Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007776.1 Hibiscus syriacus cultivar Beakdansim tig00110057_pilon, 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: 2207776
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 11
Found at i:716143 original size:25 final size:25
Alignment explanation
Indices: 716115--716192 Score: 88
Period size: 25 Copynumber: 3.0 Consensus size: 25
716105 TTCTATTTTA
716115 TTTTT-TTATTTTTTTATTTTTATT
1 TTTTTATTATTTTTTTATTTTTATT
*
716139 TTTTTATTATCTGTTTTGATTTATTATT
1 TTTTTATTAT-T-TTTTTATTT-TTATT
*
716167 TTCTTATT-TTTTTTTATTATTTATT
1 TTTTTATTATTTTTTTATT-TTTATT
716192 T
1 T
716193 ACTATTTAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
24 5 0.11
25 17 0.37
26 3 0.07
27 9 0.20
28 12 0.26
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (25 bp):
TTTTTATTATTTTTTTATTTTTATT
Found at i:720228 original size:96 final size:95
Alignment explanation
Indices: 720117--720309 Score: 314
Period size: 96 Copynumber: 2.0 Consensus size: 95
720107 TAATATTATT
*
720117 TACAATAAAGCTTGAGTTATCCCTCTAAAGCAATTGGTTAAATGCCCCGGCTTTATGGATAAGAT
1 TACAATAAAGCTTGAGTTATCCCTCTAAAGCAATTGGTTAAATGCCACGGCTTTATGGATAAGAT
720182 TCAACTAAGCCTGATAAAGGTGATTATAATA
66 TCAACT-AGCCTGATAAAGGTGATTATAATA
* * * * *
720213 TACAATAAAGCTTGAGTTGTTCCTCTAGAGCAATTGGTTAAATGCCATGGCTTTATGGATAATAT
1 TACAATAAAGCTTGAGTTATCCCTCTAAAGCAATTGGTTAAATGCCACGGCTTTATGGATAAGAT
*
720278 TCAGCTAGCCTGATAAAGGTGATTATAATA
66 TCAACTAGCCTGATAAAGGTGATTATAATA
720308 TA
1 TA
720310 TATACAATGG
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
95 26 0.29
96 64 0.71
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (95 bp):
TACAATAAAGCTTGAGTTATCCCTCTAAAGCAATTGGTTAAATGCCACGGCTTTATGGATAAGAT
TCAACTAGCCTGATAAAGGTGATTATAATA
Found at i:721634 original size:37 final size:34
Alignment explanation
Indices: 721593--721721 Score: 141
Period size: 36 Copynumber: 3.6 Consensus size: 34
721583 ACAAGGGGTC
* *
721593 GTCTCGCTTGAGACTAATTTACTCAAAACAAAGTTTT
1 GTCTCTCTTGAGAC-AATTT-CTCGAAACAAA-TTTT
*
721630 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTT
1 GTCTCTCTTGAGACAATTTCTC--GAAACAAATTTT
*
721666 GTCTCTCTTGAGACAATTTCCCTTGAAACAAATTTT
1 GTCTCTCTTGAGACAATTT--CTCGAAACAAATTTT
* *
721702 GTCTCTCTTAAGACAGTTTC
1 GTCTCTCTTGAGACAATTTC
721722 CCTTGAAACA
Statistics
Matches: 81, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
34 1 0.01
35 3 0.04
36 55 0.68
37 20 0.25
38 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (34 bp):
GTCTCTCTTGAGACAATTTCTCGAAACAAATTTT
Found at i:721673 original size:21 final size:21
Alignment explanation
Indices: 721648--721710 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
721638 TGAGACAGTT
721648 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
*
721669 TCTCTTGAGAC-AA--TT-TC
1 TCTCTTGAAACAAATTTTGTC
721686 -C-CTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
721705 TCTCTT
1 TCTCTT
721711 AAGACAGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
15 7 0.21
16 3 0.09
17 2 0.06
18 4 0.12
19 2 0.06
20 3 0.09
21 13 0.38
ACGTcount: A:0.25, C:0.22, G:0.10, T:0.43
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:721673 original size:36 final size:36
Alignment explanation
Indices: 721618--721934 Score: 289
Period size: 36 Copynumber: 9.2 Consensus size: 36
721608 AATTTACTCA
721618 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTG
* *
721655 AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* *
721691 AAACAAATTTTGTCTCTCTTAAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* *
721727 AAACAAA------ATCT-TTGA-ATATGTTT-TACATT-
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCT-C-TTG
* *
721756 AAAAAAATTTTGTCTCTCTTGAGACAGTTTCTTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * *
721792 GAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
*
721829 AAACAAATTTTG--TCT-TT------GTCTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
*
721856 AAACAAATTTT-TCCTTTCTTGAGACAGTTT-TCCTTG
1 AAACAAATTTTGT-CTCTCTTGAGACAGTTTCT-CTTG
* *
721892 AAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
721928 AAACAAA
1 AAACAAA
721935 ATCTTTGAAT
Statistics
Matches: 229, Mismatches: 24, Indels: 55
0.74 0.08 0.18
Matches are distributed among these distances:
27 20 0.09
28 2 0.01
29 16 0.07
30 7 0.03
33 2 0.01
34 3 0.01
35 6 0.03
36 130 0.57
37 43 0.19
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.41
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:721993 original size:201 final size:201
Alignment explanation
Indices: 721648--722107 Score: 663
Period size: 201 Copynumber: 2.2 Consensus size: 201
721638 TGAGACAGTT
*
721648 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCTCTTAA
1 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTTTATCTCTCTTAA
* *
721713 GACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTACATTAAAAAAATTTTGTCTCTCTTGA
66 GACAGTTTCCCTTGAAACAAAATCTTTGAATATATTTTACATTAAAAAAATTTTGTCTCCCTTGA
* *
721778 GACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAATTTTGTC
131 GACAGTTGCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTC
721843 TTTGTC
196 TTTGTC
* * * *
721849 TCTCTTGAAACAAATTTT-TCCTTTCTTGAGACAGTTTTCCTTGAAACAAATTTTATCTCTCTTG
1 TCTCTTGAAACAAATTTTGT-CTCTCTTGAGACAATTTCCCTTGAAACAAATTTTATCTCTCTTA
* *
721913 AGACAGTTTCCCTTGAAACAAAATCTTTGAATATATTTT-CCTTGAAACAAATTTTGTCTCCCTT
65 AGACAGTTTCCCTTGAAACAAAATCTTTGAATATATTTTACATT-AAAAAAATTTTGTCTCCCTT
721977 GAGACAGTTGCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTG
129 GAGACAGTTGCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTG
*
722042 TCTCTGTTGAGACATTT
194 --TCT-TT--G----TC
* * *
722059 TCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 TCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAATTTCCCTTGAAACA
722108 CCAATCTTTG
Statistics
Matches: 230, Mismatches: 16, Indels: 16
0.88 0.06 0.06
Matches are distributed among these distances:
200 4 0.02
201 176 0.77
203 3 0.01
204 2 0.01
206 1 0.00
210 14 0.06
211 29 0.13
212 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (201 bp):
TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTTTATCTCTCTTAA
GACAGTTTCCCTTGAAACAAAATCTTTGAATATATTTTACATTAAAAAAATTTTGTCTCCCTTGA
GACAGTTGCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTC
TTTGTC
Found at i:722052 original size:36 final size:36
Alignment explanation
Indices: 721949--722107 Score: 221
Period size: 37 Copynumber: 4.4 Consensus size: 36
721939 TTGAATATAT
*
721949 TTTC-CTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * * *
721984 TTGCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
* *
722021 TTTCTCTTGAAACAAATTTTGTCTCTGTTGAGACAT
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
722057 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
722094 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
722108 CCAATCTTTG
Statistics
Matches: 106, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
35 3 0.03
36 41 0.39
37 62 0.58
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:722075 original size:73 final size:73
Alignment explanation
Indices: 721949--722107 Score: 239
Period size: 73 Copynumber: 2.2 Consensus size: 73
721939 TTGAATATAT
** * *
721949 TTTC-CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTGCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTGCCCTTGAAACAAAGTTTTGTCTCTCT
722013 TGAGACAG
66 TGAGACAG
** * *
722021 TTTCTCTTGAAACAAATTTTGTCTCTGTTGAGACATTTTCCCTTGAAACAAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTGCCCTTGAAACAAAGTTTTGTCTCTCT
722086 TGAGACAG
66 TGAGACAG
722094 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
722108 CCAATCTTTG
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
72 4 0.05
73 74 0.95
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (73 bp):
TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTGCCCTTGAAACAAAGTTTTGTCTCTCT
TGAGACAG
Found at i:722143 original size:138 final size:136
Alignment explanation
Indices: 721760--722172 Score: 368
Period size: 138 Copynumber: 3.0 Consensus size: 136
721750 TACATTAAAA
** * *
721760 AAATTTTGTCTCTCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCT
1 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCT
** * *
721825 CTTGAAACAAAT-TTTGTCTTTGTCTCTCTTGAAACAAATTTT-TCCTTTCTTGAGACAGTTT-T
66 CTTGAAACAAATCTTTGAATATGT-TCTCTTGAAACAAATTTTGT-CTCTCTTGAGACAGTTTCT
721887 CCTTGAAAC
129 -CTTGAAAC
* * * *
721896 AAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAA-------ATCT-TTGAATATATTTTC
1 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTG-AGATAGTTTC
* * * *
721953 -CTTGAAACAAATTTTGTCTCCCTTGAGACA-GTTGCTTTTGGAACTAAGTTTTGTCTCTCTTGA
65 TCTTGAAACAAA-----TCT---TTGA-ATATGTT-CTCTTGAAAC-AAATTTTGTCTCTCTTGA
722016 GACAGTTTCTCTTGAAAC
119 GACAGTTTCTCTTGAAAC
* * *
722034 AAATTTTGTCTCTGTTGAGACATTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCT
1 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCT
* * *
722099 CTTGAAACACCAATCTTTGAATATGTT-TCTTGAAACAAAATTTTGCCTCCCTTGAGATAGTTTC
66 CTTGAAACA--AATCTTTGAATATGTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTC
722163 TCTTGAAAC
128 TCTTGAAAC
722172 A
1 A
722173 CAAAAAAACC
Statistics
Matches: 219, Mismatches: 31, Indels: 52
0.73 0.10 0.17
Matches are distributed among these distances:
128 14 0.06
129 11 0.05
133 1 0.00
134 1 0.00
