Multiple sequence alignment - TraesCS5A01G248900

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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 TraesCS5A01G248900 chr5A 100.000 6479 0 0 1 6479 463061582 463068060 0.000000e+00 11965.0
1 TraesCS5A01G248900 chr5A 94.118 68 4 0 3842 3909 463065359 463065426 3.200000e-18 104.0
2 TraesCS5A01G248900 chr5A 94.118 68 4 0 3778 3845 463065423 463065490 3.200000e-18 104.0
3 TraesCS5A01G248900 chr5D 95.606 3482 114 22 2051 5508 362399460 362402926 0.000000e+00 5546.0
4 TraesCS5A01G248900 chr5D 93.607 2049 98 10 1 2022 362397423 362399465 0.000000e+00 3027.0
5 TraesCS5A01G248900 chr5D 89.910 446 21 13 5507 5949 362403032 362403456 2.640000e-153 553.0
6 TraesCS5A01G248900 chr5D 80.529 529 59 23 5909 6431 362403460 362403950 3.690000e-97 366.0
7 TraesCS5A01G248900 chr5D 95.588 68 3 0 3842 3909 362401186 362401253 6.870000e-20 110.0
8 TraesCS5A01G248900 chr5D 91.071 56 5 0 4207 4262 302381684 302381739 6.970000e-10 76.8
9 TraesCS5A01G248900 chr5D 100.000 37 0 0 6424 6460 362403965 362404001 1.170000e-07 69.4
10 TraesCS5A01G248900 chr5D 97.368 38 1 0 4202 4239 362401689 362401652 1.510000e-06 65.8
11 TraesCS5A01G248900 chr5B 89.265 2925 188 50 706 3571 428127010 428129867 0.000000e+00 3546.0
12 TraesCS5A01G248900 chr5B 91.524 1640 80 36 4261 5889 428130536 428132127 0.000000e+00 2204.0
13 TraesCS5A01G248900 chr5B 86.022 465 37 11 249 700 428126340 428126789 2.110000e-129 473.0
14 TraesCS5A01G248900 chr5B 94.800 250 8 2 1 245 428125906 428126155 1.020000e-102 385.0
15 TraesCS5A01G248900 chr5B 80.541 555 52 29 5932 6479 428135212 428135717 6.130000e-100 375.0
16 TraesCS5A01G248900 chr5B 90.845 142 11 2 3841 3981 428130148 428130288 8.580000e-44 189.0
17 TraesCS5A01G248900 chr5B 92.157 51 1 3 4193 4242 35292798 35292846 1.170000e-07 69.4
18 TraesCS5A01G248900 chr5B 97.368 38 1 0 4202 4239 629934850 629934813 1.510000e-06 65.8
19 TraesCS5A01G248900 chr7D 79.052 802 123 39 1041 1807 291521920 291521129 5.800000e-140 508.0
20 TraesCS5A01G248900 chr7D 97.436 39 1 0 4207 4245 633878846 633878808 4.190000e-07 67.6
21 TraesCS5A01G248900 chr7B 85.597 486 68 2 1311 1795 361146343 361146827 5.800000e-140 508.0
22 TraesCS5A01G248900 chr7A 85.111 497 72 2 1312 1807 326046254 326045759 2.080000e-139 507.0
23 TraesCS5A01G248900 chr7A 97.561 41 1 0 4199 4239 31103420 31103460 3.240000e-08 71.3
24 TraesCS5A01G248900 chr6D 94.000 50 3 0 740 789 334250164 334250213 6.970000e-10 76.8
25 TraesCS5A01G248900 chr1B 97.619 42 1 0 4198 4239 26851602 26851561 9.010000e-09 73.1
26 TraesCS5A01G248900 chr1B 90.000 50 3 2 4195 4242 553349023 553349072 5.420000e-06 63.9


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 TraesCS5A01G248900 chr5A 463061582 463068060 6478 False 4057.666667 11965 96.078667 1 6479 3 chr5A.!!$F1 6478
1 TraesCS5A01G248900 chr5D 362397423 362404001 6578 False 1611.900000 5546 92.540000 1 6460 6 chr5D.!!$F2 6459
2 TraesCS5A01G248900 chr5B 428125906 428135717 9811 False 1195.333333 3546 88.832833 1 6479 6 chr5B.!!$F2 6478
3 TraesCS5A01G248900 chr7D 291521129 291521920 791 True 508.000000 508 79.052000 1041 1807 1 chr7D.!!$R1 766

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
858 1277 0.670546 GACACAGCGCTGCTCCTTTA 60.671 55.000 36.28 0.00 36.4 1.85 F
859 1278 0.951040 ACACAGCGCTGCTCCTTTAC 60.951 55.000 36.28 0.00 36.4 2.01 F
1597 2055 1.154016 CTTCTTCTTCGCGCGAGGA 60.154 57.895 36.39 36.39 0.0 3.71 F
2872 3357 1.193874 CCGTTGTGCTCGAAGTTAACC 59.806 52.381 0.88 0.00 0.0 2.85 F
4245 4864 0.107831 TCGTTGGGGGAGTTCAGTTG 59.892 55.000 0.00 0.00 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2030 2496 0.248702 TCTGAAACAAAAACGGCCGC 60.249 50.000 28.58 5.76 0.0 6.53 R
2162 2628 1.632920 TCATGCTAACACCCCACATCA 59.367 47.619 0.00 0.00 0.0 3.07 R
3262 3763 1.670811 CACCCATGGATTCGCAACTAC 59.329 52.381 15.22 0.00 0.0 2.73 R
4276 4912 0.453390 GCAGAGCAATTAGGGCACAC 59.547 55.000 0.00 0.00 0.0 3.82 R
6022 9811 0.233848 CGGCGTGGTTGTTTGTAGTC 59.766 55.000 0.00 0.00 0.0 2.59 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
57 58 4.143543 TCATTACGGATACCACGATACCA 58.856 43.478 0.00 0.00 34.93 3.25
64 65 3.383825 GGATACCACGATACCAGTTGACT 59.616 47.826 0.00 0.00 0.00 3.41
