Multiple sequence alignment - TraesCS2A01G312700

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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 TraesCS2A01G312700 chr2A 100.000 5026 0 0 1 5026 537399885 537404910 0.000000e+00 9282.0
1 TraesCS2A01G312700 chr2D 94.949 3425 124 22 942 4341 400051049 400054449 0.000000e+00 5321.0
2 TraesCS2A01G312700 chr2D 87.342 553 29 9 4501 5026 400054449 400054987 3.350000e-166 595.0
3 TraesCS2A01G312700 chr2D 96.721 122 4 0 784 905 400050923 400051044 2.370000e-48 204.0
4 TraesCS2A01G312700 chr2B 95.381 1797 71 5 1127 2919 474403840 474405628 0.000000e+00 2848.0
5 TraesCS2A01G312700 chr2B 94.479 1431 49 19 2918 4337 474405752 474407163 0.000000e+00 2178.0
6 TraesCS2A01G312700 chr2B 88.361 421 11 6 4644 5026 474443402 474443822 5.890000e-129 472.0
7 TraesCS2A01G312700 chr2B 93.793 290 13 3 825 1109 474403209 474403498 1.000000e-116 431.0
8 TraesCS2A01G312700 chr2B 92.169 166 10 1 4340 4505 800062976 800062814 1.090000e-56 231.0
9 TraesCS2A01G312700 chr7B 96.361 742 26 1 1 741 104082024 104081283 0.000000e+00 1219.0
10 TraesCS2A01G312700 chr7B 85.124 121 17 1 624 743 630132796 630132916 6.830000e-24 122.0
11 TraesCS2A01G312700 chrUn 89.267 587 40 9 161 742 31685756 31685188 0.000000e+00 713.0
12 TraesCS2A01G312700 chrUn 91.111 45 1 3 2905 2946 1995154 1995110 1.950000e-04 58.4
13 TraesCS2A01G312700 chr1B 88.567 586 54 10 161 742 248260381 248260957 0.000000e+00 699.0
14 TraesCS2A01G312700 chr1B 93.168 161 9 1 1 161 248260188 248260346 8.410000e-58 235.0
15 TraesCS2A01G312700 chr3D 89.400 500 47 6 245 742 498094435 498093940 4.270000e-175 625.0
16 TraesCS2A01G312700 chr3D 90.286 175 12 3 4334 4507 571465533 571465363 1.820000e-54 224.0
17 TraesCS2A01G312700 chr3D 90.286 175 12 3 4334 4507 579494787 579494957 1.820000e-54 224.0
18 TraesCS2A01G312700 chr3D 83.871 124 19 1 624 746 98598451 98598328 3.180000e-22 117.0
19 TraesCS2A01G312700 chr7D 84.138 580 62 13 173 741 460521221 460521781 7.410000e-148 534.0
20 TraesCS2A01G312700 chr7D 97.222 36 1 0 126 161 401092284 401092319 1.510000e-05 62.1
21 TraesCS2A01G312700 chr6D 92.216 167 10 1 4336 4502 229430889 229431052 3.030000e-57 233.0
22 TraesCS2A01G312700 chr4B 92.169 166 10 1 4337 4502 535345159 535344997 1.090000e-56 231.0
23 TraesCS2A01G312700 chr4A 91.716 169 11 1 4338 4506 669197976 669198141 1.090000e-56 231.0
24 TraesCS2A01G312700 chr6B 90.286 175 12 3 4334 4507 130112762 130112592 1.820000e-54 224.0
25 TraesCS2A01G312700 chr6B 89.583 48 3 2 2899 2945 135488330 135488376 5.430000e-05 60.2
26 TraesCS2A01G312700 chr3A 90.286 175 12 3 4334 4507 568001365 568001195 1.820000e-54 224.0
27 TraesCS2A01G312700 chr3B 89.071 183 15 3 4335 4516 243784042 243784220 6.550000e-54 222.0
28 TraesCS2A01G312700 chr3B 95.000 40 2 0 2902 2941 239920877 239920838 4.200000e-06 63.9
29 TraesCS2A01G312700 chr6A 85.833 120 16 1 624 742 495110612 495110731 5.280000e-25 126.0
30 TraesCS2A01G312700 chr6A 84.615 65 9 1 507 570 560376422 560376358 4.200000e-06 63.9
31 TraesCS2A01G312700 chr6A 84.375 64 10 0 507 570 560425916 560425853 4.200000e-06 63.9
32 TraesCS2A01G312700 chr6A 84.375 64 10 0 507 570 560438279 560438216 4.200000e-06 63.9
33 TraesCS2A01G312700 chr1A 85.965 114 15 1 631 743 101327583 101327470 2.460000e-23 121.0
34 TraesCS2A01G312700 chr1A 97.297 37 1 0 2902 2938 367025162 367025126 4.200000e-06 63.9
35 TraesCS2A01G312700 chr1A 83.582 67 10 1 509 574 128043211 128043277 1.510000e-05 62.1
36 TraesCS2A01G312700 chr1D 83.621 116 19 0 507 622 487204248 487204363 5.320000e-20 110.0
37 TraesCS2A01G312700 chr4D 97.368 38 1 0 2902 2939 408572549 408572512 1.170000e-06 65.8
38 TraesCS2A01G312700 chr5D 91.304 46 3 1 2895 2940 47855906 47855862 1.510000e-05 62.1
39 TraesCS2A01G312700 chr7A 89.583 48 3 2 2902 2948 591163650 591163604 5.430000e-05 60.2


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 TraesCS2A01G312700 chr2A 537399885 537404910 5025 False 9282 9282 100.0000 1 5026 1 chr2A.!!$F1 5025
1 TraesCS2A01G312700 chr2D 400050923 400054987 4064 False 2040 5321 93.0040 784 5026 3 chr2D.!!$F1 4242
