Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008245.1 Hibiscus syriacus cultivar Beakdansim tig00110895_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: 6601124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 28 of 33
Found at i:5625103 original size:199 final size:198
Alignment explanation
Indices: 5624746--5625233 Score: 688
Period size: 199 Copynumber: 2.4 Consensus size: 198
5624736 TATCAGTGTT
* * *
5624746 TTCATACTGGACAAAATGTATCGATACAACTTAAAAAATTATCGATACTTTTTCTTTACATATTC
1 TTCATACTGGACAAAA-GTATCGATACAACTTAAAAAACTATCGATACTTTTTGTTTACCTATTC
* * * * *
5624811 TCTCATTAAACCGGTATATTTTTACCGGTTACATTGTATATTTATCTATTACTTTATAATTATCA
65 TCTCATTAAACCAGTATATTTTTACCGGTTACATTGTAAAATTACCTATTACTTTATAATAATCA
* * * *
5624876 GTTTCGATGTTTTAAGGATCGATACTTATGATACATGTATCGATACTTTATTCGTCCATCTCATT
130 GTTTCAATGTTTTAAGGATCGATACTTATCA-ACATGTATCGATACTTTATGCGTACATCTCATT
*
5624941 TGGGA
194 TAGGA
* * * * * * *
5624946 TTCATACTGGACTAAAGTATCGATACTATTTAAACAAGTATCGATACTTTATGTATACCTATTCT
1 TTCATACTGGACAAAAGTATCGATACAACTTAAAAAACTATCGATACTTTTTGTTTACCTATTCT
*
5625011 CTCATTAAACTAGTATATTTTTACCGGTTACATTGTAAAATTACCTATTACTTTATAATAATCAG
66 CTCATTAAACCAGTATATTTTTACCGGTTACATTGTAAAATTACCTATTACTTTATAATAATCAG
* * *
5625076 TTTCAATGTTTTAAGGATCGATACTTATCAACTTGTATCGATACTTTATGCGTATATCTCGTTTA
131 TTTCAATGTTTTAAGGATCGATACTTATCAACATGTATCGATACTTTATGCGTACATCTCATTTA
5625141 GGA
196 GGA
**
5625144 TTCATACTGGACAAAAAGTATCGGCACAACTTAAAAAACTATCGATACTTTTTGTTTACCTATTC
1 TTCATACTGGAC-AAAAGTATCGATACAACTTAAAAAACTATCGATACTTTTTGTTTACCTATTC
* *
5625209 TCTCATTAAATCGGTATATGTTTTA
65 TCTCATTAAACCAGTATAT-TTTTA
5625234 AGGATCGATA
Statistics
Matches: 251, Mismatches: 35, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
198 44 0.18
199 187 0.75
200 20 0.08
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.41
Consensus pattern (198 bp):
TTCATACTGGACAAAAGTATCGATACAACTTAAAAAACTATCGATACTTTTTGTTTACCTATTCT
CTCATTAAACCAGTATATTTTTACCGGTTACATTGTAAAATTACCTATTACTTTATAATAATCAG
TTTCAATGTTTTAAGGATCGATACTTATCAACATGTATCGATACTTTATGCGTACATCTCATTTA
GGA
Found at i:5625620 original size:340 final size:342
Alignment explanation
Indices: 5624882--5625704 Score: 1185
Period size: 340 Copynumber: 2.4 Consensus size: 342
5624872 ATCAGTTTCG
* * * * *
5624882 ATGTTTTAAGGATCGATACTTATGATACATGTATCGATACTTTAT-TCGTCCATCTCATTTGGGA
1 ATGTTTTAAGGATCGATACTTCTCAAACATGTATCGATACATTATGT-GTCCATCTCGTTTGGGA
** * * * * * *
5624946 TTCATACTGGACTAAA-GTATCGATACTATTTAAACAAGTATCGATACTTTATGTATACCTATTC
65 TTCATACTGGAAAAAATGTATCGATACAACTGAAAAAAGTATCGATACTTTTTGTTTACCTATTC
* *
5625010 TCTCATTAAACTAGTATATTTTTACCGGTTACATTGTAAAATTACCTATTACTTTATAATAATCA
130 TCTCATTAAACGAGTATATTTTTACCAGTTA-A-T-TAAAATTACCTATTACTTTATAATAATCA
* * *
5625075 GTTTCAATGTTTTAAGGATCGATACTTATCAACTTGTATCGATACTTTATGCGTATATCTCGTTT
192 GTTTCAATGTTTTAAGGATCGATACTTATCAACATGTATCAATACTTTATGCGTACATCTCGTTT
* *
5625140 AGGATTCATACTGGACAAAAAGTATCGGCACAACTTAAAAAACTATCGATACTTTTTGTTTACCT
257 AGGATTCATACTGGACAAAAAGTATCGACACAACTTAAAAAACTAACGATACTTTTTGTTTACCT
*
5625205 ATTCTCTCATTAAATCGGTAT
322 ATTCTATCATTAAATCGGTAT
* * *
5625226 ATGTTTTAAGGATCGATA-TGTCTTAAACATGTATCTATACATTATGTTTCCATCTCGTTTGGGA
1 ATGTTTTAAGGATCGATACT-TCTCAAACATGTATCGATACATTATGTGTCCATCTCGTTTGGGA
5625290 TTCATACTGGAAAAAATGTATCGATACAACTGAAAAAAGTATCGATACTTTTTGTTTACCTATTC
65 TTCATACTGGAAAAAATGTATCGATACAACTGAAAAAAGTATCGATACTTTTTGTTTACCTATTC
* * * * *
5625355 TCTCATTAAACCGA-TATATTTTTATCAGTT-A-TATATTTACCTATTACTTTATAATTATCGGT
130 TCTCATTAAA-CGAGTATATTTTTACCAGTTAATTAAAATTACCTATTACTTTATAATAATCAGT
* * * *
5625417 TTCGATGTTTTAAGGAAT-GATACTTATTATACATGTATCAATATTTTATGCGTGCATCTCGTTT
194 TTCAATGTTTTAAGG-ATCGATACTTATCA-ACATGTATCAATACTTTATGCGTACATCTCGTTT
* *
5625481 GGGATTCATACTGGACAAAAAGTATCGATACAACTTAAAAAACTAACGATACTTTTTGTTTACCT
257 AGGATTCATACTGGACAAAAAGTATCGACACAACTTAAAAAACTAACGATACTTTTTGTTTACCT
5625546 ATTCTATCATTAAA-CGGTAT
322 ATTCTATCATTAAATCGGTAT
*
5625566 ATGTTTTAAGGATCGATACTTCTCAAACATGTATCGATACATTATGTGTCCATCTCGTTTAGGAT
1 ATGTTTTAAGGATCGATACTTCTCAAACATGTATCGATACATTATGTGTCCATCTCGTTTGGGAT
*
5625631 TCATACTGGAAAAAATGTATCGATAAAACTGAAAAAAGTATCGATACTTTTTGTTTACCTATTCT
66 TCATACTGGAAAAAATGTATCGATACAACTGAAAAAAGTATCGATACTTTTTGTTTACCTATTCT
5625696 CTCATTAAA
131 CTCATTAAA
5625705 TCAGTAACAA
Statistics
Matches: 433, Mismatches: 39, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
340 189 0.44
341 106 0.24
343 2 0.00
344 67 0.15
345 67 0.15
346 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (342 bp):
ATGTTTTAAGGATCGATACTTCTCAAACATGTATCGATACATTATGTGTCCATCTCGTTTGGGAT
TCATACTGGAAAAAATGTATCGATACAACTGAAAAAAGTATCGATACTTTTTGTTTACCTATTCT
CTCATTAAACGAGTATATTTTTACCAGTTAATTAAAATTACCTATTACTTTATAATAATCAGTTT
CAATGTTTTAAGGATCGATACTTATCAACATGTATCAATACTTTATGCGTACATCTCGTTTAGGA
TTCATACTGGACAAAAAGTATCGACACAACTTAAAAAACTAACGATACTTTTTGTTTACCTATTC
TATCATTAAATCGGTAT
Found at i:5625684 original size:145 final size:145
Alignment explanation
Indices: 5625421--5625704 Score: 410
Period size: 145 Copynumber: 2.0 Consensus size: 145
5625411 ATCGGTTTCG
* * ** * *
5625421 ATGTTTTAAGGAATGATACTTATTATACATGTATCAATATTTTATGCGTGCATCTCGTTTGGGAT
1 ATGTTTTAAGGAATGATACTTATCAAACATGTATCAATACATTATGCGTCCATCTCGTTTAGGAT
* *
5625486 TCATACTGGACAAAAAGTATCGATACAACTTAAAAAACTAACGATACTTTTTGTTTACCTATTCT
66 TCATACTGGACAAAAAGTATCGATAAAACTGAAAAAACTAACGATACTTTTTGTTTACCTATTCT
5625551 ATCATTAAACGGTAT
131 ATCATTAAACGGTAT
* * *
5625566 ATGTTTTAAGG-ATCGATACTTCTCAAACATGTATCGATACATTATGTGTCCATCTCGTTTAGGA
1 ATGTTTTAAGGAAT-GATACTTATCAAACATGTATCAATACATTATGCGTCCATCTCGTTTAGGA
* *
5625630 TTCATACTGGA-AAAAATGTATCGATAAAACTGAAAAAAGTATCGATACTTTTTGTTTACCTATT
65 TTCATACTGGACAAAAA-GTATCGATAAAACTGAAAAAACTAACGATACTTTTTGTTTACCTATT
*
5625694 CTCTCATTAAA
129 CTATCATTAAA
5625705 TCAGTAACAA
Statistics
Matches: 123, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
144 7 0.06
145 116 0.94
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (145 bp):
ATGTTTTAAGGAATGATACTTATCAAACATGTATCAATACATTATGCGTCCATCTCGTTTAGGAT
TCATACTGGACAAAAAGTATCGATAAAACTGAAAAAACTAACGATACTTTTTGTTTACCTATTCT
ATCATTAAACGGTAT
Found at i:5626297 original size:54 final size:54
Alignment explanation
Indices: 5626192--5626298 Score: 126
Period size: 54 Copynumber: 2.0 Consensus size: 54
5626182 ACTGCATCAG
* * * **
5626192 ACAATGTTAAGCAAATCGAGGAATCCAATGAAGTAAATATTATTGGTGAATCTA
1 ACAATGTTAACCAAACCAAGGAATCCAATGAAGTAAATATTATTGAAGAATCTA
* * *
5626246 ACAATGTTAACCCAACCAAGGAATGCAATGAAG-AACATATTGTTGAAGAATCT
1 ACAATGTTAACCAAACCAAGGAATCCAATGAAGTAA-ATATTATTGAAGAATCT
5626299 GACAGATTAG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
53 2 0.05
54 42 0.95
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (54 bp):
ACAATGTTAACCAAACCAAGGAATCCAATGAAGTAAATATTATTGAAGAATCTA
Found at i:5627826 original size:66 final size:65
Alignment explanation
Indices: 5627754--5627901 Score: 199
Period size: 66 Copynumber: 2.3 Consensus size: 65
5627744 CTCAAACACT
* *
5627754 CCCATCACCCCCTTAAGTTCACCCCTCAATTCCATAACTTCCTTCACCACTCCATCAAATTTTCC
1 CCCATCACCCCCTTAAGTTCACCCCACAATTCCACAACTTCCTTCACCACTCCATC-AATTTTCC
5627819 A
65 A
** * * *
5627820 CCCATCACCATCTTAAGTTCACCCCACAATTCCACAACTTCTTTCACCACTCTATCTATTTTCCA
1 CCCATCACCCCCTTAAGTTCACCCCACAATTCCACAACTTCCTTCACCACTCCATCAATTTTCCA
*
5627885 CCCA-CTTCCCCCTTAAG
1 CCCATC-ACCCCCTTAAG
5627902 CCTCTGAATT
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
64 1 0.01
65 20 0.28
66 50 0.70
ACGTcount: A:0.25, C:0.43, G:0.02, T:0.30
Consensus pattern (65 bp):
CCCATCACCCCCTTAAGTTCACCCCACAATTCCACAACTTCCTTCACCACTCCATCAATTTTCCA
Found at i:5628062 original size:9 final size:9
Alignment explanation
Indices: 5628048--5628087 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
5628038 CTTCTTCCTT
5628048 CTCCTCTTC
1 CTCCTCTTC
5628057 CTCCTCTTC
1 CTCCTCTTC
* *
5628066 CTCTTCTGC
1 CTCCTCTTC
*
5628075 CTCCTCTAC
1 CTCCTCTTC
5628084 CTCC
1 CTCC
5628088 ATGCCAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.03, C:0.55, G:0.03, T:0.40
Consensus pattern (9 bp):
CTCCTCTTC
Found at i:5628351 original size:25 final size:24
Alignment explanation
Indices: 5628321--5628370 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
5628311 ACCTACATTT
* *
5628321 ATAATTAAATTTATCATTTTATATA
1 ATAATTAAA-CTAACATTTTATATA
*
5628346 ATAATTATACTAACATTTTATATA
1 ATAATTAAACTAACATTTTATATA
5628370 A
1 A
5628371 AAAACAAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (24 bp):
ATAATTAAACTAACATTTTATATA
Found at i:5630649 original size:183 final size:183
Alignment explanation
Indices: 5630341--5630755 Score: 665
Period size: 183 Copynumber: 2.3 Consensus size: 183
5630331 ACTTATTAAA
* * *
5630341 GTATCGATACCTTCAACATATCCGGTAGT-GCTTTACCGGTTTTGTCATAATGAAATTGATTTTG
1 GTATCGATACCTTCAACATATCCGGTA-TCTCTTTACCGGTTTTGTCATAATGAAACTGATTTTA
*
5630405 TCATATTTTGACCTGTTATATTGTTATGTATCGATACATGTTTATAAAATATCGATACTTTATAG
65 TCATATTTTGACCTGTTATATTGTTATGTATCGATACAAGTTTATAAAATATCGATACTTTATAG
*
5630470 GCGCTATTATTG-TTTTCCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATG
130 GCGCTAGTATTGCTTTT-CTTTTAAATTCCAAAAGTATCGATACTTATTTGAATG
** *
5630524 GTATCGATACCTTCAACATATATGGTATCTCTTTACCGGTTTTGTCATAATGAAACTGGTTTTAT
1 GTATCGATACCTTCAACATATCCGGTATCTCTTTACCGGTTTTGTCATAATGAAACTGATTTTAT
* *
5630589 CATATTTTTACCTGTTATATTGTTATGTATCGATACAAGTTTATAAAGTATCGATACTTTATAGG
66 CATATTTTGACCTGTTATATTGTTATGTATCGATACAAGTTTATAAAATATCGATACTTTATAGG
* *
5630654 TGCTAGTATTGCTTTTCTTTTCAATTCCAAAAGTATCGATACTTATTTGAATG
131 CGCTAGTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATG
*
5630707 GTATCGATACCTTCAACATATCCGGTAGCTCTTTACTC-GTTTTGTCATA
1 GTATCGATACCTTCAACATATCCGGTATCTCTTTAC-CGGTTTTGTCATA
5630756 TTTTTACCTA
Statistics
Matches: 214, Mismatches: 15, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
182 1 0.00
183 208 0.97
184 5 0.02
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.43
Consensus pattern (183 bp):
GTATCGATACCTTCAACATATCCGGTATCTCTTTACCGGTTTTGTCATAATGAAACTGATTTTAT
CATATTTTGACCTGTTATATTGTTATGTATCGATACAAGTTTATAAAATATCGATACTTTATAGG
CGCTAGTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATG
Found at i:5631690 original size:22 final size:19
Alignment explanation
Indices: 5631644--5631713 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 19
5631634 CGTAAAAATG
5631644 GTATCGATACCATAGTAGA
1 GTATCGATACCATAGTAGA
*
5631663 GTATCGGTACCATAGTATAGTA
1 GTATCGATACCATAG--TAG-A
* *
5631685 GTATCGATACCATGGTAGGG
1 GTATCGATACCATAGTA-GA
5631705 GTATCGATA
1 GTATCGATA
5631714 TTGAGGAGCC
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 14 0.33
20 11 0.26
21 4 0.09
22 14 0.33
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (19 bp):
GTATCGATACCATAGTAGA
Found at i:5632192 original size:56 final size:56
Alignment explanation
Indices: 5632031--5632198 Score: 275
Period size: 57 Copynumber: 3.0 Consensus size: 56
5632021 ATTACATAAT
5632031 GGCACTGAGTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCTGTATG
1 GGCACTGAGTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTAT-AATTTCTGTATG
** * *
5632088 GGCACTTTGTGTGCAAAAAGTTAAGAATTTCATAATTTGTTTATAATTTCCGTATG
1 GGCACTGAGTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATAATTTCTGTATG
5632144 GGCACTGAGTGTGC-AAAAGTTAAGAAATTCATAATTTGTTTATAAATTTCTGTAT
1 GGCACTGAGTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTAT-AATTTCTGTAT
5632199 AAGAACTTTA
Statistics
Matches: 102, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
55 28 0.27
56 33 0.32
57 41 0.40
