Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 133 of 226
Found at i:44496992 original size:456 final size:454
Alignment explanation
Indices: 44496243--44497073 Score: 1280
Period size: 456 Copynumber: 1.8 Consensus size: 454
44496233 AATTATCCCC
* * *
44496243 TTGTGAATTTGGGAGTTGCTAGTTAAGGACGATGTGAATGAGCTTTTCTATTAATATTTTTCAAA
1 TTGTGAATTTGGGAGTTGCTAGTTAAAGAAGAAGTGAATGAGCTTTTCTATTAATATTTTTCAAA
* * *
44496308 ATATTTTATATTATTTTCTTTCATGAAATGTTGGTCATTTAGCATATTTAAGTATTTGAACGGTC
66 ATATTTTATATTATTTTCTTTCATGAAATGCTGGTCATGTAGCATATTTAAGTACTTGAACGGTC
* *
44496373 AAAATGTATATAAAAAAATTGGTTATTAACTTTAACGGTCAATTGTTAAATTTACCAACCCCCGA
131 AAAATGTATAT-AAAAAATTGGATATTAACTTTAACGGTCAATTGTTAAATTTACCAACCCCCAA
* * * *
44496438 TTTTTTCTTTTTCAATTAACTTCGCCACGTGTCACAACGTGCCACACCTTGGTTGTGATACATGG
195 TTTGTTCTTTTTCAATTAACTCCGCCACATGTCACAACGTGCCACACCTTGGTTGTGACACATGG
* *
44496503 CGAAAAAATAATCAACTAAAAAAATTAATAAAAATTATAAAAATATAAAAGTCTATAGACA-AAA
260 CGAAAAAATAATCAACTAAAAAAATCAATAAAAATTATAAAAATATAAAAATCTATA-ACAGAAA
*
44496567 CATAAAAAAGTATTTAATTTAAATAAAATTACAAAAATTATTATAAAATATAAAAAATTCATAAA
324 AATAAAAAAGTATTTAATTTAAATAAAATTACAAAAATTATTA-AAAATATAAAAAATTCATAAA
44496632 AGTTTTCCTTATAAATGTACTTTATTACATTTTTATAAAATTTAAAGTTATTATCCCCACAATGT
388 AGTTTTCCTTATAAATGTACTTTATTACATTTTTATAAAATTTAAAGTTATTATCCCCACAATGT
44496697 GG
453 GG
*
44496699 TTGTGAATTTGGGGGTTGCTAGTTAAAGAAGAAGTGAATGAGCTTTTCTATTAATATTTTTCAAA
1 TTGTGAATTTGGGAGTTGCTAGTTAAAGAAGAAGTGAATGAGCTTTTCTATTAATATTTTTCAAA
* **
44496764 ATATTTTATA-T-TTTT-TTTCGTGAAATGCTGGTCATGTAGCATATTTAAGTACTTGAATTGTC
66 ATATTTTATATTATTTTCTTTCATGAAATGCTGGTCATGTAGCATATTTAAGTACTTGAACGGTC
* * * *
44496826 AAAATGTAT-T-AAAAATTGCTTGATAGTTAACTTTAACTGTCAATTTTTAAATTTACTAGCCCC
131 AAAATGTATATAAAAAATTG---GATA-TTAACTTTAACGGTCAATTGTTAAATTTACCAACCCC
44496889 CAATTTGTTCTTTTTTC-ATTAACTCCGCCACATGTCACAACGTGCCACACCTTGGTTGTGACAC
192 CAATTTGTTC-TTTTTCAATTAACTCCGCCACATGTCACAACGTGCCACACCTTGGTTGTGACAC
*
44496953 ATGGCGAAAAAAATGATCAACTTAAAAAAATCAATAAAAATTATAAAAATATAAAAATCTATAAC
256 ATGGCG-AAAAAATAATCAAC-TAAAAAAATCAATAAAAATTATAAAAATATAAAAATCTATAAC
* * *
44497018 AGAAAAATAGAAAAGTATTTAATTTAAATAAATTTATAAAAATTATTAAAAATATA
319 AGAAAAATAAAAAAGTATTTAATTTAAATAAAATTACAAAAATTATTAAAAATATA
44497074 TCTAAATTAT
Statistics
Matches: 340, Mismatches: 27, Indels: 17
0.89 0.07 0.04
Matches are distributed among these distances:
450 8 0.02
452 1 0.00
453 53 0.16
454 95 0.28
455 31 0.09
456 152 0.45
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (454 bp):
TTGTGAATTTGGGAGTTGCTAGTTAAAGAAGAAGTGAATGAGCTTTTCTATTAATATTTTTCAAA
ATATTTTATATTATTTTCTTTCATGAAATGCTGGTCATGTAGCATATTTAAGTACTTGAACGGTC
AAAATGTATATAAAAAATTGGATATTAACTTTAACGGTCAATTGTTAAATTTACCAACCCCCAAT
TTGTTCTTTTTCAATTAACTCCGCCACATGTCACAACGTGCCACACCTTGGTTGTGACACATGGC
GAAAAAATAATCAACTAAAAAAATCAATAAAAATTATAAAAATATAAAAATCTATAACAGAAAAA
TAAAAAAGTATTTAATTTAAATAAAATTACAAAAATTATTAAAAATATAAAAAATTCATAAAAGT
TTTCCTTATAAATGTACTTTATTACATTTTTATAAAATTTAAAGTTATTATCCCCACAATGTGG
Found at i:44497070 original size:20 final size:20
Alignment explanation
Indices: 44497045--44497100 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
44497035 TTTAATTTAA
*
44497045 ATAAATTTATAAAAATTATT
1 ATAAAATTATAAAAATTATT
**
44497065 A-AAAATATATCTAAATTATT
1 ATAAAAT-TATAAAAATTATT
44497085 ATAAAA-TATAAAAATT
1 ATAAAATTATAAAAATT
44497101 TCATAAAAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 12 0.41
20 13 0.45
21 4 0.14
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAAAATTATAAAAATTATT
Found at i:44497332 original size:17 final size:17
Alignment explanation
Indices: 44497281--44497340 Score: 79
Period size: 18 Copynumber: 3.5 Consensus size: 17
44497271 TTTAGAAAAA
44497281 ATAA-AAAATAAAAATAT
1 ATAATAAAATAAAAAT-T
44497298 ATAATAAAATAGAAAATT
1 ATAATAAAATA-AAAATT
*
44497316 ATAGTAAAATAAAAATT
1 ATAATAAAATAAAAATT
44497333 ATAA-AAAA
1 ATAATAAAA
44497341 AATCATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
16 4 0.10
17 13 0.33
18 17 0.44
19 5 0.13
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (17 bp):
ATAATAAAATAAAAATT
Found at i:44500509 original size:13 final size:13
Alignment explanation
Indices: 44500491--44500549 Score: 75
Period size: 13 Copynumber: 4.5 Consensus size: 13
44500481 CTAAAATTTT
44500491 TCAAAAGCACTTC
1 TCAAAAGCACTTC
*
44500504 TCAAAAGCACTTT
1 TCAAAAGCACTTC
*
44500517 TCTACAA-CACTTC
1 TC-AAAAGCACTTC
*
44500530 TCAAAAGCACTTT
1 TCAAAAGCACTTC
44500543 TCAAAAG
1 TCAAAAG
44500550 TAATGAAGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
12 3 0.08
13 33 0.85
14 3 0.08
ACGTcount: A:0.39, C:0.27, G:0.07, T:0.27
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:44500796 original size:10 final size:9
Alignment explanation
Indices: 44500778--44500876 Score: 54
Period size: 10 Copynumber: 10.0 Consensus size: 9
44500768 GAACACTTAC
44500778 AAAATTTTA
1 AAAATTTTA
44500787 AAAGATTTTA
1 AAA-ATTTTA
44500797 AAAACTTTTGA
1 AAAA-TTTT-A
*
44500808 AATATTTTTA
1 AA-AATTTTA
44500818 ATAAATTTTA
1 A-AAATTTTA
* *
44500828 AATATTTTTCT
1 AA-AATTTT-A
* *
44500839 ACATTTTTA
1 AAAATTTTA
*
44500848 ATATATTTTA
1 A-AAATTTTA
44500858 TAAAATTTTA
1 -AAAATTTTA
*
44500868 ATAATTTTA
1 AAAATTTTA
44500877 TATCTATATA
Statistics
Matches: 70, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
9 14 0.20
10 45 0.64
11 10 0.14
12 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (9 bp):
AAAATTTTA
Found at i:44500869 original size:20 final size:19
Alignment explanation
Indices: 44500778--44500878 Score: 73
Period size: 20 Copynumber: 5.1 Consensus size: 19
44500768 GAACACTTAC
*
44500778 AAAATTTTAAAAGATTTTA-
1 AAAATTTT-AAATATTTTAT
44500797 AAAACTTTTGAAATATTTT-T
1 AAAA-TTTT-AAATATTTTAT
*
44500817 AATAAATTTTAAATATTTTTCT
1 -A-AAATTTTAAATA-TTTTAT
* *
44500839 ACATTTTTAATATATTTTAT
1 AAAATTTTAA-ATATTTTAT
44500859 AAAATTTT-AATAATTTTAT
1 AAAATTTTAAAT-ATTTTAT
44500878 A
1 A
44500879 TCTATATATG
Statistics
Matches: 67, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
18 2 0.03
19 13 0.19
20 35 0.52
21 13 0.19
22 4 0.06
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (19 bp):
AAAATTTTAAATATTTTAT
Found at i:44500875 original size:30 final size:30
Alignment explanation
Indices: 44500782--44500875 Score: 86
Period size: 30 Copynumber: 3.1 Consensus size: 30
44500772 ACTTACAAAA
*
44500782 TTTTAA-AAGATTTTAAAAACTTTTGAA-ATAT
1 TTTTAATAA-ATTTTAAAAA-TTTT-AATACAT
* **
44500813 TTTTAATAAATTTTAAATATTTTTCTACAT
1 TTTTAATAAATTTTAAAAATTTTAATACAT
*
44500843 TTTTAATATATTTTATAAAATTTTAATA-AT
1 TTTTAATAAATTTTA-AAAATTTTAATACAT
44500873 TTT
1 TTT
44500876 ATATCTATAT
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
30 26 0.50
31 24 0.46
32 2 0.04
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.54
Consensus pattern (30 bp):
TTTTAATAAATTTTAAAAATTTTAATACAT
Found at i:44502051 original size:20 final size:20
Alignment explanation
Indices: 44502013--44502052 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
44502003 TGAATTTTGA
*
44502013 GACTAAATTTTGGGAAGTTT
1 GACTAAATTTTAGGAAGTTT
44502033 GACTAAAATTTTAGG-AGTTT
1 GACT-AAATTTTAGGAAGTTT
44502053 AATAAGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.40
Consensus pattern (20 bp):
GACTAAATTTTAGGAAGTTT
Found at i:44503100 original size:2 final size:2
Alignment explanation
Indices: 44503093--44503120 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44503083 TTTGCTGCAG
44503093 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
44503121 TTTGTTGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44503381 original size:6 final size:6
Alignment explanation
Indices: 44503366--44503485 Score: 60
Period size: 6 Copynumber: 19.5 Consensus size: 6
44503356 TGGTAACCTG
* * * * * * *
44503366 TAAGCAA TAACAA TAAGAA TAAGAA CAATAA TAACAA TAATAA CAATAA
1 TAAG-AA TAAGAA TAAGAA TAAGAA TAAGAA TAAGAA TAAGAA TAAGAA
* * * * * * * * * *
44503415 TAACAACA AAAGAA TAACAA GAAGAA CAAGAA CAATAA TAACAA CAATAA
1 TAA-GA-A TAAGAA TAAGAA TAAGAA TAAGAA TAAGAA TAAGAA TAAGAA
44503465 TAAGAA TAAGAA TAAGAA TAA
1 TAAGAA TAAGAA TAAGAA TAA
44503486 TAATTATAAT
Statistics
Matches: 87, Mismatches: 24, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
6 79 0.91
7 5 0.06
8 3 0.03
ACGTcount: A:0.67, C:0.10, G:0.08, T:0.15
Consensus pattern (6 bp):
TAAGAA
Found at i:44503398 original size:12 final size:12
Alignment explanation
Indices: 44503371--44503467 Score: 76
Period size: 12 Copynumber: 8.4 Consensus size: 12
44503361 ACCTGTAAGC
* *
44503371 AATAACAATAAG
1 AATAACAACAAT
*
44503383 AATAAGAACAAT
1 AATAACAACAAT
44503395 AAT---AACAAT
1 AATAACAACAAT
*
44503404 AATAACAATAAT
1 AATAACAACAAT
* *
44503416 AACAACAA-AAG
1 AATAACAACAAT
* *
44503427 AATAACAAGAAG
1 AATAACAACAAT
* *
44503439 AACAAGAACAAT
1 AATAACAACAAT
44503451 AATAACAACAAT
1 AATAACAACAAT
44503463 AATAA
1 AATAA
44503468 GAATAAGAAT
Statistics
Matches: 68, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
9 9 0.13
11 9 0.13
12 50 0.74
ACGTcount: A:0.68, C:0.11, G:0.06, T:0.14
Consensus pattern (12 bp):
AATAACAACAAT
Found at i:44503401 original size:9 final size:9
Alignment explanation
Indices: 44503377--44503420 Score: 70
Period size: 9 Copynumber: 4.9 Consensus size: 9
44503367 AAGCAATAAC
*
44503377 AATAAGAAT
1 AATAACAAT
*
44503386 AAGAACAAT
1 AATAACAAT
44503395 AATAACAAT
1 AATAACAAT
44503404 AATAACAAT
1 AATAACAAT
44503413 AATAACAA
1 AATAACAA
44503421 CAAAAGAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.68, C:0.09, G:0.05, T:0.18
Consensus pattern (9 bp):
AATAACAAT
Found at i:44503487 original size:9 final size:9
Alignment explanation
Indices: 44503377--44503488 Score: 64
Period size: 9 Copynumber: 12.6 Consensus size: 9
44503367 AAGCAATAAC
44503377 AATAAGAAT
1 AATAAGAAT
* *
44503386 AAGAACAAT
1 AATAAGAAT
*
44503395 AATAACAAT
1 AATAAGAAT
*
44503404 AATAACAAT
1 AATAAGAAT
* *
44503413 AATAACAAC
1 AATAAGAAT
44503422 AA-AAGAAT
1 AATAAGAAT
* *
44503430 AACAAGAAG
1 AATAAGAAT
* *
44503439 AACAAGAAC
1 AATAAGAAT
* *
44503448 AATAATAAC
1 AATAAGAAT
* *
44503457 AACAATAAT
1 AATAAGAAT
* * *
44503466 AAGAATAAG
1 AATAAGAAT
44503475 AATAAGAAT
1 AATAAGAAT
44503484 AATAA
1 AATAA
44503489 TTATAATATA
Statistics
Matches: 85, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
8 6 0.07
9 79 0.93
ACGTcount: A:0.68, C:0.09, G:0.08, T:0.15
Consensus pattern (9 bp):
AATAAGAAT
Found at i:44516476 original size:19 final size:18
Alignment explanation
Indices: 44516444--44516479 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
44516434 TTGGGATTTT
*
44516444 ATAAATAAAGGAATAAAA
1 ATAAATAAAAGAATAAAA
44516462 ATAACATAAAAGAATAAA
1 ATAA-ATAAAAGAATAAA
44516480 CTTTGGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.17
Consensus pattern (18 bp):
ATAAATAAAAGAATAAAA
Found at i:44521757 original size:6 final size:6
Alignment explanation
Indices: 44521746--44521774 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
44521736 GGGGAAGTAA
44521746 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
44521775 AAATGAACAA
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:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:44532086 original size:15 final size:16
Alignment explanation
Indices: 44532054--44532086 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
44532044 TTTTAATAAT
44532054 GGAATTGTAATATTTA
1 GGAATTGTAATATTTA
44532070 GGAATTGTAAT-TTTA
1 GGAATTGTAATATTTA
44532085 GG
1 GG
44532087 CAGATTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.42
Consensus pattern (16 bp):
GGAATTGTAATATTTA
Found at i:44544342 original size:12 final size:13
Alignment explanation
