Multiple sequence alignment - TraesCS1D01G230800

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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 TraesCS1D01G230800 chr1D 100.000 5083 0 0 1 5083 318854894 318849812 0.000000e+00 9387.0
1 TraesCS1D01G230800 chr1D 89.506 648 67 1 4437 5083 273584552 273583905 0.000000e+00 819.0
2 TraesCS1D01G230800 chr1D 80.191 944 145 30 1072 2001 359779051 359778136 0.000000e+00 669.0
3 TraesCS1D01G230800 chr1D 84.097 698 97 12 3380 4070 359777923 359777233 0.000000e+00 662.0
4 TraesCS1D01G230800 chr1D 93.056 72 5 0 3264 3335 153773194 153773123 6.960000e-19 106.0
5 TraesCS1D01G230800 chr1A 90.791 2302 104 39 151 2408 404624779 404627016 0.000000e+00 2977.0
6 TraesCS1D01G230800 chr1A 91.601 1917 103 28 2517 4413 404627095 404628973 0.000000e+00 2595.0
7 TraesCS1D01G230800 chr1A 91.337 658 57 0 4411 5068 404629163 404629820 0.000000e+00 900.0
8 TraesCS1D01G230800 chr1A 84.748 695 88 16 3380 4065 459301758 459301073 0.000000e+00 680.0
9 TraesCS1D01G230800 chr1A 79.462 930 154 26 1072 1990 459302897 459301994 4.320000e-175 625.0
10 TraesCS1D01G230800 chr1A 90.845 142 8 3 2 142 404615916 404616053 8.690000e-43 185.0
11 TraesCS1D01G230800 chr1B 90.111 2154 138 32 2 2115 431408770 431406652 0.000000e+00 2728.0
12 TraesCS1D01G230800 chr1B 96.655 1106 29 6 3334 4435 431404331 431403230 0.000000e+00 1831.0
13 TraesCS1D01G230800 chr1B 80.659 941 143 28 1072 2001 481850407 481849495 0.000000e+00 693.0
14 TraesCS1D01G230800 chr1B 83.548 699 99 12 3380 4070 481849247 481848557 1.540000e-179 640.0
15 TraesCS1D01G230800 chr1B 96.269 268 9 1 2989 3256 431404897 431404631 6.040000e-119 438.0
16 TraesCS1D01G230800 chr1B 83.468 248 29 9 2706 2948 431405898 431405658 2.380000e-53 220.0
17 TraesCS1D01G230800 chr2B 88.923 650 68 2 4437 5083 404150179 404149531 0.000000e+00 798.0
18 TraesCS1D01G230800 chr2B 88.408 647 71 4 4437 5083 251386754 251387396 0.000000e+00 776.0
19 TraesCS1D01G230800 chr2B 76.351 592 121 17 3426 4009 95760763 95761343 2.970000e-77 300.0
20 TraesCS1D01G230800 chr2D 88.735 648 71 2 4437 5083 188893349 188893995 0.000000e+00 791.0
21 TraesCS1D01G230800 chr2D 76.441 590 124 13 3426 4009 60945716 60946296 6.390000e-79 305.0
22 TraesCS1D01G230800 chr2A 88.426 648 73 2 4437 5083 459259365 459260011 0.000000e+00 780.0
23 TraesCS1D01G230800 chr2A 76.431 594 117 21 3426 4009 61467990 61468570 2.970000e-77 300.0
24 TraesCS1D01G230800 chr2A 94.203 69 4 0 3265 3333 703051986 703052054 6.960000e-19 106.0
25 TraesCS1D01G230800 chr2A 94.203 69 4 0 3265 3333 764259869 764259937 6.960000e-19 106.0
26 TraesCS1D01G230800 chr7D 88.426 648 69 4 4437 5083 366428096 366427454 0.000000e+00 776.0
27 TraesCS1D01G230800 chr6D 88.491 643 72 2 4437 5077 334486772 334486130 0.000000e+00 776.0
28 TraesCS1D01G230800 chr7A 88.456 641 71 3 4443 5083 252160041 252159404 0.000000e+00 771.0
29 TraesCS1D01G230800 chr7A 94.286 70 3 1 3266 3335 3219497 3219429 6.960000e-19 106.0
30 TraesCS1D01G230800 chr7A 81.319 91 11 4 2694 2781 130297454 130297367 9.130000e-08 69.4
31 TraesCS1D01G230800 chr5B 74.317 549 119 18 3412 3953 54156900 54157433 3.990000e-51 213.0
32 TraesCS1D01G230800 chr5D 94.521 73 4 0 3263 3335 558380234 558380162 4.160000e-21 113.0
33 TraesCS1D01G230800 chr3A 94.444 72 4 0 3264 3335 602271258 602271329 1.500000e-20 111.0
34 TraesCS1D01G230800 chr6A 94.286 70 4 0 3264 3333 92848776 92848707 1.940000e-19 108.0
35 TraesCS1D01G230800 chr6B 93.056 72 5 0 3264 3335 21137257 21137186 6.960000e-19 106.0
36 TraesCS1D01G230800 chr7B 91.026 78 5 2 3259 3335 383736123 383736199 2.500000e-18 104.0
37 TraesCS1D01G230800 chr7B 80.583 103 18 2 2694 2796 92560091 92559991 1.520000e-10 78.7


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 TraesCS1D01G230800 chr1D 318849812 318854894 5082 True 9387.000000 9387 100.00000 1 5083 1 chr1D.!!$R3 5082
1 TraesCS1D01G230800 chr1D 273583905 273584552 647 True 819.000000 819 89.50600 4437 5083 1 chr1D.!!$R2 646
2 TraesCS1D01G230800 chr1D 359777233 359779051 1818 True 665.500000 669 82.14400 1072 4070 2 chr1D.!!$R4 2998
3 TraesCS1D01G230800 chr1A 404624779 404629820 5041 False 2157.333333 2977 91.24300 151 5068 3 chr1A.!!$F2 4917
4 TraesCS1D01G230800 chr1A 459301073 459302897 1824 True 652.500000 680 82.10500 1072 4065 2 chr1A.!!$R1 2993
5 TraesCS1D01G230800 chr1B 431403230 431408770 5540 True 1304.250000 2728 91.62575 2 4435 4 chr1B.!!$R1 4433
6 TraesCS1D01G230800 chr1B 481848557 481850407 1850 True 666.500000 693 82.10350 1072 4070 2 chr1B.!!$R2 2998
