Multiple sequence alignment - TraesCS4A01G478300

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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 TraesCS4A01G478300 chr4A 100.000 2645 0 0 1 2645 735664019 735661375 0.000000e+00 4885
1 TraesCS4A01G478300 chr4A 92.143 1260 57 17 193 1425 734384356 734385600 0.000000e+00 1740
2 TraesCS4A01G478300 chr4A 85.119 1633 214 16 1038 2645 734917494 734919122 0.000000e+00 1642
3 TraesCS4A01G478300 chr4A 87.218 1197 143 7 1457 2645 735316797 735317991 0.000000e+00 1354
4 TraesCS4A01G478300 chr4A 86.756 1193 150 6 1458 2645 735747621 735748810 0.000000e+00 1321
5 TraesCS4A01G478300 chr4A 86.555 1190 156 4 1458 2645 734583122 734584309 0.000000e+00 1308
6 TraesCS4A01G478300 chr4A 86.555 1190 156 4 1458 2645 735003911 735005098 0.000000e+00 1308
7 TraesCS4A01G478300 chr4A 85.901 1227 163 5 1421 2645 735487496 735486278 0.000000e+00 1299
8 TraesCS4A01G478300 chr4A 86.482 1191 147 10 1463 2645 736571227 736572411 0.000000e+00 1295
9 TraesCS4A01G478300 chr4A 86.398 1191 149 9 1463 2645 734731150 734732335 0.000000e+00 1290
10 TraesCS4A01G478300 chr4A 80.916 1048 156 24 387 1411 735775795 735776821 0.000000e+00 787
11 TraesCS4A01G478300 chr4A 84.459 785 115 5 630 1411 735368293 735367513 0.000000e+00 767
12 TraesCS4A01G478300 chr4A 81.038 886 128 23 259 1111 736471653 736470775 0.000000e+00 669
13 TraesCS4A01G478300 chr4A 82.873 724 85 21 124 820 736895433 736896144 4.840000e-172 614
14 TraesCS4A01G478300 chr4A 79.599 897 140 23 544 1411 735315845 735316727 1.050000e-168 603
15 TraesCS4A01G478300 chr4A 83.779 598 92 2 816 1411 736896591 736897185 1.780000e-156 562
16 TraesCS4A01G478300 chr4A 87.443 438 54 1 975 1411 734585118 734585555 1.090000e-138 503
17 TraesCS4A01G478300 chr4A 85.653 467 63 3 960 1422 736413338 736412872 3.060000e-134 488
18 TraesCS4A01G478300 chr4A 77.909 593 89 23 313 868 736755362 736755949 5.460000e-87 331
19 TraesCS4A01G478300 chr7D 85.610 1230 165 5 1421 2645 5648929 5647707 0.000000e+00 1280
20 TraesCS4A01G478300 chr7D 83.151 1187 159 23 259 1411 5449884 5448705 0.000000e+00 1046
21 TraesCS4A01G478300 chr7D 82.587 1005 139 22 432 1411 5638669 5637676 0.000000e+00 854
22 TraesCS4A01G478300 chr7D 92.857 70 3 1 473 540 5558333 5558264 1.680000e-17 100
23 TraesCS4A01G478300 chr7A 82.047 1153 163 27 282 1411 6929374 6928243 0.000000e+00 942
24 TraesCS4A01G478300 chr7A 86.842 152 5 5 124 263 6929515 6929367 3.530000e-34 156
25 TraesCS4A01G478300 chr3B 97.321 112 3 0 1 112 540175040 540174929 9.660000e-45 191
26 TraesCS4A01G478300 chr2B 96.460 113 4 0 2 114 659017161 659017049 1.250000e-43 187
27 TraesCS4A01G478300 chr2B 95.652 115 5 0 1 115 767769022 767768908 4.500000e-43 185
28 TraesCS4A01G478300 chr2B 96.429 112 4 0 1 112 800062928 800062817 4.500000e-43 185
29 TraesCS4A01G478300 chr4B 96.429 112 4 0 1 112 483266429 483266540 4.500000e-43 185
30 TraesCS4A01G478300 chr4B 94.872 117 6 0 1 117 41528207 41528091 1.620000e-42 183
31 TraesCS4A01G478300 chr5D 94.872 117 6 0 1 117 539915902 539916018 1.620000e-42 183
32 TraesCS4A01G478300 chr5D 94.828 116 6 0 2 117 517855061 517855176 5.820000e-42 182
33 TraesCS4A01G478300 chr1B 94.872 117 5 1 1 117 447163365 447163250 5.820000e-42 182


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 TraesCS4A01G478300 chr4A 735661375 735664019 2644 True 4885.0 4885 100.0000 1 2645 1 chr4A.!!$R3 2644
1 TraesCS4A01G478300 chr4A 734384356 734385600 1244 False 1740.0 1740 92.1430 193 1425 1 chr4A.!!$F1 1232
2 TraesCS4A01G478300 chr4A 734917494 734919122 1628 False 1642.0 1642 85.1190 1038 2645 1 chr4A.!!$F3 1607
