Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 183 of 187
Found at i:54901024 original size:82 final size:82
Alignment explanation
Indices: 54900887--54901051 Score: 294
Period size: 82 Copynumber: 2.0 Consensus size: 82
54900877 TTTCCACTCC
* *
54900887 TGTGGTCAATCTTTTAAAAGTATCCCATGAAACATTCCTGTCCTGGACATATGGGGAACCATAGA
1 TGTGGCCAATCTTTTAAAAGTATCCCATGAAACATTCCTGTCCTGGACATATGGGGAACCATAAA
54900952 ATCCTGTGAATCTCCAT
66 ATCCTGTGAATCTCCAT
* *
54900969 TGTGGCCAATCTTTTCAAAGTATCCCATGAAACGTTCCTGTCCTGGACATATGGGGAACCATAAA
1 TGTGGCCAATCTTTTAAAAGTATCCCATGAAACATTCCTGTCCTGGACATATGGGGAACCATAAA
54901034 ATCCTGTGAATCTCCAT
66 ATCCTGTGAATCTCCAT
54901051 T
1 T
54901052 TCACACCTTG
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.30
Consensus pattern (82 bp):
TGTGGCCAATCTTTTAAAAGTATCCCATGAAACATTCCTGTCCTGGACATATGGGGAACCATAAA
ATCCTGTGAATCTCCAT
Found at i:54902575 original size:25 final size:25
Alignment explanation
Indices: 54902539--54902586 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
54902529 CTAAAACCTA
54902539 AGAACCCATGCCAGAGACGGCAGAC
1 AGAACCCATGCCAGAGACGGCAGAC
*
54902564 AGAACCCGTGCCAGAGACGGCAG
1 AGAACCCATGCCAGAGACGGCAG
54902587 GCTTTTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.33, C:0.31, G:0.31, T:0.04
Consensus pattern (25 bp):
AGAACCCATGCCAGAGACGGCAGAC
Found at i:54909511 original size:17 final size:17
Alignment explanation
Indices: 54909489--54909525 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
54909479 TAAAAACAAT
*
54909489 ATAACTCTTGACCTTTC
1 ATAACTCTTAACCTTTC
54909506 ATAACTCTTAACCTTTC
1 ATAACTCTTAACCTTTC
54909523 ATA
1 ATA
54909526 TAACATAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.30, C:0.27, G:0.03, T:0.41
Consensus pattern (17 bp):
ATAACTCTTAACCTTTC
Found at i:54913158 original size:73 final size:73
Alignment explanation
Indices: 54913039--54913358 Score: 478
Period size: 73 Copynumber: 4.4 Consensus size: 73
54913029 TGCTCAGGGC
* * * *
54913039 TTTAGTGGCATTTTTGAGAAAGCGCCGCAAAGAACATAAGCCAAAACGACGTCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGAGCT
54913104 TTGGGGGA
66 TTGGGGGA
**
54913112 TTTAGCGGCGTTTTTAAGAAAGCATCGCAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGAGCT
54913177 TTGGGGGA
66 TTGGGGGA
*
54913185 TTTAGCGGCGTTTTTAAGAAAGTGCCGCAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGAGCT
54913250 TTGGGGGA
66 TTGGGGGA
* * * * * * * *
54913258 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAATCTAAGCTAAAACGACGCCGATTTATAAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGAGCT
**
54913323 TTCAGGGA
66 TTGGGGGA
*
54913331 TTTAGCGGCGTTTTTAGGAAAGCGCCGC
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGC
54913359 TAATGCTCAG
Statistics
Matches: 225, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 225 1.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (73 bp):
TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGAGCT
TTGGGGGA
Found at i:54913580 original size:115 final size:114
Alignment explanation
Indices: 54913258--54913573 Score: 413
Period size: 115 Copynumber: 2.8 Consensus size: 114
54913248 CTTTGGGGGA
* * * * *
54913258 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAATCTAAGCTAAAACGACGCCGATTTATAAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCT
* * *
54913323 TTCAGGGATTTAGCGGCGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGC
66 TTCAGGGATTTAGCGGCGTTTTTATGAAAGCGCCACTAATGCTCAAGGC
* * *
54913372 TTTAGCGACGTTTTTGAGAAAGCGCCGCAAAAAAACTTAAGCCAAAACAACGCCGTTTTGTGAGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGC
** * *
54913437 TTTCAACGATTTAGCGGCATTTTTATGAAAGTGCCACTAATGCTCAAGGC
65 TTTCAGGGATTTAGCGGCGTTTTTATGAAAGCGCCACTAATGCTCAAGGC
*
54913487 TTTAGCGGC-TATTTT-AGGAAAGCGCCG-AAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGA
1 TTTAGCGGCGT-TTTTGA-GAAAGCGCCGCAAAA-AACCTAAGCCAAAACGACGCCGTTTTGTGA
**
54913549 GCTTTGGGGGATTTAGCGGCGTTTT
63 GCTTTCAGGGATTTAGCGGCGTTTT
54913574 CGATGAAGCG
Statistics
Matches: 174, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
113 4 0.02
114 76 0.44
115 94 0.54
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (114 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCT
TTCAGGGATTTAGCGGCGTTTTTATGAAAGCGCCACTAATGCTCAAGGC
Found at i:54913637 original size:187 final size:188
Alignment explanation
Indices: 54913372--54913826 Score: 544
Period size: 187 Copynumber: 2.4 Consensus size: 188
54913362 TGCTCAGGGC
* * *
54913372 TTTAGCGACGTTTTTGAGAAAGCGCCGCAAAAAAACTTAAGCCAAAACAACGCCGTTTTGTGAGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCG-AAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGC
*** * * * * *
54913437 TTTCAACGATTTAGCGGCATTTTTATGAAAGTGCCACTAATGCTCAAGGCTTTAGCGGC-TATTT
65 TTTCGGGGATTTAGCGACATTTTTAGGAAAGCGCCACTAATGCTCAAGGCTTCAGCAGCGT-TTT
* * *
54913501 T-AGGAAAGCGCCG-AAAAGAACCTAAGCCAAAACGACGTC-GTTTTGTGAGCTTTGGGGGA
129 TGA-GAAAGCGCCGCAAAA-AACCTAAGCCAAAACAACGCCAGTTTTGTGAGCTTTCGGGGA
* * * *
54913560 TTTAGCGGCGTTTTCGATG-AAGCGCCGTAAAAAACCTAAGGCAAAACGACGCCGTTTTATGAGC
1 TTTAGCGGCGTTTTTGA-GAAAGCGCCGAAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGC
** * *
54913624 TTTCGGGGATTTAGCGATGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGCTTCAGCAGCGTTTTT
65 TTTCGGGGATTTAGCGACATTTTTAGGAAAGCGCCACTAATGCTCAAGGCTTCAGCAGCGTTTTT
* *
54913689 GAGAAAGCGTCGCAAAAAACCTAAGCCAAAACAACGCCATTTTTGTGAGCTTTCGGGGA
130 GAGAAAGCGCCGCAAAAAACCTAAGCCAAAACAACGCCAGTTTTGTGAGCTTTCGGGGA
* * * *
54913748 TTTAGCGGCGTTTTTTAAGAAAGCACC-ACAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGAG
1 TTTAGCGGCG-TTTTTGAGAAAGCGCCGA-AAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAG
*
54913812 CTTTGGGGGATTTAG
64 CTTTCGGGGATTTAG
54913827 TGGCGTTTAT
Statistics
Matches: 226, Mismatches: 33, Indels: 15
0.82 0.12 0.05
Matches are distributed among these distances:
187 111 0.49
188 58 0.26
189 57 0.25
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (188 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGAAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCT
TTCGGGGATTTAGCGACATTTTTAGGAAAGCGCCACTAATGCTCAAGGCTTCAGCAGCGTTTTTG
AGAAAGCGCCGCAAAAAACCTAAGCCAAAACAACGCCAGTTTTGTGAGCTTTCGGGGA
Found at i:54913656 original size:73 final size:73
Alignment explanation
Indices: 54913498--54913659 Score: 220
Period size: 73 Copynumber: 2.2 Consensus size: 73
54913488 TTAGCGGCTA
* * *
54913498 TTTTAGGAAAGCGCCGAAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGAGCTTTGGGGGATTT
1 TTTTAGGAAAGCGCCGAAAAGAACCTAAGCCAAAACGACGCCGTTTTATGAGCTTTCGGGGATTT
*
54913563 AGCGGCGT
66 AGCGACGT
* * *
54913571 TTTCGATG-AAGCGCCGTAAAA-AACCTAAGGCAAAACGACGCCGTTTTATGAGCTTTCGGGGAT
1 TTT-TAGGAAAGCGCCG-AAAAGAACCTAAGCCAAAACGACGCCGTTTTATGAGCTTTCGGGGAT
*
54913634 TTAGCGATGT
64 TTAGCGACGT
54913644 TTTTAGGAAAGCGCCG
1 TTTTAGGAAAGCGCCG
54913660 CTAATGCTCA
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
72 2 0.03
73 68 0.89
74 6 0.08
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (73 bp):
TTTTAGGAAAGCGCCGAAAAGAACCTAAGCCAAAACGACGCCGTTTTATGAGCTTTCGGGGATTT
AGCGACGT
Found at i:54913735 original size:302 final size:302
Alignment explanation
Indices: 54913185--54913762 Score: 905
Period size: 302 Copynumber: 1.9 Consensus size: 302
54913175 CTTTGGGGGA
* *
54913185 TTTAGCGGCGTTTTTAAGAAAGTGCCGCAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGAAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGAGCT
* *
54913250 TTGGGGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAATCTAAGCTAAAACGACGCCGATT
66 TTGGGGGATTTAGCGGCGTTTTCGAGAAAGCGCCGCAAAAAACCTAAGCTAAAACGACGCCGATT
* *
54913315 TATAAGCTTTCAGGGATTTAGCGGCGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGA
131 TATAAGCTTTCAGGGATTTAGCGACGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGCTTCAGCGA
*
54913380 CGTTTTTGAGAAAGCGCCGCAAAAAAACTTAAGCCAAAACAACGCCGTTTTGTGAGCTTTCAACG
196 CGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCAAAACAACGCCGTTTTGTGAGCTTTCAACG
54913445 ATTTAGCGGCATTTTTATGAAAGTGCCACTAATGCTCAAGGC
261 ATTTAGCGGCATTTTTATGAAAGTGCCACTAATGCTCAAGGC
*
54913487 TTTAGCGGC-TATTTTAGGAAAGCGCCGAAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGAGC
1 TTTAGCGGCGT-TTTTAAGAAAGCGCCGAAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGAGC
*
54913551 TTTGGGGGATTTAGCGGCGTTTTCGATG-AAGCGCCGTAAAAAACCTAAGGC-AAAACGACGCCG
65 TTTGGGGGATTTAGCGGCGTTTTCGA-GAAAGCGCCGCAAAAAACCTAA-GCTAAAACGACGCCG
* * * *
54913614 TTTTATGAGCTTTCGGGGATTTAGCGATGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGCTTCAG
128 ATTTATAAGCTTTCAGGGATTTAGCGACGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGCTTCAG
* *
54913679 C-AGCGTTTTTGAGAAAGCGTCGC-AAAAAACCTAAGCCAAAACAACGCCATTTTTGTGAGCTTT
193 CGA-CGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCAAAACAACGCC-GTTTTGTGAGCTTT
*** *
54913742 CGGGGATTTAGCGGCGTTTTT
256 CAACGATTTAGCGGCATTTTT
54913763 TAAGAAAGCA
Statistics
Matches: 252, Mismatches: 19, Indels: 10
0.90 0.07 0.04
Matches are distributed among these distances:
301 26 0.10
302 223 0.88
303 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (302 bp):
TTTAGCGGCGTTTTTAAGAAAGCGCCGAAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGAGCT
TTGGGGGATTTAGCGGCGTTTTCGAGAAAGCGCCGCAAAAAACCTAAGCTAAAACGACGCCGATT
TATAAGCTTTCAGGGATTTAGCGACGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGCTTCAGCGA
CGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCAAAACAACGCCGTTTTGTGAGCTTTCAACG
ATTTAGCGGCATTTTTATGAAAGTGCCACTAATGCTCAAGGC
Found at i:54913893 original size:72 final size:73
Alignment explanation
Indices: 54913681--54913921 Score: 297
Period size: 72 Copynumber: 3.3 Consensus size: 73
54913671 GGCTTCAGCA
* * *
54913681 GCGTTTTTGAGAAAGCGTCGCAAAAAACCTAAGCCAAAACAACGCCATTTTTGTGAGCTTTCGGG
1 GCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCC-GTTTTGTGAGCTTTCGGG
54913746 GATTTAGCG
65 GATTTAGCG
* * * * * *
54913755 GCGTTTTTTAAGAAAGCACCACAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGAGCTTTGGGG
1 GCG-TTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCTTTCGGG
*
54913820 GATTTAGTG
65 GATTTAGCG
* * * * * *
54913829 GCGTTTATGAGGAAGCGCCGCAAAAAATCT-ATCCAAAATGACGCCGTTTTATGAGCTTTCGGGG
1 GCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCTTTCGGGG
54913893 ATTTAGCG
66 ATTTAGCG
54913901 GCGTTTTT-AGAAAAGCGCCGC
1 GCGTTTTTGAG-AAAGCGCCGC
54913922 TAATGCTTAG
Statistics
Matches: 140, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
71 2 0.01
72 52 0.37
73 20 0.14
74 30 0.21
75 36 0.26
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (73 bp):
GCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCTTTCGGGG
ATTTAGCG
Found at i:54914124 original size:14 final size:14