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.39
Consensus pattern (56 bp):
GGCACTGAGTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATAATTTCTGTATG
Found at i:5632491 original size:68 final size:68
Alignment explanation
Indices: 5632402--5632676 Score: 397
Period size: 68 Copynumber: 4.0 Consensus size: 68
5632392 TAAAAGATTA
* *
5632402 GAGGTCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
1 GAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
5632467 TTT
66 TTT
*
5632470 GAGGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
1 GAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
5632535 TTT
66 TTT
* * * * *
5632538 GAGGCCTAGCTGTGTATTTGACAGAAAGTTGACAATTATGTCAGTTAGATGAAAGACTAAGTGCC
1 GAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
5632603 TTT
66 TTT
* * * * * * * * *
5632606 GAGACCTAGCGGTGCATTTGATAGAAAGATGCCAATCATGCCAGTTAAATGAAAGGTTAAATGCC
1 GAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
5632671 TTT
66 TTT
5632674 GAG
1 GAG
5632677 TAAAAGGCTA
Statistics
Matches: 187, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 187 1.00
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (68 bp):
GAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
TTT
Found at i:5632835 original size:45 final size:45
Alignment explanation
Indices: 5632710--5632836 Score: 155
Period size: 46 Copynumber: 2.8 Consensus size: 45
5632700 GCATAACATT
* * *
5632710 GTATAAAAGACATGAAAGGATACCATAAATGAAATGTATAATAGT
1 GTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGA
* * * *
5632755 GTCTAAAAAGGCATGAAAGGATGTCATAAAAGAAATGTATACTAGA
1 GTAT-AAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGA
* **
5632801 GTATACAAGGCATGAAAGGATGCCATAGTTGAAATG
1 GTATAAAAGGCATGAAAGGATGCCATAAATGAAATG
5632837 CATATGAGTG
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
45 30 0.44
46 38 0.56
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (45 bp):
GTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGA
Found at i:5632858 original size:45 final size:44
Alignment explanation
Indices: 5632809--5633031 Score: 329
Period size: 45 Copynumber: 5.0 Consensus size: 44
5632799 GAGTATACAA
*
5632809 GGCATGAAAGGATGCCATAGTTGAAATGCATATGAGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATG-GTGCATTATC
* * *
5632854 GGCATGAAATGATACCATAATTGAAATGCATATGGGTTCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATAT-GGTGCATTATC
* *
5632899 GGCATGAAAGGATGTCATAATTAAAATGCATATGAGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATG-GTGCATTATC
* *
5632944 GGCATGAAAGGGTGCCATAATTAAAATGCATATGGCTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGG-TGCATTATC
*
5632989 GGCATGAAAGGATGTCATAATTGAAATGCATATGGTGCATTAT
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGTGCATTAT
5633032 AAGTATAAAG
Statistics
Matches: 161, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
44 10 0.06
45 150 0.93
46 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.29
Consensus pattern (44 bp):
GGCATGAAAGGATGCCATAATTGAAATGCATATGGTGCATTATC
Found at i:5633060 original size:135 final size:135
Alignment explanation
Indices: 5632809--5633060 Score: 341
Period size: 135 Copynumber: 1.9 Consensus size: 135
5632799 GAGTATACAA
* * *
5632809 GGCATGAAAGGATGCCATAGTTGAAATGCATATGAGTGCATTATCGGCATGAAATGATACCATAA
1 GGCATGAAAGGATGCCATAATTAAAATGCATATGAGTGCATTATCGGCATGAAAGGATACCATAA
* ** *
5632874 TTGAAATGCATATGGGTTCATTATCGGCATGAAAGGATGTCATAATTAAAATGCATATGAGTGCA
66 TTGAAATGCATATGGGTGCATTATAAGCATGAAAGGATGTCATAATGAAAATGCATATGAGTGCA
5632939 TTATC
131 TTATC
* **
5632944 GGCATGAAAGGGTGCCATAATTAAAATGCATATG-GCTGCATTATCGGCATGAAAGGATGTCATA
1 GGCATGAAAGGATGCCATAATTAAAATGCATATGAG-TGCATTATCGGCATGAAAGGATACCATA
*
5633008 ATTGAAATGCATAT-GGTGCATTATAAGTAT-AAAGGAATGCTC-TCAATGAAAAT
65 ATTGAAATGCATATGGGTGCATTATAAGCATGAAAGG-ATG-TCAT-AATGAAAAT
5633061 AAAGAATAAT
Statistics
Matches: 102, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
133 5 0.05
134 17 0.17
135 80 0.78
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (135 bp):
GGCATGAAAGGATGCCATAATTAAAATGCATATGAGTGCATTATCGGCATGAAAGGATACCATAA
TTGAAATGCATATGGGTGCATTATAAGCATGAAAGGATGTCATAATGAAAATGCATATGAGTGCA
TTATC
Found at i:5636900 original size:17 final size:17
Alignment explanation
Indices: 5636880--5636913 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5636870 AAAAGGCTGA
*
5636880 TTTCTAAAAAATATTTT
1 TTTCCAAAAAATATTTT
*
5636897 TTTCCAAAAATTATTTT
1 TTTCCAAAAAATATTTT
5636914 AATATTTTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTCCAAAAAATATTTT
Found at i:5640170 original size:20 final size:20
Alignment explanation
Indices: 5640141--5640179 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5640131 TTTCCACAAC
*
5640141 ATGCAACTATATGCTTCTAA
1 ATGCAACTATATGATTCTAA
*
5640161 ATGCATCTATATGATTCTA
1 ATGCAACTATATGATTCTA
5640180 TATGTGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (20 bp):
ATGCAACTATATGATTCTAA
Found at i:5640505 original size:2 final size:2
Alignment explanation
Indices: 5640500--5640524 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5640490 ACACACACAC
5640500 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5640525 ATGGGATTAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5658403 original size:17 final size:17
Alignment explanation
Indices: 5658381--5658413 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5658371 TTTCATAGAA
5658381 ATATACAATAAATATAC
1 ATATACAATAAATATAC
5658398 ATATACAATAAATATA
1 ATATACAATAAATATA
5658414 AGCTTAAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (17 bp):
ATATACAATAAATATAC
Found at i:5659090 original size:22 final size:22
Alignment explanation
Indices: 5659065--5659113 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
5659055 CTACGGCGAC
5659065 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
5659087 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
5659109 ATCCG
1 ATCCG
5659114 CCTATCTCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:5661185 original size:21 final size:23
Alignment explanation
Indices: 5661161--5661258 Score: 59
Period size: 21 Copynumber: 4.6 Consensus size: 23
5661151 TGGTGCATGG
5661161 CGTGATGAGGTA-CGGT-CTTTA
1 CGTGATGAGGTAGCGGTACTTTA
* *
5661182 CGTGGTGAGGTAGAGGT--TTTA
1 CGTGATGAGGTAGCGGTACTTTA
* * ** *
5661203 CGCGATGA--AAATGGTGCTTTA
1 CGTGATGAGGTAGCGGTACTTTA
* *
5661224 CGTGGTGAGGTATC--TACTTTA
1 CGTGATGAGGTAGCGGTACTTTA
5661245 CGTGATGAGGTAGC
1 CGTGATGAGGTAGC
5661259 CACTCTATGT
Statistics
Matches: 57, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
19 4 0.07
21 49 0.86
22 3 0.05
23 1 0.02
ACGTcount: A:0.21, C:0.12, G:0.35, T:0.32
Consensus pattern (23 bp):
CGTGATGAGGTAGCGGTACTTTA
Found at i:5661575 original size:21 final size:20
Alignment explanation
Indices: 5661550--5661632 Score: 94
Period size: 21 Copynumber: 4.0 Consensus size: 20
5661540 GAAGCACCTG
* *
5661550 TCATCATTCAAGAGGCTCCT
1 TCATCGTTCAAGAGGCCCCT
*
5661570 ATCATCCTTCAAGAGGCCCCT
1 -TCATCGTTCAAGAGGCCCCT
5661591 TCCATCGTTCAAGAGGCCCCT
1 T-CATCGTTCAAGAGGCCCCT
* *
5661612 GTCATCGTTTAAGAGGTCCCT
1 -TCATCGTTCAAGAGGCCCCT
5661633 CCCACCGTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
20 1 0.02
21 53 0.96
22 1 0.02
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.28
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCCT
Found at i:5661617 original size:42 final size:42
Alignment explanation
Indices: 5661551--5661641 Score: 110
Period size: 42 Copynumber: 2.2 Consensus size: 42
5661541 AAGCACCTGT
* * *
5661551 CATCATTCAAGAGGCTCCTATCATCCTTCAAGAGGCCCCTTC
1 CATCGTTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCC
* * * *
5661593 CATCGTTCAAGAGGCCCCTGTCATCGTTTAAGAGGTCCCTCC
1 CATCGTTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCC
*
5661635 CACCGTT
1 CATCGTT
5661642 TGAGAGCCCG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.21, C:0.35, G:0.18, T:0.26
Consensus pattern (42 bp):
CATCGTTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCC
Found at i:5661641 original size:21 final size:21
Alignment explanation
Indices: 5661580--5661647 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
5661570 ATCATCCTTC
* *
5661580 AAGAGGCCCCTTCCATCGTTC
1 AAGAGGCCCCTCCCATCGTTT
**
5661601 AAGAGGCCCCTGTCATCGTTT
1 AAGAGGCCCCTCCCATCGTTT
* *
5661622 AAGAGGTCCCTCCCACCGTTT
1 AAGAGGCCCCTCCCATCGTTT
*
5661643 GAGAG
1 AAGAG
5661648 CCCGATTCAC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.21, C:0.32, G:0.24, T:0.24
Consensus pattern (21 bp):
AAGAGGCCCCTCCCATCGTTT
Found at i:5663068 original size:63 final size:64
Alignment explanation
Indices: 5662998--5663145 Score: 226
Period size: 64 Copynumber: 2.3 Consensus size: 64
5662988 AAATTGATGT
* *
5662998 ATTTGTAAAAGTTTATTTGTTTAATTGATGAGGAAATAAGAATT-TTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAAATG
* * ***
5663061 ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTGCTTGTTTAAATG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAAATG
5663125 ATTTGTAAAAGTTGATTTGTT
1 ATTTGTAAAAGTTGATTTGTT
5663146 GTTTTAAATT
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
63 38 0.49
64 39 0.51
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (64 bp):
ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAAATG
Found at i:5663293 original size:29 final size:29
Alignment explanation
Indices: 5663212--5663287 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
5663202 CTTTCGCAAC
5663212 GCGAAAGTCAAATTCGCATTGCGATGGTT
1 GCGAAAGTCAAATTCGCATTGCGATGGTT
* *
5663241 GTGAAAGTCAAATTCGCGTTGCGATGGTT
1 GCGAAAGTCAAATTCGCATTGCGATGGTT
*
5663270 GCGAAAGTTAAATTCGCA
1 GCGAAAGTCAAATTCGCA
5663288 ACGCGAAAGT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (29 bp):
GCGAAAGTCAAATTCGCATTGCGATGGTT
Found at i:5663344 original size:29 final size:29
Alignment explanation
Indices: 5663311--5663367 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
5663301 CTTCACGTTT
5663311 CGAATTTGACTTTCGCAACAATCGCAACG
1 CGAATTTGACTTTCGCAACAATCGCAACG
5663340 CGAATTTGACTTTCGCAACAATCGCAAC
1 CGAATTTGACTTTCGCAACAATCGCAAC
5663368 AAAAAATCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.25
Consensus pattern (29 bp):
CGAATTTGACTTTCGCAACAATCGCAACG
Found at i:5663561 original size:18 final size:18
Alignment explanation
Indices: 5663538--5663573 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5663528 AAGCCGGTTG
*
5663538 TGATTGTGATTTTGATTT
1 TGATTGCGATTTTGATTT
5663556 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
5663574 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.22, T:0.58
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:5665799 original size:24 final size:24
Alignment explanation
Indices: 5665772--5665818 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
5665762 CAAAATCCAA
5665772 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
5665796 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
5665819 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:5665827 original size:24 final size:24
Alignment explanation
Indices: 5665776--5665827 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
5665766 ATCCAAGTAT
** *
5665776 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
5665800 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
5665824 TGAC
1 TGAC
5665828 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:5666576 original size:16 final size:15
Alignment explanation
Indices: 5666554--5666592 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
5666544 GAAATCATTG
