Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 168 of 202
Found at i:52460131 original size:108 final size:108
Alignment explanation
Indices: 52459909--52460137 Score: 289
Period size: 108 Copynumber: 2.1 Consensus size: 108
52459899 TTCACTTTAT
* * *
52459909 TAATTTACAATCATGAACACTTCATTAAGAGTTCATCGATTTGCAATCGCAACTTCATTTAAACA
1 TAATTTACGATCATGAACACTTCATTAAGAGTTCATCGATTTACAATCGCAACTCCATTTAAACA
** * *
52459974 GCTCGTTGATTTACGATCACAACTGTCATTTTTTAAAGCTCAC
66 GCTCACTGATTTACGATCACAACTGTCATTTTTCAAACCTCAC
* * * *
52460017 TAATTTACGATCTTGAACACTTCATTAAGAGTTCGTTGATTTACGA-CTGCAACTCCATTTAAAC
1 TAATTTACGATCATGAACACTTCATTAAGAGTTCATCGATTTACAATC-GCAACTCCATTTAAAC
* * * **
52460081 AGTTCACTGATTTATGATCACAACTTTCATTTTTCAAACCTCGT
65 AGCTCACTGATTTACGATCACAACTGTCATTTTTCAAACCTCAC
*
52460125 TGATTTACGATCA
1 TAATTTACGATCA
52460138 CAGCTTCAGT
Statistics
Matches: 102, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
107 1 0.01
108 101 0.99
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (108 bp):
TAATTTACGATCATGAACACTTCATTAAGAGTTCATCGATTTACAATCGCAACTCCATTTAAACA
GCTCACTGATTTACGATCACAACTGTCATTTTTCAAACCTCAC
Found at i:52460327 original size:36 final size:36
Alignment explanation
Indices: 52460280--52460371 Score: 130
Period size: 36 Copynumber: 2.6 Consensus size: 36
52460270 TCACAACTTC
* * *
52460280 AGTTCATTGATTTATAATCATAAATAATTCATTAAA
1 AGTTCGTTGATTTATGATCATAAACAATTCATTAAA
* * *
52460316 AGTTCGTTGATTTACGATCATGAACAATTCATTAAG
1 AGTTCGTTGATTTATGATCATAAACAATTCATTAAA
52460352 AGTTCGTTGATTTATGATCA
1 AGTTCGTTGATTTATGATCA
52460372 CAACTCCATT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (36 bp):
AGTTCGTTGATTTATGATCATAAACAATTCATTAAA
Found at i:52460328 original size:135 final size:135
Alignment explanation
Indices: 52460032--52460330 Score: 393
Period size: 135 Copynumber: 2.2 Consensus size: 135
52460022 TACGATCTTG
* * * **
52460032 AACACTTCATTAAGAGTTCGTTGATTTACGACTGCAACTCCATTTAAACAGTTCACTGATTTATG
1 AACAATTCATTAAGAGTTCGTTGATTTACAACTGCAACTCCATTTAAACAGTTCACAGATTTACA
* * * *
52460097 ATCACAACTTTCATTTTTCAAACCTCGTTGATTTACGATCACAGCTTCAGTTCATTGATTTACAA
66 ATCAAAACTGTAATTTTTCAAACCTCGTTGATTTACGATCACAACTTCAGTTCATTGATTTACAA
*
52460162 TCATG
131 TCATA
* * *** *
52460167 ACCACTTCATTAAGAGTTCACCGATTTACAA-TCGCAACTCCATTTAAATAGTTCACAGATTTAC
1 AACAATTCATTAAGAGTTCGTTGATTTACAACT-GCAACTCCATTTAAACAGTTCACAGATTTAC
* * *
52460231 AATCAAAACTGTAATTTTTTAAAGCTCGTTGATTTACGATCACAACTTCAGTTCATTGATTTATA
65 AATCAAAACTGTAATTTTTCAAACCTCGTTGATTTACGATCACAACTTCAGTTCATTGATTTACA
52460296 ATCATA
130 ATCATA
* *
52460302 AATAATTCATTAAAAGTTCGTTGATTTAC
1 AACAATTCATTAAGAGTTCGTTGATTTAC
52460331 GATCATGAAC
Statistics
Matches: 139, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
134 1 0.01
135 138 0.99
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.37
Consensus pattern (135 bp):
AACAATTCATTAAGAGTTCGTTGATTTACAACTGCAACTCCATTTAAACAGTTCACAGATTTACA
ATCAAAACTGTAATTTTTCAAACCTCGTTGATTTACGATCACAACTTCAGTTCATTGATTTACAA
TCATA
Found at i:52466413 original size:113 final size:113
Alignment explanation
Indices: 52466238--52466684 Score: 392
Period size: 114 Copynumber: 3.9 Consensus size: 113
52466228 TTTACCACGC
* * * *
52466238 AGCGCCGCAAAATATC-AAGACCAACACGCAGCGTTCTGGTCTTGATGTATATTGGC-ATTAGTG
1 AGCGCCGCAAAATATCTTA-ACCAAAACGCAGAGTT-TGGTCTTGATGTATATTAGCAATTAGTG
* * *
52466301 GCGCTTATGAACAAACGCCGGTAATGTACAGTATTAGCGGCGCTTAGCGAA
64 GCGCTTATGAA-AAACGCCGCTAAAGTATAGTATTAGCGGCGCTTAGCGAA
* * * *
52466352 AGCGCCGCAAAAGATGTTAACCAAAACGTAGAGTTTAGTCTTGATGTATATT-GCAATTAGTGGC
1 AGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGCAATTAGTGGC
* * **
52466416 GCTTATAAAGAAAACGCCGCTAATGTATAGTATTAGCGGCGCAGAGCGTTAA
66 GCTTAT-GA-AAAACGCCGCTAAAGTATAGTATTAGCGGCGCTTAGCG--AA
* * ** * *
52466468 A-CGCCGCAAGATATCTTAATCAAAACGCACCGTTTTGGTCTTGATGTATACTA-TAATTAGTGG
1 AGCGCCGCAAAATATCTTAACCAAAACGCAGAG-TTTGGTCTTGATGTATATTAGCAATTAGTGG
* * ** * * * * * *
52466531 CGTTTAAGGGAAACGCCAG-TAAAGGATAGT-TATAGCAGCGTTTTGTGGTA
65 CGCTTATGAAAAACGCC-GCTAAAGTATAGTAT-TAGCGGCGCTTAG-CGAA
* * *
52466581 AGCGCCTCCAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGA-GGAGTATTAG-AATTAGTGG
1 AGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGATGTA-TATTAGCAATTAGTGG
52466644 CGCTTGATGAAAAACGCCGCTAAAGTATA-TCATTAGCGGCG
65 CGCTT-ATGAAAAACGCCGCTAAAGTATAGT-ATTAGCGGCG
52466685 TCCAGTATAC
Statistics
Matches: 265, Mismatches: 50, Indels: 36
0.75 0.14 0.10
Matches are distributed among these distances:
112 4 0.02
113 64 0.24
114 134 0.51
115 29 0.11
116 34 0.13
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26
Consensus pattern (113 bp):
AGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGCAATTAGTGGC
GCTTATGAAAAACGCCGCTAAAGTATAGTATTAGCGGCGCTTAGCGAA
Found at i:52467017 original size:18 final size:18
Alignment explanation
Indices: 52466996--52467031 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
52466986 TCATTTTATC
52466996 TGTTT-TTTATATTTAATT
1 TGTTTATTTATA-TTAATT
52467014 TGTTTATTTATATTAATT
1 TGTTTATTTATATTAATT
52467032 AAAATTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TGTTTATTTATATTAATT
Found at i:52467163 original size:20 final size:20
Alignment explanation
Indices: 52467138--52467175 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52467128 GATTGATTTG
52467138 TAATTT-ATATATATATTAAA
1 TAATTTCATATATA-ATTAAA
52467158 TAATTTCATATATAATTA
1 TAATTTCATATATAATTA
52467176 GAAAAGATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATTTCATATATAATTAAA
Found at i:52467998 original size:7 final size:7
Alignment explanation
Indices: 52467952--52467996 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
52467942 TGTTCGGGGT
52467952 TTTAGGG
1 TTTAGGG
52467959 TTTAGGG
1 TTTAGGG
*
52467966 TTTAGGC
1 TTTAGGG
52467973 TTTAGGG
1 TTTAGGG
*
52467980 TTTGGGG
1 TTTAGGG
*
52467987 TTTGGGG
1 TTTAGGG
52467994 TTT
1 TTT
52467997 GGTTTTTGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.09, C:0.02, G:0.42, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:52468660 original size:147 final size:147
Alignment explanation
Indices: 52468509--52468789 Score: 318
Period size: 147 Copynumber: 1.9 Consensus size: 147
52468499 ATTATGTTTA
** * * *
52468509 TTGAAATGTTTTCGTTTTTGTCTATTG-TATTAGTGGC-GTTTGTCAGAAACGCCACAACATTG-
1 TTGAAATGTTGCCG-TTTTGT-TAATGTTATTAGTGGCAGTTTATCAAAAACGCCACAACATTGA
* **** *
52468571 GGTAAACTGTTGGGGAAACGGGTTCGTTTTGAGTTATAGTTAGTGGCGCTTTA-CTTAAAACGCC
64 GGT-AACTGTTGAGGAAACGACCGCGTTTTGAGTGATAGTTAGTGGCGC-TTAGCTTAAAACGCC
52468635 GCAAAATTGTTCAAACATTTG
127 GCAAAATTGTTCAAACATTTG
* ****
52468656 TTGAAATGTTGCCGTTTTGTTAATGTTATTAGTGGCATTTTATCAAAAACGCCACGGGTTTGAGG
1 TTGAAATGTTGCCGTTTTGTTAATGTTATTAGTGGCAGTTTATCAAAAACGCCACAACATTGAGG
* * * *
52468721 TAAGTGTTGATGAAGCGACCGCGTTTTGAGTGATAGTTAGTGGCGCTTAGTTTAAAACGCCGCAA
66 TAACTGTTGAGGAAACGACCGCGTTTTGAGTGATAGTTAGTGGCGCTTAGCTTAAAACGCCGCAA
52468786 AATT
131 AATT
52468790 TTGACCTATA
Statistics
Matches: 110, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
145 4 0.04
146 19 0.17
147 84 0.76
148 3 0.03
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.36
Consensus pattern (147 bp):
TTGAAATGTTGCCGTTTTGTTAATGTTATTAGTGGCAGTTTATCAAAAACGCCACAACATTGAGG
TAACTGTTGAGGAAACGACCGCGTTTTGAGTGATAGTTAGTGGCGCTTAGCTTAAAACGCCGCAA
AATTGTTCAAACATTTG
Found at i:52470353 original size:15 final size:16
Alignment explanation
Indices: 52470318--52470350 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
52470308 GTATTTATAA
*
52470318 TTATCGATTTGCAATT
1 TTATCGATTTACAATT
52470334 TTATCGATTTACAATT
1 TTATCGATTTACAATT
52470350 T
1 T
52470351 ATCCGGTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (16 bp):
TTATCGATTTACAATT
Found at i:52470488 original size:67 final size:67
Alignment explanation
Indices: 52470415--52470553 Score: 244
Period size: 67 Copynumber: 2.1 Consensus size: 67
52470405 ATTAATTGAT
*
52470415 TGAATGTCAATGAATTATCAATTTTAGTTA-TCTAATTGATTGAATGTTTTATAAATTCATTATA
1 TGAATGTCAATGAATTATCAATTTTAGTTAGT-TAATTGATTGAATGTTTAATAAATTCATTATA
52470479 TAA
65 TAA
*
52470482 TGAATGTCAATGAATTATCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
1 TGAATGTCAATGAATTATCAATTTTAGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
52470547 AA
66 AA
52470549 TGAAT
1 TGAAT
52470554 TCTCAACAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
67 68 0.99
68 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.45
Consensus pattern (67 bp):
TGAATGTCAATGAATTATCAATTTTAGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
AA
Found at i:52470779 original size:76 final size:74
Alignment explanation
Indices: 52470678--52470980 Score: 588
Period size: 74 Copynumber: 4.1 Consensus size: 74
52470668 ATTTAATTTA
52470678 ACTTATTAATATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTTTTAAGTATA
1 ACTTATTAATATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTTTTAAGTATA
52470743 TTTTACATG
66 TTTTACATG
52470752 ACTTATTAATATATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTTTTAAGTA
1 ACTTATT-A-ATATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTTTTAAGTA
52470817 TATTTTACATG
64 TATTTTACATG
52470828 ACTTATTAATATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTTTTAAGTATA
1 ACTTATTAATATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTTTTAAGTATA
52470893 TTTTACATG
66 TTTTACATG
52470902 ACTTATTAATATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTTTTAAGTATA
1 ACTTATTAATATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTTTTAAGTATA
52470967 TTTTACATG
66 TTTTACATG
52470976 ACTTA
1 ACTTA
52470981 CATTACTTAC
Statistics
Matches: 227, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
74 152 0.67
75 2 0.01
76 73 0.32
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (74 bp):
ACTTATTAATATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTTTTAAGTATA
TTTTACATG
Found at i:52470873 original size:150 final size:148
Alignment explanation
Indices: 52470678--52470980 Score: 588
Period size: 150 Copynumber: 2.0 Consensus size: 148
52470668 ATTTAATTTA
52470678 ACTTATTAATATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTTTTAAGTATA
1 ACTTATTAATATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTTTTAAGTATA
52470743 TTTTACATGACTTATTAATATATATATATTTTAAAATTGATATCTTACATTACTTAAATATATAT
66 TTTTACATGACTTATT-A-ATATATATATTTTAAAATTGATATCTTACATTACTTAAATATATAT
52470808 TTTTAAGTATATTTTACATG
129 TTTTAAGTATATTTTACATG
52470828 ACTTATTAATATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTTTTAAGTATA
1 ACTTATTAATATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTTTTAAGTATA
52470893 TTTTACATGACTTATTAATATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTT
66 TTTTACATGACTTATTAATATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTT
52470958 TTAAGTATATTTTACATG
131 TTAAGTATATTTTACATG
52470976 ACTTA
1 ACTTA
52470981 CATTACTTAC
Statistics
Matches: 153, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
148 71 0.46
149 1 0.01
150 81 0.53
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (148 bp):
ACTTATTAATATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTTTTAAGTATA
TTTTACATGACTTATTAATATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTT
TTAAGTATATTTTACATG
Found at i:52471037 original size:13 final size:12
Alignment explanation
Indices: 52471011--52471059 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
52471001 TTTTTACTAA
*
52471011 AATTAACTTGAAT
1 AATT-ACTTAAAT
52471024 ATATTACTTAAAT
1 A-ATTACTTAAAT
52471037 AATTTACTTAAAT
1 AA-TTACTTAAAT
52471050 ACATTACTTA
1 A-ATTACTTA
52471060 CTAAACTGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 1 0.03
13 27 0.84
14 4 0.12
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (12 bp):
AATTACTTAAAT
Found at i:52471328 original size:16 final size:16
Alignment explanation
Indices: 52471307--52471361 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 16
52471297 ACACTTATAA
52471307 AACTTACATAATACAT
1 AACTTACATAATACAT
*
52471323 AACTTACAT-GT---T
1 AACTTACATAATACAT
52471335 AACTTACATAATACAT
1 AACTTACATAATACAT
* *
52471351 GACTTATATAA
1 AACTTACATAA
52471362 AATTCTCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
12 10 0.32
13 1 0.03
15 1 0.03
16 19 0.61
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35
Consensus pattern (16 bp):
AACTTACATAATACAT
Found at i:52471438 original size:9 final size:9
Alignment explanation
Indices: 52471400--52471528 Score: 81
Period size: 9 Copynumber: 14.6 Consensus size: 9
52471390 TAGTTACATA
*
52471400 ATAACTTAT
1 ATAACTTAC
52471409 ATAAGCTTAC
1 ATAA-CTTAC
*
52471419 ATAA-TACAC
1 ATAACT-TAC
*
52471428 ATTACTTAC
1 ATAACTTAC
* *
52471437 ATAGCATAC
1 ATAACTTAC
52471446 ATAACTTAC
1 ATAACTTAC
* *
52471455 ACAACTTAA
1 ATAACTTAC
52471464 AT-AC-TAC
1 ATAACTTAC
*
52471471 AAAACTTAC
1 ATAACTTAC
52471480 ATAACTTAC
1 ATAACTTAC
**
52471489 ATAACCGAC
1 ATAACTTAC
*
52471498 ATAATACATA-
1 AT-A-ACTTAC
52471508 ATAACTTAC
1 ATAACTTAC
52471517 --AACTTAC
1 ATAACTTAC
52471524 ATAAC
1 ATAAC
52471529 ATNNNNNNNN
Statistics
Matches: 90, Mismatches: 20, Indels: 20
0.69 0.15 0.15
Matches are distributed among these distances:
7 10 0.11
8 9 0.10
9 56 0.62
10 12 0.13
11 3 0.03
ACGTcount: A:0.47, C:0.22, G:0.02, T:0.29
Consensus pattern (9 bp):
ATAACTTAC
Found at i:52476939 original size:42 final size:42
Alignment explanation
Indices: 52476886--52477090 Score: 356
Period size: 42 Copynumber: 4.9 Consensus size: 42
52476876 TGTATAAAAA
*
52476886 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
* *
52476928 CGTCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTCTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
* *
52476970 TGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTGTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
*
52477012 CGCCGCTAAAGAACATGGTCTTTAGAGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
52477054 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTT
52477091 TTTGTAAACG
Statistics
Matches: 152, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 152 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
Found at i:52478213 original size:29 final size:29
Alignment explanation
Indices: 52478167--52478227 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
52478157 GTTAGTGATT
*
52478167 TGTGAAAATTGAATC-AAATCAAAATTTCA
1 TGTGAAAATTGAATCAAAATC-AAAGTTCA
*
52478196 TGTGCAAAATTGCA-CAAAATCAAAGTTCA
1 TGTG-AAAATTGAATCAAAATCAAAGTTCA
52478225 TGT
1 TGT
52478228 ATAACATTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (29 bp):
TGTGAAAATTGAATCAAAATCAAAGTTCA
Found at i:52484941 original size:64 final size:64
Alignment explanation
Indices: 52484873--52485214 Score: 157
Period size: 64 Copynumber: 5.2 Consensus size: 64
52484863 GTTAAGCTTC
52484873 GCTGATTTAATATCGCAACCTAAGTTCATTCGATTTAATATCATTAAAAATCTTATCTGAGTTA
1 GCTGATTTAATATCGCAACCTAAGTTCATTCGATTTAATATCATTAAAAATCTTATCTGAGTTA
* * * * * * * *
52484937 GCTGATTTTATATCACTACTCTAAATAGCTCGTT-GATTTAATATTGCAGCT-GATATCGTTA--
1 GCTGATTTAATATCGCAAC-CT--A-AGTTCATTCGATTTAATA-T-CA-TTAAAAATC-TTATC
*
52484998 AG-GTTCA
58 TGAGTT-A
* ** * * *
52485005 -CTAATTTAATATCGCAACCTAAGTTCATTTAATTTAATATCATGAACAATCTTATCTGAGTGA
1 GCTGATTTAATATCGCAACCTAAGTTCATTCGATTTAATATCATTAAAAATCTTATCTGAGTTA
* * * *** * * *
52485068 ACTGATTTAATATCCCTACTCTAA-AAAACTCGCTGATTTAATATCTCAATT-GATATCGTTA--
1 GCTGATTTAATATCGCAAC-CTAAGTTCA-T-TC-GATTTAATA--TC-ATTAAAAATC-TTATC
* *
52485129 AG-GTTC
58 TGAGTTA
* * * * * *
52485135 GCTGATTTAAGATCACAACCTAAGTTCATTTGATTTAATATCATGAACAATATTATCTGAGTTA
1 GCTGATTTAATATCGCAACCTAAGTTCATTCGATTTAATATCATTAAAAATCTTATCTGAGTTA
*
52485199 GTTGATTTAATATCGC
1 GCTGATTTAATATCGC
52485215 TACTCTAAAC
Statistics
Matches: 192, Mismatches: 58, Indels: 56
0.63 0.19 0.18
Matches are distributed among these distances:
61 8 0.04
62 9 0.05
63 10 0.05
64 68 0.35
65 7 0.04
66 7 0.04
67 53 0.28
68 10 0.05
69 11 0.06
70 9 0.05
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (64 bp):
GCTGATTTAATATCGCAACCTAAGTTCATTCGATTTAATATCATTAAAAATCTTATCTGAGTTA
Found at i:52485276 original size:131 final size:131
Alignment explanation
Indices: 52484799--52485277 Score: 636
Period size: 131 Copynumber: 3.7 Consensus size: 131
52484789 TAATTATCTT
* * * *
52484799 TGAGCTAGTTGATTTAATACCGCTACTCTAAATAGCTCGTTGATTTAATATCGCAGCTAATAAT-
1 TGAGTTAGCTGATTTAATATCGCTACTCTAAATAGCTCGTTGATTTAATATCGCAGCTGAT-ATC
* * * * *
52484863 GTTAAGCTTCGCTGATTTAATATCGCAACCTAAGTTCATTCGATTTAATATCATTAAAAATCTTA
65 GTTAAGGTTCGCTGATTTAAGATCGCAACCTAAGTTCATTTGATTTAATATCATGAACAATCTTA
52484928 TC
130 TC
* * *
52484930 TGAGTTAGCTGATTTTATATCACTACTCTAAATAGCTCGTTGATTTAATATTGCAGCTGATATCG
1 TGAGTTAGCTGATTTAATATCGCTACTCTAAATAGCTCGTTGATTTAATATCGCAGCTGATATCG
* * * *
52484995 TTAAGGTTCACTAATTTAATATCGCAACCTAAGTTCATTTAATTTAATATCATGAACAATCTTAT
66 TTAAGGTTCGCTGATTTAAGATCGCAACCTAAGTTCATTTGATTTAATATCATGAACAATCTTAT
52485060 C
131 C
* * * * * * * **
52485061 TGAGTGAACTGATTTAATATCCCTACTCTAAAAAACTCGCTGATTTAATATCTCAATTGATATCG
1 TGAGTTAGCTGATTTAATATCGCTACTCTAAATAGCTCGTTGATTTAATATCGCAGCTGATATCG
* *
52485126 TTAAGGTTCGCTGATTTAAGATCACAACCTAAGTTCATTTGATTTAATATCATGAACAATATTAT
66 TTAAGGTTCGCTGATTTAAGATCGCAACCTAAGTTCATTTGATTTAATATCATGAACAATCTTAT
52485191 C
131 C
* * * * * * *
52485192 TGAGTTAGTTGATTTAATATCGCTACTCTAAACAGCTTGTTGATTTAAGATCGTAGTTGATATCA
1 TGAGTTAGCTGATTTAATATCGCTACTCTAAATAGCTCGTTGATTTAATATCGCAGCTGATATCG
52485257 TTAAGGTTCGCTGATTTAAGA
66 TTAAGGTTCGCTGATTTAAGA
52485278 CAACCTCTCT
Statistics
Matches: 303, Mismatches: 44, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
130 2 0.01
131 301 0.99
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (131 bp):
TGAGTTAGCTGATTTAATATCGCTACTCTAAATAGCTCGTTGATTTAATATCGCAGCTGATATCG
TTAAGGTTCGCTGATTTAAGATCGCAACCTAAGTTCATTTGATTTAATATCATGAACAATCTTAT
C
Found at i:52487209 original size:2 final size:2
Alignment explanation
Indices: 52487202--52487239 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
52487192 CTACATAATC
52487202 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52487240 TATCTTCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52502266 original size:25 final size:24
Alignment explanation
Indices: 52502218--52502276 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
52502208 TTTTGAAAAG
* *
52502218 TTTTAATTTAATTTGATTTGATTT
1 TTTTAATTTAATTTAATCTGATTT
52502242 TTTATAATTTAATTTAAATCT-ATTT
1 TTT-TAATTTAATTT-AATCTGATTT
52502267 TTTTAATTTA
1 TTTTAATTTA
52502277 GTTGTATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 10 0.32
25 18 0.58
26 3 0.10
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (24 bp):
TTTTAATTTAATTTAATCTGATTT
Found at i:52505418 original size:18 final size:18
Alignment explanation
Indices: 52505395--52505429 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
52505385 ATGAATAATC
52505395 TTTTAAGAA-TTTTAAAAT
1 TTTTAA-AATTTTTAAAAT
52505413 TTTTAAAATTTTTAAAA
1 TTTTAAAATTTTTAAAA
52505430 ACTTGTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTTAAAATTTTTAAAAT
Found at i:52507888 original size:20 final size:21
Alignment explanation
Indices: 52507854--52507904 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
52507844 TTTTTAAAAA
** *
52507854 CTTTTTCCATTTTTTTC-TTT
1 CTTTTTCCAGGTTTTCCTTTT
52507874 CTTTTTCCAGGTTTTCCTTTT
1 CTTTTTCCAGGTTTTCCTTTT
52507895 CTTCTTTCCA
1 CTT-TTTCCA
52507905 ATTTCCATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 14 0.54
21 6 0.23
22 6 0.23
ACGTcount: A:0.06, C:0.25, G:0.04, T:0.65
