Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 19 of 132
Found at i:5558062 original size:46 final size:46
Alignment explanation
Indices: 5557984--5558104 Score: 165
Period size: 48 Copynumber: 2.6 Consensus size: 46
5557974 ACAAAGTACT
* * *
5557984 GAGCACACAAAGTGCTAATCAGAGAGCAC-ACGA-AGTGCTAATCGGA
1 GAGCACACACAGTGCTAATCAGAGAGCACGA-GACA-TGCTAAACAGA
5558030 GAGCACACACAGTGCTAATAACAGAGAGCACGAGACATGCTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACGAGACATGCTAAACAGA
5558078 GAGCACACACAGTGCTAATCAGAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
5558105 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
46 26 0.38
48 40 0.59
49 2 0.03
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGAGACATGCTAAACAGA
Found at i:5564314 original size:22 final size:22
Alignment explanation
Indices: 5564266--5564308 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5564256 ATTTGTAATC
* *
5564266 TTTTAATTTTTTTCTTTCTTTG
1 TTTTCATTTTTTTCTCTCTTTG
*
5564288 TTTTCATTTTTTTGTCTCTTT
1 TTTTCATTTTTTTCTCTCTTT
5564309 TCTTTCTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.07, C:0.12, G:0.05, T:0.77
Consensus pattern (22 bp):
TTTTCATTTTTTTCTCTCTTTG
Found at i:5576879 original size:84 final size:84
Alignment explanation
Indices: 5576738--5576898 Score: 295
Period size: 84 Copynumber: 1.9 Consensus size: 84
5576728 ATTCTTTTGG
*
5576738 ATCATATTCATCTTTGCCTGCATTGCTTCCATCCAACAATCTTCATTTTCAGCTTCCTCAAAAGT
1 ATCATATTCATCTCTGCCTGCATTGCTTCCATCCAACAATCTTCATTTTCAGCTTCCTCAAAAGT
5576803 AGTTGGTTTCACTATGTGA
66 AGTTGGTTTCACTATGTGA
* *
5576822 ATCATATTCATCTCTGCCTGCATTGCTTCCATTCAACAATCTTCATTTTTAGCTTCCTCAAAAGT
1 ATCATATTCATCTCTGCCTGCATTGCTTCCATCCAACAATCTTCATTTTCAGCTTCCTCAAAAGT
5576887 AGTTGGTTTCAC
66 AGTTGGTTTCAC
5576899 AATGGTCATC
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 74 1.00
ACGTcount: A:0.24, C:0.25, G:0.11, T:0.40
Consensus pattern (84 bp):
ATCATATTCATCTCTGCCTGCATTGCTTCCATCCAACAATCTTCATTTTCAGCTTCCTCAAAAGT
AGTTGGTTTCACTATGTGA
Found at i:5577517 original size:126 final size:126
Alignment explanation
Indices: 5577356--5577608 Score: 488
Period size: 126 Copynumber: 2.0 Consensus size: 126
5577346 ATTGACTGCC
5577356 TCAACCTAAAAAGTGTTGAGAAGTTTGCTCTCAAATAGTAGGCACCTGGCCATATCAAGCACTGT
1 TCAACCTAAAAAGTGTTGAGAAGTTTGCTCTCAAATAGTAGGCACCTGGCCATATCAAGCACTGT
*
5577421 CTTGTTCTTCCTTTCACATACACCATTTTACTGTGATGTGTAAATGATGGTTAGTTGATGT
66 CTTGTTCTTCCTTTCACATACACCATTTTACTGTGATGTGTAAATGATAGTTAGTTGATGT
*
5577482 TCAACCTAAAAAGTGTTGAGAAGTTTGCTCTCAAATAGTAGGCACCTGGCCATATCAAGCATTGT
1 TCAACCTAAAAAGTGTTGAGAAGTTTGCTCTCAAATAGTAGGCACCTGGCCATATCAAGCACTGT
5577547 CTTGTTCTTCCTTTCACATACACCATTTTACTGTGATGTGTAAATGATAGTTAGTTGATGT
66 CTTGTTCTTCCTTTCACATACACCATTTTACTGTGATGTGTAAATGATAGTTAGTTGATGT
5577608 T
1 T
5577609 GAACTCCAAC
Statistics
Matches: 125, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 125 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (126 bp):
TCAACCTAAAAAGTGTTGAGAAGTTTGCTCTCAAATAGTAGGCACCTGGCCATATCAAGCACTGT
CTTGTTCTTCCTTTCACATACACCATTTTACTGTGATGTGTAAATGATAGTTAGTTGATGT
Found at i:5579058 original size:20 final size:20
Alignment explanation
Indices: 5579033--5579070 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5579023 TGGACAAGGG
*
5579033 CTGGTATTGCTCGATGCTCC
1 CTGGTACTGCTCGATGCTCC
5579053 CTGGTACTGCTCGATGCT
1 CTGGTACTGCTCGATGCT
5579071 TCCTAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.11, C:0.29, G:0.26, T:0.34
Consensus pattern (20 bp):
CTGGTACTGCTCGATGCTCC
Found at i:5583518 original size:20 final size:20
Alignment explanation
Indices: 5583493--5583549 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
5583483 TGGACAATGG
5583493 CTGGTATTGCTCGATGCTCC
1 CTGGTATTGCTCGATGCTCC
* * *
5583513 CTGGTACTGCTCAATGCTTC
1 CTGGTATTGCTCGATGCTCC
* * *
5583533 CTGATGTTGTTCGATGC
1 CTGGTATTGCTCGATGC
5583550 ATGTTGGTGC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.12, C:0.26, G:0.25, T:0.37
Consensus pattern (20 bp):
CTGGTATTGCTCGATGCTCC
Found at i:5587358 original size:31 final size:32
Alignment explanation
Indices: 5587318--5587380 Score: 110
Period size: 31 Copynumber: 2.0 Consensus size: 32
5587308 CACTGCGCTG
*
5587318 ATTTCTTTTTCATATACACATATATATATTAT
1 ATTTCTTTTTCATATACACATATATAAATTAT
5587350 ATTT-TTTTTCATATACACATATATAAATTAT
1 ATTTCTTTTTCATATACACATATATAAATTAT
5587381 TTCCGGAACC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 26 0.87
32 4 0.13
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (32 bp):
ATTTCTTTTTCATATACACATATATAAATTAT
Found at i:5612267 original size:11 final size:11
Alignment explanation
Indices: 5612251--5612309 Score: 77
Period size: 11 Copynumber: 5.4 Consensus size: 11
5612241 TACTTTGAAA
*
5612251 TTAAATTTATT
1 TTAAATTTAAT
5612262 TTAAATTTTAAT
1 TTAAA-TTTAAT
5612274 TT-AATTTAAAT
1 TTAAATTT-AAT
5612285 TTAAATTT-AT
1 TTAAATTTAAT
5612295 TTAAATTTAAT
1 TTAAATTTAAT
5612306 TTAA
1 TTAA
5612310 GTTAGAATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
10 13 0.30
11 18 0.42
12 12 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:5612276 original size:5 final size:5
Alignment explanation
Indices: 5612249--5612326 Score: 59
Period size: 5 Copynumber: 14.4 Consensus size: 5
5612239 TTTACTTTGA
* *
5612249 AATTA AATTT ATTTT AAATTTT AATTT AATTT AAATTT AAATTT -ATTT
1 AATTT AATTT AATTT -AA-TTT AATTT AATTT -AATTT -AATTT AATTT
*
5612297 AAATTT AATTT AAGTTAG AATTT AATTT AA
1 -AATTT AATTT AA-TT-T AATTT AATTT AA
5612327 AATTTAATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
4 4 0.07
5 30 0.49
6 22 0.36
7 5 0.08
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (5 bp):
AATTT
Found at i:5612296 original size:27 final size:27
Alignment explanation
Indices: 5612266--5612326 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
5612256 TTTATTTTAA
*
5612266 ATTTTAATTTAATTTAAATTTA-AATTT
1 ATTTTAATTTAATTT-AAGTTAGAATTT
*
5612293 ATTTAAATTTAATTTAAGTTAGAATTT
1 ATTTTAATTTAATTTAAGTTAGAATTT
*
5612320 AATTTAA
1 ATTTTAA
5612327 AATTTAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 5 0.17
27 24 0.83
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (27 bp):
ATTTTAATTTAATTTAAGTTAGAATTT
Found at i:5612303 original size:44 final size:46
Alignment explanation
Indices: 5612251--5612351 Score: 127
Period size: 44 Copynumber: 2.2 Consensus size: 46
5612241 TACTTTGAAA
* **
5612251 TTAAATTTATTTTAAATTTTAATTTAATTTAA-ATTTAA-ATT-TAT
1 TTAAATTTAATTTAAATTAGAATTTAATTTAAAATTTAATATTAT-T
*
5612295 TTAAATTTAATTTAAGTTAGAATTTAATTTAAAATTTAATATTATT
1 TTAAATTTAATTTAAATTAGAATTTAATTTAAAATTTAATATTATT
5612341 TGTAAATTTAA
1 T-TAAATTTAA
5612352 AATGTCCATT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
44 28 0.57
45 6 0.12
46 5 0.10
47 10 0.20
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (46 bp):
TTAAATTTAATTTAAATTAGAATTTAATTTAAAATTTAATATTATT
Found at i:5612320 original size:17 final size:16
Alignment explanation
Indices: 5612237--5612326 Score: 101
Period size: 17 Copynumber: 5.4 Consensus size: 16
5612227 ACCATTTTAG
* *
5612237 AATTTACTTTGAAATTA
1 AATTTAATTT-AAATTT
*
5612254 AATTTATTTTAAATTTT
1 AATTTAATTTAAA-TTT
5612271 AATTTAATTTAAATTT
1 AATTTAATTTAAATTT
5612287 AAATTT-ATTTAAATTT
1 -AATTTAATTTAAATTT
*
5612303 AATTTAAGTTAGAATTT
1 AATTTAATTTA-AATTT
5612320 AATTTAA
1 AATTTAA
5612327 AATTTAATAT
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
15 5 0.08
16 20 0.31
17 40 0.62
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (16 bp):
AATTTAATTTAAATTT
Found at i:5614226 original size:161 final size:162
Alignment explanation
Indices: 5613917--5614254 Score: 468
Period size: 161 Copynumber: 2.1 Consensus size: 162
5613907 GCTTTTTAAT
* *
5613917 TTAATCCTTTCACAT-TTTGAATGCACCAGATGATGCCACGTGTCACTTTTTGGCTTATTTCTGC
1 TTAATCCTTTAAC-TGTTTGAATGCACCAGAGGATGCCACGTGTCACTTTTTGGCTTATTTCTGC
* * *
5613981 ATTTAGTCTTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTTAACTACA
65 ATTTAGTCTCTTTTAGTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTCTTATTTAACTACA
* * *
5614046 AAATTGGCCCAACAATTTTTCAAGGTTTATAAA
130 AAATTGCCCCAACAATTTTTCAAAGTTTACAAA
* * * *
5614079 TTAGTCCTTTGACTGTTTGACTGCACCAG-GGACTGCCACGTGTC-CATTTTTGGCTTATTTCTT
1 TTAATCCTTTAACTGTTTGAATGCACCAGAGGA-TGCCACGTGTCAC-TTTTTGGCTTATTTCTG
* * *
5614142 CATTTAGT-TCTTTTAGTTTTAATTTGTTTTAATTTAATCTCCAAATCAACTCTTATTTAATTAT
64 CATTTAGTCTCTTTTAGTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTCTTATTTAACTAC
* *
5614206 AAAATTGCCCCAAGAATTTTTCAAAGTTTACAAT
129 AAAATTGCCCCAACAATTTTTCAAAGTTTACAAA
5614240 TTAATCCTTTAACTG
1 TTAATCCTTTAACTG
5614255 CTGGATGCCT
Statistics
Matches: 155, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
161 96 0.62
162 59 0.38
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.45
Consensus pattern (162 bp):
TTAATCCTTTAACTGTTTGAATGCACCAGAGGATGCCACGTGTCACTTTTTGGCTTATTTCTGCA
TTTAGTCTCTTTTAGTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTCTTATTTAACTACAA
AATTGCCCCAACAATTTTTCAAAGTTTACAAA
Found at i:5614407 original size:59 final size:59
Alignment explanation
Indices: 5614313--5614726 Score: 454
Period size: 59 Copynumber: 7.1 Consensus size: 59
5614303 GTTTATAGGT
* * *
5614313 CCCCGAAAC-TTCCAAAATTACCATTTTACCCCCAAACCTTT-TAAAATTCTATTTTTAA
1 CCCCGAAACTTTCAAAAATTACCATTTTACCCCCAAA-CTTTCCAAAATTCCATTTTTAA
* *
5614371 CCCCGAAACTTTCAAAAATTACCATTTTACCTCCAAACTTTCCAAAATTTCATTTTTAA
1 CCCCGAAACTTTCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAA
* * * *
5614430 CCCCAAAACTTCCAAAAAATACCATTTTACCCCCAAACTTTTCAAAATTCCA-TTTTAA
1 CCCCGAAACTTTCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAA
* * * **
5614488 ACCCGAAACTTCCAAAAATTACCATTTTACCTCTGAA-TTTCCAAAATTCCATTTTTAA