71 72 4.022242 CACGATACCAGTTGACTATAGGGG 60.022 50.000 4.43 0.00 0.00 4.79
204 210 6.491403 AGAATTTTCCAACAGTATGCTGAAGT 59.509 34.615 18.40 0.00 45.28 3.01
205 211 5.689383 TTTTCCAACAGTATGCTGAAGTC 57.311 39.130 18.40 0.00 45.28 3.01
246 252 9.483489 TTTGATAGTCTCCAAGGTGTTATAGTA 57.517 33.333 0.00 0.00 0.00 1.82
247 253 8.461249 TGATAGTCTCCAAGGTGTTATAGTAC 57.539 38.462 0.00 0.00 0.00 2.73
285 472 4.667420 GCAAGCTGCTGCAAATGT 57.333 50.000 18.42 0.00 42.17 2.71
310 498 2.358737 GCAAGGACAGTCCACGGG 60.359 66.667 22.31 8.68 39.61 5.28
382 571 4.681744 GCAGGTCATTTTGTTTCACTGAA 58.318 39.130 0.00 0.00 0.00 3.02
383 572 4.504097 GCAGGTCATTTTGTTTCACTGAAC 59.496 41.667 0.00 0.00 0.00 3.18
394 592 2.084610 TCACTGAACATGGCTTCTCG 57.915 50.000 0.00 0.00 0.00 4.04
397 595 1.895798 ACTGAACATGGCTTCTCGAGA 59.104 47.619 12.08 12.08 0.00 4.04
406 604 1.271102 GGCTTCTCGAGACTTCACACT 59.729 52.381 16.36 0.00 0.00 3.55
461 663 7.271511 TCTTTGTTGGCTTGAATGTGTATTTT 58.728 30.769 0.00 0.00 0.00 1.82
467 669 5.245751 TGGCTTGAATGTGTATTTTGTGGAT 59.754 36.000 0.00 0.00 0.00 3.41
475 677 9.260002 GAATGTGTATTTTGTGGATTTCTTTGT 57.740 29.630 0.00 0.00 0.00 2.83
477 679 9.912634 ATGTGTATTTTGTGGATTTCTTTGTAG 57.087 29.630 0.00 0.00 0.00 2.74
485 687 5.705441 TGTGGATTTCTTTGTAGTGCTTAGG 59.295 40.000 0.00 0.00 0.00 2.69
491 693 5.043737 TCTTTGTAGTGCTTAGGGTTTGT 57.956 39.130 0.00 0.00 0.00 2.83
492 694 5.442391 TCTTTGTAGTGCTTAGGGTTTGTT 58.558 37.500 0.00 0.00 0.00 2.83
519 721 1.381056 ACTGGCAGGTGGTTTTGCA 60.381 52.632 20.34 0.00 42.02 4.08
526 728 1.140804 GGTGGTTTTGCAACGCTGT 59.859 52.632 0.00 0.00 33.13 4.40
535 737 1.353804 GCAACGCTGTCGGTTTCAA 59.646 52.632 0.00 0.00 40.69 2.69
626 829 1.490693 CCATTTCTCATCGGACGGCG 61.491 60.000 4.80 4.80 0.00 6.46
630 833 3.822192 CTCATCGGACGGCGGACA 61.822 66.667 13.24 0.00 0.00 4.02
781 1199 1.142667 TGAGCACCAACACAGATTCCA 59.857 47.619 0.00 0.00 0.00 3.53
857 1276 1.963338 GACACAGCGCTGCTCCTTT 60.963 57.895 36.28 14.06 36.40 3.11
858 1277 0.670546 GACACAGCGCTGCTCCTTTA 60.671 55.000 36.28 0.00 36.40 1.85
859 1278 0.951040 ACACAGCGCTGCTCCTTTAC 60.951 55.000 36.28 0.00 36.40 2.01
913 1332 2.046892 ACGGCCTCACATGTCAGC 60.047 61.111 0.00 0.00 0.00 4.26
964 1383 4.380655 GCAGATTCCGCCGTTAGTATCTAT 60.381 45.833 0.00 0.00 0.00 1.98
1034 1453 3.498661 GGGACTGAATTCTGAAACCACCT 60.499 47.826 18.13 0.00 0.00 4.00
1597 2055 1.154016 CTTCTTCTTCGCGCGAGGA 60.154 57.895 36.39 36.39 0.00 3.71
1699 2157 4.803426 CTCACCGTCAGCGAGGCC 62.803 72.222 0.00 0.00 41.33 5.19
1756 2214 2.050350 CGGAGGCGTCTTCCTACCA 61.050 63.158 6.34 0.00 36.38 3.25
1768 2226 5.624509 CGTCTTCCTACCAATCATCAAGTCA 60.625 44.000 0.00 0.00 0.00 3.41
1783 2241 2.359975 TCACTCTCGCTCTCGGCA 60.360 61.111 0.00 0.00 41.91 5.69
2162 2628 6.976934 ACATTTCTTTGTTACTGATTGGGT 57.023 33.333 0.00 0.00 0.00 4.51
2312 2778 2.182827 TGGAGCTCTAGCATGTCAGTT 58.817 47.619 14.64 0.00 45.16 3.16
2415 2881 3.242123 GCGAAACTAGAGTAGTGCATTGC 60.242 47.826 0.46 0.46 39.39 3.56
2458 2924 9.513906 TCCTGACAACATTATTCAGTAAATTGA 57.486 29.630 0.00 0.00 35.89 2.57
2591 3071 1.201429 AGGTAAGCCACTGGGAGGTG 61.201 60.000 0.00 0.00 37.19 4.00
2863 3348 3.595709 TTCTTAAAACCGTTGTGCTCG 57.404 42.857 0.00 0.00 0.00 5.03
2872 3357 1.193874 CCGTTGTGCTCGAAGTTAACC 59.806 52.381 0.88 0.00 0.00 2.85
2897 3382 2.481289 AGCAGGAAAGCTACTCAACC 57.519 50.000 0.00 0.00 44.50 3.77
2921 3406 4.053295 TGAAGATTTTGCTTCTTGCTTGC 58.947 39.130 0.00 0.00 43.60 4.01
2924 3409 4.243270 AGATTTTGCTTCTTGCTTGCATC 58.757 39.130 0.00 0.00 43.37 3.91
2962 3447 5.127491 CAGAACCCAACCTACAAGTAACAA 58.873 41.667 0.00 0.00 0.00 2.83
3262 3763 0.749649 AGCAGAGGAGCTTGGTATCG 59.250 55.000 0.00 0.00 43.70 2.92
3459 3960 5.975988 ATGAGTGGGTTATGATTGGTACT 57.024 39.130 0.00 0.00 0.00 2.73
3998 4615 4.947388 TGGGATAACTGCCTTTGTATGTTC 59.053 41.667 0.00 0.00 33.13 3.18
4041 4660 3.397955 AGTCCCAAACCCAACTCAGTATT 59.602 43.478 0.00 0.00 0.00 1.89
4210 4829 6.465035 GCATCAGAATACCATTTACTCCCTCT 60.465 42.308 0.00 0.00 0.00 3.69
4211 4830 6.485830 TCAGAATACCATTTACTCCCTCTG 57.514 41.667 0.00 0.00 0.00 3.35
4238 4857 5.071384 CCTAAATATAAGTCGTTGGGGGAGT 59.929 44.000 0.00 0.00 0.00 3.85
4239 4858 5.446260 AAATATAAGTCGTTGGGGGAGTT 57.554 39.130 0.00 0.00 0.00 3.01
