Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_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: 8285662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 35
Found at i:2410147 original size:13 final size:13
Alignment explanation
Indices: 2410129--2410164 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2410119 CTTGGCTTGG
2410129 TGTTGTGGTTTAC
1 TGTTGTGGTTTAC
*
2410142 TGTTGTGGTTTGC
1 TGTTGTGGTTTAC
*
2410155 AGTTGTGGTT
1 TGTTGTGGTT
2410165 CTCGTTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.06, C:0.06, G:0.36, T:0.53
Consensus pattern (13 bp):
TGTTGTGGTTTAC
Found at i:2410663 original size:19 final size:19
Alignment explanation
Indices: 2410633--2410681 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
2410623 CTTGACCACA
* *
2410633 AATAAAAAATAAAATTAAT
1 AATAATAAATAAAATAAAT
*
2410652 AA-AATGAAATAAGATAAAT
1 AATAAT-AAATAAAATAAAT
2410671 AATAATAAATA
1 AATAATAAATA
2410682 TATATATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 20 0.80
20 3 0.12
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (19 bp):
AATAATAAATAAAATAAAT
Found at i:2410678 original size:10 final size:9
Alignment explanation
Indices: 2410639--2410681 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
2410629 CACAAATAAA
2410639 AAATAAAAT
1 AAATAAAAT
*
2410648 TAATAAAAT
1 AAATAAAAT
*
2410657 GAAATAAGAT
1 -AAATAAAAT
2410667 AAATAATAAT
1 AAATAA-AAT
2410677 AAATA
1 AAATA
2410682 TATATATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
9 14 0.50
10 14 0.50
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (9 bp):
AAATAAAAT
Found at i:2410733 original size:36 final size:37
Alignment explanation
Indices: 2410679--2410994 Score: 203
Period size: 36 Copynumber: 8.5 Consensus size: 37
2410669 ATAATAATAA
2410679 ATATATATATATATATATTTAAAAAT-ATTTTAAAACT
1 ATATAT-TATATATATATTTAAAAATGATTTTAAAACT
2410716 ATATATTATATATATATTTTTAAAACA-G-TTTTCAAAACT
1 ATATATTATATATATA--TTTAAAA-ATGATTTT-AAAACT
* * * *
2410755 ATATATTATATA-AT-TTTCAAAATGTTTTTTAAACC
1 ATATATTATATATATATTTAAAAATGATTTTAAAACT
*
2410790 ATATATTATATAT-TTTTTCAAAAATG-TTTTAAAACT
1 ATATATTATATATATATTT-AAAAATGATTTTAAAACT
* * * *
2410826 ATATGTTATATA-AGT-TTTCAAAATAATTTCAAAACT
1 ATATATTATATATA-TATTTAAAAATGATTTTAAAACT
* *
2410862 ATATATTATATA-AGT-TTTTAAAA-GGTTTTCAAAAACT
1 ATATATTATATATA-TATTTAAAAATGATTTT--AAAACT
* * *
2410899 ATATA-T-TATGTAT-TTTCAAAATGTTTTTAAAAAAACT
1 ATATATTATATATATATTTAAAAATGATTTT---AAAACT
* * * *
2410936 ATATAATATATATACATTTTCAAAAATCAGTTTCAAAACT
1 ATATATTATATATATA-TTT-AAAAATGA-TTTTAAAACT
2410976 ATATTATATATATATATAT
1 ATA-TAT-TATATATATAT
2410995 ATATATATAT
Statistics
Matches: 226, Mismatches: 27, Indels: 48
0.75 0.09 0.16
Matches are distributed among these distances:
34 1 0.00
35 43 0.19
36 76 0.34
37 36 0.16
38 14 0.06
39 24 0.11
40 9 0.04
41 6 0.03
42 14 0.06
43 3 0.01
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (37 bp):
ATATATTATATATATATTTAAAAATGATTTTAAAACT
Found at i:2410736 original size:27 final size:25
Alignment explanation
Indices: 2410690--2410741 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
2410680 TATATATATA
2410690 TATATATTTAAAAATATTTTAAAAC
1 TATATATTTAAAAATATTTTAAAAC
* *
2410715 TATATATTATATATATATTTTTAAAAC
1 TATATATT-TAAAAATA-TTTTAAAAC
2410742 AGTTTTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 8 0.35
26 6 0.26
27 9 0.39
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (25 bp):
TATATATTTAAAAATATTTTAAAAC
Found at i:2410758 original size:72 final size:72
Alignment explanation
Indices: 2410680--2410990 Score: 294
Period size: 72 Copynumber: 4.2 Consensus size: 72
2410670 TAATAATAAA
*
2410680 TATATATATATATATATTTAAAAAT-ATTTTAAAACTATATATTATATATATATTTTTAAAACAG
1 TATATAT-TATATAT-TTTCAAAATGATTTTAAAACTATATATTATATATATATTTTTAAAA-AG
2410744 TTTTCAAAAC
63 TTTTCAAAAC
* * * *
2410754 TATATATTATATAATTTTCAAAATGTTTTTTAAACCATATATTATATAT-T-TTTTCAAAAATGT
1 TATATATTATAT-ATTTTCAAAATGATTTTAAAACTATATATTATATATATATTTTTAAAAA-GT
2410817 TTT-AAAAC
64 TTTCAAAAC
* * * * *
2410825 TATATGTTATATAAGTTTTCAAAATAATTTCAAAACTATATATTATATA-A-GTTTTTAAAAGGT
1 TATATATTATAT-A-TTTTCAAAATGATTTTAAAACTATATATTATATATATATTTTTAAAAAGT
2410888 TTTCAAAAAC
64 TTTC-AAAAC
* * * * *
2410898 TATATATTATGTATTTTCAAAATGTTTTTAAAAAAACTATATAATATATATACATTTTCAAAAA-
1 TATATATTATATATTTTCAAAATGATTTT---AAAACTATATATTATATATATATTTTTAAAAAG
2410962 TCAGTTTCAAAAC
63 T---TTTCAAAAC
2410975 TATATTATATATATAT
1 TATA-TAT-TATATAT
2410991 ATATATATAT
Statistics
Matches: 196, Mismatches: 23, Indels: 31
0.78 0.09 0.12
Matches are distributed among these distances:
71 37 0.19
72 51 0.26
73 29 0.15
74 47 0.24
75 2 0.01
76 8 0.04
77 9 0.05
78 7 0.04
79 6 0.03
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (72 bp):
TATATATTATATATTTTCAAAATGATTTTAAAACTATATATTATATATATATTTTTAAAAAGTTT
TCAAAAC
Found at i:2410795 original size:37 final size:36
Alignment explanation
Indices: 2410679--2410960 Score: 220
Period size: 36 Copynumber: 7.6 Consensus size: 36
2410669 ATAATAATAA
* *
2410679 ATATATATATATATATATTTAAAAAT-ATTTT-AAAACT
1 ATATAT-TATATA-AT-TTTCAAAATGTTTTTAAAAACT
* * *
2410716 ATATATTATATATATATTTTTAAAACAG-TTTTCAAAACT
1 ATATA-T-TATATA-ATTTTCAAAA-TGTTTTTAAAAACT
* *
2410755 ATATATTATATAATTTTCAAAATGTTTTT-TAAACC
1 ATATATTATATAATTTTCAAAATGTTTTTAAAAACT
*
2410790 ATATATTATATATTTTTTCAAAAATG-TTTT-AAAACT
1 ATATATTATATA-ATTTTC-AAAATGTTTTTAAAAACT
* ** *
2410826 ATATGTTATATAAGTTTTCAAAAT-AATTTCAAAACT
1 ATATATTATATAA-TTTTCAAAATGTTTTTAAAAACT
* * *
2410862 ATATATTATATAAGTTTTTAAAAGGTTTTCAAAAACT
1 ATATATTATATAA-TTTTCAAAATGTTTTTAAAAACT
*
2410899 ATATATTATGT-ATTTTCAAAATGTTTTTAAAAAAACT
1 ATATATTATATAATTTTCAAAATGTTTTT--AAAAACT
2410936 ATATAATATATATACATTTTCAAAA
1 ATAT-AT-TATATA-ATTTTCAAAA
2410961 ATCAGTTTCA
Statistics
Matches: 204, Mismatches: 24, Indels: 30
0.79 0.09 0.12
Matches are distributed among these distances:
35 38 0.19
36 70 0.34
37 53 0.26
38 18 0.09
39 15 0.07
41 10 0.05
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
ATATATTATATAATTTTCAAAATGTTTTTAAAAACT
Found at i:2410987 original size:2 final size:2
Alignment explanation
Indices: 2410975--2411006 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2410965 GTTTCAAAAC
2410975 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2411007 TTCAAAACTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2411023 original size:53 final size:49
Alignment explanation
Indices: 2410935--2411043 Score: 155
Period size: 52 Copynumber: 2.1 Consensus size: 49
2410925 TTAAAAAAAC
2410935 TATATAATATATATACATTTTCAAAAATCAGTTTCAAAACTATATTATATA
1 TATATAATATATATACATTTTCAAAAATCAGTTTC-AAACTATA-TATATA
* * *
2410986 TATATATATATATATATATATTTCAAAACTCATTTTCAAACTATATATATA
1 TATATA-ATATATATACAT-TTTCAAAAATCAGTTTCAAACTATATATATA
2411037 TATATAA
1 TATATAA
2411044 ATTTGGACAA
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
50 1 0.02
51 18 0.34
52 19 0.36
53 15 0.28
ACGTcount: A:0.47, C:0.09, G:0.01, T:0.43
Consensus pattern (49 bp):
TATATAATATATATACATTTTCAAAAATCAGTTTCAAACTATATATATA
Found at i:2411958 original size:85 final size:85
Alignment explanation
Indices: 2411771--2412518 Score: 966
Period size: 85 Copynumber: 8.8 Consensus size: 85
2411761 TGTCATCGAA
* * * * * * *
2411771 CTGAATGTAATTGAACTCGATA-GTTTTTGTTGACAGATAGCCTTTCTCGACTTAAGTTATACTG
1 CTGAATGTAATCGAACTCGA-AGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTG
* *
2411835 TAAATTTAACATGCCCTTT-AG
65 TAAATTTGATATG-CCTTTGAG
* * * * * * *
2411856 TTGTATGGAATCAAACTCGAAGGTATTTGTTGAAAGATAACCCTTCTCGCCTTGAGTTATGATGT
1 CTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGT
*
2411921 AAATTTGATATGTCC-TTGAA
66 AAATTTGATATG-CCTTTGAG
* *
2411941 CTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCTCCTTGAGCTATGCTGT
1 CTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGT
*
2412006 AAATTTGATGTGCCTTTGAG
66 AAATTTGATATGCCTTTGAG
* * *
2412026 CTGAATGTAATCAAACTCGAAGGTCTTTGCTGATAGATAACCCTTCTCGCCTTGAGTTATGCTGT
1 CTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGT
*
2412091 AAATTTAATATGCCTTTGAG
66 AAATTTGATATGCCTTTGAG
* * * * ** *
2412111 CTAAATGTAATCGAATTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAACTATGTTGT
1 CTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGT
2412176 AAATTTGATATGCCTTTGAG
66 AAATTTGATATGCCTTTGAG
* * *
2412196 CT-ACATGTAATCGAACTCAAAGGTCTTTGTTGACAGATAACCCTTTTCGCTTTGAGTTATGCTG
1 CTGA-ATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTG
2412260 TAAATTTGATATGCC-TTGAG
65 TAAATTTGATATGCCTTTGAG
* * * *
2412280 CTGAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACACTTCTCGCCTTGAGCTATGCTAT
1 CTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGT
2412345 AAATTTGATATGCCTTTGAG
66 AAATTTGATATGCCTTTGAG
* * * * * *
2412365 TTGAATGTAATCGAACTCAAAGGTCTTTGCTGACAGATAACCCTTTTTGCCTTGAGTTATGCGGT
1 CTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGT
2412430 AAATTTGATATGCCTTTGAG
66 AAATTTGATATGCCTTTGAG
* * * * * * *
2412450 CTGAATGTAATTGAACTCGAAGGTCTTGGTTGACATATAGCCCTTCTTGCCTTGAGCTATGCTGC
1 CTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGT
2412515 AAAT
66 AAAT
2412519 AGATCCTTTA
Statistics
Matches: 574, Mismatches: 83, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
84 81 0.14
85 493 0.86
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (85 bp):
CTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGT
AAATTTGATATGCCTTTGAG
Found at i:2412395 original size:339 final size:340
Alignment explanation
Indices: 2411774--2412510 Score: 1050
Period size: 339 Copynumber: 2.2 Consensus size: 340
2411764 CATCGAACTG
* * * * * * **
2411774 AATGTAATTGAACTCGATA-GTTTTTGTTGACAGATAGCCTTTCTCGACTT-AAGTTATACTGTA
1 AATGTAATCGAACTCGA-AGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAA-CTATGTTGTA
* * * ** * *
2411837 AATTTAACATGCCCTTT-AGTTGTATGGAATCAAACTCGAAGGTATTTGTTGAAAGATAACCCTT
64 AATTTGATATG-CCTTTGAGCTACATGTAATCAAACTCAAAGGTATTTGTTGAAAGATAACCCTT
2411901 CTCGCCTTGAGTTATGATGTAAATTTGATATGTCCTTGAACTGAATGTAATCGAACTCGAAGGTC
128 CTCGCCTTGAGTTATGATGTAAATTTGATATGTCCTTGAACTGAATGTAATCGAACTCGAAGGTC
* * * * *
2411966 TTTGTTGACAGATAACCCTTCTCTCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAA
193 TTGGTTGACAGATAACACTTCTCGCCTTGAGCTATGCTATAAATTTGATATGCCTTTGAGCTGAA
* * *
2412031 TGTAATCAAACTCGAAGGTCTTTGCTGATAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATT
258 TGTAATCAAACTCAAAGGTCTTTGCTGACAGATAACCCTTCTCGCCTTGAGTTATGCGGTAAATT
2412096 TAATATGCCTTTGAGCTA
323 TAATATGCCTTTGAGCTA
*
2412114 AATGTAATCGAATTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAACTATGTTGTAAA
1 AATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAACTATGTTGTAAA
* * * *
2412179 TTTGATATGCCTTTGAGCTACATGTAATCGAACTCAAAGGTCTTTGTTGACAGATAACCCTTTTC
66 TTTGATATGCCTTTGAGCTACATGTAATCAAACTCAAAGGTATTTGTTGAAAGATAACCCTTCTC
* * *
2412244 GCTTTGAGTTATGCTGTAAATTTGATATG-CCTTGAGCTGAATGTAATCGAACTCGAAGGTCTTG
131 GCCTTGAGTTATGATGTAAATTTGATATGTCCTTGAACTGAATGTAATCGAACTCGAAGGTCTTG
*
2412308 GTTGACAGATAACACTTCTCGCCTTGAGCTATGCTATAAATTTGATATGCCTTTGAGTTGAATGT
196 GTTGACAGATAACACTTCTCGCCTTGAGCTATGCTATAAATTTGATATGCCTTTGAGCTGAATGT
* * * *
2412373 AATCGAACTCAAAGGTCTTTGCTGACAGATAACCCTTTTTGCCTTGAGTTATGCGGTAAATTTGA
261 AATCAAACTCAAAGGTCTTTGCTGACAGATAACCCTTCTCGCCTTGAGTTATGCGGTAAATTTAA
*
2412438 TATGCCTTTGAGCTG
326 TATGCCTTTGAGCTA
* * * *
2412453 AATGTAATTGAACTCGAAGGTCTTGGTTGACATATAGCCCTTCTTGCCTTGAGCTATG
1 AATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAACTATG
2412511 CTGCAAATAG
Statistics
Matches: 352, Mismatches: 42, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
339 224 0.64
340 126 0.36
341 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (340 bp):
AATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAACTATGTTGTAAA
TTTGATATGCCTTTGAGCTACATGTAATCAAACTCAAAGGTATTTGTTGAAAGATAACCCTTCTC
GCCTTGAGTTATGATGTAAATTTGATATGTCCTTGAACTGAATGTAATCGAACTCGAAGGTCTTG
GTTGACAGATAACACTTCTCGCCTTGAGCTATGCTATAAATTTGATATGCCTTTGAGCTGAATGT
