Multiple sequence alignment - TraesCS1B01G272100

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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 TraesCS1B01G272100 chr1B 100.000 5569 0 0 1 5569 478060573 478055005 0.000000e+00 10285.0
1 TraesCS1B01G272100 chr1B 88.633 1478 115 26 1110 2548 477943673 477945136 0.000000e+00 1749.0
2 TraesCS1B01G272100 chr1B 91.826 991 71 4 3559 4539 477946777 477947767 0.000000e+00 1373.0
3 TraesCS1B01G272100 chr1B 85.596 1208 127 21 3411 4599 477947872 477949051 0.000000e+00 1223.0
4 TraesCS1B01G272100 chr1B 84.431 1002 117 21 1782 2755 477945138 477946128 0.000000e+00 950.0
5 TraesCS1B01G272100 chr1B 78.469 627 92 22 4614 5224 587035189 587035788 2.450000e-98 370.0
6 TraesCS1B01G272100 chr1B 82.701 422 56 8 5057 5471 587526518 587526929 5.300000e-95 359.0
7 TraesCS1B01G272100 chr1B 88.435 147 17 0 3411 3557 477946582 477946728 1.590000e-40 178.0
8 TraesCS1B01G272100 chr1D 94.566 4840 179 39 749 5542 355435516 355430715 0.000000e+00 7404.0
9 TraesCS1B01G272100 chr1D 91.818 990 72 3 3559 4539 355319634 355320623 0.000000e+00 1371.0
10 TraesCS1B01G272100 chr1D 86.010 1208 120 23 3411 4599 355320728 355321905 0.000000e+00 1249.0
11 TraesCS1B01G272100 chr1D 84.646 1003 112 24 1782 2755 355317979 355318968 0.000000e+00 961.0
12 TraesCS1B01G272100 chr1D 82.232 681 69 20 1903 2548 355317314 355317977 1.770000e-149 540.0
13 TraesCS1B01G272100 chr1D 81.107 614 68 27 4884 5471 434034259 434034850 1.100000e-121 448.0
14 TraesCS1B01G272100 chr1D 85.650 446 37 11 1087 1521 355316833 355317262 1.420000e-120 444.0
15 TraesCS1B01G272100 chr1D 83.102 432 49 14 5045 5471 433979452 433979864 6.810000e-99 372.0
16 TraesCS1B01G272100 chr1D 87.665 227 26 2 1 225 355435752 355435526 4.280000e-66 263.0
17 TraesCS1B01G272100 chr1D 78.249 377 61 9 4986 5349 209738954 209739322 7.260000e-54 222.0
18 TraesCS1B01G272100 chr1D 89.116 147 16 0 3411 3557 355319439 355319585 3.430000e-42 183.0
19 TraesCS1B01G272100 chr1A 93.091 5124 245 50 480 5564 455611351 455606298 0.000000e+00 7400.0
20 TraesCS1B01G272100 chr1A 89.050 484 47 4 7 484 455611913 455611430 3.710000e-166 595.0
21 TraesCS1B01G272100 chr7A 97.059 204 6 0 1159 1362 20685091 20684888 1.490000e-90 344.0
22 TraesCS1B01G272100 chr7A 95.361 194 9 0 1510 1703 20684889 20684696 5.420000e-80 309.0
23 TraesCS1B01G272100 chr7A 82.075 212 23 14 379 587 116190303 116190104 3.450000e-37 167.0
24 TraesCS1B01G272100 chr4A 96.078 204 8 0 1159 1362 603348258 603348461 3.220000e-87 333.0
25 TraesCS1B01G272100 chr4A 95.588 204 9 0 1159 1362 728411712 728411915 1.500000e-85 327.0
26 TraesCS1B01G272100 chr4A 95.939 197 8 0 1507 1703 603348457 603348653 2.500000e-83 320.0
27 TraesCS1B01G272100 chr4A 94.416 197 11 0 1507 1703 728411911 728412107 2.520000e-78 303.0
28 TraesCS1B01G272100 chr4A 88.444 225 20 4 3877 4095 67514492 67514716 3.310000e-67 267.0
29 TraesCS1B01G272100 chr2A 95.098 204 10 0 1159 1362 680893915 680893712 6.960000e-84 322.0
30 TraesCS1B01G272100 chr2A 95.361 194 9 0 1510 1703 680893713 680893520 5.420000e-80 309.0
