Multiple sequence alignment - TraesCS5D01G268000

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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 TraesCS5D01G268000 chr5D 100.000 5465 0 0 1 5465 371473642 371468178 0.000000e+00 10093.0
1 TraesCS5D01G268000 chr5D 76.511 728 105 36 1829 2504 463943270 463942557 2.440000e-88 337.0
2 TraesCS5D01G268000 chr5D 90.476 147 14 0 2579 2725 426866951 426866805 1.550000e-45 195.0
3 TraesCS5D01G268000 chr5D 89.116 147 16 0 2579 2725 398048275 398048129 3.360000e-42 183.0
4 TraesCS5D01G268000 chr5D 100.000 39 0 0 2764 2802 398048135 398048097 7.590000e-09 73.1
5 TraesCS5D01G268000 chr5D 100.000 39 0 0 2764 2802 426866811 426866773 7.590000e-09 73.1
6 TraesCS5D01G268000 chr5D 91.304 46 4 0 205 250 503961016 503960971 4.570000e-06 63.9
7 TraesCS5D01G268000 chr5A 91.149 4621 219 93 37 4558 474545818 474541289 0.000000e+00 6093.0
8 TraesCS5D01G268000 chr5A 95.385 325 12 3 4796 5119 427870018 427869696 1.050000e-141 514.0
9 TraesCS5D01G268000 chr5A 92.381 315 22 2 1575 1889 518787389 518787077 1.080000e-121 448.0
10 TraesCS5D01G268000 chr5A 92.063 315 23 2 1575 1889 155929741 155930053 5.020000e-120 442.0
11 TraesCS5D01G268000 chr5A 96.970 132 3 1 5142 5272 474540693 474540562 2.560000e-53 220.0
12 TraesCS5D01G268000 chr5A 92.523 107 5 1 5005 5111 474540796 474540693 3.410000e-32 150.0
13 TraesCS5D01G268000 chr5A 96.875 64 2 0 4941 5004 474540954 474540891 2.080000e-19 108.0
14 TraesCS5D01G268000 chr5A 94.118 68 4 0 4558 4625 427870460 427870393 2.690000e-18 104.0
15 TraesCS5D01G268000 chr5A 95.161 62 3 0 4626 4687 427870369 427870308 1.250000e-16 99.0
16 TraesCS5D01G268000 chr5A 88.372 86 3 3 4722 4800 427870130 427870045 4.510000e-16 97.1
17 TraesCS5D01G268000 chr5A 91.045 67 6 0 5399 5465 474540403 474540337 2.100000e-14 91.6
18 TraesCS5D01G268000 chr5A 100.000 49 0 0 5321 5369 474540451 474540403 2.100000e-14 91.6
19 TraesCS5D01G268000 chr5A 100.000 29 0 0 222 250 631716794 631716766 3.000000e-03 54.7
20 TraesCS5D01G268000 chr5B 95.622 2033 59 19 2523 4548 441451257 441449248 0.000000e+00 3234.0
21 TraesCS5D01G268000 chr5B 91.392 1975 112 35 567 2508 441453254 441451305 0.000000e+00 2652.0
22 TraesCS5D01G268000 chr5B 87.500 520 45 11 1 513 441453783 441453277 2.840000e-162 582.0
23 TraesCS5D01G268000 chr5B 82.392 301 34 5 3875 4173 460967176 460967459 1.520000e-60 244.0
24 TraesCS5D01G268000 chr7B 90.321 1560 151 0 2696 4255 196907161 196908720 0.000000e+00 2045.0
25 TraesCS5D01G268000 chr7B 91.892 222 16 2 1331 1552 452911948 452912167 5.320000e-80 309.0
26 TraesCS5D01G268000 chr7B 96.296 135 5 0 1034 1168 196904987 196905121 7.130000e-54 222.0
27 TraesCS5D01G268000 chr7B 77.711 166 27 9 96 253 556685559 556685396 5.830000e-15 93.5
28 TraesCS5D01G268000 chr7A 90.321 1560 151 0 2696 4255 217557422 217555863 0.000000e+00 2045.0
29 TraesCS5D01G268000 chr7A 92.381 315 22 2 1575 1889 648152093 648151781 1.080000e-121 448.0
30 TraesCS5D01G268000 chr7A 92.332 313 22 2 1575 1887 707174880 707175190 1.400000e-120 444.0
31 TraesCS5D01G268000 chr7A 95.105 143 6 1 1034 1175 217559630 217559488 1.980000e-54 224.0
32 TraesCS5D01G268000 chr7D 90.192 1560 153 0 2696 4255 205543966 205542407 0.000000e+00 2034.0
33 TraesCS5D01G268000 chr7D 95.804 143 5 1 1034 1175 205546354 205546212 4.260000e-56 230.0
34 TraesCS5D01G268000 chr7D 75.524 286 24 20 1981 2239 321515786 321515520 1.250000e-16 99.0