AATCAAACTCAAAGGTCTTTGCTGACAGATAACCCTTCTCGCCTTGAGTTATGCGGTAAATTTAA
TATGCCTTTGAGCTA
Found at i:2412778 original size:86 final size:86
Alignment explanation
Indices: 2412579--2412790 Score: 307
Period size: 86 Copynumber: 2.5 Consensus size: 86
2412569 AATTCTTTAA
**
2412579 ATGACTCCCCTTCACGGGAAAGCCAAATGGTATATTCTTCAGGTGGTTCCCCTTCGCAGGTATGA
1 ATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCAGGTATGA
* *
2412644 ATCAGGTGAGATAATCTTTGG
66 ACCAGGTGAGACAATCTTTGG
* * * * * *
2412665 ATGACTTCCCTTCATGTGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCGGGTCTGA
1 ATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCAGGTATGA
*
2412730 ACCAGGTGAGACGATCTTTGG
66 ACCAGGTGAGACAATCTTTGG
* *
2412751 ATGACTCCCCTTCACGGGAAAGCCATGTGGGATGTTCTTC
1 ATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTCTTC
2412791 GAGTGAATCC
Statistics
Matches: 109, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
86 109 1.00
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.30
Consensus pattern (86 bp):
ATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCAGGTATGA
ACCAGGTGAGACAATCTTTGG
Found at i:2414430 original size:35 final size:35
Alignment explanation
Indices: 2414356--2414427 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
2414346 GCATAAATTC
*
2414356 AAAGAAATATGAGAAAGTTCAAAAACAAGTTACAA
1 AAAGAAATATGAGAAAGTTAAAAAACAAGTTACAA
2414391 AAAGAAATATGAGAAAGTTAAAAAACAAGTT-CAA
1 AAAGAAATATGAGAAAGTTAAAAAACAAGTTACAA
2414425 AAA
1 AAA
2414428 AGAGGTTGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 6 0.17
35 30 0.83
ACGTcount: A:0.62, C:0.07, G:0.14, T:0.17
Consensus pattern (35 bp):
AAAGAAATATGAGAAAGTTAAAAAACAAGTTACAA
Found at i:2415122 original size:19 final size:19
Alignment explanation
Indices: 2415092--2415141 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
2415082 CTGGACCACA
* *
2415092 AATAAAAAATAAAATTAAT
1 AATAATAAATAAAATAAAT
*
2415111 AA-AATGAAATAAGATAAAT
1 AATAAT-AAATAAAATAAAT
2415130 AATAATAAATAA
1 AATAATAAATAA
2415142 TATATATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 21 0.81
20 3 0.12
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (19 bp):
AATAATAAATAAAATAAAT
Found at i:2415143 original size:10 final size:9
Alignment explanation
Indices: 2415098--2415141 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 9
2415088 CACAAATAAA
2415098 AAATAAAAT
1 AAATAAAAT
*
2415107 TAATAAAAT
1 AAATAAAAT
*
2415116 GAAATAAGAT
1 -AAATAAAAT
2415126 AAATAATAAT
1 AAATAA-AAT
2415136 AAATAA
1 AAATAA
2415142 TATATATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 14 0.48
10 15 0.52
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (9 bp):
AAATAAAAT
Found at i:2415190 original size:36 final size:37
Alignment explanation
Indices: 2415144--2415524 Score: 275
Period size: 36 Copynumber: 10.3 Consensus size: 37
2415134 ATAAATAATA
2415144 TATATATATATTTAAAAAT-ATTTTAAAACTATATAT
1 TATATATATATTTAAAAATAATTTTAAAACTATATAT
* * * *
2415180 TATATATATATTTTTAAAACAGTTTTCAAAACCATATAT
1 TATATATATA-TTTAAAAATAATTTT-AAAACTATATAT
* ** * *
2415219 TATATA-AT-TTTCAAAATGTTTTTTAAACCATATAT
1 TATATATATATTTAAAAATAATTTTAAAACTATATAT
* *
2415254 TATATATGT-TTTCAAAAAT-GTTTTAAAACTATATAT
1 TATATATATATTT-AAAAATAATTTTAAAACTATATAT
* * *
2415290 TATATA-AGTTTTTCAAAATAATTTCAAAACTATATAT
1 TATATATA-TATTTAAAAATAATTTTAAAACTATATAT
* *
2415327 TATATA-AGT-TTTCAAAATAATTTCAAAACTATATAT
1 TATATATA-TATTTAAAAATAATTTTAAAACTATATAT
** * **
2415363 TATATA-AGGTTTTAAAA-GGTTTTCAAAAACTATATA-
1 TATATATATATTTAAAAATAATTTT--AAAACTATATAT
* ** *
2415399 T-TATATAT-TTTCAAAATGTTTTTTAAAAACTATATAA
1 TATATATATATTTAAAAAT-AATTTT-AAAACTATATAT
* **
2415436 TATATATACATTTTCAAAAATCGTTTTCAAAACTATATAT
1 TATATATATA-TTT-AAAAATAATTTT-AAAACTATATAT
* * *
2415476 TATATATATATTTCAAAAATCATTTTCAAACTATATAA
1 TATATATATATTT-AAAAATAATTTTAAAACTATATAT
2415514 TATATATATAT
1 TATATATATAT
2415525 ATATATATAA
Statistics
Matches: 289, Mismatches: 37, Indels: 36
0.80 0.10 0.10
Matches are distributed among these distances:
35 31 0.11
36 106 0.37
37 55 0.19
38 33 0.11
39 32 0.11
40 27 0.09
41 5 0.02
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.45
Consensus pattern (37 bp):
TATATATATATTTAAAAATAATTTTAAAACTATATAT
Found at i:2415194 original size:27 final size:25
Alignment explanation
Indices: 2415148--2415199 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
2415138 ATAATATATA
2415148 TATATATTTAAAAATATTTTAAAAC
1 TATATATTTAAAAATATTTTAAAAC
* *
2415173 TATATATTATATATATATTTTTAAAAC
1 TATATATT-TAAAAATA-TTTTAAAAC
2415200 AGTTTTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 8 0.35
26 6 0.26
27 9 0.39
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (25 bp):
TATATATTTAAAAATATTTTAAAAC
Found at i:2415224 original size:73 final size:74
Alignment explanation
Indices: 2415141--2415521 Score: 269
Period size: 73 Copynumber: 5.2 Consensus size: 74
2415131 ATAATAAATA
*
2415141 ATATA-TATATATA-TTTAAAAAT-ATTTTAAAACTATATATTATATATATATTTTTAAAACAGT
1 ATATATTATATATAGTTTAAAAATAATTTTAAAACTATATATTATATATATATTTTCAAAA-AGT
*
2415203 TTTCAAAACC
65 TTTCAAAACT
* * ** * * *
2415213 ATATATTATATA-ATTTTCAAAATGTTTTTTAAACCATATA-T-TATATATGTTTTCAAAAATGT
1 ATATATTATATATAGTTTAAAAATAATTTTAAAACTATATATTATATATATATTTTCAAAAA-GT
2415275 TTT-AAAACT
65 TTTCAAAACT
* * *
2415284 ATATATTATATA-AGTTTTTCAAAATAATTTCAAAACTATATATTATATA-A-GTTTTCAAAATA
1 ATATATTATATATAG--TTTAAAAATAATTTTAAAACTATATATTATATATATATTTTCAAAA-A
*
2415346 -ATTTCAAAACT
63 GTTTTCAAAACT
* ** *
2415357 ATATATTATATA-AGGTTTTAAAA-GGTTTTCAAAA--ACTATA-TAT-TATATATTTTCAAAAT
1 ATATATTATATATA-GTTTAAAAATAATTTT-AAAACTA-TATATTATATATATATTTTCAAAAA
*
2415416 GTTTTTTAAAAACT
63 G--TTTTCAAAACT
* * **
2415430 ATATAATATATATACATTTTCAAAAATCGTTTTCAAAACTATATATTATATATATA-TTTCAAAA
1 ATAT-AT-TATATATAGTTT-AAAAATAATTTT-AAAACTATATATTATATATATATTTTCAAAA
*
2415494 ATCATTTTC-AAACT
62 A--GTTTTCAAAACT
*
2415508 ATATAATATATATA
1 ATATATTATATATA
2415522 TATATATATA
Statistics
Matches: 250, Mismatches: 30, Indels: 54
0.75 0.09 0.16
Matches are distributed among these distances:
69 2 0.01
70 5 0.02
71 35 0.14
72 40 0.16
73 78 0.31
74 19 0.08
75 13 0.05
76 12 0.05
77 11 0.04
78 13 0.05
79 16 0.06
80 6 0.02
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (74 bp):
ATATATTATATATAGTTTAAAAATAATTTTAAAACTATATATTATATATATATTTTCAAAAAGTT
TTCAAAACT
Found at i:2419513 original size:39 final size:39
Alignment explanation
Indices: 2419458--2419533 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
2419448 GACTTTACTA
2419458 TAGGCTCCTCGACTTTGTGCTCAGGATAAGTCCTTACCG
1 TAGGCTCCTCGACTTTGTGCTCAGGATAAGTCCTTACCG
* *
2419497 TAGGCTCCTCGGCTTTGTGCTCAGGGTAAGTCCTTAC
1 TAGGCTCCTCGACTTTGTGCTCAGGATAAGTCCTTAC
2419534 TGCAAGTCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.16, C:0.28, G:0.25, T:0.32
Consensus pattern (39 bp):
TAGGCTCCTCGACTTTGTGCTCAGGATAAGTCCTTACCG
Found at i:2420990 original size:18 final size:18
Alignment explanation
Indices: 2420945--2420982 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2420935 AACAGGAAAC
*
2420945 ATCGA-ACCTAAAATGGGT
1 ATCGATACC-AAAAGGGGT
2420963 ATCGATACCAAAAGGGGT
1 ATCGATACCAAAAGGGGT
2420981 AT
1 AT
2420983 TGGTACCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (18 bp):
ATCGATACCAAAAGGGGT
Found at i:2421432 original size:54 final size:54
Alignment explanation
Indices: 2421350--2422017 Score: 773
Period size: 54 Copynumber: 12.3 Consensus size: 54
2421340 ATTACCAAAT
* * * *
2421350 AGGCACCAAGTGTGCATTTCATGGAATTCATCATGAGTTAATGAATAACTGTAC
1 AGGCACTAAGTGTGCATTTCACGGAATTCATCATGAGTTGATGAATAACCGTAC
2421404 AGGCACTAAGTGTGCATTTCACGGAATTCATCATGAGTTGATGAATAACCGTAC
1 AGGCACTAAGTGTGCATTTCACGGAATTCATCATGAGTTGATGAATAACCGTAC
* * * * * *
2421458 ATGTACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTAC
1 AGGCACTAAGTGTGC-ATTTCACGGAATTCATCATGAGTTGATGAATAACCGTAC
** *
2421513 CTGCACTAAGTGTGCATTTCATGGAATTCATCATGAGTTGATGAATAACCGTAC
1 AGGCACTAAGTGTGCATTTCACGGAATTCATCATGAGTTGATGAATAACCGTAC
* *
2421567 AGACACTAAGTGTGCATTTCACGAAATTCATCATGAGTTGATGAATAACCGTAC
1 AGGCACTAAGTGTGCATTTCACGGAATTCATCATGAGTTGATGAATAACCGTAC
* ** *
2421621 ATGCACTAAGTGTGTGTTTCACGGAATTCATCATGAGTTGATGAATAACCGTAT
1 AGGCACTAAGTGTGCATTTCACGGAATTCATCATGAGTTGATGAATAACCGTAC
** *
2421675 AGGCACTAAGTGTATATTTCACGGAATTCATCATGAGTTAATGAATAACCGTAC
1 AGGCACTAAGTGTGCATTTCACGGAATTCATCATGAGTTGATGAATAACCGTAC
* * * * * * ** * *
2421729 AAGCATTATGTGTGTAAATCCACATAATTTATCATGAGTTGATGAATAACCATAC
1 AGGCACTAAGTGTG-CATTTCACGGAATTCATCATGAGTTGATGAATAACCGTAC
* * ** * *
2421784 AAGCATTAAGTGTGCATTTCATAGAATCCATCATGAGTTGATGAATAATCGTAC
1 AGGCACTAAGTGTGCATTTCACGGAATTCATCATGAGTTGATGAATAACCGTAC
* ** * *
2421838 AAGCACTAAGTGTGCATTTCAAAGAATTCATCATGAGTTGATGAATAACTGTAT
1 AGGCACTAAGTGTGCATTTCACGGAATTCATCATGAGTTGATGAATAACCGTAC
* * * *
2421892 A-ACAACTAAGTGTGTATTTCACGGAATTCATCATGAGTTGTTGAATAACTGTAC
1 AGGC-ACTAAGTGTGCATTTCACGGAATTCATCATGAGTTGATGAATAACCGTAC
* * * ** * * *
2421946 ATGCACTATGTGTACAAATCTACGAAATTCATCATGATTTGATGAACT-ACCGTAT
1 AGGCACTAAGTGTGCATTTC-ACGGAATTCATCATGAGTTGATGAA-TAACCGTAC
*
2422001 AGGCACTACGTGTGCAT
1 AGGCACTAAGTGTGCAT
2422018 CTTAATAAAT
Statistics
Matches: 526, Mismatches: 82, Indels: 11
0.85 0.13 0.02
Matches are distributed among these distances:
53 1 0.00
54 390 0.74
55 134 0.25
56 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (54 bp):
AGGCACTAAGTGTGCATTTCACGGAATTCATCATGAGTTGATGAATAACCGTAC
Found at i:2421765 original size:217 final size:213
Alignment explanation
Indices: 2421357--2422017 Score: 788
Period size: 217 Copynumber: 3.0 Consensus size: 213
2421347 AATAGGCACC
* * * *
2421357 AAGTGTGCATTTCATGGAATTCATCATGAGTTAATGAATAACTGTACAGGCACTAAGTGTGCATT
1 AAGTGTGCATTTCA-GAAATTCATCATGAGTTGATGAATAACCGTACAAGCACTAAGTGTGCATT
* * * * * *
2421422 TCACGGAATTCATCATGAGTTGATGAATAACCGTACATGTACTATGTGTGCA-AATCCACAGAAT
65 TCACGGAATTCATCATGAGTTGATGAATAACCGTATA-GCACTAAGTGT--ATATTTCACGGAAT
* * * * * **
2421486 TCATCATGAGTTGATGAATAACCGTACCTGCACTAAGTGTGCATTTCATGGAATTCATCATGAGT
127 TCATCATGAGTTGATGAATAACCGTACATGCACTATGTGTGAAATCCA-CAAATTCATCATGAGT
2421551 TGATGAATAACCGTACAGACACT
191 TGATGAATAACCGTACAGACACT
* **
2421574 AAGTGTGCATTTCACGAAATTCATCATGAGTTGATGAATAACCGTACATGCACTAAGTGTGTGTT
1 AAGTGTGCATTTCA-GAAATTCATCATGAGTTGATGAATAACCGTACAAGCACTAAGTGTGCATT
2421639 TCACGGAATTCATCATGAGTTGATGAATAACCGTATAGGCACTAAGTGTATATTTCACGGAATTC
65 TCACGGAATTCATCATGAGTTGATGAATAACCGTATA-GCACTAAGTGTATATTTCACGGAATTC
* * * *
2421704 ATCATGAGTTAATGAATAACCGTACAAGCATTATGTGTGTAAATCCACATAATTTATCATGAGTT
129 ATCATGAGTTGATGAATAACCGTACATGCACTATGTGTG-AAATCCACA-AATTCATCATGAGTT
* *
2421769 GATGAATAACCATACA-AGCATT
192 GATGAATAACCGTACAGA-CACT
* * *
2421791 AAGTGTGCATTTCATAGAATCCATCATGAGTTGATGAATAATCGTACAAGCACTAAGTGTGCATT
1 AAGTGTGCATTTCAGA-AATTCATCATGAGTTGATGAATAACCGTACAAGCACTAAGTGTGCATT
** * * *
2421856 TCAAAGAATTCATCATGAGTTGATGAATAACTGTATAACAACTAAGTGTGTATTTCACGGAATTC
65 TCACGGAATTCATCATGAGTTGATGAATAACCGTATAGC-ACTAAGTGTATATTTCACGGAATTC
* * * * *
2421921 ATCATGAGTTGTTGAATAACTGTACATGCACTATGTGTACAAATCTACGAAATTCATCATGATTT
129 ATCATGAGTTGATGAATAACCGTACATGCACTATGTGT-GAAATCCAC-AAATTCATCATGAGTT
* *
2421986 GATGAACT-ACCGTATAGGCACT
192 GATGAA-TAACCGTACAGACACT
*
2422008 ACGTGTGCAT
1 AAGTGTGCAT
2422018 CTTAATAAAT
Statistics
Matches: 382, Mismatches: 52, Indels: 20
0.84 0.11 0.04
Matches are distributed among these distances:
215 1 0.00
216 48 0.13
217 331 0.87
218 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (213 bp):
AAGTGTGCATTTCAGAAATTCATCATGAGTTGATGAATAACCGTACAAGCACTAAGTGTGCATTT
CACGGAATTCATCATGAGTTGATGAATAACCGTATAGCACTAAGTGTATATTTCACGGAATTCAT
CATGAGTTGATGAATAACCGTACATGCACTATGTGTGAAATCCACAAATTCATCATGAGTTGATG
AATAACCGTACAGACACT
Found at i:2421847 original size:271 final size:270
Alignment explanation
Indices: 2421352--2422016 Score: 922
Period size: 271 Copynumber: 2.5 Consensus size: 270
2421342 TACCAAATAG
* * * *
2421352 GCACCAAGTGTGCATTTCATGGAATTCATCATGAGTTAATGAATAACTGTACAGGCACTAAGTGT
