Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, 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: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 15 of 129
Found at i:2561085 original size:42 final size:41
Alignment explanation
Indices: 2560975--2561237 Score: 289
Period size: 42 Copynumber: 6.3 Consensus size: 41
2560965 TAATGAGCTT
* * *
2560975 TTTATTTTTCAAAGTT-TGGTGTCTCTGTTTAGAGGAGCAT
1 TTTATTTTTCAAAGTTGTGGTGCCTCTATTTAGAGGAGCAA
* * *
2561015 TTTATTTTTCAAAGTTGTGATGCTTCTATTTAGATGAGCAA
1 TTTATTTTTCAAAGTTGTGGTGCCTCTATTTAGAGGAGCAA
* *
2561056 TTTATTTTGTCAAAGTTATGGTACCTCTATTTAGAGGAGCAA
1 TTTATTTT-TCAAAGTTGTGGTGCCTCTATTTAGAGGAGCAA
* * *
2561098 TTTATTTTCCAAAGTTGTGGTACCTC-AGTTTAGAGGAGCAT
1 TTTATTTTTCAAAGTTGTGGTGCCTCTA-TTTAGAGGAGCAA
** * *
2561139 TTTATTTTTCTAAAGTTGTGGTGTTTCTGTTTAGATGAGCAA
1 TTTATTTTTC-AAAGTTGTGGTGCCTCTATTTAGAGGAGCAA
* *
2561181 TTTATTTTTTCAAAAGTTGTGATGCCTCTATTTAGAGAAGCTTAA
1 TTTA-TTTTTC-AAAGTTGTGGTGCCTCTATTTAGAGGAGC--AA
2561226 TTTA-TTTTCAAA
1 TTTATTTTTCAAA
2561238 AGTCATTGAG
Statistics
Matches: 187, Mismatches: 28, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
40 17 0.09
41 63 0.34
42 67 0.36
43 34 0.18
45 6 0.03
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (41 bp):
TTTATTTTTCAAAGTTGTGGTGCCTCTATTTAGAGGAGCAA
Found at i:2561104 original size:83 final size:80
Alignment explanation
Indices: 2560975--2561237 Score: 305
Period size: 83 Copynumber: 3.2 Consensus size: 80
2560965 TAATGAGCTT
* *
2560975 TTTATTTTTCAAAGTTTGGTGTCTCTGTTTAGAGGAGCATTTTATTTTTCAAAGTTGTGATGCTT
1 TTTATTTTTCAAAGTTTGGTGTCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTGTGATGCCT
2561040 CTATTTAGATGAGCAA
66 CTATTTAGA-GAGCAA
** * * * *
2561056 TTTATTTTGTCAAAGTTATGGTACCTCTATTTAGAGGAGCAATTTATTTTCCAAAGTTGTGGTAC
1 TTTATTTT-TCAAAGTT-TGGTGTCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTGTGATGC
*
2561121 CTC-AGTTTAGAGGAGCAT
64 CTCTA-TTTAGA-GAGCAA
* *
2561139 TTTATTTTTCTAAAGTTGTGGTGTTTCTGTTTAGATGAGCAATTTATTTTTTCAAAAGTTGTGAT
1 TTTATTTTTC-AAAGTT-TGGTGTCTCTGTTTAGAGGAGCAATTTA-TTTTTC-AAAGTTGTGAT
2561204 GCCTCTATTTAGAGAAGCTTAA
62 GCCTCTATTTAGAG-AGC--AA
2561226 TTTA-TTTTCAAA
1 TTTATTTTTCAAA
2561238 AGTCATTGAG
Statistics
Matches: 152, Mismatches: 20, Indels: 16
0.81 0.11 0.09
Matches are distributed among these distances:
81 8 0.05
82 11 0.07
83 90 0.59
84 6 0.04
85 26 0.17
86 6 0.04
87 5 0.03
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (80 bp):
TTTATTTTTCAAAGTTTGGTGTCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTGTGATGCCT
CTATTTAGAGAGCAA
Found at i:2562541 original size:26 final size:26
Alignment explanation
Indices: 2562500--2562563 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
2562490 ATTATTATCC
* *
2562500 AATGATGAAATTTATA-AAAATT-TTA
1 AATGAT-AAATTTTTATAAAATTCCTA
2562525 AATGATAAATTTTTATAAAATTCCTA
1 AATGATAAATTTTTATAAAATTCCTA
*
2562551 AGTGATAAATTTT
1 AATGATAAATTTT
2562564 GTCTAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.24
25 12 0.35
26 14 0.41
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (26 bp):
AATGATAAATTTTTATAAAATTCCTA
Found at i:2562725 original size:25 final size:25
Alignment explanation
Indices: 2562690--2562742 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
2562680 AATATTTGAT
* *
2562690 AATTTCCAATGATGAGATTCTTAA-A
1 AATTTCAAATGAT-AAATTCTTAAGA
2562715 AATTTCAAATGATAAATTCTTAAGA
1 AATTTCAAATGATAAATTCTTAAGA
2562740 AAT
1 AAT
2562743 CTCTAGGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (25 bp):
AATTTCAAATGATAAATTCTTAAGA
Found at i:2562977 original size:115 final size:111
Alignment explanation
Indices: 2562852--2563072 Score: 302
Period size: 115 Copynumber: 2.0 Consensus size: 111
2562842 CAAAAAAAAT
*
2562852 AAAGAGAAAATATTTTTAAATTGACCAAAATAGTGAAAAATTTAGAAATCCAACCAAAAAGAAAA
1 AAAGAGAAAATATTTCTAAATTGACCAAAATAGTGAAAAATTTAGAAATCCAA-C--AAA-AAAA
2562917 GAGAGA-ATTTCTAAATAGGC-CTAAATGGTGAAAAATGTAGAAATTTTGAA
62 GAGA-ATATTTCTAAATAGGCGC-AAATGGTGAAAAATGTAGAAATTTTGAA
* * * *
2562967 AAAGAGAAAATATTTCTAAATTGACCCAAATGGTGAAAAATTTAGAAATCTAACTAAAAAAGAGA
1 AAAGAGAAAATATTTCTAAATTGACCAAAATAGTGAAAAATTTAGAAATCCAACAAAAAAAGAGA
* * *
2563032 ATTTTTCTAAATAGGCGCAAATGGTGAAAAGTTTAGAAATT
66 ATATTTCTAAATAGGCGCAAATGGTGAAAAATGTAGAAATT
2563073 AAACAAAAAA
Statistics
Matches: 96, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
110 1 0.01
111 42 0.44
112 3 0.03
114 1 0.01
115 49 0.51
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (111 bp):
AAAGAGAAAATATTTCTAAATTGACCAAAATAGTGAAAAATTTAGAAATCCAACAAAAAAAGAGA
ATATTTCTAAATAGGCGCAAATGGTGAAAAATGTAGAAATTTTGAA
Found at i:2563005 original size:55 final size:53
Alignment explanation
Indices: 2562923--2563117 Score: 196
Period size: 56 Copynumber: 3.6 Consensus size: 53
2562913 AAAAGAGAGA
* *
2562923 ATTTCTAAATAGGCCTAAATGGTGAAAAATGTAGAAATTTTGAAAAAGAGAAAAT
1 ATTTCTAAATAGGCCCAAATGGTGAAAAATTTAGAAATTTT-AAAAA-AGAAAAT
* * * *
2562978 ATTTCTAAATTGACCCAAATGGTGAAAAATTTAGAAATCTAACTAAAAAAGAGAAT
1 ATTTCTAAATAGGCCCAAATGGTGAAAAATTTAGAAAT-T--TTAAAAAAGAAAAT
* * * *
2563034 TTTTCTAAATAGGCGCAAATGGTGAAAAGTTTAGAAA--TTAAACAAAAAAAAT
1 ATTTCTAAATAGGCCCAAATGGTGAAAAATTTAGAAATTTTAAA-AAAGAAAAT
* * *
2563086 ATTTCTAATTTGGCTCAAATGGTGAAATAATT
1 ATTTCTAAATAGGCCCAAATGGTGAAA-AATT
2563118 ATATATATTT
Statistics
Matches: 116, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
51 4 0.03
52 30 0.26
53 3 0.03
55 34 0.29
56 39 0.34
57 5 0.04
58 1 0.01
ACGTcount: A:0.47, C:0.08, G:0.15, T:0.29
Consensus pattern (53 bp):
ATTTCTAAATAGGCCCAAATGGTGAAAAATTTAGAAATTTTAAAAAAGAAAAT
Found at i:2563084 original size:115 final size:114
Alignment explanation
Indices: 2562846--2563093 Score: 296
Period size: 115 Copynumber: 2.2 Consensus size: 114
2562836 CGAAGACAAA
*
2562846 AAAAATAAAGAGAAAATATTTTTAAATTGACCAAAATAGTGAAAAATTTAGAAATCCAACCAAAA
1 AAAAA-AAAGAGAAAATATTTCTAAATTGACCAAAATAGTGAAAAATTTAGAAATCCAACC-AAA
2562911 AGAAAAGAGAGAATTTCTAAATAGGCCTAAATGGTGAAAAATGTAGAAATT
64 AGAAAAGAGAGAATTTCTAAATAGGCCTAAATGGTGAAAAATGTAGAAATT
*** * * * *
2562962 TTGAAAAAGAGAAAATATTTCTAAATTGACCCAAATGGTGAAAAATTTAGAAATCTAA-C-TAA-
1 AAAAAAAAGAGAAAATATTTCTAAATTGACCAAAATAGTGAAAAATTTAGAAATCCAACCAAAAG
* * *
2563024 AAAAGAGA-ATTTTTCTAAATAGGCGC-AAATGGTGAAAAGTTTAGAAATT
66 AAAAGAGAGA-ATTTCTAAATAGGC-CTAAATGGTGAAAAATGTAGAAATT
*
2563073 -AAACAAA-A-AAAATATTTCTAA
1 AAAAAAAAGAGAAAATATTTCTAA
2563094 TTTGGCTCAA
Statistics
Matches: 116, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
108 13 0.11
109 1 0.01
110 5 0.04
111 42 0.36
112 3 0.03
114 1 0.01
115 49 0.42
116 2 0.02
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.25
Consensus pattern (114 bp):
AAAAAAAAGAGAAAATATTTCTAAATTGACCAAAATAGTGAAAAATTTAGAAATCCAACCAAAAG
AAAAGAGAGAATTTCTAAATAGGCCTAAATGGTGAAAAATGTAGAAATT
Found at i:2564209 original size:3 final size:3
Alignment explanation
Indices: 2564201--2564247 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
2564191 TAGAACAAAG
2564201 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2564248 ATTAAATTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2564977 original size:24 final size:24
Alignment explanation
Indices: 2564942--2564993 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
2564932 GAGACTATAT
2564942 TCACTACACATTTTGGATATTTAG
1 TCACTACACATTTTGGATATTTAG
*
2564966 TCACTACCCATTTTGGATATTTAG
1 TCACTACACATTTTGGATATTTAG
2564990 TCAC
1 TCAC
2564994 CTCTAAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (24 bp):
TCACTACACATTTTGGATATTTAG
Found at i:2572649 original size:59 final size:56
Alignment explanation
Indices: 2572576--2573403 Score: 783
Period size: 59 Copynumber: 13.9 Consensus size: 56
2572566 TTTATATAAA
*
2572576 AAAAATTTGATACTTTCAACTTTTCCTCAAAAATTCCTTTTTGAAATCTTTATTTTTAAG
1 AAAAA-TTGATACTTTCAACTTTTCCTCAAAAATT--TTTTTGAAAT-TTTATTTTCAAG
** *
2572636 AAAAATTGATACTTTCAAC-TTTCCTTCAAAAATATTTTTTTTAATTTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTCC-TCAAAAAT-TTTTTTGAAATTTTATTTTCAAG
*
2572693 AAAAATTGATACTTTCAA-TTTCTCCTCAAAAATCTCTTTTTAAAATCTTTATTTTCAAG
1 AAAAATTGATACTTTCAACTTT-TCCTCAAAAAT-T-TTTTTGAAAT-TTTATTTTCAAG
**
2572752 AAAAATTGATACTTTCAACTTTTCCTCAAAAACGCATTTTTGAAAATTTTATTTTCAATCTTTAT
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAA--TTTTTTTG-AAATTTTATTTTC-A-----A-
*
2572817 TTTC
56 ---G
* * * *
2572821 AAGGAAAATGATACTTTCAACTTTTCTTTAAAAACGTTTTTTTGAAATTTTATTTTTAATG
1 AA--AAATTGATACTTTCAACTTTTCCTCAAAAA--TTTTTTTGAAATTTTATTTTCAA-G
* *
2572882 -AAAATTGATACTTTCAACTTTTTCTCAAAAATCCCTTTTTGAAATCTTTATTTTCAAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAAT--TTTTTTGAAAT-TTTATTTTCAAG
*
2572940 -AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTCTTGAAAATTTTATTTTCAATG
1 AAAAATTGATACTTTCAACTTTTCCTC-AAAA-ATTTTT-TTG-AAATTTTATTTTCAA-G
* * *
2573000 -AAAATTGATACTTTCAACTTTT-CTTAAAAATGTTCTTTTTTATAAATTTATTTTCAAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAA--TT-TTTTTGA-AATTTTATTTTCAAG
