Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 164 of 235
Found at i:55343599 original size:93 final size:93
Alignment explanation
Indices: 55343440--55343610 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
55343430 GGATGGTTGA
* *
55343440 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
55343505 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
55343533 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
55343598 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
55343611 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:55353103 original size:25 final size:25
Alignment explanation
Indices: 55353063--55353168 Score: 115
Period size: 25 Copynumber: 4.2 Consensus size: 25
55353053 GGATACACCA
*
55353063 CAGCTTGTATGAGCTTCTCGATTTG
1 CAGCTCGTATGAGCTTCTCGATTTG
* * * *
55353088 CAGGTCGTATGAGCTTTTCAATTTA
1 CAGCTCGTATGAGCTTCTCGATTTG
*
55353113 CAGCTTGTATGAGCTTC-CTGATTTG
1 CAGCTCGTATGAGCTTCTC-GATTTG
* * *
55353138 TAGCTCGTATGAGCTTCCCGATTTA
1 CAGCTCGTATGAGCTTCTCGATTTG
55353163 CAGCTC
1 CAGCTC
55353169 ATGAGAGCAT
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
24 1 0.02
25 63 0.97
26 1 0.02
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.38
Consensus pattern (25 bp):
CAGCTCGTATGAGCTTCTCGATTTG
Found at i:55353137 original size:50 final size:50
Alignment explanation
Indices: 55353062--55353167 Score: 151
Period size: 50 Copynumber: 2.1 Consensus size: 50
55353052 TGGATACACC
* **
55353062 ACAGCTTGTATGAGCTTCTCGATTTGCAGGTCGTATGAGCTTTTCAATTT
1 ACAGCTTGTATGAGCTTCTCGATTTGCAGCTCGTATGAGCTTCCCAATTT
* *
55353112 ACAGCTTGTATGAGCTTC-CTGATTTGTAGCTCGTATGAGCTTCCCGATTT
1 ACAGCTTGTATGAGCTTCTC-GATTTGCAGCTCGTATGAGCTTCCCAATTT
55353162 ACAGCT
1 ACAGCT
55353168 CATGAGAGCA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
49 1 0.02
50 49 0.98
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.38
Consensus pattern (50 bp):
ACAGCTTGTATGAGCTTCTCGATTTGCAGCTCGTATGAGCTTCCCAATTT
Found at i:55353184 original size:50 final size:50
Alignment explanation
Indices: 55353062--55353201 Score: 133
Period size: 50 Copynumber: 2.8 Consensus size: 50
55353052 TGGATACACC
* * * **
55353062 ACAGCTTGTATGAGC-TTCTCGATTTGCAGGTCGTATGAGCTTTTCAATTT
1 ACAGCTTGTATGAGCATACT-GATTTGTAGCTCGTATGAGCTTCCCAATTT
* * *
55353112 ACAGCTTGTATGAGCTTCCTGATTTGTAGCTCGTATGAGCTTCCCGATTT
1 ACAGCTTGTATGAGCATACTGATTTGTAGCTCGTATGAGCTTCCCAATTT
** *
55353162 ACAGCTCATG-A-GAGCATACTGATTCATAGCTTGTATGAGC
1 ACAGCT--TGTATGAGCATACTGATTTGTAGCTCGTATGAGC
55353202 ATACATGAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
50 70 0.92
51 4 0.05
52 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (50 bp):
ACAGCTTGTATGAGCATACTGATTTGTAGCTCGTATGAGCTTCCCAATTT
Found at i:55358313 original size:40 final size:40
Alignment explanation
Indices: 55358251--55358506 Score: 394
Period size: 40 Copynumber: 6.4 Consensus size: 40
55358241 AAACCAAGTA
* * *
55358251 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
55358290 CCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
55358330 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
55358370 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
55358410 CCTTCGGGACTTAGCCCAGA-ATTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
* *
55358450 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
55358490 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
55358507 CGTTATCATC
Statistics
Matches: 205, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
39 14 0.07
40 191 0.93
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:55370275 original size:48 final size:48
Alignment explanation
Indices: 55370202--55370482 Score: 249
Period size: 48 Copynumber: 5.9 Consensus size: 48
55370192 GGTAAGATGT
* * * *
55370202 CGATGCCATGTCCCAGACATCGTCTTACACTAGCTTTCATATAAACAC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATAAACAC
* * * * ** **
55370250 CAATGTCATGTTCCAAACATGGTCTTGCACTGGCTCAT-ATATCGAGGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTC-TCATATAAACAC
* * *
55370298 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTTTCATATAAACAC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATAAACAC
* * * * ** **
55370346 TGATGCCATGTTCCAAACATGGTCTTACATTGGCTCACATATCGAGGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATAAACAC
* ***
55370394 CGATGCCATGTTCCAAACATGGTCTTACACTAGGTCTCATATAAATGT
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATAAACAC
* * * * * *
55370442 TGATGTCATGTTCCAAACATGGTTTTAGACTGGCTCACATA
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATA
55370483 ACCCTAGTAT
Statistics
Matches: 181, Mismatches: 50, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
47 1 0.01
48 179 0.99
49 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (48 bp):
CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATAAACAC
Found at i:55370366 original size:96 final size:96
Alignment explanation
Indices: 55370202--55370482 Score: 411
Period size: 96 Copynumber: 2.9 Consensus size: 96
55370192 GGTAAGATGT
* **
55370202 CGATGCCATGTCCCAGACATCGTCTTACACTAGCTTTCATATAAACACCAATGTCATGTTCCAAA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTTTCATATAAACACTGATGTCATGTTCCAAA
*
55370267 CATGGTCTTGCACTGGCTCATATATCGAGGC
66 CATGGTCTTGCACTGGCTCACATATCGAGGC
*
55370298 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTTTCATATAAACACTGATGCCATGTTCCAAA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTTTCATATAAACACTGATGTCATGTTCCAAA
* *
55370363 CATGGTCTTACATTGGCTCACATATCGAGGC
66 CATGGTCTTGCACTGGCTCACATATCGAGGC
* * * * ***
55370394 CGATGCCATGTTCCAAACATGGTCTTACACTAGGTCTCATATAAATGTTGATGTCATGTTCCAAA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTTTCATATAAACACTGATGTCATGTTCCAAA
*
55370459 CATGGTTTTAG-ACTGGCTCACATA
66 CATGGTCTT-GCACTGGCTCACATA
55370483 ACCCTAGTAT
Statistics
Matches: 166, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
96 166 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (96 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTTTCATATAAACACTGATGTCATGTTCCAAA
CATGGTCTTGCACTGGCTCACATATCGAGGC
Found at i:55377264 original size:48 final size:48
Alignment explanation
Indices: 55377190--55377416 Score: 285
Period size: 48 Copynumber: 4.7 Consensus size: 48
55377180 AAAGGGTGAG
* *
55377190 ATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAA
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATAA
* * * * * * * *
55377238 ACGTCGATTCCATATACCAAACATGGTCTTACACTGGCTCACATATTGA
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATA-TAA
* * *
55377287 A-GCCGATGCCATGTCCCAGATATGGTCTTACACTAGCTCTCATATAA
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATAA
55377334 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATAA
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATAA
** * *
55377382 ATGTTGATGTCATGTTCCAAACATGATCTTACACT
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACT
55377417 GACTCACATA
Statistics
Matches: 152, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
47 3 0.02
48 146 0.96
49 3 0.02
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (48 bp):
ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATAA
Found at i:55379736 original size:27 final size:27
Alignment explanation
Indices: 55379705--55379882 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
55379695 TAAATTGTAC
55379705 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
55379732 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
55379758 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
55379786 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
55379814 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
55379841 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
55379868 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
55379883 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:55379819 original size:82 final size:81
Alignment explanation
Indices: 55379706--55379861 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
55379696 AAATTGTACA
* *
55379706 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
55379770 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
55379787 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
55379852 TGCGAGTTGA
65 TGCGAATTGA
55379862 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:55379873 original size:82 final size:81
Alignment explanation
Indices: 55379702--55379882 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
55379692 GATTAAATTG
* *
55379702 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
55379767 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
55379783 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
55379847 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
55379865 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
55379883 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:55386630 original size:25 final size:25
Alignment explanation
Indices: 55386565--55386624 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
55386555 GCAAACACAC
* *
55386565 CACAGCTCGTATGAGCTTCTCGATT
1 CACAGCTCGTATGAGCTTCCCAATT
**
55386590 TGCAGCTCGTATGAGCTTCCCAATT
1 CACAGCTCGTATGAGCTTCCCAATT
55386615 CACAGCTCGT
1 CACAGCTCGT
55386625 GAGAGCATAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (25 bp):
CACAGCTCGTATGAGCTTCCCAATT
Found at i:55386807 original size:44 final size:44
Alignment explanation
Indices: 55386744--55386837 Score: 181
Period size: 44 Copynumber: 2.2 Consensus size: 44
55386734 GGTTCAACAG
55386744 ACATAGTTCTGTTACAAGATTATATGAGTTCAATATGAACTATT
1 ACATAGTTCTGTTACAAGATTATATGAGTTCAATATGAACTATT
55386788 ACATAGTTCTGTTACAAGATTATATGAGTTCAATATGAACTATT
1 ACATAGTTCTGTTACAAGATTATATGAGTTCAATATGAACTATT
55386832 AC-TAGT
1 ACATAGT
55386838 ATTTACATGA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 4 0.08
44 46 0.92
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (44 bp):
ACATAGTTCTGTTACAAGATTATATGAGTTCAATATGAACTATT
Found at i:55386817 original size:22 final size:22
Alignment explanation
Indices: 55386748--55386818 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
55386738 CAACAGACAT
55386748 AGTTCTGTTACAAGATTATATG
1 AGTTCTGTTACAAGATTATATG
* * ** *
55386770 AGTTCAATATGA-ACTATTACAT-
1 AGTTC--TGTTACAAGATTATATG
55386792 AGTTCTGTTACAAGATTATATG
1 AGTTCTGTTACAAGATTATATG
55386814 AGTTC
1 AGTTC
55386819 AATATGAACT
Statistics
Matches: 35, Mismatches: 10, Indels: 8
0.66 0.19 0.15
Matches are distributed among these distances:
20 3 0.09
21 7 0.20
22 15 0.43
23 7 0.20
24 3 0.09
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.39
Consensus pattern (22 bp):
AGTTCTGTTACAAGATTATATG
Found at i:55391502 original size:33 final size:32
Alignment explanation
Indices: 55391465--55391578 Score: 97
Period size: 33 Copynumber: 3.5 Consensus size: 32
55391455 TACCTAAATG
*
55391465 GTACAACTT-GAAATGGTTATGTACACTTTGTGT
1 GTAC-ACTTGGAAA-GGTTAGGTACACTTTGTGT
*
55391498 GTACACTTGGAAAGGTTAGGTATACTTTGTGT
1 GTACACTTGGAAAGGTTAGGTACACTTTGTGT
* * ** * *
55391530 ATAC-CATATGAAAAGGAAAGATATACTTTGTGT
1 GTACAC-T-TGGAAAGGTTAGGTACACTTTGTGT
55391563 GTACCACTTGGAAAGG
1 GTA-CACTTGGAAAGG
55391579 AATGTACACC
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
31 1 0.01
32 25 0.37
33 38 0.57
34 2 0.03
35 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (32 bp):
GTACACTTGGAAAGGTTAGGTACACTTTGTGT
Found at i:55391579 original size:33 final size:33
Alignment explanation
Indices: 55391489--55391580 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 33
55391479 GGTTATGTAC
** *
55391489 ACTTTGTGTGTA-CACTTGGAAAGGTTAGGTAT
1 ACTTTGTGTGTACCACTTGGAAAGGAAAGATAT
* *
55391521 ACTTTGTGTATACCA-TATGAAAAGGAAAGATAT
1 ACTTTGTGTGTACCACT-TGGAAAGGAAAGATAT
55391554 ACTTTGTGTGTACCACTTGGAAAGGAA
1 ACTTTGTGTGTACCACTTGGAAAGGAA
55391581 TGTACACCTC
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
