Multiple sequence alignment - TraesCS2B01G292600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2B01G292600 chr2B 100.000 2453 0 0 1 2453 407232015 407234467 0.000000e+00 4530.0
1 TraesCS2B01G292600 chr2B 95.035 141 6 1 1889 2028 684990435 684990575 1.140000e-53 220.0
2 TraesCS2B01G292600 chr2B 96.800 125 4 0 543 667 407232498 407232622 2.470000e-50 209.0
3 TraesCS2B01G292600 chr2B 96.800 125 4 0 484 608 407232557 407232681 2.470000e-50 209.0
4 TraesCS2B01G292600 chr2B 96.970 66 2 0 602 667 407232498 407232563 7.170000e-21 111.0
5 TraesCS2B01G292600 chr2B 96.970 66 2 0 484 549 407232616 407232681 7.170000e-21 111.0
6 TraesCS2B01G292600 chr2A 92.952 979 37 9 929 1900 451807278 451808231 0.000000e+00 1397.0
7 TraesCS2B01G292600 chr2A 97.907 430 9 0 2024 2453 451808230 451808659 0.000000e+00 745.0
8 TraesCS2B01G292600 chr2A 99.565 230 0 1 1 229 230835107 230835336 3.770000e-113 418.0
9 TraesCS2B01G292600 chr2D 98.025 557 10 1 929 1484 342096564 342097120 0.000000e+00 966.0
10 TraesCS2B01G292600 chr2D 97.209 430 12 0 2024 2453 342097489 342097918 0.000000e+00 728.0
11 TraesCS2B01G292600 chr2D 95.442 373 10 2 1534 1900 342097119 342097490 2.720000e-164 588.0
12 TraesCS2B01G292600 chr2D 85.417 144 15 3 752 894 326265732 326265870 7.070000e-31 145.0
13 TraesCS2B01G292600 chr2D 83.750 80 9 4 826 902 539143006 539142928 3.380000e-09 73.1
14 TraesCS2B01G292600 chr4B 98.429 382 6 0 227 608 37553692 37554073 0.000000e+00 673.0
15 TraesCS2B01G292600 chr4B 95.918 343 14 0 543 885 37553949 37554291 7.660000e-155 556.0
16 TraesCS2B01G292600 chr4B 99.561 228 0 1 1 227 447520105 447519878 4.880000e-112 414.0
17 TraesCS2B01G292600 chr4B 99.561 228 0 1 1 227 661635664 661635437 4.880000e-112 414.0
18 TraesCS2B01G292600 chr4B 100.000 66 0 0 484 549 37554008 37554073 3.310000e-24 122.0
19 TraesCS2B01G292600 chr4B 92.424 66 5 0 602 667 37553949 37554014 7.220000e-16 95.3
20 TraesCS2B01G292600 chrUn 99.561 228 0 1 1 227 180996694 180996467 4.880000e-112 414.0
21 TraesCS2B01G292600 chrUn 99.561 228 0 1 1 227 300782730 300782957 4.880000e-112 414.0
22 TraesCS2B01G292600 chrUn 99.561 228 0 1 1 227 399897091 399896864 4.880000e-112 414.0
23 TraesCS2B01G292600 chr7B 99.561 228 0 1 1 227 320317456 320317683 4.880000e-112 414.0
24 TraesCS2B01G292600 chr7B 95.620 137 6 0 1899 2035 575370851 575370715 1.140000e-53 220.0
25 TraesCS2B01G292600 chr6B 99.561 228 0 1 1 227 43822877 43822650 4.880000e-112 414.0
26 TraesCS2B01G292600 chr6B 96.226 53 2 0 840 892 96672103 96672051 1.210000e-13 87.9
27 TraesCS2B01G292600 chr6B 85.366 82 8 4 805 884 637370702 637370781 5.620000e-12 82.4
28 TraesCS2B01G292600 chr4A 99.134 231 1 1 1 230 336016128 336016358 4.880000e-112 414.0
29 TraesCS2B01G292600 chr5B 87.613 331 20 7 229 546 690876282 690876604 4.980000e-97 364.0
30 TraesCS2B01G292600 chr5B 89.273 289 28 1 602 890 690876542 690876827 2.320000e-95 359.0
31 TraesCS2B01G292600 chr5B 93.878 147 6 2 1895 2041 670073685 670073828 4.110000e-53 219.0
32 TraesCS2B01G292600 chr5B 93.706 143 7 2 1899 2040 292392136 292392277 1.910000e-51 213.0
33 TraesCS2B01G292600 chr7A 97.015 134 4 0 1899 2032 83728728 83728595 2.450000e-55 226.0
34 TraesCS2B01G292600 chr7A 94.326 141 7 1 1893 2033 634386550 634386689 5.310000e-52 215.0
35 TraesCS2B01G292600 chr1B 90.964 166 11 4 1873 2038 409879957 409879796 1.140000e-53 220.0
36 TraesCS2B01G292600 chr5A 94.406 143 7 1 1887 2028 9840816 9840958 4.110000e-53 219.0
37 TraesCS2B01G292600 chr5A 87.730 163 16 3 732 893 512838686 512838527 1.160000e-43 187.0
38 TraesCS2B01G292600 chr3B 96.269 134 4 1 1894 2027 115549512 115549644 4.110000e-53 219.0
39 TraesCS2B01G292600 chr3B 91.803 61 4 1 840 899 654069727 654069667 1.560000e-12 84.2
40 TraesCS2B01G292600 chr6D 100.000 53 0 0 844 896 438001850 438001798 5.580000e-17 99.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G292600 chr2B 407232015 407234467 2452 False 1034.000000 4530 97.50800 1 2453 5 chr2B.!!$F2 2452
1 TraesCS2B01G292600 chr2A 451807278 451808659 1381 False 1071.000000 1397 95.42950 929 2453 2 chr2A.!!$F2 1524
2 TraesCS2B01G292600 chr2D 342096564 342097918 1354 False 760.666667 966 96.89200 929 2453 3 chr2D.!!$F2 1524
3 TraesCS2B01G292600 chr4B 37553692 37554291 599 False 361.575000 673 96.69275 227 885 4 chr4B.!!$F1 658
4 TraesCS2B01G292600 chr5B 690876282 690876827 545 False 361.500000 364 88.44300 229 890 2 chr5B.!!$F3 661

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
93 94 0.028505 GCGATCGTAACCTAGCGTGA 59.971 55.0 17.81 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1898 2015 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.0 13.64 0.0 46.06 2.59 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 4.895478 GCGGCGGTGCGGGTATTA 62.895 66.667 9.78 0.00 0.00 0.98
58 59 2.660552 CGGCGGTGCGGGTATTAG 60.661 66.667 0.00 0.00 0.00 1.73
59 60 2.280592 GGCGGTGCGGGTATTAGG 60.281 66.667 0.00 0.00 0.00 2.69
60 61 2.280592 GCGGTGCGGGTATTAGGG 60.281 66.667 0.00 0.00 0.00 3.53
61 62 3.097921 GCGGTGCGGGTATTAGGGT 62.098 63.158 0.00 0.00 0.00 4.34
62 63 1.523524 CGGTGCGGGTATTAGGGTT 59.476 57.895 0.00 0.00 0.00 4.11
63 64 0.107557 CGGTGCGGGTATTAGGGTTT 60.108 55.000 0.00 0.00 0.00 3.27