Indices: 44544325--44544353 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
44544315 CTCATACATG
44544325 AATAAATAAA-GC
1 AATAAATAAATGC
44544337 AATAAATAAATGC
1 AATAAATAAATGC
44544350 AATA
1 AATA
44544354 GTTATAGCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:44547240 original size:7 final size:7
Alignment explanation
Indices: 44547210--44547247 Score: 55
Period size: 6 Copynumber: 5.9 Consensus size: 7
44547200 GGTTTTCTCA
44547210 AAATG-G
1 AAATGAG
44547216 AAATGA-
1 AAATGAG
44547222 AAATGA-
1 AAATGAG
44547228 AAATGAG
1 AAATGAG
44547235 AAATGAG
1 AAATGAG
44547242 AAATGA
1 AAATGA
44547248 ATTCATTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 17 0.57
7 13 0.43
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.16
Consensus pattern (7 bp):
AAATGAG
Found at i:44549629 original size:29 final size:28
Alignment explanation
Indices: 44549567--44549665 Score: 146
Period size: 28 Copynumber: 3.5 Consensus size: 28
44549557 AAAAATAAAA
*
44549567 ATTTACCAAAATAGTACAACTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
*
44549595 ATTTACGAAAATATTACAACTTTTTTTTT
1 ATTTACCAAAATATTACAAC-TTTTTTTT
*
44549624 ATTTACCAAGATATATA-AACTTTTTTTT
1 ATTTACCAAAATAT-TACAACTTTTTTTT
44549652 ATTTACCAAAATAT
1 ATTTACCAAAATAT
44549666 ATCAAAAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
28 39 0.61
29 23 0.36
30 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.47
Consensus pattern (28 bp):
ATTTACCAAAATATTACAACTTTTTTTT
Found at i:44549896 original size:37 final size:37
Alignment explanation
Indices: 44549851--44549921 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
44549841 TCATTTTTTT
* *
44549851 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAAATCTATTTTAATTTAATAAAATATTCTC
*
44549888 ATTTAATAAATTTATTTTAATTTAATAAAATATT
1 ATTTAATAAATCTATTTTAATTTAATAAAATATT
44549922 AAGTAATACT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (37 bp):
ATTTAATAAATCTATTTTAATTTAATAAAATATTCTC
Found at i:44549916 original size:19 final size:19
Alignment explanation
Indices: 44549846--44549916 Score: 90
Period size: 19 Copynumber: 3.8 Consensus size: 19
44549836 TCAACTCATT
* *
44549846 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAAATCTA
44549865 TTTTAATTTAATAAA-CTA
1 TTTTAATTTAATAAATCTA
* * *
44549883 TTCTCATTTAATAAATTTA
1 TTTTAATTTAATAAATCTA
44549902 TTTTAATTTAATAAA
1 TTTTAATTTAATAAA
44549917 ATATTAAGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 16 0.36
19 28 0.64
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTAATTTAATAAATCTA
Found at i:44550268 original size:20 final size:19
Alignment explanation
Indices: 44550229--44550269 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
44550219 ACTTAATAGT
* *
44550229 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAAAAGAG
44550248 TTATTAAATAAAAAAATGAG
1 TTATTAAATAAAAAAA-GAG
44550268 TT
1 TT
44550270 GAAGGGGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (19 bp):
TTATTAAATAAAAAAAGAG
Found at i:44550521 original size:37 final size:37
Alignment explanation
Indices: 44550479--44550549 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
44550469 AGTATTACTT
*
44550479 AATAGTTTATTAAATTAAAATAGATTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
44550516 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
44550550 AAAAAAATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:44550554 original size:19 final size:19
Alignment explanation
Indices: 44550479--44550553 Score: 102
Period size: 18 Copynumber: 4.1 Consensus size: 19
44550469 AGTATTACTT
44550479 AATAG-TTTATTAAATTAA
1 AATAGATTTATTAAATTAA
* *
44550497 AATAGATTTATTAAATGAG
1 AATAGATTTATTAAATTAA
44550516 AATAG-TTTATTAAATTAA
1 AATAGATTTATTAAATTAA
*
44550534 AATAGAGTTATTAAA-TAA
1 AATAGATTTATTAAATTAA
44550552 AA
1 AA
44550554 AAATGAGTTG
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
18 26 0.52
19 24 0.48
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (19 bp):
AATAGATTTATTAAATTAA
Found at i:44550561 original size:20 final size:19
Alignment explanation
Indices: 44550485--44550562 Score: 59
Period size: 19 Copynumber: 4.1 Consensus size: 19
44550475 ACTTAATAGT
* * *
44550485 TTATTAAATTAAAATAGAT
1 TTATTAAATAAAAAAAGAG
* * * *
44550504 TTATTAAATGAGAATAG-T
1 TTATTAAATAAAAAAAGAG
* *
44550522 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAAAAGAG
44550541 TTATTAAATAAAAAAATGAG
1 TTATTAAATAAAAAAA-GAG
44550561 TT
1 TT
44550563 GAAGGGGAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
18 16 0.32
19 29 0.58
20 5 0.10
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.38
Consensus pattern (19 bp):
TTATTAAATAAAAAAAGAG
Found at i:44550676 original size:27 final size:27
Alignment explanation
Indices: 44550632--44550731 Score: 132
Period size: 27 Copynumber: 3.7 Consensus size: 27
44550622 TTTCCCTTTC
* *
44550632 GCACC-ATGGTGCCGCCAA-TGACTTTG
1 GCACCAATGGTGCCACCAATTTA-TTTG
44550658 GCACCAATGGTGCCACCAATTTATTTG
1 GCACCAATGGTGCCACCAATTTATTTG
44550685 GCACCAATGGTGCCACCAATTTATTTG
1 GCACCAATGGTGCCACCAATTTATTTG
** *
44550712 GCACCTTTGGTGCCGCCAAT
1 GCACCAATGGTGCCACCAAT
44550732 ACCATTGGGG
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
26 5 0.07
27 60 0.90
28 2 0.03
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (27 bp):
GCACCAATGGTGCCACCAATTTATTTG
Found at i:44550888 original size:27 final size:27
Alignment explanation
Indices: 44550794--44550890 Score: 140
Period size: 28 Copynumber: 3.5 Consensus size: 27
44550784 TTTTTTTGAT
44550794 ATATTTTGGTAAATAAAAAAAATTTTA
1 ATATTTTGGTAAATAAAAAAAATTTTA
44550821 TATATTTTGGTAAATAAAAAAAAATTTTA
1 -ATATTTTGGTAAAT-AAAAAAAATTTTA
** * *
44550850 ATATTTACGTAAATAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAATTTTA
44550877 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
44550891 TTTTATTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
27 23 0.37
28 26 0.42
29 13 0.21
ACGTcount: A:0.49, C:0.01, G:0.09, T:0.40
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAATTTTA
Found at i:44555624 original size:20 final size:20
Alignment explanation
Indices: 44555590--44555698 Score: 96
Period size: 20 Copynumber: 5.5 Consensus size: 20
44555580 AGCATGATTA
*
44555590 TGCTATCAGAGGCACCGTAG
1 TGCTATCAGAAGCACCGTAG
* * **
44555610 TGCTAACAAAAGCA-CAAATG
1 TGCTATCAGAAGCACCGTA-G
*
44555630 TGCTATCAGGAGCACCGTAG
1 TGCTATCAGAAGCACCGTAG
* *
44555650 TGTTATCAGAAGCACCGTAA
1 TGCTATCAGAAGCACCGTAG
* *
44555670 TGCTATCAGGAGCA-CGAATG
1 TGCTATCAGAAGCACCGTA-G
44555690 TGCTATCAG
1 TGCTATCAG
44555699 GGGTACGAAT
Statistics
Matches: 69, Mismatches: 17, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
19 5 0.07
20 62 0.90
21 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (20 bp):
TGCTATCAGAAGCACCGTAG
Found at i:44555699 original size:20 final size:20
Alignment explanation
Indices: 44555620--44555710 Score: 80
Period size: 20 Copynumber: 4.5 Consensus size: 20
44555610 TGCTAACAAA
*
44555620 AGCACAAATGTGCTATCAGG
1 AGCACGAATGTGCTATCAGG
* * *
44555640 AGCACCGTA-GTGTTATCAGA
1 AGCA-CGAATGTGCTATCAGG
44555660 AGCACCGTAA--TGCTATCAGG
1 AGCA-CG-AATGTGCTATCAGG
44555680 AGCACGAATGTGCTATCAGG
1 AGCACGAATGTGCTATCAGG
* *
44555700 GGTACGAATGT
1 AGCACGAATGT
44555711 ATTATCAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
18 2 0.03
19 2 0.03
20 51 0.88
21 3 0.05
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (20 bp):
AGCACGAATGTGCTATCAGG
Found at i:44555716 original size:60 final size:60
Alignment explanation
Indices: 44555593--44555724 Score: 149
Period size: 60 Copynumber: 2.2 Consensus size: 60
44555583 ATGATTATGC
* * * *
44555593 TATCAGAGGCACCGTAGTGCTAACAAAAGCACAAATGTGCTATCAGGAGCACCGTAGTGT
1 TATCAGAAGCACCGTAATGCTAACAAAAGCACAAATGTGCTATCAGGAGCACCGAAGTAT
* ** * * *
44555653 TATCAGAAGCACCGTAATGCTATCAGGAGCACGAATGTGCTATCAGGGGTA-CGAATGTAT
1 TATCAGAAGCACCGTAATGCTAACAAAAGCACAAATGTGCTATCAGGAGCACCGAA-GTAT
*
44555713 TATCAAAAGCAC
1 TATCAGAAGCAC
44555725 TTTTTCAAGA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 3 0.05
60 57 0.95
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.21
Consensus pattern (60 bp):
TATCAGAAGCACCGTAATGCTAACAAAAGCACAAATGTGCTATCAGGAGCACCGAAGTAT
Found at i:44560806 original size:68 final size:68
Alignment explanation
Indices: 44560697--44560837 Score: 264
Period size: 68 Copynumber: 2.1 Consensus size: 68
44560687 TAATTTATGT
*
44560697 ATGATTTTGTAGCTACCTAATTATGATTTCGAGAGTTTCCCTTTAGAACTAGCAATATTAGAGAT
1 ATGATTTTGTAGCTACCTAATTATGATCTCGAGAGTTTCCCTTTAGAACTAGCAATATTAGAGAT
44560762 GAA
66 GAA
*
44560765 ATGATTTTGTAGCTATCTAATTATGATCTCGAGAGTTTCCCTTTAGAACTAGCAATATTAGAGAT
1 ATGATTTTGTAGCTACCTAATTATGATCTCGAGAGTTTCCCTTTAGAACTAGCAATATTAGAGAT
44560830 GAA
66 GAA
44560833 ATGAT
1 ATGAT
44560838 ACATCATATT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 71 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.37
Consensus pattern (68 bp):
ATGATTTTGTAGCTACCTAATTATGATCTCGAGAGTTTCCCTTTAGAACTAGCAATATTAGAGAT
GAA
Found at i:44562502 original size:24 final size:24
Alignment explanation
Indices: 44562475--44562552 Score: 58
Period size: 26 Copynumber: 3.3 Consensus size: 24
44562465 TATATATTTT
44562475 TTATTAAATTATATTTAATAATAA
1 TTATTAAATTATATTTAATAATAA
* *
44562499 TTATTTTAAATTAT-TATTAA-ATTAT
1 TTA--TTAAATTATAT-TTAATAATAA
* *
44562524 TTATT-ATTTATA-TTAATAAT-C
1 TTATTAAATTATATTTAATAATAA
44562545 TTATTAAA
1 TTATTAAA
44562553 ATTTAATAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
21 9 0.21
22 8 0.19
23 2 0.05
24 3 0.07
25 7 0.17
26 13 0.31
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (24 bp):
TTATTAAATTATATTTAATAATAA
Found at i:44562516 original size:56 final size:57
Alignment explanation
Indices: 44562407--44562539 Score: 155
Period size: 56 Copynumber: 2.3 Consensus size: 57
44562397 TATATTATTA
* *
44562407 TATATTATGATTTTAGTAAATTAATATAAGAATAATTATATTAAGAATTTTATTAAAT
1 TATA-TATTATTTTATTAAATTAATATAAGAATAATTATATTAAGAATTTTATTAAAT
* * *
44562465 TATATATT-TTTTATTAAATTATATTTAATAATAATTAT-TTTA-AATTATTATTAAAT
1 TATATATTATTTTATTAAATTA-ATATAAGAATAATTATATTAAGAATT-TTATTAAAT
*
44562521 TATTTATTATTTATATTAA
1 TATATATTATTT-TATTAA
44562540 TAATCTTATT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
55 4 0.06
56 31 0.48
57 20 0.31
58 10 0.15
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (57 bp):
TATATATTATTTTATTAAATTAATATAAGAATAATTATATTAAGAATTTTATTAAAT
Found at i:44562524 original size:11 final size:11
Alignment explanation
Indices: 44562497--44562529 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
44562487 ATTTAATAAT
44562497 AATTATT-TTA
1 AATTATTATTA
44562507 AATTATTATTA
1 AATTATTATTA
44562518 AATTATTTATTA
1 AATTA-TTATTA
44562530 TTTATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 8 0.38
12 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
AATTATTATTA
Found at i:44562681 original size:39 final size:42
Alignment explanation
Indices: 44562636--44562736 Score: 120
Period size: 44 Copynumber: 2.4 Consensus size: 42
44562626 TTTCCTTATG
44562636 CTATTACGCCTCTATTC-T-ATTCAACCAAACACA-AGAA-TA
1 CTATTACGCCTCTATTCATAATTCAACCAAACA-ATAGAATTA
* *
44562675 CTATTACGCCTCTATTCCATTACATTCAACCAAACAATTGAATTG
1 CTATTACGCCTCTATT-CA-TA-ATTCAACCAAACAATAGAATTA
44562720 CTATTACGCCTCTATTC
1 CTATTACGCCTCTATTC
44562737 CGTTACGCCT
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
39 16 0.30
40 1 0.02
42 1 0.02
43 1 0.02
44 17 0.32
45 17 0.32
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.33
Consensus pattern (42 bp):
CTATTACGCCTCTATTCATAATTCAACCAAACAATAGAATTA
Found at i:44562744 original size:16 final size:16