Consensus pattern (21 bp):
CTTTTTCCAGGTTTTCCTTTT
Found at i:52509802 original size:31 final size:31
Alignment explanation
Indices: 52509759--52509823 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
52509749 AATCCAGAGA
52509759 TAAAGGACTTAAGGATTATTGCATGAAAGGT
1 TAAAGGACTTAAGGATTATTGCATGAAAGGT
*
52509790 TAAATGACTTAAGGATTATTGCATGAAAGGT
1 TAAAGGACTTAAGGATTATTGCATGAAAGGT
52509821 TAA
1 TAA
52509824 TCATAAAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (31 bp):
TAAAGGACTTAAGGATTATTGCATGAAAGGT
Found at i:52515464 original size:4 final size:4
Alignment explanation
Indices: 52515446--52515479 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
52515436 TTTTTGGCTC
52515446 ATTT ATTTT ATTTT ATTT ATTT ATTT ATTT ATTT
1 ATTT A-TTT A-TTT ATTT ATTT ATTT ATTT ATTT
52515480 TTAAAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 20 0.69
5 9 0.31
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
ATTT
Found at i:52519745 original size:20 final size:19
Alignment explanation
Indices: 52519709--52519747 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
52519699 GATAAAAGAA
*
52519709 ATAAAAATAAATGAAATTT
1 ATAAAAAAAAATGAAATTT
*
52519728 ATAAAAAAAATATTAAATTT
1 ATAAAAAAAA-ATGAAATTT
52519748 TAATTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
ATAAAAAAAAATGAAATTT
Found at i:52519800 original size:19 final size:18
Alignment explanation
Indices: 52519778--52519842 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 18
52519768 AAAAAACATA
52519778 AAAATCATTTAAAAATTAT
1 AAAAT-ATTTAAAAATTAT
* *
52519797 AAAAAATTGTAAAATTTTAT
1 AAAATATT-TAAAA-ATTAT
* *
52519817 AAAAATAGTAAAAAATTAT
1 -AAAATATTTAAAAATTAT
52519836 AAAATAT
1 AAAATAT
52519843 ATAGAAATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
18 9 0.25
19 13 0.36
20 8 0.22
21 6 0.17
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.34
Consensus pattern (18 bp):
AAAATATTTAAAAATTAT
Found at i:52519810 original size:29 final size:29
Alignment explanation
Indices: 52519787--52519897 Score: 120
Period size: 29 Copynumber: 3.8 Consensus size: 29
52519777 AAAAATCATT
*
52519787 TAAAAATTA-TAAAAAATTGTAAAATTTTA
1 TAAAAA-TAGTAAAAAATTATAAAATTTTA
*
52519816 TAAAAATAGTAAAAAATTATAAAA-TATA
1 TAAAAATAGTAAAAAATTATAAAATTTTA
* *
52519844 TAGAAATATGAAAAAAATTATAAAATTTTA
1 TAAAAATA-GTAAAAAATTATAAAATTTTA
* *
52519874 T-AAAGTTGTAAGAAAATTATAAAA
1 TAAAAATAGTAA-AAAATTATAAAA
52519898 AATGTAAAGA
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
28 15 0.22
29 50 0.72
30 4 0.06
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (29 bp):
TAAAAATAGTAAAAAATTATAAAATTTTA
Found at i:52519819 original size:58 final size:57
Alignment explanation
Indices: 52519757--52519877 Score: 147
Period size: 58 Copynumber: 2.1 Consensus size: 57
52519747 TTAATTAAAA
* *
52519757 ATAAAAATAGAAAAAAACATA-AAAATCATTTAAAAAT-TATAAAAAATTGTAAAATTTT
1 ATAAAAATAGAAAAAAA-ATATAAAAT-ATATAAAAATATA-AAAAAATTATAAAATTTT
* * *
52519815 ATAAAAATAGTAAAAAATTATAAAATATATAGAAATATGAAAAAAATTATAAAATTTT
1 ATAAAAATAGAAAAAAAATATAAAATATATAAAAATAT-AAAAAAATTATAAAATTTT
52519873 ATAAA
1 ATAAA
52519878 GTTGTAAGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
57 10 0.18
58 44 0.80
59 1 0.02
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (57 bp):
ATAAAAATAGAAAAAAAATATAAAATATATAAAAATATAAAAAAATTATAAAATTTT
Found at i:52519929 original size:11 final size:10
Alignment explanation
Indices: 52519788--52519940 Score: 85
Period size: 10 Copynumber: 15.9 Consensus size: 10
52519778 AAAATCATTT
52519788 AAAAATTATA
1 AAAAATTATA
*
52519798 AAAAATTGTA
1 AAAAATTATA
**
52519808 AAATTTTAT-
1 AAAAATTATA
52519817 AAAAA-TAGTA
1 AAAAATTA-TA
52519827 AAAAATTATA
1 AAAAATTATA
*
52519837 AAATA-TATA
1 AAAAATTATA
* *
52519846 GAAATATGA-A
1 -AAAAATTATA
52519856 AAAAATTAT-
1 AAAAATTATA
*
52519865 -AAAATTTTA
1 AAAAATTATA
* * *
52519874 TAAAGTTGTA
1 AAAAATTATA
52519884 AGAAAATTATA
1 A-AAAATTATA
52519895 AAAAATGTA-A
1 AAAAAT-TATA
*
52519905 AGAAA-TAT-
1 AAAAATTATA
52519913 -AAAATTCATA
1 AAAAATT-ATA
52519923 AAAAATTAT-
1 AAAAATTATA
52519932 AAAAATTAT
1 AAAAATTAT
52519941 CATACCAAAA
Statistics
Matches: 110, Mismatches: 18, Indels: 31
0.69 0.11 0.19
Matches are distributed among these distances:
7 3 0.03
8 12 0.11
9 25 0.23
10 51 0.46
11 19 0.17
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (10 bp):
AAAAATTATA
Found at i:52520159 original size:29 final size:29
Alignment explanation
Indices: 52520104--52520162 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
52520094 TTTTTGATGC
* *
52520104 ATTTTATATTTTTTTATGATTTTTATAAA
1 ATTTTATATTTTTTTAAGATTTCTATAAA
52520133 ATTTTATATTTTTTTACAG-TTTCTATAAA
1 ATTTTATATTTTTTTA-AGATTTCTATAAA
52520162 A
1 A
52520163 AATTTCTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 26 0.96
30 1 0.04
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (29 bp):
ATTTTATATTTTTTTAAGATTTCTATAAA
Found at i:52520165 original size:31 final size:29
Alignment explanation
Indices: 52520104--52520176 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 29
52520094 TTTTTGATGC
* *
52520104 ATTTTATATTTTTTTATGATTTTTATAAA
1 ATTTTATATTTTTTTAAGATTTTTAAAAA
52520133 ATTTTATATTTTTTTACAG-TTTCTATAAAAA
1 ATTTTATATTTTTTTA-AGATTT-T-TAAAAA
52520164 ATTTCTA-ATTTTT
1 ATTT-TATATTTTT
52520177 AACGAAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 19 0.50
30 2 0.05
31 15 0.39
32 2 0.05
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.62
Consensus pattern (29 bp):
ATTTTATATTTTTTTAAGATTTTTAAAAA
Found at i:52536587 original size:54 final size:54
Alignment explanation
Indices: 52536476--52536601 Score: 137
Period size: 54 Copynumber: 2.3 Consensus size: 54
52536466 GGACACAAGA
* * * * *
52536476 CTGTGTCCCAGCTCATGTCTCTGCCCATGTAACTCTCTGACTTGAGATACACGG
1 CTGTGTCCCAGCCCGTGTCTCTGACCATGTAACTCACTGACTTGAGATACACAG
* * * *
52536530 CTGTATCCCAGCCCGTGTCTCTGACCGTGTAACTCACTGACTT-AGGTCACATAG
1 CTGTGTCCCAGCCCGTGTCTCTGACCATGTAACTCACTGACTTGAGAT-ACACAG
* *
52536584 CTGTGTCGCAGGCCGTGT
1 CTGTGTCCCAGCCCGTGT
52536602 GTCAACCCAT
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
53 3 0.05
54 56 0.95
ACGTcount: A:0.17, C:0.31, G:0.23, T:0.29
Consensus pattern (54 bp):
CTGTGTCCCAGCCCGTGTCTCTGACCATGTAACTCACTGACTTGAGATACACAG
Found at i:52550524 original size:33 final size:33
Alignment explanation
Indices: 52550478--52550633 Score: 94
Period size: 33 Copynumber: 4.6 Consensus size: 33
52550468 CATATAAAGG
**
52550478 GGTTGCTGTGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
52550511 GGTTGCTAAGTGCTGATCCCACCGTATTTTAAATGTGAAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T----GGT
52550554 GGTTGCTAAGTGCTGATTCCCC----CGA--GG-
1 GGTTGCTAAGTGCTGATTCCCCGATTC-ATTGGT
*
52550581 GGTTGCTAAGTGCTGATTCCCCTAATT-ATTGGT
1 GGTTGCTAAGTGCTGATTCCCC-GATTCATTGGT
52550614 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
52550634 ACCGTANNNN
Statistics
Matches: 97, Mismatches: 7, Indels: 38
0.68 0.05 0.27
Matches are distributed among these distances:
27 22 0.23
28 2 0.02
30 1 0.01
32 2 0.02
33 37 0.38
34 3 0.03
35 2 0.02
37 2 0.02
38 2 0.02
39 1 0.01
42 2 0.02
43 21 0.22
ACGTcount: A:0.17, C:0.20, G:0.29, T:0.34
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:52564033 original size:43 final size:42
Alignment explanation
Indices: 52563964--52564049 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 42
52563954 AAGGCATAGA
* * * * *
52563964 GAAAAGAGGAATCAGTAGTTCTTTTAATGTCGTCCCTTGCAT
1 GAAAAGAGAAATCAATAGCTCCTTTAATGTCGTCCCATGCAT
*
52564006 GAAAAGGAGAAATCAATAGCTCCTTTAATGTCGTCTCATGCAT
1 GAAAA-GAGAAATCAATAGCTCCTTTAATGTCGTCCCATGCAT
52564049 G
1 G
52564050 CTTTCTTTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 5 0.14
43 32 0.86
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (42 bp):
GAAAAGAGAAATCAATAGCTCCTTTAATGTCGTCCCATGCAT
Found at i:52568931 original size:13 final size:13
Alignment explanation
Indices: 52568913--52568937 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52568903 TCCAGCAACT
52568913 ATGAATTTATTTC
1 ATGAATTTATTTC
52568926 ATGAATTTATTT
1 ATGAATTTATTT
52568938 GATGTTGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (13 bp):
ATGAATTTATTTC
Found at i:52569148 original size:50 final size:50
Alignment explanation
Indices: 52569036--52569334 Score: 391
Period size: 50 Copynumber: 5.8 Consensus size: 50
52569026 ATTTGGGTAA
* *
52569036 AGAGATCCCATGTAAGACCATGTCTGGGGCATGGCATTGGCATCCTTGAGATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAGAT---G
* *
52569092 ATAGGTCTCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
52569142 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
52569192 AAAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
52569242 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGTATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
52569292 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
52569335 TGTAATGATC
Statistics
Matches: 218, Mismatches: 24, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
50 139 0.64
51 34 0.16
53 5 0.02
55 2 0.01
56 38 0.17
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:52581688 original size:2 final size:2
Alignment explanation
Indices: 52581681--52581715 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
52581671 GTTCCCAAAT
52581681 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52581716 GTCCCATCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52582181 original size:5 final size:5
Alignment explanation
Indices: 52582171--52582201 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
52582161 TGGGCAATTG
52582171 GGTGC GGTGC GGTGC GGTGC GGTGC GGTGC G
1 GGTGC GGTGC GGTGC GGTGC GGTGC GGTGC G