Alignment explanation
Indices: 54914105--54914292 Score: 66
Period size: 14 Copynumber: 13.4 Consensus size: 14
54914095 TATCACTATA
*
54914105 GTTTAGGGTTTTTG
1 GTTTAGGGTTTATG
*
54914119 GTTTAGGGTATATG
1 GTTTAGGGTTTATG
* **
54914133 GTTTAGAGTTTAAA
1 GTTTAGGGTTTATG
*
54914147 GTTTAGGTGTTACCAT-
1 GTTTAGG-GTT--TATG
* *
54914163 -TTTAAGGTTTATT
1 GTTTAGGGTTTATG
* *
54914176 GATTATGGGTTTAAG
1 GTTTA-GGGTTTATG
* *
54914191 GGTTATGGTTTATG
1 GTTTAGGGTTTATG
* **
54914205 GTTTAAAGG-TTGGG
1 GTTT-AGGGTTTATG
*
54914219 GTTTAAGGTTTA-G
1 GTTTAGGGTTTATG
* * *
54914232 AGGTTA-TGTTCAT-
1 -GTTTAGGGTTTATG
*
54914245 GTTAAGGGTTTATG
1 GTTTAGGGTTTATG
54914259 GTTTTAGGGTTTA-G
1 G-TTTAGGGTTTATG
* *
54914273 GTTTATGGTTTAGG
1 GTTTAGGGTTTATG
54914287 GTTTAG
1 GTTTAG
54914293 ATTAACTAGT
Statistics
Matches: 127, Mismatches: 33, Indels: 28
0.68 0.18 0.15
Matches are distributed among these distances:
12 5 0.04
13 24 0.19
14 66 0.52
15 31 0.24
17 1 0.01
ACGTcount: A:0.20, C:0.02, G:0.31, T:0.47
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:54914188 original size:22 final size:21
Alignment explanation
Indices: 54914163--54914215 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
54914153 GTGTTACCAT
*
54914163 TTTAAGGTTTATTGATTATGGG
1 TTTAAGGTTTATGGATTAT-GG
* *
54914185 TTTAAGGGTTATGGTTTATGG
1 TTTAAGGTTTATGGATTATGG
54914206 TTTAAAGGTT
1 TTT-AAGGTT
54914216 GGGGTTTAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (21 bp):
TTTAAGGTTTATGGATTATGG
Found at i:54914205 original size:7 final size:7
Alignment explanation
Indices: 54914163--54914291 Score: 52
Period size: 7 Copynumber: 18.6 Consensus size: 7
54914153 GTGTTACCAT
*
54914163 TTTAAGG
1 TTTATGG
*
54914170 TTTATTG
1 TTTATGG
*
54914177 ATTATGGG
1 TTTAT-GG
*
54914185 TTTAAGG
1 TTTATGG
*
54914192 GTTATGG
1 TTTATGG
54914199 TTTATGG
1 TTTATGG
*
54914206 TTTAAAGG
1 TTT-ATGG
**
54914214 -TTGGGG
1 TTTATGG
*
54914220 TTTAAGG
1 TTTATGG
54914227 TTTA-GAG
1 TTTATG-G
*
54914234 GTTAT-G
1 TTTATGG
*
54914240 TTCAT-G
1 TTTATGG
* *
54914246 TTAAGGG
1 TTTATGG
54914253 TTTATGG
1 TTTATGG
*
54914260 TTTTAGGG
1 -TTTATGG
54914268 TTTA-GG
1 TTTATGG
54914274 TTTATGG
1 TTTATGG
*
54914281 TTTAGGG
1 TTTATGG
54914288 TTTA
1 TTTA
54914292 GATTAACTAG
Statistics
Matches: 91, Mismatches: 23, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
6 17 0.19
7 61 0.67
8 13 0.14
ACGTcount: A:0.20, C:0.01, G:0.32, T:0.47
Consensus pattern (7 bp):
TTTATGG
Found at i:54914209 original size:21 final size:21
Alignment explanation
Indices: 54914163--54914291 Score: 88
Period size: 21 Copynumber: 6.2 Consensus size: 21
54914153 GTGTTACCAT
* * *
54914163 TTTAAGGTTTATTGATTATGGG
1 TTTAAGGGTTATGGTTTAT-GG
54914185 TTTAAGGGTTATGGTTTATGG
1 TTTAAGGGTTATGGTTTATGG
* ** *
54914206 TTTAAAGGTTGGGGTTTAAGG
1 TTTAAGGGTTATGGTTTATGG
*
54914227 TTT-AGAGGTTAT-GTTCAT-G
1 TTTAAG-GGTTATGGTTTATGG
*
54914246 -TTAAGGGTTTATGGTTTTAGGG
1 TTTAAGGG-TTATGG-TTTATGG
* *
54914268 TTT-AGGTTTATGGTTTAGGG
1 TTTAAGGGTTATGGTTTATGG
54914288 TTTA
1 TTTA
54914292 GATTAACTAG
Statistics
Matches: 84, Mismatches: 15, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
18 4 0.05
19 7 0.08
20 16 0.19
21 35 0.42
22 20 0.24
23 2 0.02
ACGTcount: A:0.20, C:0.01, G:0.32, T:0.47
Consensus pattern (21 bp):
TTTAAGGGTTATGGTTTATGG
Found at i:54914292 original size:7 final size:7
Alignment explanation
Indices: 54914249--54914292 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
54914239 GTTCATGTTA
54914249 AGGGTTT
1 AGGGTTT
*
54914256 ATGGTTTT
1 A-GGGTTT
54914264 AGGGTTT
1 AGGGTTT
54914271 A-GGTTT
1 AGGGTTT
*
54914277 ATGGTTT
1 AGGGTTT
54914284 AGGGTTT
1 AGGGTTT
54914291 AG
1 AG
54914293 ATTAACTAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
6 6 0.19
7 20 0.62
8 6 0.19
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (7 bp):
AGGGTTT
Found at i:54914411 original size:26 final size:26
Alignment explanation
Indices: 54914360--54914411 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
54914350 GATAATATTA
*
54914360 ATTTGGTTCTTCAAAATCATGTGAAG
1 ATTTGGTTCTTCAAAATCATGAGAAG
54914386 ATTTGGTTCTTCAAAATCGAT-AGAAG
1 ATTTGGTTCTTCAAAATC-ATGAGAAG
54914412 CTATATCCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.37
Consensus pattern (26 bp):
ATTTGGTTCTTCAAAATCATGAGAAG
Found at i:54914606 original size:21 final size:21
Alignment explanation
Indices: 54914582--54914635 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
54914572 ATTTAAAGGT
54914582 TTAGGGGTTAGTAGTTAGGG-G
1 TTAGGGGTTAG-AGTTAGGGAG
* *
54914603 TTAGAGGTTAAGAGTTAGGGAT
1 TTAGGGGTT-AGAGTTAGGGAG
54914625 TTAGGGGTTAG
1 TTAGGGGTTAG
54914636 GATTTAGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.24, C:0.00, G:0.43, T:0.33
Consensus pattern (21 bp):
TTAGGGGTTAGAGTTAGGGAG
Found at i:54914638 original size:14 final size:14
Alignment explanation
Indices: 54914581--54914643 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
54914571 GATTTAAAGG
*
54914581 TTTAGGGGTTAGTA
1 TTTAGGGGTTAGGA
*
54914595 GTTAGGGGTTA-GA
1 TTTAGGGGTTAGGA
* * *
54914608 GGTTAAGAGTTAGGGA
1 -TTTAGGGGTTA-GGA
54914624 TTTAGGGGTTAGGA
1 TTTAGGGGTTAGGA
54914638 TTTAGG
1 TTTAGG
54914644 AATTTAAGGG
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
13 1 0.03
14 28 0.72
15 8 0.21
16 2 0.05
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.35
Consensus pattern (14 bp):
TTTAGGGGTTAGGA
Found at i:54914642 original size:22 final size:21
Alignment explanation
Indices: 54914579--54914669 Score: 87
Period size: 22 Copynumber: 4.3 Consensus size: 21
54914569 GGGATTTAAA
*
54914579 GGTTTAGGGGTTAGTAGTTAG
1 GGTTTAGGGGTTAGGAGTTAG
* * *
54914600 GGGTTAGAGGTTAAGAGTTAG
1 GGTTTAGGGGTTAGGAGTTAG
*
54914621 GGATTTAGGGGTTAGGATTTAG
1 GG-TTTAGGGGTTAGGAGTTAG
* *
54914643 GAATTTAAGGGTT-GG-GTTAG
1 G-GTTTAGGGGTTAGGAGTTAG
54914663 GGTTTAG
1 GGTTTAG
54914670 ATTAATTACT
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
19 4 0.07
20 5 0.09
21 21 0.38
22 25 0.45
ACGTcount: A:0.23, C:0.00, G:0.42, T:0.35
Consensus pattern (21 bp):
GGTTTAGGGGTTAGGAGTTAG
Found at i:54914932 original size:29 final size:29
Alignment explanation
Indices: 54914899--54914972 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 29
54914889 TATTTTTCGT
54914899 GATTTAAAATTTTAAAATAAATTTT-AAAA
1 GATTTAAAATTTTAAAA-AAATTTTAAAAA
*
54914928 GATTTCAAAATTTTTAAAAAATTTTAAAAA
1 GATTT-AAAATTTTAAAAAAATTTTAAAAA
*
54914958 GAATTTAAACTTTTA
1 G-ATTTAAAATTTTA
54914973 TTTTTATAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
29 12 0.31
30 23 0.59
31 4 0.10
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (29 bp):
GATTTAAAATTTTAAAAAAATTTTAAAAA
Found at i:54914944 original size:19 final size:19
Alignment explanation
Indices: 54914920--54914956 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
54914910 TTAAAATAAA
*
54914920 TTTTAAAAGATTTCAAAAT
1 TTTTAAAAAATTTCAAAAT
*
54914939 TTTTAAAAAATTTTAAAA
1 TTTTAAAAAATTTCAAAA
54914957 AGAATTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (19 bp):
TTTTAAAAAATTTCAAAAT
Found at i:54914947 original size:10 final size:10
Alignment explanation
Indices: 54914904--54914957 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
54914894 TTCGTGATTT
54914904 AAAATTTTAAA
1 AAAATTTT-AA
54914915 ATAAATTTTAA
1 A-AAATTTTAA
* *
54914926 AAGA-TTTCA
1 AAAATTTTAA
*
54914935 AAATTTTTAA
1 AAAATTTTAA
54914945 AAAATTTTAA
1 AAAATTTTAA
54914955 AAA
1 AAA
54914958 GAATTTAAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
9 6 0.17
10 18 0.51
11 4 0.11
12 7 0.20
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:54915500 original size:69 final size:69
Alignment explanation
Indices: 54915421--54915559 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 69
54915411 TTTGATACAG
*
54915421 AAATTTAATTTTTAGCAAAATTTATACAATTAGTGGCATTTTTTTATAAGCGCCACAAATATTTA
1 AAATTTAATTTTTAGCAAAAATTATACAATTAGTGGCATTTTTTTATAAGCGCCACAAATATTTA
54915486 CAAT
66 CAAT
*
54915490 AAATTTAATTTTTAGCAAAAATTATACAATTAGTGGCGTTTTTTTATAAGCGCCACAAATATTTA
1 AAATTTAATTTTTAGCAAAAATTATACAATTAGTGGCATTTTTTTATAAGCGCCACAAATATTTA
54915555 CAAT
66 CAAT
54915559 A
1 A
54915560 CCAAAATGGC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (69 bp):
AAATTTAATTTTTAGCAAAAATTATACAATTAGTGGCATTTTTTTATAAGCGCCACAAATATTTA
CAAT
Found at i:54917048 original size:23 final size:23
Alignment explanation
Indices: 54917022--54917089 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
54917012 ATATGTTGTT
54917022 AATTGATA-TGTTAAAGTGCTACA
1 AATTGA-AGTGTTAAAGTGCTACA
**
54917045 AATTGAAGTGTTTAAA-TGCTGTA
1 AATTGAAGTG-TTAAAGTGCTACA
*
54917068 ACTTGAAGTGTTAAAGTGCTAC
1 AATTGAAGTGTTAAAGTGCTAC
54917090 TTTCTATTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
22 6 0.16
23 26 0.70
24 5 0.14
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (23 bp):
AATTGAAGTGTTAAAGTGCTACA
Found at i:54918065 original size:42 final size:42
Alignment explanation
Indices: 54917947--54918107 Score: 206
Period size: 42 Copynumber: 3.9 Consensus size: 42
54917937 TTTTCATGAC
* *
54917947 CTTTAGCGGCGTTTTTGGGGAAAGCGTCGCT--A--TCTTGTT
1 CTTTAGCGACGTTTTT-GGGAAAGCGCCGCTAAAGGTCTTGTT
** *
54917986 CTTTAGC-AGCGTTTTTGTAAAAAGCGCTGCTAAAGGTCTTGTT
1 CTTTAGCGA-CGTTTTTG-GGAAAGCGCCGCTAAAGGTCTTGTT
54918029 CTTTAGCGACGTTTTTGGGAAAGCGCCGCTAAAGGTCTTGTT
1 CTTTAGCGACGTTTTTGGGAAAGCGCCGCTAAAGGTCTTGTT
*
54918071 CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAAAGGTC
1 CTTTAGCGACGTTTTTGGGAAAGCGCCGCTAAAGGTC
54918108 GTTTATTTTT
Statistics
Matches: 106, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
38 1 0.01
39 23 0.22
41 1 0.01
42 58 0.55
43 22 0.21
44 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.34
Consensus pattern (42 bp):
CTTTAGCGACGTTTTTGGGAAAGCGCCGCTAAAGGTCTTGTT
Found at i:54919255 original size:24 final size:24
Alignment explanation
Indices: 54919223--54919268 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
54919213 CATTAAAAAC
*
54919223 AACATAACTCTTGACCTTTCATAT
1 AACATAACTCTTGACATTTCATAT
54919247 AACATAACTCTTGACATTTCAT
1 AACATAACTCTTGACATTTCAT
54919269 TTAATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (24 bp):
AACATAACTCTTGACATTTCATAT
Found at i:54921426 original size:21 final size:21
Alignment explanation
Indices: 54921395--54921443 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
54921385 ATCATTGATT
*
54921395 TTAATCATATTACTACAA-TA
1 TTAATCTTATTACTACAATTA
*
54921415 TTCAATCTTATTGCTACAATTA
1 TT-AATCTTATTACTACAATTA
54921437 TTAATCT
1 TTAATCT
54921444 CACTGACACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 19 0.76
22 4 0.16
ACGTcount: A:0.37, C:0.16, G:0.02, T:0.45
Consensus pattern (21 bp):
TTAATCTTATTACTACAATTA
