Multiple sequence alignment - TraesCS5B01G564600

Loading Multiple Alignment...

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 TraesCS5B01G564600 chr5B 100.000 2852 0 0 1 2852 709916004 709918855 0.000000e+00 5267.0
1 TraesCS5B01G564600 chr5B 82.889 1426 175 37 615 2015 710077411 710076030 0.000000e+00 1218.0
2 TraesCS5B01G564600 chr5B 90.521 422 40 0 1 422 710077965 710077544 2.480000e-155 558.0
3 TraesCS5B01G564600 chr5B 99.355 155 1 0 1 155 710023953 710024107 6.020000e-72 281.0
4 TraesCS5B01G564600 chr5B 88.108 185 16 4 2073 2253 710076010 710075828 6.190000e-52 215.0
5 TraesCS5B01G564600 chr5B 77.447 235 42 9 221 451 448314184 448314411 2.310000e-26 130.0
6 TraesCS5B01G564600 chr5B 94.872 39 2 0 2623 2661 709918593 709918631 8.530000e-06 62.1
7 TraesCS5B01G564600 chr5B 94.872 39 2 0 2590 2628 709918626 709918664 8.530000e-06 62.1
8 TraesCS5B01G564600 chr5D 84.826 1061 137 15 1 1048 556925591 556924542 0.000000e+00 1046.0
9 TraesCS5B01G564600 chr5D 81.328 723 106 23 129 833 556922055 556921344 6.900000e-156 560.0
10 TraesCS5B01G564600 chr5D 85.373 335 47 2 1554 1887 556923961 556923628 2.100000e-91 346.0
11 TraesCS5B01G564600 chr5D 77.882 425 71 15 1084 1507 556924470 556924068 2.840000e-60 243.0
12 TraesCS5B01G564600 chr5D 86.387 191 26 0 1621 1811 556914389 556914199 2.880000e-50 209.0
13 TraesCS5B01G564600 chr5D 77.447 235 42 9 221 451 375585819 375586046 2.310000e-26 130.0
14 TraesCS5B01G564600 chr5D 83.838 99 12 3 1688 1784 559680053 559679957 1.090000e-14 91.6
15 TraesCS5B01G564600 chr4A 84.680 1077 117 19 1 1055 605424956 605423906 0.000000e+00 1031.0
16 TraesCS5B01G564600 chr4A 86.409 596 70 6 1 589 605542673 605542082 2.400000e-180 641.0
17 TraesCS5B01G564600 chr4A 77.046 941 158 32 1091 2012 605423903 605423002 3.300000e-134 488.0
18 TraesCS5B01G564600 chr4A 81.100 418 53 14 2201 2597 605422875 605422463 7.670000e-81 311.0
19 TraesCS5B01G564600 chr6A 77.433 483 83 14 4 464 611309409 611308931 6.060000e-67 265.0
20 TraesCS5B01G564600 chr6A 83.432 169 28 0 1607 1775 611307806 611307638 1.060000e-34 158.0
21 TraesCS5B01G564600 chr6D 86.111 144 20 0 1640 1783 464729165 464729022 3.800000e-34 156.0
22 TraesCS5B01G564600 chr5A 76.395 233 44 9 221 449 476767743 476767968 6.460000e-22 115.0
23 TraesCS5B01G564600 chr7B 81.731 104 19 0 1680 1783 720117920 720117817 1.410000e-13 87.9


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 TraesCS5B01G564600 chr5B 709916004 709918855 2851 False 1797.066667 5267 96.581333 1 2852 3 chr5B.!!$F3 2851
1 TraesCS5B01G564600 chr5B 710075828 710077965 2137 True 663.666667 1218 87.172667 1 2253 3 chr5B.!!$R1 2252
2 TraesCS5B01G564600 chr5D 556921344 556925591 4247 True 548.750000 1046 82.352250 1 1887 4 chr5D.!!$R3 1886
3 TraesCS5B01G564600 chr4A 605542082 605542673 591 True 641.000000 641 86.409000 1 589 1 chr4A.!!$R1 588
4 TraesCS5B01G564600 chr4A 605422463 605424956 2493 True 610.000000 1031 80.942000 1 2597 3 chr4A.!!$R2 2596
5 TraesCS5B01G564600 chr6A 611307638 611309409 1771 True 211.500000 265 80.432500 4 1775 2 chr6A.!!$R1 1771

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
466 485 0.600782 GGCTTTGTGGTGTGGCAATG 60.601 55.0 0.00 0.0 0.00 2.82 F
1297 1402 0.106708 ACACAAGATGGTGCACGAGT 59.893 50.0 11.45 0.0 42.55 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1532 1703 0.040958 CGCACCTTGCAAGTCTTCAC 60.041 55.0 24.35 7.28 45.36 3.18 R
2743 3126 0.101399 ATTGCGTCTCACGGCTCTAG 59.899 55.0 0.00 0.00 42.82 2.43 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 7.117956 ACGCTACAATTCTTTCTCTTCTTTACC 59.882 37.037 0.00 0.00 0.00 2.85
135 136 1.969923 AGATCATCAGTCTGGCTAGCC 59.030 52.381 27.71 27.71 0.00 3.93
139 140 3.161067 TCATCAGTCTGGCTAGCCTATC 58.839 50.000 33.07 21.51 36.94 2.08
148 149 0.896019 GCTAGCCTATCTGGGAGCGA 60.896 60.000 2.29 0.00 36.00 4.93
327 343 5.696822 CATCTGTTGAATCTTGTTGTCCAG 58.303 41.667 0.00 0.00 0.00 3.86
331 347 3.855255 TGAATCTTGTTGTCCAGGTGA 57.145 42.857 0.00 0.00 0.00 4.02
332 348 4.163441 TGAATCTTGTTGTCCAGGTGAA 57.837 40.909 0.00 0.00 0.00 3.18
363 379 9.492730 ACCCTGTATATCTTTTGGAAATCATTT 57.507 29.630 0.00 0.00 0.00 2.32
378 397 1.133513 TCATTTGATGGCGGCCCTAAT 60.134 47.619 17.97 7.77 0.00 1.73
446 465 5.983333 ATCAAGTATGGGGAGAGAACATT 57.017 39.130 0.00 0.00 0.00 2.71
464 483 1.260538 TTGGCTTTGTGGTGTGGCAA 61.261 50.000 0.00 0.00 41.48 4.52
466 485 0.600782 GGCTTTGTGGTGTGGCAATG 60.601 55.000 0.00 0.00 0.00 2.82
468 487 1.339610 GCTTTGTGGTGTGGCAATGTA 59.660 47.619 0.00 0.00 0.00 2.29
489 508 6.991938 TGTAAGAAACATGAGGGAAATTTGG 58.008 36.000 0.00 0.00 31.43 3.28
494 516 1.832998 CATGAGGGAAATTTGGGGTGG 59.167 52.381 0.00 0.00 0.00 4.61
500 522 2.604139 GGAAATTTGGGGTGGTTCTGA 58.396 47.619 0.00 0.00 0.00 3.27
501 523 2.969262 GGAAATTTGGGGTGGTTCTGAA 59.031 45.455 0.00 0.00 0.00 3.02
531 574 2.418746 GCGCCTTGATACCTCTTCTGAA 60.419 50.000 0.00 0.00 0.00 3.02
532 575 3.452474 CGCCTTGATACCTCTTCTGAAG 58.548 50.000 11.18 11.18 0.00 3.02
533 576 3.131223 CGCCTTGATACCTCTTCTGAAGA 59.869 47.826 18.40 18.40 35.87 2.87
602 645 2.381725 ACTAGCCTTTCGTACAAGCC 57.618 50.000 0.00 0.00 0.00 4.35
635 680 7.844493 ACCGTTGGGATATAGATAGTTTACA 57.156 36.000 0.00 0.00 36.97 2.41
636 681 7.893658 ACCGTTGGGATATAGATAGTTTACAG 58.106 38.462 0.00 0.00 36.97 2.74
