ATAACCTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 18
0.62 0.00 0.38
Matches are distributed among these distances:
13 5 0.17
14 6 0.21
16 1 0.03
17 1 0.03
19 6 0.21
20 10 0.34
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (20 bp):
TATATTATATAGTTCATTAG
Found at i:2117388 original size:112 final size:113
Alignment explanation
Indices: 2117190--2117395 Score: 276
Period size: 112 Copynumber: 1.8 Consensus size: 113
2117180 AAAACCCTCC
* *
2117190 TTTGATCTTCACAAACACCAAAATCCAAACCATTTCGTGTTTTTTTCGATCAAACACCCAAAACT
1 TTTGATCTTCACAAACACCAAAATCCAAACCATTTCGTGTTTTTTTCGATCAAACACCAAAAAAT
* * *
2117255 TCAACCCTTGTTCATCCGTGTTCATCCCAGTTCTTCCCCAAACCATTA
66 TAAACCCTTATTCATACGTGTTCATCCCAGTTCTTCCCCAAACCATTA
* *
2117303 TTTGATCTTTACAAACACCAAAA-CCTAAATC-TATTC-T-TATTTTTTCGATCAAACACCAAAA
1 TTTGATCTTCACAAACACCAAAATCC-AAACCAT-TTCGTGT-TTTTTTCGATCAAACACCAAAA
* *
2117364 AATTAAACCCTTATTCATATGTGTTCTTCCCA
63 AATTAAACCCTTATTCATACGTGTTCATCCCA
2117396 AACCCTTACA
Statistics
Matches: 81, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
111 1 0.01
112 51 0.63
113 29 0.36
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.34
Consensus pattern (113 bp):
TTTGATCTTCACAAACACCAAAATCCAAACCATTTCGTGTTTTTTTCGATCAAACACCAAAAAAT
TAAACCCTTATTCATACGTGTTCATCCCAGTTCTTCCCCAAACCATTA
Found at i:2117592 original size:6 final size:6
Alignment explanation
Indices: 2117583--2117635 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
2117573 TAACCCTAAT
* * * * * *
2117583 CCAAAC CCAAAC TCGAAC CCAAAA CCAAAC CCGAAC CCGAAT CCAAAC
1 CCAAAC CCAAAC CCAAAC CCAAAC CCAAAC CCAAAC CCAAAC CCAAAC
2117631 CCAAA
1 CCAAA
2117636 TCTGAATCCG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.47, C:0.43, G:0.06, T:0.04
Consensus pattern (6 bp):
CCAAAC
Found at i:2117610 original size:18 final size:18
Alignment explanation
Indices: 2117583--2117632 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
2117573 TAACCCTAAT
* *
2117583 CCAAACCCAAACTCGAAC
1 CCAAAACCAAACCCGAAC
2117601 CCAAAACCAAACCCGAAC
1 CCAAAACCAAACCCGAAC
* *
2117619 CCGAATCCAAACCC
1 CCAAAACCAAACCC
2117633 AAATCTGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.44, C:0.46, G:0.06, T:0.04
Consensus pattern (18 bp):
CCAAAACCAAACCCGAAC
Found at i:2117610 original size:24 final size:24
Alignment explanation
Indices: 2117574--2117635 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
2117564 CTCTAACACT
* * *
2117574 AACCCTAATCCAAACCCAAACTCG
1 AACCCAAAACCAAACCCAAACCCG
*
2117598 AACCCAAAACCAAACCCGAACCCG
1 AACCCAAAACCAAACCCAAACCCG
* *
2117622 AATCCAAACCCAAA
1 AACCCAAAACCAAA
2117636 TCTGAATCCG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.47, C:0.42, G:0.05, T:0.06
Consensus pattern (24 bp):
AACCCAAAACCAAACCCAAACCCG
Found at i:2117644 original size:18 final size:18
Alignment explanation
Indices: 2117574--2117637 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 18
2117564 CTCTAACACT
*
2117574 AACCCTAATCCAAACCCA
1 AACCCGAATCCAAACCCA
* * *
2117592 AACTCGAACCCAAAACCA
1 AACCCGAATCCAAACCCA
* * *
2117610 AACCCGAACCCGAATCCA
1 AACCCGAATCCAAACCCA
*
2117628 AACCCAAATC
1 AACCCGAATC
2117638 TGAATCCGAA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.45, C:0.42, G:0.05, T:0.08
Consensus pattern (18 bp):
AACCCGAATCCAAACCCA
Found at i:2120266 original size:20 final size:20
Alignment explanation
Indices: 2120243--2120287 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2120233 ATTTTATTTT
* * *
2120243 ATATTGTTTGCTTCTGTTTG
1 ATATTGCTTGATTCTGCTTG
2120263 ATATTGCTTGATTCTGCTTG
1 ATATTGCTTGATTCTGCTTG
2120283 ATATT
1 ATATT
2120288 TTTAAGGGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.11, G:0.18, T:0.56
Consensus pattern (20 bp):
ATATTGCTTGATTCTGCTTG
Found at i:2120386 original size:18 final size:19
Alignment explanation
Indices: 2120363--2120411 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
2120353 CACAGATTGT
*
2120363 ATGCTTTCTGAATGC-AGG
1 ATGCTTGCTGAATGCAAGG
*
2120381 ATGCTTGCTG-ATGCAATG
1 ATGCTTGCTGAATGCAAGG
2120399 ATGCTTGCTGAAT
1 ATGCTTGCTGAAT
2120412 TGATATAGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 4 0.15
18 21 0.78
19 2 0.07
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (19 bp):
ATGCTTGCTGAATGCAAGG
Found at i:2121024 original size:13 final size:13
Alignment explanation
Indices: 2121005--2121042 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
2120995 TAATTTAATG
2121005 ATTATAAATAA-A
1 ATTATAAATAAGA
2121017 ATTTATAATATAAGA
1 A-TTATAA-ATAAGA
2121032 ATTATAAATAA
1 ATTATAAATAA
2121043 TATAAAGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
ATTATAAATAAGA
Found at i:2121354 original size:35 final size:35
Alignment explanation
Indices: 2121303--2121376 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 35
2121293 TACAGCCCTC
*
2121303 AATTTTATTTTAAACCCTAAATTCTAAAATAATTT
1 AATTATATTTTAAACCCTAAATTCTAAAATAATTT
*
2121338 AATTATATTTTAAACCCTAAATTCTAAAATACTTT
1 AATTATATTTTAAACCCTAAATTCTAAAATAATTT
2121373 AATT
1 AATT
2121377 TAGGGTTTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (35 bp):
AATTATATTTTAAACCCTAAATTCTAAAATAATTT
Found at i:2121422 original size:34 final size:35
Alignment explanation
Indices: 2121373--2121446 Score: 132
Period size: 34 Copynumber: 2.1 Consensus size: 35
2121363 AAAATACTTT
*
2121373 AATTTAGGGTTTAGAATGTAATTGAAGTGTTTTGG
1 AATTTAGGGTGTAGAATGTAATTGAAGTGTTTTGG
2121408 AATTT-GGGTGTAGAATGTAATTGAAGTGTTTTGG
1 AATTTAGGGTGTAGAATGTAATTGAAGTGTTTTGG
2121442 AATTT
1 AATTT
2121447 TGAATATGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 33 0.87
35 5 0.13
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.43
Consensus pattern (35 bp):
AATTTAGGGTGTAGAATGTAATTGAAGTGTTTTGG
Found at i:2123096 original size:24 final size:24
Alignment explanation
Indices: 2123068--2123144 Score: 93
Period size: 24 Copynumber: 3.1 Consensus size: 24
2123058 TCATTTTTTC
2123068 ATTTAATT-TTTTTATTATTATTAA
1 ATTT-ATTATTTTTATTATTATTAA
*
2123092 ATTTATTATTATTATTATTATTAA
1 ATTTATTATTTTTATTATTATTAA
*
2123116 ATATTATTATTAGTATATTATTATTAA
1 AT-TTATTATT--TTTATTATTATTAA
2123143 AT
1 AT
2123145 AATTATTACA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
23 3 0.07
24 21 0.46
25 8 0.17
27 14 0.30
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (24 bp):
ATTTATTATTTTTATTATTATTAA
Found at i:2123134 original size:27 final size:25
Alignment explanation
Indices: 2123079--2123152 Score: 114
