Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 130 of 196
Found at i:38877747 original size:27 final size:26
Alignment explanation
Indices: 38877652--38877761 Score: 89
Period size: 27 Copynumber: 4.1 Consensus size: 26
38877642 ATGACACATC
*
38877652 AATA-TTTAATTATTTTTTAATTTAAAA
1 AATATTTTAA-TAATTTTTAATTT-AAA
* * * **
38877679 AATATTTTAAAAAATTATAATTT-TT
1 AATATTTTAATAATTTTTAATTTAAA
*
38877704 AATAATTTTAATGATTTTTAATTTAAA
1 AAT-ATTTTAATAATTTTTAATTTAAA
*
38877731 AATAGTTTTTATAATTTTTAAATTTAAA
1 AATA-TTTTAATAATTTTT-AATTTAAA
38877759 AAT
1 AAT
38877762 TAATTAAATG
Statistics
Matches: 64, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
25 3 0.05
26 17 0.27
27 28 0.44
28 16 0.25
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
AATATTTTAATAATTTTTAATTTAAA
Found at i:38881450 original size:26 final size:26
Alignment explanation
Indices: 38881399--38881451 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
38881389 ATTAGATATT
* * *
38881399 TTTTTTAAATTGTAAAAATATTAATA
1 TTTTTCAAATTATAAAAATATAAATA
38881425 TTTTTCAAATTATATAAAAT-TAAATA
1 TTTTTCAAATTATA-AAAATATAAATA
38881451 T
1 T
38881452 AATAATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (26 bp):
TTTTTCAAATTATAAAAATATAAATA
Found at i:38882246 original size:7 final size:7
Alignment explanation
Indices: 38882234--38882259 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
38882224 ACTTCTCAAT
38882234 TCATCCC
1 TCATCCC
38882241 TCATCCC
1 TCATCCC
38882248 TCATCCC
1 TCATCCC
38882255 TCATC
1 TCATC
38882260 TCTCTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.54, G:0.00, T:0.31
Consensus pattern (7 bp):
TCATCCC
Found at i:38884364 original size:7 final size:7
Alignment explanation
Indices: 38884352--38884377 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
38884342 ACTTCTCAAT
38884352 TCATCCC
1 TCATCCC
38884359 TCATCCC
1 TCATCCC
38884366 TCATCCC
1 TCATCCC
38884373 TCATC
1 TCATC
38884378 TCTCTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.54, G:0.00, T:0.31
Consensus pattern (7 bp):
TCATCCC
Found at i:38886482 original size:7 final size:7
Alignment explanation
Indices: 38886470--38886495 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
38886460 ACTTCTCAAT
38886470 TCATCCC
1 TCATCCC
38886477 TCATCCC
1 TCATCCC
38886484 TCATCCC
1 TCATCCC
38886491 TCATC
1 TCATC
38886496 TCTCTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.54, G:0.00, T:0.31
Consensus pattern (7 bp):
TCATCCC
Found at i:38892353 original size:46 final size:46
Alignment explanation
Indices: 38892300--38892437 Score: 249
Period size: 46 Copynumber: 3.0 Consensus size: 46
38892290 CCATGACAAA
38892300 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
38892346 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
* * *
38892392 TTGTGAAAAATAGGTATGGTATTTCAGTGAAGGAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
38892438 CTATAGCATT
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 89 1.00
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.28
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
Found at i:38898465 original size:20 final size:20
Alignment explanation
Indices: 38898440--38898482 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
38898430 AATATAAAAG
*
38898440 TATAAATATGTACATATATA
1 TATAAATAAGTACATATATA
* *
38898460 TATAAATAAGTATATATGTA
1 TATAAATAAGTACATATATA
38898480 TAT
1 TAT
38898483 GTATATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (20 bp):
TATAAATAAGTACATATATA
Found at i:38898920 original size:3 final size:3
Alignment explanation
Indices: 38898912--38898975 Score: 53
Period size: 3 Copynumber: 22.3 Consensus size: 3
38898902 ATAAATAAGT
* * * *
38898912 ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA CT- ATA TTA ATG AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
38898958 AT- ATA ATA GTA GTA ATA A
1 ATA ATA ATA ATA ATA ATA A
38898976 GACTAAAATA
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
2 5 0.10
3 44 0.90
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:38900255 original size:41 final size:41
Alignment explanation
Indices: 38900204--38900395 Score: 125
Period size: 41 Copynumber: 4.5 Consensus size: 41
38900194 TCAACTTGCC
*
38900204 CTACTGCAACTTCAGGGGGATAAGGTTTGATATGATCTACT
1 CTACTGCAACTTCAGGGAGATAAGGTTTGATATGATCTACT
* * * * * * **
38900245 CTACTACAACTTCAGAGAGATAAGATCGGTGATTTTAATCCGCT
1 CTACTGCAACTTCAGGGAGATAAGGT--TTGA-TATGATCTACT
* * * * * * * *
38900289 CCATTACATCTTCAGGGAGAT-AGGATTGGTATGTTCAACCT
1 CTACTGCAACTTCAGGGAGATAAGGTTTGATATGATCTA-CT
* * *
38900330 GCCCCACTGCAACTTTAGGGGGATAAGGTTTGATATGATCTACT
1 ---CTACTGCAACTTCAGGGAGATAAGGTTTGATATGATCTACT
*
38900374 CTACTGCAACTTCAGAGAGATA
1 CTACTGCAACTTCAGGGAGATA
38900396 GGATTGACTT
Statistics
Matches: 108, Mismatches: 35, Indels: 16
0.68 0.22 0.10
Matches are distributed among these distances:
40 4 0.04
41 44 0.41
43 5 0.05
44 42 0.39
45 13 0.12
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.30
Consensus pattern (41 bp):
CTACTGCAACTTCAGGGAGATAAGGTTTGATATGATCTACT
Found at i:38900262 original size:129 final size:129
Alignment explanation
Indices: 38900114--38900395 Score: 474
Period size: 129 Copynumber: 2.2 Consensus size: 129
38900104 GTGTGATCCG
** *
38900114 CTCTACTGCAACTTCAGAGAGATAAGATCGATGATTTTAATCCACTCCACTGTATCTTCAGGGAT
1 CTCTACTGCAACTTCAGAGAGATAAGATCGATGATTTTAATCCACTCCACTACATCTTCAGGGAG
* *
38900179 ATAGGATTGGTATGTTCAACTTGCCCTACTGCAACTTCAGGGGGATAAGGTTTGATATGATCTA
66 ATAGGATTGGTATGTTCAACCTGCCCCACTGCAACTTCAGGGGGATAAGGTTTGATATGATCTA
* * * *
38900243 CTCTACTACAACTTCAGAGAGATAAGATCGGTGATTTTAATCCGCTCCATTACATCTTCAGGGAG
1 CTCTACTGCAACTTCAGAGAGATAAGATCGATGATTTTAATCCACTCCACTACATCTTCAGGGAG
*
38900308 ATAGGATTGGTATGTTCAACCTGCCCCACTGCAACTTTAGGGGGATAAGGTTTGATATGATCTA
66 ATAGGATTGGTATGTTCAACCTGCCCCACTGCAACTTCAGGGGGATAAGGTTTGATATGATCTA
38900372 CTCTACTGCAACTTCAGAGAGATA
1 CTCTACTGCAACTTCAGAGAGATA
38900396 GGATTGACTT
Statistics
Matches: 142, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
129 142 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.30
Consensus pattern (129 bp):
CTCTACTGCAACTTCAGAGAGATAAGATCGATGATTTTAATCCACTCCACTACATCTTCAGGGAG
ATAGGATTGGTATGTTCAACCTGCCCCACTGCAACTTCAGGGGGATAAGGTTTGATATGATCTA
Found at i:38900503 original size:51 final size:50
Alignment explanation
Indices: 38900435--38900817 Score: 287
Period size: 51 Copynumber: 7.6 Consensus size: 50
38900425 AATGTCGGGG
* * * *
38900435 AAGTAAGATTCGTCGTTGTAGCTTCAATCTATTCTACTACACCATCAGGGA
1 AAGTAAGATTCGCCGTTGTAGCTTCAATCT-TTCCACTGCACCATCTGGGA
* * * ** * * *
38900486 AAGTAAGATTTGCCGTTGTGGCCTCAATCTTTTAATTGCA--ATGTCGGGG
1 AAGTAAGATTCGCCGTTGTAGCTTCAATCTTTCCACTGCACCATCT-GGGA
* * **
38900535 AAGTGAGATTCGCCATTGTAGCTTCAATCTATTCCACTGCACCGCCTGGGA
1 AAGTAAGATTCGCCGTTGTAGCTTCAATCT-TTCCACTGCACCATCTGGGA
* * ** * * *
38900586 AAGTAA-AATCTGCCGTTGTGGCTTCAATCTTTTAATTGCA--ATGCCGGGG
1 AAGTAAGATTC-GCCGTTGTAGCTTCAATCTTTCCACTGCACCAT-CTGGGA
** ** *
38900635 AAGCGAGATTTACCGTTGTAGCTTCAATCTGTTCCACTGCACC-GCTTGGGA
1 AAGTAAGATTCGCCGTTGTAGCTTCAATCT-TTCCACTGCACCATC-TGGGA
*
38900686 AAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCACCTGGG-
1 AAGTAAGATTCGCCGTTGTAGCTTCAATCT-TTCCACTGCACCATCTGGGA
* ** * ** *
38900736 AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATATC-GGGG
1 AAGTAAGATTCGCCGTTGTAGCTTCAATC-TTTCCACTGCACCATCTGGGA
* *
38900786 AAGTGAGATTCGCTGTTGTAGCTTCAATCTTT
1 AAGTAAGATTCGCCGTTGTAGCTTCAATCTTT
38900818 TTAATTGCAA
Statistics
Matches: 257, Mismatches: 61, Indels: 30
0.74 0.18 0.09
Matches are distributed among these distances:
48 2 0.01
49 59 0.23
50 96 0.37
51 98 0.38
52 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (50 bp):
AAGTAAGATTCGCCGTTGTAGCTTCAATCTTTCCACTGCACCATCTGGGA
Found at i:38900534 original size:100 final size:100
Alignment explanation
Indices: 38900406--38900765 Score: 418
Period size: 100 Copynumber: 3.6 Consensus size: 100
38900396 GGATTGACTT
* * *
38900406 CTTCAATCTGTTTAACTGCAATGTCGGGGAAGTAAGATTCGTCGTTGTAGCTTCAATCTATTCTA
1 CTTCAATCTGTTTAACTGCAATGCCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCA
* * *
38900471 CTACACCATCAGGGAAAGTAAGATTTGCCGTTGTGG
66 CTGCACC-CCTGGGAAAGTAAGATTTGCCGTTGTGG
* * * * *
38900507 CCTCAATCT-TTTAATTGCAATGTCGGGGAAGTGAGATTCGCCATTGTAGCTTCAATCTATTCCA
1 CTTCAATCTGTTTAACTGCAATGCCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCA
* *
38900571 CTGCACCGCCTGGGAAAGTAAAATCTGCCGTTGTGG
66 CTGCACC-CCTGGGAAAGTAAGATTTGCCGTTGTGG
* ** ** *
38900607 CTTCAATCT-TTTAATTGCAATGCCGGGGAAGCGAGATTTACCGTTGTAGCTTCAATCTGTTCCA
1 CTTCAATCTGTTTAACTGCAATGCCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCA
* * *
38900671 CTGCACCGCTTGGGAAAGTAAGATTCGCCGTTGTAG
66 CTGCACC-CCTGGGAAAGTAAGATTTGCCGTTGTGG
** *** * *
38900707 CTTCAATCTGTTCCACTGCACCACCTGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCT
1 CTTCAATCTGTTTAACTGCAATGCCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCT
38900766 TTTTAATTGC
Statistics
Matches: 222, Mismatches: 36, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
100 177 0.80
101 45 0.20
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (100 bp):
CTTCAATCTGTTTAACTGCAATGCCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCA
CTGCACCCCTGGGAAAGTAAGATTTGCCGTTGTGG
Found at i:38900698 original size:151 final size:151
Alignment explanation
Indices: 38900535--38900815 Score: 431
Period size: 151 Copynumber: 1.9 Consensus size: 151
38900525 AATGTCGGGG
* *
38900535 AAGTGAGATTCGCCATTGTAGCTTCAATCTATTCCACTGCACCGCCTGGGAAAGTAAAA-TCTGC
1 AAGTAAGATTCGCCATTGTAGCTTCAATCTATTCCACTGCACCACCTGGG-AAGTAAAATTC-GC
* *
38900599 CGTTGTGGCTTCAATC-TTTTAATTGCAATGCCGGGGAAGCGAGATTTACCGTTGTAGCTTCAAT
64 CGTTGTGGCTTCAATCTTTTTAATTGCAATACCGGGGAAGCGAGATTCACCGTTGTAGCTTCAAT
38900663 CTGTTCCACTGCACCGCTTGGGA
129 CTGTTCCACTGCACCGCTTGGGA
* * *
38900686 AAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCACCTGGGAAGTAAGATTCGCCG
1 AAGTAAGATTCGCCATTGTAGCTTCAATCTATTCCACTGCACCACCTGGGAAGTAAAATTCGCCG
* * * *
38900751 TTGTGGCTTCAATCTTTTTAATTGCAATATCGGGGAAGTGAGATTCGCTGTTGTAGCTTCAATCT
66 TTGTGGCTTCAATCTTTTTAATTGCAATACCGGGGAAGCGAGATTCACCGTTGTAGCTTCAATCT
