Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, 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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 17 of 109
Found at i:2748007 original size:13 final size:14
Alignment explanation
Indices: 2747980--2748012 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2747970 ACCCAACGCC
*
2747980 AAAACATACCTACA
1 AAAACATACCAACA
2747994 AAAACATA-CAACA
1 AAAACATACCAACA
2748007 AAAACA
1 AAAACA
2748013 AAAATTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.67, C:0.24, G:0.00, T:0.09
Consensus pattern (14 bp):
AAAACATACCAACA
Found at i:2748656 original size:19 final size:17
Alignment explanation
Indices: 2748618--2748659 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
2748608 GGTAAAAAAA
2748618 ATTTT-TTTTTTAATTT
1 ATTTTATTTTTTAATTT
2748634 -TTTTATTTTTTATATATT
1 ATTTTATTTTTTA-AT-TT
2748652 ATTTTATT
1 ATTTTATT
2748660 AATATTTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.18
16 7 0.32
17 2 0.09
18 2 0.09
19 7 0.32
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
ATTTTATTTTTTAATTT
Found at i:2749970 original size:21 final size:19
Alignment explanation
Indices: 2749946--2749995 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
2749936 ATAAATAAAT
2749946 AAATAAAACAAAACAAATCAA
1 AAATAAAACAAAA-AAA-CAA
2749967 AAATAAAAAGCAAAAAAACAA
1 AAAT-AAAA-CAAAAAAACAA
2749988 AAA-AAAAC
1 AAATAAAAC
2749996 TCACACATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 1 0.04
19 4 0.15
21 10 0.37
22 7 0.26
23 5 0.19
ACGTcount: A:0.80, C:0.12, G:0.02, T:0.06
Consensus pattern (19 bp):
AAATAAAACAAAAAAACAA
Found at i:2750439 original size:26 final size:26
Alignment explanation
Indices: 2750410--2750466 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
2750400 CGTTGTGTAT
* * *
2750410 AATATGAAACAAAAC-AAAACATAAAA
1 AATATCAAA-AAAACTAAAAAACAAAA
*
2750436 AATATCAAAAACACTAAAAAACAAAA
1 AATATCAAAAAAACTAAAAAACAAAA
2750462 AATAT
1 AATAT
2750467 TTTTTTCGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.72, C:0.12, G:0.02, T:0.14
Consensus pattern (26 bp):
AATATCAAAAAAACTAAAAAACAAAA
Found at i:2755259 original size:19 final size:19
Alignment explanation
Indices: 2755224--2755260 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2755214 AAAAAGCTAG
* *
2755224 AAAGAAGAAAGTCAAAGTA
1 AAAGAAGAAAATAAAAGTA
2755243 AAAGAAGAAAATAAAAGT
1 AAAGAAGAAAATAAAAGT
2755261 CAGAGTGGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.19, T:0.11
Consensus pattern (19 bp):
AAAGAAGAAAATAAAAGTA
Found at i:2761286 original size:49 final size:49
Alignment explanation
Indices: 2760992--2761590 Score: 535
Period size: 48 Copynumber: 12.5 Consensus size: 49
2760982 AAAACAAAAA
* * * *
2760992 AAAATTTTAAAGTTATTGAACTTCTGCTGAGAGGAGC-TTTCTAAGATG
1 AAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATG
* * * *
2761040 AAAATTTTAAAGCTGTTGAGCCTCTGTTGAGAGGAGTTTTTTC----T-
1 AAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATG
* * * *
2761084 AAGATTTTAAAGTTATTGAGCCTCTGCTGAGAGAAGCCATTTT-CAAGAAG
1 AAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-C-TTTTCCAAGATG
* *
2761134 AGAATTTTAAAGTTGTTGAGCCTTTGCTGAGAGGAGCTTTTCCAAGATG
1 AAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATG
* * * *
2761183 -AGATTTTAAAGTTGTTAAGCCTCTGCTGAGAAGAGCTTTTTCAAGATG
1 AAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATG
* *
2761231 -AGATTTTAAAGTTGTTGAGCCTCTGCTAAGAGGAGCTTTTCCAAGATG
1 AAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATG
* * **
2761279 AAAATTTTAAAGTTTTTGAGCCTCTACTGAGAGGAGCTTTT-TTA-AT-
1 AAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATG
* * * *
2761325 AAAATTTTAAAGTTATTGTGCCTTTGCTGAGAGGAGCTTTTTTC---A-G
1 AAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC-TTTTCCAAGATG
* * *
2761371 ---A---TAAAGTTGTTGAGCCTCTGCTGAGATGAGCCATTTCCAAGAAATTTTAA
1 AAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTCCAAG--A---T-G
*
2761421 AGAAATTTTAAAGCTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATG
1 A-AAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATG
* * * *
2761471 GAAATTTTAAAGTTGTTGTGCCTCTGCTGAGATGAGCTTTTTC-AGATG
1 AAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATG
* * * * **
2761519 AGAATTTTAAAGTTGTTGAGCCTCTGCTGAGATGAGCCATTT-CAAAAAA
1 AAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTCCAAGATG
*
2761568 AAAATTTTAAAGTTGTTAAGCCT
1 AAAATTTTAAAGTTGTTGAGCCT
2761591 ATATTAAGAG
Statistics
Matches: 451, Mismatches: 67, Indels: 65
0.77 0.11 0.11
Matches are distributed among these distances:
40 29 0.06
41 1 0.00
43 1 0.00
44 31 0.07
45 3 0.01
46 38 0.08
47 6 0.01
48 161 0.36
49 111 0.25
50 31 0.07
51 1 0.00
54 2 0.00
56 9 0.02
57 27 0.06
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (49 bp):
AAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATG
Found at i:2761316 original size:97 final size:97
Alignment explanation
Indices: 2760992--2761590 Score: 556
Period size: 97 Copynumber: 6.2 Consensus size: 97
2760982 AAAACAAAAA
* * * * *
2760992 AAAATTTTAAAGTTATTGAACTTCTGCTGAGAGGAGCTTTCT-AAGATGAAAATTTTAAAGCTGT
1 AAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATG-AAATTTTAAAGTTGT
* * *
2761056 TGAGCCTCTGTTGAGAGGAGTTTTTTC----T-
65 TGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATG
* * * * *
2761084 AAGATTTTAAAGTTATTGAGCCTCTGCTGAGAGAAGCCATTTTCAAGAAGAGAATTTTAAAGTTG
1 AAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCAAGATGA-AATTTTAAAGTTG
*
2761149 TTGAGCCTTTGCTGAGAGGAGCTTTTCCAAGATG
64 TTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATG
* * * *
2761183 -AGATTTTAAAGTTGTTAAGCCTCTGCTGAGAAGAGCTTTTTCAAGATGAGATTTTAAAGTTGTT
1 AAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATGAAATTTTAAAGTTGTT
*
2761247 GAGCCTCTGCTAAGAGGAGCTTTTCCAAGATG
66 GAGCCTCTGCTGAGAGGAGCTTTTCCAAGATG
* * * * *
2761279 AAAATTTTAAAGTTTTTGAGCCTCTACTGAGAGGAGCTTTTT-TA-ATAAAATTTTAAAGTTATT
1 AAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATGAAATTTTAAAGTTGTT
* * *
2761342 GTGCCTTTGCTGAGAGGAGCTTTTTTC---A-G
66 GAGCCTCTGCTGAGAGGAGC-TTTTCCAAGATG
* * *
2761371 ---A---TAAAGTTGTTGAGCCTCTGCTGAGATGAGCCATTTCCAAGAAATTTTAAAGAAATTTT
1 AAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCAAG--A---T---GAAATTTT
*
2761430 AAAGCTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATG
57 AAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATG
* * *
2761471 GAAATTTTAAAGTTGTTGTGCCTCTGCTGAGATGAGCTTTTTC-AGATGAGAATTTTAAAGTTGT
1 AAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATGA-AATTTTAAAGTTGT
* * * **
2761535 TGAGCCTCTGCTGAGATGAGCCATTT-CAAAAAA
65 TGAGCCTCTGCTGAGAGGAG-CTTTTCCAAGATG
*
2761568 AAAATTTTAAAGTTGTTAAGCCT
1 AAAATTTTAAAGTTGTTGAGCCT
2761591 ATATTAAGAG
Statistics
Matches: 416, Mismatches: 58, Indels: 61
0.78 0.11 0.11
Matches are distributed among these distances:
86 26 0.06
87 4 0.01
88 1 0.00
89 1 0.00
91 1 0.00
92 33 0.08
93 6 0.01
94 42 0.10
95 33 0.08
96 57 0.14
97 136 0.33
98 36 0.09
99 2 0.00
100 1 0.00
102 1 0.00
103 1 0.00
104 2 0.00
105 5 0.01
106 28 0.07
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (97 bp):
AAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATGAAATTTTAAAGTTGTT
GAGCCTCTGCTGAGAGGAGCTTTTCCAAGATG
Found at i:2761423 original size:11 final size:11
Alignment explanation
Indices: 2761409--2761433 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2761399 AGCCATTTCC
2761409 AAGAAATTTTA
1 AAGAAATTTTA
2761420 AAGAAATTTTA
1 AAGAAATTTTA
2761431 AAG
1 AAG
2761434 CTGTTGAGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (11 bp):
AAGAAATTTTA
Found at i:2761429 original size:143 final size:149
Alignment explanation
Indices: 2761280--2761561 Score: 387
Period size: 146 Copynumber: 1.9 Consensus size: 149
2761270 TCCAAGATGA
* * **
2761280 AAATTTTAAAGTTTTTGAGCCTCTACTGAGAGGAGCTTTT-TTA-AT-AAAATTTTAAAGTTATT
1 AAATTTTAAAGCTGTTGAGCCTCTACTGAGAGGAGCTTTTCCAAGATGAAAATTTTAAAGTTATT
*
2761342 GTGCCTTTGCTGAGAGGAGCTTTTT-TCAG-A-TAAAGTTGTTGAGCCTCTGCTGAGATGAGCCA
66 GTGCCTCTGCTGAGAGGAGCTTTTTATCAGAATTAAAGTTGTTGAGCCTCTGCTGAGATGAGCCA
2761404 TTTCCAAGAAATTTTAAAG
131 TTTCCAAGAAATTTTAAAG
* * *
2761423 AAATTTTAAAGCTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGGAAATTTTAAAGTTGTT
1 AAATTTTAAAGCTGTTGAGCCTCTACTGAGAGGAGCTTTTCCAAGATGAAAATTTTAAAGTTATT
* *
2761488 GTGCCTCTGCTGAGATGAGCTTTTTCAGATGAGAATTTTAAAGTTGTTGAGCCTCTGCTGAGATG
66 GTGCCTCTGCTGAGAGGAGCTTTTT---ATCAGAA--TTAAAGTTGTTGAGCCTCTGCTGAGATG
2761553 AGCCATTTC
126 AGCCATTTC
2761562 AAAAAAAAAA
Statistics
Matches: 118, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
143 37 0.31
144 1 0.01
145 2 0.02
146 38 0.32
150 3 0.03
151 1 0.01
154 36 0.31
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (149 bp):
AAATTTTAAAGCTGTTGAGCCTCTACTGAGAGGAGCTTTTCCAAGATGAAAATTTTAAAGTTATT
GTGCCTCTGCTGAGAGGAGCTTTTTATCAGAATTAAAGTTGTTGAGCCTCTGCTGAGATGAGCCA
TTTCCAAGAAATTTTAAAG
Found at i:2761801 original size:3 final size:3
Alignment explanation
Indices: 2761793--2761848 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
2761783 TAAACACCAT
2761793 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2761841 TTA TTA TT
1 TTA TTA TT
2761849 TATTTAATTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2761937 original size:22 final size:23
Alignment explanation
Indices: 2761897--2761949 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
2761887 TCTGCGTTTG
*
2761897 TCTTCTTCTCTTTTCTTTTTTTT
1 TCTTCTTCTCTTTTCTTTTTCTT
2761920 TCTT-TTCTCATTTT-TTTTTCTT
1 TCTTCTTCTC-TTTTCTTTTTCTT
2761942 TCTTCTTC
1 TCTTCTTC
2761950 ATCCTTATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (23 bp):
TCTTCTTCTCTTTTCTTTTTCTT
Found at i:2761947 original size:20 final size:19
Alignment explanation
