Multiple sequence alignment - TraesCS6D01G376800

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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 TraesCS6D01G376800 chr6D 100.000 4397 0 0 1 4397 459547212 459551608 0.000000e+00 8120.0
1 TraesCS6D01G376800 chr6D 90.470 1616 82 32 1983 3554 471274663 471276250 0.000000e+00 2065.0
2 TraesCS6D01G376800 chr6D 91.786 1120 47 12 2383 3468 471114187 471113079 0.000000e+00 1517.0
3 TraesCS6D01G376800 chr6D 93.824 340 15 5 2058 2393 471114544 471114207 1.410000e-139 507.0
4 TraesCS6D01G376800 chr6D 84.857 350 43 6 4051 4396 471276169 471276512 1.170000e-90 344.0
5 TraesCS6D01G376800 chr6D 84.839 310 36 5 4088 4396 471113078 471112779 7.150000e-78 302.0
6 TraesCS6D01G376800 chr6D 82.625 259 39 5 1296 1553 471274304 471274557 1.590000e-54 224.0
7 TraesCS6D01G376800 chr6D 75.917 436 58 27 1143 1563 471115017 471114614 3.490000e-41 180.0
8 TraesCS6D01G376800 chr6D 84.426 122 14 4 3828 3944 471276027 471276148 9.990000e-22 115.0
9 TraesCS6D01G376800 chr2B 89.835 2420 158 47 2019 4396 771418245 771415872 0.000000e+00 3025.0
10 TraesCS6D01G376800 chr2B 95.521 960 38 1 2474 3433 771488135 771487181 0.000000e+00 1530.0
11 TraesCS6D01G376800 chr2B 89.419 860 62 18 3432 4286 771480868 771480033 0.000000e+00 1057.0
12 TraesCS6D01G376800 chr2B 83.354 799 116 13 1 783 410710815 410710018 0.000000e+00 723.0
13 TraesCS6D01G376800 chr2B 84.848 363 34 13 2046 2393 771488514 771488158 3.260000e-91 346.0
14 TraesCS6D01G376800 chr2B 87.755 147 12 3 1296 1442 771420141 771420001 2.720000e-37 167.0
15 TraesCS6D01G376800 chr2B 87.162 148 11 5 1296 1442 771488939 771488799 1.270000e-35 161.0
16 TraesCS6D01G376800 chr6A 93.673 1470 61 6 1988 3431 616054237 616055700 0.000000e+00 2170.0
17 TraesCS6D01G376800 chr6A 85.380 855 92 19 3567 4396 616055319 616056165 0.000000e+00 856.0
18 TraesCS6D01G376800 chr6A 81.439 792 126 14 3 785 600271854 600272633 2.890000e-176 628.0
19 TraesCS6D01G376800 chr6A 85.641 195 23 3 1293 1487 616053868 616054057 2.680000e-47 200.0
20 TraesCS6D01G376800 chr3A 91.885 1528 82 14 2065 3561 574278793 574280309 0.000000e+00 2097.0
21 TraesCS6D01G376800 chr3A 95.888 1216 43 4 2026 3240 574320708 574319499 0.000000e+00 1962.0
22 TraesCS6D01G376800 chr3A 90.933 772 22 12 992 1722 574322221 574321457 0.000000e+00 994.0
23 TraesCS6D01G376800 chr3A 95.597 318 11 2 1727 2041 574321407 574321090 1.410000e-139 507.0
24 TraesCS6D01G376800 chr6B 90.505 1506 90 24 1997 3468 719423167 719424653 0.000000e+00 1940.0
25 TraesCS6D01G376800 chr6B 85.484 310 38 4 4088 4396 719308788 719308485 2.550000e-82 316.0
26 TraesCS6D01G376800 chr6B 80.537 447 41 22 3054 3468 719309221 719308789 7.150000e-78 302.0
27 TraesCS6D01G376800 chr6B 77.354 393 68 18 3567 3944 719424234 719424620 3.440000e-51 213.0
28 TraesCS6D01G376800 chr6B 79.828 233 29 12 1334 1563 719422934 719423151 2.120000e-33 154.0
29 TraesCS6D01G376800 chr7D 88.702 832 56 20 3567 4396 600865475 600864680 0.000000e+00 981.0
30 TraesCS6D01G376800 chr7D 84.761 794 107 6 6 785 464981982 464981189 0.000000e+00 784.0
31 TraesCS6D01G376800 chr7D 84.375 800 104 13 1 783 235150271 235151066 0.000000e+00 765.0
32 TraesCS6D01G376800 chr7D 81.589 793 128 15 4 785 17153344 17152559 1.330000e-179 640.0
33 TraesCS6D01G376800 chr2A 85.302 796 102 12 1 785 456754033 456753242 0.000000e+00 808.0
34 TraesCS6D01G376800 chr2A 77.551 784 141 25 21 783 100112118 100111349 1.450000e-119 440.0
35 TraesCS6D01G376800 chr7A 84.403 795 108 14 1 783 721077356 721078146 0.000000e+00 767.0
36 TraesCS6D01G376800 chr7A 90.343 466 30 9 3567 4032 692785343 692784893 8.140000e-167 597.0
37 TraesCS6D01G376800 chr7A 90.000 310 25 3 4087 4396 692784897 692784594 3.190000e-106 396.0
38 TraesCS6D01G376800 chr7B 81.351 992 136 30 2468 3431 680075962 680074992 0.000000e+00 761.0
39 TraesCS6D01G376800 chr7B 88.250 400 30 11 3571 3969 680075351 680074968 3.100000e-126 462.0
40 TraesCS6D01G376800 chr7B 88.761 347 27 9 3567 3912 707881467 707881132 8.800000e-112 414.0
41 TraesCS6D01G376800 chr7B 88.615 325 27 4 4076 4396 680074965 680074647 1.920000e-103 387.0
42 TraesCS6D01G376800 chr5D 83.965 792 106 13 1 785 475361840 475362617 0.000000e+00 739.0
43 TraesCS6D01G376800 chr5D 81.281 796 131 16 1 785 265527470 265528258 2.890000e-176 628.0
44 TraesCS6D01G376800 chr4B 78.105 475 83 15 324 783 431916432 431915964 9.310000e-72 281.0
45 TraesCS6D01G376800 chr4A 77.511 458 77 19 337 776 115783383 115783832 7.300000e-63 252.0
46 TraesCS6D01G376800 chr5B 85.841 113 9 6 1731 1842 494016495 494016601 3.590000e-21 113.0
47 TraesCS6D01G376800 chr2D 81.111 90 14 3 1741 1828 128461543 128461631 7.890000e-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 TraesCS6D01G376800 chr6D 459547212 459551608 4396 False 8120.000000 8120 100.000000 1 4397 1 chr6D.!!$F1 4396
1 TraesCS6D01G376800 chr6D 471274304 471276512 2208 False 687.000000 2065 85.594500 1296 4396 4 chr6D.!!$F2 3100
2 TraesCS6D01G376800 chr6D 471112779 471115017 2238 True 626.500000 1517 86.591500 1143 4396 4 chr6D.!!$R1 3253
3 TraesCS6D01G376800 chr2B 771415872 771420141 4269 True 1596.000000 3025 88.795000 1296 4396 2 chr2B.!!$R3 3100
4 TraesCS6D01G376800 chr2B 771480033 771480868 835 True 1057.000000 1057 89.419000 3432 4286 1 chr2B.!!$R2 854
5 TraesCS6D01G376800 chr2B 410710018 410710815 797 True 723.000000 723 83.354000 1 783 1 chr2B.!!$R1 782