1 CCCCGAAACTTTCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAA
* * *
5614546 CCCC--AATTTCATCAAAAATTACCATTTTACCCCCGAACCTTCCAAAATTCCATTTTTAA
1 CCCCGAAACTT--TCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAA
* *
5614605 CCTCG--ATTTCATCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCA-TTTTAA
1 CCCCGAAACTT--TCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAA
*** ** * * *
5614663 CCCCGTTTC-ACCAAAAATAACCATTTTACCCCCCGAAC-TTCCAAAATCCCATTTTTAA
1 CCCCGAAACTTTCAAAAATTACCATTTTA-CCCCCAAACTTTCCAAAATTCCATTTTTAA
5614721 CCCCGA
1 CCCCGA
5614727 TTTCATCGTT
Statistics
Matches: 309, Mismatches: 36, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
56 4 0.01
57 41 0.13
58 111 0.36
59 153 0.50
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.32
Consensus pattern (59 bp):
CCCCGAAACTTTCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAA
Found at i:5614605 original size:175 final size:174
Alignment explanation
Indices: 5614314--5614733 Score: 510
Period size: 175 Copynumber: 2.4 Consensus size: 174
5614304 TTTATAGGTC
* * *
5614314 CCCGAAACTTCC-AAAATTACCATTTTACCCCCAAACCTTT-TAAAATTCTATTTTTAACCCCGA
1 CCCGAAACTTCCAAAAATTACCATTTTACCCCCGAA--TTTCCAAAATTCCATTTTTAACCCC--
* * * *
5614377 AACTT--TCAAAAATTACCATTTTACCTCCAAACTTTCCAAAATTTCATTTTTAACCCCAAAACT
62 AATTTCATCAAAAATTACCATTTTACCCCCAAACCTTCCAAAATTCCATTTTTAACCCC--AACT
*
5614440 TC-CAAAAAATACCATTTTACCCCCAAACTTTTCAAAATTCCATTTTAAA
125 TCACAAAAAATACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTAAA
* *
5614489 CCCGAAACTTCCAAAAATTACCATTTTACCTCTGAATTTCCAAAATTCCATTTTTAACCCCAATT
1 CCCGAAACTTCCAAAAATTACCATTTTACCCCCGAATTTCCAAAATTCCATTTTTAACCCCAATT
* * * *
5614554 TCATCAAAAATTACCATTTTACCCCCGAACCTTCCAAAATTCCATTTTTAACCTCGATTTCATCA
66 TCATCAAAAATTACCATTTTACCCCCAAACCTTCCAAAATTCCATTTTTAACCCCAACTTCA-CA
* *
5614619 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTAAC
130 AAAAATACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTAAA
*** * * * * *
5614664 CCCGTTTC-ACCAAAAATAACCATTTTACCCCCCGAACTTCCAAAATCCCATTTTTAACCCCGAT
1 CCCGAAACTTCCAAAAATTACCATTTTA-CCCCCGAATTTCCAAAATTCCATTTTTAACCCCAAT
5614728 TTCATC
65 TTCATC
5614734 GTTTCTTATT
Statistics
Matches: 212, Mismatches: 26, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
173 8 0.04
174 20 0.09
175 164 0.77
176 20 0.09
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.33
Consensus pattern (174 bp):
CCCGAAACTTCCAAAAATTACCATTTTACCCCCGAATTTCCAAAATTCCATTTTTAACCCCAATT
TCATCAAAAATTACCATTTTACCCCCAAACCTTCCAAAATTCCATTTTTAACCCCAACTTCACAA
AAAATACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTAAA
Found at i:5614708 original size:29 final size:27
Alignment explanation
Indices: 5614313--5614726 Score: 188
Period size: 29 Copynumber: 14.2 Consensus size: 27
5614303 GTTTATAGGT
5614313 CCCCGAAACTTCCAAAATTACCATTTTAC
1 CCCCG-AACTTCCAAAA-TACCATTTTAC
* ** * * *
5614342 CCCCAAACCTTTTAAAATTCTATTTTTAA
1 CCCCGAA-CTTCCAAAATACCA-TTTTAC
*
5614371 CCCCGAAACTTTCAAAAATTACCATTTTAC
1 CCCCG-AAC-TTCCAAAA-TACCATTTTAC
* * **
5614401 CTCCAAACTTTCCAAAATTTCATTTTTAAC
1 CCCCGAAC-TTCCAAAATACCA-TTTT-AC
**
5614431 CCCAAAACTTCCAAAAAATACCATTTTAC
1 CCCCGAACTTCC--AAAATACCATTTTAC
* * * *
5614460 CCCCAAACTTTTCAAAATTCCATTTTAA
1 CCCCGAAC-TTCCAAAATACCATTTTAC
*
5614488 ACCCGAAACTTCCAAAAATTACCATTTTAC
1 CCCCG-AACTTCC-AAAA-TACCATTTTAC
* * * * *
5614518 CTCTGAATTTCCAAAATTCCATTTTTAA
1 CCCCGAACTTCCAAAATACCA-TTTTAC
*
5614546 CCCC-AATTTCATCAAAAATTACCATTTTAC
1 CCCCGAACTTC--C-AAAA-TACCATTTTAC
* *
5614576 CCCCGAACCTTCCAAAATTCCATTTTTAA
1 CCCCGAA-CTTCCAAAATACCA-TTTTAC
* *
5614605 CCTCG-ATTTCATCAAAAATTACCATTTTAC
1 CCCCGAACTTC--C-AAAA-TACCATTTTAC
* * *
5614635 CCCCAAACTTTCCAAAATTCCATTTTAA
1 CCCCGAAC-TTCCAAAATACCATTTTAC
*
5614663 CCCCG--TTTCACCAAAAATAACCATTTTACC
1 CCCCGAACTT--CC-AAAAT-ACCATTTTA-C
* *
5614693 CCCCGAACTTCCAAAATCCCATTTTTAA
1 CCCCGAACTTCCAAAATACCA-TTTTAC
5614721 CCCCGA
1 CCCCGA
5614727 TTTCATCGTT
Statistics
Matches: 291, Mismatches: 59, Indels: 71
0.69 0.14 0.17
Matches are distributed among these distances:
25 2 0.01
27 15 0.05
28 70 0.24
29 99 0.34
30 76 0.26
31 21 0.07
32 8 0.03
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.32
Consensus pattern (27 bp):
CCCCGAACTTCCAAAATACCATTTTAC
Found at i:5615896 original size:3 final size:3
Alignment explanation
Indices: 5615888--5615939 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
5615878 CCATAACAAT
5615888 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5615936 ATA A
1 ATA A
5615940 AGCTAACAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5618820 original size:2 final size:2
Alignment explanation
Indices: 5618813--5618867 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
5618803 TATCTTTTAA
5618813 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5618855 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
5618868 CATGTAAATG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5620913 original size:30 final size:30
Alignment explanation
Indices: 5620879--5620954 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 30
5620869 TGGCAAAATC
5620879 GGGGTAAAAATGTAATATT-AGAAAAGTTTT
1 GGGGTAAAAATGTAATATTCA-AAAAGTTTT
* *
5620909 GGGGTTAAAATGTAATTTTCAAAAAGTTTT
1 GGGGTAAAAATGTAATATTCAAAAAGTTTT
* *
5620939 GGGGTCAAAATATAAT
1 GGGGTAAAAATGTAAT
5620955 TTTTGGGCAG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 40 0.98
31 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (30 bp):
GGGGTAAAAATGTAATATTCAAAAAGTTTT
Found at i:5622072 original size:21 final size:22
Alignment explanation
Indices: 5622032--5622072 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5622022 CTTTCGTTTT
*
5622032 TTTATTTTATTATTACTAAATA
1 TTTATTTTATTATCACTAAATA
*
5622054 TTTA-TTTATTATCATTAAA
1 TTTATTTTATTATCACTAAA
5622073 CAACATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTATTTTATTATCACTAAATA
Found at i:5622882 original size:17 final size:17
Alignment explanation
Indices: 5622862--5622896 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5622852 AATTCAAATT
*
5622862 TAAATTTAATTTTAAAA
1 TAAATTTAATTTCAAAA
5622879 TAAATTTAATTTCAAAA
1 TAAATTTAATTTCAAAA
5622896 T
1 T
5622897 GGTTTGGGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAATTTAATTTCAAAA
Found at i:5622890 original size:5 final size:6
Alignment explanation
Indices: 5622841--5622887 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
5622831 AATAATATTG
* * *
5622841 AATTTA AA-TTA AATTCA AATTTA AATTTA ATTTTA AA-ATA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
5622887 A
1 A
5622888 TTTCAAAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
5 9 0.27
6 24 0.73
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:5624147 original size:18 final size:18
Alignment explanation
Indices: 5624113--5624151 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5624103 TTAATGTCCA
5624113 TATTTAATAATTAATTAT
1 TATTTAATAATTAATTAT
*
5624131 TATTTTATATATT-ATTAT
1 TATTTAATA-ATTAATTAT
5624149 TAT
1 TAT
5624152 CTTCAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTAATAATTAATTAT
Found at i:5629644 original size:16 final size:16
Alignment explanation
Indices: 5629612--5629652 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
5629602 ATAGTAAAAA
5629612 TATAATTTTATTATTT
1 TATAATTTTATTATTT
*
5629628 TATTATTTTA-TATTTT
1 TATAATTTTATTA-TTT
5629644 TATAATTTT
1 TATAATTTT
5629653 TAAAGAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 2 0.09
16 20 0.91
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATAATTTTATTATTT
Found at i:5630020 original size:17 final size:15
Alignment explanation
Indices: 5629998--5630109 Score: 89
Period size: 17 Copynumber: 6.7 Consensus size: 15
5629988 AACCATTTTA
5629998 AAATTTACTTTGAAATT
1 AAATTTA-TTT-AAATT
5630015 AAATTTATTTTAAATTT
1 AAATTTA-TTTAAA-TT
*
5630032 TAATTTAATTTAAATTT
1 AAATTT-ATTTAAA-TT
5630049 AAATTTATTTAAATTT
1 AAATTTATTTAAA-TT
*
5630065 AAATTTAATTTAAGTT
1 AAATTT-ATTTAAATT
5630081 AGAATTTAATTTAAAATT
1 A-AATTT-ATTT-AAATT
*
5630099 TAATATTATTT
1 AAAT-TTATTT
5630110 GTAAATTTAA
Statistics
Matches: 83, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
16 22 0.27
17 54 0.65
18 7 0.08
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.54
Consensus pattern (15 bp):
AAATTTATTTAAATT
Found at i:5630036 original size:22 final size:22
Alignment explanation
Indices: 5630011--5630120 Score: 100
Period size: 22 Copynumber: 4.9 Consensus size: 22
5630001 TTTACTTTGA
*
5630011 AATTAAATTT-ATTTTAAATTTT
1 AATTAAATTTAAATTTAAA-TTT
*
5630033 AATTTAATTTAAATTTAAATTT
1 AATTAAATTTAAATTTAAATTT
*
5630055 ATTTAAATTTAAATTT-AATTT
1 AATTAAATTTAAATTTAAATTT
5630076 AAGTTAGAATTT-AATTTAAAATTT
1 AA-TTA-AATTTAAATTT-AAATTT
* *
5630100 AATATTATTTGTAAATTTAAA
1 AAT-TAAATT-TAAATTTAAA
5630121 ATGTCCATTA
Statistics
Matches: 73, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
21 6 0.08
22 34 0.47
23 16 0.22
24 12 0.16
25 5 0.07
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (22 bp):
AATTAAATTTAAATTTAAATTT
Found at i:5630047 original size:6 final size:6
Alignment explanation
Indices: 5630013--5630101 Score: 84
Period size: 6 Copynumber: 15.7 Consensus size: 6
5630003 TACTTTGAAA
* *
5630013 TTAAAT TT-ATT TTAAAT TTTAAT TT-AAT TTAAAT TTAAAT TT--AT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
5630057 TTAAAT TTAAAT TT-AAT TT-AAG TTAGAAT TT-AAT TTAAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTA-AAT TTAAAT TT-AAAT TTAA
5630102 TATTATTTGT
Statistics
Matches: 70, Mismatches: 5, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.06
5 23 0.33
6 34 0.49
7 9 0.13
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (6 bp):
TTAAAT
Found at i:5630102 original size:12 final size:11
