Multiple sequence alignment - TraesCS4D01G030900

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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 TraesCS4D01G030900 chr4D 100.000 3969 0 0 1 3969 14559425 14563393 0.000000e+00 7330.0
1 TraesCS4D01G030900 chr4D 91.401 2570 138 37 990 3517 14832012 14829484 0.000000e+00 3445.0
2 TraesCS4D01G030900 chr4D 87.905 926 91 15 1018 1927 14523127 14524047 0.000000e+00 1070.0
3 TraesCS4D01G030900 chr4D 91.540 591 31 7 448 1029 14521907 14522487 0.000000e+00 797.0
4 TraesCS4D01G030900 chr4D 92.453 371 26 2 1 369 14521543 14521913 2.720000e-146 529.0
5 TraesCS4D01G030900 chr4D 89.737 380 35 4 3591 3969 17969776 17970152 2.140000e-132 483.0
6 TraesCS4D01G030900 chr4D 84.167 360 30 18 646 983 14832410 14832056 1.380000e-84 324.0
7 TraesCS4D01G030900 chr4D 89.781 137 13 1 2066 2202 14525436 14525571 1.470000e-39 174.0
8 TraesCS4D01G030900 chr4D 85.393 89 12 1 186 274 361886366 361886279 1.520000e-14 91.6
9 TraesCS4D01G030900 chr4A 92.497 2399 126 23 725 3080 456473364 456475751 0.000000e+00 3384.0
10 TraesCS4D01G030900 chr4A 92.178 2378 125 22 725 3080 586726535 586728873 0.000000e+00 3304.0
11 TraesCS4D01G030900 chr4A 86.676 698 51 18 3288 3967 456475765 456476438 0.000000e+00 736.0
12 TraesCS4D01G030900 chr4A 87.354 601 45 14 3386 3969 586728955 586729541 0.000000e+00 660.0
13 TraesCS4D01G030900 chr4B 91.670 2377 125 22 714 3054 24666283 24663944 0.000000e+00 3225.0
14 TraesCS4D01G030900 chr4B 100.000 28 0 0 3530 3557 54346118 54346091 7.000000e-03 52.8
15 TraesCS4D01G030900 chr3B 89.112 1497 86 38 633 2074 452746345 452747819 0.000000e+00 1790.0
16 TraesCS4D01G030900 chr3B 93.813 889 55 0 2066 2954 452754393 452755281 0.000000e+00 1338.0
17 TraesCS4D01G030900 chr3B 88.424 406 45 2 3564 3969 505039343 505038940 4.610000e-134 488.0
18 TraesCS4D01G030900 chr3B 89.958 239 24 0 3279 3517 783622270 783622032 3.850000e-80 309.0
19 TraesCS4D01G030900 chr3B 85.062 241 31 5 3267 3505 469631613 469631376 1.430000e-59 241.0
20 TraesCS4D01G030900 chr3B 92.308 65 3 1 411 475 452746173 452746235 1.520000e-14 91.6
21 TraesCS4D01G030900 chr1A 88.916 406 41 2 3564 3969 74327673 74328074 7.660000e-137 497.0
22 TraesCS4D01G030900 chr7D 87.500 440 42 7 3530 3969 116791191 116790765 2.750000e-136 496.0
23 TraesCS4D01G030900 chr7D 87.747 253 27 4 3268 3517 629101244 629100993 3.880000e-75 292.0
24 TraesCS4D01G030900 chr7D 79.279 222 36 9 183 397 44045645 44045427 3.200000e-31 147.0
25 TraesCS4D01G030900 chr7D 78.922 204 34 9 201 397 44095512 44095311 3.220000e-26 130.0
26 TraesCS4D01G030900 chr7B 86.449 428 46 5 3530 3956 306707807 306707391 3.610000e-125 459.0
27 TraesCS4D01G030900 chr7B 84.439 437 54 10 3530 3966 93082346 93082768 6.130000e-113 418.0
28 TraesCS4D01G030900 chr7A 85.747 442 47 11 3530 3969 86149237 86149664 1.680000e-123 453.0
29 TraesCS4D01G030900 chr7A 85.356 239 29 6 3269 3505 669483681 669483447 3.960000e-60 243.0
30 TraesCS4D01G030900 chr6D 87.724 391 44 4 3580 3969 9539796 9539409 1.680000e-123 453.0
31 TraesCS4D01G030900 chr6D 80.247 405 68 9 2 397 445815138 445814737 1.080000e-75 294.0
32 TraesCS4D01G030900 chr2D 84.773 440 54 5 3530 3969 557720986 557720560 2.830000e-116 429.0
