Multiple sequence alignment - TraesCS5B01G176600

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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 TraesCS5B01G176600 chr5B 100.000 4456 0 0 1 4456 322556759 322552304 0.000000e+00 8229.0
1 TraesCS5B01G176600 chr5D 94.320 3838 157 22 1 3806 285134621 285130813 0.000000e+00 5823.0
2 TraesCS5B01G176600 chr5D 95.312 256 12 0 4200 4455 285130044 285129789 1.490000e-109 407.0
3 TraesCS5B01G176600 chr5A 92.649 2095 112 18 52 2124 376995532 376993458 0.000000e+00 2977.0
4 TraesCS5B01G176600 chr5A 92.000 1675 95 24 2154 3806 376993460 376991803 0.000000e+00 2314.0
5 TraesCS5B01G176600 chr5A 93.305 239 6 4 4224 4456 376991477 376991243 1.190000e-90 344.0
6 TraesCS5B01G176600 chr5A 89.030 237 22 4 3951 4185 525696866 525697100 1.570000e-74 291.0
7 TraesCS5B01G176600 chr5A 98.182 55 1 0 1 55 376995608 376995554 3.670000e-16 97.1
8 TraesCS5B01G176600 chr4A 91.416 233 18 2 3951 4181 674617026 674616794 7.190000e-83 318.0
9 TraesCS5B01G176600 chr3A 90.987 233 19 2 3951 4181 603876977 603877209 3.350000e-81 313.0
10 TraesCS5B01G176600 chr6D 89.744 234 22 2 3951 4182 410373548 410373781 9.370000e-77 298.0
11 TraesCS5B01G176600 chr6D 95.556 45 1 1 3812 3856 19719481 19719524 2.220000e-08 71.3
12 TraesCS5B01G176600 chr2A 89.451 237 23 2 3951 4185 699241086 699240850 9.370000e-77 298.0
13 TraesCS5B01G176600 chr7A 89.744 234 20 4 3951 4181 79622283 79622515 3.370000e-76 296.0
14 TraesCS5B01G176600 chr7A 95.745 47 2 0 3812 3858 675053499 675053453 4.780000e-10 76.8
15 TraesCS5B01G176600 chr6A 89.121 239 22 4 3950 4185 448651632 448651869 1.210000e-75 294.0
16 TraesCS5B01G176600 chr6A 89.316 234 23 2 3951 4182 36403838 36403605 4.360000e-75 292.0
17 TraesCS5B01G176600 chr6A 87.550 249 29 2 3950 4196 421525078 421524830 2.030000e-73 287.0
18 TraesCS5B01G176600 chr7B 97.826 46 1 0 3812 3857 640269460 640269505 3.690000e-11 80.5
19 TraesCS5B01G176600 chr7B 95.455 44 1 1 3812 3855 637568868 637568826 8.000000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G176600 chr5B 322552304 322556759 4455 True 8229.000 8229 100.000 1 4456 1 chr5B.!!$R1 4455
1 TraesCS5B01G176600 chr5D 285129789 285134621 4832 True 3115.000 5823 94.816 1 4455 2 chr5D.!!$R1 4454
2 TraesCS5B01G176600 chr5A 376991243 376995608 4365 True 1433.025 2977 94.034 1 4456 4 chr5A.!!$R1 4455

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
375 401 0.179048 CAGGGCGTTATGATGCTCCA 60.179 55.0 0.00 0.00 39.19 3.86 F
1257 1290 0.178990 AGGACAAAAGGACTGGCCAC 60.179 55.0 0.00 0.00 45.38 5.01 F
2599 2655 0.094730 GGTTAAGTCGCATCGTGCAC 59.905 55.0 6.82 6.82 45.36 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2176 2223 0.178975 CCACCCAAACAGCCACCTAA 60.179 55.000 0.00 0.0 0.0 2.69 R
2991 3062 1.198637 GGTGCACTCTCAGTTTGATGC 59.801 52.381 17.98 0.0 0.0 3.91 R
4241 4998 0.110823 GCAGGAACGCAACAACTACG 60.111 55.000 0.00 0.0 0.0 3.51 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.981308 AAACGTCATCCCCAAGCG 58.019 55.556 0.00 0.00 0.00 4.68
110 136 4.803426 GTCGGCAGAGCACGAGGG 62.803 72.222 0.00 0.00 40.09 4.30
269 295 2.173519 TGGGGTTCTAGTTACGTCCTG 58.826 52.381 0.00 0.00 0.00 3.86
271 297 2.564504 GGGGTTCTAGTTACGTCCTGTT 59.435 50.000 0.00 0.00 0.00 3.16
287 313 3.345808 TTCTTGCCACTCGCGTGC 61.346 61.111 5.77 5.85 42.08 5.34
309 335 1.697432 TGACCCGTTGGATTTCTGACT 59.303 47.619 0.00 0.00 34.81 3.41
375 401 0.179048 CAGGGCGTTATGATGCTCCA 60.179 55.000 0.00 0.00 39.19 3.86
388 414 2.936919 TGCTCCATGTCAGTCTTTGT 57.063 45.000 0.00 0.00 0.00 2.83
391 417 3.578282 TGCTCCATGTCAGTCTTTGTCTA 59.422 43.478 0.00 0.00 0.00 2.59
394 420 5.645497 GCTCCATGTCAGTCTTTGTCTATTT 59.355 40.000 0.00 0.00 0.00 1.40
417 444 1.401905 GCCCGACTAATTTTCAGCTGG 59.598 52.381 15.13 0.00 0.00 4.85
418 445 1.401905 CCCGACTAATTTTCAGCTGGC 59.598 52.381 15.13 0.00 0.00 4.85
439 466 2.191802 TGTTGTTTGAATGTTGCGCTG 58.808 42.857 9.73 0.00 0.00 5.18
458 485 5.235186 GCGCTGAAAAAGAGATCTATTGCTA 59.765 40.000 2.78 0.00 0.00 3.49
