Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005680.1 Hibiscus syriacus cultivar Beakdansim tig00013285_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: 1821426
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 6
Found at i:728 original size:3 final size:3
Alignment explanation
Indices: 720--791 Score: 72
Period size: 3 Copynumber: 24.0 Consensus size: 3
710 ACTTGTTTGG
* * * ** *
720 ATC ATC ATC TTC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC AGC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* *
768 TTC ATC GTC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC
792 GTCAGCTTCA
Statistics
Matches: 54, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.25, C:0.35, G:0.06, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:773 original size:30 final size:30
Alignment explanation
Indices: 739--803 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
729 TTCATCATCA
* *
739 TCATCATCGTCATCATCTTCATCGCCAGCT
1 TCATCATCATCATCATCATCATCGCCAGCT
* *
769 TCATCGTCATCATCATCATCATCGTCAGCT
1 TCATCATCATCATCATCATCATCGCCAGCT
799 TCATC
1 TCATC
804 TGCGACCGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.22, C:0.35, G:0.09, T:0.34
Consensus pattern (30 bp):
TCATCATCATCATCATCATCATCGCCAGCT
Found at i:2629 original size:195 final size:197
Alignment explanation
Indices: 2240--3775 Score: 2556
Period size: 194 Copynumber: 7.9 Consensus size: 197
2230 TATTTAAATT
2240 AGTATCGACACAAAC--TATTAGTGTCGACACATTA-TTAGACATATTCTCTCATAAAA-CGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACA-ATTCTCTCATAAAACCGGTA
*
2301 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTGGATGA-TTTGGG
65 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
2365 ATCGA-ACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGG-
130 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTCCATTCATTCTGGGA
2428 AAAA
194 AAAA
2432 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGAC-ATTCTCTCATAAAACCGGTAT
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACAATTCTCTCATAAAACCGGTAT
2496 AATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
66 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
*
2560 TCGACACTTTTTATATATGGATCAACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAAA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAAA
2625 AA
196 AA
2627 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGAC-ATATCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACAAT-TCTCTCATAAAACCGGTA
2691 TAATTGTACCGGTTAGATTGAAAAAATTACATATTACATTATAC-TTTGGG-TCGATGATTTTGG
65 TAATTGTACCGGTTAGATTG-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
2754 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATT-TGGG
129 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTCCATTCATTCTGGG
2818 AAAAAA
193 -AAAAA
2824 AGTATCGACACAAAC--TA-TAGTGTCG--ACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACA-ATTCTCTCATAAAACCGGTA
2884 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGA-TTT-GG
65 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
2946 ATCGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCA-TCTGGGAA
130 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
3009 AAA
195 AAA
3012 AGTATCGACACAAA-TATATTAGTGTCG--ACATTATTTAGACATATTCTCTCATAAAAACCGGT
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACA-ATTCTCTCAT-AAAACCGGT
3074 ATAATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
64 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
3138 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACC-TGTTTCCATTCATTCTGGGA
129 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGA
3202 AAAA
194 AAAA
3206 AGTATCGACACAAACTATATTAGTGTCGACACATTA--TAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACA-ATTCTCTCATAAAACCGGTA
*
3269 TAATTGTACCGGTTAGATTGAAAAAATACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
65 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
3334 ATCGACACTTTTTATATATGGATCGACA-TTTATGGGTGCACCTTGTTTTCCATTCATTCTGGG-
130 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTCCATTCATTCTGGGA
3397 AAAA
194 AAAA
3401 AGTATCGACACAAACTATATTAGTGTCGAC-CATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACA-ATTCTCTCATAAAACCGGTA
3465 TAATTGTACCGGTTAGATTG--AAATTACA-A-TACA-TATACTTTTTTGGGTTCGATGATTTTG
65 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC--TTTTGGGTTCGATGATTTTG
*
3525 GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGTACCTTGTTTCCATTCATTCTGGG
128 GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGG
3590 AAAAA
193 AAAAA
**
3595 AGTATCGACACAAA-TATATTAGTGTCGACACATTATTTATGGGTTATATTCTCTCATAAAAACC
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTA---GACA-ATTCTCTCAT-AAAACC
3659 GGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT
61 GGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT
* *
3724 TGGGATTGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
126 TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
3776 GGCCATATTG
Statistics
Matches: 1286, Mismatches: 11, Indels: 85
0.93 0.01 0.06
Matches are distributed among these distances:
188 20 0.02
189 16 0.01
190 92 0.07
191 59 0.05
192 67 0.05
193 200 0.16
194 240 0.19
195 233 0.18
196 165 0.13
197 57 0.04
198 52 0.04
200 8 0.01
201 68 0.05
202 4 0.00
203 5 0.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (197 bp):
AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACAATTCTCTCATAAAACCGGTAT
AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAAA
AA
Found at i:3913 original size:19 final size:19
Alignment explanation
Indices: 3889--3933 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
3879 ATTATTTCAC
*
3889 ATACAAAAATATAAATCGT
1 ATACAAAAATATAAATAGT
* *
3908 ATACAAAATTATAAATATT
1 ATACAAAAATATAAATAGT
3927 ATACAAA
1 ATACAAA
3934 TTAACTCGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.29
Consensus pattern (19 bp):
ATACAAAAATATAAATAGT
Found at i:5732 original size:32 final size:32
Alignment explanation
Indices: 5696--5761 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
5686 CATCTTAATA
*
5696 TCACCCCTTAACACCCCAACTTCTTTCACCAC
1 TCACCCCTCAACACCCCAACTTCTTTCACCAC
* *
5728 TCACCCCTCAACACCTCTACTTCTTTCACCAC
1 TCACCCCTCAACACCCCAACTTCTTTCACCAC
5760 TC
1 TC
5762 CATCTATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.23, C:0.50, G:0.00, T:0.27
Consensus pattern (32 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCAC
Found at i:5834 original size:21 final size:21
Alignment explanation
Indices: 5794--5858 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
5784 CCCCTTATTC
* *
5794 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
5815 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
5836 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
5857 CT
1 CT
5859 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:8110 original size:19 final size:19
Alignment explanation
Indices: 8055--8101 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
8045 ATCCGGTATC
8055 ATTTTACCGGTTTTATCAT
1 ATTTTACCGGTTTTATCAT
*
8074 TTTGTTACCGGTTTTATCAT
1 ATT-TTACCGGTTTTATCAT
8094 ATTTTACC
1 ATTTTACC
8102 TGTTATATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
ATTTTACCGGTTTTATCAT
Found at i:8519 original size:146 final size:150
Alignment explanation
Indices: 8344--8611 Score: 472
Period size: 146 Copynumber: 1.8 Consensus size: 150
8334 GTAATTTAGG
8344 TTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTAC
1 TTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTAC
**
8409 A-AAATTA-TATTTGA-TGTTTTGATATTTTATAAATATTATTTAGAATTTAAATTTTTGAAAGT
66 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAATATTATTTAGAATTTAAATTTTTGAAAGT
8471 TAAGTAATTTATGTTATGAA
131 TAAGTAATTTATGTTATGAA
*
8491 TTTCAATTT-TTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
1 TTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTAC
*
8555 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAATATTATTTAGATTTTAAATTT
66 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAATATTATTTAGAATTTAAATTT
8612 AACAATATTA
Statistics
Matches: 114, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
146 55 0.48
147 13 0.11
148 7 0.06
149 39 0.34
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (150 bp):
TTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTAC
ACAAAAAATTATTTGATTGTTTTGATATTTTATAAATATTATTTAGAATTTAAATTTTTGAAAGT
TAAGTAATTTATGTTATGAA
Found at i:10678 original size:30 final size:31
Alignment explanation
Indices: 10622--10679 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
10612 AATTGTAACC
*
10622 TTTTTTACATTAGTAATCTTGTATTCAGTAT
1 TTTTTTACATTAGCAATCTTGTATTCAGTAT
*
10653 TTTTTTACAGTTTGCAA-CTTG-ATTCAG
1 TTTTTTACA-TTAGCAATCTTGTATTCAG
10680 CCGCATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 6 0.25
31 13 0.54
32 5 0.21
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.52
Consensus pattern (31 bp):
TTTTTTACATTAGCAATCTTGTATTCAGTAT
Found at i:13904 original size:39 final size:39
Alignment explanation
Indices: 13842--13930 Score: 119
Period size: 39 Copynumber: 2.3 Consensus size: 39
13832 ATCACACGCT
*
13842 CCTTTGTTTGTCGAAACACGAAGATTCGAATCTAAAAG-C
1 CCTTTGTTTGTCGAAACACGAAGACTCGAATCT-AAAGCC
*
13881 CCTTTGTTTGTC-ACAACAGGAAGACTCGAATCTAAAGCC
1 CCTTTGTTTGTCGA-AACACGAAGACTCGAATCTAAAGCC
*
13920 CCCTTGTTTGT
1 CCTTTGTTTGT
13931 TACAGTATGT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
38 5 0.11
39 40 0.89
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (39 bp):
CCTTTGTTTGTCGAAACACGAAGACTCGAATCTAAAGCC
Found at i:33864 original size:15 final size:15
Alignment explanation
Indices: 33844--33872 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
