Multiple sequence alignment - TraesCS4D01G025400

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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 TraesCS4D01G025400 chr4D 100.000 4552 0 0 1 4552 10987150 10991701 0.000000e+00 8407
1 TraesCS4D01G025400 chr4B 95.113 3724 141 22 867 4552 20743763 20747483 0.000000e+00 5830
2 TraesCS4D01G025400 chr4B 81.867 557 47 27 1 547 20743037 20743549 1.960000e-113 420
3 TraesCS4D01G025400 chr4A 93.802 3727 166 20 867 4549 591874754 591878459 0.000000e+00 5542
4 TraesCS4D01G025400 chr4A 90.097 414 18 8 1 411 591873759 591874152 2.430000e-142 516
5 TraesCS4D01G025400 chr1B 97.490 478 12 0 2609 3086 252980368 252979891 0.000000e+00 817


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 TraesCS4D01G025400 chr4D 10987150 10991701 4551 False 8407 8407 100.0000 1 4552 1 chr4D.!!$F1 4551
1 TraesCS4D01G025400 chr4B 20743037 20747483 4446 False 3125 5830 88.4900 1 4552 2 chr4B.!!$F1 4551
2 TraesCS4D01G025400 chr4A 591873759 591878459 4700 False 3029 5542 91.9495 1 4549 2 chr4A.!!$F1 4548

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
710 874 0.040692 GGCAAAAACCGGAGTCGAAC 60.041 55.0 9.46 0.00 39.00 3.95 F
811 975 0.119561 TCTGGGCAAGTAGGGGGTAA 59.880 55.0 0.00 0.00 0.00 2.85 F
1617 1871 0.250209 CATTCTCCTCAGGGCGATGG 60.250 60.0 0.00 0.00 0.00 3.51 F
2174 2435 0.258774 TTAGAAATGGAGGCAGGCCC 59.741 55.0 6.70 0.85 36.58 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1598 1852 0.250209 CCATCGCCCTGAGGAGAATG 60.250 60.0 0.00 0.0 45.90 2.67 R
2429 2690 0.684535 TCAGGCGGTGAACTGAATCA 59.315 50.0 0.00 0.0 40.51 2.57 R
2834 3095 2.063541 GATTCCAAAGCCGGGCATCG 62.064 60.0 23.09 8.2 38.88 3.84 R
3830 4124 0.039798 GTTGCATGCACACTGACAGG 60.040 55.0 22.58 0.0 0.00 4.00 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
164 166 3.152341 GGAGGCACTTATGGATTCATGG 58.848 50.000 0.00 0.00 41.55 3.66
225 229 4.159693 ACCAACTTGGGAGAAAGTGTTTTC 59.840 41.667 12.62 0.00 43.37 2.29
229 233 3.943671 TGGGAGAAAGTGTTTTCCTGA 57.056 42.857 0.00 0.00 42.99 3.86
230 234 4.453480 TGGGAGAAAGTGTTTTCCTGAT 57.547 40.909 0.00 0.00 42.99 2.90
231 235 5.576563 TGGGAGAAAGTGTTTTCCTGATA 57.423 39.130 0.00 0.00 42.99 2.15
232 236 5.313712 TGGGAGAAAGTGTTTTCCTGATAC 58.686 41.667 0.00 0.00 42.99 2.24
233 237 5.073144 TGGGAGAAAGTGTTTTCCTGATACT 59.927 40.000 0.00 0.00 42.99 2.12
234 238 5.644206 GGGAGAAAGTGTTTTCCTGATACTC 59.356 44.000 0.00 0.00 42.99 2.59
235 239 6.231211 GGAGAAAGTGTTTTCCTGATACTCA 58.769 40.000 0.00 0.00 42.99 3.41
236 240 6.881602 GGAGAAAGTGTTTTCCTGATACTCAT 59.118 38.462 0.00 0.00 42.99 2.90
237 241 8.041323 GGAGAAAGTGTTTTCCTGATACTCATA 58.959 37.037 0.00 0.00 42.99 2.15
238 242 9.606631 GAGAAAGTGTTTTCCTGATACTCATAT 57.393 33.333 0.00 0.00 42.99 1.78
251 260 3.570926 ACTCATATACACGCCATACCG 57.429 47.619 0.00 0.00 0.00 4.02
272 281 3.181506 CGAGGAGCAAGTATTTTTCTGCC 60.182 47.826 0.00 0.00 0.00 4.85
312 321 2.507471 CCCCCTTATTGAGCTGAGAAGT 59.493 50.000 0.00 0.00 0.00 3.01
322 331 5.219343 TGAGCTGAGAAGTGAAAATCTGA 57.781 39.130 0.00 0.00 0.00 3.27
327 336 6.545298 AGCTGAGAAGTGAAAATCTGAAACTT 59.455 34.615 0.00 0.00 33.91 2.66
328 337 7.067981 AGCTGAGAAGTGAAAATCTGAAACTTT 59.932 33.333 0.00 0.00 31.45 2.66
329 338 7.704047 GCTGAGAAGTGAAAATCTGAAACTTTT 59.296 33.333 0.00 0.00 31.45 2.27
335 344 8.285776 AGTGAAAATCTGAAACTTTTATTGCG 57.714 30.769 0.00 0.00 0.00 4.85
336 345 8.134895 AGTGAAAATCTGAAACTTTTATTGCGA 58.865 29.630 0.00 0.00 0.00 5.10
337 346 8.751335 GTGAAAATCTGAAACTTTTATTGCGAA 58.249 29.630 0.00 0.00 0.00 4.70
338 347 9.307121 TGAAAATCTGAAACTTTTATTGCGAAA 57.693 25.926 0.00 0.00 0.00 3.46
339 348 9.567917 GAAAATCTGAAACTTTTATTGCGAAAC 57.432 29.630 0.00 0.00 0.00 2.78
340 349 6.911484 ATCTGAAACTTTTATTGCGAAACG 57.089 33.333 0.00 0.00 0.00 3.60
341 350 6.050454 TCTGAAACTTTTATTGCGAAACGA 57.950 33.333 0.00 0.00 0.00 3.85
342 351 5.905181 TCTGAAACTTTTATTGCGAAACGAC 59.095 36.000 0.00 0.00 0.00 4.34
343 352 5.812652 TGAAACTTTTATTGCGAAACGACT 58.187 33.333 0.00 0.00 0.00 4.18
344 353 5.905181 TGAAACTTTTATTGCGAAACGACTC 59.095 36.000 0.00 0.00 0.00 3.36
410 420 3.511146 TGTCCAGAATCCATTTTTGCTCC 59.489 43.478 0.00 0.00 0.00 4.70
419 429 0.240945 ATTTTTGCTCCGCCTTGACG 59.759 50.000 0.00 0.00 0.00 4.35
420 430 0.816018 TTTTTGCTCCGCCTTGACGA 60.816 50.000 0.00 0.00 34.06 4.20
422 432 0.248012 TTTGCTCCGCCTTGACGATA 59.752 50.000 0.00 0.00 34.06 2.92
429 439 3.869065 TCCGCCTTGACGATATTTTTCT 58.131 40.909 0.00 0.00 34.06 2.52
431 441 4.094294 TCCGCCTTGACGATATTTTTCTTG 59.906 41.667 0.00 0.00 34.06 3.02