489 516 0.819259 CTGTATGTTGGGCCCATCCG 60.819 60.000 29.23 6.31 34.94 4.18
549 578 4.929819 TTGCCGCTGATAAGTAGACATA 57.070 40.909 0.00 0.00 0.00 2.29
579 608 2.039818 AGCTCTTGATGTGCATCCAG 57.960 50.000 9.39 8.06 37.61 3.86
586 615 1.814394 TGATGTGCATCCAGCTTGAAC 59.186 47.619 9.39 0.00 45.94 3.18
588 617 1.985473 TGTGCATCCAGCTTGAACTT 58.015 45.000 0.00 0.00 45.94 2.66
590 619 1.068055 GTGCATCCAGCTTGAACTTGG 60.068 52.381 0.00 0.00 45.94 3.61
591 620 1.251251 GCATCCAGCTTGAACTTGGT 58.749 50.000 0.00 0.00 41.15 3.67
592 621 1.068055 GCATCCAGCTTGAACTTGGTG 60.068 52.381 0.00 0.00 41.15 4.17
594 623 3.116091 CCAGCTTGAACTTGGTGGT 57.884 52.632 0.00 0.00 44.19 4.16
596 625 0.670162 CAGCTTGAACTTGGTGGTGG 59.330 55.000 0.00 0.00 0.00 4.61
597 626 0.550914 AGCTTGAACTTGGTGGTGGA 59.449 50.000 0.00 0.00 0.00 4.02
598 627 0.954452 GCTTGAACTTGGTGGTGGAG 59.046 55.000 0.00 0.00 0.00 3.86
599 628 1.750682 GCTTGAACTTGGTGGTGGAGT 60.751 52.381 0.00 0.00 0.00 3.85
600 629 2.486548 GCTTGAACTTGGTGGTGGAGTA 60.487 50.000 0.00 0.00 0.00 2.59
601 630 3.810743 GCTTGAACTTGGTGGTGGAGTAT 60.811 47.826 0.00 0.00 0.00 2.12
602 631 3.417069 TGAACTTGGTGGTGGAGTATG 57.583 47.619 0.00 0.00 0.00 2.39
603 632 2.708861 TGAACTTGGTGGTGGAGTATGT 59.291 45.455 0.00 0.00 0.00 2.29
604 633 3.904965 TGAACTTGGTGGTGGAGTATGTA 59.095 43.478 0.00 0.00 0.00 2.29
605 634 4.348461 TGAACTTGGTGGTGGAGTATGTAA 59.652 41.667 0.00 0.00 0.00 2.41
606 635 4.281898 ACTTGGTGGTGGAGTATGTAAC 57.718 45.455 0.00 0.00 0.00 2.50
616 645 7.876582 GTGGTGGAGTATGTAACTATTTATCCC 59.123 40.741 0.00 0.00 39.07 3.85
619 648 8.657712 GTGGAGTATGTAACTATTTATCCCCTT 58.342 37.037 0.00 0.00 39.07 3.95
630 659 9.601810 AACTATTTATCCCCTTCAAGTTTTCTT 57.398 29.630 0.00 0.00 41.31 2.52
722 755 2.062777 TGTTTGCAAAGCAGCCCCA 61.063 52.632 13.26 1.94 40.61 4.96
733 766 1.518903 GCAGCCCCACTCAAACTGAC 61.519 60.000 0.00 0.00 0.00 3.51
743 776 5.095490 CCACTCAAACTGACTTTGAACAAC 58.905 41.667 0.00 0.00 46.20 3.32
748 781 6.918626 TCAAACTGACTTTGAACAACAATGA 58.081 32.000 0.00 0.00 44.42 2.57
763 796 5.280945 CAACAATGAAAGGTTGTTCGACAT 58.719 37.500 1.60 0.00 45.24 3.06
765 798 6.627395 ACAATGAAAGGTTGTTCGACATTA 57.373 33.333 0.00 0.00 36.44 1.90
770 803 7.789273 TGAAAGGTTGTTCGACATTAAAGTA 57.211 32.000 0.00 0.00 0.00 2.24
771 804 8.211116 TGAAAGGTTGTTCGACATTAAAGTAA 57.789 30.769 0.00 0.00 0.00 2.24
772 805 8.124199 TGAAAGGTTGTTCGACATTAAAGTAAC 58.876 33.333 0.00 0.00 0.00 2.50
774 807 6.056884 AGGTTGTTCGACATTAAAGTAACCA 58.943 36.000 12.54 0.00 37.95 3.67
775 808 6.713450 AGGTTGTTCGACATTAAAGTAACCAT 59.287 34.615 12.54 0.00 37.95 3.55
776 809 6.799925 GGTTGTTCGACATTAAAGTAACCATG 59.200 38.462 7.32 0.00 36.10 3.66
777 810 5.933790 TGTTCGACATTAAAGTAACCATGC 58.066 37.500 0.00 0.00 0.00 4.06
778 811 5.703592 TGTTCGACATTAAAGTAACCATGCT 59.296 36.000 0.00 0.00 0.00 3.79
779 812 6.874664 TGTTCGACATTAAAGTAACCATGCTA 59.125 34.615 0.00 0.00 0.00 3.49
780 813 7.388224 TGTTCGACATTAAAGTAACCATGCTAA 59.612 33.333 0.00 0.00 0.00 3.09
782 815 7.745015 TCGACATTAAAGTAACCATGCTAAAC 58.255 34.615 0.00 0.00 0.00 2.01
787 820 5.705609 AAAGTAACCATGCTAAACCAGTG 57.294 39.130 0.00 0.00 0.00 3.66
792 825 3.149196 ACCATGCTAAACCAGTGACTTG 58.851 45.455 0.00 0.00 0.00 3.16
793 826 2.489329 CCATGCTAAACCAGTGACTTGG 59.511 50.000 0.00 0.48 44.09 3.61
801 834 1.086696 CCAGTGACTTGGCATTACGG 58.913 55.000 0.00 0.00 0.00 4.02
814 847 2.490509 GCATTACGGGTAGCCTTTTTGT 59.509 45.455 9.73 1.43 0.00 2.83
830 863 8.408601 AGCCTTTTTGTAAGCTTATGATATGTG 58.591 33.333 9.88 0.00 29.27 3.21
846 879 5.876460 TGATATGTGAATCCATGGCTTATCG 59.124 40.000 6.96 0.00 0.00 2.92
852 885 4.346709 TGAATCCATGGCTTATCGTCCTTA 59.653 41.667 6.96 0.00 0.00 2.69
886 919 2.302445 TGTTTTACTTGCCGGCCTACTA 59.698 45.455 26.77 0.09 0.00 1.82
922 955 3.429881 GCTAGTTTTGGCATTTGCACTTC 59.570 43.478 4.74 0.00 44.36 3.01
942 975 4.717233 TCTGTGCTTGTGATGTTGTTTT 57.283 36.364 0.00 0.00 0.00 2.43
1178 1211 6.145535 GCAAGTTCTTGAATGGTCTTGTAAG 58.854 40.000 15.52 0.00 35.96 2.34