33 TraesCS4D01G030900 chr2D 80.500 200 26 9 3530 3728 612581134 612581321 1.490000e-29 141.0
34 TraesCS4D01G030900 chr2D 76.744 172 33 6 230 397 423172067 423172235 5.460000e-14 89.8
35 TraesCS4D01G030900 chr5B 85.396 404 43 8 1 397 249562696 249563090 4.780000e-109 405.0
36 TraesCS4D01G030900 chr5B 77.143 175 35 4 2451 2624 20170562 20170392 3.260000e-16 97.1
37 TraesCS4D01G030900 chr5A 85.774 239 29 5 3269 3505 520444758 520444523 8.520000e-62 248.0
38 TraesCS4D01G030900 chr5A 85.356 239 29 6 3269 3505 704946148 704945914 3.960000e-60 243.0
39 TraesCS4D01G030900 chr5A 100.000 28 0 0 3530 3557 480299655 480299682 7.000000e-03 52.8
40 TraesCS4D01G030900 chr1B 85.654 237 30 4 3266 3500 530731002 530730768 3.060000e-61 246.0
41 TraesCS4D01G030900 chr2A 85.356 239 29 6 3269 3505 561148217 561148451 3.960000e-60 243.0
42 TraesCS4D01G030900 chr3A 79.167 120 23 2 2454 2572 488108725 488108607 9.140000e-12 82.4
43 TraesCS4D01G030900 chr3D 77.966 118 24 2 2456 2572 365928214 365928098 5.500000e-09 73.1
44 TraesCS4D01G030900 chr2B 77.686 121 23 4 2419 2537 13155114 13155232 1.980000e-08 71.3
45 TraesCS4D01G030900 chr5D 100.000 28 0 0 3530 3557 238134229 238134256 7.000000e-03 52.8
46 TraesCS4D01G030900 chr5D 100.000 28 0 0 3530 3557 379803511 379803538 7.000000e-03 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 TraesCS4D01G030900 chr4D 14559425 14563393 3968 False 7330.0 7330 100.00000 1 3969 1 chr4D.!!$F1 3968
1 TraesCS4D01G030900 chr4D 14829484 14832410 2926 True 1884.5 3445 87.78400 646 3517 2 chr4D.!!$R2 2871
2 TraesCS4D01G030900 chr4D 14521543 14525571 4028 False 642.5 1070 90.41975 1 2202 4 chr4D.!!$F3 2201
3 TraesCS4D01G030900 chr4A 456473364 456476438 3074 False 2060.0 3384 89.58650 725 3967 2 chr4A.!!$F1 3242
4 TraesCS4D01G030900 chr4A 586726535 586729541 3006 False 1982.0 3304 89.76600 725 3969 2 chr4A.!!$F2 3244
5 TraesCS4D01G030900 chr4B 24663944 24666283 2339 True 3225.0 3225 91.67000 714 3054 1 chr4B.!!$R1 2340
6 TraesCS4D01G030900 chr3B 452754393 452755281 888 False 1338.0 1338 93.81300 2066 2954 1 chr3B.!!$F1 888
7 TraesCS4D01G030900 chr3B 452746173 452747819 1646 False 940.8 1790 90.71000 411 2074 2 chr3B.!!$F2 1663

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
635 638 0.033366 TGTCCACAGACCACATGACG 59.967 55.0 0.00 0.00 42.81 4.35 F
1149 1899 0.038892 GAACTGTCCGGTTCTACGCA 60.039 55.0 10.97 0.00 41.44 5.24 F
2191 4235 0.179468 TTACCTATGGCGCCAACCTC 59.821 55.0 36.33 1.76 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2168 4212 0.034960 TTGGCGCCATAGGTAAAGCA 60.035 50.0 33.25 8.24 0.0 3.91 R
2765 4818 0.685097 CCCAGTTTCTTGTCGGAGGA 59.315 55.0 0.00 0.00 0.0 3.71 R
3809 5908 0.865769 AGGTCAACGCGAAACACATC 59.134 50.0 15.93 0.00 0.0 3.06 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
23 24 4.112634 TGGAAATTTTCTGGGTAGCAGT 57.887 40.909 8.93 0.00 0.00 4.40
45 46 1.079819 CTTGTCATCGGAGGCGTGT 60.080 57.895 0.00 0.00 0.00 4.49
72 73 3.384789 TCCATTGGTCTTGGAGACTATCG 59.615 47.826 1.86 0.00 44.46 2.92
73 74 3.133003 CCATTGGTCTTGGAGACTATCGT 59.867 47.826 7.90 0.00 44.46 3.73
91 93 1.451927 TATGCAGGAGGCTTTGGCG 60.452 57.895 0.00 0.00 45.15 5.69
107 109 2.236382 GCGCTGGCAGAAGATCTCG 61.236 63.158 20.86 11.37 39.62 4.04
110 112 0.869454 GCTGGCAGAAGATCTCGACG 60.869 60.000 20.86 0.00 0.00 5.12
