Multiple sequence alignment - TraesCS3B01G120600

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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 TraesCS3B01G120600 chr3B 100.000 4522 0 0 1443 5964 90473991 90469470 0.000000e+00 8351.0
1 TraesCS3B01G120600 chr3B 100.000 1105 0 0 1 1105 90475433 90474329 0.000000e+00 2041.0
2 TraesCS3B01G120600 chr3B 93.478 46 1 1 5385 5428 669921189 669921234 3.860000e-07 67.6
3 TraesCS3B01G120600 chr3D 93.232 4211 186 43 1443 5585 57508763 57504584 0.000000e+00 6106.0
4 TraesCS3B01G120600 chr3D 87.466 1109 56 33 1 1083 57509930 57508879 0.000000e+00 1201.0
5 TraesCS3B01G120600 chr3D 84.788 401 17 11 5584 5962 57504477 57504099 4.390000e-96 363.0
6 TraesCS3B01G120600 chr3D 79.137 139 13 7 5387 5517 589761390 589761260 1.380000e-11 82.4
7 TraesCS3B01G120600 chr3A 92.840 2053 98 14 3543 5581 66508804 66506787 0.000000e+00 2931.0
8 TraesCS3B01G120600 chr3A 93.121 1352 49 11 2223 3549 66510162 66508830 0.000000e+00 1941.0
9 TraesCS3B01G120600 chr3A 84.427 777 73 23 1443 2192 66510917 66510162 0.000000e+00 721.0
10 TraesCS3B01G120600 chr3A 94.026 385 17 1 5584 5962 66506618 66506234 4.010000e-161 579.0
11 TraesCS3B01G120600 chr3A 90.446 314 20 7 343 647 66512012 66511700 7.200000e-109 405.0
12 TraesCS3B01G120600 chr3A 84.691 405 21 23 694 1083 66511403 66511025 3.400000e-97 366.0
13 TraesCS3B01G120600 chr3A 88.438 320 16 10 15 332 66512508 66512208 3.400000e-97 366.0
14 TraesCS3B01G120600 chr3A 91.304 46 2 2 5385 5428 599863903 599863858 1.790000e-05 62.1
15 TraesCS3B01G120600 chr3A 87.500 56 2 4 5480 5531 561288510 561288456 6.450000e-05 60.2
16 TraesCS3B01G120600 chr3A 100.000 28 0 0 5581 5608 727632365 727632392 1.100000e-02 52.8
17 TraesCS3B01G120600 chr1D 100.000 37 0 0 5389 5425 311688841 311688877 1.070000e-07 69.4
18 TraesCS3B01G120600 chr6B 93.182 44 1 1 5387 5428 550272574 550272531 4.990000e-06 63.9
19 TraesCS3B01G120600 chr6B 100.000 28 0 0 5581 5608 716607806 716607779 1.100000e-02 52.8
20 TraesCS3B01G120600 chr5A 89.796 49 3 2 5385 5431 170088062 170088014 1.790000e-05 62.1
21 TraesCS3B01G120600 chr2D 93.023 43 1 1 5385 5425 484046248 484046290 1.790000e-05 62.1
22 TraesCS3B01G120600 chr4D 100.000 28 0 0 5581 5608 182067359 182067332 1.100000e-02 52.8


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 TraesCS3B01G120600 chr3B 90469470 90475433 5963 True 5196.000000 8351 100.000000 1 5964 2 chr3B.!!$R1 5963
1 TraesCS3B01G120600 chr3D 57504099 57509930 5831 True 2556.666667 6106 88.495333 1 5962 3 chr3D.!!$R2 5961
2 TraesCS3B01G120600 chr3A 66506234 66512508 6274 True 1044.142857 2931 89.712714 15 5962 7 chr3A.!!$R3 5947

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
277 287 0.027194 GCAGCAGACGCATACACATG 59.973 55.000 0.00 0.0 42.27 3.21 F
1480 2000 0.390735 CGTACCCCCTCTGGTTTTCG 60.391 60.000 0.00 0.0 39.91 3.46 F
3226 3815 0.818296 CTAGTGCACTTACCGAGCCT 59.182 55.000 27.06 0.0 0.00 4.58 F
4134 4760 1.000827 CAGCTGCTACCTCTACATCCG 60.001 57.143 0.00 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 2529 0.175760 ACCGACAGATCAATCCACGG 59.824 55.000 14.17 14.17 40.41 4.94 R