752 797 1.065998 GGGTTGCACCATACTTCGGTA 60.066 52.381 7.49 0.00 41.02 4.02
766 811 8.520351 CCATACTTCGGTACATCTCACATATTA 58.480 37.037 0.00 0.00 32.78 0.98
783 828 2.863132 TTACCTTTCTGGCCGCTTTA 57.137 45.000 0.00 0.00 40.22 1.85
858 906 4.137116 TGACACTGTAATCACCTATGGC 57.863 45.455 0.00 0.00 0.00 4.40
861 909 4.295201 ACACTGTAATCACCTATGGCCTA 58.705 43.478 3.32 0.00 0.00 3.93
927 975 1.627864 TGATGTCACCTCGGACTTGA 58.372 50.000 0.00 0.00 38.61 3.02
1000 1066 3.323775 ACTAGGTGTCCAAGGAAAAGGA 58.676 45.455 0.00 0.00 0.00 3.36
1076 1142 2.963498 GACCGGCAGTCAAGTAAAAC 57.037 50.000 0.00 0.00 45.55 2.43
1122 1227 4.523813 CGAATGTATTTTGCGGGACATAC 58.476 43.478 0.00 0.00 32.31 2.39
1134 1239 2.882137 CGGGACATACCAAAAGTTGTGT 59.118 45.455 0.00 0.00 41.20 3.72
1211 1316 0.526524 GTCGTCCAGAGGATTGCTCG 60.527 60.000 0.00 0.00 32.73 5.03
1221 1326 0.531974 GGATTGCTCGGTATCGCCAA 60.532 55.000 4.24 4.24 36.97 4.52
1222 1327 0.861837 GATTGCTCGGTATCGCCAAG 59.138 55.000 7.26 0.00 36.97 3.61
1226 1331 0.876342 GCTCGGTATCGCCAAGAAGG 60.876 60.000 0.00 0.00 41.84 3.46
1281 1386 2.789409 ATCTTGGCCCACTTCTACAC 57.211 50.000 0.00 0.00 0.00 2.90
1287 1392 2.290260 TGGCCCACTTCTACACAAGATG 60.290 50.000 0.00 0.00 33.05 2.90
1293 1398 3.187227 CACTTCTACACAAGATGGTGCAC 59.813 47.826 8.80 8.80 42.55 4.57
1294 1399 2.078849 TCTACACAAGATGGTGCACG 57.921 50.000 11.45 0.00 42.55 5.34
1297 1402 0.106708 ACACAAGATGGTGCACGAGT 59.893 50.000 11.45 0.00 42.55 4.18
1299 1404 1.726791 CACAAGATGGTGCACGAGTAC 59.273 52.381 11.45 3.21 31.10 2.73
1335 1440 8.812513 ACTTTGATCATCAGTCCATTATCAAA 57.187 30.769 0.00 0.00 39.64 2.69
1336 1441 9.417561 ACTTTGATCATCAGTCCATTATCAAAT 57.582 29.630 0.00 0.00 40.54 2.32
1372 1477 5.074652 ACAGAGGTATGGCTGAGTAGGTATA 59.925 44.000 0.00 0.00 36.07 1.47
1398 1503 2.427320 GGCACTGCTGTGGACAGA 59.573 61.111 23.15 0.00 46.59 3.41
1419 1524 4.530161 AGAGAGTCTAGTGATGCTTTGGTT 59.470 41.667 0.00 0.00 0.00 3.67
1431 1539 1.433053 CTTTGGTTCGTGTGTGCCGA 61.433 55.000 0.00 0.00 0.00 5.54
1442 1550 1.148310 GTGTGCCGAATGATATCCCG 58.852 55.000 0.00 1.56 0.00 5.14
1467 1575 6.923508 GCTATATGGTTTATCTTTTGGCCAAC 59.076 38.462 20.35 4.23 0.00 3.77
1469 1577 2.297597 TGGTTTATCTTTTGGCCAACCG 59.702 45.455 20.35 12.39 39.70 4.44
1495 1603 3.313249 TGAAATGCTGCCAATCTACGATG 59.687 43.478 0.00 0.00 0.00 3.84
1507 1618 0.179094 CTACGATGGCGGCCAAAGTA 60.179 55.000 27.70 27.23 43.17 2.24
1514 1685 1.359459 GGCGGCCAAAGTAGTCTTCG 61.359 60.000 15.62 0.00 32.90 3.79
1532 1703 0.729116 CGGTCAGTAGCATGGCTTTG 59.271 55.000 0.00 0.00 40.44 2.77
1537 1708 3.076621 TCAGTAGCATGGCTTTGTGAAG 58.923 45.455 0.00 0.00 40.44 3.02
1543 1714 2.669364 CATGGCTTTGTGAAGACTTGC 58.331 47.619 0.00 0.00 41.75 4.01
1545 1716 2.098614 TGGCTTTGTGAAGACTTGCAA 58.901 42.857 0.00 0.00 41.75 4.08
1589 1760 4.475944 CTCCATCGGACAATTTTGTTGTC 58.524 43.478 11.41 11.41 45.89 3.18
1612 1831 6.370994 GTCGACTAAAGATGATATACCGGAGA 59.629 42.308 9.46 0.00 0.00 3.71
1634 1853 3.914984 CGGAGGAGTGCAGAAAAGA 57.085 52.632 0.00 0.00 0.00 2.52
1651 1870 0.175302 AGAGCAGCTGTTGGAGATCG 59.825 55.000 16.64 0.00 0.00 3.69
1657 1876 2.094286 CAGCTGTTGGAGATCGAAGAGT 60.094 50.000 5.25 0.00 43.63 3.24
1658 1877 2.564947 AGCTGTTGGAGATCGAAGAGTT 59.435 45.455 0.00 0.00 43.63 3.01
1789 2008 1.909302 ACTACAGACTTGGGGATGTGG 59.091 52.381 0.00 0.00 0.00 4.17
1792 2011 0.692476 CAGACTTGGGGATGTGGTGA 59.308 55.000 0.00 0.00 0.00 4.02
1816 2035 1.179174 CCCCATCGAGATGACGGCTA 61.179 60.000 14.12 0.00 41.20 3.93
1822 2044 1.136110 TCGAGATGACGGCTAATGCAA 59.864 47.619 0.00 0.00 41.91 4.08
1856 2078 1.272490 CCACTACGCCTTCTGACTTCA 59.728 52.381 0.00 0.00 0.00 3.02
1869 2091 5.661056 TCTGACTTCATCCTCAACGTTAT 57.339 39.130 0.00 0.00 0.00 1.89
1889 2112 2.235891 TGACGGCTGATCGGTATGTAT 58.764 47.619 0.00 0.00 0.00 2.29
1898 2206 7.148390 CGGCTGATCGGTATGTATATATAGGAG 60.148 44.444 2.89 0.00 0.00 3.69
1940 2249 6.630443 CACGCTTGCTTACATCTATGAATTTC 59.370 38.462 0.00 0.00 0.00 2.17
2038 2353 1.340405 ACCATCAACTCTCCCATGCAC 60.340 52.381 0.00 0.00 0.00 4.57
2054 2369 5.635280 CCCATGCACGTATAGATAGAGTTTG 59.365 44.000 0.00 0.00 0.00 2.93
2056 2371 6.363626 CCATGCACGTATAGATAGAGTTTGTC 59.636 42.308 0.00 0.00 0.00 3.18
2069 2384 4.377897 AGAGTTTGTCGTCCTTACCAAAG 58.622 43.478 0.00 0.00 0.00 2.77
2071 2386 4.773013 AGTTTGTCGTCCTTACCAAAGAA 58.227 39.130 0.00 0.00 34.37 2.52
2107 2424 9.213799 AGAGTTTCTTGTCTAATGTGAATTCTC 57.786 33.333 7.05 3.61 0.00 2.87
2161 2485 6.490721 ACTTGTACCGATTTAAACCAATCCAA 59.509 34.615 0.00 0.00 30.38 3.53
2188 2512 7.039504 GCCATACATTTTCATGGATCAATAGGT 60.040 37.037 4.80 0.00 43.80 3.08
2209 2541 3.093814 TGTTCCGACTCTATTGTGCCTA 58.906 45.455 0.00 0.00 0.00 3.93
2223 2555 9.330063 TCTATTGTGCCTACTTGATCAAATAAG 57.670 33.333 9.88 6.94 0.00 1.73
2253 2585 7.336931 GCTTCAATGTGGTTTTCTTATCCTCTA 59.663 37.037 0.00 0.00 0.00 2.43
2254 2586 8.561738 TTCAATGTGGTTTTCTTATCCTCTAC 57.438 34.615 0.00 0.00 0.00 2.59
2264 2600 5.970501 TCTTATCCTCTACTTTTTCCCCC 57.029 43.478 0.00 0.00 0.00 5.40
2272 2608 5.457633 CCTCTACTTTTTCCCCCTCTTTTGA 60.458 44.000 0.00 0.00 0.00 2.69
2283 2619 1.533625 CTCTTTTGACGGCCAATGGA 58.466 50.000 2.05 0.00 34.23 3.41
2288 2652 0.322456 TTGACGGCCAATGGAGGAAG 60.322 55.000 2.05 0.00 0.00 3.46