4240 4859 4.684484 ATATAAGTCGTTGGGGGAGTTC 57.316 45.455 0.00 0.00 0.00 3.01
4242 4861 0.396811 AAGTCGTTGGGGGAGTTCAG 59.603 55.000 0.00 0.00 0.00 3.02
4244 4863 0.108019 GTCGTTGGGGGAGTTCAGTT 59.892 55.000 0.00 0.00 0.00 3.16
4245 4864 0.107831 TCGTTGGGGGAGTTCAGTTG 59.892 55.000 0.00 0.00 0.00 3.16
4246 4865 0.107831 CGTTGGGGGAGTTCAGTTGA 59.892 55.000 0.00 0.00 0.00 3.18
4247 4866 1.271379 CGTTGGGGGAGTTCAGTTGAT 60.271 52.381 0.00 0.00 0.00 2.57
4270 4906 8.363390 TGATGAACAGATGGAGTACAAGATATC 58.637 37.037 0.00 0.00 0.00 1.63
4276 4912 4.257267 TGGAGTACAAGATATCATGCCG 57.743 45.455 7.84 0.00 0.00 5.69
4296 4933 1.026182 TGTGCCCTAATTGCTCTGCG 61.026 55.000 0.00 0.00 0.00 5.18
4313 4950 3.926527 TCTGCGTCACATATTGTCTGAAC 59.073 43.478 0.00 0.00 0.00 3.18
4486 5123 2.996249 AGTCAGCATGGGATACACTG 57.004 50.000 0.00 0.00 36.16 3.66
4577 5214 0.819259 TTCTGTCGCCAAGCTGCTTT 60.819 50.000 13.10 0.00 0.00 3.51
4578 5215 1.208614 CTGTCGCCAAGCTGCTTTC 59.791 57.895 13.10 6.74 0.00 2.62
4813 5450 0.666374 GGCAAGCCGCGGTATATTTT 59.334 50.000 28.70 9.01 43.84 1.82
4821 5458 3.062042 CCGCGGTATATTTTGGAGGTAC 58.938 50.000 19.50 0.00 0.00 3.34
4919 5557 6.130298 CCGGAAAAGGCAAAAAGAAAAATT 57.870 33.333 0.00 0.00 0.00 1.82
4920 5558 5.970612 CCGGAAAAGGCAAAAAGAAAAATTG 59.029 36.000 0.00 0.00 0.00 2.32
4942 5580 9.638239 AATTGTCGCAAATAAACATGTAGAATT 57.362 25.926 0.00 0.00 0.00 2.17
5041 5679 6.151817 ACTGCTGATATCGATAAGCTCACATA 59.848 38.462 23.07 7.27 40.01 2.29
5214 5852 2.476619 CTGCACTGTTAGTCGACCAAAG 59.523 50.000 13.01 6.46 0.00 2.77
5215 5853 2.101750 TGCACTGTTAGTCGACCAAAGA 59.898 45.455 13.01 4.95 0.00 2.52
5216 5854 2.475487 GCACTGTTAGTCGACCAAAGAC 59.525 50.000 13.01 4.79 38.81 3.01
5219 5857 4.809426 CACTGTTAGTCGACCAAAGACTTT 59.191 41.667 13.01 0.00 45.74 2.66
5221 5859 4.374399 TGTTAGTCGACCAAAGACTTTCC 58.626 43.478 13.01 0.00 45.74 3.13
5237 5875 4.455606 ACTTTCCTTTGGAACTCACTGAG 58.544 43.478 4.36 4.36 41.87 3.35
5254 5892 2.438434 GCTGTCCATGGTTCCGGG 60.438 66.667 12.58 0.00 0.00 5.73
5267 5905 0.909623 TTCCGGGGTGATCTTCCTTC 59.090 55.000 0.00 0.00 0.00 3.46
5293 5931 5.297776 GTGGTCTGTTGATGATAGGGAAATG 59.702 44.000 0.00 0.00 0.00 2.32
5357 5996 5.105756 CCATCTTGTACAGTTCCCCATTTTC 60.106 44.000 0.00 0.00 0.00 2.29
5359 5998 5.070001 TCTTGTACAGTTCCCCATTTTCTG 58.930 41.667 0.00 0.00 0.00 3.02
5363 6002 4.184649 ACAGTTCCCCATTTTCTGTCTT 57.815 40.909 0.00 0.00 34.87 3.01
5377 6016 6.968131 TTTCTGTCTTGGAAATGTAGATCG 57.032 37.500 0.00 0.00 0.00 3.69
5435 6074 9.823647 ATCTTGTTACAGTATTCTCTATGGTTG 57.176 33.333 0.00 0.00 0.00 3.77
5436 6075 8.812972 TCTTGTTACAGTATTCTCTATGGTTGT 58.187 33.333 0.00 0.00 0.00 3.32
5437 6076 8.771920 TTGTTACAGTATTCTCTATGGTTGTG 57.228 34.615 0.00 0.00 0.00 3.33
5439 6078 7.179516 TGTTACAGTATTCTCTATGGTTGTGGA 59.820 37.037 0.00 0.00 0.00 4.02
5440 6079 6.227298 ACAGTATTCTCTATGGTTGTGGAG 57.773 41.667 0.00 0.00 0.00 3.86
5441 6080 5.721960 ACAGTATTCTCTATGGTTGTGGAGT 59.278 40.000 0.00 0.00 0.00 3.85
5442 6081 6.895756 ACAGTATTCTCTATGGTTGTGGAGTA 59.104 38.462 0.00 0.00 0.00 2.59
5443 6082 7.147880 ACAGTATTCTCTATGGTTGTGGAGTAC 60.148 40.741 0.00 0.00 0.00 2.73
5446 6085 5.661056 TCTCTATGGTTGTGGAGTACTTG 57.339 43.478 0.00 0.00 0.00 3.16
5448 6087 5.542635 TCTCTATGGTTGTGGAGTACTTGTT 59.457 40.000 0.00 0.00 0.00 2.83
5449 6088 5.790593 TCTATGGTTGTGGAGTACTTGTTC 58.209 41.667 0.00 0.00 0.00 3.18
5451 6090 3.804036 TGGTTGTGGAGTACTTGTTCTG 58.196 45.455 0.00 0.00 0.00 3.02
5454 6093 4.638865 GGTTGTGGAGTACTTGTTCTGTTT 59.361 41.667 0.00 0.00 0.00 2.83
5455 6094 5.220796 GGTTGTGGAGTACTTGTTCTGTTTC 60.221 44.000 0.00 0.00 0.00 2.78
5456 6095 5.353394 TGTGGAGTACTTGTTCTGTTTCT 57.647 39.130 0.00 0.00 0.00 2.52
5457 6096 5.116180 TGTGGAGTACTTGTTCTGTTTCTG 58.884 41.667 0.00 0.00 0.00 3.02
5458 6097 5.105106 TGTGGAGTACTTGTTCTGTTTCTGA 60.105 40.000 0.00 0.00 0.00 3.27
5459 6098 5.815740 GTGGAGTACTTGTTCTGTTTCTGAA 59.184 40.000 0.00 0.00 0.00 3.02
5460 6099 6.315393 GTGGAGTACTTGTTCTGTTTCTGAAA 59.685 38.462 0.00 0.00 0.00 2.69
5461 6100 7.012421 GTGGAGTACTTGTTCTGTTTCTGAAAT 59.988 37.037 6.06 0.00 0.00 2.17
5462 6101 7.226720 TGGAGTACTTGTTCTGTTTCTGAAATC 59.773 37.037 6.06 1.53 0.00 2.17