3381 3970 1.269621 GGAATGGCAGCTGATGATTGC 60.270 52.381 20.43 12.61 37.11 3.56 R
4176 4802 0.257039 ACCCTTGCATGCCTAGAAGG 59.743 55.000 21.90 21.90 38.80 3.46 R
5834 6659 1.122019 AGAACCTGGTCTCTGGCGTT 61.122 55.000 0.00 0.00 35.65 4.84 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
36 37 3.626924 AGACCTTTCCGTGCGCCT 61.627 61.111 4.18 0.00 0.00 5.52
78 79 1.669779 CAACGTCAAACCACCCGTAAA 59.330 47.619 0.00 0.00 32.49 2.01
79 80 1.298602 ACGTCAAACCACCCGTAAAC 58.701 50.000 0.00 0.00 0.00 2.01
108 111 6.895782 AGACGGGAAAGATATTAACAATCCA 58.104 36.000 0.00 0.00 0.00 3.41
159 162 3.381908 AGATCTTGGTGCTAGTAAGGACG 59.618 47.826 0.00 0.00 44.53 4.79
165 168 1.470098 GTGCTAGTAAGGACGAACCGA 59.530 52.381 0.00 0.00 44.74 4.69
170 173 4.439837 GCTAGTAAGGACGAACCGAGATTT 60.440 45.833 0.00 0.00 44.74 2.17
261 271 5.457148 GGATTAATCGAGATATACGCTGCAG 59.543 44.000 10.11 10.11 0.00 4.41
262 272 2.270275 ATCGAGATATACGCTGCAGC 57.730 50.000 29.12 29.12 37.78 5.25
263 273 0.951558 TCGAGATATACGCTGCAGCA 59.048 50.000 36.03 20.16 42.21 4.41
264 274 1.068954 TCGAGATATACGCTGCAGCAG 60.069 52.381 36.03 28.85 42.21 4.24
265 275 1.068954 CGAGATATACGCTGCAGCAGA 60.069 52.381 36.03 24.05 42.21 4.26
266 276 2.323959 GAGATATACGCTGCAGCAGAC 58.676 52.381 36.03 20.09 42.21 3.51
267 277 1.056103 GATATACGCTGCAGCAGACG 58.944 55.000 36.03 27.25 42.21 4.18
268 278 0.941463 ATATACGCTGCAGCAGACGC 60.941 55.000 36.03 10.96 42.21 5.19
269 279 2.278182 TATACGCTGCAGCAGACGCA 62.278 55.000 36.03 18.75 42.27 5.24
270 280 2.913054 ATACGCTGCAGCAGACGCAT 62.913 55.000 36.03 20.05 42.27 4.73
272 282 2.705826 GCTGCAGCAGACGCATAC 59.294 61.111 33.36 2.11 42.27 2.39
273 283 2.102438 GCTGCAGCAGACGCATACA 61.102 57.895 33.36 0.00 42.27 2.29
274 284 1.712081 CTGCAGCAGACGCATACAC 59.288 57.895 18.42 0.00 42.27 2.90
275 285 1.005156 TGCAGCAGACGCATACACA 60.005 52.632 0.00 0.00 42.27 3.72
276 286 0.391528 TGCAGCAGACGCATACACAT 60.392 50.000 0.00 0.00 42.27 3.21
277 287 0.027194 GCAGCAGACGCATACACATG 59.973 55.000 0.00 0.00 42.27 3.21
278 288 1.643880 CAGCAGACGCATACACATGA 58.356 50.000 0.00 0.00 42.27 3.07
279 289 2.207590 CAGCAGACGCATACACATGAT 58.792 47.619 0.00 0.00 42.27 2.45
280 290 2.033151 CAGCAGACGCATACACATGATG 60.033 50.000 0.00 0.00 42.27 3.07
281 291 2.159057 AGCAGACGCATACACATGATGA 60.159 45.455 0.00 0.00 42.27 2.92
282 292 2.804527 GCAGACGCATACACATGATGAT 59.195 45.455 0.00 0.00 38.36 2.45
320 330 1.128200 AAGGGCCACATATACGAGCA 58.872 50.000 6.18 0.00 0.00 4.26
329 339 4.204370 CCACATATACGAGCATTATACGCG 59.796 45.833 3.53 3.53 36.35 6.01
332 342 5.064325 ACATATACGAGCATTATACGCGAGA 59.936 40.000 15.93 0.00 34.29 4.04
333 343 2.317679 ACGAGCATTATACGCGAGAG 57.682 50.000 15.93 0.00 34.29 3.20
334 344 1.871676 ACGAGCATTATACGCGAGAGA 59.128 47.619 15.93 0.00 34.29 3.10
335 345 2.289820 ACGAGCATTATACGCGAGAGAA 59.710 45.455 15.93 3.89 34.29 2.87
337 347 3.364068 CGAGCATTATACGCGAGAGAAGA 60.364 47.826 15.93 0.00 31.59 2.87
338 348 4.537965 GAGCATTATACGCGAGAGAAGAA 58.462 43.478 15.93 0.00 0.00 2.52
339 349 4.541779 AGCATTATACGCGAGAGAAGAAG 58.458 43.478 15.93 0.00 0.00 2.85
357 552 8.682936 AGAAGAAGAGAAGAATTGTTTAGCAA 57.317 30.769 0.00 0.00 41.89 3.91