64 65 1.138661 CGGTGCGGGTATTAGGGTTTA 59.861 52.381 0.00 0.00 0.00 2.01
65 66 2.804212 CGGTGCGGGTATTAGGGTTTAG 60.804 54.545 0.00 0.00 0.00 1.85
66 67 2.435437 GGTGCGGGTATTAGGGTTTAGA 59.565 50.000 0.00 0.00 0.00 2.10
67 68 3.118298 GGTGCGGGTATTAGGGTTTAGAA 60.118 47.826 0.00 0.00 0.00 2.10
68 69 4.124970 GTGCGGGTATTAGGGTTTAGAAG 58.875 47.826 0.00 0.00 0.00 2.85
69 70 3.136763 GCGGGTATTAGGGTTTAGAAGC 58.863 50.000 0.00 0.00 0.00 3.86
70 71 3.387397 CGGGTATTAGGGTTTAGAAGCG 58.613 50.000 0.00 0.00 0.00 4.68
71 72 3.736720 GGGTATTAGGGTTTAGAAGCGG 58.263 50.000 0.00 0.00 0.00 5.52
72 73 3.389002 GGGTATTAGGGTTTAGAAGCGGA 59.611 47.826 0.00 0.00 0.00 5.54
73 74 4.141642 GGGTATTAGGGTTTAGAAGCGGAA 60.142 45.833 0.00 0.00 0.00 4.30
74 75 5.055144 GGTATTAGGGTTTAGAAGCGGAAG 58.945 45.833 0.00 0.00 0.00 3.46
88 89 2.033793 CGGAAGCGATCGTAACCTAG 57.966 55.000 17.81 2.69 0.00 3.02
89 90 1.768510 GGAAGCGATCGTAACCTAGC 58.231 55.000 17.81 0.00 0.00 3.42
90 91 1.396644 GAAGCGATCGTAACCTAGCG 58.603 55.000 17.81 0.00 0.00 4.26
91 92 0.737219 AAGCGATCGTAACCTAGCGT 59.263 50.000 17.81 0.00 0.00 5.07
92 93 0.029035 AGCGATCGTAACCTAGCGTG 59.971 55.000 17.81 0.00 0.00 5.34
93 94 0.028505 GCGATCGTAACCTAGCGTGA 59.971 55.000 17.81 0.00 0.00 4.35
94 95 1.334779 GCGATCGTAACCTAGCGTGAT 60.335 52.381 17.81 0.00 0.00 3.06
95 96 2.096069 GCGATCGTAACCTAGCGTGATA 60.096 50.000 17.81 0.00 0.00 2.15
96 97 3.477122 CGATCGTAACCTAGCGTGATAC 58.523 50.000 7.03 0.00 0.00 2.24
97 98 3.666374 CGATCGTAACCTAGCGTGATACC 60.666 52.174 7.03 0.00 0.00 2.73
98 99 2.642427 TCGTAACCTAGCGTGATACCA 58.358 47.619 0.00 0.00 0.00 3.25
99 100 3.216800 TCGTAACCTAGCGTGATACCAT 58.783 45.455 0.00 0.00 0.00 3.55
100 101 3.004002 TCGTAACCTAGCGTGATACCATG 59.996 47.826 0.00 0.00 0.00 3.66
101 102 3.243301 CGTAACCTAGCGTGATACCATGT 60.243 47.826 0.00 0.00 0.00 3.21
102 103 4.023792 CGTAACCTAGCGTGATACCATGTA 60.024 45.833 0.00 0.00 0.00 2.29
103 104 5.506151 CGTAACCTAGCGTGATACCATGTAA 60.506 44.000 0.00 0.00 0.00 2.41
104 105 4.585955 ACCTAGCGTGATACCATGTAAG 57.414 45.455 0.00 0.00 0.00 2.34
105 106 4.212716 ACCTAGCGTGATACCATGTAAGA 58.787 43.478 0.00 0.00 0.00 2.10
106 107 4.037684 ACCTAGCGTGATACCATGTAAGAC 59.962 45.833 0.00 0.00 0.00 3.01
107 108 4.037565 CCTAGCGTGATACCATGTAAGACA 59.962 45.833 0.00 0.00 0.00 3.41
108 109 4.465632 AGCGTGATACCATGTAAGACAA 57.534 40.909 0.00 0.00 0.00 3.18
109 110 5.023533 AGCGTGATACCATGTAAGACAAT 57.976 39.130 0.00 0.00 0.00 2.71
110 111 6.156748 AGCGTGATACCATGTAAGACAATA 57.843 37.500 0.00 0.00 0.00 1.90
111 112 6.578944 AGCGTGATACCATGTAAGACAATAA 58.421 36.000 0.00 0.00 0.00 1.40
112 113 6.701841 AGCGTGATACCATGTAAGACAATAAG 59.298 38.462 0.00 0.00 0.00 1.73
113 114 6.479001 GCGTGATACCATGTAAGACAATAAGT 59.521 38.462 0.00 0.00 0.00 2.24
114 115 7.011109 GCGTGATACCATGTAAGACAATAAGTT 59.989 37.037 0.00 0.00 0.00 2.66
115 116 8.879759 CGTGATACCATGTAAGACAATAAGTTT 58.120 33.333 0.00 0.00 0.00 2.66
119 120 7.227049 ACCATGTAAGACAATAAGTTTTGGG 57.773 36.000 0.00 0.00 0.00 4.12
120 121 7.007723 ACCATGTAAGACAATAAGTTTTGGGA 58.992 34.615 0.00 0.00 0.00 4.37
121 122 7.507616 ACCATGTAAGACAATAAGTTTTGGGAA 59.492 33.333 0.00 0.00 0.00 3.97
122 123 7.812669 CCATGTAAGACAATAAGTTTTGGGAAC 59.187 37.037 0.00 0.00 0.00 3.62
135 136 4.081050 GGAACCAGCACAACCCTC 57.919 61.111 0.00 0.00 0.00 4.30
136 137 1.456287 GGAACCAGCACAACCCTCT 59.544 57.895 0.00 0.00 0.00 3.69
137 138 0.690762 GGAACCAGCACAACCCTCTA 59.309 55.000 0.00 0.00 0.00 2.43
138 139 1.339151 GGAACCAGCACAACCCTCTAG 60.339 57.143 0.00 0.00 0.00 2.43
139 140 0.693049 AACCAGCACAACCCTCTAGG 59.307 55.000 0.00 0.00 43.78 3.02
151 152 2.407340 CCTCTAGGGGTGGCTTATCT 57.593 55.000 0.00 0.00 0.00 1.98
152 153 2.252714 CCTCTAGGGGTGGCTTATCTC 58.747 57.143 0.00 0.00 0.00 2.75
153 154 2.426414 CCTCTAGGGGTGGCTTATCTCA 60.426 54.545 0.00 0.00 0.00 3.27
154 155 3.515562 CTCTAGGGGTGGCTTATCTCAT 58.484 50.000 0.00 0.00 0.00 2.90
155 156 3.906846 CTCTAGGGGTGGCTTATCTCATT 59.093 47.826 0.00 0.00 0.00 2.57
156 157 5.087323 CTCTAGGGGTGGCTTATCTCATTA 58.913 45.833 0.00 0.00 0.00 1.90
157 158 5.665701 TCTAGGGGTGGCTTATCTCATTAT 58.334 41.667 0.00 0.00 0.00 1.28
158 159 6.811574 TCTAGGGGTGGCTTATCTCATTATA 58.188 40.000 0.00 0.00 0.00 0.98
159 160 7.430844 TCTAGGGGTGGCTTATCTCATTATAT 58.569 38.462 0.00 0.00 0.00 0.86
160 161 8.574853 TCTAGGGGTGGCTTATCTCATTATATA 58.425 37.037 0.00 0.00 0.00 0.86
161 162 9.386122 CTAGGGGTGGCTTATCTCATTATATAT 57.614 37.037 0.00 0.00 0.00 0.86
163 164 9.744125 AGGGGTGGCTTATCTCATTATATATAA 57.256 33.333 7.62 7.62 0.00 0.98
186 187 9.688091 ATAATGGTTGTGTTACAATATGTACCA 57.312 29.630 0.00 0.00 40.59 3.25
187 188 8.588290 AATGGTTGTGTTACAATATGTACCAT 57.412 30.769 7.28 7.28 41.43 3.55
188 189 9.688091 AATGGTTGTGTTACAATATGTACCATA 57.312 29.630 11.64 0.00 39.79 2.74
189 190 9.860650 ATGGTTGTGTTACAATATGTACCATAT 57.139 29.630 10.20 0.00 39.26 1.78
220 221 9.233649 ACATAGGTACAGAAGCTATACATAGTC 57.766 37.037 0.00 0.00 45.12 2.59
221 222 9.456147 CATAGGTACAGAAGCTATACATAGTCT 57.544 37.037 0.00 0.00 45.12 3.24
224 225 9.287373 AGGTACAGAAGCTATACATAGTCTAAC 57.713 37.037 0.00 0.00 32.98 2.34
225 226 9.064706 GGTACAGAAGCTATACATAGTCTAACA 57.935 37.037 0.00 0.00 32.96 2.41
324 325 0.764890 ACAGTGGGAGCTACAAGCAA 59.235 50.000 0.00 0.00 45.56 3.91