6 TraesCS6D01G376800 chr2B 771487181 771488939 1758 True 679.000000 1530 89.177000 1296 3433 3 chr2B.!!$R4 2137
7 TraesCS6D01G376800 chr6A 616053868 616056165 2297 False 1075.333333 2170 88.231333 1293 4396 3 chr6A.!!$F2 3103
8 TraesCS6D01G376800 chr6A 600271854 600272633 779 False 628.000000 628 81.439000 3 785 1 chr6A.!!$F1 782
9 TraesCS6D01G376800 chr3A 574278793 574280309 1516 False 2097.000000 2097 91.885000 2065 3561 1 chr3A.!!$F1 1496
10 TraesCS6D01G376800 chr3A 574319499 574322221 2722 True 1154.333333 1962 94.139333 992 3240 3 chr3A.!!$R1 2248
11 TraesCS6D01G376800 chr6B 719422934 719424653 1719 False 769.000000 1940 82.562333 1334 3944 3 chr6B.!!$F1 2610
12 TraesCS6D01G376800 chr6B 719308485 719309221 736 True 309.000000 316 83.010500 3054 4396 2 chr6B.!!$R1 1342
13 TraesCS6D01G376800 chr7D 600864680 600865475 795 True 981.000000 981 88.702000 3567 4396 1 chr7D.!!$R3 829
14 TraesCS6D01G376800 chr7D 464981189 464981982 793 True 784.000000 784 84.761000 6 785 1 chr7D.!!$R2 779
15 TraesCS6D01G376800 chr7D 235150271 235151066 795 False 765.000000 765 84.375000 1 783 1 chr7D.!!$F1 782
16 TraesCS6D01G376800 chr7D 17152559 17153344 785 True 640.000000 640 81.589000 4 785 1 chr7D.!!$R1 781
17 TraesCS6D01G376800 chr2A 456753242 456754033 791 True 808.000000 808 85.302000 1 785 1 chr2A.!!$R2 784
18 TraesCS6D01G376800 chr2A 100111349 100112118 769 True 440.000000 440 77.551000 21 783 1 chr2A.!!$R1 762
19 TraesCS6D01G376800 chr7A 721077356 721078146 790 False 767.000000 767 84.403000 1 783 1 chr7A.!!$F1 782
20 TraesCS6D01G376800 chr7A 692784594 692785343 749 True 496.500000 597 90.171500 3567 4396 2 chr7A.!!$R1 829
21 TraesCS6D01G376800 chr7B 680074647 680075962 1315 True 536.666667 761 86.072000 2468 4396 3 chr7B.!!$R2 1928
22 TraesCS6D01G376800 chr5D 475361840 475362617 777 False 739.000000 739 83.965000 1 785 1 chr5D.!!$F2 784
23 TraesCS6D01G376800 chr5D 265527470 265528258 788 False 628.000000 628 81.281000 1 785 1 chr5D.!!$F1 784

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
785 816 0.179067 TTGCTTCTCGTTGGGTTCGT 60.179 50.0 0.00 0.0 0.0 3.85 F
786 817 0.179067 TGCTTCTCGTTGGGTTCGTT 60.179 50.0 0.00 0.0 0.0 3.85 F
787 818 0.234884 GCTTCTCGTTGGGTTCGTTG 59.765 55.0 0.00 0.0 0.0 4.10 F
788 819 0.234884 CTTCTCGTTGGGTTCGTTGC 59.765 55.0 0.00 0.0 0.0 4.17 F
2755 4968 0.108804 GATCATCGACGGTGTGTGGT 60.109 55.0 8.18 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 2075 0.105224 TGCGTCTTTTTGAGTCCCGA 59.895 50.000 0.00 0.0 0.00 5.14 R
2090 4260 0.539438 AAAGCGCATGGGACCAAGAA 60.539 50.000 14.90 0.0 0.00 2.52 R
2644 4857 0.958091 CAGAGGATACCAGAGCGGAG 59.042 60.000 0.00 0.0 38.63 4.63 R
2779 4992 2.264794 GGTTGTGACCTCGGCGAT 59.735 61.111 11.27 0.0 42.99 4.58 R
3793 6684 0.109342 AACACTTCACCAGCTCCAGG 59.891 55.000 0.00 0.0 0.00 4.45 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
152 157 1.186200 TGAGGACATGGGAGAAGTCG 58.814 55.000 0.00 0.00 33.18 4.18
202 207 7.168972 TGGTTTTCGTTCAATGTTTTGATGATC 59.831 33.333 0.00 0.00 41.38 2.92
217 222 9.081997 GTTTTGATGATCTGTTGTGTTGTTTTA 57.918 29.630 0.00 0.00 0.00 1.52
278 283 2.386100 CCATGCTTGGGCCTAGGGA 61.386 63.158 16.74 0.00 39.56 4.20
282 288 0.844661 TGCTTGGGCCTAGGGAAAGA 60.845 55.000 16.74 0.00 37.74 2.52
287 297 2.853430 TGGGCCTAGGGAAAGACATTA 58.147 47.619 11.72 0.00 0.00 1.90
336 347 3.259064 CGGGAGCGACAGAAATCTAAAA 58.741 45.455 0.00 0.00 0.00 1.52
347 358 9.158233 CGACAGAAATCTAAAACCCAGTTTATA 57.842 33.333 0.00 0.00 34.43 0.98
362 374 9.582648 ACCCAGTTTATAAGTTGTTTCATAAGT 57.417 29.630 0.00 0.00 0.00 2.24
445 458 1.078848 GTGGATGCTTGCGAGAGGT 60.079 57.895 4.70 0.00 0.00 3.85
460 473 4.202121 GCGAGAGGTGGTAATCATAAGTGA 60.202 45.833 0.00 0.00 39.04 3.41
470 484 8.995220 GTGGTAATCATAAGTGAGTTGTTTGTA 58.005 33.333 0.00 0.00 37.87 2.41
513 527 1.631388 TCCGGTCCACCAACATAACAT 59.369 47.619 0.00 0.00 35.14 2.71
567 582 5.950883 TCATGGTGAAAGTAACTAGACGAG 58.049 41.667 0.00 0.00 0.00 4.18
568 583 4.778534 TGGTGAAAGTAACTAGACGAGG 57.221 45.455 0.00 0.00 0.00 4.63
590 606 1.136774 CGCGTGTCCTCGAGAATGA 59.863 57.895 15.71 0.00 32.84 2.57
664 690 1.271707 GGCCACCTTGCTACTTTGGTA 60.272 52.381 0.00 0.00 0.00 3.25
672 703 5.067283 ACCTTGCTACTTTGGTAACTTGTTG 59.933 40.000 0.00 0.00 37.61 3.33
673 704 5.298276 CCTTGCTACTTTGGTAACTTGTTGA 59.702 40.000 0.00 0.00 37.61 3.18
725 756 9.618890 ATTATCTGTTACAAGTTATGCATCAGT 57.381 29.630 0.19 0.00 0.00 3.41
726 757 7.928307 ATCTGTTACAAGTTATGCATCAGTT 57.072 32.000 0.19 0.00 0.00 3.16
727 758 7.132694 TCTGTTACAAGTTATGCATCAGTTG 57.867 36.000 21.56 21.56 0.00 3.16
752 783 3.380320 AGGAATACCTTGCAAAATACCGC 59.620 43.478 0.00 0.00 45.36 5.68
753 784 3.380320 GGAATACCTTGCAAAATACCGCT 59.620 43.478 0.00 0.00 0.00 5.52
754 785 4.142249 GGAATACCTTGCAAAATACCGCTT 60.142 41.667 0.00 0.00 0.00 4.68
755 786 5.066764 GGAATACCTTGCAAAATACCGCTTA 59.933 40.000 0.00 0.00 0.00 3.09
756 787 6.238925 GGAATACCTTGCAAAATACCGCTTAT 60.239 38.462 0.00 0.00 0.00 1.73
757 788 6.709018 ATACCTTGCAAAATACCGCTTATT 57.291 33.333 0.00 0.00 31.07 1.40
758 789 4.743493 ACCTTGCAAAATACCGCTTATTG 58.257 39.130 0.00 0.00 30.21 1.90
759 790 4.461081 ACCTTGCAAAATACCGCTTATTGA 59.539 37.500 0.00 0.00 30.21 2.57
760 791 5.127031 ACCTTGCAAAATACCGCTTATTGAT 59.873 36.000 0.00 0.00 30.21 2.57
761 792 6.042143 CCTTGCAAAATACCGCTTATTGATT 58.958 36.000 0.00 0.00 30.21 2.57
762 793 6.534793 CCTTGCAAAATACCGCTTATTGATTT 59.465 34.615 0.00 0.00 30.21 2.17