1222 1255 9.334947 TCATGATAGATTTGTCATTTCCTCTTC 57.665 33.333 0.00 0.00 33.43 2.87
1257 1290 0.178990 AGGACAAAAGGACTGGCCAC 60.179 55.000 0.00 0.00 45.38 5.01
1299 1332 4.277423 AGGGACAAAGTTACAAATGAACCG 59.723 41.667 0.00 0.00 0.00 4.44
1494 1527 4.275936 GGACAAGATGAATTGGATAACGGG 59.724 45.833 0.00 0.00 34.36 5.28
1503 1536 1.146263 GGATAACGGGTCAGGCAGG 59.854 63.158 0.00 0.00 0.00 4.85
1515 1548 3.851128 GGCAGGGGTAGAGGACGC 61.851 72.222 0.00 0.00 40.26 5.19
1949 1982 8.706322 ACTTTGTCCTTATACTTCCATTTGTT 57.294 30.769 0.00 0.00 0.00 2.83
1965 1998 1.362224 TGTTCTCCCTCCTTCCCAAG 58.638 55.000 0.00 0.00 0.00 3.61
1983 2016 3.515502 CCAAGATGTGAGGTCCTAAGTCA 59.484 47.826 0.00 0.00 0.00 3.41
1987 2021 6.380079 AGATGTGAGGTCCTAAGTCATTTT 57.620 37.500 0.00 0.00 0.00 1.82
1988 2022 6.410540 AGATGTGAGGTCCTAAGTCATTTTC 58.589 40.000 0.00 0.00 0.00 2.29
2147 2194 0.329261 TTACTTGGATGCTGCCTGCT 59.671 50.000 0.00 0.00 43.37 4.24
2149 2196 0.964358 ACTTGGATGCTGCCTGCTTC 60.964 55.000 0.00 1.47 42.86 3.86
2150 2197 0.680280 CTTGGATGCTGCCTGCTTCT 60.680 55.000 8.89 0.00 43.06 2.85
2190 2239 8.835439 ACAATTTTAAAATTAGGTGGCTGTTTG 58.165 29.630 22.44 11.64 36.52 2.93
2218 2268 6.016360 TGGCAAATGATTTTAGGATGGTATCG 60.016 38.462 0.00 0.00 0.00 2.92
2289 2339 5.490139 AATTGCTATTGTCCATTGTCTCG 57.510 39.130 0.00 0.00 0.00 4.04
2309 2359 7.147966 TGTCTCGCAAGTATTTTATAGACCTCA 60.148 37.037 0.00 0.00 39.48 3.86
2316 2366 9.099454 CAAGTATTTTATAGACCTCACAAGGAC 57.901 37.037 0.00 0.00 46.67 3.85
2333 2383 2.694109 AGGACGATACCCTCTTTGTAGC 59.306 50.000 0.00 0.00 0.00 3.58
2360 2415 8.680039 TTTTGGACCGATTAAAGTTCTTTAGA 57.320 30.769 5.39 0.00 0.00 2.10
2361 2416 7.900782 TTGGACCGATTAAAGTTCTTTAGAG 57.099 36.000 5.39 2.60 0.00 2.43
2409 2465 7.891561 ACTGTTCTATAAGGCTGTATCTGATC 58.108 38.462 0.00 0.00 0.00 2.92
2599 2655 0.094730 GGTTAAGTCGCATCGTGCAC 59.905 55.000 6.82 6.82 45.36 4.57
2609 2665 0.107214 CATCGTGCACCCCTTACCAT 60.107 55.000 12.15 0.00 0.00 3.55
2753 2824 6.730960 TTGTGTCTTACGACTTTTCTTGTT 57.269 33.333 0.68 0.00 40.86 2.83
2991 3062 4.663636 AAAGAAGTTCCGTGCTAAATCG 57.336 40.909 0.00 0.00 0.00 3.34
3081 3154 7.064609 CGTGGTAATATCTGCTCTTTTTCTTCA 59.935 37.037 0.00 0.00 0.00 3.02
3125 3198 1.494824 AAGTCGTGTGTTAGTTCCGC 58.505 50.000 0.00 0.00 0.00 5.54
3547 3625 2.086869 GCTGTGGTGTATCACATTGCT 58.913 47.619 0.00 0.00 45.26 3.91
3691 3773 4.390264 TGTCTGGATCATAGTAGACTCGG 58.610 47.826 0.00 0.00 40.07 4.63
3697 3779 2.635714 TCATAGTAGACTCGGCGAACA 58.364 47.619 12.13 0.00 0.00 3.18
3703 3785 2.665185 ACTCGGCGAACAAGGCAC 60.665 61.111 12.13 0.00 36.37 5.01
3713 3795 2.612972 CGAACAAGGCACAGTACATCCT 60.613 50.000 0.00 0.00 0.00 3.24
3751 3833 1.262683 GCAAGACGAGCCATAGATTGC 59.737 52.381 0.00 0.00 35.35 3.56
3806 3889 8.797350 TGCTTTTCTCTGATTTATCATCTCAA 57.203 30.769 0.00 0.00 36.02 3.02
3816 3899 9.591404 CTGATTTATCATCTCAATTTAGAACGC 57.409 33.333 0.00 0.00 36.02 4.84
3817 3900 9.330063 TGATTTATCATCTCAATTTAGAACGCT 57.670 29.630 0.00 0.00 0.00 5.07
3836 3919 9.989869 AGAACGCTTTTATTAAATAAAGCTCTC 57.010 29.630 23.74 20.21 36.23 3.20
3894 4651 1.381928 TTTCGCTCCCGATAGTCGCT 61.382 55.000 0.00 0.00 43.97 4.93
3898 4655 0.238817 GCTCCCGATAGTCGCTACAG 59.761 60.000 0.00 0.00 38.82 2.74
3902 4659 1.478137 CCGATAGTCGCTACAGTTGC 58.522 55.000 0.00 0.00 38.82 4.17
3909 4666 2.993899 AGTCGCTACAGTTGCATTGTAC 59.006 45.455 7.77 2.24 0.00 2.90
3910 4667 2.993899 GTCGCTACAGTTGCATTGTACT 59.006 45.455 7.77 0.00 0.00 2.73
3911 4668 3.060895 GTCGCTACAGTTGCATTGTACTC 59.939 47.826 7.77 3.30 0.00 2.59
3912 4669 2.348666 CGCTACAGTTGCATTGTACTCC 59.651 50.000 7.77 0.85 0.00 3.85
3913 4670 2.678336 GCTACAGTTGCATTGTACTCCC 59.322 50.000 1.70 0.00 0.00 4.30
3914 4671 3.619979 GCTACAGTTGCATTGTACTCCCT 60.620 47.826 1.70 0.00 0.00 4.20
3915 4672 3.508845 ACAGTTGCATTGTACTCCCTT 57.491 42.857 2.79 0.00 0.00 3.95
3918 4675 2.558359 AGTTGCATTGTACTCCCTTTGC 59.442 45.455 0.00 0.00 0.00 3.68
3919 4676 2.558359 GTTGCATTGTACTCCCTTTGCT 59.442 45.455 0.00 0.00 0.00 3.91
