Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007823.1 Hibiscus syriacus cultivar Beakdansim tig00110160_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: 6287495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 29 of 33
Found at i:5336293 original size:23 final size:23
Alignment explanation
Indices: 5336208--5336285 Score: 138
Period size: 23 Copynumber: 3.4 Consensus size: 23
5336198 ACATTTTATA
5336208 TTCGGTGCAATTCTACGCGGCAC
1 TTCGGTGCAATTCTACGCGGCAC
5336231 TTCGGTGCAATTCTACGCGGCAC
1 TTCGGTGCAATTCTACGCGGCAC
* *
5336254 TTCGGTGCAATTCTACGTGGCAT
1 TTCGGTGCAATTCTACGCGGCAC
5336277 TTCGGTGCA
1 TTCGGTGCA
5336286 TTTATACGAG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (23 bp):
TTCGGTGCAATTCTACGCGGCAC
Found at i:5346463 original size:14 final size:14
Alignment explanation
Indices: 5346446--5346491 Score: 74
Period size: 14 Copynumber: 3.2 Consensus size: 14
5346436 CACATTGGTC
5346446 ATATCTCATAGCAT
1 ATATCTCATAGCAT
5346460 ATATCTCATAGCAT
1 ATATCTCATAGCAT
*
5346474 ATATCACATATGCAT
1 ATATCTCATA-GCAT
5346489 ATA
1 ATA
5346492 ATCCTGTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 23 0.77
15 7 0.23
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.35
Consensus pattern (14 bp):
ATATCTCATAGCAT
Found at i:5347724 original size:31 final size:30
Alignment explanation
Indices: 5347684--5347742 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
5347674 GTTTACGATC
5347684 TAAATGTTTAATAATATAATTGAAATAAAAAT
1 TAAATGTTTAATAATATAATT--AATAAAAAT
*
5347716 TAAA-GTTTAATATTATAATTAATAAAA
1 TAAATGTTTAATAATATAATTAATAAAA
5347743 CAAAAAAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 7 0.27
31 15 0.58
32 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (30 bp):
TAAATGTTTAATAATATAATTAATAAAAAT
Found at i:5352738 original size:31 final size:31
Alignment explanation
Indices: 5352640--5352730 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
5352630 CAATTTAAGG
5352640 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
5352671 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
5352702 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
5352731 TTCAAAATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 12 0.20
31 37 0.62
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:5352822 original size:19 final size:19
Alignment explanation
Indices: 5352795--5352861 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
5352785 AATGTTTTTA
* *
5352795 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
5352814 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* *
5352833 TGAACAGTAAATCACTGTT
1 TGAACAGTAAATTACTATT
5352852 TGAACAGTAA
1 TGAACAGTAA
5352862 CCCGAGGCTC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.36
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:5353000 original size:21 final size:22
Alignment explanation
Indices: 5352967--5353009 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
5352957 ATTTGAATAT
*
5352967 TATGAAGGGGGTATCGATTCCC
1 TATGAAGGGGGTACCGATTCCC
5352989 TATGAA-GGGGTACCGATTCCC
1 TATGAAGGGGGTACCGATTCCC
5353010 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (22 bp):
TATGAAGGGGGTACCGATTCCC
Found at i:5353071 original size:21 final size:21
Alignment explanation
Indices: 5353038--5353077 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
5353028 TTTGAGTAGA
*
5353038 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
5353060 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
5353078 AGATACAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:5358678 original size:23 final size:21
Alignment explanation
Indices: 5358625--5358687 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
5358615 TTTTGGTGCA
*
5358625 GAGGGAATCGATTCCCCCCCT
1 GAGGGAACCGATTCCCCCCCT
**
5358646 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCCT
5358667 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
5358688 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 19 0.53
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.37, G:0.25, T:0.17
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCCT
Found at i:5358695 original size:21 final size:21
Alignment explanation
Indices: 5358627--5358708 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 21
5358617 TTGGTGCAGA
* *
5358627 GGGAATCGATTCCCCCC-CTG
1 GGGAACCGATTCCCCCCACAG
*
5358647 AGGGAACCGATTCCCCCTTTGA-AG
1 -GGGAACCGATTCCCCC---CACAG
5358671 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCACAG
* *
5358692 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
5358709 TGGGGTTCTG
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.02
21 32 0.64
23 16 0.32
24 1 0.02
ACGTcount: A:0.22, C:0.38, G:0.24, T:0.16
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCACAG
Found at i:5361155 original size:30 final size:30
Alignment explanation
Indices: 5361121--5361181 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
5361111 TTCGATATAA
*
5361121 CAAATTAAGTTAAA-TGGATTTTAAGATTTT
1 CAAATTAAGTTAAAGT-AATTTTAAGATTTT
5361151 CAAATTAAGTTAAAGTAATTTTAAGATTTT
1 CAAATTAAGTTAAAGTAATTTTAAGATTTT
5361181 C
1 C
5361182 CAAACGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (30 bp):
CAAATTAAGTTAAAGTAATTTTAAGATTTT
Found at i:5370639 original size:110 final size:112
Alignment explanation
Indices: 5370300--5370693 Score: 560
Period size: 110 Copynumber: 3.5 Consensus size: 112
5370290 TTTGCAGATT
* * * * *
5370300 TGATATTACCTTTAGAAGAAGCGGAACAAATCCCTCTCTTCCAATATTTGATATTCCCTT-GAAA
1 TGATATTCCCTTTACAAGAAGCGGAACAGATCCCTCTCTTCCAAGATTTAATATTCCCTTAGAAA
*
5370364 GAAGCGGAACAAGTCTACCCCGATTCAATTGGATCAACTCCCCCAGATC
66 -AAGCGGAACAAGTCTACCCCGATTCAA-TGGATCAACTCCCCCATATC
** * * *
5370413 TGATATTCCCTTTACAAGAAGAAGAACAGATCCCTCTATTCCAAGATTTAATAATCCCTTAGAAG
1 TGATATTCCCTTTACAAGAAGCGGAACAGATCCCTCTCTTCCAAGATTTAATATTCCCTTAGAAA
* *
5370478 AAGCGGAACAAGTCTAGCCCGATTCAATGGATCAACTCCCCCATATA
66 AAGCGGAACAAGTCTACCCCGATTCAATGGATCAACTCCCCCATATC
* * *
5370525 TGATATTCCATTTACAAGAAGCGGAACAGATCTCTCTCTTCC-A-ATTTGATATTCCCTTAGAAA
1 TGATATTCCCTTTACAAGAAGCGGAACAGATCCCTCTCTTCCAAGATTTAATATTCCCTTAGAAA
* * * *
5370588 AAACGGAAAAAGTCTACCCCGATTCAATGGATCAACTCCCACATACC
66 AAGCGGAACAAGTCTACCCCGATTCAATGGATCAACTCCCCCATATC
*
5370635 TGATATTCCCTTTACAAGAAGTGGAACAGATCCCTCTCTTCCAAGATTTAATATTCCCT
1 TGATATTCCCTTTACAAGAAGCGGAACAGATCCCTCTCTTCCAAGATTTAATATTCCCT
5370694 GAGTGACAAC
Statistics
Matches: 247, Mismatches: 31, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
110 97 0.39
111 2 0.01
112 68 0.28
113 77 0.31
114 3 0.01
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (112 bp):
TGATATTCCCTTTACAAGAAGCGGAACAGATCCCTCTCTTCCAAGATTTAATATTCCCTTAGAAA
AAGCGGAACAAGTCTACCCCGATTCAATGGATCAACTCCCCCATATC
Found at i:5373335 original size:131 final size:133
Alignment explanation
Indices: 5373083--5373391 Score: 347
Period size: 132 Copynumber: 2.3 Consensus size: 133
5373073 GCTTAAGAGG
* * * ** * * * ** * *
5373083 TCATTTA-TTCTCGATTGAAAATAATTTGATATTTTTGTTTTCTCTTTAATTAATATCGATTTTT
1 TCATTTATTTCTCGATTGGAAATAATTAGATATTATCATTTTCACTTGAGTCGATATTGAATTTT
* * * * * *
5373147 TAGACGAAATATTAATATCTCTTTTTTTTCAATTGGGGTAATAAATGATTGTTTTAATGCATGAA
66 AAGACGAAATAATAATATCTCTTTTATTTCAATTGGAGTAATAAATGACTGTTTTAATGCACGAA
5373212 AG-
131 AGA
* * * * * *
5373214 GCTGTTTA-TTCTCGATTGTAAATCATTAGATGTTATTATTTTCACTTGAGTCGATATTGAATTT
1 TC-ATTTATTTCTCGATTGGAAATAATTAGATATTATCATTTTCACTTGAGTCGATATTGAATTT
*
5373278 TAAGATGAAATAATAATATCT-TTTTATTTCAATTGGAGTAATAAATGACTGTTTTAATGCACGA
65 TAAGACGAAATAATAATATCTCTTTTATTTCAATTGGAGTAATAAATGACTGTTTTAATGCACGA
5373342 AAGA
130 AAGA
*
5373346 TCATTTATTTCTCGATTGGAAATAATTAGATATTATCGTTTTCACT
1 TCATTTATTTCTCGATTGGAAATAATTAGATATTATCATTTTCACT
5373392 CTTAAAATTA
Statistics
Matches: 146, Mismatches: 29, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
131 47 0.32
132 99 0.68
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (133 bp):
TCATTTATTTCTCGATTGGAAATAATTAGATATTATCATTTTCACTTGAGTCGATATTGAATTTT
AAGACGAAATAATAATATCTCTTTTATTTCAATTGGAGTAATAAATGACTGTTTTAATGCACGAA
AGA
Found at i:5380113 original size:32 final size:32
Alignment explanation
Indices: 5380054--5380115 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
5380044 CAGATCGAAT
* *
5380054 TCGGATCGATTGGAGGATGTAAGATTTTCGAG
1 TCGGATCGAGTGGAGGATGCAAGATTTTCGAG
* * *
5380086 TCGGGTCGAGTGGATGATGCAATATTTTCG
1 TCGGATCGAGTGGAGGATGCAAGATTTTCG
5380116 GTTTGTTCGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.23, C:0.11, G:0.34, T:0.32
Consensus pattern (32 bp):
TCGGATCGAGTGGAGGATGCAAGATTTTCGAG
Found at i:5380301 original size:2 final size:2
Alignment explanation
Indices: 5380294--5380333 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
5380284 TTTAATGTGA
*
5380294 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5380334 GATTCAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5381406 original size:15 final size:15
Alignment explanation
Indices: 5381361--5381410 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
5381351 AATTTTCGTT
*
5381361 TATTATTAATAAA-A
1 TATTATTATTAAATA
5381375 TTATTATTATT--AT-
1 -TATTATTATTAAATA
5381388 TATTATTATTAAATA
1 TATTATTATTAAATA
5381403 TATTATTA
1 TATTATTA
5381411 CAAGCCCAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
12 10 0.33
13 1 0.03
14 2 0.07
15 17 0.57
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTATTATTAAATA
Found at i:5381410 original size:3 final size:3
Alignment explanation
Indices: 5381360--5381398 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
5381350 AAATTTTCGT
* **
5381360 TTA TTA TTA ATA AAA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5381399 AATATATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:5382893 original size:31 final size:33
Alignment explanation
Indices: 5382858--5382919 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
5382848 ATAATTAAAC
5382858 ATTATAAAAATTAT-A-ATTTAGTTTTATTTAA
1 ATTATAAAAATTATAATATTTAGTTTTATTTAA
* * *
5382889 ATTATTAAAATTTTAATATTTATTTTTATTT
1 ATTATAAAAATTATAATATTTAGTTTTATTT
5382920 TTTTAATATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 12 0.46
32 1 0.04
33 13 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (33 bp):
ATTATAAAAATTATAATATTTAGTTTTATTTAA
Found at i:5387819 original size:84 final size:84
Alignment explanation
Indices: 5387721--5387935 Score: 387
Period size: 84 Copynumber: 2.6 Consensus size: 84
5387711 ATAAAACTTG
*
5387721 AGTTGTCCCTCTAGAGCAATTGGTTAATCACCCTGGCTTTATGGATAATATTCAGCCAACCTATT
1 AGTTGTCCCTCTAGAGCAATTGGTTAATCACCCCGGCTTTATGGATAATATTCAGCCAACCTATT
5387786 ATACTATTATATGCAATAA
66 ATACTATTATATGCAATAA
*
