Multiple sequence alignment - TraesCS3B01G143800

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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 TraesCS3B01G143800 chr3B 100.000 4295 0 0 1 4295 132531541 132527247 0.000000e+00 7932.0
1 TraesCS3B01G143800 chr3B 89.123 285 31 0 1417 1701 132530032 132529748 5.280000e-94 355.0
2 TraesCS3B01G143800 chr3B 89.123 285 31 0 1510 1794 132530125 132529841 5.280000e-94 355.0
3 TraesCS3B01G143800 chr3B 88.830 188 21 0 1417 1604 132529939 132529752 9.290000e-57 231.0
4 TraesCS3B01G143800 chr3B 88.830 188 21 0 1603 1790 132530125 132529938 9.290000e-57 231.0
5 TraesCS3B01G143800 chr3D 94.155 3422 154 19 776 4160 84013761 84017173 0.000000e+00 5169.0
6 TraesCS3B01G143800 chr3D 85.826 642 53 14 1 620 84012658 84013283 0.000000e+00 647.0
7 TraesCS3B01G143800 chr3D 89.123 285 31 0 1510 1794 84014405 84014689 5.280000e-94 355.0
8 TraesCS3B01G143800 chr3D 88.772 285 32 0 1417 1701 84014498 84014782 2.460000e-92 350.0
9 TraesCS3B01G143800 chr3D 88.830 188 21 0 1417 1604 84014591 84014778 9.290000e-57 231.0
10 TraesCS3B01G143800 chr3D 96.774 93 3 0 4159 4251 509255197 509255105 5.750000e-34 156.0
11 TraesCS3B01G143800 chr3D 87.500 96 11 1 1417 1511 84014683 84014778 4.540000e-20 110.0
12 TraesCS3B01G143800 chr3A 91.654 2600 123 21 1649 4160 100188919 100191512 0.000000e+00 3513.0
13 TraesCS3B01G143800 chr3A 95.740 845 23 3 776 1607 100187930 100188774 0.000000e+00 1349.0
14 TraesCS3B01G143800 chr3A 86.624 628 52 14 1 612 100187259 100187870 0.000000e+00 665.0
15 TraesCS3B01G143800 chr3A 89.474 190 20 0 1510 1699 100188584 100188773 1.540000e-59 241.0
16 TraesCS3B01G143800 chr3A 89.362 188 20 0 1603 1790 100188584 100188771 2.000000e-58 237.0
17 TraesCS3B01G143800 chr3A 90.625 96 8 1 1695 1790 100188584 100188678 4.510000e-25 126.0
18 TraesCS3B01G143800 chr7B 97.826 92 2 0 4152 4243 661996386 661996477 4.450000e-35 159.0
19 TraesCS3B01G143800 chr2D 97.826 92 2 0 4159 4250 524566912 524566821 4.450000e-35 159.0
20 TraesCS3B01G143800 chr7D 97.802 91 2 0 4158 4248 506141454 506141364 1.600000e-34 158.0
21 TraesCS3B01G143800 chr4B 95.876 97 4 0 4154 4250 107553533 107553629 1.600000e-34 158.0
22 TraesCS3B01G143800 chr4B 90.991 111 8 2 4143 4251 586463912 586464022 9.620000e-32 148.0
23 TraesCS3B01G143800 chr5D 96.774 93 3 0 4159 4251 297738342 297738434 5.750000e-34 156.0
24 TraesCS3B01G143800 chr5D 77.011 174 35 3 13 185 271679330 271679499 1.270000e-15 95.3
25 TraesCS3B01G143800 chr5B 94.949 99 5 0 4158 4256 679686674 679686576 5.750000e-34 156.0
26 TraesCS3B01G143800 chr1B 93.458 107 2 5 4158 4260 61100148 61100043 2.070000e-33 154.0


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 TraesCS3B01G143800 chr3B 132527247 132531541 4294 True 1820.800000 7932 91.181200 1 4295 5 chr3B.!!$R1 4294
1 TraesCS3B01G143800 chr3D 84012658 84017173 4515 False 1143.666667 5169 89.034333 1 4160 6 chr3D.!!$F1 4159
2 TraesCS3B01G143800 chr3A 100187259 100191512 4253 False 1021.833333 3513 90.579833 1 4160 6 chr3A.!!$F1 4159

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
20 21 0.106015 TCGAGGATCATCTGGAGGCA 60.106 55.0 5.74 0.0 33.17 4.75 F
701 1082 0.178992 CACTGCCACCTCCCTCAAAA 60.179 55.0 0.00 0.0 0.00 2.44 F
1189 1583 0.401738 CTTCCAGGCCAAGTCCAAGA 59.598 55.0 5.01 0.0 0.00 3.02 F
2707 3267 0.438830 CAGTAACTCGCGCCTTTGTC 59.561 55.0 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1860 2357 0.239082 ACTGTGTCGTCGCGTGATTA 59.761 50.000 5.77 0.00 0.00 1.75 R
2683 3243 0.246635 AGGCGCGAGTTACTGAACAT 59.753 50.000 12.10 0.00 38.10 2.71 R
2793 3365 1.338973 TCCTTACGCACACGAGTTTCT 59.661 47.619 0.00 0.00 43.93 2.52 R
4275 4873 0.183731 TCGAGAGCAGGCCATCTCTA 59.816 55.000 22.01 12.91 39.57 2.43 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
20 21 0.106015 TCGAGGATCATCTGGAGGCA 60.106 55.000 5.74 0.00 33.17 4.75
68 70 1.377202 GCGGACCATCTGCCAAAGA 60.377 57.895 0.00 0.00 42.80 2.52
77 79 2.974489 CTGCCAAAGACGCCTGCTG 61.974 63.158 0.00 0.00 0.00 4.41
122 124 1.548719 CGTGGTCCTGGTCACTTGATA 59.451 52.381 16.29 0.00 0.00 2.15
141 143 2.736670 ATTGGTATTGGAGGGAGCAC 57.263 50.000 0.00 0.00 0.00 4.40
171 173 3.234630 ATGTGGTGCGTAGGTGCGT 62.235 57.895 0.00 0.00 37.81 5.24
175 177 1.213537 GGTGCGTAGGTGCGTAAGA 59.786 57.895 0.00 0.00 43.02 2.10
185 187 5.574055 CGTAGGTGCGTAAGATTTTGTAGAA 59.426 40.000 0.00 0.00 43.02 2.10