Indices: 2761856--2761947 Score: 59
Period size: 18 Copynumber: 4.9 Consensus size: 19
2761846 ATTTATTTAA
2761856 TTTTTTTTCTTCTCTT-TCT
1 TTTTTTTTCTT-TCTTCTCT
* * *
2761875 TTTCTTTTCGTTTC-T-GCG
1 TTTTTTTTC-TTTCTTCTCT
* * *
2761893 TTTGTCTTCTTCTCTTTTCT
1 TTTTTTTTCTT-TCTTCTCT
2761913 TTTTTTTTC-TT-TTCTCAT
1 TTTTTTTTCTTTCTTCTC-T
2761931 TTTTTTTTCTTTCTTCT
1 TTTTTTTTCTTTCTTCT
2761948 TCATCCTTAT
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
17 6 0.11
18 22 0.39
19 14 0.25
20 14 0.25
ACGTcount: A:0.01, C:0.21, G:0.04, T:0.74
Consensus pattern (19 bp):
TTTTTTTTCTTTCTTCTCT
Found at i:2762962 original size:20 final size:20
Alignment explanation
Indices: 2762924--2762962 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2762914 GGTAAAAAAA
*
2762924 ATTTTTTAAAAATTTTTTTT
1 ATTTTTTAAAAATTATTTTT
* *
2762944 ATTTTTTATATATTATTTT
1 ATTTTTTAAAAATTATTTT
2762963 GTTAATATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
ATTTTTTAAAAATTATTTTT
Found at i:2764128 original size:12 final size:12
Alignment explanation
Indices: 2764102--2764202 Score: 51
Period size: 12 Copynumber: 8.2 Consensus size: 12
2764092 CTGTTTCGAC
* *
2764102 ATGGTTTGTTAA
1 ATGGTTTGCTGA
2764114 ATGGTTTGCTGA
1 ATGGTTTGCTGA
*
2764126 ATGGTGTTTCTGA
1 ATGGT-TTGCTGA
* *
2764139 ATAGTTT-TTCGA
1 ATGGTTTGCT-GA
* *
2764151 ATGGTATTTCTAA
1 ATGGT-TTGCTGA
**
2764164 ATGGTTTATTGA
1 ATGGTTTGCTGA
* *
2764176 ATGATTTGCTAA
1 ATGGTTTGCTGA
*
2764188 ATGGTGTTTCTGA
1 ATGGT-TTGCTGA
2764201 AT
1 AT
2764203 AATTTCTCGA
Statistics
Matches: 66, Mismatches: 18, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
11 1 0.02
12 39 0.59
13 25 0.38
14 1 0.02
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.47
Consensus pattern (12 bp):
ATGGTTTGCTGA
Found at i:2764152 original size:25 final size:25
Alignment explanation
Indices: 2764123--2764178 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
2764113 AATGGTTTGC
* *
2764123 TGAATGGTGTTTCTGAATAGTTT-T
1 TGAATGGTATTTCTAAATAGTTTAT
*
2764147 TCGAATGGTATTTCTAAATGGTTTAT
1 T-GAATGGTATTTCTAAATAGTTTAT
2764173 TGAATG
1 TGAATG
2764179 ATTTGCTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 24 0.89
26 2 0.07
ACGTcount: A:0.25, C:0.05, G:0.23, T:0.46
Consensus pattern (25 bp):
TGAATGGTATTTCTAAATAGTTTAT
Found at i:2764201 original size:25 final size:24
Alignment explanation
Indices: 2764156--2764251 Score: 104
Period size: 25 Copynumber: 3.9 Consensus size: 24
2764146 TTCGAATGGT
* *
2764156 ATTTCTAAATGGT-TTATTGAATG
1 ATTTCTAAATGGTGTTTTTGAATA
*
2764179 ATTTGCTAAATGGTGTTTCTGAATA
1 ATTT-CTAAATGGTGTTTTTGAATA
* *
2764204 ATTTCTCGAATGGTGTTTTTAAATA
1 ATTTCT-AAATGGTGTTTTTGAATA
*
2764229 ATTTGCTGAATGGTGTTTTTGAA
1 ATTT-CTAAATGGTGTTTTTGAA
2764252 CATATTGCTG
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
23 4 0.06
24 11 0.18
25 45 0.73
26 2 0.03
ACGTcount: A:0.27, C:0.06, G:0.20, T:0.47
Consensus pattern (24 bp):
ATTTCTAAATGGTGTTTTTGAATA
Found at i:2764239 original size:62 final size:62
Alignment explanation
Indices: 2764113--2764240 Score: 166
Period size: 62 Copynumber: 2.1 Consensus size: 62
2764103 TGGTTTGTTA
* * * * ** *
2764113 AATGGTTTGCTGAATGGTGTTTCTGAATAGTTTTTCGAATGGTATTTCTAAATGGTTTATTG
1 AATGATTTGCTAAATGGTGTTTCTGAATAATTTCTCGAATGGTATTTCTAAATAATTTACTG
* * *
2764175 AATGATTTGCTAAATGGTGTTTCTGAATAATTTCTCGAATGGTGTTTTTAAATAATTTGCTG
1 AATGATTTGCTAAATGGTGTTTCTGAATAATTTCTCGAATGGTATTTCTAAATAATTTACTG
2764237 AATG
1 AATG
2764241 GTGTTTTTGA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.26, C:0.07, G:0.22, T:0.45
Consensus pattern (62 bp):
AATGATTTGCTAAATGGTGTTTCTGAATAATTTCTCGAATGGTATTTCTAAATAATTTACTG
Found at i:2764259 original size:25 final size:24
Alignment explanation
Indices: 2764181--2764262 Score: 78
Period size: 25 Copynumber: 3.3 Consensus size: 24
2764171 ATTGAATGAT
* *
2764181 TTGCTAAATGGTGTTTCTG-AATAA
1 TTGCTGAATGGTGTTTTTGAAAT-A
*
2764205 TTTCTCGAATGGTGTTTTT-AAATAA
1 TTGCT-GAATGGTGTTTTTGAAAT-A
2764230 TTTGCTGAATGGTGTTTTTGAACATA
1 -TTGCTGAATGGTGTTTTTGAA-ATA
2764256 TTGCTGA
1 TTGCTGA
2764263 TTGATTTGCT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.08
25 36 0.73
26 7 0.14
27 2 0.04
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.45
Consensus pattern (24 bp):
TTGCTGAATGGTGTTTTTGAAATA
Found at i:2767644 original size:64 final size:62
Alignment explanation
Indices: 2767575--2767767 Score: 181
Period size: 64 Copynumber: 3.0 Consensus size: 62
2767565 TCAAAACTGT
* *
2767575 CTTCAATAATCCTTAATAAAAATTTATTATGTGGATTATTAAAGGTGTTTTGGGCCAAAAACAC
1 CTTCAATAATCC-TAATAAAAATTTATTAT-TGGATTATTAAAGGTGTTTTTGACCAAAAACAC
* * * ** * * * * * * *
2767639 TTTCAAGAAT-CTATTGCAACTTTTTTGTATGTATTATTAAAGGTGTTTTTTACCAAAATCGC
1 CTTCAATAATCCTAATAAAAATTTATTAT-TGGATTATTAAAGGTGTTTTTGACCAAAAACAC
* * *
2767701 CTTCAATAATCCCTCATAAAAATTTATTGATTGGATTATTGAAGGTGTTTTTGACCAAAAACGC
1 CTTCAATAAT-CCTAATAAAAATTTATT-ATTGGATTATTAAAGGTGTTTTTGACCAAAAACAC
2767765 CTT
1 CTT
2767768 TAAAAATCTA
Statistics
Matches: 98, Mismatches: 28, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
62 46 0.47
63 1 0.01
64 50 0.51
65 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.39
Consensus pattern (62 bp):
CTTCAATAATCCTAATAAAAATTTATTATTGGATTATTAAAGGTGTTTTTGACCAAAAACAC
Found at i:2767790 original size:126 final size:125
Alignment explanation
Indices: 2767546--2767887 Score: 325
Period size: 126 Copynumber: 2.7 Consensus size: 125
2767536 TAACAAAATG
* * * * *
2767546 TTATTGAAGGCATTTTTTATCAAAA-CTGTCTTCAATAATCCTTAATAAAAATTTATTATGTGGA
1 TTATTAAAGGCATTTTTTACCAAAATC-GCCTTCAATAATCCCTCATAAAAATTTATTAT-TGGA
* * * * ** *
2767610 TTATTAAAGGTGTTTTGGGCCAAAAACACTTTCAAGAATCTATTGCAACTTTTTTGTAT-GTA
64 TTATTGAAGGTGTTTTTGACCAAAAACACTTTCAAAAATCTATTGCAAAATTTTTCTATAG-A
**
2767672 TTATTAAAGGTGTTTTTTACCAAAATCGCCTTCAATAATCCCTCATAAAAATTTATTGATTGGAT
1 TTATTAAAGGCATTTTTTACCAAAATCGCCTTCAATAATCCCTCATAAAAATTTATT-ATTGGAT
* *
2767737 TATTGAAGGTGTTTTTGACCAAAAACGCCTTT-AAAAATCTATTTCAAAATTTTTCTATAGA
65 TATTGAAGGTGTTTTTGACCAAAAAC-ACTTTCAAAAATCTATTGCAAAATTTTTCTATAGA
* * * * * * * *
2767798 TTATTGAAGGCATTTTTCTATCGAAAAT-GCCTCCAATATTCTCTC-TCAAAATTTTTTAAATGG
1 TTATTAAAGGCATTTTT-TA-CCAAAATCGCCTTCAATAATCCCTCATAAAAATTTATT-ATTGG
** * *
2767861 ATTGGTGAAGGCGTTTTTGCCCAAAAA
63 ATTATTGAAGGTGTTTTTGACCAAAAA
2767888 ACAACTAAAA
Statistics
Matches: 179, Mismatches: 31, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
126 149 0.83
127 24 0.13
128 6 0.03
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (125 bp):
TTATTAAAGGCATTTTTTACCAAAATCGCCTTCAATAATCCCTCATAAAAATTTATTATTGGATT
ATTGAAGGTGTTTTTGACCAAAAACACTTTCAAAAATCTATTGCAAAATTTTTCTATAGA
Found at i:2770228 original size:17 final size:17
Alignment explanation
Indices: 2770206--2770241 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2770196 TTATTGATAC
* *
2770206 AATATTTATCGATTATT
1 AATATTAATCAATTATT
2770223 AATATTAATCAATTATT
1 AATATTAATCAATTATT
2770240 AA
1 AA
2770242 ATTCAAATAT
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:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (17 bp):
AATATTAATCAATTATT
Found at i:2771826 original size:52 final size:54
Alignment explanation
Indices: 2771716--2771827 Score: 149
Period size: 52 Copynumber: 2.1 Consensus size: 54
2771706 TTTTATAAGA
2771716 TTATTGAAAGAGTTTTTAACCAAAAAAAAGCCTTCAATAATCCCTAACAAAAAG
1 TTATTGAAAGAGTTTTTAACCAAAAAAAAGCCTTCAATAATCCCTAACAAAAAG
** * * *
2771770 TTATTGAAAGCA-TTTTTAACC-AAAATCA-TCTTCAATAATCCCTAATAAAAAT
1 TTATTGAAAG-AGTTTTTAACCAAAAAAAAGCCTTCAATAATCCCTAACAAAAAG
2771822 TTATTG
1 TTATTG
2771828 TGTGGATTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
52 27 0.52
53 5 0.10
54 19 0.37
55 1 0.02
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.32
Consensus pattern (54 bp):
TTATTGAAAGAGTTTTTAACCAAAAAAAAGCCTTCAATAATCCCTAACAAAAAG
Found at i:2771997 original size:126 final size:126
Alignment explanation
Indices: 2771770--2772024 Score: 318
Period size: 126 Copynumber: 2.0 Consensus size: 126
2771760 TAACAAAAAG
* * *
2771770 TTATTGAAAGCATTTTTAACCAAAATCATCTTCAATAATCCCTAATAAAAATTTATTGTGTGGAT
1 TTATTAAAAGCATTTTTAACCAAAACCACCTTCAATAATCCCTAATAAAAATTTATTGTGTGGAT
* * * * *
2771835 TATTAATGACGTTTTGGGCTAAAAATACCTTTAAAAATCCATTTCAACTTTTTTGTATGAA
66 TATTAAAGACGTTTTGAGCTAAAAATACATTCAAAAATCCATTTCAAATTTTTTGTATGAA
* * *
2771896 TTATTAAAAGTATTTTTAACCAAAACCACCTTCAATAATCTCTCATAAAAATTTATTGAT-TGGA
1 TTATTAAAAGCATTTTTAACCAAAACCACCTTCAATAATCCCTAATAAAAATTTATTG-TGTGGA
* * * * *
2771960 TTATTAAA-AGCGTTTTCGATC-AAAAATGCATTCAAAAATTCATTTCAAATTTTTTTTATGGA
65 TTATTAAAGA-CGTTTT-GAGCTAAAAATACATTCAAAAATCCATTTCAAATTTTTTGTATGAA
2772022 TTA
1 TTA
2772025 ATGAATGTGT
Statistics
Matches: 110, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
125 1 0.01
126 106 0.96
127 3 0.03
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (126 bp):
TTATTAAAAGCATTTTTAACCAAAACCACCTTCAATAATCCCTAATAAAAATTTATTGTGTGGAT
TATTAAAGACGTTTTGAGCTAAAAATACATTCAAAAATCCATTTCAAATTTTTTGTATGAA
Found at i:2772151 original size:13 final size:14
Alignment explanation
Indices: 2772123--2772151 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2772113 AAATGCTTAG
2772123 AATAATCTCTTACA
1 AATAATCTCTTACA
2772137 AATAATCTCTT-CA
1 AATAATCTCTTACA
2772150 AA
1 AA
2772152 AAATTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (14 bp):
AATAATCTCTTACA
Found at i:2772690 original size:63 final size:63
Alignment explanation
Indices: 2772607--2772739 Score: 153
Period size: 63 Copynumber: 2.1 Consensus size: 63
2772597 TAAAAATTTC
2772607 AATAATCGTCTATATTTTTTTATAAAAAAATTATTCAAAGCATTATTTATCAAAAATACTTTT
1 AATAATCGTCTATATTTTTTTATAAAAAAATTATTCAAAGCATTATTTATCAAAAATACTTTT
* ** * * ** * *
2772670 AATAATC-TCT-TATCTATTTTTTTAATGAGATTATTTAAATTATTTTTTATCAAAAATATTTTT