32 12 0.24
33 37 0.74
34 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.33
Consensus pattern (33 bp):
ACTTTGTGTGTACCACTTGGAAAGGAAAGATAT
Found at i:55391850 original size:27 final size:29
Alignment explanation
Indices: 55391819--55391876 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
55391809 TATGAATGGT
55391819 AAGTGTA-TT-TTATATGAACTTACTAAG
1 AAGTGTATTTGTTATATGAACTTACTAAG
55391846 AAGTGTATTTTGGTTATATGAACTTACTAAG
1 AAGTGTA-TTT-GTTATATGAACTTACTAAG
55391877 CATTAATGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 7 0.26
29 2 0.07
31 18 0.67
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (29 bp):
AAGTGTATTTGTTATATGAACTTACTAAG
Found at i:55392185 original size:24 final size:24
Alignment explanation
Indices: 55392157--55392273 Score: 74
Period size: 24 Copynumber: 5.2 Consensus size: 24
55392147 ATTTGTTGAA
55392157 TTGGTTGGTATATACTTATAAATT
1 TTGGTTGGTATATACTTATAAATT
* * * *
55392181 TTGGTTAG-A-A-ATTTGTTGAA--
1 TTGGTTGGTATATACTT-ATAAATT
55392201 TTGGTTGGTATATACTTATAAATT
1 TTGGTTGGTATATACTTATAAATT
* * * *
55392225 TTGGTTAG-A-A-ATTTGTTGAA--
1 TTGGTTGGTATATACTT-ATAAATT
55392245 TTGGTTGGTATATACTTATAAATT
1 TTGGTTGGTATATACTTATAAATT
55392269 TTGGT
1 TTGGT
55392274 ACAGGAAAAA
Statistics
Matches: 65, Mismatches: 16, Indels: 24
0.62 0.15 0.23
Matches are distributed among these distances:
20 14 0.22
21 8 0.12
22 16 0.25
23 8 0.12
24 19 0.29
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.49
Consensus pattern (24 bp):
TTGGTTGGTATATACTTATAAATT
Found at i:55392193 original size:44 final size:44
Alignment explanation
Indices: 55392140--55392273 Score: 268
Period size: 44 Copynumber: 3.0 Consensus size: 44
55392130 TGTTTTGAAT
55392140 GTTAGAAATTTGTTGAATTGGTTGGTATATACTTATAAATTTTG
1 GTTAGAAATTTGTTGAATTGGTTGGTATATACTTATAAATTTTG
55392184 GTTAGAAATTTGTTGAATTGGTTGGTATATACTTATAAATTTTG
1 GTTAGAAATTTGTTGAATTGGTTGGTATATACTTATAAATTTTG
55392228 GTTAGAAATTTGTTGAATTGGTTGGTATATACTTATAAATTTTG
1 GTTAGAAATTTGTTGAATTGGTTGGTATATACTTATAAATTTTG
55392272 GT
1 GT
55392274 ACAGGAAAAA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 90 1.00
ACGTcount: A:0.29, C:0.02, G:0.21, T:0.48
Consensus pattern (44 bp):
GTTAGAAATTTGTTGAATTGGTTGGTATATACTTATAAATTTTG
Found at i:55392274 original size:20 final size:20
Alignment explanation
Indices: 55392161--55392274 Score: 66
Period size: 22 Copynumber: 5.3 Consensus size: 20
55392151 GTTGAATTGG
55392161 TTGGTATATACTTATAAATT
1 TTGGTATATACTTATAAATT
* * * * *
55392181 TTGGTTAGAAATTTGTTGAATT
1 TTGG-TATATACTT-ATAAATT
55392203 GGTTGGTATATACTTATAAATT
1 --TTGGTATATACTTATAAATT
* * * * *
55392225 TTGGTTAGAAATTTGTTGAATT
1 TTGG-TATATACTT-ATAAATT
55392247 GGTTGGTATATACTTATAAATT
1 --TTGGTATATACTTATAAATT
55392269 TTGGTA
1 TTGGTA
55392275 CAGGAAAAAG
Statistics
Matches: 66, Mismatches: 20, Indels: 16
0.65 0.20 0.16
Matches are distributed among these distances:
20 14 0.21
21 12 0.18
22 20 0.30
23 12 0.18
24 8 0.12
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.48
Consensus pattern (20 bp):
TTGGTATATACTTATAAATT
Found at i:55398123 original size:15 final size:15
Alignment explanation
Indices: 55398103--55398133 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
55398093 ATATTTTTGG
55398103 TCCCAAAACCACTGT
1 TCCCAAAACCACTGT
55398118 TCCCAAAACCACTGT
1 TCCCAAAACCACTGT
55398133 T
1 T
55398134 TCGATTTAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.39, G:0.06, T:0.23
Consensus pattern (15 bp):
TCCCAAAACCACTGT
Found at i:55400725 original size:22 final size:22
Alignment explanation
Indices: 55400700--55400746 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
55400690 AATTGGTGAA
55400700 ATGTTTTGGTATTTATTTAGAG
1 ATGTTTTGGTATTTATTTAGAG
55400722 ATGTTTTGGTATTTATTTAGAG
1 ATGTTTTGGTATTTATTTAGAG
55400744 ATG
1 ATG
55400747 ACATTCCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.53
Consensus pattern (22 bp):
ATGTTTTGGTATTTATTTAGAG
Found at i:55405432 original size:67 final size:65
Alignment explanation
Indices: 55405294--55405501 Score: 210
Period size: 64 Copynumber: 3.2 Consensus size: 65
55405284 CATAATTTTG
* * * * *
55405294 GCTCTCTTGTAC-ACATGGTGAACACTTAGTACCACCCATGTGACCTAGC--CAGT-TTATCTCG
1 GCTCTCTTGT-CTACATGGTGTACACATAGAACCACCCATGCGACCTAGCTACA-TCATATCTCG
55405355 TA
64 TA
* * * *
55405357 GCTCTCTTGTCTACATGGTGTCCTTCACCTAGAACCACGCATGCGACCTAGCTACAT-ATATCCC
1 GCTCTCTTGTCTACATGGTG---TACACATAGAACCACCCATGCGACCTAGCTACATCATATCTC
55405421 GTA
63 GTA
* *
55405424 GCTCTCTTGTCTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACATCATAATGTCTC
1 GCTCTCTTGTCTACATGGTGTACACATAGAACCACCCATGCGACCTAGCTACATCAT-A--TCTC
55405489 GTA
63 GTA
55405492 GCTCTCTTGT
1 GCTCTCTTGT
55405502 ACACATGATG
Statistics
Matches: 121, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
62 1 0.01
63 18 0.15
64 29 0.24
65 2 0.02
66 24 0.20
67 29 0.24
68 18 0.15
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.31
Consensus pattern (65 bp):
GCTCTCTTGTCTACATGGTGTACACATAGAACCACCCATGCGACCTAGCTACATCATATCTCGTA
Found at i:55406246 original size:30 final size:30
Alignment explanation
Indices: 55406212--55406272 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
55406202 TCCTTAACTC
55406212 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
55406242 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
55406272 A
1 A
55406273 GGCTCAGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:55413881 original size:43 final size:43
Alignment explanation
Indices: 55413817--55414043 Score: 294
Period size: 43 Copynumber: 5.2 Consensus size: 43
55413807 CGGGTTAAAT
*
55413817 CTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTTGTGC
1 CTAGCAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTTGTGC
* *
55413860 CTAGCAGGCTTCGTGCTGGTGATGTGTATTCAGGCCTTCGTGC
1 CTAGCAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTTGTGC
* * * *
55413903 CTAGTAGGCTTCTTGCTGGTGATGTGTATTCGAGCCTTCGTGC
1 CTAGCAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTTGTGC
* *
55413946 CTAGCAGGCTTCGTTCCGGTGATGTGTATTCGGGCCTTTGTGC
1 CTAGCAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTTGTGC
* ** * *
55413989 CTAGCAGGCTAT-GATGCTAGTGAAATACTATTCGGGCCTTTGAGC
1 CTAGCAGGCT-TCG-TGCTGGTGATGT-GTATTCGGGCCTTTGTGC
55414034 CTAGCAGGCT
1 CTAGCAGGCT
55414044 ATAATGTCGG
Statistics
Matches: 161, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
43 127 0.79
44 8 0.05
45 26 0.16
ACGTcount: A:0.14, C:0.22, G:0.31, T:0.33
Consensus pattern (43 bp):
CTAGCAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTTGTGC
Found at i:55414030 original size:45 final size:44
Alignment explanation
Indices: 55413972--55414130 Score: 184
Period size: 45 Copynumber: 3.6 Consensus size: 44
55413962 CGGTGATGTG
*
55413972 TATTCGGGCCTTTGTGCCTAGCAGGCTATGATGCTAGTGAAATAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTAT-ATGCTAGTGAAATAC
* *
55414017 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATG-TCGGTGAGATAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTAT-ATGCT-AGTGAAATAC
*
55414062 TATTCGGG-CTTTCGAGCCTAGCAGGCTATAGTGCCAGTGAAATGA-
1 TATTCGGGCCTTT-GAGCCTAGCAGGCTATA-TGCTAGTGAAAT-AC
*
55414107 TA-TCGGGCC-TCGAGCCTAGCAGGC
1 TATTCGGGCCTTTGAGCCTAGCAGGC
55414131 AAAATACCGG
Statistics
Matches: 100, Mismatches: 8, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
43 13 0.13
44 12 0.12
45 74 0.74
46 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (44 bp):
TATTCGGGCCTTTGAGCCTAGCAGGCTATATGCTAGTGAAATAC
Found at i:55416690 original size:46 final size:46
Alignment explanation
Indices: 55416574--55416700 Score: 148
Period size: 46 Copynumber: 2.7 Consensus size: 46
55416564 TATGAGGGAT
* * * *
55416574 CCGAACTCGTTGAGTTACGTTCCGAGTTCACCTATGTATGCAAGCAT
1 CCGAACTCGTTGAGTTGCGTTCCGAGTTCA-TTATGGATGCAAGCAC
* * *
55416621 CCAAACTCATTGAGTTGTGTTCCGAGTTCATTATGGATGCGAA-CAC
1 CCGAACTCGTTGAGTTGCGTTCCGAGTTCATTATGGATGC-AAGCAC
* *
55416667 CCGAGCTCGTTGAGTTGCATTCCGAGTTCATTAT
1 CCGAACTCGTTGAGTTGCGTTCCGAGTTCATTAT
55416701 AGGTGAGATT
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
46 39 0.58
47 28 0.42
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGCGTTCCGAGTTCATTATGGATGCAAGCAC
Found at i:55418441 original size:21 final size:21
Alignment explanation
Indices: 55418417--55418456 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
55418407 TATGTAATTA
*
55418417 TCAG-AACAATATTTCATATAT
1 TCAGAAAC-ATATATCATATAT
55418438 TCAGAAACATATATCATAT
1 TCAGAAACATATATCATAT
55418457 CAGAGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
TCAGAAACATATATCATATAT
Found at i:55418846 original size:29 final size:29
Alignment explanation
Indices: 55418813--55418871 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
55418803 CATGTTTCTA
** *
55418813 AGCATATTAACATGTAACATACCGAACTT
1 AGCATATTAACACATAACATACAGAACTT
*
55418842 AGCATATTAACACATAATATACAGAACTT
1 AGCATATTAACACATAACATACAGAACTT
55418871 A
1 A
55418872 CTCTGTTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.27
Consensus pattern (29 bp):
AGCATATTAACACATAACATACAGAACTT
Found at i:55427839 original size:26 final size:26
Alignment explanation
Indices: 55427808--55427915 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
55427798 TGAAATGTCC
*
55427808 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
**
55427834 ATCATGGAATGTTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
55427860 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
55427886 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
55427912 ATCA
1 ATCA
55427916 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:55438438 original size:53 final size:53
Alignment explanation
Indices: 55438292--55438448 Score: 167
Period size: 53 Copynumber: 2.9 Consensus size: 53
55438282 GAGGGAAGCC
* *
55438292 AAAGTGAAAACCCGCAAAGGGCGCTTTGGGGCTTTCAGA-AAAAAAAAAAAGGGCT
1 AAAGTGAAAACCCGCAAAGGGCGCTTTGAGAC--TCA-ATAAAAAAAAAAAGGGCT
* * * *
55438347 AAAGTGAAAACCCGCAACGAGCGCTTT-AGGAC-CAAATAAAAATAGAAAGGGCT
1 AAAGTGAAAACCCGCAAAGGGCGCTTTGA-GACTC-AATAAAAAAAAAAAGGGCT
* *
55438400 AAGGTGAAAACCCGCAAAGGGCACTTTGAGACTCAATAATAAAAAAAAA
1 AAAGTGAAAACCCGCAAAGGGCGCTTTGAGACTCAATAA-AAAAAAAAA
55438449 AGAGAGAAAG
Statistics
Matches: 84, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
52 2 0.02
53 46 0.55
54 9 0.11
55 27 0.32
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (53 bp):
AAAGTGAAAACCCGCAAAGGGCGCTTTGAGACTCAATAAAAAAAAAAAGGGCT
Found at i:55440012 original size:180 final size:180
Alignment explanation
Indices: 55439503--55440081 Score: 829
Period size: 180 Copynumber: 3.2 Consensus size: 180
55439493 ATTGGTAAAG
* * * * *
55439503 ATTGAAGATCTTAACTCCTTGAAGTTGCAGCGGAGTAGATCTTCGCAGATGGTGAAAT-TTATCT
1 ATTGAAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCACAGATGGTG-AATCTTATCT
* * **
55439567 CCATGTATCGGCAATGGAGCAGATTTCACCACCAAGCCTTGTCTCTCTGAGGTAGCAAGAGAATA
65 CCATGTATCGGCAATGGAGCAGATTTTACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCA
* *
55439632 GGTTAAAGAATGAGTCTTATCTTTCTGAGGTAGCAAGGAAGCAGACTGAGA
130 GGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAGA
* * * * *
55439683 ATTGAGGATATTATCTCCCTGAAGTTGCAGCGGAGTAGATCTTTA-TGATGGTGAATCTTATCTC
1 ATTGAAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCACAGATGGTGAATCTTATCTC
* * * * *
55439747 CATGTATCAGCAATGGAGCAGATGTTACCATCAAACCTTATCTCTCTGAGATAGCAAGAGAGCAG
66 CATGTATCGGCAATGGAGCAGATTTTACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAG
*
55439812 GATGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAGA
131 GTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAGA
*
55439862 ATTGAAGATTTTATCTCCCTGAAGTTGCAGTGGAGCAGATCTTCACAGATGGTGAATCTTATCTC
1 ATTGAAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCACAGATGGTGAATCTTATCTC
* * ** *
55439927 CATGTATTGGCAATGGAGTAGATTTTATTACCAAGCCTTATCTCTCTGAGGTAGCAAAAGAGCAG
66 CATGTATCGGCAATGGAGCAGATTTTACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAG
* * *
55439992 GTTGAAGAATGAGTCTTATCTTCCTGAGATAACAAGGAAGCAGATTGAGA
131 GTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAGA
* * *
55440042 ATTGAAGATTTTATTTCCCTGAACTTGCAGTGGAGCAGAT
1 ATTGAAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGAT
55440082 TGAAAATGGA
Statistics
Matches: 356, Mismatches: 41, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
178 3 0.01
179 157 0.44
180 196 0.55
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (180 bp):
ATTGAAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCACAGATGGTGAATCTTATCTC
CATGTATCGGCAATGGAGCAGATTTTACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAG
GTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAGA
Found at i:55440686 original size:94 final size:94
Alignment explanation
Indices: 55440525--55440713 Score: 335
Period size: 94 Copynumber: 2.0 Consensus size: 94
55440515 CTTTCACGAG
*
55440525 TAAATTTTTTCTGTATAGCCGTTGCTCCATCCCTGCATTAGAATATACGAGAAGAAGGATAACAG
1 TAAATTTTTTCTGTACAGCCGTTGCTCCATCCCTGCATTAGAATATACGAGAAGAAGGATAACAG
55440590 AATTGACAGCAATGAAAATAGAATTTCAT
66 AATTGACAGCAATGAAAATAGAATTTCAT
*
55440619 TAAATTTTTT-TCGTACAGCCGTTGCTCCATCCCTGCATTAGAATATATGAGAAGAAGGATAACA
1 TAAATTTTTTCT-GTACAGCCGTTGCTCCATCCCTGCATTAGAATATACGAGAAGAAGGATAACA
*
55440683 GAATTGACAGCAATGGAAATAGAATTTCAT
65 GAATTGACAGCAATGAAAATAGAATTTCAT
55440713 T
1 T
55440714 TTTTATATAT
Statistics
Matches: 91, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
93 1 0.01
94 90 0.99
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (94 bp):
TAAATTTTTTCTGTACAGCCGTTGCTCCATCCCTGCATTAGAATATACGAGAAGAAGGATAACAG
AATTGACAGCAATGAAAATAGAATTTCAT
Found at i:55442891 original size:55 final size:53
Alignment explanation
Indices: 55442748--55442956 Score: 235
Period size: 55 Copynumber: 3.9 Consensus size: 53
55442738 ATCCTTTTGA
* *
55442748 AACTTACCACTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
* * *
55442801 AACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAG
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCC-TTGCCTTAT-G
* **
55442855 TAACTTATCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-G
1 -AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
* * *
55442908 AAACCTTTCCAATTGCCATGTCTTTG-CATGGTCTTTCATGGTATCCTTG
1 -AA-CTTACCAA-TGCCATGTC-TTGACATGGTCTTACATGGGATCCTTG
55442957 AACCCTAATG
Statistics
Matches: 133, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
52 2 0.02
53 47 0.35
54 7 0.05
55 72 0.54
56 5 0.04
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (53 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
Found at i:55442898 original size:108 final size:110
Alignment explanation
Indices: 55442748--55442948 Score: 300
Period size: 108 Copynumber: 1.8 Consensus size: 110
55442738 ATCCTTTTGA
* *
55442748 AACTTACCACTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA
55442811 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
* **
55442856 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTTTCCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
* * *
55442921 TGCCATGTCTTTGCATGGTCTTTCATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
55442949 TATCCTTGAA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 1 0.01
108 50 0.61
109 6 0.07
110 25 0.30
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.35
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
Found at i:55444060 original size:81 final size:81
Alignment explanation
Indices: 55443962--55444123 Score: 324
Period size: 81 Copynumber: 2.0 Consensus size: 81
55443952 AGAAACTTCT
55443962 AGAATGCAAGTTTTGCAACTTATTCAATTTAGTCCCAAATTTCAAATTAAGCACTTTATGCATAG
1 AGAATGCAAGTTTTGCAACTTATTCAATTTAGTCCCAAATTTCAAATTAAGCACTTTATGCATAG
55444027 AATTTCTTCACGAAAG
66 AATTTCTTCACGAAAG
55444043 AGAATGCAAGTTTTGCAACTTATTCAATTTAGTCCCAAATTTCAAATTAAGCACTTTATGCATAG
1 AGAATGCAAGTTTTGCAACTTATTCAATTTAGTCCCAAATTTCAAATTAAGCACTTTATGCATAG
55444108 AATTTCTTCACGAAAG
66 AATTTCTTCACGAAAG
55444124 TTTCACACAA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (81 bp):
AGAATGCAAGTTTTGCAACTTATTCAATTTAGTCCCAAATTTCAAATTAAGCACTTTATGCATAG
AATTTCTTCACGAAAG
Found at i:55446920 original size:50 final size:50
Alignment explanation
Indices: 55446808--55447141 Score: 343
Period size: 50 Copynumber: 6.8 Consensus size: 50
55446798 GGGTGCCGAC
* * * * *
55446808 GCCATGTCCCAGACATGGTCTTACACTG--GCTCAGACATCAAAGTCGAT
1 GCCATGTCCCAGACATGGTCTTACACTGACTCTCATATATCGAGGTCGAT
* * *
55446856 GCCATGTCCGAGACATGGTCTTACACTGACTCTCGTATATTGAGGTCGAT
1 GCCATGTCCCAGACATGGTCTTACACTGACTCTCATATATCGAGGTCGAT
* * * *
55446906 GCCATGTCCCAGACATGCTCTTACACTGGCTCTCATCTATCG-GTTCCGAT
1 GCCATGTCCCAGACATGGTCTTACACTGACTCTCATATATCGAGGT-CGAT
* *
55446956 GTCATGTCCTAGACATGGTCTTACACT-AGCTCTCATATATC-AGTGTCGAT
1 GCCATGTCCCAGACATGGTCTTACACTGA-CTCTCATATATCGAG-GTCGAT
* *
55447006 GCCATGTCCCAGACATGGTCTTACACTGA----CACATATCGA-GCCGAT
1 GCCATGTCCCAGACATGGTCTTACACTGACTCTCATATATCGAGGTCGAT
* * *
55447051 GCCATGTACCAGACATAGTCTTACACT-AGTTCTCATATATCGAGG-CTGAT
1 GCCATGTCCCAGACATGGTCTTACACTGA-CTCTCATATATCGAGGTC-GAT
*
55447101 GCCATGTCCCAGACACGGTCTTACACT-AGCTCTCATATATC
1 GCCATGTCCCAGACATGGTCTTACACTGA-CTCTCATATATC
55447142 CCTAGCGTCA
Statistics
Matches: 239, Mismatches: 32, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
44 1 0.00
45 30 0.13
46 7 0.03
47 1 0.00
48 27 0.11
49 12 0.05
50 159 0.67
51 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACACTGACTCTCATATATCGAGGTCGAT
Found at i:55468784 original size:3 final size:3
Alignment explanation
Indices: 55468776--55468832 Score: 62
Period size: 3 Copynumber: 18.7 Consensus size: 3
55468766 CATCATTCGA
* *
55468776 TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT T-T TAT GTTT TGAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT T-AT
*
55468822 TAT TAA TAT TA
1 TAT TAT TAT TA
55468833 GAATTAGAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
2 2 0.04
3 39 0.87
4 4 0.09
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:55475399 original size:143 final size:143
Alignment explanation
Indices: 55474841--55475409 Score: 762
Period size: 143 Copynumber: 4.0 Consensus size: 143
55474831 TAGATCGAAG
* * * * * * *
55474841 ATGGCGGATTTTATCTTCCTAAAGTTGCAGTTGAGCAAATTGAATCCACCAGCCTTATCTCCTTG
1 ATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTG
* * * * *
55474906 AAGTTACAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGACGTTACAGTAGAACAGATT
66 AAGTTGCAGCGAAGCAGACTGAAGACAGCGAATCTTATTTCCCTGACGTTGCAGTAGAACAAATT
55474971 AAAGCTACAAATT
131 AAAGCTACAAATT
* * *
55474984 ATGGCAGATCTTATCTTCCTGAAGTTGTAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCTCTA
1 ATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTG
* * * * * * *
55475049 AAGTTGCAGCGGAGCAGACTGAAGACAGTGAATCTTATTTCCTTGATGTTGTAGTGGAACAGATT
66 AAGTTGCAGCGAAGCAGACTGAAGACAGCGAATCTTATTTCCCTGACGTTGCAGTAGAACAAATT
55475114 AAAGCTACAAATT
131 AAAGCTACAAATT
* * * * *
55475127 ATGACAGATCTTATCTTCCTGAAATTACAGTGGAGCAGATTGAAGCCATCAGCCTTATCTCCCCG
1 ATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTG
* *
55475192 AAATTGCAGCGAAGCAGACTAAAGACAGCGAATCTTATTTCCCTGACGTTGCAGTAGAACAAATT
66 AAGTTGCAGCGAAGCAGACTGAAGACAGCGAATCTTATTTCCCTGACGTTGCAGTAGAACAAATT
55475257 AAAGCTACAAATT
131 AAAGCTACAAATT
* * *
55475270 ATGGC-GAATCTTATCTTCTTGAAGTTGTAGTGGAGCAGATTAAAGCCACCAGCCTTATCTCCCT
1 ATGGCAG-ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCT
* * * * * **
55475334 GAAGTTGCAGCGAAGCAGACTGAAGATAGCGAATATCATTTCCCTAAAGTTGCAGTAGAGTAAAT
65 GAAGTTGCAGCGAAGCAGACTGAAGACAGCGAATCTTATTTCCCTGACGTTGCAGTAGAACAAAT
*
55475399 TGAAGCTACAA
130 TAAAGCTACAA
55475410 GTTGCGAGTC
Statistics
Matches: 372, Mismatches: 53, Indels: 2
0.87 0.12 0.00
Matches are distributed among these distances:
142 1 0.00
143 371 1.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (143 bp):
ATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTG
AAGTTGCAGCGAAGCAGACTGAAGACAGCGAATCTTATTTCCCTGACGTTGCAGTAGAACAAATT
AAAGCTACAAATT
Found at i:55475441 original size:51 final size:51
Alignment explanation
Indices: 55475374--55475638 Score: 182
Period size: 51 Copynumber: 5.4 Consensus size: 51
55475364 GAATATCATT
* *
55475374 TCCCTAAAGTTGCAGTAGAGTAAATTGAAGCTACAAGTTGCGAGTCTTATC
1 TCCCTGAAGTTGCAGTAGAGTAGATTGAAGCTACAAGTTGCGAGTCTTATC
* * * * *
55475425 TCCCCGAAGTTACAGTAAGAGTAGACTGAAGATAGCAA------A-TCTTATT
1 TCCCTGAAGTTGCAGT-AGAGTAGATTGAAGCTA-CAAGTTGCGAGTCTTATC
* * * * *
55475471 TCCCTGAAATTGCCGTGGAGCAGATTGAAGCTAAAAGTTGCGAGTCTTATC
1 TCCCTGAAGTTGCAGTAGAGTAGATTGAAGCTACAAGTTGCGAGTCTTATC
* * * *
55475522 TCCCTGAAGTTGCAGTAG-G-AGCA-T--A-CTA-AAGATAGTGAATCTTATT
1 TCCCTGAAGTTGCAGTAGAGTAG-ATTGAAGCTACAAG-TTGCGAGTCTTATC
* * * *
55475568 TCCCTGAAGTTGCAGTAGAGCAGATTGAAGCTATAAGTTACG-GATCTTAGC
1 TCCCTGAAGTTGCAGTAGAGTAGATTGAAGCTACAAGTTGCGAG-TCTTATC
* *
55475619 TCTCTGAAGTAGCAGTAGAG
1 TCCCTGAAGTTGCAGTAGAG
55475639 CAAGTTAAAG
Statistics
Matches: 163, Mismatches: 32, Indels: 38
0.70 0.14 0.16
Matches are distributed among these distances:
44 2 0.01
45 16 0.10
46 49 0.30
47 4 0.02
48 3 0.02
49 3 0.02
50 4 0.02
51 62 0.38
52 17 0.10
53 3 0.02
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.28
Consensus pattern (51 bp):
TCCCTGAAGTTGCAGTAGAGTAGATTGAAGCTACAAGTTGCGAGTCTTATC
Found at i:55475498 original size:97 final size:97
Alignment explanation
Indices: 55475323--55475640 Score: 383
Period size: 97 Copynumber: 3.3 Consensus size: 97
55475313 AGCCACCAGC
** * *
55475323 CTTATCTCCCTGAAGTTGCAGCGA-AGCAGACTGAAGATAGCGAATATCATTTCCCT-AAAGTTG
1 CTTATCTCCCTGAAGTTGCAGTAAGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAA-TTG
* * *
55475386 CAGTAGAGTAAATTGAAGCTACAAGTTGCGAGT
65 CAGTAGAGCAGATTGAAGCTAAAAGTTGCGAGT
* * * *
55475419 CTTATCTCCCCGAAGTTACAGTAAGAGTAGACTGAAGATAGCAAATCTTATTTCCCTGAAATTGC
1 CTTATCTCCCTGAAGTTGCAGTAAGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAATTGC
* *
55475484 CGTGGAGCAGATTGAAGCTAAAAGTTGCGAGT
66 AGTAGAGCAGATTGAAGCTAAAAGTTGCGAGT
* * * * *
55475516 CTTATCTCCCTGAAGTTGCAGTAGGAGCATACTAAAGATAGTGAATCTTATTTCCCTGAAGTTGC
1 CTTATCTCCCTGAAGTTGCAGTAAGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAATTGC
* *
55475581 AGTAGAGCAGATTGAAGCTATAAGTTACG-GAT
66 AGTAGAGCAGATTGAAGCTAAAAGTTGCGAG-T
* * *
55475613 CTTAGCTCTCTGAAGTAGCAGT-AGAGCA
1 CTTATCTCCCTGAAGTTGCAGTAAGAGCA
55475641 AGTTAAAGTC
Statistics
Matches: 189, Mismatches: 30, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
96 26 0.14
97 160 0.85
98 3 0.02
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.27
Consensus pattern (97 bp):
CTTATCTCCCTGAAGTTGCAGTAAGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAATTGC
AGTAGAGCAGATTGAAGCTAAAAGTTGCGAGT
Found at i:55477354 original size:3 final size:3
Alignment explanation
Indices: 55477346--55477383 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
55477336 CATCATTCGA
*
55477346 TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
55477384 GTTTTGATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:55486591 original size:4 final size:4
Alignment explanation
Indices: 55486582--55486606 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
55486572 GTTTTATTTC
55486582 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
55486607 TACTTAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:55495802 original size:11 final size:11
Alignment explanation
Indices: 55495786--55495814 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
55495776 TCTACATGAC
55495786 TAAAACACACT
1 TAAAACACACT
55495797 TAAAACACACT
1 TAAAACACACT
55495808 TAAAACA
1 TAAAACA
55495815 TGCCAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.59, C:0.24, G:0.00, T:0.17
Consensus pattern (11 bp):
TAAAACACACT
Found at i:55498465 original size:47 final size:47
Alignment explanation
Indices: 55498396--55498487 Score: 175