112 114 0.452184 TGGCAGAAGATCTCGACGTC 59.548 55.000 5.18 5.18 0.00 4.34
132 134 3.248602 GTCCATCGTATTGTCATTGCCTC 59.751 47.826 0.00 0.00 0.00 4.70
161 163 5.730568 GCCAAACAGGTGATTCGTGATATTC 60.731 44.000 0.00 0.00 40.61 1.75
184 186 0.670854 GTGGGAGTCGAGGAAGCAAC 60.671 60.000 0.00 0.00 0.00 4.17
208 210 5.164012 CGGAGCAATGATTAGCGAGATTAAG 60.164 44.000 0.00 0.00 35.48 1.85
225 227 8.869897 CGAGATTAAGTTACAAGCATCTTTACA 58.130 33.333 0.00 0.00 0.00 2.41
271 274 6.684131 CGTGTTATCAATGTTGAAGCACATAG 59.316 38.462 18.42 9.80 41.13 2.23
293 296 2.166459 TCTAGCCAGGTTCTCATTGTCG 59.834 50.000 0.00 0.00 0.00 4.35
296 299 2.301870 AGCCAGGTTCTCATTGTCGTTA 59.698 45.455 0.00 0.00 0.00 3.18
306 309 3.104512 TCATTGTCGTTAGGTCTGGGAT 58.895 45.455 0.00 0.00 0.00 3.85
309 312 0.824759 GTCGTTAGGTCTGGGATGCT 59.175 55.000 0.00 0.00 0.00 3.79
315 318 0.824759 AGGTCTGGGATGCTACGTTC 59.175 55.000 0.00 0.00 0.00 3.95
322 325 0.725117 GGATGCTACGTTCGGTTTGG 59.275 55.000 0.00 0.00 0.00 3.28
338 341 2.346766 TTGGTCAATCCCATGATCCG 57.653 50.000 0.00 0.00 33.60 4.18
357 360 5.943349 TCCGAACTCTATCCCACATTTTA 57.057 39.130 0.00 0.00 0.00 1.52
363 366 6.327386 ACTCTATCCCACATTTTATGGTGT 57.673 37.500 0.00 0.00 35.23 4.16
364 367 6.731467 ACTCTATCCCACATTTTATGGTGTT 58.269 36.000 0.00 0.00 35.23 3.32
365 368 7.182060 ACTCTATCCCACATTTTATGGTGTTT 58.818 34.615 0.00 0.00 35.23 2.83
366 369 7.122650 ACTCTATCCCACATTTTATGGTGTTTG 59.877 37.037 0.00 0.00 35.23 2.93
367 370 7.178573 TCTATCCCACATTTTATGGTGTTTGA 58.821 34.615 0.00 0.00 35.23 2.69
368 371 6.872585 ATCCCACATTTTATGGTGTTTGAT 57.127 33.333 0.00 0.00 35.23 2.57
369 372 6.035368 TCCCACATTTTATGGTGTTTGATG 57.965 37.500 0.00 0.00 35.23 3.07
370 373 5.777223 TCCCACATTTTATGGTGTTTGATGA 59.223 36.000 0.00 0.00 35.23 2.92
371 374 6.268617 TCCCACATTTTATGGTGTTTGATGAA 59.731 34.615 0.00 0.00 35.23 2.57
372 375 7.038445 TCCCACATTTTATGGTGTTTGATGAAT 60.038 33.333 0.00 0.00 35.23 2.57
373 376 8.256605 CCCACATTTTATGGTGTTTGATGAATA 58.743 33.333 0.00 0.00 35.23 1.75
374 377 9.650539 CCACATTTTATGGTGTTTGATGAATAA 57.349 29.630 0.00 0.00 33.19 1.40
383 386 8.918202 TGGTGTTTGATGAATAAAGTCTAGTT 57.082 30.769 0.00 0.00 0.00 2.24
384 387 9.349713 TGGTGTTTGATGAATAAAGTCTAGTTT 57.650 29.630 0.00 0.00 0.00 2.66
399 402 9.705103 AAAGTCTAGTTTTACCCTTAAAAACCT 57.295 29.630 7.59 0.00 44.29 3.50
400 403 9.705103 AAGTCTAGTTTTACCCTTAAAAACCTT 57.295 29.630 7.59 2.74 44.29 3.50
401 404 9.705103 AGTCTAGTTTTACCCTTAAAAACCTTT 57.295 29.630 7.59 0.00 44.29 3.11
454 457 3.180584 CGATCAACCTTCATCGTTCGATC 59.819 47.826 4.67 0.00 37.67 3.69
473 476 1.670590 GCATCCTCCGATCCTCCTG 59.329 63.158 0.00 0.00 0.00 3.86
474 477 1.825281 GCATCCTCCGATCCTCCTGG 61.825 65.000 0.00 0.00 0.00 4.45
576 579 7.557724 TGTAGTATATTGTTTCATTCACGGGA 58.442 34.615 0.00 0.00 0.00 5.14
588 591 0.966920 TCACGGGAAGAAGAGGACAC 59.033 55.000 0.00 0.00 0.00 3.67
635 638 0.033366 TGTCCACAGACCACATGACG 59.967 55.000 0.00 0.00 42.81 4.35
770 776 5.940595 CGTATTTCCCACGTTTTCCATAAA 58.059 37.500 0.00 0.00 34.74 1.40
826 842 3.878778 ACTCTTGTCAATACATGGCCTC 58.121 45.455 3.32 0.00 34.97 4.70
836 857 1.238439 ACATGGCCTCGTGTTTTCTG 58.762 50.000 3.32 0.00 39.93 3.02
1007 1106 1.411977 CAAGCAACCAACCATGTCCAA 59.588 47.619 0.00 0.00 0.00 3.53
