Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000267.1 Hibiscus syriacus cultivar Beakdansim tig00000490_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 126078
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:1360 original size:14 final size:14
Alignment explanation
Indices: 1341--1367 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1331 TTTAGTCCAT
1341 TATGTATGTGTATA
1 TATGTATGTGTATA
1355 TATGTATGTGTAT
1 TATGTATGTGTAT
1368 TATTTAATTT
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:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (14 bp):
TATGTATGTGTATA
Found at i:4332 original size:18 final size:18
Alignment explanation
Indices: 4309--4343 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
4299 ACATTCCCTC
4309 TCTTTGAGACCTTGAAAT
1 TCTTTGAGACCTTGAAAT
4327 TCTTTGAGACCTTGAAA
1 TCTTTGAGACCTTGAAA
4344 CATTTTTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (18 bp):
TCTTTGAGACCTTGAAAT
Found at i:4978 original size:22 final size:24
Alignment explanation
Indices: 4952--5044 Score: 71
Period size: 22 Copynumber: 4.2 Consensus size: 24
4942 GTCCAAAGAT
*
4952 AAAATAAAAGTG-AAGAAA-AAAG
1 AAAATAAAAGAGAAAGAAACAAAG
*
4974 AAAATCAAAGAGAAAGAAACAAAG
1 AAAATAAAAGAGAAAGAAACAAAG
4998 AGAAA-AACAAGCAGAAAG-AA-AAAG
1 A-AAATAA-AAG-AGAAAGAAACAAAG
5022 --AA-AAAAGA-AAA-AAACAAAG
1 AAAATAAAAGAGAAAGAAACAAAG
5041 AAAA
1 AAAA
5045 AAGAGGACAA
Statistics
Matches: 59, Mismatches: 3, Indels: 19
0.73 0.04 0.23
Matches are distributed among these distances:
18 5 0.08
19 5 0.08
20 3 0.05
21 6 0.10
22 10 0.17
23 6 0.10
24 10 0.17
25 8 0.14
26 6 0.10
ACGTcount: A:0.75, C:0.05, G:0.16, T:0.03
Consensus pattern (24 bp):
AAAATAAAAGAGAAAGAAACAAAG
Found at i:4989 original size:16 final size:14
Alignment explanation
Indices: 4979--5041 Score: 51
Period size: 14 Copynumber: 4.4 Consensus size: 14
4969 AAAAGAAAAT
4979 CAAAGAGAAAGAAA
1 CAAAGAGAAAGAAA
*
4993 CAAAGAGAAAAACAA
1 CAAAGAGAAAGA-AA
*
5008 GCAGAAAGAAAAAGAAA
1 -C--AAAGAGAAAGAAA
5025 -AAAGA-AAA-AAA
1 CAAAGAGAAAGAAA
5036 CAAAGA
1 CAAAGA
5042 AAAAAGAGGA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
11 3 0.07
12 8 0.20
13 5 0.12
14 11 0.27
15 2 0.05
16 1 0.02
17 2 0.05
18 9 0.22
ACGTcount: A:0.75, C:0.08, G:0.17, T:0.00
Consensus pattern (14 bp):
CAAAGAGAAAGAAA
Found at i:5048 original size:32 final size:32
Alignment explanation
Indices: 4980--5048 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
4970 AAAGAAAATC
* * * *
4980 AAAGAGAAAGAAACAAAGAGAAAAACAAGCAG
1 AAAGAAAAAGAAACAAAGAAAAAAACAAGAAA
5012 AAAGAAAAAGAAA-AAAGAAAAAAACAAAGAAA
1 AAAGAAAAAGAAACAAAGAAAAAAAC-AAGAAA
5044 AAAGA
1 AAAGA
5049 GGACAAAGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 11 0.34
32 21 0.66
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (32 bp):
AAAGAAAAAGAAACAAAGAAAAAAACAAGAAA
Found at i:6258 original size:4 final size:4
Alignment explanation
Indices: 6249--8774 Score: 3868
Period size: 4 Copynumber: 634.0 Consensus size: 4
6239 ATACATCAAC
*
6249 ACAT ACAT ACAT -CAAC ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT AC-AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
6297 ACAT ACAT --AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
6343 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * *
6391 ACAT ACAT GCAT ATAT GCAT ACAT GCAT GCAT GCAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
6439 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * * * * *
6487 ACAC ACAT GCAT ACAT GCAT GCAT GCAC ACAT GCAT GCAT GCAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * * * * * *
6535 GCAT GCAT GCAC ACAT GCAT GCAT GCAT ACAT GCAC ACAT GCAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * * * *
6583 ACAT ACAT GCAC ACAT ACAT ACAC ACAT GCAT ACAT GCAT GCAT GCAC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * * * * * *
6631 ACAT GCAT GCAT GCAT ACAT GCAT GCAT GCAC ACAT GCAT GCAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * * * * *
6679 GCAT GCAC ACAT GCAT GCAT GCAT ACAT GCAC ACAT GCAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * *
6727 ACAT GCAC ACAT ACAT ACAT ACAT ACAT GCAT ACAT ACAT ACAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
6775 ACAT GCAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
6823 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
6871 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT GCAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * *
6919 ACAT GCAT GCAT GCAT ACAT ACAT GCAT GCAT ACAT ACAT ACAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
6967 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
7015 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
7063 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
7111 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT GCAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * *
7159 GCAT ACAT GCAT ACAT GCAT GCAT GCAT GCAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * *
7207 ACAT GCAT GCAT ACAT ACAT ACAT GCAT ACAT GCAT ACAT ACAT --AT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * *
7253 ACAT GCAT ACAT GCAT ACAT ACAT ACAT GCAT ACAT ACAT ACAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * *
7301 ACAT GCAT ACAT GCAT ACGT ACAT ACAT ACAT ACGT ACAT ACAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * *
7349 ACAT ACAT ACGT ACAT ACAT GCAT ACAT ACAT ACAT GCAT ACAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
7397 ACAT ACAT ACAT ACAT ACAT ACAT GCAT GCAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * *
7445 ACAT GCAT ACAT GCAT ACAT GCAT ACAT ACAT ACAT GCAT ACAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * *
7493 ACAT GCAT ACAT GCAT GCAT GCAT GCAT ACAT ACAT ACAT ACAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * *
7541 GCAT GCAT ACAT ACAT GCAT ACAT ACAT ACAT ACAT ACAT GCAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * *
7589 ACAT ACAT ACAT ACAT ACAT ACAT GCAT ACAT GCAT CCAT ACAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * * *
7637 GCAT GCAT ACAT GCAT GCAT GCAT ACAT ACAT ACAT GCAT GCAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * *
7685 GCAT ACAT GCAT ACAT ACAT GCAT ACAT GCAT ACAT GCAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
7733 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
7781 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
7829 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
7877 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
7925 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