Alignment explanation
Indices: 44562722--44562758 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
44562712 TTGAATTGCT
44562722 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
44562738 GTTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
44562754 ATTAC
1 ATTAC
44562759 AGTAAACCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.19, C:0.35, G:0.08, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:44569067 original size:3 final size:3
Alignment explanation
Indices: 44569059--44569098 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
44569049 ATGTTTTTAT
44569059 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
44569099 AGTCTTTTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:44576832 original size:25 final size:25
Alignment explanation
Indices: 44576796--44576848 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
44576786 TTACCGACAT
* *
44576796 CATGCTACTGCCTTCATTGTCGCAA
1 CATGCTACTGCCCTCAATGTCGCAA
* *
44576821 CATGCTATTGCCCTCAATGTCGCGA
1 CATGCTACTGCCCTCAATGTCGCAA
44576846 CAT
1 CAT
44576849 TCATCCTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.21, C:0.32, G:0.17, T:0.30
Consensus pattern (25 bp):
CATGCTACTGCCCTCAATGTCGCAA
Found at i:44577261 original size:20 final size:21
Alignment explanation
Indices: 44577220--44577269 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
44577210 ATTTAGTTTA
*
44577220 TTATATTATTATTTTCTTATT
1 TTATATTATTATTATCTTATT
*
44577241 TTGTATTATTATTAT-TTATT
1 TTATATTATTATTATCTTATT
44577261 TTATATTAT
1 TTATATTAT
44577270 ATCTACAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (21 bp):
TTATATTATTATTATCTTATT
Found at i:44579436 original size:41 final size:42
Alignment explanation
Indices: 44579371--44579456 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 42
44579361 AGCATAAACA
* *
44579371 GTGAGTTACACGGCCTGGACACACGTCCGTGTCCCTG-CCGT
1 GTGACTTACACGGCCTGGACACACGCCCGTGTCCCTGACCGT
** *
44579412 GTGACTTACACGGCCTGGGTACACGCCCGTGTCTCTGACCGT
1 GTGACTTACACGGCCTGGACACACGCCCGTGTCCCTGACCGT
44579454 GTG
1 GTG
44579457 GTTTTATACC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 32 0.82
42 7 0.18
ACGTcount: A:0.14, C:0.33, G:0.30, T:0.23
Consensus pattern (42 bp):
GTGACTTACACGGCCTGGACACACGCCCGTGTCCCTGACCGT
Found at i:44582966 original size:45 final size:46
Alignment explanation
Indices: 44582893--44583099 Score: 332
Period size: 46 Copynumber: 4.6 Consensus size: 46
44582883 TACGTATGAT
* * *
44582893 CACTTATTAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
44582936 CACTTATCACTTTGTCACTTGATCATATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
44582982 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-ATGCAAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
44583027 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
44583073 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
44583100 AGTACTCAAA
Statistics
Matches: 151, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
43 9 0.06
44 5 0.03
45 62 0.41
46 75 0.50
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:44583011 original size:91 final size:91
Alignment explanation
Indices: 44582893--44583099 Score: 355
Period size: 91 Copynumber: 2.3 Consensus size: 91
44582883 TACGTATGAT
* * *
44582893 CACTTATTAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCAACCACTTATCACTTTGTCACTT
*
44582956 GATCATATAAGTGTAGCTAAAGCTAC
66 GATCAGATAAGTGTAGCTAAAGCTAC
*
44582982 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTATGCAACCACTTATCACTTTGTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCAACCACTTATCACTTTGTCACTT
44583047 GATCAGATAAGTGTAGCTAAAGCTAC
66 GATCAGATAAGTGTAGCTAAAGCTAC
44583073 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
44583100 AGTACTCAAA
Statistics
Matches: 111, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
89 9 0.08
90 5 0.05
91 97 0.87
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.34
Consensus pattern (91 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCAACCACTTATCACTTTGTCACTT
GATCAGATAAGTGTAGCTAAAGCTAC
Found at i:44593533 original size:39 final size:40
Alignment explanation
Indices: 44593476--44593551 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 40
44593466 CTGAATATAA
*
44593476 TAAATATATATTTTTTTA-TTTTTTAATTTTAAAATACTT
1 TAAAAATATATTTTTTTATTTTTTTAATTTTAAAATACTT
*
44593515 TAAAAATATATTTTTTTATTTTTTTATTTTTAAAATA
1 TAAAAATATATTTTTTTATTTTTTTAATTTTAAAATA
44593552 ATTTTTTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 17 0.50
40 17 0.50
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (40 bp):
TAAAAATATATTTTTTTATTTTTTTAATTTTAAAATACTT
Found at i:44593745 original size:2 final size:2
Alignment explanation
Indices: 44593738--44593777 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
44593728 CTCTCATTAC
44593738 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
44593778 TGATGTATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44594136 original size:21 final size:21
Alignment explanation
Indices: 44594095--44594137 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
44594085 AATAACGTAC
*
44594095 ATTATATATAATTTTTATAGT
1 ATTATATATAATATTTATAGT
*
44594116 ATTATATATTATGATTT-TAGT
1 ATTATATATAAT-ATTTATAGT
44594137 A
1 A
44594138 AATTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (21 bp):
ATTATATATAATATTTATAGT
Found at i:44594451 original size:16 final size:16
Alignment explanation
Indices: 44594430--44594469 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
44594420 TTGAATTACT
44594430 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
44594446 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
44594462 ATTACAGC
1 ATTACAGC
44594470 GAACCAAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.33, G:0.05, T:0.35
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:44601896 original size:2 final size:2
Alignment explanation
Indices: 44601847--44601885 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
44601837 CATTGTCCTT
44601847 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44601886 GTTTTATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44602744 original size:8 final size:8
Alignment explanation
Indices: 44602731--44602758 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
44602721 AGTATGAATG
44602731 ATATGTAT
1 ATATGTAT
44602739 ATATGTAT
1 ATATGTAT
44602747 ATATGTAT
1 ATATGTAT
44602755 ATAT
1 ATAT
44602759 ATGTATCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:44603533 original size:41 final size:41
Alignment explanation
Indices: 44603488--44603613 Score: 153
Period size: 41 Copynumber: 3.1 Consensus size: 41
44603478 TTTATTGTCA
* * *
44603488 GTGAAATAATTCAGACTTTATGTCTAGCAGGCTTGATGCCG
1 GTGAAATAATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
* *
44603529 GTGAAATTATTCAGACTATACGTCTAGCAGGCTTAATGCCG
1 GTGAAATAATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
* * * * * *
44603570 GTGATACATTTCGGACTATAAGTCTAGCAGGCTAAAAGCCG
1 GTGAAATAATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
44603611 GTG
1 GTG
44603614 TACCGAATCA
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 73 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (41 bp):
GTGAAATAATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:44603862 original size:40 final size:40
Alignment explanation
Indices: 44603818--44603895 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
44603808 ATTGATGAGC
* * *
44603818 ATATATATATTCGGTCTAAGCA-ATTGTTAAATATATATAT
1 ATATATACATTCGGTATAAGCATA-TATTAAATATATATAT
* *
44603858 ATATATGCATTCGGTATATGCATATATTAAATATATAT
1 ATATATACATTCGGTATAAGCATATATTAAATATATAT
44603896 GCATTAGGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 31 0.97
41 1 0.03
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (40 bp):
ATATATACATTCGGTATAAGCATATATTAAATATATATAT
Found at i:44603897 original size:32 final size:31
Alignment explanation
Indices: 44603848--44603912 Score: 103
Period size: 32 Copynumber: 2.1 Consensus size: 31
44603838 CAATTGTTAA
* *
44603848 ATATATATATATATATGCATTCGGTATATGC
1 ATATATAAATATATATGCATTAGGTATATGC
44603879 ATATATTAAATATATATGCATTAGGTATATGC
1 ATATA-TAAATATATATGCATTAGGTATATGC
44603911 AT
1 AT
44603913 TTGCTAAGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 5 0.16
32 26 0.84
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (31 bp):
ATATATAAATATATATGCATTAGGTATATGC
Found at i:44604698 original size:40 final size:39
Alignment explanation
Indices: 44604652--44604791 Score: 147
Period size: 40 Copynumber: 3.5 Consensus size: 39
44604642 GCGTTTGGAC
*
44604652 AAAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTT
1 AAAAAACGCCGCTAAAAATCGAGCATTAGCGACGCTTTT
* *
44604691 CATAAAACGCCGCTAAAGATCGAGCATTAGCGACGCTTTT
1 -AAAAAACGCCGCTAAAAATCGAGCATTAGCGACGCTTTT
* * * * * *
44604731 AGGAAAGCGCCACTAAAAAT-GAGAATTAGCGCCGTTTTTT
1 A-AAAAACGCCGCTAAAAATCGAGCATTAGCGACG-CTTTT
*
44604771 GAAAAAACGCCGCAAAAAATC
1 -AAAAAACGCCGCTAAAAATC
44604792 TAAGCCCAAC
Statistics
Matches: 82, Mismatches: 14, Indels: 7
0.80 0.14 0.07
Matches are distributed among these distances:
39 13 0.16
40 68 0.83
41 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (39 bp):
AAAAAACGCCGCTAAAAATCGAGCATTAGCGACGCTTTT
Found at i:44604924 original size:40 final size:40
Alignment explanation
Indices: 44604824--44604999 Score: 203
Period size: 41 Copynumber: 4.3 Consensus size: 40
44604814 TGACCTTTTG
* * *
44604824 GGGCTTTAGTGGC-ATTTTTGAAAAATCGCCGCTAATGCTC
1 GGGCTTTAGCGGCGCTTTTTCAAAAA-CGCCGCTAATGCTC
** * *
44604864 AAGCTTTTAGCGACGCTTTTTCAAAAACGTCGCTAATGCTC
1 GGGC-TTTAGCGGCGCTTTTTCAAAAACGCCGCTAATGCTC
44604905 GGGCTTTAGCGGCGCTTTTTCAAAAACGCCGCTAATGCTC
1 GGGCTTTAGCGGCGCTTTTTCAAAAACGCCGCTAATGCTC
* **
44604945 GGGCCTTTAGCGGCG-TTTTCCAAGAAGTGCCGCTAATGCTC
1 GGG-CTTTAGCGGCGCTTTTTCAA-AAACGCCGCTAATGCTC
44604986 AGGGCTTTAGCGGC
1 -GGGCTTTAGCGGC
44605000 ATTTTGAAAA
Statistics
Matches: 117, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
40 46 0.39
41 58 0.50
42 13 0.11
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (40 bp):
GGGCTTTAGCGGCGCTTTTTCAAAAACGCCGCTAATGCTC
Found at i:44604979 original size:81 final size:82
Alignment explanation
Indices: 44604824--44605004 Score: 226
Period size: 81 Copynumber: 2.2 Consensus size: 82
44604814 TGACCTTTTG
* * * *
44604824 GGGCTTTAGTGGCATTTTTGAAAAATCGCCGCTAATGCTCAAGCTTTTAGCGACGCTTTTTCAAA
1 GGGCTTTAGCGGCATTTTTCAAAAATCGCCGCTAATGCTCAAGCCTTTAGCGACGCTTTTCCAAA
44604889 AACGTCGCTAATGCTC-
66 AACGTCGCTAATGCTCA
* ** *
44604905 GGGCTTTAGCGGCGCTTTTTCAAAAA-CGCCGCTAATGCTCGGGCCTTTAGCGGCG-TTTTCCAA
1 GGGCTTTAGCGGC-ATTTTTCAAAAATCGCCGCTAATGCTCAAGCCTTTAGCGACGCTTTTCCAA
*
44604968 GAA-GTGCCGCTAATGCTCA
65 AAACGT--CGCTAATGCTCA
44604987 GGGCTTTAGCGGCATTTT
1 GGGCTTTAGCGGCATTTT
44605005 GAAAAAGTGC
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
79 2 0.02
80 9 0.10
81 52 0.60
82 23 0.27
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.30
Consensus pattern (82 bp):
GGGCTTTAGCGGCATTTTTCAAAAATCGCCGCTAATGCTCAAGCCTTTAGCGACGCTTTTCCAAA
AACGTCGCTAATGCTCA
Found at i:44604998 original size:41 final size:41
Alignment explanation
Indices: 44604824--44605017 Score: 188
Period size: 40 Copynumber: 4.8 Consensus size: 41
44604814 TGACCTTTTG
* * *
44604824 GGGCTTTAGTGGC-ATTTTTGAAAAA-TCGCCGCTAATGCTC
1 GGGCTTTAGCGGCGCTTTTTCAAAAAGT-GCCGCTAATGCTC
** *
44604864 AAGCTTTTAGCGACGCTTTTTCAAAAACGT--CGCTAATGCTC
1 GGGC-TTTAGCGGCGCTTTTTCAAAAA-GTGCCGCTAATGCTC
*
44604905 GGGCTTTAGCGGCGCTTTTTCAAAAA-CGCCGCTAATGCTC
1 GGGCTTTAGCGGCGCTTTTTCAAAAAGTGCCGCTAATGCTC
* *
44604945 GGGCCTTTAGCGGCG-TTTTCCAAGAAGTGCCGCTAATGCTC