5387805 AGTTATCCCTCTAGAGCAATTGGTTAATCACCCCGGCTTTATGGATAATATTCAGCCAACCTATT
1 AGTTGTCCCTCTAGAGCAATTGGTTAATCACCCCGGCTTTATGGATAATATTCAGCCAACCTATT
5387870 ATACTATTATATGCAATAA
66 ATACTATTATATGCAATAA
* *
5387889 AGCTGT-CCTCTAGAGCAATTGGTTAATCGCCCCGGCTTTATGGATAA
1 AGTTGTCCCTCTAGAGCAATTGGTTAATCACCCCGGCTTTATGGATAA
5387936 GTTTCAATTA
Statistics
Matches: 126, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
83 40 0.32
84 86 0.68
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (84 bp):
AGTTGTCCCTCTAGAGCAATTGGTTAATCACCCCGGCTTTATGGATAATATTCAGCCAACCTATT
ATACTATTATATGCAATAA
Found at i:5390063 original size:114 final size:114
Alignment explanation
Indices: 5389863--5390082 Score: 377
Period size: 114 Copynumber: 1.9 Consensus size: 114
5389853 CACGTTCTCG
*
5389863 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGATTC
* *
5389928 GGTATGAACCCCAAAACCAATCATTAGATTTAAAAGATGAATTTGCTCA
66 GGTAGGAACCCCAAAACCAATCATTAGAATTAAAAGATGAATTTGCTCA
*
5389977 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGATTC
* * *
5390042 GGTAGGGACCCCAGAACCAATCATTAGAATTGAAAGATGAA
66 GGTAGGAACCCCAAAACCAATCATTAGAATTAAAAGATGAA
5390083 CTGCATGATC
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 99 1.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.30
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGATTC
GGTAGGAACCCCAAAACCAATCATTAGAATTAAAAGATGAATTTGCTCA
Found at i:5391172 original size:74 final size:75
Alignment explanation
Indices: 5391034--5391211 Score: 225
Period size: 74 Copynumber: 2.4 Consensus size: 75
5391024 ATTAACAAGA
* * * *
5391034 AGCAAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAGAAATGTTGAAATATTCTGAA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGAAATGTTGAAACATCCTGAA
*
5391099 TA-TT-TATC
66 CACTTGTATC
* * **
5391107 AGCAAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGAACTGTTGATGCATCCTGA
1 AGC-AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGAAATGTTGAAACATCCTGA
*
5391172 ACACTTGTATT
65 ACACTTGTATC
* *
5391183 AGCCAATGTTGGGGCATGCTGAAGGCCCA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCA
5391212 CAACATCCTG
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
73 3 0.03
74 55 0.62
75 25 0.28
76 6 0.07
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (75 bp):
AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGAAATGTTGAAACATCCTGAA
CACTTGTATC
Found at i:5392170 original size:54 final size:54
Alignment explanation
Indices: 5392075--5392232 Score: 164
Period size: 54 Copynumber: 3.0 Consensus size: 54
5392065 TAATTGAGAA
* * * * *
5392075 ATCTGAGTAGAAGCCACATA-AAAGGATGATTTTGTTGTCAAATGCTTTACGAAC
1 ATCTGAGCAGAAGCCACA-AGAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC
* * * *
5392129 ATCTGAGCAGAAGCCACAAGAAATGAAGAATGTGTTTTCAAATGTTTTAC-ATC
1 ATCTGAGCAGAAGCCACAAGAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC
* * *
5392182 -TC-GA-CAGAAACCACAGGAAAAGATGAATGTATTGTCAAATGTTTTACGAAC
1 ATCTGAGCAGAAGCCACAAGAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC
5392233 CAGTGATTAT
Statistics
Matches: 87, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
50 37 0.43
51 4 0.05
52 2 0.02
53 3 0.03
54 41 0.47
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (54 bp):
ATCTGAGCAGAAGCCACAAGAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC
Found at i:5392210 original size:50 final size:50
Alignment explanation
Indices: 5392127--5392228 Score: 134
Period size: 50 Copynumber: 2.0 Consensus size: 50
5392117 TGCTTTACGA
* * * *
5392127 ACATCTGAGCAGAAGCCACAAGAAATGAAGAATGTGTTTTCAAATGTTTT
1 ACATCTGAGCAGAAACCACAAGAAAAGAAGAATGTATTGTCAAATGTTTT
* *
5392177 ACATCTCGA-CAGAAACCACAGGAAAAGATGAATGTATTGTCAAATGTTTT
1 ACATCT-GAGCAGAAACCACAAGAAAAGAAGAATGTATTGTCAAATGTTTT
5392227 AC
1 AC
5392229 GAACCAGTGA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
50 43 0.96
51 2 0.04
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (50 bp):
ACATCTGAGCAGAAACCACAAGAAAAGAAGAATGTATTGTCAAATGTTTT
Found at i:5392628 original size:22 final size:22
Alignment explanation
Indices: 5392595--5392651 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
5392585 ATATCTACAA
*
5392595 TCTTCAAAGATGATAGATTCTG
1 TCTTCAAAGATGATAGATTCTC
* *
5392617 TTTTTAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
5392639 TCTTCAAAGATGA
1 TCTTCAAAGATGA
5392652 AAGCTTTATG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:5393845 original size:76 final size:76
Alignment explanation
Indices: 5393326--5393811 Score: 909
Period size: 76 Copynumber: 6.4 Consensus size: 76
5393316 CTATTTCCTA
* *
5393326 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTCTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5393391 AGCCTTAGGGT
66 AGCCTTAGGGT
*
5393402 CATCTGTAAGTCCTATAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5393467 AGCCTTAGGGT
66 AGCCTTAGGGT
*
5393478 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGTGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5393543 AGCCTTAGGGT
66 AGCCTTAGGGT
5393554 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5393619 AGCCTTAGGGT
66 AGCCTTAGGGT
5393630 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5393695 AGCCTTAGGGT
66 AGCCTTAGGGT
*
5393706 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5393771 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
5393782 CATCTGTAAGCCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
5393812 TAAAGACCTC
Statistics
Matches: 401, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 401 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:5394024 original size:12 final size:13
Alignment explanation
Indices: 5393958--5394028 Score: 62
Period size: 12 Copynumber: 5.6 Consensus size: 13
5393948 ATTTTTCGTT
5393958 TATTATTAATAA-A
1 TATTATT-ATAATA
*
5393971 -ATTATTATTAT-
1 TATTATTATAATA
5393982 TATTATTATAAT-
1 TATTATTATAATA
*
5393994 TATTATTATTAT-
1 TATTATTATAATA
5394006 TATTATTATTAAATA
1 TATTATTA-T-AATA
5394021 TATTATTA
1 TATTATTA
5394029 CAAGCCCAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
11 3 0.06
12 35 0.71
13 1 0.02
14 2 0.04
15 8 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTATTATAATA
Found at i:5394024 original size:15 final size:14
Alignment explanation
Indices: 5393977--5394028 Score: 72
Period size: 15 Copynumber: 3.7 Consensus size: 14
5393967 TAAAATTATT
5393977 ATTATTATTATTATA
1 ATTATTATTATTA-A
5393992 ATTATTATTATT--
1 ATTATTATTATTAA
5394004 ATTATTATTATTAA
1 ATTATTATTATTAA
5394018 ATATATTATTA
1 AT-TATTATTA
5394029 CAAGCCCAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 12 0.35
14 2 0.06
15 20 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTATTATTATTAA
Found at i:5394028 original size:3 final size:3
Alignment explanation
Indices: 5393957--5394016 Score: 84
Period size: 3 Copynumber: 20.0 Consensus size: 3
5393947 AATTTTTCGT
* ** *
5393957 TTA TTA TTA ATA AAA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5394005 TTA TTA TTA TTA
1 TTA TTA TTA TTA
5394017 AATATATTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:5395517 original size:31 final size:33
Alignment explanation
Indices: 5395482--5395543 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
5395472 ATAATTAAAC
5395482 ATTATAAAAATTAT-A-ATTTAGTTTTATTTAA
1 ATTATAAAAATTATAATATTTAGTTTTATTTAA
* * *
5395513 ATTATTAAAATTTTAATATTTATTTTTATTT
1 ATTATAAAAATTATAATATTTAGTTTTATTT
5395544 TTTTAATATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 12 0.46
32 1 0.04
33 13 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (33 bp):
ATTATAAAAATTATAATATTTAGTTTTATTTAA
Found at i:5397309 original size:15 final size:13
Alignment explanation
Indices: 5397289--5397326 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
5397279 AAACTTAAAG
5397289 AAAATTAAAATTTGA
1 AAAATTAAAA-TT-A
5397304 AAAATTAAAATTA
1 AAAATTAAAATTA
5397317 AAAATTAAAA
1 AAAATTAAAA
5397327 ATTTTACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 11 0.48
14 2 0.09
15 10 0.43
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (13 bp):
AAAATTAAAATTA
Found at i:5397320 original size:7 final size:7
Alignment explanation
Indices: 5397289--5397329 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
5397279 AAACTTAAAG
5397289 AAAATTA
1 AAAATTA
*
5397296 AAATTTGA
1 AAAATT-A
5397304 AAAATT-
1 AAAATTA
5397310 AAAATTA
1 AAAATTA
5397317 AAAATTA
1 AAAATTA
5397324 AAAATT
1 AAAATT
5397330 TTACAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 6 0.20
7 18 0.60
8 6 0.20
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (7 bp):
AAAATTA
Found at i:5400589 original size:13 final size:14
Alignment explanation
Indices: 5400571--5400605 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
5400561 ATATGACTAT
5400571 ATAATAATAA-TAA
1 ATAATAATAATTAA
5400584 ATAATAATAATTAA
1 ATAATAATAATTAA
5400598 ATATATAA
1 ATA-ATAA
5400606 ACATGTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.50
14 6 0.30
15 4 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATAATAATTAA
Found at i:5402086 original size:3 final size:3
Alignment explanation
Indices: 5402080--5402147 Score: 86
Period size: 3 Copynumber: 23.0 Consensus size: 3
5402070 ATTTATTATT
* *
5402080 TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA AAA TAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
*
5402126 -AA T-A TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
5402148 AGTTGGGACA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 4 0.07
3 49 0.88
4 3 0.05
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:5403177 original size:30 final size:32
Alignment explanation
Indices: 5403141--5403202 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
5403131 GACCCAACCT
* *
5403141 GATATTGATCTG-A-CAAAAATCAACCGATCC
1 GATATTGATCCGAACCAAAAAACAACCGATCC
5403171 GATATTGATCCGAACCAAAAAACAACCGATCC
1 GATATTGATCCGAACCAAAAAACAACCGATCC
5403203 AATAATCACC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 11 0.39
31 1 0.04
32 16 0.57
ACGTcount: A:0.42, C:0.26, G:0.13, T:0.19
Consensus pattern (32 bp):
GATATTGATCCGAACCAAAAAACAACCGATCC
Found at i:5404762 original size:31 final size:31
Alignment explanation
Indices: 5404722--5404792 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
5404712 GAACATAATG
* *
5404722 TATGATCACTTTCGTTTTTATTTAATTAAGA
1 TATGGTCACTTTCGTTCTTATTTAATTAAGA
5404753 TATGGTCACTTTCGTTCTTATTTAATTAAGA
1 TATGGTCACTTTCGTTCTTATTTAATTAAGA
*
5404784 TATTGTCAC
1 TATGGTCAC
5404793 CACAGGTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.49
Consensus pattern (31 bp):
TATGGTCACTTTCGTTCTTATTTAATTAAGA
Found at i:5404887 original size:67 final size:67
Alignment explanation
Indices: 5404767--5404893 Score: 168