35 TraesCS5D01G268000 chr7D 77.301 163 25 9 97 253 522871568 522871412 9.750000e-13 86.1
36 TraesCS5D01G268000 chr2A 81.673 1566 263 18 2705 4253 15003425 15001867 0.000000e+00 1280.0
37 TraesCS5D01G268000 chr2A 88.525 183 21 0 1367 1549 748030427 748030609 7.130000e-54 222.0
38 TraesCS5D01G268000 chr2A 92.562 121 9 0 1045 1165 15004451 15004331 2.020000e-39 174.0
39 TraesCS5D01G268000 chr2A 86.275 153 21 0 2573 2725 209936725 209936877 3.390000e-37 167.0
40 TraesCS5D01G268000 chr2B 80.897 1560 279 14 2705 4250 23582327 23580773 0.000000e+00 1212.0
41 TraesCS5D01G268000 chr2B 94.444 126 7 0 1040 1165 23583211 23583086 1.550000e-45 195.0
42 TraesCS5D01G268000 chr2D 80.818 1564 283 10 2705 4253 12884297 12882736 0.000000e+00 1210.0
43 TraesCS5D01G268000 chr2D 93.651 126 8 0 1040 1165 12885201 12885076 7.230000e-44 189.0
44 TraesCS5D01G268000 chr2D 87.582 153 19 0 2573 2725 25577432 25577584 1.560000e-40 178.0
45 TraesCS5D01G268000 chr2D 85.714 91 5 6 2156 2240 374549089 374549001 7.540000e-14 89.8
46 TraesCS5D01G268000 chr1D 91.168 668 31 9 4820 5461 47879042 47878377 0.000000e+00 881.0
47 TraesCS5D01G268000 chr1D 95.455 44 2 0 4752 4795 47879265 47879222 2.730000e-08 71.3
48 TraesCS5D01G268000 chr1A 90.399 677 37 8 4815 5465 47805429 47804755 0.000000e+00 865.0
49 TraesCS5D01G268000 chr1A 92.381 315 22 2 1575 1889 270717886 270717574 1.080000e-121 448.0
50 TraesCS5D01G268000 chr1A 89.674 184 19 0 1369 1552 536835713 536835530 9.150000e-58 235.0
51 TraesCS5D01G268000 chr1B 86.095 676 39 23 4820 5465 67540029 67539379 0.000000e+00 676.0
52 TraesCS5D01G268000 chr1B 87.432 183 23 0 1367 1549 293810815 293810997 1.540000e-50 211.0
53 TraesCS5D01G268000 chr3A 93.016 315 20 2 1575 1889 642859616 642859928 4.990000e-125 459.0
54 TraesCS5D01G268000 chr6B 92.063 315 23 2 1575 1889 647771803 647772115 5.020000e-120 442.0
55 TraesCS5D01G268000 chr6B 88.961 154 16 1 2573 2725 616723392 616723545 7.230000e-44 189.0
56 TraesCS5D01G268000 chr6D 76.463 735 99 42 1826 2504 10053273 10053989 1.130000e-86 331.0
57 TraesCS5D01G268000 chr6D 87.372 293 19 8 1260 1552 133887943 133887669 2.460000e-83 320.0
58 TraesCS5D01G268000 chr6D 87.372 293 18 9 1260 1551 133660911 133660637 8.830000e-83 318.0
59 TraesCS5D01G268000 chr6D 92.913 127 8 1 1039 1165 21352765 21352890 3.360000e-42 183.0
60 TraesCS5D01G268000 chr6D 89.116 147 16 0 2579 2725 27879825 27879679 3.360000e-42 183.0
61 TraesCS5D01G268000 chr6D 100.000 39 0 0 2764 2802 27879685 27879647 7.590000e-09 73.1
62 TraesCS5D01G268000 chr4A 79.869 457 58 15 1829 2258 656597182 656596733 2.470000e-78 303.0
63 TraesCS5D01G268000 chr4A 75.907 689 104 35 1832 2469 223176149 223175472 4.140000e-76 296.0
64 TraesCS5D01G268000 chr3D 88.889 153 17 0 2573 2725 164647597 164647749 7.230000e-44 189.0
65 TraesCS5D01G268000 chr3D 75.175 286 25 21 1982 2240 484481125 484481391 5.830000e-15 93.5
66 TraesCS5D01G268000 chr3D 100.000 39 0 0 2764 2802 164647743 164647781 7.590000e-09 73.1
67 TraesCS5D01G268000 chr4B 90.625 96 9 0 1367 1462 657926050 657926145 1.600000e-25 128.0
68 TraesCS5D01G268000 chr4B 85.714 91 5 6 2156 2240 420604962 420604874 7.540000e-14 89.8
69 TraesCS5D01G268000 chr4D 75.610 287 24 20 1981 2240 409950380 409950113 3.480000e-17 100.0
70 TraesCS5D01G268000 chr3B 85.714 91 5 6 2156 2240 779584856 779584768 7.540000e-14 89.8