763 794 7.254084 CCTTGCAAAATACCGCTTATTGATTTC 60.254 37.037 0.00 0.00 30.21 2.17
764 795 6.862209 TGCAAAATACCGCTTATTGATTTCT 58.138 32.000 0.00 0.00 30.21 2.52
765 796 7.319646 TGCAAAATACCGCTTATTGATTTCTT 58.680 30.769 0.00 0.00 30.21 2.52
766 797 7.816995 TGCAAAATACCGCTTATTGATTTCTTT 59.183 29.630 0.00 0.00 30.21 2.52
767 798 8.655970 GCAAAATACCGCTTATTGATTTCTTTT 58.344 29.630 0.00 0.00 30.21 2.27
768 799 9.956797 CAAAATACCGCTTATTGATTTCTTTTG 57.043 29.630 0.00 0.00 30.21 2.44
769 800 7.755582 AATACCGCTTATTGATTTCTTTTGC 57.244 32.000 0.00 0.00 0.00 3.68
770 801 5.391312 ACCGCTTATTGATTTCTTTTGCT 57.609 34.783 0.00 0.00 0.00 3.91
771 802 5.783111 ACCGCTTATTGATTTCTTTTGCTT 58.217 33.333 0.00 0.00 0.00 3.91
772 803 5.863935 ACCGCTTATTGATTTCTTTTGCTTC 59.136 36.000 0.00 0.00 0.00 3.86
773 804 6.095377 CCGCTTATTGATTTCTTTTGCTTCT 58.905 36.000 0.00 0.00 0.00 2.85
774 805 6.252228 CCGCTTATTGATTTCTTTTGCTTCTC 59.748 38.462 0.00 0.00 0.00 2.87
775 806 6.021939 CGCTTATTGATTTCTTTTGCTTCTCG 60.022 38.462 0.00 0.00 0.00 4.04
776 807 6.803807 GCTTATTGATTTCTTTTGCTTCTCGT 59.196 34.615 0.00 0.00 0.00 4.18
777 808 7.327032 GCTTATTGATTTCTTTTGCTTCTCGTT 59.673 33.333 0.00 0.00 0.00 3.85
778 809 6.998258 ATTGATTTCTTTTGCTTCTCGTTG 57.002 33.333 0.00 0.00 0.00 4.10
779 810 4.858935 TGATTTCTTTTGCTTCTCGTTGG 58.141 39.130 0.00 0.00 0.00 3.77
780 811 3.708563 TTTCTTTTGCTTCTCGTTGGG 57.291 42.857 0.00 0.00 0.00 4.12
781 812 2.341846 TCTTTTGCTTCTCGTTGGGT 57.658 45.000 0.00 0.00 0.00 4.51
782 813 2.650322 TCTTTTGCTTCTCGTTGGGTT 58.350 42.857 0.00 0.00 0.00 4.11
783 814 2.616842 TCTTTTGCTTCTCGTTGGGTTC 59.383 45.455 0.00 0.00 0.00 3.62
784 815 0.941542 TTTGCTTCTCGTTGGGTTCG 59.058 50.000 0.00 0.00 0.00 3.95
785 816 0.179067 TTGCTTCTCGTTGGGTTCGT 60.179 50.000 0.00 0.00 0.00 3.85
786 817 0.179067 TGCTTCTCGTTGGGTTCGTT 60.179 50.000 0.00 0.00 0.00 3.85
787 818 0.234884 GCTTCTCGTTGGGTTCGTTG 59.765 55.000 0.00 0.00 0.00 4.10
788 819 0.234884 CTTCTCGTTGGGTTCGTTGC 59.765 55.000 0.00 0.00 0.00 4.17
789 820 1.492319 TTCTCGTTGGGTTCGTTGCG 61.492 55.000 0.00 0.00 0.00 4.85
790 821 2.202905 TCGTTGGGTTCGTTGCGT 60.203 55.556 0.00 0.00 0.00 5.24
791 822 2.052590 CGTTGGGTTCGTTGCGTG 60.053 61.111 0.00 0.00 0.00 5.34
792 823 2.330041 GTTGGGTTCGTTGCGTGG 59.670 61.111 0.00 0.00 0.00 4.94
793 824 3.587933 TTGGGTTCGTTGCGTGGC 61.588 61.111 0.00 0.00 0.00 5.01
805 836 3.524873 CGTGGCGCAACAATTGTG 58.475 55.556 16.68 7.69 43.79 3.33
806 837 1.009108 CGTGGCGCAACAATTGTGA 60.009 52.632 16.68 0.00 43.66 3.58
807 838 0.593518 CGTGGCGCAACAATTGTGAA 60.594 50.000 16.68 0.00 43.66 3.18
808 839 1.565305 GTGGCGCAACAATTGTGAAA 58.435 45.000 12.82 0.00 43.66 2.69
809 840 1.522258 GTGGCGCAACAATTGTGAAAG 59.478 47.619 12.82 5.61 43.66 2.62
810 841 1.135915 TGGCGCAACAATTGTGAAAGT 59.864 42.857 12.82 0.00 43.66 2.66
811 842 2.200899 GGCGCAACAATTGTGAAAGTT 58.799 42.857 12.82 0.00 43.66 2.66
812 843 2.218530 GGCGCAACAATTGTGAAAGTTC 59.781 45.455 12.82 0.00 43.66 3.01
813 844 2.857152 GCGCAACAATTGTGAAAGTTCA 59.143 40.909 12.82 0.00 43.66 3.18
825 856 3.963129 TGAAAGTTCACCAACAAGAGGT 58.037 40.909 0.00 0.00 40.85 3.85
826 857 4.340617 TGAAAGTTCACCAACAAGAGGTT 58.659 39.130 0.00 0.00 37.23 3.50
827 858 4.157656 TGAAAGTTCACCAACAAGAGGTTG 59.842 41.667 0.36 0.36 43.24 3.77
828 859 6.037722 TGAAAGTTCACCAACAAGAGGTTGA 61.038 40.000 8.65 0.00 44.77 3.18
829 860 7.793398 TGAAAGTTCACCAACAAGAGGTTGAG 61.793 42.308 8.65 2.31 44.77 3.02
830 861 9.851874 TGAAAGTTCACCAACAAGAGGTTGAGA 62.852 40.741 8.65 4.02 44.77 3.27
837 868 2.417719 ACAAGAGGTTGAGATTGACGC 58.582 47.619 0.00 0.00 37.10 5.19
838 869 1.734465 CAAGAGGTTGAGATTGACGCC 59.266 52.381 0.00 0.00 35.46 5.68
839 870 0.976641 AGAGGTTGAGATTGACGCCA 59.023 50.000 0.00 0.00 0.00 5.69
840 871 1.079503 GAGGTTGAGATTGACGCCAC 58.920 55.000 0.00 0.00 0.00 5.01
841 872 0.670546 AGGTTGAGATTGACGCCACG 60.671 55.000 0.00 0.00 0.00 4.94
842 873 0.669318 GGTTGAGATTGACGCCACGA 60.669 55.000 0.00 0.00 0.00 4.35
843 874 1.359848 GTTGAGATTGACGCCACGAT 58.640 50.000 0.00 0.00 0.00 3.73
844 875 1.732259 GTTGAGATTGACGCCACGATT 59.268 47.619 0.00 0.00 0.00 3.34
845 876 2.927477 GTTGAGATTGACGCCACGATTA 59.073 45.455 0.00 0.00 0.00 1.75
846 877 3.452755 TGAGATTGACGCCACGATTAT 57.547 42.857 0.00 0.00 0.00 1.28
847 878 3.792401 TGAGATTGACGCCACGATTATT 58.208 40.909 0.00 0.00 0.00 1.40
848 879 4.188462 TGAGATTGACGCCACGATTATTT 58.812 39.130 0.00 0.00 0.00 1.40
849 880 4.634004 TGAGATTGACGCCACGATTATTTT 59.366 37.500 0.00 0.00 0.00 1.82
850 881 5.123186 TGAGATTGACGCCACGATTATTTTT 59.877 36.000 0.00 0.00 0.00 1.94
870 901 2.615929 GGGGGTAGGGGCCTCAAA 60.616 66.667 4.79 0.00 0.00 2.69
871 902 2.012794 GGGGGTAGGGGCCTCAAAT 61.013 63.158 4.79 0.00 0.00 2.32
872 903 0.699922 GGGGGTAGGGGCCTCAAATA 60.700 60.000 4.79 0.00 0.00 1.40
873 904 1.456919 GGGGTAGGGGCCTCAAATAT 58.543 55.000 4.79 0.00 0.00 1.28
874 905 1.787058 GGGGTAGGGGCCTCAAATATT 59.213 52.381 4.79 0.00 0.00 1.28
875 906 2.490902 GGGGTAGGGGCCTCAAATATTG 60.491 54.545 4.79 0.00 0.00 1.90
876 907 2.490902 GGGTAGGGGCCTCAAATATTGG 60.491 54.545 4.79 0.00 0.00 3.16
877 908 2.177016 GGTAGGGGCCTCAAATATTGGT 59.823 50.000 4.79 0.00 0.00 3.67
878 909 2.755952 AGGGGCCTCAAATATTGGTC 57.244 50.000 4.79 0.00 0.00 4.02
879 910 2.217776 AGGGGCCTCAAATATTGGTCT 58.782 47.619 4.79 0.00 0.00 3.85
880 911 2.091665 AGGGGCCTCAAATATTGGTCTG 60.092 50.000 4.79 0.00 0.00 3.51
881 912 2.310538 GGGCCTCAAATATTGGTCTGG 58.689 52.381 0.84 0.00 0.00 3.86