5463 6102 7.442666 GGAGTACTTGTTCTGTTTCTGAAATCT 59.557 37.037 6.06 0.00 0.00 2.40
5464 6103 8.147642 AGTACTTGTTCTGTTTCTGAAATCTG 57.852 34.615 6.06 5.06 0.00 2.90
5502 6141 2.528564 TGCATCTTTTCCTCCCCAAAG 58.471 47.619 0.00 0.00 0.00 2.77
5548 6294 1.918609 CGAAGCGCTCCAAGTAGTAAC 59.081 52.381 12.06 0.00 0.00 2.50
5629 6375 1.831106 ACCTGGACACGATATGAAGCA 59.169 47.619 0.00 0.00 0.00 3.91
5642 6388 5.635280 CGATATGAAGCACATCTTTACCGAT 59.365 40.000 0.00 0.00 40.07 4.18
5643 6389 6.806739 CGATATGAAGCACATCTTTACCGATA 59.193 38.462 0.00 0.00 40.07 2.92
5644 6390 7.489435 CGATATGAAGCACATCTTTACCGATAT 59.511 37.037 0.00 0.00 40.07 1.63
5645 6391 6.791887 ATGAAGCACATCTTTACCGATATG 57.208 37.500 0.00 0.00 34.56 1.78
5646 6392 5.670485 TGAAGCACATCTTTACCGATATGT 58.330 37.500 0.00 0.00 34.56 2.29
5648 6394 5.023533 AGCACATCTTTACCGATATGTGT 57.976 39.130 13.88 1.50 46.93 3.72
5649 6395 6.156748 AGCACATCTTTACCGATATGTGTA 57.843 37.500 13.88 0.00 46.93 2.90
5650 6396 6.216569 AGCACATCTTTACCGATATGTGTAG 58.783 40.000 13.88 0.00 46.93 2.74
5651 6397 5.107453 GCACATCTTTACCGATATGTGTAGC 60.107 44.000 13.88 0.00 46.93 3.58
5652 6398 5.983118 CACATCTTTACCGATATGTGTAGCA 59.017 40.000 0.00 0.00 42.62 3.49
5653 6399 5.983720 ACATCTTTACCGATATGTGTAGCAC 59.016 40.000 0.00 0.00 31.56 4.40
5654 6400 4.940463 TCTTTACCGATATGTGTAGCACC 58.060 43.478 0.00 0.00 32.73 5.01
5655 6401 4.647853 TCTTTACCGATATGTGTAGCACCT 59.352 41.667 0.00 0.00 32.73 4.00
5656 6402 2.890808 ACCGATATGTGTAGCACCTG 57.109 50.000 0.00 0.00 32.73 4.00
5657 6403 1.202533 ACCGATATGTGTAGCACCTGC 60.203 52.381 0.00 0.00 42.49 4.85
5658 6404 1.202521 CCGATATGTGTAGCACCTGCA 60.203 52.381 0.00 0.00 45.16 4.41
5659 6405 2.130395 CGATATGTGTAGCACCTGCAG 58.870 52.381 6.78 6.78 45.16 4.41
5660 6406 1.869767 GATATGTGTAGCACCTGCAGC 59.130 52.381 8.66 0.00 45.16 5.25
5661 6407 0.612744 TATGTGTAGCACCTGCAGCA 59.387 50.000 8.66 0.00 45.16 4.41
5712 6460 1.963515 GCACACACCCAAGAGGAAAAT 59.036 47.619 0.00 0.00 39.89 1.82
5788 6537 4.485163 AGCTAAAGTAATTTGCGGCAAAG 58.515 39.130 29.22 16.25 43.37 2.77
5789 6538 4.022329 AGCTAAAGTAATTTGCGGCAAAGT 60.022 37.500 29.22 28.60 43.37 2.66
5790 6539 4.684242 GCTAAAGTAATTTGCGGCAAAGTT 59.316 37.500 29.68 23.60 36.76 2.66
5791 6540 5.859648 GCTAAAGTAATTTGCGGCAAAGTTA 59.140 36.000 29.68 22.77 36.76 2.24
5792 6541 6.363896 GCTAAAGTAATTTGCGGCAAAGTTAA 59.636 34.615 29.68 13.21 36.76 2.01
5860 6610 2.005971 AAACTACTTCATCCGTCCGC 57.994 50.000 0.00 0.00 0.00 5.54
5878 6628 2.095969 CCGCAAATAACTGTCGCTCAAA 60.096 45.455 0.00 0.00 0.00 2.69
5882 6632 1.722011 ATAACTGTCGCTCAAACGGG 58.278 50.000 0.00 0.00 0.00 5.28
5883 6633 0.390124 TAACTGTCGCTCAAACGGGT 59.610 50.000 0.00 0.00 0.00 5.28
5895 8359 2.148768 CAAACGGGTGTAAGGTTCTCC 58.851 52.381 0.00 0.00 0.00 3.71
5918 8382 2.287788 GGTTGAACTTGGCACTGACATG 60.288 50.000 0.00 0.00 0.00 3.21
5943 8407 7.606456 TGAACATGCTTAAGTTAAGGGAAGTAG 59.394 37.037 21.36 0.00 36.31 2.57
5965 9754 1.084289 AAAAAGGAGCGCACGTATCC 58.916 50.000 11.47 7.46 0.00 2.59
6022 9811 3.928992 CACTGTACACCAGCATCTACAAG 59.071 47.826 0.00 0.00 45.68 3.16
6023 9812 3.832490 ACTGTACACCAGCATCTACAAGA 59.168 43.478 0.00 0.00 45.68 3.02
6024 9813 4.177026 CTGTACACCAGCATCTACAAGAC 58.823 47.826 0.00 0.00 33.59 3.01
6025 9814 3.832490 TGTACACCAGCATCTACAAGACT 59.168 43.478 0.00 0.00 0.00 3.24
6026 9815 5.014202 TGTACACCAGCATCTACAAGACTA 58.986 41.667 0.00 0.00 0.00 2.59
6027 9816 4.457834 ACACCAGCATCTACAAGACTAC 57.542 45.455 0.00 0.00 0.00 2.73
6028 9817 3.832490 ACACCAGCATCTACAAGACTACA 59.168 43.478 0.00 0.00 0.00 2.74
6029 9818 4.283467 ACACCAGCATCTACAAGACTACAA 59.717 41.667 0.00 0.00 0.00 2.41
6037 9826 6.565999 GCATCTACAAGACTACAAACAACCAC 60.566 42.308 0.00 0.00 0.00 4.16
6044 9833 0.377554 TACAAACAACCACGCCGTTG 59.622 50.000 12.32 12.32 46.94 4.10
6071 9860 3.568430 CCTACACTACACATGCCGATCTA 59.432 47.826 0.00 0.00 0.00 1.98
6072 9861 3.438297 ACACTACACATGCCGATCTAC 57.562 47.619 0.00 0.00 0.00 2.59
6087 9876 4.083961 CCGATCTACACACATCTACCTACG 60.084 50.000 0.00 0.00 0.00 3.51
6092 9881 2.096496 ACACACATCTACCTACGTACGC 59.904 50.000 16.72 0.00 0.00 4.42
6127 9916 2.331451 GTGCGCACTTCACCAACC 59.669 61.111 32.55 1.96 0.00 3.77
6130 9919 3.353836 CGCACTTCACCAACCGGG 61.354 66.667 6.32 0.00 44.81 5.73
