Multiple sequence alignment - TraesCS7B01G346500

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 TraesCS7B01G346500 chr7B 100.000 4153 0 0 1 4153 602303636 602299484 0.000000e+00 7670.0
1 TraesCS7B01G346500 chr7B 86.093 755 60 19 1681 2434 670778377 670777667 0.000000e+00 771.0
2 TraesCS7B01G346500 chr7B 89.241 316 24 7 1931 2246 648774874 648774569 1.810000e-103 387.0
3 TraesCS7B01G346500 chr7B 79.842 253 43 7 331 580 689964297 689964050 1.190000e-40 178.0
4 TraesCS7B01G346500 chr7B 88.660 97 7 4 3766 3859 522328507 522328412 9.430000e-22 115.0
5 TraesCS7B01G346500 chr7B 89.286 84 8 1 3761 3843 100382392 100382309 2.040000e-18 104.0
6 TraesCS7B01G346500 chr7D 87.882 3078 213 77 5 3018 554562521 554565502 0.000000e+00 3470.0
7 TraesCS7B01G346500 chr7D 87.871 775 41 19 3012 3746 554565571 554566332 0.000000e+00 861.0
8 TraesCS7B01G346500 chr7D 93.355 301 20 0 3853 4153 554566844 554567144 2.950000e-121 446.0
9 TraesCS7B01G346500 chr7D 86.842 76 8 2 3632 3705 447133078 447133153 2.660000e-12 84.2
10 TraesCS7B01G346500 chr7A 86.012 815 76 27 626 1427 641428816 641428027 0.000000e+00 839.0
11 TraesCS7B01G346500 chr7A 84.795 855 76 33 1461 2308 641428027 641427220 0.000000e+00 809.0
12 TraesCS7B01G346500 chr7A 87.040 679 53 16 2305 2969 641426899 641426242 0.000000e+00 734.0
13 TraesCS7B01G346500 chr7A 90.686 408 24 7 3012 3409 641426045 641425642 7.910000e-147 531.0
14 TraesCS7B01G346500 chr7A 86.792 371 30 8 1875 2245 711201188 711200837 3.010000e-106 396.0
15 TraesCS7B01G346500 chr7A 77.062 388 65 19 243 618 591874320 591874695 7.040000e-48 202.0
16 TraesCS7B01G346500 chr4A 87.332 371 27 8 1875 2245 448763482 448763132 1.390000e-109 407.0
17 TraesCS7B01G346500 chr4A 76.115 314 61 12 311 615 595400446 595400138 7.190000e-33 152.0
18 TraesCS7B01G346500 chr4A 84.375 96 12 3 3761 3854 695116239 695116333 1.590000e-14 91.6
19 TraesCS7B01G346500 chr3A 87.166 374 29 7 1872 2245 299758672 299759026 1.390000e-109 407.0
20 TraesCS7B01G346500 chr3A 88.889 117 11 1 3436 3550 57888358 57888474 4.330000e-30 143.0
21 TraesCS7B01G346500 chr3A 86.458 96 11 2 3762 3855 44305535 44305440 2.040000e-18 104.0
22 TraesCS7B01G346500 chr3A 92.958 71 3 2 3637 3705 538858263 538858333 7.350000e-18 102.0
23 TraesCS7B01G346500 chr3A 87.671 73 7 1 3634 3704 743837299 743837371 2.660000e-12 84.2
24 TraesCS7B01G346500 chr2A 87.332 371 28 7 1875 2245 39493859 39493508 1.390000e-109 407.0
25 TraesCS7B01G346500 chr2A 87.166 374 29 7 1872 2245 755547830 755548184 1.390000e-109 407.0
26 TraesCS7B01G346500 chr2A 86.735 98 8 5 3766 3859 161623684 161623780 2.040000e-18 104.0
27 TraesCS7B01G346500 chr2A 81.667 120 18 3 461 579 748435942 748436058 3.420000e-16 97.1
28 TraesCS7B01G346500 chr2B 86.792 371 30 8 1875 2245 281069231 281068880 3.010000e-106 396.0
29 TraesCS7B01G346500 chr2B 90.217 92 5 4 3771 3859 93768320 93768230 2.620000e-22 117.0
30 TraesCS7B01G346500 chr4D 80.822 146 25 2 435 579 96628373 96628516 1.220000e-20 111.0
31 TraesCS7B01G346500 chr4D 90.361 83 6 2 3625 3705 322661543 322661461 1.580000e-19 108.0
32 TraesCS7B01G346500 chr4D 91.358 81 2 3 3625 3700 47492617 47492697 5.680000e-19 106.0
33 TraesCS7B01G346500 chr6B 96.923 65 2 0 3766 3830 457776930 457776994 4.390000e-20 110.0
34 TraesCS7B01G346500 chr6B 86.458 96 10 3 3767 3859 14774433 14774528 7.350000e-18 102.0
35 TraesCS7B01G346500 chr6B 74.744 293 37 25 210 488 150770944 150771213 3.420000e-16 97.1
36 TraesCS7B01G346500 chrUn 90.361 83 6 2 3625 3705 92510152 92510234 1.580000e-19 108.0
37 TraesCS7B01G346500 chr4B 80.435 138 25 1 435 572 116485921 116486056 2.040000e-18 104.0
38 TraesCS7B01G346500 chr4B 72.105 380 85 20 210 581 4545392 4545758 1.230000e-15 95.3
39 TraesCS7B01G346500 chr5A 86.957 92 9 3 3771 3859 692700910 692700819 2.640000e-17 100.0
40 TraesCS7B01G346500 chr3B 91.781 73 3 3 3636 3705 538815448 538815376 9.500000e-17 99.0
41 TraesCS7B01G346500 chr2D 86.517 89 10 2 3619 3705 408459898 408459810 3.420000e-16 97.1
42 TraesCS7B01G346500 chr6D 81.197 117 18 4 457 572 39070174 39070287 1.590000e-14 91.6
43 TraesCS7B01G346500 chr1B 86.842 76 6 3 3634 3705 127981744 127981819 9.570000e-12 82.4
44 TraesCS7B01G346500 chr5D 93.023 43 0 3 435 475 215879421 215879380 4.480000e-05 60.2


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 TraesCS7B01G346500 chr7B 602299484 602303636 4152 True 7670.000000 7670 100.000000 1 4153 1 chr7B.!!$R3 4152
1 TraesCS7B01G346500 chr7B 670777667 670778377 710 True 771.000000 771 86.093000 1681 2434 1 chr7B.!!$R5 753
2 TraesCS7B01G346500 chr7D 554562521 554567144 4623 False 1592.333333 3470 89.702667 5 4153 3 chr7D.!!$F2 4148
3 TraesCS7B01G346500 chr7A 641425642 641428816 3174 True 728.250000 839 87.133250 626 3409 4 chr7A.!!$R2 2783


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
692 730 0.598158 TCGGAAACCACGAAGGAACG 60.598 55.0 5.7 0.0 41.22 3.95 F
1230 1276 0.340208 CCACCTCCCCTCTCCTACTT 59.660 60.0 0.0 0.0 0.00 2.24 F
