Multiple sequence alignment - TraesCS5A01G247300

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 TraesCS5A01G247300 chr5A 100.000 4624 0 0 1 4624 461496672 461492049 0.000000e+00 8540
1 TraesCS5A01G247300 chr5A 90.064 312 29 1 483 794 91550354 91550045 2.000000e-108 403
2 TraesCS5A01G247300 chr5D 90.671 2594 129 36 796 3320 360548979 360546430 0.000000e+00 3345
3 TraesCS5A01G247300 chr5D 94.323 1286 57 12 3354 4624 360546424 360545140 0.000000e+00 1956
4 TraesCS5A01G247300 chr5B 92.567 1305 67 18 796 2092 425887267 425885985 0.000000e+00 1845
5 TraesCS5A01G247300 chr5B 91.475 1220 72 18 3428 4624 425884572 425883362 0.000000e+00 1648
6 TraesCS5A01G247300 chr5B 88.231 1334 83 34 2158 3429 425885987 425884666 0.000000e+00 1526
7 TraesCS5A01G247300 chr5B 91.694 301 25 0 483 783 655135049 655135349 7.160000e-113 418
8 TraesCS5A01G247300 chr3B 87.576 491 42 9 1 485 463210356 463210833 6.760000e-153 551
9 TraesCS5A01G247300 chr3B 91.694 301 25 0 483 783 114014031 114014331 7.160000e-113 418
10 TraesCS5A01G247300 chr3B 91.362 301 26 0 483 783 636769208 636768908 3.330000e-111 412
11 TraesCS5A01G247300 chr1D 89.165 443 35 7 1 441 468235914 468236345 1.460000e-149 540
12 TraesCS5A01G247300 chr1B 87.696 447 37 8 2 441 646898463 646898898 5.340000e-139 505
13 TraesCS5A01G247300 chr1B 91.362 301 25 1 483 783 377260907 377260608 1.200000e-110 411
14 TraesCS5A01G247300 chrUn 94.040 302 13 2 1 301 10181264 10180967 1.960000e-123 453
15 TraesCS5A01G247300 chrUn 91.444 187 15 1 299 484 10180651 10180465 5.940000e-64 255
16 TraesCS5A01G247300 chr7A 91.693 313 22 3 483 794 506153344 506153035 9.190000e-117 431
17 TraesCS5A01G247300 chr7A 93.506 77 5 0 4478 4554 332416612 332416536 1.050000e-21 115
18 TraesCS5A01G247300 chr6B 91.362 301 26 0 483 783 19989033 19988733 3.330000e-111 412
19 TraesCS5A01G247300 chr6B 93.506 77 5 0 4478 4554 52023318 52023242 1.050000e-21 115
20 TraesCS5A01G247300 chr1A 89.873 316 28 3 483 797 189707091 189706779 2.000000e-108 403
21 TraesCS5A01G247300 chr1A 89.451 237 19 5 1 236 94122820 94123051 1.260000e-75 294
22 TraesCS5A01G247300 chr2B 89.809 314 30 1 483 796 77776572 77776261 7.210000e-108 401
23 TraesCS5A01G247300 chr2B 92.996 257 13 4 3 258 462938397 462938145 2.030000e-98 370
24 TraesCS5A01G247300 chr7B 77.389 429 64 15 1442 1867 16922259 16921861 1.670000e-54 224


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 TraesCS5A01G247300 chr5A 461492049 461496672 4623 True 8540.0 8540 100.000000 1 4624 1 chr5A.!!$R2 4623
1 TraesCS5A01G247300 chr5D 360545140 360548979 3839 True 2650.5 3345 92.497000 796 4624 2 chr5D.!!$R1 3828
2 TraesCS5A01G247300 chr5B 425883362 425887267 3905 True 1673.0 1845 90.757667 796 4624 3 chr5B.!!$R1 3828
3 TraesCS5A01G247300 chrUn 10180465 10181264 799 True 354.0 453 92.742000 1 484 2 chrUn.!!$R1 483

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
301 302 0.612229 TGCCCAGCTCTTTCTCTCTG 59.388 55.0 0.00 0.0 0.00 3.35 F
1321 1642 0.955919 GGTTTGGGACTTCGAGCCTG 60.956 60.0 1.82 0.0 0.00 4.85 F
1819 2148 0.609681 TTTGCACGTTATCCCCACCC 60.610 55.0 0.00 0.0 0.00 4.61 F
3091 3474 0.101040 TCACAAAGCACACAAGCTGC 59.899 50.0 0.00 0.0 45.89 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1525 1850 0.109342 ACCAAGCAGAGGAACCACAG 59.891 55.0 0.00 0.0 0.00 3.66 R
2959 3324 0.331278 TTCATGCCCAGGGTTAGTGG 59.669 55.0 7.55 0.0 34.52 4.00 R
3379 3779 0.320508 GACTGTCCCTTGTCCGAACC 60.321 60.0 0.00 0.0 0.00 3.62 R
4526 5045 0.546122 AGATCGTTGCCATTGCCCTA 59.454 50.0 0.00 0.0 36.33 3.53 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
125 126 2.203365 GGAGAGATCGGCTCCGGA 60.203 66.667 18.05 2.93 45.10 5.14
127 128 1.228003 GAGAGATCGGCTCCGGAGA 60.228 63.158 35.69 15.47 45.10 3.71
151 152 4.436998 GACCCTGTGGAGACGGCG 62.437 72.222 4.80 4.80 34.81 6.46
171 172 4.593864 GCGCCAGAGGGACGGATC 62.594 72.222 0.00 0.00 35.26 3.36
272 273 2.680352 GACAGCGGTGAGGGAGGA 60.680 66.667 23.44 0.00 0.00 3.71
287 288 2.359850 GGATTGCGTGAGTGCCCA 60.360 61.111 0.00 0.00 0.00 5.36
301 302 0.612229 TGCCCAGCTCTTTCTCTCTG 59.388 55.000 0.00 0.00 0.00 3.35
320 639 8.625651 TCTCTCTGTCTTCTTATTATTCTTCCG 58.374 37.037 0.00 0.00 0.00 4.30
322 641 8.750298 TCTCTGTCTTCTTATTATTCTTCCGTT 58.250 33.333 0.00 0.00 0.00 4.44
324 643 9.720769 TCTGTCTTCTTATTATTCTTCCGTTTT 57.279 29.630 0.00 0.00 0.00 2.43
336 655 4.148838 TCTTCCGTTTTCCCAATGAACAT 58.851 39.130 0.00 0.00 31.05 2.71
379 699 3.864789 AAACAAGAGAAGGAGAAGGCA 57.135 42.857 0.00 0.00 0.00 4.75
382 702 2.301583 ACAAGAGAAGGAGAAGGCACTC 59.698 50.000 3.66 3.66 38.49 3.51
396 716 1.880819 GCACTCCTGCCAAACCCATG 61.881 60.000 0.00 0.00 37.45 3.66
456 776 1.240256 GGACATATCGAGAGGTCGCT 58.760 55.000 17.43 0.00 46.39 4.93
484 804 8.581057 TGATGCACACGTTAATGTTTTTAATT 57.419 26.923 0.00 0.00 0.00 1.40
485 805 9.678941 TGATGCACACGTTAATGTTTTTAATTA 57.321 25.926 0.00 0.00 0.00 1.40
505 825 7.912949 AATTATACTTGCATAAATGTGTGCG 57.087 32.000 0.00 0.00 44.36 5.34