Period size: 24 Copynumber: 2.9 Consensus size: 25
2123069 TTTAATTTTT
2123079 TTATTATTATTAAAT-TTATTATTA
1 TTATTATTATTAAATATTATTATTA
2123103 TTATTATTATTAAATATTATTATTA
1 TTATTATTATTAAATATTATTATTA
2123128 GTATATTATTATTAAATAATTATTA
1 -T-TATTATTATTAAAT-ATTATTA
2123153 CAAGCCCAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
24 15 0.33
25 9 0.20
26 1 0.02
27 14 0.30
28 7 0.15
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (25 bp):
TTATTATTATTAAATATTATTATTA
Found at i:2123152 original size:3 final size:3
Alignment explanation
Indices: 2123079--2123141 Score: 67
Period size: 3 Copynumber: 21.0 Consensus size: 3
2123069 TTTAATTTTT
* *
2123079 TTA TTA TTA TTA -AA TTTA TTA TTA TTA TTA TTA TTAA ATA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
*
2123125 TTA GTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
2123142 AATAATTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
2 3 0.06
3 45 0.88
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:2124481 original size:35 final size:33
Alignment explanation
Indices: 2124407--2124490 Score: 89
Period size: 35 Copynumber: 2.4 Consensus size: 33
2124397 TTTATTTTTT
*
2124407 TTTATTTTTTAATATATTTTAAATTATTACTTTA
1 TTTATTTTTTAATATATTATAAATTATTAC-TTA
* *
2124441 ATTATTGTTTTACTATATTATAAATATATATA-TTA
1 TTTATT-TTTTAATATATTATAAAT-TAT-TACTTA
2124476 TTTATTTATTTAATA
1 TTTATTT-TTTAATA
2124491 ATGTTTATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
34 6 0.15
35 30 0.73
36 3 0.07
37 2 0.05
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (33 bp):
TTTATTTTTTAATATATTATAAATTATTACTTA
Found at i:2125189 original size:20 final size:21
Alignment explanation
Indices: 2125166--2125217 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
2125156 AGAAATTAAA
2125166 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
2125186 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
2125208 -ATT-ATTTATT
1 AATTCATTTATT
2125218 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:2131454 original size:82 final size:82
Alignment explanation
Indices: 2131317--2131548 Score: 401
Period size: 82 Copynumber: 2.8 Consensus size: 82
2131307 TCATAGTAGA
2131317 AATTGGAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 AATTGGAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
*
2131382 GGCATAACCAATCATTG
66 GGCAGAACCAATCATTG
2131399 AATTGGAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 AATTGGAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
* *
2131464 GACAGAATCAATCATTG
66 GGCAGAACCAATCATTG
* * *
2131481 AATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGATT
1 AA-TTGGAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
2131546 TGG
65 TGG
2131549 TATGAACTCC
Statistics
Matches: 142, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
82 81 0.57
83 61 0.43
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (82 bp):
AATTGGAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
GGCAGAACCAATCATTG
Found at i:2134415 original size:22 final size:22
Alignment explanation
Indices: 2134385--2134439 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
2134375 AGATTCTCAC
* *
2134385 TTCAGAGATGACAAATTTTCTT
1 TTCAAAGATGACAAATTCTCTT
* * *
2134407 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAAATTCTCTT
2134429 TTCAAAGATGA
1 TTCAAAGATGA
2134440 AAGCTTTATG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGACAAATTCTCTT
Found at i:2135220 original size:76 final size:77
Alignment explanation
Indices: 2135121--2135356 Score: 366
Period size: 83 Copynumber: 3.0 Consensus size: 77
2135111 CTATTTCCCA
*
2135121 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCCAA
2135185 AAGCCTTCGGGT
66 AAGCCTTCGGGT
*
2135197 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTCCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCC--
*
2135262 AAAAAAAAACCTTCGGGT
64 ----AAAAGCCTTCGGGT
*
2135280 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCC-A
2135345 AAAGCCTTCGGG
65 AAAGCCTTCGGG
2135357 AGCTTTTTGA
Statistics
Matches: 147, Mismatches: 6, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
76 61 0.41
78 13 0.09
83 73 0.50
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.33
Consensus pattern (77 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCCAA
AAGCCTTCGGGT
Found at i:2135337 original size:31 final size:31
Alignment explanation
Indices: 2135302--2135385 Score: 145
Period size: 31 Copynumber: 2.8 Consensus size: 31
2135292 CTTCAGTGCA
2135302 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
2135333 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
2135364 TGATGTTTTC--AAAGCCTTCGGG
1 TGATGTTTCCAAAAAGCCTTCGGG
2135386 TCATCTGTAA
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
29 12 0.23
31 40 0.77
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (31 bp):
TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
Found at i:2135416 original size:107 final size:108
Alignment explanation
Indices: 2135219--2135454 Score: 366
Period size: 107 Copynumber: 2.1 Consensus size: 108
2135209 CTTCAGTGCA
2135219 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTCCAAAAAAAAAAACCTTCGGGTCATC
1 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTCC------AAAAACCTTCGGGTCATC
2135284 TGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
60 TGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
* * *
2135333 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-AAAGCCTTCGGGTCATCTGTAAG
1 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTCCAAAAACCTTCGGGTCATCTGTAAG
* *
2135397 TCCTTCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTT
66 CCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
2135440 TGATGTTTCCAAAAA
1 TGATGTTTCCAAAAA
2135455 AAAACCTTCG
Statistics
Matches: 117, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
107 78 0.67
114 39 0.33
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (108 bp):
TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTCCAAAAACCTTCGGGTCATCTGTAAG
CCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
Found at i:2135681 original size:80 final size:79
Alignment explanation
Indices: 2135333--2136009 Score: 1086
Period size: 76 Copynumber: 8.6 Consensus size: 79
2135323 GGGAGCTTTT
* *
2135333 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC---AAAGCCTTCGGGTCATCTGTA
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCCAAAAAAACCTTCGGGTCATCTGTA
