Multiple sequence alignment - TraesCS6A01G381700

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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 TraesCS6A01G381700 chr6A 100.000 3412 0 0 1 3412 601213044 601209633 0.000000e+00 6301.0
1 TraesCS6A01G381700 chr6A 84.131 1317 163 22 1108 2415 601166361 601165082 0.000000e+00 1232.0
2 TraesCS6A01G381700 chr6A 86.667 105 14 0 1166 1270 601138263 601138159 2.150000e-22 117.0
3 TraesCS6A01G381700 chr6D 89.428 2516 198 34 96 2593 454927907 454925442 0.000000e+00 3110.0
4 TraesCS6A01G381700 chr6D 85.250 1322 167 16 1103 2415 454734220 454735522 0.000000e+00 1336.0
5 TraesCS6A01G381700 chr6D 85.915 852 80 17 2594 3411 454925119 454924274 0.000000e+00 872.0
6 TraesCS6A01G381700 chr6D 77.643 908 155 30 1339 2238 454673012 454673879 3.040000e-140 508.0
7 TraesCS6A01G381700 chr6D 75.941 1089 197 41 1166 2238 454658908 454657869 1.830000e-137 499.0
8 TraesCS6A01G381700 chr6D 74.885 1083 209 46 1166 2238 454749441 454748412 5.230000e-118 435.0
9 TraesCS6A01G381700 chr6D 82.746 284 16 18 1 284 454928171 454927921 4.430000e-54 222.0
10 TraesCS6A01G381700 chr6D 93.269 104 7 0 3309 3412 399652659 399652556 1.640000e-33 154.0
11 TraesCS6A01G381700 chr6D 84.348 115 18 0 1157 1271 454662468 454662582 2.780000e-21 113.0
12 TraesCS6A01G381700 chr6B 87.072 1578 157 20 854 2404 692017121 692015564 0.000000e+00 1740.0
13 TraesCS6A01G381700 chr6B 83.954 1315 166 21 1110 2415 691795265 691793987 0.000000e+00 1218.0
14 TraesCS6A01G381700 chr6B 85.805 472 56 9 312 776 599981227 599981694 1.100000e-134 490.0
15 TraesCS6A01G381700 chr6B 84.355 473 63 10 311 776 26217863 26218331 1.440000e-123 453.0
16 TraesCS6A01G381700 chr6B 75.894 643 112 30 1166 1788 691783807 691783188 4.310000e-74 289.0
17 TraesCS6A01G381700 chr6B 90.000 70 6 1 779 847 692017235 692017166 4.690000e-14 89.8
18 TraesCS6A01G381700 chr7D 85.084 476 62 8 311 780 478798947 478799419 8.570000e-131 477.0
19 TraesCS6A01G381700 chr7D 84.632 475 65 5 308 776 611664919 611665391 1.850000e-127 466.0
20 TraesCS6A01G381700 chr7D 80.952 357 61 6 2958 3312 387916987 387917338 3.350000e-70 276.0
21 TraesCS6A01G381700 chr7B 84.989 473 60 8 311 776 739379419 739379887 1.430000e-128 470.0
22 TraesCS6A01G381700 chr1B 84.958 472 62 7 311 776 589132576 589133044 1.430000e-128 470.0
23 TraesCS6A01G381700 chr1B 77.370 791 105 37 2557 3311 539467768 539467016 5.300000e-108 401.0
24 TraesCS6A01G381700 chr2B 84.778 473 61 8 311 776 475125011 475125479 6.670000e-127 464.0
25 TraesCS6A01G381700 chr5D 85.586 444 57 5 338 776 423231863 423231422 3.100000e-125 459.0
26 TraesCS6A01G381700 chr5D 93.333 105 7 0 3308 3412 531284401 531284505 4.560000e-34 156.0
27 TraesCS6A01G381700 chr5D 85.075 67 8 2 2601 2666 15317885 15317820 2.200000e-07 67.6
28 TraesCS6A01G381700 chrUn 76.607 731 138 24 2601 3312 40899715 40898999 4.160000e-99 372.0
29 TraesCS6A01G381700 chrUn 76.607 731 138 24 2601 3312 333713146 333713862 4.160000e-99 372.0