33834 AAACCAGACC
33844 CGACGGGTTTCGACT
1 CGACGGGTTTCGACT
33859 CGACGGGTTTCGAC
1 CGACGGGTTTCGAC
33873 CCGATCTGAC
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:0.14, C:0.28, G:0.34, T:0.24
Consensus pattern (15 bp):
CGACGGGTTTCGACT
Found at i:34309 original size:3 final size:3
Alignment explanation
Indices: 34294--34333 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
34284 TAAAACTATA
*
34294 AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
34334 TGTTTATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:52009 original size:243 final size:240
Alignment explanation
Indices: 51564--52039 Score: 893
Period size: 243 Copynumber: 2.0 Consensus size: 240
51554 ACCTGCATAT
51564 TATATGTAGAAATAGAATTATTTGGCAATTGTAGTCTCAAATAAATCATTGGAACTAGAAATTGG
1 TATATGTAGAAATAGAATTATTTGGCAATTGTAGTCTCAAATAAATCATTGGAACTAGAAATTGG
51629 TATAAATCTATTAGCGAATTGGACTCTCGATATACCTACATCTGCATTAAGAAGACTAGAACCAC
66 TATAAATCTATTAGCGAATTGGACTCTCGATATACCTACATCTGCATTAAGAAGACTAGAACCAC
51694 GACTTCCAACGCTATATGTTGGTCTGAATCCAACTCCCAGAGTGCTGGTTTACCTTGTTGTGGCT
131 GACTTCCAACGCTATATGTTGGTCTGAATCCAACTCCCAGAGTGCTGGTTTACCTTGTTGTGGCT
51759 GAAAGTGACCTAAGAACCTGC-TAAGATGATGCCAAAACCCTGCA
196 GAAAGTGACCTAAGAACCTGCATAAGATGATGCCAAAACCCTGCA
51803 TATATGTAGAAATAGAATTATTTGGCAATATGTAGTCTCAAA-AAATCATTGGAACTAGAAATTG
1 TATATGTAGAAATAGAATTATTTGGCAAT-TGTAGTCTCAAATAAATCATTGGAACTAGAAATTG
51867 GTATAAAATCTATTAGCGAATTTGGACTCTCGATATACCTAGCATCTGCATTAAGAAGACTAGAA
65 GTAT-AAATCTATTAGCGAA-TTGGACTCTCGATATACCTA-CATCTGCATTAAGAAGACTAGAA
51932 CCACGACTTCCAACGCTATAATGTTGGTCTGAATCCAACTCCCAGAGTGCTGGTTTACCTTGTTG
127 CCACGACTTCCAACGCTAT-ATGTTGGTCTGAATCCAACTCCCAGAGTGCTGGTTTACCTTGTTG
51997 TGGCTGAAAGTGACCTAAGAACCTGCATAAGATGATGCCAAAA
191 TGGCTGAAAGTGACCTAAGAACCTGCATAAGATGATGCCAAAA
52040 TCTACTAGTG
Statistics
Matches: 231, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
239 55 0.24
240 27 0.12
241 20 0.09
242 42 0.18
243 71 0.31
244 16 0.07
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (240 bp):
TATATGTAGAAATAGAATTATTTGGCAATTGTAGTCTCAAATAAATCATTGGAACTAGAAATTGG
TATAAATCTATTAGCGAATTGGACTCTCGATATACCTACATCTGCATTAAGAAGACTAGAACCAC
GACTTCCAACGCTATATGTTGGTCTGAATCCAACTCCCAGAGTGCTGGTTTACCTTGTTGTGGCT
GAAAGTGACCTAAGAACCTGCATAAGATGATGCCAAAACCCTGCA
Found at i:59865 original size:2 final size:2
Alignment explanation
Indices: 59858--59897 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
59848 TAAAAATAAT
*
59858 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59898 ATAAATTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:60718 original size:53 final size:54
Alignment explanation
Indices: 60635--60756 Score: 183
Period size: 53 Copynumber: 2.3 Consensus size: 54
60625 TACCCCCTTG
* * **
60635 GGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG-CAAAACTGTTTA
1 GGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCCAAAACCATTTA
* *
60688 GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGCCAAAACCATTTA
1 GGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCCAAAACCATTTA
60742 GGGGGAATCGGTTCC
1 GGGGGAATCGGTTCC
60757 TCCTATGGGG
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
53 37 0.60
54 25 0.40
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.23
Consensus pattern (54 bp):
GGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCCAAAACCATTTA
Found at i:61406 original size:17 final size:17
Alignment explanation
Indices: 61384--61427 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
61374 TATCATAATC
*
61384 CAAAATCCAACAATCCA
1 CAAAATCAAACAATCCA
61401 CAAAATCAAACAATCCA
1 CAAAATCAAACAATCCA
61418 -AAATATCAAA
1 CAAA-ATCAAA
61428 AGTGTTGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 3 0.12
17 22 0.88
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCAAACAATCCA
Found at i:67209 original size:22 final size:21
Alignment explanation
Indices: 67167--67206 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
67157 GAGTTTGTTT
*
67167 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
67188 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
67207 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:69234 original size:54 final size:54
Alignment explanation
Indices: 69147--69272 Score: 155
Period size: 54 Copynumber: 2.3 Consensus size: 54
69137 CGGTACCCCC
* * * * **
69147 TTGGGGGGGATCGATTCCCTCTGAGCATACTGGAATTCTCGGAG-CAAAACTGTT
1 TTGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCCAAAAC-CAT
* *
69201 TTGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGCCAAAACCAT
1 TTGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCCAAAACCAT
*
69255 TTAGGGGGAATCGGTTCC
1 TTGGGGGGAATCGGTTCC
69273 TCCTATGGGG
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 56 0.90
55 6 0.10
ACGTcount: A:0.21, C:0.22, G:0.31, T:0.25
Consensus pattern (54 bp):
TTGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCCAAAACCAT
Found at i:69615 original size:12 final size:12
Alignment explanation
Indices: 69567--69619 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 12
69557 ATTTATATAT
* *
69567 ATACCCGGCCCG
1 ATACCCAGCCCA
* *
69579 ATTCCCGGCCCA
1 ATACCCAGCCCA
*
69591 ATACCGA-CCCA
1 ATACCCAGCCCA
69602 ATACCCAGCCCA
1 ATACCCAGCCCA
69614 ATACCC
1 ATACCC
69620 GTTTAAATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 10 0.29
12 24 0.71
ACGTcount: A:0.26, C:0.49, G:0.13, T:0.11
Consensus pattern (12 bp):
ATACCCAGCCCA
Found at i:71698 original size:18 final size:18
Alignment explanation
Indices: 71675--71711 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
71665 ACTGTAATAG
*
71675 AAGGTGTGTTTATTTTAT
1 AAGGTGTGCTTATTTTAT
71693 AAGGTGTGCTTATTTTAT
1 AAGGTGTGCTTATTTTAT
71711 A
1 A
71712 CTTCCTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.51
Consensus pattern (18 bp):
AAGGTGTGCTTATTTTAT
Found at i:72835 original size:28 final size:28
Alignment explanation
Indices: 72763--72845 Score: 70
Period size: 28 Copynumber: 3.1 Consensus size: 28
72753 AGAATTAAGT
72763 ATAAA-TA-TAAA-AGATAAATA-AATAA
1 ATAAATTATTAAATAGATAAATATAAT-A
*
72788 ATAAATTATTAAATATATAAGATATAATA
1 ATAAATTATTAAATAGATAA-ATATAATA
* *
72817 A-AAATTATTTATTAGATAACA-ATAATA
1 ATAAATTATTAAATAGATAA-ATATAATA
72844 AT
1 AT
72846 TTACATATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
25 5 0.11
26 2 0.04
27 11 0.23
28 21 0.45
29 5 0.11
30 3 0.06
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (28 bp):
ATAAATTATTAAATAGATAAATATAATA
Found at i:74304 original size:29 final size:29
Alignment explanation
Indices: 74228--74304 Score: 145
Period size: 29 Copynumber: 2.7 Consensus size: 29
74218 CTTCCCAGCA
*
74228 TAGGTCGCCATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
74257 TAGGTCGCCATGCACTCCTGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
74286 TAGGTCGCCATGCACTCCT
1 TAGGTCGCCATGCACTCCT
74305 CCTGCTCCTC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.14, C:0.35, G:0.27, T:0.23
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCTGGCGACCTTG
Found at i:75892 original size:17 final size:17
Alignment explanation
Indices: 75870--75904 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
75860 AACTAGGTAT
75870 CGGGTACCCGTAAAATC
1 CGGGTACCCGTAAAATC
*
75887 CGGGTACCCGTAACATC
1 CGGGTACCCGTAAAATC
75904 C
1 C
75905 AAGTCGAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (17 bp):
CGGGTACCCGTAAAATC
Found at i:76952 original size:34 final size:33
Alignment explanation
Indices: 76898--76972 Score: 77
Period size: 34 Copynumber: 2.3 Consensus size: 33
76888 TATAATTAAA
*
76898 AAATATAAAATATAATATTATCAT-AATTATCTTT
1 AAATATAAAATATAATATTAT-ATCAATCAT-TTT
76932 AAATATATAAATACT-A-ATTATATCAATCATTTT
1 AAATATA-AAATA-TAATATTATATCAATCATTTT
76965 AAAT-TAAA
1 AAATATAAA
76973 TGTTTTTCCT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
31 2 0.05
32 2 0.05
33 9 0.24
34 17 0.46
35 6 0.16
36 1 0.03
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (33 bp):
AAATATAAAATATAATATTATATCAATCATTTT
Found at i:80395 original size:28 final size:29
Alignment explanation
Indices: 80342--80396 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
80332 AAGAGATTAA
* *
80342 GGTTTAAAGGTTATGAAGTTATGATTTAG
1 GGTTTAAAGGTTATCAAGTTAAGATTTAG
*
80371 GGTTT-AAGGTTATCAATTTAAGATTT
1 GGTTTAAAGGTTATCAAGTTAAGATTT
80397 TAAGTTAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.31, C:0.02, G:0.24, T:0.44
Consensus pattern (29 bp):
GGTTTAAAGGTTATCAAGTTAAGATTTAG
Found at i:83413 original size:19 final size:19
Alignment explanation
Indices: 83389--83438 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
83379 TAATGGGTGT
83389 ATCGATGCACTCCCTATGC
1 ATCGATGCACTCCCTATGC
83408 ATCGATGCACTCCCTATGC
1 ATCGATGCACTCCCTATGC
83427 ATCGATGCACTC
1 ATCGATGCACTC
83439 ATTTCATTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.22, C:0.36, G:0.16, T:0.26
Consensus pattern (19 bp):
ATCGATGCACTCCCTATGC
Found at i:87386 original size:21 final size:21
Alignment explanation
Indices: 87360--87409 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
87350 AAGTGGGTAT
87360 GGGAGAAGTTGAGGGACAAGA
1 GGGAGAAGTTGAGGGACAAGA
87381 GGGAGAAGTTGAGGGACAAGA
1 GGGAGAAGTTGAGGGACAAGA
*
87402 GTGAGAAG
1 GGGAGAAG
87410 ATAAGATGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.38, C:0.04, G:0.48, T:0.10
Consensus pattern (21 bp):
GGGAGAAGTTGAGGGACAAGA
Found at i:88972 original size:35 final size:29
Alignment explanation
Indices: 88903--88970 Score: 127
Period size: 29 Copynumber: 2.3 Consensus size: 29
88893 TGTTTTTCTC
88903 TATTAAAATTGACAATAATTTTAAATTTG
1 TATTAAAATTGACAATAATTTTAAATTTG
*
88932 TATTAAAATTGACAATAATTTTAATTTTG
1 TATTAAAATTGACAATAATTTTAAATTTG
88961 TATTAAAATT
1 TATTAAAATT