136 35 0.16
137 13 0.06
138 106 0.48
139 4 0.02
140 7 0.03
143 3 0.01
145 10 0.05
146 12 0.05
148 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (136 bp):
AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCT
CTTGAAACAAATCTTTGAATATGTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCT
TGAAAC
Found at i:723593 original size:38 final size:36
Alignment explanation
Indices: 723552--723787 Score: 243
Period size: 38 Copynumber: 6.5 Consensus size: 36
723542 GTTTGGCACT
723552 ATATATAGTTTTTAAAACA-TTTTGAAAACTAATATA
1 ATATATAGTTTTTAAAACATTTTTGAAAACT-ATATA
* * *
723588 GTATATAATTTTTTAAAACATTTTTGAAAAATTATATA
1 ATATAT-AGTTTTTAAAACATTTTTG-AAAACTATATA
* *
723626 ATATATAG-TTTTAAAACCATTTTTTGAAAAATTGTATA
1 ATATATAGTTTTTAAAA-CA-TTTTTG-AAAACTATATA
* * *
723664 ATATATAGTTTTAAAAACATTTTTGGAAAAATTATAAA
1 ATATATAGTTTTTAAAACATTTTT-G-AAAACTATATA
*
723702 ATATATAGTTTTAAAAACATTTTTTGAAAACT-TAT-
1 ATATATAGTTTTTAAAACA-TTTTTGAAAACTATATA
*
723737 ATA-ATA-TTTTTAAAACA-TTTTCAAAACTATATA
1 ATATATAGTTTTTAAAACATTTTTGAAAACTATATA
*
723770 ATATATAGTTTTGAAAAC
1 ATATATAGTTTTTAAAAC
723788 TTATATAATA
Statistics
Matches: 174, Mismatches: 14, Indels: 25
0.82 0.07 0.12
Matches are distributed among these distances:
31 10 0.06
32 3 0.02
33 13 0.07
34 6 0.03
35 12 0.07
36 15 0.09
37 25 0.14
38 73 0.42
39 17 0.10
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (36 bp):
ATATATAGTTTTTAAAACATTTTTGAAAACTATATA
Found at i:723770 original size:30 final size:30
Alignment explanation
Indices: 723723--723828 Score: 116
Period size: 30 Copynumber: 3.7 Consensus size: 30
723713 TAAAAACATT
723723 TTTTGAAAACTTATATAATATTTTTAAAACA
1 TTTTGAAAAC-TATATAATATTTTTAAAACA
* * *
723754 TTTTCAAAACTATATAATA----T-ATA-G
1 TTTTGAAAACTATATAATATTTTTAAAACA
*
723778 TTTTGAAAACTTATATAATATTTTTAAAACA
1 TTTTGAAAA-CTATATAATATTTTTAAAACA
723809 TTTTGAAAACTATATAATAT
1 TTTTGAAAACTATATAATAT
723829 ATAGTTTTGA
Statistics
Matches: 60, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
24 8 0.13
25 11 0.18
26 1 0.02
29 1 0.02
30 21 0.35
31 18 0.30
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (30 bp):
TTTTGAAAACTATATAATATTTTTAAAACA
Found at i:723788 original size:55 final size:55
Alignment explanation
Indices: 723723--723844 Score: 235
Period size: 55 Copynumber: 2.2 Consensus size: 55
723713 TAAAAACATT
723723 TTTTGAAAACTTATATAATATTTTTAAAACATTTTCAAAACTATATAATATATAG
1 TTTTGAAAACTTATATAATATTTTTAAAACATTTTCAAAACTATATAATATATAG
*
723778 TTTTGAAAACTTATATAATATTTTTAAAACATTTTGAAAACTATATAATATATAG
1 TTTTGAAAACTTATATAATATTTTTAAAACATTTTCAAAACTATATAATATATAG
723833 TTTTGAAAACTT
1 TTTTGAAAACTT
723845 TTTTAAAATA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
55 66 1.00
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (55 bp):
TTTTGAAAACTTATATAATATTTTTAAAACATTTTCAAAACTATATAATATATAG
Found at i:723880 original size:32 final size:32
Alignment explanation
Indices: 723820--723893 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
723810 TTTGAAAACT
* *
723820 ATATAATATATAGTTTTGAAAACTTTTTTAAA
1 ATATAATATATAGTTTTAAAAAATTTTTTAAA
*
723852 ATATAATATATAG-TTTAAAAAATATTTTTGAA
1 ATATAATATATAGTTTTAAAAAAT-TTTTTAAA
*
723884 GTAT-ATATAT
1 ATATAATATAT
723894 TATATAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 14 0.38
32 23 0.62
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (32 bp):
ATATAATATATAGTTTTAAAAAATTTTTTAAA
Found at i:723890 original size:34 final size:31
Alignment explanation
Indices: 723819--723904 Score: 82
Period size: 32 Copynumber: 2.6 Consensus size: 31
723809 TTTTGAAAAC
* *
723819 TATATAATATATAGTTTTGAAAACTTTTTTAA
1 TATATAATATATAG-TTTAAAAAATTTTTTAA
*
723851 AATATAATATATAGTTTAAAAAATATTTTTGAA
1 TATATAATATATAGTTTAAAAAAT-TTTTT-AA
*
723884 GTATATATATTATATAATTTA
1 -TATATA-A-TATATAGTTTA
723905 TATTATATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
31 8 0.18
32 18 0.41
33 2 0.05
34 5 0.11
35 1 0.02
36 10 0.23
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (31 bp):
TATATAATATATAGTTTAAAAAATTTTTTAA
Found at i:723930 original size:20 final size:20
Alignment explanation
Indices: 723905--723948 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
723895 ATATAATTTA
723905 TATTA-TATTATTATTGTTAT
1 TATTATTATT-TTATTGTTAT
* *
723925 TATTATTATTTTCTTTTTAT
1 TATTATTATTTTATTGTTAT
723945 TATT
1 TATT
723949 TTCTTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (20 bp):
TATTATTATTTTATTGTTAT
Found at i:723965 original size:15 final size:14
Alignment explanation
Indices: 723912--723958 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
723902 TTATATTATA
* *
723912 TTATTATTGTTATTA
1 TTATTATT-TTCTTT
723927 TTATTATTTTCTTT
1 TTATTATTTTCTTT
723941 TTATTATTTTCTTT
1 TTATTATTTTCTTT
723955 TTAT
1 TTAT
723959 GTTTTTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 22 0.73
15 8 0.27
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.74
Consensus pattern (14 bp):
TTATTATTTTCTTT
Found at i:724720 original size:2 final size:2
Alignment explanation
Indices: 724713--724738 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
724703 GGCTTAAGTG
724713 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
724739 CACAACCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:727217 original size:23 final size:21
Alignment explanation
Indices: 727190--727232 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
727180 ATATAAAAAA
727190 TTAT-TTTTTATTAAATATTTT
1 TTATATTTTTATTAAAT-TTTT
*
727211 TTATATTTTTATTTAATTTTT
1 TTATATTTTTATTAAATTTTT
727232 T
1 T
727233 AAATAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATATTTTTATTAAATTTTT
Found at i:730701 original size:17 final size:16
Alignment explanation
Indices: 730680--730710 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
730670 TTCTAAATTT
*
730680 TTTTTTTAGTTCAAGC
1 TTTTTTGAGTTCAAGC
730696 TTTTTTGAGTTCAAG
1 TTTTTTGAGTTCAAG
730711 TTTCAATATT
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:0.19, C:0.10, G:0.16, T:0.55
Consensus pattern (16 bp):
TTTTTTGAGTTCAAGC
Found at i:731899 original size:34 final size:33
Alignment explanation
Indices: 731805--731904 Score: 132
Period size: 33 Copynumber: 3.1 Consensus size: 33
731795 AAACATGAAA
* * *
731805 AATAAGTTGGCCGCCTACCAA-A-GAATTTTCC
1 AATAAGTTGGCCACCAACCAAGATTAATTTTCC
* *
731836 AATGAGTTGGCCACCAACCAAGATTAATTTTTC
1 AATAAGTTGGCCACCAACCAAGATTAATTTTCC
*
731869 AATAAGTTGGCCACCAACCAAGATTAAATTTCC
1 AATAAGTTGGCCACCAACCAAGATTAATTTTCC
731902 AAT
1 AAT
731905 CTTGCCAAAC
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
31 18 0.31
32 1 0.02
33 40 0.68
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (33 bp):
AATAAGTTGGCCACCAACCAAGATTAATTTTCC
Found at i:736602 original size:33 final size:33
Alignment explanation
Indices: 736530--736629 Score: 141
Period size: 33 Copynumber: 3.1 Consensus size: 33
736520 AAACATGAAA
* *
736530 AATAAGTTGGCCACCTACCAA-A-GAATTTTCC
1 AATAAGTTGGCCACCAACCAAGATTAATTTTCC
* *
736561 AATGAGTTGGCCACCAACCAAGATTAATTTTTC
1 AATAAGTTGGCCACCAACCAAGATTAATTTTCC
*
736594 AATAAGTTGGCCACCAACCAAGATTAAATTTCC
1 AATAAGTTGGCCACCAACCAAGATTAATTTTCC
736627 AAT
1 AAT
736630 CTTGCCAAAC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
31 19 0.32
32 1 0.02
33 40 0.67
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (33 bp):
AATAAGTTGGCCACCAACCAAGATTAATTTTCC
Found at i:744092 original size:20 final size:21
Alignment explanation
Indices: 744067--744107 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
744057 AACCAAATAA
744067 GTAGTATTG-GTACTAC-ATAG
1 GTAGTA-TGAGTACTACTATAG
744087 GTAGTATGAGTACTACTATAG
1 GTAGTATGAGTACTACTATAG
744108 TGTATGGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 13 0.68
21 4 0.21
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (21 bp):
GTAGTATGAGTACTACTATAG
Found at i:751947 original size:28 final size:28
Alignment explanation
Indices: 751907--751961 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
751897 ATTTTTTCAA
751907 GCATACAATAATATAGTTTGGCCTAACT
1 GCATACAATAATATAGTTTGGCCTAACT
751935 GCATACAATAATATAGTTTGGCCTAAC
1 GCATACAATAATATAGTTTGGCCTAAC
751962 AATTTTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (28 bp):
GCATACAATAATATAGTTTGGCCTAACT
Found at i:753381 original size:21 final size:21
Alignment explanation
Indices: 753356--753428 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
753346 AAAAATGTTA
*
753356 AAAAATATTAATATTTTAGAT
1 AAAAATAATAATATTTTAGAT
753377 AAAAATAATAATATTTTAGAT
1 AAAAATAATAATATTTTAGAT
*** *
753398 AATTTTTATAA-ATTTTA-AT
1 AAAAATAATAATATTTTAGAT
753417 AAAAAT-ATAATA
1 AAAAATAATAATA
753429 ACAAAACTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
18 4 0.09
19 6 0.14
20 6 0.14
21 27 0.63
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
AAAAATAATAATATTTTAGAT
Found at i:768263 original size:25 final size:25
Alignment explanation
Indices: 768229--768301 Score: 146
Period size: 25 Copynumber: 2.9 Consensus size: 25
768219 GGGTAGTGGA
768229 TAAATGCAAATGTTTGAATCAAAAC
1 TAAATGCAAATGTTTGAATCAAAAC
768254 TAAATGCAAATGTTTGAATCAAAAC
1 TAAATGCAAATGTTTGAATCAAAAC
768279 TAAATGCAAATGTTTGAATCAAA
1 TAAATGCAAATGTTTGAATCAAA
768302 TTAATTAGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.29
Consensus pattern (25 bp):
TAAATGCAAATGTTTGAATCAAAAC
Found at i:768325 original size:17 final size:17