38900816 TTTTAATTGC
Statistics
Matches: 117, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
150 25 0.21
151 92 0.79
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.31
Consensus pattern (151 bp):
AAGTAAGATTCGCCATTGTAGCTTCAATCTATTCCACTGCACCACCTGGGAAGTAAAATTCGCCG
TTGTGGCTTCAATCTTTTTAATTGCAATACCGGGGAAGCGAGATTCACCGTTGTAGCTTCAATCT
GTTCCACTGCACCGCTTGGGA
Found at i:38900818 original size:50 final size:50
Alignment explanation
Indices: 38900406--38900827 Score: 321
Period size: 50 Copynumber: 8.4 Consensus size: 50
38900396 GGATTGACTT
* *
38900406 CTTCAATCTGTTTAACTGCAATGTCGGGGAAGTAAGATTCGTCGTTGTAG
1 CTTCAATCTTTTTAACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAG
* * *** * * *
38900456 CTTCAATCTATTCT-ACTACACCATCAGGGAAAGTAAGATTTGCCGTTGTGG
1 CTTCAATCT-TTTTAACTGCAATGTC-GGGGAAGTAAGATTCGCCGTTGTAG
* * * *
38900507 CCTCAATC-TTTTAATTGCAATGTCGGGGAAGTGAGATTCGCCATTGTAG
1 CTTCAATCTTTTTAACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAG
* ** ** * * * *
38900556 CTTCAATCTATTCCACTGCACCGCCTGGGAAAGTAA-AATCTGCCGTTGTGG
1 CTTCAATCTTTTTAACTGCAATGTC-GGGGAAGTAAGATTC-GCCGTTGTAG
* * ** **
38900607 CTTCAATC-TTTTAATTGCAATGCCGGGGAAGCGAGATTTACCGTTGTAG
1 CTTCAATCTTTTTAACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAG
* ** ** * *
38900656 CTTCAATCTGTTCCACTGCACCGCTTGGGAAAGTAAGATTCGCCGTTGTAG
1 CTTCAATCTTTTTAACTGCAATG-TCGGGGAAGTAAGATTCGCCGTTGTAG
* ** **** * *
38900707 CTTCAATCTGTTCCACTGCACCACCTGGGAAGTAAGATTCGCCGTTGTGG
1 CTTCAATCTTTTTAACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAG
* * * *
38900757 CTTCAATCTTTTTAATTGCAATATCGGGGAAGTGAGATTCGCTGTTGTAG
1 CTTCAATCTTTTTAACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAG
*
38900807 CTTCAATCTTTTTAATTGCAA
1 CTTCAATCTTTTTAACTGCAA
38900828 ACTATGGTGT
Statistics
Matches: 285, Mismatches: 78, Indels: 18
0.75 0.20 0.05
Matches are distributed among these distances:
49 53 0.19
50 136 0.48
51 96 0.34
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (50 bp):
CTTCAATCTTTTTAACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAG
Found at i:38907117 original size:22 final size:22
Alignment explanation
Indices: 38907073--38907117 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
38907063 AATATAAAAG
* *
38907073 TATAAATATGTACATATATATA
1 TATAAATAAGTACATATACATA
* *
38907095 TATAAATAAGTATATATGCATA
1 TATAAATAAGTACATATACATA
38907117 T
1 T
38907118 GTATATATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (22 bp):
TATAAATAAGTACATATACATA
Found at i:38907129 original size:34 final size:32
Alignment explanation
Indices: 38907086--38907167 Score: 87
Period size: 30 Copynumber: 2.6 Consensus size: 32
38907076 AAATATGTAC
* * *
38907086 ATATATATATATAAATAAGTATATATGCATATGT
1 ATATATATATATAAATAAGCATA-A-ACATAAGT
*
38907120 ATATATATAT-TATA-AAGCATAAACATAAGT
1 ATATATATATATAAATAAGCATAAACATAAGT
*
38907150 ATGTATATATATAAATAA
1 ATATATATATATAAATAA
38907168 AAATTCGCTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
30 15 0.38
31 4 0.10
32 8 0.20
33 3 0.08
34 10 0.25
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (32 bp):
ATATATATATATAAATAAGCATAAACATAAGT
Found at i:38907349 original size:15 final size:15
Alignment explanation
Indices: 38907329--38907366 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
38907319 ACATATATAT
38907329 GTATGTATAACAAAC
1 GTATGTATAACAAAC
38907344 GTATGTATAACAAAC
1 GTATGTATAACAAAC
38907359 GTATGTAT
1 GTATGTAT
38907367 GTATATAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (15 bp):
GTATGTATAACAAAC
Found at i:38907350 original size:19 final size:18
Alignment explanation
Indices: 38907326--38907371 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 18
38907316 TAGACATATA
38907326 TATGTATGTATAACAAAC
1 TATGTATGTATAACAAAC
38907344 ---GTATGTATAACAAAC
1 TATGTATGTATAACAAAC
38907359 GTATGTATGTATA
1 -TATGTATGTATA
38907372 TAGGTTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 15 0.62
19 9 0.38
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (18 bp):
TATGTATGTATAACAAAC
Found at i:38907435 original size:12 final size:12
Alignment explanation
Indices: 38907420--38907450 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
38907410 ATATAATAAG
38907420 ATATAAAGATAT
1 ATATAAAGATAT
38907432 ATATAAAGATAT
1 ATATAAAGATAT
38907444 ATATAAA
1 ATATAAA
38907451 TAGTTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (12 bp):
ATATAAAGATAT
Found at i:38916588 original size:30 final size:30
Alignment explanation
Indices: 38916554--38916615 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
38916544 ACTTATTTTA
*
38916554 TTGTTTATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
38916584 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
38916614 TT
1 TT
38916616 ACTTGTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.24, C:0.03, G:0.13, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:38916769 original size:12 final size:12
Alignment explanation
Indices: 38916739--38916771 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
38916729 TATATATTTT
38916739 AAAATT-ATATA
1 AAAATTAATATA
38916750 AAAA-TAATATA
1 AAAATTAATATA
38916761 AAAATTAATAT
1 AAAATTAATAT
38916772 GGGTGGGACG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:38918181 original size:24 final size:24
Alignment explanation
Indices: 38918137--38918182 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
38918127 TATGAGAATT
* *
38918137 ATATATAAAAAAATACTAAAAACG
1 ATATATAAAAAAAGACAAAAAACG
38918161 ATAT-TAAAATAAAGACAAAAAA
1 ATATATAAAA-AAAGACAAAAAA
38918183 ATTATACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.70, C:0.07, G:0.04, T:0.20
Consensus pattern (24 bp):
ATATATAAAAAAAGACAAAAAACG
Found at i:38925328 original size:3 final size:3
Alignment explanation
Indices: 38925322--38925346 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
38925312 ATTGATGATG
38925322 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
38925347 TTTGTGTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:38928217 original size:72 final size:73
Alignment explanation
Indices: 38928086--38928233 Score: 271
Period size: 74 Copynumber: 2.0 Consensus size: 73
38928076 TATAGGGAAC
*
38928086 AGAGAGCTAAAGCTAATTGGTTGAAGAATGGTGATCGCAACACAAAGTTTTTTCGCAAGTTTGCA
1 AGAGAGCTAAAGCTAATTGGTTGAAGAATGGAGATCGCAACAC-AAGTTTTTTCGCAAGTTTGCA
38928151 TCAGAACAG
65 TCAGAACAG
38928160 AGAGAGCTAAAGCTAATTGGTTGAAGAATGGAGATCGCAACAC-AGTTTTTTCGCAAGTTTGCAT
1 AGAGAGCTAAAGCTAATTGGTTGAAGAATGGAGATCGCAACACAAGTTTTTTCGCAAGTTTGCAT
38928224 CAGAACAG
66 CAGAACAG
38928232 AG
1 AG
38928234 TAGAAAGAAT
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
72 31 0.42
74 42 0.58
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (73 bp):
AGAGAGCTAAAGCTAATTGGTTGAAGAATGGAGATCGCAACACAAGTTTTTTCGCAAGTTTGCAT
CAGAACAG
Found at i:38929448 original size:19 final size:19
Alignment explanation
Indices: 38929420--38929510 Score: 146
Period size: 19 Copynumber: 4.8 Consensus size: 19
38929410 ATCTTCAAGT
*
38929420 ATATGCAATCTTAAATATG
1 ATATGCAATCTTAGATATG
*
38929439 ATATGTAATCTTAGATATG
1 ATATGCAATCTTAGATATG
38929458 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
*
38929477 ATATGTAATCTTAGATATG
1 ATATGCAATCTTAGATATG
*
38929496 ATATACAATCTTAGA
1 ATATGCAATCTTAGA
38929511 AGATATGATT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 66 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (19 bp):
ATATGCAATCTTAGATATG
Found at i:38929464 original size:38 final size:38
Alignment explanation
Indices: 38929420--38929534 Score: 167
Period size: 38 Copynumber: 2.9 Consensus size: 38
38929410 ATCTTCAAGT
38929420 ATATGCAATCTTAAATATGATATGTAATCTTAGATATG
1 ATATGCAATCTTAAATATGATATGTAATCTTAGATATG
*
38929458 ATATGCAATCTTAGATATGATATGTAATCTTAGATATG
1 ATATGCAATCTTAAATATGATATGTAATCTTAGATATG
* *
38929496 ATATACAATCTTAGAAGATATGATTTTGTAATCTTAGAT
1 ATATGCAATCTT--AA-ATATGA-TATGTAATCTTAGAT
38929535 GTTTAATTTG
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
38 48 0.70
40 1 0.01
41 6 0.09
42 14 0.20
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (38 bp):
ATATGCAATCTTAAATATGATATGTAATCTTAGATATG
Found at i:38929759 original size:23 final size:23
Alignment explanation
Indices: 38929715--38929759 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
38929705 TTTTATTTCG
* *
38929715 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
38929738 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
38929760 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:38929995 original size:3 final size:3
Alignment explanation
Indices: 38929987--38930022 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
38929977 ATCTTGTATC
*
38929987 ATT ATT ATT ATT ATTT ATT ATT ATT ATT ATT TTT AT
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT AT
38930023 ATTCATGAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:38930006 original size:13 final size:13
Alignment explanation
Indices: 38929988--38930014 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
38929978 TCTTGTATCA
38929988 TTATTATTATTAT
1 TTATTATTATTAT
38930001 TTATTATTATTAT
1 TTATTATTATTAT
38930014 T
1 T
38930015 ATTTTTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATTATTATTAT
Found at i:38930008 original size:16 final size:16
Alignment explanation
Indices: 38929987--38930022 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
38929977 ATCTTGTATC
38929987 ATTATTATTATTATTT
1 ATTATTATTATTATTT
38930003 ATTATTATTATTATTT
1 ATTATTATTATTATTT
38930019 -TTAT
1 ATTAT
38930023 ATTCATGAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTATTATTATTATTT
Found at i:38935320 original size:20 final size:21
Alignment explanation
Indices: 38935276--38935313 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
38935266 AAAATATTTC
38935276 AAAATATAAAAAAATAAGAAG
1 AAAATATAAAAAAATAAGAAG
38935297 AAAA-ATAAAAAAA-AAGA
1 AAAATATAAAAAAATAAGA
38935314 GTGAAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.11
Consensus pattern (21 bp):
AAAATATAAAAAAATAAGAAG
Found at i:38936569 original size:44 final size:43
Alignment explanation
Indices: 38936521--38936663 Score: 126
Period size: 44 Copynumber: 3.3 Consensus size: 43
