Multiple sequence alignment - TraesCS6D01G293500

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6D01G293500 chr6D 100.000 7202 0 0 1 7202 404222730 404229931 0.000000e+00 13300.0
1 TraesCS6D01G293500 chr6D 100.000 1514 0 0 7380 8893 404230109 404231622 0.000000e+00 2796.0
2 TraesCS6D01G293500 chr6D 86.935 199 26 0 3096 3294 404225757 404225559 3.230000e-54 224.0
3 TraesCS6D01G293500 chr6D 87.245 196 25 0 2833 3028 404226020 404225825 3.230000e-54 224.0
4 TraesCS6D01G293500 chr6A 95.014 4392 141 36 670 5035 550739177 550743516 0.000000e+00 6826.0
5 TraesCS6D01G293500 chr6A 95.893 1534 39 5 7382 8893 550745791 550747322 0.000000e+00 2462.0
6 TraesCS6D01G293500 chr6A 96.084 1098 26 7 5033 6118 550743669 550744761 0.000000e+00 1773.0
7 TraesCS6D01G293500 chr6A 96.781 932 28 2 6222 7152 550744755 550745685 0.000000e+00 1554.0
8 TraesCS6D01G293500 chr6A 86.893 206 26 1 2823 3027 550741786 550741581 6.940000e-56 230.0
9 TraesCS6D01G293500 chr6A 79.200 250 34 10 1 246 550738716 550738951 3.320000e-34 158.0
10 TraesCS6D01G293500 chr6A 93.814 97 5 1 318 414 596540259 596540354 2.590000e-30 145.0
11 TraesCS6D01G293500 chr6B 95.558 3827 113 25 890 4703 606296172 606299954 0.000000e+00 6072.0
12 TraesCS6D01G293500 chr6B 97.031 2088 41 5 4703 6776 606303267 606305347 0.000000e+00 3493.0
13 TraesCS6D01G293500 chr6B 85.577 208 30 0 2823 3030 606298558 606298351 1.500000e-52 219.0
14 TraesCS6D01G293500 chr6B 85.500 200 28 1 3096 3294 606298285 606298086 3.250000e-49 207.0
15 TraesCS6D01G293500 chr6B 80.237 253 28 15 670 904 606290222 606290470 4.270000e-38 171.0
16 TraesCS6D01G293500 chr6B 93.103 116 7 1 6116 6231 579542426 579542312 1.540000e-37 169.0
17 TraesCS6D01G293500 chr6B 95.876 97 3 1 318 414 606290130 606290225 1.200000e-33 156.0
18 TraesCS6D01G293500 chr6B 92.784 97 6 1 318 414 684718932 684719027 1.200000e-28 139.0
19 TraesCS6D01G293500 chr6B 92.784 97 6 1 318 414 684753928 684754023 1.200000e-28 139.0
20 TraesCS6D01G293500 chr6B 92.308 65 5 0 167 231 606289956 606290020 9.510000e-15 93.5
21 TraesCS6D01G293500 chr6B 94.340 53 2 1 1 53 606289869 606289920 7.400000e-11 80.5
22 TraesCS6D01G293500 chrUn 96.755 1510 25 9 7384 8893 78930559 78929074 0.000000e+00 2495.0
23 TraesCS6D01G293500 chrUn 94.275 262 15 0 413 674 312499708 312499447 1.390000e-107 401.0
24 TraesCS6D01G293500 chrUn 92.784 97 6 1 318 414 234300572 234300477 1.200000e-28 139.0
25 TraesCS6D01G293500 chrUn 92.784 97 6 1 318 414 387880630 387880535 1.200000e-28 139.0
26 TraesCS6D01G293500 chr2D 85.036 695 92 8 6496 7181 380416529 380417220 0.000000e+00 697.0
27 TraesCS6D01G293500 chr2D 83.357 703 105 7 6492 7184 388833659 388834359 2.710000e-179 640.0
28 TraesCS6D01G293500 chr2D 82.930 703 100 12 6492 7181 249891792 249892487 4.560000e-172 616.0
29 TraesCS6D01G293500 chr2D 82.664 473 79 3 2825 3294 10222201 10221729 4.970000e-112 416.0
30 TraesCS6D01G293500 chr2D 83.607 244 36 4 2828 3067 10248799 10248556 8.980000e-55 226.0
31 TraesCS6D01G293500 chr2D 81.407 199 34 3 3096 3291 10221995 10222193 9.240000e-35 159.0
32 TraesCS6D01G293500 chr2D 81.000 200 34 3 3096 3291 10248595 10248794 1.200000e-33 156.0
33 TraesCS6D01G293500 chr2D 100.000 28 0 0 728 755 340368667 340368694 1.600000e-02 52.8
34 TraesCS6D01G293500 chr2A 84.814 698 93 9 6494 7181 515951640 515952334 0.000000e+00 689.0
35 TraesCS6D01G293500 chr3B 83.405 699 92 19 6484 7168 694031633 694030945 2.110000e-175 627.0
36 TraesCS6D01G293500 chr3B 93.916 263 16 0 413 675 677856025 677855763 1.800000e-106 398.0
37 TraesCS6D01G293500 chr4D 82.976 699 103 11 6495 7181 248930109 248930803 1.270000e-172 617.0
38 TraesCS6D01G293500 chr4D 94.231 260 15 0 414 673 419245895 419245636 1.800000e-106 398.0
39 TraesCS6D01G293500 chr4D 91.026 78 6 1 2722 2799 294454573 294454497 4.390000e-18 104.0
40 TraesCS6D01G293500 chr4D 87.500 88 10 1 2732 2819 417350082 417350168 5.680000e-17 100.0
41 TraesCS6D01G293500 chr1B 82.882 701 102 11 6494 7184 271895364 271894672 1.640000e-171 614.0
42 TraesCS6D01G293500 chr1B 93.208 265 17 1 412 675 349756358 349756622 1.080000e-103 388.0
43 TraesCS6D01G293500 chr1B 88.235 187 22 0 8705 8891 3967582 3967396 3.230000e-54 224.0
44 TraesCS6D01G293500 chr1B 87.166 187 24 0 8705 8891 4821557 4821743 6.990000e-51 213.0
45 TraesCS6D01G293500 chr1B 87.166 187 24 0 8705 8891 4841668 4841854 6.990000e-51 213.0
46 TraesCS6D01G293500 chr1B 86.096 187 26 0 8705 8891 4098605 4098419 1.510000e-47 202.0
47 TraesCS6D01G293500 chr1B 91.964 112 4 1 6117 6228 626498463 626498569 1.550000e-32 152.0
