Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009344.1 Hibiscus syriacus cultivar Beakdansim tig00113124_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: 4287485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 24
Found at i:2540171 original size:30 final size:30
Alignment explanation
Indices: 2540123--2540179 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
2540113 ATACTGCCGA
*
2540123 TGCTGCTCTAGCTGCTTCCGC-TGCTTCCGC
1 TGCTGCTCTAGCTACTTCC-CTTGCTTCCGC
**
2540153 TGCTGCTCTCTCTACTTCCCTTGCTTC
1 TGCTGCTCTAGCTACTTCCCTTGCTTC
2540180 ATTTTTCACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 1 0.04
30 22 0.96
ACGTcount: A:0.04, C:0.40, G:0.18, T:0.39
Consensus pattern (30 bp):
TGCTGCTCTAGCTACTTCCCTTGCTTCCGC
Found at i:2557720 original size:26 final size:26
Alignment explanation
Indices: 2557657--2557721 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 26
2557647 ATAAAATGAG
2557657 ATAAAGAAAAAAATAAAATGAAGACAA
1 ATAAAG-AAAAAATAAAATGAAGACAA
*
2557684 AT-AGGATAAAAATAATAAT-AAGA-AA
1 ATAAAGA-AAAAATAA-AATGAAGACAA
2557709 TATAAAGAAAAAA
1 -ATAAAGAAAAAA
2557722 GAAACAAGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
25 3 0.09
26 21 0.66
27 8 0.25
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (26 bp):
ATAAAGAAAAAATAAAATGAAGACAA
Found at i:2558058 original size:17 final size:17
Alignment explanation
Indices: 2558017--2558058 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2558007 AACGAAAAAT
*
2558017 AATAAAAATAATTAAAG
1 AATAAAAATAAATAAAG
*
2558034 AATTAAAATAAAATAAAG
1 AATAAAAAT-AAATAAAG
2558052 -ATAAAAA
1 AATAAAAA
2558059 ATAGTATCGT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (17 bp):
AATAAAAATAAATAAAG
Found at i:2558087 original size:7 final size:6
Alignment explanation
Indices: 2558073--2558126 Score: 51
Period size: 6 Copynumber: 9.0 Consensus size: 6
2558063 TATCGTATAA
*
2558073 AAAAAT AACAAAT -AAAAT AGAAAT -AAAAT AAAAAAT AAAAAT AACAAA-
1 AAAAAT AA-AAAT AAAAAT AAAAAT AAAAAT -AAAAAT AAAAAT AA-AAAT
2558121 AAAAAT
1 AAAAAT
2558127 GATTAAATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
5 11 0.28
6 17 0.43
7 12 0.30
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:2558091 original size:12 final size:12
Alignment explanation
Indices: 2558074--2558126 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
2558064 ATCGTATAAA
2558074 AAAATAACAAAT
1 AAAATAACAAAT
*
2558086 AAAAT-AGAAAT
1 AAAATAACAAAT
*
2558097 AAAATAAAAAAT
1 AAAATAACAAAT
*
2558109 AAAAATAACAAAA
1 -AAAATAACAAAT
2558122 AAAAT
1 AAAAT
2558127 GATTAAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
11 10 0.29
12 15 0.43
13 10 0.29
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.15
Consensus pattern (12 bp):
AAAATAACAAAT
Found at i:2558096 original size:18 final size:18
Alignment explanation
Indices: 2558073--2558126 Score: 74
Period size: 18 Copynumber: 3.0 Consensus size: 18
2558063 TATCGTATAA
*
2558073 AAAAATAACAAATAAAAT
1 AAAAATAACAAAAAAAAT
*
2558091 AGAAATAA-AATAAAAAAT
1 AAAAATAACAA-AAAAAAT
2558109 AAAAATAACAAAAAAAAT
1 AAAAATAACAAAAAAAAT
2558127 GATTAAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 2 0.06
18 27 0.87
19 2 0.06
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.15
Consensus pattern (18 bp):
AAAAATAACAAAAAAAAT
Found at i:2559216 original size:13 final size:13
Alignment explanation
Indices: 2559189--2559225 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
2559179 ATATATATAT
2559189 ATAAGTAATAA-AA
1 ATAA-TAATAATAA
2559202 ATAATAATAATAA
1 ATAATAATAATAA
2559215 ATAATAATAAT
1 ATAATAATAAT
2559226 TTAAAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (13 bp):
ATAATAATAATAA
Found at i:2559298 original size:38 final size:38
Alignment explanation
Indices: 2559229--2559304 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
2559219 TAATAATTTA
** *
2559229 AAAAAACTATATAATATACACTTTTTTAAAAACGTTTT
1 AAAAAACTATATAATATACAAATTTTCAAAAACGTTTT
* * *
2559267 AAAAAACTATATTATATATAAATTTTCAAAAATGTTTT
1 AAAAAACTATATAATATACAAATTTTCAAAAACGTTTT
2559305 TTTCTTAAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (38 bp):
AAAAAACTATATAATATACAAATTTTCAAAAACGTTTT
Found at i:2559332 original size:34 final size:32
Alignment explanation
Indices: 2559281--2559373 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 32
2559271 AACTATATTA
**
2559281 TATATAAATTTTCAAAAATGTTTTTTTCTTAAAC
1 TATAT-AATTTTCAAAAATGTTTTTTT-GAAAAC
2559315 TATATAATTTTCAAAAAATGTTTTTTTGAAAAC
1 TATATAATTTTC-AAAAATGTTTTTTTGAAAAC
*
2559348 TATATAATTTTCCAAAATGTTTTTTT
1 TATATAATTTTCAAAAATGTTTTTTT
2559374 AATTATATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
32 13 0.24
33 23 0.42
34 19 0.35
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.51
Consensus pattern (32 bp):
TATATAATTTTCAAAAATGTTTTTTTGAAAAC
Found at i:2559418 original size:37 final size:37
Alignment explanation
Indices: 2559377--2559615 Score: 270
Period size: 37 Copynumber: 6.4 Consensus size: 37
2559367 TTTTTTTAAT
* * *
2559377 TATATATTATAGAAGTTTTAAAAAATATTTTCAAAAC
1 TATATATTATATAAGTTTTAAAAAATGTTTTAAAAAC
* *
2559414 TATATATTATATAAGTTTATTTAAAAATTGTTTTCAATAAC
1 TATATATTATATAAG--T-TTTAAAAAATGTTTT-AAAAAC
**
2559455 TATATATTATATAAGTTTTTCAAAATGATTTTAAAAAC
1 TATATATTATATAAGTTTTAAAAAATG-TTTTAAAAAC
**
2559493 TATATATTATATATA-TTTTCTAAAATGTTTTAAAAAC
1 TATATATTATATA-AGTTTTAAAAAATGTTTTAAAAAC
* *
2559530 TATATATTATAT-AGTTTTCAAAAGTGTTTTAAAAAC
1 TATATATTATATAAGTTTTAAAAAATGTTTTAAAAAC
*
2559566 TATATATTATATACA-TTTT-CAAAATGTTTTTAAAAAC
1 TATATATTATATA-AGTTTTAAAAAATG-TTTTAAAAAC
2559603 TATATATTATATA
1 TATATATTATATA
2559616 TGTATCTTCA
Statistics
Matches: 177, Mismatches: 15, Indels: 20
0.83 0.07 0.09
Matches are distributed among these distances:
35 1 0.01
36 37 0.21
37 63 0.36
38 37 0.21
39 7 0.04
40 13 0.07
41 19 0.11
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (37 bp):
TATATATTATATAAGTTTTAAAAAATGTTTTAAAAAC
Found at i:2559564 original size:73 final size:71
Alignment explanation
Indices: 2559348--2559615 Score: 304
Period size: 73 Copynumber: 3.6 Consensus size: 71
2559338 TTTTGAAAAC
* *** * * * * *
2559348 TATATAATTTTCCAAAATGTTTTTTTAATTATATATTATAGAAGTTTTAAAAAATATTTTCAAAA
1 TATATAATTTTCTAAAATGTTTTAAAAACTATATATTATA-TAGTTTT-CAAAATGTTTTAAAAA
2559413 CTATATAT
64 CTATATAT
* *
2559421 TATATAAGTTTATTTAAAAATTGTTTTCAATAACTATATATTATATAAGTTTTTCAAAATGATTT
1 TATATAA-TTT-TCT-AAAA-TGTTTT-AAAAACTATATATTATAT-AG-TTTTCAAAATG-TTT
2559486 TAAAAACTATATAT
58 TAAAAACTATATAT
2559500 TATATATATTTTCTAAAATGTTTTAAAAACTATATATTATATAGTTTTCAAAAGTGTTTTAAAAA
1 TATATA-ATTTTCTAAAATGTTTTAAAAACTATATATTATATAGTTTTCAAAA-TGTTTTAAAAA
2559565 CTATATAT
64 CTATATAT
2559573 TATATACATTTTC-AAAATGTTTTTAAAAACTATATATTATATA
1 TATATA-ATTTTCTAAAATG-TTTTAAAAACTATATATTATATA
2559616 TGTATCTTCA
Statistics
Matches: 172, Mismatches: 12, Indels: 22
0.83 0.06 0.11
Matches are distributed among these distances:
72 6 0.03
73 68 0.40
74 7 0.04
75 18 0.10
76 10 0.06
77 10 0.06
78 23 0.13
79 29 0.17
80 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (71 bp):
TATATAATTTTCTAAAATGTTTTAAAAACTATATATTATATAGTTTTCAAAATGTTTTAAAAACT
ATATAT
Found at i:2559659 original size:4 final size:4
Alignment explanation
Indices: 2559650--2560205 Score: 1112
Period size: 4 Copynumber: 139.0 Consensus size: 4
2559640 ACTATATAAT
2559650 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
2559698 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
2559746 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
2559794 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
2559842 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
2559890 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
2559938 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
2559986 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
2560034 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
2560082 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
2560130 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
2560178 ATGG ATGG ATGG ATGG ATGG ATGG ATGG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG
2560206 TATACGATAA
Statistics
Matches: 552, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 552 1.00
ACGTcount: A:0.25, C:0.00, G:0.50, T:0.25
Consensus pattern (4 bp):
ATGG
Found at i:2567108 original size:97 final size:96
Alignment explanation
Indices: 2566979--2567207 Score: 220
Period size: 95 Copynumber: 2.4 Consensus size: 96
2566969 GAATTAAAAT
* * * *
2566979 ATCAATGATTAAAATGTAA-AA-TATCAAAATTAAAGGCTAT-ACTTCGAATTATTATAAAAATA
1 ATCAGTGATTAAAA--TAATAATTATAAAAATTAAAGGCTATGAC-TCGAA--ATAAAAAAAATA
*
2567041 TAATTACTAATAATATAATTAACCCTTAATT-ATTA
61 TAAGTACTAATAATATAATTAACCCTTAATTAATTA
* * *
2567076 ATCAGTGATTAAAATAATAATTATTAAAATTAAAGGCTCTGACTCGAAATAAAAAAAATCTAAGT
1 ATCAGTGATTAAAATAATAATTATAAAAATTAAAGGCTATGACTCGAAATAAAAAAAATATAAGT
* * * *
2567141 GCTAATAATGTAATTTAGCCTTAATTAATTA
66 ACTAATAATATAATTAACCCTTAATTAATTA
*
2567172 ATTC-G-GGTTAAAAT-ATAAATTATAAAAATTATAAGG
1 A-TCAGTGATTAAAATAAT-AATTATAAAAATTA-AAGG
2567208 GACTAATATA
Statistics
Matches: 112, Mismatches: 13, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
94 2 0.02
95 59 0.53
96 12 0.11
97 37 0.33
98 2 0.02
ACGTcount: A:0.48, C:0.08, G:0.09, T:0.34
Consensus pattern (96 bp):
ATCAGTGATTAAAATAATAATTATAAAAATTAAAGGCTATGACTCGAAATAAAAAAAATATAAGT
ACTAATAATATAATTAACCCTTAATTAATTA
Found at i:2568646 original size:45 final size:45
Alignment explanation
Indices: 2568587--2568774 Score: 313
Period size: 45 Copynumber: 4.2 Consensus size: 45
2568577 CCTGAAGGCT
* *
2568587 TTTTGAAAACATCATGCACCGAAGTGCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
2568632 TTTTAAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
2568677 TTTTGAAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* * *
2568722 TTTTGAAAACATCATACACTGAAGGTCTTACAGATGACCCAAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
2568767 TTTTGAAA
1 TTTTGAAA
2568775 GTATCAAAAA
Statistics
Matches: 134, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 134 1.00
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.24
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
Found at i:2568802 original size:121 final size:121
Alignment explanation
Indices: 2568669--2569114 Score: 693
Period size: 121 Copynumber: 3.7 Consensus size: 121
2568659 TTACAGATGA
* * ***
2568669 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
* *
2568732 ATCATACACTGAAGGTCTTACAGATGACCCAAAGGTTTTGAAAGTATCAAAAAGCT
66 ATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAGTATCAAAAAGCT
* *
2568788 CCCGAAGGCTTTTTGAAAACATCCTGCATTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
*
2568853 ATCATGCA-TTATAGGTCTTACAGATGACCCGAAGGTTTTGAAAGTATCAAAAAGCT
66 ATCATGCACTGA-AGGTCTTACAGATGACCCGAAGGTTTTGAAAGTATCAAAAAGCT
* *
2568909 CCTGAAGGCTTTTTGAAAACATCTTGCACT-ATAGGTCTTATGGATGACCCGAAGGTTTTGAAAA
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGA-AGGTCTTATGGATGACCCGAAGGTTTTGAAAA
* *
2568973 CATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAGCT
65 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAGTATCAAAAAGCT
* *
2569030 CCTGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
*
2569095 ATCATGCACTGTAGGTCTTA
66 ATCATGCACTGAAGGTCTTA
2569115 AATATGTGGG
Statistics
Matches: 302, Mismatches: 19, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
119 8 0.03
120 2 0.01
121 291 0.96
122 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (121 bp):
CCCGAAGGCTTTTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
ATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAGTATCAAAAAGCT
Found at i:2568854 original size:45 final size:45
Alignment explanation
Indices: 2568788--2568895 Score: 162
Period size: 45 Copynumber: 2.4 Consensus size: 45
2568778 TCAAAAAGCT
* * **