7973 ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8019 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8067 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8115 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8163 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8211 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8259 AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8305 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8353 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT --AT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8399 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8447 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8495 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8543 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8591 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8639 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8687 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8735 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8775 GTTAAATGAG
Statistics
Matches: 2347, Mismatches: 163, Indels: 24
0.93 0.06 0.01
Matches are distributed among these distances:
2 10 0.00
3 1 0.00
4 2335 0.99
5 1 0.00
ACGTcount: A:0.46, C:0.25, G:0.04, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:9122 original size:37 final size:38
Alignment explanation
Indices: 9081--9211 Score: 99
Period size: 37 Copynumber: 3.5 Consensus size: 38
9071 CTTTGATGTT
*
9081 GTTTCTATCGAAACA-AAATGTCGTCTCGCTAGAGACA
1 GTTTCTATCGAAAAACAAATGTCGTCTCGCTAGAGACA
* * * * *
9118 GTTTCTTTTGAAAAACAAATTTTGTCTCGCTTGAGACAA
1 GTTTCTATCGAAAAACAAATGTCGTCTCGCTAGAGAC-A
* * * * *
9157 TTTTCTA--AAAAAACAAACGTTGTCTCGCTTGAGACA
1 GTTTCTATCGAAAAACAAATGTCGTCTCGCTAGAGACA
* * *
9193 ATTTCTCT-AAAAAACAAAT
1 GTTTCTATCGAAAAACAAAT
9212 TCTATCTCGC
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
36 6 0.08
37 47 0.61
38 18 0.23
39 6 0.08
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (38 bp):
GTTTCTATCGAAAAACAAATGTCGTCTCGCTAGAGACA
Found at i:9147 original size:38 final size:38
Alignment explanation
Indices: 9103--9227 Score: 146
Period size: 37 Copynumber: 3.3 Consensus size: 38
9093 ACAAAATGTC
* * *
9103 GTCTCGCTAGAGACAGTTTCTTTTGAAAAACAAATTTT
1 GTCTCGCTTGAGACAATTTCTTTTAAAAAACAAATTTT
* * **
9141 GTCTCGCTTGAGACAATTT-TCTAAAAAAACAAACGTT
1 GTCTCGCTTGAGACAATTTCTTTTAAAAAACAAATTTT
* *
9178 GTCTCGCTTGAGACAATTTC-TCTAAAAAACAAATTCT
1 GTCTCGCTTGAGACAATTTCTTTTAAAAAACAAATTTT
*
9215 ATCTCGCTTGAGA
1 GTCTCGCTTGAGA
9228 TATTTTTCCG
Statistics
Matches: 72, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
37 55 0.76
38 17 0.24
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (38 bp):
GTCTCGCTTGAGACAATTTCTTTTAAAAAACAAATTTT
Found at i:9590 original size:28 final size:27
Alignment explanation
Indices: 9559--9660 Score: 100
Period size: 29 Copynumber: 3.6 Consensus size: 27
9549 ACAGTTTCTC
*
9559 TTGAAACAAATCTTTGAGTCTGTTCCTT
1 TTGAAAAAAATCTTTGAGT-TGTTCCTT
9587 TTGAATAAAAATCTTTGAGTTGTTTCC-T
1 TTGAA-AAAAATCTTTGAGTTG-TTCCTT
* *
9615 TTGAGAAGAAAATCGTTGAGTATGTTACTT
1 TTGA-AA-AAAATCTTTGAGT-TGTTCCTT
9645 TTGAAACAAAAT-TTTG
1 TTGAAA-AAAATCTTTG
9661 TCTCTCTTGA
Statistics
Matches: 63, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
28 16 0.25
29 40 0.63
30 7 0.11
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (27 bp):
TTGAAAAAAATCTTTGAGTTGTTCCTT
Found at i:9699 original size:92 final size:95
Alignment explanation
Indices: 9588--9772 Score: 277
Period size: 94 Copynumber: 2.0 Consensus size: 95
9578 CTGTTCCTTT
* * *
9588 TGAATAAAAATCTTTGAGTTGTTTCCTTTG-AGAAGAAAA-TCGTTGAGTATGTTACTTTTGAAA
1 TGAATAAAAATCTTTGAGTTGTTTCCTTTGAAAAAAAAAATTCGTTGAGTATGTTACTTTGGAAA
9651 CAAAATTTTGTCTCTCTTGAGACAATTTTG
66 CAAAATTTTGTCTCTCTTGAGACAATTTTG
* * * *
9681 TGAA-AAAAATCTTTGAGTTGTTTCTTTTGAAAAAAAAAATTCTTTGAGTCTGTTTCTTTGGAAA
1 TGAATAAAAATCTTTGAGTTGTTTCCTTTGAAAAAAAAAATTCGTTGAGTATGTTACTTTGGAAA
*
9745 CAAAATTTTGTTTCTCTTGAGACAATTT
66 CAAAATTTTGTCTCTCTTGAGACAATTT
9773 CTTTTGAGAA
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
92 24 0.29
93 11 0.13
94 47 0.57
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (95 bp):
TGAATAAAAATCTTTGAGTTGTTTCCTTTGAAAAAAAAAATTCGTTGAGTATGTTACTTTGGAAA
CAAAATTTTGTCTCTCTTGAGACAATTTTG
Found at i:9709 original size:29 final size:29
Alignment explanation
Indices: 9677--9754 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 29
9667 TTGAGACAAT
9677 TTTGTGAAAAAAATCTTTGAGT-TGTTTC
1 TTTGTGAAAAAAATCTTTGAGTCTGTTTC
9705 TTT-TGAAAAAAAAAATTCTTTGAGTCTGTTTC
1 TTTGTG---AAAAAAA-TCTTTGAGTCTGTTTC
9737 TTTG-GAAACAAAAT-TTTG
1 TTTGTGAAA-AAAATCTTTG
9755 TTTCTCTTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
27 2 0.05
28 7 0.16
29 4 0.09
30 11 0.26
31 9 0.21
32 10 0.23
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (29 bp):
TTTGTGAAAAAAATCTTTGAGTCTGTTTC
Found at i:9725 original size:31 final size:31
Alignment explanation
Indices: 9683--9749 Score: 100
Period size: 32 Copynumber: 2.2 Consensus size: 31
9673 CAATTTTGTG
*
9683 AAAAAAATCTTTGAGT-TGTTTCTTTTGAAA
1 AAAAAAATCTTTGAGTCTGTTTCTTTGGAAA
9713 AAAAAAATTCTTTGAGTCTGTTTCTTTGGAAA
1 AAAAAAA-TCTTTGAGTCTGTTTCTTTGGAAA
*
9745 CAAAA
1 AAAAA
9750 TTTTGTTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 7 0.21
31 9 0.27
32 17 0.52
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (31 bp):
AAAAAAATCTTTGAGTCTGTTTCTTTGGAAA
Found at i:10324 original size:133 final size:133
Alignment explanation
Indices: 10075--10416 Score: 377
Period size: 134 Copynumber: 2.6 Consensus size: 133
10065 AACCATCATC
* * * * *
10075 CCTAAAGATGGCCAGCCATCCTCATCATGTAGGAACCATGTCATCCCCTGACCAGACCTCTTCAT
1 CCTAAAGATGGCCAGCAATCCTCATCACGTAGGAACCGTGTCATCCCC-GACCAGAACTCCTCAT
** * * * *
10140 CACGTAGGATTCGTGTCAACCATAGATAACTAGTCATCCTCATCATGTAGGAACCGAGTTATCAC
65 CACGTAGGAGCCATATCAACCATAGATAACTAGTCATCCTCATCACGTAGGAACCGAGTTACCAC
10205 CACT-
130 C-CTA
** * *
10209 CCTAAAGATGGCCAGCTGTCCTCATCACGTAGGAATCGTGTCATCCCCGACCAGATCTCCTCATC
1 CCTAAAGATGGCCAGCAATCCTCATCACGTAGGAACCGTGTCATCCCCGACCAGAACTCCTCATC
* * **
10274 ACGTAGGAGCCATATCACCCTTAGATAA-TCAGTTTTCCTCATCACGTAGGAACCGAGTTACCAC
66 ACGTAGGAGCCATATCAACCATAGATAACT-AGTCATCCTCATCACGTAGGAACCGAGTTACCAC
10338 CCTA
130 CCTA
* * * * *
10342 CCTAAAGATGACCAAG-AACTCTTCATCACGTATGAGCAGTGTCATCCCC-AGCCAGAACTCCTC
1 CCTAAAGATGGCC-AGCAA-TCCTCATCACGTAGGAACCGTGTCATCCCCGA-CCAGAACTCCTC
*
10405 ATCAAGTAGGAG
63 ATCACGTAGGAG
10417 TCGTGTCACC
Statistics
Matches: 176, Mismatches: 27, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
132 3 0.02
133 81 0.46
134 92 0.52
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.23
Consensus pattern (133 bp):
CCTAAAGATGGCCAGCAATCCTCATCACGTAGGAACCGTGTCATCCCCGACCAGAACTCCTCATC
ACGTAGGAGCCATATCAACCATAGATAACTAGTCATCCTCATCACGTAGGAACCGAGTTACCACC
CTA
Found at i:10450 original size:134 final size:133
Alignment explanation
Indices: 10075--10455 Score: 322
Period size: 134 Copynumber: 2.8 Consensus size: 133
10065 AACCATCATC
* * * * * * *