6158 9947 3.417275 CTCCGTGCTCCCGCTACAG 62.417 68.421 0.00 0.00 36.97 2.74
6236 10030 2.510906 CACGTCCCATCCCATCCC 59.489 66.667 0.00 0.00 0.00 3.85
6237 10031 2.042095 ACGTCCCATCCCATCCCA 59.958 61.111 0.00 0.00 0.00 4.37
6238 10032 1.385915 ACGTCCCATCCCATCCCAT 60.386 57.895 0.00 0.00 0.00 4.00
6239 10033 1.376466 CGTCCCATCCCATCCCATC 59.624 63.158 0.00 0.00 0.00 3.51
6241 10035 1.465986 TCCCATCCCATCCCATCCC 60.466 63.158 0.00 0.00 0.00 3.85
6242 10036 1.779644 CCCATCCCATCCCATCCCA 60.780 63.158 0.00 0.00 0.00 4.37
6243 10037 1.772308 CCATCCCATCCCATCCCAG 59.228 63.158 0.00 0.00 0.00 4.45
6245 10039 2.165656 ATCCCATCCCATCCCAGCC 61.166 63.158 0.00 0.00 0.00 4.85
6246 10040 3.907130 CCCATCCCATCCCAGCCC 61.907 72.222 0.00 0.00 0.00 5.19
6247 10041 3.105248 CCATCCCATCCCAGCCCA 61.105 66.667 0.00 0.00 0.00 5.36
6248 10042 2.476078 CCATCCCATCCCAGCCCAT 61.476 63.158 0.00 0.00 0.00 4.00
6249 10043 1.076192 CATCCCATCCCAGCCCATC 59.924 63.158 0.00 0.00 0.00 3.51
6250 10044 2.165656 ATCCCATCCCAGCCCATCC 61.166 63.158 0.00 0.00 0.00 3.51
6251 10045 3.907130 CCCATCCCAGCCCATCCC 61.907 72.222 0.00 0.00 0.00 3.85
6252 10046 3.105248 CCATCCCAGCCCATCCCA 61.105 66.667 0.00 0.00 0.00 4.37
6253 10047 2.476078 CCATCCCAGCCCATCCCAT 61.476 63.158 0.00 0.00 0.00 4.00
6254 10048 1.076192 CATCCCAGCCCATCCCATC 59.924 63.158 0.00 0.00 0.00 3.51
6255 10049 2.165656 ATCCCAGCCCATCCCATCC 61.166 63.158 0.00 0.00 0.00 3.51
6256 10050 3.907130 CCCAGCCCATCCCATCCC 61.907 72.222 0.00 0.00 0.00 3.85
6257 10051 4.275508 CCAGCCCATCCCATCCCG 62.276 72.222 0.00 0.00 0.00 5.14
6258 10052 3.492353 CAGCCCATCCCATCCCGT 61.492 66.667 0.00 0.00 0.00 5.28
6259 10053 3.171388 AGCCCATCCCATCCCGTC 61.171 66.667 0.00 0.00 0.00 4.79
6260 10054 4.626081 GCCCATCCCATCCCGTCG 62.626 72.222 0.00 0.00 0.00 5.12
6261 10055 3.941188 CCCATCCCATCCCGTCGG 61.941 72.222 3.60 3.60 0.00 4.79
6262 10056 3.941188 CCATCCCATCCCGTCGGG 61.941 72.222 25.31 25.31 46.11 5.14
6263 10057 4.626081 CATCCCATCCCGTCGGGC 62.626 72.222 26.42 0.00 43.94 6.13
6303 10097 4.124351 TGTTCTAGACGGGCGCGG 62.124 66.667 27.52 9.46 0.00 6.46
6348 10161 4.100084 CATGGTCCAGCTCCGGCA 62.100 66.667 0.00 0.00 41.70 5.69
6389 10202 2.527100 GACCTGATCGTAACCAACTCG 58.473 52.381 0.00 0.00 0.00 4.18
6395 10208 3.256383 TGATCGTAACCAACTCGAAAGGA 59.744 43.478 4.63 0.00 37.16 3.36
6414 10227 0.759436 AAGCGATAGGATGGTCCCGT 60.759 55.000 0.00 0.00 37.19 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.039879 GGTATCCGTAATGAATGCCCCT 59.960 50.000 0.00 0.00 0.00 4.79
57 58 3.246387 ACAACCCTCCCCTATAGTCAACT 60.246 47.826 0.00 0.00 0.00 3.16
64 65 1.111116 CGCGACAACCCTCCCCTATA 61.111 60.000 0.00 0.00 0.00 1.31
71 72 2.027625 CTTCCACGCGACAACCCTC 61.028 63.158 15.93 0.00 0.00 4.30
204 210 0.679640 CAAAACCTATGGGCGGCTGA 60.680 55.000 9.56 0.00 35.63 4.26
205 211 0.679640 TCAAAACCTATGGGCGGCTG 60.680 55.000 9.56 0.00 35.63 4.85
246 252 5.181056 TGCAAACAATCAATGACAGATACGT 59.819 36.000 0.00 0.00 0.00 3.57
247 253 5.630061 TGCAAACAATCAATGACAGATACG 58.370 37.500 0.00 0.00 0.00 3.06
285 472 1.408702 GGACTGTCCTTGCAGCAAAAA 59.591 47.619 19.53 0.00 39.96 1.94
382 571 1.895798 TGAAGTCTCGAGAAGCCATGT 59.104 47.619 18.55 0.00 0.00 3.21
383 572 2.266554 GTGAAGTCTCGAGAAGCCATG 58.733 52.381 18.55 0.00 0.00 3.66
394 592 4.060038 TGGACAAAGAGTGTGAAGTCTC 57.940 45.455 0.00 0.00 41.96 3.36
397 595 4.589908 AGTTTGGACAAAGAGTGTGAAGT 58.410 39.130 0.00 0.00 41.96 3.01
461 663 5.705441 CCTAAGCACTACAAAGAAATCCACA 59.295 40.000 0.00 0.00 0.00 4.17
467 669 5.889289 ACAAACCCTAAGCACTACAAAGAAA 59.111 36.000 0.00 0.00 0.00 2.52
475 677 3.482436 CACCAACAAACCCTAAGCACTA 58.518 45.455 0.00 0.00 0.00 2.74
477 679 1.339929 CCACCAACAAACCCTAAGCAC 59.660 52.381 0.00 0.00 0.00 4.40
492 694 3.569210 CCTGCCAGTGGACCACCA 61.569 66.667 21.32 11.11 44.76 4.17
514 716 0.248296 GAAACCGACAGCGTTGCAAA 60.248 50.000 0.00 0.00 35.23 3.68
515 717 1.353804 GAAACCGACAGCGTTGCAA 59.646 52.632 0.00 0.00 35.23 4.08
516 718 1.369839 TTGAAACCGACAGCGTTGCA 61.370 50.000 0.00 0.00 35.23 4.08
519 721 1.782028 GCCTTGAAACCGACAGCGTT 61.782 55.000 0.00 0.00 35.23 4.84
526 728 1.988293 TTTCCATGCCTTGAAACCGA 58.012 45.000 0.00 0.00 0.00 4.69
535 737 0.960364 ACGCGACATTTTCCATGCCT 60.960 50.000 15.93 0.00 0.00 4.75