Period size: 67 Copynumber: 1.9 Consensus size: 67
5404757 GTCACTTTCG
* **
5404767 TTCTTATTTAATTAAGATATTGTCACCACAGGTTAACTGTTGTTAACAATTAATAGATTAAGTAA
1 TTCTTATTTAATTAAGATATGGTCACCACAGGTTAACTGTCATTAACAATTAATAGATTAAGTAA
5404832 CA
66 CA
* * *
5404834 TTCTTATTTAATTAAGATGTGGTCACCATAGGTTAGA-TGTCATTGAA-AGTTAATAGATTA
1 TTCTTATTTAATTAAGATATGGTCACCACAGGTTA-ACTGTCATT-AACAATTAATAGATTA
5404894 GGTGACGTGA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
67 49 0.94
68 3 0.06
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.39
Consensus pattern (67 bp):
TTCTTATTTAATTAAGATATGGTCACCACAGGTTAACTGTCATTAACAATTAATAGATTAAGTAA
CA
Found at i:5405104 original size:31 final size:30
Alignment explanation
Indices: 5405067--5405161 Score: 109
Period size: 31 Copynumber: 3.1 Consensus size: 30
5405057 TAAAAAAATA
* *
5405067 TAATATATGATTACTTTCGTTTTTATTTATT
1 TAATATATG-TCACTTTCGTTTTTATTTAAT
* * *
5405098 TTATATATGGCACTTTCGTTCTTATTTAAT
1 TAATATATGTCACTTTCGTTTTTATTTAAT
* *
5405128 TAAGATATGTCCACTTTTGTTTTTATTTAAT
1 TAATATATGT-CACTTTCGTTTTTATTTAAT
5405159 TAA
1 TAA
5405162 GATGTTGTCA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
30 24 0.45
31 29 0.55
ACGTcount: A:0.26, C:0.09, G:0.08, T:0.56
Consensus pattern (30 bp):
TAATATATGTCACTTTCGTTTTTATTTAAT
Found at i:5405115 original size:30 final size:31
Alignment explanation
Indices: 5405079--5405164 Score: 111
Period size: 30 Copynumber: 2.8 Consensus size: 31
5405069 ATATATGATT
* * * *
5405079 ACTTTCGTTTTTATTTATTTTATATATG-GC
1 ACTTTCGTTTTTATTTAATTAAGATATGTCC
*
5405109 ACTTTCGTTCTTATTTAATTAAGATATGTCC
1 ACTTTCGTTTTTATTTAATTAAGATATGTCC
*
5405140 ACTTTTGTTTTTATTTAATTAAGAT
1 ACTTTCGTTTTTATTTAATTAAGAT
5405165 GTTGTCACCA
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 24 0.50
31 24 0.50
ACGTcount: A:0.24, C:0.10, G:0.09, T:0.56
Consensus pattern (31 bp):
ACTTTCGTTTTTATTTAATTAAGATATGTCC
Found at i:5405609 original size:25 final size:25
Alignment explanation
Indices: 5405581--5405638 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
5405571 ATTTTATATA
5405581 TATTAACTTTAGGAAATAT-TTTTT
1 TATTAACTTTAGGAAATATATTTTT
**
5405605 GTATTAAC-TTATTAAATATATTTTT
1 -TATTAACTTTAGGAAATATATTTTT
5405630 TATTAACTT
1 TATTAACTT
5405639 AATTTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 16 0.55
25 13 0.45
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (25 bp):
TATTAACTTTAGGAAATATATTTTT
Found at i:5405662 original size:27 final size:25
Alignment explanation
Indices: 5405568--5405726 Score: 118
Period size: 27 Copynumber: 6.3 Consensus size: 25
5405558 TTAAATTCAT
* * *
5405568 AATATTTTATATATATTAACTTTAGGA
1 AATATTTTATTTTTATTAATTTTA--A
*
5405595 AATA-TTT-TTTGTATTAACTTATTAA
1 AATATTTTATTTTTATTAA-TT-TTAA
*
5405620 ATATATTTT-TTATTAACTTAATTTTAA
1 A-ATATTTTATT-TTTA-TTAATTTTAA
*
5405647 AATATTTTATTTTTA--AATTTAAA
1 AATATTTTATTTTTATTAATTTTAA
*
5405670 AATATTTTA--TTT-TTAATTTAAA
1 AATATTTTATTTTTATTAATTTTAA
5405692 AATATTTTATTTTTATTTTAATTTTAA
1 AATATTTTATTTTTA--TTAATTTTAA
5405719 AATATTTT
1 AATATTTT
5405727 TACTTTGGCC
Statistics
Matches: 110, Mismatches: 8, Indels: 28
0.75 0.05 0.19
Matches are distributed among these distances:
21 3 0.03
22 17 0.15
23 16 0.15
24 3 0.03
25 10 0.09
26 17 0.15
27 36 0.33
28 4 0.04
29 4 0.04
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (25 bp):
AATATTTTATTTTTATTAATTTTAA
Found at i:5405668 original size:28 final size:24
Alignment explanation
Indices: 5405594--5405726 Score: 98
Period size: 22 Copynumber: 5.4 Consensus size: 24
5405584 TAACTTTAGG
*
5405594 AAATATTTT-TTGTATTAACTTATTA
1 AAATATTTTATT-T-TTAATTTATTA
* *
5405619 AATATATTTT-TTATTAACTTAATTTTA
1 AA-ATATTTTATTTTTAA-TT--TATTA
5405646 AAATATTTTATTTTTAAATTTA--A
1 AAATATTTTATTTTT-AATTTATTA
5405669 AAATATTTTATTTTTAATTTA--A
1 AAATATTTTATTTTTAATTTATTA
*
5405691 AAATATTTTATTTTTATTTTAATTTTA
1 AAATATTTTATTTTTAATTT-A--TTA
5405718 AAATATTTT
1 AAATATTTT
5405727 TACTTTGGCC
Statistics
Matches: 91, Mismatches: 6, Indels: 20
0.78 0.05 0.17
Matches are distributed among these distances:
22 26 0.29
23 17 0.19
24 4 0.04
25 4 0.04
26 16 0.18
27 22 0.24
28 2 0.02
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (24 bp):
AAATATTTTATTTTTAATTTATTA
Found at i:5405711 original size:22 final size:22
Alignment explanation
Indices: 5405637--5405712 Score: 125
Period size: 22 Copynumber: 3.4 Consensus size: 22
5405627 TTTTATTAAC
*
5405637 TTAATTTTAAAATATTTTATTT
1 TTAATTTAAAAATATTTTATTT
5405659 TTAAATTTAAAAATATTTTATTT
1 TT-AATTTAAAAATATTTTATTT
5405682 TTAATTTAAAAATATTTTATTT
1 TTAATTTAAAAATATTTTATTT
*
5405704 TTATTTTAA
1 TTAATTTAA
5405713 TTTTAAAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
22 30 0.59
23 21 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTAATTTAAAAATATTTTATTT
Found at i:5405724 original size:22 final size:23
Alignment explanation
Indices: 5405637--5405728 Score: 98
Period size: 23 Copynumber: 3.9 Consensus size: 23
5405627 TTTTATTAAC
5405637 TTAATTTTAAAATA-TTTTATTT
1 TTAATTTTAAAATATTTTTATTT
*
5405659 TTAAATTTAAAA-ATATTTTATTT
1 TTAATTTTAAAATAT-TTTTATTT
* *
5405682 TTAATTTAAAAATATTTTATTTTTATT
1 TTAATTTTAAAATA--TT-TTTAT-TT
5405709 TTAATTTTAAAATATTTTTA
1 TTAATTTTAAAATATTTTTA
5405729 CTTTGGCCCT
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
21 1 0.02
22 11 0.19
23 18 0.32
24 4 0.07
25 3 0.05
26 5 0.09
27 15 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTAATTTTAAAATATTTTTATTT
Found at i:5406604 original size:3 final size:3
Alignment explanation
Indices: 5406591--5406642 Score: 81
Period size: 3 Copynumber: 18.0 Consensus size: 3
5406581 ATTTTTTCAT
*
5406591 TTA TT- TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5406637 TTA TTA
1 TTA TTA
5406643 CAAGCCCAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:5406617 original size:23 final size:23
Alignment explanation
Indices: 5406591--5406641 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
5406581 ATTTTTTCAT
*
5406591 TTATTTTATTATTATTATTATTA
1 TTATTTTATTATTATTATTAATA
*
5406614 TTATATTATTATTATTATTAATA
1 TTATTTTATTATTATTATTAATA
5406637 TTATT
1 TTATT
5406642 ACAAGCCCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TTATTTTATTATTATTATTAATA
Found at i:5408009 original size:6 final size:6
Alignment explanation
Indices: 5408000--5408804 Score: 1227
Period size: 6 Copynumber: 138.8 Consensus size: 6
5407990 CATTTTAGTC
5408000 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
5408048 ATATAA ATATAA ATATAA ATATAA ATAT-A A-ATAA ATATAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
5408094 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATAT-A ATAT-A
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
5408140 A-ATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATAT-A ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
5408186 ATA-AA ATATAA ATATAA ATATAA ATAT-A ATATAA ATATAA ATAT-A
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
*
5408231 ATATAA ATATAA ATATAA ATATAA AAATATA ATATAA ATATAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATA-A ATATAA ATATAA ATATAA
5408280 ATATAA A-ATAA ATATAA ATAT-A A-ATAA ATATAA ATATAA ATAAATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA AT--ATAA
5408327 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATAT-A A-ATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
5408373 ATATAA ATATAA ATATAA ATATAA ATATAA ATAATAA ATATAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA AT-ATAA ATATAA ATATAA
5408422 ATATAA ATATAA ATAT-A A-ATAA ATAT-A ATATAA ATATAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
*
5408467 ATATAA ATAT-A ATAT-A AGATAA ATATAA ATATAA ATA-AA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
5408512 ATAT-A ATATAA ATATAA ATAAATAA ATATAA ATA-AA ATATAA ATATAA
1 ATATAA ATATAA ATATAA AT--ATAA ATATAA ATATAA ATATAA ATATAA
*
5408560 ATATAATA AAATAA ATATAA ATATAA ATATAA ATATAA ATAT-A ATAT-A
1 ATAT-A-A ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
5408608 ATATAA ATAT-A ATAT-- ATATAA ATATAA ATAT-- ATATAA A-ATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
5408650 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATAT-A
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
5408697 ATATAA ATATAA ATAT-A A-ATAA ATATAA ATATAA ATATAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
5408743 ATAT-A ATAT-A A-ATAA ATATAA ATATAA ATAAATAA ATAT-A ATAT-A
1 ATATAA ATATAA ATATAA ATATAA ATATAA AT--ATAA ATATAA ATATAA
5408788 ATATAA ATATAA ATATA
1 ATATAA ATATAA ATATA
5408805 TTTGGTTAAA
Statistics
Matches: 751, Mismatches: 6, Indels: 84
0.89 0.01 0.10
Matches are distributed among these distances:
4 22 0.03
5 127 0.17
6 567 0.75
7 13 0.02
8 22 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAA
Found at i:5410657 original size:36 final size:36
Alignment explanation
Indices: 5410610--5410681 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
5410600 GAGCTCTGCA
5410610 CACAAAGATCCTGTTAGATTGATACCAAAAGTATTC
1 CACAAAGATCCTGTTAGATTGATACCAAAAGTATTC
5410646 CACAAAGATCCTGTTAGATTGATACCAAAAGTATTC
1 CACAAAGATCCTGTTAGATTGATACCAAAAGTATTC
5410682 AATGGTAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (36 bp):
CACAAAGATCCTGTTAGATTGATACCAAAAGTATTC
Found at i:5411278 original size:27 final size:27
Alignment explanation
Indices: 5411248--5411306 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
5411238 GAGTAACACC
*
5411248 TTTTTCATACATACATTTGCATTTTCA
1 TTTTTCATACATACATTTGCATTTGCA
* * **
5411275 TTTTACATCCATATTTTTGCATTTGCA
1 TTTTTCATACATACATTTGCATTTGCA
5411302 TTTTT
1 TTTTT
5411307 ATTTGCACCT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.22, C:0.17, G:0.05, T:0.56
Consensus pattern (27 bp):
TTTTTCATACATACATTTGCATTTGCA
Found at i:5413508 original size:11 final size:11
Alignment explanation
Indices: 5413488--5413537 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
5413478 CATTCATCAA
* *
5413488 AAAATAAAAAA
1 AAAAGAAAAAG
5413499 AAGAAGAAAAAG
1 AA-AAGAAAAAG
5413511 AAAAGAAAAAG
1 AAAAGAAAAAG
5413522 --AA-AAAAAG
1 AAAAGAAAAAG
5413530 AAAAGAAA
1 AAAAGAAA
5413538 TTGAATCAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
8 6 0.18
9 2 0.06
10 2 0.06
11 14 0.42
12 9 0.27
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:5413511 original size:6 final size:6
Alignment explanation
Indices: 5413487--5413537 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
5413477 TCATTCATCA
* *
5413487 AAAAAT AAAAA- AAAGAAG AAAAAG -AAAAG AAAAAG AAAAAA AGAAAAG
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A-AAAAG
5413535 AAA
1 AAA
5413538 TTGAATCAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 8 0.21
