Multiple sequence alignment - TraesCS7D01G308000

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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 TraesCS7D01G308000 chr7D 100.000 3275 0 0 1 3275 390184468 390181194 0.000000e+00 6048.0
1 TraesCS7D01G308000 chr7B 95.466 2051 80 10 864 2910 385921950 385919909 0.000000e+00 3260.0
2 TraesCS7D01G308000 chr7B 96.368 413 14 1 480 892 385922370 385921959 0.000000e+00 678.0
3 TraesCS7D01G308000 chr7B 88.128 438 31 6 2 430 385923124 385922699 4.880000e-138 501.0
4 TraesCS7D01G308000 chr7B 90.526 95 9 0 2997 3091 385919877 385919783 3.430000e-25 126.0
5 TraesCS7D01G308000 chr7A 95.963 1189 43 4 1225 2410 441587614 441586428 0.000000e+00 1925.0
6 TraesCS7D01G308000 chr7A 87.771 507 36 6 2485 2966 441571956 441571451 1.320000e-158 569.0
7 TraesCS7D01G308000 chr7A 88.372 172 14 4 3105 3274 63799542 63799709 5.540000e-48 202.0
8 TraesCS7D01G308000 chr7A 88.571 105 11 1 2998 3101 731973928 731973824 3.430000e-25 126.0
9 TraesCS7D01G308000 chr7A 93.243 74 5 0 2414 2487 441584359 441584286 3.450000e-20 110.0
10 TraesCS7D01G308000 chr7A 93.333 45 3 0 2803 2847 40735544 40735588 2.110000e-07 67.6
11 TraesCS7D01G308000 chr7A 85.714 63 9 0 2870 2932 136464477 136464415 2.110000e-07 67.6
12 TraesCS7D01G308000 chr7A 97.297 37 1 0 2928 2964 642874347 642874383 2.730000e-06 63.9
13 TraesCS7D01G308000 chr2D 85.232 237 30 4 10 243 540306468 540306702 4.220000e-59 239.0
14 TraesCS7D01G308000 chr2D 87.736 106 10 3 2998 3101 620533575 620533471 1.600000e-23 121.0
15 TraesCS7D01G308000 chr2D 89.247 93 10 0 2998 3090 422565461 422565369 2.060000e-22 117.0
16 TraesCS7D01G308000 chr2D 84.270 89 5 6 2886 2965 423809733 423809645 9.740000e-11 78.7
17 TraesCS7D01G308000 chr2A 83.730 252 34 5 10 258 29365461 29365214 7.070000e-57 231.0
18 TraesCS7D01G308000 chr2A 83.333 252 35 5 10 258 29336344 29336097 3.290000e-55 226.0
19 TraesCS7D01G308000 chr2A 83.333 252 35 5 10 258 29352930 29352683 3.290000e-55 226.0
20 TraesCS7D01G308000 chr2A 91.667 84 7 0 2998 3081 154407719 154407802 2.060000e-22 117.0
21 TraesCS7D01G308000 chrUn 83.333 252 35 5 10 258 333542405 333542652 3.290000e-55 226.0
22 TraesCS7D01G308000 chrUn 83.333 252 35 5 10 258 343431246 343431493 3.290000e-55 226.0
23 TraesCS7D01G308000 chr3B 82.072 251 40 3 10 258 259149350 259149597 3.310000e-50 209.0
24 TraesCS7D01G308000 chr5D 82.258 248 35 8 1 244 547556284 547556526 4.280000e-49 206.0
25 TraesCS7D01G308000 chr2B 87.500 104 13 0 2998 3101 207623759 207623656 1.600000e-23 121.0
26 TraesCS7D01G308000 chr2B 91.667 84 7 0 2998 3081 763335541 763335624 2.060000e-22 117.0
27 TraesCS7D01G308000 chr5B 89.362 94 10 0 2998 3091 13097082 13096989 5.740000e-23 119.0
28 TraesCS7D01G308000 chr1B 87.755 98 12 0 2998 3095 563440879 563440976 7.430000e-22 115.0
29 TraesCS7D01G308000 chr4B 80.909 110 8 6 2868 2966 125452364 125452257 1.260000e-09 75.0
30 TraesCS7D01G308000 chr5A 95.455 44 2 0 2803 2846 463604567 463604524 1.630000e-08 71.3
31 TraesCS7D01G308000 chr5A 91.489 47 4 0 2803 2849 637293576 637293530 7.590000e-07 65.8
32 TraesCS7D01G308000 chr5A 87.037 54 6 1 2803 2856 621782968 621783020 3.530000e-05 60.2
33 TraesCS7D01G308000 chr4A 91.837 49 3 1 2803 2850 627582889 627582841 2.110000e-07 67.6
34 TraesCS7D01G308000 chr4A 91.667 48 3 1 2798 2845 28603085 28603039 7.590000e-07 65.8
35 TraesCS7D01G308000 chr4A 91.667 48 3 1 2798 2845 683857906 683857952 7.590000e-07 65.8
36 TraesCS7D01G308000 chr4A 84.127 63 7 3 2800 2861 685377235 685377295 1.270000e-04 58.4
37 TraesCS7D01G308000 chr3D 83.077 65 10 1 2867 2931 354278347 354278410 1.270000e-04 58.4


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 TraesCS7D01G308000 chr7D 390181194 390184468 3274 True 6048.00 6048 100.000 1 3275 1 chr7D.!!$R1 3274
1 TraesCS7D01G308000 chr7B 385919783 385923124 3341 True 1141.25 3260 92.622 2 3091 4 chr7B.!!$R1 3089
2 TraesCS7D01G308000 chr7A 441584286 441587614 3328 True 1017.50 1925 94.603 1225 2487 2 chr7A.!!$R4 1262
3 TraesCS7D01G308000 chr7A 441571451 441571956 505 True 569.00 569 87.771 2485 2966 1 chr7A.!!$R2 481

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
846 1135 0.037734 GGGGTTTCTTCGGTGTGGAT 59.962 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2407 2734 1.963515 AGCAAAGGGCCAAAGTAGTTG 59.036 47.619 6.18 0.0 46.5 3.16 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