2568788 CCCGAAGGCTTTTTGAAAACATCCTGCATTGTAGGTCTTATGGATGA
1 CCCGAAGG--TTTTGAAAACATCATGCATTATAGGTCTTACAGATGA
2568835 CCCGAAGGTTTTGAAAACATCATGCATTATAGGTCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCATTATAGGTCTTACAGATGA
2568880 CCCGAAGGTTTTGAAA
1 CCCGAAGGTTTTGAAA
2568896 GTATCAAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
45 49 0.86
47 8 0.14
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCATTATAGGTCTTACAGATGA
Found at i:2568970 original size:166 final size:162
Alignment explanation
Indices: 2568475--2569022 Score: 547
Period size: 166 Copynumber: 3.3 Consensus size: 162
2568465 GAGGTCTTAT
* * * * * *
2568475 CATCTTGCATTGTAGGTCTTATAGATGA-CCTAGAGGATTTGAAAATATCATGCACTGAAGGGT-
1 CATCATGCACTGTAGGTCTTACAGATGACCCGA-AGGTTTTGAAAACATCATGCACTGAA-GGTC
*
2568538 TTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAGCTCCTGAAGGCTTTTTGAAAACATCATG
64 TTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAGCTCCTGAAGGCTTTTTGAAAACATCTTG
*
2568603 CACCGAAGTGCTTACAGATGACCCGAAGGTTTTAAAAA
129 CA-C-AAGT-CTTA-AGATGACCCGAAGGTTTTGAAAA
* * *
2568641 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGTCTT
* * * * ** **
2568706 ACAAATGACCCGAAGGTTTTGAAAACATC--ATA-C-ACTGAAGGTCTTACAGATGACCCAAAGG
66 ACAGATGACCCGAAGGTTTTGAAAATATCAAAAAGCTCCTGAAGG-CTT---TTTGA---AAACA
* * * * * *
2568767 TTTTG-A-AAGTATCAAAAAGCTCCCGAAGGCTTTTTGAAAA
124 TCTTGCACAAGTCTTAAGATG-ACCCGAAGG--TTTTGAAAA
* * ** *
2568807 CATCCTGCATTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCA-TTATAGGTCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGA-AGGTCT
*
2568871 TACAGATGACCCGAAGGTTTTGAAAGTATCAAAAAGCTCCTGAAGGCTTTTTGAAAACATCTTGC
65 TACAGATGACCCGAAGGTTTTGAAAATATCAAAAAGCTCCTGAAGGCTTTTTGAAAACATCTTGC
*
2568936 ACTATAGGTCTTATGGATGACCCGAAGGTTTTGAAAA
130 AC-A-A-GTCTTA-AGATGACCCGAAGGTTTTGAAAA
*
2568973 CATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAATATCA
1 CATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCA
2569023 AAAAGCTCCT
Statistics
Matches: 305, Mismatches: 54, Indels: 46
0.75 0.13 0.11
Matches are distributed among these distances:
162 7 0.02
163 14 0.05
164 13 0.04
165 8 0.03
166 225 0.74
167 4 0.01
168 15 0.05
169 12 0.04
170 7 0.02
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (162 bp):
CATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGTCTT
ACAGATGACCCGAAGGTTTTGAAAATATCAAAAAGCTCCTGAAGGCTTTTTGAAAACATCTTGCA
CAAGTCTTAAGATGACCCGAAGGTTTTGAAAA
Found at i:2568982 original size:45 final size:45
Alignment explanation
Indices: 2568919--2569022 Score: 163
Period size: 45 Copynumber: 2.3 Consensus size: 45
2568909 CCTGAAGGCT
* **
2568919 TTTTGAAAACATCTTGCACTATAGGTCTTATGGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTATAGGTCTTACAGATGACCCGAAGG
*
2568964 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTATAGGTCTTACAGATGACCCGAAGG
*
2569009 TTTTGAAAATATCA
1 TTTTGAAAACATCA
2569023 AAAAGCTCCT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTATAGGTCTTACAGATGACCCGAAGG
Found at i:2569792 original size:22 final size:22
Alignment explanation
Indices: 2569767--2569821 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
2569757 AGTAAAGCTT
*
2569767 TCATCTTTGAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAATCTA
* *
2569789 TCATCTTTGGAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
2569811 TCATCTTTGAA
1 TCATCTTTGAA
2569822 GAATGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:2570974 original size:22 final size:22
Alignment explanation
Indices: 2570949--2571003 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
2570939 AGTAAAGCTT
2570949 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
2570971 TCATCTTTGGAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
2570993 TCATCTTTGAA
1 TCATCTTTGAA
2571004 GAATGTAGAT
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:0.15, G:0.16, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:2575900 original size:19 final size:18
Alignment explanation
Indices: 2575867--2575903 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
2575857 TTGTTGATCA
*
2575867 CATTTTCAATTAATTCTC
1 CATTTTCAATAAATTCTC
2575885 CATTTATCAATAAATTCTC
1 CATTT-TCAATAAATTCTC
2575904 AAATTCCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.22, G:0.00, T:0.46
Consensus pattern (18 bp):
CATTTTCAATAAATTCTC
Found at i:2576936 original size:21 final size:20
Alignment explanation
Indices: 2576880--2576943 Score: 78
Period size: 21 Copynumber: 3.2 Consensus size: 20
2576870 CAAACTGAGC
* *
2576880 AATGCAAATAT-AAAATGTA
1 AATGAAAATATAAAAATGCA
2576899 AATGAAAATATAAAAATGCA
1 AATGAAAATATAAAAATGCA
2576919 AATGCAAACATA-AAAAATGCA
1 AATG-AAA-ATATAAAAATGCA
2576940 AATG
1 AATG
2576944 TAATGAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.25
20 11 0.28
21 16 0.40
22 3 0.08
ACGTcount: A:0.61, C:0.08, G:0.11, T:0.20
Consensus pattern (20 bp):
AATGAAAATATAAAAATGCA
Found at i:2580053 original size:18 final size:20
Alignment explanation
Indices: 2580032--2580071 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
2580022 TATTAAAAAA
*
2580032 TAAATAAATAT-TAT-TATT
1 TAAACAAATATATATATATT
2580050 TAAACAAATATATATATATT
1 TAAACAAATATATATATATT
2580070 TA
1 TA
2580072 TATGATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 3 0.16
20 6 0.32
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAACAAATATATATATATT
Found at i:2580457 original size:2 final size:2
Alignment explanation
Indices: 2580450--2580495 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2580440 TATCTTACCC
2580450 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
2580492 TA TA
1 TA TA
2580496 CCAAATTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2581614 original size:22 final size:22
Alignment explanation
Indices: 2581589--2581644 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
2581579 GACCCTAGGT
2581589 GAGTCACCATAGCTATGGTGGC
1 GAGTCACCATAGCTATGGTGGC
2581611 GAGTCACCATAGCTATGGTGGC
1 GAGTCACCATAGCTATGGTGGC
*
2581633 GACTCACCATAG
1 GAGTCACCATAG
2581645 AGCTCGACGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.21
Consensus pattern (22 bp):
GAGTCACCATAGCTATGGTGGC
Found at i:2582206 original size:14 final size:14
Alignment explanation
Indices: 2582189--2582221 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2582179 CTTCAACCAC
2582189 TTAAAA-ATATATAT
1 TTAAAAGAT-TATAT
2582203 TTAAAAGATTATAT
1 TTAAAAGATTATAT
2582217 TTAAA
1 TTAAA
2582222 CCGTTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.89
15 2 0.11
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (14 bp):
TTAAAAGATTATAT
Found at i:2583176 original size:12 final size:12
Alignment explanation
Indices: 2583159--2583265 Score: 58
Period size: 12 Copynumber: 8.5 Consensus size: 12
2583149 ATTACCTCAA
*
2583159 TATATTTTAATT
1 TATATTATAATT
2583171 TATATTATAATT
1 TATATTATAATT
* *
2583183 GATATTATAAATG
1 TATATTAT-AATT
* * *
2583196 TATCTTAAAATG
1 TATATTATAATT
2583208 T-T-TTATAATT
1 TATATTATAATT
2583218 TATATTATCATTAATT
1 TATA-T-T-A-TAATT
2583234 TCA-ATTATAATT
1 T-ATATTATAATT
*
2583246 TAAATATTAAAATT
1 T--ATATTATAATT
2583260 TATATT
1 TATATT
2583266 GATGTTAGGT
Statistics
Matches: 75, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
10 7 0.09
11 2 0.03
12 34 0.45
13 11 0.15
14 11 0.15
15 2 0.03
16 7 0.09
17 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (12 bp):
TATATTATAATT
Found at i:2599586 original size:14 final size:15
Alignment explanation
Indices: 2599569--2599615 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
2599559 TCGTTATAAA
2599569 TTTTGTTATAATT-T
1 TTTTGTTATAATTAT
* *
2599583 TTTTATTATACTTAT
1 TTTTGTTATAATTAT
*
2599598 TGTTTGTTATGATTAT
1 T-TTTGTTATAATTAT
2599614 TT
1 TT
2599616 GAAAAAATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
14 11 0.42
15 3 0.12
16 12 0.46
ACGTcount: A:0.21, C:0.02, G:0.09, T:0.68
Consensus pattern (15 bp):
TTTTGTTATAATTAT
Found at i:2602973 original size:35 final size:34
Alignment explanation
Indices: 2602888--2602974 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
2602878 AATATAATTT
*
2602888 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
2602922 TAAATAATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
2602960 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
2602975 ACTGAATACA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:2603030 original size:26 final size:24
Alignment explanation
Indices: 2603001--2603072 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
2602991 AAAGCCCAAC
2603001 AAATTTAACAAAATAAAGTAAGTATT
1 AAATTTAACAAAATAAAGTAA--ATT
*
2603027 AAA-TGAGA-AATAATAAA--AAATT
1 AAATTTA-ACAA-AATAAAGTAAATT
2603049 ACAATTTAACAAAATAAAGTAAAT
1 A-AATTTAACAAAATAAAGTAAAT
2603073 ACAAATATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 9 0.24
24 6 0.16
25 8 0.22
26 10 0.27
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.26
Consensus pattern (24 bp):
AAATTTAACAAAATAAAGTAAATT
Found at i:2603518 original size:18 final size:18
Alignment explanation
Indices: 2603497--2603540 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
2603487 TGGTGGCGGC
* *
2603497 GGCTGTGGCATCATATAT
1 GGCTGCGGCATCATAAAT
2603515 GGCTGCGGCATCATAAAT
1 GGCTGCGGCATCATAAAT
2603533 GGCTGCGG
1 GGCTGCGG
2603541 TGGCTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.25
Consensus pattern (18 bp):
GGCTGCGGCATCATAAAT
Found at i:2604668 original size:173 final size:173
Alignment explanation
Indices: 2604379--2604726 Score: 696
Period size: 173 Copynumber: 2.0 Consensus size: 173
2604369 CAATCGATCC
2604379 ATGCCCAAGACTGCAGCAGCAGGAGACATCCGCCGATAGCATTACGCTTGTAGTCAGTGGCTCCA
1 ATGCCCAAGACTGCAGCAGCAGGAGACATCCGCCGATAGCATTACGCTTGTAGTCAGTGGCTCCA
2604444 CACATTTCCCTGTATAGCAAAGCCAAAACTGTCGAGCTCAGCTAAATGATCCGGCCAGACGAAAG
66 CACATTTCCCTGTATAGCAAAGCCAAAACTGTCGAGCTCAGCTAAATGATCCGGCCAGACGAAAG
2604509 TCGCTAAGATGTCGCAACCACATGCAGTGAACTAGGTTGCGCG
131 TCGCTAAGATGTCGCAACCACATGCAGTGAACTAGGTTGCGCG
2604552 ATGCCCAAGACTGCAGCAGCAGGAGACATCCGCCGATAGCATTACGCTTGTAGTCAGTGGCTCCA
1 ATGCCCAAGACTGCAGCAGCAGGAGACATCCGCCGATAGCATTACGCTTGTAGTCAGTGGCTCCA
2604617 CACATTTCCCTGTATAGCAAAGCCAAAACTGTCGAGCTCAGCTAAATGATCCGGCCAGACGAAAG
66 CACATTTCCCTGTATAGCAAAGCCAAAACTGTCGAGCTCAGCTAAATGATCCGGCCAGACGAAAG
2604682 TCGCTAAGATGTCGCAACCACATGCAGTGAACTAGGTTGCGCG
131 TCGCTAAGATGTCGCAACCACATGCAGTGAACTAGGTTGCGCG
2604725 AT
1 AT
2604727 TTGTCCGATA
Statistics
Matches: 175, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
173 175 1.00
ACGTcount: A:0.29, C:0.28, G:0.24, T:0.19
Consensus pattern (173 bp):
ATGCCCAAGACTGCAGCAGCAGGAGACATCCGCCGATAGCATTACGCTTGTAGTCAGTGGCTCCA
CACATTTCCCTGTATAGCAAAGCCAAAACTGTCGAGCTCAGCTAAATGATCCGGCCAGACGAAAG
TCGCTAAGATGTCGCAACCACATGCAGTGAACTAGGTTGCGCG
Found at i:2605757 original size:26 final size:27
Alignment explanation
Indices: 2605728--2605780 Score: 63
Period size: 29 Copynumber: 1.9 Consensus size: 27
2605718 GCTTTACTGC
*
2605728 TATG-GGTGTTAGATCGAGAAATATAA
1 TATGAGGTGTTAGATCAAGAAATATAA
*
2605754 TATGACTGGTGTTAGATCAATAAATAT
1 TATGA--GGTGTTAGATCAAGAAATAT
2605781 GTCGGTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 4 0.18
29 18 0.82
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.34
Consensus pattern (27 bp):
TATGAGGTGTTAGATCAAGAAATATAA
Found at i:2606650 original size:13 final size:13
Alignment explanation
Indices: 2606632--2606657 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2606622 ACATAGTTCA
2606632 ACAGTCTTCATAT
1 ACAGTCTTCATAT
2606645 ACAGTCTTCATAT
1 ACAGTCTTCATAT
2606658 GCGCGTCTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
ACAGTCTTCATAT
Found at i:2608854 original size:27 final size:27
Alignment explanation
Indices: 2608803--2608866 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
2608793 AATAAATTAT
2608803 ATATTTTTAAATGAAACTAAAAATAAA
1 ATATTTTTAAATGAAACTAAAAATAAA
* ** *
2608830 ATATTTTTAAATTAAGTTAATAATAAA
1 ATATTTTTAAATGAAACTAAAAATAAA