Alignment explanation
Indices: 768303--768341 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
768293 TGAATCAAAT
768303 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
768320 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
768337 -AATTA
1 TAATTA
768342 ATTGTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:768886 original size:209 final size:209
Alignment explanation
Indices: 768526--768944 Score: 802
Period size: 209 Copynumber: 2.0 Consensus size: 209
768516 TACCCCTAGG
*
768526 TAGAAGCATCAATAGGAATGATAGTGTTAATATCACACTTTGTAATCAATGGGGTATAGTTTATT
1 TAGAAGCATCAATAGGAATGATAGTGTTAATATCACACTTTGTAATCAACGGGGTATAGTTTATT
768591 GAAGTTTGTTTTGTTGTAAATATTGATTGTAAGTTCTCGATACTTTTGTAAGAACTTATTGTTTT
66 GAAGTTTGTTTTGTTGTAAATATTGATTGTAAGTTCTCGATACTTTTGTAAGAACTTATTGTTTT
* *
768656 TTGTAGCAGTTATCTGCTCTTTGGGTAATAAAAATGATTTATCCAAAAAAATATATTGTCCCTGA
131 TTGTAGCAGTTATCTGCTCTTTGGATAATAAAAATGATTTATCCAAAAAAAAATATTGTCCCTGA
768721 ATCTATTGTTTTCA
196 ATCTATTGTTTTCA
*
768735 TAGAAGCATCAATAGGAATGATAGTGTTAATATCACACTTTGTACTCAACGGGGTATAGTTTATT
1 TAGAAGCATCAATAGGAATGATAGTGTTAATATCACACTTTGTAATCAACGGGGTATAGTTTATT
768800 GAAGTTTGTTTTGTTGTAAATATTGATTGTAAGTTCTCGATACTTTTGTAAGAACTTATTGTTTT
66 GAAGTTTGTTTTGTTGTAAATATTGATTGTAAGTTCTCGATACTTTTGTAAGAACTTATTGTTTT
768865 TTGTAGCAGTTATCTGCTCTTTGGATAATAAAAATGATTTATCCAAAAAAAAATATTGTCCCTGA
131 TTGTAGCAGTTATCTGCTCTTTGGATAATAAAAATGATTTATCCAAAAAAAAATATTGTCCCTGA
768930 ATCTATTGTTTTCA
196 ATCTATTGTTTTCA
768944 T
1 T
768945 TGTTGTTTGA
Statistics
Matches: 206, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
209 206 1.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.42
Consensus pattern (209 bp):
TAGAAGCATCAATAGGAATGATAGTGTTAATATCACACTTTGTAATCAACGGGGTATAGTTTATT
GAAGTTTGTTTTGTTGTAAATATTGATTGTAAGTTCTCGATACTTTTGTAAGAACTTATTGTTTT
TTGTAGCAGTTATCTGCTCTTTGGATAATAAAAATGATTTATCCAAAAAAAAATATTGTCCCTGA
ATCTATTGTTTTCA
Found at i:771447 original size:18 final size:18
Alignment explanation
Indices: 771424--771464 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
771414 TCACCCCAAT
*
771424 AGCTGCGACGTGTGGGGC
1 AGCTGCGACGTATGGGGC
771442 AGCTGCGACGTATGGGGC
1 AGCTGCGACGTATGGGGC
771460 AGCTG
1 AGCTG
771465 GCTCTTCTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.15, C:0.22, G:0.46, T:0.17
Consensus pattern (18 bp):
AGCTGCGACGTATGGGGC
Found at i:771745 original size:3 final size:3
Alignment explanation
Indices: 771737--771832 Score: 78
Period size: 3 Copynumber: 32.7 Consensus size: 3
771727 TTTGGGTCCG
* *
771737 TAA TAA TAA T-T TAA TTAA TAA TAA TAA TAA TAA -AA GAAA TAA -AA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA
* *
771781 TAA TAA TAA TAA TAA -AA GAAA TAA -AA TAA TAA TAA T-A TATT TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA-A TAA
771825 TAA TAA TA
1 TAA TAA TA
771833 TTAAAAAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
2 11 0.14
3 57 0.74
4 9 0.12
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:771830 original size:26 final size:26
Alignment explanation
Indices: 771753--771817 Score: 130
Period size: 26 Copynumber: 2.5 Consensus size: 26
771743 TAATTTAATT
771753 AATAATAATAATAATAAAAGAAATAA
1 AATAATAATAATAATAAAAGAAATAA
771779 AATAATAATAATAATAAAAGAAATAA
1 AATAATAATAATAATAAAAGAAATAA
771805 AATAATAATAATA
1 AATAATAATAATA
771818 TATTTAATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (26 bp):
AATAATAATAATAATAAAAGAAATAA
Found at i:772303 original size:122 final size:121
Alignment explanation
Indices: 772069--772500 Score: 467
Period size: 122 Copynumber: 3.6 Consensus size: 121
772059 CTAGCAAAAA
* * * * * * * *
772069 GTTGAACAAATTCTTCTTATTATGAATTTCTTC-TCTTTCTTAAGCTGAGTTCTTCTTATTATGA
1 GTTGAACAAACTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATAAGTTCTTCTCATTATGA
** *
772133 AC-CCCTCTGGAAAAGTTGATGTTGATCTATCTCCTTTTGTGATAGAGTCATGCAAAG
65 ACTTTCTCTGGAAAAGTTGATG-TGATCTATCTCCTTCTGTGATAGAGTCATGCAAAG
*
772190 GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAA
1 GTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAA
772255 CTTTCTCTGGAAAAGTTGATGATGATCTATCTCCTTCTGTGATAGAGTCATGCAAAG
66 CTTTCTCTGGAAAAGTTGATG-TGATCTATCTCCTTCTGTGATAGAGTCATGCAAAG
* * * * *
772312 GTTGAACAAGCTCTTCTCATTATGAACTTCATCTTCCTCTTCATATAGGTTCTTCTTATTATGAA
1 GTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAA
* * ** * **
772377 CTATCTCTGGAAAA--T--T-TGATCCA--T-C--GAGTGAT-GAATTCAAACAAAAG
66 CTTTCTCTGGAAAAGTTGATGTGATCTATCTCCTTCTGTGATAG-AGTCATGC-AAAG
* * *
772424 GTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCATATAAGTTCTTCTCATTATG
1 G-TTGAACAAACTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATG
772489 AACTTTCTCTGG
64 AACTTTCTCTGG
772501 CAATGCTGAT
Statistics
Matches: 274, Mismatches: 31, Indels: 19
0.85 0.10 0.06
Matches are distributed among these distances:
110 1 0.00
111 10 0.04
112 5 0.02
113 33 0.12
114 36 0.13
116 6 0.02
118 1 0.00
120 1 0.00
121 54 0.20
122 127 0.46
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (121 bp):
GTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAA
CTTTCTCTGGAAAAGTTGATGTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAG
Found at i:772440 original size:113 final size:113
Alignment explanation
Indices: 772308--772643 Score: 421
Period size: 113 Copynumber: 3.0 Consensus size: 113
772298 AGAGTCATGC
* * *
772308 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCATCTTCCTCTTCATATAGGTTCTTCTTATTA
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCATATAGGTTCTTCTCATTA
*
772373 TGAACTATCTCTGGAAAAT-TTGATCCATCGAGTGATGAATTCAAACA
66 TGAACTATCTCTGGAAAATCTTGATCCATCGAATGATGAATTCAAACA
* * *
772420 AAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCATATAAGTTCTTCTCAT
1 AAAGG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCATATAGGTTCTTCTCAT
* * * * *
772485 TATGAACTTTCTCTGG-CAATGC-TGATACATCAAATGATGAATTCAAGCA
64 TATGAACTATCTCTGGAAAAT-CTTGATCCATCGAATGATGAATTCAAACA
* * * *
772534 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTTTTAGAT-GAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCATATAG-GTTCTTCTCATT
* * * *
772598 ATGAACTCTATCT-GAAAATCTTGATCCATTGAATGATGGATTCAAA
65 ATGAACTATCTCTGGAAAATCTTGATCCATCGAATGATGAATTCAAA
772644 TCTTTGCTAA
Statistics
Matches: 190, Mismatches: 27, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
111 2 0.01
112 57 0.30
113 68 0.36
114 63 0.33
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (113 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCATATAGGTTCTTCTCATTA
TGAACTATCTCTGGAAAATCTTGATCCATCGAATGATGAATTCAAACA
Found at i:773803 original size:18 final size:19
Alignment explanation
Indices: 773759--773801 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
773749 GATGTTTATG
773759 AAAAA-AAATTGAATTTCGA
1 AAAAAGAAATTGAATTTC-A
773778 ACAAAAGAAATTGAATTTCA
1 A-AAAAGAAATTGAATTTCA
773798 AAAA
1 AAAA
773802 GATAATCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.18
20 6 0.27
21 12 0.55
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.23
Consensus pattern (19 bp):
AAAAAGAAATTGAATTTCA
Found at i:784790 original size:28 final size:28
Alignment explanation
Indices: 784733--784792 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
784723 AAATAAAATA
* *
784733 AAAATAAAAATACTATATATATATTATG
1 AAAATAAAAATACTATATAAAAATTATG
* *
784761 AAAATAATAAGTA-TATATAAAAATTTTG
1 AAAATAA-AAATACTATATAAAAATTATG
784789 AAAA
1 AAAA
784793 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (28 bp):
AAAATAAAAATACTATATAAAAATTATG
Found at i:785320 original size:20 final size:19
Alignment explanation
Indices: 785276--785321 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
785266 TAATTTTAAG
785276 AAAATATATTATATTTTTT
1 AAAATATATTATATTTTTT
*
785295 ACAATATATT-TATTTATTT
1 AAAATATATTATATTT-TTT
785314 AGAAATAT
1 A-AAATAT
785322 CATAAAAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
AAAATATATTATATTTTTT
Found at i:787013 original size:3 final size:3
Alignment explanation
Indices: 787005--787080 Score: 52
Period size: 3 Copynumber: 25.7 Consensus size: 3
786995 TTTGGGTCCG
* * * *
787005 TAA TAA TAA T-T TAA TTA TTA TTAA TAA TAA TAA TAA TAA -AA GAAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA -TAA
*
787050 TAA -AA TAA TAA TAA T-A TATT TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA
787081 TTAAAAAAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
2 7 0.12
3 46 0.78
4 6 0.10
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:791420 original size:22 final size:21
Alignment explanation
Indices: 791389--791439 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
791379 ATTCTAACCT
*
791389 TAAAATTAAAATATAAAATTAC
1 TAAAAATAAAA-ATAAAATTAC
*
791411 TAAAAATAAAAATTAAATTAC
1 TAAAAATAAAAATAAAATTAC
791432 TAAAAATA
1 TAAAAATA
791440 CACTAAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAATAAAAATAAAATTAC
Found at i:793958 original size:21 final size:21
Alignment explanation
Indices: 793920--793959 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
793910 CCGAATCGAG
* *
793920 TTCGAGTATTGTTGAGCTCTA
1 TTCGAGTATTGCTAAGCTCTA
793941 TTCGAGTATTGCTAAGCTC
1 TTCGAGTATTGCTAAGCTC
793960 GACTCGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (21 bp):
TTCGAGTATTGCTAAGCTCTA
Found at i:793966 original size:21 final size:21
Alignment explanation