1851 1912 0.469917 AGGGTGTCAGATTATGCCGG 59.530 55.0 0.0 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2532 2931 0.172578 TTGTGTATCTCTCGCCGTGG 59.827 55.0 0.00 0.0 0.0 4.94 R
2641 3040 0.250234 ATGGATGCGCTACACACTGT 59.750 50.0 9.73 0.0 0.0 3.55 R
3612 4201 0.179056 CACTATGGATTTCGGGCGGT 60.179 55.0 0.00 0.0 0.0 5.68 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
24 25 4.114997 CGCCGCCGCCTCATTTTT 62.115 61.111 0.00 0.00 0.00 1.94
26 27 2.700773 GCCGCCGCCTCATTTTTCT 61.701 57.895 0.00 0.00 0.00 2.52
32 33 2.747446 GCCGCCTCATTTTTCTGAGTAA 59.253 45.455 0.89 0.00 40.91 2.24
106 107 9.017509 AGAATTTCAATCAATGTAAAGCAGAGA 57.982 29.630 0.00 0.00 0.00 3.10
107 108 9.630098 GAATTTCAATCAATGTAAAGCAGAGAA 57.370 29.630 0.00 0.00 0.00 2.87
124 144 9.944376 AAGCAGAGAATAGTAACAATTTGACTA 57.056 29.630 2.79 2.14 0.00 2.59
139 159 9.823647 ACAATTTGACTATACACCATTCTAGAG 57.176 33.333 2.79 0.00 0.00 2.43
205 226 8.641499 TTACAACCTTTGATTTTGAATCACAC 57.359 30.769 3.01 0.00 0.00 3.82
207 228 6.757947 ACAACCTTTGATTTTGAATCACACAG 59.242 34.615 3.01 1.29 0.00 3.66
208 229 6.713762 ACCTTTGATTTTGAATCACACAGA 57.286 33.333 3.01 0.00 0.00 3.41
209 230 6.742109 ACCTTTGATTTTGAATCACACAGAG 58.258 36.000 3.01 0.00 0.00 3.35
221 242 3.994317 TCACACAGAGGGGAGAATATCA 58.006 45.455 0.00 0.00 0.00 2.15
222 243 4.560739 TCACACAGAGGGGAGAATATCAT 58.439 43.478 0.00 0.00 0.00 2.45
228 249 3.582208 AGAGGGGAGAATATCATGTGCTC 59.418 47.826 0.00 0.00 0.00 4.26
240 261 2.181975 CATGTGCTCCCATCCCTTTTT 58.818 47.619 0.00 0.00 0.00 1.94
241 262 1.923356 TGTGCTCCCATCCCTTTTTC 58.077 50.000 0.00 0.00 0.00 2.29
256 277 4.821805 CCCTTTTTCGTGCTACCATGATAT 59.178 41.667 0.00 0.00 36.89 1.63
258 279 5.527214 CCTTTTTCGTGCTACCATGATATCA 59.473 40.000 8.10 8.10 36.89 2.15
265 286 6.424812 TCGTGCTACCATGATATCATTTCAAG 59.575 38.462 15.74 11.42 33.61 3.02
266 287 6.424812 CGTGCTACCATGATATCATTTCAAGA 59.575 38.462 15.74 0.00 33.61 3.02
328 350 2.803203 ATGCCCACATCACATGAGC 58.197 52.632 0.00 0.00 0.00 4.26
337 359 3.433274 CACATCACATGAGCGTACAACTT 59.567 43.478 0.00 0.00 0.00 2.66
408 432 6.032094 GGACAAATCAAGCATGAATAGTGTG 58.968 40.000 0.00 0.00 39.49 3.82
409 433 6.349611 GGACAAATCAAGCATGAATAGTGTGT 60.350 38.462 0.00 0.00 39.49 3.72
412 436 5.808042 ATCAAGCATGAATAGTGTGTCAC 57.192 39.130 0.00 0.00 39.49 3.67
413 437 3.679502 TCAAGCATGAATAGTGTGTCACG 59.320 43.478 0.00 0.00 34.22 4.35
415 439 3.515630 AGCATGAATAGTGTGTCACGAG 58.484 45.455 0.00 0.00 39.64 4.18
416 440 3.193479 AGCATGAATAGTGTGTCACGAGA 59.807 43.478 0.00 0.00 39.64 4.04
417 441 3.926527 GCATGAATAGTGTGTCACGAGAA 59.073 43.478 0.00 0.00 39.64 2.87
458 482 7.530010 CCACTATTCACATTCGATTTTGTCTT 58.470 34.615 0.00 0.00 0.00 3.01
459 483 7.693951 CCACTATTCACATTCGATTTTGTCTTC 59.306 37.037 0.00 0.00 0.00 2.87
507 539 7.466746 TTTTGGACCTGAAATTTCTATGAGG 57.533 36.000 18.64 17.62 0.00 3.86
519 551 5.339008 TTTCTATGAGGTGTAGCGACATT 57.661 39.130 2.07 0.00 38.04 2.71
521 553 4.207955 TCTATGAGGTGTAGCGACATTCT 58.792 43.478 2.07 4.27 38.04 2.40
523 555 3.232213 TGAGGTGTAGCGACATTCTTC 57.768 47.619 2.07 0.00 38.04 2.87
530 562 1.060713 AGCGACATTCTTCGTGAACG 58.939 50.000 0.00 0.00 41.26 3.95
611 649 2.007608 GGAGCATTTCGGAGTTGGTAC 58.992 52.381 0.00 0.00 0.00 3.34
624 662 2.124507 TTGGTACCACCTGCTGGAGC 62.125 60.000 16.04 3.98 43.95 4.70
692 730 0.598158 TCGGAAACCACGAAGGAACG 60.598 55.000 5.70 0.00 41.22 3.95
756 794 1.212616 CTCCTCTCATAAAAGCGGCG 58.787 55.000 0.51 0.51 0.00 6.46
760 798 1.062525 CTCATAAAAGCGGCGCCAC 59.937 57.895 30.40 18.62 0.00 5.01
762 800 2.360600 ATAAAAGCGGCGCCACCA 60.361 55.556 30.40 12.53 39.03 4.17
763 801 1.752694 ATAAAAGCGGCGCCACCAT 60.753 52.632 30.40 14.42 39.03 3.55
764 802 1.724582 ATAAAAGCGGCGCCACCATC 61.725 55.000 30.40 9.37 39.03 3.51
774 812 1.451028 GCCACCATCCACTCTCTGC 60.451 63.158 0.00 0.00 0.00 4.26
799 837 3.695606 GCCAGAGTCCACGCTCCA 61.696 66.667 0.00 0.00 36.20 3.86
836 874 1.222113 CTTTCTCCGCCCTTCTCCC 59.778 63.158 0.00 0.00 0.00 4.30
849 892 3.238497 CTCCCCCGTGACACCACA 61.238 66.667 0.00 0.00 43.34 4.17
853 896 2.280797 CCCGTGACACCACACCAG 60.281 66.667 0.00 0.00 43.34 4.00
859 902 1.000283 GTGACACCACACCAGAGAGAG 60.000 57.143 0.00 0.00 42.72 3.20
869 912 3.198635 ACACCAGAGAGAGAGAGAGAGAG 59.801 52.174 0.00 0.00 0.00 3.20
885 928 3.157217 GAGAGATGGCGATGCGGGT 62.157 63.158 0.00 0.00 0.00 5.28
1207 1251 0.395724 CTGCCCCAGTAATTCACCCC 60.396 60.000 0.00 0.00 0.00 4.95
1213 1257 1.926489 AGTAATTCACCCCGCCCCA 60.926 57.895 0.00 0.00 0.00 4.96
1227 1273 2.333462 CCCCACCTCCCCTCTCCTA 61.333 68.421 0.00 0.00 0.00 2.94
1230 1276 0.340208 CCACCTCCCCTCTCCTACTT 59.660 60.000 0.00 0.00 0.00 2.24
1233 1279 2.502130 CACCTCCCCTCTCCTACTTTTC 59.498 54.545 0.00 0.00 0.00 2.29
1235 1283 3.181394 ACCTCCCCTCTCCTACTTTTCTT 60.181 47.826 0.00 0.00 0.00 2.52
1236 1284 3.847184 CCTCCCCTCTCCTACTTTTCTTT 59.153 47.826 0.00 0.00 0.00 2.52
1237 1285 4.323868 CCTCCCCTCTCCTACTTTTCTTTG 60.324 50.000 0.00 0.00 0.00 2.77
1238 1286 3.587506 TCCCCTCTCCTACTTTTCTTTGG 59.412 47.826 0.00 0.00 0.00 3.28
1239 1287 3.587506 CCCCTCTCCTACTTTTCTTTGGA 59.412 47.826 0.00 0.00 0.00 3.53
