Multiple sequence alignment - TraesCS2B01G423300

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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 TraesCS2B01G423300 chr2B 100.000 4545 0 0 1 4545 608665841 608670385 0.000000e+00 8394.0
1 TraesCS2B01G423300 chr2B 81.503 1184 155 34 2195 3331 608540772 608541938 0.000000e+00 915.0
2 TraesCS2B01G423300 chr2B 85.467 750 62 16 1268 1988 608801994 608802725 0.000000e+00 737.0
3 TraesCS2B01G423300 chr2B 83.404 711 71 17 2159 2831 608802711 608803412 2.320000e-172 616.0
4 TraesCS2B01G423300 chr2B 89.474 247 25 1 3093 3338 608803767 608804013 1.230000e-80 311.0
5 TraesCS2B01G423300 chr2B 89.855 207 17 2 2874 3076 608803506 608803712 3.490000e-66 263.0
6 TraesCS2B01G423300 chr2B 86.139 101 14 0 319 419 508409685 508409585 4.810000e-20 110.0
7 TraesCS2B01G423300 chr2B 88.421 95 6 4 2103 2195 608667911 608668002 4.810000e-20 110.0
8 TraesCS2B01G423300 chr2B 88.421 95 6 4 2071 2162 608667943 608668035 4.810000e-20 110.0
9 TraesCS2B01G423300 chr2B 87.059 85 11 0 3561 3645 523090044 523089960 3.740000e-16 97.1
10 TraesCS2B01G423300 chr2B 91.379 58 5 0 363 420 154936855 154936798 3.770000e-11 80.5
11 TraesCS2B01G423300 chr2A 92.273 1993 91 26 2103 4073 661152348 661154299 0.000000e+00 2769.0
12 TraesCS2B01G423300 chr2A 90.759 2056 107 33 127 2156 661150434 661152432 0.000000e+00 2667.0
13 TraesCS2B01G423300 chr2A 83.805 1130 123 26 2251 3338 661448215 661449326 0.000000e+00 1018.0
14 TraesCS2B01G423300 chr2A 82.623 1197 116 52 951 2095 661446582 661447738 0.000000e+00 974.0
15 TraesCS2B01G423300 chr2A 80.917 1200 163 39 2189 3331 661082602 661083792 0.000000e+00 887.0
16 TraesCS2B01G423300 chr2A 85.842 784 65 19 1291 2043 661394565 661395333 0.000000e+00 791.0
17 TraesCS2B01G423300 chr2A 94.457 433 20 2 4070 4499 661154380 661154811 0.000000e+00 664.0
18 TraesCS2B01G423300 chr2A 83.432 676 66 22 2193 2831 661395340 661396006 1.820000e-163 586.0
19 TraesCS2B01G423300 chr2A 85.904 376 43 6 426 794 661393169 661393541 4.260000e-105 392.0
20 TraesCS2B01G423300 chr2A 91.414 198 17 0 3141 3338 661403477 661403674 5.790000e-69 272.0
21 TraesCS2B01G423300 chr2A 81.429 210 31 6 592 793 480935590 480935381 1.010000e-36 165.0
22 TraesCS2B01G423300 chr2A 92.000 75 4 2 3070 3143 661396335 661396408 2.240000e-18 104.0
23 TraesCS2B01G423300 chr2A 88.235 85 10 0 3561 3645 572446254 572446338 8.040000e-18 102.0
24 TraesCS2B01G423300 chr2A 95.833 48 2 0 4491 4538 661155424 661155471 1.360000e-10 78.7
25 TraesCS2B01G423300 chr2D 93.839 1477 65 9 2103 3562 516925405 516926872 0.000000e+00 2200.0
26 TraesCS2B01G423300 chr2D 93.301 1224 52 9 951 2153 516924271 516925485 0.000000e+00 1779.0
27 TraesCS2B01G423300 chr2D 82.657 1182 118 45 951 2088 517086055 517087193 0.000000e+00 966.0
28 TraesCS2B01G423300 chr2D 81.880 1181 155 31 2195 3330 516863174 516864340 0.000000e+00 941.0
29 TraesCS2B01G423300 chr2D 89.708 719 27 20 3644 4347 516926871 516927557 0.000000e+00 874.0
30 TraesCS2B01G423300 chr2D 85.733 750 63 18 1268 1988 517037468 517038202 0.000000e+00 752.0
31 TraesCS2B01G423300 chr2D 88.937 461 43 3 2177 2629 517038206 517038666 3.070000e-156 562.0
32 TraesCS2B01G423300 chr2D 80.866 554 59 21 423 931 517085304 517085855 4.260000e-105 392.0
33 TraesCS2B01G423300 chr2D 91.481 270 21 2 3070 3338 517045911 517046179 2.000000e-98 370.0
34 TraesCS2B01G423300 chr2D 92.558 215 10 5 4335 4545 516928891 516929103 2.050000e-78 303.0
