Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007845.1 Hibiscus syriacus cultivar Beakdansim tig00110201_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: 2731752
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 12 of 13
Found at i:2369653 original size:24 final size:24
Alignment explanation
Indices: 2369626--2369679 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2369616 GTATTCGAAA
2369626 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2369650 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2369674 TTTGAT
1 TTTGAT
2369680 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2372157 original size:40 final size:40
Alignment explanation
Indices: 2372093--2372173 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
2372083 GACATTCATT
*
2372093 TGACTATCACAACGCGAATATGACTATCGCAATACGGAAA
1 TGACTATCACAACGCGAATATGACTATCGCAACACGGAAA
* * *
2372133 TGACTATCGCAATGCGGAAT-TGACTATCGCAACGCGGAAA
1 TGACTATCACAACGC-GAATATGACTATCGCAACACGGAAA
2372173 T
1 T
2372174 CACTTATGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
40 32 0.89
41 4 0.11
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (40 bp):
TGACTATCACAACGCGAATATGACTATCGCAACACGGAAA
Found at i:2372169 original size:20 final size:20
Alignment explanation
Indices: 2372092--2372171 Score: 99
Period size: 20 Copynumber: 4.0 Consensus size: 20
2372082 AGACATTCAT
*
2372092 TTGACTATCACAACGC-GAA
1 TTGACTATCGCAACGCGGAA
**
2372111 TATGACTATCGCAATACGGAA
1 T-TGACTATCGCAACGCGGAA
* *
2372132 ATGACTATCGCAATGCGGAA
1 TTGACTATCGCAACGCGGAA
2372152 TTGACTATCGCAACGCGGAA
1 TTGACTATCGCAACGCGGAA
2372172 ATCACTTATG
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
19 1 0.02
20 48 0.92
21 3 0.06
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (20 bp):
TTGACTATCGCAACGCGGAA
Found at i:2372239 original size:20 final size:20
Alignment explanation
Indices: 2372184--2372246 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
2372174 CACTTATGGT
*
2372184 GATTTACGTAATCGCATTGC
1 GATTTACGTATTCGCATTGC
* ** *
2372204 GATTTTTCAAATTCGCGTTGC
1 GA-TTTACGTATTCGCATTGC
2372225 GATTTACGTATTCGCATTGC
1 GATTTACGTATTCGCATTGC
2372245 GA
1 GA
2372247 ATTAGGAAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 18 0.55
21 15 0.45
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
GATTTACGTATTCGCATTGC
Found at i:2372267 original size:21 final size:21
Alignment explanation
Indices: 2372243--2372288 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2372233 TATTCGCATT
2372243 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
2372264 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
2372285 GCGA
1 GCGA
2372289 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:2372908 original size:21 final size:21
Alignment explanation
Indices: 2372884--2372927 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2372874 TGATAAAAAA
*
2372884 TTATATAAAATATTATTATTT
1 TTATATAAAATATTAATATTT
* *
2372905 TTATTTAAAATGTTAATATTT
1 TTATATAAAATATTAATATTT
2372926 TT
1 TT
2372928 TAACATTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TTATATAAAATATTAATATTT
Found at i:2373319 original size:21 final size:21
Alignment explanation
Indices: 2373282--2373325 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2373272 CAATGATCAC
*
2373282 TTAATTACTTATTTTTTTATT
1 TTAATTACTTATTTTTTAATT
*
2373303 TTAATTA-TTGTTCTTTTAATT
1 TTAATTACTTATT-TTTTAATT
2373324 TT
1 TT
2373326 GTTAATCAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (21 bp):
TTAATTACTTATTTTTTAATT
Found at i:2373930 original size:23 final size:24
Alignment explanation
Indices: 2373903--2373951 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
2373893 TTATATATAT
2373903 AATTTTTAAATAAAT-AAAAATAA
1 AATTTTTAAATAAATAAAAAATAA
* *
2373926 AATTTTTAGATAATTAAAAAATAA
1 AATTTTTAAATAAATAAAAAATAA
2373950 AA
1 AA
2373952 AACCTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
AATTTTTAAATAAATAAAAAATAA
Found at i:2377465 original size:9 final size:9
Alignment explanation
Indices: 2377451--2377494 Score: 63
Period size: 9 Copynumber: 4.8 Consensus size: 9
2377441 TATTTTTTTC
2377451 AAAAAAACA
1 AAAAAAACA
2377460 AAAAAAA-A
1 AAAAAAACA
2377468 CAAAAAAACA
1 -AAAAAAACA
2377478 AAAAAAACCA
1 AAAAAAA-CA
2377488 AAAAAAA
1 AAAAAAA
2377495 GCCAAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 1 0.03
9 21 0.66
10 10 0.31
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:2377466 original size:10 final size:10
Alignment explanation
Indices: 2377451--2377494 Score: 65
Period size: 10 Copynumber: 4.6 Consensus size: 10
2377441 TATTTTTTTC
2377451 AAAAAAACAA
1 AAAAAAACAA
2377461 AAAAAAAC--
1 AAAAAAACAA
2377469 AAAAAAACAA
1 AAAAAAACAA
*
2377479 AAAAAACCAA
1 AAAAAAACAA
2377489 AAAAAA
1 AAAAAA
2377495 GCCAAATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 8 0.26
10 23 0.74
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:2377473 original size:18 final size:18
Alignment explanation
Indices: 2377450--2377493 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
2377440 CTATTTTTTT
2377450 CAAAAAAACAAAAAAAAA
1 CAAAAAAACAAAAAAAAA
*
2377468 CAAAAAAACAAAAAAAAC
1 CAAAAAAACAAAAAAAAA
2377486 CAAAAAAA
1 CAAAAAAA
2377494 AGCCAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (18 bp):
CAAAAAAACAAAAAAAAA
Found at i:2377548 original size:4 final size:4
Alignment explanation
Indices: 2377539--2382330 Score: 9416
Period size: 4 Copynumber: 1204.0 Consensus size: 4
2377529 TAGGGCTGAT
2377539 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2377587 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2377635 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2377683 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2377731 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2377779 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2377827 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2377875 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2377923 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2377971 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2378019 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2378067 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2378115 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2378163 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2378211 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2378259 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TC-- TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2378305 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2378353 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2378401 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2378449 TCTA TCTA TCTA TCTA TCTA TCTA TC-- TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2378495 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2378543 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2378591 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2378639 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2378687 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2378735 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2378783 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2378831 -CTA TCTA TCTA TCTA TC-- TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2378876 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2378924 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2378972 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2379020 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2379068 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2379116 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2379164 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2379212 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2379260 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2379308 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2379356 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2379404 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2379452 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2379500 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA -CTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2379547 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2379595 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2379643 TCTA TCTA TCTA TCTA TC-- TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2379689 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2379737 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2379785 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2379833 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2379881 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2379929 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2379977 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2380025 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2380073 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2380121 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2380169 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2380217 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2380265 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2380313 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2380361 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2380409 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2380457 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2380505 TCTA TCTA TCTA TCTA --TA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2380551 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2380599 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2380647 TCTA TCTA TCTA TCTA TCTA TCTA TCTA --TA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2380693 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2380741 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2380789 TCTA TCTA TCTA TCTA TCTA TCTA TCTA --TA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2380835 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2380883 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2380931 