52582202 TTTAGTTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.61, T:0.19
Consensus pattern (5 bp):
GGTGC
Found at i:52583736 original size:16 final size:16
Alignment explanation
Indices: 52583715--52583747 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
52583705 TTCGCTGTAT
52583715 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
52583731 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
52583747 T
1 T
52583748 AGCAATTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.36, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:52583815 original size:44 final size:45
Alignment explanation
Indices: 52583727--52583816 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
52583717 GAATAGAGGC
52583727 GTAATGGAATAGAGGCGTAATAGCAATTCTATTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGCAATTCTATTGTTTGGTTGAAT
* *
52583772 GTAATGGAATAGAGGTGTAATAG-TATTCT-TCTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGCAATTCTAT-TGTTTGGTTGAAT
52583816 G
1 G
52583817 GAATAGAGGC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 19 0.45
45 22 0.52
ACGTcount: A:0.29, C:0.06, G:0.28, T:0.38
Consensus pattern (45 bp):
GTAATGGAATAGAGGCGTAATAGCAATTCTATTGTTTGGTTGAAT
Found at i:52583832 original size:39 final size:43
Alignment explanation
Indices: 52583727--52583835 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
52583717 GAATAGAGGC
52583727 GTAATGGAATAGAGGCGTAATAGCAATTCTATTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGCAATTCTATTGTTTGGTT--AT
* *
52583772 GTAATGGAATAGAGGTGTAATAG-TATTCT-TCTGTTTGG-T-T
1 GTAATGGAATAGAGGCGTAATAGCAATTCTAT-TGTTTGGTTAT
*
52583812 G-AATGGAATAGAGGCATAATAGCA
1 GTAATGGAATAGAGGCGTAATAGCA
52583836 TAAAGAAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
39 19 0.33
40 2 0.04
43 2 0.04
44 12 0.21
45 22 0.39
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.34
Consensus pattern (43 bp):
GTAATGGAATAGAGGCGTAATAGCAATTCTATTGTTTGGTTAT
Found at i:52583958 original size:18 final size:18
Alignment explanation
Indices: 52583937--52584011 Score: 57
Period size: 18 Copynumber: 4.1 Consensus size: 18
52583927 TATTAATATA
52583937 AATAATAAATAATTTAAT
1 AATAATAAATAATTTAAT
52583955 AATAATTTAAAATAA--TAATT
1 AATAA--T-AAATAATTTAA-T
* *
52583975 ATTAA-ATATAATTTAAT
1 AATAATAAATAATTTAAT
* *
52583992 AAAAATATATAATTTAAT
1 AATAATAAATAATTTAAT
52584010 AA
1 AA
52584012 AATTCTGAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
16 5 0.11
17 4 0.09
18 22 0.48
19 3 0.07
20 6 0.13
21 6 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATAATAAATAATTTAAT
Found at i:52583970 original size:13 final size:13
Alignment explanation
Indices: 52583944--52583990 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
52583934 ATAAATAATA
52583944 AATAATTT--AAT
1 AATAATTTAAAAT
52583955 AATAATTTAAAAT
1 AATAATTTAAAAT
*
52583968 AATAATTATTAAAT
1 AATAATT-TAAAAT
52583982 -ATAATTTAA
1 AATAATTTAA
52583991 TAAAAATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 8 0.26
12 2 0.06
13 16 0.52
14 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AATAATTTAAAAT
Found at i:52583972 original size:16 final size:16
Alignment explanation
Indices: 52583931--52583986 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
52583921 TAAGATTATT
*
52583931 AATATAAATAATAAAT-
1 AATAT-AATAATAATTA
*
52583947 AATTTAATAATAATTTA
1 AATATAATAATAA-TTA
*
52583964 AA-ATAATAATTATTA
1 AATATAATAATAATTA
52583979 AATATAAT
1 AATATAAT
52583987 TTAATAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 13 0.39
16 18 0.55
17 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATATAATAATAATTA
Found at i:52584010 original size:55 final size:54
Alignment explanation
Indices: 52583934--52584075 Score: 139
Period size: 55 Copynumber: 2.6 Consensus size: 54
52583924 GATTATTAAT
52583934 ATAAATAATAAATAATTTAATAATAATTTAAAATAATAATTATTAAATATAATTTA
1 ATAAA-AATAAATAATTTAATAATAATTTAAAATAATAATTATTAAAT-TAATTTA
* * * * *
52583990 ATAAAAATATATAATTTAATAA-AATTCTGAATATAATTATTCTTATATTAATTTA
1 ATAAAAATAAATAATTTAATAATAATT-T-AAAATAATAATTATTAAATTAATTTA
* * * *
52584045 CT-AAAAT-CATAATAT-ATAATAATATAAAATA
1 ATAAAAATAAATAATTTAATAATAATTTAAAATA
52584076 TTTAATCTCA
Statistics
Matches: 73, Mismatches: 10, Indels: 11
0.78 0.11 0.12
Matches are distributed among these distances:
51 5 0.07
52 5 0.07
53 9 0.12
54 9 0.12
55 25 0.34
56 20 0.27
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.41
Consensus pattern (54 bp):
ATAAAAATAAATAATTTAATAATAATTTAAAATAATAATTATTAAATTAATTTA
Found at i:52588198 original size:24 final size:24
Alignment explanation
Indices: 52588148--52588199 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
52588138 TTTCTAGAAG
* *
52588148 ATTTAGTATTTATTAGTATATTAT
1 ATTTAGCATTTATTAGCATATTAT
52588172 ATTTAGCATTTATTAGCATACTT-T
1 ATTTAGCATTTATTAGCATA-TTAT
52588196 ATTT
1 ATTT
52588200 GGCTTACGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.56
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATATTAT
Found at i:52589835 original size:24 final size:24
Alignment explanation
Indices: 52589808--52589856 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
52589798 CTAGAAGATC
*
52589808 TAGTATTTATTAGTATAATATATT
1 TAGTATTTATTAGCATAATATATT
*
52589832 TAGTATTTATTAGCATAATTTATT
1 TAGTATTTATTAGCATAATATATT
52589856 T
1 T
52589857 TACCTATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (24 bp):
TAGTATTTATTAGCATAATATATT
Found at i:52596174 original size:69 final size:69
Alignment explanation
Indices: 52596059--52596214 Score: 278
Period size: 69 Copynumber: 2.3 Consensus size: 69
52596049 CTGCAACCAG
* *
52596059 AATTCAGAGTCATTTCCGTGGTTGGCAGTTAAGAAGGAATTTTATGAAGAAGAAGCAAGCAATAA
1 AATTCAGAGTCATTTCCGTGGTTGGCAGTTAAGAAGGAATTGTATGAAGAAAAAGCAAGCAATAA
52596124 TTAA
66 TTAA
52596128 AATTCAGAGTCATTTCCGTGGTTGGCAGTTAAGAAGGAATTGTATGAAGAAAAAGCAAGCAATAA
1 AATTCAGAGTCATTTCCGTGGTTGGCAGTTAAGAAGGAATTGTATGAAGAAAAAGCAAGCAATAA
52596193 TTAA
66 TTAA
52596197 AATTCAGAG-CAATTTCCG
1 AATTCAGAGTC-ATTTCCG
52596215 GCAGCAAAAA
Statistics
Matches: 84, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
68 1 0.01
69 83 0.99
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (69 bp):
AATTCAGAGTCATTTCCGTGGTTGGCAGTTAAGAAGGAATTGTATGAAGAAAAAGCAAGCAATAA
TTAA
Found at i:52602549 original size:22 final size:22
Alignment explanation
Indices: 52602521--52602565 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
52602511 ACTTGAGAGA
52602521 ACAACAACGTTGTCATATATTT
1 ACAACAACGTTGTCATATATTT
*
52602543 ACAACAATGTTGTCATATATTT
1 ACAACAACGTTGTCATATATTT
52602565 A
1 A
52602566 AGAAGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
ACAACAACGTTGTCATATATTT
Found at i:52605208 original size:2 final size:2
Alignment explanation
Indices: 52605196--52605243 Score: 87
Period size: 2 Copynumber: 23.5 Consensus size: 2
52605186 NNNNNNNNNN
52605196 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52605239 TA TA T
1 TA TA T
52605244 CACCTAATGG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 43 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52613922 original size:39 final size:40
Alignment explanation
Indices: 52613879--52613963 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
52613869 CACGTCAAGA
* * *
52613879 AAAAAAAT-CACATAAAAATGTTTAAAAATATAAAAATAT
1 AAAAAAATCCACACAAAAATATTTAAAAATAGAAAAATAT
* * * *
52613918 AAAAAAATCCACCCCAAAATATTTAAAATTAGAAAATTAT
1 AAAAAAATCCACACAAAAATATTTAAAAATAGAAAAATAT
52613958 AAAAAA
1 AAAAAA
52613964 TAAAAAATCA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
39 8 0.21
40 30 0.79
ACGTcount: A:0.65, C:0.09, G:0.02, T:0.24
Consensus pattern (40 bp):
AAAAAAATCCACACAAAAATATTTAAAAATAGAAAAATAT
Found at i:52613962 original size:17 final size:17
Alignment explanation
Indices: 52613942--52614002 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
52613932 CAAAATATTT
*
52613942 AAAATTAGAAAATTATA
1 AAAATTAAAAAATTATA
* *
52613959 AAAAATAAAAAATCATA
1 AAAATTAAAAAATTATA
* *
52613976 ATATATTTAAAAAAGTATA
1 A-A-AATTAAAAAATTATA
52613995 AAAATTAA
1 AAAATTAA
52614003 GTTTATAAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
17 20 0.59
18 2 0.06
19 12 0.35
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (17 bp):
AAAATTAAAAAATTATA
Found at i:52615809 original size:29 final size:30
Alignment explanation
Indices: 52615756--52615812 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
52615746 TCCGAGCCTT
52615756 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGTAAAAGTTTA
* *
52615786 GGGGCAAAATTGTAATTTTG-AAAAGTT
1 GGGGCAAAAATGTAATTATGTAAAAGTT
52615813 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.32
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGTAAAAGTTTA
Found at i:52618988 original size:21 final size:21
Alignment explanation
Indices: 52618964--52619093 Score: 89
Period size: 21 Copynumber: 6.2 Consensus size: 21
52618954 ATAAGGGTTG
* *
52618964 AACGGAAGCTCGTAAGAGCTA
1 AACGGAAACTCATAAGAGCTA
* * *
52618985 AACGGAAACCCATAAGGGTTA
1 AACGGAAACTCATAAGAGCTA
* * * *
52619006 AACAGAAGCTCAAAAGAGCTG
1 AACGGAAACTCATAAGAGCTA
* * * *
52619027 AACGGAAACCCATTAGGGTTA
1 AACGGAAACTCATAAGAGCTA
* * *
52619048 AATGGAAACTCATATGAGTTA
1 AACGGAAACTCATAAGAGCTA
* * *
52619069 AACAGAAGCTCGTAAGAGCTA
1 AACGGAAACTCATAAGAGCTA
52619090 AACG
1 AACG
52619094 AAAAGTAAAC
Statistics
Matches: 77, Mismatches: 32, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 77 1.00
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (21 bp):
AACGGAAACTCATAAGAGCTA
Found at i:52618994 original size:42 final size:42
Alignment explanation
Indices: 52618947--52619049 Score: 152
Period size: 42 Copynumber: 2.5 Consensus size: 42
52618937 AGTGTTAACA
* * **
52618947 GAAACCCATAAGGGTTGAACGGAAGCTCGTAAGAGCTAAACG