506 826 4.963276 ATACTTGCATAAATGTGTGCGT 57.037 36.364 0.00 0.00 44.36 5.24
507 827 7.541122 TTATACTTGCATAAATGTGTGCGTA 57.459 32.000 0.00 0.00 44.36 4.42
508 828 4.340894 ACTTGCATAAATGTGTGCGTAG 57.659 40.909 0.00 3.01 44.36 3.51
509 829 3.126858 ACTTGCATAAATGTGTGCGTAGG 59.873 43.478 10.09 0.09 44.36 3.18
510 830 2.013400 TGCATAAATGTGTGCGTAGGG 58.987 47.619 0.00 0.00 44.36 3.53
511 831 2.285083 GCATAAATGTGTGCGTAGGGA 58.715 47.619 0.00 0.00 31.76 4.20
512 832 2.287915 GCATAAATGTGTGCGTAGGGAG 59.712 50.000 0.00 0.00 31.76 4.30
513 833 3.792401 CATAAATGTGTGCGTAGGGAGA 58.208 45.455 0.00 0.00 0.00 3.71
514 834 2.851263 AAATGTGTGCGTAGGGAGAA 57.149 45.000 0.00 0.00 0.00 2.87
515 835 3.350219 AAATGTGTGCGTAGGGAGAAT 57.650 42.857 0.00 0.00 0.00 2.40
516 836 2.604046 ATGTGTGCGTAGGGAGAATC 57.396 50.000 0.00 0.00 0.00 2.52
517 837 1.262417 TGTGTGCGTAGGGAGAATCA 58.738 50.000 0.00 0.00 36.25 2.57
518 838 1.831106 TGTGTGCGTAGGGAGAATCAT 59.169 47.619 0.00 0.00 36.25 2.45
519 839 2.205074 GTGTGCGTAGGGAGAATCATG 58.795 52.381 0.00 0.00 36.25 3.07
520 840 2.107366 TGTGCGTAGGGAGAATCATGA 58.893 47.619 0.00 0.00 36.25 3.07
521 841 2.700371 TGTGCGTAGGGAGAATCATGAT 59.300 45.455 1.18 1.18 36.25 2.45
522 842 3.062763 GTGCGTAGGGAGAATCATGATG 58.937 50.000 9.46 0.00 36.25 3.07
523 843 2.965147 TGCGTAGGGAGAATCATGATGA 59.035 45.455 9.46 0.00 36.25 2.92
524 844 3.387699 TGCGTAGGGAGAATCATGATGAA 59.612 43.478 9.46 0.00 36.25 2.57
525 845 4.040829 TGCGTAGGGAGAATCATGATGAAT 59.959 41.667 9.46 0.00 36.25 2.57
526 846 4.629200 GCGTAGGGAGAATCATGATGAATC 59.371 45.833 9.46 0.00 36.25 2.52
527 847 5.568423 GCGTAGGGAGAATCATGATGAATCT 60.568 44.000 12.55 12.55 39.20 2.40
528 848 6.462500 CGTAGGGAGAATCATGATGAATCTT 58.538 40.000 13.76 2.03 36.81 2.40
529 849 6.589523 CGTAGGGAGAATCATGATGAATCTTC 59.410 42.308 13.76 11.77 36.81 2.87
530 850 6.766997 AGGGAGAATCATGATGAATCTTCT 57.233 37.500 16.28 12.67 36.81 2.85
531 851 7.868792 AGGGAGAATCATGATGAATCTTCTA 57.131 36.000 16.28 0.00 36.81 2.10
532 852 8.272659 AGGGAGAATCATGATGAATCTTCTAA 57.727 34.615 16.28 0.00 36.81 2.10
533 853 8.721479 AGGGAGAATCATGATGAATCTTCTAAA 58.279 33.333 16.28 0.00 36.81 1.85
534 854 9.517868 GGGAGAATCATGATGAATCTTCTAAAT 57.482 33.333 16.28 0.00 36.81 1.40
565 885 8.870160 TGAGTTTTACACATTGAGAAAAATGG 57.130 30.769 2.34 0.00 41.06 3.16
566 886 8.690884 TGAGTTTTACACATTGAGAAAAATGGA 58.309 29.630 2.34 0.00 41.06 3.41
567 887 9.696917 GAGTTTTACACATTGAGAAAAATGGAT 57.303 29.630 2.34 0.00 41.06 3.41
568 888 9.480053 AGTTTTACACATTGAGAAAAATGGATG 57.520 29.630 2.34 0.00 41.06 3.51
569 889 8.711457 GTTTTACACATTGAGAAAAATGGATGG 58.289 33.333 2.34 0.00 41.06 3.51
570 890 7.537596 TTACACATTGAGAAAAATGGATGGT 57.462 32.000 2.34 0.00 41.06 3.55
571 891 6.029346 ACACATTGAGAAAAATGGATGGTC 57.971 37.500 2.34 0.00 41.06 4.02
572 892 5.776716 ACACATTGAGAAAAATGGATGGTCT 59.223 36.000 2.34 0.00 41.06 3.85
573 893 6.268387 ACACATTGAGAAAAATGGATGGTCTT 59.732 34.615 2.34 0.00 41.06 3.01
574 894 7.156673 CACATTGAGAAAAATGGATGGTCTTT 58.843 34.615 2.34 0.00 41.06 2.52
575 895 7.658575 CACATTGAGAAAAATGGATGGTCTTTT 59.341 33.333 2.34 0.00 41.06 2.27
576 896 8.869109 ACATTGAGAAAAATGGATGGTCTTTTA 58.131 29.630 2.34 0.00 41.06 1.52
577 897 9.709495 CATTGAGAAAAATGGATGGTCTTTTAA 57.291 29.630 0.00 0.00 34.50 1.52
588 908 8.561536 TGGATGGTCTTTTAATATAGGAGACA 57.438 34.615 0.00 0.00 38.72 3.41
589 909 9.170890 TGGATGGTCTTTTAATATAGGAGACAT 57.829 33.333 0.00 0.00 38.72 3.06
590 910 9.442047 GGATGGTCTTTTAATATAGGAGACATG 57.558 37.037 0.00 0.00 38.72 3.21
593 913 9.613428 TGGTCTTTTAATATAGGAGACATGTTG 57.387 33.333 0.00 0.00 38.72 3.33
594 914 9.832445 GGTCTTTTAATATAGGAGACATGTTGA 57.168 33.333 0.00 0.00 38.72 3.18
603 923 7.921041 ATAGGAGACATGTTGATTAAGGAGA 57.079 36.000 0.00 0.00 0.00 3.71
604 924 6.627087 AGGAGACATGTTGATTAAGGAGAA 57.373 37.500 0.00 0.00 0.00 2.87
605 925 7.020827 AGGAGACATGTTGATTAAGGAGAAA 57.979 36.000 0.00 0.00 0.00 2.52
606 926 7.637511 AGGAGACATGTTGATTAAGGAGAAAT 58.362 34.615 0.00 0.00 0.00 2.17
607 927 7.555554 AGGAGACATGTTGATTAAGGAGAAATG 59.444 37.037 0.00 0.00 0.00 2.32
608 928 7.554118 GGAGACATGTTGATTAAGGAGAAATGA 59.446 37.037 0.00 0.00 0.00 2.57
609 929 9.118300 GAGACATGTTGATTAAGGAGAAATGAT 57.882 33.333 0.00 0.00 0.00 2.45
635 955 6.548441 TTCAAACTATTTGTACGAGTTGGG 57.452 37.500 0.00 1.51 41.36 4.12
636 956 5.856156 TCAAACTATTTGTACGAGTTGGGA 58.144 37.500 0.00 3.26 41.36 4.37
637 957 6.289834 TCAAACTATTTGTACGAGTTGGGAA 58.710 36.000 0.00 0.00 41.36 3.97
638 958 6.938030 TCAAACTATTTGTACGAGTTGGGAAT 59.062 34.615 0.00 0.00 41.36 3.01
639 959 8.095792 TCAAACTATTTGTACGAGTTGGGAATA 58.904 33.333 0.00 0.00 41.36 1.75
640 960 8.723311 CAAACTATTTGTACGAGTTGGGAATAA 58.277 33.333 0.00 0.00 33.75 1.40
641 961 8.851541 AACTATTTGTACGAGTTGGGAATAAA 57.148 30.769 0.00 0.00 32.25 1.40
642 962 8.851541 ACTATTTGTACGAGTTGGGAATAAAA 57.148 30.769 0.00 0.00 0.00 1.52
643 963 8.943002 ACTATTTGTACGAGTTGGGAATAAAAG 58.057 33.333 0.00 0.00 0.00 2.27
644 964 7.989416 ATTTGTACGAGTTGGGAATAAAAGA 57.011 32.000 0.00 0.00 0.00 2.52