1240 1288 4.042934 CCCCTCTCCTACTTTTCTTTGGAA 59.957 45.833 0.00 0.00 0.00 3.53
1266 1314 2.590007 GCGCGGAATGCTCTCCAT 60.590 61.111 8.83 0.00 43.27 3.41
1267 1315 2.890109 GCGCGGAATGCTCTCCATG 61.890 63.158 8.83 0.00 43.27 3.66
1270 1318 1.098050 GCGGAATGCTCTCCATGTTT 58.902 50.000 5.63 0.00 41.73 2.83
1271 1319 1.474077 GCGGAATGCTCTCCATGTTTT 59.526 47.619 5.63 0.00 41.73 2.43
1272 1320 2.682856 GCGGAATGCTCTCCATGTTTTA 59.317 45.455 5.63 0.00 41.73 1.52
1273 1321 3.316308 GCGGAATGCTCTCCATGTTTTAT 59.684 43.478 5.63 0.00 41.73 1.40
1274 1322 4.202050 GCGGAATGCTCTCCATGTTTTATT 60.202 41.667 5.63 0.00 41.73 1.40
1277 1325 7.479980 CGGAATGCTCTCCATGTTTTATTTTA 58.520 34.615 5.63 0.00 34.91 1.52
1278 1326 7.645340 CGGAATGCTCTCCATGTTTTATTTTAG 59.355 37.037 5.63 0.00 34.91 1.85
1325 1375 5.502079 TCCGGTTTAGGATTTGATTTGCTA 58.498 37.500 0.00 0.00 34.92 3.49
1329 1379 6.458342 CGGTTTAGGATTTGATTTGCTAGGAC 60.458 42.308 0.00 0.00 0.00 3.85
1331 1381 4.870021 AGGATTTGATTTGCTAGGACCT 57.130 40.909 0.00 0.00 0.00 3.85
1351 1401 6.183360 GGACCTGTTAATTGTAGATGCTGAAC 60.183 42.308 0.00 0.00 0.00 3.18
1404 1457 4.840401 TTACTGCTGAATTTCGTGATCG 57.160 40.909 0.00 0.00 38.55 3.69
1412 1465 5.718649 TGAATTTCGTGATCGATCTTTCC 57.281 39.130 25.02 10.18 45.65 3.13
1456 1509 3.603965 AGATGTAGGCTAGTAGGCAGT 57.396 47.619 24.23 8.45 44.19 4.40
1457 1510 4.726035 AGATGTAGGCTAGTAGGCAGTA 57.274 45.455 24.23 10.69 44.19 2.74
1458 1511 5.263872 AGATGTAGGCTAGTAGGCAGTAT 57.736 43.478 24.23 14.54 44.19 2.12
1459 1512 5.646215 AGATGTAGGCTAGTAGGCAGTATT 58.354 41.667 24.23 7.04 44.19 1.89
1549 1604 8.998814 TCTGTTATCCAGGTAATAGGAAATTGA 58.001 33.333 0.00 0.00 41.83 2.57
1563 1618 9.525826 AATAGGAAATTGATTGATCCTGATACC 57.474 33.333 4.64 0.00 42.20 2.73
1564 1619 7.159201 AGGAAATTGATTGATCCTGATACCT 57.841 36.000 0.00 0.00 40.73 3.08
1565 1620 7.002879 AGGAAATTGATTGATCCTGATACCTG 58.997 38.462 0.00 0.00 40.73 4.00
1569 1624 3.969312 TGATTGATCCTGATACCTGCTCA 59.031 43.478 0.00 0.00 0.00 4.26
1576 1631 4.579869 TCCTGATACCTGCTCAAAGAAAC 58.420 43.478 0.00 0.00 0.00 2.78
1595 1650 2.243810 ACCCCGGTACTTACGTTTACA 58.756 47.619 0.00 0.00 0.00 2.41
1614 1669 2.674357 ACACGTTTGTTACTTCGTTGCT 59.326 40.909 0.00 0.00 34.30 3.91
1653 1709 3.820777 GTCTTCAGCAATTCTGTGACC 57.179 47.619 14.49 0.00 43.32 4.02
1684 1741 7.420800 CATCAAATGGCTGTATAGAAGGAAAC 58.579 38.462 0.00 0.00 0.00 2.78
1687 1744 7.615365 TCAAATGGCTGTATAGAAGGAAACAAT 59.385 33.333 0.00 0.00 0.00 2.71
1815 1876 6.703607 CCAGATGTGGTGCTAATCTTAGTTAG 59.296 42.308 0.00 0.00 39.30 2.34
1816 1877 7.268586 CAGATGTGGTGCTAATCTTAGTTAGT 58.731 38.462 0.00 0.00 34.80 2.24
1817 1878 8.414003 CAGATGTGGTGCTAATCTTAGTTAGTA 58.586 37.037 0.00 0.00 34.80 1.82
1828 1889 9.745880 CTAATCTTAGTTAGTAAATCCAGCGAA 57.254 33.333 0.00 0.00 0.00 4.70
1845 1906 5.116180 CAGCGAATTTAGGGTGTCAGATTA 58.884 41.667 0.00 0.00 0.00 1.75
1847 1908 5.760253 AGCGAATTTAGGGTGTCAGATTATG 59.240 40.000 0.00 0.00 0.00 1.90
1848 1909 5.560953 GCGAATTTAGGGTGTCAGATTATGC 60.561 44.000 0.00 0.00 0.00 3.14
1849 1910 5.049405 CGAATTTAGGGTGTCAGATTATGCC 60.049 44.000 0.00 0.00 0.00 4.40
1850 1911 3.469008 TTAGGGTGTCAGATTATGCCG 57.531 47.619 0.00 0.00 0.00 5.69
1851 1912 0.469917 AGGGTGTCAGATTATGCCGG 59.530 55.000 0.00 0.00 0.00 6.13
1853 1914 1.408266 GGGTGTCAGATTATGCCGGTT 60.408 52.381 1.90 0.00 0.00 4.44
1854 1915 2.365582 GGTGTCAGATTATGCCGGTTT 58.634 47.619 1.90 0.00 0.00 3.27
1855 1916 3.537580 GGTGTCAGATTATGCCGGTTTA 58.462 45.455 1.90 0.00 0.00 2.01
1856 1917 3.942748 GGTGTCAGATTATGCCGGTTTAA 59.057 43.478 1.90 1.63 0.00 1.52
1857 1918 4.578928 GGTGTCAGATTATGCCGGTTTAAT 59.421 41.667 1.90 7.03 0.00 1.40
1858 1919 5.761234 GGTGTCAGATTATGCCGGTTTAATA 59.239 40.000 1.90 0.00 0.00 0.98
1859 1920 6.430000 GGTGTCAGATTATGCCGGTTTAATAT 59.570 38.462 1.90 1.53 0.00 1.28
1860 1921 7.604927 GGTGTCAGATTATGCCGGTTTAATATA 59.395 37.037 1.90 0.00 0.00 0.86
1861 1922 8.995220 GTGTCAGATTATGCCGGTTTAATATAA 58.005 33.333 1.90 0.02 0.00 0.98
1862 1923 8.995220 TGTCAGATTATGCCGGTTTAATATAAC 58.005 33.333 1.90 1.70 0.00 1.89
1863 1924 8.995220 GTCAGATTATGCCGGTTTAATATAACA 58.005 33.333 1.90 0.00 0.00 2.41
1864 1925 9.733556 TCAGATTATGCCGGTTTAATATAACAT 57.266 29.630 1.90 0.00 0.00 2.71
1870 1931 8.685838 ATGCCGGTTTAATATAACATAGTTGT 57.314 30.769 1.90 0.00 37.82 3.32
1873 1934 8.400186 GCCGGTTTAATATAACATAGTTGTTGT 58.600 33.333 1.90 0.00 45.56 3.32
1881 1942 8.934023 ATATAACATAGTTGTTGTTATGGGGG 57.066 34.615 15.68 0.00 45.31 5.40
1883 1944 4.340617 ACATAGTTGTTGTTATGGGGGTG 58.659 43.478 0.00 0.00 32.76 4.61
1936 1997 6.864165 TGTTTTATCCATTTTACTTTGCGGTC 59.136 34.615 0.00 0.00 0.00 4.79
1944 2005 5.482686 TTTTACTTTGCGGTCGTTAAACT 57.517 34.783 0.00 0.00 0.00 2.66
2030 2091 2.331194 GCAGTAGCTGGCATTTTGTTG 58.669 47.619 0.00 0.00 37.91 3.33
2031 2092 2.030007 GCAGTAGCTGGCATTTTGTTGA 60.030 45.455 0.00 0.00 37.91 3.18
2034 2095 3.503748 AGTAGCTGGCATTTTGTTGAGAC 59.496 43.478 0.00 0.00 0.00 3.36
2035 2096 1.267806 AGCTGGCATTTTGTTGAGACG 59.732 47.619 0.00 0.00 0.00 4.18