88971 AATGAAATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (29 bp):
TATTAAAATTGACAATAATTTTAAATTTG
Found at i:90280 original size:21 final size:20
Alignment explanation
Indices: 90254--90352 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
90244 AATCAGTTTC
90254 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
90275 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
90296 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
90316 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
90337 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
90353 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.26
21 45 0.74
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:90368 original size:40 final size:40
Alignment explanation
Indices: 90319--90473 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
90309 CGATTTTCCA
* ** *
90319 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * *
90359 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
* ** *
90399 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
90439 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
90474 TATTTAAAGC
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 62 0.65
41 33 0.34
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Found at i:90381 original size:20 final size:20
Alignment explanation
Indices: 90319--90472 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
90309 CGATTTTCCA
* ** *
90319 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
90339 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
90359 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
90379 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
90399 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
90419 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
90439 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
90460 AAATCGCAACGCG
1 AAATCGCAACGCG
90473 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.82
21 17 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:90895 original size:33 final size:33
Alignment explanation
Indices: 90856--90926 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
90846 TTCACTTAGA
*
90856 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
90889 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
90922 TTTCA
1 TTTCA
90927 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:91062 original size:40 final size:36
Alignment explanation
Indices: 91004--91121 Score: 154
Period size: 40 Copynumber: 3.3 Consensus size: 36
90994 TTTGCAGAAG
*
91004 AGTCGCAACGAGATAAATGAAAATCGCAACGAGAGA
1 AGTCGCAACGAGAGAAATGAAAATCGCAACGAGAGA
91040 TGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAGAGA
1 --A--GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGA
*
91080 A-TCGCAAC--GCGAAATGAAAATCGCAACGAGAGA
1 AGTCGCAACGAGAGAAATGAAAATCGCAACGAGAGA
91113 A-TCGCAACG
1 AGTCGCAACG
91122 CGAAACCAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 10
0.86 0.02 0.11
Matches are distributed among these distances:
33 32 0.43
35 7 0.09
38 2 0.03
40 34 0.45
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.11
Consensus pattern (36 bp):
AGTCGCAACGAGAGAAATGAAAATCGCAACGAGAGA
Found at i:91077 original size:19 final size:19
Alignment explanation
Indices: 91006--91110 Score: 94
Period size: 19 Copynumber: 5.6 Consensus size: 19
90996 TGCAGAAGAG
91006 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAG--AAATGAAAA
* ***
91027 TCGCAACGAGAGATGACTG
1 TCGCAACGAGAAATGAAAA
91046 TCGCAACGAGAGAAATGAAAA
1 TCGCAAC--GAGAAATGAAAA
91067 TCGCAACGAG--A-G--AA
1 TCGCAACGAGAAATGAAAA
*
91081 TCGCAACGCGAAATGAAAA
1 TCGCAACGAGAAATGAAAA
91100 TCGCAACGAGA
1 TCGCAACGAGA
91111 GAATCGCAAC
Statistics
Matches: 67, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 27 0.40
21 25 0.37
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.11
Consensus pattern (19 bp):
TCGCAACGAGAAATGAAAA
Found at i:91084 original size:14 final size:14
Alignment explanation
Indices: 91065--91121 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
91055 GAGAAATGAA
91065 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
91079 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
91098 AATCGCAACGAGAG
1 AATCGCAACGAGAG
91112 AATCGCAACG
1 AATCGCAACG
91122 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:91097 original size:33 final size:33
Alignment explanation
Indices: 91018--91137 Score: 150
Period size: 33 Copynumber: 3.4 Consensus size: 33
91008 GCAACGAGAT
*
91018 AAATGAAAATCGCAACGAGAGATGACTGTCGCAACGAGAG
1 AAATGAAAATCGCAACGAGAGA--A---TCGCAAC--GCG
91058 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
91091 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
91124 AAACCAAAATCGCA
1 AAATGAAAATCGCA
91138 TTGCGATTTT
Statistics
Matches: 77, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
33 47 0.61
35 7 0.09
38 1 0.01
40 22 0.29
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:91155 original size:19 final size:19
Alignment explanation
Indices: 91133--91230 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
91123 GAAACCAAAA
*
91133 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
91152 TCGCGTTGTGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
91166 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
91185 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
**
91199 TCTAGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
91218 TCGCGTTGCGATT
1 TCGCGTTGCGATT
91231 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
14 18 0.30
16 6 0.10
17 6 0.10
19 30 0.50
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:91178 original size:14 final size:14
Alignment explanation
Indices: 91155--91244 Score: 54
Period size: 14 Copynumber: 5.7 Consensus size: 14
91145 TTTCATTTCG
*
91155 CGTTGTGATTCTCT
1 CGTTGCGATTCTCT
*
91169 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
91188 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
91202 AGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
91221 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
91235 CGTTGCGATT
1 CGTTGCGATT
91245 TTCATTTCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 28 0.47
16 6 0.10
17 6 0.10
19 19 0.32
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:91180 original size:33 final size:33
Alignment explanation
Indices: 91138--91252 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
91128 CAAAATCGCA
*
91138 TTGCGATTTTCATTTCGCGTTGTGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
91171 TTGCGATTTTCATTTCGCGTTGCGATTCTCTAG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
91204 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
91237 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
91253 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.10, C:0.22, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:93103 original size:93 final size:93
Alignment explanation
Indices: 92944--93412 Score: 904
Period size: 93 Copynumber: 5.1 Consensus size: 93
92934 TAGATTGCTT
*
92944 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
93009 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
93037 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
93102 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
93130 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
93195 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
93223 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
93288 TTTGTCTTTGTTTTATCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
93316 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
93381 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
93408 AGTAA
1 AGTAA
93413 TGCAATCCAT
Statistics
Matches: 371, Mismatches: 5, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
92 6 0.02
93 365 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:93504 original size:19 final size:19
Alignment explanation
Indices: 93460--93588 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
93450 TAGTTTACTT
* *
93460 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
93480 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
* **
93499 TTGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
93518 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
93532 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
93551 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
93565 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
93584 TCGCA
1 TCGCA
93589 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 44 0.50
20 13 0.15
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:93543 original size:33 final size:33
Alignment explanation
Indices: 93501--93588 Score: 142
Period size: 33 Copynumber: 2.7 Consensus size: 33
93491 AACCAAAATT
**
93501 GCAACGCGAAATGAAAATCGCAACGAC-AGAATC
1 GCAACGCGAAACCAAAATCGCAACGACAAG-ATC
93534 GCAACGCGAAACCAAAATCGCAACGACAAGATC
1 GCAACGCGAAACCAAAATCGCAACGACAAGATC
93567 GCAACGCGAAACCAAAATCGCA
1 GCAACGCGAAACCAAAATCGCA
93589 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
33 50 0.96
34 2 0.04
ACGTcount: A:0.45, C:0.28, G:0.19, T:0.07
Consensus pattern (33 bp):
GCAACGCGAAACCAAAATCGCAACGACAAGATC
Found at i:93586 original size:52 final size:52
Alignment explanation
Indices: 93460--93588 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
93450 TAGTTTACTT
** *
93460 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATTGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
93512 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
93565 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