882 913 2.310538 GGCCTCAAATATTGGTCTGGG 58.689 52.381 0.00 0.00 0.00 4.45
883 914 2.358195 GGCCTCAAATATTGGTCTGGGT 60.358 50.000 0.00 0.00 0.00 4.51
884 915 3.117663 GGCCTCAAATATTGGTCTGGGTA 60.118 47.826 0.00 0.00 0.00 3.69
885 916 4.137543 GCCTCAAATATTGGTCTGGGTAG 58.862 47.826 0.00 0.00 0.00 3.18
886 917 4.137543 CCTCAAATATTGGTCTGGGTAGC 58.862 47.826 0.00 0.00 0.00 3.58
887 918 4.385199 CCTCAAATATTGGTCTGGGTAGCA 60.385 45.833 0.00 0.00 0.00 3.49
888 919 5.186256 TCAAATATTGGTCTGGGTAGCAA 57.814 39.130 0.00 0.00 40.78 3.91
889 920 5.575157 TCAAATATTGGTCTGGGTAGCAAA 58.425 37.500 0.00 0.00 40.00 3.68
890 921 6.013379 TCAAATATTGGTCTGGGTAGCAAAA 58.987 36.000 0.00 0.00 40.00 2.44
891 922 6.667414 TCAAATATTGGTCTGGGTAGCAAAAT 59.333 34.615 0.00 0.00 40.00 1.82
892 923 7.180051 TCAAATATTGGTCTGGGTAGCAAAATT 59.820 33.333 0.00 0.00 40.00 1.82
893 924 7.494922 AATATTGGTCTGGGTAGCAAAATTT 57.505 32.000 0.00 0.00 40.00 1.82
894 925 8.602472 AATATTGGTCTGGGTAGCAAAATTTA 57.398 30.769 0.00 0.00 40.00 1.40
895 926 5.975693 TTGGTCTGGGTAGCAAAATTTAG 57.024 39.130 0.00 0.00 34.14 1.85
896 927 4.340617 TGGTCTGGGTAGCAAAATTTAGG 58.659 43.478 0.00 0.00 0.00 2.69
897 928 4.202631 TGGTCTGGGTAGCAAAATTTAGGT 60.203 41.667 0.00 0.00 0.00 3.08
898 929 4.157840 GGTCTGGGTAGCAAAATTTAGGTG 59.842 45.833 0.00 0.00 0.00 4.00
899 930 4.157840 GTCTGGGTAGCAAAATTTAGGTGG 59.842 45.833 0.00 0.00 0.00 4.61
900 931 2.829120 TGGGTAGCAAAATTTAGGTGGC 59.171 45.455 0.00 0.00 0.00 5.01
901 932 3.096852 GGGTAGCAAAATTTAGGTGGCT 58.903 45.455 0.00 0.00 35.50 4.75
902 933 4.263994 TGGGTAGCAAAATTTAGGTGGCTA 60.264 41.667 0.00 0.00 33.10 3.93
903 934 4.893524 GGGTAGCAAAATTTAGGTGGCTAT 59.106 41.667 9.90 0.00 36.39 2.97
904 935 5.009710 GGGTAGCAAAATTTAGGTGGCTATC 59.990 44.000 9.90 9.44 36.39 2.08
905 936 5.592688 GGTAGCAAAATTTAGGTGGCTATCA 59.407 40.000 11.14 0.00 35.57 2.15
906 937 6.096282 GGTAGCAAAATTTAGGTGGCTATCAA 59.904 38.462 11.14 0.00 35.57 2.57
907 938 6.796785 AGCAAAATTTAGGTGGCTATCAAT 57.203 33.333 0.00 0.00 0.00 2.57
908 939 7.186570 AGCAAAATTTAGGTGGCTATCAATT 57.813 32.000 0.00 0.00 0.00 2.32
909 940 7.623630 AGCAAAATTTAGGTGGCTATCAATTT 58.376 30.769 0.00 0.00 0.00 1.82
910 941 8.102676 AGCAAAATTTAGGTGGCTATCAATTTT 58.897 29.630 0.00 0.11 35.30 1.82
911 942 8.729756 GCAAAATTTAGGTGGCTATCAATTTTT 58.270 29.630 2.55 0.00 33.58 1.94
940 971 7.676683 ATCTCCATGTAGTTATAAGTGTGGT 57.323 36.000 15.24 1.77 0.00 4.16
941 972 6.873997 TCTCCATGTAGTTATAAGTGTGGTG 58.126 40.000 15.24 13.79 0.00 4.17
942 973 6.439375 TCTCCATGTAGTTATAAGTGTGGTGT 59.561 38.462 15.24 0.00 0.00 4.16
943 974 7.011499 TCCATGTAGTTATAAGTGTGGTGTT 57.989 36.000 15.24 0.00 0.00 3.32
944 975 8.136563 TCCATGTAGTTATAAGTGTGGTGTTA 57.863 34.615 15.24 1.53 0.00 2.41
945 976 8.595421 TCCATGTAGTTATAAGTGTGGTGTTAA 58.405 33.333 15.24 1.28 0.00 2.01
946 977 9.391006 CCATGTAGTTATAAGTGTGGTGTTAAT 57.609 33.333 2.90 0.00 0.00 1.40
1002 1033 2.142292 TTTGGGGGAGCAGAGGAAGC 62.142 60.000 0.00 0.00 0.00 3.86
1183 1224 1.534697 GGTTGGCGGGGATGGATAA 59.465 57.895 0.00 0.00 0.00 1.75
1185 1226 1.147376 TTGGCGGGGATGGATAACG 59.853 57.895 0.00 0.00 0.00 3.18
1330 1392 2.430610 CGAAGCAGGAGGAGGAGGG 61.431 68.421 0.00 0.00 0.00 4.30
1430 1498 1.721487 CAAATTCGGCGCCTTCGAT 59.279 52.632 26.68 9.83 38.10 3.59
1434 1502 4.847516 TCGGCGCCTTCGATGACG 62.848 66.667 26.68 7.80 38.10 4.35
1532 1652 3.120165 GCTAGGAAGTAAACAGTTGCAGC 60.120 47.826 0.00 0.00 0.00 5.25
1620 1844 3.835978 TGGATGTTTCTTTCTCCTCCGTA 59.164 43.478 0.00 0.00 0.00 4.02
1685 1930 1.135333 GACAGAGACCCTTTCTAGCCG 59.865 57.143 0.00 0.00 33.22 5.52
1741 2031 8.976986 AATCTGTTTTTCATGCAAGATCTTAC 57.023 30.769 7.86 2.71 0.00 2.34
1780 2070 3.003480 GGAGGCATGTACAAGACAGAAC 58.997 50.000 6.72 0.00 42.79 3.01
1785 2075 5.536161 AGGCATGTACAAGACAGAACAAAAT 59.464 36.000 6.72 0.00 42.79 1.82
1848 2138 1.588674 TTTTGGCACACACCTCTACG 58.411 50.000 0.00 0.00 39.29 3.51
1868 2158 2.095263 CGGATGTCTTTTCGTGGCAAAT 60.095 45.455 0.00 0.00 0.00 2.32
2056 4223 3.944087 AGCTCTATTTGTTCCTGTGACC 58.056 45.455 0.00 0.00 0.00 4.02
2441 4650 6.315642 TCTCGTCTTCGTTACATGATAGTCTT 59.684 38.462 0.00 0.00 38.33 3.01
2532 4745 0.310854 CGATCGTGATCATCGACCCA 59.689 55.000 18.26 2.23 44.95 4.51
2644 4857 0.523072 CTACCTTGCCACACATGTGC 59.477 55.000 25.68 12.65 44.34 4.57
2755 4968 0.108804 GATCATCGACGGTGTGTGGT 60.109 55.000 8.18 0.00 0.00 4.16
3194 5410 3.804036 TCTTTGTGTTCCTGTGTAGTGG 58.196 45.455 0.00 0.00 0.00 4.00
3201 5417 1.717032 TCCTGTGTAGTGGTCAGCTT 58.283 50.000 0.00 0.00 0.00 3.74
3410 5749 5.966742 AGAAGTAAAACCTGAAAGATGCC 57.033 39.130 0.00 0.00 34.07 4.40
3452 5799 7.439356 ACATACATACAGTGATAAGTGCACATC 59.561 37.037 21.04 14.54 38.70 3.06
3501 5848 1.672363 CAAAGCACAAGTCTCAGCACA 59.328 47.619 0.00 0.00 0.00 4.57
3504 5851 2.579873 AGCACAAGTCTCAGCACAAAT 58.420 42.857 0.00 0.00 0.00 2.32
3505 5852 2.551459 AGCACAAGTCTCAGCACAAATC 59.449 45.455 0.00 0.00 0.00 2.17
3507 5854 2.096069 CACAAGTCTCAGCACAAATCCG 60.096 50.000 0.00 0.00 0.00 4.18
3575 5924 3.579586 ACATTGCACATTTCAAGGTGGAT 59.420 39.130 6.48 0.00 40.54 3.41
3589 5938 1.609208 GTGGATGTCACTGTTGCCTT 58.391 50.000 0.00 0.00 42.86 4.35
3607 5956 1.801178 CTTGTCCCTTGTTTCGAGCTC 59.199 52.381 2.73 2.73 0.00 4.09
3699 6590 1.459812 TGCTCCACCCAAGCAATCA 59.540 52.632 0.00 0.00 46.29 2.57
3700 6591 0.040058 TGCTCCACCCAAGCAATCAT 59.960 50.000 0.00 0.00 46.29 2.45
3708 6599 2.902705 CCAAGCAATCATGGGAATGG 57.097 50.000 0.00 0.00 32.87 3.16
