Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168049.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_30, whole genome shotgun sequence
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: 11202444
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 44000 characters in sequence are not A, C, G, or T
File 33 of 64
Found at i:5154056 original size:18 final size:19
Alignment explanation
Indices: 5154037--5154087 Score: 79
Period size: 18 Copynumber: 2.8 Consensus size: 19
5154027 TATTTAAAAA
5154037 TTTTTAAGAAATTTTTAAT
1 TTTTTAAGAAATTTTTAAT
*
5154056 TTTTTTAG-AATTTTTAAT
1 TTTTTAAGAAATTTTTAAT
5154074 TTTTTAA-AAATTTT
1 TTTTTAAGAAATTTT
5154088 AAAAATTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 22 0.76
19 7 0.24
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (19 bp):
TTTTTAAGAAATTTTTAAT
Found at i:5154102 original size:21 final size:20
Alignment explanation
Indices: 5153999--5154218 Score: 143
Period size: 20 Copynumber: 11.2 Consensus size: 20
5153989 CTTTTTGAAA
*
5153999 TTTTTAAAATTTTCT-ATAA-
1 TTTTTAAAATTTT-TAAAAAT
* *
5154018 TTTTTAGAATATTTAAAAAT
1 TTTTTAAAATTTTTAAAAAT
* *
5154038 TTTTAAGAAATTTTT--AATT
1 TTTTTA-AAATTTTTAAAAAT
*
5154057 TTTTTAGAATTTTT---AAT
1 TTTTTAAAATTTTTAAAAAT
*
5154074 TTTTTAAAAATTTTAAAAAT
1 TTTTTAAAATTTTTAAAAAT
* *
5154094 TTGTTTAAAAATTTT-GAAAT
1 TT-TTTAAAATTTTTAAAAAT
* * *
5154114 TATTTTAGAGTTTTTGAAAAT
1 T-TTTTAAAATTTTTAAAAAT
*
5154135 TTTGCTAAAATTTTTAAAAAT
1 TTT-TTAAAATTTTTAAAAAT
* * *
5154156 TTGTTCAATTTTTTAAAAA-
1 TTTTTAAAATTTTTAAAAAT
**
5154175 TTTTTATTATTTTTAAAAAT
1 TTTTTAAAATTTTTAAAAAT
** *
5154195 TTTTGGAACTTTTTAAAAAT
1 TTTTTAAAATTTTTAAAAAT
5154215 TTTT
1 TTTT
5154219 AGAATCATTA
Statistics
Matches: 155, Mismatches: 35, Indels: 21
0.73 0.17 0.10
Matches are distributed among these distances:
17 14 0.09
18 8 0.05
19 36 0.23
20 58 0.37
21 39 0.25
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTTTAAAATTTTTAAAAAT
Found at i:5154195 original size:39 final size:39
Alignment explanation
Indices: 5154144--5154219 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
5154134 TTTTGCTAAA
*
5154144 ATTTTTAAAAATTTGTT-CAATTTTTTAAAAATTTTTATT
1 ATTTTTAAAAATTT-TTGCAACTTTTTAAAAATTTTTATT
*
5154183 ATTTTTAAAAATTTTTGGAACTTTTTAAAAATTTTTA
1 ATTTTTAAAAATTTTTGCAACTTTTTAAAAATTTTTA
5154220 GAATCATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 2 0.06
39 32 0.94
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.57
Consensus pattern (39 bp):
ATTTTTAAAAATTTTTGCAACTTTTTAAAAATTTTTATT
Found at i:5155629 original size:2 final size:2
Alignment explanation
Indices: 5155622--5155651 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5155612 TGTCACTTAA
*
5155622 AT AT AT AT AG 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
5155652 TCCTTTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5155857 original size:16 final size:16
Alignment explanation
Indices: 5155836--5155888 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
5155826 TAAAATTTAT
5155836 TAAATTTGAATATAAA
1 TAAATTTGAATATAAA
** * *
5155852 TAAATTAAAAT-TTAT
1 TAAATTTGAATATAAA
5155867 TAAATTTGAATATAAA
1 TAAATTTGAATATAAA
5155883 TAAATT
1 TAAATT
5155889 AAAATTTATA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 11 0.39
16 17 0.61
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (16 bp):
TAAATTTGAATATAAA
Found at i:5155862 original size:31 final size:31
Alignment explanation
Indices: 5155824--5155897 Score: 148
Period size: 31 Copynumber: 2.4 Consensus size: 31
5155814 TGTATGGGAC
5155824 ATTAAAATTTATTAAATTTGAATATAAATAA
1 ATTAAAATTTATTAAATTTGAATATAAATAA
5155855 ATTAAAATTTATTAAATTTGAATATAAATAA
1 ATTAAAATTTATTAAATTTGAATATAAATAA
5155886 ATTAAAATTTAT
1 ATTAAAATTTAT
5155898 AATTAAAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (31 bp):
ATTAAAATTTATTAAATTTGAATATAAATAA
Found at i:5159944 original size:14 final size:14
Alignment explanation
Indices: 5159921--5159950 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5159911 TTAACTTTTT
*
5159921 AAATATATTTTATA
1 AAATACATTTTATA
5159935 AAATACATTTTATA
1 AAATACATTTTATA
5159949 AA
1 AA
5159951 GAAGAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATACATTTTATA
Found at i:5163721 original size:158 final size:158
Alignment explanation
Indices: 5163433--5163750 Score: 636
Period size: 158 Copynumber: 2.0 Consensus size: 158
5163423 TTCGACTAAC
5163433 TCCGCCATCTTGACCTTAGCTTGTTGAATATTTGCCGCTATTTCTTCCAAATCATCAACCCACGC
1 TCCGCCATCTTGACCTTAGCTTGTTGAATATTTGCCGCTATTTCTTCCAAATCATCAACCCACGC
5163498 CGGTAGCAAACCCACCGTAAACGCACCACTACTGTAACAAGAATAAAATAAAATGAAATCCAATA
66 CGGTAGCAAACCCACCGTAAACGCACCACTACTGTAACAAGAATAAAATAAAATGAAATCCAATA
5163563 GTAATTATTAAGCAAATATAACAATTTT
131 GTAATTATTAAGCAAATATAACAATTTT
5163591 TCCGCCATCTTGACCTTAGCTTGTTGAATATTTGCCGCTATTTCTTCCAAATCATCAACCCACGC
1 TCCGCCATCTTGACCTTAGCTTGTTGAATATTTGCCGCTATTTCTTCCAAATCATCAACCCACGC
5163656 CGGTAGCAAACCCACCGTAAACGCACCACTACTGTAACAAGAATAAAATAAAATGAAATCCAATA
66 CGGTAGCAAACCCACCGTAAACGCACCACTACTGTAACAAGAATAAAATAAAATGAAATCCAATA
5163721 GTAATTATTAAGCAAATATAACAATTTT
131 GTAATTATTAAGCAAATATAACAATTTT
5163749 TC
1 TC
5163751 TATTAAGAAA
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
158 160 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.27
Consensus pattern (158 bp):
TCCGCCATCTTGACCTTAGCTTGTTGAATATTTGCCGCTATTTCTTCCAAATCATCAACCCACGC
CGGTAGCAAACCCACCGTAAACGCACCACTACTGTAACAAGAATAAAATAAAATGAAATCCAATA
GTAATTATTAAGCAAATATAACAATTTT
Found at i:5163999 original size:29 final size:29
Alignment explanation
Indices: 5163966--5164027 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
5163956 ATAAATAAAA
5163966 TTATAATTATAATAGTGAAAACTCTTATT
1 TTATAATTATAATAGTGAAAACTCTTATT
*
5163995 TTATAATTGTAATAGTGAAAACTCTTATT
1 TTATAATTATAATAGTGAAAACTCTTATT
5164024 TTAT
1 TTAT
5164028 GATATTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (29 bp):
TTATAATTATAATAGTGAAAACTCTTATT
Found at i:5169720 original size:3 final size:3
Alignment explanation
Indices: 5169706--5169740 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
5169696 ACACCATTTT
*
5169706 TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5169741 TCTATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:5169760 original size:12 final size:12
Alignment explanation
Indices: 5169745--5169796 Score: 70
Period size: 12 Copynumber: 4.3 Consensus size: 12
5169735 ATTATTTCTA
5169745 TTTT-TTTCTATT
1 TTTTCTTTCT-TT
5169757 TTTTCTTTCTTT
1 TTTTCTTTCTTT
*
5169769 CTTTCTTTCTTT
1 TTTTCTTTCTTT
*
5169781 CTTTCTTTCTTT
1 TTTTCTTTCTTT
5169793 TTTT
1 TTTT
5169797 TATCAGGTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
12 32 0.86
13 5 0.14
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTCTTTCTTT
Found at i:5169767 original size:4 final size:4
Alignment explanation
Indices: 5169758--5169792 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
5169748 TTTTCTATTT
5169758 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
5169793 TTTTTATCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:5169950 original size:23 final size:23
Alignment explanation
Indices: 5169915--5169959 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
5169905 TTTTGAGTTG
* *
5169915 AAAATATGGGATTCGAATCTCAA
1 AAAATATGAGATTCAAATCTCAA
* *
5169938 AAAATTTGAGATTTAAATCTCA
1 AAAATATGAGATTCAAATCTCA
5169960 GAAAGCTTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (23 bp):
AAAATATGAGATTCAAATCTCAA
Found at i:5170052 original size:16 final size:16
Alignment explanation
Indices: 5170033--5170064 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5170023 GAGATCGAAA
5170033 AAAAAAAAAACTTTAC
1 AAAAAAAAAACTTTAC
*
5170049 AAAAAAAAAAGTTTAC
1 AAAAAAAAAACTTTAC
5170065 CAGATTCAAA
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:0.69, C:0.09, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAAAAAAAACTTTAC
Found at i:5170799 original size:18 final size:19
Alignment explanation
Indices: 5170776--5170812 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5170766 GTAAAAAAAC
5170776 TATTTTTT-TAAATTTTTT
1 TATTTTTTATAAATTTTTT
*
5170794 TATTTTTTATATATTTTTT
1 TATTTTTTATAAATTTTTT
5170813 ATTAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (19 bp):
TATTTTTTATAAATTTTTT
Found at i:5170813 original size:18 final size:17
Alignment explanation
Indices: 5170779--5170815 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
5170769 AAAAAACTAT
5170779 TTTTTTAAATTTTTTTA
1 TTTTTTAAATTTTTTTA
*
5170796 TTTTTTATATATTTTTTA
1 TTTTTTAAAT-TTTTTTA
5170814 TT
1 TT
5170816 AATATTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTAAATTTTTTTA
Found at i:5171270 original size:192 final size:192
Alignment explanation
Indices: 5170934--5171281 Score: 474
Period size: 192 Copynumber: 1.8 Consensus size: 192
5170924 AATGCAAAAA
* *
5170934 TAATAAAAATGTAAGAAAAGAAAATTTTTTATTCGATGATGAGATTCAAAAGTACTCTAAGTAGT
1 TAATAAAAATG-AAGAAAAGAAAA-TTTTTATCCGATGATGAGATTCAAAAGTACTCTAAGTAGA
**
5170999 GATGCCTACAAAATCTCTAGGTGAGAAGATTTTTTTAAATATTACCAGTGTATTGGTGTATTTAT
64 GATGCCTACAAAATCTCTAGGTGAGAAGATTTTTTTAAATATTACCAGTGTATTGGAATATTTAT
*
5171064 AAAAAGTTTTCAATACAATAAAATTTATCTTTTTGTTAATAAAAATTAATAAATTAAGAATAAG
129 AAAAAGTCTTCAATACAATAAAATTTATCTTTTTGTTAATAAAAATTAATAAATTAAGAATAAG
* * * *
5171128 TAATAAAAATG-AGAAAA-AAAA-TTTTATCCGATGATGGGATTCTAAAAGTATTTTGAGTAGAG
1 TAATAAAAATGAAGAAAAGAAAATTTTTATCCGATGATGAGATTC-AAAAGTACTCTAAGTAGAG
* *
5171190 ATGCTTTA-AGAAATC-CTTAGGTGAGAAGATTTTTTTAAAATATTACTAGTGTATTGGAATATT
65 ATGC-CTACA-AAATCTC-TAGGTGAGAAGATTTTTTT-AAATATTACCAGTGTATTGGAATATT
*
5171253 TATAGAAAA-TCTTCAATATAATAAAATTT
126 TATA-AAAAGTCTTCAATACAATAAAATTT
5171282 TCATTTTCTT
Statistics
Matches: 136, Mismatches: 12, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
189 19 0.14
190 21 0.15
191 30 0.22
192 51 0.38
193 4 0.03
194 11 0.08
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (192 bp):
TAATAAAAATGAAGAAAAGAAAATTTTTATCCGATGATGAGATTCAAAAGTACTCTAAGTAGAGA
TGCCTACAAAATCTCTAGGTGAGAAGATTTTTTTAAATATTACCAGTGTATTGGAATATTTATAA
AAAGTCTTCAATACAATAAAATTTATCTTTTTGTTAATAAAAATTAATAAATTAAGAATAAG
Found at i:5172112 original size:20 final size:21
Alignment explanation
Indices: 5172074--5172113 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5172064 CTTTCAATAA
*
5172074 AAAAGAAAAAAAAATAAATTG
1 AAAACAAAAAAAAATAAATTG
*