1 GCACTAAGTGTGTATTTCACGGAATTCATCATGAGTTGATGAATAACTGTACAGGCACTAAGTGT
* * *
2421417 GCATTTCACGGAATTCATCATGAGTTGATGAATAACCGTACATGTACTATGTGTGCAAATCCACA
66 ACATTTCACGGAATTCATCATGAGTTGATGAATAACCGTACAAGCACTATGTGTGCAAATCCACA
* ** * *
2421482 GAATTCATCATGAGTTGATGAATAACCGTACCTGCACTAAGTGTGCATTTCATGGAATTCATCAT
131 GAATTCATCATGAGTTGATGAATAACCATACAAGCACTAAGTGTGCATTTCATAGAATCCATCAT
*
2421547 GAGTTGATGAATAACCGTACAGACACTAAGTGTGCATTTC-ACGAAATTCATCATGAGTTGATGA
196 GAGTTGATGAATAACCGTACAGACACTAAGTGTGCATTTCAAAG-AATTCATCATGAGTTGATGA
2421611 ATAACCGTACA
260 ATAACCGTACA
* * *
2421622 TGCACTAAGTGTGTGTTTCACGGAATTCATCATGAGTTGATGAATAACCGTATAGGCACTAAGTG
1 -GCACTAAGTGTGTATTTCACGGAATTCATCATGAGTTGATGAATAACTGTACAGGCACTAAGTG
* * * *
2421687 TATATTTCACGGAATTCATCATGAGTTAATGAATAACCGTACAAGCATTATGTGTGTAAATCCAC
65 TACATTTCACGGAATTCATCATGAGTTGATGAATAACCGTACAAGCACTATGTGTGCAAATCCAC
* * *
2421752 ATAATTTATCATGAGTTGATGAATAACCATACAAGCATTAAGTGTGCATTTCATAGAATCCATCA
130 AGAATTCATCATGAGTTGATGAATAACCATACAAGCACTAAGTGTGCATTTCATAGAATCCATCA
*
2421817 TGAGTTGATGAATAATCGTACA-AGCACTAAGTGTGCATTTCAAAGAATTCATCATGAGTTGATG
195 TGAGTTGATGAATAACCGTACAGA-CACTAAGTGTGCATTTCAAAGAATTCATCATGAGTTGATG
* *
2421881 AATAACTGTATA
259 AATAACCGTACA
* * * *
2421893 ACAACTAAGTGTGTATTTCACGGAATTCATCATGAGTTGTTGAATAACTGTACATGCACTATGTG
1 GC-ACTAAGTGTGTATTTCACGGAATTCATCATGAGTTGATGAATAACTGTACAGGCACTAAGTG
** * * * * *
2421958 TACAAATCTACGAAATTCATCATGATTTGATGAACT-ACCGTATAGGCACTACGTGTGCA
65 TACATTTC-ACGGAATTCATCATGAGTTGATGAA-TAACCGTACAAGCACTATGTGTGCA
2422017 TCTTAATAAA
Statistics
Matches: 345, Mismatches: 44, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
270 2 0.01
271 300 0.87
272 42 0.12
273 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (270 bp):
GCACTAAGTGTGTATTTCACGGAATTCATCATGAGTTGATGAATAACTGTACAGGCACTAAGTGT
ACATTTCACGGAATTCATCATGAGTTGATGAATAACCGTACAAGCACTATGTGTGCAAATCCACA
GAATTCATCATGAGTTGATGAATAACCATACAAGCACTAAGTGTGCATTTCATAGAATCCATCAT
GAGTTGATGAATAACCGTACAGACACTAAGTGTGCATTTCAAAGAATTCATCATGAGTTGATGAA
TAACCGTACA
Found at i:2422389 original size:2 final size:2
Alignment explanation
Indices: 2422382--2422412 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2422372 AGAAGGGGTG
*
2422382 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2422413 ATGTACAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2426884 original size:54 final size:53
Alignment explanation
Indices: 2426789--2426994 Score: 270
Period size: 54 Copynumber: 3.8 Consensus size: 53
2426779 TACCAAATAG
* *
2426789 GCACCAAGTGTGTATTTCACGGAATTCATCATGAGTTGATGAATAATCGTACAT
1 GCACTAAGTGTGCATTTCACGGAATTCATCATGAGTTGATGAATAA-CGTACAT
*
2426843 GCACTAAATGTGCATTTCACGGAATTCATCATGAGTTGATGAATAACCGTACA-
1 GCACTAAGTGTGCATTTCACGGAATTCATCATGAGTTGATGAATAA-CGTACAT
* *
2426896 GTCACTAAGTGTGCATTTCATGGAATTCATCATAAGTTGATGAATAACTGTACAT
1 G-CACTAAGTGTGCATTTCACGGAATTCATCATGAGTTGATGAATAAC-GTACAT
* * * * *
2426951 GCACTATGTGTGCAAATCCACGAAATTCATCATGATTTGATGAA
1 GCACTAAGTGTGC-ATTTCACGGAATTCATCATGAGTTGATGAA
2426995 CTACCGTATT
Statistics
Matches: 134, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
53 2 0.01
54 107 0.80
55 25 0.19
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (53 bp):
GCACTAAGTGTGCATTTCACGGAATTCATCATGAGTTGATGAATAACGTACAT
Found at i:2427010 original size:55 final size:54
Alignment explanation
Indices: 2426788--2427017 Score: 216
Period size: 54 Copynumber: 4.2 Consensus size: 54
2426778 TTACCAAATA
* * * * *
2426788 GGCACCAAGTGTGTATTTCACGGAATTCATCATGAGTTGATGAATAATCGTACAT
1 GGCACTAAGTGTGCAATCCACGGAATTCATCATGAGTTGATGAATAACCGTA-AT
* * *
2426843 -GCACTAAATGTGCATTTCACGGAATTCATCATGAGTTGATGAATAACCGTACA-
1 GGCACTAAGTGTGCAATCCACGGAATTCATCATGAGTTGATGAATAACCGTA-AT
* * * * * *
2426896 GTCACTAAGTGTGCATTTCATGGAATTCATCATAAGTTGATGAATAACTGTACAT
1 GGCACTAAGTGTGCAATCCACGGAATTCATCATGAGTTGATGAATAACCGTA-AT
* * * *
2426951 -GCACTATGTGTGCAAATCCACGAAATTCATCATGATTTGATGAACT-ACCGTATT
1 GGCACTAAGTGTGC-AATCCACGGAATTCATCATGAGTTGATGAA-TAACCGTAAT
*
2427005 GGCACTACGTGTG
1 GGCACTAAGTGTG
2427018 TATCTTAATA
Statistics
Matches: 150, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
54 109 0.73
55 40 0.27
56 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (54 bp):
GGCACTAAGTGTGCAATCCACGGAATTCATCATGAGTTGATGAATAACCGTAAT
Found at i:2427389 original size:2 final size:2
Alignment explanation
Indices: 2427382--2427412 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2427372 AAAAGGGGTG
*
2427382 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2427413 ATGTACAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2435265 original size:23 final size:23
Alignment explanation
Indices: 2435232--2435296 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
2435222 TAGAATTTGA
2435232 CCCGAAGGACCACGTAGAAATAT
1 CCCGAAGGACCACGTAGAAATAT
* * **
2435255 CCCGAATGACCACATAGATTTAT
1 CCCGAAGGACCACGTAGAAATAT
*
2435278 CCCGAAGGACCGCGTAGAA
1 CCCGAAGGACCACGTAGAA
2435297 CCCTCGACTC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.35, C:0.28, G:0.22, T:0.15
Consensus pattern (23 bp):
CCCGAAGGACCACGTAGAAATAT
Found at i:2435873 original size:20 final size:20
Alignment explanation
Indices: 2435850--2435897 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
2435840 CATTAGTATT
2435850 GATACCCCTCCTATAGTACC
1 GATACCCCTCCTATAGTACC
* * *
2435870 GATACTTCTCTTCTATGGTACC
1 GATAC--CCCTCCTATAGTACC
2435892 GATACC
1 GATACC
2435898 TCCTTCAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 6 0.26
22 17 0.74
ACGTcount: A:0.23, C:0.33, G:0.12, T:0.31
Consensus pattern (20 bp):
GATACCCCTCCTATAGTACC
Found at i:2440365 original size:19 final size:19
Alignment explanation
Indices: 2440341--2440390 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
2440331 ATAAAAGTGA
2440341 AAAAGTGAAAAAGTAAAGT
1 AAAAGTGAAAAAGTAAAGT
2440360 AAAAGTGAAAAAGTAAAGT
1 AAAAGTGAAAAAGTAAAGT
2440379 AAAAGT-AAAAAG
1 AAAAGTGAAAAAG
2440391 AAGATAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 6 0.19
19 25 0.81
ACGTcount: A:0.66, C:0.00, G:0.20, T:0.14
Consensus pattern (19 bp):
AAAAGTGAAAAAGTAAAGT
Found at i:2453440 original size:14 final size:14
Alignment explanation
Indices: 2453421--2453451 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2453411 AAATTTTAAA
2453421 AAATTAAGAGGTTT
1 AAATTAAGAGGTTT
*
2453435 AAATTAAGAGTTTT
1 AAATTAAGAGGTTT
2453449 AAA
1 AAA
2453452 AATTTTGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.35
Consensus pattern (14 bp):
AAATTAAGAGGTTT
Found at i:2454960 original size:66 final size:64
Alignment explanation
Indices: 2454856--2454986 Score: 199
Period size: 66 Copynumber: 2.0 Consensus size: 64
2454846 TTGTGAATTA
* * * *
2454856 AAGAAAATGGACTCTGACTTTCTTCCTCAAATCCTCAATATAAACTTAAGTCACGATACTCTTC
1 AAGAAAAGGGACTCTGACTTTCTTCCCCAAATCCTCAATATAAACTTAAGTCACCAGACTCTTC
*
2454920 AAGAAAAGGGACTCTTTGACTTTCTTCCCCAAATCCTCAATGTAAACTTAAGTCACCAGACTCTT
1 AAGAAAAGGGACTC--TGACTTTCTTCCCCAAATCCTCAATATAAACTTAAGTCACCAGACTCTT
2454985 C
64 C
2454986 A
1 A
2454987 CTAGGGTATT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
64 13 0.22
66 47 0.78
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.30
Consensus pattern (64 bp):
AAGAAAAGGGACTCTGACTTTCTTCCCCAAATCCTCAATATAAACTTAAGTCACCAGACTCTTC
Found at i:2456618 original size:18 final size:18
Alignment explanation
Indices: 2456595--2456630 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2456585 AAAAGTATTT
2456595 TTCATTTTAATAAAAACA
1 TTCATTTTAATAAAAACA
*
2456613 TTCATTTTAATTAAAACA
1 TTCATTTTAATAAAAACA
2456631 ACAAATTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (18 bp):
TTCATTTTAATAAAAACA
Found at i:2457220 original size:131 final size:130
Alignment explanation
Indices: 2456977--2457344 Score: 529
Period size: 131 Copynumber: 2.8 Consensus size: 130
2456967 ATAATTTTAA
* *
2456977 GAGAGAAAACTATAATATCTAATTATTTCCGATCGAGAATAAATGACCTCTCATACCTTAAAGTA
1 GAGAGAAAA-TATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCA
* * * *
2457042 GTCATTTATTACTCTAATCGAAATGAAGATATATCACTATTTAGTCTTAAAATTCAATATCGATT
65 GTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCAGTCTTAAAACTCAATATCGATT
2457107 C
130 C
* * *
2457108 GAGTGAAAATGATAATATCTAATGATTTTCAATCGAGAATAAATGACCTCTCATACCTTAAAGCA
1 GAGAGAAAAT-ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCA
* * *
2457173 CTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAACTCAATATTGATT
65 GTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCAGTCTTAAAACTCAATATCGATT
2457238 C
130 C
* * *
2457239 GAGAGAAAATAGTAATATCGAATTATTTCCAATCGAGAATAAATGACCTATCATGCCTTAAAGCA
1 GAGAGAAAATA-TAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCA
* ** * *
2457304 GTCATTTATTACTTCAGCCGAAATGAGGAGATATTACTATT
65 GTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATT
2457345 ATCAACATCG
Statistics
Matches: 211, Mismatches: 24, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
130 2 0.01
131 209 0.99
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (130 bp):
GAGAGAAAATATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAG
TCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCAGTCTTAAAACTCAATATCGATTC
Found at i:2459438 original size:3 final size:3
Alignment explanation
Indices: 2459430--2459472 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
2459420 AATAAACATA
2459430 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2459473 GCGGGACGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2459899 original size:136 final size:134
Alignment explanation
Indices: 2459628--2460090 Score: 484
Period size: 136 Copynumber: 3.4 Consensus size: 134
2459618 TTCACCGTAG
* * * ** *
2459628 ATCAGATCTAGAAACGTTGATTCATTCCT-CTATTCTTTAGGGAAGATTGAATCGGGACAGACTT
1 ATCAGATATAGAAATGTTGATTCATT-CTACTATTCTTCAGGGAAGATTGAATCAAGACAAACTT
* * * ** * *
2459692 TTTCCACTGTTACTAAGGGAAGATCAAATCTGGAAAGAGAGGAGATTTGTTCCATTGCTTTTTTT
65 GTTCCACTGTTACTCAGGGAAGATCAAATCTGGAAAGAGA-AAGATTTGTTCCGCTGC-TTCTTC
2459757 AAGGAAA
128 AAGGAAA
* *
2459764 ATCAGATCTAGAAATGTTGATTCATTCTACTATTCTTCAAGGAAGATTGAATCAAGACAAACTTG
1 ATCAGATATAGAAATGTTGATTCATTCTACTATTCTTCAGGGAAGATTGAATCAAGACAAACTTG
* * * *
2459829 TTCCACTGTTCCTCAGGGAAGATCAAATCTGGAAAAAAATATAGATTTGTTTCGCTGCTTCTTCA
66 TTCCACTGTTACTCAGGGAAGATCAAATCTGGAAAGAGA-A-AGATTTGTTCCGCTGCTTCTTCA
*
2459894 GGGAAA
129 AGGAAA
* * * * * ** *
2459900 ATCAGATATGGAAATATTGATTCATT-TCACTGTTCTTTAGGGAAGATTGAATCGAGGTACACTT
1 ATCAGATATAGAAATGTTGATTCATTCT-ACTATTCTTCAGGGAAGATTGAATCAAGACAAACTT
* * * * * * *
2459964 GTTCCACTGCTACTCAAGGAATATCAAATCTAGAAAGAGAGAAGATATATTCCGCTGCTTCTTGA
65 GTTCCACTGTTACTCAGGGAAGATCAAATCTGGAAAGAGA-AAGATTTGTTCCGCTGCTTCTTCA
*
2460029 AAGAAA
129 AGGAAA
*
2460035 ATCAAATAT-GTAAATGTTGATTCATTCTACTGA-TCTTCAGGGAAGATTGAATCAAG
1 ATCAGATATAG-AAATGTTGATTCATTCTACT-ATTCTTCAGGGAAGATTGAATCAAG
2460091 TTAGATTTGC
Statistics
Matches: 273, Mismatches: 48, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
134 1 0.00
135 72 0.26
136 187 0.68
137 13 0.05
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.32
Consensus pattern (134 bp):
ATCAGATATAGAAATGTTGATTCATTCTACTATTCTTCAGGGAAGATTGAATCAAGACAAACTTG
TTCCACTGTTACTCAGGGAAGATCAAATCTGGAAAGAGAAAGATTTGTTCCGCTGCTTCTTCAAG
GAAA
Found at i:2462003 original size:20 final size:20
Alignment explanation
Indices: 2461978--2462024 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
2461968 GGTTGGGGTA
2461978 TCGATACTGGATGAATAGTG
1 TCGATACTGGATGAATAGTG
2461998 TCGATACTGGATGAATAGTG
1 TCGATACTGGATGAATAGTG
2462018 TCGATAC
1 TCGATAC
2462025 CAAAAGGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.30
Consensus pattern (20 bp):
TCGATACTGGATGAATAGTG
Found at i:2462958 original size:23 final size:23
Alignment explanation
Indices: 2462924--2463024 Score: 96
Period size: 23 Copynumber: 4.4 Consensus size: 23
2462914 GAGTCGAGGG
*
2462924 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
** *
2462947 TTCTACGTGGTCCTTCAAGACAT
1 TTCTACGTGGTCCTTCGGGACAA
* *