191 193 7.279313 GGTGCGTAAGATTTTGTAGAAGGATTA 59.721 37.037 0.00 0.00 43.02 1.75
217 219 4.021016 GTGGAAGGGCGTCTTATATGAGAT 60.021 45.833 0.00 0.00 35.50 2.75
227 229 5.755375 CGTCTTATATGAGATTGCAGGTTGT 59.245 40.000 0.00 0.00 0.00 3.32
228 230 6.292542 CGTCTTATATGAGATTGCAGGTTGTG 60.293 42.308 0.00 0.00 0.00 3.33
231 233 1.896220 TGAGATTGCAGGTTGTGGTC 58.104 50.000 0.00 0.00 0.00 4.02
232 234 1.142667 TGAGATTGCAGGTTGTGGTCA 59.857 47.619 0.00 0.00 0.00 4.02
233 235 2.224843 TGAGATTGCAGGTTGTGGTCAT 60.225 45.455 0.00 0.00 0.00 3.06
235 237 2.821969 AGATTGCAGGTTGTGGTCATTC 59.178 45.455 0.00 0.00 0.00 2.67
260 270 2.168106 TGTGTGAGCTTTGGCAAACAAT 59.832 40.909 8.93 0.00 39.21 2.71
326 337 0.518195 GGCTTACGCGGCACTTTTAA 59.482 50.000 12.47 0.00 36.88 1.52
339 352 6.299604 CGGCACTTTTAATCGCTTGATATAG 58.700 40.000 0.00 0.00 0.00 1.31
439 452 4.582701 TGCAAAACCATAGTTGTGGAAG 57.417 40.909 1.63 0.00 38.48 3.46
450 463 2.031157 AGTTGTGGAAGTGCGTAATTGC 60.031 45.455 0.00 0.00 0.00 3.56
473 486 5.277683 GCATGCTTCACATCGATAAACTCAT 60.278 40.000 11.37 0.00 36.64 2.90
499 512 9.783081 TGCTAAATCATGAATGCTTAGAATAGA 57.217 29.630 15.79 0.00 30.73 1.98
645 668 5.669164 AAAAACAAAAACCCAGACAGCTA 57.331 34.783 0.00 0.00 0.00 3.32
646 669 5.669164 AAAACAAAAACCCAGACAGCTAA 57.331 34.783 0.00 0.00 0.00 3.09
647 670 5.669164 AAACAAAAACCCAGACAGCTAAA 57.331 34.783 0.00 0.00 0.00 1.85
648 671 5.669164 AACAAAAACCCAGACAGCTAAAA 57.331 34.783 0.00 0.00 0.00 1.52
649 672 5.669164 ACAAAAACCCAGACAGCTAAAAA 57.331 34.783 0.00 0.00 0.00 1.94
684 1065 0.755327 AAAGACCACCCAAGTGCCAC 60.755 55.000 0.00 0.00 43.09 5.01
685 1066 1.645402 AAGACCACCCAAGTGCCACT 61.645 55.000 0.00 0.00 43.09 4.00
686 1067 1.898574 GACCACCCAAGTGCCACTG 60.899 63.158 0.00 0.00 43.09 3.66
687 1068 3.297620 CCACCCAAGTGCCACTGC 61.298 66.667 0.00 0.00 43.09 4.40
689 1070 3.819652 ACCCAAGTGCCACTGCCA 61.820 61.111 0.00 0.00 36.33 4.92
691 1072 3.297620 CCAAGTGCCACTGCCACC 61.298 66.667 0.00 0.00 36.33 4.61
692 1073 2.203394 CAAGTGCCACTGCCACCT 60.203 61.111 0.00 0.00 36.33 4.00
693 1074 2.113986 AAGTGCCACTGCCACCTC 59.886 61.111 0.00 0.00 36.33 3.85
694 1075 3.497884 AAGTGCCACTGCCACCTCC 62.498 63.158 0.00 0.00 36.33 4.30
697 1078 4.416738 GCCACTGCCACCTCCCTC 62.417 72.222 0.00 0.00 0.00 4.30
698 1079 2.930019 CCACTGCCACCTCCCTCA 60.930 66.667 0.00 0.00 0.00 3.86
700 1081 1.455849 CACTGCCACCTCCCTCAAA 59.544 57.895 0.00 0.00 0.00 2.69
701 1082 0.178992 CACTGCCACCTCCCTCAAAA 60.179 55.000 0.00 0.00 0.00 2.44
702 1083 0.555769 ACTGCCACCTCCCTCAAAAA 59.444 50.000 0.00 0.00 0.00 1.94
724 1105 1.822615 AAAAAGTGCCACTGCCACC 59.177 52.632 0.00 0.00 36.33 4.61
747 1128 3.966665 TCTCTGGCCACTTTCCAAAATTT 59.033 39.130 0.00 0.00 32.41 1.82
754 1135 3.809279 CCACTTTCCAAAATTTGAGGCAC 59.191 43.478 7.37 0.00 0.00 5.01
760 1141 0.664166 AAAATTTGAGGCACAGCGCG 60.664 50.000 0.00 0.00 43.84 6.86
761 1142 3.615536 AATTTGAGGCACAGCGCGC 62.616 57.895 26.66 26.66 43.84 6.86
771 1152 3.425713 CAGCGCGCTGGACACAAT 61.426 61.111 45.16 15.81 40.17 2.71
772 1153 3.425713 AGCGCGCTGGACACAATG 61.426 61.111 36.13 0.00 0.00 2.82
773 1154 4.465512 GCGCGCTGGACACAATGG 62.466 66.667 26.67 0.00 0.00 3.16
774 1155 2.741985 CGCGCTGGACACAATGGA 60.742 61.111 5.56 0.00 0.00 3.41
775 1156 2.870372 GCGCTGGACACAATGGAC 59.130 61.111 0.00 0.00 0.00 4.02
780 1161 0.673644 CTGGACACAATGGACCGGAC 60.674 60.000 9.46 0.00 0.00 4.79
788 1169 1.670811 CAATGGACCGGACACAATAGC 59.329 52.381 9.46 0.00 0.00 2.97
983 1377 3.983494 CCGGCGCTCCATCGATCT 61.983 66.667 7.64 0.00 0.00 2.75
1122 1516 1.274650 ACCATCCAGGAGGTGAAGGAT 60.275 52.381 9.22 0.00 41.40 3.24
1189 1583 0.401738 CTTCCAGGCCAAGTCCAAGA 59.598 55.000 5.01 0.00 0.00 3.02
1197 1591 1.004745 GCCAAGTCCAAGATCCTCCAA 59.995 52.381 0.00 0.00 0.00 3.53
1253 1647 2.244117 GAGGATGAGTGGCGGCAGAA 62.244 60.000 13.91 0.29 0.00 3.02
1353 1747 4.149346 TCTCTCGAGGAGATGCGG 57.851 61.111 13.56 0.00 45.20 5.69
1457 1851 5.705397 ATGAAGAAAGATGAGGTGATCCA 57.295 39.130 0.00 0.00 35.89 3.41
1488 1882 1.116536 GGGAGATCGGGGAGAAGGAC 61.117 65.000 0.00 0.00 0.00 3.85
1542 1936 5.228945 AGGAGGAAATGAAGAAAGACGAA 57.771 39.130 0.00 0.00 0.00 3.85
1642 2036 6.039159 GGAAATGAAGAAAGATGAGGTGATCC 59.961 42.308 0.00 0.00 0.00 3.36
1737 2234 3.935203 TGAAGAAAGATGAGGTGATTCGC 59.065 43.478 0.00 0.00 0.00 4.70
1743 2240 2.125106 GAGGTGATTCGCCGGCTT 60.125 61.111 26.68 9.24 39.30 4.35