Indices: 793921--793966 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
793911 CGAATCGAGT
* * * *
793921 TCGAGTATTGTTGAGCTCTAT
1 TCGAGTATTGCTAAGCTCGAC
793942 TCGAGTATTGCTAAGCTCGAC
1 TCGAGTATTGCTAAGCTCGAC
793963 TCGA
1 TCGA
793967 AAACTCTGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGAGTATTGCTAAGCTCGAC
Found at i:796510 original size:25 final size:25
Alignment explanation
Indices: 796476--796523 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
796466 TGTTAAAGAC
796476 AATAACGTTAATGATCAATTTGTGA
1 AATAACGTTAATGATCAATTTGTGA
796501 AATAACGTTAATGATCAATTTGT
1 AATAACGTTAATGATCAATTTGT
796524 AACTATTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.38
Consensus pattern (25 bp):
AATAACGTTAATGATCAATTTGTGA
Found at i:797111 original size:23 final size:22
Alignment explanation
Indices: 797072--797121 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
797062 ATATTTTTAA
* *
797072 TTTTATAAAAAATTATATAAAT
1 TTTTTTAAAAAAATATATAAAT
797094 TTTTTTAAAGAAAATATATAAAT
1 TTTTTTAAA-AAAATATATAAAT
*
797117 ATTTT
1 TTTTT
797122 CCAACTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTTAAAAAAATATATAAAT
Found at i:797290 original size:18 final size:19
Alignment explanation
Indices: 797267--797303 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
797257 CCAGTAATCC
797267 TATTCCC-TGGTAATCTTT
1 TATTCCCATGGTAATCTTT
797285 TATTCCCAATGGTAATCTT
1 TATTCCC-ATGGTAATCTT
797304 ACATTCCGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.46
Consensus pattern (19 bp):
TATTCCCATGGTAATCTTT
Found at i:797771 original size:14 final size:14
Alignment explanation
Indices: 797752--797778 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
797742 TTAATTGATT
797752 AAAAAAATTCGTCA
1 AAAAAAATTCGTCA
797766 AAAAAAATTCGTC
1 AAAAAAATTCGTC
797779 TTACGTTGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (14 bp):
AAAAAAATTCGTCA
Found at i:800167 original size:31 final size:31
Alignment explanation
Indices: 800128--800196 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
800118 GATATATAAA
800128 ATATGATCACTTTCGTTTTTATTTAATTAAG
1 ATATGATCACTTTCGTTTTTATTTAATTAAG
* * *
800159 TTATGATCACTTTTGTTTTTATTTATTTAAG
1 ATATGATCACTTTCGTTTTTATTTAATTAAG
800190 ATATGAT
1 ATATGAT
800197 TACCACGGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.55
Consensus pattern (31 bp):
ATATGATCACTTTCGTTTTTATTTAATTAAG
Found at i:801320 original size:18 final size:18
Alignment explanation
Indices: 801299--801333 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
801289 TATTCTTATA
*
801299 ATTAAATTTTAATAAATG
1 ATTAAATTTAAATAAATG
801317 ATTAAATTTAAATAAAT
1 ATTAAATTTAAATAAAT
801334 CCTTATAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
ATTAAATTTAAATAAATG
Found at i:809015 original size:23 final size:20
Alignment explanation
Indices: 808964--809023 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
808954 TTTGGTGTAG
* *
808964 AGGGAATCGTTTCCCCCTTT
1 AGGGAACCGATTCCCCCTTT
808984 AGGGAACCGATTCCCCCTTT
1 AGGGAACCGATTCCCCCTTT
809004 GAAGGGGAACCGATTCCCCC
1 --A-GGGAACCGATTCCCCC
809024 CACAGGGGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.20, C:0.33, G:0.23, T:0.23
Consensus pattern (20 bp):
AGGGAACCGATTCCCCCTTT
Found at i:811307 original size:25 final size:24
Alignment explanation
Indices: 811279--811326 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
811269 AACAAAAAGG
811279 GGGAGAAGTGTTAAATGTGATAAAT
1 GGGAGAAGTGTTAAA-GTGATAAAT
*
811304 GGGAGAAGTGTTAAAGTGTTAAA
1 GGGAGAAGTGTTAAAGTGATAAA
811327 GTAAGGGGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.27
Consensus pattern (24 bp):
GGGAGAAGTGTTAAAGTGATAAAT
Found at i:814045 original size:21 final size:21
Alignment explanation
Indices: 813979--814054 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 21
813969 GTTCTAATTC
813979 TAAACAAATTAAATTACTTAT
1 TAAACAAATTAAATTACTTAT
*** ** * *
814000 TATGTAAAAAAAATGTAATT-C
1 TAAACAAATTAAAT-TACTTAT
814021 TAAACAAATTAAATTACTTAT
1 TAAACAAATTAAATTACTTAT
814042 TAAA-AATATTAAA
1 TAAACAA-ATTAAA
814055 AAGTATTGAG
Statistics
Matches: 38, Mismatches: 14, Indels: 6
0.66 0.24 0.10
Matches are distributed among these distances:
20 6 0.16
21 28 0.74
22 4 0.11
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.36
Consensus pattern (21 bp):
TAAACAAATTAAATTACTTAT
Found at i:814124 original size:41 final size:41
Alignment explanation
Indices: 814071--814148 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
814061 TGAGATATTA
*
814071 AAAAATCATAATTTTAAACAAATTAAATTACTTATTAGGTT
1 AAAAATCATAATTCTAAACAAATTAAATTACTTATTAGGTT
*
814112 AAAAATCCTAATTCTAAACAAATTAAATTACTTATTA
1 AAAAATCATAATTCTAAACAAATTAAATTACTTATTA
814149 AAAATATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.37
Consensus pattern (41 bp):
AAAAATCATAATTCTAAACAAATTAAATTACTTATTAGGTT
Found at i:814211 original size:104 final size:105
Alignment explanation
Indices: 813973--814228 Score: 390
Period size: 104 Copynumber: 2.4 Consensus size: 105
813963 TTAAAAGTTC
*
813973 TAATTCTAAACAAATTAAATTACTTATTATGTAAAAAAAAT-GTAATTCTAAACAAATTAAATTA
1 TAATTCTAAACAAATTAAATTACTTATTATGT--AAAAAATCCTAATTCTAAACAAATTAAATTA
*** *
814037 CTTATTAAAAATATTAAAAAGTATTGAGATATTAAAAAATCA
64 CTTATTAAAAATATTAAAAAGTACCAAAATATTAAAAAATCA
* * *
814079 TAATTTTAAACAAATTAAATTACTTATTAGGTTAAAAATCCTAATTCTAAACAAATTAAATTACT
1 TAATTCTAAACAAATTAAATTACTTATTATGTAAAAAATCCTAATTCTAAACAAATTAAATTACT
* *
814144 TATTAAAAATATTAAAAAGTACCAAAATGTT-AAAAATCG
66 TATTAAAAATATTAAAAAGTACCAAAATATTAAAAAATCA
814183 TAATTCTAAACAAATTAAATTACTTATTATGTAAAAAATCCTAATT
1 TAATTCTAAACAAATTAAATTACTTATTATGTAAAAAATCCTAATT
814229 ATAATGTTTT
Statistics
Matches: 136, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
104 56 0.41
105 50 0.37
106 30 0.22
ACGTcount: A:0.52, C:0.09, G:0.04, T:0.36
Consensus pattern (105 bp):
TAATTCTAAACAAATTAAATTACTTATTATGTAAAAAATCCTAATTCTAAACAAATTAAATTACT
TATTAAAAATATTAAAAAGTACCAAAATATTAAAAAATCA
Found at i:816529 original size:16 final size:16
Alignment explanation
Indices: 816508--816538 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
816498 TTTTTTGGTC
*
816508 GGGTCAATATCGGGTT
1 GGGTCAATACCGGGTT
816524 GGGTCAATACCGGGT
1 GGGTCAATACCGGGT
816539 CGCTTGATTT
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:0.19, C:0.16, G:0.39, T:0.26
Consensus pattern (16 bp):
GGGTCAATACCGGGTT
Found at i:817312 original size:16 final size:16
Alignment explanation
Indices: 817266--817347 Score: 65
Period size: 16 Copynumber: 5.1 Consensus size: 16
817256 TAGGGTTTCT
* * *
817266 TTCGAGTTAGTTTTAG
1 TTCGGGTTAATTTTGG
* *
817282 TTCAGGTTACTTTTGG
1 TTCGGGTTAATTTTGG
*
817298 TTCGGGTTAATTTTGA
1 TTCGGGTTAATTTTGG
**
817314 TTCGGGTTGTTTTTGG
1 TTCGGGTTAATTTTGG
* * *
817330 TTTGAGTTAATTTCGG
1 TTCGGGTTAATTTTGG
817346 TT
1 TT
817348 TCGGTCTGTG
Statistics
Matches: 51, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.13, C:0.07, G:0.27, T:0.52
Consensus pattern (16 bp):
TTCGGGTTAATTTTGG
Found at i:826542 original size:23 final size:24
Alignment explanation
Indices: 826508--826553 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
826498 TTTATTTTTA
826508 TTTATATTTTGA-TCACTGTTTGT
1 TTTATATTTTGACTCACTGTTTGT
*
826531 TTTA-ATTATTGACTTACTGTTTG
1 TTTATATT-TTGACTCACTGTTTG
826554 ATTTGACCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 8 0.40
24 9 0.45
ACGTcount: A:0.20, C:0.09, G:0.13, T:0.59
Consensus pattern (24 bp):
TTTATATTTTGACTCACTGTTTGT
Found at i:826925 original size:4 final size:4
Alignment explanation
Indices: 826916--826950 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
826906 ACATTTAGAT
*
826916 ATTA ATTA ATTA ATTA ATTA ATCA ATTTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA A-TTA ATTA AT
826951 AATAGGAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.89
5 3 0.11
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (4 bp):
ATTA
Found at i:831066 original size:31 final size:31
Alignment explanation
Indices: 831031--831092 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
831021 ATTAATTTCA
831031 AAATGAATTTTGATTTTGAAAAAAACTACTC
1 AAATGAATTTTGATTTTGAAAAAAACTACTC
** *
831062 AAATGAATTTTGATTTTTTAAAATACTACTC
1 AAATGAATTTTGATTTTGAAAAAAACTACTC
831093 CCCCTTACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (31 bp):
AAATGAATTTTGATTTTGAAAAAAACTACTC
Found at i:831702 original size:18 final size:18
Alignment explanation
Indices: 831679--831724 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
831669 AGGCATTTGA
* *
831679 TCCTCTGGTTGTGATTGT
1 TCCTCTGCTCGTGATTGT
*
831697 TCCTCTGCTCGTGCTTGT
1 TCCTCTGCTCGTGATTGT
831715 TCCTCGTGCT
1 TCCTC-TGCT
831725 TTTCTGGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.02, C:0.28, G:0.24, T:0.46
Consensus pattern (18 bp):
TCCTCTGCTCGTGATTGT
Found at i:833345 original size:23 final size:22
Alignment explanation
Indices: 833309--833367 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 22
833299 GGGGTATCGA
833309 TTCCCC-T-AAGGGGGAATCAG
1 TTCCCCTTCAAGGGGGAATCAG
833329 TTCCCCTTCAAAGGGGGAATCAG
1 TTCCCCTTC-AAGGGGGAATCAG
*
833352 TTCCCTTTCAAGGGGG
1 TTCCCCTTCAAGGGGG
833368 TATCGATTCC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
20 6 0.17
21 1 0.03
22 7 0.20
23 21 0.60
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24
Consensus pattern (22 bp):
TTCCCCTTCAAGGGGGAATCAG
Found at i:848753 original size:55 final size:54