2135395 AGTCCTTCAGTGCA
66 AGTCCTTCAGTGCA
*
2135409 TGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTCCAAAAAAAAACCTTCGGGTCATCTG
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCC--AAAAAAACCTTCGGGTCATCTG
*
2135474 TAAGCCCTTCAGTGCA
64 TAAGTCCTTCAGTGCA
*
2135490 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTCCAAAAAAAACCTTC-GGTCATCTGT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCC-AAAAAAACCTTCGGGTCATCTGT
2135554 AAGTCCTTCAGTGCA
65 AAGTCCTTCAGTGCA
2135569 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCCAAAAAAACCTTCGGGTCATCTGTA
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCCAAAAAAACCTTCGGGTCATCTGTA
*
2135634 AGCCCTTCAGTGCA
66 AGTCCTTCAGTGCA
2135648 TGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTCCAAAAAAAAAACCTTCGGGTCATC
1 TGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTCC---AAAAAAACCTTCGGGTCATC
2135713 TGTAAGTCCTTCAGTGCA
62 TGTAAGTCCTTCAGTGCA
* *
2135731 TGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC---AAAGCCTTCGGGTCATCTGT
1 TGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTCCAAAAAAACCTTCGGGTCATCTGT
2135793 AAGTCCTTCAGTGCA
65 AAGTCCTTCAGTGCA
* *
2135808 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC---AAAGCCTTCGGGTCATCTGTA
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCCAAAAAAACCTTCGGGTCATCTGTA
2135870 AGTCCTTCAGTGCA
66 AGTCCTTCAGTGCA
*
2135884 TGATATTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCCAAAAAAAACCTTCGGGTCATCTGT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCC-AAAAAAACCTTCGGGTCATCTGT
*
2135949 AAGCCCTTCAGTGCA
65 AAGTCCTTCAGTGCA
*
2135964 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTCTGATGTTTCCAAAAA
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCCAAAAA
2136010 GCCTTTGGGA
Statistics
Matches: 569, Mismatches: 18, Indels: 25
0.93 0.03 0.04
Matches are distributed among these distances:
76 144 0.25
77 44 0.08
78 12 0.02
79 103 0.18
80 116 0.20
81 72 0.13
83 78 0.14
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.33
Consensus pattern (79 bp):
TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCCAAAAAAACCTTCGGGTCATCTGTA
AGTCCTTCAGTGCA
Found at i:2135999 original size:31 final size:31
Alignment explanation
Indices: 2135964--2136047 Score: 127
Period size: 31 Copynumber: 2.8 Consensus size: 31
2135954 CTTCAGTGCA
2135964 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTC
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTC
* *
2135995 TGATGTTTCCAAAAAGCCTTTGGGAGCTTTT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTC
*
2136026 TGATGTTTTC--AAAGCCTTCGGG
1 TGATGTTTCCAAAAAGCCTTCGGG
2136048 TCATCTGTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 11 0.22
31 38 0.78
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (31 bp):
TGATGTTTCCAAAAAGCCTTCGGGAGCTTTC
Found at i:2136068 original size:107 final size:107
Alignment explanation
Indices: 2135884--2136190 Score: 506
Period size: 107 Copynumber: 2.8 Consensus size: 107
2135874 CTTCAGTGCA
* * *
2135884 TGATATTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCCAAAAAAAACCTTCGGGTCATCTGT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC----AAAGCCTTCGGGTCATCTGT
2135949 AAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTC
62 AAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTC
* *
2135995 TGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
* *
2136060 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTT
66 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTC
2136102 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
*
2136167 CCTTCAGTGCATGATGTTTTCAAA
66 CCTTCAGTGCATGATGTTTCCAAA
2136191 CATTTCCATC
Statistics
Matches: 186, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
107 148 0.80
111 38 0.20
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (107 bp):
TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTC
Found at i:2136106 original size:31 final size:31
Alignment explanation
Indices: 2136071--2136154 Score: 136
Period size: 31 Copynumber: 2.8 Consensus size: 31
2136061 CTTCAGTGCA
*
2136071 TGATGTTTCCAAAAAGCCTTTGGGAGCTTTT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
2136102 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
2136133 TGATGTTTTC--AAAGCCTTCGGG
1 TGATGTTTCCAAAAAGCCTTCGGG
2136155 TCATCTGTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
29 12 0.24
31 39 0.76
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (31 bp):
TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
Found at i:2136373 original size:27 final size:25
Alignment explanation
Indices: 2136318--2136391 Score: 114
Period size: 24 Copynumber: 2.9 Consensus size: 25
2136308 TTTAATTTTT
2136318 TTATTATTATTAAAT-TTATTATTA
1 TTATTATTATTAAATATTATTATTA
2136342 TTATTATTATTAAATATTATTATTA
1 TTATTATTATTAAATATTATTATTA
2136367 GTATATTATTATTAAATAATTATTA
1 -T-TATTATTATTAAAT-ATTATTA
2136392 CAAGCCCAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
24 15 0.33
25 9 0.20
26 1 0.02
27 14 0.30
28 7 0.15
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (25 bp):
TTATTATTATTAAATATTATTATTA
Found at i:2136391 original size:3 final size:3
Alignment explanation
Indices: 2136318--2136380 Score: 67
Period size: 3 Copynumber: 21.0 Consensus size: 3
2136308 TTTAATTTTT
* *
2136318 TTA TTA TTA TTA -AA TTTA TTA TTA TTA TTA TTA TTAA ATA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
*
2136364 TTA GTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
2136381 AATAATTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
2 3 0.06
3 45 0.88
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:2138989 original size:16 final size:16
Alignment explanation
Indices: 2138968--2139000 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2138958 CATTACTTAT
2138968 AAGTCAGATAAATATC
1 AAGTCAGATAAATATC
*
2138984 AAGTCAGGTAAATATC
1 AAGTCAGATAAATATC
2139000 A
1 A
2139001 TATGAGTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.24
Consensus pattern (16 bp):
AAGTCAGATAAATATC
Found at i:2141172 original size:14 final size:14
Alignment explanation
Indices: 2141153--2141179 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2141143 TTCTCCTCTC
2141153 CGCCCTTGACATAT
1 CGCCCTTGACATAT
2141167 CGCCCTTGACATA
1 CGCCCTTGACATA
2141180 CATTCAGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.37, G:0.15, T:0.26
Consensus pattern (14 bp):