3920 4677 2.875296 TGCATTGTACTCCCTTTGCTT 58.125 42.857 0.00 0.00 0.00 3.91
3921 4678 3.230134 TGCATTGTACTCCCTTTGCTTT 58.770 40.909 0.00 0.00 0.00 3.51
3922 4679 3.640967 TGCATTGTACTCCCTTTGCTTTT 59.359 39.130 0.00 0.00 0.00 2.27
3923 4680 4.830046 TGCATTGTACTCCCTTTGCTTTTA 59.170 37.500 0.00 0.00 0.00 1.52
3924 4681 5.161358 GCATTGTACTCCCTTTGCTTTTAC 58.839 41.667 0.00 0.00 0.00 2.01
3925 4682 5.048013 GCATTGTACTCCCTTTGCTTTTACT 60.048 40.000 0.00 0.00 0.00 2.24
3926 4683 6.516693 GCATTGTACTCCCTTTGCTTTTACTT 60.517 38.462 0.00 0.00 0.00 2.24
3927 4684 7.308951 GCATTGTACTCCCTTTGCTTTTACTTA 60.309 37.037 0.00 0.00 0.00 2.24
3928 4685 7.500720 TTGTACTCCCTTTGCTTTTACTTAC 57.499 36.000 0.00 0.00 0.00 2.34
3929 4686 6.834107 TGTACTCCCTTTGCTTTTACTTACT 58.166 36.000 0.00 0.00 0.00 2.24
3930 4687 6.932960 TGTACTCCCTTTGCTTTTACTTACTC 59.067 38.462 0.00 0.00 0.00 2.59
3931 4688 6.189036 ACTCCCTTTGCTTTTACTTACTCT 57.811 37.500 0.00 0.00 0.00 3.24
3932 4689 5.998363 ACTCCCTTTGCTTTTACTTACTCTG 59.002 40.000 0.00 0.00 0.00 3.35
3933 4690 4.760204 TCCCTTTGCTTTTACTTACTCTGC 59.240 41.667 0.00 0.00 0.00 4.26
3934 4691 4.518970 CCCTTTGCTTTTACTTACTCTGCA 59.481 41.667 0.00 0.00 0.00 4.41
3935 4692 5.183904 CCCTTTGCTTTTACTTACTCTGCAT 59.816 40.000 0.00 0.00 0.00 3.96
3936 4693 6.374333 CCCTTTGCTTTTACTTACTCTGCATA 59.626 38.462 0.00 0.00 0.00 3.14
3937 4694 7.067494 CCCTTTGCTTTTACTTACTCTGCATAT 59.933 37.037 0.00 0.00 0.00 1.78
3938 4695 8.462016 CCTTTGCTTTTACTTACTCTGCATATT 58.538 33.333 0.00 0.00 0.00 1.28
3941 4698 8.142994 TGCTTTTACTTACTCTGCATATTAGC 57.857 34.615 0.00 0.00 0.00 3.09
3942 4699 7.987458 TGCTTTTACTTACTCTGCATATTAGCT 59.013 33.333 0.00 0.00 34.99 3.32
3943 4700 8.831550 GCTTTTACTTACTCTGCATATTAGCTT 58.168 33.333 0.00 0.00 34.99 3.74
3945 4702 9.884636 TTTTACTTACTCTGCATATTAGCTTGA 57.115 29.630 0.00 0.00 34.99 3.02
3946 4703 8.873215 TTACTTACTCTGCATATTAGCTTGAC 57.127 34.615 0.00 0.00 34.99 3.18
3947 4704 7.118496 ACTTACTCTGCATATTAGCTTGACT 57.882 36.000 0.00 0.00 34.99 3.41
3948 4705 7.560368 ACTTACTCTGCATATTAGCTTGACTT 58.440 34.615 0.00 0.00 34.99 3.01
3949 4706 8.696374 ACTTACTCTGCATATTAGCTTGACTTA 58.304 33.333 0.00 0.00 34.99 2.24
3950 4707 9.703892 CTTACTCTGCATATTAGCTTGACTTAT 57.296 33.333 0.00 0.00 34.99 1.73
3965 4722 9.618890 AGCTTGACTTATATTAGCTTGATCAAA 57.381 29.630 9.88 0.00 38.99 2.69
3966 4723 9.875675 GCTTGACTTATATTAGCTTGATCAAAG 57.124 33.333 9.88 3.19 39.07 2.77
3988 4745 8.770438 AAAGTCAAGCTTTGTAAATTTTGACA 57.230 26.923 22.19 4.38 45.00 3.58
3989 4746 8.770438 AAGTCAAGCTTTGTAAATTTTGACAA 57.230 26.923 22.19 9.43 40.17 3.18
3990 4747 8.770438 AGTCAAGCTTTGTAAATTTTGACAAA 57.230 26.923 22.19 15.19 41.90 2.83
4000 4757 8.865590 TGTAAATTTTGACAAAGTTTAGAGGC 57.134 30.769 21.96 14.03 34.56 4.70
4001 4758 8.470805 TGTAAATTTTGACAAAGTTTAGAGGCA 58.529 29.630 21.96 15.76 34.56 4.75
4002 4759 9.308318 GTAAATTTTGACAAAGTTTAGAGGCAA 57.692 29.630 21.96 5.43 34.56 4.52
4003 4760 8.785329 AAATTTTGACAAAGTTTAGAGGCAAA 57.215 26.923 16.99 2.20 29.90 3.68
4004 4761 8.785329 AATTTTGACAAAGTTTAGAGGCAAAA 57.215 26.923 16.27 16.27 38.05 2.44
4005 4762 8.785329 ATTTTGACAAAGTTTAGAGGCAAAAA 57.215 26.923 17.32 6.32 37.47 1.94
4006 4763 8.785329 TTTTGACAAAGTTTAGAGGCAAAAAT 57.215 26.923 13.12 0.00 32.91 1.82
4007 4764 9.877178 TTTTGACAAAGTTTAGAGGCAAAAATA 57.123 25.926 13.12 0.00 32.91 1.40
4125 4882 9.833182 TTTTCTTTAAACTTGGTCAAATTTTGC 57.167 25.926 4.19 0.39 0.00 3.68
4126 4883 8.553459 TTCTTTAAACTTGGTCAAATTTTGCA 57.447 26.923 4.19 0.00 0.00 4.08
4127 4884 8.553459 TCTTTAAACTTGGTCAAATTTTGCAA 57.447 26.923 4.19 0.00 0.00 4.08
4128 4885 9.003658 TCTTTAAACTTGGTCAAATTTTGCAAA 57.996 25.926 8.05 8.05 0.00 3.68
4129 4886 9.276397 CTTTAAACTTGGTCAAATTTTGCAAAG 57.724 29.630 12.41 14.15 0.00 2.77
4130 4887 6.816134 AAACTTGGTCAAATTTTGCAAAGT 57.184 29.167 12.41 6.68 34.58 2.66
4131 4888 6.816134 AACTTGGTCAAATTTTGCAAAGTT 57.184 29.167 21.02 21.02 36.75 2.66
4132 4889 6.816134 ACTTGGTCAAATTTTGCAAAGTTT 57.184 29.167 22.59 22.59 31.44 2.66