1 AATAATCGTCTATAT-T-TTTTTATAAAAAAATTATTCAAAGCATTATTTATCAAAAATACTTTT
2772733 AATAATC
1 AATAATC
2772740 ACTTTAAATG
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
61 3 0.05
62 4 0.07
63 52 0.88
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.49
Consensus pattern (63 bp):
AATAATCGTCTATATTTTTTTATAAAAAAATTATTCAAAGCATTATTTATCAAAAATACTTTT
Found at i:2775110 original size:18 final size:17
Alignment explanation
Indices: 2775075--2775117 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
2775065 ACTTAATCTG
2775075 AATATAAAA--TTATAA
1 AATATAAAATTTTATAA
*
2775090 AATATTAAAATTTTATTA
1 AATA-TAAAATTTTATAA
2775108 AATATAAAAT
1 AATATAAAAT
2775118 AATCTATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 4 0.17
16 5 0.21
17 6 0.25
18 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATATAAAATTTTATAA
Found at i:2775446 original size:11 final size:11
Alignment explanation
Indices: 2775430--2775466 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
2775420 TTAAGAAAGA
2775430 TAAATGATTAT
1 TAAATGATTAT
2775441 TAAATGATTAT
1 TAAATGATTAT
*
2775452 TAAATG-TTAA
1 TAAATGATTAT
2775462 TAAAT
1 TAAAT
2775467 TTTTGTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (11 bp):
TAAATGATTAT
Found at i:2780708 original size:30 final size:27
Alignment explanation
Indices: 2780653--2780708 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
2780643 AAAAATTACT
* *
2780653 TTCAATAATTATATAATAAATAGAATC
1 TTCAATAATTATAAAAAAAATAGAATC
2780680 TTCAATAATTATACAAAAATAATAAGAAT
1 TTCAATAATTATA-AAAAA-AAT-AGAAT
2780709 TAATCTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 13 0.54
28 3 0.12
29 3 0.12
30 5 0.21
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.34
Consensus pattern (27 bp):
TTCAATAATTATAAAAAAAATAGAATC
Found at i:2781858 original size:24 final size:26
Alignment explanation
Indices: 2781830--2781878 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
2781820 AAAAATGTTT
*
2781830 TTCCATCTTTTCA-CTTTTC-TTTTC
1 TTCCAACTTTTCATCTTTTCATTTTC
2781854 TTCCAACTTTTCATCTTTTCATTTT
1 TTCCAACTTTTCATCTTTTCATTTT
2781879 TTTATACCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.55
25 6 0.27
26 4 0.18
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.61
Consensus pattern (26 bp):
TTCCAACTTTTCATCTTTTCATTTTC
Found at i:2790490 original size:16 final size:16
Alignment explanation
Indices: 2790471--2790529 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 16
2790461 TATAATATTA
2790471 TAATTATCTAATTAAT
1 TAATTATCTAATTAAT
*
2790487 TAATTATCTAATAAAT
1 TAATTATCTAATTAAT
*
2790503 TAATTA-ATAATTAACT
1 TAATTATCTAATTAA-T
*
2790519 T-ATTTTCTAAT
1 TAATTATCTAAT
2790530 GAAACTATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 9 0.25
16 27 0.75
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATTATCTAATTAAT
Found at i:2791540 original size:15 final size:15
Alignment explanation
Indices: 2791478--2791541 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 15
2791468 AAAAATATTG
*
2791478 TTTTATAAATGAGTGA
1 TTTTATAAAT-AGTTA
* *
2791494 TTTTTTGAATAGTTA
1 TTTTATAAATAGTTA
** * *
2791509 TTCCATAAAGAGCTA
1 TTTTATAAATAGTTA
2791524 TTTTATAAATAGTTA
1 TTTTATAAATAGTTA
2791539 TTT
1 TTT
2791542 CGTGAACATC
Statistics
Matches: 35, Mismatches: 13, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
15 27 0.77
16 8 0.23
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.48
Consensus pattern (15 bp):
TTTTATAAATAGTTA
Found at i:2792200 original size:14 final size:14
Alignment explanation
Indices: 2792181--2792207 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2792171 AATAGATAAA
2792181 AATATTTATGATAG
1 AATATTTATGATAG
2792195 AATATTTATGATA
1 AATATTTATGATA
2792208 TTTTAAGTAC
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:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (14 bp):
AATATTTATGATAG
Found at i:2794538 original size:36 final size:35
Alignment explanation
Indices: 2794141--2794540 Score: 186
Period size: 36 Copynumber: 11.4 Consensus size: 35
2794131 ATTGGAAGCA
* *
2794141 TTTCCC-AAAAAATAG-AGAATAAATAATTAGAATG
1 TTTCCCTAAAAAATAGAAGAACAAGTAA-TAGAATG
* * *
2794175 TTT-CCTTAAAAATAGAAGAACAAGCAATGAGAGTG
1 TTTCCCTAAAAAATAGAAGAACAAGTAAT-AGAATG
* * *
2794210 TTTCTCTAAAAAATAAGAA-AAAAAATAAT-GATAT-
1 TTTCCCTAAAAAAT-AGAAGAACAAGTAATAGA-ATG
* * * * *
2794244 TGTT-CCTTAAAAATAGGATAACAAATAATAGATTG
1 T-TTCCCTAAAAAATAGAAGAACAAGTAATAGAATG
* *
2794279 CTTT-CCT-AAAAATAAAAGAACAAGTAATATAAGTG
1 -TTTCCCTAAAAAATAGAAGAACAAGTAATAGAA-TG
* * *
2794314 TTTCCTTAAAAAATAG-AGCAACAAGTAATGGATATA
1 TTTCCCTAAAAAATAGAAG-AACAAGTAATAGA-ATG
** * * * *
2794350 TTTATCT-AAAAATAGGAGAATAATTAATGGAAATG
1 TTTCCCTAAAAAATAGAAGAACAAGTAATAG-AATG
* *
2794385 TTTCCCCTAAAAAATAGGAA-AATAAGTAAT-GCTAATA
1 TTT-CCCTAAAAAATA-GAAGAACAAGTAATAG--AATG
* * *
2794422 TTTCCCTAAAATATA-AGAGAATAAGCAAT-GTAAATG
1 TTTCCCTAAAAAATAGA-AGAACAAGTAATAG--AATG
** * *
2794458 TTTTTCTAAAAAATAAAAGAACAAGTAACAAGAATG
1 TTTCCCTAAAAAATAGAAGAACAAGTAA-TAGAATG
*
2794494 TTT--CTAAAAAATAGAAGAATAAGTAATAAGAATG
1 TTTCCCTAAAAAATAGAAGAACAAGTAAT-AGAATG
**
2794528 TTTCTTTAAAAAA
1 TTTCCCTAAAAAA
2794541 GATAAGAGAA
Statistics
Matches: 282, Mismatches: 54, Indels: 58
0.72 0.14 0.15
Matches are distributed among these distances:
33 5 0.02
34 86 0.30
35 56 0.20
36 104 0.37
37 28 0.10
38 3 0.01
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.28
Consensus pattern (35 bp):
TTTCCCTAAAAAATAGAAGAACAAGTAATAGAATG
Found at i:2796014 original size:16 final size:16
Alignment explanation
Indices: 2795990--2796044 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
2795980 ATTTATTTAT
*
2795990 ATATATTTATATAATA
1 ATATATTTAAATAATA
*
2796006 ATATTTTTAAAT-AT-
1 ATATATTTAAATAATA
* *
2796020 TTATATTTAAAAAATA
1 ATATATTTAAATAATA
*
2796036 ATATTTTTA
1 ATATATTTA
2796045 TTAATTTCGG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
14 9 0.30
15 4 0.13
16 17 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATATTTAAATAATA
Found at i:2801071 original size:16 final size:15
Alignment explanation
Indices: 2801035--2801084 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
2801025 AGTTATTTTG
*
2801035 TGAATAATTGTTTTA
1 TGAATAATTGTTTCA
*
2801050 TAAATAAATTGTTTCA
1 TGAAT-AATTGTTTCA
* *
2801066 TGAATAGTTGTTCCA
1 TGAATAATTGTTTCA
2801081 TGAA
1 TGAA
2801085 CAACTATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
15 16 0.55
16 13 0.45
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (15 bp):
TGAATAATTGTTTCA
Found at i:2803679 original size:156 final size:156
Alignment explanation
Indices: 2803395--2803707 Score: 608
Period size: 156 Copynumber: 2.0 Consensus size: 156
2803385 TCTTGAAGTA
*
2803395 GAATATATATTGATGGTCAGGTGAGTCACAACATAACTTTGAGCTGGAAATGGCTCGCAAGATGG
1 GAATATATATTGAGGGTCAGGTGAGTCACAACATAACTTTGAGCTGGAAATGGCTCGCAAGATGG
2803460 GGGTATAATTCTGGTTCTTTATAGCTGCAACCTCTGCTGCTACTCGGAATGTTTTTCTTTTTGTT
66 GGGTATAATTCTGGTTCTTTATAGCTGCAACCTCTGCTGCTACTCGGAATGTTTTTCTTTTTGTT
*
2803525 CCTTCTCTTTTGAGTGAATAGTACTT
131 CCTTCACTTTTGAGTGAATAGTACTT
2803551 GAATATATATTGAGGGTCAGGTGAGTCACAACATAACTTTGAGCTGGAAATGGCTCGCAAGATGG
1 GAATATATATTGAGGGTCAGGTGAGTCACAACATAACTTTGAGCTGGAAATGGCTCGCAAGATGG
2803616 GGGTATAATTCTGGTTCTTTATAGCTGCAACCTCTGCTGCTACTCGGAATGTTTTTCTTTTTGTT
66 GGGTATAATTCTGGTTCTTTATAGCTGCAACCTCTGCTGCTACTCGGAATGTTTTTCTTTTTGTT
2803681 CCTTCACTTTTGAGTGAATAGTACTT
131 CCTTCACTTTTGAGTGAATAGTACTT
2803707 G
1 G
2803708 GATTTAAAGT
Statistics
Matches: 155, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 155 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (156 bp):
GAATATATATTGAGGGTCAGGTGAGTCACAACATAACTTTGAGCTGGAAATGGCTCGCAAGATGG
GGGTATAATTCTGGTTCTTTATAGCTGCAACCTCTGCTGCTACTCGGAATGTTTTTCTTTTTGTT
CCTTCACTTTTGAGTGAATAGTACTT
Found at i:2805142 original size:17 final size:18
Alignment explanation
Indices: 2805122--2805160 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
2805112 AATTTACATT
*
2805122 TATAT-AAAATAAAAATA
1 TATATAAAAACAAAAATA
2805139 TATATGAAAAACAAAAATA
1 TATAT-AAAAACAAAAATA
2805158 TAT
1 TAT
2805161 TTGACAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
19 14 0.74
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (18 bp):
TATATAAAAACAAAAATA
Found at i:2805697 original size:29 final size:30
Alignment explanation
Indices: 2805622--2805701 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
2805612 TTCATATATG
*
2805622 AAATAATCAAAATAAAATAATTTTAAATAATC
1 AAAT-ATCAAAATAAAAT-TTTTTAAATAATC
* * * *
2805654 AAAGATCCAATTAAAATTTTTTAAA-AATT
1 AAATATCAAAATAAAATTTTTTAAATAATC
2805683 AAATATCAAAATAAAATTT
1 AAATATCAAAATAAAATTT
2805702 GATTCAAAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 19 0.47
30 7 0.17
31 11 0.28
32 3 0.08
ACGTcount: A:0.59, C:0.06, G:0.01, T:0.34
Consensus pattern (30 bp):
AAATATCAAAATAAAATTTTTTAAATAATC
Found at i:2806542 original size:30 final size:29
Alignment explanation
Indices: 2806498--2806580 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
2806488 GATTTGGGTA
* *
2806498 TTTTAGTTTGTTGTTGAATTTGTTTTTGGG
1 TTTTAATTT-TTGTTGAATTTGTTTATGGG
* *
2806528 TTTTAATTTCTTGTTGAATCTG-ATATGGG
1 TTTTAATTT-TTGTTGAATTTGTTTATGGG
* *
2806557 TTTTTAGTTTTGATTGAATTTGTT
1 TTTTAATTTTTG-TTGAATTTGTT
2806581 ATTTTTTAAG
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
28 3 0.07
29 20 0.48
30 19 0.45
ACGTcount: A:0.16, C:0.02, G:0.22, T:0.60
Consensus pattern (29 bp):
TTTTAATTTTTGTTGAATTTGTTTATGGG
Found at i:2807381 original size:2 final size:2
Alignment explanation
Indices: 2807374--2807402 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2807364 TTTGAGTTAT
2807374 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2807403 CTTAAACTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2807853 original size:21 final size:21