38936511 GACACTAGCA
38936521 TTGCCTCCCTGGGTTACAGCGGAGCAGGTTAAAAATAGCAGATC
1 TTGCCTCCCTGGGTTACAGCGGAGCAGGTTAAAAATA-CAGATC
* ** * * * * * * * *
38936565 TTGCCTTCCTGCATCGACAGCGAAGTAGATTGAAGACACCAG-CC
1 TTGCCTCCCTGGGT-TACAGCGGAGCAGGTTAAAAATA-CAGATC
*
38936609 TTGCCTCCCTGGGTTACAGCGGAGCAGGTTAAAAGTTACAGATC
1 TTGCCTCCCTGGGTTACAGCGGAGCAGGTTAAAA-ATACAGATC
*
38936653 TTGCCTTCCTG
1 TTGCCTCCCTG
38936664 CACCGACAGC
Statistics
Matches: 71, Mismatches: 25, Indels: 6
0.70 0.25 0.06
Matches are distributed among these distances:
43 17 0.24
44 35 0.49
45 19 0.27
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.24
Consensus pattern (43 bp):
TTGCCTCCCTGGGTTACAGCGGAGCAGGTTAAAAATACAGATC
Found at i:38936613 original size:88 final size:88
Alignment explanation
Indices: 38936382--38936961 Score: 795
Period size: 88 Copynumber: 6.6 Consensus size: 88
38936372 GTGAAGATAA
* * * *
38936382 CAGATCTTGCCTTCCTGCACAGACAGCGAAGTAGATCGAAGACACCAACCTTGCTTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
**
38936447 GTAGCGGAGCAGGTTAAAAAATAG
66 ACAGCGGAGCAGGTT-AAAAATAG
* * * * * * *
38936471 CATATCTTGTCTTCATGCACCGACAACGAAGCAGATCAAAGACACTAGCATTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
38936536 ACAGCGGAGCAGGTTAAAAATAG
66 ACAGCGGAGCAGGTTAAAAATAG
* * *
38936559 CAGATCTTGCCTTCCTGCATCGACAGCGAAGTAGATTGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
38936624 ACAGCGGAGCAGGTTAAAAGTTA-
66 ACAGCGGAGCAGGTTAAAA-ATAG
* *
38936647 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCTTTGCCTCCCTAGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
** *
38936712 GTAGCGGAGCAGGTTAAAAATAA
66 ACAGCGGAGCAGGTTAAAAATAG
* * * *
38936735 CAGATCTTACCTTCCTGCACCGACAGCGAAGCAGATCGAGGACACCAACCTTGCCTCCCTCGG-T
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
38936799 AGTAGCGGAGCAAGTTAAAAAATAG
66 A-CAGCGGAGCAGGTT-AAAAATAG
* *
38936824 TAGATCTTACCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
38936889 GCAGCAGAGCAGGTTAAAAATAG
66 ACAGCGGAGCAGGTTAAAAATAG
* * *
38936912 CAGATCTTGCCTTCCTGCACCGACAGCGAAACAGATCGATGACCCCAGCC
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC
38936962 CTATCTCTCT
Statistics
Matches: 433, Mismatches: 53, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
87 3 0.01
88 283 0.65
89 146 0.34
90 1 0.00
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.20
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
ACAGCGGAGCAGGTTAAAAATAG
Found at i:38936701 original size:44 final size:44
Alignment explanation
Indices: 38936565--38936702 Score: 100
Period size: 44 Copynumber: 3.1 Consensus size: 44
38936555 ATAGCAGATC
* * * *
38936565 TTGCCTTCCTGCATCGACAGCGAAGTAGATTGAAGACACCAGCC
1 TTGCCTTCCTGCACCGACAGCGAAGCAGATAGAAGACACCAGCT
* **** * * * ** *
38936609 TTGCCTCCCTG-GGTTACAGCGGAGCAGGTTAAAAGTTA-CAGAT
1 TTGCCTTCCTGCACCGACAGCGAAGCA-GATAGAAGACACCAGCT
*
38936652 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCT
1 -TTGCCTTCCTGCACCGACAGCGAAGCAGATAGAAGACACCAGCT
38936697 TTGCCT
1 TTGCCT
38936703 CCCTAGGTTG
Statistics
Matches: 64, Mismatches: 26, Indels: 8
0.65 0.27 0.08
Matches are distributed among these distances:
43 12 0.19
44 38 0.59
45 14 0.22
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (44 bp):
TTGCCTTCCTGCACCGACAGCGAAGCAGATAGAAGACACCAGCT
Found at i:38936854 original size:265 final size:264
Alignment explanation
Indices: 38936381--38936961 Score: 833
Period size: 265 Copynumber: 2.2 Consensus size: 264
38936371 AGTGAAGATA
* * * * *
38936381 ACAGATCTTGCCTTCCTGCACAGACAGCGAAGTAGATCGAAGACACCAACCTTGCTTCCCTGGGT
1 ACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGT
* * **
38936446 TGTAGCGGAGCAGGTTAAAAAATAGCATATCTTGTCTTCATGCACCGACAACGAAGCAGATCAAA
66 TGTAGCGGAGCAGGTTAAAAAATAACAGATCTTACCTTCATGCACCGACAACGAAGCAGATCAAA
* * * * *
38936511 GACACTAGCATTGCCTCCCTGGGTTACAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTG
131 GACACCAACATTGCCTCCCTCGGTTACAGCGGAGCAAGTTAAAAATAGCAGATCTTACCTTCCTG
* * * *
38936576 CATCGACAGCGAAGTAGATTGAAGACACCAGCCTTGCCTCCCTGGGTTACAGCGGAGCAGGTTAA
196 CACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTACAGCAGAGCAGGTTAA
*
38936641 AAGTT
261 AA-AT
*
38936646 ACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCTTTGCCTCCCTAGGT
1 ACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGT
* * * *
38936711 TGTAGCGGAGCAGGTT-AAAAATAACAGATCTTACCTTCCTGCACCGACAGCGAAGCAGATCGAG
66 TGTAGCGGAGCAGGTTAAAAAATAACAGATCTTACCTTCATGCACCGACAACGAAGCAGATCAAA
* * *
38936775 GACACCAACCTTGCCTCCCTCGG-TAGTAGCGGAGCAAGTTAAAAAATAGTAGATCTTACCTTCC
131 GACACCAACATTGCCTCCCTCGGTTA-CAGCGGAGCAAGTT-AAAAATAGCAGATCTTACCTTCC
*
38936839 TGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCAGAGCAGGTT
194 TGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTACAGCAGAGCAGGTT
38936904 AAAAAT
259 AAAAAT
* * *
38936910 AGCAGATCTTGCCTTCCTGCACCGACAGCGAAACAGATCGATGACCCCAGCC
1 A-CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC
38936962 CTATCTCTCT
Statistics
Matches: 281, Mismatches: 32, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
263 2 0.01
264 73 0.26
265 206 0.73
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.20
Consensus pattern (264 bp):
ACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGT
TGTAGCGGAGCAGGTTAAAAAATAACAGATCTTACCTTCATGCACCGACAACGAAGCAGATCAAA
GACACCAACATTGCCTCCCTCGGTTACAGCGGAGCAAGTTAAAAATAGCAGATCTTACCTTCCTG
CACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTACAGCAGAGCAGGTTAA
AAAT
Found at i:38936909 original size:177 final size:177
Alignment explanation
Indices: 38936378--38936950 Score: 835
Period size: 177 Copynumber: 3.2 Consensus size: 177
38936368 ATCAGTGAAG
* * *
38936378 ATAACAGATCTTGCCTTCCTGCACAGACAGCGAAGTAGATCGAAGACACCAACCTTGCTTCCCTG
1 ATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTG
* * * * *
38936443 GGTTGTAGCGGAGCAGGTTAAAAAATAGCATATCTTGTCTTCATGCACCGACAACGAAGCAGATC
66 GGTAGTAGCGGAGCAGGTTAAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATC
* * *
38936508 AAAGACACTAGCATTGCCTCCCTGGGTTACAGCGGAGCAGGTTAAAA
131 GAAGACACCAGCATTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAA
* * * * *
38936555 ATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGTAGATTGAAGACACCAGCCTTGCCTCCCTG
1 ATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTG
* **
38936620 GGTTA-CAGCGGAGCAGGTTAAAAGTTA-CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGAT
66 GG-TAGTAGCGGAGCAGGTTAAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGAT
* * *
38936683 CGAAGACACCAGCTTTGCCTCCCTAGGTTGTAGCGGAGCAGGTTAAAA
130 CGAAGACACCAGCATTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAA
* * *
38936731 ATAACAGATCTTACCTTCCTGCACCGACAGCGAAGCAGATCGAGGACACCAACCTTGCCTCCCTC
1 ATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTG
* * *
38936796 GGTAGTAGCGGAGCAAGTTAAAAAATAGTAGATCTTACCTTCCTGCACCGACAGCGAAGCAGATC
66 GGTAGTAGCGGAGCAGGTTAAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATC
* *
38936861 GAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCAGAGCAGGTTAAAA
131 GAAGACACCAGCATTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAA
* *
38936908 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAACAGATCGA
1 ATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGA
38936951 TGACCCCAGC
Statistics
Matches: 352, Mismatches: 41, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
175 2 0.01
176 151 0.43
177 198 0.56
178 1 0.00
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.20
Consensus pattern (177 bp):
ATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTG
GGTAGTAGCGGAGCAGGTTAAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATC
GAAGACACCAGCATTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAA
Found at i:38937008 original size:44 final size:45
Alignment explanation
Indices: 38936958--38937059 Score: 163
Period size: 44 Copynumber: 2.3 Consensus size: 45
38936948 CGATGACCCC
38936958 AGCCCTATCTCTCTGGACAGTAGTGGAATAGGTTGAAGATTGT-A
1 AGCCCTATCTCTCTGGACAGTAGTGGAATAGGTTGAAGATTGTGA
* *
38937002 AGCCCTATCTCCCTGGTCAGTAGTGGAATAGGTTGAAGATTGTGA
1 AGCCCTATCTCTCTGGACAGTAGTGGAATAGGTTGAAGATTGTGA
*
38937047 A-TCCTATCTCTCT
1 AGCCCTATCTCTCT
38937060 AAGCAACAGT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 51 0.96
45 2 0.04
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (45 bp):
AGCCCTATCTCTCTGGACAGTAGTGGAATAGGTTGAAGATTGTGA
Found at i:38937071 original size:44 final size:44
Alignment explanation
Indices: 38936979--38937082 Score: 122
Period size: 44 Copynumber: 2.4 Consensus size: 44
38936969 TCTGGACAGT
* **
38936979 AGTGGAATAGGTTGAAGATTGTAAGCCCTATCTCCCTGGTCAGT
1 AGTGGAATAGGTTGAAGATTGTAAGCCCTATCTCCCTAGTCAAC
* *
38937023 AGTGGAATAGGTTGAAGATTGTGAA-TCCTATCTCTCTAAG-CAAC
1 AGTGGAATAGGTTGAAGATTGT-AAGCCCTATCTCCCT-AGTCAAC
*
38937067 AGTGGAGTAGGTTGAA
1 AGTGGAATAGGTTGAA
38937083 AATAGCAGAT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
44 49 0.94
45 3 0.06
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (44 bp):
AGTGGAATAGGTTGAAGATTGTAAGCCCTATCTCCCTAGTCAAC
Found at i:38937695 original size:45 final size:45
Alignment explanation
Indices: 38937576--38937907 Score: 149
Period size: 45 Copynumber: 7.6 Consensus size: 45
38937566 TCGTATCTAG
* *
38937576 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACT-AAG-TAAG-TAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAT-AGCGAA
* * * *
38937619 GCCTTATC-CTCCTGAAGTTGTAGT-GAGGCAGACTGAAGATGGCGAA
1 -TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTCAAGATAGCGAA
* * ** **
38937665 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-ATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGATAGCGAA
** ** * *
38937709 T-TCTATCTAGCTGAAGTTGCAGTGGAGTGGA-TTAAAATCA-C-AGA
1 TCT-TATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAT-AGCGA-A
* * * **
38937753 TCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T--TGCAT--CGGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAG-ATAGCGAA
* * * * * *
38937793 TCATATCTTCTTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGATAGCGAA
* * *
38937838 TCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTCAAGAAATC-AA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGATAGCGAA
* * *
38937882 GTATTATCCCCCTGAAATTGCAGTGG
1 -TCTTATCTCCCTGAAGTTGCAGTGG
38937908 GTAGACTAAA
Statistics
Matches: 218, Mismatches: 50, Indels: 39
0.71 0.16 0.13
Matches are distributed among these distances:
40 19 0.09
41 7 0.03
42 2 0.01
43 15 0.07
44 74 0.34
45 95 0.44
46 6 0.03
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.27
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGATAGCGAA
Found at i:38937760 original size:44 final size:44
Alignment explanation
Indices: 38937446--38937784 Score: 162
Period size: 44 Copynumber: 7.8 Consensus size: 44
38937436 GAAAATGGCG
* * * *
38937446 AATCTTATCTACCTGAAGTTGCAATGGAGTAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAAT
* * * * * *
38937490 AATCCTATCTCTCTAAAGTCGCAGTGGAGCGGATTAAAATC-AT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAAT
* * * *** *
38937533 AGATCTTATCTCTCTGAAGTTGCAG-AGAGTAGA-TCGTATC--T
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAAT
* * * * *
38937574 AGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTA--AGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA-AACCAAT
* * * * *****
38937617 AAGCCTTATC-CTCCTGAAGTTGTAGT-GAGGCAGACTGAAGATGGCG
1 AA-TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAACCAAT
*
38937663 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAAT
** ** *
38937707 AAT-TCTATCTAGCTGAAGTTGCAGTGGAGTGGATTAAAATCACA-
1 AATCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCA-AT
* * *
38937751 GATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
38937785 GCATCGGGTC
Statistics
Matches: 220, Mismatches: 58, Indels: 35
0.70 0.19 0.11
Matches are distributed among these distances:
40 20 0.09
41 8 0.04
42 5 0.02
43 23 0.10
44 131 0.60
45 28 0.13
46 5 0.02
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAAT
Found at i:38937810 original size:217 final size:217
Alignment explanation
Indices: 38937431--38937824 Score: 608
Period size: 217 Copynumber: 1.8 Consensus size: 217
38937421 GCAATTTAAA
*
38937431 AGACTGAAAATGGCGAATCTTATCTACCTGAAGTTGCAATGGAGTAGATTAAAGCCAATAATCCT
1 AGACTGAAAATGGCGAATCTTATCTACCTGAAGTTGCAATGGAGCAGATTAAAGCCAATAATCCT
** *
38937496 ATCTCTCTAAAGTCGCAGTGGAGCGGATTAAAATCATAGATCTTATCTCTCTGAAGTTGCAGAGA
66 ATCTAGCTAAAGTCGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGA
* * * *
38937561 GTAGATCGTATCTAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTAAGTAAGCCTTAT
131 GCAGATCGCATCGAGTCATATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTAAGTAAGCCTTAT
38937626 CCTCCTGAAGTTGTAGTGAGGC
196 CCTCCTGAAGTTGTAGTGAGGC
* * * *
38937648 AGACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATTCT
1 AGACTGAAAATGGCGAATCTTATCTACCTGAAGTTGCAATGGAGCAGATTAAAGCCAATAATCCT
* * *
38937713 ATCTAGCTGAAGTTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGA
66 ATCTAGCTAAAGTCGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGA
* * * * *
38937778 GCAGATTGCATCGGGTCATATCTTCTTGAAGTTGCAGTGGAGCAGAC
131 GCAGATCGCATCGAGTCATATCTCCCTGAAGTTACAGTGGAGCAGAC
38937825 CCAAGAAAGC
Statistics
Matches: 157, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
217 157 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (217 bp):
AGACTGAAAATGGCGAATCTTATCTACCTGAAGTTGCAATGGAGCAGATTAAAGCCAATAATCCT
ATCTAGCTAAAGTCGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGA
GCAGATCGCATCGAGTCATATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTAAGTAAGCCTTAT
CCTCCTGAAGTTGTAGTGAGGC
Found at i:38937954 original size:217 final size:217
Alignment explanation
Indices: 38937443--38937964 Score: 498
Period size: 217 Copynumber: 2.4 Consensus size: 217
38937433 ACTGAAAATG
* ** * * * * * * * *
38937443 GCGAATCTTATCTACCTGAAGTTGCAATGGAGTAGATTAAAGCCAATAATCCTATCT-CTCTAAA
1 GCGAATATTATCCCCCTGAAATTGCAGTGGAGCAGACTAAAGCAAAAAATCCCATCTAC-CTGAA
* * * * * *
38937507 GTCGCAGTGGAGCGGATTAAAATCATAGATCTTATCTCTCTGAAGTTGCAGAGAGTAGATCGTAT
65 GTTGCAATGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCAT
* * * * *
38937572 CTAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTAAGTAAGCCTTATCCTCCTGAAGT
130 CGAGTCATATCTCCCTGAAGTTACAGTGGAGCAGACCAAGAAAGCAAGCCTTATCCTCCTGAAGT
* * **
38937637 TGTAGTGAGGCAGACTGAAGATG
195 TGCAGTGAGGCAGACTCAAGAAA
* * * * * * * * *
38937660 GCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATTCTATCTAGCTGAAG
1 GCGAATATTATCCCCCTGAAATTGCAGTGGAGCAGACTAAAGCAAAAAATCCCATCTACCTGAAG
* *
38937725 TTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATTGCATC
66 TTGCAATGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATC
* * * * * *
38937790 GGGTCATATCTTCTTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCGAGTCTTAT-CTCCTTGAAG
131 GAGTCATATCTCCCTGAAGTTACAGTGGAGCAGA-CCAAGAAAGCAAGCCTTATCCTCC-TGAAG
38937854 TTGCAGTG-GAGCAGACTCAAGAAA
194 TTGCAGTGAG-GCAGACTCAAGAAA
* * * * *
38937878 TC-AAGTATTATCCCCCTGAAATTGCAGTGG-GTAGACTAAA-TAAACAAATCCCATCTCCCTTA
1 GCGAA-TATTATCCCCCTGAAATTGCAGTGGAGCAGACTAAAGCAAA-AAATCCCATCTACCTGA
* *
38937940 AGTTGTAATGGAGTGGATTAGAATC
64 AGTTGCAATGGAGTGGATTAAAATC
38937965 TCTCTGAAAT
Statistics
Matches: 255, Mismatches: 44, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
216 2 0.01
217 193 0.76
218 60 0.24
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (217 bp):
GCGAATATTATCCCCCTGAAATTGCAGTGGAGCAGACTAAAGCAAAAAATCCCATCTACCTGAAG
TTGCAATGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATC
GAGTCATATCTCCCTGAAGTTACAGTGGAGCAGACCAAGAAAGCAAGCCTTATCCTCCTGAAGTT
GCAGTGAGGCAGACTCAAGAAA
Found at i:38938485 original size:19 final size:19
Alignment explanation
Indices: 38938461--38938533 Score: 146
Period size: 19 Copynumber: 3.8 Consensus size: 19
38938451 AATCTTCAAG
38938461 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
38938480 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
38938499 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
38938518 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
38938534 AGATATGATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 54 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:38938559 original size:22 final size:22
Alignment explanation
Indices: 38938461--38938556 Score: 102
Period size: 19 Copynumber: 4.7 Consensus size: 22
38938451 AATCTTCAAG
38938461 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
38938480 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
38938499 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
38938518 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
38938540 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
38938557 GATTTAATTT
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
19 51 0.72
22 8 0.11
23 12 0.17
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:38938779 original size:23 final size:23
Alignment explanation
Indices: 38938735--38938779 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
38938725 TCTTATTTTG
* *
38938735 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
38938758 TTGATTTGTATATGGTTGATTT
1 TTGATTTGTATATAATTGATTT
38938780 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.18, T:0.60
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:38939016 original size:3 final size:3
Alignment explanation
Indices: 38939008--38939046 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
38938998 ATCTTGTATC
* *
38939008 ATT ATT ATT ATT ATTT ATT ATT ATT ATT TTT ATT TTT AT
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT AT
38939047 ATTCATGCGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
ATT
Found at i:38939027 original size:13 final size:13
Alignment explanation
Indices: 38939009--38939046 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
38938999 TCTTGTATCA
38939009 TTATTATTATTAT
1 TTATTATTATTAT
38939022 TTATTATTATTAT
1 TTATTATTATTAT
*
38939035 TT-TTATTTTTAT
1 TTATTATTATTAT
38939047 ATTCATGCGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTATTATTATTAT
Found at i:38941208 original size:19 final size:19
Alignment explanation
Indices: 38941184--38941229 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
38941174 TAGATGTAGT
38941184 TATTAAATTGTGATTGCAG
1 TATTAAATTGTGATTGCAG
*
38941203 TATTAAATTGTGATTGTAG
1 TATTAAATTGTGATTGCAG
38941222 TATTAAAT
1 TATTAAAT
38941230 ACGATTCGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.46
Consensus pattern (19 bp):
TATTAAATTGTGATTGCAG
Found at i:38942292 original size:25 final size:24
Alignment explanation
Indices: 38942247--38942293 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
38942237 GCTTTTAGAC
* * *
38942247 TAAATTGAATGTTTATGTATATTA
1 TAAATTGAATATGTATATATATTA
38942271 TAAATTCGAATATGTATATATAT
1 TAAATT-GAATATGTATATATAT
38942294 ACGTACAGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 6 0.32
25 13 0.68
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (24 bp):
TAAATTGAATATGTATATATATTA
Found at i:38942756 original size:42 final size:42
Alignment explanation
Indices: 38942691--38942865 Score: 244
Period size: 42 Copynumber: 4.2 Consensus size: 42
38942681 CCTAGCTTGT
* * *
38942691 TGCCAGTGAAAT-CATTCAGACTTTACGTCTAGTAGGCTTAA
1 TGCCGGTGAAATAAATTCAGACTTTACGTCTAGCAGGCTTAA
*
38942732 TGCCGGTGAAATAAATTCAAACTTTACGTCTAGCAGGCTTAA
1 TGCCGGTGAAATAAATTCAGACTTTACGTCTAGCAGGCTTAA
*
38942774 TGCCGGTGAAATAAATTCAGACTTCACGTCTAGCAGGCTTAA
1 TGCCGGTGAAATAAATTCAGACTTTACGTCTAGCAGGCTTAA
** * * *
38942816 TGCTAGTGAAATAAATTCGGACTATAAGTCTAGCAGGCTTAA
1 TGCCGGTGAAATAAATTCAGACTTTACGTCTAGCAGGCTTAA
*
38942858 AGCCGGTG
1 TGCCGGTG
38942866 TACTGAATCA
Statistics
Matches: 118, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
41 11 0.09
42 107 0.91
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (42 bp):
TGCCGGTGAAATAAATTCAGACTTTACGTCTAGCAGGCTTAA
Found at i:38950943 original size:42 final size:42
Alignment explanation
Indices: 38950885--38951029 Score: 182
Period size: 42 Copynumber: 3.5 Consensus size: 42
38950875 CAGTGAAACC
* * *
38950885 ATTCAGACTTTACGTCTAGCAGGCTCAATGCCAGTGAAATAA
1 ATTCAAACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAA
*
38950927 ATTCAAAGTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAA
1 ATTCAAACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAA
* * * * *
38950969 ATTCAGACTTCAAGTTTAGCATGCTTAATGCCGGTGAAATAA
1 ATTCAAACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAA
* * *
38951011 ATTCAGACTATAAGTCTAG
1 ATTCAAACTTTACGTCTAG
38951030 TCGACTTAAA
Statistics
Matches: 90, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 90 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (42 bp):
ATTCAAACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAA
Found at i:38953378 original size:17 final size:17
Alignment explanation
Indices: 38953356--38953399 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
38953346 TCCCAAGTCC
38953356 CATGCAATATATCATGG
1 CATGCAATATATCATGG
38953373 CATGCAATATATCATGG
1 CATGCAATATATCATGG
38953390 CATGC-ATATA
1 CATGCAATATA
38953400 CAGAAGCAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.19
17 22 0.81
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (17 bp):
CATGCAATATATCATGG
Found at i:38956645 original size:13 final size:13
Alignment explanation
Indices: 38956627--38956651 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38956617 TAATTGATGT
38956627 ATTTTATTTTTAA
1 ATTTTATTTTTAA
38956640 ATTTTATTTTTA
1 ATTTTATTTTTA
38956652 TATGAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTATTTTTAA
Found at i:38966486 original size:24 final size:25
Alignment explanation
Indices: 38966424--38966476 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
38966414 ATTATATTTA
*
38966424 TAAT-AAATATATAAAATTAAAAAT
1 TAATAAAATCTATAAAATTAAAAAT
* *
38966448 TATTAAAATCTATAAAATTAAAATT
1 TAATAAAATCTATAAAATTAAAAAT
38966473 TAAT
1 TAAT
38966477 GATACTATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
TAATAAAATCTATAAAATTAAAAAT
Found at i:38966609 original size:28 final size:30
Alignment explanation
Indices: 38966560--38966632 Score: 89
Period size: 28 Copynumber: 2.5 Consensus size: 30
38966550 ATACTAAATT
* *
38966560 CATATATTACTAATACATAAAATAAT-ATA
1 CATATATAACTATTACATAAAATAATAATA
*
38966589 -ATATATAACTATTAC-TGAAAATATTAATA
1 CATATATAACTATTACAT-AAAATAATAATA
38966618 CATATATAACTATTA
1 CATATATAACTATTA
38966633 TTATAACATA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
27 1 0.03
28 20 0.53
29 3 0.08
30 14 0.37
ACGTcount: A:0.52, C:0.10, G:0.01, T:0.37
Consensus pattern (30 bp):
CATATATAACTATTACATAAAATAATAATA
Found at i:38967490 original size:24 final size:26
Alignment explanation
Indices: 38967436--38967491 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 26
38967426 ATTGTTATCG
*
38967436 TATAAAAATAAAATGAATTATTACAT
1 TATAAAAATAAAATGAATTATAACAT
*
38967462 T-TAAAAATAAAAT-ATTTATAAC-T
1 TATAAAAATAAAATGAATTATAACAT
38967485 TATAAAA
1 TATAAAA
38967492 TTCAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 2 0.07
24 12 0.44
25 12 0.44
26 1 0.04
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.36
Consensus pattern (26 bp):
TATAAAAATAAAATGAATTATAACAT
Found at i:38970281 original size:21 final size:22
Alignment explanation
Indices: 38970257--38970297 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
38970247 AGCTATGATC
38970257 AATAAATTTA-TTATAAAAAAT
1 AATAAATTTATTTATAAAAAAT
*
38970278 AATATATTTATTTATAAAAA
1 AATAAATTTATTTATAAAAA
38970298 GTTATGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AATAAATTTATTTATAAAAAAT
Found at i:38980136 original size:41 final size:41
Alignment explanation
Indices: 38980081--38980319 Score: 299
Period size: 41 Copynumber: 5.8 Consensus size: 41
38980071 GAATGTAATA
* *
38980081 CAGACGTTACGTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG-A-TACATTT
38980122 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
38980163 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* *
38980204 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* * *
38980245 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG-TAC-TGAAT
1 CAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTGATACAT--TT
* * **
38980286 CAGGCTTTAAGCCTAGCAGGCAAAATGCCGGTGA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
38980320 ATCTGTTTAA
Statistics
Matches: 181, Mismatches: 10, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
39 3 0.02
40 8 0.04
41 168 0.93
42 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (41 bp):
CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
Found at i:38987292 original size:41 final size:41
Alignment explanation
Indices: 38987237--38987475 Score: 299
Period size: 41 Copynumber: 5.8 Consensus size: 41
38987227 GAATGTAATA
* *
38987237 CAGACGTTACGTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG-A-TACATTT
38987278 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
38987319 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* *
38987360 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* * *
38987401 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG-TAC-TGAAT
1 CAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTGATACAT--TT
* * **
38987442 CAGGCTTTAAGCCTAGCAGGCAAAATGCCGGTGA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
38987476 ATCTGTTTAA
Statistics
Matches: 181, Mismatches: 10, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
39 3 0.02
40 8 0.04
41 168 0.93
42 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (41 bp):
CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
Found at i:38988634 original size:23 final size:24
Alignment explanation
Indices: 38988581--38988674 Score: 102
Period size: 26 Copynumber: 3.8 Consensus size: 24
38988571 AGCCATGATC
*
38988581 GGTAAGCTCATTCCGAGCTGAAGAAT
1 GGTAAGCTCA-TACGAGCTG-AGAAT
38988607 GGTAAGCTC-TATCGAGCTGA-AAT
1 GGTAAGCTCATA-CGAGCTGAGAAT
* *
38988630 GGTAAGCTCATAAGAGCTGATATATT
1 GGTAAGCTCATACGAGCTGAGA-A-T
38988656 GGTAAGCTCATACGAGCTG
1 GGTAAGCTCATACGAGCTG
38988675 TGGTGAGTCT
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
23 19 0.32
24 5 0.08
25 8 0.13
26 28 0.47
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.26
Consensus pattern (24 bp):
GGTAAGCTCATACGAGCTGAGAAT
Found at i:38988640 original size:49 final size:49
Alignment explanation
Indices: 38988581--38988674 Score: 120
Period size: 49 Copynumber: 1.9 Consensus size: 49
38988571 AGCCATGATC
**
38988581 GGTAAGCTCATTCCGAGCTGA-AGAATGGTAAGCTC-TATCGAGCTGAAAT
1 GGTAAGCTCA-TAAGAGCTGATAGAATGGTAAGCTCATA-CGAGCTGAAAT
* *
38988630 GGTAAGCTCATAAGAGCTGATATATTGGTAAGCTCATACGAGCTG
1 GGTAAGCTCATAAGAGCTGATAGAATGGTAAGCTCATACGAGCTG
38988675 TGGTGAGTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
48 8 0.21
49 29 0.74
50 2 0.05
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.26
Consensus pattern (49 bp):
GGTAAGCTCATAAGAGCTGATAGAATGGTAAGCTCATACGAGCTGAAAT
Found at i:38996471 original size:21 final size:21
Alignment explanation
Indices: 38996444--38996500 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
38996434 TTAACTCTAA
38996444 AAAATATTTAAAAACAATACAT
1 AAAATATTTAAAAA-AATACAT
38996466 -AAATATGTT-AAAAAATACAT
1 AAAATAT-TTAAAAAAATACAT
38996486 AAAAATATTTAAAAA
1 -AAAATATTTAAAAA
38996501 TTCAAAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
20 7 0.23
21 12 0.39
22 12 0.39
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (21 bp):
AAAATATTTAAAAAAATACAT
Found at i:38997445 original size:19 final size:18
Alignment explanation
Indices: 38997423--38997482 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 18
38997413 TAAAAAATTG
38997423 AAAATGATATAAAGTATAT
1 AAAAT-ATATAAAGTATAT
*
38997442 AAAATTATAAAAAG-ATTAT
1 AAAA-TATATAAAGTA-TAT
*
38997461 AAATATATATAAA-TACAT
1 AAA-ATATATAAAGTATAT
38997479 AAAA
1 AAAA
38997483 AAAAATCTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
17 1 0.03
18 6 0.18
19 25 0.74
20 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (18 bp):
AAAATATATAAAGTATAT
Found at i:39005547 original size:15 final size:15
Alignment explanation
Indices: 39005502--39005549 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
39005492 AGTGTCAATC
39005502 TTGTACATGTTCATG
1 TTGTACATGTTCATG
* * *
39005517 TTGCACATATCCATG
1 TTGTACATGTTCATG
*
39005532 TTGTACATGTTGATG
1 TTGTACATGTTCATG
39005547 TTG
1 TTG
39005550 CATATATTAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (15 bp):
TTGTACATGTTCATG
Found at i:39005570 original size:30 final size:30
Alignment explanation
Indices: 39005496--39005572 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 30
39005486 GCAGTTAGTG
39005496 TCAATCTTGTACATGTTCATGTTGCACATA
1 TCAATCTTGTACATGTTCATGTTGCACATA
* * * *
39005526 TCCATGTTGTACATGTTGATGTTGCATATA
1 TCAATCTTGTACATGTTCATGTTGCACATA
* *
39005556 TTAATCTTGGACATGTT
1 TCAATCTTGTACATGTT
39005573 ACTCTTCATT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.43
Consensus pattern (30 bp):
TCAATCTTGTACATGTTCATGTTGCACATA
Found at i:39006175 original size:18 final size:17
Alignment explanation
Indices: 39006144--39006188 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
39006134 ATTGATTGAA
39006144 TTAA-ATTTTATATTTT
1 TTAATATTTTATATTTT
*
39006160 TTAATACTTTTTTATTTT
1 TTAATA-TTTTATATTTT
39006178 TTAATATTTTA
1 TTAATATTTTA
39006189 AAATTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 4 0.16
17 5 0.20
18 16 0.64
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (17 bp):
TTAATATTTTATATTTT
Found at i:39010263 original size:15 final size:14
Alignment explanation
Indices: 39010242--39010277 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
39010232 ATAATCCTTA
*
39010242 ATAATTATCTTAAT
1 ATAATTATCCTAAT
39010256 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
39010271 ATAATTA
1 ATAATTA
39010278 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:39012451 original size:29 final size:31
Alignment explanation
Indices: 39012417--39012480 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 31
39012407 TATAAATTTG
* *
39012417 GAATTTAGTTCTTATA-TTTTTAT-TTTTAA
1 GAATTTAGTCCTTATACTTTTCATATTTTAA
*
39012446 GAATTTAGTCCTTTTACTTTTCATATTTTAA
1 GAATTTAGTCCTTATACTTTTCATATTTTAA
39012477 -AATT
1 GAATT
39012481 CAGATCCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 14 0.47
30 10 0.33
31 6 0.20
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.58
Consensus pattern (31 bp):
GAATTTAGTCCTTATACTTTTCATATTTTAA
