Multiple sequence alignment - TraesCS7D01G530900

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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 TraesCS7D01G530900 chr7D 100.000 4415 0 0 1 4415 625356402 625351988 0.000000e+00 8154.0
1 TraesCS7D01G530900 chr7D 85.779 2658 337 26 777 3417 625250301 625252934 0.000000e+00 2776.0
2 TraesCS7D01G530900 chr7D 85.111 2485 330 24 975 3446 625227727 625225270 0.000000e+00 2503.0
3 TraesCS7D01G530900 chr7D 84.588 2563 339 29 989 3534 448855404 448857927 0.000000e+00 2494.0
4 TraesCS7D01G530900 chr7D 91.228 114 10 0 357 470 34756857 34756970 5.910000e-34 156.0
5 TraesCS7D01G530900 chr7D 92.593 81 6 0 487 567 568370009 568370089 2.790000e-22 117.0
6 TraesCS7D01G530900 chr7D 100.000 31 0 0 568 598 404056843 404056813 1.720000e-04 58.4
7 TraesCS7D01G530900 chr7B 96.290 4178 102 24 250 4415 724956692 724952556 0.000000e+00 6807.0
8 TraesCS7D01G530900 chr7B 85.333 2659 345 28 777 3417 723903179 723900548 0.000000e+00 2708.0
9 TraesCS7D01G530900 chr7B 85.539 2607 319 33 950 3534 466668834 466671404 0.000000e+00 2673.0
10 TraesCS7D01G530900 chr7B 96.725 397 12 1 4019 4414 23678578 23678974 0.000000e+00 660.0
11 TraesCS7D01G530900 chr7B 89.904 208 12 2 6 213 724956886 724956688 4.380000e-65 259.0
12 TraesCS7D01G530900 chr7B 100.000 31 0 0 568 598 413571165 413571135 1.720000e-04 58.4
13 TraesCS7D01G530900 chr7A 86.793 2476 291 23 950 3417 720864396 720861949 0.000000e+00 2728.0
14 TraesCS7D01G530900 chr7A 83.399 2542 366 28 1012 3534 547114128 547111624 0.000000e+00 2305.0
15 TraesCS7D01G530900 chr7A 85.127 2286 295 22 1180 3446 720885032 720887291 0.000000e+00 2296.0
16 TraesCS7D01G530900 chr7A 93.519 108 7 0 363 470 206959856 206959963 1.270000e-35 161.0
17 TraesCS7D01G530900 chr7A 90.244 82 8 0 487 568 571702544 571702625 1.680000e-19 108.0
18 TraesCS7D01G530900 chr7A 100.000 31 0 0 568 598 462978616 462978586 1.720000e-04 58.4
19 TraesCS7D01G530900 chr1B 84.378 2791 375 29 649 3408 623547164 623549924 0.000000e+00 2682.0
20 TraesCS7D01G530900 chr1B 94.595 111 5 1 4305 4414 33322916 33322806 2.110000e-38 171.0
21 TraesCS7D01G530900 chr1D 84.447 2739 373 23 695 3408 453113031 453115741 0.000000e+00 2649.0
22 TraesCS7D01G530900 chr1D 83.012 830 105 20 2509 3328 452681527 452680724 0.000000e+00 719.0
23 TraesCS7D01G530900 chr1D 92.035 113 9 0 364 476 471593834 471593722 4.570000e-35 159.0
24 TraesCS7D01G530900 chr6A 83.738 2515 353 35 956 3445 608493844 608491361 0.000000e+00 2327.0
25 TraesCS7D01G530900 chr2B 96.725 397 12 1 4019 4414 642414460 642414856 0.000000e+00 660.0
26 TraesCS7D01G530900 chr2B 86.458 96 12 1 484 578 214312031 214312126 2.170000e-18 104.0
27 TraesCS7D01G530900 chrUn 96.474 397 13 1 4019 4414 200831425 200831821 0.000000e+00 654.0
28 TraesCS7D01G530900 chr5B 96.222 397 14 1 4019 4414 594290790 594291186 0.000000e+00 649.0
29 TraesCS7D01G530900 chr5B 93.694 111 7 0 366 476 208523451 208523341 2.730000e-37 167.0
30 TraesCS7D01G530900 chr3B 95.718 397 16 1 4019 4414 34317914 34318310 4.820000e-179 638.0
31 TraesCS7D01G530900 chr3B 94.789 403 14 2 4019 4414 34313358 34312956 4.850000e-174 621.0