645 965 7.989416 TTTGTACGAGTTGGGAATAAAAGAT 57.011 32.000 0.00 0.00 0.00 2.40
646 966 7.989416 TTGTACGAGTTGGGAATAAAAGATT 57.011 32.000 0.00 0.00 0.00 2.40
647 967 7.372451 TGTACGAGTTGGGAATAAAAGATTG 57.628 36.000 0.00 0.00 0.00 2.67
648 968 6.938030 TGTACGAGTTGGGAATAAAAGATTGT 59.062 34.615 0.00 0.00 0.00 2.71
649 969 6.254281 ACGAGTTGGGAATAAAAGATTGTG 57.746 37.500 0.00 0.00 0.00 3.33
650 970 5.768164 ACGAGTTGGGAATAAAAGATTGTGT 59.232 36.000 0.00 0.00 0.00 3.72
651 971 6.938030 ACGAGTTGGGAATAAAAGATTGTGTA 59.062 34.615 0.00 0.00 0.00 2.90
652 972 7.094933 ACGAGTTGGGAATAAAAGATTGTGTAC 60.095 37.037 0.00 0.00 0.00 2.90
653 973 7.119262 CGAGTTGGGAATAAAAGATTGTGTACT 59.881 37.037 0.00 0.00 0.00 2.73
654 974 8.706322 AGTTGGGAATAAAAGATTGTGTACTT 57.294 30.769 0.00 0.00 0.00 2.24
655 975 9.143155 AGTTGGGAATAAAAGATTGTGTACTTT 57.857 29.630 0.00 0.00 37.85 2.66
774 1094 7.892778 TTAATCTAAATAGACGTGTGTTGCA 57.107 32.000 0.00 0.00 34.72 4.08
775 1095 5.779806 ATCTAAATAGACGTGTGTTGCAC 57.220 39.130 0.00 0.00 38.18 4.57
790 1110 3.453559 GCACGGGCATACACTTAGT 57.546 52.632 3.77 0.00 40.72 2.24
791 1111 2.589798 GCACGGGCATACACTTAGTA 57.410 50.000 3.77 0.00 40.72 1.82
792 1112 2.470821 GCACGGGCATACACTTAGTAG 58.529 52.381 3.77 0.00 40.72 2.57
793 1113 2.159142 GCACGGGCATACACTTAGTAGT 60.159 50.000 3.77 0.00 40.72 2.73
795 1115 6.462000 GCACGGGCATACACTTAGTAGTGA 62.462 50.000 3.77 0.00 46.26 3.41
796 1116 7.849447 GCACGGGCATACACTTAGTAGTGAA 62.849 48.000 3.77 0.00 46.26 3.18
886 1207 1.814793 TCCAATCATCGCACGGAAAA 58.185 45.000 0.00 0.00 0.00 2.29
902 1223 1.521423 GAAAACACCACGTCTCGTCTG 59.479 52.381 0.00 0.00 38.32 3.51
921 1242 3.888323 TCTGTCCATGTAGCAAAAGCAAA 59.112 39.130 0.00 0.00 0.00 3.68
922 1243 4.022935 TCTGTCCATGTAGCAAAAGCAAAG 60.023 41.667 0.00 0.00 0.00 2.77
923 1244 2.989166 GTCCATGTAGCAAAAGCAAAGC 59.011 45.455 0.00 0.00 0.00 3.51
924 1245 2.627221 TCCATGTAGCAAAAGCAAAGCA 59.373 40.909 0.00 0.00 0.00 3.91
925 1246 3.069300 TCCATGTAGCAAAAGCAAAGCAA 59.931 39.130 0.00 0.00 0.00 3.91
926 1247 3.998341 CCATGTAGCAAAAGCAAAGCAAT 59.002 39.130 0.00 0.00 0.00 3.56
927 1248 4.453136 CCATGTAGCAAAAGCAAAGCAATT 59.547 37.500 0.00 0.00 0.00 2.32
928 1249 5.638657 CCATGTAGCAAAAGCAAAGCAATTA 59.361 36.000 0.00 0.00 0.00 1.40
929 1250 6.183360 CCATGTAGCAAAAGCAAAGCAATTAG 60.183 38.462 0.00 0.00 0.00 1.73
930 1251 5.841810 TGTAGCAAAAGCAAAGCAATTAGT 58.158 33.333 0.00 0.00 0.00 2.24
932 1253 7.083858 TGTAGCAAAAGCAAAGCAATTAGTAG 58.916 34.615 0.00 0.00 0.00 2.57
933 1254 4.925646 AGCAAAAGCAAAGCAATTAGTAGC 59.074 37.500 0.00 0.00 0.00 3.58
935 1256 5.164022 GCAAAAGCAAAGCAATTAGTAGCAG 60.164 40.000 0.00 0.00 0.00 4.24
995 1316 1.069258 CTCCGGCGATAGGGTTTCC 59.931 63.158 9.30 0.00 0.00 3.13
1288 1609 2.993264 CCACGGACCAGGTACGGT 60.993 66.667 28.42 11.15 45.14 4.83
1289 1610 1.678635 CCACGGACCAGGTACGGTA 60.679 63.158 28.42 0.00 45.14 4.02
1290 1611 1.508088 CACGGACCAGGTACGGTAC 59.492 63.158 28.42 9.82 45.14 3.34
1318 1639 2.842320 GAGGTTTGGGACTTCGAGC 58.158 57.895 0.00 0.00 0.00 5.03
1320 1641 1.128188 AGGTTTGGGACTTCGAGCCT 61.128 55.000 1.82 0.00 0.00 4.58
1321 1642 0.955919 GGTTTGGGACTTCGAGCCTG 60.956 60.000 1.82 0.00 0.00 4.85
1418 1742 5.826208 ACCAAGTTCTCGTTATTTCAGGTTT 59.174 36.000 0.00 0.00 0.00 3.27
1505 1829 7.682865 CGTAACTAGTTAAAAAGTGCTTCGATG 59.317 37.037 16.82 0.00 0.00 3.84
1525 1850 6.697455 TCGATGCTACTGTTCTCATATTTGTC 59.303 38.462 0.00 0.00 0.00 3.18
1680 2006 4.012374 GTTGACATCTGTGATGGTGGAAT 58.988 43.478 11.55 0.00 0.00 3.01
1788 2114 2.540101 GGATCAGTATAGCACGTGCAAC 59.460 50.000 39.21 30.98 45.16 4.17
1806 2132 6.297694 TGCAACCATTTTTCTATTTTGCAC 57.702 33.333 2.11 0.00 42.06 4.57
1818 2147 1.249407 TTTTGCACGTTATCCCCACC 58.751 50.000 0.00 0.00 0.00 4.61
1819 2148 0.609681 TTTGCACGTTATCCCCACCC 60.610 55.000 0.00 0.00 0.00 4.61
1822 2151 1.029947 GCACGTTATCCCCACCCTTG 61.030 60.000 0.00 0.00 0.00 3.61
1892 2221 4.649267 TCTCGAGTGATATGAGGGAGAT 57.351 45.455 13.13 0.00 0.00 2.75
1947 2277 3.322514 GCTGTTAGCTGTCCCAACA 57.677 52.632 0.00 0.00 38.45 3.33
2072 2402 3.436704 AGTCTGTATGTCAAAATGGTGCG 59.563 43.478 0.00 0.00 0.00 5.34
2082 2412 0.751643 AAATGGTGCGGGTATGCCTC 60.752 55.000 0.00 0.00 34.45 4.70
2098 2428 2.012673 GCCTCCTACTGAATGCACTTG 58.987 52.381 0.00 0.00 0.00 3.16
2099 2429 2.616510 GCCTCCTACTGAATGCACTTGT 60.617 50.000 0.00 0.00 0.00 3.16
2100 2430 3.679389 CCTCCTACTGAATGCACTTGTT 58.321 45.455 0.00 0.00 0.00 2.83
2101 2431 4.832248 CCTCCTACTGAATGCACTTGTTA 58.168 43.478 0.00 0.00 0.00 2.41
2102 2432 4.631813 CCTCCTACTGAATGCACTTGTTAC 59.368 45.833 0.00 0.00 0.00 2.50
2103 2433 5.482908 CTCCTACTGAATGCACTTGTTACT 58.517 41.667 0.00 0.00 0.00 2.24
2104 2434 5.865085 TCCTACTGAATGCACTTGTTACTT 58.135 37.500 0.00 0.00 0.00 2.24
2105 2435 6.296026 TCCTACTGAATGCACTTGTTACTTT 58.704 36.000 0.00 0.00 0.00 2.66
2106 2436 6.204688 TCCTACTGAATGCACTTGTTACTTTG 59.795 38.462 0.00 0.00 0.00 2.77
2107 2437 5.835113 ACTGAATGCACTTGTTACTTTGT 57.165 34.783 0.00 0.00 0.00 2.83