3 TraesCS4A01G478300 chr4A 735747621 735748810 1189 False 1321.0 1321 86.7560 1458 2645 1 chr4A.!!$F5 1187
4 TraesCS4A01G478300 chr4A 735003911 735005098 1187 False 1308.0 1308 86.5550 1458 2645 1 chr4A.!!$F4 1187
5 TraesCS4A01G478300 chr4A 735486278 735487496 1218 True 1299.0 1299 85.9010 1421 2645 1 chr4A.!!$R2 1224
6 TraesCS4A01G478300 chr4A 736571227 736572411 1184 False 1295.0 1295 86.4820 1463 2645 1 chr4A.!!$F7 1182
7 TraesCS4A01G478300 chr4A 734731150 734732335 1185 False 1290.0 1290 86.3980 1463 2645 1 chr4A.!!$F2 1182
8 TraesCS4A01G478300 chr4A 735315845 735317991 2146 False 978.5 1354 83.4085 544 2645 2 chr4A.!!$F10 2101
9 TraesCS4A01G478300 chr4A 734583122 734585555 2433 False 905.5 1308 86.9990 975 2645 2 chr4A.!!$F9 1670
10 TraesCS4A01G478300 chr4A 735775795 735776821 1026 False 787.0 787 80.9160 387 1411 1 chr4A.!!$F6 1024
11 TraesCS4A01G478300 chr4A 735367513 735368293 780 True 767.0 767 84.4590 630 1411 1 chr4A.!!$R1 781
12 TraesCS4A01G478300 chr4A 736470775 736471653 878 True 669.0 669 81.0380 259 1111 1 chr4A.!!$R5 852
13 TraesCS4A01G478300 chr4A 736895433 736897185 1752 False 588.0 614 83.3260 124 1411 2 chr4A.!!$F11 1287
14 TraesCS4A01G478300 chr4A 736755362 736755949 587 False 331.0 331 77.9090 313 868 1 chr4A.!!$F8 555
15 TraesCS4A01G478300 chr7D 5647707 5648929 1222 True 1280.0 1280 85.6100 1421 2645 1 chr7D.!!$R4 1224
16 TraesCS4A01G478300 chr7D 5448705 5449884 1179 True 1046.0 1046 83.1510 259 1411 1 chr7D.!!$R1 1152
17 TraesCS4A01G478300 chr7D 5637676 5638669 993 True 854.0 854 82.5870 432 1411 1 chr7D.!!$R3 979
18 TraesCS4A01G478300 chr7A 6928243 6929515 1272 True 549.0 942 84.4445 124 1411 2 chr7A.!!$R1 1287

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
562 604 0.88649 CTGCAACCTTGGCTCGTCTT 60.886 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2160 2743 0.039165 CTTTTGCCGCCAAAGGAGAC 60.039 55.0 8.71 0.0 41.58 3.36 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
29 30 6.931838 ACGGAGTAAAATGAGTGAATCTACA 58.068 36.000 0.00 0.00 41.94 2.74
30 31 6.812160 ACGGAGTAAAATGAGTGAATCTACAC 59.188 38.462 0.00 0.00 41.94 2.90
43 44 8.430801 AGTGAATCTACACTCTAAAATGCATC 57.569 34.615 0.00 0.00 46.36 3.91
44 45 8.263640 AGTGAATCTACACTCTAAAATGCATCT 58.736 33.333 0.00 0.00 46.36 2.90
45 46 9.534565 GTGAATCTACACTCTAAAATGCATCTA 57.465 33.333 0.00 0.00 37.73 1.98
55 56 9.809096 ACTCTAAAATGCATCTATATACATCCG 57.191 33.333 0.00 0.00 0.00 4.18
56 57 9.809096 CTCTAAAATGCATCTATATACATCCGT 57.191 33.333 0.00 0.00 0.00 4.69
61 62 8.877808 AATGCATCTATATACATCCGTATGTG 57.122 34.615 3.56 0.00 45.99 3.21
62 63 6.805713 TGCATCTATATACATCCGTATGTGG 58.194 40.000 3.56 0.00 45.99 4.17
63 64 6.379988 TGCATCTATATACATCCGTATGTGGT 59.620 38.462 3.56 0.00 45.99 4.16
64 65 6.918569 GCATCTATATACATCCGTATGTGGTC 59.081 42.308 3.56 0.00 45.99 4.02
65 66 7.426410 CATCTATATACATCCGTATGTGGTCC 58.574 42.308 3.56 0.00 45.99 4.46
66 67 6.486941 TCTATATACATCCGTATGTGGTCCA 58.513 40.000 3.56 0.00 45.99 4.02
67 68 7.123383 TCTATATACATCCGTATGTGGTCCAT 58.877 38.462 3.56 0.00 45.99 3.41
68 69 8.276477 TCTATATACATCCGTATGTGGTCCATA 58.724 37.037 3.56 0.00 45.99 2.74
69 70 5.661056 ATACATCCGTATGTGGTCCATAG 57.339 43.478 3.56 0.00 45.99 2.23
70 71 3.305720 ACATCCGTATGTGGTCCATAGT 58.694 45.455 0.00 0.00 44.79 2.12
71 72 3.069586 ACATCCGTATGTGGTCCATAGTG 59.930 47.826 0.00 0.00 44.79 2.74
72 73 3.021177 TCCGTATGTGGTCCATAGTGA 57.979 47.619 0.00 0.00 36.71 3.41
73 74 3.367321 TCCGTATGTGGTCCATAGTGAA 58.633 45.455 0.00 0.00 36.71 3.18
74 75 3.770388 TCCGTATGTGGTCCATAGTGAAA 59.230 43.478 0.00 0.00 36.71 2.69