1749 2246 1.305219 TGATTCGCCGGCTTGAAAGG 61.305 55.000 26.68 6.92 0.00 3.11
1755 2252 1.379642 GCCGGCTTGAAAGGGAGATG 61.380 60.000 22.15 0.00 0.00 2.90
1878 2375 1.333115 TTAATCACGCGACGACACAG 58.667 50.000 15.93 0.00 0.00 3.66
2054 2599 4.886496 AGAGAAAGCTAAAAGGTACCGT 57.114 40.909 6.18 0.00 0.00 4.83
2057 2602 3.581770 AGAAAGCTAAAAGGTACCGTCCT 59.418 43.478 6.18 0.00 39.84 3.85
2059 2604 4.462508 AAGCTAAAAGGTACCGTCCTAC 57.537 45.455 6.18 0.00 36.74 3.18
2206 2761 9.084164 GCATTATATTCTGATGAATGCCAATTC 57.916 33.333 6.62 0.00 44.17 2.17
2209 2764 2.646930 TCTGATGAATGCCAATTCGCT 58.353 42.857 0.00 0.00 44.47 4.93
2233 2788 7.437862 GCTAGTATCTCTTTTCTGTCAATCCTG 59.562 40.741 0.00 0.00 0.00 3.86
2247 2802 2.363038 CAATCCTGGCACATAACATGGG 59.637 50.000 0.00 0.00 38.20 4.00
2260 2815 6.037720 CACATAACATGGGCGTGTCTTAAATA 59.962 38.462 0.00 0.00 33.60 1.40
2286 2844 8.410673 TGTAGGAGTTACTGATTGGATATCTC 57.589 38.462 2.05 0.00 33.23 2.75
2291 2849 7.870445 GGAGTTACTGATTGGATATCTCTGTTC 59.130 40.741 2.05 0.00 0.00 3.18
2320 2878 7.000472 TCTCACTTGTTTGATTTCCAGATTCT 59.000 34.615 0.00 0.00 0.00 2.40
2365 2924 8.684386 TTATCCAGTATCACACTTTTGTTTCA 57.316 30.769 0.00 0.00 34.26 2.69
2366 2925 6.618287 TCCAGTATCACACTTTTGTTTCAG 57.382 37.500 0.00 0.00 34.26 3.02
2377 2936 4.037446 ACTTTTGTTTCAGAATTGCCGCTA 59.963 37.500 0.00 0.00 0.00 4.26
2439 2998 6.040616 TGTGCAAATATGATCAATGGTGCATA 59.959 34.615 22.42 18.90 0.00 3.14
2440 2999 7.094631 GTGCAAATATGATCAATGGTGCATAT 58.905 34.615 22.42 3.77 35.95 1.78
2441 3000 7.062956 GTGCAAATATGATCAATGGTGCATATG 59.937 37.037 22.42 0.00 34.97 1.78
2443 3002 7.979537 GCAAATATGATCAATGGTGCATATGAT 59.020 33.333 6.97 0.00 34.97 2.45
2444 3003 9.301153 CAAATATGATCAATGGTGCATATGATG 57.699 33.333 6.97 0.00 34.97 3.07
2497 3056 7.619698 TCTCTTTTCTGTCAATCCTATCACCTA 59.380 37.037 0.00 0.00 0.00 3.08
2528 3087 8.338259 GCACATGTCTTAAATATGTAGGAGTTG 58.662 37.037 0.00 0.00 37.59 3.16
2537 3097 5.791336 ATATGTAGGAGTTGCTGATTCGA 57.209 39.130 0.00 0.00 0.00 3.71
2541 3101 6.161855 TGTAGGAGTTGCTGATTCGATATT 57.838 37.500 0.00 0.00 0.00 1.28
2542 3102 5.985530 TGTAGGAGTTGCTGATTCGATATTG 59.014 40.000 0.00 0.00 0.00 1.90
2707 3267 0.438830 CAGTAACTCGCGCCTTTGTC 59.561 55.000 0.00 0.00 0.00 3.18
2739 3299 1.600023 CAACTAACCCTCCGCACAAA 58.400 50.000 0.00 0.00 0.00 2.83
2793 3365 1.267121 GCCCAAGTCTACACTGGAGA 58.733 55.000 3.50 0.00 31.06 3.71
2862 3434 7.257790 TGATTTTCTTGATACTCCTCTGGAA 57.742 36.000 0.00 0.00 0.00 3.53
2910 3482 4.503991 CCCACAACTAGAGAAGAAGCACTT 60.504 45.833 0.00 0.00 42.03 3.16
3024 3596 1.764571 TACCAGTTCCCAAGCAGCGT 61.765 55.000 0.00 0.00 0.00 5.07
3144 3716 4.841422 AGCAGTGCAAGAAGTTCTATGAT 58.159 39.130 19.20 0.00 0.00 2.45
3288 3860 6.914654 TGGAACATTGGATTTGAATCAGAA 57.085 33.333 6.11 0.00 37.15 3.02
3334 3906 5.569413 CAAACTTCTTTGGTGTACAGTGTC 58.431 41.667 0.00 0.00 34.20 3.67
3374 3946 3.290710 TCGGTTACCCCTGTATACTGTC 58.709 50.000 4.17 0.00 0.00 3.51
3388 3960 5.643348 TGTATACTGTCAATGGTGCAGAAAG 59.357 40.000 4.17 0.00 34.74 2.62
3389 3961 1.610522 ACTGTCAATGGTGCAGAAAGC 59.389 47.619 0.00 0.00 45.96 3.51
3446 4018 4.996758 TGGTGATCATTACAGTGTCAGTTG 59.003 41.667 0.00 0.00 0.00 3.16
3449 4021 5.470098 GTGATCATTACAGTGTCAGTTGGTT 59.530 40.000 0.00 0.00 0.00 3.67
3457 4036 8.771920 TTACAGTGTCAGTTGGTTGATAATAG 57.228 34.615 0.00 0.00 0.00 1.73
3464 4043 7.097192 GTCAGTTGGTTGATAATAGTGTCAGA 58.903 38.462 0.00 0.00 0.00 3.27
3511 4091 6.146021 CAGAAAAGTTGAACAGTTGCTTGTTT 59.854 34.615 0.00 0.00 41.15 2.83
3512 4092 6.705825 AGAAAAGTTGAACAGTTGCTTGTTTT 59.294 30.769 0.00 0.00 41.15 2.43
3526 4106 8.682710 AGTTGCTTGTTTTCTTATTTACACTCA 58.317 29.630 0.00 0.00 0.00 3.41
3594 4174 1.691434 TGAATCAACTTTGTTGCCCCC 59.309 47.619 5.65 0.00 0.00 5.40
3627 4207 5.659440 TCAAAATAACATGGAAGGAAGCC 57.341 39.130 0.00 0.00 0.00 4.35
3681 4261 1.866880 GCCTGTTGCTTCTGCTGTTTG 60.867 52.381 0.00 0.00 40.48 2.93
3753 4340 6.320926 TGGCATTTATCTGCTGCTTACATTAA 59.679 34.615 0.00 0.00 41.95 1.40
3821 4408 7.857885 CAGAGAGTTTGTGTTTGGAGTTTTATC 59.142 37.037 0.00 0.00 0.00 1.75
3838 4425 9.362539 GAGTTTTATCGAGTAGGTGAATTTGTA 57.637 33.333 0.00 0.00 0.00 2.41
3883 4470 3.548268 GTGACTAGTATCAGCGCTTGTTC 59.452 47.826 7.50 0.00 0.00 3.18
3928 4515 8.912988 TCTTGTGTAAAATCCACTGAAGAATTT 58.087 29.630 0.00 0.00 33.92 1.82
3956 4543 1.146774 TGGGGTGGATTTGCTTCAGAA 59.853 47.619 0.00 0.00 0.00 3.02