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2380979 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2381027 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2381075 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2381123 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2381171 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2381219 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2381267 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2381315 TCTA TCTA TCTA TCTA TCTA TCTA TCTA --TA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2381361 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2381409 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2381457 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA --TA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2381503 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2381551 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2381599 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2381647 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2381695 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2381743 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2381791 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2381839 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2381887 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2381935 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2381983 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2382031 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2382079 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2382127 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2382175 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2382223 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2382271 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TC-A TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
2382318 --TA TCTA T-TA TCTA
1 TCTA TCTA TCTA TCTA
2382331 ATTAGATTAT
Statistics
Matches: 4764, Mismatches: 0, Indels: 48
0.99 0.00 0.01
Matches are distributed among these distances:
2 20 0.00
3 12 0.00
4 4732 0.99
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
TCTA
Found at i:2388196 original size:24 final size:25
Alignment explanation
Indices: 2388150--2388204 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
2388140 ACATCAAATA
*
2388150 TTAACTTAAAAAACTCAAATAAAGT
1 TTAATTTAAAAAACTCAAATAAAGT
**
2388175 TTAATTTAAAAAA-TCATGTAAAGT
1 TTAATTTAAAAAACTCAAATAAAGT
*
2388199 TAAATT
1 TTAATT
2388205 ATATCGAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (25 bp):
TTAATTTAAAAAACTCAAATAAAGT
Found at i:2401026 original size:21 final size:22
Alignment explanation
Indices: 2400993--2401033 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2400983 AAGCTTAATC
**
2400993 ATAAAACTTTTTAA-ACTACAA
1 ATAAAACAATTTAACACTACAA
2401014 ATAAAACAATTTAACACTAC
1 ATAAAACAATTTAACACTAC
2401034 TTAAAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (22 bp):
ATAAAACAATTTAACACTACAA
Found at i:2406556 original size:646 final size:646
Alignment explanation
Indices: 2405326--2406622 Score: 2594
Period size: 646 Copynumber: 2.0 Consensus size: 646
2405316 GCACCCCCAC
2405326 TCTAATAAGCTTCCAACAAATCTCAGGGTTCCGTGAAGAGTCCTTATGTTCCGATTCTTTCTTAG
1 TCTAATAAGCTTCCAACAAATCTCAGGGTTCCGTGAAGAGTCCTTATGTTCCGATTCTTTCTTAG
2405391 AAAGAAAAAGGAGTTTGTAATTTAAGTTTAGGGAAAATTACACAGTTCCTCACTCAACTTTTATT
66 AAAGAAAAAGGAGTTTGTAATTTAAGTTTAGGGAAAATTACACAGTTCCTCACTCAACTTTTATT
2405456 TTTTCTAATTTGTTCACTGAACTTTACAAATTGAATCATTTTGCTCACTCTCTTGTTATTTTTCT
131 TTTTCTAATTTGTTCACTGAACTTTACAAATTGAATCATTTTGCTCACTCTCTTGTTATTTTTCT
2405521 AACGTCGTTAACAAAAAAACTGAAGGTGACTGGATGCCACTGTCAGCCACCGTCGACCATCGCAG
196 AACGTCGTTAACAAAAAAACTGAAGGTGACTGGATGCCACTGTCAGCCACCGTCGACCATCGCAG
2405586 ATGGTGGTCATTCGGTCTCAAATTTCATGGGTCGCTTCACCTTGACACTGTGAGTCTGAACCCGA
261 ATGGTGGTCATTCGGTCTCAAATTTCATGGGTCGCTTCACCTTGACACTGTGAGTCTGAACCCGA
2405651 CCTCTATTTTGTCGGAACTTGCTCCTAAGTCTACGAATTTGAGATTGAAAGTGACAAATACAAAA
326 CCTCTATTTTGTCGGAACTTGCTCCTAAGTCTACGAATTTGAGATTGAAAGTGACAAATACAAAA
2405716 CGTTTCAATCCAGATTCACGGGTTTCGGGATATTTTTCTGCGAAACAACCACTAGATTCAGACTC
391 CGTTTCAATCCAGATTCACGGGTTTCGGGATATTTTTCTGCGAAACAACCACTAGATTCAGACTC
2405781 AATGGGTCATGATGAACCGACCTATGAAATTTGAGATCGAACGACCACCATCAACAACGATGGAC
456 AATGGGTCATGATGAACCGACCTATGAAATTTGAGATCGAACGACCACCATCAACAACGATGGAC
2405846 GTTGGCCATAATGAAAATGTCGTAGTGGCCGGCGGCAACAACCGGTTGCAAAGTAGAGAGAAAGT
521 GTTGGCCATAATGAAAATGTCGTAGTGGCCGGCGGCAACAACCGGTTGCAAAGTAGAGAGAAAGT
2405911 AGGGGGAAGAAAAAGGACAAATACAGAAAAATGAAGAAGAATAAAAGATTTCATAATTAAT
586 AGGGGGAAGAAAAAGGACAAATACAGAAAAATGAAGAAGAATAAAAGATTTCATAATTAAT
2405972 TCTAATAAGCTTCCAACAAATCTCAGGGTTCCGTGAAGAGTCCTTATGTTCCGATTCTTTCTTAG
1 TCTAATAAGCTTCCAACAAATCTCAGGGTTCCGTGAAGAGTCCTTATGTTCCGATTCTTTCTTAG
2406037 AAAGAAAAAGGAGTTTGTAATTTAAGTTTAGGGAAAATTACACAGTTCCTCACTCAACTTTTATT
66 AAAGAAAAAGGAGTTTGTAATTTAAGTTTAGGGAAAATTACACAGTTCCTCACTCAACTTTTATT
2406102 TTTTCTAATTTGTTCACTGAACTTTACAAATTGAATCATTTTGCTCACTCTCTTGTTATTTTTCT
131 TTTTCTAATTTGTTCACTGAACTTTACAAATTGAATCATTTTGCTCACTCTCTTGTTATTTTTCT
2406167 AACGTCGTTAACAAAAAAACTGAAGGTGACTGGATGCCACTGTCAGCCACCGTCGACCATCGCAG
196 AACGTCGTTAACAAAAAAACTGAAGGTGACTGGATGCCACTGTCAGCCACCGTCGACCATCGCAG
2406232 ATGGTGGTCATTCGGTCTCAAATTTCATGGGTCGCTTCACCTTGACACTGTGAGTCTGAACCCGA
261 ATGGTGGTCATTCGGTCTCAAATTTCATGGGTCGCTTCACCTTGACACTGTGAGTCTGAACCCGA
2406297 CCTCTATTTTGTCGGAACTTGCTCCTAAGTCTACGAATTTGAGATTGAAAGTGACAAATACAAAA
326 CCTCTATTTTGTCGGAACTTGCTCCTAAGTCTACGAATTTGAGATTGAAAGTGACAAATACAAAA
2406362 CGTTTCAATCCAGATTCACGGGTTTCGGGATATTTTTCTGCGAAACAACCACTAGATTCAGACTC
391 CGTTTCAATCCAGATTCACGGGTTTCGGGATATTTTTCTGCGAAACAACCACTAGATTCAGACTC
2406427 AATGGGTCATGATGAACCGACCTATGAAATTTGAGATCGAACGACCACCATCAACAACGATGGAC
456 AATGGGTCATGATGAACCGACCTATGAAATTTGAGATCGAACGACCACCATCAACAACGATGGAC
2406492 GTTGGCCATAATGAAAATGTCGTAGTGGCCGGCGGCAACAACCGGTTGCAAAGTAGAGAGAAAGT
521 GTTGGCCATAATGAAAATGTCGTAGTGGCCGGCGGCAACAACCGGTTGCAAAGTAGAGAGAAAGT
2406557 AGGGGGAAGAAAAAGGACAAATACAGAAAAATGAAGAAGAATAAAAGATTTCATAATTAAT
586 AGGGGGAAGAAAAAGGACAAATACAGAAAAATGAAGAAGAATAAAAGATTTCATAATTAAT
2406618 TCTAA
1 TCTAA
2406623 ATGACGTCGT
Statistics
Matches: 651, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
646 651 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (646 bp):
TCTAATAAGCTTCCAACAAATCTCAGGGTTCCGTGAAGAGTCCTTATGTTCCGATTCTTTCTTAG
AAAGAAAAAGGAGTTTGTAATTTAAGTTTAGGGAAAATTACACAGTTCCTCACTCAACTTTTATT
TTTTCTAATTTGTTCACTGAACTTTACAAATTGAATCATTTTGCTCACTCTCTTGTTATTTTTCT
AACGTCGTTAACAAAAAAACTGAAGGTGACTGGATGCCACTGTCAGCCACCGTCGACCATCGCAG
ATGGTGGTCATTCGGTCTCAAATTTCATGGGTCGCTTCACCTTGACACTGTGAGTCTGAACCCGA
CCTCTATTTTGTCGGAACTTGCTCCTAAGTCTACGAATTTGAGATTGAAAGTGACAAATACAAAA
CGTTTCAATCCAGATTCACGGGTTTCGGGATATTTTTCTGCGAAACAACCACTAGATTCAGACTC
AATGGGTCATGATGAACCGACCTATGAAATTTGAGATCGAACGACCACCATCAACAACGATGGAC
GTTGGCCATAATGAAAATGTCGTAGTGGCCGGCGGCAACAACCGGTTGCAAAGTAGAGAGAAAGT
AGGGGGAAGAAAAAGGACAAATACAGAAAAATGAAGAAGAATAAAAGATTTCATAATTAAT
Found at i:2409170 original size:2 final size:2
Alignment explanation
Indices: 2409165--2409279 Score: 92
Period size: 2 Copynumber: 56.5 Consensus size: 2
2409155 AAAACAACTA
*
2409165 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AGT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * * * *
2409207 AT AA AGT AT CT GT A- AT AT AT AT AT AA ACT AT AT AGT TT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT
* *
2409249 AT AT AT AT AT AT -T AT GT AT AA ACT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
2409280 CCATGTATAA
Statistics
Matches: 90, Mismatches: 15, Indels: 16
0.74 0.12 0.13
Matches are distributed among these distances:
1 3 0.03
2 82 0.91
3 5 0.06
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2409285 original size:20 final size:20
Alignment explanation
Indices: 2409252--2409299 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
2409242 TTTATATATA
**
2409252 TATATATATTATGTATAAAC
1 TATATATACCATGTATAAAC
2409272 TATATATACCATGTATAAAC
1 TATATATACCATGTATAAAC
2409292 TATA-ATAC
1 TATATATAC
2409300 TATATAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (20 bp):
TATATATACCATGTATAAAC
Found at i:2409359 original size:11 final size:11
Alignment explanation
Indices: 2409345--2409374 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2409335 ACTACATAGT
2409345 TTATATATAAA
1 TTATATATAAA
*
2409356 TTATATATGAA
1 TTATATATAAA
2409367 TTATATAT
1 TTATATAT
2409375 TATATAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (11 bp):
TTATATATAAA
Found at i:2409456 original size:22 final size:21
Alignment explanation
Indices: 2409430--2409491 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
2409420 ATATATACTG
*
2409430 TATAAATTATATAGTTTATTAA
1 TATAAGTTATATAGTTTATT-A
*
2409452 TATAAGCTATATAGTTT-TTA
1 TATAAGTTATATAGTTTATTA
2409472 TATATAGTATATATAGTTTA
1 TATA-AGT-TATATAGTTTA
2409492 GGGTTTAGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 5 0.15
21 4 0.12
22 25 0.74
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (21 bp):
TATAAGTTATATAGTTTATTA
Found at i:2409497 original size:7 final size:7
Alignment explanation
Indices: 2409487--2409526 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
2409477 AGTATATATA
2409487 GTTTAGG
1 GTTTAGG
2409494 GTTTAGG
1 GTTTAGG
*
2409501 GGTTAGG
1 GTTTAGG
*
2409508 GGTTAGG
1 GTTTAGG
2409515 GTTTAGG
1 GTTTAGG
2409522 GTTTA
1 GTTTA
2409527 TATTTATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.15, C:0.00, G:0.45, T:0.40
Consensus pattern (7 bp):
GTTTAGG
Found at i:2409574 original size:20 final size:20
Alignment explanation
Indices: 2409549--2409622 Score: 78
Period size: 20 Copynumber: 3.5 Consensus size: 20
2409539 TATAAACTAC
2409549 ATACTATGA-TTTATATTTAT
1 ATACTAT-ATTTTATATTTAT
2409569 ATACTATATTTTATACTATTTAT
1 ATACTATA-TTT-TA-TATTTAT
*
2409592 ATAAACTATAGTTTATATTTAT
1 AT--ACTATATTTTATATTTAT
2409614 ATACTATAT
1 ATACTATAT
2409623 ATATGAACTA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
19 1 0.02
20 13 0.28
21 2 0.04
22 11 0.24
23 11 0.24
24 2 0.04
25 6 0.13
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (20 bp):
