Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007867.1 Hibiscus syriacus cultivar Beakdansim tig00110239_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: 3477501
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 18
Found at i:2334087 original size:84 final size:84
Alignment explanation
Indices: 2333698--2334640 Score: 621
Period size: 84 Copynumber: 11.4 Consensus size: 84
2333688 AATTTATTGA
* * * * * * * * * * *
2333698 CAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATGATGTACCTTCGG-GATGAGTGGAATCGA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTT-GGAGCTGAGCGTAGTCAA
2333762 ACTCGAAGGTC---T-TTGG
65 ACTCGAAGGTCTTTTGTTGG
* * * * * * * * * *
2333778 CAGATAACCCTTCTTGACTTAAGCTATGCTGGAAATGATGGTGCCTTTGAGCTAAGTGGAATCCA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGAT-ATGCCTTGGAGCTGAGCGTAGTCAA
*
2333843 ACTCGAAGGTC---T-TTGA
65 ACTCGAAGGTCTTTTGTTGG
* * * * * * * *
2333859 CAGATAACCCTTCTCG-CTTTCAGTTATGCTGCAAATGATGTACCTCT-GAGTTGAGTGTAATCG
1 CAGATAACCCTTCTAGAC-TTAAGTTATGCTGCAAATGATATGCCT-TGGAGCTGAGCGTAGTCA
2333922 AACTCGAAGGTC---T-TTGG
64 AACTCGAAGGTCTTTTGTTGG
* * * * * * * * *
2333939 CAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAACGATGGTGCCTCT-AAACTGAGCGTGGTCA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGAT-ATGCCT-TGGAGCTGAGCGTAGTCA
*
2334003 AACTTGAAGGTCTTTTGTTGG
64 AACTCGAAGGTCTTTTGTTGG
* * * * *
2334024 TAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATATGCCTTGGAGCTAAGCGTAGTCAAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAA
* *
2334089 CTTGAAGGTCTTTTAG-TGA
66 CTCGAAGGTCTTTT-GTTGG
* * ** * * * * * * *
2334108 TAAATAACCCTTCTAGTA-TTGGGTTATGTTGTAAATGATATTCCCTCGAAGCTGAGTGTAATCA
1 CAGATAACCCTTCTAG-ACTTAAGTTATGCTGCAAATGATA-TGCCTTGGAGCTGAGCGTAGTCA
*
2334172 AACTCGAGGGTC---T-TTGG
64 AACTCGAAGGTCTTTTGTTGG
* * * *
2334189 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAA
* * *
2334254 CTCGAATGTCTTTTGGTGA
66 CTCGAAGGTCTTTTGTTGG
* * ** * * * * * *
2334273 CAGATAACCCTTCTAGCCTTGAGTTATATTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCAA
*
2334338 ACTCGAGGGTC---T-TTGG
65 ACTCGAAGGTCTTTTGTTGG
** * ** * * * *
2334354 CAGATAGTCCTTATCTACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGATCGTGGTCGAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAA
*
2334419 CTCGAAGGTCTTTGGTTGG
66 CTCGAAGGTCTTTTGTTGG
* * * * * * * *
2334438 CATATAACCCTTATCGACTTAAGTTATGCTGCAAATGATATACCTTGGACCTGAGTGTAATCGAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAA
*
2334503 CTCGAAGGTCCTTTT-ATGG
66 CTCGAAGGT-CTTTTGTTGG
* * * * * * *
2334522 CAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTACCTTGG-GAC-GAGCATAGTCAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAG-CTGAGCGTAGTCAA
*
2334585 ACTTGAAGGTCTTTTGTTGG
65 ACTCGAAGGTCTTTTGTTGG
* *
2334605 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAAT
2334641 AGTTTCTTAA
Statistics
Matches: 684, Mismatches: 151, Indels: 53
0.77 0.17 0.06
Matches are distributed among these distances:
80 155 0.23
81 159 0.23
82 7 0.01
83 52 0.08
84 218 0.32
85 93 0.14
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (84 bp):
CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAA
CTCGAAGGTCTTTTGTTGG
Found at i:2334202 original size:165 final size:164
Alignment explanation
Indices: 2334020--2334632 Score: 658
Period size: 165 Copynumber: 3.7 Consensus size: 164
2334010 AGGTCTTTTG
* * * * * *
2334020 TTGGTAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATATGCCTTGGAGCTAAGCGTAGT
1 TTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTACAAATGATATGCCTTGGAGCTGAGCGTAGT
* * * *
2334085 CAAACTTGAAGGTCTTTTAGTGATAAATAACCCTTCTAGTATTGGGTTATGTTGTAAATGATATT
66 CAAACTCGAAGGTCTTTTGGTGACAAATAACCCTTCTAG-ATTGAGTTATGTTGTAAATGATATT
*
2334150 CCCTCGAAGCTGAGTGTAATCAAACTCGAGGGTCT
130 CCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCT
* *
2334185 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTACAAATGATATGCCTTGGAGCTGAGCGTAGT
* * * * * *
2334250 CGAACTCGAATGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATATTGTAAATGATATG
66 CAAACTCGAAGGTCTTTTGGTGACAAATAACCCTTCTAG-ATTGAGTTATGTTGTAAATGATATT
2334315 CCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCT
130 CCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCT
* * ** * * * * *
2334350 TTGGCAGATAGTCCTTATCTACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGATCGTGGT
1 TTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTACAAATGATATGCCTTGGAGCTGAGCGTAGT
* * * * * * * *
2334415 CGAACTCGAAGGTC-TTTGGTTGGCATATAACCCTTATCGACTTAAGTTATGCTGCAAATGATA-
66 CAAACTCGAAGGTCTTTTGG-TGACAAATAACCCTTCTAGA-TTGAGTTATGTTGTAAATGATAT
* * * * *
2334478 TACCTTGGACCTGAGTGTAATCGAACTCGAAGGTCCTTT
129 TCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGT-C--T
* * * *
2334517 TATGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTACCTTGG-GAC-GAGCATA
1 T-TGGCAGATAGCCCTTCTAGACTTAAGCTATGCTACAAATGATATGCCTTGGAG-CTGAGCGTA
* * * * *
2334580 GTCAAACTTGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATG
64 GTCAAACTCGAAGGTCTTTTGGTGACAAATAACCCTTCTAG-ATTGAGTTATG
2334633 CTGCAAATAG
Statistics
Matches: 379, Mismatches: 60, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
164 33 0.09
165 250 0.66
167 46 0.12
168 50 0.13
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (164 bp):
TTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTACAAATGATATGCCTTGGAGCTGAGCGTAGT
CAAACTCGAAGGTCTTTTGGTGACAAATAACCCTTCTAGATTGAGTTATGTTGTAAATGATATTC
CCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCT
Found at i:2335868 original size:36 final size:38
Alignment explanation
Indices: 2335822--2335899 Score: 108
Period size: 36 Copynumber: 2.1 Consensus size: 38
2335812 ACAAAATGAG
*
2335822 AAAAAGGAAAAAAATAAT-A-AGT-AATAAATAATAATA
1 AAAAAAGAAAAAAATAATAATAGTAAATAAAT-ATAATA
*
2335858 AAAAAAGAAAATAATAATAATAGTAAATAAATATAATA
1 AAAAAAGAAAAAAATAATAATAGTAAATAAATATAATA
2335896 AAAA
1 AAAA
2335900 CTATTTTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
36 16 0.43
37 1 0.03
38 13 0.35
39 7 0.19
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (38 bp):
AAAAAAGAAAAAAATAATAATAGTAAATAAATATAATA
Found at i:2335895 original size:25 final size:26
Alignment explanation
Indices: 2335829--2335896 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 26
2335819 GAGAAAAAGG
2335829 AAAAAAATAATAAGTAATAAATAATAAT
1 AAAAAAAT-ATAA-TAATAAATAATAAT
* * *
2335857 AAAAAAAGAAAATAAT-AATAATAGT
1 AAAAAAATATAATAATAAATAATAAT
*
2335882 AAATAAATATAATAA
1 AAAAAAATATAATAA
2335897 AAACTATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
25 20 0.59
26 4 0.12
27 3 0.09
28 7 0.21
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (26 bp):
AAAAAAATATAATAATAAATAATAAT
Found at i:2335934 original size:36 final size:35
Alignment explanation
Indices: 2335894--2335972 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 35
2335884 ATAAATATAA
*
2335894 TAAAAACT-ATTTTTAAAACCATATAATATATATGTT
1 TAAAAA-TAATTTTCAAAACCATATAATATATAT-TT
**
2335930 TAAAAATAATTTTCAAAATTATATAATATATATTT
1 TAAAAATAATTTTCAAAACCATATAATATATATTT
2335965 TCAAAAAT
1 T-AAAAAT
2335973 TGTTTTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 4 0.11
36 34 0.89
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (35 bp):
TAAAAATAATTTTCAAAACCATATAATATATATTT
Found at i:2336000 original size:39 final size:38
Alignment explanation
Indices: 2335939--2336039 Score: 127
Period size: 39 Copynumber: 2.7 Consensus size: 38
2335929 TTAAAAATAA
* *
2335939 TTTTCAAAATTATATA--ATATATATTTT-CAAAAATTG
1 TTTTAAAAATTATATACTATATATATTTTACAAAAA-CG
* *
2335975 TTTTAAAAACTTATTTATTATATATATTTTACAAAAACG
1 TTTTAAAAA-TTATATACTATATATATTTTACAAAAACG
2336014 TTTTAAAAATTATATACTATATATAT
1 TTTTAAAAATTATATACTATATATAT
2336040 ATATATATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
36 8 0.14
37 6 0.11
38 15 0.27
39 21 0.38
40 6 0.11
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.48
Consensus pattern (38 bp):
TTTTAAAAATTATATACTATATATATTTTACAAAAACG
Found at i:2336041 original size:40 final size:39
Alignment explanation
Indices: 2335914--2336039 Score: 129
Period size: 36 Copynumber: 3.3 Consensus size: 39
2335904 TTTTAAAACC
* ** *
2335914 ATATAATATATATGTTT-AAAAATAATTTTCAAAA-TTAT
1 ATATTATATATAT-TTTCAAAAATCGTTTTAAAAACTTAT
*
2335952 ATA--ATATATATTTTCAAAAATTGTTTTAAAAACTTAT
1 ATATTATATATATTTTCAAAAATCGTTTTAAAAACTTAT
*
2335989 TTATTATATATATTTTACAAAAA-CGTTTTAAAAA-TTAT
1 ATATTATATATATTTT-CAAAAATCGTTTTAAAAACTTAT
*
2336027 ATACTATATATAT
1 ATATTATATATAT
2336040 ATATATATAT
Statistics
Matches: 76, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
35 3 0.04
36 22 0.29
37 6 0.08
38 18 0.24
39 21 0.28
40 6 0.08
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (39 bp):
ATATTATATATATTTTCAAAAATCGTTTTAAAAACTTAT
Found at i:2336081 original size:11 final size:11
Alignment explanation
Indices: 2336048--2336080 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
2336038 ATATATATAT
2336048 ATGTTTTTAAA
1 ATGTTTTTAAA
2336059 ATGTTTTTAAA
1 ATGTTTTTAAA
2336070 ATG-TTTTAAA
1 ATGTTTTTAAA
2336080 A
1 A
2336081 ACTATATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (11 bp):
ATGTTTTTAAA
Found at i:2336087 original size:38 final size:38
Alignment explanation
Indices: 2336057--2336129 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
2336047 TATGTTTTTA
* *
2336057 AAATGTTTTTAAAATGTTTTAAAAACTATATAATATAT
1 AAATGTTTTCAAAATGTCTTAAAAACTATATAATATAT
*
2336095 ATATGTTTTCAAAATGTCTTAAAAACTATATAATA
1 AAATGTTTTCAAAATGTCTTAAAAACTATATAATA
2336130 GATATTAGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (38 bp):
AAATGTTTTCAAAATGTCTTAAAAACTATATAATATAT
Found at i:2336867 original size:15 final size:15
Alignment explanation
Indices: 2336847--2336889 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
2336837 GCTAGATGGG
2336847 CGGATGCGGGGCGGA
1 CGGATGCGGGGCGGA
2336862 CGGATGCGGGGCGGA
1 CGGATGCGGGGCGGA
*
2336877 TGGATGCGGGGCG
1 CGGATGCGGGGCG
2336890 AGTAATGACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.12, C:0.19, G:0.60, T:0.09
Consensus pattern (15 bp):
CGGATGCGGGGCGGA
Found at i:2337130 original size:37 final size:36
Alignment explanation
Indices: 2337052--2337279 Score: 296
Period size: 37 Copynumber: 6.1 Consensus size: 36
2337042 TCCCTAATAG
*
2337052 ATATATA-TTTCAAAATGTTTTAAAAACTATATGATAC
1 ATATATATTTTCAAAATGTTTTAAAAACTATAT-AT-T
* * *
2337089 ATATATGTTTTTAAAAATGTTTTAAAAATTATATATT
1 ATATAT-ATTTTCAAAATGTTTTAAAAACTATATATT
2337126 ATATATATTTTCAAAATGTTTTTAAAAACTATATATT
1 ATATATATTTTCAAAATG-TTTTAAAAACTATATATT
2337163 ATATATATTTTCAAAATGTTTTAAAAACTATATAATAT
1 ATATATATTTTCAAAATGTTTTAAAAACTATAT-AT-T
* *
2337201 ATATATGTTTTCAAAAATGTTTTAAAAACTTATATATC
1 ATATATATTTTC-AAAATGTTTTAAAAAC-TATATATT
* * *
2337239 ATATATATTTTCAAAATGTTTTCAAAATTATATAAT
1 ATATATATTTTCAAAATGTTTTAAAAACTATATATT
2337275 ATATA
1 ATATA
2337280 CATATATATA
Statistics
Matches: 170, Mismatches: 14, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
36 36 0.21
37 63 0.37
38 25 0.15
39 41 0.24
40 5 0.03
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (36 bp):
ATATATATTTTCAAAATGTTTTAAAAACTATATATT
Found at i:2337219 original size:76 final size:73
Alignment explanation
Indices: 2337046--2337279 Score: 326
Period size: 76 Copynumber: 3.1 Consensus size: 73
2337036 TTGCCATCCC
* * * *
2337046 TAATAGATATATATTTCAAAATGTTTTAAAAACTATATGATACATATATGTTTTTAAAAATGTTT
1 TAATATATATATTTTTCAAAATGTTTTAAAAACTATAT-AT-CATATAT-ATTTTCAAAATGTTT
2337111 TAAAAATTATA