37 38 3.867055 CGATGCATTAACGCTCATCTT 57.133 42.857 0.00 0.00 34.68 2.40
45 46 6.148645 TGCATTAACGCTCATCTTGTTTCTTA 59.851 34.615 0.00 0.00 0.00 2.10
52 53 8.547967 ACGCTCATCTTGTTTCTTATTTCTTA 57.452 30.769 0.00 0.00 0.00 2.10
90 91 2.215942 ACCAGTAAAAGATGTGGGGC 57.784 50.000 0.00 0.00 34.07 5.80
97 98 1.750193 AAAGATGTGGGGCGTGTATG 58.250 50.000 0.00 0.00 0.00 2.39
108 109 2.163412 GGGCGTGTATGCTTTCAATGAA 59.837 45.455 0.00 0.00 34.52 2.57
129 130 9.715121 AATGAATTTTTAGACTACCTAACACGA 57.285 29.630 0.00 0.00 37.10 4.35
136 137 3.447586 AGACTACCTAACACGACATGCAT 59.552 43.478 0.00 0.00 0.00 3.96
138 139 5.126545 AGACTACCTAACACGACATGCATTA 59.873 40.000 0.00 0.00 0.00 1.90
143 144 4.268644 CCTAACACGACATGCATTAGTCAG 59.731 45.833 15.25 10.14 34.48 3.51
146 147 2.674852 CACGACATGCATTAGTCAGCTT 59.325 45.455 15.25 0.00 34.48 3.74
151 152 5.007039 CGACATGCATTAGTCAGCTTATTGT 59.993 40.000 15.25 0.00 34.48 2.71
154 155 7.868775 ACATGCATTAGTCAGCTTATTGTATG 58.131 34.615 0.00 11.87 0.00 2.39
203 204 7.241628 ACATTTAGTTCTCTCATTTTCCCCTT 58.758 34.615 0.00 0.00 0.00 3.95
204 205 7.394641 ACATTTAGTTCTCTCATTTTCCCCTTC 59.605 37.037 0.00 0.00 0.00 3.46
205 206 3.944087 AGTTCTCTCATTTTCCCCTTCG 58.056 45.455 0.00 0.00 0.00 3.79
210 211 1.474077 CTCATTTTCCCCTTCGCCTTG 59.526 52.381 0.00 0.00 0.00 3.61
248 250 9.988815 AACCTAGATAACTAATGCACTGATAAG 57.011 33.333 0.00 0.00 0.00 1.73
249 251 8.589338 ACCTAGATAACTAATGCACTGATAAGG 58.411 37.037 0.00 0.00 0.00 2.69
250 252 8.807118 CCTAGATAACTAATGCACTGATAAGGA 58.193 37.037 0.00 0.00 0.00 3.36
251 253 9.853555 CTAGATAACTAATGCACTGATAAGGAG 57.146 37.037 0.00 0.00 0.00 3.69
252 254 7.675062 AGATAACTAATGCACTGATAAGGAGG 58.325 38.462 0.00 0.00 0.00 4.30
253 255 4.696479 ACTAATGCACTGATAAGGAGGG 57.304 45.455 0.00 0.00 0.00 4.30
254 256 4.298626 ACTAATGCACTGATAAGGAGGGA 58.701 43.478 0.00 0.00 0.00 4.20
255 257 3.853355 AATGCACTGATAAGGAGGGAG 57.147 47.619 0.00 0.00 0.00 4.30
256 258 2.254152 TGCACTGATAAGGAGGGAGT 57.746 50.000 0.00 0.00 0.00 3.85
257 259 3.398318 TGCACTGATAAGGAGGGAGTA 57.602 47.619 0.00 0.00 0.00 2.59
258 260 3.719871 TGCACTGATAAGGAGGGAGTAA 58.280 45.455 0.00 0.00 0.00 2.24
274 276 8.314021 GGAGGGAGTAAATGAAATTGATTGTTT 58.686 33.333 0.00 0.00 36.10 2.83
296 304 4.654091 ATTTTGACACACCAACTTCAGG 57.346 40.909 0.00 0.00 0.00 3.86
302 310 1.676006 CACACCAACTTCAGGTTCACC 59.324 52.381 0.00 0.00 37.23 4.02
305 313 0.179029 CCAACTTCAGGTTCACCCGT 60.179 55.000 0.00 0.00 38.74 5.28
314 322 2.280524 TTCACCCGTTGCCGTCTG 60.281 61.111 0.00 0.00 0.00 3.51
329 337 4.095334 TGCCGTCTGAATTCATCTTTCATG 59.905 41.667 8.96 0.00 32.94 3.07
346 354 7.928873 TCTTTCATGTAGAGAATTTAACCCCT 58.071 34.615 0.00 0.00 0.00 4.79
435 445 6.272698 GCAATAGGCAAAATAAAATGGTCG 57.727 37.500 0.00 0.00 43.97 4.79
436 446 5.234116 GCAATAGGCAAAATAAAATGGTCGG 59.766 40.000 0.00 0.00 43.97 4.79
437 447 3.885724 AGGCAAAATAAAATGGTCGGG 57.114 42.857 0.00 0.00 0.00 5.14
438 448 2.093711 AGGCAAAATAAAATGGTCGGGC 60.094 45.455 0.00 0.00 0.00 6.13
439 449 1.923864 GCAAAATAAAATGGTCGGGCG 59.076 47.619 0.00 0.00 0.00 6.13
440 450 2.416162 GCAAAATAAAATGGTCGGGCGA 60.416 45.455 0.00 0.00 0.00 5.54
441 451 3.839293 CAAAATAAAATGGTCGGGCGAA 58.161 40.909 0.00 0.00 0.00 4.70
442 452 3.775661 AAATAAAATGGTCGGGCGAAG 57.224 42.857 0.00 0.00 0.00 3.79
457 467 0.657840 CGAAGCACCGAATCATTCCC 59.342 55.000 0.00 0.00 0.00 3.97
458 468 1.025041 GAAGCACCGAATCATTCCCC 58.975 55.000 0.00 0.00 0.00 4.81
459 469 0.625849 AAGCACCGAATCATTCCCCT 59.374 50.000 0.00 0.00 0.00 4.79
460 470 0.181350 AGCACCGAATCATTCCCCTC 59.819 55.000 0.00 0.00 0.00 4.30
461 471 0.107214 GCACCGAATCATTCCCCTCA 60.107 55.000 0.00 0.00 0.00 3.86
462 472 1.668419 CACCGAATCATTCCCCTCAC 58.332 55.000 0.00 0.00 0.00 3.51
463 473 0.546598 ACCGAATCATTCCCCTCACC 59.453 55.000 0.00 0.00 0.00 4.02
464 474 0.179018 CCGAATCATTCCCCTCACCC 60.179 60.000 0.00 0.00 0.00 4.61
465 475 0.179018 CGAATCATTCCCCTCACCCC 60.179 60.000 0.00 0.00 0.00 4.95
466 476 0.186143 GAATCATTCCCCTCACCCCC 59.814 60.000 0.00 0.00 0.00 5.40
467 477 0.554865 AATCATTCCCCTCACCCCCA 60.555 55.000 0.00 0.00 0.00 4.96
468 478 1.289244 ATCATTCCCCTCACCCCCAC 61.289 60.000 0.00 0.00 0.00 4.61
469 479 2.212761 ATTCCCCTCACCCCCACA 59.787 61.111 0.00 0.00 0.00 4.17
