Multiple sequence alignment - TraesCS5D01G369500

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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 TraesCS5D01G369500 chr5D 100.000 4178 0 0 1 4178 444887032 444891209 0.000000e+00 7716.0
1 TraesCS5D01G369500 chr5D 77.723 202 30 4 2537 2723 198466869 198466668 4.420000e-20 110.0
2 TraesCS5D01G369500 chr5B 91.553 2557 144 35 715 3228 541916043 541918570 0.000000e+00 3459.0
3 TraesCS5D01G369500 chr5B 93.566 544 25 9 3225 3759 541918596 541919138 0.000000e+00 802.0
4 TraesCS5D01G369500 chr5B 83.240 716 25 30 7 718 541915332 541915956 1.690000e-158 569.0
5 TraesCS5D01G369500 chr5B 91.864 295 19 2 3885 4178 541938159 541938449 1.400000e-109 407.0
6 TraesCS5D01G369500 chr5B 87.843 255 9 4 3885 4135 541935613 541935849 3.180000e-71 279.0
7 TraesCS5D01G369500 chr5A 89.423 1872 110 38 941 2750 561810493 561812338 0.000000e+00 2279.0
8 TraesCS5D01G369500 chr5A 82.381 1067 97 45 2754 3758 561812425 561813462 0.000000e+00 845.0
9 TraesCS5D01G369500 chr5A 83.673 343 32 8 377 718 561809899 561810218 6.790000e-78 302.0
10 TraesCS5D01G369500 chr5A 83.650 263 19 18 54 293 561809270 561809531 4.200000e-55 226.0
11 TraesCS5D01G369500 chr5A 96.667 90 3 0 1917 2006 605801410 605801321 2.600000e-32 150.0
12 TraesCS5D01G369500 chr5A 86.154 130 18 0 3754 3883 116568858 116568987 1.570000e-29 141.0
13 TraesCS5D01G369500 chr5A 96.203 79 3 0 1756 1834 605801486 605801408 3.390000e-26 130.0
14 TraesCS5D01G369500 chr5A 79.882 169 27 3 3885 4047 561814998 561814831 2.640000e-22 117.0
15 TraesCS5D01G369500 chr5A 87.097 93 6 2 715 807 561810304 561810390 2.660000e-17 100.0
16 TraesCS5D01G369500 chr5A 85.915 71 4 4 1735 1799 625752395 625752325 2.080000e-08 71.3
17 TraesCS5D01G369500 chr5A 93.478 46 2 1 7 52 561809236 561809280 2.700000e-07 67.6
18 TraesCS5D01G369500 chr2D 83.612 299 22 9 1307 1603 643078861 643079134 5.360000e-64 255.0
19 TraesCS5D01G369500 chr2D 85.976 164 15 5 1654 1812 643079145 643079305 7.180000e-38 169.0
20 TraesCS5D01G369500 chr1A 92.793 111 8 0 1332 1442 9479165 9479275 1.200000e-35 161.0
21 TraesCS5D01G369500 chr3B 80.693 202 21 9 2538 2723 522283521 522283720 1.570000e-29 141.0
22 TraesCS5D01G369500 chr1B 94.444 90 5 0 1917 2006 453199612 453199523 5.630000e-29 139.0
23 TraesCS5D01G369500 chr1B 77.778 207 28 7 2534 2723 545085147 545085352 1.230000e-20 111.0
24 TraesCS5D01G369500 chr1B 100.000 34 0 0 1801 1834 453199643 453199610 3.490000e-06 63.9
25 TraesCS5D01G369500 chrUn 89.623 106 5 4 1735 1834 129540936 129541041 3.390000e-26 130.0
26 TraesCS5D01G369500 chr2B 78.744 207 26 7 2534 2723 20559605 20559400 5.670000e-24 122.0
27 TraesCS5D01G369500 chr7A 100.000 31 0 0 1770 1800 645410616 645410646 1.620000e-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 TraesCS5D01G369500 chr5D 444887032 444891209 4177 False 7716.0 7716 100.0000 1 4178 1 chr5D.!!$F1 4177
1 TraesCS5D01G369500 chr5B 541915332 541919138 3806 False 1610.0 3459 89.4530 7 3759 3 chr5B.!!$F1 3752
2 TraesCS5D01G369500 chr5B 541935613 541938449 2836 False 343.0 407 89.8535 3885 4178 2 chr5B.!!$F2 293
3 TraesCS5D01G369500 chr5A 561809236 561813462 4226 False 636.6 2279 86.6170 7 3758 6 chr5A.!!$F2 3751

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
576 904 0.032540 CGCTGCCTTTTGAGCCTTTT 59.967 50.0 0.00 0.0 30.98 2.27 F
877 1296 0.177604 CCTCAAGCGGCAGATCTTCT 59.822 55.0 1.45 0.0 0.00 2.85 F
937 1364 0.319040 CCACAGAGTCACACGGTCTG 60.319 60.0 0.00 0.0 42.91 3.51 F
2019 2477 0.667792 GCTCGTCTCAAGTGGACACC 60.668 60.0 0.00 0.0 33.73 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 2336 0.251832 TCTCGCCCTTCTTCACCTCT 60.252 55.000 0.0 0.0 0.00 3.69 R
1995 2453 1.005748 CACTTGAGACGAGCTGCCA 60.006 57.895 0.0 0.0 0.00 4.92 R
2829 3441 1.527311 GACCTCGGATCGCTTTAATGC 59.473 52.381 3.3 3.3 0.00 3.56 R
3817 4501 0.109597 GCGTTGGAATGCTTGGTCTG 60.110 55.000 0.0 0.0 37.92 3.51 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.034687 CACTCCCACCCAGCAAGG 59.965 66.667 0.00 0.00 37.03 3.61
22 23 2.673523 CTCCCACCCAGCAAGGAG 59.326 66.667 0.00 0.00 41.22 3.69
52 53 3.423253 CCACCACGGTTGGGGTTGA 62.423 63.158 0.00 0.00 46.34 3.18
62 63 1.595058 TTGGGGTTGAGGTTGGGGTT 61.595 55.000 0.00 0.00 0.00 4.11
63 64 1.533033 GGGGTTGAGGTTGGGGTTG 60.533 63.158 0.00 0.00 0.00 3.77
64 65 1.533033 GGGTTGAGGTTGGGGTTGG 60.533 63.158 0.00 0.00 0.00 3.77
65 66 1.533033 GGTTGAGGTTGGGGTTGGG 60.533 63.158 0.00 0.00 0.00 4.12
66 67 1.533033 GTTGAGGTTGGGGTTGGGG 60.533 63.158 0.00 0.00 0.00 4.96
67 68 2.015726 TTGAGGTTGGGGTTGGGGT 61.016 57.895 0.00 0.00 0.00 4.95
124 125 1.070577 CGACGAATCAATCAATCCGCC 60.071 52.381 0.00 0.00 0.00 6.13
126 127 2.213499 ACGAATCAATCAATCCGCCTC 58.787 47.619 0.00 0.00 0.00 4.70