Found at i:54924483 original size:6 final size:6
Alignment explanation
Indices: 54924472--54924500 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
54924462 ACTTGCTTGA
54924472 CCTCTC CCTCTC CCTCTC CCTCTC CCTCT
1 CCTCTC CCTCTC CCTCTC CCTCTC CCTCT
54924501 TCTTCTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
CCTCTC
Found at i:54931434 original size:120 final size:120
Alignment explanation
Indices: 54931295--54931535 Score: 448
Period size: 120 Copynumber: 2.0 Consensus size: 120
54931285 TGGACCTTCA
*
54931295 TATTTTTTGGGTTTGTTAGGGGGAATTCCAGGGTTGGTGTTTAAGAGGGTGAGGGTTCG-TCAAA
1 TATTTTTTGGGTTTGTTAGGGGGAATTCCAGGGTTGGTGTTTAAAAGGGTGAGGGTT-GATCAAA
54931359 AATGGTTGGTGTTGACTAGTGAAATTGAAGGCTTTGCCTCAAGGCTAAACAAACCT
65 AATGGTTGGTGTTGACTAGTGAAATTGAAGGCTTTGCCTCAAGGCTAAACAAACCT
54931415 TATTTTTTGGGTTTGTTAGGGGGAATTCCAGGGTTGGTGTTTAAAAGGGTGAGGGTTGATCAAAA
1 TATTTTTTGGGTTTGTTAGGGGGAATTCCAGGGTTGGTGTTTAAAAGGGTGAGGGTTGATCAAAA
*
54931480 ATGGTTGGTGTTGTCTAGTGAAATTGAAGGCTTTGCCTCAAGGCTAAACAAACCT
66 ATGGTTGGTGTTGACTAGTGAAATTGAAGGCTTTGCCTCAAGGCTAAACAAACCT
54931535 T
1 T
54931536 TGCCTTTTAA
Statistics
Matches: 118, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
119 1 0.01
120 117 0.99
ACGTcount: A:0.24, C:0.10, G:0.31, T:0.34
Consensus pattern (120 bp):
TATTTTTTGGGTTTGTTAGGGGGAATTCCAGGGTTGGTGTTTAAAAGGGTGAGGGTTGATCAAAA
ATGGTTGGTGTTGACTAGTGAAATTGAAGGCTTTGCCTCAAGGCTAAACAAACCT
Found at i:54933997 original size:21 final size:21
Alignment explanation
Indices: 54933966--54934014 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
54933956 ATCATTGATT
*
54933966 TTAATCATATTACTACAA-TA
1 TTAATCTTATTACTACAATTA
*
54933986 TTCAATCTTATTGCTACAATTA
1 TT-AATCTTATTACTACAATTA
54934008 TTAATCT
1 TTAATCT
54934015 CACTGACACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 19 0.76
22 4 0.16
ACGTcount: A:0.37, C:0.16, G:0.02, T:0.45
Consensus pattern (21 bp):
TTAATCTTATTACTACAATTA
Found at i:54935670 original size:6 final size:6
Alignment explanation
Indices: 54935659--54935684 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
54935649 ATTTCATTTC
54935659 TTCATT TTCATT TTCATT TTCATT TT
1 TTCATT TTCATT TTCATT TTCATT TT
54935685 GGAGAAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (6 bp):
TTCATT
Found at i:54935672 original size:63 final size:64
Alignment explanation
Indices: 54935593--54935733 Score: 203
Period size: 63 Copynumber: 2.2 Consensus size: 64
54935583 TTTCAGGTCA
*
54935593 TCTTCATTTTTCATTTTCATTTTCATTTTGGAGAAAACCACATTAATTTCCAAATGATTT-CATT
1 TCTTCA-TTTTCATTTTCATTTTCATTTTGGAGAAAACCACAATAATTTCCAAATGATTTCCATT
* * * *
54935657 TCTTCATTTTCATTTTCATTTTCATTTTGGAGAAAACTATAATCATTTTCAAATGATTTCCCATT
1 TCTTCATTTTCATTTTCATTTTCATTTTGGAGAAAACCACAATAATTTCCAAATGATTT-CCATT
*
54935722 TCTCCATTTTCA
1 TCTTCATTTTCA
54935734 CCATTTCTAT
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
63 48 0.70
64 6 0.09
65 15 0.22
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.49
Consensus pattern (64 bp):
TCTTCATTTTCATTTTCATTTTCATTTTGGAGAAAACCACAATAATTTCCAAATGATTTCCATT
Found at i:54943954 original size:20 final size:21
Alignment explanation
Indices: 54943929--54943969 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
54943919 TTTGATTTAA
54943929 TTTTATAAT-ACTAATATTTT
1 TTTTATAATAACTAATATTTT
* *
54943949 TTTTATAGTAATTAATATTTT
1 TTTTATAATAACTAATATTTT
54943970 AAAAATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTTATAATAACTAATATTTT
Found at i:54951249 original size:2 final size:2
Alignment explanation
Indices: 54951242--54951276 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
54951232 TAACTCCATA
54951242 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54951277 ACTTATGGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54951765 original size:58 final size:58
Alignment explanation
Indices: 54951695--54951810 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
54951685 TTAAAGCTCC
*
54951695 TAGAACATGGCCAAACAAACTCAACTTGAACTCATTTGAAGCAAATCTTAATGACACA
1 TAGAACATGGCCAAACAAACTCAACTTGAACTCATGTGAAGCAAATCTTAATGACACA
54951753 TAGAACATGGCCAAACAAACTCAACTTGAACTCATGTGAAGCAAATCTTAATGACACA
1 TAGAACATGGCCAAACAAACTCAACTTGAACTCATGTGAAGCAAATCTTAATGACACA
54951811 GGTCGCGGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.43, C:0.22, G:0.13, T:0.22
Consensus pattern (58 bp):
TAGAACATGGCCAAACAAACTCAACTTGAACTCATGTGAAGCAAATCTTAATGACACA
Found at i:54954213 original size:25 final size:25
Alignment explanation
Indices: 54954185--54954241 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
54954175 AATAACTTTC
54954185 CAGATAATACGCCATAAT-GGTTTTT
1 CAGATAATACGCCA-AATAGGTTTTT
* *
54954210 CAGATAATACTCCACATAGGTTTTT
1 CAGATAATACGCCAAATAGGTTTTT
*
54954235 CAAATAA
1 CAGATAA
54954242 CTTGACACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 2 0.07
25 26 0.93
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (25 bp):
CAGATAATACGCCAAATAGGTTTTT
Found at i:54959179 original size:26 final size:25
Alignment explanation
Indices: 54959150--54959227 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 25
54959140 GTGATGGAGG
54959150 TTATTTATTTTAAATTGCTGTGTATA
1 TTATTTATTTTAAATTG-TGTGTATA
* * * *
54959176 TTATTCATTTTAATTTGTTTTGCATA
1 TTATTTATTTTAAATTG-TGTGTATA
*
54959202 TTATTTACTTTAAAATTGTGT-TATA
1 TTATTTA-TTTTAAATTGTGTGTATA
54959227 T
1 T
54959228 ATTATGTCGT
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
25 4 0.10
26 29 0.71
27 8 0.20
ACGTcount: A:0.27, C:0.05, G:0.09, T:0.59
Consensus pattern (25 bp):
TTATTTATTTTAAATTGTGTGTATA
Found at i:54961983 original size:20 final size:20
Alignment explanation
Indices: 54961942--54961984 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
54961932 TTGTTTGGAA
**
54961942 CTTTTTCCAGGATTCTTGAT
1 CTTTTTCCAGGATTCTCCAT
*
54961962 CTTTTTCTAGGATTCTCCAT
1 CTTTTTCCAGGATTCTCCAT
54961982 CTT
1 CTT
54961985 AAAATATCAT
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:0.14, C:0.23, G:0.12, T:0.51
Consensus pattern (20 bp):
CTTTTTCCAGGATTCTCCAT
Found at i:54972900 original size:16 final size:16
Alignment explanation
Indices: 54972874--54972906 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
54972864 TTTAGTAAAT
54972874 TTATATAAGAATATTTA
1 TTATATAAGAAT-TTTA
54972891 TTAT-TAAGAATTTTA
1 TTATATAAGAATTTTA
54972906 T
1 T
54972907 GAATTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 7 0.44
17 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
TTATATAAGAATTTTA
Found at i:54973046 original size:94 final size:92
Alignment explanation
Indices: 54972869--54973159 Score: 424
Period size: 93 Copynumber: 3.1 Consensus size: 92
54972859 ATGATTTTAG
* * * *
54972869 TAAATTTATATAAG-AATATTTATTATTAAGAATTTTATG-AATTATATATCATTAGTTAAATGA
1 TAAATTCATATAAGAAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTA-TTAAATTA
*
54972932 TATTTAATATTAATTATTTTAAATGATA
65 TATTTAATATTAATTATTTTAAATTATA
54972960 TAAATTCATATAAGGAAAAATTTATTATCAAGAATTTTATGAAATTTATATATCATTATTAAATT
1 TAAATTCATATAA-GAAAAATTTATTATCAAGAATTTTATGAAA-TTATATATCATTATTAAATT
54973025 ATATTTAATATTAATTATTTTAAATTATA
64 ATATTTAATATTAATTATTTTAAATTATA
* * *
54973054 TAAATTCATATAACAAAAATTTATTTATCAAGAATTTGATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAAATTTA-TTATCAAGAATTTTATGAAATTATATATCATTATTAAATTA
* *
54973119 TATTTAATAATAATTATATTAAATTATA
65 TATTTAATATTAATTATTTTAAATTATA
* *
54973147 CAAACTCATATAA
1 TAAATTCATATAA
54973160 TTAAATTATA
Statistics
Matches: 183, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
91 12 0.07
92 1 0.01
93 89 0.49
94 68 0.37
95 13 0.07
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (92 bp):
TAAATTCATATAAGAAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
ATTTAATATTAATTATTTTAAATTATA
Found at i:54973171 original size:49 final size:48
Alignment explanation
Indices: 54972908--54973251 Score: 218
Period size: 49 Copynumber: 7.2 Consensus size: 48
54972898 GAATTTTATG
* * * *
54972908 AATTATAT--ATCAT-TAGTTAAATGATATTTAATATTAATTATTTTA
1 AATTATATAAATCATATAATTAAATTATATTTAATAATAATTATATTA
* ** * * *
54972953 AATGATATAAATTCATATAAGGAAA--A-ATTTATTATCAAGAATTTTATGA
1 AATTATATAAA-TCATATAATTAAATTATATTTA--AT-AATAATTATATTA
* * *
54973002 AATT-TATATATCAT-T-ATTAAATTATATTTAATATTAATTATTTTA
1 AATTATATAAATCATATAATTAAATTATATTTAATAATAATTATATTA
** * *
54973047 AATTATATAAATTCATATAACAAAAATT-TATTT-ATCAAGAATT-TGATGA
1 AATTATATAAA-TCATATAA-TTAAATTATATTTAAT-AATAATTAT-ATTA
*
54973096 AATTATAT--AT--TATTATTAAATTATATTTAATAATAATTATATTA
1 AATTATATAAATCATATAATTAAATTATATTTAATAATAATTATATTA
* * *
54973140 AATTATACAAACTCATATAATTAAATTATATTTAATAATAATAATTTTA
1 AATTATATAAA-TCATATAATTAAATTATATTTAATAATAATTATATTA
*
54973189 AATTATTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTCA
1 AATTA-TA-TAAATC--ATA---TAATTAAATTATATTTAATAATAATTATATT-A
54973244 AATTATAT
1 AATTATAT
54973252 TTTATACTAT
Statistics
Matches: 229, Mismatches: 37, Indels: 58
0.71 0.11 0.18
Matches are distributed among these distances:
43 5 0.02
44 25 0.11
45 26 0.11
46 15 0.07
47 13 0.06
48 20 0.09
49 73 0.32
50 9 0.04
51 3 0.01
52 3 0.01
53 1 0.00
54 4 0.02
55 32 0.14
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (48 bp):
AATTATATAAATCATATAATTAAATTATATTTAATAATAATTATATTA
Found at i:54973177 original size:18 final size:17
Alignment explanation
Indices: 54973155--54973233 Score: 52
Period size: 18 Copynumber: 4.4 Consensus size: 17
54973145 TACAAACTCA
54973155 TATAATTAAATTATATT
1 TATAATTAAATTATATT
* * *
54973172 TAATAATAATAATTTTAAAT
1 T-ATAATTA-AATTAT-ATT
*
54973192 TATTATTAAATCATATATT
1 TATAATTAAAT--TATATT
*
54973211 T-TAATTAAAATATATT
1 TATAATTAAATTATATT
54973227 TAATAAT
1 T-ATAAT
54973234 AATTATTTCA
Statistics
Matches: 46, Mismatches: 9, Indels: 13
0.68 0.13 0.19
Matches are distributed among these distances:
16 7 0.15
17 1 0.02
18 20 0.43
19 13 0.28
20 5 0.11
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (17 bp):
TATAATTAAATTATATT
Found at i:54973192 original size:93 final size:92
Alignment explanation
Indices: 54972884--54973194 Score: 321
Period size: 93 Copynumber: 3.3 Consensus size: 92
54972874 TTATATAAGA
* *
54972884 ATATTTATTATTAAGAATTTTATGAATTATATATCATTAGTTAAATGATATTTAATATTAATTAT
1 ATATTTA-TAATAAGAATTTTA--AATTATATATCATTA-TTAAATTATATTTAATATTAATTAT
*
54972949 TTTAAATGATATAAATTCATATAAGGAAAAATT
62 TTTAAATTATATAAATTCATATAA--AAAAATT
*
54972982 -TA-TTAT--CAAGAATTTTATGAAATTTATATATCATTATTAAATTATATTTAATATTAATTAT
1 ATATTTATAATAAGAA-TTT-T-AAA-TTATATATCATTATTAAATTATATTTAATATTAATTAT
54973043 TTTAAATTATATAAATTCATATAACAAAAATT
62 TTTAAATTATATAAATTCATATAA-AAAAATT
* * * *
54973075 -TATTTAT--CAAGAATTTGATGAAATTATATATTATTATTAAATTATATTTAATAATAATTATA