Alignment explanation
Indices: 5630013--5630102 Score: 96
Period size: 12 Copynumber: 8.0 Consensus size: 11
5630003 TACTTTGAAA
*
5630013 TTAAATTTATT
1 TTAAATTTAAT
5630024 TTAAATTTTAAT
1 TTAAA-TTTAAT
5630036 TT-AATTTAAAT
1 TTAAATTT-AAT
5630047 TTAAATTT-AT
1 TTAAATTTAAT
5630057 TTAAATTTAAAT
1 TTAAATTT-AAT
*
5630069 TT-AATTTAAG
1 TTAAATTTAAT
5630079 TTAGAATTTAAT
1 TTA-AATTTAAT
5630091 TTAAAATTTAAT
1 TT-AAATTTAAT
5630103 ATTATTTGTA
Statistics
Matches: 68, Mismatches: 3, Indels: 15
0.79 0.03 0.17
Matches are distributed among these distances:
10 17 0.25
11 17 0.25
12 33 0.49
13 1 0.01
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:5630825 original size:10 final size:10
Alignment explanation
Indices: 5630810--5630878 Score: 56
Period size: 10 Copynumber: 7.2 Consensus size: 10
5630800 TTTGAATAGC
*
5630810 ATTAATAATT
1 ATTAATAATA
5630820 ATTAATGAA-A
1 ATTAAT-AATA
* *
5630830 A-TATTAACA
1 ATTAATAATA
5630839 A-TAATAATA
1 ATTAATAATA
5630848 ATT-ATAATA
1 ATTAATAATA
*
5630857 AATAATAATA
1 ATTAATAATA
*
5630867 ATAAATAATA
1 ATTAATAATA
5630877 AT
1 AT
5630879 GAATTTTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
8 2 0.04
9 20 0.42
10 24 0.50
11 2 0.04
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (10 bp):
ATTAATAATA
Found at i:5630862 original size:13 final size:13
Alignment explanation
Indices: 5630838--5630878 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
5630828 AAATATTAAC
5630838 AATAAT-AATAAT
1 AATAATAAATAAT
*
5630850 TATAATAAATAAT
1 AATAATAAATAAT
5630863 AATAATAAATAAT
1 AATAATAAATAAT
5630876 AAT
1 AAT
5630879 GAATTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 5 0.19
13 21 0.81
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AATAATAAATAAT
Found at i:5630898 original size:3 final size:3
Alignment explanation
Indices: 5630838--5630878 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
5630828 AAATATTAAC
*
5630838 AAT AAT AAT AAT TAT AAT AAAT AAT AAT AAT AAAT AAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT -AAT AAT AAT
5630879 GAATTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 28 0.82
4 6 0.18
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:5631969 original size:28 final size:27
Alignment explanation
Indices: 5631931--5632212 Score: 134
Period size: 29 Copynumber: 9.7 Consensus size: 27
5631921 TGAAACTTCC
*
5631931 AAAATTACCATTTTACCACCAAACCTTTT
1 AAAATTACCATTTTACC-CCAAA-CTTTA
*
5631960 AAAATT-CCATTTTAACCCCGAAACTTCCA
1 AAAATTACCATTTT-ACCCC-AAACTT-TA
*
5631989 AAAATTACCATTTTACCCCCGAACTTTCA
1 AAAATTACCATTTTA-CCCCAAACTTT-A
*
5632018 AAAATT-CCATTTTTAACCCC-GA-TTTCACCA
1 AAAATTACCA-TTTT-ACCCCAAACTTT----A
5632048 AAAATTACCATTTTACCCCTAAACTTTCA
1 AAAATTACCATTTTACCCC-AAACTTT-A
* *
5632077 AAAATT-CCATTTTTAACCCC-GATTTCATCA
1 AAAATTACCA-TTTT-ACCCCAAACTT--T-A
**
5632107 AAAATTACCATTTTACCCCTAAACTTCC
1 AAAATTACCATTTTACCCC-AAACTTTA
*
5632135 AAAATT-CCATTTTTAACCCC-GA-TTTCACCA
1 AAAATTACCA-TTTT-ACCCCAAACTTT----A
*
5632165 AAAATTACCATTTTACCCCCAAACTTTCC
1 AAAATTACCATTTTA-CCCCAAACTTT-A
5632194 AAAATT-CCATTTTAACCCC
1 AAAATTACCATTTT-ACCCC
5632213 GATTTCACCA
Statistics
Matches: 203, Mismatches: 17, Indels: 67
0.71 0.06 0.23
Matches are distributed among these distances:
26 2 0.01
27 7 0.03
28 43 0.21
29 75 0.37
30 56 0.28
31 14 0.07
32 6 0.03
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.33
Consensus pattern (27 bp):
AAAATTACCATTTTACCCCAAACTTTA
Found at i:5632061 original size:59 final size:59
Alignment explanation
Indices: 5631931--5632241 Score: 456
Period size: 59 Copynumber: 5.3 Consensus size: 59
5631921 TGAAACTTCC
* * *
5631931 AAAATTACCATTTTACCACCAAACCTTT-TAAAATTCCA-TTTTAACCCCGAAACTT--CCA
1 AAAATTACCATTTTACCCCCAAA-CTTTCAAAAATTCCATTTTTAACCCCG--ATTTCACCA
*
5631989 AAAATTACCATTTTACCCCCGAACTTTCAAAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCAAACTTTCAAAAATTCCATTTTTAACCCCGATTTCACCA
* *
5632048 AAAATTACCATTTTACCCCTAAACTTTCAAAAATTCCATTTTTAACCCCGATTTCATCA
1 AAAATTACCATTTTACCCCCAAACTTTCAAAAATTCCATTTTTAACCCCGATTTCACCA
* *
5632107 AAAATTACCATTTTACCCCTAAAC-TTCCAAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCAAACTTTCAAAAATTCCATTTTTAACCCCGATTTCACCA
*
5632165 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCACC-
1 AAAATTACCATTTTACCCCCAAACTTTCAAAAATTCCATTTTTAACCCCGATTTCACCA
*
5632222 AAAATTACCATTTTGCCCCC
1 AAAATTACCATTTTACCCCC
5632242 GGGTATCCAA
Statistics
Matches: 237, Mismatches: 11, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
57 26 0.11
58 104 0.44
59 107 0.45
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.32
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCAAACTTTCAAAAATTCCATTTTTAACCCCGATTTCACCA
Found at i:5632147 original size:117 final size:115
Alignment explanation
Indices: 5631931--5632241 Score: 457
Period size: 117 Copynumber: 2.7 Consensus size: 115
5631921 TGAAACTTCC
* *
5631931 AAAATTACCATTTTACCACCAAACCTTT-TAAAATTCCATTTTAACCCCGAAACTTC-CAAAAAT
1 AAAATTACCATTTTACC-CCAAA-CTTTCAAAAATTCCATTTTAACCCCG--ATTTCACAAAAAT
*
5631994 TACCATTTTACCCCCGAACTTTCAAAAATTCCATTTTTAACCCCGATTTCACCA
62 TACCATTTTACCCCCAAACTTTCAAAAATTCCATTTTTAACCCCGATTTCACCA
5632048 AAAATTACCATTTTACCCCTAAACTTTCAAAAATTCCATTTTTAACCCCGATTTCATCAAAAATT
1 AAAATTACCATTTTACCCC-AAACTTTCAAAAATTCCA-TTTTAACCCCGATTTCA-CAAAAATT
* *
5632113 ACCATTTTACCCCTAAAC-TTCCAAAATTCCATTTTTAACCCCGATTTCACCA
63 ACCATTTTACCCCCAAACTTTCAAAAATTCCATTTTTAACCCCGATTTCACCA
* *
5632165 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTAACCCCGATTTCACCAAAATTAC
1 AAAATTACCATTTTA-CCCCAAACTTTCAAAAATTCCATTTTAACCCCGATTTCACAAAAATTAC
*
5632230 CATTTTGCCCCC
65 CATTTTACCCCC
5632242 GGGTATCCAA
Statistics
Matches: 179, Mismatches: 9, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
115 19 0.11
116 27 0.15
117 94 0.53
118 39 0.22
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.32
Consensus pattern (115 bp):
AAAATTACCATTTTACCCCAAACTTTCAAAAATTCCATTTTAACCCCGATTTCACAAAAATTACC
ATTTTACCCCCAAACTTTCAAAAATTCCATTTTTAACCCCGATTTCACCA
Found at i:5633634 original size:42 final size:43
Alignment explanation
Indices: 5633574--5633688 Score: 160
Period size: 42 Copynumber: 2.7 Consensus size: 43
5633564 GTTTATGAGG
*
5633574 AAAAACGCCGCTATAGAACATGGTCTTTAGCGACGC-TTCCCC
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTTCCCC
* * * * *
5633616 AAAAACGCCACTAAAGAACATGATCTTTAGCGGCGCTTTTCTC
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTTCCCC
*
5633659 ACAAACGCCGCTAAAGAACATGGTCTTTAG
1 AAAAACGCCGCTAAAGAACATGGTCTTTAG
5633689 TGGCATTTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
42 32 0.51
43 31 0.49
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTTCCCC
Found at i:5633679 original size:43 final size:43
Alignment explanation
Indices: 5633576--5633715 Score: 165
Period size: 43 Copynumber: 3.3 Consensus size: 43
5633566 TTATGAGGAA
* * * * * *
5633576 AAACGCCGCTATAGAACATGGTCTTTAGCGACGC-TTCCCCAA
1 AAACGCCACTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCAC
*
5633618 AAACGCCACTAAAGAACATGATCTTTAGCGGCGCTTTTCTCAC
1 AAACGCCACTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCAC
* * ** *
5633661 AAACGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTGTCAC
1 AAACGCCACTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCAC
5633704 AAACGCCACTAA
1 AAACGCCACTAA
5633716 TATTAACAAA
Statistics
Matches: 83, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 30 0.36
43 53 0.64
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (43 bp):
AAACGCCACTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCAC
Found at i:5633985 original size:41 final size:41
Alignment explanation
Indices: 5633928--5634069 Score: 214
Period size: 41 Copynumber: 3.5 Consensus size: 41
5633918 ACAAGCTAAA
* * *
5633928 ATTGCTCTGACCTTTAGCTGCGCTAGGCCATAAGCGCCGCT
1 ATTGCTCTGACCTTTAGCGGTGCTTGGCCATAAGCGCCGCT
*
5633969 ATTGCTCTGACCTTTAGCGGTGCTTGGCCTTAAGCGCCGCT
1 ATTGCTCTGACCTTTAGCGGTGCTTGGCCATAAGCGCCGCT
* *
5634010 ATTGCTCTGACCTTTAGCGGTGCTTGACCGTAAGCGCCGCT
1 ATTGCTCTGACCTTTAGCGGTGCTTGGCCATAAGCGCCGCT
*
5634051 ATTGCTCT-ACCTTTTGCGG
1 ATTGCTCTGACCTTTAGCGG
5634070 CGTTTTTTGT
Statistics
Matches: 94, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
40 10 0.11
41 84 0.89
ACGTcount: A:0.14, C:0.30, G:0.25, T:0.31
Consensus pattern (41 bp):
ATTGCTCTGACCTTTAGCGGTGCTTGGCCATAAGCGCCGCT
Found at i:5640390 original size:30 final size:30
Alignment explanation
Indices: 5640356--5640435 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 30
5640346 AAAGAAACAA
5640356 TTTTAAAAAATAAATATGTTATATAAATAT-
1 TTTTAAAAAATAAATATGTTATATAAAT-TC
* *
5640386 TTTTAAAATATATATAT-TCTATATAAATTC
1 TTTTAAAAAATAAATATGT-TATATAAATTC
5640416 TTTTAAAAAAATAAA-ATGTT
1 TTTT-AAAAAATAAATATGTT
5640436 GTTTCAACTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
29 2 0.05
30 31 0.74
31 9 0.21
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (30 bp):
TTTTAAAAAATAAATATGTTATATAAATTC
Found at i:5646545 original size:18 final size:18
Alignment explanation
Indices: 5646511--5646565 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
5646501 AATTAAAAAG
*
5646511 TATAAAT-TTTGAAATTT
1 TATAAATATTTTAAATTT
5646528 TATAAATATTTTAAATTT
1 TATAAATATTTTAAATTT
*
5646546 TAAAAATTATTTTAAATTT
1 TATAAA-TATTTTAAATTT
5646565 T
1 T
5646566 TGAAAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.21
18 14 0.41
19 13 0.38
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
TATAAATATTTTAAATTT
Found at i:5646571 original size:20 final size:19
Alignment explanation
Indices: 5646516--5646578 Score: 83
Period size: 20 Copynumber: 3.3 Consensus size: 19
5646506 AAAAGTATAA
*
5646516 ATTTTGAAATTTTATAAA-T