221 254 2.203509 CCTCTCCCCGTCGGCTAT 60.204 66.667 5.50 0.00 0.00 2.97
348 382 4.075793 CGAGTCCTCCCTCCCCCA 62.076 72.222 0.00 0.00 0.00 4.96
350 384 2.876858 AGTCCTCCCTCCCCCACT 60.877 66.667 0.00 0.00 0.00 4.00
351 385 2.125225 GTCCTCCCTCCCCCACTT 59.875 66.667 0.00 0.00 0.00 3.16
353 387 1.229853 TCCTCCCTCCCCCACTTTC 60.230 63.158 0.00 0.00 0.00 2.62
354 388 2.309504 CCTCCCTCCCCCACTTTCC 61.310 68.421 0.00 0.00 0.00 3.13
355 389 2.609610 TCCCTCCCCCACTTTCCG 60.610 66.667 0.00 0.00 0.00 4.30
356 390 4.426313 CCCTCCCCCACTTTCCGC 62.426 72.222 0.00 0.00 0.00 5.54
357 391 3.330720 CCTCCCCCACTTTCCGCT 61.331 66.667 0.00 0.00 0.00 5.52
358 392 2.269241 CTCCCCCACTTTCCGCTC 59.731 66.667 0.00 0.00 0.00 5.03
359 393 3.327404 TCCCCCACTTTCCGCTCC 61.327 66.667 0.00 0.00 0.00 4.70
360 394 4.426313 CCCCCACTTTCCGCTCCC 62.426 72.222 0.00 0.00 0.00 4.30
361 395 3.646715 CCCCACTTTCCGCTCCCA 61.647 66.667 0.00 0.00 0.00 4.37
362 396 2.359975 CCCACTTTCCGCTCCCAC 60.360 66.667 0.00 0.00 0.00 4.61
363 397 2.359975 CCACTTTCCGCTCCCACC 60.360 66.667 0.00 0.00 0.00 4.61
364 398 2.429930 CACTTTCCGCTCCCACCA 59.570 61.111 0.00 0.00 0.00 4.17
365 399 1.966451 CACTTTCCGCTCCCACCAC 60.966 63.158 0.00 0.00 0.00 4.16
366 400 2.359975 CTTTCCGCTCCCACCACC 60.360 66.667 0.00 0.00 0.00 4.61
367 401 2.852075 TTTCCGCTCCCACCACCT 60.852 61.111 0.00 0.00 0.00 4.00
368 402 2.804828 CTTTCCGCTCCCACCACCTC 62.805 65.000 0.00 0.00 0.00 3.85
371 405 3.775654 CGCTCCCACCACCTCCTC 61.776 72.222 0.00 0.00 0.00 3.71
372 406 3.403558 GCTCCCACCACCTCCTCC 61.404 72.222 0.00 0.00 0.00 4.30
373 407 2.452114 CTCCCACCACCTCCTCCT 59.548 66.667 0.00 0.00 0.00 3.69
374 408 1.687493 CTCCCACCACCTCCTCCTC 60.687 68.421 0.00 0.00 0.00 3.71
375 409 2.689034 CCCACCACCTCCTCCTCC 60.689 72.222 0.00 0.00 0.00 4.30
403 721 2.443016 CCCCCACGGAGAGGAGAG 60.443 72.222 0.00 0.00 42.26 3.20
404 722 2.443016 CCCCACGGAGAGGAGAGG 60.443 72.222 0.00 0.00 42.26 3.69
405 723 2.684104 CCCACGGAGAGGAGAGGA 59.316 66.667 0.00 0.00 42.26 3.71
406 724 1.454847 CCCACGGAGAGGAGAGGAG 60.455 68.421 0.00 0.00 42.26 3.69
407 725 2.124693 CCACGGAGAGGAGAGGAGC 61.125 68.421 0.00 0.00 42.26 4.70
464 783 2.757077 CGCCACCCTCCCTTTTCT 59.243 61.111 0.00 0.00 0.00 2.52
542 861 0.039437 TTGACTCTTCTCCACGACGC 60.039 55.000 0.00 0.00 0.00 5.19
543 862 1.153997 GACTCTTCTCCACGACGCC 60.154 63.158 0.00 0.00 0.00 5.68
544 863 2.182030 CTCTTCTCCACGACGCCC 59.818 66.667 0.00 0.00 0.00 6.13
545 864 3.358076 CTCTTCTCCACGACGCCCC 62.358 68.421 0.00 0.00 0.00 5.80
546 865 4.796231 CTTCTCCACGACGCCCCG 62.796 72.222 0.00 0.00 0.00 5.73
570 898 3.064324 CCCCCGCTGCCTTTTGAG 61.064 66.667 0.00 0.00 0.00 3.02
572 900 3.752339 CCCGCTGCCTTTTGAGCC 61.752 66.667 0.00 0.00 30.98 4.70
573 901 2.674380 CCGCTGCCTTTTGAGCCT 60.674 61.111 0.00 0.00 30.98 4.58
575 903 1.662044 CGCTGCCTTTTGAGCCTTT 59.338 52.632 0.00 0.00 30.98 3.11
576 904 0.032540 CGCTGCCTTTTGAGCCTTTT 59.967 50.000 0.00 0.00 30.98 2.27
577 905 1.505425 GCTGCCTTTTGAGCCTTTTG 58.495 50.000 0.00 0.00 0.00 2.44
579 907 2.747436 CTGCCTTTTGAGCCTTTTGAC 58.253 47.619 0.00 0.00 0.00 3.18
581 909 1.602920 GCCTTTTGAGCCTTTTGACCG 60.603 52.381 0.00 0.00 0.00 4.79
582 910 1.602920 CCTTTTGAGCCTTTTGACCGC 60.603 52.381 0.00 0.00 0.00 5.68
583 911 1.338020 CTTTTGAGCCTTTTGACCGCT 59.662 47.619 0.00 0.00 34.97 5.52
585 913 4.379174 GAGCCTTTTGACCGCTCA 57.621 55.556 3.51 0.00 46.63 4.26
586 914 2.629002 GAGCCTTTTGACCGCTCAA 58.371 52.632 3.51 0.00 46.63 3.02
587 915 0.951558 GAGCCTTTTGACCGCTCAAA 59.048 50.000 1.72 1.72 46.63 2.69
599 927 1.196354 CCGCTCAAACTTGCTTCTCTG 59.804 52.381 0.00 0.00 0.00 3.35
605 933 2.437359 CTTGCTTCTCTGCCCCCG 60.437 66.667 0.00 0.00 0.00 5.73
623 952 1.289066 GTGATCGCGGCTAGCCATA 59.711 57.895 32.47 17.51 44.76 2.74
624 953 0.734253 GTGATCGCGGCTAGCCATAG 60.734 60.000 32.47 21.76 44.76 2.23
653 982 1.996292 TATGAGTGACACAGCGCTTC 58.004 50.000 7.50 3.27 0.00 3.86
741 1160 0.392998 TTTCCGATCCCAGCTTCAGC 60.393 55.000 0.00 0.00 42.49 4.26
801 1220 0.465278 GGCTTCCAGCTTCAGGGATC 60.465 60.000 0.00 0.00 41.99 3.36
805 1224 0.324738 TCCAGCTTCAGGGATCGAGT 60.325 55.000 0.00 0.00 0.00 4.18
806 1225 0.179089 CCAGCTTCAGGGATCGAGTG 60.179 60.000 0.00 0.00 0.00 3.51
850 1269 2.584835 ATTAAAGCTCTGGTGCACCA 57.415 45.000 35.49 35.49 45.30 4.17
875 1294 4.950479 CCTCAAGCGGCAGATCTT 57.050 55.556 1.45 0.00 0.00 2.40
877 1296 0.177604 CCTCAAGCGGCAGATCTTCT 59.822 55.000 1.45 0.00 0.00 2.85
879 1298 1.932511 CTCAAGCGGCAGATCTTCTTC 59.067 52.381 1.45 0.00 0.00 2.87
901 1320 2.516906 CGGAGGGGAAGATAGTAGTCC 58.483 57.143 0.00 0.00 0.00 3.85
902 1321 2.158505 CGGAGGGGAAGATAGTAGTCCA 60.159 54.545 0.00 0.00 32.70 4.02
903 1322 3.232662 GGAGGGGAAGATAGTAGTCCAC 58.767 54.545 0.00 0.00 34.84 4.02
904 1323 3.232662 GAGGGGAAGATAGTAGTCCACC 58.767 54.545 0.00 0.00 35.23 4.61