1 GAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTAAACG
*
52618989 GAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTGAACG
1 GAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTAAACG
*
52619031 GAAACCCATTAGGGTTAAA
1 GAAACCCATAAGGGTTAAA
52619050 TGGAAACTCA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.42, C:0.18, G:0.25, T:0.15
Consensus pattern (42 bp):
GAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTAAACG
Found at i:52619031 original size:63 final size:63
Alignment explanation
Indices: 52618962--52619093 Score: 147
Period size: 63 Copynumber: 2.1 Consensus size: 63
52618952 CCATAAGGGT
* * * *
52618962 TGAACGGAAGCTCGTAAGAGCTAAACGGAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGC
1 TGAACGGAAACCCATAAGAGCTAAACGGAAACCCATAAGAGTTAAACAGAAGCTCAAAAGAGC
* * * * * * **
52619025 TGAACGGAAACCCATTAGGGTTAAATGGAAACTCATATGAGTTAAACAGAAGCTCGTAAGAGC
1 TGAACGGAAACCCATAAGAGCTAAACGGAAACCCATAAGAGTTAAACAGAAGCTCAAAAGAGC
*
52619088 TAAACG
1 TGAACG
52619094 AAAAGTAAAC
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.17
Consensus pattern (63 bp):
TGAACGGAAACCCATAAGAGCTAAACGGAAACCCATAAGAGTTAAACAGAAGCTCAAAAGAGC
Found at i:52626265 original size:19 final size:19
Alignment explanation
Indices: 52626241--52626277 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
52626231 TATTTTTTTA
52626241 CTTAAAAA-ATTCAAAATTC
1 CTTAAAAATATT-AAAATTC
52626260 CTTAAAAATATTAAAATT
1 CTTAAAAATATTAAAATT
52626278 TTCATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (19 bp):
CTTAAAAATATTAAAATTC
Found at i:52626937 original size:43 final size:43
Alignment explanation
Indices: 52626888--52626980 Score: 150
Period size: 43 Copynumber: 2.2 Consensus size: 43
52626878 ATAAAATGTT
52626888 AGAATTTTATGAAAAAATTTAAAAATTTATGTATTGTTTTGAG
1 AGAATTTTATGAAAAAATTTAAAAATTTATGTATTGTTTTGAG
***
52626931 AGAATTTTATGAAATTTTTTAAAAATTTATGTATTGTTTTGAG
1 AGAATTTTATGAAAAAATTTAAAAATTTATGTATTGTTTTGAG
*
52626974 AAAATTT
1 AGAATTT
52626981 AGGGTTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (43 bp):
AGAATTTTATGAAAAAATTTAAAAATTTATGTATTGTTTTGAG
Found at i:52626977 original size:22 final size:22
Alignment explanation
Indices: 52626909--52626981 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 22
52626899 AAAAAATTTA
52626909 AAAATTTATGTATTGTTTTGAG
1 AAAATTTATGTATTGTTTTGAG
* *
52626931 AGAATTTTATGAAATT-TTTT-A-
1 A-AAATTTATG-TATTGTTTTGAG
52626952 AAAATTTATGTATTGTTTTGAG
1 AAAATTTATGTATTGTTTTGAG
52626974 AAAATTTA
1 AAAATTTA
52626982 GGGTTTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 3 0.07
20 12 0.29
21 2 0.05
22 10 0.24
23 12 0.29
24 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (22 bp):
AAAATTTATGTATTGTTTTGAG
Found at i:52627072 original size:20 final size:21
Alignment explanation
Indices: 52627047--52627096 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
52627037 TTTTCTTAAG
52627047 TAAAAAATA-CCATAAAATTC
1 TAAAAAATATCCATAAAATTC
* * *
52627067 TAAAAAAAAATTCATAATATTC
1 T-AAAAAATATCCATAAAATTC
52627089 TAAAAAAT
1 TAAAAAAT
52627097 TTAAAAGCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 13 0.54
22 10 0.42
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAAAAATATCCATAAAATTC
Found at i:52627082 original size:22 final size:23
Alignment explanation
Indices: 52627048--52627095 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
52627038 TTTCTTAAGT
52627048 AAAAAATACCATAAAATTCTAAA
1 AAAAAATACCATAAAATTCTAAA
* *
52627071 AAAAAAT-TCATAATATTCTAAA
1 AAAAAATACCATAAAATTCTAAA
52627093 AAA
1 AAA
52627096 TTTAAAAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (23 bp):
AAAAAATACCATAAAATTCTAAA
Found at i:52627596 original size:13 final size:13
Alignment explanation
Indices: 52627578--52627607 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
52627568 GAAAGTTAAC
52627578 CCCATAAATCTAT
1 CCCATAAATCTAT
52627591 CCCATAAATCTAT
1 CCCATAAATCTAT
52627604 CCCA
1 CCCA
52627608 GTATAAGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.27
Consensus pattern (13 bp):
CCCATAAATCTAT
Found at i:52634486 original size:15 final size:15
Alignment explanation
Indices: 52634477--52634510 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
52634467 CAAATGCTAT
52634477 AATAATAAATACAAC
1 AATAATAAATACAAC
*
52634492 AATAATAAATACATC
1 AATAATAAATACAAC
52634507 AATA
1 AATA
52634511 GCATAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAAATACAAC
Found at i:52634535 original size:13 final size:14
Alignment explanation
Indices: 52634517--52634553 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
52634507 AATAGCATAA
52634517 AAATAATATAAAC-
1 AAATAATATAAACG
52634530 AAATAA-ATAAACG
1 AAATAATATAAACG
52634543 AAATGAATATA
1 AAAT-AATATA
52634554 TATAAAAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 10 0.48
14 2 0.10
15 3 0.14
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (14 bp):
AAATAATATAAACG
Found at i:52634927 original size:2 final size:2
Alignment explanation
Indices: 52634864--52634910 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
52634854 AAAACATACG
52634864 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52634906 TA TA T
1 TA TA T
52634911 GAACATATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52635032 original size:2 final size:2
Alignment explanation
Indices: 52635027--52635071 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
52635017 ATGAAGAATA
52635027 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52635069 AT A
1 AT A
52635072 AATGTATAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52635198 original size:3 final size:3
Alignment explanation
Indices: 52635192--52635302 Score: 195
Period size: 3 Copynumber: 37.0 Consensus size: 3
52635182 TTACAATACC
* *
52635192 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
52635240 AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
52635288 AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
52635303 NNNNNNNNNN
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 102 1.00
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:52637693 original size:44 final size:43
Alignment explanation
Indices: 52637530--52637957 Score: 111
Period size: 44 Copynumber: 9.7 Consensus size: 43
52637520 TAAGACTTAC
* * *
52637530 AATCTTCAATCTATTCCACTGTTGCCCGGGGA-AGTAGAATTACTG
1 AATCTTCAATCTACTCCACTGTTGCCCAGGGAGA-TA-AAAT-CTG
* * ** * * *
52637575 --GCTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCCG
1 AATCTTCAATCTACTCCACTGTTGCC-CAGGGAGATAAAATCTG
* * * * **
52637617 CCATCTTCGATCTACTCTACTATTGCTTAGGGAGATAAAATCTG
1 -AATCTTCAATCTACTCCACTGTTGCCCAGGGAGATAAAATCTG
* *
52637661 AAATCTTCAATCTATTCCACTGTTGCCCAGGGA-AGTAGAATTACTG
1 -AATCTTCAATCTACTCCACTGTTGCCCAGGGAGA-TA-AAAT-CTG
* * * ** * *
52637707 --GCTTCAATGTACTCCACTATAACCACAGGGAGCTAAAATC-C
1 AATCTTCAATCTACTCCACTGTTGCC-CAGGGAGATAAAATCTG
* * ** ** * * *
52637748 ACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGTTGAGATCTG
1 A--ATCTTCAATCTACTCCACTGTTGCCCAGGGAGATAAAATCTG
* * * * *
52637793 AAATCTTCAATCTATTCCATTTTTGTCCAGGGA-AGTAGAATTACTG
1 -AATCTTCAATCTACTCCACTGTTGCCCAGGGAGA-TA-AAAT-CTG
* * * ** * *
52637839 --GCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCG
1 AATCTTCAATCTACTCCACTGTTGCC-CAGGGAGATAAAATCTG
* * * ** ** *
52637881 CCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
1 -AATCTTCAATCTACTCCACTGTTGCCCAGGGAGATAAAATCTG
* *
52637925 AAATCTTCAATCTATTCCACTGTTGTCCAGGGA
1 -AATCTTCAATCTACTCCACTGTTGCCCAGGGA
52637958 TGTAGAATTA
Statistics
Matches: 260, Mismatches: 99, Indels: 49
0.64 0.24 0.12
Matches are distributed among these distances:
42 5 0.02
43 63 0.24
44 132 0.51
45 53 0.20
46 7 0.03
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (43 bp):
AATCTTCAATCTACTCCACTGTTGCCCAGGGAGATAAAATCTG
Found at i:52637694 original size:132 final size:132
Alignment explanation
Indices: 52637515--52637969 Score: 741
Period size: 132 Copynumber: 3.4 Consensus size: 132
52637505 GCAACTGCAA
* *
52637515 GGAGATAAGA-CTTACAATCTTCAATCTATTCCACTGTTGCCCGGGGAAGTAGAATTACTGGCTT
1 GGAGATAAGATCTGA-AATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGCTT
* * * * *
52637579 CAATGTACTCCACTGTAACCACAGAGAGGTAAAATCCGCCATCTTCGATCTACTCTACTATTGCT
65 CAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCT
52637644 TAG
130 TAG
*
52637647 GGAGATAAAATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGCTTC
1 GGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGCTTC
* *
52637712 AATGTACTCCACTATAACCACAGGGAGCTAAAATCCACCATCTTCGATCTGCTCCACTACTGCTT
66 AATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTT
52637777 AG
131 AG
* * * * *
52637779 GGAGTTGAGATCTGAAATCTTCAATCTATTCCATTTTTGTCCAGGGAAGTAGAATTACTGGCTTC
1 GGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGCTTC
52637844 AATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTT
66 AATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTT
52637909 AG
131 AG
* *
52637911 GGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGATGTAGAATTACT
1 GGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACT
52637970 NNNNNNNNNN
Statistics
Matches: 299, Mismatches: 23, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
132 296 0.99
133 3 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (132 bp):
GGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGCTTC
AATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTT
AG
Found at i:52640799 original size:23 final size:22
Alignment explanation
Indices: 52640742--52640801 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
52640732 ATTGCAAAAC
* *
52640742 AGAAAAAGAAAGAAAAGCAATCG
1 AGAAAAGGAAA-AAAACCAATCG
*
52640765 A-AAAAGAAAAAAAAACCCAATCG
1 AGAAAAG-GAAAAAAA-CCAATCG
52640788 AGAAAAGGAAAAAA