* * * *
2573058 AAAAATTGACATTTTCAACTTTTCCTCAAAAATCCCTTTTCGAAATCTTTATTTTCAAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAAT--TTTTTTGAAAT-TTTATTTTCAAG
*
2573117 AAAAATTGATACTTTCAACTTTTTCTCAAAAATGCTTTTTTGAAAATTTTATTTTCAAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAAT--TTTTTTG-AAATTTTATTTTCAAG
* * *
2573176 AAAAATTAATATTTTCAACTTTTTCTCAAAAATATTTTTT-AAAGTTTTTATTTT-AAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAAT-TTTTTTGAAA--TTTTATTTTCAAG
* * *
2573233 AAAAATTGATACTTTCAATTTTTCCTCAAAAACATTTTTTTGAAGTTTTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTCCTC-AAAA-ATTTTTTTGAA-ATTTTATTTTCAAG
* *
2573292 AAAAATTGATAATTTCAACATTTCCTCAAAAATATTTTTT-AAATTTTTATTTTCAAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAAT-TTTTTTGAAA-TTTTATTTTCAAG
* *
2573349 AAAAATTGATACTTTCAACTTTTCTTCAAAAATATTTTTTTAAAATTTTTATTTT
1 AAAAATTGATACTTTCAACTTTTCCTC-AAAA-ATTTTTTTGAAA-TTTTATTTT
2573404 AAGGAGATTA
Statistics
Matches: 660, Mismatches: 56, Indels: 105
0.80 0.07 0.13
Matches are distributed among these distances:
56 4 0.01
57 108 0.16
58 153 0.23
59 284 0.43
60 58 0.09
61 1 0.00
64 1 0.00
65 1 0.00
69 3 0.00
70 12 0.02
71 35 0.05
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.47
Consensus pattern (56 bp):
AAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTGAAATTTTATTTTCAAG
Found at i:2572706 original size:116 final size:115
Alignment explanation
Indices: 2572576--2573403 Score: 774
Period size: 116 Copynumber: 7.0 Consensus size: 115
2572566 TTTATATAAA
*
2572576 AAAAATTTGATACTTTCAACTTTTCCTCAAAAATTCCTTTTTGAAATCTTTATTTTTAAGAAAAA
1 AAAAA-TTGATACTTTCAACTTTTCCTCAAAAATT--TTTTTGAAATCTTTATTTTCAAGAAAAA
* *
2572641 TTGATACTTTCAACTTTCCTTCAAAAAT-ATTTTTTTTAATTTTATTTTTAAG
63 TTGATACTTTCAACTTTCCTTCAAAAATAATTTTTTTAAATTTTATTTTCAAG
*
2572693 AAAAATTGATACTTTCAA-TTTCTCCTCAAAAATCTCTTTTTAAAATCTTTATTTTCAAGAAAAA
1 AAAAATTGATACTTTCAACTTT-TCCTCAAAAAT-T-TTTTTGAAATCTTTATTTTCAAGAAAAA
*
2572757 TTGATACTTTCAACTTTTCC-TCAAAAACGCATTTTTGAAAATTTTATTTTCAATCTTTATTTTC
63 TTGATACTTTCAAC-TTTCCTTC-AAAA---A----T---AA-TTT-TTTTAAAT-TTTATTTTC
2572821 AAG
113 AAG
* * * *
2572824 GAAAA-TGATACTTTCAACTTTTCTTTAAAAACGTTTTTTTGAAAT-TTTATTTTTAATG-AAAA
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAA--TTTTTTTGAAATCTTTATTTTCAA-GAAAAA
* *** *
2572886 TTGATACTTTCAACTTT-TTCTCAAAAATCCCTTTTTGAAATCTTTATTTTCAAG
63 TTGATACTTTCAACTTTCCT-TCAAAAATAATTTTTTTAAAT-TTTATTTTCAAG
*
2572940 -AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTCTTGAAAAT-TTTATTTTCAATG-AA
1 AAAAATTGATACTTTCAACTTTTCCTC-AAAA-ATTTTT-TTG-AAATCTTTATTTTCAA-GAAA
* ** *
2573002 AATTGATACTTTCAACTTTTCTT-AAAAATGTTCTTTTTTATAAATTTATTTTCAAG
61 AATTGATACTTTCAACTTTCCTTCAAAAATAAT-TTTTTTA-AATTTTATTTTCAAG
* * * *
2573058 AAAAATTGACATTTTCAACTTTTCCTCAAAAATCCCTTTTCGAAATCTTTATTTTCAAGAAAAAT
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAAT--TTTTTTGAAATCTTTATTTTCAAGAAAAAT
* ** *
2573123 TGATACTTTCAACTTT-TTCTCAAAAATGCTTTTTTGAAAATTTTATTTTCAAG
64 TGATACTTTCAACTTTCCT-TCAAAAATAATTTTTT-TAAATTTTATTTTCAAG
* * * *
2573176 AAAAATTAATATTTTCAACTTTTTCTCAAAAATATTTTTT-AAAGTTTTTATTTT-AAGAAAAAT
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAAT-TTTTTTGAAA-TCTTTATTTTCAAGAAAAAT
* * * *
2573239 TGATACTTTCAATTTTTCC-TCAAAAA-CATTTTTTTGAAGTTTTTATTTTTAAG
64 TGATACTTTCAA-CTTTCCTTCAAAAATAATTTTTTT-AA-ATTTTATTTTCAAG
* * *
2573292 AAAAATTGATAATTTCAACATTTCCTCAAAAATATTTTTT-AAATTTTTATTTTCAAGAAAAATT
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAAT-TTTTTTGAAATCTTTATTTTCAAGAAAAATT
*
2573356 GATACTTTCAACTTTTCTTCAAAAAT-ATTTTTTTAAAATTTTTATTTT
65 GATACTTTCAACTTTCCTTCAAAAATAATTTTTTT-AAA-TTTTATTTT
2573404 AAGGAGATTA
Statistics
Matches: 606, Mismatches: 56, Indels: 99
0.80 0.07 0.13
Matches are distributed among these distances:
115 29 0.05
116 238 0.39
117 54 0.09
118 145 0.24
119 38 0.06
120 1 0.00
121 1 0.00
124 1 0.00
125 1 0.00
128 8 0.01
129 33 0.05
130 37 0.06
131 19 0.03
132 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.47
Consensus pattern (115 bp):
AAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTGAAATCTTTATTTTCAAGAAAAATTG
ATACTTTCAACTTTCCTTCAAAAATAATTTTTTTAAATTTTATTTTCAAG
Found at i:2572854 original size:71 final size:71
Alignment explanation
Indices: 2572736--2572876 Score: 221
Period size: 71 Copynumber: 2.0 Consensus size: 71
2572726 CTCTTTTTAA
2572736 AATCTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAACGCATTTTTGAAAATTT
1 AATCTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAACGCATTTTTG-AAATTT
2572801 TATTTTC
65 TATTTTC
* * * **
2572808 AATCTTTATTTTCAAGGAAAA-TGATACTTTCAACTTTTCTTTAAAAACGTTTTTTTGAAATTTT
1 AATCTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAACGCATTTTTGAAATTTT
2572872 ATTTT
66 ATTTT
2572877 TAATGAAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
70 12 0.19
71 32 0.50
72 20 0.31
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (71 bp):
AATCTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAACGCATTTTTGAAATTTT
ATTTTC
Found at i:2572912 original size:27 final size:27
Alignment explanation
Indices: 2572882--2572971 Score: 74
Period size: 27 Copynumber: 3.2 Consensus size: 27
2572872 ATTTTTAATG
2572882 AAAATTGATACTTTCAACTTTTTCTCA
1 AAAATTGATACTTTCAACTTTTTCTCA
*** * * *
2572909 AAAATCCCT-TTTTGAAATCTTTATTTTCAA
1 AAAATTGATACTTT-CAA-CTTT-TTCTC-A
2572939 GAAAATTGATACTTTCAACTTTTTCTCA
1 -AAAATTGATACTTTCAACTTTTTCTCA
2572967 AAAAT
1 AAAAT
2572972 ATTTTTCTTG
Statistics
Matches: 45, Mismatches: 12, Indels: 12
0.65 0.17 0.17
Matches are distributed among these distances:
26 3 0.07
27 13 0.29
28 5 0.11
29 8 0.18
30 5 0.11
31 8 0.18
32 3 0.07
ACGTcount: A:0.36, C:0.17, G:0.04, T:0.43
Consensus pattern (27 bp):
AAAATTGATACTTTCAACTTTTTCTCA
Found at i:2575249 original size:171 final size:171
Alignment explanation
Indices: 2574962--2575402 Score: 661
Period size: 171 Copynumber: 2.6 Consensus size: 171
2574952 AAATAATATG
* * * * *
2574962 ACAATTATTTTTATTGAAATTTCATCTAAATTATTTCATCATTTGGGTCAAATTTAGATAAAATT
1 ACAATTACTTGTATTGAAATTTCATCTAAATCATTTCACCATTTGGGTCAAATTTAAATAAAATT
* *
2575027 TCTCACCTAGAGATTTCTTAAAAATTTACCATTTGAAATTTCTATGAATCTCATCCTTAGATAAT
66 TCTCACCTAGAGATTTCTTAAAAATTTACCATTTGAAATTTCCAAGAATCTCATCCTTAGATAAT
*
2575092 TATCAAATATTTTCAATCTAAATTTTTATTTGGAAAAGAAC
131 TATCAAATATTTTCAATCCAAATTTTTATTTGGAAAAGAAC
* *
2575133 ACAATTACTTGTATTGAAATTTCATCTAAATCA-TTCTACCATTTGGGCCAAATTTAAAGAAAAT
1 ACAATTACTTGTATTGAAATTTCATCTAAATCATTTC-ACCATTTGGGTCAAATTTAAATAAAAT
* * *
2575197 TTCTCACCTAGAGATTTCTTAGAAATTTACCATTTGAAGTTTCCAAGAATCTCATCCTTGGATAA
65 TTCTCACCTAGAGATTTCTTAAAAATTTACCATTTGAAATTTCCAAGAATCTCATCCTTAGATAA
2575262 TTATCAAATATTTTCAATCCAAATTTTTATTTGGAAAAGAAC
130 TTATCAAATATTTTCAATCCAAATTTTTATTTGGAAAAGAAC
* **
2575304 ACAATTACTTGTATTGAAATTTCATTTAAATCATTTCACCATTTAAGTCAAATTTAAATAAAATT
1 ACAATTACTTGTATTGAAATTTCATCTAAATCATTTCACCATTTGGGTCAAATTTAAATAAAATT
* * * * *
2575369 TTTCACTTAAAAATTT-TATAAAAATTTACTATTT
66 TCTCACCTAGAGATTTCT-TAAAAATTTACCATTT
2575403 TTCGTATCTA
Statistics
Matches: 243, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
170 4 0.02
171 236 0.97
172 3 0.01
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (171 bp):
ACAATTACTTGTATTGAAATTTCATCTAAATCATTTCACCATTTGGGTCAAATTTAAATAAAATT
TCTCACCTAGAGATTTCTTAAAAATTTACCATTTGAAATTTCCAAGAATCTCATCCTTAGATAAT
TATCAAATATTTTCAATCCAAATTTTTATTTGGAAAAGAAC
Found at i:2576484 original size:22 final size:24
Alignment explanation
Indices: 2576424--2576485 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 24
2576414 TAGATAGATC
2576424 ATAAAAA-AAATAAAAATGATAAAT
1 ATAAAAATAAAT-AAAATGATAAAT
* * *
2576448 AGAAAAATAGA-AAAAT-CTAAA-
1 ATAAAAATAAATAAAATGATAAAT
2576469 ATAAAAATAAATAAAAT
1 ATAAAAATAAATAAAAT
2576486 TTTTTACACC
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
21 9 0.29
22 9 0.29
23 5 0.16
24 6 0.19
25 2 0.06
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (24 bp):
ATAAAAATAAATAAAATGATAAAT
Found at i:2576484 original size:23 final size:22
Alignment explanation
Indices: 2576424--2576484 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
2576414 TAGATAGATC
2576424 ATAAAAAAAATAAAAATGATAA
1 ATAAAAAAAATAAAAATGATAA
* * *
2576446 ATAGAAAAATAGAAAAAT-CTAAA
1 ATA-AAAAAAATAAAAATGAT-AA
2576469 ATAAAAATAAATAAAA
1 ATAAAAA-AAATAAAA
2576485 TTTTTTACAC
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 8 0.26
23 23 0.74
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (22 bp):
ATAAAAAAAATAAAAATGATAA
Found at i:2578361 original size:19 final size:17
Alignment explanation
Indices: 2578324--2578362 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2578314 GGATCCTCAA
2578324 TATTATAAACATATATT
1 TATTATAAACATATATT
2578341 TATTCATAAAC-TATATT
1 TATT-ATAAACATATATT
2578358 T-TTAT
1 TATTAT
2578363 CATTTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.10
16 2 0.10
17 11 0.52
18 6 0.29
