Multiple sequence alignment - TraesCS6A01G071100

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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 TraesCS6A01G071100 chr6A 100.000 3541 0 0 1 3541 38771462 38767922 0.000000e+00 6540.0
1 TraesCS6A01G071100 chr6A 76.870 575 114 15 2832 3401 242209147 242209707 1.230000e-79 307.0
2 TraesCS6A01G071100 chr6A 75.185 270 60 4 1967 2231 61890398 61890665 1.730000e-23 121.0
3 TraesCS6A01G071100 chr6A 87.273 55 6 1 2354 2408 34289866 34289813 1.060000e-05 62.1
4 TraesCS6A01G071100 chr6D 92.452 1921 101 20 1 1905 34542459 34540567 0.000000e+00 2704.0
5 TraesCS6A01G071100 chr6D 84.156 486 47 18 2371 2828 34538129 34537646 9.020000e-121 444.0
6 TraesCS6A01G071100 chr6B 92.478 1356 50 22 563 1908 71309808 71308495 0.000000e+00 1892.0
7 TraesCS6A01G071100 chr6B 82.912 673 101 7 2832 3501 339351086 339351747 8.460000e-166 593.0
8 TraesCS6A01G071100 chr6B 82.577 683 105 6 2822 3502 101274058 101274728 1.090000e-164 590.0
9 TraesCS6A01G071100 chr6B 81.872 673 110 3 2832 3502 719752485 719751823 1.110000e-154 556.0
10 TraesCS6A01G071100 chr6B 86.053 380 34 12 158 533 71310173 71309809 1.190000e-104 390.0
11 TraesCS6A01G071100 chr6B 90.141 71 6 1 2761 2830 71305371 71305301 1.350000e-14 91.6
12 TraesCS6A01G071100 chr2D 83.531 674 91 11 2832 3502 430469586 430470242 2.340000e-171 612.0
13 TraesCS6A01G071100 chr2D 77.899 276 49 9 1965 2234 399900038 399899769 1.020000e-35 161.0
14 TraesCS6A01G071100 chr2D 91.071 56 4 1 2354 2409 649591942 649591888 1.360000e-09 75.0
15 TraesCS6A01G071100 chr3D 83.186 678 101 8 2827 3502 18777794 18777128 3.020000e-170 608.0
16 TraesCS6A01G071100 chr3D 76.727 275 55 7 1966 2234 7510666 7510395 1.020000e-30 145.0
17 TraesCS6A01G071100 chr3D 78.571 210 38 5 2027 2232 121667618 121667824 7.980000e-27 132.0
18 TraesCS6A01G071100 chr7D 83.333 672 96 7 2833 3502 107676127 107676784 1.090000e-169 606.0
19 TraesCS6A01G071100 chr7D 77.033 209 45 2 1967 2172 133328880 133329088 2.230000e-22 117.0
20 TraesCS6A01G071100 chr7D 89.831 59 6 0 1143 1201 427621435 427621493 3.790000e-10 76.8
21 TraesCS6A01G071100 chr1B 83.210 673 91 10 2832 3502 496071619 496072271 6.540000e-167 597.0
22 TraesCS6A01G071100 chr1D 83.384 656 94 7 2849 3502 340669250 340669892 8.460000e-166 593.0
23 TraesCS6A01G071100 chr1D 84.375 576 73 12 2931 3502 378733885 378733323 1.860000e-152 549.0
24 TraesCS6A01G071100 chr1D 84.884 86 11 1 2149 2232 485481387 485481302 6.300000e-13 86.1
25 TraesCS6A01G071100 chr2B 83.489 642 94 4 2832 3471 522825139 522824508 3.940000e-164 588.0
26 TraesCS6A01G071100 chr2B 82.641 674 103 5 2824 3495 651133971 651134632 5.090000e-163 584.0
27 TraesCS6A01G071100 chr2B 89.286 56 5 1 2354 2408 634202361 634202306 6.340000e-08 69.4
28 TraesCS6A01G071100 chr5B 82.467 673 106 3 2832 3502 614364916 614364254 2.370000e-161 579.0
29 TraesCS6A01G071100 chr5B 82.301 452 66 8 2824 3273 678322045 678321606 2.580000e-101 379.0
30 TraesCS6A01G071100 chr4A 82.267 688 105 8 2820 3502 668795280 668795955 2.370000e-161 579.0
31 TraesCS6A01G071100 chr4A 87.273 55 6 1 2354 2408 684398782 684398835 1.060000e-05 62.1
32 TraesCS6A01G071100 chr4D 82.318 673 106 9 2832 3502 485512435 485513096 3.970000e-159 571.0
33 TraesCS6A01G071100 chr4D 79.545 176 33 2 1973 2145 465600340 465600165 4.800000e-24 122.0
34 TraesCS6A01G071100 chr4D 100.000 29 0 0 941 969 277203328 277203356 2.000000e-03 54.7
35 TraesCS6A01G071100 chr4B 83.535 413 55 5 2818 3230 522339066 522338667 1.200000e-99 374.0
36 TraesCS6A01G071100 chr7A 77.491 271 55 6 1966 2232 501033349 501033617 1.320000e-34 158.0
37 TraesCS6A01G071100 chr7A 88.710 62 7 0 1143 1204 505025404 505025343 3.790000e-10 76.8
38 TraesCS6A01G071100 chr2A 79.909 219 39 5 2019 2234 701014833 701014617 4.730000e-34 156.0
39 TraesCS6A01G071100 chr2A 74.806 258 45 12 1979 2232 406745726 406745967 8.090000e-17 99.0
40 TraesCS6A01G071100 chrUn 74.897 243 51 10 1981 2218 109049559 109049322 6.250000e-18 102.0
41 TraesCS6A01G071100 chrUn 89.091 55 6 0 2354 2408 101381202 101381256 6.340000e-08 69.4
42 TraesCS6A01G071100 chr7B 89.831 59 6 0 1143 1201 445288340 445288398 3.790000e-10 76.8
43 TraesCS6A01G071100 chr1A 86.364 66 9 0 2360 2425 499637712 499637777 4.900000e-09 73.1
44 TraesCS6A01G071100 chr3B 89.286 56 4 2 2354 2408 768735857 768735803 6.340000e-08 69.4
45 TraesCS6A01G071100 chr5A 90.000 50 3 2 2354 2402 524984191 524984143 2.950000e-06 63.9


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 TraesCS6A01G071100 chr6A 38767922 38771462 3540 True 6540.0 6540 100.000000 1 3541 1 chr6A.!!$R2 3540
1 TraesCS6A01G071100 chr6A 242209147 242209707 560 False 307.0 307 76.870000 2832 3401 1 chr6A.!!$F2 569
2 TraesCS6A01G071100 chr6D 34537646 34542459 4813 True 1574.0 2704 88.304000 1 2828 2 chr6D.!!$R1 2827