1 GGG-CTTTAGCGGCGCTTTTTCAAAAAGTGCCGCTAATGCTC
* *
44604986 AGGGCTTTAGC-G-GCATTTTGAAAAAGTGCCGC
1 -GGGCTTTAGCGGCGCTTTTTCAAAAAGTGCCGC
44605018 AAAAATATTT
Statistics
Matches: 127, Mismatches: 17, Indels: 20
0.77 0.10 0.12
Matches are distributed among these distances:
39 1 0.01
40 61 0.48
41 51 0.40
42 13 0.10
44 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (41 bp):
GGGCTTTAGCGGCGCTTTTTCAAAAAGTGCCGCTAATGCTC
Found at i:44605351 original size:14 final size:14
Alignment explanation
Indices: 44605332--44605365 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
44605322 TATAGTTTAG
*
44605332 GGTTTAATATATAT
1 GGTTTAAGATATAT
*
44605346 GGTTTAAGGTATAT
1 GGTTTAAGATATAT
44605360 GGTTTA
1 GGTTTA
44605366 GGGTATAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (14 bp):
GGTTTAAGATATAT
Found at i:44605370 original size:14 final size:14
Alignment explanation
Indices: 44605341--44605377 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
44605331 GGGTTTAATA
44605341 TATATGGTTTAAGG
1 TATATGGTTTAAGG
*
44605355 TATATGGTTTAGGG
1 TATATGGTTTAAGG
*
44605369 TATAGGGTT
1 TATATGGTT
44605378 AATTTAAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.43
Consensus pattern (14 bp):
TATATGGTTTAAGG
Found at i:44605454 original size:14 final size:15
Alignment explanation
Indices: 44605426--44605458 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
44605416 AAGGTTTATA
44605426 GATTATGGAATTAGG
1 GATTATGGAATTAGG
44605441 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
44605455 GATT
1 GATT
44605459 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:44610249 original size:42 final size:42
Alignment explanation
Indices: 44610185--44610418 Score: 319
Period size: 42 Copynumber: 5.5 Consensus size: 42
44610175 TCTTGGCGTT
* * * *
44610185 TAAAGGTCTTGGTTTTTTGCGGCATTTGTGGGAAAAGCGCCAC
1 TAAAGGTCTTGGTCTTTAGCGGCATTT-TGGGTAAAGCGCCGC
*
44610228 TAAA-GTC-TGGTTCTTTAGCGGCGTTTTTGGGTAAAGCGCCGC
1 TAAAGGTCTTGG-TCTTTAGCGGC-ATTTTGGGTAAAGCGCCGC
* * *
44610270 TAAAGATCTTGGTCTTTAGCGGCGTTTTTGGTAAAGCGCCGC
1 TAAAGGTCTTGGTCTTTAGCGGCATTTTGGGTAAAGCGCCGC
*
44610312 TAAAGGTCTTGGTCTTTAGCGGCATTTTTGGTAAAGCGCCGC
1 TAAAGGTCTTGGTCTTTAGCGGCATTTTGGGTAAAGCGCCGC
* * *
44610354 TAAAGGTCTTGGTCTTTAACGACATTTTTGGTAAAGCGCCGC
1 TAAAGGTCTTGGTCTTTAGCGGCATTTTGGGTAAAGCGCCGC
44610396 TAAAGGTCTTGGTCTTTAGCGGC
1 TAAAGGTCTTGGTCTTTAGCGGC
44610419 GTTTGTGTGA
Statistics
Matches: 173, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
41 3 0.02
42 147 0.85
43 20 0.12
44 3 0.02
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (42 bp):
TAAAGGTCTTGGTCTTTAGCGGCATTTTGGGTAAAGCGCCGC
Found at i:44614696 original size:31 final size:31
Alignment explanation
Indices: 44614656--44614756 Score: 130
Period size: 31 Copynumber: 3.3 Consensus size: 31
44614646 GGCATCAATA
* * *
44614656 ATTCATATTTACATATTCATACCCTATAATC
1 ATTCATATTTGCATATTCATACCTTGTAATC
* * *
44614687 ATTCGTATTTGCATATTCACATCTTGTAATC
1 ATTCATATTTGCATATTCATACCTTGTAATC
* *
44614718 ATTCATATTTGCATTTTTATACCTTGTAATC
1 ATTCATATTTGCATATTCATACCTTGTAATC
44614749 ATTCATAT
1 ATTCATAT
44614757 AAATTTTCGG
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.47
Consensus pattern (31 bp):
ATTCATATTTGCATATTCATACCTTGTAATC
Found at i:44617710 original size:7 final size:7
Alignment explanation
Indices: 44617693--44617722 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
44617683 ATTTTTAAAC
44617693 ATAATTAT
1 ATAA-TAT
44617701 ATAATAT
1 ATAATAT
44617708 ATAATAT
1 ATAATAT
44617715 ATAATAT
1 ATAATAT
44617722 A
1 A
44617723 CAAATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATAATAT
Found at i:44623563 original size:15 final size:14
Alignment explanation
Indices: 44623541--44623571 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
44623531 AATTAGATAT
44623541 TATTTATTATAAAA
1 TATTTATTATAAAA
44623555 TATTATATTATAAAA
1 TATT-TATTATAAAA
44623570 TA
1 TA
44623572 AATTTCGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TATTTATTATAAAA
Found at i:44626798 original size:7 final size:7
Alignment explanation
Indices: 44626788--44626902 Score: 53
Period size: 7 Copynumber: 16.7 Consensus size: 7
44626778 ATCTAGAATT
44626788 TTGAACC
1 TTGAACC
44626795 TTGAACC
1 TTGAACC
44626802 TTGAACC
1 TTGAACC
* *
44626809 TTAAACT
1 TTGAACC
44626816 TTGAA-C
1 TTGAACC
** *
44626822 TCAAATC
1 TTGAACC
*
44626829 TTGAACA
1 TTGAACC
44626836 TTGAA--
1 TTGAACC
*
44626841 TTCCAGACC
1 TT-GA-ACC
*
44626850 TCGAACC
1 TTGAACC
* *
44626857 TTAAACT
1 TTGAACC
44626864 TTGAACC
1 TTGAACC
44626871 TTGAA-C
1 TTGAACC
44626877 TCTGAA--
1 T-TGAACC
44626883 TTCGAACC
1 TT-GAACC
*
44626891 TTAAACC
1 TTGAACC
44626898 TTGAA
1 TTGAA
44626903 ACCCAATTTT
Statistics
Matches: 79, Mismatches: 20, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
5 3 0.04
6 10 0.13
7 62 0.78
8 3 0.04
9 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.30
Consensus pattern (7 bp):
TTGAACC
Found at i:44634392 original size:20 final size:18
Alignment explanation
Indices: 44634361--44634397 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
44634351 AAGCAAACAT
44634361 AAAAAAATAAAACTAAAG
1 AAAAAAATAAAACTAAAG
44634379 AAAAAAATTGAAAACTAAA
1 AAAAAAA-T-AAAACTAAA
44634398 TTTAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 1 0.06
20 9 0.53
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (18 bp):
AAAAAAATAAAACTAAAG
Found at i:44635725 original size:11 final size:11
Alignment explanation
Indices: 44635711--44635774 Score: 110
Period size: 11 Copynumber: 5.7 Consensus size: 11
44635701 ATTTTTTAAA
44635711 TTTTAAAATAT
1 TTTTAAAATAT
44635722 TTTTAAAATAT
1 TTTTAAAATAT
44635733 TTTTAAAATAT
1 TTTTAAAATAT
44635744 TTTTAAAATACT
1 TTTTAAAATA-T
*
44635756 TTTTAAAATTT
1 TTTTAAAATAT
44635767 TTTTAAAA
1 TTTTAAAA
44635775 AATTGGTGTT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
11 41 0.80
12 10 0.20
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:44636491 original size:6 final size:6
Alignment explanation
Indices: 44636482--44636515 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
44636472 CAATGGGACG
44636482 GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA GGGA
1 GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA GGGA
44636516 TGGTGGGGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGGAGA
Found at i:44643063 original size:7 final size:7
Alignment explanation
Indices: 44643053--44643092 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
44643043 TTGGGGTAGA
44643053 TGGGAGG
1 TGGGAGG
44643060 TGGGAGG
1 TGGGAGG
44643067 TGGGAGG
1 TGGGAGG
*
44643074 TCGGAGG
1 TGGGAGG
*
44643081 TCGGAGG
1 TGGGAGG
44643088 TGGGA
1 TGGGA
44643093 TGGGAAGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.15, C:0.05, G:0.65, T:0.15
Consensus pattern (7 bp):
TGGGAGG
Found at i:44643152 original size:30 final size:31
Alignment explanation
Indices: 44643093--44643152 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
44643083 GGAGGTGGGA
*
44643093 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGAGAATAAAAATTTTAGGGGAAAAG
*
44643124 TGGGAAG-GAGTAAAAATTTT-GGGAGAAAA
1 TGGGAAGAGAATAAAAATTTTAGGG-GAAAA
44643153 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 16 0.62
31 7 0.27
ACGTcount: A:0.45, C:0.00, G:0.35, T:0.20
Consensus pattern (31 bp):
TGGGAAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:44643463 original size:9 final size:9
Alignment explanation
Indices: 44643446--44643476 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
44643436 TCGAGTTGAT
44643446 TCGAATAAC
1 TCGAATAAC
*
44643455 TCGATTAAC
1 TCGAATAAC
44643464 TCGAATAAC
1 TCGAATAAC
44643473 TCGA
1 TCGA
44643477 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:44643671 original size:18 final size:19
Alignment explanation
Indices: 44643645--44643681 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
44643635 TTGTGGGTGT
44643645 TTTAAAAATT-TTATTTTA
1 TTTAAAAATTATTATTTTA
*
44643663 TTTATAAATTATTATTTTA
1 TTTAAAAATTATTATTTTA
44643682 ATAAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTAAAAATTATTATTTTA
Found at i:44648596 original size:22 final size:22
Alignment explanation
Indices: 44648571--44648648 Score: 122
Period size: 22 Copynumber: 3.5 Consensus size: 22
44648561 TGCACTAATG
*
44648571 AACAGAGAGCAC-TAAAGTGCTA
1 AACAGAGAGCACAT-ATGTGCTA
44648593 AACAGAGAGCACATATGTGCTA
1 AACAGAGAGCACATATGTGCTA
44648615 AACAGAGAGCACATATGTGCTA
1 AACAGAGAGCACATATGTGCTA
*
44648637 AACGGAGAGCAC
1 AACAGAGAGCAC
44648649 TGTCGTGTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
22 52 0.98
23 1 0.02
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.14
Consensus pattern (22 bp):
AACAGAGAGCACATATGTGCTA
Found at i:44648674 original size:25 final size:25
Alignment explanation
Indices: 44648565--44648695 Score: 79
Period size: 22 Copynumber: 5.6 Consensus size: 25
44648555 TTATTATGCA
*
44648565 CTAATGAA-CAGAGAGCACTAAAGTG
1 CTAAT-AATCAGAGAGCACTAACGTG
*
44648590 CT-A-AA-CAGAGAGCAC-ATATGTG
1 CTAATAATCAGAGAGCACTA-ACGTG
*
44648612 CT-A-AA-CAGAGAGCAC-ATATGTG
1 CTAATAATCAGAGAGCACTA-ACGTG
* **
44648634 CT-A-AA-CGGAGAGCACTGTCGTG
1 CTAATAATCAGAGAGCACTAACGTG
* *
44648656 TTAGTAATCAGAGAGCACTAACGTG
1 CTAATAATCAGAGAGCACTAACGTG
44648681 CTAATAATCAGAGAG
1 CTAATAATCAGAGAG
44648696 TGCTAAAGTT
Statistics
Matches: 89, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.01
22 56 0.63
24 3 0.03
25 29 0.33
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (25 bp):
CTAATAATCAGAGAGCACTAACGTG
Found at i:44649197 original size:8 final size:8
Alignment explanation
Indices: 44649184--44649219 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
44649174 TGTTTTATAT
44649184 ATATAATA
1 ATATAATA
44649192 ATATAATA
1 ATATAATA
44649200 ATATAATA
1 ATATAATA
44649208 ATATAATA
1 ATATAATA
44649216 ATAT
1 ATAT
44649220 TTTAATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAATA
Found at i:44653687 original size:41 final size:41
Alignment explanation
Indices: 44653618--44653735 Score: 145
Period size: 41 Copynumber: 3.0 Consensus size: 41
44653608 AAGGACGCCA
* *
44653618 CAAAAGGCTAG-ACTATAGCGGCATTTTTCTCATAAATGCTG
1 CAAAAGGTTAGAACTATAGCGGC-GTTTTCTCATAAATGCTG
* *
44653659 CAAAAGGTTAGAACTATAGCGGCGTTTTCTCACAAACGCTG
1 CAAAAGGTTAGAACTATAGCGGCGTTTTCTCATAAATGCTG
* *
44653700 CAAAAGGTAAGAA--ATAACGGCGTTTT-TCATAAATGC
1 CAAAAGGTTAGAACTATAGCGGCGTTTTCTCATAAATGC
44653736 CACGAATATT
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
38 8 0.12
39 12 0.18
41 37 0.54
42 11 0.16
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (41 bp):
CAAAAGGTTAGAACTATAGCGGCGTTTTCTCATAAATGCTG
Found at i:44655426 original size:43 final size:43
Alignment explanation
Indices: 44655378--44655494 Score: 153
Period size: 43 Copynumber: 2.7 Consensus size: 43
44655368 CAAGCCCGTG
* * *
44655378 TGGCTCACATGGCCAAGAGACACACCTGTGTGGTCAGGACGTA
1 TGGCTCACACGACCAAGAGACACGCCTGTGTGGTCAGGACGTA
* * * * * *
44655421 TGGCTCACACAACCAAGAGATATGCCCGTGTGGTCAGGCCGTG
1 TGGCTCACACGACCAAGAGACACGCCTGTGTGGTCAGGACGTA
44655464 TGGCTCACACGACCAAGAGACACGCCTGTGT
1 TGGCTCACACGACCAAGAGACACGCCTGTGT
44655495 CTCAGGCCGT
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 61 1.00
ACGTcount: A:0.25, C:0.28, G:0.29, T:0.18
Consensus pattern (43 bp):
TGGCTCACACGACCAAGAGACACGCCTGTGTGGTCAGGACGTA
Found at i:44656936 original size:23 final size:23
Alignment explanation
Indices: 44656892--44656939 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
44656882 GGATAGCCAT
* * *
44656892 ATATCGGGAAGTTCAAGCGAGCC
1 ATATCGGAAAGCTCAAGAGAGCC
*
44656915 ATATCGGAAAGCTCTAGAGAGCC
1 ATATCGGAAAGCTCAAGAGAGCC