7 TraesCS1D01G230800 chr2B 404149531 404150179 648 True 798.000000 798 88.92300 4437 5083 1 chr2B.!!$R1 646
8 TraesCS1D01G230800 chr2B 251386754 251387396 642 False 776.000000 776 88.40800 4437 5083 1 chr2B.!!$F2 646
9 TraesCS1D01G230800 chr2B 95760763 95761343 580 False 300.000000 300 76.35100 3426 4009 1 chr2B.!!$F1 583
10 TraesCS1D01G230800 chr2D 188893349 188893995 646 False 791.000000 791 88.73500 4437 5083 1 chr2D.!!$F2 646
11 TraesCS1D01G230800 chr2D 60945716 60946296 580 False 305.000000 305 76.44100 3426 4009 1 chr2D.!!$F1 583
12 TraesCS1D01G230800 chr2A 459259365 459260011 646 False 780.000000 780 88.42600 4437 5083 1 chr2A.!!$F2 646
13 TraesCS1D01G230800 chr2A 61467990 61468570 580 False 300.000000 300 76.43100 3426 4009 1 chr2A.!!$F1 583
14 TraesCS1D01G230800 chr7D 366427454 366428096 642 True 776.000000 776 88.42600 4437 5083 1 chr7D.!!$R1 646
15 TraesCS1D01G230800 chr6D 334486130 334486772 642 True 776.000000 776 88.49100 4437 5077 1 chr6D.!!$R1 640
16 TraesCS1D01G230800 chr7A 252159404 252160041 637 True 771.000000 771 88.45600 4443 5083 1 chr7A.!!$R3 640
17 TraesCS1D01G230800 chr5B 54156900 54157433 533 False 213.000000 213 74.31700 3412 3953 1 chr5B.!!$F1 541

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
97 98 0.244994 TTTTGGTGGTGTGTGTGTGC 59.755 50.000 0.00 0.0 0.00 4.57 F
177 199 0.319211 TTTGTCAGGTCGATCGCGTT 60.319 50.000 11.09 0.0 38.98 4.84 F
711 744 0.400381 TCCATATGGCCAGCCTCTCA 60.400 55.000 17.58 0.0 36.94 3.27 F
728 761 0.471780 TCAACTCCACTCTCCAGCCA 60.472 55.000 0.00 0.0 0.00 4.75 F
1260 1295 1.214589 CGAACACTACCTGTCCCGG 59.785 63.158 0.00 0.0 30.29 5.73 F
2604 3241 1.066656 CACGCACATGCAACAATCGG 61.067 55.000 4.49 0.0 42.21 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 1820 1.286880 CCCGACCGACGTGTAGTTT 59.713 57.895 0.00 0.0 40.78 2.66 R
2054 2121 1.295792 TGTGTTTCTCTGGTCGTTGC 58.704 50.000 0.00 0.0 0.00 4.17 R
2523 3152 2.169352 AGAGCAATAGTGAATGCCGAGT 59.831 45.455 0.00 0.0 43.57 4.18 R
2524 3153 2.831333 AGAGCAATAGTGAATGCCGAG 58.169 47.619 0.00 0.0 43.57 4.63 R
2953 4373 0.319297 CCAGCTTGCCTCTTGTTTGC 60.319 55.000 0.00 0.0 0.00 3.68 R
4550 6408 0.460284 CGAAGGGTAACAGATGCGCT 60.460 55.000 9.73 0.0 38.57 5.92 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
27 28 6.238538 GGAAGGTGTTCGTGATTTCTTAACAA 60.239 38.462 0.00 0.00 32.32 2.83
46 47 3.019564 CAAATGGCCCTAAGTCTCTTGG 58.980 50.000 0.00 0.00 0.00 3.61
47 48 2.270434 ATGGCCCTAAGTCTCTTGGA 57.730 50.000 0.00 0.00 0.00 3.53
52 53 1.204941 CCCTAAGTCTCTTGGACCGTG 59.795 57.143 0.00 0.00 45.54 4.94
72 73 4.616802 CGTGCTTATGATTTGGTTTGTCAC 59.383 41.667 0.00 0.00 0.00 3.67
93 94 2.364970 CCATGATTTTGGTGGTGTGTGT 59.635 45.455 0.00 0.00 31.74 3.72
94 95 3.382855 CATGATTTTGGTGGTGTGTGTG 58.617 45.455 0.00 0.00 0.00 3.82
95 96 2.451490 TGATTTTGGTGGTGTGTGTGT 58.549 42.857 0.00 0.00 0.00 3.72
96 97 2.165234 TGATTTTGGTGGTGTGTGTGTG 59.835 45.455 0.00 0.00 0.00 3.82
97 98 0.244994 TTTTGGTGGTGTGTGTGTGC 59.755 50.000 0.00 0.00 0.00 4.57
98 99 0.610509 TTTGGTGGTGTGTGTGTGCT 60.611 50.000 0.00 0.00 0.00 4.40
99 100 1.311651 TTGGTGGTGTGTGTGTGCTG 61.312 55.000 0.00 0.00 0.00 4.41
100 101 1.748879 GGTGGTGTGTGTGTGCTGT 60.749 57.895 0.00 0.00 0.00 4.40
101 102 1.429021 GTGGTGTGTGTGTGCTGTG 59.571 57.895 0.00 0.00 0.00 3.66
102 103 1.002746 TGGTGTGTGTGTGCTGTGT 60.003 52.632 0.00 0.00 0.00 3.72
103 104 0.607762 TGGTGTGTGTGTGCTGTGTT 60.608 50.000 0.00 0.00 0.00 3.32
118 119 6.540551 TGTGCTGTGTTTAGTTGAATTGTCTA 59.459 34.615 0.00 0.00 0.00 2.59
142 143 3.695830 AGGAGTTCCTTTGCGATGTAA 57.304 42.857 0.00 0.00 46.09 2.41
174 196 1.007336 ACGTTTGTCAGGTCGATCGC 61.007 55.000 11.09 5.58 0.00 4.58
177 199 0.319211 TTTGTCAGGTCGATCGCGTT 60.319 50.000 11.09 0.00 38.98 4.84
185 207 0.800683 GTCGATCGCGTTGTCATGGA 60.801 55.000 11.09 0.00 38.98 3.41
198 220 5.334802 CGTTGTCATGGAGTTTCATGCTTTA 60.335 40.000 0.00 0.00 42.96 1.85
213 235 6.237901 TCATGCTTTAAGTAGTCCACATGTT 58.762 36.000 0.00 0.00 36.08 2.71
214 236 6.714810 TCATGCTTTAAGTAGTCCACATGTTT 59.285 34.615 0.00 0.00 36.08 2.83
217 239 7.422399 TGCTTTAAGTAGTCCACATGTTTTTC 58.578 34.615 0.00 0.00 0.00 2.29
219 241 7.591426 GCTTTAAGTAGTCCACATGTTTTTCTG 59.409 37.037 0.00 0.00 0.00 3.02
221 243 9.616156 TTTAAGTAGTCCACATGTTTTTCTGTA 57.384 29.630 0.00 0.00 0.00 2.74
223 245 7.907214 AGTAGTCCACATGTTTTTCTGTATC 57.093 36.000 0.00 0.00 0.00 2.24
224 246 6.879458 AGTAGTCCACATGTTTTTCTGTATCC 59.121 38.462 0.00 0.00 0.00 2.59
225 247 5.880901 AGTCCACATGTTTTTCTGTATCCT 58.119 37.500 0.00 0.00 0.00 3.24