Alignment explanation
Indices: 2807812--2807855 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2807802 AAGATTAATT
* *
2807812 TAGTGATATTAATTATTATAA
1 TAGTGAGATTAATAATTATAA
2807833 TAGTGAGATTAA-AATTAATAA
1 TAGTGAGATTAATAATT-ATAA
2807854 TA
1 TA
2807856 AAATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (21 bp):
TAGTGAGATTAATAATTATAA
Found at i:2807974 original size:21 final size:23
Alignment explanation
Indices: 2807934--2807975 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
2807924 TAAATACATT
2807934 AAATTATAAACTTATGTAATAAA
1 AAATTATAAACTTATGTAATAAA
*
2807957 AAATT-TAAA-TTATTTAATA
1 AAATTATAAACTTATGTAATA
2807976 TTTATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 4 0.22
23 5 0.28
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
AAATTATAAACTTATGTAATAAA
Found at i:2808047 original size:18 final size:20
Alignment explanation
Indices: 2808013--2808050 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
2808003 TTATGAAATT
2808013 ATTTTTAGATCAAATAATAA
1 ATTTTTAGATCAAATAATAA
2808033 ATTTTTA-AT-AAATAATAA
1 ATTTTTAGATCAAATAATAA
2808051 TAATAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 2 0.11
20 7 0.39
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
ATTTTTAGATCAAATAATAA
Found at i:2808155 original size:20 final size:19
Alignment explanation
Indices: 2808121--2808236 Score: 64
Period size: 20 Copynumber: 6.1 Consensus size: 19
2808111 TGCAATTTGT
*
2808121 AAGTAAAAAATAAAA-ACGA
1 AAGTAAAAAATAAAATA-AA
2808140 AAGTAAAAAATCAAAATAAA
1 AAGTAAAAAAT-AAAATAAA
* *
2808160 AAGTAAAAAGGACAAAAATCAA
1 AAGTAAAAA--A-TAAAATAAA
**
2808182 AA-T-AAAAAGGAAATAAA
1 AAGTAAAAAATAAAATAAA
* *
2808199 AAG-ATCAAGAT-AAA-AAA
1 AAGTA-AAAAATAAAATAAA
2808216 AAGTAAAAAATCAAAATAAA
1 AAGTAAAAAAT-AAAATAAA
2808236 A
1 A
2808237 GAGATTAAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 23
0.69 0.10 0.21
Matches are distributed among these distances:
17 18 0.24
18 5 0.07
19 17 0.23
20 22 0.30
21 2 0.03
22 10 0.14
ACGTcount: A:0.73, C:0.05, G:0.09, T:0.12
Consensus pattern (19 bp):
AAGTAAAAAATAAAATAAA
Found at i:2808206 original size:53 final size:48
Alignment explanation
Indices: 2808127--2808236 Score: 132
Period size: 53 Copynumber: 2.2 Consensus size: 48
2808117 TTGTAAGTAA
2808127 AAAATAAAAACGAAAGTAAAAAATCAAAATAAAAAGTAAAAAGGACAAAAATC
1 AAAATAAAAACGAAAGTAAAAAATCAAAAT--AAA--AAAAAGGA-AAAAATC
* * *
2808180 AAAATAAAAAGGAAA-TAAAAAGATCAAGATAAAAAAAAGTAAAAAATC
1 AAAATAAAAACGAAAGTAAAAA-ATCAAAATAAAAAAAAGGAAAAAATC
2808228 AAAATAAAA
1 AAAATAAAA
2808237 GAGATTAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
48 16 0.30
49 7 0.13
51 3 0.06
52 6 0.11
53 21 0.40
ACGTcount: A:0.74, C:0.05, G:0.09, T:0.12
Consensus pattern (48 bp):
AAAATAAAAACGAAAGTAAAAAATCAAAATAAAAAAAAGGAAAAAATC
Found at i:2808245 original size:23 final size:22
Alignment explanation
Indices: 2808173--2808271 Score: 76
Period size: 25 Copynumber: 4.2 Consensus size: 22
2808163 TAAAAAGGAC
2808173 AAAAATCAAAATAAAAAGGAAATA
1 AAAAATCAAAATAAAAA-G-AATA
* *
2808197 AAAAGATCAAGATAAAAAAAAGTA
1 AAAA-ATCAAAATAAAAAGAA-TA
2808221 AAAAATCAAAAT-AAAAGAGAT-
1 AAAAATCAAAATAAAAAGA-ATA
* *
2808242 TAAAATCAAACTAATAAAAATAATA
1 AAAAATC-AA--AATAAAAAGAATA
2808267 AAAAA
1 AAAAA
2808272 AAGGGTGAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
21 6 0.10
22 8 0.13
23 10 0.17
24 15 0.25
25 21 0.35
ACGTcount: A:0.73, C:0.05, G:0.07, T:0.15
Consensus pattern (22 bp):
AAAAATCAAAATAAAAAGAATA
Found at i:2809820 original size:20 final size:20
Alignment explanation
Indices: 2809797--2809835 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2809787 TGTATACTTT
* *
2809797 TATATGTGTGTATATATATA
1 TATATATGTGTACATATATA
2809817 TATATATGTGTACATATAT
1 TATATATGTGTACATATAT
2809836 TTTAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.03, G:0.13, T:0.49
Consensus pattern (20 bp):
TATATATGTGTACATATATA
Found at i:2811066 original size:94 final size:94
Alignment explanation
Indices: 2810964--2811146 Score: 312
Period size: 94 Copynumber: 1.9 Consensus size: 94
2810954 CCATATTGTT
** * * *
2810964 AAGTTATGGTTAAAATACTAAAAAAATTAAACTATTTTATTTTTCTTAAATAAATTCTTATTGTA
1 AAGTTATGGTTAAAATACTAAAAAAACAAAACTATTTTACTTTTCTTAAACAAACTCTTATTGTA
2811029 TTCAAATGAATCCTTATCCTTTAACAAAA
66 TTCAAATGAATCCTTATCCTTTAACAAAA
2811058 AAGTTATGGTTAAAATACTAAAAAAACAAAACTATTTTACTTTTCTTAAACAAACTCTTATTGTA
1 AAGTTATGGTTAAAATACTAAAAAAACAAAACTATTTTACTTTTCTTAAACAAACTCTTATTGTA
*
2811123 TTCAAATGAATCCTTATCTTTTAA
66 TTCAAATGAATCCTTATCCTTTAA
2811147 TTTTGTTAAA
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 83 1.00
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.40
Consensus pattern (94 bp):
AAGTTATGGTTAAAATACTAAAAAAACAAAACTATTTTACTTTTCTTAAACAAACTCTTATTGTA
TTCAAATGAATCCTTATCCTTTAACAAAA
Found at i:2821833 original size:14 final size:14
Alignment explanation
Indices: 2821814--2821841 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2821804 AGTTAAAAAT
2821814 AATTTTTGAAATTA
1 AATTTTTGAAATTA
2821828 AATTTTTGAAATTA
1 AATTTTTGAAATTA
2821842 TTGGAGGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATTTTTGAAATTA
Found at i:2825969 original size:18 final size:20
Alignment explanation
Indices: 2825948--2825991 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
2825938 AATAATCAAG
2825948 TCAATTTAACAATT-A-TTC
1 TCAATTTAACAATTAATTTC
* *
2825966 TCAAATTATCAATTAATTTC
1 TCAATTTAACAATTAATTTC
2825986 TCAATT
1 TCAATT
2825992 AATCATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 12 0.57
19 1 0.05
20 8 0.38
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (20 bp):
TCAATTTAACAATTAATTTC
Found at i:2825996 original size:20 final size:19
Alignment explanation
Indices: 2825963--2826000 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
2825953 TTAACAATTA
2825963 TTCTCAAATTATCAATTAAT
1 TTCTCAAATTATC-ATTAAT
2825983 TTCTC-AATTAATCATTAA
1 TTCTCAAATT-ATCATTAA
2826001 ATCCCAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (19 bp):
TTCTCAAATTATCATTAAT
Found at i:2828822 original size:20 final size:21
Alignment explanation
Indices: 2828782--2828832 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 21
2828772 CTCGAAATTA
2828782 ATAAAATATTATTTTTAAAAT
1 ATAAAATATTATTTTTAAAAT
2828803 ATAAAATATTATTTTT-AAAT
1 ATAAAATATTATTTTTAAAAT
2828823 ATAAATATAT
1 ATAAA-ATAT
2828833 AATTATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 9 0.31
21 20 0.69
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:2828855 original size:21 final size:20
Alignment explanation
Indices: 2828782--2828855 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 20
2828772 CTCGAAATTA
*
2828782 ATAAAATATTATTTTTAAAAT
1 ATAAAATATAATTTTT-AAAT
*
2828803 ATAAAATATTATTTTTAAAT
1 ATAAAATATAATTTTTAAAT
*
2828823 ATAAATATATAATTATATATAA-
1 ATAAA-ATATAATT-TTTA-AAT
2828845 ATAAAATATAA
1 ATAAAATATAA
2828856 AAAAATAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
20 9 0.19
21 29 0.60
22 8 0.17
23 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAAAATATAATTTTTAAAT
Found at i:2832599 original size:20 final size:20
Alignment explanation
Indices: 2832553--2832606 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
2832543 TTAATCTGAA
*
2832553 ATTTAATGATTTGTTAATTT
1 ATTTAATGATTTGTTAATAT
* *
2832573 ATATAATTATTT-TTAATAAT
1 ATTTAATGATTTGTTAAT-AT
2832593 ATTTAATAGATTTG
1 ATTTAAT-GATTTG
2832607 ATATTTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 5 0.19
20 17 0.65
21 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (20 bp):
ATTTAATGATTTGTTAATAT
Found at i:2836507 original size:23 final size:23
Alignment explanation
Indices: 2836463--2836507 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2836453 GTAAAATCAT
*
2836463 ATTTAAAATGTAATATTTAATAA
1 ATTTAAAATGTAATATTCAATAA
*
2836486 ATTTAAAATTTAA-ATCTCAATA
1 ATTTAAAATGTAATAT-TCAATA
2836508 TTTATAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (23 bp):
ATTTAAAATGTAATATTCAATAA
Found at i:2839524 original size:21 final size:22
Alignment explanation
Indices: 2839500--2839543 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2839490 CTGATCCTGT
*
2839500 AGTAGGAAAAAGAA-AGAAAAA
1 AGTAAGAAAAAGAACAGAAAAA
* *
2839521 AGTAAGAAGAGGAACAGAAAAA
1 AGTAAGAAAAAGAACAGAAAAA
2839543 A
1 A
2839544 AGGGTTCTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.68, C:0.02, G:0.25, T:0.05
Consensus pattern (22 bp):
AGTAAGAAAAAGAACAGAAAAA
Found at i:2841803 original size:10 final size:10
Alignment explanation
Indices: 2841790--2841828 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
2841780 TCCAAAAGAG
*
2841790 TTTTTATTCA
1 TTTTTATTTA
*
2841800 TTTTATTTTTA
1 TTTT-TATTTA
2841811 TTTTTATTTA
1 TTTTTATTTA
2841821 TTTTTATT
1 TTTTTATT
2841829 AAGTCAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:2851772 original size:14 final size:14
Alignment explanation
Indices: 2851753--2851779 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2851743 ACCAAACACA
2851753 TTATGTAGTATTAG
1 TTATGTAGTATTAG
2851767 TTATGTAGTATTA
1 TTATGTAGTATTA
2851780 TTTTGAAAAA
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:0.30, C:0.00, G:0.19, T:0.52
Consensus pattern (14 bp):
TTATGTAGTATTAG
Found at i:2853251 original size:255 final size:255
Alignment explanation
Indices: 2852799--2853265 Score: 830
Period size: 255 Copynumber: 1.8 Consensus size: 255
2852789 ATCCCAGCAG
*
2852799 CAAAGCACATGTCTTATAAAAATAATTTTTTTTTTTATATAATAACATTGTTGCTTCATTGAAAT
1 CAAAGCACATGTCTTATAAAAATAATTTTTTTTTATATATAATAACATTGTTGCTTCATTGAAAT
2852864 ATAAAATTATTTTAATATTTTTTTATTGAATAGGTTCATCGTTCATGTTAGATTTATTTTAGCTT
66 ATAAAATTATTTTAATATTTTTTTATTGAATAGGTTCATCGTTCATGTTAGATTTATTTTAGCTT
*