35 TraesCS2B01G423300 chr2D 93.333 195 10 1 2885 3076 517045678 517045872 7.440000e-73 285.0
36 TraesCS2B01G423300 chr2D 90.476 168 15 1 426 593 516970233 516970399 2.130000e-53 220.0
37 TraesCS2B01G423300 chr2D 89.922 129 13 0 2703 2831 517045445 517045573 2.810000e-37 167.0
38 TraesCS2B01G423300 chr2D 88.235 102 11 1 423 524 516870497 516870597 2.220000e-23 121.0
39 TraesCS2B01G423300 chr2D 84.167 120 18 1 812 931 516924013 516924131 1.030000e-21 115.0
40 TraesCS2B01G423300 chr2D 85.246 61 5 2 979 1035 516856628 516856688 4.910000e-05 60.2
41 TraesCS2B01G423300 chr5A 76.670 913 124 45 1152 2039 419361131 419361979 1.510000e-114 424.0
42 TraesCS2B01G423300 chr5A 92.466 146 9 2 1 145 396212773 396212917 1.660000e-49 207.0
43 TraesCS2B01G423300 chr5A 87.059 85 11 0 3561 3645 538319347 538319263 3.740000e-16 97.1
44 TraesCS2B01G423300 chr5A 85.870 92 11 2 329 419 693652575 693652485 3.740000e-16 97.1
45 TraesCS2B01G423300 chr4A 80.757 317 35 12 1751 2056 541336410 541336109 1.650000e-54 224.0
46 TraesCS2B01G423300 chr4A 94.286 140 6 2 1 138 683674658 683674519 3.560000e-51 213.0
47 TraesCS2B01G423300 chr4A 80.751 213 33 5 591 795 140303543 140303331 4.710000e-35 159.0
48 TraesCS2B01G423300 chr4A 80.374 214 32 8 591 795 81267530 81267742 2.190000e-33 154.0
49 TraesCS2B01G423300 chr4A 94.545 55 2 1 365 419 731474505 731474558 2.910000e-12 84.2
50 TraesCS2B01G423300 chr4D 96.947 131 4 0 1 131 96114494 96114364 2.130000e-53 220.0
51 TraesCS2B01G423300 chr4D 95.556 135 5 1 1 135 102126250 102126383 9.900000e-52 215.0
52 TraesCS2B01G423300 chr4D 91.503 153 7 6 1 150 348983325 348983474 5.960000e-49 206.0
53 TraesCS2B01G423300 chr4D 83.099 213 26 6 591 794 470431977 470431766 7.760000e-43 185.0
54 TraesCS2B01G423300 chr4D 80.365 219 33 6 584 794 464843129 464842913 1.690000e-34 158.0
55 TraesCS2B01G423300 chr4D 85.714 84 9 2 3561 3641 58394133 58394050 8.100000e-13 86.1
56 TraesCS2B01G423300 chr3D 96.241 133 4 1 1 133 178391181 178391050 2.750000e-52 217.0
57 TraesCS2B01G423300 chr3D 90.000 90 9 0 3556 3645 351116939 351117028 2.870000e-22 117.0
58 TraesCS2B01G423300 chr3D 87.059 85 11 0 3561 3645 515677268 515677184 3.740000e-16 97.1
59 TraesCS2B01G423300 chr3D 81.522 92 13 4 329 419 550509692 550509604 6.310000e-09 73.1
60 TraesCS2B01G423300 chr6A 92.466 146 9 2 1 145 168894666 168894810 1.660000e-49 207.0
61 TraesCS2B01G423300 chr5D 91.391 151 11 2 1 149 54327818 54327968 5.960000e-49 206.0
62 TraesCS2B01G423300 chr5D 82.418 91 16 0 329 419 232623899 232623809 3.770000e-11 80.5
63 TraesCS2B01G423300 chr4B 88.166 169 12 6 1 168 504703225 504703064 1.290000e-45 195.0
64 TraesCS2B01G423300 chr4B 86.813 91 11 1 3561 3650 631841551 631841461 2.890000e-17 100.0
65 TraesCS2B01G423300 chr1D 79.000 300 39 14 131 419 439127535 439127821 2.790000e-42 183.0
66 TraesCS2B01G423300 chr7B 80.930 215 29 9 591 795 71396287 71396499 4.710000e-35 159.0
67 TraesCS2B01G423300 chr7B 91.837 98 8 0 3664 3761 413560050 413560147 2.210000e-28 137.0
68 TraesCS2B01G423300 chr1A 80.374 214 32 7 591 795 25949939 25949727 2.190000e-33 154.0
69 TraesCS2B01G423300 chr6D 87.778 90 10 1 3560 3648 128256984 128257073 2.240000e-18 104.0
70 TraesCS2B01G423300 chr3A 77.576 165 32 5 259 420 432259942 432259780 1.350000e-15 95.3


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 TraesCS2B01G423300 chr2B 608665841 608670385 4544 False 2871.333333 8394 92.280667 1 4545 3 chr2B.!!$F2 4544
1 TraesCS2B01G423300 chr2B 608540772 608541938 1166 False 915.000000 915 81.503000 2195 3331 1 chr2B.!!$F1 1136