6 23 0.59
7 8 0.21
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:5413519 original size:19 final size:18
Alignment explanation
Indices: 5413486--5413537 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 18
5413476 CTCATTCATC
*
5413486 AAAAAATAAAA-AAAAGA
1 AAAAAAGAAAAGAAAAGA
5413503 AGAAAAAGAAAAGAAAAAGA
1 A-AAAAAGAAAAG-AAAAGA
5413523 AAAAAAGAAAAGAAA
1 AAAAAAGAAAAGAAA
5413538 TTGAATCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 1 0.03
18 12 0.39
19 11 0.35
20 7 0.23
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (18 bp):
AAAAAAGAAAAGAAAAGA
Found at i:5415212 original size:39 final size:39
Alignment explanation
Indices: 5415166--5415268 Score: 172
Period size: 39 Copynumber: 2.6 Consensus size: 39
5415156 CAGATCCATG
5415166 TGGGGCATTTTGAAGTCTCACATCAGTATGAAGAAACGT
1 TGGGGCATTTTGAAGTCTCACATCAGTATGAAGAAACGT
*
5415205 TGGGGCATTTTGAAGTCTCACACCAGTATGAAGAAACGT
1 TGGGGCATTTTGAAGTCTCACATCAGTATGAAGAAACGT
*
5415244 TGGGGAATTTTGAAAG-CTCACATCA
1 TGGGGCATTTTG-AAGTCTCACATCA
5415269 ACAAGAAGTA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
39 57 0.95
40 3 0.05
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (39 bp):
TGGGGCATTTTGAAGTCTCACATCAGTATGAAGAAACGT
Found at i:5415721 original size:54 final size:54
Alignment explanation
Indices: 5415638--5415952 Score: 386
Period size: 54 Copynumber: 5.8 Consensus size: 54
5415628 GAGAAATCTA
* *
5415638 GGCAAAAGCCACATGAAATGATGAGTGTGTTGTCAAATATTTTACGAACATATG
1 GGCAAAAGCCACATGAAAGGATGAATGTGTTGTCAAATATTTTACGAACATATG
5415692 GGCAAAAGCCACATGAAAGGATGAATGTGTTGTCAAATATTTTACGAACATATG
1 GGCAAAAGCCACATGAAAGGATGAATGTGTTGTCAAATATTTTACGAACATATG
* * * * *
5415746 AGCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATATG
1 GGCAAAAGCCACATGAAAGGATGAATGTGTTGTCAAATATTTTACGAACATATG
* * * *
5415800 GGCAGAAGCCACATGAAAGGATGAATGTGTTGTCAAATGA-TTTATGAATATCTG
1 GGCAAAAGCCACATGAAAGGATGAATGTGTTGTCAAAT-ATTTTACGAACATATG
* * * * * *
5415854 TGTAGAAA-CCACAGGGAATGATGAATGTGTTGTCAAA-ATGTTTACGAACATCTG
1 GGCA-AAAGCCACATGAAAGGATGAATGTGTTGTCAAATAT-TTTACGAACATATG
* * *
5415908 TGCAGAAA-CCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 GGCA-AAAGCCACATGAAAGGATGAATGTGTTGTCAAATATTTTAC
5415953 AAACCAGTGA
Statistics
Matches: 229, Mismatches: 27, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
52 1 0.00
54 225 0.98
55 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (54 bp):
GGCAAAAGCCACATGAAAGGATGAATGTGTTGTCAAATATTTTACGAACATATG
Found at i:5415832 original size:108 final size:108
Alignment explanation
Indices: 5415643--5415952 Score: 444
Period size: 108 Copynumber: 2.9 Consensus size: 108
5415633 ATCTAGGCAA
* * * *
5415643 AAGCCACATGAAATGATGAGTGTGTTGTCAAATATTTTACGAACATATGGGCAAAAGCCACATGA
1 AAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATATGGGCAGAAGCCACATGA
5415708 AAGGATGAATGTGTTGTCAAATATTTTACGAACATATGAGCAG
66 AAGGATGAATGTGTTGTCAAATATTTTACGAACATATGAGCAG
5415751 AAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATATGGGCAGAAGCCACATGA
1 AAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATATGGGCAGAAGCCACATGA
* * * * *
5415816 AAGGATGAATGTGTTGTCAAATGA-TTTATGAATATCTGTGTAG
66 AAGGATGAATGTGTTGTCAAAT-ATTTTACGAACATATGAGCAG
* * * * * *
5415859 AAACCACAGGGAATGATGAATGTGTTGTCAAAATG-TTTACGAACATCTGTGCAGAAACCACAAG
1 AAGCCACAGGAAATGATGAATGTGTTGTC-AAATGTTTTACGAACATATGGGCAGAAGCCACATG
*
5415923 AAAGGATGAATGTGTTGTCAAATGTTTTAC
65 AAAGGATGAATGTGTTGTCAAATATTTTAC
5415953 AAACCAGTGA
Statistics
Matches: 182, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
108 176 0.97
109 6 0.03
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (108 bp):
AAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATATGGGCAGAAGCCACATGA
AAGGATGAATGTGTTGTCAAATATTTTACGAACATATGAGCAG
Found at i:5415933 original size:162 final size:162
Alignment explanation
Indices: 5415638--5415952 Score: 438
Period size: 162 Copynumber: 1.9 Consensus size: 162
5415628 GAGAAATCTA
* *
5415638 GGCAAAAGCCACATGAAATGATGAGTGTGTTGTCAAATATTTTACGAACATATGGGCAAAAGCCA
1 GGCAAAAGCCACATGAAAGGATGAATGTGTTGTCAAATATTTTACGAACATATGGGCAAAAGCCA
* * * *
5415703 CATGAAAGGATGAATGTGTTGTCAAATATTTTACGAACATATGAGCAGAAGCCACAGGAAATGAT
66 CAGGAAAGGATGAATGTGTTGTCAAATATTTTACGAACATATGAGCAGAAACCACAAGAAAGGAT
5415768 GAATGTGTTGTCAAATGTTTTACGAACATATG
131 GAATGTGTTGTCAAATGTTTTACGAACATATG
* * * * * *
5415800 GGCAGAAGCCACATGAAAGGATGAATGTGTTGTCAAATGA-TTTATGAATATCTGTGTAGAAA-C
1 GGCAAAAGCCACATGAAAGGATGAATGTGTTGTCAAAT-ATTTTACGAACATATGGGCA-AAAGC
* * * *
5415863 CACAGGGAATGATGAATGTGTTGTCAAA-ATGTTTACGAACATCTGTGCAGAAACCACAAGAAAG
64 CACAGGAAAGGATGAATGTGTTGTCAAATAT-TTTACGAACATATGAGCAGAAACCACAAGAAAG
5415927 GATGAATGTGTTGTCAAATGTTTTAC
128 GATGAATGTGTTGTCAAATGTTTTAC
5415953 AAACCAGTGA
Statistics
Matches: 134, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
161 2 0.01
162 128 0.96
163 4 0.03
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (162 bp):
GGCAAAAGCCACATGAAAGGATGAATGTGTTGTCAAATATTTTACGAACATATGGGCAAAAGCCA
CAGGAAAGGATGAATGTGTTGTCAAATATTTTACGAACATATGAGCAGAAACCACAAGAAAGGAT
GAATGTGTTGTCAAATGTTTTACGAACATATG
Found at i:5416347 original size:22 final size:22
Alignment explanation
Indices: 5416319--5416399 Score: 83
Period size: 22 Copynumber: 3.7 Consensus size: 22
5416309 CTACATCTAT
*
5416319 ATTCTTCAAAGATTATAGATTC
1 ATTCTTCAAAGATGATAGATTC
* *
5416341 ATTCTTCAAAAAGGATAGATTC
1 ATTCTTCAAAGATGATAGATTC
** *
5416363 CCTCTTCAAAGATGATATATTC
1 ATTCTTCAAAGATGATAGATTC
*
5416385 -TCTTTTCAAAGATGA
1 AT-TCTTCAAAGATGA
5416400 AAGCTCTATT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (22 bp):
ATTCTTCAAAGATGATAGATTC
Found at i:5417018 original size:123 final size:121
Alignment explanation
Indices: 5416797--5417484 Score: 865
Period size: 123 Copynumber: 5.6 Consensus size: 121
5416787 GATGGATCAA
* * *
5416797 CATTTTCAGATAGAGTTCATAATAAGAAGAACTCATCTGAAGAGGTAGAAGAAGTTCATAGTCTG
1 CATTTCCAGATAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTCTG
*
5416862 AAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAGTATATC
66 AAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCA--AAATC
* *
5416920 CATTTCCAGATAAAGTTCGTAATAAGAAGAACTCATATGAAGAGGAAGAAGAAGTTCATAGTCTG
1 CATTTCCAGATAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTCTG
* * * * * * * *
5416985 AAGAACATGTTCAACCTTTCGCTTGATTTTATCGCAGAAGGAGATAAAACAACATC
66 AAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAAAATC
* * * * * *
5417041 AATATTTACAGACAAAGTTTGTAATAAGAAGAATTCATCTGAAGAGGAAGAAGAAGTTCATAGTC
1 --CATTTCCAGATAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTC
* * * *
5417106 TGAAGAACTTATTCAACCTTTTGCTTAACTTTATCGTAGAAGGAGATAGAGCAACATC
64 TGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAAAATC
* * * *
5417164 AACATTTTCAGATAGAGTTCATAATAAGAATAACTCATCTGAAGAGGAAGAAAAAGTTCATAGTC
1 --CATTTCCAGATAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTC
* * *
5417229 TGAAGAACTTATTCAATCTTTTGATTGACTCTATCGCAGAAGGAGATAGAGCAATAAAGC
64 TGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGC-A-AAATC
* * *
5417289 CATTTCCAAGATAGAGTTCGTAATAAAAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAATCT
1 CATTTCC-AGATAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTCT
** * * * *
5417354 GAAGAACTTATTCAATATTTTGATTGACTCCATCGCAGAAGGAGGTAGAGCAGCAAAGC
65 GAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCA--AAATC
* * * *
5417413 CATTT-TATATAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAATAAGTTCATAATCTG
1 CATTTCCAGATAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTCTG
*
5417477 AATAACTT
66 AAGAACTT
5417485 GTTTAACTTT
Statistics
Matches: 499, Mismatches: 60, Indels: 13
0.87 0.10 0.02
Matches are distributed among these distances:
121 4 0.01
122 61 0.12
123 321 0.64
124 110 0.22
125 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (121 bp):
CATTTCCAGATAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTCTG
AAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAAAATC
Found at i:5417471 original size:369 final size:368
Alignment explanation
Indices: 5416792--5417484 Score: 1014
Period size: 369 Copynumber: 1.9 Consensus size: 368
5416782 CACTCGATGG
* *
5416792 ATCAACATTTTCAGATAGAGTTCATAATAAGAAGAACTCATCTGAAGAGGTAGAAGAAGTTCATA
1 ATCAACATTTTCAGATAGAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATA
* * * *
5416857 GTCTGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAGTATATCCA
66 GTCTGAAGAACTTATTCAACCTTTTGATTGACTCTATCGCAGAAGGAGATAGAGCAATAAAGCCA
* * *
5416922 TTTCCAGATAAAGTTCGTAATAAGAAGAACTCATATGAAGAGGAAGAAGAAGTTCATAGTCTGAA
131 TTTCCAGATAAAGTTCGTAATAAAAAGAACTCATATGAAGAGAAAGAAGAAGTTCATAATCTGAA
* * * * ** *
5416987 GAACATGTTCAACCTTTCGCTTGATTTTATCGCAGAAGGAGATAAAACAACATCAATATTTACAG
196 GAACATATTCAACATTTCGATTGACTCCATCGCAGAAGGAGATAAAACAACAGCAATATTTA-AG
* * *
5417052 ACAAAGTTTGTAATAAGAAGAATTCATCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTA
260 ACAAAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACTTA
5417117 TTCAACCTTTTGCTTAACTTTATCGTAGAAGGAGATAGAGCAAC
325 TTCAACCTTTTGCTTAACTTTATCGTAGAAGGAGATAGAGCAAC
*
5417161 ATCAACATTTTCAGATAGAGTTCATAATAAGAATAACTCATCTGAAGAGGAAGAAAAAGTTCATA
1 ATCAACATTTTCAGATAGAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATA
*
5417226 GTCTGAAGAACTTATTCAATCTTTTGATTGACTCTATCGCAGAAGGAGATAGAGCAATAAAGCCA
66 GTCTGAAGAACTTATTCAACCTTTTGATTGACTCTATCGCAGAAGGAGATAGAGCAATAAAGCCA
* *
5417291 TTTCCAAGATAGAGTTCGTAATAAAAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAATCTGA
131 TTTCC-AGATAAAGTTCGTAATAAAAAGAACTCATATGAAGAGAAAGAAGAAGTTCATAATCTGA
* * * * * *
5417356 AGAACTTATTCAATATTTTGATTGACTCCATCGCAGAAGGAGGTAGAGCAGCAA-AGCCAT-TTT
195 AGAACATATTCAACATTTCGATTGACTCCATCGCAGAAGGAGATA-A--AACAACAGCAATATTT
* * * * *
5417419 -ATATAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAATAAGTTCATAATCTGAATAAC
257 AAGACAAAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAAC
5417483 TT
322 TT
5417485 GTTTAACTTT
Statistics
Matches: 286, Mismatches: 34, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
369 185 0.65
370 89 0.31
371 4 0.01
372 4 0.01
373 4 0.01
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (368 bp):
ATCAACATTTTCAGATAGAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATA
GTCTGAAGAACTTATTCAACCTTTTGATTGACTCTATCGCAGAAGGAGATAGAGCAATAAAGCCA
TTTCCAGATAAAGTTCGTAATAAAAAGAACTCATATGAAGAGAAAGAAGAAGTTCATAATCTGAA
GAACATATTCAACATTTCGATTGACTCCATCGCAGAAGGAGATAAAACAACAGCAATATTTAAGA
CAAAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACTTAT
TCAACCTTTTGCTTAACTTTATCGTAGAAGGAGATAGAGCAAC
Found at i:5417683 original size:3 final size:3
Alignment explanation
Indices: 5417670--5417734 Score: 93