2044 2105 6.370593 GCATTTTGTTGAGACGATTTCAGTA 58.629 36.000 0.00 0.00 0.00 2.74
2045 2106 6.303259 GCATTTTGTTGAGACGATTTCAGTAC 59.697 38.462 0.00 0.00 0.00 2.73
2088 2149 6.040247 TGCTGATCTCATTGCATTTTCAATC 58.960 36.000 0.00 0.00 34.68 2.67
2099 2160 1.337118 TTTTCAATCCACAGGCACCC 58.663 50.000 0.00 0.00 0.00 4.61
2126 2187 3.519913 GACCAAGTCTCCTCCAGGTAATT 59.480 47.826 0.00 0.00 36.34 1.40
2127 2188 4.695606 ACCAAGTCTCCTCCAGGTAATTA 58.304 43.478 0.00 0.00 36.34 1.40
2128 2189 5.098663 ACCAAGTCTCCTCCAGGTAATTAA 58.901 41.667 0.00 0.00 36.34 1.40
2129 2190 5.731678 ACCAAGTCTCCTCCAGGTAATTAAT 59.268 40.000 0.00 0.00 36.34 1.40
2133 2194 9.930693 CAAGTCTCCTCCAGGTAATTAATATAC 57.069 37.037 0.00 0.00 36.34 1.47
2140 2201 7.310485 CCTCCAGGTAATTAATATACGCCTCTT 60.310 40.741 0.00 0.00 0.00 2.85
2143 2204 9.530633 CCAGGTAATTAATATACGCCTCTTATC 57.469 37.037 0.00 0.00 0.00 1.75
2286 2351 2.489285 GCGGCGGCAAATTGATGA 59.511 55.556 9.78 0.00 39.62 2.92
2290 2355 1.322538 GGCGGCAAATTGATGAGGGT 61.323 55.000 3.07 0.00 0.00 4.34
2294 2359 2.170166 GGCAAATTGATGAGGGTCACA 58.830 47.619 0.00 0.00 0.00 3.58
2354 2743 3.491964 GGTCGGTTATCGGATGATTGTGA 60.492 47.826 0.00 0.00 39.77 3.58
2363 2752 1.202110 GGATGATTGTGACTGCTTGCG 60.202 52.381 0.00 0.00 0.00 4.85
2375 2764 6.861572 TGTGACTGCTTGCGATTATACTATAC 59.138 38.462 0.00 0.00 0.00 1.47
2441 2840 3.255888 GTCATATGAGCATAGGACGTGGA 59.744 47.826 16.40 0.00 42.62 4.02
2488 2887 6.947644 TTTACTTTTGGGAAACTAGACACC 57.052 37.500 0.00 0.00 0.00 4.16
2504 2903 3.822607 ACCGCATGTGAGAAGAGTC 57.177 52.632 8.11 0.00 0.00 3.36
2523 2922 9.862371 GAAGAGTCAAGACATATTCAGACTTTA 57.138 33.333 2.72 0.00 40.20 1.85
2527 2926 7.978975 AGTCAAGACATATTCAGACTTTAGAGC 59.021 37.037 2.72 0.00 38.18 4.09
2532 2931 7.930865 AGACATATTCAGACTTTAGAGCCAATC 59.069 37.037 0.00 0.00 0.00 2.67
2535 2934 4.207891 TCAGACTTTAGAGCCAATCCAC 57.792 45.455 0.00 0.00 0.00 4.02
2601 3000 1.271856 TTCCGTCAGGCATGTAAGGA 58.728 50.000 0.00 3.19 37.47 3.36
2608 3007 4.321304 CGTCAGGCATGTAAGGATAGTAGG 60.321 50.000 0.00 0.00 0.00 3.18
2638 3037 2.885135 AGGATTGATGTGGACAAGCA 57.115 45.000 0.00 0.00 35.71 3.91
2639 3038 2.440409 AGGATTGATGTGGACAAGCAC 58.560 47.619 0.00 0.00 35.71 4.40
2640 3039 1.474077 GGATTGATGTGGACAAGCACC 59.526 52.381 0.00 0.00 35.71 5.01
2641 3040 2.161855 GATTGATGTGGACAAGCACCA 58.838 47.619 0.00 0.00 34.43 4.17
2669 3068 0.666913 AGCGCATCCATTTGCAGATC 59.333 50.000 11.47 0.00 42.91 2.75
2674 3073 1.335810 CATCCATTTGCAGATCGGGTG 59.664 52.381 5.12 5.12 0.00 4.61
2682 3081 3.558931 TGCAGATCGGGTGATTGTATT 57.441 42.857 0.00 0.00 34.09 1.89
2683 3082 3.884895 TGCAGATCGGGTGATTGTATTT 58.115 40.909 0.00 0.00 34.09 1.40
2714 3113 6.590068 TCCATTTGGAAACATGTTCATTTGT 58.410 32.000 12.39 0.00 42.18 2.83
2716 3115 8.373981 TCCATTTGGAAACATGTTCATTTGTAT 58.626 29.630 12.39 0.00 42.18 2.29
2717 3116 8.658609 CCATTTGGAAACATGTTCATTTGTATC 58.341 33.333 12.39 2.80 42.32 2.24
2718 3117 9.205719 CATTTGGAAACATGTTCATTTGTATCA 57.794 29.630 12.39 0.00 42.32 2.15
2734 3133 7.536895 TTTGTATCACAATAAATGCATTGCC 57.463 32.000 13.82 0.00 38.00 4.52
2819 3218 1.602668 CCTCACCAAACAACCGCAATG 60.603 52.381 0.00 0.00 0.00 2.82
2845 3244 4.391830 TGCAACTTTAGCATCGTTTAGGAG 59.608 41.667 0.00 0.00 37.02 3.69
2858 3257 3.502211 CGTTTAGGAGTTGGATGCAACTT 59.498 43.478 30.05 19.28 44.53 2.66
2859 3258 4.693566 CGTTTAGGAGTTGGATGCAACTTA 59.306 41.667 30.05 18.32 44.53 2.24
2860 3259 5.163854 CGTTTAGGAGTTGGATGCAACTTAG 60.164 44.000 30.05 14.28 44.53 2.18
2893 3292 2.143925 GCCTTGTTCCACTCACTGTAC 58.856 52.381 0.00 0.00 0.00 2.90
2901 3300 4.067972 TCCACTCACTGTACCTGAAAAC 57.932 45.455 0.00 0.00 0.00 2.43
2902 3301 3.139077 CCACTCACTGTACCTGAAAACC 58.861 50.000 0.00 0.00 0.00 3.27
2912 3311 4.942483 TGTACCTGAAAACCGAAACTGAAA 59.058 37.500 0.00 0.00 0.00 2.69
2950 3354 6.093404 GCCAGCATGATCATATTTTCTCATG 58.907 40.000 8.15 6.95 44.93 3.07
3005 3495 6.845302 TGATTATTAGCTCAAAACACAGCTG 58.155 36.000 13.48 13.48 45.81 4.24
3199 3785 9.809096 CTAGACATGTTCTTCTTTCAGCTTATA 57.191 33.333 0.00 0.00 35.55 0.98
3201 3787 9.323985 AGACATGTTCTTCTTTCAGCTTATATC 57.676 33.333 0.00 0.00 0.00 1.63
3202 3788 8.443953 ACATGTTCTTCTTTCAGCTTATATCC 57.556 34.615 0.00 0.00 0.00 2.59
3211 3799 4.226427 TCAGCTTATATCCATCCCATGC 57.774 45.455 0.00 0.00 0.00 4.06
3288 3877 2.360801 GCTGTGTATTGGTTGGTGTTGT 59.639 45.455 0.00 0.00 0.00 3.32
3290 3879 2.614520 TGTGTATTGGTTGGTGTTGTCG 59.385 45.455 0.00 0.00 0.00 4.35
3304 3893 3.734735 GTGTTGTCGGTTCAGTAGACTTC 59.265 47.826 0.00 0.00 36.01 3.01
3330 3919 5.105106 TGTGAATAAGGATTTCGGCACTCTA 60.105 40.000 0.00 0.00 0.00 2.43
3368 3957 1.065926 CAGAGCAGAGTGGGCATTGTA 60.066 52.381 0.00 0.00 0.00 2.41
3497 4086 4.207165 ACCAAAACAAGTCACAGCAGTAT 58.793 39.130 0.00 0.00 0.00 2.12
3537 4126 1.973281 ACAAGCGCCAACATCCAGG 60.973 57.895 2.29 0.00 0.00 4.45
3553 4142 7.443302 ACATCCAGGAATCAAGAGAGAAATA 57.557 36.000 0.00 0.00 0.00 1.40
3554 4143 7.507829 ACATCCAGGAATCAAGAGAGAAATAG 58.492 38.462 0.00 0.00 0.00 1.73
3555 4144 7.346698 ACATCCAGGAATCAAGAGAGAAATAGA 59.653 37.037 0.00 0.00 0.00 1.98