5172095 AAAACAAAAAGAAA-AAATT
1 AAAACAAAAAAAAATAAATT
5172114 CACACACGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.78, C:0.03, G:0.07, T:0.12
Consensus pattern (21 bp):
AAAACAAAAAAAAATAAATTG
Found at i:5182281 original size:11 final size:11
Alignment explanation
Indices: 5182265--5182289 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5182255 TATTTTGCTT
5182265 AAAAAAAAGAA
1 AAAAAAAAGAA
5182276 AAAAAAAAGAA
1 AAAAAAAAGAA
5182287 AAA
1 AAA
5182290 TGATGACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:5183167 original size:53 final size:50
Alignment explanation
Indices: 5183108--5183426 Score: 287
Period size: 53 Copynumber: 6.4 Consensus size: 50
5183098 AATAGATGAA
*
5183108 TTTTAAAGTTGTTGAGTCTTTGCTGAGATGAGCTTCTTTCAAGATGAGAATT
1 TTTTAAAGTTGTTGAGCCTTTGCTGAGATGAGCTT-TTTCAAGATGAGAA-T
* * * *
5183160 TCTTTAAAGTTGTTGAACCTTTGCTTAGAGGAGCTTTTTTC-AGATAATGAA-
1 T-TTTAAAGTTGTTGAGCCTTTGCTGAGATGAGC-TTTTTCAAGATGA-GAAT
* * ** *
5183211 TTTTAAAGTTATTGAGCCTTTGTTGAGAAAAGCTTTTTCAAGATGAAAATTT
1 TTTTAAAGTTGTTGAGCCTTTGCTGAGATGAGCTTTTTCAAGATGAGAA--T
* * * *
5183263 TTTTAAAGTTTTTAAGCCTCTGCTGAGAGGAGCTTTTTTCAAGATGA-AAT
1 TTTTAAAGTTGTTGAGCCTTTGCTGAGATGAGC-TTTTTCAAGATGAGAAT
* * *
5183313 TTTT-AAGTTGTTGAG-TTTCTGCTTATATGAGCTTTTTCAAGATG-G-A-
1 TTTTAAAGTTGTTGAGCCTT-TGCTGAGATGAGCTTTTTCAAGATGAGAAT
* * * * *
5183359 TTTTAAAGTTGTTGAGCTTTTACGGATATGAGCTTTTTCAAGATGA-CAT
1 TTTTAAAGTTGTTGAGCCTTTGCTGAGATGAGCTTTTTCAAGATGAGAAT
*
5183408 TTTTAAAGTTGATGAGCCT
1 TTTTAAAGTTGTTGAGCCT
5183427 CTACTTAAAG
Statistics
Matches: 221, Mismatches: 31, Indels: 33
0.78 0.11 0.12
Matches are distributed among these distances:
46 4 0.02
47 34 0.15
48 17 0.08
49 44 0.20
50 36 0.16
51 1 0.00
52 35 0.16
53 48 0.22
54 2 0.01
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (50 bp):
TTTTAAAGTTGTTGAGCCTTTGCTGAGATGAGCTTTTTCAAGATGAGAAT
Found at i:5183317 original size:102 final size:101
Alignment explanation
Indices: 5183101--5183327 Score: 289
Period size: 102 Copynumber: 2.2 Consensus size: 101
5183091 TTTCGAGAAT
* ** *
5183101 AGATG-AATTTTAAAGTTGTTGAGTCTTTGCTGAGATGAGCTTCTTTCAAGATGAGAATTTCTTT
1 AGATGAAATTTTAAAGTTGTTGAGCCTTTGCTGAGAAAAGCTTCTTTCAAGATGAAAATTTCTTT
* *
5183165 AAAGTTGTTGAACCTTTGCTTAGAGGAGCTTTTTTC
66 AAAGTTGTTGAACCTCTGCTGAGAGGAGCTTTTTTC
* * * *
5183201 AGATAATGAATTTTAAAGTTATTGAGCCTTTGTTGAGAAAAGCTT-TTTCAAGATGAAAATTTTT
1 AGATGA--AATTTTAAAGTTGTTGAGCCTTTGCTGAGAAAAGCTTCTTTCAAGATGAAAATTTCT
*
5183265 TTAAAGTT-TTTAAGCCTCTGCTGAGAGGAGCTTTTTTC
64 TTAAAGTTGTTGAA-CCTCTGCTGAGAGGAGCTTTTTTC
*
5183303 AAGATGAAATTTTTAAGTTGTTGAG
1 -AGATGAAATTTTAAAGTTGTTGAG
5183328 TTTCTGCTTA
Statistics
Matches: 108, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
100 4 0.04
101 20 0.19
102 47 0.44
103 37 0.34
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (101 bp):
AGATGAAATTTTAAAGTTGTTGAGCCTTTGCTGAGAAAAGCTTCTTTCAAGATGAAAATTTCTTT
AAAGTTGTTGAACCTCTGCTGAGAGGAGCTTTTTTC
Found at i:5183441 original size:49 final size:49
Alignment explanation
Indices: 5183101--5183442 Score: 212
Period size: 49 Copynumber: 6.9 Consensus size: 49
5183091 TTTCGAGAAT
* * * * *
5183101 AGATG-AA-TTTTAAAGTTGTTGAGTCTTTGCTGAGATGAGCTTCTTTCA
1 AGATGAAATTTTTAAAGTTGTTGAGCCTCTACTGATAGGAGCTT-TTTCA
* * * * *
5183149 AGATGAGAATTTCTTTAAAGTTGTTGAACCTTTGCTTAGAGGAGCTTTTTTC-
1 AGATGA-AA-TT-TTTAAAGTTGTTGAGCCTCTACTGATAGGAGC-TTTTTCA
* * * ** * **
5183201 AGAT-AATGAATTTTAAAGTTATTGAGCCTTTGTTGAGAAAAGCTTTTTCA
1 AGATGAA--ATTTTTAAAGTTGTTGAGCCTCTACTGATAGGAGCTTTTTCA
* * * *
5183251 AGATGAAAATTTTTTTAAAGTTTTTAAGCCTCTGCTGAGAGGAGCTTTTTTCA
1 AGATG-AAA--TTTTTAAAGTTGTTGAGCCTCTACTGATAGGAGC-TTTTTCA
** * * *
5183304 AGATGAAATTTTT-AAGTTGTTGAGTTTCTGCTTATATGAGCTTTTTCA
1 AGATGAAATTTTTAAAGTTGTTGAGCCTCTACTGATAGGAGCTTTTTCA
* * * * *
5183352 AGATG-GA-TTTTAAAGTTGTTGAGCTTTTACGGATATGAGCTTTTTCA
1 AGATGAAATTTTTAAAGTTGTTGAGCCTCTACTGATAGGAGCTTTTTCA
* * * *
5183399 AGATGACATTTTTAAAGTTGATGAGCCTCTACTTAAAGGAGCTT
1 AGATGAAATTTTTAAAGTTGTTGAGCCTCTACTGATAGGAGCTT
5183443 GTTGAGCATC
Statistics
Matches: 238, Mismatches: 39, Indels: 33
0.77 0.13 0.11
Matches are distributed among these distances:
46 4 0.02
47 36 0.15
48 18 0.08
49 55 0.23
50 39 0.16
51 2 0.01
52 38 0.16
53 44 0.18
54 2 0.01
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (49 bp):
AGATGAAATTTTTAAAGTTGTTGAGCCTCTACTGATAGGAGCTTTTTCA
Found at i:5183454 original size:25 final size:25
Alignment explanation
Indices: 5183420--5183467 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
5183410 TTAAAGTTGA
*
5183420 TGAGCCTCTACTTAAAGGAGCTTGT
1 TGAGCATCTACTTAAAGGAGCTTGT
* *
5183445 TGAGCATCTACTTAGATGAGCTT
1 TGAGCATCTACTTAAAGGAGCTT
5183468 TTCAAGATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (25 bp):
TGAGCATCTACTTAAAGGAGCTTGT
Found at i:5183508 original size:48 final size:48
Alignment explanation
Indices: 5183441--5183750 Score: 367
Period size: 48 Copynumber: 6.5 Consensus size: 48
5183431 TTAAAGGAGC
*
5183441 TTGTTGAGCATCTACTTAGATGAGC-TTTTCAAGATGAGATTTTTAAAG
1 TTGTTGAGCCTCTACTTAGATGAGCTTTTTCAAGATGAGA-TTTTAAAG
* **
5183489 TTGTTGAGCCTCTATTTAGAAAAGCTTTTTCAAGATG-GATTTTAAAG
1 TTGTTGAGCCTCTACTTAGATGAGCTTTTTCAAGATGAGATTTTAAAG
* * *
5183536 TTGTTGAGCCTCTACTGAAAGGAGCTTTTTCAAGATGAGATTTTAAAG
1 TTGTTGAGCCTCTACTTAGATGAGCTTTTTCAAGATGAGATTTTAAAG
* * * * * * *
5183584 TTGTTGAGCCTCT-GTTGATATTAGTTTTTTTAATATGAGATTTTAAAA
1 TTGTTGAGCCTCTACTT-AGATGAGCTTTTTCAAGATGAGATTTTAAAG
* *
5183632 TTGTTGAGCCTCTGCTGAGATGAGCTTTTTCAAGATGAGATTTTTAAAG
1 TTGTTGAGCCTCTACTTAGATGAGCTTTTTCAAGATGAGA-TTTTAAAG
** * * *
5183681 TTGTTGAGCCTCTGTTTAGAAGAGCTTTTCCAAGATGATA-TTTAAAG
1 TTGTTGAGCCTCTACTTAGATGAGCTTTTTCAAGATGAGATTTTAAAG
*
5183728 TTGTTGAGCCTTTACTTAGATGA
1 TTGTTGAGCCTCTACTTAGATGA
5183751 ACCTTTTTAA
Statistics
Matches: 222, Mismatches: 35, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
47 67 0.30
48 101 0.45
49 54 0.24
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (48 bp):
TTGTTGAGCCTCTACTTAGATGAGCTTTTTCAAGATGAGATTTTAAAG
Found at i:5183549 original size:120 final size:121
Alignment explanation
Indices: 5183320--5183562 Score: 312
Period size: 120 Copynumber: 2.0 Consensus size: 121
5183310 AATTTTTAAG
** * * * *
5183320 TTGTTGAGTTTCTGCTTATATGAGCTTTTTCAAGATGGATTTTAAAGTTGTTGAGCTTTTACGGA
1 TTGTTGAGCATCTACTTAGATGAGCTTTTTCAAGATGGATTTTAAAGTTGTTGAGCCTCTACGGA
* ** *
5183385 TATGAGCTTTTTCAAGATGACATTTTTAAAGTTGATGAGCCTCTACTTAAAGGAGC
66 GAAAAGCTTTTTCAAGATGACATTTTTAAAGTTGATGAGCCTCTACTGAAAGGAGC
**
5183441 TTGTTGAGCATCTACTTAGATGAGC-TTTTCAAGATGAGATTTTTAAAGTTGTTGAGCCTCTATT
1 TTGTTGAGCATCTACTTAGATGAGCTTTTTCAAGATG-GA-TTTTAAAGTTGTTGAGCCTCTACG
* * *
5183505 TAGAAAAGCTTTTTCAAGATG-GA-TTTTAAAGTTGTTGAGCCTCTACTGAAAGGAGC
64 GAGAAAAGCTTTTTCAAGATGACATTTTTAAAGTTGATGAGCCTCTACTGAAAGGAGC
5183561 TT
1 TT
5183563 TTTCAAGATG
Statistics
Matches: 105, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
120 44 0.42
121 24 0.23
122 37 0.35
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (121 bp):
TTGTTGAGCATCTACTTAGATGAGCTTTTTCAAGATGGATTTTAAAGTTGTTGAGCCTCTACGGA
GAAAAGCTTTTTCAAGATGACATTTTTAAAGTTGATGAGCCTCTACTGAAAGGAGC
Found at i:5183691 original size:265 final size:267
Alignment explanation
Indices: 5183211--5183693 Score: 668
Period size: 265 Copynumber: 1.8 Consensus size: 267
5183201 AGATAATGAA
* * *
5183211 TTTTAAAGTTATTGAGCCTTTGTTGAGAAAAGCTTTTTCAAGATGAAAATTTTTTTAAAGTTTTT
1 TTTTAAAGTTATTGAGCCTCTATTGAGAAAAGCTTTTTCAAGATG-AAA--TTTTTAAAGTTGTT
* * * **
5183276 AAGCCTCTGCTGAGAGGAGCTTTTTTCAAGATGAAATTTTTAAGTTGTTGAGTTTCTGCTTATAT
63 AAGCCTCTACTGAAAGGAGCTTTTTTCAAGATGAAATTTTAAAGTTGTTGAGCCTCTGCTTATAT
* * * *
5183341 GAGCTTTTTCAAGATGGATTTTAAAGTTGTTGAGCTTTTACGGATATGAGCTTTTTCAAGATGAC
128 GAGCTTTTTCAAGATGGATTTTAAAATTGTTGAGCCTCTACGGAGATGAGCTTTTTCAAGATGAC
5183406 ATTTTTAAAGTTGATGAGCCTCTACTTAAAGGAGCTTGTTGAGCATCTACTTAGATGAGCTTTTC
193 ATTTTTAAAGTTGATGAGCCTCTACTTAAAGGAGCTTGTTGAGCATCTACTTAGATGAGCTTTTC
5183471 AAGATGAGAT
258 AAGATGAGAT
* * * *
5183481 TTTTAAAGTTGTTGAGCCTCTATTTAGAAAAGCTTTTTCAAGATG-GA-TTTTAAAGTTGTTGAG
1 TTTTAAAGTTATTGAGCCTCTATTGAGAAAAGCTTTTTCAAGATGAAATTTTTAAAGTTGTTAAG
* *
5183544 CCTCTACTGAAAGGAGC-TTTTTCAAGATGAGATTTTAAAGTTGTTGAGCCTCTG-TTGATATTA
66 CCTCTACTGAAAGGAGCTTTTTTCAAGATGAAATTTTAAAGTTGTTGAGCCTCTGCTT-ATATGA
* * * * * *
5183607 GTTTTTTTAATATGAGATTTTAAAATTGTTGAGCCTCTGCTGAGATGAGCTTTTTCAAGATGAGA
130 GCTTTTTCAAGATG-GATTTTAAAATTGTTGAGCCTCTACGGAGATGAGCTTTTTCAAGATGACA
*
5183672 TTTTTAAAGTTGTTGAGCCTCT
194 TTTTTAAAGTTGATGAGCCTCT
5183694 GTTTAGAAGA
Statistics
Matches: 186, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
263 2 0.01
264 49 0.26
265 93 0.50
268 1 0.01
270 41 0.22
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.41
Consensus pattern (267 bp):
TTTTAAAGTTATTGAGCCTCTATTGAGAAAAGCTTTTTCAAGATGAAATTTTTAAAGTTGTTAAG
CCTCTACTGAAAGGAGCTTTTTTCAAGATGAAATTTTAAAGTTGTTGAGCCTCTGCTTATATGAG
CTTTTTCAAGATGGATTTTAAAATTGTTGAGCCTCTACGGAGATGAGCTTTTTCAAGATGACATT
TTTAAAGTTGATGAGCCTCTACTTAAAGGAGCTTGTTGAGCATCTACTTAGATGAGCTTTTCAAG
ATGAGAT
Found at i:5183960 original size:9 final size:8
Alignment explanation
Indices: 5183946--5183999 Score: 54
Period size: 9 Copynumber: 6.2 Consensus size: 8
5183936 GCTTTAAACA
5183946 TTATTATTT
1 TTATT-TTT
5183955 TTATTATTT
1 TTATT-TTT
5183964 TTATTTTT
1 TTATTTTT
*
5183972 CTATTTTTT
1 TTA-TTTTT
*
5183981 TTCTTTTT
1 TTATTTTT
5183989 TCTATTTTT
1 T-TATTTTT
5183998 TT
1 TT
5184000 TTCTTCTTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
8 12 0.31
9 27 0.69
ACGTcount: A:0.13, C:0.06, G:0.00, T:0.81
Consensus pattern (8 bp):
TTATTTTT
Found at i:5183976 original size:26 final size:26
Alignment explanation
Indices: 5183947--5183997 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
5183937 CTTTAAACAT
5183947 TATTATTTTTATTATTTT-TATTTTTC
1 TATTATTTTTATT-TTTTCTATTTTTC
* *
5183973 TATTTTTTTTCTTTTTTCTATTTTT
1 TATTATTTTTATTTTTTCTATTTTT
5183998 TTTTCTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (26 bp):
TATTATTTTTATTTTTTCTATTTTTC
Found at i:5183981 original size:17 final size:17
Alignment explanation
Indices: 5183946--5184000 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
5183936 GCTTTAAACA
* *
5183946 TTATTATTTTTATTATTT
1 TTATT-TTTCTATTTTTT
5183964 TTATTTTTCTATTTTTT
1 TTATTTTTCTATTTTTT
*
5183981 TTCTTTTTTCTATTTTTT
1 TT-ATTTTTCTATTTTTT
5183999 TT
1 TT
5184001 TCTTCTTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 12 0.36