5666554 AAAAATTATATAAAA
1 AAAAATTATATAAAA
*
5666569 ATAAAATTATGTAAAA
1 A-AAAATTATATAAAA
5666585 AAAAATTA
1 AAAAATTA
5666593 GAGATGGGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:5666773 original size:20 final size:20
Alignment explanation
Indices: 5666748--5666855 Score: 78
Period size: 20 Copynumber: 5.3 Consensus size: 20
5666738 AACTAAAACC
5666748 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
*
5666768 TGTTGCG-AATTCAAAAATCG
1 TGTTGCGAAATT-AAAATTCG
* * *
5666788 AGTTGCTACAA-CAAAATTCG
1 TGTTGCGA-AATTAAAATTCG
* *
5666808 CGTTGCG-AATTCAAAAATCG
1 TGTTGCGAAATT-AAAATTCG
* * *
5666828 AGTTGCGAATTTGAAATTCAG
1 TGTTGCGAAATTAAAATTC-G
5666849 TGTTGCG
1 TGTTGCG
5666856 GATTTGGAAA
Statistics
Matches: 67, Mismatches: 14, Indels: 13
0.71 0.15 0.14
Matches are distributed among these distances:
18 2 0.03
19 4 0.06
20 49 0.73
21 10 0.15
22 2 0.03
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:5666845 original size:40 final size:39
Alignment explanation
Indices: 5666749--5666855 Score: 133
Period size: 40 Copynumber: 2.6 Consensus size: 39
5666739 ACTAAAACCT
5666749 GTTGCGAAATTAAAATTCGTGTTGCGAATTCAAAAATCGA
1 GTTGCG-AATTAAAATTCGTGTTGCGAATTCAAAAATCGA
* ** *
5666789 GTTGCTACAACAAAATTCGCGTTGCGAATTCAAAAATCGA
1 GTTGCGA-ATTAAAATTCGTGTTGCGAATTCAAAAATCGA
*
5666829 GTTGCGAATTTGAAATTCAGTGTTGCG
1 GTTGCGAA-TTAAAATTC-GTGTTGCG
5666856 GATTTGGAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
39 2 0.04
40 46 0.84
41 7 0.13
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (39 bp):
GTTGCGAATTAAAATTCGTGTTGCGAATTCAAAAATCGA
Found at i:5666916 original size:20 final size:20
Alignment explanation
Indices: 5666868--5666909 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
5666858 TTTGGAAATT
*
5666868 GCAACGCGATTTACAGATTC
1 GCAATGCGATTTACAGATTC
*
5666888 GCAATGCGATTTACATATTC
1 GCAATGCGATTTACAGATTC
5666908 GC
1 GC
5666910 GTTGCGAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (20 bp):
GCAATGCGATTTACAGATTC
Found at i:5668824 original size:20 final size:20
Alignment explanation
Indices: 5668801--5668850 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
5668791 TTTGGTATTT
5668801 TTATTTAATTTTTTAAATAA
1 TTATTTAATTTTTTAAATAA
5668821 TTATTTAATTTTTTAAATAA
1 TTATTTAATTTTTTAAATAA
5668841 TTATTTAATT
1 TTATTTAATT
5668851 ATGACGTCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTAATTTTTTAAATAA
Found at i:5671465 original size:182 final size:182
Alignment explanation
Indices: 5671099--5671738 Score: 842
Period size: 182 Copynumber: 3.6 Consensus size: 182
5671089 ATCGATACAA
* * * *
5671099 AAAAATGTATCGATCTATAACAGTATAACAGGTAAAAATATGATC-AAACCGGTTTC-ATTATGA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGA-CAAAACCGGTCTCGA-AATGA
* * * * * * * *
5671162 CAAAACCGGTAAAGCACTACCTTATATATTTAAAGTATCGATTCCATTGAAATAAGTATCAAAAC
64 CAAAACCGGTAAAGCGCTACCTAATATGTTGAAAGTATCGAATACATTGAAATAAGTATCGACAC
5671227 TTATGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
129 TTATGGAATTTAAAAGAGAAGCAGTAATAG-GCCTATAAAGTGTCGATACTTTAT
* *
5671282 AAAAATGTATCGATCCATAATAATATAACAGGTAAAAATATGACAAAACCGGTCTTGAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
* * *
5671347 AAACCGGTAAAGCGTTACCTAATATGTTGAAAGTGTC-AATAC-TTTAATATAAGTATCGACACT
66 AAACCGGTAAAGCGCTACCTAATATGTTGAAAGTATCGAATACATTGAA-ATAAGTATCGACACT
*
5671410 TTTGGAATTTAAAAGAGAAGCAGTAATAGTGCCTATAAAGTGTCGATACTTTAT
130 TATGGAATTTAAAAGAGAAGCAGTAATAG-GCCTATAAAGTGTCGATACTTTAT
*
5671464 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCGGTCTCGAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
* * *
5671529 AAACCGGTAAAGCGCTACCTAATATGTTTAAAGTATCGATTCCATTGAAATAAGTATCGACAC-T
66 AAACCGGTAAAGCGCTACCTAATATGTTGAAAGTATCGAATACATTGAAATAAGTATCGACACTT
* * *
5671593 ATGGAATTTAAAAGATAAACAGTAATA-G-C--------GTCAATACTTTAT
131 ATGGAATTTAAAAGAGAAGCAGTAATAGGCCTATAAAGTGTCGATACTTTAT
* * *
5671635 AAAAATGTATCGATCCATAACAATACAACATGTAAAAATATGACAAAACTGGTCTCGAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
* ** *
5671700 AAACCGGTAAAACGCTACCGGATATGTTGAAAGTGTCGA
66 AAACCGGTAAAGCGCTACCTAATATGTTGAAAGTATCGA
5671739 TACTTCAATA
Statistics
Matches: 411, Mismatches: 41, Indels: 22
0.87 0.09 0.05
Matches are distributed among these distances:
171 107 0.26
179 1 0.00
180 1 0.00
181 4 0.01
182 190 0.46
183 103 0.25
184 5 0.01
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
AAACCGGTAAAGCGCTACCTAATATGTTGAAAGTATCGAATACATTGAAATAAGTATCGACACTT
ATGGAATTTAAAAGAGAAGCAGTAATAGGCCTATAAAGTGTCGATACTTTAT
Found at i:5674489 original size:13 final size:13
Alignment explanation
Indices: 5674448--5674490 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
5674438 TCGATTTTAC
5674448 TGACCCGACC-AGT
1 TGACCCGACCTA-T
5674461 TGACCCGACCCT-T
1 TGACCCGA-CCTAT
5674474 TGACCCGACCTAT
1 TGACCCGACCTAT
5674487 TGAC
1 TGAC
5674491 AGTTAACCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 3 0.11
13 22 0.81
14 2 0.07
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.21
Consensus pattern (13 bp):
TGACCCGACCTAT
Found at i:5674773 original size:135 final size:135
Alignment explanation
Indices: 5674511--5674759 Score: 313
Period size: 135 Copynumber: 1.8 Consensus size: 135
5674501 TTGTTGACCG
* * * *
5674511 TTGACTTTGACCAAAAAGTTAAATTTTTTGAAAAGTCATATTTTATGTTTTTCAACGTTCTGAGT
1 TTGACTTTGACCAAAAAGTCAAAATTTTTGAAAAGTCATATTTTATGTTTTTCAACATACTGAGT
** * * *
5674576 CCGAATCCGAAGTTTGGTTTTCGAAATTCGAACCCGAAAGCCTCGAAATCATCAGTCAAACCCGT
66 CCGAATCCGAAGTTCCGTTTTCCAAATTCAAACCCGAAAGCCTCCAAATCATCAGTCAAACCCGT
5674641 TGACT
131 TGACT
*
5674646 TTGACTTTGACCAAAAAGTCAAAATTTTTGAAAA-TACATGTTTTATGTTTTTCAACATACTGAG
1 TTGACTTTGACCAAAAAGTCAAAATTTTTGAAAAGT-CATATTTTATGTTTTTCAACATACTGAG
* ** ** * *
5674710 TTCGCTTTTGTAG-TCCGTTTTGCCAAATTCAAAGCCGAAAGCCTCCAAAT
65 TCCGAATCCGAAGTTCCGTTTT-CCAAATTCAAACCCGAAAGCCTCCAAAT
5674760 TGTCTATTAA
Statistics
Matches: 95, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
134 7 0.07
135 88 0.93
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (135 bp):
TTGACTTTGACCAAAAAGTCAAAATTTTTGAAAAGTCATATTTTATGTTTTTCAACATACTGAGT
CCGAATCCGAAGTTCCGTTTTCCAAATTCAAACCCGAAAGCCTCCAAATCATCAGTCAAACCCGT
TGACT
Found at i:5682475 original size:200 final size:202
Alignment explanation
Indices: 5681845--5682506 Score: 1073
Period size: 201 Copynumber: 3.3 Consensus size: 202
5681835 ACAATCATTA
*
5681845 TTAATTAGAAAACAGGTCAACATAATGTATCGACACTTTTTAAATTTGTGTCGATACGTGTTGTC
1 TTAATTAGAAAACAGGTCAACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTGTTGTC
* *
5681910 CATAAATGAATGCCCAAACGAGGTGTACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATC
66 CAGAAATGAATGCCCAAACGAGGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATC
* * * *
5681975 CCAAAAACATTGAAACCCATAATTATAGTGTAATAGGCAATTTTGCAATGTAACTGGTATAAATA
131 CCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGCAATGTAACAGGTATAAATA
5682040 TACC-AGT
196 TACCGA-T
* *
5682047 TTAATTAGAAAACAGGTCAACATAATGTATCGACACTTTTTATATTTGTGTTGATACTTGTTGTC
1 TTAATTAGAAAACAGGTCAACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTGTTGTC
*
5682112 TAG-AATGAATGCCCAAACGAGGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATC
66 CAGAAATGAATGCCCAAACGAGGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATC
*
5682176 CCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGCAATGTAACCGGTATAAATA
131 CCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGCAATGTAACAGGTATAAATA
*
5682241 TACATG-T
196 TAC-CGAT
*
5682248 TTAATTAGAAAACAGGTCAACATAATGTATCGACACTTTTTATATTTGTGTCGATACTTGTTGTC
1 TTAATTAGAAAACAGGTCAACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTGTTGTC
* * * * **
5682313 CAGAAATGAATG-ACAAACTAGTTGCACGCATGAAGTGTCGATACATTTA-AAATTGTATCGATC
66 CAGAAATGAATGCCCAAACGAGGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATC
*
5682376 CCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAATTTTGCAATGTAACAGGTATAAATA
131 CCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGCAATGTAACAGGTATAAATA
5682441 TACCGAT
196 TACCGAT
* *
5682448 TTAATTAGAAAACAGATCAATATAATGTATCGACACTTTTTAAATTTGTGTCGATACTT
1 TTAATTAGAAAACAGGTCAACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTT
5682507 TTTTTAAATT
Statistics
Matches: 431, Mismatches: 25, Indels: 10
0.92 0.05 0.02
Matches are distributed among these distances:
199 1 0.00
200 135 0.31
201 224 0.52
202 71 0.16
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (202 bp):
TTAATTAGAAAACAGGTCAACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTGTTGTC
CAGAAATGAATGCCCAAACGAGGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATC
CCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGCAATGTAACAGGTATAAATA
TACCGAT
Found at i:5683168 original size:2 final size:2
Alignment explanation
Indices: 5683161--5683208 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
5683151 ATGGGGAAGA
5683161 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
5683203 AT AT AT
1 AT AT AT
5683209 CTCCGGATAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5684042 original size:3 final size:3
Alignment explanation
Indices: 5684029--5684090 Score: 97
Period size: 3 Copynumber: 20.7 Consensus size: 3
5684019 CAAGCGCTCA
* * *
5684029 ATG AAG ATG ATG ATG AAG ATG ATG ATG ATG ATG AAG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
5684077 ATG ATG ATG ATG AT
1 ATG ATG ATG ATG AT
5684091 CCAAACAAGT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (3 bp):
ATG
Found at i:5686166 original size:200 final size:199
Alignment explanation
Indices: 5685782--5686467 Score: 885
Period size: 200 Copynumber: 3.4 Consensus size: 199
5685772 ATACATTTTC
* * * *
5685782 TAAAAGTATCGACCCCAAAAACATCGAAACCAATAATTATATTGTAATAGGTAAATTAACAATGT
1 TAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGT
* * * **
5685847 AACCGGTATAAATATACCGG-TTAATTAGAAAACAAATCAACATAATGTATCGACACTTGTGGAA
66 AACCGGTATAAATATACCGGTTTTATGAGAAAACAAATCAACATAATGTATCGACACTTTTTAAA
* * * * *
5685911 TTTGTGTTGATACTTATTGTCCAGAATAAATGCTCAAATGAGGTGTACACATAAAGTGACGATAA
131 TTTGTGTCGATACTT-TTGTCCAGAATGAATG-TCAAATGAGGTGCACGCATAAAGTGTCGATAA
5685976 ATTTAT
194 ATTTAT
* * *
5685982 TAAAAGTATCGATCCCAAAAATATCGAAACCGATAATTATAATGTAATAGGTAAATTTATAATTT
1 TAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGT
* * * **
5686047 AACCAGTATAAATATACCGGTTTTATGAGAGAATAGGTCAACATAATGTATCGACACTTTTTAAA
66 AACCGGTATAAATATACCGGTTTTATGAGAAAACAAATCAACATAATGTATCGACACTTTTTAAA
*
5686112 TTTGTGTCGATACATTTTGTCCAGAATGAATGTCAAACGAGGTGCACGCATAAAGTGTCGATACA
131 TTTGTGTCGATAC-TTTTGTCCAGAATGAATGTCAAATGAGGTGCACGCATAAAGTGTCGATA-A
5686177 A-TTAT
194 ATTTAT
* * *
5686182 TAAAAGTATAGATCCCAAAAACATCGGAACCGATAATTACAATGTAATAGGTAAATTTACAATGT
1 TAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGT
* * * * * *
5686247 ACCCGGTAGAAATATACCGTTTTTATGAGAAAACATATCTACATAATGTATCGACACTTTTTAAG
66 AACCGGTATAAATATACCGGTTTTATGAGAAAACAAATCAACATAATGTATCGACACTTTTTAAA
* * * * *
5686312 TTTGTGTCGATACTTTTTTCTAGAATGAATGCCCAATGAGGTGCACGCATAAAGTGTCGATACAT
131 TTTGTGTCGATACTTTTGTCCAGAATGAATGTCAAATGAGGTGCACGCATAAAGTGTCGATAAAT
5686377 TTA-
196 TTAT
* * * * * **
5686380 -AAATTGTATCAATCCTAAAAACATCAAAATCGATAATTATAATGTAATAGGTAAATTTGTAATG
1 TAAA-AGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATG
* *
5686444 TTACCCGTATAAATATACCGGTTT
65 TAACCGGTATAAATATACCGGTTT
5686468 AGTTAGAAAA
Statistics
Matches: 421, Mismatches: 60, Indels: 12
0.85 0.12 0.02
Matches are distributed among these distances:
197 3 0.01
198 70 0.17
199 47 0.11
200 235 0.56
201 64 0.15