48 TraesCS6D01G293500 chr1B 90.517 116 6 1 6113 6228 229263272 229263162 2.000000e-31 148.0
49 TraesCS6D01G293500 chr1A 82.783 697 107 8 6495 7181 508148979 508148286 2.120000e-170 610.0
50 TraesCS6D01G293500 chr1A 85.561 187 27 0 8705 8891 3500839 3501025 7.040000e-46 196.0
51 TraesCS6D01G293500 chr5D 97.388 268 5 2 406 673 228058609 228058344 1.050000e-123 455.0
52 TraesCS6D01G293500 chr5D 83.636 275 28 6 3038 3296 58507586 58507313 8.920000e-60 243.0
53 TraesCS6D01G293500 chr5D 89.286 140 15 0 2824 2963 58507309 58507448 9.180000e-40 176.0
54 TraesCS6D01G293500 chr5D 91.071 112 5 2 6117 6228 547057318 547057212 7.190000e-31 147.0
55 TraesCS6D01G293500 chr5D 92.405 79 6 0 2721 2799 268905800 268905722 7.300000e-21 113.0
56 TraesCS6D01G293500 chr7D 94.253 261 15 0 413 673 600893774 600893514 5.000000e-107 399.0
57 TraesCS6D01G293500 chr7D 93.893 262 15 1 413 674 33204291 33204031 2.330000e-105 394.0
58 TraesCS6D01G293500 chr7D 93.487 261 17 0 413 673 456373366 456373106 1.080000e-103 388.0
59 TraesCS6D01G293500 chr7D 94.792 96 4 1 319 414 613431928 613431834 2.000000e-31 148.0
60 TraesCS6D01G293500 chr7D 88.618 123 7 4 6113 6234 536146621 536146505 9.310000e-30 143.0
61 TraesCS6D01G293500 chr7A 92.884 267 18 1 412 677 313682205 313682471 3.890000e-103 387.0
62 TraesCS6D01G293500 chr7A 75.574 479 103 12 2823 3296 620400499 620400968 3.230000e-54 224.0
63 TraesCS6D01G293500 chr7A 91.837 98 7 1 318 415 566027831 566027927 1.560000e-27 135.0
64 TraesCS6D01G293500 chr1D 92.105 114 4 1 6115 6228 273817500 273817392 1.200000e-33 156.0
65 TraesCS6D01G293500 chr1D 86.667 90 10 2 2710 2799 269365929 269366016 2.040000e-16 99.0
66 TraesCS6D01G293500 chr5B 90.435 115 6 1 6114 6228 511610740 511610849 7.190000e-31 147.0
67 TraesCS6D01G293500 chr5B 81.646 158 27 2 8705 8861 517800766 517800610 7.250000e-26 130.0
68 TraesCS6D01G293500 chr5B 92.405 79 6 0 2721 2799 304628732 304628654 7.300000e-21 113.0
69 TraesCS6D01G293500 chr3A 88.618 123 8 3 6117 6239 530186804 530186688 2.590000e-30 145.0
70 TraesCS6D01G293500 chr7B 89.908 109 10 1 318 426 528017100 528017207 1.200000e-28 139.0
71 TraesCS6D01G293500 chr5A 80.892 157 30 0 8705 8861 544505442 544505286 3.370000e-24 124.0
72 TraesCS6D01G293500 chr3D 86.813 91 9 3 2709 2799 151805132 151805219 2.040000e-16 99.0
73 TraesCS6D01G293500 chr4A 83.495 103 13 4 2699 2799 115567258 115567158 9.510000e-15 93.5


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 TraesCS6D01G293500 chr6D 404222730 404231622 8892 False 8048.0 13300 100.0000 1 8893 2 chr6D.!!$F1 8892
1 TraesCS6D01G293500 chr6A 550738716 550747322 8606 False 2554.6 6826 92.5944 1 8893 5 chr6A.!!$F2 8892
2 TraesCS6D01G293500 chr6B 606296172 606305347 9175 False 4782.5 6072 96.2945 890 6776 2 chr6B.!!$F4 5886
3 TraesCS6D01G293500 chrUn 78929074 78930559 1485 True 2495.0 2495 96.7550 7384 8893 1 chrUn.!!$R1 1509
4 TraesCS6D01G293500 chr2D 380416529 380417220 691 False 697.0 697 85.0360 6496 7181 1 chr2D.!!$F5 685
5 TraesCS6D01G293500 chr2D 388833659 388834359 700 False 640.0 640 83.3570 6492 7184 1 chr2D.!!$F6 692
6 TraesCS6D01G293500 chr2D 249891792 249892487 695 False 616.0 616 82.9300 6492 7181 1 chr2D.!!$F3 689
7 TraesCS6D01G293500 chr2A 515951640 515952334 694 False 689.0 689 84.8140 6494 7181 1 chr2A.!!$F1 687
8 TraesCS6D01G293500 chr3B 694030945 694031633 688 True 627.0 627 83.4050 6484 7168 1 chr3B.!!$R2 684
9 TraesCS6D01G293500 chr4D 248930109 248930803 694 False 617.0 617 82.9760 6495 7181 1 chr4D.!!$F1 686
10 TraesCS6D01G293500 chr1B 271894672 271895364 692 True 614.0 614 82.8820 6494 7184 1 chr1B.!!$R4 690
11 TraesCS6D01G293500 chr1A 508148286 508148979 693 True 610.0 610 82.7830 6495 7181 1 chr1A.!!$R1 686

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
720 816 0.117340 ATATAGGCGGCTCCCCTTCT 59.883 55.000 17.67 0.0 33.88 2.85 F
1762 1897 0.323451 AAACCCCGAATGGAAGGAGC 60.323 55.000 0.00 0.0 37.49 4.70 F
3007 3151 1.202806 TCTGTAGCTGCCAGTGCTTTT 60.203 47.619 13.11 0.0 41.46 2.27 F
3359 3504 0.250295 TTTCGCACCAGGAACTCCAG 60.250 55.000 0.00 0.0 34.60 3.86 F
4181 4326 3.504906 AGCACTTGAGATGTGTTGGATTG 59.495 43.478 0.00 0.0 37.70 2.67 F
5255 8870 0.533755 GACTCTGGTTGCACACTGCT 60.534 55.000 0.00 0.0 45.31 4.24 F
5441 9065 0.109723 GACACACCCTTGGCCACTAA 59.890 55.000 3.88 0.0 0.00 2.24 F
6234 9872 1.136500 GGACGGAGGGAGTAACACATC 59.864 57.143 0.00 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2449 2585 0.535780 CCAGGCTTGAGCTCAACACA 60.536 55.000 25.16 5.27 41.70 3.72 R