18 21 0.64
ACGTcount: A:0.13, C:0.05, G:0.00, T:0.82
Consensus pattern (17 bp):
TTATTTTTCTATTTTTT
Found at i:5183982 original size:18 final size:17
Alignment explanation
Indices: 5183952--5184001 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
5183942 AACATTATTA
* *
5183952 TTTT-TATTATTTTTAT
1 TTTTCTATTTTTTTTTT
5183968 TTTTCTATTTTTTTTCTT
1 TTTTCTATTTTTTTT-TT
5183986 TTTTCTATTTTTTTTT
1 TTTTCTATTTTTTTTT
5184002 CTTCTTCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 4 0.13
17 10 0.33
18 16 0.53
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTCTATTTTTTTTTT
Found at i:5184009 original size:18 final size:18
Alignment explanation
Indices: 5183956--5184009 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
5183946 TTATTATTTT
* *
5183956 TATTATTTTTATTT-TTC
1 TATTTTTTTTCTTTCTTC
*
5183973 TATTTTTTTTCTTTTTTC
1 TATTTTTTTTCTTTCTTC
5183991 TATTTTTTTT-TCTTCTTC
1 TATTTTTTTTCT-TTCTTC
5184009 T
1 T
5184010 TTCCTTATCC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 13 0.41
18 19 0.59
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (18 bp):
TATTTTTTTTCTTTCTTC
Found at i:5184168 original size:22 final size:22
Alignment explanation
Indices: 5184134--5184175 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5184124 TTTTGGGTTG
5184134 AAAATATGGGATTCGAATCCCA
1 AAAATATGGGATTCGAATCCCA
* * *
5184156 AAAATTTGTGATTTGAATCC
1 AAAATATGGGATTCGAATCC
5184176 TAGAATAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (22 bp):
AAAATATGGGATTCGAATCCCA
Found at i:5186003 original size:18 final size:18
Alignment explanation
Indices: 5185974--5186023 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
5185964 AAATTATCTT
5185974 TTTAATAAATTTTAATTAA
1 TTTAATAAATTTT-ATTAA
5185993 TTTAA-AAATTTTATTAA
1 TTTAATAAATTTTATTAA
** *
5186010 AATGATAAATTTTA
1 TTTAATAAATTTTA
5186024 ATAAGTGACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 7 0.26
18 15 0.56
19 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TTTAATAAATTTTATTAA
Found at i:5186752 original size:27 final size:28
Alignment explanation
Indices: 5186718--5186830 Score: 117
Period size: 27 Copynumber: 4.0 Consensus size: 28
5186708 GTTTTATTCT
**
5186718 TTTATTAAATTATAATTA-TAATTATAA
1 TTTATTAAAAAATAATTATTAATTATAA
5186745 TTTATTAAAAAATAA-TATTAATTATAA
1 TTTATTAAAAAATAATTATTAATTATAA
5186772 -TTACTTAATAAAAGTAATTATTAATTATAA
1 TTTA-TTAA-AAAA-TAATTATTAATTATAA
* *
5186802 TTAATTAATAAAAATAA-AATTAATTATAA
1 TTTATT-A-AAAAATAATTATTAATTATAA
5186831 CAAAATAAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 14
0.80 0.04 0.15
Matches are distributed among these distances:
26 5 0.07
27 26 0.35
28 4 0.05
29 14 0.19
30 17 0.23
31 7 0.09
32 1 0.01
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (28 bp):
TTTATTAAAAAATAATTATTAATTATAA
Found at i:5186794 original size:30 final size:27
Alignment explanation
Indices: 5186736--5186830 Score: 120
Period size: 30 Copynumber: 3.3 Consensus size: 27
5186726 ATTATAATTA
5186736 TAATTATAATTTATTAA-AAAATAATAT
1 TAATTATAA-TTATTAATAAAATAATAT
5186763 TAATTATAATTACTTAATAAAAGTAATTAT
1 TAATTATAATTA-TTAATAAAA-TAA-TAT
*
5186793 TAATTATAATTAATTAATAAAAATAAAAT
1 TAATTATAATT-ATTAAT-AAAATAATAT
5186822 TAATTATAA
1 TAATTATAA
5186831 CAAAATAAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 10
0.85 0.01 0.14
Matches are distributed among these distances:
26 3 0.05
27 13 0.21
28 4 0.07
29 14 0.23
30 22 0.36
31 5 0.08
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (27 bp):
TAATTATAATTATTAATAAAATAATAT
Found at i:5186824 original size:19 final size:20
Alignment explanation
Indices: 5186800--5186840 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
5186790 TATTAATTAT
5186800 AATTAATTA-ATA-AAAATAA
1 AATTAATTATA-ACAAAATAA
5186819 AATTAATTATAACAAAATAA
1 AATTAATTATAACAAAATAA
5186839 AA
1 AA
5186841 ATTACTAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AATTAATTATAACAAAATAA
Found at i:5186885 original size:25 final size:25
Alignment explanation
Indices: 5186799--5186885 Score: 63
Period size: 25 Copynumber: 3.4 Consensus size: 25
5186789 TTATTAATTA
* *
5186799 TAATTAATTAATAAAAA-TA-AAAT
1 TAATTAATAAATAAAAATTACTAAT
*
5186822 TAATTATAACAAAATAAAAATTACTAGA-
1 TAA-T-TAA-TAAATAAAAATTACTA-AT
* * *
5186850 CAAATATTAAATAAAAATTACTAAT
1 TAATTAATAAATAAAAATTACTAAT
5186875 TAATTAATAAA
1 TAATTAATAAA
5186886 GTTGAGAAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 12
0.68 0.14 0.17
Matches are distributed among these distances:
23 3 0.06
24 2 0.04
25 26 0.55
26 10 0.21
27 2 0.04
28 3 0.06
29 1 0.02
ACGTcount: A:0.62, C:0.05, G:0.01, T:0.32
Consensus pattern (25 bp):
TAATTAATAAATAAAAATTACTAAT
Found at i:5189165 original size:12 final size:12
Alignment explanation
Indices: 5189150--5189186 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
5189140 TATTGATCAG
5189150 AATTTTTTATTA
1 AATTTTTTATTA
5189162 AA-TTTTTATTA
1 AATTTTTTATTA
5189173 AATTATTTT-TTA
1 AATT-TTTTATTA
5189185 AA
1 AA
5189187 AAAATTTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 11 0.48
12 8 0.35
13 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
AATTTTTTATTA
Found at i:5190922 original size:17 final size:15
Alignment explanation
Indices: 5190879--5190921 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
5190869 TCCAAGTATT
5190879 AAATAAAAAATAATA
1 AAATAAAAAATAATA
*
5190894 AAATTTGAAAAATAATA
1 AAA--TAAAAAATAATA
5190911 GAAATAAAAAA
1 -AAATAAAAAA
5190922 AAACTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 3 0.13
16 6 0.26
17 11 0.48
18 3 0.13
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (15 bp):
AAATAAAAAATAATA
Found at i:5192377 original size:26 final size:26
Alignment explanation
Indices: 5192348--5192400 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
5192338 AAATAGTTGG
*
5192348 ATTTAATTGGTTTTATTTGATATTTA
1 ATTTAATTGCTTTTATTTGATATTTA
* * *
5192374 ATTTAATTTCTTTTATTTTATTTTTA
1 ATTTAATTGCTTTTATTTGATATTTA
5192400 A
1 A
5192401 AAAATATAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (26 bp):
ATTTAATTGCTTTTATTTGATATTTA
Found at i:5192894 original size:16 final size:16
Alignment explanation
Indices: 5192875--5192905 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5192865 CATTTTTTTG
5192875 TTTATTGATTTACTTA
1 TTTATTGATTTACTTA
*
5192891 TTTATTTATTTACTT
1 TTTATTGATTTACTT
5192906 GTTTTATTAA
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:0.23, C:0.06, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTATTGATTTACTTA
Found at i:5202615 original size:20 final size:20
Alignment explanation
Indices: 5202590--5202645 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
5202580 TATTTTACTT
*
5202590 AAAAAAAAGAAAAAAGATGC
1 AAAAAAAAGAAAAAAGATAC
* *
5202610 AAAAAAATGAAAAAAAATAC
1 AAAAAAAAGAAAAAAGATAC
5202630 AAAAAAGAA-AAAAAAG
1 AAAAAA-AAGAAAAAAG
5202646 GAGATGATTC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.80, C:0.04, G:0.11, T:0.05
Consensus pattern (20 bp):
AAAAAAAAGAAAAAAGATAC
Found at i:5203736 original size:5 final size:5
Alignment explanation
Indices: 5203726--5203776 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
5203716 AATAATATTT
* * *
5203726 AACAA AACAA AACAA AAAAA GAAAAA AATAA AACAGA AA-AA AACAA AACAA
1 AACAA AACAA AACAA AACAA -AACAA AACAA AACA-A AACAA AACAA AACAA
5203777 GTAAACAAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
4 3 0.08
5 29 0.73
6 8 0.20
ACGTcount: A:0.82, C:0.12, G:0.04, T:0.02
Consensus pattern (5 bp):
AACAA
Found at i:5203769 original size:36 final size:36
Alignment explanation
Indices: 5203729--5203803 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
5203719 AATATTTAAC
* *
5203729 AAAACAAAACAAAAAAAGAAA-AAAATAAAACAGAAA
1 AAAACAAAACAAAAAAACAAACAAAA-AAAAAAGAAA
**
5203765 AAAACAAAACAAGTAAACAAACAAAAAAAAAAGAAA
1 AAAACAAAACAAAAAAACAAACAAAAAAAAAAGAAA
5203801 AAA
1 AAA
5203804 GTTAAGGAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 30 0.88
37 4 0.12
ACGTcount: A:0.83, C:0.09, G:0.05, T:0.03
Consensus pattern (36 bp):
AAAACAAAACAAAAAAACAAACAAAAAAAAAAGAAA
Found at i:5203782 original size:23 final size:22
Alignment explanation
Indices: 5203729--5203796 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 22
5203719 AATATTTAAC
* *
5203729 AAAACAAAAC-AAAAAAAGAAA
1 AAAATAAAACAAAAAAAAAAAA
5203750 AAAATAAAACAGAAAAAAACAAAA
1 AAAATAAAACA-AAAAAAA-AAAA
* * *
5203774 CAAGT-AAACAAACAAAAAAAA
1 AAAATAAAACAAAAAAAAAAAA
5203795 AA
1 AA
5203797 GAAAAAAGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 14 0.37
22 6 0.16
23 12 0.32
24 6 0.16
ACGTcount: A:0.82, C:0.10, G:0.04, T:0.03
Consensus pattern (22 bp):
AAAATAAAACAAAAAAAAAAAA
Found at i:5204056 original size:32 final size:31
Alignment explanation
Indices: 5203999--5204077 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 31
5203989 AAAAAAAAGA
*
5203999 AGAAA-AAAAAAATTTTTCATGTGAGAGTTC
1 AGAAACAAAAAAATTTTGCATGTGAGAGTTC
*
5204029 TGAAACAAAAAAATTTTGCA-GCTTGAGAGTTC
1 AGAAACAAAAAAATTTTGCATG--TGAGAGTTC
* *
5204061 AGGAAC-GAAAAATTTTG
1 AGAAACAAAAAAATTTTG
5204078 ATCTACCCAC
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 5 0.12
31 23 0.56
32 13 0.32
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (31 bp):
AGAAACAAAAAAATTTTGCATGTGAGAGTTC
Found at i:5205648 original size:141 final size:142
Alignment explanation
Indices: 5205489--5205771 Score: 532
Period size: 142 Copynumber: 2.0 Consensus size: 142
5205479 TCATAATTCA
*
5205489 TATTAATAATAAGATTAATAAAT-AAAAAGTATAATAAAATTGAGATTTTAAATATAAACAGTCG
1 TATTAATAATAAGATTAATAAATAAAAAAGTATAATAAAATTGAGATCTTAAATATAAACAGTCG
5205553 CACCTAAACTCTGCCTAGATGTTGGAGAGTCGGGGTGGTCTCATTATATTTAAGAATCCAACTCT
66 CACCTAAACTCTGCCTAGATGTTGGAGAGTCGGGGTGGTCTCATTATATTTAAGAATCCAACTCT
5205618 TAAATTGCATTT
131 TAAATTGCATTT
*
5205630 TATTAATAATAAGATTAATAAATAAAAAAGTATAATAAAATTGGGATCTTAAATATAAACAGTCG
1 TATTAATAATAAGATTAATAAATAAAAAAGTATAATAAAATTGAGATCTTAAATATAAACAGTCG
*
5205695 CACCTAAGCTCTGCCTAGATGTTGGAGAGTCGGGGTGGTCTCATTATATTTAAGAATCCAACTCT
66 CACCTAAACTCTGCCTAGATGTTGGAGAGTCGGGGTGGTCTCATTATATTTAAGAATCCAACTCT
5205760 TAAATTGCATTT
131 TAAATTGCATTT
5205772 CATTTTACAT
Statistics
Matches: 138, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
141 23 0.17
142 115 0.83
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (142 bp):
TATTAATAATAAGATTAATAAATAAAAAAGTATAATAAAATTGAGATCTTAAATATAAACAGTCG