2852929 TCCAAGAAGAAAGTTTTAACTTAGTTTCTTTTGGTAACCAAAGTTCAATCCATTACAACTTTAAG
131 TCCAAGAAGAAAGTTTTAACTTAGTTTCTGTTGGTAACCAAAGTTCAATCCATTACAACTTTAAG
2852994 TATAAAAAAATTATCAATTACTTTTATATAATAACATTGTTGTTTCATTGAAATTTAAAAT
196 TAT-AAAAAATTATCAATTACTTTTATATAATAACATTGTTGTTTCATTGAAATTTAAAAT
*
2853055 CAAAGCACATGTCTTATAAAAATAA-TTTTTTTTATATATAATAACATTGTTGTTTCATTGAAAT
1 CAAAGCACATGTCTTATAAAAATAATTTTTTTTTATATATAATAACATTGTTGCTTCATTGAAAT
*
2853119 TTAAAATTATTTTAATATTTTTTTATTGAATAGGTTCATCGTTCATGTTAGATTTATTTTAGCTT
66 ATAAAATTATTTTAATATTTTTTTATTGAATAGGTTCATCGTTCATGTTAGATTTATTTTAGCTT
* * * *
2853184 TCCAAGATGAAAGTTTTAATTTGGTTTCTGTTGGTAACCAAAGTTCAATCCATGT-TAACTTTAA
131 TCCAAGAAGAAAGTTTTAACTTAGTTTCTGTTGGTAACCAAAGTTCAATCCAT-TACAACTTTAA
2853248 GTATAAAAAATTATCAAT
195 GTATAAAAAATTATCAAT
2853266 AATTAAAAAA
Statistics
Matches: 202, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
254 14 0.07
255 162 0.80
256 26 0.13
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.45
Consensus pattern (255 bp):
CAAAGCACATGTCTTATAAAAATAATTTTTTTTTATATATAATAACATTGTTGCTTCATTGAAAT
ATAAAATTATTTTAATATTTTTTTATTGAATAGGTTCATCGTTCATGTTAGATTTATTTTAGCTT
TCCAAGAAGAAAGTTTTAACTTAGTTTCTGTTGGTAACCAAAGTTCAATCCATTACAACTTTAAG
TATAAAAAATTATCAATTACTTTTATATAATAACATTGTTGTTTCATTGAAATTTAAAAT
Found at i:2853317 original size:11 final size:11
Alignment explanation
Indices: 2853275--2853341 Score: 57
Period size: 11 Copynumber: 6.1 Consensus size: 11
2853265 TAATTAAAAA
* *
2853275 ATTAAATTATC
1 ATTAATTTATT
* *
2853286 ATTTATTTACT
1 ATTAATTTATT
2853297 ATT-ATGTTATT
1 ATTAAT-TTATT
2853308 ATTAATTTATT
1 ATTAATTTATT
*
2853319 ATTAAATTATT
1 ATTAATTTATT
2853330 AATT-ATTTATT
1 -ATTAATTTATT
2853341 A
1 A
2853342 CTAAATTATC
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
10 3 0.07
11 38 0.83
12 5 0.11
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.58
Consensus pattern (11 bp):
ATTAATTTATT
Found at i:2853328 original size:22 final size:22
Alignment explanation
Indices: 2853275--2853424 Score: 83
Period size: 22 Copynumber: 6.9 Consensus size: 22
2853265 TAATTAAAAA
* * *
2853275 ATTAAATTATCATTTATTTACT
1 ATTAAATTATTATTAATTTATT
**
2853297 ATTATGTTATTATTAATTTATT
1 ATTAAATTATTATTAATTTATT
2853319 ATTAAATTATTAATT-ATTTATT
1 ATTAAATTATT-ATTAATTTATT
* * * * *
2853341 ACTAAATTATCAATGATTTACT
1 ATTAAATTATTATTAATTTATT
*
2853363 ACTAAATTATTGATT--TTT-TT
1 ATTAAATTATT-ATTAATTTATT
* * * * *
2853383 ACTAAGTTACTAATAATTCATT
1 ATTAAATTATTATTAATTTATT
* * *
2853405 ATAAAATTATAACTAATTTA
1 ATTAAATTATTATTAATTTA
2853425 CTAGTAATTT
Statistics
Matches: 97, Mismatches: 25, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
19 2 0.02
20 10 0.10
21 7 0.07
22 73 0.75
23 5 0.05
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (22 bp):
ATTAAATTATTATTAATTTATT
Found at i:2853360 original size:44 final size:44
Alignment explanation
Indices: 2853312--2853466 Score: 140
Period size: 44 Copynumber: 3.6 Consensus size: 44
2853302 GTTATTATTA
*
2853312 ATTTATTATTAAATTATTAATTATTTATTACTAAATTATCAATG
1 ATTTATTATAAAATTATTAATTATTTATTACTAAATTATCAATG
* * * *
2853356 ATTTACTACT-AAATTATTGATT-TTT-TTACTAAGTTA-CTAATA
1 ATTTATTA-TAAAATTATTAATTATTTATTACTAAATTATC-AATG
* * * * *
2853398 ATTCATTATAAAATTA-TAACTAATTTACTAGTAATTTATCAATG
1 ATTTATTATAAAATTATTAA-TTATTTATTACTAAATTATCAATG
* *
2853442 ATTGAATATAAAATTATTAATTATT
1 ATTTATTATAAAATTATTAATTATT
2853467 AACTAATTTA
Statistics
Matches: 88, Mismatches: 15, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
41 4 0.05
42 26 0.30
43 6 0.07
44 47 0.53
45 5 0.06
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.48
Consensus pattern (44 bp):
ATTTATTATAAAATTATTAATTATTTATTACTAAATTATCAATG
Found at i:2853497 original size:22 final size:22
Alignment explanation
Indices: 2853479--2853557 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 22
2853469 CTAATTTATT
2853479 ACTAAATTATCACTTATTTACA
1 ACTAAATTATCACTTATTTACA
*
2853501 ATTAAATTATCA-TTGATTTACA
1 ACTAAATTATCACTT-ATTTACA
* * * * **
2853523 ATTAAGTTATCAATAATTTATT
1 ACTAAATTATCACTTATTTACA
*
2853545 ACAAAATTATCAC
1 ACTAAATTATCAC
2853558 AAATCAAATT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 2 0.04
22 43 0.93
23 1 0.02
ACGTcount: A:0.43, C:0.13, G:0.03, T:0.42
Consensus pattern (22 bp):
ACTAAATTATCACTTATTTACA
Found at i:2853821 original size:22 final size:22
Alignment explanation
Indices: 2853796--2853880 Score: 80
Period size: 22 Copynumber: 3.9 Consensus size: 22
2853786 AAACTAAAAT
*
2853796 TAATTTACTGTTAAGTTATCGC
1 TAATTTACTATTAAGTTATCGC
* **
2853818 TAATTTACTATTAATTTATCAT
1 TAATTTACTATTAAGTTATCGC
* * * **
2853840 TGATTTATTATGAAGTTATCAA
1 TAATTTACTATTAAGTTATCGC
*
2853862 TAATTAACTATTAAGTTAT
1 TAATTTACTATTAAGTTAT
2853881 TATTTATAAA
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.48
Consensus pattern (22 bp):
TAATTTACTATTAAGTTATCGC
Found at i:2854263 original size:19 final size:19
Alignment explanation
Indices: 2854241--2854278 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2854231 AAGCTATAAA
2854241 TAATTTACTACTAAATTAT
1 TAATTTACTACTAAATTAT
* *
2854260 TAATTTATTACTAATTTAT
1 TAATTTACTACTAAATTAT
2854279 AAATGATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (19 bp):
TAATTTACTACTAAATTAT
Found at i:2854486 original size:22 final size:22
Alignment explanation
Indices: 2854170--2854516 Score: 150
Period size: 22 Copynumber: 16.2 Consensus size: 22
2854160 AAAAAAAAAA
* * *
2854170 ATTAAAGATTGACAATTAAGTT
1 ATTAATGATTTACTATTAAGTT
* *
2854192 ATTATTGATTTATTATTATA-TT
1 ATTAATGATTTACTATTA-AGTT
* * * *
2854214 ATCATTGATTTACTACTAAGCT
1 ATTAATGATTTACTATTAAGTT
* * * *
2854236 ATAAATAATTTACTACTAAATT
1 ATTAATGATTTACTATTAAGTT
* * *
2854258 ATT-A--ATTTATTACTAATTT
1 ATTAATGATTTACTATTAAGTT
* *
2854277 ATAAATGATATACTATTAAGTT
1 ATTAATGATTTACTATTAAGTT
*
2854299 CTTAATGATTTA-TCATTAAGTT
1 ATTAATGATTTACT-ATTAAGTT
* * * *
2854321 GTAAATGATTTATTATTAAATT
1 ATTAATGATTTACTATTAAGTT
* * *
2854343 ATTGATAATTTACTACTAAG--
1 ATTAATGATTTACTATTAAGTT
* *
2854363 -TTAATGATTTATTATAAAAGTT
1 ATTAATGATTTACTAT-TAAGTT
* * *
2854385 A-TAATTGATTTACAACTAAATT
1 ATTAA-TGATTTACTATTAAGTT
*
2854407 ATTAGT-ACTTTACTATTATA-TT
1 ATTAATGA-TTTACTATTA-AGTT
* * * *
2854429 ATTAGTGATTTACGACTAAATT
1 ATTAATGATTTACTATTAAGTT
* *
2854451 A-TCA--ATTTATTATTAAGTT
1 ATTAATGATTTACTATTAAGTT
* *
2854470 ATCAATAATTTACTATTAA-TT
1 ATTAATGATTTACTATTAAGTT
*
2854491 ATCAATGATTTACTATTATA-TT
1 ATTAATGATTTACTATTA-AGTT
2854513 ATTA
1 ATTA
2854517 TGTATTTTTT
Statistics
Matches: 243, Mismatches: 61, Indels: 42
0.70 0.18 0.12
Matches are distributed among these distances:
19 38 0.16
20 5 0.02
21 25 0.10
22 161 0.66
23 14 0.06
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (22 bp):
ATTAATGATTTACTATTAAGTT
Found at i:2854494 original size:21 final size:21
Alignment explanation
Indices: 2854454--2854514 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 21
2854444 CTAAATTATC
*
2854454 AATTTATTATTAAGTTATCAAT
1 AATTTACTATTAA-TTATCAAT
2854476 AATTTACTATTAATTATCAAT
1 AATTTACTATTAATTATCAAT
*
2854497 GATTTACTATTATATTAT
1 AATTTACTATTA-ATTAT
2854515 TATGTATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 19 0.53
22 17 0.47
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (21 bp):
AATTTACTATTAATTATCAAT
Found at i:2854677 original size:22 final size:22
Alignment explanation
Indices: 2854652--2854831 Score: 109
Period size: 22 Copynumber: 8.3 Consensus size: 22
2854642 ACTATCTACA
*
2854652 AAATTATTACTAATTTACAATT
1 AAATTATTACTAATTTACTATT
* *
2854674 AAATTA-TCCATAATTTACTATC
1 AAATTATTAC-TAATTTACTATT
* *
2854696 AAATTATTACTGATTTA-TAAT
1 AAATTATTACTAATTTACTATT
*
2854717 AAATTATT-CATAATTTATTATT
1 AAATTATTAC-TAATTTACTATT
* * *
2854739 AAGTTATCACTAATTGACTATT
1 AAATTATTACTAATTTACTATT
* ** * *
2854761 AAGTTATTGGTGATTTACTACT
1 AAATTATTACTAATTTACTATT
* * *
2854783 AAGTTA-TATTAATTTACTCTT
1 AAATTATTACTAATTTACTATT
* * * * *
2854804 -AATTTTTAATTATTAACTACT
1 AAATTATTACTAATTTACTATT
2854825 AAATTAT
1 AAATTAT
2854832 CAATTGTTTA
Statistics
Matches: 119, Mismatches: 32, Indels: 14
0.72 0.19 0.08
Matches are distributed among these distances:
20 4 0.03
21 38 0.32
22 74 0.62
23 3 0.03
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.47
Consensus pattern (22 bp):
AAATTATTACTAATTTACTATT
Found at i:2854731 original size:65 final size:65
Alignment explanation
Indices: 2854652--2854799 Score: 149
Period size: 65 Copynumber: 2.3 Consensus size: 65
2854642 ACTATCTACA
*
2854652 AAATTATTACTAATTTACAATTAAATTATC-CATAATTTACTATCAAATTATTACTGATTTATAA
1 AAATTATTACTAATTTACAATTAAATTATCAC-TAATTGACTATCAAATTATTACTGATTTATAA
2854716 T
65 T
** * * * **
2854717 AAATTATT-CATAATTTATTATTAAGTTATCACTAATTGACTATTAAGTTATTGGTGATTTACTA
1 AAATTATTAC-TAATTTACAATTAAATTATCACTAATTGACTATCAAATTATTACTGATTTA-TA
*
2854781 CT
64 AT
* *
2854783 AAGTTA-TATTAATTTAC
1 AAATTATTACTAATTTAC
2854800 TCTTAATTTT
Statistics
Matches: 67, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
64 1 0.01
65 57 0.85
66 9 0.13
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.46
Consensus pattern (65 bp):
AAATTATTACTAATTTACAATTAAATTATCACTAATTGACTATCAAATTATTACTGATTTATAAT
Found at i:2854836 original size:22 final size:22
Alignment explanation
Indices: 2854773--2855009 Score: 84
Period size: 22 Copynumber: 11.2 Consensus size: 22
2854763 GTTATTGGTG
*
2854773 ATTTACTACTAAGTTAT--ATT
1 ATTTACTACTAAATTATCAATT
* * *
2854793 AATTTACT-CTTAATTTTTAATT
1 -ATTTACTACTAAATTATCAATT
*
2854815 ATTAACTACTAAATTATCAATT
1 ATTTACTACTAAATTATCAATT
* * * * *
2854837 GTTTAGTACTAAGTTATTATTT
1 ATTTACTACTAAATTATCAATT
* * **
2854859 ATTTACTACTAAGTTCTTTA-T
1 ATTTACTACTAAATTATCAATT
*
2854880 AATT--TACT--A-TATCAATT
1 ATTTACTACTAAATTATCAATT
* * * *
2854897 AATTACTATTAAATCA-AAACTT
1 ATTTACTACTAAATTATCAA-TT