3709 6600 2.390696 CCAAGCAATCATGGGAATGGA 58.609 47.619 0.00 0.00 32.87 3.41
3710 6601 2.364324 CCAAGCAATCATGGGAATGGAG 59.636 50.000 0.00 0.00 32.87 3.86
3711 6602 3.293337 CAAGCAATCATGGGAATGGAGA 58.707 45.455 0.00 0.00 0.00 3.71
3712 6603 3.225177 AGCAATCATGGGAATGGAGAG 57.775 47.619 0.00 0.00 0.00 3.20
3770 6661 4.752101 TGCTCTTGTCTGCTTAGTTTCTTC 59.248 41.667 0.00 0.00 0.00 2.87
3771 6662 4.143221 GCTCTTGTCTGCTTAGTTTCTTCG 60.143 45.833 0.00 0.00 0.00 3.79
3772 6663 4.307432 TCTTGTCTGCTTAGTTTCTTCGG 58.693 43.478 0.00 0.00 0.00 4.30
3773 6664 3.746045 TGTCTGCTTAGTTTCTTCGGT 57.254 42.857 0.00 0.00 0.00 4.69
3774 6665 4.067972 TGTCTGCTTAGTTTCTTCGGTT 57.932 40.909 0.00 0.00 0.00 4.44
3775 6666 4.056050 TGTCTGCTTAGTTTCTTCGGTTC 58.944 43.478 0.00 0.00 0.00 3.62
3776 6667 4.202223 TGTCTGCTTAGTTTCTTCGGTTCT 60.202 41.667 0.00 0.00 0.00 3.01
3777 6668 4.150804 GTCTGCTTAGTTTCTTCGGTTCTG 59.849 45.833 0.00 0.00 0.00 3.02
3778 6669 2.806244 TGCTTAGTTTCTTCGGTTCTGC 59.194 45.455 0.00 0.00 0.00 4.26
3779 6670 2.806244 GCTTAGTTTCTTCGGTTCTGCA 59.194 45.455 0.00 0.00 0.00 4.41
3780 6671 3.120511 GCTTAGTTTCTTCGGTTCTGCAG 60.121 47.826 7.63 7.63 0.00 4.41
3781 6672 2.622064 AGTTTCTTCGGTTCTGCAGT 57.378 45.000 14.67 0.00 0.00 4.40
3782 6673 3.746045 AGTTTCTTCGGTTCTGCAGTA 57.254 42.857 14.67 0.00 0.00 2.74
3783 6674 3.391049 AGTTTCTTCGGTTCTGCAGTAC 58.609 45.455 14.67 14.63 0.00 2.73
3784 6675 3.069729 AGTTTCTTCGGTTCTGCAGTACT 59.930 43.478 21.00 0.00 0.00 2.73
3785 6676 3.746045 TTCTTCGGTTCTGCAGTACTT 57.254 42.857 21.00 0.00 0.00 2.24
3786 6677 3.746045 TCTTCGGTTCTGCAGTACTTT 57.254 42.857 21.00 0.00 0.00 2.66
3787 6678 4.067972 TCTTCGGTTCTGCAGTACTTTT 57.932 40.909 21.00 0.00 0.00 2.27
3788 6679 4.448210 TCTTCGGTTCTGCAGTACTTTTT 58.552 39.130 21.00 0.00 0.00 1.94
3789 6680 4.510340 TCTTCGGTTCTGCAGTACTTTTTC 59.490 41.667 21.00 5.24 0.00 2.29
3790 6681 4.067972 TCGGTTCTGCAGTACTTTTTCT 57.932 40.909 21.00 0.00 0.00 2.52
3791 6682 5.204409 TCGGTTCTGCAGTACTTTTTCTA 57.796 39.130 21.00 0.00 0.00 2.10
3792 6683 5.790593 TCGGTTCTGCAGTACTTTTTCTAT 58.209 37.500 21.00 0.00 0.00 1.98
3793 6684 5.867716 TCGGTTCTGCAGTACTTTTTCTATC 59.132 40.000 21.00 2.65 0.00 2.08
3794 6685 5.063564 CGGTTCTGCAGTACTTTTTCTATCC 59.936 44.000 21.00 3.18 0.00 2.59
3795 6686 6.174049 GGTTCTGCAGTACTTTTTCTATCCT 58.826 40.000 21.00 0.00 0.00 3.24
3796 6687 6.092807 GGTTCTGCAGTACTTTTTCTATCCTG 59.907 42.308 21.00 0.00 0.00 3.86
3803 6694 4.227864 ACTTTTTCTATCCTGGAGCTGG 57.772 45.455 1.52 0.00 0.00 4.85
3806 6697 2.550277 TTCTATCCTGGAGCTGGTGA 57.450 50.000 1.52 0.00 0.00 4.02
3812 6703 0.109342 CCTGGAGCTGGTGAAGTGTT 59.891 55.000 0.00 0.00 0.00 3.32
3816 6707 2.092429 TGGAGCTGGTGAAGTGTTTCTT 60.092 45.455 0.00 0.00 39.32 2.52
3818 6709 3.243201 GGAGCTGGTGAAGTGTTTCTTTG 60.243 47.826 0.00 0.00 36.40 2.77
3851 6749 7.816945 TTTTTAATTATCTTTGCTCAGCTGC 57.183 32.000 9.47 0.00 0.00 5.25
3861 6759 1.202806 TGCTCAGCTGCAAGTAAACCT 60.203 47.619 9.47 0.00 40.29 3.50
4093 7003 2.354510 ACGCAAATTCACCCACATATCG 59.645 45.455 0.00 0.00 0.00 2.92
4122 7032 6.690957 CAGGTTTTGCGGTACAACATAATATG 59.309 38.462 0.00 0.00 38.23 1.78
4125 7035 5.666969 TTGCGGTACAACATAATATGCTC 57.333 39.130 0.00 0.00 31.73 4.26
4223 7134 2.094545 GGCCAGAAAGATTTGCATCGTT 60.095 45.455 0.00 0.00 34.19 3.85
4301 7224 3.242220 CGCTATCGCTGCCATCAAATATC 60.242 47.826 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 157 9.988350 CCAACTTCACATGATTACTTATAACAC 57.012 33.333 0.00 0.00 0.00 3.32
202 207 6.238374 CCACTAGAGGTAAAACAACACAACAG 60.238 42.308 0.00 0.00 0.00 3.16
217 222 2.958818 TCACAAGACACCACTAGAGGT 58.041 47.619 5.96 5.96 44.48 3.85
287 297 7.586349 ACCCATCATCTACAAACTAATTCCAT 58.414 34.615 0.00 0.00 0.00 3.41
336 347 9.582648 ACTTATGAAACAACTTATAAACTGGGT 57.417 29.630 0.00 0.00 0.00 4.51
347 358 7.872483 CCAAAATAGCCACTTATGAAACAACTT 59.128 33.333 0.00 0.00 0.00 2.66
362 374 8.774546 TTAAACATATGGATCCAAAATAGCCA 57.225 30.769 20.67 0.00 0.00 4.75
409 421 9.023962 AGCATCCACAAATACAAGAAAAGAATA 57.976 29.630 0.00 0.00 0.00 1.75
416 428 4.615682 CGCAAGCATCCACAAATACAAGAA 60.616 41.667 0.00 0.00 0.00 2.52
445 458 8.995220 GTACAAACAACTCACTTATGATTACCA 58.005 33.333 0.00 0.00 33.22 3.25
470 484 5.681639 AGCTAAGGTGTTGTTCTTACTTGT 58.318 37.500 0.00 0.00 0.00 3.16
513 527 7.492524 AGATCGCATTCACTACTTTGATAAGA 58.507 34.615 0.00 0.00 35.30 2.10
568 583 4.477975 CTCGAGGACACGCGGGAC 62.478 72.222 19.19 9.60 43.53 4.46
628 644 4.597075 AGGTGGCCAAATCCTTTTTATTGT 59.403 37.500 7.24 0.00 0.00 2.71
718 749 3.019564 AGGTATTCCTTGCAACTGATGC 58.980 45.455 2.62 2.62 44.67 3.91
731 762 3.380320 AGCGGTATTTTGCAAGGTATTCC 59.620 43.478 0.00 2.05 0.00 3.01
732 763 4.632538 AGCGGTATTTTGCAAGGTATTC 57.367 40.909 0.00 0.00 0.00 1.75
733 764 6.709018 ATAAGCGGTATTTTGCAAGGTATT 57.291 33.333 0.00 0.00 0.00 1.89
734 765 6.320164 TCAATAAGCGGTATTTTGCAAGGTAT 59.680 34.615 0.00 0.00 29.38 2.73
735 766 5.648526 TCAATAAGCGGTATTTTGCAAGGTA 59.351 36.000 0.00 0.00 29.38 3.08
736 767 4.461081 TCAATAAGCGGTATTTTGCAAGGT 59.539 37.500 0.00 0.00 29.38 3.50
737 768 4.992688 TCAATAAGCGGTATTTTGCAAGG 58.007 39.130 0.00 0.00 29.38 3.61
738 769 7.489113 AGAAATCAATAAGCGGTATTTTGCAAG 59.511 33.333 0.00 0.00 29.38 4.01
739 770 7.319646 AGAAATCAATAAGCGGTATTTTGCAA 58.680 30.769 0.00 0.00 29.38 4.08
740 771 6.862209 AGAAATCAATAAGCGGTATTTTGCA 58.138 32.000 0.00 0.00 29.38 4.08
741 772 7.755582 AAGAAATCAATAAGCGGTATTTTGC 57.244 32.000 0.00 0.00 29.38 3.68