3984 4571 0.034089 GCCCTTACCAGCTTGTCCAT 60.034 55.000 0.00 0.00 0.00 3.41
4026 4614 7.342026 AGTTCCAATTCAGGACAGTTTTAACTT 59.658 33.333 0.00 0.00 37.42 2.66
4091 4689 4.731313 AGTCTTCTGGTCCCTCAATTTT 57.269 40.909 0.00 0.00 0.00 1.82
4092 4690 5.066913 AGTCTTCTGGTCCCTCAATTTTT 57.933 39.130 0.00 0.00 0.00 1.94
4100 4698 3.552890 GGTCCCTCAATTTTTGTGTGCTC 60.553 47.826 0.00 0.00 0.00 4.26
4104 4702 4.503643 CCCTCAATTTTTGTGTGCTCCATT 60.504 41.667 0.00 0.00 0.00 3.16
4106 4704 4.378774 TCAATTTTTGTGTGCTCCATTGG 58.621 39.130 0.00 0.00 0.00 3.16
4107 4705 4.128643 CAATTTTTGTGTGCTCCATTGGT 58.871 39.130 1.86 0.00 0.00 3.67
4114 4712 0.807496 GTGCTCCATTGGTGCTTCTC 59.193 55.000 25.44 12.64 42.02 2.87
4125 4723 3.173151 TGGTGCTTCTCTCTTATCCACA 58.827 45.455 0.00 0.00 0.00 4.17
4160 4758 9.601217 TTAGATATTTTCTCAGCTGTTTCCTAC 57.399 33.333 14.67 0.00 35.79 3.18
4161 4759 7.856415 AGATATTTTCTCAGCTGTTTCCTACT 58.144 34.615 14.67 2.12 0.00 2.57
4162 4760 7.984617 AGATATTTTCTCAGCTGTTTCCTACTC 59.015 37.037 14.67 4.47 0.00 2.59
4163 4761 3.963428 TTCTCAGCTGTTTCCTACTCC 57.037 47.619 14.67 0.00 0.00 3.85
4164 4762 2.180276 TCTCAGCTGTTTCCTACTCCC 58.820 52.381 14.67 0.00 0.00 4.30
4165 4763 2.183679 CTCAGCTGTTTCCTACTCCCT 58.816 52.381 14.67 0.00 0.00 4.20
4166 4764 2.167487 CTCAGCTGTTTCCTACTCCCTC 59.833 54.545 14.67 0.00 0.00 4.30
4167 4765 1.208293 CAGCTGTTTCCTACTCCCTCC 59.792 57.143 5.25 0.00 0.00 4.30
4168 4766 0.175989 GCTGTTTCCTACTCCCTCCG 59.824 60.000 0.00 0.00 0.00 4.63
4169 4767 1.558233 CTGTTTCCTACTCCCTCCGT 58.442 55.000 0.00 0.00 0.00 4.69
4170 4768 1.477295 CTGTTTCCTACTCCCTCCGTC 59.523 57.143 0.00 0.00 0.00 4.79
4171 4769 0.822811 GTTTCCTACTCCCTCCGTCC 59.177 60.000 0.00 0.00 0.00 4.79
4172 4770 0.325016 TTTCCTACTCCCTCCGTCCC 60.325 60.000 0.00 0.00 0.00 4.46
4173 4771 1.512201 TTCCTACTCCCTCCGTCCCA 61.512 60.000 0.00 0.00 0.00 4.37
4174 4772 1.233369 CCTACTCCCTCCGTCCCAT 59.767 63.158 0.00 0.00 0.00 4.00
4175 4773 0.481567 CCTACTCCCTCCGTCCCATA 59.518 60.000 0.00 0.00 0.00 2.74
4176 4774 1.133262 CCTACTCCCTCCGTCCCATAA 60.133 57.143 0.00 0.00 0.00 1.90
4177 4775 2.492940 CCTACTCCCTCCGTCCCATAAT 60.493 54.545 0.00 0.00 0.00 1.28
4178 4776 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
4179 4777 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
4180 4778 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
4181 4779 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
4182 4780 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
4183 4781 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
4184 4782 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
4185 4783 3.386726 CCTCCGTCCCATAATGTAAGACA 59.613 47.826 0.00 0.00 0.00 3.41
4186 4784 4.040461 CCTCCGTCCCATAATGTAAGACAT 59.960 45.833 0.00 0.00 41.31 3.06
4188 4786 5.996644 TCCGTCCCATAATGTAAGACATTT 58.003 37.500 9.92 0.00 45.80 2.32
4189 4787 6.419791 TCCGTCCCATAATGTAAGACATTTT 58.580 36.000 9.92 0.33 45.80 1.82
4190 4788 6.887545 TCCGTCCCATAATGTAAGACATTTTT 59.112 34.615 9.92 0.00 45.80 1.94
4235 4833 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
4236 4834 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
4237 4835 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
4238 4836 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
4239 4837 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
4240 4838 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
4241 4839 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
4242 4840 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
4243 4841 3.173965 CATTATGGGACGGAGGGAGTAT 58.826 50.000 0.00 0.00 0.00 2.12
4244 4842 3.339713 TTATGGGACGGAGGGAGTATT 57.660 47.619 0.00 0.00 0.00 1.89
4245 4843 2.191981 ATGGGACGGAGGGAGTATTT 57.808 50.000 0.00 0.00 0.00 1.40
4246 4844 1.961133 TGGGACGGAGGGAGTATTTT 58.039 50.000 0.00 0.00 0.00 1.82
4247 4845 3.119009 TGGGACGGAGGGAGTATTTTA 57.881 47.619 0.00 0.00 0.00 1.52
4248 4846 3.660959 TGGGACGGAGGGAGTATTTTAT 58.339 45.455 0.00 0.00 0.00 1.40
4249 4847 4.818447 TGGGACGGAGGGAGTATTTTATA 58.182 43.478 0.00 0.00 0.00 0.98
4250 4848 4.836736 TGGGACGGAGGGAGTATTTTATAG 59.163 45.833 0.00 0.00 0.00 1.31
4251 4849 4.837298 GGGACGGAGGGAGTATTTTATAGT 59.163 45.833 0.00 0.00 0.00 2.12
4252 4850 5.047448 GGGACGGAGGGAGTATTTTATAGTC 60.047 48.000 0.00 0.00 0.00 2.59
4253 4851 5.774184 GGACGGAGGGAGTATTTTATAGTCT 59.226 44.000 0.00 0.00 0.00 3.24