ATACTATATTTTATATTTAT
Found at i:2409585 original size:12 final size:13
Alignment explanation
Indices: 2409560--2409609 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
2409550 TACTATGATT
2409560 TATATTTATATAC
1 TATATTTATATAC
2409573 TATATTT-TATAC
1 TATATTTATATAC
*
2409585 TAT-TTATATAAAC
1 TATATT-TATATAC
2409598 TATAGTTTATAT
1 TATA-TTTATAT
2409610 TTATATACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 2 0.06
12 9 0.29
13 14 0.45
14 4 0.13
15 2 0.06
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (13 bp):
TATATTTATATAC
Found at i:2409600 original size:25 final size:23
Alignment explanation
Indices: 2409562--2409621 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
2409552 CTATGATTTA
*
2409562 TATTTATATACTATATTTTATAC
1 TATTTATATACTATAGTTTATAC
2409585 TATTTATATAAACTATAG-TT-TA-
1 TATTTATAT--ACTATAGTTTATAC
2409607 TATTTATATACTATA
1 TATTTATATACTATA
2409622 TATATGAACT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
20 6 0.18
22 9 0.26
23 11 0.32
24 2 0.06
25 6 0.18
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (23 bp):
TATTTATATACTATAGTTTATAC
Found at i:2409620 original size:33 final size:32
Alignment explanation
Indices: 2409573--2409639 Score: 107
Period size: 33 Copynumber: 2.1 Consensus size: 32
2409563 ATTTATATAC
*
2409573 TATATTTTATACTATTTATATAAACTATAGTT
1 TATATTTTATACTATATATATAAACTATAGTT
*
2409605 TATATTTATATACTATATATATGAACTATAGTT
1 TATATTT-TATACTATATATATAAACTATAGTT
2409638 TA
1 TA
2409640 CGTATGAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 7 0.22
33 25 0.78
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (32 bp):
TATATTTTATACTATATATATAAACTATAGTT
Found at i:2409634 original size:20 final size:20
Alignment explanation
Indices: 2409611--2409694 Score: 66
Period size: 20 Copynumber: 4.3 Consensus size: 20
2409601 AGTTTATATT
* *
2409611 TATATACTATATATATGAAC
1 TATATAGTATACATATGAAC
* *
2409631 --TATAGTTTACGTATGAAC
1 TATATAGTATACATATGAAC
* * *
2409649 TATAT-GTAAATATAGTAAAC
1 TATATAGTATACATA-TGAAC
*
2409669 TATATAGTTTACATATGAAC
1 TATATAGTATACATATGAAC
2409689 TATATA
1 TATATA
2409695 AATTTTATAT
Statistics
Matches: 47, Mismatches: 13, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
18 14 0.30
19 5 0.11
20 22 0.47
21 6 0.13
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (20 bp):
TATATAGTATACATATGAAC
Found at i:2409686 original size:40 final size:40
Alignment explanation
Indices: 2409628--2409732 Score: 126
Period size: 40 Copynumber: 2.6 Consensus size: 40
2409618 TATATATATG
*
2409628 AACTATAGTTTACGTATGAACTATATGTAAA-TATAGTAAACT
1 AACTATAGTTTACATATGAACTATA--TAAATTATA-TAAACT
* *
2409670 -A-TATAGTTTACATATGAACTATATAAATTTTATATACT
1 AACTATAGTTTACATATGAACTATATAAATTATATAAACT
*
2409708 AACTATAGTTTACATATAAACTATA
1 AACTATAGTTTACATATGAACTATA
2409733 GTTGATATTT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
38 9 0.16
39 4 0.07
40 42 0.75
41 1 0.02
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.39
Consensus pattern (40 bp):
AACTATAGTTTACATATGAACTATATAAATTATATAAACT
Found at i:2409719 original size:18 final size:18
Alignment explanation
Indices: 2409698--2409740 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2409688 CTATATAAAT
2409698 TTTATATACT-AACTATAG
1 TTTATATA-TAAACTATAG
*
2409716 TTTACATATAAACTATAG
1 TTTATATATAAACTATAG
*
2409734 TTGATAT
1 TTTATAT
2409741 TTACATATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (18 bp):
TTTATATATAAACTATAG
Found at i:2409822 original size:22 final size:22
Alignment explanation
Indices: 2409797--2409839 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2409787 AGTTTACGTA
2409797 TAAACTATATAGACTAACTATG
1 TAAACTATATAGACTAACTATG
* * *
2409819 TAAATTTTATATACTAACTAT
1 TAAACTATATAGACTAACTAT
2409840 AGTTTACGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.40
Consensus pattern (22 bp):
TAAACTATATAGACTAACTATG
Found at i:2409834 original size:53 final size:53
Alignment explanation
Indices: 2409760--2409861 Score: 195
Period size: 53 Copynumber: 1.9 Consensus size: 53
2409750 AACTATATAG
*
2409760 ACTATGTAAATTTTATGTACTAACTATAGTTTACGTATAAACTATATAGACTA
1 ACTATGTAAATTTTATATACTAACTATAGTTTACGTATAAACTATATAGACTA
2409813 ACTATGTAAATTTTATATACTAACTATAGTTTACGTATAAACTATATAG
1 ACTATGTAAATTTTATATACTAACTATAGTTTACGTATAAACTATATAG
2409862 TTTACGTATA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (53 bp):
ACTATGTAAATTTTATATACTAACTATAGTTTACGTATAAACTATATAGACTA
Found at i:2409855 original size:18 final size:18
Alignment explanation
Indices: 2409834--2409881 Score: 78
Period size: 20 Copynumber: 2.6 Consensus size: 18
2409824 TTTATATACT
2409834 AACTATAGTTTACGTATA
1 AACTATAGTTTACGTATA
2409852 AACTATATAGTTTACGTATA
1 AAC--TATAGTTTACGTATA
2409872 AACTATAGTT
1 AACTATAGTT
2409882 AGTATATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.36
20 18 0.64
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (18 bp):
AACTATAGTTTACGTATA
Found at i:2409860 original size:20 final size:20
Alignment explanation
Indices: 2409837--2409878 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2409827 ATATACTAAC
2409837 TATAGTTTACGTATAAACTA
1 TATAGTTTACGTATAAACTA
2409857 TATAGTTTACGTATAAACTA
1 TATAGTTTACGTATAAACTA
2409877 TA
1 TA
2409879 GTTAGTATAT
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:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (20 bp):
TATAGTTTACGTATAAACTA
Found at i:2410016 original size:23 final size:24
Alignment explanation
Indices: 2409974--2410018 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
2409964 TAGTATATAA
*
2409974 ATAAACTATAGTTATATAAATAGT
1 ATAAAATATAGTTATATAAATAGT
2409998 ATAAAATATAG-TATATAAATA
1 ATAAAATATAGTTATATAAATA
2410019 TAAATCATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (24 bp):
ATAAAATATAGTTATATAAATAGT
Found at i:2410050 original size:6 final size:6
Alignment explanation
Indices: 2410039--2410063 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2410029 TATGTAGTTT
2410039 ATATAA ATATAA ATATAA ATATAA A
1 ATATAA ATATAA ATATAA ATATAA A
2410064 CCCTAAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAA
Found at i:2410124 original size:28 final size:27
Alignment explanation
Indices: 2410059--2410153 Score: 100
Period size: 28 Copynumber: 3.4 Consensus size: 27
2410049 AAATATAAAT
* *
2410059 ATAAACCCTAAATCCTAGATCCTAAACC
1 ATAAACCCT-AATCTTAAATCCTAAACC
* * *
2410087 CTAGATCCTAACTCTTAAATCCTAAACC
1 ATAAACCCTAA-TCTTAAATCCTAAACC
*
2410115 ATAAACCCTAATCTATAAATGCTAAACC
1 ATAAACCCTAATCT-TAAATCCTAAACC
*
2410143 CTAAACCCTAA
1 ATAAACCCTAA
2410154 ACTATATATA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
27 5 0.09
28 50 0.91
ACGTcount: A:0.42, C:0.31, G:0.03, T:0.24
Consensus pattern (27 bp):
ATAAACCCTAATCTTAAATCCTAAACC
Found at i:2410155 original size:7 final size:7
Alignment explanation
Indices: 2410060--2410155 Score: 59
Period size: 7 Copynumber: 13.7 Consensus size: 7
2410050 AATATAAATA
2410060 TAAACCC
1 TAAACCC
*
2410067 TAAATCC
1 TAAACCC
* *
2410074 TAGATCC
1 TAAACCC
2410081 TAAACCC
1 TAAACCC
* *
2410088 TAGATCC
1 TAAACCC
*
2410095 T-AACTCT
1 TAAAC-CC
*
2410102 TAAATCC
1 TAAACCC
*
2410109 TAAACCA
1 TAAACCC
2410116 TAAACCC
1 TAAACCC
* **
2410123 TAATCTA
1 TAAACCC
**
2410130 TAAATGC
1 TAAACCC
2410137 TAAACCC
1 TAAACCC
2410144 TAAACCC
1 TAAACCC
2410151 TAAAC
1 TAAAC
2410156 TATATATACT
Statistics
Matches: 64, Mismatches: 23, Indels: 4
0.70 0.25 0.04
Matches are distributed among these distances:
6 1 0.02
7 61 0.95
8 2 0.03
ACGTcount: A:0.42, C:0.31, G:0.03, T:0.24
Consensus pattern (7 bp):
TAAACCC
Found at i:2410181 original size:20 final size:22
Alignment explanation
Indices: 2410158--2410205 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
2410148 CCCTAAACTA
2410158 TATATACTATATA-TAA-AAAC
1 TATATACTATATATTAATAAAC
* *
2410178 TATATAGTTTATATTAATAAAC
1 TATATACTATATATTAATAAAC
2410200 TATATA
1 TATATA
2410206 ATTTATACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 11 0.46
21 3 0.12
22 10 0.42
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (22 bp):
TATATACTATATATTAATAAAC
Found at i:2410210 original size:22 final size:23
Alignment explanation
Indices: 2410151--2410301 Score: 78
Period size: 22 Copynumber: 7.0 Consensus size: 23
2410141 CCCTAAACCC
*
2410151 TAAACTATAT-ATACTATATATAA
1 TAAACTATATAAT-TTATATATAA
*
2410174 -AAACTATATAGTTTATAT-TAA
1 TAAACTATATAATTTATATATAA
*
2410195 TAAACTATATAA-TT-TATACAA
1 TAAACTATATAATTTATATATAA
* * * *
2410216 TATATTATTATAATTATAGATAATCTA
1 TAAACTA-TATAATT-TATAT-AT-AA
2410243 TAAACTATAT--TTTATATAT-A
1 TAAACTATATAATTTATATATAA
*
2410263 T-AA-TACAT-ATTTAT-T-TAA
1 TAAACTATATAATTTATATATAA
*
2410281 TAAACTAT-TTATTTATATATA
1 TAAACTATATAATTTATATATA
2410302 TATATATAGT
Statistics
Matches: 98, Mismatches: 14, Indels: 33
0.68 0.10 0.23
Matches are distributed among these distances:
17 1 0.01
18 7 0.07
19 10 0.10
20 13 0.13
21 13 0.13
22 33 0.34
23 6 0.06
24 3 0.03
25 2 0.02
26 4 0.04
27 6 0.06
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (23 bp):
TAAACTATATAATTTATATATAA
Found at i:2410272 original size:20 final size:20
Alignment explanation
Indices: 2410241--2410303 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
2410231 ATAGATAATC
2410241 TATAAACTATATTTTATATA
1 TATAAACTATATTTTATATA
*
2410261 TATAATAC-ATA-TTTATTTA
1 TATAA-ACTATATTTTATATA
*
2410280 -ATAAACTATTTATTTATATA
1 TATAAACTATAT-TTTATATA
2410300 TATA
1 TATA
2410304 TATATAGTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
17 2 0.06
18 6 0.17
19 7 0.20
20 15 0.43
21 5 0.14
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
TATAAACTATATTTTATATA
Found at i:2413431 original size:31 final size:31
Alignment explanation
Indices: 2413394--2413702 Score: 299
Period size: 31 Copynumber: 9.7 Consensus size: 31
2413384 ATATCATTAC
* *
2413394 TATTATTAAATCATTAAAGTTAACTACTAAT
1 TATTATCAAATCATTAAAGTTAACTAATAAT
* *
2413425 TATTATTAAATCATTAAAGTTATCTAATAAT
1 TATTATCAAATCATTAAAGTTAACTAATAAT
*
2413456 TAGTATCAAATCATTAAAGTTAACTAATAAT
1 TATTATCAAATCATTAAAGTTAACTAATAAT
*
2413487 T-TGTATCAAATCA-TAAAGTTAAATCGTTAA-AGT
1 TAT-TATCAAATCATTAAAGTT-AA-C--TAATAAT
* * *
2413520 TAATTA-CTAATTATTATTAAA-TT-ATTAAAGTTAT
1 T-ATTATC-AA--ATCATTAAAGTTAACT-AA-TAAT
*
2413554 CTATTAATTAAATCATTAAAGTTAAC-AACTAAT