2108 2438 6.207691 ACTGAATGCACTTGTTACTTTGTT 57.792 33.333 0.00 0.00 0.00 2.83
2109 2439 7.328277 ACTGAATGCACTTGTTACTTTGTTA 57.672 32.000 0.00 0.00 0.00 2.41
2225 2557 5.864628 AACCTTTCTCGAAATAGAGTTGC 57.135 39.130 0.00 0.00 39.21 4.17
2257 2589 4.425577 AGTTCATTCGATGTTCTTTGCC 57.574 40.909 0.00 0.00 0.00 4.52
2287 2619 8.859090 GTTGAATTGGATAAATCATGGGATGTA 58.141 33.333 0.00 0.00 32.92 2.29
2395 2727 7.065803 GCTTTCTTTGTAGCCACATACTTATCA 59.934 37.037 0.00 0.00 33.76 2.15
2525 2879 4.505556 CGTCTGTCCACATGATAATCAGTG 59.494 45.833 0.00 0.00 0.00 3.66
2559 2913 1.600023 TGGTTCATTTCCGTGTCACC 58.400 50.000 0.00 0.00 0.00 4.02
2560 2914 1.134068 TGGTTCATTTCCGTGTCACCA 60.134 47.619 0.00 0.00 33.81 4.17
2561 2915 1.265905 GGTTCATTTCCGTGTCACCAC 59.734 52.381 0.00 0.00 38.27 4.16
2568 2923 0.888619 TCCGTGTCACCACATCTCTC 59.111 55.000 0.00 0.00 41.93 3.20
2587 2942 4.820775 TCTCTATAAGAGATGCCCCAGTT 58.179 43.478 2.50 0.00 45.77 3.16
2633 2990 9.083422 ACTTGTGCTGCTCTTCTCTATAATATA 57.917 33.333 0.00 0.00 0.00 0.86
2637 2994 9.734620 GTGCTGCTCTTCTCTATAATATATCAG 57.265 37.037 0.00 0.00 0.00 2.90
2937 3302 0.921896 ATGTAGCTTCATGGGGTGCT 59.078 50.000 4.87 0.52 39.30 4.40
2959 3324 5.064834 GCTACAGCTGTTGGGTAAGTTATTC 59.935 44.000 27.06 1.59 38.21 1.75
2961 3326 4.202524 ACAGCTGTTGGGTAAGTTATTCCA 60.203 41.667 15.25 4.42 0.00 3.53
2968 3333 5.440207 TGGGTAAGTTATTCCACTAACCC 57.560 43.478 0.00 0.00 33.02 4.11
2984 3349 0.482446 ACCCTGGGCATGAACTTTCA 59.518 50.000 14.08 0.00 42.14 2.69
3016 3381 1.203052 CCCAACCTGCATAGCTTGTTG 59.797 52.381 13.45 13.45 38.98 3.33
3017 3382 1.203052 CCAACCTGCATAGCTTGTTGG 59.797 52.381 20.34 20.34 45.83 3.77
3035 3403 0.255033 GGTAAGCTTGGGTTCCCGAT 59.745 55.000 9.86 0.00 0.00 4.18
3091 3474 0.101040 TCACAAAGCACACAAGCTGC 59.899 50.000 0.00 0.00 45.89 5.25
3109 3495 5.032100 GCTGCTGAGCATAGTCAAATATG 57.968 43.478 7.94 0.00 45.46 1.78
3122 3508 2.555325 TCAAATATGCTGCCAGCTATGC 59.445 45.455 18.96 0.55 42.97 3.14
3138 3524 4.006319 GCTATGCCTTCAGAGTTTGTCTT 58.994 43.478 0.00 0.00 34.19 3.01
3139 3525 5.046304 AGCTATGCCTTCAGAGTTTGTCTTA 60.046 40.000 0.00 0.00 34.19 2.10
3144 3530 4.688413 GCCTTCAGAGTTTGTCTTAGTCAG 59.312 45.833 0.00 0.00 30.64 3.51
3147 3533 2.989840 CAGAGTTTGTCTTAGTCAGCCG 59.010 50.000 0.00 0.00 30.64 5.52
3150 3536 4.280174 AGAGTTTGTCTTAGTCAGCCGTTA 59.720 41.667 0.00 0.00 27.07 3.18
3151 3537 5.047235 AGAGTTTGTCTTAGTCAGCCGTTAT 60.047 40.000 0.00 0.00 27.07 1.89
3158 3544 5.690857 GTCTTAGTCAGCCGTTATGTAATCC 59.309 44.000 0.00 0.00 0.00 3.01
3160 3546 3.039011 AGTCAGCCGTTATGTAATCCCT 58.961 45.455 0.00 0.00 0.00 4.20
3173 3559 8.429641 GTTATGTAATCCCTTCCAATCTAGTGA 58.570 37.037 0.00 0.00 0.00 3.41
3182 3568 7.069578 TCCCTTCCAATCTAGTGAGTTACATAC 59.930 40.741 0.00 0.00 0.00 2.39
3205 3595 3.890756 TGAAGCTTCAAAATGCTCCTGAA 59.109 39.130 26.61 0.00 38.75 3.02
3224 3614 6.041409 TCCTGAAGAGAGGTTATGCTCTATTG 59.959 42.308 0.00 0.00 40.43 1.90
3237 3627 5.584253 TGCTCTATTGGTCTTCACTAGTC 57.416 43.478 0.00 0.00 32.44 2.59
3242 3639 7.642082 TCTATTGGTCTTCACTAGTCCTAAC 57.358 40.000 0.00 0.00 33.70 2.34
3264 3661 3.473113 AACCCTGGGAGCAAATATGTT 57.527 42.857 22.23 0.00 0.00 2.71
3274 3671 7.939782 TGGGAGCAAATATGTTATATGTGTTG 58.060 34.615 0.00 0.00 0.00 3.33
3277 3674 7.255590 GGAGCAAATATGTTATATGTGTTGGCT 60.256 37.037 0.00 0.00 0.00 4.75
3297 3694 3.564644 GCTCCATGATTGATCACTTCCAG 59.435 47.826 0.00 0.00 40.03 3.86
3298 3695 4.778579 CTCCATGATTGATCACTTCCAGT 58.221 43.478 0.00 0.00 40.03 4.00
3310 3707 3.386078 TCACTTCCAGTATCTGATGGAGC 59.614 47.826 0.00 0.00 46.01 4.70
3315 3712 2.171237 CCAGTATCTGATGGAGCCAACA 59.829 50.000 0.00 0.00 39.02 3.33
3330 3727 4.327680 AGCCAACAAATCTAGACTGGTTC 58.672 43.478 0.00 0.00 0.00 3.62
3335 3732 2.932614 CAAATCTAGACTGGTTCTGGCG 59.067 50.000 0.00 0.00 35.55 5.69
3356 3755 5.411361 GGCGTATGTAAGATTGCCATATTGA 59.589 40.000 0.00 0.00 42.03 2.57
3379 3779 1.682854 CATCAATTGGGAATGGGACCG 59.317 52.381 5.42 0.00 0.00 4.79
3400 3800 1.002087 GTTCGGACAAGGGACAGTCAT 59.998 52.381 2.17 0.00 37.37 3.06
3541 4037 7.116075 TGGTAACAGCATCTACAATAACCAAT 58.884 34.615 0.00 0.00 46.17 3.16
3631 4127 1.495148 TGGGTGGTGGTGATTGTTGTA 59.505 47.619 0.00 0.00 0.00 2.41
3718 4219 6.992123 TGATATACTGCCGATTGAAGAATTGT 59.008 34.615 0.00 0.00 0.00 2.71
3729 4230 7.258441 CGATTGAAGAATTGTGGTCTAGAGTA 58.742 38.462 0.00 0.00 0.00 2.59
3735 4238 7.106439 AGAATTGTGGTCTAGAGTATGTCTG 57.894 40.000 0.00 0.00 36.64 3.51
3744 4247 5.361285 GTCTAGAGTATGTCTGTTGGGATGT 59.639 44.000 0.00 0.00 36.64 3.06
3788 4291 4.497473 TTAGGTTTGTTGATTGAAGGCG 57.503 40.909 0.00 0.00 0.00 5.52
3841 4344 6.265422 GGTGCTAGAATGTAAATAGGCCATTT 59.735 38.462 5.01 11.64 40.10 2.32
3844 4347 9.231297 TGCTAGAATGTAAATAGGCCATTTATC 57.769 33.333 17.68 13.28 40.39 1.75
3855 4358 2.857592 CCATTTATCTGGCTGTGTGC 57.142 50.000 0.00 0.00 41.94 4.57
3856 4359 1.064505 CCATTTATCTGGCTGTGTGCG 59.935 52.381 0.00 0.00 44.05 5.34
3870 4373 3.043713 TGCGGCAACTGAAGCTCG 61.044 61.111 0.00 0.00 0.00 5.03