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTATAAACATATATT
Found at i:2578365 original size:18 final size:18
Alignment explanation
Indices: 2578324--2578358 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2578314 GGATCCTCAA
2578324 TATT-ATAAACATATATT
1 TATTCATAAACATATATT
2578341 TATTCATAAAC-TATATT
1 TATTCATAAACATATATT
2578358 T
1 T
2578359 TTATCATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTCATAAACATATATT
Found at i:2584546 original size:1 final size:1
Alignment explanation
Indices: 2584540--2584581 Score: 84
Period size: 1 Copynumber: 42.0 Consensus size: 1
2584530 CATTTCAAGG
2584540 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2584582 GAGAAATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2584774 original size:2 final size:2
Alignment explanation
Indices: 2584767--2584805 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2584757 ATGGTACGTA
2584767 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2584806 ATTTCAGAAT
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2592994 original size:26 final size:24
Alignment explanation
Indices: 2592946--2593011 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 24
2592936 TAAAAAAGCT
*
2592946 TATTCATGAATAT-TAAATAAATA
1 TATTCATAAATATATAAATAAATA
* *
2592969 TGTTCACTAATATATATAAATGAATA
1 TATTCA-TAA-ATATATAAATAAATA
2592995 TATTCATAAATA-ATAAA
1 TATTCATAAATATATAAA
2593012 CAGATCATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 10 0.28
24 5 0.14
25 7 0.19
26 14 0.39
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.38
Consensus pattern (24 bp):
TATTCATAAATATATAAATAAATA
Found at i:2597435 original size:29 final size:27
Alignment explanation
Indices: 2597395--2597470 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 27
2597385 GTCTTATTTA
* *
2597395 TTTATTTATTTATTTTAACATCTAAAATT
1 TTTATTTTTTTATTTTAAAAT-T-AAATT
*
2597424 TTTATTTTTTTATAGTTTAAAATTATATT
1 TTTATTTTTTTAT--TTTAAAATTAAATT
2597453 TTATATATTTTTTATTTT
1 TT-TAT-TTTTTTATTTT
2597471 TTGACATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
29 21 0.52
30 4 0.10
31 15 0.38
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (27 bp):
TTTATTTTTTTATTTTAAAATTAAATT
Found at i:2597794 original size:26 final size:27
Alignment explanation
Indices: 2597708--2597799 Score: 116
Period size: 27 Copynumber: 3.4 Consensus size: 27
2597698 TTTATATATA
*
2597708 TATTTATCTAATAATATATATTTTTAT
1 TATTTATCTATTAATATATATTTTTAT
* *
2597735 TAGTTATCCATTAATAT-TATTTTTTAT
1 TATTTATCTATTAATATATA-TTTTTAT
* *
2597762 TACTTATCTATTAATGTATATTTTTA-
1 TATTTATCTATTAATATATATTTTTAT
2597788 TATTTATCTATT
1 TATTTATCTATT
2597800 TTTTTATTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
26 13 0.23
27 41 0.73
28 2 0.04
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.60
Consensus pattern (27 bp):
TATTTATCTATTAATATATATTTTTAT
Found at i:2597801 original size:16 final size:16
Alignment explanation
Indices: 2597780--2597815 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
2597770 TATTAATGTA
2597780 TATTTTTATATTTATC
1 TATTTTTATATTTATC
*
2597796 TATTTTTTTATTTATC
1 TATTTTTATATTTATC
2597812 TATT
1 TATT
2597816 CTGAATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (16 bp):
TATTTTTATATTTATC
Found at i:2598552 original size:3 final size:3
Alignment explanation
Indices: 2598546--2598597 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
2598536 TTTTTCTTAT
2598546 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TCT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
2598590 TTA TTA TT
1 TTA TTA TT
2598598 TATTGATTAG
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2598585 original size:23 final size:23
Alignment explanation
Indices: 2598555--2598598 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
2598545 TTTATTATTA
2598555 TTATTATTATTATTATTATTTCT
1 TTATTATTATTATTATTATTTCT
2598578 TTATTATTATTATTATTATTT
1 TTATTATTATTATTATTATTT
2598599 ATTGATTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
TTATTATTATTATTATTATTTCT
Found at i:2598657 original size:11 final size:11
Alignment explanation
Indices: 2598623--2598656 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
2598613 AATTATTTAG
2598623 TATTCTTTATTT
1 TATT-TTTATTT
2598635 TATTTTTATTT
1 TATTTTTATTT
2598646 TA-TTTTATTT
1 TATTTTTATTT
2598656 T
1 T
2598657 TTTAAAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.41
11 9 0.41
12 4 0.18
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:2598671 original size:14 final size:14
Alignment explanation
Indices: 2598652--2598678 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2598642 ATTTTATTTT
2598652 ATTTTTTTAAAATG
1 ATTTTTTTAAAATG
2598666 ATTTTTTTAAAAT
1 ATTTTTTTAAAAT
2598679 AAAATTTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (14 bp):
ATTTTTTTAAAATG
Found at i:2598766 original size:58 final size:56
Alignment explanation
Indices: 2598671--2598851 Score: 204
Period size: 58 Copynumber: 3.1 Consensus size: 56
2598661 AAATGATTTT
* * *
2598671 TTTAAAATAAAATTTCAAAAAAATATATTTTTAAAAAAAAGTTGAAAGTATCAATTTTCC
1 TTTAAAAT-AATTTTC-TAAAAA-ATA-TTTTGAAAAAAAGTTGAAAGTATCAATTTTCC
* **
2598731 TTGAAAATAAGTTTTCTAAAAAATATTTTCGAAAAAAAGTTGAAAGTATCAATTTTTT
1 TTTAAAATAA-TTTTCTAAAAAATATTTT-GAAAAAAAGTTGAAAGTATCAATTTTCC
* *
2598789 TTTAAAATAATTTTCTAAAAAATATTTTGATGAAAAA-TT-AGAAGTACCAATTTTCC
1 TTTAAAATAATTTTCTAAAAAATATTTTGA-AAAAAAGTTGA-AAGTATCAATTTTCC
2598845 TTTAAAA
1 TTTAAAA
2598852 AAAATTATTT
Statistics
Matches: 106, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
55 1 0.01
56 23 0.22
57 27 0.25
58 37 0.35
59 7 0.07
60 11 0.10
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (56 bp):
TTTAAAATAATTTTCTAAAAAATATTTTGAAAAAAAGTTGAAAGTATCAATTTTCC
Found at i:2603268 original size:83 final size:82
Alignment explanation
Indices: 2603173--2603345 Score: 310
Period size: 83 Copynumber: 2.1 Consensus size: 82
2603163 TGTTGCTATA
2603173 TAAGTTAATATTTTTCATCAAAAATCATCAATAAAATTATTAATTTTTACATTTAATAGAAAATT
1 TAAGTTAATATTTTTCATCAAAAATCATCAATAAAATTATTAATTTTTACATTTAATAGAAAATT
2603238 ATTATTATAAATAATAT
66 ATTATTATAAATAATAT
* *
2603255 GTAAGTTAATATTTTTCATCGAAAATCATCAATAAATTTATTAATTTTTACATTTAATAGAAAAT
1 -TAAGTTAATATTTTTCATCAAAAATCATCAATAAAATTATTAATTTTTACATTTAATAGAAAAT
2603320 TATTATTATAAATAATAT
65 TATTATTATAAATAATAT
*
2603338 TAACTTAA
1 TAAGTTAA
2603346 CTTTTACATT
Statistics
Matches: 87, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
82 7 0.08
83 80 0.92
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.44
Consensus pattern (82 bp):
TAAGTTAATATTTTTCATCAAAAATCATCAATAAAATTATTAATTTTTACATTTAATAGAAAATT
ATTATTATAAATAATAT
Found at i:2603352 original size:47 final size:48
Alignment explanation
Indices: 2603295--2603390 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
2603285 AATAAATTTA
* *
2603295 TTAATTTTTACATTTAATAG-AAAATTATTATTATAAATAATATTAAC
1 TTAACTTTTACATTTAATAGAAAAATCATTATTATAAATAATATTAAC
*
2603342 TTAACTTTTACATTTAATAGAAAAATCATTATTTTAAATAATATTAAC
1 TTAACTTTTACATTTAATAGAAAAATCATTATTATAAATAATATTAAC
2603390 T
1 T
2603391 AATATTAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 19 0.42
48 26 0.58
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (48 bp):
TTAACTTTTACATTTAATAGAAAAATCATTATTATAAATAATATTAAC
Found at i:2604289 original size:42 final size:43
Alignment explanation
Indices: 2604239--2604323 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 43
2604229 TAATTTATTC
** *
2604239 ATTAATTTTTTCAGTCACGAATTTTTAT-TTTAATTTTGAAAA
1 ATTAATTTTCACAATCACGAATTTTTATATTTAATTTTGAAAA
** *
2604281 ATTAATTTTCACAATCACGGTTTTTTATATTTATTTTTGAAAA
1 ATTAATTTTCACAATCACGAATTTTTATATTTAATTTTGAAAA
2604324 TACGGTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 23 0.64
43 13 0.36
ACGTcount: A:0.33, C:0.08, G:0.07, T:0.52
Consensus pattern (43 bp):
ATTAATTTTCACAATCACGAATTTTTATATTTAATTTTGAAAA
Found at i:2606574 original size:42 final size:42
Alignment explanation
Indices: 2606515--2606605 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
2606505 AACAGCTTCC
2606515 TAAACCATCCAAGAAACCACGATCCAAGAATCCCATATTCTT
1 TAAACCATCCAAGAAACCACGATCCAAGAATCCCATATTCTT
2606557 TAAACCATCCAAGAAACCACGATCCAAGAATCCCATATTCTT
1 TAAACCATCCAAGAAACCACGATCCAAGAATCCCATATTCTT
2606599 T-AACCAT
1 TAAACCAT
2606606 AAGTAGTCGA
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 6 0.12
42 43 0.88
ACGTcount: A:0.41, C:0.31, G:0.07, T:0.22
Consensus pattern (42 bp):
TAAACCATCCAAGAAACCACGATCCAAGAATCCCATATTCTT
Found at i:2620040 original size:2 final size:2
Alignment explanation
Indices: 2620033--2620072 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2620023 CATACCACGA
2620033 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
2620073 TTGCAAGCAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2632158 original size:30 final size:30
Alignment explanation
Indices: 2632093--2632160 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
2632083 ATTAATTTTT
* *