2 TraesCS2B01G423300 chr2B 608801994 608804013 2019 False 481.750000 737 87.050000 1268 3338 4 chr2B.!!$F3 2070
3 TraesCS2B01G423300 chr2A 661150434 661155471 5037 False 1544.675000 2769 93.330500 127 4538 4 chr2A.!!$F4 4411
4 TraesCS2B01G423300 chr2A 661446582 661449326 2744 False 996.000000 1018 83.214000 951 3338 2 chr2A.!!$F6 2387
5 TraesCS2B01G423300 chr2A 661082602 661083792 1190 False 887.000000 887 80.917000 2189 3331 1 chr2A.!!$F2 1142
6 TraesCS2B01G423300 chr2A 661393169 661396408 3239 False 468.250000 791 86.794500 426 3143 4 chr2A.!!$F5 2717
7 TraesCS2B01G423300 chr2D 516924013 516929103 5090 False 1054.200000 2200 90.714600 812 4545 5 chr2D.!!$F5 3733
8 TraesCS2B01G423300 chr2D 516863174 516864340 1166 False 941.000000 941 81.880000 2195 3330 1 chr2D.!!$F2 1135
9 TraesCS2B01G423300 chr2D 517085304 517087193 1889 False 679.000000 966 81.761500 423 2088 2 chr2D.!!$F8 1665
10 TraesCS2B01G423300 chr2D 517037468 517038666 1198 False 657.000000 752 87.335000 1268 2629 2 chr2D.!!$F6 1361
11 TraesCS2B01G423300 chr2D 517045445 517046179 734 False 274.000000 370 91.578667 2703 3338 3 chr2D.!!$F7 635
12 TraesCS2B01G423300 chr5A 419361131 419361979 848 False 424.000000 424 76.670000 1152 2039 1 chr5A.!!$F2 887

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
935 1385 0.108774 TGTGGGGCAAACGTATGTCA 59.891 50.0 0.0 0.0 0.0 3.58 F
937 1387 0.398696 TGGGGCAAACGTATGTCACT 59.601 50.0 0.0 0.0 0.0 3.41 F
938 1388 0.802494 GGGGCAAACGTATGTCACTG 59.198 55.0 0.0 0.0 0.0 3.66 F
939 1389 0.802494 GGGCAAACGTATGTCACTGG 59.198 55.0 0.0 0.0 0.0 4.00 F
1735 2585 0.878416 GTGGTTTGCGTGGCTTCATA 59.122 50.0 0.0 0.0 0.0 2.15 F
3172 4647 0.744771 GAAGGGGACATCGAAGCACC 60.745 60.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2433 3741 0.950555 TGATGGTCAACTGCGTCAGC 60.951 55.000 6.74 0.00 45.41 4.26 R
2905 4306 1.061566 GGATTTCGCGTAACCTTTCCG 59.938 52.381 5.77 0.00 0.00 4.30 R
3056 4471 5.129485 ACATTTAGTACTAGCTGCTCCACAT 59.871 40.000 4.91 0.00 0.00 3.21 R
3172 4647 2.432628 GAAGTCCACGGCCGTCTG 60.433 66.667 31.80 22.88 0.00 3.51 R
3374 4852 2.663188 GCTTAGATCAGGGCGCGG 60.663 66.667 8.83 0.00 0.00 6.46 R
4258 5837 2.554032 AGACACATTTTTCGAGGCAAGG 59.446 45.455 0.00 0.00 0.00 3.61 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 5.605564 TTCACACATGTATCAAGTTTCCG 57.394 39.130 0.00 0.00 0.00 4.30
30 31 4.000325 TCACACATGTATCAAGTTTCCGG 59.000 43.478 0.00 0.00 0.00 5.14
31 32 3.751175 CACACATGTATCAAGTTTCCGGT 59.249 43.478 0.00 0.00 0.00 5.28
32 33 4.215399 CACACATGTATCAAGTTTCCGGTT 59.785 41.667 0.00 0.00 0.00 4.44
33 34 5.410132 CACACATGTATCAAGTTTCCGGTTA 59.590 40.000 0.00 0.00 0.00 2.85
34 35 5.998981 ACACATGTATCAAGTTTCCGGTTAA 59.001 36.000 0.00 0.00 0.00 2.01
35 36 6.657541 ACACATGTATCAAGTTTCCGGTTAAT 59.342 34.615 0.00 0.00 0.00 1.40
36 37 7.825270 ACACATGTATCAAGTTTCCGGTTAATA 59.175 33.333 0.00 0.00 0.00 0.98
37 38 8.120465 CACATGTATCAAGTTTCCGGTTAATAC 58.880 37.037 0.00 0.00 0.00 1.89
38 39 7.825270 ACATGTATCAAGTTTCCGGTTAATACA 59.175 33.333 0.00 0.88 34.10 2.29
39 40 8.670135 CATGTATCAAGTTTCCGGTTAATACAA 58.330 33.333 0.00 0.00 33.52 2.41
40 41 8.795842 TGTATCAAGTTTCCGGTTAATACAAT 57.204 30.769 0.00 0.00 0.00 2.71
41 42 9.233649 TGTATCAAGTTTCCGGTTAATACAATT 57.766 29.630 0.00 0.00 0.00 2.32
42 43 9.712359 GTATCAAGTTTCCGGTTAATACAATTC 57.288 33.333 0.00 0.00 0.00 2.17
43 44 7.989416 TCAAGTTTCCGGTTAATACAATTCT 57.011 32.000 0.00 0.00 0.00 2.40