75 76 4.407621 TCCGTATGTGGTCCATAGTGAAAT 59.592 41.667 0.00 0.00 36.71 2.17
76 77 4.750098 CCGTATGTGGTCCATAGTGAAATC 59.250 45.833 0.00 0.00 36.71 2.17
77 78 5.453339 CCGTATGTGGTCCATAGTGAAATCT 60.453 44.000 0.00 0.00 36.71 2.40
78 79 5.692204 CGTATGTGGTCCATAGTGAAATCTC 59.308 44.000 0.00 0.00 36.71 2.75
79 80 5.965033 ATGTGGTCCATAGTGAAATCTCT 57.035 39.130 0.00 0.00 29.82 3.10
80 81 7.255486 CGTATGTGGTCCATAGTGAAATCTCTA 60.255 40.741 0.00 0.00 36.71 2.43
81 82 6.222038 TGTGGTCCATAGTGAAATCTCTAC 57.778 41.667 0.00 0.00 0.00 2.59
82 83 5.163550 TGTGGTCCATAGTGAAATCTCTACG 60.164 44.000 0.00 0.00 0.00 3.51
83 84 5.067413 GTGGTCCATAGTGAAATCTCTACGA 59.933 44.000 0.00 0.00 0.00 3.43
84 85 5.655090 TGGTCCATAGTGAAATCTCTACGAA 59.345 40.000 0.00 0.00 0.00 3.85
85 86 6.183360 TGGTCCATAGTGAAATCTCTACGAAG 60.183 42.308 0.00 0.00 0.00 3.79
86 87 6.039493 GGTCCATAGTGAAATCTCTACGAAGA 59.961 42.308 0.00 0.00 0.00 2.87
87 88 6.913673 GTCCATAGTGAAATCTCTACGAAGAC 59.086 42.308 0.00 0.00 0.00 3.01
88 89 6.829298 TCCATAGTGAAATCTCTACGAAGACT 59.171 38.462 0.00 0.00 0.00 3.24
89 90 7.339721 TCCATAGTGAAATCTCTACGAAGACTT 59.660 37.037 0.00 0.00 0.00 3.01
90 91 8.622157 CCATAGTGAAATCTCTACGAAGACTTA 58.378 37.037 0.00 0.00 0.00 2.24
102 103 9.596677 CTCTACGAAGACTTATATTTAGGAACG 57.403 37.037 0.00 0.00 0.00 3.95
103 104 9.330063 TCTACGAAGACTTATATTTAGGAACGA 57.670 33.333 0.00 0.00 0.00 3.85
104 105 9.941664 CTACGAAGACTTATATTTAGGAACGAA 57.058 33.333 0.00 0.00 0.00 3.85
105 106 8.853469 ACGAAGACTTATATTTAGGAACGAAG 57.147 34.615 0.00 0.00 0.00 3.79
106 107 7.919621 ACGAAGACTTATATTTAGGAACGAAGG 59.080 37.037 0.00 0.00 0.00 3.46
107 108 7.381678 CGAAGACTTATATTTAGGAACGAAGGG 59.618 40.741 0.00 0.00 0.00 3.95
108 109 7.909485 AGACTTATATTTAGGAACGAAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
109 110 7.953752 AGACTTATATTTAGGAACGAAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
110 111 7.564292 AGACTTATATTTAGGAACGAAGGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
111 112 8.773033 ACTTATATTTAGGAACGAAGGGAGTA 57.227 34.615 0.00 0.00 0.00 2.59
112 113 9.377238 ACTTATATTTAGGAACGAAGGGAGTAT 57.623 33.333 0.00 0.00 0.00 2.12
117 118 4.338379 AGGAACGAAGGGAGTATTATGC 57.662 45.455 0.00 0.00 0.00 3.14
118 119 3.709653 AGGAACGAAGGGAGTATTATGCA 59.290 43.478 0.00 0.00 0.00 3.96
119 120 4.348168 AGGAACGAAGGGAGTATTATGCAT 59.652 41.667 3.79 3.79 0.00 3.96
120 121 5.542635 AGGAACGAAGGGAGTATTATGCATA 59.457 40.000 1.16 1.16 0.00 3.14
121 122 5.869888 GGAACGAAGGGAGTATTATGCATAG 59.130 44.000 6.50 0.00 0.00 2.23
122 123 4.822026 ACGAAGGGAGTATTATGCATAGC 58.178 43.478 6.50 2.08 0.00 2.97
257 270 3.210227 TCACAATTTTCCTTGCGAGTGA 58.790 40.909 0.00 0.00 32.91 3.41
274 287 5.107298 GCGAGTGAAACATCTATAAGGATGC 60.107 44.000 4.63 0.00 44.81 3.91
295 308 3.947868 CTTCCTGGAAAGCATGAAGAGA 58.052 45.455 10.86 0.00 35.56 3.10
300 313 2.224597 TGGAAAGCATGAAGAGACAGCA 60.225 45.455 0.00 0.00 0.00 4.41
333 356 7.160049 TGGATACCAACTCGTTGTTTGTATTA 58.840 34.615 15.64 9.65 43.28 0.98
334 357 7.118101 TGGATACCAACTCGTTGTTTGTATTAC 59.882 37.037 15.64 13.39 43.28 1.89
405 429 2.635427 TGTGTGTCCATGTTGGCTACTA 59.365 45.455 0.01 0.00 37.47 1.82
448 474 9.171877 CTCCATCTCAGCTAAACTTAAAGAAAT 57.828 33.333 0.00 0.00 0.00 2.17
494 525 1.211703 TGTCTTGACCTGCTGTTTGGA 59.788 47.619 0.00 0.00 0.00 3.53
562 604 0.886490 CTGCAACCTTGGCTCGTCTT 60.886 55.000 0.00 0.00 0.00 3.01
618 673 1.995484 CATCTGTGTAAGCTCACCACG 59.005 52.381 3.31 1.15 37.51 4.94
681 754 2.584791 GTCGTTTGCAACCTGCTAATG 58.415 47.619 0.00 8.21 45.31 1.90
729 804 4.449068 GGTGTTCATCCACTGCTATATTCG 59.551 45.833 0.00 0.00 35.63 3.34