*
2608857 ATATATTTAA
1 ATATTTTTAA
2608867 TAAGTTGGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (27 bp):
ATATTTTTAAATGAAACTAAAAATAAA
Found at i:2608879 original size:27 final size:25
Alignment explanation
Indices: 2608824--2608895 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 25
2608814 TGAAACTAAA
2608824 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATA-TTTT-AATTAAGTTAAT
**
2608851 AATAAAATATATTTAA-TAAGTTGGT
1 AATAAAATAT-TTTAATTAAGTTAAT
2608876 -ATAAAAATATTTTAAGTTAA
1 AAT-AAAATATTTTAA-TTAA
2608896 TATATATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
24 7 0.18
25 14 0.36
26 6 0.15
27 12 0.31
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (25 bp):
AATAAAATATTTTAATTAAGTTAAT
Found at i:2612380 original size:192 final size:197
Alignment explanation
Indices: 2612043--2612420 Score: 538
Period size: 192 Copynumber: 1.9 Consensus size: 197
2612033 TTAGGGTCAT
* *
2612043 ATGGTTGTCCCTTGTTTACATATGTAATGGGATAAGGAGGAGGTAAGATTAGATAGTAGGCTGCC
1 ATGGTTGTCCCTTGTTCACATATGTAATGGGATAAGGAGGAGGTAAGATTA-ATAGTAGGCTGAC
*
2612108 CCCAACATCAGGATGAGATGCAGCTTCCGTAGAAGACCTTCGAATTATGAAATGCCCTCCGCGAG
65 CCCAACATCAGGATGAGATGCAGCTTCCGTAGAAGACCTTCGAATTATGAAATGCCCTCCACGAG
* * *
2612173 ATTCGATCTCACGACCTCAAGGTTAAGAACCTTGTACTCTACCAACTGAGCTGGATAGTCATTTC
130 ACTCGATCACACGACCTCAAGGTTAAGAACCTTATACTCTACCAACTGAGCTGGATAGTCATTTC
2612238 AAA
195 AAA
* * * * *
2612241 ATGGTTGTCTCTTGTTCCCATATGTAATGGGGTAAATGA-GAGGTAAGA-T-A-A-TAGGCTTAC
1 ATGGTTGTCCCTTGTTCACATATGTAATGGGAT-AAGGAGGAGGTAAGATTAATAGTAGGCTGAC
* *
2612301 CCCAACA-CTAGGTTGAGA-GCAGCTTCCGTA-AGAGACCTTCGAATTATGAAATGCCCTCCATG
65 CCCAACATC-AGGATGAGATGCAGCTTCCGTAGA-AGACCTTCGAATTATGAAATGCCCTCCACG
*
2612363 AGACTCGATCACACGACCTCAAGGTTAAGAACCTTATGCTCTACCAACTGAGCTGGAT
128 AGACTCGATCACACGACCTCAAGGTTAAGAACCTTATACTCTACCAACTGAGCTGGAT
2612421 GGCCATTTAA
Statistics
Matches: 163, Mismatches: 14, Indels: 12
0.86 0.07 0.06
Matches are distributed among these distances:
191 1 0.01
192 95 0.58
193 22 0.13
194 1 0.01
195 1 0.01
197 1 0.01
198 38 0.23
199 4 0.02
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (197 bp):
ATGGTTGTCCCTTGTTCACATATGTAATGGGATAAGGAGGAGGTAAGATTAATAGTAGGCTGACC
CCAACATCAGGATGAGATGCAGCTTCCGTAGAAGACCTTCGAATTATGAAATGCCCTCCACGAGA
CTCGATCACACGACCTCAAGGTTAAGAACCTTATACTCTACCAACTGAGCTGGATAGTCATTTCA
AA
Found at i:2615168 original size:16 final size:16
Alignment explanation
Indices: 2615147--2615192 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
2615137 GAACATTATT
2615147 AATTTAATTTATAAAA
1 AATTTAATTTATAAAA
* *
2615163 AATTTAAATTATGAAA
1 AATTTAATTTATAAAA
* *
2615179 GATTTAATGTATAA
1 AATTTAATTTATAA
2615193 TTATAAATTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (16 bp):
AATTTAATTTATAAAA
Found at i:2615212 original size:29 final size:30
Alignment explanation
Indices: 2615162--2615226 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
2615152 AATTTATAAA
2615162 AAATT-TAAATTATGAAAGA-TTT-AATGT
1 AAATTATAAATTATGAAAGATTTTAAATGT
*
2615189 ATAATTATAAATTAGTTAAA-ATTTTAAATGT
1 A-AATTATAAATTA-TGAAAGATTTTAAATGT
2615220 AAATTAT
1 AAATTAT
2615227 TTAAAATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
27 1 0.03
28 4 0.12
29 8 0.25
30 13 0.41
31 6 0.19
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (30 bp):
AAATTATAAATTATGAAAGATTTTAAATGT
Found at i:2617203 original size:19 final size:18
Alignment explanation
Indices: 2617142--2617217 Score: 54
Period size: 19 Copynumber: 4.3 Consensus size: 18
2617132 TTTATGTTAG
*
2617142 TATTTTTTTTAAATAGTTA
1 TATTTTTATTAAATA-TTA
2617161 T-TATTTT-TT--ATATTAA
1 TAT-TTTTATTAAATATT-A
*
2617177 TATATTTATGTAAATATTA
1 TATTTTTAT-TAAATATTA
*
2617196 TATTTTTATTAAA-ATAA
1 TATTTTTATTAAATATTA
2617213 TATTT
1 TATTT
2617218 ATAATTATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 16
0.71 0.05 0.24
Matches are distributed among these distances:
15 2 0.04
16 8 0.17
17 10 0.21
18 8 0.17
19 14 0.30
20 5 0.11
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TATTTTTATTAAATATTA
Found at i:2617215 original size:17 final size:19
Alignment explanation
Indices: 2617174--2617217 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2617164 TTTTTTATAT
*
2617174 TAATATATTTATGTAAATA
1 TAATATTTTTATGTAAATA
*
2617193 TTATATTTTTAT-TAAA-A
1 TAATATTTTTATGTAAATA
2617210 TAATATTT
1 TAATATTT
2617218 ATAATTATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
19 10 0.45
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TAATATTTTTATGTAAATA
Found at i:2617227 original size:32 final size:31
Alignment explanation
Indices: 2617158--2617235 Score: 79
Period size: 32 Copynumber: 2.4 Consensus size: 31
2617148 TTTTAAATAG
*
2617158 TTATTATTTTTTATATTAATATATTTATGTAA
1 TTATTATTTTTTATATAAATATATTTA-GTAA
*
2617190 ATATTATATTTTTAT-TAAAATAATATTTA-TAA
1 TTATTAT-TTTTTATAT-AAAT-ATATTTAGTAA
2617222 TTATTATTTATTTA
1 TTATTATTT-TTTA
2617236 GAATTATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
31 2 0.05
32 20 0.51
33 10 0.26
34 7 0.18
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (31 bp):
TTATTATTTTTTATATAAATATATTTAGTAA
Found at i:2617393 original size:17 final size:17
Alignment explanation
Indices: 2617371--2617424 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
2617361 AATGTTAATA
2617371 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
2617388 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
2617405 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
2617422 TTT
1 TTT
2617425 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:2618270 original size:94 final size:94
Alignment explanation
Indices: 2618109--2618296 Score: 351
Period size: 94 Copynumber: 2.0 Consensus size: 94
2618099 ATGCCCGATC
*
2618109 GTGAATGAACCATACTATTACCCTTATTGTTTAGAGTAATTTTCGAACTAAATTTTGATTTAAAT
1 GTGAATGAACCATACTATTACCCTTATTGTTGAGAGTAATTTTCGAACTAAATTTTGATTTAAAT
2618174 ATTTTCAATTAAATAGGGTGATATTTAGT
66 ATTTTCAATTAAATAGGGTGATATTTAGT
2618203 GTGAATGAACCATACGTATTACCCTTATTGTTGAG-GTAATTTTCGAACTAAATTTTGATTTAAA
1 GTGAATGAACCATAC-TATTACCCTTATTGTTGAGAGTAATTTTCGAACTAAATTTTGATTTAAA
2618267 TATTTTCAATTAAATAGGGTGATATTTAGT
65 TATTTTCAATTAAATAGGGTGATATTTAGT
2618297 TTATATTATA
Statistics
Matches: 92, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
94 74 0.80
95 18 0.20
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.42
Consensus pattern (94 bp):
GTGAATGAACCATACTATTACCCTTATTGTTGAGAGTAATTTTCGAACTAAATTTTGATTTAAAT
ATTTTCAATTAAATAGGGTGATATTTAGT
Found at i:2619093 original size:21 final size:21
Alignment explanation
Indices: 2619067--2619160 Score: 143
Period size: 21 Copynumber: 4.5 Consensus size: 21
2619057 TATGCCATCT
2619067 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
* *
2619088 CCGCAGGGTTACATTCTGAGG
1 CCGCAGGGTTACATTCCGAGC
*
2619109 CTGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
* *
2619130 CCGCAGGGTTACATACCTAGC
1 CCGCAGGGTTACATTCCGAGC
2619151 CCGCAGGGTT
1 CCGCAGGGTT
2619161 TTATACCATA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 65 1.00
ACGTcount: A:0.19, C:0.30, G:0.30, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:2619779 original size:34 final size:32
Alignment explanation
Indices: 2619705--2619772 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
2619695 ATATCATTCG
2619705 AAATTTAAAATAAAAAAATAATATTCAAATTT
1 AAATTTAAAATAAAAAAATAATATTCAAATTT
** *
2619737 AAATTTAAAATATAAATTATAGTATTCGAAATTT
1 AAATTTAAAATA-AAAAAATAATATTC-AAATTT
2619771 AA
1 AA
2619773 CATTAAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 12 0.39
33 11 0.35
34 8 0.26
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (32 bp):
AAATTTAAAATAAAAAAATAATATTCAAATTT
Found at i:2620405 original size:128 final size:128
Alignment explanation
Indices: 2620172--2621310 Score: 2073
Period size: 128 Copynumber: 8.9 Consensus size: 128
2620162 TTACCTGATT
*
2620172 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *** *
2620237 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCACCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
2620300 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
2620365 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
2620428 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
2620493 TGACGAAATAATGGAAGGCGCCCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
** *
2620556 TACTGATATATCGGGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
2620621 TGACAAAATAATGGAAGGCGCCCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
2620684 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
2620749 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
2620812 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
2620877 TGACGAAATAATGGAAGGCGCGCCCCCGGGAATGCGCCTTCATGTGAATAGTGAAATAACAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
2620940 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
2621005 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
2621068 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
2621133 TGACAAAATAATGGAAGGCGTGCCCCCGGGAACACGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
2621196 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
2621261 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATA
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATA
2621311 ATACTCCGAT
Statistics
Matches: 977, Mismatches: 33, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
127 1 0.00
128 976 1.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:2621396 original size:8 final size:8
Alignment explanation
Indices: 2621383--2621423 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
2621373 TCACAATCTT
2621383 TCAAATTC
1 TCAAATTC
2621391 TCAAATTC
1 TCAAATTC
* *
2621399 CCAAACTC
1 TCAAATTC
2621407 T-AAATTC
1 TCAAATTC
2621414 TCAAATTC
1 TCAAATTC
2621422 TC
1 TC
2621424 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:2631966 original size:21 final size:21
Alignment explanation
Indices: 2631940--2632084 Score: 80
Period size: 21 Copynumber: 6.9 Consensus size: 21
2631930 TATATAAAAT
*
2631940 TGTCCC-AAATAACCTCATATA
1 TGTCCCGAAA-AACCACATATA
*
2631961 TGTCCCGAAAGACCACATATA
1 TGTCCCGAAAAACCACATATA
* * ** *
2631982 TGTCTCTAAGGACCATATATA
1 TGTCCCGAAAAACCACATATA
* * *
2632003 TGTTCC-AAAGGACCACATACA
1 TGTCCCGAAA-AACCACATATA
* * *
2632024 TGTCCTGAAAGACCTCATATA
1 TGTCCCGAAAAACCACATATA
* * *
2632045 TGTTCC-AAAGGATCACATATA
1 TGTCCCGAAA-AACCACATATA
**
2632066 TGTCCCGAAGGACCACATA
1 TGTCCCGAAAAACCACATA
2632085 GAACCCTCGA
Statistics
Matches: 97, Mismatches: 22, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
20 5 0.05
21 84 0.87
22 8 0.08
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.25
Consensus pattern (21 bp):
TGTCCCGAAAAACCACATATA
Found at i:2632004 original size:42 final size:42
Alignment explanation
Indices: 2631954--2632084 Score: 153
Period size: 42 Copynumber: 3.1 Consensus size: 42
2631944 CCAAATAACC
*
2631954 TCATATATGTCCCGAAA-GACCACATATATGTCTCTAAGGACCA
1 TCATATATGTTCC-AAAGGACCACATATATGTC-CTAAGGACCA
* *
2631997 T-ATATATGTTCCAAAGGACCACATACATGTCCTGAAAGACC-
1 TCATATATGTTCCAAAGGACCACATATATGTCCT-AAGGACCA
* *
2632038 TCATATATGTTCCAAAGGATCACATATATGTCCCGAAGGACCA
1 TCATATATGTTCCAAAGGACCACATATATGT-CCTAAGGACCA
2632081 -CATA
1 TCATA
2632085 GAACCCTCGA
Statistics
Matches: 76, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
41 6 0.08
42 67 0.88
43 3 0.04
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (42 bp):
TCATATATGTTCCAAAGGACCACATATATGTCCTAAGGACCA
Found at i:2632027 original size:63 final size:63
Alignment explanation
Indices: 2631940--2632084 Score: 175
Period size: 63 Copynumber: 2.3 Consensus size: 63
2631930 TATATAAAAT
** * * * *
2631940 TGTCCCAAATAACCTCATATATGTCCCGAAAGACCACATATATG-TCTCTAAGGACCATATATA
1 TGTCCCAAAGGACCACATACATGTCCCGAAAGACCACATATATGTTC-CAAAGGACCACATATA
* * * *