Alignment explanation
Indices: 848668--848883 Score: 281
Period size: 55 Copynumber: 3.9 Consensus size: 54
848658 TGGAGTAGAC
* * * *
848668 CCATTTTTCGAAGAATTTTCAAGTCCTATACTCCCTGGAAGGAGAGGGAGCGGGT
1 CCATTTTTCGAAGATTTTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGC-GGA
* * * *
848723 CCATTTTTCTAAGATTGTTCGAGTCTTATACTCCCTGAAAGAAGAGGGAGCGGA
1 CCATTTTTCGAAGATTTTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGA
* * * *
848777 CCAATTTTCCAAAGATTTTTCAAGGCCTATACTCCCTGAAAGAAGAGGGAGCGAA
1 CC-ATTTTTCGAAGATTTTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGA
848832 CC-TGATTTTCGAAGATTTTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGC
1 CCAT--TTTTCGAAGATTTTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGC
848884 ATACCATTCT
Statistics
Matches: 140, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
53 1 0.01
54 4 0.03
55 135 0.96
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (54 bp):
CCATTTTTCGAAGATTTTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGA
Found at i:850536 original size:33 final size:33
Alignment explanation
Indices: 850499--850688 Score: 142
Period size: 33 Copynumber: 5.8 Consensus size: 33
850489 AATTTTGGGT
850499 TCGGGTTTTTTAAAGTTTGATATTCGGGTCGGG
1 TCGGGTTTTTTAAAGTTTGATATTCGGGTCGGG
* * *
850532 TCGGGTTTTTGT-AAGTGTGATATTAGGGTAGGG
1 TCGGGTTTTT-TAAAGTTTGATATTCGGGTCGGG
* *
850565 TCGGGTTTTTTTCAAA----AAAATTCGGGATCGGG
1 TCGGG-TTTTTT-AAAGTTTGATATTCGGG-TCGGG
** ***
850597 TCAGATTTTTTTTAAA-TTTCG-GGCTCGGGTCGGG
1 TC-G-GGTTTTTTAAAGTTT-GATATTCGGGTCGGG
* *
850631 TCGGGTTTTTTTAAGTTTGATATTCGGGTTGGG
1 TCGGGTTTTTTAAAGTTTGATATTCGGGTCGGG
* *
850664 TCGGGTTTTTTTAAGTGTGATATTC
1 TCGGGTTTTTTAAAGTTTGATATTC
850689 AAGTCAGGTT
Statistics
Matches: 123, Mismatches: 21, Indels: 26
0.72 0.12 0.15
Matches are distributed among these distances:
31 7 0.06
32 18 0.15
33 78 0.63
34 13 0.11
35 7 0.06
ACGTcount: A:0.17, C:0.09, G:0.32, T:0.43
Consensus pattern (33 bp):
TCGGGTTTTTTAAAGTTTGATATTCGGGTCGGG
Found at i:850702 original size:34 final size:33
Alignment explanation
Indices: 850628--850705 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
850618 GGCTCGGGTC
* ** *
850628 GGGTCGGGTTTTTTTAAGTTTGATATTCGGGTT
1 GGGTCGGGTTTTTTTAAGTGTGATATTCAAGTA
850661 GGGTCGGGTTTTTTTAAGTGTGATATTCAAGTCA
1 GGGTCGGGTTTTTTTAAGTGTGATATTCAAGT-A
*
850695 GGTTCGGGTTT
1 GGGTCGGGTTT
850706 AGGGTGAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 29 0.74
34 10 0.26
ACGTcount: A:0.14, C:0.08, G:0.33, T:0.45
Consensus pattern (33 bp):
GGGTCGGGTTTTTTTAAGTGTGATATTCAAGTA
Found at i:851282 original size:16 final size:16
Alignment explanation
Indices: 851261--851291 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
851251 ATTTCAGATT
*
851261 CATATTCCAATTCCTA
1 CATATTCAAATTCCTA
851277 CATATTCAAATTCCT
1 CATATTCAAATTCCT
851292 TCACAGATTT
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:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (16 bp):
CATATTCAAATTCCTA
Found at i:853125 original size:29 final size:30
Alignment explanation
Indices: 853041--853137 Score: 135
Period size: 29 Copynumber: 3.2 Consensus size: 30
853031 CGTAAATTTG
*
853041 ATTACATGAAAATCATTTTATGTAAAAATGA
1 ATTACATGAAAATTATTTTATGT-AAAATGA
853072 ATTACATGAAAATTATTTTATGTAAAATGA
1 ATTACATGAAAATTATTTTATGTAAAATGA
* *
853102 ATTAGC-T-AAAATTGTTTTAGGTAAAATGA
1 ATTA-CATGAAAATTATTTTATGTAAAATGA
853131 ATTACAT
1 ATTACAT
853138 TTTCTAGGAA
Statistics
Matches: 61, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
28 1 0.02
29 25 0.41
30 12 0.20
31 23 0.38
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.38
Consensus pattern (30 bp):
ATTACATGAAAATTATTTTATGTAAAATGA
Found at i:853426 original size:19 final size:19
Alignment explanation
Indices: 853404--853446 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
853394 TTTATTAACA
*
853404 TAATACTAAAT-TATTATAT
1 TAATACTAAATATA-TAAAT
*
853423 TAATATTAAATATATAAAT
1 TAATACTAAATATATAAAT
853442 TAATA
1 TAATA
853447 TTACTCATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATACTAAATATATAAAT
Found at i:854236 original size:37 final size:37
Alignment explanation
Indices: 854162--854236 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
854152 TACTATAAAT
* **
854162 AATTTATATATTTTCTTTAAAAAATTTAAATTCATAA
1 AATTTATATATTTTCTTTAAAAAATTGAAATAAATAA
* *
854199 AATTTATATAATTTTTTTTACAAAATTGAAA-AAATAA
1 AATTTATAT-ATTTTCTTTAAAAAATTGAAATAAATAA
854236 A
1 A
854237 TATGTTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 14 0.44
38 18 0.56
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
AATTTATATATTTTCTTTAAAAAATTGAAATAAATAA
Found at i:858618 original size:73 final size:74
Alignment explanation
Indices: 858531--858678 Score: 174
Period size: 74 Copynumber: 2.0 Consensus size: 74
858521 CTCATCTTAT
* * * * * *
858531 TTACAACCCTAAATTTATTCTTACGAGTGT-T-TCGAGCTTGAATGTTAAACCATGCTTGATATT
1 TTACAACCCCAAATTCATTCGTACG-GTGTATCTCGAGCTTGAATGTCAAACCATGCTTAATACT
858594 GTATGAAAGA
65 GTATGAAAGA
* * * * *
858604 TTACAACCCCAAATTCATTCGTACGGTGTATCTTGAGTTTGAATGTCAGACCATGTTTAATGCTG
1 TTACAACCCCAAATTCATTCGTACGGTGTATCTCGAGCTTGAATGTCAAACCATGCTTAATACTG
858669 TATGAAAGA
66 TATGAAAGA
858678 T
1 T
858679 GGGATTAGTT
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
72 4 0.06
73 23 0.37
74 35 0.56
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (74 bp):
TTACAACCCCAAATTCATTCGTACGGTGTATCTCGAGCTTGAATGTCAAACCATGCTTAATACTG
TATGAAAGA
Found at i:859190 original size:13 final size:13
Alignment explanation
Indices: 859172--859198 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
859162 TTTTAAATGT
859172 GTGTCATCTTTAG
1 GTGTCATCTTTAG
859185 GTGTCATCTTTAG
1 GTGTCATCTTTAG
859198 G
1 G
859199 AGTCGTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.44
Consensus pattern (13 bp):
GTGTCATCTTTAG
Found at i:863926 original size:2 final size:2
Alignment explanation
Indices: 863919--864023 Score: 87
Period size: 2 Copynumber: 55.0 Consensus size: 2
863909 ATTATAGTTA
*
863919 AT AT AT AT AT AT CT -T 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
** * * * * *
863960 AT AT AT CC AC CT -T AG A- AA AA AT -T AT AGT -T A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
863998 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
864024 TCACCTTAAA
Statistics
Matches: 88, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
1 6 0.07
2 81 0.92
3 1 0.01
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:866019 original size:183 final size:183
Alignment explanation
Indices: 865631--866019 Score: 570
Period size: 183 Copynumber: 2.1 Consensus size: 183
865621 ATCAAATTTT
*
865631 AAATATTAAATATATTATATATATAACATATGAACTCAACCCAAATCATTAAAACCCCAATTAAT
1 AAATATTAAATATA-T-TATATATAACATATGAACTCAACCCAAACCATTAAAACCCCAATTAAT
* *
865696 ACTTTAAAATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAATTT
64 AATTTAAAATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATT
* *
865761 TTTAATTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTCTAATTAAA
129 TTTAATTTATAATGATATATTATTTAAATTAATTATAAACTGTTTTCTAATTAAA
**
865816 AAATATTAAATATATTATATATAACATATGGGCT-AAGCCCAAACCATTTAAAA-CCCAATTAAT
1 AAATATTAAATATATTATATATAACATATGAACTCAA-CCCAAACCA-TTAAAACCCCAATTAAT
* *
865879 AATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATCTAAAAT
64 AATTTAAAATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAA-TTATATAAAAT
* * *
865944 TTTTATTTTATAATGATTTATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
128 TTTTAATTTATAATGATATATTATTTAAATTAATTATAAACTGTTTTCT-AATTAAA
* *
866000 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
866020 AATTAGAAAA
Statistics
Matches: 186, Mismatches: 14, Indels: 10
0.89 0.07 0.05
Matches are distributed among these distances:
182 2 0.01
183 99 0.53
184 71 0.38
185 14 0.08
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.42
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAACATATGAACTCAACCCAAACCATTAAAACCCCAATTAATAA
TTTAAAATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
TAATTTATAATGATATATTATTTAAATTAATTATAAACTGTTTTCTAATTAAA
Found at i:867887 original size:2 final size:2
Alignment explanation
Indices: 867882--867939 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
867872 ATTATTTCCT
867882 TA TA TA T- 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
867923 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
867940 TATTTATTAT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:868061 original size:25 final size:25
Alignment explanation
Indices: 868012--868064 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
868002 ATTTCTCGAC
*
868012 TATTATTAATATTTAGTATTATTTT
1 TATTATTAATATGTAGTATTATTTT
*
868037 TATTATTAAATATGTA-TA-TACTTT
1 TATTATT-AATATGTAGTATTATTTT
868061 TATT
1 TATT
868065 TATTTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.36
25 9 0.36
26 7 0.28
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (25 bp):
TATTATTAATATGTAGTATTATTTT
Found at i:868092 original size:25 final size:25
Alignment explanation
Indices: 868059--868121 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
868049 TGTATATACT
*
868059 TTTATTTATTTTA-TTTTTTA-ATATA
1 TTTA-TTATTTTACTATTTTACAT-TA
868084 TTCTATTATTTTACTATTTTACATTA
1 TT-TATTATTTTACTATTTTACATTA
*
868110 TTTTTTATTTTA
1 TTTATTATTTTA