365 560 7.710896 AGAAGAATTGTTTAGCAATATCTGGC 58.289 34.615 0.00 0.00 46.29 4.85
366 561 7.559170 AGAAGAATTGTTTAGCAATATCTGGCT 59.441 33.333 0.00 0.00 46.29 4.75
434 639 3.857764 CCGATCTTACCCGGCTCT 58.142 61.111 0.00 0.00 39.22 4.09
564 772 2.418628 CCAATAACGCCGTGAGTCAAAT 59.581 45.455 0.00 0.00 0.00 2.32
582 790 4.157120 CCCTCCTTACACGCGGGG 62.157 72.222 15.46 5.75 0.00 5.73
637 852 3.936372 ATCTTCCCGTGTATCCGTATG 57.064 47.619 0.00 0.00 0.00 2.39
650 865 1.536766 TCCGTATGCGACCCTAATACG 59.463 52.381 4.21 7.32 45.40 3.06
656 1149 2.309613 TGCGACCCTAATACGTACCAT 58.690 47.619 0.00 0.00 0.00 3.55
700 1193 3.838795 GGCGACACGTGCGTCATC 61.839 66.667 24.72 11.52 35.54 2.92
702 1195 3.532792 CGACACGTGCGTCATCCG 61.533 66.667 17.22 4.30 35.54 4.18
719 1214 4.029809 GCGTGGCCCCCTACTTGT 62.030 66.667 0.00 0.00 0.00 3.16
722 1217 2.208640 TGGCCCCCTACTTGTCCA 59.791 61.111 0.00 0.00 0.00 4.02
726 1221 1.898154 CCCCCTACTTGTCCAGACG 59.102 63.158 0.00 0.00 0.00 4.18
959 1466 1.760480 GCTCTCACCCTCTCCCTCC 60.760 68.421 0.00 0.00 0.00 4.30
961 1468 1.862138 TCTCACCCTCTCCCTCCCA 60.862 63.158 0.00 0.00 0.00 4.37
1017 1533 4.400251 CCCACCGTCTCCCTCCCT 62.400 72.222 0.00 0.00 0.00 4.20
1018 1534 2.760385 CCACCGTCTCCCTCCCTC 60.760 72.222 0.00 0.00 0.00 4.30
1019 1535 2.760385 CACCGTCTCCCTCCCTCC 60.760 72.222 0.00 0.00 0.00 4.30
1020 1536 4.077180 ACCGTCTCCCTCCCTCCC 62.077 72.222 0.00 0.00 0.00 4.30
1021 1537 3.756783 CCGTCTCCCTCCCTCCCT 61.757 72.222 0.00 0.00 0.00 4.20
1022 1538 2.123640 CGTCTCCCTCCCTCCCTC 60.124 72.222 0.00 0.00 0.00 4.30
1023 1539 2.284151 GTCTCCCTCCCTCCCTCC 59.716 72.222 0.00 0.00 0.00 4.30
1024 1540 3.036959 TCTCCCTCCCTCCCTCCC 61.037 72.222 0.00 0.00 0.00 4.30
1025 1541 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
1026 1542 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
1027 1543 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
1028 1544 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
1029 1545 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
1030 1546 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
1031 1547 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
1032 1548 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
1075 1591 0.673644 CTTCCCTGCGTACAACCCAG 60.674 60.000 0.00 0.00 0.00 4.45
1077 1593 2.031919 CCTGCGTACAACCCAGCA 59.968 61.111 0.00 0.00 38.03 4.41
1079 1595 2.668212 TGCGTACAACCCAGCAGC 60.668 61.111 0.00 0.00 34.39 5.25
1080 1596 2.668212 GCGTACAACCCAGCAGCA 60.668 61.111 0.00 0.00 0.00 4.41
1081 1597 2.680913 GCGTACAACCCAGCAGCAG 61.681 63.158 0.00 0.00 0.00 4.24
1083 1599 1.016130 CGTACAACCCAGCAGCAGAG 61.016 60.000 0.00 0.00 0.00 3.35
1084 1600 1.003355 TACAACCCAGCAGCAGAGC 60.003 57.895 0.00 0.00 0.00 4.09
1085 1601 2.469465 TACAACCCAGCAGCAGAGCC 62.469 60.000 0.00 0.00 34.23 4.70
1086 1602 4.357279 AACCCAGCAGCAGAGCCC 62.357 66.667 0.00 0.00 34.23 5.19
1480 2000 0.390735 CGTACCCCCTCTGGTTTTCG 60.391 60.000 0.00 0.00 39.91 3.46
1487 2007 1.574428 CTCTGGTTTTCGGTTGCGG 59.426 57.895 0.00 0.00 0.00 5.69
1488 2008 2.050442 CTGGTTTTCGGTTGCGGC 60.050 61.111 0.00 0.00 0.00 6.53
1490 2010 2.050442 GGTTTTCGGTTGCGGCTG 60.050 61.111 0.00 0.00 0.00 4.85