3 TraesCS6A01G071100 chr6B 71305301 71310173 4872 True 791.2 1892 89.557333 158 2830 3 chr6B.!!$R2 2672
4 TraesCS6A01G071100 chr6B 339351086 339351747 661 False 593.0 593 82.912000 2832 3501 1 chr6B.!!$F2 669
5 TraesCS6A01G071100 chr6B 101274058 101274728 670 False 590.0 590 82.577000 2822 3502 1 chr6B.!!$F1 680
6 TraesCS6A01G071100 chr6B 719751823 719752485 662 True 556.0 556 81.872000 2832 3502 1 chr6B.!!$R1 670
7 TraesCS6A01G071100 chr2D 430469586 430470242 656 False 612.0 612 83.531000 2832 3502 1 chr2D.!!$F1 670
8 TraesCS6A01G071100 chr3D 18777128 18777794 666 True 608.0 608 83.186000 2827 3502 1 chr3D.!!$R2 675
9 TraesCS6A01G071100 chr7D 107676127 107676784 657 False 606.0 606 83.333000 2833 3502 1 chr7D.!!$F1 669
10 TraesCS6A01G071100 chr1B 496071619 496072271 652 False 597.0 597 83.210000 2832 3502 1 chr1B.!!$F1 670
11 TraesCS6A01G071100 chr1D 340669250 340669892 642 False 593.0 593 83.384000 2849 3502 1 chr1D.!!$F1 653
12 TraesCS6A01G071100 chr1D 378733323 378733885 562 True 549.0 549 84.375000 2931 3502 1 chr1D.!!$R1 571
13 TraesCS6A01G071100 chr2B 522824508 522825139 631 True 588.0 588 83.489000 2832 3471 1 chr2B.!!$R1 639
14 TraesCS6A01G071100 chr2B 651133971 651134632 661 False 584.0 584 82.641000 2824 3495 1 chr2B.!!$F1 671
15 TraesCS6A01G071100 chr5B 614364254 614364916 662 True 579.0 579 82.467000 2832 3502 1 chr5B.!!$R1 670
16 TraesCS6A01G071100 chr4A 668795280 668795955 675 False 579.0 579 82.267000 2820 3502 1 chr4A.!!$F1 682
17 TraesCS6A01G071100 chr4D 485512435 485513096 661 False 571.0 571 82.318000 2832 3502 1 chr4D.!!$F2 670

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
271 272 0.179059 TGCCTTGAACAGCACGAGAA 60.179 50.0 0.0 0.0 33.08 2.87 F
283 284 0.232303 CACGAGAAAAGTGGCGTGTC 59.768 55.0 0.0 0.0 46.28 3.67 F
1576 1604 0.248907 ATCTATCCGCAACCACGACG 60.249 55.0 0.0 0.0 34.06 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1979 2035 0.179202 GCGTGTGCGTGCATTCATAA 60.179 50.0 0.00 0.0 40.81 1.90 R
2108 2164 0.391130 TAGGTGTTCCAGCGATGTGC 60.391 55.0 0.00 0.0 46.98 4.57 R
2663 4773 0.254178 CACCCTCACATGCTAGCCTT 59.746 55.0 13.29 0.0 0.00 4.35 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
23 24 5.077134 AGAGATGAATCATGTCGACACAA 57.923 39.130 22.71 12.46 38.85 3.33
31 32 3.983741 TCATGTCGACACAACACATGTA 58.016 40.909 22.71 1.21 45.16 2.29
83 84 4.009675 ACGGTGAACATGCAAGTATTCAT 58.990 39.130 0.00 0.00 33.85 2.57
93 94 2.961062 GCAAGTATTCATCCCTGCCATT 59.039 45.455 0.00 0.00 0.00 3.16
127 128 5.730568 GCTTATAAGATGGTTGACGCCTTTG 60.731 44.000 16.85 0.00 0.00 2.77
132 133 1.106351 TGGTTGACGCCTTTGTGCAT 61.106 50.000 0.00 0.00 0.00 3.96
138 139 0.734889 ACGCCTTTGTGCATATGCTC 59.265 50.000 27.13 23.57 42.66 4.26
192 193 2.618709 CAGTCTCTGAAACCAAACCACC 59.381 50.000 0.00 0.00 32.44 4.61
226 227 5.008712 GTCCAACGGATCTCAAGTTTTTCTT 59.991 40.000 0.00 0.00 32.73 2.52
239 240 6.544564 TCAAGTTTTTCTTAACGGATCAAGGT 59.455 34.615 0.00 0.00 34.66 3.50
256 257 3.244887 AGGTAAGCCTTTCTTTTGCCT 57.755 42.857 0.00 0.00 44.18 4.75
257 258 3.576861 AGGTAAGCCTTTCTTTTGCCTT 58.423 40.909 0.00 0.00 44.18 4.35
259 260 3.320826 GGTAAGCCTTTCTTTTGCCTTGA 59.679 43.478 0.00 0.00 36.25 3.02
260 261 4.202212 GGTAAGCCTTTCTTTTGCCTTGAA 60.202 41.667 0.00 0.00 36.25 2.69
261 262 3.459232 AGCCTTTCTTTTGCCTTGAAC 57.541 42.857 0.00 0.00 0.00 3.18
262 263 2.765699 AGCCTTTCTTTTGCCTTGAACA 59.234 40.909 0.00 0.00 0.00 3.18
263 264 3.126073 GCCTTTCTTTTGCCTTGAACAG 58.874 45.455 0.00 0.00 0.00 3.16
264 265 3.126073 CCTTTCTTTTGCCTTGAACAGC 58.874 45.455 0.00 0.00 0.00 4.40
265 266 3.430651 CCTTTCTTTTGCCTTGAACAGCA 60.431 43.478 0.00 0.00 37.18 4.41
266 267 2.869233 TCTTTTGCCTTGAACAGCAC 57.131 45.000 0.00 0.00 39.10 4.40
267 268 1.065401 TCTTTTGCCTTGAACAGCACG 59.935 47.619 0.00 0.00 39.10 5.34
268 269 1.065401 CTTTTGCCTTGAACAGCACGA 59.935 47.619 0.00 0.00 39.10 4.35
269 270 0.662619 TTTGCCTTGAACAGCACGAG 59.337 50.000 0.00 0.00 39.10 4.18
271 272 0.179059 TGCCTTGAACAGCACGAGAA 60.179 50.000 0.00 0.00 33.08 2.87
272 273 0.944386 GCCTTGAACAGCACGAGAAA 59.056 50.000 0.00 0.00 0.00 2.52
274 275 2.603173 GCCTTGAACAGCACGAGAAAAG 60.603 50.000 0.00 0.00 0.00 2.27
277 278 1.939934 TGAACAGCACGAGAAAAGTGG 59.060 47.619 0.00 0.00 39.80 4.00
278 279 0.663153 AACAGCACGAGAAAAGTGGC 59.337 50.000 0.00 0.00 39.80 5.01
279 280 1.205064 CAGCACGAGAAAAGTGGCG 59.795 57.895 0.00 0.00 39.80 5.69
280 281 1.227556 AGCACGAGAAAAGTGGCGT 60.228 52.632 0.00 0.00 39.80 5.68
282 283 2.307363 CACGAGAAAAGTGGCGTGT 58.693 52.632 0.00 0.00 46.28 4.49
283 284 0.232303 CACGAGAAAAGTGGCGTGTC 59.768 55.000 0.00 0.00 46.28 3.67
370 371 8.752187 AGTGTTAACATATGATTTTGCCTTGAT 58.248 29.630 12.26 0.00 0.00 2.57
378 379 3.057104 TGATTTTGCCTTGATCAGCACAG 60.057 43.478 9.01 0.00 39.10 3.66