Period size: 47 Copynumber: 2.0 Consensus size: 47
55498386 AACATTCGAC
55498396 AACATAACTTGAATATAGCATAAATACTTTTACGAGCCTTAAATCAT
1 AACATAACTTGAATATAGCATAAATACTTTTACGAGCCTTAAATCAT
*
55498443 AACATAACTTGAGTATAGCATAAATACTTTTACGAGCCTTAAATC
1 AACATAACTTGAATATAGCATAAATACTTTTACGAGCCTTAAATC
55498488 GAGCCTAAGG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (47 bp):
AACATAACTTGAATATAGCATAAATACTTTTACGAGCCTTAAATCAT
Found at i:55500052 original size:41 final size:41
Alignment explanation
Indices: 55499992--55500629 Score: 497
Period size: 41 Copynumber: 15.5 Consensus size: 41
55499982 TACCTAATAC
* * *
55499992 AATACACT-AGCACGAAGCCTGTTAAGCTCAAAACCTGATAT
1 AATACACTGA-CACGAAGCCTGCTAAGCACAAAGCCTGATAT
* * * * *
55500033 AACACACTGACACGAAGCCTACTAGGCTCAAAGTCTGATAT
1 AATACACTGACACGAAGCCTGCTAAGCACAAAGCCTGATAT
* * * * ** * * *
55500074 AACACACCAGA-ACAAAGCTTTTTAGGCACAAAGCTTAATAT
1 AATACA-CTGACACGAAGCCTGCTAAGCACAAAGCCTGATAT
* *
55500115 AATACACTGACACGAAGCCTACT-AGTCAGAAAGCCTGATAT
1 AATACACTGACACGAAGCCTGCTAAG-CACAAAGCCTGATAT
* *
55500156 AATACACT-AGCACGAAGCCTGCTAAGCCCAAAGCTTGATAT
1 AATACACTGA-CACGAAGCCTGCTAAGCACAAAGCCTGATAT
* * *
55500197 AATACAC-CAGCACAAAGCCTGCTAGGCACAAAGCCTGATAT
1 AATACACTGA-CACGAAGCCTGCTAAGCACAAAGCCTGATAT
* * * ** *
55500238 AATACACTGGCACGAAACCTAC-AAGGCACAACTCCTAATAT
1 AATACACTGACACGAAGCCTGCTAA-GCACAAAGCCTGATAT
* * *
55500279 AATACACCGACACGAAGCCTGCTAAGCCCAAAGCTTGATAT
1 AATACACTGACACGAAGCCTGCTAAGCACAAAGCCTGATAT
* * *
55500320 AATACAC-CAGCACAAAGCCTGCTAGGCACAAAGCCTGATAT
1 AATACACTGA-CACGAAGCCTGCTAAGCACAAAGCCTGATAT
* * * ** *
55500361 AATACACTGGCACGAAACCTAC-AAGGCACAACTCCTAATAT
1 AATACACTGACACGAAGCCTGCTAA-GCACAAAGCCTGATAT
* * * *
55500402 AATACACCGACACGAAGCCTGCTAAGAATAAAGCTTGATAT
1 AATACACTGACACGAAGCCTGCTAAGCACAAAGCCTGATAT
* * * *
55500443 AATACACT-AGCATGAAGCCTACTAGGCATAAAGGCCTGATAT
1 AATACACTGA-CACGAAGCCTGCTAAGCACAAA-GCCTGATAT
* *
55500485 AATACA-TCGACATGAAGCTTGCTAAGCACAAAGCCTGATAT
1 AATACACT-GACACGAAGCCTGCTAAGCACAAAGCCTGATAT
* * * * * * *
55500526 AATACATTGGCACAAAGCCTGCTAGGAATAAAGCCTGATAC
1 AATACACTGACACGAAGCCTGCTAAGCACAAAGCCTGATAT
* * * *
55500567 AATACACT-AGCACGAAACTTGCTAGGCACAAAGCTTGATAT
1 AATACACTGA-CACGAAGCCTGCTAAGCACAAAGCCTGATAT
* * *
55500608 AATACACCGGCATGAAGCCTGC
1 AATACACTGACACGAAGCCTGC
55500630 AGGACTTAAT
Statistics
Matches: 469, Mismatches: 107, Indels: 42
0.76 0.17 0.07
Matches are distributed among these distances:
40 9 0.02
41 416 0.89
42 43 0.09
43 1 0.00
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.19
Consensus pattern (41 bp):
AATACACTGACACGAAGCCTGCTAAGCACAAAGCCTGATAT
Found at i:55500188 original size:82 final size:82
Alignment explanation
Indices: 55499992--55500614 Score: 590
Period size: 82 Copynumber: 7.6 Consensus size: 82
55499982 TACCTAATAC
* * * *
55499992 AATACACTAGCACGAAGCCTGTTAAGCTCAAAACCTGATATAACACACTGACACGAAGCCTACTA
1 AATACACTAGCACGAAGCCTGCTAAGCACAAAGCCTGATATAATACACTGACACGAAGCCTACTA
* *
55500057 GGCTCAAAGTCTGATAT
66 GGCACAAAGCCTGATAT
* * * * * ** * * *
55500074 AACACACCAGAACAAAGCTTTTTAGGCACAAAGCTTAATATAATACACTGACACGAAGCCTACTA
1 AATACACTAGCACGAAGCCTGCTAAGCACAAAGCCTGATATAATACACTGACACGAAGCCTACTA
* *
55500139 GTCAGAAAGCCTGATAT
66 GGCACAAAGCCTGATAT
* * * * *
55500156 AATACACTAGCACGAAGCCTGCTAAGCCCAAAGCTTGATATAATACAC-CAGCACAAAGCCTGCT
1 AATACACTAGCACGAAGCCTGCTAAGCACAAAGCCTGATATAATACACTGA-CACGAAGCCTACT
55500220 AGGCACAAAGCCTGATAT
65 AGGCACAAAGCCTGATAT
* * * ** * * *
55500238 AATACACTGGCACGAAACCTAC-AAGGCACAACTCCTAATATAATACACCGACACGAAGCCTGCT
1 AATACACTAGCACGAAGCCTGCTAA-GCACAAAGCCTGATATAATACACTGACACGAAGCCTACT
* * *
55500302 AAGCCCAAAGCTTGATAT
65 AGGCACAAAGCCTGATAT
* * * * * *
55500320 AATACACCAGCACAAAGCCTGCTAGGCACAAAGCCTGATATAATACACTGGCACGAAACCTACAA
1 AATACACTAGCACGAAGCCTGCTAAGCACAAAGCCTGATATAATACACTGACACGAAGCCTACTA
** *
55500385 GGCACAACTCCTAATAT
66 GGCACAAAGCCTGATAT
* * * * *
55500402 AATACAC-CGACACGAAGCCTGCTAAGAATAAAGCTTGATATAATACACT-AGCATGAAGCCTAC
1 AATACACTAG-CACGAAGCCTGCTAAGCACAAAGCCTGATATAATACACTGA-CACGAAGCCTAC
*
55500465 TAGGCATAAAGGCCTGATAT
64 TAGGCACAAA-GCCTGATAT
* * * * * * *
55500485 AATACA-TCGACATGAAGCTTGCTAAGCACAAAGCCTGATATAATACATTGGCACAAAGCCTGCT
1 AATACACTAG-CACGAAGCCTGCTAAGCACAAAGCCTGATATAATACACTGACACGAAGCCTACT
* * *
55500549 AGGAATAAAGCCTGATAC
65 AGGCACAAAGCCTGATAT
* * * *
55500567 AATACACTAGCACGAAACTTGCTAGGCACAAAGCTTGATATAATACAC
1 AATACACTAGCACGAAGCCTGCTAAGCACAAAGCCTGATATAATACAC
55500615 CGGCATGAAG
Statistics
Matches: 435, Mismatches: 96, Indels: 20
0.79 0.17 0.04
Matches are distributed among these distances:
81 4 0.01
82 360 0.83
83 71 0.16
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.19
Consensus pattern (82 bp):
AATACACTAGCACGAAGCCTGCTAAGCACAAAGCCTGATATAATACACTGACACGAAGCCTACTA
GGCACAAAGCCTGATAT
Found at i:55500205 original size:123 final size:124
Alignment explanation
Indices: 55499992--55500614 Score: 643
Period size: 123 Copynumber: 5.1 Consensus size: 124
55499982 TACCTAATAC
** * * * * *
55499992 AATACACT-AGCACGAAGCCTGTTAAGCTCAAAACCTGATATAACACACT-GACACGAAGCCTAC
1 AATACACTGA-CACGAAGCCTACTAGGCACAAAGCCTGATATAATACACTCGACACGAAGCCTGC
* * * * * ** * *
55500055 TAGGCTCAAAG-TCTGATATAACACACCAGAACAAAGCTTTTTAGGCACAAAGCTTAATAT
65 TAAGCACAAAGCT-TGATATAATACACCAGCACAAAGCCTGCTAGGCACAAAGCCTGATAT
* * *
55500115 AATACACTGACACGAAGCCTACTAGTCAGAAAGCCTGATATAATACACTAG-CACGAAGCCTGCT
1 AATACACTGACACGAAGCCTACTAGGCACAAAGCCTGATATAATACACTCGACACGAAGCCTGCT
*
55500179 AAGCCCAAAGCTTGATATAATACACCAGCACAAAGCCTGCTAGGCACAAAGCCTGATAT
66 AAGCACAAAGCTTGATATAATACACCAGCACAAAGCCTGCTAGGCACAAAGCCTGATAT
* * * ** *
55500238 AATACACTGGCACGAAACCTACAAGGCACAACTCCTAATATAATACAC-CGACACGAAGCCTGCT
1 AATACACTGACACGAAGCCTACTAGGCACAAAGCCTGATATAATACACTCGACACGAAGCCTGCT
*
55500302 AAGCCCAAAGCTTGATATAATACACCAGCACAAAGCCTGCTAGGCACAAAGCCTGATAT
66 AAGCACAAAGCTTGATATAATACACCAGCACAAAGCCTGCTAGGCACAAAGCCTGATAT
* * * ** *
55500361 AATACACTGGCACGAAACCTACAAGGCACAACTCCTAATATAATACAC-CGACACGAAGCCTGCT
1 AATACACTGACACGAAGCCTACTAGGCACAAAGCCTGATATAATACACTCGACACGAAGCCTGCT
* * * ** * *
55500425 AAGAATAAAGCTTGATATAATACACTAGCATGAAGCCTACTAGGCATAAAGGCCTGATAT
66 AAGCACAAAGCTTGATATAATACACCAGCACAAAGCCTGCTAGGCACAAA-GCCTGATAT
* * * * * * *
55500485 AATACA-TCGACATGAAGCTTGCTAAGCACAAAGCCTGATATAATACA-TTGGCACAAAGCCTGC
1 AATACACT-GACACGAAGCCTACTAGGCACAAAGCCTGATATAATACACTCGACACGAAGCCTGC
* * * * * * * *
55500548 TAGGAATAAAGCCTGATACAATACACTAGCACGAAA-CTTGCTAGGCACAAAGCTTGATAT
65 TAAGCACAAAGCTTGATATAATACACCAGCAC-AAAGCCTGCTAGGCACAAAGCCTGATAT
55500608 AATACAC
1 AATACAC
55500615 CGGCATGAAG
Statistics
Matches: 434, Mismatches: 57, Indels: 17
0.85 0.11 0.03
Matches are distributed among these distances:
122 1 0.00
123 332 0.76
124 99 0.23
125 2 0.00
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.19
Consensus pattern (124 bp):
AATACACTGACACGAAGCCTACTAGGCACAAAGCCTGATATAATACACTCGACACGAAGCCTGCT
AAGCACAAAGCTTGATATAATACACCAGCACAAAGCCTGCTAGGCACAAAGCCTGATAT
Found at i:55502788 original size:44 final size:44
Alignment explanation
Indices: 55502725--55502824 Score: 182
Period size: 44 Copynumber: 2.3 Consensus size: 44
55502715 ACAAGGGATG
*
55502725 ATGGGCAAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACAGGTTGTGTTAATGGAAAAATAAAATAAGAAGC
55502769 ATGGGCAAAACAGGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACAGGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
55502813 ATGGGCGAAACA
1 ATGGGCAAAACA
55502825 TGTCATGAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.47, C:0.08, G:0.25, T:0.20
Consensus pattern (44 bp):
ATGGGCAAAACAGGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:55504523 original size:47 final size:47
Alignment explanation
Indices: 55504472--55504694 Score: 322
Period size: 47 Copynumber: 4.7 Consensus size: 47
55504462 TTAGGATTCT
* * *
55504472 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
55504519 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
55504566 ATGTGATGAATGTGAGAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
55504613 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
55504660 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
55504695 TCCCGAAGGG
Statistics
Matches: 160, Mismatches: 15, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
46 1 0.01
47 159 0.99
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:55504869 original size:37 final size:37
Alignment explanation
Indices: 55504813--55504891 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
55504803 CCGAGCTCTA
* * *
55504813 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
55504850 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
55504887 AAGAC
1 AAGAC
55504892 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:55507336 original size:13 final size:13
Alignment explanation
Indices: 55507316--55507351 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
55507306 TTTGTTGCGA
55507316 ACTCTCATGTTAT
1 ACTCTCATGTTAT
*
55507329 ATTCTCATGTTAT
1 ACTCTCATGTTAT
55507342 ACTCTC-TGTT
1 ACTCTCATGTT
55507352 TGGTGTGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.19, C:0.22, G:0.08, T:0.50
Consensus pattern (13 bp):
ACTCTCATGTTAT
Found at i:55507462 original size:36 final size:36
Alignment explanation
Indices: 55507393--55507463 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
55507383 ATTGCTGTGT
* * **
55507393 TGGAGGGATTGGCTCGTGTGAGCATCTGGTGTGTTC
1 TGGAAGGATTGACTCGTGTGAGCATCTACTGTGTTC
55507429 TGGAAGGATTGACTCGTGTGAGCATCTACTGTGTT
1 TGGAAGGATTGACTCGTGTGAGCATCTACTGTGTT
55507464 TGGTTGGACT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.15, C:0.14, G:0.37, T:0.34
Consensus pattern (36 bp):
TGGAAGGATTGACTCGTGTGAGCATCTACTGTGTTC
Found at i:55508338 original size:17 final size:16
Alignment explanation
Indices: 55508316--55508347 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
55508306 TTACAAATTA
55508316 TTGGAAGCTCGATCGGG
1 TTGGAAGCTC-ATCGGG
55508333 TTGGAAGCTCATCGG
1 TTGGAAGCTCATCGG
55508348 AGATCTATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.25
Consensus pattern (16 bp):
TTGGAAGCTCATCGGG
Found at i:55510818 original size:42 final size:42
Alignment explanation
Indices: 55510708--55510822 Score: 133
Period size: 43 Copynumber: 2.7 Consensus size: 42
55510698 AAAGCTCGTA
* *
55510708 CAATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAAATAT
1 CAATGCC-ATGTCCCAGACATGGTCTTACATGAAATCAAATAT
** * *
55510751 CAATGCCACTGTCATAGACAGGGTCTTACATGAAATCATATA-
1 CAATGCCA-TGTCCCAGACATGGTCTTACATGAAATCAAATAT
*
55510793 CGATGCCTATGTCCCAGACATGGTCTTACA
1 CAATGCC-ATGTCCCAGACATGGTCTTACA
55510823 CGTAGATCTC
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
42 25 0.42
43 35 0.58
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.27
Consensus pattern (42 bp):
CAATGCCATGTCCCAGACATGGTCTTACATGAAATCAAATAT
Found at i:55514211 original size:23 final size:21
Alignment explanation
Indices: 55514166--55514210 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
55514156 TGGTCTGCGT
*
55514166 ACATGGGTGTGTGAAGTAGAC
1 ACATGGGAGTGTGAAGTAGAC
* *
55514187 ACATGGGAGTGTGGAGTAGCC
1 ACATGGGAGTGTGAAGTAGAC
55514208 ACA
1 ACA
55514211 CGACCATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.13, G:0.38, T:0.20
Consensus pattern (21 bp):
ACATGGGAGTGTGAAGTAGAC
Found at i:55517472 original size:5 final size:5
Alignment explanation
Indices: 55517462--55517500 Score: 71
Period size: 5 Copynumber: 8.0 Consensus size: 5
55517452 GATACCAACC
55517462 ATAAA ATAAA ATAAA ATAAA AT-AA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
55517501 TTTTTATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:55517489 original size:14 final size:14
Alignment explanation
Indices: 55517462--55517501 Score: 71
Period size: 14 Copynumber: 2.8 Consensus size: 14
55517452 GATACCAACC
55517462 ATAAAATAAAATAAA
1 ATAAAAT-AAATAAA
55517477 ATAAAATAAATAAA
1 ATAAAATAAATAAA
55517491 ATAAAATAAAT
1 ATAAAATAAAT