3359 3504 0.657840 GGCATGACCAATCGCTACAC 59.342 55.000 0.00 0.00 38.86 2.90 R
4181 4326 2.592861 GATGGAGTGGCGGCATCC 60.593 66.667 24.07 24.07 0.00 3.51 R
5141 8756 1.376037 GAGTTGGAGGAGGGCAACG 60.376 63.158 0.00 0.00 33.26 4.10 R
5317 8932 1.758862 TCCATCACTGTCGCATCTGAT 59.241 47.619 0.00 0.00 0.00 2.90 R
6202 9826 0.517316 CTCCGTCCGAAAAAGCTTGG 59.483 55.000 0.00 0.00 0.00 3.61 R
6516 10164 1.068474 CTACCTCAACTTGTTCGGCG 58.932 55.000 0.00 0.00 0.00 6.46 R
7893 11580 2.032549 GCAGCCGATGTAGCTTACAATG 60.033 50.000 0.00 0.00 42.76 2.82 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
39 40 6.744112 TCCCAACAAATTTCATTACTCACAC 58.256 36.000 0.00 0.00 0.00 3.82
40 41 6.322456 TCCCAACAAATTTCATTACTCACACA 59.678 34.615 0.00 0.00 0.00 3.72
61 62 8.193438 CACACAGATAAGTCTCATCACATTCTA 58.807 37.037 0.00 0.00 30.42 2.10
62 63 8.922237 ACACAGATAAGTCTCATCACATTCTAT 58.078 33.333 0.00 0.00 30.42 1.98
63 64 9.761504 CACAGATAAGTCTCATCACATTCTATT 57.238 33.333 0.00 0.00 30.42 1.73
93 94 1.429463 AAAGTCTCGTCACATTCCGC 58.571 50.000 0.00 0.00 0.00 5.54
94 95 0.317160 AAGTCTCGTCACATTCCGCA 59.683 50.000 0.00 0.00 0.00 5.69
95 96 0.388649 AGTCTCGTCACATTCCGCAC 60.389 55.000 0.00 0.00 0.00 5.34
96 97 0.666274 GTCTCGTCACATTCCGCACA 60.666 55.000 0.00 0.00 0.00 4.57
97 98 0.246360 TCTCGTCACATTCCGCACAT 59.754 50.000 0.00 0.00 0.00 3.21
98 99 1.078709 CTCGTCACATTCCGCACATT 58.921 50.000 0.00 0.00 0.00 2.71
99 100 2.094442 TCTCGTCACATTCCGCACATTA 60.094 45.455 0.00 0.00 0.00 1.90
100 101 2.866156 CTCGTCACATTCCGCACATTAT 59.134 45.455 0.00 0.00 0.00 1.28
102 103 2.032894 CGTCACATTCCGCACATTATCC 60.033 50.000 0.00 0.00 0.00 2.59
104 105 3.002656 GTCACATTCCGCACATTATCCTG 59.997 47.826 0.00 0.00 0.00 3.86
107 108 4.096231 CACATTCCGCACATTATCCTGAAA 59.904 41.667 0.00 0.00 0.00 2.69
126 127 4.080582 TGAAAGGAAAACAGAGTCTGGACA 60.081 41.667 23.79 7.48 35.51 4.02
132 163 0.683973 ACAGAGTCTGGACAGGCAAG 59.316 55.000 23.79 0.00 34.98 4.01
164 195 5.068198 ACTGATGTTGAAAAACACATCTGCT 59.932 36.000 15.20 4.71 38.21 4.24
165 196 5.522456 TGATGTTGAAAAACACATCTGCTC 58.478 37.500 12.28 0.00 37.62 4.26
194 225 1.474077 GCGCAGATGAAAAACCAGGAT 59.526 47.619 0.30 0.00 0.00 3.24
197 228 4.662145 CGCAGATGAAAAACCAGGATTAC 58.338 43.478 0.00 0.00 0.00 1.89
201 232 6.587608 GCAGATGAAAAACCAGGATTACAAAG 59.412 38.462 0.00 0.00 0.00 2.77
213 244 5.185635 CAGGATTACAAAGAGGATTTGGCAA 59.814 40.000 0.00 0.00 33.92 4.52
214 245 5.420104 AGGATTACAAAGAGGATTTGGCAAG 59.580 40.000 0.00 0.00 33.92 4.01
216 247 2.250924 ACAAAGAGGATTTGGCAAGGG 58.749 47.619 0.00 0.00 33.92 3.95
223 254 2.027385 GGATTTGGCAAGGGCTAGAAG 58.973 52.381 0.00 0.00 40.87 2.85
240 271 4.889832 AGAAGAGCAAAAGACACACTTG 57.110 40.909 0.00 0.00 38.98 3.16
241 272 4.517285 AGAAGAGCAAAAGACACACTTGA 58.483 39.130 0.00 0.00 38.98 3.02
246 277 6.095377 AGAGCAAAAGACACACTTGAAAAAG 58.905 36.000 0.00 0.00 38.98 2.27
248 279 6.454795 AGCAAAAGACACACTTGAAAAAGAA 58.545 32.000 0.00 0.00 38.98 2.52
249 280 6.928492 AGCAAAAGACACACTTGAAAAAGAAA 59.072 30.769 0.00 0.00 38.98 2.52
256 315 7.340487 AGACACACTTGAAAAAGAAAAGAGGAT 59.660 33.333 0.00 0.00 0.00 3.24
303 362 1.375523 GAATTGACAGGGACCGCGT 60.376 57.895 4.92 0.00 0.00 6.01
308 367 4.657824 ACAGGGACCGCGTGAACG 62.658 66.667 4.92 0.00 43.27 3.95
344 440 0.532862 AGACCAACGCACTCACCAAG 60.533 55.000 0.00 0.00 0.00 3.61
388 484 3.470888 ACGGCCCCCTCTTGATCG 61.471 66.667 0.00 0.00 0.00 3.69
392 488 4.241555 CCCCCTCTTGATCGGCCG 62.242 72.222 22.12 22.12 0.00 6.13
395 491 2.721167 CCCTCTTGATCGGCCGTCA 61.721 63.158 27.15 23.72 0.00 4.35
414 510 1.066645 CAACCCCGTCCAGGTAAGTAC 60.067 57.143 0.00 0.00 36.27 2.73
415 511 0.411058 ACCCCGTCCAGGTAAGTACT 59.589 55.000 0.00 0.00 35.24 2.73
416 512 1.109609 CCCCGTCCAGGTAAGTACTC 58.890 60.000 0.00 0.00 38.74 2.59
417 513 1.109609 CCCGTCCAGGTAAGTACTCC 58.890 60.000 0.00 0.00 38.74 3.85
418 514 1.109609 CCGTCCAGGTAAGTACTCCC 58.890 60.000 0.00 0.00 34.51 4.30
419 515 1.341778 CCGTCCAGGTAAGTACTCCCT 60.342 57.143 7.99 7.99 34.51 4.20
420 516 2.022934 CGTCCAGGTAAGTACTCCCTC 58.977 57.143 10.38 1.33 0.00 4.30
421 517 2.386779 GTCCAGGTAAGTACTCCCTCC 58.613 57.143 10.38 4.73 0.00 4.30
423 519 1.341778 CCAGGTAAGTACTCCCTCCGT 60.342 57.143 10.38 0.00 0.00 4.69
424 520 2.454538 CAGGTAAGTACTCCCTCCGTT 58.545 52.381 10.38 0.00 0.00 4.44
425 521 2.426381 CAGGTAAGTACTCCCTCCGTTC 59.574 54.545 10.38 0.00 0.00 3.95
426 522 1.753649 GGTAAGTACTCCCTCCGTTCC 59.246 57.143 0.00 0.00 0.00 3.62
427 523 2.450476 GTAAGTACTCCCTCCGTTCCA 58.550 52.381 0.00 0.00 0.00 3.53