Period size: 3 Copynumber: 23.0 Consensus size: 3
5417660 ATTTTTTCAT
5417670 TTA TT- TTA TTA TTA TTA TTA TTA TT- TTA TTA TTA TTA -TA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
5417714 TTA TTA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
5417735 CAGGTCCAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
2 8 0.14
3 48 0.86
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:5417684 original size:11 final size:11
Alignment explanation
Indices: 5417670--5417725 Score: 73
Period size: 11 Copynumber: 5.3 Consensus size: 11
5417660 ATTTTTTCAT
5417670 TTATTTTATTA
1 TTATTTTATTA
5417681 TTA--TTATTA
1 TTATTTTATTA
5417690 TTATTTTATTA
1 TTATTTTATTA
*
5417701 TTATTATATTA
1 TTATTTTATTA
5417712 -TATTATTATTA
1 TTATT-TTATTA
5417723 TTA
1 TTA
5417726 ATATTATTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
9 9 0.23
10 4 0.10
11 24 0.62
12 2 0.05
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:5417947 original size:55 final size:55
Alignment explanation
Indices: 5417881--5417991 Score: 168
Period size: 55 Copynumber: 2.0 Consensus size: 55
5417871 ACCCTAAACC
* * *
5417881 CAACTAAGGTTTCATCATCTCAGCATCTAGCCGCCAACATCATCAGTCGTTGGAT
1 CAACTAAGGTTTCATCATCTCAGCATCCAGCCGCCAACATCATCAGCCATTGGAT
* * *
5417936 CAACTAGGGTTTCATCATCTCAGCATCCAGCTGCCAATATCATCAGCCATTGGAT
1 CAACTAAGGTTTCATCATCTCAGCATCCAGCCGCCAACATCATCAGCCATTGGAT
5417991 C
1 C
5417992 TGGCAAGATC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (55 bp):
CAACTAAGGTTTCATCATCTCAGCATCCAGCCGCCAACATCATCAGCCATTGGAT
Found at i:5419104 original size:23 final size:22
Alignment explanation
Indices: 5419050--5419105 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
5419040 GAATCATTGA
5419050 TTTTAATTTTTTTACCATAAGT
1 TTTTAATTTTTTTACCATAAGT
* *
5419072 TTTCTTATTTTTTTACTCCTATAG-
1 TTT-TAATTTTTTTAC-CATA-AGT
5419096 TTTTAATTTT
1 TTTTAATTTT
5419106 CTCTATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 3 0.11
23 17 0.61
24 6 0.21
25 2 0.07
ACGTcount: A:0.21, C:0.11, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTTAATTTTTTTACCATAAGT
Found at i:5421346 original size:70 final size:73
Alignment explanation
Indices: 5421231--5421381 Score: 263
Period size: 70 Copynumber: 2.1 Consensus size: 73
5421221 CAAAAGAAAT
*
5421231 TGTTGACGTAGTAGTGAAGTGAAGGTGCTACCTAGGCAGCTGTGTCCATCTA-TTCTA-CGAGTT
1 TGTTGATGTAGTAG-GAAGTGAAGGTGCTACCTAGGCAGCTGTGTCCATCTATTTCTACCGAGTT
5421294 AATTTCAGA
65 AATTTCAGA
5421303 TGTTGATGTAGTA-GAAGTGAAGGTGCTACCTAGGCAGCTGTGTCCATCTATTTCTACCGAGTTA
1 TGTTGATGTAGTAGGAAGTGAAGGTGCTACCTAGGCAGCTGTGTCCATCTATTTCTACCGAGTTA
5421367 ATTTCAGA
66 ATTTCAGA
5421375 TGTTGAT
1 TGTTGAT
5421382 CGTTGTTGAC
Statistics
Matches: 76, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
70 37 0.49
71 5 0.07
72 34 0.45
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.34
Consensus pattern (73 bp):
TGTTGATGTAGTAGGAAGTGAAGGTGCTACCTAGGCAGCTGTGTCCATCTATTTCTACCGAGTTA
ATTTCAGA
Found at i:5425825 original size:113 final size:112
Alignment explanation
Indices: 5425436--5425899 Score: 786
Period size: 113 Copynumber: 4.1 Consensus size: 112
5425426 TCGGTTTGTA
* * *
5425436 TCGATACTTTATAAAAATATATTGATTCATAACAATATAACAGGTAAAAAAAATGACAAAAACGG
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGAC-AAAACGG
* *
5425501 TCTATAAATGACAAAACAGGTAAAGCGCTACTGAATATATTGAAAGTG
65 TCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
5425549 TCGATACTTTATAAAAATGTA-CGATCCATAACAATATAACAGGTAAAAAAAATGACAAAACGGT
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAACGGT
5425613 CTATAAATGACCAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
66 CTATAAATGA-CAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
5425661 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAACCG
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGAC-AAAA-CG
*
5425726 ATCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
64 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
5425775 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAACCGG
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAA-CGG
* * *
5425840 TCTATAAATGACAAAACAGGTAAAGCACTACCGGATATGTTGATAGTG
65 TCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
*
5425888 TCGATATTTTAT
1 TCGATACTTTAT
5425900 TATAAGTATC
Statistics
Matches: 336, Mismatches: 11, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
111 18 0.05
112 89 0.26
113 118 0.35
114 98 0.29
115 13 0.04
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (112 bp):
TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAACGGT
CTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
Found at i:5426102 original size:179 final size:180
Alignment explanation
Indices: 5425769--5426213 Score: 698
Period size: 179 Copynumber: 2.5 Consensus size: 180
5425759 GGATATATTG
*
5425769 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAATATGACAA
** * *
5425834 AACCGGTCTATAAATGACAAAACAGGTAAAGCACTACCGGATATGTTGATAGTGTCGATATTTTA
65 AACCGGTCTCGAAATGAC--AACAGGTAAAGCACTACCAGATATGTTGAAAGTGTCGATATTTTA
* * ***
5425899 TTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCTTTAAT
128 TTATAAGTATCAACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
*
5425952 AAAGTGTCGATACTTTATAAAACTGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
*
5426017 ACCGGTCTCGAAATGACAAC-GGTAAAG-AGCTACCATATATGTTGAAAGTGTCGATATTTTATT
66 ACCGGTCTCGAAATGACAACAGGTAAAGCA-CTACCAGATATGTTGAAAGTGTCGATATTTTATT
5426080 ATAAGTATCAACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
130 ATAAGTATCAACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
*
5426131 AAA-TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* *
5426195 ATCGCTCTCGAAATGACAA
66 ACCGGTCTCGAAATGACAA
5426214 AACCGATAGT
Statistics
Matches: 245, Mismatches: 16, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
178 77 0.31
179 87 0.36
180 3 0.01
182 28 0.11
183 50 0.20
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.28
Consensus pattern (180 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCGGTCTCGAAATGACAACAGGTAAAGCACTACCAGATATGTTGAAAGTGTCGATATTTTATTA
TAAGTATCAACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
Found at i:5426701 original size:23 final size:23
Alignment explanation
Indices: 5426655--5426702 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
5426645 AAATAGGTCA
* * *
5426655 ATATAAGCGTTACCTATTACATT
1 ATATAAGCGCTACATAATACATT
*
5426678 ATATAAGCGCTACATAATATATT
1 ATATAAGCGCTACATAATACATT
5426701 AT
1 AT
5426703 TGTACTTGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.38
Consensus pattern (23 bp):
ATATAAGCGCTACATAATACATT
Found at i:5429029 original size:3 final size:3
Alignment explanation
Indices: 5429021--5429078 Score: 64
Period size: 3 Copynumber: 19.3 Consensus size: 3
5429011 TCGTCCCGAC
* ** *
5429021 ATT ATT ATT TTT ATT ATT ATT ATT ATT ACC ATT ATT ACT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5429069 ACTT -TT ATT A
1 A-TT ATT ATT A
5429079 ATTTGTGCAT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 2 0.04
3 41 0.91
4 2 0.04
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:5430710 original size:62 final size:58
Alignment explanation
Indices: 5430629--5430763 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 58
5430619 ATTAAAAATG
* * * *
5430629 TTTATTTTAGTCACTTTTGCATTTTATTTTGTTTTAATTTTTGACATGATGATTTGTTTGTT-
1 TTTATTTTAGTC-CTTTTGCATGTT-GTTT-TTTCAATTTTTG-CATGATGATTT-TATGTTA
* *
5430691 TTTATTTTAGTCCTATTTGCATGTTGTTTTTTCAATTTTTGCATGTTGCTTTTATGTTA
1 TTTATTTTAGTCCT-TTTGCATGTTGTTTTTTCAATTTTTGCATGATGATTTTATGTTA
5430750 TTTCATTTTAGTCC
1 TTT-ATTTTAGTCC
5430764 CTGATTAGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
58 5 0.08
59 12 0.19
60 21 0.33
61 5 0.08
62 21 0.33
ACGTcount: A:0.16, C:0.10, G:0.13, T:0.61
Consensus pattern (58 bp):
TTTATTTTAGTCCTTTTGCATGTTGTTTTTTCAATTTTTGCATGATGATTTTATGTTA
Found at i:5431650 original size:133 final size:132
Alignment explanation
Indices: 5431210--5431684 Score: 785
Period size: 132 Copynumber: 3.6 Consensus size: 132
5431200 TTAATACATT
* * *
5431210 TTCATTTCGGTTGGAGTAAT-AATGATTGCTTAAAGGCATGAGAGGTCA-TTATTCTCGATTGGA
1 TTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGA
** * * *
5431273 AATAATTAGATATTATAATTTTCTCTCGAATCAATATTGA-ATTTTAAGACTAAATAGTGATATC
66 AATAATTAGATATTATGGTTTTCTCTCGAATCAACATTGAGTTTTTAAGACAAAATAGTGATATC
5431337 TC
131 TC
* *
5431339 TTCGTTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCAATTGGA
1 TTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGA
* *
5431404 AATAATTATATATTATGGTTTTCTCTCGAATCAACATTGAGTTTTTAAGACAAAATATTGATATC
66 AATAATTAGATATTATGGTTTTCTCTCGAATCAACATTGAGTTTTTAAGACAAAATAGTGATATC
5431469 TC
131 TC
*
5431471 TTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGAATGAGAGGTCATTTATTCTCGATTGGA
1 TTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGA
* *
5431536 ATTAATTATATATTATGGTTTTCTCTCGAATCAACATTGAGTTTTTTAAGACAAAATAGTGATAT
66 AATAATTAGATATTATGGTTTTCTCTCGAATCAACATTGAG-TTTTTAAGACAAAATAGTGATAT
5431601 CTC
130 CTC
5431604 TTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGA
1 TTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGA
5431669 AATAATTAGATATTAT
66 AATAATTAGATATTAT
5431685 TATTTTCTTT
Statistics
Matches: 322, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
129 18 0.06
130 26 0.08
131 50 0.16
132 125 0.39
133 103 0.32
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.39
Consensus pattern (132 bp):
TTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGA
AATAATTAGATATTATGGTTTTCTCTCGAATCAACATTGAGTTTTTAAGACAAAATAGTGATATC
TC
Found at i:5444060 original size:38 final size:37
Alignment explanation
Indices: 5444002--5444074 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
5443992 CAACCCGATA
*
5444002 AATATTAAAAATAATTATTTATATATATATATATATAT
1 AATATTAAAAAT-ATTATTTAAATATATATATATATAT
5444040 AATATTAATAAAT-TTAATTTAAATATATATATATA
1 AATATTAA-AAATATT-ATTTAAATATATATATATA
5444075 CCCGGCCCGA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 2 0.06
38 26 0.81
39 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (37 bp):
AATATTAAAAATATTATTTAAATATATATATATATAT
Found at i:5444136 original size:12 final size:12
Alignment explanation
Indices: 5444072--5444137 Score: 80
Period size: 12 Copynumber: 5.6 Consensus size: 12
5444062 ATATATATAT
*
5444072 ATACCCGGCCCG
1 ATACCCGGCCCA
*
5444084 ATTCCCGGCCCA
1 ATACCCGGCCCA
*
5444096 ATA-CCGACCCA
1 ATACCCGGCCCA
* *
5444107 ATACTCGACCCA
1 ATACCCGGCCCA
5444119 ATACCCGGCCCA
1 ATACCCGGCCCA
5444131 ATACCCG
1 ATACCCG
5444138 TTTAAATAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
11 10 0.22
12 36 0.78
ACGTcount: A:0.26, C:0.47, G:0.15, T:0.12