415 420 4.773323 AAGCCCGAATTTCTCTTCTTTG 57.227 40.909 0.00 0.00 0.00 2.77
469 475 7.254117 CCTTCAGTTTATGTTCTAGTATGTGCG 60.254 40.741 0.00 0.00 0.00 5.34
556 562 4.675114 GTGCACAAAAAGAAATACACCTCG 59.325 41.667 13.17 0.00 0.00 4.63
618 624 1.308998 AGTTTCCCGTGTGAAGCAAG 58.691 50.000 0.00 0.00 0.00 4.01
641 647 3.253432 ACCTTTCATTTTCTCCAAGCGTC 59.747 43.478 0.00 0.00 0.00 5.19
663 669 1.002069 AAATGGACATGGAGGGCTCA 58.998 50.000 0.00 0.00 0.00 4.26
666 672 1.452833 GGACATGGAGGGCTCAAGC 60.453 63.158 0.00 0.00 41.14 4.01
690 696 2.414481 CACGAACAAGAGCCATCAGAAG 59.586 50.000 0.00 0.00 0.00 2.85
740 755 2.892640 GCCCATTTCCCTTTCGGC 59.107 61.111 0.00 0.00 0.00 5.54
753 768 0.817013 TTTCGGCCAGAATCATTGCC 59.183 50.000 2.24 0.00 38.86 4.52
773 788 5.445964 TGCCCCTTTATGGAAATTCTACTC 58.554 41.667 0.00 0.00 38.35 2.59
813 828 3.596046 ACTTTCAGGGGAATATTGGGTGA 59.404 43.478 0.00 0.00 31.93 4.02
897 912 1.535462 ACATTTCCTTTTCTGCGTCCG 59.465 47.619 0.00 0.00 0.00 4.79
1003 1027 2.703536 TCATTGGTATACCGTGCCATCT 59.296 45.455 17.13 0.00 42.56 2.90
1005 1029 3.738830 TTGGTATACCGTGCCATCTAC 57.261 47.619 17.13 0.00 42.56 2.59
1026 1051 4.732784 ACAACAAAACAAGCAGTAGTGTG 58.267 39.130 0.00 0.00 30.30 3.82
1029 1054 4.513442 ACAAAACAAGCAGTAGTGTGAGA 58.487 39.130 0.00 0.00 0.00 3.27
1033 1058 3.919216 ACAAGCAGTAGTGTGAGATCAC 58.081 45.455 6.01 6.01 46.59 3.06
1058 1083 6.763610 CCTTGAGATTAGGATACAAGTTCCAC 59.236 42.308 0.00 0.00 37.02 4.02
1059 1084 6.867519 TGAGATTAGGATACAAGTTCCACA 57.132 37.500 0.00 0.00 41.41 4.17
1107 1135 5.892348 AGAAATTAGCCTCTTTCCTGGAAA 58.108 37.500 20.06 20.06 32.90 3.13
1209 1237 1.067669 TGTAGCGCAGGTGATCATCTC 59.932 52.381 11.47 0.48 40.22 2.75
1216 1244 3.655486 GCAGGTGATCATCTCATCTCTG 58.345 50.000 5.21 0.00 41.77 3.35
1217 1245 3.321396 GCAGGTGATCATCTCATCTCTGA 59.679 47.826 5.21 0.00 41.77 3.27
1218 1246 4.559906 GCAGGTGATCATCTCATCTCTGAG 60.560 50.000 5.21 0.00 41.77 3.35
1219 1247 3.575256 AGGTGATCATCTCATCTCTGAGC 59.425 47.826 1.50 0.00 41.77 4.26
1231 1259 2.696506 TCTCTGAGCAGCAAGTTCATG 58.303 47.619 0.00 0.00 36.83 3.07
1232 1260 1.738350 CTCTGAGCAGCAAGTTCATGG 59.262 52.381 0.00 0.00 36.83 3.66
1246 1274 5.894298 AGTTCATGGTCTTCATAGCCATA 57.106 39.130 0.00 0.00 36.66 2.74
1264 1292 5.886474 AGCCATAACCATCATCATCATCATC 59.114 40.000 0.00 0.00 0.00 2.92
1267 1295 7.682021 GCCATAACCATCATCATCATCATCATG 60.682 40.741 0.00 0.00 0.00 3.07
1270 1298 5.010282 ACCATCATCATCATCATCATGGTG 58.990 41.667 0.00 0.00 40.80 4.17
1528 1556 3.773560 CCCTCACCATTTCCAAGGTAAA 58.226 45.455 0.00 0.00 36.07 2.01
1576 1604 0.248907 ATCTATCCGCAACCACGACG 60.249 55.000 0.00 0.00 34.06 5.12
1584 1612 1.941476 GCAACCACGACGACGATGAC 61.941 60.000 15.32 0.00 42.66 3.06
1609 1637 2.621407 GGTGATGGTGGTGATGATGGTT 60.621 50.000 0.00 0.00 0.00 3.67
1771 1799 1.016627 CACAAGTACGCCATGGGATG 58.983 55.000 15.13 6.29 0.00 3.51
1772 1800 0.908910 ACAAGTACGCCATGGGATGA 59.091 50.000 15.13 0.00 0.00 2.92
1773 1801 1.134401 ACAAGTACGCCATGGGATGAG 60.134 52.381 15.13 0.00 0.00 2.90
1774 1802 1.138859 CAAGTACGCCATGGGATGAGA 59.861 52.381 15.13 0.00 0.00 3.27
1775 1803 1.722034 AGTACGCCATGGGATGAGAT 58.278 50.000 15.13 0.00 0.00 2.75
1780 1808 3.713003 ACGCCATGGGATGAGATAGATA 58.287 45.455 15.13 0.00 0.00 1.98
1787 1815 7.550906 GCCATGGGATGAGATAGATAACTAAAC 59.449 40.741 15.13 0.00 32.04 2.01
1849 1877 7.442969 TGGAAACCATGTACCGATGAATAATAC 59.557 37.037 0.00 0.00 0.00 1.89
1903 1931 6.857777 GCTGATGCTGAGTATGAACTTAAT 57.142 37.500 0.00 0.00 34.18 1.40
1904 1932 6.886307 GCTGATGCTGAGTATGAACTTAATC 58.114 40.000 0.00 0.00 34.18 1.75
1905 1933 6.073331 GCTGATGCTGAGTATGAACTTAATCC 60.073 42.308 0.00 0.00 34.18 3.01
1906 1934 6.291377 TGATGCTGAGTATGAACTTAATCCC 58.709 40.000 0.00 0.00 35.56 3.85
1907 1935 5.036117 TGCTGAGTATGAACTTAATCCCC 57.964 43.478 0.00 0.00 35.56 4.81
1908 1936 4.141482 TGCTGAGTATGAACTTAATCCCCC 60.141 45.833 0.00 0.00 35.56 5.40
1946 1974 9.877178 AAAAGAGTATGAACTTAATCATCGTCT 57.123 29.630 0.00 0.00 40.44 4.18
1995 2051 1.093972 CCCTTATGAATGCACGCACA 58.906 50.000 0.00 0.00 0.00 4.57
2006 2062 3.918977 ACGCACACGCACCCTACA 61.919 61.111 0.00 0.00 45.53 2.74
2008 2064 2.032634 CGCACACGCACCCTACATT 61.033 57.895 0.00 0.00 38.40 2.71
2012 2068 3.199677 GCACACGCACCCTACATTTATA 58.800 45.455 0.00 0.00 38.36 0.98
2015 2071 5.113383 CACACGCACCCTACATTTATAAGA 58.887 41.667 0.00 0.00 0.00 2.10
2017 2073 6.260050 CACACGCACCCTACATTTATAAGAAT 59.740 38.462 0.00 0.00 0.00 2.40
2021 2077 6.369065 CGCACCCTACATTTATAAGAATCTCC 59.631 42.308 0.00 0.00 0.00 3.71
2022 2078 6.369065 GCACCCTACATTTATAAGAATCTCCG 59.631 42.308 0.00 0.00 0.00 4.63
2027 2083 9.015367 CCTACATTTATAAGAATCTCCGAGAGA 57.985 37.037 4.07 6.14 43.20 3.10
2034 2090 1.336755 GAATCTCCGAGAGACTGAGCC 59.663 57.143 4.07 0.00 41.76 4.70