CACCTAAACTCTGCCTAGATGTTGGAGAGTCGGGGTGGTCTCATTATATTTAAGAATCCAACTCT
TAAATTGCATTT
Found at i:5207917 original size:8 final size:8
Alignment explanation
Indices: 5207904--5207933 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
5207894 TATTTTGCTT
5207904 AAAAAAAG
1 AAAAAAAG
5207912 AAAAAAAG
1 AAAAAAAG
5207920 -AAAAAAG
1 AAAAAAAG
5207927 AAAAAAA
1 AAAAAAA
5207934 TGATGACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:5207925 original size:15 final size:15
Alignment explanation
Indices: 5207905--5207933 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5207895 ATTTTGCTTA
5207905 AAAAAAGAAAAAAAG
1 AAAAAAGAAAAAAAG
5207920 AAAAAAGAAAAAAA
1 AAAAAAGAAAAAAA
5207934 TGATGACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:5208781 original size:48 final size:48
Alignment explanation
Indices: 5208713--5209662 Score: 1139
Period size: 48 Copynumber: 19.7 Consensus size: 48
5208703 CAAATGAGAT
* *
5208713 TTTTAAAGTTGTTGAGCCTCTGTTGAGATGAGCTTTTTCAAGAAAAGA
1 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAGA
** *
5208761 TTTTAAAGTCATTGAGCCTCTGTTGAGAGGAGCTTTTTCAAG-AAAGAA
1 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAG-A
*
5208809 TTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTTCAAG-AAAGAA
1 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAG-A
*
5208857 TTTTTAAAGTTGTGGAACCTCTGTTGAGAGGAGCTTTTTCAAG-AAAGAA
1 -TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAG-A
*
5208906 TTTTAAAGTTGTAGAGCCTCTGTTGAGAGGAGCTTTTTCAA-AATGAA-A
1 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAA--AAGA
* **
5208954 TTTTAAAGTTATGGAGCCTCTGTTGAGAGGAGCTTTTTC-AGATGAGA
1 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAGA
5209001 TTTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAG-AAAGAA
1 -TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAG-A
* * * *
5209050 TTTTTAAGTTGTTGAGCCTCTGCTGAGAGGAGC-TTTCCAA-AATGAA-A
1 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAA--AAGA
5209097 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAG-AAAGAA
1 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAG-A
*
5209145 TTTTAAAGTTGTGGAGCCTCTGTTGAGATGAGCTTTTTCAAG-AAAGAA
1 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAG-A
* * * *
5209193 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTCCAA-AATGAA-A
1 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAA--AAGA
* * * *
5209241 TTTTAAAGTTGTGGAACCTCTGCTGAAAGGAGCTTTTCCAA-AATGAA-A
1 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAA--AAGA
* *
5209289 TTTTAAAGTGGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAAA
1 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAGA
* * * **
5209337 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAA-ATGAGA
1 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAGA
*
5209384 TTTTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAATAAA
1 --TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAA-AGA
* * **
5209435 TTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTCCAA-ATGAGA
1 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAGA
*
5209482 TTTTTTAAAGTTATGGAGCCTCTGTTGAGAGGAGCTTTTTCAAG-AAAGAA
1 --TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAG-A
* *
5209532 TTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTTTAAG-AAAGAA
1 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAG-A
* *
5209580 TTTTTAAAGTTGTGGAACCTCTGTTGAGAGGAGCTTTTTCAAGAAAAAA
1 -TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAGA
* * *
5209629 TTTTAAAGTTGATTGAGCCTCTGCTAAGAGGAGC
1 TTTTAAAGTTG-TGGAGCCTCTGTTGAGAGGAGC
5209663 CCTTTTCTGT
Statistics
Matches: 796, Mismatches: 73, Indels: 65
0.85 0.08 0.07
Matches are distributed among these distances:
46 3 0.00
47 51 0.06
48 503 0.63
49 228 0.29
50 9 0.01
51 2 0.00
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.35
Consensus pattern (48 bp):
TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAGA
Found at i:5208896 original size:97 final size:97
Alignment explanation
Indices: 5208713--5209662 Score: 1307
Period size: 96 Copynumber: 9.8 Consensus size: 97
5208703 CAAATGAGAT
* * * **
5208713 TTTTAAAGTTGTTGAGCCTCTGTTGAGATGAGCTTTTTCAAGAAA-AGATTTTAAAGTCATTGAG
1 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAAATTTTAAAGTTGTTGAG
5208777 CCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAA
66 CCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAA
* * * *
5208809 TTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAATTTTTAAAGTTGTGGAA
1 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAAATTTTAAAGTTGTTGAG
5208874 CCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAA
66 CCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAA
* * * *
5208906 TTTTAAAGTTGTAGAGCCTCTGTTGAGAGGAGCTTTTTCAA-AATGAAATTTTAAAGTTATGGAG
1 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAAATTTTAAAGTTGTTGAG
* *
5208970 CCTCTGTTGAGAGGAGCTTTTTC-AGATGAGAT
66 CCTCTGTTGAGAGGAGCTTTTTCAAGA-AAGAA
*
5209002 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAG-AATTTTTAAGTTGTTGAG
1 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAAATTTTAAAGTTGTTGAG
* * *
5209066 CCTCTGCTGAGAGGAGC-TTTCCAA-AATGAAA
66 CCTCTGTTGAGAGGAGCTTTTTCAAGAAAG-AA
*
5209097 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAG-AATTTTAAAGTTGTGGAG
1 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAAATTTTAAAGTTGTTGAG
*
5209161 CCTCTGTTGAGATGAGCTTTTTCAAGAAAGAA
66 CCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAA
* * * * * * *
5209193 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTCCAA-AATGAAATTTTAAAGTTGTGGAA
1 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAAATTTTAAAGTTGTTGAG
* * * *
5209257 CCTCTGCTGAAAGGAGCTTTTCCAA-AATGAAA
66 CCTCTGTTGAGAGGAGCTTTTTCAAGAAAG-AA
*
5209289 TTTTAAAGTGGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAA-AAATTTTAAAGTTGTTGAG
1 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAAATTTTAAAGTTGTTGAG
* * * *
5209353 CCTCTGCTGAGAGGAGCTTTTCCAA-ATGAGATT
66 CCTCTGTTGAGAGGAGCTTTTTCAAGA-AAGA-A
*
5209386 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAATAAATTTTAAAGTTGTTGAG
1 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAAATTTTAAAGTTGTTGAG
* * *
5209451 CCTCTGTTGAGAGGAGCTTTTCCAA-ATGAGATT
66 CCTCTGTTGAGAGGAGCTTTTTCAAGA-AAGA-A
*
5209484 TTTTAAAGTTATGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAG-AATTTTAAAGTTGTTGAG
1 TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAAATTTTAAAGTTGTTGAG
*
5209548 CCTCTGTTGAGAGGAGCTTTTTTAAGAAAGAA
66 CCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAA
*
5209580 TTTTTAAAGTTGTGGAACCTCTGTTGAGAGGAGCTTTTTCAAGAAA-AAATTTTAAAGTTGATTG
1 -TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAAATTTTAAAGTTG-TTG
* *
5209644 AGCCTCTGCTAAGAGGAGC
64 AGCCTCTGTTGAGAGGAGC
5209663 CCTTTTCTGT
Statistics
Matches: 772, Mismatches: 65, Indels: 32
0.89 0.07 0.04
Matches are distributed among these distances:
94 1 0.00
95 92 0.12
96 325 0.42
97 238 0.31
98 116 0.15
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.35
Consensus pattern (97 bp):
TTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAAATTTTAAAGTTGTTGAG
CCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAA
Found at i:5209839 original size:5 final size:5
Alignment explanation
Indices: 5209829--5209879 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
5209819 AATAATATTT
* * *
5209829 AACAA AACAA AACAA AAAAA GAAAAA AATAA AACAGA AA-AA AACAA AACAA
1 AACAA AACAA AACAA AACAA -AACAA AACAA AACA-A AACAA AACAA AACAA
5209880 GTAAACAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
4 3 0.08
5 29 0.73
6 8 0.20
ACGTcount: A:0.82, C:0.12, G:0.04, T:0.02
Consensus pattern (5 bp):
AACAA
Found at i:5209853 original size:8 final size:8
Alignment explanation
Indices: 5209837--5209900 Score: 51
Period size: 8 Copynumber: 8.0 Consensus size: 8
5209827 TTAACAAAAC
*
5209837 AAAACAAA
1 AAAAGAAA
5209845 AAAAGAAA
1 AAAAGAAA
*
5209853 AAAA-TAA
1 AAAAGAAA
*
5209860 AACAGAAA
1 AAAAGAAA
*
5209868 AAAACAAA
1 AAAAGAAA
*
5209876 ACAAGTAAA
1 AAAAG-AAA
5209885 CAAAA-AAA
1 -AAAAGAAA
5209893 AAAAGAAA
1 AAAAGAAA
5209901 GAAGTCAAGG
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
7 9 0.21
8 28 0.65
9 3 0.07
10 3 0.07
ACGTcount: A:0.83, C:0.08, G:0.06, T:0.03
Consensus pattern (8 bp):
AAAAGAAA
Found at i:5209876 original size:23 final size:23
Alignment explanation
Indices: 5209842--5209894 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
5209832 AAAACAAAAC
* *
5209842 AAAAAAAGAAAA-AAATAAAACAG
1 AAAAAAACAAAACAAAT-AAACAA
*
5209865 AAAAAAACAAAACAAGTAAACAA
1 AAAAAAACAAAACAAATAAACAA
5209888 AAAAAAA
1 AAAAAAA
5209895 AAGAAAGAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.83, C:0.08, G:0.06, T:0.04
Consensus pattern (23 bp):
AAAAAAACAAAACAAATAAACAA
Found at i:5210167 original size:33 final size:31
Alignment explanation
Indices: 5210098--5210167 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 31
5210088 AAAAAAAGAA
*
5210098 AAAAAAATTTTTCATGTGAGAGTTCTGAAAC
1 AAAAAAATTTTTCATGTGAGAGTTCAGAAAC
*
5210129 AAAAAAATTTTTCCA-GCTTGAGAGTTCAGGAAC
1 AAAAAAATTTTT-CATG--TGAGAGTTCAGAAAC
*
5210162 GAAAAA
1 AAAAAA
5210168 TTTCGATCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 13 0.39
32 2 0.06
33 18 0.55
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.27
Consensus pattern (31 bp):
AAAAAAATTTTTCATGTGAGAGTTCAGAAAC
Found at i:5211424 original size:16 final size:16
Alignment explanation
Indices: 5211367--5211424 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
5211357 AAACCCTTAA
5211367 AAATCCAAAATCCATT-
1 AAATCCAAAATCC-TTG
* *
5211383 AAATCCAAAACCGCTCG
1 AAATCCAAAATC-CTTG
5211400 AAATCCAAAATCCTTG
1 AAATCCAAAATCCTTG
*
5211416 AAGTCCAAA
1 AAATCCAAA
5211425 GTCCGAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 23 0.66
17 12 0.34
ACGTcount: A:0.47, C:0.28, G:0.07, T:0.19
Consensus pattern (16 bp):
AAATCCAAAATCCTTG
Found at i:5211709 original size:141 final size:142
Alignment explanation
Indices: 5211553--5211835 Score: 523
Period size: 142 Copynumber: 2.0 Consensus size: 142
5211543 TCATAATTCA
*
5211553 TATTAATAATAAGATTAATAAAT-AAAAAGTATAATAAAATTGAGATTTTAAATATAAACAGTCG
1 TATTAATAATAAGATTAATAAATAAAAAAGTATAATAAAATTGAGATCTTAAATATAAACAGTCG
*
5211617 CACCTCAGCTCTGCCTAGATGTTGGAGAGTCAGGGTGGTCTCATTATATTTAAGAATCCAACTCT