44656938 AT
1 AT
44656940 TAATCAGGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (23 bp):
ATATCGGAAAGCTCAAGAGAGCC
Found at i:44661076 original size:23 final size:23
Alignment explanation
Indices: 44661050--44661094 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
44661040 TTGCAAACTA
44661050 TTAAAGCCTTCATTGTCCTATAT
1 TTAAAGCCTTCATTGTCCTATAT
*
44661073 TTAAAGCTTTCATTGTCCTATA
1 TTAAAGCCTTCATTGTCCTATA
44661095 CTTGCAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (23 bp):
TTAAAGCCTTCATTGTCCTATAT
Found at i:44661600 original size:73 final size:73
Alignment explanation
Indices: 44661508--44661710 Score: 185
Period size: 73 Copynumber: 2.8 Consensus size: 73
44661498 TTTCAGAAGC
** *
44661508 TTAATTTAGTTTGATTTATTGAAATTTGATACAAAGTAAAACAGCTTGTTCAATTATGCGTTTTA
1 TTAATTTAGTTCAATTTATTGAAATTTGATACAAAGTAAAACAGCTTATTCAATTATGCGTTTTA
44661573 AAAAAAAG
66 AAAAAAAG
* ** * * * *
44661581 TTAATTTAGTTCAATTTATTGAATTTTGATATTAAGTAGAACCGTTTATTCAATTATGTGTTTT-
1 TTAATTTAGTTCAATTTATTGAAATTTGATACAAAGTAAAACAGCTTATTCAATTATGCGTTTTA
** *
44661645 TTAAAAGG
66 AAAAAAAG
* * * * ** **
44661653 CTATTTTAGTTCAATTCATTG-AGTTTCGATATTAAGTAAAACAATTTATTCAAGTTAT
1 TTAATTTAGTTCAATTTATTGAAATTT-GATACAAAGTAAAACAGCTTATTCAA-TTAT
44661711 ATGTTTTGAG
Statistics
Matches: 108, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
71 4 0.04
72 46 0.43
73 58 0.54
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.44
Consensus pattern (73 bp):
TTAATTTAGTTCAATTTATTGAAATTTGATACAAAGTAAAACAGCTTATTCAATTATGCGTTTTA
AAAAAAAG
Found at i:44661684 original size:72 final size:72
Alignment explanation
Indices: 44661409--44661775 Score: 276
Period size: 72 Copynumber: 5.1 Consensus size: 72
44661399 AGTAAAATTA
* *
44661409 TTTATTTAATTATGTGTTTTTAAAAAGGTTAATTTAGTTCAATTTATT-AAGTTTTGATATTAAG
1 TTTATTCAATTATGTGTTTTTAAAAAGGCTAATTTAGTTCAATTTATTGAA-TTTTGATATTAAG
** *
44661473 CGAAACCG
65 TAAAACAG
* * *** * * ** * **
44661481 TTTATTTAGTTAT-ACATTTTCAGAA-GCTTAATTTAGTTTGATTTATTGAAATTTGATACAAAG
1 TTTATTCAATTATGTGTTTTTAAAAAGGC-TAATTTAGTTCAATTTATTGAATTTTGATATTAAG
44661544 TAAAACAG
65 TAAAACAG
* * * * * *
44661552 CTTGTTCAATTATGCGTTTTAAAAAAAAGTTAATTTAGTTCAATTTATTGAATTTTGATATTAAG
1 TTTATTCAATTATGTGTTTT-TAAAAAGGCTAATTTAGTTCAATTTATTGAATTTTGATATTAAG
* *
44661617 TAGAACCG
65 TAAAACAG
* * * * *
44661625 TTTATTCAATTATGTGTTTTTTAAAAGGCTATTTTAGTTCAATTCATTGAGTTTCGATATTAAGT
1 TTTATTCAATTATGTGTTTTTAAAAAGGCTAATTTAGTTCAATTTATTGAATTTTGATATTAAGT
*
44661690 AAAACAA
66 AAAACAG
* * * ** * * ** * *
44661697 TTTATTCAAGTTATATG-TTTTGAGAAGATTAAATTAATTTGATTTATTGAGTTGTGATATTAAG
1 TTTATTCAA-TTATGTGTTTTTAAAAAGGCTAATTTAGTTCAATTTATTGAATTTTGATATTAAG
44661761 TAAAATC-G
65 TAAAA-CAG
44661769 TTTATTC
1 TTTATTC
44661776 GGTGATATTA
Statistics
Matches: 227, Mismatches: 61, Indels: 14
0.75 0.20 0.05
Matches are distributed among these distances:
70 1 0.00
71 48 0.21
72 114 0.50
73 63 0.28
74 1 0.00
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.46
Consensus pattern (72 bp):
TTTATTCAATTATGTGTTTTTAAAAAGGCTAATTTAGTTCAATTTATTGAATTTTGATATTAAGT
AAAACAG
Found at i:44662663 original size:35 final size:35
Alignment explanation
Indices: 44662613--44662679 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
44662603 AGATTTAAAG
* *
44662613 ATGATAATCATAACTTACAAAAATATTTAAAGTTT
1 ATGATAATCAAAACTTACAAAAACATTTAAAGTTT
* *
44662648 ATGATTATCAAAACTTACATAAACATTTAAAG
1 ATGATAATCAAAACTTACAAAAACATTTAAAG
44662680 AATAAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.34
Consensus pattern (35 bp):
ATGATAATCAAAACTTACAAAAACATTTAAAGTTT
Found at i:44662714 original size:9 final size:9
Alignment explanation
Indices: 44662700--44662834 Score: 70
Period size: 9 Copynumber: 15.6 Consensus size: 9
44662690 AACTTTGGAT
44662700 TATAACTTA
1 TATAACTTA
44662709 TATAACTTA
1 TATAACTTA
*
44662718 CATAA-TTCA
1 TATAACTT-A
44662727 TA-AA--TA
1 TATAACTTA
44662733 TATAACTTA
1 TATAACTTA
*
44662742 CATAA--TA
1 TATAACTTA
* *
44662749 CATAA-ATA
1 TATAACTTA
* *
44662757 TATATCATA
1 TATAACTTA
44662766 TCATAACTTA
1 T-ATAACTTA
*
44662776 CATAACTTA
1 TATAACTTA
*
44662785 TATAA-ATA
1 TATAACTTA
* *
44662793 TATATCATA
1 TATAACTTA
44662802 TCATAACTTA
1 T-ATAACTTA
*
44662812 CATAACTTA
1 TATAACTTA
*
44662821 CATAACTTA
1 TATAACTTA
*
44662830 CATAA
1 TATAA
44662835 ATAAATATCA
Statistics
Matches: 103, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
6 3 0.03
7 10 0.10
8 15 0.15
9 63 0.61
10 12 0.12
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (9 bp):
TATAACTTA
Found at i:44662738 original size:24 final size:24
Alignment explanation
Indices: 44662707--44662760 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
44662697 GATTATAACT
*
44662707 TATATAACTTACATAATTCATAAA
1 TATATAACTTACATAATACATAAA
44662731 TATATAACTTACATAATACATAAA
1 TATATAACTTACATAATACATAAA
44662755 TATATA
1 TATATA
44662761 TCATATCATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (24 bp):
TATATAACTTACATAATACATAAA
Found at i:44662797 original size:36 final size:36
Alignment explanation
Indices: 44662701--44662825 Score: 172
Period size: 36 Copynumber: 3.6 Consensus size: 36
44662691 ACTTTGGATT
* *
44662701 ATAACTTATATAACTTACAT-AAT-TCATA-AATAT-
1 ATAACTTACATAACTTACATAAATAT-ATATCATATC
44662734 ATAACTTACATAA--TACATAAATATATATCATATC
1 ATAACTTACATAACTTACATAAATATATATCATATC
*
44662768 ATAACTTACATAACTTATATAAATATATATCATATC
1 ATAACTTACATAACTTACATAAATATATATCATATC
44662804 ATAACTTACATAACTTACATAA
1 ATAACTTACATAACTTACATAA
44662826 CTTACATAAA
Statistics
Matches: 82, Mismatches: 4, Indels: 9
0.86 0.04 0.09
Matches are distributed among these distances:
31 5 0.06
32 6 0.07
33 17 0.21
34 13 0.16
36 41 0.50
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (36 bp):
ATAACTTACATAACTTACATAAATATATATCATATC
Found at i:44662819 original size:45 final size:45
Alignment explanation
Indices: 44662734--44662861 Score: 154
Period size: 45 Copynumber: 2.9 Consensus size: 45
44662724 TCATAAATAT
* * * *
44662734 ATAACTTACAT-AATACATA-AATAT-ATATCATATCATAACTTAC
1 ATAACTTACATAAATAAATATCATATAATAACTTA-CATAACTTAC
* * *
44662777 ATAACTTATATAAATATATATCATATCATAACTTACATAACTTAC
1 ATAACTTACATAAATAAATATCATATAATAACTTACATAACTTAC
*
44662822 ATAACTTACATAAATAAATATCATATAATAACTTCCATAA
1 ATAACTTACATAAATAAATATCATATAATAACTTACATAA
44662862 AACTTTGGAT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
43 10 0.14
44 7 0.10
45 50 0.68
46 6 0.08
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (45 bp):
ATAACTTACATAAATAAATATCATATAATAACTTACATAACTTAC
Found at i:44662853 original size:36 final size:36
Alignment explanation
Indices: 44662701--44662861 Score: 134
Period size: 45 Copynumber: 4.4 Consensus size: 36
44662691 ACTTTGGATT
* ** *
44662701 ATAACTTATATAACTTACAT-AATTCATA-AATAT-
1 ATAACTTACATAACTTACATAAATAAATATCATATA
* *
44662734 ATAACTTACATAA--TACATAAATATATATCATATC
1 ATAACTTACATAACTTACATAAATAAATATCATATA
*
44662768 ATAACTTACATAACTTATATAAATATATATCATATCATAACTTA
1 ATAACTTACATAACTTACAT-AA-ATA-A--ATATCAT-A--TA
44662812 CATAACTTACATAACTTACATAAATAAATATCATATA
1 -ATAACTTACATAACTTACATAAATAAATATCATATA
*
44662849 ATAACTTCCATAA
1 ATAACTTACATAA
44662862 AACTTTGGAT
Statistics
Matches: 105, Mismatches: 9, Indels: 25
0.76 0.06 0.18
Matches are distributed among these distances:
31 5 0.05
32 6 0.06
33 16 0.15
34 13 0.12
36 16 0.15
37 4 0.04
38 3 0.03
39 1 0.01
40 7 0.07
41 7 0.07
42 2 0.02
43 3 0.03
44 3 0.03
45 19 0.18
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (36 bp):
ATAACTTACATAACTTACATAAATAAATATCATATA
Found at i:44668593 original size:66 final size:65
Alignment explanation
Indices: 44668479--44668617 Score: 190
Period size: 66 Copynumber: 2.1 Consensus size: 65
44668469 TCACATTGCT
* * *
44668479 CAACTTAAAGTGGAGGTAGCATCGAGAGAAGCAAAGGCTCAAATAAAATATGAAGAACTCCAGCT
1 CAACTTAAAGTGGAGGCAGCAGCGAGAGAAGCAAAGGC-CAAAAAAAATATGAAGAACTCCAGCT
44668544 A
65 A
* * *
44668545 CAACTTAAAGTGGAGGCAGCAGCGAGGGAAGCAGAGG-CAAGCAAAAAATATGACGAACTCCAGC
1 CAACTTAAAGTGGAGGCAGCAGCGAGAGAAGCAAAGGCCAA--AAAAAATATGAAGAACTCCAGC
44668609 TA
64 TA
44668611 CAACTTA
1 CAACTTA
44668618 CGAATATGAT
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
64 3 0.05
66 62 0.95
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.14
Consensus pattern (65 bp):
CAACTTAAAGTGGAGGCAGCAGCGAGAGAAGCAAAGGCCAAAAAAAATATGAAGAACTCCAGCTA
Found at i:44669013 original size:43 final size:42
Alignment explanation
Indices: 44668966--44669110 Score: 168
Period size: 43 Copynumber: 3.4 Consensus size: 42
44668956 AGAACATGAC
44668966 CTTTAGCGGCGTTTTTGGGTAAAGAGCCGCTAAAGGTCATGTT
1 CTTTAGCGGCGTTTTTGGG-AAAGAGCCGCTAAAGGTCATGTT
* *
44669009 CTTTAGCGACATTTTTGGGGAAAGCA-CCGCTAAAGGTCATGTT
1 CTTTAGCGGCGTTTTT-GGGAAAG-AGCCGCTAAAGGTCATGTT
* * * *
44669052 CTGTAGCGGCGTTTGTAGGGAAA-ACGCCGCTAAATGTCTTGTT
1 CTTTAGCGGCGTTT-TTGGGAAAGA-GCCGCTAAAGGTCATGTT
*
44669095 CTATAGCGGCGTTTTT
1 CTTTAGCGGCGTTTTT
44669111 CCACATAAAT
Statistics
Matches: 87, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 80 0.92
44 5 0.06
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.32
Consensus pattern (42 bp):
CTTTAGCGGCGTTTTTGGGAAAGAGCCGCTAAAGGTCATGTT
Found at i:44672190 original size:23 final size:23
Alignment explanation
Indices: 44672164--44672213 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
44672154 TATCCCCACA
*
44672164 TGGAGTGTAG-GGTTGGACGGAGT
1 TGGAGTGTAGAGGCTGGACGG-GT
*
44672187 TGGAGTGTAGAGGCTGGATGGGT
1 TGGAGTGTAGAGGCTGGACGGGT
44672210 TGGA
1 TGGA
44672214 TTTGATACTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.18, C:0.04, G:0.52, T:0.26
Consensus pattern (23 bp):
TGGAGTGTAGAGGCTGGACGGGT
Found at i:44672769 original size:17 final size:18
Alignment explanation
Indices: 44672718--44672775 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
44672708 GCAATAAGTG
*
44672718 ACGTTTTGAAAATTAATA
1 ACGTTTTGAAAATGAATA
*
44672736 ACGTTTTGAAAAAGAATA
1 ACGTTTTGAAAATGAATA
* *
44672754 AC-TTTTGAATATGAATC
1 ACGTTTTGAAAATGAATA
44672771 ACGTT
1 ACGTT
44672776 GAAATTAATC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
17 14 0.41
18 20 0.59
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (18 bp):
ACGTTTTGAAAATGAATA
Found at i:44680662 original size:6 final size:6
Alignment explanation
Indices: 44680651--44680685 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
44680641 TGATATTAAC
44680651 AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT
44680686 CAGTCAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:44686260 original size:37 final size:37
Alignment explanation
Indices: 44686218--44686294 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
44686208 ATGCCATGTC
*
44686218 CCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTG
1 CCAGACATGGTCATACAGGGGACCTCTCATCTCGGTG
*
44686255 CCAGACATGGTCATACATGGGACCTCTCATCTCGGTG
1 CCAGACATGGTCATACAGGGGACCTCTCATCTCGGTG
44686292 CCA
1 CCA
44686295 ATGACATGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.21, C:0.31, G:0.25, T:0.23
Consensus pattern (37 bp):
CCAGACATGGTCATACAGGGGACCTCTCATCTCGGTG
Found at i:44686314 original size:87 final size:87
Alignment explanation
Indices: 44686168--44686334 Score: 228
Period size: 87 Copynumber: 1.9 Consensus size: 87
44686158 ATGCCATATC
* * ** *
44686168 CCAGATATGGTCTTACATGGGAGTTATCATATAGGTGTCCATGCCATGTCCCAGACATGGTCTTA
1 CCAGACATGGTCATACATGGGACCTATCATATAGGTGTCCATGACATGTCCCAGACATGGTCTTA
44686233 CAGGGGACCTCTCATCTCGGTG
66 CAGGGGACCTCTCATCTCGGTG
* * * *
44686255 CCAGACATGGTCATACATGGGACCTCTCATCTCGGTG-CCAATGACATGTCCGAGACATGGTCTT
1 CCAGACATGGTCATACATGGGACCTATCATATAGGTGTCC-ATGACATGTCCCAGACATGGTCTT
*