2 TraesCS2A01G312700 chr2B 474403209 474407163 3954 False 1819 2848 94.5510 825 4337 3 chr2B.!!$F2 3512
3 TraesCS2A01G312700 chr7B 104081283 104082024 741 True 1219 1219 96.3610 1 741 1 chr7B.!!$R1 740
4 TraesCS2A01G312700 chrUn 31685188 31685756 568 True 713 713 89.2670 161 742 1 chrUn.!!$R2 581
5 TraesCS2A01G312700 chr1B 248260188 248260957 769 False 467 699 90.8675 1 742 2 chr1B.!!$F1 741
6 TraesCS2A01G312700 chr7D 460521221 460521781 560 False 534 534 84.1380 173 741 1 chr7D.!!$F2 568

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
764 814 0.321671 ATGAGTGCTTGCGTGGTACT 59.678 50.0 0.00 0.0 32.67 2.73 F
769 819 0.462937 TGCTTGCGTGGTACTGTGTT 60.463 50.0 0.00 0.0 0.00 3.32 F
1528 1917 0.704076 TTGGGGAGTCAAATCAGGGG 59.296 55.0 0.00 0.0 0.00 4.79 F
2712 3114 2.234908 GTGGAGCAGTACTGAGGATGTT 59.765 50.0 27.08 0.0 0.00 2.71 F
3741 4271 2.169769 CCCAAGGAAGATTACTACGCCA 59.830 50.0 0.00 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1989 2390 0.678048 GTCCCATCAGGCAGTCCAAC 60.678 60.000 0.0 0.0 34.51 3.77 R
2039 2440 1.072331 GGCTCAGGAAGTTGAACAGGA 59.928 52.381 0.0 0.0 0.00 3.86 R
3087 3615 2.582636 AGGAATGTTGCCCATCTTACCT 59.417 45.455 0.0 0.0 31.75 3.08 R
3788 4318 0.394899 CCTCTTTGCCACCATCCTCC 60.395 60.000 0.0 0.0 0.00 4.30 R
4883 5448 0.038744 CTGGGATGCTGGTGGAGTTT 59.961 55.000 0.0 0.0 0.00 2.66 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
152 153 3.709587 ACTCCCTCCGTCTCAAGATAAA 58.290 45.455 0.00 0.00 0.00 1.40
266 309 4.082841 ACACATCTTCACAAAATATGCGCA 60.083 37.500 14.96 14.96 0.00 6.09
286 329 3.062909 GCAGGGAACAAAAACGGAAAAAC 59.937 43.478 0.00 0.00 0.00 2.43
567 617 6.806668 TGAAGTGGGTTCATATGTATCTGA 57.193 37.500 1.90 0.00 40.45 3.27
571 621 7.200434 AGTGGGTTCATATGTATCTGAGTTT 57.800 36.000 1.90 0.00 0.00 2.66
673 723 7.116805 GTCTTGAATCATTTCTTCGGCATTTTT 59.883 33.333 0.00 0.00 32.78 1.94
686 736 9.921637 TCTTCGGCATTTTTATGTCTTATTTTT 57.078 25.926 0.00 0.00 0.00 1.94
747 797 6.718389 CGTGCACGCATACTAGTATATATG 57.282 41.667 28.16 13.26 32.83 1.78
748 798 6.483687 CGTGCACGCATACTAGTATATATGA 58.516 40.000 28.16 2.62 31.54 2.15
749 799 6.629252 CGTGCACGCATACTAGTATATATGAG 59.371 42.308 28.16 9.86 35.46 2.90
750 800 7.473366 GTGCACGCATACTAGTATATATGAGT 58.527 38.462 15.03 10.47 40.92 3.41
752 802 7.900299 CACGCATACTAGTATATATGAGTGC 57.100 40.000 20.20 15.29 45.85 4.40
753 803 7.698628 CACGCATACTAGTATATATGAGTGCT 58.301 38.462 20.20 6.97 45.85 4.40
754 804 8.184848 CACGCATACTAGTATATATGAGTGCTT 58.815 37.037 20.20 9.55 45.85 3.91
755 805 8.184848 ACGCATACTAGTATATATGAGTGCTTG 58.815 37.037 15.03 5.02 39.43 4.01
756 806 7.166638 CGCATACTAGTATATATGAGTGCTTGC 59.833 40.741 15.03 10.02 31.54 4.01
757 807 7.166638 GCATACTAGTATATATGAGTGCTTGCG 59.833 40.741 15.03 0.00 31.54 4.85
758 808 6.576662 ACTAGTATATATGAGTGCTTGCGT 57.423 37.500 0.00 0.00 0.00 5.24
759 809 6.382608 ACTAGTATATATGAGTGCTTGCGTG 58.617 40.000 0.00 0.00 0.00 5.34
760 810 4.560128 AGTATATATGAGTGCTTGCGTGG 58.440 43.478 0.00 0.00 0.00 4.94
761 811 2.979814 TATATGAGTGCTTGCGTGGT 57.020 45.000 0.00 0.00 0.00 4.16
762 812 2.979814 ATATGAGTGCTTGCGTGGTA 57.020 45.000 0.00 0.00 0.00 3.25
763 813 2.004583 TATGAGTGCTTGCGTGGTAC 57.995 50.000 0.00 0.00 0.00 3.34
764 814 0.321671 ATGAGTGCTTGCGTGGTACT 59.678 50.000 0.00 0.00 32.67 2.73
765 815 0.599991 TGAGTGCTTGCGTGGTACTG 60.600 55.000 0.00 0.00 30.31 2.74
766 816 0.600255 GAGTGCTTGCGTGGTACTGT 60.600 55.000 0.00 0.00 30.31 3.55
767 817 0.880278 AGTGCTTGCGTGGTACTGTG 60.880 55.000 0.00 0.00 0.00 3.66
768 818 1.145156 TGCTTGCGTGGTACTGTGT 59.855 52.632 0.00 0.00 0.00 3.72
769 819 0.462937 TGCTTGCGTGGTACTGTGTT 60.463 50.000 0.00 0.00 0.00 3.32
770 820 1.202545 TGCTTGCGTGGTACTGTGTTA 60.203 47.619 0.00 0.00 0.00 2.41
771 821 1.868498 GCTTGCGTGGTACTGTGTTAA 59.132 47.619 0.00 0.00 0.00 2.01
772 822 2.288458 GCTTGCGTGGTACTGTGTTAAA 59.712 45.455 0.00 0.00 0.00 1.52
773 823 3.242804 GCTTGCGTGGTACTGTGTTAAAA 60.243 43.478 0.00 0.00 0.00 1.52
774 824 4.555906 GCTTGCGTGGTACTGTGTTAAAAT 60.556 41.667 0.00 0.00 0.00 1.82
775 825 5.334260 GCTTGCGTGGTACTGTGTTAAAATA 60.334 40.000 0.00 0.00 0.00 1.40
776 826 6.615264 TTGCGTGGTACTGTGTTAAAATAA 57.385 33.333 0.00 0.00 0.00 1.40