868122 ACACACACAC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 19 0.58
26 12 0.36
27 2 0.06
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTATTATTTTACTATTTTACATTA
Found at i:868141 original size:2 final size:2
Alignment explanation
Indices: 868136--868196 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
868126 ACACACACAC
868136 AT AT AT AT AT AT AT AT -T 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
868177 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
868197 TGTTTGGTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:868343 original size:30 final size:31
Alignment explanation
Indices: 868307--868377 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 31
868297 ATTTATATTT
* *
868307 TTTTATTATT-TTTCT-CTTATATTTGTTTAA
1 TTTTATTATTACTTCTGATTATATTTGTTT-A
*
868337 TTTTATT-TTACTTCTGATTCTATTTGTTTA
1 TTTTATTATTACTTCTGATTATATTTGTTTA
868367 TTTTATGTATT
1 TTTTAT-TATT
868378 GTCTTCCTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
29 2 0.06
30 18 0.53
31 12 0.35
32 2 0.06
ACGTcount: A:0.18, C:0.07, G:0.06, T:0.69
Consensus pattern (31 bp):
TTTTATTATTACTTCTGATTATATTTGTTTA
Found at i:871770 original size:26 final size:28
Alignment explanation
Indices: 871731--871782 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
871721 ACATTACATA
*
871731 TTTTGTATTTTATA-TTT-CATGTTTGT
1 TTTTGTATTATATATTTTCCATGTTTGT
*
871757 TTTTTTATTATATATTTTCCATGTTT
1 TTTTGTATTATATATTTTCCATGTTT
871783 TTACATTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 12 0.55
27 3 0.14
28 7 0.32
ACGTcount: A:0.17, C:0.06, G:0.08, T:0.69
Consensus pattern (28 bp):
TTTTGTATTATATATTTTCCATGTTTGT
Found at i:872645 original size:3 final size:3
Alignment explanation
Indices: 872637--872692 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
872627 AATATTATAT
* * * *
872637 TTA TTA TTA TTA TAA TTA TTT TTCA TTA TTA TTA TTA TTA ATG TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
872683 TTA TTA TTA T
1 TTA TTA TTA T
872693 ATTTTTATGC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
3 42 0.95
4 2 0.05
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:874691 original size:2 final size:2
Alignment explanation
Indices: 874686--874710 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
874676 TAATAAATCG
874686 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 T
874711 TTATTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:874860 original size:2 final size:2
Alignment explanation
Indices: 874853--874877 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
874843 TATGGATTAG
874853 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 T
874878 TAAAATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:879390 original size:35 final size:35
Alignment explanation
Indices: 879344--879484 Score: 237
Period size: 35 Copynumber: 4.0 Consensus size: 35
879334 GCAAACTCAA
*
879344 GTGGGGCGTCAAAGCACATAATGTAACATCCGTTT
1 GTGGGGCGTCAAAGCACATAATGTAGCATCCGTTT
*
879379 GTGGGGCGTCAAAGCATATAATGTAGCATCCGTTT
1 GTGGGGCGTCAAAGCACATAATGTAGCATCCGTTT
*
879414 GTAGGGCGTCAAAGCACATAATGTAGCATCCGTTT
1 GTGGGGCGTCAAAGCACATAATGTAGCATCCGTTT
* *
879449 ATGGGGCATCAAAGCACATAATGTAGCATCCGTTT
1 GTGGGGCGTCAAAGCACATAATGTAGCATCCGTTT
879484 G
1 G
879485 GGTCAAGTGT
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 98 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (35 bp):
GTGGGGCGTCAAAGCACATAATGTAGCATCCGTTT
Found at i:882487 original size:29 final size:30
Alignment explanation
Indices: 882417--882474 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
882407 CAATTTAAGG
882417 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
882448 CAAAATGTTTTTGGACTT-AATTGAATT
1 CAAAATGTTTTTGGACTTGAATTGAATT
882475 AATTCAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 9 0.33
30 12 0.44
31 6 0.22
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:882584 original size:21 final size:21
Alignment explanation
Indices: 882558--882609 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
882548 GGTGTCAAAG
882558 TGCATCCATGCACCCCTGCAA
1 TGCATCCATGCACCCCTGCAA
* *
882579 TGCATCCATGCATCCCTGCAG
1 TGCATCCATGCACCCCTGCAA
882600 TGCATCCATG
1 TGCATCCATG
882610 TACCTGCACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.23
Consensus pattern (21 bp):
TGCATCCATGCACCCCTGCAA
Found at i:882603 original size:42 final size:42
Alignment explanation
Indices: 882556--882654 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
882546 AGGGTGTCAA
*
882556 AGTGCATCCATGCACCCCTGCA-A-TGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGCACAGTGCATCCATGCA-CCATGC
* *
882598 AGTGCATCCATGTA-CCTGCACTAGTGCATCGATGCACCATGC
1 AGTGCATCCATGCACCCTGCAC-AGTGCATCCATGCACCATGC
*
882640 AGTGCATCCTTGCAC
1 AGTGCATCCATGCAC
882655 TCCATTTCGA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
40 6 0.12
42 31 0.65
43 11 0.23
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.23
Consensus pattern (42 bp):
AGTGCATCCATGCACCCTGCACAGTGCATCCATGCACCATGC
Found at i:882700 original size:20 final size:20
Alignment explanation
Indices: 882674--882747 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
882664 AATGCACTTA
882674 GTGCATCGATGCATCCTGAT
1 GTGCATCGATGCATCCTGAT
* **
882694 ATGCATCGATGCATCAAGGAT
1 GTGCATCGATGCATC-CTGAT
*
882715 GTGCATCGATGCATCCTGTT
1 GTGCATCGATGCATCCTGAT
*
882735 GTGCATCCATGCA
1 GTGCATCGATGCA
882748 AGAAGGCTGC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 28 0.62
21 17 0.38
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.28
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGAT
Found at i:882721 original size:21 final size:20
Alignment explanation
Indices: 882674--882729 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
882664 AATGCACTTA
**
882674 GTGCATCGATGCATCCTGAT
1 GTGCATCGATGCATCAGGAT
*
882694 ATGCATCGATGCATCAAGGAT
1 GTGCATCGATGCATC-AGGAT
882715 GTGCATCGATGCATC
1 GTGCATCGATGCATC
882730 CTGTTGTGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (20 bp):
GTGCATCGATGCATCAGGAT
Found at i:882814 original size:13 final size:13
Alignment explanation
Indices: 882796--882857 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 13
882786 GGGGTATCGA
882796 TGCACCATGATAG
1 TGCACCATGATAG
882809 TGCACC--G--A-
1 TGCACCATGATAG
882817 TGCACCATGATAG
1 TGCACCATGATAG
882830 TGCACC---A-A-
1 TGCACCATGATAG
882838 TGCACCATGATAG
1 TGCACCATGATAG
882851 TGCACCA
1 TGCACCA
882858 ATGCACCATG
Statistics
Matches: 39, Mismatches: 0, Indels: 20
0.66 0.00 0.34
Matches are distributed among these distances:
8 12 0.31
9 2 0.05
10 2 0.05
11 2 0.05
12 2 0.05
13 19 0.49
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (13 bp):
TGCACCATGATAG
Found at i:882817 original size:21 final size:21
Alignment explanation
Indices: 882795--882867 Score: 137
Period size: 21 Copynumber: 3.5 Consensus size: 21
882785 AGGGGTATCG
*
882795 ATGCACCATGATAGTGCACCG
1 ATGCACCATGATAGTGCACCA
882816 ATGCACCATGATAGTGCACCA
1 ATGCACCATGATAGTGCACCA
882837 ATGCACCATGATAGTGCACCA
1 ATGCACCATGATAGTGCACCA
882858 ATGCACCATG
1 ATGCACCATG
882868 TTATGGGCAG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.19
Consensus pattern (21 bp):
ATGCACCATGATAGTGCACCA
Found at i:884213 original size:13 final size:16
Alignment explanation
Indices: 884177--884214 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
884167 CTCACTCATG
884177 AGATGATGGTGAAGGA
1 AGATGATGGTGAAGGA
884193 AGATGATGGTGAAGGA
1 AGATGATGGTGAAGGA
884209 AGATGA
1 AGATGA
884215 AGAAAGGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.42, T:0.18
Consensus pattern (16 bp):
AGATGATGGTGAAGGA
Found at i:886072 original size:34 final size:30
Alignment explanation
Indices: 886034--886102 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
886024 TTGATATAAC
886034 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
886068 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
886097 AATTTA
1 AATTTA
886103 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:886113 original size:29 final size:30
Alignment explanation
Indices: 886043--886102 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
886033 CAATTTAAGG
886043 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
886074 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
886103 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:886211 original size:21 final size:20
Alignment explanation
Indices: 886182--886280 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 20
886172 AGGGTGTCAA
*
886182 AGTGAATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
886203 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
886224 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
* *
886245 TAGTGCATCGATGCACCATGC
1 -AGTGCATCCATGCACCCTGC
886266 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
886281 TCCATTTCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.06
20 14 0.20
21 35 0.51
22 13 0.19
23 3 0.04
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.21
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:886216 original size:13 final size:14
Alignment explanation
Indices: 886213--886280 Score: 54
Period size: 13 Copynumber: 4.9 Consensus size: 14
886203 AGTGCATCCA
*
886213 TGCATCCCTGCA-G
1 TGCATCCATGCACG
*
886226 TGCATCCATGCACC
1 TGCATCCATGCACG
*
886240 TGCA-CTAGTGCATCG
1 TGCATCCA-TGCA-CG