2289 2653 1.198094 TGACGGCCAATGGAGGAAGA 61.198 55.000 2.05 0.00 0.00 2.87
2302 2666 5.407407 TGGAGGAAGACAGAGTATTGTTC 57.593 43.478 0.00 0.00 0.00 3.18
2356 2721 5.006153 TGTCATTATCTTCACCGATCGTT 57.994 39.130 15.09 0.00 0.00 3.85
2361 2729 0.245539 TCTTCACCGATCGTTGACCC 59.754 55.000 15.44 0.00 0.00 4.46
2375 2743 4.082300 TCGTTGACCCGTGCTAGTTATTTA 60.082 41.667 0.00 0.00 0.00 1.40
2384 2752 6.370718 CCCGTGCTAGTTATTTACACTTTCTT 59.629 38.462 0.00 0.00 0.00 2.52
2387 2755 9.953825 CGTGCTAGTTATTTACACTTTCTTTAG 57.046 33.333 0.00 0.00 0.00 1.85
2421 2789 9.280174 CACTAGGTGGTTTGTTTCTATTTTCTA 57.720 33.333 0.00 0.00 0.00 2.10
2424 2792 8.706322 AGGTGGTTTGTTTCTATTTTCTACAT 57.294 30.769 0.00 0.00 0.00 2.29
2438 2806 9.650539 CTATTTTCTACATATATGAGCTGCACT 57.349 33.333 19.63 0.00 0.00 4.40
2439 2807 7.719778 TTTTCTACATATATGAGCTGCACTG 57.280 36.000 19.63 0.00 0.00 3.66
2462 2838 6.450545 TGTATCCGAATTTGCAATTTCAACA 58.549 32.000 25.56 20.49 0.00 3.33
2470 2846 8.157813 CGAATTTGCAATTTCAACAGTGAATAG 58.842 33.333 25.56 8.16 43.29 1.73
2471 2847 6.768029 TTTGCAATTTCAACAGTGAATAGC 57.232 33.333 0.00 0.00 43.29 2.97
2489 2869 9.626045 GTGAATAGCACTAATTAAACAAAAGCT 57.374 29.630 0.00 0.00 44.27 3.74
2514 2894 5.689383 TCTTTTGGTAGTCAAGCATGAAC 57.311 39.130 0.00 0.00 37.30 3.18
2583 2966 7.841915 TGTGAGATGAATATTTCTTTGCGTA 57.158 32.000 0.00 0.00 0.00 4.42
2593 2976 9.465494 GAATATTTCTTTGCGTATACATCATCG 57.535 33.333 3.32 0.00 0.00 3.84
2598 2981 3.612472 TGCGTATACATCATCGTCGAA 57.388 42.857 0.00 0.00 0.00 3.71
2601 2984 3.727227 GCGTATACATCATCGTCGAACAA 59.273 43.478 0.00 0.00 0.00 2.83
2604 2987 6.111696 CGTATACATCATCGTCGAACAAAAC 58.888 40.000 0.00 0.00 0.00 2.43
2605 2988 3.806316 ACATCATCGTCGAACAAAACC 57.194 42.857 0.00 0.00 0.00 3.27
2606 2989 3.135225 ACATCATCGTCGAACAAAACCA 58.865 40.909 0.00 0.00 0.00 3.67
2607 2990 3.751175 ACATCATCGTCGAACAAAACCAT 59.249 39.130 0.00 0.00 0.00 3.55
2608 2991 4.932799 ACATCATCGTCGAACAAAACCATA 59.067 37.500 0.00 0.00 0.00 2.74
2611 2994 4.992319 TCATCGTCGAACAAAACCATAAGT 59.008 37.500 0.00 0.00 0.00 2.24
2612 2995 4.718858 TCGTCGAACAAAACCATAAGTG 57.281 40.909 0.00 0.00 0.00 3.16
2615 2998 5.293814 TCGTCGAACAAAACCATAAGTGAAA 59.706 36.000 0.00 0.00 0.00 2.69
2616 2999 5.966503 CGTCGAACAAAACCATAAGTGAAAA 59.033 36.000 0.00 0.00 0.00 2.29
2617 3000 6.635239 CGTCGAACAAAACCATAAGTGAAAAT 59.365 34.615 0.00 0.00 0.00 1.82
2618 3001 7.799447 CGTCGAACAAAACCATAAGTGAAAATA 59.201 33.333 0.00 0.00 0.00 1.40
2626 3009 9.887406 AAAACCATAAGTGAAAATAGTACAACG 57.113 29.630 0.00 0.00 0.00 4.10
2627 3010 8.836268 AACCATAAGTGAAAATAGTACAACGA 57.164 30.769 0.00 0.00 0.00 3.85
2628 3011 8.248117 ACCATAAGTGAAAATAGTACAACGAC 57.752 34.615 0.00 0.00 0.00 4.34
2629 3012 7.062605 ACCATAAGTGAAAATAGTACAACGACG 59.937 37.037 0.00 0.00 0.00 5.12
2630 3013 7.274033 CCATAAGTGAAAATAGTACAACGACGA 59.726 37.037 0.00 0.00 0.00 4.20
2631 3014 8.641155 CATAAGTGAAAATAGTACAACGACGAA 58.359 33.333 0.00 0.00 0.00 3.85
2632 3015 6.443876 AGTGAAAATAGTACAACGACGAAC 57.556 37.500 0.00 0.00 0.00 3.95
2633 3016 5.978919 AGTGAAAATAGTACAACGACGAACA 59.021 36.000 0.00 0.00 0.00 3.18
2634 3017 6.476380 AGTGAAAATAGTACAACGACGAACAA 59.524 34.615 0.00 0.00 0.00 2.83
2635 3018 7.010367 AGTGAAAATAGTACAACGACGAACAAA 59.990 33.333 0.00 0.00 0.00 2.83
2636 3019 7.635587 GTGAAAATAGTACAACGACGAACAAAA 59.364 33.333 0.00 0.00 0.00 2.44
2637 3020 7.635587 TGAAAATAGTACAACGACGAACAAAAC 59.364 33.333 0.00 0.00 0.00 2.43
2638 3021 3.931285 AGTACAACGACGAACAAAACC 57.069 42.857 0.00 0.00 0.00 3.27
2640 3023 3.872771 AGTACAACGACGAACAAAACCAT 59.127 39.130 0.00 0.00 0.00 3.55
2641 3024 5.049167 AGTACAACGACGAACAAAACCATA 58.951 37.500 0.00 0.00 0.00 2.74
2642 3025 4.879104 ACAACGACGAACAAAACCATAA 57.121 36.364 0.00 0.00 0.00 1.90
2643 3026 4.839796 ACAACGACGAACAAAACCATAAG 58.160 39.130 0.00 0.00 0.00 1.73
2644 3027 4.333372 ACAACGACGAACAAAACCATAAGT 59.667 37.500 0.00 0.00 0.00 2.24
2645 3028 4.461992 ACGACGAACAAAACCATAAGTG 57.538 40.909 0.00 0.00 0.00 3.16
2646 3029 4.121317 ACGACGAACAAAACCATAAGTGA 58.879 39.130 0.00 0.00 0.00 3.41
2647 3030 4.571580 ACGACGAACAAAACCATAAGTGAA 59.428 37.500 0.00 0.00 0.00 3.18
2649 3032 5.966503 CGACGAACAAAACCATAAGTGAAAA 59.033 36.000 0.00 0.00 0.00 2.29
2651 3034 7.799447 CGACGAACAAAACCATAAGTGAAAATA 59.201 33.333 0.00 0.00 0.00 1.40
2652 3035 9.113876 GACGAACAAAACCATAAGTGAAAATAG 57.886 33.333 0.00 0.00 0.00 1.73
2653 3036 8.626526 ACGAACAAAACCATAAGTGAAAATAGT 58.373 29.630 0.00 0.00 0.00 2.12
2659 3042 9.887406 AAAACCATAAGTGAAAATAGTACAACG 57.113 29.630 0.00 0.00 0.00 4.10
2660 3043 8.836268 AACCATAAGTGAAAATAGTACAACGA 57.164 30.769 0.00 0.00 0.00 3.85
2661 3044 8.836268 ACCATAAGTGAAAATAGTACAACGAA 57.164 30.769 0.00 0.00 0.00 3.85
2662 3045 8.932791 ACCATAAGTGAAAATAGTACAACGAAG 58.067 33.333 0.00 0.00 0.00 3.79
2663 3046 7.903431 CCATAAGTGAAAATAGTACAACGAAGC 59.097 37.037 0.00 0.00 0.00 3.86
2664 3047 6.854496 AAGTGAAAATAGTACAACGAAGCA 57.146 33.333 0.00 0.00 0.00 3.91
2665 3048 6.467723 AGTGAAAATAGTACAACGAAGCAG 57.532 37.500 0.00 0.00 0.00 4.24
2666 3049 6.220930 AGTGAAAATAGTACAACGAAGCAGA 58.779 36.000 0.00 0.00 0.00 4.26
2667 3050 6.366332 AGTGAAAATAGTACAACGAAGCAGAG 59.634 38.462 0.00 0.00 0.00 3.35
2668 3051 5.120208 TGAAAATAGTACAACGAAGCAGAGC 59.880 40.000 0.00 0.00 0.00 4.09