1539 2059 4.947147 GTGCGGTGGGTGGCTTGA 62.947 66.667 0.00 0.00 0.00 3.02
1540 2060 3.965258 TGCGGTGGGTGGCTTGAT 61.965 61.111 0.00 0.00 0.00 2.57
1541 2061 3.134127 GCGGTGGGTGGCTTGATC 61.134 66.667 0.00 0.00 0.00 2.92
1542 2062 2.438434 CGGTGGGTGGCTTGATCC 60.438 66.667 0.00 0.00 0.00 3.36
1543 2063 2.438434 GGTGGGTGGCTTGATCCG 60.438 66.667 0.00 0.00 0.00 4.18
1545 2065 2.040544 GTGGGTGGCTTGATCCGTG 61.041 63.158 0.00 0.00 0.00 4.94
1546 2066 2.351276 GGGTGGCTTGATCCGTGT 59.649 61.111 0.00 0.00 0.00 4.49
1547 2067 1.303317 GGGTGGCTTGATCCGTGTT 60.303 57.895 0.00 0.00 0.00 3.32
1580 2111 0.996727 GTGTTTGCGCCGTTTAGCTG 60.997 55.000 4.18 0.00 0.00 4.24
1696 2243 8.674607 GGAAACGTGTAGATTTATCCTGATTTT 58.325 33.333 0.00 0.00 0.00 1.82
1720 2271 4.574674 TGATTGATTCCCACTAGTTGCT 57.425 40.909 0.00 0.00 0.00 3.91
1760 2314 5.881447 AGTACGAGTAGTATCTTGCTTGTG 58.119 41.667 0.00 0.00 37.69 3.33
1788 2342 2.496817 CGTGTAGCAGGAGGAGCC 59.503 66.667 0.00 0.00 0.00 4.70
1789 2343 2.496817 GTGTAGCAGGAGGAGCCG 59.503 66.667 0.00 0.00 43.43 5.52
1790 2344 3.461773 TGTAGCAGGAGGAGCCGC 61.462 66.667 0.00 0.00 43.43 6.53
1791 2345 3.151022 GTAGCAGGAGGAGCCGCT 61.151 66.667 0.00 0.00 44.65 5.52
1792 2346 2.835431 TAGCAGGAGGAGCCGCTC 60.835 66.667 12.27 12.27 42.66 5.03
1793 2347 3.366406 TAGCAGGAGGAGCCGCTCT 62.366 63.158 19.68 6.22 42.66 4.09
1794 2348 4.219999 GCAGGAGGAGCCGCTCTC 62.220 72.222 19.68 14.10 43.43 3.20
1795 2349 3.898509 CAGGAGGAGCCGCTCTCG 61.899 72.222 19.68 1.17 42.82 4.04
1807 2361 3.059603 GCTCTCGGCGACCATTTTA 57.940 52.632 4.99 0.00 0.00 1.52
1933 2488 3.189287 CAGGTTCAAAACTCTGGAATCGG 59.811 47.826 0.00 0.00 0.00 4.18
1992 2547 1.154205 GCCGTGGATTGATCTGTCGG 61.154 60.000 13.22 13.22 37.34 4.79
2001 2556 4.502259 GGATTGATCTGTCGGTATGCTCTT 60.502 45.833 0.00 0.00 0.00 2.85
2040 2595 6.238925 GGGATGCTTGTTTGTACTGTTTAGTT 60.239 38.462 0.00 0.00 38.36 2.24
2041 2596 6.856426 GGATGCTTGTTTGTACTGTTTAGTTC 59.144 38.462 0.00 0.00 38.36 3.01
2043 2598 7.011828 TGCTTGTTTGTACTGTTTAGTTCTC 57.988 36.000 0.00 0.00 38.36 2.87
2046 2605 4.508861 TGTTTGTACTGTTTAGTTCTCGCC 59.491 41.667 0.00 0.00 38.36 5.54
2084 2646 4.530875 TGATGATAGAGCAGAGTCAGTCA 58.469 43.478 0.00 0.00 0.00 3.41
2098 2660 1.890979 AGTCATGCGCATGCTAGGC 60.891 57.895 39.11 25.69 43.34 3.93
2107 2670 3.554342 ATGCTAGGCTGCTCCCCG 61.554 66.667 0.00 0.00 34.51 5.73
2192 2756 2.414481 CTCTCAGCAATCAGTTTGGTCG 59.586 50.000 0.00 0.00 44.02 4.79
2197 2761 2.362077 AGCAATCAGTTTGGTCGCTTTT 59.638 40.909 0.00 0.00 42.23 2.27
2204 2768 4.339814 TCAGTTTGGTCGCTTTTGGTTAAT 59.660 37.500 0.00 0.00 0.00 1.40
2213 2777 6.089417 GGTCGCTTTTGGTTAATTGATCAAAG 59.911 38.462 13.09 2.97 31.89 2.77
2288 2852 4.712476 CCCTGTTTCTATCAGCTGCTATT 58.288 43.478 9.47 0.00 0.00 1.73
2300 2864 3.135530 CAGCTGCTATTTCTAGGGGAACT 59.864 47.826 0.00 0.00 33.13 3.01
2437 3019 6.899393 ATAGCACAAAGTCCATTTCTTTCA 57.101 33.333 0.00 0.00 33.58 2.69
2487 3069 7.676683 TCAATCTACCTTCCTAGCTTTGTAT 57.323 36.000 0.00 0.00 0.00 2.29
2497 3079 8.807118 CCTTCCTAGCTTTGTATGAGTATATGA 58.193 37.037 0.00 0.00 0.00 2.15
2526 3108 5.939883 CAGTTTCATGTTTGGATACCTGAGA 59.060 40.000 0.00 0.00 0.00 3.27