2632003 TGTTCCAAAGGACCACATACATGTCCTGAAAGACCTCATATATGTTCCAAAGGATCACATATA
1 TGTCCCAAAGGACCACATACATGTCCCGAAAGACCACATATATGTTCCAAAGGACCACATATA
*
2632066 TGTCCCGAAGGACCACATA
1 TGTCCCAAAGGACCACATA
2632085 GAACCCTCGA
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
63 67 0.97
64 2 0.03
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.25
Consensus pattern (63 bp):
TGTCCCAAAGGACCACATACATGTCCCGAAAGACCACATATATGTTCCAAAGGACCACATATA
Found at i:2637305 original size:23 final size:24
Alignment explanation
Indices: 2637270--2637315 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2637260 TTGTATTGAT
2637270 TAATAATTATT-AAAAAATTAATA
1 TAATAATTATTAAAAAAATTAATA
* *
2637293 TAATTATTTTTAAAAAAATTAAT
1 TAATAATTATTAAAAAAATTAAT
2637316 TCTTGCTGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TAATAATTATTAAAAAAATTAATA
Found at i:2641690 original size:41 final size:41
Alignment explanation
Indices: 2641644--2641725 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
2641634 TCTGGAATCA
2641644 GCTTTAAAAGAAACGACAGCTCCTGCTGTGAGAACTGCACC
1 GCTTTAAAAGAAACGACAGCTCCTGCTGTGAGAACTGCACC
2641685 GCTTTAAAAGAAACGACAGCTCCTGCTGTGAGAACTGCACC
1 GCTTTAAAAGAAACGACAGCTCCTGCTGTGAGAACTGCACC
2641726 TTCGACTTCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.20
Consensus pattern (41 bp):
GCTTTAAAAGAAACGACAGCTCCTGCTGTGAGAACTGCACC
Found at i:2646453 original size:21 final size:21
Alignment explanation
Indices: 2646411--2646453 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2646401 TTTCTGGGTT
* * *
2646411 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
2646432 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
2646453 A
1 A
2646454 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:2646519 original size:67 final size:65
Alignment explanation
Indices: 2646433--2646581 Score: 174
Period size: 68 Copynumber: 2.2 Consensus size: 65
2646423 ACCCATTCAA
* * * *
2646433 GGGGAACCGATACCCCCTCAACG-AAATGAATTTTCAGAATGCTAGAGGGGAATCGGTACCCCCA
1 GGGGAACCGATA-CCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGAGGAATCGATA-CCCCA
2646497 GGG
64 -GG
* * * *
2646500 GGGGAAACCGATACCCCTCATCGTATATGAAATTCCAGATTGCTTGAGAGGAATCGATACCCCAG
1 GGGG-AACCGATACCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGAGGAATCGATACCCCAG
2646565 G
65 G
*
2646566 GGGGAACCGATTCCCC
1 GGGGAACCGATACCCC
2646582 CATGAGAAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
65 11 0.15
66 6 0.08
67 18 0.25
68 36 0.51
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.18
Consensus pattern (65 bp):
GGGGAACCGATACCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGAGGAATCGATACCCCAGG
Found at i:2646914 original size:29 final size:29
Alignment explanation
Indices: 2646880--2646951 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
2646870 CATATTATGA
**
2646880 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
2646909 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
2646938 TACATGACATGAAT
1 TACATGACATGAAT
2646952 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:2647008 original size:30 final size:31
Alignment explanation
Indices: 2646966--2647025 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
2646956 AGAAAAAGTT
*
2646966 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
2646997 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
2647026 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:2647273 original size:22 final size:22
Alignment explanation
Indices: 2647245--2647311 Score: 118
Period size: 22 Copynumber: 3.0 Consensus size: 22
2647235 TTATGGACAT
2647245 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
2647267 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
2647289 AA-TCTACGGGGCACTTCGGTGC
1 AATTCTAC-GGGCACTTCGGTGC
2647311 A
1 A
2647312 TTTATACGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
21 5 0.11
22 39 0.89
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:2651167 original size:52 final size:51
Alignment explanation
Indices: 2651102--2651205 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 51
2651092 GATGGTCTTT
2651102 GTGCAGATTAACCCTTAACCAGCATGGTTGGAACGAATAGGAGAATTGCAA
1 GTGCAGATTAACCCTTAACCAGCATGGTTGGAACGAATAGGAGAATTGCAA
2651153 GTGCAGAATTAACCCTTAACCAGCATGGTTGGAACGAATAGGAGAATTGCAA
1 GTGCAG-ATTAACCCTTAACCAGCATGGTTGGAACGAATAGGAGAATTGCAA
2651205 G
1 G
2651206 GTAAAGATGA
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 6 0.12
52 46 0.88
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (51 bp):
GTGCAGATTAACCCTTAACCAGCATGGTTGGAACGAATAGGAGAATTGCAA
Found at i:2653238 original size:21 final size:21
Alignment explanation
Indices: 2653196--2653238 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2653186 TTTCTGGGTT
* * *
2653196 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
2653217 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
2653238 A
1 A
2653239 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:2653304 original size:67 final size:67
Alignment explanation
Indices: 2653218--2653368 Score: 214
Period size: 67 Copynumber: 2.3 Consensus size: 67
2653208 ACCCATTCAA
* * *
2653218 GGGGAACCGATACCCCCTCAACG-AAATGAATTTCCAGAATGCTAGAGGGGAATCGGTACCCCCA
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGAGGAATCGATACCCCCA
2653282 GGG
66 -GG
* * * *
2653285 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGAGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGAGGAATCGATACCCCCA
2653350 GG
66 GG
*
2653352 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
2653369 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
67 40 0.53
68 35 0.47
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.17
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGAGGAATCGATACCCCCA
GG
Found at i:2653704 original size:29 final size:29
Alignment explanation
Indices: 2653670--2653741 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
2653660 CATATTATGA
**
2653670 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
2653699 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
2653728 TACATGACATGAAT
1 TACATGACATGAAT
2653742 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:2653798 original size:30 final size:31
Alignment explanation
Indices: 2653756--2653815 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
2653746 AGAAAAAGTT
*
2653756 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
2653787 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
2653816 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:2654095 original size:23 final size:22
Alignment explanation
Indices: 2654035--2654102 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
2654025 TTATGGACAT
2654035 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
2654057 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
2654079 AATTCTACGGGGCACTTCGGTGC
1 AATTCTAC-GGGCACTTCGGTGC
2654102 A
1 A
2654103 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 30 0.67
23 15 0.33
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.26
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:2656125 original size:39 final size:39
Alignment explanation
Indices: 2656079--2656155 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
2656069 TTATTTTTTT
*
2656079 AATCCTTTTTGGTATAAGTATCATATTTGATTTATTAAA
1 AATCCTTTTTGGTATAAGTATCATATTCGATTTATTAAA
2656118 AATCCTTTTTGGTATAAGTATCATATTCGATTTATTAA
1 AATCCTTTTTGGTATAAGTATCATATTCGATTTATTAA
2656156 TCGATTAATC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.32, C:0.09, G:0.10, T:0.48
Consensus pattern (39 bp):
AATCCTTTTTGGTATAAGTATCATATTCGATTTATTAAA
Found at i:2657328 original size:182 final size:181
Alignment explanation
Indices: 2656774--2657494 Score: 946
Period size: 182 Copynumber: 4.0 Consensus size: 181
2656764 GATACAAATG
* * ** * * * * * *
2656774 AAAAATGTATCGCTCTATAGTAATATTACAGGTAAAAATATGATAAATCCGGTTTCGAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCAAAATGACA
* * *
2656839 AAATCGGTAAA-ACGATATCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTT
66 AAACCGATAAAGA-AATATCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTT
2656903 TTGGAATTTAAAAGAGAAGAAGTTATAGCGCATATAAAGTGTCGATACTTTA
130 TTGGAATTTAAAAGAGAAGAAGTTATAGCGCATATAAAGTGTCGATACTTTA
* * ** *
2656955 AAAAATGTATTGATCCATAACAATATAACATGTAAAACTATGACAAAACATGTCTAAAAAATGAC
1 AAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCT-CAAAATGAC
* * * * *
2657020 AAAACCGATAAAAAAATATCAGATATGTTGAAGGTGTCGATAATTTAATATAAGTATCGAATATT
65 AAAACCGATAAAGAAATATCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCG-ACACT
2657085 TTTGGAATTTAAAAGAGAAGAAGTTATAGCGCATATAAAGTGTCGATACTTTAA
129 TTTGGAATTTAAAAGAGAAGAAGTTATAGCGCATATAAAGTGTCGATACTTT-A
*
2657139 AAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCCCAAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCAAAATGACA
* * * ** * *
2657204 AATCTGGTAAAGAGCTA-CTGGATATGTTGAATGTGTTGATAATTTAATATAAGTATCGACACTT
66 AAACCGATAAAGAAATATC-GGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTT
* * * **
2657268 TCT-GAATTTAAAAGAGAATAAGTTATAGCGCCTAAAAAGTGTTAATACTTTA
130 T-TGGAATTTAAAAGAGAAGAAGTTATAGCGCATATAAAGTGTCGATACTTTA
* * *
2657320 TGAAAATGTATCGATCTATAACAATATAACA-GCTAAAAATATGACAAAACCGATCTCAAAATGA
1 -AAAAATGTATCGATCCATAACAATATAACATG-TAAAAATATGACAAAACCGGTCTCAAAATGA
* * *
2657384 CAAAACCGATAAAGAACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACT
64 CAAAACCGATAAAGAAATATCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACT
* *
2657449 TTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTATCGA
129 TTTGGAATTTAAAAGAGAAGAAGTTATAGCGCATATAAAGTGTCGA
2657495 CACTCTTTAA
Statistics
Matches: 470, Mismatches: 60, Indels: 19
0.86 0.11 0.03
Matches are distributed among these distances:
181 45 0.10
182 260 0.55
183 114 0.24
184 51 0.11
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.29
Consensus pattern (181 bp):
AAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCAAAATGACA
AAACCGATAAAGAAATATCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
TGGAATTTAAAAGAGAAGAAGTTATAGCGCATATAAAGTGTCGATACTTTA
Found at i:2657444 original size:365 final size:364
Alignment explanation
Indices: 2656774--2657494 Score: 1006
Period size: 365 Copynumber: 2.0 Consensus size: 364
2656764 GATACAAATG
* * ** * * * ** *
2656774 AAAAATGTATCGCTCTATAGTAATATTACAGGTAAAAATATGATAAATCCGGTTTCGAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCCCAAAATGACA
2656839 AAATCGGTAAAACGATATCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
66 AAATCGGTAAAACGATATCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
* * *
2656904 TGGAATTTAAAAGAGAAGAAGTTATAGCGCATATAAAGTGTCGATACTTTAAAAAATGTATTGAT
131 TGGAATTTAAAAGAGAAGAAGTTATAGCGCATAAAAAGTGTCAATACTTTAAAAAATGTATCGAT
* *
2656969 CCATAACAATATAACATGTAAAACTATGACAAAACATGTCTAAAAAATGACAAAACCGATAAAAA
196 CCATAACAATATAACATGTAAAAATATGACAAAACACGTCTAAAAAATGACAAAACCGATAAAAA
* * * *
2657034 AATATCAGATATGTTGAAGGTGTCGATAATTTAATATAAGTATCGAATATTTTTGGAATTTAAAA
261 AATACCAGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCG-ACACTTTTGGAATTTAAAA
*
2657099 GAGAAGAAGTTATAGCGCATATAAAGTGTCGATACTTTAA
325 GAGAAGAAGTTATAGCGCATATAAAGTATCGATACTTTAA
*
2657139 AAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCCCAAAATGAC-
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCCCAAAATGACA
* * *
2657203 AAATCTGGTAAAGA-GCTA-CTGGATATGTTGAATGTGTTGATAATTTAATATAAGTATCGACAC
66 AAATC-GGTAAA-ACGATATC-GGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACAC
* * * *
2657266 TTTCT-GAATTTAAAAGAGAATAAGTTATAGCGCCTAAAAAGTGTTAATACTTTATGAAAATGTA
128 TTT-TGGAATTTAAAAGAGAAGAAGTTATAGCGCATAAAAAGTGTCAATACTTTA-AAAAATGTA
* *
2657330 TCGATCTATAACAATATAACA-GCTAAAAATATGACAAAAC-CGATCT-CAAAATGACAAAACCG
191 TCGATCCATAACAATATAACATG-TAAAAATATGACAAAACACG-TCTAAAAAATGACAAAACCG
* * * *
2657392 ATAAAGAACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTTGGAAT
254 ATAAAAAAATACCAGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTTGGAAT
*
2657457 TTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTATCGA
319 TTAAAAGAGAAGAAGTTATAGCGCATATAAAGTATCGA
2657495 CACTCTTTAA
Statistics
Matches: 314, Mismatches: 35, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
364 53 0.17
365 213 0.68
366 48 0.15
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.29
Consensus pattern (364 bp):
AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCCCAAAATGACA
AAATCGGTAAAACGATATCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
TGGAATTTAAAAGAGAAGAAGTTATAGCGCATAAAAAGTGTCAATACTTTAAAAAATGTATCGAT
CCATAACAATATAACATGTAAAAATATGACAAAACACGTCTAAAAAATGACAAAACCGATAAAAA
AATACCAGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTTGGAATTTAAAAG
AGAAGAAGTTATAGCGCATATAAAGTATCGATACTTTAA
Found at i:2657960 original size:23 final size:23
Alignment explanation
Indices: 2657930--2657981 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
2657920 TCCTGTTAAA
** *
2657930 TACCTATTTTATTATATAAGCAC
1 TACCTATTACATTATATAAGAAC
*
2657953 TACCTATTACATTATATAAGAAT
1 TACCTATTACATTATATAAGAAC
2657976 TACCTA
1 TACCTA
2657982 ATATGTTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.40
Consensus pattern (23 bp):
TACCTATTACATTATATAAGAAC
Found at i:2667152 original size:16 final size:16
Alignment explanation
Indices: 2667131--2667171 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
2667121 TATTCACATA
*
2667131 AATAGTGAATTTCGTT
1 AATAGTAAATTTCGTT
*
2667147 AATAGTAAATTTCGTG
1 AATAGTAAATTTCGTT
*
2667163 AAAAGTAAA
1 AATAGTAAA
2667172 ATTTGGTCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.44, C:0.05, G:0.17, T:0.34
Consensus pattern (16 bp):
AATAGTAAATTTCGTT
Found at i:2669491 original size:22 final size:22
Alignment explanation
Indices: 2669465--2669509 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
2669455 CAGGTTGAAG
2669465 AAGAGCTT-GTATGGTTTAAAAC
1 AAGAGCTTCG-ATGGTTTAAAAC
*
2669487 AAGAGGTTCGATGGTTTAAAAC
1 AAGAGCTTCGATGGTTTAAAAC
2669509 A
1 A
2669510 TCAGGAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (22 bp):
AAGAGCTTCGATGGTTTAAAAC
Found at i:2672025 original size:19 final size:19
Alignment explanation
Indices: 2672001--2672038 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2671991 CATATACTCA
2672001 CCATGCAGACGAGCCATAC
1 CCATGCAGACGAGCCATAC
2672020 CCATGCAGACGAGCCATAC
1 CCATGCAGACGAGCCATAC
2672039 AAGCCATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.37, G:0.21, T:0.11
Consensus pattern (19 bp):
CCATGCAGACGAGCCATAC
Found at i:2672097 original size:32 final size:32
Alignment explanation
Indices: 2672053--2672123 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
2672043 CATATACTCA
* *
2672053 CCATGCAGACGAGCCAGCCAACGGAGAGGTCG
1 CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
*
2672085 CCATGCAAACGAGCCAGCCAATAGAGAGGTCG
1 CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
2672117 CCATGCA
1 CCATGCA
2672124 GTCTGGGCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.31, C:0.31, G:0.30, T:0.08
Consensus pattern (32 bp):
CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
Found at i:2672215 original size:29 final size:29
Alignment explanation
Indices: 2672111--2672205 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
2672101 GCCAATAGAG
* **
2672111 AGGTCGCCATGCAGTCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
2672140 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
2672169 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
2672198 AGGTCGCC
1 AGGTCGCC
2672206 CCGGCGTCCC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.14, C:0.31, G:0.33, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:2672274 original size:50 final size:50
Alignment explanation
Indices: 2672232--2672347 Score: 170
Period size: 50 Copynumber: 2.4 Consensus size: 50
2672222 CCCGAGACCA
*
2672232 TGCATG-C-ACATGCA-GCCAA-ATAACTTCACGTGCTCCTGCTCCCCGC
1 TGCATGCCTACATGCATGCCAAGATAACTTCACGTGCTCCTGCTCCCAGC
* *
2672278 TGCATGCCTGCATGCATGCCAAGATAACTTCACGTGCTCCTGCTCCCCGC
1 TGCATGCCTACATGCATGCCAAGATAACTTCACGTGCTCCTGCTCCCAGC
2672328 TGCATGCCTACA-GCATGCCA
1 TGCATGCCTACATGCATGCCA
2672348 TGTGATCCTA
Statistics
Matches: 64, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
46 6 0.09
47 1 0.02
48 6 0.09
49 13 0.20
50 38 0.59
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.22
Consensus pattern (50 bp):
TGCATGCCTACATGCATGCCAAGATAACTTCACGTGCTCCTGCTCCCAGC
Found at i:2672495 original size:16 final size:16
Alignment explanation
Indices: 2672474--2672536 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
2672464 CACACATAAA
2672474 AGAAAGAAAGAAAGGG
1 AGAAAGAAAGAAAGGG
** * *
2672490 AGAAAGATTG-CAGCCG
1 AGAAAGAAAGAAAG-GG
2672506 AGAAAGAAAGAAAGGG
1 AGAAAGAAAGAAAGGG
2672522 AGAAAGAAAGGAAAG
1 AGAAAGAAA-GAAAG
2672537 TAAGAAGAAG
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
15 2 0.06
16 27 0.75
17 7 0.19
ACGTcount: A:0.57, C:0.05, G:0.35, T:0.03
Consensus pattern (16 bp):
AGAAAGAAAGAAAGGG
Found at i:2672761 original size:43 final size:41
Alignment explanation
Indices: 2672657--2672765 Score: 116
Period size: 41 Copynumber: 2.6 Consensus size: 41
2672647 TACATAAATT
*
2672657 AAAAATTATTTAATTAGTATATGTT-TGATAGTTATAGTTAAA
1 AAAAATTATTTAATTAGT-TTTGTTATGATAGTTATAG-TAAA
* * *
2672699 AAAAATTAATTAGTT-GTTTTGTTAATAGTTAGTTATA-TAAA
1 AAAAATTATTTAATTAGTTTTGTT-AT-GATAGTTATAGTAAA
2672740 AAAAATTATTTAATTAGGTTTTGTTA
1 AAAAATTATTTAATTA-GTTTTGTTA
2672766 GTTAAATAGT
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
40 5 0.09
41 19 0.34
42 15 0.27
43 17 0.30
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (41 bp):
AAAAATTATTTAATTAGTTTTGTTATGATAGTTATAGTAAA
Found at i:2672855 original size:30 final size:32
Alignment explanation
Indices: 2672820--2672893 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
2672810 TTAGTTAGTA
2672820 AGTTTATTAGTAG-TATA-TTA-ATGAAAAAAT
1 AGTTTATTAGTAGTTATAGTTATAT-AAAAAAT
*
2672850 AGTTTATTAGTTAGTTTTAGTTATATAAAAAAT
1 AGTTTATTAG-TAGTTATAGTTATATAAAAAAT
*
2672883 ATTTTATTAGT
1 AGTTTATTAGT
2672894 TGTTTAAGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 10 0.26
31 3 0.08
32 4 0.11
33 19 0.50
34 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (32 bp):
AGTTTATTAGTAGTTATAGTTATATAAAAAAT
Found at i:2674379 original size:26 final size:25
Alignment explanation
Indices: 2674343--2674807 Score: 275
Period size: 26 Copynumber: 18.7 Consensus size: 25
2674333 ATCCAATTTT
2674343 TATAATGATTATTACTAAATCATTAC
1 TATAATGATTATTA-TAAATCATTAC
2674369 TATAATGATTATTATCAAATCATTAC
1 TATAATGATTATTAT-AAATCATTAC
* * *
2674395 TA-AATCATCAAATCATTAAAT-ATT--
1 TATAATGAT--TATTA-TAAATCATTAC
* **
2674419 TA-AATCATTA-T-TAAATCATTTT
1 TATAATGATTATTATAAATCATTAC
*
2674441 TATAATGATTATTACTAAATCATTAT
1 TATAATGATTATTA-TAAATCATTAC
2674467 TATAATGATTATTATCAAATCATTAC
1 TATAATGATTATTAT-AAATCATTAC
2674493 TATAATGATTATTATCAAATCATTAC
1 TATAATGATTATTAT-AAATCATTAC
* * *
2674519 TA-AATCATCAAATCATTAAAT-ATT--
1 TATAATGAT--TATTA-TAAATCATTAC
* *
2674543 TA-AATCATTA-T-TAAA-CATT-T
1 TATAATGATTATTATAAATCATTAC
2674563 TATAATGATTATTACTAAATCATTAC
1 TATAATGATTATTA-TAAATCATTAC
2674589 TATAATGATTATTATCAAATCATTAC
1 TATAATGATTATTAT-AAATCATTAC
* * *
2674615 TA-AATCATCAAATCATTAAAT-ATT--
1 TATAATGAT--TATTA-TAAATCATTAC
* **
2674639 TA-AATCATTA-T-TAAATCATTTT
1 TATAATGATTATTATAAATCATTAC
*
2674661 TATAATGATTATTACT-AAT-ATTAT
1 TATAATGATTATTA-TAAATCATTAC
2674685 TATAATGATTATTATCAAATCATTAC
1 TATAATGATTATTAT-AAATCATTAC
2674711 TATAATGATTATTATCAAATCATTAC
1 TATAATGATTATTAT-AAATCATTAC
* * *
2674737 TAATCAAATCATTAAATATTAAATCATTAT
1 T-AT--AATGATT-ATTA-TAAATCATTAC
* *
2674767 TA-AATCATTTTTATAATGAT-ATTAC
1 TATAATGATTATTATAA--ATCATTAC
*
2674792 TA-AATCATTATTATAA
1 TATAATGATTATTATAA
2674808 TGATTATTAT
Statistics
Matches: 365, Mismatches: 30, Indels: 89
0.75 0.06 0.18
Matches are distributed among these distances:
19 17 0.05
20 8 0.02
21 7 0.02
22 8 0.02
23 15 0.04
24 51 0.14
25 49 0.13
26 163 0.45
27 23 0.06
28 3 0.01
29 7 0.02
30 13 0.04
31 1 0.00
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.43
Consensus pattern (25 bp):
TATAATGATTATTATAAATCATTAC
Found at i:2674550 original size:35 final size:33
Alignment explanation
Indices: 2674500--2674657 Score: 98
Period size: 35 Copynumber: 4.8 Consensus size: 33
2674490 TACTATAATG
* *
2674500 ATTATTATCAAATCATTACTAAATCATCAAATC
1 ATTAATATTAAATCATTACTAAATCATCAAATC
* * *
2674533 ATTAAATATTTAAATCATTATTAAA-CATTTTATAATG
1 ATT-AATA-TTAAATCATTACTAAATCA--TCA-AATC
* * *
2674570 ATTATTACTAAATCATTAC----T-AT--AATG
1 ATTAATATTAAATCATTACTAAATCATCAAATC
* *
2674596 ATTATTATCAAATCATTACTAAATCATCAAATC
1 ATTAATATTAAATCATTACTAAATCATCAAATC
*
2674629 ATTAAATATTTAAATCATTATTAAATCAT
1 ATT-AATA-TTAAATCATTACTAAATCAT
2674658 TTTTATAATG
Statistics
Matches: 96, Mismatches: 14, Indels: 28
0.70 0.10 0.20
Matches are distributed among these distances:
26 21 0.22
29 1 0.01
30 1 0.01
31 3 0.03
33 9 0.09
34 8 0.08
35 42 0.44
36 5 0.05
37 6 0.06
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.41
Consensus pattern (33 bp):
ATTAATATTAAATCATTACTAAATCATCAAATC
Found at i:2674575 original size:21 final size:19
Alignment explanation
Indices: 2674533--2674576 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
2674523 TCATCAAATC
*
2674533 ATTAAATATTTAAATCATT
1 ATTAAACATTTAAATCATT
*
2674552 ATTAAACATTTTATAATGATT
1 ATTAAACA-TTTA-AATCATT
2674573 ATTA
1 ATTA
2674577 CTAAATCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.33
20 4 0.19
21 10 0.48
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (19 bp):
ATTAAACATTTAAATCATT
Found at i:2674591 original size:96 final size:97
Alignment explanation
Indices: 2674451--2674830 Score: 455
Period size: 96 Copynumber: 3.7 Consensus size: 97
2674441 TATAATGATT
*
2674451 ATTACTAAATCATTATTATAATGATTATTA-TCAAATCATTACTATAATGATTATTATCAAATCA
1 ATTATTAAATCATT-TTATAATGATTATTACT-AAATCATTACTATAATGATTATTATCAAATCA
2674515 TTACTAAATCATCAAATCATTAAATATTTAAATC
64 TTACTAAATCATCAAATCATTAAATATTTAAATC
2674549 ATTATTAAA-CATTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATT
1 ATTATTAAATCATTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATT
2674613 ACTAAATCATCAAATCATTAAATATTTAAATC
66 ACTAAATCATCAAATCATTAAATATTTAAATC
*
2674645 ATTATTAAATCATTTTTATAATGATTATTACT-AAT-ATTATTATAATGATTATTATCAAATCAT
1 ATTATTAAATCA-TTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCAT
* *
2674708 TACTATAATGATTATTATCAAATCATTACTAATCAAATCATTAAATATTAA
65 TAC--T-A--A--ATCATCAAATCATTA--AAT---AT--TT-AA-A-T-C
*
2674759 ATCATTATTAAATCATTTTTATAATGA-TATTACTAAATCATTATTATAATGATTATTATCAAAT
1 A---TTATTAAATCA-TTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAAT
2674823 CATTACTA
62 CATTACTA
2674831 TAATGATTAT
Statistics
Matches: 252, Mismatches: 4, Indels: 35
0.87 0.01 0.12
Matches are distributed among these distances:
96 120 0.48
97 10 0.04
98 28 0.11
99 1 0.00
101 1 0.00
103 14 0.06
105 3 0.01
108 2 0.01
110 2 0.01
111 2 0.01
112 1 0.00
113 1 0.00
114 1 0.00
115 1 0.00
116 8 0.03
117 26 0.10
118 31 0.12
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (97 bp):
ATTATTAAATCATTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATT
ACTAAATCATCAAATCATTAAATATTTAAATC
Found at i:2674688 original size:122 final size:121
Alignment explanation
Indices: 2674427--2674855 Score: 335
Period size: 122 Copynumber: 3.5 Consensus size: 121
2674417 TTTAAATCAT
2674427 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCA-TTTTATAATGATTATTACT-AAT-ATTATTATAATGATTATTATCAAATCATTA
2674492 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
63 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
*
2674551 TATTAAA-CATTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTAC
1 TATTAAATCATTTTATAATGATTATTACT-AAT-ATTATTATAATGATTATTATCAAATCATTAC
* * * * *