4254 4852 6.267242 GGACGGAGGGAGTATTTTATAGTCTT 59.733 42.308 0.00 0.00 0.00 3.01
4255 4853 7.052142 ACGGAGGGAGTATTTTATAGTCTTG 57.948 40.000 0.00 0.00 0.00 3.02
4256 4854 6.837568 ACGGAGGGAGTATTTTATAGTCTTGA 59.162 38.462 0.00 0.00 0.00 3.02
4257 4855 7.509659 ACGGAGGGAGTATTTTATAGTCTTGAT 59.490 37.037 0.00 0.00 0.00 2.57
4258 4856 8.368668 CGGAGGGAGTATTTTATAGTCTTGATT 58.631 37.037 0.00 0.00 0.00 2.57
4259 4857 9.495572 GGAGGGAGTATTTTATAGTCTTGATTG 57.504 37.037 0.00 0.00 0.00 2.67
4260 4858 8.910351 AGGGAGTATTTTATAGTCTTGATTGC 57.090 34.615 0.00 0.00 0.00 3.56
4261 4859 7.939588 AGGGAGTATTTTATAGTCTTGATTGCC 59.060 37.037 0.00 0.00 0.00 4.52
4262 4860 7.095187 GGGAGTATTTTATAGTCTTGATTGCCG 60.095 40.741 0.00 0.00 0.00 5.69
4263 4861 7.095187 GGAGTATTTTATAGTCTTGATTGCCGG 60.095 40.741 0.00 0.00 0.00 6.13
4264 4862 7.280356 AGTATTTTATAGTCTTGATTGCCGGT 58.720 34.615 1.90 0.00 0.00 5.28
4265 4863 8.426489 AGTATTTTATAGTCTTGATTGCCGGTA 58.574 33.333 1.90 0.00 0.00 4.02
4266 4864 9.048446 GTATTTTATAGTCTTGATTGCCGGTAA 57.952 33.333 7.65 7.65 0.00 2.85
4267 4865 6.913873 TTTATAGTCTTGATTGCCGGTAAC 57.086 37.500 7.28 2.46 0.00 2.50
4268 4866 4.755266 ATAGTCTTGATTGCCGGTAACT 57.245 40.909 7.28 1.94 0.00 2.24
4269 4867 2.699954 AGTCTTGATTGCCGGTAACTG 58.300 47.619 7.28 0.00 0.00 3.16
4279 4877 3.081329 GCCGGTAACTGCTAAGTAGAG 57.919 52.381 1.90 0.00 44.37 2.43
4280 4878 2.686915 GCCGGTAACTGCTAAGTAGAGA 59.313 50.000 1.90 0.00 44.37 3.10
4281 4879 3.318557 GCCGGTAACTGCTAAGTAGAGAT 59.681 47.826 1.90 0.00 44.37 2.75
4282 4880 4.793353 GCCGGTAACTGCTAAGTAGAGATG 60.793 50.000 1.90 0.00 44.37 2.90
4283 4881 4.261656 CCGGTAACTGCTAAGTAGAGATGG 60.262 50.000 0.00 0.00 34.77 3.51
4284 4882 4.623002 GGTAACTGCTAAGTAGAGATGGC 58.377 47.826 0.00 0.00 34.77 4.40
4285 4883 3.828875 AACTGCTAAGTAGAGATGGCC 57.171 47.619 0.00 0.00 34.77 5.36
4286 4884 3.039252 ACTGCTAAGTAGAGATGGCCT 57.961 47.619 3.32 0.00 33.79 5.19
4287 4885 2.697751 ACTGCTAAGTAGAGATGGCCTG 59.302 50.000 3.32 0.00 33.79 4.85
4288 4886 1.414181 TGCTAAGTAGAGATGGCCTGC 59.586 52.381 3.32 0.00 0.00 4.85
4289 4887 1.691434 GCTAAGTAGAGATGGCCTGCT 59.309 52.381 3.32 0.00 0.00 4.24
4290 4888 2.288763 GCTAAGTAGAGATGGCCTGCTC 60.289 54.545 15.11 15.11 0.00 4.26
4291 4889 2.173126 AAGTAGAGATGGCCTGCTCT 57.827 50.000 24.67 24.67 43.48 4.09
4292 4890 1.703411 AGTAGAGATGGCCTGCTCTC 58.297 55.000 24.91 21.18 41.46 3.20
4293 4891 0.313672 GTAGAGATGGCCTGCTCTCG 59.686 60.000 24.91 0.00 42.21 4.04
4294 4892 0.183731 TAGAGATGGCCTGCTCTCGA 59.816 55.000 24.91 16.55 42.21 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.290197 GGAATGCCTCCAGATGATCCTC 60.290 54.545 0.00 0.00 44.67 3.71
47 48 3.950794 TTGGCAGATGGTCCGCGAC 62.951 63.158 8.23 3.56 0.00 5.19
48 49 3.247056 TTTGGCAGATGGTCCGCGA 62.247 57.895 8.23 0.00 0.00 5.87
49 50 2.745884 TTTGGCAGATGGTCCGCG 60.746 61.111 0.00 0.00 0.00 6.46
50 51 1.377202 TCTTTGGCAGATGGTCCGC 60.377 57.895 0.00 0.00 0.00 5.54
51 52 1.361668 CGTCTTTGGCAGATGGTCCG 61.362 60.000 0.00 0.00 35.11 4.79
91 93 2.438434 GACCACGCCCCATGGAAG 60.438 66.667 15.22 5.21 39.87 3.46
99 101 4.699522 GTGACCAGGACCACGCCC 62.700 72.222 0.00 0.00 0.00 6.13
122 124 1.922447 TGTGCTCCCTCCAATACCAAT 59.078 47.619 0.00 0.00 0.00 3.16
175 177 9.853177 CCTTCCACTATAATCCTTCTACAAAAT 57.147 33.333 0.00 0.00 0.00 1.82
185 187 2.633481 GACGCCCTTCCACTATAATCCT 59.367 50.000 0.00 0.00 0.00 3.24
191 193 5.084519 TCATATAAGACGCCCTTCCACTAT 58.915 41.667 0.00 0.00 36.34 2.12
199 201 3.324846 TGCAATCTCATATAAGACGCCCT 59.675 43.478 0.00 0.00 0.00 5.19
217 219 0.950836 CGAATGACCACAACCTGCAA 59.049 50.000 0.00 0.00 0.00 4.08
227 229 1.877637 CTCACACAACCGAATGACCA 58.122 50.000 0.00 0.00 0.00 4.02
228 230 0.517316 GCTCACACAACCGAATGACC 59.483 55.000 0.00 0.00 0.00 4.02
231 233 2.605338 CCAAAGCTCACACAACCGAATG 60.605 50.000 0.00 0.00 0.00 2.67
232 234 1.608590 CCAAAGCTCACACAACCGAAT 59.391 47.619 0.00 0.00 0.00 3.34
233 235 1.021202 CCAAAGCTCACACAACCGAA 58.979 50.000 0.00 0.00 0.00 4.30
235 237 1.008538 GCCAAAGCTCACACAACCG 60.009 57.895 0.00 0.00 35.50 4.44
361 374 1.070914 TGTTGTACCACTTGATCGGCA 59.929 47.619 0.00 0.00 0.00 5.69
415 428 5.543507 TCCACAACTATGGTTTTGCAAAT 57.456 34.783 13.65 0.00 40.95 2.32
417 430 4.404073 ACTTCCACAACTATGGTTTTGCAA 59.596 37.500 0.00 0.00 40.95 4.08
435 448 1.133025 AGCATGCAATTACGCACTTCC 59.867 47.619 21.98 0.00 46.56 3.46