2669 3052 2.257974 TAGTACAACGAAGCAGAGCG 57.742 50.000 0.00 0.00 0.00 5.03
2670 3053 0.388649 AGTACAACGAAGCAGAGCGG 60.389 55.000 0.00 0.00 0.00 5.52
2671 3054 0.388134 GTACAACGAAGCAGAGCGGA 60.388 55.000 0.00 0.00 0.00 5.54
2692 3075 3.837112 GGCAAAATCCGGCGCCAT 61.837 61.111 28.98 10.88 44.25 4.40
2693 3076 2.583045 GCAAAATCCGGCGCCATG 60.583 61.111 28.98 17.39 0.00 3.66
2694 3077 2.884367 CAAAATCCGGCGCCATGT 59.116 55.556 28.98 5.24 0.00 3.21
2695 3078 1.516821 CAAAATCCGGCGCCATGTG 60.517 57.895 28.98 9.99 0.00 3.21
2696 3079 3.355203 AAAATCCGGCGCCATGTGC 62.355 57.895 28.98 0.00 38.45 4.57
2703 3086 2.126346 GCGCCATGTGCCAAACTC 60.126 61.111 0.00 0.00 36.24 3.01
2704 3087 2.629656 GCGCCATGTGCCAAACTCT 61.630 57.895 0.00 0.00 36.24 3.24
2705 3088 1.305219 GCGCCATGTGCCAAACTCTA 61.305 55.000 0.00 0.00 36.24 2.43
2706 3089 1.164411 CGCCATGTGCCAAACTCTAA 58.836 50.000 0.00 0.00 36.24 2.10
2707 3090 1.131126 CGCCATGTGCCAAACTCTAAG 59.869 52.381 0.00 0.00 36.24 2.18
2708 3091 2.436417 GCCATGTGCCAAACTCTAAGA 58.564 47.619 0.00 0.00 0.00 2.10
2709 3092 3.019564 GCCATGTGCCAAACTCTAAGAT 58.980 45.455 0.00 0.00 0.00 2.40
2710 3093 3.181493 GCCATGTGCCAAACTCTAAGATG 60.181 47.826 0.00 0.00 0.00 2.90
2711 3094 3.379372 CCATGTGCCAAACTCTAAGATGG 59.621 47.826 0.00 0.00 36.00 3.51
2712 3095 3.071874 TGTGCCAAACTCTAAGATGGG 57.928 47.619 0.00 0.00 33.45 4.00
2713 3096 2.290896 TGTGCCAAACTCTAAGATGGGG 60.291 50.000 0.00 0.00 33.45 4.96
2714 3097 1.340991 TGCCAAACTCTAAGATGGGGC 60.341 52.381 0.00 0.00 40.51 5.80
2715 3098 2.024306 GCCAAACTCTAAGATGGGGCC 61.024 57.143 0.00 0.00 34.17 5.80
2716 3099 1.566231 CCAAACTCTAAGATGGGGCCT 59.434 52.381 0.84 0.00 0.00 5.19
2717 3100 2.777692 CCAAACTCTAAGATGGGGCCTA 59.222 50.000 0.84 0.00 0.00 3.93
2718 3101 3.433740 CCAAACTCTAAGATGGGGCCTAC 60.434 52.174 0.84 0.00 0.00 3.18
2719 3102 3.423058 AACTCTAAGATGGGGCCTACT 57.577 47.619 0.84 0.00 0.00 2.57
2722 3105 2.370189 CTCTAAGATGGGGCCTACTTGG 59.630 54.545 0.84 8.94 39.35 3.61
2730 3113 3.081409 GCCTACTTGGGCGAGGGA 61.081 66.667 0.00 0.00 42.82 4.20
2740 3123 4.816984 GCGAGGGACGGAGGGAGA 62.817 72.222 0.00 0.00 42.83 3.71
2741 3124 2.517402 CGAGGGACGGAGGGAGAG 60.517 72.222 0.00 0.00 38.46 3.20
2743 3126 4.467107 AGGGACGGAGGGAGAGGC 62.467 72.222 0.00 0.00 0.00 4.70
2744 3127 4.467107 GGGACGGAGGGAGAGGCT 62.467 72.222 0.00 0.00 0.00 4.58
2745 3128 2.601868 GGACGGAGGGAGAGGCTA 59.398 66.667 0.00 0.00 0.00 3.93
2746 3129 1.529713 GGACGGAGGGAGAGGCTAG 60.530 68.421 0.00 0.00 0.00 3.42
2747 3130 1.532728 GACGGAGGGAGAGGCTAGA 59.467 63.158 0.00 0.00 0.00 2.43
2759 3142 2.278271 GCTAGAGCCGTGAGACGC 60.278 66.667 0.00 0.00 40.91 5.19
2760 3143 3.052620 GCTAGAGCCGTGAGACGCA 62.053 63.158 0.00 0.00 40.91 5.24
2762 3145 0.101399 CTAGAGCCGTGAGACGCAAT 59.899 55.000 0.00 0.00 40.91 3.56
2763 3146 1.333931 CTAGAGCCGTGAGACGCAATA 59.666 52.381 0.00 0.00 40.91 1.90
2764 3147 0.179134 AGAGCCGTGAGACGCAATAC 60.179 55.000 0.00 0.00 40.91 1.89
2774 3157 4.758692 CGCAATACGCTCCCATCT 57.241 55.556 0.00 0.00 39.08 2.90
2775 3158 2.992089 CGCAATACGCTCCCATCTT 58.008 52.632 0.00 0.00 39.08 2.40
2776 3159 1.299541 CGCAATACGCTCCCATCTTT 58.700 50.000 0.00 0.00 39.08 2.52
2777 3160 2.479837 CGCAATACGCTCCCATCTTTA 58.520 47.619 0.00 0.00 39.08 1.85
2778 3161 3.067106 CGCAATACGCTCCCATCTTTAT 58.933 45.455 0.00 0.00 39.08 1.40
2779 3162 3.123621 CGCAATACGCTCCCATCTTTATC 59.876 47.826 0.00 0.00 39.08 1.75
2783 3166 2.398588 ACGCTCCCATCTTTATCCAGA 58.601 47.619 0.00 0.00 0.00 3.86
2784 3167 2.103263 ACGCTCCCATCTTTATCCAGAC 59.897 50.000 0.00 0.00 0.00 3.51
2785 3168 2.103094 CGCTCCCATCTTTATCCAGACA 59.897 50.000 0.00 0.00 0.00 3.41
2786 3169 3.432186 CGCTCCCATCTTTATCCAGACAA 60.432 47.826 0.00 0.00 0.00 3.18
2787 3170 3.879892 GCTCCCATCTTTATCCAGACAAC 59.120 47.826 0.00 0.00 0.00 3.32
2788 3171 4.626287 GCTCCCATCTTTATCCAGACAACA 60.626 45.833 0.00 0.00 0.00 3.33
2789 3172 5.688807 CTCCCATCTTTATCCAGACAACAT 58.311 41.667 0.00 0.00 0.00 2.71
2791 3174 6.493166 TCCCATCTTTATCCAGACAACATTT 58.507 36.000 0.00 0.00 0.00 2.32
2793 3176 7.556275 TCCCATCTTTATCCAGACAACATTTAC 59.444 37.037 0.00 0.00 0.00 2.01
2794 3177 7.339212 CCCATCTTTATCCAGACAACATTTACA 59.661 37.037 0.00 0.00 0.00 2.41
2795 3178 8.184192 CCATCTTTATCCAGACAACATTTACAC 58.816 37.037 0.00 0.00 0.00 2.90
2796 3179 8.729756 CATCTTTATCCAGACAACATTTACACA 58.270 33.333 0.00 0.00 0.00 3.72
2798 3181 9.295825 TCTTTATCCAGACAACATTTACACAAT 57.704 29.630 0.00 0.00 0.00 2.71
2799 3182 9.559958 CTTTATCCAGACAACATTTACACAATC 57.440 33.333 0.00 0.00 0.00 2.67
2800 3183 8.628630 TTATCCAGACAACATTTACACAATCA 57.371 30.769 0.00 0.00 0.00 2.57
2804 3187 8.081633 TCCAGACAACATTTACACAATCATTTC 58.918 33.333 0.00 0.00 0.00 2.17
2805 3188 7.866898 CCAGACAACATTTACACAATCATTTCA 59.133 33.333 0.00 0.00 0.00 2.69
2806 3189 9.414295 CAGACAACATTTACACAATCATTTCAT 57.586 29.630 0.00 0.00 0.00 2.57
2807 3190 9.630098 AGACAACATTTACACAATCATTTCATC 57.370 29.630 0.00 0.00 0.00 2.92
2808 3191 9.409312 GACAACATTTACACAATCATTTCATCA 57.591 29.630 0.00 0.00 0.00 3.07
2809 3192 9.195411 ACAACATTTACACAATCATTTCATCAC 57.805 29.630 0.00 0.00 0.00 3.06
2810 3193 9.194271 CAACATTTACACAATCATTTCATCACA 57.806 29.630 0.00 0.00 0.00 3.58
2811 3194 9.932207 AACATTTACACAATCATTTCATCACAT 57.068 25.926 0.00 0.00 0.00 3.21