3556 4145 7.739995 TCCAGGAATCAAGAGAGAAATAGAA 57.260 36.000 0.00 0.00 0.00 2.10
3557 4146 7.560368 TCCAGGAATCAAGAGAGAAATAGAAC 58.440 38.462 0.00 0.00 0.00 3.01
3564 4153 7.316393 TCAAGAGAGAAATAGAACCAGGAAA 57.684 36.000 0.00 0.00 0.00 3.13
3595 4184 3.637769 GCCCCAGACCCATTTTACATAA 58.362 45.455 0.00 0.00 0.00 1.90
3600 4189 5.482175 CCCAGACCCATTTTACATAAAACCA 59.518 40.000 0.00 0.00 37.92 3.67
3601 4190 6.350949 CCCAGACCCATTTTACATAAAACCAG 60.351 42.308 0.00 0.00 37.92 4.00
3602 4191 6.350949 CCAGACCCATTTTACATAAAACCAGG 60.351 42.308 0.00 3.91 37.92 4.45
3605 4194 7.511028 AGACCCATTTTACATAAAACCAGGAAA 59.489 33.333 12.46 0.00 37.92 3.13
3607 4196 8.154203 ACCCATTTTACATAAAACCAGGAAAAG 58.846 33.333 12.46 2.70 37.92 2.27
3608 4197 7.606073 CCCATTTTACATAAAACCAGGAAAAGG 59.394 37.037 0.00 0.00 37.92 3.11
3609 4198 7.606073 CCATTTTACATAAAACCAGGAAAAGGG 59.394 37.037 0.00 0.00 37.92 3.95
3611 4200 3.582164 ACATAAAACCAGGAAAAGGGCA 58.418 40.909 0.00 0.00 0.00 5.36
3612 4201 3.970640 ACATAAAACCAGGAAAAGGGCAA 59.029 39.130 0.00 0.00 0.00 4.52
3613 4202 4.202315 ACATAAAACCAGGAAAAGGGCAAC 60.202 41.667 0.00 0.00 0.00 4.17
3648 4259 6.493802 TCCATAGTGGGAGTAACATAGATGAC 59.506 42.308 0.00 0.00 38.32 3.06
3692 4304 5.130975 TGGCAGCTAATTAATGAGGAGAGAA 59.869 40.000 1.84 0.00 0.00 2.87
3738 4350 7.595819 TTGTTCTGGTTTATTGGTCTTCATT 57.404 32.000 0.00 0.00 0.00 2.57
3795 4610 7.994425 TCACACATACCAATACAAAATGAGT 57.006 32.000 0.00 0.00 0.00 3.41
3874 4891 5.900437 TGAGTAGTCTAAAGAGGGGAGAAA 58.100 41.667 0.00 0.00 0.00 2.52
3877 4894 4.421574 AGTCTAAAGAGGGGAGAAAGGA 57.578 45.455 0.00 0.00 0.00 3.36
3910 4927 2.231235 GGCTGACAAAAGGGTTACATGG 59.769 50.000 0.00 0.00 0.00 3.66
3916 4933 5.359576 TGACAAAAGGGTTACATGGATATGC 59.640 40.000 0.00 0.00 37.85 3.14
3919 4936 1.165270 GGGTTACATGGATATGCGGC 58.835 55.000 0.00 0.00 37.85 6.53
3934 4951 1.153188 CGGCCACCATAGCATCACA 60.153 57.895 2.24 0.00 0.00 3.58
3976 4993 3.056250 GCACTCCATCAGAGAAGAACTCA 60.056 47.826 0.00 0.00 46.50 3.41
4010 5027 0.324738 TCCTTCGTCAGCCTGGATCT 60.325 55.000 0.00 0.00 0.00 2.75
4028 5045 0.543277 CTGGCCAGAGCAACATAGGA 59.457 55.000 29.88 0.00 42.56 2.94
4030 5047 0.179034 GGCCAGAGCAACATAGGAGG 60.179 60.000 0.00 0.00 42.56 4.30
4031 5048 0.817229 GCCAGAGCAACATAGGAGGC 60.817 60.000 0.00 0.00 39.53 4.70
4033 5050 0.531532 CAGAGCAACATAGGAGGCCG 60.532 60.000 0.00 0.00 0.00 6.13
4038 5055 1.138266 GCAACATAGGAGGCCGTCTTA 59.862 52.381 6.22 1.91 0.00 2.10
4149 5166 1.442526 CTCAGCACATCCCGCAATCC 61.443 60.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 8.822805 TCTCTGGGTCTATTACATTTTGTAACT 58.177 33.333 2.42 0.00 44.54 2.24
109 110 9.959721 AGAATGGTGTATAGTCAAATTGTTACT 57.040 29.630 0.00 0.00 0.00 2.24
139 159 3.971871 CGACGAATGCTCTCTGTATTCTC 59.028 47.826 0.00 0.00 42.90 2.87
193 214 3.394274 TCTCCCCTCTGTGTGATTCAAAA 59.606 43.478 0.00 0.00 0.00 2.44
205 226 3.327172 AGCACATGATATTCTCCCCTCTG 59.673 47.826 0.00 0.00 0.00 3.35
207 228 3.307339 GGAGCACATGATATTCTCCCCTC 60.307 52.174 0.00 0.00 37.85 4.30
208 229 2.641815 GGAGCACATGATATTCTCCCCT 59.358 50.000 0.00 0.00 37.85 4.79
209 230 3.064900 GGAGCACATGATATTCTCCCC 57.935 52.381 0.00 0.00 37.85 4.81
221 242 2.460669 GAAAAAGGGATGGGAGCACAT 58.539 47.619 0.00 0.00 0.00 3.21
222 243 1.886222 CGAAAAAGGGATGGGAGCACA 60.886 52.381 0.00 0.00 0.00 4.57
228 249 1.743394 GTAGCACGAAAAAGGGATGGG 59.257 52.381 0.00 0.00 0.00 4.00
240 261 5.852827 TGAAATGATATCATGGTAGCACGA 58.147 37.500 18.85 0.00 36.56 4.35
241 262 6.424812 TCTTGAAATGATATCATGGTAGCACG 59.575 38.462 18.85 10.14 36.56 5.34
288 309 9.333724 GGCATCCATGATTTTTCAGAATTATTT 57.666 29.630 0.00 0.00 0.00 1.40
291 312 6.383436 TGGGCATCCATGATTTTTCAGAATTA 59.617 34.615 0.00 0.00 38.32 1.40
313 335 1.290203 GTACGCTCATGTGATGTGGG 58.710 55.000 0.00 0.00 40.93 4.61
382 406 6.094603 ACACTATTCATGCTTGATTTGTCCTC 59.905 38.462 2.75 0.00 0.00 3.71
384 408 6.032094 CACACTATTCATGCTTGATTTGTCC 58.968 40.000 2.75 0.00 0.00 4.02
393 417 3.925379 TCGTGACACACTATTCATGCTT 58.075 40.909 6.37 0.00 31.34 3.91
397 421 4.621460 CGTTTCTCGTGACACACTATTCAT 59.379 41.667 6.37 0.00 31.34 2.57
408 432 4.509915 TTTGACTTTCGTTTCTCGTGAC 57.490 40.909 0.00 0.00 40.80 3.67
409 433 4.491280 CGTTTTGACTTTCGTTTCTCGTGA 60.491 41.667 0.00 0.00 40.80 4.35
412 436 2.707469 GCGTTTTGACTTTCGTTTCTCG 59.293 45.455 0.00 0.00 41.41 4.04
413 437 3.033873 GGCGTTTTGACTTTCGTTTCTC 58.966 45.455 0.00 0.00 0.00 2.87
415 439 2.528688 GTGGCGTTTTGACTTTCGTTTC 59.471 45.455 0.00 0.00 0.00 2.78
416 440 2.162809 AGTGGCGTTTTGACTTTCGTTT 59.837 40.909 0.00 0.00 0.00 3.60
417 441 1.741145 AGTGGCGTTTTGACTTTCGTT 59.259 42.857 0.00 0.00 0.00 3.85
432 456 5.640732 ACAAAATCGAATGTGAATAGTGGC 58.359 37.500 0.00 0.00 0.00 5.01
434 458 8.446273 AGAAGACAAAATCGAATGTGAATAGTG 58.554 33.333 0.00 0.00 0.00 2.74
481 513 8.534496 CCTCATAGAAATTTCAGGTCCAAAATT 58.466 33.333 19.99 8.46 36.81 1.82
503 535 2.415491 CGAAGAATGTCGCTACACCTCA 60.415 50.000 0.00 0.00 38.78 3.86
507 539 2.592194 TCACGAAGAATGTCGCTACAC 58.408 47.619 0.00 0.00 45.00 2.90