610 813 2.183300 CCGCCGTCCGATGAGAAA 59.817 61.111 0.00 0.00 40.02 2.52
626 829 4.284550 TGGTTGCCAGCCCTGTCC 62.285 66.667 0.00 0.00 0.00 4.02
781 1199 4.057428 GGACCAGTCGCAGTCGCT 62.057 66.667 0.00 0.00 35.30 4.93
938 1357 0.597637 CTAACGGCGGAATCTGCGAT 60.598 55.000 13.24 1.46 30.86 4.58
1597 2055 1.218316 GAGGCCGGTCTTGACGAAT 59.782 57.895 11.49 0.00 0.00 3.34
1621 2079 1.141019 GAAGTAGGTGGCGATGCGA 59.859 57.895 0.00 0.00 0.00 5.10
1753 2211 3.854666 CGAGAGTGACTTGATGATTGGT 58.145 45.455 0.00 0.00 31.94 3.67
1756 2214 3.446873 AGAGCGAGAGTGACTTGATGATT 59.553 43.478 0.00 0.00 31.94 2.57
1982 2448 3.730715 GTGTTGTGACAATTAGCAACTGC 59.269 43.478 0.00 0.00 41.04 4.40
2030 2496 0.248702 TCTGAAACAAAAACGGCCGC 60.249 50.000 28.58 5.76 0.00 6.53
2036 2502 6.090763 CACTGAACCCTTTCTGAAACAAAAAC 59.909 38.462 0.00 0.00 35.28 2.43
2127 2593 4.190772 CAAAGAAATGTTGCACCACCTTT 58.809 39.130 0.00 0.00 0.00 3.11
2162 2628 1.632920 TCATGCTAACACCCCACATCA 59.367 47.619 0.00 0.00 0.00 3.07
2332 2798 3.499918 AGGCTGTTGAGAAATCACGAAAG 59.500 43.478 0.00 0.00 0.00 2.62
2371 2837 4.202223 GCCGTAGAATCCTCCAACTGATAA 60.202 45.833 0.00 0.00 0.00 1.75
2415 2881 3.453717 TCAGGAATCAGGAATCAGGTGAG 59.546 47.826 0.00 0.00 0.00 3.51
2591 3071 4.871993 ACAGTTGATCAGATTGATTCGC 57.128 40.909 9.35 0.00 37.20 4.70
2674 3154 9.374838 CCAGTAAAACAAATACTCCGTACTTAT 57.625 33.333 0.00 0.00 31.33 1.73
2853 3338 1.862201 TGGTTAACTTCGAGCACAACG 59.138 47.619 5.42 0.00 0.00 4.10
2863 3348 4.755266 TCCTGCTAGGATGGTTAACTTC 57.245 45.455 5.42 3.29 40.06 3.01
2872 3357 3.386078 TGAGTAGCTTTCCTGCTAGGATG 59.614 47.826 0.00 4.33 45.34 3.51
2921 3406 8.265055 TGGGTTCTGTTTAGTTAAGATAGGATG 58.735 37.037 0.00 0.00 0.00 3.51
2924 3409 7.336176 GGTTGGGTTCTGTTTAGTTAAGATAGG 59.664 40.741 0.00 0.00 0.00 2.57
2962 3447 3.084786 GGCTTTAACCTCACTCTTGCAT 58.915 45.455 0.00 0.00 0.00 3.96
3080 3581 9.166173 CTGGATGAATTTAATTAGTCAGTCACA 57.834 33.333 0.00 0.00 0.00 3.58
3081 3582 8.125448 GCTGGATGAATTTAATTAGTCAGTCAC 58.875 37.037 0.00 0.00 0.00 3.67
3262 3763 1.670811 CACCCATGGATTCGCAACTAC 59.329 52.381 15.22 0.00 0.00 2.73
3412 3913 2.821366 CACTGGACCCATGCGCTC 60.821 66.667 9.73 0.00 0.00 5.03
3423 3924 2.038952 CCACTCATTCTTGGTCACTGGA 59.961 50.000 0.00 0.00 0.00 3.86
3459 3960 6.487668 CCCATAATGACACTGCAAGAATCATA 59.512 38.462 3.60 0.00 39.79 2.15
3587 4171 9.739276 AACCTATGAAAATCTCAATCAACACTA 57.261 29.630 0.00 0.00 37.67 2.74
3589 4173 9.994432 CTAACCTATGAAAATCTCAATCAACAC 57.006 33.333 0.00 0.00 37.67 3.32
3667 4251 0.037590 TCCCCACAATTTCCCGTCAG 59.962 55.000 0.00 0.00 0.00 3.51
3805 4390 9.956720 AGATTACAAACATATAGCTGAATTTGC 57.043 29.630 0.00 0.00 31.69 3.68
3998 4615 6.128795 GGACTGAGATACAAGTTTTCACTTCG 60.129 42.308 0.00 0.00 41.69 3.79
4041 4660 5.165652 AGGATTAGGAGCAGAAATGGGATA 58.834 41.667 0.00 0.00 0.00 2.59
4162 4781 2.681848 CTGTCTGATTCATGGTTCTGGC 59.318 50.000 0.00 0.00 0.00 4.85
4210 4829 6.350906 CCCCAACGACTTATATTTAGGAACA 58.649 40.000 0.00 0.00 0.00 3.18
4211 4830 5.761726 CCCCCAACGACTTATATTTAGGAAC 59.238 44.000 0.00 0.00 0.00 3.62
4238 4857 5.233083 ACTCCATCTGTTCATCAACTGAA 57.767 39.130 0.00 0.00 42.02 3.02
4239 4858 4.897509 ACTCCATCTGTTCATCAACTGA 57.102 40.909 0.00 0.00 42.66 3.41
4240 4859 5.482006 TGTACTCCATCTGTTCATCAACTG 58.518 41.667 0.00 0.00 33.17 3.16
4242 4861 6.166279 TCTTGTACTCCATCTGTTCATCAAC 58.834 40.000 0.00 0.00 0.00 3.18
4244 4863 6.550938 ATCTTGTACTCCATCTGTTCATCA 57.449 37.500 0.00 0.00 0.00 3.07
4245 4864 8.363390 TGATATCTTGTACTCCATCTGTTCATC 58.637 37.037 3.98 0.00 0.00 2.92
4246 4865 8.255111 TGATATCTTGTACTCCATCTGTTCAT 57.745 34.615 3.98 0.00 0.00 2.57
4247 4866 7.660030 TGATATCTTGTACTCCATCTGTTCA 57.340 36.000 3.98 0.00 0.00 3.18
4276 4912 0.453390 GCAGAGCAATTAGGGCACAC 59.547 55.000 0.00 0.00 0.00 3.82
4296 4933 5.482908 AGTCCAGTTCAGACAATATGTGAC 58.517 41.667 0.00 0.00 36.68 3.67
4313 4950 5.163374 TGAGACATCATGACCAATAGTCCAG 60.163 44.000 0.00 0.00 45.68 3.86
4486 5123 3.127425 ACTAGAACTGCAAACCAGGAC 57.873 47.619 0.00 0.00 46.14 3.85
4577 5214 4.012374 GGCCAACTCAATGAGAAAGATGA 58.988 43.478 18.20 0.00 33.32 2.92
4578 5215 4.015084 AGGCCAACTCAATGAGAAAGATG 58.985 43.478 18.20 7.37 33.32 2.90
4801 5438 2.727798 CGTACCTCCAAAATATACCGCG 59.272 50.000 0.00 0.00 0.00 6.46