66 CACCTAAGCTCTGCCTAGATGTTGGAGAGTCAGGGTGGTCTCATTATATTTAAGAATCCAACTCT
5211682 TAAATTGCATTT
131 TAAATTGCATTT
*
5211694 TATTAATAATAAGATTAATAAATAAAAAAGTATAATAAAATTGGGATCTTAAATATAAACAGTCG
1 TATTAATAATAAGATTAATAAATAAAAAAGTATAATAAAATTGAGATCTTAAATATAAACAGTCG
*
5211759 CACCTAAGCTCTGCCTAGATGTTGGAGAGTCGGGGTGGTCTCATTATATTTAAGAATCCAACTCT
66 CACCTAAGCTCTGCCTAGATGTTGGAGAGTCAGGGTGGTCTCATTATATTTAAGAATCCAACTCT
5211824 TAAATTGCATTT
131 TAAATTGCATTT
5211836 CATTTTACAT
Statistics
Matches: 137, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
141 23 0.17
142 114 0.83
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.33
Consensus pattern (142 bp):
TATTAATAATAAGATTAATAAATAAAAAAGTATAATAAAATTGAGATCTTAAATATAAACAGTCG
CACCTAAGCTCTGCCTAGATGTTGGAGAGTCAGGGTGGTCTCATTATATTTAAGAATCCAACTCT
TAAATTGCATTT
Found at i:5212553 original size:35 final size:35
Alignment explanation
Indices: 5212509--5212580 Score: 83
Period size: 35 Copynumber: 2.1 Consensus size: 35
5212499 ATTTATTCTC
* * *
5212509 TTGATTCACGGTTTAATCCC-GATCATTGCTATTTT
1 TTGAATCACGATTCAATCCCAG-TCATTGCTATTTT
**
5212544 TTGAATCACGATTCAATCCCAGTCATTTTTATTTT
1 TTGAATCACGATTCAATCCCAGTCATTGCTATTTT
5212579 TT
1 TT
5212581 ACTTGTGGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 30 0.97
36 1 0.03
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.47
Consensus pattern (35 bp):
TTGAATCACGATTCAATCCCAGTCATTGCTATTTT
Found at i:5212885 original size:102 final size:102
Alignment explanation
Indices: 5212761--5212993 Score: 326
Period size: 102 Copynumber: 2.3 Consensus size: 102
5212751 AATTTCAGTC
* * * *
5212761 ATTTTTA-TTTTTAAATTATGATTCAATCTCGATCTTTTTAATTCTAAATCACAATTTAATCCCA
1 ATTTTTATTTTTTGACTTGTGATTCAATCCCGATCTTTTTAATTCTAAATCACAATTTAATCCCA
* *
5212825 ATCGTTGCTATTCTCTGACTCACGGCTTAATCCTGAT
66 ATCGTTACTATTCTCTGACTCACAGCTTAATCCTGAT
* * *
5212862 CTTTTTATTTTTTGACTTGTGATTCAATCCCTATCTTTTTAATTCTAAATCACGATTTAATCCCA
1 ATTTTTATTTTTTGACTTGTGATTCAATCCCGATCTTTTTAATTCTAAATCACAATTTAATCCCA
* ** *
5212927 ATTGTTACTATTCTCTGACTCGTAGTTTAATCCTGAT
66 ATCGTTACTATTCTCTGACTCACAGCTTAATCCTGAT
*
5212964 ATTTTTATTTTTTGACTTG-GGTTCAATCCC
1 ATTTTTATTTTTTGACTTGTGATTCAATCCC
5212994 TATCGTCTTT
Statistics
Matches: 116, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 16 0.14
102 100 0.86
ACGTcount: A:0.24, C:0.19, G:0.09, T:0.47
Consensus pattern (102 bp):
ATTTTTATTTTTTGACTTGTGATTCAATCCCGATCTTTTTAATTCTAAATCACAATTTAATCCCA
ATCGTTACTATTCTCTGACTCACAGCTTAATCCTGAT
Found at i:5213037 original size:34 final size:34
Alignment explanation
Indices: 5212967--5213038 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
5212957 TCCTGATATT
* * *
5212967 TTTATTTTTTGACTTGGGTTCAATCCCTATCGTC
1 TTTATTTTTTGACTCGGATTCAATCCCGATCGTC
**
5213001 TTTATTTTTTGACTCGCGATTCAATTTCGATC-TC
1 TTTATTTTTTGACTCG-GATTCAATCCCGATCGTC
5213035 TTTA
1 TTTA
5213039 ATTCTAAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
34 21 0.66
35 11 0.34
ACGTcount: A:0.17, C:0.19, G:0.12, T:0.51
Consensus pattern (34 bp):
TTTATTTTTTGACTCGGATTCAATCCCGATCGTC
Found at i:5213107 original size:136 final size:136
Alignment explanation
Indices: 5212865--5213117 Score: 319
Period size: 136 Copynumber: 1.9 Consensus size: 136
5212855 TCCTGATCTT
* * * * *
5212865 TTTATTTTTTGACTTGTGATTCAATCCCTATCTTTTTAATTCTAAATCACGATTTAATCCCAATT
1 TTTATTTTTTGACTCGCGATTCAATCCCGATCTCTTTAATTCTAAATCACGATTTAATCCCAATC
* * * *
5212930 GTTACTATTCTCTGACTCGTAGTTTAATCCTGATATTTTTATTTTTTGACTTGGGTTCAATCCCT
66 GTCACTATTCTCTGACTCGTAGTTTAATCCAGATATCTTTATTTTCTGACTTGGGTTCAATCCCT
5212995 ATCGTC
131 ATCGTC
** * * **
5213001 TTTATTTTTTGACTCGCGATTCAATTTCGATCTCTTTAATTCTAAATCATGGTTTAATCCTGATC
1 TTTATTTTTTGACTCGCGATTCAATCCCGATCTCTTTAATTCTAAATCACGATTTAATCCCAATC
** * *
5213066 GTCGTTATTCTTTGACTCGTAGTTTAATCACAG-TCTCTTTATTTTCTGACTT
66 GTCACTATTCTCTGACTCGTAGTTTAATC-CAGATATCTTTATTTTCTGACTT
5213118 ATCATTCAAT
Statistics
Matches: 97, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
136 95 0.98
137 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.11, T:0.49
Consensus pattern (136 bp):
TTTATTTTTTGACTCGCGATTCAATCCCGATCTCTTTAATTCTAAATCACGATTTAATCCCAATC
GTCACTATTCTCTGACTCGTAGTTTAATCCAGATATCTTTATTTTCTGACTTGGGTTCAATCCCT
ATCGTC
Found at i:5213229 original size:34 final size:34
Alignment explanation
Indices: 5213157--5213231 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
5213147 TTACTCGTGG
* *
5213157 TTTAATCTCGGTCTCATTATTTTTTGACTCGCAG
1 TTTAATCTCGGTCTCATTATTTTTTGACTCACAA
* * * *
5213191 TTTAATTTTGGTCTCTTTATTTTTTGACTTACAA
1 TTTAATCTCGGTCTCATTATTTTTTGACTCACAA
5213225 TTTAATC
1 TTTAATC
5213232 CCAATCGTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.20, C:0.16, G:0.11, T:0.53
Consensus pattern (34 bp):
TTTAATCTCGGTCTCATTATTTTTTGACTCACAA
Found at i:5213279 original size:34 final size:34
Alignment explanation
Indices: 5213202--5213283 Score: 92
Period size: 35 Copynumber: 2.4 Consensus size: 34
5213192 TTAATTTTGG
** * *
5213202 TCTCTTTATTTTTTGACTTACAATTTAATCCCAA
1 TCTCTTTATTTTTCAACTCACAATTTAACCCCAA
* **
5213236 TCGTTTTTATTTTTCAACTCACGGTTTAACCCCAA
1 TC-TCTTTATTTTTCAACTCACAATTTAACCCCAA
5213271 TCTCTTTATTTTT
1 TCTCTTTATTTTT
5213284 AAGATGCAGT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
34 12 0.31
35 27 0.69
ACGTcount: A:0.22, C:0.22, G:0.05, T:0.51
Consensus pattern (34 bp):
TCTCTTTATTTTTCAACTCACAATTTAACCCCAA
Found at i:5213414 original size:34 final size:35
Alignment explanation
Indices: 5213339--5213491 Score: 93
Period size: 35 Copynumber: 4.5 Consensus size: 35
5213329 TTAATTCGTC
*
5213339 TCTTTATTTTTTAACTCGTGATTTAATCCTGATCA
1 TCTTTATTTTTTAACTCGTGATTCAATCCTGATCA
* *
5213374 TTTTTATTTTTTGACTCGT-AGTTCAAT-CTCGAT-A
1 TCTTTATTTTTTAACTCGTGA-TTCAATCCT-GATCA
* * * * * **
5213408 TCTTTA-TTTCTAAGTCGCGGTTTAATCCCAATCA
1 TCTTTATTTTTTAACTCGTGATTCAATCCTGATCA
* * * * * *
5213442 TCATTATTTTCTAACTTGCGATTTAAT-CTCGGTC-
1 TCTTTATTTTTTAACTCGTGATTCAATCCT-GATCA
5213476 TCTTTATTTTTTAACT
1 TCTTTATTTTTTAACT
5213492 TGTAGTTTAA
Statistics
Matches: 90, Mismatches: 21, Indels: 15
0.71 0.17 0.12
Matches are distributed among these distances:
33 15 0.17
34 31 0.34
35 44 0.49
ACGTcount: A:0.22, C:0.18, G:0.10, T:0.50
Consensus pattern (35 bp):
TCTTTATTTTTTAACTCGTGATTCAATCCTGATCA
Found at i:5213492 original size:34 final size:34
Alignment explanation
Indices: 5213329--5213560 Score: 118
Period size: 34 Copynumber: 6.8 Consensus size: 34
5213319 GACCCGTAGA
* *
5213329 TTAAT-TCG-TCTCTTTATTTTTTAACTCGTGAT
1 TTAATCTCGATCTCTTTATTTTTTAACTTGCGAT
* *
5213361 TTAATC-CTGATCATTTTTATTTTTTGAC-T-CGTAGT
1 TTAATCTC-GATC-TCTTTATTTTTTAACTTGCG-A-T
* * * * * *
5213396 TCAATCTCGATATCTTTA-TTTCTAAGTCGCGGT
1 TTAATCTCGATCTCTTTATTTTTTAACTTGCGAT
* * * *
5213429 TTAATCCCAATCATCATTATTTTCTAACTTGCGAT
1 TTAATCTCGATC-TCTTTATTTTTTAACTTGCGAT
* *
5213464 TTAATCTCGGTCTCTTTATTTTTTAACTTG-TAGT
1 TTAATCTCGATCTCTTTATTTTTTAACTTGCGA-T
* * ***** * * *
5213498 TTAATTTCGATCTCGTTATCCACCAACTCGTGGT
1 TTAATCTCGATCTCTTTATTTTTTAACTTGCGAT
5213532 TTAATCTCGATCGTCTTTATTTTTTAACT
1 TTAATCTCGATC-TCTTTATTTTTTAACT
5213561 CATGGTAACA
Statistics
Matches: 142, Mismatches: 44, Indels: 25
0.67 0.21 0.12
Matches are distributed among these distances:
32 6 0.04
33 17 0.12
34 63 0.44
35 55 0.39
36 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.11, T:0.49
Consensus pattern (34 bp):
TTAATCTCGATCTCTTTATTTTTTAACTTGCGAT
Found at i:5215008 original size:14 final size:16
Alignment explanation
Indices: 5214989--5215023 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
5214979 TAAAAAAAAA
5214989 TTTTT-TTTCATTATT
1 TTTTTCTTTCATTATT
5215004 TTTTTCCTTTCATTATT
1 TTTTT-CTTTCATTATT
5215021 TTT
1 TTT
5215024 GTATATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
17 13 0.72
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTCTTTCATTATT
Found at i:5215557 original size:13 final size:13
Alignment explanation
Indices: 5215539--5215563 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5215529 CTTTACCTTT
5215539 CAAATCCTAAAAG
1 CAAATCCTAAAAG
5215552 CAAATCCTAAAA
1 CAAATCCTAAAA
5215564 CTTTTAAACC
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:0.56, C:0.24, G:0.04, T:0.16
Consensus pattern (13 bp):
CAAATCCTAAAAG
Found at i:5215599 original size:13 final size:13
Alignment explanation
Indices: 5215569--5215607 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
5215559 TAAAACTTTT
*
5215569 AAACCCTAAAATCA
1 AAACCCT-AAATTA
*
5215583 AAACCCTAAATTG
1 AAACCCTAAATTA
5215596 AAACCCTAAATT
1 AAACCCTAAATT
5215608 CTCTAAACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 16 0.70
14 7 0.30
ACGTcount: A:0.51, C:0.26, G:0.03, T:0.21
Consensus pattern (13 bp):
AAACCCTAAATTA
Found at i:5217396 original size:20 final size:20
Alignment explanation
Indices: 5217371--5217411 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
5217361 TTCATTAGAA
*
5217371 TTACTGACATGATTATTAAT
1 TTACTGACATGATTATCAAT
5217391 TTACTGACATGATTATCAAT
1 TTACTGACATGATTATCAAT
5217411 T
1 T
5217412 GATTTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (20 bp):
TTACTGACATGATTATCAAT
Found at i:5217604 original size:28 final size:29
Alignment explanation
Indices: 5217564--5217622 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
5217554 CTTTATCTCT
*
5217564 CTAATTATTAACTG-AAAAGATTAAATAA
1 CTAATTATTAACTGAAAAAAATTAAATAA
5217592 CTAATTATTAACTGAAAAAAATTAAATAA
1 CTAATTATTAACTGAAAAAAATTAAATAA
5217621 CT
1 CT
5217623 CTGCAATTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.32
Consensus pattern (29 bp):
CTAATTATTAACTGAAAAAAATTAAATAA
Found at i:5220104 original size:29 final size:29
Alignment explanation
Indices: 5220072--5220138 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 29
5220062 CACTTTTAGG
* * *
5220072 TAAATTTTAATATTT-TTATTATATTCAAA
1 TAAATTTTAATCTTTGAT-TTACATTCAAA
*
5220101 TAAATTATTAATCTTTGATTTACATTTAAA
1 TAAATT-TTAATCTTTGATTTACATTCAAA
5220131 TAAATTTT
1 TAAATTTT
5220139 TTAAATTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 8 0.25
30 23 0.72
31 1 0.03
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.54
Consensus pattern (29 bp):
TAAATTTTAATCTTTGATTTACATTCAAA
Found at i:5222169 original size:5 final size:5
Alignment explanation
Indices: 5222138--5222194 Score: 55
Period size: 5 Copynumber: 11.4 Consensus size: 5
5222128 CTCACCTTTC
* * *
5222138 TTTTC TTTTC TTTTC TTTTG -TTT- TTTTG TTTTG TTTTG TTTTG TTGTTG