10075 CCTAAAGATGGCCAG-CCATCCTCATCATGTAGGAACCATGTCATCCCCTGACCAGACCTCTTCA
1 CCTAAAGATGACCAGAAC-TCCTCATCACGTAGGAAGCGTGTCATCCCC-GACCAGAACTCCTCA
* ** * * * * * * * * *
10139 TCACGTAGGATTCGTGTCAACCATAGATAACTAGTCATCCTCATCATGTAGGAACCGAGTTATCA
64 TCAAGTAGGAGCCATATCACCCTTAGATAACCAGACCTCCTCATCACGTAGGAACCGAGTTACCA
10204 CCACT
129 CCACT
* *** * *
10209 CCTAAAGATGGCCAGCTGTCCTCATCACGTAGGAATCGTGTCATCCCCGACCAGATCTCCTCATC
1 CCTAAAGATGACCAGAACTCCTCATCACGTAGGAAGCGTGTCATCCCCGACCAGAACTCCTCATC
* * ***
10274 ACGTAGGAGCCATATCACCCTTAGATAATCAGTTTTCCTCATCACGTAGGAACCGAGTTACCACC
66 AAGTAGGAGCCATATCACCCTTAGATAACCAGACCTCCTCATCACGTAGGAACCGAGTTACCACC
10339 -CT
131 ACT
* *
10341 ACCTAAAGATGACCAAGAACTCTTCATCACGTATG-AGCAGTGTCATCCCC-AGCCAGAACTCCT
1 -CCTAAAGATGACC-AGAACTCCTCATCACGTAGGAAGC-GTGTCATCCCCGA-CCAGAACTCCT
* * * * * *
10404 CATCAAGTAGGAGTCGTGTCACCTTTAG-TCGACCAGACCTCTTCATCACGTA
62 CATCAAGTAGGAGCCATATCACCCTTAGAT-AACCAGACCTCCTCATCACGTA
10456 TGAGCAGTGT
Statistics
Matches: 203, Mismatches: 38, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
132 2 0.01
133 84 0.41
134 117 0.58
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (133 bp):
CCTAAAGATGACCAGAACTCCTCATCACGTAGGAAGCGTGTCATCCCCGACCAGAACTCCTCATC
AAGTAGGAGCCATATCACCCTTAGATAACCAGACCTCCTCATCACGTAGGAACCGAGTTACCACC
ACT
Found at i:10466 original size:43 final size:40
Alignment explanation
Indices: 10351--10474 Score: 110
Period size: 39 Copynumber: 3.0 Consensus size: 40
10341 ACCTAAAGAT
10351 GACCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCA
1 GACC-AGAACTCTTCATCACGTATGAGCAGTGTCATCCCCA
* * * **
10392 G-CCAGAACTCCTCATCAAGTAGGAGTC-GTGTCA-CCTTTA
1 GACCAGAACTCTTCATCACGTATGAG-CAGTGTCATCC-CCA
* *
10431 GTCGACCAGACCTCTTCATCACGTATGAGCAGTGTCGTCCCCA
1 ---GACCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCA
10474 G
1 G
10475 CAACCAACAT
Statistics
Matches: 63, Mismatches: 12, Indels: 17
0.68 0.13 0.18
Matches are distributed among these distances:
38 2 0.03
39 26 0.41
40 4 0.06
41 1 0.02
42 2 0.03
43 26 0.41
44 2 0.03
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.23
Consensus pattern (40 bp):
GACCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCA
Found at i:10631 original size:3 final size:3
Alignment explanation
Indices: 10625--10685 Score: 81
Period size: 3 Copynumber: 21.0 Consensus size: 3
10615 TTTTTTTAAT
* *
10625 TTA TTA TT- TTA TT- TTA TTA GTA TTA TTA TTA TTA TTA TTA TTA GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
10671 ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
10686 ATTTACATGT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
2 4 0.08
3 47 0.92
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:13296 original size:21 final size:20
Alignment explanation
Indices: 13272--13310 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
13262 ATTTTTTTAC
13272 TATTTAAATTTAAATATATAT
1 TATTTAAATTTAAA-ATATAT
*
13293 TATTTTAATTTAAAATAT
1 TATTTAAATTTAAAATAT
13311 TTAAAAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTTAAATTTAAAATATAT
Found at i:16515 original size:182 final size:182
Alignment explanation
Indices: 16208--16656 Score: 726
Period size: 182 Copynumber: 2.5 Consensus size: 182
16198 TTTTAATACA
* * *
16208 GGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGATACA
1 GGTTTTGTCATTTTGAGATCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACA
* *
16273 TTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGTC
66 TTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTC
*
16338 GATACTTATAATAAAGTA-TCGACACTATCAACATATCCGGTAGC-TCTTTATC
131 GATACTTATAATAAAGTAGT-GACACTATCAACATATCCGGTAGCGT-TTTACC
* *
16390 GGTTTTGTCATTTTGAGATCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACA
1 GGTTTTGTCATTTTGAGATCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACA
16455 TTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTC
66 TTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTC
*
16520 GATACTTATAATAAAGTAGTGACACTATTAACATATCCGGTAGCGTTTTACC
131 GATACTTATAATAAAGTAGTGACACTATCAACATATCCGGTAGCGTTTTACC
** * *
16572 TATTTTGTCATTTAT-AGACCGGTTTTGTCAT-TTTTTACATGTTTTATTGTTATGGATCGATAC
1 GGTTTTGTCATTT-TGAGATCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATAC
16635 ATTTTTATAAAGTATCGACACT
65 ATTTTTATAAAGTATCGACACT
16657 ATCAACATAT
Statistics
Matches: 250, Mismatches: 14, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
181 52 0.21
182 195 0.78
183 3 0.01
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (182 bp):
GGTTTTGTCATTTTGAGATCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACA
TTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTC
GATACTTATAATAAAGTAGTGACACTATCAACATATCCGGTAGCGTTTTACC
Found at i:16786 original size:112 final size:112
Alignment explanation
Indices: 16530--16992 Score: 698
Period size: 112 Copynumber: 4.1 Consensus size: 112
16520 GATACTTATA
* * *
16530 ATAAAGTAGT-GACACTATT-AACATATCCGGTAGCGTTTTACCTATTTTGTCATTTATAGACCG
1 ATAAAGTA-TCGACACT-TTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCG
* *
16593 GTTTTGTCA-TTTTTTACATGTTTTATTGTTATGGATCGATACATTTTT
64 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * *
16641 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
16706 TTTGTCATTTTTTTACCTGTTATATAGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
16753 ATAAAGTATCGACCCTTTCAATATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
16818 TTTGTCATTTTTTTTACCTGTTATATTGTTATGGATAGATATATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
16866 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGGCCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * ** *
16931 TTTATCATTTTTTTACTTGTTATATTGTTATGGATTAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
16978 ATAAAATATCGACAC
1 ATAAAGTATCGACAC
16993 AAACCGACAA
Statistics
Matches: 327, Mismatches: 21, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
110 2 0.01
111 64 0.20
112 156 0.48
113 105 0.32
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:16919 original size:225 final size:223
Alignment explanation
Indices: 16552--16990 Score: 698
Period size: 225 Copynumber: 2.0 Consensus size: 223
16542 CACTATTAAC
* *
16552 ATATCCGGTAGCGTTTTACCTATTTTGTCATTTATAGACCGGTTTTGTCATTTTTTACATGTTTT
1 ATATCCGGTAGCGCTTTACCTATTTTGTCATTTATAGACCGGTTTTGTCATTTTTTACATGTTAT
*
16617 ATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTAC
66 ATTGTTATGGATAGATACATTTTTATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTAC
* * *
16682 TTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATAGTTATGGATCGATAC
131 CTGTTTTGTCATTTATAGACCGGTTTTATCATTTTTTTACCTGTTATATAGTTATGGATCAATAC
*
16747 ATTTTTATAAAGTATCGACCCTTTCAAT
196 ATTTTTATAAAATATCGACCCTTTCAAT
* * *
16775 ATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTTACCTGTT
1 ATATCCGGTAGCGCTTTACCTATTTTGTCATTTATAGACCGGTTTTGTCA--TTTTTTACATGTT