905 1324 1.962100 GGGGAAGATAGTAGTCCACCG 59.038 57.143 0.00 0.00 32.70 4.94
906 1325 2.664015 GGGAAGATAGTAGTCCACCGT 58.336 52.381 0.00 0.00 32.70 4.83
913 1332 4.580995 AGATAGTAGTCCACCGTGATCTTG 59.419 45.833 0.00 0.00 0.00 3.02
915 1334 2.897969 AGTAGTCCACCGTGATCTTGTT 59.102 45.455 0.00 0.00 0.00 2.83
919 1346 1.586154 CCACCGTGATCTTGTTGCCC 61.586 60.000 0.00 0.00 0.00 5.36
929 1356 0.947244 CTTGTTGCCCACAGAGTCAC 59.053 55.000 0.00 0.00 36.48 3.67
937 1364 0.319040 CCACAGAGTCACACGGTCTG 60.319 60.000 0.00 0.00 42.91 3.51
938 1365 2.808598 ACAGAGTCACACGGTCTGT 58.191 52.632 0.00 0.00 44.86 3.41
939 1366 3.967886 CAGAGTCACACGGTCTGTT 57.032 52.632 0.00 0.00 34.24 3.16
940 1367 1.772182 CAGAGTCACACGGTCTGTTC 58.228 55.000 0.00 0.00 34.24 3.18
943 1370 1.301479 GTCACACGGTCTGTTCCCC 60.301 63.158 0.00 0.00 0.00 4.81
944 1371 1.458777 TCACACGGTCTGTTCCCCT 60.459 57.895 0.00 0.00 0.00 4.79
945 1372 1.301716 CACACGGTCTGTTCCCCTG 60.302 63.158 0.00 0.00 0.00 4.45
946 1373 2.358737 CACGGTCTGTTCCCCTGC 60.359 66.667 0.00 0.00 0.00 4.85
949 1388 1.987855 CGGTCTGTTCCCCTGCCTA 60.988 63.158 0.00 0.00 0.00 3.93
951 1390 1.602771 GTCTGTTCCCCTGCCTACC 59.397 63.158 0.00 0.00 0.00 3.18
1206 1652 2.422231 CCACTGCTCCTCCTCCGAG 61.422 68.421 0.00 0.00 35.72 4.63
1207 1653 1.680651 CACTGCTCCTCCTCCGAGT 60.681 63.158 0.00 0.00 33.93 4.18
1208 1654 1.379309 ACTGCTCCTCCTCCGAGTC 60.379 63.158 0.00 0.00 33.93 3.36
1210 1656 3.213402 GCTCCTCCTCCGAGTCCG 61.213 72.222 0.00 0.00 33.93 4.79
1211 1657 3.213402 CTCCTCCTCCGAGTCCGC 61.213 72.222 0.00 0.00 33.93 5.54
1467 1916 1.934463 GCCGAGTTACGATGGCATG 59.066 57.895 3.81 0.00 46.76 4.06
1728 2177 2.722201 GGAGGTGGAGGCGAACGAT 61.722 63.158 0.00 0.00 0.00 3.73
1754 2209 3.374402 CGAGGAGGTGGACACGCT 61.374 66.667 0.00 0.00 0.00 5.07
1819 2274 4.742201 TGCTGGCGAGCTCGTTCC 62.742 66.667 34.46 27.69 46.39 3.62
1870 2325 2.501610 GGGACACGGAGAGGATGC 59.498 66.667 0.00 0.00 0.00 3.91
1995 2453 4.071875 TGCGTCGGCGGTAATGGT 62.072 61.111 13.05 0.00 44.10 3.55
2019 2477 0.667792 GCTCGTCTCAAGTGGACACC 60.668 60.000 0.00 0.00 33.73 4.16
2215 2707 7.979786 TGTCTGGAGTTCCTTTTCTATCTAT 57.020 36.000 0.00 0.00 36.82 1.98
2217 2709 8.826765 TGTCTGGAGTTCCTTTTCTATCTATTT 58.173 33.333 0.00 0.00 36.82 1.40
2261 2753 2.519771 AGGAAATTGCAGCATGAGGA 57.480 45.000 0.00 0.00 39.69 3.71
2331 2829 8.994429 TGAATTCACTTTAGTTTTTGCTTCAA 57.006 26.923 3.38 0.00 0.00 2.69
2332 2830 9.598517 TGAATTCACTTTAGTTTTTGCTTCAAT 57.401 25.926 3.38 0.00 0.00 2.57
2333 2831 9.853921 GAATTCACTTTAGTTTTTGCTTCAATG 57.146 29.630 0.00 0.00 0.00 2.82
2343 2846 7.433680 AGTTTTTGCTTCAATGGTACTAAAGG 58.566 34.615 0.00 0.00 0.00 3.11
2360 2863 7.674471 ACTAAAGGAGCTTTTCATTCTGTAC 57.326 36.000 0.00 0.00 35.21 2.90
2568 3081 7.201600 CCATTCGGGTTATTTTATTGGCAAAAG 60.202 37.037 3.01 0.00 31.29 2.27
2589 3102 2.726241 GCAAAGAGAAAAACCGCATGTC 59.274 45.455 0.00 0.00 0.00 3.06
2606 3119 5.098211 GCATGTCAGAACTAAAATCTTGGC 58.902 41.667 0.00 0.00 0.00 4.52
2650 3177 4.572795 GCTAGAAGAGGGTGTATTTTGAGC 59.427 45.833 0.00 0.00 0.00 4.26
2657 3185 3.689649 AGGGTGTATTTTGAGCATCGTTC 59.310 43.478 0.00 0.00 38.61 3.95
2829 3441 3.758554 CAGGGGCCAAAATATAATCTCCG 59.241 47.826 4.39 0.00 0.00 4.63
2837 3449 7.542130 GGCCAAAATATAATCTCCGCATTAAAG 59.458 37.037 0.00 0.00 0.00 1.85
2838 3450 7.062255 GCCAAAATATAATCTCCGCATTAAAGC 59.938 37.037 0.00 0.00 0.00 3.51
2887 3516 3.641046 TGGGGGTCAATGGACAATTATG 58.359 45.455 1.86 0.00 46.17 1.90
2900 3529 8.697507 ATGGACAATTATGGAACTTAATCCTC 57.302 34.615 0.00 0.00 40.35 3.71
2902 3531 6.766467 GGACAATTATGGAACTTAATCCTCGT 59.234 38.462 0.00 0.00 40.35 4.18
2984 3613 4.159377 TCTCAAAATTTAGGCGTGCTTG 57.841 40.909 0.00 0.00 0.00 4.01
2992 3621 4.477302 TTTAGGCGTGCTTGTTTAGTTC 57.523 40.909 0.00 0.00 0.00 3.01
2999 3628 3.311322 CGTGCTTGTTTAGTTCCAAGACA 59.689 43.478 3.72 0.00 40.36 3.41
3015 3644 9.912634 GTTCCAAGACAGATTTTCATTTTATCA 57.087 29.630 0.00 0.00 0.00 2.15
3087 3726 5.704515 TCTCTTTGAAATCTTGCAGGAGAAG 59.295 40.000 4.35 3.98 0.00 2.85
3110 3749 6.441274 AGTGCATGTAACTCATCTTGTTTTG 58.559 36.000 0.00 0.00 34.09 2.44
3114 3753 7.012799 TGCATGTAACTCATCTTGTTTTGTACA 59.987 33.333 0.00 0.00 34.09 2.90
3115 3754 7.535258 GCATGTAACTCATCTTGTTTTGTACAG 59.465 37.037 0.00 0.00 34.64 2.74
3189 3828 0.679002 CAGGGTGACTGGCCAATCAG 60.679 60.000 19.00 1.37 43.70 2.90
3467 4143 2.376808 AAGATGCTGTGGTTCTCTCG 57.623 50.000 0.00 0.00 0.00 4.04
3500 4176 1.134098 CCGGATGCTTCAGGTGGTATT 60.134 52.381 10.15 0.00 33.01 1.89
3526 4205 5.178061 TGTGTGACTGTTGATGGTATGATC 58.822 41.667 0.00 0.00 0.00 2.92
3634 4313 3.004629 TGTGCTGTACATGGCTTCAAAAG 59.995 43.478 8.39 0.00 33.42 2.27
3685 4364 1.831286 GAGGCGACGGGGATTCCTA 60.831 63.158 2.01 0.00 0.00 2.94