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TT-TTG
5222187 TTGTTG TT
1 TT-TTG TT
5222195 GTTGGTTTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
4 6 0.12
5 31 0.65
6 11 0.23
ACGTcount: A:0.00, C:0.05, G:0.16, T:0.79
Consensus pattern (5 bp):
TTTTG
Found at i:5222186 original size:3 final size:3
Alignment explanation
Indices: 5222163--5222198 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
5222153 TTTTGTTTTT
5222163 TTG TT- TTG TT- TTG TT- TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
5222199 GTTTTTTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
2 6 0.20
3 24 0.80
ACGTcount: A:0.00, C:0.00, G:0.28, T:0.72
Consensus pattern (3 bp):
TTG
Found at i:5228448 original size:27 final size:27
Alignment explanation
Indices: 5228416--5228488 Score: 76
Period size: 28 Copynumber: 2.7 Consensus size: 27
5228406 AAGTATAATA
* *
5228416 AAATATTTAATTTAATATTTTAATTTT
1 AAATATTTAATTTAATATTTAAATTAT
* *
5228443 AAATATTTAAATATAATACTTAAATTAT
1 AAATATTT-AATTTAATATTTAAATTAT
*
5228471 AAATTTATTAA-TTAATAT
1 AAATAT-TTAATTTAATAT
5228489 AATATTTAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
27 13 0.35
28 22 0.59
29 2 0.05
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (27 bp):
AAATATTTAATTTAATATTTAAATTAT
Found at i:5228569 original size:28 final size:29
Alignment explanation
Indices: 5228523--5228609 Score: 88
Period size: 28 Copynumber: 3.0 Consensus size: 29
5228513 TCATATGTTG
*
5228523 TATCACATTAATAAA-TTTATAATTTAAA
1 TATCATATTAATAAATTTTATAATTTAAA
* **
5228551 TATCATATTAA-AAATTTTAAAATCCAAA
1 TATCATATTAATAAATTTTATAATTTAAA
**
5228579 TATCATATCTAATATTTTATTATAATTTAAA
1 TATCATAT-TAATAAATT-TTATAATTTAAA
5228610 AATAATTCAT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
27 3 0.07
28 28 0.61
29 3 0.07
30 3 0.07
31 9 0.20
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (29 bp):
TATCATATTAATAAATTTTATAATTTAAA
Found at i:5229687 original size:16 final size:16
Alignment explanation
Indices: 5229666--5229699 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
5229656 CCACCTGTAT
5229666 GGAGTCGATGACAGAC
1 GGAGTCGATGACAGAC
5229682 GGAGTCGATGACAGAC
1 GGAGTCGATGACAGAC
5229698 GG
1 GG
5229700 CTTATAGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.18, G:0.41, T:0.12
Consensus pattern (16 bp):
GGAGTCGATGACAGAC
Found at i:5235144 original size:19 final size:20
Alignment explanation
Indices: 5235107--5235147 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5235097 AAATTTTAAA
*
5235107 TTATTTAATATTTATAAAAT
1 TTATTTAATATATATAAAAT
*
5235127 TTATTTATTATATA-AAAAT
1 TTATTTAATATATATAAAAT
5235146 TT
1 TT
5235148 CTAATAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATTTAATATATATAAAAT
Found at i:5236050 original size:40 final size:40
Alignment explanation
Indices: 5235995--5236073 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
5235985 ATCGCACAAA
*
5235995 TTTAAAATTTGAGTCTCGACCCGTAACAACTGCACCTCAC
1 TTTAAAATTTAAGTCTCGACCCGTAACAACTGCACCTCAC
5236035 TTTAAAATTTAAGTCTCGACCCGTAACAACTGCACCTCA
1 TTTAAAATTTAAGTCTCGACCCGTAACAACTGCACCTCA
5236074 GTGGTGCTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.32, C:0.29, G:0.11, T:0.28
Consensus pattern (40 bp):
TTTAAAATTTAAGTCTCGACCCGTAACAACTGCACCTCAC
Found at i:5237830 original size:18 final size:18
Alignment explanation
Indices: 5237802--5237846 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
5237792 AATCAAACCG
*
5237802 AATTATATATATATTTTA
1 AATTTTATATATATTTTA
*
5237820 ATTTTTATATATATTTTA
1 AATTTTATATATATTTTA
5237838 AATTTTATA
1 AATTTTATA
5237847 AAATAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
AATTTTATATATATTTTA
Found at i:5243602 original size:16 final size:16
Alignment explanation
Indices: 5243576--5243617 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
5243566 GGGTTCAATT
*
5243576 AGGCTCATTTTAGTT-
1 AGGCCCATTTTAGTTC
*
5243591 ATGGCCCATTTTGGTTC
1 A-GGCCCATTTTAGTTC
5243608 AGGCCCATTT
1 AGGCCCATTT
5243618 AGATCTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 1 0.04
16 21 0.91
17 1 0.04
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.40
Consensus pattern (16 bp):
AGGCCCATTTTAGTTC
Found at i:5243644 original size:3 final size:3
Alignment explanation
Indices: 5243636--5243664 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5243626 TTAGATGCTT
5243636 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5243665 CATTTTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5244533 original size:8 final size:8
Alignment explanation
Indices: 5244520--5244567 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
5244510 AATTACAGGT
5244520 TTTTTTTA
1 TTTTTTTA
5244528 TTTTTTTA
1 TTTTTTTA
*
5244536 TTTTTTGA
1 TTTTTTTA
*
5244544 TTTTGTTTT
1 TTTT-TTTA
5244553 TTTGATTTTA
1 TTT--TTTTA
5244563 TTTTT
1 TTTTT
5244568 AACCTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
8 21 0.64
9 5 0.15
10 6 0.18
11 1 0.03
ACGTcount: A:0.10, C:0.00, G:0.06, T:0.83
Consensus pattern (8 bp):
TTTTTTTA
Found at i:5244547 original size:13 final size:13
Alignment explanation
Indices: 5244531--5244567 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
5244521 TTTTTTATTT
5244531 TTTTATTTTTTGA
1 TTTTATTTTTTGA
*
5244544 TTTTGTTTTTTTGA
1 TTTT-ATTTTTTGA
5244558 TTTTATTTTT
1 TTTTATTTTT
5244568 AACCTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.11, C:0.00, G:0.08, T:0.81
Consensus pattern (13 bp):
TTTTATTTTTTGA
Found at i:5244588 original size:13 final size:12
Alignment explanation
Indices: 5244519--5244603 Score: 55
Period size: 13 Copynumber: 6.6 Consensus size: 12
5244509 CAATTACAGG
5244519 TTTTTTTTATTT-
1 TTTTTTTT-TTTA
*
5244531 TTTTATTTTTTGA
1 TTTT-TTTTTTTA
5244544 TTTTGTTTTTTTGA
1 TTTT-TTTTTTT-A
* *
5244558 TTTTATTTTTAA
1 TTTTTTTTTTTA
*
5244570 CCTTTTTTTTGTTA
1 --TTTTTTTTTTTA
*
5244584 TTTTTTGGTTTTA
1 TTTTTT-TTTTTA
5244597 TTTTTTT
1 TTTTTTT
5244604 ATGGGAAGAT
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
12 13 0.23
13 29 0.52
14 14 0.25
ACGTcount: A:0.11, C:0.02, G:0.07, T:0.80
Consensus pattern (12 bp):
TTTTTTTTTTTA
Found at i:5255409 original size:13 final size:13
Alignment explanation
Indices: 5255393--5255417 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5255383 TAAAAAAAAA
5255393 AGAAAAAAATGAG
1 AGAAAAAAATGAG
5255406 AGAAAAAAATGA
1 AGAAAAAAATGA
5255418 TTTTCATGGC
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:0.72, C:0.00, G:0.20, T:0.08
Consensus pattern (13 bp):
AGAAAAAAATGAG
Found at i:5256184 original size:236 final size:235
Alignment explanation
Indices: 5255768--5256228 Score: 638
Period size: 236 Copynumber: 2.0 Consensus size: 235
5255758 TTATCCACCC
* * * * *
5255768 ACTTGATCTTGGCTCAGTTCAGATCATTTTTTATGATTCGTGATTTCATTTCGATGATTTATTTT
1 ACTTGATATTGGCTCAATTCAGATCATTTCTTATGATTCGTGATTTCATCTCGATCATTTATTTT
* * ** **
5255833 TACCTCAACTCGGTCTTGGTTGCCTCAGTTGACTCGTGATTTTGTCTCGGTCACTTGATCTTGAC
66 TACCTCAACTCGGTCTCGGTCGCCTCAGTTGACTCGTGATTCCGTCTCAATCACTTGATCTTGAC
* * * * * *
5255898 TCAGTCTAGATCATTTTTTATGATTCGTGGTTTCACCCTGATCATTTATTTTCGACCTCAACTTG
131 TCAATCCAAATAATTTCTTATGATTCATGGTTTCACCCTGATCATTTATTTTCGACCTCAACTTG
* *
5255963 GTCCTGGTTACTTCATTTGACTCTTGGTTTGGTCTTGATT
196 GTCCTGGTCACTTCATTTGACTCGTGGTTTGGTCTTGATT
5256003 ACTTGATATTGGCTCAATTCAGATCATTTCTTATGATTCGTGATTTCATCTCGATCATTTATTTT
1 ACTTGATATTGGCTCAATTCAGATCATTTCTTATGATTCGTGATTTCATCTCGATCATTTATTTT
* * *
5256068 TAACCTCGACTCGGTCTCGGTCGCCTTATTTGACAT-GTGATTCCGTC-CTAATCACTTGATCTT
66 T-ACCTCAACTCGGTCTCGGTCGCCTCAGTTGAC-TCGTGATTCCGTCTC-AATCACTTGATCTT
* * *
5256131 GACTCAATCCAAATAATTTCTTATGATTCATGGTTTCATCTTGATCATTTATTTTCGACCTTAAC
128 GACTCAATCCAAATAATTTCTTATGATTCATGGTTTCACCCTGATCATTTATTTTCGACCTCAAC
* *
5256196 TTGGTCCTTGTCACTTTATTTGACTCGTGGTTT
193 TTGGTCCTGGTCACTTCATTTGACTCGTGGTTT
5256229 AGTCCCGGTC
Statistics
Matches: 196, Mismatches: 27, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
235 62 0.32
236 133 0.68
237 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.45
Consensus pattern (235 bp):
ACTTGATATTGGCTCAATTCAGATCATTTCTTATGATTCGTGATTTCATCTCGATCATTTATTTT
TACCTCAACTCGGTCTCGGTCGCCTCAGTTGACTCGTGATTCCGTCTCAATCACTTGATCTTGAC
TCAATCCAAATAATTTCTTATGATTCATGGTTTCACCCTGATCATTTATTTTCGACCTCAACTTG
GTCCTGGTCACTTCATTTGACTCGTGGTTTGGTCTTGATT
Found at i:5256241 original size:118 final size:118
Alignment explanation
Indices: 5255767--5256249 Score: 434
Period size: 118 Copynumber: 4.1 Consensus size: 118
5255757 ATTATCCACC
* * * * * *
5255767 CACTTGATCTTGGCTCAGTTCAGATCATTTTTTATGATTCGTGATTTCAT-TTCGATGATTTATT
1 CACTTGATCTTGACTCAATCCAGATCATTTCTTATGATTCGTGGTTTCATCTT-GATCATTTATT
* * * ** * * * * * *
5255831 TT-TACCTCAACTCGGTCTTGGTTGCCTCAGTTGACTCGTGATTTTGTCTCGGT
65 TTCGACCTCAACTTGGTCCTGGTCACTTTATTTGACTCGTGATTTAGTCCCGAT
* * * * *
5255884 CACTTGATCTTGACTCAGTCTAGATCATTTTTTATGATTCGTGGTTTCACCCTGATCATTTATTT
1 CACTTGATCTTGACTCAATCCAGATCATTTCTTATGATTCGTGGTTTCATCTTGATCATTTATTT
* * * * * **
5255949 TCGACCTCAACTTGGTCCTGGTTACTTCATTTGACTCTTGGTTTGGTCTTGAT
66 TCGACCTCAACTTGGTCCTGGTCACTTTATTTGACTCGTGATTTAGTCCCGAT
* * * * * *
5256002 TACTTGATATTGGCTCAATTCAGATCATTTCTTATGATTCGTGATTTCATCTCGATCATTTATTT
1 CACTTGATCTTGACTCAATCCAGATCATTTCTTATGATTCGTGGTTTCATCTTGATCATTTATTT
** * * * * ** **
5256067 TTAACCTCGACTCGGT-CTCGGTCGCCTTATTTGACAT-GTGATTCCGTCCTAAT
66 TCGACCTCAACTTGGTCCT-GGTCACTTTATTTGAC-TCGTGATTTAGTCCCGAT
* * *
5256120 CACTTGATCTTGACTCAATCCAAATAATTTCTTATGATTCATGGTTTCATCTTGATCATTTATTT
1 CACTTGATCTTGACTCAATCCAGATCATTTCTTATGATTCGTGGTTTCATCTTGATCATTTATTT
* * * *
5256185 TCGACCTTAACTTGGTCCTTGTCACTTTATTTGACTCGTGGTTTAGTCCCGGT
66 TCGACCTCAACTTGGTCCTGGTCACTTTATTTGACTCGTGATTTAGTCCCGAT
*
5256238 CACTTGACCTTG
1 CACTTGATCTTG
5256250 GTTTAGTCCA
Statistics
Matches: 293, Mismatches: 67, Indels: 11
0.79 0.18 0.03
Matches are distributed among these distances:
117 60 0.20
118 230 0.78
119 3 0.01
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.44
Consensus pattern (118 bp):
CACTTGATCTTGACTCAATCCAGATCATTTCTTATGATTCGTGGTTTCATCTTGATCATTTATTT
TCGACCTCAACTTGGTCCTGGTCACTTTATTTGACTCGTGATTTAGTCCCGAT
Found at i:5257430 original size:19 final size:20
Alignment explanation
Indices: 5257402--5257442 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
5257392 CAATCGTAAG
5257402 TTTTACTTTTTCT-ATTTTAT
1 TTTTACTTTTT-TGATTTTAT
5257422 TTTTA-TTTTTTGATTTTAT