* * *
16840 ATATTGTTATGGATAGATATATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTT
64 ATATTGTTATGGATAGATACATTTTTATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTT
* * * *
16905 ACCTGTTTTGTCATTTATAGGCCGGTTTTATCATTTTTTTACTTGTTATATTGTTATGGATTAAT
129 ACCTGTTTTGTCATTTATAGACCGGTTTTATCATTTTTTTACCTGTTATATAGTTATGGATCAAT
*
16970 ATATTTTTATAAAATATCGAC
194 ACATTTTTATAAAATATCGAC
16991 ACAAACCGAC
Statistics
Matches: 196, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
223 47 0.24
225 149 0.76
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.47
Consensus pattern (223 bp):
ATATCCGGTAGCGCTTTACCTATTTTGTCATTTATAGACCGGTTTTGTCATTTTTTACATGTTAT
ATTGTTATGGATAGATACATTTTTATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTAC
CTGTTTTGTCATTTATAGACCGGTTTTATCATTTTTTTACCTGTTATATAGTTATGGATCAATAC
ATTTTTATAAAATATCGACCCTTTCAAT
Found at i:17168 original size:18 final size:20
Alignment explanation
Indices: 17127--17166 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17117 GCGGTTCATG
*
17127 GAATGTAAGATTACCAGTGA
1 GAATGTAAGATTACCAGAGA
*
17147 GAATGTAAGATTACAAGAGA
1 GAATGTAAGATTACCAGAGA
17167 ATATAATTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.07, G:0.25, T:0.23
Consensus pattern (20 bp):
GAATGTAAGATTACCAGAGA
Found at i:17394 original size:37 final size:37
Alignment explanation
Indices: 17321--17394 Score: 87
Period size: 38 Copynumber: 2.0 Consensus size: 37
17311 GTTAAAAAAT
* * *
17321 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTAAATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
17358 ATTTAAATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTAAAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
17395 GAGGTTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 12 0.39
38 19 0.61
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (37 bp):
ATTTAAATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:18565 original size:12 final size:12
Alignment explanation
Indices: 18548--18583 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
18538 GCCGATTTAG
18548 AAAATTAAAAAT
1 AAAATTAAAAAT
18560 AAAATTAAAAAT
1 AAAATTAAAAAT
18572 AAAATTAAAAAT
1 AAAATTAAAAAT
18584 TGTAATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
AAAATTAAAAAT
Found at i:18575 original size:5 final size:6
Alignment explanation
Indices: 18548--18581 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
18538 GCCGATTTAG
* *
18548 AAAATT AAAAAT AAAATT AAAAAT AAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAA
18582 ATTGTAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (6 bp):
AAAATT
Found at i:19402 original size:36 final size:35
Alignment explanation
Indices: 19320--19404 Score: 100
Period size: 36 Copynumber: 2.4 Consensus size: 35
19310 AATTATATTT
* *
19320 TAAACCCTAAATTCCAAAATACTTCAATTACATCC
1 TAAACCCCAAATTCCAAAATACTTCAATTACATCA
** *
19355 TAAACATCAAATTCCAAAAATACTTTAATTACAT-A
1 TAAACCCCAAATTCC-AAAATACTTCAATTACATCA
19390 TACAACCCCAAATTC
1 TA-AACCCCAAATTC
19405 ATAATCCATT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
35 14 0.34
36 27 0.66
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (35 bp):
TAAACCCCAAATTCCAAAATACTTCAATTACATCA
Found at i:22932 original size:35 final size:35
Alignment explanation
Indices: 22893--22969 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
22883 GTTGGGCATG
* *
22893 TAATTGAAGTATTTTGGAATTTGAGGTTTAGAATA
1 TAATTGAAGTATTTTAGAATTTGAGGTTTAAAATA
** * *
22928 TAATTGAAGTATTTTAGTTTTTGGGGTTTAAAATG
1 TAATTGAAGTATTTTAGAATTTGAGGTTTAAAATA
22963 TAATTGA
1 TAATTGA
22970 TGATTGTGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.45
Consensus pattern (35 bp):
TAATTGAAGTATTTTAGAATTTGAGGTTTAAAATA
Found at i:23854 original size:85 final size:83
Alignment explanation
Indices: 23742--23906 Score: 233
Period size: 85 Copynumber: 2.0 Consensus size: 83
23732 GGAATTTCGA
* * *
23742 GAGAGTTTTACTCCACCTAAATCTCTTTTAATATCTAAATTTAAAAAAGATAAATAATATATTTT
1 GAGAGATTTACTCCACCTAAATATCTTTTAATATCCAAATTT-AAAAAGAT-AATAATATATTTT
23807 AAATGTAAAATATTAAATCT
64 AAATGTAAAATATTAAATCT
* * *
23827 GAGAGATTTACTCCAACC-AAATATCTTTTAATATCCAAATTTAAACATATAATAATATCTTTTA
1 GAGAGATTTACTCC-ACCTAAATATCTTTTAATATCCAAATTTAAAAAGATAATAATATATTTTA
*
23891 AATTTAAAATATTAAA
65 AATGTAAAATATTAAA
23907 CATATATGCA
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
83 28 0.39
84 6 0.08
85 35 0.49
86 3 0.04
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (83 bp):
GAGAGATTTACTCCACCTAAATATCTTTTAATATCCAAATTTAAAAAGATAATAATATATTTTAA
ATGTAAAATATTAAATCT
Found at i:28780 original size:3 final size:3
Alignment explanation
Indices: 28772--28846 Score: 105
Period size: 3 Copynumber: 24.7 Consensus size: 3
28762 TTAATATATT
* * *
28772 TAA TAA TAA TGA TAA TGAA TAA TAA TAA TAA TAA TAA TTA TAG TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
28818 TAA TAA TAA TTA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
28847 TTTATAATAT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
3 60 0.95
4 3 0.05
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:29312 original size:112 final size:111
Alignment explanation
Indices: 29178--29955 Score: 1267
Period size: 112 Copynumber: 7.0 Consensus size: 111
29168 TATGCAAAAA
* *
29178 GTTGAACAAGTTCTTCTTATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * * * *
29243 TC-TTCTCTGGAAATGCTGATCGATCAATTGATGAATTCATGTA-AAAG
66 ACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATT--TG-ACAAAG
* *
29290 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
*
29355 ACTTTCTTTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAG
66 ACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA-CAAAG
*
29402 GTTGAACAAGCTCTTCTTATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
29467 ACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAG
66 ACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA-CAAAG
29514 GTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
29579 ACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAG
66 ACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA-CAAAG
29626 GTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * * *
29691 AC-TTCTCTGGAAATGCTGATCGATCAATTGATGAATTCATGTA-AAAG
66 ACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATT--TG-ACAAAG
* *
29738 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
*
29803 ACTTTCTTTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAG
66 ACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA-CAAAG
*
29850 GTTGAACAAGCTCTTCTTATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
29915 ACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
29956 ATCTTTGCTA
Statistics
Matches: 629, Mismatches: 28, Indels: 18
0.93 0.04 0.03
Matches are distributed among these distances:
110 2 0.00
111 35 0.06