886255 ATGCA-CCATGCA-G
1 -TGCATCCATGCACG
886268 TGCATCCATGCAC
1 TGCATCCATGCAC
886281 TCCATTTCGA
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
12 4 0.09
13 21 0.48
14 8 0.18
15 5 0.11
16 6 0.14
ACGTcount: A:0.22, C:0.35, G:0.21, T:0.22
Consensus pattern (14 bp):
TGCATCCATGCACG
Found at i:886381 original size:21 final size:20
Alignment explanation
Indices: 886352--886450 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 20
886342 AGGGTGTCAA
*
886352 AGTGAATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
886373 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
886394 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
* *
886415 TAGTGCATCGATGCACCATGC
1 -AGTGCATCCATGCACCCTGC
886436 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
886451 TCCATTTCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.06
20 14 0.20
21 35 0.51
22 13 0.19
23 3 0.04
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.21
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:886386 original size:13 final size:14
Alignment explanation
Indices: 886383--886450 Score: 54
Period size: 13 Copynumber: 4.9 Consensus size: 14
886373 AGTGCATCCA
*
886383 TGCATCCCTGCA-G
1 TGCATCCATGCACG
*
886396 TGCATCCATGCACC
1 TGCATCCATGCACG
*
886410 TGCA-CTAGTGCATCG
1 TGCATCCA-TGCA-CG
886425 ATGCA-CCATGCA-G
1 -TGCATCCATGCACG
886438 TGCATCCATGCAC
1 TGCATCCATGCAC
886451 TCCATTTCGA
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
12 4 0.09
13 21 0.48
14 8 0.18
15 5 0.11
16 6 0.14
ACGTcount: A:0.22, C:0.35, G:0.21, T:0.22
Consensus pattern (14 bp):
TGCATCCATGCACG
Found at i:886434 original size:170 final size:170
Alignment explanation
Indices: 886152--886492 Score: 682
Period size: 170 Copynumber: 2.0 Consensus size: 170
886142 ATTAAATTCG
886152 GATTTGAGCCAAAATGCTAAAGGGTGTCAAAGTGAATCCATGCACCCCTGCAGTGCATCCATGCA
1 GATTTGAGCCAAAATGCTAAAGGGTGTCAAAGTGAATCCATGCACCCCTGCAGTGCATCCATGCA
886217 TCCCTGCAGTGCATCCATGCACCTGCACTAGTGCATCGATGCACCATGCAGTGCATCCATGCACT
66 TCCCTGCAGTGCATCCATGCACCTGCACTAGTGCATCGATGCACCATGCAGTGCATCCATGCACT
886282 CCATTTCGAATGCACTTAGTGCATCGATGCATCCTGATGT
131 CCATTTCGAATGCACTTAGTGCATCGATGCATCCTGATGT
886322 GATTTGAGCCAAAATGCTAAAGGGTGTCAAAGTGAATCCATGCACCCCTGCAGTGCATCCATGCA
1 GATTTGAGCCAAAATGCTAAAGGGTGTCAAAGTGAATCCATGCACCCCTGCAGTGCATCCATGCA
886387 TCCCTGCAGTGCATCCATGCACCTGCACTAGTGCATCGATGCACCATGCAGTGCATCCATGCACT
66 TCCCTGCAGTGCATCCATGCACCTGCACTAGTGCATCGATGCACCATGCAGTGCATCCATGCACT
886452 CCATTTCGAATGCACTTAGTGCATCGATGCATCCTGATGT
131 CCATTTCGAATGCACTTAGTGCATCGATGCATCCTGATGT
886492 G
1 G
886493 CATCGATGCA
Statistics
Matches: 171, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
170 171 1.00
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (170 bp):
GATTTGAGCCAAAATGCTAAAGGGTGTCAAAGTGAATCCATGCACCCCTGCAGTGCATCCATGCA
TCCCTGCAGTGCATCCATGCACCTGCACTAGTGCATCGATGCACCATGCAGTGCATCCATGCACT
CCATTTCGAATGCACTTAGTGCATCGATGCATCCTGATGT
Found at i:886495 original size:20 final size:20
Alignment explanation
Indices: 886470--886544 Score: 105
Period size: 20 Copynumber: 3.7 Consensus size: 20
886460 AATGCACTTA
886470 GTGCATCGATGCATCCTGAT
1 GTGCATCGATGCATCCTGAT
**
886490 GTGCATCGATGCATCAAGATT
1 GTGCATCGATGCATCCTGA-T
*
886511 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGAT
*
886531 GTGCATCCATGCAT
1 GTGCATCGATGCAT
886545 GAAGGCTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 31 0.65
21 17 0.35
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGAT
Found at i:887859 original size:43 final size:43
Alignment explanation
Indices: 887738--887888 Score: 191
Period size: 43 Copynumber: 3.6 Consensus size: 43
887728 CTTGATTTTC
* * * *
887738 AGGGGTTCCTTGATGACACGCTTAAAAGACCATCGTGATATGT
1 AGGGGTTCCTTGATGAAAAGCTTGAGAGACCATCGTGATATGT
* *
887781 AGGGGTT-CTT--TGATAAGCTTGAGAAACCATCGTGATATGT
1 AGGGGTTCCTTGATGAAAAGCTTGAGAGACCATCGTGATATGT
* * *
887821 AGGGGTTTCTTGATGAAAAGCTTGAGGGACCATTGTGATATGT
1 AGGGGTTCCTTGATGAAAAGCTTGAGAGACCATCGTGATATGT
*
887864 AGGGGTTCCTTGATGAAAAACTTGA
1 AGGGGTTCCTTGATGAAAAGCTTGA
887889 TGAACATTTG
Statistics
Matches: 94, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
40 32 0.34
41 3 0.03
42 3 0.03
43 56 0.60
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.30
Consensus pattern (43 bp):
AGGGGTTCCTTGATGAAAAGCTTGAGAGACCATCGTGATATGT
Found at i:888117 original size:90 final size:90
Alignment explanation
Indices: 887964--888444 Score: 687
Period size: 90 Copynumber: 5.3 Consensus size: 90
887954 ATTTTCAAGA
* * * *
887964 GTTTCTTGATTTCTAAGTCCTTCGGGTCATCTATAAAACCTTCAGTGCAGGATATTTTCAAATGA
1 GTTTCTTGATTTTTAAGTCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGA
* *
888029 AATTTTAAAAACTAAGCCTTCGGGG
66 GATTTTAAAAACTAAGCCTTCAGGG
* *
888054 GTTTCTTGATTTTTAAGTCCTTCGGGTCATCCATAAGACCTTCAGTGCATGATATTTTCAAATGA
1 GTTTCTTGATTTTTAAGTCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGA
* *
888119 GA-TCTAAGAAACTGAGCCTTCAGGG
66 GATTTTAA-AAACTAAGCCTTCAGGG
*
888144 GTTTCTTGATTTTTAAGTCCTTCGGGTCATCCATAAGACCTTCAGTGCATGATGTTTTCAAATGA
1 GTTTCTTGATTTTTAAGTCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGA
* * *
888209 GA-TCTAAGAAACTGAGCCTTCGGGG
66 GATTTTAA-AAACTAAGCCTTCAGGG
* * *
888234 GTTTCTAGATTTTTATGTCTTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGA
1 GTTTCTTGATTTTTAAGTCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGA
* * * *
888299 AATTTTAGAAACTAAGACTTCCGGG
66 GATTTTAAAAACTAAGCCTTCAGGG
* *
888324 GTTTCTTGATTTTTAAGTCCTTTGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGA
1 GTTTCTTGATTTTTAAGTCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGA
*
888389 GATTTTAGAAACTAAGCCTTCAGGG
66 GATTTTAAAAACTAAGCCTTCAGGG
* * *
888414 GTTTCTTAATTTTTAAATCCTACGGGTCATC
1 GTTTCTTGATTTTTAAGTCCTTCGGGTCATC
888445 AGTAAATCTT
Statistics
Matches: 356, Mismatches: 33, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
89 4 0.01
90 349 0.98
91 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (90 bp):
GTTTCTTGATTTTTAAGTCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGA
GATTTTAAAAACTAAGCCTTCAGGG
Found at i:896190 original size:32 final size:32
Alignment explanation
Indices: 896153--896225 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
896143 CAAATTTTCT
*
896153 TTTATTTCTTTTTAAATTTATTATCTATCTTC
1 TTTATTTCATTTTAAATTTATTATCTATCTTC
*
896185 TTTATTTCATTTTAAATTTATTGTCTATCTTC
1 TTTATTTCATTTTAAATTTATTATCTATCTTC
896217 TTTATTTCA
1 TTTATTTCA
896226 GTACGTTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.22, C:0.12, G:0.01, T:0.64
Consensus pattern (32 bp):
TTTATTTCATTTTAAATTTATTATCTATCTTC
Found at i:896220 original size:16 final size:15
Alignment explanation
Indices: 896169--896224 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
896159 TCTTTTTAAA
896169 TTTATTATCTATCTTC
1 TTTATT-TCTATCTTC
* *
896185 TTTATTTC-ATTTTAAA
1 TTTATTTCTATCTT--C
896201 TTTATTGTCTATCTTC
1 TTTATT-TCTATCTTC
896217 TTTATTTC
1 TTTATTTC
896225 AGTACGTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
14 4 0.12
15 4 0.12
16 18 0.56
17 2 0.06
18 4 0.12
ACGTcount: A:0.20, C:0.14, G:0.02, T:0.64
Consensus pattern (15 bp):
TTTATTTCTATCTTC
Found at i:899816 original size:13 final size:13
Alignment explanation
Indices: 899798--899836 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
899788 TAGAAAGAAG
899798 AAAAAACAAAAAC
1 AAAAAACAAAAAC
*
899811 AAAAAACAAAAAG
1 AAAAAACAAAAAC
*
899824 AGAAAA-AAAAAC
1 AAAAAACAAAAAC
899836 A
1 A
899837 TTTAGAGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.85, C:0.10, G:0.05, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAAAC
Found at i:899897 original size:8 final size:7
Alignment explanation
Indices: 899872--899928 Score: 53
Period size: 7 Copynumber: 8.0 Consensus size: 7
899862 ATCTAAATTG
899872 AAAAA-A
1 AAAAAGA
*
899878 AAAGAGA
1 AAAAAGA
899885 AAAAAGA
1 AAAAAGA
899892 ACAAAAGA
1 A-AAAAGA
*
899900 GAAAAGA
1 AAAAAGA
*
899907 GAAAAGA
1 AAAAAGA
*
899914 GAAAAGA
1 AAAAAGA
899921 AAATAAGA
1 AAA-AAGA
899929 TGGGTTAAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
6 4 0.09
7 30 0.68
8 10 0.23
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (7 bp):
AAAAAGA
Found at i:899899 original size:17 final size:17
Alignment explanation
Indices: 899877--899909 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
899867 AATTGAAAAA
899877 AAAAGAGAAAAAAGAAC
1 AAAAGAGAAAAAAGAAC
*
899894 AAAAGAGAAAAGAGAA
1 AAAAGAGAAAAAAGAA
899910 AAGAGAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAAGAGAAAAAAGAAC
Found at i:901180 original size:106 final size:107
Alignment explanation
Indices: 901019--901262 Score: 359
Period size: 106 Copynumber: 2.3 Consensus size: 107
901009 ACGAAGGGGC
* *
901019 TTCCCAGTTTCAAAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCAAGACAACACAAGCT
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTAGACTCAAGACAACACAAGCT
* * *
901084 CAACTTCATGAG-GAAGGGGCGGCTGATTGTC-AACAAACAACT
66 CAACTTCA-CAGCGAAGGGGCAGCTGACTGTCAAACAAACAA-T
* * *
901126 TT-CCAGTTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTAGACTCGAGACATCACAAGCT
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTAGACTCAAGACAACACAAGCT
*
901190 CAACTTCACAGCGAAGGGGCAGCTGGCTGTCAAACAAACAAT
66 CAACTTCACAGCGAAGGGGCAGCTGACTGTCAAACAAACAAT
*
901232 TTCCCAGTTCCAGAGCCAATTTCAACTTCAC