1 ATTTT-AAATTTTAAAAATT
5646535 ATTTTAAATTTTAAAAATT
1 ATTTTAAATTTTAAAAATT
*
5646554 ATTTTAAATTTTTGAAAATT
1 ATTTTAAA-TTTTAAAAATT
5646574 ATTTT
1 ATTTT
5646579 GATTGTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
18 11 0.28
19 14 0.35
20 15 0.38
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
ATTTTAAATTTTAAAAATT
Found at i:5650815 original size:2 final size:2
Alignment explanation
Indices: 5650808--5650841 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5650798 TCCCTTTCAA
*
5650808 AT AT AT AT AT AT AT AT AT GT 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
5650842 TTTTGTAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5652319 original size:22 final size:23
Alignment explanation
Indices: 5652294--5652341 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
5652284 ACATATTTTT
*
5652294 AAATATACTTAAT-TTTTTACTC
1 AAATAAACTTAATATTTTTACTC
5652316 AAATAAACTTAATATTTTTACTC
1 AAATAAACTTAATATTTTTACTC
5652339 AAA
1 AAA
5652342 CTATTTTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATAAACTTAATATTTTTACTC
Found at i:5658900 original size:2 final size:2
Alignment explanation
Indices: 5658893--5658933 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5658883 ATACATCTAT
5658893 TA 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 TA T
5658934 TAAATACAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5660285 original size:111 final size:110
Alignment explanation
Indices: 5660133--5660356 Score: 385
Period size: 111 Copynumber: 2.0 Consensus size: 110
5660123 GGTGTTCATA
*
5660133 TTGGATGTTCATTGCTTAATAGATGGTTCTGTATTGAATATTAATAATGGCTCCTACAATAATGA
1 TTGGATATTCATTGCTTAATAGATGGTTCTGTATTGAATATTAATAATGGCTCCTACAATAATGA
* *
5660198 AAAGTGATTATTGTTCTTTTTTCTTCTTCAAGCTTTCAAGATATT
66 AAAATAATTATTGTTCTTTTTTCTTCTTCAAGCTTTCAAGATATT
*
5660243 TTGGATATTCATTGCTTAATTAGATGGTTCTGTATTGAATATTAATAATGGCTCCTACAGTAATG
1 TTGGATATTCATTGCTTAA-TAGATGGTTCTGTATTGAATATTAATAATGGCTCCTACAATAATG
* *
5660308 AAAAATAATTGTTGTTCTTTTTTCTTCTTCAAGCTTTTAAGATATT
65 AAAAATAATTATTGTTCTTTTTTCTTCTTCAAGCTTTCAAGATATT
5660354 TTG
1 TTG
5660357 ATTATATATG
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
110 18 0.17
111 89 0.83
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (110 bp):
TTGGATATTCATTGCTTAATAGATGGTTCTGTATTGAATATTAATAATGGCTCCTACAATAATGA
AAAATAATTATTGTTCTTTTTTCTTCTTCAAGCTTTCAAGATATT
Found at i:5671527 original size:33 final size:33
Alignment explanation
Indices: 5671485--5671551 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
5671475 CCAATATAAT
5671485 AATTTTCATTTGTTCTCGTTCTTTTAAAGTTTA
1 AATTTTCATTTGTTCTCGTTCTTTTAAAGTTTA
5671518 AATTTTCATTTGTTCTCGTTCTTTTAAAGTTTA
1 AATTTTCATTTGTTCTCGTTCTTTTAAAGTTTA
5671551 A
1 A
5671552 CCCTCAATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.22, C:0.12, G:0.09, T:0.57
Consensus pattern (33 bp):
AATTTTCATTTGTTCTCGTTCTTTTAAAGTTTA
Found at i:5681332 original size:7 final size:7
Alignment explanation
Indices: 5681320--5681391 Score: 117
Period size: 7 Copynumber: 10.3 Consensus size: 7
5681310 CCAACCCATC
5681320 TTCCTAA
1 TTCCTAA
5681327 TTCCTAA
1 TTCCTAA
5681334 TTCCTAA
1 TTCCTAA
5681341 TTCCTAA
1 TTCCTAA
5681348 TTCCTAA
1 TTCCTAA
5681355 TTCCTAA
1 TTCCTAA
*
5681362 TTCTTAA
1 TTCCTAA
*
5681369 TTCCTAC
1 TTCCTAA
5681376 TTCCTAA
1 TTCCTAA
*
5681383 GTCCTAA
1 TTCCTAA
5681390 TT
1 TT
5681392 ATGTTCTTAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 59 1.00
ACGTcount: A:0.26, C:0.28, G:0.01, T:0.44
Consensus pattern (7 bp):
TTCCTAA
Found at i:5688613 original size:23 final size:23
Alignment explanation
Indices: 5688586--5688629 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
5688576 TTCCTTTAAC
5688586 TTAATCGAACATGTTCACGAACA
1 TTAATCGAACATGTTCACGAACA
*
5688609 TTAATCGAATATGTTCACGAA
1 TTAATCGAACATGTTCACGAA
5688630 TAATATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAACA
Found at i:5694475 original size:22 final size:23
Alignment explanation
Indices: 5694428--5694476 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 23
5694418 GATTTCAAAG
5694428 TTAATCTACTTCAAATATGAAATT
1 TTAATCTACTTCAAATA-GAAATT
5694452 TTAATCTACTTCAAATA-AAATT
1 TTAATCTACTTCAAATAGAAATT
5694474 TTA
1 TTA
5694477 TTTTTGGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 8 0.32
24 17 0.68
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43
Consensus pattern (23 bp):
TTAATCTACTTCAAATAGAAATT
Found at i:5695365 original size:27 final size:28
Alignment explanation
Indices: 5695324--5695386 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
5695314 AATGATTTAA
* * *
5695324 TTTTAATAAATTTTACCACTTTTAATAT
1 TTTTAATAAACTTTAACAATTTTAATAT
* *
5695352 TTTTAA-AAACTTTAATAATTTTTATAT
1 TTTTAATAAACTTTAACAATTTTAATAT
5695379 TTTTAATA
1 TTTTAATA
5695387 TTTTTTATGG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTTAATAAACTTTAACAATTTTAATAT
Found at i:5695382 original size:8 final size:9
Alignment explanation
Indices: 5695343--5695391 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
5695333 ATTTTACCAC
5695343 TTTTAATAT
1 TTTTAATAT
* *
5695352 TTTTAAAAA
1 TTTTAATAT
*
5695361 CTTTAATAAT
1 TTTTAAT-AT
5695371 TTTT-ATAT
1 TTTTAATAT
5695379 TTTTAATAT
1 TTTTAATAT
5695388 TTTT
1 TTTT
5695392 TATGGCTGGT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
8 6 0.19
9 22 0.69
10 4 0.12
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTTAATAT
Found at i:5695383 original size:18 final size:18
Alignment explanation
Indices: 5695298--5695394 Score: 58
Period size: 18 Copynumber: 5.4 Consensus size: 18
5695288 AAATTTAATT
5695298 TTTTTATGATTTTT-ATAA
1 TTTTTAT-ATTTTTAATAA
*
5695316 TGATTTA-A-TTTTAATAA
1 T-TTTTATATTTTTAATAA
* * *
5695333 ATTTTACCACTTTTAAT-A
1 TTTTTA-TATTTTTAATAA
* **
5695351 TTTTTAAAAACTTTAATAA
1 TTTTT-ATATTTTTAATAA
*
5695370 TTTTTATATTTTTAATAT
1 TTTTTATATTTTTAATAA
5695388 TTTTTAT
1 TTTTTAT
5695395 GGCTGGTCAA
Statistics
Matches: 61, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
16 8 0.13
17 5 0.08
18 30 0.49
19 18 0.30
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTTATATTTTTAATAA
Found at i:5696811 original size:3 final size:3
Alignment explanation
Indices: 5696803--5696851 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
5696793 TTCCTTTCTT
5696803 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5696851 T
1 T
5696852 CTTTCTGACG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5712325 original size:15 final size:16
Alignment explanation
Indices: 5712297--5712334 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
5712287 AAGGACAAAA
*
5712297 AGAAATTCCTTTACTT
1 AGAAATTCCTTTACAT
*
5712313 AGAATTTCC-TTACAT
1 AGAAATTCCTTTACAT
5712328 AGAAATT
1 AGAAATT
5712335 AAAAAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (16 bp):
AGAAATTCCTTTACAT
Found at i:5722786 original size:30 final size:30
Alignment explanation
Indices: 5722733--5722816 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 30
5722723 AGTTTTTAAG
**
5722733 AGTTTAG-GGTCAAAATGCGATTTTGGGAA
1 AGTTTAGAGGTCAAAATGTAATTTTGGGAA
* *
5722762 AGTTTAGAGGTCAAAATATAATTTTTGGAA
1 AGTTTAGAGGTCAAAATGTAATTTTGGGAA
* *
5722792 AGCTCA-AGGGTCAAAATGTAATTTT
1 AGTTTAGA-GGTCAAAATGTAATTTT
5722817 TGAGAAGTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
29 8 0.17
30 38 0.83
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (30 bp):
AGTTTAGAGGTCAAAATGTAATTTTGGGAA
Found at i:5722839 original size:30 final size:30
Alignment explanation
Indices: 5722804--5722916 Score: 136
Period size: 30 Copynumber: 3.8 Consensus size: 30
5722794 CTCAAGGGTC
* *
5722804 AAAATGTAATTTTTGAGAAGTTCGAGAGTT
1 AAAATGTAATTTTAGAGAAGTTTGAGAGTT
* * * **
5722834 GAAATGTAATTTTAGAGAATTTTAAGAGAC
1 AAAATGTAATTTTAGAGAAGTTTGAGAGTT
* *
5722864 AAAATGTAATTTTAGAGAACTTTGAGGGTT
1 AAAATGTAATTTTAGAGAAGTTTGAGAGTT
*
5722894 AAAATGTAATTTTAAAGAAGTTT
1 AAAATGTAATTTTAGAGAAGTTT
5722917 AGGGGTCGAT
Statistics
Matches: 68, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 68 1.00
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.36
Consensus pattern (30 bp):
AAAATGTAATTTTAGAGAAGTTTGAGAGTT
Found at i:5722844 original size:60 final size:61
Alignment explanation
Indices: 5722774--5722906 Score: 144
Period size: 60 Copynumber: 2.2 Consensus size: 61
5722764 TTTAGAGGTC
* * * * * *
5722774 AAAATATAATTTTTGGA-AAGCTCAAGGGTCAAAATGTAATTTTTGAGAAGTTCGAGAGTT
1 AAAATGTAATTTTTAGAGAAGCTCAAGAGACAAAATGTAATTTTAGAGAACTTCGAGAGTT
* ** * * *
5722834 GAAATGTAA-TTTTAGAGAATTTTAAGAGACAAAATGTAATTTTAGAGAACTTTGAGGGTT
1 AAAATGTAATTTTTAGAGAAGCTCAAGAGACAAAATGTAATTTTAGAGAACTTCGAGAGTT
5722894 AAAATGTAATTTT
1 AAAATGTAATTTT
5722907 AAAGAAGTTT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
59 6 0.10
60 49 0.84
61 3 0.05
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.35
Consensus pattern (61 bp):
AAAATGTAATTTTTAGAGAAGCTCAAGAGACAAAATGTAATTTTAGAGAACTTCGAGAGTT
Found at i:5722907 original size:60 final size:60
Alignment explanation
Indices: 5722803--5722917 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
5722793 GCTCAAGGGT
* * * * *
5722803 CAAAATGTAATTTTTGAGAAGTTCGAGAGTTGAAATGTAATTTTAGAGAATTTTAAGAGA
1 CAAAATGTAATTTTAGAGAACTTCGAGAGTTAAAATGTAATTTTAAAGAAGTTTAAGAGA
* *
5722863 CAAAATGTAATTTTAGAGAACTTTGAGGGTTAAAATGTAATTTTAAAGAAGTTTA
1 CAAAATGTAATTTTAGAGAACTTCGAGAGTTAAAATGTAATTTTAAAGAAGTTTA
5722918 GGGGTCGATT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.36
Consensus pattern (60 bp):
CAAAATGTAATTTTAGAGAACTTCGAGAGTTAAAATGTAATTTTAAAGAAGTTTAAGAGA
Found at i:5723250 original size:203 final size:203
Alignment explanation
Indices: 5722901--5723300 Score: 755
Period size: 203 Copynumber: 2.0 Consensus size: 203
5722891 GTTAAAATGT