777 827 6.804770 TGCGTGGTACTGTGTTAAAATAAT 57.195 33.333 0.00 0.00 0.00 1.28
778 828 7.902387 TGCGTGGTACTGTGTTAAAATAATA 57.098 32.000 0.00 0.00 0.00 0.98
779 829 7.741198 TGCGTGGTACTGTGTTAAAATAATAC 58.259 34.615 0.00 0.00 0.00 1.89
780 830 7.387122 TGCGTGGTACTGTGTTAAAATAATACA 59.613 33.333 0.00 0.81 0.00 2.29
781 831 7.901377 GCGTGGTACTGTGTTAAAATAATACAG 59.099 37.037 19.19 19.19 42.63 2.74
782 832 7.901377 CGTGGTACTGTGTTAAAATAATACAGC 59.099 37.037 20.16 9.84 41.28 4.40
783 833 8.943002 GTGGTACTGTGTTAAAATAATACAGCT 58.057 33.333 20.16 13.04 41.28 4.24
784 834 8.941977 TGGTACTGTGTTAAAATAATACAGCTG 58.058 33.333 20.16 13.48 41.28 4.24
785 835 9.158233 GGTACTGTGTTAAAATAATACAGCTGA 57.842 33.333 23.35 4.31 41.28 4.26
807 857 3.006967 ACTTCACAGTCAGGCGTAAAGAT 59.993 43.478 0.00 0.00 0.00 2.40
821 871 3.071602 CGTAAAGATGGGGGACTCATGAT 59.928 47.826 0.00 0.00 0.00 2.45
909 959 3.118519 ACGTAATAAATCACCCGGCTTCT 60.119 43.478 0.00 0.00 0.00 2.85
920 970 1.612395 CCGGCTTCTCTGCTCCTTCT 61.612 60.000 0.00 0.00 0.00 2.85
929 979 2.235650 CTCTGCTCCTTCTGATTGGTCA 59.764 50.000 0.00 0.00 0.00 4.02
977 1027 2.891191 TCAAAACCCTATTTCCGGCT 57.109 45.000 0.00 0.00 0.00 5.52
1021 1076 4.933064 CCGACGGCATCCTCTCGC 62.933 72.222 0.00 0.00 0.00 5.03
1063 1118 2.181021 CCCCGGAGTTCGTCTTCG 59.819 66.667 0.73 4.58 44.16 3.79
1068 1123 1.737008 GGAGTTCGTCTTCGGGCAC 60.737 63.158 0.00 0.00 37.69 5.01
1173 1552 2.791383 TTTTTCACGCTGATGGTTGG 57.209 45.000 0.00 0.00 0.00 3.77
1180 1559 3.823873 TCACGCTGATGGTTGGTTTTATT 59.176 39.130 0.00 0.00 0.00 1.40
1215 1597 2.159028 GCAGATGTGGAGGAGTTCTACC 60.159 54.545 0.00 0.00 36.52 3.18
1287 1669 3.195610 GGGGAGATGGAATTTGTGGTTTC 59.804 47.826 0.00 0.00 0.00 2.78
1411 1793 6.336842 AGTTGCTGATTCCATAATATTGGC 57.663 37.500 0.00 0.00 36.66 4.52
1419 1801 7.424803 TGATTCCATAATATTGGCAGTTTTCG 58.575 34.615 0.00 0.00 36.66 3.46
1424 1806 3.932545 ATATTGGCAGTTTTCGTTGCA 57.067 38.095 0.00 0.00 42.02 4.08
1448 1837 7.423199 CATTACCAGTGGAATGATTGATGAAG 58.577 38.462 18.40 0.00 35.46 3.02
1528 1917 0.704076 TTGGGGAGTCAAATCAGGGG 59.296 55.000 0.00 0.00 0.00 4.79
1535 1924 4.166144 GGGAGTCAAATCAGGGGAGAATTA 59.834 45.833 0.00 0.00 0.00 1.40
1591 1980 2.807967 TGTATGCCTTATCTGATTGCGC 59.192 45.455 0.00 0.00 0.00 6.09
1616 2005 6.976934 ACCAGAACATTTAACCATCACTTT 57.023 33.333 0.00 0.00 0.00 2.66
1667 2068 7.707893 AGAAATTGCCATGAATACTAACAATGC 59.292 33.333 0.00 0.00 0.00 3.56
1678 2079 7.337184 TGAATACTAACAATGCGGGTAAATTGA 59.663 33.333 2.60 0.00 37.26 2.57
1689 2090 3.056179 CGGGTAAATTGAAATGGCCTGTT 60.056 43.478 3.32 0.00 0.00 3.16
1714 2115 2.380064 TTGAGTGGCCAAAGGATTGT 57.620 45.000 7.24 0.00 34.60 2.71
1756 2157 2.905415 ATTCCCAATTGCCTCTGTCA 57.095 45.000 0.00 0.00 0.00 3.58
1880 2281 4.409570 CACTAGCATGCTCATTTTGTGTC 58.590 43.478 26.57 0.00 0.00 3.67
1915 2316 4.956700 TGGGTTACTTGTGGAATGAACAAA 59.043 37.500 0.00 0.00 37.10 2.83
2037 2438 2.494073 GTGAGTCAACTACCTGAGGAGG 59.506 54.545 4.99 0.00 46.21 4.30
2191 2592 2.410053 GTCGTGTCTCATTTGACAGAGC 59.590 50.000 0.00 0.00 46.09 4.09
2320 2722 7.524912 CATGATATAGTCCATACTTTGCTTGC 58.475 38.462 0.00 0.00 37.15 4.01
2321 2723 6.830912 TGATATAGTCCATACTTTGCTTGCT 58.169 36.000 0.00 0.00 37.15 3.91
2322 2724 7.962441 TGATATAGTCCATACTTTGCTTGCTA 58.038 34.615 0.00 0.00 37.15 3.49
2664 3066 9.591792 CTCTACTAATTGAATGATGTCTGAACA 57.408 33.333 0.00 0.00 40.38 3.18
2712 3114 2.234908 GTGGAGCAGTACTGAGGATGTT 59.765 50.000 27.08 0.00 0.00 2.71
2842 3244 3.520569 TCAATCGACGAATGCTTCATCA 58.479 40.909 8.06 0.00 0.00 3.07
2952 3479 7.030165 CGGAGGTAGTATATGTCATGATTGTC 58.970 42.308 0.00 0.00 0.00 3.18
3019 3547 9.955208 GATTGCAGTATTGTCATTATCATTTCA 57.045 29.630 0.00 0.00 0.00 2.69
3386 3916 3.552684 CGGAGTACGGTGTTTAGTTTGGA 60.553 47.826 0.00 0.00 39.42 3.53
3613 4143 6.072948 CCACACGACATTCCTTATTTGTTGTA 60.073 38.462 0.00 0.00 36.15 2.41
3741 4271 2.169769 CCCAAGGAAGATTACTACGCCA 59.830 50.000 0.00 0.00 0.00 5.69
3788 4318 2.117156 CCGGCCAATGCTCAAGGAG 61.117 63.158 2.24 0.00 37.74 3.69
3812 4342 2.283173 GGTGGCAAAGAGGGTGGG 60.283 66.667 0.00 0.00 0.00 4.61
3852 4382 4.326766 CCAAGTGTGCCGGTTGCG 62.327 66.667 1.90 0.00 45.60 4.85