32 TraesCS7D01G530900 chr3B 82.845 239 35 4 366 598 507132190 507132428 4.470000e-50 209.0
33 TraesCS7D01G530900 chr3B 96.875 32 1 0 568 599 610174431 610174462 2.000000e-03 54.7
34 TraesCS7D01G530900 chr6B 97.188 320 8 1 4096 4414 31387746 31387427 1.400000e-149 540.0
35 TraesCS7D01G530900 chr6B 100.000 28 0 0 570 597 169481793 169481766 8.000000e-03 52.8
36 TraesCS7D01G530900 chr3D 86.134 238 28 3 366 598 389633010 389633247 7.330000e-63 252.0
37 TraesCS7D01G530900 chr3D 91.304 115 10 0 362 476 482857263 482857377 1.640000e-34 158.0
38 TraesCS7D01G530900 chr2D 92.105 114 9 0 363 476 122864108 122864221 1.270000e-35 161.0
39 TraesCS7D01G530900 chr2D 92.593 81 6 0 487 567 61023715 61023795 2.790000e-22 117.0
40 TraesCS7D01G530900 chr1A 85.276 163 17 4 3287 3447 547567654 547567497 1.270000e-35 161.0
41 TraesCS7D01G530900 chr1A 91.228 114 10 0 363 476 459273228 459273341 5.910000e-34 156.0
42 TraesCS7D01G530900 chr1A 92.208 77 6 0 493 569 568391275 568391199 4.670000e-20 110.0
43 TraesCS7D01G530900 chr4A 91.304 115 10 0 362 476 30742890 30742776 1.640000e-34 158.0
44 TraesCS7D01G530900 chr4A 100.000 32 0 0 568 599 649809687 649809656 4.770000e-05 60.2
45 TraesCS7D01G530900 chr5D 91.250 80 7 0 487 566 492288312 492288233 4.670000e-20 110.0
46 TraesCS7D01G530900 chr3A 96.970 33 1 0 565 597 456377826 456377858 6.170000e-04 56.5


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 TraesCS7D01G530900 chr7D 625351988 625356402 4414 True 8154 8154 100.000 1 4415 1 chr7D.!!$R3 4414
1 TraesCS7D01G530900 chr7D 625250301 625252934 2633 False 2776 2776 85.779 777 3417 1 chr7D.!!$F4 2640
2 TraesCS7D01G530900 chr7D 625225270 625227727 2457 True 2503 2503 85.111 975 3446 1 chr7D.!!$R2 2471
3 TraesCS7D01G530900 chr7D 448855404 448857927 2523 False 2494 2494 84.588 989 3534 1 chr7D.!!$F2 2545
4 TraesCS7D01G530900 chr7B 724952556 724956886 4330 True 3533 6807 93.097 6 4415 2 chr7B.!!$R3 4409
5 TraesCS7D01G530900 chr7B 723900548 723903179 2631 True 2708 2708 85.333 777 3417 1 chr7B.!!$R2 2640
6 TraesCS7D01G530900 chr7B 466668834 466671404 2570 False 2673 2673 85.539 950 3534 1 chr7B.!!$F2 2584
7 TraesCS7D01G530900 chr7A 720861949 720864396 2447 True 2728 2728 86.793 950 3417 1 chr7A.!!$R3 2467
8 TraesCS7D01G530900 chr7A 547111624 547114128 2504 True 2305 2305 83.399 1012 3534 1 chr7A.!!$R2 2522
9 TraesCS7D01G530900 chr7A 720885032 720887291 2259 False 2296 2296 85.127 1180 3446 1 chr7A.!!$F3 2266
10 TraesCS7D01G530900 chr1B 623547164 623549924 2760 False 2682 2682 84.378 649 3408 1 chr1B.!!$F1 2759
11 TraesCS7D01G530900 chr1D 453113031 453115741 2710 False 2649 2649 84.447 695 3408 1 chr1D.!!$F1 2713
12 TraesCS7D01G530900 chr1D 452680724 452681527 803 True 719 719 83.012 2509 3328 1 chr1D.!!$R1 819
13 TraesCS7D01G530900 chr6A 608491361 608493844 2483 True 2327 2327 83.738 956 3445 1 chr6A.!!$R1 2489

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
228 229 0.106708 TACATCAGCCATCCGGAAGC 59.893 55.0 19.44 19.44 0.00 3.86 F
240 241 0.250727 CCGGAAGCCCTGAAAGACAA 60.251 55.0 0.00 0.00 34.07 3.18 F