1 -TATT-ATCAAATCATTAAAGTTAACTAA-TAAT
* *
2413587 TATTATTAAATTATTAAAGTTAACTAATAAT
1 TATTATCAAATCATTAAAGTTAACTAATAAT
* *
2413618 TAGTATCAAATCATTAAAGTTAATTAATAAT
1 TATTATCAAATCATTAAAGTTAACTAATAAT
*
2413649 TAGTATCAAATCATTAAAGTTAACTAATAAT
1 TATTATCAAATCATTAAAGTTAACTAATAAT
*
2413680 TAGTATCAAATCATTAAAGTTAA
1 TATTATCAAATCATTAAAGTTAA
2413703 ATCATTAAAG
Statistics
Matches: 236, Mismatches: 22, Indels: 40
0.79 0.07 0.13
Matches are distributed among these distances:
30 7 0.03
31 174 0.74
32 9 0.04
33 17 0.07
34 14 0.06
35 6 0.03
36 5 0.02
37 4 0.02
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.40
Consensus pattern (31 bp):
TATTATCAAATCATTAAAGTTAACTAATAAT
Found at i:2413588 original size:131 final size:137
Alignment explanation
Indices: 2413394--2413640 Score: 373
Period size: 131 Copynumber: 1.8 Consensus size: 137
2413384 ATATCATTAC
*
2413394 TATTATTAAATCATTAAAGTTAACTACTAATTATTATTAAATCATTAAAGTTATCTAATAATTAG
1 TATTATTAAATCATTAAAGTTAACTACTAATTA-TATTAAATCATTAAAGTTAACTAATAATTAG
*
2413459 TATCAAATCATTAAAGTTAACTAATAATTTGTATCAAATCA-TAAAGTTAAATCGTTAAAGTTAA
65 TATCAAATCATTAAAGTTAACTAATAATTAGTATCAAATCATTAAAGTTAAATCGTTAAAGTTAA
2413523 TTACTAAT
130 TTACTAAT
* *
2413531 TATTATTAAATTATTAAAGTT-A-T-CT-ATTA-ATTAAATCATTAAAGTTAAC-AACTAATTAT
1 TATTATTAAATCATTAAAGTTAACTACTAATTATATTAAATCATTAAAGTTAACTAA-TAATTAG
* *
2413590 TATTAAATTATTAAAGTTAACTAATAATTAGTATCAAATCATTAAAGTTAA
65 TATCAAATCATTAAAGTTAACTAATAATTAGTATCAAATCATTAAAGTTAA
2413641 TTAATAATTA
Statistics
Matches: 102, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
130 2 0.02
131 63 0.62
132 9 0.09
133 4 0.04
134 2 0.02
135 1 0.01
136 1 0.01
137 20 0.20
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (137 bp):
TATTATTAAATCATTAAAGTTAACTACTAATTATATTAAATCATTAAAGTTAACTAATAATTAGT
ATCAAATCATTAAAGTTAACTAATAATTAGTATCAAATCATTAAAGTTAAATCGTTAAAGTTAAT
TACTAAT
Found at i:2413591 original size:56 final size:56
Alignment explanation
Indices: 2413505--2413681 Score: 194
Period size: 56 Copynumber: 3.1 Consensus size: 56
2413495 AATCATAAAG
* *
2413505 TTAAATCGTTAAAGTTAATTACTAATTATTATTAAATTATTAAAGTTATCTATTAA
1 TTAAATCATTAAAGTTAATAACTAATTATTATTAAATTATTAAAGTTATCTATTAA
* *
2413561 TTAAATCATTAAAGTTAACAACTAATTATTATTAAATTATTAAAGTTAACTAATAATTAGTA
1 TTAAATCATTAAAGTTAATAACTAATTATTATTAAATTATTAAAGTT-A-T-CT-ATTA--A
* * * * * *
2413623 TCAAATCATTAAAGTTAATTAA-TAATTAGTATCAAATCATTAAAGTTAACTAATAA
1 TTAAATCATTAAAGTTAA-TAACTAATTATTATTAAATTATTAAAGTTATCTATTAA
2413679 TTA
1 TTA
2413682 GTATCAAATC
Statistics
Matches: 101, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
56 47 0.47
57 1 0.01
58 4 0.04
59 2 0.02
60 4 0.04
61 1 0.01
62 40 0.40
63 2 0.02
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (56 bp):
TTAAATCATTAAAGTTAATAACTAATTATTATTAAATTATTAAAGTTATCTATTAA
Found at i:2413619 original size:25 final size:25
Alignment explanation
Indices: 2413535--2413619 Score: 89
Period size: 25 Copynumber: 3.2 Consensus size: 25
2413525 ACTAATTATT
* *
2413535 ATTAAATTATTAAAGTTATCTATTA
1 ATTAAATTATTAAAGTTAACTAATA
*
2413560 ATTAAATCATTAAAGTTAACAACTAATTA
1 ATTAAATTATTAAAGTT---AACTAA-TA
2413589 TTATTAAATTATTAAAGTTAACTAATA
1 --ATTAAATTATTAAAGTTAACTAATA
2413616 ATTA
1 ATTA
2413620 GTATCAAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
25 20 0.40
27 2 0.04
28 10 0.20
29 2 0.04
31 16 0.32
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (25 bp):
ATTAAATTATTAAAGTTAACTAATA
Found at i:2413725 original size:45 final size:45
Alignment explanation
Indices: 2413656--2413742 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
2413646 AATTAGTATC
2413656 AAATCATTAAAGTTAACTAATAATTAGTATCAAATCATTAAAGTT
1 AAATCATTAAAGTTAACTAATAATTAGTATCAAATCATTAAAGTT
* * *
2413701 AAATCATTAAAGTTAACTACTAATTATTATTAAATCATTAAA
1 AAATCATTAAAGTTAACTAATAATTAGTATCAAATCATTAAA
2413743 TTTATCTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (45 bp):
AAATCATTAAAGTTAACTAATAATTAGTATCAAATCATTAAAGTT
Found at i:2413734 original size:31 final size:31
Alignment explanation
Indices: 2413699--2413778 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
2413689 ATCATTAAAG
2413699 TTAAATCATTAAAGTTAACTACTAATTATTA
1 TTAAATCATTAAAGTTAACTACTAATTATTA
* * *
2413730 TTAAATCATTAAATTTATCTATTAATTATTA
1 TTAAATCATTAAAGTTAACTACTAATTATTA
* *
2413761 TCAAATTATTAAAGTTAA
1 TTAAATCATTAAAGTTAA
2413779 AATTTAATAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (31 bp):
TTAAATCATTAAAGTTAACTACTAATTATTA
Found at i:2413798 original size:107 final size:107
Alignment explanation
Indices: 2413401--2413818 Score: 296
Period size: 107 Copynumber: 3.8 Consensus size: 107
2413391 TACTATTATT
* * * * *
2413401 AAATCATTAAAGTTAACTACTAATTATTATTAAATCATTAAAGTTATCTAATAATTAGTATCAAA
1 AAATCATTAAAGTTAATTAATAATTAGTATCAAATCATTAAAGTTAACTAATAATTAGTATCAAA
* * ** * * * *
2413466 TCATTA-AAGTTAACT-AATAATTTGTATCAAATCATAAAGT-T-
66 TCATTATAA-TTAAATCATTAAAGT-TAACTAATAAT-TAGTATC
* * * * * *
2413507 AAATCGTTAAAGTTAATTACTAATTATTATTAAATTATTAAAGTTATCTATTAATTAAATCATTA
1 AAATCATTAAAGTTAATTAATAATTAGTATCAAATCATTAAAGTTA---ACTAA-T--A--ATT-
* * * * *
2413572 AAGTTAACAACTAATTATTATTAAATTATTAAAGTTAACTAATAATTAGTATC
57 -AG-TATCAAATCATTATAATTAAATCATTAAAGTTAACTAATAATTAGTATC
2413625 AAATCATTAAAGTTAATTAATAATTAGTATCAAATCATTAAAGTTAACTAATAATTAGTATCAAA
1 AAATCATTAAAGTTAATTAATAATTAGTATCAAATCATTAAAGTTAACTAATAATTAGTATCAAA
* * *
2413690 TCATTA-AAGTTAAATCATTAAAGTTAACTACTAATTATTATT
66 TCATTATAA-TTAAATCATTAAAGTTAACTAATAATTAGTATC
* * * * *
2413732 AAATCATTAAA-TTTATCTATTAATTATTATCAAATTATTAAAGTTAA--AATTTAA-TAATGAT
1 AAATCATTAAAGTTAAT-TAATAATTAGTATCAAATCATTAAAGTTAACTAA--TAATTAGT-AT
* *
2413793 TAAATCATTATTATTAAATCATTAAA
62 CAAATCATTATAATTAAATCATTAAA
2413819 TTTTACCATT
Statistics
Matches: 253, Mismatches: 38, Indels: 41
0.76 0.11 0.12
Matches are distributed among these distances:
105 2 0.01
106 51 0.20
107 104 0.41
108 3 0.01
109 3 0.01
110 4 0.02
112 2 0.01
114 4 0.02
115 4 0.02
116 5 0.02
117 24 0.09
118 47 0.19
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.41
Consensus pattern (107 bp):
AAATCATTAAAGTTAATTAATAATTAGTATCAAATCATTAAAGTTAACTAATAATTAGTATCAAA
TCATTATAATTAAATCATTAAAGTTAACTAATAATTAGTATC
Found at i:2413803 original size:76 final size:75
Alignment explanation
Indices: 2413399--2413821 Score: 272
Period size: 76 Copynumber: 5.6 Consensus size: 75
2413389 ATTACTATTA
* * *
2413399 TTAAATCATTAAAGTTAACTACTAATTATTATTAAATCATTAAAGTTATCTAATAATTAGTATCA
1 TTAAATCAATAAAGTTAAC-ACTAATTATTATTAAATCATTAAATTTAACTAATAATTAGTATCA
2413464 AATCATTAAAG
65 AATCATTAAAG
* ** * * * * *
2413475 TTAACT-AATAATTTGTATCA--AATCATAAAGTTAAATCGTTAAAGTTAATTACTAATTATTAT
1 TTAAATCAATAAAGT-TAACACTAATTAT-TA-TTAAATCATTAAA-TT--TAACTAA-TA--AT
* * *
2413537 TAAATTATTAAAGTTATCTATTAA-
57 T--AGTATCAAA-TCAT-TA--AAG
* * *
2413561 TTAAATCATTAAAGTTAACAACTAATTATTATTAAATTATTAAAGTTAACTAATAATTAGTATCA
1 TTAAATCAATAAAGTTAAC-ACTAATTATTATTAAATCATTAAATTTAACTAATAATTAGTATCA
2413626 AATCATTAAAG
65 AATCATTAAAG
* * *
2413637 TT-AAT---T-AA--T---A--A-TTAGTATCAAATCATTAAAGTTAACTAATAATTAGTATCAA
1 TTAAATCAATAAAGTTAACACTAATTATTATTAAATCATTAAATTTAACTAATAATTAGTATCAA
2413689 ATCATTAAAG
66 ATCATTAAAG
* * * *
2413699 TTAAATCATTAAAGTTAACTACTAATTATTATTAAATCATTAAATTTATCTATTAATTATTATCA
1 TTAAATCAATAAAGTTAAC-ACTAATTATTATTAAATCATTAAATTTAACTAATAATTAGTATCA
*
2413764 AATTATTAAAG
65 AATCATTAAAG
* * *
2413775 TTAAAATTTAATAATGATTAA-A-TCATTATTATTAAATCATTAAATTT
1 TT-AAA-TCAATAAAG-TTAACACTAATTATTATTAAATCATTAAATTT
2413822 TACCATTTCA
Statistics
Matches: 268, Mismatches: 42, Indels: 74
0.70 0.11 0.19
Matches are distributed among these distances:
62 50 0.19
63 4 0.01
65 1 0.00
66 1 0.00
67 2 0.01
69 2 0.01
71 2 0.01
72 1 0.00
73 6 0.02
74 1 0.00
75 24 0.09
76 81 0.30
77 6 0.02
78 14 0.05
79 13 0.05
81 6 0.02
83 9 0.03
84 9 0.03
85 2 0.01
86 9 0.03
87 19 0.07
88 1 0.00
89 5 0.02
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (75 bp):
TTAAATCAATAAAGTTAACACTAATTATTATTAAATCATTAAATTTAACTAATAATTAGTATCAA
ATCATTAAAG
Found at i:2417350 original size:18 final size:18
Alignment explanation
Indices: 2417327--2417362 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2417317 AGTATGTTCA
2417327 GGGGGTATCGATTCCCCT
1 GGGGGTATCGATTCCCCT
2417345 GGGGGTATCGATTCCCCT
1 GGGGGTATCGATTCCCCT
2417363 CTAAATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.28, G:0.33, T:0.28
Consensus pattern (18 bp):
GGGGGTATCGATTCCCCT
Found at i:2418698 original size:17 final size:16
Alignment explanation
Indices: 2418662--2418730 Score: 72
Period size: 15 Copynumber: 4.3 Consensus size: 16
2418652 AACCGGGTAT
2418662 CGGGTACCCG-AT-TCC
1 CGGGTACCCGAATAT-C
*
2418677 CGGGTACCCGCAAAATC
1 CGGGTACCCG-AATATC
*
2418694 CGGGTACCCGATTA-C
1 CGGGTACCCGAATATC
2418709 CGGGTACCCGTAATATC
1 CGGGTACCCG-AATATC
2418726 CGGGT
1 CGGGT
2418731 CGGGACACGG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
15 21 0.47
16 5 0.11
17 18 0.40
18 1 0.02
ACGTcount: A:0.20, C:0.33, G:0.28, T:0.19
Consensus pattern (16 bp):
CGGGTACCCGAATATC
Found at i:2418703 original size:32 final size:32
Alignment explanation
Indices: 2418662--2418730 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
2418652 AACCGGGTAT
*
2418662 CGGGTACCCGATTCCCGGGTACCCGCAAAATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
* *
2418694 CGGGTACCCGATTACCGGGTACCCGTAATATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
2418726 CGGGT
1 CGGGT
2418731 CGGGACACGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.20, C:0.33, G:0.28, T:0.19
Consensus pattern (32 bp):
CGGGTACCCGATTACCGGGTACCCGCAAAATC
Found at i:2419170 original size:15 final size:15
Alignment explanation
Indices: 2419146--2419175 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2419136 GGGGTTTTTC
*
2419146 TTTAAGAGTCAAAGT
1 TTTAAAAGTCAAAGT
2419161 TTTAAAAGTCAAAGT
1 TTTAAAAGTCAAAGT
2419176 GATACCTCGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (15 bp):
TTTAAAAGTCAAAGT
Found at i:2421383 original size:60 final size:60
Alignment explanation
Indices: 2421262--2421386 Score: 155
Period size: 60 Copynumber: 2.1 Consensus size: 60
2421252 GTAGAGTGAT
* * * * *
2421262 CATTTTGTAACTTTTAATAGTTGAGGGACTCAACAAAATAACATCTTATAGTCAATGGAC
1 CATTTTGTAACTTTTAATAGTTGAGGGACTAAACAAAACAACATCATATAATCAAGGGAC