3854 4384 3.276846 AAGTGTGCCGGTTGCGAC 61.277 61.111 1.90 0.00 45.60 5.19
3942 4472 1.577468 CAAGTGTGTTGGCGTGACTA 58.423 50.000 0.00 0.00 0.00 2.59
4032 4562 3.676093 TCTGACTCGATATAGCGGTGAT 58.324 45.455 10.94 0.00 0.00 3.06
4215 4753 0.608130 GGCTTGGGTTCAAACATCCC 59.392 55.000 0.00 0.00 41.41 3.85
4284 4822 1.043816 ATCTGAGGGGACATAGTGCG 58.956 55.000 0.00 0.00 0.00 5.34
4306 4844 4.641989 CGGGTAGTACTGTACTATGTTGGT 59.358 45.833 25.61 4.50 42.68 3.67
4329 4867 5.068215 AGTAGTATGAGTAGGCCATCTGT 57.932 43.478 5.01 0.00 0.00 3.41
4333 4871 1.279496 TGAGTAGGCCATCTGTTGCT 58.721 50.000 5.01 0.00 0.00 3.91
4340 4878 2.307098 AGGCCATCTGTTGCTTTCTACT 59.693 45.455 5.01 0.00 0.00 2.57
4341 4879 2.680339 GGCCATCTGTTGCTTTCTACTC 59.320 50.000 0.00 0.00 0.00 2.59
4342 4880 2.680339 GCCATCTGTTGCTTTCTACTCC 59.320 50.000 0.00 0.00 0.00 3.85
4343 4881 3.274288 CCATCTGTTGCTTTCTACTCCC 58.726 50.000 0.00 0.00 0.00 4.30
4344 4882 3.054802 CCATCTGTTGCTTTCTACTCCCT 60.055 47.826 0.00 0.00 0.00 4.20
4345 4883 3.963428 TCTGTTGCTTTCTACTCCCTC 57.037 47.619 0.00 0.00 0.00 4.30
4346 4884 2.567615 TCTGTTGCTTTCTACTCCCTCC 59.432 50.000 0.00 0.00 0.00 4.30
4347 4885 1.275291 TGTTGCTTTCTACTCCCTCCG 59.725 52.381 0.00 0.00 0.00 4.63
4348 4886 1.275573 GTTGCTTTCTACTCCCTCCGT 59.724 52.381 0.00 0.00 0.00 4.69
4349 4887 1.640917 TGCTTTCTACTCCCTCCGTT 58.359 50.000 0.00 0.00 0.00 4.44
4350 4888 1.549170 TGCTTTCTACTCCCTCCGTTC 59.451 52.381 0.00 0.00 0.00 3.95
4351 4889 1.134759 GCTTTCTACTCCCTCCGTTCC 60.135 57.143 0.00 0.00 0.00 3.62
4352 4890 2.458620 CTTTCTACTCCCTCCGTTCCT 58.541 52.381 0.00 0.00 0.00 3.36
4353 4891 3.629087 CTTTCTACTCCCTCCGTTCCTA 58.371 50.000 0.00 0.00 0.00 2.94
4354 4892 3.744940 TTCTACTCCCTCCGTTCCTAA 57.255 47.619 0.00 0.00 0.00 2.69
4355 4893 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
4356 4894 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
4357 4895 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
4358 4896 5.136105 TCTACTCCCTCCGTTCCTAAATAC 58.864 45.833 0.00 0.00 0.00 1.89
4359 4897 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
4360 4898 5.134725 ACTCCCTCCGTTCCTAAATACTA 57.865 43.478 0.00 0.00 0.00 1.82
4361 4899 5.713807 ACTCCCTCCGTTCCTAAATACTAT 58.286 41.667 0.00 0.00 0.00 2.12
4362 4900 6.856757 ACTCCCTCCGTTCCTAAATACTATA 58.143 40.000 0.00 0.00 0.00 1.31
4363 4901 7.300658 ACTCCCTCCGTTCCTAAATACTATAA 58.699 38.462 0.00 0.00 0.00 0.98
4364 4902 7.450944 ACTCCCTCCGTTCCTAAATACTATAAG 59.549 40.741 0.00 0.00 0.00 1.73
4365 4903 7.300658 TCCCTCCGTTCCTAAATACTATAAGT 58.699 38.462 0.00 0.00 0.00 2.24
4366 4904 7.449704 TCCCTCCGTTCCTAAATACTATAAGTC 59.550 40.741 0.00 0.00 0.00 3.01
4367 4905 7.450944 CCCTCCGTTCCTAAATACTATAAGTCT 59.549 40.741 0.00 0.00 0.00 3.24
4368 4906 8.858094 CCTCCGTTCCTAAATACTATAAGTCTT 58.142 37.037 0.00 0.00 0.00 3.01
4371 4909 9.813446 CCGTTCCTAAATACTATAAGTCTTTGT 57.187 33.333 0.00 0.00 29.19 2.83
4399 4937 8.768501 AGATTTCACTATGGACTACATACAGA 57.231 34.615 0.00 0.00 41.03 3.41
4400 4938 8.855110 AGATTTCACTATGGACTACATACAGAG 58.145 37.037 0.00 0.00 41.03 3.35
4401 4939 7.956328 TTTCACTATGGACTACATACAGAGT 57.044 36.000 0.00 0.00 41.03 3.24
4402 4940 9.642343 ATTTCACTATGGACTACATACAGAGTA 57.358 33.333 0.00 0.00 41.03 2.59
4403 4941 9.470399 TTTCACTATGGACTACATACAGAGTAA 57.530 33.333 0.00 0.00 41.03 2.24
4404 4942 9.470399 TTCACTATGGACTACATACAGAGTAAA 57.530 33.333 0.00 0.00 41.03 2.01
4405 4943 9.470399 TCACTATGGACTACATACAGAGTAAAA 57.530 33.333 0.00 0.00 41.03 1.52
4436 4974 9.842775 TGAATCTTCACTCTAAAATGCATCTAT 57.157 29.630 0.00 0.00 31.01 1.98
4452 4990 9.828039 AATGCATCTATATACATCTGTATGTGG 57.172 33.333 12.10 8.21 45.99 4.17
4453 4991 8.366359 TGCATCTATATACATCTGTATGTGGT 57.634 34.615 12.10 0.00 45.99 4.16
4454 4992 8.815912 TGCATCTATATACATCTGTATGTGGTT 58.184 33.333 12.10 1.86 45.99 3.67
4455 4993 9.307121 GCATCTATATACATCTGTATGTGGTTC 57.693 37.037 12.10 0.75 45.99 3.62
4464 5002 8.806429 ACATCTGTATGTGGTTCATAATGAAA 57.194 30.769 0.00 0.00 44.79 2.69
4465 5003 9.412460 ACATCTGTATGTGGTTCATAATGAAAT 57.588 29.630 0.00 0.00 44.79 2.17
4466 5004 9.888878 CATCTGTATGTGGTTCATAATGAAATC 57.111 33.333 0.00 0.00 38.22 2.17