297 323 8.831715 AATTAATCGAAAGGCAAATCTTTTGT 57.168 26.923 0.00 0.00 38.58 2.83
410 438 7.838771 GCAAATCTTTTGCCTCTATTTCAAT 57.161 32.000 12.74 0.00 39.38 2.57
542 570 2.799126 ACACAAGTCAGGTCAACCAA 57.201 45.000 1.33 0.00 38.89 3.67
558 586 1.959282 ACCAAGAGCTCTGGCAAAAAG 59.041 47.619 19.06 2.39 41.70 2.27
559 587 2.233271 CCAAGAGCTCTGGCAAAAAGA 58.767 47.619 19.06 0.00 41.70 2.52
711 744 0.400381 TCCATATGGCCAGCCTCTCA 60.400 55.000 17.58 0.00 36.94 3.27
712 745 0.475475 CCATATGGCCAGCCTCTCAA 59.525 55.000 13.05 0.00 36.94 3.02
713 746 1.602311 CATATGGCCAGCCTCTCAAC 58.398 55.000 13.05 0.00 36.94 3.18
714 747 1.142465 CATATGGCCAGCCTCTCAACT 59.858 52.381 13.05 0.00 36.94 3.16
715 748 0.833287 TATGGCCAGCCTCTCAACTC 59.167 55.000 13.05 0.00 36.94 3.01
728 761 0.471780 TCAACTCCACTCTCCAGCCA 60.472 55.000 0.00 0.00 0.00 4.75
738 771 2.203337 TCCAGCCAAAGCGTGCTT 60.203 55.556 0.24 0.24 46.67 3.91
774 807 3.056313 GCCGCCCACTTGCATTCTC 62.056 63.158 0.00 0.00 0.00 2.87
916 949 5.762218 CCCTGCTCATCTTCACCTATAAAAG 59.238 44.000 0.00 0.00 0.00 2.27
1260 1295 1.214589 CGAACACTACCTGTCCCGG 59.785 63.158 0.00 0.00 30.29 5.73
1771 1830 1.291272 GGCTCCGGAAACTACACGT 59.709 57.895 5.23 0.00 0.00 4.49
1953 2012 3.284449 GGCAACCGGAGCGTTGTT 61.284 61.111 9.46 0.00 44.10 2.83
1980 2039 2.526873 ACCACCTTCCACTCGGCT 60.527 61.111 0.00 0.00 0.00 5.52
2027 2094 8.094174 CATATATGCATACGACTCGTTACTTC 57.906 38.462 8.99 0.00 41.54 3.01
2031 2098 3.790288 GCATACGACTCGTTACTTCCTTC 59.210 47.826 9.84 0.00 41.54 3.46
2054 2121 5.570973 TCGTAAAATGAAATGCAATCGTTGG 59.429 36.000 10.14 3.16 0.00 3.77
2090 2157 2.872245 ACACATCGAACACTTCAACCTG 59.128 45.455 0.00 0.00 0.00 4.00
2093 2160 3.312421 ACATCGAACACTTCAACCTGTTG 59.688 43.478 3.61 3.61 41.71 3.33
2123 2193 3.443976 CCTTTTGGTCTTTTGTTCACCG 58.556 45.455 0.00 0.00 32.27 4.94
2127 2197 2.712709 TGGTCTTTTGTTCACCGTCAA 58.287 42.857 0.00 0.00 32.27 3.18
2129 2199 4.452825 TGGTCTTTTGTTCACCGTCAATA 58.547 39.130 0.00 0.00 32.27 1.90
2139 2209 9.804758 TTTGTTCACCGTCAATAATTTTTACTT 57.195 25.926 0.00 0.00 0.00 2.24
2173 2738 7.711339 GTCTTTTGGGTATAGAACATACTCCTG 59.289 40.741 0.00 0.00 0.00 3.86
2183 2748 6.128138 AGAACATACTCCTGCTTTTTACCT 57.872 37.500 0.00 0.00 0.00 3.08
2195 2760 6.013293 CCTGCTTTTTACCTATATAGGAGGCT 60.013 42.308 31.53 14.16 46.63 4.58
2213 2778 1.815003 GCTGGTGCTCTACTTTTGCAT 59.185 47.619 0.00 0.00 39.00 3.96
2231 2833 4.215109 TGCATTAAGAAGGGGGAAATAGC 58.785 43.478 0.00 0.00 0.00 2.97
2237 2839 4.242336 AGAAGGGGGAAATAGCTTCAAG 57.758 45.455 0.00 0.00 35.55 3.02
2269 2871 9.967451 AAAAACAAAGAAGAAGGGGAAAATAAA 57.033 25.926 0.00 0.00 0.00 1.40
2296 2898 9.504708 TTCGTTACAAATTTTGGATTACCTAGA 57.495 29.630 13.42 0.00 37.04 2.43
2316 2918 9.196139 ACCTAGATATATAAGAGCAAGGTCATC 57.804 37.037 1.84 0.00 28.80 2.92
2323 2925 4.615588 AAGAGCAAGGTCATCTATAGCC 57.384 45.455 1.84 0.00 0.00 3.93
2324 2926 3.855668 AGAGCAAGGTCATCTATAGCCT 58.144 45.455 1.84 0.00 0.00 4.58
2327 2929 5.421693 AGAGCAAGGTCATCTATAGCCTATG 59.578 44.000 1.84 0.00 0.00 2.23
2345 2947 7.841956 AGCCTATGTAATAGCGAACTCATATT 58.158 34.615 0.00 0.00 45.64 1.28
2376 2978 9.696917 TTAGTCATACTTGCATACTATGTCATG 57.303 33.333 0.00 0.00 0.00 3.07
2389 2991 3.598693 ATGTCATGAATATGTGGCCCA 57.401 42.857 0.00 0.00 35.73 5.36
2413 3040 8.025445 CCATCTTTTCTTTCACAAAGGACTATG 58.975 37.037 0.00 0.00 39.01 2.23
2417 3044 6.968131 TTCTTTCACAAAGGACTATGATCG 57.032 37.500 0.00 0.00 39.01 3.69
2422 3049 7.827819 TTCACAAAGGACTATGATCGTAAAG 57.172 36.000 0.00 0.00 0.00 1.85
2456 3085 5.751243 TGTCTCCTCAAACTAAGCAAAAC 57.249 39.130 0.00 0.00 0.00 2.43
2462 3091 9.959721 TCTCCTCAAACTAAGCAAAACTATAAT 57.040 29.630 0.00 0.00 0.00 1.28
2484 3113 6.859112 ATATGACATCTCTTTATAGCCCGT 57.141 37.500 0.00 0.00 0.00 5.28
2485 3114 5.552870 ATGACATCTCTTTATAGCCCGTT 57.447 39.130 0.00 0.00 0.00 4.44
2486 3115 5.353394 TGACATCTCTTTATAGCCCGTTT 57.647 39.130 0.00 0.00 0.00 3.60
2487 3116 6.474140 TGACATCTCTTTATAGCCCGTTTA 57.526 37.500 0.00 0.00 0.00 2.01
2488 3117 6.278363 TGACATCTCTTTATAGCCCGTTTAC 58.722 40.000 0.00 0.00 0.00 2.01
2489 3118 5.287226 ACATCTCTTTATAGCCCGTTTACG 58.713 41.667 0.00 0.00 39.44 3.18
2490 3119 4.989279 TCTCTTTATAGCCCGTTTACGT 57.011 40.909 0.00 0.00 37.74 3.57
2491 3120 4.925068 TCTCTTTATAGCCCGTTTACGTC 58.075 43.478 0.00 0.00 37.74 4.34
2492 3121 4.398988 TCTCTTTATAGCCCGTTTACGTCA 59.601 41.667 0.00 0.00 37.74 4.35
2493 3122 5.070770 TCTTTATAGCCCGTTTACGTCAA 57.929 39.130 0.00 0.00 37.74 3.18
2494 3123 4.864247 TCTTTATAGCCCGTTTACGTCAAC 59.136 41.667 2.44 2.44 37.74 3.18