* * *
2854919 ATTTACTATTAAATTATCACTA
1 ATTTACTACTAAATTATCAATT
* *
2854941 ATTTATTA-TAAGTTAT-AATT
1 ATTTACTACTAAATTATCAATT
* * * *
2854961 GATTTATTATTAAGTTATCAATG
1 -ATTTACTACTAAATTATCAATT
* * *
2854984 ATTAATTACTAAATTATCACTT
1 ATTTACTACTAAATTATCAATT
2855006 ATTT
1 ATTT
2855010 TTTAATGGTT
Statistics
Matches: 160, Mismatches: 42, Indels: 27
0.70 0.18 0.12
Matches are distributed among these distances:
16 3 0.02
17 5 0.03
19 7 0.04
20 8 0.05
21 35 0.22
22 98 0.61
23 4 0.03
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.49
Consensus pattern (22 bp):
ATTTACTACTAAATTATCAATT
Found at i:2855189 original size:44 final size:42
Alignment explanation
Indices: 2855121--2855222 Score: 118
Period size: 44 Copynumber: 2.4 Consensus size: 42
2855111 ACTAATTTAC
*
2855121 TACTAATTAAGTTATCAATTATTTA-TTACTAAATTATTATTCATT
1 TACT-ATTAAGTTATCAATTATTTATTTA-TAAATT-TCA-TCATT
* *
2855166 TACTATTAAGTTATC-ATTAATTTATTTATAAGTTTCATGATT
1 TACTATTAAGTTATCAATT-ATTTATTTATAAATTTCATCATT
2855208 TACTATTAAGTTATC
1 TACTATTAAGTTATC
2855223 GATAATTACT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
42 19 0.37
43 5 0.10
44 21 0.40
45 7 0.13
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (42 bp):
TACTATTAAGTTATCAATTATTTATTTATAAATTTCATCATT
Found at i:2855197 original size:22 final size:21
Alignment explanation
Indices: 2855128--2855242 Score: 83
Period size: 22 Copynumber: 5.4 Consensus size: 21
2855118 TACTACTAAT
2855128 TAAGTTATCAATTATTTATTAC
1 TAAGTTATC-ATTATTTATTAC
* * * *
2855150 TAAATTATTATTCATTTACTAT
1 TAAGTTATCATT-ATTTATTAC
2855172 TAAGTTATCATTAATTTATTTA-
1 TAAGTTATCATT-ATTTA-TTAC
* * *
2855194 TAAGTT-TCATGATTTACTAT
1 TAAGTTATCATTATTTATTAC
* *
2855214 TAAGTTATCGA-TAATTACTAC
1 TAAGTTATC-ATTATTTATTAC
2855235 TAAGTTAT
1 TAAGTTAT
2855243 ACCGATTACT
Statistics
Matches: 75, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
19 2 0.03
20 11 0.15
21 24 0.32
22 36 0.48
23 2 0.03
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.50
Consensus pattern (21 bp):
TAAGTTATCATTATTTATTAC
Found at i:2855233 original size:21 final size:20
Alignment explanation
Indices: 2855165--2855242 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 20
2855155 TATTATTCAT
2855165 TTACTATTAAGTTATCATTAA
1 TTACTATTAAGTTATCA-TAA
* *
2855186 TTTA-TTTATAAGTT-TCATGAT
1 -TTACTAT-TAAGTTATCAT-AA
2855207 TTACTATTAAGTTATCGATAA
1 TTACTATTAAGTTATC-ATAA
*
2855228 TTACTACTAAGTTAT
1 TTACTATTAAGTTAT
2855243 ACCGATTACT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
20 10 0.22
21 25 0.54
22 11 0.24
ACGTcount: A:0.35, C:0.09, G:0.08, T:0.49
Consensus pattern (20 bp):
TTACTATTAAGTTATCATAA
Found at i:2856179 original size:20 final size:19
Alignment explanation
Indices: 2856135--2856175 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
2856125 AAAATATTTA
2856135 TAATTATTAAAAAAACTTG
1 TAATTATTAAAAAAACTTG
* *
2856154 TAATTATTTAAGAAACTTG
1 TAATTATTAAAAAAACTTG
2856173 TAA
1 TAA
2856176 ATTACATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (19 bp):
TAATTATTAAAAAAACTTG
Found at i:2857254 original size:26 final size:26
Alignment explanation
Indices: 2857217--2857281 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
2857207 TAGTTGATCA
* *
2857217 ACAA-TCACAATACACAATCATTATC
1 ACAATTCAAAATACACAATAATTATC
* *
2857242 ACAATTCAAAATACGCAATAATTTTC
1 ACAATTCAAAATACACAATAATTATC
*
2857268 ACATTTCACAAATA
1 ACAATTCA-AAATA
2857282 TCATCTCATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
25 4 0.12
26 24 0.73
27 5 0.15
ACGTcount: A:0.48, C:0.23, G:0.02, T:0.28
Consensus pattern (26 bp):
ACAATTCAAAATACACAATAATTATC
Found at i:2858756 original size:12 final size:12
Alignment explanation
Indices: 2858735--2858764 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2858725 CAAACATATA
2858735 TAAT-ATTATGT
1 TAATAATTATGT
2858746 TAATAATTATGT
1 TAATAATTATGT
2858758 TAATAAT
1 TAATAAT
2858765 ACAAGATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (12 bp):
TAATAATTATGT
Found at i:2860120 original size:21 final size:23
Alignment explanation
Indices: 2860094--2860145 Score: 90
Period size: 21 Copynumber: 2.3 Consensus size: 23
2860084 TATTCTACAA
2860094 AAAAAAAATTACTCAAC-A-AAT
1 AAAAAAAATTACTCAACAATAAT
2860115 AAAAAAAATTACTCAACAATAAT
1 AAAAAAAATTACTCAACAATAAT
2860138 AAAAAAAA
1 AAAAAAAA
2860146 CCCAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 17 0.59
22 1 0.03
23 11 0.38
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.17
Consensus pattern (23 bp):
AAAAAAAATTACTCAACAATAAT
Found at i:2860232 original size:23 final size:23
Alignment explanation
Indices: 2860206--2860255 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
2860196 TTAACCCAAC
2860206 AAAAA-CTCAACAAATATATAACA
1 AAAAACCT-AACAAATATATAACA
* *
2860229 AAAAACCTAACAAATTTATAATA
1 AAAAACCTAACAAATATATAACA
2860252 AAAA
1 AAAA
2860256 TTAAACAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.66, C:0.14, G:0.00, T:0.20
Consensus pattern (23 bp):
AAAAACCTAACAAATATATAACA
Found at i:2860272 original size:13 final size:13
Alignment explanation
Indices: 2860251--2860295 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
2860241 AATTTATAAT
2860251 AAAAA-TTAAACA
1 AAAAACTTAAACA
*
2860263 ATAAACTT-AACA
1 AAAAACTTAAACA
2860275 AAAATAC-TAAACA
1 AAAA-ACTTAAACA
2860288 AAAAACTT
1 AAAAACTT
2860296 TCAGCCGGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
12 14 0.52
13 13 0.48
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAAACTTAAACA
Found at i:2861932 original size:25 final size:25
Alignment explanation
Indices: 2861898--2861945 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
2861888 TGAAAAATCA
* *
2861898 AAATTTAAAATGATTGAAATACTTG
1 AAATTCAAAATGATTAAAATACTTG
2861923 AAATTCAAAATGATTAAAATACT
1 AAATTCAAAATGATTAAAATACT
2861946 AAATACACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.33
Consensus pattern (25 bp):
AAATTCAAAATGATTAAAATACTTG
Found at i:2862450 original size:17 final size:17
Alignment explanation
Indices: 2862417--2862451 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2862407 ATTTGAAATT
**
2862417 TTTTATTATATGTAAAA
1 TTTTATTATATAAAAAA
2862434 TTTTATTATATAAAAAA
1 TTTTATTATATAAAAAA
2862451 T
1 T
2862452 ATTAAAATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
TTTTATTATATAAAAAA
Found at i:2863182 original size:31 final size:31
Alignment explanation
Indices: 2863147--2863210 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
2863137 GAAGAATTTA
* *
2863147 ATTATGTTTTTAATGATAAAACAATCAACTC
1 ATTATATTATTAATGATAAAACAATCAACTC
* *
2863178 ATTATATTATTAATGATCAAACTATCAACTC
1 ATTATATTATTAATGATAAAACAATCAACTC
2863209 AT
1 AT
2863211 AAAACATACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.39
Consensus pattern (31 bp):
ATTATATTATTAATGATAAAACAATCAACTC
Found at i:2870139 original size:7 final size:7
Alignment explanation
Indices: 2870127--2870160 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
2870117 CACATTCAAT
2870127 AAATTTA
1 AAATTTA
2870134 AAATTTA
1 AAATTTA
2870141 AAATTTA
1 AAATTTA
*
2870148 ATATTTA
1 AAATTTA
*
2870155 TAATTT
1 AAATTT
2870161 TTTTCTGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (7 bp):
AAATTTA
Found at i:2870684 original size:20 final size:20
Alignment explanation
Indices: 2870659--2870700 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2870649 TGCCAATTCA
2870659 CCGGTCATCCCTTTGCTTTG
1 CCGGTCATCCCTTTGCTTTG
2870679 CCGGTCATCCCTTTGCTTTG
1 CCGGTCATCCCTTTGCTTTG
2870699 CC
1 CC
2870701 AGGTAGCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.05, C:0.38, G:0.19, T:0.38
Consensus pattern (20 bp):
CCGGTCATCCCTTTGCTTTG
Found at i:2872073 original size:21 final size:21
Alignment explanation
Indices: 2872038--2872087 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2872028 TGCCACTGTC
*
2872038 CTTGGTGCTCAAGCCT-TGGCT
1 CTTGGTGCTCAAGCCTGT-GCA
**
2872059 CTTGGTGCTTGAGCCTGTGCA
1 CTTGGTGCTCAAGCCTGTGCA
2872080 CTTGGTGC
1 CTTGGTGC
2872088 GCCTACCCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.08, C:0.26, G:0.32, T:0.34
Consensus pattern (21 bp):
CTTGGTGCTCAAGCCTGTGCA
Found at i:2879137 original size:2 final size:2
Alignment explanation
Indices: 2879130--2879155 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2879120 ATTGCGGTAC
2879130 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
2879156 TAGATTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2880554 original size:55 final size:54
Alignment explanation
Indices: 2880479--2880592 Score: 131
Period size: 55 Copynumber: 2.1 Consensus size: 54
2880469 TAATATATCC
* * *
2880479 AAAAAGAATCAAAGCTAAAGACAAATGA-CTTACCGTAAAGACATTCAAAAGAAA
1 AAAAAGAATCAAAGCTAAAGACAAATGATC-TACCCTAAAAACATACAAAAGAAA
* * * * *
2880533 AAAAAGGAATTAAAGTTAAAGATAAATGATCTACCCTAAAAACCTACCAAAGAAA
1 AAAAA-GAATCAAAGCTAAAGACAAATGATCTACCCTAAAAACATACAAAAGAAA
2880588 AAAAA
1 AAAAA
2880593 TACTTATGTA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
54 5 0.10
55 44 0.88
56 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.11, T:0.16
Consensus pattern (54 bp):
AAAAAGAATCAAAGCTAAAGACAAATGATCTACCCTAAAAACATACAAAAGAAA
Found at i:2880912 original size:59 final size:59
Alignment explanation
Indices: 2880809--2880955 Score: 203
Period size: 59 Copynumber: 2.5 Consensus size: 59
2880799 ATTTAAAAAG
*
2880809 ATATATATCTAAATTATTA-AAAAATAATTTTAAAAAATAGAAAGATAT-TATTTAAATT
1 ATATATATCTAAATTATTAGAAAAATAATTTTAAAAAATAAAAAGATATATATTT-AATT
* ** *
2880867 ATATATATCTAAATTATTAGAAAATTAATTTTAGGAGATAAAAAGATATATATTTAATT
1 ATATATATCTAAATTATTAGAAAAATAATTTTAAAAAATAAAAAGATATATATTTAATT
*
2880926 ATATATA--TAAATTATTAGAAAAGTAATTTT
1 ATATATATCTAAATTATTAGAAAAATAATTTT
2880956 GGATAACTAA
Statistics