1149 1899 0.038892 GAACTGTCCGGTTCTACGCA 60.039 55.000 10.97 0.00 41.44 5.24
1191 1941 3.350909 CTCCGATGGCCACGACGAA 62.351 63.158 23.58 8.17 0.00 3.85
1247 1997 1.158466 TGGAGAGGCTGGAGTCCAA 59.842 57.895 14.17 0.00 36.11 3.53
1362 2112 4.436998 CTGGGTCTGTCGGCCGTC 62.437 72.222 27.15 21.30 0.00 4.79
1425 2175 2.978824 GTCAACTCCGGGCTGCTA 59.021 61.111 0.00 0.00 0.00 3.49
1428 2178 0.687757 TCAACTCCGGGCTGCTAGAT 60.688 55.000 0.00 0.00 0.00 1.98
1669 2428 8.498054 TTTTGGTTTCAAATGCTGATGTTTTA 57.502 26.923 0.00 0.00 41.84 1.52
1670 2429 8.674263 TTTGGTTTCAAATGCTGATGTTTTAT 57.326 26.923 0.00 0.00 37.89 1.40
1671 2430 7.887996 TGGTTTCAAATGCTGATGTTTTATC 57.112 32.000 0.00 0.00 32.78 1.75
1672 2431 7.669427 TGGTTTCAAATGCTGATGTTTTATCT 58.331 30.769 0.00 0.00 32.78 1.98
1673 2432 8.801299 TGGTTTCAAATGCTGATGTTTTATCTA 58.199 29.630 0.00 0.00 32.78 1.98
2022 3031 5.902613 TTGATGGGCTTAAAATGAGTCAG 57.097 39.130 0.00 0.00 0.00 3.51
2097 4141 0.322816 GTTCTGGATGGGCTGAAGCA 60.323 55.000 4.43 0.00 44.36 3.91
2157 4201 2.106332 GGCCGTCGATGATTCCGT 59.894 61.111 6.11 0.00 0.00 4.69
2179 4223 2.223203 CGACGTCGACTGCTTTACCTAT 60.223 50.000 33.35 0.00 43.02 2.57
2191 4235 0.179468 TTACCTATGGCGCCAACCTC 59.821 55.000 36.33 1.76 0.00 3.85
2195 4239 1.971505 CTATGGCGCCAACCTCCTCA 61.972 60.000 36.33 6.47 0.00 3.86
2196 4240 1.971505 TATGGCGCCAACCTCCTCAG 61.972 60.000 36.33 0.00 0.00 3.35
2272 4316 1.448540 CGTCTCCTTCGGCAGCAAT 60.449 57.895 0.00 0.00 0.00 3.56
2308 4352 3.644719 CAGATGGAGGAGCTGGCT 58.355 61.111 0.00 0.00 34.18 4.75
2572 4622 2.125512 GACCAGCCGATCAACGCT 60.126 61.111 0.00 0.00 41.07 5.07
2576 4626 4.135153 AGCCGATCAACGCTCGCT 62.135 61.111 0.00 0.00 41.07 4.93
2854 4907 4.832608 GAACCTTCCCCGCGCGAT 62.833 66.667 34.63 6.19 0.00 4.58
2936 4989 0.966920 GAACCTGGAGGAGTTCGTGA 59.033 55.000 0.00 0.00 38.94 4.35
2978 5031 3.244249 CGGGGAGAAGTGAAGAAAGTCTT 60.244 47.826 0.00 0.00 39.87 3.01
3035 5097 0.094730 GCATTACTTCGTCGTGGTGC 59.905 55.000 0.00 0.00 0.00 5.01
3131 5204 1.002087 CTAGGGTCGTGGCTTTTGAGT 59.998 52.381 0.00 0.00 0.00 3.41
3132 5205 0.182775 AGGGTCGTGGCTTTTGAGTT 59.817 50.000 0.00 0.00 0.00 3.01
3133 5206 1.029681 GGGTCGTGGCTTTTGAGTTT 58.970 50.000 0.00 0.00 0.00 2.66
3134 5207 1.407618 GGGTCGTGGCTTTTGAGTTTT 59.592 47.619 0.00 0.00 0.00 2.43
3135 5208 2.459934 GGTCGTGGCTTTTGAGTTTTG 58.540 47.619 0.00 0.00 0.00 2.44
3137 5210 3.363178 GTCGTGGCTTTTGAGTTTTGAG 58.637 45.455 0.00 0.00 0.00 3.02
3138 5211 2.119457 CGTGGCTTTTGAGTTTTGAGC 58.881 47.619 0.00 0.00 0.00 4.26
3139 5212 2.479389 CGTGGCTTTTGAGTTTTGAGCA 60.479 45.455 0.00 0.00 35.12 4.26
3140 5213 3.118542 GTGGCTTTTGAGTTTTGAGCAG 58.881 45.455 0.00 0.00 35.12 4.24
3141 5214 2.130395 GGCTTTTGAGTTTTGAGCAGC 58.870 47.619 0.00 0.00 35.12 5.25
3164 5237 5.522097 GCTATCTTCTTGTTCTTCTAGTGCC 59.478 44.000 0.00 0.00 0.00 5.01
3166 5239 2.080286 TCTTGTTCTTCTAGTGCCGC 57.920 50.000 0.00 0.00 0.00 6.53
3167 5240 0.716108 CTTGTTCTTCTAGTGCCGCG 59.284 55.000 0.00 0.00 0.00 6.46
3168 5241 0.032952 TTGTTCTTCTAGTGCCGCGT 59.967 50.000 4.92 0.00 0.00 6.01
3170 5243 0.109226 GTTCTTCTAGTGCCGCGTCT 60.109 55.000 4.92 3.00 0.00 4.18
3181 5262 0.664767 GCCGCGTCTCATATCACCTC 60.665 60.000 4.92 0.00 0.00 3.85
3189 5270 3.378742 GTCTCATATCACCTCTGTCGTGT 59.621 47.826 0.00 0.00 32.86 4.49