2632093 TAAT-TTTTTAATTATATATATTTATATAA
1 TAATATTTTTAAATATATATATTTATAAAA
* *
2632122 TGATATTTTTAAATATTTATATTT-TAAAAA
1 TAATATTTTTAAATATATATATTTAT-AAAA
2632152 TAATATTTT
1 TAATATTTT
2632161 ATTAATTTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (30 bp):
TAATATTTTTAAATATATATATTTATAAAA
Found at i:2634015 original size:31 final size:31
Alignment explanation
Indices: 2633959--2634017 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
2633949 TACTTTATTA
*
2633959 TTGGCTAAATACTCAAATCAAGATCAAACAT
1 TTGGATAAATACTCAAATCAAGATCAAACAT
* * *
2633990 TTGGATAATTACTCAATTCAGGATCAAA
1 TTGGATAAATACTCAAATCAAGATCAAA
2634018 TATTATCGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (31 bp):
TTGGATAAATACTCAAATCAAGATCAAACAT
Found at i:2634716 original size:42 final size:41
Alignment explanation
Indices: 2634610--2634749 Score: 145
Period size: 42 Copynumber: 3.3 Consensus size: 41
2634600 GCATATTCTG
* *
2634610 ATTTATGATTTTTTGTTATTATTCTTAATTGTTCAAATTTAT
1 ATTTA-GATTTTCTGTTATTGTTCTTAATTGTTCAAATTTAT
* * * *
2634652 AGTTAAAGTTTTTTATTATTGTTCTTAATTGTTCAAATTTAT
1 ATTTAGA-TTTTCTGTTATTGTTCTTAATTGTTCAAATTTAT
* * * *
2634694 ATTTGAGATTTTCTGTTGTTGTTCTTAATTGCTCAAAATAAT
1 ATTT-AGATTTTCTGTTATTGTTCTTAATTGTTCAAATTTAT
*
2634736 ATTTAAGGTTTTCT
1 ATTT-AGATTTTCT
2634750 ACTATTCTTA
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
41 1 0.01
42 79 0.96
43 2 0.02
ACGTcount: A:0.26, C:0.06, G:0.11, T:0.56
Consensus pattern (41 bp):
ATTTAGATTTTCTGTTATTGTTCTTAATTGTTCAAATTTAT
Found at i:2634836 original size:81 final size:82
Alignment explanation
Indices: 2634628--2634836 Score: 210
Period size: 81 Copynumber: 2.5 Consensus size: 82
2634618 TTTTTTGTTA
* * * * *
2634628 TTATTCTTAATTGTTCAAATTTATAGTTAAAGTTTTTTATTATTGTTCTTAATTGTTCAAATTTA
1 TTATTCTTAATTGCTCAAATTTATAGTT-AAGGTTTTT-TTACTATTCTTAATTGCTCAAATTTA
**
2634693 TATTTGAGATTTTCTGTTG
64 TATTTGAGATTTTCTACTG
* * * * * *
2634712 TTGTTCTTAATTGCTCAAAATAATATTTAAGG-TTTTCTACTATTCTTAATTGCCTGAAA-TTAT
1 TTATTCTTAATTGCTCAAATTTATAGTTAAGGTTTTTTTACTATTCTTAATTG-CTCAAATTTAT
2634775 AGTTTG-GATTTTCTACTG
65 A-TTTGAGATTTTCTACTG
* * *
2634793 TTATTCTTAATTACTCGAATTTATAGTT-AGGTTTTTTTGCTATT
1 TTATTCTTAATTGCTCAAATTTATAGTTAAGGTTTTTTTACTATT
2634837 TAGGCATATT
Statistics
Matches: 101, Mismatches: 21, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
80 3 0.03
81 60 0.59
82 12 0.12
83 3 0.03
84 23 0.23
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.54
Consensus pattern (82 bp):
TTATTCTTAATTGCTCAAATTTATAGTTAAGGTTTTTTTACTATTCTTAATTGCTCAAATTTATA
TTTGAGATTTTCTACTG
Found at i:2635343 original size:32 final size:32
Alignment explanation
Indices: 2635273--2635343 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
2635263 ACCCTTGGTT
* ** **
2635273 ATAACAAAGTAAAAGCTTATAACTGAAATTTT
1 ATAACAAAGTAAAAGATTATAACAAAAATTAA
*
2635305 AGAACAAAGTAAAAGATTATAACAAAAATTAA
1 ATAACAAAGTAAAAGATTATAACAAAAATTAA
2635337 ATAACAA
1 ATAACAA
2635344 TGTACGAGAC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.24
Consensus pattern (32 bp):
ATAACAAAGTAAAAGATTATAACAAAAATTAA
Found at i:2635965 original size:42 final size:41
Alignment explanation
Indices: 2635883--2635986 Score: 102
Period size: 42 Copynumber: 2.5 Consensus size: 41
2635873 TAAGATATAG
* *
2635883 TTGAGGTAATTAGGAATGAACGAGGTAGAAATTAACATGTAA
1 TTGAGGTAATAAGGAATGAAC-AGGTAGAAATCAACATGTAA
* *
2635925 TTGATGTAATAAGGAATGAA-AGGATAGAAAATCAATATGTAA
1 TTGAGGTAATAAGGAATGAACAGG-TAG-AAATCAACATGTAA
* * * *
2635967 GTAAGGCAATAGGGAATGAA
1 TTGAGGTAATAAGGAATGAA
2635987 AGATATGAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
40 3 0.06
41 3 0.06
42 45 0.88
ACGTcount: A:0.46, C:0.04, G:0.26, T:0.24
Consensus pattern (41 bp):
TTGAGGTAATAAGGAATGAACAGGTAGAAATCAACATGTAA
Found at i:2639386 original size:72 final size:75
Alignment explanation
Indices: 2639309--2639452 Score: 172
Period size: 72 Copynumber: 2.0 Consensus size: 75
2639299 TAAATAGTAC
* * * *
2639309 CCTACAATCAAACCAAAGAAATATC-AGCAAATAAATTCCAGC-AAAACACCAAA-AAA-AT-AA
1 CCTACAATCAAACCAAA-AAAAATCAAG-AAACAAATACCAACAAAAACACCAAAGAAATATCAA
2639369 TAAATTTACTAG
64 TAAATTTACTAG
* * *
2639381 CCTACAATCACACTAAAAAAAATCAAGAAACGAATACCAACAAAAACACCAAAGAAATATCAATA
1 CCTACAATCAAACCAAAAAAAATCAAGAAACAAATACCAACAAAAACACCAAAGAAATATCAATA
2639446 AATTTAC
66 AATTTAC
2639453 CGAACAATGT
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
71 16 0.27
72 28 0.47
73 3 0.05
74 2 0.03
75 11 0.18
ACGTcount: A:0.57, C:0.22, G:0.05, T:0.17
Consensus pattern (75 bp):
CCTACAATCAAACCAAAAAAAATCAAGAAACAAATACCAACAAAAACACCAAAGAAATATCAATA
AATTTACTAG
Found at i:2639694 original size:26 final size:26
Alignment explanation
Indices: 2639665--2639714 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
2639655 TGCTACTAGT
*
2639665 TGAATTGATATTTGAAGAAAATATCA
1 TGAATTGATATTTAAAGAAAATATCA
2639691 TGAATTGATATTTAAAGAAAATAT
1 TGAATTGATATTTAAAGAAAATAT
2639715 TATGTTCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (26 bp):
TGAATTGATATTTAAAGAAAATATCA
Found at i:2642913 original size:24 final size:24
Alignment explanation
Indices: 2642871--2642923 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2642861 TTTAAATATA
*
2642871 AAAAATAAGAATTTTAAATATTTT
1 AAAAATAAGAATTTTAAATATTTC
*
2642895 AAAAAT-AGGATTTTGAAATATTTC
1 AAAAATAAGAATTTT-AAATATTTC
2642919 AAAAA
1 AAAAA
2642924 AATATGGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.36
Consensus pattern (24 bp):
AAAAATAAGAATTTTAAATATTTC
Found at i:2653772 original size:44 final size:44
Alignment explanation
Indices: 2653709--2653798 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
2653699 CTGGAAACTA
*
2653709 AACCTATAATTTCAAGTAAAAACACATGTCCATAAGATAATGCC
1 AACCTATAATTCCAAGTAAAAACACATGTCCATAAGATAATGCC
* *
2653753 AACCTATAATTCCAAGTAAAAAGACATGTCCATAAGTTAATGCC
1 AACCTATAATTCCAAGTAAAAACACATGTCCATAAGATAATGCC
2653797 AA
1 AA
2653799 ATGTCAGAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (44 bp):
AACCTATAATTCCAAGTAAAAACACATGTCCATAAGATAATGCC
Found at i:2666423 original size:14 final size:14
Alignment explanation
Indices: 2666404--2666432 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2666394 AAACAGAGTT
2666404 ATATCTCACCTTTC
1 ATATCTCACCTTTC
2666418 ATATCTCACCTTTC
1 ATATCTCACCTTTC
2666432 A
1 A
2666433 ACCCATTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.24, C:0.34, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATCTCACCTTTC
Found at i:2668388 original size:24 final size:24
Alignment explanation
Indices: 2668344--2668397 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 24
2668334 TTATTCTAAT
2668344 ATATATTTTTTATTTCTC-TTTGA
1 ATATATTTTTTATTTCTCTTTTGA
2668367 A-ATATTTTTTATTAT-TAACTTTTGA
1 ATATATTTTTTATT-TCT--CTTTTGA
2668392 ATATAT
1 ATATAT
2668398 GTATGATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
22 13 0.50
23 2 0.08
24 1 0.04
25 6 0.23
26 4 0.15
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.61
Consensus pattern (24 bp):
ATATATTTTTTATTTCTCTTTTGA
Found at i:2668633 original size:30 final size:29
Alignment explanation
Indices: 2668572--2668644 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
2668562 TTTTTAATTA
* * * *
2668572 ATTTTTAAATTTTTTATTTATATAATGAT
1 ATTTTTAAATTTTATATTTAAAAAATAAT
2668601 ATTTTTAAATATTTATATTTAAAAAATAAT
1 ATTTTTAAAT-TTTATATTTAAAAAATAAT
*
2668631 ATTTTATTAATTTT
1 ATTTT-TAAATTTT
2668645 GAGTCGAGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 10 0.27
30 23 0.62
31 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (29 bp):
ATTTTTAAATTTTATATTTAAAAAATAAT
Found at i:2669390 original size:6 final size:7
Alignment explanation
Indices: 2669370--2669398 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2669360 TGTATCAATT
2669370 AATAAAA
1 AATAAAA
2669377 AATAAAA
1 AATAAAA
2669384 AATAAAA
1 AATAAAA
2669391 AATAAAA
1 AATAAAA
2669398 A
1 A
2669399 CCCATAAAGA
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:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AATAAAA
Found at i:2674569 original size:19 final size:19
Alignment explanation
Indices: 2674531--2674569 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2674521 CAACCCCACC
*
2674531 TCACAAAAACCAGAAGGCT
1 TCACAAAAACCAGAAAGCT
*
2674550 TCACAAAAACCGGAAAGCT
1 TCACAAAAACCAGAAAGCT
2674569 T
1 T
2674570 TATTGTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.26, G:0.15, T:0.13
Consensus pattern (19 bp):
TCACAAAAACCAGAAAGCT
Found at i:2679976 original size:27 final size:27
Alignment explanation
Indices: 2679923--2679978 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
2679913 AAATTGAAAA
*
2679923 TAATAATAAAAGTGAAATTAATTATTG
1 TAATAATAAAAGTGAAATTAATAATTG
* *
2679950 TAATAATAAAA-TTAAATATTATAATTG
1 TAATAATAAAAGTGAAAT-TAATAATTG
2679977 TA
1 TA
2679979 GATGAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (27 bp):
TAATAATAAAAGTGAAATTAATAATTG
Found at i:2680091 original size:28 final size:27
Alignment explanation