31 TraesCS1B01G272100 chr6A 95.074 203 10 0 1159 1361 60063016 60062814 2.500000e-83 320.0
32 TraesCS1B01G272100 chr6B 93.909 197 12 0 1507 1703 104568100 104568296 1.170000e-76 298.0
33 TraesCS1B01G272100 chr3A 94.330 194 11 0 1510 1703 459525643 459525450 1.170000e-76 298.0
34 TraesCS1B01G272100 chr3A 80.478 251 31 12 375 614 36669496 36669739 5.730000e-40 176.0
35 TraesCS1B01G272100 chr3A 80.478 251 31 13 375 614 36670985 36671228 5.730000e-40 176.0
36 TraesCS1B01G272100 chr4D 80.645 372 56 8 4989 5349 319546521 319546155 1.980000e-69 274.0
37 TraesCS1B01G272100 chr7B 88.000 225 21 4 3877 4095 52983548 52983772 1.540000e-65 261.0
38 TraesCS1B01G272100 chr7B 88.479 217 21 2 3877 4089 52956882 52956666 5.530000e-65 259.0
39 TraesCS1B01G272100 chr5B 80.161 373 55 11 4989 5349 665948989 665948624 1.540000e-65 261.0
40 TraesCS1B01G272100 chr5B 79.752 242 35 12 379 614 3483393 3483626 4.460000e-36 163.0
41 TraesCS1B01G272100 chr5B 100.000 36 0 0 3355 3390 64309944 64309909 3.600000e-07 67.6
42 TraesCS1B01G272100 chr2B 81.933 238 34 7 379 614 151646097 151645867 5.690000e-45 193.0
43 TraesCS1B01G272100 chr2B 80.120 166 27 6 5399 5562 449679341 449679502 9.800000e-23 119.0
44 TraesCS1B01G272100 chr2D 83.105 219 21 14 379 592 99740781 99740574 9.530000e-43 185.0
45 TraesCS1B01G272100 chr3D 79.675 246 35 12 379 614 517012043 517011803 4.460000e-36 163.0
46 TraesCS1B01G272100 chr3D 78.495 279 37 15 379 638 487225204 487225478 1.610000e-35 161.0


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 TraesCS1B01G272100 chr1B 478055005 478060573 5568 True 10285.000000 10285 100.000000 1 5569 1 chr1B.!!$R1 5568
1 TraesCS1B01G272100 chr1B 477943673 477949051 5378 False 1094.600000 1749 87.784200 1110 4599 5 chr1B.!!$F3 3489
2 TraesCS1B01G272100 chr1B 587035189 587035788 599 False 370.000000 370 78.469000 4614 5224 1 chr1B.!!$F1 610
3 TraesCS1B01G272100 chr1D 355430715 355435752 5037 True 3833.500000 7404 91.115500 1 5542 2 chr1D.!!$R1 5541
4 TraesCS1B01G272100 chr1D 355316833 355321905 5072 False 791.333333 1371 86.578667 1087 4599 6 chr1D.!!$F4 3512
5 TraesCS1B01G272100 chr1D 434034259 434034850 591 False 448.000000 448 81.107000 4884 5471 1 chr1D.!!$F3 587
6 TraesCS1B01G272100 chr1A 455606298 455611913 5615 True 3997.500000 7400 91.070500 7 5564 2 chr1A.!!$R1 5557

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
384 390 0.582005 GTGCTCACAGACGTTTGGTC 59.418 55.000 11.17 0.0 46.45 4.02 F
903 1009 1.000359 GCCCTAGCCCACCAAATGT 60.000 57.895 0.00 0.0 0.00 2.71 F
1662 1799 1.153823 CTTCGTGCCTCCGTACCTG 60.154 63.158 0.00 0.0 0.00 4.00 F
2305 3263 0.394762 ACCACGCGTAGTCAGGGATA 60.395 55.000 13.44 0.0 0.00 2.59 F
3394 4575 0.392193 ATGAGGAGGCTCGTTGCTTG 60.392 55.000 11.50 0.0 42.39 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1527 1662 0.036952 CGGATTCAGACCACAGCAGT 60.037 55.0 0.00 0.0 0.00 4.40 R
2220 3152 0.839946 AAGGAGGCGAGCAATGGTAT 59.160 50.0 0.00 0.0 0.00 2.73 R
3222 4403 0.108662 ACGACGATCAAGCATGAGCA 60.109 50.0 8.04 0.0 42.11 4.26 R
3905 5144 0.397941 CACAGCCAACAGGAGGAAGA 59.602 55.0 0.00 0.0 0.00 2.87 R