3947 4451 6.215121 TGTGCCAGAATAAACTTTGTGAATG 58.785 36.000 0.00 0.00 0.00 2.67
3969 4473 4.220163 TGAACTGCACCAAATGAATATGCA 59.780 37.500 0.00 0.00 43.70 3.96
3979 4483 6.991531 ACCAAATGAATATGCACACTTGTTTT 59.008 30.769 0.00 0.00 0.00 2.43
4008 4512 2.286365 ATTTCCGTGCCAGAAAAGGA 57.714 45.000 0.00 0.00 36.83 3.36
4044 4549 6.442952 TGATTGCAAACAATTGTACTACCAC 58.557 36.000 12.39 3.23 46.59 4.16
4094 4600 7.492669 AGAATACAGTGGTGATATTGAAACTCG 59.507 37.037 0.00 0.00 0.00 4.18
4170 4688 0.242017 AAAGCACAAGGAGCAATCGC 59.758 50.000 0.00 0.00 38.99 4.58
4297 4816 2.295909 CCAAAACGCAAAGATGAAGGGA 59.704 45.455 0.00 0.00 0.00 4.20
4298 4817 3.243704 CCAAAACGCAAAGATGAAGGGAA 60.244 43.478 0.00 0.00 0.00 3.97
4446 4965 8.741603 TCATCTCAATCTGATGCAAATAAAGA 57.258 30.769 0.00 0.00 40.59 2.52
4611 5130 7.749570 CAGCTGAAAGAGAACAAGAAACATATG 59.250 37.037 8.42 0.00 34.07 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.579127 GCCCTAAATGTGGCCGAT 57.421 55.556 0.00 0.00 41.97 4.18
108 109 2.203365 TCCGGAGCCGATCTCTCC 60.203 66.667 11.05 16.63 45.12 3.71
125 126 2.227036 CCACAGGGTCCAGCCTTCT 61.227 63.158 0.00 0.00 37.43 2.85
127 128 2.121963 TCCACAGGGTCCAGCCTT 60.122 61.111 0.00 0.00 37.43 4.35
158 159 1.202663 TCTACTCGATCCGTCCCTCTG 60.203 57.143 0.00 0.00 0.00 3.35
159 160 1.071071 CTCTACTCGATCCGTCCCTCT 59.929 57.143 0.00 0.00 0.00 3.69
160 161 1.515081 CTCTACTCGATCCGTCCCTC 58.485 60.000 0.00 0.00 0.00 4.30
161 162 0.535553 GCTCTACTCGATCCGTCCCT 60.536 60.000 0.00 0.00 0.00 4.20
162 163 1.843734 CGCTCTACTCGATCCGTCCC 61.844 65.000 0.00 0.00 0.00 4.46
166 167 1.863491 CCTCGCTCTACTCGATCCG 59.137 63.158 0.00 0.00 35.25 4.18
170 171 2.895865 CCGCCTCGCTCTACTCGA 60.896 66.667 0.00 0.00 34.52 4.04
171 172 2.887889 CTCCGCCTCGCTCTACTCG 61.888 68.421 0.00 0.00 0.00 4.18
242 243 2.795297 CTGTCTCGTCTCCTCCGC 59.205 66.667 0.00 0.00 0.00 5.54
272 273 3.058160 GCTGGGCACTCACGCAAT 61.058 61.111 0.00 0.00 31.47 3.56
287 288 7.480760 AATAAGAAGACAGAGAGAAAGAGCT 57.519 36.000 0.00 0.00 0.00 4.09
301 302 8.396390 GGGAAAACGGAAGAATAATAAGAAGAC 58.604 37.037 0.00 0.00 0.00 3.01
317 636 2.823154 GGATGTTCATTGGGAAAACGGA 59.177 45.455 0.00 0.00 37.23 4.69
320 639 4.954875 TGTTGGATGTTCATTGGGAAAAC 58.045 39.130 0.00 0.00 37.23 2.43
322 641 4.040217 CCTTGTTGGATGTTCATTGGGAAA 59.960 41.667 0.00 0.00 35.95 3.13
324 643 3.164268 CCTTGTTGGATGTTCATTGGGA 58.836 45.455 0.00 0.00 38.35 4.37
379 699 0.038744 CTCATGGGTTTGGCAGGAGT 59.961 55.000 0.00 0.00 0.00 3.85
382 702 2.353610 GGCTCATGGGTTTGGCAGG 61.354 63.158 0.00 0.00 0.00 4.85
415 735 3.371898 CACGTCGACACAGGTATACACTA 59.628 47.826 17.16 0.00 0.00 2.74
416 736 2.161012 CACGTCGACACAGGTATACACT 59.839 50.000 17.16 0.00 0.00 3.55
418 738 1.469703 CCACGTCGACACAGGTATACA 59.530 52.381 17.16 0.00 0.00 2.29
456 776 5.431420 AAACATTAACGTGTGCATCAAGA 57.569 34.783 8.62 0.00 31.49 3.02
484 804 6.201997 CCTACGCACACATTTATGCAAGTATA 59.798 38.462 0.00 0.00 42.17 1.47
485 805 4.963276 ACGCACACATTTATGCAAGTAT 57.037 36.364 0.00 0.00 42.17 2.12
486 806 4.331443 CCTACGCACACATTTATGCAAGTA 59.669 41.667 0.00 0.00 42.17 2.24
487 807 3.126858 CCTACGCACACATTTATGCAAGT 59.873 43.478 0.00 0.00 42.17 3.16
488 808 3.487376 CCCTACGCACACATTTATGCAAG 60.487 47.826 0.00 0.00 42.17 4.01
489 809 2.421775 CCCTACGCACACATTTATGCAA 59.578 45.455 0.00 0.00 42.17 4.08
490 810 2.013400 CCCTACGCACACATTTATGCA 58.987 47.619 0.00 0.00 42.17 3.96
491 811 2.285083 TCCCTACGCACACATTTATGC 58.715 47.619 0.00 0.00 38.52 3.14
492 812 3.792401 TCTCCCTACGCACACATTTATG 58.208 45.455 0.00 0.00 0.00 1.90
493 813 4.481368 TTCTCCCTACGCACACATTTAT 57.519 40.909 0.00 0.00 0.00 1.40
494 814 3.965379 TTCTCCCTACGCACACATTTA 57.035 42.857 0.00 0.00 0.00 1.40
495 815 2.851263 TTCTCCCTACGCACACATTT 57.149 45.000 0.00 0.00 0.00 2.32
496 816 2.236146 TGATTCTCCCTACGCACACATT 59.764 45.455 0.00 0.00 0.00 2.71
497 817 1.831106 TGATTCTCCCTACGCACACAT 59.169 47.619 0.00 0.00 0.00 3.21
498 818 1.262417 TGATTCTCCCTACGCACACA 58.738 50.000 0.00 0.00 0.00 3.72
499 819 2.159099 TCATGATTCTCCCTACGCACAC 60.159 50.000 0.00 0.00 0.00 3.82
500 820 2.107366 TCATGATTCTCCCTACGCACA 58.893 47.619 0.00 0.00 0.00 4.57
501 821 2.890808 TCATGATTCTCCCTACGCAC 57.109 50.000 0.00 0.00 0.00 5.34
502 822 2.965147 TCATCATGATTCTCCCTACGCA 59.035 45.455 5.16 0.00 0.00 5.24
503 823 3.667497 TCATCATGATTCTCCCTACGC 57.333 47.619 5.16 0.00 0.00 4.42
504 824 6.035368 AGATTCATCATGATTCTCCCTACG 57.965 41.667 5.16 0.00 33.31 3.51
505 825 7.678837 AGAAGATTCATCATGATTCTCCCTAC 58.321 38.462 11.62 3.74 36.44 3.18
506 826 7.868792 AGAAGATTCATCATGATTCTCCCTA 57.131 36.000 11.62 0.00 36.44 3.53
507 827 6.766997 AGAAGATTCATCATGATTCTCCCT 57.233 37.500 11.62 9.47 36.44 4.20
508 828 8.915057 TTTAGAAGATTCATCATGATTCTCCC 57.085 34.615 11.62 7.75 36.44 4.30
539 859 9.311916 CCATTTTTCTCAATGTGTAAAACTCAA 57.688 29.630 2.82 0.00 32.95 3.02
540 860 8.690884 TCCATTTTTCTCAATGTGTAAAACTCA 58.309 29.630 2.82 0.00 32.95 3.41
541 861 9.696917 ATCCATTTTTCTCAATGTGTAAAACTC 57.303 29.630 2.82 0.00 32.95 3.01