1 ATATTTATAATAAGAATTT--T-AAATTATATATCATTATTAAATTATATTTAATATTAATTATT
* * **
54973137 TTAAATTATACAAACTCATATAATTAAATT
63 TTAAATTATATAAATTCATATAAAAAAATT
*
54973167 ATATTTAATAATAATAATTTTAAATTAT
1 ATATTT-ATAATAAGAATTTTAAATTAT
54973195 TATTAAATCA
Statistics
Matches: 190, Mismatches: 13, Indels: 25
0.83 0.06 0.11
Matches are distributed among these distances:
92 5 0.03
93 86 0.45
94 71 0.37
95 15 0.08
96 11 0.06
97 2 0.01
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (92 bp):
ATATTTATAATAAGAATTTTAAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTA
AATTATATAAATTCATATAAAAAAATT
Found at i:54973319 original size:120 final size:120
Alignment explanation
Indices: 54973189--54973485 Score: 488
Period size: 120 Copynumber: 2.5 Consensus size: 120
54973179 AATAATTTTA
54973189 AATTATTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTCAAATTATATT
1 AATT-TTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATCTT-AAATTATATT
* *
54973253 TTATACTATCATATATTATGATTTTAGGAAATTCATATAAGAATATTGATTATTAAG
64 TTATACTATCATATATTATGATTTGAGGAAATTCATATAACAATATTGATTATTAAG
*
54973310 AATTTTATTAAATCATATATTTTAATTAAAATATATTGAATAATAATTATCTTAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATCTTAAATTATATTTT
* *
54973375 ATAGTATCATATATTATGATTTGAGTAAATTCATATAACAATATTGATTATTAAG
66 ATACTATCATATATTATGATTTGAGGAAATTCATATAACAATATTGATTATTAAG
* * * *
54973430 ATTTTTATTAAATTATATATTTTAATTAAAATATATTTAATAACAATTATGTTAAA
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATCTTAAA
54973486 ATATGATTAA
Statistics
Matches: 165, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
120 159 0.96
121 6 0.04
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (120 bp):
AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATCTTAAATTATATTTT
ATACTATCATATATTATGATTTGAGGAAATTCATATAACAATATTGATTATTAAG
Found at i:54973325 original size:61 final size:60
Alignment explanation
Indices: 54973260--54973450 Score: 162
Period size: 61 Copynumber: 3.2 Consensus size: 60
54973250 ATTTTATACT
54973260 ATCATATATTATGATTTTAGGAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
1 ATCATATATTATGATTTTA-GAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
* * * * * *
54973321 ATCATATATT-TTA-ATTA-AAA-T-ATAT-TGAATAATAATTATCTTAAATTATATTTTA-TAG
1 ATCATATATTATGATTTTAGAAATTCATATAAGAATATTGATTA--TT-AA-GA-ATTTTATTA-
*
54973379 T
60 A
* * *
54973380 ATCATATATTATGATTTGAGTAAATTCATATAACAATATTGATTATTAAGATTTTTATTAA
1 ATCATATATTATGATTTTAG-AAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
*
54973441 ATTATATATT
1 ATCATATATT
54973451 TTAATTAAAA
Statistics
Matches: 98, Mismatches: 18, Indels: 28
0.68 0.12 0.19
Matches are distributed among these distances:
54 10 0.10
55 4 0.04
56 3 0.03
57 5 0.05
58 3 0.03
59 19 0.19
60 4 0.04
61 26 0.27
62 3 0.03
63 5 0.05
64 3 0.03
65 4 0.04
66 9 0.09
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (60 bp):
ATCATATATTATGATTTTAGAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
Found at i:54973447 original size:59 final size:59
Alignment explanation
Indices: 54973264--54973447 Score: 133
Period size: 59 Copynumber: 3.1 Consensus size: 59
54973254 TATACTATCA
* * * *
54973264 TATATTATGATTTTAGGAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
1 TATATTATGATTTAAGTAAATTCATATAACAATATTGATTATTAAGATTTTTATTAAAT
* * * * * * * * * * * *
54973323 CATATATTTTAATTAAAATATATTGA-ATAATAATTATCTTA-AATT-ATATTTTATAGTATCA-
1 --TATATTATGATTTAAGTAAATTCATATAACAA-TAT-TGATTATTAAGATTTT-TATTA-AAT
*
54973384 TATATTATGATTTGAGTAAATTCATATAACAATATTGATTATTAAGATTTTTATTAAAT
1 TATATTATGATTTAAGTAAATTCATATAACAATATTGATTATTAAGATTTTTATTAAAT
54973443 TATAT
1 TATAT
54973448 ATTTTAATTA
Statistics
Matches: 87, Mismatches: 28, Indels: 18
0.65 0.21 0.14
Matches are distributed among these distances:
58 3 0.03
59 32 0.37
60 23 0.26
61 26 0.30
62 3 0.03
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (59 bp):
TATATTATGATTTAAGTAAATTCATATAACAATATTGATTATTAAGATTTTTATTAAAT
Found at i:54973457 original size:18 final size:18
Alignment explanation
Indices: 54973430--54973465 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
54973420 GATTATTAAG
* *
54973430 ATTTTTATTAAATTATAT
1 ATTTTAATTAAAATATAT
54973448 ATTTTAATTAAAATATAT
1 ATTTTAATTAAAATATAT
54973466 TTAATAACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTAATTAAAATATAT
Found at i:54976180 original size:12 final size:12
Alignment explanation
Indices: 54976163--54976187 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54976153 GGGTAGAGAG
54976163 TTTTTTTTGTTT
1 TTTTTTTTGTTT
54976175 TTTTTTTTGTTT
1 TTTTTTTTGTTT
54976187 T
1 T
54976188 AAAGAAGGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTTTTTTTGTTT
Found at i:54976666 original size:15 final size:15
Alignment explanation
Indices: 54976646--54976695 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
54976636 ACTAATTAAG
*
54976646 TTATTATTGCTGTTA
1 TTATTATTGCTATTA
*
54976661 TTATTATTGTTATTA
1 TTATTATTGCTATTA
* *
54976676 TTATTATGGGTATTA
1 TTATTATTGCTATTA
54976691 TTATT
1 TTATT
54976696 GTGTTGGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.24, C:0.02, G:0.12, T:0.62
Consensus pattern (15 bp):
TTATTATTGCTATTA
Found at i:54976679 original size:12 final size:12
Alignment explanation
Indices: 54976645--54976680 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
54976635 AACTAATTAA
**
54976645 GTTATTATTGCT
1 GTTATTATTATT
54976657 GTTATTATTATT
1 GTTATTATTATT
54976669 GTTATTATTATT
1 GTTATTATTATT
54976681 ATGGGTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.22, C:0.03, G:0.11, T:0.64
Consensus pattern (12 bp):
GTTATTATTATT
Found at i:54981975 original size:16 final size:17
Alignment explanation
Indices: 54981954--54981991 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
54981944 TTTTATATGG
*
54981954 ATTTTACT-TTTATTTT
1 ATTTTACTATGTATTTT
54981970 ATTTTACTAATGTATTTT
1 ATTTTACT-ATGTATTTT
54981988 ATTT
1 ATTT
54981992 AAATAAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTTACTATGTATTTT
Found at i:54984514 original size:16 final size:18
Alignment explanation
Indices: 54984479--54984517 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
54984469 TTGTTTGATA
54984479 TTATTATATTTTATAAAAT
1 TTATTATATTTTAT-AAAT
*
54984498 TTATT-TATTTTATAATT
1 TTATTATATTTTATAAAT
54984515 TTA
1 TTA
54984518 ATCTTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 8 0.42
19 5 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATTATATTTTATAAAT
Found at i:55002619 original size:30 final size:29
Alignment explanation
Indices: 55002578--55002634 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
55002568 AAAGTAAGAC
55002578 ATGATAATACATA-TAAAAATATAAAAATA
1 ATGATAATACATACT-AAAATATAAAAATA
*
55002607 ATGATACATACATACTAATATATAAAAA
1 ATGATA-ATACATACTAAAATATAAAAA
55002635 AAGTAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 6 0.24
30 18 0.72
31 1 0.04
ACGTcount: A:0.61, C:0.07, G:0.04, T:0.28
Consensus pattern (29 bp):
ATGATAATACATACTAAAATATAAAAATA
Found at i:55003776 original size:17 final size:17
Alignment explanation
Indices: 55003754--55003792 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
55003744 TGAAACCATG
* *
55003754 AAAAAAGAAAGGAAAAC
1 AAAAAAAAAAAGAAAAC
55003771 AAAAAAAAAAAGAAAAC
1 AAAAAAAAAAAGAAAAC
55003788 AAAAA
1 AAAAA
55003793 TAATATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAGAAAAC
Found at i:55004443 original size:17 final size:17
Alignment explanation
Indices: 55004409--55004456 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
55004399 TTAAAATCTT
*
55004409 GATAAATGAAT-A-TTC
1 GATAAATTAATAATTTC
55004424 GATAAATTAATAATTTC
1 GATAAATTAATAATTTC
55004441 GATTAAA-TAATAATTT
1 GA-TAAATTAATAATTT
55004457 TTTGGGTCCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 10 0.34
16 1 0.03
17 14 0.48
18 4 0.14
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (17 bp):
GATAAATTAATAATTTC
Found at i:55005829 original size:18 final size:17
Alignment explanation
Indices: 55005805--55006124 Score: 122
Period size: 18 Copynumber: 17.6 Consensus size: 17
55005795 ACACAATAAT
55005805 AATTTTTGAAAACACGA
1 AATTTTTGAAAACACGA
55005822 AGATTTTTG-AAACACGA
1 A-ATTTTTGAAAACACGA
* *
55005839 GATTTTTTTG-AAATACGAA
1 -A-ATTTTTGAAAACACG-A
* *
55005858 AATTTATG-AAACACGGTC
1 AATTTTTGAAAACAC-G-A
*
55005876 AATTTTTTAAAACACGAA
1 AATTTTTGAAAACACG-A
55005894 AATTTTTGAAAA-ACGGGA
1 AATTTTTGAAAACAC--GA
*
55005912 ATTTTTTTTTGAAAACACGGA
1 A---ATTTTTGAAAACAC-GA
* *
55005933 AATTTATG-AAACATGGA
1 AATTTTTGAAAACA-CGA
* *
55005950 ATTTTTTTTTTGAAAACAAGAA
1 A----ATTTTTGAAAACACG-A
* *
55005972 AATTTTCGATATACGA-GA
1 AATTTTTGA-AAAC-ACGA
* *
55005990 ATTTTTTAAAAACACGGGA
1 AATTTTTGAAAACAC--GA
55006009 AATTTTTTTGAAAACAC-A
1 AA--TTTTTGAAAACACGA
*
55006027 AA-TTTTG-AAACACTGG
1 AATTTTTGAAAACAC-GA
55006043 AATTTTT-AAAACACGA
1 AATTTTTGAAAACACGA
*
55006059 AGATTTTTG-AAACATGA
1 A-ATTTTTGAAAACACGA
55006076 AAGTTTTTGAAAACACGA
1 AA-TTTTTGAAAACACGA
* *
55006094 ATTTTTTTTTAAAACACGGA
1 A--ATTTTTGAAAACAC-GA
55006114 AATTTTTGAAA
1 AATTTTTGAAA
55006125 CCCGATTTTT
Statistics
Matches: 230, Mismatches: 37, Indels: 71
0.68 0.11 0.21
Matches are distributed among these distances:
14 6 0.03
15 5 0.02
16 6 0.03
17 62 0.27
18 79 0.34
19 27 0.12
20 4 0.02
21 32 0.14
22 9 0.04
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (17 bp):
AATTTTTGAAAACACGA
Found at i:55005922 original size:21 final size:22
Alignment explanation
Indices: 55005896--55005977 Score: 68
Period size: 22 Copynumber: 4.0 Consensus size: 22
55005886 AACACGAAAA
*
55005896 TTTTTGAAAA-ACGGGAATTTT
1 TTTTTGAAAACACGGAAATTTT
55005917 TTTTTGAAAACACGGAAA----
1 TTTTTGAAAACACGGAAATTTT
* * *
55005935 TTTATG-AAACATGGAATTTTT
1 TTTTTGAAAACACGGAAATTTT
* *
55005956 TTTTTGAAAACAAGAAAATTTT
1 TTTTTGAAAACACGGAAATTTT
55005978 CGATATACGA
Statistics
Matches: 47, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
17 9 0.19
18 5 0.11
21 15 0.32
22 18 0.38
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.40
Consensus pattern (22 bp):
TTTTTGAAAACACGGAAATTTT
Found at i:55005931 original size:22 final size:21
Alignment explanation
Indices: 55005896--55005937 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
55005886 AACACGAAAA
*
55005896 TTTTTGAAAAACGGGAATTTT
1 TTTTTGAAAAACGGAAATTTT
55005917 TTTTTGAAAACACGGAAATTT
1 TTTTTGAAAA-ACGGAAATTT
55005938 ATGAAACATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.40
Consensus pattern (21 bp):
TTTTTGAAAAACGGAAATTTT
Found at i:55006119 original size:20 final size:19
Alignment explanation
Indices: 55005807--55006120 Score: 99
Period size: 17 Copynumber: 17.2 Consensus size: 19
55005797 ACAATAATAA