470 480 2.238701 ATTCCCCTCACCCCCACAC 61.239 63.158 0.00 0.00 0.00 3.82
471 481 4.995058 TCCCCTCACCCCCACACC 62.995 72.222 0.00 0.00 0.00 4.16
491 780 2.581354 CCGCCTCTCCTCCACTTG 59.419 66.667 0.00 0.00 0.00 3.16
492 781 2.125350 CGCCTCTCCTCCACTTGC 60.125 66.667 0.00 0.00 0.00 4.01
496 785 1.601171 CTCTCCTCCACTTGCCCAG 59.399 63.158 0.00 0.00 0.00 4.45
571 860 1.573932 CCAGCAACATTTGACGCGA 59.426 52.632 15.93 0.00 0.00 5.87
578 867 1.153353 ACATTTGACGCGACGGAATT 58.847 45.000 15.93 0.00 0.00 2.17
580 869 0.179200 ATTTGACGCGACGGAATTGC 60.179 50.000 15.93 0.00 0.00 3.56
662 951 4.002982 TCTTCATTGTTTATCGCTGCTGT 58.997 39.130 0.00 0.00 0.00 4.40
714 1003 8.586879 AATGGAAAAATAAGAAGAAGAGAGGG 57.413 34.615 0.00 0.00 0.00 4.30
800 1089 5.003160 TGATTGAATCAGTTTCGTGTCCAT 58.997 37.500 3.29 0.00 37.13 3.41
846 1135 0.037734 GGGGTTTCTTCGGTGTGGAT 59.962 55.000 0.00 0.00 0.00 3.41
854 1143 2.069273 CTTCGGTGTGGATCAAGTGTC 58.931 52.381 0.00 0.00 0.00 3.67
866 1155 1.691976 TCAAGTGTCGGTCCTGTTGAT 59.308 47.619 0.00 0.00 0.00 2.57
955 1279 2.123589 TGGATCCGTATGGGTGTGAAT 58.876 47.619 7.39 0.00 37.00 2.57
959 1283 3.704800 TCCGTATGGGTGTGAATCAAA 57.295 42.857 0.00 0.00 37.00 2.69
981 1305 0.317269 GATGAATGTGCGGCCGATTG 60.317 55.000 33.48 0.00 0.00 2.67
982 1306 2.278142 GAATGTGCGGCCGATTGC 60.278 61.111 33.48 12.12 40.16 3.56
994 1318 3.612860 CGGCCGATTGCTTGTAGATATAC 59.387 47.826 24.07 0.00 40.92 1.47
995 1319 4.618460 CGGCCGATTGCTTGTAGATATACT 60.618 45.833 24.07 0.00 40.92 2.12
996 1320 5.392703 CGGCCGATTGCTTGTAGATATACTA 60.393 44.000 24.07 0.00 40.92 1.82
1094 1418 1.499056 GGCATGCACAACTCAGACG 59.501 57.895 21.36 0.00 0.00 4.18
1240 1564 1.453235 CTGATGGCGATGATGGGGT 59.547 57.895 0.00 0.00 0.00 4.95
1244 1568 1.644437 ATGGCGATGATGGGGTGGAA 61.644 55.000 0.00 0.00 0.00 3.53
1348 1672 5.300792 TCACTGGAGATGCGTGTACAATATA 59.699 40.000 0.00 0.00 0.00 0.86
1384 1708 3.368236 GTGCCGAATCAGTTCAAGTCTAC 59.632 47.826 0.00 0.00 33.86 2.59
1623 1947 3.567164 AGCAGATGTGACCTTCAAAGTTG 59.433 43.478 0.00 0.00 0.00 3.16
1862 2186 1.263484 CATCTATTTGCAGCAGCGGAG 59.737 52.381 0.00 0.00 46.23 4.63
1925 2249 2.363306 TGTGCCTGAACCTTGATGTT 57.637 45.000 0.00 0.00 0.00 2.71
1954 2278 1.067776 GGCTGTTGTACTGCGTCTAGT 60.068 52.381 0.00 0.00 42.94 2.57
2084 2408 2.158740 GGTTTCTCCCTCTCCATTAGCC 60.159 54.545 0.00 0.00 0.00 3.93
2273 2599 1.517832 CTAAGTGTCTCTGCCCCGG 59.482 63.158 0.00 0.00 0.00 5.73
2363 2689 6.470557 TGTTTAAGCGTGTAACTGGAATAC 57.529 37.500 0.00 0.00 31.75 1.89
2407 2734 5.622233 GCCTATCTTGTCAATGTTTTGGACC 60.622 44.000 0.00 0.00 33.44 4.46
2448 4840 0.690192 TGATTCGCAACTTGGGGAGA 59.310 50.000 6.03 0.00 0.00 3.71
2449 4841 1.339055 TGATTCGCAACTTGGGGAGAG 60.339 52.381 6.03 0.00 0.00 3.20
2504 4896 6.166279 TGTGAGAAGTGATAATCCTTGTGAC 58.834 40.000 0.00 0.00 0.00 3.67
2571 4963 5.363562 TCAGTTCCTATTGTCATCTGCAT 57.636 39.130 0.00 0.00 0.00 3.96
2620 5012 2.791383 TCGTGGCATCCTTTTTGTTG 57.209 45.000 0.00 0.00 0.00 3.33
2624 5016 3.192422 CGTGGCATCCTTTTTGTTGGATA 59.808 43.478 0.00 0.00 40.76 2.59
2709 5101 6.758806 AAGTTCCTTTCTAGACCTTTGGTA 57.241 37.500 0.00 0.00 35.25 3.25
2737 5129 1.003233 ACGGAGGAATCAACCCTTCAC 59.997 52.381 0.00 0.00 33.36 3.18
2752 5144 7.333174 TCAACCCTTCACATTTCAAAGAAAAAC 59.667 33.333 0.00 0.00 0.00 2.43
2811 5219 7.786178 TCAAACGTCATCTTAATTCCTATGG 57.214 36.000 0.00 0.00 0.00 2.74
2865 5273 4.657814 AGGGTGGATAATGTGAACTTGT 57.342 40.909 0.00 0.00 0.00 3.16
2872 5280 7.174253 GGTGGATAATGTGAACTTGTGTTAGAA 59.826 37.037 0.00 0.00 36.39 2.10
2879 5287 9.730420 AATGTGAACTTGTGTTAGAACATTTAC 57.270 29.630 0.00 0.00 39.29 2.01
2882 5290 9.006215 GTGAACTTGTGTTAGAACATTTACAAC 57.994 33.333 0.00 0.00 41.59 3.32
2898 5306 1.247567 CAACCGGACTTGGCAAATCT 58.752 50.000 9.46 0.00 0.00 2.40
2901 5309 1.004745 ACCGGACTTGGCAAATCTGAT 59.995 47.619 18.43 0.00 0.00 2.90
2912 5320 3.009723 GCAAATCTGATCCCTCAAACGA 58.990 45.455 0.00 0.00 0.00 3.85
2966 5383 6.404734 GGTCACGCCTCAAATATTTGATTCTT 60.405 38.462 26.83 14.37 45.26 2.52
2967 5384 7.029563 GTCACGCCTCAAATATTTGATTCTTT 58.970 34.615 26.83 11.12 45.26 2.52
2968 5385 7.542130 GTCACGCCTCAAATATTTGATTCTTTT 59.458 33.333 26.83 10.23 45.26 2.27
2969 5386 8.087750 TCACGCCTCAAATATTTGATTCTTTTT 58.912 29.630 26.83 8.92 45.26 1.94
2990 5407 5.371115 TTTTTGCGGGAGACTCAAATAAG 57.629 39.130 4.53 0.00 34.55 1.73