2821 3204 9.710979 CAATCATTTCATCACATAATTTTTGGC 57.289 29.630 0.00 0.00 0.00 4.52
2822 3205 9.451002 AATCATTTCATCACATAATTTTTGGCA 57.549 25.926 0.00 0.00 0.00 4.92
2823 3206 8.843885 TCATTTCATCACATAATTTTTGGCAA 57.156 26.923 0.00 0.00 0.00 4.52
2824 3207 8.719648 TCATTTCATCACATAATTTTTGGCAAC 58.280 29.630 0.00 0.00 0.00 4.17
2826 3209 5.486526 TCATCACATAATTTTTGGCAACCC 58.513 37.500 0.00 0.00 0.00 4.11
2829 3212 4.020662 TCACATAATTTTTGGCAACCCCTC 60.021 41.667 0.00 0.00 0.00 4.30
2831 3214 4.222810 ACATAATTTTTGGCAACCCCTCTC 59.777 41.667 0.00 0.00 0.00 3.20
2832 3215 2.702270 ATTTTTGGCAACCCCTCTCT 57.298 45.000 0.00 0.00 0.00 3.10
2833 3216 2.470057 TTTTTGGCAACCCCTCTCTT 57.530 45.000 0.00 0.00 0.00 2.85
2834 3217 2.470057 TTTTGGCAACCCCTCTCTTT 57.530 45.000 0.00 0.00 0.00 2.52
2835 3218 1.703411 TTTGGCAACCCCTCTCTTTG 58.297 50.000 0.00 0.00 0.00 2.77
2836 3219 0.827507 TTGGCAACCCCTCTCTTTGC 60.828 55.000 0.00 0.00 44.05 3.68
2837 3220 1.228552 GGCAACCCCTCTCTTTGCA 60.229 57.895 7.74 0.00 46.12 4.08
2838 3221 1.527433 GGCAACCCCTCTCTTTGCAC 61.527 60.000 7.74 0.00 46.12 4.57
2839 3222 0.823356 GCAACCCCTCTCTTTGCACA 60.823 55.000 0.76 0.00 44.17 4.57
2840 3223 1.915141 CAACCCCTCTCTTTGCACAT 58.085 50.000 0.00 0.00 0.00 3.21
2841 3224 1.815003 CAACCCCTCTCTTTGCACATC 59.185 52.381 0.00 0.00 0.00 3.06
2842 3225 1.067295 ACCCCTCTCTTTGCACATCA 58.933 50.000 0.00 0.00 0.00 3.07
2843 3226 1.637553 ACCCCTCTCTTTGCACATCAT 59.362 47.619 0.00 0.00 0.00 2.45
2844 3227 2.295885 CCCCTCTCTTTGCACATCATC 58.704 52.381 0.00 0.00 0.00 2.92
2845 3228 2.356432 CCCCTCTCTTTGCACATCATCA 60.356 50.000 0.00 0.00 0.00 3.07
2846 3229 2.943690 CCCTCTCTTTGCACATCATCAG 59.056 50.000 0.00 0.00 0.00 2.90
2847 3230 3.607741 CCTCTCTTTGCACATCATCAGT 58.392 45.455 0.00 0.00 0.00 3.41
2848 3231 4.008330 CCTCTCTTTGCACATCATCAGTT 58.992 43.478 0.00 0.00 0.00 3.16
2849 3232 4.458295 CCTCTCTTTGCACATCATCAGTTT 59.542 41.667 0.00 0.00 0.00 2.66
2850 3233 5.391736 CCTCTCTTTGCACATCATCAGTTTC 60.392 44.000 0.00 0.00 0.00 2.78
2851 3234 5.065235 TCTCTTTGCACATCATCAGTTTCA 58.935 37.500 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.379972 AGTAGTTGGATCTCCCACTCG 58.620 52.381 6.26 0.00 46.62 4.18
54 55 7.413109 CCGGTAAAGAAGAGAAAGAATTGTAGC 60.413 40.741 0.00 0.00 0.00 3.58
60 61 3.933332 CGCCGGTAAAGAAGAGAAAGAAT 59.067 43.478 1.90 0.00 0.00 2.40
124 125 0.972883 CCCAGATAGGCTAGCCAGAC 59.027 60.000 34.70 23.00 38.92 3.51
135 136 1.482593 ACCAAGTTCGCTCCCAGATAG 59.517 52.381 0.00 0.00 0.00 2.08
139 140 0.741221 GCTACCAAGTTCGCTCCCAG 60.741 60.000 0.00 0.00 0.00 4.45
148 149 2.629051 GACATAAGCGGCTACCAAGTT 58.371 47.619 1.35 0.00 0.00 2.66
331 347 5.491078 TCCAAAAGATATACAGGGTGAGGTT 59.509 40.000 0.00 0.00 0.00 3.50
332 348 5.036916 TCCAAAAGATATACAGGGTGAGGT 58.963 41.667 0.00 0.00 0.00 3.85
363 379 0.322456 GCATATTAGGGCCGCCATCA 60.322 55.000 12.58 0.00 0.00 3.07
399 418 5.830991 AGTGCCAGTAACAAACAAAAGGATA 59.169 36.000 0.00 0.00 0.00 2.59
446 465 1.047596 ATTGCCACACCACAAAGCCA 61.048 50.000 0.00 0.00 0.00 4.75
466 485 6.398095 CCCAAATTTCCCTCATGTTTCTTAC 58.602 40.000 0.00 0.00 0.00 2.34
468 487 4.286808 CCCCAAATTTCCCTCATGTTTCTT 59.713 41.667 0.00 0.00 0.00 2.52
477 496 1.899814 GAACCACCCCAAATTTCCCTC 59.100 52.381 0.00 0.00 0.00 4.30
483 502 2.825532 CGATTCAGAACCACCCCAAATT 59.174 45.455 0.00 0.00 0.00 1.82
484 503 2.446435 CGATTCAGAACCACCCCAAAT 58.554 47.619 0.00 0.00 0.00 2.32
486 505 0.037590 CCGATTCAGAACCACCCCAA 59.962 55.000 0.00 0.00 0.00 4.12
488 507 0.326927 TTCCGATTCAGAACCACCCC 59.673 55.000 0.00 0.00 0.00 4.95
489 508 1.810755 GTTTCCGATTCAGAACCACCC 59.189 52.381 0.00 0.00 0.00 4.61
494 516 0.518559 GCGCGTTTCCGATTCAGAAC 60.519 55.000 8.43 0.00 35.63 3.01
500 522 1.024579 ATCAAGGCGCGTTTCCGATT 61.025 50.000 13.51 0.00 35.63 3.34
501 523 0.179094 TATCAAGGCGCGTTTCCGAT 60.179 50.000 13.51 14.76 35.63 4.18
531 574 3.507622 GCAAGGCATAGAAAACAAGGTCT 59.492 43.478 0.00 0.00 0.00 3.85
532 575 3.367395 GGCAAGGCATAGAAAACAAGGTC 60.367 47.826 0.00 0.00 0.00 3.85
533 576 2.562738 GGCAAGGCATAGAAAACAAGGT 59.437 45.455 0.00 0.00 0.00 3.50
602 645 0.108329 ATCCCAACGGTTAGCGTGAG 60.108 55.000 10.94 6.46 0.00 3.51
635 680 1.215423 ACTTGGTTGAAAGGTCTGGCT 59.785 47.619 0.00 0.00 0.00 4.75
636 681 1.692411 ACTTGGTTGAAAGGTCTGGC 58.308 50.000 0.00 0.00 0.00 4.85
752 797 6.058183 GCCAGAAAGGTAATATGTGAGATGT 58.942 40.000 0.00 0.00 40.61 3.06
766 811 0.400594 ACTAAAGCGGCCAGAAAGGT 59.599 50.000 2.24 0.00 40.61 3.50
783 828 7.671302 TGTTTCTTATTACAGAGAAGAGCACT 58.329 34.615 0.00 0.00 33.77 4.40
867 915 1.416401 ACTTCAAGAGAGAAACCGCCA 59.584 47.619 0.00 0.00 0.00 5.69
927 975 4.013050 GAGTCTTTTCCTTTAGCCATGCT 58.987 43.478 0.00 0.00 43.41 3.79
1000 1066 2.036217 CCATGCAGTTTGACCACAACAT 59.964 45.455 0.00 0.00 35.63 2.71
1076 1142 0.461870 TTTCCTGATCACGGCCATCG 60.462 55.000 2.24 0.00 45.88 3.84
1122 1227 6.560253 AGCTTACTGATACACAACTTTTGG 57.440 37.500 0.00 0.00 34.12 3.28
1211 1316 0.539986 TCCACCTTCTTGGCGATACC 59.460 55.000 0.00 0.00 40.22 2.73
1221 1326 1.840635 GGGCTACTTGATCCACCTTCT 59.159 52.381 0.00 0.00 0.00 2.85
1222 1327 1.134068 GGGGCTACTTGATCCACCTTC 60.134 57.143 0.00 0.00 0.00 3.46
1226 1331 0.181350 CTGGGGGCTACTTGATCCAC 59.819 60.000 0.00 0.00 0.00 4.02
1269 1374 3.338249 CACCATCTTGTGTAGAAGTGGG 58.662 50.000 11.84 7.27 37.47 4.61