93589 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 41 0.67
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:93606 original size:19 final size:19
Alignment explanation
Indices: 93584--93718 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
93574 GAAACCAAAA
*
93584 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
93603 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
93619 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
93636 TCGCATTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
93652 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
93669 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
93688 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
93708 TCGTGTTGCGA
1 TCGCGTTGCGA
93719 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 15 0.15
16 12 0.12
17 12 0.12
19 46 0.47
20 12 0.12
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:93625 original size:14 final size:14
Alignment explanation
Indices: 93606--93662 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
93596 TTTCATTTCG
93606 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
93620 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
93637 CGCATTGCGATTCTTT
1 CG--TTGCGATTCTTT
93653 CGTTGCGATT
1 CGTTGCGATT
93663 TTCATTTCGC
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 16 0.42
16 8 0.21
17 8 0.21
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:93631 original size:33 final size:33
Alignment explanation
Indices: 93589--93681 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
93579 CAAAATCGCA
93589 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
*
93622 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
93655 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
93682 TTGGTTTCGC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
Found at i:95016 original size:14 final size:14
Alignment explanation
Indices: 94997--95032 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
94987 ATTGTTTAAT
94997 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
95011 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
95025 TGATTTGT
1 TGATTTGT
95033 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:95163 original size:19 final size:19
Alignment explanation
Indices: 95139--95236 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
95129 AAAATTGACT
95139 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
95158 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
95177 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
95191 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
95210 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
95230 ATCGCAA
1 ATCGCAA
95237 CGGGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:95217 original size:52 final size:53
Alignment explanation
Indices: 95139--95256 Score: 211
Period size: 52 Copynumber: 2.2 Consensus size: 53
95129 AAAATTGACT
95139 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
95191 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
95244 ATCGCAATTGCGA
1 ATCGCAA-TGCGA
95257 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 29 0.46
53 29 0.46
54 5 0.08
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:95274 original size:19 final size:19
Alignment explanation
Indices: 95245--95486 Score: 281
Period size: 19 Copynumber: 13.7 Consensus size: 19
95235 AACGGGAGAA
95245 TCGCAATTGCGATTTTCATT
1 TCGC-ATTGCGATTTTCATT
*
95265 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
95281 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
95298 TCGCATTGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
95317 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
95333 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
95350 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
95369 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
95385 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
95402 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
95421 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
95440 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
95458 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
95474 TCGCATTGCGATT
1 TCGCATTGCGATT
95487 CTCTCGTTGC
Statistics
Matches: 191, Mismatches: 10, Indels: 43
0.78 0.04 0.18
Matches are distributed among these distances:
14 29 0.15
16 23 0.12
17 21 0.11
18 1 0.01
19 97 0.51
20 20 0.10
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:95310 original size:52 final size:52
Alignment explanation
Indices: 95245--95500 Score: 387
Period size: 52 Copynumber: 4.9 Consensus size: 52
95235 AACGGGAGAA
95245 TCGCAATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGC-ATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
95298 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
95350 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
95402 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCA--
1 TCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--TTGCGATTTTCATT
*
95458 T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
95501 GTAATTTCCG
Statistics
Matches: 192, Mismatches: 5, Indels: 18
0.89 0.02 0.08
Matches are distributed among these distances:
47 8 0.04
49 2 0.01
50 2 0.01
51 3 0.02
52 128 0.67
53 28 0.15
54 3 0.02
55 3 0.02
56 3 0.02
58 12 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:95359 original size:71 final size:69
Alignment explanation
Indices: 95249--95486 Score: 263
Period size: 71 Copynumber: 3.4 Consensus size: 69
95239 GGAGAATCGC
* *
95249 AATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGA
1 AATTGCGATTTGCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA
95309 TTTT
66 TTTT
* * *
95313 AATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTG
1 AATTGCG-ATTTGC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTG
95377 CGATTCTCT
63 CGATT-T-T
** *
95386 CGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCG
1 AATTGCGATTTGCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCG
95451 ATTTT
65 ATTTT
* * *
95456 CATGTTGGGATTTTCATTTCGCATTGCGATT
1 -A-ATTGCGATTTGCATTTCGCATTGCGATT
95487 CTCTCGTTGC
Statistics
Matches: 147, Mismatches: 13, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
64 9 0.06
65 4 0.03
66 9 0.06
68 3 0.02
69 4 0.03
70 1 0.01
71 65 0.44
72 44 0.30
73 8 0.05
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (69 bp):
AATTGCGATTTGCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA
TTTT
Found at i:95508 original size:33 final size:33
Alignment explanation
Indices: 95251--95500 Score: 247
Period size: 33 Copynumber: 7.2 Consensus size: 33
95241 AGAATCGCAA
95251 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* *
95284 TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TT-CTCTCG
* * * * *
95320 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
95355 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
95388 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
95424 CATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
95460 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
95493 TTGCGATT
1 TTGCGATT
95501 GTAATTTCCG
Statistics
Matches: 179, Mismatches: 19, Indels: 38
0.76 0.08 0.16
Matches are distributed among these distances:
31 9 0.05
32 6 0.03
33 83 0.46
34 14 0.08
35 7 0.04
36 10 0.06
37 5 0.03
38 23 0.13
39 13 0.07
40 9 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:97961 original size:24 final size:24
Alignment explanation
Indices: 97927--97973 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
97917 CTGAAACATC
97927 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
97951 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
97974 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:98684 original size:20 final size:20
Alignment explanation
Indices: 98656--98905 Score: 286
Period size: 20 Copynumber: 12.5 Consensus size: 20
98646 AAATTTCAGT
* *
98656 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
98676 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
98696 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
98716 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
98736 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
98756 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
98776 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
98796 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
98816 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
98836 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
98856 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* *
98876 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
98896 GTTGCGATTT
1 GTTGCGATTT
98906 TCCATATTTT
Statistics
Matches: 205, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
20 204 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:98951 original size:21 final size:21
Alignment explanation
Indices: 98921--99003 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
98911 ATTTTCATAT
*
98921 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
98942 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
98963 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
98984 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
99004 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:106632 original size:2 final size:2
Alignment explanation
Indices: 106625--106657 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
106615 CAATAATACC
106625 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
106658 TTAATTAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:117313 original size:16 final size:16