2462970 TTATACGCGGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
* ** *
2462993 TACTATATGGTCCTTCGGAAC-A
1 TTCTACGTGGTCCTTCGGGACAA
*
2463015 TTCTATGTGG
1 TTCTACGTGG
2463025 CACTTCGATG
Statistics
Matches: 61, Mismatches: 17, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
22 9 0.15
23 52 0.85
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.32
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAA
Found at i:2463043 original size:24 final size:24
Alignment explanation
Indices: 2463015--2463069 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
2463005 CTTCGGAACA
*
2463015 TTCTATGTGGCACTTCGATGCAAT
1 TTCTATGCGGCACTTCGATGCAAT
** *
2463039 TTCTACACGGCACTTCGTTGCAAT
1 TTCTATGCGGCACTTCGATGCAAT
*
2463063 TTATATG
1 TTCTATG
2463070 AGCTGTGGTG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (24 bp):
TTCTATGCGGCACTTCGATGCAAT
Found at i:2465152 original size:20 final size:20
Alignment explanation
Indices: 2465127--2465174 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
2465117 GTTGTTTGAC
2465127 CGGTCTGAACTGGATTAAAA
1 CGGTCTGAACTGGATTAAAA
*
2465147 CGGTCTGAACTGGATTAAAC
1 CGGTCTGAACTGGATTAAAA
2465167 CGGTCTGA
1 CGGTCTGA
2465175 CCAGTCCGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (20 bp):
CGGTCTGAACTGGATTAAAA
Found at i:2465240 original size:17 final size:18
Alignment explanation
Indices: 2465197--2465247 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
2465187 GGGTTGACCC
2465197 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
2465215 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
2465233 GA-CCGACCCGACCCG
1 GACCCGACCCGACCCG
2465248 GTGATATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 13 0.39
18 20 0.61
ACGTcount: A:0.18, C:0.51, G:0.24, T:0.08
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:2465247 original size:5 final size:5
Alignment explanation
Indices: 2465192--2465230 Score: 51
Period size: 5 Copynumber: 7.2 Consensus size: 5
2465182 GAACCGGGTT
2465192 GACCC GACCC GACCC GACCC GTTGACCC GACCC GACCC G
1 GACCC GACCC GACCC GACCC ---GACCC GACCC GACCC G
2465231 TTGACCGACC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 26 0.84
8 5 0.16
ACGTcount: A:0.18, C:0.54, G:0.23, T:0.05
Consensus pattern (5 bp):
GACCC
Found at i:2465290 original size:29 final size:28
Alignment explanation
Indices: 2465248--2465407 Score: 187
Period size: 29 Copynumber: 5.6 Consensus size: 28
2465238 ACCCGACCCG
2465248 GTGATATTTTAGTAATTATTTTGAAACCA
1 GTGATATTTTAGTAATTATTTTGAAA-CA
*
2465277 GTGATATTTTAGTAATTATTTTGAAACC
1 GTGATATTTTAGTAATTATTTTGAAACA
*
2465305 GATGATATTTT-GTTAATTATTTTGAAAAA
1 G-TGATATTTTAG-TAATTATTTTGAAACA
* *
2465334 GTGATATTTTGGTAATTATTTTGAAAAA
1 GTGATATTTTAGTAATTATTTTGAAACA
* * *
2465362 TGTGATATTTTGGTAATTATTTTTAAAACG
1 -GTGATATTTTAGTAATTA-TTTTGAAACA
* *
2465392 GTGCTATTTTCGTAAT
1 GTGATATTTTAGTAAT
2465408 AGTTGACTGT
Statistics
Matches: 118, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
28 28 0.24
29 83 0.70
30 7 0.06
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (28 bp):
GTGATATTTTAGTAATTATTTTGAAACA
Found at i:2465356 original size:57 final size:56
Alignment explanation
Indices: 2465248--2465407 Score: 187
Period size: 57 Copynumber: 2.8 Consensus size: 56
2465238 ACCCGACCCG
* *
2465248 GTGATATTTTAGTAATTATTTTGAAACCAGTGATATTTTAGTAATTATTTTG-AAACC
1 GTGATATTTT-GTAATTATTTTGAAA-AAGTGATATTTTAGTAATTATTTTGAAAAAC
* *
2465305 GATGATATTTTGTTAATTATTTTGAAAAAGTGATATTTTGGTAATTATTTTGAAAAAT
1 G-TGATATTTTG-TAATTATTTTGAAAAAGTGATATTTTAGTAATTATTTTGAAAAAC
* * * *
2465363 GTGATATTTTGGTAATTATTTTTAAAACGGTGCTATTTTCGTAAT
1 GTGATATTTT-GTAATTATTTTGAAAA-AGTGATATTTTAGTAAT
2465408 AGTTGACTGT
Statistics
Matches: 90, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
57 48 0.53
58 42 0.47
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (56 bp):
GTGATATTTTGTAATTATTTTGAAAAAGTGATATTTTAGTAATTATTTTGAAAAAC
Found at i:2469149 original size:23 final size:24
Alignment explanation
Indices: 2469066--2469151 Score: 147
Period size: 24 Copynumber: 3.6 Consensus size: 24
2469056 ATATTTGTCT
2469066 CGAATGACCACATAGGATTGTCCC
1 CGAATGACCACATAGGATTGTCCC
2469090 CGAATGACCACATAGGATTGTCCC
1 CGAATGACCACATAGGATTGTCCC
2469114 CGAATGACCACATAGGATTGT-CC
1 CGAATGACCACATAGGATTGTCCC
* *
2469137 TGAAGGACCACATAG
1 CGAATGACCACATAG
2469152 AACCCTCGAC
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
23 15 0.25
24 45 0.75
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (24 bp):
CGAATGACCACATAGGATTGTCCC
Found at i:2479598 original size:74 final size:74
Alignment explanation
Indices: 2479477--2479625 Score: 253
Period size: 74 Copynumber: 2.0 Consensus size: 74
2479467 ATGTTAATCT
* *
2479477 AGCCCTAATAATGCTCAAAACTCCCTATAAAATCTCATTAAAAGCATTCTCATTTACCTTTTTCT
1 AGCCCTAATAATGCCCAAAACTCCCTATAAAATCTCATCAAAAGCATTCTCATTTACCTTTTTCT
*
2479542 TACTACACA
66 TACGACACA
*
2479551 AGCCCTAGTAATGCCCAAAACTCCCTATAAAATCTCATCAAAAGCATTCTCATTTACCTTTTTCT
1 AGCCCTAATAATGCCCAAAACTCCCTATAAAATCTCATCAAAAGCATTCTCATTTACCTTTTTCT
*
2479616 TGCGACACA
66 TACGACACA
2479625 A
1 A
2479626 AGCAGTGATT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (74 bp):
AGCCCTAATAATGCCCAAAACTCCCTATAAAATCTCATCAAAAGCATTCTCATTTACCTTTTTCT
TACGACACA
Found at i:2487794 original size:14 final size:15
Alignment explanation
Indices: 2487770--2487798 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2487760 GTGTATGATA
2487770 TGTATTATGATTATG
1 TGTATTATGATTATG
2487785 TGTA-TATGATTATG
1 TGTATTATGATTATG
2487799 GAAATGTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TGTATTATGATTATG
Found at i:2488124 original size:14 final size:14
Alignment explanation
Indices: 2488101--2488170 Score: 67
Period size: 14 Copynumber: 5.3 Consensus size: 14
2488091 TGAACAATAA
*
2488101 AATACAGTATGAAC
1 AATACCGTATGAAC
2488115 AATACCGTATGAAC
1 AATACCGTATGAAC
*
2488129 AGTA----ATGAAC
1 AATACCGTATGAAC
* *
2488139 ATTACCATATGAAC
1 AATACCGTATGAAC
*
2488153 AGTACCGTATGAAC
1 AATACCGTATGAAC
2488167 AATA
1 AATA
2488171 TTGTAAACAG
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
10 9 0.20
14 37 0.80
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (14 bp):
AATACCGTATGAAC
Found at i:2488138 original size:24 final size:24
Alignment explanation
Indices: 2488104--2488156 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2488094 ACAATAAAAT
*
2488104 ACAGT-ATGAACAATACCGTATGA
1 ACAGTAATGAACAATACCATATGA
*
2488127 ACAGTAATGAACATTACCATATGA
1 ACAGTAATGAACAATACCATATGA
2488151 ACAGTA
1 ACAGTA
2488157 CCGTATGAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23
Consensus pattern (24 bp):
ACAGTAATGAACAATACCATATGA
Found at i:2488256 original size:21 final size:23
Alignment explanation
Indices: 2488207--2488258 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
2488197 TTTTCCAGAT
* *
2488207 TGCTTCAGGCGAACCGATTCCCC
1 TGCTACAGGCGAACCGATTACCC
*
2488230 TTCTACAGG-GAACCGA-TACCC
1 TGCTACAGGCGAACCGATTACCC
2488251 TGCTACAG
1 TGCTACAG
2488259 TACTGCTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 11 0.44
22 7 0.28
23 7 0.28
ACGTcount: A:0.23, C:0.35, G:0.21, T:0.21
Consensus pattern (23 bp):
TGCTACAGGCGAACCGATTACCC
Found at i:2489029 original size:32 final size:32
Alignment explanation
Indices: 2488912--2489034 Score: 128
Period size: 31 Copynumber: 3.9 Consensus size: 32
2488902 ACCTCGGCAA
* * * *
2488912 CTGTCCATA-GGTCCGAAGAACCTAGGTAAAT
1 CTGTCCATATGTTCCGTAGAACATAGGTAATT
* *
2488943 -TGTCCATATGTTCCTTAGAACATAGGT-ATA
1 CTGTCCATATGTTCCGTAGAACATAGGTAATT
* * *
2488973 CTGTCCATATATCCCG-AAATACATAGGTAATT
1 CTGTCCATATGTTCCGTAGA-ACATAGGTAATT
2489005 CTGTCCATATGTTCCGTAGAACATAGGTAA
1 CTGTCCATATGTTCCGTAGAACATAGGTAA
2489035 ACCCTCAACT
Statistics
Matches: 73, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
30 11 0.15
31 34 0.47
32 26 0.36
33 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (32 bp):
CTGTCCATATGTTCCGTAGAACATAGGTAATT
Found at i:2496857 original size:248 final size:243
Alignment explanation
Indices: 2496416--2496898 Score: 894
Period size: 248 Copynumber: 2.0 Consensus size: 243
2496406 GTAGTTTCTG
2496416 GAGAAATTGATTTTTTTTAAACCTATACTTCTCATTTTTTTATATAAAAAATAATTCAACTTTAA
1 GAGAAATTGATTTTTTTTAAACCTATACTTCTCATTTTTTTATATAAAAAATAATTCAACTTTAA
*
2496481 GGTTCAAACTAACAATGGAGAGTAAGTAGCTTTAAATCATAAAATAATTTGAAAATCAAAGCTCC
66 GGTTCAAACTAACAATAGAGAGTAAGTAGCTTTAAATCATAAAATAATTTGAAAATCAAAGCTCC
2496546 CCCTCAATAAAAACATTCCAAGAAAACTTTTGACACAAAAGTTTAACACTTAAAAGACTATTGAA
131 CCCTCAATAAAAACATTCCAAGAAAACTTTTGACACAAAAGTTTAACACTTAAAAGACTATTGAA
2496611 TTTCAATAAGATAAGAAAGAAAACACATTAGTAGAACATTGAGAAATT
196 TTTCAATAAGATAAGAAAGAAAACACATTAGTAGAACATTGAGAAATT
2496659 GAGAAATTGATTTTTTTTAAACCTATACTTCTCATCATTTTTTTATATAAAAAATAATTCAACTT
1 GAGAAATTGATTTTTTTTAAACCTATAC-T-TC-TCATTTTTTTATATAAAAAATAATTCAACTT
2496724 TAAGGTTCAAACTAACAATAGAGAGTAAGTAGCTTTAAATCATAAAAATAATTTGAAAAATCAAA
63 TAAGGTTCAAACTAACAATAGAGAGTAAGTAGCTTTAAATCAT-AAAATAATTTG-AAAATCAAA
*
2496789 GCTCCCCCTCAATAAAAGCATTCCAAGAAAACTTTTGACACAAAAGTTTAACACTTAAAAGACTA
126 GCTCCCCCTCAATAAAAACATTCCAAGAAAACTTTTGACACAAAAGTTTAACACTTAAAAGACTA
*
2496854 TTGAATTTCAATAAGATAAGAAAGAAAACACATTAGTAGCACATT
191 TTGAATTTCAATAAGATAAGAAAGAAAACACATTAGTAGAACATT
2496899 AAATTCAATA
Statistics
Matches: 232, Mismatches: 3, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
243 28 0.12
244 1 0.00
245 2 0.01
246 73 0.31
247 11 0.05
248 117 0.50
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (243 bp):
GAGAAATTGATTTTTTTTAAACCTATACTTCTCATTTTTTTATATAAAAAATAATTCAACTTTAA
GGTTCAAACTAACAATAGAGAGTAAGTAGCTTTAAATCATAAAATAATTTGAAAATCAAAGCTCC
CCCTCAATAAAAACATTCCAAGAAAACTTTTGACACAAAAGTTTAACACTTAAAAGACTATTGAA
TTTCAATAAGATAAGAAAGAAAACACATTAGTAGAACATTGAGAAATT
Found at i:2497711 original size:21 final size:20
Alignment explanation
Indices: 2497687--2497735 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2497677 CTCAAAATAA
* *
2497687 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATCTAATTTTG
2497707 TTTTTCAAAATCTAATTTTG
1 TTTTTCAAAATCTAATTTTG
*
2497727 CTTTT-AAAA
1 TTTTTCAAAA
2497736 GAAAATCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTTTCAAAATCTAATTTTG
Found at i:2500944 original size:2 final size:2
Alignment explanation
Indices: 2500937--2500964 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2500927 ATATCTACAA
2500937 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2500965 GTTTCTATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2505693 original size:24 final size:24
Alignment explanation
Indices: 2505661--2505790 Score: 111
Period size: 24 Copynumber: 5.5 Consensus size: 24
2505651 CACCGAAGTG
*
2505661 CCACATAGAATTTGTCCCAAAGGA
1 CCACGTAGAATTTGTCCCAAAGGA
* * *
2505685 CCGCGTAGAATTTGTCCCGAATGA
1 CCACGTAGAATTTGTCCCAAAGGA
* * *
2505709 CAATGTAGAA-ATGTCCCAAAGGA
1 CCACGTAGAATTTGTCCCAAAGGA
* * *
2505732 CCACATAGAATTTGTCTCGAAGGA
1 CCACGTAGAATTTGTCCCAAAGGA
* ** * *
2505756 CAATATAGAA-TTATCCCGAAGGA
1 CCACGTAGAATTTGTCCCAAAGGA
2505779 CCACGTAGAATT
1 CCACGTAGAATT
2505791 GTCTTGAAAG
Statistics
Matches: 81, Mismatches: 23, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
23 35 0.43
24 46 0.57
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (24 bp):
CCACGTAGAATTTGTCCCAAAGGA
Found at i:2505741 original size:47 final size:47
Alignment explanation
Indices: 2505673--2505790 Score: 164
Period size: 47 Copynumber: 2.5 Consensus size: 47
2505663 ACATAGAATT
* * *
2505673 TGTCCCAAAGGACCGCGTAGAATTTGTCCCGAATGACAATGTAGAAA
1 TGTCCCAAAGGACCACGTAGAATTTGTCCCGAAGGACAATATAGAAA
* * *
2505720 TGTCCCAAAGGACCACATAGAATTTGTCTCGAAGGACAATATAGAAT
1 TGTCCCAAAGGACCACGTAGAATTTGTCCCGAAGGACAATATAGAAA
* *
2505767 TATCCCGAAGGACCACGTAGAATT
1 TGTCCCAAAGGACCACGTAGAATT
2505791 GTCTTGAAAG
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 62 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (47 bp):
TGTCCCAAAGGACCACGTAGAATTTGTCCCGAAGGACAATATAGAAA