*
5722901 AATTTTAAAGAAGTTTAGGGGTCGATTGGGCAATAAACCCAAAAAATTTTGACACGTGATAGCTT
1 AATTTTAAAGAAGTTTAAGGGTCGATTGGGCAATAAACCCAAAAAATTTTGACACGTGATAGCTT
5722966 TTTAGGCCTCCAAAATGTTGAGGGACCAATTTGAAAAACAATTAAAATTATTGGGCCAATTTGTA
66 TTTAGGCCTCCAAAATGTTGAGGGACCAATTTGAAAAACAATTAAAATTATTGGGCCAATTTGTA
*
5723031 ATAAATTAAAAAATGAATTAAGGATTAAACTGAAATAAATAAAAATGAAGAAGGGCTAACTACAT
131 ATAAATTAAAAAATGAATTAAGAATTAAACTGAAATAAATAAAAATGAAGAAGGGCTAACTACAT
5723096 AAGTTAAA
196 AAGTTAAA
* *
5723104 AATTTTAGAGAAGTTTAAGGGTCGATTGGGCAATAAACCCAAAAAATTTTGACACGTGGTAGCTT
1 AATTTTAAAGAAGTTTAAGGGTCGATTGGGCAATAAACCCAAAAAATTTTGACACGTGATAGCTT
*
5723169 TTTAGGCCTCCAAAATGTTGAGGGACCAATTTGAAAAATAATTAAAATTATTGGGCCAATTTGTA
66 TTTAGGCCTCCAAAATGTTGAGGGACCAATTTGAAAAACAATTAAAATTATTGGGCCAATTTGTA
5723234 ATAAATTAAAAAATGAATTAAGAATTAAACTGAAATAAATAAAAATGAAGAAGGGCTAACTACAT
131 ATAAATTAAAAAATGAATTAAGAATTAAACTGAAATAAATAAAAATGAAGAAGGGCTAACTACAT
5723299 AA
196 AA
5723301 ATAAACCAAA
Statistics
Matches: 192, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
203 192 1.00
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.28
Consensus pattern (203 bp):
AATTTTAAAGAAGTTTAAGGGTCGATTGGGCAATAAACCCAAAAAATTTTGACACGTGATAGCTT
TTTAGGCCTCCAAAATGTTGAGGGACCAATTTGAAAAACAATTAAAATTATTGGGCCAATTTGTA
ATAAATTAAAAAATGAATTAAGAATTAAACTGAAATAAATAAAAATGAAGAAGGGCTAACTACAT
AAGTTAAA
Found at i:5723984 original size:20 final size:20
Alignment explanation
Indices: 5723955--5723993 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5723945 CCTTTAATTC
5723955 TTTTAAATTTATT-TTTGTTG
1 TTTTAAATTT-TTATTTGTTG
*
5723975 TTTTATATTTTTATTTGTT
1 TTTTAAATTTTTATTTGTT
5723994 ATTAATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (20 bp):
TTTTAAATTTTTATTTGTTG
Found at i:5729784 original size:24 final size:24
Alignment explanation
Indices: 5729756--5729830 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
5729746 TCCAAAGCAC
5729756 TCAAGGAGCTTATTCTTAAGCAAT
1 TCAAGGAGCTTATTCTTAAGCAAT
* * *
5729780 TCAAGTG-TCTT-TTC-TATGC-TT
1 TCAAG-GAGCTTATTCTTAAGCAAT
* *
5729801 TTATTGGAGCTTATTCTTAAGCAAT
1 TCA-AGGAGCTTATTCTTAAGCAAT
5729826 TCAAG
1 TCAAG
5729831 TGTCTTTTCT
Statistics
Matches: 35, Mismatches: 10, Indels: 12
0.61 0.18 0.21
Matches are distributed among these distances:
21 4 0.11
22 8 0.23
23 6 0.17
24 13 0.37
25 4 0.11
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (24 bp):
TCAAGGAGCTTATTCTTAAGCAAT
Found at i:5729827 original size:46 final size:46
Alignment explanation
Indices: 5729760--5729852 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
5729750 AAGCACTCAA
5729760 GGAGCTTATTCTTAAGCAATTCAAGTGTCTTTTCTATGCTTTTATT
1 GGAGCTTATTCTTAAGCAATTCAAGTGTCTTTTCTATGCTTTTATT
5729806 GGAGCTTATTCTTAAGCAATTCAAGTGTCTTTTCTATGCTTTTATT
1 GGAGCTTATTCTTAAGCAATTCAAGTGTCTTTTCTATGCTTTTATT
5729852 G
1 G
5729853 AGTTTTAGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.47
Consensus pattern (46 bp):
GGAGCTTATTCTTAAGCAATTCAAGTGTCTTTTCTATGCTTTTATT
Found at i:5731526 original size:17 final size:16
Alignment explanation
Indices: 5731506--5731544 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
5731496 ATAAAAATAA
5731506 AAAAAAAATATTTTTT
1 AAAAAAAATATTTTTT
*
5731522 GAAAATAAATATTTTTT
1 -AAAAAAAATATTTTTT
5731539 AAAAAA
1 AAAAAA
5731545 TTAGGACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AAAAAAAATATTTTTT
Found at i:5738969 original size:119 final size:119
Alignment explanation
Indices: 5738758--5738996 Score: 478
Period size: 119 Copynumber: 2.0 Consensus size: 119
5738748 TGATAAGCCT
5738758 TACCTCTCTTGTTTCAAGCTAGCCGATTTAACCTTACCCTCTATTTGTGTTTCAGGATTGACCTA
1 TACCTCTCTTGTTTCAAGCTAGCCGATTTAACCTTACCCTCTATTTGTGTTTCAGGATTGACCTA
5738823 ATCTTGTGATTCACTTTTTATCAGTGTATATCTCATCTAATGCTTCATTTTCCA
66 ATCTTGTGATTCACTTTTTATCAGTGTATATCTCATCTAATGCTTCATTTTCCA
5738877 TACCTCTCTTGTTTCAAGCTAGCCGATTTAACCTTACCCTCTATTTGTGTTTCAGGATTGACCTA
1 TACCTCTCTTGTTTCAAGCTAGCCGATTTAACCTTACCCTCTATTTGTGTTTCAGGATTGACCTA
5738942 ATCTTGTGATTCACTTTTTATCAGTGTATATCTCATCTAATGCTTCATTTTCCA
66 ATCTTGTGATTCACTTTTTATCAGTGTATATCTCATCTAATGCTTCATTTTCCA
5738996 T
1 T
5738997 GCATTTTAAT
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 120 1.00
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (119 bp):
TACCTCTCTTGTTTCAAGCTAGCCGATTTAACCTTACCCTCTATTTGTGTTTCAGGATTGACCTA
ATCTTGTGATTCACTTTTTATCAGTGTATATCTCATCTAATGCTTCATTTTCCA
Found at i:5741560 original size:18 final size:20
Alignment explanation
Indices: 5741533--5741571 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
5741523 TTAATGAGAT
5741533 TTTTAGTATA-TA-ATTTTA
1 TTTTAGTATATTATATTTTA
*
5741551 TTTTATTATATTATATTTTA
1 TTTTAGTATATTATATTTTA
5741571 T
1 T
5741572 ATATTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 2 0.11
20 7 0.39
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTTAGTATATTATATTTTA
Found at i:5741767 original size:14 final size:14
Alignment explanation
Indices: 5741748--5741776 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5741738 TTCTAAAGAC
5741748 GATGATTTGTCTAA
1 GATGATTTGTCTAA
5741762 GATGATTTGTCTAA
1 GATGATTTGTCTAA
5741776 G
1 G
5741777 TTCGGGTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (14 bp):
GATGATTTGTCTAA
Found at i:5742434 original size:37 final size:37
Alignment explanation
Indices: 5742384--5742458 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
5742374 ACTCTTTGCT
5742384 AATGTGGTTTTAGTTGCCTTTCTTACCTGCCAAGAAG
1 AATGTGGTTTTAGTTGCCTTTCTTACCTGCCAAGAAG
5742421 AATGTGGTTTTAGTTGCCTTTCTTACCTGCCAAGAAG
1 AATGTGGTTTTAGTTGCCTTTCTTACCTGCCAAGAAG
5742458 A
1 A
5742459 CTTGGATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (37 bp):
AATGTGGTTTTAGTTGCCTTTCTTACCTGCCAAGAAG
Found at i:5742518 original size:50 final size:50
Alignment explanation
Indices: 5742460--5742556 Score: 176
Period size: 50 Copynumber: 1.9 Consensus size: 50
5742450 CCAAGAAGAC
*
5742460 TTGGATTTTGGTTGATATATACCTTTACAAATTTTCTTCTTCTTCTTGAT
1 TTGGATTTTGGTTGATACATACCTTTACAAATTTTCTTCTTCTTCTTGAT
*
5742510 TTGGATTTTGGTTGATACATGCCTTTACAAATTTTCTTCTTCTTCTT
1 TTGGATTTTGGTTGATACATACCTTTACAAATTTTCTTCTTCTTCTT
5742557 CCTCTTCCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.19, C:0.15, G:0.12, T:0.54
Consensus pattern (50 bp):
TTGGATTTTGGTTGATACATACCTTTACAAATTTTCTTCTTCTTCTTGAT
Found at i:5742894 original size:19 final size:21
Alignment explanation
Indices: 5742867--5742908 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 21
5742857 AAAATGTATA
5742867 AAAAGATAT-TAAT-AAAATT
1 AAAAGATATGTAATAAAAATT
* *
5742886 AAAATATATGTCATAAAAATT
1 AAAAGATATGTAATAAAAATT
5742907 AA
1 AA
5742909 GAAATCATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 8 0.42
20 3 0.16
21 8 0.42
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (21 bp):
AAAAGATATGTAATAAAAATT
Found at i:5744385 original size:3 final size:3
Alignment explanation
Indices: 5744377--5744421 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
5744367 ATGTGATTCA
5744377 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5744422 TGTAGCCTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5752003 original size:15 final size:17
Alignment explanation
Indices: 5751985--5752022 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 17
5751975 CCCCCCCCCC
5751985 AAAAAAAAAA-AAA-AG
1 AAAAAAAAAAGAAAGAG
5752000 AAAAAAAAAAGAAAGAG
1 AAAAAAAAAAGAAAGAG
5752017 AAAAAA
1 AAAAAA
5752023 TCATTGCCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 10 0.48
16 3 0.14
17 8 0.38
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGAAAGAG
Found at i:5752007 original size:17 final size:17
Alignment explanation
Indices: 5751985--5752022 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
5751975 CCCCCCCCCC
5751985 AAAAAAAAAAAAAAGAA
1 AAAAAAAAAAAAAAGAA
* *
5752002 AAAAAAAAGAAAGAGAA
1 AAAAAAAAAAAAAAGAA
5752019 AAAA
1 AAAA
5752023 TCATTGCCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAAGAA
Found at i:5752020 original size:11 final size:11
Alignment explanation
Indices: 5751985--5752013 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5751975 CCCCCCCCCC
5751985 AAAA-AAAAAA
1 AAAAGAAAAAA
5751995 AAAAGAAAAAA
1 AAAAGAAAAAA
5752006 AAAAGAAA
1 AAAAGAAA
5752014 GAGAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:5753218 original size:61 final size:61
Alignment explanation
Indices: 5753141--5753257 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
5753131 CATTGTTGTT
* ** *
5753141 AAAATCAAAAACTCATTTGTTTGATAAAGCAAATTTCATCATATGGGTTTGAATCAAAATC
1 AAAATAAAAAACTCATTTACTTGATAAAACAAATTTCATCATATGGGTTTGAATCAAAATC
* * *
5753202 AAAATAAAAAATTCATTTACTTGATAAAACAAATTTCCTCATTTGGGTTTGAATCA
1 AAAATAAAAAACTCATTTACTTGATAAAACAAATTTCATCATATGGGTTTGAATCA
5753258 CGCATGCAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (61 bp):
AAAATAAAAAACTCATTTACTTGATAAAACAAATTTCATCATATGGGTTTGAATCAAAATC
Found at i:5755437 original size:17 final size:17
Alignment explanation
Indices: 5755415--5755453 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5755405 CTCCACCTTG
* * *
5755415 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACAA
5755432 ACAAGAACTCTCAACAA
1 ACAAGAACTCTCAACAA
5755449 ACAAG
1 ACAAG
5755454 TTCTCCACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.26, G:0.10, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACAA
Found at i:5761452 original size:14 final size:14
Alignment explanation
Indices: 5761435--5761461 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5761425 CTGGTATTTT
5761435 TACATATATATATA
1 TACATATATATATA
5761449 TACATATATATAT
1 TACATATATATAT
5761462 TTCTCTCGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (14 bp):
TACATATATATATA