563 595 9.813446 ACGGTACCATTAAAACAACAATTTTAA 57.187 25.926 13.54 6.04 44.17 1.52
574 606 3.502979 TGCTCCAACGGTACCATTAAAAC 59.497 43.478 13.54 0.00 0.00 2.43
624 662 1.376424 ATCGACACTTGGCAGCCTG 60.376 57.895 14.15 5.18 0.00 4.85
756 794 1.451028 GCAGAGAGTGGATGGTGGC 60.451 63.158 0.00 0.00 0.00 5.01
760 798 0.179116 CGTCTGCAGAGAGTGGATGG 60.179 60.000 18.89 0.00 0.00 3.51
762 800 0.613292 ACCGTCTGCAGAGAGTGGAT 60.613 55.000 18.89 5.29 31.78 3.41
763 801 1.228583 ACCGTCTGCAGAGAGTGGA 60.229 57.895 18.89 0.00 31.78 4.02
764 802 1.080230 CACCGTCTGCAGAGAGTGG 60.080 63.158 27.37 22.85 33.04 4.00
766 804 2.653702 GCACCGTCTGCAGAGAGT 59.346 61.111 18.89 14.75 46.29 3.24
774 812 2.262915 GGACTCTGGCACCGTCTG 59.737 66.667 10.22 0.00 0.00 3.51
836 874 2.280797 CTGGTGTGGTGTCACGGG 60.281 66.667 0.00 0.00 46.42 5.28
849 892 3.708631 CTCTCTCTCTCTCTCTCTCTGGT 59.291 52.174 0.00 0.00 0.00 4.00
853 896 4.802248 GCCATCTCTCTCTCTCTCTCTCTC 60.802 54.167 0.00 0.00 0.00 3.20
859 902 2.254546 TCGCCATCTCTCTCTCTCTC 57.745 55.000 0.00 0.00 0.00 3.20
869 912 2.969238 CACCCGCATCGCCATCTC 60.969 66.667 0.00 0.00 0.00 2.75
1171 1215 4.057428 GCTGCTGACGTCCTCGGT 62.057 66.667 14.12 0.00 41.85 4.69
1213 1257 2.387510 AGAAAAGTAGGAGAGGGGAGGT 59.612 50.000 0.00 0.00 0.00 3.85
1227 1273 5.460748 CGCGGTAAAAATTCCAAAGAAAAGT 59.539 36.000 0.00 0.00 35.09 2.66
1230 1276 3.736759 GCGCGGTAAAAATTCCAAAGAAA 59.263 39.130 8.83 0.00 35.09 2.52
1233 1279 1.646726 CGCGCGGTAAAAATTCCAAAG 59.353 47.619 24.84 0.00 0.00 2.77
1235 1283 0.109689 CCGCGCGGTAAAAATTCCAA 60.110 50.000 39.71 0.00 0.00 3.53
1236 1284 0.954449 TCCGCGCGGTAAAAATTCCA 60.954 50.000 44.16 21.74 36.47 3.53
1237 1285 0.168568 TTCCGCGCGGTAAAAATTCC 59.831 50.000 44.16 0.00 36.47 3.01
1238 1286 1.843753 CATTCCGCGCGGTAAAAATTC 59.156 47.619 44.16 0.00 36.47 2.17
1239 1287 1.902840 CATTCCGCGCGGTAAAAATT 58.097 45.000 44.16 20.37 36.47 1.82
1240 1288 0.524604 GCATTCCGCGCGGTAAAAAT 60.525 50.000 44.16 33.06 36.47 1.82
1259 1307 9.013490 CGCATTTCTAAAATAAAACATGGAGAG 57.987 33.333 0.00 0.00 0.00 3.20
1261 1309 8.909708 TCGCATTTCTAAAATAAAACATGGAG 57.090 30.769 0.00 0.00 0.00 3.86
1262 1310 9.868277 AATCGCATTTCTAAAATAAAACATGGA 57.132 25.926 0.00 0.00 0.00 3.41
1266 1314 9.482627 ACCAAATCGCATTTCTAAAATAAAACA 57.517 25.926 0.00 0.00 0.00 2.83
1271 1319 9.575783 GGTAAACCAAATCGCATTTCTAAAATA 57.424 29.630 0.00 0.00 35.64 1.40
1272 1320 7.547722 GGGTAAACCAAATCGCATTTCTAAAAT 59.452 33.333 0.81 0.00 39.85 1.82
1273 1321 6.869388 GGGTAAACCAAATCGCATTTCTAAAA 59.131 34.615 0.81 0.00 39.85 1.52
1274 1322 6.391537 GGGTAAACCAAATCGCATTTCTAAA 58.608 36.000 0.81 0.00 39.85 1.85
1277 1325 3.119637 CGGGTAAACCAAATCGCATTTCT 60.120 43.478 0.81 0.00 40.22 2.52
1278 1326 3.119779 TCGGGTAAACCAAATCGCATTTC 60.120 43.478 0.81 0.00 40.22 2.17
1280 1328 2.438411 TCGGGTAAACCAAATCGCATT 58.562 42.857 0.81 0.00 40.22 3.56
1314 1364 7.232534 ACAATTAACAGGTCCTAGCAAATCAAA 59.767 33.333 0.00 0.00 0.00 2.69
1317 1367 6.759497 ACAATTAACAGGTCCTAGCAAATC 57.241 37.500 0.00 0.00 0.00 2.17
1325 1375 5.189736 TCAGCATCTACAATTAACAGGTCCT 59.810 40.000 0.00 0.00 0.00 3.85
1329 1379 6.992063 AGTTCAGCATCTACAATTAACAGG 57.008 37.500 0.00 0.00 0.00 4.00
1331 1381 7.064609 GCACTAGTTCAGCATCTACAATTAACA 59.935 37.037 0.00 0.00 0.00 2.41
1351 1401 4.176271 TCGTCAGATCAAACATGCACTAG 58.824 43.478 0.00 0.00 0.00 2.57
1412 1465 9.155975 TCTTAGCTAATCTTTCTTAGTTGCTTG 57.844 33.333 6.64 0.00 32.39 4.01
1456 1509 7.482474 CACATTTTGATCTGCCATGTGTAATA 58.518 34.615 14.63 0.00 39.84 0.98
1457 1510 6.334989 CACATTTTGATCTGCCATGTGTAAT 58.665 36.000 14.63 0.00 39.84 1.89
1458 1511 5.712004 CACATTTTGATCTGCCATGTGTAA 58.288 37.500 14.63 0.00 39.84 2.41
1459 1512 4.380761 GCACATTTTGATCTGCCATGTGTA 60.381 41.667 19.81 0.00 44.38 2.90
1534 1589 8.924511 TCAGGATCAATCAATTTCCTATTACC 57.075 34.615 0.00 0.00 36.45 2.85
1540 1595 7.002879 CAGGTATCAGGATCAATCAATTTCCT 58.997 38.462 0.00 0.00 39.18 3.36
1547 1602 3.969312 TGAGCAGGTATCAGGATCAATCA 59.031 43.478 0.00 0.00 0.00 2.57
1549 1604 5.131642 TCTTTGAGCAGGTATCAGGATCAAT 59.868 40.000 0.00 0.00 0.00 2.57
1561 1616 0.537371 CGGGGTTTCTTTGAGCAGGT 60.537 55.000 0.00 0.00 0.00 4.00
1562 1617 1.244019 CCGGGGTTTCTTTGAGCAGG 61.244 60.000 0.00 0.00 0.00 4.85
1563 1618 0.537371 ACCGGGGTTTCTTTGAGCAG 60.537 55.000 6.32 0.00 0.00 4.24
1564 1619 0.766131 TACCGGGGTTTCTTTGAGCA 59.234 50.000 6.32 0.00 0.00 4.26
1565 1620 1.162698 GTACCGGGGTTTCTTTGAGC 58.837 55.000 6.32 0.00 0.00 4.26
1569 1624 3.044235 CGTAAGTACCGGGGTTTCTTT 57.956 47.619 6.32 0.00 0.00 2.52
1595 1650 2.031191 CCAGCAACGAAGTAACAAACGT 59.969 45.455 0.00 0.00 45.00 3.99
1614 1669 1.695242 ACCAACTTCCATACGACACCA 59.305 47.619 0.00 0.00 0.00 4.17
1684 1741 9.582431 AAGATTTCACATCTAGATTTTGCATTG 57.418 29.630 1.33 0.00 0.00 2.82
1687 1744 7.394077 TCCAAGATTTCACATCTAGATTTTGCA 59.606 33.333 1.33 0.00 0.00 4.08
1815 1876 4.638865 ACACCCTAAATTCGCTGGATTTAC 59.361 41.667 0.00 0.00 0.00 2.01
1816 1877 4.850680 ACACCCTAAATTCGCTGGATTTA 58.149 39.130 3.20 3.20 0.00 1.40
1817 1878 3.694566 GACACCCTAAATTCGCTGGATTT 59.305 43.478 1.43 1.43 0.00 2.17