4133 4890 6.610456 ACTTGGTCAAATTTTGCAAAGTTTG 58.390 32.000 35.84 35.84 43.05 2.93
4134 4891 6.429385 ACTTGGTCAAATTTTGCAAAGTTTGA 59.571 30.769 38.06 38.06 45.89 2.69
4141 4898 9.213799 TCAAATTTTGCAAAGTTTGACTTTAGT 57.786 25.926 38.06 14.73 45.84 2.24
4142 4899 9.476761 CAAATTTTGCAAAGTTTGACTTTAGTC 57.523 29.630 37.27 2.92 45.84 2.59
4178 4935 8.964476 TGCAGACTAAATAAAAATAGAGGGAG 57.036 34.615 0.00 0.00 0.00 4.30
4179 4936 8.548877 TGCAGACTAAATAAAAATAGAGGGAGT 58.451 33.333 0.00 0.00 0.00 3.85
4190 4947 6.633325 AAATAGAGGGAGTATCATGGATGG 57.367 41.667 0.00 0.00 36.25 3.51
4191 4948 2.264455 AGAGGGAGTATCATGGATGGC 58.736 52.381 0.00 0.00 36.25 4.40
4192 4949 1.280421 GAGGGAGTATCATGGATGGCC 59.720 57.143 0.00 0.00 36.25 5.36
4193 4950 1.132267 AGGGAGTATCATGGATGGCCT 60.132 52.381 3.32 0.00 36.25 5.19
4194 4951 1.707427 GGGAGTATCATGGATGGCCTT 59.293 52.381 3.32 0.00 36.25 4.35
4195 4952 2.553904 GGGAGTATCATGGATGGCCTTG 60.554 54.545 3.32 0.00 39.92 3.61
4198 4955 4.993307 TCATGGATGGCCTTGAGC 57.007 55.556 3.32 0.00 41.80 4.26
4213 4970 1.288188 TGAGCCCTTGATGATGTGGA 58.712 50.000 0.00 0.00 0.00 4.02
4214 4971 1.848388 TGAGCCCTTGATGATGTGGAT 59.152 47.619 0.00 0.00 0.00 3.41
4241 4998 1.792367 GGGCATCTTGTTTTTGAACGC 59.208 47.619 0.00 0.00 0.00 4.84
4380 5143 3.947132 CTGCTGCCACTCGTCCCTG 62.947 68.421 0.00 0.00 0.00 4.45
4400 5163 1.075536 GGGTTTCATGGAGGAACACCT 59.924 52.381 0.00 0.00 40.67 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
309 335 4.632688 GTCCTCGATAAAAATTTGACCGGA 59.367 41.667 9.46 0.00 0.00 5.14
358 384 0.877071 CATGGAGCATCATAACGCCC 59.123 55.000 0.00 0.00 36.25 6.13
375 401 5.581085 GGCGTAAATAGACAAAGACTGACAT 59.419 40.000 0.00 0.00 0.00 3.06
388 414 6.339730 TGAAAATTAGTCGGGCGTAAATAGA 58.660 36.000 0.00 0.00 0.00 1.98
391 417 4.201881 GCTGAAAATTAGTCGGGCGTAAAT 60.202 41.667 1.26 0.00 0.00 1.40
394 420 2.093869 AGCTGAAAATTAGTCGGGCGTA 60.094 45.455 0.00 0.00 0.00 4.42
417 444 1.071305 GCGCAACATTCAAACAACAGC 60.071 47.619 0.30 0.00 0.00 4.40
418 445 2.216940 CAGCGCAACATTCAAACAACAG 59.783 45.455 11.47 0.00 0.00 3.16
458 485 6.295067 GGCCCAACATACAGTTCAAAGTTAAT 60.295 38.462 0.00 0.00 38.74 1.40
476 503 1.001887 TACAACGGATGGGCCCAAC 60.002 57.895 32.58 27.70 0.00 3.77
489 516 5.503520 GCAGATATTTAACCAGCCGTACAAC 60.504 44.000 0.00 0.00 0.00 3.32
530 559 5.060662 TGATATGTCTACTTATCAGCGGC 57.939 43.478 12.29 0.00 37.78 6.53
549 578 5.163581 GCACATCAAGAGCTACCAATTTGAT 60.164 40.000 0.00 0.00 38.60 2.57
579 608 0.954452 CTCCACCACCAAGTTCAAGC 59.046 55.000 0.00 0.00 0.00 4.01
586 615 4.553330 AGTTACATACTCCACCACCAAG 57.447 45.455 0.00 0.00 28.23 3.61
588 617 6.630203 AAATAGTTACATACTCCACCACCA 57.370 37.500 0.00 0.00 38.33 4.17
590 619 7.876582 GGGATAAATAGTTACATACTCCACCAC 59.123 40.741 2.88 0.00 38.33 4.16
591 620 7.016858 GGGGATAAATAGTTACATACTCCACCA 59.983 40.741 2.88 0.00 38.33 4.17
592 621 7.237055 AGGGGATAAATAGTTACATACTCCACC 59.763 40.741 0.00 0.79 38.33 4.61
593 622 8.203681 AGGGGATAAATAGTTACATACTCCAC 57.796 38.462 2.88 0.00 38.33 4.02
594 623 8.808240 AAGGGGATAAATAGTTACATACTCCA 57.192 34.615 2.88 0.00 38.33 3.86
600 629 9.990868 AAACTTGAAGGGGATAAATAGTTACAT 57.009 29.630 0.00 0.00 0.00 2.29
601 630 9.816787 AAAACTTGAAGGGGATAAATAGTTACA 57.183 29.630 0.00 0.00 0.00 2.41
604 633 9.601810 AAGAAAACTTGAAGGGGATAAATAGTT 57.398 29.630 0.00 0.00 0.00 2.24
605 634 9.244292 GAAGAAAACTTGAAGGGGATAAATAGT 57.756 33.333 0.00 0.00 0.00 2.12
606 635 9.467796 AGAAGAAAACTTGAAGGGGATAAATAG 57.532 33.333 0.00 0.00 0.00 1.73
616 645 6.420008 CAGCATTTCAGAAGAAAACTTGAAGG 59.580 38.462 0.00 0.00 46.06 3.46
619 648 6.455360 ACAGCATTTCAGAAGAAAACTTGA 57.545 33.333 0.00 0.00 46.06 3.02
630 659 6.631971 TTTGTGATGTTACAGCATTTCAGA 57.368 33.333 6.57 0.00 30.83 3.27
677 706 8.182227 GGTAAACATGAAGGCATTCTTAGTTAC 58.818 37.037 12.92 14.88 35.50 2.50
678 707 8.107095 AGGTAAACATGAAGGCATTCTTAGTTA 58.893 33.333 12.92 5.32 35.50 2.24
743 776 7.647715 ACTTTAATGTCGAACAACCTTTCATTG 59.352 33.333 0.00 0.00 0.00 2.82