112 529 0.84
113 62 0.10
114 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (111 bp):
GTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGACAAAG
Found at i:30817 original size:83 final size:83
Alignment explanation
Indices: 30675--31294 Score: 1102
Period size: 83 Copynumber: 7.5 Consensus size: 83
30665 TAGTTCCTAC
*
30675 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTTATCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAA
*
30740 TTCAATGATTGGTTCTGC
66 TTCAATGATTGGTTCTGT
30758 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAA
*
30823 TTTAATGATTGGTTCTGT
66 TTCAATGATTGGTTCTGT
30841 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAA
30906 TTCAATGATTGGTTCTGT
66 TTCAATGATTGGTTCTGT
* *
30924 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAATACATTCATCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAA
30989 TTCAATGATTGGTTCTGT
66 TTCAATGATTGGTTCTGT
* *
31007 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAATACATTCATCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAA
31072 TTCAATGATTGGTTCTGT
66 TTCAATGATTGGTTCTGT
** * * *
31090 -AGTTCCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAATACATTCATATTCCAA
1 CA-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
31154 ATTCAATGATTGGTTCTGT
65 ATTCAATGATTGGTTCTGT
31173 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG-A-ACATTCATCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAA
31236 TTCAATGATTGGTTCTGT
66 TTCAATGATTGGTTCTGT
31254 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
31295 TTATTGGCCA
Statistics
Matches: 522, Mismatches: 13, Indels: 6
0.96 0.02 0.01
Matches are distributed among these distances:
81 74 0.14
82 2 0.00
83 445 0.85
84 1 0.00
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (83 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAA
TTCAATGATTGGTTCTGT
Found at i:32478 original size:25 final size:25
Alignment explanation
Indices: 32450--32516 Score: 91
Period size: 25 Copynumber: 2.6 Consensus size: 25
32440 CTTGACCCCC
32450 CTTTTTTCTTTTTTTCTTTTTC-TTT
1 CTTTTTT-TTTTTTTCTTTTTCTTTT
32475 CTTTTTTTTTTCTTTCTTTTTCTTTT
1 CTTTTTTTTTT-TTTCTTTTTCTTTT
32501 CTCTTTTTTTTCTTTT
1 CT-TTTTTTTT-TTTT
32517 TCTTCAAGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
24 4 0.11
25 17 0.45
26 5 0.13
27 11 0.29
28 1 0.03
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (25 bp):
CTTTTTTTTTTTTTCTTTTTCTTTT
Found at i:32520 original size:15 final size:16
Alignment explanation
Indices: 32452--32520 Score: 101
Period size: 15 Copynumber: 4.5 Consensus size: 16
32442 TGACCCCCCT
32452 TTTTTC-TT-TTTTTC
1 TTTTTCTTTCTTTTTC
32466 TTTTTCTTTCTTTTT-
1 TTTTTCTTTCTTTTTC
32481 TTTTTCTTTCTTTTTC
1 TTTTTCTTTCTTTTTC
32497 TTTTCTCTTT-TTTTTC
1 TTTT-TCTTTCTTTTTC
32513 TTTTTCTT
1 TTTTTCTT
32521 CAAGCATAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.12
15 21 0.41
16 19 0.37
17 5 0.10
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTCTTTCTTTTTC
Found at i:43143 original size:15 final size:13
Alignment explanation
Indices: 43111--43148 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
43101 TTTGACAGTA
43111 AAAT-AAATAATG
1 AAATAAAATAATG
43123 AAATAAAATAATTG
1 AAATAAAATAA-TG
43137 CAAATAAAATAA
1 -AAATAAAATAA
43149 AATAAAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 6 0.26
14 2 0.09
15 11 0.48
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (13 bp):
AAATAAAATAATG
Found at i:45281 original size:3 final size:3
Alignment explanation
Indices: 45273--45355 Score: 121
Period size: 3 Copynumber: 27.7 Consensus size: 3
45263 TTAATATATT
* * *
45273 TAA TAA TAA TAA TGA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
45321 TAG TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
45356 TTTATAATAT
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:45364 original size:15 final size:15
Alignment explanation
Indices: 45264--45349 Score: 68
Period size: 15 Copynumber: 5.5 Consensus size: 15
45254 TATATGTATT
45264 TAAT-ATATTTAATAA
1 TAATAATATTT-ATAA
*
45279 TAATAATGATAATGATAA
1 TAATAAT-AT--TTATAA
* *
45297 TAATAATAATAATAA
1 TAATAATATTTATAA
*
45312 TAATAAT-TATAGTAA
1 TAATAATATTTA-TAA
*
45327 TAATAATAATTATAA
1 TAATAATATTTATAA
45342 TAATAATA
1 TAATAATA
45350 ATAATATTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
14 1 0.02
15 37 0.65
16 4 0.07
17 3 0.05
18 11 0.19
19 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
TAATAATATTTATAA
Found at i:50890 original size:19 final size:20
Alignment explanation
Indices: 50850--50890 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
50840 GTAGGAAAAG
50850 AATATTTTCTAAGGAGAGAA
1 AATATTTTCTAAGGAGAGAA
50870 AATATTTTC-AA-GAGAAGAA
1 AATATTTTCTAAGGAG-AGAA
50889 AA
1 AA
50891 CTTCTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.15
19 8 0.40
20 9 0.45
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.27
Consensus pattern (20 bp):
AATATTTTCTAAGGAGAGAA
Found at i:55254 original size:3 final size:3
Alignment explanation
Indices: 55246--55275 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
55236 AATTATTTTT
55246 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55276 AATGAGTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:55695 original size:113 final size:113
Alignment explanation
Indices: 55501--56826 Score: 2145
Period size: 113 Copynumber: 11.8 Consensus size: 113
55491 TAGAGTCATT
* ** *
55501 CAAAAGGTTGAATAAGCTCTTCTTATTATGAAC-T-TTC-T-CTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
55562 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATAATGAATTCAAG
66 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAG
55610 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
55675 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATCATGAATTCAAG
66 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAG
55723 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
55788 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAG
66 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAG
* *
55836 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTTTTCCTTGTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
** * *
55901 TTATGAACTCGATTTGGAAAAGCTGATCCATCAAATGATGAATTCAAG
66 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAG
55949 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
56014 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAG
66 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAG
56062 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
56127 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAG
66 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAG
* ** *
56175 CAAAAGGTTGAATAAGCTCTTCTTATTATGAAC-T-TTC-T-CTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * * *
56236 TTATGAACTTTCTCT-GTAAAGGTTGATCCATTAAGTGATGAATTTGAA-