438 448 7.119846 CCTTGACGATATTTTTCTTGTTCCTCT 59.880 37.037 0.00 0.00 0.00 3.69
449 459 2.724977 TGTTCCTCTTACTGTGCTCG 57.275 50.000 0.00 0.00 0.00 5.03
453 463 0.737715 CCTCTTACTGTGCTCGTGGC 60.738 60.000 0.00 0.00 42.22 5.01
468 478 1.823470 TGGCTGCTGTTTTCGCTGT 60.823 52.632 0.00 0.00 0.00 4.40
470 480 0.249031 GGCTGCTGTTTTCGCTGTTT 60.249 50.000 0.00 0.00 0.00 2.83
471 481 0.848305 GCTGCTGTTTTCGCTGTTTG 59.152 50.000 0.00 0.00 0.00 2.93
491 502 9.113876 CTGTTTGTGTTTTCGGTATCTATTTTC 57.886 33.333 0.00 0.00 0.00 2.29
493 504 6.411630 TGTGTTTTCGGTATCTATTTTCCG 57.588 37.500 0.00 0.00 43.65 4.30
503 514 6.530534 CGGTATCTATTTTCCGTATCATCCAC 59.469 42.308 0.00 0.00 38.45 4.02
506 517 9.436957 GTATCTATTTTCCGTATCATCCACAAT 57.563 33.333 0.00 0.00 0.00 2.71
513 524 2.061773 GTATCATCCACAATCCGCGAG 58.938 52.381 8.23 0.00 0.00 5.03
515 526 0.534873 TCATCCACAATCCGCGAGAA 59.465 50.000 8.23 0.00 0.00 2.87
529 540 3.722123 CGCGAGAACGGATTATTAATGC 58.278 45.455 0.00 0.00 40.15 3.56
530 541 3.183574 CGCGAGAACGGATTATTAATGCA 59.816 43.478 0.00 0.00 40.15 3.96
534 545 6.715464 CGAGAACGGATTATTAATGCAAAGT 58.285 36.000 8.41 0.00 35.72 2.66
571 609 3.815401 GGCTGCTGAGACAAGTCTTTAAA 59.185 43.478 3.96 0.00 40.61 1.52
572 610 4.319839 GGCTGCTGAGACAAGTCTTTAAAC 60.320 45.833 3.96 0.00 40.61 2.01
573 611 4.319839 GCTGCTGAGACAAGTCTTTAAACC 60.320 45.833 3.96 0.00 40.61 3.27
574 612 3.807622 TGCTGAGACAAGTCTTTAAACCG 59.192 43.478 3.96 0.00 40.61 4.44
575 613 4.056050 GCTGAGACAAGTCTTTAAACCGA 58.944 43.478 3.96 0.00 40.61 4.69
576 614 4.691216 GCTGAGACAAGTCTTTAAACCGAT 59.309 41.667 3.96 0.00 40.61 4.18
578 616 6.035112 GCTGAGACAAGTCTTTAAACCGATAG 59.965 42.308 3.96 0.00 40.61 2.08
581 619 8.579006 TGAGACAAGTCTTTAAACCGATAGTTA 58.421 33.333 3.96 0.00 40.61 2.24
595 633 8.445275 AACCGATAGTTAATTATGTTGATGCA 57.555 30.769 0.00 0.00 36.74 3.96
596 634 8.621532 ACCGATAGTTAATTATGTTGATGCAT 57.378 30.769 0.00 0.00 0.00 3.96
597 635 9.719355 ACCGATAGTTAATTATGTTGATGCATA 57.281 29.630 0.00 0.00 0.00 3.14
602 640 8.752005 AGTTAATTATGTTGATGCATAGTGGT 57.248 30.769 0.00 0.00 33.48 4.16
604 642 9.801873 GTTAATTATGTTGATGCATAGTGGTTT 57.198 29.630 0.00 0.00 33.48 3.27
605 643 9.800433 TTAATTATGTTGATGCATAGTGGTTTG 57.200 29.630 0.00 0.00 33.48 2.93
606 644 6.832520 TTATGTTGATGCATAGTGGTTTGT 57.167 33.333 0.00 0.00 33.48 2.83
607 645 7.929941 TTATGTTGATGCATAGTGGTTTGTA 57.070 32.000 0.00 0.00 33.48 2.41
608 646 8.518430 TTATGTTGATGCATAGTGGTTTGTAT 57.482 30.769 0.00 0.00 33.48 2.29
609 647 6.193514 TGTTGATGCATAGTGGTTTGTATG 57.806 37.500 0.00 0.00 0.00 2.39
610 648 5.125257 TGTTGATGCATAGTGGTTTGTATGG 59.875 40.000 0.00 0.00 0.00 2.74
611 649 3.631686 TGATGCATAGTGGTTTGTATGGC 59.368 43.478 0.00 0.00 0.00 4.40
612 650 3.078891 TGCATAGTGGTTTGTATGGCA 57.921 42.857 0.00 0.00 0.00 4.92
613 651 3.630168 TGCATAGTGGTTTGTATGGCAT 58.370 40.909 4.88 4.88 0.00 4.40
614 652 4.786425 TGCATAGTGGTTTGTATGGCATA 58.214 39.130 2.32 2.32 0.00 3.14
667 831 7.823799 TGAAAGAGTTCCTGCAAAAAGAAAAAT 59.176 29.630 0.00 0.00 32.28 1.82
668 832 8.565896 AAAGAGTTCCTGCAAAAAGAAAAATT 57.434 26.923 0.00 0.00 0.00 1.82
669 833 7.776933 AGAGTTCCTGCAAAAAGAAAAATTC 57.223 32.000 0.00 0.00 0.00 2.17
692 856 7.596749 TCTTAGAAAGCGAGTTTATTCAAGG 57.403 36.000 0.00 0.00 0.00 3.61
693 857 4.686839 AGAAAGCGAGTTTATTCAAGGC 57.313 40.909 0.00 0.00 0.00 4.35
695 859 4.518970 AGAAAGCGAGTTTATTCAAGGCAA 59.481 37.500 0.00 0.00 0.00 4.52
696 860 4.846779 AAGCGAGTTTATTCAAGGCAAA 57.153 36.364 0.00 0.00 0.00 3.68
699 863 4.982295 AGCGAGTTTATTCAAGGCAAAAAC 59.018 37.500 0.00 0.00 0.00 2.43
700 864 4.149922 GCGAGTTTATTCAAGGCAAAAACC 59.850 41.667 0.00 0.00 31.87 3.27
701 865 4.381566 CGAGTTTATTCAAGGCAAAAACCG 59.618 41.667 0.00 0.00 31.87 4.44
702 866 4.627058 AGTTTATTCAAGGCAAAAACCGG 58.373 39.130 0.00 0.00 31.87 5.28
704 868 4.513198 TTATTCAAGGCAAAAACCGGAG 57.487 40.909 9.46 0.00 33.69 4.63
705 869 1.770294 TTCAAGGCAAAAACCGGAGT 58.230 45.000 9.46 0.00 33.69 3.85
706 870 1.314730 TCAAGGCAAAAACCGGAGTC 58.685 50.000 9.46 0.00 33.69 3.36
709 873 0.179040 AGGCAAAAACCGGAGTCGAA 60.179 50.000 9.46 0.00 39.00 3.71
710 874 0.040692 GGCAAAAACCGGAGTCGAAC 60.041 55.000 9.46 0.00 39.00 3.95
711 875 0.383860 GCAAAAACCGGAGTCGAACG 60.384 55.000 9.46 0.00 39.00 3.95
717 881 3.495124 CCGGAGTCGAACGGTTAAA 57.505 52.632 14.27 0.00 44.85 1.52
718 882 2.000429 CCGGAGTCGAACGGTTAAAT 58.000 50.000 14.27 0.00 44.85 1.40
719 883 3.149436 CCGGAGTCGAACGGTTAAATA 57.851 47.619 14.27 0.00 44.85 1.40