1 TTTTACTTTTTTGATTTTAT
5257441 TT
1 TT
5257443 GATTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 1 0.05
19 14 0.70
20 5 0.25
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTTACTTTTTTGATTTTAT
Found at i:5258192 original size:28 final size:29
Alignment explanation
Indices: 5258160--5258227 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
5258150 TACCATGTTA
*
5258160 ATTAATAAATTTATAA-TTC-AAATATCAT
1 ATTAA-AAATTTATAACATCAAAATATCAT
* *
5258188 ATTAAAAATTTTTAACATCAAAATATTAT
1 ATTAAAAATTTATAACATCAAAATATCAT
*
5258217 ATTAAACATTT
1 ATTAAAAATTT
5258228 CATTATAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 9 0.26
28 7 0.21
29 18 0.53
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (29 bp):
ATTAAAAATTTATAACATCAAAATATCAT
Found at i:5262163 original size:18 final size:17
Alignment explanation
Indices: 5262142--5262185 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
5262132 TTCTTTTGCT
*
5262142 TTTTATTTTCTATTTTGA
1 TTTTATTTT-TATGTTGA
5262160 TTTTGATTTTTATGTTGA
1 TTTT-ATTTTTATGTTGA
5262178 TTTT-TTTT
1 TTTTATTTT
5262186 ATTTTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 4 0.17
18 15 0.62
19 5 0.21
ACGTcount: A:0.14, C:0.02, G:0.09, T:0.75
Consensus pattern (17 bp):
TTTTATTTTTATGTTGA
Found at i:5273695 original size:40 final size:38
Alignment explanation
Indices: 5273642--5274058 Score: 262
Period size: 40 Copynumber: 10.4 Consensus size: 38
5273632 CCTCTCAGCT
* * *
5273642 TTTTGAATTTAAAGTTCGTTACCTCTTGTCAAAGGAGCC
1 TTTTAAATTTAAAGTTCGTTGCCT-TTGTGAAAGGAGCC
* * * *
5273681 TTTTAACATTTAAAGTTTGTTGCCTTTGGTTAAATGAGCT
1 TTTTAA-ATTTAAAGTTCGTTGCCTTT-GTGAAAGGAGCC
* **
5273721 TTTTAATATTTAAAGTTTGTTGCCTTTGATGGTAGTGCAGCAC
1 TTTTAA-ATTTAAAGTTCGTTGCCTTTG-TGAAAG-G-AGC-C
* * *
5273764 TTTTGAATTTAAAGTTCGTTGCCTCTAGTGAGAGGAGCC
1 TTTTAAATTTAAAGTTCGTTGCCT-TTGTGAAAGGAGCC
* * * * *
5273803 TTTTAATATTTAAAGTTTGTTACCTTTAGTTAAAAGAGCA
1 TTTTAA-ATTTAAAGTTCGTTGCCTTT-GTGAAAGGAGCC
* * * * *
5273843 TTGTTGAATTTAAAGTTCATTGCCTCTGGTGAGAA-TAACC
1 TT-TTAAATTTAAAGTTCGTTGCCT-TTGTGA-AAGGAGCC
* * * *
5273883 TTTTAATATTTAAAGTTTGTTGCCTTTAGTTAAAAGAGCAT
1 TTTTAA-ATTTAAAGTTCGTTGCCTTT-GTGAAAGGAGC-C
* * * *
5273924 TTTTGAATTTAAAGTTCGTTACCTCTGGTGAGAA-TAGCC
1 TTTTAAATTTAAAGTTCGTTGCCT-TTGTGA-AAGGAGCC
* * *
5273963 TTTTAATATTTAAAGTTTGTTGCCTTTGGTTAAATGAGCTC
1 TTTTAA-ATTTAAAGTTCGTTGCCTTT-GTGAAAGGAGC-C
* * **
5274004 TTTTGAATTTAAAGTTCGTTGCCTTTGATCAAAGGAGTT
1 TTTTAAATTTAAAGTTCGTTGCCTTTG-TGAAAGGAGCC
*
5274043 TTTTTAATTTAAAGTT
1 TTTTAAATTTAAAGTT
5274059 TCATAGCTTC
Statistics
Matches: 293, Mismatches: 62, Indels: 46
0.73 0.15 0.11
Matches are distributed among these distances:
39 45 0.15
40 195 0.67
41 22 0.08
42 24 0.08
43 7 0.02
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (38 bp):
TTTTAAATTTAAAGTTCGTTGCCTTTGTGAAAGGAGCC
Found at i:5273875 original size:80 final size:79
Alignment explanation
Indices: 5273648--5274027 Score: 433
Period size: 80 Copynumber: 4.7 Consensus size: 79
5273638 AGCTTTTTGA
* * * * * * * * *
5273648 ATTTAAAGTTCGTTACCTCTT-GTCAAAGGAGCCTTTTAACATTTAAAGTTTGTTGCCTTTGGTT
1 ATTTAAAGTTTGTTGCCT-TTAGTTAAAAGAGCATTTTGA-ATTTAAAGTTCGTTGCCTCTGGTG
*
5273712 A-AATGAGCTTTTTAAT
64 AGAA-GAGCCTTTTAAT
* ** *
5273728 ATTTAAAGTTTGTTGCCTTTGATGGT-AGTGCAGCACTTTTGAATTTAAAGTTCGTTGCCTCTAG
1 ATTTAAAGTTTGTTGCCTTT-A-GTTAAAAG-AGCA-TTTTGAATTTAAAGTTCGTTGCCTCTGG
*
5273792 TGAGAGGAGCCTTTTAAT
62 TGAGAAGAGCCTTTTAAT
* *
5273810 ATTTAAAGTTTGTTACCTTTAGTTAAAAGAGCATTGTTGAATTTAAAGTTCATTGCCTCTGGTGA
1 ATTTAAAGTTTGTTGCCTTTAGTTAAAAGAGCATT-TTGAATTTAAAGTTCGTTGCCTCTGGTGA
* *
5273875 GAATAACCTTTTAAT
65 GAAGAGCCTTTTAAT
*
5273890 ATTTAAAGTTTGTTGCCTTTAGTTAAAAGAGCATTTTTGAATTTAAAGTTCGTTACCTCTGGTGA
1 ATTTAAAGTTTGTTGCCTTTAGTTAAAAGAGCA-TTTTGAATTTAAAGTTCGTTGCCTCTGGTGA
*
5273955 GAATAGCCTTTTAAT
65 GAAGAGCCTTTTAAT
* * *
5273970 ATTTAAAGTTTGTTGCCTTTGGTTAAATGAGCTCTTTTGAATTTAAAGTTCGTTGCCT
1 ATTTAAAGTTTGTTGCCTTTAGTTAAAAGAGC-ATTTTGAATTTAAAGTTCGTTGCCT
5274028 TTGATCAAAG
Statistics
Matches: 259, Mismatches: 31, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
79 4 0.02
80 187 0.72
81 7 0.03
82 55 0.21
83 6 0.02
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (79 bp):
ATTTAAAGTTTGTTGCCTTTAGTTAAAAGAGCATTTTGAATTTAAAGTTCGTTGCCTCTGGTGAG
AAGAGCCTTTTAAT
Found at i:5274269 original size:12 final size:12
Alignment explanation
Indices: 5274249--5274284 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
5274239 AACTATTTTT
5274249 TTATATATTAATA
1 TTAT-TATTAATA
*
5274262 TTATTATTGATA
1 TTATTATTAATA
5274274 TTATTATTAAT
1 TTATTATTAAT
5274285 TTTTTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:5275110 original size:12 final size:11
Alignment explanation
Indices: 5275095--5275168 Score: 57
Period size: 10 Copynumber: 6.8 Consensus size: 11
5275085 AGGTTTTCCC
*
5275095 TTTTATTTTCTA
1 TTTTATTTT-GA
5275107 TTTTAATTTTGA
1 TTTT-ATTTTGA
5275119 TTTTA-TTT-A
1 TTTTATTTTGA
* *
5275128 TTTTGTGTTGA
1 TTTTATTTTGA
*
5275139 TTTTTATGTTGA
1 -TTTTATTTTGA
5275151 -TTTATTTT-A
1 TTTTATTTTGA
5275160 TTTTATTTT
1 TTTTATTTT
5275169 TTCATGATAT
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
9 6 0.12
10 20 0.38
11 2 0.04
12 19 0.37
13 5 0.10
ACGTcount: A:0.18, C:0.01, G:0.08, T:0.73
Consensus pattern (11 bp):
TTTTATTTTGA
Found at i:5275404 original size:16 final size:17
Alignment explanation
Indices: 5275382--5275424 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
5275372 ATTTTATTAC
5275382 AAAAAATAAAT-AATAA
1 AAAAAATAAATAAATAA
* *
5275398 GAAAAAT-GATAAATAA
1 AAAAAATAAATAAATAA
5275414 AAAAAATAAAT
1 AAAAAATAAAT
5275425 TATTTAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
15 2 0.10
16 17 0.81
17 2 0.10
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.19
Consensus pattern (17 bp):
AAAAAATAAATAAATAA
Found at i:5280143 original size:15 final size:16
Alignment explanation
Indices: 5280123--5280154 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
5280113 TCATTTTCTA
5280123 TTAAGTACAAAA-ATG
1 TTAAGTACAAAAGATG
5280138 TTAAGTACAAAAGATG
1 TTAAGTACAAAAGATG
5280154 T
1 T
5280155 CAGACAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (16 bp):
TTAAGTACAAAAGATG
Found at i:5290246 original size:18 final size:18
Alignment explanation
Indices: 5290223--5290261 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5290213 GAAACGAGAT
*
5290223 AACCAACTGTAACCAACC
1 AACCAACCGTAACCAACC
*
5290241 AACCAACCGTAACCGACC
1 AACCAACCGTAACCAACC
5290259 AAC
1 AAC
5290262 TTAAGTCAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.44, C:0.41, G:0.08, T:0.08
Consensus pattern (18 bp):
AACCAACCGTAACCAACC
Found at i:5292221 original size:50 final size:50
Alignment explanation
Indices: 5292162--5292261 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
5292152 TGGTTGGCTT
*
5292162 CAGATCCTAATGCAATTATCAGAATGGTCAGCATAAGACTATAAGTTTGA
1 CAGATCCTAATGCAATTATCAGAATGATCAGCATAAGACTATAAGTTTGA
5292212 CAGATCCTAATGCAATTATCAGAATGATCAGCATAAGACTATAAGTTTGA
1 CAGATCCTAATGCAATTATCAGAATGATCAGCATAAGACTATAAGTTTGA
5292262 ACATATCATA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (50 bp):
CAGATCCTAATGCAATTATCAGAATGATCAGCATAAGACTATAAGTTTGA
Found at i:5308068 original size:26 final size:26
Alignment explanation
Indices: 5308039--5308101 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
5308029 GATTGATTTG
*
5308039 GTGGCTAGTCTAGTTTGGTCACAAGC
1 GTGGCTAGTCTAGTTTGATCACAAGC
5308065 GTGGCTAGTCTAGTTTGATCACAAGC
1 GTGGCTAGTCTAGTTTGATCACAAGC
5308091 GTGGCTAGTCT
1 GTGGCTAGTCT
5308102 GATGGGACTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.32
Consensus pattern (26 bp):
GTGGCTAGTCTAGTTTGATCACAAGC
Found at i:5308377 original size:28 final size:28
Alignment explanation
Indices: 5308310--5308377 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
5308300 GAATCAGATT
* *
5308310 AGGCCTAAAACCTAGTTGAATCAAAATC
1 AGGCTTAAAGCCTAGTTGAATCAAAATC
* ** *
5308338 AAGCTTGGAGCCTAGTTGAGTCAAAATC
1 AGGCTTAAAGCCTAGTTGAATCAAAATC
5308366 AGGCTTAAAGCC
1 AGGCTTAAAGCC
5308378 CAGTCAAATC
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (28 bp):
AGGCTTAAAGCCTAGTTGAATCAAAATC
Found at i:5308838 original size:35 final size:35
Alignment explanation
Indices: 5308797--5308936 Score: 122
Period size: 35 Copynumber: 4.0 Consensus size: 35
5308787 AAGTCAAAAA
* *
5308797 AATAATGAGGATCGGGGATGAACCGCAAGTCAAGG
1 AATAATGAAGATCGGGGATGAACCACAAGTCAAGG
* * * *
5308832 AATAATGATGATTGGGGATGAATCATAAGTCAAGAG
1 AATAATGAAGATCGGGGATGAACCACAAGTCAAG-G
* * * * *
5308868 GATAAAGACGATC-GTGATTAAACCACAAGTCAAGG
1 AATAATGAAGATCGGGGA-TGAACCACAAGTCAAGG
* *
5308903 AATAATGAAGA-CTGGGAAAGAACCACAAGTCAAG
1 AATAATGAAGATC-GGGGATGAACCACAAGTCAAG
5308937 AGGATAAAGA
Statistics
Matches: 81, Mismatches: 20, Indels: 8
0.74 0.18 0.07
Matches are distributed among these distances:
34 1 0.01
35 55 0.68
36 25 0.31
ACGTcount: A:0.43, C:0.13, G:0.27, T:0.17
Consensus pattern (35 bp):
AATAATGAAGATCGGGGATGAACCACAAGTCAAGG
Found at i:5309037 original size:71 final size:70
Alignment explanation
Indices: 5308828--5309119 Score: 260
Period size: 71 Copynumber: 4.1 Consensus size: 70
5308818 ACCGCAAGTC
* * *
5308828 AAGGAATAATGATGATTGGGGATGAATCATAAGTCAAGAGGATAAAGACGATCGTGATTAAACCA
1 AAGGAATAATGATGATT-GGGATGAACCACAAGTCAAGAGGATAAAGACGATCGAGATTAAACCA
* *
5308893 CAAGTC
65 CGAGTT
* * * *
5308899 AAGGAATAATGAAGACTGGGAAAGAACCACAAGTCAAGAGGATAAAGACGATCGAGATTAAATCA
1 AAGGAATAATGATGATTGGG-ATGAACCACAAGTCAAGAGGATAAAGACGATCGAGATTAAACCA
5308964 CGAGTT
65 CGAGTT
* * * * * * *
5308970 AAGGAATAATGATGATTAAGGATGAACCGCAAGTTAAAAGGATAAAGATGACCGAGACTAAACCA
1 AAGGAATAATGATGATT-GGGATGAACCACAAGTCAAGAGGATAAAGACGATCGAGATTAAACCA
5309035 CGAGTT
65 CGAGTT
** * ** * * * * * * * * *
5309041 AAAAAGATAAAGACAACTGGGACTGAATCATAAATCAAGAAGATAAAGACGATTGGGACTGAACC
1 AAGGA-ATAATGATGATTGGGA-TGAACCACAAGTCAAGAGGATAAAGACGATCGAGATTAAACC
*
5309106 ACGAGTC
64 ACGAGTT
5309113 AAGGAAT
1 AAGGAAT
5309120 CACAGAGACT
Statistics
Matches: 175, Mismatches: 42, Indels: 8
0.78 0.19 0.04
Matches are distributed among these distances:
70 3 0.02
71 123 0.70
72 49 0.28
ACGTcount: A:0.46, C:0.13, G:0.24, T:0.17
Consensus pattern (70 bp):
AAGGAATAATGATGATTGGGATGAACCACAAGTCAAGAGGATAAAGACGATCGAGATTAAACCAC
GAGTT
Found at i:5309115 original size:36 final size:36
Alignment explanation
Indices: 5308811--5309115 Score: 129