44 45 9.675464 ATCAAGTTTCCGGTTAATACAATTCTA 57.325 29.630 0.00 0.00 0.00 2.10
45 46 9.158233 TCAAGTTTCCGGTTAATACAATTCTAG 57.842 33.333 0.00 0.00 0.00 2.43
46 47 7.549615 AGTTTCCGGTTAATACAATTCTAGC 57.450 36.000 0.00 0.00 0.00 3.42
47 48 7.107542 AGTTTCCGGTTAATACAATTCTAGCA 58.892 34.615 0.00 0.00 0.00 3.49
48 49 7.773690 AGTTTCCGGTTAATACAATTCTAGCAT 59.226 33.333 0.00 0.00 0.00 3.79
49 50 7.490962 TTCCGGTTAATACAATTCTAGCATG 57.509 36.000 0.00 0.00 0.00 4.06
50 51 6.822442 TCCGGTTAATACAATTCTAGCATGA 58.178 36.000 0.00 0.00 0.00 3.07
51 52 7.276658 TCCGGTTAATACAATTCTAGCATGAA 58.723 34.615 0.00 0.00 0.00 2.57
52 53 7.225931 TCCGGTTAATACAATTCTAGCATGAAC 59.774 37.037 0.00 0.00 0.00 3.18
53 54 7.011950 CCGGTTAATACAATTCTAGCATGAACA 59.988 37.037 0.00 0.00 0.00 3.18
54 55 8.394877 CGGTTAATACAATTCTAGCATGAACAA 58.605 33.333 0.00 0.00 0.00 2.83
111 112 8.739972 AGTAACAACTTTATTATTGCCTCTTGG 58.260 33.333 0.00 0.00 0.00 3.61
112 113 6.530019 ACAACTTTATTATTGCCTCTTGGG 57.470 37.500 0.00 0.00 38.36 4.12
125 126 3.902218 CCTCTTGGGCATATTTCCTTCA 58.098 45.455 0.00 0.00 0.00 3.02
186 191 2.700773 GGATTTGCACTGTCCGCCC 61.701 63.158 0.00 0.00 0.00 6.13
195 200 1.122019 ACTGTCCGCCCTTGAACTCT 61.122 55.000 0.00 0.00 0.00 3.24
199 204 0.537188 TCCGCCCTTGAACTCTGATC 59.463 55.000 0.00 0.00 0.00 2.92
221 226 4.282449 TCAACTATGTTCCTCTTGTTCGGA 59.718 41.667 0.00 0.00 0.00 4.55
222 227 4.457834 ACTATGTTCCTCTTGTTCGGAG 57.542 45.455 0.00 0.00 0.00 4.63
237 242 5.244755 TGTTCGGAGATGAAATGTTGATCA 58.755 37.500 0.00 0.00 35.04 2.92
246 251 8.981724 AGATGAAATGTTGATCAATTGAACTG 57.018 30.769 13.09 0.00 0.00 3.16
248 253 6.514063 TGAAATGTTGATCAATTGAACTGCA 58.486 32.000 13.09 12.60 0.00 4.41
259 264 6.327154 TCAATTGAACTGCACATTGATCATC 58.673 36.000 5.45 0.00 33.33 2.92
266 271 4.927425 ACTGCACATTGATCATCTTTTTGC 59.073 37.500 0.00 0.97 0.00 3.68
267 272 4.884247 TGCACATTGATCATCTTTTTGCA 58.116 34.783 0.00 3.68 35.19 4.08
301 306 7.228108 GCATGATTTGAGGTTTCAGATATGAGA 59.772 37.037 0.00 0.00 34.15 3.27
314 319 0.678684 TATGAGAGACGCGGGTGTGA 60.679 55.000 10.96 0.00 0.00 3.58
329 334 4.201910 CGGGTGTGAAAGGCAACATATAAG 60.202 45.833 0.00 0.00 41.41 1.73
332 337 5.393027 GGTGTGAAAGGCAACATATAAGGTG 60.393 44.000 0.00 0.00 41.41 4.00
333 338 5.183140 GTGTGAAAGGCAACATATAAGGTGT 59.817 40.000 0.00 0.00 41.41 4.16
334 339 5.182950 TGTGAAAGGCAACATATAAGGTGTG 59.817 40.000 0.00 0.00 41.41 3.82
335 340 4.157656 TGAAAGGCAACATATAAGGTGTGC 59.842 41.667 0.00 2.07 41.41 4.57
336 341 2.654863 AGGCAACATATAAGGTGTGCC 58.345 47.619 16.98 16.98 40.69 5.01
337 342 1.681264 GGCAACATATAAGGTGTGCCC 59.319 52.381 15.39 0.15 37.58 5.36
338 343 1.333619 GCAACATATAAGGTGTGCCCG 59.666 52.381 0.00 0.00 38.74 6.13
339 344 1.946768 CAACATATAAGGTGTGCCCGG 59.053 52.381 0.00 0.00 38.74 5.73
340 345 1.209621 ACATATAAGGTGTGCCCGGT 58.790 50.000 0.00 0.00 38.74 5.28
341 346 2.400573 ACATATAAGGTGTGCCCGGTA 58.599 47.619 0.00 0.00 38.74 4.02
354 359 2.433664 CGGTAAGTGCCCGTGGAC 60.434 66.667 0.00 0.00 40.59 4.02
369 374 3.643978 GACGCGCCCAGATGCATC 61.644 66.667 19.37 19.37 0.00 3.91
406 411 0.609131 CCGGATTTGCCAAGTCTGGT 60.609 55.000 17.33 0.00 45.53 4.00
420 425 4.899352 AGTCTGGTTGTAGATGCTCTTT 57.101 40.909 0.00 0.00 0.00 2.52
421 426 5.234466 AGTCTGGTTGTAGATGCTCTTTT 57.766 39.130 0.00 0.00 0.00 2.27
469 474 6.409524 TGAAAGCATTTGGTGAGAGAAAAT 57.590 33.333 0.00 0.00 39.27 1.82
826 885 7.916077 ACAACCAGCCTACTAAGATATAAGT 57.084 36.000 0.00 0.00 0.00 2.24
842 901 7.210174 AGATATAAGTATTGAAAGTGCAGCGA 58.790 34.615 0.00 0.00 0.00 4.93