3689 4368 1.509703 GCGACGGGGATTCCTATTTC 58.490 55.000 2.01 0.00 0.00 2.17
3737 4420 1.274703 CCCATCTGCCAGTGTACCCT 61.275 60.000 0.00 0.00 0.00 4.34
3743 4426 2.154462 CTGCCAGTGTACCCTTGAAAG 58.846 52.381 0.00 0.00 0.00 2.62
3744 4427 0.881796 GCCAGTGTACCCTTGAAAGC 59.118 55.000 0.00 0.00 0.00 3.51
3759 4443 3.976015 TGAAAGCCCCCAATACTTTAGG 58.024 45.455 0.00 0.00 33.91 2.69
3760 4444 3.296854 GAAAGCCCCCAATACTTTAGGG 58.703 50.000 0.00 0.00 42.44 3.53
3763 4447 2.838637 CCCCCAATACTTTAGGGCAA 57.161 50.000 0.00 0.00 41.42 4.52
3764 4448 2.384828 CCCCCAATACTTTAGGGCAAC 58.615 52.381 0.00 0.00 41.42 4.17
3765 4449 2.024369 CCCCCAATACTTTAGGGCAACT 60.024 50.000 0.00 0.00 41.42 3.16
3766 4450 3.288092 CCCCAATACTTTAGGGCAACTC 58.712 50.000 0.00 0.00 41.42 3.01
3767 4451 3.288092 CCCAATACTTTAGGGCAACTCC 58.712 50.000 0.00 0.00 35.44 3.85
3778 4462 4.988598 CAACTCCCACGCACGGCT 62.989 66.667 0.00 0.00 0.00 5.52
3779 4463 4.681978 AACTCCCACGCACGGCTC 62.682 66.667 0.00 0.00 0.00 4.70
3784 4468 3.055719 CCACGCACGGCTCCAAAT 61.056 61.111 0.00 0.00 0.00 2.32
3785 4469 2.480555 CACGCACGGCTCCAAATC 59.519 61.111 0.00 0.00 0.00 2.17
3786 4470 3.118454 ACGCACGGCTCCAAATCG 61.118 61.111 0.00 0.00 0.00 3.34
3787 4471 3.118454 CGCACGGCTCCAAATCGT 61.118 61.111 0.00 0.00 37.64 3.73
3788 4472 2.785258 GCACGGCTCCAAATCGTC 59.215 61.111 0.00 0.00 34.73 4.20
3789 4473 2.750888 GCACGGCTCCAAATCGTCC 61.751 63.158 0.00 0.00 34.73 4.79
3790 4474 2.125673 ACGGCTCCAAATCGTCCG 60.126 61.111 0.00 0.00 45.04 4.79
3791 4475 2.125673 CGGCTCCAAATCGTCCGT 60.126 61.111 0.00 0.00 35.75 4.69
3792 4476 2.452813 CGGCTCCAAATCGTCCGTG 61.453 63.158 0.00 0.00 35.75 4.94
3793 4477 2.106683 GGCTCCAAATCGTCCGTGG 61.107 63.158 0.00 0.00 0.00 4.94
3794 4478 2.106683 GCTCCAAATCGTCCGTGGG 61.107 63.158 0.00 0.00 32.95 4.61
3795 4479 1.295423 CTCCAAATCGTCCGTGGGT 59.705 57.895 0.00 0.00 32.95 4.51
3796 4480 1.004320 TCCAAATCGTCCGTGGGTG 60.004 57.895 0.00 0.00 32.95 4.61
3797 4481 1.302192 CCAAATCGTCCGTGGGTGT 60.302 57.895 0.00 0.00 0.00 4.16
3798 4482 1.296056 CCAAATCGTCCGTGGGTGTC 61.296 60.000 0.00 0.00 0.00 3.67
3799 4483 1.004200 AAATCGTCCGTGGGTGTCC 60.004 57.895 0.00 0.00 0.00 4.02
3800 4484 2.775032 AAATCGTCCGTGGGTGTCCG 62.775 60.000 0.00 0.00 35.24 4.79
3802 4486 4.289245 CGTCCGTGGGTGTCCGTT 62.289 66.667 0.00 0.00 35.24 4.44
3803 4487 2.109593 GTCCGTGGGTGTCCGTTT 59.890 61.111 0.00 0.00 35.24 3.60
3804 4488 2.109387 TCCGTGGGTGTCCGTTTG 59.891 61.111 0.00 0.00 35.24 2.93
3805 4489 2.975799 CCGTGGGTGTCCGTTTGG 60.976 66.667 0.00 0.00 35.24 3.28
3806 4490 2.975799 CGTGGGTGTCCGTTTGGG 60.976 66.667 0.00 0.00 35.24 4.12
3807 4491 2.596338 GTGGGTGTCCGTTTGGGG 60.596 66.667 0.00 0.00 36.01 4.96
3808 4492 3.097830 TGGGTGTCCGTTTGGGGT 61.098 61.111 0.00 0.00 36.01 4.95
3809 4493 2.196502 GGGTGTCCGTTTGGGGTT 59.803 61.111 0.00 0.00 36.01 4.11
3810 4494 1.351080 TGGGTGTCCGTTTGGGGTTA 61.351 55.000 0.00 0.00 36.01 2.85
3811 4495 0.178995 GGGTGTCCGTTTGGGGTTAA 60.179 55.000 0.00 0.00 36.01 2.01
3812 4496 1.689984 GGTGTCCGTTTGGGGTTAAA 58.310 50.000 0.00 0.00 36.01 1.52
3813 4497 1.337703 GGTGTCCGTTTGGGGTTAAAC 59.662 52.381 0.00 0.00 37.23 2.01
3820 4504 2.574450 GTTTGGGGTTAAACGGACAGA 58.426 47.619 0.00 0.00 31.67 3.41
3821 4505 2.259266 TTGGGGTTAAACGGACAGAC 57.741 50.000 0.00 0.00 0.00 3.51
3822 4506 0.397564 TGGGGTTAAACGGACAGACC 59.602 55.000 0.00 0.00 0.00 3.85
3823 4507 0.397564 GGGGTTAAACGGACAGACCA 59.602 55.000 0.00 0.00 38.90 4.02
3824 4508 1.202794 GGGGTTAAACGGACAGACCAA 60.203 52.381 0.00 0.00 38.90 3.67
3825 4509 2.148768 GGGTTAAACGGACAGACCAAG 58.851 52.381 0.00 0.00 38.90 3.61
3826 4510 1.534163 GGTTAAACGGACAGACCAAGC 59.466 52.381 0.00 0.00 38.90 4.01
3827 4511 2.215196 GTTAAACGGACAGACCAAGCA 58.785 47.619 0.00 0.00 38.90 3.91
3828 4512 2.812011 GTTAAACGGACAGACCAAGCAT 59.188 45.455 0.00 0.00 38.90 3.79
3829 4513 1.981256 AAACGGACAGACCAAGCATT 58.019 45.000 0.00 0.00 38.90 3.56
3830 4514 1.523758 AACGGACAGACCAAGCATTC 58.476 50.000 0.00 0.00 38.90 2.67
3831 4515 0.321653 ACGGACAGACCAAGCATTCC 60.322 55.000 0.00 0.00 38.90 3.01
3832 4516 0.321564 CGGACAGACCAAGCATTCCA 60.322 55.000 0.00 0.00 38.90 3.53
3833 4517 1.881925 CGGACAGACCAAGCATTCCAA 60.882 52.381 0.00 0.00 38.90 3.53
3834 4518 1.541588 GGACAGACCAAGCATTCCAAC 59.458 52.381 0.00 0.00 38.79 3.77
3835 4519 1.197721 GACAGACCAAGCATTCCAACG 59.802 52.381 0.00 0.00 0.00 4.10
3836 4520 0.109597 CAGACCAAGCATTCCAACGC 60.110 55.000 0.00 0.00 0.00 4.84
3837 4521 1.154225 GACCAAGCATTCCAACGCG 60.154 57.895 3.53 3.53 0.00 6.01
3838 4522 2.504681 CCAAGCATTCCAACGCGC 60.505 61.111 5.73 0.00 0.00 6.86
3839 4523 2.871080 CAAGCATTCCAACGCGCG 60.871 61.111 30.96 30.96 0.00 6.86
3840 4524 4.101790 AAGCATTCCAACGCGCGG 62.102 61.111 35.22 17.35 0.00 6.46