542 862 9.480053 CATCCATTTTTCTCAATGTGTAAAACT 57.520 29.630 2.82 0.00 32.95 2.66
543 863 8.711457 CCATCCATTTTTCTCAATGTGTAAAAC 58.289 33.333 2.82 0.00 32.95 2.43
544 864 8.428063 ACCATCCATTTTTCTCAATGTGTAAAA 58.572 29.630 3.16 3.16 32.95 1.52
545 865 7.961351 ACCATCCATTTTTCTCAATGTGTAAA 58.039 30.769 0.00 0.00 32.95 2.01
546 866 7.451255 AGACCATCCATTTTTCTCAATGTGTAA 59.549 33.333 0.00 0.00 32.95 2.41
547 867 6.947733 AGACCATCCATTTTTCTCAATGTGTA 59.052 34.615 0.00 0.00 32.95 2.90
548 868 5.776716 AGACCATCCATTTTTCTCAATGTGT 59.223 36.000 0.00 0.00 32.95 3.72
549 869 6.276832 AGACCATCCATTTTTCTCAATGTG 57.723 37.500 0.00 0.00 32.95 3.21
550 870 6.923199 AAGACCATCCATTTTTCTCAATGT 57.077 33.333 0.00 0.00 32.95 2.71
551 871 9.709495 TTAAAAGACCATCCATTTTTCTCAATG 57.291 29.630 0.00 0.00 34.39 2.82
562 882 9.170890 TGTCTCCTATATTAAAAGACCATCCAT 57.829 33.333 0.00 0.00 36.39 3.41
563 883 8.561536 TGTCTCCTATATTAAAAGACCATCCA 57.438 34.615 0.00 0.00 36.39 3.41
564 884 9.442047 CATGTCTCCTATATTAAAAGACCATCC 57.558 37.037 0.00 0.00 36.39 3.51
567 887 9.613428 CAACATGTCTCCTATATTAAAAGACCA 57.387 33.333 0.00 0.00 36.39 4.02
568 888 9.832445 TCAACATGTCTCCTATATTAAAAGACC 57.168 33.333 0.00 0.00 36.39 3.85
577 897 9.607333 TCTCCTTAATCAACATGTCTCCTATAT 57.393 33.333 0.00 0.00 0.00 0.86
578 898 9.434275 TTCTCCTTAATCAACATGTCTCCTATA 57.566 33.333 0.00 0.00 0.00 1.31
579 899 7.921041 TCTCCTTAATCAACATGTCTCCTAT 57.079 36.000 0.00 0.00 0.00 2.57
580 900 7.733773 TTCTCCTTAATCAACATGTCTCCTA 57.266 36.000 0.00 0.00 0.00 2.94
581 901 6.627087 TTCTCCTTAATCAACATGTCTCCT 57.373 37.500 0.00 0.00 0.00 3.69
582 902 7.554118 TCATTTCTCCTTAATCAACATGTCTCC 59.446 37.037 0.00 0.00 0.00 3.71
583 903 8.498054 TCATTTCTCCTTAATCAACATGTCTC 57.502 34.615 0.00 0.00 0.00 3.36
609 929 8.723311 CCCAACTCGTACAAATAGTTTGAAATA 58.277 33.333 9.21 0.00 43.26 1.40
610 930 7.446013 TCCCAACTCGTACAAATAGTTTGAAAT 59.554 33.333 9.21 0.00 43.26 2.17
611 931 6.766944 TCCCAACTCGTACAAATAGTTTGAAA 59.233 34.615 9.21 0.00 43.26 2.69
612 932 6.289834 TCCCAACTCGTACAAATAGTTTGAA 58.710 36.000 9.21 0.00 43.26 2.69
613 933 5.856156 TCCCAACTCGTACAAATAGTTTGA 58.144 37.500 9.21 0.00 43.26 2.69
614 934 6.548441 TTCCCAACTCGTACAAATAGTTTG 57.452 37.500 1.15 1.15 45.95 2.93
615 935 8.851541 TTATTCCCAACTCGTACAAATAGTTT 57.148 30.769 0.00 0.00 31.21 2.66
616 936 8.851541 TTTATTCCCAACTCGTACAAATAGTT 57.148 30.769 0.00 0.00 33.82 2.24
617 937 8.851541 TTTTATTCCCAACTCGTACAAATAGT 57.148 30.769 0.00 0.00 0.00 2.12
618 938 9.158233 TCTTTTATTCCCAACTCGTACAAATAG 57.842 33.333 0.00 0.00 0.00 1.73
619 939 9.675464 ATCTTTTATTCCCAACTCGTACAAATA 57.325 29.630 0.00 0.00 0.00 1.40
620 940 7.989416 TCTTTTATTCCCAACTCGTACAAAT 57.011 32.000 0.00 0.00 0.00 2.32
621 941 7.989416 ATCTTTTATTCCCAACTCGTACAAA 57.011 32.000 0.00 0.00 0.00 2.83
622 942 7.446013 ACAATCTTTTATTCCCAACTCGTACAA 59.554 33.333 0.00 0.00 0.00 2.41
623 943 6.938030 ACAATCTTTTATTCCCAACTCGTACA 59.062 34.615 0.00 0.00 0.00 2.90
624 944 7.094933 ACACAATCTTTTATTCCCAACTCGTAC 60.095 37.037 0.00 0.00 0.00 3.67
625 945 6.938030 ACACAATCTTTTATTCCCAACTCGTA 59.062 34.615 0.00 0.00 0.00 3.43
626 946 5.768164 ACACAATCTTTTATTCCCAACTCGT 59.232 36.000 0.00 0.00 0.00 4.18
627 947 6.254281 ACACAATCTTTTATTCCCAACTCG 57.746 37.500 0.00 0.00 0.00 4.18
628 948 8.336801 AGTACACAATCTTTTATTCCCAACTC 57.663 34.615 0.00 0.00 0.00 3.01
629 949 8.706322 AAGTACACAATCTTTTATTCCCAACT 57.294 30.769 0.00 0.00 0.00 3.16
748 1068 9.589111 TGCAACACACGTCTATTTAGATTAATA 57.411 29.630 0.00 0.00 34.39 0.98
749 1069 8.388103 GTGCAACACACGTCTATTTAGATTAAT 58.612 33.333 0.00 0.00 40.07 1.40
750 1070 7.735500 GTGCAACACACGTCTATTTAGATTAA 58.264 34.615 0.00 0.00 40.07 1.40
751 1071 7.285783 GTGCAACACACGTCTATTTAGATTA 57.714 36.000 0.00 0.00 40.07 1.75
752 1072 6.165659 GTGCAACACACGTCTATTTAGATT 57.834 37.500 0.00 0.00 40.07 2.40
753 1073 5.779806 GTGCAACACACGTCTATTTAGAT 57.220 39.130 0.00 0.00 40.07 1.98
770 1090 6.129111 ACTACTAAGTGTATGCCCGTGCAA 62.129 45.833 0.00 0.00 42.55 4.08
771 1091 4.688897 ACTACTAAGTGTATGCCCGTGCA 61.689 47.826 0.00 0.00 43.12 4.57
772 1092 2.159142 ACTACTAAGTGTATGCCCGTGC 60.159 50.000 0.00 0.00 33.57 5.34
773 1093 3.444916 CACTACTAAGTGTATGCCCGTG 58.555 50.000 0.00 0.00 46.76 4.94
774 1094 3.795623 CACTACTAAGTGTATGCCCGT 57.204 47.619 0.00 0.00 46.76 5.28
781 1101 8.864472 GCACACGGTGTTCACTACTAAGTGTA 62.864 46.154 11.82 0.00 43.36 2.90
783 1103 5.836003 GCACACGGTGTTCACTACTAAGTG 61.836 50.000 11.82 0.00 43.77 3.16
784 1104 3.797865 GCACACGGTGTTCACTACTAAGT 60.798 47.826 11.82 0.00 35.75 2.24
785 1105 2.729882 GCACACGGTGTTCACTACTAAG 59.270 50.000 11.82 0.00 35.75 2.18
786 1106 2.101082 TGCACACGGTGTTCACTACTAA 59.899 45.455 11.82 0.00 35.75 2.24
787 1107 1.682323 TGCACACGGTGTTCACTACTA 59.318 47.619 11.82 0.00 35.75 1.82
788 1108 0.462375 TGCACACGGTGTTCACTACT 59.538 50.000 11.82 0.00 35.75 2.57
789 1109 0.859232 CTGCACACGGTGTTCACTAC 59.141 55.000 11.82 0.00 35.75 2.73
790 1110 0.249699 CCTGCACACGGTGTTCACTA 60.250 55.000 11.82 0.00 35.75 2.74