4467 5005 9.857656 ATCTGTATGTGGTTCATAATGAAATCT 57.142 29.630 0.00 0.00 38.22 2.40
4468 5006 9.330063 TCTGTATGTGGTTCATAATGAAATCTC 57.670 33.333 0.00 0.00 38.22 2.75
4469 5007 9.334947 CTGTATGTGGTTCATAATGAAATCTCT 57.665 33.333 0.00 0.00 38.22 3.10
4473 5011 9.685276 ATGTGGTTCATAATGAAATCTCTACAA 57.315 29.630 0.00 0.00 38.22 2.41
4474 5012 9.513906 TGTGGTTCATAATGAAATCTCTACAAA 57.486 29.630 0.00 0.00 38.22 2.83
4475 5013 9.994432 GTGGTTCATAATGAAATCTCTACAAAG 57.006 33.333 0.00 0.00 38.22 2.77
4476 5014 9.958180 TGGTTCATAATGAAATCTCTACAAAGA 57.042 29.630 0.00 0.00 38.22 2.52
4538 5076 0.250338 AGCGTGAAAACCCACCTCTC 60.250 55.000 0.00 0.00 33.67 3.20
4539 5077 0.250338 GCGTGAAAACCCACCTCTCT 60.250 55.000 0.00 0.00 33.67 3.10
4546 5084 6.473758 GTGAAAACCCACCTCTCTAGTAATT 58.526 40.000 0.00 0.00 0.00 1.40
4586 5124 0.099436 GACATGCCATCCGTTTGCTC 59.901 55.000 0.00 0.00 0.00 4.26
4605 5144 1.630369 TCTGCCTGCCATTGTTACTCT 59.370 47.619 0.00 0.00 0.00 3.24
4609 5148 2.875672 GCCTGCCATTGTTACTCTCACA 60.876 50.000 0.00 0.00 0.00 3.58
4610 5149 2.744202 CCTGCCATTGTTACTCTCACAC 59.256 50.000 0.00 0.00 0.00 3.82
4628 5167 3.002791 ACACTGGATACACATCTTTGCG 58.997 45.455 0.00 0.00 46.17 4.85
4650 5189 1.208052 TGGCATCTGGAGTGCTACTTC 59.792 52.381 0.00 0.00 42.16 3.01
4655 5194 4.622695 GCATCTGGAGTGCTACTTCTCTTT 60.623 45.833 0.00 0.00 39.45 2.52
4661 5200 5.702670 TGGAGTGCTACTTCTCTTTGAAATG 59.297 40.000 0.00 0.00 33.79 2.32
4662 5201 5.934625 GGAGTGCTACTTCTCTTTGAAATGA 59.065 40.000 0.00 0.00 33.79 2.57
4663 5202 6.428159 GGAGTGCTACTTCTCTTTGAAATGAA 59.572 38.462 0.00 0.00 33.79 2.57
4664 5203 7.120432 GGAGTGCTACTTCTCTTTGAAATGAAT 59.880 37.037 0.00 0.00 33.79 2.57
4665 5204 8.038492 AGTGCTACTTCTCTTTGAAATGAATC 57.962 34.615 0.00 0.00 33.79 2.52
4666 5205 7.120432 AGTGCTACTTCTCTTTGAAATGAATCC 59.880 37.037 0.00 0.00 33.79 3.01
4667 5206 6.092670 TGCTACTTCTCTTTGAAATGAATCCG 59.907 38.462 0.00 0.00 33.79 4.18
4668 5207 6.092807 GCTACTTCTCTTTGAAATGAATCCGT 59.907 38.462 0.00 0.00 33.79 4.69
4669 5208 6.246420 ACTTCTCTTTGAAATGAATCCGTG 57.754 37.500 0.00 0.00 33.79 4.94
4670 5209 5.997746 ACTTCTCTTTGAAATGAATCCGTGA 59.002 36.000 0.00 0.00 33.79 4.35
4671 5210 6.656693 ACTTCTCTTTGAAATGAATCCGTGAT 59.343 34.615 0.00 0.00 33.79 3.06
4672 5211 7.824289 ACTTCTCTTTGAAATGAATCCGTGATA 59.176 33.333 0.00 0.00 33.79 2.15
4695 5234 9.153721 GATAGATGCTCTCAGAAAGAATATTGG 57.846 37.037 0.00 0.00 32.23 3.16
4698 5237 8.219178 AGATGCTCTCAGAAAGAATATTGGATT 58.781 33.333 0.00 0.00 32.23 3.01
4747 5305 3.766545 ACATGAACTACAGCCAAATGGT 58.233 40.909 0.00 0.00 37.57 3.55
4768 5326 4.848757 GTTTGATGAACCTAATGATCGGC 58.151 43.478 0.00 0.00 31.85 5.54
4841 5406 2.465920 CGTTGTGCTTCGTCGAGC 59.534 61.111 9.00 9.00 43.00 5.03
4844 5409 4.717629 TGTGCTTCGTCGAGCGGG 62.718 66.667 10.62 3.45 45.64 6.13
4850 5415 3.851845 TTCGTCGAGCGGGGTGTTG 62.852 63.158 0.00 0.00 41.72 3.33
4862 5427 2.515901 GTGTTGCCCCACCTGTCT 59.484 61.111 0.00 0.00 0.00 3.41
4864 5429 2.985847 GTTGCCCCACCTGTCTGC 60.986 66.667 0.00 0.00 0.00 4.26
4865 5430 4.641645 TTGCCCCACCTGTCTGCG 62.642 66.667 0.00 0.00 0.00 5.18
4873 5438 3.052082 CCTGTCTGCGGCCACAAG 61.052 66.667 2.24 0.00 0.00 3.16
4883 5448 2.203337 GCCACAAGGTCAGCACCA 60.203 61.111 0.00 0.00 46.68 4.17
4901 5466 0.251297 CAAACTCCACCAGCATCCCA 60.251 55.000 0.00 0.00 0.00 4.37
4907 5472 4.457496 ACCAGCATCCCAGCGACG 62.457 66.667 0.00 0.00 40.15 5.12
5000 5565 1.220477 GAACCTGAGCAGCCTCCTC 59.780 63.158 0.00 0.00 37.29 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 153 3.182887 ACTCCCTCTGTCTTGAGTCAT 57.817 47.619 0.00 0.00 32.85 3.06
266 309 4.538746 TGTTTTTCCGTTTTTGTTCCCT 57.461 36.364 0.00 0.00 0.00 4.20
286 329 4.085107 GCGGCGGCAAAATAAAAAGATATG 60.085 41.667 9.78 0.00 39.62 1.78
322 365 3.527533 ACGCTATTTCGAAGCACCAATA 58.472 40.909 8.23 0.00 40.08 1.90
701 751 1.330521 CAATGCGCGCCTTTACACTAT 59.669 47.619 30.77 9.00 0.00 2.12
742 792 2.979814 ACCACGCAAGCACTCATATA 57.020 45.000 0.00 0.00 45.62 0.86
743 793 2.168521 AGTACCACGCAAGCACTCATAT 59.831 45.455 0.00 0.00 45.62 1.78
744 794 1.548719 AGTACCACGCAAGCACTCATA 59.451 47.619 0.00 0.00 45.62 2.15