2036 2092 1.450491 CTCCGAGAGACTGAGCCGA 60.450 63.158 0.00 0.00 0.00 5.54
2043 2099 0.528017 GAGACTGAGCCGACACATCA 59.472 55.000 0.00 0.00 0.00 3.07
2052 2108 2.433604 AGCCGACACATCATCTTGAGAT 59.566 45.455 0.00 0.00 34.56 2.75
2054 2110 4.100035 AGCCGACACATCATCTTGAGATTA 59.900 41.667 0.00 0.00 31.21 1.75
2062 2118 9.107177 ACACATCATCTTGAGATTAATGAAGTC 57.893 33.333 15.09 0.00 30.20 3.01
2063 2119 9.106070 CACATCATCTTGAGATTAATGAAGTCA 57.894 33.333 15.09 0.00 30.20 3.41
2064 2120 9.848710 ACATCATCTTGAGATTAATGAAGTCAT 57.151 29.630 15.09 0.00 33.18 3.06
2080 2136 5.680151 TGAAGTCATCATAAACGCATCCGTA 60.680 40.000 0.00 0.00 39.02 4.02
2094 2150 4.110482 GCATCCGTAGTCAATAAGAACGT 58.890 43.478 0.00 0.00 30.42 3.99
2099 2155 4.096081 CCGTAGTCAATAAGAACGTCTCCT 59.904 45.833 0.00 0.00 30.42 3.69
2100 2156 5.295292 CCGTAGTCAATAAGAACGTCTCCTA 59.705 44.000 0.00 0.00 30.42 2.94
2108 2164 3.555917 AGAACGTCTCCTAACTGAACG 57.444 47.619 0.00 0.00 0.00 3.95
2115 2171 1.920574 CTCCTAACTGAACGCACATCG 59.079 52.381 0.00 0.00 45.38 3.84
2116 2172 0.370273 CCTAACTGAACGCACATCGC 59.630 55.000 0.00 0.00 43.23 4.58
2118 2174 1.059692 CTAACTGAACGCACATCGCTG 59.940 52.381 0.00 0.00 43.23 5.18
2119 2175 1.568612 AACTGAACGCACATCGCTGG 61.569 55.000 0.00 0.00 43.23 4.85
2120 2176 1.737735 CTGAACGCACATCGCTGGA 60.738 57.895 0.00 0.00 43.23 3.86
2123 2179 1.565156 GAACGCACATCGCTGGAACA 61.565 55.000 0.00 0.00 43.23 3.18
2124 2180 1.841663 AACGCACATCGCTGGAACAC 61.842 55.000 0.00 0.00 43.23 3.32
2125 2181 2.870372 GCACATCGCTGGAACACC 59.130 61.111 0.00 0.00 37.77 4.16
2126 2182 1.672356 GCACATCGCTGGAACACCT 60.672 57.895 0.00 0.00 37.77 4.00
2127 2183 0.391130 GCACATCGCTGGAACACCTA 60.391 55.000 0.00 0.00 37.77 3.08
2128 2184 1.943968 GCACATCGCTGGAACACCTAA 60.944 52.381 0.00 0.00 37.77 2.69
2139 3773 7.825270 TCGCTGGAACACCTAAAATAAATCTAA 59.175 33.333 0.00 0.00 0.00 2.10
2173 3807 5.854010 ACAAGTGTGAAGTCTAAGACTCA 57.146 39.130 0.00 0.00 42.59 3.41
2181 3815 7.653713 GTGTGAAGTCTAAGACTCAAAATCTGA 59.346 37.037 0.00 0.00 42.59 3.27
2211 3846 4.279145 GAGATACCACTGTCCTCCTAACA 58.721 47.826 0.00 0.00 0.00 2.41
2218 3853 4.324563 CCACTGTCCTCCTAACAATCCAAT 60.325 45.833 0.00 0.00 0.00 3.16
2221 3856 5.192522 ACTGTCCTCCTAACAATCCAATCAT 59.807 40.000 0.00 0.00 0.00 2.45
2231 3866 6.530019 AACAATCCAATCATAGGTTGGTTC 57.470 37.500 8.75 0.00 45.05 3.62
2232 3867 5.579047 ACAATCCAATCATAGGTTGGTTCA 58.421 37.500 8.75 0.00 45.05 3.18
2238 3873 4.811969 ATCATAGGTTGGTTCACGTACA 57.188 40.909 0.00 0.00 0.00 2.90
2241 3876 1.944032 AGGTTGGTTCACGTACACAC 58.056 50.000 0.00 0.00 0.00 3.82
2247 4215 3.446799 TGGTTCACGTACACACAAGTAC 58.553 45.455 0.00 0.00 40.68 2.73
2274 4242 0.036388 ATCGACACGCCCATTTCTGT 60.036 50.000 0.00 0.00 0.00 3.41
2282 4250 4.462483 ACACGCCCATTTCTGTCAATATTT 59.538 37.500 0.00 0.00 0.00 1.40
2292 4260 8.664798 CATTTCTGTCAATATTTTGTACTCCGA 58.335 33.333 0.00 0.00 34.32 4.55
2319 4288 8.993121 TGACTAACTATTGCTTTTTCTCTTGAG 58.007 33.333 0.00 0.00 0.00 3.02
2321 4290 9.998106 ACTAACTATTGCTTTTTCTCTTGAGTA 57.002 29.630 0.00 0.00 0.00 2.59
2359 4328 8.634444 TGGTTGATGGGTATTAAATTAAATCGG 58.366 33.333 0.00 0.00 0.00 4.18
2360 4329 8.852135 GGTTGATGGGTATTAAATTAAATCGGA 58.148 33.333 0.00 0.00 0.00 4.55
2361 4330 9.893305 GTTGATGGGTATTAAATTAAATCGGAG 57.107 33.333 0.00 0.00 0.00 4.63
2362 4331 8.630054 TGATGGGTATTAAATTAAATCGGAGG 57.370 34.615 0.00 0.00 0.00 4.30
2367 4450 7.865889 GGGTATTAAATTAAATCGGAGGCAAAG 59.134 37.037 0.00 0.00 0.00 2.77
2426 4509 4.304048 TTGAATTTAAAGGCCCCGAGTA 57.696 40.909 0.00 0.00 0.00 2.59
2428 4511 4.664392 TGAATTTAAAGGCCCCGAGTAAA 58.336 39.130 0.00 0.00 0.00 2.01
2429 4512 4.460034 TGAATTTAAAGGCCCCGAGTAAAC 59.540 41.667 0.00 0.00 0.00 2.01
2430 4513 3.505480 TTTAAAGGCCCCGAGTAAACA 57.495 42.857 0.00 0.00 0.00 2.83
2436 4525 1.538512 GGCCCCGAGTAAACAAAAGTC 59.461 52.381 0.00 0.00 0.00 3.01
2462 4551 5.615289 ACTCTCCTGAAATAATGATTCCCG 58.385 41.667 0.00 0.00 0.00 5.14
2472 4561 7.282224 TGAAATAATGATTCCCGATTCTTTCGT 59.718 33.333 0.00 0.00 46.65 3.85
2473 4562 4.882671 AATGATTCCCGATTCTTTCGTG 57.117 40.909 0.00 0.00 46.65 4.35
2498 4588 2.940158 GGTAACCCACAACTTGTCCTT 58.060 47.619 0.00 0.00 0.00 3.36
2574 4664 2.151502 TCCAAAGCAAGGGACAAACA 57.848 45.000 0.00 0.00 0.00 2.83
2608 4718 3.620419 ATGGCCACGACCGCATCAA 62.620 57.895 8.16 0.00 0.00 2.57
2611 4721 3.039202 GCCACGACCGCATCAAAGG 62.039 63.158 0.00 0.00 0.00 3.11
2615 4725 0.960364 ACGACCGCATCAAAGGCATT 60.960 50.000 0.00 0.00 0.00 3.56
2682 5461 0.254178 AAGGCTAGCATGTGAGGGTG 59.746 55.000 18.24 0.00 0.00 4.61
2684 5463 2.176273 GCTAGCATGTGAGGGTGCG 61.176 63.158 10.63 0.00 45.69 5.34
2715 6860 3.840124 GGGGGAGACGAACAGATTAAT 57.160 47.619 0.00 0.00 0.00 1.40
2720 6865 5.068723 GGGGAGACGAACAGATTAATAGTCA 59.931 44.000 0.00 0.00 0.00 3.41