581 582 3.414700 GACGGCGACTTGGTGCAG 61.415 66.667 16.62 0.00 0.00 4.41
606 607 4.072088 GCACGAGCAAACCGACGG 62.072 66.667 13.61 13.61 41.58 4.79
607 608 4.072088 CACGAGCAAACCGACGGC 62.072 66.667 15.39 0.00 0.00 5.68
610 611 3.774702 GAGCAAACCGACGGCGAC 61.775 66.667 15.16 6.59 40.82 5.19
613 614 2.663852 CAAACCGACGGCGACCTT 60.664 61.111 15.16 0.00 40.82 3.50
614 615 2.663852 AAACCGACGGCGACCTTG 60.664 61.111 15.16 0.00 40.82 3.61
634 635 3.512452 CGCGACGACGACGACTTG 61.512 66.667 22.94 5.72 42.66 3.16
635 636 3.164011 GCGACGACGACGACTTGG 61.164 66.667 22.94 0.00 42.66 3.61
636 637 2.250485 CGACGACGACGACTTGGT 59.750 61.111 15.32 0.00 42.66 3.67
637 638 2.073220 CGACGACGACGACTTGGTG 61.073 63.158 15.32 0.00 42.66 4.17
638 639 2.354305 ACGACGACGACTTGGTGC 60.354 61.111 15.32 0.00 42.66 5.01
639 640 2.354188 CGACGACGACTTGGTGCA 60.354 61.111 0.00 0.00 42.66 4.57
704 705 2.995482 CCGACGAGCGTATGTTGC 59.005 61.111 0.00 0.00 38.67 4.17
740 741 4.148825 GGCGAGTGCGGATGAGGT 62.149 66.667 0.00 0.00 44.10 3.85
741 742 2.583593 GCGAGTGCGGATGAGGTC 60.584 66.667 0.00 0.00 38.16 3.85
742 743 2.278206 CGAGTGCGGATGAGGTCG 60.278 66.667 0.00 0.00 0.00 4.79
743 744 2.761195 CGAGTGCGGATGAGGTCGA 61.761 63.158 0.00 0.00 0.00 4.20
744 745 1.064946 GAGTGCGGATGAGGTCGAG 59.935 63.158 0.00 0.00 0.00 4.04
745 746 2.583593 GTGCGGATGAGGTCGAGC 60.584 66.667 6.48 6.48 33.50 5.03
746 747 4.193334 TGCGGATGAGGTCGAGCG 62.193 66.667 9.28 0.00 34.98 5.03
747 748 4.933064 GCGGATGAGGTCGAGCGG 62.933 72.222 9.28 0.00 0.00 5.52
748 749 3.518998 CGGATGAGGTCGAGCGGT 61.519 66.667 9.28 0.00 0.00 5.68
749 750 2.893398 GGATGAGGTCGAGCGGTT 59.107 61.111 9.28 0.00 0.00 4.44
750 751 1.519455 GGATGAGGTCGAGCGGTTG 60.519 63.158 9.28 0.00 0.00 3.77
751 752 2.125512 ATGAGGTCGAGCGGTTGC 60.126 61.111 9.28 0.00 43.24 4.17
761 762 4.821589 GCGGTTGCGCTAGGCTCT 62.822 66.667 9.73 0.00 44.05 4.09
762 763 2.805546 CGGTTGCGCTAGGCTCTA 59.194 61.111 9.73 0.00 44.05 2.43
763 764 1.364171 CGGTTGCGCTAGGCTCTAT 59.636 57.895 9.73 0.00 44.05 1.98
764 765 0.664767 CGGTTGCGCTAGGCTCTATC 60.665 60.000 9.73 0.00 44.05 2.08
765 766 0.319986 GGTTGCGCTAGGCTCTATCC 60.320 60.000 9.73 0.00 44.05 2.59
766 767 0.676736 GTTGCGCTAGGCTCTATCCT 59.323 55.000 9.73 0.00 44.05 3.24
767 768 0.962489 TTGCGCTAGGCTCTATCCTC 59.038 55.000 9.73 0.00 44.05 3.71
768 769 0.111446 TGCGCTAGGCTCTATCCTCT 59.889 55.000 9.73 0.00 44.05 3.69
769 770 1.253100 GCGCTAGGCTCTATCCTCTT 58.747 55.000 0.00 0.00 37.66 2.85
770 771 1.201414 GCGCTAGGCTCTATCCTCTTC 59.799 57.143 0.00 0.00 37.66 2.87
771 772 2.790433 CGCTAGGCTCTATCCTCTTCT 58.210 52.381 0.00 0.00 37.66 2.85
772 773 3.153919 CGCTAGGCTCTATCCTCTTCTT 58.846 50.000 0.00 0.00 37.66 2.52
773 774 3.190535 CGCTAGGCTCTATCCTCTTCTTC 59.809 52.174 0.00 0.00 37.66 2.87
774 775 4.407365 GCTAGGCTCTATCCTCTTCTTCT 58.593 47.826 0.00 0.00 37.66 2.85
775 776 4.832823 GCTAGGCTCTATCCTCTTCTTCTT 59.167 45.833 0.00 0.00 37.66 2.52
776 777 5.304357 GCTAGGCTCTATCCTCTTCTTCTTT 59.696 44.000 0.00 0.00 37.66 2.52
777 778 6.183360 GCTAGGCTCTATCCTCTTCTTCTTTT 60.183 42.308 0.00 0.00 37.66 2.27
778 779 6.634889 AGGCTCTATCCTCTTCTTCTTTTT 57.365 37.500 0.00 0.00 0.00 1.94
820 821 5.541766 CGAATGATCGTACGGTCTAAAAG 57.458 43.478 27.43 12.39 44.06 2.27
821 822 4.085721 CGAATGATCGTACGGTCTAAAAGC 60.086 45.833 27.43 11.06 44.06 3.51
830 831 1.850441 CGGTCTAAAAGCGGTGTATCG 59.150 52.381 0.00 0.00 44.98 2.92
831 832 2.733227 CGGTCTAAAAGCGGTGTATCGT 60.733 50.000 0.00 0.00 44.98 3.73
832 833 2.601763 GGTCTAAAAGCGGTGTATCGTG 59.398 50.000 0.00 0.00 0.00 4.35
833 834 3.504863 GTCTAAAAGCGGTGTATCGTGA 58.495 45.455 0.00 0.00 0.00 4.35
834 835 3.546670 GTCTAAAAGCGGTGTATCGTGAG 59.453 47.826 0.00 0.00 0.00 3.51
835 836 1.722011 AAAAGCGGTGTATCGTGAGG 58.278 50.000 0.00 0.00 0.00 3.86
836 837 0.606604 AAAGCGGTGTATCGTGAGGT 59.393 50.000 0.00 0.00 0.00 3.85
837 838 1.466856 AAGCGGTGTATCGTGAGGTA 58.533 50.000 0.00 0.00 0.00 3.08
838 839 1.466856 AGCGGTGTATCGTGAGGTAA 58.533 50.000 0.00 0.00 0.00 2.85
839 840 1.133790 AGCGGTGTATCGTGAGGTAAC 59.866 52.381 0.00 0.00 0.00 2.50
840 841 1.818850 CGGTGTATCGTGAGGTAACG 58.181 55.000 0.00 0.00 44.92 3.18
841 842 1.553308 GGTGTATCGTGAGGTAACGC 58.447 55.000 0.00 0.00 43.26 4.84
848 849 2.260434 TGAGGTAACGCAGCGACC 59.740 61.111 24.65 19.77 43.45 4.79
849 850 2.879462 GAGGTAACGCAGCGACCG 60.879 66.667 24.65 0.00 40.15 4.79
850 851 4.430765 AGGTAACGCAGCGACCGG 62.431 66.667 24.65 0.00 40.15 5.28
858 859 3.061848 CAGCGACCGGCCCAAATT 61.062 61.111 0.00 0.00 45.17 1.82
859 860 2.282887 AGCGACCGGCCCAAATTT 60.283 55.556 0.00 0.00 45.17 1.82
860 861 2.126110 GCGACCGGCCCAAATTTG 60.126 61.111 11.40 11.40 34.80 2.32
891 892 2.582498 GCGCGTATCACTCGCCTT 60.582 61.111 8.43 0.00 45.44 4.35
892 893 1.298863 GCGCGTATCACTCGCCTTA 60.299 57.895 8.43 0.00 45.44 2.69
893 894 0.868602 GCGCGTATCACTCGCCTTAA 60.869 55.000 8.43 0.00 45.44 1.85
894 895 2.386888 GCGCGTATCACTCGCCTTAAA 61.387 52.381 8.43 0.00 45.44 1.52
895 896 3.860388 GCGCGTATCACTCGCCTTAAAA 61.860 50.000 8.43 0.00 45.44 1.52
896 897 5.294668 GCGCGTATCACTCGCCTTAAAAA 62.295 47.826 8.43 0.00 45.44 1.94
1395 1498 1.378778 CGTCCTCTCCTCGGGTTCT 60.379 63.158 0.00 0.00 0.00 3.01
1410 1513 2.029290 GGGTTCTCTCGTCAAGCACTTA 60.029 50.000 0.00 0.00 0.00 2.24