745 795 0.321671 AGTACCACGCAAGCACTCAT 59.678 50.000 0.00 0.00 45.62 2.90
746 796 0.599991 CAGTACCACGCAAGCACTCA 60.600 55.000 0.00 0.00 45.62 3.41
747 797 0.600255 ACAGTACCACGCAAGCACTC 60.600 55.000 0.00 0.00 45.62 3.51
748 798 0.880278 CACAGTACCACGCAAGCACT 60.880 55.000 0.00 0.00 45.62 4.40
749 799 1.157870 ACACAGTACCACGCAAGCAC 61.158 55.000 0.00 0.00 45.62 4.40
750 800 0.462937 AACACAGTACCACGCAAGCA 60.463 50.000 0.00 0.00 45.62 3.91
751 801 1.504359 TAACACAGTACCACGCAAGC 58.496 50.000 0.00 0.00 45.62 4.01
753 803 6.615264 TTATTTTAACACAGTACCACGCAA 57.385 33.333 0.00 0.00 0.00 4.85
754 804 6.804770 ATTATTTTAACACAGTACCACGCA 57.195 33.333 0.00 0.00 0.00 5.24
755 805 7.741198 TGTATTATTTTAACACAGTACCACGC 58.259 34.615 0.00 0.00 0.00 5.34
756 806 7.901377 GCTGTATTATTTTAACACAGTACCACG 59.099 37.037 7.34 0.00 39.03 4.94
757 807 8.943002 AGCTGTATTATTTTAACACAGTACCAC 58.057 33.333 7.34 0.00 39.03 4.16
758 808 8.941977 CAGCTGTATTATTTTAACACAGTACCA 58.058 33.333 5.25 0.00 39.03 3.25
759 809 9.158233 TCAGCTGTATTATTTTAACACAGTACC 57.842 33.333 14.67 0.00 39.03 3.34
760 810 9.968743 GTCAGCTGTATTATTTTAACACAGTAC 57.031 33.333 14.67 0.00 39.03 2.73
761 811 9.938280 AGTCAGCTGTATTATTTTAACACAGTA 57.062 29.630 14.67 0.00 39.03 2.74
762 812 8.848474 AGTCAGCTGTATTATTTTAACACAGT 57.152 30.769 14.67 0.00 39.03 3.55
763 813 9.760660 GAAGTCAGCTGTATTATTTTAACACAG 57.239 33.333 14.67 2.15 39.65 3.66
764 814 9.278978 TGAAGTCAGCTGTATTATTTTAACACA 57.721 29.630 14.67 2.75 0.00 3.72
765 815 9.543018 GTGAAGTCAGCTGTATTATTTTAACAC 57.457 33.333 14.67 8.22 0.00 3.32
766 816 9.278978 TGTGAAGTCAGCTGTATTATTTTAACA 57.721 29.630 14.67 5.80 0.00 2.41
767 817 9.760660 CTGTGAAGTCAGCTGTATTATTTTAAC 57.239 33.333 14.67 0.00 0.00 2.01
768 818 9.502091 ACTGTGAAGTCAGCTGTATTATTTTAA 57.498 29.630 14.67 0.00 38.84 1.52
769 819 9.151471 GACTGTGAAGTCAGCTGTATTATTTTA 57.849 33.333 14.67 0.00 38.84 1.52
770 820 7.661437 TGACTGTGAAGTCAGCTGTATTATTTT 59.339 33.333 14.67 0.00 43.09 1.82
771 821 7.161404 TGACTGTGAAGTCAGCTGTATTATTT 58.839 34.615 14.67 0.00 43.09 1.40
772 822 6.701340 TGACTGTGAAGTCAGCTGTATTATT 58.299 36.000 14.67 2.61 43.09 1.40
773 823 6.286240 TGACTGTGAAGTCAGCTGTATTAT 57.714 37.500 14.67 0.00 43.09 1.28
774 824 5.722021 TGACTGTGAAGTCAGCTGTATTA 57.278 39.130 14.67 0.00 43.09 0.98
775 825 4.607293 TGACTGTGAAGTCAGCTGTATT 57.393 40.909 14.67 9.72 43.09 1.89
783 833 1.324383 TACGCCTGACTGTGAAGTCA 58.676 50.000 8.21 8.21 45.41 3.41
784 834 2.433868 TTACGCCTGACTGTGAAGTC 57.566 50.000 0.00 0.00 39.15 3.01
785 835 2.364324 TCTTTACGCCTGACTGTGAAGT 59.636 45.455 0.00 0.00 34.42 3.01
799 849 2.434336 TCATGAGTCCCCCATCTTTACG 59.566 50.000 0.00 0.00 0.00 3.18
807 857 0.343018 TGGAGATCATGAGTCCCCCA 59.657 55.000 19.57 14.35 0.00 4.96
909 959 2.259917 TGACCAATCAGAAGGAGCAGA 58.740 47.619 0.00 0.00 0.00 4.26
920 970 4.324254 GGGATTCCACTACTTGACCAATCA 60.324 45.833 4.80 0.00 0.00 2.57
929 979 1.628327 GGGGAGGGGATTCCACTACTT 60.628 57.143 17.00 0.00 37.68 2.24
985 1035 3.792047 CATCGCCGCCACACAGTG 61.792 66.667 0.00 0.00 0.00 3.66
1012 1067 3.532155 GACGGCAGGCGAGAGGAT 61.532 66.667 25.17 0.00 0.00 3.24
1134 1513 2.566010 CCCGCACCAAAATCCACG 59.434 61.111 0.00 0.00 0.00 4.94
1173 1552 6.864165 TCTGCGGACCAATAAACAAATAAAAC 59.136 34.615 0.00 0.00 0.00 2.43
1180 1559 3.190327 CACATCTGCGGACCAATAAACAA 59.810 43.478 0.00 0.00 0.00 2.83
1411 1793 3.974401 CACTGGTAATGCAACGAAAACTG 59.026 43.478 0.00 0.00 0.00 3.16
1419 1801 4.989279 ATCATTCCACTGGTAATGCAAC 57.011 40.909 12.16 0.00 33.91 4.17
1424 1806 7.121382 ACTTCATCAATCATTCCACTGGTAAT 58.879 34.615 0.00 0.00 0.00 1.89
1508 1897 1.077005 CCCCTGATTTGACTCCCCAAA 59.923 52.381 0.00 0.00 39.93 3.28
1535 1924 4.574828 GCACCATATTATCACCAAACTCGT 59.425 41.667 0.00 0.00 0.00 4.18
1591 1980 7.687941 AAGTGATGGTTAAATGTTCTGGTAG 57.312 36.000 0.00 0.00 0.00 3.18
1616 2005 8.518430 TCCAATTTACAGCTGAATATAAGCAA 57.482 30.769 23.35 0.00 43.37 3.91
1667 2068 2.495669 ACAGGCCATTTCAATTTACCCG 59.504 45.455 5.01 0.00 0.00 5.28
1678 2079 2.298163 CTCAAAGCTCAACAGGCCATTT 59.702 45.455 5.01 0.00 0.00 2.32
1689 2090 1.321474 CTTTGGCCACTCAAAGCTCA 58.679 50.000 3.88 0.00 44.44 4.26