CGCCCTTGACATAT
Found at i:2142454 original size:29 final size:29
Alignment explanation
Indices: 2142422--2142587 Score: 144
Period size: 29 Copynumber: 5.8 Consensus size: 29
2142412 ACAATAAAGA
2142422 CCAAAACTTTTATAAATTACAAACAAATG
1 CCAAAACTTTTATAAATTACAAACAAATG
*
2142451 CC-AAACTTTTTATAAATTACAAACAAATA
1 CCAAAAC-TTTTATAAATTACAAACAAATG
2142480 CCAAAACTTTTTATAAATTAC-AACAAATG
1 CCAAAAC-TTTTATAAATTACAAACAAATG
* *** * *
2142509 ACAAAAAAATTAAAAATTAC-AACAAATT
1 CCAAAACTTTTATAAATTACAAACAAATG
*** *
2142537 CCAATTGTTTTTATAAATTACAATCAAA-G
1 CCAA-AACTTTTATAAATTACAAACAAATG
* *
2142566 -AAAAACTTCTAATAAATTACAA
1 CCAAAACTT-TTATAAATTACAA
2142588 TAATGACTTG
Statistics
Matches: 110, Mismatches: 22, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
27 2 0.02
28 38 0.35
29 47 0.43
30 23 0.21
ACGTcount: A:0.53, C:0.15, G:0.02, T:0.30
Consensus pattern (29 bp):
CCAAAACTTTTATAAATTACAAACAAATG
Found at i:2142583 original size:57 final size:56
Alignment explanation
Indices: 2142409--2142587 Score: 175
Period size: 57 Copynumber: 3.1 Consensus size: 56
2142399 TTTTTGATAT
* * ** *
2142409 ATTACAATAAAGACCAAAAC-TTTTATAAATTACAAACAAATGCCAAACTTTTTATAA
1 ATTACAACAAATACCAAAACTTTTTATAAATTAC-AACAAATGAAAAAC-TTTAATAA
**
2142466 ATTACAAACAAATACCAAAACTTTTTATAAATTACAACAAATGACAAAAAAATTAA-AA
1 ATTAC-AACAAATACCAAAACTTTTTATAAATTACAACAAATG--AAAAACTTTAATAA
* ***
2142524 ATTACAACAAATTCCAATTGTTTTTATAAATTACAATCAAA-GAAAAACTTCTAATAA
1 ATTACAACAAATACCAAAACTTTTTATAAATTACAA-CAAATGAAAAACTT-TAATAA
2142581 ATTACAA
1 ATTACAA
2142588 TAATGACTTG
Statistics
Matches: 102, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
55 6 0.06
56 3 0.03
57 42 0.41
58 32 0.31
59 16 0.16
60 3 0.03
ACGTcount: A:0.54, C:0.15, G:0.03, T:0.29
Consensus pattern (56 bp):
ATTACAACAAATACCAAAACTTTTTATAAATTACAACAAATGAAAAACTTTAATAA
Found at i:2144899 original size:18 final size:20
Alignment explanation
Indices: 2144856--2144900 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
2144846 TATTTAAAAA
2144856 TAAAAATA-TTAAATATTAT
1 TAAAAATATTTAAATATTAT
*
2144875 T-ATAATATTTAAA-ATT-T
1 TAAAAATATTTAAATATTAT
2144892 TAAAAATAT
1 TAAAAATAT
2144901 AAAGAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
17 2 0.09
18 14 0.64
19 6 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAAAATATTTAAATATTAT
Found at i:2147328 original size:2 final size:2
Alignment explanation
Indices: 2147321--2147391 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
2147311 ATAGTCCTTT
2147321 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2147363 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2147392 TCAATTTAGA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2148127 original size:55 final size:55
Alignment explanation
Indices: 2148061--2148171 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
2148051 GGGTGGCCTT
2148061 CATTTGGAAGAAGTAATAATAACCACTAGAATTAATGCATAGGCTTGAAACCAGA
1 CATTTGGAAGAAGTAATAATAACCACTAGAATTAATGCATAGGCTTGAAACCAGA
2148116 CATTTGGAAGAAGTAATAATAACCACTAGAATTAATGCATAGGCTTGAAACCAGA
1 CATTTGGAAGAAGTAATAATAACCACTAGAATTAATGCATAGGCTTGAAACCAGA
2148171 C
1 C
2148172 GTGTGTCTCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.23
Consensus pattern (55 bp):
CATTTGGAAGAAGTAATAATAACCACTAGAATTAATGCATAGGCTTGAAACCAGA
Found at i:2149452 original size:3 final size:3
Alignment explanation
Indices: 2149438--2149506 Score: 57
Period size: 3 Copynumber: 22.7 Consensus size: 3
2149428 AATCGACTGT
* * * * * *
2149438 TAA TAGA TAA TAA TAA TAA TCA TCA TCA TCA TAA TCA TAA TCA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
2149484 TCA TAA TCA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
2149507 TTTGTCTGTG
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
3 52 0.95
4 3 0.05
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2149506 original size:6 final size:6
Alignment explanation
Indices: 2149444--2149502 Score: 73
Period size: 6 Copynumber: 9.8 Consensus size: 6
2149434 CTGTTAATAG
* * * *
2149444 ATAATA ATAATA ATCATC ATCATC ATAATC ATAATC ATAATC ATAATC
1 ATAATC ATAATC ATAATC ATAATC ATAATC ATAATC ATAATC ATAATC
*
2149492 ATAATA ATAAT
1 ATAATC ATAAT
2149503 AATATTTGTC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
ATAATC
Found at i:2149611 original size:86 final size:86
Alignment explanation
Indices: 2149471--2149637 Score: 325
Period size: 86 Copynumber: 1.9 Consensus size: 86
2149461 CATCATCATA
2149471 ATCATAATCATAATCATAATCATAATAATAATAATATTTGTCTGTGAAAGCAAATCGTAAACTCT
1 ATCATAATCATAATCATAATCATAATAATAATAATATTTGTCTGTGAAAGCAAATCGTAAACTCT
2149536 GAAACAGCATACACGGTAATC
66 GAAACAGCATACACGGTAATC
*
2149557 ATCATAATCATAATCATAATTATAATAATAATAATATTTGTCTGTGAAAGCAAATCGTAAACTCT
1 ATCATAATCATAATCATAATCATAATAATAATAATATTTGTCTGTGAAAGCAAATCGTAAACTCT
2149622 GAAACAGCATACACGG
66 GAAACAGCATACACGG
2149638 GGATTGTCCA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 80 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (86 bp):
ATCATAATCATAATCATAATCATAATAATAATAATATTTGTCTGTGAAAGCAAATCGTAAACTCT
GAAACAGCATACACGGTAATC
Found at i:2156599 original size:19 final size:20
Alignment explanation
Indices: 2156545--2156607 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 20
2156535 GTTAAAAATG
*
2156545 ATAAT-AAATAATAAAGAAA
1 ATAATCAAAGAATAAAGAAA
* * *
2156564 AAAATGAATGAAGTAAAGAAA
1 ATAATCAAAGAA-TAAAGAAA
2156585 ATAA-CAAAGAATAAAGAAA
1 ATAATCAAAGAATAAAGAAA
2156604 ATAA
1 ATAA
2156608 AAAAATTTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 16 0.44
20 9 0.25
21 11 0.31
ACGTcount: A:0.71, C:0.02, G:0.11, T:0.16
Consensus pattern (20 bp):
ATAATCAAAGAATAAAGAAA
Found at i:2156793 original size:13 final size:13
Alignment explanation
Indices: 2156777--2156842 Score: 64
Period size: 13 Copynumber: 5.2 Consensus size: 13
2156767 AGATAGAAAT
*
2156777 AAAAGAAAAATAA
1 AAAAGAAAAGTAA
2156790 AAAAG-AAAGTAA
1 AAAAGAAAAGTAA
*
2156802 AAATGAATAAGTAA
1 AAAAGAA-AAGTAA
* *
2156816 AATATAAAAGTAA
1 AAAAGAAAAGTAA
*
2156829 AATAGAAAA-TAA
1 AAAAGAAAAGTAA
2156841 AA
1 AA
2156843 TAATAATAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
12 15 0.33
13 20 0.44
14 10 0.22
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (13 bp):
AAAAGAAAAGTAA
Found at i:2156831 original size:44 final size:44
Alignment explanation
Indices: 2156774--2156868 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 44
2156764 GAAAGATAGA
*