2721 6866 6.406624 GGGGAGACGAACAGATTAATAGTCAA 60.407 42.308 0.00 0.00 0.00 3.18
2742 6887 1.686052 TCCCCAAAATAATCGCATGCC 59.314 47.619 13.15 0.00 0.00 4.40
2749 6894 2.869233 ATAATCGCATGCCCACAAAC 57.131 45.000 13.15 0.00 0.00 2.93
2756 6901 2.030363 CGCATGCCCACAAACTAAAAGA 60.030 45.455 13.15 0.00 0.00 2.52
2759 6904 1.950909 TGCCCACAAACTAAAAGACGG 59.049 47.619 0.00 0.00 0.00 4.79
2810 7165 6.036577 AGAATTGTGGTTTGACTTGTTGTT 57.963 33.333 0.00 0.00 0.00 2.83
2819 7174 1.339247 TGACTTGTTGTTGTGTCCGGT 60.339 47.619 0.00 0.00 0.00 5.28
2902 7257 4.931661 ATTACGTAAGGACCGACATGAT 57.068 40.909 14.25 0.00 46.39 2.45
2903 7258 2.865343 ACGTAAGGACCGACATGATC 57.135 50.000 0.00 0.00 46.39 2.92
2908 7263 4.261447 CGTAAGGACCGACATGATCATACA 60.261 45.833 8.15 0.00 0.00 2.29
2910 7266 2.630098 AGGACCGACATGATCATACAGG 59.370 50.000 8.15 13.43 0.00 4.00
2924 7281 7.971201 TGATCATACAGGAAAGATAGCAGAAT 58.029 34.615 0.00 0.00 0.00 2.40
2985 7342 1.748879 CCACCACAATAGCCACCGG 60.749 63.158 0.00 0.00 0.00 5.28
3007 7364 5.495640 GGAGAATAGAATGATGGATCACCC 58.504 45.833 0.00 0.00 40.03 4.61
3018 7375 1.993391 GATCACCCCCTCACCCGAA 60.993 63.158 0.00 0.00 0.00 4.30
3019 7376 1.307866 ATCACCCCCTCACCCGAAT 60.308 57.895 0.00 0.00 0.00 3.34
3025 7382 0.037590 CCCCTCACCCGAATTTGACA 59.962 55.000 0.00 0.00 0.00 3.58
3106 7463 2.159393 CCATTGCCGTTGAACGAATCAT 60.159 45.455 20.47 2.71 46.05 2.45
3107 7464 3.064682 CCATTGCCGTTGAACGAATCATA 59.935 43.478 20.47 5.83 46.05 2.15
3108 7465 4.261155 CCATTGCCGTTGAACGAATCATAT 60.261 41.667 20.47 7.55 46.05 1.78
3122 7479 4.327357 CGAATCATATATCGAGGCAACACC 59.673 45.833 0.00 0.00 41.43 4.16
3123 7480 3.678056 TCATATATCGAGGCAACACCC 57.322 47.619 0.00 0.00 40.58 4.61
3124 7481 2.301870 TCATATATCGAGGCAACACCCC 59.698 50.000 0.00 0.00 40.58 4.95
3125 7482 0.677288 TATATCGAGGCAACACCCCG 59.323 55.000 0.00 0.00 40.58 5.73
3126 7483 2.040009 ATATCGAGGCAACACCCCGG 62.040 60.000 0.00 0.00 40.58 5.73
3129 7486 3.948719 GAGGCAACACCCCGGACA 61.949 66.667 0.73 0.00 40.58 4.02
3177 7536 0.393820 GACACCCCACCACGACTAAA 59.606 55.000 0.00 0.00 0.00 1.85
3198 7557 1.276421 ACATTGAAGGAGGAGACCACG 59.724 52.381 0.00 0.00 0.00 4.94
3199 7558 1.276421 CATTGAAGGAGGAGACCACGT 59.724 52.381 0.00 0.00 0.00 4.49
3200 7559 2.297698 TTGAAGGAGGAGACCACGTA 57.702 50.000 0.00 0.00 0.00 3.57
3236 7597 2.203480 AACCCAGCACATGCCGTT 60.203 55.556 0.00 0.00 43.38 4.44
3262 7623 2.093288 AGATGTTGTCGATGCAGACCAT 60.093 45.455 3.85 1.58 40.26 3.55
3281 7642 3.072038 CCATAATCTGCATCCACTCCTGA 59.928 47.826 0.00 0.00 0.00 3.86
3313 7674 0.592754 GCTCCATGTCGACGCTAGAC 60.593 60.000 11.62 0.00 38.98 2.59
3351 7712 2.182842 GGAGCCCGATGACACATGC 61.183 63.158 0.00 0.00 0.00 4.06
3358 7719 1.371337 CGATGACACATGCCCACCAG 61.371 60.000 0.00 0.00 0.00 4.00
3423 7787 2.889170 TTTCAAATCCATCCCCGACA 57.111 45.000 0.00 0.00 0.00 4.35
3504 7868 2.437359 CTGCCGAAGCCAAGAGGG 60.437 66.667 0.00 0.00 38.69 4.30
3514 7878 1.762370 AGCCAAGAGGGTTTTGTTTGG 59.238 47.619 0.00 0.00 45.14 3.28
3515 7879 1.484653 GCCAAGAGGGTTTTGTTTGGT 59.515 47.619 3.79 0.00 40.27 3.67
3516 7880 2.741553 GCCAAGAGGGTTTTGTTTGGTG 60.742 50.000 3.79 0.00 40.27 4.17
3517 7881 2.158971 CCAAGAGGGTTTTGTTTGGTGG 60.159 50.000 0.00 0.00 34.88 4.61
3518 7882 2.763448 CAAGAGGGTTTTGTTTGGTGGA 59.237 45.455 0.00 0.00 0.00 4.02
3519 7883 3.328535 AGAGGGTTTTGTTTGGTGGAT 57.671 42.857 0.00 0.00 0.00 3.41
3520 7884 3.653164 AGAGGGTTTTGTTTGGTGGATT 58.347 40.909 0.00 0.00 0.00 3.01
3521 7885 3.387699 AGAGGGTTTTGTTTGGTGGATTG 59.612 43.478 0.00 0.00 0.00 2.67
3522 7886 3.111484 AGGGTTTTGTTTGGTGGATTGT 58.889 40.909 0.00 0.00 0.00 2.71
3523 7887 3.118445 AGGGTTTTGTTTGGTGGATTGTG 60.118 43.478 0.00 0.00 0.00 3.33
3524 7888 3.369997 GGGTTTTGTTTGGTGGATTGTGT 60.370 43.478 0.00 0.00 0.00 3.72
3525 7889 3.868661 GGTTTTGTTTGGTGGATTGTGTC 59.131 43.478 0.00 0.00 0.00 3.67
3526 7890 3.428746 TTTGTTTGGTGGATTGTGTCG 57.571 42.857 0.00 0.00 0.00 4.35
3527 7891 1.313772 TGTTTGGTGGATTGTGTCGG 58.686 50.000 0.00 0.00 0.00 4.79
3528 7892 1.134068 TGTTTGGTGGATTGTGTCGGA 60.134 47.619 0.00 0.00 0.00 4.55
3529 7893 1.950909 GTTTGGTGGATTGTGTCGGAA 59.049 47.619 0.00 0.00 0.00 4.30
3530 7894 1.600023 TTGGTGGATTGTGTCGGAAC 58.400 50.000 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.152223 TGTGTTGTGTCGACATGATTCATC 59.848 41.667 23.12 13.34 29.89 2.92
14 15 4.725556 ATGTTACATGTGTTGTGTCGAC 57.274 40.909 9.11 9.11 39.48 4.20
106 107 4.634004 CACAAAGGCGTCAACCATCTTATA 59.366 41.667 0.00 0.00 0.00 0.98
132 133 2.079158 GCTCACTTGCAGTTGAGCATA 58.921 47.619 31.68 0.00 45.19 3.14
138 139 2.843077 CAATACGCTCACTTGCAGTTG 58.157 47.619 0.00 0.00 0.00 3.16
192 193 3.353836 CGTTGGACCAAGCCACCG 61.354 66.667 7.31 3.29 37.50 4.94
253 254 0.944386 TTTCTCGTGCTGTTCAAGGC 59.056 50.000 0.00 0.00 0.00 4.35