55005807 TTTTTGAAAACACGAAGA--
1 TTTTTGAAAACACGAA-ATT
*
55005825 TTTTTG-AAACACGAGATT
1 TTTTTGAAAACACGAAATT
* *
55005843 TTTTTG-AAATACGAAA-A
1 TTTTTGAAAACACGAAATT
* *
55005860 TTTATG-AAACACGGTCAA-T
1 TTTTTGAAAACAC-G-AAATT
*
55005879 TTTTT-AAAACACGAAA-A
1 TTTTTGAAAACACGAAATT
*
55005896 TTTTTGAAAA-ACGGGAATTTT
1 TTTTTGAAAACAC--GAA-ATT
55005917 TTTTTGAAAACACGGAAA--
1 TTTTTGAAAACAC-GAAATT
* * *
55005935 TTTATG-AAACATGGAATTTTT
1 TTTTTGAAAACA-CGAA--ATT
* *
55005956 TTTTTGAAAACAAGAAA-A
1 TTTTTGAAAACACGAAATT
* * *
55005974 TTTTCG-ATATACGAGAA-T
1 TTTTTGAAAACACGA-AATT
*
55005992 TTTTTAAAAACACGGGAAATT
1 TTTTTGAAAACAC--GAAATT
55006013 TTTTTGAAAACAC-AAA--
1 TTTTTGAAAACACGAAATT
*
55006029 -TTTTG-AAACACTGGAA--
1 TTTTTGAAAACAC-GAAATT
55006045 TTTTT-AAAACACGAAGA--
1 TTTTTGAAAACACGAA-ATT
* *
55006062 TTTTTG-AAACATGAAA-G
1 TTTTTGAAAACACGAAATT
*
55006079 TTTTTGAAAACACGAATTT
1 TTTTTGAAAACACGAAATT
*
55006098 TTTTTTAAAACACGGAAATT
1 TTTTTGAAAACAC-GAAATT
55006118 TTT
1 TTT
55006121 GAAACCCGAT
Statistics
Matches: 225, Mismatches: 39, Indels: 62
0.69 0.12 0.19
Matches are distributed among these distances:
14 6 0.03
15 5 0.02
16 6 0.03
17 70 0.31
18 53 0.24
19 31 0.14
20 10 0.04
21 37 0.16
22 7 0.03
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.36
Consensus pattern (19 bp):
TTTTTGAAAACACGAAATT
Found at i:55006636 original size:7 final size:7
Alignment explanation
Indices: 55006609--55006650 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
55006599 AATTGAACAA
*
55006609 TTTTTCC
1 TTTTTTC
55006616 TTTTTTC
1 TTTTTTC
55006623 TTCTTTT-
1 TT-TTTTC
55006630 TCTTTTTC
1 T-TTTTTC
55006638 TTTTTTC
1 TTTTTTC
55006645 TTTTTT
1 TTTTTT
55006651 TCTCTCTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
7 25 0.81
8 6 0.19
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTTC
Found at i:55006640 original size:22 final size:22
Alignment explanation
Indices: 55006609--55006653 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
55006599 AATTGAACAA
55006609 TTTTTCCTTTTTTCTTCTTTTTC
1 TTTTTCCTTTTTTCTT-TTTTTC
55006632 TTTTT-CTTTTTTCTTTTTTTC
1 TTTTTCCTTTTTTCTTTTTTTC
55006653 T
1 T
55006654 CTCTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 7 0.32
22 10 0.45
23 5 0.23
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTTTCCTTTTTTCTTTTTTTC
Found at i:55006647 original size:19 final size:19
Alignment explanation
Indices: 55006615--55006662 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 19
55006605 ACAATTTTTC
*
55006615 CTTTTTTCTTCTTTTTCTTTTT
1 CTTTTTTCTT-TTTTTC--TCT
55006637 CTTTTTTCTTTTTTTCTCT
1 CTTTTTTCTTTTTTTCTCT
55006656 CTTTTTT
1 CTTTTTT
55006663 TGGGCCTGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 9 0.36
21 6 0.24
22 10 0.40
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (19 bp):
CTTTTTTCTTTTTTTCTCT
Found at i:55006663 original size:15 final size:14
Alignment explanation
Indices: 55006616--55006663 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 14
55006606 CAATTTTTCC
55006616 TTTTTTCTTCTTTT
1 TTTTTTCTTCTTTT
*
55006630 TCTTTTTCTTTTTTCT
1 T-TTTTTCTTCTTT-T
55006646 TTTTTTCTCTCTTTT
1 TTTTTTCT-TCTTTT
55006661 TTT
1 TTT
55006664 GGGCCTGCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 1 0.03
15 22 0.76
16 6 0.21
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTCTTCTTTT
Found at i:55006685 original size:16 final size:16
Alignment explanation
Indices: 55006662--55006704 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
55006652 CTCTCTTTTT
55006662 TTGGGCCTGCTGCCT-
1 TTGGGCCTGCTGCCTA
55006677 TTGGGGCCTG-TG-CTA
1 TT-GGGCCTGCTGCCTA
55006692 TTGGGCCTGCTGC
1 TTGGGCCTGCTGC
55006705 TGGTGTTGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 9 0.38
15 8 0.33
16 7 0.29
ACGTcount: A:0.02, C:0.28, G:0.37, T:0.33
Consensus pattern (16 bp):
TTGGGCCTGCTGCCTA
Found at i:55006705 original size:15 final size:14
Alignment explanation
Indices: 55006661--55006705 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
55006651 TCTCTCTTTT
55006661 TTTGGGCCTGCTGCC
1 TTTGGGCCTGCTG-C
55006676 TTTGGGGCCTG-TGC
1 TTT-GGGCCTGCTGC
55006690 TATTGGGCCTGCTGC
1 T-TTGGGCCTGCTGC
55006705 T
1 T
55006706 GGTGTTGGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 9 0.33
15 11 0.41
16 7 0.26
ACGTcount: A:0.02, C:0.27, G:0.36, T:0.36
Consensus pattern (14 bp):
TTTGGGCCTGCTGC
Found at i:55006724 original size:26 final size:26
Alignment explanation
Indices: 55006695--55006754 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
55006685 TGTGCTATTG
*
55006695 GGCCTGCTGCTGGTGTTGGGCTGGCT
1 GGCCTGCTGCTGGCGTTGGGCTGGCT
55006721 GGCCTGCTGCTGGCGTTGGGCTGGCT
1 GGCCTGCTGCTGGCGTTGGGCTGGCT
55006747 GGCCTGCT
1 GGCCTGCT
55006755 AGGCCTGCCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.00, C:0.27, G:0.45, T:0.28
Consensus pattern (26 bp):
GGCCTGCTGCTGGCGTTGGGCTGGCT
Found at i:55006786 original size:17 final size:17
Alignment explanation
Indices: 55006764--55006798 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
55006754 TAGGCCTGCC
55006764 GTTGGGCCTAGCG-TTGG
1 GTTGGGCCT-GCGCTTGG
55006781 GTTGGGCCTGCGCTTGG
1 GTTGGGCCTGCGCTTGG
55006798 G
1 G
55006799 CTGTTTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.03, C:0.20, G:0.49, T:0.29
Consensus pattern (17 bp):
GTTGGGCCTGCGCTTGG
Found at i:55006846 original size:26 final size:26
Alignment explanation
Indices: 55006803--55006857 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
55006793 CTTGGGCTGT
* *
55006803 TTTTGGCCTGTTTCTTTTTTTTTTTGC
1 TTTTGGCCTCTTTCTTTTGTTTTTT-C
*
55006830 TTTT-GCCTCTTTTTTTTGTTTTTTC
1 TTTTGGCCTCTTTCTTTTGTTTTTTC
55006855 TTT
1 TTT
55006858 GGGCTGCTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 4 0.16
26 17 0.68
27 4 0.16
ACGTcount: A:0.00, C:0.15, G:0.11, T:0.75
Consensus pattern (26 bp):
TTTTGGCCTCTTTCTTTTGTTTTTTC
Found at i:55006978 original size:6 final size:6
Alignment explanation
Indices: 55006959--55007030 Score: 67
Period size: 6 Copynumber: 11.8 Consensus size: 6
55006949 AAAAAAATAT
* *
55006959 TTTTTC -TTTT- TTTTTC TTTTTC TTTTTTC TTTTTC TTCCTTC TTCTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC -TTTTTC TTTTTC TT-TTTC TTTTTC
* *
55007007 TTCCTTC TTTTTC TTCTTC TTTTT
1 TT-TTTC TTTTTC TTTTTC TTTTT
55007031 TCTCCTTCTT
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
5 8 0.14
6 32 0.56
7 17 0.30
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:55006986 original size:13 final size:13
Alignment explanation
Indices: 55006972--55007030 Score: 75
Period size: 13 Copynumber: 4.6 Consensus size: 13
55006962 TTCTTTTTTT
*
55006972 TTCTTTTTCTTTT
1 TTCTTTTTCTTTC
*
55006985 TTCTTTTTCTTCC
1 TTCTTTTTCTTTC
* *
55006998 TTCTTCTTCTTCC
1 TTCTTTTTCTTTC
55007011 TTCTTTTTC-TTC
1 TTCTTTTTCTTTC
55007023 TTCTTTTT
1 TTCTTTTT
55007031 TCTCCTTCTT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
12 10 0.24
13 31 0.76
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (13 bp):
TTCTTTTTCTTTC
Found at i:55007005 original size:3 final size:3
Alignment explanation
Indices: 55006972--55007045 Score: 66
Period size: 3 Copynumber: 25.3 Consensus size: 3
55006962 TTCTTTTTTT
* * *
55006972 TTC TTT TTC TT- TT- TTC TTT TTC TTCC TTC TTC TTC TTCC TTC TTT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC TTC TT-C TTC TTC
*
55007017 TTC TTC TTC TT- TT- TTC TCC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
55007046 CCGTTCGGCC
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
2 8 0.14
3 45 0.76
4 6 0.10
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:55007031 original size:13 final size:13
Alignment explanation
Indices: 55006958--55007040 Score: 69
Period size: 13 Copynumber: 6.0 Consensus size: 13
55006948 AAAAAAAATA
*
55006958 TTTT-TTCTTTTT
1 TTTTCTTCTTCTT
*
55006970 TTTTCTTTTTCTT
1 TTTTCTTCTTCTT
*
55006983 TTTTCTTTTTCTT
1 TTTTCTTCTTCTT
55006996 CCTTCTTCTTCTTCCTTCT
1 --TT-TTCTTCTT-C-T-T
55007015 TTTTCTTCTTCTT
1 TTTTCTTCTTCTT
*
55007028 TTTTCTCCTTCTT
1 TTTTCTTCTTCTT
55007041 CTTCTCCGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
12 4 0.07
13 32 0.53
14 1 0.02
15 3 0.05
16 15 0.25
17 3 0.05
18 1 0.02
19 1 0.02
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTCTTCTTCTT
Found at i:55007038 original size:16 final size:15
Alignment explanation
Indices: 55006962--55007043 Score: 66
Period size: 16 Copynumber: 5.5 Consensus size: 15
55006952 AAAATATTTT
55006962 TTCTT-TTTTTT-TC
1 TTCTTCTTTTTTCTC
*
55006975 TTTTTCTTTTTTCT-
1 TTCTTCTTTTTTCTC
**
55006989 TT-TTCTTCCTTCTTC
1 TTCTTCTTTTTTC-TC
55007004 TTCTTCCTTCTTTT-TC
1 TTCTT-CTT-TTTTCTC
55007020 TTCTTCTTTTTTCTCC
1 TTCTTCTTTTTTCT-C
55007036 TTCTTCTT
1 TTCTTCTT
55007044 CTCCGTTCGG
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
13 12 0.22
14 13 0.24
15 7 0.13
16 18 0.33
17 3 0.05
18 2 0.04
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
TTCTTCTTTTTTCTC
Found at i:55007039 original size:19 final size:19
Alignment explanation
Indices: 55006988--55007045 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
55006978 TTCTTTTTTC
55006988 TTTTTCTTCCTTCTTCTTCT
1 TTTTTC-TCCTTCTTCTTCT
** **
55007008 TCCTTCTTTTTCTTCTTCT
1 TTTTTCTCCTTCTTCTTCT
55007027 TTTTTCTCCTTCTTCTTCT
1 TTTTTCTCCTTCTTCTTCT
55007046 CCGTTCGGCC
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
19 26 0.87
20 4 0.13
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTCTCCTTCTTCTTCT
Found at i:55007443 original size:29 final size:29
Alignment explanation
Indices: 55007402--55007514 Score: 147
Period size: 29 Copynumber: 3.9 Consensus size: 29
55007392 AAATTTTGAG
*
55007402 AAAGTTTAGGGGTCAAAACGTAATTTCAA
1 AAAGTTTAGGGGTCAAAATGTAATTTCAA
* * *
55007431 AAAGTTTATGGGTCAAAATGTAATTTTATG
1 AAAGTTTAGGGGTCAAAATGTAATTTCA-A
* *
55007461 AAA-TTTAGGGGTTAAAATGCAATTTCAA
1 AAAGTTTAGGGGTCAAAATGTAATTTCAA
*
55007489 AAAGTTTAGGGGTTAAAATGTAATTT
1 AAAGTTTAGGGGTCAAAATGTAATTT
55007515 TTTATTTTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
28 3 0.04
29 66 0.92
30 3 0.04
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.35
Consensus pattern (29 bp):
AAAGTTTAGGGGTCAAAATGTAATTTCAA
Found at i:55007485 original size:58 final size:59
Alignment explanation
Indices: 55007393--55007515 Score: 178
Period size: 58 Copynumber: 2.1 Consensus size: 59
55007383 GCCAAAACAA
* *
55007393 AATTTTGAGAAAGTTTAGGGGTCAAAACGTAATTTCAAAAAGTTTATGGGTCAAAATGT
1 AATTTTGAGAAAGTTTAGGGGTCAAAACGCAATTTCAAAAAGTTTAGGGGTCAAAATGT
* * *
55007452 AATTTT-ATGAAA-TTTAGGGGTTAAAATGCAATTTCAAAAAGTTTAGGGGTTAAAATGT
1 AATTTTGA-GAAAGTTTAGGGGTCAAAACGCAATTTCAAAAAGTTTAGGGGTCAAAATGT
55007510 AATTTT
1 AATTTT
55007516 TTATTTTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