1433 1536 1.601419 ATGGTACGTGTGCCGCTACT 61.601 55.000 0.00 0.00 41.42 2.57
1475 1578 2.564771 TGCATGCTAGTTATGGTCAGC 58.435 47.619 20.33 0.00 34.56 4.26
1503 1614 4.664267 TGCTGGGCAGGGAGAGGT 62.664 66.667 0.00 0.00 33.32 3.85
1504 1615 4.106925 GCTGGGCAGGGAGAGGTG 62.107 72.222 0.00 0.00 0.00 4.00
1505 1616 3.406200 CTGGGCAGGGAGAGGTGG 61.406 72.222 0.00 0.00 0.00 4.61
1506 1617 4.270153 TGGGCAGGGAGAGGTGGT 62.270 66.667 0.00 0.00 0.00 4.16
1507 1618 3.721706 GGGCAGGGAGAGGTGGTG 61.722 72.222 0.00 0.00 0.00 4.17
1508 1619 2.607750 GGCAGGGAGAGGTGGTGA 60.608 66.667 0.00 0.00 0.00 4.02
1509 1620 1.997874 GGCAGGGAGAGGTGGTGAT 60.998 63.158 0.00 0.00 0.00 3.06
1510 1621 1.566298 GGCAGGGAGAGGTGGTGATT 61.566 60.000 0.00 0.00 0.00 2.57
1511 1622 0.329596 GCAGGGAGAGGTGGTGATTT 59.670 55.000 0.00 0.00 0.00 2.17
1512 1623 1.272147 GCAGGGAGAGGTGGTGATTTT 60.272 52.381 0.00 0.00 0.00 1.82
1513 1624 2.819348 GCAGGGAGAGGTGGTGATTTTT 60.819 50.000 0.00 0.00 0.00 1.94
1565 1676 9.696917 GGATTTTAGAAATAATGCTACATTGGG 57.303 33.333 3.11 0.00 0.00 4.12
1710 1821 1.400242 GCAGAAAACATGGCGTCTCAC 60.400 52.381 0.00 0.00 0.00 3.51
1858 1975 7.581213 TTGGACATTTTAGTGTTGATGAAGT 57.419 32.000 0.00 0.00 31.16 3.01
1898 2015 5.964958 ACACATTGTTGCTGCTTTATACT 57.035 34.783 0.00 0.00 0.00 2.12
1899 2016 8.554835 TTACACATTGTTGCTGCTTTATACTA 57.445 30.769 0.00 0.00 0.00 1.82
1900 2017 6.842163 ACACATTGTTGCTGCTTTATACTAC 58.158 36.000 0.00 0.00 0.00 2.73
1901 2018 6.655003 ACACATTGTTGCTGCTTTATACTACT 59.345 34.615 0.00 0.00 0.00 2.57
1902 2019 7.148407 ACACATTGTTGCTGCTTTATACTACTC 60.148 37.037 0.00 0.00 0.00 2.59
1903 2020 6.316390 ACATTGTTGCTGCTTTATACTACTCC 59.684 38.462 0.00 0.00 0.00 3.85
1904 2021 4.766375 TGTTGCTGCTTTATACTACTCCC 58.234 43.478 0.00 0.00 0.00 4.30
1905 2022 4.469945 TGTTGCTGCTTTATACTACTCCCT 59.530 41.667 0.00 0.00 0.00 4.20
1906 2023 4.939052 TGCTGCTTTATACTACTCCCTC 57.061 45.455 0.00 0.00 0.00 4.30
1907 2024 3.641906 TGCTGCTTTATACTACTCCCTCC 59.358 47.826 0.00 0.00 0.00 4.30
1908 2025 3.305471 GCTGCTTTATACTACTCCCTCCG 60.305 52.174 0.00 0.00 0.00 4.63
1909 2026 3.890147 CTGCTTTATACTACTCCCTCCGT 59.110 47.826 0.00 0.00 0.00 4.69
1910 2027 3.887716 TGCTTTATACTACTCCCTCCGTC 59.112 47.826 0.00 0.00 0.00 4.79
1911 2028 3.255395 GCTTTATACTACTCCCTCCGTCC 59.745 52.174 0.00 0.00 0.00 4.79
1912 2029 2.847327 TATACTACTCCCTCCGTCCG 57.153 55.000 0.00 0.00 0.00 4.79
1913 2030 0.110104 ATACTACTCCCTCCGTCCGG 59.890 60.000 0.00 0.00 0.00 5.14
1914 2031 0.982852 TACTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
1915 2032 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
1916 2033 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
1917 2034 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
1918 2035 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
1919 2036 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
1920 2037 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
1921 2038 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
1922 2039 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
1923 2040 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
1924 2041 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
1925 2042 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
1926 2043 1.997606 CCGTCCGGAAATACTTGTCAC 59.002 52.381 5.23 0.00 37.50 3.67
1927 2044 1.997606 CGTCCGGAAATACTTGTCACC 59.002 52.381 5.23 0.00 0.00 4.02
1928 2045 2.610976 CGTCCGGAAATACTTGTCACCA 60.611 50.000 5.23 0.00 0.00 4.17
1929 2046 3.404899 GTCCGGAAATACTTGTCACCAA 58.595 45.455 5.23 0.00 0.00 3.67
1930 2047 3.816523 GTCCGGAAATACTTGTCACCAAA 59.183 43.478 5.23 0.00 0.00 3.28
1931 2048 4.276431 GTCCGGAAATACTTGTCACCAAAA 59.724 41.667 5.23 0.00 0.00 2.44
1932 2049 5.048294 GTCCGGAAATACTTGTCACCAAAAT 60.048 40.000 5.23 0.00 0.00 1.82
1933 2050 5.048364 TCCGGAAATACTTGTCACCAAAATG 60.048 40.000 0.00 0.00 0.00 2.32
1934 2051 5.048364 CCGGAAATACTTGTCACCAAAATGA 60.048 40.000 0.00 0.00 0.00 2.57
1935 2052 6.442952 CGGAAATACTTGTCACCAAAATGAA 58.557 36.000 0.00 0.00 0.00 2.57
1936 2053 7.090173 CGGAAATACTTGTCACCAAAATGAAT 58.910 34.615 0.00 0.00 0.00 2.57
1937 2054 8.240682 CGGAAATACTTGTCACCAAAATGAATA 58.759 33.333 0.00 0.00 0.00 1.75
1938 2055 9.921637 GGAAATACTTGTCACCAAAATGAATAA 57.078 29.630 0.00 0.00 0.00 1.40
1944 2061 8.143835 ACTTGTCACCAAAATGAATAAAAGAGG 58.856 33.333 0.00 0.00 0.00 3.69
1945 2062 7.831691 TGTCACCAAAATGAATAAAAGAGGA 57.168 32.000 0.00 0.00 0.00 3.71
1946 2063 8.421249 TGTCACCAAAATGAATAAAAGAGGAT 57.579 30.769 0.00 0.00 0.00 3.24
1947 2064 8.306038 TGTCACCAAAATGAATAAAAGAGGATG 58.694 33.333 0.00 0.00 0.00 3.51
1948 2065 8.306761 GTCACCAAAATGAATAAAAGAGGATGT 58.693 33.333 0.00 0.00 0.00 3.06
1949 2066 9.527157 TCACCAAAATGAATAAAAGAGGATGTA 57.473 29.630 0.00 0.00 0.00 2.29
1987 2104 9.802039 TTTAGTTCTACATACATCCCTTTTTGT 57.198 29.630 0.00 0.00 0.00 2.83
1988 2105 9.802039 TTAGTTCTACATACATCCCTTTTTGTT 57.198 29.630 0.00 0.00 0.00 2.83
1989 2106 8.336801 AGTTCTACATACATCCCTTTTTGTTC 57.663 34.615 0.00 0.00 0.00 3.18
1990 2107 7.942341 AGTTCTACATACATCCCTTTTTGTTCA 59.058 33.333 0.00 0.00 0.00 3.18
1991 2108 8.739972 GTTCTACATACATCCCTTTTTGTTCAT 58.260 33.333 0.00 0.00 0.00 2.57
1992 2109 8.877864 TCTACATACATCCCTTTTTGTTCATT 57.122 30.769 0.00 0.00 0.00 2.57