2991 5408 3.695830 TTGCGGGAGACTCAAATAAGT 57.304 42.857 4.53 0.00 0.00 2.24
2992 5409 3.247006 TGCGGGAGACTCAAATAAGTC 57.753 47.619 4.53 0.00 44.96 3.01
3002 5419 6.654793 GACTCAAATAAGTCGAGCTTGATT 57.345 37.500 7.00 0.00 36.61 2.57
3003 5420 6.654793 ACTCAAATAAGTCGAGCTTGATTC 57.345 37.500 7.00 0.00 38.05 2.52
3004 5421 6.402222 ACTCAAATAAGTCGAGCTTGATTCT 58.598 36.000 7.00 0.00 38.05 2.40
3011 5428 2.599082 GTCGAGCTTGATTCTACAACCG 59.401 50.000 7.00 0.00 0.00 4.44
3012 5429 2.490509 TCGAGCTTGATTCTACAACCGA 59.509 45.455 0.00 0.00 0.00 4.69
3030 5447 5.684550 ACCGAACACCTCAAATTAGAAAC 57.315 39.130 0.00 0.00 0.00 2.78
3037 5454 7.039313 ACACCTCAAATTAGAAACCTCAAAC 57.961 36.000 0.00 0.00 0.00 2.93
3038 5455 6.040504 ACACCTCAAATTAGAAACCTCAAACC 59.959 38.462 0.00 0.00 0.00 3.27
3074 5491 5.302360 TGCAACGTGAAACCTAATCTAAGT 58.698 37.500 0.00 0.00 0.00 2.24
3075 5492 5.407387 TGCAACGTGAAACCTAATCTAAGTC 59.593 40.000 0.00 0.00 0.00 3.01
3084 5501 3.702045 ACCTAATCTAAGTCGAGCTTGCT 59.298 43.478 9.58 0.00 38.05 3.91
3085 5502 4.202070 ACCTAATCTAAGTCGAGCTTGCTC 60.202 45.833 12.20 12.20 38.05 4.26
3094 5511 2.013021 GAGCTTGCTCGATTCTGCC 58.987 57.895 6.88 0.00 0.00 4.85
3095 5512 1.760268 GAGCTTGCTCGATTCTGCCG 61.760 60.000 6.88 0.00 0.00 5.69
3096 5513 2.705826 CTTGCTCGATTCTGCCGC 59.294 61.111 0.00 0.00 0.00 6.53
3097 5514 3.147889 CTTGCTCGATTCTGCCGCG 62.148 63.158 0.00 0.00 0.00 6.46
3102 5519 4.585526 CGATTCTGCCGCGCCCTA 62.586 66.667 0.00 0.00 0.00 3.53
3103 5520 2.203015 GATTCTGCCGCGCCCTAA 60.203 61.111 0.00 0.00 0.00 2.69
3104 5521 2.203070 ATTCTGCCGCGCCCTAAG 60.203 61.111 0.00 0.00 0.00 2.18
3114 5531 2.886124 GCCCTAAGCGAGACGTGC 60.886 66.667 0.00 0.00 0.00 5.34
3115 5532 2.579787 CCCTAAGCGAGACGTGCG 60.580 66.667 0.00 0.00 37.44 5.34
3116 5533 2.178521 CCTAAGCGAGACGTGCGT 59.821 61.111 0.00 0.00 37.44 5.24
3117 5534 1.868251 CCTAAGCGAGACGTGCGTC 60.868 63.158 15.92 15.92 44.86 5.19
3118 5535 1.868251 CTAAGCGAGACGTGCGTCC 60.868 63.158 19.35 11.00 45.59 4.79
3119 5536 3.656243 TAAGCGAGACGTGCGTCCG 62.656 63.158 19.35 20.75 45.59 4.79
3142 5559 4.430765 GAGCGGCTTCGACGGGAA 62.431 66.667 2.97 0.00 32.98 3.97
3143 5560 3.927163 GAGCGGCTTCGACGGGAAA 62.927 63.158 2.97 0.00 32.98 3.13
3144 5561 2.818274 GCGGCTTCGACGGGAAAT 60.818 61.111 0.00 0.00 32.98 2.17
3145 5562 3.089784 CGGCTTCGACGGGAAATG 58.910 61.111 0.00 0.00 33.34 2.32
3146 5563 1.447140 CGGCTTCGACGGGAAATGA 60.447 57.895 0.00 0.00 33.34 2.57
3147 5564 0.810031 CGGCTTCGACGGGAAATGAT 60.810 55.000 0.00 0.00 33.34 2.45
3148 5565 0.657840 GGCTTCGACGGGAAATGATG 59.342 55.000 0.00 0.00 33.34 3.07
3149 5566 1.369625 GCTTCGACGGGAAATGATGT 58.630 50.000 0.00 0.00 33.34 3.06
3150 5567 2.546778 GCTTCGACGGGAAATGATGTA 58.453 47.619 0.00 0.00 33.34 2.29
3151 5568 2.284417 GCTTCGACGGGAAATGATGTAC 59.716 50.000 0.00 0.00 33.34 2.90
3152 5569 3.782046 CTTCGACGGGAAATGATGTACT 58.218 45.455 0.00 0.00 33.34 2.73
3153 5570 3.880047 TCGACGGGAAATGATGTACTT 57.120 42.857 0.00 0.00 0.00 2.24
3154 5571 3.777478 TCGACGGGAAATGATGTACTTC 58.223 45.455 1.85 1.85 0.00 3.01
3155 5572 2.534349 CGACGGGAAATGATGTACTTCG 59.466 50.000 4.48 0.00 0.00 3.79
3156 5573 2.864343 GACGGGAAATGATGTACTTCGG 59.136 50.000 4.48 0.00 0.00 4.30
3157 5574 2.235402 ACGGGAAATGATGTACTTCGGT 59.765 45.455 4.48 0.00 0.00 4.69
3158 5575 3.267483 CGGGAAATGATGTACTTCGGTT 58.733 45.455 4.48 1.29 0.00 4.44
3159 5576 3.687698 CGGGAAATGATGTACTTCGGTTT 59.312 43.478 9.99 9.99 0.00 3.27
3160 5577 4.155280 CGGGAAATGATGTACTTCGGTTTT 59.845 41.667 10.96 7.93 0.00 2.43
3161 5578 5.335348 CGGGAAATGATGTACTTCGGTTTTT 60.335 40.000 10.96 6.18 0.00 1.94
3162 5579 6.090783 GGGAAATGATGTACTTCGGTTTTTC 58.909 40.000 10.96 11.89 0.00 2.29
3163 5580 6.090783 GGAAATGATGTACTTCGGTTTTTCC 58.909 40.000 18.59 18.59 34.63 3.13
3164 5581 6.294286 GGAAATGATGTACTTCGGTTTTTCCA 60.294 38.462 23.06 3.52 39.42 3.53
3165 5582 6.834168 AATGATGTACTTCGGTTTTTCCAT 57.166 33.333 4.48 0.00 35.57 3.41
3166 5583 5.873179 TGATGTACTTCGGTTTTTCCATC 57.127 39.130 4.48 0.00 35.57 3.51
3167 5584 4.390603 TGATGTACTTCGGTTTTTCCATCG 59.609 41.667 4.48 0.00 35.57 3.84
3168 5585 3.068560 TGTACTTCGGTTTTTCCATCGG 58.931 45.455 0.00 0.00 35.57 4.18
3169 5586 2.265589 ACTTCGGTTTTTCCATCGGT 57.734 45.000 0.00 0.00 35.57 4.69
3170 5587 3.405823 ACTTCGGTTTTTCCATCGGTA 57.594 42.857 0.00 0.00 35.57 4.02