877 936 7.657336 ACACATTCAATTTGGAACGATTTAGT 58.343 30.769 0.00 0.00 0.00 2.24
879 938 9.061610 CACATTCAATTTGGAACGATTTAGTAC 57.938 33.333 0.00 0.00 0.00 2.73
886 945 9.661563 AATTTGGAACGATTTAGTACTACATCA 57.338 29.630 22.68 7.37 0.00 3.07
890 1340 5.746307 ACGATTTAGTACTACATCAGCGA 57.254 39.130 22.68 0.00 0.00 4.93
896 1346 2.809119 AGTACTACATCAGCGAGATCGG 59.191 50.000 4.18 0.00 40.23 4.18
931 1381 5.470047 TTTATTTTGTGGGGCAAACGTAT 57.530 34.783 0.00 0.00 45.70 3.06
932 1382 2.802787 TTTTGTGGGGCAAACGTATG 57.197 45.000 0.00 0.00 45.70 2.39
934 1384 1.240256 TTGTGGGGCAAACGTATGTC 58.760 50.000 0.00 0.00 33.53 3.06
935 1385 0.108774 TGTGGGGCAAACGTATGTCA 59.891 50.000 0.00 0.00 0.00 3.58
937 1387 0.398696 TGGGGCAAACGTATGTCACT 59.601 50.000 0.00 0.00 0.00 3.41
938 1388 0.802494 GGGGCAAACGTATGTCACTG 59.198 55.000 0.00 0.00 0.00 3.66
939 1389 0.802494 GGGCAAACGTATGTCACTGG 59.198 55.000 0.00 0.00 0.00 4.00
1072 1843 1.542030 TCCACAACAGTTTTGCACGTT 59.458 42.857 0.00 0.00 0.00 3.99
1194 1993 3.458189 GGATTCATCCGTAGTTGACAGG 58.542 50.000 0.00 0.00 37.19 4.00
1249 2055 4.948621 TGATCAATTGACCATGCATGTGTA 59.051 37.500 24.58 7.83 0.00 2.90
1431 2255 1.266718 GACGACACCAAGGTACGTACA 59.733 52.381 26.02 0.00 39.13 2.90
1616 2461 1.375326 GGCCAAGTCCTTCCTCGTT 59.625 57.895 0.00 0.00 0.00 3.85
1735 2585 0.878416 GTGGTTTGCGTGGCTTCATA 59.122 50.000 0.00 0.00 0.00 2.15
1912 2780 3.582120 ACGTGGTGGCGCAACAAG 61.582 61.111 18.47 12.68 36.66 3.16
1960 2834 5.371526 ACTCATCTCTTGCAAGAAAGAACA 58.628 37.500 28.16 13.17 35.79 3.18
1963 2837 6.498304 TCATCTCTTGCAAGAAAGAACAAAC 58.502 36.000 28.16 0.00 35.79 2.93
2249 3547 6.346758 CGACGGTTAGTACAAACATAAGCAAA 60.347 38.462 0.00 0.00 0.00 3.68
2433 3741 1.376942 CCAGAGCAGCAAGGTCCAG 60.377 63.158 0.00 0.00 45.87 3.86
2508 3816 1.135139 CACATCGACCGGAGTGAAGAT 59.865 52.381 9.46 0.10 33.99 2.40
2529 3837 2.101185 CGCGTCAGCAGATCGACT 59.899 61.111 0.00 0.00 45.49 4.18
2533 3841 1.002359 GCGTCAGCAGATCGACTATCA 60.002 52.381 0.00 0.00 44.35 2.15
2682 4027 1.542030 TGCACTCGAAGAAGAGGAGTC 59.458 52.381 0.00 0.00 42.31 3.36
2869 4253 3.935828 GCCTTCTCTTACTAACAAGCTGG 59.064 47.826 0.00 0.00 0.00 4.85
2871 4255 4.563580 CCTTCTCTTACTAACAAGCTGGCA 60.564 45.833 0.00 0.00 0.00 4.92
2905 4306 0.884704 TTTCTTCGCACTGCAGGGTC 60.885 55.000 19.18 9.10 0.00 4.46
3056 4471 5.654603 AACTGTTGGACGATCTGTATACA 57.345 39.130 5.25 5.25 0.00 2.29
3172 4647 0.744771 GAAGGGGACATCGAAGCACC 60.745 60.000 0.00 0.00 0.00 5.01
3338 4813 3.484407 CCAAGATCCCTTGCCTTAGATG 58.516 50.000 0.00 0.00 46.42 2.90
3360 4838 9.815306 AGATGATAATAACTAGCAGGTAGAAGA 57.185 33.333 13.77 0.00 32.41 2.87
3363 4841 7.501559 TGATAATAACTAGCAGGTAGAAGACGT 59.498 37.037 13.77 0.00 32.41 4.34
3367 4845 1.185618 AGCAGGTAGAAGACGTGGCA 61.186 55.000 0.00 0.00 42.94 4.92
3517 4996 7.439381 ACAGACTTCAGAAATTTTCATTGCAT 58.561 30.769 11.53 0.00 0.00 3.96
3537 5016 8.437360 TTGCATACTGGTAGACTATGAAATTG 57.563 34.615 0.00 0.00 0.00 2.32
3564 5043 9.321562 GAATCCGGAATCAGTTGTTTATTACTA 57.678 33.333 14.86 0.00 0.00 1.82
3566 5045 7.613585 TCCGGAATCAGTTGTTTATTACTACA 58.386 34.615 0.00 0.00 35.32 2.74
3569 5048 8.548721 CGGAATCAGTTGTTTATTACTACATCC 58.451 37.037 0.00 0.00 35.32 3.51
3572 5051 9.444600 AATCAGTTGTTTATTACTACATCCGTT 57.555 29.630 0.00 0.00 35.32 4.44
3574 5053 7.546667 TCAGTTGTTTATTACTACATCCGTTCC 59.453 37.037 0.00 0.00 35.32 3.62
3621 5101 4.698583 AGTATAGTGTCGAAAACGCTCT 57.301 40.909 0.00 0.00 45.69 4.09