742 773 9.956797 CAAAAGAAATCAATAAGCGGTATTTTG 57.043 29.630 0.00 0.00 29.38 2.44
743 774 8.655970 GCAAAAGAAATCAATAAGCGGTATTTT 58.344 29.630 0.00 0.00 29.38 1.82
744 775 8.034804 AGCAAAAGAAATCAATAAGCGGTATTT 58.965 29.630 0.00 0.00 29.38 1.40
745 776 7.547227 AGCAAAAGAAATCAATAAGCGGTATT 58.453 30.769 0.00 0.00 32.25 1.89
746 777 7.100458 AGCAAAAGAAATCAATAAGCGGTAT 57.900 32.000 0.00 0.00 0.00 2.73
747 778 6.509418 AGCAAAAGAAATCAATAAGCGGTA 57.491 33.333 0.00 0.00 0.00 4.02
748 779 5.391312 AGCAAAAGAAATCAATAAGCGGT 57.609 34.783 0.00 0.00 0.00 5.68
749 780 6.095377 AGAAGCAAAAGAAATCAATAAGCGG 58.905 36.000 0.00 0.00 0.00 5.52
750 781 6.021939 CGAGAAGCAAAAGAAATCAATAAGCG 60.022 38.462 0.00 0.00 0.00 4.68
751 782 6.803807 ACGAGAAGCAAAAGAAATCAATAAGC 59.196 34.615 0.00 0.00 0.00 3.09
752 783 8.633408 CAACGAGAAGCAAAAGAAATCAATAAG 58.367 33.333 0.00 0.00 0.00 1.73
753 784 7.594758 CCAACGAGAAGCAAAAGAAATCAATAA 59.405 33.333 0.00 0.00 0.00 1.40
754 785 7.083858 CCAACGAGAAGCAAAAGAAATCAATA 58.916 34.615 0.00 0.00 0.00 1.90
755 786 5.922544 CCAACGAGAAGCAAAAGAAATCAAT 59.077 36.000 0.00 0.00 0.00 2.57
756 787 5.280945 CCAACGAGAAGCAAAAGAAATCAA 58.719 37.500 0.00 0.00 0.00 2.57
757 788 4.261572 CCCAACGAGAAGCAAAAGAAATCA 60.262 41.667 0.00 0.00 0.00 2.57
758 789 4.229876 CCCAACGAGAAGCAAAAGAAATC 58.770 43.478 0.00 0.00 0.00 2.17
759 790 3.636764 ACCCAACGAGAAGCAAAAGAAAT 59.363 39.130 0.00 0.00 0.00 2.17
760 791 3.020984 ACCCAACGAGAAGCAAAAGAAA 58.979 40.909 0.00 0.00 0.00 2.52
761 792 2.650322 ACCCAACGAGAAGCAAAAGAA 58.350 42.857 0.00 0.00 0.00 2.52
762 793 2.341846 ACCCAACGAGAAGCAAAAGA 57.658 45.000 0.00 0.00 0.00 2.52
763 794 2.602217 CGAACCCAACGAGAAGCAAAAG 60.602 50.000 0.00 0.00 0.00 2.27
764 795 1.332375 CGAACCCAACGAGAAGCAAAA 59.668 47.619 0.00 0.00 0.00 2.44
765 796 0.941542 CGAACCCAACGAGAAGCAAA 59.058 50.000 0.00 0.00 0.00 3.68
766 797 0.179067 ACGAACCCAACGAGAAGCAA 60.179 50.000 0.00 0.00 34.70 3.91
767 798 0.179067 AACGAACCCAACGAGAAGCA 60.179 50.000 0.00 0.00 34.70 3.91
768 799 0.234884 CAACGAACCCAACGAGAAGC 59.765 55.000 0.00 0.00 34.70 3.86
769 800 0.234884 GCAACGAACCCAACGAGAAG 59.765 55.000 0.00 0.00 34.70 2.85
770 801 1.492319 CGCAACGAACCCAACGAGAA 61.492 55.000 0.00 0.00 34.70 2.87
771 802 1.952133 CGCAACGAACCCAACGAGA 60.952 57.895 0.00 0.00 34.70 4.04
772 803 2.241880 ACGCAACGAACCCAACGAG 61.242 57.895 0.00 0.00 34.70 4.18
773 804 2.202905 ACGCAACGAACCCAACGA 60.203 55.556 0.00 0.00 34.70 3.85
774 805 2.052590 CACGCAACGAACCCAACG 60.053 61.111 0.00 0.00 0.00 4.10
775 806 2.330041 CCACGCAACGAACCCAAC 59.670 61.111 0.00 0.00 0.00 3.77
776 807 3.587933 GCCACGCAACGAACCCAA 61.588 61.111 0.00 0.00 0.00 4.12
788 819 0.593518 TTCACAATTGTTGCGCCACG 60.594 50.000 8.77 0.00 0.00 4.94
789 820 1.522258 CTTTCACAATTGTTGCGCCAC 59.478 47.619 8.77 4.28 0.00 5.01
790 821 1.135915 ACTTTCACAATTGTTGCGCCA 59.864 42.857 8.77 0.00 0.00 5.69
791 822 1.851658 ACTTTCACAATTGTTGCGCC 58.148 45.000 8.77 0.00 0.00 6.53
792 823 2.857152 TGAACTTTCACAATTGTTGCGC 59.143 40.909 8.77 0.00 31.01 6.09
804 835 3.963129 ACCTCTTGTTGGTGAACTTTCA 58.037 40.909 0.00 0.00 36.30 2.69
805 836 4.983671 AACCTCTTGTTGGTGAACTTTC 57.016 40.909 0.00 0.00 37.93 2.62
816 847 2.808543 GCGTCAATCTCAACCTCTTGTT 59.191 45.455 0.00 0.00 37.80 2.83
817 848 2.417719 GCGTCAATCTCAACCTCTTGT 58.582 47.619 0.00 0.00 0.00 3.16
818 849 1.734465 GGCGTCAATCTCAACCTCTTG 59.266 52.381 0.00 0.00 0.00 3.02
819 850 1.347707 TGGCGTCAATCTCAACCTCTT 59.652 47.619 0.00 0.00 0.00 2.85
820 851 0.976641 TGGCGTCAATCTCAACCTCT 59.023 50.000 0.00 0.00 0.00 3.69
821 852 1.079503 GTGGCGTCAATCTCAACCTC 58.920 55.000 0.00 0.00 0.00 3.85
822 853 0.670546 CGTGGCGTCAATCTCAACCT 60.671 55.000 0.00 0.00 0.00 3.50
823 854 0.669318 TCGTGGCGTCAATCTCAACC 60.669 55.000 0.00 0.00 0.00 3.77
824 855 1.359848 ATCGTGGCGTCAATCTCAAC 58.640 50.000 0.00 0.00 0.00 3.18
825 856 2.093306 AATCGTGGCGTCAATCTCAA 57.907 45.000 0.00 0.00 0.00 3.02
826 857 2.951457 TAATCGTGGCGTCAATCTCA 57.049 45.000 0.00 0.00 0.00 3.27
827 858 4.795970 AAATAATCGTGGCGTCAATCTC 57.204 40.909 0.00 0.00 0.00 2.75
828 859 5.560966 AAAAATAATCGTGGCGTCAATCT 57.439 34.783 0.00 0.00 0.00 2.40
853 884 0.699922 TATTTGAGGCCCCTACCCCC 60.700 60.000 0.00 0.00 0.00 5.40
854 885 1.456919 ATATTTGAGGCCCCTACCCC 58.543 55.000 0.00 0.00 0.00 4.95
855 886 2.490902 CCAATATTTGAGGCCCCTACCC 60.491 54.545 0.00 0.00 0.00 3.69
856 887 2.177016 ACCAATATTTGAGGCCCCTACC 59.823 50.000 0.00 0.00 0.00 3.18
857 888 3.138468 AGACCAATATTTGAGGCCCCTAC 59.862 47.826 0.00 0.00 0.00 3.18
858 889 3.138283 CAGACCAATATTTGAGGCCCCTA 59.862 47.826 0.00 0.00 0.00 3.53
859 890 2.091665 CAGACCAATATTTGAGGCCCCT 60.092 50.000 0.00 0.00 0.00 4.79
860 891 2.310538 CAGACCAATATTTGAGGCCCC 58.689 52.381 0.00 0.00 0.00 5.80
861 892 2.310538 CCAGACCAATATTTGAGGCCC 58.689 52.381 0.00 0.00 0.00 5.80
862 893 2.310538 CCCAGACCAATATTTGAGGCC 58.689 52.381 0.00 0.00 0.00 5.19
863 894 3.018423 ACCCAGACCAATATTTGAGGC 57.982 47.619 0.00 0.00 0.00 4.70
864 895 4.137543 GCTACCCAGACCAATATTTGAGG 58.862 47.826 0.00 0.00 0.00 3.86
865 896 4.780815 TGCTACCCAGACCAATATTTGAG 58.219 43.478 0.00 0.00 0.00 3.02
866 897 4.853468 TGCTACCCAGACCAATATTTGA 57.147 40.909 0.00 0.00 0.00 2.69
867 898 5.913137 TTTGCTACCCAGACCAATATTTG 57.087 39.130 0.00 0.00 0.00 2.32
868 899 7.494922 AATTTTGCTACCCAGACCAATATTT 57.505 32.000 0.00 0.00 0.00 1.40
869 900 7.494922 AAATTTTGCTACCCAGACCAATATT 57.505 32.000 0.00 0.00 0.00 1.28