Alignment explanation
Indices: 117292--117327 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
117282 ATCTCTAGGA
117292 TAGCGGCTTCTTGATG
1 TAGCGGCTTCTTGATG
117308 TAGCGGCTTCTTGATG
1 TAGCGGCTTCTTGATG
117324 TAGC
1 TAGC
117328 CGCTATGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.14, C:0.19, G:0.31, T:0.36
Consensus pattern (16 bp):
TAGCGGCTTCTTGATG
Found at i:124011 original size:60 final size:60
Alignment explanation
Indices: 123959--124073 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
123949 ACTATTACTA
* ** * *
123959 TCATCCTAAATTAGTCCTTAAAC-TTTTAAATATTTCAATTTCATCCCCAAACTATGACCT
1 TCATCCTAAACTAGTCCCCAAACATTTTAAACATTCCAATTTCAT-CCCAAACTATGACCT
* * *
124019 TTATTCTAAACTAGTCCCCAAACATTTTGAACATTCCAATTTCATCCCAAACTAT
1 TCATCCTAAACTAGTCCCCAAACATTTTAAACATTCCAATTTCATCCCAAACTAT
124074 ATGTATATAC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
60 28 0.61
61 18 0.39
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (60 bp):
TCATCCTAAACTAGTCCCCAAACATTTTAAACATTCCAATTTCATCCCAAACTATGACCT
Found at i:124288 original size:60 final size:60
Alignment explanation
Indices: 124190--124349 Score: 189
Period size: 60 Copynumber: 2.7 Consensus size: 60
124180 TTACATATTT
* ** *
124190 GGATGAAACTGGAATATTCAAAAGTTTGGGGACCAATTT-GGAA-AGAAGGTCATAGTTTGA
1 GGATGAAATTGGAATATTCAAAAGTTTAAGGACTAATTTAGGAAGAG-A-GTCATAGTTTGA
* * * * *
124250 GGATGAAATTGGAATGTTCAAATGTTTAAGGATTAATTTAGGATGAGATTCATAGTTTGA
1 GGATGAAATTGGAATATTCAAAAGTTTAAGGACTAATTTAGGAAGAGAGTCATAGTTTGA
* *
124310 GGATAAAATTAGAATATTCAAAAGTTTAAGGACTAATTTA
1 GGATGAAATTGGAATATTCAAAAGTTTAAGGACTAATTTA
124350 AAATGAAGTT
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
60 78 0.93
61 4 0.05
62 2 0.02
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.32
Consensus pattern (60 bp):
GGATGAAATTGGAATATTCAAAAGTTTAAGGACTAATTTAGGAAGAGAGTCATAGTTTGA
Found at i:124336 original size:29 final size:29
Alignment explanation
Indices: 124243--124341 Score: 74
Period size: 29 Copynumber: 3.3 Consensus size: 29
124233 AGAAGGTCAT
* * * *
124243 AGTTTGAGGATGAAATTGGAATGTTCAAA
1 AGTTTAAGGATAAAATTAGAATATTCAAA
* * * * *
124272 TGTTTAAGGATTAATTTAGGATGAGATTC-AT
1 AGTTTAAGGATAAAATTA-GA--ATATTCAAA
*
124303 AGTTTGAGGATAAAATTAGAATATTCAAA
1 AGTTTAAGGATAAAATTAGAATATTCAAA
124332 AGTTTAAGGA
1 AGTTTAAGGA
124342 CTAATTTAAA
Statistics
Matches: 51, Mismatches: 15, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
28 5 0.10
29 23 0.45
30 4 0.08
31 15 0.29
32 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.34
Consensus pattern (29 bp):
AGTTTAAGGATAAAATTAGAATATTCAAA
Found at i:124596 original size:29 final size:29
Alignment explanation
Indices: 124558--124656 Score: 78
Period size: 29 Copynumber: 3.3 Consensus size: 29
124548 AGAATGTCAT
*
124558 AGTTTGAGGATGAAATTGGAATGTTCAAA
1 AGTTTAAGGATGAAATTGGAATGTTCAAA
* *
124587 AGTTTAAGGACT-AATTTAGG-ATGAGATTC-AT
1 AGTTTAAGGA-TGAAATT-GGAAT--G-TTCAAA
* * *
124618 AGTTTGAGGATGAAATTAGAATATTCAAA
1 AGTTTAAGGATGAAATTGGAATGTTCAAA
124647 AGTTTAAGGA
1 AGTTTAAGGA
124657 CTAATTTAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 16
0.68 0.12 0.21
Matches are distributed among these distances:
28 3 0.06
29 25 0.47
30 5 0.09
31 17 0.32
32 3 0.06
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.32
Consensus pattern (29 bp):
AGTTTAAGGATGAAATTGGAATGTTCAAA
Found at i:124618 original size:60 final size:60
Alignment explanation
Indices: 124554--124686 Score: 207
Period size: 60 Copynumber: 2.2 Consensus size: 60
124544 GGAAAGAATG
* * **
124554 TCATAGTTTGAGGATGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAGGATG-AGAT
1 TCATAGTTTGAGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAAG-T
124614 TCATAGTTTGAGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAAGT
1 TCATAGTTTGAGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAAGT
124674 T-ATAGTTTGAGGA
1 TCATAGTTTGAGGA
124687 CATATGATCC
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
59 12 0.18
60 54 0.79
61 2 0.03
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.34
Consensus pattern (60 bp):
TCATAGTTTGAGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAAGT
Found at i:124622 original size:31 final size:29
Alignment explanation
Indices: 124581--124664 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 29
124571 AATTGGAATG
124581 TTCAAAAGTTTAAGGACTAATTTAGGATGAGA
1 TTCAAAAGTTTAAGGACTAATTTA-GA--AGA
* * * *
124613 TTC-ATAGTTTGAGGA-TGAAATTAGAATA
1 TTCAAAAGTTTAAGGACT-AATTTAGAAGA
124641 TTCAAAAGTTTAAGGACTAATTTA
1 TTCAAAAGTTTAAGGACTAATTTA
124665 AAATGAAGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
28 5 0.12
29 15 0.36
30 4 0.10
31 15 0.36
32 3 0.07
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (29 bp):
TTCAAAAGTTTAAGGACTAATTTAGAAGA
Found at i:124658 original size:315 final size:315
Alignment explanation
Indices: 124086--124717 Score: 1131
Period size: 315 Copynumber: 2.0 Consensus size: 315
124076 GTATATACTA
*
124086 ATCACATTCATTGTTAATACAATTGTTAGGCCAAGTTATATTATTATATGTTAGAAAAAAACACA
1 ATCACATTCATTGTTAATACAATTGTTAGGCCAAGTTATATCATTATATGTTAGAAAAAAACACA
* * *
124151 AATTTAGGTTAGACTATGGTTGAAACTAATTACATATTTGGATGAAACTGGAATATTCAAAAGTT
66 AATTTAGGTTAGAATACGATTGAAACTAATTACATATTTGGATGAAACTGGAATATTCAAAAGTT
*
124216 TGGGGACCAATTTGGAAAGAAGGTCATAGTTTGAGGATGAAATTGGAATGTTCAAATGTTTAAGG
131 TGGGGACCAATTTGGAAAGAAGGTCATAGTTTGAGGATGAAATTGGAATGTTCAAAAGTTTAAGG
*
124281 ATTAATTTAGGATGAGATTCATAGTTTGAGGATAAAATTAGAATATTCAAAAGTTTAAGGACTAA
196 ACTAATTTAGGATGAGATTCATAGTTTGAGGATAAAATTAGAATATTCAAAAGTTTAAGGACTAA
*
124346 TTTAAAATGAAGTTATAGTTTGGGGACATATGATACAATTAACTCAATTATTTAG
261 TTTAAAATGAAGTTATAGTTTGAGGACATATGATACAATTAACTCAATTATTTAG
*
124401 ATCACATTCATTGTTAATACAATTGTTAGGCCAAGTTATATCATTATATGTTTG-AAAAAACACA
1 ATCACATTCATTGTTAATACAATTGTTAGGCCAAGTTATATCATTATATGTTAGAAAAAAACAC-
*
124465 AAATTTAGGTTAGAATACGATTGAAACTAATTACATATTTGGATTAAACTGGAATATTCAAAAGT
65 AAATTTAGGTTAGAATACGATTGAAACTAATTACATATTTGGATGAAACTGGAATATTCAAAAGT
* *
124530 TTGGGGTCCAATTTGGAAAGAATGTCATAGTTTGAGGATGAAATTGGAATGTTCAAAAGTTTAAG
130 TTGGGGACCAATTTGGAAAGAAGGTCATAGTTTGAGGATGAAATTGGAATGTTCAAAAGTTTAAG
*
124595 GACTAATTTAGGATGAGATTCATAGTTTGAGGATGAAATTAGAATATTCAAAAGTTTAAGGACTA
195 GACTAATTTAGGATGAGATTCATAGTTTGAGGATAAAATTAGAATATTCAAAAGTTTAAGGACTA
*
124660 ATTTAAAATGAAGTTATAGTTTGAGGACATATGATCCAATTAACTCAATTATTTAG
260 ATTTAAAATGAAGTTATAGTTTGAGGACATATGATACAATTAACTCAATTATTTAG
124716 AT
1 AT
124718 AGGTTTGACA
Statistics
Matches: 303, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
314 9 0.03
315 294 0.97
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.34
Consensus pattern (315 bp):
ATCACATTCATTGTTAATACAATTGTTAGGCCAAGTTATATCATTATATGTTAGAAAAAAACACA
AATTTAGGTTAGAATACGATTGAAACTAATTACATATTTGGATGAAACTGGAATATTCAAAAGTT
TGGGGACCAATTTGGAAAGAAGGTCATAGTTTGAGGATGAAATTGGAATGTTCAAAAGTTTAAGG
ACTAATTTAGGATGAGATTCATAGTTTGAGGATAAAATTAGAATATTCAAAAGTTTAAGGACTAA
TTTAAAATGAAGTTATAGTTTGAGGACATATGATACAATTAACTCAATTATTTAG
Found at i:126617 original size:37 final size:38
Alignment explanation
Indices: 126529--126620 Score: 98
Period size: 37 Copynumber: 2.4 Consensus size: 38
126519 TTTAATTAAA
* * *
126529 AAATTTATATAAAATTTTATTTATAATTATATATTATTT
1 AAATTTATAT-AAATTGTATTTATAATTATAAAATATTT
*
126568 AAATTAATTATAAATTGT-TTT-TAATTATAAAATATTT
1 AAATTTA-TATAAATTGTATTTATAATTATAAAATATTT
*
126605 AATTTTTATATAAATT
1 AA-ATTTATATAAATT
126621 AGAAAATTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
37 24 0.53
38 6 0.13
39 12 0.27
40 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (38 bp):
AAATTTATATAAATTGTATTTATAATTATAAAATATTT
Found at i:128348 original size:29 final size:29
Alignment explanation
Indices: 128312--128400 Score: 117
Period size: 29 Copynumber: 3.1 Consensus size: 29
128302 AGTGTTGACC
*
128312 GTAGGTCGCCATGTC-CTCCGGGCGACCTT
1 GTAGGTCGCCATG-CACGCCGGGCGACCTT
* * *
128341 GTAGGTCGCCATGCACGCCAGGCGACATG
1 GTAGGTCGCCATGCACGCCGGGCGACCTT
*
128370 GTAGGTCGCCATGCACGCTGGGCGACCTT
1 GTAGGTCGCCATGCACGCCGGGCGACCTT
128399 GT
1 GT
128401 CCTACGCCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
28 1 0.02
29 50 0.98
ACGTcount: A:0.15, C:0.31, G:0.34, T:0.20
Consensus pattern (29 bp):
GTAGGTCGCCATGCACGCCGGGCGACCTT
Found at i:128479 original size:22 final size:22
Alignment explanation
Indices: 128452--128497 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
128442 TGCATGCAAA
128452 CGACCTCTTCCGACGTGCATGG
1 CGACCTCTTCCGACGTGCATGG
128474 CGACCTCTTCCGACGTGCATGG
1 CGACCTCTTCCGACGTGCATGG
128496 CG
1 CG
128498 CATGCAAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.13, C:0.37, G:0.28, T:0.22
Consensus pattern (22 bp):
CGACCTCTTCCGACGTGCATGG
Found at i:128536 original size:31 final size:31
Alignment explanation
Indices: 128501--128562 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
128491 CATGGCGCAT
* *
128501 GCAAAGCTTCATTCTCTCGCCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
*
128532 GCAAAGCTTCATCCTCTCACTACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
128563 TAGAACACTT
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:0.24, C:0.35, G:0.15, T:0.26
Consensus pattern (31 bp):
GCAAAGCTTCATCCTCTCACCACAGCTCGTA
Found at i:144333 original size:13 final size:13
Alignment explanation
Indices: 144315--144342 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
144305 ATCATTACAA
144315 AAGCCAGACAAGT
1 AAGCCAGACAAGT
144328 AAGCCAGACAAGT
1 AAGCCAGACAAGT
144341 AA
1 AA
144343 AGAAATTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.21, G:0.21, T:0.07
Consensus pattern (13 bp):
AAGCCAGACAAGT
Found at i:145086 original size:113 final size:113
Alignment explanation