1 AGAAAAGGAAAAAA
52640802 GAAAACCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
22 8 0.27
23 17 0.57
24 5 0.17
ACGTcount: A:0.70, C:0.10, G:0.17, T:0.03
Consensus pattern (22 bp):
AGAAAAGGAAAAAAACCAATCG
Found at i:52641347 original size:17 final size:17
Alignment explanation
Indices: 52641327--52641388 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
52641317 GTTTAGAATC
52641327 GGGTTTGTGTTAGATTT
1 GGGTTTGTGTTAGATTT
* * *
52641344 GGGTATTGGGTTTAGAATC
1 GGGT-TTGTG-TTAGATTT
52641363 GGGTTTGTGTTAGATTT
1 GGGTTTGTGTTAGATTT
52641380 GGGCTTTGT
1 GGG-TTTGT
52641389 AATACTAAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
17 13 0.36
18 13 0.36
19 10 0.28
ACGTcount: A:0.13, C:0.03, G:0.37, T:0.47
Consensus pattern (17 bp):
GGGTTTGTGTTAGATTT
Found at i:52641352 original size:36 final size:36
Alignment explanation
Indices: 52641310--52641382 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
52641300 GTTCGGTATT
52641310 GTATTGGGTTTAGAATCGGGTTTGTGTTAGATTTGG
1 GTATTGGGTTTAGAATCGGGTTTGTGTTAGATTTGG
52641346 GTATTGGGTTTAGAATCGGGTTTGTGTTAGATTTGG
1 GTATTGGGTTTAGAATCGGGTTTGTGTTAGATTTGG
52641382 G
1 G
52641383 CTTTGTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.16, C:0.03, G:0.37, T:0.44
Consensus pattern (36 bp):
GTATTGGGTTTAGAATCGGGTTTGTGTTAGATTTGG
Found at i:52642335 original size:31 final size:31
Alignment explanation
Indices: 52642300--52642372 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
52642290 TCGAACACAT
* *
52642300 GGCTGTGTGGACGAATTGTGTAACAGGTTGA
1 GGCTGTGTGGACAAACTGTGTAACAGGTTGA
*
52642331 GGCTGTGTGGACAAACTGTGTAACTGGTTGA
1 GGCTGTGTGGACAAACTGTGTAACAGGTTGA
*
52642362 GGCCGTGTGGA
1 GGCTGTGTGGA
52642373 GATGGAGTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.21, C:0.12, G:0.40, T:0.27
Consensus pattern (31 bp):
GGCTGTGTGGACAAACTGTGTAACAGGTTGA
Found at i:52645547 original size:30 final size:30
Alignment explanation
Indices: 52645485--52645547 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
52645475 ACTTTTCCCT
*
52645485 CAAAACTTTTACTCCTTCCCACTTCCCCCC
1 CAAAACTTTTACTCCCTCCCACTTCCCCCC
52645515 CAAAACTTTTACTCCCCTCCC-C-TCCCCTCC
1 CAAAACTTTTACT-CCCTCCCACTTCCCC-CC
52645545 CAA
1 CAA
52645548 CCCCCTAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 5 0.17
30 19 0.63
31 6 0.20
ACGTcount: A:0.21, C:0.52, G:0.00, T:0.27
Consensus pattern (30 bp):
CAAAACTTTTACTCCCTCCCACTTCCCCCC
Found at i:52645680 original size:30 final size:31
Alignment explanation
Indices: 52645645--52645704 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
52645635 TAACCTTTTA
*
52645645 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
52645675 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
52645705 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:52651574 original size:15 final size:14
Alignment explanation
Indices: 52651554--52651584 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
52651544 AAGTACAATC
52651554 ATCCAAAAACTGAAA
1 ATCCAAAAACT-AAA
52651569 ATCCAAAAACTAAA
1 ATCCAAAAACTAAA
52651583 AT
1 AT
52651585 AATAGTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.61, C:0.19, G:0.03, T:0.16
Consensus pattern (14 bp):
ATCCAAAAACTAAA
Found at i:52651719 original size:33 final size:33
Alignment explanation
Indices: 52651653--52651719 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
52651643 TTACAATGTC
* * *
52651653 ACAAATATGCTACAAATTTGACAAAAGCAACTA
1 ACAAATATACTACAAATGTGACAAAAACAACTA
*
52651686 ACAAATATACTACAAATGTGACAAAAACTACTA
1 ACAAATATACTACAAATGTGACAAAAACAACTA
52651719 A
1 A
52651720 GCGTCACATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.54, C:0.18, G:0.07, T:0.21
Consensus pattern (33 bp):
ACAAATATACTACAAATGTGACAAAAACAACTA
Found at i:52655742 original size:16 final size:16
Alignment explanation
Indices: 52655721--52655752 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
52655711 GTTTTGTTGC
*
52655721 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
52655737 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
52655753 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:52656075 original size:50 final size:50
Alignment explanation
Indices: 52656006--52656246 Score: 268
Period size: 50 Copynumber: 4.8 Consensus size: 50
52655996 TTTTGTCATT
* * * **
52656006 CGATACACGTAGTAGCCTTCACATAGTACCACACACGTGATTAAGTTTTA
1 CGATTCACATAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTA
* *
52656056 CGGTTCACATAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
1 CGATTCACATAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTA
* **
52656106 CGGTTCACGCAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTT-
1 CGATTCACATAGTAGCCTTCACATAGTACTACACACGTGACC-AAG-TTTTA
* * * * ***
52656157 CGATACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
1 CGATTCACATAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTA
* * *
52656207 TCTATTCACGTAGTAGCCTTCACACAGTACTACACACGTG
1 -CGATTCACATAGTAGCCTTCACATAGTACTACACACGTG
52656247 TTCATCGATA
Statistics
Matches: 162, Mismatches: 25, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
49 3 0.02
50 85 0.52
51 70 0.43
52 4 0.02
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (50 bp):
CGATTCACATAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTA
Found at i:52656750 original size:30 final size:30
Alignment explanation
Indices: 52656716--52656773 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
52656706 CCTTGACTCG
52656716 AACTTTAGCAAAATTACAATTTTGCCCCTA
1 AACTTTAGCAAAATTACAATTTTGCCCCTA
* * * *
52656746 AACTTTTGCATATTTACACTTTTGCCCC
1 AACTTTAGCAAAATTACAATTTTGCCCC
52656774 AAAGATCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.29, C:0.26, G:0.07, T:0.38
Consensus pattern (30 bp):
AACTTTAGCAAAATTACAATTTTGCCCCTA
Found at i:52662024 original size:22 final size:24
Alignment explanation
Indices: 52661994--52662037 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
52661984 CGGGACAAAA
52661994 ATTTGAATTAATG-AAATGGTGGC
1 ATTTGAATTAATGAAAATGGTGGC
52662017 ATTT-AATTAATGAAAATGGTG
1 ATTTGAATTAATGAAAATGGTG
52662038 CATAGAAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (24 bp):
ATTTGAATTAATGAAAATGGTGGC
Found at i:52681050 original size:20 final size:20
Alignment explanation
Indices: 52681022--52681091 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
52681012 TATTGATCTT
* *
52681022 GTATTGATACTTTTTTTAAG
1 GTATCGATACTTTTCTTAAG
52681042 GTATCGATACTTTTCTTAAG
1 GTATCGATACTTTTCTTAAG
* *
52681062 ATATCGATA-TATTTCCTAAAG
1 GTATCGATACT-TTT-CTTAAG
52681083 GTATCGATA
1 GTATCGATA
52681092 TTCCTGCTCC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.02
20 29 0.67
21 13 0.30
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.44
Consensus pattern (20 bp):
GTATCGATACTTTTCTTAAG
Found at i:52683109 original size:28 final size:29
Alignment explanation
Indices: 52683064--52683124 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
52683054 ATTTATTTGT
*
52683064 TTAAGGTTTAGGGATTTTAAAA-AATAAA
1 TTAAGGTTTAGGAATTTTAAAATAATAAA
*
52683092 TTAAGGTTTA-GAATTTTTAAAATAATTAA
1 TTAAGGTTTAGGAA-TTTTAAAATAATAAA
52683121 TTAA
1 TTAA
52683125 ATTAGGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 2 0.07
28 18 0.62
29 9 0.31
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (29 bp):
TTAAGGTTTAGGAATTTTAAAATAATAAA
Found at i:52683143 original size:33 final size:32
Alignment explanation
Indices: 52683088--52683206 Score: 123
Period size: 33 Copynumber: 3.6 Consensus size: 32
52683078 TTTTAAAAAA
**
52683088 TAAATTAAGGTTTAGAATTTTTAAAATAATTAAT
1 TAAATT-AGGTTTAG-GGTTTTAAAATAATTAAT
*
52683122 TAAATTAGGTTTTAGGGTTTT-AAGTAAATTAAT
1 TAAATTAGG-TTTAGGGTTTTAAAAT-AATTAAT
* * *
52683155 TAAATTAAAGTTTAGAGTTTTAAAAAAATTAAT
1 TAAATT-AGGTTTAGGGTTTTAAAATAATTAAT
52683188 TAAATTAGGGTTTAGGGTT
1 TAAATTA-GGTTTAGGGTT
52683207 GAGTGTTGAA
Statistics
Matches: 71, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
32 4 0.06
33 52 0.73
34 15 0.21
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.43
Consensus pattern (32 bp):
TAAATTAGGTTTAGGGTTTTAAAATAATTAAT
Found at i:52683223 original size:67 final size:66
Alignment explanation
Indices: 52683081--52683206 Score: 175
Period size: 66 Copynumber: 1.9 Consensus size: 66
52683071 TTAGGGATTT
* * * * *
52683081 TAAAAAA-TAAATTAAGGTTTAGAATTTTTAAAATAATTAATTAAATTAGGTTTTAGGGTTTTAA
1 TAAAAAATTAAATTAAAGTTTAGAAGTTTTAAAAAAATTAATTAAATTAGGGTTTAGGGTTTGAA
52683145 G
66 G
*
52683146 TAAATTAATTAAATTAAAGTTTAG-AGTTTTAAAAAAATTAATTAAATTAGGGTTTAGGGTT
1 TAAA-AAATTAAATTAAAGTTTAGAAGTTTTAAAAAAATTAATTAAATTAGGGTTTAGGGTT
52683207 GAGTGTTGAA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
65 4 0.07
66 36 0.67
67 14 0.26
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.41
Consensus pattern (66 bp):
TAAAAAATTAAATTAAAGTTTAGAAGTTTTAAAAAAATTAATTAAATTAGGGTTTAGGGTTTGAA
G
Found at i:52683534 original size:127 final size:125
Alignment explanation
Indices: 52683249--52683756 Score: 518
Period size: 127 Copynumber: 4.1 Consensus size: 125
52683239 TTTTGTTTCT
* * * **
52683249 TTTTTCTAGAGTAGTTTCAGAAAATTTAATTTTGAGAAGACGGTTCTG-AAAAATAGTG-ACAAA
1 TTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTA-AAA
* * *
52683312 AACGCTTCAAGCAAG-ATGCACTGTCAACAAAAGTACTGAAAAAAGCTCCTACGTGGACGCTC
65 AACGCTTCAAGC-AGTATGCACTGTCAACAAAATTACTAAAAAAAACTCC-ACGTGGACGCTC
* * * * * *
52683374 TTTTACTACAGTAGTTTCTAAAAAAATAATTTTGAGAAGACGGTTTTGAAAAAATAATGTAAAAA
1 TTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTAAAAA
* * * * * *
52683439 ATGCTTCAAGCAGTATGCACTCTCAGCAGAATTACTAAAAAAAAACTCTCATGTGGATGCTC
66 ACGCTTCAAGCAGTATGCACTGTCAACAAAATTACT-AAAAAAAACTC-CACGTGGACGCTC
* *
52683501 TTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAAAAGACGGTTCTGAAAAAATAGTGTCAAAA