254 255 2.614057 ACTTTTCTCGTGCTGTTCAAGG 59.386 45.455 0.00 0.00 0.00 3.61
255 256 3.546815 CCACTTTTCTCGTGCTGTTCAAG 60.547 47.826 0.00 0.00 0.00 3.02
256 257 2.354510 CCACTTTTCTCGTGCTGTTCAA 59.645 45.455 0.00 0.00 0.00 2.69
257 258 1.939934 CCACTTTTCTCGTGCTGTTCA 59.060 47.619 0.00 0.00 0.00 3.18
259 260 0.663153 GCCACTTTTCTCGTGCTGTT 59.337 50.000 0.00 0.00 0.00 3.16
260 261 1.498865 CGCCACTTTTCTCGTGCTGT 61.499 55.000 0.00 0.00 0.00 4.40
261 262 1.205064 CGCCACTTTTCTCGTGCTG 59.795 57.895 0.00 0.00 0.00 4.41
262 263 1.227556 ACGCCACTTTTCTCGTGCT 60.228 52.632 0.00 0.00 33.59 4.40
263 264 1.082756 CACGCCACTTTTCTCGTGC 60.083 57.895 0.72 0.00 44.20 5.34
265 266 0.878961 GGACACGCCACTTTTCTCGT 60.879 55.000 0.00 0.00 36.34 4.18
266 267 1.860078 GGACACGCCACTTTTCTCG 59.140 57.895 0.00 0.00 36.34 4.04
267 268 1.860078 CGGACACGCCACTTTTCTC 59.140 57.895 0.00 0.00 35.94 2.87
268 269 4.043168 CGGACACGCCACTTTTCT 57.957 55.556 0.00 0.00 35.94 2.52
278 279 1.484227 TTTTCTCACACGCGGACACG 61.484 55.000 12.47 0.00 44.63 4.49
279 280 0.232303 CTTTTCTCACACGCGGACAC 59.768 55.000 12.47 0.00 0.00 3.67
280 281 0.179094 ACTTTTCTCACACGCGGACA 60.179 50.000 12.47 0.00 0.00 4.02
281 282 0.232303 CACTTTTCTCACACGCGGAC 59.768 55.000 12.47 0.00 0.00 4.79
282 283 0.878523 CCACTTTTCTCACACGCGGA 60.879 55.000 12.47 0.00 0.00 5.54
283 284 1.157870 ACCACTTTTCTCACACGCGG 61.158 55.000 12.47 1.27 0.00 6.46
321 322 4.234574 TGCTGATTCTTACGTGTGTACTG 58.765 43.478 0.00 0.00 0.00 2.74
370 371 2.775911 CTGGAAGAATCCTGTGCTGA 57.224 50.000 0.00 0.00 46.70 4.26
378 379 3.481453 GGGCTTATCACTGGAAGAATCC 58.519 50.000 0.00 0.00 46.76 3.01
415 420 1.648504 GCGTGGGTATGTTACTGTCC 58.351 55.000 0.00 0.00 0.00 4.02
469 475 6.435430 AATGGCAAAGGAAAAAGTGAAAAC 57.565 33.333 0.00 0.00 0.00 2.43
618 624 3.253432 ACGCTTGGAGAAAATGAAAGGTC 59.747 43.478 0.00 0.00 0.00 3.85
641 647 1.064166 AGCCCTCCATGTCCATTTCAG 60.064 52.381 0.00 0.00 0.00 3.02
663 669 2.919971 GCTCTTGTTCGTGGAGCTT 58.080 52.632 6.89 0.00 46.04 3.74
666 672 1.338105 TGATGGCTCTTGTTCGTGGAG 60.338 52.381 0.00 0.00 0.00 3.86
740 755 3.322828 CCATAAAGGGGCAATGATTCTGG 59.677 47.826 0.00 0.00 0.00 3.86
753 768 4.515567 GCCGAGTAGAATTTCCATAAAGGG 59.484 45.833 0.00 0.00 38.24 3.95
773 788 2.584418 CTCATCGAGTGGCTGCCG 60.584 66.667 14.98 1.57 0.00 5.69
897 912 1.772836 AGGCATTGGATTCTTGAGCC 58.227 50.000 0.00 0.00 40.85 4.70
986 1009 2.668625 TGTAGATGGCACGGTATACCA 58.331 47.619 21.76 1.94 37.99 3.25
1003 1027 5.644206 TCACACTACTGCTTGTTTTGTTGTA 59.356 36.000 0.00 0.00 0.00 2.41
1005 1029 4.980590 TCACACTACTGCTTGTTTTGTTG 58.019 39.130 0.00 0.00 0.00 3.33
1026 1051 7.531857 TGTATCCTAATCTCAAGGTGATCTC 57.468 40.000 0.00 0.00 35.48 2.75
1029 1054 7.682787 ACTTGTATCCTAATCTCAAGGTGAT 57.317 36.000 0.00 0.00 39.49 3.06
1033 1058 6.763610 GTGGAACTTGTATCCTAATCTCAAGG 59.236 42.308 0.00 0.00 39.49 3.61
1058 1083 3.276857 CTGTTCTTGGGTGAGATGGATG 58.723 50.000 0.00 0.00 0.00 3.51
1059 1084 2.240667 CCTGTTCTTGGGTGAGATGGAT 59.759 50.000 0.00 0.00 0.00 3.41
1209 1237 2.696506 TGAACTTGCTGCTCAGAGATG 58.303 47.619 0.00 0.00 0.00 2.90
1216 1244 1.818642 AGACCATGAACTTGCTGCTC 58.181 50.000 0.00 0.00 0.00 4.26
1217 1245 2.157738 GAAGACCATGAACTTGCTGCT 58.842 47.619 0.00 0.00 0.00 4.24
1218 1246 1.881973 TGAAGACCATGAACTTGCTGC 59.118 47.619 8.60 0.00 0.00 5.25
1219 1247 4.201891 GCTATGAAGACCATGAACTTGCTG 60.202 45.833 8.60 0.52 36.71 4.41
1231 1259 4.973168 TGATGGTTATGGCTATGAAGACC 58.027 43.478 0.00 0.00 0.00 3.85
1232 1260 6.233434 TGATGATGGTTATGGCTATGAAGAC 58.767 40.000 0.00 0.00 0.00 3.01
1246 1274 5.476945 CACCATGATGATGATGATGATGGTT 59.523 40.000 12.70 0.00 40.05 3.67
1264 1292 3.622612 TGCATACAAGAACGATCACCATG 59.377 43.478 0.00 0.00 0.00 3.66
1267 1295 2.609459 CCTGCATACAAGAACGATCACC 59.391 50.000 0.00 0.00 0.00 4.02
1270 1298 1.599542 GCCCTGCATACAAGAACGATC 59.400 52.381 0.00 0.00 0.00 3.69
1549 1577 5.352284 GTGGTTGCGGATAGATAGATATGG 58.648 45.833 0.00 0.00 0.00 2.74
1576 1604 1.202417 ACCATCACCATCGTCATCGTC 60.202 52.381 0.00 0.00 38.33 4.20
1584 1612 1.134431 TCATCACCACCATCACCATCG 60.134 52.381 0.00 0.00 0.00 3.84
1773 1801 8.760569 GCTCAAGCTCTTGTTTAGTTATCTATC 58.239 37.037 9.20 0.00 41.16 2.08
1774 1802 8.655651 GCTCAAGCTCTTGTTTAGTTATCTAT 57.344 34.615 9.20 0.00 41.16 1.98
1808 1836 3.813166 GGTTTCCACATCTTTGAGTTCGA 59.187 43.478 0.00 0.00 0.00 3.71
1809 1837 3.563808 TGGTTTCCACATCTTTGAGTTCG 59.436 43.478 0.00 0.00 0.00 3.95
1810 1838 5.010012 ACATGGTTTCCACATCTTTGAGTTC 59.990 40.000 0.00 0.00 35.80 3.01
1811 1839 4.895297 ACATGGTTTCCACATCTTTGAGTT 59.105 37.500 0.00 0.00 35.80 3.01
1812 1840 4.473444 ACATGGTTTCCACATCTTTGAGT 58.527 39.130 0.00 0.00 35.80 3.41
1849 1877 7.486802 AATTTGAAGCAAAAGGTTGATTGAG 57.513 32.000 0.00 0.00 43.24 3.02
1920 1948 9.877178 AGACGATGATTAAGTTCATACTCTTTT 57.123 29.630 0.00 0.00 36.48 2.27