66 TTATGAACTCTCTCTGGCAAA-GCTGATCCATCAAATGATGAA-TTCAAG
* * *
56284 CAAAGGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
56349 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAG
66 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAG
56397 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
** * *
56462 TTATGAACTCGATTTGGAAAAGCTGATCCATCAAATGATGAATTCAAG
66 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAG
56510 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
56575 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAG
66 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAG
56623 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTTC
* * * * * * *
56688 TCATTATGACCTCTAC-CTGGCAATGTTAATCCATCAATTGATGAATTTAAA
63 TCATTATGAACTCT-CTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAG
*
56739 TAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTTC
56804 TCATTATGAACTCTAC-CTGGCAA
63 TCATTATGAACTCT-CTCTGGCAA
56827 TATTAATCCA
Statistics
Matches: 1142, Mismatches: 59, Indels: 25
0.93 0.05 0.02
Matches are distributed among these distances:
108 4 0.00
109 112 0.10
110 7 0.01
111 9 0.01
112 7 0.01
113 857 0.75
114 4 0.00
115 1 0.00
116 140 0.12
117 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAG
Found at i:56563 original size:561 final size:565
Alignment explanation
Indices: 55501--56826 Score: 2217
Period size: 561 Copynumber: 2.4 Consensus size: 565
55491 TAGAGTCATT
* ** *
55501 CAAAAGGTTGAATAAGCTCTTCTTATTATGAAC-T-TTC-T-CTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
55562 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATAATGAATTCAAGCAAAAGGTTGAACAAAT
66 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAAT
55627 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGG
131 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGG
*
55692 CAAAGCTGATCCATCAAATCATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACT
196 CAAAGCTGATCCATCAAATCATGAATTCAAGCAAAAGGTTAAACAAATTCTTCTCATTATGAACT
55757 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGCAAAGCTGATCCATCAA
261 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGCAAAGCTGATCCATCAA
* *
55822 ATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTTTTCCTTGTTCAG
326 ATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
55887 ATGAGTTCTTCTCATTATGAACTCGATTTGGAAAAGCTGATCCATCAAATGATGAATTCAAGCAA
391 ATGAGTTCTTCTCATTATGAACTCGATTTGGAAAAGCTGATCCATCAAATGATGAATTCAAGCAA
55952 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
456 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
56017 TGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAG
521 TGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAG
56062 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* **
56127 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAATAAGC
66 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAAT
* *
56192 TCTTCTTATTATGAAC-T-TTC-T-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT-G
131 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGG
* * * * * * * *
56252 TAAAGGTTGATCCATTAAGTGATGAATTTGAA-CAAAGGGTTAAACAAGTTCTTCTCATTATGAA
196 CAAA-GCTGATCCATCAAATCATGAA-TTCAAGCAAAAGGTTAAACAAATTCTTCTCATTATGAA
56316 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGCAAAGCTGATCCATC
259 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGCAAAGCTGATCCATC
56381 AAATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
324 AAATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
56446 AGATGAGTTCTTCTCATTATGAACTCGATTTGGAAAAGCTGATCCATCAAATGATGAATTCAAGC
389 AGATGAGTTCTTCTCATTATGAACTCGATTTGGAAAAGCTGATCCATCAAATGATGAATTCAAGC
56511 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
454 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
56576 TATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAG
519 TATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAG
56623 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTTC
* * * * * * **
56688 TCATTATGACCTCTAC-CTGGCAATGTTAATCCATCAATTGATGAATTTAAATAAAAGGTTGAAC
63 TCATTATGAACTCT-CTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAAC
56752 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACTC
127 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTTCTCATTATGAACTC
56817 TAC-CTGGCAA
189 T-CTCTGGCAA
56827 TATTAATCCA
Statistics
Matches: 711, Mismatches: 35, Indels: 27
0.92 0.05 0.03
Matches are distributed among these distances:
560 4 0.01
561 466 0.66
562 6 0.01
563 7 0.01
564 84 0.12
565 101 0.14
566 3 0.00
567 1 0.00
568 7 0.01
570 1 0.00
571 27 0.04
572 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (565 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAAT
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGG
CAAAGCTGATCCATCAAATCATGAATTCAAGCAAAAGGTTAAACAAATTCTTCTCATTATGAACT
TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGCAAAGCTGATCCATCAA
ATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
ATGAGTTCTTCTCATTATGAACTCGATTTGGAAAAGCTGATCCATCAAATGATGAATTCAAGCAA
AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAG
Found at i:57326 original size:52 final size:52
Alignment explanation
Indices: 57248--57352 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
57238 TTGAATTCTG
57248 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCAC
1 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCAC
57300 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCAC
1 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCAC
57352 A
1 A
57353 GATATCGATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.36
Consensus pattern (52 bp):
ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCAC
Found at i:57862 original size:115 final size:115
Alignment explanation
Indices: 57689--58118 Score: 808
Period size: 115 Copynumber: 3.7 Consensus size: 115
57679 GATCATGCAG
* * * *
57689 TTCATCTTTTAATTCCAATGATTGGTTCTGTAG-TTCCTACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
*
57753 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTATACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
57803 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
57868 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
57918 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
57983 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
58033 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
58098 AACACTTCCAGAAGATGCTAT
66 AACACTTCCAGAAGATGCTAT
58119 GAGCAAATTC
Statistics
Matches: 310, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
114 30 0.10
115 280 0.90
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.32
Consensus pattern (115 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:58181 original size:93 final size:93
Alignment explanation