3209 5290 4.309950 GTCCGGCCGGTTGTCAGT 62.310 66.667 41.57 0.00 36.47 3.41
3246 5327 4.217767 ACTTGATCTGTAGCGTTGTAGTCA 59.782 41.667 0.00 0.00 0.00 3.41
3260 5341 3.852286 TGTAGTCAGTGTCGTTTGTGTT 58.148 40.909 0.00 0.00 0.00 3.32
3322 5403 4.036144 GCCTTTTCTGTCTAGCCATTCATC 59.964 45.833 0.00 0.00 0.00 2.92
3326 5407 5.946942 TTCTGTCTAGCCATTCATCTTCT 57.053 39.130 0.00 0.00 0.00 2.85
3331 5412 4.820716 GTCTAGCCATTCATCTTCTGCATT 59.179 41.667 0.00 0.00 0.00 3.56
3356 5437 5.170270 GCGATTCATGCAAGTATTTTTCTCG 59.830 40.000 0.00 0.00 0.00 4.04
3423 5504 3.305608 GCAGCACAACAAAGCCTTCTAAT 60.306 43.478 0.00 0.00 0.00 1.73
3429 5510 6.582672 GCACAACAAAGCCTTCTAATTAGAAC 59.417 38.462 21.46 13.98 37.40 3.01
3441 5522 9.169592 CCTTCTAATTAGAACGTGGGATAAAAA 57.830 33.333 21.46 0.00 37.40 1.94
3531 5613 8.812972 TGTTAGTATTTACTAGCAGATATGGGG 58.187 37.037 9.42 0.00 42.49 4.96
3532 5614 9.032624 GTTAGTATTTACTAGCAGATATGGGGA 57.967 37.037 6.71 0.00 39.69 4.81
3533 5615 7.726033 AGTATTTACTAGCAGATATGGGGAG 57.274 40.000 0.00 0.00 34.13 4.30
3534 5616 7.479579 AGTATTTACTAGCAGATATGGGGAGA 58.520 38.462 0.00 0.00 34.13 3.71
3562 5658 5.530171 ACAATCAGATTATGCAGATGTGGTC 59.470 40.000 9.27 0.00 0.00 4.02
3563 5659 4.758773 TCAGATTATGCAGATGTGGTCA 57.241 40.909 9.27 0.00 0.00 4.02
3564 5660 5.300411 TCAGATTATGCAGATGTGGTCAT 57.700 39.130 9.27 0.00 36.95 3.06
3565 5661 5.061179 TCAGATTATGCAGATGTGGTCATG 58.939 41.667 9.27 0.00 34.06 3.07
3566 5662 4.820173 CAGATTATGCAGATGTGGTCATGT 59.180 41.667 0.00 0.00 34.06 3.21
3567 5663 4.820173 AGATTATGCAGATGTGGTCATGTG 59.180 41.667 0.00 1.82 44.71 3.21
3568 5664 1.758936 ATGCAGATGTGGTCATGTGG 58.241 50.000 0.00 0.00 42.96 4.17
3569 5665 0.401356 TGCAGATGTGGTCATGTGGT 59.599 50.000 7.30 0.00 42.96 4.16
3576 5672 4.718774 AGATGTGGTCATGTGGTAGAGATT 59.281 41.667 0.00 0.00 34.06 2.40
3616 5712 5.074102 TCAATTGCCAGGATGAGATAAGGAT 59.926 40.000 0.00 0.00 39.69 3.24
3620 5716 5.380043 TGCCAGGATGAGATAAGGATTTTC 58.620 41.667 0.00 0.00 39.69 2.29
3624 5720 7.147846 GCCAGGATGAGATAAGGATTTTCAAAA 60.148 37.037 0.00 0.00 39.69 2.44
3647 5743 9.467258 AAAATGTCATTTCACAAACTATGTCTG 57.533 29.630 11.19 0.00 41.46 3.51
3669 5765 9.269453 GTCTGAATGATGTCATGATGAGATAAA 57.731 33.333 4.95 0.00 36.56 1.40
3672 5768 7.664318 TGAATGATGTCATGATGAGATAAAGGG 59.336 37.037 4.95 0.00 36.56 3.95
3674 5770 5.072736 TGATGTCATGATGAGATAAAGGGCT 59.927 40.000 4.95 0.00 29.83 5.19
3739 5835 7.821652 TCATAACGATTTGATTTTGTAAGGCA 58.178 30.769 0.00 0.00 0.00 4.75
3754 5850 4.762765 TGTAAGGCACCACAACGAAATATT 59.237 37.500 0.00 0.00 0.00 1.28
3806 5905 2.924757 TGCCTGAGCTAGATTGATGG 57.075 50.000 0.00 0.00 40.80 3.51
3809 5908 3.244457 TGCCTGAGCTAGATTGATGGATG 60.244 47.826 0.00 0.00 40.80 3.51
3816 5915 5.938279 AGCTAGATTGATGGATGATGTGTT 58.062 37.500 0.00 0.00 0.00 3.32
3821 5920 1.665169 TGATGGATGATGTGTTTCGCG 59.335 47.619 0.00 0.00 0.00 5.87
3827 5926 0.584396 TGATGTGTTTCGCGTTGACC 59.416 50.000 5.77 0.00 0.00 4.02
3853 5952 4.023021 GCGTAAAGGTGTTTTCCATAACCA 60.023 41.667 0.00 0.00 35.01 3.67
3865 5964 7.928706 TGTTTTCCATAACCAGTAAAATTGTGG 59.071 33.333 0.00 0.00 36.29 4.17
3869 5968 7.232188 TCCATAACCAGTAAAATTGTGGTACA 58.768 34.615 0.00 0.00 44.07 2.90
3876 5975 9.010029 ACCAGTAAAATTGTGGTACAAGAATAG 57.990 33.333 0.00 0.00 42.99 1.73