3843 4527 3.864686 CATTCCAACGCGCGGGAG 61.865 66.667 35.22 21.97 34.02 4.30
3874 4558 4.974368 TTTTTGTCTGATTTGTGTCCGT 57.026 36.364 0.00 0.00 0.00 4.69
3875 4559 4.974368 TTTTGTCTGATTTGTGTCCGTT 57.026 36.364 0.00 0.00 0.00 4.44
3876 4560 4.545823 TTTGTCTGATTTGTGTCCGTTC 57.454 40.909 0.00 0.00 0.00 3.95
3877 4561 3.469008 TGTCTGATTTGTGTCCGTTCT 57.531 42.857 0.00 0.00 0.00 3.01
3878 4562 4.594123 TGTCTGATTTGTGTCCGTTCTA 57.406 40.909 0.00 0.00 0.00 2.10
3879 4563 4.304110 TGTCTGATTTGTGTCCGTTCTAC 58.696 43.478 0.00 0.00 0.00 2.59
3880 4564 4.038763 TGTCTGATTTGTGTCCGTTCTACT 59.961 41.667 0.00 0.00 0.00 2.57
3881 4565 4.621886 GTCTGATTTGTGTCCGTTCTACTC 59.378 45.833 0.00 0.00 0.00 2.59
3882 4566 3.921677 TGATTTGTGTCCGTTCTACTCC 58.078 45.455 0.00 0.00 0.00 3.85
3883 4567 2.427232 TTTGTGTCCGTTCTACTCCG 57.573 50.000 0.00 0.00 0.00 4.63
3902 4586 9.804758 CTACTCCGTTTCTCTCTTGTTTATATT 57.195 33.333 0.00 0.00 0.00 1.28
3927 4611 5.355071 TGATCATGCACTGAAAACCACTATC 59.645 40.000 0.00 0.00 37.44 2.08
3959 4643 1.002366 CAATCACGCGCTTTAGAGCT 58.998 50.000 5.73 0.00 46.96 4.09
4072 7302 3.520290 TTGGAGCTCTACCAATACACG 57.480 47.619 14.64 0.00 41.64 4.49
4088 7318 9.490379 ACCAATACACGATATTCCTTCTTTATC 57.510 33.333 0.00 0.00 0.00 1.75
4136 7366 7.915293 TCTCTAAAAACAACTGTCAACTCAA 57.085 32.000 0.00 0.00 0.00 3.02
4140 7371 8.519526 TCTAAAAACAACTGTCAACTCAATGTT 58.480 29.630 0.00 0.00 39.92 2.71
4154 7385 8.632679 TCAACTCAATGTTTTCTCTTAATGCTT 58.367 29.630 0.00 0.00 36.63 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.590553 TGCTGGGTGGGAGTGGGA 62.591 66.667 0.00 0.00 0.00 4.37
1 2 3.574074 CTTGCTGGGTGGGAGTGGG 62.574 68.421 0.00 0.00 0.00 4.61
2 3 2.034687 CTTGCTGGGTGGGAGTGG 59.965 66.667 0.00 0.00 0.00 4.00
3 4 2.034687 CCTTGCTGGGTGGGAGTG 59.965 66.667 0.00 0.00 0.00 3.51
4 5 2.121963 TCCTTGCTGGGTGGGAGT 60.122 61.111 0.00 0.00 36.20 3.85
5 6 2.673523 CTCCTTGCTGGGTGGGAG 59.326 66.667 0.00 0.00 39.22 4.30
20 21 1.603739 GGTGGTTGGTTGCCTCCTC 60.604 63.158 0.00 0.00 36.87 3.71
22 23 2.197324 TGGTGGTTGGTTGCCTCC 59.803 61.111 0.00 0.00 39.43 4.30
52 53 2.370403 TGACCCCAACCCCAACCT 60.370 61.111 0.00 0.00 0.00 3.50
206 219 2.792947 GCAATAGCCGACGGGGAGA 61.793 63.158 17.22 0.00 38.47 3.71
331 365 4.075793 TGGGGGAGGGAGGACTCG 62.076 72.222 0.00 0.00 38.39 4.18
340 374 3.330720 AGCGGAAAGTGGGGGAGG 61.331 66.667 0.00 0.00 0.00 4.30
348 382 2.430367 GTGGTGGGAGCGGAAAGT 59.570 61.111 0.00 0.00 0.00 2.66
350 384 2.852075 AGGTGGTGGGAGCGGAAA 60.852 61.111 0.00 0.00 0.00 3.13
351 385 3.319198 GAGGTGGTGGGAGCGGAA 61.319 66.667 0.00 0.00 0.00 4.30
354 388 3.775654 GAGGAGGTGGTGGGAGCG 61.776 72.222 0.00 0.00 0.00 5.03
355 389 3.403558 GGAGGAGGTGGTGGGAGC 61.404 72.222 0.00 0.00 0.00 4.70
356 390 1.687493 GAGGAGGAGGTGGTGGGAG 60.687 68.421 0.00 0.00 0.00 4.30
357 391 2.450243 GAGGAGGAGGTGGTGGGA 59.550 66.667 0.00 0.00 0.00 4.37
358 392 2.689034 GGAGGAGGAGGTGGTGGG 60.689 72.222 0.00 0.00 0.00 4.61
359 393 2.689034 GGGAGGAGGAGGTGGTGG 60.689 72.222 0.00 0.00 0.00 4.61
360 394 0.842467 AAAGGGAGGAGGAGGTGGTG 60.842 60.000 0.00 0.00 0.00 4.17
361 395 0.547954 GAAAGGGAGGAGGAGGTGGT 60.548 60.000 0.00 0.00 0.00 4.16
362 396 1.275421 GGAAAGGGAGGAGGAGGTGG 61.275 65.000 0.00 0.00 0.00 4.61
363 397 1.275421 GGGAAAGGGAGGAGGAGGTG 61.275 65.000 0.00 0.00 0.00 4.00
364 398 1.083141 GGGAAAGGGAGGAGGAGGT 59.917 63.158 0.00 0.00 0.00 3.85
365 399 1.694525 GGGGAAAGGGAGGAGGAGG 60.695 68.421 0.00 0.00 0.00 4.30
366 400 0.253394 AAGGGGAAAGGGAGGAGGAG 60.253 60.000 0.00 0.00 0.00 3.69
367 401 0.253207 GAAGGGGAAAGGGAGGAGGA 60.253 60.000 0.00 0.00 0.00 3.71
368 402 1.282653 GGAAGGGGAAAGGGAGGAGG 61.283 65.000 0.00 0.00 0.00 4.30
369 403 1.282653 GGGAAGGGGAAAGGGAGGAG 61.283 65.000 0.00 0.00 0.00 3.69
370 404 1.230182 GGGAAGGGGAAAGGGAGGA 60.230 63.158 0.00 0.00 0.00 3.71
371 405 2.317378 GGGGAAGGGGAAAGGGAGG 61.317 68.421 0.00 0.00 0.00 4.30
372 406 2.317378 GGGGGAAGGGGAAAGGGAG 61.317 68.421 0.00 0.00 0.00 4.30
373 407 2.204401 GGGGGAAGGGGAAAGGGA 60.204 66.667 0.00 0.00 0.00 4.20
374 408 2.536897 TGGGGGAAGGGGAAAGGG 60.537 66.667 0.00 0.00 0.00 3.95
375 409 2.770827 GTGGGGGAAGGGGAAAGG 59.229 66.667 0.00 0.00 0.00 3.11
464 783 2.993899 GACTTGATTCGAGCTCGGAAAA 59.006 45.455 33.98 22.73 40.29 2.29
548 867 4.722535 AAGGCAGCGGGGGAGAGA 62.723 66.667 0.00 0.00 0.00 3.10
549 868 3.273788 AAAAGGCAGCGGGGGAGAG 62.274 63.158 0.00 0.00 0.00 3.20
550 869 3.256960 AAAAGGCAGCGGGGGAGA 61.257 61.111 0.00 0.00 0.00 3.71
562 890 1.602920 GCGGTCAAAAGGCTCAAAAGG 60.603 52.381 0.00 0.00 0.00 3.11
575 903 1.333619 GAAGCAAGTTTGAGCGGTCAA 59.666 47.619 25.16 25.16 41.13 3.18
576 904 0.944386 GAAGCAAGTTTGAGCGGTCA 59.056 50.000 14.39 14.39 35.48 4.02
577 905 1.195674 GAGAAGCAAGTTTGAGCGGTC 59.804 52.381 7.89 7.89 35.48 4.79