55517502 TTTTATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 18 0.72
15 7 0.28
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
ATAAAATAAATAAA
Found at i:55520961 original size:47 final size:48
Alignment explanation
Indices: 55520893--55521255 Score: 209
Period size: 47 Copynumber: 7.7 Consensus size: 48
55520883 AGATATGTGC
* *
55520893 GCCAGTGTTAGACATGTCTGGGACAT-GCATCCACCACATA-ATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGGCATCCGCCACATAGATGAGA
* * * *
55520939 GCCAGTGTAAGACCATGTCTGGGACATGGCAT-CGGCATAGAGACGA-A
1 GCCAGTGTAAGA-CATGTCTGGGACATGGCATCCGCCACATAGATGAGA
* * **
55520986 TGCTAGTGTAAGACATGTCTGGGACAT-GCAT-CGGC-TTTGAGATGAGA
1 -GCCAGTGTAAGACATGTCTGGGACATGGCATCCGCCACAT-AGATGAGA
* * * * * *
55521033 GCCAGTGTAAGACATGTCTGGGACAT-ACATCCGCCTCGAGATATGCGT
1 GCCAGTGTAAGACATGTCTGGGACATGGCATCCGCCAC-ATAGATGAGA
* * * * * *
55521081 GCTAGTGTAAGACCATATCTGGGCCATGGCAT-TG--ACATTGAGACGAGT
1 GCCAGTGTAAGA-CATGTCTGGGACATGGCATCCGCCACA-T-AGATGAGA
* * * * * *
55521129 GCGAGTGTAAGACGTGTCTAGGACAT-GCATCGGCCTCGAT-GATGATA
1 GCCAGTGTAAGACATGTCTGGGACATGGCATCCGCCAC-ATAGATGAGA
* * * *
55521176 GTCAGTGTAAGACCATATCTGGGACATGGCAT-CG--ACTTGAGATGTGA
1 GCCAGTGTAAGA-CATGTCTGGGACATGGCATCCGCCACAT-AGATGAGA
* *
55521223 GCTAGTGTAAGACCATGTTTGGGACATGGCATC
1 GCCAGTGTAAGA-CATGTCTGGGACATGGCATC
55521256 GGCTTGACAT
Statistics
Matches: 242, Mismatches: 53, Indels: 42
0.72 0.16 0.12
Matches are distributed among these distances:
45 2 0.01
46 58 0.24
47 97 0.40
48 62 0.26
49 19 0.08
50 4 0.02
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (48 bp):
GCCAGTGTAAGACATGTCTGGGACATGGCATCCGCCACATAGATGAGA
Found at i:55521084 original size:94 final size:96
Alignment explanation
Indices: 55520933--55521258 Score: 364
Period size: 96 Copynumber: 3.4 Consensus size: 96
55520923 CCACCACATA
* * * *
55520933 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT--AGAGACGAATGCTAGTGTA
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCCTCGAGATATGAGTGCTAGTGTA
* *
55520996 AGA-CATGTCTGGGACAT-GCATCGGCTTTGAG
65 AGACCATATCTGGGACATGGCATCGAC-TTGAG
* * *
55521027 ATGAGAGCCAGTGTAAGA-CATGTCTGGGACATACATCCGCCTCGAGATATGCGTGCTAGTGTAA
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGAGATATGAGTGCTAGTGTAA
* *
55521091 GACCATATCTGGGCCATGGCATTGACATTGAG
66 GACCATATCTGGGACATGGCATCGAC-TTGAG
* * * * *
55521123 ACGAGTGCGAGTGTAAGA-CGTGTCTAGGACATGCATCGGCCTCGATGATGAT-AGT-C-AGTGT
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGA-GAT-ATGAGTGCTAGTGT
55521184 AAGACCATATCTGGGACATGGCATCGACTTGAG
64 AAGACCATATCTGGGACATGGCATCGACTTGAG
* * *
55521217 ATGTGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGC
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGC
55521259 TTGACATGTG
Statistics
Matches: 195, Mismatches: 29, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
92 7 0.04
93 14 0.07
94 55 0.28
95 54 0.28
96 58 0.30
97 5 0.03
98 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.24
Consensus pattern (96 bp):
ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGAGATATGAGTGCTAGTGTAA
GACCATATCTGGGACATGGCATCGACTTGAG
Found at i:55521109 original size:142 final size:142
Alignment explanation
Indices: 55520893--55521258 Score: 443
Period size: 142 Copynumber: 2.6 Consensus size: 142
55520883 AGATATGTGC
* * * * *
55520893 GCCAGTGTTAGACATGTCTGGGACATGCATCCACCAC-ATAATGAGAGCCAGTGTAAGACCATGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCCGCCTCGAGAATGAGAGCTAGTGTAAGACCATGT
* * *
55520957 CTGGGACATGGCATCGGCATAGAGACGAATGCTAGTGTAAGACATGTCTGGGACATGCATCGGCT
66 CTGGGACATGGCATCGGCATAGAGACGAATGCGAGTGTAAGACATGTCTAGGACATGCATCGGCC
*
55521022 TTGA-GATGAGA
131 TCGATGATGAGA
* * * *
55521033 GCCAGTGTAAGACATGTCTGGGACATACATCCGCCTCGAGATATGCGTGCTAGTGTAAGACCATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCCGCCTCGAGA-ATGAGAGCTAGTGTAAGACCATG
* * * * * *
55521098 TCTGGGCCATGGCATTGACATTGAGACGAGTGCGAGTGTAAGACGTGTCTAGGACATGCATCGGC
65 TCTGGGACATGGCATCGGCATAGAGACGAATGCGAGTGTAAGACATGTCTAGGACATGCATCGGC
*
55521163 CTCGATGATGATA
130 CTCGATGATGAGA
* * * * *
55521176 GTCAGTGTAAGACCATATCTGGGACATGGCAT-CGACTTGAG-ATGTGAGCTAGTGTAAGACCAT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCCGCCTCGAGAATGAGAGCTAGTGTAAGACCAT
*
55521239 GTTTGGGACATGGCATCGGC
64 GTCTGGGACATGGCATCGGC
55521259 TTGACATGTG
Statistics
Matches: 189, Mismatches: 32, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
140 33 0.17
141 2 0.01
142 114 0.60
143 17 0.09
144 20 0.11
145 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (142 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCCGCCTCGAGAATGAGAGCTAGTGTAAGACCATGT
CTGGGACATGGCATCGGCATAGAGACGAATGCGAGTGTAAGACATGTCTAGGACATGCATCGGCC
TCGATGATGAGA
Found at i:55521139 original size:96 final size:96
Alignment explanation
Indices: 55520933--55521249 Score: 337
Period size: 95 Copynumber: 3.3 Consensus size: 96
55520923 CCACCACATA
* * * * *
55520933 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGA-GACGA-A-TGCTAGTGT
1 ATGAGAGCCAGTGTAAGA-CATGTCTGGGACAT-ACATCCGCCTCGATGATGATAGTGCTAGTGT
* *
55520995 AAGA-CATGTCTGGGACAT-GCATCGGCTTTGAG
64 AAGACCATATCTGGGACATGGCATCGAC-TTGAG
*
55521027 ATGAGAGCCAGTGTAAGACATGTCTGGGACATACATCCGCCTCGA-GAT-ATGCGTGCTAGTGTA
1 ATGAGAGCCAGTGTAAGACATGTCTGGGACATACATCCGCCTCGATGATGAT-AGTGCTAGTGTA
* *
55521090 AGACCATATCTGGGCCATGGCATTGACATTGAG
65 AGACCATATCTGGGACATGGCATCGAC-TTGAG
* * * * * * *
55521123 ACGAGTGCGAGTGTAAGACGTGTCTAGGACATGCATCGGCCTCGATGATGATAGT-C-AGTGTAA
1 ATGAGAGCCAGTGTAAGACATGTCTGGGACATACATCCGCCTCGATGATGATAGTGCTAGTGTAA
55521186 GACCATATCTGGGACATGGCATCGACTTGAG
66 GACCATATCTGGGACATGGCATCGACTTGAG
* * *
55521217 ATGTGAGCTAGTGTAAGACCATGTTTGGGACAT
1 ATGAGAGCCAGTGTAAGA-CATGTCTGGGACAT
55521250 GGCATCGGCT
Statistics
Matches: 187, Mismatches: 28, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
91 1 0.01
92 11 0.06
93 14 0.07
94 50 0.27
95 54 0.29
96 50 0.27
97 5 0.03
98 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (96 bp):
ATGAGAGCCAGTGTAAGACATGTCTGGGACATACATCCGCCTCGATGATGATAGTGCTAGTGTAA
GACCATATCTGGGACATGGCATCGACTTGAG
Found at i:55521256 original size:47 final size:47
Alignment explanation
Indices: 55520937--55521302 Score: 261
Period size: 47 Copynumber: 7.8 Consensus size: 47
55520927 CACATAATGA
* * * *
55520937 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGAGACG-
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGAC-TTGAGATGT
* * *
55520984 AATGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTTTGAGATGA
1 GA-GCTAGTGTAAGACCATGTCTGGGACATGGCATCGAC-TTGAGATGT
* * * * *
55521031 GAGCCAGTGTAAGA-CATGTCTGGGACAT-ACATCCGCCTCGAGATATGC
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCAT-CGACTTGAG--ATGT
* * * * * *
55521079 GTGCTAGTGTAAGACCATATCTGGGCCATGGCATTGACATTGAGACGA
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGAC-TTGAGATGT
* * * * * *
55521127 GTGCGAGTGTAAGA-CGTGTCTAGGACAT-GCATCGGCCTCGATGATGAT
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATC-GACTTGA-GATG-T
*
55521175 -AG-TCAGTGTAAGACCATATCTGGGACATGGCATCGACTTGAGATGT
1 GAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATGT
* * *
55521221 GAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCTTGACATGT
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATGT
* * * *
55521268 G-TC-AGTGTAAGACC-TGTTTGGGACACGGTATCGAC
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGAC
55521303 ACAAATGGAC
Statistics
Matches: 257, Mismatches: 46, Indels: 35
0.76 0.14 0.10
Matches are distributed among these distances:
44 18 0.07
45 11 0.04
46 55 0.21
47 89 0.35
48 58 0.23
49 19 0.07
50 7 0.03
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (47 bp):
GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATGT
Found at i:55521746 original size:59 final size:59
Alignment explanation
Indices: 55521675--55521794 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
55521665 CTTCACCTCC
55521675 TTACCAGAATAGAGTTATATGAGGAAATTCACGAGAGATATTTTGTATAAACTTACAAA
1 TTACCAGAATAGAGTTATATGAGGAAATTCACGAGAGATATTTTGTATAAACTTACAAA
55521734 TTACCAGAATAGAGTTATATGAGGAAATTCACGAGAGATATTTTGTATAAACTTACAAA
1 TTACCAGAATAGAGTTATATGAGGAAATTCACGAGAGATATTTTGTATAAACTTACAAA
55521793 TT
1 TT
55521795 GGAAACTAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.32
Consensus pattern (59 bp):
TTACCAGAATAGAGTTATATGAGGAAATTCACGAGAGATATTTTGTATAAACTTACAAA
Found at i:55526692 original size:46 final size:47
Alignment explanation
Indices: 55526606--55526926 Score: 278
Period size: 47 Copynumber: 6.8 Consensus size: 47
55526596 AATGAGAGCC
*
55526606 AGTGTAAGACCATGTCTAGGACATGGCATCGGCATTGAGACGAGTGCT
1 AGTGTAAGA-CATGTCTGGGACATGGCATCGGCATTGAGACGAGTGCT
* * * * *
55526654 AGTGTAAGACATGTTTGGGACAT-GCTTCGGCTTTGAGACGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGGCATCGGCATTGAGACGAGTGCT
* * * * * *
55526700 AGTGTAAGACATGTCTGGGACAT-GCATCAGCCTCAAGATATGTGTGCT
1 AGTGTAAGACATGTCTGGGACATGGCATCGGCAT--TGAGACGAGTGCT
* *
55526748 TGTGTAAGACAATGTCTGGGACATGGCATCGGCATTGAGACAAGTGCT
1 AGTGTAAGAC-ATGTCTGGGACATGGCATCGGCATTGAGACGAGTGCT
* * * * * *
55526796 AGTGTAAGACGTGTCTAGGACA-CGCATCGGCCTCGATGATGA-TAG-T
1 AGTGTAAGACATGTCTGGGACATGGCATCGGCATTGA-GACGAGT-GCT
* * * * * *
55526842 CAGTGTAAGACCATATCTGGGACATGGCACCGAC-TTGAGATGTGAGCT
1 -AGTGTAAGA-CATGTCTGGGACATGGCATCGGCATTGAGACGAGTGCT
55526890 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-TTGA
1 AGTGTAAGA-CATGTCTGGGACATGGCATCGGCATTGA
55526927 CATGTGTCAG
Statistics
Matches: 218, Mismatches: 44, Indels: 23
0.76 0.15 0.08
Matches are distributed among these distances:
46 61 0.28
47 74 0.34
48 56 0.26
49 19 0.09
50 8 0.04
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.25
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGGCATCGGCATTGAGACGAGTGCT
Found at i:55526697 original size:94 final size:93
Alignment explanation
Indices: 55526599--55526944 Score: 312
Period size: 94 Copynumber: 3.7 Consensus size: 93
55526589 ACCACATAAT
* *
55526599 GAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCATTGAGACGAGTGCTAGTGTAAGAC
1 GAGAGCCAGTGTAAGA-CATGTCTAGGACATGGCATCGGCCTTGAGATGAGTGCTAGTGTAAGAC
* *
55526664 ATGTTTGGGACAT-GCTTCGGCTTTGAGAC
65 ATGTCTGGGACATGGCATCGGC-TTGAGAC
* * * * * *
55526693 GAGAGCCAGTGTAAGACATGTCTGGGACAT-GCATCAGCCTCAAGATATGTGTGCTTGTGTAAGA
1 GAGAGCCAGTGTAAGACATGTCTAGGACATGGCATCGGCCT--TGAGATGAGTGCTAGTGTAAGA
55526757 CAATGTCTGGGACATGGCATCGGCATTGAGAC
64 C-ATGTCTGGGACATGGCATCGGC-TTGAGAC
* * * * * *
55526789 AAGTGCTAGTGTAAGACGTGTCTAGGACA-CGCATCGGCCTCGATGATGA-TAG-TCAGTGTAAG
1 GAGAGCCAGTGTAAGACATGTCTAGGACATGGCATCGGCCTTGA-GATGAGT-GCT-AGTGTAAG
* * * *
55526851 ACCATATCTGGGACATGGCACCGACTTGAGAT
63 A-CATGTCTGGGACATGGCATCGGCTTGAGAC
* * * * *
55526883 GTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGG-CTTGACATGTGT-C-AGTGTAAGAC
1 GAGAGCCAGTGTAAGA-CATGTCTAGGACATGGCATCGGCCTTGAGATGAGTGCTAGTGTAAGAC
55526945 CTTTTTGGGA
Statistics
Matches: 205, Mismatches: 34, Indels: 29
0.76 0.13 0.11
Matches are distributed among these distances:
91 1 0.00
92 17 0.08
93 13 0.06
94 60 0.29
95 59 0.29
96 55 0.27
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (93 bp):
GAGAGCCAGTGTAAGACATGTCTAGGACATGGCATCGGCCTTGAGATGAGTGCTAGTGTAAGACA
TGTCTGGGACATGGCATCGGCTTGAGAC
Found at i:55526773 original size:142 final size:141
Alignment explanation
Indices: 55526558--55526957 Score: 434
Period size: 142 Copynumber: 2.8 Consensus size: 141
55526548 GATATGTGCT
* * * * * * *
55526558 CCAGTGTTAGACATGTTTGGGACATGCATCAACCACATAATGAGAGCCAGTGTAAGACCATGTCT
1 CCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCAGAATGTGAGCTAGTGTAAGACCATGTCT
* * * * *
55526623 AGGACATGGCATCGGCATTGAGACGAGTGCTAGTGTAAGACATGTTTGGGACATGCTTCGGCTTT
66 GGGACATGGCATCGGCATTGAGACGAGTGCTAGTGTAAGACATGTTTGGGACACGCATCGGCCTC
55526688 GA-GACGAGAG
131 GATGACGAGAG
* * *
55526698 CCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCAAGATATGTGTGCTTGTGTAAGACAATGT