3947 6046 4.457949 AGCTTACAAAAACGAACCCATAGG 59.542 41.667 0.00 0.00 40.04 2.57
3957 6056 3.181448 ACGAACCCATAGGAAGTTGTGTT 60.181 43.478 0.00 0.00 36.73 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 0.389817 CGCCTCCGATGACAAGTGAA 60.390 55.000 0.00 0.00 36.29 3.18
45 46 4.971282 AGTCTCCAAGACCAATGGATCATA 59.029 41.667 6.16 0.00 46.18 2.15
72 73 1.718757 CGCCAAAGCCTCCTGCATAC 61.719 60.000 0.00 0.00 44.83 2.39
73 74 1.451927 CGCCAAAGCCTCCTGCATA 60.452 57.895 0.00 0.00 44.83 3.14
91 93 0.869454 CGTCGAGATCTTCTGCCAGC 60.869 60.000 0.00 0.00 0.00 4.85
110 112 3.206150 AGGCAATGACAATACGATGGAC 58.794 45.455 0.00 0.00 0.00 4.02
112 114 3.205338 TGAGGCAATGACAATACGATGG 58.795 45.455 0.00 0.00 0.00 3.51
132 134 1.197721 GAATCACCTGTTTGGCGTCTG 59.802 52.381 0.00 0.00 40.22 3.51
161 163 1.658686 CTTCCTCGACTCCCACTCCG 61.659 65.000 0.00 0.00 0.00 4.63
184 186 2.140065 TCTCGCTAATCATTGCTCCG 57.860 50.000 0.00 0.00 0.00 4.63
241 243 6.425417 TGCTTCAACATTGATAACACGACTTA 59.575 34.615 0.00 0.00 37.00 2.24
252 255 6.259608 GCTAGACTATGTGCTTCAACATTGAT 59.740 38.462 0.00 0.00 41.09 2.57
271 274 3.526534 GACAATGAGAACCTGGCTAGAC 58.473 50.000 0.00 0.00 0.00 2.59
293 296 1.755380 ACGTAGCATCCCAGACCTAAC 59.245 52.381 0.00 0.00 0.00 2.34
296 299 0.824759 GAACGTAGCATCCCAGACCT 59.175 55.000 0.00 0.00 0.00 3.85
306 309 0.104487 TGACCAAACCGAACGTAGCA 59.896 50.000 0.00 0.00 0.00 3.49
309 312 2.415776 GGATTGACCAAACCGAACGTA 58.584 47.619 0.00 0.00 38.79 3.57
315 318 1.832883 TCATGGGATTGACCAAACCG 58.167 50.000 0.00 0.00 45.13 4.44
322 325 3.134458 GAGTTCGGATCATGGGATTGAC 58.866 50.000 0.00 0.00 32.67 3.18
338 341 6.828785 ACACCATAAAATGTGGGATAGAGTTC 59.171 38.462 0.00 0.00 41.14 3.01
357 360 9.520515 AACTAGACTTTATTCATCAAACACCAT 57.479 29.630 0.00 0.00 0.00 3.55
373 376 9.705103 AGGTTTTTAAGGGTAAAACTAGACTTT 57.295 29.630 0.00 0.00 42.36 2.66
374 377 9.705103 AAGGTTTTTAAGGGTAAAACTAGACTT 57.295 29.630 0.00 3.99 42.36 3.01
375 378 9.705103 AAAGGTTTTTAAGGGTAAAACTAGACT 57.295 29.630 0.00 0.00 42.36 3.24
399 402 9.777297 CATTTCATCCTTTCCCTTTTCTTAAAA 57.223 29.630 0.00 0.00 0.00 1.52
400 403 8.933653 ACATTTCATCCTTTCCCTTTTCTTAAA 58.066 29.630 0.00 0.00 0.00 1.52
401 404 8.491045 ACATTTCATCCTTTCCCTTTTCTTAA 57.509 30.769 0.00 0.00 0.00 1.85
402 405 8.491045 AACATTTCATCCTTTCCCTTTTCTTA 57.509 30.769 0.00 0.00 0.00 2.10
403 406 7.379059 AACATTTCATCCTTTCCCTTTTCTT 57.621 32.000 0.00 0.00 0.00 2.52
404 407 6.294731 CGAACATTTCATCCTTTCCCTTTTCT 60.295 38.462 0.00 0.00 0.00 2.52
405 408 5.863935 CGAACATTTCATCCTTTCCCTTTTC 59.136 40.000 0.00 0.00 0.00 2.29
406 409 5.783111 CGAACATTTCATCCTTTCCCTTTT 58.217 37.500 0.00 0.00 0.00 2.27
407 410 4.321974 GCGAACATTTCATCCTTTCCCTTT 60.322 41.667 0.00 0.00 0.00 3.11
408 411 3.193479 GCGAACATTTCATCCTTTCCCTT 59.807 43.478 0.00 0.00 0.00 3.95
409 412 2.755103 GCGAACATTTCATCCTTTCCCT 59.245 45.455 0.00 0.00 0.00 4.20
424 427 1.000394 TGAAGGTTGATCGAGCGAACA 60.000 47.619 8.98 0.00 0.00 3.18
473 476 2.094762 ATAGCTGGTTGTCGTTCACC 57.905 50.000 0.00 0.00 0.00 4.02
474 477 2.159627 CCAATAGCTGGTTGTCGTTCAC 59.840 50.000 0.00 0.00 40.78 3.18
523 526 3.670625 AGAAACACAGCGGTATTGCTAA 58.329 40.909 0.00 0.00 45.23 3.09
526 529 2.031157 ACAAGAAACACAGCGGTATTGC 60.031 45.455 0.00 0.00 0.00 3.56