Consensus pattern (12 bp):
ATACCCGGCCCA
Found at i:5453898 original size:17 final size:18
Alignment explanation
Indices: 5453878--5453919 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
5453868 TTGACCGTTG
*
5453878 ACTTTGACTAAAAGTTA-
1 ACTTTGACTAAAAGTCAT
**
5453895 ACTTTTTCTAAAAGTCAT
1 ACTTTGACTAAAAGTCAT
5453913 ACTTTGA
1 ACTTTGA
5453920 TTTTTTTTTC
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (18 bp):
ACTTTGACTAAAAGTCAT
Found at i:5457305 original size:18 final size:19
Alignment explanation
Indices: 5457282--5457324 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
5457272 CAGTAATCCT
*
5457282 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGAAATCTTAC
5457300 ATTCCCACTGGAAATCTTAC
1 ATT-CCACTGGAAATCTTAC
5457320 ATTCC
1 ATTCC
5457325 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.26, C:0.30, G:0.09, T:0.35
Consensus pattern (19 bp):
ATTCCACTGGAAATCTTAC
Found at i:5457315 original size:20 final size:20
Alignment explanation
Indices: 5457287--5457324 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5457277 ATCCTATTCC
*
5457287 CTGGTAATCTTACATTCCCA
1 CTGGAAATCTTACATTCCCA
5457307 CTGGAAATCTTACATTCC
1 CTGGAAATCTTACATTCC
5457325 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (20 bp):
CTGGAAATCTTACATTCCCA
Found at i:5457852 original size:2 final size:2
Alignment explanation
Indices: 5457845--5457896 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
5457835 CTTTAAACTC
5457845 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
5457887 AT AT AT AT AT
1 AT AT AT AT AT
5457897 CATCAAACCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5458456 original size:130 final size:125
Alignment explanation
Indices: 5458195--5458457 Score: 278
Period size: 130 Copynumber: 2.1 Consensus size: 125
5458185 TTAAGTTCTA
* * * ** * *
5458195 ATAGGTATGTATGTCATCAAAGCAGCATCCATTTTTAACATCAAAACTAAGTCACTGAAATTAAC
1 ATAGGTATGTATGTCAACAAAACAGCATCCAATAATAACATCAAAACTAACTCACTGAAATCAAC
* * ** ***
5458260 TTGTTTAGTCCTAATTCAACACACTACAAAATTTGGATGCTACACCCTTTTTGAACTCTG
66 TTGTTTAATCCTAATTCAACAAACTACAAAATTTGGATGCTACACCCACTGCAAACTCTG
* *
5458320 AGAGGTATGTATGTCAACAAAACAAGCATCCAATAATAACATCAAAAGC-AACTCATTGAAATCA
1 ATAGGTATGTATGTCAACAAAAC-AGCATCCAATAATAACATCAAAA-CTAACTCACTGAAATCA
* * *
5458384 ACTTGTTATATAATCCTAATTGCAACATAAC-GCATAATTTGGATGTTACACCCACTGCAAACTC
64 ACTTG-T-T-TAATCCTAATT-CAACA-AACTACAAAATTTGGATGCTACACCCACTGCAAACTC
5458448 TG
124 TG
5458450 ATAGGTAT
1 ATAGGTAT
5458458 ACATACTTGT
Statistics
Matches: 111, Mismatches: 20, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
125 20 0.18
126 37 0.33
127 2 0.02
128 1 0.01
129 10 0.09
130 39 0.35
131 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.30
Consensus pattern (125 bp):
ATAGGTATGTATGTCAACAAAACAGCATCCAATAATAACATCAAAACTAACTCACTGAAATCAAC
TTGTTTAATCCTAATTCAACAAACTACAAAATTTGGATGCTACACCCACTGCAAACTCTG
Found at i:5466090 original size:31 final size:33
Alignment explanation
Indices: 5466028--5466091 Score: 80
Period size: 31 Copynumber: 2.0 Consensus size: 33
5466018 TGAGCAGCTT
* *
5466028 GAAAATATAATATATTAAGATTTTATTTTTTTA
1 GAAAATATAATATATTAAAATTTTATATTTTTA
5466061 GAAAATA-AAT-TATTAATAATTTTA-ATTTTTA
1 GAAAATATAATATATTAA-AATTTTATATTTTTA
5466092 TGTATTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 12 0.43
32 9 0.32
33 7 0.25
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (33 bp):
GAAAATATAATATATTAAAATTTTATATTTTTA
Found at i:5466090 original size:32 final size:33
Alignment explanation
Indices: 5466028--5466090 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
5466018 TGAGCAGCTT
* *
5466028 GAAAATATAATATATTAAGATTTTATTTTTTTA
1 GAAAATATAATATATTAAAATTTTAATTTTTTA
5466061 GAAAATA-AAT-TATTAATAATTTTAATTTTT
1 GAAAATATAATATATTAA-AATTTTAATTTTT
5466091 ATGTATTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 6 0.22
32 14 0.52
33 7 0.26
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (33 bp):
GAAAATATAATATATTAAAATTTTAATTTTTTA
Found at i:5477688 original size:29 final size:29
Alignment explanation
Indices: 5477651--5477762 Score: 107
Period size: 29 Copynumber: 3.8 Consensus size: 29
5477641 TAGTTTAATA
*
5477651 AAAAAAAGAATAAAATATATTTTTAAGTT
1 AAAATAAGAATAAAATATATTTTTAAGTT
* * *
5477680 AAAATAAGAATAAAATATACTCTCTAAGTG
1 AAAATAAGAATAAAATATA-TTTTTAAGTT
* * * *
5477710 AAGATAAGATTAAAACATATATTCTTATGTT
1 AAAATAAGAAT-AAA-ATATATTTTTAAGTT
* *
5477741 CAAATAAAAATAAAATATATTT
1 AAAATAAGAATAAAATATATTT
5477763 CCAGTCGTTC
Statistics
Matches: 64, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
29 25 0.39
30 19 0.30
31 15 0.23
32 5 0.08
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.33
Consensus pattern (29 bp):
AAAATAAGAATAAAATATATTTTTAAGTT
Found at i:5478548 original size:30 final size:31
Alignment explanation
Indices: 5478503--5478581 Score: 106
Period size: 30 Copynumber: 2.6 Consensus size: 31
5478493 TAATGCAAAA
* * * *
5478503 AATAAAAGACATTTTTAAAATTTAAGATAAT
1 AATAAAATAAATTTTTAAAATTTAAAATAAG
*
5478534 AAT-AAATATATTTTTAAAATTTAAAATAAG
1 AATAAAATAAATTTTTAAAATTTAAAATAAG
5478564 AATAAAATAAATTTTTAA
1 AATAAAATAAATTTTTAA
5478582 GTGAGGATGA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 26 0.62
31 16 0.38
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (31 bp):
AATAAAATAAATTTTTAAAATTTAAAATAAG
Found at i:5478666 original size:13 final size:13
Alignment explanation
Indices: 5478650--5478677 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5478640 ATTTTAAGTT
5478650 AATATATTTTTAA
1 AATATATTTTTAA
5478663 AATATATTTTTAA
1 AATATATTTTTAA
5478676 AA
1 AA
5478678 ATTAAGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AATATATTTTTAA
Found at i:5478698 original size:31 final size:31
Alignment explanation
Indices: 5478469--5478823 Score: 139
Period size: 29 Copynumber: 11.7 Consensus size: 31
5478459 TTTCTATCAA
5478469 AAAAATAAAATATA--TTTAATAAGTTAATGCA-
1 AAAAATAAAATATATTTTTAA-AAGTTAA-G-AT
* * *
5478500 AAAAATAAAAGACATTTTTAAAATTTAAGAT
1 AAAAATAAAATATATTTTTAAAAGTTAAGAT
* * *
5478531 AATAAT-AAATATATTTTTAAAATTTAAAAT
1 AAAAATAAAATATATTTTTAAAAGTTAAGAT
* * * *
5478561 AAGAATAAAATAAATTTTT--AAGTGAGGAT
1 AAAAATAAAATATATTTTTAAAAGTTAAGAT
* * * *
5478590 GAGAATAAAATATATATTTATATTAAA-ATAATAAT
1 AAAAATAAAATATAT-TTT-TA--AAAGTTAA-GAT
* *
5478625 AAAATATTTAAATATA-TTTT--AAGTTAATAT
1 AAAA-A-TAAAATATATTTTTAAAAGTTAAGAT
**** *
5478655 ATTTTTAAAATATATTTTTAAAAATTAAGAT
1 AAAAATAAAATATATTTTTAAAAGTTAAGAT
* *
5478686 AAAAATAAAATATACTTTT--AAGTGAAGAT
1 AAAAATAAAATATATTTTTAAAAGTTAAGAT
* * *
5478715 AAAGATAAAATATATATTTT--TACTCT-A-AT
1 AAAAATAAAATATAT-TTTTAAAAGT-TAAGAT
*
5478744 -AAAATAAAAT-T-TATTTAATAAGTT-A-AT
1 AAAAATAAAATATATTTTTAA-AAGTTAAGAT
5478771 ACAAAATAAAATATA--TTTAATAAGTTAA-A-
1 A-AAAATAAAATATATTTTTAA-AAGTTAAGAT
5478800 AAGAATATAAAATATATTTTTAAA
1 AA-AA-ATAAAATATATTTTTAAA
5478824 TTTAATATAT
Statistics
Matches: 246, Mismatches: 47, Indels: 62
0.69 0.13 0.17
Matches are distributed among these distances:
25 3 0.01
26 1 0.00
27 5 0.02
28 20 0.08
29 70 0.28
30 55 0.22
31 56 0.23
32 11 0.04
33 5 0.02
34 2 0.01
35 9 0.04
36 1 0.00
37 8 0.03
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.38
Consensus pattern (31 bp):
AAAAATAAAATATATTTTTAAAAGTTAAGAT
Found at i:5479218 original size:42 final size:45
Alignment explanation
Indices: 5479171--5479275 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 45
5479161 GATAATTTTA
*
5479171 ATAATATAAAATTATATATTTTATTGTT-ATAAT-TAT-AT-TATT
1 ATAATATAAAATTATATATTTTATT-TTAATAATATATGATAAATT
* *
5479213 ATAATATGTAAATTATA-CTTTTATTTTAATAATATATGATAAATT
1 ATAATAT-AAAATTATATATTTTATTTTAATAATATATGATAAATT
*
5479258 ATTA-ATAAAATTA-ATATT
1 ATAATATAAAATTATATATT
5479276 ATTTATTAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
41 2 0.04
42 20 0.39
43 19 0.37
44 4 0.08
45 6 0.12
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (45 bp):
ATAATATAAAATTATATATTTTATTTTAATAATATATGATAAATT
Found at i:5479564 original size:35 final size:32
Alignment explanation
Indices: 5479497--5479564 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 32
5479487 ATTAATTATT
*
5479497 AAATTATATTTATTGATAATTTTAATAATATA
1 AAATTATATTTATTGATAATTATAATAATATA
* *
5479529 AAATTATATTTTATTGTTATAATTATATTAGTATA
1 AAATTATA-TTTATTG--ATAATTATAATAATATA
5479564 A
1 A
5479565 TATGTAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 8 0.27
33 7 0.23
35 15 0.50
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (32 bp):
AAATTATATTTATTGATAATTATAATAATATA
Found at i:5479736 original size:17 final size:17
Alignment explanation
Indices: 5479714--5479775 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
5479704 TTATTTTTAA
5479714 TATTTTAATAATATTAT
1 TATTTTAATAATATTAT
*
5479731 TATTTTAATAAATAATTAA
1 TATTTTAAT-AAT-ATTAT
*
5479750 TATAATTAATAATA-TAT
1 TAT-TTTAATAATATTAT
*
5479767 TATTCTAAT
1 TATTTTAAT
5479776 TTTAATAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
16 4 0.11
17 14 0.38
18 4 0.11
19 10 0.27
20 5 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTTTAATAATATTAT
Found at i:5479750 original size:25 final size:25
Alignment explanation
Indices: 5479682--5479794 Score: 66
Period size: 25 Copynumber: 4.8 Consensus size: 25
5479672 ATATATACTC
*
5479682 TTTAA-AACATAATATAATATTCTTATT
1 TTTAATAA-ATAAT-TAATATTATTA-T
**
5479709 TTTAATATTTTAA-TAATATTATTAT
1 TTTAATA-AATAATTAATATTATTAT
5479734 TTTAATAAATAATTAATA-TA--A-
1 TTTAATAAATAATTAATATTATTAT
* * *
5479755 -TTAAT-AAT-A-TATTATTCTAAT
1 TTTAATAAATAATTAATATTATTAT
5479776 TTTAATAAATAATTAATAT
1 TTTAATAAATAATTAATAT
5479795 ATTTAAAATA
Statistics
Matches: 67, Mismatches: 8, Indels: 24
0.68 0.08 0.24
Matches are distributed among these distances:
17 4 0.06
18 2 0.03
19 3 0.04
20 6 0.09
22 6 0.09
23 3 0.04
24 6 0.09
25 18 0.27
26 10 0.15
27 5 0.07
28 4 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTAATAAATAATTAATATTATTAT
Found at i:5479760 original size:20 final size:20
Alignment explanation
Indices: 5479735--5479800 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
5479725 TATTATTATT
5479735 TTAATAAATAATTAATATAA
1 TTAATAAATAATTAATATAA
* *
5479755 TTAAT-AATATATTATTCTAA
1 TTAATAAATA-ATTAATATAA
*
5479775 TTTTAATAAATAATTAATATAT
1 --TTAATAAATAATTAATATAA
5479797 TTAA
1 TTAA
5479801 AATAATTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
19 4 0.11
20 17 0.46
22 12 0.32
23 4 0.11
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAATAAATAATTAATATAA
Found at i:5483106 original size:18 final size:18
Alignment explanation
Indices: 5483085--5483125 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
5483075 ATGGTGGTTG
5483085 TGATGTTGCAG-CTTGTGA
1 TGATGTTGCAGTCTT-TGA