* *
2421322 CATTTTGTAACTTTTAATAGTT-AGGGGACTAAACAAAGCAACATCATATAAT-TAGGAGAC
1 CATTTTGTAACTTTTAATAGTTGA-GGGACTAAACAAAACAACATCATATAATCAAGG-GAC
2421382 CATTT
1 CATTT
2421387 GTATAATTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
59 3 0.05
60 53 0.95
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAGTTGAGGGACTAAACAAAACAACATCATATAATCAAGGGAC
Found at i:2423811 original size:22 final size:22
Alignment explanation
Indices: 2423786--2423854 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
2423776 TCTGTAATTT
*
2423786 AGTTGCAAAATTTGCGAATTCG
1 AGTTGCAAAATTGGCGAATTCG
*
2423808 AGTTGCGAAATTGGCGAATTCG
1 AGTTGCAAAATTGGCGAATTCG
* * * * *
2423830 AATCGCGAAATTGGTGAATTTG
1 AGTTGCAAAATTGGCGAATTCG
2423852 AGT
1 AGT
2423855 CGTGAAATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (22 bp):
AGTTGCAAAATTGGCGAATTCG
Found at i:2423861 original size:22 final size:22
Alignment explanation
Indices: 2423793--2423863 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
2423783 TTTAGTTGCA
* * *
2423793 AAATTTGCGAATTCGAGTTGCG
1 AAATTGGCGAATTCGAATCGCG
2423815 AAATTGGCGAATTCGAATCGCG
1 AAATTGGCGAATTCGAATCGCG
* * * *
2423837 AAATTGGTGAATTTGAGTCGTG
1 AAATTGGCGAATTCGAATCGCG
2423859 AAATT
1 AAATT
2423864 TGCGTTGCGA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.31
Consensus pattern (22 bp):
AAATTGGCGAATTCGAATCGCG
Found at i:2423990 original size:20 final size:20
Alignment explanation
Indices: 2423965--2424002 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2423955 TGAAGAATCA
2423965 CGTTGCGAAATTAAAAACTG
1 CGTTGCGAAATTAAAAACTG
*
2423985 CGTTGCGAATTTAAAAAC
1 CGTTGCGAAATTAAAAAC
2424003 CGCATTACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.26
Consensus pattern (20 bp):
CGTTGCGAAATTAAAAACTG
Found at i:2424013 original size:20 final size:20
Alignment explanation
Indices: 2423970--2424041 Score: 99
Period size: 20 Copynumber: 3.6 Consensus size: 20
2423960 AATCACGTTG
* * * *
2423970 CGAAATTAAAAACTGCGTTG
1 CGAATTTAAAAACCGCATTA
2423990 CGAATTTAAAAACCGCATTA
1 CGAATTTAAAAACCGCATTA
*
2424010 CGAATTTGAAAACCGCATTA
1 CGAATTTAAAAACCGCATTA
2424030 CGAATTTAAAAA
1 CGAATTTAAAAA
2424042 TTTAAAAACC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (20 bp):
CGAATTTAAAAACCGCATTA
Found at i:2424052 original size:28 final size:28
Alignment explanation
Indices: 2424012--2424069 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
2424002 CCGCATTACG
*
2424012 AATTTGAAAACCGCATTACGAATTTAAA
1 AATTTAAAAACCGCATTACGAATTTAAA
* *
2424040 AATTTAAAAACCGCGTTGCGAATTTAAA
1 AATTTAAAAACCGCATTACGAATTTAAA
2424068 AA
1 AA
2424070 CCGGTGGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.28
Consensus pattern (28 bp):
AATTTAAAAACCGCATTACGAATTTAAA
Found at i:2424580 original size:2 final size:2
Alignment explanation
Indices: 2424573--2424620 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2424563 AGCAATCACT
2424573 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
2424615 TA TA TA
1 TA TA TA
2424621 ATAAAACCTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2425794 original size:164 final size:164
Alignment explanation
Indices: 2425523--2425851 Score: 633
Period size: 164 Copynumber: 2.0 Consensus size: 164
2425513 TAATATCATG
2425523 CAGGAAATCTCTCTTTTTCCATTTATTTTATTTTTTATAGGTGATCAGTTCACTTACCTAATATG
1 CAGGAAATCTCTCTTTTTCCATTTATTTTATTTTTTATAGGTGATCAGTTCACTTACCTAATATG
2425588 CTCACAAAATCCCTACAAGAACTTACCCCACCACCAACGCCCATCAGTCCGGATTCCCAATTGTC
66 CTCACAAAATCCCTACAAGAACTTACCCCACCACCAACGCCCATCAGTCCGGATT-CCAATTGTC
*
2425653 -ACATTTCATCGGCTTACCCCAAATCTCTATCTTT
130 AACATTTCATCGGCTTACCCAAAATCTCTATCTTT
2425687 CAGGAAATCTCTCTTTTTCCATTTATTTTATTTTTTATAGGTGATCAGTTCACTTACCTAATATG
1 CAGGAAATCTCTCTTTTTCCATTTATTTTATTTTTTATAGGTGATCAGTTCACTTACCTAATATG
2425752 CTCACAAAATCCCTACAAGAACTTACCCCACCACCAACGCCCATCAGTCCGGATTCCAATTGTCA
66 CTCACAAAATCCCTACAAGAACTTACCCCACCACCAACGCCCATCAGTCCGGATTCCAATTGTCA
2425817 ACATTTCATCGGCTTACCCAAAATCTCTATCTTT
131 ACATTTCATCGGCTTACCCAAAATCTCTATCTTT
2425851 C
1 C
2425852 TGAATTTTGA
Statistics
Matches: 163, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
163 9 0.06
164 154 0.94
ACGTcount: A:0.27, C:0.29, G:0.09, T:0.34
Consensus pattern (164 bp):
CAGGAAATCTCTCTTTTTCCATTTATTTTATTTTTTATAGGTGATCAGTTCACTTACCTAATATG
CTCACAAAATCCCTACAAGAACTTACCCCACCACCAACGCCCATCAGTCCGGATTCCAATTGTCA
ACATTTCATCGGCTTACCCAAAATCTCTATCTTT
Found at i:2426882 original size:20 final size:21
Alignment explanation
Indices: 2426844--2426883 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2426834 CTTTAGATTA
2426844 ATATTTTTAATTATTAAACAT
1 ATATTTTTAATTATTAAACAT
2426865 ATATCTTTT-ATT-TTAAACA
1 ATAT-TTTTAATTATTAAACA
2426884 AAAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATTTTTAATTATTAAACAT
Found at i:2427519 original size:179 final size:182
Alignment explanation
Indices: 2427275--2427649 Score: 632
Period size: 179 Copynumber: 2.1 Consensus size: 182
2427265 AAGTGTGATA
* *
2427275 TTCGGCTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAATCAGACCGACCTGAAAATATATATAAT
1 TTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAATCAGACCAACCTGAAAATATATATAAT
*
2427340 TCAGGTCGGGTCGGATTAATTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTC
66 TCAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTC
*
2427405 -G-G-ATTTCTAATACATATATTCGGGTCGGGTCGGATGAAACTTTTTTTTG
131 GGCGAATTTCTAATACATATATTCGGGTCGGGTCGGATGAAACTTTATTTTG
*
2427454 TTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAATCGGACCAACCTGAAAAT-TAATATAA
1 TTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAATCAGACCAACCTGAAAATAT-ATATAA
*
2427518 TTCCGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGT
65 TTCAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGT
*
2427583 CGGGTCGAATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTG
130 C-GG-CGAATTTCTAATACATATATTCGGGTCGGGTCGGATGAAACTTTATTTTG
2427638 TTCGGGTCGGGT
1 TTCGGGTCGGGT
2427650 TTTTTAAGTG
Statistics
Matches: 183, Mismatches: 7, Indels: 7
0.93 0.04 0.04
Matches are distributed among these distances:
178 1 0.01
179 123 0.67
181 1 0.01
183 1 0.01
184 57 0.31
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (182 bp):
TTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAATCAGACCAACCTGAAAATATATATAAT
TCAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTC
GGCGAATTTCTAATACATATATTCGGGTCGGGTCGGATGAAACTTTATTTTG
Found at i:2427679 original size:27 final size:28
Alignment explanation
Indices: 2427638--2427702 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
2427628 CTTTATTTTG
2427638 TTCGGGTCGGG-TTTTTTAAGTGTGATA
1 TTCGGGTCGGGTTTTTTTAAGTGTGATA
*
2427665 TTTGGGTCGGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTTTTTTTAAGTGTGATA
2427693 TTCGGGTCGG
1 TTCGGGTCGG
2427703 ATTGGGTCGG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 10 0.29
28 25 0.71
ACGTcount: A:0.12, C:0.08, G:0.35, T:0.45
Consensus pattern (28 bp):
TTCGGGTCGGGTTTTTTTAAGTGTGATA
Found at i:2427852 original size:37 final size:38
Alignment explanation
Indices: 2427797--2427869 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
2427787 TTTTGTTCGG
* *
2427797 GTCGGGTCGGGTC-GGGTTTTTTAAGTGTGATATTCAA
1 GTCGAGTCGGGTCAGGTTTTTTTAAGTGTGATATTCAA
2427834 GTCGAGTCGGGTCAGGTTTTTTTAAGTGTGATATTC
1 GTCGAGTCGGGTCAGGTTTTTTTAAGTGTGATATTC
2427870 GGGTCAGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
37 12 0.36
38 21 0.64
ACGTcount: A:0.16, C:0.11, G:0.33, T:0.40
Consensus pattern (38 bp):
GTCGAGTCGGGTCAGGTTTTTTTAAGTGTGATATTCAA
Found at i:2428439 original size:38 final size:38
Alignment explanation
Indices: 2428392--2428469 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 38
2428382 TCTGACATGT
*
2428392 CTGCGAACCAAACAGAATATGAAATT-GTATTCCAATTC
1 CTGCCAACCAAACAGAATATGAAATTAG-ATTCCAATTC
* *
2428430 CTGCCAACCAAACAGAATATGGAATTAGATTCTAATTC
1 CTGCCAACCAAACAGAATATGAAATTAGATTCCAATTC
2428468 CT
1 CT
2428470 ACATATTACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 35 0.97
39 1 0.03
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (38 bp):
CTGCCAACCAAACAGAATATGAAATTAGATTCCAATTC
Found at i:2437282 original size:2 final size:2
Alignment explanation
Indices: 2437275--2437301 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2437265 TGTCCATCAC
2437275 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 T
2437302 GATTTTTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2437806 original size:3 final size:3
Alignment explanation
Indices: 2437798--2437823 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2437788 AATCTCTTAT
2437798 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2437824 TATGAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2437894 original size:22 final size:22
Alignment explanation
Indices: 2437869--2437912 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2437859 AATTTTTTAT
*
2437869 ATAAATCCAAATTCTACTGTGA
1 ATAAACCCAAATTCTACTGTGA
*
2437891 ATAAACCCAACTTCTACTGTGA
1 ATAAACCCAAATTCTACTGTGA
2437913 GGAAAGGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.30
Consensus pattern (22 bp):
ATAAACCCAAATTCTACTGTGA
Found at i:2443738 original size:21 final size:21
Alignment explanation
Indices: 2443714--2443758 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2443704 GTAACAGTTA
* * *
2443714 ATAATTTTGATATAATATTTT
1 ATAAATTTAATATAATAATTT
*
2443735 ATAAATTTAATATGATAATTT
1 ATAAATTTAATATAATAATTT
2443756 ATA
1 ATA
2443759 TATAAATAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (21 bp):
ATAAATTTAATATAATAATTT
Found at i:2450564 original size:14 final size:14
Alignment explanation
Indices: 2450547--2450575 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2450537 TACACTTGCA
2450547 AACTGAAAAAAGGG
1 AACTGAAAAAAGGG
2450561 AACTGAAAAAAGGG
1 AACTGAAAAAAGGG
2450575 A
1 A
2450576 TTGCAGGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.28, T:0.07
Consensus pattern (14 bp):
AACTGAAAAAAGGG
Found at i:2452094 original size:3 final size:3
Alignment explanation
Indices: 2452086--2452115 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2452076 CTTGCTATAT
2452086 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2452116 TCTCATCTCT
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):