44686319 ACATGGGACCTCTCAT
65 ACAGGGGACCTCTCAT
44686335 AATCTCAATG
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
86 2 0.03
87 67 0.97
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (87 bp):
CCAGACATGGTCATACATGGGACCTATCATATAGGTGTCCATGACATGTCCCAGACATGGTCTTA
CAGGGGACCTCTCATCTCGGTG
Found at i:44686315 original size:50 final size:51
Alignment explanation
Indices: 44686255--44686389 Score: 168
Period size: 56 Copynumber: 2.6 Consensus size: 51
44686245 CATCTCGGTG
* *
44686255 CCAGACATGGTCATACATGGGACCTCTCATCTC-GGTGCCAATGACATGTC
1 CCAGACATGGTCTTACATGGGACCTCTCATCTCAGATGCCAATGACATGTC
* *
44686305 CGAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCCATGTC
1 CCAGACATGGTCTTACATGGGACCTCTC---ATCTC-A-GATGCCAATGACATGTC
44686361 CCAGACATGGTCTTACATGGGA--TCTCATC
1 CCAGACATGGTCTTACATGGGACCTCTCATC
44686390 CTCTTAATGT
Statistics
Matches: 74, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
50 26 0.35
51 3 0.04
53 5 0.07
54 4 0.05
56 36 0.49
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (51 bp):
CCAGACATGGTCTTACATGGGACCTCTCATCTCAGATGCCAATGACATGTC
Found at i:44689044 original size:22 final size:22
Alignment explanation
Indices: 44689019--44689063 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
44689009 TAGTTTTTCT
44689019 CTTAAATGAATCTGGACACTGG
1 CTTAAATGAATCTGGACACTGG
44689041 CTTAAATGAATCTGGACACTGG
1 CTTAAATGAATCTGGACACTGG
44689063 C
1 C
44689064 ACTTAATCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (22 bp):
CTTAAATGAATCTGGACACTGG
Found at i:44690335 original size:27 final size:27
Alignment explanation
Indices: 44690297--44690542 Score: 336
Period size: 27 Copynumber: 9.1 Consensus size: 27
44690287 CGTGGGCAAG
44690297 TGATCGAAATACCCTCGAAGGGTAAAA
1 TGATCGAAATACCCTCGAAGGGTAAAA
*
44690324 TGATCGAAATACCCTCGAAGGTTAAAA
1 TGATCGAAATACCCTCGAAGGGTAAAA
*
44690351 TGA-CTGAAATACCCTCGAAAGGTAAAA
1 TGATC-GAAATACCCTCGAAGGGTAAAA
*
44690378 TGATCAAAATACCCTCGAAGGGTAAAA
1 TGATCGAAATACCCTCGAAGGGTAAAA
*
44690405 TGACCGAAATACCCTCGAAGGGTAAAA
1 TGATCGAAATACCCTCGAAGGGTAAAA
* **
44690432 TGACCGAAATACCCTTAAAGGGTAAAA
1 TGATCGAAATACCCTCGAAGGGTAAAA
* *
44690459 TGATCGAAATACCCTCAAAAGGTAAAA
1 TGATCGAAATACCCTCGAAGGGTAAAA
* *
44690486 TGATCGAAATACCCCCAAAGGGTAAAA
1 TGATCGAAATACCCTCGAAGGGTAAAA
*
44690513 TGA-CTGAAATACCC-CCATAGGGTAAAA
1 TGATC-GAAATACCCTCGA-AGGGTAAAA
44690540 TGA
1 TGA
44690543 CTGATATACC
Statistics
Matches: 200, Mismatches: 15, Indels: 8
0.90 0.07 0.04
Matches are distributed among these distances:
26 4 0.02
27 195 0.98
28 1 0.00
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.18
Consensus pattern (27 bp):
TGATCGAAATACCCTCGAAGGGTAAAA
Found at i:44690942 original size:28 final size:28
Alignment explanation
Indices: 44690902--44690995 Score: 100
Period size: 28 Copynumber: 3.4 Consensus size: 28
44690892 ACTACACTGT
44690902 ACTGTTACTGTATTGGGCTAAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
* * *
44690930 ACTGCTACTGTATTAGGCTCAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
* * * * *
44690958 CCTGATACTGCT-TAGGGCTTAGGCCCAG
1 ACTGTTACTG-TATTGGGCTAAGGCCCAC
44690986 ACTGTTACTG
1 ACTGTTACTG
44690996 CATGTCGTAT
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 53 0.98
29 1 0.02
ACGTcount: A:0.20, C:0.28, G:0.24, T:0.28
Consensus pattern (28 bp):
ACTGTTACTGTATTGGGCTAAGGCCCAC
Found at i:44693775 original size:18 final size:17
Alignment explanation
Indices: 44693738--44693771 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
44693728 ATTTCATTTT
44693738 CACAAACCATTTTCAAA
1 CACAAACCATTTTCAAA
*
44693755 CACAAATCATTTTCAAA
1 CACAAACCATTTTCAAA
44693772 ACACTATGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (17 bp):
CACAAACCATTTTCAAA
Found at i:44697443 original size:13 final size:11
Alignment explanation
Indices: 44697407--44697437 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
44697397 CTGTCCGTAT
44697407 TAATTTTTATA
1 TAATTTTTATA
*
44697418 TTATTTTTATA
1 TAATTTTTATA
44697429 TAATTTTTA
1 TAATTTTTA
44697438 AATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:44697603 original size:29 final size:30
Alignment explanation
Indices: 44697559--44697616 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
44697549 CTTAACAAGA
*
44697559 AAATGCCTCTACAAT-ATAACAAAATTAAT
1 AAATGCCTCTAAAATAATAACAAAATTAAT
*
44697588 AAATGCCTTTAAAATAATAACAAAATTAA
1 AAATGCCTCTAAAATAATAACAAAATTAA
44697617 CAATAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.28
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAT
Found at i:44697649 original size:25 final size:23
Alignment explanation
Indices: 44697598--44697651 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 23
44697588 AAATGCCTTT
* *
44697598 AAAATAATAACAAAATTAACAAT
1 AAAATAATAACAAAAATAACAAC
*
44697621 AAAATAATATCCAAACAATAACAAC
1 AAAATAATA-ACAAA-AATAACAAC
44697646 AAAATA
1 AAAATA
44697652 GTAGCAACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 9 0.35
24 4 0.15
25 13 0.50
ACGTcount: A:0.69, C:0.13, G:0.00, T:0.19
Consensus pattern (23 bp):
AAAATAATAACAAAAATAACAAC
Found at i:44710167 original size:27 final size:27
Alignment explanation
Indices: 44710120--44710453 Score: 342
Period size: 27 Copynumber: 12.4 Consensus size: 27
44710110 AGGCCGTAAC
**
44710120 AGTCATTTTATCTCCTA--GGGGTATAAT
1 AGTCATTTTA-C-CCTATGGGGGTATTTT
44710147 AGTCATTTTACCCTATGGGGGTA-TTT
1 AGTCATTTTACCCTATGGGGGTATTTT
*
44710173 CGATCATTTTACCCTATGGGGGTATTTT
1 AG-TCATTTTACCCTATGGGGGTATTTT
* * *
44710201 GGTCATTCTACCCTATGCGGGTA-TTT
1 AGTCATTTTACCCTATGGGGGTATTTT
*
44710227 CGATCATTTTACCCTAT-GGGGTA-TTT
1 AG-TCATTTTACCCTATGGGGGTATTTT
* **
44710253 CGATCATTTTACCCTATGGAAGTATTTT
1 AG-TCATTTTACCCTATGGGGGTATTTT
** *
44710281 AGTCATTTTACCCTATAAGGGTATTTC
1 AGTCATTTTACCCTATGGGGGTATTTT
* *
44710308 AGTCATTTTACCTTATGGGGTTATTTTT
1 AGTCATTTTACCCTATGGGGGTA-TTTT
*
44710336 A-TCATTTTACCCTATGGGGGTATTTC
1 AGTCATTTTACCCTATGGGGGTATTTT
* * *
44710362 GGTCATTCTA-CCTATGAGGGTATTTT
1 AGTCATTTTACCCTATGGGGGTATTTT
* **
44710388 GGTCATTTTACTTTATGGGGGTATTTT
1 AGTCATTTTACCCTATGGGGGTATTTT
* *
44710415 AGTCATTTTATCCTATTGGGGTATTTT
1 AGTCATTTTACCCTATGGGGGTATTTT
44710442 AGTCATTTTACC
1 AGTCATTTTACC
44710454 TATTTTGGGG
Statistics
Matches: 258, Mismatches: 39, Indels: 20
0.81 0.12 0.06
Matches are distributed among these distances:
25 4 0.02
26 58 0.22
27 184 0.71
28 12 0.05
ACGTcount: A:0.20, C:0.16, G:0.19, T:0.44
Consensus pattern (27 bp):
AGTCATTTTACCCTATGGGGGTATTTT
Found at i:44710278 original size:80 final size:81
Alignment explanation
Indices: 44710149--44710453 Score: 384
Period size: 80 Copynumber: 3.8 Consensus size: 81
44710139 GGTATAATAG
*
44710149 TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTGGTCATTCTACCC
1 TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTAGTCATTCTACCC
*
44710214 TATGCGGGTATTTCGA
66 TATGAGGGTATTTCGA
** *
44710230 TCATTTTACCCTAT-GGGGTATTTCGATCATTTTACCCTATGGAAGTATTTTAGTCATTTTACCC
1 TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTAGTCATTCTACCC
*
44710294 TATAAGGGTATTTC-A
66 TATGAGGGTATTTCGA
* * ** **
44710309 GTCATTTTACCTTATGGGGTTATTTTTATCATTTTACCCTATGGGGGTATTTCGGTCATTCTA-C
1 -TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTAGTCATTCTACC
* *
44710373 CTATGAGGGTATTTTGG
65 CTATGAGGGTATTTCGA
** * * * *
44710390 TCATTTTACTTTATGGGGGTATTT-TAGTCATTTTATCCTATTGGGGTATTTTAGTCATTTTACC
1 TCATTTTACCCTATGGGGGTATTTCGA-TCATTTTACCCTATGGGGGTATTTTAGTCATTCTACC
44710454 TATTTTGGGG
Statistics
Matches: 194, Mismatches: 25, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
79 3 0.02
80 137 0.71
81 54 0.28
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.45
Consensus pattern (81 bp):
TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTAGTCATTCTACCC
TATGAGGGTATTTCGA
Found at i:44710469 original size:26 final size:26
Alignment explanation
Indices: 44710413--44710470 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
44710403 TGGGGGTATT
*
44710413 TTAGTCATTTTATCCTATTGGGGTATT
1 TTAGTCATTTTATCCTATTGGGG-ATC
44710440 TTAGTCATTTTA-CCTATTTTGGGG-TC
1 TTAGTCATTTTATCCTA--TTGGGGATC
44710466 TTAGT
1 TTAGT
44710471 GTAGATATCG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 10 0.36
27 12 0.43
28 6 0.21
ACGTcount: A:0.17, C:0.12, G:0.19, T:0.52
Consensus pattern (26 bp):
TTAGTCATTTTATCCTATTGGGGATC
Found at i:44713650 original size:598 final size:593
Alignment explanation
Indices: 44712482--44713660 Score: 1833
Period size: 598 Copynumber: 2.0 Consensus size: 593
44712472 AGTCGACAAA
* * * * *
44712482 CCCCAATTTTGGCTTTCTCTGTTCGCTGGTTTTTGGGTTTCTCGTTACGCACCTAGGCAAAATCG
1 CCCCAATTTCGGCTTTCTCTGTTCGCTGGTTTTTGGGTTCCTCATTACACACCTAGGCAAAATCA
* * ** *
44712547 ATGTAGAACTCAACAATCGAGTATTCTGGTACCTAGATTGACAATTTACATGATTTTTTAACCAA
66 ATGTAGAACTCAACAATCAAGTATTCTGGTACCTAGATTGACAATTCACACAAGTTTTTAACCAA
44712612 AATCTTACCAAACCCAAATGAAAAATTCACAAGAGCAACACTAATTGAACCTATATTCAACCATT
131 AATCTTACCAAACCCAAATGAAAAATTCACAAGAGCAACACTAATTGAACCTATATTCAACCATT
* * *
44712677 AACAACCCCTAAATGATATGAAACACTTACACTTGAATGAAAACACCATACAACTCTTAATTTGC
196 AACAACCCCTAAATGATATGAAACACTTACACTTGAATGAAAACACCACACAACTCCTAATTAGC
* *
44712742 TGGTAGATGGACTATCTCATGAAATTCAACTAAAACCAATCAATCGGTTAACATCGATACAACTC
261 TAGTAGATGGACTATCCCATGAAATTCAACTAAAACCAATCAATCGGTTAACATCGATACAACTC
* *
44712807 CACCACCACACCTCAACAAGTTGAAAACTAAAGAAGAAAAACTCCATAACATAAGAGAAGAAGTC
326 CACCACCACACCTCAACAAGTTGAAAACTAAAGAAGAAAAACACCAAAACATAAGAGAAGAAGTC
* *
44712872 AAGACTTACACACGAATCAGGTTGTAATCTATACAATCAAACATCACCACCGAACTTGAATAGTA
391 AAGACTTACACACGAATCAGGTTGCAATCTATACAATCAAACATCACCACCAAACTTGAATAGTA
* * * *
44712937 AGAACAATGGAAGTAAGGGCTCTAAAGACCAAGAAACCAACAGAGTAAGTTGCTACCAAGAACTC
456 AGAACAATGGAAGTAAGGGCACTAAAGACCAAGAAACCAAAAGAGCAAGTTGATACCAAGAACTC
* *
44713002 ACATGAAAAGAAAGAAAATAAAACTGGGAAAAATAAAAGGAACGTGGAAAAAGGGAAGAGATGGC
521 ACATGAAAAGAAAGAAAATAAAACTGGGAAAAACAAAAGGAACATGG-AAAAGGGAAGAGATGGC
44713067 GTTGACAGG
585 GTTGACAGG
* *
44713076 CCCCAATTTCGGCTTTCTCTGTTTGCT-GTTTTTATGGTTCCTCATTACACACCTAGGCAAAATC
1 CCCCAATTTCGGCTTTCTCTGTTCGCTGGTTTTT-GGGTTCCTCATTACACACCTAGGCAAAATC
44713140 AATGTAGAACTCAACAATCAAGTATTCTGGTACCTAGATTGACAATTCACACAAGTTTTTAACCA
65 AATGTAGAACTCAACAATCAAGTATTCTGGTACCTAGATTGACAATTCACACAAGTTTTTAACCA
* * * * *
44713205 AAGTCTTATCAAACCCAAATGACAAGTTCACAAGAGCAACACTAATTGGACCTATATTCAACCAT
130 AAATCTTACCAAACCCAAATGAAAAATTCACAAGAGCAACACTAATTGAACCTATATTCAACCAT
*
44713270 TAACAACCCCTAAAATGATATG-AACACTTACCCTTGAATGAAAACAACACCACACAACTCCTAA
195 TAACAACCCCT-AAATGATATGAAACACTTACACTTGAATG--AA-AACACCACACAACTCCTAA
* * * * * * *
44713334 TTAGCTAGTAGATGGATTGTCCCGTGAACTTCACCTAAAACCGATCAATCGGTTAATATCGATAC
256 TTAGCTAGTAGATGGACTATCCCATGAAATTCAACTAAAACCAATCAATCGGTTAACATCGATAC
* *
44713399 AACTCCCCCACCACACCTCAACAAAGTTGAAAACTGAAGAAGAAAAACACCAAAACATAAGA-AA
321 AACTCCACCACCACACCTCAAC-AAGTTGAAAACTAAAGAAGAAAAACACCAAAACATAAGAGAA
* * *
44713463 GGATGTCAAGACTTACACACGAATCAGGTTGCAATCTATACAATCGAACATCACTACCAAACTTG
385 -GAAGTCAAGACTTACACACGAATCAGGTTGCAATCTATACAATCAAACATCACCACCAAACTTG
* * *
44713528 AATAGTAAGAACATTGGAAGTAAGGGCACTAAAGACCAAGAAACCAAAAGAGCAATTTGATACTA
449 AATAGTAAGAACAATGGAAGTAAGGGCACTAAAGACCAAGAAACCAAAAGAGCAAGTTGATACCA
44713593 AGAACTCACATGAAAAGAAAGAAAATAAAACTGGGAAAAACAAAAGGAACATGGAAAAGGGAAGA
514 AGAACTCACATGAAAAGAAAGAAAATAAAACTGGGAAAAACAAAAGGAACATGGAAAAGGGAAGA
44713658 GAT
579 GAT
44713661 TTTTGGTATA
Statistics
Matches: 530, Mismatches: 48, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
593 6 0.01
594 198 0.37
595 10 0.02
596 2 0.00
597 109 0.21
598 205 0.39
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.22
Consensus pattern (593 bp):