Found at i:2506434 original size:24 final size:24
Alignment explanation
Indices: 2506406--2506459 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
2506396 TCTCTTCTAT
2506406 GATACCGATACCCACTTCAGTATC
1 GATACCGATACCCACTTCAGTATC
2506430 GATACCGATACCCACTTCAGTATC
1 GATACCGATACCCACTTCAGTATC
2506454 GATACC
1 GATACC
2506460 ATTTTTCGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.30, C:0.33, G:0.13, T:0.24
Consensus pattern (24 bp):
GATACCGATACCCACTTCAGTATC
Found at i:2518903 original size:30 final size:30
Alignment explanation
Indices: 2518844--2518975 Score: 194
Period size: 30 Copynumber: 4.4 Consensus size: 30
2518834 CCCGAAGGAC
* *
2518844 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
2518873 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
2518903 CTATCCAGAGGTCATAAAGATCCTTGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
2518933 CTGTCCATAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
2518963 CTGTCCATAGGTC
1 CTATCCAGAGGTC
2518976 TCGAAGAACC
Statistics
Matches: 96, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
29 19 0.20
30 77 0.80
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:2518992 original size:30 final size:30
Alignment explanation
Indices: 2518889--2519011 Score: 115
Period size: 30 Copynumber: 4.1 Consensus size: 30
2518879 AGAGGTCATA
* * * *
2518889 AAGATCCTCGGTAACTATCCAGAGGTCAT-A
1 AAGATCCTAGGTAACTGTCCATAGGTC-TCG
* *
2518919 AAGATCCTTGGTAACTGTCCATAGGTCAT-A
1 AAGATCCTAGGTAACTGTCCATAGGTC-TCG
*
2518949 AAGATCCTCGGTAACTGTCCATAGGTCTCG
1 AAGATCCTAGGTAACTGTCCATAGGTCTCG
* * *
2518979 AAGAACCTAGGTAAACTGTTCATATGTCTCG
1 AAGATCCTAGGT-AACTGTCCATAGGTCTCG
2519010 AA
1 AA
2519012 AGACATAGGT
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
29 1 0.01
30 63 0.77
31 18 0.22
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (30 bp):
AAGATCCTAGGTAACTGTCCATAGGTCTCG
Found at i:2518992 original size:60 final size:60
Alignment explanation
Indices: 2518844--2519002 Score: 187
Period size: 60 Copynumber: 2.6 Consensus size: 60
2518834 CCCGAAGGAC
* ** * *
2518844 CTATCCAGAGGTCACAAAG-ACCCCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGAACCTAGGTAACTGTCCATAGGTCATAAAGATCCTCGGTAA
* *
2518903 CTATCCAGAGGTCATAAAGATCCTTGGTAACTGTCCATAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGAACCTAGGTAACTGTCCATAGGTCATAAAGATCCTCGGTAA
* * * *
2518963 CTGTCCATAGGTC-TCGAAGAACCTAGGTAAACTGTTCATA
1 CTATCCAGAGGTCAT-AAAGAACCTAGGT-AACTGTCCATA
2519003 TGTCTCGAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
59 19 0.22
60 56 0.66
61 10 0.12
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (60 bp):
CTATCCAGAGGTCATAAAGAACCTAGGTAACTGTCCATAGGTCATAAAGATCCTCGGTAA
Found at i:2519008 original size:31 final size:31
Alignment explanation
Indices: 2518931--2519025 Score: 90
Period size: 31 Copynumber: 3.1 Consensus size: 31
2518921 GATCCTTGGT
* *
2518931 AACTGTCCATAGGTCAT--AAAGATCCTCGGT-
1 AACTGTCCATAGGTC-TCGAAAGA-CATAGGTA
*
2518961 AACTGTCCATAGGTCTCG-AAGAACCTAGGTA
1 AACTGTCCATAGGTCTCGAAAG-ACATAGGTA
* *
2518992 AACTGTTCATATGTCTCGAAAGACATAGGTA
1 AACTGTCCATAGGTCTCGAAAGACATAGGTA
2519023 AAC
1 AAC
2519026 CCTTGACTCT
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
29 1 0.02
30 24 0.43
31 28 0.50
32 3 0.05
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (31 bp):
AACTGTCCATAGGTCTCGAAAGACATAGGTA
Found at i:2523270 original size:2 final size:2
Alignment explanation
Indices: 2523263--2523288 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2523253 TGCACCTTTC
2523263 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2523289 CCACGCATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2523617 original size:30 final size:30
Alignment explanation
Indices: 2523561--2523689 Score: 197
Period size: 30 Copynumber: 4.3 Consensus size: 30
2523551 GAAGGACCTA
* * *
2523561 TCCAGAGGTCACAAAGA-CCCCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
2523590 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
2523620 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
* *
2523650 TCCATAGGTCATAAAGATCATCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
2523680 TCCATAGGTC
1 TCCAGAGGTC
2523690 TCGAAGAACC
Statistics
Matches: 94, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 16 0.17
30 78 0.83
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:2523706 original size:60 final size:60
Alignment explanation
Indices: 2523561--2523716 Score: 190
Period size: 60 Copynumber: 2.6 Consensus size: 60
2523551 GAAGGACCTA
* ** * *
2523561 TCCAGAGGTCACAAAG-ACCCCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGAACCTAGGTAACTATCCATAGGTCATAAAGATCATCGGTAACTG
* * *
2523620 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCATAGGTCATAAAGATCATCGGTAACTG
1 TCCAGAGGTCATAAAGAACCTAGGTAACTATCCATAGGTCATAAAGATCATCGGTAACTG
* *
2523680 TCCATAGGTC-TCGAAGAACCTAGGTAAACTATCCATA
1 TCCAGAGGTCAT-AAAGAACCTAGGT-AACTATCCATA
2523717 TGTCTCGAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
59 16 0.19
60 57 0.69
61 10 0.12
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (60 bp):
TCCAGAGGTCATAAAGAACCTAGGTAACTATCCATAGGTCATAAAGATCATCGGTAACTG
Found at i:2523722 original size:31 final size:31
Alignment explanation
Indices: 2523645--2523739 Score: 90
Period size: 31 Copynumber: 3.1 Consensus size: 31
2523635 GATCCTCGGT
* *
2523645 AACTGTCCATAGGTCAT--AAAGATCATCGGT-
1 AACTATCCATAGGTC-TCGAAAGA-CATAGGTA
* *
2523675 AACTGTCCATAGGTCTCG-AAGAACCTAGGTA
1 AACTATCCATAGGTCTCGAAAG-ACATAGGTA
*
2523706 AACTATCCATATGTCTCGAAAGACATAGGTA
1 AACTATCCATAGGTCTCGAAAGACATAGGTA
2523737 AAC
1 AAC
2523740 CCTCGACTCT
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
29 1 0.02
30 23 0.42
31 28 0.51
32 3 0.05
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (31 bp):
AACTATCCATAGGTCTCGAAAGACATAGGTA
Found at i:2524800 original size:19 final size:19
Alignment explanation
Indices: 2524776--2524823 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
2524766 GATTAAAAGA
2524776 GTGCATCGATGCACTACTT
1 GTGCATCGATGCACTACTT
2524795 GTGCATCGATGCACTACTT
1 GTGCATCGATGCACTACTT
2524814 GTGCATCGAT
1 GTGCATCGAT
2524824 ACACCTTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCACTACTT
Found at i:2526723 original size:21 final size:22
Alignment explanation
Indices: 2526684--2526724 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2526674 CAGATTGCCC
2526684 AGAGGGAACCGATTTCCCCCAA
1 AGAGGGAACCGATTTCCCCCAA
*
2526706 AGAGGGAACTGA-TTCCCCC
1 AGAGGGAACCGATTTCCCCC
2526725 TGAATGGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.29, C:0.32, G:0.24, T:0.15
Consensus pattern (22 bp):
AGAGGGAACCGATTTCCCCCAA
Found at i:2526786 original size:19 final size:20
Alignment explanation
Indices: 2526762--2526800 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
2526752 ATATTACTCG
2526762 AAGGGA-ACCGATTCCCCCC
1 AAGGGAGACCGATTCCCCCC
2526781 AAGGGAGTACCGATTCCCCC
1 AAGGGAG-ACCGATTCCCCC
2526801 TGTATAATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
21 12 0.67
ACGTcount: A:0.26, C:0.38, G:0.23, T:0.13
Consensus pattern (20 bp):
AAGGGAGACCGATTCCCCCC
Found at i:2528668 original size:19 final size:19
Alignment explanation
Indices: 2528619--2528672 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
2528609 GCTCTACTTT
*
2528619 TATTAAAATGATATTAAAA
1 TATTAAAATAATATTAAAA
* *
2528638 TATTATATTAATATT-AAA
1 TATTAAAATAATATTAAAA
2528656 TATATAAAATAATATTA
1 TAT-TAAAATAATATTA
2528673 TTTTTGGTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TATTAAAATAATATTAAAA
Found at i:2538292 original size:22 final size:22
Alignment explanation
Indices: 2538209--2538285 Score: 120
Period size: 22 Copynumber: 3.5 Consensus size: 22
2538199 TGGGCTAGGA
*
2538209 GAATCGGTACCCATTC-AATGG
1 GAATCGGTACCCATTCAAAGGG
*
2538230 GAATCGGTACCCATTCAAGGGG
1 GAATCGGTACCCATTCAAAGGG
2538252 GAATCGGTACCCATTCAAAGGG
1 GAATCGGTACCCATTCAAAGGG
*
2538274 GAATCGATACCC
1 GAATCGGTACCC
2538286 CCTCAAACGA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
21 16 0.31
22 35 0.69
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (22 bp):
GAATCGGTACCCATTCAAAGGG
Found at i:2539958 original size:23 final size:23
Alignment explanation
Indices: 2539932--2539991 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
2539922 ATGGAACTAC
* *
2539932 GGTGTAATTCTATGCGGCACTCT
1 GGTGCAATTCTACGCGGCACTCT
*
2539955 GGTGCAATTCTACGTGGCACT-T
1 GGTGCAATTCTACGCGGCACTCT
*
2539977 CGGTGCAATTATACG
1 -GGTGCAATTCTACG
2539992 AGCTATGGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.32
Consensus pattern (23 bp):
GGTGCAATTCTACGCGGCACTCT
Found at i:2545235 original size:93 final size:93
Alignment explanation
Indices: 2545076--2545264 Score: 369
Period size: 93 Copynumber: 2.0 Consensus size: 93
2545066 CTACAATCCT
*
2545076 TAACACTCCCTAGGAAAAAACTTTACAATCAATCGATCCCCTCCTTAGTTAATTTATCTACCTCC
1 TAACACTCCCTAGGAAAAAACTTTACAATCAATCGATCCCCTCCTTAGCTAATTTATCTACCTCC
2545141 CAATTACAACCCCTTGGAATAAATCTAA
66 CAATTACAACCCCTTGGAATAAATCTAA
2545169 TAACACTCCCTAGGAAAAAACTTTACAATCAATCGATCCCCTCCTTAGCTAATTTATCTACCTCC
1 TAACACTCCCTAGGAAAAAACTTTACAATCAATCGATCCCCTCCTTAGCTAATTTATCTACCTCC
2545234 CAATTACAACCCCTTGGAATAAATCTAA
66 CAATTACAACCCCTTGGAATAAATCTAA
2545262 TAA
1 TAA
2545265 TAACCGCCCT
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 95 1.00
ACGTcount: A:0.36, C:0.29, G:0.06, T:0.29
Consensus pattern (93 bp):
TAACACTCCCTAGGAAAAAACTTTACAATCAATCGATCCCCTCCTTAGCTAATTTATCTACCTCC
CAATTACAACCCCTTGGAATAAATCTAA
Found at i:2550008 original size:33 final size:34
Alignment explanation
Indices: 2549969--2550035 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
2549959 ATATATTGAG
* *
2549969 GTATATTCAT-TTTCT-TCATTTAAAATCTAATTT
1 GTATATTCATATTT-TATAATTTAAAATCGAATTT
*
2550002 GTATATTTATATTTTATAATTTAAAATCGAATTT
1 GTATATTCATATTTTATAATTTAAAATCGAATTT
2550036 TTTATCTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 10 0.34
34 19 0.66
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.54
Consensus pattern (34 bp):
GTATATTCATATTTTATAATTTAAAATCGAATTT
Found at i:2551873 original size:131 final size:129
Alignment explanation
Indices: 2551630--2551998 Score: 438
Period size: 131 Copynumber: 2.8 Consensus size: 129
2551620 ATAATTTTAA
2551630 GAGAGAAAATTATAATATCTAATTATTTCTG-ATCGAGAATAAATGATCTTTCATGCCTTAAAGC
1 GAGAGAAAA-TATAATATCTAATTATTTC-GAATCGAGAATAAATGATCTTT-ATGCCTTAAAGC
* * * * * *
2551694 ATTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATAT-AGTCTTAAAATTTAATATCTA
63 AATCATTTATTACTCCAATCGAAATGAAGAAATATCATTAT-TCAGTCTTAAAAATCAATATCGA
2551758 TTC
127 TTC
* * * * *
2551761 GAGTGAAAATGATCATATCTAATGATTTTC-AATCGAGAATAAATGACCTCTTATACCTTAAAGC
1 GAGAGAAAAT-ATAATATCTAATTA-TTTCGAATCGAGAATAAATGATCT-TTATGCCTTAAAGC
* * *
2551825 AGTCATTTATTACTCCAATCGAAATGAAAAAATATCATTATTCCGTCTTAAAAATCAATATCGAT
63 AATCATTTATTACTCCAATCGAAATGAAGAAATATCATTATTCAGTCTTAAAAATCAATATCGAT
2551890 TC
128 TC
* * * * *
2551892 GAGAGAAAATAGTAATATCGAATTATTTCGAATCAAGAATAAATGATATATCATGTCTTAAAGCA
1 GAGAGAAAATA-TAATATCTAATTATTTCGAATCGAGAATAAATGATCT-TTATGCCTTAAAGCA
* * *
2551957 ATCATTTATTACTCCAGTCGAAATGAAGATATATTATTATTC
64 ATCATTTATTACTCCAATCGAAATGAAGAAATATCATTATTC
2551999 TCAACATCGA
Statistics
Matches: 202, Mismatches: 29, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
130 7 0.03
131 189 0.94
132 6 0.03
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (129 bp):
GAGAGAAAATATAATATCTAATTATTTCGAATCGAGAATAAATGATCTTTATGCCTTAAAGCAAT
CATTTATTACTCCAATCGAAATGAAGAAATATCATTATTCAGTCTTAAAAATCAATATCGATTC
Found at i:2554113 original size:3 final size:3
Alignment explanation
Indices: 2554105--2554135 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2554095 AATAAACATA
*
2554105 AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2554136 GTAGCGGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:2554515 original size:135 final size:133
Alignment explanation
Indices: 2554293--2554753 Score: 465