870 901 7.287696 CCTAAATTTTGCTACCCAGACCAATAT 59.712 37.037 0.00 0.00 0.00 1.28
871 902 6.605594 CCTAAATTTTGCTACCCAGACCAATA 59.394 38.462 0.00 0.00 0.00 1.90
872 903 5.422012 CCTAAATTTTGCTACCCAGACCAAT 59.578 40.000 0.00 0.00 0.00 3.16
873 904 4.770010 CCTAAATTTTGCTACCCAGACCAA 59.230 41.667 0.00 0.00 0.00 3.67
874 905 4.202631 ACCTAAATTTTGCTACCCAGACCA 60.203 41.667 0.00 0.00 0.00 4.02
875 906 4.157840 CACCTAAATTTTGCTACCCAGACC 59.842 45.833 0.00 0.00 0.00 3.85
876 907 4.157840 CCACCTAAATTTTGCTACCCAGAC 59.842 45.833 0.00 0.00 0.00 3.51
877 908 4.340617 CCACCTAAATTTTGCTACCCAGA 58.659 43.478 0.00 0.00 0.00 3.86
878 909 3.119137 GCCACCTAAATTTTGCTACCCAG 60.119 47.826 0.00 0.00 0.00 4.45
879 910 2.829120 GCCACCTAAATTTTGCTACCCA 59.171 45.455 0.00 0.00 0.00 4.51
880 911 3.096852 AGCCACCTAAATTTTGCTACCC 58.903 45.455 0.00 0.00 0.00 3.69
881 912 5.592688 TGATAGCCACCTAAATTTTGCTACC 59.407 40.000 0.00 0.00 34.48 3.18
882 913 6.693315 TGATAGCCACCTAAATTTTGCTAC 57.307 37.500 0.00 0.00 34.48 3.58
883 914 7.896383 ATTGATAGCCACCTAAATTTTGCTA 57.104 32.000 0.00 2.70 35.95 3.49
884 915 6.796785 ATTGATAGCCACCTAAATTTTGCT 57.203 33.333 0.00 0.47 0.00 3.91
885 916 7.848223 AAATTGATAGCCACCTAAATTTTGC 57.152 32.000 0.00 0.00 27.40 3.68
914 945 9.381038 ACCACACTTATAACTACATGGAGATAT 57.619 33.333 13.29 12.54 0.00 1.63
915 946 8.638873 CACCACACTTATAACTACATGGAGATA 58.361 37.037 13.29 4.30 0.00 1.98
916 947 7.125811 ACACCACACTTATAACTACATGGAGAT 59.874 37.037 13.29 1.42 0.00 2.75
917 948 6.439375 ACACCACACTTATAACTACATGGAGA 59.561 38.462 13.29 0.00 0.00 3.71
918 949 6.640518 ACACCACACTTATAACTACATGGAG 58.359 40.000 2.41 2.41 0.00 3.86
919 950 6.614694 ACACCACACTTATAACTACATGGA 57.385 37.500 0.00 0.00 0.00 3.41
920 951 8.780846 TTAACACCACACTTATAACTACATGG 57.219 34.615 0.00 0.00 0.00 3.66
968 999 6.544197 GCTCCCCCAAAACATCTTTTTAAAAA 59.456 34.615 12.62 12.62 0.00 1.94
969 1000 6.058833 GCTCCCCCAAAACATCTTTTTAAAA 58.941 36.000 0.00 0.00 0.00 1.52
970 1001 5.131142 TGCTCCCCCAAAACATCTTTTTAAA 59.869 36.000 0.00 0.00 0.00 1.52
971 1002 4.656112 TGCTCCCCCAAAACATCTTTTTAA 59.344 37.500 0.00 0.00 0.00 1.52
972 1003 4.227197 TGCTCCCCCAAAACATCTTTTTA 58.773 39.130 0.00 0.00 0.00 1.52
973 1004 3.044894 TGCTCCCCCAAAACATCTTTTT 58.955 40.909 0.00 0.00 0.00 1.94
974 1005 2.634453 CTGCTCCCCCAAAACATCTTTT 59.366 45.455 0.00 0.00 0.00 2.27
975 1006 2.158325 TCTGCTCCCCCAAAACATCTTT 60.158 45.455 0.00 0.00 0.00 2.52
976 1007 1.428912 TCTGCTCCCCCAAAACATCTT 59.571 47.619 0.00 0.00 0.00 2.40
977 1008 1.005215 CTCTGCTCCCCCAAAACATCT 59.995 52.381 0.00 0.00 0.00 2.90
978 1009 1.467920 CTCTGCTCCCCCAAAACATC 58.532 55.000 0.00 0.00 0.00 3.06
979 1010 0.040204 CCTCTGCTCCCCCAAAACAT 59.960 55.000 0.00 0.00 0.00 2.71
980 1011 1.065410 TCCTCTGCTCCCCCAAAACA 61.065 55.000 0.00 0.00 0.00 2.83
981 1012 0.112412 TTCCTCTGCTCCCCCAAAAC 59.888 55.000 0.00 0.00 0.00 2.43
982 1013 0.405585 CTTCCTCTGCTCCCCCAAAA 59.594 55.000 0.00 0.00 0.00 2.44
983 1014 2.078452 CTTCCTCTGCTCCCCCAAA 58.922 57.895 0.00 0.00 0.00 3.28
984 1015 2.606587 GCTTCCTCTGCTCCCCCAA 61.607 63.158 0.00 0.00 0.00 4.12
985 1016 3.011517 GCTTCCTCTGCTCCCCCA 61.012 66.667 0.00 0.00 0.00 4.96
986 1017 2.264120 GAAGCTTCCTCTGCTCCCCC 62.264 65.000 15.97 0.00 40.22 5.40
987 1018 1.223211 GAAGCTTCCTCTGCTCCCC 59.777 63.158 15.97 0.00 40.22 4.81
988 1019 1.223211 GGAAGCTTCCTCTGCTCCC 59.777 63.158 33.98 8.71 44.11 4.30
989 1020 1.153469 CGGAAGCTTCCTCTGCTCC 60.153 63.158 36.30 14.59 45.33 4.70
990 1021 1.153469 CCGGAAGCTTCCTCTGCTC 60.153 63.158 36.30 14.05 45.33 4.26
1002 1033 3.895232 TCCAGATCTTTCTTCCGGAAG 57.105 47.619 34.19 34.19 39.71 3.46
1050 1081 0.469070 TTCTTTTCGTTCGGGGGTGA 59.531 50.000 0.00 0.00 0.00 4.02
1052 1083 2.055684 TTTTCTTTTCGTTCGGGGGT 57.944 45.000 0.00 0.00 0.00 4.95
1053 1084 3.653539 ATTTTTCTTTTCGTTCGGGGG 57.346 42.857 0.00 0.00 0.00 5.40
1058 1089 8.496872 TCGGATTGTTATTTTTCTTTTCGTTC 57.503 30.769 0.00 0.00 0.00 3.95
1059 1090 7.114388 GCTCGGATTGTTATTTTTCTTTTCGTT 59.886 33.333 0.00 0.00 0.00 3.85
1185 1226 4.918201 CTCCCCGCGGAAGATGGC 62.918 72.222 30.73 0.00 37.86 4.40
1330 1392 0.689412 CCACTCCTCCTTCTCCTCCC 60.689 65.000 0.00 0.00 0.00 4.30
1422 1490 2.541999 CCTTACTCTCGTCATCGAAGGC 60.542 54.545 0.00 0.00 45.61 4.35
1430 1498 2.040012 AGAGGTGTCCTTACTCTCGTCA 59.960 50.000 0.00 0.00 36.96 4.35
1532 1652 4.158394 ACGGTTCCCATGAATGAATGAAAG 59.842 41.667 0.00 0.00 31.98 2.62
1567 1791 6.343703 CACCTCACTCACAGATCAATTATGA 58.656 40.000 0.00 0.00 40.57 2.15
1568 1792 5.526479 CCACCTCACTCACAGATCAATTATG 59.474 44.000 0.00 0.00 0.00 1.90
1569 1793 5.426509 TCCACCTCACTCACAGATCAATTAT 59.573 40.000 0.00 0.00 0.00 1.28
1620 1844 1.556451 TCACATGGCTACACTGATGCT 59.444 47.619 0.00 0.00 0.00 3.79
1658 1902 4.678256 AGAAAGGGTCTCTGTCAGTATCA 58.322 43.478 0.00 0.00 32.01 2.15
1665 1910 1.135333 CGGCTAGAAAGGGTCTCTGTC 59.865 57.143 0.00 0.00 37.84 3.51
1722 1967 7.523293 TCAAGGTAAGATCTTGCATGAAAAA 57.477 32.000 22.75 5.16 40.82 1.94
1723 1968 7.523293 TTCAAGGTAAGATCTTGCATGAAAA 57.477 32.000 26.61 14.95 40.82 2.29
1741 2031 4.797275 GCCTCCACAAATGTCTTTTCAAGG 60.797 45.833 0.00 0.00 0.00 3.61
1780 2070 4.219033 CGTCTTTTTGAGTCCCGATTTTG 58.781 43.478 0.00 0.00 0.00 2.44
1785 2075 0.105224 TGCGTCTTTTTGAGTCCCGA 59.895 50.000 0.00 0.00 0.00 5.14
1841 2131 3.179830 CACGAAAAGACATCCGTAGAGG 58.820 50.000 0.00 0.00 42.97 3.69
1848 2138 3.575965 ATTTGCCACGAAAAGACATCC 57.424 42.857 0.00 0.00 0.00 3.51
1890 2180 8.652810 AATCAAAAGAATCAGACTTTTTGTGG 57.347 30.769 0.00 0.00 42.95 4.17