791 1111 1.523711 CCTGCACACGGTGTTCACT 60.524 57.895 11.82 0.00 35.75 3.41
792 1112 2.542907 CCCTGCACACGGTGTTCAC 61.543 63.158 11.82 4.95 35.75 3.18
793 1113 2.203139 CCCTGCACACGGTGTTCA 60.203 61.111 11.82 12.37 35.75 3.18
794 1114 1.961277 CTCCCTGCACACGGTGTTC 60.961 63.158 11.82 7.59 35.75 3.18
795 1115 2.111043 CTCCCTGCACACGGTGTT 59.889 61.111 11.82 0.00 35.75 3.32
796 1116 3.941188 CCTCCCTGCACACGGTGT 61.941 66.667 8.21 8.21 35.75 4.16
797 1117 3.177194 TTCCTCCCTGCACACGGTG 62.177 63.158 6.58 6.58 36.51 4.94
798 1118 2.847234 TTCCTCCCTGCACACGGT 60.847 61.111 0.00 0.00 0.00 4.83
799 1119 2.046892 CTTCCTCCCTGCACACGG 60.047 66.667 0.00 0.00 0.00 4.94
800 1120 2.743928 GCTTCCTCCCTGCACACG 60.744 66.667 0.00 0.00 0.00 4.49
836 1156 2.866156 GGAAAGGTGTTTTTGCTGCTTC 59.134 45.455 0.00 0.00 0.00 3.86
886 1207 1.653115 GACAGACGAGACGTGGTGT 59.347 57.895 0.00 5.20 41.37 4.16
921 1242 3.190874 GCGTCTTCTGCTACTAATTGCT 58.809 45.455 0.00 0.00 0.00 3.91
922 1243 2.285488 GGCGTCTTCTGCTACTAATTGC 59.715 50.000 0.00 0.00 0.00 3.56
923 1244 3.307242 GTGGCGTCTTCTGCTACTAATTG 59.693 47.826 0.00 0.00 40.27 2.32
924 1245 3.522553 GTGGCGTCTTCTGCTACTAATT 58.477 45.455 0.00 0.00 40.27 1.40
925 1246 2.479730 CGTGGCGTCTTCTGCTACTAAT 60.480 50.000 0.00 0.00 41.13 1.73
926 1247 1.135489 CGTGGCGTCTTCTGCTACTAA 60.135 52.381 0.00 0.00 41.13 2.24
927 1248 0.450583 CGTGGCGTCTTCTGCTACTA 59.549 55.000 0.00 0.00 41.13 1.82
928 1249 1.213013 CGTGGCGTCTTCTGCTACT 59.787 57.895 0.00 0.00 41.13 2.57
929 1250 2.445438 GCGTGGCGTCTTCTGCTAC 61.445 63.158 0.00 0.00 40.06 3.58
930 1251 2.126071 GCGTGGCGTCTTCTGCTA 60.126 61.111 0.00 0.00 0.00 3.49
932 1253 2.770587 CTTTGCGTGGCGTCTTCTGC 62.771 60.000 0.00 0.00 0.00 4.26
933 1254 1.205064 CTTTGCGTGGCGTCTTCTG 59.795 57.895 0.00 0.00 0.00 3.02
935 1256 2.127232 GCTTTGCGTGGCGTCTTC 60.127 61.111 0.00 0.00 0.00 2.87
1215 1536 3.771491 CCGTCGTCGTCGTCGTCT 61.771 66.667 17.80 0.00 44.09 4.18
1288 1609 3.009192 AAACCTCGCCGCATCCGTA 62.009 57.895 0.00 0.00 0.00 4.02
1289 1610 4.388499 AAACCTCGCCGCATCCGT 62.388 61.111 0.00 0.00 0.00 4.69
1290 1611 3.864686 CAAACCTCGCCGCATCCG 61.865 66.667 0.00 0.00 0.00 4.18
1291 1612 3.508840 CCAAACCTCGCCGCATCC 61.509 66.667 0.00 0.00 0.00 3.51
1292 1613 3.508840 CCCAAACCTCGCCGCATC 61.509 66.667 0.00 0.00 0.00 3.91
1293 1614 4.028490 TCCCAAACCTCGCCGCAT 62.028 61.111 0.00 0.00 0.00 4.73
1320 1641 0.516877 CCTCGTGCGCTGAATTTTCA 59.483 50.000 9.73 0.00 35.57 2.69
1321 1642 0.794605 GCCTCGTGCGCTGAATTTTC 60.795 55.000 9.73 0.00 0.00 2.29
1332 1656 2.854185 GCAATTCATTAAAGCCTCGTGC 59.146 45.455 0.00 0.00 41.71 5.34
1359 1683 0.941542 GCTCAACAGTTACACGCCAA 59.058 50.000 0.00 0.00 0.00 4.52
1418 1742 3.928727 ACCGATCAAGTTAGTTCGACA 57.071 42.857 0.00 0.00 33.72 4.35
1505 1829 6.036517 CCACAGACAAATATGAGAACAGTAGC 59.963 42.308 0.00 0.00 0.00 3.58
1525 1850 0.109342 ACCAAGCAGAGGAACCACAG 59.891 55.000 0.00 0.00 0.00 3.66
1589 1915 4.510167 AAGGACATCTTTCCATGGTAGG 57.490 45.455 12.58 2.31 38.25 3.18
1680 2006 4.227300 AGCCTAAACCATCACATTCCACTA 59.773 41.667 0.00 0.00 0.00 2.74
1788 2114 7.010091 GGGATAACGTGCAAAATAGAAAAATGG 59.990 37.037 0.00 0.00 0.00 3.16
1806 2132 1.453197 GGCAAGGGTGGGGATAACG 60.453 63.158 0.00 0.00 0.00 3.18
1818 2147 3.514645 GCACACATTCTAAATGGCAAGG 58.485 45.455 0.00 0.00 0.00 3.61
1819 2148 3.514645 GGCACACATTCTAAATGGCAAG 58.485 45.455 0.00 0.00 35.99 4.01
1822 2151 1.742831 TCGGCACACATTCTAAATGGC 59.257 47.619 4.82 0.00 0.00 4.40
1947 2277 1.333177 AGCCGTTCAGACTTCAGAGT 58.667 50.000 0.00 0.00 39.32 3.24
2066 2396 2.882403 TAGGAGGCATACCCGCACCA 62.882 60.000 0.00 0.00 39.21 4.17
2072 2402 2.551071 GCATTCAGTAGGAGGCATACCC 60.551 54.545 0.00 0.00 36.11 3.69
2082 2412 6.017109 ACAAAGTAACAAGTGCATTCAGTAGG 60.017 38.462 0.00 0.00 0.00 3.18
2098 2428 8.996271 ACCAGCAGTAATAACTAACAAAGTAAC 58.004 33.333 0.00 0.00 37.50 2.50
2100 2430 9.865321 CTACCAGCAGTAATAACTAACAAAGTA 57.135 33.333 0.00 0.00 37.50 2.24
2101 2431 8.373220 ACTACCAGCAGTAATAACTAACAAAGT 58.627 33.333 0.00 0.00 41.49 2.66
2102 2432 8.656849 CACTACCAGCAGTAATAACTAACAAAG 58.343 37.037 0.00 0.00 33.48 2.77
2103 2433 7.118680 GCACTACCAGCAGTAATAACTAACAAA 59.881 37.037 0.00 0.00 33.48 2.83
2104 2434 6.592607 GCACTACCAGCAGTAATAACTAACAA 59.407 38.462 0.00 0.00 33.48 2.83
2105 2435 6.103997 GCACTACCAGCAGTAATAACTAACA 58.896 40.000 0.00 0.00 33.48 2.41
2106 2436 5.522824 GGCACTACCAGCAGTAATAACTAAC 59.477 44.000 0.00 0.00 38.86 2.34
2107 2437 5.424252 AGGCACTACCAGCAGTAATAACTAA 59.576 40.000 0.00 0.00 43.14 2.24
2108 2438 4.960469 AGGCACTACCAGCAGTAATAACTA 59.040 41.667 0.00 0.00 43.14 2.24
2109 2439 3.775316 AGGCACTACCAGCAGTAATAACT 59.225 43.478 0.00 0.00 43.14 2.24
2158 2490 6.434028 ACACAACATTCCACTGCATTAGTTAT 59.566 34.615 0.00 0.00 37.60 1.89
2164 2496 4.370917 GAAACACAACATTCCACTGCATT 58.629 39.130 0.00 0.00 0.00 3.56
2225 2557 7.916128 ACATCGAATGAACTTTAGAGTATCG 57.084 36.000 0.00 0.00 42.67 2.92
2257 2589 6.982141 CCCATGATTTATCCAATTCAACTGTG 59.018 38.462 0.00 0.00 30.21 3.66