63 TAAAAATTATA
* *
2337122 TATTATATATA-TTTTCAAAATGTTTTTAAAAACTATATATTATATATATTTTCAAAATGTTTTA
1 TAATATATATATTTTTCAAAATG-TTTTAAAAACTATATATCATATATATTTTCAAAATGTTTTA
*
2337186 AAAACTATA
65 AAAATTATA
2337195 TAATATATATATGTTTTCAAAAATGTTTTAAAAACTTATATATCATATATATTTTCAAAATGTTT
1 TAATATATATAT-TTTTC-AAAATGTTTTAAAAAC-TATATATCATATATATTTTCAAAATGTTT
*
2337260 TCAAAATTATA
63 TAAAAATTATA
2337271 TAATATATA
1 TAATATATA
2337280 CATATATATA
Statistics
Matches: 142, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
73 33 0.23
74 6 0.04
75 27 0.19
76 76 0.54
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (73 bp):
TAATATATATATTTTTCAAAATGTTTTAAAAACTATATATCATATATATTTTCAAAATGTTTTAA
AAATTATA
Found at i:2337271 original size:112 final size:111
Alignment explanation
Indices: 2337052--2337279 Score: 368
Period size: 112 Copynumber: 2.0 Consensus size: 111
2337042 TCCCTAATAG
* *
2337052 ATATATATTTCAAAATGTTTTAAAAACTATATGATACATATATGTTTTTAAAAATGTTTTAAAAA
1 ATATATATTTCAAAATGTTTTAAAAACTATATAATACATATATGTTTTCAAAAATGTTTTAAAAA
* *
2337117 TTATATATTATATATATTTTCAAAATGTTTTTAAAAACTATATATT
66 TTATATATCATATATATTTTCAAAATGTTTTTAAAAACTATATAAT
*
2337163 ATATATATTTTCAAAATGTTTTAAAAACTATATAATATATATATGTTTTCAAAAATGTTTTAAAA
1 ATATATA-TTTCAAAATGTTTTAAAAACTATATAATACATATATGTTTTCAAAAATGTTTTAAAA
* *
2337228 ACTTATATATCATATATATTTTCAAAATG-TTTTCAAAATTATATAAT
65 A-TTATATATCATATATATTTTCAAAATGTTTTTAAAAACTATATAAT
2337275 ATATA
1 ATATA
2337280 CATATATATA
Statistics
Matches: 108, Mismatches: 7, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
111 7 0.06
112 75 0.69
113 26 0.24
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (111 bp):
ATATATATTTCAAAATGTTTTAAAAACTATATAATACATATATGTTTTCAAAAATGTTTTAAAAA
TTATATATCATATATATTTTCAAAATGTTTTTAAAAACTATATAAT
Found at i:2338525 original size:21 final size:20
Alignment explanation
Indices: 2338501--2338540 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2338491 ATGGAGTAAA
2338501 AAATAAAAAAAAAAGTAAAAT
1 AAATAAAAAAAAAA-TAAAAT
* *
2338522 AAATTAAAAAAGAATAAAA
1 AAATAAAAAAAAAATAAAA
2338541 ATAATGTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (20 bp):
AAATAAAAAAAAAATAAAAT
Found at i:2338653 original size:36 final size:37
Alignment explanation
Indices: 2338570--2338671 Score: 104
Period size: 37 Copynumber: 2.8 Consensus size: 37
2338560 TAGTATTTAC
* *
2338570 TAAAATAAATAAAAAATAATAAATATATAATACTAAG
1 TAAAACAAATAAAAAATAATAAATATAAAATACTAAG
* *
2338607 TAAAACAAATAAAAAATAA-AGATATACAAGATATTAAG
1 TAAAACAAATAAAAAATAATAAATATA-AA-ATACTAAG
*
2338645 -AAAA-AAATAATAAAAAAATAAA-ATAAA
1 TAAAACAAATAA-AAAATAATAAATATAAA
2338672 GTAAAAATAT
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
36 14 0.25
37 32 0.58
38 9 0.16
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.22
Consensus pattern (37 bp):
TAAAACAAATAAAAAATAATAAATATAAAATACTAAG
Found at i:2338703 original size:42 final size:42
Alignment explanation
Indices: 2338649--2338780 Score: 94
Period size: 44 Copynumber: 3.1 Consensus size: 42
2338639 ATTAAGAAAA
2338649 AAAT-AATAAAAAAATAAAATAAAGTAAAAATATAATATATAT
1 AAATAAAT-AAAAAATAAAATAAAGTAAAAATATAATATATAT
* * *
2338691 AAATAAATAAAAACAAAAAATGAATATTAAGAAA-A-AATATATAA
1 AAATAAATAAAAA-ATAAAAT-AA-AGTAA-AAATATAATATATAT
* * * * * *
2338735 AAACATATAAAATATAATATTAAG-AAAAATAT-ATACATAGT
1 AAATAAATAAAAAATAAAATAAAGTAAAAATATAATATATA-T
2338776 AAATA
1 AAATA
2338781 GAGAAAAATT
Statistics
Matches: 69, Mismatches: 13, Indels: 17
0.70 0.13 0.17
Matches are distributed among these distances:
39 3 0.04
40 9 0.13
41 5 0.07
42 10 0.14
43 14 0.20
44 20 0.29
45 5 0.07
46 3 0.04
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (42 bp):
AAATAAATAAAAAATAAAATAAAGTAAAAATATAATATATAT
Found at i:2338711 original size:17 final size:17
Alignment explanation
Indices: 2338691--2338753 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
2338681 TAATATATAT
2338691 AAATAAATAAAAACAAA
1 AAATAAATAAAAACAAA
* ** *
2338708 AAATGAATATTAAGAAA
1 AAATAAATAAAAACAAA
*
2338725 AAATATATAAAAACATATA
1 AAATAAATAAAAACA-A-A
2338744 AAATATAATA
1 AAATA-AATA
2338754 TTAAGAAAAA
Statistics
Matches: 33, Mismatches: 10, Indels: 3
0.72 0.22 0.07
Matches are distributed among these distances:
17 23 0.70
18 1 0.03
19 6 0.18
20 3 0.09
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.22
Consensus pattern (17 bp):
AAATAAATAAAAACAAA
Found at i:2338735 original size:34 final size:36
Alignment explanation
Indices: 2338691--2338769 Score: 110
Period size: 36 Copynumber: 2.2 Consensus size: 36
2338681 TAATATATAT
*
2338691 AAATAAATAAAAACA-A-AAAAT-GAATATTAAGAAA
1 AAATATATAAAAACATATAAAATAGAATATTAAG-AA
*
2338725 AAATATATAAAAACATATAAAATATAATATTAAGAA
1 AAATATATAAAAACATATAAAATAGAATATTAAGAA
2338761 AAATATATA
1 AAATATATA
2338770 CATAGTAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
34 14 0.35
35 1 0.03
36 16 0.40
37 9 0.22
ACGTcount: A:0.70, C:0.03, G:0.04, T:0.24
Consensus pattern (36 bp):
AAATATATAAAAACATATAAAATAGAATATTAAGAA
Found at i:2340604 original size:106 final size:106
Alignment explanation
Indices: 2340347--2340821 Score: 500
Period size: 106 Copynumber: 4.6 Consensus size: 106
2340337 AATTGGCTCT
* * * * * *
2340347 GGAAATTGTTTGTTGACAGTCAGCCGCCCCTTCACTGTGAAGTTAAGCTTGTGCTGTCTCGAGTC
1 GGAAATTGTTTGTTGACAATCAGCTGCCCCTTCGCTGTGAAGTTGAGATTGTGTTGTCTCGAGTC
* *
2340412 TAATATCCTT--C-GT----TTGAAATTGACTCTG-AA-T-
66 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG
* * * *
2340443 -GAAA-T-TTTATTGACAATCAGCCT-CCCCTTCG-TCGTGAAGTTGAGCTTGTGTTGTCTTGGG
1 GGAAATTGTTTGTTGACAATCAG-CTGCCCCTTCGCT-GTGAAGTTGAGATTGTGTTGTCTCGAG
* * *
2340503 TCCAATATCCTTCGATGGGAAGTTGAAATTGGCCCTGAAATTG
64 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG
* * * *
2340546 GGAAATTGTTTATTGACAGTCAGCTGCCCCTTCGCTGTGAAGTTGAGATTGTGCTGTCTTGAGTC
1 GGAAATTGTTTGTTGACAATCAGCTGCCCCTTCGCTGTGAAGTTGAGATTGTGTTGTCTCGAGTC
2340611 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG
66 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG
* * * * * * *
2340652 GGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTATGAAGTTGA-ACTTGTGTTGTCTCGAAT
1 GGAAATTGTTTGTTGACAATCAGCTGCCCCTTCGCTGTGAAGTTGAGA-TTGTGTTGTCTCGAGT
* *
2340716 CCAATATCCTTTGCTGTGAAGTTGAAATTGGTTCTGAAATTG
65 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG
* * *
2340758 GGAAATTGTTTGTTGACAACCAG-TCGTCCCTTCGTTGTGAAGTTGA-ACTTGTGTTGTCTCGAG
1 GGAAATTGTTTGTTGACAATCAGCT-GCCCCTTCGCTGTGAAGTTGAGA-TTGTGTTGTCTCGAG
2340821 T
64 T
2340822 GGCAAGATAT
Statistics
Matches: 323, Mismatches: 37, Indels: 28
0.83 0.10 0.07
Matches are distributed among these distances:
92 1 0.00
93 54 0.17
94 2 0.01
95 4 0.01
96 1 0.00
100 13 0.04
101 2 0.01
102 1 0.00
104 4 0.01
105 4 0.01
106 236 0.73
107 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.36
Consensus pattern (106 bp):
GGAAATTGTTTGTTGACAATCAGCTGCCCCTTCGCTGTGAAGTTGAGATTGTGTTGTCTCGAGTC
CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG
Found at i:2341610 original size:67 final size:65
Alignment explanation
Indices: 2341494--2341814 Score: 225
Period size: 65 Copynumber: 4.8 Consensus size: 65
2341484 AAGATATATG
* * * **
2341494 TTGTTTCATGA-AAACGGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTTAAGGGAAATAAATTCAAAGA-
2341558 TT
64 TT
*
2341560 TGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
2341625 T
65 T
* * ** * * *
2341626 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACGGAATTTGTTTCAAGAGAAACTGTCTCAAGAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T--A-A-AT
* *
2341691 ACAAA-ACT
57 TCAAAGATT
* * * * * * * *** * * * *
2341699 TAGTTCCAAAAGAAGCTGTCTCAAGGGAGACGAAATTTATTTCAAATAAAACATATTCAAATAAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
* *
2341764 TTGTTTCAAG-GAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
1 TTGTTTCAAGAG-AAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA
2341815 CTGTCTCAAG
Statistics
Matches: 200, Mismatches: 42, Indels: 27
0.74 0.16 0.10
Matches are distributed among these distances:
64 6 0.03
65 84 0.42
66 5 0.03
67 34 0.17
68 21 0.10
70 1 0.00
72 1 0.00
73 43 0.22
74 5 0.03
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:2341663 original size:65 final size:67
Alignment explanation
Indices: 2341468--2341676 Score: 219
Period size: 65 Copynumber: 3.1 Consensus size: 67
2341458 AATTCATTTC
* * * * * *
2341468 AAGGGAAAT-GATCTCAAAGATATATGTTGTTTCATGA-AAACGGTCTCAAGGGAAACAAAATTT
1 AAGGGAAATAAAT-TCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
2341531 TGTTTT
62 TGTTTT
** *
2341537 AAGGGAAATAAATTTGAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTT
1 AAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTT
2341602 TT
66 TT
* * **
2341604 AGGGGAAATAAATTCAAAGA-TTT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACGGAATTTGTT
1 AAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTT
*
2341667 TC
66 TT
*
2341669 AAGAGAAA
1 AAGGGAAA
2341677 CTGTCTCAAG
Statistics
Matches: 121, Mismatches: 17, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
65 43 0.36
66 3 0.02
67 34 0.28
68 24 0.20
69 15 0.12
70 2 0.02
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.30
Consensus pattern (67 bp):
AAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTT
TT
Found at i:2341677 original size:36 final size:36
Alignment explanation
Indices: 2341625--2341952 Score: 199
Period size: 36 Copynumber: 9.4 Consensus size: 36
2341615 ATTCAAAGAT
* *
2341625 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGGAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
*
2341661 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* * * * *
2341697 CTTAGTTCCAAAAGAAGCTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* * * *
2341734 TTTATTTCAA-ATAAAACATAT-TC---A-A-A--TAA
1 TTTGTTTCAAGA-GAAAC-TGTCTCAAGAGAGACGAAA
*
2341763 TTTGTTTCAAG-GAAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAG-AAACTGTCTCAAGAGAGACGAAA
* *
2341799 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* * * * *
2341835 TTTATTTCAAGGGAAA-TGTTTTC-----A-ATG--T
1 TTTGTTTCAAGAGAAACTG-TCTCAAGAGAGACGAAA
* * *
2341863 TTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAA
1 TT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* * * *
2341900 TTTTGTTTTAAGGGAAACTATCTCAAGAGAGACAAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* *
2341937 TTCGTTTCAAGGGAAA
1 TTTGTTTCAAGAGAAA
2341953 TGTTTTCAAT
Statistics
Matches: 228, Mismatches: 38, Indels: 52
0.72 0.12 0.16
Matches are distributed among these distances:
28 4 0.02
29 32 0.14
30 4 0.02
31 2 0.01
32 2 0.01
33 1 0.00
34 2 0.01
35 4 0.02
36 111 0.49
37 64 0.28
38 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
Found at i:2341728 original size:138 final size:138
Alignment explanation
Indices: 2341571--2341829 Score: 374
Period size: 138 Copynumber: 1.9 Consensus size: 138
2341561 GTGTTTCAAG
* * ** * * *
2341571 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTATTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
* **
2341636 GGAAACTGTCTCAAGAGAGACGGAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
66 GAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
2341701 GTTCCAAA
131 GTTCCAAA
* * * * *
2341709 AGAAGCTGTCTCAAGGGAGACGAAATTTATTTCAAATAAAACATATTCAAATAATTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTATTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
*
2341774 GAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
66 GAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
2341830 TGAAATTTAT