2156774 AATAAAAGAAAAATAAAAAAGAAAGTAAAAATGAATAAGTA-AAAT
1 AATAAAAGAAAAATAAAAAAGAAAATAAAAAT-AATAA-TAGAAAT
* * * *
2156819 -ATAAAAGTAAAATAGAAAATAAAATAATAATAATAATAGAAAT
1 AATAAAAGAAAAATAAAAAAGAAAATAAAAATAATAATAGAAAT
2156862 AATAAAA
1 AATAAAA
2156869 TAGTAAAAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
42 2 0.05
43 9 0.21
44 32 0.74
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (44 bp):
AATAAAAGAAAAATAAAAAAGAAAATAAAAATAATAATAGAAAT
Found at i:2156843 original size:12 final size:12
Alignment explanation
Indices: 2156769--2156876 Score: 71
Period size: 12 Copynumber: 8.7 Consensus size: 12
2156759 GAGATGAAAG
2156769 ATAG-AAATAAA
1 ATAGAAAATAAA
*
2156780 AGA-AAAATAAA
1 ATAGAAAATAAA
* *
2156791 AAAGAAAGTAAA
1 ATAGAAAATAAA
2156803 A-ATGAATAAGTAAA
1 ATA-GAA-AA-TAAA
*
2156817 ATATAAAAGTAAA
1 ATAGAAAA-TAAA
2156830 ATAGAAAATAAA
1 ATAGAAAATAAA
*
2156842 ATA-ATAATAATA
1 ATAGAAAATAA-A
2156854 ATAGAAATAATAAA
1 ATAG-AA-AATAAA
2156868 ATAGTAAAA
1 ATAG-AAAA
2156877 GAGTATAGAA
Statistics
Matches: 78, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
11 18 0.23
12 22 0.28
13 17 0.22
14 15 0.19
15 6 0.08
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.19
Consensus pattern (12 bp):
ATAGAAAATAAA
Found at i:2156850 original size:18 final size:17
Alignment explanation
Indices: 2156801--2156866 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 17
2156791 AAAGAAAGTA
2156801 AAAATGAATAAGTAAAATAT
1 AAAAT-AATAA-TAAAA-AT
2156821 AAAAGTAA-AATAGAAAAT
1 AAAA-TAATAATA-AAAAT
*
2156839 AAAATAATAATAATAAT
1 AAAATAATAATAAAAAT
2156856 AGAAATAATAA
1 A-AAATAATAA
2156867 AATAGTAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
17 8 0.20
18 21 0.51
19 5 0.12
20 6 0.15
21 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.23
Consensus pattern (17 bp):
AAAATAATAATAAAAAT
Found at i:2156855 original size:9 final size:8
Alignment explanation
Indices: 2156836--2156876 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
2156826 TAAAATAGAA
2156836 AATAAAAT
1 AATAAAAT
2156844 AATAATAAT
1 AATAA-AAT
2156853 AATAGAAAT
1 AATA-AAAT
2156862 AATAAAAT
1 AATAAAAT
*
2156870 AGTAAAA
1 AATAAAA
2156877 GAGTATAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 15 0.50
9 14 0.47
10 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:2156984 original size:18 final size:17
Alignment explanation
Indices: 2156963--2157006 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
2156953 AATAGTTATA
2156963 ATAAAAATAAATAAAAAT
1 ATAAAAATAAA-AAAAAT
* *
2156981 ATAAATATAAAACAAAT
1 ATAAAAATAAAAAAAAT
2156998 AGTAAAAAT
1 A-TAAAAAT
2157007 GACCATGACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (17 bp):
ATAAAAATAAAAAAAAT
Found at i:2158065 original size:2 final size:2
Alignment explanation
Indices: 2158058--2158099 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2158048 TAAAACAATA
2158058 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
2158100 GTTTATGTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2158683 original size:15 final size:15
Alignment explanation
Indices: 2158665--2158724 Score: 52
Period size: 15 Copynumber: 3.8 Consensus size: 15
2158655 AAAGATTTTG
2158665 TGTCTCAAGAGAAAT
1 TGTCTCAAGAGAAAT
2158680 TGTCTCAAGGGAGACAAAAT
1 TGTCTCAA--GAG---AAAT
2158700 T-T-TCAAGAGAAAT
1 TGTCTCAAGAGAAAT
*
2158713 TGTCTCGAGAGA
1 TGTCTCAAGAGA
2158725 GACGAAATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
13 5 0.14
14 1 0.03
15 15 0.41
16 3 0.08
17 3 0.08
18 4 0.11
19 1 0.03
20 5 0.14
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.25
Consensus pattern (15 bp):
TGTCTCAAGAGAAAT
Found at i:2158706 original size:33 final size:33
Alignment explanation
Indices: 2158669--2158734 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2158659 ATTTTGTGTC
*
2158669 TCAAGAGAAATTGTCTCAAGGGAGACAAAATTT
1 TCAAGAGAAATTGTCTCAAGAGAGACAAAATTT
* *
2158702 TCAAGAGAAATTGTCTCGAGAGAGACGAAATTT
1 TCAAGAGAAATTGTCTCAAGAGAGACAAAATTT
2158735 GTTTAAATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.24
Consensus pattern (33 bp):
TCAAGAGAAATTGTCTCAAGAGAGACAAAATTT
Found at i:2158828 original size:51 final size:51
Alignment explanation
Indices: 2158764--2158876 Score: 172
Period size: 51 Copynumber: 2.2 Consensus size: 51
2158754 AAAAGATTTT
* * *
2158764 GTTTCAAGGGAAACTGTCTCAATAGAGACAAAATTTGTTTAAAGGGAAACC
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTGTTTAAAGGGAAACC
* *
2158815 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTGTTTCAAGGGAAACT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTGTTTAAAGGGAAACC
*
2158866 GTCTCAAGAGA
1 GTTTCAAGAGA
2158877 GACAAAATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (51 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTGTTTAAAGGGAAACC
Found at i:2158855 original size:36 final size:36
Alignment explanation
Indices: 2158815--2158894 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 36
2158805 AAGGGAAACC
2158815 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATT
* *
2158851 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATT
2158887 GTTTCAAG
1 GTTTCAAG
2158895 TTGGGTCAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (36 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATT
Found at i:2159587 original size:106 final size:105
Alignment explanation
Indices: 2159266--2159639 Score: 487
Period size: 106 Copynumber: 3.5 Consensus size: 105
2159256 GTATTGTTCC
* * * * * *
2159266 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGTTCTGGAACTAGGAAATTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAG
* *
2159331 TCAGCCGCCCCTTCCCTGTGAAGTTGAGCTTGTGTTGTCTC
66 TCAG-CGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
* * * *
2159372 GAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATAAAACTGAAGAAGTTTTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTG----AAACTG-GGAAGTTGTTTGTT
* * *
2159437 AACAGTCAGCTGCCCCTTCGCTATGAAGTTGAGCTTGTGATGTCTT
61 GACAGTCAGC-GCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
* *
2159483 GAGTCCAATTTCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAG
* *
2159548 CCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTT
66 TCAG-CGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
* *
2159589 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGAAACTGGGAAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAG
2159640 CTCATTCGTC
Statistics