Indices: 2680054--2680138 Score: 72
Period size: 28 Copynumber: 3.1 Consensus size: 27
2680044 ATAAATGATT
2680054 ATTAA-AAATATTAAATTAAATTTGAT-AA
1 ATTAATAAATATTAAATT--ATTT-ATAAA
2680082 A-TAATAAATATTTTAAATTATTTATAAA
1 ATTAATAAATA--TTAAATTATTTATAAA
*
2680110 ATTAATAAATAATTAAA-AATTTA-AAA
1 ATTAATAAAT-ATTAAATTATTTATAAA
2680136 ATT
1 ATT
2680139 TATTTTTATA
Statistics
Matches: 50, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
26 6 0.12
27 10 0.20
28 18 0.36
29 8 0.16
30 8 0.16
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (27 bp):
ATTAATAAATATTAAATTATTTATAAA
Found at i:2686255 original size:16 final size:17
Alignment explanation
Indices: 2686234--2686265 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2686224 ATTTTTAATG
2686234 TTAAAAAAT-TAAAAAC
1 TTAAAAAATATAAAAAC
2686250 TTAAAAAATATAAAAA
1 TTAAAAAATATAAAAA
2686266 TAAAAATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (17 bp):
TTAAAAAATATAAAAAC
Found at i:2693379 original size:17 final size:17
Alignment explanation
Indices: 2693357--2693390 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2693347 TAAAAAAAAT
2693357 TTAATTTTCTTT-TTTCC
1 TTAATTTT-TTTGTTTCC
2693374 TTAATTTTTTTGTTTCC
1 TTAATTTTTTTGTTTCC
2693391 ATTTTTCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.12, C:0.15, G:0.03, T:0.71
Consensus pattern (17 bp):
TTAATTTTTTTGTTTCC
Found at i:2702567 original size:2 final size:2
Alignment explanation
Indices: 2702562--2702598 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2702552 TAAAAAAGTG
*
2702562 TA TA TA -A TA TA TA TA TA TA TA TA TT 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
2702599 GAAAAAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2702720 original size:1 final size:1
Alignment explanation
Indices: 2702714--2702741 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
2702704 GGCACTCTTC
2702714 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
2702742 CAAGTTTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2703044 original size:36 final size:37
Alignment explanation
Indices: 2703004--2703080 Score: 129
Period size: 37 Copynumber: 2.1 Consensus size: 37
2702994 TACGCTCTTC
* *
2703004 TTCTTTTCTTTTC-TTTTCAAGGCCAAATATAGGAGA
1 TTCTTTTCTTTTCTTTTTCAAAGCCAAATATAAGAGA
2703040 TTCTTTTCTTTTCTTTTTCAAAGCCAAATATAAGAGA
1 TTCTTTTCTTTTCTTTTTCAAAGCCAAATATAAGAGA
2703077 TTCT
1 TTCT
2703081 ATAAATGGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 13 0.34
37 25 0.66
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.47
Consensus pattern (37 bp):
TTCTTTTCTTTTCTTTTTCAAAGCCAAATATAAGAGA
Found at i:2704394 original size:24 final size:23
Alignment explanation
Indices: 2704348--2704415 Score: 57
Period size: 24 Copynumber: 2.8 Consensus size: 23
2704338 TATAAAAAAT
* * *
2704348 TATTTTTTAATTAATTATTTAAT-
1 TATTTTATAA-TATTTATATAATA
2704371 TATTTATATATATATTTATATAATGA
1 TATTT-TATA-ATATTTATATAAT-A
*
2704397 TATTTTTTAATATTTATAT
1 TATTTTATAATATTTATAT
2704416 TTAAAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 5 0.14
24 23 0.62
25 4 0.11
26 5 0.14
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (23 bp):
TATTTTATAATATTTATATAATA
Found at i:2704415 original size:30 final size:31
Alignment explanation
Indices: 2704370--2704438 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 31
2704360 AATTATTTAA
* * * *
2704370 TTATTTATATATATATTTATATAATGATATT
1 TTATTAATATATATATTTAAAAAATAATATT
*
2704401 TT-TTAATATTTATATTTAAAAAATAATATT
1 TTATTAATATATATATTTAAAAAATAATATT
2704431 TTATTAAT
1 TTATTAAT
2704439 TTCGGGTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 25 0.78
31 7 0.22
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (31 bp):
TTATTAATATATATATTTAAAAAATAATATT
Found at i:2707905 original size:30 final size:31
Alignment explanation
Indices: 2707869--2707942 Score: 78
Period size: 37 Copynumber: 2.2 Consensus size: 31
2707859 AAATACTTGT
*
2707869 AATCTAAT-ATCAATGATCTATCAAAGAAAA
1 AATCTAATGATCAATGATCTAGCAAAGAAAA
2707899 AATCTAAGGTATGGAATCAATGATCTAGCAAAGAAAA
1 AATCT-A---AT-G-ATCAATGATCTAGCAAAGAAAA
2707936 AATCTAA
1 AATCTAA
2707943 GATATGGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
30 5 0.14
31 1 0.03
33 1 0.03
34 2 0.06
36 1 0.03
37 26 0.72
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.24
Consensus pattern (31 bp):
AATCTAATGATCAATGATCTAGCAAAGAAAA
Found at i:2707931 original size:37 final size:37
Alignment explanation
Indices: 2707877--2707952 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
2707867 GTAATCTAAT
* *
2707877 ATCAATGATCTATCAAAGAAAAAATCTAAGGTATGGA
1 ATCAATGATCTAGCAAAGAAAAAATCTAAGATATGGA
2707914 ATCAATGATCTAGCAAAGAAAAAATCTAAGATATGGA
1 ATCAATGATCTAGCAAAGAAAAAATCTAAGATATGGA
2707951 AT
1 AT
2707953 TTCCTTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.50, C:0.11, G:0.16, T:0.24
Consensus pattern (37 bp):
ATCAATGATCTAGCAAAGAAAAAATCTAAGATATGGA
Found at i:2708056 original size:2 final size:2
Alignment explanation
Indices: 2708049--2708078 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2708039 AAGACTTAGA
2708049 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
2708079 TGGTTCTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2712366 original size:12 final size:12
Alignment explanation
Indices: 2712349--2712373 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2712339 AAATATTGTT
2712349 TTTAATTTTTAA
1 TTTAATTTTTAA
2712361 TTTAATTTTTAA
1 TTTAATTTTTAA
2712373 T
1 T
2712374 ATTTTTAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTAATTTTTAA
Found at i:2712884 original size:2 final size:2
Alignment explanation
Indices: 2712877--2712906 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2712867 AGTGCTATGA
2712877 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
2712907 TGTTCTAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2713872 original size:23 final size:22
Alignment explanation
Indices: 2713834--2713876 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
2713824 ATTTTAAATT
2713834 TTTTAATATAAATTTTATTATA
1 TTTTAATATAAATTTTATTATA
2713856 TTTTAAT-TAAAGTTTTTATTA
1 TTTTAATATAAA--TTTTATTA
2713877 ATTCAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 7 0.37
23 8 0.42
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTAATATAAATTTTATTATA
Found at i:2725837 original size:10 final size:10
Alignment explanation
Indices: 2725822--2725852 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2725812 CGCATACTGT
2725822 TGCACAATTA
1 TGCACAATTA
*
2725832 TGCACAATTG
1 TGCACAATTA
2725842 TGCACAATTA
1 TGCACAATTA
2725852 T
1 T
2725853 ACGCCTGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (10 bp):
TGCACAATTA
Found at i:2734567 original size:31 final size:32
Alignment explanation
Indices: 2734529--2734588 Score: 113
Period size: 31 Copynumber: 1.9 Consensus size: 32
2734519 TAATTTCATA
2734529 AAATTTCAAAAGATCCTAACTA-GAAAATATG
1 AAATTTCAAAAGATCCTAACTAGGAAAATATG
2734560 AAATTTCAAAAGATCCTAACTAGGAAAAT
1 AAATTTCAAAAGATCCTAACTAGGAAAAT
2734589 TTTCTAGGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 22 0.79
32 6 0.21
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.25
Consensus pattern (32 bp):
AAATTTCAAAAGATCCTAACTAGGAAAATATG
Found at i:2754377 original size:18 final size:17
Alignment explanation
Indices: 2754351--2754414 Score: 53
Period size: 18 Copynumber: 3.8 Consensus size: 17
2754341 TGTAAAATAT
*
2754351 TAAACATTATATTTTATA
1 TAAAAATTATA-TTTATA
2754369 TAAAAATTA-A-TTAT-
1 TAAAAATTATATTTATA
* * *
2754383 TATAATTTATATTAATA
1 TAAAAATTATATTTATA
2754400 TAAAAATATATATTT
1 TAAAAAT-TATATTT
2754415 TAATAAACTT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
14 7 0.20
15 5 0.14
16 3 0.09
17 6 0.17
18 14 0.40
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAAAATTATATTTATA
Found at i:2754377 original size:25 final size:25
Alignment explanation
Indices: 2754343--2754421 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
2754333 GTTATTCGTG
*
2754343 TAAAATATTAAACATTATATTTTATA
1 TAAAA-ATTAAAAATTATATTTTATA
** *
2754369 TAAAAATTAATTATTATAATTTATA
1 TAAAAATTAAAAATTATATTTTATA
* *
2754394 TTAATA-TAAAAATATATATTTTA-A
1 TAAAAATTAAAAAT-TATATTTTATA
2754418 TAAA
1 TAAA
2754422 CTTATATATA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
24 9 0.21
25 29 0.67
26 5 0.12
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (25 bp):
TAAAAATTAAAAATTATATTTTATA
Found at i:2756916 original size:13 final size:14
Alignment explanation
Indices: 2756898--2756937 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
2756888 AAAATGATTA
2756898 AAAAAATTAAAA-T
1 AAAAAATTAAAATT
2756911 AAAAAATTAAAATT
1 AAAAAATTAAAATT
*
2756925 AATAAATTGAAAA
1 AAAAAATT-AAAA
2756938 ATCTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
14 8 0.33
15 4 0.17
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (14 bp):
AAAAAATTAAAATT
Found at i:2759344 original size:16 final size:16