1 TTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTAAAAA
* * * * * *
52683566 ACGCTTCAAGCAGGATGCACTGTCAGCAAAGTTACTGAAAAAATCTCCCACATGGACGCTC
66 ACGCTTCAAGCAGTATGCACTGTCAACAAAATTACTAAAAAAAACT-CCACGTGGACGCTC
* * * *
52683627 ---TT-T-T--T--TTCCTGGAAAAATAATTTTAAGAAGACGGTTTTGAAAAAATAGTGCAAAAA
1 TTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTAAAAA
* * * * * *
52683683 ATGCTTCAAGCAGTATGCACTATCAACAAAATTACTGAAAAAAGCTCCCACATGGACTCTC
66 ACGCTTCAAGCAGTATGCACTGTCAACAAAATTACTAAAAAAAACT-CCACGTGGACGCTC
*
52683744 TTTTTCTACAGTA
1 TTTTTCTATAGTA
52683757 TTTCTTGCTT
Statistics
Matches: 320, Mismatches: 49, Indels: 28
0.81 0.12 0.07
Matches are distributed among these distances:
117 99 0.31
119 1 0.00
120 2 0.01
121 2 0.01
122 1 0.00
123 2 0.01
124 1 0.00
125 43 0.13
126 59 0.18
127 109 0.34
128 1 0.00
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.29
Consensus pattern (125 bp):
TTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTAAAAA
ACGCTTCAAGCAGTATGCACTGTCAACAAAATTACTAAAAAAAACTCCACGTGGACGCTC
Found at i:52683643 original size:117 final size:117
Alignment explanation
Indices: 52683515--52683748 Score: 355
Period size: 117 Copynumber: 2.0 Consensus size: 117
52683505 TCTATAGTAG
52683515 TTCCTGAAAAAATAATTTTGAA-AAGACGGTTCTGAAAAAATAGTGTC-AAAAACGCTTCAAGCA
1 TTCCTGAAAAAATAATTTT-AAGAAGACGGTTCTGAAAAAATAGTG-CAAAAAACGCTTCAAGCA
* * * *
52683578 GGATGCACTGTCAGCAAAGTTACTGAAAAAATCTCCCACATGGACGCTCTTTTT
64 GGATGCACTATCAACAAAATTACTGAAAAAAGCTCCCACATGGACGCTCTTTTT
* * * *
52683632 TTCCTGGAAAAATAATTTTAAGAAGACGGTTTTGAAAAAATAGTGCAAAAAATGCTTCAAGCAGT
1 TTCCTGAAAAAATAATTTTAAGAAGACGGTTCTGAAAAAATAGTGCAAAAAACGCTTCAAGCAGG
*
52683697 ATGCACTATCAACAAAATTACTGAAAAAAGCTCCCACATGGACTCTCTTTTT
66 ATGCACTATCAACAAAATTACTGAAAAAAGCTCCCACATGGACGCTCTTTTT
52683749 CTACAGTATT
Statistics
Matches: 106, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
116 3 0.03
117 103 0.97
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (117 bp):
TTCCTGAAAAAATAATTTTAAGAAGACGGTTCTGAAAAAATAGTGCAAAAAACGCTTCAAGCAGG
ATGCACTATCAACAAAATTACTGAAAAAAGCTCCCACATGGACGCTCTTTTT
Found at i:52687384 original size:25 final size:24
Alignment explanation
Indices: 52687347--52687398 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
52687337 ACTGTTATAA
* *
52687347 AAAATTATAAAAT-AAAAATTAATT
1 AAAATTACAAAATGAAAAA-AAATT
52687371 AAAATTACATAAATGAAAAAAAATT
1 AAAATTACA-AAATGAAAAAAAATT
52687396 AAA
1 AAA
52687399 TAATATTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.33
25 11 0.46
26 5 0.21
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (24 bp):
AAAATTACAAAATGAAAAAAAATT
Found at i:52703425 original size:16 final size:18
Alignment explanation
Indices: 52703406--52703442 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
52703396 TTTATTATAA
*
52703406 AAATATTTA-TAATTT-T
1 AAATAATTATTAATTTGT
52703422 AAATAATTATTAATTTGT
1 AAATAATTATTAATTTGT
52703440 AAA
1 AAA
52703443 AATAGTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 6 0.33
18 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
AAATAATTATTAATTTGT
Found at i:52703837 original size:20 final size:20
Alignment explanation
Indices: 52703812--52703850 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
52703802 TTTTAAATTT
*
52703812 AAATTA-GTTTTTGGAAAAAA
1 AAATTATGTTATT-GAAAAAA
52703832 AAATTATGTTATTGAAAAA
1 AAATTATGTTATTGAAAAA
52703851 TATTTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (20 bp):
AAATTATGTTATTGAAAAAA
Found at i:52705525 original size:31 final size:32
Alignment explanation
Indices: 52705480--52705542 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
52705470 AGATAATTTT
52705480 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
52705512 AAAGAG-TTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
52705543 TAATTTGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.43
Consensus pattern (32 bp):
AAAGAGTTTTTATTAGGATTCAATTACTCTTG
Found at i:52706157 original size:18 final size:18
Alignment explanation
Indices: 52706099--52706151 Score: 79
Period size: 18 Copynumber: 2.8 Consensus size: 18
52706089 TTAAAAAAAC
52706099 AAAAAAAGCAAAAAAGCGCA
1 AAAAAAAGC--AAAAGCGCA
*
52706119 AAAAAAAGTAAAAGCGCA
1 AAAAAAAGCAAAAGCGCA
52706137 AAAAAAAGCAAAAGC
1 AAAAAAAGCAAAAGC
52706152 AAAAAAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 23 0.74
20 8 0.26
ACGTcount: A:0.70, C:0.13, G:0.15, T:0.02
Consensus pattern (18 bp):
AAAAAAAGCAAAAGCGCA
Found at i:52711841 original size:31 final size:32
Alignment explanation
Indices: 52711796--52711858 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
52711786 AGATAATTTT
52711796 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
52711828 AAAGAG-TTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
52711859 TAATTTGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.43
Consensus pattern (32 bp):
AAAGAGTTTTTATTAGGATTCAATTACTCTTG
Found at i:52717515 original size:6 final size:6
Alignment explanation
Indices: 52717504--52717529 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
52717494 CATAAATGAT
52717504 TAATTA TAATTA TAATTA TAATTA TA
1 TAATTA TAATTA TAATTA TAATTA TA
52717530 TAAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAATTA
Found at i:52718317 original size:7 final size:7
Alignment explanation
Indices: 52718305--52718330 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
52718295 TAGAAACTAG
52718305 GGTTTAT
1 GGTTTAT
52718312 GGTTTAT
1 GGTTTAT
52718319 GGTTTAT
1 GGTTTAT
52718326 GGTTT
1 GGTTT
52718331 TGAGAGTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.31, T:0.58
Consensus pattern (7 bp):
GGTTTAT
Found at i:52726176 original size:19 final size:18
Alignment explanation
Indices: 52726152--52726195 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
52726142 ATTTTTAATT
*
52726152 TTTTTTGGATATTTATGTA
1 TTTTTTAGATATTTATG-A
* *
52726171 TTTTTTATATTTTTATGA
1 TTTTTTAGATATTTATGA
52726189 TTTTTTA
1 TTTTTTA
52726196 AAGAAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.70
Consensus pattern (18 bp):
TTTTTTAGATATTTATGA
Found at i:52726823 original size:31 final size:30
Alignment explanation
Indices: 52726780--52726887 Score: 110
Period size: 31 Copynumber: 3.5 Consensus size: 30
52726770 ATAATTAATC
* *
52726780 ACATTAATATTAAATTAACAAAATATTATCT
1 ACATAAATATTAAATTAA-AAAATAATATCT
* **
52726811 AGATAAATATTAAATT-AAATTTAATATCTT
1 ACATAAATATTAAATTAAAAAATAATATC-T
* * *
52726841 ATATTAATAATAAATTAATAAAATAATATCT
1 ACATAAATATTAAATTAA-AAAATAATATCT
52726872 ACATAAATATTAAATT
1 ACATAAATATTAAATT
52726888 TAAGTTTAAT
Statistics
Matches: 61, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
29 8 0.13
30 15 0.25
31 29 0.48
32 9 0.15
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.40
Consensus pattern (30 bp):
ACATAAATATTAAATTAAAAAATAATATCT
Found at i:52726878 original size:61 final size:62
Alignment explanation
Indices: 52726782--52726899 Score: 184
Period size: 61 Copynumber: 1.9 Consensus size: 62
52726772 AATTAATCAC
* * *
52726782 ATTAATATTAAATTAACAAAATATTATCTAGATAAATATTAAA-TTAAATTTAATATCTTAT
1 ATTAATAATAAATTAACAAAATAATATCTACATAAATATTAAATTTAAATTTAATATCTTAT
* *
52726843 ATTAATAATAAATTAATAAAATAATATCTACATAAATATTAAATTTAAGTTTAATAT
1 ATTAATAATAAATTAACAAAATAATATCTACATAAATATTAAATTTAAATTTAATAT
52726900 TAAATTCATT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
61 39 0.76
62 12 0.24
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (62 bp):
ATTAATAATAAATTAACAAAATAATATCTACATAAATATTAAATTTAAATTTAATATCTTAT
Found at i:52747640 original size:13 final size:14
Alignment explanation
Indices: 52747617--52747646 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
52747607 ACTAAGAATA
52747617 TAAATATAAATACT
1 TAAATATAAATACT
52747631 TAAA-ATAAATACT
1 TAAATATAAATACT
52747644 TAA
1 TAA
52747647 GAAAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAATATAAATACT
Found at i:52756986 original size:13 final size:13
Alignment explanation
Indices: 52756964--52756994 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
52756954 ATTAAATAGA
52756964 TATT-TATTAAAT
1 TATTATATTAAAT
52756976 TATTATATTAAAT
1 TATTATATTAAAT
52756989 TATTAT
1 TATTAT
52756995 TGTAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTATATTAAAT
Found at i:52757165 original size:19 final size:20
Alignment explanation
Indices: 52757141--52757184 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
52757131 AAGATATTTA
* *
52757141 TAAATATTAATT-AATTAAT
1 TAAATATAAATTAAATAAAT
52757160 TAAATATAAATTAAATAAAT
1 TAAATATAAATTAAATAAAT
52757180 TAAAT
1 TAAAT
52757185 GGTGCCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAATATAAATTAAATAAAT
Found at i:52759055 original size:2 final size:2
Alignment explanation
Indices: 52759048--52759080 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
52759038 TACATGAGTC
52759048 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
52759081 CTAAATGATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52763077 original size:15 final size:15
Alignment explanation
Indices: 52763057--52763100 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
52763047 TTTAGGGGTT
* *
52763057 TGTTCTGTTCTGTTC
1 TGTTCTGTTATGTTA
52763072 TGTTCTGTTATGTTA
1 TGTTCTGTTATGTTA
*
52763087 TGTTATGTTATGTT
1 TGTTCTGTTATGTT
52763101 TTTTTGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.09, C:0.09, G:0.20, T:0.61
Consensus pattern (15 bp):
TGTTCTGTTATGTTA
Found at i:52763110 original size:5 final size:5
Alignment explanation
Indices: 52763057--52763100 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
52763047 TTTAGGGGTT
* * * *
52763057 TGTTC TGTTC TGTTC TGTTC TGTTA TGTTA TGTTA TGTTA TGTT