Found at i:39013122 original size:17 final size:17
Alignment explanation
Indices: 39013090--39013143 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 17
39013080 GTTGAATTAG
39013090 ATTTTATATTTTTTTAAAT
1 ATTTTATA--TTTTTAAAT
39013109 ATTTTATATTTTT-AAT
1 ATTTTATATTTTTAAAT
* *
39013125 AATTTATTTATTTTAAAT
1 ATTTTATAT-TTTTAAAT
39013143 A
1 A
39013144 GATAAACTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 10 0.32
17 9 0.29
18 4 0.13
19 8 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTATATTTTTAAAT
Found at i:39014578 original size:7 final size:7
Alignment explanation
Indices: 39014566--39014628 Score: 74
Period size: 7 Copynumber: 8.9 Consensus size: 7
39014556 GTAGAGGTTT
39014566 TTTTTTG
1 TTTTTTG
*
39014573 TTTTTTA
1 TTTTTTG
39014580 TTTTCTTG
1 TTTT-TTG
*
39014588 TTTTTTT
1 TTTTTTG
39014595 TGTTTTTG
1 T-TTTTTG
39014603 -TTTTTG
1 TTTTTTG
*
39014609 TTTTGTG
1 TTTTTTG
39014616 TTTTTTG
1 TTTTTTG
39014623 TTTTTT
1 TTTTTT
39014629 TTCTCCACTC
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
6 6 0.13
7 30 0.64
8 11 0.23
ACGTcount: A:0.02, C:0.02, G:0.13, T:0.84
Consensus pattern (7 bp):
TTTTTTG
Found at i:39014588 original size:15 final size:14
Alignment explanation
Indices: 39014563--39014629 Score: 73
Period size: 15 Copynumber: 4.6 Consensus size: 14
39014553 CCGGTAGAGG
39014563 TTTTTTTTTGTTTT
1 TTTTTTTTTGTTTT
*
39014577 TTATTTTCTTGTTTT
1 TT-TTTTTTTGTTTT
39014592 TTTTGTTTTTG-TTT
1 TTTT-TTTTTGTTTT
* *
39014606 TTGTTTTGTGTTTT
1 TTTTTTTTTGTTTT
39014620 TTGTTTTTTT
1 TT-TTTTTTT
39014630 TCTCCACTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
13 5 0.12
14 15 0.35
15 23 0.53
ACGTcount: A:0.01, C:0.01, G:0.12, T:0.85
Consensus pattern (14 bp):
TTTTTTTTTGTTTT
Found at i:39014600 original size:6 final size:6
Alignment explanation
Indices: 39014563--39014627 Score: 64
Period size: 6 Copynumber: 10.7 Consensus size: 6
39014553 CCGGTAGAGG
*
39014563 TTTT-T TTTTGT TTTT-T ATTTTCT TGTTT-T TTTTGT TTTTGT TTTTGT
1 TTTTGT TTTTGT TTTTGT -TTTTGT T-TTTGT TTTTGT TTTTGT TTTTGT
39014610 TTTGTGTT TTTTGT TTTT
1 TTT-TG-T TTTTGT TTTT
39014628 TTTCTCCACT
Statistics
Matches: 53, Mismatches: 0, Indels: 13
0.80 0.00 0.20
Matches are distributed among these distances:
5 8 0.15
6 33 0.62
7 8 0.15
8 4 0.08
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.85
Consensus pattern (6 bp):
TTTTGT
Found at i:39014614 original size:26 final size:24
Alignment explanation
Indices: 39014564--39014628 Score: 85
Period size: 26 Copynumber: 2.6 Consensus size: 24
39014554 CGGTAGAGGT
39014564 TTTTTTTTGTTTTTTATTTTCTTG
1 TTTTTTTTGTTTTTTATTTTCTTG
* *
39014588 TTTTTTTTGTTTTTGTTTTTGTTTTG
1 TTTTTTTTGTTTTT-TATTT-TCTTG
*
39014614 TGTTTTTTGTTTTTT
1 TTTTTTTTGTTTTTT
39014629 TTCTCCACTC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 14 0.39
25 5 0.14
26 17 0.47
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.85
Consensus pattern (24 bp):
TTTTTTTTGTTTTTTATTTTCTTG
Found at i:39032503 original size:15 final size:15
Alignment explanation
Indices: 39032483--39032512 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39032473 GAAGAGGATG
39032483 ATGCTTGTGAAGTTT
1 ATGCTTGTGAAGTTT
39032498 ATGCTTGTGAAGTTT
1 ATGCTTGTGAAGTTT
39032513 TCCTCATCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.27, T:0.47
Consensus pattern (15 bp):
ATGCTTGTGAAGTTT
Found at i:39037275 original size:19 final size:19
Alignment explanation
Indices: 39037251--39037297 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
39037241 GCAACTCACC
39037251 CCACTGCCTCGCAGTAGCT
1 CCACTGCCTCGCAGTAGCT
39037270 CCACTGCCTCGCAGTAGCT
1 CCACTGCCTCGCAGTAGCT
39037289 CCACTGCCT
1 CCACTGCCT
39037298 GTAGAGAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.15, C:0.45, G:0.19, T:0.21
Consensus pattern (19 bp):
CCACTGCCTCGCAGTAGCT
Found at i:39039212 original size:30 final size:31
Alignment explanation
Indices: 39039162--39039223 Score: 117
Period size: 30 Copynumber: 2.0 Consensus size: 31
39039152 ACGCTCATTA
39039162 TGATATTATTATTATTTATTTACATAGCTAG
1 TGATATTATTATTATTTATTTACATAGCTAG
39039193 TGATATTATTATT-TTTATTTACATAGCTAG
1 TGATATTATTATTATTTATTTACATAGCTAG
39039223 T
1 T
39039224 AAGTGAGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 18 0.58
31 13 0.42
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.53
Consensus pattern (31 bp):
TGATATTATTATTATTTATTTACATAGCTAG
Found at i:39049399 original size:26 final size:27
Alignment explanation
Indices: 39049341--39049404 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 27
39049331 TCGTAAAAGT
* * *
39049341 TATATATATATTTATATAAGAAATATG
1 TATATATATATCTATATAAAAAATACG
*
39049368 TATATATATA-CTATATAAAAAATGCG
1 TATATATATATCTATATAAAAAATACG
* *
39049394 TGTATAAATAT
1 TATATATATAT
39049405 AGAAATAGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
26 20 0.67
27 10 0.33
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41
Consensus pattern (27 bp):
TATATATATATCTATATAAAAAATACG
Found at i:39122645 original size:20 final size:20
Alignment explanation
Indices: 39122622--39122782 Score: 104
Period size: 21 Copynumber: 8.0 Consensus size: 20
39122612 AAATTGTAAA
39122622 AAATATTGTAAAAAATTATT
1 AAATATTGTAAAAAATTATT
* *
39122642 AAATATTTTTAAAAATATTTTT
1 AAATA-TTGTAAAAA-ATTATT
39122664 AAAT-TT-T-AAAAATTATT
1 AAATATTGTAAAAAATTATT
* * *
39122681 AAAAATTATAAAACATTATTT
1 AAATATTGTAAAAAATTA-TT
39122702 AAACT-TTGT-AAAAATTATT
1 AAA-TATTGTAAAAAATTATT
**
39122721 AAA-ATT-TTGAAAATTATTT
1 AAATATTGTAAAAAATTA-TT
*
39122740 AAAAAATTG-AAAATAATTATT
1 -AAATATTGTAAAA-AATTATT
*
39122761 AAAAAATTGTAAAAAAATTATT
1 -AAATATTGT-AAAAAATTATT
39122783 TAATTAGAAA
Statistics
Matches: 114, Mismatches: 11, Indels: 30
0.74 0.07 0.19
Matches are distributed among these distances:
17 9 0.08
18 15 0.13
19 9 0.08
20 24 0.21
21 32 0.28
22 21 0.18
23 4 0.04
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (20 bp):
AAATATTGTAAAAAATTATT
Found at i:39122659 original size:12 final size:12
Alignment explanation
Indices: 39122642--39122666 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39122632 AAAAATTATT
39122642 AAATATTTTTAA
1 AAATATTTTTAA
39122654 AAATATTTTTAA
1 AAATATTTTTAA
39122666 A
1 A
39122667 TTTTAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATATTTTTAA
Found at i:39122678 original size:39 final size:40
Alignment explanation
Indices: 39122627--39122739 Score: 133
Period size: 40 Copynumber: 2.8 Consensus size: 40
39122617 GTAAAAAATA
39122627 TTGTAAAAAATTATTAAATATTTTTAAAAATATTTTTAAA-T
1 TTGT-AAAAATTATTAAA-ATTTTTAAAAATATTTTTAAACT
* * *
39122668 TT-TAAAAATTATTAAAAATTATAAAACAT-TATTTAAACT
1 TTGTAAAAATTATTAAAATTTTTAAAA-ATATTTTTAAACT
* *
39122707 TTGTAAAAATTATTAAAATTTTGAAAATTATTT
1 TTGTAAAAATTATTAAAATTTTTAAAAATATTT
39122740 AAAAAATTGA
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
38 15 0.25
39 19 0.32
40 24 0.40
41 2 0.03
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.46
Consensus pattern (40 bp):
TTGTAAAAATTATTAAAATTTTTAAAAATATTTTTAAACT
Found at i:39122682 original size:10 final size:10
Alignment explanation
Indices: 39122632--39122765 Score: 86
Period size: 10 Copynumber: 13.5 Consensus size: 10
39122622 AAATATTGTA
39122632 AAAAATTATT
1 AAAAATTATT
* *
39122642 AAATATTTTT
1 AAAAATTATT
39122652 AAAAA-TATTT
1 AAAAATTA-TT
**
39122662 TTAAATT-TT
1 AAAAATTATT
39122671 AAAAATTATT
1 AAAAATTATT
39122681 AAAAATTA-T
1 AAAAATTATT
39122690 AAAACATTATT
1 AAAA-ATTATT
* *
39122701 TAAACTT-TGT
1 AAAAATTAT-T
39122711 AAAAATTATT
1 AAAAATTATT
39122721 -AAAATT-TT
1 AAAAATTATT
*
39122729 GAAAATTATTT
1 AAAAATTA-TT
39122740 AAAAA--ATT
1 AAAAATTATT
39122748 GAAAATAATTATT
1 --AAA-AATTATT
39122761 AAAAA
1 AAAAA
39122766 ATTGTAAAAA
Statistics
Matches: 96, Mismatches: 13, Indels: 30
0.69 0.09 0.22
Matches are distributed among these distances:
8 4 0.04
9 27 0.28
10 45 0.47
11 17 0.18
13 3 0.03
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (10 bp):
AAAAATTATT
Found at i:39122760 original size:22 final size:23
Alignment explanation
Indices: 39122730--39122785 Score: 89
Period size: 22 Copynumber: 2.5 Consensus size: 23
39122720 TAAAATTTTG
39122730 AAAATTATTTAAAAAATTG-AAA
1 AAAATTATTTAAAAAATTGTAAA
*
39122752 ATAATTA-TTAAAAAATTGTAAA
1 AAAATTATTTAAAAAATTGTAAA
39122774 AAAATTATTTAA
1 AAAATTATTTAA
39122786 TTAGAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 11 0.37
22 15 0.50
23 4 0.13
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.36
Consensus pattern (23 bp):
AAAATTATTTAAAAAATTGTAAA
Found at i:39122769 original size:21 final size:21
Alignment explanation
Indices: 39122714--39122782 Score: 79
Period size: 19 Copynumber: 3.3 Consensus size: 21
39122704 ACTTTGTAAA
**
39122714 AATTATTAAAATTTTGAAAAT
1 AATTATTAAAAAATTGAAAAT
*
39122735 TA-T-TTAAAAAATTGAAAAT
1 AATTATTAAAAAATTGAAAAT
*
39122754 AATTATTAAAAAATTGTAAAAA
1 AATTATTAAAAAATTG-AAAAT
39122776 AATTATT
1 AATTATT
39122783 TAATTAGAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 15 0.38
20 2 0.05
21 12 0.30
22 11 0.28
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (21 bp):
AATTATTAAAAAATTGAAAAT
Found at i:39122878 original size:11 final size:10
Alignment explanation
Indices: 39122802--39122970 Score: 87
Period size: 10 Copynumber: 16.6 Consensus size: 10
39122792 ATTTCACAAT
39122802 TTTTTAATAA
1 TTTTTAATAA
* *
39122812 TTATTTACT-G
1 TT-TTTAATAA
*
39122822 TTGTTAATAA
1 TTTTTAATAA
*
39122832 TTTTTAACAA
1 TTTTTAATAA
* * *
39122842 ATTTAAATGATT
1 TTTTTAAT-A-A
*
39122854 TTTTTTATAA
1 TTTTTAATAA
39122864 TTTTTAATAA
1 TTTTTAATAA
*
39122874 TTTTT-TTACA
1 TTTTTAATA-A
* *
39122884 ATTTTAAAATA
1 TTTTTAATA-A
* *
39122895 TTTTTGACAA
1 TTTTTAATAA
*
39122905 TATTTAATAA
1 TTTTTAATAA
*
39122915 TTATTT-ACAA
1 TT-TTTAATAA
39122925 TTTTTAATACA
1 TTTTTAATA-A
39122936 TTTTTAA-AA
1 TTTTTAATAA
39122945 TTTTTTAA-AA
1 -TTTTTAATAA
*
39122955 TTTTTAATAT
1 TTTTTAATAA
39122965 TTTTTA
1 TTTTTA
39122971 TAACCTTTTT
Statistics
Matches: 117, Mismatches: 31, Indels: 22
0.69 0.18 0.13
Matches are distributed among these distances:
9 17 0.15
10 69 0.59
11 26 0.22
12 5 0.04