579 907 1.196354 CAGAGAAGCAAGTTTGAGCGG 59.804 52.381 0.00 0.00 35.48 5.52
581 909 1.068679 GGCAGAGAAGCAAGTTTGAGC 60.069 52.381 0.00 0.00 35.83 4.26
582 910 1.538950 GGGCAGAGAAGCAAGTTTGAG 59.461 52.381 0.00 0.00 35.83 3.02
583 911 1.609208 GGGCAGAGAAGCAAGTTTGA 58.391 50.000 0.00 0.00 35.83 2.69
585 913 0.540597 GGGGGCAGAGAAGCAAGTTT 60.541 55.000 0.00 0.00 35.83 2.66
586 914 1.075659 GGGGGCAGAGAAGCAAGTT 59.924 57.895 0.00 0.00 35.83 2.66
587 915 2.759795 GGGGGCAGAGAAGCAAGT 59.240 61.111 0.00 0.00 35.83 3.16
605 933 0.734253 CTATGGCTAGCCGCGATCAC 60.734 60.000 28.28 2.72 38.15 3.06
623 952 1.212935 GTCACTCATAACCCCATGGCT 59.787 52.381 6.09 0.00 33.59 4.75
624 953 1.064758 TGTCACTCATAACCCCATGGC 60.065 52.381 6.09 0.00 33.59 4.40
625 954 2.026356 TGTGTCACTCATAACCCCATGG 60.026 50.000 4.14 4.14 37.80 3.66
626 955 3.273434 CTGTGTCACTCATAACCCCATG 58.727 50.000 4.27 0.00 0.00 3.66
627 956 2.356125 GCTGTGTCACTCATAACCCCAT 60.356 50.000 4.27 0.00 0.00 4.00
628 957 1.003118 GCTGTGTCACTCATAACCCCA 59.997 52.381 4.27 0.00 0.00 4.96
653 982 1.576421 GAACAGCTGCGTCCAAAGG 59.424 57.895 15.27 0.00 0.00 3.11
741 1160 2.354259 GAAGATGGTGTGCCTCTGAAG 58.646 52.381 0.00 0.00 35.27 3.02
742 1161 1.003580 GGAAGATGGTGTGCCTCTGAA 59.996 52.381 0.00 0.00 35.27 3.02
743 1162 0.615331 GGAAGATGGTGTGCCTCTGA 59.385 55.000 0.00 0.00 35.27 3.27
744 1163 0.393537 GGGAAGATGGTGTGCCTCTG 60.394 60.000 0.00 0.00 35.27 3.35
745 1164 1.566298 GGGGAAGATGGTGTGCCTCT 61.566 60.000 0.00 0.00 35.27 3.69
747 1166 1.542375 AGGGGAAGATGGTGTGCCT 60.542 57.895 0.00 0.00 35.27 4.75
748 1167 1.379044 CAGGGGAAGATGGTGTGCC 60.379 63.158 0.00 0.00 0.00 5.01
749 1168 0.257039 ATCAGGGGAAGATGGTGTGC 59.743 55.000 0.00 0.00 0.00 4.57
850 1269 3.763671 CCGCTTGAGGCCAAAACT 58.236 55.556 5.01 0.00 37.74 2.66
858 1277 0.177604 AGAAGATCTGCCGCTTGAGG 59.822 55.000 0.00 0.00 0.00 3.86
861 1280 1.012841 GGAAGAAGATCTGCCGCTTG 58.987 55.000 0.00 0.00 31.20 4.01
865 1284 1.227380 CCGGGAAGAAGATCTGCCG 60.227 63.158 5.76 5.76 43.61 5.69
889 1308 4.794334 AGATCACGGTGGACTACTATCTT 58.206 43.478 8.50 0.00 0.00 2.40
890 1309 4.440826 AGATCACGGTGGACTACTATCT 57.559 45.455 8.50 4.50 0.00 1.98
891 1310 4.338682 ACAAGATCACGGTGGACTACTATC 59.661 45.833 8.50 2.17 0.00 2.08
892 1311 4.279145 ACAAGATCACGGTGGACTACTAT 58.721 43.478 8.50 0.00 0.00 2.12
893 1312 3.693807 ACAAGATCACGGTGGACTACTA 58.306 45.455 8.50 0.00 0.00 1.82
894 1313 2.526432 ACAAGATCACGGTGGACTACT 58.474 47.619 8.50 0.00 0.00 2.57
895 1314 2.993899 CAACAAGATCACGGTGGACTAC 59.006 50.000 8.50 0.00 0.00 2.73
896 1315 2.611971 GCAACAAGATCACGGTGGACTA 60.612 50.000 8.50 0.00 0.00 2.59
897 1316 1.878102 GCAACAAGATCACGGTGGACT 60.878 52.381 8.50 5.33 0.00 3.85
898 1317 0.517316 GCAACAAGATCACGGTGGAC 59.483 55.000 8.50 3.02 0.00 4.02
899 1318 0.605319 GGCAACAAGATCACGGTGGA 60.605 55.000 8.50 0.00 0.00 4.02
900 1319 1.586154 GGGCAACAAGATCACGGTGG 61.586 60.000 8.50 0.00 39.74 4.61
901 1320 0.888736 TGGGCAACAAGATCACGGTG 60.889 55.000 0.56 0.56 39.74 4.94
902 1321 0.889186 GTGGGCAACAAGATCACGGT 60.889 55.000 0.00 0.00 39.74 4.83
903 1322 0.888736 TGTGGGCAACAAGATCACGG 60.889 55.000 0.00 0.00 35.24 4.94
904 1323 0.518636 CTGTGGGCAACAAGATCACG 59.481 55.000 0.00 0.00 38.67 4.35
905 1324 1.808945 CTCTGTGGGCAACAAGATCAC 59.191 52.381 0.00 0.00 38.67 3.06
906 1325 1.421268 ACTCTGTGGGCAACAAGATCA 59.579 47.619 10.06 0.00 38.67 2.92
913 1332 1.498865 CGTGTGACTCTGTGGGCAAC 61.499 60.000 0.00 0.00 0.00 4.17
915 1334 2.421314 CGTGTGACTCTGTGGGCA 59.579 61.111 0.00 0.00 0.00 5.36
919 1346 0.385751 ACAGACCGTGTGACTCTGTG 59.614 55.000 2.08 0.00 42.45 3.66
929 1356 2.358737 GCAGGGGAACAGACCGTG 60.359 66.667 0.00 0.00 44.48 4.94
937 1364 0.180642 GCTTAGGTAGGCAGGGGAAC 59.819 60.000 0.00 0.00 0.00 3.62
938 1365 0.044244 AGCTTAGGTAGGCAGGGGAA 59.956 55.000 0.00 0.00 0.00 3.97
939 1366 0.398664 GAGCTTAGGTAGGCAGGGGA 60.399 60.000 0.00 0.00 0.00 4.81
940 1367 0.399233 AGAGCTTAGGTAGGCAGGGG 60.399 60.000 0.00 0.00 0.00 4.79
943 1370 2.159028 GGAACAGAGCTTAGGTAGGCAG 60.159 54.545 0.00 0.00 0.00 4.85
944 1371 1.831736 GGAACAGAGCTTAGGTAGGCA 59.168 52.381 0.00 0.00 0.00 4.75
945 1372 1.831736 TGGAACAGAGCTTAGGTAGGC 59.168 52.381 0.00 0.00 0.00 3.93
997 1443 4.506255 GGGAAGGCCGTCCATGGG 62.506 72.222 34.59 0.00 39.70 4.00
999 1445 3.781307 TCGGGAAGGCCGTCCATG 61.781 66.667 34.59 26.42 39.70 3.66
1065 1511 2.795297 CTCTCGCTCCACTCGTCC 59.205 66.667 0.00 0.00 0.00 4.79
1625 2074 4.492160 GCGTGGCCAGATCGACGA 62.492 66.667 17.59 0.00 33.64 4.20
1754 2209 0.898320 CGGGCTCTTCCTCTTTCTCA 59.102 55.000 0.00 0.00 34.39 3.27
1819 2274 2.279784 GGCCCGCTCGATCTTCAG 60.280 66.667 0.00 0.00 0.00 3.02
1881 2336 0.251832 TCTCGCCCTTCTTCACCTCT 60.252 55.000 0.00 0.00 0.00 3.69
1995 2453 1.005748 CACTTGAGACGAGCTGCCA 60.006 57.895 0.00 0.00 0.00 4.92