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTT
52763101 TTTTTGTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.09, C:0.09, G:0.20, T:0.61
Consensus pattern (5 bp):
TGTTA
Found at i:52766075 original size:43 final size:43
Alignment explanation
Indices: 52766009--52766111 Score: 188
Period size: 43 Copynumber: 2.4 Consensus size: 43
52765999 AAAACTTTGG
52766009 ATCATAACTTACATTAACTTACATAATACATAAATATATATCAT
1 ATCATAACTTACA-TAACTTACATAATACATAAATATATATCAT
*
52766053 ATCATAACTTGCATAACTTACATAATACATAAATATATATCAT
1 ATCATAACTTACATAACTTACATAATACATAAATATATATCAT
52766096 ATCATAACTTACATAA
1 ATCATAACTTACATAA
52766112 ATATATACAA
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
43 45 0.79
44 12 0.21
ACGTcount: A:0.48, C:0.17, G:0.01, T:0.35
Consensus pattern (43 bp):
ATCATAACTTACATAACTTACATAATACATAAATATATATCAT
Found at i:52782104 original size:24 final size:24
Alignment explanation
Indices: 52782089--52782140 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
52782079 AATCAATGTC
*
52782089 AAATATATTATGCTAATAAATACT
1 AAATATATTATACTAATAAATACT
*
52782113 AAATATATTATACTAATAAATATT
1 AAATATATTATACTAATAAATACT
52782137 AAAT
1 AAAT
52782141 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:52782264 original size:29 final size:29
Alignment explanation
Indices: 52782231--52782289 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
52782221 TCCACATTGA
* *
52782231 CACAAATTCTCAACGAACAAGTTCTTCAC
1 CACAAACTCTCAACGAACAAGTTCTCCAC
52782260 CACAAACTCTCAACGAACAAGTTCTCCAC
1 CACAAACTCTCAACGAACAAGTTCTCCAC
52782289 C
1 C
52782290 TCTTTCACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.37, C:0.36, G:0.07, T:0.20
Consensus pattern (29 bp):
CACAAACTCTCAACGAACAAGTTCTCCAC
Found at i:52782967 original size:17 final size:17
Alignment explanation
Indices: 52782945--52782980 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
52782935 TTATTTCAAG
52782945 AAAGGATTAAATTGTAA
1 AAAGGATTAAATTGTAA
52782962 AAAGGATTAAATTGTAA
1 AAAGGATTAAATTGTAA
52782979 AA
1 AA
52782981 GTGACAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.17, T:0.28
Consensus pattern (17 bp):
AAAGGATTAAATTGTAA
Found at i:52785035 original size:56 final size:59
Alignment explanation
Indices: 52784929--52785074 Score: 174
Period size: 56 Copynumber: 2.5 Consensus size: 59
52784919 AATTGACAGT
*
52784929 AAAAGGATCTAGCCCGGACGGGTGATCCTATCCTGAAATAGCCCTCCCGAAGAATATGTGTG
1 AAAAAGATCTAGCCCGGACGGGTGATCC-AT-CTGAAATAGCCCTCCCGAAGAATATGTG-G
*
52784991 AAAAAGATCTAG-CCGGACGGGTGAT-C-T-TGATATAGCCCTCCCGAAGAATATGTGG
1 AAAAAGATCTAGCCCGGACGGGTGATCCATCTGAAATAGCCCTCCCGAAGAATATGTGG
* * * *
52785046 AAAATGGATTTAGCCCAGACGGGTAATCC
1 AAAA-AGATCTAGCCCGGACGGGTGATCC
52785075 GAATTAGGGT
Statistics
Matches: 75, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
55 5 0.07
56 32 0.43
57 11 0.15
58 2 0.03
60 1 0.01
61 13 0.17
62 11 0.15
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (59 bp):
AAAAAGATCTAGCCCGGACGGGTGATCCATCTGAAATAGCCCTCCCGAAGAATATGTGG
Found at i:52785304 original size:67 final size:67
Alignment explanation
Indices: 52785196--52785327 Score: 246
Period size: 67 Copynumber: 2.0 Consensus size: 67
52785186 GTTTATATTA
*
52785196 CAGGGGATTTAGCCTGGACTGGTAATCCCGTTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
52785261 TG
66 TG
*
52785263 CAGGGGGTTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
52785328 GAATTGAAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.19, C:0.19, G:0.35, T:0.27
Consensus pattern (67 bp):
CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
TG
Found at i:52790010 original size:24 final size:24
Alignment explanation
Indices: 52789995--52790046 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
52789985 AATCAATGTC
*
52789995 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATGCT
*
52790019 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAATAAATGCT
52790043 AAAT
1 AAAT
52790047 CTATCTGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATGCT
Found at i:52791966 original size:17 final size:16
Alignment explanation
Indices: 52791936--52791967 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
52791926 ATCTGTTGTT
52791936 TTAATTTTTTATATTA
1 TTAATTTTTTATATTA
52791952 TTAATTTTATTATATT
1 TTAATTTT-TTATATT
52791968 GTATATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTAATTTTTTATATTA
Found at i:52792241 original size:23 final size:24
Alignment explanation
Indices: 52792212--52792259 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
52792202 TAATTTATTA
52792212 ATATATTTTTACTTA-TATTTTTT
1 ATATATTTTTACTTATTATTTTTT
*
52792235 ATATATTTTTATTTATTTATTTTTT
1 ATATATTTTTACTTA-TTATTTTTT
52792260 GATACCTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.64
25 8 0.36
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (24 bp):
ATATATTTTTACTTATTATTTTTT
Found at i:52804383 original size:44 final size:42
Alignment explanation
Indices: 52804333--52804615 Score: 164
Period size: 41 Copynumber: 6.7 Consensus size: 42
52804323 ACTTCAGTCT
*
52804333 TATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGAAAATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATT--AGAAAATAATCC
* * * *
52804377 TATCTCCCTGAAGTTGCAATGGAGCGGATTA-AAATTAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAAAATA-ATCC
** * ** * * *** * *
52804419 TATCTCTTTAAAGTTGCAGAAGAGCAGA-TCGCATCCAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAAAATAATCC
52804460 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGAAAATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATT--AGAAAATAATCC
* * *
52804504 TATCTCTCTAAAGTTGCAGTGGAGC-GAATT--AAAATCAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAG-ATTAGAAAAT-A-ATCC
* * ** * * ** * **
52804546 TATCTCTCTGAAGTTACAGAAGAGCAGA-TCGCATCTAGTTT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAAAATAATCC
*
52804587 TATCTCCCTGAAGTTACAGTGGAGCAGAT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAT
52804616 CAAGATGATA
Statistics
Matches: 182, Mismatches: 45, Indels: 26
0.72 0.18 0.10
Matches are distributed among these distances:
40 5 0.03
41 61 0.34
42 54 0.30
43 4 0.02
44 58 0.32
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (42 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAAAATAATCC
Found at i:52804650 original size:127 final size:127
Alignment explanation
Indices: 52804327--52804615 Score: 461
Period size: 127 Copynumber: 2.3 Consensus size: 127
52804317 GGTGAAACTT
* * *
52804327 CAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGAAAATAATCCTATCTCCCTGAAGTT
1 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGAAAATAATCCTATCTCTCTGAAGTT
* * * * *
52804392 GCAATGGAGCGGATTAAAATTAGATCTTATCTCTTTAAAGTTGCAGAAGAGCAGATCGCATC
66 GCAGTGGAGCGAATTAAAATCAGATCTTATCTCTCTAAAGTTACAGAAGAGCAGATCGCATC
*
52804454 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGAAAATAATCCTATCTCTCTAAAGTT
1 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGAAAATAATCCTATCTCTCTGAAGTT
*
52804519 GCAGTGGAGCGAATTAAAATCAGATCTTATCTCTCTGAAGTTACAGAAGAGCAGATCGCATC
66 GCAGTGGAGCGAATTAAAATCAGATCTTATCTCTCTAAAGTTACAGAAGAGCAGATCGCATC
* * *
52804581 TAGTTTTATCTCCCTGAAGTTACAGTGGAGCAGAT
1 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
52804616 CAAGATGATA
Statistics
Matches: 149, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
127 149 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (127 bp):
CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGAAAATAATCCTATCTCTCTGAAGTT
GCAGTGGAGCGAATTAAAATCAGATCTTATCTCTCTAAAGTTACAGAAGAGCAGATCGCATC
Found at i:52805984 original size:3 final size:3
Alignment explanation
Indices: 52805967--52806069 Score: 147
Period size: 3 Copynumber: 34.0 Consensus size: 3
52805957 AATTTTTTCA
* *
52805967 TAT TAT TAAT T-T TAT TA- TAT TGT ATAT TGT ATAT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT -TAT TAT -TAT TAT TAT TAT TAT
52806013 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
52806061 TAT TAT TAT
1 TAT TAT TAT
52806070 ATCTATATAT
Statistics
Matches: 91, Mismatches: 4, Indels: 10
0.87 0.04 0.10
Matches are distributed among these distances:
2 4 0.04
3 80 0.88
4 7 0.08
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:52806153 original size:28 final size:27
Alignment explanation
Indices: 52806095--52806158 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
52806085 CAAAGGTATG
* * *
52806095 TTAATATATATATATTTTTAAATGTTT
1 TTAATATATACATATTTTCAAATGTTA
52806122 TTAAATATATACATATTTTCATAAT-TTA
1 TT-AATATATACATATTTTCA-AATGTTA
52806150 TTAATATAT
1 TTAATATAT
52806159 TTTCACTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 9 0.28
28 20 0.62
29 3 0.09
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (27 bp):
TTAATATATACATATTTTCAAATGTTA
Found at i:52806193 original size:25 final size:25
Alignment explanation
Indices: 52806153--52806202 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
52806143 TAATTTATTA
52806153 ATATATTTTCACTTATATT-TTTTTT
1 ATATATTTTCACTTAT-TTATTTTTT
* *
52806178 ATATATTTTTATTTATTTATTTTTT
1 ATATATTTTCACTTATTTATTTTTT
52806203 GATACCTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (25 bp):
ATATATTTTCACTTATTTATTTTTT
Found at i:52811861 original size:15 final size:15
Alignment explanation
Indices: 52811841--52811895 Score: 73
Period size: 15 Copynumber: 3.9 Consensus size: 15
52811831 TAAAAGTATA
52811841 TATTTAATATATTAT
1 TATTTAATATATTAT
52811856 TATTT-A-ATA-TA-
1 TATTTAATATATTAT
52811867 TATTTAATATATTAT
1 TATTTAATATATTAT
52811882 TATTTAAATATATT
1 TATTT-AATATATT
52811896 TAATATTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
11 5 0.14
12 3 0.09
13 6 0.17
14 3 0.09
15 10 0.29
16 8 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATTTAATATATTAT
Done.