3171 5588 3.946606 ACTTCGGTTTTTCCATCGGTAT 58.053 40.909 0.00 0.00 35.57 2.73
3172 5589 4.329392 ACTTCGGTTTTTCCATCGGTATT 58.671 39.130 0.00 0.00 35.57 1.89
3173 5590 4.393990 ACTTCGGTTTTTCCATCGGTATTC 59.606 41.667 0.00 0.00 35.57 1.75
3174 5591 2.931325 TCGGTTTTTCCATCGGTATTCG 59.069 45.455 0.00 0.00 36.69 3.34
3175 5592 2.031191 CGGTTTTTCCATCGGTATTCGG 59.969 50.000 0.00 0.00 36.26 4.30
3176 5593 3.011818 GGTTTTTCCATCGGTATTCGGT 58.988 45.455 0.00 0.00 36.41 4.69
3177 5594 3.441222 GGTTTTTCCATCGGTATTCGGTT 59.559 43.478 0.00 0.00 36.41 4.44
3178 5595 4.635324 GGTTTTTCCATCGGTATTCGGTTA 59.365 41.667 0.00 0.00 36.41 2.85
3179 5596 5.123661 GGTTTTTCCATCGGTATTCGGTTAA 59.876 40.000 0.00 0.00 36.41 2.01
3180 5597 6.349197 GGTTTTTCCATCGGTATTCGGTTAAA 60.349 38.462 0.00 0.00 36.41 1.52
3181 5598 7.252708 GTTTTTCCATCGGTATTCGGTTAAAT 58.747 34.615 0.00 0.00 39.77 1.40
3182 5599 8.397148 GTTTTTCCATCGGTATTCGGTTAAATA 58.603 33.333 0.00 0.00 39.77 1.40
3183 5600 7.481275 TTTCCATCGGTATTCGGTTAAATAC 57.519 36.000 0.00 0.00 40.07 1.89
3206 5623 4.992381 GAACCTATCGATTCCAATTCGG 57.008 45.455 1.71 0.00 0.00 4.30
3207 5624 4.377897 GAACCTATCGATTCCAATTCGGT 58.622 43.478 1.71 0.00 35.57 4.69
3208 5625 4.417426 ACCTATCGATTCCAATTCGGTT 57.583 40.909 1.71 0.00 35.57 4.44
3209 5626 5.540400 ACCTATCGATTCCAATTCGGTTA 57.460 39.130 1.71 0.00 35.57 2.85
3210 5627 6.110411 ACCTATCGATTCCAATTCGGTTAT 57.890 37.500 1.71 0.00 35.57 1.89
3211 5628 6.531021 ACCTATCGATTCCAATTCGGTTATT 58.469 36.000 1.71 0.00 35.57 1.40
3212 5629 6.649557 ACCTATCGATTCCAATTCGGTTATTC 59.350 38.462 1.71 0.00 35.57 1.75
3213 5630 6.649141 CCTATCGATTCCAATTCGGTTATTCA 59.351 38.462 1.71 0.00 35.57 2.57
3214 5631 6.935741 ATCGATTCCAATTCGGTTATTCAA 57.064 33.333 0.00 0.00 35.57 2.69
3215 5632 6.114221 TCGATTCCAATTCGGTTATTCAAC 57.886 37.500 0.00 0.00 35.57 3.18
3216 5633 5.644206 TCGATTCCAATTCGGTTATTCAACA 59.356 36.000 0.00 0.00 36.29 3.33
3217 5634 6.317642 TCGATTCCAATTCGGTTATTCAACAT 59.682 34.615 0.00 0.00 36.29 2.71
3218 5635 7.496263 TCGATTCCAATTCGGTTATTCAACATA 59.504 33.333 0.00 0.00 36.29 2.29
3219 5636 8.126074 CGATTCCAATTCGGTTATTCAACATAA 58.874 33.333 0.00 0.00 36.29 1.90
3220 5637 9.796120 GATTCCAATTCGGTTATTCAACATAAA 57.204 29.630 0.00 0.00 36.29 1.40
3222 5639 9.982651 TTCCAATTCGGTTATTCAACATAAAAA 57.017 25.926 0.00 0.00 36.29 1.94
3223 5640 9.413048 TCCAATTCGGTTATTCAACATAAAAAC 57.587 29.630 0.00 0.00 36.29 2.43
3224 5641 8.652463 CCAATTCGGTTATTCAACATAAAAACC 58.348 33.333 0.00 0.00 36.29 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.706432 CGTTAATGCATCGCGCCA 59.294 55.556 0.00 0.00 41.33 5.69
18 19 4.542662 ACAAGATGAGCGTTAATGCATC 57.457 40.909 21.31 15.36 37.88 3.91
19 20 4.970662 AACAAGATGAGCGTTAATGCAT 57.029 36.364 21.31 7.28 37.31 3.96
75 76 1.530323 ACACGCCCCACATCTTTTAC 58.470 50.000 0.00 0.00 0.00 2.01
79 80 0.748005 GCATACACGCCCCACATCTT 60.748 55.000 0.00 0.00 0.00 2.40
84 85 0.958382 TGAAAGCATACACGCCCCAC 60.958 55.000 0.00 0.00 0.00 4.61
90 91 9.340695 TCTAAAAATTCATTGAAAGCATACACG 57.659 29.630 2.68 0.00 0.00 4.49
108 109 7.064253 GCATGTCGTGTTAGGTAGTCTAAAAAT 59.936 37.037 0.00 0.00 39.43 1.82
127 128 5.007039 ACAATAAGCTGACTAATGCATGTCG 59.993 40.000 0.00 2.68 36.10 4.35
129 130 7.521099 GCATACAATAAGCTGACTAATGCATGT 60.521 37.037 0.00 0.00 37.67 3.21
138 139 9.784531 AATACTATTGCATACAATAAGCTGACT 57.215 29.630 0.18 0.00 45.73 3.41
203 204 4.228567 TGCACGTGACCAAGGCGA 62.229 61.111 22.23 0.00 0.00 5.54
204 205 4.012895 GTGCACGTGACCAAGGCG 62.013 66.667 22.23 0.00 0.00 5.52
205 206 2.477176 TTGTGCACGTGACCAAGGC 61.477 57.895 22.23 1.55 0.00 4.35
210 211 0.032952 TCTAGGTTGTGCACGTGACC 59.967 55.000 22.23 22.30 0.00 4.02
248 250 7.410120 ACAATCAATTTCATTTACTCCCTCC 57.590 36.000 0.00 0.00 0.00 4.30
274 276 5.197451 ACCTGAAGTTGGTGTGTCAAAATA 58.803 37.500 0.00 0.00 36.30 1.40
305 313 4.071423 TGAAAGATGAATTCAGACGGCAA 58.929 39.130 14.54 0.00 33.15 4.52
329 337 7.986320 GGAAACTCTAGGGGTTAAATTCTCTAC 59.014 40.741 0.00 0.00 0.00 2.59
433 443 4.077184 ATTCGGTGCTTCGCCCGA 62.077 61.111 12.26 12.26 44.68 5.14
434 444 3.564027 GATTCGGTGCTTCGCCCG 61.564 66.667 8.73 8.73 41.33 6.13
435 445 1.376609 AATGATTCGGTGCTTCGCCC 61.377 55.000 0.00 0.00 0.00 6.13
436 446 0.028110 GAATGATTCGGTGCTTCGCC 59.972 55.000 0.00 0.00 0.00 5.54
437 447 0.028110 GGAATGATTCGGTGCTTCGC 59.972 55.000 0.00 0.00 0.00 4.70