58 48 0.83
59 10 0.17
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (59 bp):
AATTTTGAGAAAGTTTAGGGGTCAAAACGCAATTTCAAAAAGTTTAGGGGTCAAAATGT
Found at i:55008662 original size:27 final size:27
Alignment explanation
Indices: 55008615--55008678 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
55008605 AAATGTTCTC
**
55008615 TAAATTAAT-AAATATTAATTTATTGA
1 TAAATTAATAAAATATTAATTTATCAA
*
55008641 TAAATTAATAAAATATTCATTTATCAA
1 TAAATTAATAAAATATTAATTTATCAA
*
55008668 TAAACTAATAA
1 TAAATTAATAA
55008679 CCTCGATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 9 0.27
27 24 0.73
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (27 bp):
TAAATTAATAAAATATTAATTTATCAA
Found at i:55009466 original size:14 final size:14
Alignment explanation
Indices: 55009431--55009472 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
55009421 GGCTCACCAT
55009431 AAACCAAA-AAATA
1 AAACCAAATAAATA
*
55009444 ATA--AAATAAATA
1 AAACCAAATAAATA
55009456 AAACCAAATAAATA
1 AAACCAAATAAATA
55009470 AAA
1 AAA
55009473 GTTCAAGTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
11 3 0.12
12 7 0.29
13 2 0.08
14 12 0.50
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (14 bp):
AAACCAAATAAATA
Found at i:55010731 original size:18 final size:18
Alignment explanation
Indices: 55010700--55010752 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
55010690 GCAATATATG
55010700 TAAAAATA-ATTTAAAATA
1 TAAAAATATA-TTAAAATA
* *
55010718 TAAAAATTTATTAATATA
1 TAAAAATATATTAAAATA
*
55010736 TAACAATATATGTAAAA
1 TAAAAATATAT-TAAAA
55010753 AAAATTTTCG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 23 0.82
19 5 0.18
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
TAAAAATATATTAAAATA
Found at i:55010884 original size:34 final size:35
Alignment explanation
Indices: 55010829--55010895 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
55010819 CAAACACCAG
*
55010829 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
55010864 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
55010896 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:55016848 original size:106 final size:106
Alignment explanation
Indices: 55016658--55016870 Score: 354
Period size: 106 Copynumber: 2.0 Consensus size: 106
55016648 TTAATAACAG
* * * *
55016658 GTTGCCAATAGTGATATTGTGCTTAAGGTGTCTATGCTCGCTTTTAATTTGATTTTTATCTCCCT
1 GTTGACAATAGTGATATTGTCCTTAAGGTGTCTATGCTCGCTTTTAACTTGAATTTTATCTCCCT
*
55016723 ACTTTGAGGAGAGCTCACGAAATTTGACAGGATTAAGTAGA
66 ACTTCGAGGAGAGCTCACGAAATTTGACAGGATTAAGTAGA
* *
55016764 GTTGACAATAGTGATATTGTCCTTAAGGTGTCTATGCTTGGTTTTAACTTGAATTTTATCTCCCT
1 GTTGACAATAGTGATATTGTCCTTAAGGTGTCTATGCTCGCTTTTAACTTGAATTTTATCTCCCT
*
55016829 ACTTCGAGGAGAGCTCACGAAATTTGACGGGATTAAGTAGA
66 ACTTCGAGGAGAGCTCACGAAATTTGACAGGATTAAGTAGA
55016870 G
1 G
55016871 ATAAATTGAT
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 99 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.37
Consensus pattern (106 bp):
GTTGACAATAGTGATATTGTCCTTAAGGTGTCTATGCTCGCTTTTAACTTGAATTTTATCTCCCT
ACTTCGAGGAGAGCTCACGAAATTTGACAGGATTAAGTAGA
Found at i:55021089 original size:17 final size:17
Alignment explanation
Indices: 55021067--55021129 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
55021057 ATTGAATCAC
55021067 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
55021084 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
*
55021104 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
55021121 TACATAATT
1 TACATAATT
55021130 CTTGAAATTA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 17 0.50
18 4 0.12
19 5 0.15
20 8 0.24
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:55021102 original size:37 final size:37
Alignment explanation
Indices: 55021058--55021132 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
55021048 ATTCCCCGAA
*
55021058 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
*
55021095 TTGAATCACTACATAATTAAAAACATTACATAATTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
55021132 T
1 T
55021133 GAAATTAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:55021339 original size:44 final size:45
Alignment explanation
Indices: 55021271--55021369 Score: 157
Period size: 45 Copynumber: 2.2 Consensus size: 45
55021261 AGAGTCAGAC
*
55021271 TTTAGTTTTATTTTTATTGAGTT-GGTAATTGGGTAGACTTTAGT
1 TTTAGTTTTAGTTTTATTGAGTTGGGTAATTGGGTAGACTTTAGT
*
55021315 TTTAGTTTTAGTTTTATT-AGGTTGGGTAATTGGGTAGATTTTAGT
1 TTTAGTTTTAGTTTTATTGA-GTTGGGTAATTGGGTAGACTTTAGT
55021360 TTTAGTTTTA
1 TTTAGTTTTA
55021370 TTGGGTTGGG
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
43 1 0.02
44 20 0.39
45 30 0.59
ACGTcount: A:0.20, C:0.01, G:0.23, T:0.56
Consensus pattern (45 bp):
TTTAGTTTTAGTTTTATTGAGTTGGGTAATTGGGTAGACTTTAGT
Found at i:55022313 original size:23 final size:23
Alignment explanation
Indices: 55022279--55022322 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
55022269 TTCTACCCAT
55022279 AATTATCATCTCAACA-CAAAGG
1 AATTATCATCTCAACATCAAAGG
* *
55022301 AATTGATCTTCTCTACATCAAA
1 AATT-ATCATCTCAACATCAAA
55022323 CCAAATCCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.30
Consensus pattern (23 bp):
AATTATCATCTCAACATCAAAGG
Found at i:55028384 original size:2 final size:2
Alignment explanation
Indices: 55028379--55028426 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
55028369 ATAAGAAGAC
55028379 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55028421 AT AT AT
1 AT AT AT
55028427 GATAATTATT
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):
AT
Found at i:55028878 original size:16 final size:17
Alignment explanation
Indices: 55028852--55028884 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
55028842 TTCTAAAATG
*
55028852 TATGCCAAAAATTCAAA
1 TATGCCAAAAACTCAAA
55028869 TATG-CAAAAACTCAAA
1 TATGCCAAAAACTCAAA
55028885 AAAAATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.55, C:0.18, G:0.06, T:0.21
Consensus pattern (17 bp):
TATGCCAAAAACTCAAA
Found at i:55032781 original size:3 final size:3
Alignment explanation
Indices: 55032773--55032839 Score: 109
Period size: 3 Copynumber: 22.3 Consensus size: 3
55032763 CATTTTTGCC
55032773 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
55032821 ATT ATT -TAT ATT AGT ATT A
1 ATT ATT AT-T ATT ATT ATT A
55032840 GAGTAGTAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 1 0.02
3 58 0.97
4 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:55036556 original size:4 final size:4
Alignment explanation
Indices: 55036547--55036579 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
55036537 TACCTCTTTT
55036547 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA T
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA T
55036580 CAGTATTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TTCA
Found at i:55043499 original size:44 final size:44
Alignment explanation
Indices: 55043423--55043831 Score: 317
Period size: 44 Copynumber: 9.0 Consensus size: 44
55043413 ATAGAGAATT
* * * * *
55043423 TTATATCCCTGAAGTTACAGTGTATCATATTAAAGCTACAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATC
*
55043467 TTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCTACAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATC
*
55043511 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATC
*
55043555 TTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAA-CTACAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCTACAAATC
* * * *
55043599 CTATAC-CCCTAAAGTTGCAGTTGG-TC-GAATTGAAGCCAGAACAACAAATC
1 TTAT-CTCCCTGAAGTTGCAG-TGGAGCAG-ATT-AA---AG--CTACAAATC
* * * * * *
55043649 TTACCTCTCTAAACTTGCAGTGGAGCAGATTGAAGCTACGAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATC
* ** * *
55043693 TTAACTCCCTGAAGTTGTTGTGGAGTAGATTGAAGCTACAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATC
* * * * * * *
55043737 CTATAC-CCCTCAAGTTGTAGTGG-GTCGGATTGAATCTACCATAGCGAACC
1 TTAT-CTCCCTGAAGTTGCAGTGGAG-CAGATT-AA---AGC-TA-CAAATC
* * *
55043787 TTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCTACGAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATC
55043831 T
1 T
55043832 CAGTTCCTTA
Statistics
Matches: 295, Mismatches: 47, Indels: 46
0.76 0.12 0.12
Matches are distributed among these distances:
43 2 0.01
44 210 0.71
45 11 0.04
46 4 0.01
47 1 0.00
48 2 0.01
49 9 0.03
50 54 0.18
51 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.28
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATC
Found at i:55043646 original size:138 final size:138
Alignment explanation
Indices: 55043504--55043941 Score: 472
Period size: 138 Copynumber: 3.2 Consensus size: 138
55043494 GATTAAAGCT
* **
55043504 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCCCTGAAG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACGAATCTTATCTCCCTGAAG
* *
55043569 TTGCAATGGAGCAGATTGAAACTACAAATCCTATACCCCTAAAGTTGCAGTTGGTCGAATTGAAG
66 TTGCAGTGGAGTAGATTGAAACTACAAATCCTATACCCCTAAAGTTGCAGTTGGTCGAATTGAAG
* *
55043634 CCAGAACA
131 CTACAACA
* * * * *
55043642 ACAAATCTTACCTCTCTAAACTTGCAGTGGAGCAGATTGAAGCTACGAATCTTAACTCCCTGAAG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACGAATCTTATCTCCCTGAAG
** * * * * * *
55043707 TTGTTGTGGAGTAGATTGAAGCTACAAATCCTATACCCCTCAAGTTGTAGTGGGTCGGATTGAAT
66 TTGCAGTGGAGTAGATTGAAACTACAAATCCTATACCCCTAAAGTTGCAGTTGGTCGAATTGAAG
* *
55043772 CTACCATA
131 CTACAACA
* * * * * * *
55043780 GCGAACCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCTACGAATCTCAGT-TCCTTAAA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACGAATCTTA-TCTCCCTGAA
* * * * *
55043844 GTTACAGCGGAGTAGATTGAAACTACAATTCGC-ATACCCCTGAAGTTGCA-TTGGGTTAGAA-T
65 GTTGCAGTGGAGTAGATTGAAACTACAAATC-CTATACCCCTAAAGTTGCAGTT-GG-TCGAATT
55043906 GAAGCTACAACGA
127 GAAGCTACAAC-A
**
55043919 A-AAATCTTATCTCTTTGAAGTTG
1 ACAAATCTTATCTCCCTGAAGTTG
55043942 GAAAGAAGCA
Statistics
Matches: 242, Mismatches: 53, Indels: 10
0.79 0.17 0.03
Matches are distributed among these distances:
137 1 0.00
138 236 0.98
139 5 0.02
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (138 bp):
ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACGAATCTTATCTCCCTGAAG
TTGCAGTGGAGTAGATTGAAACTACAAATCCTATACCCCTAAAGTTGCAGTTGGTCGAATTGAAG
CTACAACA
Found at i:55044485 original size:7 final size:7
Alignment explanation
Indices: 55044469--55044509 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
55044459 AGAAGCCCCA
55044469 AAACCCT
1 AAACCCT
*
55044476 AAACCTT
1 AAACCCT
55044483 AAACCCT
1 AAACCCT
55044490 AAACCCT
1 AAACCCT
55044497 AAACCCT
1 AAACCCT
55044504 AAACCC
1 AAACCC
55044510 GAATCACCCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.15
Consensus pattern (7 bp):
AAACCCT