2232 2724 7.557358 TCATGCTGCAATTTCCTATTCTCTAAA 59.443 33.333 6.36 0.00 0.00 1.85
2234 2726 6.594744 TCATGCTGCAATTTCCTATTCTCTA 58.405 36.000 6.36 0.00 0.00 2.43
2236 2728 5.278364 CCTCATGCTGCAATTTCCTATTCTC 60.278 44.000 6.36 0.00 0.00 2.87
2242 2734 2.519771 TCCTCATGCTGCAATTTCCT 57.480 45.000 6.36 0.00 0.00 3.36
2331 2829 7.337942 CAGAATGAAAAGCTCCTTTAGTACCAT 59.662 37.037 0.00 0.00 39.69 3.55
2332 2830 6.655003 CAGAATGAAAAGCTCCTTTAGTACCA 59.345 38.462 0.00 0.00 39.69 3.25
2333 2831 6.655425 ACAGAATGAAAAGCTCCTTTAGTACC 59.345 38.462 0.00 0.00 39.69 3.34
2360 2863 5.008217 GTCTGAGCCATCACAGTACTAGTAG 59.992 48.000 1.87 0.00 35.84 2.57
2568 3081 2.726241 GACATGCGGTTTTTCTCTTTGC 59.274 45.455 0.00 0.00 0.00 3.68
2589 3102 9.167311 ACTACTTATGCCAAGATTTTAGTTCTG 57.833 33.333 2.41 0.00 0.00 3.02
2650 3177 3.122780 TGCGTTTATGTCAGTGAACGATG 59.877 43.478 16.39 0.00 45.44 3.84
2657 3185 2.964123 CGTGTTTGCGTTTATGTCAGTG 59.036 45.455 0.00 0.00 0.00 3.66
2727 3255 6.856426 CAGAGCATGCATTATATGTCAACAAG 59.144 38.462 21.98 0.00 0.00 3.16
2829 3441 1.527311 GACCTCGGATCGCTTTAATGC 59.473 52.381 3.30 3.30 0.00 3.56
2902 3531 1.679153 TCGCAGCAGGTTCGTATCATA 59.321 47.619 0.00 0.00 0.00 2.15
2909 3538 2.507992 CTCCTCGCAGCAGGTTCG 60.508 66.667 9.83 0.00 34.76 3.95
2930 3559 3.131396 CAAAGTCGAAGCAACACCTAGT 58.869 45.455 0.00 0.00 0.00 2.57
2984 3613 9.750125 AAATGAAAATCTGTCTTGGAACTAAAC 57.250 29.630 0.00 0.00 0.00 2.01
3015 3644 5.008019 CCGTACAAGATGCTGCTTTTCATAT 59.992 40.000 0.00 0.00 0.00 1.78
3087 3726 6.208644 ACAAAACAAGATGAGTTACATGCAC 58.791 36.000 0.00 0.00 39.56 4.57
3189 3828 4.130118 AGAATCACAGTTCACAGGTGTTC 58.870 43.478 0.00 0.00 34.27 3.18
3228 3867 0.810648 TTTCCGCACATGAATGGAGC 59.189 50.000 0.00 0.00 0.00 4.70
3300 3969 7.410800 TCCGTTATTGCGTTTCGATATTTAT 57.589 32.000 0.00 0.00 0.00 1.40
3305 3974 3.000523 GCTTCCGTTATTGCGTTTCGATA 59.999 43.478 0.00 0.00 0.00 2.92
3467 4143 3.984193 ATCCGGCTTCCAGCACTGC 62.984 63.158 0.00 0.00 44.75 4.40
3490 4166 4.338118 ACAGTCACACAAAAATACCACCTG 59.662 41.667 0.00 0.00 0.00 4.00
3500 4176 5.825151 TCATACCATCAACAGTCACACAAAA 59.175 36.000 0.00 0.00 0.00 2.44
3526 4205 3.258228 TGCATACACAGTACACGAATGG 58.742 45.455 0.00 0.00 0.00 3.16
3600 4279 3.957497 TGTACAGCACATGGAAAAAGGTT 59.043 39.130 0.00 0.00 30.04 3.50
3634 4313 8.716909 TCTGAAAAGTTTCAAAACAAAATGACC 58.283 29.630 7.80 0.00 45.61 4.02
3685 4364 2.368548 GGCAAAAAGGGTGTCCAGAAAT 59.631 45.455 0.00 0.00 34.83 2.17
3689 4368 1.118838 TTGGCAAAAAGGGTGTCCAG 58.881 50.000 0.00 0.00 34.83 3.86
3714 4393 2.357154 GGTACACTGGCAGATGGGATTT 60.357 50.000 23.66 2.40 0.00 2.17
3717 4396 1.271840 GGGTACACTGGCAGATGGGA 61.272 60.000 23.66 3.78 0.00 4.37
3718 4397 1.224592 GGGTACACTGGCAGATGGG 59.775 63.158 23.66 9.89 0.00 4.00
3737 4420 4.349365 CCTAAAGTATTGGGGGCTTTCAA 58.651 43.478 0.00 0.00 33.71 2.69
3761 4445 4.988598 AGCCGTGCGTGGGAGTTG 62.989 66.667 0.00 0.00 0.00 3.16
3762 4446 4.681978 GAGCCGTGCGTGGGAGTT 62.682 66.667 0.00 0.00 0.00 3.01
3767 4451 3.039202 GATTTGGAGCCGTGCGTGG 62.039 63.158 0.00 0.00 0.00 4.94
3768 4452 2.480555 GATTTGGAGCCGTGCGTG 59.519 61.111 0.00 0.00 0.00 5.34
3769 4453 3.118454 CGATTTGGAGCCGTGCGT 61.118 61.111 0.00 0.00 0.00 5.24
3770 4454 3.083600 GACGATTTGGAGCCGTGCG 62.084 63.158 0.00 0.00 36.60 5.34
3771 4455 2.750888 GGACGATTTGGAGCCGTGC 61.751 63.158 0.00 0.00 36.60 5.34
3772 4456 2.452813 CGGACGATTTGGAGCCGTG 61.453 63.158 0.00 0.00 36.60 4.94
3773 4457 2.125673 CGGACGATTTGGAGCCGT 60.126 61.111 0.00 0.00 39.41 5.68
3774 4458 2.125673 ACGGACGATTTGGAGCCG 60.126 61.111 0.00 0.00 46.83 5.52
3775 4459 2.106683 CCACGGACGATTTGGAGCC 61.107 63.158 0.00 0.00 31.39 4.70
3776 4460 2.106683 CCCACGGACGATTTGGAGC 61.107 63.158 0.00 0.00 31.39 4.70
3777 4461 1.019278 CACCCACGGACGATTTGGAG 61.019 60.000 0.00 0.00 31.39 3.86
3778 4462 1.004320 CACCCACGGACGATTTGGA 60.004 57.895 0.00 0.00 31.39 3.53
3779 4463 1.296056 GACACCCACGGACGATTTGG 61.296 60.000 0.00 0.00 0.00 3.28
3780 4464 1.296056 GGACACCCACGGACGATTTG 61.296 60.000 0.00 0.00 0.00 2.32
3781 4465 1.004200 GGACACCCACGGACGATTT 60.004 57.895 0.00 0.00 0.00 2.17
3782 4466 2.660802 GGACACCCACGGACGATT 59.339 61.111 0.00 0.00 0.00 3.34
3783 4467 3.755628 CGGACACCCACGGACGAT 61.756 66.667 0.00 0.00 0.00 3.73
3785 4469 3.795499 AAACGGACACCCACGGACG 62.795 63.158 0.00 0.00 0.00 4.79
3786 4470 2.109593 AAACGGACACCCACGGAC 59.890 61.111 0.00 0.00 0.00 4.79
3787 4471 2.109387 CAAACGGACACCCACGGA 59.891 61.111 0.00 0.00 0.00 4.69
3788 4472 2.975799 CCAAACGGACACCCACGG 60.976 66.667 0.00 0.00 0.00 4.94
3789 4473 2.975799 CCCAAACGGACACCCACG 60.976 66.667 0.00 0.00 0.00 4.94
3790 4474 2.596338 CCCCAAACGGACACCCAC 60.596 66.667 0.00 0.00 0.00 4.61
3791 4475 1.351080 TAACCCCAAACGGACACCCA 61.351 55.000 0.00 0.00 0.00 4.51