1828 1889 4.389374 CGGCATAATCTGACACCCTAAAT 58.611 43.478 0.00 0.00 29.06 1.40
1845 1906 8.685838 ACAACTATGTTATATTAAACCGGCAT 57.314 30.769 0.00 0.00 35.91 4.40
1861 1922 4.202631 ACACCCCCATAACAACAACTATGT 60.203 41.667 0.00 0.00 43.14 2.29
1862 1923 4.340617 ACACCCCCATAACAACAACTATG 58.659 43.478 0.00 0.00 0.00 2.23
1863 1924 4.668138 ACACCCCCATAACAACAACTAT 57.332 40.909 0.00 0.00 0.00 2.12
1864 1925 4.456662 AACACCCCCATAACAACAACTA 57.543 40.909 0.00 0.00 0.00 2.24
1865 1926 3.322191 AACACCCCCATAACAACAACT 57.678 42.857 0.00 0.00 0.00 3.16
1866 1927 4.146564 ACTAACACCCCCATAACAACAAC 58.853 43.478 0.00 0.00 0.00 3.32
1867 1928 4.105057 AGACTAACACCCCCATAACAACAA 59.895 41.667 0.00 0.00 0.00 2.83
1868 1929 3.653836 AGACTAACACCCCCATAACAACA 59.346 43.478 0.00 0.00 0.00 3.33
1869 1930 4.296621 AGACTAACACCCCCATAACAAC 57.703 45.455 0.00 0.00 0.00 3.32
1870 1931 5.572066 GCTTAGACTAACACCCCCATAACAA 60.572 44.000 0.00 0.00 0.00 2.83
1873 1934 3.457012 GGCTTAGACTAACACCCCCATAA 59.543 47.826 0.00 0.00 0.00 1.90
1881 1942 4.246458 CAAGACTGGGCTTAGACTAACAC 58.754 47.826 0.00 0.00 0.00 3.32
1883 1944 3.514309 TCCAAGACTGGGCTTAGACTAAC 59.486 47.826 0.00 0.00 43.71 2.34
1908 1969 8.716909 CCGCAAAGTAAAATGGATAAAACAATT 58.283 29.630 0.00 0.00 0.00 2.32
1944 2005 9.010029 GGTCAAACTAGATAATTTTCAGAACCA 57.990 33.333 0.00 0.00 0.00 3.67
1972 2033 9.823647 AATAGATTATGACAGTTGGACAAGTAG 57.176 33.333 0.00 0.00 0.00 2.57
2034 2095 9.077674 GGCAGTAAGATATATGTACTGAAATCG 57.922 37.037 24.62 8.38 44.94 3.34
2035 2096 9.077674 CGGCAGTAAGATATATGTACTGAAATC 57.922 37.037 24.62 13.60 44.94 2.17
2044 2105 5.924475 GCAAACGGCAGTAAGATATATGT 57.076 39.130 0.00 0.00 43.97 2.29
2099 2160 1.324005 GGAGGAGACTTGGTCGGAGG 61.324 65.000 0.00 0.00 44.43 4.30
2129 2190 9.186837 CCTTATAGAAAGGATAAGAGGCGTATA 57.813 37.037 0.00 0.00 38.60 1.47
2133 2194 6.209788 ACTCCTTATAGAAAGGATAAGAGGCG 59.790 42.308 6.93 0.00 44.75 5.52
2151 2212 5.832539 AGCCCGTATACTACTACTCCTTA 57.167 43.478 0.56 0.00 0.00 2.69
2153 2214 5.832539 TTAGCCCGTATACTACTACTCCT 57.167 43.478 0.56 0.00 0.00 3.69
2154 2215 6.000840 AGTTTAGCCCGTATACTACTACTCC 58.999 44.000 0.56 0.00 0.00 3.85
2156 2217 6.652900 GCTAGTTTAGCCCGTATACTACTACT 59.347 42.308 0.56 0.63 45.95 2.57
2157 2218 6.836953 GCTAGTTTAGCCCGTATACTACTAC 58.163 44.000 0.56 0.00 45.95 2.73
2354 2743 5.399858 CCGTATAGTATAATCGCAAGCAGT 58.600 41.667 0.00 0.00 37.18 4.40
2441 2840 3.862877 TTCATAGGCCATAGCACATGT 57.137 42.857 5.01 0.00 42.56 3.21
2488 2887 2.665537 GTCTTGACTCTTCTCACATGCG 59.334 50.000 0.00 0.00 0.00 4.73
2504 2903 7.044181 TGGCTCTAAAGTCTGAATATGTCTTG 58.956 38.462 0.00 0.00 0.00 3.02
2527 2926 0.673985 TATCTCTCGCCGTGGATTGG 59.326 55.000 0.00 0.00 0.00 3.16
2532 2931 0.172578 TTGTGTATCTCTCGCCGTGG 59.827 55.000 0.00 0.00 0.00 4.94
2535 2934 2.282555 CACATTTGTGTATCTCTCGCCG 59.717 50.000 2.48 0.00 40.96 6.46
2601 3000 2.057922 CCTTGGGACCATGCCTACTAT 58.942 52.381 0.00 0.00 0.00 2.12
2608 3007 1.684983 CATCAATCCTTGGGACCATGC 59.315 52.381 0.00 0.00 32.98 4.06
2636 3035 3.244105 CGCTACACACTGTGGTGC 58.756 61.111 13.77 14.36 46.57 5.01
2638 3037 0.670546 GATGCGCTACACACTGTGGT 60.671 55.000 9.73 9.59 37.94 4.16
2639 3038 1.361668 GGATGCGCTACACACTGTGG 61.362 60.000 9.73 3.85 37.94 4.17
2640 3039 0.670239 TGGATGCGCTACACACTGTG 60.670 55.000 9.73 7.68 39.75 3.66
2641 3040 0.250234 ATGGATGCGCTACACACTGT 59.750 50.000 9.73 0.00 0.00 3.55
2642 3041 1.372582 AATGGATGCGCTACACACTG 58.627 50.000 9.73 0.00 0.00 3.66
2643 3042 1.739466 CAAATGGATGCGCTACACACT 59.261 47.619 9.73 0.00 0.00 3.55
2644 3043 1.795162 GCAAATGGATGCGCTACACAC 60.795 52.381 9.73 0.00 36.45 3.82
2645 3044 0.451383 GCAAATGGATGCGCTACACA 59.549 50.000 9.73 2.73 36.45 3.72
2669 3068 5.294799 TGGACGAATAAAATACAATCACCCG 59.705 40.000 0.00 0.00 0.00 5.28
2674 3073 9.796120 TTCCAAATGGACGAATAAAATACAATC 57.204 29.630 0.54 0.00 45.39 2.67
2682 3081 6.987386 ACATGTTTCCAAATGGACGAATAAA 58.013 32.000 0.54 0.00 45.39 1.40
2683 3082 6.582677 ACATGTTTCCAAATGGACGAATAA 57.417 33.333 0.54 0.00 45.39 1.40
2711 3110 6.876155 AGGCAATGCATTTATTGTGATACAA 58.124 32.000 9.83 0.00 42.95 2.41
2712 3111 6.468333 AGGCAATGCATTTATTGTGATACA 57.532 33.333 9.83 0.00 39.62 2.29
2713 3112 7.920151 TGTAAGGCAATGCATTTATTGTGATAC 59.080 33.333 11.19 0.00 39.62 2.24
2714 3113 8.005192 TGTAAGGCAATGCATTTATTGTGATA 57.995 30.769 11.19 0.00 39.62 2.15
2716 3115 6.278172 TGTAAGGCAATGCATTTATTGTGA 57.722 33.333 11.19 0.00 39.62 3.58
2717 3116 6.964741 TTGTAAGGCAATGCATTTATTGTG 57.035 33.333 11.19 0.00 39.62 3.33
2718 3117 7.160726 ACTTTGTAAGGCAATGCATTTATTGT 58.839 30.769 11.19 1.68 39.62 2.71
2819 3218 2.969443 ACGATGCTAAAGTTGCACAC 57.031 45.000 0.00 0.00 43.59 3.82
2827 3226 5.175859 TCCAACTCCTAAACGATGCTAAAG 58.824 41.667 0.00 0.00 0.00 1.85
2858 3257 6.828273 TGGAACAAGGCGTACTACTAATACTA 59.172 38.462 0.00 0.00 31.92 1.82
2859 3258 5.653769 TGGAACAAGGCGTACTACTAATACT 59.346 40.000 0.00 0.00 31.92 2.12
2860 3259 5.745769 GTGGAACAAGGCGTACTACTAATAC 59.254 44.000 0.00 0.00 44.16 1.89
2893 3292 4.632538 AGTTTCAGTTTCGGTTTTCAGG 57.367 40.909 0.00 0.00 0.00 3.86