4612 7082 1.249407 ACTGAACTCCGTGACTCTCC 58.751 55.0 0.00 0.0 0.00 3.71 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
52 53 5.181056 AGAACACATTTGTCATGCACGATAA 59.819 36.000 0.00 0.00 33.55 1.75
57 58 0.718904 TGTCATGCACGATAACACGC 59.281 50.000 0.00 0.00 36.70 5.34
61 63 1.135831 CATGCACGATAACACGCCAAA 60.136 47.619 0.00 0.00 36.70 3.28
64 66 2.030717 TGCACGATAACACGCCAAATTT 60.031 40.909 0.00 0.00 36.70 1.82
94 96 3.073798 TGTGATCCCACCTCAAGCTTTAA 59.926 43.478 0.00 0.00 42.53 1.52
124 126 3.190874 CTCTCGGGCAATAGACAACTTC 58.809 50.000 0.00 0.00 0.00 3.01
135 137 2.180276 AGACAACTTCGAGCACCCTAT 58.820 47.619 0.00 0.00 0.00 2.57
136 138 2.093973 AGACAACTTCGAGCACCCTATG 60.094 50.000 0.00 0.00 0.00 2.23
143 145 1.837439 TCGAGCACCCTATGACCAATT 59.163 47.619 0.00 0.00 0.00 2.32
145 147 2.355756 CGAGCACCCTATGACCAATTTG 59.644 50.000 0.00 0.00 0.00 2.32
159 161 2.554032 CCAATTTGTCAGGCTTTCGACT 59.446 45.455 5.24 0.00 33.18 4.18
169 171 3.194968 CAGGCTTTCGACTAGTTTCCCTA 59.805 47.826 0.00 0.00 0.00 3.53
191 193 7.283354 CCCTAATAAACTGACCAATTCTCTTCC 59.717 40.741 0.00 0.00 0.00 3.46
285 291 3.866651 TGATGAAAAGTAGAGCTCCTGC 58.133 45.455 10.93 0.47 40.05 4.85
287 293 1.279271 TGAAAAGTAGAGCTCCTGCCC 59.721 52.381 10.93 0.00 40.80 5.36
365 371 7.716799 AAGCTCAGTATCTATGAATCCTAGG 57.283 40.000 0.82 0.82 0.00 3.02
366 372 6.799827 AGCTCAGTATCTATGAATCCTAGGT 58.200 40.000 9.08 0.00 0.00 3.08
369 375 6.556639 TCAGTATCTATGAATCCTAGGTGCT 58.443 40.000 9.08 0.00 0.00 4.40
372 378 5.736951 ATCTATGAATCCTAGGTGCTCAC 57.263 43.478 9.08 0.00 0.00 3.51
384 390 0.582005 GTGCTCACAGACGTTTGGTC 59.418 55.000 11.17 0.00 46.45 4.02
485 493 9.965824 AATAAACTTGACCTTTCATTGTACTTG 57.034 29.630 0.00 0.00 0.00 3.16
486 494 7.404671 AAACTTGACCTTTCATTGTACTTGT 57.595 32.000 0.00 0.00 0.00 3.16
487 495 6.619801 ACTTGACCTTTCATTGTACTTGTC 57.380 37.500 0.00 0.00 0.00 3.18
488 496 6.119536 ACTTGACCTTTCATTGTACTTGTCA 58.880 36.000 0.00 0.00 0.00 3.58
489 497 6.601613 ACTTGACCTTTCATTGTACTTGTCAA 59.398 34.615 0.00 0.00 38.67 3.18
516 605 8.978874 AAAAATTCACAAAAATAAGAAGGCCT 57.021 26.923 0.00 0.00 0.00 5.19
573 662 4.836125 AAATAGTGCAAACAGTGACCTG 57.164 40.909 0.00 0.00 44.68 4.00
604 694 8.541899 ACAAATAACTTTTCCCCTAAAGTCAA 57.458 30.769 0.00 0.00 45.13 3.18
605 695 8.418662 ACAAATAACTTTTCCCCTAAAGTCAAC 58.581 33.333 0.00 0.00 45.13 3.18
607 697 4.160642 ACTTTTCCCCTAAAGTCAACGT 57.839 40.909 0.00 0.00 43.04 3.99
736 842 9.550406 CTATCCTAGACCTCCTATTCTTATACG 57.450 40.741 0.00 0.00 0.00 3.06
786 892 6.837992 TCTTATACGTTTTGTCATTCTTGGC 58.162 36.000 0.00 0.00 0.00 4.52
869 975 1.508632 TTCCGCTACTGTTTGCTGAC 58.491 50.000 0.00 0.00 0.00 3.51
883 989 2.182827 TGCTGACTTGCTCTAGTCCAT 58.817 47.619 8.54 0.00 43.11 3.41
903 1009 1.000359 GCCCTAGCCCACCAAATGT 60.000 57.895 0.00 0.00 0.00 2.71
975 1085 3.459969 AGTCCATCCTCTTCCATAAACCC 59.540 47.826 0.00 0.00 0.00 4.11
990 1100 3.459063 CCCGACCGGTCTTCTCCC 61.459 72.222 30.92 5.00 0.00 4.30
1492 1627 7.984422 TCATGACTACTGATGATTGTTTGTT 57.016 32.000 0.00 0.00 0.00 2.83
1493 1628 8.394971 TCATGACTACTGATGATTGTTTGTTT 57.605 30.769 0.00 0.00 0.00 2.83