Found at i:5763103 original size:19 final size:20
Alignment explanation
Indices: 5763034--5763132 Score: 69
Period size: 20 Copynumber: 5.0 Consensus size: 20
5763024 ATTTGATAGT
*
5763034 CCCTCATAGT-TTTTGGTAAT
1 CCCTCATA-TATTTTGGTAAG
* * * *
5763054 CGCACATA-ACTTTTTGTAAT
1 CCCTCATATA-TTTTGGTAAG
* *
5763074 CCCTAATATATTTTGGTATG
1 CCCTCATATATTTTGGTAAG
*
5763094 CTCTCA-ATATTTTTGGTAAG
1 CCCTCATATA-TTTTGGTAAG
*
5763114 CCCTCATATTTTTTGGTAA
1 CCCTCATATATTTTGGTAA
5763133 TCCGACCAAA
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
19 3 0.05
20 54 0.90
21 3 0.05
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.44
Consensus pattern (20 bp):
CCCTCATATATTTTGGTAAG
Found at i:5763470 original size:22 final size:21
Alignment explanation
Indices: 5763445--5763503 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
5763435 TCCTTACTTC
*
5763445 GAAAGCATACAAAATAAATTAT
1 GAAAGAATACAAAA-AAATTAT
* *
5763467 GAAATAATAC-TAAAAATTAT
1 GAAAGAATACAAAAAAATTAT
* *
5763487 GAGAGTATACAAAAAAA
1 GAAAGAATACAAAAAAA
5763504 CATGATGGAA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
20 14 0.48
21 7 0.24
22 8 0.28
ACGTcount: A:0.61, C:0.07, G:0.10, T:0.22
Consensus pattern (21 bp):
GAAAGAATACAAAAAAATTAT
Found at i:5763593 original size:20 final size:20
Alignment explanation
Indices: 5763534--5763594 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
5763524 TTTTAATAGT
*
5763534 GTACCAAAAATTCTGAAAGAA
1 GTACCAAAAATTATG-AAGAA
* *
5763555 -TACCAAAAAAATATTAAGAA
1 GTACC-AAAAATTATGAAGAA
5763575 GTACCAAAAATTATGAAGAA
1 GTACCAAAAATTATGAAGAA
5763595 ACATCAAGGA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
20 22 0.67
21 11 0.33
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.20
Consensus pattern (20 bp):
GTACCAAAAATTATGAAGAA
Found at i:5763887 original size:22 final size:22
Alignment explanation
Indices: 5763862--5763933 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
5763852 ATGCAATACT
*
5763862 AAAAATTATAAGAGAATAAAAA
1 AAAAATTATAAGAGAATAACAA
* *
5763884 AAAATATTACAAG-GGAT-ACAA
1 AAAA-ATTATAAGAGAATAACAA
* *
5763905 AAAAATTATGAGAGAATATCAA
1 AAAAATTATAAGAGAATAACAA
5763927 AAAAATT
1 AAAAATT
5763934 TGAAGGAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
20 6 0.15
21 10 0.25
22 17 0.43
23 7 0.17
ACGTcount: A:0.64, C:0.04, G:0.11, T:0.21
Consensus pattern (22 bp):
AAAAATTATAAGAGAATAACAA
Found at i:5763929 original size:23 final size:22
Alignment explanation
Indices: 5763862--5763931 Score: 72
Period size: 23 Copynumber: 3.2 Consensus size: 22
5763852 ATGCAATACT
*
5763862 AAAAATTATAAGAGAATAAAAA
1 AAAAATTATAAGAGAATACAAA
* *
5763884 AAAATATTACAAG-GGATAC-AA
1 AAAA-ATTATAAGAGAATACAAA
*
5763905 AAAAATTATGAGAGAATATCAAA
1 AAAAATTATAAGAGAATA-CAAA
5763928 AAAA
1 AAAA
5763932 TTTGAAGGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
20 6 0.16
21 10 0.26
22 9 0.24
23 13 0.34
ACGTcount: A:0.66, C:0.04, G:0.11, T:0.19
Consensus pattern (22 bp):
AAAAATTATAAGAGAATACAAA
Found at i:5763942 original size:21 final size:22
Alignment explanation
Indices: 5763841--5763944 Score: 69
Period size: 22 Copynumber: 4.9 Consensus size: 22
5763831 TGAAACTTAC
* *
5763841 AAAAAATTATGATGCAATA-C-
1 AAAAAATTATGAAGGAATATCA
* **
5763861 TAAAAATTAT-AAGAGAATAAAA
1 AAAAAATTATGAAG-GAATATCA
* *
5763883 AAAAATATTA-CAAGGGATA-CA
1 AAAAA-ATTATGAAGGAATATCA
5763904 AAAAAATTATG-AGAGAATATCA
1 AAAAAATTATGAAG-GAATATCA
5763926 AAAAAATT-TGAAGGAATAT
1 AAAAAATTATGAAGGAATAT
5763945 ATACTAAAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
19 2 0.03
20 19 0.29
21 18 0.27
22 20 0.30
23 7 0.11
ACGTcount: A:0.60, C:0.05, G:0.12, T:0.23
Consensus pattern (22 bp):
AAAAAATTATGAAGGAATATCA
Found at i:5766218 original size:26 final size:23
Alignment explanation
Indices: 5766187--5766253 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 23
5766177 ACATTAAAAT
5766187 AAAATTTAAAATTTAATATATTTATA
1 AAAATTTAAAATTT-ATAT-TTT-TA
*
5766213 AAAATTCTAAAATTTGTATTTTTA
1 AAAATT-TAAAATTTATATTTTTA
* *
5766237 AAAATCTAAAATATATA
1 AAAATTTAAAATTTATA
5766254 AAAAATTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 9 0.25
24 7 0.19
25 3 0.08
26 9 0.25
27 8 0.22
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (23 bp):
AAAATTTAAAATTTATATTTTTA
Found at i:5767910 original size:45 final size:44
Alignment explanation
Indices: 5767859--5767999 Score: 138
Period size: 45 Copynumber: 3.2 Consensus size: 44
5767849 ATTTGTAGTT
*
5767859 ACTGCCACTTGTTGTGGGTGCACAACATATTTAG-AGATTAAACAA
1 ACTGCCACTTGTTGTGGATGCACAACATATTT-GCAGATTAAA-AA
*
5767904 ACTGCCACTTGGTTCGT-GAT-CAAACCACATATTTGCAG-TT-----
1 ACTGCCACTT-GTT-GTGGATGC--ACAACATATTTGCAGATTAAAAA
5767944 ACTGCCACTTGTTGTGGATGCACAACATATTTGCAGATTAAATAA
1 ACTGCCACTTGTTGTGGATGCACAACATATTTGCAGATTAAA-AA
5767989 ACTGCCACTTG
1 ACTGCCACTTG
5768000 GTTTGTGATC
Statistics
Matches: 79, Mismatches: 3, Indels: 28
0.72 0.03 0.25
Matches are distributed among these distances:
38 16 0.20
39 8 0.10
40 11 0.14
45 22 0.28
46 8 0.10
47 14 0.18
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (44 bp):
ACTGCCACTTGTTGTGGATGCACAACATATTTGCAGATTAAAAA
Found at i:5767992 original size:85 final size:85
Alignment explanation
Indices: 5767849--5768017 Score: 277
Period size: 85 Copynumber: 2.0 Consensus size: 85
5767839 ACCATCGTTG
* *
5767849 ATTTGTAGTTACTGCCACTTGTTGTGGGTGCACAACATATTTAGAGATTAAACAAACTGCCACTT
1 ATTTGCAGTTACTGCCACTTGTTGTGGATGCACAACATATTTAGAGATTAAACAAACTGCCACTT
5767914 GGTTCGTGATCAAACCACAT
66 GGTTCGTGATCAAACCACAT
*
5767934 ATTTGCAGTTACTGCCACTTGTTGTGGATGCACAACATATTT-GCAGATTAAATAAACTGCCACT
1 ATTTGCAGTTACTGCCACTTGTTGTGGATGCACAACATATTTAG-AGATTAAACAAACTGCCACT
* *
5767998 TGGTTTGTGATCGAACCACA
65 TGGTTCGTGATCAAACCACA
5768018 CTGTTTGTAG
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
84 1 0.01
85 77 0.99
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (85 bp):
ATTTGCAGTTACTGCCACTTGTTGTGGATGCACAACATATTTAGAGATTAAACAAACTGCCACTT
GGTTCGTGATCAAACCACAT
Found at i:5768800 original size:21 final size:22
Alignment explanation
Indices: 5768767--5768811 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
5768757 ACAAGTTAAC
* * *
5768767 GATTGATTTAAAGATTTATCAA
1 GATTGATTGAAAGATATAGCAA
5768789 GATT-ATTGAAAGATATAGCAA
1 GATTGATTGAAAGATATAGCAA
5768810 GA
1 GA
5768812 ACTGAAAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.33
Consensus pattern (22 bp):
GATTGATTGAAAGATATAGCAA
Found at i:5779963 original size:23 final size:24
Alignment explanation
Indices: 5779937--5779984 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
5779927 TCACGCCAGT
5779937 TAAAAAA-ATCAATTTAAAAAAAA
1 TAAAAAATATCAATTTAAAAAAAA
*
5779960 TAAAAAATATCATTTTAAAAAAAA
1 TAAAAAATATCAATTTAAAAAAAA
5779984 T
1 T
5779985 CATTTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (24 bp):
TAAAAAATATCAATTTAAAAAAAA
Found at i:5779978 original size:15 final size:16
Alignment explanation
Indices: 5779960--5780000 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
5779950 TTAAAAAAAA
5779960 TAAAAAATATCA-TTT
1 TAAAAAATATCATTTT
*
5779975 TAAAAAAAATCATTTTT
1 TAAAAAATATCA-TTTT
5779992 TAAAAAATA
1 TAAAAAATA
5780001 AAATGAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 11 0.50
17 11 0.50
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAAAATATCATTTT
Found at i:5779983 original size:17 final size:17
Alignment explanation
Indices: 5779961--5779998 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
5779951 TAAAAAAAAT
5779961 AAAAAAT-ATCATTTTAA
1 AAAAAATCAT-ATTTTAA
*
5779978 AAAAAATCATTTTTTAA
1 AAAAAATCATATTTTAA
5779995 AAAA
1 AAAA
5779999 TAAAATGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAAAATCATATTTTAA
Found at i:5780109 original size:18 final size:19
Alignment explanation
Indices: 5780077--5780130 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 19
5780067 AAGTATTTTT
*
5780077 AATTTTTTAAA-ATTA-TA
1 AATTTTTAAAATATTATTA
5780094 AATTTTTAAAATATTATTA
1 AATTTTTAAAATATTATTA
5780113 AATTTTATAAGAATATTA
1 AATTTT-TAA-AATATTA
5780131 AATAAAGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 10 0.31
18 4 0.12
19 8 0.25
20 3 0.09
21 7 0.22
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
AATTTTTAAAATATTATTA
Found at i:5783189 original size:9 final size:9
Alignment explanation
Indices: 5783166--5783207 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
5783156 AAATTATTTT
*
5783166 TTAAAAATA
1 TTAAAATTA
5783175 -TAAAATTA
1 TTAAAATTA
5783183 TTAAAATTAA
1 TTAAAATT-A
5783193 TTTAAAATTA
1 -TTAAAATTA
5783203 TTAAA
1 TTAAA
5783208 TAATTTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
8 7 0.24
9 12 0.41
10 2 0.07
11 8 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
TTAAAATTA
Found at i:5783461 original size:99 final size:99
Alignment explanation
Indices: 5783328--5783522 Score: 291
Period size: 99 Copynumber: 2.0 Consensus size: 99
5783318 TGAACCAAAT
* *
5783328 CATGACTACTTCTCTACTTGAATTCTGAACCAAACCATGGCATCTTCTTCTTCCATCGCTCTCCC
1 CATGACTACTTCTCCACTTGAATTCTGAACCAAACCATGGCATCTTCTTCTTCCATCACTCTCCC
*
5783393 AACCCTTCAAGGTTCTCTATTTTAATCTCATAAC
66 AACCCTTCAAGGTTCTCTATTTCAATCTCATAAC
* * * * * **
5783427 CATGACTACTTCTCCACTTGGATTTTGAATCAAACTATGGCTTCTTCTTCTTCCATCACTCTCTT
1 CATGACTACTTCTCCACTTGAATTCTGAACCAAACCATGGCATCTTCTTCTTCCATCACTCTCCC
*
5783492 AACCGTTCAAGGTTCTCTATTTCAATCTCAT
66 AACCCTTCAAGGTTCTCTATTTCAATCTCAT
5783523 TTCTTAGGAA
Statistics
Matches: 85, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
99 85 1.00
ACGTcount: A:0.23, C:0.30, G:0.09, T:0.38
Consensus pattern (99 bp):
CATGACTACTTCTCCACTTGAATTCTGAACCAAACCATGGCATCTTCTTCTTCCATCACTCTCCC
AACCCTTCAAGGTTCTCTATTTCAATCTCATAAC
Found at i:5784133 original size:16 final size:16
Alignment explanation