428 524 2.249309 AAGTACTCCCTCCGTTCCAT 57.751 50.000 0.00 0.00 0.00 3.41
429 525 3.393426 AAGTACTCCCTCCGTTCCATA 57.607 47.619 0.00 0.00 0.00 2.74
430 526 3.393426 AGTACTCCCTCCGTTCCATAA 57.607 47.619 0.00 0.00 0.00 1.90
431 527 3.924922 AGTACTCCCTCCGTTCCATAAT 58.075 45.455 0.00 0.00 0.00 1.28
432 528 3.641906 AGTACTCCCTCCGTTCCATAATG 59.358 47.826 0.00 0.00 0.00 1.90
433 529 2.478292 ACTCCCTCCGTTCCATAATGT 58.522 47.619 0.00 0.00 0.00 2.71
434 530 3.649843 ACTCCCTCCGTTCCATAATGTA 58.350 45.455 0.00 0.00 0.00 2.29
435 531 3.641906 ACTCCCTCCGTTCCATAATGTAG 59.358 47.826 0.00 0.00 0.00 2.74
436 532 3.641906 CTCCCTCCGTTCCATAATGTAGT 59.358 47.826 0.00 0.00 0.00 2.73
437 533 3.386726 TCCCTCCGTTCCATAATGTAGTG 59.613 47.826 0.00 0.00 0.00 2.74
438 534 3.131396 CCTCCGTTCCATAATGTAGTGC 58.869 50.000 0.00 0.00 0.00 4.40
439 535 3.131396 CTCCGTTCCATAATGTAGTGCC 58.869 50.000 0.00 0.00 0.00 5.01
440 536 2.769663 TCCGTTCCATAATGTAGTGCCT 59.230 45.455 0.00 0.00 0.00 4.75
441 537 3.962063 TCCGTTCCATAATGTAGTGCCTA 59.038 43.478 0.00 0.00 0.00 3.93
442 538 4.056050 CCGTTCCATAATGTAGTGCCTAC 58.944 47.826 5.65 5.65 37.46 3.18
480 576 9.495572 AAATTCAAACTTTACAAACTTTGACCA 57.504 25.926 8.55 0.00 33.51 4.02
481 577 9.495572 AATTCAAACTTTACAAACTTTGACCAA 57.504 25.926 8.55 0.00 33.51 3.67
482 578 8.527567 TTCAAACTTTACAAACTTTGACCAAG 57.472 30.769 8.55 8.83 33.51 3.61
497 593 9.628500 ACTTTGACCAAGTTTATAGAGAAAACT 57.372 29.630 0.00 0.00 43.89 2.66
626 722 7.769272 CTTGATCAAAGTTTGCAAGGTTTAA 57.231 32.000 20.01 0.70 34.00 1.52
627 723 8.369218 CTTGATCAAAGTTTGCAAGGTTTAAT 57.631 30.769 20.01 4.79 34.00 1.40
628 724 8.729805 TTGATCAAAGTTTGCAAGGTTTAATT 57.270 26.923 10.90 0.00 0.00 1.40
629 725 8.729805 TGATCAAAGTTTGCAAGGTTTAATTT 57.270 26.923 10.90 0.00 0.00 1.82
630 726 9.171877 TGATCAAAGTTTGCAAGGTTTAATTTT 57.828 25.926 10.90 0.00 0.00 1.82
664 760 3.194005 AGGCACTACATTATGGAACGG 57.806 47.619 0.00 0.00 36.02 4.44
665 761 2.769663 AGGCACTACATTATGGAACGGA 59.230 45.455 0.00 0.00 36.02 4.69
666 762 3.131396 GGCACTACATTATGGAACGGAG 58.869 50.000 0.00 0.00 0.00 4.63
667 763 3.131396 GCACTACATTATGGAACGGAGG 58.869 50.000 0.00 0.00 0.00 4.30
668 764 3.728845 CACTACATTATGGAACGGAGGG 58.271 50.000 0.00 0.00 0.00 4.30
669 765 3.386726 CACTACATTATGGAACGGAGGGA 59.613 47.826 0.00 0.00 0.00 4.20
670 766 3.641906 ACTACATTATGGAACGGAGGGAG 59.358 47.826 0.00 0.00 0.00 4.30
671 767 2.478292 ACATTATGGAACGGAGGGAGT 58.522 47.619 0.00 0.00 0.00 3.85
672 768 3.649843 ACATTATGGAACGGAGGGAGTA 58.350 45.455 0.00 0.00 0.00 2.59
673 769 4.232091 ACATTATGGAACGGAGGGAGTAT 58.768 43.478 0.00 0.00 0.00 2.12
674 770 4.040461 ACATTATGGAACGGAGGGAGTATG 59.960 45.833 0.00 0.00 0.00 2.39
675 771 2.176247 ATGGAACGGAGGGAGTATGT 57.824 50.000 0.00 0.00 0.00 2.29
676 772 1.946984 TGGAACGGAGGGAGTATGTT 58.053 50.000 0.00 0.00 0.00 2.71
677 773 1.553248 TGGAACGGAGGGAGTATGTTG 59.447 52.381 0.00 0.00 0.00 3.33
678 774 1.653151 GAACGGAGGGAGTATGTTGC 58.347 55.000 0.00 0.00 0.00 4.17
679 775 0.981183 AACGGAGGGAGTATGTTGCA 59.019 50.000 0.00 0.00 0.00 4.08
680 776 0.249398 ACGGAGGGAGTATGTTGCAC 59.751 55.000 0.00 0.00 0.00 4.57
681 777 0.462047 CGGAGGGAGTATGTTGCACC 60.462 60.000 0.00 0.00 0.00 5.01
682 778 0.618458 GGAGGGAGTATGTTGCACCA 59.382 55.000 0.00 0.00 0.00 4.17
683 779 1.212935 GGAGGGAGTATGTTGCACCAT 59.787 52.381 1.21 1.21 0.00 3.55
697 793 0.249238 CACCATCGCACCTAGAGCTC 60.249 60.000 5.27 5.27 0.00 4.09
708 804 4.098807 GCACCTAGAGCTCCTTATATAGGC 59.901 50.000 19.36 7.36 44.37 3.93
720 816 0.117340 ATATAGGCGGCTCCCCTTCT 59.883 55.000 17.67 0.00 33.88 2.85
722 818 3.914921 TATAGGCGGCTCCCCTTCTCC 62.915 61.905 17.67 0.00 33.88 3.71
724 820 3.855853 GCGGCTCCCCTTCTCCTC 61.856 72.222 0.00 0.00 0.00 3.71
730 826 2.040359 CCCCTTCTCCTCCTCCCC 60.040 72.222 0.00 0.00 0.00 4.81
760 856 3.928992 GCGAGGTGGTACTAAACTAAACC 59.071 47.826 0.00 0.00 0.00 3.27
764 860 3.681417 GGTGGTACTAAACTAAACCAGCG 59.319 47.826 6.77 0.00 46.77 5.18
765 861 4.309933 GTGGTACTAAACTAAACCAGCGT 58.690 43.478 0.00 0.00 42.47 5.07
766 862 4.386954 GTGGTACTAAACTAAACCAGCGTC 59.613 45.833 0.00 0.00 42.47 5.19
767 863 3.609807 GGTACTAAACTAAACCAGCGTCG 59.390 47.826 0.00 0.00 32.04 5.12
768 864 3.375782 ACTAAACTAAACCAGCGTCGT 57.624 42.857 0.00 0.00 0.00 4.34
769 865 3.054878 ACTAAACTAAACCAGCGTCGTG 58.945 45.455 0.00 0.00 0.00 4.35
770 866 0.584876 AAACTAAACCAGCGTCGTGC 59.415 50.000 0.00 0.00 46.98 5.34
828 924 3.524648 GAACGGTCGTGGGCCTCAA 62.525 63.158 4.53 0.00 0.00 3.02
829 925 2.999739 GAACGGTCGTGGGCCTCAAA 63.000 60.000 4.53 0.00 0.00 2.69