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:39122957 original size:30 final size:29
Alignment explanation
Indices: 39122854--39122989 Score: 103
Period size: 30 Copynumber: 4.5 Consensus size: 29
39122844 TTAAATGATT
* *
39122854 TTTTTTATAATTTTTAATAATTTTTTTACAA
1 TTTTTTAAAATTTTTAATAA--TTTTTAAAA
* * * *
39122885 -TTTTAAAATATTTTTGACAATATTTAATAA
1 TTTTTTAAA-ATTTTTAATAATTTTTAA-AA
* *
39122915 TTATTTACAATTTTTAATACATTTTTAAAA
1 TTTTTTAAAATTTTTAATA-ATTTTTAAAA
* *
39122945 TTTTTTAAAATTTTTAATATTTTTTATAAC
1 TTTTTTAAAATTTTTAATAATTTTTA-AAA
*
39122975 CTTTTTACAAATTTT
1 TTTTTTA-AAATTTT
39122990 CAACGTGGTC
Statistics
Matches: 82, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
29 11 0.13
30 43 0.52
31 28 0.34
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.58
Consensus pattern (29 bp):
TTTTTTAAAATTTTTAATAATTTTTAAAA
Found at i:39126933 original size:23 final size:23
Alignment explanation
Indices: 39126907--39126982 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
39126897 ATAAGTGCCA
39126907 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
39126930 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
39126953 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
39126976 CACTGAT
1 CACTGAT
39126983 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:39127082 original size:8 final size:8
Alignment explanation
Indices: 39127069--39127097 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
39127059 ACCCGGGACT
39127069 CACTGTAA
1 CACTGTAA
39127077 CACTGTAA
1 CACTGTAA
39127085 CACTGTAA
1 CACTGTAA
39127093 CACTG
1 CACTG
39127098 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:39127228 original size:18 final size:17
Alignment explanation
Indices: 39127202--39127240 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
39127192 ATTTTCCTTC
39127202 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
39127219 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
39127237 CACA
1 CACA
39127241 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:39134266 original size:23 final size:23
Alignment explanation
Indices: 39134240--39134315 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
39134230 ATAAGTGCCA
39134240 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
39134263 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
39134286 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
39134309 CACTGAT
1 CACTGAT
39134316 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:39134415 original size:8 final size:8
Alignment explanation
Indices: 39134402--39134430 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
39134392 ACCCGGGACT
39134402 CACTGTAA
1 CACTGTAA
39134410 CACTGTAA
1 CACTGTAA
39134418 CACTGTAA
1 CACTGTAA
39134426 CACTG
1 CACTG
39134431 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:39134561 original size:18 final size:17
Alignment explanation
Indices: 39134535--39134573 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
39134525 ATTTTCCTTC
39134535 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
39134552 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
39134570 CACA
1 CACA
39134574 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:39136724 original size:21 final size:21
Alignment explanation
Indices: 39136686--39136735 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
39136676 GTCACACGGT
*
39136686 CGTGTGGC-TTCACACATGGC
1 CGTGTGGCTTTCACACATGCC
* *
39136706 TGTGTGGCTTTCCCACATGCC
1 CGTGTGGCTTTCACACATGCC
39136727 CGTGTGGCT
1 CGTGTGGCT
39136736 AGACCGTGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.10, C:0.30, G:0.30, T:0.30
Consensus pattern (21 bp):
CGTGTGGCTTTCACACATGCC
Found at i:39140524 original size:11 final size:11
Alignment explanation
Indices: 39140489--39140524 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
39140479 AAATACGTAC
39140489 AAATAT-TATA
1 AAATATATATA
39140499 TAAATATATATA
1 -AAATATATATA
39140511 AAATATATATA
1 AAATATATATA
39140522 AAA
1 AAA
39140525 ATGTGCATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 20 0.83
12 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AAATATATATA
Found at i:39140676 original size:16 final size:16
Alignment explanation
Indices: 39140655--39140690 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
39140645 AAATGGAAAG
39140655 TATATAGATATACATA
1 TATATAGATATACATA
39140671 TATATAGATATACATA
1 TATATAGATATACATA
39140687 TATA
1 TATA
39140691 AAAAAGGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
TATATAGATATACATA
Found at i:39141602 original size:14 final size:13
Alignment explanation
Indices: 39141573--39141598 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39141563 TACAAAAGTT
39141573 GAAAAAAAGAAAA
1 GAAAAAAAGAAAA
39141586 GAAAAAAAGAAAA
1 GAAAAAAAGAAAA
39141599 AGAACCCCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
GAAAAAAAGAAAA
Found at i:39147921 original size:26 final size:26
Alignment explanation
Indices: 39147889--39147942 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
39147879 ACATAGTTTT
39147889 TATATTAT-TTATAAAGGTTATAATAA
1 TATATTATATTATAAA-GTTATAATAA
*
39147915 TATATTATATTATAAAGTTATTATAA
1 TATATTATATTATAAAGTTATAATAA
39147941 TA
1 TA
39147943 AAAGACAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (26 bp):
TATATTATATTATAAAGTTATAATAA
Found at i:39150533 original size:46 final size:46
Alignment explanation
Indices: 39150466--39150605 Score: 210
Period size: 46 Copynumber: 3.0 Consensus size: 46
39150456 ACAATGCTAT
* * * *
39150466 AACTCAATATGGTTTCCTTCACTGAAATACCATACCTACTTTTCTC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
39150512 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTATTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
39150558 AACTTAGTATGAGTTTT-TTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATG-GTTTTCTTCACTGAAACACCATACCTACTTTTCAC
39150604 AA
1 AA
39150606 TTTTCCATGG
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
46 81 0.94
47 5 0.06
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:39152121 original size:43 final size:43
Alignment explanation
Indices: 39152006--39152132 Score: 152
Period size: 44 Copynumber: 2.9 Consensus size: 43
39151996 AGGATTCCGT
*
39152006 TATGTG-TTATCATGTAAGACCACGTCTAGGACGTTGGCATCGA
1 TATGTGATTA-CATGTAAGACCACGTCTGGGACGTTGGCATCGA
* * * *
39152049 TTTATGATTTGCGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGA
1 TATGTGA-TTACATGTAAGACCAC-GTCTGGGAC-GTTGGCATCGA
39152093 TATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 TATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
39152133 TGTACCACTA
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
42 1 0.01
43 32 0.46
44 33 0.48
45 3 0.04
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.31
Consensus pattern (43 bp):
TATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCATCGA
Found at i:39158844 original size:43 final size:42
Alignment explanation
Indices: 39158573--39158843 Score: 283
Period size: 43 Copynumber: 6.3 Consensus size: 42
39158563 TTTTAGACAT
* * ****
39158573 AAACGCAGCTAAAGATCATGACTTTTAGCGGCGCTTTTTTTAC
1 AAACGCCGCTAAAGAACATGAC-TTTAGCGGCGCTTTACCCAC
* * **
39158616 AAACGCCGCTATAGAGCATGACTTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGAACATGAC-TTTAGCGGCGCTTTACCCAC
* *
39158659 AAACGTCGCTATAGAACATGAGCTTTAGCGGCGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGA-CTTTAGCGGCGCTTTACCCAC
*
39158702 AAATGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGA-CTTTAGCGGCGCTTTACCCAC
* * *
39158745 AAACGTCGCTAAAGAACATGACCTTTAGCGACGCTTTACCCAA
1 AAACGCCGCTAAAGAACATGA-CTTTAGCGGCGCTTTACCCAC
** * * *
39158788 AAATACCGCTAAAAAACATGATCTTTAGCTGCGCTTTTA-TCAC
1 AAACGCCGCTAAAGAACATGA-CTTTAGCGGCGC-TTTACCCAC
39158831 AAACGCCGCTAAA
1 AAACGCCGCTAAA
39158844 AGTACGATTC
Statistics
Matches: 198, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
43 193 0.97
44 5 0.03
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.25
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATGACTTTAGCGGCGCTTTACCCAC
Found at i:39160081 original size:40 final size:40
Alignment explanation
Indices: 39160018--39160102 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
39160008 TAGCTTGAAT
* * *
39160018 ATCAACACTTCAATATTTAATATGTAAGGAATTATCAAAA
1 ATCAACACTTCAATATTTAATATGCAAGAAATTAACAAAA
* *
39160058 ATCAACATTTCAATAATTT-ATATGCAAGAAATTAACACAA
1 ATCAACACTTCAAT-ATTTAATATGCAAGAAATTAACAAAA
39160098 ATCAA
1 ATCAA
39160103 TCTTACAACA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 35 0.90
41 4 0.10
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (40 bp):
ATCAACACTTCAATATTTAATATGCAAGAAATTAACAAAA
Found at i:39160296 original size:87 final size:86
Alignment explanation
Indices: 39160168--39160447 Score: 393
Period size: 86 Copynumber: 3.2 Consensus size: 86
39160158 GGCAATAGGG
* * *
39160168 CTAAATCTTCAATTTCTATAACGATTTATATGCAACAAATTAGCAAAAAATCAATGGTTCAAGTT
1 CTAAATTTTCAATTT-TATAACAACTTATATGCAACAAATTAGCAAAAAATCAATGGTTCAAGTT
* * *
39160233 CATGTATTTACCAAAAATCAGA
65 CATGCATTTACCAACAACCAGA
* *
39160255 CTAATTTTTCAATATTTATAACAACTTATATGCAACAAATTAGC-AAAAATAAATGGTTCAAGTT
1 CTAAATTTTCAAT-TTTATAACAACTTATATGCAACAAATTAGCAAAAAATCAATGGTTCAAGTT
39160319 CATGCATTTACCAACAACCAGA
65 CATGCATTTACCAACAACCAGA
* **
39160341 CTAAATTTTCAATTTTTATAACAACTTATGTGCAACAAATTAG-AAAAAATCAACAGTTCAAGTT
1 CTAAATTTTCAA-TTTTATAACAACTTATATGCAACAAATTAGCAAAAAATCAATGGTTCAAGTT
*
39160405 CATGCATTCACCAACAACCAGA
65 CATGCATTTACCAACAACCAGA
*
39160427 CCAAATTTTCAACTTTTATAA
1 CTAAATTTTCAA-TTTTATAA
39160448 AGTAGAAAAA
Statistics
Matches: 174, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
86 134 0.77
87 38 0.22
88 2 0.01
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (86 bp):
CTAAATTTTCAATTTTATAACAACTTATATGCAACAAATTAGCAAAAAATCAATGGTTCAAGTTC
ATGCATTTACCAACAACCAGA
Found at i:39164112 original size:14 final size:14
Alignment explanation
Indices: 39164082--39164138 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
39164072 ACATGAACTA
*
39164082 TAAATCCTTAACTCC
1 TAAATCCTAAAC-CC
39164097 TAAATCCTAAACCC
1 TAAATCCTAAACCC
**
39164111 TAACCCCTAAACCC
1 TAAATCCTAAACCC