Period size: 36 Copynumber: 8.6 Consensus size: 36
5308801 ATGAGGATCG
* * * *
5308811 GGGA-TGAACCGCAAGTCAAGGA-ATAATGATGATT
1 GGGACTGAACCACAAGTCAAGAAGATAAAGACGATT
* * * *
5308845 GGGGA-TGAATCATAAGTCAAGAGGATAAAGACGATC
1 -GGGACTGAACCACAAGTCAAGAAGATAAAGACGATT
* * * * * * *
5308881 GTGATTAAACCACAAGTCAAGGA-ATAATGAAGACT
1 GGGACTGAACCACAAGTCAAGAAGATAAAGACGATT
** * *
5308916 GGGAAAGAACCACAAGTCAAGAGGATAAAGACGATC
1 GGGACTGAACCACAAGTCAAGAAGATAAAGACGATT
* * * * * * * * *
5308952 GAGATTAAATCACGAGTTAAGGA-ATAATGATGATT
1 GGGACTGAACCACAAGTCAAGAAGATAAAGACGATT
* * * * **
5308987 AAGGA-TGAACCGCAAGTTAA-AAGGATAAAGATGACC
1 -GGGACTGAACCACAAGTCAAGAA-GATAAAGACGATT
* * * * * * *
5309023 GAGACTAAACCACGAGTTAAAAAGATAAAGACAACT
1 GGGACTGAACCACAAGTCAAGAAGATAAAGACGATT
* * *
5309059 GGGACTGAATCATAAATCAAGAAGATAAAGACGATT
1 GGGACTGAACCACAAGTCAAGAAGATAAAGACGATT
*
5309095 GGGACTGAACCACGAGTCAAG
1 GGGACTGAACCACAAGTCAAG
5309116 GAATCACAGA
Statistics
Matches: 190, Mismatches: 72, Indels: 15
0.69 0.26 0.05
Matches are distributed among these distances:
34 1 0.01
35 67 0.35
36 120 0.63
37 2 0.01
ACGTcount: A:0.45, C:0.13, G:0.25, T:0.17
Consensus pattern (36 bp):
GGGACTGAACCACAAGTCAAGAAGATAAAGACGATT
Found at i:5309275 original size:34 final size:35
Alignment explanation
Indices: 5309237--5309317 Score: 103
Period size: 34 Copynumber: 2.3 Consensus size: 35
5309227 ACATTAACTT
**
5309237 AGATTAAATCATAAGTCAGA-AAGTAAGGA-GATCG
1 AGATTAAATCATAAGTCAGAGAA-TAACAATGATCG
**
5309271 AGATTAAATCACGAGTCAGAGAATAACAATGATCG
1 AGATTAAATCATAAGTCAGAGAATAACAATGATCG
5309306 AGATTAAATCAT
1 AGATTAAATCAT
5309318 GATTTGGAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
34 22 0.55
35 18 0.45
ACGTcount: A:0.47, C:0.11, G:0.20, T:0.22
Consensus pattern (35 bp):
AGATTAAATCATAAGTCAGAGAATAACAATGATCG
Found at i:5309406 original size:34 final size:33
Alignment explanation
Indices: 5309362--5309436 Score: 80
Period size: 34 Copynumber: 2.2 Consensus size: 33
5309352 TGTCAAGAAA
* *
5309362 AAAGATGATAGAGATTGAATCACAAGTCA-GAAAAT
1 AAAGA-GATAGAGATTAAACCACAA-T-ATGAAAAT
* *
5309397 AAAGAGATAGGGATTAAACCACAATATGGAAAT
1 AAAGAGATAGAGATTAAACCACAATATGAAAAT
5309430 AAAGAGA
1 AAAGAGA
5309437 CTGTGATTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
32 1 0.03
33 13 0.37
34 16 0.46
35 5 0.14
ACGTcount: A:0.53, C:0.08, G:0.21, T:0.17
Consensus pattern (33 bp):
AAAGAGATAGAGATTAAACCACAATATGAAAAT
Found at i:5312295 original size:3 final size:3
Alignment explanation
Indices: 5312281--5312351 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
5312271 AATTTTTTAA
* * * * *
5312281 ATT ATT AGT ATT ATT ATT TTT TTT ATT ATT ATT ATT -TT TTT ACT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
5312328 -TT ATT TTT ATT -TT ATT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
5312352 TTTTTGGTCC
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
2 8 0.15
3 47 0.85
ACGTcount: A:0.24, C:0.01, G:0.01, T:0.73
Consensus pattern (3 bp):
ATT
Found at i:5312311 original size:27 final size:25
Alignment explanation
Indices: 5312273--5312356 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 25
5312263 TAATTTTTAA
*
5312273 TTTTTTA-AATTATTAGTATTATTATT
1 TTTTTTATTATTATTA-TATT-TTATT
*
5312299 TTTTTTATTATTATTATTTTTTTACTAT
1 TTTTTTATTATTATTA-TATTTTA-T-T
5312327 TTTATTT-TTATT-TTATTATTTTATT
1 TTT-TTTATTATTATTA-TATTTTATT
5312352 TTTTT
1 TTTTT
5312357 GGTCCAAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
24 2 0.04
25 4 0.08
26 11 0.22
27 21 0.42
28 9 0.18
29 3 0.06
ACGTcount: A:0.23, C:0.01, G:0.01, T:0.75
Consensus pattern (25 bp):
TTTTTTATTATTATTATATTTTATT
Found at i:5312312 original size:18 final size:18
Alignment explanation
Indices: 5312289--5312356 Score: 88
Period size: 18 Copynumber: 3.8 Consensus size: 18
5312279 AAATTATTAG
5312289 TATTATTATTTTTTTTAT
1 TATTATTATTTTTTTTAT
5312307 TATTATTATTTTTTTACTAT
1 TATTATTATTTTTTT--TAT
*
5312327 T-TTATT-TTTATTTTAT
1 TATTATTATTTTTTTTAT
5312343 TATT-TTATTTTTTT
1 TATTATTATTTTTTT
5312357 GGTCCAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
16 6 0.14
17 8 0.18
18 21 0.48
19 5 0.11
20 4 0.09
ACGTcount: A:0.21, C:0.01, G:0.00, T:0.78
Consensus pattern (18 bp):
TATTATTATTTTTTTTAT
Found at i:5313138 original size:13 final size:13
Alignment explanation
Indices: 5313104--5313147 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
5313094 TGGTATTTTC
5313104 TTATTTATTTTAT
1 TTATTTATTTTAT
**
5313117 TTAAGTATTTTAT
1 TTATTTATTTTAT
*
5313130 TTATTTATTTTAA
1 TTATTTATTTTAT
5313143 TTATT
1 TTATT
5313148 AAATTAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (13 bp):
TTATTTATTTTAT
Found at i:5313263 original size:25 final size:26
Alignment explanation
Indices: 5313208--5313261 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
5313198 AATGATGGAA
*
5313208 TTTATAAAAATTTTAATTGGTAAATT
1 TTTATAAAAATTTTAAGTGGTAAATT
5313234 TTTAT-AAAATTCTTAAGTGAG-AAATT
1 TTTATAAAAATT-TTAAGTG-GTAAATT
5313260 TT
1 TT
5313262 ATCTAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 6 0.24
26 18 0.72
27 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (26 bp):
TTTATAAAAATTTTAAGTGGTAAATT
Found at i:5322264 original size:33 final size:33
Alignment explanation
Indices: 5322204--5322267 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
5322194 GAAGGCAACA
* **
5322204 AAATAATTAAACAAATCAATATGTAAATAAAAC
1 AAATAATTAAACAAATAAATAAATAAATAAAAC
* *
5322237 AAATAATTAAAGAAGTAAATAAATAAATAAA
1 AAATAATTAAACAAATAAATAAATAAATAAA
5322268 CAAGTATGTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (33 bp):
AAATAATTAAACAAATAAATAAATAAATAAAAC
Found at i:5323972 original size:15 final size:15
Alignment explanation
Indices: 5323954--5323985 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5323944 GATTTTTGGA
5323954 TTTGAATTTTAAGGT
1 TTTGAATTTTAAGGT
*
5323969 TTTGGATTTTAAGGT
1 TTTGAATTTTAAGGT
5323984 TT
1 TT
5323986 GGGATTTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (15 bp):
TTTGAATTTTAAGGT
Found at i:5323990 original size:15 final size:15
Alignment explanation
Indices: 5323959--5323993 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
5323949 TTGGATTTGA
*
5323959 ATTTTAAGGTTTTGG
1 ATTTTAAGGTTTGGG
5323974 ATTTTAAGGTTTGGG
1 ATTTTAAGGTTTGGG
5323989 ATTTT
1 ATTTT
5323994 GGATTTTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.26, T:0.54
Consensus pattern (15 bp):
ATTTTAAGGTTTGGG
Found at i:5323996 original size:22 final size:22
Alignment explanation
Indices: 5323968--5324015 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
5323958 AATTTTAAGG
5323968 TTTTGGATTTTAAGGTTTGGGA
1 TTTTGGATTTTAAGGTTTGGGA
*
5323990 TTTTGGATTTTAGGGTTTGGGA
1 TTTTGGATTTTAAGGTTTGGGA
5324012 TTTT
1 TTTT
5324016 AGAAAACATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (22 bp):
TTTTGGATTTTAAGGTTTGGGA
Found at i:5325379 original size:52 final size:52
Alignment explanation
Indices: 5325314--5325412 Score: 135
Period size: 52 Copynumber: 1.9 Consensus size: 52
5325304 TGTTTGTAGG
* * *
5325314 GATGGCTAATTTGGTTAGGTCACAAGCGTGGCTAGTCTGATGGGACTAGTTT
1 GATGGCTAATTTGGTTAGATCACAAGCGTGGCTAGTCTAATAGGACTAGTTT
** * *
5325366 GATGGCTGGTTTGGTTTGATCACAAGCGTGGCTGGTCTAATAGGACT
1 GATGGCTAATTTGGTTAGATCACAAGCGTGGCTAGTCTAATAGGACT
5325413 GGTCTAGTGG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 40 1.00
ACGTcount: A:0.20, C:0.14, G:0.33, T:0.32
Consensus pattern (52 bp):
GATGGCTAATTTGGTTAGATCACAAGCGTGGCTAGTCTAATAGGACTAGTTT
Found at i:5325424 original size:52 final size:52
Alignment explanation
Indices: 5325314--5325426 Score: 129
Period size: 52 Copynumber: 2.2 Consensus size: 52
5325304 TGTTTGTAGG
** * * * *
5325314 GATGGCTAATTTGGTTAGGTCACAAGCGTGGCTAGTCTGATGGGACTAGTTT
1 GATGGCTGGTTTGGTTAGATCACAAGCGTGGCTAGTCTAATAGGACTAGTTA
* * *
5325366 GATGGCTGGTTTGGTTTGATCACAAGCGTGGCTGGTCTAATAGGACTGGTCTA
1 GATGGCTGGTTTGGTTAGATCACAAGCGTGGCTAGTCTAATAGGACTAGT-TA
5325419 G-TGGCTGG
1 GATGGCTGG
5325427 ATAGGGTTGG
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
52 49 0.96
53 2 0.04
ACGTcount: A:0.19, C:0.14, G:0.35, T:0.32
Consensus pattern (52 bp):
GATGGCTGGTTTGGTTAGATCACAAGCGTGGCTAGTCTAATAGGACTAGTTA
Found at i:5326017 original size:20 final size:20
Alignment explanation
Indices: 5325994--5326060 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 20
5325984 TCTAACTAAT
5325994 TATT-TTTTAAGTAATAAAAA
1 TATTATTTTAA-TAATAAAAA
* *
5326014 TATTATTATAAAAATAATAAA
1 TATTATTTTAATAATAA-AAA
5326035 -ATTATTTTAAATAAATAAAATA
1 TATTATTTT-AAT-AATAAAA-A
5326057 TATT
1 TATT
5326061 TATAAGGGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
20 16 0.43
21 12 0.32
22 6 0.16
23 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (20 bp):
TATTATTTTAATAATAAAAA
Found at i:5326061 original size:20 final size:21
Alignment explanation
Indices: 5326005--5326061 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
5325995 ATTTTTTAAG
*
5326005 TAATAAAAATATTATTATAAAAA
1 TAAT-AAAATA-TATTTTAAAAA
*
5326028 TAATAAAAT-TATTTTAAATA
1 TAATAAAATATATTTTAAAAA
5326048 -AATAAAATATATTT
1 TAATAAAATATATTT
5326062 ATAAGGGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 8 0.26
20 14 0.45
22 5 0.16
23 4 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAATAAAATATATTTTAAAAA
Found at i:5326062 original size:19 final size:20
Alignment explanation
Indices: 5326005--5326062 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 20
5325995 ATTTTTTAAG
5326005 TAATAAAAATATTATTATAAAAA
1 TAAT-AAAATA-TATT-TAAAAA
*
5326028 TAATAAAAT-TATTT-TAAA
1 TAATAAAATATATTTAAAAA
5326046 TAAATAAAATATATTTA
1 T-AATAAAATATATTTA
5326063 TAAGGGAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 4 0.13
19 9 0.29
20 9 0.29
22 5 0.16
23 4 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAATAAAATATATTTAAAAA
Found at i:5329574 original size:43 final size:44
Alignment explanation
Indices: 5329537--5329619 Score: 132
Period size: 43 Copynumber: 1.9 Consensus size: 44
5329527 TAAAAGGTTC
5329537 ATCTAAACAGAAGTTCAACAACTTTT-AAAAATATAAAAAAACT
1 ATCTAAACAGAAGTTCAACAACTTTTGAAAAATATAAAAAAACT
* * *
5329580 ATCTCAATAGAGGTTCAACAACTTTTGAAAAATATAAAAA
1 ATCTAAACAGAAGTTCAACAACTTTTGAAAAATATAAAAA
5329620 GCTTCTTTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
43 23 0.64
44 13 0.36
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.27
Consensus pattern (44 bp):
ATCTAAACAGAAGTTCAACAACTTTTGAAAAATATAAAAAAACT
Done.