2564 3146 4.935808 AGTCCATAATCCGTGTTCAACTTC 59.064 41.667 0.00 0.00 0.00 3.01
2628 3211 9.809096 GTCTGATTCTAGACTATTGATGTTCAA 57.191 33.333 0.00 0.00 42.93 2.69
2704 3288 3.272574 TCATCTGAACCATCTCCAAGC 57.727 47.619 0.00 0.00 0.00 4.01
2806 3393 7.623089 GCTCTGTTCTGCTGTTTATCTTAGTTG 60.623 40.741 0.00 0.00 0.00 3.16
2885 3474 2.504175 GGTAGTGATGCACCCCTTAGAA 59.496 50.000 0.00 0.00 34.49 2.10
2929 3518 6.939163 GGAGTATGGCAAGTAGATCAAATGAT 59.061 38.462 0.00 0.00 37.51 2.45
3014 3603 7.309990 CCTCACATGTTTCATTTGTTCCCTATT 60.310 37.037 0.00 0.00 0.00 1.73
3226 3815 0.818296 CTAGTGCACTTACCGAGCCT 59.182 55.000 27.06 0.00 0.00 4.58
3237 3826 4.228097 CGAGCCTTTGCATCCGCG 62.228 66.667 0.00 0.00 42.97 6.46
3258 3847 3.851403 CGAATGCCTTTAAACATTGGTCG 59.149 43.478 8.35 3.85 36.65 4.79
3297 3886 7.990886 TGACCAACACTTAGTTAATCAAGAAGT 59.009 33.333 6.14 0.00 38.74 3.01
3381 3970 5.050091 CAGCTTCAACTTACACACCAAGTAG 60.050 44.000 0.00 0.00 35.19 2.57
3559 4179 4.337555 GCTAATGCATCTCATGTGGTCTTT 59.662 41.667 0.00 0.00 39.41 2.52
3560 4180 4.978083 AATGCATCTCATGTGGTCTTTC 57.022 40.909 0.00 0.00 35.13 2.62
3610 4230 8.642908 AGGTTGCTTTTGTGACTTTATTTTAC 57.357 30.769 0.00 0.00 0.00 2.01
4134 4760 1.000827 CAGCTGCTACCTCTACATCCG 60.001 57.143 0.00 0.00 0.00 4.18
4176 4802 2.690497 TCTCCTATCAGTACTGCTGCAC 59.310 50.000 18.45 0.00 44.66 4.57
4283 4909 3.829601 CTGAGACACAGGTAGAGGTCTTT 59.170 47.826 0.00 0.00 40.48 2.52
4508 5134 5.839063 TCTTCTACTCAGGAAACTTCAGGAA 59.161 40.000 0.00 0.00 40.21 3.36
4562 5189 0.111253 AACTGTTGGCCTTGGAGGAG 59.889 55.000 3.32 0.00 37.67 3.69
4609 5236 1.196808 TGCCGACGAAAAGATTTCAGC 59.803 47.619 0.00 1.82 0.00 4.26
4640 5267 1.604278 GAAGTGGTCTGTTGCAGTTCC 59.396 52.381 0.00 2.15 32.61 3.62
4692 5319 2.035632 GCTGTCTAGTCTGCCTGGTAT 58.964 52.381 7.46 0.00 0.00 2.73
4702 5329 4.946157 AGTCTGCCTGGTATGAATTTCTTG 59.054 41.667 0.00 0.00 0.00 3.02
4724 5351 3.440522 GTGCTCCTAATTTCCAGTTCCAC 59.559 47.826 0.00 0.00 0.00 4.02
4737 5364 3.288242 CAGTTCCACGTTGAACAATTCG 58.712 45.455 28.07 11.55 45.62 3.34
4758 5385 0.918258 TACAGCCATGCCCTGAATCA 59.082 50.000 15.80 0.00 34.47 2.57
4766 5393 1.097232 TGCCCTGAATCATTTGCTCG 58.903 50.000 0.00 0.00 0.00 5.03
4775 5402 4.142403 TGAATCATTTGCTCGTCCAATTCC 60.142 41.667 0.00 0.00 0.00 3.01
4813 5448 3.844211 ACTATGGCAGGAGGAGTACAAAA 59.156 43.478 0.00 0.00 0.00 2.44
4954 5589 4.443598 GGAGAGGAAGCAGAATAACCGATT 60.444 45.833 0.00 0.00 0.00 3.34
5254 5895 1.893808 AGCTGTCAGGTTGTTGGCG 60.894 57.895 0.00 0.00 0.00 5.69
5383 6026 8.671028 TCTGTGAAACTAGTAAAACAAAAGGTC 58.329 33.333 0.00 0.00 38.04 3.85
5391 6034 8.702819 ACTAGTAAAACAAAAGGTCAGTACTCT 58.297 33.333 0.00 0.00 0.00 3.24
5394 6037 7.927092 AGTAAAACAAAAGGTCAGTACTCTCTC 59.073 37.037 0.00 0.00 0.00 3.20
5644 6463 2.529780 TGGGCTTCACAAAATTGCAG 57.470 45.000 0.00 0.00 0.00 4.41
5673 6492 6.961359 TCATAAACTGTGATTACCAAGTCG 57.039 37.500 0.00 0.00 0.00 4.18
5674 6493 5.350365 TCATAAACTGTGATTACCAAGTCGC 59.650 40.000 0.00 0.00 0.00 5.19
5834 6659 6.675026 TCGAGAAGAACTCTAACAATTTCGA 58.325 36.000 0.00 0.00 42.92 3.71
5935 6776 1.386533 GCTGTGGCATTGTATCAGCT 58.613 50.000 15.75 0.00 45.14 4.24