438 448 0.657840 GGGAATGATTCGGTGCTTCG 59.342 55.000 0.00 0.00 0.00 3.79
439 449 1.025041 GGGGAATGATTCGGTGCTTC 58.975 55.000 0.00 0.00 0.00 3.86
440 450 0.625849 AGGGGAATGATTCGGTGCTT 59.374 50.000 0.00 0.00 0.00 3.91
441 451 0.181350 GAGGGGAATGATTCGGTGCT 59.819 55.000 0.00 0.00 0.00 4.40
442 452 0.107214 TGAGGGGAATGATTCGGTGC 60.107 55.000 0.00 0.00 0.00 5.01
443 453 1.668419 GTGAGGGGAATGATTCGGTG 58.332 55.000 0.00 0.00 0.00 4.94
444 454 0.546598 GGTGAGGGGAATGATTCGGT 59.453 55.000 0.00 0.00 0.00 4.69
445 455 0.179018 GGGTGAGGGGAATGATTCGG 60.179 60.000 0.00 0.00 0.00 4.30
446 456 0.179018 GGGGTGAGGGGAATGATTCG 60.179 60.000 0.00 0.00 0.00 3.34
447 457 0.186143 GGGGGTGAGGGGAATGATTC 59.814 60.000 0.00 0.00 0.00 2.52
448 458 0.554865 TGGGGGTGAGGGGAATGATT 60.555 55.000 0.00 0.00 0.00 2.57
449 459 1.086565 TGGGGGTGAGGGGAATGAT 59.913 57.895 0.00 0.00 0.00 2.45
450 460 1.928567 GTGGGGGTGAGGGGAATGA 60.929 63.158 0.00 0.00 0.00 2.57
451 461 2.237965 TGTGGGGGTGAGGGGAATG 61.238 63.158 0.00 0.00 0.00 2.67
452 462 2.212761 TGTGGGGGTGAGGGGAAT 59.787 61.111 0.00 0.00 0.00 3.01
453 463 2.856988 GTGTGGGGGTGAGGGGAA 60.857 66.667 0.00 0.00 0.00 3.97
454 464 4.995058 GGTGTGGGGGTGAGGGGA 62.995 72.222 0.00 0.00 0.00 4.81
473 483 3.394836 AAGTGGAGGAGAGGCGGC 61.395 66.667 0.00 0.00 0.00 6.53
474 484 2.581354 CAAGTGGAGGAGAGGCGG 59.419 66.667 0.00 0.00 0.00 6.13
475 485 2.125350 GCAAGTGGAGGAGAGGCG 60.125 66.667 0.00 0.00 0.00 5.52
476 486 2.270527 GGCAAGTGGAGGAGAGGC 59.729 66.667 0.00 0.00 0.00 4.70
477 487 1.908340 CTGGGCAAGTGGAGGAGAGG 61.908 65.000 0.00 0.00 0.00 3.69
478 488 0.906756 TCTGGGCAAGTGGAGGAGAG 60.907 60.000 0.00 0.00 0.00 3.20
487 776 0.404426 GGTTAGGGTTCTGGGCAAGT 59.596 55.000 0.00 0.00 0.00 3.16
491 780 2.681591 GGGGTTAGGGTTCTGGGC 59.318 66.667 0.00 0.00 0.00 5.36
492 781 0.924226 ATGGGGGTTAGGGTTCTGGG 60.924 60.000 0.00 0.00 0.00 4.45
496 785 1.145119 GATCCATGGGGGTTAGGGTTC 59.855 57.143 13.02 0.00 38.11 3.62
662 951 4.020573 ACAAATGTTACCACGAGGATCAGA 60.021 41.667 5.68 0.00 38.69 3.27
714 1003 5.451590 AGGCAACATAGGTACACCACCAC 62.452 52.174 0.38 0.00 46.15 4.16
820 1109 1.340697 ACCGAAGAAACCCCAATAGCC 60.341 52.381 0.00 0.00 0.00 3.93
846 1135 1.116308 TCAACAGGACCGACACTTGA 58.884 50.000 0.00 0.00 0.00 3.02
854 1143 2.401583 TGAATGGATCAACAGGACCG 57.598 50.000 0.00 0.00 34.30 4.79
955 1279 1.739466 GCCGCACATTCATCTCTTTGA 59.261 47.619 0.00 0.00 0.00 2.69
959 1283 1.522355 CGGCCGCACATTCATCTCT 60.522 57.895 14.67 0.00 0.00 3.10
1077 1401 1.230635 ACCGTCTGAGTTGTGCATGC 61.231 55.000 11.82 11.82 0.00 4.06
1187 1511 3.277142 ACAATAACCCAGTCGAATCCC 57.723 47.619 0.00 0.00 0.00 3.85
1289 1613 0.038892 TCAGGTCTACGAACGCCAAC 60.039 55.000 0.00 0.00 0.00 3.77
1295 1619 3.690139 TGATCAGTCTCAGGTCTACGAAC 59.310 47.826 0.00 0.00 0.00 3.95
1348 1672 1.001641 GGCACCCTGTTCTCTGCAT 60.002 57.895 0.00 0.00 0.00 3.96
1384 1708 0.742635 GGAAGCCTCTTCGAAGCTGG 60.743 60.000 20.56 22.51 36.84 4.85
1623 1947 2.095461 GGCAGGAAACATTTCTCCTCC 58.905 52.381 4.45 0.00 40.22 4.30
1862 2186 5.537300 TCAACCTCTCTAGACCATATTGC 57.463 43.478 0.00 0.00 0.00 3.56
1877 2201 4.377431 CGTTCACACATAAGCTTCAACCTC 60.377 45.833 0.00 0.00 0.00 3.85
1925 2249 3.689161 GCAGTACAACAGCCACATTATCA 59.311 43.478 0.00 0.00 0.00 2.15
1954 2278 2.021457 TCTGGCAGTCGTATCGATCAA 58.979 47.619 15.27 0.00 38.42 2.57
2084 2408 4.504461 CGAGTATTCTTCTCCCACAAATCG 59.496 45.833 0.00 0.00 0.00 3.34
2281 2607 4.093011 AGACTAAAGAGACATCAGCAGGT 58.907 43.478 0.00 0.00 0.00 4.00
2287 2613 7.279615 TCAACCAAAAGACTAAAGAGACATCA 58.720 34.615 0.00 0.00 0.00 3.07
2299 2625 6.657541 TCACTAACAGTTTCAACCAAAAGACT 59.342 34.615 0.00 0.00 0.00 3.24
2363 2689 5.420409 AGGCAGAATTAAAAGAGACCTACG 58.580 41.667 0.00 0.00 0.00 3.51
2407 2734 1.963515 AGCAAAGGGCCAAAGTAGTTG 59.036 47.619 6.18 0.00 46.50 3.16
2448 4840 2.353406 CGACCGTGAACTAAATCCACCT 60.353 50.000 0.00 0.00 0.00 4.00
2449 4841 1.997606 CGACCGTGAACTAAATCCACC 59.002 52.381 0.00 0.00 0.00 4.61
2504 4896 4.384056 CACATACTAGCAAATCTCCTGGG 58.616 47.826 0.00 0.00 0.00 4.45
2620 5012 5.248380 ACAAATCAAGGAGGCCTATATCC 57.752 43.478 4.42 1.94 31.13 2.59
2624 5016 4.307259 TCCTACAAATCAAGGAGGCCTAT 58.693 43.478 4.42 0.00 36.97 2.57
2697 5089 4.403432 CCGTTCCTACATACCAAAGGTCTA 59.597 45.833 0.00 0.00 37.09 2.59