1275 1380 1.616374 TCGTGCACCATCTTGTGTAGA 59.384 47.619 12.15 0.00 38.52 2.59
1281 1386 1.359848 GGTACTCGTGCACCATCTTG 58.640 55.000 12.15 0.00 34.77 3.02
1287 1392 0.249398 AATCAGGGTACTCGTGCACC 59.751 55.000 12.15 0.00 0.00 5.01
1293 1398 3.611766 AAGTTGGAATCAGGGTACTCG 57.388 47.619 0.00 0.00 0.00 4.18
1294 1399 4.906618 TCAAAGTTGGAATCAGGGTACTC 58.093 43.478 0.00 0.00 0.00 2.59
1297 1402 5.512942 TGATCAAAGTTGGAATCAGGGTA 57.487 39.130 0.00 0.00 0.00 3.69
1299 1404 4.951715 TGATGATCAAAGTTGGAATCAGGG 59.048 41.667 0.00 0.00 0.00 4.45
1335 1440 9.062367 AGCCATACCTCTGTAATTATATGGAAT 57.938 33.333 18.53 8.04 40.98 3.01
1336 1441 8.321353 CAGCCATACCTCTGTAATTATATGGAA 58.679 37.037 18.53 0.00 40.98 3.53
1345 1450 4.835615 CCTACTCAGCCATACCTCTGTAAT 59.164 45.833 0.00 0.00 0.00 1.89
1347 1452 3.204606 ACCTACTCAGCCATACCTCTGTA 59.795 47.826 0.00 0.00 0.00 2.74
1357 1462 4.752621 TGGGTATATACCTACTCAGCCA 57.247 45.455 27.24 13.78 45.72 4.75
1372 1477 3.009115 AGCAGTGCCGGTGGGTAT 61.009 61.111 12.58 0.00 34.97 2.73
1398 1503 4.619394 CGAACCAAAGCATCACTAGACTCT 60.619 45.833 0.00 0.00 0.00 3.24
1419 1524 2.469826 GATATCATTCGGCACACACGA 58.530 47.619 0.00 0.00 38.78 4.35
1431 1539 8.938883 AGATAAACCATATAGCGGGATATCATT 58.061 33.333 4.83 0.00 33.24 2.57
1442 1550 6.648879 TGGCCAAAAGATAAACCATATAGC 57.351 37.500 0.61 0.00 0.00 2.97
1467 1575 3.830192 GGCAGCATTTCAGGGCGG 61.830 66.667 0.00 0.00 34.54 6.13
1469 1577 0.179092 GATTGGCAGCATTTCAGGGC 60.179 55.000 0.00 0.00 0.00 5.19
1495 1603 1.359459 CGAAGACTACTTTGGCCGCC 61.359 60.000 1.04 1.04 36.39 6.13
1507 1618 1.478510 CCATGCTACTGACCGAAGACT 59.521 52.381 0.00 0.00 0.00 3.24
1514 1685 1.470098 CACAAAGCCATGCTACTGACC 59.530 52.381 5.42 0.00 38.25 4.02
1532 1703 0.040958 CGCACCTTGCAAGTCTTCAC 60.041 55.000 24.35 7.28 45.36 3.18
1537 1708 1.237285 ACATCCGCACCTTGCAAGTC 61.237 55.000 24.35 12.18 45.36 3.01
1543 1714 2.746904 TGTCATTAACATCCGCACCTTG 59.253 45.455 0.00 0.00 31.20 3.61
1545 1716 2.779755 TGTCATTAACATCCGCACCT 57.220 45.000 0.00 0.00 31.20 4.00
1569 1740 3.058570 TCGACAACAAAATTGTCCGATGG 60.059 43.478 12.82 1.06 44.29 3.51
1589 1760 6.403418 GGTCTCCGGTATATCATCTTTAGTCG 60.403 46.154 0.00 0.00 0.00 4.18
1612 1831 3.846405 TTCTGCACTCCTCCGGGGT 62.846 63.158 0.00 0.00 36.25 4.95
1628 1847 2.498167 TCTCCAACAGCTGCTCTTTTC 58.502 47.619 15.27 0.00 0.00 2.29
1630 1849 2.709213 GATCTCCAACAGCTGCTCTTT 58.291 47.619 15.27 0.00 0.00 2.52
1634 1853 0.610174 TTCGATCTCCAACAGCTGCT 59.390 50.000 15.27 0.00 0.00 4.24
1651 1870 3.707102 AGCAGACCTACCCATAACTCTTC 59.293 47.826 0.00 0.00 0.00 2.87
1657 1876 2.679082 GAGGAGCAGACCTACCCATAA 58.321 52.381 0.00 0.00 40.73 1.90
1658 1877 1.133136 GGAGGAGCAGACCTACCCATA 60.133 57.143 0.00 0.00 40.73 2.74
1713 1932 1.305633 TCCTCTGGCTAGCAGTGCT 60.306 57.895 23.44 23.44 43.41 4.40
1716 1935 1.382420 CCCTCCTCTGGCTAGCAGT 60.382 63.158 18.24 0.00 0.00 4.40
1789 2008 0.179000 ATCTCGATGGGGCAGTTCAC 59.821 55.000 0.00 0.00 0.00 3.18
1792 2011 0.179000 GTCATCTCGATGGGGCAGTT 59.821 55.000 7.03 0.00 39.24 3.16
1816 2035 1.133025 GCGCTGACCAATAGTTGCATT 59.867 47.619 0.00 0.00 0.00 3.56
1822 2044 1.134788 GTAGTGGCGCTGACCAATAGT 60.135 52.381 11.58 0.00 40.68 2.12
1869 2091 1.682740 TACATACCGATCAGCCGTCA 58.317 50.000 0.00 0.00 0.00 4.35
1889 2112 7.813148 GCGTGCAGAAAGAAATACTCCTATATA 59.187 37.037 0.00 0.00 0.00 0.86
1898 2206 2.495939 CGTGCGTGCAGAAAGAAATAC 58.504 47.619 0.00 0.00 0.00 1.89
1940 2249 8.839343 TGCATCAAGTGATAAATACATACCAAG 58.161 33.333 0.00 0.00 32.63 3.61
2027 2342 4.918588 TCTATCTATACGTGCATGGGAGA 58.081 43.478 11.36 9.70 0.00 3.71
2038 2353 6.542574 AGGACGACAAACTCTATCTATACG 57.457 41.667 0.00 0.00 0.00 3.06
2077 2392 6.978338 TCACATTAGACAAGAAACTCTACGT 58.022 36.000 0.00 0.00 0.00 3.57
2078 2393 7.869016 TTCACATTAGACAAGAAACTCTACG 57.131 36.000 0.00 0.00 0.00 3.51
2107 2424 5.916883 CAGCATAACCTGACAAAGAAACAAG 59.083 40.000 0.00 0.00 34.77 3.16
2161 2485 6.989155 ATTGATCCATGAAAATGTATGGCT 57.011 33.333 0.00 0.00 42.82 4.75
2188 2512 1.899814 AGGCACAATAGAGTCGGAACA 59.100 47.619 0.00 0.00 0.00 3.18
2209 2541 6.882610 TGAAGCACACTTATTTGATCAAGT 57.117 33.333 8.41 8.52 35.82 3.16
2223 2555 4.045636 AGAAAACCACATTGAAGCACAC 57.954 40.909 0.00 0.00 0.00 3.82
2253 2585 2.956333 CGTCAAAAGAGGGGGAAAAAGT 59.044 45.455 0.00 0.00 0.00 2.66
2254 2586 2.296190 CCGTCAAAAGAGGGGGAAAAAG 59.704 50.000 0.00 0.00 0.00 2.27
2264 2600 1.470098 CTCCATTGGCCGTCAAAAGAG 59.530 52.381 0.00 0.00 39.05 2.85
2272 2608 1.299976 GTCTTCCTCCATTGGCCGT 59.700 57.895 0.00 0.00 0.00 5.68
2283 2619 6.672266 TGAAGAACAATACTCTGTCTTCCT 57.328 37.500 8.74 0.00 35.21 3.36
2335 2699 5.041287 TCAACGATCGGTGAAGATAATGAC 58.959 41.667 32.43 0.00 39.10 3.06
2349 2714 0.866061 CTAGCACGGGTCAACGATCG 60.866 60.000 14.88 14.88 37.61 3.69
2356 2721 4.221262 AGTGTAAATAACTAGCACGGGTCA 59.779 41.667 0.00 0.00 35.46 4.02
2361 2729 9.953825 CTAAAGAAAGTGTAAATAACTAGCACG 57.046 33.333 0.00 0.00 35.46 5.34
2375 2743 5.193679 AGTGGTTGCTTCTAAAGAAAGTGT 58.806 37.500 0.00 0.00 33.07 3.55
2421 2789 5.623141 CGGATACAGTGCAGCTCATATATGT 60.623 44.000 12.42 0.00 0.00 2.29
2424 2792 4.079253 TCGGATACAGTGCAGCTCATATA 58.921 43.478 0.00 0.00 0.00 0.86
2430 2798 2.679837 CAAATTCGGATACAGTGCAGCT 59.320 45.455 0.00 0.00 0.00 4.24