3792 4476 0.178995 TTAACCCCAAACGGACACCC 60.179 55.000 0.00 0.00 0.00 4.61
3793 4477 1.337703 GTTTAACCCCAAACGGACACC 59.662 52.381 0.00 0.00 0.00 4.16
3794 4478 2.780065 GTTTAACCCCAAACGGACAC 57.220 50.000 0.00 0.00 0.00 3.67
3800 4484 2.291465 GTCTGTCCGTTTAACCCCAAAC 59.709 50.000 0.00 0.00 35.49 2.93
3801 4485 2.574450 GTCTGTCCGTTTAACCCCAAA 58.426 47.619 0.00 0.00 0.00 3.28
3802 4486 1.202794 GGTCTGTCCGTTTAACCCCAA 60.203 52.381 0.00 0.00 0.00 4.12
3803 4487 0.397564 GGTCTGTCCGTTTAACCCCA 59.602 55.000 0.00 0.00 0.00 4.96
3804 4488 0.397564 TGGTCTGTCCGTTTAACCCC 59.602 55.000 0.00 0.00 39.52 4.95
3805 4489 2.148768 CTTGGTCTGTCCGTTTAACCC 58.851 52.381 0.00 0.00 39.52 4.11
3806 4490 1.534163 GCTTGGTCTGTCCGTTTAACC 59.466 52.381 0.00 0.00 39.52 2.85
3807 4491 2.215196 TGCTTGGTCTGTCCGTTTAAC 58.785 47.619 0.00 0.00 39.52 2.01
3808 4492 2.623878 TGCTTGGTCTGTCCGTTTAA 57.376 45.000 0.00 0.00 39.52 1.52
3809 4493 2.851263 ATGCTTGGTCTGTCCGTTTA 57.149 45.000 0.00 0.00 39.52 2.01
3810 4494 1.880027 GAATGCTTGGTCTGTCCGTTT 59.120 47.619 0.00 0.00 39.52 3.60
3811 4495 1.523758 GAATGCTTGGTCTGTCCGTT 58.476 50.000 0.00 0.00 39.52 4.44
3812 4496 0.321653 GGAATGCTTGGTCTGTCCGT 60.322 55.000 0.00 0.00 39.52 4.69
3813 4497 0.321564 TGGAATGCTTGGTCTGTCCG 60.322 55.000 0.00 0.00 39.52 4.79
3814 4498 1.541588 GTTGGAATGCTTGGTCTGTCC 59.458 52.381 0.00 0.00 0.00 4.02
3815 4499 1.197721 CGTTGGAATGCTTGGTCTGTC 59.802 52.381 0.00 0.00 0.00 3.51
3816 4500 1.238439 CGTTGGAATGCTTGGTCTGT 58.762 50.000 0.00 0.00 0.00 3.41
3817 4501 0.109597 GCGTTGGAATGCTTGGTCTG 60.110 55.000 0.00 0.00 37.92 3.51
3818 4502 1.577328 CGCGTTGGAATGCTTGGTCT 61.577 55.000 0.00 0.00 38.77 3.85
3819 4503 1.154225 CGCGTTGGAATGCTTGGTC 60.154 57.895 0.00 0.00 38.77 4.02
3820 4504 2.953821 CGCGTTGGAATGCTTGGT 59.046 55.556 0.00 0.00 38.77 3.67
3821 4505 2.504681 GCGCGTTGGAATGCTTGG 60.505 61.111 8.43 0.00 38.77 3.61
3822 4506 2.871080 CGCGCGTTGGAATGCTTG 60.871 61.111 24.19 0.00 38.77 4.01
3823 4507 4.101790 CCGCGCGTTGGAATGCTT 62.102 61.111 29.95 0.00 38.77 3.91
3826 4510 3.864686 CTCCCGCGCGTTGGAATG 61.865 66.667 29.95 13.84 0.00 2.67
3853 4537 4.974368 ACGGACACAAATCAGACAAAAA 57.026 36.364 0.00 0.00 0.00 1.94
3854 4538 4.638421 AGAACGGACACAAATCAGACAAAA 59.362 37.500 0.00 0.00 0.00 2.44
3855 4539 4.196193 AGAACGGACACAAATCAGACAAA 58.804 39.130 0.00 0.00 0.00 2.83
3856 4540 3.804036 AGAACGGACACAAATCAGACAA 58.196 40.909 0.00 0.00 0.00 3.18
3857 4541 3.469008 AGAACGGACACAAATCAGACA 57.531 42.857 0.00 0.00 0.00 3.41
3858 4542 4.557205 AGTAGAACGGACACAAATCAGAC 58.443 43.478 0.00 0.00 0.00 3.51
3859 4543 4.321750 GGAGTAGAACGGACACAAATCAGA 60.322 45.833 0.00 0.00 0.00 3.27
3860 4544 3.927142 GGAGTAGAACGGACACAAATCAG 59.073 47.826 0.00 0.00 0.00 2.90
3861 4545 3.613193 CGGAGTAGAACGGACACAAATCA 60.613 47.826 0.00 0.00 0.00 2.57
3862 4546 2.921754 CGGAGTAGAACGGACACAAATC 59.078 50.000 0.00 0.00 0.00 2.17
3863 4547 2.298163 ACGGAGTAGAACGGACACAAAT 59.702 45.455 0.00 0.00 41.94 2.32
3864 4548 1.682854 ACGGAGTAGAACGGACACAAA 59.317 47.619 0.00 0.00 41.94 2.83
3865 4549 1.321474 ACGGAGTAGAACGGACACAA 58.679 50.000 0.00 0.00 41.94 3.33
3866 4550 1.321474 AACGGAGTAGAACGGACACA 58.679 50.000 0.00 0.00 45.00 3.72
3867 4551 2.030451 AGAAACGGAGTAGAACGGACAC 60.030 50.000 0.00 0.00 45.00 3.67
3868 4552 2.227388 GAGAAACGGAGTAGAACGGACA 59.773 50.000 0.00 0.00 45.00 4.02
3869 4553 2.487372 AGAGAAACGGAGTAGAACGGAC 59.513 50.000 0.00 0.00 45.00 4.79
3870 4554 2.746362 GAGAGAAACGGAGTAGAACGGA 59.254 50.000 0.00 0.00 45.00 4.69
3871 4555 2.748532 AGAGAGAAACGGAGTAGAACGG 59.251 50.000 0.00 0.00 45.00 4.44
3872 4556 4.159857 CAAGAGAGAAACGGAGTAGAACG 58.840 47.826 0.00 0.00 45.00 3.95
3873 4557 5.123805 ACAAGAGAGAAACGGAGTAGAAC 57.876 43.478 0.00 0.00 45.00 3.01
3874 4558 5.786264 AACAAGAGAGAAACGGAGTAGAA 57.214 39.130 0.00 0.00 45.00 2.10
3875 4559 5.786264 AAACAAGAGAGAAACGGAGTAGA 57.214 39.130 0.00 0.00 45.00 2.59
3876 4560 9.804758 AATATAAACAAGAGAGAAACGGAGTAG 57.195 33.333 0.00 0.00 45.00 2.57
3879 4563 9.151471 TCAAATATAAACAAGAGAGAAACGGAG 57.849 33.333 0.00 0.00 0.00 4.63
3880 4564 9.667107 ATCAAATATAAACAAGAGAGAAACGGA 57.333 29.630 0.00 0.00 0.00 4.69
3881 4565 9.922305 GATCAAATATAAACAAGAGAGAAACGG 57.078 33.333 0.00 0.00 0.00 4.44
3902 4586 3.890756 AGTGGTTTTCAGTGCATGATCAA 59.109 39.130 0.00 0.00 37.89 2.57
3927 4611 4.196349 CGCGTGATTGAAGAAATATCGTG 58.804 43.478 0.00 0.00 32.70 4.35
3992 4676 7.772292 ACACTCCAATATATATCCATGCATCAC 59.228 37.037 0.00 0.00 0.00 3.06
4042 7272 7.432148 TTGGTAGAGCTCCAATATACAAAGA 57.568 36.000 10.93 0.00 39.62 2.52
4052 7282 3.093814 TCGTGTATTGGTAGAGCTCCAA 58.906 45.455 10.93 9.11 46.82 3.53


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

AutoCloner maintained by Alex Coulton.