806 884 1.995542 AGGTCATTCCACACTCCCAAT 59.004 47.619 0.00 0.00 39.02 3.16
812 890 5.760253 GTCATTCCACACTCCCAATATAGTG 59.240 44.000 2.43 2.43 46.84 2.74
965 1496 6.749923 AAGCAATTCTGGTTCTATCTTCAC 57.250 37.500 0.00 0.00 38.98 3.18
993 1536 3.707102 TCAACCCAAAAAGTAAACCCTGG 59.293 43.478 0.00 0.00 0.00 4.45
1050 1593 1.259316 GCGTTAGCTTGAAATTGGCG 58.741 50.000 0.00 0.00 41.01 5.69
1101 1644 2.766263 TGATGCTTCAACCTACCTCGAT 59.234 45.455 0.00 0.00 0.00 3.59
1218 1761 3.007182 CCAAGTTGGACAAATGGCTTCAT 59.993 43.478 17.60 0.00 40.96 2.57
1335 1878 1.305219 CCAATGCGTCCACCGTCAAT 61.305 55.000 0.00 0.00 39.32 2.57
1417 1960 6.658816 TGAGAACAGAAAGCTAATTTGCCATA 59.341 34.615 8.30 0.00 0.00 2.74
1430 2003 7.014230 GCTAATTTGCCATATAAAGGACTTCCA 59.986 37.037 0.00 0.00 38.89 3.53
1435 2008 6.613699 TGCCATATAAAGGACTTCCATCAAT 58.386 36.000 0.00 0.00 38.89 2.57
1440 2013 9.288576 CATATAAAGGACTTCCATCAATTGCTA 57.711 33.333 0.00 0.00 38.89 3.49
1442 2015 6.705863 AAAGGACTTCCATCAATTGCTATC 57.294 37.500 0.00 0.00 38.89 2.08
1450 2023 5.624159 TCCATCAATTGCTATCCTTACCAG 58.376 41.667 0.00 0.00 0.00 4.00
1451 2024 4.217118 CCATCAATTGCTATCCTTACCAGC 59.783 45.833 0.00 0.00 35.82 4.85
1452 2025 4.778213 TCAATTGCTATCCTTACCAGCT 57.222 40.909 0.00 0.00 36.26 4.24
1453 2026 4.454678 TCAATTGCTATCCTTACCAGCTG 58.545 43.478 6.78 6.78 36.26 4.24
1454 2027 3.498774 ATTGCTATCCTTACCAGCTGG 57.501 47.619 31.60 31.60 42.17 4.85
1469 2042 3.885297 CCAGCTGGTTCTGGTTATAATGG 59.115 47.826 25.53 0.00 46.59 3.16
1473 2046 4.816925 GCTGGTTCTGGTTATAATGGAGAC 59.183 45.833 0.00 0.00 0.00 3.36
1474 2047 5.396884 GCTGGTTCTGGTTATAATGGAGACT 60.397 44.000 0.00 0.00 0.00 3.24
1492 2065 0.751277 CTGCCCCGCCATAACATCAA 60.751 55.000 0.00 0.00 0.00 2.57
1541 2114 4.104102 ACCACCTCTGAAAGTAATTGGTCA 59.896 41.667 0.00 0.00 31.54 4.02
1546 2119 5.063944 CCTCTGAAAGTAATTGGTCATGACG 59.936 44.000 19.33 1.27 33.76 4.35
1611 2193 5.531659 TGCTATTACTGAGTCTAGTACAGCC 59.468 44.000 19.41 10.88 38.97 4.85
1631 2213 1.812571 CATGTACTCAGGTTTGGCCAC 59.187 52.381 3.88 0.00 40.61 5.01
1650 2232 2.624838 CACTGTTGGAGTTTGAGGCATT 59.375 45.455 0.00 0.00 29.75 3.56
1672 2254 2.238521 GAAAATCCACCTTGGCACAGA 58.761 47.619 0.00 0.00 42.39 3.41
1674 2256 2.134789 AATCCACCTTGGCACAGATC 57.865 50.000 0.00 0.00 42.39 2.75
1694 2276 3.071479 TCGTTTACAATGACAAGAGGGC 58.929 45.455 0.00 0.00 0.00 5.19
1711 2293 9.034800 ACAAGAGGGCAAAAGAATATTTTGATA 57.965 29.630 16.16 0.00 40.73 2.15
1776 2358 3.004419 GTCATACACGGGAGATCATCGAA 59.996 47.826 0.00 0.00 0.00 3.71
1777 2359 3.004419 TCATACACGGGAGATCATCGAAC 59.996 47.826 0.00 0.00 0.00 3.95
1782 2364 0.755686 GGGAGATCATCGAACCTGCT 59.244 55.000 0.00 0.00 0.00 4.24
1788 2371 3.196469 AGATCATCGAACCTGCTTCTCAA 59.804 43.478 0.00 0.00 0.00 3.02
1881 2464 3.552890 GGAAATTCCTGCTTGTGTTGGAC 60.553 47.826 4.46 0.00 32.53 4.02
1911 2494 1.133363 TTGAACCCGGGAGTGAAAGA 58.867 50.000 32.02 0.88 0.00 2.52
1926 2509 3.753797 GTGAAAGAGAATGGGACCAACTC 59.246 47.826 15.96 15.96 35.41 3.01
1936 2519 2.043939 TGGGACCAACTCTTAGCTCCTA 59.956 50.000 0.00 0.00 0.00 2.94
1938 2521 3.070302 GGGACCAACTCTTAGCTCCTATG 59.930 52.174 0.00 0.00 0.00 2.23
1965 2548 3.820467 CACAACAGATGGGAAGCAAAGTA 59.180 43.478 0.00 0.00 32.54 2.24
1981 2564 6.407202 AGCAAAGTATTGGTAACTTCTCGAT 58.593 36.000 0.00 0.00 45.01 3.59
1997 2580 3.324846 TCTCGATGGGATACATTTCCAGG 59.675 47.826 0.00 0.00 40.72 4.45
2039 2622 2.040278 TGTGTCCTCTGGAAAAGATGGG 59.960 50.000 0.00 0.00 33.29 4.00
2044 2627 4.656112 GTCCTCTGGAAAAGATGGGAGATA 59.344 45.833 0.00 0.00 31.57 1.98
2049 2632 5.726308 TCTGGAAAAGATGGGAGATACTCAA 59.274 40.000 0.00 0.00 30.42 3.02