30 TraesCS6A01G381700 chr7A 84.034 357 54 3 2957 3312 438145730 438146084 1.170000e-89 340.0
31 TraesCS6A01G381700 chr7A 81.870 353 58 6 2962 3312 439634149 439634497 3.330000e-75 292.0
32 TraesCS6A01G381700 chr2D 76.538 699 108 39 2651 3305 318582805 318582119 7.060000e-87 331.0
33 TraesCS6A01G381700 chr2D 96.154 104 4 0 3309 3412 329002125 329002022 1.630000e-38 171.0
34 TraesCS6A01G381700 chr3D 81.375 349 62 3 2957 3304 532129280 532129626 7.210000e-72 281.0
35 TraesCS6A01G381700 chr3D 92.523 107 7 1 3306 3412 402740868 402740973 5.900000e-33 152.0
36 TraesCS6A01G381700 chr5B 81.197 351 62 4 2959 3307 501358932 501359280 2.590000e-71 279.0
37 TraesCS6A01G381700 chr2A 75.758 594 94 29 2668 3223 412458886 412459467 1.570000e-63 254.0
38 TraesCS6A01G381700 chr5A 95.192 104 4 1 3309 3412 442515614 442515512 2.720000e-36 163.0
39 TraesCS6A01G381700 chr4D 95.192 104 4 1 3309 3412 134291941 134292043 2.720000e-36 163.0
40 TraesCS6A01G381700 chr4A 93.333 105 7 0 3308 3412 641312215 641312111 4.560000e-34 156.0
41 TraesCS6A01G381700 chr3B 93.333 105 6 1 3308 3412 647702284 647702181 1.640000e-33 154.0


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 TraesCS6A01G381700 chr6A 601209633 601213044 3411 True 6301.000000 6301 100.000000 1 3412 1 chr6A.!!$R3 3411
1 TraesCS6A01G381700 chr6A 601165082 601166361 1279 True 1232.000000 1232 84.131000 1108 2415 1 chr6A.!!$R2 1307
2 TraesCS6A01G381700 chr6D 454924274 454928171 3897 True 1401.333333 3110 86.029667 1 3411 3 chr6D.!!$R4 3410
3 TraesCS6A01G381700 chr6D 454734220 454735522 1302 False 1336.000000 1336 85.250000 1103 2415 1 chr6D.!!$F3 1312
4 TraesCS6A01G381700 chr6D 454673012 454673879 867 False 508.000000 508 77.643000 1339 2238 1 chr6D.!!$F2 899
5 TraesCS6A01G381700 chr6D 454657869 454658908 1039 True 499.000000 499 75.941000 1166 2238 1 chr6D.!!$R2 1072
6 TraesCS6A01G381700 chr6D 454748412 454749441 1029 True 435.000000 435 74.885000 1166 2238 1 chr6D.!!$R3 1072
7 TraesCS6A01G381700 chr6B 691793987 691795265 1278 True 1218.000000 1218 83.954000 1110 2415 1 chr6B.!!$R2 1305
8 TraesCS6A01G381700 chr6B 692015564 692017235 1671 True 914.900000 1740 88.536000 779 2404 2 chr6B.!!$R3 1625
9 TraesCS6A01G381700 chr6B 691783188 691783807 619 True 289.000000 289 75.894000 1166 1788 1 chr6B.!!$R1 622
10 TraesCS6A01G381700 chr1B 539467016 539467768 752 True 401.000000 401 77.370000 2557 3311 1 chr1B.!!$R1 754
11 TraesCS6A01G381700 chrUn 40898999 40899715 716 True 372.000000 372 76.607000 2601 3312 1 chrUn.!!$R1 711
12 TraesCS6A01G381700 chrUn 333713146 333713862 716 False 372.000000 372 76.607000 2601 3312 1 chrUn.!!$F1 711
13 TraesCS6A01G381700 chr2D 318582119 318582805 686 True 331.000000 331 76.538000 2651 3305 1 chr2D.!!$R1 654
14 TraesCS6A01G381700 chr2A 412458886 412459467 581 False 254.000000 254 75.758000 2668 3223 1 chr2A.!!$F1 555

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
964 1179 0.107643 TCATGTTGGGCTGAACGTGA 59.892 50.0 16.07 16.07 45.42 4.35 F