4813 5450 3.627395 AAATGAATCTGCGTACCTCCA 57.373 42.857 0.00 0.00 0.00 3.86
4821 5458 7.801547 AATACAGAAACAAAATGAATCTGCG 57.198 32.000 13.20 0.00 37.22 5.18
4896 5534 5.749596 ATTTTTCTTTTTGCCTTTTCCGG 57.250 34.783 0.00 0.00 0.00 5.14
4919 5557 9.157104 TCTAATTCTACATGTTTATTTGCGACA 57.843 29.630 2.30 0.00 0.00 4.35
4920 5558 9.982291 TTCTAATTCTACATGTTTATTTGCGAC 57.018 29.630 2.30 0.00 0.00 5.19
4956 5594 9.383519 AGATGATCGACACAACATAAACTAAAT 57.616 29.630 0.00 0.00 0.00 1.40
5174 5812 2.609459 CAGCTACTGTCAATAAAGCCCG 59.391 50.000 0.00 0.00 33.63 6.13
5202 5840 4.950205 AAGGAAAGTCTTTGGTCGACTA 57.050 40.909 16.46 6.50 40.65 2.59
5214 5852 4.451900 TCAGTGAGTTCCAAAGGAAAGTC 58.548 43.478 0.00 1.81 43.86 3.01
5215 5853 4.455606 CTCAGTGAGTTCCAAAGGAAAGT 58.544 43.478 12.28 0.00 43.86 2.66
5216 5854 3.251972 GCTCAGTGAGTTCCAAAGGAAAG 59.748 47.826 21.06 0.00 43.86 2.62
5219 5857 2.050144 AGCTCAGTGAGTTCCAAAGGA 58.950 47.619 21.06 0.00 31.39 3.36
5221 5859 2.805099 GACAGCTCAGTGAGTTCCAAAG 59.195 50.000 21.06 5.93 31.39 2.77
5237 5875 2.438434 CCCGGAACCATGGACAGC 60.438 66.667 21.47 4.02 0.00 4.40
5267 5905 2.483714 CCCTATCATCAACAGACCACCG 60.484 54.545 0.00 0.00 0.00 4.94
5357 5996 5.011090 TCCGATCTACATTTCCAAGACAG 57.989 43.478 0.00 0.00 0.00 3.51
5359 5998 3.804873 GCTCCGATCTACATTTCCAAGAC 59.195 47.826 0.00 0.00 0.00 3.01
5363 6002 3.031013 TCAGCTCCGATCTACATTTCCA 58.969 45.455 0.00 0.00 0.00 3.53
5377 6016 0.312102 GCACCAAACTGTTCAGCTCC 59.688 55.000 0.00 0.00 0.00 4.70
5431 6070 3.805207 ACAGAACAAGTACTCCACAACC 58.195 45.455 0.00 0.00 0.00 3.77
5435 6074 5.357257 TCAGAAACAGAACAAGTACTCCAC 58.643 41.667 0.00 0.00 0.00 4.02
5436 6075 5.607939 TCAGAAACAGAACAAGTACTCCA 57.392 39.130 0.00 0.00 0.00 3.86
5437 6076 6.920569 TTTCAGAAACAGAACAAGTACTCC 57.079 37.500 0.00 0.00 0.00 3.85
5439 6078 7.987458 TCAGATTTCAGAAACAGAACAAGTACT 59.013 33.333 0.00 0.00 0.00 2.73
5440 6079 8.142994 TCAGATTTCAGAAACAGAACAAGTAC 57.857 34.615 0.00 0.00 0.00 2.73
5441 6080 8.612619 GTTCAGATTTCAGAAACAGAACAAGTA 58.387 33.333 21.02 0.00 35.47 2.24
5442 6081 7.337942 AGTTCAGATTTCAGAAACAGAACAAGT 59.662 33.333 24.50 11.78 37.25 3.16
5443 6082 7.701445 AGTTCAGATTTCAGAAACAGAACAAG 58.299 34.615 24.50 4.66 37.25 3.16
5446 6085 6.416161 GCAAGTTCAGATTTCAGAAACAGAAC 59.584 38.462 19.60 19.60 35.58 3.01
5448 6087 5.589855 TGCAAGTTCAGATTTCAGAAACAGA 59.410 36.000 0.00 0.00 0.00 3.41
5449 6088 5.824429 TGCAAGTTCAGATTTCAGAAACAG 58.176 37.500 0.00 0.00 0.00 3.16
5451 6090 7.704789 AATTGCAAGTTCAGATTTCAGAAAC 57.295 32.000 4.94 0.00 0.00 2.78
5454 6093 9.248291 GTAAAAATTGCAAGTTCAGATTTCAGA 57.752 29.630 13.16 0.00 0.00 3.27
5455 6094 9.033481 TGTAAAAATTGCAAGTTCAGATTTCAG 57.967 29.630 13.16 0.00 0.00 3.02
5456 6095 8.939201 TGTAAAAATTGCAAGTTCAGATTTCA 57.061 26.923 13.16 4.98 0.00 2.69
5457 6096 9.801714 CATGTAAAAATTGCAAGTTCAGATTTC 57.198 29.630 13.16 2.45 0.00 2.17
5458 6097 8.284693 GCATGTAAAAATTGCAAGTTCAGATTT 58.715 29.630 13.16 5.72 36.40 2.17
5459 6098 7.441760 TGCATGTAAAAATTGCAAGTTCAGATT 59.558 29.630 13.16 6.08 42.95 2.40
5460 6099 6.930164 TGCATGTAAAAATTGCAAGTTCAGAT 59.070 30.769 13.16 5.43 42.95 2.90
5461 6100 6.279123 TGCATGTAAAAATTGCAAGTTCAGA 58.721 32.000 13.16 3.21 42.95 3.27
5462 6101 6.528014 TGCATGTAAAAATTGCAAGTTCAG 57.472 33.333 13.16 3.07 42.95 3.02
5502 6141 9.763465 GATTCTTCGCTCAGATAATACTAGTAC 57.237 37.037 4.31 0.00 0.00 2.73
5548 6294 4.202101 TGTTTTTACACATGTTGCCCTGAG 60.202 41.667 0.00 0.00 0.00 3.35
5629 6375 5.983720 GTGCTACACATATCGGTAAAGATGT 59.016 40.000 0.00 0.00 34.08 3.06
5642 6388 0.612744 TGCTGCAGGTGCTACACATA 59.387 50.000 17.12 0.00 42.66 2.29
5643 6389 0.250858 TTGCTGCAGGTGCTACACAT 60.251 50.000 17.12 0.00 42.66 3.21
5644 6390 0.465278 TTTGCTGCAGGTGCTACACA 60.465 50.000 17.12 0.00 42.66 3.72
5645 6391 0.883833 ATTTGCTGCAGGTGCTACAC 59.116 50.000 17.12 0.00 42.66 2.90
5646 6392 1.619654 AATTTGCTGCAGGTGCTACA 58.380 45.000 17.12 0.00 42.66 2.74
5647 6393 2.730550 AAATTTGCTGCAGGTGCTAC 57.269 45.000 17.12 0.00 42.66 3.58
5648 6394 2.364970 ACAAAATTTGCTGCAGGTGCTA 59.635 40.909 17.12 0.00 42.66 3.49
5649 6395 1.139455 ACAAAATTTGCTGCAGGTGCT 59.861 42.857 17.12 0.00 42.66 4.40
5650 6396 1.585297 ACAAAATTTGCTGCAGGTGC 58.415 45.000 17.12 2.02 42.50 5.01