2056 2639 7.443302 AAGATGGGAGATACTCAATTCTTGA 57.557 36.000 0.00 0.00 38.17 3.02
2057 2640 7.630005 AGATGGGAGATACTCAATTCTTGAT 57.370 36.000 0.00 0.00 39.30 2.57
2061 2644 7.730084 TGGGAGATACTCAATTCTTGATACTG 58.270 38.462 0.00 0.00 39.30 2.74
2140 2723 3.795688 TGGAAGATTTTGCAGAGGAGT 57.204 42.857 0.00 0.00 30.57 3.85
2157 2740 3.069586 AGGAGTTTGTTAAAAGGCTTGGC 59.930 43.478 0.00 0.00 0.00 4.52
2181 2764 1.202830 TCTCCTTTGGCGGCAAAAGTA 60.203 47.619 32.93 21.14 33.61 2.24
2216 2799 6.701400 CAGTTGAAAGGGAAAACAAATACCAG 59.299 38.462 0.00 0.00 0.00 4.00
2265 2848 5.234466 AGATTGACAAACTAAGTGAGCCT 57.766 39.130 0.00 0.00 0.00 4.58
2308 2891 8.861086 GGAGTTATGAGAAGTTAGATCCATGTA 58.139 37.037 0.00 0.00 0.00 2.29
2360 2943 1.892474 TCCAAAAGGCCACAAGTATGC 59.108 47.619 5.01 0.00 0.00 3.14
2491 3074 6.262601 TCTGTTTCGTTCTTTCAACCATTTC 58.737 36.000 0.00 0.00 0.00 2.17
2521 3110 7.454260 AGATACTATGTTATGCACGATCTCA 57.546 36.000 0.00 0.00 0.00 3.27
2525 3114 4.979564 ATGTTATGCACGATCTCATTCG 57.020 40.909 0.00 0.00 44.56 3.34
2540 3129 4.160439 TCTCATTCGTGACCTAGCAGAATT 59.840 41.667 0.00 0.00 30.10 2.17
2541 3130 4.183865 TCATTCGTGACCTAGCAGAATTG 58.816 43.478 0.00 0.00 30.10 2.32
2572 3161 7.559170 CCAAAGAGGAATACTTCAGATTGGAAT 59.441 37.037 0.00 0.00 41.22 3.01
2573 3162 8.404000 CAAAGAGGAATACTTCAGATTGGAATG 58.596 37.037 0.00 0.00 0.00 2.67
2587 3176 5.882557 AGATTGGAATGTGATAAGGTGACAC 59.117 40.000 0.00 0.00 35.45 3.67
2598 3187 6.823689 GTGATAAGGTGACACAAATACCATCT 59.176 38.462 8.08 0.00 36.94 2.90
2601 3190 5.099042 AGGTGACACAAATACCATCTACC 57.901 43.478 8.08 0.00 36.94 3.18
2619 3208 3.422417 ACCGTTCGACATCTATCTGTG 57.578 47.619 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 6.812160 GTGTAGATTCACTCATTTTACTCCGT 59.188 38.462 0.00 0.00 35.68 4.69
6 7 7.036220 AGTGTAGATTCACTCATTTTACTCCG 58.964 38.462 0.00 0.00 44.07 4.63
19 20 8.430801 AGATGCATTTTAGAGTGTAGATTCAC 57.569 34.615 0.00 0.00 38.46 3.18
29 30 9.809096 CGGATGTATATAGATGCATTTTAGAGT 57.191 33.333 11.19 0.00 38.38 3.24
30 31 9.809096 ACGGATGTATATAGATGCATTTTAGAG 57.191 33.333 11.19 0.00 38.38 2.43
34 35 9.890629 ACATACGGATGTATATAGATGCATTTT 57.109 29.630 12.79 0.00 44.77 1.82
35 36 9.317936 CACATACGGATGTATATAGATGCATTT 57.682 33.333 14.23 0.00 44.82 2.32
36 37 7.928167 CCACATACGGATGTATATAGATGCATT 59.072 37.037 14.23 1.23 44.82 3.56
37 38 7.069950 ACCACATACGGATGTATATAGATGCAT 59.930 37.037 14.23 0.00 44.82 3.96
38 39 6.379988 ACCACATACGGATGTATATAGATGCA 59.620 38.462 14.23 0.00 44.82 3.96
39 40 6.806751 ACCACATACGGATGTATATAGATGC 58.193 40.000 14.23 0.00 44.82 3.91
40 41 7.068226 TGGACCACATACGGATGTATATAGATG 59.932 40.741 14.23 0.00 44.82 2.90
41 42 7.123383 TGGACCACATACGGATGTATATAGAT 58.877 38.462 14.23 0.00 44.82 1.98
42 43 6.486941 TGGACCACATACGGATGTATATAGA 58.513 40.000 14.23 0.00 44.82 1.98
43 44 6.769134 TGGACCACATACGGATGTATATAG 57.231 41.667 14.23 0.00 44.82 1.31
44 45 8.057011 ACTATGGACCACATACGGATGTATATA 58.943 37.037 14.23 7.10 44.82 0.86
45 46 6.895756 ACTATGGACCACATACGGATGTATAT 59.104 38.462 14.23 1.16 44.82 0.86
46 47 6.152154 CACTATGGACCACATACGGATGTATA 59.848 42.308 14.23 6.48 44.82 1.47
47 48 5.047306 CACTATGGACCACATACGGATGTAT 60.047 44.000 14.23 4.48 44.82 2.29
48 49 4.279922 CACTATGGACCACATACGGATGTA 59.720 45.833 14.23 0.00 44.82 2.29
50 51 3.320826 TCACTATGGACCACATACGGATG 59.679 47.826 5.94 5.94 41.03 3.51
51 52 3.572642 TCACTATGGACCACATACGGAT 58.427 45.455 0.00 0.00 41.03 4.18
52 53 3.021177 TCACTATGGACCACATACGGA 57.979 47.619 0.00 0.00 41.03 4.69
53 54 3.812156 TTCACTATGGACCACATACGG 57.188 47.619 0.00 0.00 41.03 4.02