Indices: 5784112--5784164 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
5784102 TATTAAAATA
5784112 ATTTTAATAATTTTAT
1 ATTTTAATAATTTTAT
*
5784128 ATTTTAA-AA-ATTA-
1 ATTTTAATAATTTTAT
5784141 ATTTTAAAATAATTTTAT
1 ATTTT--AATAATTTTAT
5784159 ATTTTA
1 ATTTTA
5784165 TATTTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
13 5 0.17
14 3 0.10
15 4 0.13
16 10 0.33
17 3 0.10
18 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTTAATAATTTTAT
Found at i:5784144 original size:29 final size:29
Alignment explanation
Indices: 5784106--5784164 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 29
5784096 TTAAAATATT
5784106 AAAATAATTTT-AATAATTTTATATTTTA
1 AAAATAATTTTAAATAATTTTATATTTTA
5784134 AAAATTAATTTTAAAATAATTTTATATTTTA
1 AAAA-TAATTTT-AAATAATTTTATATTTTA
5784165 TATTTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 4 0.14
29 7 0.25
31 17 0.61
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
AAAATAATTTTAAATAATTTTATATTTTA
Found at i:5784149 original size:40 final size:39
Alignment explanation
Indices: 5784104--5784194 Score: 143
Period size: 38 Copynumber: 2.4 Consensus size: 39
5784094 GATTAAAATA
*
5784104 TTAAAATAATTTTAATAATTTTATATTTTAAAAATTAATT
1 TTAAAATAATTTTAAT-ATTTTATATTTTAAAAAATAATT
5784144 TTAAAATAATTTT-ATATTTTATATTTTAAAAAATAATT
1 TTAAAATAATTTTAATATTTTATATTTTAAAAAATAATT
5784182 TT--AATAATTTTAA
1 TTAAAATAATTTTAA
5784195 AATCATTTGC
Statistics
Matches: 49, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
36 9 0.18
37 1 0.02
38 24 0.49
39 2 0.04
40 13 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (39 bp):
TTAAAATAATTTTAATATTTTATATTTTAAAAAATAATT
Found at i:5784601 original size:18 final size:16
Alignment explanation
Indices: 5784569--5784604 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
5784559 ATAGAATGAG
5784569 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
5784585 AATAAATTTAATTAATTA
1 AATAAATTT--TTAATTA
5784603 AA
1 AA
5784605 ACTTTTAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:5784946 original size:24 final size:25
Alignment explanation
Indices: 5784911--5784961 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
5784901 TACTTTCTAT
* *
5784911 ATTACACAATAATTATAATA-TAAA
1 ATTACACAATAATCAAAATATTAAA
5784935 ATTACA-AGATAATCAAAATATTAAA
1 ATTACACA-ATAATCAAAATATTAAA
5784960 AT
1 AT
5784962 CTAAACACCG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 1 0.04
24 16 0.70
25 6 0.26
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (25 bp):
ATTACACAATAATCAAAATATTAAA
Found at i:5788164 original size:2 final size:2
Alignment explanation
Indices: 5788157--5788190 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5788147 TGCAATGCTG
5788157 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5788191 AACAGGTGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5790306 original size:2 final size:2
Alignment explanation
Indices: 5790299--5790351 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
5790289 TTGCTATTAC
5790299 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5790341 AT AT GT AT AT A
1 AT AT AT AT AT A
5790352 ATACCAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5792456 original size:21 final size:21
Alignment explanation
Indices: 5792432--5792476 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
5792422 TCTAACCTCG
*
5792432 CTGCATTCATTAATTTTTTGC
1 CTGCATTCATTAAATTTTTGC
5792453 CTGCATTCATTAAATTTTTGC
1 CTGCATTCATTAAATTTTTGC
5792474 CTG
1 CTG
5792477 GTCATTTCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.49
Consensus pattern (21 bp):
CTGCATTCATTAAATTTTTGC
Found at i:5796495 original size:24 final size:26
Alignment explanation
Indices: 5796451--5796508 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
5796441 CAAACCACGC
5796451 TTGTGGCAAATTTTTTAGG-AAGCCT
1 TTGTGGCAAATTTTTTAGGAAAGCCT
* *
5796476 TTGTGGC-GATTTATTT-GGAAAGTCT
1 TTGTGGCAAATTT-TTTAGGAAAGCCT
5796501 TTGTGGCA
1 TTGTGGCA
5796509 GGTTATCTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 6 0.21
25 22 0.79
ACGTcount: A:0.21, C:0.10, G:0.28, T:0.41
Consensus pattern (26 bp):
TTGTGGCAAATTTTTTAGGAAAGCCT
Found at i:5796514 original size:25 final size:25
Alignment explanation
Indices: 5796474--5796547 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 25
5796464 TTTAGGAAGC
* * *
5796474 CTTTGTGGCGATTTATTTGGAAAGT
1 CTTTGTGGCAAGTTATTTGTAAAGT
* * * *
5796499 CTTTGTGGCAGGTTATCTATAAAAT
1 CTTTGTGGCAAGTTATTTGTAAAGT
*
5796524 CTTTGTGGCAAGTTACTTGTAAAG
1 CTTTGTGGCAAGTTATTTGTAAAG
5796548 CCTATGTAGC
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.41
Consensus pattern (25 bp):
CTTTGTGGCAAGTTATTTGTAAAGT
Found at i:5798527 original size:2 final size:2
Alignment explanation
Indices: 5798520--5798549 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5798510 TATAAAAATA
5798520 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
5798550 TTAAAGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5800580 original size:2 final size:2
Alignment explanation
Indices: 5800573--5800624 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
5800563 TGCAATGCTG
5800573 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5800615 CT CT CT CT CT
1 CT CT CT CT CT
5800625 AACAGGTGGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5804417 original size:29 final size:29
Alignment explanation
Indices: 5804385--5804494 Score: 184
Period size: 29 Copynumber: 3.8 Consensus size: 29
5804375 TTTGTCTCAA
* *
5804385 GTTACATTTTAATCACTTATGTTTGAAAT
1 GTTACGTTTTAGTCACTTATGTTTGAAAT
5804414 GTTACGTTTTAGTCACTTATGTTTGAAAT
1 GTTACGTTTTAGTCACTTATGTTTGAAAT
* *
5804443 GTTACGTTTTAGTCACTTATGTTTAAAAC
1 GTTACGTTTTAGTCACTTATGTTTGAAAT
5804472 GTTACGTTTTAGTCACTTATGTT
1 GTTACGTTTTAGTCACTTATGTT
5804495 AGTATTTTAG
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 77 1.00
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.48
Consensus pattern (29 bp):
GTTACGTTTTAGTCACTTATGTTTGAAAT
Found at i:5804641 original size:14 final size:14
Alignment explanation
Indices: 5804622--5804651 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5804612 GAATAAATCT
5804622 TTAATTAAATAAAA
1 TTAATTAAATAAAA
*
5804636 TTAATTAATTAAAA
1 TTAATTAAATAAAA
5804650 TT
1 TT
5804652 TTAAAACCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAATTAAATAAAA
Found at i:5805015 original size:18 final size:16
Alignment explanation
Indices: 5804988--5805028 Score: 59
Period size: 14 Copynumber: 2.7 Consensus size: 16
5804978 TTAGGGTTTA
*
5804988 AAAAATTTAATTAATT
1 AAAAATTTATTTAATT
5805004 --AAATTTATTTAATT
1 AAAAATTTATTTAATT
5805018 AAAAATTTATT
1 AAAAATTTATT
5805029 CTCATTCCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 13 0.59
16 9 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAAAATTTATTTAATT
Found at i:5820378 original size:122 final size:122
Alignment explanation
Indices: 5820227--5820472 Score: 492
Period size: 122 Copynumber: 2.0 Consensus size: 122
5820217 CACCTAACTG
5820227 ATCTCTCTTTATAGTGGAAACTATGGACTAAAATGCATCTCCAAGATATACACATCACTAGTAGG
1 ATCTCTCTTTATAGTGGAAACTATGGACTAAAATGCATCTCCAAGATATACACATCACTAGTAGG
5820292 CTTCATCTTCATCTCTTTTGACTAATAATAATAATACCTTGAGAAAAGTCTTCGCAC
66 CTTCATCTTCATCTCTTTTGACTAATAATAATAATACCTTGAGAAAAGTCTTCGCAC
5820349 ATCTCTCTTTATAGTGGAAACTATGGACTAAAATGCATCTCCAAGATATACACATCACTAGTAGG
1 ATCTCTCTTTATAGTGGAAACTATGGACTAAAATGCATCTCCAAGATATACACATCACTAGTAGG
5820414 CTTCATCTTCATCTCTTTTGACTAATAATAATAATACCTTGAGAAAAGTCTTCGCAC
66 CTTCATCTTCATCTCTTTTGACTAATAATAATAATACCTTGAGAAAAGTCTTCGCAC
5820471 AT
1 AT
5820473 TATCAATGAG
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 124 1.00
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (122 bp):
ATCTCTCTTTATAGTGGAAACTATGGACTAAAATGCATCTCCAAGATATACACATCACTAGTAGG
CTTCATCTTCATCTCTTTTGACTAATAATAATAATACCTTGAGAAAAGTCTTCGCAC
Found at i:5822699 original size:18 final size:17
Alignment explanation
Indices: 5822672--5822719 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
5822662 TGATTTTCAC
5822672 AAATATTTTTTAGATAAA
1 AAAT-TTTTTTAGATAAA
* *
5822690 AAATTATTTTTAAATAAT
1 AAATT-TTTTTAGATAAA
*
5822708 ATATTTTTTTAG
1 AAATTTTTTTAG
5822720 CTTTTTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (17 bp):
AAATTTTTTTAGATAAA
Found at i:5825875 original size:23 final size:24
Alignment explanation
Indices: 5825839--5825901 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
5825829 TAACACTCCA
*
5825839 CAGAATGTAA-TGCACTGA-AGTGT
1 CAGAATG-AATTGCACTGATAGTGC
* *
5825862 TAGAATGAATTGCAC-CATAGTGC
1 CAGAATGAATTGCACTGATAGTGC
5825885 CAGAATGAATTGCACTG
1 CAGAATGAATTGCACTG
5825902 TAATGCTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 3 0.09
23 29 0.91
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (24 bp):
CAGAATGAATTGCACTGATAGTGC
Found at i:5829877 original size:30 final size:30
Alignment explanation
Indices: 5829822--5830137 Score: 242
Period size: 29 Copynumber: 10.8 Consensus size: 30
5829812 CTTCAGACGC
* **
5829822 TTCGAGGGCAAAACGGTAA-TTTTGGAAAA
1 TTCGAGGGTAAAAATGTAATTTTTGGAAAA
*
5829851 TTCGAGGGTAAAAATGTAATTTTTGGAAAC
1 TTCGAGGGTAAAAATGTAATTTTTGGAAAA
* * *
5829881 TTC-AAGGTCAAAAATGGAA-TTTTGGAAAG
1 TTCGAGGGT-AAAAATGTAATTTTTGGAAAA
** *
5829910 TTTAAGGGTAAAATTGTAATTTTTGGAAAA
1 TTCGAGGGTAAAAATGTAATTTTTGGAAAA
* * * *
5829940 TTTG-GGGTTTAAAATGGAA-TTTTGGAAAG
1 TTCGAGGG-TAAAAATGTAATTTTTGGAAAA
*
5829969 TTCGAGGGTAAAAATGTAATTTTTGGAAAC
1 TTCGAGGGTAAAAATGTAATTTTTGGAAAA
** *
5829999 TTCGA-GGTCAAAAA-CAAAATTTTGGAAAA
1 TTCGAGGGT-AAAAATGTAATTTTTGGAAAA
* *
5830028 TT-TAGGGGT-AAAATGTAATTTTTGAAAAA
1 TTCGA-GGGTAAAAATGTAATTTTTGGAAAA
* * * *
5830057 TTC-AAGGTTAAAATGGAA-TTTTGGAAAG
1 TTCGAGGGTAAAAATGTAATTTTTGGAAAA
* *