748 781 7.067251 TGGTTACTTTAATGTCGAACAACCTTT 59.933 33.333 17.38 0.00 35.15 3.11
763 796 6.999272 TCACTGGTTTAGCATGGTTACTTTAA 59.001 34.615 1.12 0.00 0.00 1.52
765 798 5.240844 GTCACTGGTTTAGCATGGTTACTTT 59.759 40.000 1.12 0.00 0.00 2.66
770 803 3.508845 AGTCACTGGTTTAGCATGGTT 57.491 42.857 1.12 0.00 0.00 3.67
771 804 3.149196 CAAGTCACTGGTTTAGCATGGT 58.851 45.455 1.62 1.62 0.00 3.55
772 805 2.489329 CCAAGTCACTGGTTTAGCATGG 59.511 50.000 0.00 0.00 0.00 3.66
774 807 2.162681 GCCAAGTCACTGGTTTAGCAT 58.837 47.619 0.00 0.00 38.86 3.79
775 808 1.133945 TGCCAAGTCACTGGTTTAGCA 60.134 47.619 0.00 0.00 38.86 3.49
776 809 1.604604 TGCCAAGTCACTGGTTTAGC 58.395 50.000 0.00 0.00 38.86 3.09
777 810 4.142902 CGTAATGCCAAGTCACTGGTTTAG 60.143 45.833 0.00 0.00 38.86 1.85
778 811 3.749088 CGTAATGCCAAGTCACTGGTTTA 59.251 43.478 0.00 0.00 38.86 2.01
779 812 2.552315 CGTAATGCCAAGTCACTGGTTT 59.448 45.455 0.00 0.00 38.86 3.27
780 813 2.151202 CGTAATGCCAAGTCACTGGTT 58.849 47.619 0.00 0.00 38.86 3.67
782 815 1.086696 CCGTAATGCCAAGTCACTGG 58.913 55.000 0.00 0.00 39.71 4.00
787 820 1.296727 GCTACCCGTAATGCCAAGTC 58.703 55.000 0.00 0.00 0.00 3.01
792 825 1.758936 AAAAGGCTACCCGTAATGCC 58.241 50.000 0.00 0.00 45.21 4.40
793 826 2.490509 ACAAAAAGGCTACCCGTAATGC 59.509 45.455 0.00 0.00 35.76 3.56
801 834 6.753107 TCATAAGCTTACAAAAAGGCTACC 57.247 37.500 8.70 0.00 34.40 3.18
814 847 7.337689 GCCATGGATTCACATATCATAAGCTTA 59.662 37.037 18.40 8.99 0.00 3.09
830 863 3.409026 AGGACGATAAGCCATGGATTC 57.591 47.619 20.60 4.88 0.00 2.52
852 885 7.148239 CGGCAAGTAAAACAGGAAGAAGATAAT 60.148 37.037 0.00 0.00 0.00 1.28
874 907 2.969950 AGAATAACATAGTAGGCCGGCA 59.030 45.455 30.85 7.48 0.00 5.69
886 919 6.622896 GCCAAAACTAGCAACGAGAATAACAT 60.623 38.462 0.00 0.00 0.00 2.71
922 955 4.422840 TCAAAACAACATCACAAGCACAG 58.577 39.130 0.00 0.00 0.00 3.66
942 975 5.236911 GCAATTCCTCAAAGCATGTTTTTCA 59.763 36.000 4.61 0.00 0.00 2.69
1178 1211 5.976458 TCATGAAATGGAATTAACAAGGGC 58.024 37.500 0.00 0.00 46.73 5.19
1222 1255 7.065563 CCTTTTGTCCTTCTGTTGAGATATGAG 59.934 40.741 0.00 0.00 0.00 2.90
1299 1332 1.537202 GTGACTGTTGCATCACCCTTC 59.463 52.381 6.88 0.00 39.49 3.46
1320 1353 1.875576 GCAGCATGGGGATCTTCGTAG 60.876 57.143 0.00 0.00 35.86 3.51
1323 1356 0.465097 AAGCAGCATGGGGATCTTCG 60.465 55.000 0.00 0.00 35.86 3.79
1350 1383 6.935741 TCCTTATTATTGAACCATTCCACG 57.064 37.500 0.00 0.00 0.00 4.94
1453 1486 4.338012 TGTCCAACAATCTCAGCATCAAT 58.662 39.130 0.00 0.00 0.00 2.57
1455 1488 3.421919 TGTCCAACAATCTCAGCATCA 57.578 42.857 0.00 0.00 0.00 3.07
1494 1527 1.001760 TCCTCTACCCCTGCCTGAC 59.998 63.158 0.00 0.00 0.00 3.51
1503 1536 2.125961 ATCACCGCGTCCTCTACCC 61.126 63.158 4.92 0.00 0.00 3.69
1515 1548 0.523072 CTTTTGCTGGACCATCACCG 59.477 55.000 0.00 0.00 0.00 4.94
1615 1648 8.834004 AGACTACATAGTAAAGACCATACCAA 57.166 34.615 0.00 0.00 36.50 3.67
1936 1969 4.175962 AGGAGGGAGAACAAATGGAAGTA 58.824 43.478 0.00 0.00 0.00 2.24
1949 1982 1.081174 ACATCTTGGGAAGGAGGGAGA 59.919 52.381 0.00 0.00 0.00 3.71
1965 1998 6.173339 TGAAAATGACTTAGGACCTCACATC 58.827 40.000 0.00 0.00 0.00 3.06
2076 2123 6.717289 AGGCACATAAATGTTGTCCTAAGTA 58.283 36.000 6.55 0.00 39.39 2.24
2176 2223 0.178975 CCACCCAAACAGCCACCTAA 60.179 55.000 0.00 0.00 0.00 2.69
2177 2224 1.458486 CCACCCAAACAGCCACCTA 59.542 57.895 0.00 0.00 0.00 3.08
2178 2225 2.198426 CCACCCAAACAGCCACCT 59.802 61.111 0.00 0.00 0.00 4.00
2190 2239 4.443315 CCATCCTAAAATCATTTGCCACCC 60.443 45.833 0.00 0.00 0.00 4.61
2218 2268 6.968904 CCTGTAACAAGAATCATACAACATGC 59.031 38.462 0.00 0.00 0.00 4.06
2289 2339 7.769044 TCCTTGTGAGGTCTATAAAATACTTGC 59.231 37.037 0.00 0.00 43.97 4.01
2309 2359 2.904434 ACAAAGAGGGTATCGTCCTTGT 59.096 45.455 6.82 6.82 37.51 3.16
2316 2366 3.821421 AAGGCTACAAAGAGGGTATCG 57.179 47.619 0.00 0.00 0.00 2.92
2333 2383 5.959618 AGAACTTTAATCGGTCCAAAAGG 57.040 39.130 0.00 0.00 34.07 3.11
2599 2655 1.479389 GGGCATCAGAATGGTAAGGGG 60.479 57.143 0.00 0.00 36.16 4.79
2668 2724 6.828273 TGCTTAGCTTTGACCATAACATATGT 59.172 34.615 1.41 1.41 0.00 2.29