1921 1949 9.307121 CAGACGATGATTAAGTTCATACTCTTT 57.693 33.333 0.00 0.00 36.48 2.52
1922 1950 8.470805 ACAGACGATGATTAAGTTCATACTCTT 58.529 33.333 0.00 0.00 36.48 2.85
1923 1951 8.001881 ACAGACGATGATTAAGTTCATACTCT 57.998 34.615 0.00 0.00 36.48 3.24
1924 1952 7.380065 GGACAGACGATGATTAAGTTCATACTC 59.620 40.741 0.00 0.00 36.48 2.59
1946 1974 2.154798 CTTTCGCACGGGAGAGGACA 62.155 60.000 0.00 0.00 0.00 4.02
1970 2026 2.648059 GTGCATTCATAAGGGTGAGCT 58.352 47.619 0.00 0.00 0.00 4.09
1971 2027 1.331756 CGTGCATTCATAAGGGTGAGC 59.668 52.381 0.00 0.00 0.00 4.26
1979 2035 0.179202 GCGTGTGCGTGCATTCATAA 60.179 50.000 0.00 0.00 40.81 1.90
1995 2051 6.827727 AGATTCTTATAAATGTAGGGTGCGT 58.172 36.000 0.00 0.00 0.00 5.24
1997 2053 6.369065 CGGAGATTCTTATAAATGTAGGGTGC 59.631 42.308 0.00 0.00 0.00 5.01
2006 2062 8.698973 TCAGTCTCTCGGAGATTCTTATAAAT 57.301 34.615 8.39 0.00 40.98 1.40
2008 2064 6.205853 GCTCAGTCTCTCGGAGATTCTTATAA 59.794 42.308 8.39 0.00 40.98 0.98
2012 2068 2.687935 GCTCAGTCTCTCGGAGATTCTT 59.312 50.000 8.39 0.00 40.98 2.52
2015 2071 1.398692 GGCTCAGTCTCTCGGAGATT 58.601 55.000 8.39 0.93 40.98 2.40
2017 2073 1.450491 CGGCTCAGTCTCTCGGAGA 60.450 63.158 7.60 7.60 40.01 3.71
2021 2077 1.135731 GTGTCGGCTCAGTCTCTCG 59.864 63.158 0.00 0.00 0.00 4.04
2022 2078 0.814457 ATGTGTCGGCTCAGTCTCTC 59.186 55.000 0.00 0.00 0.00 3.20
2027 2083 1.189752 AGATGATGTGTCGGCTCAGT 58.810 50.000 0.00 0.00 0.00 3.41
2034 2090 7.704789 TCATTAATCTCAAGATGATGTGTCG 57.295 36.000 12.59 0.00 34.49 4.35
2036 2092 9.107177 GACTTCATTAATCTCAAGATGATGTGT 57.893 33.333 8.00 12.32 37.16 3.72
2052 2108 7.518211 CGGATGCGTTTATGATGACTTCATTAA 60.518 37.037 8.94 4.28 42.62 1.40
2054 2110 5.277490 CGGATGCGTTTATGATGACTTCATT 60.277 40.000 8.94 0.00 42.62 2.57
2062 2118 4.048504 TGACTACGGATGCGTTTATGATG 58.951 43.478 19.82 2.75 0.00 3.07
2063 2119 4.316205 TGACTACGGATGCGTTTATGAT 57.684 40.909 19.82 0.00 0.00 2.45
2064 2120 3.786516 TGACTACGGATGCGTTTATGA 57.213 42.857 19.82 0.00 0.00 2.15
2072 2128 4.110482 ACGTTCTTATTGACTACGGATGC 58.890 43.478 0.00 0.00 34.32 3.91
2074 2130 5.221009 GGAGACGTTCTTATTGACTACGGAT 60.221 44.000 0.00 0.00 34.32 4.18
2076 2132 4.096081 AGGAGACGTTCTTATTGACTACGG 59.904 45.833 0.00 0.00 34.32 4.02
2080 2136 6.433404 TCAGTTAGGAGACGTTCTTATTGACT 59.567 38.462 0.00 0.00 0.00 3.41
2084 2140 6.091437 CGTTCAGTTAGGAGACGTTCTTATT 58.909 40.000 0.00 0.00 0.00 1.40
2087 2143 3.856267 GCGTTCAGTTAGGAGACGTTCTT 60.856 47.826 0.00 0.00 0.00 2.52
2089 2145 1.984297 GCGTTCAGTTAGGAGACGTTC 59.016 52.381 0.00 0.00 0.00 3.95
2090 2146 1.338973 TGCGTTCAGTTAGGAGACGTT 59.661 47.619 0.00 0.00 0.00 3.99
2094 2150 2.415491 CGATGTGCGTTCAGTTAGGAGA 60.415 50.000 0.00 0.00 34.64 3.71
2108 2164 0.391130 TAGGTGTTCCAGCGATGTGC 60.391 55.000 0.00 0.00 46.98 4.57
2139 3773 8.034804 AGACTTCACACTTGTGCTTAAATTTTT 58.965 29.630 4.38 0.00 45.25 1.94
2145 3779 6.479001 GTCTTAGACTTCACACTTGTGCTTAA 59.521 38.462 4.94 0.00 45.25 1.85
2146 3780 5.983720 GTCTTAGACTTCACACTTGTGCTTA 59.016 40.000 4.94 0.00 45.25 3.09
2147 3781 4.811557 GTCTTAGACTTCACACTTGTGCTT 59.188 41.667 4.94 0.00 45.25 3.91
2153 3787 8.207545 AGATTTTGAGTCTTAGACTTCACACTT 58.792 33.333 16.60 0.00 43.53 3.16
2159 3793 7.279758 CCCATCAGATTTTGAGTCTTAGACTTC 59.720 40.741 16.60 9.37 43.53 3.01
2167 3801 3.618351 CAGCCCATCAGATTTTGAGTCT 58.382 45.455 0.00 0.00 39.68 3.24
2172 3806 3.008835 TCTCCAGCCCATCAGATTTTG 57.991 47.619 0.00 0.00 0.00 2.44
2173 3807 3.967467 ATCTCCAGCCCATCAGATTTT 57.033 42.857 0.00 0.00 0.00 1.82
2218 3853 3.321396 TGTGTACGTGAACCAACCTATGA 59.679 43.478 0.00 0.00 0.00 2.15
2221 3856 2.429971 TGTGTGTACGTGAACCAACCTA 59.570 45.455 0.00 0.00 0.00 3.08
2231 3866 3.243301 ACCTCAGTACTTGTGTGTACGTG 60.243 47.826 0.00 0.00 45.23 4.49
2232 3867 2.954318 ACCTCAGTACTTGTGTGTACGT 59.046 45.455 0.00 0.00 45.23 3.57
2238 3873 3.057456 GTCGATCACCTCAGTACTTGTGT 60.057 47.826 13.69 0.75 0.00 3.72
2241 3876 3.502920 GTGTCGATCACCTCAGTACTTG 58.497 50.000 0.00 0.00 40.84 3.16
2247 4215 1.517257 GGCGTGTCGATCACCTCAG 60.517 63.158 11.01 1.42 43.51 3.35
2265 4233 7.910162 CGGAGTACAAAATATTGACAGAAATGG 59.090 37.037 0.00 0.00 38.94 3.16
2274 4242 9.309516 GTTAGTCATCGGAGTACAAAATATTGA 57.690 33.333 0.00 0.00 38.94 2.57
2282 4250 6.096423 AGCAATAGTTAGTCATCGGAGTACAA 59.904 38.462 0.00 0.00 0.00 2.41
2292 4260 9.507329 TCAAGAGAAAAAGCAATAGTTAGTCAT 57.493 29.630 0.00 0.00 0.00 3.06
2319 4288 4.685924 CATCAACCATGGGAGCAAAATAC 58.314 43.478 18.09 0.00 0.00 1.89
2321 4290 3.899052 CATCAACCATGGGAGCAAAAT 57.101 42.857 18.09 0.00 0.00 1.82
2426 4509 8.753497 ATTTCAGGAGAGTAAGACTTTTGTTT 57.247 30.769 0.00 0.00 0.00 2.83
2436 4525 7.386299 CGGGAATCATTATTTCAGGAGAGTAAG 59.614 40.741 0.00 0.00 0.00 2.34
2462 4551 2.660189 TACCCGGACACGAAAGAATC 57.340 50.000 0.73 0.00 44.60 2.52