1 CCAGTGTAAGACATGTCTGGGACATGCATCAGCCTC-AGA-ATGTGAGCTAGTGTAAGACCATGT
* * * *
55526763 CTGGGACATGGCATCGGCATTGAGACAAGTGCTAGTGTAAGACGTGTCTAGGACACGCATCGGCC
64 CTGGGACATGGCATCGGCATTGAGACGAGTGCTAGTGTAAGACATGTTTGGGACACGCATCGGCC
* *
55526828 TCGATGATGATAG
129 TCGATGACGAGAG
* * * * *
55526841 TCAGTGTAAGACCATATCTGGGACATGGCA-CCGACT-TGAGATGTGAGCTAGTGTAAGACCATG
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCTCAGA-ATGTGAGCTAGTGTAAGACCATG
* * * * *
55526904 TCTGGGACATGGCATCGGC-TTGACATGTGT-C-AGTGTAAGACCTTTTTGGGACAC
63 TCTGGGACATGGCATCGGCATTGAGACGAGTGCTAGTGTAAGACATGTTTGGGACAC
55526958 AGTATCAACA
Statistics
Matches: 217, Mismatches: 38, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
139 19 0.09
140 33 0.15
141 9 0.04
142 120 0.55
143 16 0.07
144 17 0.08
145 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (141 bp):
CCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCAGAATGTGAGCTAGTGTAAGACCATGTCT
GGGACATGGCATCGGCATTGAGACGAGTGCTAGTGTAAGACATGTTTGGGACACGCATCGGCCTC
GATGACGAGAG
Found at i:55527464 original size:92 final size:92
Alignment explanation
Indices: 55527307--55527491 Score: 370
Period size: 92 Copynumber: 2.0 Consensus size: 92
55527297 TGTGAGAGTC
55527307 GAAAATTTAGAGGCTTTACAATCTTCACCCCCTTACCAGAATAGAGTTATATGAGGAAATTCACG
1 GAAAATTTAGAGGCTTTACAATCTTCACCCCCTTACCAGAATAGAGTTATATGAGGAAATTCACG
55527372 AGAGATATGTTGTATAAACTTACAAAT
66 AGAGATATGTTGTATAAACTTACAAAT
55527399 GAAAATTTAGAGGCTTTACAATCTTCACCCCCTTACCAGAATAGAGTTATATGAGGAAATTCACG
1 GAAAATTTAGAGGCTTTACAATCTTCACCCCCTTACCAGAATAGAGTTATATGAGGAAATTCACG
55527464 AGAGATATGTTGTATAAACTTACAAAT
66 AGAGATATGTTGTATAAACTTACAAAT
55527491 G
1 G
55527492 GGAAACTAAA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 93 1.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (92 bp):
GAAAATTTAGAGGCTTTACAATCTTCACCCCCTTACCAGAATAGAGTTATATGAGGAAATTCACG
AGAGATATGTTGTATAAACTTACAAAT
Found at i:55532852 original size:47 final size:45
Alignment explanation
Indices: 55532745--55533048 Score: 172
Period size: 47 Copynumber: 6.6 Consensus size: 45
55532735 CTTGTGTGCT
* * * * *
55532745 AGTGTAAGACATGTCTGGGACATGGATTGGCCACATTATGAGTGA-C
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTAGA-GATGAGT-ACC
* *
55532791 TGTATAAGACCATGTCTGGGACATGGCATCGGCGTAGAGATGAGTACC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-TAGAGATGAGTACC
* * *
55532839 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGATGATGA-TAGCT
1 AGTGTAAGACATGTCTGGGACATGCATC-GGCTAGA-GATGAGTA-CC
** * * * * *
55532886 AGTGTAAGATGTGTCTAGGATACGCATCGGCTA-AGA-GTTGTGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTAGAGATG-AGTACC
* * *
55532930 AGTGTATGACATGTCTGGGACATGCATCAGCTTCGATGATGA-TAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGC-TAGA-GATGAGTA-CC
* ** * ** * * * *
55532977 AGTGTAATATGTGTCTAGGACACACATCAGCTA-AGA-GTTGTGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTAGAGATG-AGTACC
55533021 AGTGTAAGACATGTCTGGGACATGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
55533049 AGCACGTATA
Statistics
Matches: 193, Mismatches: 49, Indels: 34
0.70 0.18 0.12
Matches are distributed among these distances:
43 2 0.01
44 52 0.27
45 5 0.03
46 23 0.12
47 88 0.46
48 21 0.11
49 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.26
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTAGAGATGAGTACC
Found at i:55532945 original size:44 final size:44
Alignment explanation
Indices: 55532897--55533051 Score: 141
Period size: 44 Copynumber: 3.5 Consensus size: 44
55532887 GTGTAAGATG
* *
55532897 TGTCTAGGATACGCATCGGCTAAGAGTTGTGCCAGTGTATGACA
1 TGTCTAGGACACGCATCAGCTAAGAGTTGTGCCAGTGTATGACA
* * ** * **
55532941 TGTCTGGGACATGCATCAGCTTCGATGATGATAGCCAGTGTAAT-ATG
1 TGTCTAGGACACGCATCAGCTAAGA-GTTG-T-GCCAGTGT-ATGACA
* * *
55532988 TGTCTAGGACACACATCAGCTAAGAGTTGTGCTAGTGTAAGACA
1 TGTCTAGGACACGCATCAGCTAAGAGTTGTGCCAGTGTATGACA
* *
55533032 TGTCTGGGACATGCATCAGC
1 TGTCTAGGACACGCATCAGC
55533052 ACGTATATAT
Statistics
Matches: 84, Mismatches: 22, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
43 1 0.01
44 44 0.52
45 4 0.05
46 4 0.05
47 29 0.35
48 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (44 bp):
TGTCTAGGACACGCATCAGCTAAGAGTTGTGCCAGTGTATGACA
Found at i:55532973 original size:91 final size:91
Alignment explanation
Indices: 55532837--55533051 Score: 358
Period size: 91 Copynumber: 2.4 Consensus size: 91
55532827 GAGATGAGTA
*
55532837 CCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGATGATGATAGCTAGTGTAAGATGTGTCT
1 CCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGATGATGATAGCCAGTGTAAGATGTGTCT
* * *
55532902 AGGATACGCATCGGCTAAGAGTTGTG
66 AGGACACACATCAGCTAAGAGTTGTG
* * *
55532928 CCAGTGTATGACATGTCTGGGACATGCATCAGCTTCGATGATGATAGCCAGTGTAATATGTGTCT
1 CCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGATGATGATAGCCAGTGTAAGATGTGTCT
55532993 AGGACACACATCAGCTAAGAGTTGTG
66 AGGACACACATCAGCTAAGAGTTGTG
*
55533019 CTAGTGTAAGACATGTCTGGGACATGCATCAGC
1 CCAGTGTAAGACATGTCTGGGACATGCATCAGC
55533052 ACGTATATAT
Statistics
Matches: 115, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 115 1.00
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.27
Consensus pattern (91 bp):
CCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGATGATGATAGCCAGTGTAAGATGTGTCT
AGGACACACATCAGCTAAGAGTTGTG
Found at i:55534534 original size:14 final size:14
Alignment explanation
Indices: 55534515--55534544 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
55534505 CATTCCGAAG
55534515 TATATATATATACA
1 TATATATATATACA
55534529 TATATATATATACA
1 TATATATATATACA
55534543 TA
1 TA
55534545 AGTATGCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TATATATATATACA
Found at i:55535057 original size:27 final size:27
Alignment explanation
Indices: 55535026--55535203 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
55535016 TAAATTGTAC
55535026 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
55535053 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
55535079 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
55535107 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
55535135 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
55535162 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
55535189 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
55535204 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:55535140 original size:82 final size:81
Alignment explanation
Indices: 55535027--55535182 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
55535017 AAATTGTACA
* *
55535027 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
55535091 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
55535108 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
55535173 TGCGAGTTGA
65 TGCGAATTGA
55535183 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:55535194 original size:82 final size:81
Alignment explanation
Indices: 55535023--55535203 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
55535013 GATTAAATTG
* *
55535023 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
55535088 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
55535104 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
55535168 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
55535186 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
55535204 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:55537073 original size:14 final size:13
Alignment explanation
Indices: 55537050--55537081 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
55537040 TGGATATCAA
55537050 AACAATAATTAAG
1 AACAATAATTAAG
55537063 AACACATAATTAAG
1 AACA-ATAATTAAG
55537077 AACAA
1 AACAA
55537082 GTTAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (13 bp):
AACAATAATTAAG
Found at i:55544470 original size:20 final size:18
Alignment explanation
Indices: 55544445--55544484 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
55544435 ACCTAACAAA
*
55544445 AATTAAACTTAAGCCATATT
1 AATTAAA-TTAA-ACATATT
55544465 AATTAAATTAAACATATT
1 AATTAAATTAAACATATT
55544483 AA
1 AA
55544485 CATAACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 4 0.21
20 7 0.37
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.35
Consensus pattern (18 bp):
AATTAAATTAAACATATT
Found at i:55545743 original size:27 final size:25
Alignment explanation
Indices: 55545711--55545790 Score: 99
Period size: 27 Copynumber: 3.0 Consensus size: 25
55545701 CAGAACAATA
55545711 AATGTGGCA-ATGCCACCAGTATCAGT
1 AATGTGGCATA-GCCACCAGTA-CAGT
55545737 AATTGTGGCATAGCCACCAGTAACAGT
1 AA-TGTGGCATAGCCACCAGT-ACAGT
*
55545764 GAATGTGACATAGCCACCAGTACAGT
1 -AATGTGGCATAGCCACCAGTACAGT
55545790 A
1 A
55545791 CTTCCTCCAT
Statistics
Matches: 49, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
25 1 0.02
26 7 0.14
27 37 0.76
28 4 0.08
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.21
Consensus pattern (25 bp):
AATGTGGCATAGCCACCAGTACAGT
Found at i:55545976 original size:27 final size:27
Alignment explanation
Indices: 55545926--55546086 Score: 180
Period size: 27 Copynumber: 6.0 Consensus size: 27
55545916 GGCATAATCG
* * *
55545926 TCATGTTACCATACAGGAGTATTAC-A
1 TCATTTTACCCTACAGGGGTATTACGA
* *
55545952 GTCATTTTACCCTACCGGGGCATTACGA
1 -TCATTTTACCCTACAGGGGTATTACGA
* * *
55545980 TGATTTTACCCTATAAGGGTATTACGA
1 TCATTTTACCCTACAGGGGTATTACGA
**
55546007 TCATTTTACCCTACAAAGGTATTACGA
1 TCATTTTACCCTACAGGGGTATTACGA
* * * *
55546034 TCATTTTAGCCAACAGGGGTGTTACGG
1 TCATTTTACCCTACAGGGGTATTACGA
55546061 TCATTTTACCCTACAGGGGTATTACG
1 TCATTTTACCCTACAGGGGTATTACG
55546087 GTCAGATAAC
Statistics
Matches: 111, Mismatches: 22, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
27 110 0.99
28 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (27 bp):
TCATTTTACCCTACAGGGGTATTACGA
Found at i:55549651 original size:5 final size:5
Alignment explanation
Indices: 55549634--55549666 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
55549624 ATGCTCTCTT
55549634 TTTTC TTTT- TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
55549667 TTTACGAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTTC
Found at i:55552584 original size:16 final size:15
Alignment explanation
Indices: 55552563--55552599 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
55552553 TATAAAGTTG
*
55552563 ATTATAATTAATATA
1 ATTATAATAAATATA
55552578 TATTATAATAAATATA
1 -ATTATAATAAATATA
55552594 ATTATA
1 ATTATA
55552600 CATGAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTATAATAAATATA
Found at i:55560421 original size:48 final size:48
Alignment explanation
Indices: 55560361--55560585 Score: 247
Period size: 48 Copynumber: 4.7 Consensus size: 48
55560351 ACTTGTCGAG
* *
55560361 GCCGATGCCATGTCCTAGACGTGGTCTTACA-TAGGCTCTTATAATGTC
1 GCCGATGCCATGTCCTAGACATGGTCTTACACTA-GCTCTCATAATGTC
* * * * * * ****
55560409 GCTGATGTCATGTCCCAGACACGGTCTTACACTAGCACACATAGCAAC
1 GCCGATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCATAATGTC
* * *
55560457 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTG
1 GCCGATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCATAATGTC
* *
55560505 GCCGATGCCATGT-CTCAGACATGGTCTTACACTAGCTCTTATAATGTG
1 GCCGATGCCATGTCCT-AGACATGGTCTTACACTAGCTCTCATAATGTC
**
55560553 GCTAATGCCATGTCCTAGACATGGTCTTACACT
1 GCCGATGCCATGTCCTAGACATGGTCTTACACT
55560586 GGCACACATA
Statistics
Matches: 146, Mismatches: 28, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
47 1 0.01
48 141 0.97
49 4 0.03
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (48 bp):
GCCGATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCATAATGTC
Found at i:55560494 original size:96 final size:96
Alignment explanation
Indices: 55560361--55560540 Score: 272
Period size: 96 Copynumber: 1.9 Consensus size: 96
55560351 ACTTGTCGAG
* * * * *
55560361 GCCGATGCCATGTCCTAGACGTGGTCTTACATAGGCTCTTATAATGTCGCTGATGTCATGTCCCA