71 TraesCS5D01G268000 chrUn 86.047 86 4 6 2161 2240 275300815 275300732 9.750000e-13 86.1


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 TraesCS5D01G268000 chr5D 371468178 371473642 5464 True 10093.000 10093 100.000000 1 5465 1 chr5D.!!$R1 5464
1 TraesCS5D01G268000 chr5D 463942557 463943270 713 True 337.000 337 76.511000 1829 2504 1 chr5D.!!$R2 675
2 TraesCS5D01G268000 chr5A 474540337 474545818 5481 True 1125.700 6093 94.760333 37 5465 6 chr5A.!!$R4 5428
3 TraesCS5D01G268000 chr5A 427869696 427870460 764 True 203.525 514 93.259000 4558 5119 4 chr5A.!!$R3 561
4 TraesCS5D01G268000 chr5B 441449248 441453783 4535 True 2156.000 3234 91.504667 1 4548 3 chr5B.!!$R1 4547
5 TraesCS5D01G268000 chr7B 196904987 196908720 3733 False 1133.500 2045 93.308500 1034 4255 2 chr7B.!!$F2 3221
6 TraesCS5D01G268000 chr7A 217555863 217559630 3767 True 1134.500 2045 92.713000 1034 4255 2 chr7A.!!$R2 3221
7 TraesCS5D01G268000 chr7D 205542407 205546354 3947 True 1132.000 2034 92.998000 1034 4255 2 chr7D.!!$R3 3221
8 TraesCS5D01G268000 chr2A 15001867 15004451 2584 True 727.000 1280 87.117500 1045 4253 2 chr2A.!!$R1 3208
9 TraesCS5D01G268000 chr2B 23580773 23583211 2438 True 703.500 1212 87.670500 1040 4250 2 chr2B.!!$R1 3210
10 TraesCS5D01G268000 chr2D 12882736 12885201 2465 True 699.500 1210 87.234500 1040 4253 2 chr2D.!!$R2 3213
11 TraesCS5D01G268000 chr1D 47878377 47879265 888 True 476.150 881 93.311500 4752 5461 2 chr1D.!!$R1 709
12 TraesCS5D01G268000 chr1A 47804755 47805429 674 True 865.000 865 90.399000 4815 5465 1 chr1A.!!$R1 650
13 TraesCS5D01G268000 chr1B 67539379 67540029 650 True 676.000 676 86.095000 4820 5465 1 chr1B.!!$R1 645
14 TraesCS5D01G268000 chr6D 10053273 10053989 716 False 331.000 331 76.463000 1826 2504 1 chr6D.!!$F1 678
15 TraesCS5D01G268000 chr4A 223175472 223176149 677 True 296.000 296 75.907000 1832 2469 1 chr4A.!!$R1 637

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
129 130 1.130561 GCCATTTGTAGAAGTCGTGGC 59.869 52.381 0.00 0.0 43.09 5.01 F
1429 2287 0.966179 TCACGGACAAGAGCAAGCTA 59.034 50.000 0.00 0.0 0.00 3.32 F
1827 3024 0.543277 TGCAGTCCAAGCCTCCTATG 59.457 55.000 0.00 0.0 0.00 2.23 F
3279 5482 0.404426 TCTCCCGTGAGACTCTCCAA 59.596 55.000 3.68 0.0 42.73 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1510 2368 0.179134 CGAGGTCGGACTTGGTCATC 60.179 60.0 8.23 0.0 33.68 2.92 R
2280 4060 0.747255 TAATCGAGCTCAGTCCAGGC 59.253 55.0 15.40 0.0 0.00 4.85 R
3825 6031 1.092348 CCACACGGTCAGAGACGATA 58.908 55.0 1.64 0.0 32.65 2.92 R
5277 7961 0.315886 ATGCTGTGTGTGTTGCCATG 59.684 50.0 0.00 0.0 0.00 3.66 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
27 28 8.630917 TCGGGTGAACAGTAAATTCAAAAATAA 58.369 29.630 0.00 0.00 37.80 1.40
28 29 9.418045 CGGGTGAACAGTAAATTCAAAAATAAT 57.582 29.630 0.00 0.00 37.80 1.28
129 130 1.130561 GCCATTTGTAGAAGTCGTGGC 59.869 52.381 0.00 0.00 43.09 5.01
133 134 3.955771 TTTGTAGAAGTCGTGGCAAAC 57.044 42.857 0.00 0.00 0.00 2.93
136 137 3.472652 TGTAGAAGTCGTGGCAAACAAT 58.527 40.909 0.00 0.00 0.00 2.71
137 138 3.496884 TGTAGAAGTCGTGGCAAACAATC 59.503 43.478 0.00 0.00 0.00 2.67
138 139 1.531149 AGAAGTCGTGGCAAACAATCG 59.469 47.619 0.00 0.00 0.00 3.34
143 147 1.659794 GTGGCAAACAATCGGTGCT 59.340 52.632 0.00 0.00 38.36 4.40
156 160 5.047377 ACAATCGGTGCTCCAAAAATGTTAT 60.047 36.000 5.52 0.00 0.00 1.89
220 228 3.629855 ACGACCACAAATGTCAATTCACA 59.370 39.130 0.00 0.00 32.91 3.58