1502 1637 7.040823 ACTGATGATTGTTTGTTTCTTCTCCTC 60.041 37.037 0.00 0.00 0.00 3.71
1527 1662 4.594123 TGTTCCGTGTAATCTTCTGTCA 57.406 40.909 0.00 0.00 0.00 3.58
1582 1717 2.213499 CCCATGCGACATTCCTAGTTC 58.787 52.381 0.00 0.00 0.00 3.01
1602 1737 5.252630 AGTTCCCCTTCTCTTGATTTCTGAT 59.747 40.000 0.00 0.00 0.00 2.90
1614 1749 6.550854 TCTTGATTTCTGATCCCTTTTGTTGT 59.449 34.615 0.00 0.00 0.00 3.32
1662 1799 1.153823 CTTCGTGCCTCCGTACCTG 60.154 63.158 0.00 0.00 0.00 4.00
1804 1941 3.319198 GTTCTCCCACCGCTCCCA 61.319 66.667 0.00 0.00 0.00 4.37
1884 2021 3.003482 GGATGATTCTGCTGTCAATCTGC 59.997 47.826 6.58 0.00 40.62 4.26
1922 2059 2.799126 TTGATGCTAATCGGTTGGGT 57.201 45.000 0.00 0.00 35.37 4.51
2220 3152 4.100963 TCTTGCTCCTCAGTTTGTTCTGTA 59.899 41.667 0.00 0.00 36.85 2.74
2305 3263 0.394762 ACCACGCGTAGTCAGGGATA 60.395 55.000 13.44 0.00 0.00 2.59
2322 3280 7.808856 GTCAGGGATATCTGTAACTACGAATTC 59.191 40.741 2.05 0.00 36.25 2.17
2427 3412 4.340950 TGAATGAGGTTTCCTTGTTGGTTC 59.659 41.667 0.00 0.00 31.76 3.62
2461 3447 2.973694 TAACGCCTTCACCTATGGTC 57.026 50.000 0.00 0.00 31.02 4.02
2469 3455 4.344102 GCCTTCACCTATGGTCTACATACA 59.656 45.833 0.00 0.00 41.03 2.29
2495 3497 4.710324 TGTTCTTACTGTCGAATTTGGGT 58.290 39.130 0.00 0.00 0.00 4.51
2643 3645 7.235804 AGGTGTAATGGTGTTTAGTTGGTATT 58.764 34.615 0.00 0.00 0.00 1.89
2649 3651 8.715190 AATGGTGTTTAGTTGGTATTTAAGGT 57.285 30.769 0.00 0.00 0.00 3.50
2663 3665 9.914834 TGGTATTTAAGGTTATATATGGATGGC 57.085 33.333 0.00 0.00 0.00 4.40
2675 3677 0.968405 TGGATGGCAGCCAAAACTTC 59.032 50.000 24.33 11.09 36.95 3.01
2758 3767 1.352622 TGGCCAACTCAAGGACCAGT 61.353 55.000 0.61 0.00 31.11 4.00
2999 4177 4.953579 AGCCCAACTGAAAAACTGAAACTA 59.046 37.500 0.00 0.00 0.00 2.24
3046 4225 4.215613 CGAGCTACACCACAGCATACTATA 59.784 45.833 0.00 0.00 41.66 1.31
3140 4321 8.879759 CAAGTTAAGTCTGTTGTACTTTCAGAA 58.120 33.333 13.56 0.00 39.42 3.02
3159 4340 3.528905 AGAATTCATGGATGGAACCCTCA 59.471 43.478 8.44 0.00 0.00 3.86
3164 4345 3.117776 TCATGGATGGAACCCTCATTCTG 60.118 47.826 0.00 0.00 0.00 3.02
3183 4364 5.692115 TCTGGGATGCAGTGTTTTATCTA 57.308 39.130 0.00 0.00 0.00 1.98
3222 4403 4.974645 TCACTGGTCTGTAATTTCTGGT 57.025 40.909 0.00 0.00 0.00 4.00
3256 4437 1.512926 GTCGTGTTTGATCTGCCTGT 58.487 50.000 0.00 0.00 0.00 4.00
3261 4442 0.953727 GTTTGATCTGCCTGTGTGCA 59.046 50.000 0.00 0.00 39.37 4.57
3394 4575 0.392193 ATGAGGAGGCTCGTTGCTTG 60.392 55.000 11.50 0.00 42.39 4.01
3665 4902 9.859427 TTTGTGTTCATTCCATAATCTCATTTC 57.141 29.630 0.00 0.00 0.00 2.17
3887 5126 6.931281 AGAATCTGTACAATATCAATGTCCGG 59.069 38.462 0.00 0.00 32.27 5.14
3905 5144 1.296715 GAAGGTCGTGCTGATGGGT 59.703 57.895 0.00 0.00 0.00 4.51
4134 5374 2.549329 CGCTATGGTGAGCAAATGCATA 59.451 45.455 8.28 0.00 42.99 3.14
4164 5404 4.082245 ACTGCATTTAAATTGAGTTCCGGG 60.082 41.667 0.00 0.00 0.00 5.73
4165 5405 3.829601 TGCATTTAAATTGAGTTCCGGGT 59.170 39.130 0.00 0.00 0.00 5.28
4294 5536 3.211963 GGCAAGTATGGCGGGCTG 61.212 66.667 2.38 0.00 42.73 4.85
4518 5760 5.294552 AGTTACTTGCTCAACTTCTGTGTTC 59.705 40.000 0.00 0.00 30.89 3.18
4572 7042 4.177026 ACAGTGAAATGTGTATCGAGAGC 58.823 43.478 0.00 0.00 30.46 4.09