2495 3124 4.454728 TTATAGCCCGTTTACGTCAACT 57.545 40.909 10.64 0.00 37.74 3.16
2496 3125 2.818130 TAGCCCGTTTACGTCAACTT 57.182 45.000 10.64 0.00 37.74 2.66
2497 3126 2.818130 AGCCCGTTTACGTCAACTTA 57.182 45.000 10.64 0.00 37.74 2.24
2498 3127 3.323751 AGCCCGTTTACGTCAACTTAT 57.676 42.857 10.64 0.00 37.74 1.73
2499 3128 3.667360 AGCCCGTTTACGTCAACTTATT 58.333 40.909 10.64 0.00 37.74 1.40
2500 3129 4.819769 AGCCCGTTTACGTCAACTTATTA 58.180 39.130 10.64 0.00 37.74 0.98
2501 3130 5.422145 AGCCCGTTTACGTCAACTTATTAT 58.578 37.500 10.64 0.00 37.74 1.28
2502 3131 6.572519 AGCCCGTTTACGTCAACTTATTATA 58.427 36.000 10.64 0.00 37.74 0.98
2503 3132 6.476706 AGCCCGTTTACGTCAACTTATTATAC 59.523 38.462 10.64 0.00 37.74 1.47
2504 3133 6.476706 GCCCGTTTACGTCAACTTATTATACT 59.523 38.462 10.64 0.00 37.74 2.12
2505 3134 7.010460 GCCCGTTTACGTCAACTTATTATACTT 59.990 37.037 10.64 0.00 37.74 2.24
2506 3135 8.323140 CCCGTTTACGTCAACTTATTATACTTG 58.677 37.037 10.64 0.00 37.74 3.16
2507 3136 7.842721 CCGTTTACGTCAACTTATTATACTTGC 59.157 37.037 10.64 0.00 37.74 4.01
2508 3137 8.589629 CGTTTACGTCAACTTATTATACTTGCT 58.410 33.333 10.64 0.00 34.11 3.91
2509 3138 9.897349 GTTTACGTCAACTTATTATACTTGCTC 57.103 33.333 5.36 0.00 0.00 4.26
2510 3139 9.865321 TTTACGTCAACTTATTATACTTGCTCT 57.135 29.630 0.00 0.00 0.00 4.09
2511 3140 9.865321 TTACGTCAACTTATTATACTTGCTCTT 57.135 29.630 0.00 0.00 0.00 2.85
2513 3142 9.517609 ACGTCAACTTATTATACTTGCTCTTAG 57.482 33.333 0.00 0.00 0.00 2.18
2514 3143 8.969267 CGTCAACTTATTATACTTGCTCTTAGG 58.031 37.037 0.00 0.00 0.00 2.69
2527 3156 7.259161 ACTTGCTCTTAGGAAAGTTATACTCG 58.741 38.462 0.00 0.00 34.13 4.18
2528 3157 6.145338 TGCTCTTAGGAAAGTTATACTCGG 57.855 41.667 0.00 0.00 34.13 4.63
2529 3158 4.983538 GCTCTTAGGAAAGTTATACTCGGC 59.016 45.833 0.00 0.00 34.13 5.54
2530 3159 5.451520 GCTCTTAGGAAAGTTATACTCGGCA 60.452 44.000 0.00 0.00 34.13 5.69
2531 3160 6.726490 TCTTAGGAAAGTTATACTCGGCAT 57.274 37.500 0.00 0.00 34.13 4.40
2532 3161 7.120923 TCTTAGGAAAGTTATACTCGGCATT 57.879 36.000 0.00 0.00 34.13 3.56
2533 3162 7.208080 TCTTAGGAAAGTTATACTCGGCATTC 58.792 38.462 0.00 0.00 34.13 2.67
2534 3163 5.353394 AGGAAAGTTATACTCGGCATTCA 57.647 39.130 0.00 0.00 0.00 2.57
2535 3164 5.116882 AGGAAAGTTATACTCGGCATTCAC 58.883 41.667 0.00 0.00 0.00 3.18
2536 3165 5.104900 AGGAAAGTTATACTCGGCATTCACT 60.105 40.000 0.00 0.00 0.00 3.41
2537 3166 6.097839 AGGAAAGTTATACTCGGCATTCACTA 59.902 38.462 0.00 0.00 0.00 2.74
2541 3170 5.696724 AGTTATACTCGGCATTCACTATTGC 59.303 40.000 0.00 0.00 38.14 3.56
2561 3190 3.003275 TGCTCTTCTTGTTTTTAGGCACG 59.997 43.478 0.00 0.00 0.00 5.34
2604 3241 1.066656 CACGCACATGCAACAATCGG 61.067 55.000 4.49 0.00 42.21 4.18
2626 3310 7.705214 TCGGTTTCGAAAAAGAAAAATAGGAA 58.295 30.769 13.10 0.00 43.03 3.36
2628 3312 7.358105 CGGTTTCGAAAAAGAAAAATAGGAAGC 60.358 37.037 13.10 0.00 41.18 3.86
2630 3314 6.642707 TCGAAAAAGAAAAATAGGAAGCCA 57.357 33.333 0.00 0.00 0.00 4.75
2669 3353 4.779696 ACAATTGGCCAAAGTGATGTTTT 58.220 34.783 29.63 13.09 37.30 2.43
2678 3362 5.813672 GCCAAAGTGATGTTTTCATGCATAT 59.186 36.000 0.00 0.00 41.05 1.78
2681 3365 7.222031 CCAAAGTGATGTTTTCATGCATATCTG 59.778 37.037 0.00 0.00 41.05 2.90
2695 3379 8.210265 TCATGCATATCTGAATTAACTACCACA 58.790 33.333 0.00 0.00 0.00 4.17
2696 3380 9.006839 CATGCATATCTGAATTAACTACCACAT 57.993 33.333 0.00 0.00 0.00 3.21
2734 3418 7.389803 ACTTTGCAAACATGCACTATACATA 57.610 32.000 8.05 0.00 45.32 2.29
2769 3456 9.672086 TGTACGTATTCTTTTCAGAATTTTTGG 57.328 29.630 0.00 0.00 46.07 3.28
2827 3514 8.767478 CTCCAATAGCAATTTCACAAAAGAAT 57.233 30.769 0.00 0.00 0.00 2.40
2836 3524 7.201496 GCAATTTCACAAAAGAATAGCTCATGG 60.201 37.037 0.00 0.00 0.00 3.66
2877 3566 9.165035 TGGAGGAATTATGCAAAATCAAATTTC 57.835 29.630 0.00 0.00 0.00 2.17
2953 4373 4.989875 ATGGAGGGACTAAATGGATGAG 57.010 45.455 0.00 0.00 41.55 2.90
2975 4395 0.251077 AACAAGAGGCAAGCTGGGAG 60.251 55.000 0.00 0.00 0.00 4.30
3025 4445 4.798574 AGCTTTGCACTTCGAATAAAAGG 58.201 39.130 16.85 2.43 0.00 3.11
3220 4640 4.987285 CACATCATCATGCACTACCTAGTC 59.013 45.833 0.00 0.00 31.77 2.59
3223 4643 1.763968 TCATGCACTACCTAGTCGCT 58.236 50.000 0.00 0.00 33.46 4.93
3275 4695 5.049198 TGCGTATATTACAGTACTCCCTTCG 60.049 44.000 0.00 0.00 0.00 3.79
3276 4696 5.049129 GCGTATATTACAGTACTCCCTTCGT 60.049 44.000 0.00 0.00 0.00 3.85
3278 4698 6.348050 CGTATATTACAGTACTCCCTTCGTCC 60.348 46.154 0.00 0.00 0.00 4.79
3279 4699 1.742761 TACAGTACTCCCTTCGTCCG 58.257 55.000 0.00 0.00 0.00 4.79
3281 4701 1.171308 CAGTACTCCCTTCGTCCGAA 58.829 55.000 1.81 1.81 0.00 4.30