Found at i:55051012 original size:3 final size:3
Alignment explanation
Indices: 55051004--55051042 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
55050994 AAATTCAAAC
55051004 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
55051043 TATAGAGCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:55052591 original size:7 final size:7
Alignment explanation
Indices: 55052579--55052604 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
55052569 ATTAGTTTTG
55052579 TTTATAA
1 TTTATAA
55052586 TTTATAA
1 TTTATAA
55052593 TTTATAA
1 TTTATAA
55052600 TTTAT
1 TTTAT
55052605 TTTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTATAA
Found at i:55060158 original size:22 final size:22
Alignment explanation
Indices: 55060133--55060174 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
55060123 GAGGAATAAA
*
55060133 AATTGAGTGAGAA-TTAAAAGGG
1 AATTGAGAGA-AATTTAAAAGGG
55060155 AATTGAGAGAAATTTAAAAG
1 AATTGAGAGAAATTTAAAAG
55060175 AGCTTTGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.50, C:0.00, G:0.26, T:0.24
Consensus pattern (22 bp):
AATTGAGAGAAATTTAAAAGGG
Found at i:55060552 original size:42 final size:42
Alignment explanation
Indices: 55060495--55060595 Score: 159
Period size: 42 Copynumber: 2.4 Consensus size: 42
55060485 GTTTACAAAC
55060495 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTA-AA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGC-TTAGAA
* * *
55060537 AAAAACACCGTTAAAGACCATGTTGTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
55060579 AAAAACGCCGCTAAAGA
1 AAAAACGCCGCTAAAGA
55060596 ACTAAAGATC
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
41 3 0.06
42 50 0.94
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
Found at i:55061056 original size:21 final size:21
Alignment explanation
Indices: 55061029--55061078 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
55061019 TTTTGGCCTG
* *
55061029 CTCTGCTTCTCTTGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
55061050 TTCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
55061071 CTCTGCTT
1 CTCTGCTT
55061079 TAAGTTGTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.02, C:0.42, G:0.18, T:0.38
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:55066642 original size:9 final size:9
Alignment explanation
Indices: 55066628--55067020 Score: 317
Period size: 9 Copynumber: 42.9 Consensus size: 9
55066618 TTTTTATGTA
55066628 TTATGTAAG
1 TTATGTAAG
55066637 TTATGTAAG
1 TTATGTAAG
* *
55066646 TTATTTAAT
1 TTATGTAAG
55066655 TTATGTAAG
1 TTATGTAAG
* *
55066664 ATAAGTAAG
1 TTATGTAAG
*
55066673 TTAT-TTAG
1 TTATGTAAG
55066681 TTTATGTAAG
1 -TTATGTAAG
* *
55066691 TTATTTAAT
1 TTATGTAAG
*
55066700 TTATGCAAG
1 TTATGTAAG
55066709 TTTATGTAAG
1 -TTATGTAAG
55066719 TTATGTAAG
1 TTATGTAAG
* * * *
55066728 TCCACGGAAT
1 T-TATGTAAG
55066738 TTATGTCAA-
1 TTATGT-AAG
*
55066747 TTATTTAAG
1 TTATGTAAG
* *
55066756 TTATTTAAT
1 TTATGTAAG
55066765 TTATGTAAG
1 TTATGTAAG
55066774 TTATGTAAG
1 TTATGTAAG
* * *
55066783 TAATTTAAT
1 TTATGTAAG
*
55066792 TTATGCAAG
1 TTATGTAAG
55066801 TTTATGTAAG
1 -TTATGTAAG
55066811 TTATGTAAG
1 TTATGTAAG
* *
55066820 TTATTTAAT
1 TTATGTAAG
55066829 TTATGTAAG
1 TTATGTAAG
55066838 TTATGTAAG
1 TTATGTAAG
*
55066847 TTAT-TTAG
1 TTATGTAAG
55066855 TTTATGTAAG
1 -TTATGTAAG
* *
55066865 TTATTTAAT
1 TTATGTAAG
*
55066874 TTATGCAAG
1 TTATGTAAG
55066883 TTTTATGTAAG
1 --TTATGTAAG
55066894 TTATGTAAG
1 TTATGTAAG
* * * *
55066903 TCCACGGAAT
1 T-TATGTAAG
55066913 TTATGTCAA-
1 TTATGT-AAG
*
55066922 TTATTTAAG
1 TTATGTAAG
* *
55066931 TTATTTAAT
1 TTATGTAAG
55066940 TTATGTAAG
1 TTATGTAAG
*
55066949 TTATGTAAA
1 TTATGTAAG
* *
55066958 TTATTTAAT
1 TTATGTAAG
*
55066967 TTATGCAAG
1 TTATGTAAG
55066976 TTTATGTAAG
1 -TTATGTAAG
55066986 TTATGTAAG
1 TTATGTAAG
* *
55066995 TTATTTAAT
1 TTATGTAAG
55067004 TTATGTAAG
1 TTATGTAAG
55067013 TTATGTAA
1 TTATGTAA
55067021 CTTAATACAC
Statistics
Matches: 300, Mismatches: 69, Indels: 30
0.75 0.17 0.08
Matches are distributed among these distances:
8 10 0.03
9 238 0.79
10 44 0.15
11 8 0.03
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:55067104 original size:16 final size:16
Alignment explanation
Indices: 55067079--55067116 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
55067069 GAAAACGAAG
*
55067079 TAAA-TTTAATACTAA
1 TAAATTTTAATACAAA
55067094 TAAATTTTAATACAAA
1 TAAATTTTAATACAAA
55067110 TAAATTT
1 TAAATTT
55067117 AGAAAACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTTAATACAAA
Found at i:55069161 original size:22 final size:23
Alignment explanation
Indices: 55069136--55069193 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
55069126 CTTTAACCAA
*
55069136 AAAACCTTAAACCAC-TT-ACTCT
1 AAAACCTTAAACC-CTTTAACACT
*
55069158 AAAACCCTAAACCCTTTAACACT
1 AAAACCTTAAACCCTTTAACACT
*
55069181 TAAACCTTAAACC
1 AAAACCTTAAACC
55069194 TTAGCCCCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 1 0.03
22 14 0.47
23 15 0.50
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (23 bp):
AAAACCTTAAACCCTTTAACACT
Found at i:55069215 original size:14 final size:14
Alignment explanation
Indices: 55069198--55069228 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
55069188 TAAACCTTAG
55069198 CCCCAACCTCTAAA
1 CCCCAACCTCTAAA
*
55069212 CCCCAATCTCTAAA
1 CCCCAACCTCTAAA
55069226 CCC
1 CCC
55069229 ATAATCCCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (14 bp):
CCCCAACCTCTAAA
Found at i:55069314 original size:21 final size:21
Alignment explanation
Indices: 55069290--55069333 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
55069280 AACCCCTATC
* *
55069290 CCTTAATCTCCAACC-TCTAAA
1 CCTTAAACTCAAACCAT-TAAA
55069311 CCTTAAACTCAAACCATTAAA
1 CCTTAAACTCAAACCATTAAA
55069332 CC
1 CC
55069334 AAGTACCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (21 bp):
CCTTAAACTCAAACCATTAAA
Found at i:55069550 original size:21 final size:21
Alignment explanation
Indices: 55069526--55069595 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
55069516 ATAAACTATA
*
55069526 AACCCTAAACCCCTAACCCTT
1 AACCATAAACCCCTAACCCTT
* *
55069547 AACCATTAACCCGTAACACC-T
1 AACCATAAACCCCTAAC-CCTT
*
55069568 ATACAATAAACCCC-AACCCTT
1 A-ACCATAAACCCCTAACCCTT
55069589 AAACCAT
1 -AACCAT
55069596 GGCCTGTAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
20 2 0.05
21 24 0.63
22 12 0.32
ACGTcount: A:0.40, C:0.40, G:0.01, T:0.19
Consensus pattern (21 bp):
AACCATAAACCCCTAACCCTT
Found at i:55070051 original size:114 final size:114
Alignment explanation
Indices: 55069837--55070591 Score: 1027
Period size: 114 Copynumber: 6.6 Consensus size: 114
55069827 GTTTCGGTTT
** * *
55069837 AAAACGATGCGTTTTGGTTAAGATTTATTTGCGGCGCTCAGTATAATGCGCCGCTAATGATGTAC
1 AAAACGATGCGTTTTGGTTAAGATTT-TTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGC
* * *
55069902 TTTAGCGGC-GTTTTAC-TATAGCGCCACTAATTCTAAAATACCTAAACCA
65 TTTAGCGGCATTTTTACTTA-AGCGCCACTAATTCTAAAATACCTCAACCC
* * * *
55069951 AAAACGACGCGTTTTGGTTAAG-TTTTCTTGCGGCGCTTTGAATAATGCGCCGCTAATTGTGTTC
1 AAAACGATGCGTTTTGGTTAAGATTTT-TTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGC
* * *
55070015 TTTAGCGGCATTTATCCTTAAGCGCCACTAAATCTAAAATACCTCAACCC
65 TTTAGCGGCATTTTTACTTAAGCGCCACTAATTCTAAAATACCTCAACCC
* * *
55070065 AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGAATGATGCACCGCTAATGGTGTGCT
1 AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
** * * * *
55070130 TTTCCGGCGTTTTTAGTCAAGCGCCACTAATTCTAAAATACATCAACCC
66 TTAGCGGCATTTTTACTTAAGCGCCACTAATTCTAAAATACCTCAACCC
* * **
55070179 AGAACGATGCGTTTTGGTTAAGATTTTTTGCGTCGCTTTGTACGATGCGCCGCTAATGGTGTGCT
1 AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
* * * *
55070244 TCT-GCGGCATTTTTAGTTAAGCGCCAGTAATTCTAAATTACATCAACCC
66 T-TAGCGGCATTTTTACTTAAGCGCCACTAATTCTAAAATACCTCAACCC
* * * *
55070293 AGAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGTATTATGCGCCGCTAATGGTCTACT
1 AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
*
55070358 TTAGCGGCGTTTTTACTTAAGCGCCACTAATTCTAAAATACCTCAACCC
66 TTAGCGGCATTTTTACTTAAGCGCCACTAATTCTAAAATACCTCAACCC
* * * * * *
55070407 AGAACGATGCGTTTTGGTTATGA-TTTTTGCGGCGCTCTCTCTAACGCGCCGCTAATGGTGTGCT
1 AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
* * *
55070471 TTAGCGGCATTTATCCTTAAGCGCCACTAATTCTAATATACCTCAACCC
66 TTAGCGGCATTTTTACTTAAGCGCCACTAATTCTAAAATACCTCAACCC
55070520 AAAACGATGCGTTTTGGTTAAGA-TTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
1 AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
55070584 TTAGCGGC
66 TTAGCGGC
55070592 GTTTGTCGAA
Statistics
Matches: 570, Mismatches: 65, Indels: 13
0.88 0.10 0.02
Matches are distributed among these distances:
112 1 0.00
113 189 0.33
114 373 0.65
115 7 0.01
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.34
Consensus pattern (114 bp):
AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
TTAGCGGCATTTTTACTTAAGCGCCACTAATTCTAAAATACCTCAACCC
Found at i:55070818 original size:28 final size:29
Alignment explanation
Indices: 55070762--55070819 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
55070752 TTTTGTTTTT
55070762 TCGACCTAATTCAGTAAATTTTGAAAAAA
1 TCGACCTAATTCAGTAAATTTTGAAAAAA
* *
55070791 TCGACCTAA-TCTAGTAATTTTTCAAAAAA
1 TCGACCTAATTC-AGTAAATTTTGAAAAAA
55070820 AAAACAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.33
Consensus pattern (29 bp):
TCGACCTAATTCAGTAAATTTTGAAAAAA
Found at i:55073041 original size:5 final size:5
Alignment explanation
Indices: 55073031--55073058 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
55073021 ACACACAAAA
55073031 ATTAT ATTAT ATTAT ATTAT ATTAT ATT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATT
55073059 GTTATATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATTAT
Found at i:55079084 original size:20 final size:19
Alignment explanation
Indices: 55079039--55079094 Score: 71
Period size: 18 Copynumber: 3.0 Consensus size: 19
55079029 AAATAACTTA
*
55079039 TTAATATATATTTTAA-AG
1 TTAATATATATTTTAATAT
55079057 TTAATATATATTTTCAATAT
1 TTAATATATATTTT-AATAT
*
55079077 TTATTATAT-TTTTAATAT
1 TTAATATATATTTTAATAT
55079095 ATTTTTACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 19 0.56
19 6 0.18
20 9 0.26
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
TTAATATATATTTTAATAT
Found at i:55079248 original size:45 final size:43
Alignment explanation
Indices: 55079165--55079248 Score: 96
Period size: 45 Copynumber: 1.9 Consensus size: 43
55079155 AAATTTATAT
* * * * *
55079165 CTTACATTACTTAAATATATATTTTTAAGTATATTTTACATGA
1 CTTACATTACTTAAAAACATATTTTTAACTAAAATTTACATGA
*
55079208 CTTACATTACTTACTAAAACATATTTTTTACTAAAATTTAC
1 CTTACATTACTTA--AAAACATATTTTTAACTAAAATTTAC