1993 2110 9.308000 TCTACATACATCCCTTTTTGTTCATTT 57.692 29.630 0.00 0.00 0.00 2.32
1994 2111 9.927668 CTACATACATCCCTTTTTGTTCATTTT 57.072 29.630 0.00 0.00 0.00 1.82
1995 2112 8.606040 ACATACATCCCTTTTTGTTCATTTTG 57.394 30.769 0.00 0.00 0.00 2.44
1996 2113 8.428063 ACATACATCCCTTTTTGTTCATTTTGA 58.572 29.630 0.00 0.00 0.00 2.69
1997 2114 9.439500 CATACATCCCTTTTTGTTCATTTTGAT 57.561 29.630 0.00 0.00 0.00 2.57
1998 2115 7.733402 ACATCCCTTTTTGTTCATTTTGATG 57.267 32.000 0.00 0.00 33.80 3.07
1999 2116 7.507829 ACATCCCTTTTTGTTCATTTTGATGA 58.492 30.769 0.00 0.00 32.39 2.92
2000 2117 7.442062 ACATCCCTTTTTGTTCATTTTGATGAC 59.558 33.333 0.00 0.00 32.39 3.06
2001 2118 6.882656 TCCCTTTTTGTTCATTTTGATGACA 58.117 32.000 0.00 0.00 0.00 3.58
2002 2119 7.334090 TCCCTTTTTGTTCATTTTGATGACAA 58.666 30.769 0.00 0.00 0.00 3.18
2003 2120 7.495279 TCCCTTTTTGTTCATTTTGATGACAAG 59.505 33.333 0.00 0.00 37.32 3.16
2004 2121 7.280652 CCCTTTTTGTTCATTTTGATGACAAGT 59.719 33.333 0.00 0.00 37.32 3.16
2005 2122 9.311916 CCTTTTTGTTCATTTTGATGACAAGTA 57.688 29.630 0.00 0.00 37.32 2.24
2011 2128 9.179552 TGTTCATTTTGATGACAAGTATTTTCG 57.820 29.630 0.00 0.00 37.32 3.46
2012 2129 8.638565 GTTCATTTTGATGACAAGTATTTTCGG 58.361 33.333 0.00 0.00 37.32 4.30
2013 2130 8.105097 TCATTTTGATGACAAGTATTTTCGGA 57.895 30.769 0.00 0.00 37.32 4.55
2014 2131 8.020819 TCATTTTGATGACAAGTATTTTCGGAC 58.979 33.333 0.00 0.00 37.32 4.79
2015 2132 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
2016 2133 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
2017 2134 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
2018 2135 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
2019 2136 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2020 2137 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2021 2138 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
2022 2139 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
2269 2386 7.306983 GGTCTTCATATGCTTGCATTTTATTGC 60.307 37.037 13.52 1.18 43.07 3.56
2309 2426 4.577693 CACCATCGGTTTCATTCATCTCAT 59.422 41.667 0.00 0.00 31.02 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 4.895478 TAATACCCGCACCGCCGC 62.895 66.667 0.00 0.00 0.00 6.53
41 42 2.660552 CTAATACCCGCACCGCCG 60.661 66.667 0.00 0.00 0.00 6.46
42 43 2.280592 CCTAATACCCGCACCGCC 60.281 66.667 0.00 0.00 0.00 6.13
43 44 2.280592 CCCTAATACCCGCACCGC 60.281 66.667 0.00 0.00 0.00 5.68
44 45 0.107557 AAACCCTAATACCCGCACCG 60.108 55.000 0.00 0.00 0.00 4.94
45 46 2.435437 TCTAAACCCTAATACCCGCACC 59.565 50.000 0.00 0.00 0.00 5.01
46 47 3.825143 TCTAAACCCTAATACCCGCAC 57.175 47.619 0.00 0.00 0.00 5.34
47 48 3.432608 GCTTCTAAACCCTAATACCCGCA 60.433 47.826 0.00 0.00 0.00 5.69
48 49 3.136763 GCTTCTAAACCCTAATACCCGC 58.863 50.000 0.00 0.00 0.00 6.13
49 50 3.387397 CGCTTCTAAACCCTAATACCCG 58.613 50.000 0.00 0.00 0.00 5.28
50 51 3.389002 TCCGCTTCTAAACCCTAATACCC 59.611 47.826 0.00 0.00 0.00 3.69
51 52 4.677673 TCCGCTTCTAAACCCTAATACC 57.322 45.455 0.00 0.00 0.00 2.73
52 53 4.510711 GCTTCCGCTTCTAAACCCTAATAC 59.489 45.833 0.00 0.00 0.00 1.89
53 54 4.700700 GCTTCCGCTTCTAAACCCTAATA 58.299 43.478 0.00 0.00 0.00 0.98
54 55 3.542648 GCTTCCGCTTCTAAACCCTAAT 58.457 45.455 0.00 0.00 0.00 1.73
55 56 2.675889 CGCTTCCGCTTCTAAACCCTAA 60.676 50.000 0.00 0.00 0.00 2.69
56 57 1.134907 CGCTTCCGCTTCTAAACCCTA 60.135 52.381 0.00 0.00 0.00 3.53
57 58 0.391263 CGCTTCCGCTTCTAAACCCT 60.391 55.000 0.00 0.00 0.00 4.34
58 59 0.390735 TCGCTTCCGCTTCTAAACCC 60.391 55.000 0.00 0.00 0.00 4.11
59 60 1.593469 GATCGCTTCCGCTTCTAAACC 59.407 52.381 0.00 0.00 0.00 3.27
60 61 1.255600 CGATCGCTTCCGCTTCTAAAC 59.744 52.381 0.26 0.00 0.00 2.01
61 62 1.135199 ACGATCGCTTCCGCTTCTAAA 60.135 47.619 16.60 0.00 0.00 1.85
62 63 0.454600 ACGATCGCTTCCGCTTCTAA 59.545 50.000 16.60 0.00 0.00 2.10
63 64 1.302366 TACGATCGCTTCCGCTTCTA 58.698 50.000 16.60 0.00 0.00 2.10
64 65 0.454600 TTACGATCGCTTCCGCTTCT 59.545 50.000 16.60 0.00 0.00 2.85
65 66 0.571197 GTTACGATCGCTTCCGCTTC 59.429 55.000 16.60 0.00 0.00 3.86
66 67 0.804933 GGTTACGATCGCTTCCGCTT 60.805 55.000 16.60 0.00 0.00 4.68
67 68 1.226888 GGTTACGATCGCTTCCGCT 60.227 57.895 16.60 0.00 0.00 5.52
68 69 0.029834 TAGGTTACGATCGCTTCCGC 59.970 55.000 16.60 0.00 0.00 5.54
69 70 1.925068 GCTAGGTTACGATCGCTTCCG 60.925 57.143 16.60 4.59 0.00 4.30
70 71 1.768510 GCTAGGTTACGATCGCTTCC 58.231 55.000 16.60 14.35 0.00 3.46
71 72 1.268437 ACGCTAGGTTACGATCGCTTC 60.268 52.381 16.60 5.25 0.00 3.86
72 73 0.737219 ACGCTAGGTTACGATCGCTT 59.263 50.000 16.60 0.00 0.00 4.68
73 74 0.029035 CACGCTAGGTTACGATCGCT 59.971 55.000 16.60 6.62 0.00 4.93
74 75 0.028505 TCACGCTAGGTTACGATCGC 59.971 55.000 16.60 0.00 0.00 4.58
75 76 2.682952 ATCACGCTAGGTTACGATCG 57.317 50.000 14.88 14.88 0.00 3.69
76 77 3.251729 TGGTATCACGCTAGGTTACGATC 59.748 47.826 0.00 0.00 0.00 3.69
77 78 3.216800 TGGTATCACGCTAGGTTACGAT 58.783 45.455 0.00 0.00 0.00 3.73
78 79 2.642427 TGGTATCACGCTAGGTTACGA 58.358 47.619 0.00 0.00 0.00 3.43
79 80 3.243301 ACATGGTATCACGCTAGGTTACG 60.243 47.826 0.00 0.00 0.00 3.18
80 81 4.317671 ACATGGTATCACGCTAGGTTAC 57.682 45.455 0.00 0.00 0.00 2.50
81 82 5.829391 TCTTACATGGTATCACGCTAGGTTA 59.171 40.000 0.00 0.00 0.00 2.85
82 83 4.647853 TCTTACATGGTATCACGCTAGGTT 59.352 41.667 0.00 0.00 0.00 3.50