3284 4704 2.629617 AGTACTCCCTTCGTCCGAAAAA 59.370 45.455 3.52 0.00 33.34 1.94
3306 4726 4.983671 ACTTGTCCCAAACTTGTTTCTC 57.016 40.909 0.00 0.00 0.00 2.87
3308 4728 4.770010 ACTTGTCCCAAACTTGTTTCTCAA 59.230 37.500 0.00 0.66 34.61 3.02
3311 4731 5.659463 TGTCCCAAACTTGTTTCTCAAATG 58.341 37.500 0.00 0.00 35.48 2.32
3313 4733 4.959210 TCCCAAACTTGTTTCTCAAATGGA 59.041 37.500 0.00 0.00 36.92 3.41
3316 4736 7.454380 TCCCAAACTTGTTTCTCAAATGGATAT 59.546 33.333 0.00 0.00 36.92 1.63
3917 5576 2.290093 GCTCTACTACGCCGAGTACAAT 59.710 50.000 0.00 0.00 0.00 2.71
4083 5742 3.879295 CACCAGCGGATTGAAGTATTGAT 59.121 43.478 1.50 0.00 0.00 2.57
4112 5774 9.586150 GTCAACTTATCATATATGCTTTGAACG 57.414 33.333 7.92 0.00 0.00 3.95
4129 5791 8.493547 GCTTTGAACGGTAGACATATATTTACC 58.506 37.037 7.38 7.38 33.74 2.85
4155 5817 5.874895 GGTAAATCACCTACTGTTTGTCC 57.125 43.478 0.00 0.00 44.79 4.02
4451 6309 7.769507 TCTGACTGTATCTACTACGTGAAGATT 59.230 37.037 12.47 0.00 32.39 2.40
4490 6348 1.072173 CCTTCGTGGATGATGGCCATA 59.928 52.381 20.84 7.82 37.81 2.74
4539 6397 3.636231 CCTTCGTGGGTGGAGCCA 61.636 66.667 0.00 0.00 39.65 4.75
4543 6401 3.402681 CGTGGGTGGAGCCATCCT 61.403 66.667 19.10 0.00 46.93 3.24
4550 6408 1.204146 GTGGAGCCATCCTTGGACTA 58.796 55.000 0.00 0.00 46.92 2.59
4616 6474 4.515191 GGACGTACGATAACACCACCTATA 59.485 45.833 24.41 0.00 0.00 1.31
4833 6697 4.901849 TCAAGTAGTCTAATCATCCCCCTG 59.098 45.833 0.00 0.00 0.00 4.45
4850 6714 4.101119 CCCCCTGTAGACATACTTTCGATT 59.899 45.833 0.00 0.00 32.75 3.34
4864 6728 9.314321 CATACTTTCGATTCTACAAGTGGTATT 57.686 33.333 7.93 0.00 31.83 1.89
4904 6768 7.665690 TGTTAGCCTTGATTTTCATTGCTTTA 58.334 30.769 6.60 0.00 35.87 1.85
4905 6769 8.147058 TGTTAGCCTTGATTTTCATTGCTTTAA 58.853 29.630 6.60 0.00 35.87 1.52
4943 6807 6.282199 GTTTCACAACCTAGGAGAGTATGA 57.718 41.667 17.98 7.25 0.00 2.15
4945 6809 4.930696 TCACAACCTAGGAGAGTATGACA 58.069 43.478 17.98 0.00 0.00 3.58
4956 6820 7.090319 AGGAGAGTATGACATCTAGTGAGAT 57.910 40.000 0.00 0.00 43.63 2.75
4977 6841 8.158132 TGAGATTAACTATCATCGTAGAGGTCT 58.842 37.037 0.00 0.00 43.63 3.85
4986 6850 5.962433 TCATCGTAGAGGTCTTTACTTTGG 58.038 41.667 0.00 0.00 43.63 3.28
5008 6872 4.367450 GTGGCACAAATTTTGCTAGTTGA 58.633 39.130 13.86 2.21 44.16 3.18
5078 6942 3.190535 GGATGTTGTTCGTATTGGCTTGT 59.809 43.478 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.086706 AGAAATCACGAACACCTTCCTT 57.913 40.909 0.00 0.00 0.00 3.36
9 10 5.344933 GGCCATTTGTTAAGAAATCACGAAC 59.655 40.000 7.57 0.00 0.00 3.95
13 14 5.405935 AGGGCCATTTGTTAAGAAATCAC 57.594 39.130 6.18 3.56 0.00 3.06
27 28 2.239907 GTCCAAGAGACTTAGGGCCATT 59.760 50.000 6.18 0.00 42.69 3.16
46 47 4.165779 CAAACCAAATCATAAGCACGGTC 58.834 43.478 0.00 0.00 0.00 4.79
47 48 3.572255 ACAAACCAAATCATAAGCACGGT 59.428 39.130 0.00 0.00 0.00 4.83
72 73 2.364970 ACACACACCACCAAAATCATGG 59.635 45.455 0.00 0.00 46.38 3.66
81 82 1.748500 CAGCACACACACACCACCA 60.749 57.895 0.00 0.00 0.00 4.17
93 94 5.356751 AGACAATTCAACTAAACACAGCACA 59.643 36.000 0.00 0.00 0.00 4.57
94 95 5.821204 AGACAATTCAACTAAACACAGCAC 58.179 37.500 0.00 0.00 0.00 4.40
95 96 7.744087 ATAGACAATTCAACTAAACACAGCA 57.256 32.000 0.00 0.00 0.00 4.41
142 143 1.140252 ACAAACGTACACAAGCCCTCT 59.860 47.619 0.00 0.00 0.00 3.69
174 196 2.485426 AGCATGAAACTCCATGACAACG 59.515 45.455 7.94 0.00 44.98 4.10
177 199 5.769662 ACTTAAAGCATGAAACTCCATGACA 59.230 36.000 7.94 0.00 44.98 3.58
185 207 6.296026 TGTGGACTACTTAAAGCATGAAACT 58.704 36.000 0.00 0.00 0.00 2.66
198 220 7.390718 GGATACAGAAAAACATGTGGACTACTT 59.609 37.037 0.00 0.00 0.00 2.24
260 285 9.170584 GCCTTTCGATTAATTAAGCATAAGAAC 57.829 33.333 18.66 10.96 0.00 3.01
381 409 4.596311 GCAAAAGATTTGCCCCGG 57.404 55.556 15.12 0.00 39.38 5.73
420 448 9.374838 GTAAGATGCTTCCATTCATTTCATTTT 57.625 29.630 0.00 0.00 0.00 1.82
421 449 8.533657 TGTAAGATGCTTCCATTCATTTCATTT 58.466 29.630 0.00 0.00 0.00 2.32
424 452 7.649533 ATGTAAGATGCTTCCATTCATTTCA 57.350 32.000 0.00 0.00 0.00 2.69
425 453 8.937634 AAATGTAAGATGCTTCCATTCATTTC 57.062 30.769 11.35 0.00 31.58 2.17
426 454 9.374838 GAAAATGTAAGATGCTTCCATTCATTT 57.625 29.630 11.35 11.35 34.48 2.32
428 456 7.198390 CGAAAATGTAAGATGCTTCCATTCAT 58.802 34.615 0.00 0.00 0.00 2.57
429 457 6.554419 CGAAAATGTAAGATGCTTCCATTCA 58.446 36.000 0.00 0.00 0.00 2.57
430 458 5.456822 GCGAAAATGTAAGATGCTTCCATTC 59.543 40.000 0.00 0.00 0.00 2.67
507 535 8.746922 TGACTTGTGTACTTAGTATAAAACCG 57.253 34.615 0.00 0.00 0.00 4.44
542 570 4.202192 CCTTTTTCTTTTTGCCAGAGCTCT 60.202 41.667 11.45 11.45 40.80 4.09
558 586 1.269569 CGGCTTGGGTTGACCTTTTTC 60.270 52.381 0.00 0.00 41.11 2.29