5962 6803 1.000955 TCGAGAAGAAGCCAGTGTTCC 59.999 52.381 0.00 0.00 0.00 3.62
5963 6804 1.814793 GAGAAGAAGCCAGTGTTCCC 58.185 55.000 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 6.070995 TGTTAATATCTTTCCCGTCTCTGTGT 60.071 38.462 0.00 0.00 0.00 3.72
79 80 6.338146 TGTTAATATCTTTCCCGTCTCTGTG 58.662 40.000 0.00 0.00 0.00 3.66
108 111 4.664150 ATTGGTGTGTGGATTTCGTTTT 57.336 36.364 0.00 0.00 0.00 2.43
159 162 5.420409 AGTAGGTGATTGAAATCTCGGTTC 58.580 41.667 4.76 0.00 36.39 3.62
261 271 2.204237 TCATCATGTGTATGCGTCTGC 58.796 47.619 0.00 0.00 43.20 4.26
262 272 6.716898 ATAATCATCATGTGTATGCGTCTG 57.283 37.500 0.00 0.00 34.21 3.51
263 273 8.831715 TTAATAATCATCATGTGTATGCGTCT 57.168 30.769 0.00 0.00 34.21 4.18
320 330 6.483974 TCTTCTCTTCTTCTCTCGCGTATAAT 59.516 38.462 5.77 0.00 0.00 1.28
329 339 8.655970 GCTAAACAATTCTTCTCTTCTTCTCTC 58.344 37.037 0.00 0.00 0.00 3.20
332 342 8.682936 TTGCTAAACAATTCTTCTCTTCTTCT 57.317 30.769 0.00 0.00 31.73 2.85
357 552 3.296854 TGTCACCTTCGTAGCCAGATAT 58.703 45.455 0.00 0.00 0.00 1.63
358 553 2.730382 TGTCACCTTCGTAGCCAGATA 58.270 47.619 0.00 0.00 0.00 1.98
359 554 1.557099 TGTCACCTTCGTAGCCAGAT 58.443 50.000 0.00 0.00 0.00 2.90
360 555 1.272490 CTTGTCACCTTCGTAGCCAGA 59.728 52.381 0.00 0.00 0.00 3.86
361 556 1.272490 TCTTGTCACCTTCGTAGCCAG 59.728 52.381 0.00 0.00 0.00 4.85
365 560 4.238514 CCTTTCTCTTGTCACCTTCGTAG 58.761 47.826 0.00 0.00 0.00 3.51
366 561 3.006537 CCCTTTCTCTTGTCACCTTCGTA 59.993 47.826 0.00 0.00 0.00 3.43
544 752 3.485216 GGATTTGACTCACGGCGTTATTG 60.485 47.826 11.19 0.00 0.00 1.90
637 852 3.375782 AATGGTACGTATTAGGGTCGC 57.624 47.619 0.00 0.00 0.00 5.19
650 865 3.609258 CGCGGCTCGTAATGGTAC 58.391 61.111 0.00 0.00 0.00 3.34
702 1195 3.971109 GACAAGTAGGGGGCCACGC 62.971 68.421 4.39 2.15 0.00 5.34
703 1196 2.267961 GACAAGTAGGGGGCCACG 59.732 66.667 4.39 0.00 0.00 4.94
704 1197 2.198304 CTGGACAAGTAGGGGGCCAC 62.198 65.000 4.39 0.00 0.00 5.01
705 1198 1.923395 CTGGACAAGTAGGGGGCCA 60.923 63.158 4.39 0.00 0.00 5.36
706 1199 1.615424 TCTGGACAAGTAGGGGGCC 60.615 63.158 0.00 0.00 0.00 5.80
714 1209 2.201022 ACGAGGCGTCTGGACAAGT 61.201 57.895 5.89 0.00 33.69 3.16
716 1211 2.338620 CACGAGGCGTCTGGACAA 59.661 61.111 5.89 0.00 38.32 3.18
876 1378 4.426313 GCGTGGGAAGGGAAGGGG 62.426 72.222 0.00 0.00 0.00 4.79
898 1400 1.099879 GGCGGAGAAGGAGTAGCGTA 61.100 60.000 0.00 0.00 0.00 4.42
940 1447 1.000993 GAGGGAGAGGGTGAGAGCA 59.999 63.158 0.00 0.00 0.00 4.26
941 1448 1.760480 GGAGGGAGAGGGTGAGAGC 60.760 68.421 0.00 0.00 0.00 4.09
942 1449 1.075600 GGGAGGGAGAGGGTGAGAG 60.076 68.421 0.00 0.00 0.00 3.20
943 1450 1.862138 TGGGAGGGAGAGGGTGAGA 60.862 63.158 0.00 0.00 0.00 3.27
959 1466 3.649502 AGAGGGGTATTTATAACGGGTGG 59.350 47.826 0.00 0.00 0.00 4.61
961 1468 3.072038 GCAGAGGGGTATTTATAACGGGT 59.928 47.826 0.00 0.00 0.00 5.28
1018 1534 4.825679 GTGGGGAGGGAGGGAGGG 62.826 77.778 0.00 0.00 0.00 4.30
1019 1535 4.825679 GGTGGGGAGGGAGGGAGG 62.826 77.778 0.00 0.00 0.00 4.30
1020 1536 4.825679 GGGTGGGGAGGGAGGGAG 62.826 77.778 0.00 0.00 0.00 4.30
1031 1547 4.939368 TTTGTCCGCGTGGGTGGG 62.939 66.667 16.49 0.00 44.27 4.61