Statistics
Matches: 105, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
138 105 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.26
Consensus pattern (138 bp):
AGAAACTGTCTCAAGGGAGACAAAATTTATTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
GAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
GTTCCAAA
Found at i:2341729 original size:37 final size:36
Alignment explanation
Indices: 2341637--2341735 Score: 117
Period size: 37 Copynumber: 2.7 Consensus size: 36
2341627 TGTTTCAAGG
** * * *
2341637 GAAACTGTCTCAAGAGAGACGGAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
2341673 GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAAA
* * *
2341710 GAAGCTGTCTCAAGGGAGACGAAATT
1 GAAACTGTCTCAAGAGAGACAAAATT
2341736 TATTTCAAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
36 24 0.44
37 30 0.56
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.21
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
Found at i:2341872 original size:101 final size:102
Alignment explanation
Indices: 2341663--2342039 Score: 427
Period size: 102 Copynumber: 3.7 Consensus size: 102
2341653 AGACGGAATT
* * * ** * * *
2341663 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAGCTGTCTCAAGGGAG
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* *** ** * **
2341728 ACGAAATTTATTTCAAATAAAACATATTCAAATAATT-
66 ACAAAATTTATTTCAAGGGAAATGTTTTC-AATGTTTA
* *
2341765 TGTTTCAAG-GAAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TGTTTCAAGAG-AAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGAGA
**
2341828 GATGAAATTTATTTCAAGGGAAATGTTTTCAATGTTTA
65 GACAAAATTTATTTCAAGGGAAATGTTTTCAATGTTTA
* * *
2341866 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTGTTTTAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGAGAG
**
2341931 ACAAAATTCGTTTCAAGGGAAATGTTTTCAATGTTTA
66 ACAAAATTTATTTCAAGGGAAATGTTTTCAATGTTTA
* * * * *
2341968 TGTTTCAAGAGAAACTATCTCAAGGGAGACAATATTTTATTTCAAGGGAAACTATCTCAAGCGAG
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
2342033 ATAAAAT
66 ACAAAAT
2342040 CTTCTTTTTA
Statistics
Matches: 243, Mismatches: 28, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
100 5 0.02
101 77 0.32
102 161 0.66
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (102 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGAGAG
ACAAAATTTATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:2341917 original size:37 final size:36
Alignment explanation
Indices: 2341866--2341952 Score: 129
Period size: 37 Copynumber: 2.4 Consensus size: 36
2341856 TCAATGTTTA
* *
2341866 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
*
2341903 TGTTTTAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
*
2341939 CGTTTCAAGGGAAA
1 TGTTTCAAGGGAAA
2341953 TGTTTTCAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 14 0.31
37 31 0.69
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
Found at i:2341926 original size:203 final size:204
Alignment explanation
Indices: 2341663--2342039 Score: 454
Period size: 203 Copynumber: 1.9 Consensus size: 204
2341653 AGACGGAATT
* * * *
2341663 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAGCTGTCTCAAGGGAG
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAGAGAG
* * * *
2341728 ACGAAATTTATTTCAAATAAAACATATTCAAATAATT-TGTTTCAAG-GAAAACTGTCTCAAGAG
66 ACAAAATTCATTTCAAAGAAAACATATTC-AATAATTATGTTTCAAGAG-AAACTATCTCAAGAG
* * *
2341791 AGACAA-AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGATGAAATTTATTTCAAGGGAAATGTT
129 AGACAATAATTTATTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTATTTCAAGGGAAATGTT
2341855 TTCAATGTTTA
194 TTCAATGTTTA
* * * ** **
2341866 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTGTTTTAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAGAGAG
* * * ** * ** *
2341931 ACAAAATTCGTTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAG
66 ACAAAATTCATTTCAAAGAAAACATATTCAATAATTATGTTTCAAGAGAAACTATCTCAAGAGAG
* *
2341996 ACAATATTTTATTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
131 ACAATAATTTATTTCAAGGGAAACTATCTCAAGAGAGATAAAAT
2342040 CTTCTTTTTA
Statistics
Matches: 142, Mismatches: 29, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
202 5 0.04
203 102 0.72
204 35 0.25
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (204 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAGAGAG
ACAAAATTCATTTCAAAGAAAACATATTCAATAATTATGTTTCAAGAGAAACTATCTCAAGAGAG
ACAATAATTTATTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTATTTCAAGGGAAATGTTTT
CAATGTTTA
Found at i:2341945 original size:102 final size:102
Alignment explanation
Indices: 2341765--2342039 Score: 428
Period size: 102 Copynumber: 2.7 Consensus size: 102
2341755 TCAAATAATT
* * *
2341765 TGTTTCAAG-GAAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TGTTTCAAGAG-AAACTATCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
* *
2341828 GATGAAATTTATTTCAAGGGAAATGTTTTCAATGTTTA
65 GATAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
2341866 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTGTTTTAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* *
2341931 ACAAAATTCGTTTCAAGGGAAATGTTTTCAATGTTTA
66 ATAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* * *
2341968 TGTTTCAAGAGAAACTATCTCAAGGGAGACAATATTTTATTTCAAGGGAAACTATCTCAAGCGAG
1 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
2342033 ATAAAAT
66 ATAAAAT
2342040 CTTCTTTTTA
Statistics
Matches: 159, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
101 30 0.19
102 129 0.81
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31
Consensus pattern (102 bp):
TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
ATAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:2343727 original size:28 final size:27
Alignment explanation
Indices: 2343686--2343751 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 27
2343676 GCATCTCGTC
*
2343686 TTTTTTTTTCAATTT-TCCTTTGTTTTT
1 TTTTTTTTTCAATTTCT-CTTTGCTTTT
*
2343713 TTTTTCTTTTTAATTTCTCTTTGCTTTT
1 TTTTT-TTTTCAATTTCTCTTTGCTTTT
2343741 TCTCTTTTTTT
1 T-T-TTTTTTT
2343752 TTTCTCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 5 0.15
28 19 0.58
29 6 0.18
30 3 0.09
ACGTcount: A:0.06, C:0.14, G:0.03, T:0.77
Consensus pattern (27 bp):
TTTTTTTTTCAATTTCTCTTTGCTTTT
Found at i:2343740 original size:26 final size:26
Alignment explanation
Indices: 2343711--2343760 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2343701 TCCTTTGTTT
*
2343711 TTTTTTTCTTTTTAATTTCTCTTTGC
1 TTTTTCTCTTTTTAATTTCTCTTTGC
**
2343737 TTTTTCTCTTTTTTTTTTCTCTTT
1 TTTTTCTCTTTTTAATTTCTCTTT
2343761 TTGTTCTGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (26 bp):
TTTTTCTCTTTTTAATTTCTCTTTGC
Found at i:2344996 original size:7 final size:7
Alignment explanation
Indices: 2344984--2345012 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2344974 TGAAATGTAG
2344984 ATGCAAA
1 ATGCAAA
2344991 ATGCAAA
1 ATGCAAA
2344998 ATGCAAA
1 ATGCAAA
2345005 ATGCAAA
1 ATGCAAA
2345012 A
1 A
2345013 ACGCATGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (7 bp):
ATGCAAA
Found at i:2347133 original size:12 final size:12
Alignment explanation
Indices: 2347038--2347133 Score: 53
Period size: 12 Copynumber: 8.1 Consensus size: 12
2347028 AATAAAAAAT
2347038 TAAAATA-AAGTA
1 TAAAATATAA-TA
2347050 -AAAATATAATA
1 TAAAATATAATA
*
2347061 T-ATATAT-ATA
1 TAAAATATAATA
*
2347071 TATAAATA-AAAA
1 TA-AAATATAATA
*
2347083 TTAAAATAGAATA
1 -TAAAATATAATA
*
2347096 TTAAGAAAATATATA
1 -TAA-AATATA-ATA
2347111 TAAAA-AT-ATA
1 TAAAATATAATA
2347121 TAAAATATAATA
1 TAAAATATAATA
2347133 T
1 T
2347134 TAAGAAAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
10 12 0.18
11 15 0.22
12 19 0.28
13 11 0.16
14 7 0.10
15 3 0.04
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (12 bp):
TAAAATATAATA
Found at i:2347134 original size:37 final size:38
Alignment explanation
Indices: 2347066--2347149 Score: 118
Period size: 37 Copynumber: 2.2 Consensus size: 38
2347056 TAATATATAT
2347066 ATATATATAAATAAAAATTAAAATAGAATATTAAGAAA
1 ATATATATAAATAAAAATTAAAATAGAATATTAAGAAA
* *
2347104 ATATATAT-AA-AAATATATAAAATATAATATTAAGAAA
1 ATATATATAAATAAAAAT-TAAAATAGAATATTAAGAAA
*
2347141 AAATATATA
1 ATATATATA
2347150 CATAGTAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
36 5 0.12
37 28 0.68
38 8 0.20
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (38 bp):
ATATATATAAATAAAAATTAAAATAGAATATTAAGAAA
Found at i:2347206 original size:15 final size:15
Alignment explanation
Indices: 2347186--2347215 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2347176 ATCTATACAT
2347186 ATATATATATATATA
1 ATATATATATATATA
2347201 ATATATATATATATA
1 ATATATATATATATA
2347216 TAATAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:2347206 original size:17 final size:17
Alignment explanation
Indices: 2347179--2347233 Score: 78
Period size: 17 Copynumber: 3.3 Consensus size: 17
2347169 TTAATACATC
2347179 TATACATATATATATATA
1 TATA-ATATATATATATA
2347197 TATAATATATATATATA
1 TATAATATATATATATA
*
2347214 TATAATA-AAAT-TATA
1 TATAATATATATATATA
2347229 TATAA
1 TATAA
2347234 AGAGGAATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
15 9 0.25
16 3 0.08
17 20 0.56
18 4 0.11
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
TATAATATATATATATA
Found at i:2347232 original size:2 final size:2
Alignment explanation
Indices: 2347179--2347217 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
2347169 TTAATACATC
*
2347179 TA TA CA TA TA TA TA TA TA TA TA -A 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
2347218 ATAAAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2356226 original size:2 final size:2
Alignment explanation
Indices: 2356221--2356334 Score: 214
Period size: 2 Copynumber: 58.0 Consensus size: 2
2356211 ATTCGTATGA
2356221 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2356263 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2356304 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2356335 TTTTCTAAAT
Statistics
Matches: 110, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
1 2 0.02
2 108 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2356490 original size:2 final size:2
Alignment explanation
Indices: 2356485--2356519 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2356475 TTTGGAAAAT
2356485 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2356520 TATTTTTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2358301 original size:19 final size:19
Alignment explanation
Indices: 2358262--2358301 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2358252 GTTGTAAATG
* * *
2358262 ATTTGGTTTTGAAAGAGAA
1 ATTTGATTTTGAAAAACAA
2358281 ATTTGATTTTGAAAAACAA
1 ATTTGATTTTGAAAAACAA
2358300 AT
1 AT
2358302 GAAACTTTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.38
Consensus pattern (19 bp):
ATTTGATTTTGAAAAACAA
Found at i:2360009 original size:20 final size:20
Alignment explanation
Indices: 2359986--2360035 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
2359976 GTTCTTACAG
*
2359986 TATCAATACTATATGAACAT
1 TATCGATACTATATGAACAT
2360006 TATCGATACTATATGAACAT
1 TATCGATACTATATGAACAT
2360026 TATCGATACT
1 TATCGATACT
2360036 GTTCATATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (20 bp):
TATCGATACTATATGAACAT
Found at i:2361926 original size:24 final size:24
Alignment explanation
Indices: 2361897--2362011 Score: 135
Period size: 24 Copynumber: 4.8 Consensus size: 24
2361887 TGTTCTGTAA
*
2361897 TATGTTCGTTCATTTATATTTGTT
1 TATGTTCGTTCATTTATATTCGTT