2674615 TA-AATCATCAAATCATTAAAT-ATT--TAAATCAT----T-ATTAAATCATTTTTATAATGAT
64 TATAATGAT--TATTATCAAATCATTACTAAATCATCAAATCATTAAAT-A--TTTA-AATCAT
* *
2674670 TATTACTAAT-ATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
1 TATTA--AATCATT-TTATAATGATTATTA-CTAAT-ATTATTATAATGATTATTATCAAATCAT
* * * * * * *
2674734 TACTAATCAAATCATTAAATATTAAATCATTATTAAATCAT----T--TT-TATA-AT-GAT-AT
61 TACT-AT--AATGATT-ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
* * *
2674789 TACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATC-AATCATTA
1 TATTAAATCATT-TTATAATGATTATTA-CTAAT-ATTATTATAATGATTATTATCAAATCATTA
2674853 CTA
63 CTA
2674856 AATCATCAAA
Statistics
Matches: 271, Mismatches: 14, Indels: 48
0.81 0.04 0.14
Matches are distributed among these distances:
115 7 0.03
116 3 0.01
117 13 0.05
118 51 0.19
119 16 0.06
120 10 0.04
121 10 0.04
122 111 0.41
123 12 0.04
124 7 0.03
125 9 0.03
126 11 0.04
127 2 0.01
128 9 0.03
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (121 bp):
TATTAAATCATTTTATAATGATTATTACTAATATTATTATAATGATTATTATCAAATCATTACTA
TAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
Found at i:2674742 original size:15 final size:14
Alignment explanation
Indices: 2674692--2674855 Score: 79
Period size: 12 Copynumber: 12.5 Consensus size: 14
2674682 TATTATAATG
*
2674692 ATTATTATCAAATC
1 ATTACTATCAAATC
*
2674706 ATTACTAT--AATG
1 ATTACTATCAAATC
*
2674718 ATTATTATCAAATC
1 ATTACTATCAAATC
2674732 ATTACTAATCAAATC
1 ATTACT-ATCAAATC
* *
2674747 ATTAAATATTAAATC
1 ATT-ACTATCAAATC
2674762 ATTA-T-T-AAATC
1 ATTACTATCAAATC
**
2674773 ATTTTTAT-AATGAT-
1 ATTACTATCAA--ATC
2674787 ATTAC--T-AAATC
1 ATTACTATCAAATC
* *
2674798 ATTATTAT--AATG
1 ATTACTATCAAATC
*
2674810 ATTATTATCAAATC
1 ATTACTATCAAATC
*
2674824 ATTACTAT--AATG
1 ATTACTATCAAATC
*
2674836 ATTATTATC-AATC
1 ATTACTATCAAATC
2674849 ATTACTA
1 ATTACTA
2674856 AATCATCAAA
Statistics
Matches: 118, Mismatches: 18, Indels: 29
0.72 0.11 0.18
Matches are distributed among these distances:
10 2 0.02
11 12 0.10
12 36 0.31
13 14 0.12
14 29 0.25
15 23 0.19
16 2 0.02
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.43
Consensus pattern (14 bp):
ATTACTATCAAATC
Found at i:2674795 original size:25 final size:25
Alignment explanation
Indices: 2674635--2674852 Score: 139
Period size: 26 Copynumber: 8.6 Consensus size: 25
2674625 AATCATTAAA
*
2674635 TATT-TAAATCATTATTA-AATCAT
1 TATTATAAATCATTATTATAATGAT
* *
2674658 TTTTAT-AATGATTATTACTAAT-AT
1 TATTATAAATCATTATTA-TAATGAT
* *
2674682 TATTAT-AATGATTATTATCAAATCAT
1 TATTATAAATCATTATTAT--AATGAT
* * *
2674708 TACTAT-AATGATTATTATCAAATCAT
1 TATTATAAATCATTATTAT--AATGAT
* *
2674734 TACTAATCAAATCATTAAATATTAA--AT
1 TA-TTAT-AAATCATT-ATTA-TAATGAT
* *
2674761 CATTATTAAATCATTTTTATAATGA-
1 TATTA-TAAATCATTATTATAATGAT
2674786 TATTACTAAATCATTATTATAATGAT
1 TATTA-TAAATCATTATTATAATGAT
*
2674812 TATTATCAAATCATTACTATAATGAT
1 TATTAT-AAATCATTATTATAATGAT
*
2674838 TATTATCAATCATTA
1 TATTATAAATCATTA
2674853 CTAAATCATC
Statistics
Matches: 162, Mismatches: 17, Indels: 30
0.78 0.08 0.14
Matches are distributed among these distances:
23 14 0.09
24 22 0.14
25 39 0.24
26 69 0.43
27 6 0.04
29 8 0.05
30 3 0.02
31 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (25 bp):
TATTATAAATCATTATTATAATGAT
Found at i:2674852 original size:220 final size:219
Alignment explanation
Indices: 2674338--2674830 Score: 901
Period size: 220 Copynumber: 2.3 Consensus size: 219
2674328 TTGAGATCCA
2674338 ATTTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCAT
1 ATTTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCAT
2674403 CAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATT
66 CAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATT
2674468 ATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATC
131 ATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACT-AA-CATCAAATC
2674533 ATTAAATATTTAAATCATTATTAAAC
194 ATTAAATATTTAAATCATTATTAAAC
2674559 A-TTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCAT
1 ATTTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCAT
2674623 CAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATTACT-AAT-ATTATT
66 CAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATT
2674686 ATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACT-A-ATCAAATCAT
131 ATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAACATCAAATCAT
2674749 TAAATA-TTAAATCATTATTAAATC
196 TAAATATTTAAATCATTATTAAA-C
*
2674773 ATTTTTATAATGA-TATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTA
1 ATTTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTACTA
2674831 TAATGATTAT
Statistics
Matches: 269, Mismatches: 1, Indels: 11
0.96 0.00 0.04
Matches are distributed among these distances:
213 16 0.06
214 62 0.23
215 11 0.04
216 1 0.00
218 58 0.22
219 3 0.01
220 117 0.43
221 1 0.00
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (219 bp):
ATTTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCAT
CAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATT
ATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAACATCAAATCAT
TAAATATTTAAATCATTATTAAAC
Found at i:2676756 original size:75 final size:75
Alignment explanation
Indices: 2676633--2676782 Score: 300
Period size: 75 Copynumber: 2.0 Consensus size: 75
2676623 ACTTGCACTC
2676633 TGGGCCATATTTTACACACTTTGCGTATAGGGTTTTCTGGTTGGACTCTGCAACATGGACATCAA
1 TGGGCCATATTTTACACACTTTGCGTATAGGGTTTTCTGGTTGGACTCTGCAACATGGACATCAA
2676698 CATGGCATTT
66 CATGGCATTT
2676708 TGGGCCATATTTTACACACTTTGCGTATAGGGTTTTCTGGTTGGACTCTGCAACATGGACATCAA
1 TGGGCCATATTTTACACACTTTGCGTATAGGGTTTTCTGGTTGGACTCTGCAACATGGACATCAA
2676773 CATGGCATTT
66 CATGGCATTT
2676783 GATGCAGTAC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (75 bp):
TGGGCCATATTTTACACACTTTGCGTATAGGGTTTTCTGGTTGGACTCTGCAACATGGACATCAA
CATGGCATTT
Found at i:2677821 original size:26 final size:24
Alignment explanation
Indices: 2677761--2677821 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 24
2677751 TTACTATATT
*
2677761 ATTAATAATGATTTAATAATTATT
1 ATTAATAATGATTTAATAATTATG
* *
2677785 ATTAATCTAATGATTTGATATTTAATG
1 ATTAA--TAATGATTTAATAATT-ATG
2677812 ATTTAATAAT
1 A-TTAATAAT
2677822 AATATGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 5 0.17
26 18 0.60
27 3 0.10
28 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (24 bp):
ATTAATAATGATTTAATAATTATG
Found at i:2678639 original size:21 final size:21
Alignment explanation
Indices: 2678606--2678654 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2678596 AATATAATAT
*
2678606 ATAACTTAAACTAACCAACTA
1 ATAACTTAAACTAACAAACTA
* *
2678627 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
2678648 ATTAACT
1 A-TAACT
2678655 AGATTTTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:2679123 original size:35 final size:35
Alignment explanation
Indices: 2679083--2679150 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
2679073 TGGATGCAAC
*
2679083 GCATGCATGAGTGATACAGTTAAAGCTTGGTCGTT
1 GCATGCATGAGTGATACAGTTAAAGCTGGGTCGTT
*
2679118 GCATGCATGAGTGCTACAGTTAAAGCTGGGTCG
1 GCATGCATGAGTGATACAGTTAAAGCTGGGTCG
2679151 CGATGCAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.28
Consensus pattern (35 bp):
GCATGCATGAGTGATACAGTTAAAGCTGGGTCGTT
Found at i:2679204 original size:12 final size:12
Alignment explanation
Indices: 2679187--2679211 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2679177 TCCATGGCGA
2679187 CCTACCACCTAC
1 CCTACCACCTAC
2679199 CCTACCACCTAC
1 CCTACCACCTAC
2679211 C
1 C
2679212 ATGTCGTCGG
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:0.24, C:0.60, G:0.00, T:0.16
Consensus pattern (12 bp):
CCTACCACCTAC
Found at i:2679495 original size:13 final size:13
Alignment explanation
Indices: 2679477--2679533 Score: 78
Period size: 13 Copynumber: 4.1 Consensus size: 13
2679467 GATGGACGAG
2679477 CAACAGCGGCCAC
1 CAACAGCGGCCAC
2679490 CAACAGCGGCCACCC
1 CAACAGCGGCCA--C
2679505 CAAAGCAGCGGCCAC
1 C-AA-CAGCGGCCAC
2679520 CAACAGCGGCCAC
1 CAACAGCGGCCAC
2679533 C
1 C
2679534 CCAAGCAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
13 23 0.57
14 2 0.05
15 4 0.10
16 2 0.05
17 9 0.22
ACGTcount: A:0.30, C:0.47, G:0.23, T:0.00
Consensus pattern (13 bp):
CAACAGCGGCCAC
Found at i:2679516 original size:30 final size:30
Alignment explanation
Indices: 2679480--2679537 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
2679470 GGACGAGCAA
2679480 CAGCGGCCACCAACAGCGGCCACCCCAAAG
1 CAGCGGCCACCAACAGCGGCCACCCCAAAG
2679510 CAGCGGCCACCAACAGCGGCCACCCCAA
1 CAGCGGCCACCAACAGCGGCCACCCCAA
2679538 GCAAATAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.29, C:0.48, G:0.22, T:0.00
Consensus pattern (30 bp):
CAGCGGCCACCAACAGCGGCCACCCCAAAG
Found at i:2679592 original size:29 final size:29
Alignment explanation
Indices: 2679551--2679723 Score: 312
Period size: 29 Copynumber: 6.0 Consensus size: 29
2679541 AATAACTTAT
*
2679551 AGGACGCCGGGCGTGCATGGCGTCCT-TA
1 AGGACGCCGGGCGTGCATGGCGACCTATA
*
2679579 TAGGACGCCAGGCGTGCATGGCGACCTATA
1 -AGGACGCCGGGCGTGCATGGCGACCTATA
2679609 AGGACGCCGGGCGTGCATGGCGACCTATA
1 AGGACGCCGGGCGTGCATGGCGACCTATA
2679638 AGGACGCCGGGCGTGCATGGCGACCTATA
1 AGGACGCCGGGCGTGCATGGCGACCTATA
2679667 AGGACGCCGGGCGTGCATGGCGACCTATA
1 AGGACGCCGGGCGTGCATGGCGACCTATA
2679696 AGGACGCCGGGCGTGCATGGCGACCTAT
1 AGGACGCCGGGCGTGCATGGCGACCTAT
2679724 GTTGCCACTG
Statistics
Matches: 140, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
29 138 0.99
30 2 0.01
ACGTcount: A:0.20, C:0.28, G:0.38, T:0.15
Consensus pattern (29 bp):
AGGACGCCGGGCGTGCATGGCGACCTATA
Found at i:2680080 original size:60 final size:60
Alignment explanation
Indices: 2680006--2680155 Score: 185
Period size: 60 Copynumber: 2.5 Consensus size: 60
2679996 TTGTATCATG
* * * *
2680006 TCCCCAAACTATGACCCTCATTTTAAATT-GATCTTTATACTTTTGAATATTTCAATTTCA
1 TCCCCAAACTATGACCCTCATTTTAAATTAGA-CTTTAAACTTTTGAAAAATCCAATTTCA
* * **
2680066 TCCCCAAATTATGACTCTCATTCAAAATTAGACTTTAAACTTTTGAAAAATCCAATTTCA
1 TCCCCAAACTATGACCCTCATTTTAAATTAGACTTTAAACTTTTGAAAAATCCAATTTCA
* * *
2680126 TCCTCAAACTATGAACCTAATTTTAAATTA
1 TCCCCAAACTATGACCCTCATTTTAAATTA
2680156 ATCCTCAAAA
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
60 72 0.97
61 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (60 bp):
TCCCCAAACTATGACCCTCATTTTAAATTAGACTTTAAACTTTTGAAAAATCCAATTTCA
Found at i:2682774 original size:3 final size:3
Alignment explanation
Indices: 2682761--2682846 Score: 108
Period size: 3 Copynumber: 30.0 Consensus size: 3
2682751 TATATATATT
* *
2682761 TAA TAA T-A TAA TAA TAA T-A TTA TAG TAA TAA TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
2682806 TGA TAA -AA TAA TAA TAA TAA TAA TAA AAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2682847 ATCATATGGG
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
2 8 0.11
3 65 0.89
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2682827 original size:37 final size:37
Alignment explanation
Indices: 2682761--2682842 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 37
2682751 TATATATATT
* * *
2682761 TAATAATATAATAATAATATTATAGTAATAATAATAA
1 TAATAATATAATAATAATATAATAATAATAATAAAAA
*
2682798 TAATAATATGATAA-AATAATAATAATAATAATAAAAA
1 TAATAATATAATAATAAT-ATAATAATAATAATAAAAA
2682835 TAATAATA
1 TAATAATA
2682843 ATAAATCATA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 3 0.08
37 37 0.93
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (37 bp):
TAATAATATAATAATAATATAATAATAATAATAAAAA
Found at i:2683350 original size:113 final size:112
Alignment explanation
Indices: 2683097--2683636 Score: 679
Period size: 113 Copynumber: 4.8 Consensus size: 112
2683087 CTCTGATGAG
* * *
2683097 TTCTTCTCA-TATGAACTTCTTCATCCTTCTTTC-GATGAGTTCTTCTCATTATGAACTTTCTCT
1 TTCTTCTCATTATGAACTTCTTCATCCTTC-TTCAGATGAGTTCTTCTTATTATGAACTCTATCT
** * *
2683160 AAAAAAGTTGAT-CATCAAGTGATGGATTTGAGCAAAA-ATCTGAACAAA