ATA
Found at i:2459413 original size:20 final size:20
Alignment explanation
Indices: 2459384--2459426 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2459374 TTTCCACCAC
*
2459384 ATGCAACTACATGCTTCTAA
1 ATGCAACTACATGCTCCTAA
* *
2459404 ATGCATCTACATGGTCCTAA
1 ATGCAACTACATGCTCCTAA
2459424 ATG
1 ATG
2459427 AGCTCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTACATGCTCCTAA
Found at i:2464465 original size:7 final size:7
Alignment explanation
Indices: 2464445--2464530 Score: 106
Period size: 7 Copynumber: 12.7 Consensus size: 7
2464435 GTTAGATTAC
2464445 ACCCTAA
1 ACCCTAA
2464452 A-CCTAA
1 ACCCTAA
2464458 ACCCTAA
1 ACCCTAA
2464465 ACCCTAA
1 ACCCTAA
**
2464472 ACTATAA
1 ACCCTAA
*
2464479 ATCCTAA
1 ACCCTAA
2464486 A-CCTAA
1 ACCCTAA
2464492 ACCCTAA
1 ACCCTAA
*
2464499 ACCCTTA
1 ACCCTAA
*
2464506 ATCCTAA
1 ACCCTAA
2464513 A-CCTAA
1 ACCCTAA
2464519 ACCCTAA
1 ACCCTAA
2464526 ACCCT
1 ACCCT
2464531 TAATCCGATT
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
6 18 0.26
7 50 0.74
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (7 bp):
ACCCTAA
Found at i:2464529 original size:27 final size:27
Alignment explanation
Indices: 2464445--2464536 Score: 132
Period size: 27 Copynumber: 3.4 Consensus size: 27
2464435 GTTAGATTAC
*
2464445 ACCC-TAAACCTAAACCCTAAACCCTAA
1 ACCCTTAATCCTAAA-CCTAAACCCTAA
** *
2464472 ACTATAAATCCTAAACCTAAACCCTAA
1 ACCCTTAATCCTAAACCTAAACCCTAA
2464499 ACCCTTAATCCTAAACCTAAACCCTAA
1 ACCCTTAATCCTAAACCTAAACCCTAA
2464526 ACCCTTAATCC
1 ACCCTTAATCC
2464537 GATTATATGA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
27 49 0.86
28 8 0.14
ACGTcount: A:0.42, C:0.37, G:0.00, T:0.21
Consensus pattern (27 bp):
ACCCTTAATCCTAAACCTAAACCCTAA
Found at i:2464665 original size:14 final size:14
Alignment explanation
Indices: 2464624--2464690 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 14
2464614 AACCCTAAAC
*
2464624 TAAA-TATAAACCC
1 TAAACTATAAACCT
*
2464637 TAAATCT-CAAACCT
1 TAAA-CTATAAACCT
*
2464651 TAAACTATAAGCCT
1 TAAACTATAAACCT
*
2464665 TAAACTATAAACCA
1 TAAACTATAAACCT
*
2464679 TAAACCATAAAC
1 TAAACTATAAAC
2464691 TCTAAGCCTT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
13 6 0.14
14 37 0.84
15 1 0.02
ACGTcount: A:0.51, C:0.24, G:0.01, T:0.24
Consensus pattern (14 bp):
TAAACTATAAACCT
Found at i:2464675 original size:21 final size:21
Alignment explanation
Indices: 2464651--2464691 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2464641 TCTCAAACCT
* * *
2464651 TAAACTATAAGCCTTAAACTA
1 TAAACCATAAACCATAAACTA
2464672 TAAACCATAAACCATAAACT
1 TAAACCATAAACCATAAACT
2464692 CTAAGCCTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.22, G:0.02, T:0.24
Consensus pattern (21 bp):
TAAACCATAAACCATAAACTA
Found at i:2464683 original size:156 final size:154
Alignment explanation
Indices: 2464396--2464684 Score: 406
Period size: 156 Copynumber: 1.9 Consensus size: 154
2464386 CATTGTATAT
2464396 TACTAAAAGAAAAATAAAAGCTCATTTAATTAAGCACATGTTAGATTACACCCTAAACCTAAACC
1 TACTAAAAGAAAAATAAAAGCTCATTTAATTAAGCACATGTTAGATTACACCCTAAACCTAAACC
* * * *
2464461 CTAAACCCTAAACTATAAATCCTAAACCTAAACCCTAAACCCTTAATCCTAAACCTAAACCCTAA
66 CTAAA-CCTAAACTATAAACCCTAAACCTAAACCCTAAA-CCTTAAGCCTAAACATAAACCATAA
2464526 ACCCTTAATCCGATTATATGACAGGG
129 ACCCTTAATCCGATTATATGACAGGG
* *
2464552 TACTAAAAGAAAAATAAAAGC-CTATTTAATTATGCCCATGTTAGATTACACCCTAAATCCTAAA
1 TACTAAAAGAAAAATAAAAGCTC-ATTTAATTAAGCACATGTTAGATTACACCCTAAA-CCTAAA
* *
2464616 CCCTAAA-CTAAA-TATAAACCCTAAATCTCAAACCTTAAA-CTATAAGCCTTAAACTATAAACC
64 CCCTAAACCTAAACTATAAACCCTAAACCT-AAACCCTAAACCT-TAAGCC-TAAAC-ATAAACC
2464678 ATAAACC
125 ATAAACC
2464685 ATAAACTCTA
Statistics
Matches: 119, Mismatches: 8, Indels: 12
0.86 0.06 0.09
Matches are distributed among these distances:
153 2 0.02
154 19 0.16
155 20 0.17
156 65 0.55
157 13 0.11
ACGTcount: A:0.45, C:0.25, G:0.06, T:0.25
Consensus pattern (154 bp):
TACTAAAAGAAAAATAAAAGCTCATTTAATTAAGCACATGTTAGATTACACCCTAAACCTAAACC
CTAAACCTAAACTATAAACCCTAAACCTAAACCCTAAACCTTAAGCCTAAACATAAACCATAAAC
CCTTAATCCGATTATATGACAGGG
Found at i:2464709 original size:14 final size:13
Alignment explanation
Indices: 2464692--2464734 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
2464682 ACCATAAACT
*
2464692 CTAAGCCTTAAGCC
1 CTAACCCTTAA-CC
2464706 CTAAACCCTTAACC
1 CT-AACCCTTAACC
2464720 CTTAACCCTTAACC
1 C-TAACCCTTAACC
2464734 C
1 C
2464735 AATTATGTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 17 0.65
15 9 0.35
ACGTcount: A:0.30, C:0.42, G:0.05, T:0.23
Consensus pattern (13 bp):
CTAACCCTTAACC
Found at i:2464710 original size:21 final size:21
Alignment explanation
Indices: 2464658--2464728 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 21
2464648 CCTTAAACTA
* * *
2464658 TAAGCCTTAAACTATAAACCA
1 TAAGCCCTAAACTCTAAACCT
* * *
2464679 TAAACCATAAACTCTAAGCCT
1 TAAGCCCTAAACTCTAAACCT
* *
2464700 TAAGCCCTAAACCCTTAACCCT
1 TAAGCCCTAAACTC-TAAACCT
2464722 TAA-CCCT
1 TAAGCCCT
2464729 TAACCCAATT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 31 0.77
22 9 0.22
ACGTcount: A:0.39, C:0.32, G:0.04, T:0.24
Consensus pattern (21 bp):
TAAGCCCTAAACTCTAAACCT
Found at i:2464732 original size:7 final size:7
Alignment explanation
Indices: 2464697--2464734 Score: 58
Period size: 7 Copynumber: 5.3 Consensus size: 7
2464687 AAACTCTAAG
2464697 CCTTAAGC
1 CCTTAA-C
*
2464705 CCTAAAC
1 CCTTAAC
2464712 CCTTAAC
1 CCTTAAC
2464719 CCTTAAC
1 CCTTAAC
2464726 CCTTAAC
1 CCTTAAC
2464733 CC
1 CC
2464735 AATTATGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
7 23 0.82
8 5 0.18
ACGTcount: A:0.29, C:0.45, G:0.03, T:0.24
Consensus pattern (7 bp):
CCTTAAC
Found at i:2467699 original size:21 final size:21
Alignment explanation
Indices: 2467670--2467722 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2467660 ATTCTGACTA
2467670 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
2467691 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
2467712 TCGCAATGCGA
1 TCGCATTGCGA
2467723 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:2467737 original size:20 final size:21
Alignment explanation
Indices: 2467712--2467922 Score: 148
Period size: 20 Copynumber: 10.4 Consensus size: 21
2467702 TTTTCCTAAT
2467712 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGTAAA
* * *
2467732 TCGCAATGCAAATTAGGAAAA
1 TCGCAATGCGAATTACGTAAA
2467753 TCGCAATGC-AATTACGTAAA
1 TCGCAATGCGAATTACGTAAA
* *
2467773 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGTAAA
* *
2467794 TCGTAATGCG-ATTGCGTAAA
1 TCGCAATGCGAATTACGTAAA
* *
2467814 TCGCATTGTG-ATTACGT-AA
1 TCGCAATGCGAATTACGTAAA
* * * * *
2467833 TCGCATTGCGATTTTCCTAAT
1 TCGCAATGCGAATTACGTAAA
* * * * * *
2467854 TCGTATTGCGATTTTCCTAAT
1 TCGCAATGCGAATTACGTAAA
* * *
2467875 TCGCACTTCGATTTACGT-AA
1 TCGCAATGCGAATTACGTAAA
* *
2467895 TCGCATTGCGATTTA-GTAAA
1 TCGCAATGCGAATTACGTAAA
2467915 TCGCAATG
1 TCGCAATG
2467923 AGATTCTGAC
Statistics
Matches: 156, Mismatches: 30, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
19 13 0.08
20 76 0.49
21 67 0.43
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (21 bp):
TCGCAATGCGAATTACGTAAA
Found at i:2467758 original size:41 final size:41
Alignment explanation
Indices: 2467712--2467818 Score: 162
Period size: 41 Copynumber: 2.6 Consensus size: 41
2467702 TTTTCCTAAT
2467712 TCGCAATGCGAATACGTAAATCGCAATGCAAATTAGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCAAATTAGGAAAA
*
2467753 TCGCAATGC-AATTACGTAAATCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAATCGCAATGCAAATTAGGAAAA
* * *
2467794 TCGTAATGCGATTGCGTAAATCGCA
1 TCGCAATGCGAATACGTAAATCGCA
2467819 TTGTGATTAC
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
40 2 0.03
41 57 0.95
42 1 0.02
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (41 bp):
TCGCAATGCGAATACGTAAATCGCAATGCAAATTAGGAAAA
Found at i:2467861 original size:21 final size:21
Alignment explanation
Indices: 2467833--2467908 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
2467823 GATTACGTAA
2467833 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
*
2467854 TCGTATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
* *
2467875 TCGCACTT-CGATTTACGTAA-
1 TCGCA-TTGCGATTTTCCTAAT
2467895 TCGCATTGCGATTT
1 TCGCATTGCGATTT
2467909 AGTAAATCGC
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
19 2 0.04
20 11 0.22
21 34 0.69
22 2 0.04
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCTAAT
Found at i:2467927 original size:20 final size:20
Alignment explanation
Indices: 2467884--2467927 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2467874 TTCGCACTTC
* *
2467884 GATTTACGTAATCGCATTGC
1 GATTTACGTAATCGCAATGA
2467904 GATTTA-GTAAATCGCAATGA
1 GATTTACGT-AATCGCAATGA
2467924 GATT
1 GATT
2467928 CTGACTATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (20 bp):
GATTTACGTAATCGCAATGA
Found at i:2471384 original size:19 final size:19
Alignment explanation
Indices: 2471349--2471423 Score: 70
Period size: 19 Copynumber: 4.2 Consensus size: 19
2471339 CTTAATGTCT
* *
2471349 ATCGCAACGCGGAAATGAGA
1 ATCGCAATGC-GAAATGAAA
2471369 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2471388 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
2471402 ATTGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2471421 ATC
1 ATC
2471424 TTAATGTCGT
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
14 9 0.20
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 20 0.45
20 9 0.20
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2471598 original size:14 final size:14
Alignment explanation
Indices: 2471579--2471615 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2471569 CATCAATTAA
2471579 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2471593 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2471607 ACAAATCAA
1 ACAAATCAA
2471616 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2473603 original size:20 final size:20
Alignment explanation
Indices: 2473578--2473687 Score: 103
Period size: 19 Copynumber: 5.9 Consensus size: 20
2473568 CGCGATTATA
*
2473578 GTTTCGCGTTGCGATTTTTG
1 GTTTCGCGTTGCGATTTTTC
2473598 GTTTCGCGTTGCGA-TTTTC
1 GTTTCGCGTTGCGATTTTTC
*
2473617 ATTTCGCGTTGCGA---TTC
1 GTTTCGCGTTGCGATTTTTC
*
2473634 ---TCTCGTTGCGA-TTTTC
1 GTTTCGCGTTGCGATTTTTC