Indices: 144888--145117 Score: 460
Period size: 113 Copynumber: 2.0 Consensus size: 113
144878 TCTAGCGTGT
144888 CCGGCCTGGAATATGAACAAAAAAAAGGACATACCAAATCCATAAGCATCTCCTGTGCACATTCA
1 CCGGCCTGGAATATGAACAAAAAAAAGGACATACCAAATCCATAAGCATCTCCTGTGCACATTCA
144953 AATCCTTTGTCGAATAAATCAAAATTAAACCTTTTGTGAACATTATAC
66 AATCCTTTGTCGAATAAATCAAAATTAAACCTTTTGTGAACATTATAC
145001 CCGGCCTGGAATATGAACAAAAAAAAGGACATACCAAATCCATAAGCATCTCCTGTGCACATTCA
1 CCGGCCTGGAATATGAACAAAAAAAAGGACATACCAAATCCATAAGCATCTCCTGTGCACATTCA
145066 AATCCTTTGTCGAATAAATCAAAATTAAACCTTTTGTGAACATTATAC
66 AATCCTTTGTCGAATAAATCAAAATTAAACCTTTTGTGAACATTATAC
145114 CCGG
1 CCGG
145118 GTTGGGATGT
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 117 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (113 bp):
CCGGCCTGGAATATGAACAAAAAAAAGGACATACCAAATCCATAAGCATCTCCTGTGCACATTCA
AATCCTTTGTCGAATAAATCAAAATTAAACCTTTTGTGAACATTATAC
Found at i:155869 original size:30 final size:30
Alignment explanation
Indices: 155835--155932 Score: 76
Period size: 29 Copynumber: 3.3 Consensus size: 30
155825 ACATCATATG
155835 TCTTTAAATATAATATTTATTTTAAATTAT
1 TCTTTAAATATAATATTTATTTTAAATTAT
** ** *
155865 TCTTTAAA-ATTTTAAATATTTT-AATTTT
1 TCTTTAAATATAATATTTATTTTAAATTAT
* * *
155893 ATCCTCAAATTATGAAT-TTCATTTTAAATTAT
1 -TCTTTAAA-TAT-AATATTTATTTTAAATTAT
155925 TCTTTAAA
1 TCTTTAAA
155933 CTGTTGATCA
Statistics
Matches: 48, Mismatches: 15, Indels: 9
0.67 0.21 0.12
Matches are distributed among these distances:
28 5 0.10
29 16 0.33
30 8 0.17
31 13 0.27
32 6 0.12
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.54
Consensus pattern (30 bp):
TCTTTAAATATAATATTTATTTTAAATTAT
Found at i:156015 original size:60 final size:59
Alignment explanation
Indices: 155850--156021 Score: 177
Period size: 60 Copynumber: 2.9 Consensus size: 59
155840 AAATATAATA
* * * * * *
155850 TTTATTTTAAATTATTCTTTAAAATTTTAAATATTTTAATTTTATCCTCAAATTATGAAT
1 TTTATTTTAAATTATTCTTTAAACTTTT-AATCTTTCAATTTCATTCTCAAACTATGAAT
* * * *
155910 TTCATTTTAAATTATTCTTTAAACTGTTGATCATTTCAATTTCATTTTCAAACTAT-AACT
1 TTTATTTTAAATTATTCTTTAAACTTTTAATC-TTTCAATTTCATTCTCAAACTATGAA-T
* *
155970 TTTATTTTAAATTGA-TCTTCAAACTTTTCAATCTTTCAATTTCATTCCCAAA
1 TTTATTTTAAATT-ATTCTTTAAACTTTT-AATCTTTCAATTTCATTCTCAAA
156022 TCCATATAGA
Statistics
Matches: 92, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
59 4 0.04
60 84 0.91
61 4 0.04
ACGTcount: A:0.33, C:0.13, G:0.02, T:0.51
Consensus pattern (59 bp):
TTTATTTTAAATTATTCTTTAAACTTTTAATCTTTCAATTTCATTCTCAAACTATGAAT
Found at i:156588 original size:22 final size:21
Alignment explanation
Indices: 156536--156595 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
156526 TTACATATTC
**
156536 GCATTGCGATAGTTGAAGTTT
1 GCATTGCGATAGTCCAAGTTT
156557 GCATTGCGATAGTCCAAGTTT
1 GCATTGCGATAGTCCAAGTTT
*
156578 GCATTTGCGATATTCCAA
1 GCA-TTGCGATAGTCCAA
156596 AATCGCAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
21 22 0.63
22 13 0.37
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (21 bp):
GCATTGCGATAGTCCAAGTTT
Found at i:157231 original size:6 final size:5
Alignment explanation
Indices: 157202--157241 Score: 53
Period size: 5 Copynumber: 7.4 Consensus size: 5
157192 CCGTCTCGTC
157202 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG TC
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG TC
157242 ATACGTGTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.53
6 16 0.47
ACGTcount: A:0.00, C:0.20, G:0.53, T:0.28
Consensus pattern (5 bp):
TCGGG
Found at i:157371 original size:23 final size:21
Alignment explanation
Indices: 157333--157492 Score: 207
Period size: 21 Copynumber: 7.4 Consensus size: 21
157323 ATTTTGGACT
157333 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
157354 ATCGCAACGCGAATTTGGAATAA
1 ATCGCAA--CGAACTTGGAATAA
*
157377 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
157398 ATCGCAACGCGAACTTGGAATAA
1 ATCGCAA--CGAACTTGGAATAA
*
157421 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
157442 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
157463 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
157484 ATCGCAACG
1 ATCGCAACG
157493 CGAACTTAGA
Statistics
Matches: 123, Mismatches: 8, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
19 10 0.08
21 64 0.52
23 49 0.40
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:157386 original size:44 final size:44
Alignment explanation
Indices: 157333--157499 Score: 275
Period size: 44 Copynumber: 3.8 Consensus size: 44
157323 ATTTTGGACT
*
157333 ATCGCAACGAACTTGGAATAAATCGCAACGCGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGAATAA
*
157377 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGAATAA
* * *
157421 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT--
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGAATAA
157463 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTT
157500 AGACTATCGC
Statistics
Matches: 118, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
42 36 0.31
44 82 0.69
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (44 bp):
ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGAATAA
Found at i:157508 original size:21 final size:21
Alignment explanation
Indices: 157442--157517 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
157432 TTTGGAATAA
*
157442 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTAGACT
* *
157463 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTAGACT
157482 AAATCGCAACGCGAACTTAGACT
1 --ATCGCAACGCGAACTTAGACT
*
157505 ATCGCAATGCGAA
1 ATCGCAACGCGAA
157518 TATGTAAATC
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
19 10 0.22
21 26 0.57
23 10 0.22
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGAACTTAGACT
Found at i:170804 original size:17 final size:15
Alignment explanation
Indices: 170758--170811 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 15
170748 CTCTATACAA
170758 TAATAACTCTTTAAAT
1 TAATAACTC-TTAAAT
170774 TAAT-ACTCATTAAAT
1 TAATAACTC-TTAAAT
*
170789 TAATAAACTCTCTAAAA
1 TAAT-AACTCT-TAAAT
170806 TAATAA
1 TAATAA
170812 ATTTGTCCGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 14 0.42
16 7 0.21
17 12 0.36
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (15 bp):
TAATAACTCTTAAAT
Found at i:175191 original size:16 final size:16
Alignment explanation
Indices: 175170--175203 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
175160 AAGTAAGTAA
175170 ATCTTCAATTTTAATC
1 ATCTTCAATTTTAATC
175186 ATCTTCAATTTTAATC
1 ATCTTCAATTTTAATC
175202 AT
1 AT
175204 AGTTTAATTG
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:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (16 bp):
ATCTTCAATTTTAATC
Found at i:176774 original size:20 final size:20
Alignment explanation
Indices: 176749--176786 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
176739 AAACGTCGAG
176749 AACATAAAAAATAATACACT
1 AACATAAAAAATAATACACT
*
176769 AACATAAAAATTAATACA
1 AACATAAAAAATAATACA
176787 AATTTTAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.66, C:0.13, G:0.00, T:0.21
Consensus pattern (20 bp):
AACATAAAAAATAATACACT
Found at i:177680 original size:6 final size:7
Alignment explanation
Indices: 177654--177678 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
177644 GGGGCGGTCG
177654 TTTTTAA
1 TTTTTAA
177661 TTTTTAA
1 TTTTTAA
177668 TTTTTAA
1 TTTTTAA
177675 TTTT
1 TTTT
177679 AAAATAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTAA
Found at i:179203 original size:6 final size:6
Alignment explanation
Indices: 179192--179235 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
179182 CACCCAAGTC
179192 AACCCT AACCCT AACCCT AACCCT AACCCT AACCCT AACCCT AA
1 AACCCT AACCCT AACCCT AACCCT AACCCT AACCCT AACCCT AA
179236 AACCTAGACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.36, C:0.48, G:0.00, T:0.16
Consensus pattern (6 bp):
AACCCT
Found at i:180934 original size:2 final size:2
Alignment explanation
Indices: 180927--180970 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
180917 TTTCTTTTAA
180927 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
180969 AT
1 AT
180971 TGGTCATAGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:181096 original size:2 final size:2
Alignment explanation
Indices: 181089--181132 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
181079 TTGTAAGAAC
181089 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
181131 TA
1 TA
181133 GACAGAGAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:181141 original size:2 final size:2
Alignment explanation
Indices: 181136--181163 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
181126 ATATATAGAC
181136 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
181164 GTGGAGGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:182389 original size:13 final size:13
Alignment explanation
Indices: 182371--182396 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
182361 ACATGCATAC
182371 ACATAATAGATCA
1 ACATAATAGATCA
182384 ACATAATAGATCA
1 ACATAATAGATCA
182397 TCAACAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (13 bp):
ACATAATAGATCA
Found at i:185719 original size:3 final size:3
Alignment explanation
Indices: 185713--185758 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
185703 TAGTATTCTC
* * *
185713 AAT AAT AAT AAT AAT GAT AAT AAC AAT AAT AAT GAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
185759 GTTCATTTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:186777 original size:26 final size:27
Alignment explanation
Indices: 186719--186778 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 27
186709 ATATGTAATA
*
186719 ATTTACTGTCATGATCACTAATAAACTT
1 ATTTACTGTCATCATCACTAATAAAC-T