833 956 4.323477 TCGTGGGCCTCAAACGGG 62.323 66.667 13.34 0.00 37.87 5.28
841 964 2.668632 CTCAAACGGGCTGGGCTA 59.331 61.111 0.00 0.00 0.00 3.93
863 986 2.158957 GGCCGAAAGATATGAGTCCACA 60.159 50.000 0.00 0.00 0.00 4.17
944 1070 1.335051 GCGTGCTTTGTCTTTCCTTCC 60.335 52.381 0.00 0.00 0.00 3.46
1207 1338 2.280186 CCCCTAATCCGACGCAGC 60.280 66.667 0.00 0.00 0.00 5.25
1471 1602 5.578727 TCGTGCAAATTGTTTTACTGCTTTT 59.421 32.000 0.00 0.00 0.00 2.27
1472 1603 5.671997 CGTGCAAATTGTTTTACTGCTTTTG 59.328 36.000 0.00 0.00 0.00 2.44
1495 1626 5.065859 TGTGACAAGATTGTTCACGATGTTT 59.934 36.000 16.33 0.00 42.43 2.83
1552 1684 6.292811 GCAACATTGTTGTAAGTTGAATTGGG 60.293 38.462 25.88 0.71 42.87 4.12
1572 1704 4.466015 TGGGTTGAAGCTTTGAAGACTTTT 59.534 37.500 0.00 0.00 0.00 2.27
1757 1892 1.617533 GCCCTAAAACCCCGAATGGAA 60.618 52.381 0.00 0.00 37.49 3.53
1762 1897 0.323451 AAACCCCGAATGGAAGGAGC 60.323 55.000 0.00 0.00 37.49 4.70
1767 1902 2.102578 CCCGAATGGAAGGAGCAATTT 58.897 47.619 0.00 0.00 37.49 1.82
2120 2256 2.121948 TGCAGGGCAGTAGAGATTGAT 58.878 47.619 0.00 0.00 33.32 2.57
2137 2273 5.887598 AGATTGATGCAACTATAAACCAGCA 59.112 36.000 0.00 0.00 36.34 4.41
2407 2543 4.002982 GACACATCACATGAGCAAACCTA 58.997 43.478 0.00 0.00 0.00 3.08
2416 2552 2.771089 TGAGCAAACCTAGAGCAAGTG 58.229 47.619 0.00 0.00 0.00 3.16
2449 2585 5.045578 AGGCTCATAACAAAGTGTCATAGGT 60.046 40.000 0.00 0.00 0.00 3.08
2582 2724 4.853924 AATTGATTTCGAGCTTGTGGTT 57.146 36.364 0.00 0.00 0.00 3.67
2634 2776 3.864789 TTGAGCTTCTTGGTCTTCCTT 57.135 42.857 0.00 0.00 43.13 3.36
2692 2835 8.287439 TCTTCATTGTTTTCTTCACTACCAAA 57.713 30.769 0.00 0.00 0.00 3.28
2785 2928 7.201741 GGCTAAAGTTGAAACCCATAAGATCTC 60.202 40.741 0.00 0.00 0.00 2.75
2809 2952 6.073167 TCGAAACCAACGCATTTATCTGTTAA 60.073 34.615 0.00 0.00 0.00 2.01
2943 3087 2.403252 AGAAATACCCCTGAGCAACG 57.597 50.000 0.00 0.00 0.00 4.10
3007 3151 1.202806 TCTGTAGCTGCCAGTGCTTTT 60.203 47.619 13.11 0.00 41.46 2.27
3020 3164 7.268586 TGCCAGTGCTTTTTATTCTTTTGTAA 58.731 30.769 0.00 0.00 38.71 2.41
3119 3263 5.241728 AGGGATGCTACAAAAGAACTGAAAC 59.758 40.000 0.00 0.00 0.00 2.78
3210 3354 6.388689 TCAGGGGTATTTCTATAACACCACAT 59.611 38.462 0.00 0.00 35.00 3.21
3359 3504 0.250295 TTTCGCACCAGGAACTCCAG 60.250 55.000 0.00 0.00 34.60 3.86
3529 3674 7.630242 TGATCATGGGAATTTAGTGTTCTTC 57.370 36.000 0.00 0.00 0.00 2.87
4181 4326 3.504906 AGCACTTGAGATGTGTTGGATTG 59.495 43.478 0.00 0.00 37.70 2.67
4476 4622 9.180678 GGTATGTGCTTATTTTGATATTTTCCG 57.819 33.333 0.00 0.00 0.00 4.30
4548 4694 7.487822 TGGCCTTTATGGATGAAAACATTTA 57.512 32.000 3.32 0.00 38.35 1.40
4840 8299 6.804783 CGTCCAAAAAGACAAGTTAACAAAGT 59.195 34.615 8.61 2.84 36.52 2.66
5255 8870 0.533755 GACTCTGGTTGCACACTGCT 60.534 55.000 0.00 0.00 45.31 4.24
5287 8902 0.955428 GTTCACTGAGCATCCCGCAA 60.955 55.000 0.00 0.00 46.13 4.85
5441 9065 0.109723 GACACACCCTTGGCCACTAA 59.890 55.000 3.88 0.00 0.00 2.24
5681 9305 5.957842 TCATTCAGAAACCATTAACGCTT 57.042 34.783 0.00 0.00 0.00 4.68
6017 9641 9.936759 TGTATGTGAAATTCAACATGTAGTAGA 57.063 29.630 15.95 0.00 0.00 2.59
6022 9646 8.443937 GTGAAATTCAACATGTAGTAGAAGACC 58.556 37.037 0.00 0.00 0.00 3.85
6076 9700 3.013921 GGACAAATCCCAGTCGCAATTA 58.986 45.455 0.00 0.00 39.39 1.40
6202 9826 4.006319 GCTAGATACATCCATTTGAGGGC 58.994 47.826 0.00 0.00 0.00 5.19
6234 9872 1.136500 GGACGGAGGGAGTAACACATC 59.864 57.143 0.00 0.00 0.00 3.06
6399 10037 7.331687 GCATGTTTTATTTGTTCACCAGCTTAT 59.668 33.333 0.00 0.00 0.00 1.73
6428 10066 5.970317 AAGCATTTGACTGATTGTGATCA 57.030 34.783 0.00 0.00 39.92 2.92
6516 10164 2.584492 ACAAGAACAACAAAGCCTGC 57.416 45.000 0.00 0.00 0.00 4.85
6694 10345 3.073678 TCATGTCAAGTTTGGTCCATCG 58.926 45.455 0.00 0.00 0.00 3.84
6784 10441 1.026718 GCCCAAACCATCTCAGACGG 61.027 60.000 0.00 0.00 0.00 4.79
7067 10725 5.022122 TGCCACTTCATCCATCCAAATTTA 58.978 37.500 0.00 0.00 0.00 1.40
7699 11386 0.320247 CACACACCAGAGAGGCAGAC 60.320 60.000 0.00 0.00 43.14 3.51
7893 11580 5.915196 GCAATGGTTGTTTTCTCACTTAGAC 59.085 40.000 0.00 0.00 32.51 2.59
7952 11640 0.242017 GTGAATGCACAAGGGTCAGC 59.758 55.000 0.00 0.00 44.51 4.26
8090 11778 7.541783 GCACTTAGTGTTGATTGCATTTATTGA 59.458 33.333 14.23 0.00 35.75 2.57
8175 11863 1.953559 TGCCGGAAATCAGCTGTATC 58.046 50.000 14.67 10.26 0.00 2.24
8218 11906 5.545723 CAGAGAGGTAATCATCCCTACCATT 59.454 44.000 1.41 0.00 40.16 3.16
8432 12120 0.966179 GGCCGTTGGTCCAAGATTTT 59.034 50.000 3.96 0.00 0.00 1.82
8433 12121 1.336795 GGCCGTTGGTCCAAGATTTTG 60.337 52.381 3.96 0.00 0.00 2.44