2709 5101 3.118371 GGTTGATTCCTCCGTTCCTACAT 60.118 47.826 0.00 0.00 0.00 2.29
2783 5175 9.712305 ATAGGAATTAAGATGACGTTTGATAGG 57.288 33.333 0.00 0.00 0.00 2.57
2834 5242 2.889522 TATCCACCCTTTAGGCCTCT 57.110 50.000 9.68 0.00 40.58 3.69
2837 5245 3.117663 TCACATTATCCACCCTTTAGGCC 60.118 47.826 0.00 0.00 40.58 5.19
2865 5273 5.613329 AGTCCGGTTGTAAATGTTCTAACA 58.387 37.500 0.00 0.00 44.06 2.41
2872 5280 1.883926 GCCAAGTCCGGTTGTAAATGT 59.116 47.619 0.00 0.00 0.00 2.71
2876 5284 2.054232 TTTGCCAAGTCCGGTTGTAA 57.946 45.000 0.00 0.00 0.00 2.41
2879 5287 1.068333 CAGATTTGCCAAGTCCGGTTG 60.068 52.381 0.00 0.00 0.00 3.77
2882 5290 1.672881 GATCAGATTTGCCAAGTCCGG 59.327 52.381 0.00 0.00 0.00 5.14
2898 5306 1.079405 GCGGTCGTTTGAGGGATCA 60.079 57.895 0.00 0.00 0.00 2.92
2901 5309 4.367023 CCGCGGTCGTTTGAGGGA 62.367 66.667 19.50 0.00 0.00 4.20
2968 5385 4.825085 ACTTATTTGAGTCTCCCGCAAAAA 59.175 37.500 0.00 0.00 44.36 1.94
2969 5386 4.394729 ACTTATTTGAGTCTCCCGCAAAA 58.605 39.130 0.00 0.00 44.36 2.44
2970 5387 4.000988 GACTTATTTGAGTCTCCCGCAAA 58.999 43.478 0.00 0.00 45.09 3.68
2971 5388 3.596214 GACTTATTTGAGTCTCCCGCAA 58.404 45.455 0.00 0.00 42.18 4.85
2972 5389 2.416836 CGACTTATTTGAGTCTCCCGCA 60.417 50.000 0.00 0.00 43.05 5.69
2973 5390 2.159282 TCGACTTATTTGAGTCTCCCGC 60.159 50.000 0.00 0.00 43.05 6.13
2974 5391 3.696898 CTCGACTTATTTGAGTCTCCCG 58.303 50.000 0.00 0.00 43.05 5.14
2975 5392 3.131400 AGCTCGACTTATTTGAGTCTCCC 59.869 47.826 0.00 0.00 43.05 4.30
2976 5393 4.379339 AGCTCGACTTATTTGAGTCTCC 57.621 45.455 0.00 0.00 43.05 3.71
2977 5394 5.403246 TCAAGCTCGACTTATTTGAGTCTC 58.597 41.667 3.84 0.00 43.05 3.36
2978 5395 5.392767 TCAAGCTCGACTTATTTGAGTCT 57.607 39.130 3.84 0.00 43.05 3.24
2979 5396 6.533367 AGAATCAAGCTCGACTTATTTGAGTC 59.467 38.462 5.21 5.21 40.90 3.36
2980 5397 6.402222 AGAATCAAGCTCGACTTATTTGAGT 58.598 36.000 0.00 0.00 37.98 3.41
2981 5398 6.900568 AGAATCAAGCTCGACTTATTTGAG 57.099 37.500 0.00 0.00 36.04 3.02
2982 5399 7.320399 TGTAGAATCAAGCTCGACTTATTTGA 58.680 34.615 0.00 0.00 36.04 2.69
2983 5400 7.525688 TGTAGAATCAAGCTCGACTTATTTG 57.474 36.000 0.00 0.00 36.04 2.32
2984 5401 7.064728 GGTTGTAGAATCAAGCTCGACTTATTT 59.935 37.037 0.00 0.00 40.98 1.40
2985 5402 6.535508 GGTTGTAGAATCAAGCTCGACTTATT 59.464 38.462 0.00 2.84 40.98 1.40
2986 5403 6.043411 GGTTGTAGAATCAAGCTCGACTTAT 58.957 40.000 0.00 0.00 40.98 1.73
2987 5404 5.408356 GGTTGTAGAATCAAGCTCGACTTA 58.592 41.667 0.00 0.00 40.98 2.24
2988 5405 4.246458 GGTTGTAGAATCAAGCTCGACTT 58.754 43.478 0.00 0.00 40.98 3.01
2989 5406 3.673594 CGGTTGTAGAATCAAGCTCGACT 60.674 47.826 0.00 0.00 41.68 4.18
2990 5407 2.599082 CGGTTGTAGAATCAAGCTCGAC 59.401 50.000 0.00 0.00 41.68 4.20
2991 5408 2.490509 TCGGTTGTAGAATCAAGCTCGA 59.509 45.455 0.00 0.00 41.68 4.04
2992 5409 2.876091 TCGGTTGTAGAATCAAGCTCG 58.124 47.619 0.00 0.00 41.68 5.03
2993 5410 3.994392 TGTTCGGTTGTAGAATCAAGCTC 59.006 43.478 0.00 0.30 41.68 4.09
2994 5411 3.746492 GTGTTCGGTTGTAGAATCAAGCT 59.254 43.478 6.96 0.00 41.68 3.74
2995 5412 3.120304 GGTGTTCGGTTGTAGAATCAAGC 60.120 47.826 0.00 0.00 40.84 4.01
2996 5413 4.315803 AGGTGTTCGGTTGTAGAATCAAG 58.684 43.478 0.00 0.00 0.00 3.02
2997 5414 4.202274 TGAGGTGTTCGGTTGTAGAATCAA 60.202 41.667 0.00 0.00 0.00 2.57
2998 5415 3.322541 TGAGGTGTTCGGTTGTAGAATCA 59.677 43.478 0.00 0.00 0.00 2.57
2999 5416 3.921677 TGAGGTGTTCGGTTGTAGAATC 58.078 45.455 0.00 0.00 0.00 2.52
3000 5417 4.345859 TTGAGGTGTTCGGTTGTAGAAT 57.654 40.909 0.00 0.00 0.00 2.40
3001 5418 3.823281 TTGAGGTGTTCGGTTGTAGAA 57.177 42.857 0.00 0.00 0.00 2.10
3002 5419 3.823281 TTTGAGGTGTTCGGTTGTAGA 57.177 42.857 0.00 0.00 0.00 2.59
3003 5420 5.929992 TCTAATTTGAGGTGTTCGGTTGTAG 59.070 40.000 0.00 0.00 0.00 2.74
3004 5421 5.856156 TCTAATTTGAGGTGTTCGGTTGTA 58.144 37.500 0.00 0.00 0.00 2.41
3011 5428 6.877611 TGAGGTTTCTAATTTGAGGTGTTC 57.122 37.500 0.00 0.00 0.00 3.18
3012 5429 7.417456 GGTTTGAGGTTTCTAATTTGAGGTGTT 60.417 37.037 0.00 0.00 0.00 3.32
3030 5447 7.523293 TGCATGTAATAATATGGGTTTGAGG 57.477 36.000 0.00 0.00 0.00 3.86
3037 5454 6.552859 TCACGTTGCATGTAATAATATGGG 57.447 37.500 0.00 0.00 0.00 4.00
3038 5455 7.378461 GGTTTCACGTTGCATGTAATAATATGG 59.622 37.037 0.00 0.00 0.00 2.74
3085 5502 4.585526 TAGGGCGCGGCAGAATCG 62.586 66.667 34.30 0.00 0.00 3.34
3097 5514 2.886124 GCACGTCTCGCTTAGGGC 60.886 66.667 0.00 0.00 37.64 5.19