2753 2824 6.350949 GGCCACCTCTGCAAAGAAAATAATTA 60.351 38.462 0.00 0.00 0.00 1.40
2882 2953 8.641541 GGAAACCCAATATCATGACACAAATAT 58.358 33.333 0.00 0.00 0.00 1.28
2991 3062 1.198637 GGTGCACTCTCAGTTTGATGC 59.801 52.381 17.98 0.00 0.00 3.91
3081 3154 7.423844 AATCAAAAGAAAAGGTCTTCAAGGT 57.576 32.000 0.00 0.00 46.36 3.50
3125 3198 9.132521 CAGAATTTAAAGTGCTTCAATAACCTG 57.867 33.333 0.00 0.00 0.00 4.00
3317 3395 2.587194 CGCCGCTCTCTTCCATGG 60.587 66.667 4.97 4.97 0.00 3.66
3691 3773 1.128692 GATGTACTGTGCCTTGTTCGC 59.871 52.381 0.00 0.00 0.00 4.70
3713 3795 1.506309 GCATCAGACACCGCAACACA 61.506 55.000 0.00 0.00 0.00 3.72
3810 3893 9.989869 GAGAGCTTTATTTAATAAAAGCGTTCT 57.010 29.630 20.56 18.97 35.72 3.01
3811 3894 9.769093 TGAGAGCTTTATTTAATAAAAGCGTTC 57.231 29.630 20.56 20.36 35.72 3.95
3821 3904 8.352942 CGGGCTAAATTGAGAGCTTTATTTAAT 58.647 33.333 0.00 0.00 38.79 1.40
3824 3907 5.450550 GCGGGCTAAATTGAGAGCTTTATTT 60.451 40.000 0.00 0.00 38.79 1.40
3826 3909 3.565902 GCGGGCTAAATTGAGAGCTTTAT 59.434 43.478 0.00 0.00 38.79 1.40
3827 3910 2.943033 GCGGGCTAAATTGAGAGCTTTA 59.057 45.455 0.00 0.00 38.79 1.85
3828 3911 1.745653 GCGGGCTAAATTGAGAGCTTT 59.254 47.619 0.00 0.00 38.79 3.51
3829 3912 1.340017 TGCGGGCTAAATTGAGAGCTT 60.340 47.619 0.00 0.00 38.79 3.74
3830 3913 0.253044 TGCGGGCTAAATTGAGAGCT 59.747 50.000 0.00 0.00 38.79 4.09
3832 3915 3.848272 TTTTGCGGGCTAAATTGAGAG 57.152 42.857 0.00 0.00 0.00 3.20
3858 4368 0.532115 AAATGCCCGAAATGCCTGTC 59.468 50.000 0.00 0.00 0.00 3.51
3859 4369 0.532115 GAAATGCCCGAAATGCCTGT 59.468 50.000 0.00 0.00 0.00 4.00
3860 4370 0.526096 CGAAATGCCCGAAATGCCTG 60.526 55.000 0.00 0.00 0.00 4.85
3862 4372 1.878069 GCGAAATGCCCGAAATGCC 60.878 57.895 0.00 0.00 37.76 4.40
3863 4373 3.691965 GCGAAATGCCCGAAATGC 58.308 55.556 0.00 0.00 37.76 3.56
3894 4651 4.634012 AAGGGAGTACAATGCAACTGTA 57.366 40.909 7.70 7.70 0.00 2.74
3898 4655 2.558359 AGCAAAGGGAGTACAATGCAAC 59.442 45.455 0.00 0.00 36.30 4.17
3902 4659 6.575162 AGTAAAAGCAAAGGGAGTACAATG 57.425 37.500 0.00 0.00 0.00 2.82
3909 4666 5.106515 GCAGAGTAAGTAAAAGCAAAGGGAG 60.107 44.000 0.00 0.00 0.00 4.30
3910 4667 4.760204 GCAGAGTAAGTAAAAGCAAAGGGA 59.240 41.667 0.00 0.00 0.00 4.20
3911 4668 4.518970 TGCAGAGTAAGTAAAAGCAAAGGG 59.481 41.667 0.00 0.00 0.00 3.95
3912 4669 5.689383 TGCAGAGTAAGTAAAAGCAAAGG 57.311 39.130 0.00 0.00 0.00 3.11
3915 4672 8.612619 GCTAATATGCAGAGTAAGTAAAAGCAA 58.387 33.333 0.00 0.00 33.91 3.91
3919 4676 9.884636 TCAAGCTAATATGCAGAGTAAGTAAAA 57.115 29.630 0.00 0.00 34.99 1.52
3920 4677 9.314321 GTCAAGCTAATATGCAGAGTAAGTAAA 57.686 33.333 0.00 0.00 34.99 2.01
3921 4678 8.696374 AGTCAAGCTAATATGCAGAGTAAGTAA 58.304 33.333 0.00 0.00 34.99 2.24
3922 4679 8.239038 AGTCAAGCTAATATGCAGAGTAAGTA 57.761 34.615 0.00 0.00 34.99 2.24
3923 4680 7.118496 AGTCAAGCTAATATGCAGAGTAAGT 57.882 36.000 0.00 0.00 34.99 2.24
3924 4681 9.703892 ATAAGTCAAGCTAATATGCAGAGTAAG 57.296 33.333 0.00 0.00 34.99 2.34
3939 4696 9.618890 TTTGATCAAGCTAATATAAGTCAAGCT 57.381 29.630 8.41 0.00 45.12 3.74
3940 4697 9.875675 CTTTGATCAAGCTAATATAAGTCAAGC 57.124 33.333 8.41 0.00 0.00 4.01
3964 4721 8.770438 TTGTCAAAATTTACAAAGCTTGACTT 57.230 26.923 20.78 0.00 40.48 3.01
3965 4722 8.770438 TTTGTCAAAATTTACAAAGCTTGACT 57.230 26.923 20.78 0.00 39.88 3.41
3974 4731 9.308318 GCCTCTAAACTTTGTCAAAATTTACAA 57.692 29.630 7.65 2.98 33.92 2.41
3975 4732 8.470805 TGCCTCTAAACTTTGTCAAAATTTACA 58.529 29.630 7.65 3.11 0.00 2.41
3976 4733 8.865590 TGCCTCTAAACTTTGTCAAAATTTAC 57.134 30.769 7.65 0.95 0.00 2.01
3977 4734 9.877178 TTTGCCTCTAAACTTTGTCAAAATTTA 57.123 25.926 10.57 10.57 0.00 1.40
3978 4735 8.785329 TTTGCCTCTAAACTTTGTCAAAATTT 57.215 26.923 9.47 9.47 0.00 1.82
3979 4736 8.785329 TTTTGCCTCTAAACTTTGTCAAAATT 57.215 26.923 0.00 0.00 30.32 1.82
3980 4737 8.785329 TTTTTGCCTCTAAACTTTGTCAAAAT 57.215 26.923 0.00 0.00 33.84 1.82
3981 4738 8.785329 ATTTTTGCCTCTAAACTTTGTCAAAA 57.215 26.923 0.00 0.00 32.50 2.44
4099 4856 9.833182 GCAAAATTTGACCAAGTTTAAAGAAAA 57.167 25.926 10.26 0.00 31.37 2.29