*
186747 AATTTACTGTCATCATCACTAATTAAC-
1 -ATTTACTGTCATCATCACTAATAAACT
186774 ATTTA
1 ATTTA
186779 AATAAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 5 0.17
29 24 0.83
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (27 bp):
ATTTACTGTCATCATCACTAATAAACT
Found at i:186915 original size:16 final size:16
Alignment explanation
Indices: 186896--186936 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
186886 GTAAAAGATA
186896 AAAATAAATA-AATATT
1 AAAATAAATATAAT-TT
186912 AAAATAAATATAATTT
1 AAAATAAATATAATTT
186928 AAACATAAA
1 AAA-ATAAA
186937 ATCATAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATAAATATAATTT
Found at i:188335 original size:36 final size:36
Alignment explanation
Indices: 188269--188388 Score: 116
Period size: 36 Copynumber: 3.3 Consensus size: 36
188259 ATGGAGATTC
* * *
188269 AGATGGTGGATTAGTGCTTGGTTTAGCCTTGGATGG
1 AGATGGTGCATTAATGCTTGGTTTAACCTTGGATGG
* *
188305 AGATAGTGCATTAATGCTTGGTTTAACCTTGGGTGG
1 AGATGGTGCATTAATGCTTGGTTTAACCTTGGATGG
* ** * * * *
188341 AGGTGGTGCATTGTTGATTGAG-TTAGCGTTGGACGG
1 AGATGGTGCATTAATGCTTG-GTTTAACCTTGGATGG
188377 AGATGGTGCATT
1 AGATGGTGCATT
188389 GTTGCTTGAT
Statistics
Matches: 68, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
36 67 0.99
37 1 0.01
ACGTcount: A:0.19, C:0.09, G:0.37, T:0.35
Consensus pattern (36 bp):
AGATGGTGCATTAATGCTTGGTTTAACCTTGGATGG
Found at i:189649 original size:28 final size:28
Alignment explanation
Indices: 189609--189670 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
189599 ACAGAAAAAA
189609 TGCAACCTCTTACT-CCTTTGCTCTTCTC
1 TGCAACCTCTTACTCCCTTT-CTCTTCTC
*
189637 TGCAGCCTCTTACTCCCTTTCTCTTCTC
1 TGCAACCTCTTACTCCCTTTCTCTTCTC
*
189665 TTCAAC
1 TGCAAC
189671 AATCCTACCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 25 0.83
29 5 0.17
ACGTcount: A:0.11, C:0.40, G:0.06, T:0.42
Consensus pattern (28 bp):
TGCAACCTCTTACTCCCTTTCTCTTCTC
Found at i:193877 original size:46 final size:47
Alignment explanation
Indices: 193816--193917 Score: 152
Period size: 46 Copynumber: 2.2 Consensus size: 47
193806 TGTTATCCAC
193816 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTATTCAA
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTATTCAA
* * * *
193863 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCTTGTTCGA
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTATTCAA
*
193909 AAAATGAAA
1 AAAAAGAAA
193918 ATAAATGACT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
46 41 0.84
47 8 0.16
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (47 bp):
AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTATTCAA
Found at i:203558 original size:36 final size:36
Alignment explanation
Indices: 203507--203599 Score: 132
Period size: 36 Copynumber: 2.6 Consensus size: 36
203497 TATATTAATG
*
203507 CTTGGGTGAAGATGGTGCATTGTTGCTCGGTTTAGC
1 CTTGGGTGAAGATGGTGCATTGTTGCTCGGGTTAGC
* * *
203543 CTTGGGTGAACATGGTGCATTGTTGCTCGGGTTGGT
1 CTTGGGTGAAGATGGTGCATTGTTGCTCGGGTTAGC
* *
203579 CTTGGATGAAGATGGTCCATT
1 CTTGGGTGAAGATGGTGCATT
203600 TTTGTTTGGT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.15, C:0.14, G:0.35, T:0.35
Consensus pattern (36 bp):
CTTGGGTGAAGATGGTGCATTGTTGCTCGGGTTAGC
Found at i:203769 original size:30 final size:30
Alignment explanation
Indices: 203735--203803 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
203725 TCAGGGCTAG
*
203735 AGATGGGATTAGCTTAGGAGTAGGGGTCAA
1 AGATGGGATTAGCTTAGGAGTAGGGGCCAA
* * * *
203765 AGATGGGGTTGGCTTAGGGGTAGGGGCCAG
1 AGATGGGATTAGCTTAGGAGTAGGGGCCAA
203795 AGATGGGAT
1 AGATGGGAT
203804 CAACTTTGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.25, C:0.07, G:0.46, T:0.22
Consensus pattern (30 bp):
AGATGGGATTAGCTTAGGAGTAGGGGCCAA
Found at i:208804 original size:36 final size:36
Alignment explanation
Indices: 208753--208880 Score: 138
Period size: 36 Copynumber: 3.6 Consensus size: 36
208743 GGGCTGCAGA
*
208753 TGGTGCATTA-ATGCTTGGTTTAGTCTTGGATGGAGG
1 TGGTGCATTAGTTGCTTGGTTTAG-CTTGGATGGAGG
* *
208789 TGGTGCATTAG-TGCTTGTTTTAACCTTGGATGGAGG
1 TGGTGCATTAGTTGCTTGGTTT-AGCTTGGATGGAGG
* * *
208825 TGGTGCA-TCGTTGCTTGGGTTAGCGTTGGATGGAGT
1 TGGTGCATTAGTTGCTTGGTTTAGC-TTGGATGGAGG
*
208861 TGGTGCGTT-GTTGCTTGGTT
1 TGGTGCATTAGTTGCTTGGTT
208881 CAGCCTTTAA
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
35 4 0.05
36 72 0.92
37 2 0.03
ACGTcount: A:0.12, C:0.10, G:0.38, T:0.40
Consensus pattern (36 bp):
TGGTGCATTAGTTGCTTGGTTTAGCTTGGATGGAGG
Found at i:208967 original size:36 final size:36
Alignment explanation
Indices: 208894--208980 Score: 104
Period size: 36 Copynumber: 2.4 Consensus size: 36
208884 CCTTTAATGT
* * * * *
208894 AGATGATGCATTGTTGCTGGGTTTGGTCTTTGGTGA
1 AGATGGTGCATTGTTGCTCGATTTCGTCTTGGGTGA
208930 AGATGGTGCATTGTTGCTCGATTTCGT-TTGGGATGA
1 AGATGGTGCATTGTTGCTCGATTTCGTCTTGGG-TGA
*
208966 AGATGGTCCATTGTT
1 AGATGGTGCATTGTT
208981 TCTTGGTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
35 4 0.09
36 40 0.91
ACGTcount: A:0.16, C:0.10, G:0.33, T:0.40
Consensus pattern (36 bp):
AGATGGTGCATTGTTGCTCGATTTCGTCTTGGGTGA
Found at i:209117 original size:30 final size:29
Alignment explanation
Indices: 209081--209199 Score: 157
Period size: 30 Copynumber: 4.0 Consensus size: 29
209071 GGTAGGCGTC
*
209081 GGGGCCGGAGATGGAGTTGGCTTAGGGGAA
1 GGGGCCGGAGATGG-GTTGGCTTAGGGGTA
*
209111 GGGGCCGGAGATGGGCTGGGCTTAGGGGTA
1 GGGGCCGGAGATGGG-TTGGCTTAGGGGTA
*
209141 GGGGTCGGAGATGGGGTTGGCTTAGGGGTA
1 GGGGCCGGAGAT-GGGTTGGCTTAGGGGTA
* *
209171 GGGGCCGGAGATGAGGTGGGCTTTGGGGT
1 GGGGCCGGAGATG-GGTTGGCTTAGGGGT
209200 CGGAGAAGGG
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
29 2 0.03
30 74 0.94
31 3 0.04
ACGTcount: A:0.14, C:0.10, G:0.56, T:0.19
Consensus pattern (29 bp):
GGGGCCGGAGATGGGTTGGCTTAGGGGTA
Found at i:209166 original size:24 final size:24
Alignment explanation
Indices: 209139--209214 Score: 62
Period size: 30 Copynumber: 2.9 Consensus size: 24
209129 GGCTTAGGGG
209139 TAGGGGTCGGAGATGGGGTTGGCT
1 TAGGGGTCGGAGATGGGGTTGGCT
* *
209163 TAGGGGTAGGGGCCGGAGATGAGGTGGGCT
1 TAGGGGT------CGGAGATGGGGTTGGCT
* *
209193 TTGGGGTCGGAGAAGGGGTTGG
1 TAGGGGTCGGAGATGGGGTTGG
209215 GATCGGGGTC
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
24 19 0.47
30 21 0.52
ACGTcount: A:0.14, C:0.08, G:0.57, T:0.21
Consensus pattern (24 bp):
TAGGGGTCGGAGATGGGGTTGGCT
Found at i:209179 original size:60 final size:60
Alignment explanation
Indices: 209081--209199 Score: 186
Period size: 60 Copynumber: 2.0 Consensus size: 60
209071 GGTAGGCGTC
209081 GGGGCCGGAGATGGAGTTGGCTTAGGGGAAGGGGCCGGAGATG-GGCTGGGCTTAGGGGTA
1 GGGGCCGGAGATGGAGTTGGCTTAGGGGAAGGGGCCGGAGATGAGG-TGGGCTTAGGGGTA
* * * *
209141 GGGGTCGGAGATGGGGTTGGCTTAGGGGTAGGGGCCGGAGATGAGGTGGGCTTTGGGGT
1 GGGGCCGGAGATGGAGTTGGCTTAGGGGAAGGGGCCGGAGATGAGGTGGGCTTAGGGGT
209200 CGGAGAAGGG
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
60 52 0.96
61 2 0.04
ACGTcount: A:0.14, C:0.10, G:0.56, T:0.19
Consensus pattern (60 bp):
GGGGCCGGAGATGGAGTTGGCTTAGGGGAAGGGGCCGGAGATGAGGTGGGCTTAGGGGTA
Found at i:211002 original size:30 final size:31
Alignment explanation
Indices: 210968--211029 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
210958 ATATATATAT
*
210968 ATATTATAAAAAAAATTGAGA-ATCAAATTA
1 ATATTATAAAAAAAATTCAGAGATCAAATTA
* * *
210998 ATATTTTATATAAAATTCAGAGATCAAATTA
1 ATATTATAAAAAAAATTCAGAGATCAAATTA
211029 A
1 A
211030 AAATTAACTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (31 bp):
ATATTATAAAAAAAATTCAGAGATCAAATTA
Found at i:219505 original size:130 final size:130
Alignment explanation
Indices: 219364--219611 Score: 408
Period size: 130 Copynumber: 1.9 Consensus size: 130
219354 TATTTATATA
*
219364 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * *
219429 TTAGCACATGATCATGACACGTGTCATTAGTGACACGTGTTACCA-CCTAATTATTTATATATGC
66 TTAACACATGATCATGACACGTGTCATTAGTGACACATGTCA-CATCCTAATTATTTATATATGC
219493 T
130 T
219494 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
219559 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACATCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTAGTGACACATGTCACATCCTAATTA
219612 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
129 2 0.02
130 107 0.98
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTAGTGACACATGTCACATCCTAATTATTTATATATGCT
Found at i:219642 original size:130 final size:129
Alignment explanation
Indices: 219378--219642 Score: 293
Period size: 130 Copynumber: 2.0 Consensus size: 129
219368 ATTTGGTCCT
* *
219378 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * **** *
219443 TGACACGTGTCATTAGTGACACGTGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTAGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
219508 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
219573 TGATATGTGTTATTGGTGACACATGTCA-CATCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAG
66 TGACACGTGTCATTAGTGACACATGTCACCA-CCTAATT--AAGAAAA-TAAGCTATCAAAGAAG
219636 T-A
127 TCA
219638 AAATT
1 AAATT
219643 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 19, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
129 2 0.02
130 97 0.87
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTAGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:220097 original size:15 final size:16
Alignment explanation
Indices: 220073--220109 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
220063 TTTAATTTCT
220073 TATT-AAAAATA-AAA
1 TATTCAAAAATATAAA
220087 TATTCAAAAATATAAA
1 TATTCAAAAATATAAA
220103 TGATTCA
1 T-ATTCA
220110 TACATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
TATTCAAAAATATAAA
Found at i:220292 original size:35 final size:35
Alignment explanation
Indices: 220243--220328 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