Period size: 135 Copynumber: 3.4 Consensus size: 133
2554283 TTCACCGTAG
* * * * * * * * *
2554293 ATCATATCTGGAAACGTTGATTCATTCCTCTATTCTTTAGGGAATATTGAATCGGGACAAACTTG
1 ATCAGATCTAGAAATGTTGATTCATTCCACTATTCTTCAGGGAAGATTAAATCGAGACATACTTG
* * * **
2554358 TTTCATTGTTACTAAGTGAAGATCAAATATGGAAAGAGATGGGATATGTTCCACTACTTTTTCAA
66 TTCCACTGTTACTCAG-GAAGATCAAATATGGAAAGAGATGGGATATGTTCTGCTA-TTTTTCAA
2554423 GGAAA
129 GGAAA
* * * *
2554428 ATCATATGTAGAAATGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCAAGACATACTTG
1 ATCAGATCTAGAAATGTTGATTCATTCCACTATTCTTCAGGGAAGATTAAATCGAGACATACTTG
* * * * * * * * **
2554493 TTCCACTATTCCTCAGGAAAGATCAAGTCTAG-AAGAAATAGAGATTTGTTCTGCTGATTCATCA
66 TTCCACTGTTACTCAGG-AAGATCAAATATGGAAAGAGAT-GGGATATGTTCTGCT-ATTTTTCA
*
2554557 GGGAAA
128 AGGAAA
* * **
2554563 ATCAGATCTAGAAATATTCATTCATTCCACTATTCTTCAGGGAAGATTAAATCGAGGTATACTTG
1 ATCAGATCTAGAAATGTTGATTCATTCCACTATTCTTCAGGGAAGATTAAATCGAGACATACTTG
* * * * *
2554628 TTCCACTGCTACTCAGGGAAGATCAAATTTGGAAAGAGAGGGGATATGTTCTGCTGTTTCTTGAA
66 TTCCACTGTTACTCA-GGAAGATCAAATATGGAAAGAGATGGGATATGTTCTGCTATTT-TTCAA
*
2554693 AGAAA
129 GGAAA
* * * *
2554698 ATCAGATCTGGAAATGTTGATTTATTCCACTGTTCTTTAGGGAAGATTAAATCGAG
1 ATCAGATCTAGAAATGTTGATTCATTCCACTATTCTTCAGGGAAGATTAAATCGAG
2554754 TTCGATTTGC
Statistics
Matches: 265, Mismatches: 55, Indels: 12
0.80 0.17 0.04
Matches are distributed among these distances:
134 9 0.03
135 248 0.94
136 8 0.03
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (133 bp):
ATCAGATCTAGAAATGTTGATTCATTCCACTATTCTTCAGGGAAGATTAAATCGAGACATACTTG
TTCCACTGTTACTCAGGAAGATCAAATATGGAAAGAGATGGGATATGTTCTGCTATTTTTCAAGG
AAA
Found at i:2557592 original size:23 final size:23
Alignment explanation
Indices: 2557561--2557666 Score: 108
Period size: 23 Copynumber: 4.7 Consensus size: 23
2557551 TCAAGGGTTT
*
2557561 TACGCGGTCCTTCGGGACAATTC
1 TACGTGGTCCTTCGGGACAATTC
* *
2557584 TACGTGGTCCTTCTGGACATTTC
1 TACGTGGTCCTTCGGGACAATTC
* * * *
2557607 TACGCGGTCCTTTGGGAAAATAC
1 TACGTGGTCCTTCGGGACAATTC
*
2557630 TATGTGGTCCTTCGGGAC-ATTC
1 TACGTGGTCCTTCGGGACAATTC
*
2557652 TATGTGG-CACTTCGG
1 TACGTGGTC-CTTCGG
2557667 TGCAATTTCT
Statistics
Matches: 68, Mismatches: 14, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
21 1 0.01
22 16 0.24
23 51 0.75
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.32
Consensus pattern (23 bp):
TACGTGGTCCTTCGGGACAATTC
Found at i:2557637 original size:46 final size:46
Alignment explanation
Indices: 2557561--2557650 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
2557551 TCAAGGGTTT
* * *
2557561 TACGCGGTCCTTCGGGACAATTCTACGTGGTCCTTCTGGACATTTC
1 TACGCGGTCCTTCGGGAAAATACTACGTGGTCCTTCGGGACATTTC
* *
2557607 TACGCGGTCCTTTGGGAAAATACTATGTGGTCCTTCGGGACATT
1 TACGCGGTCCTTCGGGAAAATACTACGTGGTCCTTCGGGACATT
2557651 CTATGTGGCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (46 bp):
TACGCGGTCCTTCGGGAAAATACTACGTGGTCCTTCGGGACATTTC
Found at i:2561545 original size:23 final size:23
Alignment explanation
Indices: 2561519--2561576 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
2561509 TGTCTTGAAT
2561519 GACCACATAGGATTGTCCCAAAG
1 GACCACATAGGATTGTCCCAAAG
* ** ** *
2561542 GACCATATAGTTTTGTCCTGAAT
1 GACCACATAGGATTGTCCCAAAG
2561565 GACCACATAGGA
1 GACCACATAGGA
2561577 ATGACCACAT
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (23 bp):
GACCACATAGGATTGTCCCAAAG
Found at i:2561580 original size:14 final size:14
Alignment explanation
Indices: 2561561--2561588 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2561551 GTTTTGTCCT
2561561 GAATGACCACATAG
1 GAATGACCACATAG
2561575 GAATGACCACATAG
1 GAATGACCACATAG
2561589 AACCCTCGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
GAATGACCACATAG
Found at i:2571697 original size:19 final size:19
Alignment explanation
Indices: 2571649--2571701 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
2571639 GCTCTATTTT
2571649 TATTAAAAT-ATATTAAAA
1 TATTAAAATAATATTAAAA
* *
2571667 TATTATATTAATATT-AAA
1 TATTAAAATAATATTAAAA
2571685 TATATAAAATAATATTA
1 TAT-TAAAATAATATTA
2571702 TTTTTGGTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 13 0.46
19 15 0.54
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TATTAAAATAATATTAAAA
Found at i:2572167 original size:16 final size:16
Alignment explanation
Indices: 2572146--2572200 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
2572136 TAATAAATGT
*
2572146 CACGTCATCACCAAGC
1 CACGTCATCATCAAGC
2572162 CACGTCATCATCAAGC
1 CACGTCATCATCAAGC
*
2572178 CACGTCATCATCAAGT
1 CACGTCATCATCAAGC
2572194 CACGTCA
1 CACGTCA
2572201 GTAATGACGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.31, C:0.38, G:0.13, T:0.18
Consensus pattern (16 bp):
CACGTCATCATCAAGC
Found at i:2584161 original size:36 final size:36
Alignment explanation
Indices: 2584114--2584222 Score: 200
Period size: 36 Copynumber: 3.0 Consensus size: 36
2584104 TGAGATCCTG
2584114 AAAGTGCCTTTTATCTCATGAACAATGATGTTACAT
1 AAAGTGCCTTTTATCTCATGAACAATGATGTTACAT
2584150 AAAGTGCCTTTTATCTCATGAACAATGATGTTACAT
1 AAAGTGCCTTTTATCTCATGAACAATGATGTTACAT
* *
2584186 AAAGTGCCTTTTATCTCGTTAACAATGATGTTACAT
1 AAAGTGCCTTTTATCTCATGAACAATGATGTTACAT
2584222 A
1 A
2584223 CTCAGAACTT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.37
Consensus pattern (36 bp):
AAAGTGCCTTTTATCTCATGAACAATGATGTTACAT
Found at i:2588905 original size:15 final size:15
Alignment explanation
Indices: 2588885--2588919 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2588875 TAGCCTATCT
2588885 GTTATTCCTTTAGAA
1 GTTATTCCTTTAGAA
2588900 GTTATTCCTTTAGAA
1 GTTATTCCTTTAGAA
*
2588915 ATTAT
1 GTTAT
2588920 CCCTCTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (15 bp):
GTTATTCCTTTAGAA
Found at i:2597364 original size:23 final size:23
Alignment explanation
Indices: 2597337--2597401 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
2597327 CTTATATAGA
*
2597337 ACTTCGGTGCAATTATACGTGGT
1 ACTTCGGTGCAATTATACGTGGC
* *
2597360 ACTTCGGTGCAATTCTATGTGGC
1 ACTTCGGTGCAATTATACGTGGC
* *
2597383 ACTTTGGTGCATTTATACG
1 ACTTCGGTGCAATTATACG
2597402 AGTTGTGGTG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (23 bp):
ACTTCGGTGCAATTATACGTGGC
Found at i:2598838 original size:23 final size:23
Alignment explanation
Indices: 2598812--2598862 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
2598802 AATAACATAT
* **
2598812 TAGGTACCTCTTATATAATGTAA
1 TAGGTACCGCTTATATAATAAAA
*
2598835 TAGGTAGCGCTTATATAATAAAA
1 TAGGTACCGCTTATATAATAAAA
2598858 TAGGT
1 TAGGT
2598863 TAATTACTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (23 bp):
TAGGTACCGCTTATATAATAAAA
Found at i:2598932 original size:87 final size:87
Alignment explanation
Indices: 2598786--2598957 Score: 292
Period size: 87 Copynumber: 2.0 Consensus size: 87
2598776 ATTTAACCGG
* * *
2598786 AAATATTATCAAGTACAATAACATATTAGGTACCTCTTATATAATGTAATAGGTAGCGCTTATAT
1 AAATATTATCAAGCACAATAACATATTAGGTACCTCTTATATAACGTAATAGATAGCGCTTATAT
2598851 AATAAAATAGGTTAATTACTAA
66 AATAAAATAGGTTAATTACTAA
*
2598873 AAATATTATCAAGCACAATAACATATTAGGTA-GTGCTTATATAACGTAATAGATAGCGCTTATA
1 AAATATTATCAAGCACAATAACATATTAGGTACCT-CTTATATAACGTAATAGATAGCGCTTATA
2598937 TAATAAAATAGGTTAATTACT
65 TAATAAAATAGGTTAATTACT
2598958 TAATTTGTTA
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
86 1 0.01
87 79 0.99
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (87 bp):
AAATATTATCAAGCACAATAACATATTAGGTACCTCTTATATAACGTAATAGATAGCGCTTATAT
AATAAAATAGGTTAATTACTAA
Found at i:2601480 original size:20 final size:21
Alignment explanation
Indices: 2601434--2601493 Score: 77
Period size: 20 Copynumber: 2.8 Consensus size: 21
2601424 TTCCCCTGTG
2601434 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
2601457 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
2601477 GGGGGGATCGATTCCCT
1 GGGGGAATCGGTTCCCT
2601494 ATGCACCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.18, C:0.25, G:0.35, T:0.22
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:2607618 original size:199 final size:197
Alignment explanation
Indices: 2607273--2607959 Score: 948
Period size: 199 Copynumber: 3.4 Consensus size: 197
2607263 AACATAAAAG
* * * *
2607273 GTTATATTGTAAAGTTACCTATTACATTATAATTATCGGTTTTGATGTTTTTGGGATTGATACAA
1 GTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAA
** * * *
2607338 TTTTAAACATATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGAATCG
66 TTTTAAATGTATCGACACTTTATGCGTGCACCTAGTT-GTCATTCATTCTGGACAAAAAGTATCG
* * *
2607403 ACACAAATTTAAAAAGTGACGGTATATTATGTAGACCTATTTTCTCATAAAACCAGTATATTTAT
130 ACACAAATTTAAAAAGTGACGATACATTATGTAGACCTATTTTCTCATAAAACCAGTATATTTCT
2607468 ATCA
195 A-CA
* *
2607472 GTTACATTGTAAATTTACCTATTATATTATAATTATCGGTTTCAATGTTTTTGGGATCGATACAA
1 GTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAA
* *
2607537 TTTTAAATGTATCGACACTTTATGTGTGCACCTAATATGTCATTCATTCTGGACAAAAAGTATCG
66 TTTTAAATGTATCGACACTTTATGCGTGCACCTAGT-TGTCATTCATTCTGGACAAAAAGTATCG
* * * **
2607602 ACACAAATTTAAAAAGT-ATTGATACATTATGTTGACCTATTCTCTCATAAAATTAGTATATTTC
130 ACACAAATTTAAAAAGTGA-CGATACATTATGTAGACCTATTTTCTCATAAAACCAGTATATTTC
2607666 TACCA
194 TA-CA
* * * * * *
2607671 ATTACATTTTAAATTTACTTATTACATTGTAATTATCGATTTCGATGTTTTTGAGATCGATACAA
1 GTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAA
* * *
2607736 TTTTAAATGTATCTACACTTTATGCGTGCACCTAGTTTCTCATTTATTCTGGACAAAAAGTATCG
66 TTTTAAATGTATCGACACTTTATGCGTGCACCTAG-TTGTCATTCATTCTGGACAAAAAGTATCG
* *
2607801 ACACAAATTTAAAAAGTGTCGATACATTATGTAGACATATTTTCTCATAAAACC-GATATATTTC
130 ACACAAATTTAAAAAGTGACGATACATTATGTAGACCTATTTTCTCATAAAACCAG-TATATTTC
*
2607865 TACTG
194 TAC-A
*
2607870 GTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATAC-T
1 GTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAA
2607934 TTTAATAAATGTATCGACACATTTAT
66 TTT--TAAATGTATCGACAC-TTTAT
2607960 TTATCTATTC
Statistics
Matches: 428, Mismatches: 51, Indels: 16
0.86 0.10 0.03
Matches are distributed among these distances:
198 6 0.01
199 401 0.94
200 16 0.04
201 5 0.01
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (197 bp):
GTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAA
TTTTAAATGTATCGACACTTTATGCGTGCACCTAGTTGTCATTCATTCTGGACAAAAAGTATCGA
CACAAATTTAAAAAGTGACGATACATTATGTAGACCTATTTTCTCATAAAACCAGTATATTTCTA
CA
Found at i:2608062 original size:15 final size:15
Alignment explanation
Indices: 2608042--2608070 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2608032 TCGACACATT
2608042 TTTGGAAACTTTATC
1 TTTGGAAACTTTATC
2608057 TTTGGAAACTTTAT
1 TTTGGAAACTTTAT
2608071 GTGTCGATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.48
Consensus pattern (15 bp):
TTTGGAAACTTTATC
Found at i:2609498 original size:24 final size:24
Alignment explanation
Indices: 2609479--2609534 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
2609469 CTAAATTTAT
2609479 ATTGAAATTCAAACTCAAATTGAA
1 ATTGAAATTCAAACTCAAATTGAA
* *
2609503 ATTTAAATTCAAACTCCAATT-AA
1 ATTGAAATTCAAACTCAAATTGAA
2609526 ATATGAAAT
1 AT-TGAAAT
2609535 AAACATGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.32
Consensus pattern (24 bp):
ATTGAAATTCAAACTCAAATTGAA
Found at i:2609502 original size:18 final size:18
Alignment explanation
Indices: 2609479--2609515 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2609469 CTAAATTTAT
2609479 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
2609497 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
2609515 A
1 A
2609516 CTCCAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:2610061 original size:10 final size:10
Alignment explanation
Indices: 2610046--2610075 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
2610036 GAAAGCTACA
2610046 TTCTTCTTCC
1 TTCTTCTTCC
2610056 TTCTTCTTCC
1 TTCTTCTTCC
2610066 TTCTTCTTCC
1 TTCTTCTTCC
2610076 CGTGGGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (10 bp):
TTCTTCTTCC
Found at i:2610545 original size:21 final size:21
Alignment explanation
Indices: 2610519--2610563 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2610509 GATTTCTGGG