* *
2361921 TATGTTCGTTCATTTATGTTCCTT
1 TATGTTCGTTCATTTATATTCGTT
* *
2361945 TATGTTCGTTCGTTTATATTCATT
1 TATGTTCGTTCATTTATATTCGTT
* *
2361969 TATGTTC-TTCGTTTATGTTCGTT
1 TATGTTCGTTCATTTATATTCGTT
*
2361992 TATGCGT-GTTCATTTATATT
1 TATG-TTCGTTCATTTATATT
2362012 TAGCCTAATC
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
23 18 0.23
24 60 0.77
ACGTcount: A:0.15, C:0.12, G:0.14, T:0.59
Consensus pattern (24 bp):
TATGTTCGTTCATTTATATTCGTT
Found at i:2361938 original size:14 final size:14
Alignment explanation
Indices: 2361919--2361991 Score: 56
Period size: 10 Copynumber: 5.9 Consensus size: 14
2361909 TTTATATTTG
2361919 TTTATGTTCGTTCA
1 TTTATGTTCGTTCA
2361933 TTTATGTTC---C-
1 TTTATGTTCGTTCA
*
2361943 TTTATGTTCGTTCG
1 TTTATGTTCGTTCA
*
2361957 TTTA---T-ATTCA
1 TTTATGTTCGTTCA
*
2361967 TTTATGTTC-TTCG
1 TTTATGTTCGTTCA
2361980 TTTATGTTCGTT
1 TTTATGTTCGTT
2361992 TATGCGTGTT
Statistics
Matches: 47, Mismatches: 3, Indels: 18
0.69 0.04 0.26
Matches are distributed among these distances:
10 16 0.34
11 2 0.04
13 14 0.30
14 15 0.32
ACGTcount: A:0.12, C:0.14, G:0.14, T:0.60
Consensus pattern (14 bp):
TTTATGTTCGTTCA
Found at i:2362213 original size:23 final size:23
Alignment explanation
Indices: 2362185--2362265 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
2362175 TTTTCATTTA
*
2362185 TGTTCGTTTACGTTAATTTATTG
1 TGTTCGTTTACGTTAGTTTATTG
* * *
2362208 TGTTCGTTTACATTGGTTCATTTG
1 TGTTCGTTTACGTTAGTTTA-TTG
*
2362232 TGTTCGTTTACGTTTGTTTATTG
1 TGTTCGTTTACGTTAGTTTATTG
2362255 TGTTCGTTTAC
1 TGTTCGTTTAC
2362266 ATCCGTTCGT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 30 0.60
24 20 0.40
ACGTcount: A:0.12, C:0.11, G:0.20, T:0.57
Consensus pattern (23 bp):
TGTTCGTTTACGTTAGTTTATTG
Found at i:2362252 original size:47 final size:47
Alignment explanation
Indices: 2362177--2362283 Score: 160
Period size: 47 Copynumber: 2.3 Consensus size: 47
2362167 AAAATATATT
2362177 TTCATTTATGTTCGTTTACGTTAATTTATTGTGTTCGTTTACATTGG
1 TTCATTTATGTTCGTTTACGTTAATTTATTGTGTTCGTTTACATTGG
* ** **
2362224 TTCATTTGTGTTCGTTTACGTTTGTTTATTGTGTTCGTTTACATCCG
1 TTCATTTATGTTCGTTTACGTTAATTTATTGTGTTCGTTTACATTGG
*
2362271 TTCGTTTATGTTC
1 TTCATTTATGTTC
2362284 ATTCATTTGT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 53 1.00
ACGTcount: A:0.13, C:0.13, G:0.18, T:0.56
Consensus pattern (47 bp):
TTCATTTATGTTCGTTTACGTTAATTTATTGTGTTCGTTTACATTGG
Found at i:2368752 original size:15 final size:16
Alignment explanation
Indices: 2368734--2368772 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
2368724 AATAATAATA
2368734 ATAATAATA-TATCAT
1 ATAATAATATTATCAT
*
2368749 ATAATAATATTATTAT
1 ATAATAATATTATCAT
2368765 AT-ATAATA
1 ATAATAATA
2368773 GATACGTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATAATATTATCAT
Found at i:2368754 original size:18 final size:18
Alignment explanation
Indices: 2368731--2368772 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
2368721 GTAAATAATA
2368731 ATAATAATAATA-TATCAT
1 ATAATAATAATATTAT-AT
*
2368749 ATAATAATATTATTATAT
1 ATAATAATAATATTATAT
2368767 ATAATA
1 ATAATA
2368773 GATACGTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAATAATAATATTATAT
Found at i:2369151 original size:99 final size:93
Alignment explanation
Indices: 2368987--2369275 Score: 336
Period size: 93 Copynumber: 3.0 Consensus size: 93
2368977 AGGATGATAA
* * *
2368987 ACTTGAGA-AGAATATGTTTCACTACTCTTCCGTGAAGATCAGATTCGAGGTTGTAA--TACTT-
1 ACTTGA-ACAGAATCTGTTTCACTACTCTTCCGTGAAGATCAGATTC-AAG-T-TAATTTATTTC
* *
2369048 CACTACTCTTTCGTGAAGGTTAAATTTGAATG
62 CACTACTCTTTTGTGAAGGTTGAATTTGAATG
* *
2369080 ACTTGAACAGAATCTGTTTCTGTTTCACTACTCTTCCTTCAAGATCAGATTCAAGTTAATTTATT
1 ACTTGAACAGAA------TCTGTTTCACTACTCTTCCGTGAAGATCAGATTCAAGTTAATTTATT
*
2369145 TCCACTACTCTTTTAT-AGAGGTTGAATTTGAATG
60 TCCACTACTCTTTTGTGA-AGGTTGAATTTGAATG
* * *
2369179 ACTTGATCAGAATCTGTTTCACTACTCTTCCGTGAAGATCAGATTCAAGTTGATTTGTTTCCACT
1 ACTTGAACAGAATCTGTTTCACTACTCTTCCGTGAAGATCAGATTCAAGTTAATTTATTTCCACT
*
2369244 ACTCTTTTGTGGAGGTTGAATTTGAATG
66 ACTCTTTTGTGAAGGTTGAATTTGAATG
2369272 ACTT
1 ACTT
2369276 CACTACTCTT
Statistics
Matches: 169, Mismatches: 15, Indels: 24
0.81 0.07 0.12
Matches are distributed among these distances:
92 1 0.01
93 88 0.52
96 3 0.02
97 1 0.01
98 7 0.04
99 69 0.41
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (93 bp):
ACTTGAACAGAATCTGTTTCACTACTCTTCCGTGAAGATCAGATTCAAGTTAATTTATTTCCACT
ACTCTTTTGTGAAGGTTGAATTTGAATG
Found at i:2369328 original size:43 final size:41
Alignment explanation
Indices: 2369193--2369616 Score: 297
Period size: 43 Copynumber: 10.6 Consensus size: 41
2369183 GATCAGAATC
2369193 TGTTT-CACTACTCTTCCGTGAAGATCAGATTCAAGTTGATT
1 TGTTTCCACTACTCTTCCGTGAAGATCAGATTCAAGTTGA-T
** * * * *
2369234 TGTTTCCACTACTCTTTTGTG--G---AGGTTGAATTTGAA
1 TGTTTCCACTACTCTTCCGTGAAGATCAGATTCAAGTTGAT
*
2369270 TGACTT-CACTACTCTTCCGTGAAGATCAGATTCAAGTATGATT
1 TG-TTTCCACTACTCTTCCGTGAAGATCAGATTCAAGT-TGA-T
2369313 TGTTTCCACTACTCTTCCGTGAAGATCAGATTCAAGTATGATT
1 TGTTTCCACTACTCTTCCGTGAAGATCAGATTCAAGT-TGA-T
* * * * *
2369356 TGTTTCCACTACTCTTCCATG--G---AGGTTGAATTTGAA
1 TGTTTCCACTACTCTTCCGTGAAGATCAGATTCAAGTTGAT
*
2369392 TGACTT-CACTACTCTTCCGTGAAGATCAGATTCAAGTTGGAAT
1 TG-TTTCCACTACTCTTCCGTGAAGATCAGATTCAAGTT-G-AT
* * * *
2369435 TGTTTCCACTACTTTTCCGTG--G---AGGTTGAA-TTCGAA
1 TGTTTCCACTACTCTTCCGTGAAGATCAGATTCAAGTT-GAT
*
2369471 TGACTT-CACTACTCTTCCGTGAAGATCAGATTCAAGTTGGAAT
1 TG-TTTCCACTACTCTTCCGTGAAGATCAGATTCAAGTT-G-AT
* * * *
2369514 TGTTTCCACTACTCTTCCGTG--G---AGGTTGAATTTGAA
1 TGTTTCCACTACTCTTCCGTGAAGATCAGATTCAAGTTGAT
* *
2369550 TGACTT-CACTACTCTTCCGTGAAGATCATATTCAAGTTGGAAT
1 TG-TTTCCACTACTCTTCCGTGAAGATCAGATTCAAGTT-G-AT
*
2369593 TGTTTCCACTACTCTTCCATGAAG
1 TGTTTCCACTACTCTTCCGTGAAG
2369617 GTTTTTATGA
Statistics
Matches: 296, Mismatches: 50, Indels: 72
0.71 0.12 0.17
Matches are distributed among these distances:
36 66 0.22
37 25 0.08
38 25 0.08
40 1 0.00
41 36 0.12
42 29 0.10
43 114 0.39
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.37
Consensus pattern (41 bp):
TGTTTCCACTACTCTTCCGTGAAGATCAGATTCAAGTTGAT
Found at i:2369384 original size:122 final size:121
Alignment explanation
Indices: 2369188--2369455 Score: 450
Period size: 122 Copynumber: 2.2 Consensus size: 121
2369178 GACTTGATCA
**
2369188 GAATCTGTTT-CACTACTCTTCCGTGAAGATCAGATTCAAGTTGATTTGTTTCCACTACTCTTTT
1 GAAT-TGTTTCCACTACTCTTCCGTGAAGATCAGATTCAAGTTGATTTGTTTCCACTACTCTTCC
*
2369252 GTGGAGGTTGAATTTGAATGACTTCACTACTCTTCCGTGAAGATCAGATTCAAGTAT-
65 ATGGAGGTTGAATTTGAATGACTTCACTACTCTTCCGTGAAGATCAGATTCAAGT-TG
*
2369309 GATTTGTTTCCACTACTCTTCCGTGAAGATCAGATTCAAGTATGATTTGTTTCCACTACTCTTCC
1 GAATTGTTTCCACTACTCTTCCGTGAAGATCAGATTCAAGT-TGATTTGTTTCCACTACTCTTCC
2369374 ATGGAGGTTGAATTTGAATGACTTCACTACTCTTCCGTGAAGATCAGATTCAAGTTG
65 ATGGAGGTTGAATTTGAATGACTTCACTACTCTTCCGTGAAGATCAGATTCAAGTTG
*
2369431 GAATTGTTTCCACTACTTTTCCGTG
1 GAATTGTTTCCACTACTCTTCCGTG
2369456 GAGGTTGAAT
Statistics
Matches: 138, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
120 5 0.04
121 35 0.25
122 98 0.71
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (121 bp):
GAATTGTTTCCACTACTCTTCCGTGAAGATCAGATTCAAGTTGATTTGTTTCCACTACTCTTCCA
TGGAGGTTGAATTTGAATGACTTCACTACTCTTCCGTGAAGATCAGATTCAAGTTG
Found at i:2369402 original size:36 final size:36
Alignment explanation
Indices: 2369362--2369570 Score: 161
Period size: 36 Copynumber: 5.4 Consensus size: 36
2369352 GATTTGTTTC
* *
2369362 CACTACTCTTCCATGGAGGTTGAATTTGAATGACTT
1 CACTACTCTTCCGTGGAGGTTGAATTGGAATGACTT
* * *
2369398 CACTACTCTTCCGTGAAGATCAGATTCAAGTTGGAATTG-TTT
1 CACTACTCTTCCGTG--G---AGGTTGAA-TTGGAA-TGACTT
* *
2369440 CCACTACTTTTCCGTGGAGGTTGAATTCGAATGACTT
1 -CACTACTCTTCCGTGGAGGTTGAATTGGAATGACTT
* * *
2369477 CACTACTCTTCCGTGAAGATCAGATTCAAGTTGGAATTG-TTT
1 CACTACTCTTCCGTG--G---AGGTTGAA-TTGGAA-TGACTT
*
2369519 CCACTACTCTTCCGTGGAGGTTGAATTTGAATGACTT
1 -CACTACTCTTCCGTGGAGGTTGAATTGGAATGACTT
2369556 CACTACTCTTCCGTG
1 CACTACTCTTCCGTG
2369571 AAGATCATAT
Statistics
Matches: 136, Mismatches: 19, Indels: 36
0.71 0.10 0.19
Matches are distributed among these distances:
36 47 0.35
37 14 0.10
38 14 0.10
41 14 0.10
42 14 0.10
43 33 0.24
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (36 bp):
CACTACTCTTCCGTGGAGGTTGAATTGGAATGACTT
Found at i:2369402 original size:79 final size:79
Alignment explanation
Indices: 2369319--2369619 Score: 523
Period size: 79 Copynumber: 3.8 Consensus size: 79
2369309 GATTTGTTTC
*
2369319 CACTACTCTTCCGTGAAGATCAGATTCAAGTAT-GATTTGTTTCCACTACTCTTCCATGGAGGTT
1 CACTACTCTTCCGTGAAGATCAGATTCAAGT-TGGAATTGTTTCCACTACTCTTCCATGGAGGTT
2369383 GAATTTGAATGACTT
65 GAATTTGAATGACTT
* *
2369398 CACTACTCTTCCGTGAAGATCAGATTCAAGTTGGAATTGTTTCCACTACTTTTCCGTGGAGGTTG
1 CACTACTCTTCCGTGAAGATCAGATTCAAGTTGGAATTGTTTCCACTACTCTTCCATGGAGGTTG
*
2369463 AATTCGAATGACTT
66 AATTTGAATGACTT
*
2369477 CACTACTCTTCCGTGAAGATCAGATTCAAGTTGGAATTGTTTCCACTACTCTTCCGTGGAGGTTG
1 CACTACTCTTCCGTGAAGATCAGATTCAAGTTGGAATTGTTTCCACTACTCTTCCATGGAGGTTG
2369542 AATTTGAATGACTT
66 AATTTGAATGACTT
* *
2369556 CACTACTCTTCCGTGAAGATCATATTCAAGTTGGAATTGTTTCCACTACTCTTCCATGAAGGTT
1 CACTACTCTTCCGTGAAGATCAGATTCAAGTTGGAATTGTTTCCACTACTCTTCCATGGAGGTT
2369620 TTTATGAATG
Statistics
Matches: 212, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
78 1 0.00
79 211 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.36
Consensus pattern (79 bp):
CACTACTCTTCCGTGAAGATCAGATTCAAGTTGGAATTGTTTCCACTACTCTTCCATGGAGGTTG
AATTTGAATGACTT
Found at i:2369694 original size:20 final size:20
Alignment explanation
Indices: 2369671--2369770 Score: 103
Period size: 20 Copynumber: 5.0 Consensus size: 20
2369661 CTAACAGATG
*
2369671 ACCCGAAGGACTTACAAATT
1 ACCCGAAGGATTTACAAATT
2369691 ACCCGAA-GATTTTACAAATT
1 ACCCGAAGGA-TTTACAAATT
* *
2369711 ACCCGAAGGTTTTACAAATG
1 ACCCGAAGGATTTACAAATT
* * * *
2369731 ACCTGGAGGCTTTACAAATG
1 ACCCGAAGGATTTACAAATT
* *
2369751 ACCCGGAGGTTTTACAAATT
1 ACCCGAAGGATTTACAAATT
2369771 CGTGGGAAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.03
20 66 0.96
21 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (20 bp):
ACCCGAAGGATTTACAAATT
Found at i:2369726 original size:40 final size:40
Alignment explanation
Indices: 2369668--2369770 Score: 125
Period size: 40 Copynumber: 2.6 Consensus size: 40
2369658 AGACTAACAG
** *
2369668 ATGACCCGAAGGACTTACAAATTACCCGAAGATTTTACAA
1 ATGACCCGAAGGTTTTACAAATTACCCGAAGACTTTACAA
* * * * *
2369708 ATTACCCGAAGGTTTTACAAATGACCTGGAGGCTTTACAA
1 ATGACCCGAAGGTTTTACAAATTACCCGAAGACTTTACAA
*
2369748 ATGACCCGGAGGTTTTACAAATT
1 ATGACCCGAAGGTTTTACAAATT
2369771 CGTGGGAAAT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (40 bp):
ATGACCCGAAGGTTTTACAAATTACCCGAAGACTTTACAA
Found at i:2375480 original size:81 final size:81
Alignment explanation
Indices: 2375345--2375503 Score: 264
Period size: 81 Copynumber: 2.0 Consensus size: 81
2375335 AGTCTCTTGC
* *
2375345 ACAACCGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTTT
1 ACAACCGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTATCGATCCGCCATTTCGTGT
*
2375410 GCGAACCATTCTCGGT
66 GCAAACCATTCTCGGT
***
2375426 ACAACCGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTATTTCTCCGCCATTTCGTGT
1 ACAACCGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTATCGATCCGCCATTTCGTGT
2375491 GCAAACCATTCTC
66 GCAAACCATTCTC
2375504 TGTAACTCGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 72 1.00
ACGTcount: A:0.19, C:0.33, G:0.18, T:0.30
Consensus pattern (81 bp):
ACAACCGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTATCGATCCGCCATTTCGTGT
GCAAACCATTCTCGGT
Found at i:2375678 original size:55 final size:54
Alignment explanation
Indices: 2375619--2375916 Score: 280
Period size: 55 Copynumber: 5.5 Consensus size: 54
2375609 TTTAATTAAC
* * *
2375619 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCCAAAGT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGCAG-CAAAAAT
* * * *
2375674 GATTGAGCACCTCTGTGCTTCAGTCGAGAACTGACACCTCTGTACAGTTAAAAAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGCAG-CAAAAAT
* * * * * * *
2375729 GACTGAGCACCTCTGTGCTTCAA-CCAGGAGCTCACACCTCTAT-TAGCTAAGACT
1 GATTGAGCACCTCTGTGCTTCAATCGA-GAGCTGACACCTCTGTGCAGC-AAAAAT
*
2375783 GATTGAGCACGTCTGTGCTTCAATCGAG-GACTGACACCTCTGTGCAGTCAAAAAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAG-CTGACACCTCTGTGCAG-CAAAAAT
* * * * * * * **
2375838 GACTGAGCACCTCTATGCTTCAGTCTAAAATCTGGCACCTCTGTGCA-TTAAAAT
1 GATTGAGCACCTCTGTGCTTCAATC-GAGAGCTGACACCTCTGTGCAGCAAAAAT
*
2375892 GATTGAGCACCTCTGTGCTACAATC
1 GATTGAGCACCTCTGTGCTTCAATC
2375917 TAAAATCAAG
Statistics
Matches: 195, Mismatches: 40, Indels: 17
0.77 0.16 0.07
Matches are distributed among these distances:
53 1 0.01
54 67 0.34
55 110 0.56
56 17 0.09
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (54 bp):
GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGCAGCAAAAAT
Found at i:2375836 original size:109 final size:110
Alignment explanation
Indices: 2375622--2375859 Score: 338
Period size: 109 Copynumber: 2.2 Consensus size: 110
2375612 AATTAACGAT
* * * *
2375622 TGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCCAAAGTGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAGAGCTCACACCTCTATGTAGCCCAAACTGATTGAGCACCTC
* *
2375687 TGTGCTTCAGTCGAGAACTGACACCTCTGTACAGTTAAAAATGAC
66 TGTGCTTCAATCGAGAACTGACACCTCTGTACAGTCAAAAATGAC
* *
2375732 TGAGCACCTCTGTGCTTCAACC-AGGAGCTCACACCTCTAT-TAG-CTAAGACTGATTGAGCACG
1 TGAGCACCTCTGTGCTTCAACCGA-GAGCTCACACCTCTATGTAGCCCAA-ACTGATTGAGCACC
* *
2375794 TCTGTGCTTCAATCGAGGACTGACACCTCTGTGCAGTCAAAAATGAC
64 TCTGTGCTTCAATCGAGAACTGACACCTCTGTACAGTCAAAAATGAC
*
2375841 TGAGCACCTCTATGCTTCA
1 TGAGCACCTCTGTGCTTCA
2375860 GTCTAAAATC
Statistics
Matches: 115, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
108 3 0.03
109 77 0.67
110 35 0.30
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (110 bp):
TGAGCACCTCTGTGCTTCAACCGAGAGCTCACACCTCTATGTAGCCCAAACTGATTGAGCACCTC
TGTGCTTCAATCGAGAACTGACACCTCTGTACAGTCAAAAATGAC
Found at i:2375849 original size:28 final size:28
Alignment explanation
Indices: 2375811--2375909 Score: 102
Period size: 26 Copynumber: 3.6 Consensus size: 28
2375801 TTCAATCGAG
*
2375811 GACTGA-CACCTCTGTGCAGTCAAAAAT
1 GACTGAGCACCTCTGTGCAGTCTAAAAT
*
2375838 GACTGAGCACCTCTATGCTTCAGTCTAAAAT
1 GACTGAGCACCTC--TG-TGCAGTCTAAAAT
2375869 --CTG-GCACCTCTGTGCA-T-TAAAAT
1 GACTGAGCACCTCTGTGCAGTCTAAAAT
*
2375892 GATTGAGCACCTCTGTGC
1 GACTGAGCACCTCTGTGC
2375910 TACAATCTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
23 6 0.10
24 1 0.02
25 5 0.08
26 14 0.23
27 6 0.10
28 13 0.21
29 3 0.05
30 2 0.03
31 11 0.18
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.27
Consensus pattern (28 bp):
GACTGAGCACCTCTGTGCAGTCTAAAAT
Found at i:2375868 original size:31 final size:30
Alignment explanation
Indices: 2375811--2375922 Score: 82
Period size: 31 Copynumber: 4.0 Consensus size: 30
2375801 TTCAATCGAG
* *
2375811 GACTGA-CACCTC-TG-TGCAGTCAAAAAT
1 GACTGAGCACCTCTTGCTACAGTCTAAAAT
*
2375838 GACTGAGCACCTCTATGCTTCAGTCTAAAAT
1 GACTGAGCACCTCT-TGCTACAGTCTAAAAT
*
2375869 --CTG-GCACCTC-TG-TGCA-T-TAAAAT
1 GACTGAGCACCTCTTGCTACAGTCTAAAAT
* *
2375892 GATTGAGCACCTCTGTGCTACAATCTAAAAT
1 GACTGAGCACCTCT-TGCTACAGTCTAAAAT
2375923 CAAGCACCTC
Statistics
Matches: 68, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
23 6 0.09
24 1 0.01
25 5 0.07
26 9 0.13
27 6 0.09
28 15 0.22
29 6 0.09
30 3 0.04
31 17 0.25
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (30 bp):
GACTGAGCACCTCTTGCTACAGTCTAAAAT
Found at i:2375895 original size:109 final size:109
Alignment explanation
Indices: 2375622--2375916 Score: 301
Period size: 109 Copynumber: 2.7 Consensus size: 109
2375612 AATTAACGAT
* * * * * * * *
2375622 TGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCCAA-AGTGATTGAGCACCT
1 TGAGCACCTCTATGCTTCAACCAAAAGCTCACACCTCT-AGTAG-CTAAGAATGATTGAGCACCT
* *
2375686 CTGTGCTTCAGTCGAGAACTGACACCTCTGTACAGTTAAAAATGAC
64 CTGTGCTTCAATCGAGAACTGACACCTCTGTACAGTCAAAAATGAC
* ** * * *
2375732 TGAGCACCTCTGTGCTTCAACCAGGAGCTCACACCTCTATTAGCTAAGACTGATTGAGCACGTCT
1 TGAGCACCTCTATGCTTCAACCAAAAGCTCACACCTCTAGTAGCTAAGAATGATTGAGCACCTCT
* *
2375797 GTGCTTCAATCGAGGACTGACACCTCTGTGCAGTCAAAAATGAC
66 GTGCTTCAATCGAGAACTGACACCTCTGTACAGTCAAAAATGAC
* * * **
2375841 TGAGCACCTCTATGCTTCAGTCTAAAATCTGGCACCTCT-GT-GCATTAA-AATGATTGAGCACC
1 TGAGCACCTCTATGCTTCA-ACCAAAAGCTCACACCTCTAGTAGC--TAAGAATGATTGAGCACC
*
2375903 TCTGTGCTACAATC
63 TCTGTGCTTCAATC
2375917 TAAAATCAAG
Statistics
Matches: 156, Mismatches: 25, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
108 5 0.03
109 102 0.65
110 49 0.31
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.26
Consensus pattern (109 bp):
TGAGCACCTCTATGCTTCAACCAAAAGCTCACACCTCTAGTAGCTAAGAATGATTGAGCACCTCT
GTGCTTCAATCGAGAACTGACACCTCTGTACAGTCAAAAATGAC
Found at i:2379989 original size:17 final size:18
Alignment explanation
Indices: 2379963--2379996 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2379953 TTAATTTAAA
*
2379963 TAAATATATTATTTATTT
1 TAAATATATTAATTATTT
2379981 TAAAT-TATTAATTATT
1 TAAATATATTAATTATT
2379997 AATAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TAAATATATTAATTATTT
Found at i:2380668 original size:22 final size:22
Alignment explanation
Indices: 2380618--2380671 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
2380608 TAACTAATTC
* *
2380618 CTAACTATACAAGAATAGCTAA
1 CTAACTTTTCAAGAATAGCTAA
2380640 CTAACTTTTCAAGAATAGCTAA
1 CTAACTTTTCAAGAATAGCTAA
2380662 CTAACTTTTC
1 CTAACTTTTC
2380672 TATGCTCAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.31
Consensus pattern (22 bp):
CTAACTTTTCAAGAATAGCTAA
Found at i:2383247 original size:18 final size:18
Alignment explanation
Indices: 2383224--2383266 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
2383214 ATTCATCTTC
2383224 TTCCCACCTTCCATGGCT
1 TTCCCACCTTCCATGGCT
2383242 TTCCCACCTTCCATGGCT
1 TTCCCACCTTCCATGGCT
2383260 TTCCCAC
1 TTCCCAC
2383267 TAAAGATCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.12, C:0.47, G:0.09, T:0.33
Consensus pattern (18 bp):
TTCCCACCTTCCATGGCT
Found at i:2385447 original size:17 final size:17
Alignment explanation
Indices: 2385422--2385454 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2385412 CATACACAAG
*
2385422 ATCATAGTCGAAGAAGA
1 ATCAAAGTCGAAGAAGA
2385439 ATCAAAGTCGAAGAAG
1 ATCAAAGTCGAAGAAG
2385455 GAGCAAAGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.12, G:0.24, T:0.15
Consensus pattern (17 bp):
ATCAAAGTCGAAGAAGA
Found at i:2385461 original size:17 final size:17
Alignment explanation
Indices: 2385427--2385462 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2385417 ACAAGATCAT
*
2385427 AGTCGAAGAAGAATCAA
1 AGTCGAAGAAGAAGCAA
*
2385444 AGTCGAAGAAGGAGCAA
1 AGTCGAAGAAGAAGCAA
2385461 AG
1 AG
2385463 CCATCACGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.11, G:0.31, T:0.08
Consensus pattern (17 bp):
AGTCGAAGAAGAAGCAA
Found at i:2388207 original size:11 final size:11
Alignment explanation
Indices: 2388191--2388225 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2388181 AGGCAACCCA
2388191 TTTTGTTTTAT
1 TTTTGTTTTAT
2388202 TTTTGTTTTAT
1 TTTTGTTTTAT
**
2388213 TTTCATTTTAT
1 TTTTGTTTTAT
2388224 TT
1 TT
2388226 ATTTCATTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.11, C:0.03, G:0.06, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTAT
Found at i:2389698 original size:74 final size:75
Alignment explanation
Indices: 2389614--2389763 Score: 196
Period size: 75 Copynumber: 2.0 Consensus size: 75
2389604 TGGAATAAAC
** *
2389614 TCAAGTTTAGGATAATATTTTAAACATTATAT-TTTATTTT-TTTATTTTAGTTTAAATATGTTT
1 TCAAGTTTAGGATAATATTTT-AACATTATATCTTTATTTTAGGTATTTTAGTTTAAATAGGTTT
2389677 TAGTATTTTAA
65 TAGTATTTTAA
* * * * * *
2389688 TCAATTTTAGGATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT
1 TCAAGTTTAGGATAATATTTTAACATTATATCTTTATTTTAGGTATTTTAGTTTAAATAGGTTTT
2389753 AGTATTTTAA
66 AGTATTTTAA
2389763 T
1 T
2389764 TAGGATTTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
73 7 0.11
74 26 0.40
75 32 0.49
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.58
Consensus pattern (75 bp):
TCAAGTTTAGGATAATATTTTAACATTATATCTTTATTTTAGGTATTTTAGTTTAAATAGGTTTT
AGTATTTTAA
Found at i:2390388 original size:19 final size:20
Alignment explanation
Indices: 2390364--2390409 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
2390354 CTTTAATTTG
2390364 TTTATTTAATTATT-TTTCT
1 TTTATTTAATTATTATTTCT
* *
2390383 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTCT
2390403 TTTATTT
1 TTTATTT
2390410 TAAAAACAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTATTTAATTATTATTTCT
Found at i:2394589 original size:18 final size:18
Alignment explanation
Indices: 2394566--2394600 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2394556 CAGGACTCAA
2394566 GTGTACAGAGAAAAAATG
1 GTGTACAGAGAAAAAATG
2394584 GTGTACAGAGAAAAAAT
1 GTGTACAGAGAAAAAAT
2394601 TATGGGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.06, G:0.26, T:0.17
Consensus pattern (18 bp):
GTGTACAGAGAAAAAATG
Found at i:2398187 original size:18 final size:18
Alignment explanation
Indices: 2398166--2398202 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2398156 ATCTTTATTT
*
2398166 ATTTAATCTCTTTTTACC
1 ATTTAATCTCATTTTACC
*
2398184 ATTTAATTTCATTTTACC
1 ATTTAATCTCATTTTACC
2398202 A
1 A
2398203 AACCCCCCAT
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:0.27, C:0.19, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTAATCTCATTTTACC
Found at i:2403781 original size:17 final size:15
Alignment explanation
Indices: 2403747--2403804 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
2403737 ATTTTATTAG
2403747 TATGTGAAAATGTTA
1 TATGTGAAAATGTTA
* *
2403762 TATGTGAATATGTTT
1 TATGTGAAAATGTTA
*
2403777 TATATGAAAATGTTA
1 TATGTGAAAATGTTA
2403792 TATGTGAAAATGT
1 TATGTGAAAATGT
2403805 GCTAAGTGGA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (15 bp):
TATGTGAAAATGTTA
Found at i:2403820 original size:45 final size:45
Alignment explanation
Indices: 2403747--2403832 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
2403737 ATTTTATTAG
* * * *
2403747 TATGTGAAAATGTTATATGTGAATATGTTTTATATGAAAATGTTA
1 TATGTGAAAATGTGATAAGTGAATATGTTCTACATGAAAATGTTA
*
2403792 TATGTGAAAATGTGCTAAGTGGAA-ATGTTCTACATGAAAAT
1 TATGTGAAAATGTGATAAGT-GAATATGTTCTACATGAAAAT
2403833 ACTCTATGTG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
45 32 0.91
46 3 0.09
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.38
Consensus pattern (45 bp):
TATGTGAAAATGTGATAAGTGAATATGTTCTACATGAAAATGTTA
Found at i:2403841 original size:45 final size:45
Alignment explanation
Indices: 2403747--2403844 Score: 108
Period size: 45 Copynumber: 2.2 Consensus size: 45
2403737 ATTTTATTAG
* * * * **
2403747 TATGTGAAAATGTTATATGTGAATATGTTTTATATGAAAATGTTA
1 TATGTGAAAATGTGATAAGTGAATATGTTCTACATGAAAATACTA
* *
2403792 TATGTGAAAATGTGCTAAGTGGAA-ATGTTCTACATGAAAATACTC
1 TATGTGAAAATGTGATAAGT-GAATATGTTCTACATGAAAATACTA
2403837 TATGTGAA
1 TATGTGAA
2403845 TGTGCTCTAC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