54 55 5.601662 AGATTTCACTATGGACCACATACG 58.398 41.667 0.00 0.00 41.03 3.06
55 56 6.821388 AGAGATTTCACTATGGACCACATAC 58.179 40.000 0.00 0.00 41.03 2.39
56 57 7.255486 CGTAGAGATTTCACTATGGACCACATA 60.255 40.741 0.00 0.00 41.03 2.29
57 58 5.965033 AGAGATTTCACTATGGACCACAT 57.035 39.130 0.00 0.00 43.68 3.21
58 59 5.163550 CGTAGAGATTTCACTATGGACCACA 60.164 44.000 0.00 0.00 0.00 4.17
59 60 5.067413 TCGTAGAGATTTCACTATGGACCAC 59.933 44.000 0.00 0.00 30.34 4.16
60 61 5.198207 TCGTAGAGATTTCACTATGGACCA 58.802 41.667 0.00 0.00 30.34 4.02
61 62 5.769484 TCGTAGAGATTTCACTATGGACC 57.231 43.478 4.96 0.00 30.34 4.46
62 63 6.913673 GTCTTCGTAGAGATTTCACTATGGAC 59.086 42.308 0.00 2.91 38.43 4.02
63 64 6.829298 AGTCTTCGTAGAGATTTCACTATGGA 59.171 38.462 0.00 0.00 38.43 3.41
64 65 7.033530 AGTCTTCGTAGAGATTTCACTATGG 57.966 40.000 0.00 0.00 38.43 2.74
76 77 9.596677 CGTTCCTAAATATAAGTCTTCGTAGAG 57.403 37.037 0.00 0.00 38.43 2.43
77 78 9.330063 TCGTTCCTAAATATAAGTCTTCGTAGA 57.670 33.333 0.00 0.00 0.00 2.59
78 79 9.941664 TTCGTTCCTAAATATAAGTCTTCGTAG 57.058 33.333 0.00 0.00 0.00 3.51
79 80 9.941664 CTTCGTTCCTAAATATAAGTCTTCGTA 57.058 33.333 0.00 0.00 0.00 3.43
80 81 7.919621 CCTTCGTTCCTAAATATAAGTCTTCGT 59.080 37.037 0.00 0.00 0.00 3.85
81 82 7.381678 CCCTTCGTTCCTAAATATAAGTCTTCG 59.618 40.741 0.00 0.00 0.00 3.79
82 83 8.419442 TCCCTTCGTTCCTAAATATAAGTCTTC 58.581 37.037 0.00 0.00 0.00 2.87
83 84 8.315220 TCCCTTCGTTCCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
84 85 7.564292 ACTCCCTTCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
85 86 7.724287 ACTCCCTTCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
86 87 7.672122 ACTCCCTTCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
91 92 8.092687 GCATAATACTCCCTTCGTTCCTAAATA 58.907 37.037 0.00 0.00 0.00 1.40
92 93 6.935208 GCATAATACTCCCTTCGTTCCTAAAT 59.065 38.462 0.00 0.00 0.00 1.40
93 94 6.126997 TGCATAATACTCCCTTCGTTCCTAAA 60.127 38.462 0.00 0.00 0.00 1.85
94 95 5.364446 TGCATAATACTCCCTTCGTTCCTAA 59.636 40.000 0.00 0.00 0.00 2.69
95 96 4.897076 TGCATAATACTCCCTTCGTTCCTA 59.103 41.667 0.00 0.00 0.00 2.94
96 97 3.709653 TGCATAATACTCCCTTCGTTCCT 59.290 43.478 0.00 0.00 0.00 3.36
97 98 4.067972 TGCATAATACTCCCTTCGTTCC 57.932 45.455 0.00 0.00 0.00 3.62
98 99 5.348997 GCTATGCATAATACTCCCTTCGTTC 59.651 44.000 8.00 0.00 0.00 3.95
99 100 5.221641 TGCTATGCATAATACTCCCTTCGTT 60.222 40.000 8.00 0.00 31.71 3.85
100 101 4.283467 TGCTATGCATAATACTCCCTTCGT 59.717 41.667 8.00 0.00 31.71 3.85
101 102 4.820897 TGCTATGCATAATACTCCCTTCG 58.179 43.478 8.00 0.00 31.71 3.79
102 103 5.123027 GCTTGCTATGCATAATACTCCCTTC 59.877 44.000 8.00 0.00 38.76 3.46
103 104 5.006386 GCTTGCTATGCATAATACTCCCTT 58.994 41.667 8.00 0.00 38.76 3.95
104 105 4.042062 TGCTTGCTATGCATAATACTCCCT 59.958 41.667 8.00 0.00 38.76 4.20
105 106 4.154918 GTGCTTGCTATGCATAATACTCCC 59.845 45.833 8.00 0.00 42.69 4.30
106 107 4.999950 AGTGCTTGCTATGCATAATACTCC 59.000 41.667 8.00 0.00 42.69 3.85
107 108 5.121454 GGAGTGCTTGCTATGCATAATACTC 59.879 44.000 8.00 13.17 42.69 2.59
108 109 4.999950 GGAGTGCTTGCTATGCATAATACT 59.000 41.667 8.00 5.99 42.69 2.12
109 110 4.143030 CGGAGTGCTTGCTATGCATAATAC 60.143 45.833 8.00 1.22 42.69 1.89
110 111 3.996363 CGGAGTGCTTGCTATGCATAATA 59.004 43.478 8.00 0.00 42.69 0.98
111 112 2.810274 CGGAGTGCTTGCTATGCATAAT 59.190 45.455 8.00 0.00 42.69 1.28
112 113 2.212652 CGGAGTGCTTGCTATGCATAA 58.787 47.619 8.00 0.00 42.69 1.90
113 114 1.138859 ACGGAGTGCTTGCTATGCATA 59.861 47.619 6.20 6.20 42.51 3.14
114 115 0.107508 ACGGAGTGCTTGCTATGCAT 60.108 50.000 3.79 3.79 42.51 3.96
115 116 1.296392 ACGGAGTGCTTGCTATGCA 59.704 52.632 0.00 0.00 42.51 3.96