Indices: 58022--58232 Score: 395
Period size: 93 Copynumber: 2.3 Consensus size: 93
58012 CTTATTTCTA
58022 CTATGAGCAAATTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
1 CTATGAGCAAATTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
58087 ATAACTCAAAGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
58115 CTATGAGCAAATTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
1 CTATGAGCAAATTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
*
58180 ATAACTCAAAGAACACTTCTAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
* *
58208 CTATGAGCACATTCATCTTCCAAAT
1 CTATGAGCAAATTCATCTTTCAAAT
58233 AATGTTTGGA
Statistics
Matches: 115, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 115 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (93 bp):
CTATGAGCAAATTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
ATAACTCAAAGAACACTTCCAGAAGATG
Found at i:59604 original size:4 final size:4
Alignment explanation
Indices: 59595--59645 Score: 52
Period size: 4 Copynumber: 12.8 Consensus size: 4
59585 TTTTTTCCTT
* *
59595 TTTC TTTC TTT- TTTC TTTTC TTT- TTTT TTTC TTTTT TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC -TTTC TTTC TTTC TTTC -TTTC TTTC TTTC TTTC
59643 TTT
1 TTT
59646 TTCTCTTCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
3 6 0.15
4 27 0.68
5 7 0.17
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (4 bp):
TTTC
Found at i:59607 original size:11 final size:11
Alignment explanation
Indices: 59588--59645 Score: 66
Period size: 11 Copynumber: 5.3 Consensus size: 11
59578 ACCTCCCTTT
*
59588 TTTCCTTTTTC
1 TTTCTTTTTTC
59599 TTTCTTTTTTC
1 TTTCTTTTTTC
*
59610 TTTTCTTTTTTT
1 -TTTCTTTTTTC
59622 TTTC-TTTTT-
1 TTTCTTTTTTC
59631 TTTCTTTCTTTC
1 TTTCTTT-TTTC
59643 TTT
1 TTT
59646 TTCTCTTCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
9 4 0.10
10 7 0.17
11 17 0.41
12 13 0.32
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:59613 original size:23 final size:23
Alignment explanation
Indices: 59587--59631 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
59577 GACCTCCCTT
59587 TTTTCCTTTTTCTTTCTTTTTTC
1 TTTTCCTTTTTCTTTCTTTTTTC
* *
59610 TTTTCTTTTTTTTTTCTTTTTT
1 TTTTCCTTTTTCTTTCTTTTTT
59632 TTCTTTCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTCCTTTTTCTTTCTTTTTTC
Found at i:59646 original size:23 final size:21
Alignment explanation
Indices: 59585--59649 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 21
59575 TTGACCTCCC
*
59585 TTTTTTCCTTTTTCTTTCTTT-T
1 TTTTTTTCTTTTT-TTT-TTTCT
*
59607 TTCTTTTC-TTTTTTTTTTCT
1 TTTTTTTCTTTTTTTTTTTCT
59627 TTTTTTTCTTTCTTTCTTTTTCT
1 TTTTTTTCTTT-TTT-TTTTTCT
59650 CTTCAAGCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
19 3 0.08
20 11 0.31
21 6 0.17
22 9 0.25
23 7 0.19
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTTTTTCTTTTTTTTTTTCT
Found at i:59647 original size:16 final size:16
Alignment explanation
Indices: 59584--59646 Score: 81
Period size: 16 Copynumber: 3.8 Consensus size: 16
59574 ATTGACCTCC
59584 CTTTTTTCCTTTTTCTTT
1 CTTTTTT-C-TTTTCTTT
59602 CTTTTTTCTTTTCTTT
1 CTTTTTTCTTTTCTTT
* *
59618 TTTTTTTCTTTTTTTT
1 CTTTTTTCTTTTCTTT
59634 CTTTCTTTCTTTT
1 CTTT-TTTCTTTT
59647 TCTCTTCAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
16 25 0.61
17 9 0.22
18 7 0.17
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
CTTTTTTCTTTTCTTT
Found at i:66928 original size:15 final size:15
Alignment explanation
Indices: 66905--66936 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
66895 TGAAATGAAT
66905 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
66920 AATGCATGTATGCAA
1 AATGAATGTATGCAA
66935 AA
1 AA
66937 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:72372 original size:3 final size:3
Alignment explanation
Indices: 72364--72405 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
72354 AATTATTTTT
*
72364 TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
72406 AATGAGTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:72688 original size:15 final size:15
Alignment explanation
Indices: 72668--72710 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 15
72658 TTTTAACCAT
*
72668 ACTCTCAAGCATTTG
1 ACTCTCAACCATTTG
72683 ACTCTCAACCA--T-
1 ACTCTCAACCATTTG
72695 ACTCTCAACCATTTG
1 ACTCTCAACCATTTG
72710 A
1 A
72711 ACAATTCTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
12 11 0.46
13 1 0.04
14 1 0.04
15 11 0.46
ACGTcount: A:0.30, C:0.33, G:0.07, T:0.30
Consensus pattern (15 bp):
ACTCTCAACCATTTG
Found at i:72700 original size:12 final size:12
Alignment explanation
Indices: 72662--72706 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
72652 AAATACTTTT
72662 AACCATACTCTC
1 AACCATACTCTC
*
72674 AAGCATTTGACTCTC
1 AACCA--T-ACTCTC
72689 AACCATACTCTC
1 AACCATACTCTC
72701 AACCAT
1 AACCAT
72707 TTGAACAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 16 0.57
13 1 0.04
14 1 0.04
15 10 0.36
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (12 bp):
AACCATACTCTC
Found at i:72700 original size:27 final size:29
Alignment explanation
Indices: 72662--72732 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 29
72652 AAATACTTTT
*
72662 AACCATACTCTCAAGCATTTG-AC-TCTC
1 AACCATACTCTCAACCATTTGAACATCTC
72689 AACCATACTCTCAACCATTTGAACAATTCTC
1 AACCATACTCTCAACCATTTGAAC-A-TCTC
72720 AACCATACTCTCA
1 AACCATACTCTCA
72733 GTCATGTGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
27 20 0.51
28 2 0.05
31 17 0.44
ACGTcount: A:0.34, C:0.34, G:0.04, T:0.28
Consensus pattern (29 bp):
AACCATACTCTCAACCATTTGAACATCTC
Found at i:72743 original size:31 final size:31
Alignment explanation
Indices: 72662--72744 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 31
72652 AAATACTTTT
* *
72662 AACCATACTCTCAAGCATTTG-AC---TCTC
1 AACCATACTCTCAACCATGTGAACAATTCTC
*
72689 AACCATACTCTCAACCATTTGAACAATTCTC
1 AACCATACTCTCAACCATGTGAACAATTCTC
**
72720 AACCATACTCTCAGTCATGTGAACA
1 AACCATACTCTCAACCATGTGAACA
72745 TTGAACGTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
27 20 0.42
28 2 0.04
31 26 0.54
ACGTcount: A:0.34, C:0.31, G:0.07, T:0.28
Consensus pattern (31 bp):
AACCATACTCTCAACCATGTGAACAATTCTC
Found at i:73131 original size:98 final size:98
Alignment explanation
Indices: 72962--73150 Score: 326
Period size: 98 Copynumber: 1.9 Consensus size: 98
72952 AGTTGCGTGC
* * *
72962 TGAGTTTATCTCAATTATCAATGGACTAATTTTTAAGTACCACATGCTATTACTATTAGAAAATG
1 TGAGTCTATCTCAATTATCAATGGACTAATTTTTAAGCACCACATGCTATTACTACTAGAAAATG
*
73027 GATTATGAACTAGGTTGAGTATTTTTTTTACGA
66 GATTATGAACTAGGTTGAGCATTTTTTTTACGA
73060 TGAGTCTATCTCAATTATCAATGGACT-ATTTTCTAAGCACCACATGCTATTACTACTAGAAAAT
1 TGAGTCTATCTCAATTATCAATGGACTAATTTT-TAAGCACCACATGCTATTACTACTAGAAAAT
73124 GGATTATGAACTAGGTTGAGCATTTTT
65 GGATTATGAACTAGGTTGAGCATTTTT
73151 CTTTGAAAGG
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