65 GGAAAAGCTGATCCATCAAGTGAT-GATTTGAGCAAAAGGT-TGAACAAA
* * *
2683208 -T-TTCTCATTATGGACTTCTTCATCCTTCTTCAGATGAGTTCTTCTTATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTTATTATGAACTCTATCTG
* *
2683271 GAAAAGCTAATCTATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGAT-GATTTGAGCAAAAGGTTGAACAAA
* *
2683319 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTTATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTTATTATGAACTCTATCTG
* *
2683384 GAAAAGCTAATCTATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGAT-GATTTGAGCAAAAGGTTGAACAAA
* *
2683432 TTC-TCTCATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTTCTT-TTCATTATGAACT-TTTCT
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTT-ATTATGAACTCTATCT
* * * * *
2683493 GGAAAGGCTGATCCATCAA-TGATGAATTCAGGTAAAAGGTTGAACAAG
65 GGAAAAGCTGATCCATCAAGTGATGATTTGA-GCAAAAGGTTGAACAAA
* * * * *
2683541 TTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTTATTATGAACTCTATCTG
2683606 GAAAAGCTGATCCATCAAGTGATGAATTTGA
66 GAAAAGCTGATCCATCAAGTGATG-ATTTGA
2683637 ATCTTTGCTA
Statistics
Matches: 384, Mismatches: 31, Indels: 25
0.87 0.07 0.06
Matches are distributed among these distances:
108 5 0.01
109 31 0.08
110 85 0.22
111 104 0.27
112 38 0.10
113 117 0.30
114 4 0.01
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (112 bp):
TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTTATTATGAACTCTATCTG
GAAAAGCTGATCCATCAAGTGATGATTTGAGCAAAAGGTTGAACAAA
Found at i:2683595 original size:222 final size:222
Alignment explanation
Indices: 2683095--2683636 Score: 722
Period size: 222 Copynumber: 2.4 Consensus size: 222
2683085 AGCTCTGATG
2683095 AGTTCTTCTCA-TATGAACTTCTTCATCCTTCTTTC-GATGAGTTCTTCTCATTATGAACTTTCT
1 AGTTCTTCTCATTATGAACTTCTTCATCCTTC-TTCAGATGAGTTCTTCTCATTATGAACTTTCT
** * *
2683158 CTAAAAAAGTTGATCATCAAGTGATGGATTTGAGCAAAAATCTGAACAAATTTCTCATTATGGAC
65 CTGGAAAAGCTGATCATCAAGTGAT-GATTTGAGCAAAAATCTGAACAAATTTCTCATTATGAAC
*
2683223 TTCTTCATCCTTCTTCAGATGAGTTCTTCTTATTATGAACTCGAACTGGAAAAGCTAATCTATCA
129 TTCTTCATCCTTCTTCAGATGAGTTCTTCTTATTATGAACTCGAACTGGAAAAGCTAATCCATCA
* *
2683288 AGTGATAGATTTGAGCAAAAGGTTGAACA
194 AGTGATAGAATTCAGCAAAAGGTTGAACA
* * ****
2683317 AATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTTATTATGAACTCGAAC
1 AGTTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* *
2683382 TGGAAAAGCTAATCTATCAAGTGATAGATTTGAGCAAAAGGT-TGAACAAATTCTCTCATTATGA
66 TGGAAAAGCTGATC-ATCAAGTGAT-GATTTGAGCAAAA-ATCTGAACAAATT-TCTCATTATGA
* *** * *
2683446 AC-TCTTCTTCCTTCTTCAGATGAGTTCTT-TTCATTATGAACT-TTTCTGGAAAGGCTGATCCA
127 ACTTCTTCATCCTTCTTCAGATGAGTTCTTCTT-ATTATGAACTCGAACTGGAAAAGCTAATCCA
*
2683508 TCAA-TGAT-GAATTCAGGTAAAAGGTTGAACA
191 TCAAGTGATAGAATTCA-GCAAAAGGTTGAACA
* *
2683539 AGTTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
2683604 TGGAAAAGCTGATCCATCAAGTGATGAATTTGA
66 TGGAAAAGCTGAT-CATCAAGTGATG-ATTTGA
2683637 ATCTTTGCTA
Statistics
Matches: 279, Mismatches: 32, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
221 6 0.02
222 116 0.42
223 75 0.27
224 69 0.25
225 13 0.05
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (222 bp):
AGTTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAAAGCTGATCATCAAGTGATGATTTGAGCAAAAATCTGAACAAATTTCTCATTATGAACTT
CTTCATCCTTCTTCAGATGAGTTCTTCTTATTATGAACTCGAACTGGAAAAGCTAATCCATCAAG
TGATAGAATTCAGCAAAAGGTTGAACA
Found at i:2684489 original size:82 final size:82
Alignment explanation
Indices: 2684349--2684642 Score: 434
Period size: 82 Copynumber: 3.6 Consensus size: 82
2684339 CTGTAGTTCC
*
2684349 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTT
* *
2684413 TAAATTCAATAATTGGTT
65 CAAATTCAATGATTGGTT
* * *
2684431 TACCAAACCAGATCAGATGACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
2684496 AAATTCAATGATTGGTT
66 AAATTCAATGATTGGTT
* * * *
2684513 CTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAACACATTC--CTC
1 -T-ACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTT
2684575 TCAAATTCAATGATTGGTTT
64 TCAAATTCAATGATTGG-TT
2684595 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
2684643 TGAGTCTCTT
Statistics
Matches: 192, Mismatches: 15, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
80 2 0.01
81 62 0.32
82 75 0.39
83 51 0.27
84 2 0.01
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (82 bp):
TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
AAATTCAATGATTGGTT
Found at i:2684563 original size:83 final size:82
Alignment explanation
Indices: 2684351--2685077 Score: 627
Period size: 83 Copynumber: 8.5 Consensus size: 82
2684341 GTAGTTCCTA
* * *
2684351 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTTTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCCTTCA
* *
2684415 AATTCAATAATTGGTTTA
65 AATTCAATGATTGGTTTT
* *
2684433 CCAAACCAGATCAGATGACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTTCAA
2684498 ATTCAATGATTGGTTCTGT
66 ATTCAATGATTGGTT-T-T
* * *
2684517 CC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAACACATTCCT-C-TCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTTCAA
2684579 ATTCAATGATTGGTTTT
66 ATTCAATGATTGGTTTT
* *
2684596 ACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTC-TTTAT--TT
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAG-CACATTCATCCTT
* * ** *
2684658 CTACTATGAGCAA--ATTCATCTT
63 C-A-AAT--TCAATGATTGGTTTT
* * * * * * * ** * * *
2684680 CCAAATTCAATGAT-TGGT-TCTGCCAAACCAGATCAGATAACTCA-AAGAACACT-TCCAGAAG
1 CCAAA--CCA-GATCAGATAACT--C-AA--AGAACA-CT-TC-CAGAAG-ATGCTAT-GAGCAC
* *
2684741 ATGCTATGAGCACATTCATCCTTCAATTTCAATGACTGGTTTT
53 ATTC-AT---C-C-TTCA------AAT-TCAATGATTGGTTTT
*
2684784 ACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTTTA
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTTCA
* *
2684849 ATTTCAATGATTGGTTCTG
65 AATTCAATGATTGGTT-TT
* *
2684868 CCAAACCATATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATGAGCACATTCATCCTTCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTTCAA
* *
2684933 TTTCAATGATTAGTTCTGT
66 ATTCAATGATTGGTT-T-T
2684952 -CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTTCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTTCAA
* *
2685016 TTTCAATGACTGGTTTT
66 ATTCAATGATTGGTTTT
2685033 ACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
2685078 TTTCCATTGA
Statistics
Matches: 525, Mismatches: 70, Indels: 99
0.76 0.10 0.14
Matches are distributed among these distances:
79 1 0.00
80 3 0.01
81 62 0.12
82 81 0.15
83 268 0.51
84 15 0.03
85 4 0.01
86 7 0.01
87 2 0.00
89 5 0.01
90 5 0.01
91 8 0.02
92 8 0.02
95 2 0.00
96 11 0.02
97 5 0.01
98 2 0.00
99 8 0.02
101 2 0.00
102 7 0.01
103 7 0.01
104 7 0.01
105 5 0.01
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.27
Consensus pattern (82 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTTCAA
ATTCAATGATTGGTTTT
Found at i:2684789 original size:105 final size:105
Alignment explanation
Indices: 2684576--2684767 Score: 282
Period size: 105 Copynumber: 1.8 Consensus size: 105
2684566 ACATTCCTCT
*
2684576 CAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 CAAATTCAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
* * * * *
2684641 ATTGAGTCTCTTTATTTCTACTATGAGCAAATTCATCTTC
66 ATTGAGTCACTTCATTCCTACAATGAGCAAACTCATCTTC
*
2684681 CAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 CAAATTCAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
*
2684746 A-TGAG-CACATTCA-TCCTTCAAT
66 ATTGAGTCAC-TTCATTCCTACAAT
2684768 TTCAATGACT
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
103 8 0.10
104 7 0.09
105 64 0.81
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.29
Consensus pattern (105 bp):
CAAATTCAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
ATTGAGTCACTTCATTCCTACAATGAGCAAACTCATCTTC
Found at i:2684935 original size:166 final size:166
Alignment explanation
Indices: 2684661--2685077 Score: 701
Period size: 166 Copynumber: 2.5 Consensus size: 166
2684651 TTTATTTCTA
* *
2684661 CTATGAGCAAATTCAT-CTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAA
1 CTATGAGCACATTCATCCTT-CAATTTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAA
* *
2684725 AGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTTCAATTTCAATGACTGGTTTTACCAAA
65 AGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTTCAATTTCAATGACTAGTTCTACCAAA
2684790 CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
130 CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
* *
2684827 CTATGAGCACATTCATCCTTTAATTTCAATGATTGGTTCTGCCAAACCATATCAGATAACTCAAA
1 CTATGAGCACATTCATCCTTCAATTTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
* * **
2684892 GAACACTTCTAGAAGATGCTATGAGCACATTCATCCTTCAATTTCAATGATTAGTTCTGTCAAAC
66 GAACACTTCCAGAAGATGCTATGAGCACATTCATCCTTCAATTTCAATGACTAGTTCTACCAAAC
2684957 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
131 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
* * *
2684993 CTATGAGCACATTCATCCTTCAATTTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCCTTCAATTTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
2685058 GAACACTTCCAGAAGATGCT
66 GAACACTTCCAGAAGATGCT
2685078 TTTCCATTGA
Statistics
Matches: 234, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
166 231 0.99
167 3 0.01
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.27
Consensus pattern (166 bp):
CTATGAGCACATTCATCCTTCAATTTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATGAGCACATTCATCCTTCAATTTCAATGACTAGTTCTACCAAAC
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
Found at i:2686061 original size:1 final size:1
Alignment explanation
Indices: 2686051--2686122 Score: 54
Period size: 1 Copynumber: 72.0 Consensus size: 1
2686041 TGACCTCCCC
* * * * * * * * *
2686051 TTTTTCTTTTTTCTTTTTCTTTTTTTTCTTTTTTCTCTTTTTTCTTTCTTTTTTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
2686116 TTCTTTT
1 TTTTTTT
2686123 CTTCAAGCAT
Statistics
Matches: 51, Mismatches: 20, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:2686078 original size:9 final size:9
Alignment explanation
Indices: 2686050--2686122 Score: 76
Period size: 9 Copynumber: 7.6 Consensus size: 9
2686040 TTGACCTCCC
2686050 CTTTTTCTTT
1 CTTTTT-TTT
2686060 -TTTCTTTTT
1 CTTT-TTTTT
2686069 CTTTTTTTT
1 CTTTTTTTT
*
2686078 CTTTTTTCT
1 CTTTTTTTT
2686087 CTTTTTTCTTT
1 C-TTTTT-TTT
2686098 CTTTTTTTTT
1 C-TTTTTTTT
2686108 CTTTTTTTTT
1 C-TTTTTTTT
2686118 CTTTT
1 CTTTT
2686123 CTTCAAGCAT
Statistics
Matches: 57, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
9 24 0.42
10 24 0.42
11 9 0.16
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:2686091 original size:29 final size:32
Alignment explanation
Indices: 2686051--2686126 Score: 106
Period size: 29 Copynumber: 2.5 Consensus size: 32
2686041 TGACCTCCCC
*
2686051 TTTTTCTTTTTTCTT-TTTC-TTTTTTTTC-T
1 TTTTTCTCTTTTCTTCTTTCTTTTTTTTTCTT
2686080 TTTTTCTCTTTT-TTCTTTCTTTTTTTTTCTT
1 TTTTTCTCTTTTCTTCTTTCTTTTTTTTTCTT
*
2686111 TTTTTTTCTTTTCTTC
1 TTTTTCTCTTTTCTTC
2686127 AAGCATAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
28 2 0.05
29 15 0.37
30 9 0.22
31 12 0.29
32 3 0.07
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (32 bp):
TTTTTCTCTTTTCTTCTTTCTTTTTTTTTCTT
Found at i:2686115 original size:31 final size:30
Alignment explanation
Indices: 2686051--2686125 Score: 109
Period size: 30 Copynumber: 2.5 Consensus size: 30
2686041 TGACCTCCCC
*
2686051 TTTTTCTTTTTTCTTTTTCTTTTTTTTCTT
1 TTTTTCTTTTTTCTTTCTCTTTTTTTTCTT
2686081 TTTTCTCTTTTTTCTTTCT-TTTTTTTTCTT
1 TTTT-TCTTTTTTCTTTCTCTTTTTTTTCTT
2686111 TTTTT-TTCTTTTCTT
1 TTTTTCTT-TTTTCTT
2686126 CAAGCATAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
28 2 0.05
29 8 0.19
30 19 0.45
31 13 0.31
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (30 bp):
TTTTTCTTTTTTCTTTCTCTTTTTTTTCTT
Found at i:2693461 original size:15 final size:15
Alignment explanation
Indices: 2693438--2693469 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2693428 TGAGATGAAT