722 886 4.201618 CCGGAGTCGAACGGTTAAATAAAC 60.202 45.833 14.27 0.00 44.85 2.01
723 887 4.201618 CGGAGTCGAACGGTTAAATAAACC 60.202 45.833 0.00 0.00 45.75 3.27
740 904 8.463930 AAATAAACCGGTCATATGAATGATGT 57.536 30.769 8.04 0.00 43.87 3.06
741 905 9.567776 AAATAAACCGGTCATATGAATGATGTA 57.432 29.630 8.04 0.00 43.87 2.29
742 906 9.567776 AATAAACCGGTCATATGAATGATGTAA 57.432 29.630 8.04 0.00 43.87 2.41
743 907 7.873719 AAACCGGTCATATGAATGATGTAAA 57.126 32.000 8.04 0.00 43.87 2.01
744 908 7.873719 AACCGGTCATATGAATGATGTAAAA 57.126 32.000 8.04 0.00 43.87 1.52
745 909 8.463930 AACCGGTCATATGAATGATGTAAAAT 57.536 30.769 8.04 0.00 43.87 1.82
747 911 8.352201 ACCGGTCATATGAATGATGTAAAATTG 58.648 33.333 7.07 0.00 43.87 2.32
748 912 8.567104 CCGGTCATATGAATGATGTAAAATTGA 58.433 33.333 7.07 0.00 43.87 2.57
749 913 9.603298 CGGTCATATGAATGATGTAAAATTGAG 57.397 33.333 7.07 0.00 43.87 3.02
795 959 7.869016 TTTTAGAGATGTAACGTGAACTCTG 57.131 36.000 15.85 0.00 36.39 3.35
796 960 4.442375 AGAGATGTAACGTGAACTCTGG 57.558 45.455 0.00 0.00 34.19 3.86
797 961 3.193691 AGAGATGTAACGTGAACTCTGGG 59.806 47.826 0.00 0.00 34.19 4.45
798 962 2.000447 GATGTAACGTGAACTCTGGGC 59.000 52.381 0.00 0.00 0.00 5.36
799 963 0.753867 TGTAACGTGAACTCTGGGCA 59.246 50.000 0.00 0.00 0.00 5.36
801 965 1.798813 GTAACGTGAACTCTGGGCAAG 59.201 52.381 0.00 0.00 0.00 4.01
803 967 1.045407 ACGTGAACTCTGGGCAAGTA 58.955 50.000 0.00 0.00 0.00 2.24
804 968 1.000955 ACGTGAACTCTGGGCAAGTAG 59.999 52.381 0.00 0.00 0.00 2.57
805 969 1.673033 CGTGAACTCTGGGCAAGTAGG 60.673 57.143 0.00 0.00 0.00 3.18
806 970 0.984230 TGAACTCTGGGCAAGTAGGG 59.016 55.000 0.00 0.00 0.00 3.53
807 971 0.253327 GAACTCTGGGCAAGTAGGGG 59.747 60.000 0.00 0.00 0.00 4.79
810 974 0.326238 CTCTGGGCAAGTAGGGGGTA 60.326 60.000 0.00 0.00 0.00 3.69
811 975 0.119561 TCTGGGCAAGTAGGGGGTAA 59.880 55.000 0.00 0.00 0.00 2.85
812 976 0.996583 CTGGGCAAGTAGGGGGTAAA 59.003 55.000 0.00 0.00 0.00 2.01
813 977 1.356398 CTGGGCAAGTAGGGGGTAAAA 59.644 52.381 0.00 0.00 0.00 1.52
815 979 2.291930 TGGGCAAGTAGGGGGTAAAATG 60.292 50.000 0.00 0.00 0.00 2.32
816 980 1.754803 GGCAAGTAGGGGGTAAAATGC 59.245 52.381 0.00 0.00 0.00 3.56
819 983 3.368013 GCAAGTAGGGGGTAAAATGCAAC 60.368 47.826 0.00 0.00 33.00 4.17
820 984 4.086457 CAAGTAGGGGGTAAAATGCAACT 58.914 43.478 0.00 0.00 0.00 3.16
821 985 4.397919 AGTAGGGGGTAAAATGCAACTT 57.602 40.909 0.00 0.00 0.00 2.66
822 986 4.747583 AGTAGGGGGTAAAATGCAACTTT 58.252 39.130 0.00 0.00 0.00 2.66
823 987 4.770531 AGTAGGGGGTAAAATGCAACTTTC 59.229 41.667 0.00 0.00 0.00 2.62
824 988 2.903784 AGGGGGTAAAATGCAACTTTCC 59.096 45.455 0.00 0.00 0.00 3.13
825 989 2.027561 GGGGGTAAAATGCAACTTTCCC 60.028 50.000 14.18 14.18 0.00 3.97
826 990 2.903784 GGGGTAAAATGCAACTTTCCCT 59.096 45.455 19.09 0.00 34.63 4.20
827 991 3.056107 GGGGTAAAATGCAACTTTCCCTC 60.056 47.826 19.09 7.72 34.63 4.30
828 992 3.832490 GGGTAAAATGCAACTTTCCCTCT 59.168 43.478 14.90 0.00 0.00 3.69
829 993 4.321974 GGGTAAAATGCAACTTTCCCTCTG 60.322 45.833 14.90 0.00 0.00 3.35
835 1010 3.149196 TGCAACTTTCCCTCTGAATGAC 58.851 45.455 0.00 0.00 33.50 3.06
838 1013 4.566004 CAACTTTCCCTCTGAATGACGTA 58.434 43.478 0.00 0.00 33.50 3.57
841 1016 5.420409 ACTTTCCCTCTGAATGACGTATTC 58.580 41.667 0.00 0.00 44.45 1.75
844 1019 4.537751 TCCCTCTGAATGACGTATTCTCT 58.462 43.478 14.56 0.00 44.49 3.10
859 1034 4.724602 TCTCGCTGCTGCACGGTC 62.725 66.667 16.29 1.85 39.64 4.79
883 1105 4.933064 GGCAGCCGTCGGATCGAG 62.933 72.222 17.49 0.00 36.23 4.04
909 1133 1.654023 CGTCCCAGGATTTTTCCCGC 61.654 60.000 0.00 0.00 0.00 6.13
920 1144 2.919960 TTTTCCCGCAACCGTCACGA 62.920 55.000 0.00 0.00 0.00 4.35
921 1145 2.919960 TTTCCCGCAACCGTCACGAA 62.920 55.000 0.00 0.00 0.00 3.85
983 1224 1.262640 ACACGTATCCACCCACCTCC 61.263 60.000 0.00 0.00 0.00 4.30
1256 1503 0.322456 CCTCAACGGCCTCAATTCCA 60.322 55.000 0.00 0.00 0.00 3.53
1407 1660 4.357947 GACGTGGCGCAGTCTGGA 62.358 66.667 10.83 0.00 34.74 3.86
1468 1721 3.818773 CCAGGTTCGAACTACCAAACATT 59.181 43.478 26.32 0.00 38.16 2.71
1495 1748 1.633852 CGAGAGGTGAAAGCAGCAGC 61.634 60.000 0.00 0.00 44.77 5.25
1496 1749 0.604780 GAGAGGTGAAAGCAGCAGCA 60.605 55.000 3.17 0.00 44.77 4.41
1499 1752 0.466922 AGGTGAAAGCAGCAGCAGTT 60.467 50.000 3.17 0.00 44.77 3.16
1500 1753 0.318445 GGTGAAAGCAGCAGCAGTTG 60.318 55.000 3.17 0.00 45.49 3.16
1534 1788 2.109181 GTACCCTGCCGGCATCTC 59.891 66.667 32.87 14.95 33.26 2.75
1550 1804 5.220989 CGGCATCTCTCATGTGAATTTTGAT 60.221 40.000 0.00 0.00 0.00 2.57
1553 1807 8.358148 GGCATCTCTCATGTGAATTTTGATAAT 58.642 33.333 0.00 0.00 0.00 1.28