97 5 0.06
98 81 0.94
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (98 bp):
TGAGTCTATCTCAATTATCAATGGACTAATTTTTAAGCACCACATGCTATTACTACTAGAAAATG
GATTATGAACTAGGTTGAGCATTTTTTTTACGA
Found at i:73180 original size:2 final size:2
Alignment explanation
Indices: 73173--73215 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
73163 GTAAGTTTTG
73173 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
73215 T
1 T
73216 TTAAGGGTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:80387 original size:11 final size:11
Alignment explanation
Indices: 80373--80401 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
80363 AGAGATTTTA
80373 GAGAGTTTCTT
1 GAGAGTTTCTT
80384 GAGAGTTTCTT
1 GAGAGTTTCTT
80395 GAGAGTT
1 GAGAGTT
80402 GTTTTCTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.21, C:0.07, G:0.31, T:0.41
Consensus pattern (11 bp):
GAGAGTTTCTT
Found at i:80388 original size:13 final size:12
Alignment explanation
Indices: 80360--80401 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
80350 CTTCCAATAC
*
80360 TAGAGAGATT-T
1 TAGAGAGTTTCT
80371 TAGAGAGTTTCT
1 TAGAGAGTTTCT
80383 T-GAGAGTTTCT
1 TAGAGAGTTTCT
80394 T-GAGAGTT
1 TAGAGAGTT
80402 GTTTTCTCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.26, C:0.05, G:0.29, T:0.40
Consensus pattern (12 bp):
TAGAGAGTTTCT
Found at i:83095 original size:136 final size:137
Alignment explanation
Indices: 82944--83266 Score: 380
Period size: 136 Copynumber: 2.3 Consensus size: 137
82934 ATATTAAAAT
* * * * *
82944 CTAATCAATTTTAACAAATTATTGAAACGAATATTTAAAATGGAACCTCAGACATTAATGTGATG
1 CTAACCAATTTTAACAAATTATTGAAA-GAATAATTAAAATGGAACCTCAGACATAAATGCGAGG
*
83009 ATCAAATAAAAAATTCTTCTAAATTAAAAGACTAAGGTAAAATTAAACTAAAATGAAGGCTCT-A
65 ACCAAATAAAAAATTCTTCTAAATTAAAAGACTAAGGTAAAATTAAACTAAAATGAAGGCTCTAA
83073 -ATCAATC
130 TATCAATC
* * * * * *
83080 CTAACTAATTTTAACAAATTTTTTACTAGAATAATTAAAATGGAACCTCGGGCATAAATGCGAGG
1 CTAACCAATTTTAACAAATTATTGA-AAGAATAATTAAAATGGAACCTCAGACATAAATGCGAGG
* * * * * * *
83145 ACCAAATCAAAACTTCTTTTAAATTAAAGGATTAAGGTGAAATTAGACTAAAATGAAGGCTCTAA
65 ACCAAATAAAAAATTCTTCTAAATTAAAAGACTAAGGTAAAATTAAACTAAAATGAAGGCTCT-A
*
83210 ATATTAATC
129 ATATCAATC
* * * *
83219 CTAACCAATTTTAGCCATTTATTGAATTGAATAATTAAAATGGAACCT
1 CTAACCAATTTTAACAAATTATTGAA-AGAATAATTAAAATGGAACCT
83267 TAAGCATAAC
Statistics
Matches: 154, Mismatches: 28, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
136 107 0.69
137 1 0.01
138 1 0.01
139 45 0.29
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.31
Consensus pattern (137 bp):
CTAACCAATTTTAACAAATTATTGAAAGAATAATTAAAATGGAACCTCAGACATAAATGCGAGGA
CCAAATAAAAAATTCTTCTAAATTAAAAGACTAAGGTAAAATTAAACTAAAATGAAGGCTCTAAT
ATCAATC
Found at i:83648 original size:16 final size:16
Alignment explanation
Indices: 83617--83664 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
83607 CTGGAAATTA
83617 AGTACTGAAATTTAAAAT
1 AGTA-TGAAA-TTAAAAT
83635 AGTA-GAAATGTAAAAT
1 AGTATGAAAT-TAAAAT
*
83651 TGTATGAAATTAAA
1 AGTATGAAATTAAA
83665 GGTTAAAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 1 0.04
16 17 0.63
17 5 0.19
18 4 0.15
ACGTcount: A:0.52, C:0.02, G:0.15, T:0.31
Consensus pattern (16 bp):
AGTATGAAATTAAAAT
Found at i:87279 original size:16 final size:16
Alignment explanation
Indices: 87258--87290 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
87248 TTAACGGTGG
87258 TTGGGAAAGTCAAAAC
1 TTGGGAAAGTCAAAAC
*
87274 TTGGGAAAGTCGAAAC
1 TTGGGAAAGTCAAAAC
87290 T
1 T
87291 CAAACCCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.21
Consensus pattern (16 bp):
TTGGGAAAGTCAAAAC
Found at i:88208 original size:77 final size:79
Alignment explanation
Indices: 88111--88255 Score: 190
Period size: 77 Copynumber: 1.9 Consensus size: 79
88101 AATACATTTC
**
88111 TTATTTAATTAATTCAAATTAAATAT-ACATT-AAAGAATTATAATCTGAATTACAATC-TTTAA
1 TTATTTAATTAATTCAAATTAAATATCA-ATTAAAAGAATTATAATCAAAATTACAATCTTTTAA
88173 TGTTCATTTAAAATA
65 TGTTCATTTAAAATA
* * * *
88188 TTATTTAATT-ATTCTGAATTAAATATCAATTAAAAGAGTTGTAATCAAAATTACATTCTTTTAA
1 TTATTTAATTAATTC-AAATTAAATATCAATTAAAAGAATTATAATCAAAATTACAATCTTTTAA
88252 TGTT
65 TGTT
88256 TACTTACTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
76 4 0.07
77 23 0.40
78 22 0.38
79 9 0.16
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.44
Consensus pattern (79 bp):
TTATTTAATTAATTCAAATTAAATATCAATTAAAAGAATTATAATCAAAATTACAATCTTTTAAT
GTTCATTTAAAATA
Found at i:98666 original size:19 final size:20
Alignment explanation
Indices: 98615--98667 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
98605 TGTCCTCACA
*
98615 TTTTCTTTTTCC-TCTCTTG
1 TTTTCTTTTTCCTTTTCTTG
* **
98634 TTTTCTCTCCCCTTTTCTT-
1 TTTTCTTTTTCCTTTTCTTG
98653 TTTTCTTTTTCCTTT
1 TTTTCTTTTTCCTTT
98668 GCCTCAGGGA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTCTTTTTCCTTTTCTTG
Found at i:122175 original size:20 final size:20
Alignment explanation
Indices: 122152--122244 Score: 161
Period size: 20 Copynumber: 4.7 Consensus size: 20
122142 ATTAAGCCTT
*
122152 TGGTATGGATTCCAGTCCTC
1 TGGTATGGATACCAGTCCTC
122172 TGGTATGGATACCAGTCCTC
1 TGGTATGGATACCAGTCCTC
122192 TGGTATGGATACCAGTCCTC
1 TGGTATGGATACCAGTCCTC
122212 TGGTATGGATA-CAGTCCTC
1 TGGTATGGATACCAGTCCTC
*
122231 TGGTATGAATACCA
1 TGGTATGGATACCA
122245 TAACTCTGAT
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
19 18 0.26
20 52 0.74
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.31
Consensus pattern (20 bp):
TGGTATGGATACCAGTCCTC
Found at i:122252 original size:39 final size:40
Alignment explanation
Indices: 122152--122264 Score: 140
Period size: 39 Copynumber: 2.9 Consensus size: 40
122142 ATTAAGCCTT
* * *
122152 TGGTATGGATTCCAGTCCTCTGGTATGGATACCAGTCCTC
1 TGGTATGAATACCAGTACTCTGGTATGGATACCAGTCCTC
* *
122192 TGGTATGGATACCAGTCCTCTGGTATGGATA-CAGTCCTC
1 TGGTATGAATACCAGTACTCTGGTATGGATACCAGTCCTC
* *
122231 TGGTATGAATACCA-TAACTCTGATATGGAGACCA
1 TGGTATGAATACCAGT-ACTCTGGTATGGATACCA
122265 ATTTATCCGT
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.02
39 33 0.50
40 32 0.48
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (40 bp):
TGGTATGAATACCAGTACTCTGGTATGGATACCAGTCCTC
Found at i:122252 original size:59 final size:60
Alignment explanation
Indices: 122152--122264 Score: 158
Period size: 59 Copynumber: 1.9 Consensus size: 60
122142 ATTAAGCCTT
* * * * *
122152 TGGTATGGATTCCAGTCCTCTGGTATGGATACCAGTCCTCTGGTATGGATACCAGTCCTC
1 TGGTATGGATTACAGTCCTCTGGTATGAATACCAGTACTCTGATATGGAGACCAGTCCTC
122212 TGGTATGGA-TACAGTCCTCTGGTATGAATACCA-TAACTCTGATATGGAGACCA
1 TGGTATGGATTACAGTCCTCTGGTATGAATACCAGT-ACTCTGATATGGAGACCA
122265 ATTTATCCGT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
58 1 0.02
59 37 0.79
60 9 0.19
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (60 bp):
TGGTATGGATTACAGTCCTCTGGTATGAATACCAGTACTCTGATATGGAGACCAGTCCTC
Done.