3628 5108 6.963049 AGTGTCGAAAACGCTCTTATATTT 57.037 33.333 0.00 0.00 45.69 1.40
3643 5123 7.419711 TCTTATATTTTGAGACGGAGGAAGT 57.580 36.000 0.00 0.00 0.00 3.01
3810 5297 6.808829 TGTACCTTATAACCAATCCAGTACG 58.191 40.000 0.00 0.00 0.00 3.67
3916 5411 8.413229 CCCATTAAAAGAAATTCATGTACGGAT 58.587 33.333 0.00 0.00 0.00 4.18
3955 5450 7.849804 AAGAGATGCTAAAATCATAACGTGT 57.150 32.000 0.00 0.00 0.00 4.49
4012 5507 0.869880 GCACGTGCACCCTTTTGAAC 60.870 55.000 34.52 0.00 41.59 3.18
4171 5750 8.917088 TGTTTATATAGTACAGTAGTTCCCACC 58.083 37.037 0.00 0.00 0.00 4.61
4193 5772 7.255801 CCACCTCAAAGAAGCCAAACTTATTAA 60.256 37.037 0.00 0.00 38.86 1.40
4258 5837 7.543520 GGAAAACATCAATGGAGAATTCTGAAC 59.456 37.037 14.00 3.60 0.00 3.18
4319 5898 3.494626 CGTGCAATTAGGCTACTATGTGG 59.505 47.826 0.00 0.00 34.04 4.17
4413 7337 5.006746 GGTGGCTGATTCAGAACTAATAACG 59.993 44.000 17.87 0.00 32.44 3.18
4541 8089 6.879458 ACTTTTGGCTATAGAAAGTTCATCGT 59.121 34.615 3.21 0.00 39.79 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.040939 CGGAAACTTGATACATGTGTGAATATA 57.959 33.333 9.11 0.00 0.00 0.86
4 5 7.012327 CCGGAAACTTGATACATGTGTGAATAT 59.988 37.037 9.11 0.00 0.00 1.28
5 6 6.315144 CCGGAAACTTGATACATGTGTGAATA 59.685 38.462 9.11 0.00 0.00 1.75
6 7 5.123820 CCGGAAACTTGATACATGTGTGAAT 59.876 40.000 9.11 0.00 0.00 2.57
7 8 4.454161 CCGGAAACTTGATACATGTGTGAA 59.546 41.667 9.11 0.70 0.00 3.18
8 9 4.000325 CCGGAAACTTGATACATGTGTGA 59.000 43.478 9.11 0.00 0.00 3.58
9 10 3.751175 ACCGGAAACTTGATACATGTGTG 59.249 43.478 9.46 0.00 0.00 3.82
10 11 4.015872 ACCGGAAACTTGATACATGTGT 57.984 40.909 9.46 0.10 0.00 3.72
11 12 6.489127 TTAACCGGAAACTTGATACATGTG 57.511 37.500 9.46 0.00 0.00 3.21
12 13 7.825270 TGTATTAACCGGAAACTTGATACATGT 59.175 33.333 9.46 2.69 28.53 3.21
13 14 8.203937 TGTATTAACCGGAAACTTGATACATG 57.796 34.615 9.46 0.00 28.53 3.21
14 15 8.795842 TTGTATTAACCGGAAACTTGATACAT 57.204 30.769 9.46 0.00 31.55 2.29
15 16 8.795842 ATTGTATTAACCGGAAACTTGATACA 57.204 30.769 9.46 11.96 30.33 2.29
16 17 9.712359 GAATTGTATTAACCGGAAACTTGATAC 57.288 33.333 9.46 9.36 0.00 2.24
17 18 9.675464 AGAATTGTATTAACCGGAAACTTGATA 57.325 29.630 9.46 0.00 0.00 2.15
18 19 8.575649 AGAATTGTATTAACCGGAAACTTGAT 57.424 30.769 9.46 0.00 0.00 2.57
19 20 7.989416 AGAATTGTATTAACCGGAAACTTGA 57.011 32.000 9.46 0.00 0.00 3.02
20 21 7.908601 GCTAGAATTGTATTAACCGGAAACTTG 59.091 37.037 9.46 0.00 0.00 3.16
21 22 7.608761 TGCTAGAATTGTATTAACCGGAAACTT 59.391 33.333 9.46 0.00 0.00 2.66
22 23 7.107542 TGCTAGAATTGTATTAACCGGAAACT 58.892 34.615 9.46 0.00 0.00 2.66
23 24 7.311364 TGCTAGAATTGTATTAACCGGAAAC 57.689 36.000 9.46 0.00 0.00 2.78
24 25 7.771361 TCATGCTAGAATTGTATTAACCGGAAA 59.229 33.333 9.46 1.61 0.00 3.13
25 26 7.276658 TCATGCTAGAATTGTATTAACCGGAA 58.723 34.615 9.46 0.00 0.00 4.30
26 27 6.822442 TCATGCTAGAATTGTATTAACCGGA 58.178 36.000 9.46 0.00 0.00 5.14
27 28 7.011950 TGTTCATGCTAGAATTGTATTAACCGG 59.988 37.037 0.00 0.00 0.00 5.28
28 29 7.915508 TGTTCATGCTAGAATTGTATTAACCG 58.084 34.615 0.00 0.00 0.00 4.44
85 86 8.739972 CCAAGAGGCAATAATAAAGTTGTTACT 58.260 33.333 0.00 0.00 35.68 2.24
86 87 7.973944 CCCAAGAGGCAATAATAAAGTTGTTAC 59.026 37.037 0.00 0.00 0.00 2.50
87 88 8.062065 CCCAAGAGGCAATAATAAAGTTGTTA 57.938 34.615 0.00 0.00 0.00 2.41
88 89 6.935167 CCCAAGAGGCAATAATAAAGTTGTT 58.065 36.000 0.00 0.00 0.00 2.83
89 90 6.530019 CCCAAGAGGCAATAATAAAGTTGT 57.470 37.500 0.00 0.00 0.00 3.32
104 105 3.633986 GTGAAGGAAATATGCCCAAGAGG 59.366 47.826 0.00 0.00 39.47 3.69