Matches: 81, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
57 22 0.27
58 19 0.23
59 35 0.43
60 5 0.06
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (59 bp):
ATATATATCTAAATTATTAGAAAAATAATTTTAAAAAATAAAAAGATATATATTTAATT
Found at i:2882675 original size:28 final size:28
Alignment explanation
Indices: 2882631--2882704 Score: 107
Period size: 28 Copynumber: 2.7 Consensus size: 28
2882621 TAAGTATTAA
2882631 ATTA-ATTAATAAA-TTTATAATTCAAAT
1 ATTACATTAA-AAATTTTATAATTCAAAT
*
2882658 ATTACATTAAAAATTTTAAAATTCAAAT
1 ATTACATTAAAAATTTTATAATTCAAAT
*
2882686 ATTACATTAAATATTTTAT
1 ATTACATTAAAAATTTTAT
2882705 TTTAATTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 7 0.17
28 35 0.83
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTACATTAAAAATTTTATAATTCAAAT
Found at i:2884338 original size:17 final size:17
Alignment explanation
Indices: 2884316--2884354 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
2884306 TATTGAAGTA
2884316 TAATTAGTCGATTTTAT
1 TAATTAGTCGATTTTAT
*
2884333 TAATTAGTTGATTTTAT
1 TAATTAGTCGATTTTAT
2884350 TAATT
1 TAATT
2884355 GGTTTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.56
Consensus pattern (17 bp):
TAATTAGTCGATTTTAT
Found at i:2885755 original size:22 final size:20
Alignment explanation
Indices: 2885730--2885773 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
2885720 AGTTGCAGAG
2885730 AGTGAAGCAACAGATCCAAGAA
1 AGTGAAGC-ACA-ATCCAAGAA
* *
2885752 AGTGTATCACAATCCAAGAA
1 AGTGAAGCACAATCCAAGAA
2885772 AG
1 AG
2885774 AGAGGTTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.55
21 3 0.15
22 6 0.30
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.14
Consensus pattern (20 bp):
AGTGAAGCACAATCCAAGAA
Found at i:2887497 original size:17 final size:17
Alignment explanation
Indices: 2887456--2887505 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 17
2887446 TCAGATATAA
2887456 ATATTATAATACGTAA-
1 ATATTATAATACGTAAT
*
2887472 CTA-TATAATACGTAAT
1 ATATTATAATACGTAAT
2887488 ATATTATAATACGTAAT
1 ATATTATAATACGTAAT
2887505 A
1 A
2887506 ATGGTATCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 12 0.40
16 4 0.13
17 14 0.47
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (17 bp):
ATATTATAATACGTAAT
Found at i:2893798 original size:7 final size:6
Alignment explanation
Indices: 2893782--2893854 Score: 69
Period size: 6 Copynumber: 11.3 Consensus size: 6
2893772 CCCAATTTGG
2893782 TTTTTA TTTTGTA TTTTTA TTTTTA TTTATT- TTTTTA TTTTGTA -TTTTA
1 TTTTTA TTTT-TA TTTTTA TTTTTA TTT-TTA TTTTTA TTTT-TA TTTTTA
2893831 TGTATTTA TTATTTA TTTATTA TT
1 T-T-TTTA TT-TTTA TTT-TTA TT
2893855 ACTATGTATT
Statistics
Matches: 59, Mismatches: 0, Indels: 15
0.80 0.00 0.20
Matches are distributed among these distances:
5 4 0.07
6 26 0.44
7 24 0.41
8 5 0.08
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:2893812 original size:4 final size:4
Alignment explanation
Indices: 2893803--2894004 Score: 60
Period size: 4 Copynumber: 49.5 Consensus size: 4
2893793 TATTTTTATT
* * *
2893803 TTTA TTTA TTTT TTTA TTT- TGTA TTTTA TGTA TTTA -TTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA
* * * * * *
2893850 -TTA TTACTA TGTA TTAA TATA TGTA TATC TTTA TTTA TTTA TTT- TTT-
1 TTTA TT--TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * * ** *
2893897 TTCTG TTAATA TCTA TATA TGTA TTTTA TTTA TCTA GCTA TATA TTTA
1 TT-TA TT--TA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA
* * *
2893945 -TTA TTATAA TTTA TTTA -TTA TTTT TTTA TTTA TCTTG TAATA TTT-
1 TTTA TT-T-A TTTA TTTA TTTA TTTA TTTA TTTA T-TTA T-TTA TTTA
2893990 TTTA TTTA TCTTA TT
1 TTTA TTTA T-TTA TT
2894005 ATTATTTTTA
Statistics
Matches: 147, Mismatches: 34, Indels: 34
0.68 0.16 0.16
Matches are distributed among these distances:
3 22 0.15
4 98 0.67
5 19 0.13
6 8 0.05
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:2893818 original size:31 final size:31
Alignment explanation
Indices: 2893782--2893851 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
2893772 CCCAATTTGG
2893782 TTTTTATTTTGTATTTTTAT-T-TTTATTTATT
1 TTTTTATTTTGTA-TTTTATGTATTTA-TTATT
2893813 TTTTTATTTTGTATTTTATGTATTTATTATT
1 TTTTTATTTTGTATTTTATGTATTTATTATT
*
2893844 TATTTATT
1 TTTTTATT
2893852 ATTACTATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
30 6 0.17
31 26 0.72
32 4 0.11
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (31 bp):
TTTTTATTTTGTATTTTATGTATTTATTATT
Found at i:2893973 original size:48 final size:44
Alignment explanation
Indices: 2893920--2894013 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 44
2893910 TATATATGTA
2893920 TTTTATTTATCTAGCTATATATTTATTATTATAAT-TTATTTATTATTT
1 TTTTATTTATCTAG-TA-ATATTTATTATT-T-ATCTTA-TTATTATTT
* *
2893968 TTTTATTTATCTTGTAATATTTTTTATTTATCTTATTATTATTT
1 TTTTATTTATCTAGTAATATTTATTATTTATCTTATTATTATTT
2894012 TT
1 TT
2894014 AATTATCTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
44 13 0.30
45 4 0.09
46 11 0.26
47 2 0.05
48 13 0.30
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (44 bp):
TTTTATTTATCTAGTAATATTTATTATTTATCTTATTATTATTT
Found at i:2893992 original size:21 final size:21
Alignment explanation
Indices: 2893953--2894033 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
2893943 TATTATTATA
*
2893953 ATTTAT-TTATTAT-TTTTTT
1 ATTTATCTTGTTATATTTTTT
*
2893972 ATTTATCTTGTAATATTTTTT
1 ATTTATCTTGTTATATTTTTT
*
2893993 ATTTATCTTATTAT-TATTTTT
1 ATTTATCTTGTTATAT-TTTTT
*
2894014 AATTATC-TGTTATATTTTTT
1 ATTTATCTTGTTATATTTTTT
2894034 TTCTTTTTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
19 6 0.12
20 16 0.31
21 30 0.58
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.70
Consensus pattern (21 bp):
ATTTATCTTGTTATATTTTTT
Found at i:2894029 original size:41 final size:40
Alignment explanation
Indices: 2893953--2894033 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 40
2893943 TATTATTATA
*
2893953 ATTTATTTATTATTTTTTTATTTATCTTGTAATATTTTTT
1 ATTTATTTATTATTTTTTTAATTATCTTGTAATATTTTTT
*
2893993 ATTTATCTTATTATTATTTTTAATTATC-TGTTATATTTTTT
1 ATTTAT-TTATTATT-TTTTTAATTATCTTGTAATATTTTTT
2894034 TTCTTTTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 6 0.16
41 20 0.54
42 11 0.30
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.70
Consensus pattern (40 bp):
ATTTATTTATTATTTTTTTAATTATCTTGTAATATTTTTT
Found at i:2894062 original size:20 final size:20
Alignment explanation
Indices: 2894037--2894083 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2894027 ATTTTTTTTC
2894037 TTTTTTCGTTTATCTA-ATTT
1 TTTTTTCGTTTATC-AGATTT
2894057 TTTTTTCGTTTATCAGATTT
1 TTTTTTCGTTTATCAGATTT
2894077 TTTTTTC
1 TTTTTTC
2894084 TTTTTTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.13, C:0.11, G:0.06, T:0.70
Consensus pattern (20 bp):
TTTTTTCGTTTATCAGATTT
Found at i:2894410 original size:11 final size:11
Alignment explanation
Indices: 2894396--2894432 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
2894386 GGCGAATTTT
*
2894396 TTTTTTGAAAA
1 TTTTTGGAAAA
2894407 TTTTTGGAAAA
1 TTTTTGGAAAA
2894418 TTTTTGGAAAA
1 TTTTTGGAAAA
2894429 TTTT
1 TTTT
2894433 CAGATTCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (11 bp):
TTTTTGGAAAA
Found at i:2895008 original size:11 final size:10
Alignment explanation
Indices: 2894984--2895042 Score: 50
Period size: 11 Copynumber: 5.7 Consensus size: 10
2894974 TTCTTTTATC
2894984 TTTATTTTATT
1 TTTATTTT-TT
2894995 TTTATTTTTGT
1 TTTATTTTT-T
2895006 TTTATTTTTT
1 TTTATTTTTT
*
2895016 ATTT-TTTTAAT
1 -TTTATTTT-TT
*
2895027 TTT-TTTATT
1 TTTATTTTTT
2895036 TTTATTT
1 TTTATTT
2895043 CTCACTTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
9 4 0.10
10 15 0.37
11 22 0.54
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (10 bp):
TTTATTTTTT
Found at i:2895016 original size:18 final size:18
Alignment explanation
Indices: 2894977--2895074 Score: 80
Period size: 17 Copynumber: 5.5 Consensus size: 18
2894967 TTTAATGTTC
*
2894977 TTTTATCTTTATTTTA-T
1 TTTTATTTTTATTTTATT
*
2894994 TTTTATTTTTGTTTTATT
1 TTTTATTTTTATTTTATT
*
2895012 TTTTA-TTTT-TTTAATTT
1 TTTTATTTTTATTTTA-TT
*
2895029 TTTTATTTTTATTTCTCA-C
1 TTTTATTTTTATTT-T-ATT
*
2895048 TTTTA-TTTTGTTTTATT
1 TTTTATTTTTATTTTATT
2895065 ATTTTATTTT
1 -TTTTATTTT
2895075 CTTTAAATAA
Statistics
Matches: 65, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
16 5 0.08
17 26 0.40
18 22 0.34
19 11 0.17
21 1 0.02
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTATTTTTATTTTATT
Found at i:2895028 original size:9 final size:8
Alignment explanation
Indices: 2894988--2895038 Score: 61
Period size: 8 Copynumber: 6.2 Consensus size: 8
2894978 TTTATCTTTA
2894988 TTTTATTT
1 TTTTATTT
2894996 TTATT-TTT
1 TT-TTATTT
2895004 GTTTTA-TT
1 -TTTTATTT
2895012 TTTTATTT
1 TTTTATTT
2895020 TTTTAATTT
1 TTTT-ATTT
2895029 TTTTATTT
1 TTTTATTT
2895037 TT
1 TT
2895039 ATTTCTCACT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
7 5 0.13
8 21 0.55
9 12 0.32
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.84
Consensus pattern (8 bp):
TTTTATTT
Found at i:2895264 original size:59 final size:59
Alignment explanation
Indices: 2895090--2895426 Score: 359
Period size: 59 Copynumber: 5.7 Consensus size: 59
2895080 AATAAAATCC
* ** *
2895090 AAAAAATATTTTTTGGAAAAAGTTGAAAGTATCAATTTTTTTTTAAA-TAAAA-TTTC-
1 AAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAATTTTCA
*** * * *
2895146 AAAAAA-GGGTTTGAGG-AAAATTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTTCA
1 AAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTTG-AAATTAAAATTTTCA
2895205 AAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAATTTTCAA
1 AAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAATTTTC-A
* * * * * *
2895265 AAAAAAAAGTTTTTGAGG-AAAAGTTGAAATTATCAATTTTCCTTGAAAATCAAAGTTTCC