5483103 TGATGTTGCAGTCTTTGA
1 TGATGTTGCAGTCTTTGA
5483121 TGATG
1 TGATG
5483126 GTGTAATCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.17, C:0.10, G:0.32, T:0.41
Consensus pattern (18 bp):
TGATGTTGCAGTCTTTGA
Found at i:5484002 original size:19 final size:19
Alignment explanation
Indices: 5483978--5484025 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
5483968 CATTTGATGT
5483978 ATCGATGCACCAGCCATGC
1 ATCGATGCACCAGCCATGC
5483997 ATCGATGCACCAGCCATGC
1 ATCGATGCACCAGCCATGC
5484016 ATCGATGCAC
1 ATCGATGCAC
5484026 TCTGGCTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.27, C:0.35, G:0.21, T:0.17
Consensus pattern (19 bp):
ATCGATGCACCAGCCATGC
Found at i:5484006 original size:84 final size:83
Alignment explanation
Indices: 5483908--5484070 Score: 195
Period size: 84 Copynumber: 2.0 Consensus size: 83
5483898 AAATGCATTT
* * * *
5483908 CATGCATCGTTGCA-CATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCAT
1 CATGCATCGATGCACCA-ACCATGCACCGATGCACTCAGGATGTTT-TG-AAACATAGAATGCAC
*
5483971 TTGATGTATCGATGCACCAGC
63 TTGATGCATCGATGCACCAGC
* * * * *
5483992 CATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTGTTTTGAAACATATAATGCACTTG
1 CATGCATCGATGCACCAACCATGCACCGATGCACTCAGGATGTTTTGAAACATAGAATGCACTTG
5484057 ATGCATCGATGCAC
66 ATGCATCGATGCAC
5484071 GCTTAGTGCA
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
83 28 0.42
84 34 0.51
85 5 0.07
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.26
Consensus pattern (83 bp):
CATGCATCGATGCACCAACCATGCACCGATGCACTCAGGATGTTTTGAAACATAGAATGCACTTG
ATGCATCGATGCACCAGC
Found at i:5492763 original size:64 final size:66
Alignment explanation
Indices: 5492609--5492768 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 66
5492599 AATTAAATTG
* * * *
5492609 AACATCGGATGCATTTCATGCATCGATGCA-CATACCATGCACCGATGCACTGAGGATTTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATCCACTCAGGATTTTATGA
5492673 A
66 A
* * * *
5492674 AACATCGAATGCATTTGATGCATCGATGCACCA-GCCATGCATCGATCCACTCTGGCTATTT-TG
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATCCACTCAGGAT-TTTATG
5492737 -A
65 AA
*
5492738 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
5492769 GCTTAGTGCA
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 31 0.37
65 48 0.57
66 5 0.06
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.26
Consensus pattern (66 bp):
AACATCGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATCCACTCAGGATTTTATGA
A
Found at i:5495369 original size:18 final size:18
Alignment explanation
Indices: 5495327--5495371 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
5495317 TTCCTCAACC
*
5495327 ATCAGAGTCGGACTCAGA
1 ATCAGATTCGGACTCAGA
5495345 ATCAGATTCGGACTCAGA
1 ATCAGATTCGGACTCAGA
5495363 ATCAGATTC
1 ATCAGATTC
5495372 AGTTTCAGTA
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:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (18 bp):
ATCAGATTCGGACTCAGA
Found at i:5496646 original size:23 final size:22
Alignment explanation
Indices: 5496615--5496673 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
5496605 TGTTTTCATA
5496615 AAAAAATCCTTAAAAGTATTTC-
1 AAAAAATCCTTAAAA-TATTTCG
*
5496637 AGAAAAATCCCTAAAATATTTCG
1 A-AAAAATCCTTAAAATATTTCG
5496660 AAAAAAT-CTTAAAA
1 AAAAAATCCTTAAAA
5496674 AGCGTCAGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 6 0.18
22 13 0.39
23 14 0.42
ACGTcount: A:0.54, C:0.14, G:0.05, T:0.27
Consensus pattern (22 bp):
AAAAAATCCTTAAAATATTTCG
Found at i:5496665 original size:22 final size:22
Alignment explanation
Indices: 5496615--5496667 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
5496605 TGTTTTCATA
*
5496615 AAAAAATCCTTAAAAGTATTTC
1 AAAAAATCCCTAAAAGTATTTC
5496637 AGAAAAATCCCTAAAA-TATTTC
1 A-AAAAATCCCTAAAAGTATTTC
5496659 GAAAAAATC
1 -AAAAAATC
5496668 TTAAAAAGCG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.53, C:0.15, G:0.06, T:0.26
Consensus pattern (22 bp):
AAAAAATCCCTAAAAGTATTTC
Found at i:5496674 original size:22 final size:22
Alignment explanation
Indices: 5496615--5496674 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
5496605 TGTTTTCATA
*
5496615 AAAAAATCCTTAAAAGTATTTC
1 AAAAAATCCTTAAAAATATTTC
*
5496637 AGAAAAATCCCT-AAAATATTTC
1 A-AAAAATCCTTAAAAATATTTC
5496659 GAAAAAAT-CTTAAAAA
1 -AAAAAATCCTTAAAAA
5496675 GCGTCAGTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 2 0.06
22 20 0.62
23 10 0.31
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.27
Consensus pattern (22 bp):
AAAAAATCCTTAAAAATATTTC
Found at i:5500744 original size:27 final size:27
Alignment explanation
Indices: 5500709--5500765 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
5500699 CCGGCTGCAC
* * *
5500709 CTTCGAATCTTCAATGTCCAGCTGAGG
1 CTTCAAATCATCAATCTCCAGCTGAGG
*
5500736 CTTCAAATCATCACTCTCCAGCTGAGG
1 CTTCAAATCATCAATCTCCAGCTGAGG
5500763 CTT
1 CTT
5500766 TGAACTCACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.30
Consensus pattern (27 bp):
CTTCAAATCATCAATCTCCAGCTGAGG
Found at i:5500781 original size:27 final size:27
Alignment explanation
Indices: 5500725--5500786 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
5500715 ATCTTCAATG
*
5500725 TCCAGCTGAGGCTTCAAATCATCACTC
1 TCCAGCTGAGGCTTCAAATCATCACAC
* *
5500752 TCCAGCTGAGGCTTTGAACTCA-CACAC
1 TCCAGCTGAGGC-TTCAAATCATCACAC
5500779 TCCAGCTG
1 TCCAGCTG
5500787 GCCCTTGGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 24 0.77
28 7 0.23
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.24
Consensus pattern (27 bp):
TCCAGCTGAGGCTTCAAATCATCACAC
Found at i:5503607 original size:156 final size:154
Alignment explanation
Indices: 5503278--5503748 Score: 584
Period size: 156 Copynumber: 3.0 Consensus size: 154
5503268 TAAATGACAC
* *
5503278 ATTGAAGGAATAAGGAGATTATGAAAAATTGAAAGACTAAATTGAAAAATAAAAAAATCTTATCA
1 ATTGAA-GAATAAGGAGATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTCTTATC-
* *
5503343 AAAAGATGAATTGAAAGTACAAATGTATTCTA-TA-GTTTAGGAGCATGTG-CTCAAATTAGGT-
64 -AAAGAGGAATTGAAAGTACAAATGTATTCTACTATGTTTAGGAGCATGTGACTCAAATTTGGTA
*
5503404 AAAAACA-GACTTAAAATAAATGATGA
128 AAAAAAATGACTTAAAATAAATGATGA
* * * * *
5503430 ATTGAAGAAATAAGGATATTATGACAAATTGAAGGACTAAATTGAAAACTAATAAATTTTTTATC
1 ATTGAAG-AATAAGGAGATTATGAAAAATTGAAGGACTAAATTGAAAAATAA-AAAATTCTTATC
*
5503495 -AAGAGGAATTGAAAGTACACATGTATTCTACTATGTTTTAGGAGCATGTGACTCAAATTTGGTA
64 AAAGAGGAATTGAAAGTACAAATGTATTCTACTATG-TTTAGGAGCATGTGACTCAAATTTGGTA
*
5503559 AAAAAAATGACTTAAAATAAATAATGA
128 AAAAAAATGACTTAAAATAAATGATGA
* *
5503586 ATTGAAGAATTAAGTAGATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTGTTATCA
1 ATTGAAGAA-TAAGGAGATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTCTTATC-
* * *
5503651 AAACGTGGAATCGAAAGTA-AATATGTATTCTACTATGGTTTAGGAGCATGT-AGTTCAAATTT-
64 AAA-GAGGAATTGAAAGTACAA-ATGTATTCTACTAT-GTTTAGGAGCATGTGA-CTCAAATTTG
* *
5503713 G-AAAAAAAATGGACTTAAAATGAATGAGGA
125 GTAAAAAAAAT-GACTTAAAATAAATGATGA
5503743 ATTGAA
1 ATTGAA
5503749 TAAATAATGA
Statistics
Matches: 278, Mismatches: 25, Indels: 27
0.84 0.08 0.08
Matches are distributed among these distances:
150 28 0.10
151 3 0.01
152 47 0.17
153 23 0.08
154 11 0.04
155 18 0.06
156 72 0.26
157 27 0.10
158 48 0.17
159 1 0.00
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.29
Consensus pattern (154 bp):
ATTGAAGAATAAGGAGATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTCTTATCAA
AGAGGAATTGAAAGTACAAATGTATTCTACTATGTTTAGGAGCATGTGACTCAAATTTGGTAAAA
AAAATGACTTAAAATAAATGATGA
Found at i:5504424 original size:35 final size:35
Alignment explanation
Indices: 5504385--5504451 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
5504375 AACATAGTCA
5504385 TCAATTACATTCTAAATCC-TAAAATCCAAAATGTT
1 TCAATTACATTCTAAA-CCTTAAAATCCAAAATGTT
*
5504420 TCAATTACATTCTAAACCTTAAATTCCAAAAT
1 TCAATTACATTCTAAACCTTAAAATCCAAAAT
5504452 ACTTTAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 2 0.07
35 28 0.93
ACGTcount: A:0.43, C:0.21, G:0.01, T:0.34
Consensus pattern (35 bp):
TCAATTACATTCTAAACCTTAAAATCCAAAATGTT
Found at i:5504461 original size:35 final size:35
Alignment explanation
Indices: 5504385--5504461 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 35
5504375 AACATAGTCA
*
5504385 TCAATTACATTCTAAATCCTAAAATCCAAAATGTT
1 TCAATTACATTCTAAATCCTAAAATCCAAAATCTT
*
5504420 TCAATTACATTCTAAA-CCTTAAATTCCAAAATACTT
1 TCAATTACATTCTAAATCC-TAAAATCCAAAAT-CTT
5504456 T-AATTA
1 TCAATTA
5504462 TGCCCAACCC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
34 2 0.05
35 33 0.87
36 3 0.08
ACGTcount: A:0.43, C:0.19, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTACATTCTAAATCCTAAAATCCAAAATCTT
Found at i:5505521 original size:31 final size:31
Alignment explanation
Indices: 5505483--5505607 Score: 164
Period size: 31 Copynumber: 4.0 Consensus size: 31
5505473 CCCGAAGGAC
* * *
5505483 CAGTCCATAGATTCCGAAGAACCTAGGTAAT
1 CAGTCCATAGATCCCGAAGAACATAGGTAAA
*
5505514 CAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATAGATCCCGAAGAACATAGGTAAA
*
5505545 CAGTCCATATG-TCCTGAAGAACATAGGTAAA
1 CAGTCCATA-GATCCCGAAGAACATAGGTAAA
*
5505576 CAGTCTATATG-TCCCGAAGAACATAGGTAAA
1 CAGTCCATA-GATCCCGAAGAACATAGGTAAA
5505607 C
1 C
5505608 CCTCGACCCT
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
31 85 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (31 bp):
CAGTCCATAGATCCCGAAGAACATAGGTAAA
Found at i:5506504 original size:21 final size:21
Alignment explanation
Indices: 5506480--5506524 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5506470 TTTTGTTCGT
* *
5506480 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
5506501 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
5506522 TTG
1 TTG
5506525 CCAGAAATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:5510302 original size:31 final size:31
Alignment explanation
Indices: 5510264--5510388 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
5510254 CCCGAAGGAC
* * * *
5510264 CAGTCCATA-GATTCCGAAAAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
5510295 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
5510326 CAGTCCATATGTCCCGAAGAATATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
5510357 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
5510388 C
1 C
5510389 CCTCGACCCT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:5514344 original size:13 final size:14
Alignment explanation
Indices: 5514323--5514417 Score: 63
Period size: 14 Copynumber: 6.9 Consensus size: 14
5514313 GGGCATGTAA
*
5514323 AATTGTAATAAT-T
1 AATTATAATAATAT
5514336 AATTATAATAATAT
1 AATTATAATAATAT
5514350 AA-TATAAT--TAT
1 AATTATAATAATAT
* * *
5514361 AATAATATTTATTAT
1 AATTATA-ATAATAT
* * *
5514376 ATTTATTATGTATAT