5651 6397 3.196463 TCAACAAAATTTGCTGCAGGTG 58.804 40.909 17.12 0.00 0.00 4.00
5652 6398 3.540314 TCAACAAAATTTGCTGCAGGT 57.460 38.095 17.12 0.00 0.00 4.00
5653 6399 4.312443 AGATCAACAAAATTTGCTGCAGG 58.688 39.130 17.12 0.00 0.00 4.85
5654 6400 5.107220 GGAAGATCAACAAAATTTGCTGCAG 60.107 40.000 10.11 10.11 0.00 4.41
5655 6401 4.751098 GGAAGATCAACAAAATTTGCTGCA 59.249 37.500 5.52 0.00 0.00 4.41
5656 6402 4.751098 TGGAAGATCAACAAAATTTGCTGC 59.249 37.500 5.52 0.00 0.00 5.25
5657 6403 5.178067 GGTGGAAGATCAACAAAATTTGCTG 59.822 40.000 5.52 4.13 0.00 4.41
5658 6404 5.299949 GGTGGAAGATCAACAAAATTTGCT 58.700 37.500 5.52 0.00 0.00 3.91
5659 6405 4.452114 GGGTGGAAGATCAACAAAATTTGC 59.548 41.667 5.52 0.00 0.00 3.68
5660 6406 4.996758 GGGGTGGAAGATCAACAAAATTTG 59.003 41.667 3.89 3.89 0.00 2.32
5661 6407 4.907269 AGGGGTGGAAGATCAACAAAATTT 59.093 37.500 0.00 0.00 0.00 1.82
5704 6452 5.927689 TGATGCAATTGTGTGAATTTTCCTC 59.072 36.000 7.40 0.00 0.00 3.71
5742 6491 0.942252 CATGGATGGACATCGCAGTG 59.058 55.000 6.24 0.00 38.69 3.66
5788 6537 8.352942 ACTGAAATTGTTGTGGATCTTCTTAAC 58.647 33.333 0.00 0.00 0.00 2.01
5789 6538 8.352201 CACTGAAATTGTTGTGGATCTTCTTAA 58.648 33.333 0.00 0.00 0.00 1.85
5790 6539 7.874940 CACTGAAATTGTTGTGGATCTTCTTA 58.125 34.615 0.00 0.00 0.00 2.10
5791 6540 6.742109 CACTGAAATTGTTGTGGATCTTCTT 58.258 36.000 0.00 0.00 0.00 2.52
5792 6541 6.323203 CACTGAAATTGTTGTGGATCTTCT 57.677 37.500 0.00 0.00 0.00 2.85
5818 6568 1.980765 ACAGCAGATGTTGGAGGAAGA 59.019 47.619 1.71 0.00 39.96 2.87
5860 6610 3.479006 CCGTTTGAGCGACAGTTATTTG 58.521 45.455 0.00 0.00 0.00 2.32
5878 6628 0.974383 CAGGAGAACCTTACACCCGT 59.026 55.000 0.00 0.00 45.36 5.28
5882 6632 3.764237 TCAACCAGGAGAACCTTACAC 57.236 47.619 0.00 0.00 45.36 2.90
5883 6633 3.714798 AGTTCAACCAGGAGAACCTTACA 59.285 43.478 19.46 0.00 45.36 2.41
5895 8359 1.334869 GTCAGTGCCAAGTTCAACCAG 59.665 52.381 0.00 0.00 0.00 4.00
5918 8382 6.819397 ACTTCCCTTAACTTAAGCATGTTC 57.181 37.500 1.29 0.00 34.46 3.18
5951 9737 2.954868 CGTGGATACGTGCGCTCC 60.955 66.667 9.73 7.41 44.99 4.70
6022 9811 0.233848 CGGCGTGGTTGTTTGTAGTC 59.766 55.000 0.00 0.00 0.00 2.59
6023 9812 0.462403 ACGGCGTGGTTGTTTGTAGT 60.462 50.000 13.76 0.00 0.00 2.73
6024 9813 0.658897 AACGGCGTGGTTGTTTGTAG 59.341 50.000 15.70 0.00 0.00 2.74
6025 9814 0.377554 CAACGGCGTGGTTGTTTGTA 59.622 50.000 15.70 0.00 41.77 2.41
6026 9815 1.137825 CAACGGCGTGGTTGTTTGT 59.862 52.632 15.70 0.00 41.77 2.83
6027 9816 2.227568 GCAACGGCGTGGTTGTTTG 61.228 57.895 15.70 7.36 46.93 2.93
6028 9817 2.103340 GCAACGGCGTGGTTGTTT 59.897 55.556 15.70 0.00 46.93 2.83
6044 9833 1.922570 CATGTGTAGTGTAGGTCCGC 58.077 55.000 0.00 0.00 0.00 5.54
6071 9860 2.096496 GCGTACGTAGGTAGATGTGTGT 59.904 50.000 17.90 0.00 0.00 3.72
6072 9861 2.713011 GCGTACGTAGGTAGATGTGTG 58.287 52.381 17.90 0.00 0.00 3.82
6232 10026 2.165656 GGATGGGCTGGGATGGGAT 61.166 63.158 0.00 0.00 0.00 3.85
6236 10030 1.076192 GATGGGATGGGCTGGGATG 59.924 63.158 0.00 0.00 0.00 3.51
6237 10031 2.165656 GGATGGGATGGGCTGGGAT 61.166 63.158 0.00 0.00 0.00 3.85
6238 10032 2.778278 GGATGGGATGGGCTGGGA 60.778 66.667 0.00 0.00 0.00 4.37
6239 10033 3.907130 GGGATGGGATGGGCTGGG 61.907 72.222 0.00 0.00 0.00 4.45
6241 10035 3.482232 GACGGGATGGGATGGGCTG 62.482 68.421 0.00 0.00 0.00 4.85
6242 10036 3.171388 GACGGGATGGGATGGGCT 61.171 66.667 0.00 0.00 0.00 5.19
6243 10037 4.626081 CGACGGGATGGGATGGGC 62.626 72.222 0.00 0.00 0.00 5.36
6306 10100 1.948138 CGCATACGGCTGAGCTGAG 60.948 63.158 21.86 10.27 41.67 3.35
6308 10102 3.634072 GCGCATACGGCTGAGCTG 61.634 66.667 12.53 12.53 41.67 4.24
6357 10170 3.706373 CAGGTCGGGTGGTCCAGG 61.706 72.222 0.00 0.00 34.36 4.45
6359 10172 1.987855 GATCAGGTCGGGTGGTCCA 60.988 63.158 0.00 0.00 34.36 4.02
6360 10173 2.901042 GATCAGGTCGGGTGGTCC 59.099 66.667 0.00 0.00 0.00 4.46
6361 10174 2.494918 CGATCAGGTCGGGTGGTC 59.505 66.667 0.00 0.00 46.47 4.02
6369 10182 2.163010 TCGAGTTGGTTACGATCAGGTC 59.837 50.000 0.00 0.00 0.00 3.85
6389 10202 3.394719 GACCATCCTATCGCTTCCTTTC 58.605 50.000 0.00 0.00 0.00 2.62
6395 10208 0.759436 ACGGGACCATCCTATCGCTT 60.759 55.000 0.00 0.00 36.57 4.68


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

AutoCloner maintained by Alex Coulton.