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCAC
901263 GGCAGAATAT
Statistics
Matches: 124, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
105 2 0.02
106 84 0.68
107 38 0.31
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.22
Consensus pattern (107 bp):
TTCCCAGTTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTAGACTCAAGACAACACAAGCT
CAACTTCACAGCGAAGGGGCAGCTGACTGTCAAACAAACAAT
Found at i:902899 original size:2 final size:2
Alignment explanation
Indices: 902894--902942 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
902884 TTTATTTCCT
902894 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
902936 TA TA TA T
1 TA TA TA T
902943 TGTATTTCTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:903005 original size:25 final size:25
Alignment explanation
Indices: 902956--903008 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
902946 ATTTCTCGAC
*
902956 TATTATTAATATTTAGTATTATTTT
1 TATTATTAATATGTAGTATTATTTT
*
902981 TATTATTAAATATGTA-TA-TACTTT
1 TATTATT-AATATGTAGTATTATTTT
903005 TATT
1 TATT
903009 TATTTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.36
25 9 0.36
26 7 0.28
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (25 bp):
TATTATTAATATGTAGTATTATTTT
Found at i:903024 original size:17 final size:17
Alignment explanation
Indices: 903002--903040 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
902992 ATGTATATAC
* * *
903002 TTTTATTTATTTTATTT
1 TTTTATATATTCTATTA
903019 TTTTATATATTCTATTA
1 TTTTATATATTCTATTA
903036 TTTTA
1 TTTTA
903041 CTATTTTACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTATATATTCTATTA
Found at i:903047 original size:25 final size:25
Alignment explanation
Indices: 903003--903065 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
902993 TGTATATACT
* * *
903003 TTTATTTATTTTATTTTTTTATA-TA
1 TTTA-TTATTTTACTATTTTACATTA
903028 TTCTATTATTTTACTATTTTACATTA
1 TT-TATTATTTTACTATTTTACATTA
*
903054 TTTTTTATTTTA
1 TTTATTATTTTA
903066 ACATATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 26 0.81
26 6 0.19
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (25 bp):
TTTATTATTTTACTATTTTACATTA
Found at i:903073 original size:2 final size:2
Alignment explanation
Indices: 903068--903103 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
903058 TTATTTTAAC
903068 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
903104 TTTCGGGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:903445 original size:14 final size:13
Alignment explanation
Indices: 903420--903444 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
903410 TCTCACCTTT
903420 TTTTATTTTTTTG
1 TTTTATTTTTTTG
903433 TTTTATTTTTTT
1 TTTTATTTTTTT
903445 TACTTATTTT
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:0.08, C:0.00, G:0.04, T:0.88
Consensus pattern (13 bp):
TTTTATTTTTTTG
Found at i:906332 original size:10 final size:10
Alignment explanation
Indices: 906314--906368 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
906304 TACCTTTTAA
*
906314 TTTAATTATT
1 TTTAGTTATT
*
906324 TTTAGTTATA
1 TTTAGTTATT
906334 TTT-GTTGATT
1 TTTAGTT-ATT
*
906344 TTTAGTTATA
1 TTTAGTTATT
906354 TTT-GTTAATT
1 TTTAGTT-ATT
906364 TTTAG
1 TTTAG
906369 AACCTATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
9 6 0.17
10 26 0.72
11 4 0.11
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.65
Consensus pattern (10 bp):
TTTAGTTATT
Found at i:906344 original size:20 final size:20
Alignment explanation
Indices: 906321--906368 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
906311 TAATTTAATT
*
906321 ATTTTTAGTTATATTTGTTG
1 ATTTTTAGTTATATTTGTTA
906341 ATTTTTAGTTATATTTGTTA
1 ATTTTTAGTTATATTTGTTA
906361 ATTTTTAG
1 ATTTTTAG
906369 AACCTATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.12, T:0.65
Consensus pattern (20 bp):
ATTTTTAGTTATATTTGTTA
Found at i:915536 original size:50 final size:48
Alignment explanation
Indices: 915482--915586 Score: 124
Period size: 47 Copynumber: 2.1 Consensus size: 48
915472 AGATGCGATA
** *
915482 AATTTT-AATAAAAAATTATATTTTATTAAAACTCATCACTTCAAGATTAC-
1 AATTTTAAAT-AAAAA--ATATTTT-TTAAAACTCATCACCCCAAGATAACG
*
915532 AATTTTAAATAAAAAATATTTTTTAGAACTCATCACCCCAAGATAACG
1 AATTTTAAATAAAAAATATTTTTTAAAACTCATCACCCCAAGATAACG
915580 AATTTTA
1 AATTTTA
915587 TGGACACCGT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
47 21 0.43
48 14 0.29
50 11 0.22
51 3 0.06
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (48 bp):
AATTTTAAATAAAAAATATTTTTTAAAACTCATCACCCCAAGATAACG
Found at i:915681 original size:16 final size:16
Alignment explanation
Indices: 915652--915731 Score: 106
Period size: 16 Copynumber: 5.0 Consensus size: 16
915642 TTAGTTAAGT
915652 CGAAAGTAACCTGAAC
1 CGAAAGTAACCTGAAC
* *
915668 CGAAAATAAGCTGAAC
1 CGAAAGTAACCTGAAC
*
915684 TGAAAGTAACCTGAAC
1 CGAAAGTAACCTGAAC
* *
915700 CGAAAATAAGCTGAAC
1 CGAAAGTAACCTGAAC
*
915716 TGAAAGTAACCTGAAC
1 CGAAAGTAACCTGAAC
915732 ATAAAGCAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 53 1.00
ACGTcount: A:0.46, C:0.20, G:0.19, T:0.15
Consensus pattern (16 bp):
CGAAAGTAACCTGAAC
Found at i:915689 original size:32 final size:32
Alignment explanation
Indices: 915653--915731 Score: 158
Period size: 32 Copynumber: 2.5 Consensus size: 32
915643 TAGTTAAGTC
915653 GAAAGTAACCTGAACCGAAAATAAGCTGAACT
1 GAAAGTAACCTGAACCGAAAATAAGCTGAACT
915685 GAAAGTAACCTGAACCGAAAATAAGCTGAACT
1 GAAAGTAACCTGAACCGAAAATAAGCTGAACT
915717 GAAAGTAACCTGAAC
1 GAAAGTAACCTGAAC
915732 ATAAAGCAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.15
Consensus pattern (32 bp):
GAAAGTAACCTGAACCGAAAATAAGCTGAACT
Found at i:915762 original size:16 final size:16
Alignment explanation
Indices: 915741--915772 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
915731 CATAAAGCAA
915741 TCAAATCGAAAATAAC
1 TCAAATCGAAAATAAC
*
915757 TCAAATCGAAAGTAAC
1 TCAAATCGAAAATAAC
915773 CCGAATTTAA
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:0.53, C:0.19, G:0.09, T:0.19
Consensus pattern (16 bp):
TCAAATCGAAAATAAC
Found at i:916318 original size:83 final size:83
Alignment explanation
Indices: 916161--916320 Score: 184
Period size: 83 Copynumber: 1.9 Consensus size: 83
916151 TTTTATTTTT
* *
916161 AATAATAATTTATTAATTTAATATCTATTTTAGATTTCATTAATTAATGAACCAAAATATTATAT
1 AATAATAATTTATTAATTCAATATCTATTTTAGATTTCATTAACTAATGAACCAAAATATTATAT
*
916226 TAATCTTTAAATAATCTA
66 AAATCTTTAAATAATCTA
* * * **
916244 AATAATAA-TTATTAATTCAATATTTCATTTTGGA-TTCTATTACCTAATGATTCAAAA-ATTAT
1 AATAATAATTTATTAATTCAATATCT-ATTTTAGATTTC-ATTAACTAATGAACCAAAATATTAT
916306 -TAAATTCGTTTAAAT
64 ATAAA-TC-TTTAAAT
916321 CAAAATATGA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
81 3 0.05
82 25 0.38
83 37 0.57
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (83 bp):
AATAATAATTTATTAATTCAATATCTATTTTAGATTTCATTAACTAATGAACCAAAATATTATAT
AAATCTTTAAATAATCTA
Found at i:916515 original size:27 final size:29
Alignment explanation
Indices: 916483--916549 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
916473 ATAACTTATT
*
916483 TTTATAATAT-AAAGGT-AAATATTTTTA
1 TTTATAATATAAAAAGTAAAATATTTTTA
* *
916510 TTTATAATTTAAAAATTAAAATATTTTTA
1 TTTATAATATAAAAAGTAAAATATTTTTA
916539 TTGATATAATA
1 TT--TATAATA
916550 ATATAATATC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 9 0.28
28 4 0.12
29 13 0.41
31 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (29 bp):
TTTATAATATAAAAAGTAAAATATTTTTA
Found at i:916703 original size:32 final size:32
Alignment explanation
Indices: 916667--916727 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
916657 GTTAAACATC
* *
916667 TAATTTAAAGTTTTAATTAATAATAAAATTAA
1 TAATTAAAAATTTTAATTAATAATAAAATTAA
* **
916699 TAATTAAAAATTTTATTTTTTAATAAAAT
1 TAATTAAAAATTTTAATTAATAATAAAAT
916728 AGATTGTACC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (32 bp):
TAATTAAAAATTTTAATTAATAATAAAATTAA
Found at i:917522 original size:22 final size:21
Alignment explanation
Indices: 917497--917537 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
917487 ATAATTTCAG
*
917497 TAAAAAAATTAGATTTTTTTTA
1 TAAAAAAATTA-AGTTTTTTTA
*
917519 TAAATAAATTAAGTTTTTT
1 TAAAAAAATTAAGTTTTTT
917538 ATTTTTTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (21 bp):
TAAAAAAATTAAGTTTTTTTA
Found at i:934474 original size:19 final size:19
Alignment explanation
Indices: 934430--934480 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 19
934420 TATAAGGTAC
934430 TAATTAAAA-AAATAAC-A
1 TAATTAAAATAAATAACAA
*
934447 T-A-GAAAATAAATAACAA
1 TAATTAAAATAAATAACAA
934464 TAATTAAAATAAA-AACA
1 TAATTAAAATAAATAACA
934481 TAAAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 4 0.14
16 8 0.29
17 3 0.11
18 5 0.18
19 8 0.29
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.22
Consensus pattern (19 bp):
TAATTAAAATAAATAACAA
Found at i:934492 original size:33 final size:34
Alignment explanation
Indices: 934430--934493 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
934420 TATAAGGTAC
934430 TAATTAAAAAAATAACATAGAAAATAAATAACAA
1 TAATTAAAAAAATAACATAGAAAATAAATAACAA
934464 TAATTAAAATAAA-AACATA-AAAATAAATAA
1 TAATTAAAA-AAATAACATAGAAAATAAATAA
934494 AGTACAAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 11 0.38
34 15 0.52
35 3 0.10
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.22
Consensus pattern (34 bp):
TAATTAAAAAAATAACATAGAAAATAAATAACAA
Done.