264 272 6.991485 ACAACATTTGTCGCAATTTTAGAG 57.009 33.333 0.00 0.00 40.56 2.43
307 319 9.490663 CATTATTCTTGGATTTTACTGTTCGTC 57.509 33.333 0.00 0.00 0.00 4.20
309 321 4.320870 TCTTGGATTTTACTGTTCGTCCC 58.679 43.478 0.00 0.00 0.00 4.46
313 325 3.367703 GGATTTTACTGTTCGTCCCGAGA 60.368 47.826 0.00 0.00 37.14 4.04
341 353 3.158676 GAGCTCGGGACCATAAGAGTAT 58.841 50.000 0.00 0.00 33.57 2.12
447 459 6.575162 ATGTAAGAGGGTTTCAACATGTTC 57.425 37.500 8.48 0.00 34.95 3.18
448 460 4.513692 TGTAAGAGGGTTTCAACATGTTCG 59.486 41.667 8.48 4.95 0.00 3.95
456 468 6.095720 AGGGTTTCAACATGTTCGACTTAAAA 59.904 34.615 8.48 0.00 0.00 1.52
532 546 7.446632 CAACACTTTTACCGGTTGTTTAAAAC 58.553 34.615 15.04 0.00 36.70 2.43
534 548 6.807720 ACACTTTTACCGGTTGTTTAAAACTG 59.192 34.615 15.04 13.80 36.38 3.16
536 550 7.219344 CACTTTTACCGGTTGTTTAAAACTGAG 59.781 37.037 15.04 3.57 38.48 3.35
537 551 6.756299 TTTACCGGTTGTTTAAAACTGAGT 57.244 33.333 15.04 1.24 38.48 3.41
540 554 6.122850 ACCGGTTGTTTAAAACTGAGTAAC 57.877 37.500 0.00 0.00 38.48 2.50
541 555 5.066375 ACCGGTTGTTTAAAACTGAGTAACC 59.934 40.000 0.00 1.97 38.48 2.85
542 556 5.297527 CCGGTTGTTTAAAACTGAGTAACCT 59.702 40.000 8.91 0.00 38.48 3.50
543 557 6.482973 CCGGTTGTTTAAAACTGAGTAACCTA 59.517 38.462 8.91 0.00 38.48 3.08
544 558 7.173735 CCGGTTGTTTAAAACTGAGTAACCTAT 59.826 37.037 8.91 0.00 38.48 2.57
553 567 8.605325 AAAACTGAGTAACCTATAAGCTAGGA 57.395 34.615 8.06 0.00 38.09 2.94
554 568 7.826918 AACTGAGTAACCTATAAGCTAGGAG 57.173 40.000 8.06 0.00 38.09 3.69
562 576 7.619512 AACCTATAAGCTAGGAGTATTTGCT 57.380 36.000 8.06 0.00 38.09 3.91
563 577 7.234661 ACCTATAAGCTAGGAGTATTTGCTC 57.765 40.000 8.06 0.00 38.09 4.26
565 579 2.517650 AGCTAGGAGTATTTGCTCGC 57.482 50.000 0.00 0.00 36.38 5.03
578 592 1.446966 GCTCGCACCTGAGGAGAAC 60.447 63.158 4.99 0.00 36.47 3.01
633 647 3.107402 TCCTCTGCAGAAGACACCTAT 57.893 47.619 18.85 0.00 0.00 2.57
634 648 4.251103 TCCTCTGCAGAAGACACCTATA 57.749 45.455 18.85 0.00 0.00 1.31
662 676 4.141018 ACTGGTTTGGAATCCACCTAAACT 60.141 41.667 0.00 0.00 34.47 2.66
784 814 2.119484 AAAGGCCGACGACCATTCCA 62.119 55.000 2.14 0.00 0.00 3.53
900 930 3.179830 CATGTAGAACCTTCGAGAACCG 58.820 50.000 0.00 0.00 40.25 4.44
957 987 1.896465 CTCTCGTCCTCTCAAAACCCT 59.104 52.381 0.00 0.00 0.00 4.34
1188 1222 2.040884 CCCCGGATCCCCTTCTCA 60.041 66.667 0.73 0.00 0.00 3.27
1189 1223 1.462238 CCCCGGATCCCCTTCTCAT 60.462 63.158 0.73 0.00 0.00 2.90
1190 1224 1.484444 CCCCGGATCCCCTTCTCATC 61.484 65.000 0.73 0.00 0.00 2.92
1196 1230 2.112691 GGATCCCCTTCTCATCCCTCTA 59.887 54.545 0.00 0.00 31.31 2.43
1202 1240 6.217297 TCCCCTTCTCATCCCTCTATTTTTA 58.783 40.000 0.00 0.00 0.00 1.52
1343 1942 1.338200 GCGTTTCAGATCTGTGTCCCT 60.338 52.381 21.92 0.00 0.00 4.20
1377 1976 5.040635 GGTGTGTTTACTGGTGTGATTTTG 58.959 41.667 0.00 0.00 0.00 2.44
1429 2287 0.966179 TCACGGACAAGAGCAAGCTA 59.034 50.000 0.00 0.00 0.00 3.32
1510 2368 2.568090 GTTGACAGCGGCATTGGG 59.432 61.111 1.45 0.00 0.00 4.12
1827 3024 0.543277 TGCAGTCCAAGCCTCCTATG 59.457 55.000 0.00 0.00 0.00 2.23
1870 3265 4.271696 TGTCTTGATGTAGGTTCTGTGG 57.728 45.455 0.00 0.00 0.00 4.17
1966 3362 4.264253 TGTCTGCACTGCATAAGCTTAAT 58.736 39.130 10.85 0.00 42.74 1.40
1973 3369 4.025396 CACTGCATAAGCTTAATCCTGTCG 60.025 45.833 10.85 2.78 42.74 4.35
1997 3393 6.404844 CGGTTCTGTGATCTACTTGTCTATGT 60.405 42.308 0.00 0.00 0.00 2.29
2035 3431 4.558226 ACTGTGATGATTGGCTTACTGA 57.442 40.909 0.00 0.00 0.00 3.41