2287 2619 2.643551 CACACATCTCCCGCCTTTATT 58.356 47.619 0.00 0.00 0.00 1.40
2395 2727 6.189133 TCCTACCTTGGTTTTTGTAAGTGTT 58.811 36.000 0.00 0.00 0.00 3.32
2443 2797 2.019807 AGGGAACAGGAACGAAGGTA 57.980 50.000 0.00 0.00 0.00 3.08
2568 2923 4.593206 TGGTAACTGGGGCATCTCTTATAG 59.407 45.833 0.00 0.00 37.61 1.31
2587 2942 6.070653 ACAAGTATAAAGTCCGGAACATGGTA 60.071 38.462 5.23 0.00 0.00 3.25
2937 3302 5.013287 TGGAATAACTTACCCAACAGCTGTA 59.987 40.000 22.01 0.00 0.00 2.74
2959 3324 0.331278 TTCATGCCCAGGGTTAGTGG 59.669 55.000 7.55 0.00 34.52 4.00
2961 3326 1.372501 AGTTCATGCCCAGGGTTAGT 58.627 50.000 7.55 0.00 0.00 2.24
2968 3333 4.589216 TTTCTTGAAAGTTCATGCCCAG 57.411 40.909 0.00 0.00 37.00 4.45
2984 3349 2.365293 GCAGGTTGGGTCAACATTTCTT 59.635 45.455 12.06 0.00 45.11 2.52
3035 3403 8.637986 ACAGAAAACTAATTTGCAGTATTTCCA 58.362 29.630 2.03 0.00 31.11 3.53
3071 3454 1.862815 GCAGCTTGTGTGCTTTGTGAG 60.863 52.381 0.00 0.00 41.98 3.51
3122 3508 4.688413 GCTGACTAAGACAAACTCTGAAGG 59.312 45.833 0.00 0.00 0.00 3.46
3138 3524 4.220724 AGGGATTACATAACGGCTGACTA 58.779 43.478 0.00 0.00 0.00 2.59
3139 3525 3.039011 AGGGATTACATAACGGCTGACT 58.961 45.455 0.00 0.00 0.00 3.41
3144 3530 3.202829 TGGAAGGGATTACATAACGGC 57.797 47.619 0.00 0.00 0.00 5.68
3147 3533 8.429641 TCACTAGATTGGAAGGGATTACATAAC 58.570 37.037 0.00 0.00 0.00 1.89
3150 3536 6.617371 ACTCACTAGATTGGAAGGGATTACAT 59.383 38.462 0.00 0.00 0.00 2.29
3151 3537 5.964477 ACTCACTAGATTGGAAGGGATTACA 59.036 40.000 0.00 0.00 0.00 2.41
3158 3544 7.923344 CAGTATGTAACTCACTAGATTGGAAGG 59.077 40.741 0.00 0.00 35.76 3.46
3160 3546 8.589701 TCAGTATGTAACTCACTAGATTGGAA 57.410 34.615 0.00 0.00 35.76 3.53
3173 3559 7.175641 AGCATTTTGAAGCTTCAGTATGTAACT 59.824 33.333 31.78 24.25 38.01 2.24
3182 3568 3.504906 TCAGGAGCATTTTGAAGCTTCAG 59.495 43.478 27.02 17.45 42.04 3.02
3205 3595 5.463154 AGACCAATAGAGCATAACCTCTCT 58.537 41.667 0.00 0.00 41.15 3.10
3224 3614 5.126869 GGGTTAGTTAGGACTAGTGAAGACC 59.873 48.000 0.00 0.00 39.43 3.85
3237 3627 1.580059 TGCTCCCAGGGTTAGTTAGG 58.420 55.000 5.01 0.00 0.00 2.69
3242 3639 4.170468 ACATATTTGCTCCCAGGGTTAG 57.830 45.455 5.01 0.00 0.00 2.34
3264 3661 5.939447 TCAATCATGGAGCCAACACATATA 58.061 37.500 0.00 0.00 0.00 0.86
3274 3671 2.883386 GGAAGTGATCAATCATGGAGCC 59.117 50.000 0.00 0.00 39.30 4.70
3297 3694 5.128919 AGATTTGTTGGCTCCATCAGATAC 58.871 41.667 3.79 0.00 0.00 2.24
3298 3695 5.378230 AGATTTGTTGGCTCCATCAGATA 57.622 39.130 3.79 0.00 0.00 1.98
3310 3707 4.697352 CCAGAACCAGTCTAGATTTGTTGG 59.303 45.833 9.12 8.48 33.56 3.77
3315 3712 2.567615 ACGCCAGAACCAGTCTAGATTT 59.432 45.455 0.00 0.00 33.56 2.17
3330 3727 2.560504 TGGCAATCTTACATACGCCAG 58.439 47.619 0.00 0.00 44.27 4.85
3356 3755 1.291637 TCCCATTCCCAATTGATGCCT 59.708 47.619 7.12 0.00 0.00 4.75
3366 3765 2.961893 CGAACCGGTCCCATTCCCA 61.962 63.158 8.04 0.00 0.00 4.37
3379 3779 0.320508 GACTGTCCCTTGTCCGAACC 60.321 60.000 0.00 0.00 0.00 3.62
3541 4037 2.094675 GCCTGCTGCCTTAAGAATTGA 58.905 47.619 3.36 0.00 0.00 2.57
3631 4127 5.065988 CCTAAATAAATGTAGCACGCCAGTT 59.934 40.000 0.00 0.00 0.00 3.16
3718 4219 4.023980 CCCAACAGACATACTCTAGACCA 58.976 47.826 0.00 0.00 0.00 4.02
3729 4230 3.828451 CCTTCAAACATCCCAACAGACAT 59.172 43.478 0.00 0.00 0.00 3.06
3735 4238 4.082026 CCTCAATCCTTCAAACATCCCAAC 60.082 45.833 0.00 0.00 0.00 3.77
3744 4247 3.009723 CGCTAAGCCTCAATCCTTCAAA 58.990 45.455 0.00 0.00 0.00 2.69
3788 4291 7.655732 ACATAATTTATTTAAATGGGCTTCCGC 59.344 33.333 11.05 0.00 36.14 5.54
3822 4325 8.641498 CCAGATAAATGGCCTATTTACATTCT 57.359 34.615 17.28 14.41 42.39 2.40
3841 4344 2.125147 GCCGCACACAGCCAGATA 60.125 61.111 0.00 0.00 41.38 1.98
3844 4347 4.332637 GTTGCCGCACACAGCCAG 62.333 66.667 0.00 0.00 41.38 4.85
3851 4354 2.203195 AGCTTCAGTTGCCGCACA 60.203 55.556 0.00 0.00 0.00 4.57
3855 4358 3.793144 GCCGAGCTTCAGTTGCCG 61.793 66.667 0.00 0.00 0.00 5.69
3856 4359 0.744414 TATGCCGAGCTTCAGTTGCC 60.744 55.000 0.00 0.00 0.00 4.52
3870 4373 6.909550 TTACATTTTGGGGATACATATGCC 57.090 37.500 1.58 0.90 42.77 4.40
3947 4451 4.563976 GTGCATATTCATTTGGTGCAGTTC 59.436 41.667 0.00 0.00 45.32 3.01
4008 4512 7.908827 TTGTTTGCAATCAATTGAGCATATT 57.091 28.000 19.52 4.57 40.14 1.28
4044 4549 1.730501 AGCTCCATTCGACACACATG 58.269 50.000 0.00 0.00 0.00 3.21
4094 4600 7.807907 CAGTTACAAAACAATGGAGATGTTACC 59.192 37.037 0.00 0.00 39.98 2.85
4170 4688 4.433186 TTCTTATTTGGTTGTGATGGCG 57.567 40.909 0.00 0.00 0.00 5.69
4297 4816 7.441836 TGCAATGTAGACGACCTATGATTATT 58.558 34.615 0.00 0.00 0.00 1.40
4298 4817 6.993079 TGCAATGTAGACGACCTATGATTAT 58.007 36.000 0.00 0.00 0.00 1.28
4347 4866 2.415608 TAGCTGCGGTTCTCCTCGG 61.416 63.158 0.00 0.00 0.00 4.63
4446 4965 9.903682 GCAATATCTTAACTCATGCATTATGTT 57.096 29.630 0.00 5.24 38.01 2.71
4496 5015 6.945435 TGTAATTTCACCTTTCTCATGCCTTA 59.055 34.615 0.00 0.00 0.00 2.69
4526 5045 0.546122 AGATCGTTGCCATTGCCCTA 59.454 50.000 0.00 0.00 36.33 3.53


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

AutoCloner maintained by Alex Coulton.