571 574 0.826672 ACGTGTCCTCTTCTTCCCGT 60.827 55.000 0.00 0.00 0.00 5.28
572 575 0.109226 GACGTGTCCTCTTCTTCCCG 60.109 60.000 0.00 0.00 0.00 5.14
576 579 2.159142 ACAAACGACGTGTCCTCTTCTT 60.159 45.455 0.00 0.00 0.00 2.52
588 591 0.299300 TCTGCGTGAAACAAACGACG 59.701 50.000 0.00 0.00 43.68 5.12
650 653 6.411376 TGACCATAATCGTCAAATTACTGGT 58.589 36.000 0.00 0.00 37.31 4.00
748 754 6.679843 TGTTTATGGAAAACGTGGGAAATAC 58.320 36.000 0.00 0.00 33.05 1.89
770 776 4.074970 GGATCGGATTTATGCCATTCTGT 58.925 43.478 0.00 0.00 0.00 3.41
826 842 5.163652 ACTCCCTTCTTTTTCAGAAAACACG 60.164 40.000 7.89 0.86 41.25 4.49
1007 1106 4.379243 CGAGCAGGACGTTGGCCT 62.379 66.667 3.32 0.00 35.75 5.19
1212 1962 0.589229 CCACATACTCGTCGACGCTC 60.589 60.000 32.19 0.00 39.60 5.03
1362 2112 2.660064 CGACTGGGTGGAGAAGGGG 61.660 68.421 0.00 0.00 0.00 4.79
1823 2592 2.223377 CACGTGCAGTTTCCTTCTTACC 59.777 50.000 0.82 0.00 0.00 2.85
1831 2600 1.104577 TTTCCCCACGTGCAGTTTCC 61.105 55.000 10.91 0.00 0.00 3.13
2022 3031 2.171448 ACTCATGTAGGCCCAACTCATC 59.829 50.000 0.00 0.00 0.00 2.92
2097 4141 2.750350 CTCGGGCCTTGAAGTGGT 59.250 61.111 0.84 0.00 0.00 4.16
2168 4212 0.034960 TTGGCGCCATAGGTAAAGCA 60.035 50.000 33.25 8.24 0.00 3.91
2173 4217 1.692173 GGAGGTTGGCGCCATAGGTA 61.692 60.000 33.25 12.81 0.00 3.08
2179 4223 4.020617 CTGAGGAGGTTGGCGCCA 62.021 66.667 29.03 29.03 0.00 5.69
2545 4595 3.626924 GGCTGGTCGGTCCACAGT 61.627 66.667 6.97 0.00 41.93 3.55
2572 4622 2.808315 GCCTCCTCGATGAAGCGA 59.192 61.111 0.00 0.00 38.74 4.93
2576 4626 2.721167 CCCACGCCTCCTCGATGAA 61.721 63.158 0.00 0.00 0.00 2.57
2765 4818 0.685097 CCCAGTTTCTTGTCGGAGGA 59.315 55.000 0.00 0.00 0.00 3.71
2936 4989 1.364171 CGCTAGCCCGCAGATAGTT 59.636 57.895 9.66 0.00 0.00 2.24
2978 5031 2.439135 ACCATGCATGCCAGATACAGTA 59.561 45.455 21.69 0.00 0.00 2.74
3131 5204 6.000219 AGAACAAGAAGATAGCTGCTCAAAA 59.000 36.000 4.91 0.00 0.00 2.44
3132 5205 5.555017 AGAACAAGAAGATAGCTGCTCAAA 58.445 37.500 4.91 0.00 0.00 2.69
3133 5206 5.157940 AGAACAAGAAGATAGCTGCTCAA 57.842 39.130 4.91 0.00 0.00 3.02
3134 5207 4.815533 AGAACAAGAAGATAGCTGCTCA 57.184 40.909 4.91 0.00 0.00 4.26
3135 5208 5.418676 AGAAGAACAAGAAGATAGCTGCTC 58.581 41.667 4.91 0.00 0.00 4.26
3137 5210 6.255453 CACTAGAAGAACAAGAAGATAGCTGC 59.745 42.308 0.00 0.00 0.00 5.25
3138 5211 6.255453 GCACTAGAAGAACAAGAAGATAGCTG 59.745 42.308 0.00 0.00 0.00 4.24
3139 5212 6.337356 GCACTAGAAGAACAAGAAGATAGCT 58.663 40.000 0.00 0.00 0.00 3.32
3140 5213 5.522097 GGCACTAGAAGAACAAGAAGATAGC 59.478 44.000 0.00 0.00 0.00 2.97
3141 5214 5.746245 CGGCACTAGAAGAACAAGAAGATAG 59.254 44.000 0.00 0.00 0.00 2.08
3164 5237 1.335182 ACAGAGGTGATATGAGACGCG 59.665 52.381 3.53 3.53 0.00 6.01
3166 5239 2.614520 ACGACAGAGGTGATATGAGACG 59.385 50.000 0.00 0.00 0.00 4.18
3167 5240 3.378742 ACACGACAGAGGTGATATGAGAC 59.621 47.826 0.00 0.00 38.73 3.36
3168 5241 3.378427 CACACGACAGAGGTGATATGAGA 59.622 47.826 0.00 0.00 38.73 3.27
3170 5243 3.352648 TCACACGACAGAGGTGATATGA 58.647 45.455 0.00 0.00 36.69 2.15
3181 5262 2.430921 GCCGGACTCACACGACAG 60.431 66.667 5.05 0.00 0.00 3.51
3209 5290 3.785486 GATCAAGTGATCGACCACATGA 58.215 45.455 19.42 19.42 45.08 3.07
3246 5327 2.147958 ACACACAACACAAACGACACT 58.852 42.857 0.00 0.00 0.00 3.55
3260 5341 4.442375 AAAACATGTTTTCGGACACACA 57.558 36.364 27.01 0.00 38.27 3.72