1032 1548 1.801309 AAATTTGTCCGCGTGGGTGG 61.801 55.000 16.49 0.00 45.56 4.61
1075 1591 3.123620 CTTCGTGGGCTCTGCTGC 61.124 66.667 0.00 0.00 0.00 5.25
1077 1593 3.602513 CTGCTTCGTGGGCTCTGCT 62.603 63.158 0.00 0.00 0.00 4.24
1078 1594 3.123620 CTGCTTCGTGGGCTCTGC 61.124 66.667 0.00 0.00 0.00 4.26
1079 1595 3.123620 GCTGCTTCGTGGGCTCTG 61.124 66.667 0.00 0.00 0.00 3.35
1080 1596 4.400961 GGCTGCTTCGTGGGCTCT 62.401 66.667 0.00 0.00 0.00 4.09
1458 1978 3.857521 AACCAGAGGGGGTACGGCA 62.858 63.158 0.00 0.00 41.32 5.69
1463 1983 0.474273 ACCGAAAACCAGAGGGGGTA 60.474 55.000 0.00 0.00 41.32 3.69
1464 1984 1.358051 AACCGAAAACCAGAGGGGGT 61.358 55.000 0.00 0.00 45.04 4.95
1480 2000 4.481112 CCAATCGCAGCCGCAACC 62.481 66.667 0.00 0.00 38.40 3.77
1523 2043 3.918253 GATCAAGCCACCCACCGCA 62.918 63.158 0.00 0.00 0.00 5.69
1542 2062 1.947642 GTATCCCGCCGCTAACACG 60.948 63.158 0.00 0.00 0.00 4.49
1543 2063 1.947642 CGTATCCCGCCGCTAACAC 60.948 63.158 0.00 0.00 0.00 3.32
1545 2065 1.947642 CACGTATCCCGCCGCTAAC 60.948 63.158 0.00 0.00 41.42 2.34
1546 2066 1.947597 AACACGTATCCCGCCGCTAA 61.948 55.000 0.00 0.00 41.42 3.09
1547 2067 1.947597 AAACACGTATCCCGCCGCTA 61.948 55.000 0.00 0.00 41.42 4.26
1557 2088 1.127213 CTAAACGGCGCAAACACGTAT 59.873 47.619 10.83 0.00 40.31 3.06
1615 2149 0.396417 ACGGGCTCTGCTCTATCACT 60.396 55.000 0.00 0.00 0.00 3.41
1696 2243 5.774690 AGCAACTAGTGGGAATCAATCAAAA 59.225 36.000 0.00 0.00 0.00 2.44
1720 2271 8.289939 ACTCGTACTATAATTGGAGAGAAACA 57.710 34.615 0.00 0.00 0.00 2.83
1760 2314 2.450345 GCTACACGGCGCCTAACAC 61.450 63.158 26.68 5.62 0.00 3.32
1789 2343 0.931005 CTAAAATGGTCGCCGAGAGC 59.069 55.000 0.00 3.63 46.92 4.09
1790 2344 2.194271 GACTAAAATGGTCGCCGAGAG 58.806 52.381 0.00 0.00 0.00 3.20
1791 2345 2.288961 GACTAAAATGGTCGCCGAGA 57.711 50.000 0.00 0.00 0.00 4.04
1807 2361 4.729856 GCGGTACCCAACGCGACT 62.730 66.667 15.93 0.00 46.58 4.18
1813 2368 4.726334 TTGGATGCGGTACCCAAC 57.274 55.556 6.25 4.32 35.25 3.77
1933 2488 3.057526 GCCAGGGATTCTACAACAAACAC 60.058 47.826 0.00 0.00 0.00 3.32
1974 2529 0.175760 ACCGACAGATCAATCCACGG 59.824 55.000 14.17 14.17 40.41 4.94
1992 2547 0.447801 CCACGCCAACAAGAGCATAC 59.552 55.000 0.00 0.00 0.00 2.39
2040 2595 9.645059 CATCAAATTAATCTTATCTAGGCGAGA 57.355 33.333 0.00 0.00 39.01 4.04
2041 2596 9.645059 TCATCAAATTAATCTTATCTAGGCGAG 57.355 33.333 0.00 0.00 0.00 5.03
2084 2646 3.285215 GCAGCCTAGCATGCGCAT 61.285 61.111 19.28 19.28 42.27 4.73
2098 2660 0.671781 CTTTGTCAGACGGGGAGCAG 60.672 60.000 0.00 0.00 0.00 4.24
2107 2670 7.253422 CAATCCATATGTTTCCTTTGTCAGAC 58.747 38.462 1.24 0.00 0.00 3.51
2181 2745 1.757682 ACCAAAAGCGACCAAACTGA 58.242 45.000 0.00 0.00 0.00 3.41
2192 2756 9.650371 GTTTTCTTTGATCAATTAACCAAAAGC 57.350 29.630 9.40 1.98 0.00 3.51
2288 2852 9.108111 TGTTCTAGAATTTAAGTTCCCCTAGAA 57.892 33.333 8.75 12.79 38.60 2.10
2334 2898 9.739276 CATTGCCCTTCTAAATGGAGTATATTA 57.261 33.333 0.00 0.00 0.00 0.98
2367 2931 6.540438 AGGTGAGATATTACGACAAAAGGA 57.460 37.500 0.00 0.00 0.00 3.36
2497 3079 6.777580 AGGTATCCAAACATGAAACTGACTTT 59.222 34.615 0.00 0.00 0.00 2.66
2526 3108 3.432051 GACTGAGCTACCGCCGCAT 62.432 63.158 0.00 0.00 36.60 4.73