83 84 4.037684 GTCTTACATGGTATCACGCTAGGT 59.962 45.833 0.00 0.00 0.00 3.08
84 85 4.037565 TGTCTTACATGGTATCACGCTAGG 59.962 45.833 0.00 0.00 0.00 3.02
85 86 5.183014 TGTCTTACATGGTATCACGCTAG 57.817 43.478 0.00 0.00 0.00 3.42
86 87 5.585820 TTGTCTTACATGGTATCACGCTA 57.414 39.130 0.00 0.00 0.00 4.26
87 88 4.465632 TTGTCTTACATGGTATCACGCT 57.534 40.909 0.00 0.00 0.00 5.07
88 89 6.479001 ACTTATTGTCTTACATGGTATCACGC 59.521 38.462 0.00 0.00 0.00 5.34
89 90 8.420374 AACTTATTGTCTTACATGGTATCACG 57.580 34.615 0.00 0.00 0.00 4.35
93 94 8.966868 CCCAAAACTTATTGTCTTACATGGTAT 58.033 33.333 0.00 0.00 0.00 2.73
94 95 8.164733 TCCCAAAACTTATTGTCTTACATGGTA 58.835 33.333 0.00 0.00 0.00 3.25
95 96 7.007723 TCCCAAAACTTATTGTCTTACATGGT 58.992 34.615 0.00 0.00 0.00 3.55
96 97 7.461182 TCCCAAAACTTATTGTCTTACATGG 57.539 36.000 0.00 0.00 0.00 3.66
97 98 7.812669 GGTTCCCAAAACTTATTGTCTTACATG 59.187 37.037 0.00 0.00 0.00 3.21
98 99 7.507616 TGGTTCCCAAAACTTATTGTCTTACAT 59.492 33.333 0.00 0.00 0.00 2.29
99 100 6.834451 TGGTTCCCAAAACTTATTGTCTTACA 59.166 34.615 0.00 0.00 0.00 2.41
100 101 7.279750 TGGTTCCCAAAACTTATTGTCTTAC 57.720 36.000 0.00 0.00 0.00 2.34
101 102 6.015772 GCTGGTTCCCAAAACTTATTGTCTTA 60.016 38.462 0.00 0.00 30.80 2.10
102 103 5.221441 GCTGGTTCCCAAAACTTATTGTCTT 60.221 40.000 0.00 0.00 30.80 3.01
103 104 4.280929 GCTGGTTCCCAAAACTTATTGTCT 59.719 41.667 0.00 0.00 30.80 3.41
104 105 4.038642 TGCTGGTTCCCAAAACTTATTGTC 59.961 41.667 0.00 0.00 30.80 3.18
105 106 3.964031 TGCTGGTTCCCAAAACTTATTGT 59.036 39.130 0.00 0.00 30.80 2.71
106 107 4.202202 TGTGCTGGTTCCCAAAACTTATTG 60.202 41.667 0.00 0.00 30.80 1.90
107 108 3.964031 TGTGCTGGTTCCCAAAACTTATT 59.036 39.130 0.00 0.00 30.80 1.40
108 109 3.571590 TGTGCTGGTTCCCAAAACTTAT 58.428 40.909 0.00 0.00 30.80 1.73
109 110 3.019799 TGTGCTGGTTCCCAAAACTTA 57.980 42.857 0.00 0.00 30.80 2.24
110 111 1.859302 TGTGCTGGTTCCCAAAACTT 58.141 45.000 0.00 0.00 30.80 2.66
111 112 1.480545 GTTGTGCTGGTTCCCAAAACT 59.519 47.619 0.00 0.00 30.80 2.66
112 113 1.472552 GGTTGTGCTGGTTCCCAAAAC 60.473 52.381 0.00 0.00 30.80 2.43
113 114 0.827368 GGTTGTGCTGGTTCCCAAAA 59.173 50.000 0.00 0.00 30.80 2.44
114 115 1.045911 GGGTTGTGCTGGTTCCCAAA 61.046 55.000 0.00 0.00 38.15 3.28
115 116 1.456705 GGGTTGTGCTGGTTCCCAA 60.457 57.895 0.00 0.00 38.15 4.12
116 117 2.197324 GGGTTGTGCTGGTTCCCA 59.803 61.111 0.00 0.00 38.15 4.37
117 118 1.603739 GAGGGTTGTGCTGGTTCCC 60.604 63.158 0.00 0.00 38.50 3.97
118 119 0.690762 TAGAGGGTTGTGCTGGTTCC 59.309 55.000 0.00 0.00 0.00 3.62
119 120 1.339151 CCTAGAGGGTTGTGCTGGTTC 60.339 57.143 0.00 0.00 0.00 3.62
120 121 0.693049 CCTAGAGGGTTGTGCTGGTT 59.307 55.000 0.00 0.00 0.00 3.67
121 122 2.377136 CCTAGAGGGTTGTGCTGGT 58.623 57.895 0.00 0.00 0.00 4.00
132 133 2.252714 GAGATAAGCCACCCCTAGAGG 58.747 57.143 0.00 0.00 0.00 3.69
133 134 2.964209 TGAGATAAGCCACCCCTAGAG 58.036 52.381 0.00 0.00 0.00 2.43
134 135 3.637821 ATGAGATAAGCCACCCCTAGA 57.362 47.619 0.00 0.00 0.00 2.43
135 136 7.682787 ATATAATGAGATAAGCCACCCCTAG 57.317 40.000 0.00 0.00 0.00 3.02
137 138 9.744125 TTATATATAATGAGATAAGCCACCCCT 57.256 33.333 0.81 0.00 0.00 4.79
160 161 9.688091 TGGTACATATTGTAACACAACCATTAT 57.312 29.630 1.37 0.00 44.80 1.28
194 195 9.233649 GACTATGTATAGCTTCTGTACCTATGT 57.766 37.037 0.00 0.00 33.68 2.29
195 196 9.456147 AGACTATGTATAGCTTCTGTACCTATG 57.544 37.037 0.00 0.00 33.68 2.23
198 199 9.287373 GTTAGACTATGTATAGCTTCTGTACCT 57.713 37.037 0.00 0.00 33.68 3.08
199 200 9.064706 TGTTAGACTATGTATAGCTTCTGTACC 57.935 37.037 0.00 0.00 33.68 3.34
324 325 0.811616 GCTTTCCATCTCGCCATCGT 60.812 55.000 0.00 0.00 36.96 3.73
382 383 3.660111 GCAACTCCGCCACCACAC 61.660 66.667 0.00 0.00 0.00 3.82
589 590 4.072088 CCGTCGGTTTGCTCGTGC 62.072 66.667 2.08 1.71 40.20 5.34
590 591 4.072088 GCCGTCGGTTTGCTCGTG 62.072 66.667 13.94 0.00 0.00 4.35
593 594 3.774702 GTCGCCGTCGGTTTGCTC 61.775 66.667 13.94 0.00 36.13 4.26
596 597 2.663852 AAGGTCGCCGTCGGTTTG 60.664 61.111 13.94 3.52 36.13 2.93
597 598 2.663852 CAAGGTCGCCGTCGGTTT 60.664 61.111 13.94 0.00 36.13 3.27
617 618 3.512452 CAAGTCGTCGTCGTCGCG 61.512 66.667 0.00 0.00 38.33 5.87
618 619 3.164011 CCAAGTCGTCGTCGTCGC 61.164 66.667 7.01 3.07 38.33 5.19
619 620 2.073220 CACCAAGTCGTCGTCGTCG 61.073 63.158 5.50 5.50 38.33 5.12
620 621 2.362800 GCACCAAGTCGTCGTCGTC 61.363 63.158 1.33 0.00 38.33 4.20
621 622 2.354305 GCACCAAGTCGTCGTCGT 60.354 61.111 1.33 0.00 38.33 4.34
622 623 2.354188 TGCACCAAGTCGTCGTCG 60.354 61.111 0.00 0.00 38.55 5.12
623 624 2.658707 GCTGCACCAAGTCGTCGTC 61.659 63.158 0.00 0.00 0.00 4.20
624 625 2.661866 GCTGCACCAAGTCGTCGT 60.662 61.111 0.00 0.00 0.00 4.34
625 626 3.767230 CGCTGCACCAAGTCGTCG 61.767 66.667 0.00 0.00 0.00 5.12
626 627 4.077188 GCGCTGCACCAAGTCGTC 62.077 66.667 0.00 0.00 0.00 4.20
725 726 2.278206 CGACCTCATCCGCACTCG 60.278 66.667 0.00 0.00 0.00 4.18
726 727 1.064946 CTCGACCTCATCCGCACTC 59.935 63.158 0.00 0.00 0.00 3.51
727 728 3.069980 GCTCGACCTCATCCGCACT 62.070 63.158 0.00 0.00 0.00 4.40
728 729 2.583593 GCTCGACCTCATCCGCAC 60.584 66.667 0.00 0.00 0.00 5.34
729 730 4.193334 CGCTCGACCTCATCCGCA 62.193 66.667 0.00 0.00 0.00 5.69
730 731 4.933064 CCGCTCGACCTCATCCGC 62.933 72.222 0.00 0.00 0.00 5.54
731 732 3.064987 AACCGCTCGACCTCATCCG 62.065 63.158 0.00 0.00 0.00 4.18