3098 5515 2.579787 CGCACGTCTCGCTTAGGG 60.580 66.667 0.00 0.00 0.00 3.53
3099 5516 1.868251 GACGCACGTCTCGCTTAGG 60.868 63.158 15.56 0.00 41.57 2.69
3100 5517 1.868251 GGACGCACGTCTCGCTTAG 60.868 63.158 21.19 0.00 44.04 2.18
3101 5518 2.177531 GGACGCACGTCTCGCTTA 59.822 61.111 21.19 0.00 44.04 3.09
3125 5542 3.927163 TTTCCCGTCGAAGCCGCTC 62.927 63.158 0.00 0.00 35.37 5.03
3126 5543 3.310860 ATTTCCCGTCGAAGCCGCT 62.311 57.895 0.00 0.00 35.37 5.52
3127 5544 2.818274 ATTTCCCGTCGAAGCCGC 60.818 61.111 0.00 0.00 35.37 6.53
3128 5545 0.810031 ATCATTTCCCGTCGAAGCCG 60.810 55.000 0.00 0.00 37.07 5.52
3129 5546 0.657840 CATCATTTCCCGTCGAAGCC 59.342 55.000 0.00 0.00 0.00 4.35
3130 5547 1.369625 ACATCATTTCCCGTCGAAGC 58.630 50.000 0.00 0.00 0.00 3.86
3131 5548 3.782046 AGTACATCATTTCCCGTCGAAG 58.218 45.455 0.00 0.00 0.00 3.79
3132 5549 3.880047 AGTACATCATTTCCCGTCGAA 57.120 42.857 0.00 0.00 0.00 3.71
3133 5550 3.732774 CGAAGTACATCATTTCCCGTCGA 60.733 47.826 0.00 0.00 0.00 4.20
3134 5551 2.534349 CGAAGTACATCATTTCCCGTCG 59.466 50.000 0.00 0.00 0.00 5.12
3135 5552 2.864343 CCGAAGTACATCATTTCCCGTC 59.136 50.000 0.00 0.00 0.00 4.79
3136 5553 2.235402 ACCGAAGTACATCATTTCCCGT 59.765 45.455 0.00 0.00 0.00 5.28
3137 5554 2.901249 ACCGAAGTACATCATTTCCCG 58.099 47.619 0.00 0.00 0.00 5.14
3138 5555 5.638596 AAAACCGAAGTACATCATTTCCC 57.361 39.130 0.00 0.00 0.00 3.97
3139 5556 6.090783 GGAAAAACCGAAGTACATCATTTCC 58.909 40.000 13.87 13.87 37.29 3.13
3140 5557 6.674066 TGGAAAAACCGAAGTACATCATTTC 58.326 36.000 0.00 2.07 42.61 2.17
3141 5558 6.642707 TGGAAAAACCGAAGTACATCATTT 57.357 33.333 0.00 0.00 42.61 2.32
3142 5559 6.403200 CGATGGAAAAACCGAAGTACATCATT 60.403 38.462 0.00 0.00 42.61 2.57
3143 5560 5.064707 CGATGGAAAAACCGAAGTACATCAT 59.935 40.000 0.00 0.00 42.61 2.45
3144 5561 4.390603 CGATGGAAAAACCGAAGTACATCA 59.609 41.667 0.00 0.00 42.61 3.07
3145 5562 4.201783 CCGATGGAAAAACCGAAGTACATC 60.202 45.833 0.00 0.00 42.61 3.06
3146 5563 3.687698 CCGATGGAAAAACCGAAGTACAT 59.312 43.478 0.00 0.00 42.61 2.29
3147 5564 3.068560 CCGATGGAAAAACCGAAGTACA 58.931 45.455 0.00 0.00 42.61 2.90
3148 5565 3.069289 ACCGATGGAAAAACCGAAGTAC 58.931 45.455 0.00 0.00 42.61 2.73
3149 5566 3.405823 ACCGATGGAAAAACCGAAGTA 57.594 42.857 0.00 0.00 42.61 2.24
3150 5567 2.265589 ACCGATGGAAAAACCGAAGT 57.734 45.000 0.00 0.00 42.61 3.01
3151 5568 4.493545 CGAATACCGATGGAAAAACCGAAG 60.494 45.833 0.00 0.00 40.46 3.79
3152 5569 3.371591 CGAATACCGATGGAAAAACCGAA 59.628 43.478 0.00 0.00 40.46 4.30
3153 5570 2.931325 CGAATACCGATGGAAAAACCGA 59.069 45.455 0.00 0.00 40.46 4.69
3154 5571 2.031191 CCGAATACCGATGGAAAAACCG 59.969 50.000 0.00 0.00 40.46 4.44
3155 5572 3.011818 ACCGAATACCGATGGAAAAACC 58.988 45.455 0.00 0.00 41.76 3.27
3156 5573 4.690184 AACCGAATACCGATGGAAAAAC 57.310 40.909 0.00 0.00 41.76 2.43
3157 5574 6.814506 TTTAACCGAATACCGATGGAAAAA 57.185 33.333 0.00 0.00 41.76 1.94
3158 5575 7.012232 GGTATTTAACCGAATACCGATGGAAAA 59.988 37.037 10.12 0.00 46.78 2.29
3159 5576 6.482973 GGTATTTAACCGAATACCGATGGAAA 59.517 38.462 10.12 0.00 46.78 3.13
3160 5577 5.990996 GGTATTTAACCGAATACCGATGGAA 59.009 40.000 10.12 0.00 46.78 3.53
3161 5578 5.540911 GGTATTTAACCGAATACCGATGGA 58.459 41.667 10.12 0.00 46.78 3.41
3162 5579 5.851047 GGTATTTAACCGAATACCGATGG 57.149 43.478 10.12 0.00 46.78 3.51
3186 5603 4.417426 ACCGAATTGGAATCGATAGGTT 57.583 40.909 0.00 0.00 46.41 3.50
3187 5604 4.417426 AACCGAATTGGAATCGATAGGT 57.583 40.909 0.00 0.00 42.76 3.08
3188 5605 6.649141 TGAATAACCGAATTGGAATCGATAGG 59.351 38.462 0.00 0.00 42.76 2.57
3189 5606 7.652300 TGAATAACCGAATTGGAATCGATAG 57.348 36.000 0.00 0.00 42.76 2.08
3190 5607 7.496263 TGTTGAATAACCGAATTGGAATCGATA 59.504 33.333 0.00 0.00 42.00 2.92
3191 5608 6.317642 TGTTGAATAACCGAATTGGAATCGAT 59.682 34.615 0.00 0.00 42.00 3.59
3192 5609 5.644206 TGTTGAATAACCGAATTGGAATCGA 59.356 36.000 0.00 0.00 42.00 3.59
3193 5610 5.874831 TGTTGAATAACCGAATTGGAATCG 58.125 37.500 0.00 0.00 42.00 3.34
3194 5611 9.796120 TTTATGTTGAATAACCGAATTGGAATC 57.204 29.630 0.00 0.00 42.00 2.52
3196 5613 9.982651 TTTTTATGTTGAATAACCGAATTGGAA 57.017 25.926 0.00 0.00 42.00 3.53
3197 5614 9.413048 GTTTTTATGTTGAATAACCGAATTGGA 57.587 29.630 0.00 0.00 42.00 3.53
3198 5615 8.652463 GGTTTTTATGTTGAATAACCGAATTGG 58.348 33.333 0.00 0.00 46.41 3.16


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

AutoCloner maintained by Alex Coulton.