2057 3454 5.068855 TGACCATGTGTTGATGTGATTTGTT 59.931 36.000 0.00 0.00 0.00 2.83
2062 3459 7.326789 CCATGTGTTGATGTGATTTGTTCTTAC 59.673 37.037 0.00 0.00 0.00 2.34
2069 3466 5.412526 TGTGATTTGTTCTTACAACGGTC 57.587 39.130 0.00 0.00 43.66 4.79
2150 3548 2.555757 GCATGAGAAAACTCTGTTGCCT 59.444 45.455 0.00 0.00 0.00 4.75
2151 3549 3.365767 GCATGAGAAAACTCTGTTGCCTC 60.366 47.826 0.00 0.00 0.00 4.70
2153 3551 4.955811 TGAGAAAACTCTGTTGCCTCTA 57.044 40.909 0.00 0.93 0.00 2.43
2154 3552 4.632153 TGAGAAAACTCTGTTGCCTCTAC 58.368 43.478 0.00 0.00 0.00 2.59
2164 3581 2.235155 TGTTGCCTCTACTATGCGGAAA 59.765 45.455 0.00 0.00 0.00 3.13
2194 3611 7.315247 TGGTAATGTGATTAGTTGTGTATGC 57.685 36.000 0.00 0.00 0.00 3.14
2195 3612 7.109501 TGGTAATGTGATTAGTTGTGTATGCT 58.890 34.615 0.00 0.00 0.00 3.79
2299 4354 0.747255 GCCTGGACTGAGCTCGATTA 59.253 55.000 9.64 0.00 0.00 1.75
2315 4370 4.183865 TCGATTAAGATCTGTGCTGGTTG 58.816 43.478 0.00 0.00 0.00 3.77
2469 4614 6.683715 TCATATGTAAGCAATGCATGGATTG 58.316 36.000 29.55 29.55 34.97 2.67
2474 4619 1.674441 AGCAATGCATGGATTGACTCG 59.326 47.619 35.56 15.27 35.65 4.18
2479 4625 3.610040 TGCATGGATTGACTCGTACTT 57.390 42.857 0.00 0.00 0.00 2.24
2624 4817 7.701539 TGATGTATGTTTGGCTGTTCTTTAT 57.298 32.000 0.00 0.00 0.00 1.40
2671 4864 3.644823 TGCACATGCTTTCTGTTCATTG 58.355 40.909 5.31 0.00 42.66 2.82
2672 4865 2.410730 GCACATGCTTTCTGTTCATTGC 59.589 45.455 0.00 0.00 38.21 3.56
2952 5155 1.165907 TGGTCAACAAGCAGAAGCCG 61.166 55.000 0.00 0.00 43.56 5.52
3183 5386 1.807755 CGCCGTGTCTTCATCATGGAT 60.808 52.381 8.15 0.00 42.63 3.41
3279 5482 0.404426 TCTCCCGTGAGACTCTCCAA 59.596 55.000 3.68 0.00 42.73 3.53
3825 6031 1.594331 GCGACAAGGTTGAGAAGGTT 58.406 50.000 0.00 0.00 0.00 3.50
3843 6049 2.516923 GTTATCGTCTCTGACCGTGTG 58.483 52.381 0.00 0.00 0.00 3.82
3876 6082 1.367471 CTGTCTGGTGACTGGCGAA 59.633 57.895 0.00 0.00 43.29 4.70
4020 6226 2.104331 CTCCGTAAGCGTGCCGAT 59.896 61.111 0.00 0.00 36.15 4.18
4170 6379 1.202903 GGCCTGAGCATTGATGAGGAT 60.203 52.381 11.83 0.00 42.56 3.24
4182 6391 3.838271 GAGGATGACGAGGCGCCA 61.838 66.667 31.54 7.75 0.00 5.69
4260 6472 1.810030 GGTCGACTAAGCGCCAAGG 60.810 63.158 16.46 0.00 0.00 3.61
4283 6495 3.249973 CTGTCGGCTGTCGTCGTCA 62.250 63.158 0.09 0.00 39.73 4.35
4350 6563 0.387565 GTTGGATGGTTTTGGCACGT 59.612 50.000 0.00 0.00 0.00 4.49
4459 6672 8.911918 TTGTTGGTTCTACAATATGTGTTAGT 57.088 30.769 0.00 0.00 41.98 2.24
4460 6673 8.911918 TGTTGGTTCTACAATATGTGTTAGTT 57.088 30.769 0.00 0.00 41.98 2.24
4461 6674 9.999660 TGTTGGTTCTACAATATGTGTTAGTTA 57.000 29.630 0.00 0.00 41.98 2.24
4573 6787 5.770663 TGGATTCGTTTTTGAATTGTCCCTA 59.229 36.000 0.00 0.00 38.65 3.53
4622 6836 5.249393 ACATAGGAATGACTTCTGTTGGACT 59.751 40.000 0.00 0.00 36.54 3.85
4705 7105 2.131972 CTTGTGGATCAACGACGAACA 58.868 47.619 0.00 0.00 32.18 3.18
4706 7106 2.226602 TGTGGATCAACGACGAACAA 57.773 45.000 0.00 0.00 0.00 2.83
4707 7107 2.761559 TGTGGATCAACGACGAACAAT 58.238 42.857 0.00 0.00 0.00 2.71
4708 7108 2.734606 TGTGGATCAACGACGAACAATC 59.265 45.455 0.00 0.00 0.00 2.67
4709 7109 2.734606 GTGGATCAACGACGAACAATCA 59.265 45.455 0.00 0.00 0.00 2.57
4710 7110 2.993220 TGGATCAACGACGAACAATCAG 59.007 45.455 0.00 0.00 0.00 2.90
4711 7111 2.222819 GGATCAACGACGAACAATCAGC 60.223 50.000 0.00 0.00 0.00 4.26
4712 7112 1.144969 TCAACGACGAACAATCAGCC 58.855 50.000 0.00 0.00 0.00 4.85
4713 7113 0.865111 CAACGACGAACAATCAGCCA 59.135 50.000 0.00 0.00 0.00 4.75