8660 12368 6.348540 GCTATGGAACCATAAAAGCGGATAAG 60.349 42.308 13.51 2.31 38.30 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 2.223377 GCGGAATGTGACGAGACTTTTT 59.777 45.455 0.00 0.00 0.00 1.94
73 74 1.798813 GCGGAATGTGACGAGACTTTT 59.201 47.619 0.00 0.00 0.00 2.27
74 75 1.270094 TGCGGAATGTGACGAGACTTT 60.270 47.619 0.00 0.00 0.00 2.66
75 76 0.317160 TGCGGAATGTGACGAGACTT 59.683 50.000 0.00 0.00 0.00 3.01
76 77 0.388649 GTGCGGAATGTGACGAGACT 60.389 55.000 0.00 0.00 0.00 3.24
77 78 0.666274 TGTGCGGAATGTGACGAGAC 60.666 55.000 0.00 0.00 0.00 3.36
78 79 0.246360 ATGTGCGGAATGTGACGAGA 59.754 50.000 0.00 0.00 0.00 4.04
79 80 1.078709 AATGTGCGGAATGTGACGAG 58.921 50.000 0.00 0.00 0.00 4.18
80 81 2.371910 TAATGTGCGGAATGTGACGA 57.628 45.000 0.00 0.00 0.00 4.20
81 82 2.032894 GGATAATGTGCGGAATGTGACG 60.033 50.000 0.00 0.00 0.00 4.35
82 83 3.002656 CAGGATAATGTGCGGAATGTGAC 59.997 47.826 0.00 0.00 0.00 3.67
83 84 3.118445 TCAGGATAATGTGCGGAATGTGA 60.118 43.478 0.00 0.00 0.00 3.58
84 85 3.205338 TCAGGATAATGTGCGGAATGTG 58.795 45.455 0.00 0.00 0.00 3.21
85 86 3.558931 TCAGGATAATGTGCGGAATGT 57.441 42.857 0.00 0.00 0.00 2.71
86 87 4.261322 CCTTTCAGGATAATGTGCGGAATG 60.261 45.833 0.00 0.00 37.67 2.67
87 88 3.885297 CCTTTCAGGATAATGTGCGGAAT 59.115 43.478 0.00 0.00 37.67 3.01
88 89 3.054728 TCCTTTCAGGATAATGTGCGGAA 60.055 43.478 0.00 0.00 40.06 4.30
89 90 2.503765 TCCTTTCAGGATAATGTGCGGA 59.496 45.455 0.00 0.00 40.06 5.54
90 91 2.917933 TCCTTTCAGGATAATGTGCGG 58.082 47.619 0.00 0.00 40.06 5.69
91 92 4.963276 TTTCCTTTCAGGATAATGTGCG 57.037 40.909 0.00 0.00 45.34 5.34
92 93 6.024552 TGTTTTCCTTTCAGGATAATGTGC 57.975 37.500 0.00 0.00 45.34 4.57
93 94 7.175641 ACTCTGTTTTCCTTTCAGGATAATGTG 59.824 37.037 0.00 0.00 45.34 3.21
94 95 7.234355 ACTCTGTTTTCCTTTCAGGATAATGT 58.766 34.615 0.00 0.00 45.34 2.71
95 96 7.609532 AGACTCTGTTTTCCTTTCAGGATAATG 59.390 37.037 0.00 0.00 45.34 1.90
96 97 7.609532 CAGACTCTGTTTTCCTTTCAGGATAAT 59.390 37.037 0.00 0.00 45.34 1.28
97 98 6.936900 CAGACTCTGTTTTCCTTTCAGGATAA 59.063 38.462 0.00 0.00 45.34 1.75
98 99 6.467677 CAGACTCTGTTTTCCTTTCAGGATA 58.532 40.000 0.00 0.00 45.34 2.59
99 100 5.312079 CAGACTCTGTTTTCCTTTCAGGAT 58.688 41.667 0.00 0.00 45.34 3.24
100 101 4.444876 CCAGACTCTGTTTTCCTTTCAGGA 60.445 45.833 5.32 0.00 44.10 3.86
102 103 4.513318 GTCCAGACTCTGTTTTCCTTTCAG 59.487 45.833 5.32 0.00 0.00 3.02
104 105 4.451900 TGTCCAGACTCTGTTTTCCTTTC 58.548 43.478 5.32 0.00 0.00 2.62
107 108 2.370189 CCTGTCCAGACTCTGTTTTCCT 59.630 50.000 5.32 0.00 0.00 3.36
109 110 2.147150 GCCTGTCCAGACTCTGTTTTC 58.853 52.381 5.32 0.00 0.00 2.29
116 117 2.027745 TCATTCTTGCCTGTCCAGACTC 60.028 50.000 0.00 0.00 0.00 3.36
122 123 4.517285 TCAGTTATCATTCTTGCCTGTCC 58.483 43.478 0.00 0.00 0.00 4.02
126 127 6.182627 TCAACATCAGTTATCATTCTTGCCT 58.817 36.000 0.00 0.00 35.85 4.75
132 163 9.462174 TGTGTTTTTCAACATCAGTTATCATTC 57.538 29.630 0.00 0.00 44.85 2.67
164 195 3.592898 TTCATCTGCGCTTCAGTTAGA 57.407 42.857 9.73 0.43 43.32 2.10
165 196 4.668576 TTTTCATCTGCGCTTCAGTTAG 57.331 40.909 9.73 0.00 43.32 2.34
186 217 5.716703 CCAAATCCTCTTTGTAATCCTGGTT 59.283 40.000 0.00 0.00 0.00 3.67
194 225 3.831911 CCCTTGCCAAATCCTCTTTGTAA 59.168 43.478 0.00 0.00 0.00 2.41
197 228 1.066645 GCCCTTGCCAAATCCTCTTTG 60.067 52.381 0.00 0.00 0.00 2.77
201 232 1.212935 TCTAGCCCTTGCCAAATCCTC 59.787 52.381 0.00 0.00 38.69 3.71
216 247 4.513318 AAGTGTGTCTTTTGCTCTTCTAGC 59.487 41.667 0.00 0.00 41.77 3.42
223 254 6.092748 TCTTTTTCAAGTGTGTCTTTTGCTC 58.907 36.000 0.00 0.00 33.63 4.26
231 262 6.852664 TCCTCTTTTCTTTTTCAAGTGTGTC 58.147 36.000 0.00 0.00 0.00 3.67
232 263 6.834168 TCCTCTTTTCTTTTTCAAGTGTGT 57.166 33.333 0.00 0.00 0.00 3.72
275 334 6.428771 CGGTCCCTGTCAATTCTTAAAACTAA 59.571 38.462 0.00 0.00 0.00 2.24
276 335 5.935789 CGGTCCCTGTCAATTCTTAAAACTA 59.064 40.000 0.00 0.00 0.00 2.24
277 336 4.760204 CGGTCCCTGTCAATTCTTAAAACT 59.240 41.667 0.00 0.00 0.00 2.66
278 337 4.615223 GCGGTCCCTGTCAATTCTTAAAAC 60.615 45.833 0.00 0.00 0.00 2.43
285 344 1.375523 ACGCGGTCCCTGTCAATTC 60.376 57.895 12.47 0.00 0.00 2.17
308 367 0.820891 TCTACCATCTCGGGGTACGC 60.821 60.000 0.29 0.29 43.86 4.42
310 369 1.326328 GGTCTACCATCTCGGGGTAC 58.674 60.000 0.00 0.00 39.85 3.34
372 468 4.241555 CCGATCAAGAGGGGGCCG 62.242 72.222 0.00 0.00 0.00 6.13
378 474 1.084370 GTTGACGGCCGATCAAGAGG 61.084 60.000 35.90 0.00 36.76 3.69
379 475 1.084370 GGTTGACGGCCGATCAAGAG 61.084 60.000 35.90 0.00 36.76 2.85
392 488 0.036671 CTTACCTGGACGGGGTTGAC 60.037 60.000 0.00 0.00 38.19 3.18
395 491 1.203225 AGTACTTACCTGGACGGGGTT 60.203 52.381 0.00 0.00 38.19 4.11