3302 5383 6.596888 CAGAAGATGAATGGCTAGACAGAAAA 59.403 38.462 3.72 0.00 0.00 2.29
3322 5403 2.117137 GCATGAATCGCAATGCAGAAG 58.883 47.619 5.91 0.00 39.61 2.85
3331 5412 5.953183 AGAAAAATACTTGCATGAATCGCA 58.047 33.333 6.60 0.00 37.68 5.10
3529 5611 6.866480 TGCATAATCTGATTGTTTTTCTCCC 58.134 36.000 13.01 0.00 0.00 4.30
3530 5612 7.765307 TCTGCATAATCTGATTGTTTTTCTCC 58.235 34.615 13.01 0.00 0.00 3.71
3531 5613 9.234384 CATCTGCATAATCTGATTGTTTTTCTC 57.766 33.333 13.01 0.00 0.00 2.87
3532 5614 8.746530 ACATCTGCATAATCTGATTGTTTTTCT 58.253 29.630 13.01 0.00 0.00 2.52
3533 5615 8.804743 CACATCTGCATAATCTGATTGTTTTTC 58.195 33.333 13.01 0.00 0.00 2.29
3534 5616 7.762615 CCACATCTGCATAATCTGATTGTTTTT 59.237 33.333 13.01 0.00 0.00 1.94
3583 5679 6.189859 TCATCCTGGCAATTGATTTAGACTT 58.810 36.000 10.34 0.00 0.00 3.01
3584 5680 5.759059 TCATCCTGGCAATTGATTTAGACT 58.241 37.500 10.34 0.00 0.00 3.24
3585 5681 5.824624 TCTCATCCTGGCAATTGATTTAGAC 59.175 40.000 10.34 0.00 0.00 2.59
3586 5682 6.005066 TCTCATCCTGGCAATTGATTTAGA 57.995 37.500 10.34 0.00 0.00 2.10
3587 5683 6.896021 ATCTCATCCTGGCAATTGATTTAG 57.104 37.500 10.34 0.90 0.00 1.85
3588 5684 7.449395 CCTTATCTCATCCTGGCAATTGATTTA 59.551 37.037 10.34 0.00 0.00 1.40
3596 5692 5.393068 AAATCCTTATCTCATCCTGGCAA 57.607 39.130 0.00 0.00 0.00 4.52
3599 5695 7.886629 TTTGAAAATCCTTATCTCATCCTGG 57.113 36.000 0.00 0.00 0.00 4.45
3602 5698 9.741647 GACATTTTGAAAATCCTTATCTCATCC 57.258 33.333 0.00 0.00 0.00 3.51
3620 5716 9.467258 AGACATAGTTTGTGAAATGACATTTTG 57.533 29.630 14.46 8.07 39.18 2.44
3624 5720 7.984422 TCAGACATAGTTTGTGAAATGACAT 57.016 32.000 0.00 0.00 39.18 3.06
3647 5743 7.361885 GCCCTTTATCTCATCATGACATCATTC 60.362 40.741 0.00 0.00 33.61 2.67
3692 5788 6.738114 TGAGACCATCACATTTTCAGTTTTC 58.262 36.000 0.00 0.00 31.12 2.29
3754 5850 8.873215 TCAAATGCAATTTACTCCGTTAAAAA 57.127 26.923 0.00 0.00 46.64 1.94
3759 5855 5.184864 TCCATCAAATGCAATTTACTCCGTT 59.815 36.000 0.00 0.00 46.64 4.44
3760 5856 4.704540 TCCATCAAATGCAATTTACTCCGT 59.295 37.500 0.00 0.00 46.64 4.69
3761 5857 5.036737 GTCCATCAAATGCAATTTACTCCG 58.963 41.667 0.00 0.00 46.64 4.63
3763 5859 5.964758 TGGTCCATCAAATGCAATTTACTC 58.035 37.500 0.00 0.00 46.64 2.59
3764 5860 5.999205 TGGTCCATCAAATGCAATTTACT 57.001 34.783 0.00 0.00 46.64 2.24
3765 5861 5.006941 GCATGGTCCATCAAATGCAATTTAC 59.993 40.000 0.00 0.00 46.64 2.01
3766 5862 5.117584 GCATGGTCCATCAAATGCAATTTA 58.882 37.500 0.00 0.00 46.64 1.40
3770 5869 1.207570 GGCATGGTCCATCAAATGCAA 59.792 47.619 14.74 0.00 45.72 4.08
3806 5905 2.495939 GTCAACGCGAAACACATCATC 58.504 47.619 15.93 0.00 0.00 2.92
3809 5908 0.865769 AGGTCAACGCGAAACACATC 59.134 50.000 15.93 0.00 0.00 3.06
3821 5920 3.036075 ACACCTTTACGCTAGGTCAAC 57.964 47.619 1.07 0.00 44.12 3.18
3827 5926 6.402875 GGTTATGGAAAACACCTTTACGCTAG 60.403 42.308 0.00 0.00 29.25 3.42
3836 5935 7.849322 ATTTTACTGGTTATGGAAAACACCT 57.151 32.000 0.00 0.00 0.00 4.00
3853 5952 9.787435 TGTCTATTCTTGTACCACAATTTTACT 57.213 29.630 0.00 0.00 37.48 2.24
3876 5975 7.801716 TTTTGCCTCCATACATAACTATGTC 57.198 36.000 5.64 0.00 45.11 3.06
3919 6018 7.079182 TGGGTTCGTTTTTGTAAGCTATATG 57.921 36.000 0.00 0.00 0.00 1.78
3930 6029 5.219633 CAACTTCCTATGGGTTCGTTTTTG 58.780 41.667 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.