2693438 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
2693453 AATGCATGTATGCAA
1 AATGAATGTATGCAA
2693468 AA
1 AA
2693470 AGGTATTGAT
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:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:2697435 original size:17 final size:18
Alignment explanation
Indices: 2697413--2697450 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2697403 CTCTCTGGGG
2697413 TCTGTTGT-TTC-CTCGTC
1 TCTGTTGTGTTCTCT-GTC
2697430 TCTGTTGTGTTCTCTGTC
1 TCTGTTGTGTTCTCTGTC
2697448 TCT
1 TCT
2697451 CCGTTCTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 9 0.47
19 2 0.11
ACGTcount: A:0.00, C:0.26, G:0.18, T:0.55
Consensus pattern (18 bp):
TCTGTTGTGTTCTCTGTC
Found at i:2697450 original size:18 final size:17
Alignment explanation
Indices: 2697413--2697450 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2697403 CTCTCTGGGG
2697413 TCTGTTGTTTCCTCGTC
1 TCTGTTGTTTCCTCGTC
2697430 TCTGTTGTGTT-CTCTGTC
1 TCTGTTGT-TTCCTC-GTC
2697448 TCT
1 TCT
2697451 CCGTTCTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.00, C:0.26, G:0.18, T:0.55
Consensus pattern (17 bp):
TCTGTTGTTTCCTCGTC
Found at i:2697830 original size:3 final size:3
Alignment explanation
Indices: 2697822--2697935 Score: 192
Period size: 3 Copynumber: 38.0 Consensus size: 3
2697812 TATATATATT
* * *
2697822 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2697870 TAA TAA TAA TGA 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
2697918 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
2697936 ATCAATATGG
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 103 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2699199 original size:25 final size:27
Alignment explanation
Indices: 2699152--2699227 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 27
2699142 AAAAATAACA
* *
2699152 AATAAAATATTTTTTAAATTAAGTTTAT
1 AATAAAATA-TATTTAAATTAAGTTAAT
2699180 AATAAAATATATTT-AA-TAAGTTAAT
1 AATAAAATATATTTAAATTAAGTTAAT
2699205 -ATAAAA-ATATTT---TTAAGTTAAT
1 AATAAAATATATTTAAATTAAGTTAAT
2699227 A
1 A
2699228 TATATATATA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
22 9 0.20
23 6 0.14
24 6 0.14
25 8 0.18
26 2 0.05
27 4 0.09
28 9 0.20
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (27 bp):
AATAAAATATATTTAAATTAAGTTAAT
Found at i:2699204 original size:22 final size:22
Alignment explanation
Indices: 2699179--2699241 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
2699169 ATTAAGTTTA
2699179 TAATA-AAATATATTTAATAAGT
1 TAATATAAATATATTT-ATAAGT
* *
2699201 TAATATAAAAATATTTTTAAGT
1 TAATATAAATATATTTATAAGT
* *
2699223 TAATATATATATATATATA
1 TAATATAAATATATTTATA
2699242 TATATATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 25 0.74
23 9 0.26
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (22 bp):
TAATATAAATATATTTATAAGT
Found at i:2699232 original size:2 final size:2
Alignment explanation
Indices: 2699225--2699266 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
2699215 TTTTAAGTTA
2699225 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT AT CAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
2699266 A
1 A
2699267 ATCCTTGTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.05
2 33 0.89
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2699571 original size:39 final size:39
Alignment explanation
Indices: 2699482--2699571 Score: 110
Period size: 39 Copynumber: 2.3 Consensus size: 39
2699472 AAAAACTAAT
2699482 GTGAAATAATTTAAGAAATTAAGAATTTAGAACGTTATG
1 GTGAAATAATTTAAGAAATTAAGAATTTAGAACGTTATG
** * * * *
2699521 GTGTCAGAATTTTAGAAATTAAGATTTTAGAATGTTA-G
1 GTGAAATAATTTAAGAAATTAAGAATTTAGAACGTTATG
2699559 AGTGAAATAATTT
1 -GTGAAATAATTT
2699572 GTGAATTATG
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
38 1 0.02
39 40 0.98
ACGTcount: A:0.42, C:0.02, G:0.19, T:0.37
Consensus pattern (39 bp):
GTGAAATAATTTAAGAAATTAAGAATTTAGAACGTTATG
Found at i:2701304 original size:21 final size:20
Alignment explanation
Indices: 2701258--2701323 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
2701248 CACGAACTCA
* *
2701258 AAATTTACAATACAATTTTC
1 AAATTTACAACACAAATTTC
*
2701278 AAATTTACAACACATAATTTG
1 AAATTTACAACACA-AATTTC
* **
2701299 AAATTTGCAACTTAAATTT-
1 AAATTTACAACACAAATTTC
2701318 AAATTT
1 AAATTT
2701324 TCGCAAAGCG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
19 6 0.15
20 18 0.46
21 15 0.38
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.39
Consensus pattern (20 bp):
AAATTTACAACACAAATTTC
Found at i:2702000 original size:21 final size:20
Alignment explanation
Indices: 2701975--2702027 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 20
2701965 AAGAGATGAG
*
2701975 CTTGCGAAAATTTAAATTTTC
1 CTTGCGAAAATTTAAA-TTCC
2701996 CTTGCGAAAATTTAAATTCC
1 CTTGCGAAAATTTAAATTCC
2702016 CGTTGCGAAAAT
1 C-TTGCGAAAAT
2702028 AGACATGGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (20 bp):
CTTGCGAAAATTTAAATTCC
Found at i:2711819 original size:80 final size:80
Alignment explanation
Indices: 2711723--2711883 Score: 304
Period size: 80 Copynumber: 2.0 Consensus size: 80
2711713 TTCATTCGAA
2711723 TGACCCGGATTTTGTTTATCATCATGTTGGAAGTTGGATTTCCATTTGTTTGGTGTGCAGGTTAA
1 TGACCCGGATTTTGTTTATCATCATGTTGGAAGTTGGATTTCCATTTGTTTGGTGTGCAGGTTAA
2711788 GGATAAGAGTAATTT
66 GGATAAGAGTAATTT
* *
2711803 TGACCCGGATTTTGTTTATCATCATGTTGGAAGTTGGATTTTCATTTGTTTGGTGTGCAGGTTAT
1 TGACCCGGATTTTGTTTATCATCATGTTGGAAGTTGGATTTCCATTTGTTTGGTGTGCAGGTTAA
2711868 GGATAAGAGTAATTT
66 GGATAAGAGTAATTT
2711883 T
1 T
2711884 AAGATAGTTT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.43
Consensus pattern (80 bp):
TGACCCGGATTTTGTTTATCATCATGTTGGAAGTTGGATTTCCATTTGTTTGGTGTGCAGGTTAA
GGATAAGAGTAATTT
Found at i:2715075 original size:175 final size:173
Alignment explanation
Indices: 2714784--2715162 Score: 584
Period size: 175 Copynumber: 2.2 Consensus size: 173
2714774 TTTAAGTGAG
* * *
2714784 GAAATGTAAACAAGGATGAATGGTGTTGGATGTTGTGCTACGGGGTCATTACCCTACTTTCAAAA
1 GAAATGTAAACAAGGATGAATGGTGTTGGATGTTGTGCTACAGGATCATTACCCCACTTTCAAAA
** *
2714849 GACATGTCTGATGGGATATGAATCATCACCATTACCGTTTTTAAACTTCAGGACCTTCATTTTTT
66 GACATGTCTGATAAGATAAGAATCATCACCATTACCGTTTTTAAACTTCAGGA-C--CATTTTTT
2714914 TTT-ACGATGTGGGATTAATATCCTCTCCATGGCGTTACAACTGCA
128 TTTCACGATGTGGGATTAATATCCTCTCCATGGCGTTACAACTGCA
* *
2714959 GAAATGTAAACAAGGATGAATGGTTTTGGATGTTGTG-TCACAGGATCATTACCCCATTTTCAAA
1 GAAATGTAAACAAGGATGAATGGTGTTGGATGTTGTGCT-ACAGGATCATTACCCCACTTTCAAA
*
2715023 AGACATGTCTGATAAGATAAGAATCATCATCATTA-CGTTTTTTAAACTTCAGGACCATTTTTTT
65 AGACATGTCTGATAAGATAAGAATCATCACCATTACCG-TTTTTAAACTTCAGGACCATTTTTTT
* **
2715087 TTCACGATGTGGGATTAATATCCTCTCCATGGCGTTACAAGTGTG
129 TTCACGATGTGGGATTAATATCCTCTCCATGGCGTTACAACTGCA
2715132 GAAATGTAAACAAGGATGAATGGTGTTGGAT
1 GAAATGTAAACAAGGATGAATGGTGTTGGAT
2715163 CTTGCACCTT
Statistics
Matches: 188, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
172 11 0.06
173 69 0.37
174 4 0.02
175 104 0.55
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.34
Consensus pattern (173 bp):
GAAATGTAAACAAGGATGAATGGTGTTGGATGTTGTGCTACAGGATCATTACCCCACTTTCAAAA
GACATGTCTGATAAGATAAGAATCATCACCATTACCGTTTTTAAACTTCAGGACCATTTTTTTTT
CACGATGTGGGATTAATATCCTCTCCATGGCGTTACAACTGCA
Found at i:2719083 original size:252 final size:252
Alignment explanation
Indices: 2718638--2719409 Score: 928
Period size: 252 Copynumber: 3.1 Consensus size: 252
2718628 TTCGGGTCTG
*
2718638 GTCGGGTCGGATGAAACTTTATTTTGGTCGGGTCGGTTTTTTTAAGTATGATATTTGGGTCGGGT
1 GTCGGGTCGG-TGAAACTTTATTTTGGTCGGGTCGGTTTTTTTAAGTATGATATTCGGGTCGGGT
* * *
2718703 TGAGTTCAGTTTTAAGGTGAAAAATACCCGATCCGAAAATATATATAATTTTACCTTATATATTC
65 CGAGTTCAGGTTTAAGGTGAAAAATACCCGACCCGAAAATATATATAATTTTACCTTATATATTC
*
2718768 AGGAATAATTACAATAATACCCCTCTATATATATATTTTTTCAATTAAGTCACTATTTTTATTGA
130 AGGAATAATTACAATAATACCCATCTATATATATATTTTTTCAATTAAGTCACTATTTTTATTGA
* *
2718833 ATAAAAAT-ATTTTTTTATTATTTCGGGTC-GGATCGGGTTTCTAATTCATATATTCAA
195 ATAAAAATAATTTTTTTATTATTTCGGGTCGGGA-CAGATTTCTAATTCATATATTCAA
*
2718890 GTCGGGTCGTGTGAAACTTTATTTTGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGGGT
1 GTCGGGTCG-GTGAAACTTTATTTTGGTCGGGTCGGTTTTTTTAAGTATGATATTCGGGTCGGGT
* * *
2718955 CGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAATATATATAATTTTACCTTATATATTT
65 CGAGTTCAGGTTTAAGGTGAAAAATACCCGACCCGAAAATATATATAATTTTACCTTATATATTC
* *
2719020 AGGAATAATTACAATAATACCCATCTATATATA-ATTTTTTTCAATTAAGTCATTGTTTTTATTG
130 AGGAATAATTACAATAATACCCATCTATATATATA-TTTTTTCAATTAAGTCACTATTTTTATTG
**
2719084 AATAAAAATAATTTTTTTATTATTTCGGGTCGGGACAGATTTCTAATTCATATATTCGG
194 AATAAAAATAATTTTTTTATTATTTCGGGTCGGGACAGATTTCTAATTCATATATTCAA
* * ** *
2719143 GTCAGGTCGGGTGAAACTTTATTTTGGTCGGGTCGG---------GT-CG-GGTTCGGGTTTAGG
1 GTCGGGTC-GGTGAAACTTTATTTTGGTCGGGTCGGTTTTTTTAAGTATGATATTCGGG--TCGG
*** *** **** * *
2719197 GT-GA----A-AAAT-ACCCG-ACCCGACCCGACCC-AAAAAATATATAATTTTACCTGATATAT
63 GTCGAGTTCAGGTTTAAGGTGAAAAATACCCGACCCGAAAATATATATAATTTTACCTTATATAT
* * * * *
2719253 TTAGAAATAATTACAATAATACCCCTCTATATAT-T-TTTTTTCAATTAAGCCACTGTTTTTATT
128 TCAGGAATAATTACAATAATACCCATCTATATATATATTTTTTCAATTAAGTCACTATTTTTATT
* * * *
2719316 GAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATTCAG
193 GAATAAAAATAATTTTTTTATTATTTCGGGTCGGGACAGATTTCTAATTCATATATTCAA
2719376 GTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTC
1 GTCGGGTC-GGTGAAACTTTATTTTGGTCGGGTC
2719410 AGGTCTCTGA
Statistics
Matches: 469, Mismatches: 43, Indels: 35
0.86 0.08 0.06
Matches are distributed among these distances:
233 115 0.25
235 58 0.12
236 10 0.02
237 1 0.00
238 1 0.00
242 6 0.01
243 3 0.01
244 7 0.01
251 1 0.00
252 188 0.40
253 75 0.16
254 4 0.01
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (252 bp):
GTCGGGTCGGTGAAACTTTATTTTGGTCGGGTCGGTTTTTTTAAGTATGATATTCGGGTCGGGTC
GAGTTCAGGTTTAAGGTGAAAAATACCCGACCCGAAAATATATATAATTTTACCTTATATATTCA
GGAATAATTACAATAATACCCATCTATATATATATTTTTTCAATTAAGTCACTATTTTTATTGAA
TAAAAATAATTTTTTTATTATTTCGGGTCGGGACAGATTTCTAATTCATATATTCAA
Found at i:2719344 original size:233 final size:225
Alignment explanation
Indices: 2718944--2719414 Score: 728
Period size: 233 Copynumber: 2.1 Consensus size: 225
2718934 AGTGTGATAT
*
2718944 TCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAATATATATAATTTTAC
1 TCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTAC
* * * *
2719009 CTTATATATTTAGGAATAATTACAATAATACCCATCTATATATAATTTTTTTCAATTAAGTCATT
66 CTGATATATTTAGAAATAATTACAATAATACCCATCTATATAT-ATTTTTTTCAATTAAGCCACT
2719074 GTTTTTATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGACAGATTTCTAATTCATATAT
130 GTTTTTATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGACAGATTTCTAATTCATATAT
*
2719139 TCGGGTCAGGTCGGGTGAAACTTTATTTTGG
195 TCAGGTCAGGTCGGGTGAAACTTTATTTTGG
*
2719170 TCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCGACCCAAAAAATATA
1 TCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAAT-----ACCCGACCCG----AAAAAATATA
*
2719235 TAATTTTACCTGATATATTTAGAAATAATTACAATAATACCCCTCTATATAT-TTTTTTTCAATT
57 TAATTTTACCTGATATATTTAGAAATAATTACAATAATACCCATCTATATATATTTTTTTCAATT
* * *
2719299 AAGCCACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCGGGTTTCTAAT
122 AAGCCACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGACAGATTTCTAAT
*
2719364 TCATATATTCAGGTCGGGTCGGGTGAAACTTTATTTTGG
187 TCATATATTCAGGTCAGGTCGGGTGAAACTTTATTTTGG
*
2719403 TCGGGTCAGGTC
1 TCGGGTCGGGTC
2719415 TCTGATGGAG
Statistics
Matches: 223, Mismatches: 13, Indels: 11
0.90 0.05 0.04
Matches are distributed among these distances:
226 35 0.16
231 10 0.04
233 120 0.54
235 58 0.26
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (225 bp):
TCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTAC
CTGATATATTTAGAAATAATTACAATAATACCCATCTATATATATTTTTTTCAATTAAGCCACTG
TTTTTATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGACAGATTTCTAATTCATATATT
CAGGTCAGGTCGGGTGAAACTTTATTTTGG
Done.