995 1217 0.946221 GTGTCCGTGCTCCTGTTCAG 60.946 60.0 0.00 0.00 0.00 3.02 F
1860 2151 0.370273 GTGAACTAAGCGCACCGATG 59.630 55.0 11.47 0.00 0.00 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1860 2151 0.454600 TACGCACGACAAGAGGATCC 59.545 55.0 2.48 2.48 33.66 3.36 R
2000 2305 0.940126 CACTGCTGAAGTTGAGCGTT 59.060 50.0 9.84 0.00 39.47 4.84 R
3121 3840 0.539438 AAATGGGAAGTTGCGCCTCA 60.539 50.0 4.18 0.00 0.00 3.86 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
21 22 1.680735 ACATGATGCGTGTTTGTGGTT 59.319 42.857 0.00 0.00 28.11 3.67
34 35 6.039616 GTGTTTGTGGTTGCTAGAAAATTCA 58.960 36.000 0.00 0.00 0.00 2.57
72 73 2.313427 ACAGGTTGTGGGTGTGGGT 61.313 57.895 0.00 0.00 0.00 4.51
73 74 1.827789 CAGGTTGTGGGTGTGGGTG 60.828 63.158 0.00 0.00 0.00 4.61
74 75 2.277404 GGTTGTGGGTGTGGGTGT 59.723 61.111 0.00 0.00 0.00 4.16
76 77 1.379309 GTTGTGGGTGTGGGTGTGT 60.379 57.895 0.00 0.00 0.00 3.72
78 79 2.143575 TTGTGGGTGTGGGTGTGTGT 62.144 55.000 0.00 0.00 0.00 3.72
80 81 2.274104 GGGTGTGGGTGTGTGTGT 59.726 61.111 0.00 0.00 0.00 3.72
82 83 2.118404 GGTGTGGGTGTGTGTGTGG 61.118 63.158 0.00 0.00 0.00 4.17
83 84 2.118404 GTGTGGGTGTGTGTGTGGG 61.118 63.158 0.00 0.00 0.00 4.61
84 85 2.518349 GTGGGTGTGTGTGTGGGG 60.518 66.667 0.00 0.00 0.00 4.96
85 86 3.814906 TGGGTGTGTGTGTGGGGG 61.815 66.667 0.00 0.00 0.00 5.40
108 278 4.454678 GGGATGATCAAGCATGAACAGTA 58.545 43.478 7.92 0.00 41.03 2.74
122 292 9.683069 AGCATGAACAGTACAAAAAGATAAAAG 57.317 29.630 0.00 0.00 0.00 2.27
126 296 8.637986 TGAACAGTACAAAAAGATAAAAGGCAT 58.362 29.630 0.00 0.00 0.00 4.40
170 340 5.885912 TGGCTTTGTCTTCTTTTGTTACTCT 59.114 36.000 0.00 0.00 0.00 3.24
229 399 1.425066 TGCCATTGGTGAAGAAGAGGT 59.575 47.619 4.26 0.00 0.00 3.85
235 405 6.183360 GCCATTGGTGAAGAAGAGGTAATTAC 60.183 42.308 7.09 7.09 0.00 1.89
245 415 0.527565 AGGTAATTACGGTGTCGCGT 59.472 50.000 5.77 0.00 40.63 6.01
250 420 0.241749 ATTACGGTGTCGCGTCTTCA 59.758 50.000 5.77 0.00 40.63 3.02
256 426 0.933509 GTGTCGCGTCTTCAACTCGT 60.934 55.000 5.77 0.00 37.37 4.18
264 434 3.218398 CGTCTTCAACTCGTTTCATTGC 58.782 45.455 0.00 0.00 0.00 3.56
270 440 5.342806 TCAACTCGTTTCATTGCTTGTAG 57.657 39.130 0.00 0.00 0.00 2.74
273 443 3.428870 ACTCGTTTCATTGCTTGTAGTCG 59.571 43.478 0.00 0.00 0.00 4.18
275 445 3.805422 TCGTTTCATTGCTTGTAGTCGTT 59.195 39.130 0.00 0.00 0.00 3.85
276 446 3.900116 CGTTTCATTGCTTGTAGTCGTTG 59.100 43.478 0.00 0.00 0.00 4.10
284 454 2.352421 GCTTGTAGTCGTTGCTAGGTGA 60.352 50.000 0.00 0.00 0.00 4.02
286 456 4.495422 CTTGTAGTCGTTGCTAGGTGATT 58.505 43.478 0.00 0.00 0.00 2.57
299 469 2.766345 GGTGATTTACGGTACCACCA 57.234 50.000 13.54 0.00 44.83 4.17
300 470 2.349590 GGTGATTTACGGTACCACCAC 58.650 52.381 13.54 9.28 44.83 4.16
301 471 2.289569 GGTGATTTACGGTACCACCACA 60.290 50.000 13.54 1.21 44.83 4.17
302 472 2.997986 GTGATTTACGGTACCACCACAG 59.002 50.000 13.54 0.00 38.47 3.66
309 480 1.412710 CGGTACCACCACAGCATATCT 59.587 52.381 13.54 0.00 38.47 1.98