116 117 4.208632 ACGGAGTGCTTGCTATGC 57.791 55.556 0.00 0.00 42.51 3.14
234 247 4.097135 TCACTCGCAAGGAAAATTGTGAAA 59.903 37.500 4.49 0.00 46.04 2.69
236 249 3.210227 TCACTCGCAAGGAAAATTGTGA 58.790 40.909 3.06 3.06 44.98 3.58
237 250 3.624326 TCACTCGCAAGGAAAATTGTG 57.376 42.857 0.00 0.00 41.10 3.33
238 251 4.142271 TGTTTCACTCGCAAGGAAAATTGT 60.142 37.500 0.00 0.00 32.85 2.71
239 252 4.358851 TGTTTCACTCGCAAGGAAAATTG 58.641 39.130 0.00 0.00 32.85 2.32
241 254 4.520492 AGATGTTTCACTCGCAAGGAAAAT 59.480 37.500 0.00 0.00 32.85 1.82
242 255 3.882888 AGATGTTTCACTCGCAAGGAAAA 59.117 39.130 0.00 0.00 32.85 2.29
295 308 2.241941 TGGTATCCATCACCATTGCTGT 59.758 45.455 0.00 0.00 41.17 4.40
300 313 3.199946 ACGAGTTGGTATCCATCACCATT 59.800 43.478 0.00 0.00 45.32 3.16
320 333 7.129622 ACATTGTGTGAGTAATACAAACAACG 58.870 34.615 0.00 0.00 44.59 4.10
333 356 4.019860 AGCAGAGGATAACATTGTGTGAGT 60.020 41.667 0.00 0.00 0.00 3.41
334 357 4.511527 AGCAGAGGATAACATTGTGTGAG 58.488 43.478 0.00 0.00 0.00 3.51
384 408 1.419762 AGTAGCCAACATGGACACACA 59.580 47.619 0.00 0.00 40.96 3.72
385 409 2.185004 AGTAGCCAACATGGACACAC 57.815 50.000 0.00 0.00 40.96 3.82
405 429 9.422681 TGAGATGGAGTAGCTAATAAACTAACT 57.577 33.333 0.00 0.00 0.00 2.24
448 474 0.253044 GATGGTCCAGCTACTTGCCA 59.747 55.000 0.00 0.00 44.23 4.92
494 525 3.946558 GCAAGAGAATGAGGCAGAAATCT 59.053 43.478 0.00 0.00 0.00 2.40
562 604 1.302192 GTTGTAGGAGCCGGCACAA 60.302 57.895 31.54 26.11 0.00 3.33
618 673 7.659390 ACTTTACAGCCAGATTATGAGAATAGC 59.341 37.037 0.00 0.00 0.00 2.97
681 754 7.860872 CCTGTTGGAGTAAGAAACACAAAATAC 59.139 37.037 0.00 0.00 31.66 1.89
729 804 5.644636 TGGAACGGATGTAGAAATAACCAAC 59.355 40.000 0.00 0.00 0.00 3.77
806 884 6.978659 CGATGGCAAAGACTAAGAACACTATA 59.021 38.462 0.00 0.00 0.00 1.31
812 890 4.246458 AGACGATGGCAAAGACTAAGAAC 58.754 43.478 0.00 0.00 0.00 3.01
916 1446 8.807118 TCTAGACACAGTGATGAATAAGAAAGT 58.193 33.333 7.81 0.00 0.00 2.66
965 1496 8.208224 AGGGTTTACTTTTTGGGTTGAATAAAG 58.792 33.333 0.00 0.00 33.27 1.85
993 1536 0.893727 ACGCCACTTCCATTGGGTTC 60.894 55.000 2.09 0.00 34.35 3.62
1050 1593 2.479566 TCTTCAAGACAGGTGATGCC 57.520 50.000 0.00 0.00 37.58 4.40
1101 1644 1.303948 CTCATGGGCCATGTCCACA 59.696 57.895 38.04 22.27 41.42 4.17
1193 1736 1.341080 CCATTTGTCCAACTTGGGCT 58.659 50.000 13.62 0.00 44.07 5.19
1218 1761 4.348168 AGGTAGAAGCCTTCTTTGAGTTCA 59.652 41.667 13.04 0.00 41.14 3.18
1323 1866 4.499037 AAAAGCTTTATTGACGGTGGAC 57.501 40.909 13.10 0.00 0.00 4.02
1327 1870 6.322491 GCTTCATAAAAGCTTTATTGACGGT 58.678 36.000 13.10 0.00 40.01 4.83
1330 1873 7.699812 CAGAGGCTTCATAAAAGCTTTATTGAC 59.300 37.037 13.10 7.54 42.62 3.18
1335 1878 4.094887 CGCAGAGGCTTCATAAAAGCTTTA 59.905 41.667 13.10 1.49 42.62 1.85
1417 1960 7.449704 GGATAGCAATTGATGGAAGTCCTTTAT 59.550 37.037 10.34 0.00 36.82 1.40
1430 2003 5.068636 CAGCTGGTAAGGATAGCAATTGAT 58.931 41.667 10.34 5.28 38.93 2.57
1450 2023 4.816925 GTCTCCATTATAACCAGAACCAGC 59.183 45.833 0.00 0.00 0.00 4.85
1451 2024 6.051717 CAGTCTCCATTATAACCAGAACCAG 58.948 44.000 0.00 0.00 0.00 4.00
1452 2025 5.629133 GCAGTCTCCATTATAACCAGAACCA 60.629 44.000 0.00 0.00 0.00 3.67
1453 2026 4.816925 GCAGTCTCCATTATAACCAGAACC 59.183 45.833 0.00 0.00 0.00 3.62
1454 2027 4.816925 GGCAGTCTCCATTATAACCAGAAC 59.183 45.833 0.00 0.00 0.00 3.01
1455 2028 4.141482 GGGCAGTCTCCATTATAACCAGAA 60.141 45.833 0.00 0.00 0.00 3.02
1469 2042 1.523938 GTTATGGCGGGGCAGTCTC 60.524 63.158 0.45 0.00 0.00 3.36
1473 2046 0.751277 TTGATGTTATGGCGGGGCAG 60.751 55.000 0.45 0.00 0.00 4.85
1474 2047 0.106268 ATTGATGTTATGGCGGGGCA 60.106 50.000 0.00 0.00 0.00 5.36