45 41 0.93
46 3 0.07
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (45 bp):
TATGTGAAAATGTGATAAGTGAATATGTTCTACATGAAAATACTA
Found at i:2404023 original size:24 final size:23
Alignment explanation
Indices: 2403963--2404024 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
2403953 GAATCGAGGG
* * *
2403963 TTCTACACGATCCTTCGGGACAA
1 TTCTACGCGATCCTTCGAGAAAA
* *
2403986 TTCTACGTGGTCCTTCGAGAAACA
1 TTCTACGCGATCCTTCGAGAAA-A
2404010 TTCTACGCGATCCTT
1 TTCTACGCGATCCTT
2404025 TAGGACATAT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 17 0.55
24 14 0.45
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.31
Consensus pattern (23 bp):
TTCTACGCGATCCTTCGAGAAAA
Found at i:2404062 original size:24 final size:24
Alignment explanation
Indices: 2404030--2404099 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
2404020 TCCTTTAGGA
2404030 CATA-TCTATGTGGCACTTCGGTG
1 CATATTCTATGTGGCACTTCGGTG
*
2404053 CATATTCTATGTGACACTTCGGTG
1 CATATTCTATGTGGCACTTCGGTG
* *
2404077 CATATTCTACGTGGTACTTCGGT
1 CATATTCTATGTGGCACTTCGGT
2404100 AAAAATTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 4 0.10
24 38 0.90
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (24 bp):
CATATTCTATGTGGCACTTCGGTG
Found at i:2405087 original size:21 final size:21
Alignment explanation
Indices: 2405061--2405100 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2405051 ATTTTGCACT
2405061 GAGTGTACCGATACACCTAGA
1 GAGTGTACCGATACACCTAGA
2405082 GAGTGTACCGATACACCTA
1 GAGTGTACCGATACACCTA
2405101 CACTCCCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.20
Consensus pattern (21 bp):
GAGTGTACCGATACACCTAGA
Found at i:2411368 original size:12 final size:13
Alignment explanation
Indices: 2411342--2411372 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
2411332 GTATCGTAAT
2411342 TTTTCAAACATTG
1 TTTTCAAACATTG
2411355 TTTTCAAA-ATTG
1 TTTTCAAACATTG
2411367 TTTTCA
1 TTTTCA
2411373 CATATTGCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (13 bp):
TTTTCAAACATTG
Found at i:2411856 original size:18 final size:18
Alignment explanation
Indices: 2411833--2411872 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
2411823 TTTCTATTCC
2411833 AATGCGGTTTGTGTCCAA
1 AATGCGGTTTGTGTCCAA
2411851 AATGCGGTTTGTGTCCAA
1 AATGCGGTTTGTGTCCAA
2411869 AATG
1 AATG
2411873 AGTCTCGTAC
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:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (18 bp):
AATGCGGTTTGTGTCCAA
Found at i:2413147 original size:14 final size:14
Alignment explanation
Indices: 2413115--2413150 Score: 58
Period size: 12 Copynumber: 2.7 Consensus size: 14
2413105 AGGGGGAGTA
2413115 ATTTTTCAAAAATG
1 ATTTTTCAAAAATG
2413129 A--TTTCAAAAATG
1 ATTTTTCAAAAATG
2413141 ATTTTTCAAA
1 ATTTTTCAAA
2413151 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 12 0.60
14 8 0.40
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (14 bp):
ATTTTTCAAAAATG
Found at i:2416150 original size:24 final size:23
Alignment explanation
Indices: 2416109--2416156 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
2416099 TGCTTTTATA
*
2416109 ATTATATTATCATAATATTTAAT
1 ATTATATTATCATAATATATAAT
*
2416132 ATTATATTTTTCATAATATATAAT
1 ATTATA-TTATCATAATATATAAT
2416156 A
1 A
2416157 AAATATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTATATTATCATAATATATAAT
Found at i:2416162 original size:24 final size:24
Alignment explanation
Indices: 2416118--2416163 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2416108 AATTATATTA
* **
2416118 TCATAATATTTAATATTATATTTT
1 TCATAATATATAATAAAATATTTT
2416142 TCATAATATATAATAAAATATT
1 TCATAATATATAATAAAATATT
2416164 AATAAAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (24 bp):
TCATAATATATAATAAAATATTTT
Found at i:2433942 original size:18 final size:18
Alignment explanation
Indices: 2433919--2433960 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2433909 TTTTGGTTAT
2433919 TCTGCTTATATGTATGTA
1 TCTGCTTATATGTATGTA
*
2433937 TCTGCTTATGTGTATGTA
1 TCTGCTTATATGTATGTA
*
2433955 CCTGCT
1 TCTGCT
2433961 AATGAGAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.48
Consensus pattern (18 bp):
TCTGCTTATATGTATGTA
Found at i:2436643 original size:18 final size:19
Alignment explanation
Indices: 2436606--2436643 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2436596 CACGGAATGT
*
2436606 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GAGAATAA
2436626 AAGATTACCA-GAGAATAA
1 AAGATTACCAGGAGAATAA
2436644 GATTACTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.50, C:0.11, G:0.21, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGGAGAATAA
Found at i:2438136 original size:19 final size:19
Alignment explanation
Indices: 2438098--2438137 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2438088 CGAATAATTT
* * *
2438098 AATCGAATATATAATTTTA
1 AATCGAATAGAAAATCTTA
2438117 AATCGAATAGAAAATCTTA
1 AATCGAATAGAAAATCTTA
2438136 AA
1 AA
2438138 ATTCATTTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (19 bp):
AATCGAATAGAAAATCTTA
Found at i:2438254 original size:13 final size:13
Alignment explanation
Indices: 2438238--2438268 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
2438228 TAAAATTTTC
2438238 TTTGAAAATCATT
1 TTTGAAAATCATT
2438251 TTTG-AAATCATT
1 TTTGAAAATCATT
2438263 TTTGAA
1 TTTGAA
2438269 CATTACTCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (13 bp):
TTTGAAAATCATT
Found at i:2438328 original size:13 final size:13
Alignment explanation
Indices: 2438310--2438340 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
2438300 TTAAAATTTC
2438310 TTTGAAAATCATT
1 TTTGAAAATCATT
2438323 TTTG-AAATCATT
1 TTTGAAAATCATT
2438335 TTTGAA
1 TTTGAA
2438341 CATTACTCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (13 bp):
TTTGAAAATCATT
Found at i:2438343 original size:72 final size:73
Alignment explanation
Indices: 2438225--2438373 Score: 291
Period size: 72 Copynumber: 2.1 Consensus size: 73
2438215 ATTTTAGTAA
2438225 TTTTAAAATTTTCTTTGAAAATCATTTTTGAAATCATTTTTGAACATTACTCCCCCTTACTTTAT
1 TTTTAAAATTTTCTTTGAAAATCATTTTTGAAATCATTTTTGAACATTACTCCCCCTTACTTTAT
2438290 TCTCCCCC
66 TCTCCCCC
2438298 TTTTAAAA-TTTCTTTGAAAATCATTTTTGAAATCATTTTTGAACATTACTCCCCCTTACTTTAT
1 TTTTAAAATTTTCTTTGAAAATCATTTTTGAAATCATTTTTGAACATTACTCCCCCTTACTTTAT
2438362 TCTCCCCC
66 TCTCCCCC
2438370 TTTT
1 TTTT
2438374 TTTATTAAAT
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
72 68 0.89
73 8 0.11
ACGTcount: A:0.26, C:0.23, G:0.04, T:0.48
Consensus pattern (73 bp):
TTTTAAAATTTTCTTTGAAAATCATTTTTGAAATCATTTTTGAACATTACTCCCCCTTACTTTAT
TCTCCCCC
Found at i:2438401 original size:72 final size:72
Alignment explanation
Indices: 2438242--2438406 Score: 199
Period size: 72 Copynumber: 2.3 Consensus size: 72
2438232 ATTTTCTTTG
* *
2438242 AAAATCATTTTTGAAATCATTTTTGAACATTACTCCCCCTTACTTTATTCTCCCCCTTTTAAAAT
1 AAAATCATCTATGAAATCATTTTTGAACATTACTCCCCCTTACTTTATTCTCCCCCTTTTAAAAT
*** **
2438307 TTCTTTG
66 TAAATCA
* * ***
2438314 AAAATCATTTTTGAAATCATTTTTGAACATTACTCCCCCTTACTTTATTCTCCCCCTTTTTTTAT
1 AAAATCATCTATGAAATCATTTTTGAACATTACTCCCCCTTACTTTATTCTCCCCCTTTTAAAAT
2438379 TAAATCA
66 TAAATCA
2438386 AAAAGTC-TCTATGAAAT-ATTT
1 AAAA-TCATCTATGAAATCATTT
2438407 AAACAAGGTT
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
71 4 0.05
72 76 0.93
73 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.04, T:0.45
Consensus pattern (72 bp):
AAAATCATCTATGAAATCATTTTTGAACATTACTCCCCCTTACTTTATTCTCCCCCTTTTAAAAT
TAAATCA
Found at i:2438450 original size:2 final size:2
Alignment explanation
Indices: 2438443--2438481 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2438433 ATTGATTTAA
2438443 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2438482 GCTTAAGCTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2440647 original size:21 final size:20
Alignment explanation
Indices: 2440590--2440647 Score: 53
Period size: 23 Copynumber: 2.7 Consensus size: 20
2440580 TACACCTGTG
*
2440590 AGTGTATCAATACACATTCA
1 AGTGTATCGATACACATTCA
* *
2440610 AGGAATGTATTGGTACACATTCA
1 A-G--TGTATCGATACACATTCA
2440633 TAGTGTATCGATACA
1 -AGTGTATCGATACA
2440648 TAGTAAGGAG
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
20 1 0.03
21 11 0.38
23 16 0.55
24 1 0.03
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (20 bp):
AGTGTATCGATACACATTCA
Found at i:2442697 original size:12 final size:12
Alignment explanation
Indices: 2442680--2442704 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2442670 ATGATGGTTC
2442680 TCCAACGTCATG
1 TCCAACGTCATG
2442692 TCCAACGTCATG
1 TCCAACGTCATG
2442704 T
1 T
2442705 GTATTTACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.28
Consensus pattern (12 bp):
TCCAACGTCATG
Found at i:2448078 original size:89 final size:90
Alignment explanation
Indices: 2447921--2448179 Score: 380
Period size: 89 Copynumber: 2.9 Consensus size: 90
2447911 CTAAGAAAAC
* * * * *
2447921 CCTTGGGTAGGCTCATAGGCCCCGAGGCATATCCTTAGGTTGGTTTCCTTTTGCTGTGAGCTTA-
1 CCTTGGGTAGGCTCATAGGCCCCAAGGCATATCCTTAGGTTGGCTTCCCTTTGATGTGTGCTTAG
2447985 GGTAACCCTACGGATCTAAGGATAT
66 GGTAACCCTACGGATCTAAGGATAT
* *
2448010 CCTTGGGTAGGCCCATAGGCCCCAAGGCATATCCTTAGGTTGG-TTCCCTTTGGTGTGTGCTTAG
1 CCTTGGGTAGGCTCATAGGCCCCAAGGCATATCCTTAGGTTGGCTTCCCTTTGATGTGTGCTTAG
2448074 GGTAACCCTACGGATCTAAGGATAT
66 GGTAACCCTACGGATCTAAGGATAT
* * * *
2448099 CCTTGGGTAGGCTCATAGG-CCCAAGGTATATCCTTAGGTTGGCTCCCCTTTTGATGTGTACTGA
1 CCTTGGGTAGGCTCATAGGCCCCAAGGCATATCCTTAGGTTGGCTTCCC-TTTGATGTGTGCTTA
2448163 GGGTAAGCCCTACGGAT
65 GGGTAA-CCCTACGGAT
2448180 ACAGTTCTGG
Statistics
Matches: 155, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
88 39 0.25
89 88 0.57
90 18 0.12
91 10 0.06
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (90 bp):
CCTTGGGTAGGCTCATAGGCCCCAAGGCATATCCTTAGGTTGGCTTCCCTTTGATGTGTGCTTAG
GGTAACCCTACGGATCTAAGGATAT
Found at i:2453022 original size:89 final size:89
Alignment explanation
Indices: 2452864--2453200 Score: 468
Period size: 89 Copynumber: 3.8 Consensus size: 89
2452854 TGTAAGACCT
* * * * *
2452864 TACGGA-CATAAGGATA-CTCTTGGGTAGGCTCATAGGCCCCGAGGCATATCCTTATGTTGGTTT
1 TACGGATC-TAAGGATATC-CTTGGGTAGACCCATAGGCCCCAAGGCATATCCTTAGGTTGGTTC
*
2452927 CATTTTGATGTGTGCTTAGGTAACCC
64 CCTTTTGATGTGTGCTTAGGTAACCC
* *
2452953 TACGGATCTAAGGATATCCATGGGTAGACCCATAGGCCCCAAGCCATATCCTTAGGTTGGTTCCC
1 TACGGATCTAAGGATATCCTTGGGTAGACCCATAGGCCCCAAGGCATATCCTTAGGTTGGTTCCC
*
2453018 TTTTGCTGTGTGCTTAGGTAACCC
66 TTTTGATGTGTGCTTAGGTAACCC
*
2453042 TACGGATCTAAGGATATCCTTGGGTAGGCCCATAGGCCCCAAGGCATATCCTTAGGTTGGTTCCC
1 TACGGATCTAAGGATATCCTTGGGTAGACCCATAGGCCCCAAGGCATATCCTTAGGTTGGTTCCC
*
2453107 -TTTGGTGTGTGCTTAGGGTAACCC
66 TTTTGATGTGTGCTTA-GGTAACCC
* * *
2453131 TACGGATCTAAGGATATCCTTGGGTA-AGCTCATAGG-CCCAAGGTATATCCTTAGGTTGGCTCC
1 TACGGATCTAAGGATATCCTTGGGTAGA-CCCATAGGCCCCAAGGCATATCCTTAGGTTGG-TTC
2453194 CCTTTTG
64 CCTTTTG
2453201 TCGTGCGCTA
Statistics
Matches: 225, Mismatches: 17, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
88 36 0.16
89 183 0.81
90 6 0.03
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.31
Consensus pattern (89 bp):
TACGGATCTAAGGATATCCTTGGGTAGACCCATAGGCCCCAAGGCATATCCTTAGGTTGGTTCCC
TTTTGATGTGTGCTTAGGTAACCC
Found at i:2457284 original size:25 final size:24
Alignment explanation
Indices: 2457236--2457281 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2457226 TGATGAGGGA
2457236 TGAAATTGAATTAATTATAAAATG
1 TGAAATTGAATTAATTATAAAATG
*
2457260 TGAAGTTGATATTAA-TATAAAA
1 TGAAATTGA-ATTAATTATAAAA