39164125 -ATAATCCATAAACC
1 TA-AATCC-TAAACC
39164139 TTAAGATAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
13 1 0.03
14 17 0.49
15 17 0.49
ACGTcount: A:0.40, C:0.37, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAATCCTAAACCC
Found at i:39164118 original size:7 final size:7
Alignment explanation
Indices: 39164095--39164201 Score: 54
Period size: 7 Copynumber: 15.0 Consensus size: 7
39164085 ATCCTTAACT
*
39164095 CCTAAAT
1 CCTAAAC
39164102 CCTAAAC
1 CCTAAAC
*
39164109 CCTAACC
1 CCTAAAC
39164116 CCTAAAC
1 CCTAAAC
*
39164123 CCATAATC
1 CC-TAAAC
*
39164131 CATAAAC
1 CCTAAAC
* *
39164138 CTTAAGAT
1 CCTAA-AC
**
39164146 AAT-AAC
1 CCTAAAC
*
39164152 TCATAAAC
1 -CCTAAAC
*
39164160 CTTAAAC
1 CCTAAAC
39164167 CCTAAAC
1 CCTAAAC
* * *
39164174 CATATAT
1 CCTAAAC
39164181 CCTAAAC
1 CCTAAAC
*
39164188 CATAAAC
1 CCTAAAC
39164195 CCTAAAC
1 CCTAAAC
39164202 TATAATGATA
Statistics
Matches: 74, Mismatches: 22, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
6 1 0.01
7 63 0.85
8 10 0.14
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.21
Consensus pattern (7 bp):
CCTAAAC
Found at i:39164174 original size:14 final size:14
Alignment explanation
Indices: 39164095--39164206 Score: 75
Period size: 14 Copynumber: 7.9 Consensus size: 14
39164085 ATCCTTAACT
39164095 CCTAAATCC-TAAAC
1 CCTAAA-CCATAAAC
* *
39164109 CCTAACCCCTAAAC
1 CCTAAACCATAAAC
*
39164123 CCATAATCCATAAAC
1 CC-TAAACCATAAAC
* **
39164138 CTTAAGATAAT-AAC
1 CCTAA-ACCATAAAC
* *
39164152 TCATAAACCTTAAAC
1 -CCTAAACCATAAAC
* *
39164167 CCTAAACCATATAT
1 CCTAAACCATAAAC
39164181 CCTAAACCATAAAC
1 CCTAAACCATAAAC
*
39164195 CCTAAACTATAA
1 CCTAAACCATAA
39164207 TGATAATTAA
Statistics
Matches: 75, Mismatches: 18, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
13 2 0.03
14 53 0.71
15 20 0.27
ACGTcount: A:0.46, C:0.31, G:0.01, T:0.22
Consensus pattern (14 bp):
CCTAAACCATAAAC
Found at i:39164290 original size:8 final size:7
Alignment explanation
Indices: 39164252--39164300 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
39164242 CTAGTTACTC
*
39164252 TAAACCT
1 TAAACCA
39164259 TAAACCA
1 TAAACCA
39164266 TAAACC-
1 TAAACCA
*
39164272 TAAACCC
1 TAAACCA
39164279 TAAAACCA
1 T-AAACCA
39164287 TAAACTCA
1 TAAAC-CA
39164295 TAAACC
1 TAAACC
39164301 CTTAACACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
6 6 0.16
7 18 0.49
8 13 0.35
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.18
Consensus pattern (7 bp):
TAAACCA
Found at i:39164350 original size:7 final size:7
Alignment explanation
Indices: 39164338--39164391 Score: 63
Period size: 7 Copynumber: 7.6 Consensus size: 7
39164328 CCCCAGCCTT
39164338 TAAACCA
1 TAAACCA
39164345 TAAACCA
1 TAAACCA
*
39164352 TAAATCA
1 TAAACCA
*
39164359 TAACCCA
1 TAAACCA
39164366 TAAACCCA
1 TAAA-CCA
*
39164374 TAATCCA
1 TAAACCA
*
39164381 TAAACCT
1 TAAACCA
39164388 TAAA
1 TAAA
39164392 ATGGTAACAC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
7 33 0.85
8 6 0.15
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAACCA
Found at i:39164421 original size:14 final size:14
Alignment explanation
Indices: 39164402--39164435 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
39164392 ATGGTAACAC
*
39164402 CTAAACCTTAAACT
1 CTAAACCATAAACT
*
39164416 CTAAACCATATACT
1 CTAAACCATAAACT
39164430 CTAAAC
1 CTAAAC
39164436 TAAAAACCCT
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:0.44, C:0.29, G:0.00, T:0.26
Consensus pattern (14 bp):
CTAAACCATAAACT
Found at i:39164801 original size:40 final size:41
Alignment explanation
Indices: 39164755--39164984 Score: 234
Period size: 41 Copynumber: 5.7 Consensus size: 41
39164745 AATAGTTTTT
* *
39164755 GCGGCGCTTTTTCAAAAACGTCGCTAAA-AATAGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGACTAGAGCATTA
*
39164795 GCGGCGCTTTTTCAAAAACGCCGCTAAA-AATAGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGACTAGAGCATTA
* * ** * *
39164835 GAGTCGCTTTTTCAAAAACGATGCTAAAGCCCAGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGACTAGAGCATTA
* * * *
39164876 GCGAGAC-C-TTTTCACAAATGCCGCTAAAGCCCAGAGCATTA
1 GCG-G-CGCTTTTTCAAAAACGCCGCTAAAGACTAGAGCATTA
* ** *
39164917 GCGGTGCTTTTTCAAAAACGCCGCTAAATTCTCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGACTAGAGCATTA
* **
39164958 GTGGCATTTTTTCAAAAACGCCGCTAA
1 GCGGCGCTTTTTCAAAAACGCCGCTAA
39164985 CGCCTCAAAA
Statistics
Matches: 160, Mismatches: 25, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
40 65 0.41
41 93 0.58
42 1 0.01
43 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGACTAGAGCATTA
Found at i:39170443 original size:18 final size:18
Alignment explanation
Indices: 39170422--39170456 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39170412 TGATCATAGT
*
39170422 CATGGTCACGGTCATGGC
1 CATGATCACGGTCATGGC
39170440 CATGATCACGGTCATGG
1 CATGATCACGGTCATGG
39170457 TCATAGCCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.26, G:0.31, T:0.23
Consensus pattern (18 bp):
CATGATCACGGTCATGGC
Found at i:39170472 original size:30 final size:30
Alignment explanation
Indices: 39170408--39170472 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
39170398 CTATTATTGG
* * * *
39170408 GCCATGATCATAGTCATGGTCACGGTCATG
1 GCCATGATCACAGTCATGGTCACAGCCATA
* *
39170438 GCCATGATCACGGTCATGGTCATAGCCATA
1 GCCATGATCACAGTCATGGTCACAGCCATA
39170468 GCCAT
1 GCCAT
39170473 AGCCATAGCC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.25
Consensus pattern (30 bp):
GCCATGATCACAGTCATGGTCACAGCCATA
Found at i:39170505 original size:6 final size:6
Alignment explanation
Indices: 39170458--39170492 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
39170448 CGGTCATGGT
39170458 CATAGC CATAGC CATAGC CATAGC CATAGC CATAG
1 CATAGC CATAGC CATAGC CATAGC CATAGC CATAG
39170493 TGATCATAGT
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:0.34, C:0.31, G:0.17, T:0.17
Consensus pattern (6 bp):
CATAGC
Found at i:39172589 original size:18 final size:19
Alignment explanation
Indices: 39172566--39172601 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
39172556 AATGAACTAT
*
39172566 TAAAAACAATTA-AAAAAG
1 TAAAAAAAATTATAAAAAG
39172584 TAAAAAAAATTATAAAAA
1 TAAAAAAAATTATAAAAA
39172602 TCGGATCAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (19 bp):
TAAAAAAAATTATAAAAAG
Found at i:39178592 original size:18 final size:18
Alignment explanation
Indices: 39178569--39178604 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
39178559 AGACCAATCT
39178569 GTTATTCGAATTATTCGA
1 GTTATTCGAATTATTCGA
* *
39178587 GTTATTTGAGTTATTCGA
1 GTTATTCGAATTATTCGA
39178605 ATTGTAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.47
Consensus pattern (18 bp):
GTTATTCGAATTATTCGA
Found at i:39180632 original size:21 final size:22
Alignment explanation
Indices: 39180597--39180638 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
39180587 CAAATGTGCA
39180597 AGCTCACCAAAGCATGAGAGCG
1 AGCTCACCAAAGCATGAGAGCG
39180619 AGCTCACC-AAGCATGAGAGC
1 AGCTCACCAAAGCATGAGAGC
39180639 TTACCTGCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.36, C:0.29, G:0.26, T:0.10
Consensus pattern (22 bp):
AGCTCACCAAAGCATGAGAGCG
Found at i:39180679 original size:8 final size:8
Alignment explanation
Indices: 39180666--39180693 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
39180656 ACTCTGTAAG
39180666 TTGCCAAC
1 TTGCCAAC
39180674 TTGCCAAC
1 TTGCCAAC
39180682 TTGCCAAC
1 TTGCCAAC
39180690 TTGC
1 TTGC
39180694 ACTAAAACTA
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:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (8 bp):
TTGCCAAC
Found at i:39180884 original size:16 final size:16
Alignment explanation
Indices: 39180863--39180896 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
39180853 AACTATGCAT
*
39180863 CAGTTTTTTAATGAAA
1 CAGTTTTTTAACGAAA
39180879 CAGTTTTTTAACGAAA
1 CAGTTTTTTAACGAAA
39180895 CA
1 CA
39180897 ATTCACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (16 bp):
CAGTTTTTTAACGAAA
Found at i:39181799 original size:71 final size:71
Alignment explanation
Indices: 39181693--39181835 Score: 286
Period size: 71 Copynumber: 2.0 Consensus size: 71
39181683 TTTGCATCCA
39181693 ATTCCTGGTTTAGGAGCAAAAGAAACAATGTATCGTATACCCTCGCATATGATCAAACACGTTTG
1 ATTCCTGGTTTAGGAGCAAAAGAAACAATGTATCGTATACCCTCGCATATGATCAAACACGTTTG
39181758 CAACAT
66 CAACAT
39181764 ATTCCTGGTTTAGGAGCAAAAGAAACAATGTATCGTATACCCTCGCATATGATCAAACACGTTTG
1 ATTCCTGGTTTAGGAGCAAAAGAAACAATGTATCGTATACCCTCGCATATGATCAAACACGTTTG
39181829 CAACAT
66 CAACAT
39181835 A
1 A
39181836 GCCTAAGACA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.27
Consensus pattern (71 bp):
ATTCCTGGTTTAGGAGCAAAAGAAACAATGTATCGTATACCCTCGCATATGATCAAACACGTTTG
CAACAT
Found at i:39187167 original size:34 final size:34
Alignment explanation
Indices: 39187128--39187200 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
39187118 ACTAAGTAGA
39187128 TATAAGCCCTAAACTTCCACCACATAAAGGAGAT
1 TATAAGCCCTAAACTTCCACCACATAAAGGAGAT
39187162 TATAAGCCCTAAACTTCCACCACATAAAGGAGAT
1 TATAAGCCCTAAACTTCCACCACATAAAGGAGAT
*
39187196 AATAA
1 TATAA
39187201 AAAGTAGGTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.44, C:0.25, G:0.11, T:0.21
Consensus pattern (34 bp):
TATAAGCCCTAAACTTCCACCACATAAAGGAGAT
Found at i:39192354 original size:9 final size:10
Alignment explanation
Indices: 39192342--39192383 Score: 52
Period size: 9 Copynumber: 4.4 Consensus size: 10
39192332 CTTTTCGTTC
39192342 TTTTAATGAT
1 TTTTAATGAT
*
39192352 TTTT-ATAAT
1 TTTTAATGAT
*
39192361 TTTTAATTAT
1 TTTTAATGAT
39192371 TTTTAA-GAT
1 TTTTAATGAT
39192380 TTTT
1 TTTT
39192384 TAAAAGATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 14 0.50
10 14 0.50
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (10 bp):
TTTTAATGAT
Found at i:39201785 original size:6 final size:6
Alignment explanation
Indices: 39201774--39201802 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
39201764 AACCATTGAA
39201774 CATAAG CATAAG CATAAG CATAAG CATAA
1 CATAAG CATAAG CATAAG CATAAG CATAA
39201803 ACAAGAAGGA
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:0.52, C:0.17, G:0.14, T:0.17
Consensus pattern (6 bp):
CATAAG
Done.