4612 7082 9.467258 AGTCAAATTTTGAGTGAAATGTGTATG 57.533 29.630 16.75 0.00 41.59 2.39
4686 7156 6.639686 CACGTATATTCGCCTGTAAATGTACT 59.360 38.462 1.22 0.00 31.23 2.73
4784 7262 0.971386 AAATTGCCCAGCTGTTGAGG 59.029 50.000 13.81 7.70 0.00 3.86
4806 7284 5.483937 AGGTGATGTGTACCATTTCTCACTA 59.516 40.000 11.90 0.00 40.74 2.74
4880 7358 9.033481 CAAAAATTTGTACTGTGAACATGATGT 57.967 29.630 0.00 0.00 33.59 3.06
5015 7507 3.290710 GGTTATGTCCCTGCATCACAAT 58.709 45.455 0.00 0.00 0.00 2.71
5050 7556 6.040955 TGTCAGTCAAGAGTAATGTTCTCAGT 59.959 38.462 0.00 0.00 34.73 3.41
5053 7559 6.364706 CAGTCAAGAGTAATGTTCTCAGTCAC 59.635 42.308 0.00 0.00 34.73 3.67
5055 7561 6.584563 GTCAAGAGTAATGTTCTCAGTCACTC 59.415 42.308 0.00 0.00 34.73 3.51
5076 7583 8.084073 TCACTCTTTTCCAAAGCTGAAAATATG 58.916 33.333 9.99 9.04 40.01 1.78
5077 7584 8.084073 CACTCTTTTCCAAAGCTGAAAATATGA 58.916 33.333 9.99 5.08 40.01 2.15
5144 7654 4.379918 GCTGGATTCTTACTTGCAAACTCC 60.380 45.833 0.00 0.00 0.00 3.85
5326 7837 2.611292 GACGGCATCATCAGAAAGAAGG 59.389 50.000 0.00 0.00 0.00 3.46
5353 7864 3.379372 CCGATTCATTCAGGATTGCAAGT 59.621 43.478 4.94 0.00 0.00 3.16
5410 7921 5.064707 TCAGTAAGTGCTCAAACTGTCAAAC 59.935 40.000 15.68 0.00 40.18 2.93
5414 7925 3.758554 AGTGCTCAAACTGTCAAACTGTT 59.241 39.130 0.00 0.00 41.12 3.16
5426 7938 5.120399 TGTCAAACTGTTAAGGTAGTGTGG 58.880 41.667 0.00 0.00 33.81 4.17
5438 7950 3.705072 AGGTAGTGTGGGTGCTATACTTC 59.295 47.826 0.00 0.00 0.00 3.01
5442 7954 0.179119 GTGGGTGCTATACTTCGCGT 60.179 55.000 5.77 0.00 0.00 6.01
5445 7957 2.287970 TGGGTGCTATACTTCGCGTATG 60.288 50.000 5.77 0.00 39.15 2.39
5474 7986 4.749598 GGCTTTGTGTTATTTTTCCAGTGG 59.250 41.667 1.40 1.40 0.00 4.00
5476 7988 5.691754 GCTTTGTGTTATTTTTCCAGTGGAG 59.308 40.000 12.67 0.00 31.21 3.86
5478 7990 4.469657 TGTGTTATTTTTCCAGTGGAGCT 58.530 39.130 12.67 1.27 31.21 4.09
5479 7991 4.278170 TGTGTTATTTTTCCAGTGGAGCTG 59.722 41.667 12.67 0.00 44.63 4.24
5496 8008 1.661112 GCTGAATGTAACGACAGAGCC 59.339 52.381 0.00 0.00 39.50 4.70
5497 8009 1.920574 CTGAATGTAACGACAGAGCCG 59.079 52.381 0.00 0.00 39.50 5.52
5502 8014 3.463527 ATGTAACGACAGAGCCGAAGGA 61.464 50.000 0.00 0.00 46.82 3.36
5503 8015 4.747580 ATGTAACGACAGAGCCGAAGGAT 61.748 47.826 0.00 0.00 46.82 3.24
5504 8016 5.465584 ATGTAACGACAGAGCCGAAGGATA 61.466 45.833 0.00 0.00 46.82 2.59
5529 8041 2.031682 AGCATCTAAATCGGCAAATCGC 60.032 45.455 0.00 0.00 41.28 4.58
5548 8060 2.666508 CGCAGTGTGTGGTAGTATGTTC 59.333 50.000 0.00 0.00 0.00 3.18
5566 8078 5.581126 TGTTCAAAACATCTTGAAGTGCT 57.419 34.783 0.00 0.00 44.00 4.40
5567 8079 6.691754 TGTTCAAAACATCTTGAAGTGCTA 57.308 33.333 0.00 0.00 44.00 3.49
5568 8080 7.275888 TGTTCAAAACATCTTGAAGTGCTAT 57.724 32.000 0.00 0.00 44.00 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 6.131544 ACAAATGTGTTCTACAACAAGGAC 57.868 37.500 0.00 0.00 44.32 3.85
52 53 0.678950 CCCCTCAAAATTTGGCGTGT 59.321 50.000 5.83 0.00 0.00 4.49
57 58 3.055891 GGATCACACCCCTCAAAATTTGG 60.056 47.826 5.83 0.00 0.00 3.28
61 63 2.532250 GGGATCACACCCCTCAAAAT 57.468 50.000 0.00 0.00 43.81 1.82
88 90 4.437524 GCCCGAGAGTTGATTTCTTAAAGC 60.438 45.833 0.00 0.00 0.00 3.51