327 498 6.571344 GCATATCTGTCACCTATCTTCGACAT 60.571 42.308 0.00 0.00 37.72 3.06
330 501 4.705023 TCTGTCACCTATCTTCGACATCAA 59.295 41.667 0.00 0.00 37.72 2.57
342 513 1.726791 CGACATCAACACAGTAGCCAC 59.273 52.381 0.00 0.00 0.00 5.01
369 543 0.395862 ACGACGGATCACCTCCTCAT 60.396 55.000 0.00 0.00 42.47 2.90
403 577 1.875514 GGCTTCATCGCTGATATGCAA 59.124 47.619 0.00 0.00 0.00 4.08
417 591 2.954611 GCAACTTTGCGGACCTCC 59.045 61.111 0.00 0.00 45.11 4.30
418 592 1.896660 GCAACTTTGCGGACCTCCA 60.897 57.895 0.00 0.00 45.11 3.86
419 593 1.452145 GCAACTTTGCGGACCTCCAA 61.452 55.000 0.00 0.00 45.11 3.53
420 594 0.593128 CAACTTTGCGGACCTCCAAG 59.407 55.000 0.00 0.00 35.14 3.61
421 595 0.472471 AACTTTGCGGACCTCCAAGA 59.528 50.000 2.48 0.00 35.14 3.02
422 596 0.693049 ACTTTGCGGACCTCCAAGAT 59.307 50.000 2.48 0.00 35.14 2.40
423 597 1.906574 ACTTTGCGGACCTCCAAGATA 59.093 47.619 2.48 0.00 35.14 1.98
449 623 1.962807 CCAAAGGTGAAGCCATTGACA 59.037 47.619 3.19 0.00 45.93 3.58
496 670 2.175811 GGACACGCCATCGCAAAC 59.824 61.111 0.00 0.00 39.84 2.93
500 674 2.031919 ACGCCATCGCAAACTCCA 59.968 55.556 0.00 0.00 39.84 3.86
501 675 1.599518 ACGCCATCGCAAACTCCAA 60.600 52.632 0.00 0.00 39.84 3.53
511 685 0.954452 CAAACTCCAAGTCTGGCACC 59.046 55.000 0.00 0.00 43.17 5.01
527 701 0.902531 CACCCCACCACGACTAAGAT 59.097 55.000 0.00 0.00 0.00 2.40
551 725 0.408700 AAGGAGGAGACCGTACCTGT 59.591 55.000 0.00 0.00 36.57 4.00
578 752 0.802494 CAACCACGAACCCAGCATAC 59.198 55.000 0.00 0.00 0.00 2.39
590 764 1.659098 CCAGCATACGTTCGGTCTTTC 59.341 52.381 0.00 0.00 0.00 2.62
616 790 2.604914 GTCGTCGATGCAGATCACAATT 59.395 45.455 0.00 0.00 0.00 2.32
624 798 3.503891 TGCAGATCACAATTTGCATTCG 58.496 40.909 1.25 0.00 45.22 3.34
625 799 2.280708 GCAGATCACAATTTGCATTCGC 59.719 45.455 0.00 0.00 41.46 4.70
640 814 0.809385 TTCGCTCTTGGACTACCTCG 59.191 55.000 0.00 0.00 37.04 4.63
652 826 2.214181 CTACCTCGCAAGCTCCACGT 62.214 60.000 0.00 0.00 37.18 4.49
675 849 2.584418 CTGGAGCAGACGCCATCG 60.584 66.667 0.00 0.00 45.48 3.84
683 857 3.507924 GACGCCATCGCAATGCCA 61.508 61.111 0.00 0.00 39.84 4.92
688 862 1.519898 CCATCGCAATGCCAAAGCC 60.520 57.895 0.00 0.00 38.69 4.35
718 892 0.405198 AGTCCACCACAATGATGCCA 59.595 50.000 0.00 0.00 0.00 4.92
725 899 3.133464 CAATGATGCCACCGCCGT 61.133 61.111 0.00 0.00 0.00 5.68
726 900 2.824041 AATGATGCCACCGCCGTC 60.824 61.111 0.00 0.00 0.00 4.79
727 901 3.620419 AATGATGCCACCGCCGTCA 62.620 57.895 0.00 0.00 34.40 4.35
748 922 5.352569 GTCACCACATCTCTATTTGAACAGG 59.647 44.000 0.00 0.00 0.00 4.00
755 929 4.579869 TCTCTATTTGAACAGGCTGGTTC 58.420 43.478 20.34 18.54 45.75 3.62
771 946 0.458025 GTTCCGAGTCCATCACCGAC 60.458 60.000 0.00 0.00 0.00 4.79
773 948 2.348104 CCGAGTCCATCACCGACCA 61.348 63.158 0.00 0.00 0.00 4.02
924 1138 5.761165 TGACATCATGCATGACCAATTAG 57.239 39.130 30.92 16.11 40.03 1.73
964 1179 0.107643 TCATGTTGGGCTGAACGTGA 59.892 50.000 16.07 16.07 45.42 4.35
995 1217 0.946221 GTGTCCGTGCTCCTGTTCAG 60.946 60.000 0.00 0.00 0.00 3.02