2901 3300 7.017645 CACTTGATATGAAGTTTCAGTTTCGG 58.982 38.462 4.67 0.00 41.08 4.30
2902 3301 6.521133 GCACTTGATATGAAGTTTCAGTTTCG 59.479 38.462 4.67 0.00 41.08 3.46
2912 3311 3.354948 TGCTGGCACTTGATATGAAGT 57.645 42.857 1.25 1.25 36.58 3.01
3005 3495 4.137543 AGATGTTTGTGAGGTCAGGTTTC 58.862 43.478 0.00 0.00 0.00 2.78
3120 3703 0.693049 GACCACAGGACCAGGAACAT 59.307 55.000 0.00 0.00 0.00 2.71
3158 3741 1.301244 CTAGCATGCCGAATCGCCT 60.301 57.895 15.66 0.00 0.00 5.52
3192 3778 5.283763 TCTAGCATGGGATGGATATAAGCT 58.716 41.667 0.00 0.00 0.00 3.74
3225 3813 1.543208 CCAAGAACTACCACAGCTGCA 60.543 52.381 15.27 0.00 0.00 4.41
3226 3814 1.160137 CCAAGAACTACCACAGCTGC 58.840 55.000 15.27 0.00 0.00 5.25
3227 3815 2.146342 CACCAAGAACTACCACAGCTG 58.854 52.381 13.48 13.48 0.00 4.24
3228 3816 1.072331 CCACCAAGAACTACCACAGCT 59.928 52.381 0.00 0.00 0.00 4.24
3229 3817 1.202770 ACCACCAAGAACTACCACAGC 60.203 52.381 0.00 0.00 0.00 4.40
3230 3818 2.158813 ACACCACCAAGAACTACCACAG 60.159 50.000 0.00 0.00 0.00 3.66
3231 3819 1.841277 ACACCACCAAGAACTACCACA 59.159 47.619 0.00 0.00 0.00 4.17
3288 3877 2.557056 CACAGGAAGTCTACTGAACCGA 59.443 50.000 10.52 0.00 38.09 4.69
3290 3879 4.602340 TTCACAGGAAGTCTACTGAACC 57.398 45.455 10.52 0.00 38.09 3.62
3304 3893 3.065371 GTGCCGAAATCCTTATTCACAGG 59.935 47.826 0.00 0.00 0.00 4.00
3330 3919 3.176411 TCTGGTCATCACAGGTCTGAAT 58.824 45.455 4.84 0.00 36.62 2.57
3368 3957 3.119101 AGTGAAGCCGAAATACGTCTCAT 60.119 43.478 0.00 0.00 40.78 2.90
3451 4040 6.098266 GTCTCATTTATAAAATGGGGCCAAGT 59.902 38.462 4.39 0.00 26.71 3.16
3488 4077 4.261072 CCGAGTACGATAACATACTGCTGT 60.261 45.833 0.66 0.66 42.66 4.40
3497 4086 1.958579 CCCATCCCGAGTACGATAACA 59.041 52.381 0.00 0.00 42.66 2.41
3537 4126 7.560368 TCCTGGTTCTATTTCTCTCTTGATTC 58.440 38.462 0.00 0.00 0.00 2.52
3553 4142 1.704641 GTTGCCCTTTTCCTGGTTCT 58.295 50.000 0.00 0.00 0.00 3.01
3554 4143 0.679505 GGTTGCCCTTTTCCTGGTTC 59.320 55.000 0.00 0.00 0.00 3.62
3555 4144 1.112916 CGGTTGCCCTTTTCCTGGTT 61.113 55.000 0.00 0.00 0.00 3.67
3556 4145 1.530655 CGGTTGCCCTTTTCCTGGT 60.531 57.895 0.00 0.00 0.00 4.00
3557 4146 2.931068 GCGGTTGCCCTTTTCCTGG 61.931 63.158 0.00 0.00 33.98 4.45
3595 4184 1.128200 GGTTGCCCTTTTCCTGGTTT 58.872 50.000 0.00 0.00 0.00 3.27
3609 4198 1.098712 TATGGATTTCGGGCGGTTGC 61.099 55.000 0.00 0.00 41.71 4.17
3611 4200 0.544697 ACTATGGATTTCGGGCGGTT 59.455 50.000 0.00 0.00 0.00 4.44
3612 4201 0.179056 CACTATGGATTTCGGGCGGT 60.179 55.000 0.00 0.00 0.00 5.68
3613 4202 0.884704 CCACTATGGATTTCGGGCGG 60.885 60.000 0.00 0.00 40.96 6.13
3614 4203 0.884704 CCCACTATGGATTTCGGGCG 60.885 60.000 0.00 0.00 40.96 6.13
3616 4205 1.768870 ACTCCCACTATGGATTTCGGG 59.231 52.381 0.00 0.00 40.96 5.14
3617 4206 4.141801 TGTTACTCCCACTATGGATTTCGG 60.142 45.833 0.00 0.00 40.96 4.30
3618 4207 5.018539 TGTTACTCCCACTATGGATTTCG 57.981 43.478 0.00 0.00 40.96 3.46
3619 4208 7.963532 TCTATGTTACTCCCACTATGGATTTC 58.036 38.462 0.00 0.00 40.96 2.17
3622 4211 7.179338 GTCATCTATGTTACTCCCACTATGGAT 59.821 40.741 0.00 0.00 40.96 3.41
3623 4212 6.493802 GTCATCTATGTTACTCCCACTATGGA 59.506 42.308 0.00 0.00 40.96 3.41
3672 4284 9.692325 ATTTGTTTCTCTCCTCATTAATTAGCT 57.308 29.630 0.00 0.00 0.00 3.32
3709 4321 9.974980 GAAGACCAATAAACCAGAACAAAAATA 57.025 29.630 0.00 0.00 0.00 1.40
3710 4322 8.482128 TGAAGACCAATAAACCAGAACAAAAAT 58.518 29.630 0.00 0.00 0.00 1.82
3711 4323 7.841956 TGAAGACCAATAAACCAGAACAAAAA 58.158 30.769 0.00 0.00 0.00 1.94
3712 4324 7.411486 TGAAGACCAATAAACCAGAACAAAA 57.589 32.000 0.00 0.00 0.00 2.44
3713 4325 7.595819 ATGAAGACCAATAAACCAGAACAAA 57.404 32.000 0.00 0.00 0.00 2.83
3714 4326 7.595819 AATGAAGACCAATAAACCAGAACAA 57.404 32.000 0.00 0.00 0.00 2.83
3715 4327 8.877864 ATAATGAAGACCAATAAACCAGAACA 57.122 30.769 0.00 0.00 0.00 3.18
3845 4661 6.159928 TCCCCTCTTTAGACTACTCATAGTGA 59.840 42.308 0.00 0.00 41.98 3.41
3897 4914 3.486383 CCGCATATCCATGTAACCCTTT 58.514 45.455 0.00 0.00 34.40 3.11
3910 4927 0.321564 TGCTATGGTGGCCGCATATC 60.322 55.000 19.98 10.01 0.00 1.63
3916 4933 1.153188 TGTGATGCTATGGTGGCCG 60.153 57.895 0.00 0.00 0.00 6.13
3919 4936 0.466189 GGGGTGTGATGCTATGGTGG 60.466 60.000 0.00 0.00 0.00 4.61
3976 4993 1.353091 AAGGAGTCGGCTTCCTTCTT 58.647 50.000 13.04 1.16 39.45 2.52
4010 5027 0.543277 CTCCTATGTTGCTCTGGCCA 59.457 55.000 4.71 4.71 37.74 5.36
4028 5045 1.049402 GGGAGCTTATAAGACGGCCT 58.951 55.000 16.85 3.05 0.00 5.19
4030 5047 2.210961 GTTGGGAGCTTATAAGACGGC 58.789 52.381 16.85 1.39 0.00 5.68
4031 5048 2.484947 GGGTTGGGAGCTTATAAGACGG 60.485 54.545 16.85 0.00 0.00 4.79
4033 5050 3.433740 CCAGGGTTGGGAGCTTATAAGAC 60.434 52.174 16.85 8.80 41.05 3.01
4113 5130 2.980233 GAAGCGTTGCAGGCTGGT 60.980 61.111 17.64 0.93 38.53 4.00
4119 5136 1.206072 GTGCTGAGAAGCGTTGCAG 59.794 57.895 0.00 0.00 37.69 4.41
4124 5141 1.078848 GGGATGTGCTGAGAAGCGT 60.079 57.895 0.00 0.00 37.69 5.07
4126 5143 2.467826 GCGGGATGTGCTGAGAAGC 61.468 63.158 0.00 0.00 0.00 3.86



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

AutoCloner maintained by Alex Coulton.