94 96 2.859165 TTGCCCGAGAGTTGATTTCT 57.141 45.000 0.00 0.00 0.00 2.52
124 126 2.332063 AATTGGTCATAGGGTGCTCG 57.668 50.000 0.00 0.00 0.00 5.03
135 137 2.293122 CGAAAGCCTGACAAATTGGTCA 59.707 45.455 14.98 14.98 45.06 4.02
136 138 2.552315 TCGAAAGCCTGACAAATTGGTC 59.448 45.455 5.98 5.98 38.29 4.02
143 145 3.746045 AACTAGTCGAAAGCCTGACAA 57.254 42.857 0.00 0.00 37.58 3.18
145 147 2.994578 GGAAACTAGTCGAAAGCCTGAC 59.005 50.000 0.00 0.00 35.33 3.51
159 161 9.457436 GAATTGGTCAGTTTATTAGGGAAACTA 57.543 33.333 0.75 0.00 43.59 2.24
169 171 7.694093 AGAGGAAGAGAATTGGTCAGTTTATT 58.306 34.615 0.00 0.00 0.00 1.40
246 249 8.503458 TTTCATCATCAAGAAGAGGATTTCTC 57.497 34.615 0.00 0.00 44.84 2.87
247 250 8.874744 TTTTCATCATCAAGAAGAGGATTTCT 57.125 30.769 0.00 0.00 44.84 2.52
248 251 8.738106 ACTTTTCATCATCAAGAAGAGGATTTC 58.262 33.333 0.00 0.00 44.84 2.17
249 252 8.647256 ACTTTTCATCATCAAGAAGAGGATTT 57.353 30.769 0.00 0.00 44.84 2.17
253 257 7.011295 GCTCTACTTTTCATCATCAAGAAGAGG 59.989 40.741 0.00 0.00 32.14 3.69
311 317 1.659098 GCTATGCTCACGCGTTAAACT 59.341 47.619 10.22 0.00 39.65 2.66
316 322 1.361668 CTTGGCTATGCTCACGCGTT 61.362 55.000 10.22 0.00 39.65 4.84
335 341 9.418045 GGATTCATAGATACTGAGCTTTTCTAC 57.582 37.037 0.00 0.00 0.00 2.59
365 371 0.582005 GACCAAACGTCTGTGAGCAC 59.418 55.000 0.00 0.00 38.57 4.40
366 372 2.986311 GACCAAACGTCTGTGAGCA 58.014 52.632 0.00 0.00 38.57 4.26
495 584 8.210265 TCAAAAGGCCTTCTTATTTTTGTGAAT 58.790 29.630 20.79 0.00 38.91 2.57
500 589 7.928167 AGAAGTCAAAAGGCCTTCTTATTTTTG 59.072 33.333 20.79 17.20 41.53 2.44
579 668 8.418662 GTTGACTTTAGGGGAAAAGTTATTTGT 58.581 33.333 3.71 0.00 46.92 2.83
604 694 4.705337 TTCTTTTGCACTAAACCAACGT 57.295 36.364 0.00 0.00 0.00 3.99
605 695 5.099575 ACTTTCTTTTGCACTAAACCAACG 58.900 37.500 0.00 0.00 0.00 4.10
607 697 7.832769 ACTTACTTTCTTTTGCACTAAACCAA 58.167 30.769 0.00 0.00 0.00 3.67
706 812 5.494706 AGAATAGGAGGTCTAGGATAGGGAG 59.505 48.000 0.00 0.00 39.78 4.30
715 821 9.680315 CAAAACGTATAAGAATAGGAGGTCTAG 57.320 37.037 0.00 0.00 0.00 2.43
752 858 9.058174 TGACAAAACGTATAAGAATCCTCAAAA 57.942 29.630 0.00 0.00 0.00 2.44
753 859 8.610248 TGACAAAACGTATAAGAATCCTCAAA 57.390 30.769 0.00 0.00 0.00 2.69
786 892 5.063944 CCTGTTTGACATCCTTACTTGATCG 59.936 44.000 0.00 0.00 0.00 3.69
801 907 3.777556 CCCCTTGGCCTGTTTGAC 58.222 61.111 3.32 0.00 0.00 3.18
848 954 1.871039 TCAGCAAACAGTAGCGGAAAC 59.129 47.619 0.00 0.00 32.20 2.78
855 961 3.397482 AGAGCAAGTCAGCAAACAGTAG 58.603 45.455 0.00 0.00 36.85 2.57
869 975 2.324541 AGGGCTATGGACTAGAGCAAG 58.675 52.381 7.77 0.00 45.40 4.01
883 989 0.550914 CATTTGGTGGGCTAGGGCTA 59.449 55.000 0.00 0.00 38.73 3.93
903 1009 2.127708 GAGGATGGAGGAAAAGGCCTA 58.872 52.381 5.16 0.00 38.73 3.93
975 1085 3.459063 GGGGGAGAAGACCGGTCG 61.459 72.222 28.26 0.00 34.09 4.79
990 1100 2.119611 GGGTTGGGAAAGGTGGGG 59.880 66.667 0.00 0.00 0.00 4.96
1353 1468 1.372838 CCGAGAGAAGCGAGCAGAGA 61.373 60.000 0.00 0.00 0.00 3.10
1354 1469 1.063972 CCGAGAGAAGCGAGCAGAG 59.936 63.158 0.00 0.00 0.00 3.35
1358 1474 0.109039 AGAAACCGAGAGAAGCGAGC 60.109 55.000 0.00 0.00 0.00 5.03