1057 1288 3.197766 TGGCTCACGTCTCATCCTAATTT 59.802 43.478 0.00 0.00 0.00 1.82
1084 1315 5.386958 TTGTTATCTCGTTCTAGCACACT 57.613 39.130 0.00 0.00 0.00 3.55
1087 1318 1.905637 TCTCGTTCTAGCACACTCCA 58.094 50.000 0.00 0.00 0.00 3.86
1089 1320 1.813178 CTCGTTCTAGCACACTCCAGA 59.187 52.381 0.00 0.00 0.00 3.86
1304 1549 2.481854 CATCCAGCTCTCTCATTTCCG 58.518 52.381 0.00 0.00 0.00 4.30
1335 1595 4.151157 GCTTGACTGATTGGTTCAATTTGC 59.849 41.667 0.00 0.00 33.90 3.68
1359 1619 4.626081 AGCTGGCCGCAAGAACGT 62.626 61.111 19.30 0.00 42.61 3.99
1511 1771 2.203596 ACCCCGTCGGTTCACTCT 60.204 61.111 11.06 0.00 45.36 3.24
1569 1837 3.685265 GCCTAACATGGACATGGACATGA 60.685 47.826 27.93 13.02 45.55 3.07
1576 1844 2.012673 GGACATGGACATGAAGCACTC 58.987 52.381 18.38 4.82 41.20 3.51
1580 1848 2.462456 TGGACATGAAGCACTCACTC 57.538 50.000 0.00 0.00 36.69 3.51
1636 1923 1.823041 CCGTAGAGGGGACGAGGAC 60.823 68.421 0.00 0.00 42.98 3.85
1641 1928 2.283966 AGGGGACGAGGACTGTGG 60.284 66.667 0.00 0.00 0.00 4.17
1718 2005 1.678635 CGTGCACATGGACCCCAAT 60.679 57.895 18.64 0.00 36.95 3.16
1795 2082 1.950630 AAACCGGCGTACGTGTGAC 60.951 57.895 17.90 0.00 42.24 3.67
1796 2083 2.354074 AAACCGGCGTACGTGTGACT 62.354 55.000 17.90 0.00 42.24 3.41
1860 2151 0.370273 GTGAACTAAGCGCACCGATG 59.630 55.000 11.47 0.00 0.00 3.84
1878 2177 1.215647 GGATCCTCTTGTCGTGCGT 59.784 57.895 3.84 0.00 0.00 5.24
1883 2182 1.816835 TCCTCTTGTCGTGCGTAGAAT 59.183 47.619 0.00 0.00 0.00 2.40
1919 2218 1.300233 GATGATGGCGGAGGTCGTC 60.300 63.158 0.00 0.00 44.94 4.20
2000 2305 2.954684 CGGTCCTGCCCTACAGCAA 61.955 63.158 0.00 0.00 45.78 3.91
2018 2323 1.331756 CAAACGCTCAACTTCAGCAGT 59.668 47.619 0.00 0.00 36.61 4.40
2042 2347 3.755628 GTCGCCCGCTACCTCACA 61.756 66.667 0.00 0.00 0.00 3.58
2068 2373 4.078516 GCCGGCCTACCAGAACGT 62.079 66.667 18.11 0.00 34.57 3.99
2333 2638 3.389329 AGTTCACTGACATGAGGACAAGT 59.611 43.478 0.00 0.00 0.00 3.16
2351 2656 3.655276 AGTTTGTACGAGACGGTGATT 57.345 42.857 0.00 0.00 0.00 2.57
2353 2658 3.985925 AGTTTGTACGAGACGGTGATTTC 59.014 43.478 0.00 0.00 0.00 2.17
2523 2828 2.100216 CAACGGCAATAGCGCACC 59.900 61.111 11.47 1.30 43.41 5.01
2544 2849 7.497595 GCACCGTGATATCCAAATCCTATATA 58.502 38.462 1.65 0.00 0.00 0.86
2547 2852 9.931698 ACCGTGATATCCAAATCCTATATACTA 57.068 33.333 0.00 0.00 0.00 1.82
2570 2879 2.808906 ACCTCAGGGCATTTCTAACC 57.191 50.000 0.00 0.00 35.63 2.85
2649 3280 3.318275 CGATCCCAAATCGGTCTTAGAGA 59.682 47.826 0.00 0.00 37.84 3.10
2697 3328 6.349445 CGCGGTTCTCTCTATATTTACTCCAT 60.349 42.308 0.00 0.00 0.00 3.41
2745 3377 3.399644 CCACTCTCTCTTCCCCTCCTATA 59.600 52.174 0.00 0.00 0.00 1.31
2781 3468 4.729856 CCCCGTCCCGTTGTCGAC 62.730 72.222 9.11 9.11 39.71 4.20
2790 3477 4.754667 GTTGTCGACGCCTCCCCC 62.755 72.222 11.62 0.00 0.00 5.40
2842 3532 3.319198 GAAGTGGCTGGACCCCGA 61.319 66.667 0.00 0.00 37.83 5.14
3062 3781 2.418356 GTCGGGTCGTTCCACACA 59.582 61.111 2.42 0.00 38.11 3.72
3063 3782 1.227321 GTCGGGTCGTTCCACACAA 60.227 57.895 2.42 0.00 38.11 3.33