1554 1808 9.745880 GCATCTCTCATGTGAATTTTGATAATT 57.254 29.630 0.00 0.00 0.00 1.40
1569 1823 7.514784 TTTGATAATTGCCATGATCGATTCT 57.485 32.000 0.00 0.00 0.00 2.40
1575 1829 2.945008 TGCCATGATCGATTCTTGTTCC 59.055 45.455 0.00 0.00 0.00 3.62
1578 1832 4.194640 CCATGATCGATTCTTGTTCCTGT 58.805 43.478 0.00 0.00 0.00 4.00
1588 1842 3.184628 TCTTGTTCCTGTCCTGATGGAT 58.815 45.455 0.00 0.00 45.29 3.41
1598 1852 3.118629 TGTCCTGATGGATGTGAAGCTAC 60.119 47.826 0.00 0.00 45.29 3.58
1612 1866 1.127343 AGCTACATTCTCCTCAGGGC 58.873 55.000 0.00 0.00 0.00 5.19
1617 1871 0.250209 CATTCTCCTCAGGGCGATGG 60.250 60.000 0.00 0.00 0.00 3.51
1630 1884 1.532868 GGCGATGGCATCTACATGTTC 59.467 52.381 23.97 0.00 42.47 3.18
1650 1904 2.482296 TTCGAGACGAAGAACCCCGC 62.482 60.000 2.48 0.00 41.05 6.13
1660 1914 1.883084 GAACCCCGCTACATCGCAG 60.883 63.158 0.00 0.00 0.00 5.18
1793 2047 2.025037 AGCAAGGCAAATATCCCACTCA 60.025 45.455 0.00 0.00 0.00 3.41
1827 2086 4.603231 TGTAACCAACAAGTTCGTGTTC 57.397 40.909 1.58 0.00 39.73 3.18
1828 2087 3.374678 TGTAACCAACAAGTTCGTGTTCC 59.625 43.478 1.58 0.00 39.73 3.62
1842 2101 3.745975 TCGTGTTCCAATCATTCTCACAC 59.254 43.478 0.00 0.00 0.00 3.82
1845 2104 2.470983 TCCAATCATTCTCACACGCA 57.529 45.000 0.00 0.00 0.00 5.24
1860 2119 1.372128 CGCACTTCTTTGCTTGCCC 60.372 57.895 0.00 0.00 40.62 5.36
1861 2120 1.005748 GCACTTCTTTGCTTGCCCC 60.006 57.895 0.00 0.00 39.59 5.80
1862 2121 1.667722 CACTTCTTTGCTTGCCCCC 59.332 57.895 0.00 0.00 0.00 5.40
1863 2122 1.114722 CACTTCTTTGCTTGCCCCCA 61.115 55.000 0.00 0.00 0.00 4.96
1877 2138 1.265454 CCCCCACTCCACAGGTCTAC 61.265 65.000 0.00 0.00 0.00 2.59
1895 2156 5.395768 GGTCTACATGATGCCTGAAAGTAGT 60.396 44.000 0.00 0.00 31.81 2.73
2021 2282 1.213296 TCAGGGGTTCCTATTGGCTC 58.787 55.000 0.00 0.00 42.67 4.70
2022 2283 0.918983 CAGGGGTTCCTATTGGCTCA 59.081 55.000 0.00 0.00 42.67 4.26
2054 2315 7.389330 TCAGATTTAAGTTCTTATGGTGCGAAA 59.611 33.333 0.00 0.00 0.00 3.46
2099 2360 0.758123 ATAGCAGCTCTCCTCTTGCC 59.242 55.000 0.00 0.00 0.00 4.52
2174 2435 0.258774 TTAGAAATGGAGGCAGGCCC 59.741 55.000 6.70 0.85 36.58 5.80
2399 2660 4.330250 CATCAAGTCAACTCTGGATTGGT 58.670 43.478 0.00 0.00 0.00 3.67
2421 2682 5.163301 GGTGTAATGGATGGTGATAGAGTGT 60.163 44.000 0.00 0.00 0.00 3.55
2429 2690 6.070021 TGGATGGTGATAGAGTGTCTTCAAAT 60.070 38.462 0.00 0.00 0.00 2.32
2569 2830 2.531771 TCCACATACTGAGAAACGGGA 58.468 47.619 0.00 0.00 0.00 5.14
2618 2879 9.646427 CAGTTCTTTCTGAAGTATAAGCTAAGT 57.354 33.333 0.00 0.00 36.63 2.24
2834 3095 6.530534 AGTTCACGCTGTTAACTATGACATAC 59.469 38.462 7.22 1.90 29.66 2.39
2843 3104 1.272490 ACTATGACATACGATGCCCGG 59.728 52.381 0.00 0.00 43.93 5.73
3014 3275 8.037382 ACACTCTGAACAATAGATTCAACATG 57.963 34.615 0.00 0.00 35.70 3.21
3504 3765 9.807921 AATTTTCAGAAGTCTATGGGAACTTAA 57.192 29.630 0.00 0.00 0.00 1.85
3557 3821 4.682778 TGGCTGGGATGTATAGTAACAC 57.317 45.455 0.00 0.00 30.75 3.32
3591 3856 8.049117 TGGATATTTTGTCTTGAGACTAGCATT 58.951 33.333 12.00 0.00 44.99 3.56
3606 3871 7.786030 AGACTAGCATTGTCTGATTAGCTAAA 58.214 34.615 10.85 0.00 42.46 1.85
3618 3883 9.346725 GTCTGATTAGCTAAATTTTCAAGTTGG 57.653 33.333 10.85 0.00 0.00 3.77
3619 3884 9.077885 TCTGATTAGCTAAATTTTCAAGTTGGT 57.922 29.630 10.85 0.00 0.00 3.67
3624 3889 7.946655 AGCTAAATTTTCAAGTTGGTAAAGC 57.053 32.000 2.34 4.47 0.00 3.51
3625 3890 7.496747 AGCTAAATTTTCAAGTTGGTAAAGCA 58.503 30.769 2.34 0.00 0.00 3.91
3626 3891 7.653311 AGCTAAATTTTCAAGTTGGTAAAGCAG 59.347 33.333 2.34 4.81 0.00 4.24
3627 3892 7.651704 GCTAAATTTTCAAGTTGGTAAAGCAGA 59.348 33.333 2.34 0.00 0.00 4.26
3628 3893 9.185192 CTAAATTTTCAAGTTGGTAAAGCAGAG 57.815 33.333 2.34 0.00 0.00 3.35
3629 3894 6.959639 ATTTTCAAGTTGGTAAAGCAGAGA 57.040 33.333 2.34 0.00 0.00 3.10
3630 3895 6.377327 TTTTCAAGTTGGTAAAGCAGAGAG 57.623 37.500 2.34 0.00 0.00 3.20
3631 3896 3.403038 TCAAGTTGGTAAAGCAGAGAGC 58.597 45.455 2.34 0.00 46.19 4.09
3830 4124 4.509970 GGGTTTGCAAACTGTAATTTGTCC 59.490 41.667 34.39 21.81 40.92 4.02
4067 4364 6.020440 GCGTGAACCATGATCAATAACAATTG 60.020 38.462 3.24 3.24 0.00 2.32
4220 4520 7.729124 ATCAAACCATCAAGAATCAGGAAAT 57.271 32.000 0.00 0.00 0.00 2.17
4225 4525 4.160814 CCATCAAGAATCAGGAAATGCCAA 59.839 41.667 0.00 0.00 40.02 4.52
4322 4623 8.186821 GGGTCAATGTTTGATTCTCAATCTAAG 58.813 37.037 0.00 0.00 42.47 2.18
4344 4645 5.241662 AGAATTCTGCTGTAGTTTCAGGAC 58.758 41.667 7.30 0.00 36.12 3.85
4414 4715 4.811364 GCAGCCCCAGGGAAGAGC 62.811 72.222 7.25 0.69 37.50 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
151 153 5.599242 ACAATGTCATGCCATGAATCCATAA 59.401 36.000 9.36 0.00 41.69 1.90