Alignment explanation
Indices: 2759323--2759356 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2759313 ATAAATTGTA
2759323 ATTCTTGTCATTAGCC
1 ATTCTTGTCATTAGCC
* *
2759339 ATTCTTGTTATTGGCC
1 ATTCTTGTCATTAGCC
2759355 AT
1 AT
2759357 AAGTTATAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.47
Consensus pattern (16 bp):
ATTCTTGTCATTAGCC
Found at i:2764897 original size:13 final size:13
Alignment explanation
Indices: 2764879--2764920 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2764869 AATATTTTTA
2764879 TTAAATTAATATT
1 TTAAATTAATATT
* *
2764892 TTAAATTAAAATA
1 TTAAATTAATATT
2764905 TTAAA-TAATAATT
1 TTAAATTAAT-ATT
2764918 TTA
1 TTA
2764921 TTAATATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 3 0.12
13 21 0.88
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAAATTAATATT
Found at i:2764899 original size:18 final size:18
Alignment explanation
Indices: 2764862--2764901 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
2764852 TAATTATGTA
*
2764862 TAAATATAATATTTTTAT
1 TAAATATAATATTTTAAT
2764880 TAAAT-TAATATTTTAAAT
1 TAAATATAATATTTT-AAT
2764898 TAAA
1 TAAA
2764902 ATATTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAAATATAATATTTTAAT
Found at i:2773530 original size:24 final size:24
Alignment explanation
Indices: 2773498--2773554 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
2773488 AAATTGACTT
2773498 CTGCAGCTGTTGCAATA-GCAGCAG
1 CTGCAGCTGTTGCAA-AGGCAGCAG
* *
2773522 CTGCTGCTGTTGCAAAGGCTGCAG
1 CTGCAGCTGTTGCAAAGGCAGCAG
*
2773546 CTGCGGCTG
1 CTGCAGCTG
2773555 CTAATGTTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 1 0.03
24 28 0.97
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.23
Consensus pattern (24 bp):
CTGCAGCTGTTGCAAAGGCAGCAG
Found at i:2781360 original size:2 final size:2
Alignment explanation
Indices: 2781353--2781382 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2781343 ACAAAACCAG
2781353 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2781383 AGAAATTGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2786928 original size:14 final size:14
Alignment explanation
Indices: 2786911--2786944 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2786901 ACCTTTTGGG
*
2786911 TTTTTTTTTTTTTC
1 TTTTTGTTTTTTTC
2786925 TTTTTGTTTTTTTC
1 TTTTTGTTTTTTTC
*
2786939 TGTTTG
1 TTTTTG
2786945 GAAGGAGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.85
Consensus pattern (14 bp):
TTTTTGTTTTTTTC
Found at i:2791334 original size:25 final size:24
Alignment explanation
Indices: 2791306--2791358 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
2791296 AATATTATTT
2791306 TTAATATAAATATAAAATTAAATA-A
1 TTAAT-TAAA-ATAAAATTAAATATA
* *
2791331 TTAATTAAAATATAATTATATATA
1 TTAATTAAAATAAAATTAAATATA
2791355 TTAA
1 TTAA
2791359 ATCAAATCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 11 0.44
24 9 0.36
25 5 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TTAATTAAAATAAAATTAAATATA
Found at i:2792749 original size:12 final size:12
Alignment explanation
Indices: 2792732--2792757 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2792722 CCGTACTGAC
2792732 TCATCTTCTTCA
1 TCATCTTCTTCA
2792744 TCATCTTCTTCA
1 TCATCTTCTTCA
2792756 TC
1 TC
2792758 TGGTGAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.35, G:0.00, T:0.50
Consensus pattern (12 bp):
TCATCTTCTTCA
Found at i:2792797 original size:24 final size:23
Alignment explanation
Indices: 2792766--2792812 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2792756 TCTGGTGAAG
2792766 AGCAAGAACTAGGAGAAGAGAAA
1 AGCAAGAACTAGGAGAAGAGAAA
* **
2792789 AGCAGAGAAGTAGTTGAAGAGAAA
1 AGCA-AGAACTAGGAGAAGAGAAA
2792813 TCTTTGGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.53, C:0.06, G:0.32, T:0.09
Consensus pattern (23 bp):
AGCAAGAACTAGGAGAAGAGAAA
Found at i:2795140 original size:24 final size:24
Alignment explanation
Indices: 2795112--2795161 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
2795102 GTATGTAACT
* * *
2795112 TTCGTATCTTATTTTTGTATTATA
1 TTCGTATCATATTATTATATTATA
*
2795136 TTCGTATCATGTTATTATATTATA
1 TTCGTATCATATTATTATATTATA
2795160 TT
1 TT
2795162 TTAGATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (24 bp):
TTCGTATCATATTATTATATTATA
Found at i:2796495 original size:8 final size:8
Alignment explanation
Indices: 2796482--2796521 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
2796472 TTTTTATTTA
2796482 TATATATT
1 TATATATT
*
2796490 TATATAAT
1 TATATATT
2796498 TATATATT
1 TATATATT
*
2796506 TAAATATT
1 TATATATT
2796514 T-TATATT
1 TATATATT
2796521 T
1 T
2796522 TTAAAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TATATATT
Found at i:2796496 original size:26 final size:25
Alignment explanation
Indices: 2796467--2796519 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
2796457 TTATATAAAA
* * *
2796467 ATAATTTTTTATTTATATATATTTAT
1 ATAATTATATATTTAAATAT-TTTAT
2796493 ATAATTATATATTTAAATATTTTAT
1 ATAATTATATATTTAAATATTTTAT
2796518 AT
1 AT
2796520 TTTTAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
ATAATTATATATTTAAATATTTTAT
Found at i:2796534 original size:23 final size:22
Alignment explanation
Indices: 2796508--2796563 Score: 87
Period size: 21 Copynumber: 2.5 Consensus size: 22
2796498 TATATATTTA
*
2796508 AATATTTTATATTTTTAAAAAAT
1 AATATTTTAT-TATTTAAAAAAT
2796531 AATATTTT-TTATTTAAAAAAT
1 AATATTTTATTATTTAAAAAAT
2796552 AATATTTTATTA
1 AATATTTTATTA
2796564 ATTTTAGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
21 19 0.61
22 4 0.13
23 8 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATATTTTATTATTTAAAAAAT
Found at i:2797036 original size:32 final size:33
Alignment explanation
Indices: 2797007--2797074 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
2796997 TGTTATAAGT
* *
2797007 AATAAAATAAATACATCTTGTC-TATTATAAAA
1 AATAAAATAAATACACCTTATCATATTATAAAA
* *
2797039 AATAAAGTAAATAGACCTTATCATATTATAATAA
1 AATAAAATAAATACACCTTATCATATTATAA-AA
2797073 AA
1 AA
2797075 ATATTTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 18 0.60
33 8 0.27
34 4 0.13
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.32
Consensus pattern (33 bp):
AATAAAATAAATACACCTTATCATATTATAAAA
Found at i:2799155 original size:15 final size:15
Alignment explanation
Indices: 2799126--2799154 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2799116 GAATTTACAA
2799126 ATTTATTGAATTTTT
1 ATTTATTGAATTTTT
2799141 ATTTA-TGAATTTTT
1 ATTTATTGAATTTTT
2799155 TTGAATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (15 bp):
ATTTATTGAATTTTT
Found at i:2800502 original size:13 final size:12
Alignment explanation
Indices: 2800475--2800543 Score: 70
Period size: 13 Copynumber: 5.8 Consensus size: 12
2800465 TTTAAATTTG
*
2800475 ATAATTTAAAAT
1 ATAATATAAAAT
2800487 ATAATATAATAAT
1 ATAATATAA-AAT
*
2800500 ATATTAT-AAAT
1 ATAATATAAAAT
2800511 ATAATATTAAAAT
1 ATAATA-TAAAAT
*
2800524 AAAATATAAAA-
1 ATAATATAAAAT
*
2800535 ATGATATAA
1 ATAATATAA
2800544 TTTAAAATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
11 15 0.31
12 15 0.31
13 18 0.38
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (12 bp):
ATAATATAAAAT
Found at i:2800514 original size:24 final size:24
Alignment explanation
Indices: 2800483--2800544 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
2800473 TGATAATTTA
* *
2800483 AAATATAATATAATAATATATTAT
1 AAATATAATATAATAATAAAATAT
2800507 AAATATAATATTAA-AATAAAATAT
1 AAATATAATA-TAATAATAAAATAT
* *
2800531 AAAAATGATATAAT
1 AAATATAATATAAT
2800545 TTAAAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 3 0.09
24 26 0.81
25 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATATAATATAATAATAAAATAT
Found at i:2800590 original size:23 final size:22
Alignment explanation
Indices: 2800543--2800591 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
2800533 AAATGATATA
* *
2800543 ATTTAAAATTTTAATAATAATT
1 ATTTAAAATTTTAATAAAAAAT
2800565 ATTTAAAGA-TTTAATAAAAAAAT
1 ATTTAAA-ATTTTAAT-AAAAAAT
2800588 ATTT
1 ATTT
2800592 TATATTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTTAAAATTTTAATAAAAAAT
Found at i:2800653 original size:20 final size:20
Alignment explanation
Indices: 2800630--2800686 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
2800620 TATATATTTT
2800630 TTATATAAAATATAATATAA
1 TTATATAAAATATAATATAA
* * *
2800650 TTATATAAATTTTAATAT-T
1 TTATATAAAATATAATATAA
*
2800669 TTATATAATATA-AATATA
1 TTATATAAAATATAATATA
2800687 CTTTTTCAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 5 0.17
19 9 0.30
20 16 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATATAAAATATAATATAA
Found at i:2823330 original size:27 final size:29
Alignment explanation
Indices: 2823299--2823372 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 29
2823289 AAATACATTG
* *
2823299 AATAAAAATGAATAAA-A-TAATTTTTTT
1 AATAAAAATGAATAAACACGAATATTTTT
*
2823326 AATAAAAAAGAACTAAACACGAATATTTTT
1 AATAAAAATGAA-TAAACACGAATATTTTT
*