2457282 ATGGAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (24 bp):
TGAAATTGAATTAATTATAAAATG
Found at i:2458439 original size:30 final size:30
Alignment explanation
Indices: 2458401--2458782 Score: 147
Period size: 30 Copynumber: 12.9 Consensus size: 30
2458391 TCATAAGTAT
2458401 TAAA-TATAAAGTATATATATATATATATA
1 TAAAGTATAAAGTATATATATATATATATA
2458430 TAAAGTATAAAGTATA-AGTATATATATATA
1 TAAAGTATAAAGTATATA-TATATATATATA
* *
2458460 TAAAGTTTTACTATAAAGTATATGTACATATATA-A
1 TAAAG------TATAAAGTATATATATATATATATA
*
2458495 T-AA-TATAAAGTATA-AGTATAAATATATTA
1 TAAAGTATAAAGTATATA-TATATATATA-TA
* *
2458524 TATA-TATAAAGTATA-AT-TATA-A-AGA
1 TAAAGTATAAAGTATATATATATATATATA
* * *
2458549 CTAAAGCATATAAGTATATAAATATAAAGTATA
1 -TAAAGTATA-AAGTATATATATATATA-TATA
* *
2458582 TATATGTATATAA-TA-ATATAAAGTATATAAGTA
1 TA-AAGTATA-AAGTATATATATA-TATAT-A-TA
* *
2458615 TATAA-TATAAAGTATATA-AGCAT-TACATA
1 TA-AAGTATAAAGTATATATA-TATATATATA
*
2458644 T-AAGTATATAAGTAT-TATATATAAAGTATA
1 TAAAGTATA-AAGTATATATATATATA-TATA
*
2458674 TAAA-TATAAAAGTATATATATA-A-A-CTA
1 TAAAGTAT-AAAGTATATATATATATATATA
* * ** *
2458701 TAAAGTGTATA-TATATA-AGGT-TTTAGTA
1 TAAAGTATAAAGTATATATATATATATA-TA
* *
2458729 TAAAGTATATA-TACATATATA-ATA-ATA
1 TAAAGTATAAAGTATATATATATATATATA
* *
2458756 TAAAGTAT-AAGTATGTGTATATATATA
1 TAAAGTATAAAGTATATATATATATATA
2458783 AACACACGTA
Statistics
Matches: 268, Mismatches: 39, Indels: 92
0.67 0.10 0.23
Matches are distributed among these distances:
25 2 0.01
26 11 0.04
27 50 0.19
28 41 0.15
29 24 0.09
30 60 0.22
31 20 0.07
32 16 0.06
33 20 0.07
34 2 0.01
35 2 0.01
36 20 0.07
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.38
Consensus pattern (30 bp):
TAAAGTATAAAGTATATATATATATATATA
Found at i:2458492 original size:40 final size:38
Alignment explanation
Indices: 2458448--2458532 Score: 100
Period size: 40 Copynumber: 2.2 Consensus size: 38
2458438 AAAGTATAAG
* *
2458448 TATAT-ATATATATAAAGTTTTACTATAAAGTATATGTACA
1 TATATAATA-ATATAAAGTATAACTATAAA-TATAT-TACA
* *
2458488 TATATAATAATATAAAGTATAAGTATAAATATATTATA
1 TATATAATAATATAAAGTATAACTATAAATATATTACA
2458526 TATATAA
1 TATATAA
2458533 AGTATAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
38 10 0.25
39 5 0.12
40 22 0.55
41 3 0.08
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (38 bp):
TATATAATAATATAAAGTATAACTATAAATATATTACA
Found at i:2458569 original size:8 final size:8
Alignment explanation
Indices: 2458556--2458691 Score: 112
Period size: 8 Copynumber: 17.6 Consensus size: 8
2458546 AGACTAAAGC
2458556 ATATAAGT
1 ATATAAGT
*
2458564 ATATAAAT
1 ATATAAGT
2458572 ATA-AAGT
1 ATATAAGT
2458579 ATATATATGT
1 ATATA-A-GT
2458589 ATATAA-T
1 ATATAAGT
2458596 AATATAAAGT
1 -ATAT-AAGT
2458606 ATATAAGT
1 ATATAAGT
2458614 ATATAA-T
1 ATATAAGT
2458621 ATA-AAGT
1 ATATAAGT
*
2458628 ATATAAGC
1 ATATAAGT
*
2458636 AT-T-A-C
1 ATATAAGT
2458641 ATATAAGT
1 ATATAAGT
2458649 ATATAAGT
1 ATATAAGT
2458657 AT-T-A-T
1 ATATAAGT
2458662 ATATAAAGT
1 ATAT-AAGT
*
2458671 ATATAAAT
1 ATATAAGT
*
2458679 ATAAAAGT
1 ATATAAGT
2458687 ATATA
1 ATATA
2458692 TATAAACTAT
Statistics
Matches: 105, Mismatches: 8, Indels: 30
0.73 0.06 0.21
Matches are distributed among these distances:
5 6 0.06
6 6 0.06
7 18 0.17
8 54 0.51
9 13 0.12
10 8 0.08
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.37
Consensus pattern (8 bp):
ATATAAGT
Found at i:2458598 original size:58 final size:51
Alignment explanation
Indices: 2458471--2458718 Score: 138
Period size: 50 Copynumber: 5.1 Consensus size: 51
2458461 AAAGTTTTAC
* * *
2458471 TATAAAGTATATGTACATATATA-ATAATATAAAG--TATAAG--TATAAA
1 TATAAAGTATATATATATATAAAGATAATATAAAGTATATAAGTATATAAA
* * ** * *
2458517 TATATTA-TATATATAAAGTATAATTATAAAGACTAAAGCATATAAGTATATAAA
1 TATA-AAGTATATATATA-TATAAAGAT-AATA-TAAAGTATATAAGTATATAAA
* *
2458571 TATAAAGTATATATATGTATATA-ATAATATAAAGTATATAAGTATAT-AA
1 TATAAAGTATATATATATATAAAGATAATATAAAGTATATAAGTATATAAA
* * *
2458620 TATAAAGTATATA-AGCAT-T----A-CATAT-AAGTATATAAGTAT-TATA
1 TATAAAGTATATATA-TATATAAAGATAATATAAAGTATATAAGTATATAAA
* * * *
2458663 TATAAAGTATATAAATATA-AAAGTATATATATAAACTATA-AAGTGTATATA
1 TATAAAGTATATATATATATAAAG-ATA-ATATAAAGTATATAAGTATATAAA
2458714 TATAA
1 TATAA
2458719 GGTTTTAGTA
Statistics
Matches: 158, Mismatches: 21, Indels: 41
0.72 0.10 0.19
Matches are distributed among these distances:
42 1 0.01
43 30 0.19
44 5 0.03
45 1 0.01
46 12 0.08
47 5 0.03
48 5 0.03
49 19 0.12
50 31 0.20
51 18 0.11
52 8 0.05
53 5 0.03
54 18 0.11
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.36
Consensus pattern (51 bp):
TATAAAGTATATATATATATAAAGATAATATAAAGTATATAAGTATATAAA
Found at i:2458644 original size:22 final size:21
Alignment explanation
Indices: 2458550--2458676 Score: 130
Period size: 22 Copynumber: 5.6 Consensus size: 21
2458540 TTATAAAGAC
*
2458550 TAAAGCATATAAGTATATAAATA
1 TAAAGTATATAAGTAT-T-AATA
2458573 TAAAGTATATATATGTATATAATAATA
1 TAAAGTATATA-A-G--TAT--TAATA
2458600 TAAAGTATATAAGTATATAATA
1 TAAAGTATATAAGTAT-TAATA
*
2458622 TAAAGTATATAAGCATTACATA
1 TAAAGTATATAAGTATTA-ATA
2458644 T-AAGTATATAAGTATTATATA
1 TAAAGTATATAAGTATTA-ATA
2458665 TAAAGTATATAA
1 TAAAGTATATAA
2458677 ATATAAAAGT
Statistics
Matches: 93, Mismatches: 4, Indels: 15
0.83 0.04 0.13
Matches are distributed among these distances:
21 21 0.23
22 35 0.38
23 13 0.14
24 1 0.01
25 2 0.02
26 1 0.01
27 18 0.19
28 2 0.02
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (21 bp):
TAAAGTATATAAGTATTAATA
Found at i:2458653 original size:43 final size:48
Alignment explanation
Indices: 2458403--2458676 Score: 174
Period size: 43 Copynumber: 5.8 Consensus size: 48
2458393 ATAAGTATTA
2458403 AATATAAAGTATATATA-TATATATATATAAAGTATA-AA-G--TATAAGT
1 AATATAAAGTATATA-AGTATATA-ATATAAAGTATATAATGCATATAA-T
* * *
2458449 -ATATATA-TATATAAAGT-TTTACTATAAAGTATATGTACAT--ATATAAT
1 AATATAAAGTATAT-AAGTATATAATATAAAGTATA--TA-ATGCATATAAT
* * *
2458496 AATATAAAG--TATAAGTATA-AATATATTATA-TATATAAAGTATAATTAT
1 AATATAAAGTATATAAGTATATAATATA--A-AGTATATAATGCAT-ATAAT
* * *
2458544 AAAGACTAAAGCATATAAGTATATAAATATAAAGTATATATATGTATATAAT
1 -AATA-TAAAGTATATAAGTATAT-AATATAAAGTATATA-ATGCATATAAT
2458596 AATATAAAGTATATAAGTATATAATATAAAGTATATAA-GCAT-T-A-
1 AATATAAAGTATATAAGTATATAATATAAAGTATATAATGCATATAAT
*
2458640 CATAT-AAGTATATAAGTAT-TATATATAAAGTATATAA
1 AATATAAAGTATATAAGTATATA-ATATAAAGTATATAA
2458677 ATATAAAAGT
Statistics
Matches: 187, Mismatches: 15, Indels: 55
0.73 0.06 0.21
Matches are distributed among these distances:
42 2 0.01
43 40 0.21
44 13 0.07
45 10 0.05
46 13 0.07
47 11 0.06
48 21 0.11
49 19 0.10
50 22 0.12
51 4 0.02
52 21 0.11
53 5 0.03
54 6 0.03
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (48 bp):
AATATAAAGTATATAAGTATATAATATAAAGTATATAATGCATATAAT
Found at i:2458695 original size:22 final size:21
Alignment explanation
Indices: 2458401--2458718 Score: 99
Period size: 22 Copynumber: 15.1 Consensus size: 21
2458391 TCATAAGTAT
2458401 TAAATATAAAGTATATATATA
1 TAAATATAAAGTATATATATA
2458422 TATATATATAAAGTATA-A-AGTA
1 TA-A-ATATAAAGTATATATA-TA
* * *
2458444 TAAGTATATATA-TATATAAAGTT
1 TAA--ATATAAAGTATATATA-TA
* *
2458467 TTACTATAAAGTATATGTACATATA
1 TAAATATAAAGTATA--T--ATATA
*
2458492 TAATAATATAAAGTATA-A-GTA
1 T-A-AATATAAAGTATATATATA
2458513 TAAATAT--A-T-TATATATA
1 TAAATATAAAGTATATATATA
* *
2458530 TAAAGTAT-AA-T-TATAAAGA
1 TAAA-TATAAAGTATATATATA
* *
2458549 CTAAAGCATATAAGTATATAAATA
1 -TAAA-TATA-AAGTATATATATA
* *
2458573 TAAAGTATATA-TATGTATATA
1 TAAA-TATAAAGTATATATATA
2458594 -ATAATATAAAGTATATA-AGTA
1 TA-AATATAAAGTATATATA-TA
*
2458615 TATAATATAAAGTATATA-AGCA
1 TA-AATATAAAGTATATATA-TA
*
2458637 TTACATAT-AAGTATATA-AGTA
1 -TAAATATAAAGTATATATA-TA
*
2458658 TTATATATAAAGTATATA-A-A
1 -TAAATATAAAGTATATATATA
2458678 T--ATA-AAAGTATATATATA
1 TAAATATAAAGTATATATATA
* *
2458696 -AACTATAAAGTGTATATATA
1 TAAATATAAAGTATATATATA
2458716 TAA
1 TAA
2458719 GGTTTTAGTA
Statistics
Matches: 236, Mismatches: 27, Indels: 68
0.71 0.08 0.21
Matches are distributed among these distances:
15 2 0.01
16 12 0.05
17 11 0.05
18 4 0.02
19 16 0.07
20 29 0.12
21 54 0.23
22 56 0.24
23 28 0.12
24 8 0.03
25 2 0.01
26 2 0.01
27 12 0.05
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (21 bp):
TAAATATAAAGTATATATATA
Found at i:2458873 original size:9 final size:9
Alignment explanation
Indices: 2458856--2459019 Score: 61
Period size: 8 Copynumber: 19.1 Consensus size: 9
2458846 TCTTTATAAT
2458856 TATACTTTA
1 TATACTTTA
2458865 TATA-TTT-
1 TATACTTTA
2458872 TATA-TTTA
1 TATACTTTA
2458880 -ATAC-TTA
1 TATACTTTA
2458887 TATACTTTA
1 TATACTTTA
2458896 TAT--TATTA
1 TATACT-TTA
*
2458904 TATAC-ATA
1 TATACTTTA
*
2458912 TATA-TATA
1 TATACTTTA
*
2458920 TATA-TATA
1 TATACTTTA
**
2458928 TATAC-ACA
1 TATACTTTA
* * *
2458936 CACACGTATA
1 TATAC-TTTA
*
2458946 TATAGTTTA
1 TATACTTTA
2458955 TATA-TATATA
1 TATACT-T-TA
*
2458965 TATAC-ATA
1 TATACTTTA
2458973 CTTATACTTTA
1 --TATACTTTA
2458984 TAT--TTATA
1 TATACTT-TA
2458992 TATACTTTA
1 TATACTTTA
*
2459001 TATATTTTA
1 TATACTTTA
2459010 TATACTTTA
1 TATACTTTA
2459019 T
1 T
2459020 TCCTTATAAT
Statistics
Matches: 122, Mismatches: 13, Indels: 40
0.70 0.07 0.23
Matches are distributed among these distances:
7 16 0.13
8 47 0.39
9 40 0.33
10 17 0.14
11 2 0.02
ACGTcount: A:0.39, C:0.09, G:0.01, T:0.51
Consensus pattern (9 bp):
TATACTTTA
Found at i:2458873 original size:22 final size:21
Alignment explanation
Indices: 2458847--2458901 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
2458837 ATGCTTTAGT
2458847 CTTTATAATTATACTTTATATA
1 CTTTATAATTATAC-TTATATA
* *
2458869 TTTTATATTTAATACTTATATA
1 CTTTATAATT-ATACTTATATA
2458891 CTTTAT-ATTAT
1 CTTTATAATTAT
2458902 TATATACATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 2 0.07
21 2 0.07
22 20 0.71
23 4 0.14
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (21 bp):
CTTTATAATTATACTTATATA
Found at i:2458907 original size:2 final size:2
Alignment explanation
Indices: 2458894--2459602 Score: 176
Period size: 2 Copynumber: 364.0 Consensus size: 2
2458884 TTATATACTT
* *
2458894 TA TA T- TA T- TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * ** * *
2458934 CA CA CA CG TA TA TA TA GTT TA TA TA TA TA TA TA TA CA TA CT- TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * *
2458977 TA CTT TA TA TT TA TA TA TA CTT TA TA TA T- TT TA TA TA CTT TA
1 TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA
* *
2459019 T- TCC T- TA TA -A T- TA TA CT- TA TA TA TA TA TA TA -A TA TA CTT
1 TA T-A TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA
*
2459058 TA TT TA TA T- TA TA T- TA TA T- TA TA T- TA TA T- 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
*
2459095 T- TA TA T- TA TA T- TA TA TT TA TA TA T- TA TA T- 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
*
2459132 TA TA T- TA TA TA TA T- TA TA T- TA T- TA T- TA TA T- TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
2459168 TA TA T- TA TA T- TA TA TA TA TA CA CT- TA TA TA CA T- TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * *
2459207 TA AA CTA TA TA -A TT TA TA CA TA GTA TA TA TA -A TT TA TA -A T-
1 TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * * * *
2459247 TA TA CA TA -A TA TA TA AA TG TA -A GT- TT TA TA TA TT TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * *
2459287 TA -A T- TCA TA TA TA -A TT TA TA TA TA AA CTA TA TA GTC TA TA
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* * * *
2459327 TA TA GT- TCA -A TA GT- TCA TA TA TA AA CTC TA TA T- TT TA TA CA
1 TA TA -TA T-A TA TA -TA T-A TA TA TA TA -TA TA TA TA TA TA TA TA