559 587 0.750249 CGGCTTGGGTTGACCTTTTT 59.250 50.000 0.00 0.00 41.11 1.94
711 744 1.072965 CTTTGGCTGGAGAGTGGAGTT 59.927 52.381 0.00 0.00 0.00 3.01
712 745 0.689623 CTTTGGCTGGAGAGTGGAGT 59.310 55.000 0.00 0.00 0.00 3.85
713 746 0.676151 GCTTTGGCTGGAGAGTGGAG 60.676 60.000 0.00 0.00 35.22 3.86
714 747 1.376466 GCTTTGGCTGGAGAGTGGA 59.624 57.895 0.00 0.00 35.22 4.02
715 748 2.037136 CGCTTTGGCTGGAGAGTGG 61.037 63.158 0.00 0.00 36.09 4.00
728 761 0.955919 GTCTAGGCCAAGCACGCTTT 60.956 55.000 5.01 0.00 33.42 3.51
738 771 2.970639 GAGTGTGCGTCTAGGCCA 59.029 61.111 5.01 0.00 0.00 5.36
774 807 1.130613 CTCGAAAAAGCGCGTGGAG 59.869 57.895 8.43 0.00 0.00 3.86
856 889 4.067944 ACTGATCTTTAGGTCCAGAGGT 57.932 45.455 0.00 0.00 0.00 3.85
862 895 5.598830 TGGTGATCTACTGATCTTTAGGTCC 59.401 44.000 10.30 4.39 46.84 4.46
864 897 6.841229 TCATGGTGATCTACTGATCTTTAGGT 59.159 38.462 7.42 0.00 46.84 3.08
936 969 1.659211 GCGTGTGTTTTGGTGATCGAC 60.659 52.381 0.00 0.00 0.00 4.20
1245 1280 2.203728 TGCCGGGACAGGTAGTGT 60.204 61.111 2.18 0.00 44.49 3.55
1675 1734 1.750930 CCATCCTCCGGACCATCTG 59.249 63.158 0.00 0.00 32.98 2.90
1761 1820 1.286880 CCCGACCGACGTGTAGTTT 59.713 57.895 0.00 0.00 40.78 2.66
1794 1853 2.124109 TTGAGGTTTGTGGGCGCA 60.124 55.556 10.83 0.00 0.00 6.09
1803 1862 3.660111 GCGCTGCCGTTGAGGTTT 61.660 61.111 0.00 0.00 43.70 3.27
1845 1904 2.986979 TCCTCGTACACGCCTGCA 60.987 61.111 0.00 0.00 39.60 4.41
1953 2012 2.847234 AAGGTGGTCCAGCCGTCA 60.847 61.111 17.55 0.00 41.21 4.35
1980 2039 2.616634 TTGTGCACTTACCAACGGTA 57.383 45.000 19.41 0.00 37.09 4.02
2018 2085 7.712264 TTTCATTTTACGAAGGAAGTAACGA 57.288 32.000 0.00 0.00 34.25 3.85
2020 2087 7.806014 TGCATTTCATTTTACGAAGGAAGTAAC 59.194 33.333 0.00 0.00 34.25 2.50
2027 2094 5.799936 ACGATTGCATTTCATTTTACGAAGG 59.200 36.000 0.00 0.00 0.00 3.46
2031 2098 5.720971 GCCAACGATTGCATTTCATTTTACG 60.721 40.000 0.00 0.00 0.00 3.18
2054 2121 1.295792 TGTGTTTCTCTGGTCGTTGC 58.704 50.000 0.00 0.00 0.00 4.17
2090 2157 4.816392 AGACCAAAAGGTTTGACAACAAC 58.184 39.130 2.30 0.00 35.63 3.32
2093 2160 5.699001 ACAAAAGACCAAAAGGTTTGACAAC 59.301 36.000 2.30 0.00 34.16 3.32
2139 2209 7.780745 TGTTCTATACCCAAAAGACCAAAAGAA 59.219 33.333 0.00 0.00 0.00 2.52
2173 2738 6.174049 CCAGCCTCCTATATAGGTAAAAAGC 58.826 44.000 25.06 18.67 44.02 3.51
2183 2748 3.835478 AGAGCACCAGCCTCCTATATA 57.165 47.619 0.00 0.00 43.56 0.86
2195 2760 5.312895 TCTTAATGCAAAAGTAGAGCACCA 58.687 37.500 10.86 0.00 41.60 4.17
2213 2778 5.789574 TGAAGCTATTTCCCCCTTCTTAA 57.210 39.130 0.00 0.00 35.80 1.85
2246 2848 9.778741 GAATTTATTTTCCCCTTCTTCTTTGTT 57.221 29.630 0.00 0.00 0.00 2.83
2247 2849 8.088365 CGAATTTATTTTCCCCTTCTTCTTTGT 58.912 33.333 0.00 0.00 0.00 2.83
2248 2850 8.088365 ACGAATTTATTTTCCCCTTCTTCTTTG 58.912 33.333 0.00 0.00 0.00 2.77
2249 2851 8.190326 ACGAATTTATTTTCCCCTTCTTCTTT 57.810 30.769 0.00 0.00 0.00 2.52
2250 2852 7.776618 ACGAATTTATTTTCCCCTTCTTCTT 57.223 32.000 0.00 0.00 0.00 2.52
2251 2853 7.776618 AACGAATTTATTTTCCCCTTCTTCT 57.223 32.000 0.00 0.00 0.00 2.85
2291 2893 9.420118 AGATGACCTTGCTCTTATATATCTAGG 57.580 37.037 0.00 0.00 0.00 3.02
2313 2915 8.625651 AGTTCGCTATTACATAGGCTATAGATG 58.374 37.037 6.72 0.00 33.43 2.90
2315 2917 7.827729 TGAGTTCGCTATTACATAGGCTATAGA 59.172 37.037 6.72 0.00 33.43 1.98
2316 2918 7.986562 TGAGTTCGCTATTACATAGGCTATAG 58.013 38.462 6.72 1.78 33.43 1.31
2318 2920 6.835819 TGAGTTCGCTATTACATAGGCTAT 57.164 37.500 0.00 0.00 33.43 2.97
2321 2923 9.751542 ATAATATGAGTTCGCTATTACATAGGC 57.248 33.333 0.00 0.00 33.43 3.93
2359 2961 8.448615 CCACATATTCATGACATAGTATGCAAG 58.551 37.037 10.16 6.73 35.96 4.01
2376 2978 5.859205 AAGAAAAGATGGGCCACATATTC 57.141 39.130 9.28 11.97 39.95 1.75
2389 2991 8.924511 TCATAGTCCTTTGTGAAAGAAAAGAT 57.075 30.769 0.00 0.00 41.02 2.40
2462 3091 6.665992 AACGGGCTATAAAGAGATGTCATA 57.334 37.500 0.00 0.00 0.00 2.15
2463 3092 5.552870 AACGGGCTATAAAGAGATGTCAT 57.447 39.130 0.00 0.00 0.00 3.06
2465 3094 5.401674 CGTAAACGGGCTATAAAGAGATGTC 59.598 44.000 0.00 0.00 35.37 3.06
2466 3095 5.163478 ACGTAAACGGGCTATAAAGAGATGT 60.163 40.000 7.50 0.00 44.95 3.06
2467 3096 5.287226 ACGTAAACGGGCTATAAAGAGATG 58.713 41.667 7.50 0.00 44.95 2.90
2468 3097 5.068198 TGACGTAAACGGGCTATAAAGAGAT 59.932 40.000 7.50 0.00 44.95 2.75
2469 3098 4.398988 TGACGTAAACGGGCTATAAAGAGA 59.601 41.667 7.50 0.00 44.95 3.10
2470 3099 4.675510 TGACGTAAACGGGCTATAAAGAG 58.324 43.478 7.50 0.00 44.95 2.85
2471 3100 4.717233 TGACGTAAACGGGCTATAAAGA 57.283 40.909 7.50 0.00 44.95 2.52
2472 3101 4.866486 AGTTGACGTAAACGGGCTATAAAG 59.134 41.667 10.18 0.00 44.95 1.85