1920 2211 7.291566 TGACAGTAAATTCCCCAAAAGAGTTA 58.708 34.615 0.00 0.00 0.00 2.24
1921 2212 6.133356 TGACAGTAAATTCCCCAAAAGAGTT 58.867 36.000 0.00 0.00 0.00 3.01
1922 2213 5.701224 TGACAGTAAATTCCCCAAAAGAGT 58.299 37.500 0.00 0.00 0.00 3.24
2056 4223 4.439289 GCAGGAAGCAAAGTTAAGCTATGG 60.439 45.833 3.45 0.00 44.79 2.74
2090 4260 0.539438 AAAGCGCATGGGACCAAGAA 60.539 50.000 14.90 0.00 0.00 2.52
2380 4554 8.929260 ATATATCAAATTCATGCTCCAACTCA 57.071 30.769 0.00 0.00 0.00 3.41
2532 4745 3.005554 CAGCTGGAACTCAATCGTGATT 58.994 45.455 5.57 0.00 31.85 2.57
2644 4857 0.958091 CAGAGGATACCAGAGCGGAG 59.042 60.000 0.00 0.00 38.63 4.63
2755 4968 4.075793 CCCCCGGAGACCCTCTGA 62.076 72.222 0.73 0.00 39.05 3.27
2779 4992 2.264794 GGTTGTGACCTCGGCGAT 59.735 61.111 11.27 0.00 42.99 4.58
2910 5126 1.761174 GGAGACAACCAGCTTCCCA 59.239 57.895 0.00 0.00 0.00 4.37
3145 5361 0.105760 TCATGCCCTCTCCTCTCCTC 60.106 60.000 0.00 0.00 0.00 3.71
3146 5362 0.341258 TTCATGCCCTCTCCTCTCCT 59.659 55.000 0.00 0.00 0.00 3.69
3147 5363 1.072015 CATTCATGCCCTCTCCTCTCC 59.928 57.143 0.00 0.00 0.00 3.71
3148 5364 2.037511 CTCATTCATGCCCTCTCCTCTC 59.962 54.545 0.00 0.00 0.00 3.20
3201 5417 1.003839 CCGTTCCAGTGCTTGCCTA 60.004 57.895 0.00 0.00 0.00 3.93
3228 5444 8.589701 TGAATAAACTACCAGACTAGACATCA 57.410 34.615 0.00 0.00 0.00 3.07
3410 5749 4.930963 TGTATGTTTTTGCTGGAACACTG 58.069 39.130 2.33 0.00 38.46 3.66
3479 5826 2.098117 GTGCTGAGACTTGTGCTTTGTT 59.902 45.455 0.00 0.00 0.00 2.83
3481 5828 1.672363 TGTGCTGAGACTTGTGCTTTG 59.328 47.619 0.00 0.00 0.00 2.77
3487 5834 2.146342 CGGATTTGTGCTGAGACTTGT 58.854 47.619 0.00 0.00 0.00 3.16
3501 5848 4.641541 TGAAATGACATGATGAGCGGATTT 59.358 37.500 0.00 0.00 0.00 2.17
3504 5851 3.200483 CTGAAATGACATGATGAGCGGA 58.800 45.455 0.00 0.00 0.00 5.54
3505 5852 2.289820 CCTGAAATGACATGATGAGCGG 59.710 50.000 0.00 0.00 0.00 5.52
3507 5854 4.978083 AACCTGAAATGACATGATGAGC 57.022 40.909 0.00 0.00 0.00 4.26
3575 5924 0.465460 GGGACAAGGCAACAGTGACA 60.465 55.000 0.00 0.00 33.83 3.58
3589 5938 0.319555 CGAGCTCGAAACAAGGGACA 60.320 55.000 32.06 0.00 43.02 4.02
3696 6587 4.614967 AAAACCTCTCCATTCCCATGAT 57.385 40.909 0.00 0.00 31.07 2.45
3699 6590 4.293368 AGAGAAAAACCTCTCCATTCCCAT 59.707 41.667 0.00 0.00 42.51 4.00
3700 6591 3.657727 AGAGAAAAACCTCTCCATTCCCA 59.342 43.478 0.00 0.00 42.51 4.37
3709 6600 5.760743 GCTAAACACAGAGAGAAAAACCTCT 59.239 40.000 0.00 0.00 45.53 3.69
3710 6601 5.049336 GGCTAAACACAGAGAGAAAAACCTC 60.049 44.000 0.00 0.00 0.00 3.85
3711 6602 4.822350 GGCTAAACACAGAGAGAAAAACCT 59.178 41.667 0.00 0.00 0.00 3.50
3712 6603 4.822350 AGGCTAAACACAGAGAGAAAAACC 59.178 41.667 0.00 0.00 0.00 3.27
3725 6616 3.565902 AGCTCTGAAACAAGGCTAAACAC 59.434 43.478 0.00 0.00 0.00 3.32
3770 6661 5.063564 GGATAGAAAAAGTACTGCAGAACCG 59.936 44.000 23.35 0.00 0.00 4.44
3771 6662 6.092807 CAGGATAGAAAAAGTACTGCAGAACC 59.907 42.308 23.35 7.33 0.00 3.62
3772 6663 6.092807 CCAGGATAGAAAAAGTACTGCAGAAC 59.907 42.308 23.35 2.27 0.00 3.01
3773 6664 6.013725 TCCAGGATAGAAAAAGTACTGCAGAA 60.014 38.462 23.35 0.00 0.00 3.02
3774 6665 5.483937 TCCAGGATAGAAAAAGTACTGCAGA 59.516 40.000 23.35 0.48 0.00 4.26
3775 6666 5.734720 TCCAGGATAGAAAAAGTACTGCAG 58.265 41.667 13.48 13.48 0.00 4.41
3776 6667 5.734720 CTCCAGGATAGAAAAAGTACTGCA 58.265 41.667 0.00 0.00 0.00 4.41
3777 6668 4.572795 GCTCCAGGATAGAAAAAGTACTGC 59.427 45.833 0.00 0.00 0.00 4.40
3778 6669 5.814705 CAGCTCCAGGATAGAAAAAGTACTG 59.185 44.000 0.00 0.00 0.00 2.74
3779 6670 5.104735 CCAGCTCCAGGATAGAAAAAGTACT 60.105 44.000 0.00 0.00 0.00 2.73
3780 6671 5.119694 CCAGCTCCAGGATAGAAAAAGTAC 58.880 45.833 0.00 0.00 0.00 2.73
3781 6672 4.783227 ACCAGCTCCAGGATAGAAAAAGTA 59.217 41.667 0.00 0.00 0.00 2.24
3782 6673 3.589288 ACCAGCTCCAGGATAGAAAAAGT 59.411 43.478 0.00 0.00 0.00 2.66
3783 6674 3.944015 CACCAGCTCCAGGATAGAAAAAG 59.056 47.826 0.00 0.00 0.00 2.27
3784 6675 3.587061 TCACCAGCTCCAGGATAGAAAAA 59.413 43.478 0.00 0.00 0.00 1.94
3785 6676 3.181329 TCACCAGCTCCAGGATAGAAAA 58.819 45.455 0.00 0.00 0.00 2.29
3786 6677 2.832838 TCACCAGCTCCAGGATAGAAA 58.167 47.619 0.00 0.00 0.00 2.52
3787 6678 2.550277 TCACCAGCTCCAGGATAGAA 57.450 50.000 0.00 0.00 0.00 2.10
3788 6679 2.292521 ACTTCACCAGCTCCAGGATAGA 60.293 50.000 0.00 0.00 0.00 1.98
3789 6680 2.114616 ACTTCACCAGCTCCAGGATAG 58.885 52.381 0.00 0.00 0.00 2.08
3790 6681 1.833630 CACTTCACCAGCTCCAGGATA 59.166 52.381 0.00 0.00 0.00 2.59
3791 6682 0.617413 CACTTCACCAGCTCCAGGAT 59.383 55.000 0.00 0.00 0.00 3.24
3792 6683 0.764369 ACACTTCACCAGCTCCAGGA 60.764 55.000 0.00 0.00 0.00 3.86
3793 6684 0.109342 AACACTTCACCAGCTCCAGG 59.891 55.000 0.00 0.00 0.00 4.45
3794 6685 1.876156 GAAACACTTCACCAGCTCCAG 59.124 52.381 0.00 0.00 0.00 3.86
3795 6686 1.490490 AGAAACACTTCACCAGCTCCA 59.510 47.619 0.00 0.00 33.64 3.86
3796 6687 2.262423 AGAAACACTTCACCAGCTCC 57.738 50.000 0.00 0.00 33.64 4.70
3848 6746 2.543653 GCCAACACAGGTTTACTTGCAG 60.544 50.000 0.00 0.00 34.21 4.41
3851 6749 2.306847 AGGCCAACACAGGTTTACTTG 58.693 47.619 5.01 0.00 34.21 3.16
3861 6759 0.825840 GCCCAAAGTAGGCCAACACA 60.826 55.000 5.01 0.00 45.16 3.72
3896 6794 6.738114 TGCATCTTTCAGGTTTTACTTCTTG 58.262 36.000 0.00 0.00 0.00 3.02
4093 7003 3.110358 GTTGTACCGCAAAACCTGAAAC 58.890 45.455 0.00 0.00 39.03 2.78
4256 7170 3.371285 GGGAACTAGACTTGCGACATTTC 59.629 47.826 0.00 0.00 0.00 2.17
4301 7224 1.213537 CAGCCCGGTGAAAATGCAG 59.786 57.895 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.