4714 7114 0.865769 AACGACGAACAATCAGCCAC 59.134 50.000 0.00 0.00 0.00 5.01
4715 7115 0.249699 ACGACGAACAATCAGCCACA 60.250 50.000 0.00 0.00 0.00 4.17
4716 7116 0.439985 CGACGAACAATCAGCCACAG 59.560 55.000 0.00 0.00 0.00 3.66
4717 7117 1.795768 GACGAACAATCAGCCACAGA 58.204 50.000 0.00 0.00 0.00 3.41
4718 7118 2.350522 GACGAACAATCAGCCACAGAT 58.649 47.619 0.00 0.00 0.00 2.90
4719 7119 2.349886 GACGAACAATCAGCCACAGATC 59.650 50.000 0.00 0.00 0.00 2.75
4720 7120 2.027745 ACGAACAATCAGCCACAGATCT 60.028 45.455 0.00 0.00 0.00 2.75
4812 7277 3.545633 CTTGCGACTAAAAGTGCTTGAC 58.454 45.455 0.00 0.00 0.00 3.18
4943 7505 5.126222 TGATCTCATCTGTGTAGACAAGGAC 59.874 44.000 0.00 0.00 35.34 3.85
5057 7714 2.675317 CGACCCTGAAGTCCTTCACATC 60.675 54.545 5.64 3.75 43.90 3.06
5139 7806 1.469308 CCTTATAGAGCCGAGGTAGCG 59.531 57.143 0.00 0.00 34.64 4.26
5277 7961 6.366061 TGTCAGTAACTCAATGCATATATCGC 59.634 38.462 0.00 1.55 0.00 4.58
5302 7986 2.480073 GCAACACACACAGCATGAAGTT 60.480 45.455 0.00 0.00 39.69 2.66
5372 8140 5.007682 GTGCTAATGGAGAACTTGGGTTTA 58.992 41.667 0.00 0.00 35.58 2.01
5386 8154 5.425862 ACTTGGGTTTACTCCTAGGATTCTC 59.574 44.000 13.12 2.13 32.68 2.87
5432 8209 7.912250 AGAATTGCTTGAATAAAGTATTCGCTG 59.088 33.333 4.10 0.00 45.82 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 6.913170 ACTTGGTAAGCATAGACAACATTTG 58.087 36.000 0.00 0.00 0.00 2.32
129 130 2.791383 TTTGGAGCACCGATTGTTTG 57.209 45.000 0.00 0.00 39.42 2.93
133 134 3.302365 ACATTTTTGGAGCACCGATTG 57.698 42.857 0.00 0.00 39.42 2.67
136 137 5.461032 AAATAACATTTTTGGAGCACCGA 57.539 34.783 0.00 0.00 39.42 4.69
137 138 6.201806 TGAAAAATAACATTTTTGGAGCACCG 59.798 34.615 12.89 0.00 34.29 4.94
138 139 7.489574 TGAAAAATAACATTTTTGGAGCACC 57.510 32.000 12.89 0.00 32.85 5.01
180 184 5.221342 TGGTCGTGGCAAATAAACAAAATCT 60.221 36.000 0.00 0.00 0.00 2.40
288 300 4.680171 GGGACGAACAGTAAAATCCAAG 57.320 45.455 0.00 0.00 0.00 3.61
305 317 2.478831 GAGCTCATTTGATCTCGGGAC 58.521 52.381 9.40 0.00 29.21 4.46
313 325 0.911769 TGGTCCCGAGCTCATTTGAT 59.088 50.000 15.40 0.00 0.00 2.57
341 353 5.362556 GAGAGCTATGTTGCACTCAAAAA 57.637 39.130 8.58 0.00 45.50 1.94
365 377 2.356382 TGTGCTAAACCCTTTGTTGTCG 59.644 45.455 0.00 0.00 37.23 4.35
427 439 4.753107 GTCGAACATGTTGAAACCCTCTTA 59.247 41.667 17.58 0.00 0.00 2.10
504 518 4.099380 ACAACCGGTAAAAGTGTTGTTG 57.901 40.909 8.00 0.00 46.59 3.33
529 543 7.840210 ACTCCTAGCTTATAGGTTACTCAGTTT 59.160 37.037 0.00 0.00 36.16 2.66
532 546 9.523168 AATACTCCTAGCTTATAGGTTACTCAG 57.477 37.037 0.00 0.00 36.16 3.35
536 550 8.586744 AGCAAATACTCCTAGCTTATAGGTTAC 58.413 37.037 0.00 0.00 36.16 2.50
537 551 8.722622 AGCAAATACTCCTAGCTTATAGGTTA 57.277 34.615 0.00 0.00 36.16 2.85
540 554 6.326375 CGAGCAAATACTCCTAGCTTATAGG 58.674 44.000 0.00 0.00 35.36 2.57
541 555 5.802956 GCGAGCAAATACTCCTAGCTTATAG 59.197 44.000 0.00 0.00 35.36 1.31
542 556 5.243060 TGCGAGCAAATACTCCTAGCTTATA 59.757 40.000 0.00 0.00 35.36 0.98
543 557 4.039245 TGCGAGCAAATACTCCTAGCTTAT 59.961 41.667 0.00 0.00 35.36 1.73
544 558 3.383505 TGCGAGCAAATACTCCTAGCTTA 59.616 43.478 0.00 0.00 35.36 3.09
546 560 1.757118 TGCGAGCAAATACTCCTAGCT 59.243 47.619 0.00 0.00 38.43 3.32
548 562 2.101582 AGGTGCGAGCAAATACTCCTAG 59.898 50.000 0.00 0.00 32.79 3.02
549 563 2.108168 AGGTGCGAGCAAATACTCCTA 58.892 47.619 0.00 0.00 32.79 2.94
552 566 1.929836 CTCAGGTGCGAGCAAATACTC 59.070 52.381 0.00 0.00 0.00 2.59