3089 3808 2.545952 GCTCGTGGTGATGGAATACGAT 60.546 50.000 0.00 0.00 42.04 3.73
3152 3871 2.745884 CCATTTGAGACGGCGCCA 60.746 61.111 28.98 4.72 0.00 5.69
3273 3992 0.601558 CGTATATGGTGGACCTCCGG 59.398 60.000 8.06 0.00 39.43 5.14
3347 4066 8.842358 TTTACACTCATTCACCCTTAGTTTAG 57.158 34.615 0.00 0.00 0.00 1.85
3360 4079 9.110502 CACCCTTAGTTTAGACCAAGATATTTC 57.889 37.037 0.00 0.00 27.40 2.17
3384 4103 9.773328 TTCATTTAAACAGAGATATTCGCTTTG 57.227 29.630 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 3.440173 CCCACAACCTGTGCTTACATTAG 59.560 47.826 1.12 0.00 46.51 1.73
64 65 2.118404 CCACACACACACCCACACC 61.118 63.158 0.00 0.00 0.00 4.16
68 69 3.814906 CCCCCACACACACACCCA 61.815 66.667 0.00 0.00 0.00 4.51
84 85 1.959282 GTTCATGCTTGATCATCCCCC 59.041 52.381 2.75 0.00 0.00 5.40
85 86 2.621998 CTGTTCATGCTTGATCATCCCC 59.378 50.000 12.29 0.00 32.54 4.81
87 88 4.877823 TGTACTGTTCATGCTTGATCATCC 59.122 41.667 12.29 5.92 32.54 3.51
88 89 6.426980 TTGTACTGTTCATGCTTGATCATC 57.573 37.500 12.29 8.03 32.54 2.92
89 90 6.822667 TTTGTACTGTTCATGCTTGATCAT 57.177 33.333 12.29 7.09 32.54 2.45
90 91 6.631971 TTTTGTACTGTTCATGCTTGATCA 57.368 33.333 11.57 11.57 32.15 2.92
91 92 7.362662 TCTTTTTGTACTGTTCATGCTTGATC 58.637 34.615 2.75 3.56 0.00 2.92
93 94 6.691754 TCTTTTTGTACTGTTCATGCTTGA 57.308 33.333 0.00 0.00 0.00 3.02
94 95 9.462174 TTTATCTTTTTGTACTGTTCATGCTTG 57.538 29.630 0.00 0.00 0.00 4.01
201 371 4.219115 TCTTCACCAATGGCAGGTAAAAA 58.781 39.130 0.00 0.00 37.23 1.94
202 372 3.838565 TCTTCACCAATGGCAGGTAAAA 58.161 40.909 0.00 0.00 37.23 1.52
204 374 3.073798 TCTTCTTCACCAATGGCAGGTAA 59.926 43.478 0.00 0.00 37.23 2.85
205 375 2.642311 TCTTCTTCACCAATGGCAGGTA 59.358 45.455 0.00 0.00 37.23 3.08
206 376 1.425066 TCTTCTTCACCAATGGCAGGT 59.575 47.619 0.00 0.00 40.85 4.00
207 377 2.089980 CTCTTCTTCACCAATGGCAGG 58.910 52.381 0.00 0.00 0.00 4.85
209 379 1.425066 ACCTCTTCTTCACCAATGGCA 59.575 47.619 0.00 0.00 0.00 4.92
210 380 2.206576 ACCTCTTCTTCACCAATGGC 57.793 50.000 0.00 0.00 0.00 4.40
211 381 6.037172 CGTAATTACCTCTTCTTCACCAATGG 59.963 42.308 10.01 0.00 0.00 3.16
212 382 6.037172 CCGTAATTACCTCTTCTTCACCAATG 59.963 42.308 10.01 0.00 0.00 2.82
213 383 6.113411 CCGTAATTACCTCTTCTTCACCAAT 58.887 40.000 10.01 0.00 0.00 3.16
214 384 5.012354 ACCGTAATTACCTCTTCTTCACCAA 59.988 40.000 10.01 0.00 0.00 3.67
218 388 5.620654 CGACACCGTAATTACCTCTTCTTCA 60.621 44.000 10.01 0.00 0.00 3.02
229 399 2.095314 TGAAGACGCGACACCGTAATTA 60.095 45.455 15.93 0.00 42.24 1.40
235 405 1.606350 GAGTTGAAGACGCGACACCG 61.606 60.000 15.93 0.00 39.16 4.94
245 415 4.335315 ACAAGCAATGAAACGAGTTGAAGA 59.665 37.500 0.00 0.00 0.00 2.87
250 420 4.084537 CGACTACAAGCAATGAAACGAGTT 60.085 41.667 0.00 0.00 0.00 3.01
256 426 3.563808 AGCAACGACTACAAGCAATGAAA 59.436 39.130 0.00 0.00 0.00 2.69
264 434 3.570926 TCACCTAGCAACGACTACAAG 57.429 47.619 0.00 0.00 0.00 3.16
270 440 2.601763 CCGTAAATCACCTAGCAACGAC 59.398 50.000 0.00 0.00 0.00 4.34
273 443 3.867493 GGTACCGTAAATCACCTAGCAAC 59.133 47.826 0.00 0.00 0.00 4.17