1490 1625 3.368236 CGGAACAATCGAGGAGAAGAAAC 59.632 47.826 0.00 0.00 0.00 2.78
1491 1626 3.006537 ACGGAACAATCGAGGAGAAGAAA 59.993 43.478 0.00 0.00 0.00 2.52
1492 1627 2.561419 ACGGAACAATCGAGGAGAAGAA 59.439 45.455 0.00 0.00 0.00 2.52
1493 1628 2.094700 CACGGAACAATCGAGGAGAAGA 60.095 50.000 0.00 0.00 0.00 2.87
1502 1637 4.625742 ACAGAAGATTACACGGAACAATCG 59.374 41.667 0.00 0.00 34.55 3.34
1527 1662 0.036952 CGGATTCAGACCACAGCAGT 60.037 55.000 0.00 0.00 0.00 4.40
1568 1703 2.766828 AGAAGGGGAACTAGGAATGTCG 59.233 50.000 0.00 0.00 0.00 4.35
1582 1717 4.459330 GGATCAGAAATCAAGAGAAGGGG 58.541 47.826 0.00 0.00 0.00 4.79
1602 1737 3.697045 CTGTGGTACAACAACAAAAGGGA 59.303 43.478 4.26 0.00 44.16 4.20
1614 1749 0.320421 GCTTCTCCGCTGTGGTACAA 60.320 55.000 7.20 0.00 44.16 2.41
1884 2021 4.677584 TCAAATTTGGTGTGAAGAAACCG 58.322 39.130 17.90 0.00 39.47 4.44
2220 3152 0.839946 AAGGAGGCGAGCAATGGTAT 59.160 50.000 0.00 0.00 0.00 2.73
2322 3280 7.198306 AGAAACTAAGTTATGTCCAAAACGG 57.802 36.000 0.00 0.00 0.00 4.44
2366 3350 9.473007 TTCATGTGTTAATTTCCCAGATAATGA 57.527 29.630 0.00 0.00 0.00 2.57
2461 3447 9.135843 TCGACAGTAAGAACAATTTGTATGTAG 57.864 33.333 1.76 3.11 0.00 2.74
2469 3455 7.145323 CCCAAATTCGACAGTAAGAACAATTT 58.855 34.615 0.00 0.00 0.00 1.82
2543 3545 1.655484 TGCCGCATCTAACATCAGTG 58.345 50.000 0.00 0.00 0.00 3.66
2643 3645 6.012069 TGGCTGCCATCCATATATAACCTTAA 60.012 38.462 19.30 0.00 0.00 1.85
2649 3651 6.314120 AGTTTTGGCTGCCATCCATATATAA 58.686 36.000 24.03 7.40 31.53 0.98
2655 3657 1.551883 GAAGTTTTGGCTGCCATCCAT 59.448 47.619 24.03 8.19 31.53 3.41
2663 3665 4.861102 AATTGGAGAGAAGTTTTGGCTG 57.139 40.909 0.00 0.00 0.00 4.85
2750 3759 4.513406 TTTTGGTCAAAGTACTGGTCCT 57.487 40.909 0.00 0.00 0.00 3.85
2780 3804 3.558958 GCCCATGTTTGCCTTACCAAAAT 60.559 43.478 0.00 0.00 36.55 1.82
2844 3872 5.860182 CACATTTAAGTGTGCATTTGAGAGG 59.140 40.000 16.89 0.00 42.51 3.69
2999 4177 1.349026 AGCATGAGTAGCACCTTGTGT 59.651 47.619 0.00 0.00 35.75 3.72
3074 4253 3.435105 CACAAACAAAAGTGCTGCCTA 57.565 42.857 0.00 0.00 0.00 3.93
3088 4267 4.298332 CCAAAACAGATGGTAGCACAAAC 58.702 43.478 0.00 0.00 33.08 2.93
3140 4321 4.169461 AGAATGAGGGTTCCATCCATGAAT 59.831 41.667 0.00 0.00 0.00 2.57
3159 4340 5.513233 AGATAAAACACTGCATCCCAGAAT 58.487 37.500 0.00 0.00 44.64 2.40
3164 4345 5.376625 TCCATAGATAAAACACTGCATCCC 58.623 41.667 0.00 0.00 0.00 3.85
3183 4364 6.721208 ACCAGTGAAAATACATCAAGTTCCAT 59.279 34.615 0.00 0.00 0.00 3.41
3222 4403 0.108662 ACGACGATCAAGCATGAGCA 60.109 50.000 8.04 0.00 42.11 4.26
3256 4437 0.840617 TACCAGGAACCAACTGCACA 59.159 50.000 0.00 0.00 34.65 4.57
3261 4442 1.774856 AGCAACTACCAGGAACCAACT 59.225 47.619 0.00 0.00 0.00 3.16
3421 4604 9.953565 AAGGTGTTATACAGTTATAGCTGAAAA 57.046 29.630 21.85 10.25 39.62 2.29
3780 5019 7.628234 AGACATCAAAAGTGGAGTAATCTGAT 58.372 34.615 0.00 0.00 0.00 2.90
3887 5126 0.741221 GACCCATCAGCACGACCTTC 60.741 60.000 0.00 0.00 0.00 3.46
3905 5144 0.397941 CACAGCCAACAGGAGGAAGA 59.602 55.000 0.00 0.00 0.00 2.87
4159 5399 1.180456 TACAGTTGCGAAGACCCGGA 61.180 55.000 0.73 0.00 0.00 5.14
4164 5404 4.844267 ACAAATGTTACAGTTGCGAAGAC 58.156 39.130 22.73 0.00 42.16 3.01