164 166 2.221517 GCACACCAAAACAATGTCATGC 59.778 45.455 0.00 0.00 0.00 4.06
229 233 4.945543 TCGGTATGGCGTGTATATGAGTAT 59.054 41.667 0.00 0.00 0.00 2.12
230 234 4.325972 TCGGTATGGCGTGTATATGAGTA 58.674 43.478 0.00 0.00 0.00 2.59
231 235 3.151554 TCGGTATGGCGTGTATATGAGT 58.848 45.455 0.00 0.00 0.00 3.41
232 236 3.427638 CCTCGGTATGGCGTGTATATGAG 60.428 52.174 0.00 0.00 0.00 2.90
233 237 2.490509 CCTCGGTATGGCGTGTATATGA 59.509 50.000 0.00 0.00 0.00 2.15
234 238 2.490509 TCCTCGGTATGGCGTGTATATG 59.509 50.000 0.00 0.00 0.00 1.78
235 239 2.753452 CTCCTCGGTATGGCGTGTATAT 59.247 50.000 0.00 0.00 0.00 0.86
236 240 2.156917 CTCCTCGGTATGGCGTGTATA 58.843 52.381 0.00 0.00 0.00 1.47
237 241 0.959553 CTCCTCGGTATGGCGTGTAT 59.040 55.000 0.00 0.00 0.00 2.29
238 242 1.731433 GCTCCTCGGTATGGCGTGTA 61.731 60.000 0.00 0.00 0.00 2.90
251 260 3.758554 TGGCAGAAAAATACTTGCTCCTC 59.241 43.478 0.00 0.00 0.00 3.71
272 281 2.231235 GGGTAACATTCCCAGCAAAGTG 59.769 50.000 0.00 0.00 44.05 3.16
312 321 8.864069 TTCGCAATAAAAGTTTCAGATTTTCA 57.136 26.923 0.00 0.00 31.41 2.69
322 331 5.008316 AGGAGTCGTTTCGCAATAAAAGTTT 59.992 36.000 0.00 0.00 0.00 2.66
327 336 5.427036 AAAAGGAGTCGTTTCGCAATAAA 57.573 34.783 11.02 0.00 0.00 1.40
328 337 6.730960 ATAAAAGGAGTCGTTTCGCAATAA 57.269 33.333 11.02 0.00 0.00 1.40
329 338 6.369340 TCAATAAAAGGAGTCGTTTCGCAATA 59.631 34.615 11.02 1.00 0.00 1.90
330 339 5.180492 TCAATAAAAGGAGTCGTTTCGCAAT 59.820 36.000 11.02 0.00 0.00 3.56
331 340 4.512198 TCAATAAAAGGAGTCGTTTCGCAA 59.488 37.500 11.02 0.00 0.00 4.85
332 341 4.059511 TCAATAAAAGGAGTCGTTTCGCA 58.940 39.130 11.02 1.39 0.00 5.10
333 342 4.657075 TCAATAAAAGGAGTCGTTTCGC 57.343 40.909 11.02 0.00 0.00 4.70
334 343 6.165659 ACATCAATAAAAGGAGTCGTTTCG 57.834 37.500 11.02 2.01 0.00 3.46
335 344 8.718734 AGTAACATCAATAAAAGGAGTCGTTTC 58.281 33.333 11.02 0.00 0.00 2.78
336 345 8.504005 CAGTAACATCAATAAAAGGAGTCGTTT 58.496 33.333 4.99 4.99 0.00 3.60
337 346 7.876068 TCAGTAACATCAATAAAAGGAGTCGTT 59.124 33.333 0.00 0.00 0.00 3.85
338 347 7.383687 TCAGTAACATCAATAAAAGGAGTCGT 58.616 34.615 0.00 0.00 0.00 4.34
339 348 7.827819 TCAGTAACATCAATAAAAGGAGTCG 57.172 36.000 0.00 0.00 0.00 4.18
340 349 9.383519 TCATCAGTAACATCAATAAAAGGAGTC 57.616 33.333 0.00 0.00 0.00 3.36
341 350 9.911788 ATCATCAGTAACATCAATAAAAGGAGT 57.088 29.630 0.00 0.00 0.00 3.85
386 395 5.337813 GGAGCAAAAATGGATTCTGGACATT 60.338 40.000 0.00 0.00 36.46 2.71
410 420 4.969816 ACAAGAAAAATATCGTCAAGGCG 58.030 39.130 0.00 0.00 0.00 5.52
420 430 8.515414 GCACAGTAAGAGGAACAAGAAAAATAT 58.485 33.333 0.00 0.00 0.00 1.28
422 432 6.547510 AGCACAGTAAGAGGAACAAGAAAAAT 59.452 34.615 0.00 0.00 0.00 1.82
429 439 2.364324 ACGAGCACAGTAAGAGGAACAA 59.636 45.455 0.00 0.00 0.00 2.83
431 441 2.329379 CACGAGCACAGTAAGAGGAAC 58.671 52.381 0.00 0.00 0.00 3.62
449 459 1.370900 CAGCGAAAACAGCAGCCAC 60.371 57.895 0.00 0.00 37.01 5.01
453 463 1.847999 CACAAACAGCGAAAACAGCAG 59.152 47.619 0.00 0.00 37.01 4.24
468 478 7.041235 ACGGAAAATAGATACCGAAAACACAAA 60.041 33.333 11.27 0.00 46.94 2.83
470 480 5.933463 ACGGAAAATAGATACCGAAAACACA 59.067 36.000 11.27 0.00 46.94 3.72
471 481 6.413018 ACGGAAAATAGATACCGAAAACAC 57.587 37.500 11.27 0.00 46.94 3.32
491 502 1.148310 GCGGATTGTGGATGATACGG 58.852 55.000 0.00 0.00 30.36 4.02
493 504 2.061773 CTCGCGGATTGTGGATGATAC 58.938 52.381 6.13 0.00 0.00 2.24
513 524 9.434559 GAAGTACTTTGCATTAATAATCCGTTC 57.565 33.333 10.02 0.00 0.00 3.95
515 526 8.612619 CAGAAGTACTTTGCATTAATAATCCGT 58.387 33.333 10.02 0.00 0.00 4.69
523 534 9.891828 CAATACAACAGAAGTACTTTGCATTAA 57.108 29.630 10.02 0.00 0.00 1.40
529 540 6.373779 CAGCCAATACAACAGAAGTACTTTG 58.626 40.000 10.02 11.96 0.00 2.77
530 541 5.048713 GCAGCCAATACAACAGAAGTACTTT 60.049 40.000 10.02 0.00 0.00 2.66
534 545 4.002982 CAGCAGCCAATACAACAGAAGTA 58.997 43.478 0.00 0.00 0.00 2.24
547 558 0.761187 AGACTTGTCTCAGCAGCCAA 59.239 50.000 0.00 0.00 0.00 4.52
571 609 8.621532 ATGCATCAACATAATTAACTATCGGT 57.378 30.769 0.00 0.00 0.00 4.69
576 614 9.845740 ACCACTATGCATCAACATAATTAACTA 57.154 29.630 0.19 0.00 32.29 2.24
578 616 9.801873 AAACCACTATGCATCAACATAATTAAC 57.198 29.630 0.19 0.00 32.29 2.01
581 619 7.839907 ACAAACCACTATGCATCAACATAATT 58.160 30.769 0.19 0.00 32.29 1.40
590 628 3.631686 TGCCATACAAACCACTATGCATC 59.368 43.478 0.19 0.00 0.00 3.91
592 630 3.078891 TGCCATACAAACCACTATGCA 57.921 42.857 0.00 0.00 0.00 3.96
593 631 5.766150 TTATGCCATACAAACCACTATGC 57.234 39.130 0.00 0.00 0.00 3.14
594 632 8.412456 TGATTTTATGCCATACAAACCACTATG 58.588 33.333 0.00 0.00 0.00 2.23