2473650 GTTTCGCGTTGCGA-TTTTC
1 GTTTCGCGTTGCGATTTTTC
* *
2473669 ATTCTCTCGTTGCGATTTT
1 GTT-TCGCGTTGCGATTTT
2473688 CATTTCAACC
Statistics
Matches: 77, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
14 10 0.13
16 3 0.04
17 3 0.04
19 34 0.44
20 24 0.31
21 3 0.04
ACGTcount: A:0.07, C:0.21, G:0.24, T:0.48
Consensus pattern (20 bp):
GTTTCGCGTTGCGATTTTTC
Found at i:2473623 original size:39 final size:36
Alignment explanation
Indices: 2473579--2473693 Score: 128
Period size: 39 Copynumber: 3.1 Consensus size: 36
2473569 GCGATTATAG
*
2473579 TTTCGCGTTGCGATTTTTGGTTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGA-TTTT--TTTCTCGTTGCGATTTTCA
* *
2473618 TTTCGCGTTGCGA---TTCTCTCGTTGCGATTTTCG
1 TTTCGCGTTGCGATTTTTTTCTCGTTGCGATTTTCA
2473651 TTTCGCGTTGCGATTTTCATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTT--TT-TCTCGTTGCGATTTTCA
2473690 TTTC
1 TTTC
2473694 AACCAAAAGA
Statistics
Matches: 65, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
33 29 0.45
35 1 0.02
36 1 0.02
38 1 0.02
39 33 0.51
ACGTcount: A:0.08, C:0.22, G:0.22, T:0.49
Consensus pattern (36 bp):
TTTCGCGTTGCGATTTTTTTCTCGTTGCGATTTTCA
Found at i:2473646 original size:33 final size:34
Alignment explanation
Indices: 2473604--2473693 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 34
2473594 TTTGGTTTCG
2473604 CGTTGCGATTTTCATTTCGCGTTGCG-ATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGTATTCTCT
*
2473637 CGTTGCGATTTTCGTTTCGCGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCG----T-ATTCTCT
2473676 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
2473694 AACCAAAAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
33 25 0.51
39 24 0.49
ACGTcount: A:0.09, C:0.23, G:0.20, T:0.48
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTCGCGTTGCGTATTCTCT
Found at i:2473688 original size:20 final size:20
Alignment explanation
Indices: 2473630--2473691 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
2473620 TCGCGTTGCG
2473630 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
* *
2473650 GTT-TCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
2473669 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
2473689 ATT
1 ATT
2473692 TCAACCAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 17 0.46
20 20 0.54
ACGTcount: A:0.10, C:0.23, G:0.18, T:0.50
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:2473893 original size:94 final size:93
Alignment explanation
Indices: 2473783--2474061 Score: 394
Period size: 94 Copynumber: 3.1 Consensus size: 93
2473773 ATGGATTGCA
* *
2473783 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
2473848 TAGCAGAATTGGCAGCAAACGAACAAAT
66 TAGCAGAATTGGCAGCAAACGAACAAAT
2473876 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
2473941 TTAGCAGAATTGGCAG-TAAC---CGAAT
65 TTAGCAGAATTGGCAGCAAACGAACAAAT
* *
2473966 ATACTTCAACCAAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT-AATAA-ACA-A-
1 TTACTTCAACC-AAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* * *
2474027 TTTAGCAGTATTGGCAGCAACCGAATAAAT
64 TTTAGCAGAATTGGCAGCAAACGAACAAAT
2474057 TTACT
1 TTACT
2474062 AAGCAATCTA
Statistics
Matches: 167, Mismatches: 12, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
87 16 0.10
88 3 0.02
89 10 0.06
90 23 0.14
91 34 0.20
93 7 0.04
94 74 0.44
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.22
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAAACGAACAAAT
Found at i:2474899 original size:21 final size:22
Alignment explanation
Indices: 2474857--2474899 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2474847 AATAACAAAC
*
2474857 ATTAGTAATTGTTAAATAATTA
1 ATTAGTAATTGTTAAAAAATTA
2474879 ATTA-TAATT-TTAAAAATATTA
1 ATTAGTAATTGTTAAAAA-ATTA
2474900 TATAGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (22 bp):
ATTAGTAATTGTTAAAAAATTA
Found at i:2475771 original size:20 final size:20
Alignment explanation
Indices: 2475746--2475801 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
2475736 CTTTTGGTTG
2475746 AAATGAAAATCGCAACGAGA
1 AAATGAAAATCGCAACGAGA
* *
2475766 AAATGAAAATCGCAACGCGG
1 AAATGAAAATCGCAACGAGA
**
2475786 AAATGACTATCGCAAC
1 AAATGAAAATCGCAAC
2475802 AAGAGAATCG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.12
Consensus pattern (20 bp):
AAATGAAAATCGCAACGAGA
Found at i:2475789 original size:40 final size:37
Alignment explanation
Indices: 2475745--2475838 Score: 97
Period size: 33 Copynumber: 2.6 Consensus size: 37
2475735 TCTTTTGGTT
*
2475745 GAAATGAAAATCGCAACGAGAAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAG-AAA-GAAAATCGCAACAC
** *
2475784 GGAAATGACTATCGCAAC----AAGAGAATCGCAACAC
1 -GAAATGAAAATCGCAACGAGAAAGAAAATCGCAACAC
2475818 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
2475839 GAATCACAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
33 15 0.34
34 12 0.27
35 2 0.05
40 15 0.34
ACGTcount: A:0.49, C:0.19, G:0.21, T:0.11
Consensus pattern (37 bp):
GAAATGAAAATCGCAACGAGAAAGAAAATCGCAACAC
Found at i:2475831 original size:33 final size:34
Alignment explanation
Indices: 2475773--2475843 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 34
2475763 AGAAAATGAA
* **
2475773 AATCGCAACGCGGAAATGACTATCGCAACAAGAG
1 AATCGCAACACGGAAATGAAAATCGCAACAAGAG
*
2475807 AATCGCAACAC-GAAATGAAAATCGCAACGAGAG
1 AATCGCAACACGGAAATGAAAATCGCAACAAGAG
2475840 AATC
1 AATC
2475844 ACAATGCGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 23 0.70
34 10 0.30
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (34 bp):
AATCGCAACACGGAAATGAAAATCGCAACAAGAG
Found at i:2475903 original size:33 final size:33
Alignment explanation
Indices: 2475848--2475928 Score: 99
Period size: 33 Copynumber: 2.5 Consensus size: 33
2475838 AGAATCACAA
** * *
2475848 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCACATTGCGATTATCTCGT
*
2475881 TGCGATTTTCATTTCACATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCACATTGCGATTATCTCGT
**
2475914 TGCGATAGTCATTTC
1 TGCGATTTTCATTTC
2475929 CGCGTTGCGA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCACATTGCGATTATCTCGT
Found at i:2476515 original size:20 final size:20
Alignment explanation
Indices: 2476474--2476585 Score: 129
Period size: 20 Copynumber: 5.5 Consensus size: 20
2476464 GCTATGTAAA
2476474 TCGCATTGCGATAGTTA-G-AT
1 TCGCATTGCGAT--TTACGTAT
*
2476494 TCACATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
2476514 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
* *
2476535 TCGCATTGCGATTTACTTAA
1 TCGCATTGCGATTTACGTAT
*
2476555 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
2476575 TCGCATTGCGA
1 TCGCATTGCGA
2476586 ATTAGGAAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
18 3 0.04
19 1 0.01
20 56 0.72
21 18 0.23
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:2476549 original size:41 final size:40
Alignment explanation
Indices: 2476492--2476585 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
2476482 CGATAGTTAG
* * *
2476492 ATTCACATTGCGATTTACGTATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* * *
2476532 AATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
2476573 ATTCGCATTGCGA
1 ATTCGCATTGCGA
2476586 ATTAGGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 13 0.28
41 34 0.72
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
Found at i:2476607 original size:22 final size:21
Alignment explanation
Indices: 2476582--2476628 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2476572 TATTCGCATT
2476582 GCGAATTAGGAAAAATCGCAAC
1 GCGAATTAGG-AAAATCGCAAC
* * *
2476604 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
2476625 GCGA
1 GCGA
2476629 TAGTCAGACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.38, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:2481243 original size:10 final size:12
Alignment explanation
Indices: 2481218--2481246 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2481208 AATAGTTTCC
2481218 TAAAAAAAATTA
1 TAAAAAAAATTA
2481230 TAAAAAAAATTA
1 TAAAAAAAATTA
2481242 -AAAAA
1 TAAAAA
2481247 CTTACTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
TAAAAAAAATTA
Found at i:2485957 original size:45 final size:45
Alignment explanation
Indices: 2485893--2485985 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
2485883 TGTCCTTTAA
2485893 CATATTGCTTTTATTACTTTATATACTCACCTTAGTTACTGACTC
1 CATATTGCTTTTATTACTTTATATACTCACCTTAGTTACTGACTC
2485938 CATATTGCTTTTATTACTTTATATACTCACCTTAGTTACTGACTC
1 CATATTGCTTTTATTACTTTATATACTCACCTTAGTTACTGACTC
2485983 CAT
1 CAT
2485986 CTCTACATTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.25, C:0.23, G:0.06, T:0.46
Consensus pattern (45 bp):
CATATTGCTTTTATTACTTTATATACTCACCTTAGTTACTGACTC
Found at i:2486546 original size:20 final size:20
Alignment explanation
Indices: 2486523--2486560 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2486513 TCCAATAAAA
* *
2486523 TCAAATATTTTTTTACCAAT
1 TCAAATATGTTATTACCAAT
2486543 TCAAATATGTTATTACCA
1 TCAAATATGTTATTACCA
2486561 CTACTTTTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.16, G:0.03, T:0.45
Consensus pattern (20 bp):
TCAAATATGTTATTACCAAT
Found at i:2494999 original size:17 final size:19
Alignment explanation
Indices: 2494977--2495020 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
2494967 CAACTATGTT
2494977 AATATTT-TACAA-ATTGA
1 AATATTTATACAACATTGA
*
2494994 AATATTTATGCAACATTGA
1 AATATTTATACAACATTGA
2495013 AATTATTT
1 AA-TATTT
2495021 GGAATAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 7 0.30
18 4 0.17
19 7 0.30
20 5 0.22
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (19 bp):
AATATTTATACAACATTGA
Found at i:2497308 original size:19 final size:20
Alignment explanation
Indices: 2497255--2497310 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
2497245 AATAACGATT
*
2497255 TTAAATTTTTAAATTTAAATA
1 TTAATTTTTTAAA-TTAAATA
***
2497276 TTAATTTAAAAAATTAAATA
1 TTAATTTTTTAAATTAAATA
2497296 TT-ATTTTTTAAATTA
1 TTAATTTTTTAAATTA
2497311 TAAATTTAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
19 10 0.36
20 9 0.32
21 9 0.32
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTAATTTTTTAAATTAAATA
Found at i:2499835 original size:102 final size:102
Alignment explanation
Indices: 2499691--2499889 Score: 292