732 733 1.519455 CAACCGCTCGACCTCATCC 60.519 63.158 0.00 0.00 0.00 3.51
733 734 2.167861 GCAACCGCTCGACCTCATC 61.168 63.158 0.00 0.00 34.30 2.92
734 735 2.125512 GCAACCGCTCGACCTCAT 60.126 61.111 0.00 0.00 34.30 2.90
735 736 4.717629 CGCAACCGCTCGACCTCA 62.718 66.667 0.00 0.00 35.30 3.86
745 746 0.664767 GATAGAGCCTAGCGCAACCG 60.665 60.000 11.47 0.00 41.38 4.44
746 747 0.319986 GGATAGAGCCTAGCGCAACC 60.320 60.000 11.47 0.00 41.38 3.77
747 748 0.676736 AGGATAGAGCCTAGCGCAAC 59.323 55.000 11.47 0.00 41.38 4.17
748 749 0.962489 GAGGATAGAGCCTAGCGCAA 59.038 55.000 11.47 0.00 38.73 4.85
749 750 0.111446 AGAGGATAGAGCCTAGCGCA 59.889 55.000 11.47 0.00 38.73 6.09
750 751 1.201414 GAAGAGGATAGAGCCTAGCGC 59.799 57.143 0.00 0.00 38.73 5.92
751 752 2.790433 AGAAGAGGATAGAGCCTAGCG 58.210 52.381 0.00 0.00 38.73 4.26
752 753 4.407365 AGAAGAAGAGGATAGAGCCTAGC 58.593 47.826 0.00 0.00 38.73 3.42
753 754 6.976934 AAAGAAGAAGAGGATAGAGCCTAG 57.023 41.667 0.00 0.00 38.73 3.02
754 755 7.741554 AAAAAGAAGAAGAGGATAGAGCCTA 57.258 36.000 0.00 0.00 38.73 3.93
755 756 6.634889 AAAAAGAAGAAGAGGATAGAGCCT 57.365 37.500 0.00 0.00 42.17 4.58
799 800 4.085721 CGCTTTTAGACCGTACGATCATTC 60.086 45.833 18.76 4.86 0.00 2.67
800 801 3.795101 CGCTTTTAGACCGTACGATCATT 59.205 43.478 18.76 0.00 0.00 2.57
801 802 3.369385 CGCTTTTAGACCGTACGATCAT 58.631 45.455 18.76 1.59 0.00 2.45
802 803 2.478370 CCGCTTTTAGACCGTACGATCA 60.478 50.000 18.76 0.00 0.00 2.92
803 804 2.114825 CCGCTTTTAGACCGTACGATC 58.885 52.381 18.76 9.86 0.00 3.69
804 805 1.474077 ACCGCTTTTAGACCGTACGAT 59.526 47.619 18.76 0.00 0.00 3.73
805 806 0.881118 ACCGCTTTTAGACCGTACGA 59.119 50.000 18.76 0.00 0.00 3.43
806 807 0.986992 CACCGCTTTTAGACCGTACG 59.013 55.000 8.69 8.69 0.00 3.67
807 808 2.070262 ACACCGCTTTTAGACCGTAC 57.930 50.000 0.00 0.00 0.00 3.67
808 809 3.487376 CGATACACCGCTTTTAGACCGTA 60.487 47.826 0.00 0.00 0.00 4.02
809 810 2.733227 CGATACACCGCTTTTAGACCGT 60.733 50.000 0.00 0.00 0.00 4.83
810 811 1.850441 CGATACACCGCTTTTAGACCG 59.150 52.381 0.00 0.00 0.00 4.79
811 812 2.601763 CACGATACACCGCTTTTAGACC 59.398 50.000 0.00 0.00 0.00 3.85
812 813 3.504863 TCACGATACACCGCTTTTAGAC 58.495 45.455 0.00 0.00 0.00 2.59
813 814 3.428452 CCTCACGATACACCGCTTTTAGA 60.428 47.826 0.00 0.00 0.00 2.10
814 815 2.858344 CCTCACGATACACCGCTTTTAG 59.142 50.000 0.00 0.00 0.00 1.85
815 816 2.231964 ACCTCACGATACACCGCTTTTA 59.768 45.455 0.00 0.00 0.00 1.52
816 817 1.001633 ACCTCACGATACACCGCTTTT 59.998 47.619 0.00 0.00 0.00 2.27
817 818 0.606604 ACCTCACGATACACCGCTTT 59.393 50.000 0.00 0.00 0.00 3.51
818 819 1.466856 TACCTCACGATACACCGCTT 58.533 50.000 0.00 0.00 0.00 4.68
819 820 1.133790 GTTACCTCACGATACACCGCT 59.866 52.381 0.00 0.00 0.00 5.52
820 821 1.553308 GTTACCTCACGATACACCGC 58.447 55.000 0.00 0.00 0.00 5.68
821 822 1.818850 CGTTACCTCACGATACACCG 58.181 55.000 0.00 0.00 43.15 4.94
822 823 1.135315 TGCGTTACCTCACGATACACC 60.135 52.381 0.00 0.00 43.15 4.16
823 824 2.182825 CTGCGTTACCTCACGATACAC 58.817 52.381 0.00 0.00 43.15 2.90
824 825 1.468565 GCTGCGTTACCTCACGATACA 60.469 52.381 0.00 0.00 43.15 2.29
825 826 1.197910 GCTGCGTTACCTCACGATAC 58.802 55.000 0.00 0.00 43.15 2.24
826 827 0.248336 CGCTGCGTTACCTCACGATA 60.248 55.000 14.93 0.00 43.15 2.92
827 828 1.516386 CGCTGCGTTACCTCACGAT 60.516 57.895 14.93 0.00 43.15 3.73
828 829 2.126618 CGCTGCGTTACCTCACGA 60.127 61.111 14.93 0.00 43.15 4.35
829 830 2.126618 TCGCTGCGTTACCTCACG 60.127 61.111 22.48 0.00 43.36 4.35
830 831 2.092882 GGTCGCTGCGTTACCTCAC 61.093 63.158 22.48 10.46 0.00 3.51
831 832 2.260434 GGTCGCTGCGTTACCTCA 59.740 61.111 22.48 0.00 0.00 3.86
832 833 2.879462 CGGTCGCTGCGTTACCTC 60.879 66.667 24.45 10.10 0.00 3.85
833 834 4.430765 CCGGTCGCTGCGTTACCT 62.431 66.667 24.45 0.00 0.00 3.08
841 842 2.635443 AAATTTGGGCCGGTCGCTG 61.635 57.895 1.90 0.00 37.74 5.18
842 843 2.282887 AAATTTGGGCCGGTCGCT 60.283 55.556 1.90 0.00 37.74 4.93
843 844 2.126110 CAAATTTGGGCCGGTCGC 60.126 61.111 10.49 4.53 0.00 5.19
844 845 2.571231 CCAAATTTGGGCCGGTCG 59.429 61.111 26.87 1.10 44.70 4.79
937 938 0.958382 CCGCCTTGAAATGGACGGAA 60.958 55.000 8.99 0.00 46.15 4.30
1395 1498 3.317150 CATGTGTAAGTGCTTGACGAGA 58.683 45.455 0.00 0.00 0.00 4.04
1475 1578 2.516930 CCCAGCAGCCCATAACCG 60.517 66.667 0.00 0.00 0.00 4.44
1518 1629 1.133730 ACCACCTCTTACCCGCAAAAA 60.134 47.619 0.00 0.00 0.00 1.94
1519 1630 0.475044 ACCACCTCTTACCCGCAAAA 59.525 50.000 0.00 0.00 0.00 2.44
1520 1631 0.250553 CACCACCTCTTACCCGCAAA 60.251 55.000 0.00 0.00 0.00 3.68
1521 1632 1.373435 CACCACCTCTTACCCGCAA 59.627 57.895 0.00 0.00 0.00 4.85
1522 1633 2.589157 CCACCACCTCTTACCCGCA 61.589 63.158 0.00 0.00 0.00 5.69
1523 1634 1.623542 ATCCACCACCTCTTACCCGC 61.624 60.000 0.00 0.00 0.00 6.13
1524 1635 0.909623 AATCCACCACCTCTTACCCG 59.090 55.000 0.00 0.00 0.00 5.28
1525 1636 3.451402 AAAATCCACCACCTCTTACCC 57.549 47.619 0.00 0.00 0.00 3.69
1526 1637 5.431179 TCTAAAATCCACCACCTCTTACC 57.569 43.478 0.00 0.00 0.00 2.85
1527 1638 7.939784 ATTTCTAAAATCCACCACCTCTTAC 57.060 36.000 0.00 0.00 0.00 2.34
1529 1640 8.971073 CATTATTTCTAAAATCCACCACCTCTT 58.029 33.333 0.00 0.00 0.00 2.85
1530 1641 7.068716 GCATTATTTCTAAAATCCACCACCTCT 59.931 37.037 0.00 0.00 0.00 3.69
1531 1642 7.068716 AGCATTATTTCTAAAATCCACCACCTC 59.931 37.037 0.00 0.00 0.00 3.85