275 445 3.098377 TGGTACCGTAAATCACCTAGCA 58.902 45.455 7.57 0.00 32.04 3.49
276 446 3.451526 GTGGTACCGTAAATCACCTAGC 58.548 50.000 7.57 0.00 32.04 3.42
284 454 1.348366 TGCTGTGGTGGTACCGTAAAT 59.652 47.619 7.57 0.00 42.58 1.40
286 456 0.978151 ATGCTGTGGTGGTACCGTAA 59.022 50.000 7.57 0.00 42.58 3.18
300 470 7.059256 GTCGAAGATAGGTGACAGATATGCTG 61.059 46.154 0.00 0.00 45.48 4.41
301 471 5.048364 GTCGAAGATAGGTGACAGATATGCT 60.048 44.000 0.00 0.00 40.67 3.79
302 472 5.157781 GTCGAAGATAGGTGACAGATATGC 58.842 45.833 0.00 0.00 40.67 3.14
309 480 4.219725 TGTTGATGTCGAAGATAGGTGACA 59.780 41.667 0.00 0.00 44.58 3.58
317 488 4.177026 GCTACTGTGTTGATGTCGAAGAT 58.823 43.478 0.00 0.00 40.67 2.40
318 489 3.575630 GCTACTGTGTTGATGTCGAAGA 58.424 45.455 0.00 0.00 0.00 2.87
327 498 2.719531 TTTGGTGGCTACTGTGTTGA 57.280 45.000 0.00 0.00 0.00 3.18
403 577 0.693049 ATCTTGGAGGTCCGCAAAGT 59.307 50.000 9.37 0.00 39.43 2.66
449 623 1.816224 CCCCGGTTTGATTCGTTCAAT 59.184 47.619 0.00 0.00 43.73 2.57
500 674 2.776526 TGGTGGGGTGCCAGACTT 60.777 61.111 0.00 0.00 0.00 3.01
501 675 3.570212 GTGGTGGGGTGCCAGACT 61.570 66.667 0.00 0.00 36.57 3.24
511 685 0.462047 GGCATCTTAGTCGTGGTGGG 60.462 60.000 0.00 0.00 0.00 4.61
527 701 2.488771 TACGGTCTCCTCCTTCGGCA 62.489 60.000 0.00 0.00 0.00 5.69
544 718 3.270877 GTGGTTGATGGATGACAGGTAC 58.729 50.000 0.00 0.00 0.00 3.34
551 725 1.339631 GGGTTCGTGGTTGATGGATGA 60.340 52.381 0.00 0.00 0.00 2.92
590 764 2.049959 GATCTGCATCGACGACATCTG 58.950 52.381 0.00 0.00 0.00 2.90
616 790 2.346803 GTAGTCCAAGAGCGAATGCAA 58.653 47.619 0.00 0.00 46.23 4.08
624 798 0.246635 TTGCGAGGTAGTCCAAGAGC 59.753 55.000 0.00 0.00 35.89 4.09
625 799 1.737363 GCTTGCGAGGTAGTCCAAGAG 60.737 57.143 2.37 0.00 36.38 2.85
640 814 2.551270 CGTCAACGTGGAGCTTGC 59.449 61.111 0.00 0.00 34.11 4.01
652 826 2.049156 CGTCTGCTCCAGCGTCAA 60.049 61.111 0.00 0.00 45.83 3.18
675 849 1.217244 CCTCAGGCTTTGGCATTGC 59.783 57.895 0.00 0.00 40.87 3.56
683 857 2.262423 GACTTGTGTCCTCAGGCTTT 57.738 50.000 0.00 0.00 37.24 3.51
708 882 3.112126 GACGGCGGTGGCATCATTG 62.112 63.158 13.24 0.00 42.47 2.82
718 892 3.296709 GAGATGTGGTGACGGCGGT 62.297 63.158 13.24 0.00 0.00 5.68
725 899 5.491070 CCTGTTCAAATAGAGATGTGGTGA 58.509 41.667 0.00 0.00 0.00 4.02
726 900 4.095483 GCCTGTTCAAATAGAGATGTGGTG 59.905 45.833 0.00 0.00 0.00 4.17
727 901 4.018960 AGCCTGTTCAAATAGAGATGTGGT 60.019 41.667 0.00 0.00 0.00 4.16
729 903 4.334759 CCAGCCTGTTCAAATAGAGATGTG 59.665 45.833 0.00 0.00 0.00 3.21
748 922 0.741221 GTGATGGACTCGGAACCAGC 60.741 60.000 10.74 10.74 42.07 4.85
755 929 1.676678 ATGGTCGGTGATGGACTCGG 61.677 60.000 0.00 0.00 34.82 4.63
771 946 2.868044 GCTCGCCACTTGGAGTATATGG 60.868 54.545 0.00 0.00 37.39 2.74
773 948 2.320781 AGCTCGCCACTTGGAGTATAT 58.679 47.619 0.00 0.00 37.39 0.86
842 1018 4.789075 TTGGCTCGCCGACTACGC 62.789 66.667 3.14 0.00 39.42 4.42
886 1100 4.864334 CATGGAGGACCGGCTGGC 62.864 72.222 12.89 4.26 39.70 4.85
918 1132 8.443160 TCGTCAAGCTGAAATCTTAACTAATTG 58.557 33.333 0.00 0.00 0.00 2.32