1 AATTATAAT-AATAT
*
5514391 AATAATAATAATAT
1 AATTATAATAATAT
*
5514405 AAATATAATAATA
1 AATTATAATAATA
5514418 ACATATATAT
Statistics
Matches: 61, Mismatches: 15, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
11 5 0.08
12 3 0.05
13 18 0.30
14 19 0.31
15 16 0.26
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
AATTATAATAATAT
Found at i:5514359 original size:19 final size:18
Alignment explanation
Indices: 5514330--5514368 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
5514320 TAAAATTGTA
5514330 ATAATTAATTATAATAAT
1 ATAATTAATTATAATAAT
5514348 ATAATATAATTATAATAAT
1 ATAAT-TAATTATAATAAT
5514367 AT
1 AT
5514369 TTATTATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAATTAATTATAATAAT
Found at i:5514427 original size:17 final size:17
Alignment explanation
Indices: 5514386--5514427 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
5514376 ATTTATTATG
*
5514386 TATATAATAATAATAATA
1 TATAT-ATAATAATAACA
*
5514404 TAAATATAATAATAACA
1 TATATATAATAATAACA
5514421 TATATAT
1 TATATAT
5514428 GTATAAACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
TATATATAATAATAACA
Found at i:5516880 original size:14 final size:14
Alignment explanation
Indices: 5516861--5516895 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
5516851 TCATTCTTCT
5516861 CAGCTTTTGTTGCA
1 CAGCTTTTGTTGCA
5516875 CAGCTTTTGTTGCA
1 CAGCTTTTGTTGCA
5516889 CAGCTTT
1 CAGCTTT
5516896 ACATTCTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (14 bp):
CAGCTTTTGTTGCA
Found at i:5517285 original size:64 final size:64
Alignment explanation
Indices: 5517188--5517332 Score: 177
Period size: 64 Copynumber: 2.2 Consensus size: 64
5517178 TTTTCAAAGG
* * *
5517188 CATGCACCGATGCATCAATCCATGCATCGATGCACCATT-GAATAAATT-GAACATCGAATGCAT
1 CATGCATCGATGCA-CTATCCATGCATCGATGCA-C-TTGGAATAAATTAAAACATCGAATGCAT
5517251 TT
63 TT
* ** **
5517253 CATGCATCGATGCACTATCTATGCATCGATGCACTTGGGTTTTATTAAAACATCGAATGCATTT
1 CATGCATCGATGCACTATCCATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTT
5517317 CATGCATCGATGCACT
1 CATGCATCGATGCACT
5517333 CAGGCTATTT
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
62 2 0.03
63 6 0.09
64 49 0.70
65 13 0.19
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (64 bp):
CATGCATCGATGCACTATCCATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTT
Found at i:5517323 original size:45 final size:45
Alignment explanation
Indices: 5517273--5517376 Score: 129
Period size: 45 Copynumber: 2.3 Consensus size: 45
5517263 TGCACTATCT
* * * *
5517273 ATGCATCGATGCACT-TGGGTTTTATTAAAACATCGAATGCATTTC
1 ATGCATCGATGCACTCAGGCTATT-TTAAAACATCGAATACATTTC
* * *
5517318 ATGCATCGATGCACTCAGGCTATTTTCAAACATCGAATACCTTTT
1 ATGCATCGATGCACTCAGGCTATTTTAAAACATCGAATACATTTC
5517363 ATGCATCGATGCAC
1 ATGCATCGATGCAC
5517377 ACTTGGTGCG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
45 46 0.90
46 5 0.10
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGGCTATTTTAAAACATCGAATACATTTC
Found at i:5526055 original size:64 final size:64
Alignment explanation
Indices: 5525913--5526036 Score: 187
Period size: 64 Copynumber: 1.9 Consensus size: 64
5525903 TGCTTTCTCT
* **
5525913 ATGCATCGATGCACTTGGGTTTTATTAAAACATCGAATGCATTTCATGCATCGATGCACAAGAA
1 ATGCACCGATGCACTCAGGTTTTATTAAAACATCGAATGCATTTCATGCATCGATGCACAAGAA
* *
5525977 ATGCACCGATGCACTCAGGTTATT-TTCAAACATCGAATGCATTTTATGCATCGATGCACA
1 ATGCACCGATGCACTCAGGTT-TTATTAAAACATCGAATGCATTTCATGCATCGATGCACA
5526037 CTTGGTGCAC
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
64 52 0.96
65 2 0.04
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (64 bp):
ATGCACCGATGCACTCAGGTTTTATTAAAACATCGAATGCATTTCATGCATCGATGCACAAGAA
Found at i:5535493 original size:3 final size:3
Alignment explanation
Indices: 5535485--5535538 Score: 85
Period size: 3 Copynumber: 18.3 Consensus size: 3
5535475 TATTAAGTAT
5535485 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA A-A TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
5535532 ATA ATA A
1 ATA ATA A
5535539 CATATATATA
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 3 0.06
3 44 0.92
4 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5537802 original size:13 final size:13
Alignment explanation
Indices: 5537780--5537844 Score: 94
Period size: 13 Copynumber: 5.0 Consensus size: 13
5537770 GTCATAAATC
*
5537780 TATGAAGCGCATT
1 TATGACGCGCATT
5537793 TATGACGCGCATT
1 TATGACGCGCATT
*
5537806 TATGACACGCATT
1 TATGACGCGCATT
*
5537819 TATGACGCTCATT
1 TATGACGCGCATT
*
5537832 TATGACGCTCATT
1 TATGACGCGCATT
5537845 GAGCATCATT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 48 1.00
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:5537993 original size:2 final size:2
Alignment explanation
Indices: 5537986--5538021 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5537976 TTTCGTAAAT
5537986 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5538022 TAGATTGACA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5539730 original size:2 final size:2
Alignment explanation
Indices: 5539718--5539752 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
5539708 TATTTGGTGC
5539718 AT AT GAT 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
5539753 GTCCGCCAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5547368 original size:99 final size:97
Alignment explanation
Indices: 5547186--5547383 Score: 378
Period size: 99 Copynumber: 2.0 Consensus size: 97
5547176 AACAGATGTT
5547186 AATATGTATATAGCCAACATGAAGCTTCATATAAGTGCCACAAGCATGAGACGATGCTGAGCTAG
1 AATATGTATATAGCCAACATGAAGCTTCATATAAGTGCCACAAGCATGAGACGATGCTGAGCTAG
5547251 ATTCCACTAGAACCAGGAACAAGACATTGATG
66 ATTCCACTAGAACCAGGAACAAGACATTGATG
5547283 AATATGTATATAGCCAACATGGAAGCTTCATATAAGTGCCACAAGCATGAGACTGATGCTGAGCT
1 AATATGTATATAGCCAACAT-GAAGCTTCATATAAGTGCCACAAGCATGAGAC-GATGCTGAGCT
5547348 AGATTCCACTAGAACCAGGAACAAGACATTGATG
64 AGATTCCACTAGAACCAGGAACAAGACATTGATG
5547382 AA
1 AA
5547384 GATTGTAGAT
Statistics
Matches: 99, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
97 20 0.20
98 32 0.32
99 47 0.47
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (97 bp):
AATATGTATATAGCCAACATGAAGCTTCATATAAGTGCCACAAGCATGAGACGATGCTGAGCTAG
ATTCCACTAGAACCAGGAACAAGACATTGATG
Found at i:5552109 original size:41 final size:42
Alignment explanation
Indices: 5552015--5552130 Score: 141
Period size: 41 Copynumber: 2.8 Consensus size: 42
5552005 TATTAAGTTA
*
5552015 TTCGGGTCATC-AGTAAGTCTTTCGAGCATGATGATTAAATCC
1 TTCGGGTCATCTA-TAAGTCTTTCGAGCATGATGAGTAAATCC
*
5552057 TTCGGGTCATCTATAAGTCTTTCGAGC-TAGAT-AGTAAGTCC
1 TTCGGGTCATCTATAAGTCTTTCGAGCAT-GATGAGTAAATCC
* *
5552098 TTCGGGCCATCTATAAGTCCTTC-AGGCATGATG
1 TTCGGGTCATCTATAAGTCTTTCGA-GCATGATG
5552131 TTTCCGCATG
Statistics
Matches: 65, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
40 1 0.02
41 34 0.52
42 29 0.45
43 1 0.02
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (42 bp):
TTCGGGTCATCTATAAGTCTTTCGAGCATGATGAGTAAATCC
Found at i:5552116 original size:20 final size:20
Alignment explanation
Indices: 5552054--5552120 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
5552044 GATGATTAAA
*
5552054 TCCTTCGGGTCATCTATAAG
1 TCCTTCGGGCCATCTATAAG
* * * **
5552074 TCTTTCGAGCTAGATAGTAAG
1 TCCTTCGGGCCATCTA-TAAG
5552095 TCCTTCGGGCCATCTATAAG
1 TCCTTCGGGCCATCTATAAG
5552115 TCCTTC
1 TCCTTC
5552121 AGGCATGATG
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
20 20 0.57
21 15 0.43
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.34
Consensus pattern (20 bp):
TCCTTCGGGCCATCTATAAG
Found at i:5552305 original size:197 final size:197
Alignment explanation
Indices: 5551944--5552368 Score: 584
Period size: 197 Copynumber: 2.2 Consensus size: 197
5551934 TGAAAATGAA
* * * * * *
5551944 ATTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTATTACCCAGTAAATTATTTCCAAAATTATT
1 ATTTTCGAAAAATGAGAAAACGATTTCCAAAATTTATTACCCAGTAAATTATTTCCAAAACTAGT
* * * *
5552009 AAGTTATTCGGGTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAG
66 AAGTCATTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCAGGTCATCTATAAG
* * * * * *
5552074 TCTTTCGAGCTAGATAGTAAGTCCTTCGGGCCATCTATAAGTCCTTCAGGCATGATGTTTCCGCA
131 TCTTTCGAGCAAGATAGTAAGTCATTCGGGCCATCTATAAGACCTTCAGGCAGGATATTTCCACA
5552139 TG
196 TG
* *
5552141 ATTTTCGAAAAATGAGAAAACGATTTCCAAAATTTTTTACCTAGTAAATTATTTCCAAAACTAGT
1 ATTTTCGAAAAATGAGAAAACGATTTCCAAAATTTATTACCCAGTAAATTATTTCCAAAACTAGT
* * *
5552206 ATGTCCTTCGGGCCATCAGTAAGTTTTTCAAGCATGATGATTAAATCCTTCAGGTCATCT-TACA
66 AAGTCATTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCAGGTCATCTATA-A
* * *
5552270 GTCTTTCGAGCAAGAT-GATAAGTCATTCTGGCCATCTATAAGACCTTCGGGCAGGATATTTTCA
130 GTCTTTCGAGCAAGATAG-TAAGTCATTCGGGCCATCTATAAGACCTTCAGGCAGGATATTTCCA
5552334 CATG
194 CATG
* *
5552338 ATTTTCAAAAAATGAGAAAGCGATTTCCAAA
1 ATTTTCGAAAAATGAGAAAACGATTTCCAAA
5552369 GTTTCTCATT
Statistics
Matches: 200, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
196 3 0.01
197 197 0.99
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (197 bp):
ATTTTCGAAAAATGAGAAAACGATTTCCAAAATTTATTACCCAGTAAATTATTTCCAAAACTAGT
AAGTCATTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCAGGTCATCTATAAG
TCTTTCGAGCAAGATAGTAAGTCATTCGGGCCATCTATAAGACCTTCAGGCAGGATATTTCCACA
TG
Found at i:5552661 original size:3 final size:3
Alignment explanation
Indices: 5552653--5552698 Score: 67
Period size: 3 Copynumber: 15.0 Consensus size: 3
5552643 TTTGTCCAGG
5552653 TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TT- TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA T-TA TTA TTA
5552699 ATTTTTTATA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 1 0.03
3 35 0.88
4 4 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5552677 original size:16 final size:16
Alignment explanation
Indices: 5552656--5552698 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
5552646 GTCCAGGTTA
5552656 TTATTATTATTATTAT
1 TTATTATTATTATTAT
5552672 TTATTATTATTATTAT
1 TTATTATTATTATTAT
5552688 TTA-TATTATTA
1 TTATTATTATTA
5552699 ATTTTTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 8 0.30
16 19 0.70
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTATTATTATTAT
Found at i:5552702 original size:13 final size:14
Alignment explanation
Indices: 5552659--5552707 Score: 57
Period size: 13 Copynumber: 3.5 Consensus size: 14
5552649 CAGGTTATTA
5552659 TTATTATTATT-AT
1 TTATTATTATTAAT
5552672 TTATTATTATTATTAT
1 TTATTATTATTA--AT
5552688 TTA-TATTATTAAT
1 TTATTATTATTAAT
*
5552701 TTTTTAT
1 TTATTAT
5552708 AGACCCAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 15 0.48
14 3 0.10
15 8 0.26
16 5 0.16
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATTATTATTAAT
Done.