2823356 AAAAATAAATGAATAAA
1 AATAA-AAATGAATAAA
2823373 TTATAAATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
27 11 0.29
28 4 0.11
29 1 0.03
30 16 0.42
31 6 0.16
ACGTcount: A:0.61, C:0.04, G:0.05, T:0.30
Consensus pattern (29 bp):
AATAAAAATGAATAAACACGAATATTTTT
Found at i:2827695 original size:15 final size:15
Alignment explanation
Indices: 2827675--2827704 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2827665 GTTTCTGCCG
2827675 CCACTAGATGAGAAA
1 CCACTAGATGAGAAA
2827690 CCACTAGATGAGAAA
1 CCACTAGATGAGAAA
2827705 GTCATGATTT
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:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (15 bp):
CCACTAGATGAGAAA
Found at i:2827965 original size:15 final size:15
Alignment explanation
Indices: 2827947--2827991 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
2827937 AAATATAAAA
2827947 ATAATTATTATATTT
1 ATAATTATTATATTT
2827962 ATAATTAATTA-ATTT
1 ATAATT-ATTATATTT
2827977 -TAATT-TTAATATTT
1 ATAATTATT-ATATTT
2827991 A
1 A
2827992 ATATGATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
12 2 0.08
13 1 0.04
14 9 0.35
15 10 0.38
16 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATAATTATTATATTT
Found at i:2828282 original size:10 final size:10
Alignment explanation
Indices: 2828267--2828296 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2828257 AGCAATAATA
2828267 ATTTTAATTT
1 ATTTTAATTT
2828277 ATTTTAATTT
1 ATTTTAATTT
*
2828287 AATTTAATTT
1 ATTTTAATTT
2828297 TTTAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
ATTTTAATTT
Found at i:2828338 original size:28 final size:30
Alignment explanation
Indices: 2828307--2828370 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 30
2828297 TTTAAATAAT
2828307 ATATAAAATTATA-AATTTTTACA-ATTCA
1 ATATAAAATTATATAATTTTTACATATTCA
* *
2828335 ATATAAATTTATATTGAATTTTTATATATTCA
1 ATATAAAATTATA-T-AATTTTTACATATTCA
2828367 ATAT
1 ATAT
2828371 GATTCTAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 12 0.40
31 9 0.30
32 9 0.30
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (30 bp):
ATATAAAATTATATAATTTTTACATATTCA
Found at i:2831449 original size:2 final size:2
Alignment explanation
Indices: 2831442--2831471 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2831432 CCCAAGGAAC
2831442 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
2831472 CGAAAACAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2842756 original size:26 final size:26
Alignment explanation
Indices: 2842716--2842807 Score: 86
Period size: 26 Copynumber: 3.7 Consensus size: 26
2842706 AATTAGTTAA
*
2842716 ATTTAAATATCAATTTTAATGATATTC
1 ATTTAAATATAAATTTTAAT-ATATTC
*
2842743 ATTT-AATATAAATTTTAAT-TA--A
1 ATTTAAATATAAATTTTAATATATTC
* *
2842765 ATTTAAATATTAATTTTAATAAGATTC
1 ATTTAAATATAAATTTTAAT-ATATTC
*
2842792 ATTT-AATATAATTTTT
1 ATTTAAATATAAATTTT
2842808 TGATCAAATT
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
22 4 0.08
23 14 0.26
24 2 0.04
25 1 0.02
26 24 0.45
27 8 0.15
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.51
Consensus pattern (26 bp):
ATTTAAATATAAATTTTAATATATTC
Found at i:2842777 original size:17 final size:17
Alignment explanation
Indices: 2842737--2842779 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2842727 AATTTTAATG
* *
2842737 ATATTCATTTAATATAA
1 ATATTAATTAAATATAA
* *
2842754 ATTTTAATTAAATTTAA
1 ATATTAATTAAATATAA
2842771 ATATTAATT
1 ATATTAATT
2842780 TTAATAAGAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTAATTAAATATAA
Found at i:2842780 original size:49 final size:49
Alignment explanation
Indices: 2842712--2842807 Score: 156
Period size: 49 Copynumber: 2.0 Consensus size: 49
2842702 GTAAAATTAG
* *
2842712 TTAAATTTAAATATCAATTTTAATGATATTCATTTAATATAAATTTTAA
1 TTAAATTTAAATATCAATTTTAATAAGATTCATTTAATATAAATTTTAA
* *
2842761 TTAAATTTAAATATTAATTTTAATAAGATTCATTTAATATAATTTTT
1 TTAAATTTAAATATCAATTTTAATAAGATTCATTTAATATAAATTTT
2842808 TGATCAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (49 bp):
TTAAATTTAAATATCAATTTTAATAAGATTCATTTAATATAAATTTTAA
Found at i:2843127 original size:6 final size:6
Alignment explanation
Indices: 2843116--2843155 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
2843106 TGCTTTCAGA
* *
2843116 ATATAT ATATAT ATATTT ATATTT ATATTT ATATTT ATAT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATAT
2843156 GAAGATGCCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (6 bp):
ATATTT
Found at i:2850029 original size:23 final size:25
Alignment explanation
Indices: 2849988--2850038 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
2849978 TCCATCTCAA
2849988 TTTTTTAGATATATTAAAT-TATAT
1 TTTTTTAGATATATTAAATCTATAT
*
2850012 TTTTTTA-ATAT-TTAAAATCTTTAT
1 TTTTTTAGATATATT-AAATCTATAT
2850036 TTT
1 TTT
2850039 ATATAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 2 0.08
23 8 0.33
24 14 0.58
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (25 bp):
TTTTTTAGATATATTAAATCTATAT
Found at i:2850687 original size:13 final size:13
Alignment explanation
Indices: 2850644--2850692 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
2850634 TAATTTATGT
2850644 ATTTATATT-ATA
1 ATTTATATTAATA
*
2850656 TTTTATA-TAA-A
1 ATTTATATTAATA
*
2850667 AATTATATTAATA
1 ATTTATATTAATA
*
2850680 ATTTATATAAATA
1 ATTTATATTAATA
2850693 TAAAAATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
11 7 0.24
12 10 0.34
13 12 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATTTATATTAATA
Found at i:2850688 original size:24 final size:23
Alignment explanation
Indices: 2850646--2850690 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
2850636 ATTTATGTAT
*
2850646 TTATATTATATTTTATATAAAAA
1 TTATATTATAATTTATATAAAAA
2850669 TTATATTAATAATTTATATAAA
1 TTATATT-ATAATTTATATAAA
2850691 TATAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTATATTATAATTTATATAAAAA
Found at i:2850776 original size:24 final size:24
Alignment explanation
Indices: 2850730--2850795 Score: 87
Period size: 24 Copynumber: 2.7 Consensus size: 24
2850720 CATTGAATTT
2850730 AATTATATTTATTTATTAAAATTTTA
1 AATTATA-TTATTT-TTAAAATTTTA
* *
2850756 AATTATATTATTTTTATAATTTTT
1 AATTATATTATTTTTAAAATTTTA
*
2850780 ATTTATATTATTTTTA
1 AATTATATTATTTTTA
2850796 CATCTAATCG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 24 0.65
25 6 0.16
26 7 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
AATTATATTATTTTTAAAATTTTA
Found at i:2851531 original size:14 final size:14
Alignment explanation
Indices: 2851521--2851559 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
2851511 ATTATTTTGA
2851521 TTTAATAATTTTAT
1 TTTAATAATTTTAT
*
2851535 TTTAATAA-TTAAT
1 TTTAATAATTTTAT
2851548 TTTAATAATTTT
1 TTTAATAATTTT
2851560 TTGTCATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTAATAATTTTAT
Found at i:2851812 original size:16 final size:16
Alignment explanation
Indices: 2851776--2851819 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
2851766 ACAAAAAAAT
* *
2851776 ATTTTAAATATTTTAT
1 ATTTTAAAAATTTTAA
*
2851792 TTTTTAAAAATTTTAA
1 ATTTTAAAAATTTTAA
2851808 ATTTTAAAAATT
1 ATTTTAAAAATT
2851820 ATCACAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTTAAAAATTTTAA
Found at i:2852132 original size:16 final size:17
Alignment explanation
Indices: 2852104--2852148 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
2852094 TTGATCTAAA
2852104 TTTAATA-AAATATT-T
1 TTTAATATAAATATTAT
2852119 TTTAATATAAATATTAT
1 TTTAATATAAATATTAT
2852136 TTTAA-ATAAATAT
1 TTTAATATAAATAT
2852149 ATAAATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.25
16 15 0.54
17 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTAATATAAATATTAT
Found at i:2852143 original size:18 final size:17
Alignment explanation
Indices: 2852107--2852160 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
2852097 ATCTAAATTT
2852107 AATAAAATATT-TTTT-
1 AATAAAATATTATTTTA
2852122 AATATAAATATTATTTTA
1 AATA-AAATATTATTTTA
* *
2852140 AATAAATATATAAATTTA
1 AATAAA-ATATTATTTTA
2852158 AAT
1 AAT
2852161 TTAAATAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
15 4 0.12
16 7 0.21
17 6 0.18
18 16 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATAAAATATTATTTTA
Found at i:2852152 original size:24 final size:24
Alignment explanation
Indices: 2852123--2852199 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
2852113 ATATTTTTTA
2852123 ATATAAATATTATTTTAAATAAAT
1 ATATAAATATTATTTTAAATAAAT
* *
2852147 ATATAAAT-TTAAATTTAAATAATT
1 ATATAAATATT-ATTTTAAATAAAT
* *
2852171 AATTACAAATATT-TTTT-TATAAAT
1 -A-TATAAATATTATTTTAAATAAAT
2852195 ATATA
1 ATATA
2852200 TTAGGTTGGG
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
22 3 0.07
23 3 0.07
24 24 0.57
25 4 0.10
26 6 0.14
27 2 0.05
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (24 bp):
ATATAAATATTATTTTAAATAAAT
Found at i:2856363 original size:14 final size:14
Alignment explanation
Indices: 2856334--2856376 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2856324 AAATTATATC