1 GCCGATGCCATGTCCCAGACATGGTCTTACATAGGCTCTCATAATGTCGCCGATGCCATGTCCCA
55560426 GACACGGTCTTACACTAGCACACATAGCAAC
66 GACACGGTCTTACACTAGCACACATAGCAAC
* *
55560457 GCCGATGCCATGTCCCAGACATGGTCTTACACT-GGCTCTCATAATGTGGCCGATGCCATGTCTC
1 GCCGATGCCATGTCCCAGACATGGTCTTACA-TAGGCTCTCATAATGTCGCCGATGCCATGTCCC
*
55560521 AGACATGGTCTTACACTAGC
65 AGACACGGTCTTACACTAGC
55560541 TCTTATAATG
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
96 74 0.99
97 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (96 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACATAGGCTCTCATAATGTCGCCGATGCCATGTCCCA
GACACGGTCTTACACTAGCACACATAGCAAC
Found at i:55560573 original size:144 final size:144
Alignment explanation
Indices: 55560313--55560595 Score: 392
Period size: 144 Copynumber: 2.0 Consensus size: 144
55560303 AGGGTAAATT
* **
55560313 GCCGATGCCATATCCCAGATATGGTCTTACAATGGCTCACTTGTCGAGGCCGATGCCATGTCCTA
1 GCCGATGCCATATCCCAGACATGGTCTTACAATGGCTCACTAATCGAGGCCGATGCCATGTCCTA
* * *
55560378 GACGTGGTCTTACATAGGCTCTTATAATGTCGCTGATGTCATGTCCCAGACACGGTCTTACACTA
66 GACATGGTCTTACATAGGCTCTTATAATGTCGCTAATGCCATGTCCCAGACACGGTCTTACACTA
55560443 GCACACATAGCAAC
131 GCACACATAGCAAC
* * * *
55560457 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCCGATGCCATGT-CT
1 GCCGATGCCATATCCCAGACATGGTCTTACAATGGCTCAC-TAATCGAGGCCGATGCCATGTCCT
* * *
55560520 CAGACATGGTCTTACACTA-GCTCTTATAATGTGGCTAATGCCATGTCCTAGACATGGTCTTACA
65 -AGACATGGTCTTACA-TAGGCTCTTATAATGTCGCTAATGCCATGTCCCAGACACGGTCTTACA
*
55560584 CTGGCACACATA
128 CTAGCACACATA
55560596 TCACCCAATT
Statistics
Matches: 122, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
143 2 0.02
144 116 0.95
145 4 0.03
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (144 bp):
GCCGATGCCATATCCCAGACATGGTCTTACAATGGCTCACTAATCGAGGCCGATGCCATGTCCTA
GACATGGTCTTACATAGGCTCTTATAATGTCGCTAATGCCATGTCCCAGACACGGTCTTACACTA
GCACACATAGCAAC
Found at i:55565812 original size:25 final size:26
Alignment explanation
Indices: 55565773--55565847 Score: 86
Period size: 25 Copynumber: 3.0 Consensus size: 26
55565763 TGGACACACC
55565773 ACAGCTTGT-ATGAGCTTACCGATTCT
1 ACAGCTTGTGA-GAGCTTACCGATTCT
55565799 -CAGCTTGTGAGAGCTTACCGATT-T
1 ACAGCTTGTGAGAGCTTACCGATTCT
* *
55565823 ACTA-CTCGTGAGAGCATACCGATTC
1 AC-AGCTTGTGAGAGCTTACCGATTC
55565848 ATAGCTCGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
24 1 0.02
25 40 0.93
26 2 0.05
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (26 bp):
ACAGCTTGTGAGAGCTTACCGATTCT
Found at i:55565855 original size:25 final size:25
Alignment explanation
Indices: 55565784--55565866 Score: 82
Period size: 25 Copynumber: 3.3 Consensus size: 25
55565774 CAGCTTGTAT
* *
55565784 GAGCTTACCGATTC-TCAGCTTGTGA
1 GAGCATACCGATTCAT-AGCTCGTGA
* *
55565809 GAGCTTACCGATTTACTA-CTCGTGA
1 GAGCATACCGATTCA-TAGCTCGTGA
55565834 GAGCATACCGATTCATAGCTCGT-A
1 GAGCATACCGATTCATAGCTCGTGA
55565858 TGAGCATAC
1 -GAGCATAC
55565867 ATGTACAGGA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
24 3 0.06
25 45 0.90
26 1 0.02
27 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (25 bp):
GAGCATACCGATTCATAGCTCGTGA
Found at i:55577050 original size:42 final size:42
Alignment explanation
Indices: 55576899--55577053 Score: 113
Period size: 42 Copynumber: 3.7 Consensus size: 42
55576889 AGCTCATACA
* **
55576899 ATGCCAACGTCCTAGATGTGGTCTTACATGT-AATCAAATATCG
1 ATGCCAACGTCCTAGACGTGGTCTTACACATAAATCAAAT-T-G
* **
55576942 ATGCC-ACTGTCGC-AGACAG-GATCTTACACA-AAATCAAAAACG
1 ATGCCAAC-GTC-CTAGAC-GTGGTCTTACACATAAATC-AAATTG
** * * * *
55576984 ATTTCAATGTCCCAGACATAGTCTTACACATAAATCAAATTG
1 ATGCCAACGTCCTAGACGTGGTCTTACACATAAATCAAATTG
55577026 ATGCCAACGTCCTAGACGTGGTCTTACA
1 ATGCCAACGTCCTAGACGTGGTCTTACA
55577054 GGAAATCACA
Statistics
Matches: 83, Mismatches: 20, Indels: 19
0.68 0.16 0.16
Matches are distributed among these distances:
41 1 0.01
42 48 0.58
43 29 0.35
44 5 0.06
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (42 bp):
ATGCCAACGTCCTAGACGTGGTCTTACACATAAATCAAATTG
Found at i:55579358 original size:21 final size:20
Alignment explanation
Indices: 55579330--55579368 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
55579320 CAAAACTTGT
*
55579330 ATAACTATCATCAAACATTC
1 ATAACTATAATCAAACATTC
*
55579350 ATAATCTATAATTAAACAT
1 ATAA-CTATAATCAAACAT
55579369 CAAAATACTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAACTATAATCAAACATTC
Found at i:55582941 original size:27 final size:27
Alignment explanation
Indices: 55582911--55583085 Score: 190
Period size: 27 Copynumber: 6.4 Consensus size: 27
55582901 TTGAGTCCGT
* * * *
55582911 ACACTCAGTGCTATATAATCAACTCGC
1 ACACTTAGTGCTACATAGTCAAATCGC
* *
55582938 ACACTTAGTGCTACGTAATCAAATCGC
1 ACACTTAGTGCTACATAGTCAAATCGC
*
55582965 ACACTTAGTGCTACATAGTCAAACTCAC
1 ACACTTAGTGCTACATAGTCAAA-TCGC
** * *
55582993 ACACTTAGTGCCGCATGGTCAATTCGC
1 ACACTTAGTGCTACATAGTCAAATCGC
* **
55583020 ACACTTAGTGC-ATCATATTCATTTCGC
1 ACACTTAGTGCTA-CATAGTCAAATCGC
*
55583047 ACACTTAGTGCAACATAGTCAAATCGC
1 ACACTTAGTGCTACATAGTCAAATCGC
55583074 ACACTTAGTGCT
1 ACACTTAGTGCT
55583086 GTACAATTTA
Statistics
Matches: 125, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 102 0.82
28 23 0.18
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.27
Consensus pattern (27 bp):
ACACTTAGTGCTACATAGTCAAATCGC
Found at i:55583048 original size:82 final size:81
Alignment explanation
Indices: 55582929--55583084 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
55582919 TGCTATATAA
* *
55582929 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCACA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCACA
55582994 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
55583011 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCACA
55583075 CACTTAGTGC
65 CACTTAGTGC
55583085 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 51 0.77
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCACAC
ACTTAGTGCCGCATGG
Found at i:55591113 original size:27 final size:27
Alignment explanation
Indices: 55591083--55591260 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
55591073 ATATTGAGTC
* * * *
55591083 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
55591110 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
55591137 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
55591165 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
55591192 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
55591219 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
55591246 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
55591261 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:55591222 original size:82 final size:81
Alignment explanation
Indices: 55591104--55591259 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
55591094 TGCTATATAA
* *
55591104 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
55591169 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
55591186 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
55591250 CACTTAGTGC
65 CACTTAGTGC
55591260 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:55597466 original size:27 final size:27
Alignment explanation
Indices: 55597436--55597744 Score: 447
Period size: 27 Copynumber: 11.4 Consensus size: 27
55597426 AACCCTCATT
55597436 TGATAAAATGACGATTTTGCCCTTATG
1 TGATAAAATGACGATTTTGCCCTTATG
* *
55597463 TGATAAAATGATGATTTTGTCCTTATG
1 TGATAAAATGACGATTTTGCCCTTATG
*
55597490 TGATAAAATGACGATTTTGCCTTTATG
1 TGATAAAATGACGATTTTGCCCTTATG
* *
55597517 TGATAAAATGATGATTTTGCCCTCATG
1 TGATAAAATGACGATTTTGCCCTTATG
* * * *
55597544 TGATAAAATTATGATTTTTCCCTTAAG
1 TGATAAAATGACGATTTTGCCCTTATG
55597571 TGATAAAATGACGATTTTGCCCTTATG
1 TGATAAAATGACGATTTTGCCCTTATG
*
55597598 TGATAAAATGACGATTTTGCCCTCATG
1 TGATAAAATGACGATTTTGCCCTTATG
*
55597625 TGATAAAATGACGATTTTGCCCTTAGG
1 TGATAAAATGACGATTTTGCCCTTATG
* * *
55597652 TGATAAAATGATGATTTTGCCTTTAGG
1 TGATAAAATGACGATTTTGCCCTTATG
* *
55597679 TGATAAAATGACAATTTTTCCCTTATG
1 TGATAAAATGACGATTTTGCCCTTATG
* * *
55597706 TGGTAAAATGATGATTTTACCCTTATG
1 TGATAAAATGACGATTTTGCCCTTATG
55597733 TGATAAAATGAC
1 TGATAAAATGAC
55597745 CGAAATACCC
Statistics
Matches: 250, Mismatches: 32, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 250 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.39
Consensus pattern (27 bp):
TGATAAAATGACGATTTTGCCCTTATG
Found at i:55597766 original size:27 final size:27
Alignment explanation
Indices: 55597736--55597797 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
55597726 CCTTATGTGA
* *
55597736 TAAAATGACCGAAATACCCCTGTAGGG
1 TAAAATGACCGAAATACCCCAGTAAGG
* * *
55597763 TAAAATGACTGTAATACCTCAGTAAGG
1 TAAAATGACCGAAATACCCCAGTAAGG
55597790 TAAAATGA
1 TAAAATGA
55597798 TAGATTTGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCCAGTAAGG
Found at i:55598164 original size:18 final size:18
Alignment explanation
Indices: 55598141--55598199 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
55598131 TCTGTTTGCA
55598141 TACTGCACTGATTACTGT
1 TACTGCACTGATTACTGT
* *
55598159 TACTGCATTGATCA-TGGT
1 TACTGCACTGATTACT-GT
*
55598177 TACTGCACTGATTACTAT
1 TACTGCACTGATTACTGT
55598195 TACTG
1 TACTG
55598200 AAATGGGCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
17 1 0.03
18 32 0.94
19 1 0.03
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (18 bp):
TACTGCACTGATTACTGT
Found at i:55598228 original size:35 final size:35
Alignment explanation
Indices: 55598183--55598279 Score: 124
Period size: 35 Copynumber: 2.8 Consensus size: 35
55598173 TGGTTACTGC
*
55598183 ACTGATTACTATTACTGAAATGGGCTAAAACCTAG
1 ACTGATTACTATTACTGAAATGGGCTAAAACCCAG
* * *
55598218 ATTGATTACTATTACTGAACTGGGTTAAAACCCAG
1 ACTGATTACTATTACTGAAATGGGCTAAAACCCAG
* * *
55598253 GCTG-CTACTGTTACTGAAATGGGCTAA
1 ACTGATTACTATTACTGAAATGGGCTAA
55598280 TGCCCAGATT
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
34 19 0.37
35 33 0.63
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (35 bp):
ACTGATTACTATTACTGAAATGGGCTAAAACCCAG
Found at i:55598286 original size:34 final size:34
Alignment explanation
Indices: 55598189--55598309 Score: 116
Period size: 34 Copynumber: 3.5 Consensus size: 34
55598179 CTGCACTGAT
* * * *
55598189 TACTATTACTGAAATGGGCTAAAACCTAGATTGAT
1 TACTGTTACTGAAATGGGCTAAAACCCAGACTG-C
* * * *
55598224 TACTATTACTGAACTGGGTTAAAACCCAGGCTGC
1 TACTGTTACTGAAATGGGCTAAAACCCAGACTGC
** *
55598258 TACTGTTACTGAAATGGGCTAATGCCCAGATTGC
1 TACTGTTACTGAAATGGGCTAAAACCCAGACTGC
* *
55598292 CACTGTTACTGATATGGG
1 TACTGTTACTGAAATGGG
55598310 TTTAGGCCCC
Statistics
Matches: 71, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
34 43 0.61
35 28 0.39
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (34 bp):
TACTGTTACTGAAATGGGCTAAAACCCAGACTGC
Found at i:55599698 original size:44 final size:43
Alignment explanation
Indices: 55599549--55599710 Score: 129
Period size: 42 Copynumber: 3.8 Consensus size: 43
55599539 AGCTCGTATA
* * ** *
55599549 ATGCCAACGTCCTAGACG-GGTCTTACATGT-AATCAAATATCA
1 ATGCCAACGTCCCAGAAGTGGTCTTACACATAAATCAAATA-CG
* *
55599591 ATGCC-ACTTTCCCAGACAG-GGTCTTACAC-GAAATCAAATACG
1 ATGCCAAC-GTCCCAGA-AGTGGTCTTACACATAAATCAAATACG
* * * *
55599633 ATGTCAATGTCCTAGATGTGGTCTTACACATAAATCATAAGT-CG
1 ATGCCAACGTCCCAGAAGTGGTCTTACACATAAATCA-AA-TACG
55599677 ATGCCAACGTCCCAGAAGTGGTCTTACACGATAA
1 ATGCCAACGTCCCAGAAGTGGTCTTACAC-ATAA
55599711 CACATATCAG
Statistics
Matches: 95, Mismatches: 16, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
41 3 0.03
42 32 0.34
43 26 0.27
44 29 0.31
45 5 0.05
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGAAGTGGTCTTACACATAAATCAAATACG
Found at i:55602222 original size:15 final size:17
Alignment explanation
Indices: 55602188--55602221 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55602178 CTCTACTATT
55602188 ATTATTATTTTGATAGAA
1 ATTATTATTTTGATA-AA
55602206 ATTATTATTTT-ATAAA
1 ATTATTATTTTGATAAA
55602222 TATTGAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 3 0.19