2432 2800 2.419673 TGCAAATTCGGATACAGTGCAG 59.580 45.455 0.00 0.00 35.72 4.41
2438 2806 6.450545 TGTTGAAATTGCAAATTCGGATACA 58.549 32.000 19.58 16.83 0.00 2.29
2439 2807 6.586082 ACTGTTGAAATTGCAAATTCGGATAC 59.414 34.615 19.58 14.99 0.00 2.24
2489 2869 7.360861 CGTTCATGCTTGACTACCAAAAGAATA 60.361 37.037 1.02 0.00 33.76 1.75
2496 2876 2.224426 ACCGTTCATGCTTGACTACCAA 60.224 45.455 1.02 0.00 0.00 3.67
2499 2879 3.064207 TGAACCGTTCATGCTTGACTAC 58.936 45.455 9.99 0.00 34.08 2.73
2514 2894 4.701956 ATGCTTTACTGGAAATGAACCG 57.298 40.909 0.00 0.00 0.00 4.44
2575 2958 3.972502 TCGACGATGATGTATACGCAAAG 59.027 43.478 0.00 1.33 0.00 2.77
2579 2962 3.294102 TGTTCGACGATGATGTATACGC 58.706 45.455 0.00 0.00 0.00 4.42
2583 2966 4.932799 TGGTTTTGTTCGACGATGATGTAT 59.067 37.500 0.00 0.00 0.00 2.29
2593 2976 7.924103 ATTTTCACTTATGGTTTTGTTCGAC 57.076 32.000 0.00 0.00 0.00 4.20
2601 2984 9.275398 TCGTTGTACTATTTTCACTTATGGTTT 57.725 29.630 0.00 0.00 0.00 3.27
2604 2987 7.274033 TCGTCGTTGTACTATTTTCACTTATGG 59.726 37.037 0.00 0.00 0.00 2.74
2605 2988 8.165212 TCGTCGTTGTACTATTTTCACTTATG 57.835 34.615 0.00 0.00 0.00 1.90
2606 2989 8.642020 GTTCGTCGTTGTACTATTTTCACTTAT 58.358 33.333 0.00 0.00 0.00 1.73
2607 2990 7.647318 TGTTCGTCGTTGTACTATTTTCACTTA 59.353 33.333 0.00 0.00 0.00 2.24
2608 2991 6.476380 TGTTCGTCGTTGTACTATTTTCACTT 59.524 34.615 0.00 0.00 0.00 3.16
2611 2994 6.825284 TTGTTCGTCGTTGTACTATTTTCA 57.175 33.333 0.00 0.00 0.00 2.69
2612 2995 7.110628 GGTTTTGTTCGTCGTTGTACTATTTTC 59.889 37.037 0.00 0.00 0.00 2.29
2615 2998 5.523188 TGGTTTTGTTCGTCGTTGTACTATT 59.477 36.000 0.00 0.00 0.00 1.73
2616 2999 5.049167 TGGTTTTGTTCGTCGTTGTACTAT 58.951 37.500 0.00 0.00 0.00 2.12
2617 3000 4.428209 TGGTTTTGTTCGTCGTTGTACTA 58.572 39.130 0.00 0.00 0.00 1.82
2618 3001 3.260740 TGGTTTTGTTCGTCGTTGTACT 58.739 40.909 0.00 0.00 0.00 2.73
2621 3004 4.333372 ACTTATGGTTTTGTTCGTCGTTGT 59.667 37.500 0.00 0.00 0.00 3.32
2622 3005 4.668837 CACTTATGGTTTTGTTCGTCGTTG 59.331 41.667 0.00 0.00 0.00 4.10
2624 3007 4.121317 TCACTTATGGTTTTGTTCGTCGT 58.879 39.130 0.00 0.00 0.00 4.34
2626 3009 7.924103 ATTTTCACTTATGGTTTTGTTCGTC 57.076 32.000 0.00 0.00 0.00 4.20
2627 3010 8.626526 ACTATTTTCACTTATGGTTTTGTTCGT 58.373 29.630 0.00 0.00 0.00 3.85
2633 3016 9.887406 CGTTGTACTATTTTCACTTATGGTTTT 57.113 29.630 0.00 0.00 0.00 2.43
2634 3017 9.275398 TCGTTGTACTATTTTCACTTATGGTTT 57.725 29.630 0.00 0.00 0.00 3.27
2635 3018 8.836268 TCGTTGTACTATTTTCACTTATGGTT 57.164 30.769 0.00 0.00 0.00 3.67
2636 3019 8.836268 TTCGTTGTACTATTTTCACTTATGGT 57.164 30.769 0.00 0.00 0.00 3.55
2637 3020 7.903431 GCTTCGTTGTACTATTTTCACTTATGG 59.097 37.037 0.00 0.00 0.00 2.74
2638 3021 8.440059 TGCTTCGTTGTACTATTTTCACTTATG 58.560 33.333 0.00 0.00 0.00 1.90
2640 3023 7.868922 TCTGCTTCGTTGTACTATTTTCACTTA 59.131 33.333 0.00 0.00 0.00 2.24
2641 3024 6.704493 TCTGCTTCGTTGTACTATTTTCACTT 59.296 34.615 0.00 0.00 0.00 3.16
2642 3025 6.220930 TCTGCTTCGTTGTACTATTTTCACT 58.779 36.000 0.00 0.00 0.00 3.41
2643 3026 6.462073 TCTGCTTCGTTGTACTATTTTCAC 57.538 37.500 0.00 0.00 0.00 3.18
2644 3027 5.120208 GCTCTGCTTCGTTGTACTATTTTCA 59.880 40.000 0.00 0.00 0.00 2.69
2645 3028 5.551893 GCTCTGCTTCGTTGTACTATTTTC 58.448 41.667 0.00 0.00 0.00 2.29
2646 3029 4.091509 CGCTCTGCTTCGTTGTACTATTTT 59.908 41.667 0.00 0.00 0.00 1.82
2647 3030 3.612860 CGCTCTGCTTCGTTGTACTATTT 59.387 43.478 0.00 0.00 0.00 1.40
2649 3032 2.479730 CCGCTCTGCTTCGTTGTACTAT 60.480 50.000 0.00 0.00 0.00 2.12
2651 3034 0.388649 CCGCTCTGCTTCGTTGTACT 60.389 55.000 0.00 0.00 0.00 2.73
2652 3035 0.388134 TCCGCTCTGCTTCGTTGTAC 60.388 55.000 0.00 0.00 0.00 2.90
2653 3036 0.109272 CTCCGCTCTGCTTCGTTGTA 60.109 55.000 0.00 0.00 0.00 2.41
2654 3037 1.373497 CTCCGCTCTGCTTCGTTGT 60.373 57.895 0.00 0.00 0.00 3.32
2655 3038 2.734673 GCTCCGCTCTGCTTCGTTG 61.735 63.158 0.00 0.00 0.00 4.10
2657 3040 4.443266 GGCTCCGCTCTGCTTCGT 62.443 66.667 0.00 0.00 0.00 3.85
2664 3047 3.628646 ATTTTGCCGGCTCCGCTCT 62.629 57.895 29.70 2.61 38.24 4.09
2665 3048 3.113386 GATTTTGCCGGCTCCGCTC 62.113 63.158 29.70 13.89 38.24 5.03
2666 3049 3.134127 GATTTTGCCGGCTCCGCT 61.134 61.111 29.70 8.49 38.24 5.52
2667 3050 4.193334 GGATTTTGCCGGCTCCGC 62.193 66.667 29.70 12.90 38.24 5.54
2676 3059 2.583045 CATGGCGCCGGATTTTGC 60.583 61.111 23.90 0.00 0.00 3.68
2677 3060 1.516821 CACATGGCGCCGGATTTTG 60.517 57.895 23.90 14.05 0.00 2.44
2679 3062 3.825611 GCACATGGCGCCGGATTT 61.826 61.111 23.90 0.00 0.00 2.17
2686 3069 1.305219 TAGAGTTTGGCACATGGCGC 61.305 55.000 0.00 0.00 46.16 6.53
2687 3070 1.131126 CTTAGAGTTTGGCACATGGCG 59.869 52.381 0.00 0.00 46.16 5.69
2689 3072 3.379372 CCATCTTAGAGTTTGGCACATGG 59.621 47.826 0.00 0.00 39.30 3.66
2690 3073 3.379372 CCCATCTTAGAGTTTGGCACATG 59.621 47.826 0.00 0.00 39.30 3.21
2692 3075 2.290896 CCCCATCTTAGAGTTTGGCACA 60.291 50.000 0.00 0.00 0.00 4.57
2693 3076 2.369394 CCCCATCTTAGAGTTTGGCAC 58.631 52.381 0.00 0.00 0.00 5.01
2694 3077 1.340991 GCCCCATCTTAGAGTTTGGCA 60.341 52.381 9.10 0.00 37.58 4.92
2695 3078 1.393603 GCCCCATCTTAGAGTTTGGC 58.606 55.000 0.00 0.00 0.00 4.52
2696 3079 1.566231 AGGCCCCATCTTAGAGTTTGG 59.434 52.381 0.00 0.00 0.00 3.28
2697 3080 3.456277 AGTAGGCCCCATCTTAGAGTTTG 59.544 47.826 0.00 0.00 0.00 2.93
2698 3081 3.737263 AGTAGGCCCCATCTTAGAGTTT 58.263 45.455 0.00 0.00 0.00 2.66