105 106 4.530875 AGTGAAGGAAATATGCCCAAGAG 58.469 43.478 0.00 0.00 0.00 2.85
106 107 4.591321 AGTGAAGGAAATATGCCCAAGA 57.409 40.909 0.00 0.00 0.00 3.02
107 108 6.966534 AATAGTGAAGGAAATATGCCCAAG 57.033 37.500 0.00 0.00 0.00 3.61
165 170 0.099436 GCGGACAGTGCAAATCCATC 59.901 55.000 11.56 0.97 32.35 3.51
186 191 7.102346 AGGAACATAGTTGATCAGAGTTCAAG 58.898 38.462 19.73 3.82 36.52 3.02
195 200 5.869344 CGAACAAGAGGAACATAGTTGATCA 59.131 40.000 0.00 0.00 0.00 2.92
199 204 4.566004 TCCGAACAAGAGGAACATAGTTG 58.434 43.478 0.00 0.00 32.86 3.16
221 226 7.544566 GCAGTTCAATTGATCAACATTTCATCT 59.455 33.333 11.07 0.00 0.00 2.90
222 227 7.329962 TGCAGTTCAATTGATCAACATTTCATC 59.670 33.333 11.07 0.00 0.00 2.92
237 242 6.525578 AGATGATCAATGTGCAGTTCAATT 57.474 33.333 0.00 0.00 0.00 2.32
246 251 6.292168 GCTATGCAAAAAGATGATCAATGTGC 60.292 38.462 0.00 4.53 0.00 4.57
248 253 5.975344 CGCTATGCAAAAAGATGATCAATGT 59.025 36.000 0.00 0.00 0.00 2.71
266 271 3.065786 ACCTCAAATCATGCAACGCTATG 59.934 43.478 0.00 0.00 0.00 2.23
267 272 3.282021 ACCTCAAATCATGCAACGCTAT 58.718 40.909 0.00 0.00 0.00 2.97
301 306 2.030562 CCTTTCACACCCGCGTCT 59.969 61.111 4.92 0.00 0.00 4.18
314 319 3.447229 GGCACACCTTATATGTTGCCTTT 59.553 43.478 3.13 0.00 39.31 3.11
329 334 3.053896 GCACTTACCGGGCACACC 61.054 66.667 6.32 0.00 0.00 4.16
338 343 2.433664 CGTCCACGGGCACTTACC 60.434 66.667 0.00 0.00 35.37 2.85
339 344 3.116531 GCGTCCACGGGCACTTAC 61.117 66.667 0.55 0.00 40.23 2.34
340 345 4.728102 CGCGTCCACGGGCACTTA 62.728 66.667 0.00 0.00 44.83 2.24
367 372 4.077184 TCTGAAACGCCCGCGGAT 62.077 61.111 30.73 9.03 44.69 4.18
450 455 8.125978 TCATAAATTTTCTCTCACCAAATGCT 57.874 30.769 0.00 0.00 0.00 3.79
626 639 5.105917 ACGCCACCTCATAAAAATTGGTTAG 60.106 40.000 0.00 0.00 0.00 2.34
630 643 3.866883 ACGCCACCTCATAAAAATTGG 57.133 42.857 0.00 0.00 0.00 3.16
786 810 5.739358 GCTGGTTGTACTGGGAGTATGATAC 60.739 48.000 0.00 0.00 32.65 2.24
826 885 5.527951 ACAATTTTCGCTGCACTTTCAATA 58.472 33.333 0.00 0.00 0.00 1.90
839 898 8.881231 CAAATTGAATGTGTAAACAATTTTCGC 58.119 29.630 0.00 0.00 44.76 4.70
877 936 2.806818 GTCCGATCTCGCTGATGTAGTA 59.193 50.000 0.00 0.00 35.14 1.82
879 938 1.399087 CGTCCGATCTCGCTGATGTAG 60.399 57.143 0.00 0.00 35.14 2.74
886 945 2.975266 AGATATACGTCCGATCTCGCT 58.025 47.619 0.00 0.00 38.18 4.93
931 1381 1.185618 CCGGAAGTCTCCCAGTGACA 61.186 60.000 0.00 0.00 38.71 3.58
932 1382 0.898789 TCCGGAAGTCTCCCAGTGAC 60.899 60.000 0.00 0.00 38.71 3.67
934 1384 1.592223 GTCCGGAAGTCTCCCAGTG 59.408 63.158 5.23 0.00 38.71 3.66
935 1385 1.977544 CGTCCGGAAGTCTCCCAGT 60.978 63.158 5.23 0.00 38.71 4.00
937 1387 3.379445 GCGTCCGGAAGTCTCCCA 61.379 66.667 18.88 0.00 38.71 4.37
938 1388 2.560051 GAAGCGTCCGGAAGTCTCCC 62.560 65.000 18.88 1.58 38.71 4.30
939 1389 1.153804 GAAGCGTCCGGAAGTCTCC 60.154 63.158 18.88 1.96 38.52 3.71
974 1743 0.394938 AAATGTTTTTCCGTGGGGGC 59.605 50.000 0.00 0.00 34.94 5.80
1072 1843 1.588082 GGCTCGTAAGGTCGTCCAA 59.412 57.895 0.51 0.00 35.89 3.53
1136 1935 5.284079 AGCAAACTTTGTGAAATGCAGTAG 58.716 37.500 3.48 0.00 36.30 2.57
1194 1993 3.502211 AGCACACATTGGTTGTTACTAGC 59.498 43.478 0.00 0.00 36.00 3.42
1249 2055 2.558795 AGTAAGCACGTCTCACACAGAT 59.441 45.455 0.00 0.00 32.08 2.90
1353 2177 3.509137 GAACACGCCGTCCACCTCA 62.509 63.158 0.00 0.00 0.00 3.86
1380 2204 2.697761 GCCTCGAGCACCGTAGTCA 61.698 63.158 6.99 0.00 42.97 3.41
1616 2461 3.106609 TTGAACCTGGTGGGGCCA 61.107 61.111 4.39 0.00 46.95 5.36
1735 2585 4.722700 AGCAAGGGCCGCACGAAT 62.723 61.111 6.19 0.00 42.56 3.34