2474 3103 4.454728 AGTTGACGTAAACGGGCTATAA 57.545 40.909 10.18 0.00 44.95 0.98
2476 3105 3.323751 AAGTTGACGTAAACGGGCTAT 57.676 42.857 10.18 0.00 44.95 2.97
2477 3106 2.818130 AAGTTGACGTAAACGGGCTA 57.182 45.000 10.18 0.00 44.95 3.93
2480 3109 7.992180 AGTATAATAAGTTGACGTAAACGGG 57.008 36.000 10.18 0.00 44.95 5.28
2481 3110 7.842721 GCAAGTATAATAAGTTGACGTAAACGG 59.157 37.037 10.18 0.00 35.75 4.44
2482 3111 8.589629 AGCAAGTATAATAAGTTGACGTAAACG 58.410 33.333 10.18 0.04 36.59 3.60
2483 3112 9.897349 GAGCAAGTATAATAAGTTGACGTAAAC 57.103 33.333 7.79 7.79 32.51 2.01
2484 3113 9.865321 AGAGCAAGTATAATAAGTTGACGTAAA 57.135 29.630 0.00 0.00 32.51 2.01
2485 3114 9.865321 AAGAGCAAGTATAATAAGTTGACGTAA 57.135 29.630 0.00 0.00 32.51 3.18
2487 3116 9.517609 CTAAGAGCAAGTATAATAAGTTGACGT 57.482 33.333 0.00 0.00 32.51 4.34
2488 3117 8.969267 CCTAAGAGCAAGTATAATAAGTTGACG 58.031 37.037 0.00 0.00 32.51 4.35
2501 3130 8.404000 CGAGTATAACTTTCCTAAGAGCAAGTA 58.596 37.037 0.00 0.00 35.30 2.24
2502 3131 7.259161 CGAGTATAACTTTCCTAAGAGCAAGT 58.741 38.462 0.00 0.00 35.30 3.16
2503 3132 6.697892 CCGAGTATAACTTTCCTAAGAGCAAG 59.302 42.308 0.00 0.00 35.30 4.01
2504 3133 6.570692 CCGAGTATAACTTTCCTAAGAGCAA 58.429 40.000 0.00 0.00 35.30 3.91
2505 3134 5.451520 GCCGAGTATAACTTTCCTAAGAGCA 60.452 44.000 0.00 0.00 35.30 4.26
2506 3135 4.983538 GCCGAGTATAACTTTCCTAAGAGC 59.016 45.833 0.00 0.00 35.30 4.09
2507 3136 6.145338 TGCCGAGTATAACTTTCCTAAGAG 57.855 41.667 0.00 0.00 35.30 2.85
2508 3137 6.726490 ATGCCGAGTATAACTTTCCTAAGA 57.274 37.500 0.00 0.00 35.30 2.10
2509 3138 6.984474 TGAATGCCGAGTATAACTTTCCTAAG 59.016 38.462 0.00 0.00 37.40 2.18
2510 3139 6.759827 GTGAATGCCGAGTATAACTTTCCTAA 59.240 38.462 0.00 0.00 0.00 2.69
2511 3140 6.097839 AGTGAATGCCGAGTATAACTTTCCTA 59.902 38.462 0.00 0.00 0.00 2.94
2512 3141 5.104900 AGTGAATGCCGAGTATAACTTTCCT 60.105 40.000 0.00 0.00 0.00 3.36
2513 3142 5.116882 AGTGAATGCCGAGTATAACTTTCC 58.883 41.667 0.00 0.00 0.00 3.13
2514 3143 7.948278 ATAGTGAATGCCGAGTATAACTTTC 57.052 36.000 0.00 0.00 0.00 2.62
2515 3144 7.254795 GCAATAGTGAATGCCGAGTATAACTTT 60.255 37.037 0.00 0.00 36.56 2.66
2516 3145 6.202954 GCAATAGTGAATGCCGAGTATAACTT 59.797 38.462 0.00 0.00 36.56 2.66
2517 3146 5.696724 GCAATAGTGAATGCCGAGTATAACT 59.303 40.000 0.00 0.00 36.56 2.24
2518 3147 5.696724 AGCAATAGTGAATGCCGAGTATAAC 59.303 40.000 0.00 0.00 43.57 1.89
2519 3148 5.853936 AGCAATAGTGAATGCCGAGTATAA 58.146 37.500 0.00 0.00 43.57 0.98
2520 3149 5.243954 AGAGCAATAGTGAATGCCGAGTATA 59.756 40.000 0.00 0.00 43.57 1.47
2521 3150 4.039730 AGAGCAATAGTGAATGCCGAGTAT 59.960 41.667 0.00 0.00 43.57 2.12
2522 3151 3.384789 AGAGCAATAGTGAATGCCGAGTA 59.615 43.478 0.00 0.00 43.57 2.59
2523 3152 2.169352 AGAGCAATAGTGAATGCCGAGT 59.831 45.455 0.00 0.00 43.57 4.18
2524 3153 2.831333 AGAGCAATAGTGAATGCCGAG 58.169 47.619 0.00 0.00 43.57 4.63
2525 3154 2.988010 AGAGCAATAGTGAATGCCGA 57.012 45.000 0.00 0.00 43.57 5.54
2526 3155 3.201290 AGAAGAGCAATAGTGAATGCCG 58.799 45.455 0.00 0.00 43.57 5.69
2527 3156 4.397417 ACAAGAAGAGCAATAGTGAATGCC 59.603 41.667 0.00 0.00 43.57 4.40
2528 3157 5.557891 ACAAGAAGAGCAATAGTGAATGC 57.442 39.130 0.00 0.00 42.87 3.56
2529 3158 8.807667 AAAAACAAGAAGAGCAATAGTGAATG 57.192 30.769 0.00 0.00 0.00 2.67
2531 3160 8.567948 CCTAAAAACAAGAAGAGCAATAGTGAA 58.432 33.333 0.00 0.00 0.00 3.18
2532 3161 7.308589 GCCTAAAAACAAGAAGAGCAATAGTGA 60.309 37.037 0.00 0.00 0.00 3.41
2533 3162 6.803807 GCCTAAAAACAAGAAGAGCAATAGTG 59.196 38.462 0.00 0.00 0.00 2.74
2534 3163 6.490040 TGCCTAAAAACAAGAAGAGCAATAGT 59.510 34.615 0.00 0.00 0.00 2.12
2535 3164 6.803807 GTGCCTAAAAACAAGAAGAGCAATAG 59.196 38.462 0.00 0.00 0.00 1.73
2536 3165 6.567701 CGTGCCTAAAAACAAGAAGAGCAATA 60.568 38.462 0.00 0.00 0.00 1.90
2537 3166 5.532557 GTGCCTAAAAACAAGAAGAGCAAT 58.467 37.500 0.00 0.00 0.00 3.56
2541 3170 3.251004 AGCGTGCCTAAAAACAAGAAGAG 59.749 43.478 0.00 0.00 0.00 2.85
2561 3190 4.569162 TGTGTGTGTTACTTTGTACTCAGC 59.431 41.667 0.00 0.00 0.00 4.26
2604 3241 7.436970 TGGCTTCCTATTTTTCTTTTTCGAAAC 59.563 33.333 10.79 0.00 32.99 2.78
2630 3314 9.768662 GGCCAATTGTAAATAATTCAATCATCT 57.231 29.630 4.43 0.00 32.39 2.90
2669 3353 8.210265 TGTGGTAGTTAATTCAGATATGCATGA 58.790 33.333 10.16 0.00 0.00 3.07
2690 3374 7.546667 GCAAAGTTTCATGATGAAATATGTGGT 59.453 33.333 21.91 3.38 46.55 4.16
2691 3375 7.546316 TGCAAAGTTTCATGATGAAATATGTGG 59.454 33.333 21.91 11.68 46.55 4.17
2695 3379 9.491675 TGTTTGCAAAGTTTCATGATGAAATAT 57.508 25.926 21.91 12.18 46.55 1.28
2696 3380 8.883954 TGTTTGCAAAGTTTCATGATGAAATA 57.116 26.923 21.91 0.00 46.55 1.40