414 510 3.641906 ACTACATTATGGAACGGAGGGAG 59.358 47.826 0.00 0.00 0.00 4.30
415 511 3.386726 CACTACATTATGGAACGGAGGGA 59.613 47.826 0.00 0.00 0.00 4.20
416 512 3.728845 CACTACATTATGGAACGGAGGG 58.271 50.000 0.00 0.00 0.00 4.30
417 513 3.131396 GCACTACATTATGGAACGGAGG 58.869 50.000 0.00 0.00 0.00 4.30
418 514 3.131396 GGCACTACATTATGGAACGGAG 58.869 50.000 0.00 0.00 0.00 4.63
419 515 2.769663 AGGCACTACATTATGGAACGGA 59.230 45.455 0.00 0.00 36.02 4.69
420 516 3.194005 AGGCACTACATTATGGAACGG 57.806 47.619 0.00 0.00 36.02 4.44
602 698 7.769272 TTAAACCTTGCAAACTTTGATCAAG 57.231 32.000 8.41 9.53 38.64 3.02
603 699 8.729805 AATTAAACCTTGCAAACTTTGATCAA 57.270 26.923 3.38 3.38 0.00 2.57
604 700 8.729805 AAATTAAACCTTGCAAACTTTGATCA 57.270 26.923 5.65 0.00 0.00 2.92
637 733 8.999431 CGTTCCATAATGTAGTGCCTATAAATT 58.001 33.333 0.00 0.00 0.00 1.82
638 734 7.606456 CCGTTCCATAATGTAGTGCCTATAAAT 59.394 37.037 0.00 0.00 0.00 1.40
639 735 6.932400 CCGTTCCATAATGTAGTGCCTATAAA 59.068 38.462 0.00 0.00 0.00 1.40
640 736 6.268158 TCCGTTCCATAATGTAGTGCCTATAA 59.732 38.462 0.00 0.00 0.00 0.98
641 737 5.776208 TCCGTTCCATAATGTAGTGCCTATA 59.224 40.000 0.00 0.00 0.00 1.31
642 738 4.591498 TCCGTTCCATAATGTAGTGCCTAT 59.409 41.667 0.00 0.00 0.00 2.57
643 739 3.962063 TCCGTTCCATAATGTAGTGCCTA 59.038 43.478 0.00 0.00 0.00 3.93
644 740 2.769663 TCCGTTCCATAATGTAGTGCCT 59.230 45.455 0.00 0.00 0.00 4.75
645 741 3.131396 CTCCGTTCCATAATGTAGTGCC 58.869 50.000 0.00 0.00 0.00 5.01
646 742 3.131396 CCTCCGTTCCATAATGTAGTGC 58.869 50.000 0.00 0.00 0.00 4.40
647 743 3.386726 TCCCTCCGTTCCATAATGTAGTG 59.613 47.826 0.00 0.00 0.00 2.74
648 744 3.641906 CTCCCTCCGTTCCATAATGTAGT 59.358 47.826 0.00 0.00 0.00 2.73
649 745 3.641906 ACTCCCTCCGTTCCATAATGTAG 59.358 47.826 0.00 0.00 0.00 2.74
650 746 3.649843 ACTCCCTCCGTTCCATAATGTA 58.350 45.455 0.00 0.00 0.00 2.29
651 747 2.478292 ACTCCCTCCGTTCCATAATGT 58.522 47.619 0.00 0.00 0.00 2.71
652 748 4.040461 ACATACTCCCTCCGTTCCATAATG 59.960 45.833 0.00 0.00 0.00 1.90
653 749 4.232091 ACATACTCCCTCCGTTCCATAAT 58.768 43.478 0.00 0.00 0.00 1.28
654 750 3.649843 ACATACTCCCTCCGTTCCATAA 58.350 45.455 0.00 0.00 0.00 1.90
655 751 3.323774 ACATACTCCCTCCGTTCCATA 57.676 47.619 0.00 0.00 0.00 2.74
656 752 2.170607 CAACATACTCCCTCCGTTCCAT 59.829 50.000 0.00 0.00 0.00 3.41
657 753 1.553248 CAACATACTCCCTCCGTTCCA 59.447 52.381 0.00 0.00 0.00 3.53
658 754 1.742750 GCAACATACTCCCTCCGTTCC 60.743 57.143 0.00 0.00 0.00 3.62
659 755 1.066430 TGCAACATACTCCCTCCGTTC 60.066 52.381 0.00 0.00 0.00 3.95
660 756 0.981183 TGCAACATACTCCCTCCGTT 59.019 50.000 0.00 0.00 0.00 4.44
661 757 0.249398 GTGCAACATACTCCCTCCGT 59.751 55.000 0.00 0.00 36.32 4.69
662 758 0.462047 GGTGCAACATACTCCCTCCG 60.462 60.000 0.00 0.00 39.98 4.63
663 759 0.618458 TGGTGCAACATACTCCCTCC 59.382 55.000 0.00 0.00 39.98 4.30
664 760 2.565841 GATGGTGCAACATACTCCCTC 58.434 52.381 19.28 0.00 39.98 4.30
665 761 1.134401 CGATGGTGCAACATACTCCCT 60.134 52.381 19.28 0.00 39.98 4.20
666 762 1.299541 CGATGGTGCAACATACTCCC 58.700 55.000 19.28 3.50 39.98 4.30
667 763 0.657840 GCGATGGTGCAACATACTCC 59.342 55.000 19.28 3.92 39.98 3.85
668 764 1.368641 TGCGATGGTGCAACATACTC 58.631 50.000 19.28 10.16 43.02 2.59
669 765 3.549412 TGCGATGGTGCAACATACT 57.451 47.368 19.28 0.00 43.02 2.12
676 772 1.517361 CTCTAGGTGCGATGGTGCA 59.483 57.895 0.00 0.00 43.95 4.57
677 773 1.884926 GCTCTAGGTGCGATGGTGC 60.885 63.158 0.00 0.00 0.00 5.01
678 774 0.249238 GAGCTCTAGGTGCGATGGTG 60.249 60.000 6.43 0.00 35.28 4.17
679 775 1.395826 GGAGCTCTAGGTGCGATGGT 61.396 60.000 14.64 0.00 35.28 3.55
680 776 1.112315 AGGAGCTCTAGGTGCGATGG 61.112 60.000 14.64 0.00 38.92 3.51
681 777 0.749649 AAGGAGCTCTAGGTGCGATG 59.250 55.000 14.64 0.00 38.92 3.84
682 778 2.366640 TAAGGAGCTCTAGGTGCGAT 57.633 50.000 14.64 0.00 38.92 4.58
683 779 2.366640 ATAAGGAGCTCTAGGTGCGA 57.633 50.000 14.64 0.00 38.92 5.10
697 793 1.622725 AGGGGAGCCGCCTATATAAGG 60.623 57.143 8.71 0.00 45.12 2.69
708 804 3.157949 GGAGGAGAAGGGGAGCCG 61.158 72.222 0.00 0.00 0.00 5.52
720 816 4.507916 CGAGCGAGGGGAGGAGGA 62.508 72.222 0.00 0.00 0.00 3.71
785 881 3.470567 GCTGAACCACGACGCTCG 61.471 66.667 0.00 5.97 46.93 5.03
786 882 3.112709 GGCTGAACCACGACGCTC 61.113 66.667 0.00 0.00 38.86 5.03
841 964 2.103263 GTGGACTCATATCTTTCGGCCT 59.897 50.000 0.00 0.00 0.00 5.19
845 968 5.817296 TCCATTTGTGGACTCATATCTTTCG 59.183 40.000 0.00 0.00 32.09 3.46
863 986 1.004745 ACGAGGCCTGACAATCCATTT 59.995 47.619 12.00 0.00 0.00 2.32
1215 1346 0.736325 CCAGCTGGAGAACCGTAACG 60.736 60.000 29.88 0.00 39.42 3.18