220233 ATTGAAGTAT
** * *
220243 TTTAGAATTTAATTGAAGTATTTTAGAACTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
220278 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
220313 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
220329 TGATTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.02, G:0.21, T:0.40
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:222414 original size:2 final size:2
Alignment explanation
Indices: 222407--222452 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
222397 CGAAAGAAGA
222407 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
222449 TC TC
1 TC TC
222453 GTAGGGTTCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:224251 original size:14 final size:15
Alignment explanation
Indices: 224232--224260 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
224222 AACGTATTTC
224232 TTACGTTT-ATGTTT
1 TTACGTTTGATGTTT
224246 TTACGTTTGATGTTT
1 TTACGTTTGATGTTT
224261 AATTGGGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.14, C:0.07, G:0.17, T:0.62
Consensus pattern (15 bp):
TTACGTTTGATGTTT
Found at i:228268 original size:19 final size:20
Alignment explanation
Indices: 228244--228294 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
228234 AATGACCAAT
228244 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
228263 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
228283 AAAATCGCAACG
1 AAAATCGCAACG
228295 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:228288 original size:20 final size:20
Alignment explanation
Indices: 228244--228482 Score: 92
Period size: 20 Copynumber: 11.6 Consensus size: 20
228234 AATGACCAAT
* *
228244 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
228263 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
228283 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
228303 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
**
228323 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
228343 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
228364 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
*
228387 AAAATCGCAATGCGATTGATTAAG
1 AAAATCGCAACGCGA-T--TT-AG
* * * *
228411 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
228431 AGATTCGCAACGCGACTGAG
1 AAAATCGCAACGCGATTTAG
*
228451 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
*
228471 AGAATCGCAACG
1 AAAATCGCAACG
228483 TTAAAAAGAA
Statistics
Matches: 178, Mismatches: 30, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
19 17 0.10
20 114 0.64
21 15 0.08
23 12 0.07
24 18 0.10
26 2 0.01
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:228314 original size:40 final size:41
Alignment explanation
Indices: 228263--228357 Score: 124
Period size: 40 Copynumber: 2.4 Consensus size: 41
228253 ACGCGATATC
** *
228263 AAAATCGCAACGCGAT-TTAGAAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATAAAAGAAAATCGCAACGGTAAAAAG
*
228303 AAAATCGCAACG-G-TCAAAAGAAAATCGCAACGGTCAAAAG
1 AAAATCGCAACGCGAT-AAAAGAAAATCGCAACGGTAAAAAG
228343 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
228358 GCTTCCAAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
38 1 0.02
39 1 0.02
40 44 0.94
41 1 0.02
ACGTcount: A:0.48, C:0.20, G:0.19, T:0.13
Consensus pattern (41 bp):
AAAATCGCAACGCGATAAAAGAAAATCGCAACGGTAAAAAG
Found at i:228401 original size:23 final size:24
Alignment explanation
Indices: 228368--228425 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
228358 GCTTCCAAGT
* *
228368 TCGCAACGCGATTTA-GAAGAAAA
1 TCGCAATGCGATTGATGAAGAAAA
* *
228391 TCGCAATGCGATTGATTAAGAGAA
1 TCGCAATGCGATTGATGAAGAAAA
228415 TCGCAATGCGA
1 TCGCAATGCGA
228426 CTGAGAGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 13 0.43
24 17 0.57
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (24 bp):
TCGCAATGCGATTGATGAAGAAAA
Found at i:228496 original size:20 final size:20
Alignment explanation
Indices: 228473--228512 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
228463 CGATTTAGAG
*
228473 AATCGCAACGTTAAAAAGAA
1 AATCGCAACGGTAAAAAGAA
*
228493 AATCGCAACGGTCAAAAGAA
1 AATCGCAACGGTAAAAAGAA
228513 TAGTTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.17, G:0.17, T:0.12
Consensus pattern (20 bp):
AATCGCAACGGTAAAAAGAA
Found at i:228601 original size:6 final size:6
Alignment explanation
Indices: 228590--228694 Score: 210
Period size: 6 Copynumber: 17.5 Consensus size: 6
228580 GACACGTATT
228590 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
228638 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
228686 ACCACG ACC
1 ACCACG ACC
228695 CGAGACGAGA
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 99 1.00
ACGTcount: A:0.33, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:229530 original size:20 final size:20
Alignment explanation
Indices: 229507--229657 Score: 176
Period size: 20 Copynumber: 7.4 Consensus size: 20
229497 CTTTTTAGCG
*
229507 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCA
*
229527 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCA
* *
229547 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TCTCAATCGCA
*
229570 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCA
* *
229590 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAATCGCA
* *
229610 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAATCGCA
**
229630 TTGCGATTCAATCAATCGCA
1 TTGCGATTCTCTCAATCGCA
229650 TTGCGATT
1 TTGCGATT
229658 TTCTTATAAA
Statistics
Matches: 117, Mismatches: 11, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
20 98 0.84
21 2 0.02
22 3 0.03
23 14 0.12
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (20 bp):
TTGCGATTCTCTCAATCGCA
Found at i:229755 original size:20 final size:20
Alignment explanation
Indices: 229485--229782 Score: 116
Period size: 20 Copynumber: 14.6 Consensus size: 20
229475 AATTTTTGAC
*** *
229485 CGTTGCGATTTTCTTTTTAG
1 CGTTGCGATTTTCTAAATCG
* * *
229505 CGTTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
229525 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
229545 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
229568 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
229588 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
229608 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* *** *
229628 CATTGCGATTCAATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
229648 CATTGCGATTTTCTTATAAATCG
1 CGTTGCGATTTTC---TAAATCG
* ** ** *
229671 TGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
229692 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
229710 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
229732 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
229752 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
229771 CGTTGCGATTTT
1 CGTTGCGATTTT
229783 ATTGATCATT
Statistics
Matches: 221, Mismatches: 46, Indels: 23
0.76 0.16 0.08
Matches are distributed among these distances:
18 2 0.01
19 17 0.08
20 157 0.71
21 13 0.06
22 4 0.02
23 28 0.13
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:229772 original size:19 final size:20
Alignment explanation
Indices: 229732--229782 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
229722 TTCTTTTTAA
*
229732 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
229752 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
229771 CGTTGCGATTTT
1 CGTTGCGATTTT
229783 ATTGATCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:236892 original size:4 final size:4
Alignment explanation
Indices: 236870--236941 Score: 63
Period size: 4 Copynumber: 18.0 Consensus size: 4
236860 CTGAAGGTAT
* * * * * * * * *
236870 TCTC TCCC TCTC CCTC TCTC TCTC CCCC TCCC TCCC TCCC TCCC TCCC
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC
236918 TCTC TCTC TCTC TCTC TCTC TCTC
1 TCTC TCTC TCTC TCTC TCTC TCTC
236942 CTTGTACATA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 60 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (4 bp):
TCTC
Found at i:236941 original size:12 final size:12
Alignment explanation
Indices: 236871--236939 Score: 79
Period size: 12 Copynumber: 5.9 Consensus size: 12
236861 TGAAGGTATT
*
236871 CTCTCCCTCTCC
1 CTCTCTCTCTCC
236883 CTCTCTCTCTCC
1 CTCTCTCTCTCC
*
236895 C-C-CTCCCTCC
1 CTCTCTCTCTCC
* *
236905 CTCCCTCCCTCC
1 CTCTCTCTCTCC
*
236917 CTCTCTCTCTCT
1 CTCTCTCTCTCC
236929 CTCTCTCTCTC
1 CTCTCTCTCTC
236940 TCCTTGTACA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
10 8 0.16
11 2 0.04
12 40 0.80
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (12 bp):
CTCTCTCTCTCC
Found at i:239322 original size:16 final size:18
Alignment explanation
Indices: 239291--239324 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
239281 GCAAACTGAA
239291 ATTTTCAAATTATTTTAT
1 ATTTTCAAATTATTTTAT
239309 ATTTT-AAA-TATTTTAT
1 ATTTTCAAATTATTTTAT
239325 TTATATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTCAAATTATTTTAT
Found at i:244207 original size:60 final size:59
Alignment explanation
Indices: 244075--244212 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 59
244065 AACATAATGA
* * *
244075 ATAGTCAAGTGACCATTTTATAAATTTTAATAGTCGAGGGACCCAACAAAGTAACTCCCT
1 ATAGTC-AGGGACCATTTTATAAATTTTAATAGTCGAAGGACCCAACAAAGCAACTCCCT
* * * * *
244135 ATAGTCAGGGGACCATTTTATAACTTTTAATAGTCTAAGGACTCAACAAAGCAA-TATCTT
1 ATAGTCA-GGGACCATTTTATAAATTTTAATAGTCGAAGGACCCAACAAAGCAACT-CCCT
244195 ATAGTCGAGGGACCATTT
1 ATAGTC-AGGGACCATTT
244213 GTGTACTTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
59 2 0.03
60 64 0.96
61 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Consensus pattern (59 bp):
ATAGTCAGGGACCATTTTATAAATTTTAATAGTCGAAGGACCCAACAAAGCAACTCCCT
Done.