924 1138 6.408858 TGATCGTCAAGCTGAAATCTTAAC 57.591 37.500 0.00 0.00 0.00 2.01
980 1202 0.588252 CAAACTGAACAGGAGCACGG 59.412 55.000 6.76 0.00 0.00 4.94
1057 1288 7.274904 GTGTGCTAGAACGAGATAACAATAACA 59.725 37.037 0.00 0.00 0.00 2.41
1084 1315 3.312404 GCTGTTTGCAGAGTCTGGA 57.688 52.632 21.54 16.58 45.28 3.86
1103 1334 1.987855 ATGGTGATGGTCGACGGGT 60.988 57.895 9.92 0.00 0.00 5.28
1104 1335 1.521457 CATGGTGATGGTCGACGGG 60.521 63.158 9.92 0.00 0.00 5.28
1105 1336 2.173669 GCATGGTGATGGTCGACGG 61.174 63.158 9.92 0.00 0.00 4.79
1257 1494 1.144057 CTTGCGCTTACCGGGATCT 59.856 57.895 9.73 0.00 37.44 2.75
1304 1549 1.734465 CAATCAGTCAAGCGAAGGGAC 59.266 52.381 0.00 0.00 0.00 4.46
1347 1607 3.181169 AAGTGCACGTTCTTGCGGC 62.181 57.895 12.01 0.00 46.20 6.53
1511 1771 0.117140 TTTCAGAGGGGCAGAGGAGA 59.883 55.000 0.00 0.00 0.00 3.71
1569 1837 3.616721 ACGGGCGAGTGAGTGCTT 61.617 61.111 0.00 0.00 0.00 3.91
1622 1909 1.304547 CACAGTCCTCGTCCCCTCT 60.305 63.158 0.00 0.00 0.00 3.69
1674 1961 2.036733 CGTAGGAGGAAGTGAACACCAA 59.963 50.000 1.11 0.00 0.00 3.67
1795 2082 4.322567 GGGGCAGATAGAATTGAGCTTAG 58.677 47.826 0.00 0.00 0.00 2.18
1796 2083 3.073062 GGGGGCAGATAGAATTGAGCTTA 59.927 47.826 0.00 0.00 0.00 3.09
1860 2151 0.454600 TACGCACGACAAGAGGATCC 59.545 55.000 2.48 2.48 33.66 3.36
1935 2234 2.612115 CTCCAGCCCCCTCTTGGT 60.612 66.667 0.00 0.00 0.00 3.67
2000 2305 0.940126 CACTGCTGAAGTTGAGCGTT 59.060 50.000 9.84 0.00 39.47 4.84
2112 2417 1.542187 GGGTGCTCGTAGACAAGGGT 61.542 60.000 0.00 0.00 0.00 4.34
2154 2459 2.433145 CACGGCACTGACGCAGAT 60.433 61.111 3.53 0.00 37.73 2.90
2238 2543 3.827784 CTTGCCGTCGTCTTCGCG 61.828 66.667 0.00 0.00 36.77 5.87
2260 2565 1.229082 AACCTGTACTCCCTCGCCA 60.229 57.895 0.00 0.00 0.00 5.69
2333 2638 3.319755 GGAAATCACCGTCTCGTACAAA 58.680 45.455 0.00 0.00 0.00 2.83
2448 2753 9.553064 CAGAGTACTTATCCTCATTTATTTGCT 57.447 33.333 0.00 0.00 0.00 3.91
2544 2849 7.038231 GGTTAGAAATGCCCTGAGGTATATAGT 60.038 40.741 0.00 0.00 37.52 2.12
2547 2852 5.280011 CGGTTAGAAATGCCCTGAGGTATAT 60.280 44.000 0.00 0.00 37.52 0.86
2555 2860 3.545703 AGAATCGGTTAGAAATGCCCTG 58.454 45.455 0.00 0.00 0.00 4.45
2649 3280 4.338400 GGCGGCTGAGGATAATTTTTACTT 59.662 41.667 0.00 0.00 0.00 2.24
2745 3377 3.369388 GGGGAGGGGAGGAGAGGT 61.369 72.222 0.00 0.00 0.00 3.85
2943 3634 1.934220 CTCTGCGAGTAGGCGAACCA 61.934 60.000 0.00 0.00 39.06 3.67
2952 3643 3.068165 CCAATGTATGTCCTCTGCGAGTA 59.932 47.826 0.00 0.00 0.00 2.59
3076 3795 1.270094 GCCACCGATCGTATTCCATCA 60.270 52.381 15.09 0.00 0.00 3.07
3121 3840 0.539438 AAATGGGAAGTTGCGCCTCA 60.539 50.000 4.18 0.00 0.00 3.86
3127 3846 1.200020 CCGTCTCAAATGGGAAGTTGC 59.800 52.381 0.00 0.00 0.00 4.17
3273 3992 4.756458 AGCTCAGAGTGCTGGCGC 62.756 66.667 0.00 0.00 42.53 6.53
3336 4055 9.853177 ATGAAATATCTTGGTCTAAACTAAGGG 57.147 33.333 2.46 0.00 42.52 3.95
3360 4079 9.941664 ATCAAAGCGAATATCTCTGTTTAAATG 57.058 29.630 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.