202 2 0.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (199 bp):
TAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGT
AACCGGTATAAATATACCGGTTTTATGAGAAAACAAATCAACATAATGTATCGACACTTTTTAAA
TTTGTGTCGATACTTTTGTCCAGAATGAATGTCAAATGAGGTGCACGCATAAAGTGTCGATAAAT
TTAT
Found at i:5687979 original size:20 final size:21
Alignment explanation
Indices: 5687956--5688024 Score: 52
Period size: 20 Copynumber: 3.2 Consensus size: 21
5687946 TATCTAGAGT
5687956 TAATTAAATATATGTTTTAA-
1 TAATTAAATATATGTTTTAAC
* * *
5687976 TAATCTCGAATATTTAATTTTAAC
1 TAAT-T-AAATATAT-GTTTTAAC
* *
5688000 TAATTAAATATA-GATTTAAT
1 TAATTAAATATATGTTTTAAC
5688020 TAATT
1 TAATT
5688025 TGAAATAATA
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
20 14 0.38
21 1 0.03
22 11 0.30
23 7 0.19
24 4 0.11
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (21 bp):
TAATTAAATATATGTTTTAAC
Found at i:5688107 original size:90 final size:89
Alignment explanation
Indices: 5687986--5688158 Score: 301
Period size: 90 Copynumber: 1.9 Consensus size: 89
5687976 TAATCTCGAA
*
5687986 TATTTAATTTTAACTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTTTAACTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAT-CCTAATATGAT
5688051 TAGGGTAACTTGGATATAAGAGGAT
65 TAGGGTAACTTGGATATAAGAGGAT
* *
5688076 TATTAAATTTTAATTAATTAAATATATATTTAATTAATTTGAAATAATAAAATCCTAATATGATT
1 TATTAAATTTTAACTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCTAATATGATT
*
5688141 AGGGTAACTTGGCTATAA
66 AGGGTAACTTGGATATAA
5688159 AAGGGTGTGT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 29 0.37
90 50 0.63
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.40
Consensus pattern (89 bp):
TATTAAATTTTAACTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCTAATATGATT
AGGGTAACTTGGATATAAGAGGAT
Found at i:5689429 original size:2 final size:2
Alignment explanation
Indices: 5689422--5689478 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
5689412 TTTGGTGCGT
5689422 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
5689464 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
5689479 GAGAACCCAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5689924 original size:12 final size:11
Alignment explanation
Indices: 5689887--5689925 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
5689877 TCTGTCTCTC
5689887 TGTTTTTTTTT
1 TGTTTTTTTTT
*
5689898 TCTTTTTTTTCT
1 TGTTTTTTTT-T
5689910 TGTTTTCTTTTT
1 TGTTTT-TTTTT
5689922 TGTT
1 TGTT
5689926 CTCTCCCCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 9 0.38
12 11 0.46
13 4 0.17
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (11 bp):
TGTTTTTTTTT
Found at i:5690373 original size:20 final size:20
Alignment explanation
Indices: 5690348--5690394 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
5690338 GGGTCTGATC
*
5690348 TTGGGTCGGGTTT-ATTATAA
1 TTGGGTCGAGTTTGA-TATAA
5690368 TTGGGTCGAGTTTGATATAA
1 TTGGGTCGAGTTTGATATAA
*
5690388 TCGGGTC
1 TTGGGTC
5690395 AACTTCTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.19, C:0.09, G:0.32, T:0.40
Consensus pattern (20 bp):
TTGGGTCGAGTTTGATATAA
Found at i:5690467 original size:3 final size:3
Alignment explanation
Indices: 5690459--5690487 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
5690449 GTAAAATTAA
5690459 AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5690488 TAAATAAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:5690476 original size:14 final size:14
Alignment explanation
Indices: 5690459--5690485 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5690449 GTAAAATTAA
5690459 AATAATAATAATAT
1 AATAATAATAATAT
5690473 AATAATAATAATA
1 AATAATAATAATA
5690486 ATTAAATAAG
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAATAATAATAT
Found at i:5690494 original size:14 final size:15
Alignment explanation
Indices: 5690453--5690491 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 15
5690443 AAAAATGTAA
5690453 AATTAAAATAATAAT
1 AATTAAAATAATAAT
5690468 AATATAATAATAATAAT
1 AAT-TAA-AATAATAAT
5690485 AATTAAA
1 AATTAAA
5690492 TAAGACCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.18
16 6 0.27
17 12 0.55
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AATTAAAATAATAAT
Found at i:5691417 original size:22 final size:24
Alignment explanation
Indices: 5691382--5691427 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
5691372 CTAACTTTTA
5691382 TTTTATTGTATATTA-ACTACTAAC
1 TTTTATTGTATATTACACT-CTAAC
5691406 TTTTATT-T-TATTACACTCTAAC
1 TTTTATTGTATATTACACTCTAAC
5691428 CATTGTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 10 0.48
23 4 0.19
24 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTTATTGTATATTACACTCTAAC
Found at i:5691661 original size:15 final size:15
Alignment explanation
Indices: 5691641--5691686 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
5691631 GCGCTAACTT
5691641 TTCTAACAACTAACA
1 TTCTAACAACTAACA
*
5691656 TTCTAACAGCT-A-A
1 TTCTAACAACTAACA
*
5691669 TTACTAACTACTAACA
1 TT-CTAACAACTAACA
5691685 TT
1 TT
5691687 TTTATTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
13 3 0.12
14 8 0.32
15 11 0.44
16 3 0.12
ACGTcount: A:0.41, C:0.24, G:0.02, T:0.33
Consensus pattern (15 bp):
TTCTAACAACTAACA
Found at i:5695830 original size:18 final size:18
Alignment explanation
Indices: 5695809--5695934 Score: 68
Period size: 18 Copynumber: 7.0 Consensus size: 18
5695799 TAGAGTAAAG
5695809 AGAAAAAAACAAAGAAGA
1 AGAAAAAAACAAAGAAGA
* *
5695827 AGAAAAGAGCAAAGAAGA
1 AGAAAAAAACAAAGAAGA
* * *
5695845 AGAAAAGAGCACAGAA-A
1 AGAAAAAAACAAAGAAGA
5695862 A-AAACAAAGAGCAAAG-AGCA
1 AGAAA-AAA-A-CAAAGAAG-A
* *
5695882 AAAAAAGAAAGAAA-AAGA
1 AGAAAA-AAACAAAGAAGA
*
5695900 AGAAGAAAAAGAAA-AAGA
1 AGAA-AAAAACAAAGAAGA
5695918 A-AAAAAGAA-AAAGAAGA
1 AGAAAAA-AACAAAGAAGA
5695935 CAAGAAGCAC
Statistics
Matches: 89, Mismatches: 8, Indels: 23
0.74 0.07 0.19
Matches are distributed among these distances:
16 9 0.10
17 12 0.13
18 48 0.54
19 11 0.12
20 4 0.04
21 5 0.06
ACGTcount: A:0.74, C:0.06, G:0.21, T:0.00
Consensus pattern (18 bp):
AGAAAAAAACAAAGAAGA
Found at i:5695832 original size:15 final size:16
Alignment explanation
Indices: 5695782--5695851 Score: 56
Period size: 17 Copynumber: 4.3 Consensus size: 16
5695772 AAATAAATAA
*
5695782 AAAAGCAAAGAA-AAA
1 AAAAGCAAAGAAGAAG
*
5695797 AATAGAGTAAAG-AGAA-
1 AA-A-AGCAAAGAAGAAG
*
5695813 AAAAACAAAGAAGAAG
1 AAAAGCAAAGAAGAAG
5695829 AAAAGAGCAAAGAAGAAG
1 -AAA-AGCAAAGAAGAAG
5695847 AAAAG
1 AAAAG
5695852 AGCACAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
14 5 0.11
15 7 0.16
16 6 0.14
17 14 0.32
18 12 0.27
ACGTcount: A:0.71, C:0.04, G:0.21, T:0.03
Consensus pattern (16 bp):
AAAAGCAAAGAAGAAG
Found at i:5695872 original size:19 final size:18
Alignment explanation
Indices: 5695780--5695889 Score: 79
Period size: 18 Copynumber: 6.4 Consensus size: 18
5695770 GCAAATAAAT
5695780 AAAAA-AGCAAAG-AAAA
1 AAAAAGAGCAAAGAAAAA
* * *
5695796 AAATAGAGTAAAG--AGA
1 AAAAAGAGCAAAGAAAAA
*
5695812 AAAAA-A-CAAAGAAGAA
1 AAAAAGAGCAAAGAAAAA
* *
5695828 GAAAAGAGCAAAGAAGAA
1 AAAAAGAGCAAAGAAAAA
* *
5695846 GAAAAGAGCACAGAAAAA
1 AAAAAGAGCAAAGAAAAA
**
5695864 AACAAAGAGCAAAGAGCAA
1 AA-AAAGAGCAAAGAAAAA
5695883 AAAAAGA
1 AAAAAGA
5695890 AAGAAAAAGA
Statistics
Matches: 74, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
14 4 0.05
15 1 0.01
16 15 0.20
17 7 0.09
18 32 0.43
19 15 0.20
ACGTcount: A:0.71, C:0.07, G:0.20, T:0.02
Consensus pattern (18 bp):
AAAAAGAGCAAAGAAAAA
Found at i:5695893 original size:70 final size:68
Alignment explanation
Indices: 5695792--5695920 Score: 170
Period size: 70 Copynumber: 1.9 Consensus size: 68
5695782 AAAAGCAAAG
* * * * *
5695792 AAAAAAATAGAGTAAAGAGAAAAAAACAAAGAAGAAGAA-AAGAGCAAAGAAGAAGAAAAGAGCA
1 AAAAAAAAAGAGCAAAGAGAAAAAAACAAAGAAAAAGAAGAAGA-AAAAGAAAAAGAAAAGAGCA
5695856 CAGA
65 CAGA
*
5695860 AAAAAACAAAGAGCAAAGAGCAAAAAAAGAAAGAAAAAGAAGAAGAAAAAGAAAAAGAAAA
1 AAAAAA-AAAGAGCAAAGAG-AAAAAAACAAAGAAAAAGAAGAAGAAAAAGAAAAAGAAAA
5695921 AAAGAAAAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
68 6 0.12
69 11 0.21
70 31 0.60
71 4 0.08
ACGTcount: A:0.73, C:0.05, G:0.20, T:0.02
Consensus pattern (68 bp):
AAAAAAAAAGAGCAAAGAGAAAAAAACAAAGAAAAAGAAGAAGAAAAAGAAAAAGAAAAGAGCAC
AGA
Found at i:5695900 original size:6 final size:6
Alignment explanation
Indices: 5695889--5695932 Score: 61
Period size: 6 Copynumber: 7.0 Consensus size: 6
5695879 GCAAAAAAAG
*
5695889 AAAGAA AAAGAA GAAGAA AAAGAA AAAGAAAA AAAGAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG--AA AAAGAA AAAGAA
5695933 GACAAGAAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 28 0.82
8 6 0.18
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:5695905 original size:12 final size:11
Alignment explanation
Indices: 5695881--5695926 Score: 56
Period size: 12 Copynumber: 3.9 Consensus size: 11
5695871 AGCAAAGAGC
5695881 AAAAAAAGAAAG
1 AAAAAAAG-AAG
5695893 AAAAAGAAGAAG
1 AAAAA-AAGAAG
*
5695905 AAAAAGAAAAAG
1 AAAAA-AAGAAG
5695917 AAAAAAAGAA
1 AAAAAAAGAA
5695927 AAAGAAGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
11 4 0.13
12 24 0.77
13 3 0.10
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAG
Found at i:5699044 original size:27 final size:27
Alignment explanation
Indices: 5699014--5699066 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 27
5699004 TCTCTCTTGA
5699014 GAAA-GTTTCA-TTCGAAACACAAATTTT
1 GAAATGTTTCACTT-GAAACA-AAATTTT
5699041 GAAATTGTTTCACTTGAAACAAAATT
1 GAAA-TGTTTCACTTGAAACAAAATT
5699067 GCTGACATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
27 4 0.17
28 5 0.22
29 12 0.52
30 2 0.09
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (27 bp):
GAAATGTTTCACTTGAAACAAAATTTT
Found at i:5699214 original size:36 final size:36
Alignment explanation
Indices: 5699129--5699255 Score: 114
Period size: 36 Copynumber: 3.5 Consensus size: 36
5699119 TTTGAAATTG
* * ***
5699129 TTTCACTTGAAAC-AAAATTGATATCACTTGAGATTG
1 TTTCTCTTGAAACAAAAATTG-TCTCACTTGAGAAAA
* *
5699165 TTT-TCTCTAAAACAAAAATTGTCTCACTTGAGACAA
1 TTTCTCT-TGAAACAAAAATTGTCTCACTTGAGAAAA
** * * *
5699201 TTTCTCTTGAAACAAATTTTATCTCGCATGAGAAAA
1 TTTCTCTTGAAACAAAAATTGTCTCACTTGAGAAAA
5699237 TTTCTCTTGAAACAAAAAT
1 TTTCTCTTGAAACAAAAAT
5699256 CCTTGAGATT
Statistics
Matches: 73, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
35 2 0.03
36 61 0.84
37 10 0.14
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (36 bp):
TTTCTCTTGAAACAAAAATTGTCTCACTTGAGAAAA
Found at i:5699340 original size:160 final size:160
Alignment explanation
Indices: 5699171--5699468 Score: 366
Period size: 160 Copynumber: 1.9 Consensus size: 160
5699161 ATTGTTTTCT
* * *
5699171 CTAAAACAAAAATTG-TCTCACTTGAGACAATTTCTCTTGAAACAAATTTTATCTCGCATGAGAA
1 CTAAAAC-AAAATTGATCTCACTTGAGACAATTTCTCTTGAAACAAATTTCATATCACATGAGAA
* * * * *
5699235 AATTTCTCTTGAAACAAAA-ATCCTTGAGATTGTTTCTCTCGAAACAAATTTCGTCTCGCTTGAG
65 AATTTCTCTTGAAACAAAAGCT-CTTGAGATTATTTCCCTCAAAACAAATTTCGGCTCGCTTGAG
*
5699299 ACAGTTTTCCACAAATTTTGAAATTTTTGCAC
129 AAAGTTTTCCACAAATTTTGAAATTTTTGCAC
*** * * ** *
5699331 CTAAAACAAAATTGATCTCACTTGAGATTGTTTTTCTTGAAACAAATTTCGTATCATTTGAGACA
1 CTAAAACAAAATTGATCTCACTTGAGACAATTTCTCTTGAAACAAATTTCATATCACATGAGAAA
* * * * *
5699396 TTTTCTTTTGAAACATAAGCTTTTGAGATTATTTCCCTCAAAACAAATTTTGGCTCGCTTGAGAA
66 ATTTCTCTTGAAACAAAAGCTCTTGAGATTATTTCCCTCAAAACAAATTTCGGCTCGCTTGAGAA
5699461 AGTTTTCC
131 AGTTTTCC
5699469 CTTGAGATGC
Statistics
Matches: 114, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
159 7 0.06
160 106 0.93