2747 3434 9.463443 AGTTCCAAAAATTCTGAAAAGAATACG 57.537 29.630 1.59 0.00 37.52 3.06
2787 3474 3.658757 TTGGAGCCCGATTTTCAAAAG 57.341 42.857 0.00 0.00 0.00 2.27
2820 3507 8.763984 AAGATGATTCCATGAGCTATTCTTTT 57.236 30.769 0.00 0.00 32.09 2.27
2824 3511 7.093354 TCGTAAGATGATTCCATGAGCTATTC 58.907 38.462 0.00 0.00 45.01 1.75
2825 3512 6.997655 TCGTAAGATGATTCCATGAGCTATT 58.002 36.000 0.00 0.00 45.01 1.73
2877 3566 6.940831 ACCAAAAATCATCCAAACCTTTTG 57.059 33.333 0.00 0.00 34.87 2.44
2912 3601 9.987272 CCTCCATTCTTAAACTGATTTTCTTTT 57.013 29.630 0.00 0.00 0.00 2.27
2916 3605 7.394641 AGTCCCTCCATTCTTAAACTGATTTTC 59.605 37.037 0.00 0.00 0.00 2.29
2953 4373 0.319297 CCAGCTTGCCTCTTGTTTGC 60.319 55.000 0.00 0.00 0.00 3.68
2975 4395 6.837471 AATGCCCACTACTAGTAGTATAGC 57.163 41.667 30.34 28.87 43.98 2.97
2977 4397 7.781219 TCACAAATGCCCACTACTAGTAGTATA 59.219 37.037 30.34 18.50 43.98 1.47
2978 4398 6.610020 TCACAAATGCCCACTACTAGTAGTAT 59.390 38.462 30.34 19.42 43.98 2.12
2979 4399 5.953548 TCACAAATGCCCACTACTAGTAGTA 59.046 40.000 30.34 18.15 43.98 1.82
2980 4400 4.775780 TCACAAATGCCCACTACTAGTAGT 59.224 41.667 26.61 26.61 46.52 2.73
2981 4401 5.339008 TCACAAATGCCCACTACTAGTAG 57.661 43.478 25.30 25.30 39.04 2.57
2982 4402 4.382685 GCTCACAAATGCCCACTACTAGTA 60.383 45.833 1.89 1.89 0.00 1.82
2983 4403 3.619979 GCTCACAAATGCCCACTACTAGT 60.620 47.826 0.00 0.00 0.00 2.57
2984 4404 2.939103 GCTCACAAATGCCCACTACTAG 59.061 50.000 0.00 0.00 0.00 2.57
2985 4405 2.571653 AGCTCACAAATGCCCACTACTA 59.428 45.455 0.00 0.00 0.00 1.82
2986 4406 1.352352 AGCTCACAAATGCCCACTACT 59.648 47.619 0.00 0.00 0.00 2.57
2987 4407 1.826385 AGCTCACAAATGCCCACTAC 58.174 50.000 0.00 0.00 0.00 2.73
3025 4445 9.937175 GCTAGTGTCACTCCAATTTTATATTTC 57.063 33.333 9.26 0.00 0.00 2.17
3037 4457 1.475403 GCCTAGCTAGTGTCACTCCA 58.525 55.000 19.31 0.00 0.00 3.86
3223 4643 3.254629 GCATGTTTGCTCTCTGGGA 57.745 52.632 0.00 0.00 45.77 4.37
3256 4676 4.518211 CGGACGAAGGGAGTACTGTAATAT 59.482 45.833 0.00 0.00 0.00 1.28
3257 4677 3.879295 CGGACGAAGGGAGTACTGTAATA 59.121 47.826 0.00 0.00 0.00 0.98
3258 4678 2.686915 CGGACGAAGGGAGTACTGTAAT 59.313 50.000 0.00 0.00 0.00 1.89
3263 4683 1.915141 TTTCGGACGAAGGGAGTACT 58.085 50.000 7.25 0.00 35.38 2.73
3284 4704 5.245075 TTGAGAAACAAGTTTGGGACAAGTT 59.755 36.000 2.45 0.00 37.48 2.66
3288 4708 5.395103 CCATTTGAGAAACAAGTTTGGGACA 60.395 40.000 2.45 0.00 39.77 4.02
3289 4709 5.049828 CCATTTGAGAAACAAGTTTGGGAC 58.950 41.667 2.45 0.00 39.77 4.46
3290 4710 4.959210 TCCATTTGAGAAACAAGTTTGGGA 59.041 37.500 2.45 0.00 39.77 4.37
3347 4991 6.526325 GCGTGCATTCAAATTAAGTTCATACA 59.474 34.615 0.00 0.00 0.00 2.29
3348 4992 6.526325 TGCGTGCATTCAAATTAAGTTCATAC 59.474 34.615 0.00 0.00 0.00 2.39
3368 5012 3.646554 ACAGCTGTGACATGCGTG 58.353 55.556 20.97 3.82 0.00 5.34
3917 5576 2.288025 GGCACCCGGACCAGAGTTA 61.288 63.158 0.73 0.00 0.00 2.24
4058 5717 1.523758 ACTTCAATCCGCTGGTGAAC 58.476 50.000 0.00 0.00 0.00 3.18
4083 5742 8.147704 TCAAAGCATATATGATAAGTTGACGGA 58.852 33.333 17.10 0.00 0.00 4.69
4165 5827 9.662947 CAGACCACATCATCAATATGTATGTAT 57.337 33.333 0.00 0.00 35.82 2.29
4170 5832 7.365497 AGTCAGACCACATCATCAATATGTA 57.635 36.000 0.00 0.00 35.82 2.29
4490 6348 3.525800 AGCAACCTTGTCTAACCCATT 57.474 42.857 0.00 0.00 0.00 3.16
4539 6397 1.069823 CAGATGCGCTAGTCCAAGGAT 59.930 52.381 9.73 0.00 0.00 3.24
4543 6401 2.418197 GGTAACAGATGCGCTAGTCCAA 60.418 50.000 9.73 0.00 0.00 3.53
4550 6408 0.460284 CGAAGGGTAACAGATGCGCT 60.460 55.000 9.73 0.00 38.57 5.92
4605 6463 1.829222 CGTGGTTCCTATAGGTGGTGT 59.171 52.381 18.51 0.00 36.34 4.16
4657 6515 0.826256 AAGGGAAGGGTTTGGCGAAC 60.826 55.000 9.21 9.21 37.53 3.95
4661 6519 2.304221 AGTAAAGGGAAGGGTTTGGC 57.696 50.000 0.00 0.00 0.00 4.52
4833 6697 9.011407 CACTTGTAGAATCGAAAGTATGTCTAC 57.989 37.037 0.00 0.00 38.50 2.59
4850 6714 8.591114 ACTAAAGCTCTAATACCACTTGTAGA 57.409 34.615 0.00 0.00 31.61 2.59
4864 6728 5.511363 AGGCTAACAGAGACTAAAGCTCTA 58.489 41.667 0.00 0.00 44.27 2.43
4904 6768 5.263599 TGTGAAACCAAGGCTATGATCATT 58.736 37.500 14.65 0.00 34.36 2.57
4905 6769 4.858850 TGTGAAACCAAGGCTATGATCAT 58.141 39.130 13.81 13.81 34.36 2.45
4943 6807 9.290988 ACGATGATAGTTAATCTCACTAGATGT 57.709 33.333 0.00 0.00 41.81 3.06
4956 6820 9.624373 AGTAAAGACCTCTACGATGATAGTTAA 57.376 33.333 0.00 0.00 0.00 2.01
4977 6841 5.163713 GCAAAATTTGTGCCACCAAAGTAAA 60.164 36.000 7.60 0.00 37.71 2.01
4986 6850 4.367450 TCAACTAGCAAAATTTGTGCCAC 58.633 39.130 7.96 0.00 43.27 5.01


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

AutoCloner maintained by Alex Coulton.