439 452 1.913403 GTGAAGCATGCAATTACGCAC 59.087 47.619 21.98 12.19 46.56 5.34
450 463 5.723492 TGAGTTTATCGATGTGAAGCATG 57.277 39.130 8.54 0.00 38.06 4.06
473 486 9.783081 TCTATTCTAAGCATTCATGATTTAGCA 57.217 29.630 0.00 0.00 37.59 3.49
509 522 8.954950 TTTTGATTGACACAATGTTTACCAAT 57.045 26.923 1.64 0.00 0.00 3.16
560 573 1.285078 GTGGGCTATTTTGGAGAGGGT 59.715 52.381 0.00 0.00 0.00 4.34
623 646 4.551702 AGCTGTCTGGGTTTTTGTTTTT 57.448 36.364 0.00 0.00 0.00 1.94
624 647 5.669164 TTAGCTGTCTGGGTTTTTGTTTT 57.331 34.783 0.00 0.00 0.00 2.43
625 648 5.669164 TTTAGCTGTCTGGGTTTTTGTTT 57.331 34.783 0.00 0.00 0.00 2.83
626 649 5.669164 TTTTAGCTGTCTGGGTTTTTGTT 57.331 34.783 0.00 0.00 0.00 2.83
627 650 5.669164 TTTTTAGCTGTCTGGGTTTTTGT 57.331 34.783 0.00 0.00 0.00 2.83
684 1065 3.437642 TTTTTGAGGGAGGTGGCAG 57.562 52.632 0.00 0.00 0.00 4.85
712 1093 2.527624 AGAGAGGTGGCAGTGGCA 60.528 61.111 16.56 16.56 43.71 4.92
713 1094 2.046507 CAGAGAGGTGGCAGTGGC 60.047 66.667 10.30 10.30 40.13 5.01
714 1095 2.667418 CCAGAGAGGTGGCAGTGG 59.333 66.667 0.00 0.00 0.00 4.00
720 1101 0.322008 GAAAGTGGCCAGAGAGGTGG 60.322 60.000 5.11 0.00 40.61 4.61
721 1102 0.322008 GGAAAGTGGCCAGAGAGGTG 60.322 60.000 5.11 0.00 40.61 4.00
724 1105 2.276732 TTTGGAAAGTGGCCAGAGAG 57.723 50.000 5.11 0.00 36.64 3.20
732 1113 3.809279 GTGCCTCAAATTTTGGAAAGTGG 59.191 43.478 9.18 4.31 0.00 4.00
754 1135 3.425713 ATTGTGTCCAGCGCGCTG 61.426 61.111 45.54 45.54 43.26 5.18
760 1141 2.040544 CCGGTCCATTGTGTCCAGC 61.041 63.158 0.00 0.00 0.00 4.85
761 1142 0.673644 GTCCGGTCCATTGTGTCCAG 60.674 60.000 0.00 0.00 0.00 3.86
762 1143 1.373435 GTCCGGTCCATTGTGTCCA 59.627 57.895 0.00 0.00 0.00 4.02
763 1144 0.953960 GTGTCCGGTCCATTGTGTCC 60.954 60.000 0.00 0.00 0.00 4.02
764 1145 0.250124 TGTGTCCGGTCCATTGTGTC 60.250 55.000 0.00 0.00 0.00 3.67
765 1146 0.181587 TTGTGTCCGGTCCATTGTGT 59.818 50.000 0.00 0.00 0.00 3.72
766 1147 1.533625 ATTGTGTCCGGTCCATTGTG 58.466 50.000 0.00 0.00 0.00 3.33
767 1148 2.939640 GCTATTGTGTCCGGTCCATTGT 60.940 50.000 0.00 0.00 0.00 2.71
768 1149 1.670811 GCTATTGTGTCCGGTCCATTG 59.329 52.381 0.00 0.00 0.00 2.82
769 1150 1.559682 AGCTATTGTGTCCGGTCCATT 59.440 47.619 0.00 0.00 0.00 3.16
770 1151 1.204146 AGCTATTGTGTCCGGTCCAT 58.796 50.000 0.00 0.00 0.00 3.41
771 1152 0.981183 AAGCTATTGTGTCCGGTCCA 59.019 50.000 0.00 0.00 0.00 4.02
772 1153 1.737793 CAAAGCTATTGTGTCCGGTCC 59.262 52.381 0.00 0.00 0.00 4.46
773 1154 2.695359 TCAAAGCTATTGTGTCCGGTC 58.305 47.619 0.00 0.00 0.00 4.79
774 1155 2.851263 TCAAAGCTATTGTGTCCGGT 57.149 45.000 0.00 0.00 0.00 5.28
775 1156 4.497473 TTTTCAAAGCTATTGTGTCCGG 57.503 40.909 0.00 0.00 0.00 5.14
780 1161 3.181550 CGCGCTTTTTCAAAGCTATTGTG 60.182 43.478 16.95 6.39 40.94 3.33
788 1169 2.594529 TAGAGCGCGCTTTTTCAAAG 57.405 45.000 36.87 0.00 0.00 2.77
973 1365 2.142761 CCAGGGGCAGATCGATGGA 61.143 63.158 0.54 0.00 0.00 3.41
983 1377 3.521765 ATTTCGGCAACCAGGGGCA 62.522 57.895 7.59 0.00 0.00 5.36
1189 1583 2.185350 CAGACGCGCTTGGAGGAT 59.815 61.111 5.73 0.00 0.00 3.24
1353 1747 3.195698 GCGTTCACGAGCATCCCC 61.196 66.667 2.87 0.00 43.02 4.81
1457 1851 1.677637 GATCTCCCTTTCGAGCCGGT 61.678 60.000 1.90 0.00 0.00 5.28
1488 1882 0.247460 TCACCCTTGACATCTCAGCG 59.753 55.000 0.00 0.00 0.00 5.18
1542 1936 0.320374 TTTGGAGCCGACGAATCACT 59.680 50.000 0.00 0.00 0.00 3.41
1737 2234 0.749454 CCATCTCCCTTTCAAGCCGG 60.749 60.000 0.00 0.00 0.00 6.13
1743 2240 0.421495 TCTCCCCCATCTCCCTTTCA 59.579 55.000 0.00 0.00 0.00 2.69
1749 2246 1.385206 AGCCTTCTCCCCCATCTCC 60.385 63.158 0.00 0.00 0.00 3.71
1755 2252 3.011517 TCAGCAGCCTTCTCCCCC 61.012 66.667 0.00 0.00 0.00 5.40
1860 2357 0.239082 ACTGTGTCGTCGCGTGATTA 59.761 50.000 5.77 0.00 0.00 1.75
2206 2761 6.419413 GGATTGACAGAAAAGAGATACTAGCG 59.581 42.308 0.00 0.00 0.00 4.26
2209 2764 7.633772 GCCAGGATTGACAGAAAAGAGATACTA 60.634 40.741 0.00 0.00 0.00 1.82
2233 2788 1.312371 ACACGCCCATGTTATGTGCC 61.312 55.000 0.00 0.00 33.96 5.01
2247 2802 7.919621 AGTAACTCCTACATATTTAAGACACGC 59.080 37.037 0.00 0.00 32.37 5.34
2260 2815 8.964533 AGATATCCAATCAGTAACTCCTACAT 57.035 34.615 0.00 0.00 32.37 2.29
2286 2844 5.739752 TCAAACAAGTGAGATGTGAACAG 57.260 39.130 0.00 0.00 0.00 3.16
2291 2849 6.016860 TCTGGAAATCAAACAAGTGAGATGTG 60.017 38.462 0.00 0.00 0.00 3.21
2320 2878 8.812972 TGGATAAGAAAACTCAAGTAGCTCTAA 58.187 33.333 0.00 0.00 0.00 2.10
2365 2924 9.289782 AGATTCTTAAATTATAGCGGCAATTCT 57.710 29.630 1.45 0.00 0.00 2.40