*
2856334 AATATTTTTACTAAA
1 AATATTTAT-CTAAA
2856349 AATATTTATCTAAA
1 AATATTTATCTAAA
*
2856363 AATATATATC-AAA
1 AATATTTATCTAAA
2856376 A
1 A
2856377 TTTACTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 4 0.15
14 14 0.54
15 8 0.31
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATTTATCTAAA
Found at i:2856381 original size:37 final size:37
Alignment explanation
Indices: 2856321--2856391 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
2856311 TATCTAATAA
*
2856321 TAAAAATTATATCAATATTTTTACTAAAAATATTTATC
1 TAAAAATTATATCAATATATTTACTAAAAA-ATTTATC
2856359 TAAAAATATATATCAA-A-ATTTACTAAAAAATTT
1 TAAAAAT-TATATCAATATATTTACTAAAAAATTT
2856392 TAAAATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 4 0.13
37 11 0.35
38 8 0.26
39 8 0.26
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (37 bp):
TAAAAATTATATCAATATATTTACTAAAAAATTTATC
Found at i:2857255 original size:14 final size:15
Alignment explanation
Indices: 2857236--2857269 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
2857226 AAATTTATTA
2857236 ATTTTTAAT-ATAAT
1 ATTTTTAATGATAAT
2857250 ATTTTTAATGATAAT
1 ATTTTTAATGATAAT
2857265 -TTTTT
1 ATTTTT
2857270 TTTCATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
ATTTTTAATGATAAT
Found at i:2858296 original size:18 final size:18
Alignment explanation
Indices: 2858275--2858309 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2858265 AATATATAAA
2858275 AAATATTATTT-ATAATTT
1 AAAT-TTATTTGATAATTT
2858293 AAATTTATTTGATAATT
1 AAATTTATTTGATAATT
2858310 ATTTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
AAATTTATTTGATAATTT
Found at i:2867009 original size:15 final size:16
Alignment explanation
Indices: 2866969--2867009 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
2866959 ATTTCAGCTC
*
2866969 TAAATTATTTCTATAA
1 TAAATTTTTTCTATAA
2866985 TAAATTTTTTC-ATAA
1 TAAATTTTTTCTATAA
2867000 -AAATTCTTTT
1 TAAATT-TTTT
2867010 ATCAATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 5 0.22
15 8 0.35
16 10 0.43
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (16 bp):
TAAATTTTTTCTATAA
Found at i:2876886 original size:27 final size:27
Alignment explanation
Indices: 2876847--2876900 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
2876837 TGAAAACGTG
* *
2876847 TTTGATAATTAAAAATAAAAATAAGTT
1 TTTGAAAAATAAAAATAAAAATAAGTT
*
2876874 TTTGAAAAATAAAAATAAAAATGAGTT
1 TTTGAAAAATAAAAATAAAAATAAGTT
2876901 GAAATATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.33
Consensus pattern (27 bp):
TTTGAAAAATAAAAATAAAAATAAGTT
Found at i:2876909 original size:24 final size:25
Alignment explanation
Indices: 2876846--2876918 Score: 78
Period size: 27 Copynumber: 2.9 Consensus size: 25
2876836 GTGAAAACGT
2876846 GTTTGATAAT-TAAAAATAAAAATAA
1 GTTTGA-AATATAAAAATAAAAATAA
* *
2876871 GTTTTTGAAAAATAAAAATAAAAATGA
1 G--TTTGAAATATAAAAATAAAAATAA
*
2876898 G-TTGAAATATAAAAACAAAAA
1 GTTTGAAATATAAAAATAAAAA
2876919 AAATATTTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
24 18 0.44
25 1 0.02
26 2 0.05
27 20 0.49
ACGTcount: A:0.62, C:0.01, G:0.10, T:0.27
Consensus pattern (25 bp):
GTTTGAAATATAAAAATAAAAATAA
Found at i:2887968 original size:2 final size:2
Alignment explanation
Indices: 2887961--2887997 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2887951 TTGATAATTT
**
2887961 TA TA TA TA TA TA CG 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 TA T
2887998 TAATCTTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2894978 original size:22 final size:22
Alignment explanation
Indices: 2894947--2894989 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
2894937 ACTTTAAGCT
2894947 CAAATTTAA-TTCAATCGGGGC
1 CAAATTTAATTTCAATCGGGGC
2894968 CAAAGTTTAATTTTCAATCGGG
1 CAAA-TTTAA-TTTCAATCGGG
2894990 CCTGAAGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 5 0.26
24 10 0.53
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (22 bp):
CAAATTTAATTTCAATCGGGGC
Found at i:2896180 original size:18 final size:18
Alignment explanation
Indices: 2896159--2896200 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2896149 TGTTAATTTT
*
2896159 AAAATAAACTTTAAAATA
1 AAAATAAACCTTAAAATA
*
2896177 AAAATAAACCTTATAATA
1 AAAATAAACCTTAAAATA
*
2896195 ATAATA
1 AAAATA
2896201 TAAATTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATAAACCTTAAAATA
Found at i:2908596 original size:49 final size:50
Alignment explanation
Indices: 2908468--2908889 Score: 315
Period size: 49 Copynumber: 8.7 Consensus size: 50
2908458 GACATCTCGA
* * * * *
2908468 TTTT-AAGATAAAAATTTTAAAGTTGTCGAG-TCTCTATTGAAATGAGCCT
1 TTTTCAAGATAAGACTTTTAAAGTTGTTGAGCTCTCTACTGAGATGAG-CT
* *
2908517 TTTTCAATATAAGACTTTTAAAGTTGTTGAGCTC-CTGCTGAGATGAGTCT
1 TTTTCAAGATAAGACTTTTAAAGTTGTTGAGCTCTCTACTGAGATGAG-CT
* * * * *
2908567 TTTTTAATATGAGA-TTTTAAAGTTGTTGAG-TCTCTACTTAGATGAGCC
1 TTTTCAAGATAAGACTTTTAAAGTTGTTGAGCTCTCTACTGAGATGAGCT
* * * * *
2908615 TTTTC-AGATGAGATTTTTAAAGTTGTTGAGC-CTCTATTAAGAGGAGACT
1 TTTTCAAGATAAGACTTTTAAAGTTGTTGAGCTCTCTACTGAGATGAG-CT
* * * * *
2908664 TTTTCAAGATAAGACTTTTAAAGTTATTAAGC-ATCTGCTTAGA-GAAGCT
1 TTTTCAAGATAAGACTTTTAAAGTTGTTGAGCTCTCTACTGAGATG-AGCT
*
2908713 TTTTCAAGATAAAACTTTTAAAGTTGTTGAGC-CTCTACTGAGA-GAAGCCT
1 TTTTCAAGATAAGACTTTTAAAGTTGTTGAGCTCTCTACTGAGATG-AG-CT
* *
2908763 TTTTCAAGATGAGA-TTTTAAAGTTGTTGAGC-CTCTACTTAGA-GAAGC-
1 TTTTCAAGATAAGACTTTTAAAGTTGTTGAGCTCTCTACTGAGATG-AGCT
* * * * * * * *
2908810 ATTTC-ATATGAGATTTTTAAATTTGTTGAG-TTTCTAATGAGAAGAGCCT
1 TTTTCAAGATAAGACTTTTAAAGTTGTTGAGCTCTCTACTGAGATGAG-CT
* * *
2908859 TTTTCAA-ATGAGA-TTTTAATGTTATTGAGCT
1 TTTTCAAGATAAGACTTTTAAAGTTGTTGAGCT
2908890 TTTACTTAGA
Statistics
Matches: 311, Mismatches: 46, Indels: 32
0.80 0.12 0.08
Matches are distributed among these distances:
46 7 0.02
47 36 0.12
48 51 0.16
49 123 0.40
50 92 0.30
51 2 0.01
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (50 bp):
TTTTCAAGATAAGACTTTTAAAGTTGTTGAGCTCTCTACTGAGATGAGCT
Found at i:2908749 original size:147 final size:148
Alignment explanation
Indices: 2908481--2908798 Score: 407
Period size: 147 Copynumber: 2.2 Consensus size: 148
2908471 TAAGATAAAA
* * * * * * *
2908481 ATTTTAAAGTTGTCGAGTCTCTATTGAAATGAGCCTTTTTCAATATAAGACTTTTAAAGTTGTTG
1 ATTTTAAAGTTGTTGAGCCTCTATTGAAAGGAGACTTTTTCAAGATAAGACTTTTAAAGTTATTA
* * * * * *
2908546 AGCTCCTGCTGAGATGAGTCTTTTTTAATATGAGATTTTAAAGTTGTTGAGTCTCTACTTAGATG
66 AGCTCCTGCTGAGATGAGTCTTTTTCAAGATAAAATTTTAAAGTTGTTGAGCCTCTACTGAGA-G
2908611 -AGCC-TTTTC-AGATGAG
130 AAGCCTTTTTCAAGATGAG
2908627 ATTTTTAAAGTTGTTGAGCCTCTATT-AAGAGGAGACTTTTTCAAGATAAGACTTTTAAAGTTAT
1 A-TTTTAAAGTTGTTGAGCCTCTATTGAA-AGGAGACTTTTTCAAGATAAGACTTTTAAAGTTAT
*
2908691 TAAGCAT-CTGCTTAGA-GAAG-CTTTTTCAAGATAAAACTTTTAAAGTTGTTGAGCCTCTACTG
64 TAAGC-TCCTGCTGAGATG-AGTCTTTTTCAAGATAAAA-TTTTAAAGTTGTTGAGCCTCTACTG
2908753 AGAGAAGCCTTTTTCAAGATGAG
126 AGAGAAGCCTTTTTCAAGATGAG
2908776 ATTTTAAAGTTGTTGAGCCTCTA
1 ATTTTAAAGTTGTTGAGCCTCTA
2908799 CTTAGAGAAG
Statistics
Matches: 150, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
146 17 0.11
147 97 0.65
148 28 0.19
149 8 0.05
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (148 bp):
ATTTTAAAGTTGTTGAGCCTCTATTGAAAGGAGACTTTTTCAAGATAAGACTTTTAAAGTTATTA
AGCTCCTGCTGAGATGAGTCTTTTTCAAGATAAAATTTTAAAGTTGTTGAGCCTCTACTGAGAGA
AGCCTTTTTCAAGATGAG
Found at i:2908953 original size:96 final size:96
Alignment explanation
Indices: 2908532--2908953 Score: 422
Period size: 96 Copynumber: 4.4 Consensus size: 96
2908522 AATATAAGAC
* * * * * *
2908532 TTTTAAAGTTGTTGAG-CTCCTGCTGAGATGAGTCTTTTTTAATATGAGATTTTAAAGTTGTTGA
1 TTTTAAAGTTGTTGAGCCT-CTACTAAGATGAGCCTTTTTCAAGATGAGATTTTAAAGTTATTGA
*
2908596 G-TCTCTACTTAGATGAGCCTTTTCAGATGAGAT
65 GCT-TCTACTTAGA-GAACCTTTTCAGATGAGAT
* * * * *
2908629 TTTTAAAGTTGTTGAGCCTCTATTAAGAGGAGACTTTTTCAAGATAAGACTTTTAAAGTTATTAA
1 TTTTAAAGTTGTTGAGCCTCTACTAAGATGAGCCTTTTTCAAGATGAGA-TTTTAAAGTTATTGA
* * * * * *
2908694 GCATCTGCTTAGAGAAGCTTTTTCAAGATAAAAC
65 GCTTCTACTTAGAGAA-CCTTTTC-AGATGAGAT
* *
2908728 TTTTAAAGTTGTTGAGCCTCTACTGAGA-GAAGCCTTTTTCAAGATGAGATTTTAAAGTTGTTGA
1 TTTTAAAGTTGTTGAGCCTCTACTAAGATG-AGCCTTTTTCAAGATGAGATTTTAAAGTTATTGA
* * * *
2908792 GCCTCTACTTAGAGAAGCATTTCATATGAGAT
65 GCTTCTACTTAGAGAACCTTTTCAGATGAGAT
* ** * * * *
2908824 TTTTAAATTTGTTGAGTTTCTAATGAGAAGAGCCTTTTTCAA-ATGAGATTTTAATGTTATTGAG
1 TTTTAAAGTTGTTGAGCCTCTACTAAGATGAGCCTTTTTCAAGATGAGATTTTAAAGTTATTGAG
*
2908888 CTTTTACTTAGAGGAACCTCTTT-AGATGAGAT
66 CTTCTACTTAGA-GAACCT-TTTCAGATGAGAT
* *
2908920 TTTTAAAGTTATTGAGCCTCTACCAAGATGAGCC
1 TTTTAAAGTTGTTGAGCCTCTACTAAGATGAGCC
2908954 GTTCTTTAGA
Statistics
Matches: 265, Mismatches: 51, Indels: 19
0.79 0.15 0.06
Matches are distributed among these distances:
95 30 0.11
96 79 0.30
97 48 0.18
98 59 0.22
99 49 0.18
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.39
Consensus pattern (96 bp):
TTTTAAAGTTGTTGAGCCTCTACTAAGATGAGCCTTTTTCAAGATGAGATTTTAAAGTTATTGAG
CTTCTACTTAGAGAACCTTTTCAGATGAGAT
Done.