1532 1643 6.897413 AGCATTATTTCTAAAATCCACCACCT 59.103 34.615 0.00 0.00 0.00 4.00
1564 1675 4.718940 AACTATTTGCAGGCAACATACC 57.281 40.909 6.14 0.00 41.41 2.73
1565 1676 7.812669 ACTTAAAACTATTTGCAGGCAACATAC 59.187 33.333 6.14 0.00 41.41 2.39
1870 1987 3.213506 AGCAGCAACAATGTGTAAGACA 58.786 40.909 0.00 0.00 39.53 3.41
1898 2015 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
1899 2016 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
1900 2017 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
1901 2018 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
1902 2019 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
1903 2020 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
1904 2021 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
1905 2022 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
1906 2023 1.997606 GTGACAAGTATTTCCGGACGG 59.002 52.381 1.83 3.96 0.00 4.79
1907 2024 1.997606 GGTGACAAGTATTTCCGGACG 59.002 52.381 1.83 0.00 0.00 4.79
1908 2025 3.048337 TGGTGACAAGTATTTCCGGAC 57.952 47.619 1.83 0.00 37.44 4.79
1921 2038 7.831691 TCCTCTTTTATTCATTTTGGTGACA 57.168 32.000 0.00 0.00 39.83 3.58
1922 2039 8.306761 ACATCCTCTTTTATTCATTTTGGTGAC 58.693 33.333 0.00 0.00 0.00 3.67
1923 2040 8.421249 ACATCCTCTTTTATTCATTTTGGTGA 57.579 30.769 0.00 0.00 0.00 4.02
1961 2078 9.802039 ACAAAAAGGGATGTATGTAGAACTAAA 57.198 29.630 0.00 0.00 0.00 1.85
1962 2079 9.802039 AACAAAAAGGGATGTATGTAGAACTAA 57.198 29.630 0.00 0.00 0.00 2.24
1963 2080 9.444600 GAACAAAAAGGGATGTATGTAGAACTA 57.555 33.333 0.00 0.00 0.00 2.24
1964 2081 7.942341 TGAACAAAAAGGGATGTATGTAGAACT 59.058 33.333 0.00 0.00 0.00 3.01
1965 2082 8.106247 TGAACAAAAAGGGATGTATGTAGAAC 57.894 34.615 0.00 0.00 0.00 3.01
1966 2083 8.877864 ATGAACAAAAAGGGATGTATGTAGAA 57.122 30.769 0.00 0.00 0.00 2.10
1967 2084 8.877864 AATGAACAAAAAGGGATGTATGTAGA 57.122 30.769 0.00 0.00 0.00 2.59
1968 2085 9.927668 AAAATGAACAAAAAGGGATGTATGTAG 57.072 29.630 0.00 0.00 0.00 2.74
1969 2086 9.703892 CAAAATGAACAAAAAGGGATGTATGTA 57.296 29.630 0.00 0.00 0.00 2.29
1970 2087 8.428063 TCAAAATGAACAAAAAGGGATGTATGT 58.572 29.630 0.00 0.00 0.00 2.29
1971 2088 8.830201 TCAAAATGAACAAAAAGGGATGTATG 57.170 30.769 0.00 0.00 0.00 2.39
1972 2089 9.439500 CATCAAAATGAACAAAAAGGGATGTAT 57.561 29.630 0.00 0.00 34.61 2.29
1973 2090 8.646004 TCATCAAAATGAACAAAAAGGGATGTA 58.354 29.630 0.00 0.00 38.97 2.29
1974 2091 7.442062 GTCATCAAAATGAACAAAAAGGGATGT 59.558 33.333 0.00 0.00 43.42 3.06
1975 2092 7.441760 TGTCATCAAAATGAACAAAAAGGGATG 59.558 33.333 0.00 0.00 43.42 3.51
1976 2093 7.507829 TGTCATCAAAATGAACAAAAAGGGAT 58.492 30.769 0.00 0.00 43.42 3.85
1977 2094 6.882656 TGTCATCAAAATGAACAAAAAGGGA 58.117 32.000 0.00 0.00 43.42 4.20
1978 2095 7.280652 ACTTGTCATCAAAATGAACAAAAAGGG 59.719 33.333 0.87 0.00 43.42 3.95
1979 2096 8.200364 ACTTGTCATCAAAATGAACAAAAAGG 57.800 30.769 0.87 0.00 43.42 3.11
1985 2102 9.179552 CGAAAATACTTGTCATCAAAATGAACA 57.820 29.630 0.00 0.00 43.42 3.18
1986 2103 8.638565 CCGAAAATACTTGTCATCAAAATGAAC 58.361 33.333 0.00 0.00 43.42 3.18
1987 2104 8.572185 TCCGAAAATACTTGTCATCAAAATGAA 58.428 29.630 0.00 0.00 43.42 2.57
1988 2105 8.020819 GTCCGAAAATACTTGTCATCAAAATGA 58.979 33.333 0.00 0.00 39.63 2.57
1989 2106 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
1990 2107 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
1991 2108 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
1992 2109 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
1993 2110 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
1994 2111 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
1995 2112 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
1996 2113 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
1997 2114 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
1998 2115 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
1999 2116 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2000 2117 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2001 2118 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
2002 2119 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
2003 2120 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
2004 2121 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2005 2122 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
2006 2123 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
2007 2124 1.856629 AATACTCCCTCCGTCCGAAA 58.143 50.000 0.00 0.00 0.00 3.46
2008 2125 1.856629 AAATACTCCCTCCGTCCGAA 58.143 50.000 0.00 0.00 0.00 4.30
2009 2126 2.734755 TAAATACTCCCTCCGTCCGA 57.265 50.000 0.00 0.00 0.00 4.55
2010 2127 5.458041 TTAATAAATACTCCCTCCGTCCG 57.542 43.478 0.00 0.00 0.00 4.79
2011 2128 8.687292 AAAATTAATAAATACTCCCTCCGTCC 57.313 34.615 0.00 0.00 0.00 4.79
2012 2129 9.333724 TGAAAATTAATAAATACTCCCTCCGTC 57.666 33.333 0.00 0.00 0.00 4.79
2013 2130 9.862149 ATGAAAATTAATAAATACTCCCTCCGT 57.138 29.630 0.00 0.00 0.00 4.69
2269 2386 2.361757 TGGTGCCACAGAAAACATCAAG 59.638 45.455 0.00 0.00 0.00 3.02
2377 2494 4.667519 ACTCGGTCCATATGAAGGTAAC 57.332 45.455 3.65 0.00 0.00 2.50
2393 2510 4.156190 TGCTTCTCTCTAGTTGTAACTCGG 59.844 45.833 0.00 0.00 40.37 4.63


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.