Matches: 232, Mismatches: 29, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
106 133 0.57
107 7 0.03
110 5 0.02
111 87 0.38
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAG
TCAGCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
Found at i:2164838 original size:33 final size:31
Alignment explanation
Indices: 2164801--2164894 Score: 83
Period size: 33 Copynumber: 3.1 Consensus size: 31
2164791 AAATGATAAT
2164801 AAATAATAAAGAAAAAAATGAATGAAGTAAAGA
1 AAATAATAAAGAAAAAAATGAATGAA-TAAA-A
* *
2164834 AAATAACAAAG-AATAAA-GAA--AATAAAA
1 AAATAATAAAGAAAAAAATGAATGAATAAAA
*
2164861 AAAT--TAAAGATAAAAATGAATGAAATAAATA
1 AAATAATAAAGAAAAAAATGAATG-AATAAA-A
2164892 AAA
1 AAA
2164895 CAAAAAAATG
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
25 4 0.08
26 4 0.08
27 8 0.16
28 4 0.08
29 2 0.04
30 6 0.12
31 7 0.14
32 5 0.10
33 10 0.20
ACGTcount: A:0.72, C:0.01, G:0.11, T:0.16
Consensus pattern (31 bp):
AAATAATAAAGAAAAAAATGAATGAATAAAA
Found at i:2164917 original size:3 final size:3
Alignment explanation
Indices: 2164911--2164951 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2164901 AATGGAGAAC
2164911 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2164952 CATACATAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2165108 original size:18 final size:18
Alignment explanation
Indices: 2165082--2165136 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
2165072 GAATAAGTAA
2165082 AATAGAAAAGTAAAATAAC
1 AATAGAAAA-TAAAATAAC
*
2165101 AA-AGAAAATAATAATAAT
1 AATAGAAAATAA-AATAAC
2165119 AATAGAAATAATAAAATA
1 AATAG-AA-AATAAAATA
2165137 GTAAAAGAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 3 0.10
18 13 0.42
19 4 0.13
20 6 0.19
21 5 0.16
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.20
Consensus pattern (18 bp):
AATAGAAAATAAAATAAC
Found at i:2165246 original size:17 final size:16
Alignment explanation
Indices: 2165226--2165268 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
2165216 AATAATAGTT
*
2165226 ATAAAAAATAAATAGAA
1 ATAAAAAATAAA-ACAA
2165243 ATAAAAATATAAAACAA
1 ATAAAAA-ATAAAACAA
2165260 ATAGAAAAA
1 ATA-AAAAA
2165269 ATGACCATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (16 bp):
ATAAAAAATAAAACAA
Found at i:2166322 original size:2 final size:2
Alignment explanation
Indices: 2166315--2166351 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2166305 AATAATAATT
*
2166315 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2166352 GATTATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 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):
TA
Found at i:2173603 original size:55 final size:55
Alignment explanation
Indices: 2173445--2173643 Score: 290
Period size: 56 Copynumber: 3.6 Consensus size: 55
2173435 CCCTATTTTC
* * *
2173445 TAGATAGATTCGATTTCGGAGCCTCTATTTTTATGCTTCTTAATGGCAACAACTGA
1 TAGATATATTCGATTTCGG-GCCCCTATTTTTATGCTTATTAATGGCAACAACTGA
* * *
2173501 TAGATATACTCGATTTCAGGGCCCCTATTTTTATGCTTATTAATGGCAATAATTGA
1 TAGATATATTCGATTTC-GGGCCCCTATTTTTATGCTTATTAATGGCAACAACTGA
*
2173557 TAGATATATTCGATTTCGGGCCCTTATTTTTATGCTTATTAATGGCAACAACTGA
1 TAGATATATTCGATTTCGGGCCCCTATTTTTATGCTTATTAATGGCAACAACTGA
* *
2173612 AAGATATATTCGATTTTGGGTCCCCTATTTTT
1 TAGATATATTCGATTTCGGG-CCCCTATTTTT
2173644 TGAGGCCATG
Statistics
Matches: 128, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
55 53 0.41
56 73 0.57
57 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (55 bp):
TAGATATATTCGATTTCGGGCCCCTATTTTTATGCTTATTAATGGCAACAACTGA
Found at i:2174633 original size:20 final size:20
Alignment explanation
Indices: 2174608--2174660 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
2174598 ACATATGAAA
2174608 ATATGACTATGAGATAAGA-C
1 ATATGACTATGAGATAA-ACC
2174628 ATATGACTATGAGATAAACC
1 ATATGACTATGAGATAAACC
2174648 ATATGACTATGAG
1 ATATGACTATGAG
2174661 CTATGTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.26
Consensus pattern (20 bp):
ATATGACTATGAGATAAACC
Found at i:2177188 original size:4 final size:4
Alignment explanation
Indices: 2177179--2177349 Score: 270
Period size: 4 Copynumber: 42.8 Consensus size: 4
2177169 ATGTAACAAT
2177179 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * *
2177227 TACA TACA TATA TACA TATA TATA TACA TACA TACA TATA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * *
2177275 TACA TATA TACA TATA TACA TACA TACA TACA TACA TATA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
2177323 TACA TACA TACA TATA TACA TACA TAC
1 TACA TACA TACA TACA TACA TACA TAC
2177350 CCGCCATCAT
Statistics
Matches: 153, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 153 1.00
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (4 bp):
TACA
Found at i:2183972 original size:57 final size:58
Alignment explanation
Indices: 2183902--2184225 Score: 350
Period size: 59 Copynumber: 5.5 Consensus size: 58
2183892 AATCCACTTC
* * * * * * *
2183902 CTTATTATGAATTTCTTATATTTATA-TACATATATTTCCC-ATACGGAACTTCATACA
1 CTTAGTATGAATTTCTTACATTT-TAGCACATAAAGTGCCCAATACGGAAATTCATACA
*
2183959 CTTAGTATAAATTTCTTAACATTTTAGCACATAAAGTGCCCAATACGGAAATTCATACA
1 CTTAGTATGAATTTCTT-ACATTTTAGCACATAAAGTGCCCAATACGGAAATTCATACA
** ** *
2184018 CTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCAATACAAAAATTTATACA
1 CTTAGTATGAATTTCTT-ACATTTTAGCACATAAAGTGCCCAATACGGAAATTCATACA
* * * * *
2184077 CTTAATATGAATTTTTTAACATTTTAGCAC-TCGAAGTGCCCAATACGAAAAATCATACA
1 CTTAGTATGAATTTCTT-ACATTTTAGCACAT-AAAGTGCCCAATACGGAAATTCATACA
* * * *
2184136 CTTAGTAT-ATATTTCTTAACATTTTAGCATACAAAGTGCCTAATACGAAAATTCATACA
1 CTTAGTATGA-ATTTCTT-ACATTTTAGCACATAAAGTGCCCAATACGGAAATTCATACA
2184195 CTTAGTATGAATTTCTTAACATTTTAGCACA
1 CTTAGTATGAATTTCTT-ACATTTTAGCACA
2184226 CTTAATGCCA
Statistics
Matches: 232, Mismatches: 28, Indels: 12
0.85 0.10 0.04
Matches are distributed among these distances:
57 17 0.07
58 16 0.07
59 198 0.85
60 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (58 bp):
CTTAGTATGAATTTCTTACATTTTAGCACATAAAGTGCCCAATACGGAAATTCATACA
Found at i:2184014 original size:59 final size:59
Alignment explanation
Indices: 2183942--2184226 Score: 419
Period size: 59 Copynumber: 4.8 Consensus size: 59
2183932 TATATTTCCC
* * * *
2183942 ATACGGAACTTCATACACTTAGTATAAATTTCTTAACATTTTAGCACATAAAGTGCCCA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCA
* *
2184001 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCA
* * * * * *
2184060 ATACAAAAATTTATACACTTAATATGAATTTTTTAACATTTTAGCACTCGAAGTGCCCA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCA
* * *
2184119 ATACGAAAAATCATACACTTAGTAT-ATATTTCTTAACATTTTAGCATACAAAGTGCCTA
1 ATACGAAAATTCATACACTTAGTATGA-ATTTCTTAACATTTTAGCACACAAAGTGCCCA
2184178 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACAC
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACAC
2184227 TTAATGCCAT
Statistics
Matches: 203, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
58 1 0.00
59 201 0.99
60 1 0.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (59 bp):
ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCA
Found at i:2184749 original size:20 final size:21
Alignment explanation
Indices: 2184724--2184774 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
2184714 GTTTCAAAAT
*
2184724 GGTATCGATACCTT-CCCTTC
1 GGTATCGATACCTTCCCCTCC
2184744 GGTATCGATA-CTTCCCCTCC
1 GGTATCGATACCTTCCCCTCC
*
2184764 GATATCGATAC
1 GGTATCGATAC
2184775 TGATTGAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.20, C:0.33, G:0.16, T:0.31
Consensus pattern (21 bp):
GGTATCGATACCTTCCCCTCC
Found at i:2185929 original size:36 final size:36
Alignment explanation
Indices: 2185881--2185949 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
2185871 TATAAATGAG
* *
2185881 CATCCGTGTAATTAACCTAAAACTTCAATATTTGAT
1 CATCCGTATAATTAACCTAAAACTTCAACATTTGAT
*
2185917 CATCCGTATAATTAACTTAAAACTTCAACATTT
1 CATCCGTATAATTAACCTAAAACTTCAACATTT
2185950 TGACCTATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (36 bp):
CATCCGTATAATTAACCTAAAACTTCAACATTTGAT
Found at i:2189807 original size:2 final size:2
Alignment explanation
Indices: 2189800--2189837 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2189790 TTAACTTCTT
2189800 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2189838 GGGTCGAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2190494 original size:28 final size:27
Alignment explanation
Indices: 2190462--2190519 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
2190452 CAATTTTTTA
* *
2190462 TTAATCGACACTCTATCAAATAATAGTT
1 TTAATCGACACTATACCAAATAAT-GTT
* *
2190490 TTAATTGACATTATACCAAATAATGTT
1 TTAATCGACACTATACCAAATAATGTT
2190517 TTA
1 TTA
2190520 TATAAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (27 bp):
TTAATCGACACTATACCAAATAATGTT
Found at i:2190656 original size:17 final size:17
Alignment explanation
Indices: 2190613--2190657 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
2190603 ATTATTTATC
2190613 AAATAATCTTTTTTATAT
1 AAATAAT-TTTTTTATAT
*
2190631 ACATAATTTTTTTATAT
1 AAATAATTTTTTTATAT
*
2190648 AAATTATTTT
1 AAATAATTTT
2190658 AACTCATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (17 bp):
AAATAATTTTTTTATAT
Found at i:2195177 original size:26 final size:26
Alignment explanation
Indices: 2195121--2195183 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 26
2195111 CAGATAATTA
*
2195121 AGTACATTTTAAAATTTTAAATTGAT
1 AGTATATTTTAAAATTTTAAATTGAT
* *
2195147 A-TATATTTTAAATATTTT-ATTTTAT
1 AGTATATTTTAAA-ATTTTAAATTGAT
2195172 AGTATAATTTTA
1 AGTAT-ATTTTA
2195184 TCCCTAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 16 0.52
26 9 0.29
27 6 0.19
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.54
Consensus pattern (26 bp):
AGTATATTTTAAAATTTTAAATTGAT
Found at i:2195711 original size:23 final size:23
Alignment explanation
Indices: 2195683--2195743 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
2195673 CTCATACTAG
**
2195683 TTTGAATAGAATAATATAAAATT
1 TTTGAATAGAATAATATAAAAAA
2195706 TTTGAATAGAATAATATAAAAAA
1 TTTGAATAGAATAATATAAAAAA
2195729 TTTGAATAGAA-AATA
1 TTTGAATAGAATAATA
2195744 AAACATGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 4 0.11
23 32 0.89
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (23 bp):
TTTGAATAGAATAATATAAAAAA
Found at i:2196175 original size:25 final size:23
Alignment explanation
Indices: 2196139--2196206 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 23
2196129 CATCCAATAC
2196139 AATAAATAAATATTATTTATTAACA
1 AATAAAT-AATATTATTTATTAA-A
2196164 AATATAATAATATTATTT-TTAAA
1 AATA-AATAATATTATTTATTAAA
2196187 ATATTAGAATAAT-TTATTTA
1 A-A-TA-AATAATATTATTTA
2196207 ATATTATTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
23 2 0.05
24 11 0.29
25 22 0.58
26 3 0.08
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (23 bp):
AATAAATAATATTATTTATTAAA
Found at i:2196190 original size:22 final size:26
Alignment explanation
Indices: 2196139--2196185 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
2196129 CATCCAATAC
2196139 AATA-AATAAATATTATTTATTAACA
1 AATATAATAAATATTATTTATTAACA
2196164 AATATAAT-AATATTATTT-TTAA
1 AATATAATAAATATTATTTATTAA
2196186 AATATTAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.19
25 14 0.67
26 3 0.14
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
AATATAATAAATATTATTTATTAACA
Found at i:2196197 original size:22 final size:25
Alignment explanation
Indices: 2196147--2196206 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 25
2196137 ACAATAAATA
*
2196147 AATATTATTTATTAACAAATATAAT
1 AATATTATTTATTAACAAATATAAG
*
2196172 AATATTATTT-TT-A-AAATATTAG
1 AATATTATTTATTAACAAATATAAG
2196194 AATAATTTATTTA
1 AAT-A-TTATTTA
2196207 ATATTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 10 0.33
23 2 0.07
24 8 0.27
25 10 0.33
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (25 bp):
AATATTATTTATTAACAAATATAAG
Found at i:2198067 original size:45 final size:45
Alignment explanation
Indices: 2198009--2198244 Score: 285
Period size: 45 Copynumber: 5.2 Consensus size: 45
2197999 AAATGAATGA
* * *
2198009 ATAAATAAAATGCATAACGGTGCATTATCGGCATGAAATGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCAGCATGAAAGGATGCC
* * * * *
2198054 GTAACTGATATGCATAACGATGCATTATCAGCATGAAAGGATACC
1 ATAAATGAAATGCATAACGGTGCATTATCAGCATGAAAGGATGCC
* *
2198099 ATAAATGAAATGCATAACGGTGCATTATCATCATGAAAGAATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCAGCATGAAAGGATGCC
* *
2198144 ATAAATTAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCAGCATGAAAGGATGCC
** * * *
2198189 ATAAATGAAAATGTGTAACGGTGTATTATAAGTATGAACA-GATGCC
1 ATAAATG-AAATGCATAACGGTGCATTATCAGCATGAA-AGGATGCC
*
2198235 ATCAATGAAA
1 ATAAATGAAA
2198245 ATAAAGAATA
Statistics
Matches: 162, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
45 125 0.77
46 36 0.22
47 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (45 bp):
ATAAATGAAATGCATAACGGTGCATTATCAGCATGAAAGGATGCC