553 567 1.406069 CCTCAGGTGCGAGCAAATACT 60.406 52.381 0.00 0.00 0.00 2.12
554 568 1.009829 CCTCAGGTGCGAGCAAATAC 58.990 55.000 0.00 0.00 0.00 1.89
562 576 1.533033 TGGTTCTCCTCAGGTGCGA 60.533 57.895 0.00 0.00 34.23 5.10
563 577 1.374758 GTGGTTCTCCTCAGGTGCG 60.375 63.158 0.00 0.00 34.23 5.34
565 579 1.339438 CCATGTGGTTCTCCTCAGGTG 60.339 57.143 0.00 0.00 39.98 4.00
578 592 8.477256 ACAATTCCTTATTACAAATCCATGTGG 58.523 33.333 0.00 0.00 34.75 4.17
633 647 4.770010 GGTGGATTCCAAACCAGTTGATTA 59.230 41.667 7.05 0.00 39.87 1.75
634 648 3.578282 GGTGGATTCCAAACCAGTTGATT 59.422 43.478 7.05 0.00 39.87 2.57
662 676 3.118186 TGGTTTTGGAAGGAAAGACGAGA 60.118 43.478 0.00 0.00 0.00 4.04
784 814 2.351706 TAGGGTTGCGGTGAGTTTTT 57.648 45.000 0.00 0.00 0.00 1.94
900 930 2.544267 GCCTATTTATGTGTGGTCTCGC 59.456 50.000 0.00 0.00 0.00 5.03
957 987 1.002533 AGGCGGCTAGGGTTAGGAA 59.997 57.895 11.03 0.00 0.00 3.36
1030 1060 4.457496 CTCCGTCGCCATGGCTGT 62.457 66.667 33.07 0.00 39.32 4.40
1172 1205 1.484444 GGATGAGAAGGGGATCCGGG 61.484 65.000 5.45 0.00 38.33 5.73
1188 1222 4.042174 TCACGGGGTAAAAATAGAGGGAT 58.958 43.478 0.00 0.00 0.00 3.85
1189 1223 3.452878 TCACGGGGTAAAAATAGAGGGA 58.547 45.455 0.00 0.00 0.00 4.20
1190 1224 3.918294 TCACGGGGTAAAAATAGAGGG 57.082 47.619 0.00 0.00 0.00 4.30
1196 1230 1.385528 GCGGATCACGGGGTAAAAAT 58.614 50.000 0.00 0.00 44.51 1.82
1256 1294 2.100418 GACGGAATCTAAACCCTAGCGT 59.900 50.000 0.00 0.00 0.00 5.07
1343 1942 2.544590 AAACACACCACGTCAGCCCA 62.545 55.000 0.00 0.00 0.00 5.36
1377 1976 1.000396 ATCTTGTCCAAGGCCTGCC 60.000 57.895 5.69 0.00 38.88 4.85
1510 2368 0.179134 CGAGGTCGGACTTGGTCATC 60.179 60.000 8.23 0.00 33.68 2.92
1522 2719 1.002250 CGAGGTTGTTGACGAGGTCG 61.002 60.000 0.00 0.00 46.33 4.79
1827 3024 7.065563 AGACATGAAGAGTAAATCAATCACAGC 59.934 37.037 0.00 0.00 31.33 4.40
1870 3265 7.434602 GCAACCTACTAATACAGCTACACTAAC 59.565 40.741 0.00 0.00 0.00 2.34
1966 3362 1.924731 AGATCACAGAACCGACAGGA 58.075 50.000 0.00 0.00 41.02 3.86
1973 3369 6.868622 ACATAGACAAGTAGATCACAGAACC 58.131 40.000 0.00 0.00 0.00 3.62
1997 3393 5.686753 TCACAGTTTAAAAGGCTTGGACTA 58.313 37.500 0.00 0.00 0.00 2.59
2035 3431 5.302568 AGAACAAATCACATCAACACATGGT 59.697 36.000 0.00 0.00 0.00 3.55
2057 3454 4.885907 CCTATCTACCAGACCGTTGTAAGA 59.114 45.833 0.00 0.00 0.00 2.10
2062 3459 2.032620 AGCCTATCTACCAGACCGTTG 58.967 52.381 0.00 0.00 0.00 4.10
2069 3466 7.716799 AGATCAAGATAAGCCTATCTACCAG 57.283 40.000 5.26 0.00 42.95 4.00
2150 3548 5.680619 ACCATCAAATTTCCGCATAGTAGA 58.319 37.500 0.00 0.00 0.00 2.59
2151 3549 7.490962 TTACCATCAAATTTCCGCATAGTAG 57.509 36.000 0.00 0.00 0.00 2.57
2153 3551 6.321181 ACATTACCATCAAATTTCCGCATAGT 59.679 34.615 0.00 0.00 0.00 2.12
2154 3552 6.638063 CACATTACCATCAAATTTCCGCATAG 59.362 38.462 0.00 0.00 0.00 2.23
2164 3581 9.023962 ACACAACTAATCACATTACCATCAAAT 57.976 29.630 0.00 0.00 0.00 2.32
2194 3611 0.835941 AGTGCAGCCTCCCAGATAAG 59.164 55.000 0.00 0.00 0.00 1.73
2195 3612 0.543277 CAGTGCAGCCTCCCAGATAA 59.457 55.000 0.00 0.00 0.00 1.75
2199 3620 2.189191 TAAGCAGTGCAGCCTCCCAG 62.189 60.000 19.20 0.00 34.23 4.45
2280 4060 0.747255 TAATCGAGCTCAGTCCAGGC 59.253 55.000 15.40 0.00 0.00 4.85
2299 4354 5.108187 ACATATCAACCAGCACAGATCTT 57.892 39.130 0.00 0.00 0.00 2.40
2339 4473 7.786030 TCATGGTTAAAATGTTGGAAAGTCAA 58.214 30.769 0.00 0.00 0.00 3.18
2344 4486 7.976135 CCAATCATGGTTAAAATGTTGGAAA 57.024 32.000 17.63 0.00 42.18 3.13