4100 4857 9.003658 TGCAAAATTTGACCAAGTTTAAAGAAA 57.996 25.926 10.26 0.00 31.37 2.52
4101 4858 8.553459 TGCAAAATTTGACCAAGTTTAAAGAA 57.447 26.923 10.26 0.00 31.37 2.52
4102 4859 8.553459 TTGCAAAATTTGACCAAGTTTAAAGA 57.447 26.923 10.26 0.00 31.37 2.52
4103 4860 9.276397 CTTTGCAAAATTTGACCAAGTTTAAAG 57.724 29.630 13.84 6.79 31.37 1.85
4104 4861 8.787852 ACTTTGCAAAATTTGACCAAGTTTAAA 58.212 25.926 13.84 2.11 31.37 1.52
4105 4862 8.329203 ACTTTGCAAAATTTGACCAAGTTTAA 57.671 26.923 13.84 0.00 31.37 1.52
4106 4863 7.913674 ACTTTGCAAAATTTGACCAAGTTTA 57.086 28.000 13.84 0.00 31.37 2.01
4107 4864 6.816134 ACTTTGCAAAATTTGACCAAGTTT 57.184 29.167 13.84 0.00 32.66 2.66
4108 4865 6.816134 AACTTTGCAAAATTTGACCAAGTT 57.184 29.167 13.84 14.80 32.94 2.66
4109 4866 6.429385 TCAAACTTTGCAAAATTTGACCAAGT 59.571 30.769 33.20 14.31 36.42 3.16
4110 4867 6.840075 TCAAACTTTGCAAAATTTGACCAAG 58.160 32.000 33.20 15.61 36.42 3.61
4111 4868 6.808008 TCAAACTTTGCAAAATTTGACCAA 57.192 29.167 33.20 18.66 36.42 3.67
4115 4872 9.213799 ACTAAAGTCAAACTTTGCAAAATTTGA 57.786 25.926 33.20 33.20 46.83 2.69
4116 4873 9.476761 GACTAAAGTCAAACTTTGCAAAATTTG 57.523 29.630 30.47 30.47 46.83 2.32
4152 4909 9.566432 CTCCCTCTATTTTTATTTAGTCTGCAT 57.434 33.333 0.00 0.00 0.00 3.96
4153 4910 8.548877 ACTCCCTCTATTTTTATTTAGTCTGCA 58.451 33.333 0.00 0.00 0.00 4.41
4154 4911 8.966069 ACTCCCTCTATTTTTATTTAGTCTGC 57.034 34.615 0.00 0.00 0.00 4.26
4164 4921 8.605947 CCATCCATGATACTCCCTCTATTTTTA 58.394 37.037 0.00 0.00 0.00 1.52
4165 4922 7.465116 CCATCCATGATACTCCCTCTATTTTT 58.535 38.462 0.00 0.00 0.00 1.94
4166 4923 6.523150 GCCATCCATGATACTCCCTCTATTTT 60.523 42.308 0.00 0.00 0.00 1.82
4167 4924 5.045286 GCCATCCATGATACTCCCTCTATTT 60.045 44.000 0.00 0.00 0.00 1.40
4168 4925 4.472833 GCCATCCATGATACTCCCTCTATT 59.527 45.833 0.00 0.00 0.00 1.73
4169 4926 4.036518 GCCATCCATGATACTCCCTCTAT 58.963 47.826 0.00 0.00 0.00 1.98
4170 4927 3.445008 GCCATCCATGATACTCCCTCTA 58.555 50.000 0.00 0.00 0.00 2.43
4171 4928 2.264455 GCCATCCATGATACTCCCTCT 58.736 52.381 0.00 0.00 0.00 3.69
4172 4929 1.280421 GGCCATCCATGATACTCCCTC 59.720 57.143 0.00 0.00 0.00 4.30
4173 4930 1.132267 AGGCCATCCATGATACTCCCT 60.132 52.381 5.01 0.00 33.74 4.20
4174 4931 1.366319 AGGCCATCCATGATACTCCC 58.634 55.000 5.01 0.00 33.74 4.30
4175 4932 2.373169 TCAAGGCCATCCATGATACTCC 59.627 50.000 5.01 0.00 35.36 3.85
4176 4933 3.672808 CTCAAGGCCATCCATGATACTC 58.327 50.000 5.01 0.00 39.14 2.59
4177 4934 2.224719 GCTCAAGGCCATCCATGATACT 60.225 50.000 5.01 0.00 39.14 2.12
4178 4935 2.157738 GCTCAAGGCCATCCATGATAC 58.842 52.381 5.01 0.00 39.14 2.24
4179 4936 2.574006 GCTCAAGGCCATCCATGATA 57.426 50.000 5.01 0.00 39.14 2.15
4180 4937 3.434053 GCTCAAGGCCATCCATGAT 57.566 52.632 5.01 0.00 39.14 2.45
4181 4938 4.993307 GCTCAAGGCCATCCATGA 57.007 55.556 5.01 0.00 37.71 3.07
4190 4947 1.030457 CATCATCAAGGGCTCAAGGC 58.970 55.000 0.00 0.00 40.90 4.35
4191 4948 2.022195 CACATCATCAAGGGCTCAAGG 58.978 52.381 0.00 0.00 0.00 3.61
4192 4949 2.022195 CCACATCATCAAGGGCTCAAG 58.978 52.381 0.00 0.00 0.00 3.02
4193 4950 1.634973 TCCACATCATCAAGGGCTCAA 59.365 47.619 0.00 0.00 0.00 3.02
4194 4951 1.288188 TCCACATCATCAAGGGCTCA 58.712 50.000 0.00 0.00 0.00 4.26
4195 4952 2.621998 CAATCCACATCATCAAGGGCTC 59.378 50.000 0.00 0.00 0.00 4.70
4196 4953 2.662866 CAATCCACATCATCAAGGGCT 58.337 47.619 0.00 0.00 0.00 5.19
4197 4954 1.684983 CCAATCCACATCATCAAGGGC 59.315 52.381 0.00 0.00 0.00 5.19
4198 4955 2.313317 CCCAATCCACATCATCAAGGG 58.687 52.381 0.00 0.00 0.00 3.95
4213 4970 0.712380 AACAAGATGCCCTCCCCAAT 59.288 50.000 0.00 0.00 0.00 3.16
4214 4971 0.486879 AAACAAGATGCCCTCCCCAA 59.513 50.000 0.00 0.00 0.00 4.12
4241 4998 0.110823 GCAGGAACGCAACAACTACG 60.111 55.000 0.00 0.00 0.00 3.51
4380 5143 1.075536 AGGTGTTCCTCCATGAAACCC 59.924 52.381 0.00 0.00 40.58 4.11
4400 5163 1.986757 GAGAGCAGAGCAGGGGTCA 60.987 63.158 0.00 0.00 34.11 4.02


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

AutoCloner maintained by Alex Coulton.