1414 1545 1.363744 CTGTTGAATCCAGAGTCGCC 58.636 55.000 0.00 0.00 31.38 5.54
1471 1602 4.126437 ACATCGTGAACAATCTTGTCACA 58.874 39.130 17.59 10.41 41.31 3.58
1472 1603 4.732285 ACATCGTGAACAATCTTGTCAC 57.268 40.909 11.99 11.99 41.31 3.67
1495 1626 3.336997 AGGGATCTGGGATATTCTACCGA 59.663 47.826 0.00 0.00 0.00 4.69
1552 1684 7.818493 AAGAAAAAGTCTTCAAAGCTTCAAC 57.182 32.000 0.00 0.00 43.49 3.18
1589 1722 2.210961 CAGCAGTGATCATGTAGCTGG 58.789 52.381 22.96 11.78 44.10 4.85
1636 1771 3.593442 TGGGGAAGACTTTGACACATT 57.407 42.857 0.00 0.00 0.00 2.71
1757 1892 4.751767 TTTGGAACAACAAATTGCTCCT 57.248 36.364 10.06 0.00 46.99 3.69
2120 2256 3.712016 TCCTGCTGGTTTATAGTTGCA 57.288 42.857 9.73 0.00 34.23 4.08
2137 2273 7.680730 CAAGGCTATTATACACCTACATTCCT 58.319 38.462 0.00 0.00 0.00 3.36
2322 2458 6.288294 AGCCACGTATGAACATACAATGTAT 58.712 36.000 20.11 0.00 44.07 2.29
2325 2461 6.418956 GTTAGCCACGTATGAACATACAATG 58.581 40.000 20.11 16.91 42.82 2.82
2407 2543 1.027357 CTTTGTGCCACACTTGCTCT 58.973 50.000 0.00 0.00 35.11 4.09
2416 2552 1.885887 TGTTATGAGCCTTTGTGCCAC 59.114 47.619 0.00 0.00 0.00 5.01
2449 2585 0.535780 CCAGGCTTGAGCTCAACACA 60.536 55.000 25.16 5.27 41.70 3.72
2582 2724 7.608153 TCCATATTAAACTCGAGTTCAACTGA 58.392 34.615 29.82 17.14 37.25 3.41
2634 2776 2.005606 TTTGTCTGCTTGGGCTGGGA 62.006 55.000 0.00 0.00 39.59 4.37
2717 2860 1.172180 AAAGGCGCTGCTGCTGTAAA 61.172 50.000 14.03 0.00 36.97 2.01
2785 2928 4.078363 ACAGATAAATGCGTTGGTTTCG 57.922 40.909 0.00 0.00 0.00 3.46
2943 3087 3.879892 AGCAGAGAAGACCTGACAAAAAC 59.120 43.478 0.00 0.00 33.65 2.43
3041 3185 4.715534 TGGTGTTTATGTTCTCAGGGAA 57.284 40.909 0.00 0.00 0.00 3.97
3094 3238 4.985538 TCAGTTCTTTTGTAGCATCCCTT 58.014 39.130 0.00 0.00 0.00 3.95
3095 3239 4.640771 TCAGTTCTTTTGTAGCATCCCT 57.359 40.909 0.00 0.00 0.00 4.20
3119 3263 0.976641 TCCTCTGTAGTTGCCAGTGG 59.023 55.000 4.20 4.20 42.33 4.00
3210 3354 3.009253 TCAGTTTTGCCCCTATTCCGTTA 59.991 43.478 0.00 0.00 0.00 3.18
3343 3488 1.669115 CACTGGAGTTCCTGGTGCG 60.669 63.158 9.48 0.00 39.04 5.34
3359 3504 0.657840 GGCATGACCAATCGCTACAC 59.342 55.000 0.00 0.00 38.86 2.90
3488 3633 4.722194 TGATCAAATCAGTTGCGTTAAGC 58.278 39.130 0.00 0.00 39.50 3.09
4181 4326 2.592861 GATGGAGTGGCGGCATCC 60.593 66.667 24.07 24.07 0.00 3.51
4476 4622 4.060900 TGCAGACAGATCAAACTGAAGAC 58.939 43.478 14.19 1.53 40.63 3.01
4548 4694 5.044105 AGGAGTGGGCAAATACTAAGGAAAT 60.044 40.000 0.00 0.00 0.00 2.17
4840 8299 9.872721 TCAACACTTACAATATTACATCGGTTA 57.127 29.630 0.00 0.00 0.00 2.85
5141 8756 1.376037 GAGTTGGAGGAGGGCAACG 60.376 63.158 0.00 0.00 33.26 4.10
5287 8902 4.965814 CATGGACTGCTTGGATATGTAGT 58.034 43.478 0.00 0.00 31.31 2.73
5317 8932 1.758862 TCCATCACTGTCGCATCTGAT 59.241 47.619 0.00 0.00 0.00 2.90
5681 9305 1.765314 GAGGCTTCTATGGCTTCCTCA 59.235 52.381 0.00 0.00 43.09 3.86
6017 9641 5.122396 GTGACATTATTGAAAGAGCGGTCTT 59.878 40.000 23.57 23.57 45.56 3.01
6019 9643 4.201822 GGTGACATTATTGAAAGAGCGGTC 60.202 45.833 6.48 6.48 0.00 4.79
6022 9646 4.944962 TGGTGACATTATTGAAAGAGCG 57.055 40.909 0.00 0.00 33.40 5.03
6153 9777 6.699575 AACTTGGTGCTAAATACATCCATC 57.300 37.500 0.00 0.00 0.00 3.51
6202 9826 0.517316 CTCCGTCCGAAAAAGCTTGG 59.483 55.000 0.00 0.00 0.00 3.61
6234 9872 7.552458 TGTGTTACTACCATATGATTTGCAG 57.448 36.000 3.65 0.00 0.00 4.41
6399 10037 7.013178 TCACAATCAGTCAAATGCTTTTGTAGA 59.987 33.333 20.69 16.97 42.37 2.59
6428 10066 4.256920 GCCTGATTACATCACACTTGACT 58.743 43.478 0.00 0.00 33.38 3.41
6516 10164 1.068474 CTACCTCAACTTGTTCGGCG 58.932 55.000 0.00 0.00 0.00 6.46
6694 10345 4.046938 TGATAATGTCAAGAGAGGTCGC 57.953 45.455 0.00 0.00 32.78 5.19
6784 10441 3.206150 TGAAGAGAAGCTTGTCCAACAC 58.794 45.455 19.26 7.78 36.83 3.32
7415 11102 9.364989 TGTACTCTGTTTTTCTTTGGAAAATTG 57.635 29.630 5.03 0.76 46.57 2.32
7699 11386 3.311322 CCAATTGCCAATGCTGCTTATTG 59.689 43.478 0.00 3.46 38.71 1.90
7893 11580 2.032549 GCAGCCGATGTAGCTTACAATG 60.033 50.000 0.00 0.00 42.76 2.82
7952 11640 6.690098 CACTTGAACTTCTTTCACTGTGATTG 59.310 38.462 11.86 7.67 44.28 2.67
8090 11778 8.362639 CAGGCATAAAATATGCAGGTTTATCTT 58.637 33.333 20.37 0.00 46.21 2.40
8175 11863 7.060600 TCTCTGTTTGTTGTAATGAATAGCG 57.939 36.000 0.00 0.00 0.00 4.26
8218 11906 5.245977 TCGATGAACTATGGGATGCATAAGA 59.754 40.000 0.00 0.00 0.00 2.10
8432 12120 5.187772 ACAGAGCCATATACTCTTGTCAACA 59.812 40.000 4.99 0.00 41.79 3.33
8433 12121 5.665459 ACAGAGCCATATACTCTTGTCAAC 58.335 41.667 4.99 0.00 41.79 3.18


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

AutoCloner maintained by Alex Coulton.