* *
2610519 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2610540 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2610561 CAA
1 CAA
2610564 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2611166 original size:18 final size:18
Alignment explanation
Indices: 2611143--2611177 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2611133 CTAGGAGATT
2611143 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
2611161 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
2611178 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:2611263 original size:21 final size:22
Alignment explanation
Indices: 2611234--2611277 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2611224 GTTGTATGAT
2611234 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
2611255 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
2611277 A
1 A
2611278 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:2612176 original size:149 final size:148
Alignment explanation
Indices: 2611990--2612292 Score: 543
Period size: 149 Copynumber: 2.0 Consensus size: 148
2611980 GAGTCGAGGG
2611990 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
* *
2612055 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
*
2612120 TATGGCACTACGGTGCAAT
131 TATGGCACTAC-GTACAAT
* * *
2612139 TCTATGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
2612204 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
2612269 TATGGCACTACGTACAAT
131 TATGGCACTACGTACAAT
2612287 TCTACG
1 TCTACG
2612293 GGGCACTTCG
Statistics
Matches: 147, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
148 11 0.07
149 136 0.93
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (148 bp):
TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
TATGGCACTACGTACAAT
Found at i:2615539 original size:21 final size:21
Alignment explanation
Indices: 2615513--2615557 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2615503 GATTTCTGGG
* *
2615513 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2615534 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2615555 CAA
1 CAA
2615558 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2616160 original size:18 final size:18
Alignment explanation
Indices: 2616137--2616171 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2616127 CTAGGAGATT
2616137 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
2616155 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
2616172 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:2616256 original size:21 final size:22
Alignment explanation
Indices: 2616227--2616270 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2616217 GTTGTATGAT
2616227 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
2616248 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
2616270 A
1 A
2616271 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:2617172 original size:149 final size:149
Alignment explanation
Indices: 2616986--2617289 Score: 554
Period size: 149 Copynumber: 2.0 Consensus size: 149
2616976 GAGTCGAGGG
2616986 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
* *
2617051 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
2617116 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* * *
2617135 TCTATGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
*
2617200 ACTTGATCCCTAGCATATGTATATGATTCTTAAATAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
2617265 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2617284 TCTACG
1 TCTACG
2617290 GGGCACTTCG
Statistics
Matches: 148, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
149 148 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:2617312 original size:23 final size:23
Alignment explanation
Indices: 2617268--2617312 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2617258 ATCATTATAT
*
2617268 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
2617291 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
2617313 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:2621265 original size:21 final size:22
Alignment explanation
Indices: 2621236--2621279 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2621226 GTTGTATGAT
2621236 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
2621257 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
2621279 A
1 A
2621280 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:2622183 original size:149 final size:149
Alignment explanation
Indices: 2621997--2622300 Score: 554
Period size: 149 Copynumber: 2.0 Consensus size: 149
2621987 GAGTCGAGGG
2621997 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
* *
2622062 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
2622127 TATGGCACTACGGTACAAT
131 TATGGCACTACGGTACAAT
* * *
2622146 TCTATGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
2622211 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
*
2622276 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTACAAT
2622295 TCTACG
1 TCTACG
2622301 GGGCACTTCG
Statistics
Matches: 148, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
149 148 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTACAAT
Found at i:2622323 original size:23 final size:23
Alignment explanation
Indices: 2622279--2622323 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2622269 ATCATTATAT
*
2622279 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
2622302 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
2622324 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:2624015 original size:3 final size:3
Alignment explanation
Indices: 2624007--2624050 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
2623997 ACTTGTTTGG
* * * *
2624007 ATC ATC ATC ATC ATT ATC ATC CTC ATC TTC ATC ATC ATC TTC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
2624051 TAAGCGCTTG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.27, C:0.32, G:0.00, T:0.41
Consensus pattern (3 bp):
ATC
Found at i:2624863 original size:2 final size:2
Alignment explanation
Indices: 2624856--2624940 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
2624846 ATAGTATCCG
2624856 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
2624898 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
2624940 T
1 T
2624941 CATTCCCCAT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2625952 original size:199 final size:199
Alignment explanation
Indices: 2625610--2627038 Score: 2065
Period size: 199 Copynumber: 7.2 Consensus size: 199
2625600 GTATTGACAT
* * *
2625610 ATTTTAAAAGTGTCGATACATTATGTAGAGCTATTTTCTCATAAAACCGGTATATTTATATCGGT
1 ATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTAT-TTTATACCGGT
* * * * **
2625675 TACATTGTAAATTTACCTATTACATTATAATTATCGATTTCTATGATTTTGGGATCGACCCAATT
65 TACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATACAATT
* ** *
2625740 TTAAATGTATCGACACTTTATGCGTGCACCTAGTTT-CTCATTCATTTCTAGACAAAAAGTATCG
130 TTAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCA-TTCTGGACAAAAAGTATCG
*
2625804 ACAAAA
194 ACACAA
*
2625810 ATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATTTTCTACCGGTT
1 ATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATTTTATACCGGTT
*
2625875 ACATTGTAAATTTACCTATTACATTGTAATAATCGGTTTTC-ATGTTTTTGGGATCGATACAATT
66 ACATTGTAAATTTACCTATTACATTGTAATTATCGG-TTTCGATGTTTTTGGGATCGATACAATT
* * * *
2625939 TTAAATGTATCGACAATTTGTGTGTGCACCTCGTTTGGGCATTCATTCTGGACAAAGAGTATCGA
130 TTAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTCTGGACAAAAAGTATCGA
2626004 CACAA
195 CACAA
* * * * * *
2626009 ATTTAAAAAGTGTCGATACATTATGTTGACATATTTTATCATAAAACCTGTATTTTCTACCAGTT
1 ATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATTTTATACCGGTT
* * * * **
2626074 ACATTGCAAAATTACCTATTACATTCTAATTATCGGTTTCGATGTTATTGGGATCGATACTTTTT
66 ACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTT
* *
2626139 ATAAATGTATCGACACTTTACGCGTGCACCTCGTTTGGGCATTCATTTTGGACAAAAAGTATCGA
131 -TAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTCTGGACAAAAAGTATCGA
2626204 CACAA
195 CACAA
* * *
2626209 ATTTTAAAAGTGTCGATATATTATGTAGACCTATTTTCTCATAAAACCGGTATTTTATACTGGTT
1 ATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATTTTATACCGGTT
* * * * *
2626274 ACATTGCAAAATTACCTACTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGAAACATTTT
66 ACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTT
*
2626339 ATAAATGTATCGACACTTTATGCGTGCACCTCGTTT-GTCATTCATTTCTGGACAAAAAGTATCG
131 -TAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCA-TTCTGGACAAAAAGTATCG
2626403 ACACAA
194 ACACAA
* *
2626409 ATTTAAAAAGTGTTGATACATTATGTAGACCTATTTTCTCATAAAATCGGTATTTTATACCGGTT
1 ATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATTTTATACCGGTT
* * * *
2626474 ATATTATAAATTTATCTATTACATTGTAAGTATCGGTTTCGATGTTTTTGGGATCGATACAATTT
66 ACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTT
* *
2626539 TTAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTATGGACAAAAAGTATCGAC
131 TAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTCTGGACAAAAAGTATCGAC
*
2626604 ACGA
196 ACAA
**
2626608 ATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAATTGGTATTTTATACCGGTT
1 ATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATTTTATACCGGTT
* * * *
2626673 TCATTGTAAATTTATCTATTCCATTGTAATTATCGGTTTCGATGTTTTTGGGATTGATACAATTT
66 ACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTT
* * * * *
2626738 TAAATGTATTGACACTTTATGCGTGTACCTCGTTTGGGAATTCATTATGGACAAAAAGTGTCGAC
131 TAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTCTGGACAAAAAGTATCGAC
2626803 ACAA
196 ACAA
* * * * * * *
2626807 ATTTTAAAATTGTCAATACATTATGTTGACCTATTTTCTCATAAAACCAGTATTTTCTACGGGTT
1 ATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATTTTATACCGGTT
* * * *
2626872 ACATTGTAAAATTACCTATTACATTCTAATTATCGGTTTCGATATTTTTGGGATCGATA-ATTTT
66 ACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATACA-ATT
*
2626936 TATAAATGTATCGACACTTTATGCGTGTACCTCGTTTGGGCATTCATTCTGGACAAAAAGTATCG
130 T-TAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTCTGGACAAAAAGTATCG
2627001 ACACAA
194 ACACAA
* *
2627007 ATTTTAAAAGTGTCGATACATTATGTTGACCT
1 ATTTAAAAAGTGTCGATACATTATGTAGACCT
2627039 GTTACTTTAA
Statistics
Matches: 1112, Mismatches: 109, Indels: 16
0.90 0.09 0.01
Matches are distributed among these distances:
198 5 0.00
199 590 0.53
200 517 0.46
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (199 bp):
ATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATTTTATACCGGTT
ACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTT
TAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTCTGGACAAAAAGTATCGAC
ACAA
Found at i:2626383 original size:399 final size:398
Alignment explanation
Indices: 2625610--2627038 Score: 2076
Period size: 399 Copynumber: 3.6 Consensus size: 398
2625600 GTATTGACAT
* * *
2625610 ATTTTAAAAGTGTCGATACATTATGTAGAGCTATTTTCTCATAAAACCGGTATATTTATATCGGT
1 ATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTAT-TTTATACCGGT
* * * * * ** *
2625675 TACATTGTAAATTTACCTATTACATTATAATTATCGATTTCTATGATTTTGGGATCGACCCAATT
65 TACATTGTAAAATTACCTATTACATTCTAATTATCGGTTTCGATGTTTTTGGGATCGATACATTT
* ** *
2625740 TTAAATGTATCGACACTTTATGCGTGCACCTAGTTT-CTCATTCATTTCTAGACAAAAAGTATCG
130 TTAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTT-TGGACAAAAAGTATCG
* *
2625804 ACAAAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATTTTCTA
194 ACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATTTTATA
*
2625869 CCGGTTACATTGTAAATTTACCTATTACATTGTAATAATCGGTTTTC-ATGTTTTTGGGATCGAT
259 CCGGTTACATTGTAAATTTACCTATTACATTGTAATTATCGG-TTTCGATGTTTTTGGGATCGAT
* * * *
2625933 ACAATTTTAAATGTATCGACAATTTGTGTGTGCACCTCGTTTGGGCATTCATTCTGGACAAAGAG
323 ACAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTCTGGACAAAAAG
2625998 TATCGACACAA
388 TATCGACACAA
* * * * * *
2626009 ATTTAAAAAGTGTCGATACATTATGTTGACATATTTTATCATAAAACCTGTATTTTCTACCAGTT