Found at i:2204687 original size:24 final size:24
Alignment explanation
Indices: 2204636--2204687 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
2204626 ATTGAAACTG
* **
2204636 CCACGTAGAATTTGCACAGAAGTG
1 CCACGTAGAATATGCACAGAAGCA
* *
2204660 CCACGTAGAATATGTACCGAAGCA
1 CCACGTAGAATATGCACAGAAGCA
2204684 CCAC
1 CCAC
2204688 ATAGTTTTGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (24 bp):
CCACGTAGAATATGCACAGAAGCA
Found at i:2204742 original size:24 final size:24
Alignment explanation
Indices: 2204676--2204745 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 24
2204666 AGAATATGTA
*
2204676 CCGAAGCACCACATAG--TTTTGTC
1 CCGAAGGACCACATAGAATTTT-TC
* * * *
2204699 CCAAAGGACCGCGTATAATTTTTC
1 CCGAAGGACCACATAGAATTTTTC
2204723 CCGAAGGACCACATAGAATTTTT
1 CCGAAGGACCACATAGAATTTTT
2204746 ATGAAGGACC
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
23 11 0.31
24 21 0.58
25 4 0.11
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (24 bp):
CCGAAGGACCACATAGAATTTTTC
Found at i:2205450 original size:21 final size:21
Alignment explanation
Indices: 2205408--2205459 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
2205398 CTTACTCTTG
2205408 GTATCGATAC-CTCTATATCA
1 GTATCGATACTCTCTATATCA
*
2205428 GTATCGATACTACTTTA-ATCA
1 GTATCGATACT-CTCTATATCA
2205449 GTATCGATACT
1 GTATCGATACT
2205460 GTTCATCCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 10 0.34
21 15 0.52
22 4 0.14
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (21 bp):
GTATCGATACTCTCTATATCA
Found at i:2211407 original size:22 final size:22
Alignment explanation
Indices: 2211376--2211422 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
2211366 CCCATATCGC
*
2211376 AAATCGCTCTTAGAAAAGACTG
1 AAATCACTCTTAGAAAAGACTG
2211398 AAATCACTCTTAGAAAAGACTG
1 AAATCACTCTTAGAAAAGACTG
2211420 AAA
1 AAA
2211423 CTCCCTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (22 bp):
AAATCACTCTTAGAAAAGACTG
Found at i:2214695 original size:54 final size:54
Alignment explanation
Indices: 2214637--2214989 Score: 242
Period size: 54 Copynumber: 6.5 Consensus size: 54
2214627 TAAACAAATT
*** * **
2214637 ATGAATTTCGTCCCTTGCACACCTAGTGCTGAAATTGATATTCATCCT-CATAGG
1 ATGAATTTCGTCAAATGCACACCTAGTGCCGAAACGGATATTCAT-CTACATAGG
* * * *
2214691 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCTACATAGG
1 ATGAATTTCGTCAAATGCACACCTAGTGCCGAAACGGATATTCATCTACATAGG
* * * * * * *
2214745 ATGAATTTCGTGAAATGCACACTTAGTGTCGAAACAGTTATTCATCCACATAAG
1 ATGAATTTCGTCAAATGCACACCTAGTGCCGAAACGGATATTCATCTACATAGG
* * * * * * * * *
2214799 ATGAATTCCGTGAAATGCACACTTAGTACCAAAATGGTTATTCATCCACATATG
1 ATGAATTTCGTCAAATGCACACCTAGTGCCGAAACGGATATTCATCTACATAGG
* * * * * ** * * * * *
2214853 ATAAATTCCGTGAAATGCACACTTAATTTCGAAACAGTTATTCATCCATATAAG
1 ATGAATTTCGTCAAATGCACACCTAGTGCCGAAACGGATATTCATCTACATAGG
* * * * * * *
2214907 ATGAATTAT-GTGAAATGCACACTTACTGCCGAAACGGTTATTCATCCATATATG
1 ATGAATT-TCGTCAAATGCACACCTAGTGCCGAAACGGATATTCATCTACATAGG
* * *
2214961 ATGAATTCCGTGAAATGCACACTTAGTGC
1 ATGAATTTCGTCAAATGCACACCTAGTGC
2214990 TTATTGGGTA
Statistics
Matches: 256, Mismatches: 40, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
53 2 0.01
54 254 0.99
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.30
Consensus pattern (54 bp):
ATGAATTTCGTCAAATGCACACCTAGTGCCGAAACGGATATTCATCTACATAGG
Found at i:2214811 original size:108 final size:108
Alignment explanation
Indices: 2214675--2214988 Score: 484
Period size: 108 Copynumber: 2.9 Consensus size: 108
2214665 CTGAAATTGA
* * *
2214675 TATTCATCCTCATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCTAC
1 TATTCATCCACATAAGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCAC
* *
2214740 ATAGGATGAATTTCGTGAAATGCACACTTAGTGTCGAAACAGT
66 ATATGATGAATTCCGTGAAATGCACACTTAGTGTCGAAACAGT
* * *
2214783 TATTCATCCACATAAGATGAATTCCGTGAAATGCACACTTAGTACCAAAATGGTTATTCATCCAC
1 TATTCATCCACATAAGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCAC
* * *
2214848 ATATGATAAATTCCGTGAAATGCACACTTAATTTCGAAACAGT
66 ATATGATGAATTCCGTGAAATGCACACTTAGTGTCGAAACAGT
* ** * *
2214891 TATTCATCCATATAAGATGAATTATGTGAAATGCACACTTACTGCCGAAACGGTTATTCATCCAT
1 TATTCATCCACATAAGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCAC
2214956 ATATGATGAATTCCGTGAAATGCACACTTAGTG
66 ATATGATGAATTCCGTGAAATGCACACTTAGTG
2214989 CTTATTGGGT
Statistics
Matches: 184, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
108 184 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (108 bp):
TATTCATCCACATAAGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCAC
ATATGATGAATTCCGTGAAATGCACACTTAGTGTCGAAACAGT
Found at i:2214912 original size:162 final size:162
Alignment explanation
Indices: 2214675--2214987 Score: 475
Period size: 162 Copynumber: 1.9 Consensus size: 162
2214665 CTGAAATTGA
* * * * *
2214675 TATTCATCCTCATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCTAC
1 TATTCATCCACATAGGATAAATTCCGTGAAATGCACACTTAATGCCGAAACAGTTATTCATCCAC
* * *
2214740 ATAGGATGAATT-TCGTGAAATGCACACTTAGTGTCGAAACAGTTATTCATCCACATAAGATGAA
66 ATAAGATGAATTAT-GTGAAATGCACACTTACTGCCGAAACAGTTATTCATCCACATAAGATGAA
2214804 TTCCGTGAAATGCACACTTAGTACCAAAATGGT
130 TTCCGTGAAATGCACACTTAGTACCAAAATGGT
* ** *
2214837 TATTCATCCACATATGATAAATTCCGTGAAATGCACACTTAATTTCGAAACAGTTATTCATCCAT
1 TATTCATCCACATAGGATAAATTCCGTGAAATGCACACTTAATGCCGAAACAGTTATTCATCCAC
* * *
2214902 ATAAGATGAATTATGTGAAATGCACACTTACTGCCGAAACGGTTATTCATCCATATATGATGAAT
66 ATAAGATGAATTATGTGAAATGCACACTTACTGCCGAAACAGTTATTCATCCACATAAGATGAAT
2214967 TCCGTGAAATGCACACTTAGT
131 TCCGTGAAATGCACACTTAGT
2214988 GCTTATTGGG
Statistics
Matches: 135, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
162 134 0.99
163 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (162 bp):
TATTCATCCACATAGGATAAATTCCGTGAAATGCACACTTAATGCCGAAACAGTTATTCATCCAC
ATAAGATGAATTATGTGAAATGCACACTTACTGCCGAAACAGTTATTCATCCACATAAGATGAAT
TCCGTGAAATGCACACTTAGTACCAAAATGGT
Found at i:2215339 original size:20 final size:21
Alignment explanation
Indices: 2215313--2215364 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2215303 TGGCCCTTCA
2215313 ATATCGATACCTA-TACTATG
1 ATATCGATACCTACTACTATG
*
2215333 GTATCGATA-CTACCTACTATG
1 ATATCGATACCTA-CTACTATG
*
2215354 ATATCAATACC
1 ATATCGATACC
2215365 CCCATCTAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 3 0.12
20 8 0.31
21 14 0.54
22 1 0.04
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.33
Consensus pattern (21 bp):
ATATCGATACCTACTACTATG
Done.