1894 2759 3.805385 CTTGTTGCGCCACCACGTG 62.805 63.158 9.08 9.08 34.88 4.49
1912 2780 1.131883 CTCACAGCATAGCCTTTGCAC 59.868 52.381 9.81 0.00 42.62 4.57
1960 2834 7.301868 TGCAAGGAGGAATTAAAAGATGTTT 57.698 32.000 0.00 0.00 0.00 2.83
1963 2837 7.820872 ACAAATGCAAGGAGGAATTAAAAGATG 59.179 33.333 0.00 0.00 0.00 2.90
2012 2888 3.971245 ACTTTCTCTCAGCCGAAGATT 57.029 42.857 0.00 0.00 0.00 2.40
2013 2889 5.606348 AATACTTTCTCTCAGCCGAAGAT 57.394 39.130 0.00 0.00 0.00 2.40
2155 3034 6.037281 TGAGTGCAAACGTATGTACAGAAAAA 59.963 34.615 0.33 0.00 38.25 1.94
2156 3035 5.524281 TGAGTGCAAACGTATGTACAGAAAA 59.476 36.000 0.33 0.00 38.25 2.29
2157 3036 5.050634 GTGAGTGCAAACGTATGTACAGAAA 60.051 40.000 0.33 0.00 38.25 2.52
2158 3037 4.446385 GTGAGTGCAAACGTATGTACAGAA 59.554 41.667 0.33 0.00 38.25 3.02
2159 3038 3.985279 GTGAGTGCAAACGTATGTACAGA 59.015 43.478 0.33 0.00 38.25 3.41
2169 3048 5.545658 ACAATAATAGGTGAGTGCAAACG 57.454 39.130 0.00 0.00 0.00 3.60
2174 3053 8.045176 AGAAAAGAACAATAATAGGTGAGTGC 57.955 34.615 0.00 0.00 0.00 4.40
2433 3741 0.950555 TGATGGTCAACTGCGTCAGC 60.951 55.000 6.74 0.00 45.41 4.26
2529 3837 3.135457 TCGTCGCCGGTGCTGATA 61.135 61.111 11.05 0.00 34.43 2.15
2682 4027 2.035421 CCCGGCCATCACATCATTG 58.965 57.895 2.24 0.00 0.00 2.82
2869 4253 4.882671 AGAAACAATATGATCACCGTGC 57.117 40.909 0.00 0.00 0.00 5.34
2871 4255 4.034048 GCGAAGAAACAATATGATCACCGT 59.966 41.667 0.00 0.00 0.00 4.83
2905 4306 1.061566 GGATTTCGCGTAACCTTTCCG 59.938 52.381 5.77 0.00 0.00 4.30
3056 4471 5.129485 ACATTTAGTACTAGCTGCTCCACAT 59.871 40.000 4.91 0.00 0.00 3.21
3172 4647 2.432628 GAAGTCCACGGCCGTCTG 60.433 66.667 31.80 22.88 0.00 3.51
3338 4813 7.804129 CACGTCTTCTACCTGCTAGTTATTATC 59.196 40.741 0.00 0.00 0.00 1.75
3374 4852 2.663188 GCTTAGATCAGGGCGCGG 60.663 66.667 8.83 0.00 0.00 6.46
3426 4904 6.888088 GCCACCCCTTCTCTTACTTTAAAATA 59.112 38.462 0.00 0.00 0.00 1.40
3427 4905 5.715279 GCCACCCCTTCTCTTACTTTAAAAT 59.285 40.000 0.00 0.00 0.00 1.82
3517 4996 8.429641 GGATTCCAATTTCATAGTCTACCAGTA 58.570 37.037 0.00 0.00 0.00 2.74
3537 5016 6.451064 AATAAACAACTGATTCCGGATTCC 57.549 37.500 20.71 7.47 0.00 3.01
3564 5043 5.394224 CGCTCCTATATTATGGAACGGATGT 60.394 44.000 0.00 0.00 38.02 3.06
3566 5045 4.710375 ACGCTCCTATATTATGGAACGGAT 59.290 41.667 15.73 2.04 43.64 4.18
3569 5048 6.780706 AAAACGCTCCTATATTATGGAACG 57.219 37.500 12.40 12.40 44.53 3.95
3617 5097 5.844004 TCCTCCGTCTCAAAATATAAGAGC 58.156 41.667 0.00 0.00 0.00 4.09
3628 5108 4.282449 TGTCAAATACTTCCTCCGTCTCAA 59.718 41.667 0.00 0.00 0.00 3.02
3659 5139 9.499479 CACCAGATTTTGATAGCTAGACATAAT 57.501 33.333 14.27 14.27 0.00 1.28
3683 5163 6.452872 GCGTTGAATTTCTGTTAATGATGCAC 60.453 38.462 0.00 0.00 0.00 4.57
3810 5297 6.597832 ATCATAATACTACAGGAGAGTGCC 57.402 41.667 0.00 0.00 0.00 5.01
3916 5411 7.288810 AGCATCTCTTTTATTGAACAAACCA 57.711 32.000 0.00 0.00 0.00 3.67
3997 5492 5.656480 TCTAAAAAGTTCAAAAGGGTGCAC 58.344 37.500 8.80 8.80 0.00 4.57
4171 5750 8.110860 TCCTTAATAAGTTTGGCTTCTTTGAG 57.889 34.615 0.00 0.00 38.57 3.02
4258 5837 2.554032 AGACACATTTTTCGAGGCAAGG 59.446 45.455 0.00 0.00 0.00 3.61
4319 5898 9.998106 ATGTGGTATAGTGTAATTGTAGGATTC 57.002 33.333 0.00 0.00 0.00 2.52
4353 7277 3.343617 CTTCCGGCTTTCATGTTAGGAA 58.656 45.455 0.00 0.78 35.34 3.36
4413 7337 5.061064 CGGCTCTATCTATGAACGTTTATGC 59.939 44.000 15.22 8.03 0.00 3.14
4466 7390 4.580167 TGCATTATGTCTGTCCTTTATGCC 59.420 41.667 0.00 0.00 37.05 4.40


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

AutoCloner maintained by Alex Coulton.