55079249 TTTAATATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
43 13 0.39
45 20 0.61
ACGTcount: A:0.38, C:0.13, G:0.02, T:0.46
Consensus pattern (43 bp):
CTTACATTACTTAAAAACATATTTTTAACTAAAATTTACATGA
Found at i:55079261 original size:13 final size:13
Alignment explanation
Indices: 55079245--55079409 Score: 136
Period size: 13 Copynumber: 12.5 Consensus size: 13
55079235 TTACTAAAAT
*
55079245 TTACTTTAATATA
1 TTACTTAAATATA
*
55079258 TTACTTGAATATA
1 TTACTTAAATATA
*
55079271 TTACTTAAATAAA
1 TTACTTAAATATA
*
55079284 TTACTTAAATACA
1 TTACTTAAATATA
*
55079297 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** *
55079311 TTGGTTAAATTTA
1 TTACTTAAATATA
*
55079324 TTACTTAAATATG
1 TTACTTAAATATA
*
55079337 TTACTTAAATACA
1 TTACTTAAATATA
*
55079350 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** *
55079364 TTGTTTAAATTTA
1 TTACTTAAATATA
*
55079377 TTACTTAAATATG
1 TTACTTAAATATA
*
55079390 TTACTTAAATACA
1 TTACTTAAATATA
55079403 TTACTTA
1 TTACTTA
55079410 CTAAANNNNN
Statistics
Matches: 118, Mismatches: 28, Indels: 12
0.75 0.18 0.08
Matches are distributed among these distances:
12 6 0.05
13 96 0.81
14 10 0.08
15 6 0.05
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.46
Consensus pattern (13 bp):
TTACTTAAATATA
Found at i:55079326 original size:53 final size:53
Alignment explanation
Indices: 55079269--55079414 Score: 265
Period size: 53 Copynumber: 2.8 Consensus size: 53
55079259 TACTTGAATA
**
55079269 TATTACTTAAATAAATTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
*
55079322 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGTTTAAATT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
55079375 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAA
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAA
55079415 NNNNNNNNNN
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 90 1.00
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (53 bp):
TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
Found at i:55079874 original size:9 final size:9
Alignment explanation
Indices: 55079860--55080084 Score: 213
Period size: 9 Copynumber: 25.8 Consensus size: 9
55079850 ATAATACATT
55079860 TAACTTACA
1 TAACTTACA
55079869 TAACTTACA
1 TAACTTACA
55079878 TAACTTACA
1 TAACTTACA
55079887 TAA--TACA
1 TAACTTACA
*
55079894 AAACTTACA
1 TAACTTACA
*
55079903 TAACTTAAA
1 TAACTTACA
*
55079912 TATCTTACA
1 TAACTTACA
*
55079921 CAACTTACA
1 TAACTTACA
*
55079930 TAACCTACA
1 TAACTTACA
55079939 TAA--TACA
1 TAACTTACA
*
55079946 TTTAACTTAGA
1 --TAACTTACA
55079957 TAACTTACA
1 TAACTTACA
55079966 TAACTTACA
1 TAACTTACA
*
55079975 TAATACATA-A
1 T-A-ACTTACA
55079985 TAACTTAC-
1 TAACTTACA
55079993 -AACTTACA
1 TAACTTACA
*
55080001 TAACATACA
1 TAACTTACA
*
55080010 TTACTT-CGA
1 TAACTTAC-A
55080019 TAACTTACA
1 TAACTTACA
55080028 TAACTTACA
1 TAACTTACA
55080037 TAA--TACA
1 TAACTTACA
*
55080044 CAACTTACA
1 TAACTTACA
* *
55080053 TAGCTTACT
1 TAACTTACA
55080062 TAA--TACA
1 TAACTTACA
55080069 TAACTTACA
1 TAACTTACA
55080078 TAACTTA
1 TAACTTA
55080085 TACACGTACA
Statistics
Matches: 176, Mismatches: 23, Indels: 34
0.76 0.10 0.15
Matches are distributed among these distances:
7 29 0.16
8 5 0.03
9 131 0.74
10 4 0.02
11 7 0.04
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.32
Consensus pattern (9 bp):
TAACTTACA
Found at i:55079907 original size:43 final size:43
Alignment explanation
Indices: 55079860--55080084 Score: 221
Period size: 43 Copynumber: 5.2 Consensus size: 43
55079850 ATAATACATT
*
55079860 TAACTTACATAACTTACATAACTTACATAATACAAAACTTACA
1 TAACTTACATAACTTACATAACTTACATAATACATAACTTACA
* * *
55079903 TAACTTAAATATCTTACACAACTTACATAACCTACATAA--TACA
1 TAACTTACATAACTTACATAACTTACATAA--TACATAACTTACA
*
55079946 TTTAACTTAGATAACTTACATAACTTACATAATACATAATAACTTAC-
1 --TAACTTACATAACTTACATAACTTACATAATAC---ATAACTTACA
* *
55079993 -AACTTACATAACATACATTACTT-CGATAACTTACATAACTTACA
1 TAACTTACATAACTTACATAACTTAC-ATAA--TACATAACTTACA
* * *
55080037 TAA--TACACAACTTACATAGCTTACTTAATACATAACTTACA
1 TAACTTACATAACTTACATAACTTACATAATACATAACTTACA
55080078 TAACTTA
1 TAACTTA
55080085 TACACGTACA
Statistics
Matches: 150, Mismatches: 15, Indels: 34
0.75 0.08 0.17
Matches are distributed among these distances:
41 16 0.11
43 64 0.43
44 25 0.17
45 35 0.23
46 7 0.05
48 3 0.02
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.32
Consensus pattern (43 bp):
TAACTTACATAACTTACATAACTTACATAATACATAACTTACA
Found at i:55080004 original size:71 final size:62
Alignment explanation
Indices: 55079847--55080043 Score: 192
Period size: 62 Copynumber: 3.2 Consensus size: 62
55079837 NNCATAACCC
* * * * *
55079847 TACATAATACAT-TTAACTTACATAACTTACATAACTTACA-TA-ATACAAAACTTACATAACT
1 TACATAATACATAATAACTTAC--AACTTACATAACATACATTACTTAGATAACTTACATAACT
* * * *
55079908 TAAAT-AT-CTTACACAACTTACATAACCTACAT-A-ATACATTTAACTTAGATAACTTACATAA
1 TACATAATACATA-ATAACTTAC--AACTTACATAACATACA-TT-ACTTAGATAACTTACATAA
55079969 CT
61 CT
*
55079971 TACATAATACATAATAACTTACAACTTACATAACATACATTACTTCGATAACTTACATAACT
1 TACATAATACATAATAACTTACAACTTACATAACATACATTACTTAGATAACTTACATAACT
55080033 TACATAATACA
1 TACATAATACA
55080044 CAACTTACAT
Statistics
Matches: 112, Mismatches: 14, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
59 6 0.05
60 3 0.03
61 22 0.20
62 40 0.36
63 23 0.21
64 15 0.13
65 3 0.03
ACGTcount: A:0.46, C:0.20, G:0.01, T:0.32
Consensus pattern (62 bp):
TACATAATACATAATAACTTACAACTTACATAACATACATTACTTAGATAACTTACATAACT
Found at i:55080073 original size:25 final size:25
Alignment explanation
Indices: 55079847--55080084 Score: 173
Period size: 25 Copynumber: 9.1 Consensus size: 25
55079837 NNCATAACCC
55079847 TACATAATACATTTAACTTACATAACT
1 TACATAATACA--TAACTTACATAACT
*
55079874 TACATAACTTACATAA--TACAAAACT
1 TACATAA--TACATAACTTACATAACT
* * *
55079899 TACATAACTTAAATATCTTACACAACT
1 TACATAA--TACATAACTTACATAACT
55079926 TACATAACCTACATAA--TACATTTAACT
1 TACATAA--TACATAACTTACA--TAACT
*
55079953 TAGATAACTTACATAACTTACATAA--
1 TACATAA--TACATAACTTACATAACT
* *
55079978 TACATAATAACTTACAACTTACATAACA
1 TACATAAT-AC--ATAACTTACATAACT
* *
55080006 TACATTACTTCGATAACTTACATAACT
1 TACA-TAATAC-ATAACTTACATAACT
* *
55080033 TACATAATACACAACTTACATAGCT
1 TACATAATACATAACTTACATAACT
*
55080058 TACTTAATACATAACTTACATAACT
1 TACATAATACATAACTTACATAACT
55080083 TA
1 TA
55080085 TACACGTACA
Statistics
Matches: 173, Mismatches: 24, Indels: 30
0.76 0.11 0.13
Matches are distributed among these distances:
23 1 0.01
24 2 0.01
25 69 0.40
26 16 0.09
27 69 0.40
28 5 0.03
29 11 0.06
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.33
Consensus pattern (25 bp):
TACATAATACATAACTTACATAACT
Found at i:55082161 original size:21 final size:21
Alignment explanation
Indices: 55082110--55082161 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
55082100 TACAACTTAG
* *
55082110 AGCAGAGGCGGCAGCGAGGGA
1 AGCAGAGGCTGCAGCGAGAGA
*
55082131 AGCAGAGGCTGTAGCGAGAGA
1 AGCAGAGGCTGCAGCGAGAGA
55082152 AGCAGAGGCT
1 AGCAGAGGCT
55082162 CAAAAGAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.17, G:0.46, T:0.06
Consensus pattern (21 bp):
AGCAGAGGCTGCAGCGAGAGA
Found at i:55082599 original size:41 final size:41
Alignment explanation
Indices: 55082545--55082668 Score: 176
Period size: 41 Copynumber: 3.0 Consensus size: 41
55082535 TTTTTCACAA
* *
55082545 AAGCGCTGCTAAAGAACATGATCTTTAGTGGCATTTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTT
* *
55082586 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTT-T
* * *
55082628 AAACGTCGCTAAAGAACATGACCTTTAGCGGCATTTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTT
55082669 GTAAACGTTG
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
41 37 0.51
42 36 0.49
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (41 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTT
Found at i:55082638 original size:42 final size:41
Alignment explanation
Indices: 55082552--55082668 Score: 171
Period size: 42 Copynumber: 2.8 Consensus size: 41
55082542 CAAAAGCGCT
* * *
55082552 GCTAAAGAACATGATCTTTAGTGGCATTTTTTTTAAGCGCC
1 GCTAAAGAACATGATCTTTAGCGGCATTTTTTTTAAACGTC
* *
55082593 GCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAACGTC
1 GCTAAAGAACATGATCTTTAGCGGCATTTTTTT-TAAACGTC
*
55082635 GCTAAAGAACATGACCTTTAGCGGCATTTTTTTT
1 GCTAAAGAACATGATCTTTAGCGGCATTTTTTTT
55082669 GTAAACGTTG
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 31 0.46
42 36 0.54
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.37
Consensus pattern (41 bp):
GCTAAAGAACATGATCTTTAGCGGCATTTTTTTTAAACGTC
Found at i:55083999 original size:22 final size:22
Alignment explanation
Indices: 55083974--55084043 Score: 122
Period size: 22 Copynumber: 3.2 Consensus size: 22
55083964 AAATTCAATA
55083974 TCAATTTCCTTCAAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
*
55083996 TCAATTCCCTTCAAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
*
55084018 TCAATTTCCTTCCAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
55084040 TCAA
1 TCAA
55084044 ACTCTCAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.31, C:0.30, G:0.00, T:0.39
Consensus pattern (22 bp):
TCAATTTCCTTCAAAAATTCTC
Found at i:55084049 original size:30 final size:30
Alignment explanation
Indices: 55084015--55084073 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
55084005 TTCAAAAATT
* *
55084015 CTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
55084045 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
55084074 TTTCCTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.34
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:55084050 original size:52 final size:51
Alignment explanation
Indices: 55083993--55084095 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 51
55083983 TTCAAAAATT
* * *
55083993 CTCTC-AATTCCCTTCAAAAATTCTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATT-CCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTC-CAAA
*
55084045 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTCAAATTCCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
55084096 TCCATATTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
51 4 0.09
52 38 0.83
53 4 0.09
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.34
Consensus pattern (51 bp):
CTCTCAAATTCCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
Found at i:55084084 original size:21 final size:22
Alignment explanation
Indices: 55084045--55084086 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
55084035 TTCTCTCAAA
55084045 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
55084067 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
55084087 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Done.