1714 2115 1.538047 GGACTTCCAATTCTGCAGCA 58.462 50.000 9.47 0.00 35.64 4.41
1756 2157 1.128200 TGCAGTGACACCCAACTACT 58.872 50.000 0.84 0.00 0.00 2.57
1868 2269 6.141211 CAGAAAACGACATGACACAAAATGAG 59.859 38.462 0.00 0.00 0.00 2.90
1880 2281 4.274950 ACAAGTAACCCAGAAAACGACATG 59.725 41.667 0.00 0.00 0.00 3.21
1915 2316 2.299013 TGTGCCTACGAAGATGACAACT 59.701 45.455 0.00 0.00 0.00 3.16
1989 2390 0.678048 GTCCCATCAGGCAGTCCAAC 60.678 60.000 0.00 0.00 34.51 3.77
2037 2438 2.550180 GCTCAGGAAGTTGAACAGGAAC 59.450 50.000 0.00 0.00 0.00 3.62
2039 2440 1.072331 GGCTCAGGAAGTTGAACAGGA 59.928 52.381 0.00 0.00 0.00 3.86
2262 2664 3.614092 ACACATAGAATGTCCTGCTTGG 58.386 45.455 0.00 0.00 42.70 3.61
2281 2683 9.002600 GGACTATATCATGCAATACATTCAACA 57.997 33.333 0.00 0.00 36.64 3.33
2296 2698 7.456725 AGCAAGCAAAGTATGGACTATATCAT 58.543 34.615 0.00 0.00 33.58 2.45
2302 2704 5.677319 AGTAGCAAGCAAAGTATGGACTA 57.323 39.130 0.00 0.00 33.58 2.59
2320 2722 8.861101 GTCTTTGTGCATAGTAAGTTGTAGTAG 58.139 37.037 0.00 0.00 0.00 2.57
2321 2723 7.539710 CGTCTTTGTGCATAGTAAGTTGTAGTA 59.460 37.037 0.00 0.00 0.00 1.82
2322 2724 6.365247 CGTCTTTGTGCATAGTAAGTTGTAGT 59.635 38.462 0.00 0.00 0.00 2.73
2489 2891 6.319715 AGGTAAAAGGGAGAAAAGGCATTTA 58.680 36.000 0.00 0.00 0.00 1.40
2952 3479 5.689514 TGTGAAACTGTTGCAAAATTATCCG 59.310 36.000 2.00 0.00 38.04 4.18
3087 3615 2.582636 AGGAATGTTGCCCATCTTACCT 59.417 45.455 0.00 0.00 31.75 3.08
3150 3680 6.515523 CAGCATGAGTTGAAGTGAAAAGCAC 61.516 44.000 0.00 0.00 43.74 4.40
3280 3810 3.562557 GCAAGAACGTAAAGGAGAACCAA 59.437 43.478 0.00 0.00 38.94 3.67
3386 3916 5.755375 CCATGATAGCAATCAGTACTTCGTT 59.245 40.000 0.00 0.00 45.17 3.85
3613 4143 7.701539 TTGATAAAGCCTGTGTTTGATATGT 57.298 32.000 0.00 0.00 0.00 2.29
3741 4271 5.047092 CCATTACCTTCCAGCTGTTGAAATT 60.047 40.000 13.81 2.54 0.00 1.82
3788 4318 0.394899 CCTCTTTGCCACCATCCTCC 60.395 60.000 0.00 0.00 0.00 4.30
3852 4382 2.641912 GTTAGCGCTGTAGATCTCGTC 58.358 52.381 22.90 0.00 0.00 4.20
3854 4384 1.260825 TCGTTAGCGCTGTAGATCTCG 59.739 52.381 22.90 12.23 38.14 4.04
3932 4462 0.817654 CCATCTCAGTAGTCACGCCA 59.182 55.000 0.00 0.00 0.00 5.69
3942 4472 0.537188 ATTCCGTTCGCCATCTCAGT 59.463 50.000 0.00 0.00 0.00 3.41
4032 4562 1.272490 ACGAGTCGGAAGCTTTCATCA 59.728 47.619 18.30 0.00 0.00 3.07
4132 4670 5.476599 CCAAAATCCTAACATGTCACCAAGA 59.523 40.000 0.00 0.00 0.00 3.02
4180 4718 1.579429 GCCAACGGCCTGTACAAAG 59.421 57.895 0.00 0.00 44.06 2.77
4238 4776 7.602517 TTTTGATTTGAAACGGTGTCAAAAT 57.397 28.000 25.59 15.98 45.43 1.82
4241 4779 6.333416 TGATTTTGATTTGAAACGGTGTCAA 58.667 32.000 9.66 9.66 33.21 3.18
4284 4822 6.830838 ACTACCAACATAGTACAGTACTACCC 59.169 42.308 20.68 0.00 43.46 3.69
4306 4844 6.202202 ACAGATGGCCTACTCATACTACTA 57.798 41.667 3.32 0.00 0.00 1.82
4329 4867 1.640917 ACGGAGGGAGTAGAAAGCAA 58.359 50.000 0.00 0.00 0.00 3.91
4333 4871 2.617840 AGGAACGGAGGGAGTAGAAA 57.382 50.000 0.00 0.00 0.00 2.52
4340 4878 7.300658 ACTTATAGTATTTAGGAACGGAGGGA 58.699 38.462 0.00 0.00 0.00 4.20
4341 4879 7.450944 AGACTTATAGTATTTAGGAACGGAGGG 59.549 40.741 0.00 0.00 0.00 4.30
4342 4880 8.406730 AGACTTATAGTATTTAGGAACGGAGG 57.593 38.462 0.00 0.00 0.00 4.30
4345 4883 9.813446 ACAAAGACTTATAGTATTTAGGAACGG 57.187 33.333 0.00 0.00 37.52 4.44
4373 4911 9.862149 TCTGTATGTAGTCCATAGTGAAATCTA 57.138 33.333 0.00 0.00 36.71 1.98
4374 4912 8.768501 TCTGTATGTAGTCCATAGTGAAATCT 57.231 34.615 0.00 0.00 36.71 2.40
4375 4913 8.634444 ACTCTGTATGTAGTCCATAGTGAAATC 58.366 37.037 0.00 0.00 36.71 2.17
4376 4914 8.540507 ACTCTGTATGTAGTCCATAGTGAAAT 57.459 34.615 0.00 0.00 36.71 2.17
4377 4915 7.956328 ACTCTGTATGTAGTCCATAGTGAAA 57.044 36.000 0.00 0.00 36.71 2.69
4378 4916 9.470399 TTTACTCTGTATGTAGTCCATAGTGAA 57.530 33.333 0.00 0.00 36.71 3.18
4379 4917 9.470399 TTTTACTCTGTATGTAGTCCATAGTGA 57.530 33.333 0.00 0.00 36.71 3.41
4410 4948 9.842775 ATAGATGCATTTTAGAGTGAAGATTCA 57.157 29.630 0.00 0.00 34.20 2.57
4426 4964 9.828039 CCACATACAGATGTATATAGATGCATT 57.172 33.333 0.00 0.00 44.82 3.56
4427 4965 8.985922 ACCACATACAGATGTATATAGATGCAT 58.014 33.333 0.00 0.00 44.82 3.96
4428 4966 8.366359 ACCACATACAGATGTATATAGATGCA 57.634 34.615 5.21 0.00 44.82 3.96