1492 2065 3.576078 TGTGGTCTCAGGAACAACAAT 57.424 42.857 0.00 0.00 41.23 2.71
1546 2119 8.779303 ACGATCTATTATATGATCACGATCCTC 58.221 37.037 0.00 0.00 39.06 3.71
1581 2154 6.857956 ACTAGACTCAGTAATAGCAGTTGTG 58.142 40.000 0.00 0.00 0.00 3.33
1611 2193 1.812571 GTGGCCAAACCTGAGTACATG 59.187 52.381 7.24 0.00 40.22 3.21
1631 2213 2.029649 CCAATGCCTCAAACTCCAACAG 60.030 50.000 0.00 0.00 0.00 3.16
1650 2232 1.337118 GTGCCAAGGTGGATTTTCCA 58.663 50.000 0.00 0.00 45.98 3.53
1672 2254 3.689649 GCCCTCTTGTCATTGTAAACGAT 59.310 43.478 0.00 0.00 0.00 3.73
1674 2256 2.811431 TGCCCTCTTGTCATTGTAAACG 59.189 45.455 0.00 0.00 0.00 3.60
1711 2293 5.590259 GTGAGATGCTTACCCACATTGTTAT 59.410 40.000 0.00 0.00 0.00 1.89
1713 2295 3.758554 GTGAGATGCTTACCCACATTGTT 59.241 43.478 0.00 0.00 0.00 2.83
1776 2358 1.005215 CATTCCCCTTGAGAAGCAGGT 59.995 52.381 0.00 0.00 0.00 4.00
1777 2359 1.760192 CATTCCCCTTGAGAAGCAGG 58.240 55.000 0.00 0.00 0.00 4.85
1809 2392 1.662629 CGCTGCAGAGTATCAAGGTTG 59.337 52.381 20.43 0.00 37.82 3.77
1842 2425 6.321181 GGAATTTCCCTGATTGTTGCAGTATA 59.679 38.462 3.89 0.00 0.00 1.47
1899 2482 1.555075 TCCCATTCTCTTTCACTCCCG 59.445 52.381 0.00 0.00 0.00 5.14
1902 2485 3.703001 TGGTCCCATTCTCTTTCACTC 57.297 47.619 0.00 0.00 0.00 3.51
1911 2494 3.185455 AGCTAAGAGTTGGTCCCATTCT 58.815 45.455 0.00 0.00 0.00 2.40
1926 2509 5.245531 TGTTGTGAAACCATAGGAGCTAAG 58.754 41.667 0.00 0.00 34.36 2.18
1936 2519 3.524095 TCCCATCTGTTGTGAAACCAT 57.476 42.857 0.00 0.00 34.36 3.55
1938 2521 2.029918 GCTTCCCATCTGTTGTGAAACC 60.030 50.000 0.00 0.00 34.36 3.27
1965 2548 5.365605 TGTATCCCATCGAGAAGTTACCAAT 59.634 40.000 0.00 0.00 0.00 3.16
1981 2564 1.922447 AGCACCTGGAAATGTATCCCA 59.078 47.619 0.00 0.00 38.82 4.37
2056 2639 2.794103 TGCATGGTGCTTGAACAGTAT 58.206 42.857 3.41 0.00 45.31 2.12
2057 2640 2.268762 TGCATGGTGCTTGAACAGTA 57.731 45.000 3.41 0.00 45.31 2.74
2061 2644 2.490903 AGAGAATGCATGGTGCTTGAAC 59.509 45.455 0.00 0.00 45.31 3.18
2067 2650 0.737219 GTCCAGAGAATGCATGGTGC 59.263 55.000 0.00 0.00 45.29 5.01
2107 2690 0.884704 TCTTCCAGCCTTTCACGCAC 60.885 55.000 0.00 0.00 0.00 5.34
2137 2720 3.390135 GGCCAAGCCTTTTAACAAACTC 58.610 45.455 0.00 0.00 46.69 3.01
2157 2740 2.747855 GCCGCCAAAGGAGACTGG 60.748 66.667 0.00 0.00 42.68 4.00
2160 2743 0.039165 CTTTTGCCGCCAAAGGAGAC 60.039 55.000 8.71 0.00 41.58 3.36
2265 2848 4.623932 ACTCCACAAAAGAGCACTCATA 57.376 40.909 0.00 0.00 34.56 2.15
2491 3074 6.868339 TCGTGCATAACATAGTATCTTCCATG 59.132 38.462 0.00 0.00 0.00 3.66
2496 3079 7.886338 TGAGATCGTGCATAACATAGTATCTT 58.114 34.615 0.00 0.00 0.00 2.40
2498 3081 8.694975 AATGAGATCGTGCATAACATAGTATC 57.305 34.615 0.00 0.00 0.00 2.24
2521 3110 2.939103 GCAATTCTGCTAGGTCACGAAT 59.061 45.455 0.00 0.00 45.74 3.34
2540 3129 6.384015 TCTGAAGTATTCCTCTTTGGATAGCA 59.616 38.462 0.00 0.00 46.93 3.49
2541 3130 6.821388 TCTGAAGTATTCCTCTTTGGATAGC 58.179 40.000 0.00 0.00 46.93 2.97
2544 3133 7.059156 CCAATCTGAAGTATTCCTCTTTGGAT 58.941 38.462 0.00 0.00 46.93 3.41
2556 3145 8.497745 ACCTTATCACATTCCAATCTGAAGTAT 58.502 33.333 0.00 0.00 0.00 2.12
2572 3161 5.870706 TGGTATTTGTGTCACCTTATCACA 58.129 37.500 0.00 0.00 39.76 3.58
2573 3162 6.823689 AGATGGTATTTGTGTCACCTTATCAC 59.176 38.462 0.00 0.00 33.28 3.06
2587 3176 4.426416 TGTCGAACGGTAGATGGTATTTG 58.574 43.478 0.00 0.00 0.00 2.32
2598 3187 3.242969 GCACAGATAGATGTCGAACGGTA 60.243 47.826 0.00 0.00 0.00 4.02
2601 3190 1.775770 CGCACAGATAGATGTCGAACG 59.224 52.381 0.00 0.00 0.00 3.95
2619 3208 4.092821 TGTTGCTTCATACTATCAACACGC 59.907 41.667 0.00 0.00 41.12 5.34


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

AutoCloner maintained by Alex Coulton.