* * * *
2459368 TGA TA TA TA TA GTT TA AA CA TA -A TA TA TA TA GTT TA TA TA TA
1 T-A TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * *
2459410 GTA TA TA -A TGA TA TA AA TA TA AA CTA TA TA GTT TA TA TA TA TA
1 -TA TA TA TA T-A TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA
* * * *
2459453 TA TA GTT TA TA CA TA TA -A TA TA TA TA CTT TA TA TA TA CA T- TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * * * *
2459495 TA T- TG TT TA TA AA TA GTT TA TA T- TA -A TA AA CTA TA TA GTT
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA
* * *
2459535 TA TA TA TA TA TA TA TA -A TA TA CTT TA TA TA TA AA CTA TA GTT
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA -TA
* *
2459577 TA TA CA TA -A AA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2459603 ATTGTTTCAA
Statistics
Matches: 513, Mismatches: 105, Indels: 178
0.64 0.13 0.22
Matches are distributed among these distances:
1 54 0.11
2 424 0.83
3 35 0.07
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2459069 original size:5 final size:5
Alignment explanation
Indices: 2459023--2459186 Score: 193
Period size: 5 Copynumber: 33.2 Consensus size: 5
2459013 ACTTTATTCC
*
2459023 TTATAA TTATA CTTATA -TATA TATATA ATATA CTT-TA TTTATA TTATA
1 TTAT-A TTATA -TTATA TTATA T-TATA TTATA -TTATA -TTATA TTATA
2459071 TTATA TTATA TTATA TTATA -TATA TTATA TTATA TTATA TT-TA -TATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
2459118 TTATA TTATA -TATA -TATA TTATA -TATA TTATA TTATTA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTA-TA TTATA TTATA
2459166 TTTATA TTATA TTATA -TATA T
1 -TTATA TTATA TTATA TTATA T
2459187 ACACTTATAT
Statistics
Matches: 142, Mismatches: 3, Indels: 27
0.83 0.02 0.16
Matches are distributed among these distances:
3 1 0.01
4 28 0.20
5 87 0.61
6 26 0.18
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:2459407 original size:11 final size:11
Alignment explanation
Indices: 2459391--2459566 Score: 65
Period size: 11 Copynumber: 16.7 Consensus size: 11
2459381 TTAAACATAA
2459391 TATATATAGTT
1 TATATATAGTT
*
2459402 TATATATAGTA
1 TATATATAGTT
*
2459413 TATA-AT-G-A
1 TATATATAGTT
* *
2459421 TATAAATA-TA
1 TATATATAGTT
*
2459431 AACTATATAG-T
1 TA-TATATAGTT
2459442 T-TATATA--T
1 TATATATAGTT
2459450 -ATATATAGTT
1 TATATATAGTT
* *
2459460 TATACATA-TAA
1 TATATATAGT-T
*
2459471 TATATATACTT
1 TATATATAGTT
**
2459482 TATATATACAT
1 TATATATAGTT
2459493 TATAT-T-GTT
1 TATATATAGTT
*
2459502 TATAAATAGTT
1 TATATATAGTT
* *
2459513 TATAT-TAATA
1 TATATATAGTT
*
2459523 AACTATATAGTT
1 TA-TATATAGTT
2459535 TATATATA-TAT
1 TATATATAGT-T
*
2459546 ATATAATATACTT
1 -TAT-ATATAGTT
2459559 TATATATA
1 TATATATA
2459567 AACTATAGTT
Statistics
Matches: 126, Mismatches: 20, Indels: 38
0.68 0.11 0.21
Matches are distributed among these distances:
8 12 0.10
9 14 0.11
10 13 0.10
11 69 0.55
12 11 0.09
13 6 0.05
14 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (11 bp):
TATATATAGTT
Found at i:2459592 original size:75 final size:74
Alignment explanation
Indices: 2459451--2459592 Score: 187
Period size: 75 Copynumber: 1.9 Consensus size: 74
2459441 TTTATATATA
* * ***
2459451 TATATAGTTTATACATATAATATATATACTTTATATATACATTATATTGTTTATAAATAGTTTAT
1 TATATAGTTTATACATATAATATATATACTTTATATATAAACTATA-TGTTTATAAATAAAATAT
2459516 ATTAATAAAC
65 ATTAATAAAC
* *
2459526 TATATAGTTTATATATATATATATAATATACTTTATATATAAACTATA-GTTTATACATAAAATA
1 TATATAGTTTATACATATA-ATAT-ATATACTTTATATATAAACTATATGTTTATAAATAAAATA
2459590 TAT
64 TAT
2459593 ATATATTATA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
75 33 0.57
76 4 0.07
77 21 0.36
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (74 bp):
TATATAGTTTATACATATAATATATATACTTTATATATAAACTATATGTTTATAAATAAAATATA
TTAATAAAC
Found at i:2467642 original size:3 final size:3
Alignment explanation
Indices: 2467624--2467677 Score: 51
Period size: 3 Copynumber: 18.3 Consensus size: 3
2467614 TAAAGATTGT
* *
2467624 TAA TAA -AA TGA TAA TAA TAA TAA TAA TAA TAAA TAA -AA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
2467668 GT-A TAA TAA T
1 -TAA TAA TAA T
2467678 TAATTAAGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
2 5 0.12
3 33 0.79
4 4 0.10
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2468899 original size:24 final size:24
Alignment explanation
Indices: 2468861--2468907 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
2468851 GAGACAAATT
2468861 TGTTTTGAAAAAAACAATCTCAAG
1 TGTTTTGAAAAAAACAATCTCAAG
* *
2468885 TGTTTTGAGAGAAACAATCTCAA
1 TGTTTTGAAAAAAACAATCTCAA
2468908 AGGCTTAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (24 bp):
TGTTTTGAAAAAAACAATCTCAAG
Found at i:2471435 original size:44 final size:44
Alignment explanation
Indices: 2471309--2471446 Score: 179
Period size: 44 Copynumber: 3.2 Consensus size: 44
2471299 TGATCTTGTC
* * * * * *
2471309 TTTCTGGAAGATACATGCCTTCAAAAATGCCCCAACATTTATCA
1 TTTCTGGATGATATAGGCCTTAAAAAATACCCCAACACTTATCA
*
2471353 TTTCTGGATGATATAGGCC-TAAAAAATATCCCAACACTTATCA
1 TTTCTGGATGATATAGGCCTTAAAAAATACCCCAACACTTATCA
* * *
2471396 TTTCTGGATGATATGGGCCTTAAAAAATACCCCTACACTTTTCA
1 TTTCTGGATGATATAGGCCTTAAAAAATACCCCAACACTTATCA
2471440 TTTCTGG
1 TTTCTGG
2471447 CTCTATCACT
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
43 38 0.46
44 44 0.54
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (44 bp):
TTTCTGGATGATATAGGCCTTAAAAAATACCCCAACACTTATCA
Found at i:2478545 original size:18 final size:18
Alignment explanation
Indices: 2478522--2478556 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2478512 TTCTGAGTAC
2478522 TGGCAGTG-TCAGGAACAA
1 TGGCAGTGAT-AGGAACAA
2478540 TGGCAGTGATAGGAACA
1 TGGCAGTGATAGGAACA
2478557 GTCGGAGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.34, C:0.14, G:0.34, T:0.17
Consensus pattern (18 bp):
TGGCAGTGATAGGAACAA
Found at i:2481521 original size:47 final size:44
Alignment explanation
Indices: 2481423--2481548 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 44
2481413 GTAACCATGC
* * *
2481423 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATTGGA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGA
*
2481466 AAATTAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAA-TAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATTGG-A
* *
2481514 AAATAAGCTTACAAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
2481549 AGATTTTATA
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
43 3 0.04
44 19 0.26
45 11 0.15
46 1 0.01
47 34 0.47
48 4 0.06
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGA
Found at i:2488678 original size:47 final size:44
Alignment explanation
Indices: 2488580--2488712 Score: 169
Period size: 47 Copynumber: 2.9 Consensus size: 44
2488570 GTAACCATGC
* * * *
2488580 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATTGGA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATTTTGGA
2488623 AAATTAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAA-TAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATTTTGG-A
*
2488671 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGATATTTT
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG-TATTTT
2488713 ATATTATTTT
Statistics
Matches: 79, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
43 3 0.04
44 19 0.24
45 11 0.14
46 7 0.09
47 35 0.44
48 4 0.05
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.33
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATTTTGGA
Found at i:2489524 original size:18 final size:18
Alignment explanation
Indices: 2489501--2489557 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
2489491 ATGGAATTTA
2489501 AGATAAAAATAAATAAAT
1 AGATAAAAATAAATAAAT
* *
2489519 ATATAAAAATAAA-AGAT
1 AGATAAAAATAAATAAAT
2489536 GAGATAAAAATAAAATAAAT
1 -AGATAAAAAT-AAATAAAT
2489556 AG
1 AG
2489558 GGGGTTTGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
17 3 0.09
18 21 0.66
19 5 0.16
20 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
AGATAAAAATAAATAAAT
Found at i:2490004 original size:26 final size:25
Alignment explanation
Indices: 2489951--2490004 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 25
2489941 TAGCATGTTT
*
2489951 AAAAATAAAACTTAAAATAAAATAA
1 AAAAATAAAACTTAAAAGAAAATAA
*
2489976 AAAAATGAAAACTTGAAAAGAAAAGAA
1 AAAAAT-AAAACTT-AAAAGAAAATAA
2490003 AA
1 AA
2490005 TAGAGAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 6 0.24
26 7 0.28
27 12 0.48
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (25 bp):
AAAAATAAAACTTAAAAGAAAATAA
Found at i:2501681 original size:22 final size:22
Alignment explanation
Indices: 2501656--2501702 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
2501646 TGGGCCGTTG
2501656 GATCTTGCCAGATCCAACGGCT
1 GATCTTGCCAGATCCAACGGCT
2501678 GATCTTGCCAGATCCAACGGCT
1 GATCTTGCCAGATCCAACGGCT
2501700 GAT
1 GAT
2501703 GATGTGGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.23
Consensus pattern (22 bp):
GATCTTGCCAGATCCAACGGCT
Found at i:2501836 original size:3 final size:3
Alignment explanation
Indices: 2501828--2501961 Score: 191
Period size: 3 Copynumber: 44.7 Consensus size: 3
2501818 GTAATATTTA
*
2501828 AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAAT AAT AAT AAT -AT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
*
2501874 AAT -AT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* **
2501921 ACT AAT AAT AAT AAT AAT AAT TTT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2501962 ATTTAAATGA
Statistics
Matches: 117, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
2 4 0.03
3 107 0.91
4 6 0.05
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:2511757 original size:72 final size:72
Alignment explanation
Indices: 2511640--2511784 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
2511630 ATGAGATGTA
2511640 ATATACTTCCAAACATGAAACCTATGGTGAAAAATGCTATCAAAACTCCTAGTCTCGTCGCCATT
1 ATATACTTCCAAACATGAAACCTATGGTGAAAAATGCTATCAAAACTCCTAGTCTCGTCGCCATT
2511705 AAAATCG
66 AAAATCG
2511712 ATATACTTCCAAACATGAAACCTATGGTGAAAAATGCTATCAAAACTCCTAGTCTCGTCGCCATT
1 ATATACTTCCAAACATGAAACCTATGGTGAAAAATGCTATCAAAACTCCTAGTCTCGTCGCCATT
2511777 AAAATCG
66 AAAATCG
2511784 A
1 A
2511785 GGTAACCTTG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.26
Consensus pattern (72 bp):
ATATACTTCCAAACATGAAACCTATGGTGAAAAATGCTATCAAAACTCCTAGTCTCGTCGCCATT
AAAATCG
Found at i:2517024 original size:21 final size:21
Alignment explanation
Indices: 2517000--2517046 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2516990 GCTCTGGAAT
*
2517000 TTTTCCTAGGATGCAACCAGC
1 TTTTCCTAGGATGCAACCAAC
* * *
2517021 TTTTCTTGGGATGTAACCAAC
1 TTTTCCTAGGATGCAACCAAC
2517042 TTTTC
1 TTTTC
2517047 TTGTGAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TTTTCCTAGGATGCAACCAAC
Found at i:2517047 original size:21 final size:21
Alignment explanation
Indices: 2517008--2517049 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2516998 ATTTTTCCTA
*
2517008 GGATGCAACCAGCTTTTCTTG
1 GGATGCAACCAACTTTTCTTG
*
2517029 GGATGTAACCAACTTTTCTTG
1 GGATGCAACCAACTTTTCTTG
2517050 TGAAATTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (21 bp):
GGATGCAACCAACTTTTCTTG
Found at i:2518613 original size:17 final size:16
Alignment explanation
Indices: 2518586--2518617 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2518576 AAAGACAAAG
2518586 TAGAAAAAATAATAAA
1 TAGAAAAAATAATAAA
2518602 TAGAATAAAATAATAA
1 TAGAA-AAAATAATAA
2518618 TTGGAGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (16 bp):
TAGAAAAAATAATAAA
Done.