4429 4967 9.307121 GAACCACATACAGATGTATATAGATGC 57.693 37.037 5.21 0.00 44.82 3.91
4438 4976 9.898152 TTTCATTATGAACCACATACAGATGTA 57.102 29.630 7.19 0.00 39.04 2.29
4439 4977 8.806429 TTTCATTATGAACCACATACAGATGT 57.194 30.769 7.19 0.00 40.51 3.06
4440 4978 9.888878 GATTTCATTATGAACCACATACAGATG 57.111 33.333 7.19 0.00 40.62 2.90
4441 4979 9.857656 AGATTTCATTATGAACCACATACAGAT 57.142 29.630 7.19 0.00 40.62 2.90
4442 4980 9.330063 GAGATTTCATTATGAACCACATACAGA 57.670 33.333 7.19 0.00 40.62 3.41
4443 4981 9.334947 AGAGATTTCATTATGAACCACATACAG 57.665 33.333 7.19 0.00 40.62 2.74
4447 4985 9.685276 TTGTAGAGATTTCATTATGAACCACAT 57.315 29.630 7.19 0.00 35.89 3.21
4448 4986 9.513906 TTTGTAGAGATTTCATTATGAACCACA 57.486 29.630 7.19 0.00 35.89 4.17
4449 4987 9.994432 CTTTGTAGAGATTTCATTATGAACCAC 57.006 33.333 7.19 2.67 35.89 4.16
4450 4988 9.958180 TCTTTGTAGAGATTTCATTATGAACCA 57.042 29.630 7.19 0.00 35.89 3.67
4474 5012 9.440761 ACTCCATCTGTTCCTAAATATAAGTCT 57.559 33.333 0.00 0.00 0.00 3.24
4481 5019 9.667107 CAAAACTACTCCATCTGTTCCTAAATA 57.333 33.333 0.00 0.00 0.00 1.40
4482 5020 8.383175 TCAAAACTACTCCATCTGTTCCTAAAT 58.617 33.333 0.00 0.00 0.00 1.40
4483 5021 7.741785 TCAAAACTACTCCATCTGTTCCTAAA 58.258 34.615 0.00 0.00 0.00 1.85
4484 5022 7.311092 TCAAAACTACTCCATCTGTTCCTAA 57.689 36.000 0.00 0.00 0.00 2.69
4485 5023 6.928348 TCAAAACTACTCCATCTGTTCCTA 57.072 37.500 0.00 0.00 0.00 2.94
4486 5024 5.825593 TCAAAACTACTCCATCTGTTCCT 57.174 39.130 0.00 0.00 0.00 3.36
4487 5025 5.355350 CCATCAAAACTACTCCATCTGTTCC 59.645 44.000 0.00 0.00 0.00 3.62
4488 5026 6.173339 TCCATCAAAACTACTCCATCTGTTC 58.827 40.000 0.00 0.00 0.00 3.18
4489 5027 6.126863 TCCATCAAAACTACTCCATCTGTT 57.873 37.500 0.00 0.00 0.00 3.16
4490 5028 5.762179 TCCATCAAAACTACTCCATCTGT 57.238 39.130 0.00 0.00 0.00 3.41
4491 5029 6.600822 ACAATCCATCAAAACTACTCCATCTG 59.399 38.462 0.00 0.00 0.00 2.90
4492 5030 6.725364 ACAATCCATCAAAACTACTCCATCT 58.275 36.000 0.00 0.00 0.00 2.90
4493 5031 7.121168 TCAACAATCCATCAAAACTACTCCATC 59.879 37.037 0.00 0.00 0.00 3.51
4494 5032 6.947733 TCAACAATCCATCAAAACTACTCCAT 59.052 34.615 0.00 0.00 0.00 3.41
4495 5033 6.303054 TCAACAATCCATCAAAACTACTCCA 58.697 36.000 0.00 0.00 0.00 3.86
4496 5034 6.623767 GCTCAACAATCCATCAAAACTACTCC 60.624 42.308 0.00 0.00 0.00 3.85
4497 5035 6.317857 GCTCAACAATCCATCAAAACTACTC 58.682 40.000 0.00 0.00 0.00 2.59
4498 5036 5.106555 CGCTCAACAATCCATCAAAACTACT 60.107 40.000 0.00 0.00 0.00 2.57
4499 5037 5.088739 CGCTCAACAATCCATCAAAACTAC 58.911 41.667 0.00 0.00 0.00 2.73
4546 5084 7.825331 TGTCAATTCACTAACCAACCATTTA 57.175 32.000 0.00 0.00 0.00 1.40
4586 5124 2.012673 GAGAGTAACAATGGCAGGCAG 58.987 52.381 1.89 0.00 0.00 4.85
4605 5144 4.002982 GCAAAGATGTGTATCCAGTGTGA 58.997 43.478 0.00 0.00 33.64 3.58
4609 5148 3.610040 TCGCAAAGATGTGTATCCAGT 57.390 42.857 0.00 0.00 38.25 4.00
4628 5167 1.415659 AGTAGCACTCCAGATGCCATC 59.584 52.381 0.00 0.00 44.53 3.51
4633 5172 4.734398 AAGAGAAGTAGCACTCCAGATG 57.266 45.455 0.00 0.00 34.13 2.90
4637 5176 4.955811 TTCAAAGAGAAGTAGCACTCCA 57.044 40.909 0.00 0.00 34.13 3.86
4640 5179 7.120432 GGATTCATTTCAAAGAGAAGTAGCACT 59.880 37.037 0.00 0.00 37.57 4.40
4650 5189 7.776933 TCTATCACGGATTCATTTCAAAGAG 57.223 36.000 0.00 0.00 0.00 2.85
4655 5194 5.614308 AGCATCTATCACGGATTCATTTCA 58.386 37.500 0.00 0.00 0.00 2.69
4695 5234 5.710567 GGGGTAGGAACTATTATTGGCAATC 59.289 44.000 17.41 0.65 45.60 2.67
4698 5237 4.312487 AGGGGTAGGAACTATTATTGGCA 58.688 43.478 0.00 0.00 45.60 4.92
4747 5305 4.522114 TGCCGATCATTAGGTTCATCAAA 58.478 39.130 0.00 0.00 0.00 2.69
4762 5320 3.574445 CTGCTGCTGCTGCCGATC 61.574 66.667 25.44 2.06 40.48 3.69
4864 5429 3.357079 GTGCTGACCTTGTGGCCG 61.357 66.667 0.00 0.00 36.63 6.13
4865 5430 2.985847 GGTGCTGACCTTGTGGCC 60.986 66.667 0.00 0.00 39.47 5.36
4869 5434 1.680338 GAGTTTGGTGCTGACCTTGT 58.320 50.000 0.00 0.00 43.58 3.16
4873 5438 1.172812 GGTGGAGTTTGGTGCTGACC 61.173 60.000 0.00 0.00 43.48 4.02
4880 5445 0.251341 GGATGCTGGTGGAGTTTGGT 60.251 55.000 0.00 0.00 0.00 3.67
4883 5448 0.038744 CTGGGATGCTGGTGGAGTTT 59.961 55.000 0.00 0.00 0.00 2.66
5000 5565 1.817099 GGGCAAGATCGACCTGCTG 60.817 63.158 13.15 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.