18 11 0.69
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
ATTATTATTTTGATAAA
Found at i:55602601 original size:26 final size:24
Alignment explanation
Indices: 55602566--55602617 Score: 77
Period size: 26 Copynumber: 2.1 Consensus size: 24
55602556 ATTTGTTTTC
*
55602566 AAAATTAGTTGAATATTAACTTCAAA
1 AAAATCAGTTGAATATTAA-TT-AAA
55602592 AAAATCAGTTGAATATTAATTAAA
1 AAAATCAGTTGAATATTAATTAAA
55602616 AA
1 AA
55602618 TTATTATCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 5 0.20
25 2 0.08
26 18 0.72
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.33
Consensus pattern (24 bp):
AAAATCAGTTGAATATTAATTAAA
Found at i:55604686 original size:6 final size:6
Alignment explanation
Indices: 55604669--55604712 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
55604659 TAGGTTTCCA
* * * *
55604669 GAAAAT GGAAAT GAAAAT GGAAAT GGAAAT GAAAAT GGAAAT GA
1 GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GA
55604713 TCCGTTTGCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.16
Consensus pattern (6 bp):
GAAAAT
Found at i:55604694 original size:18 final size:18
Alignment explanation
Indices: 55604671--55604711 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
55604661 GGTTTCCAGA
55604671 AAATGGAAATGAAAATGG
1 AAATGGAAATGAAAATGG
55604689 AAATGGAAATGAAAATGG
1 AAATGGAAATGAAAATGG
55604707 AAATG
1 AAATG
55604712 ATCCGTTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.27, T:0.17
Consensus pattern (18 bp):
AAATGGAAATGAAAATGG
Found at i:55604712 original size:12 final size:12
Alignment explanation
Indices: 55604669--55604711 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
55604659 TAGGTTTCCA
55604669 GAAAATGGAAAT
1 GAAAATGGAAAT
55604681 GAAAATGGAAAT
1 GAAAATGGAAAT
* *
55604693 GGAAATGAAAAT
1 GAAAATGGAAAT
*
55604705 GGAAATG
1 GAAAATG
55604712 ATCCGTTTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.16
Consensus pattern (12 bp):
GAAAATGGAAAT
Found at i:55604912 original size:26 final size:26
Alignment explanation
Indices: 55604883--55604944 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
55604873 GGCAAAGTCA
* *
55604883 TCAAAATTTTATTAAGGGGAAAATCG
1 TCAAAATTTTATCAAAGGGAAAATCG
* *
55604909 TCAAAATTTTATCAAAGGTAAAATTG
1 TCAAAATTTTATCAAAGGGAAAATCG
*
55604935 CCAAAATTTT
1 TCAAAATTTT
55604945 GTTGGGGTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.34
Consensus pattern (26 bp):
TCAAAATTTTATCAAAGGGAAAATCG
Found at i:55608454 original size:37 final size:37
Alignment explanation
Indices: 55608399--55608473 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
55608389 CAATTATATT
55608399 ACTCTACCATCGAGAGACGATTTCACTTGAGGGAAAG
1 ACTCTACCATCGAGAGACGATTTCACTTGAGGGAAAG
* * *
55608436 ACTCTACCATCGATAGACGATTTTACTTGTGGGAAAG
1 ACTCTACCATCGAGAGACGATTTCACTTGAGGGAAAG
55608473 A
1 A
55608474 GGTAATTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (37 bp):
ACTCTACCATCGAGAGACGATTTCACTTGAGGGAAAG
Found at i:55630897 original size:48 final size:48
Alignment explanation
Indices: 55630823--55630957 Score: 171
Period size: 48 Copynumber: 2.8 Consensus size: 48
55630813 TAGGGTTATG
*
55630823 TGTGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
* * * **
55630871 TGTGATCCCATGTAAGACCATATCTGGGATAGGGCATTGGCATTTATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
** * * *
55630919 TGTGATTTCGTGTAAGACCATGTTTGGAACATGGCATTG
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTG
55630958 ATATGAGACG
Statistics
Matches: 73, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 73 1.00
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.31
Consensus pattern (48 bp):
TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
Found at i:55639435 original size:16 final size:16
Alignment explanation
Indices: 55639416--55639446 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55639406 CTTCTTCACT
55639416 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
55639432 TACTTACTTACTTAA
1 TACTCACTTACTTAA
55639447 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:55639452 original size:20 final size:20
Alignment explanation
Indices: 55639413--55639452 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
55639403 AAACTTCTTC
* *
55639413 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
55639433 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
55639453 TTATTAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:55639766 original size:53 final size:54
Alignment explanation
Indices: 55639639--55639892 Score: 229
Period size: 53 Copynumber: 4.8 Consensus size: 54
55639629 ACACGGGTAC
* * * * *
55639639 CTTACCATTTCCATGACATGTCATGGTCTTACGTGGTATCCTT---TT-T-AAA
1 CTTACCAATTCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* * * * *
55639688 CTTACCATTTCCATGTCTCGACATGGTTTTATATGGTATCCTTGCCTTATG-AA
1 CTTACCAATTCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* * *
55639741 CTCACCAATTCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGAAA
1 CTTACCAATTCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTAT-GAAA
** * * *
55639796 CTTATTAATGCCATGTCTTGACATGGTCTTAC-TGATATCCTTGCCTTA-GAAA
1 CTTACCAATTCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* *
55639848 CCTTACCAATTTCCATGCCTTGGCATAGTCTTACATGGTATCCTT
1 -CTTACCAA-TTCCATGCCTTGACATGGTCTTACATGGTATCCTT
55639893 AAACCCTAAT
Statistics
Matches: 163, Mismatches: 30, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
49 36 0.22
52 8 0.05
53 48 0.29
54 32 0.20
55 39 0.24
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.38
Consensus pattern (54 bp):
CTTACCAATTCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
Found at i:55639821 original size:55 final size:53
Alignment explanation
Indices: 55639698--55639892 Score: 153
Period size: 55 Copynumber: 3.6 Consensus size: 53
55639688 CTTACCATTT
* * * * *
55639698 CCATGTCTCGACATGGTTTTATATGGTATCCTTGCCTTATGAACTCACCAATT
1 CCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACCAATG
* * * **
55639751 CCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGAAACTTATTAATG
1 CCATGTCTTGACATGGTCTTACATGGGATCC-TTGCCTTAT-G-AACTCACCAATG
** * *
55639806 CCATGTCTTGACATGGTCTTAC-TGATATCCTTGCCTTA-GAAACCTTACCAATTT
1 CCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG-AA-CTCACCAA-TG
* * * *
55639860 CCATGCCTTGGCATAGTCTTACATGGTATCCTT
1 CCATGTCTTGACATGGTCTTACATGGGATCCTT
55639893 AAACCCTAAT
Statistics
Matches: 114, Mismatches: 21, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
52 6 0.05
53 37 0.32
54 32 0.28
55 39 0.34
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (53 bp):
CCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACCAATG
Found at i:55645157 original size:26 final size:27
Alignment explanation
Indices: 55645107--55645160 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 27
55645097 TTGCCTCAAG
55645107 TTCAAATCTTTTTGAGTCATCAAATAT
1 TTCAAATCTTTTTGAGTCATCAAATAT
55645134 TTCAAA-CTTTTGTGA-TCAGT-AAATAT
1 TTCAAATCTTTT-TGAGTCA-TCAAATAT
55645160 T
1 T
55645161 CGGCACTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.44
Consensus pattern (27 bp):
TTCAAATCTTTTTGAGTCATCAAATAT
Found at i:55649928 original size:55 final size:55
Alignment explanation
Indices: 55649768--55649977 Score: 205
Period size: 55 Copynumber: 3.9 Consensus size: 55
55649758 GTATCCTTTT
* * ** * *
55649768 GAAACTTACCATTGCCATGAATCGACATGGTCTTGCATGGTATCCTTGCCTTAT-
1 GAAACTTACCAATGTCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
* * * *
55649822 G-AACTCACCAATGTCATGCCTTGGCATGGTCTTACATGGGA-CCTTTTCCTTATA
1 GAAACTTACCAATGTCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTATA
* * * * *
55649876 GAAACTTATCAATGCCATGTCTTAACATGGTCTTACATGATATCCTTGCC-T-TA
1 GAAACTTACCAATGTCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
* *
55649929 GAAACCTTACCAATTTTCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 GAAA-CTTACCAA-TGTCATGCCTTGACATGGTCTTACATGGTATCCTT
55649978 AAACCCTAAT
Statistics
Matches: 124, Mismatches: 26, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
52 2 0.02
53 45 0.36
54 10 0.08
55 65 0.52
56 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (55 bp):
GAAACTTACCAATGTCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
Found at i:55656493 original size:18 final size:19
Alignment explanation
Indices: 55656467--55656502 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
55656457 GGGGTTAATG
*
55656467 ATGATACTTT-TAGGGAAT
1 ATGAAACTTTCTAGGGAAT
55656485 ATGAAACTTTCTAGGGAA
1 ATGAAACTTTCTAGGGAA
55656503 GTTTGTGACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.33
Consensus pattern (19 bp):
ATGAAACTTTCTAGGGAAT
Found at i:55663459 original size:6 final size:6
Alignment explanation
Indices: 55663445--55663476 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
55663435 CAAAAGGAGT
*
55663445 TTTTTA TTTTAA TTTTAA TTTTAA TTTTAA TT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TT
55663477 GTTTGTGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTTAA
Found at i:55671601 original size:19 final size:19
Alignment explanation
Indices: 55671577--55671616 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
55671567 ATCTCATCTC
*
55671577 ATTCA-TTGTATTTAGATTA
1 ATTCATTTGCATTTAG-TTA
55671596 ATTCATTTGCATTTAGTTA
1 ATTCATTTGCATTTAGTTA
55671615 AT
1 AT
55671617 ATTAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (19 bp):
ATTCATTTGCATTTAGTTA
Found at i:55673488 original size:42 final size:43
Alignment explanation
Indices: 55673432--55673544 Score: 160
Period size: 43 Copynumber: 2.7 Consensus size: 43
55673422 GAGATTTATG
*
55673432 TGTAAGACCATGTCTGGGACA-TCGGCATCG-TATTTGATTTCA
1 TGTAAGACCATGTCTGGGACAGT-GGCATCGATATTTGATTACA
*
55673474 TGTAAGACCCTGTCTGGGACAGTGGCATCGATATTTGATTACA
1 TGTAAGACCATGTCTGGGACAGTGGCATCGATATTTGATTACA
*
55673517 TGTATGACCATGTCTGGGAC-GTTGGCAT
1 TGTAAGACCATGTCTGGGACAG-TGGCAT
55673545 TGTACGAGCT
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
42 28 0.44
43 36 0.56
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.32
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACAGTGGCATCGATATTTGATTACA
Found at i:55675645 original size:33 final size:33
Alignment explanation
Indices: 55675608--55675670 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
55675598 ATGTTCTTGC
*
55675608 GATGATTAAATATGGTGTGTTACAATTAGTTGT
1 GATGATTAAATATGGTCTGTTACAATTAGTTGT
55675641 GATGATTAAATATGGTCTGTTACAATTAGT
1 GATGATTAAATATGGTCTGTTACAATTAGT
55675671 CACATATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.41
Consensus pattern (33 bp):
GATGATTAAATATGGTCTGTTACAATTAGTTGT
Found at i:55681798 original size:25 final size:25
Alignment explanation
Indices: 55681766--55681813 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
55681756 TTATAACATG
* *
55681766 AAAATGACCGTTTTACCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
55681791 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
55681814 GTTTATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:55681897 original size:11 final size:11
Alignment explanation
Indices: 55681861--55681916 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
55681851 CATGGTATGT
55681861 ATGATATGCAC
1 ATGATATGCAC
* *
55681872 ATGACATG--T
1 ATGATATGCAC
55681881 ATGATATGCAC
1 ATGATATGCAC
*
55681892 ATGATATG--T
1 ATGATATGCAC
55681901 ATGATATGCAC
1 ATGATATGCAC
55681912 ATGAT
1 ATGAT
55681917 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:55681916 original size:20 final size:20
Alignment explanation
Indices: 55681850--55681916 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
55681840 ATTTTCATAA
*
55681850 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
55681870 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
55681890 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
55681910 ACATGAT
1 ACATGAT
55681917 GTATTCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Done.