1 AAAAAATA-TTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAATTTTCA
* *
2895325 AAAAAATATTTTT-GGAGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTT-A
1 AAAAAATATTTTTGGGA-AAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAATTTTCA
* * *
2895383 AAAGAATATTTTT-TGAGAAAAGTTGAAAGTATCAATTTTTCTTG
1 AAAAAATATTTTTGGGA-AAAAGTTGAAAGTATCAATTTTCCTTG
2895427 CACAAGAATA
Statistics
Matches: 235, Mismatches: 34, Indels: 22
0.81 0.12 0.08
Matches are distributed among these distances:
55 26 0.11
56 11 0.05
57 5 0.02
58 44 0.19
59 59 0.25
60 45 0.19
61 43 0.18
62 2 0.01
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (59 bp):
AAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAATTTTCA
Found at i:2895362 original size:27 final size:27
Alignment explanation
Indices: 2895332--2895423 Score: 71
Period size: 27 Copynumber: 3.3 Consensus size: 27
2895322 TCCAAAAAAT
*
2895332 ATTTTTGGAGAAAAGTTGAAAGTATCA
1 ATTTTTCGAGAAAAGTTGAAAGTATCA
* * *
2895359 ATTTTCCTCGAAATTAAAGTTTTAAAAGAAT--
1 ATTTT--TCGAGA--AAAG--TTGAAAGTATCA
*
2895390 ATTTTTTGAGAAAAGTTGAAAGTATCA
1 ATTTTTCGAGAAAAGTTGAAAGTATCA
2895417 ATTTTTC
1 ATTTTTC
2895424 TTGCACAAGA
Statistics
Matches: 48, Mismatches: 9, Indels: 16
0.66 0.12 0.22
Matches are distributed among these distances:
25 8 0.17
27 15 0.31
29 8 0.17
31 9 0.19
33 8 0.17
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (27 bp):
ATTTTTCGAGAAAAGTTGAAAGTATCA
Found at i:2895378 original size:58 final size:58
Alignment explanation
Indices: 2895087--2895426 Score: 354
Period size: 58 Copynumber: 5.8 Consensus size: 58
2895077 TTAAATAAAA
** * *
2895087 TCCAAAAAATATTTTTTGGA-AAAAGTTGAAAGTATCAATTTTTTTTTAAA-TAAAATT
1 TCCAAAAAATA-TTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAGTT
*** * *
2895144 T-CAAAAAA-GGGTTT-GAGGAAAATTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTT
1 TCCAAAAAATATTTTTGGA-GAAAAGTTGAAAGTATCAATTTTCCTTG-AAATTAAAG-TT
* *
2895202 TCAAAAAAATATTTTTGG-GAAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAATTT
1 TCCAAAAAATATTTTTGGAG-AAAAGTTGAAAGTATCAATTTTCCTTGAAATT-AAAGTT
* * * *
2895261 TCAAAAAAAAAAGTTTTT-GAGGAAAAGTTGAAATTATCAATTTTCCTTGAAAATCAAAGTT
1 TC-CAAAAAATA-TTTTTGGA-GAAAAGTTGAAAGTATCAATTTTCCTTG-AAATTAAAGTT
*
2895322 TCCAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTT
1 TCCAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAGTT
* * *
2895380 T-TAAAAGAATATTTTTTGAGAAAAGTTGAAAGTATCAATTTTTCTTG
1 TCCAAAA-AATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTTG
2895427 CACAAGAATA
Statistics
Matches: 237, Mismatches: 29, Indels: 33
0.79 0.10 0.11
Matches are distributed among these distances:
53 2 0.01
54 3 0.01
55 23 0.10
56 10 0.04
57 8 0.03
58 51 0.22
59 46 0.19
60 50 0.21
61 39 0.16
62 5 0.02
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (58 bp):
TCCAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAGTT
Found at i:2899693 original size:21 final size:22
Alignment explanation
Indices: 2899637--2899706 Score: 61
Period size: 24 Copynumber: 3.0 Consensus size: 22
2899627 ATAGTTATTG
**
2899637 ATAAATATTTATTTTAATAAATTT
1 ATAAATATTT-TGATAATAAA-TT
2899661 ATAAATGATTTTGATAATAAATT
1 ATAAAT-ATTTTGATAATAAATT
* *
2899684 ATTAAT-TTTTTATAATATAATT
1 ATAAATATTTTGATAATA-AATT
2899706 A
1 A
2899707 CATGTCATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 10 0.25
22 5 0.12
23 7 0.17
24 14 0.35
25 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (22 bp):
ATAAATATTTTGATAATAAATT
Found at i:2900802 original size:13 final size:13
Alignment explanation
Indices: 2900780--2900817 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
2900770 CCGATTCAAT
2900780 AAAATCTAAAATTA
1 AAAAT-TAAAATTA
2900794 AAAATTAAAATTA
1 AAAATTAAAATTA
2900807 ATAAATTAAAA
1 A-AAATTAAAA
2900818 GTTTTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAATTAAAATTA
Found at i:2901057 original size:14 final size:12
Alignment explanation
Indices: 2901023--2901065 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
2901013 ACCTATTAAT
*
2901023 TTAAATTTTTTA
1 TTAAAATTTTTA
2901035 TTAAAATTTTTA
1 TTAAAATTTTTA
2901047 TTAAATCATTTTTA
1 TTAAA--ATTTTTA
*
2901061 ATAAA
1 TTAAA
2901066 GAATTTTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 16 0.59
14 11 0.41
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (12 bp):
TTAAAATTTTTA
Found at i:2901198 original size:21 final size:21
Alignment explanation
Indices: 2901174--2901229 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
2901164 GATGAATATG
2901174 TATTT-TAATAAATTAATTAAT
1 TATTTATAATAAA-TAATTAAT
*
2901195 TATTTTATAATAAATAATTCAT
1 TA-TTTATAATAAATAATTAAT
*
2901217 TTTTTATAATAAA
1 TATTTATAATAAA
2901230 ACCATGTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 13 0.42
22 11 0.35
23 7 0.23
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTTATAATAAATAATTAAT
Found at i:2902080 original size:21 final size:21
Alignment explanation
Indices: 2902054--2902125 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 21
2902044 AGAAAATTTC
2902054 AAAAAAATTTTAAAAGTTCC-
1 AAAAAAATTTTAAAAGTTCCA
**
2902074 AAAAAAATTCTTAAAAAGTTTTA
1 AAAAAAATT-TT-AAAAGTTCCA
**
2902097 AAATAATTTTTTAAAA-TTCCA
1 AAA-AAAATTTTAAAAGTTCCA
*
2902118 AAATAAAT
1 AAAAAAAT
2902126 AAATATTTAT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
20 11 0.28
21 8 0.21
22 11 0.28
23 5 0.13
24 4 0.10
ACGTcount: A:0.56, C:0.07, G:0.03, T:0.35
Consensus pattern (21 bp):
AAAAAAATTTTAAAAGTTCCA
Found at i:2902090 original size:22 final size:20
Alignment explanation
Indices: 2902053--2902125 Score: 67
Period size: 22 Copynumber: 3.5 Consensus size: 20
2902043 AAGAAAATTT
2902053 CAAAAAAATTTTAAAAGTTC
1 CAAAAAAATTTTAAAAGTTC
*
2902073 CAAAAAAATTCTTAAAAAGTTT
1 CAAAAAAATT-TT-AAAAGTTC
* *
2902095 TAAAATAATTTTTTAAAA-TTC
1 CAAAA-AA-ATTTTAAAAGTTC
2902116 CAAAATAAAT
1 CAAAA-AAAT
2902126 AAATATTTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
20 11 0.26
21 11 0.26
22 15 0.35
23 4 0.09
24 2 0.05
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
CAAAAAAATTTTAAAAGTTC
Found at i:2902158 original size:19 final size:18
Alignment explanation
Indices: 2902136--2902181 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
2902126 AAATATTTAT
*
2902136 AAAAATTATAAAAAGATTC
1 AAAAAATATAAAAAG-TTC
*
2902155 AAAAAATCTAAAAAGTTC
1 AAAAAATATAAAAAGTTC
2902173 AAAAAATAT
1 AAAAAATAT
2902182 CCAAAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.65, C:0.07, G:0.04, T:0.24
Consensus pattern (18 bp):
AAAAAATATAAAAAGTTC
Found at i:2902197 original size:20 final size:19
Alignment explanation
Indices: 2902145--2902188 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2902135 TAAAAATTAT
*
2902145 AAAAAGATTC-AAAAAATCT
1 AAAAAG-TTCAAAAAAATCC
2902164 AAAAAGTTCAAAAAATATCC
1 AAAAAGTTCAAAAAA-ATCC
2902184 AAAAA
1 AAAAA
2902189 TTTGAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 11 0.50
20 8 0.36
ACGTcount: A:0.66, C:0.11, G:0.05, T:0.18
Consensus pattern (19 bp):
AAAAAGTTCAAAAAAATCC
Found at i:2902402 original size:21 final size:21
Alignment explanation
Indices: 2902363--2902418 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
2902353 AACTTTTTTG
*
2902363 AAATATTTTAAAAAA-TTAT-A
1 AAATA-TTAAAAAAATTTATGA
2902383 AAATATTGAAAAAAATTTATGA
1 AAATATT-AAAAAAATTTATGA
*
2902405 ACA-ATTAAAAAAAT
1 AAATATTAAAAAAAT
2902419 ACAAAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 2 0.06
20 19 0.61
21 7 0.23
22 3 0.10
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (21 bp):
AAATATTAAAAAAATTTATGA
Found at i:2902531 original size:17 final size:18
Alignment explanation
Indices: 2902502--2902535 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2902492 GATTTTTTAA
2902502 AATTTTCATAAAATTTTT
1 AATTTTCATAAAATTTTT
2902520 AATTTT-ATAAAATTTT
1 AATTTTCATAAAATTTT
2902536 AAAATGTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTTTCATAAAATTTTT
Found at i:2902731 original size:21 final size:21
Alignment explanation
Indices: 2902694--2902749 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
2902684 TTTAATTTTT
* * *
2902694 ATTTTAGATATTCTTTTGAAT
1 ATTTTAGATTTTTTTTTGAAA
* *
2902715 TTTTTGGATTTTTTTTTGAAA
1 ATTTTAGATTTTTTTTTGAAA
2902736 ATTTTAGATTTTTT
1 ATTTTAGATTTTTT
2902750 ATTTTTTATA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.23, C:0.02, G:0.11, T:0.64
Consensus pattern (21 bp):
ATTTTAGATTTTTTTTTGAAA
Found at i:2902790 original size:24 final size:23
Alignment explanation
Indices: 2902734--2902791 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 23
2902724 TTTTTTTTGA
**
2902734 AAATTTTAGATTTTTTATTTTTT
1 AAATTTTTTATTTTTTATTTTTT
*
2902757 ATAAGCTTTTTATTTTTATATTTTTT
1 A-AA-TTTTTTATTTTT-TATTTTTT
2902783 AAATTTTTT
1 AAATTTTTT
2902792 CAAAATTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
23 1 0.04
24 7 0.25
25 11 0.39
26 9 0.32
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (23 bp):
AAATTTTTTATTTTTTATTTTTT
Found at i:2903452 original size:31 final size:30
Alignment explanation
Indices: 2903414--2903474 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
2903404 ATGATACATA
2903414 ATTTGAAAGA-TTAAGGTACAAATTATATATT
1 ATTTGAAA-ATTTAA-GTACAAATTATATATT
* *
2903445 ATTTGAAAATTTTAGTGCAAATTATATATT
1 ATTTGAAAATTTAAGTACAAATTATATATT
2903475 TTATTTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (30 bp):
ATTTGAAAATTTAAGTACAAATTATATATT
Found at i:2904287 original size:11 final size:11
Alignment explanation
Indices: 2904271--2904303 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2904261 TCTATTTAAA
2904271 TATATTAAAAT
1 TATATTAAAAT
2904282 TATATTAAAAT
1 TATATTAAAAT
*
2904293 AATA-TAAAAT
1 TATATTAAAAT
2904303 T
1 T
2904304 TTAAATTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TATATTAAAAT
Done.