161 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (160 bp):
CTAAAACAAAATTGATCTCACTTGAGACAATTTCTCTTGAAACAAATTTCATATCACATGAGAAA
ATTTCTCTTGAAACAAAAGCTCTTGAGATTATTTCCCTCAAAACAAATTTCGGCTCGCTTGAGAA
AGTTTTCCACAAATTTTGAAATTTTTGCAC
Found at i:5699544 original size:168 final size:167
Alignment explanation
Indices: 5699310--5699671 Score: 432
Period size: 168 Copynumber: 2.1 Consensus size: 167
5699300 CAGTTTTCCA
* * *
5699310 CAAATTTTGAAATTT-TTGCACCTAAAACAAAATTGATCTCACTTGAGATTGTTTTTCTTGAAAC
1 CAAATTTTG-AATTTGTTTCACTTGAAACAAAATTGATCTCACTTGAGATTGTTTTTCTTGAAAC
* * * **
5699374 AAATTTCGTATCATTTGAGACA-TTTTCTTTTGAA-A-CATAAGCTTTTGAGATTATTTCCCTCA
65 AAATTTCGTATCATTTGAGACAGTCTTC-CTT-AATAGC-GAA-CACTTGAGATTATTTCCCTCA
* *
5699436 AAACAAATTTTGGCTCGCTTGAGA-AAGTTTTCCCTT-GAGATG
126 AAACAAATTTCGGCTCGCTTGAGATAA-TTTTCCCTTGGA-ACG
5699478 CAAATTTTGAATTTGTTTCACTTGAAACAAAATTGATCTCACTTGAGATTGTTTTTCTCT-AAAC
1 CAAATTTTGAATTTGTTTCACTTGAAACAAAATTGATCTCACTTGAGATTGTTTTTCT-TGAAAC
* * * *
5699542 AAATTTTGTCTCATTTGAGACAGTCTTCCTTAATATGCGAACACTTGAGATTGTTTCTCTCAAAA
65 AAATTTCGTATCATTTGAGACAGTCTTCCTTAATA-GCGAACACTTGAGATTATTTCCCTCAAAA
*
5699607 CAAATTTCGTCTCGCTTGAGATAATTTTCCCTTGGAACG
129 CAAATTTCGGCTCGCTTGAGATAATTTTCCCTTGGAACG
* *
5699646 TAAATTTTGAAATTGTTCTCACTTGA
1 CAAATTTTGAATTTGTT-TCACTTGA
5699672 GATTGTTTTT
Statistics
Matches: 168, Mismatches: 17, Indels: 17
0.83 0.08 0.08
Matches are distributed among these distances:
167 7 0.04
168 141 0.84
169 19 0.11
170 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.40
Consensus pattern (167 bp):
CAAATTTTGAATTTGTTTCACTTGAAACAAAATTGATCTCACTTGAGATTGTTTTTCTTGAAACA
AATTTCGTATCATTTGAGACAGTCTTCCTTAATAGCGAACACTTGAGATTATTTCCCTCAAAACA
AATTTCGGCTCGCTTGAGATAATTTTCCCTTGGAACG
Found at i:5699818 original size:84 final size:84
Alignment explanation
Indices: 5699583--5699919 Score: 414
Period size: 84 Copynumber: 4.0 Consensus size: 84
5699573 AATATGCGAA
* * *
5699583 CACTTGAGATTGTTTCTC-T-CAAAACAAATTTCGTCTCGCTTGAGATAATTTTCCCTTGGAACG
1 CACTTGAGATTGTTTTTCTTAAAAAACAAATTTCGTCTCGCTTGAGATAATTTTCCCTTGAAACG
* *
5699646 TAAATTTTGAAATTGTTCT
66 CAAATTTTGAAAATGTTCT
* *
5699665 CACTTGAGATTGTTTTTTCTTAAAAAACTAATTTTGTCTCGCTTGAGATAATTTTCCCTTGAAAC
1 CACTTGAGATTG-TTTTTCTTAAAAAACAAATTTCGTCTCGCTTGAGATAATTTTCCCTTGAAAC
*
5699730 GCAAATTTTGAAAATGTTTT
65 GCAAATTTTGAAAATGTTCT
* * * * * * * *
5699750 CACTTGAGATTGTTTTTCTTAAAAATCAAACTCCGCCTCTCTTGAGATAATTTTCCTTTTAAATG
1 CACTTGAGATTGTTTTTCTTAAAAAACAAATTTCGTCTCGCTTGAGATAATTTTCCCTTGAAACG
*
5699815 CAAATTTTGAAACTGTTCT
66 CAAATTTTGAAAATGTTCT
* * * *
5699834 CACTTGATATTGTTCTTCTTAAAAAACAAAATTT-GTCTCGCTTGAGATAGTTTTCCCTTAAAAC
1 CACTTGAGATTGTTTTTCTTAAAAAAC-AAATTTCGTCTCGCTTGAGATAATTTTCCCTTGAAAC
* *
5699898 GTAAATTCT-AAAATGTT-T
65 GCAAATTTTGAAAATGTTCT
5699916 CACT
1 CACT
5699920 CGAAACAAAA
Statistics
Matches: 217, Mismatches: 34, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
82 17 0.08
83 12 0.06
84 116 0.53
85 72 0.33
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (84 bp):
CACTTGAGATTGTTTTTCTTAAAAAACAAATTTCGTCTCGCTTGAGATAATTTTCCCTTGAAACG
CAAATTTTGAAAATGTTCT
Found at i:5700540 original size:140 final size:140
Alignment explanation
Indices: 5700093--5700595 Score: 645
Period size: 139 Copynumber: 3.6 Consensus size: 140
5700083 AACTGATCAT
* * * *
5700093 ATCTCCTCAACGCGAAGGAGCAGTGTCACCCTCAGATAACCAGACTTCATCATCACGTAGGAACT
1 ATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAACCAGACTTCCTCATCACGTAGGAACC
* * *
5700158 GTGTTCTCTCCAAATTATCCC-TAAAGACGGCTAGACATCCTCATCAAGTAGGAACAATGTCGTC
66 GTGTTGTCTCCAAATTATCCCATAAAGACGGCTAGACGTCCTCATCAAGTAGGAACAATGTCATC
5700222 CACCGACCAG
131 CACCGACCAG
* ** *
5700232 ATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGACAATTAGACTTCCTCATCACGTAGGAATC
1 ATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAACCAGACTTCCTCATCACGTAGGAACC
* * * *
5700297 GTGTTGTCTCCAAATTAT-CTATAAAGACGGCTAGACGTTCTCATCACGTAGGAGA-AATGTCCT
66 GTGTTGTCTCCAAATTATCCCATAAAGACGGCTAGACGTCCTCATCAAGTAGGA-ACAATGTCAT
5700360 CCACCGACCAG
130 CCACCGACCAG
** * * * *
5700371 ATCTCCTCAACGCTTAGGAGTAGCT-TCATCCTCAGATAACCAGGCTTCCTCGTCACGTAGGAAC
1 ATCTCCTCAACGCGAAGGAGCAG-TGTCATCCTCAGACAACCAGACTTCCTCATCACGTAGGAAC
* * * * *
5700435 CGTGTTGTCTCCAAATTATCCCAAAAAAATGGCTAAACGTCCTCATCATGTAGGAACAATGTCAT
65 CGTGTTGTCTCCAAATTATCCCATAAAGACGGCTAGACGTCCTCATCAAGTAGGAACAATGTCAT
*
5700500 CCACCGACCAA
130 CCACCGACCAG
* * * * * *
5700511 ATCTCCTCAACGCGAAGAAGCAGTGTCATCCTTAGACAATCAGACTTCCTCAACGCGTAGGAATC
1 ATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAACCAGACTTCCTCATCACGTAGGAACC
*
5700576 GTATTGTCTCCAAAATTATC
66 GTGTTGTCTCC-AAATTATC
5700596 TCCAGGTTGA
Statistics
Matches: 313, Mismatches: 44, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
138 1 0.00
139 196 0.63
140 108 0.35
141 8 0.03
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.24
Consensus pattern (140 bp):
ATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAACCAGACTTCCTCATCACGTAGGAACC
GTGTTGTCTCCAAATTATCCCATAAAGACGGCTAGACGTCCTCATCAAGTAGGAACAATGTCATC
CACCGACCAG
Found at i:5701955 original size:5 final size:5
Alignment explanation
Indices: 5701945--5701969 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5701935 ACCACTAACT
5701945 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
5701970 ATTAATTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:5702071 original size:16 final size:16
Alignment explanation
Indices: 5702052--5702094 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
5702042 TCAAACTCTG
*
5702052 CTAACCGCTAACTTTT
1 CTAACCGCTAACCTTT
*
5702068 CTAACAGCTAACCTTT
1 CTAACCGCTAACCTTT
5702084 CTAACCGCTAA
1 CTAACCGCTAA
5702095 TTACTAACTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.30, C:0.33, G:0.07, T:0.30
Consensus pattern (16 bp):
CTAACCGCTAACCTTT
Found at i:5706774 original size:20 final size:19
Alignment explanation
Indices: 5706722--5706774 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
5706712 TTTTAGTATT
*
5706722 TTAT-TTTTAATATATTTAT
1 TTATATTTTAA-ATATTTAA
*
5706741 TTATATTTTGAATATTTGAA
1 TTATATTTTAAATATTT-AA
5706761 TTATATTTTAAATA
1 TTATATTTTAAATA
5706775 ACTTTAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 10 0.34
20 19 0.66
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (19 bp):
TTATATTTTAAATATTTAA
Found at i:5709138 original size:26 final size:26
Alignment explanation
Indices: 5709102--5709172 Score: 133
Period size: 26 Copynumber: 2.7 Consensus size: 26
5709092 GAGTATTGCT
5709102 GAGCTCGACTCGAAAACTCTAAAATA
1 GAGCTCGACTCGAAAACTCTAAAATA
*
5709128 GAGCTCGACTCGAAAACTCTGAAATA
1 GAGCTCGACTCGAAAACTCTAAAATA
5709154 GAGCTCGACTCGAAAACTC
1 GAGCTCGACTCGAAAACTC
5709173 GCGAGCTTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (26 bp):
GAGCTCGACTCGAAAACTCTAAAATA
Found at i:5709771 original size:18 final size:18
Alignment explanation
Indices: 5709744--5709788 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
5709734 TTAGTTACCT
*
5709744 AATCAGACCCATATATAA
1 AATCATACCCATATATAA
5709762 AATCATACCCATATATAA
1 AATCATACCCATATATAA
5709780 AATCATACC
1 AATCATACC
5709789 TGAATCTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.49, C:0.24, G:0.02, T:0.24
Consensus pattern (18 bp):
AATCATACCCATATATAA
Found at i:5716040 original size:10 final size:11
Alignment explanation
Indices: 5716005--5716067 Score: 69
Period size: 10 Copynumber: 5.8 Consensus size: 11
5715995 AATAAGAAGA
5716005 AAGAAAAATAG
1 AAGAAAAATAG
5716016 AAGAAAAATAG
1 AAGAAAAATAG
* *
5716027 AA-AAAGAAGAAA
1 AAGAAA-AA-TAG
5716039 AAGAAAAATAG
1 AAGAAAAATAG
5716050 -AGAAAAATAG
1 AAGAAAAATAG
5716060 -AGAAAAAT
1 AAGAAAAAT
5716068 GAAAAATGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
10 21 0.47
11 16 0.36
12 5 0.11
13 3 0.07
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (11 bp):
AAGAAAAATAG
Found at i:5716042 original size:34 final size:34
Alignment explanation
Indices: 5715998--5716093 Score: 124
Period size: 34 Copynumber: 2.8 Consensus size: 34
5715988 TAAAAAGAAT
5715998 AAGAAGAAAGAAAAATAGAAGAAAAATAGA-AAAA
1 AAGAA-AAAGAAAAATAGAAGAAAAATAGAGAAAA
5716032 GAAGAAAAAGAAAAATAG-AGAAAAATAGAGAAAA
1 -AAGAAAAAGAAAAATAGAAGAAAAATAGAGAAAA
* *
5716066 ATGAAAAATGAAAAATGAGAAAAAAAAT
1 AAGAAAAA-GAAAAAT-AGAAGAAAAAT
5716094 TAAGATAAGC
Statistics
Matches: 55, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
33 18 0.33
34 23 0.42
35 7 0.13
36 7 0.13
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (34 bp):
AAGAAAAAGAAAAATAGAAGAAAAATAGAGAAAA
Found at i:5716059 original size:33 final size:33
Alignment explanation
Indices: 5715976--5716089 Score: 130
Period size: 33 Copynumber: 3.5 Consensus size: 33
5715966 AATTCATTAA
*
5715976 AAAATATAGAGATAAAA-AGAATAAGAAG--AAAG
1 AAAA-ATAGAGA-AAAATAGAAAAAGAAGAAAAAG
5716008 AAAAATAGAAGAAAAATAGAAAAAGAAGAAAAAG
1 AAAAATAG-AGAAAAATAGAAAAAGAAGAAAAAG
*
5716042 AAAAATAGAGAAAAATAGAGAAAA-ATGAAAAATG
1 AAAAATAGAGAAAAATAGA-AAAAGAAGAAAAA-G
5716076 AAAAAT-GAGAAAAA
1 AAAAATAGAGAAAAA
5716090 AAATTAAGAT
Statistics
Matches: 74, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
31 8 0.11
32 17 0.23
33 26 0.35
34 23 0.31
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.10
Consensus pattern (33 bp):
AAAAATAGAGAAAAATAGAAAAAGAAGAAAAAG
Found at i:5716080 original size:14 final size:15
Alignment explanation
Indices: 5716020--5716088 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 15
5716010 AAATAGAAGA
5716020 AAAATAGAAAAA-GAAG
1 AAAAT-GAAAAATG-AG
*
5716036 AAAAAGAAAAATAGAG
1 AAAATGAAAAAT-GAG
5716052 AAAAATAGAGAAAAATGA-
1 -AAAAT---GAAAAATGAG
5716070 AAAATGAAAAATGAG
1 AAAATGAAAAATGAG
5716085 AAAA
1 AAAA
5716089 AAAATTAAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
14 9 0.20
15 10 0.23
16 6 0.14
17 10 0.23
19 2 0.05
20 7 0.16
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (15 bp):
AAAATGAAAAATGAG
Found at i:5718044 original size:38 final size:37
Alignment explanation
Indices: 5717980--5718320 Score: 340
Period size: 38 Copynumber: 8.8 Consensus size: 37
5717970 GAAGCTTCAA
* * *
5717980 CTTGACTCCATTGTAAAGATAAGTCAATTTTTGTTATT
1 CTTGACTCC-TCGTGAAGAGAAGTCAATTTTTGTTATT
** *
5718018 CTTGACTCACTCGTGAAGAGGGGTCAATCTTTGTTATT
1 CTTGACTC-CTCGTGAAGAGAAGTCAATTTTTGTTATT
* * *
5718056 CTTGACTTCCTTGTGAAGAGAGGTTAATTTTTGTTATT
1 CTTGAC-TCCTCGTGAAGAGAAGTCAATTTTTGTTATT
*
5718094 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
1 CTTGAC-TCCTCGTGAAGAGAAGTCAATTTTTGTTATT
* * *
5718132 CTTGACTCCCTCATGAAGAGAAGCCAATCTTTGTTATT
1 CTTGACT-CCTCGTGAAGAGAAGTCAATTTTTGTTATT
* * *
5718170 CTTGACTCCCTTGTGAAGAGAGGTCAATTTTTTTTATT
1 CTTGACT-CCTCGTGAAGAGAAGTCAATTTTTGTTATT
* * *
5718208 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTATTTTT
1 CTTGAC-TCCTCGTGAAGAGAAGTCAATTTTTGTTATT
* *
5718246 CTTGACTCCCTCGTGAAGAGGATTCAATCTTTCAATGTTATT
1 CTTGACT-CCTCGTGAAGAGAAGTCAAT-TTT---TGTTATT
* * *
5718288 ATTGACTTTCTCGTGAAGAGGAGTCAATATTTT
1 CTTGAC-TCCTCGTGAAGAGAAGTCAAT-TTTT
5718321 AGTGCTGTCC
Statistics
Matches: 257, Mismatches: 36, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
37 2 0.01
38 216 0.84
39 7 0.03
42 31 0.12
43 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.41
Consensus pattern (37 bp):
CTTGACTCCTCGTGAAGAGAAGTCAATTTTTGTTATT
Found at i:5718095 original size:76 final size:76
Alignment explanation
Indices: 5717995--5718315 Score: 390
Period size: 76 Copynumber: 4.2 Consensus size: 76
5717985 CTCCATTGTA
* * * **
5717995 AAGATAAGTCAATTTTTGTTATTCTTGACTCACTCGTGAAGAGGGGTCAATCTTTGTTATTCTTG