2366 2925 9.899226 AAGATTCTTAAATTATAGCGGCAATTC 57.101 29.630 1.45 0.00 0.00 2.17
2519 3078 5.986135 ACAATATCGAATCAGCAACTCCTAC 59.014 40.000 0.00 0.00 0.00 3.18
2567 3127 0.606401 CGTGTCCTGCAAATCTGGGT 60.606 55.000 0.00 0.00 34.80 4.51
2568 3128 0.321564 TCGTGTCCTGCAAATCTGGG 60.322 55.000 0.00 0.00 34.80 4.45
2683 3243 0.246635 AGGCGCGAGTTACTGAACAT 59.753 50.000 12.10 0.00 38.10 2.71
2707 3267 3.270877 GGTTAGTTGCATGAGGTGGTAG 58.729 50.000 0.00 0.00 0.00 3.18
2793 3365 1.338973 TCCTTACGCACACGAGTTTCT 59.661 47.619 0.00 0.00 43.93 2.52
2889 3461 4.084118 GCAAGTGCTTCTTCTCTAGTTGTG 60.084 45.833 0.00 0.00 38.21 3.33
2910 3482 4.039092 GGAGGGGCAGCAAGAGCA 62.039 66.667 0.00 0.00 45.49 4.26
3024 3596 4.380531 GTGGATGGATTGAAATCGAGCTA 58.619 43.478 3.82 0.00 36.27 3.32
3030 3602 6.633500 TTATTCGGTGGATGGATTGAAATC 57.367 37.500 0.00 0.00 34.66 2.17
3144 3716 1.676635 GCCATCAGGAAGCACAGCA 60.677 57.895 0.00 0.00 36.89 4.41
3288 3860 4.399303 GGCTCCTGCTTTATGTGTTACATT 59.601 41.667 0.00 0.00 38.42 2.71
3294 3866 2.558359 GTTTGGCTCCTGCTTTATGTGT 59.442 45.455 0.00 0.00 39.59 3.72
3300 3872 2.371658 AGAAGTTTGGCTCCTGCTTT 57.628 45.000 0.00 0.00 39.59 3.51
3334 3906 3.379240 CGAGGATCTATGCTGTGACAAG 58.621 50.000 0.00 0.00 0.00 3.16
3374 3946 2.230508 ACATGAGCTTTCTGCACCATTG 59.769 45.455 0.00 0.00 45.94 2.82
3446 4018 8.492673 TGAACAATCTGACACTATTATCAACC 57.507 34.615 0.00 0.00 0.00 3.77
3449 4021 9.371136 GAACTGAACAATCTGACACTATTATCA 57.629 33.333 0.00 0.00 0.00 2.15
3457 4036 8.534333 TTACATAGAACTGAACAATCTGACAC 57.466 34.615 0.00 0.00 0.00 3.67
3511 4091 8.076178 GCTGCTTCTTTTGAGTGTAAATAAGAA 58.924 33.333 0.00 0.00 0.00 2.52
3512 4092 7.445402 AGCTGCTTCTTTTGAGTGTAAATAAGA 59.555 33.333 0.00 0.00 0.00 2.10
3526 4106 2.224137 GGGCAAGAAAGCTGCTTCTTTT 60.224 45.455 16.28 7.66 41.81 2.27
3594 4174 8.741101 TCCATGTTATTTTGAATTGTTTCTCG 57.259 30.769 0.00 0.00 32.78 4.04
3627 4207 6.920569 AGTACAACTGTAAAAGGTTCAGTG 57.079 37.500 0.00 0.00 41.37 3.66
3657 4237 0.541296 AGCAGAAGCAACAGGCCATT 60.541 50.000 5.01 0.00 46.50 3.16
3753 4340 5.564550 AGATCCTGAGTTTGCTACATGTTT 58.435 37.500 2.30 0.00 0.00 2.83
3851 4438 6.090763 CGCTGATACTAGTCACATTGTGAAAA 59.909 38.462 20.57 10.89 44.49 2.29
3863 4450 4.035278 AGAACAAGCGCTGATACTAGTC 57.965 45.455 12.58 0.08 0.00 2.59
3928 4515 2.635427 GCAAATCCACCCCAAAAAGGTA 59.365 45.455 0.00 0.00 35.24 3.08
3971 4558 2.042162 AGGATCAAATGGACAAGCTGGT 59.958 45.455 0.00 0.00 0.00 4.00
4026 4614 1.896183 CACACGATGCAACCACCCA 60.896 57.895 0.00 0.00 0.00 4.51
4091 4689 0.467844 AGCACCAATGGAGCACACAA 60.468 50.000 22.86 0.00 41.64 3.33
4092 4690 0.467844 AAGCACCAATGGAGCACACA 60.468 50.000 22.86 0.00 41.64 3.72
4100 4698 4.133078 GGATAAGAGAGAAGCACCAATGG 58.867 47.826 0.00 0.00 0.00 3.16
4104 4702 3.055819 GTGTGGATAAGAGAGAAGCACCA 60.056 47.826 0.00 0.00 0.00 4.17
4106 4704 3.929610 GTGTGTGGATAAGAGAGAAGCAC 59.070 47.826 0.00 0.00 0.00 4.40
4107 4705 3.834813 AGTGTGTGGATAAGAGAGAAGCA 59.165 43.478 0.00 0.00 0.00 3.91
4114 4712 7.340122 TCTAAGATGAGTGTGTGGATAAGAG 57.660 40.000 0.00 0.00 0.00 2.85
4125 4723 8.703743 AGCTGAGAAAATATCTAAGATGAGTGT 58.296 33.333 0.00 0.00 38.80 3.55
4160 4758 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
4161 4759 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
4162 4760 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
4163 4761 3.386726 TGTCTTACATTATGGGACGGAGG 59.613 47.826 0.00 0.00 0.00 4.30
4164 4762 4.665833 TGTCTTACATTATGGGACGGAG 57.334 45.455 0.00 0.00 0.00 4.63
4165 4763 5.623956 AATGTCTTACATTATGGGACGGA 57.376 39.130 3.51 0.00 46.11 4.69
4210 4808 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
4211 4809 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
4212 4810 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
4213 4811 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
4214 4812 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
4216 4814 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
4217 4815 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
4218 4816 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
4219 4817 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
4220 4818 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
4221 4819 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
4222 4820 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
4223 4821 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