595 633 8.413229 GTGATTTTATGCCATACAAACCACTAT 58.587 33.333 9.99 0.00 0.00 2.12
596 634 7.394641 TGTGATTTTATGCCATACAAACCACTA 59.605 33.333 14.72 5.31 0.00 2.74
597 635 6.210385 TGTGATTTTATGCCATACAAACCACT 59.790 34.615 14.72 0.00 0.00 4.00
598 636 6.393990 TGTGATTTTATGCCATACAAACCAC 58.606 36.000 10.20 10.20 0.00 4.16
599 637 6.596309 TGTGATTTTATGCCATACAAACCA 57.404 33.333 0.00 0.00 0.00 3.67
600 638 6.870965 TGTTGTGATTTTATGCCATACAAACC 59.129 34.615 0.00 0.00 0.00 3.27
601 639 7.881643 TGTTGTGATTTTATGCCATACAAAC 57.118 32.000 0.00 0.00 0.00 2.93
604 642 8.965819 ACTTATGTTGTGATTTTATGCCATACA 58.034 29.630 0.00 0.00 0.00 2.29
607 645 9.407380 TCTACTTATGTTGTGATTTTATGCCAT 57.593 29.630 0.00 0.00 0.00 4.40
608 646 8.800370 TCTACTTATGTTGTGATTTTATGCCA 57.200 30.769 0.00 0.00 0.00 4.92
632 670 7.383102 TGCAGGAACTCTTTCAAAAGATATC 57.617 36.000 5.69 7.20 43.52 1.63
641 679 5.913137 TTCTTTTTGCAGGAACTCTTTCA 57.087 34.783 0.00 0.00 34.60 2.69
642 680 7.595311 TTTTTCTTTTTGCAGGAACTCTTTC 57.405 32.000 0.00 0.00 34.60 2.62
645 683 7.559486 AGAATTTTTCTTTTTGCAGGAACTCT 58.441 30.769 0.00 0.00 36.36 3.24
646 684 7.776933 AGAATTTTTCTTTTTGCAGGAACTC 57.223 32.000 0.00 0.00 36.36 3.01
667 831 7.360946 GCCTTGAATAAACTCGCTTTCTAAGAA 60.361 37.037 0.00 0.00 0.00 2.52
668 832 6.092259 GCCTTGAATAAACTCGCTTTCTAAGA 59.908 38.462 0.00 0.00 0.00 2.10
669 833 6.128282 TGCCTTGAATAAACTCGCTTTCTAAG 60.128 38.462 0.00 0.00 0.00 2.18
671 835 5.242434 TGCCTTGAATAAACTCGCTTTCTA 58.758 37.500 0.00 0.00 0.00 2.10
672 836 4.072131 TGCCTTGAATAAACTCGCTTTCT 58.928 39.130 0.00 0.00 0.00 2.52
673 837 4.419522 TGCCTTGAATAAACTCGCTTTC 57.580 40.909 0.00 0.00 0.00 2.62
674 838 4.846779 TTGCCTTGAATAAACTCGCTTT 57.153 36.364 0.00 0.00 0.00 3.51
676 840 4.846779 TTTTGCCTTGAATAAACTCGCT 57.153 36.364 0.00 0.00 0.00 4.93
677 841 4.149922 GGTTTTTGCCTTGAATAAACTCGC 59.850 41.667 0.00 0.00 0.00 5.03
679 843 4.684242 CCGGTTTTTGCCTTGAATAAACTC 59.316 41.667 0.00 0.00 0.00 3.01
681 845 4.623002 TCCGGTTTTTGCCTTGAATAAAC 58.377 39.130 0.00 0.00 0.00 2.01
683 847 3.892588 ACTCCGGTTTTTGCCTTGAATAA 59.107 39.130 0.00 0.00 0.00 1.40
685 849 2.296190 GACTCCGGTTTTTGCCTTGAAT 59.704 45.455 0.00 0.00 0.00 2.57
686 850 1.679153 GACTCCGGTTTTTGCCTTGAA 59.321 47.619 0.00 0.00 0.00 2.69
687 851 1.314730 GACTCCGGTTTTTGCCTTGA 58.685 50.000 0.00 0.00 0.00 3.02
689 853 0.179040 TCGACTCCGGTTTTTGCCTT 60.179 50.000 0.00 0.00 36.24 4.35
690 854 0.179040 TTCGACTCCGGTTTTTGCCT 60.179 50.000 0.00 0.00 36.24 4.75
691 855 0.040692 GTTCGACTCCGGTTTTTGCC 60.041 55.000 0.00 0.00 36.24 4.52
692 856 0.383860 CGTTCGACTCCGGTTTTTGC 60.384 55.000 0.00 0.00 36.24 3.68
693 857 0.233848 CCGTTCGACTCCGGTTTTTG 59.766 55.000 0.00 0.00 39.38 2.44
695 859 4.348857 CCGTTCGACTCCGGTTTT 57.651 55.556 0.00 0.00 39.38 2.43
699 863 7.133643 GGTTTATTTAACCGTTCGACTCCGG 62.134 48.000 14.00 14.00 46.48 5.14
700 864 4.201618 GGTTTATTTAACCGTTCGACTCCG 60.202 45.833 0.00 0.00 46.48 4.63
701 865 5.208624 GGTTTATTTAACCGTTCGACTCC 57.791 43.478 0.00 0.00 46.48 3.85
711 875 8.842280 TCATTCATATGACCGGTTTATTTAACC 58.158 33.333 9.42 0.00 42.79 2.85
714 878 9.567776 ACATCATTCATATGACCGGTTTATTTA 57.432 29.630 9.42 0.62 43.29 1.40
715 879 8.463930 ACATCATTCATATGACCGGTTTATTT 57.536 30.769 9.42 0.00 43.29 1.40
716 880 9.567776 TTACATCATTCATATGACCGGTTTATT 57.432 29.630 9.42 0.00 43.29 1.40
717 881 9.567776 TTTACATCATTCATATGACCGGTTTAT 57.432 29.630 9.42 9.66 43.29 1.40
718 882 8.966069 TTTACATCATTCATATGACCGGTTTA 57.034 30.769 9.42 4.37 43.29 2.01
719 883 7.873719 TTTACATCATTCATATGACCGGTTT 57.126 32.000 9.42 1.66 43.29 3.27
722 886 8.567104 TCAATTTTACATCATTCATATGACCGG 58.433 33.333 4.48 0.00 43.29 5.28
723 887 9.603298 CTCAATTTTACATCATTCATATGACCG 57.397 33.333 4.48 0.00 43.29 4.79
770 934 7.384115 CCAGAGTTCACGTTACATCTCTAAAAA 59.616 37.037 0.00 0.00 32.17 1.94
771 935 6.866770 CCAGAGTTCACGTTACATCTCTAAAA 59.133 38.462 0.00 0.00 32.17 1.52
772 936 6.387465 CCAGAGTTCACGTTACATCTCTAAA 58.613 40.000 0.00 0.00 32.17 1.85
773 937 5.105877 CCCAGAGTTCACGTTACATCTCTAA 60.106 44.000 0.00 0.00 32.17 2.10
774 938 4.398358 CCCAGAGTTCACGTTACATCTCTA 59.602 45.833 0.00 0.00 32.17 2.43
776 940 3.512680 CCCAGAGTTCACGTTACATCTC 58.487 50.000 0.00 0.00 0.00 2.75
777 941 2.353803 GCCCAGAGTTCACGTTACATCT 60.354 50.000 0.00 0.00 0.00 2.90
778 942 2.000447 GCCCAGAGTTCACGTTACATC 59.000 52.381 0.00 0.00 0.00 3.06
779 943 1.346395 TGCCCAGAGTTCACGTTACAT 59.654 47.619 0.00 0.00 0.00 2.29
780 944 0.753867 TGCCCAGAGTTCACGTTACA 59.246 50.000 0.00 0.00 0.00 2.41