CCCCAATTTCGGCTTTCTCTGTTCGCTGGTTTTTGGGTTCCTCATTACACACCTAGGCAAAATCA
ATGTAGAACTCAACAATCAAGTATTCTGGTACCTAGATTGACAATTCACACAAGTTTTTAACCAA
AATCTTACCAAACCCAAATGAAAAATTCACAAGAGCAACACTAATTGAACCTATATTCAACCATT
AACAACCCCTAAATGATATGAAACACTTACACTTGAATGAAAACACCACACAACTCCTAATTAGC
TAGTAGATGGACTATCCCATGAAATTCAACTAAAACCAATCAATCGGTTAACATCGATACAACTC
CACCACCACACCTCAACAAGTTGAAAACTAAAGAAGAAAAACACCAAAACATAAGAGAAGAAGTC
AAGACTTACACACGAATCAGGTTGCAATCTATACAATCAAACATCACCACCAAACTTGAATAGTA
AGAACAATGGAAGTAAGGGCACTAAAGACCAAGAAACCAAAAGAGCAAGTTGATACCAAGAACTC
ACATGAAAAGAAAGAAAATAAAACTGGGAAAAACAAAAGGAACATGGAAAAGGGAAGAGATGGCG
TTGACAGG
Found at i:44720434 original size:20 final size:20
Alignment explanation
Indices: 44720403--44720469 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
44720393 TGTAGCATGC
*
44720403 ACACGGGCATGTAAACCATT
1 ACACGAGCATGTAAACCATT
*
44720423 ACATGAGCATGTAAACCATT
1 ACACGAGCATGTAAACCATT
* * *
44720443 ACACGGGCATGTAGACCATC
1 ACACGAGCATGTAAACCATT
44720463 ACACGAG
1 ACACGAG
44720470 AGTGTAGACA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.18
Consensus pattern (20 bp):
ACACGAGCATGTAAACCATT
Found at i:44722564 original size:656 final size:656
Alignment explanation
Indices: 44721085--44723430 Score: 3326
Period size: 656 Copynumber: 3.6 Consensus size: 656
44721075 TGTCGTGTGC
**
44721085 AGGGTGGACGAAGAGGTGTTTGGATGGTTGGGGTGTCTTTTTGACTTAATGCATTCGGTTTGCAT
1 AGGGTGGACGAAGAGGTGTTTGGATGGTTGGGGTGGGTTTTTGACTTAATGCATTCGGTTTGCAT
* *
44721150 TTGAGCATATGTGTCTGATTATGAAATTTTCAAATTGTTTGCGAATGGTATATTAATTTGAAGTG
66 TTGAGCATATGTGTCTGATTATGAAAATTTCAAATTGTTTGCGAATGGTATATTAATTTGATGTG
* *
44721215 -TCTGTACCTCTGTTTACCGCTTCAAGGTTTTTATGCTCTGTCTATGCGTTCTTATCTAGGATAA
131 TTC-GTACCTCTGTTTACCACTTCAAGGTTTTTATGCTCTGTCTATGTGTTCTTATCTAGGATAA
** * * * *
44721279 TTGTTTTTGAAATCTCGTCTTTTGTCATTCATTTTTGGTTTCAAACACACACTGAGCTCCCGTAG
195 TTGTTTTTGAAATCTCACCTTTTGTCATTCATTTTTGGTTTCAGACTCACACTGAACTCGCGTAG
* * * * * * * *
44721344 CTCGCCTTCCTTTAGTTTCTCTATTTCAGGTAACTCGTGGTTTAAGGCTAGACTCAATAGTCGGA
260 CTCACCTCCCTTCAGTTTCTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGACAGTCGGA
* * *
44721409 GGTCTCAGAGAGATAGTGTTTGATTCAATTTAAGTAAAATTTTTATATA-TTTTATACAGTTGGT
325 GGTCTCAGAGAGATAGTGTTTGATTCGATTTAAGTAAAATTTTCATA-AGTTTTATACGGTTGGT
* * *
44721473 TTAAGACTGCTTGTAAAGCGATTATATAAACTGTGGTACAAAGTTTTTATGTTGGACTTTTGTAA
389 TTAAGACTGTTTCTAAAGCGATTATATAAACTGTGGTACAAAGTTTTTATGTTGGACTTTCGTAA
* * * * *
44721538 AGTGTTATTTGGACTAAACTTTAGAAATTGTGGATTTTATGGCTGAATGTTTTGACGCCAGTTTA
454 AGTGTTATTTGGATTGAACTTTAGAAACTGTGGATTTTATGTCTGAATGTTTTGACGCCGGTTTA
* *
44721603 ATATTTGTTTCAAAACATAGCTAAGTTTTATTTAGTTTCCTTAAGTTGAAATGAAGAAAAGGGTT
519 ATA-TTGTTTCAAAACATAGCTAAGTTTTATTTAGTTTCCTTAAGTTGAAATGAACAAAAGGATT
* *
44721668 TTCCTGATTTGAATTAAAGTTTTTGTTTCCGCCACCATTGGTGGCTAAATGTAACCT-TCAGAAT
583 TTCTTGATTTGAATTAAAGTTTTTGTTTCCGCCACCTTTGGTGGCTAAATGTAACCTCT-AGAAT
*
44721732 CCGGTCTAAA
647 TCGGTCTAAA
* * * * *
44721742 AGGGTGGACGAAGAGGTGTTTGAATGGTTGGGGTGGGTTTTTTACTTAACGTATTCGGTTTGTAT
1 AGGGTGGACGAAGAGGTGTTTGGATGGTTGGGGTGGGTTTTTGACTTAATGCATTCGGTTTGCAT
* * * * *
44721807 TTTAGCATATGTGTCTGATGATGAAATTTTCAAATTGTTTGCGAATAGTATATTAATTTAATGTG
66 TTGAGCATATGTGTCTGATTATGAAAATTTCAAATTGTTTGCGAATGGTATATTAATTTGATGTG
* * * *
44721872 TTCGTACCTATGTTTATCACTTTAAGG-TTCTATGCTCTGTCTATGTGTTCTTATCTAGGATAAT
131 TTCGTACCTCTGTTTACCACTTCAAGGTTTTTATGCTCTGTCTATGTGTTCTTATCTAGGATAAT
* *
44721936 TGTTTCTGAAATCACACCTTTTGTCATTCATTTTTGGTTTCAGACTCACACTGAACTCGCGTAGC
196 TGTTTTTGAAATCTCACCTTTTGTCATTCATTTTTGGTTTCAGACTCACACTGAACTCGCGTAGC
* * * * * * * *
44722001 CCACCTTCCTTTAGTTTCTCTCTTTCAAGTAACTCGTCGTTTGAGGTTGGACTCGCCAGTCGGAT
261 TCACCTCCCTTCAGTTTCTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGACAGTCGGAG
*
44722066 GTCTTAGAGAGATAGTGTTTGACTT-GATTTAAGTAAAATTTTCATAAGTTTTATACGGTTGGTT
326 GTCTCAGAGAGATAGTGTTTGA-TTCGATTTAAGTAAAATTTTCATAAGTTTTATACGGTTGGTT
* * * *
44722130 TAAGACTGTTTCTAAAGCGACTATATAAACTGTTGTACAATGTTTTTATGTTGGACTTTCATAAA
390 TAAGACTGTTTCTAAAGCGATTATATAAACTGTGGTACAAAGTTTTTATGTTGGACTTTCGTAAA
* * *
44722195 GTGTTATTTGGATTGAACTTTAAAAACTGTAGATTTTATGTCTGAATGTTTTGATGCCGGTTTAA
455 GTGTTATTTGGATTGAACTTTAGAAACTGTGGATTTTATGTCTGAATGTTTTGACGCCGGTTTAA
* * * *
44722260 TATTGTTTCAAAACATAACTAAGTTTTATTTAGTTTCCTTCAGTTAAAACGAACAAAAGGATTTT
520 TATTGTTTCAAAACATAGCTAAGTTTTATTTAGTTTCCTTAAGTTGAAATGAACAAAAGGATTTT
*
44722325 CTTGATTTGAATTAAAGTTTTTGTTTCCACCACCTTTGGTGGCTAAATGTAACCTCTAGAATTCG
585 CTTGATTTGAATTAAAGTTTTTGTTTCCGCCACCTTTGGTGGCTAAATGTAACCTCTAGAATTCG
44722390 GTCTAAA
650 GTCTAAA
* ** * *
44722397 AGGGTGGACGAAGAGGTGTTTGGATGGTTAGGGTGGGTTTTTTTCTTAATGTATTCAGTTTGCAT
1 AGGGTGGACGAAGAGGTGTTTGGATGGTTGGGGTGGGTTTTTGACTTAATGCATTCGGTTTGCAT
* * *
44722462 TTGAGCATATGTGTCTGATTATGAAAATTACAAATTATTTGCAAATGGTATATTAATTTGATGTG
66 TTGAGCATATGTGTCTGATTATGAAAATTTCAAATTGTTTGCGAATGGTATATTAATTTGATGTG
* * * * * *
44722527 TTCATACCTCTGTTTACCGCTTCAAGGTTTTTATGCTCTATTTGTGTGTTCTTATCTGGGATAAT
131 TTCGTACCTCTGTTTACCACTTCAAGGTTTTTATGCTCTGTCTATGTGTTCTTATCTAGGATAAT
* * * *
44722592 TGTTTTTGAAATCTCACCTTTTGTAATTCATTTTTGCTTTCAGACTCACA-TTAAGCTTGCGTAG
196 TGTTTTTGAAATCTCACCTTTTGTCATTCATTTTTGGTTTCAGACTCACACTGAA-CTCGCGTAG
* * *
44722656 CTCAGCTCCCTTCAGTTTCTCTCTTTTAGGTAACTCGTGGTTTGAGGCTGGACTC-AGCAATCGG
260 CTCACCTCCCTTCAGTTTCTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGA-CAGTCGG
* * *
44722720 AGGTCTCAGAGAGATAGTGTTTGATTCGGTTTAAGT-AAATATTTCATATGTTTTATACGGTTTG
324 AGGTCTCAGAGAGATAGTGTTTGATTCGATTTAAGTAAAAT-TTTCATAAGTTTTATACGGTTGG
* *
44722784 TTTAAGACTATTTTTAAAGCGATTATATAAACTGTGGTACAAAGTTTTTATGTTGGACTTTCGTA
388 TTTAAGACTGTTTCTAAAGCGATTATATAAACTGTGGTACAAAGTTTTTATGTTGGACTTTCGTA
* * *
44722849 AAATGTTATTTGGATTGAACTTTAGAAACTGTGGATTTTATGTCTCAATGTTTTGACGCTGGTTT
453 AAGTGTTATTTGGATTGAACTTTAGAAACTGTGGATTTTATGTCTGAATGTTTTGACGCCGGTTT
* * * **
44722914 AATATTATTTCAAAACATAGCTAAGTTTTATTTAGTTTTCTTAAGTTGAAATGCACAAAACTATT
518 AATATTGTTTCAAAACATAGCTAAGTTTTATTTAGTTTCCTTAAGTTGAAATGAACAAAAGGATT
* **
44722979 TTCTTGATTTGAATTAAAGTTTTTGTTTCCGCCACCTTTGGTGGCTAAATGTAACCACCGGAATT
583 TTCTTGATTTGAATTAAAGTTTTTGTTTCCGCCACCTTTGGTGGCTAAATGTAACCTCTAGAATT
44723044 CGGTCTAAA
648 CGGTCTAAA
** * * * *
44723053 ATTGTGGACCAAGAGGTGTTCGGATGGTTGGGGTGGGTTTTTGACTTAATACATTCGGTTTGCAC
1 AGGGTGGACGAAGAGGTGTTTGGATGGTTGGGGTGGGTTTTTGACTTAATGCATTCGGTTTGCAT
* * *
44723118 TTGAGCATATGTGTCTGATTATGAAAATTTCAGATTGTTTACGAATTGTATATTAATTTGATGTG
66 TTGAGCATATGTGTCTGATTATGAAAATTTCAAATTGTTTGCGAATGGTATATTAATTTGATGTG
* * * * *
44723183 TTCGTACATCTGTTTACCACTTCAAGGTTTTTATGCTTTGTCTATGTGTTCTAACCTGGGATAAT
131 TTCGTACCTCTGTTTACCACTTCAAGGTTTTTATGCTCTGTCTATGTGTTCTTATCTAGGATAAT
* * ** * * * *
44723248 TATTTTTTACCTCTCGCCTTTTGTCATTCATTTTT-TTTTCAGACTCATACTGAGCTCGCGTAGC
196 TGTTTTTGAAATCTCACCTTTTGTCATTCATTTTTGGTTTCAGACTCACACTGAACTCGCGTAGC
* *
44723312 TCACCTCCCTTCAATTTTTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGACAGTCGGAG
261 TCACCTCCCTTCAGTTTCTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGACAGTCGGAG
*
44723377 GTCAT-AGAGAGATAGTGTTTGATTCGGTTTAAGTAAAATTTTCATAAGTTTTAT
326 GTC-TCAGAGAGATAGTGTTTGATTCGATTTAAGTAAAATTTTCATAAGTTTTAT
44723431 TTAGTTTCCT
Statistics
Matches: 1496, Mismatches: 180, Indels: 28
0.88 0.11 0.02
Matches are distributed among these distances:
655 396 0.26
656 958 0.64
657 140 0.09
658 2 0.00
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (656 bp):
AGGGTGGACGAAGAGGTGTTTGGATGGTTGGGGTGGGTTTTTGACTTAATGCATTCGGTTTGCAT
TTGAGCATATGTGTCTGATTATGAAAATTTCAAATTGTTTGCGAATGGTATATTAATTTGATGTG
TTCGTACCTCTGTTTACCACTTCAAGGTTTTTATGCTCTGTCTATGTGTTCTTATCTAGGATAAT
TGTTTTTGAAATCTCACCTTTTGTCATTCATTTTTGGTTTCAGACTCACACTGAACTCGCGTAGC
TCACCTCCCTTCAGTTTCTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGACAGTCGGAG
GTCTCAGAGAGATAGTGTTTGATTCGATTTAAGTAAAATTTTCATAAGTTTTATACGGTTGGTTT
AAGACTGTTTCTAAAGCGATTATATAAACTGTGGTACAAAGTTTTTATGTTGGACTTTCGTAAAG
TGTTATTTGGATTGAACTTTAGAAACTGTGGATTTTATGTCTGAATGTTTTGACGCCGGTTTAAT
ATTGTTTCAAAACATAGCTAAGTTTTATTTAGTTTCCTTAAGTTGAAATGAACAAAAGGATTTTC
TTGATTTGAATTAAAGTTTTTGTTTCCGCCACCTTTGGTGGCTAAATGTAACCTCTAGAATTCGG
TCTAAA
Found at i:44723860 original size:485 final size:486
Alignment explanation
Indices: 44722935--44723903 Score: 1246
Period size: 485 Copynumber: 2.0 Consensus size: 486
44722925 AAAACATAGC
* * * * * * *
44722935 TAAGTTTTATTTAGTTTTCTTAAGTTGAAATGCACAAAACTATTTTCTTGATTTGAATTAAAGTT
1 TAAGTTTTATTTAGTTTCCTTAAGTTGAAACGAACAAAACGACTTTCTAGAGTTGAATTAAAGTT
* **
44723000 TTTGTTTCCGCCACCTTTGGTGGCTAAATGTAACCACCGGAATTCGGTCTAAAATTGTGGACCAA
66 TTTGTTTCCGCCACCTTTGGTGGCTAAATGTAACCACCAGAATTCGGTCTAAAAGGGTGGACCAA
* *
44723065 GAGGTGTTCGGATGGTTGGGGTGGGTTTTTGACTTAATACATTCGGTTTGCACTTGAGCATATGT
131 AAGGTGTTCGAATGGTTGGGGTGGGTTTTTGACTTAATACATTCGGTTTGCACTTGAGCATATGT
* * * * *
44723130 GTCTGATTATGAAAATTTCAGATTGTTTACGAATTGTATATTAATTTGATGTGTTCGTACATCTG
196 GTCTGATTATGAAAATTTCAAATTGTTTACGAATGGTATATCAATTTGATGTATTCATACATCTG
* * * * * * **
44723195 TTTACCACTTCAAGGTTTTTATGCTTTGTCTATGTGTTCTAACCTGGGATAATTATTTTTTACCT
261 TTTACCACTTCAAGGTTTTTATACTCTATATATGTGTTCTAACCTGGGATAATTAGTTTTGAAAT
** * * * *
44723260 CTCGCCTTTTGTCATTCATTTTTTTTTCAGACTCATACTGAGCTCGCGTAGCTCACCTCCCTTCA
326 AACGCATTTTGTCATTCATTTTTGTTTCAGACTCAAACTGAACTCGCGTAGCTCACCTCCCTTCA
* * * *
44723325 ATTTTTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGACAGTCGGAGGTCATAGAGAGAT
391 ATTTCTCTCTTACAGGTAACTCGTAGTTTGAGGCTGGACTCGACAGTCGGAGGGCATAGAGAGAT
*
44723390 AGTGTTTGATTCGGTTTAAGTAAAATTTTCA
456 AGTGTTTGATTCGATTTAAGTAAAATTTTCA
* * *
44723421 TAAGTTTTATTTAGTTTCCTTAAGTTGAAACGAACAAAAGGGCTTTCTAGAGTTGAATTAGAGTT
1 TAAGTTTTATTTAGTTTCCTTAAGTTGAAACGAACAAAACGACTTTCTAGAGTTGAATTAAAGTT
* * * * *
44723486 TTTGTTTTCTCTACCTTTGGTGGCTAAATGTAACCTCTAGAATTC-GTCTAAAAGGGTGGA-CAA
66 TTTGTTTCCGCCACCTTTGGTGGCTAAATGTAACCACCAGAATTCGGTCTAAAAGGGTGGACCAA
* * ** *
44723549 AATGGTGTTTGAATGGTTGGGGTGGGTTTTTTACTTAATGTATTCGGTTTGCATTTGAGCATATG
131 AA-GGTGTTCGAATGGTTGGGGTGGGTTTTTGACTTAATACATTCGGTTTGCACTTGAGCATATG
* * ** * *
44723614 TGTCTGATTATGGAATTTTCAAATTGTTTGTGAATGGTATATCAATTTGATGTATTCATACCTTT
195 TGTCTGATTATGAAAATTTCAAATTGTTTACGAATGGTATATCAATTTGATGTATTCATACATCT
* * * * *
44723679 GTTTACCATTTCAAGG-TTTTATACTCTATATGTGTGTTCTTATCTGGGATAATTGGTTTTGAAA
260 GTTTACCACTTCAAGGTTTTTATACTCTATATATGTGTTCTAACCTGGGATAATTAGTTTTGAAA
* * **
44723743 TAACGCATTTTGTCATTTATTTGTTGTTTCAGACTCAAATTGAACTCTTGTAGCTCACCTCCC-T
325 TAACGCATTTTGTCATTCATTT-TTGTTTCAGACTCAAACTGAACTCGCGTAGCTCACCTCCCTT
* * ** *
44723807 CTAGA-TTCTCTCTTACAGGTAACTCGTAGTTTGAGGTTGGACTTGGTAGTCGGAGGGCTTAGAG
389 C-A-ATTTCTCTCTTACAGGTAACTCGTAGTTTGAGGCTGGACTCGACAGTCGGAGGGCATAGAG
44723871 AGATAGTGTTTGATTCGATTTAAGTAAAATTTT
452 AGATAGTGTTTGATTCGATTTAAGTAAAATTTT
44723904 AACTTTTATT
Statistics
Matches: 410, Mismatches: 69, Indels: 9
0.84 0.14 0.02
Matches are distributed among these distances:
484 60 0.15
485 255 0.62
486 95 0.23
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (486 bp):
TAAGTTTTATTTAGTTTCCTTAAGTTGAAACGAACAAAACGACTTTCTAGAGTTGAATTAAAGTT
TTTGTTTCCGCCACCTTTGGTGGCTAAATGTAACCACCAGAATTCGGTCTAAAAGGGTGGACCAA
AAGGTGTTCGAATGGTTGGGGTGGGTTTTTGACTTAATACATTCGGTTTGCACTTGAGCATATGT
GTCTGATTATGAAAATTTCAAATTGTTTACGAATGGTATATCAATTTGATGTATTCATACATCTG
TTTACCACTTCAAGGTTTTTATACTCTATATATGTGTTCTAACCTGGGATAATTAGTTTTGAAAT
AACGCATTTTGTCATTCATTTTTGTTTCAGACTCAAACTGAACTCGCGTAGCTCACCTCCCTTCA
ATTTCTCTCTTACAGGTAACTCGTAGTTTGAGGCTGGACTCGACAGTCGGAGGGCATAGAGAGAT
AGTGTTTGATTCGATTTAAGTAAAATTTTCA
Found at i:44724785 original size:656 final size:651
Alignment explanation
Indices: 44723421--44725216 Score: 2364
Period size: 656 Copynumber: 2.7 Consensus size: 651
44723411 AAAATTTTCA