1 AAGAGAAGTCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTG
*
5718060 ACTTCCTTGTG
66 ACTTCCTCGTG
* * * *
5718071 AAGAGAGGTTAATTTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTG
1 AAGAGAAGTCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTG
* *
5718136 ACTCCCTCATG
66 ACTTCCTCGTG
* * * * *
5718147 AAGAGAAGCCAATCTTTGTTATTCTTGACTCCCTTGTGAAGAGAGGTCAATTTTTTTTATTCTTG
1 AAGAGAAGTCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTG
5718212 ACTTCCTCGTG
66 ACTTCCTCGTG
* * * *
5718223 AAGAGAAGTCAATCTTTATTTTTCTTGACTCCCTCGTGAAGAGGATTCAATCTTTCAATGTTATT
1 AAGAGAAGTCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGAAGTCAATC-TT---TGTTATT
* *
5718288 ATTGACTTTCTCGTG
62 CTTGACTTCCTCGTG
*
5718303 AAGAGGAGTCAAT
1 AAGAGAAGTCAAT
5718316 ATTTTAGTGC
Statistics
Matches: 208, Mismatches: 33, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
76 175 0.84
77 2 0.01
80 31 0.15
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (76 bp):
AAGAGAAGTCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTG
ACTTCCTCGTG
Found at i:5718274 original size:114 final size:114
Alignment explanation
Indices: 5717995--5718277 Score: 449
Period size: 114 Copynumber: 2.5 Consensus size: 114
5717985 CTCCATTGTA
* * * *
5717995 AAGATAAGTCAATTTTTGTTATTCTTGACTCACTCGTGAAGAGGGGTCAATCTTTGTTATTCTTG
1 AAGAGAAGTCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCTTTGTTATTCTTG
* *
5718060 ACTTCCTTGTGAAGAGAGGTTAATTTTTGTTATTCTTGACTTCCTCGTG
66 ACTCCCTTGTGAAGAGAGGTCAATTTTTGTTATTCTTGACTTCCTCGTG
* * *
5718109 AAGAGAAGTCAATCTTTGTTATTCTTGACTCCCTCATGAAGAGAAGCCAATCTTTGTTATTCTTG
1 AAGAGAAGTCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCTTTGTTATTCTTG
*
5718174 ACTCCCTTGTGAAGAGAGGTCAATTTTTTTTATTCTTGACTTCCTCGTG
66 ACTCCCTTGTGAAGAGAGGTCAATTTTTGTTATTCTTGACTTCCTCGTG
* * *
5718223 AAGAGAAGTCAATCTTTATTTTTCTTGACTCCCTCGTGAAGAGGATTCAATCTTT
1 AAGAGAAGTCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCTTT
5718278 CAATGTTATT
Statistics
Matches: 153, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 153 1.00
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.41
Consensus pattern (114 bp):
AAGAGAAGTCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCTTTGTTATTCTTG
ACTCCCTTGTGAAGAGAGGTCAATTTTTGTTATTCTTGACTTCCTCGTG
Found at i:5718351 original size:45 final size:45
Alignment explanation
Indices: 5718289--5718621 Score: 391
Period size: 45 Copynumber: 7.4 Consensus size: 45
5718279 AATGTTATTA
* * *
5718289 TTGACTTTCTCGTGAAGAGGAGTCAATATTTTAGTGCTGTCCTTC
1 TTGACTTTCTCGCGAAGAGGAGTCAATCTTTTAGTGTTGTCCTTC
* * *
5718334 TTAACTTTCTCGCGAAGAGGAGTTAATCTTTCAGTGTTGT-CTTCC
1 TTGACTTTCTCGCGAAGAGGAGTCAATCTTTTAGTGTTGTCCTT-C
** * * *
5718379 TTGACTTTCTCATGAAGATGTGTCAATATTTTAGTGTTGTCCTTC
1 TTGACTTTCTCGCGAAGAGGAGTCAATCTTTTAGTGTTGTCCTTC
*
5718424 TTGACTTTCTCGCGAAGAGGAGTCAATCTTTTAGTGTCGTCCTTC
1 TTGACTTTCTCGCGAAGAGGAGTCAATCTTTTAGTGTTGTCCTTC
* * *
5718469 TTGACTTTCTCGCGAAGAAGAGTTAATCTTTTACTGTTGTCCTT-
1 TTGACTTTCTCGCGAAGAGGAGTCAATCTTTTAGTGTTGTCCTTC
* * *
5718513 TATGACTTTCTCGCGAAGAGGAGTCAATCTTTCAGTATTGTCATTC
1 T-TGACTTTCTCGCGAAGAGGAGTCAATCTTTTAGTGTTGTCCTTC
* * * * ** * *
5718559 TTGAATTTTTCACGAAGAGAAGTTGATATTTTAGTGTTGTCCTTT
1 TTGACTTTCTCGCGAAGAGGAGTCAATCTTTTAGTGTTGTCCTTC
*
5718604 TTGACTTTCTCACGAAGA
1 TTGACTTTCTCGCGAAGA
5718622 ATAGTGAACT
Statistics
Matches: 241, Mismatches: 43, Indels: 8
0.83 0.15 0.03
Matches are distributed among these distances:
44 4 0.02
45 233 0.97
46 4 0.02
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (45 bp):
TTGACTTTCTCGCGAAGAGGAGTCAATCTTTTAGTGTTGTCCTTC
Found at i:5718404 original size:90 final size:88
Alignment explanation
Indices: 5718244--5718621 Score: 420
Period size: 90 Copynumber: 4.2 Consensus size: 88
5718234 ATCTTTATTT
** * * * * * **
5718244 TTCTTGACTCCCTCGTGAAGAGGATTCAATCTTTCAATG-T-TATTATTGACTTTCTCGTGAAGA
1 TTCTTGACTTTCTCGCGAAGAGGAGTCAATCTTTCAGTGTTGTCTTCTTGACTTTCTCACGAAGA
*
5718307 GGAGTCAATATTTTAGTGCTGTCC
66 -GAGTCAATATTTTAGTGTTGTCC
* * *
5718331 TTCTTAACTTTCTCGCGAAGAGGAGTTAATCTTTCAGTGTTGTCTTCCTTGACTTTCTCATGAAG
1 TTCTTGACTTTCTCGCGAAGAGGAGTCAATCTTTCAGTGTTGTCTT-CTTGACTTTCTCACGAAG
*
5718396 ATGTGTCAATATTTTAGTGTTGTCC
65 A-GAGTCAATATTTTAGTGTTGTCC
* * *
5718421 TTCTTGACTTTCTCGCGAAGAGGAGTCAATCTTTTAGTGTCGTCCTTCTTGACTTTCTCGCGAAG
1 TTCTTGACTTTCTCGCGAAGAGGAGTCAATCTTTCAGTGTTGT-CTTCTTGACTTTCTCACGAAG
* * *
5718486 AAGAGTTAATCTTTTACTGTTGTCC
65 -AGAGTCAATATTTTAGTGTTGTCC
* * *
5718511 TT-TATGACTTTCTCGCGAAGAGGAGTCAATCTTTCAGTATTGTCATTCTTGAATTTTTCACGAA
1 TTCT-TGACTTTCTCGCGAAGAGGAGTCAATCTTTCAGTGTTGTC-TTCTTGACTTTCTCACGAA
**
5718575 GAGAAGTTGATATTTTAGTGTTGTCC
64 GAG-AGTCAATATTTTAGTGTTGTCC
* *
5718601 TTTTTGACTTTCTCACGAAGA
1 TTCTTGACTTTCTCGCGAAGA
5718622 ATAGTGAACT
Statistics
Matches: 249, Mismatches: 33, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
87 32 0.13
88 1 0.00
89 7 0.03
90 204 0.82
91 5 0.02
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (88 bp):
TTCTTGACTTTCTCGCGAAGAGGAGTCAATCTTTCAGTGTTGTCTTCTTGACTTTCTCACGAAGA
GAGTCAATATTTTAGTGTTGTCC
Found at i:5719430 original size:133 final size:133
Alignment explanation
Indices: 5719283--5720096 Score: 1064
Period size: 133 Copynumber: 6.1 Consensus size: 133
5719273 AAATTTCTAT
* *
5719283 AGTCTAATCTCCCCTAAAGTGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAG
1 AGTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAG
* *
5719348 AGCAGTGAAGCAAATC-ACTTTTGATTCAATCTTCCCTGAAGAGCAATGAAGTGAATCAAGTTTT
66 AGCAGTAAAGCAAATCGA-TTCTGATTCAATCTTCCCTGAAGAGCAATGAAGTGAATCAAGTTTT
5719412 CTCG
130 CTCG
* * * * *
5719416 AGTCTGATCTCCCCTAAAGAGTAGTGGAACAAATTCTTCTTCTTTCAAATTTGGTCTTCTTAAAG
1 AGTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAG
* * * * * *
5719481 AGCAATTAAGCAAATCGATTCGGATTCAATCTTCCTTGAAGAG-AA-GTAATATAAATCAAGTTT
66 AGCAGTAAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAGCAATG-AA-GTGAATCAAGTTT
5719544 TCTCG
129 TCTCG
* * * *
5719549 AGTCTGATATCCCCTAAAGAGTAGTGGAACATATTCTTCTTCTTTTAGATTTGGTCTTCCTGAAG
1 AGTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAG
* * * * *
5719614 AGTAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAACAGTGAAGTGGATCAACGTTTT
66 AGCAGTAAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAGCAATGAAGTGAATCAA-GTTTT
*
5719679 CTTG
130 CTCG
* * * * *
5719683 AGTCTGATATCCCCTAAAGAGTAGTGGAGTAGATTCTTCTTCTTTTAGATTTGGTATTCCTGAAA
1 AGTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAG
* *
5719748 AGCAGTTAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAGCATTGAAGTGAATCAAGTTTTC
66 AGCAGTAAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAGCAATGAAGTGAATCAAGTTTTC
*
5719813 TAG
131 TCG
* * *
5719816 AGTCTAATCTCCCCTAAAGAGTAGTGGAGAAGATTATTCTTCTTTCAGATTTGGTCTTCCTGAAG
1 AGTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAG
* *
5719881 AGCAGTAAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAGCAGTGAAGTGGATCAAAGTTTT
66 AGCAGTAAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAGCAATGAAGTGAATC-AAGTTTT
5719946 CTCG
130 CTCG
* * * * * * * *
5719950 AGTCTGATATCCCCTAAAGAGTAGTGAAGCATATCCTTATTCTGTCATATTTGGTCTTTCTGAAG
1 AGTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAG
* ** *
5720015 AGCAATAAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAATAATGGAA-TGAATTAACG-TT
66 AGCAGTAAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAGCAAT-GAAGTGAATCAA-GTTT
5720078 TCTCG
129 TCTCG
*
5720083 A-TCTGATCTACCCT
1 AGTCTGATCTCCCCT
5720097 GCAAAAAATA
Statistics
Matches: 600, Mismatches: 72, Indels: 19
0.87 0.10 0.03
Matches are distributed among these distances:
131 1 0.00
132 15 0.03
133 342 0.57
134 238 0.40
135 4 0.01
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (133 bp):
AGTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAG
AGCAGTAAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAGCAATGAAGTGAATCAAGTTTTC
TCG
Found at i:5719807 original size:267 final size:265
Alignment explanation
Indices: 5719276--5720056 Score: 1118
Period size: 267 Copynumber: 2.9 Consensus size: 265
5719266 TGGATCAAAA
* * *
5719276 TTTCTATAGTCTAATCTCCCCTAAAGTGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTCTT
1 TTTCTAGAGTCTAATCTCCCCTAAAGAGTAGTGGAACAGATTCTTCTTCTTTCAGATTTGGTCTT
* * *
5719341 CCTGAAGAGCAGTGAAGCAAATC-ACTTTTGATTCAATCTTCCCTGAAGAGCAATGAAGTGAATC
66 CCTGAAGAGCAGTGAAGCAAATCGA-TTCTGATTCAATCTTCCCTGAAGAGCAGTGAAGTGGATC
* *
5719405 AAGTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAACAAATTCTTCTTCTTTCAAATTTGG
130 AAGTTTTCTCGAGTCTGATATCCCCTAAAGAGTAGTGGAGCAAATTCTTCTTCTTTCAAATTTGG
* * *
5719470 TCTTCTTAAAGAGCAATTAAGCAAATCGATTCGGATTCAATCTTCCTTGAAGAGAAGTAATATAA
195 TCTTCTGAAA-AGCAATTAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAGAAGTAATATAA
5719535 ATCAAGT
259 ATCAAGT
* * * * *
5719542 TTTCTCGAGTCTGATATCCCCTAAAGAGTAGTGGAACATATTCTTCTTCTTTTAGATTTGGTCTT
1 TTTCTAGAGTCTAATCTCCCCTAAAGAGTAGTGGAACAGATTCTTCTTCTTTCAGATTTGGTCTT
* *
5719607 CCTGAAGAGTAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAACAGTGAAGTGGATCA
66 CCTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAGCAGTGAAGTGGATCA
* * * * *
5719672 ACGTTTTCTTGAGTCTGATATCCCCTAAAGAGTAGTGGAGTAGATTCTTCTTCTTTTAGATTTGG
131 A-GTTTTCTCGAGTCTGATATCCCCTAAAGAGTAGTGGAGCAAATTCTTCTTCTTTCAAATTTGG
* * * * * *
5719737 TATTCCTGAAAAGCAGTTAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAGCATTGAA-GTG
195 TCTT-CTGAAAAGCAATTAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAGAAGT-AATATA
5719801 AATCAAGT
258 AATCAAGT
*
5719809 TTTCTAGAGTCTAATCTCCCCTAAAGAGTAGTGGAGA-AGATTATTCTTCTTTCAGATTTGGTCT
1 TTTCTAGAGTCTAATCTCCCCTAAAGAGTAGTGGA-ACAGATTCTTCTTCTTTCAGATTTGGTCT
*
5719873 TCCTGAAGAGCAGTAAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAGCAGTGAAGTGGATC
65 TCCTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAGCAGTGAAGTGGATC
* * * * * *
5719938 AAAGTTTTCTCGAGTCTGATATCCCCTAAAGAGTAGTGAAGCATATCCTTATTCTGTCATATTTG
130 -AAGTTTTCTCGAGTCTGATATCCCCTAAAGAGTAGTGGAGCAAATTCTTCTTCTTTCAAATTTG
* *
5720003 GTCTTTCTGAAGAGCAATAAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
194 GTC-TTCTGAAAAGCAATTAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
5720057 ATAATGGAAT
Statistics
Matches: 457, Mismatches: 51, Indels: 13
0.88 0.10 0.02
Matches are distributed among these distances:
266 116 0.25
267 329 0.72
268 12 0.03
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (265 bp):
TTTCTAGAGTCTAATCTCCCCTAAAGAGTAGTGGAACAGATTCTTCTTCTTTCAGATTTGGTCTT
CCTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAGCAGTGAAGTGGATCA
AGTTTTCTCGAGTCTGATATCCCCTAAAGAGTAGTGGAGCAAATTCTTCTTCTTTCAAATTTGGT
CTTCTGAAAAGCAATTAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAGAAGTAATATAAAT
CAAGT
Found at i:5724414 original size:29 final size:29
Alignment explanation
Indices: 5724353--5724438 Score: 102
Period size: 29 Copynumber: 3.0 Consensus size: 29
5724343 CCCAACCCAT
* ****
5724353 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACTCCCGGCGACCAAGG
*
5724382 AGGTCGCCATGCACTCCGGGCGACCAAGG
1 AGGTCGCCATGCACTCCCGGCGACCAAGG
5724411 AGGTCGCCATGCA-TGCCCGGCGACCAAG
1 AGGTCGCCATGCACT-CCCGGCGACCAAG
5724439 CTTTTAACCC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
28 1 0.02
29 48 0.98
ACGTcount: A:0.20, C:0.38, G:0.29, T:0.13
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCGGCGACCAAGG
Found at i:5724643 original size:29 final size:29
Alignment explanation
Indices: 5724593--5724665 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 29
5724583 GTTGCCGGGC
* **