4224 4822 3.339713 AATACTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
4225 4823 3.339713 AAATACTCCCTCCGTCCCATA 57.660 47.619 0.00 0.00 0.00 2.74
4226 4824 2.191981 AAATACTCCCTCCGTCCCAT 57.808 50.000 0.00 0.00 0.00 4.00
4227 4825 1.961133 AAAATACTCCCTCCGTCCCA 58.039 50.000 0.00 0.00 0.00 4.37
4228 4826 4.837298 ACTATAAAATACTCCCTCCGTCCC 59.163 45.833 0.00 0.00 0.00 4.46
4229 4827 5.774184 AGACTATAAAATACTCCCTCCGTCC 59.226 44.000 0.00 0.00 0.00 4.79
4230 4828 6.897706 AGACTATAAAATACTCCCTCCGTC 57.102 41.667 0.00 0.00 0.00 4.79
4231 4829 6.837568 TCAAGACTATAAAATACTCCCTCCGT 59.162 38.462 0.00 0.00 0.00 4.69
4232 4830 7.286215 TCAAGACTATAAAATACTCCCTCCG 57.714 40.000 0.00 0.00 0.00 4.63
4233 4831 9.495572 CAATCAAGACTATAAAATACTCCCTCC 57.504 37.037 0.00 0.00 0.00 4.30
4234 4832 8.994170 GCAATCAAGACTATAAAATACTCCCTC 58.006 37.037 0.00 0.00 0.00 4.30
4235 4833 7.939588 GGCAATCAAGACTATAAAATACTCCCT 59.060 37.037 0.00 0.00 0.00 4.20
4236 4834 7.095187 CGGCAATCAAGACTATAAAATACTCCC 60.095 40.741 0.00 0.00 0.00 4.30
4237 4835 7.095187 CCGGCAATCAAGACTATAAAATACTCC 60.095 40.741 0.00 0.00 0.00 3.85
4238 4836 7.441458 ACCGGCAATCAAGACTATAAAATACTC 59.559 37.037 0.00 0.00 0.00 2.59
4239 4837 7.280356 ACCGGCAATCAAGACTATAAAATACT 58.720 34.615 0.00 0.00 0.00 2.12
4240 4838 7.492352 ACCGGCAATCAAGACTATAAAATAC 57.508 36.000 0.00 0.00 0.00 1.89
4241 4839 9.048446 GTTACCGGCAATCAAGACTATAAAATA 57.952 33.333 0.00 0.00 0.00 1.40
4242 4840 7.773690 AGTTACCGGCAATCAAGACTATAAAAT 59.226 33.333 0.00 0.00 0.00 1.82
4243 4841 7.065324 CAGTTACCGGCAATCAAGACTATAAAA 59.935 37.037 0.00 0.00 0.00 1.52
4244 4842 6.537301 CAGTTACCGGCAATCAAGACTATAAA 59.463 38.462 0.00 0.00 0.00 1.40
4245 4843 6.046593 CAGTTACCGGCAATCAAGACTATAA 58.953 40.000 0.00 0.00 0.00 0.98
4246 4844 5.597806 CAGTTACCGGCAATCAAGACTATA 58.402 41.667 0.00 0.00 0.00 1.31
4247 4845 4.442706 CAGTTACCGGCAATCAAGACTAT 58.557 43.478 0.00 0.00 0.00 2.12
4248 4846 3.857052 CAGTTACCGGCAATCAAGACTA 58.143 45.455 0.00 0.00 0.00 2.59
4249 4847 2.699954 CAGTTACCGGCAATCAAGACT 58.300 47.619 0.00 0.00 0.00 3.24
4250 4848 1.130561 GCAGTTACCGGCAATCAAGAC 59.869 52.381 0.00 0.00 0.00 3.01
4251 4849 1.003118 AGCAGTTACCGGCAATCAAGA 59.997 47.619 0.00 0.00 33.84 3.02
4252 4850 1.453155 AGCAGTTACCGGCAATCAAG 58.547 50.000 0.00 0.00 33.84 3.02
4253 4851 2.772077 TAGCAGTTACCGGCAATCAA 57.228 45.000 0.00 0.00 33.84 2.57
4254 4852 2.027561 ACTTAGCAGTTACCGGCAATCA 60.028 45.455 0.00 0.00 33.84 2.57
4255 4853 2.629051 ACTTAGCAGTTACCGGCAATC 58.371 47.619 0.00 0.00 33.84 2.67
4256 4854 2.781681 ACTTAGCAGTTACCGGCAAT 57.218 45.000 0.00 0.00 33.84 3.56
4257 4855 2.827322 TCTACTTAGCAGTTACCGGCAA 59.173 45.455 0.00 0.00 34.06 4.52
4258 4856 2.426024 CTCTACTTAGCAGTTACCGGCA 59.574 50.000 0.00 0.00 34.06 5.69
4259 4857 2.686915 TCTCTACTTAGCAGTTACCGGC 59.313 50.000 0.00 0.00 34.06 6.13
4260 4858 4.261656 CCATCTCTACTTAGCAGTTACCGG 60.262 50.000 0.00 0.00 34.06 5.28
4261 4859 4.793353 GCCATCTCTACTTAGCAGTTACCG 60.793 50.000 0.00 0.00 34.06 4.02
4262 4860 4.501743 GGCCATCTCTACTTAGCAGTTACC 60.502 50.000 0.00 0.00 34.06 2.85
4263 4861 4.342665 AGGCCATCTCTACTTAGCAGTTAC 59.657 45.833 5.01 0.00 34.06 2.50
4264 4862 4.342378 CAGGCCATCTCTACTTAGCAGTTA 59.658 45.833 5.01 0.00 34.06 2.24
4265 4863 3.133721 CAGGCCATCTCTACTTAGCAGTT 59.866 47.826 5.01 0.00 34.06 3.16
4266 4864 2.697751 CAGGCCATCTCTACTTAGCAGT 59.302 50.000 5.01 0.00 36.99 4.40
4267 4865 2.547642 GCAGGCCATCTCTACTTAGCAG 60.548 54.545 5.01 0.00 0.00 4.24
4268 4866 1.414181 GCAGGCCATCTCTACTTAGCA 59.586 52.381 5.01 0.00 0.00 3.49
4269 4867 1.691434 AGCAGGCCATCTCTACTTAGC 59.309 52.381 5.01 0.00 0.00 3.09
4270 4868 3.230134 AGAGCAGGCCATCTCTACTTAG 58.770 50.000 21.02 0.00 37.86 2.18
4271 4869 3.226777 GAGAGCAGGCCATCTCTACTTA 58.773 50.000 22.01 0.00 39.57 2.24
4272 4870 2.038659 GAGAGCAGGCCATCTCTACTT 58.961 52.381 22.01 5.38 39.57 2.24
4273 4871 1.703411 GAGAGCAGGCCATCTCTACT 58.297 55.000 22.01 5.69 39.57 2.57
4274 4872 0.313672 CGAGAGCAGGCCATCTCTAC 59.686 60.000 22.01 15.56 39.57 2.59
4275 4873 0.183731 TCGAGAGCAGGCCATCTCTA 59.816 55.000 22.01 12.91 39.57 2.43
4276 4874 1.076412 TCGAGAGCAGGCCATCTCT 60.076 57.895 22.11 22.11 41.95 3.10
4277 4875 3.531283 TCGAGAGCAGGCCATCTC 58.469 61.111 18.09 18.09 38.87 2.75


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

AutoCloner maintained by Alex Coulton.