5830085 TTTGGGGGTAAAAATGTAATTTTTTGGAAAA
1 TTCGAGGGTAAAAATGTAA-TTTTTGGAAAA
* * *
5830116 ATC-AGGGTCAAAATGGAATTTT
1 TTCGAGGGTAAAAATGTAATTTT
5830138 AAGAAGTTTG
Statistics
Matches: 226, Mismatches: 45, Indels: 32
0.75 0.15 0.11
Matches are distributed among these distances:
28 18 0.08
29 116 0.51
30 82 0.36
31 10 0.04
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.33
Consensus pattern (30 bp):
TTCGAGGGTAAAAATGTAATTTTTGGAAAA
Found at i:5830145 original size:59 final size:58
Alignment explanation
Indices: 5829826--5830167 Score: 352
Period size: 59 Copynumber: 5.8 Consensus size: 58
5829816 AGACGCTTCG
* * * *
5829826 AGGG-CAAAACGGTAATTTTGGAAAATTCGAGGGTAAAAATGTAATTTTTGGAAACTTC
1 AGGGTCAAAATGG-AATTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTGGAAAATTC
* * * *
5829884 AAGGTCAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATTGTAATTTTTGGAAAATTT
1 AGGGTC-AAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTGGAAAATTC
* * * *
5829943 GGGGTTTAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAACTTC
1 AGGG-TCAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTGGAAAATTC
*** * *
5830002 -GAGGTCAAAAACAAAATTTTGGAAAATTT-AGGGGT-AAAATGTAATTTTTGAAAAATTC
1 AG-GGTC-AAAATGGAATTTTGGAAAGTTTGA-GGGTAAAAATGTAATTTTTGGAAAATTC
* * * *
5830060 AAGGTTAAAATGGAATTTTGGAAAGTTTGGGGGTAAAAATGTAATTTTTTGGAAAAATC
1 AGGGTCAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATGTAA-TTTTTGGAAAATTC
* * * *
5830119 AGGGTCAAAATGGAATTTT-AAGAAGTTTGAGGGTCAAAATATGATTTTT
1 AGGGTCAAAATGGAATTTTGGA-AAGTTTGAGGGTAAAAATGTAATTTTT
5830168 AGATAGTTTA
Statistics
Matches: 233, Mismatches: 40, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
57 22 0.09
58 45 0.19
59 159 0.68
60 7 0.03
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (58 bp):
AGGGTCAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTGGAAAATTC
Found at i:5830165 original size:29 final size:30
Alignment explanation
Indices: 5830119--5830176 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
5830109 TGGAAAAATC
5830119 AGGGTCAAAATGGAATTTTAAGA-AGTTTG
1 AGGGTCAAAATGGAATTTTAAGATAGTTTG
* *
5830148 AGGGTCAAAATATG-ATTTTTAGATAGTTT
1 AGGGTCAAAAT-GGAATTTTAAGATAGTTT
5830177 AGAGACCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.36
Consensus pattern (30 bp):
AGGGTCAAAATGGAATTTTAAGATAGTTTG
Found at i:5830208 original size:25 final size:25
Alignment explanation
Indices: 5830170--5830220 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
5830160 TGATTTTTAG
5830170 ATAGTTTAGAGACCTTTTGGGCAAT
1 ATAGTTTAGAGACCTTTTGGGCAAT
*
5830195 ATAGTTTAGGGACCTTTTGGGCAAT
1 ATAGTTTAGAGACCTTTTGGGCAAT
5830220 A
1 A
5830221 AAACCTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.35
Consensus pattern (25 bp):
ATAGTTTAGAGACCTTTTGGGCAAT
Found at i:5832003 original size:49 final size:47
Alignment explanation
Indices: 5831931--5832307 Score: 251
Period size: 49 Copynumber: 7.7 Consensus size: 47
5831921 ATGTTTTTGT
* * *
5831931 GGTACTAGATTCGCCATTGCGGCTTAAATCTTTCTCTTCATGCTTTCAA
1 GGTACAAGGTTCGCCATTGCGGCTTAAATCTTTC-CTTCAT-CTTTCGA
* ** * *
5831980 GGTACAAGGTTCGCCATTGCGGCTTAAACCTTTCCTATTGTACCTTCGT
1 GGTACAAGGTTCGCCATTGCGGCTTAAATCTTTCCT-TCAT-CTTTCGA
* * *
5832029 GGTAC-TGGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCAT-TTTCTGA
1 GGTACAAGG-TTCGCCATTGCGGCTTAAATCTTT-CCTTCATCTTTC-GA
* * * * *
5832077 GGTACAAGGTTCGCCATTGCGGTTTAAACCTTTCCTTTGATATCTTCGT
1 GGTACAAGGTTCGCCATTGCGGCTTAAATCTTTCC-TTCATCT-TTCGA
** * ** * * *
5832126 GGTATTAGATTTACCGTTGCGGCTTAAATCTTTCCTTTTAT-TTTCTTA
1 GGTACAAGGTTCGCCATTGCGGCTTAAATCTTTCC-TTCATCTTTC-GA
* * * *
5832174 GGTACAAGGTTCGCCGTTGCGGCTTAAATCTTTCCTTTGATATCTTCGT
1 GGTACAAGGTTCGCCATTGCGGCTTAAATCTTTCC-TTCATCT-TTCGA
* **
5832223 GGTAC-TGGATTCGCTGTTGCGGCTTAAATCTTTCCCTTAACATCCTTT-GA
1 GGTACAAGG-TTCGCCATTGCGGCTTAAATCTTT-CCTT--CAT-CTTTCGA
* * *
5832273 GGTATAAGGTTCGCCATTGCGACTTAAACCTTTCC
1 GGTACAAGGTTCGCCATTGCGGCTTAAATCTTTCC
5832308 CTTTGTATTT
Statistics
Matches: 257, Mismatches: 54, Indels: 34
0.74 0.16 0.10
Matches are distributed among these distances:
47 8 0.03
48 72 0.28
49 134 0.52
50 36 0.14
51 6 0.02
52 1 0.00
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.39
Consensus pattern (47 bp):
GGTACAAGGTTCGCCATTGCGGCTTAAATCTTTCCTTCATCTTTCGA
Found at i:5832124 original size:97 final size:97
Alignment explanation
Indices: 5831929--5832363 Score: 563
Period size: 97 Copynumber: 4.4 Consensus size: 97
5831919 CAATGTTTTT
* * *
5831929 GTGGTACTAGATTCGCCATTGCGGCTTAAATCTTTCTCTTCATGCTTTC-AAGGTACAAGGTTCG
1 GTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT-CTTTCTGAGGTACAAGGTTCG
*
5831993 CCATTGCGGCTTAAACCTTTCCTATTGTACCTTC
65 CCATTGCGGCTTAAACCTTTCCT-TTGTATCTTC
* *
5832027 GTGGTACTGGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCAT-TTTCTGAGGTACAAGGTTCGC
1 GTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATCTTTCTGAGGTACAAGGTTCGC
*
5832091 CATTGCGGTTTAAACCTTTCCTTTGATATCTTC
66 CATTGCGGCTTAAACCTTTCCTTTG-TATCTTC
* ** * * *
5832124 GTGGTATTAGATTTACCGTTGCGGCTTAAATCTTTCCTTTTAT-TTTCTTAGGTACAAGGTTCGC
1 GTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATCTTTCTGAGGTACAAGGTTCGC
* *
5832188 CGTTGCGGCTTAAATCTTTCCTTTGATATCTTC
66 CATTGCGGCTTAAACCTTTCCTTTG-TATCTTC
* * * *
5832221 GTGGTACTGGATTCGCTGTTGCGGCTTAAATCTTTCCCTTAACATCCTT-TGAGGTATAAGGTTC
1 GTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTT--CATCTTTCTGAGGTACAAGGTTC
* *
5832285 GCCATTGCGACTTAAACCTTTCCCTTTGTATTTTC
64 GCCATTGCGGCTTAAACCTTT-CCTTTGTATCTTC
* *
5832320 GTGGTACTAGATTCACCGTTGCGACTTAAATCTTTTCCCTTCAT
1 GTGGTACTAGATTCGCCGTTGCGGCTTAAATC-TTTCCCTTCAT
5832364 GGTGATGAAA
Statistics
Matches: 294, Mismatches: 36, Indels: 14
0.85 0.10 0.04
Matches are distributed among these distances:
96 7 0.02
97 162 0.55
98 42 0.14
99 67 0.23
100 16 0.05
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.40
Consensus pattern (97 bp):
GTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATCTTTCTGAGGTACAAGGTTCGC
CATTGCGGCTTAAACCTTTCCTTTGTATCTTC
Found at i:5844011 original size:29 final size:30
Alignment explanation
Indices: 5843948--5844237 Score: 201
Period size: 29 Copynumber: 9.9 Consensus size: 30
5843938 CTTCGGACAC
5843948 TTCGAGGGTAAAACA--TAA-TTTTGGAAAA
1 TTCGAGGGTAAAA-ATGTAATTTTTGGAAAA
*
5843976 TTCGAGGGTAAAAATGTAATTTTTGG-AAC
1 TTCGAGGGTAAAAATGTAATTTTTGGAAAA
* * *
5844005 TTTGA-GGTCAAAAATGGAA-TTTTGGAAAG
1 TTCGAGGGT-AAAAATGTAATTTTTGGAAAA
* * * *
5844034 TTCGGGGAGT-AAAATATAATTTTTAGAAAC
1 TTCGAGG-GTAAAAATGTAATTTTTGGAAAA
* * ** *
5844064 TT-TAAGGTCAAAAA-CAAAATTTTGG-AAA
1 TTCGAGGGT-AAAAATGTAATTTTTGGAAAA
**
5844092 TTTAAGGGTAAAAATGTAATTTTTGGAAAA
1 TTCGAGGGTAAAAATGTAATTTTTGGAAAA
* * * *
5844122 TTC-AAGATCAAAAATG-AAATTTTGGAAAG
1 TTCGAGGGT-AAAAATGTAATTTTTGGAAAA
*
5844151 TTCGAGGGTAAAAATATAATTTTTTGGAAAA
1 TTCGAGGGTAAAAATGTAA-TTTTTGGAAAA
* * * *
5844182 TTCTAGGTTAAAAATGGAA-TTTTGGAAAG
1 TTCGAGGGTAAAAATGTAATTTTTGGAAAA
* *
5844211 TTCGAGGGTCAAAATATAATTTTTGGA
1 TTCGAGGGTAAAAATGTAATTTTTGGA
5844238 TAGTTTAGGG
Statistics
Matches: 201, Mismatches: 43, Indels: 34
0.72 0.15 0.12
Matches are distributed among these distances:
27 1 0.00
28 33 0.16
29 96 0.48
30 45 0.22
31 26 0.13
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (30 bp):
TTCGAGGGTAAAAATGTAATTTTTGGAAAA
Found at i:5844075 original size:59 final size:59
Alignment explanation
Indices: 5843964--5844237 Score: 331
Period size: 58 Copynumber: 4.7 Consensus size: 59
5843954 GGTAAAACAT
* * * * *
5843964 AATTTTGGAAAATTCGAGGGTAAAAATGTAATTTTTGG-AACTTTGAGGTCAAAAATGG
1 AATTTTGGAAAGTTCGAGGGTAAAAATATAATTTTTGGAAAATTTAAGGTCAAAAATGA
* * * **
5844022 AATTTTGGAAAGTTCGGGGAGT-AAAATATAATTTTTAGAAACTTTAAGGTCAAAAACAA
1 AATTTTGGAAAGTTCGAGG-GTAAAAATATAATTTTTGGAAAATTTAAGGTCAAAAATGA
** * * *
5844081 AATTTTGGAAA-TTTAAGGGTAAAAATGTAATTTTTGGAAAATTCAAGATCAAAAATGA
1 AATTTTGGAAAGTTCGAGGGTAAAAATATAATTTTTGGAAAATTTAAGGTCAAAAATGA
* *
5844139 AATTTTGGAAAGTTCGAGGGTAAAAATATAATTTTTTGGAAAATTCT-AGGTTAAAAATGG
1 AATTTTGGAAAGTTCGAGGGTAAAAATATAA-TTTTTGGAAAATT-TAAGGTCAAAAATGA
*
5844199 AATTTTGGAAAGTTCGAGGGTCAAAATATAATTTTTGGA
1 AATTTTGGAAAGTTCGAGGGTAAAAATATAATTTTTGGA
5844238 TAGTTTAGGG
Statistics
Matches: 184, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
57 2 0.01
58 76 0.41
59 53 0.29
60 53 0.29
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (59 bp):
AATTTTGGAAAGTTCGAGGGTAAAAATATAATTTTTGGAAAATTTAAGGTCAAAAATGA
Found at i:5845350 original size:3 final size:3
Alignment explanation
Indices: 5845344--5845368 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5845334 GTTTTTTTTA
5845344 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
5845369 ATGCCTTTAA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:5845941 original size:9 final size:10
Alignment explanation
Indices: 5845926--5845971 Score: 60
Period size: 9 Copynumber: 4.8 Consensus size: 10
5845916 AATGGTCAGC
5845926 CACGTGGCTG
1 CACGTGGCTG
*
5845936 -ACGTGGATG
1 CACGTGGCTG
5845945 CACGTGGCTG
1 CACGTGGCTG
*
5845955 -ACGTGGATG
1 CACGTGGCTG
5845964 CACGTGGC
1 CACGTGGC
5845972 AAGGGTTGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
9 16 0.53
10 14 0.47
ACGTcount: A:0.15, C:0.24, G:0.41, T:0.20
Consensus pattern (10 bp):
CACGTGGCTG
Found at i:5845950 original size:19 final size:19
Alignment explanation
Indices: 5845926--5845971 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
5845916 AATGGTCAGC
5845926 CACGTGGCTGACGTGGATG
1 CACGTGGCTGACGTGGATG
5845945 CACGTGGCTGACGTGGATG
1 CACGTGGCTGACGTGGATG
5845964 CACGTGGC
1 CACGTGGC
5845972 AAGGGTTGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.15, C:0.24, G:0.41, T:0.20
Consensus pattern (19 bp):
CACGTGGCTGACGTGGATG
Done.