2469 4614 7.760340 AGAAGGTCAAATCAATAAGTACGAGTC 59.240 37.037 0.00 0.00 0.00 3.36
2602 4795 9.632638 AGATATAAAGAACAGCCAAACATACAT 57.367 29.630 0.00 0.00 0.00 2.29
2643 4836 4.444536 ACAGAAAGCATGTGCAAACAAAT 58.555 34.783 7.83 0.00 45.16 2.32
2671 4864 6.202570 TGAAAGCAAATTGTAACAAATCAGGC 59.797 34.615 0.00 0.00 0.00 4.85
2672 4865 7.652909 TCTGAAAGCAAATTGTAACAAATCAGG 59.347 33.333 0.00 0.00 32.42 3.86
3183 5386 3.515502 CAGGGATCAACTCCTCACAGTTA 59.484 47.826 0.00 0.00 44.28 2.24
3279 5482 3.648067 TGACCTTGAGGATCTTGTTCTGT 59.352 43.478 3.59 0.00 38.94 3.41
3825 6031 1.092348 CCACACGGTCAGAGACGATA 58.908 55.000 1.64 0.00 32.65 2.92
3843 6049 2.352805 CAGCAAGGGGAGTCCACC 59.647 66.667 8.15 8.24 38.24 4.61
3876 6082 1.226262 GTTGGCGGTCCACCCATAT 59.774 57.895 0.00 0.00 43.33 1.78
3924 6130 1.992277 AGCCATGCTCGAGTCCCTT 60.992 57.895 15.13 0.00 30.62 3.95
4020 6226 0.179094 ACTTGTCGTTCTTGTCGGCA 60.179 50.000 0.00 0.00 41.07 5.69
4170 6379 2.989253 TTCTCTGGCGCCTCGTCA 60.989 61.111 29.70 5.44 39.83 4.35
4182 6391 0.388649 GCATGTCGGTGTCGTTCTCT 60.389 55.000 0.00 0.00 37.69 3.10
4283 6495 3.418687 TGCAGGGCATGGACATCT 58.581 55.556 0.00 0.00 31.71 2.90
4350 6563 6.870971 AAGACAAAACCGATACAGCTAAAA 57.129 33.333 0.00 0.00 0.00 1.52
4478 6691 1.864435 GCAGATGCAAGCAATAGCAGC 60.864 52.381 0.00 0.00 46.70 5.25
4529 6743 0.596082 GAAGCGGCCAAACAAGCTAA 59.404 50.000 2.24 0.00 39.25 3.09
4538 6752 1.745115 CGAATCCAGAAGCGGCCAA 60.745 57.895 2.24 0.00 0.00 4.52
4573 6787 3.173953 TGGCAATTCCTTTGTCATCCT 57.826 42.857 0.00 0.00 44.80 3.24
4607 6821 3.194861 CGAACAAGTCCAACAGAAGTCA 58.805 45.455 0.00 0.00 0.00 3.41
4617 6831 5.751509 GCACATATATGTACGAACAAGTCCA 59.248 40.000 17.86 0.00 39.39 4.02
4642 6879 1.941325 CCATTCACGGCCTCTAGAAC 58.059 55.000 0.00 0.00 0.00 3.01
4705 7105 7.039504 ACAACAATTTTAGATCTGTGGCTGATT 60.040 33.333 5.18 0.00 0.00 2.57
4706 7106 6.435277 ACAACAATTTTAGATCTGTGGCTGAT 59.565 34.615 5.18 0.00 0.00 2.90
4707 7107 5.769662 ACAACAATTTTAGATCTGTGGCTGA 59.230 36.000 5.18 0.00 0.00 4.26
4708 7108 6.017400 ACAACAATTTTAGATCTGTGGCTG 57.983 37.500 5.18 0.06 0.00 4.85
4709 7109 6.655078 AACAACAATTTTAGATCTGTGGCT 57.345 33.333 5.18 0.00 0.00 4.75
4710 7110 7.115378 CAGAAACAACAATTTTAGATCTGTGGC 59.885 37.037 5.18 0.00 0.00 5.01
4711 7111 8.352201 TCAGAAACAACAATTTTAGATCTGTGG 58.648 33.333 5.18 0.00 34.77 4.17
4712 7112 9.173939 GTCAGAAACAACAATTTTAGATCTGTG 57.826 33.333 5.18 0.00 34.77 3.66
4713 7113 9.125026 AGTCAGAAACAACAATTTTAGATCTGT 57.875 29.630 5.18 0.00 34.77 3.41
4714 7114 9.604626 GAGTCAGAAACAACAATTTTAGATCTG 57.395 33.333 5.18 0.00 34.54 2.90
4715 7115 9.566432 AGAGTCAGAAACAACAATTTTAGATCT 57.434 29.630 0.00 0.00 0.00 2.75
4748 7153 9.905713 AAAAATACTCTGTTCCTGCATCTTATA 57.094 29.630 0.00 0.00 0.00 0.98
4812 7277 1.003718 GTTGACGGAGGGTTCAGGG 60.004 63.158 0.00 0.00 0.00 4.45
4921 7483 4.404073 GGTCCTTGTCTACACAGATGAGAT 59.596 45.833 0.00 0.00 32.71 2.75
5030 7686 2.526873 ACTTCAGGGTCGGCAGGT 60.527 61.111 0.00 0.00 0.00 4.00
5139 7806 1.302033 CCCCTGTGAGTGAGTGTGC 60.302 63.158 0.00 0.00 0.00 4.57
5277 7961 0.315886 ATGCTGTGTGTGTTGCCATG 59.684 50.000 0.00 0.00 0.00 3.66
5302 7986 4.801330 TTGAATCTCAGAACCGAAGCTA 57.199 40.909 0.00 0.00 0.00 3.32
5386 8154 1.518325 TCACTGGCACGTTACAATGG 58.482 50.000 0.00 0.00 0.00 3.16
5432 8209 9.691362 TCAAATAAGCTTTTACTGTTTCATTCC 57.309 29.630 3.20 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.