1 ATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATTTTATACCGGTT
* * *
2626074 ACATTGCAAAATTACCTATTACATTCTAATTATCGGTTTCGATGTTATTGGGATCGATACTTTTT
66 ACATTGTAAAATTACCTATTACATTCTAATTATCGGTTTCGATGTTTTTGGGATCGATACATTTT
*
2626139 ATAAATGTATCGACACTTTACGCGTGCACCTCGTTTGGGCATTCATTTTGGACAAAAAGTATCGA
131 -TAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTTTGGACAAAAAGTATCGA
* *
2626204 CACAAATTTTAAAAGTGTCGATATATTATGTAGACCTATTTTCTCATAAAACCGGTATTTTATAC
195 CACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATTTTATAC
* * * * *
2626269 TGGTTACATTGCAAAATTACCTACTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGAAAC
260 CGGTTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATAC
* *
2626334 ATTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTT-GTCATTCATTTCTGGACAAAAAG
325 AATTT-TAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCA-TTCTGGACAAAAAG
2626398 TATCGACACAA
388 TATCGACACAA
* *
2626409 ATTTAAAAAGTGTTGATACATTATGTAGACCTATTTTCTCATAAAATCGGTATTTTATACCGGTT
1 ATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATTTTATACCGGTT
* * * * * *
2626474 ATATTATAAATTTATCTATTACATTGTAAGTATCGGTTTCGATGTTTTTGGGATCGATACAATTT
66 ACATTGTAAAATTACCTATTACATTCTAATTATCGGTTTCGATGTTTTTGGGATCGATAC-ATTT
*
2626539 TT-AATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTATGGACAAAAAGTATCGA
130 TTAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTTTGGACAAAAAGTATCGA
* **
2626603 CACGAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAATTGGTATTTTATAC
195 CACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATTTTATAC
* * * *
2626668 CGGTTTCATTGTAAATTTATCTATTCCATTGTAATTATCGGTTTCGATGTTTTTGGGATTGATAC
260 CGGTTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATAC
* * * * *
2626733 AATTTTAAATGTATTGACACTTTATGCGTGTACCTCGTTTGGGAATTCATTATGGACAAAAAGTG
325 AATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTCTGGACAAAAAGTA
2626798 TCGACACAA
390 TCGACACAA
* * * * * * *
2626807 ATTTTAAAATTGTCAATACATTATGTTGACCTATTTTCTCATAAAACCAGTATTTTCTACGGGTT
1 ATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATTTTATACCGGTT
*
2626872 ACATTGTAAAATTACCTATTACATTCTAATTATCGGTTTCGATATTTTTGGGATCGATA-ATTTT
66 ACATTGTAAAATTACCTATTACATTCTAATTATCGGTTTCGATGTTTTTGGGATCGATACA-TTT
* *
2626936 TATAAATGTATCGACACTTTATGCGTGTACCTCGTTTGGGCATTCATTCTGGACAAAAAGTATCG
130 T-TAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTTTGGACAAAAAGTATCG
* *
2627001 ACACAAATTTTAAAAGTGTCGATACATTATGTTGACCT
194 ACACAAATTTAAAAAGTGTCGATACATTATGTAGACCT
2627039 GTTACTTTAA
Statistics
Matches: 918, Mismatches: 102, Indels: 20
0.88 0.10 0.02
Matches are distributed among these distances:
396 1 0.00
397 4 0.00
398 232 0.25
399 502 0.55
400 175 0.19
401 4 0.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (398 bp):
ATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATTTTATACCGGTT
ACATTGTAAAATTACCTATTACATTCTAATTATCGGTTTCGATGTTTTTGGGATCGATACATTTT
TAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTTTGGACAAAAAGTATCGAC
ACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATTTTATACC
GGTTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATACA
ATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTCTGGACAAAAAGTAT
CGACACAA
Found at i:2633436 original size:63 final size:63
Alignment explanation
Indices: 2633334--2633457 Score: 146
Period size: 63 Copynumber: 2.0 Consensus size: 63
2633324 CTAATGTGAC
** *
2633334 TCTTAGGTAGGCTCTACGGCCTTGAGATCATTCTCGGGTAGGCCCTGCA-GCCCTAAGATGTGT
1 TCTTAGGTAGGCTCTACGGCCCCGAAATCATTCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* * *
2633397 TCTTAGGTAGGC-CTCACGGCCCCGAAATC-TATCTTGGGTAGGCTCTCAGGCCTTAAGATGT
1 TCTTAGGTAGGCTCT-ACGGCCCCGAAATCAT-TCTCGGGTAGGCCCTCAGGCCCTAAGATGT
2633458 TCCCTTAGGT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
62 5 0.10
63 47 0.90
ACGTcount: A:0.19, C:0.26, G:0.27, T:0.28
Consensus pattern (63 bp):
TCTTAGGTAGGCTCTACGGCCCCGAAATCATTCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:2636155 original size:18 final size:18
Alignment explanation
Indices: 2636132--2636171 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
2636122 TTCCTCCTAA
2636132 CTTCCTCCATCTTTTCTT
1 CTTCCTCCATCTTTTCTT
2636150 CTTCCTCCATCTTTTCTT
1 CTTCCTCCATCTTTTCTT
2636168 CTTC
1 CTTC
2636172 ATATTTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.05, C:0.40, G:0.00, T:0.55
Consensus pattern (18 bp):
CTTCCTCCATCTTTTCTT
Found at i:2641989 original size:340 final size:339
Alignment explanation
Indices: 2641368--2642047 Score: 1053
Period size: 340 Copynumber: 2.0 Consensus size: 339
2641358 CGTGTACTTA
* * * *
2641368 TTAAAGTATCTACACTTTTAACATATCCGGTAGCGCTTAACCGGTTTTGTCATATTTTTACCTAT
1 TTAAAGTATCGACACTTTCAACATATCCGATAGCGCTTAACCGGTTTTGTCATATTTTTACATAT
* *
2641433 TATATTGTTATGGATCGATACATTTTTATAAAGATCGACACTTTATAGGCGGTATTATTGCTTCT
66 TATATTGTTATGGATCGATACATTTTTATAAAGATCGACACTTTATAGGCGCTATTACTGCTTCT
*
2641498 CTTTTAAATTACAAAAGTGTCGATACTTATATTAAAGTATCGATACTTTCAACATATTCGGTAGC
131 CTTTTAAATTACAAAAGTGTCGATACTTATATTAAAGTATCGACACTTTCAACATATTCGGTAGC
*
2641563 GTTTTACCCGTTTTGTCATTTCGAAATCGGTTTTGTCATATTTTTACAAGTTATATTGTTATGGA
196 GTTTTACCCGTTTTATCATTTCGAAATCGGTTTTGTCATATTTTTACAAGTTATATTGTTATGGA
* * * *
2641628 TCGATACATTTTTACAAAGTATCAACACTTTATAGGCGCTA-TATCTGCTTCTTTTTTAAATTCC
261 TCGATACATTTTTACAAAGTATCAACACTTTACAAGCGCTATTAT-TGCTTCTCTTTTAAATTAC
*
2641692 AAAAGTGTTGATACT
325 AAAAGTGTCGATACT
* * * *
2641707 TTAAAGTATCGACACTTTCAACATATTCGATAGCTCTTTACCGGTTTTGTCATATTTTTACATGT
1 TTAAAGTATCGACACTTTCAACATATCCGATAGCGCTTAACCGGTTTTGTCATATTTTTACATAT
*
2641772 TATATTGTTATGGATTGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTC
66 TATATTGTTATGGATCGATACATTTTTATAAAG-ATCGACACTTTATAGGCGCTATTACTGCTTC
* *
2641837 TCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATCGACACTTTTAACATA-TCAGGTA
130 TCTTTTAAATTACAAAAGTGTCGATACTTATATTAAAGTATCGACACTTTCAACATATTC-GGTA
* *
2641901 GC-TCTTTA-CCGATTTTATCATTTCGAGATCGGTTTTGTCATATTTTTACATGTTATATTGTTA
194 GCGT-TTTACCCG-TTTTATCATTTCGAAATCGGTTTTGTCATATTTTTACAAGTTATATTGTTA
* ** *
2641964 TGGATCGATATATTTTTTTAAAGTATCGACACTTTACAAGCGCTATTATTGCTTCTCTTTTAAAT
257 TGGATCGATACATTTTTACAAAGTATCAACACTTTACAAGCGCTATTATTGCTTCTCTTTTAAAT
2642029 TACAAAAGTGTCGATACT
322 TACAAAAGTGTCGATACT
2642047 T
1 T
2642048 ATTTCAATCT
Statistics
Matches: 310, Mismatches: 26, Indels: 9
0.90 0.08 0.03
Matches are distributed among these distances:
339 95 0.31
340 212 0.68
341 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.43
Consensus pattern (339 bp):
TTAAAGTATCGACACTTTCAACATATCCGATAGCGCTTAACCGGTTTTGTCATATTTTTACATAT
TATATTGTTATGGATCGATACATTTTTATAAAGATCGACACTTTATAGGCGCTATTACTGCTTCT
CTTTTAAATTACAAAAGTGTCGATACTTATATTAAAGTATCGACACTTTCAACATATTCGGTAGC
GTTTTACCCGTTTTATCATTTCGAAATCGGTTTTGTCATATTTTTACAAGTTATATTGTTATGGA
TCGATACATTTTTACAAAGTATCAACACTTTACAAGCGCTATTATTGCTTCTCTTTTAAATTACA
AAAGTGTCGATACT
Found at i:2642165 original size:182 final size:181
Alignment explanation
Indices: 2641748--2642165 Score: 534
Period size: 182 Copynumber: 2.3 Consensus size: 181
2641738 AGCTCTTTAC
* *
2641748 CGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATTGATACATTTTTATAAAGTATCGACA
1 CGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATATATTTTT-TAAAGTATCGACA
* * * *
2641813 CTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTAT
65 CTTTACAAGCGCTATTACTGCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAAACTAT
* * * * * *
2641878 CGACACTTTTAACATATCAGGTAGCTCTTTACCGATTTTATCATTTCGAGAT
130 CGACACTTTCAACATATCAGGTACCACTTAACCGATTTTATCATATCGAAAT
2641930 CGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATATATTTTTTTAAAGTATCGACA
1 CGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATATA-TTTTTTAAAGTATCGACA
* *
2641995 CTTTACAAGCGCTATTATTGCTTCTCTTTTAAATTACAAAAGTGTCGATACTTAT-TTCAATCTA
65 CTTTACAAGCGCTATTACTGCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATT-AAACT-
* * * * * *
2642059 ATTGATACTTTCAACATATCCGGTACCACTTAATCGGTTTTGTCATAAT-GAAAT
128 ATCGACACTTTCAACATATCAGGTACCACTTAACCGATTTTATCAT-ATCGAAAT
* * * * ** *
2642113 TGGTTTTGTCATATTTTAACCTATTATATTACTATGGATCAATATATTTTTTA
1 CGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATATATTTTTTA
2642166 TTTGTATCGA
Statistics
Matches: 205, Mismatches: 27, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
181 2 0.01
182 118 0.58
183 84 0.41
184 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (181 bp):
CGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATATATTTTTTAAAGTATCGACAC
TTTACAAGCGCTATTACTGCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAAACTATC
GACACTTTCAACATATCAGGTACCACTTAACCGATTTTATCATATCGAAAT
Found at i:2643715 original size:16 final size:16
Alignment explanation
Indices: 2643694--2643752 Score: 109
Period size: 16 Copynumber: 3.7 Consensus size: 16
2643684 CCAACGTTTA
2643694 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
2643710 TGTTCGTTTATATTCG
1 TGTTCGTTTATGTTCG
2643726 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2643742 TGTTCGTTTAT
1 TGTTCGTTTAT
2643753 TTGTTAAATG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.08, C:0.12, G:0.22, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:2650989 original size:21 final size:21
Alignment explanation
Indices: 2650965--2651011 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
2650955 CAATAAGATA
2650965 AGGTCGGAACCCGTCGGGATC
1 AGGTCGGAACCCGTCGGGATC
*
2650986 AGGTCGGAACCCGTCGGGTTC
1 AGGTCGGAACCCGTCGGGATC
2651007 AGGTC
1 AGGTC
2651012 TTGTGCCCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.28, G:0.38, T:0.17
Consensus pattern (21 bp):
AGGTCGGAACCCGTCGGGATC
Found at i:2651733 original size:62 final size:62
Alignment explanation
Indices: 2651636--2651760 Score: 223
Period size: 62 Copynumber: 2.0 Consensus size: 62
2651626 AGTCACCCTT
* *
2651636 GCTGATGTTATCATGATACGCAACCTCTTAAAAGTAGAATGACTTATTGTGTTGTAATATAA
1 GCTGATGTTATCATGACACGCAACCTCCTAAAAGTAGAATGACTTATTGTGTTGTAATATAA
*
2651698 GCTGATGTTATCTTGACACGCAACCTCCTAAAAGTAGAATGACTTATTGTGTTGTAATATAA
1 GCTGATGTTATCATGACACGCAACCTCCTAAAAGTAGAATGACTTATTGTGTTGTAATATAA
2651760 G
1 G
2651761 TCGTCGTCTT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.34
Consensus pattern (62 bp):
GCTGATGTTATCATGACACGCAACCTCCTAAAAGTAGAATGACTTATTGTGTTGTAATATAA
Found at i:2655950 original size:2 final size:2
Alignment explanation
Indices: 2655943--2655980 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2655933 CATTCGTTCA
2655943 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2655981 CTTATAAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2658265 original size:13 final size:13
Alignment explanation
Indices: 2658222--2658257 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
2658212 AAAACATTGA
2658222 AAATTTTTAAAAT
1 AAATTTTTAAAAT
2658235 AAATTTTTAAAAT
1 AAATTTTTAAAAT
2658248 AAATTTTTAA
1 AAATTTTTAA
2658258 TTATAATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AAATTTTTAAAAT
Found at i:2671136 original size:20 final size:20
Alignment explanation
Indices: 2671107--2671144 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2671097 TACAAAAGTT
*
2671107 ATAATGATTTATGTAATTTG
1 ATAATCATTTATGTAATTTG
2671127 ATAATCATTTATGTAATT
1 ATAATCATTTATGTAATT
2671145 GTCTTTAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.50
Consensus pattern (20 bp):
ATAATCATTTATGTAATTTG
Found at i:2682341 original size:17 final size:17
Alignment explanation
Indices: 2682319--2682368 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
2682309 AAATTCTTCT
2682319 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
*
2682336 AACA-T--T-GATACTCA
1 AACATTCATAGAAAC-CA
2682350 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
2682367 AA
1 AA
2682369 ACATGAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 4 0.15
14 7 0.27
15 1 0.04
16 1 0.04
17 9 0.35
18 4 0.15
ACGTcount: A:0.52, C:0.22, G:0.06, T:0.20
Consensus pattern (17 bp):
AACATTCATAGAAACCA
Done.