2564 3146 4.619760 CACTGAAAACAATGTGCTAGCATG 59.380 41.667 22.51 17.61 0.00 4.06
2628 3211 5.245977 CCTTAACCTGGAACCACAAATTGAT 59.754 40.000 0.00 0.00 0.00 2.57
2704 3288 2.560105 TGAGTATGATCCATCTCTGGCG 59.440 50.000 0.00 0.00 42.80 5.69
2885 3474 3.677963 CAAAGCCTGGAGGACCAAT 57.322 52.632 0.00 0.00 46.32 3.16
3014 3603 2.036571 CGCTGGATCTTGCAGTGCA 61.037 57.895 15.37 15.37 39.34 4.57
3237 3826 5.054390 TCGACCAATGTTTAAAGGCATTC 57.946 39.130 2.02 0.00 33.55 2.67
3297 3886 4.340666 GTGCTCTGACATTCCTCTGAGATA 59.659 45.833 6.17 0.00 38.09 1.98
3381 3970 1.269621 GGAATGGCAGCTGATGATTGC 60.270 52.381 20.43 12.61 37.11 3.56
3559 4179 9.825109 TCATACCATAATTAAAGATGTGAACGA 57.175 29.630 0.00 0.00 0.00 3.85
3662 4282 4.814224 AGGGCCACTAATAATCCACATT 57.186 40.909 6.18 0.00 0.00 2.71
3663 4283 5.922960 TTAGGGCCACTAATAATCCACAT 57.077 39.130 6.18 0.00 36.76 3.21
4032 4658 0.977395 GGATGGCCGTAGCTAGGAAT 59.023 55.000 14.94 5.62 39.73 3.01
4134 4760 3.204306 TGGCAGATTGATGATCCTCAC 57.796 47.619 0.00 0.00 35.21 3.51
4176 4802 0.257039 ACCCTTGCATGCCTAGAAGG 59.743 55.000 21.90 21.90 38.80 3.46
4283 4909 8.141268 CAGCTAAATTACCTGAAAACAGGAAAA 58.859 33.333 20.85 14.49 45.00 2.29
4331 4957 7.484007 CACAAACAGCAGCTAGATCAATAAAAG 59.516 37.037 0.00 0.00 0.00 2.27
4508 5134 6.376299 ACAAGACGGAAAAGGTTAAGAAAAGT 59.624 34.615 0.00 0.00 0.00 2.66
4562 5189 3.675228 CGGTGTTCACAGTACCTATGGAC 60.675 52.174 5.32 0.00 32.28 4.02
4609 5236 3.941483 ACAGACCACTTCTTTCACACAAG 59.059 43.478 0.00 0.00 28.96 3.16
4640 5267 1.406219 CGTCGTCTTGTGCCTCATCG 61.406 60.000 0.00 0.00 0.00 3.84
4692 5319 6.493115 TGGAAATTAGGAGCACAAGAAATTCA 59.507 34.615 0.00 0.00 0.00 2.57
4702 5329 3.440522 GTGGAACTGGAAATTAGGAGCAC 59.559 47.826 0.00 0.00 0.00 4.40
4724 5351 3.223157 GGCTGTAACGAATTGTTCAACG 58.777 45.455 0.00 0.00 42.09 4.10
4737 5364 1.678101 GATTCAGGGCATGGCTGTAAC 59.322 52.381 19.78 1.47 0.00 2.50
4758 5385 2.107950 TCGGAATTGGACGAGCAAAT 57.892 45.000 0.00 0.00 34.67 2.32
4766 5393 8.807581 GTTCAAAAATCATAATCGGAATTGGAC 58.192 33.333 0.00 0.00 0.00 4.02
4775 5402 7.592533 CCTGCCATAGTTCAAAAATCATAATCG 59.407 37.037 0.00 0.00 0.00 3.34
4813 5448 5.044624 TCAGAATTCCCAGGAGATCATTGTT 60.045 40.000 0.65 0.00 0.00 2.83
4954 5589 8.094284 TCAATCTAGAATCAATGGAGAGGAAA 57.906 34.615 0.00 0.00 0.00 3.13
5143 5784 6.112734 ACGGCTCAACATGTGATAGAAATAA 58.887 36.000 0.00 0.00 35.07 1.40
5145 5786 4.517285 ACGGCTCAACATGTGATAGAAAT 58.483 39.130 0.00 0.00 35.07 2.17
5147 5788 3.610040 ACGGCTCAACATGTGATAGAA 57.390 42.857 0.00 0.00 35.07 2.10
5149 5790 3.002791 ACAACGGCTCAACATGTGATAG 58.997 45.455 0.00 0.00 35.07 2.08
5254 5895 4.092968 GTCAAACCACATTATCGGTCTCAC 59.907 45.833 0.00 0.00 33.17 3.51
5581 6234 6.351966 GGCAAGTACTCCCTCTGTAAACTAAT 60.352 42.308 0.00 0.00 0.00 1.73
5582 6235 5.046807 GGCAAGTACTCCCTCTGTAAACTAA 60.047 44.000 0.00 0.00 0.00 2.24
5659 6478 3.994392 TGAGAAAGCGACTTGGTAATCAC 59.006 43.478 0.00 0.00 0.00 3.06
5742 6561 2.342279 CAGGTGGCTCGGTCGAAA 59.658 61.111 0.00 0.00 0.00 3.46
5834 6659 1.122019 AGAACCTGGTCTCTGGCGTT 61.122 55.000 0.00 0.00 35.65 4.84
5935 6776 1.734477 GCTTCTTCTCGAGCGCACA 60.734 57.895 11.47 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.