2537 4627 4.764050 TGGATGGACGGCTCTTATTTTA 57.236 40.909 0.00 0.00 0.00 1.52
2544 4634 1.078143 GCTTTGGATGGACGGCTCT 60.078 57.895 0.00 0.00 0.00 4.09
2574 4664 2.893489 GGCCATGACCTCTTTGTTTTCT 59.107 45.455 0.00 0.00 0.00 2.52
2604 4714 2.894919 GCCCGCAATGCCTTTGAT 59.105 55.556 0.00 0.00 37.53 2.57
2608 4718 3.443045 CTTCGCCCGCAATGCCTT 61.443 61.111 0.00 0.00 0.00 4.35
2611 4721 4.481112 CACCTTCGCCCGCAATGC 62.481 66.667 0.00 0.00 0.00 3.56
2633 4743 2.223021 CGGATGCACATGTTAACCTTCG 60.223 50.000 2.48 0.00 0.00 3.79
2663 4773 0.254178 CACCCTCACATGCTAGCCTT 59.746 55.000 13.29 0.00 0.00 4.35
2665 4775 1.821332 GCACCCTCACATGCTAGCC 60.821 63.158 13.29 0.00 38.84 3.93
2715 6860 5.441500 TGCGATTATTTTGGGGATTGACTA 58.558 37.500 0.00 0.00 0.00 2.59
2720 6865 3.244181 GGCATGCGATTATTTTGGGGATT 60.244 43.478 12.44 0.00 0.00 3.01
2721 6866 2.299867 GGCATGCGATTATTTTGGGGAT 59.700 45.455 12.44 0.00 0.00 3.85
2742 6887 6.607735 TTTCTACCGTCTTTTAGTTTGTGG 57.392 37.500 0.00 0.00 0.00 4.17
2756 6901 9.282569 ACGAAGACTATTCTATATTTCTACCGT 57.717 33.333 0.00 0.00 0.00 4.83
2780 7135 4.929808 AGTCAAACCACAATTCTAGCTACG 59.070 41.667 0.00 0.00 0.00 3.51
2830 7185 9.128404 AGTGAGACATGTATTATCATGCAAAAT 57.872 29.630 0.00 0.00 46.15 1.82
2864 7219 9.968743 CTTACGTAATTTGTACTTTGATCCTTC 57.031 33.333 8.76 0.00 0.00 3.46
2867 7222 8.385858 GTCCTTACGTAATTTGTACTTTGATCC 58.614 37.037 8.76 0.00 0.00 3.36
2902 7257 9.319060 AGATATTCTGCTATCTTTCCTGTATGA 57.681 33.333 0.00 0.00 35.39 2.15
2903 7258 9.585099 GAGATATTCTGCTATCTTTCCTGTATG 57.415 37.037 0.00 0.00 38.33 2.39
2924 7281 5.597806 ACGTTGTTGTCAAACTCAGAGATA 58.402 37.500 3.79 0.00 37.19 1.98
2941 7298 1.302511 GGCAGGTGATGGACGTTGT 60.303 57.895 0.00 0.00 0.00 3.32
2985 7342 5.495640 GGGGTGATCCATCATTCTATTCTC 58.504 45.833 0.00 0.00 39.30 2.87
3007 7364 1.165270 GTGTCAAATTCGGGTGAGGG 58.835 55.000 0.00 0.00 0.00 4.30
3018 7375 1.003580 AGTGATGGAGCCGTGTCAAAT 59.996 47.619 0.00 0.00 0.00 2.32
3019 7376 0.396435 AGTGATGGAGCCGTGTCAAA 59.604 50.000 0.00 0.00 0.00 2.69
3025 7382 1.270518 GCATATCAGTGATGGAGCCGT 60.271 52.381 16.15 0.00 0.00 5.68
3072 7429 2.612471 CGGCAATGGCTTCATTTTTGGA 60.612 45.455 5.02 0.00 38.92 3.53
3177 7536 2.289694 CGTGGTCTCCTCCTTCAATGTT 60.290 50.000 0.00 0.00 0.00 2.71
3198 7557 3.489355 TCATGGTTGATGGATGGCATAC 58.511 45.455 1.67 1.67 32.26 2.39
3199 7558 3.880168 TCATGGTTGATGGATGGCATA 57.120 42.857 0.00 0.00 32.26 3.14
3200 7559 2.696707 GTTCATGGTTGATGGATGGCAT 59.303 45.455 0.00 0.00 32.26 4.40
3236 7597 4.064388 TCTGCATCGACAACATCTGAAAA 58.936 39.130 0.00 0.00 0.00 2.29
3262 7623 3.776969 AGTTCAGGAGTGGATGCAGATTA 59.223 43.478 0.00 0.00 0.00 1.75
3281 7642 3.118531 ACATGGAGCTTGGGAGATAGTT 58.881 45.455 0.00 0.00 0.00 2.24
3351 7712 2.124570 CGGCATCCTTCTGGTGGG 60.125 66.667 0.00 0.00 34.23 4.61
3378 7742 9.647918 ATCTAGTCTGTTCAAGTAAGGATGATA 57.352 33.333 0.00 0.00 0.00 2.15
3423 7787 6.558014 ACTCTGATGAGATGATTGGTCCTATT 59.442 38.462 0.00 0.00 42.73 1.73
3488 7852 2.351924 AAACCCTCTTGGCTTCGGCA 62.352 55.000 0.00 0.00 43.96 5.69
3502 7866 3.202097 CACAATCCACCAAACAAAACCC 58.798 45.455 0.00 0.00 0.00 4.11
3503 7867 3.867857 ACACAATCCACCAAACAAAACC 58.132 40.909 0.00 0.00 0.00 3.27
3504 7868 3.549873 CGACACAATCCACCAAACAAAAC 59.450 43.478 0.00 0.00 0.00 2.43
3505 7869 3.429547 CCGACACAATCCACCAAACAAAA 60.430 43.478 0.00 0.00 0.00 2.44
3506 7870 2.099921 CCGACACAATCCACCAAACAAA 59.900 45.455 0.00 0.00 0.00 2.83
3507 7871 1.678627 CCGACACAATCCACCAAACAA 59.321 47.619 0.00 0.00 0.00 2.83
3508 7872 1.134068 TCCGACACAATCCACCAAACA 60.134 47.619 0.00 0.00 0.00 2.83
3509 7873 1.600023 TCCGACACAATCCACCAAAC 58.400 50.000 0.00 0.00 0.00 2.93
3510 7874 1.950909 GTTCCGACACAATCCACCAAA 59.049 47.619 0.00 0.00 0.00 3.28
3511 7875 1.600023 GTTCCGACACAATCCACCAA 58.400 50.000 0.00 0.00 0.00 3.67
3512 7876 0.601576 CGTTCCGACACAATCCACCA 60.602 55.000 0.00 0.00 0.00 4.17
3513 7877 1.296056 CCGTTCCGACACAATCCACC 61.296 60.000 0.00 0.00 0.00 4.61
3514 7878 0.320073 TCCGTTCCGACACAATCCAC 60.320 55.000 0.00 0.00 0.00 4.02
3515 7879 0.320073 GTCCGTTCCGACACAATCCA 60.320 55.000 0.00 0.00 32.74 3.41
3516 7880 0.320073 TGTCCGTTCCGACACAATCC 60.320 55.000 0.00 0.00 37.85 3.01
3517 7881 1.393539 CATGTCCGTTCCGACACAATC 59.606 52.381 0.00 0.00 45.19 2.67
3518 7882 1.438651 CATGTCCGTTCCGACACAAT 58.561 50.000 0.00 0.00 45.19 2.71
3519 7883 1.225376 GCATGTCCGTTCCGACACAA 61.225 55.000 0.00 0.00 45.19 3.33
3520 7884 1.666553 GCATGTCCGTTCCGACACA 60.667 57.895 0.00 0.00 45.19 3.72
3521 7885 2.726691 CGCATGTCCGTTCCGACAC 61.727 63.158 0.00 0.00 45.19 3.67
3522 7886 2.431771 CGCATGTCCGTTCCGACA 60.432 61.111 0.00 0.00 46.36 4.35
3523 7887 2.431942 ACGCATGTCCGTTCCGAC 60.432 61.111 0.00 0.00 38.47 4.79


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

AutoCloner maintained by Alex Coulton.