2699 3082 3.423058 AGTAGGCCCCATCTTAGAGTT 57.577 47.619 0.00 0.00 0.00 3.01
2700 3083 3.041946 CAAGTAGGCCCCATCTTAGAGT 58.958 50.000 0.00 0.00 0.00 3.24
2701 3084 2.370189 CCAAGTAGGCCCCATCTTAGAG 59.630 54.545 0.00 0.00 0.00 2.43
2702 3085 2.408565 CCAAGTAGGCCCCATCTTAGA 58.591 52.381 0.00 0.00 0.00 2.10
2703 3086 1.421646 CCCAAGTAGGCCCCATCTTAG 59.578 57.143 0.00 0.00 35.39 2.18
2704 3087 1.518367 CCCAAGTAGGCCCCATCTTA 58.482 55.000 0.00 0.00 35.39 2.10
2705 3088 2.321720 CCCAAGTAGGCCCCATCTT 58.678 57.895 0.00 0.00 35.39 2.40
2706 3089 4.089839 CCCAAGTAGGCCCCATCT 57.910 61.111 0.00 0.00 35.39 2.90
2714 3097 2.901042 GTCCCTCGCCCAAGTAGG 59.099 66.667 0.00 0.00 37.03 3.18
2715 3098 2.494918 CGTCCCTCGCCCAAGTAG 59.505 66.667 0.00 0.00 0.00 2.57
2716 3099 3.072468 CCGTCCCTCGCCCAAGTA 61.072 66.667 0.00 0.00 38.35 2.24
2718 3101 4.148825 CTCCGTCCCTCGCCCAAG 62.149 72.222 0.00 0.00 38.35 3.61
2729 3112 0.536460 CTCTAGCCTCTCCCTCCGTC 60.536 65.000 0.00 0.00 0.00 4.79
2730 3113 1.534697 CTCTAGCCTCTCCCTCCGT 59.465 63.158 0.00 0.00 0.00 4.69
2743 3126 0.101399 ATTGCGTCTCACGGCTCTAG 59.899 55.000 0.00 0.00 42.82 2.43
2744 3127 1.065102 GTATTGCGTCTCACGGCTCTA 59.935 52.381 0.00 0.00 42.82 2.43
2745 3128 0.179134 GTATTGCGTCTCACGGCTCT 60.179 55.000 0.00 0.00 42.82 4.09
2746 3129 1.472276 CGTATTGCGTCTCACGGCTC 61.472 60.000 0.00 0.00 42.82 4.70
2747 3130 1.516386 CGTATTGCGTCTCACGGCT 60.516 57.895 0.00 0.00 42.82 5.52
2758 3141 3.437049 GGATAAAGATGGGAGCGTATTGC 59.563 47.826 0.00 0.00 46.98 3.56
2759 3142 4.641396 TGGATAAAGATGGGAGCGTATTG 58.359 43.478 0.00 0.00 0.00 1.90
2760 3143 4.593206 TCTGGATAAAGATGGGAGCGTATT 59.407 41.667 0.00 0.00 0.00 1.89
2762 3145 3.321111 GTCTGGATAAAGATGGGAGCGTA 59.679 47.826 0.00 0.00 0.00 4.42
2763 3146 2.103263 GTCTGGATAAAGATGGGAGCGT 59.897 50.000 0.00 0.00 0.00 5.07
2764 3147 2.103094 TGTCTGGATAAAGATGGGAGCG 59.897 50.000 0.00 0.00 0.00 5.03
2766 3149 5.102953 TGTTGTCTGGATAAAGATGGGAG 57.897 43.478 0.00 0.00 0.00 4.30
2768 3151 6.780457 AAATGTTGTCTGGATAAAGATGGG 57.220 37.500 0.00 0.00 0.00 4.00
2769 3152 8.184192 GTGTAAATGTTGTCTGGATAAAGATGG 58.816 37.037 0.00 0.00 0.00 3.51
2770 3153 8.729756 TGTGTAAATGTTGTCTGGATAAAGATG 58.270 33.333 0.00 0.00 0.00 2.90
2771 3154 8.862325 TGTGTAAATGTTGTCTGGATAAAGAT 57.138 30.769 0.00 0.00 0.00 2.40
2772 3155 8.684386 TTGTGTAAATGTTGTCTGGATAAAGA 57.316 30.769 0.00 0.00 0.00 2.52
2774 3157 9.072375 TGATTGTGTAAATGTTGTCTGGATAAA 57.928 29.630 0.00 0.00 0.00 1.40
2775 3158 8.628630 TGATTGTGTAAATGTTGTCTGGATAA 57.371 30.769 0.00 0.00 0.00 1.75
2776 3159 8.806429 ATGATTGTGTAAATGTTGTCTGGATA 57.194 30.769 0.00 0.00 0.00 2.59
2777 3160 7.707624 ATGATTGTGTAAATGTTGTCTGGAT 57.292 32.000 0.00 0.00 0.00 3.41
2778 3161 7.523293 AATGATTGTGTAAATGTTGTCTGGA 57.477 32.000 0.00 0.00 0.00 3.86
2779 3162 7.866898 TGAAATGATTGTGTAAATGTTGTCTGG 59.133 33.333 0.00 0.00 0.00 3.86
2783 3166 9.195411 GTGATGAAATGATTGTGTAAATGTTGT 57.805 29.630 0.00 0.00 0.00 3.32
2784 3167 9.194271 TGTGATGAAATGATTGTGTAAATGTTG 57.806 29.630 0.00 0.00 0.00 3.33
2785 3168 9.932207 ATGTGATGAAATGATTGTGTAAATGTT 57.068 25.926 0.00 0.00 0.00 2.71
2795 3178 9.710979 GCCAAAAATTATGTGATGAAATGATTG 57.289 29.630 0.00 0.00 0.00 2.67
2796 3179 9.451002 TGCCAAAAATTATGTGATGAAATGATT 57.549 25.926 0.00 0.00 0.00 2.57
2798 3181 8.719648 GTTGCCAAAAATTATGTGATGAAATGA 58.280 29.630 0.00 0.00 0.00 2.57
2799 3182 7.964011 GGTTGCCAAAAATTATGTGATGAAATG 59.036 33.333 0.00 0.00 0.00 2.32
2800 3183 7.121020 GGGTTGCCAAAAATTATGTGATGAAAT 59.879 33.333 0.00 0.00 0.00 2.17
2804 3187 4.635324 GGGGTTGCCAAAAATTATGTGATG 59.365 41.667 0.00 0.00 0.00 3.07
2805 3188 4.535692 AGGGGTTGCCAAAAATTATGTGAT 59.464 37.500 0.00 0.00 0.00 3.06
2806 3189 3.906846 AGGGGTTGCCAAAAATTATGTGA 59.093 39.130 0.00 0.00 0.00 3.58
2807 3190 4.020307 AGAGGGGTTGCCAAAAATTATGTG 60.020 41.667 0.00 0.00 0.00 3.21
2808 3191 4.167319 AGAGGGGTTGCCAAAAATTATGT 58.833 39.130 0.00 0.00 0.00 2.29
2809 3192 4.467438 AGAGAGGGGTTGCCAAAAATTATG 59.533 41.667 0.00 0.00 0.00 1.90
2810 3193 4.687976 AGAGAGGGGTTGCCAAAAATTAT 58.312 39.130 0.00 0.00 0.00 1.28
2811 3194 4.126520 AGAGAGGGGTTGCCAAAAATTA 57.873 40.909 0.00 0.00 0.00 1.40
2812 3195 2.976440 AGAGAGGGGTTGCCAAAAATT 58.024 42.857 0.00 0.00 0.00 1.82
2813 3196 2.702270 AGAGAGGGGTTGCCAAAAAT 57.298 45.000 0.00 0.00 0.00 1.82
2814 3197 2.433970 CAAAGAGAGGGGTTGCCAAAAA 59.566 45.455 0.00 0.00 0.00 1.94
2815 3198 2.038659 CAAAGAGAGGGGTTGCCAAAA 58.961 47.619 0.00 0.00 0.00 2.44
2816 3199 1.703411 CAAAGAGAGGGGTTGCCAAA 58.297 50.000 0.00 0.00 0.00 3.28
2817 3200 0.827507 GCAAAGAGAGGGGTTGCCAA 60.828 55.000 0.00 0.00 41.41 4.52
2819 3202 1.228552 TGCAAAGAGAGGGGTTGCC 60.229 57.895 5.26 0.00 45.60 4.52
2820 3203 0.823356 TGTGCAAAGAGAGGGGTTGC 60.823 55.000 0.00 0.76 46.21 4.17
2821 3204 1.815003 GATGTGCAAAGAGAGGGGTTG 59.185 52.381 0.00 0.00 0.00 3.77
2822 3205 1.425066 TGATGTGCAAAGAGAGGGGTT 59.575 47.619 0.00 0.00 0.00 4.11
2823 3206 1.067295 TGATGTGCAAAGAGAGGGGT 58.933 50.000 0.00 0.00 0.00 4.95
2824 3207 2.295885 GATGATGTGCAAAGAGAGGGG 58.704 52.381 0.00 0.00 0.00 4.79
2826 3209 3.607741 ACTGATGATGTGCAAAGAGAGG 58.392 45.455 0.00 0.00 0.00 3.69
2829 3212 5.366829 TGAAACTGATGATGTGCAAAGAG 57.633 39.130 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.