4165 5405 5.756347 ACTACAAATGTTACAGTTGCGAAGA 59.244 36.000 22.73 5.31 42.16 2.87
4518 5760 5.622856 GCAGAAGTTCTTTGTCGAAAATGAG 59.377 40.000 1.56 0.00 0.00 2.90
4572 7042 8.306038 TCAAAATTTGACTATTGAACTCCATGG 58.694 33.333 4.97 4.97 34.08 3.66
4608 7078 2.753452 TGAACTCCGTGACTCTCCATAC 59.247 50.000 0.00 0.00 0.00 2.39
4612 7082 1.249407 ACTGAACTCCGTGACTCTCC 58.751 55.000 0.00 0.00 0.00 3.71
4686 7156 6.543465 CAGTTTGGCCATATAGATTCTTCACA 59.457 38.462 6.09 0.00 0.00 3.58
4744 7218 2.570415 TTTTGTCACCGAATGGGCTA 57.430 45.000 0.00 0.00 40.62 3.93
4784 7262 8.216387 TGTGTAGTGAGAAATGGTACACATCAC 61.216 40.741 9.06 1.08 45.24 3.06
4880 7358 3.196469 CCTCTCAAGTCTCAGGCATACAA 59.804 47.826 0.00 0.00 0.00 2.41
5015 7507 3.165071 TCTTGACTGACACCTGAGCATA 58.835 45.455 0.00 0.00 0.00 3.14
5024 7516 6.216569 TGAGAACATTACTCTTGACTGACAC 58.783 40.000 0.00 0.00 35.66 3.67
5050 7556 5.913137 TTTTCAGCTTTGGAAAAGAGTGA 57.087 34.783 6.39 3.23 38.82 3.41
5053 7559 9.136952 CTTCATATTTTCAGCTTTGGAAAAGAG 57.863 33.333 13.79 7.90 44.62 2.85
5055 7561 7.601508 AGCTTCATATTTTCAGCTTTGGAAAAG 59.398 33.333 13.79 3.93 44.62 2.27
5076 7583 7.287235 TCTCCCATACCTAAAGTAAGTAGCTTC 59.713 40.741 0.00 0.00 33.70 3.86
5077 7584 7.130775 TCTCCCATACCTAAAGTAAGTAGCTT 58.869 38.462 0.00 0.00 33.70 3.74
5144 7654 3.367498 GGATAGATCCCGACGAATGGAAG 60.367 52.174 0.00 0.00 41.20 3.46
5244 7755 5.450592 TGAAATGTTGCTGCACAAGAATA 57.549 34.783 0.00 0.00 39.50 1.75
5326 7837 3.760580 ATCCTGAATGAATCGGACCTC 57.239 47.619 0.00 0.00 36.44 3.85
5353 7864 4.661222 TCATGCAGTTGAAGGAAATGGTA 58.339 39.130 0.00 0.00 30.01 3.25
5410 7921 2.038557 AGCACCCACACTACCTTAACAG 59.961 50.000 0.00 0.00 0.00 3.16
5414 7925 4.875389 AGTATAGCACCCACACTACCTTA 58.125 43.478 0.00 0.00 0.00 2.69
5426 7938 3.009301 ACATACGCGAAGTATAGCACC 57.991 47.619 15.93 0.00 43.78 5.01
5438 7950 1.668751 ACAAAGCCCATTACATACGCG 59.331 47.619 3.53 3.53 0.00 6.01
5442 7954 9.646427 GAAAAATAACACAAAGCCCATTACATA 57.354 29.630 0.00 0.00 0.00 2.29
5445 7957 6.931840 TGGAAAAATAACACAAAGCCCATTAC 59.068 34.615 0.00 0.00 0.00 1.89
5474 7986 2.600867 GCTCTGTCGTTACATTCAGCTC 59.399 50.000 0.00 0.00 34.37 4.09
5476 7988 1.661112 GGCTCTGTCGTTACATTCAGC 59.339 52.381 0.00 0.00 34.37 4.26
5478 7990 1.542472 TCGGCTCTGTCGTTACATTCA 59.458 47.619 0.00 0.00 34.37 2.57
5479 7991 2.273370 TCGGCTCTGTCGTTACATTC 57.727 50.000 0.00 0.00 34.37 2.67
5486 7998 1.471119 TTATCCTTCGGCTCTGTCGT 58.529 50.000 0.00 0.00 30.45 4.34
5487 7999 2.802787 ATTATCCTTCGGCTCTGTCG 57.197 50.000 0.00 0.00 0.00 4.35
5496 8008 7.464710 GCCGATTTAGATGCTTATTATCCTTCG 60.465 40.741 0.00 0.00 0.00 3.79
5497 8009 7.334421 TGCCGATTTAGATGCTTATTATCCTTC 59.666 37.037 0.00 0.00 0.00 3.46
5502 8014 8.177663 CGATTTGCCGATTTAGATGCTTATTAT 58.822 33.333 0.00 0.00 0.00 1.28
5503 8015 7.518161 CGATTTGCCGATTTAGATGCTTATTA 58.482 34.615 0.00 0.00 0.00 0.98
5504 8016 6.373779 CGATTTGCCGATTTAGATGCTTATT 58.626 36.000 0.00 0.00 0.00 1.40
5529 8041 6.037720 TGTTTTGAACATACTACCACACACTG 59.962 38.462 0.00 0.00 36.25 3.66


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

AutoCloner maintained by Alex Coulton.