781 945 1.798813 CTTGCCCAGAGTTCACGTTAC 59.201 52.381 0.00 0.00 0.00 2.50
782 946 1.414919 ACTTGCCCAGAGTTCACGTTA 59.585 47.619 0.00 0.00 0.00 3.18
783 947 0.180406 ACTTGCCCAGAGTTCACGTT 59.820 50.000 0.00 0.00 0.00 3.99
784 948 1.000955 CTACTTGCCCAGAGTTCACGT 59.999 52.381 0.00 0.00 0.00 4.49
785 949 1.673033 CCTACTTGCCCAGAGTTCACG 60.673 57.143 0.00 0.00 0.00 4.35
786 950 1.339151 CCCTACTTGCCCAGAGTTCAC 60.339 57.143 0.00 0.00 0.00 3.18
787 951 0.984230 CCCTACTTGCCCAGAGTTCA 59.016 55.000 0.00 0.00 0.00 3.18
788 952 0.253327 CCCCTACTTGCCCAGAGTTC 59.747 60.000 0.00 0.00 0.00 3.01
789 953 1.208165 CCCCCTACTTGCCCAGAGTT 61.208 60.000 0.00 0.00 0.00 3.01
790 954 1.616628 CCCCCTACTTGCCCAGAGT 60.617 63.158 0.00 0.00 0.00 3.24
791 955 0.326238 TACCCCCTACTTGCCCAGAG 60.326 60.000 0.00 0.00 0.00 3.35
792 956 0.119561 TTACCCCCTACTTGCCCAGA 59.880 55.000 0.00 0.00 0.00 3.86
793 957 0.996583 TTTACCCCCTACTTGCCCAG 59.003 55.000 0.00 0.00 0.00 4.45
794 958 1.458017 TTTTACCCCCTACTTGCCCA 58.542 50.000 0.00 0.00 0.00 5.36
795 959 2.384828 CATTTTACCCCCTACTTGCCC 58.615 52.381 0.00 0.00 0.00 5.36
796 960 1.754803 GCATTTTACCCCCTACTTGCC 59.245 52.381 0.00 0.00 0.00 4.52
797 961 2.452505 TGCATTTTACCCCCTACTTGC 58.547 47.619 0.00 0.00 0.00 4.01
798 962 4.086457 AGTTGCATTTTACCCCCTACTTG 58.914 43.478 0.00 0.00 0.00 3.16
799 963 4.397919 AGTTGCATTTTACCCCCTACTT 57.602 40.909 0.00 0.00 0.00 2.24
801 965 4.081862 GGAAAGTTGCATTTTACCCCCTAC 60.082 45.833 0.00 0.00 0.00 3.18
803 967 2.903784 GGAAAGTTGCATTTTACCCCCT 59.096 45.455 0.00 0.00 0.00 4.79
804 968 2.027561 GGGAAAGTTGCATTTTACCCCC 60.028 50.000 12.41 8.29 33.21 5.40
805 969 2.903784 AGGGAAAGTTGCATTTTACCCC 59.096 45.455 17.54 13.89 39.00 4.95
806 970 3.832490 AGAGGGAAAGTTGCATTTTACCC 59.168 43.478 17.54 16.59 39.00 3.69
807 971 4.522789 TCAGAGGGAAAGTTGCATTTTACC 59.477 41.667 14.68 14.68 38.57 2.85
810 974 5.305128 TCATTCAGAGGGAAAGTTGCATTTT 59.695 36.000 0.00 0.00 39.39 1.82
811 975 4.834496 TCATTCAGAGGGAAAGTTGCATTT 59.166 37.500 0.00 0.00 39.39 2.32
812 976 4.219288 GTCATTCAGAGGGAAAGTTGCATT 59.781 41.667 0.00 0.00 39.39 3.56
813 977 3.760684 GTCATTCAGAGGGAAAGTTGCAT 59.239 43.478 0.00 0.00 39.39 3.96
815 979 2.160417 CGTCATTCAGAGGGAAAGTTGC 59.840 50.000 0.00 0.00 39.39 4.17
816 980 3.403038 ACGTCATTCAGAGGGAAAGTTG 58.597 45.455 0.00 0.00 39.39 3.16
819 983 5.665459 AGAATACGTCATTCAGAGGGAAAG 58.335 41.667 15.43 0.00 44.81 2.62
820 984 5.422331 AGAGAATACGTCATTCAGAGGGAAA 59.578 40.000 15.43 0.00 44.81 3.13
821 985 4.956700 AGAGAATACGTCATTCAGAGGGAA 59.043 41.667 15.43 0.00 44.81 3.97
822 986 4.537751 AGAGAATACGTCATTCAGAGGGA 58.462 43.478 15.43 0.00 44.81 4.20
823 987 4.555708 CGAGAGAATACGTCATTCAGAGGG 60.556 50.000 15.43 3.14 44.81 4.30
824 988 4.532276 CGAGAGAATACGTCATTCAGAGG 58.468 47.826 15.43 0.00 44.81 3.69
825 989 3.971871 GCGAGAGAATACGTCATTCAGAG 59.028 47.826 15.43 8.21 44.81 3.35
826 990 3.628032 AGCGAGAGAATACGTCATTCAGA 59.372 43.478 15.43 0.00 44.81 3.27
827 991 3.728221 CAGCGAGAGAATACGTCATTCAG 59.272 47.826 15.43 8.22 44.81 3.02
828 992 3.695816 CAGCGAGAGAATACGTCATTCA 58.304 45.455 15.43 0.00 44.81 2.57
829 993 2.469516 GCAGCGAGAGAATACGTCATTC 59.530 50.000 0.00 0.21 43.02 2.67
835 1010 0.526310 TGCAGCAGCGAGAGAATACG 60.526 55.000 0.00 0.00 46.23 3.06
838 1013 1.808799 CGTGCAGCAGCGAGAGAAT 60.809 57.895 10.72 0.00 46.23 2.40
841 1016 4.731612 ACCGTGCAGCAGCGAGAG 62.732 66.667 16.05 5.25 46.23 3.20
863 1038 4.241555 GATCCGACGGCTGCCCAT 62.242 66.667 14.12 0.53 0.00 4.00
882 1104 1.330655 AATCCTGGGACGTCGATGCT 61.331 55.000 9.92 0.00 0.00 3.79
883 1105 0.462047 AAATCCTGGGACGTCGATGC 60.462 55.000 9.92 0.00 0.00 3.91
920 1144 4.678743 GCTTCAAGGGCCCCCGTT 62.679 66.667 21.43 2.73 41.95 4.44
983 1224 3.106986 ATCGGCGGTTGGAGATGGG 62.107 63.158 7.21 0.00 0.00 4.00
1248 1495 1.912220 CGCCTAGGGGTGGAATTGA 59.088 57.895 17.58 0.00 39.31 2.57
1296 1543 1.841663 CGAACCACACGGAAAGCCAG 61.842 60.000 0.00 0.00 35.59 4.85
1404 1657 2.614969 AAGCTGCTGGGGGATCCA 60.615 61.111 15.23 0.00 44.79 3.41
1407 1660 3.011517 ACGAAGCTGCTGGGGGAT 61.012 61.111 1.35 0.00 0.00 3.85
1488 1741 0.101040 TTCACAACAACTGCTGCTGC 59.899 50.000 8.89 8.89 40.20 5.25
1495 1748 5.273170 ACGAATCACAATTCACAACAACTG 58.727 37.500 0.00 0.00 41.22 3.16
1496 1749 5.499139 ACGAATCACAATTCACAACAACT 57.501 34.783 0.00 0.00 41.22 3.16
1499 1752 4.214545 GGGTACGAATCACAATTCACAACA 59.785 41.667 0.00 0.00 41.22 3.33
1500 1753 4.454504 AGGGTACGAATCACAATTCACAAC 59.545 41.667 0.00 0.00 41.22 3.32