Period size: 102 Copynumber: 2.0 Consensus size: 102
2499681 AAATAAAACC
* *
2499691 CTTTTTAAATATCACCGATATATAAGTTCTGGTTTCTAATCCCTTTTAATTCAAGTTTGAGGAAG
1 CTTTTTAAATATCACCGATATATAAGTTCTGGTTTCTAATCCCGTTTAATTCAAGTTCGAGGAAG
2499756 ACAGGGAACTTTTGTGAATGTGGTTAGTTTCTAATCT
66 ACAGGGAACTTTTGTGAATGTGGTTAGTTTCTAATCT
* * * **
2499793 CTTTTTAAATATCACCTATTTATTAA-TTTTGGTTTCTAATCCCGTTTAATTTGAGTTCGAGGAA
1 CTTTTTAAATATCACCGATATA-TAAGTTCTGGTTTCTAATCCCGTTTAATTCAAGTTCGAGGAA
* * *
2499857 GATAGGGAACTTTTGTGGATGTGGTTGGTTTCT
65 GACAGGGAACTTTTGTGAATGTGGTTAGTTTCT
2499890 TTTCATCTGT
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
102 83 0.97
103 3 0.03
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.43
Consensus pattern (102 bp):
CTTTTTAAATATCACCGATATATAAGTTCTGGTTTCTAATCCCGTTTAATTCAAGTTCGAGGAAG
ACAGGGAACTTTTGTGAATGTGGTTAGTTTCTAATCT
Found at i:2500050 original size:22 final size:22
Alignment explanation
Indices: 2500025--2500096 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
2500015 TAAAGTAATT
2500025 CCTTCTTGTCTTTCTTCTTTTC
1 CCTTCTTGTCTTTCTTCTTTTC
* * ** * *
2500047 CCTTTTTGTATTTAGTGTAGTT-
1 CCTTCTTGTCTTTCTTCT-TTTC
2500069 CCTTCTTGTCTTTCTTCTTTTC
1 CCTTCTTGTCTTTCTTCTTTTC
2500091 CCTTCT
1 CCTTCT
2500097 CCAGAGAGCA
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.04, C:0.26, G:0.08, T:0.61
Consensus pattern (22 bp):
CCTTCTTGTCTTTCTTCTTTTC
Found at i:2500071 original size:44 final size:44
Alignment explanation
Indices: 2500005--2500094 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
2499995 TTTATATTTG
2500005 TTTTTGTATTTAAAGTAATTCCTTCTTGTCTTTCTTCTTTTCCC
1 TTTTTGTATTTAAAGTAATTCCTTCTTGTCTTTCTTCTTTTCCC
** *
2500049 TTTTTGTATTTAGTGTAGTTCCTTCTTGTCTTTCTTCTTTTCCC
1 TTTTTGTATTTAAAGTAATTCCTTCTTGTCTTTCTTCTTTTCCC
2500093 TT
1 TT
2500095 CTCCAGAGAG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.10, C:0.20, G:0.09, T:0.61
Consensus pattern (44 bp):
TTTTTGTATTTAAAGTAATTCCTTCTTGTCTTTCTTCTTTTCCC
Found at i:2505260 original size:20 final size:20
Alignment explanation
Indices: 2505235--2505286 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
2505225 CAACGCGATC
2505235 CCAGAATCGCAAATAAGTTT
1 CCAGAATCGCAAATAAGTTT
*
2505255 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATAAGTTT
*
2505275 CCAAAATCGCAA
1 CCAGAATCGCAA
2505287 CGCGATTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATAAGTTT
Found at i:2505303 original size:21 final size:20
Alignment explanation
Indices: 2505276--2505374 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
2505266 AATCAGTTTC
2505276 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
2505297 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
2505318 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
2505338 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
2505359 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2505375 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:2505403 original size:20 final size:20
Alignment explanation
Indices: 2505341--2505534 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
2505331 CGATTTTCCA
* ** *
2505341 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
2505361 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
2505381 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2505401 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
2505421 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
2505441 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2505461 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
2505481 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
2505501 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
2505522 AAATCGCAACGCG
1 AAATCGCAACGCG
2505535 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:2505425 original size:60 final size:60
Alignment explanation
Indices: 2505341--2505534 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
2505331 CGATTTTCCA
* ** * *
2505341 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
2505401 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
2505461 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
2505522 AAATCGCAACGCG
1 AAATCGCAACGCG
2505535 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:2505955 original size:33 final size:33
Alignment explanation
Indices: 2505916--2505986 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2505906 TTCACTTAGA
*
2505916 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
2505949 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
2505982 TTTCA
1 TTTCA
2505987 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:2506126 original size:14 final size:14
Alignment explanation
Indices: 2506107--2506161 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2506097 AGAATGACTG
2506107 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
2506121 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
2506140 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
2506154 TCGCAACG
1 TCGCAACG
2506162 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:2506199 original size:19 final size:18
Alignment explanation
Indices: 2506172--2506289 Score: 80
Period size: 14 Copynumber: 7.1 Consensus size: 18
2506162 CGAAACCAAA
*
2506172 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCA-T
2506191 TCGCGTTGCGA--TTC--
1 TCGCGTTGCGATTTTCAT
*
2506205 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCA-T
2506224 TCGCGTTGCGA--TTC--
1 TCGCGTTGCGATTTTCAT
* *
2506238 TCTCGTTGCGATTGTCAT
1 TCGCGTTGCGATTTTCAT
2506256 CTCGCGTTGCGA--TTC--
1 -TCGCGTTGCGATTTTCAT
*
2506271 TCTCGTTGCGATTTTCAT
1 TCGCGTTGCGATTTTCAT
2506289 T
1 T
2506290 TCAACCAAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 29
0.68 0.07 0.25
Matches are distributed among these distances:
14 30 0.39
16 8 0.10
17 8 0.10
18 1 0.01
19 30 0.39
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCAT
Found at i:2506213 original size:14 final size:14
Alignment explanation
Indices: 2506194--2506283 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
2506184 TTTCATTTCG
2506194 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2506208 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2506227 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2506241 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
2506258 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
2506274 CGTTGCGATT
1 CGTTGCGATT
2506284 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2506219 original size:33 final size:33
Alignment explanation
Indices: 2506177--2506291 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
2506167 CCAAATCGCA
2506177 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2506210 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
2506243 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2506276 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2506292 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2508297 original size:184 final size:186
Alignment explanation
Indices: 2507988--2508366 Score: 744
Period size: 184 Copynumber: 2.0 Consensus size: 186
2507978 TAGATTGCTT
2507988 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2508053 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
2508118 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTG-TTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2508172 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2508237 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
2508302 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2508358 AGTAAATTT
1 AGTAAATTT
2508367 ATCCATTCAA
Statistics
Matches: 193, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
184 155 0.80
185 12 0.06
186 26 0.13
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2508314 original size:93 final size:93
Alignment explanation
Indices: 2507988--2508366 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
2507978 TAGATTGCTT
2507988 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2508053 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2508081 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2508145 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2508172 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2508237 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2508265 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2508330 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2508358 AGTAAATTT
1 AGTAAATTT
2508367 ATCCATTCAA
Statistics
Matches: 284, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
91 79 0.28
92 24 0.08
93 181 0.64
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2508450 original size:19 final size:19
Alignment explanation
Indices: 2508410--2508538 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2508400 TAGTTTACTT
* *
2508410 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
2508430 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
2508449 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
2508468 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
2508482 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
2508501 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
2508515 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
2508534 TCGCA
1 TCGCA
2508539 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:2508489 original size:33 final size:32
Alignment explanation
Indices: 2508446--2508538 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
2508436 CGCGAAACCA
**
2508446 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
2508478 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
2508511 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
2508539 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:2508536 original size:52 final size:52
Alignment explanation
Indices: 2508410--2508538 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
2508400 TAGTTTACTT
**
2508410 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
2508462 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
2508515 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
2508539 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Done.