5724593 GTGCATGGCGACCTCCTTGGTCGCCCGGA
1 GTGCATGGCGACCTACGAGGTCGCCCGGA
* **
5724622 GTGCATGGCGACCTAGGAGGTCGCTGGGA
1 GTGCATGGCGACCTACGAGGTCGCCCGGA
* *
5724651 ATGCATGACGACCTA
1 GTGCATGGCGACCTA
5724666 TGGGTTGGGT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.18, C:0.27, G:0.36, T:0.19
Consensus pattern (29 bp):
GTGCATGGCGACCTACGAGGTCGCCCGGA
Found at i:5729908 original size:12 final size:12
Alignment explanation
Indices: 5729893--5729956 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
5729883 AGGTATATTT
5729893 TATTATATTTAA
1 TATTATATTTAA
*
5729905 TATT-T-TGTTAG
1 TATTATAT-TTAA
*
5729916 TATTTTATTTAA
1 TATTATATTTAA
5729928 TTATTTAATATTTAA
1 -TA-TT-ATATTTAA
*
5729943 TATTTTATTTAA
1 TATTATATTTAA
5729955 TA
1 TA
5729957 ATTTTTTTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
10 1 0.02
11 8 0.19
12 17 0.40
13 5 0.12
14 4 0.10
15 7 0.17
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (12 bp):
TATTATATTTAA
Found at i:5729941 original size:15 final size:13
Alignment explanation
Indices: 5729916--5729961 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
5729906 ATTTTGTTAG
5729916 TATTTTATTTAAT
1 TATTTTATTTAAT
5729929 TATTTAATATTTAA-
1 TATTT--TATTTAAT
5729943 TATTTTATTTAAT
1 TATTTTATTTAAT
*
5729956 AATTTT
1 TATTTT
5729962 TTTGTCCAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
12 7 0.24
13 10 0.34
14 5 0.17
15 7 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:5732244 original size:13 final size:13
Alignment explanation
Indices: 5732226--5732250 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5732216 TTTGTTGGAC
5732226 TTTTGTTAATTTA
1 TTTTGTTAATTTA
5732239 TTTTGTTAATTT
1 TTTTGTTAATTT
5732251 TGTTTATTAT
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:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (13 bp):
TTTTGTTAATTTA
Found at i:5735601 original size:9 final size:9
Alignment explanation
Indices: 5735587--5735611 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5735577 TAACACATTA
5735587 AAATAATTT
1 AAATAATTT
5735596 AAATAATTT
1 AAATAATTT
5735605 AAATAAT
1 AAATAAT
5735612 AATAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AAATAATTT
Found at i:5736166 original size:41 final size:41
Alignment explanation
Indices: 5736078--5736172 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
5736068 AAGGTGCGAT
* *
5736078 CTATGCATCGCGCTCTATCCCTACATGACAGAAAGCATGAC
1 CTATGCACCGCGCTATATCCCTACATGACAGAAAGCATGAC
* * *
5736119 CCATGCACCGCGCTATATCCCTACGTGGCAGAAAG--TGCAGC
1 CTATGCACCGCGCTATATCCCTACATGACAGAAAGCATG-A-C
5736160 CTATGCACCGCGC
1 CTATGCACCGCGC
5736173 CTTACTCAGC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
39 2 0.04
40 1 0.02
41 43 0.93
ACGTcount: A:0.25, C:0.35, G:0.21, T:0.19
Consensus pattern (41 bp):
CTATGCACCGCGCTATATCCCTACATGACAGAAAGCATGAC
Found at i:5740711 original size:26 final size:26
Alignment explanation
Indices: 5740659--5740727 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
5740649 AATTAAAATC
*
5740659 ATAAAAACAACAAATAAATAATAAAA
1 ATAAAAACAACAAATAAATAACAAAA
**
5740685 ATAAAAACAGTAAA-AAATAACATAAA
1 ATAAAAACAACAAATAAATAACA-AAA
* *
5740711 ACAAAAATAA-AAATAAA
1 ATAAAAACAACAAATAAA
5740728 ATATGAGGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
25 10 0.29
26 25 0.71
ACGTcount: A:0.77, C:0.07, G:0.01, T:0.14
Consensus pattern (26 bp):
ATAAAAACAACAAATAAATAACAAAA
Found at i:5742542 original size:23 final size:23
Alignment explanation
Indices: 5742516--5742560 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5742506 TCTACAGAAT
*
5742516 ATGTGCGTTGTCAATAATTAATA
1 ATGTGCATTGTCAATAATTAATA
*
5742539 ATGTGCATTGTCATTAATTAAT
1 ATGTGCATTGTCAATAATTAAT
5742561 TAATATTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (23 bp):
ATGTGCATTGTCAATAATTAATA
Found at i:5743107 original size:36 final size:37
Alignment explanation
Indices: 5743067--5743149 Score: 105
Period size: 37 Copynumber: 2.3 Consensus size: 37
5743057 ACTAAACCCG
* *
5743067 TCCCCGTCCCC-ATCTCCATTTAACATAAACAATTTT
1 TCCCCGTCCCCGACCCCCATTTAACATAAACAATTTT
* * *
5743103 TCCCCGTCCCCGACCCCCGTTTAGCATAAACGATTTT
1 TCCCCGTCCCCGACCCCCATTTAACATAAACAATTTT
*
5743140 TCCCCATCCC
1 TCCCCGTCCC
5743150 GTTTAATTCG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
36 11 0.28
37 29 0.73
ACGTcount: A:0.22, C:0.42, G:0.07, T:0.29
Consensus pattern (37 bp):
TCCCCGTCCCCGACCCCCATTTAACATAAACAATTTT
Found at i:5743264 original size:3 final size:3
Alignment explanation
Indices: 5743256--5743289 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
5743246 AAACATGTTT
5743256 TTA TTA TTA TTA TTA TTA -TA GTTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T
5743290 GGGATGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.86
4 2 0.07
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:5749085 original size:64 final size:64
Alignment explanation
Indices: 5748946--5749103 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 64
5748936 AATTGTTCAG
* *
5748946 TGTGTATCGATGCACAGGAAGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATT
1 TGTGTATCGATGCACAGGAAGTGCATCGATACACCCATTAAAAATGGAAACATCGAAGGCAATT
* * * * * **
5749010 AGTGCATCGATGCACAAGG-AGTGCATCGATACACCCCCTT-AAGATTGAAACATCGAAGGTGAT
1 TGTGTATCGATGCAC-AGGAAGTGCATCGATACA-CCCATTAAAAATGGAAACATCGAAGGCAAT
5749073 T
64 T
* ** *
5749074 TGTGTACCGATGCATGGGTAGTGCATCGAT
1 TGTGTATCGATGCACAGGAAGTGCATCGAT
5749104 GCACATGTTA
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
63 2 0.03
64 67 0.87
65 8 0.10
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.24
Consensus pattern (64 bp):
TGTGTATCGATGCACAGGAAGTGCATCGATACACCCATTAAAAATGGAAACATCGAAGGCAATT
Found at i:5750640 original size:23 final size:23
Alignment explanation
Indices: 5750574--5750640 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
5750564 ACCTTATATA
*
5750574 GCACTTCGGTGCATTTCTAAGCG
1 GCACTTCGGTGCATTTCTACGCG
* * *
5750597 GCACTTCGGTACAATTCTACGTG
1 GCACTTCGGTGCATTTCTACGCG
*
5750620 GCACTTCGGTGCATTTATACG
1 GCACTTCGGTGCATTTCTACG
5750641 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.31
Consensus pattern (23 bp):
GCACTTCGGTGCATTTCTACGCG
Found at i:5754848 original size:19 final size:18
Alignment explanation
Indices: 5754816--5754853 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5754806 ATATCTACAT
*
5754816 ATAATAAAAAAACAAAAA
1 ATAACAAAAAAACAAAAA
5754834 ATAACAAAAATAACAAAAA
1 ATAACAAAAA-AACAAAAA
5754853 A
1 A
5754854 ACTCTATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.82, C:0.08, G:0.00, T:0.11
Consensus pattern (18 bp):
ATAACAAAAAAACAAAAA
Found at i:5757505 original size:15 final size:15
Alignment explanation
Indices: 5757485--5757515 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5757475 CTATTAGCGC
5757485 TTTTATTTAATAAAA
1 TTTTATTTAATAAAA
*
5757500 TTTTATTTTATAAAA
1 TTTTATTTAATAAAA
5757515 T
1 T
5757516 GGGTGTTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTTATTTAATAAAA
Found at i:5760559 original size:20 final size:20
Alignment explanation
Indices: 5760477--5760546 Score: 140
Period size: 20 Copynumber: 3.5 Consensus size: 20
5760467 GAATGAAGTA
5760477 GTATCGATACTAATGTGGAG
1 GTATCGATACTAATGTGGAG
5760497 GTATCGATACTAATGTGGAG
1 GTATCGATACTAATGTGGAG
5760517 GTATCGATACTAATGTGGAG
1 GTATCGATACTAATGTGGAG
5760537 GTATCGATAC
1 GTATCGATAC
5760547 CAATAGTAAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.30, C:0.11, G:0.29, T:0.30
Consensus pattern (20 bp):
GTATCGATACTAATGTGGAG
Found at i:5760559 original size:40 final size:40
Alignment explanation
Indices: 5760477--5760559 Score: 132
Period size: 40 Copynumber: 2.1 Consensus size: 40
5760467 GAATGAAGTA
* *
5760477 GTATCGATACTAATGTGGAGGTATCGATACTAATGTGGAG
1 GTATCGATACTAATGTGGAGGTATCGATACCAATGTGAAG
5760517 GTATCGATACTAATGTGGAGGTATCGATACCAATAGT-AAG
1 GTATCGATACTAATGTGGAGGTATCGATACCAAT-GTGAAG
5760557 GTA
1 GTA
5760560 CCTATACTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 38 0.95
41 2 0.05
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.29
Consensus pattern (40 bp):
GTATCGATACTAATGTGGAGGTATCGATACCAATGTGAAG
Found at i:5761051 original size:15 final size:15
Alignment explanation
Indices: 5761031--5761115 Score: 125
Period size: 15 Copynumber: 5.7 Consensus size: 15
5761021 ACTTTATTAG
*
5761031 TATGTGAATATGTTA
1 TATGTGAATATGTTC
*
5761046 TATGTGAATATGTTA
1 TATGTGAATATGTTC
* *
5761061 TACGTGAAAATGTTC
1 TATGTGAATATGTTC
5761076 TATGTGAATATGTTC
1 TATGTGAATATGTTC
*
5761091 TATGTGAATGTGTTC
1 TATGTGAATATGTTC
5761106 TATGTGAATA
1 TATGTGAATA
5761116 GATGATACTT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 63 1.00
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.44
Consensus pattern (15 bp):
TATGTGAATATGTTC
Found at i:5761263 original size:23 final size:23
Alignment explanation
Indices: 5761237--5761286 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
5761227 GTCCTTCGGA
*
5761237 ACAATTTTATATGGTCATTCAGG
1 ACAATTCTATATGGTCATTCAGG
* *
5761260 ACAATTCTATATGGTCCTTCGGG
1 ACAATTCTATATGGTCATTCAGG
5761283 ACAA
1 ACAA
5761287 ATCTTTGTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (23 bp):
ACAATTCTATATGGTCATTCAGG
Found at i:5761331 original size:24 final size:24
Alignment explanation
Indices: 5761293--5761346 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
5761283 ACAAATCTTT
** * *
5761293 GTGGCACTTTGGTGCATATTTTAC
1 GTGGCACTTCAGTGCAAATTCTAC
5761317 GTGGCACTTCAGTGCAAATTCTAC
1 GTGGCACTTCAGTGCAAATTCTAC
*
5761341 GCGGCA
1 GTGGCA
5761347 GTTTCGACTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.31
Consensus pattern (24 bp):
GTGGCACTTCAGTGCAAATTCTAC
Found at i:5763384 original size:19 final size:20
Alignment explanation
Indices: 5763360--5763410 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
5763350 AATGACCAAT
5763360 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
5763379 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
5763399 AAAATCGCAACG
1 AAAATCGCAACG
5763411 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:5763404 original size:20 final size:20
Alignment explanation
Indices: 5763360--5763657 Score: 159
Period size: 20 Copynumber: 14.6 Consensus size: 20
5763350 AATGACCAAT
* *
5763360 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
5763379 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
5763399 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
***
5763419 AAAATCGCAACG-GACAAAAG
1 AAAATCGCAACGCGA-TTTAG
* * **
5763439 AAAATCGCAACACGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
5763460 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
5763483 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
** * *
5763503 TCAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
5763523 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
5763543 AGAGTCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * *
5763563 AAGAGAATCGCAATGCGACTGAG
1 -A-A-AATCGCAACGCGATTTAG
* * * *
5763586 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
5763606 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
5763626 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
5763646 AAAATCGCAACG
1 AAAATCGCAACG
5763658 TTAAAAAGAA
Statistics
Matches: 224, Mismatches: 46, Indels: 17
0.78 0.16 0.06
Matches are distributed among these distances:
19 18 0.08
20 162 0.72
21 15 0.07
22 1 0.00
23 28 0.12
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:5763538 original size:40 final size:40
Alignment explanation
Indices: 5763464--5763655 Score: 231