1534 1788 8.547894 CATGGCAATTATCAAAATTCACATGAG 58.452 33.333 0.00 0.00 35.26 2.90
1550 1804 6.238731 GGAACAAGAATCGATCATGGCAATTA 60.239 38.462 0.00 0.00 31.00 1.40
1553 1807 3.378112 GGAACAAGAATCGATCATGGCAA 59.622 43.478 0.00 0.00 31.00 4.52
1554 1808 2.945008 GGAACAAGAATCGATCATGGCA 59.055 45.455 0.00 0.00 31.00 4.92
1555 1809 3.003068 CAGGAACAAGAATCGATCATGGC 59.997 47.826 0.00 0.00 31.00 4.40
1588 1842 3.196469 CCTGAGGAGAATGTAGCTTCACA 59.804 47.826 0.00 0.00 0.00 3.58
1598 1852 0.250209 CCATCGCCCTGAGGAGAATG 60.250 60.000 0.00 0.00 45.90 2.67
1612 1866 3.183172 CGAAGAACATGTAGATGCCATCG 59.817 47.826 0.00 3.39 32.14 3.84
1617 1871 3.483922 CGTCTCGAAGAACATGTAGATGC 59.516 47.826 0.00 0.00 34.09 3.91
1793 2047 4.582656 TGTTGGTTACAAATAAGCAGCTGT 59.417 37.500 16.64 0.00 46.55 4.40
1822 2081 3.667960 GCGTGTGAGAATGATTGGAACAC 60.668 47.826 0.00 0.00 39.29 3.32
1827 2086 2.079158 AGTGCGTGTGAGAATGATTGG 58.921 47.619 0.00 0.00 0.00 3.16
1828 2087 3.434641 AGAAGTGCGTGTGAGAATGATTG 59.565 43.478 0.00 0.00 0.00 2.67
1845 2104 1.115326 GTGGGGGCAAGCAAAGAAGT 61.115 55.000 0.00 0.00 0.00 3.01
1860 2119 1.208052 CATGTAGACCTGTGGAGTGGG 59.792 57.143 0.00 0.00 0.00 4.61
1861 2120 2.179427 TCATGTAGACCTGTGGAGTGG 58.821 52.381 0.00 0.00 0.00 4.00
1862 2121 3.790091 CATCATGTAGACCTGTGGAGTG 58.210 50.000 0.00 0.00 0.00 3.51
1863 2122 2.169352 GCATCATGTAGACCTGTGGAGT 59.831 50.000 0.00 0.00 0.00 3.85
1877 2138 7.255035 CCATTCTTACTACTTTCAGGCATCATG 60.255 40.741 0.00 0.00 0.00 3.07
2021 2282 8.408601 CCATAAGAACTTAAATCTGACCCAATG 58.591 37.037 0.00 0.00 0.00 2.82
2022 2283 8.116026 ACCATAAGAACTTAAATCTGACCCAAT 58.884 33.333 0.00 0.00 0.00 3.16
2054 2315 4.341806 CAGATACTGAGCTCTCCATTCTGT 59.658 45.833 16.19 0.00 32.44 3.41
2099 2360 0.967380 GCCTGTGTGGATTCCAAGGG 60.967 60.000 19.22 13.96 38.35 3.95
2399 2660 5.899547 AGACACTCTATCACCATCCATTACA 59.100 40.000 0.00 0.00 0.00 2.41
2421 2682 4.083324 GCGGTGAACTGAATCATTTGAAGA 60.083 41.667 0.00 0.00 0.00 2.87
2429 2690 0.684535 TCAGGCGGTGAACTGAATCA 59.315 50.000 0.00 0.00 40.51 2.57
2569 2830 4.082354 GCTGCTTTGAATGGAAGAAGTCAT 60.082 41.667 0.00 0.00 33.15 3.06
2834 3095 2.063541 GATTCCAAAGCCGGGCATCG 62.064 60.000 23.09 8.20 38.88 3.84
2843 3104 5.632347 CACAAACATCTTCAGATTCCAAAGC 59.368 40.000 0.00 0.00 31.21 3.51
3557 3821 9.605275 TCTCAAGACAAAATATCCAGTTATCTG 57.395 33.333 0.00 0.00 41.01 2.90
3575 3840 5.065704 TCAGACAATGCTAGTCTCAAGAC 57.934 43.478 1.79 1.79 44.11 3.01
3586 3851 8.742777 TGAAAATTTAGCTAATCAGACAATGCT 58.257 29.630 7.08 0.00 34.92 3.79
3591 3856 9.897744 CAACTTGAAAATTTAGCTAATCAGACA 57.102 29.630 7.08 3.39 0.00 3.41
3606 3871 6.515696 GCTCTCTGCTTTACCAACTTGAAAAT 60.516 38.462 0.00 0.00 38.95 1.82
3610 3875 3.403038 GCTCTCTGCTTTACCAACTTGA 58.597 45.455 0.00 0.00 38.95 3.02
3623 3888 3.697045 TCCTGAACTACTAAGCTCTCTGC 59.303 47.826 0.00 0.00 43.29 4.26
3624 3889 5.592282 TCATCCTGAACTACTAAGCTCTCTG 59.408 44.000 0.00 0.00 0.00 3.35
3625 3890 5.761205 TCATCCTGAACTACTAAGCTCTCT 58.239 41.667 0.00 0.00 0.00 3.10
3626 3891 6.648879 ATCATCCTGAACTACTAAGCTCTC 57.351 41.667 0.00 0.00 0.00 3.20
3627 3892 7.782644 ACTAATCATCCTGAACTACTAAGCTCT 59.217 37.037 0.00 0.00 0.00 4.09
3628 3893 7.865385 CACTAATCATCCTGAACTACTAAGCTC 59.135 40.741 0.00 0.00 0.00 4.09
3629 3894 7.685641 GCACTAATCATCCTGAACTACTAAGCT 60.686 40.741 0.00 0.00 0.00 3.74
3630 3895 6.422400 GCACTAATCATCCTGAACTACTAAGC 59.578 42.308 0.00 0.00 0.00 3.09
3631 3896 7.492524 TGCACTAATCATCCTGAACTACTAAG 58.507 38.462 0.00 0.00 0.00 2.18
3632 3897 7.418337 TGCACTAATCATCCTGAACTACTAA 57.582 36.000 0.00 0.00 0.00 2.24
3633 3898 7.093509 TGTTGCACTAATCATCCTGAACTACTA 60.094 37.037 0.00 0.00 0.00 1.82
3634 3899 5.939764 TGCACTAATCATCCTGAACTACT 57.060 39.130 0.00 0.00 0.00 2.57
3830 4124 0.039798 GTTGCATGCACACTGACAGG 60.040 55.000 22.58 0.00 0.00 4.00
4220 4520 2.100584 AGTTTTGATTCAAGCGTTGGCA 59.899 40.909 0.00 0.00 43.41 4.92
4225 4525 3.374745 CTGCAAGTTTTGATTCAAGCGT 58.625 40.909 0.00 0.00 0.00 5.07
4322 4623 4.997395 TGTCCTGAAACTACAGCAGAATTC 59.003 41.667 0.00 0.00 36.67 2.17
4411 4712 1.421382 TACAACTTTGGTACGCGCTC 58.579 50.000 5.73 0.00 0.00 5.03
4414 4715 3.058777 ACCATTTACAACTTTGGTACGCG 60.059 43.478 3.53 3.53 40.62 6.01
4417 4718 7.485810 AGTTTCACCATTTACAACTTTGGTAC 58.514 34.615 0.00 0.00 40.44 3.34
4483 4784 7.631717 AAGCTCACCTCTTTTTATGATAACC 57.368 36.000 0.00 0.00 0.00 2.85
4512 4813 4.030977 GCTACGAAATGCAGCAAAGAAATG 59.969 41.667 0.00 0.00 35.35 2.32


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

AutoCloner maintained by Alex Coulton.