* * * *
44723421 TAAGTTTTATTTAGTTTCCTTAAGTTGAAACGAACAAAAGGGCTTTCTAGAGTTGAATT-AGAGT
1 TAAGTTTTATTTAGTTTTCTTAAGTTGAAACGAACAAAAGGGTTTTCTTGATTTGAATTAAG-GT
* * * * *
44723485 TTTTGTTTTCTCTACCTTTGGTGGCTAAATGTAACCTCTAGAATTCGTCTAAAAGGGTGGACAAA
65 TTTTGTTTCCACCACCTTTGGTGGCTAAATGTAACCTCTGGAATTCGTCTAAAAGGGTGGACAAG
* * *
44723550 ATGGTGTTTGAATGGTTGGGGTGGGTTTTTT-ACTTAATGTATTCGGTTTGCATTTGAGCATATG
130 A-GGTGTTTGGATGGTTGGGGT-GGTTTTTTGACTTAATGCATTCGGTTTGCATTTGAGCAAATG
* * * * *
44723614 TGTCTGATTATGGAATTTTCAAATTGTTTGTGAATGGTATATCAATTTGATGTATTCATACCTTT
193 TGTCTGATTATGAAATTTTCAAATTGTTTGTGAATGGTATATTAATTTGATGTGTTCGTACCTCT
** * *
44723679 GTTTACCATTTCAAGG-TTTTATACTCTATATGTGTGTTCTTATCTGGGATAATTGGTTTTGAAA
258 GTTTACCGCTTCAAGGTTTTTATGCTCTATATGTGTGTTCTTATCTGGGATAATTGTTTTTGAAA
** * * * * * * *
44723743 TAACGCATTTTGTCATTTATTTGTTGTTTCAGACTCAAATTGAACTCT-TGTAGCTCACCTCCCT
323 TCTCGCCTTTTGTCATTCATTT-TTGTTTCAAACTCAAACTGAGCT-TGCGTAGCTCACCTCCTT
* * * * * ** * * *
44723807 CTAGATTCTCTCTTACAGGTAACTCGTAGTTTGAGGTTGGACTTGGTAGTCGGAGGGCTTAGAGA
386 C-AGTTTCTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGACAGTCAGAGGTCTCAGAGA
*
44723872 GATAGTGTTTGATTCGATTTAAGTAAAATTTT-A-ACTTTTATTCTGTTGGTTGAAGACTGTTTC
450 GATAGTGTTTGATTCGATTTAAGTAAAATTTTCATACTTTTATACTGTTGGTTGAAGACTGTTTC
* * * * * *
44723935 TAAAGCGATTATATAATCTGTGGTACACAGTTTTTATGTTGGACTTTCGTAAAGTGTTATTTGGA
515 TAAAGCGATTATATAAGCTGTGCTACAAAGTTTTTATGTTGAACTTTCATAAAGTATTATTTGGA
* * * *
44724000 CTGAACTTTAGAAACTGTACATTTTATGTTTGAATGTTTTGATGCCGGTTTAATATTGTTTCAAA
580 CTGAACTTTAGAAACTATACATTTTATGTATGAATGTTTTGATGCCAGTTTAATATTATTTCAAA
44724065 ACATAGC
645 ACATAGC
*
44724072 TAAGTTTTATTTAGTTTTCTTAAGTTGATACGAACAAAAGGGTTTTCTTGATTTGAATTAAGGTT
1 TAAGTTTTATTTAGTTTTCTTAAGTTGAAACGAACAAAAGGGTTTTCTTGATTTGAATTAAGGTT
** *
44724137 TTTGTTTCCACCACCTTTGGTGGCTAAATGTAACCTCTGGAATTCAACCTAAAAGGGTGGACGAG
66 TTTGTTTCCACCACCTTTGGTGGCTAAATGTAACCTCTGGAATTC-GTCTAAAAGGGTGGAC-AA
*
44724202 GAGGTGTTTGGATGGTTGGGGTGGTTTTTTGACTTAATGCATTCGGTTTGCATTTGAGCAGATGT
129 GAGGTGTTTGGATGGTTGGGGTGGTTTTTTGACTTAATGCATTCGGTTTGCATTTGAGCAAATGT
* *
44724267 GTCTGATTATGAAATTTTCAAATTATTTGTGAACGGTATATTAATTTGATGTGTTCGTACCTCTG
194 GTCTGATTATGAAATTTTCAAATTGTTTGTGAATGGTATATTAATTTGATGTGTTCGTACCTCTG
* *
44724332 TTTACCGCGTCAAGGTTTTTATGCTCTATCTGTGTGTTCTTATCTGGGATAATTGTTTTTGAAAT
259 TTTACCGCTTCAAGGTTTTTATGCTCTATATGTGTGTTCTTATCTGGGATAATTGTTTTTGAAAT
* *
44724397 CTCTCCTTTTGTCATTCATTTTTGGTTTCAAACTCACACTGAGCTTGCGTAGCTCACCTCCTTTC
324 CTCGCCTTTTGTCATTCATTTTT-GTTTCAAACTCAAACTGAGCTTGCGTAGCTCACCTCC-TTC
* * * ** *
44724462 AGTTTCTCTCTTTTAGGTAACTCATGGTTTGAGCCTACACTCGACAGTCAAAGGTCTCAGAGAGA
387 AGTTTCTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGACAGTCAGAGGTCTCAGAGAGA
* * * * * * *
44724527 TAGTGTTTGATTCGGTATAAGTAAATTTTTCATATGTTTTATAC-GATTTGTTTAAGACTGTTTG
452 TAGTGTTTGATTCGATTTAAGTAAAATTTTCATA-CTTTTATACTG-TTGGTTGAAGACTGTTTC
* * *
44724591 TAAAGCGATTGTATAAGCTGTGCTACAAATTTTTTATGTTGAACTTTCATAAAGTATTATTTTGA
515 TAAAGCGATTATATAAGCTGTGCTACAAAGTTTTTATGTTGAACTTTCATAAAGTATTATTTGGA
* * **
44724656 TTGAACTTTCGAAACTATGGATTTTATGTATGAATGTTTTGATGCCAGTTTAATATTATTTCAAA
580 CTGAACTTTAGAAACTATACATTTTATGTATGAATGTTTTGATGCCAGTTTAATATTATTTCAAA
44724721 ACATAGC
645 ACATAGC
* * * * *
44724728 TAAGTTTTATTTAGTTTTCTTAAGTTGAAATGCACAAAAGTGTTTTCTTGATTTGAATTAAAGAT
1 TAAGTTTTATTTAGTTTTCTTAAGTTGAAACGAACAAAAGGGTTTTCTTGATTTGAATTAAGGTT
* * * *
44724793 TTTGTTTCCGCCACCTTTGGTGGCTAAATGTAACCTCCGAAATTCGGTCTAAAATGGTGGACCAA
66 TTTGTTTCCACCACCTTTGGTGGCTAAATGTAACCTCTGGAATTC-GTCTAAAAGGGTGGA-CAA
* * *
44724858 GAGGTGTTTGGATGGTTGGGGTGGGTTTTTGACTTAATACATTCGGTTTGCATTTAAGCAAATGT
129 GAGGTGTTTGGATGGTTGGGGTGGTTTTTTGACTTAATGCATTCGGTTTGCATTTGAGCAAATGT
* * *
44724923 GTCTTATTATGAAATTTTCAAATTGTTTGCGAATGGTATATTAATTTGATGTGTTCGTACCTCTA
194 GTCTGATTATGAAATTTTCAAATTGTTTGTGAATGGTATATTAATTTGATGTGTTCGTACCTCTG
* * * * * * * * *
44724988 TTTACCGCTTTAATGTTTTTATGCTCTGTTTGTCTGTTCTGACCTGGGATAATTATTTTTGACAT
259 TTTACCGCTTCAAGGTTTTTATGCTCTATATGTGTGTTCTTATCTGGGATAATTGTTTTTGAAAT
* * * *
44725053 CTCGCCTTTTGTCATTCATTTTTTGTTTCAAACTCATACTAAGCTCGCATAGCTCACCTCCCTTC
324 CTCGCCTTTTGTCATTCA-TTTTTGTTTCAAACTCAAACTGAGCTTGCGTAGCTCACCT-CCTTC
* * *
44725118 AATTTCTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGACAGTCAGATGTCACAGAGAGA
387 AGTTTCTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGACAGTCAGAGGTCTCAGAGAGA
* *
44725183 TAATGTTTGATTTGATTTAAGTAAAATTTTCATA
452 TAGTGTTTGATTCGATTTAAGTAAAATTTTCATA
44725217 AGTTGTATTT
Statistics
Matches: 997, Mismatches: 133, Indels: 25
0.86 0.12 0.02
Matches are distributed among these distances:
651 106 0.11
652 140 0.14
653 170 0.17
654 3 0.00
655 2 0.00
656 568 0.57
657 8 0.01
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.42
Consensus pattern (651 bp):
TAAGTTTTATTTAGTTTTCTTAAGTTGAAACGAACAAAAGGGTTTTCTTGATTTGAATTAAGGTT
TTTGTTTCCACCACCTTTGGTGGCTAAATGTAACCTCTGGAATTCGTCTAAAAGGGTGGACAAGA
GGTGTTTGGATGGTTGGGGTGGTTTTTTGACTTAATGCATTCGGTTTGCATTTGAGCAAATGTGT
CTGATTATGAAATTTTCAAATTGTTTGTGAATGGTATATTAATTTGATGTGTTCGTACCTCTGTT
TACCGCTTCAAGGTTTTTATGCTCTATATGTGTGTTCTTATCTGGGATAATTGTTTTTGAAATCT
CGCCTTTTGTCATTCATTTTTGTTTCAAACTCAAACTGAGCTTGCGTAGCTCACCTCCTTCAGTT
TCTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGACAGTCAGAGGTCTCAGAGAGATAGT
GTTTGATTCGATTTAAGTAAAATTTTCATACTTTTATACTGTTGGTTGAAGACTGTTTCTAAAGC
GATTATATAAGCTGTGCTACAAAGTTTTTATGTTGAACTTTCATAAAGTATTATTTGGACTGAAC
TTTAGAAACTATACATTTTATGTATGAATGTTTTGATGCCAGTTTAATATTATTTCAAAACATAG
C
Found at i:44730593 original size:26 final size:26
Alignment explanation
Indices: 44730564--44730615 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
44730554 AATAAAAGAA
44730564 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTTTAATTAG
44730590 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTTTAATTAG
44730616 CATTAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (26 bp):
AACATTCAATATTTCAGTTTAATTAG
Found at i:44732811 original size:50 final size:50
Alignment explanation
Indices: 44732668--44732909 Score: 182
Period size: 50 Copynumber: 4.7 Consensus size: 50
44732658 GGTAAAGAGA
* *
44732668 TCCCATGTAAGACCATGTCTGGGACATGGCATTAGCATCATCGAGGTTATGAGAAG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA-C-T-GA-G--ATGAGAAG
* * * * * *
44732724 TCTCACGCAAGACCATGTCAGGGACATGCCGTTGGCACTGAGATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAAG
* * * * *
44732774 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAAG
* * * * * * * *
44732824 TCCCATGTAAGACCATATCTGGGATATGACATTGGCAGT-ACAAGA-AACA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAA-G
*** *
44732873 TCCTGTGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
44732910 TGTTATTATC
Statistics
Matches: 149, Mismatches: 36, Indels: 9
0.77 0.19 0.05
Matches are distributed among these distances:
48 2 0.01
49 35 0.23
50 77 0.52
52 1 0.01
53 2 0.01
54 1 0.01
55 1 0.01
56 30 0.20
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (50 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAAG
Found at i:44734908 original size:75 final size:75
Alignment explanation
Indices: 44734783--44734931 Score: 264
Period size: 75 Copynumber: 2.0 Consensus size: 75
44734773 TAGCTTTTGA
* *
44734783 AACGACCTACACCTTTAGGTTTCCTTTTGGTTCTCCCATTAGCTTGGGTTGAACCACCTTAGTTT
1 AACGACCTACACCTTTAGGTTTCCTTTTGGTTCTCCAATTAGCTTCGGTTGAACCACCTTAGTTT
44734848 ATGGGCTATT
66 ATGGGCTATT
44734858 AACGACCTACACCTTTAGGTTTCCTTTTGGTTCTCCAATT-GCTTTCGGTTGAACCACCTTAGTT
1 AACGACCTACACCTTTAGGTTTCCTTTTGGTTCTCCAATTAGC-TTCGGTTGAACCACCTTAGTT
44734922 TATGGGCTAT
65 TATGGGCTAT
44734932 AATTATTGCA
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
74 2 0.03
75 69 0.97
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.39
Consensus pattern (75 bp):
AACGACCTACACCTTTAGGTTTCCTTTTGGTTCTCCAATTAGCTTCGGTTGAACCACCTTAGTTT
ATGGGCTATT
Found at i:44734959 original size:12 final size:13
Alignment explanation
Indices: 44734934--44734963 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
44734924 TGGGCTATAA
44734934 TTATTGCATTTAT
1 TTATTGCATTTAT
44734947 TTATTGC-TTTAT
1 TTATTGCATTTAT
44734959 TTATT
1 TTATT
44734964 CATGTATGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (13 bp):
TTATTGCATTTAT
Found at i:44739849 original size:22 final size:22
Alignment explanation
Indices: 44739824--44739872 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
44739814 TGCAGTTGAT
44739824 TCATGGCTAACGTACTAAGCTC
1 TCATGGCTAACGTACTAAGCTC
** *
44739846 TCATGTTTCACGTACTAAGCTC
1 TCATGGCTAACGTACTAAGCTC
44739868 TCATG
1 TCATG
44739873 TTTGAACAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (22 bp):
TCATGGCTAACGTACTAAGCTC
Found at i:44739873 original size:22 final size:22
Alignment explanation
Indices: 44739833--44739875 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
44739823 TTCATGGCTA
44739833 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTC
44739855 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
44739876 GAACAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTC
Found at i:44741939 original size:24 final size:25
Alignment explanation
Indices: 44741911--44741958 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
44741901 TCTGACCCAA
*
44741911 TTTTACTGGAATATG-AATGGAACC
1 TTTTACTGGAATAAGTAATGGAACC
* *
44741935 TTTTAGTGGGATAAGTAATGGAAC
1 TTTTACTGGAATAAGTAATGGAAC
44741959 TTGGAAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.33
Consensus pattern (25 bp):
TTTTACTGGAATAAGTAATGGAACC
Found at i:44743366 original size:26 final size:26
Alignment explanation
Indices: 44743332--44743383 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
44743322 AATAAAAGAA
44743332 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTTTAATTAG
44743358 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTTTAATTAG
44743384 CTTTAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (26 bp):
AACATTCAATATTTCAGTTTAATTAG
Found at i:44744047 original size:24 final size:25
Alignment explanation
Indices: 44744019--44744065 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
44744009 TCCGACCCAA
*
44744019 TTTTACTGGAATATG-AATGGAAGC
1 TTTTACTGGAATAAGTAATGGAAGC
* *
44744043 TTTTAGTGGGATAAGTAATGGAA
1 TTTTACTGGAATAAGTAATGGAA
44744066 CTTGGAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (25 bp):
TTTTACTGGAATAAGTAATGGAAGC
Found at i:44745432 original size:26 final size:26
Alignment explanation
Indices: 44745403--44745452 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
44745393 TAAAAGCAAA
* *
44745403 CATTCAATATTTTAGTTTAATTAGAC
1 CATTCAATATATCAGTTTAATTAGAC
44745429 CATTCAATATATCAGTTTAATTAG
1 CATTCAATATATCAGTTTAATTAG
44745453 CATGAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (26 bp):
CATTCAATATATCAGTTTAATTAGAC
Found at i:44747548 original size:26 final size:26
Alignment explanation
Indices: 44747519--44747570 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
44747509 AATAAAAGAA
*
44747519 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTCTAATTAG
44747545 AACATTCAATATTTCAGTCTAATTAG
1 AACATTCAATATTTCAGTCTAATTAG
44747571 CATTAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (26 bp):
AACATTCAATATTTCAGTCTAATTAG
Found at i:44754013 original size:26 final size:26
Alignment explanation
Indices: 44753979--44754030 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
44753969 AATAAAAGAA
*
44753979 AACATTCAACATTTCAGTTTAATTAG
1 AACATTCAACATTTCAGTCTAATTAG
*
44754005 AACATTCAATATTTCAGTCTAATTAG
1 AACATTCAACATTTCAGTCTAATTAG
44754031 CATTAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (26 bp):
AACATTCAACATTTCAGTCTAATTAG
Done.