Period size: 40 Copynumber: 4.7 Consensus size: 40
5763454 GCTTCCAAGT
***
5763464 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTCAA
1 TCGCAACGCGATTTAG-AG--AATCGCAATGCGATTGAGAGAA
* * *
5763507 TCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
*
5763547 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAGAA
1 TCGCAACGCGATTT---AGAGAATCGCAATGCGATTGAGAGAA
* * *
5763590 TCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
1 TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
*
5763630 TCGCAACGCGATTTAGAAAATCGCAA
1 TCGCAACGCGATTTAGAGAATCGCAA
5763656 CGTTAAAAAG
Statistics
Matches: 128, Mismatches: 18, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
40 78 0.61
42 2 0.02
43 48 0.38
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (40 bp):
TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
Found at i:5763575 original size:83 final size:83
Alignment explanation
Indices: 5763464--5763647 Score: 287
Period size: 83 Copynumber: 2.2 Consensus size: 83
5763454 GCTTCCAAGT
* ** * * *
5763464 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTCAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGACAATCGCAATGCGACTGAGAGAATC
*
5763529 GCAATGCGATTGAGAGAG
66 GCAATGCGATTGAGAGAA
* *
5763547 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGACAATCGCAATGCGACTGAGAGAATC
5763612 GCAATGCGATTGAGAGAA
66 GCAATGCGATTGAGAGAA
5763630 TCGCAACGCGATTTAGAA
1 TCGCAACGCGATTTAGAA
5763648 AATCGCAACG
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 92 1.00
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (83 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGACAATCGCAATGCGACTGAGAGAATC
GCAATGCGATTGAGAGAA
Found at i:5763667 original size:20 final size:20
Alignment explanation
Indices: 5763644--5763687 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
5763634 AACGCGATTT
*
5763644 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
5763664 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
5763684 AGAA
1 AGAA
5763688 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.18, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:5763776 original size:6 final size:6
Alignment explanation
Indices: 5763765--5763808 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
5763755 GACACGTATT
5763765 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
5763809 CGAGACGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:5764520 original size:6 final size:6
Alignment explanation
Indices: 5764499--5764590 Score: 170
Period size: 6 Copynumber: 15.7 Consensus size: 6
5764489 TCTCGTCTCG
5764499 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
5764545 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
5764591 ATACGTGTCT
Statistics
Matches: 86, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 10 0.12
6 76 0.88
ACGTcount: A:0.00, C:0.17, G:0.51, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:5764692 original size:20 final size:20
Alignment explanation
Indices: 5764667--5764710 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
5764657 TTTTTAACTA
*
5764667 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
5764687 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
5764707 TTCT
1 TTCT
5764711 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:5764720 original size:20 final size:20
Alignment explanation
Indices: 5764697--5765098 Score: 184
Period size: 20 Copynumber: 19.6 Consensus size: 20
5764687 TTCTTTTTAA
5764697 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
5764717 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
5764737 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
5764757 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
5764777 CATTGCGATTCTCTTCTAAATCG
1 CGTTGCGA-T-T-TTCTAAATCG
* * *
5764800 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
5764820 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* *** *
5764840 CATTGCGATTCAATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
5764860 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
5764883 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
5764904 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
5764922 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
5764944 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
5764964 CGTTGCGATTTT-GATATACG
1 CGTTGCGATTTTCTAAAT-CG
* **
5764984 CGTTGCGATTTATGT-GTTCG
1 CGTTGCGATTT-TCTAAATCG
*
5765004 CGTTGCGATTTTC-ATATTCG
1 CGTTGCGATTTTCTA-AATCG
**
5765024 CGTTGCGATTTTGGAAAATCG
1 CGTTGCGATTTT-CTAAATCG
** * * *
5765045 CAATGCGAATTTGTACTATCG
1 CGTTGCGATTTTCTA-AATCG
* *
5765066 CATTGCGATTTTCAAGAATCG
1 CGTTGCGATTTTCTA-AATCG
5765087 CGTTGCGATTTT
1 CGTTGCGATTTT
5765099 GGAAACTGAT
Statistics
Matches: 302, Mismatches: 61, Indels: 37
0.75 0.15 0.09
Matches are distributed among these distances:
18 2 0.01
19 4 0.01
20 203 0.67
21 60 0.20
22 6 0.02
23 27 0.09
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:5764743 original size:40 final size:40
Alignment explanation
Indices: 5764699--5764890 Score: 231
Period size: 40 Copynumber: 4.7 Consensus size: 40
5764689 CTTTTTAACG
5764699 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * * *
5764739 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
*
5764779 TTGCGATTCTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGA-T-T-TTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * **
5764822 TTGCGATTCTATAAATCGCATTGCGATTCAATCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
5764862 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGA--TT-TTCTAAATCGCGTTGCGA
5764891 ACTTGGAAGC
Statistics
Matches: 126, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
40 73 0.58
41 2 0.02
42 4 0.03
43 47 0.37
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (40 bp):
TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
Found at i:5764805 original size:83 final size:83
Alignment explanation
Indices: 5764707--5764890 Score: 296
Period size: 83 Copynumber: 2.2 Consensus size: 83
5764697 CGTTGCGATT
* * * * **
5764707 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCAATC
*
5764772 AGTCGCATTGCGATTCTC
66 AATCGCATTGCGATTCTC
5764790 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCAATC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCAATC
*
5764855 AATCGCATTGCGATTTTC
66 AATCGCATTGCGATTCTC
5764873 TTCTAAATCGCGTTGCGA
1 TTCTAAATCGCGTTGCGA
5764891 ACTTGGAAGC
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 93 1.00
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (83 bp):
TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCAATC
AATCGCATTGCGATTCTC
Found at i:5765051 original size:21 final size:21
Alignment explanation
Indices: 5765021--5765103 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
5765011 ATTTTCATAT
*
5765021 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
5765042 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
5765063 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
5765084 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
5765104 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:5770808 original size:21 final size:21
Alignment explanation
Indices: 5770779--5770822 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5770769 AATTTAGTTA
*
5770779 ATTATTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
5770800 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
5770821 AT
1 AT
5770823 ATTATATTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.57
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:5770823 original size:28 final size:28
Alignment explanation
Indices: 5770792--5770857 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
5770782 ATTTTGTTAG
*
5770792 TATAAATTATTAGTTTGTTAGTTTAAGT
1 TATAAATTATTAGTTTATTAGTTTAAGT
*
5770820 TAT-ATTATATTAGTTTATTAGTTTAAGT
1 TATAAAT-TATTAGTTTATTAGTTTAAGT
*
5770848 TATATATTAT
1 TATAAATTAT
5770858 ATTATAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.91
29 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (28 bp):
TATAAATTATTAGTTTATTAGTTTAAGT
Found at i:5771389 original size:22 final size:22
Alignment explanation
Indices: 5771354--5771395 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
5771344 TTTAAAAAAA
5771354 TGTTGTGTTTAAAAATATTTAG
1 TGTTGTGTTTAAAAATATTTAG
5771376 TGTTGT-TTTAAAAAATATTT
1 TGTTGTGTTT-AAAAATATTT
5771396 TTTTTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.52
Consensus pattern (22 bp):
TGTTGTGTTTAAAAATATTTAG
Found at i:5771658 original size:26 final size:25
Alignment explanation
Indices: 5771603--5771658 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
5771593 ATAAATAGTT
* *
5771603 ATTATTAATCATTACTAAATCATATT
1 ATTATTAATCATTAC-AAATCAAATC
5771629 ATTATTAAATCATTA-AATATCAAATC
1 ATTATT-AATCATTACAA-ATCAAATC
5771655 ATTA
1 ATTA
5771659 GATTAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 2 0.08
26 16 0.62
27 8 0.31
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (25 bp):
ATTATTAATCATTACAAATCAAATC
Found at i:5774668 original size:15 final size:15
Alignment explanation
Indices: 5774648--5774686 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
5774638 AATGATTTAA
*
5774648 TAATGATTTTATTTT
1 TAATGATTTTATATT
5774663 TAATGATTTTATATT
1 TAATGATTTTATATT
5774678 TAATGATTT
1 TAATGATTT
5774687 AGTAATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (15 bp):
TAATGATTTTATATT
Found at i:5774869 original size:21 final size:23
Alignment explanation
Indices: 5774843--5774884 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5774833 ATAATAATGA
5774843 TTAT-AATA-GTCGAATTTATCT
1 TTATAAATATGTCGAATTTATCT
5774864 TTATAAATATGTCGAATTTAT
1 TTATAAATATGTCGAATTTAT
5774885 TTTTTTACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 4 0.21
23 11 0.58
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.48
Consensus pattern (23 bp):
TTATAAATATGTCGAATTTATCT
Found at i:5775048 original size:14 final size:13
Alignment explanation
Indices: 5775029--5775076 Score: 55
Period size: 14 Copynumber: 3.7 Consensus size: 13
5775019 TATTAATATT
5775029 TAATGATTTGATGG
1 TAATGATTTGAT-G
5775043 TAATGATTT-A-G
1 TAATGATTTGATG
*
5775054 TAATGAATTGATAG
1 TAATGATTTGAT-G
5775068 TAATGATTT
1 TAATGATTT
5775077 ATTATTAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 9 0.31
12 1 0.03
13 1 0.03
14 18 0.62
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (13 bp):
TAATGATTTGATG
Found at i:5775058 original size:25 final size:25
Alignment explanation
Indices: 5775029--5775077 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
5775019 TATTAATATT
* *
5775029 TAATGATTTGATGGTAATGATTTAG
1 TAATGAATTGATAGTAATGATTTAG
5775054 TAATGAATTGATAGTAATGATTTA
1 TAATGAATTGATAGTAATGATTTA
5775078 TTATTAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (25 bp):
TAATGAATTGATAGTAATGATTTAG
Found at i:5775298 original size:11 final size:11
Alignment explanation
Indices: 5775282--5775347 Score: 60
Period size: 11 Copynumber: 5.5 Consensus size: 11
5775272 TGATATCATT
*
5775282 TGATTTAGTAA
1 TGATTTAATAA
5775293 TGATTTGATAATAA
1 TGA-TT--TAATAA
5775307 TGATTTAATAA
1 TGATTTAATAA
*
5775318 TGATTTTATATTTA
1 TGA-TTTA-A-TAA
5775332 TGATTTAATAA
1 TGATTTAATAA
5775343 TGATT
1 TGATT
5775348 ATTATTAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
11 19 0.41
12 7 0.15
13 7 0.15
14 13 0.28
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (11 bp):
TGATTTAATAA
Done.