385 386 0.321671 ACTCCCTCCGTTCACACATG 59.678 55.0 0.00 0.00 0.00 3.21 F
1161 1213 0.537143 TCACCTGCGGCTTCAACAAT 60.537 50.0 0.00 0.00 0.00 2.71 F
1270 1322 0.686441 CGTGTACTCCTGGGGATCCA 60.686 60.0 15.23 0.00 41.58 3.41 F
1271 1323 1.807814 GTGTACTCCTGGGGATCCAT 58.192 55.0 15.23 0.00 43.11 3.41 F
2145 2214 3.070603 AGGAAGTGGAAGTTGCTTTCCG 61.071 50.0 18.35 0.00 46.45 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2141 2210 0.754472 AACAAGGGACGACTTCGGAA 59.246 50.000 3.30 0.0 44.95 4.30 R
2145 2214 1.226746 CACCAACAAGGGACGACTTC 58.773 55.000 0.00 0.0 43.89 3.01 R
2177 2246 2.262637 AGATAGAACGACCCAAACCCA 58.737 47.619 0.00 0.0 0.00 4.51 R
2380 2458 3.871594 ACCTCTACACAAAATATCGCTGC 59.128 43.478 0.00 0.0 0.00 5.25 R
3172 3259 1.614413 GACTGTCTCCACTTCCTCGTT 59.386 52.381 0.00 0.0 0.00 3.85 R
3315 3405 1.674962 GCCAGCTTGACCATCATTCTC 59.325 52.381 0.00 0.0 0.00 2.87 R
3916 4014 0.108186 CCCGCATGTGACTAGCTGAA 60.108 55.000 8.11 0.0 0.00 3.02 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
44 45 5.931441 AAAAATGAAGACTTCTCCGTCTG 57.069 39.130 16.02 0.00 43.14 3.51
45 46 4.608948 AAATGAAGACTTCTCCGTCTGT 57.391 40.909 16.02 0.00 43.14 3.41
46 47 3.859411 ATGAAGACTTCTCCGTCTGTC 57.141 47.619 16.02 0.00 43.14 3.51
47 48 2.865079 TGAAGACTTCTCCGTCTGTCT 58.135 47.619 16.02 0.00 43.14 3.41
48 49 2.554462 TGAAGACTTCTCCGTCTGTCTG 59.446 50.000 16.02 0.00 43.14 3.51
49 50 0.885196 AGACTTCTCCGTCTGTCTGC 59.115 55.000 0.00 0.00 42.39 4.26
50 51 0.598562 GACTTCTCCGTCTGTCTGCA 59.401 55.000 0.00 0.00 0.00 4.41
51 52 0.315568 ACTTCTCCGTCTGTCTGCAC 59.684 55.000 0.00 0.00 0.00 4.57
52 53 0.389166 CTTCTCCGTCTGTCTGCACC 60.389 60.000 0.00 0.00 0.00 5.01
79 80 6.007076 TGAAGTCCATATGTTGCCAAGTTTA 58.993 36.000 1.24 0.00 0.00 2.01
91 92 3.067040 TGCCAAGTTTACGGTTTCTTTCC 59.933 43.478 0.00 0.00 0.00 3.13
107 108 0.613260 TTCCGATAGCAGCCAACTGT 59.387 50.000 0.00 0.00 46.30 3.55
118 119 6.199937 AGCAGCCAACTGTTGAAATAATAG 57.800 37.500 21.49 3.70 46.30 1.73
144 145 4.455877 ACTTATTTCACTTGCCAGCTGTAC 59.544 41.667 13.81 4.91 0.00 2.90
158 159 1.532868 GCTGTACGATGGATGATTGGC 59.467 52.381 0.00 0.00 0.00 4.52
188 189 0.468226 GTGGCTCGAATCATACCCCA 59.532 55.000 0.00 0.00 0.00 4.96
190 191 1.562008 TGGCTCGAATCATACCCCAAA 59.438 47.619 0.00 0.00 0.00 3.28
196 197 4.340617 TCGAATCATACCCCAAAAGCTTT 58.659 39.130 5.69 5.69 0.00 3.51
212 213 7.148086 CCAAAAGCTTTATTGCAGGAGTATACA 60.148 37.037 13.10 0.00 34.99 2.29
213 214 8.408601 CAAAAGCTTTATTGCAGGAGTATACAT 58.591 33.333 13.10 0.00 34.99 2.29
214 215 7.736447 AAGCTTTATTGCAGGAGTATACATC 57.264 36.000 5.50 0.04 34.99 3.06
215 216 6.830912 AGCTTTATTGCAGGAGTATACATCA 58.169 36.000 5.50 0.00 34.99 3.07
216 217 6.933521 AGCTTTATTGCAGGAGTATACATCAG 59.066 38.462 5.50 0.00 34.99 2.90
217 218 6.348050 GCTTTATTGCAGGAGTATACATCAGC 60.348 42.308 5.50 5.87 0.00 4.26
218 219 3.475566 TTGCAGGAGTATACATCAGCC 57.524 47.619 5.50 0.00 0.00 4.85
219 220 2.397597 TGCAGGAGTATACATCAGCCA 58.602 47.619 5.50 0.00 0.00 4.75
220 221 2.974794 TGCAGGAGTATACATCAGCCAT 59.025 45.455 5.50 0.00 0.00 4.40
221 222 3.007290 TGCAGGAGTATACATCAGCCATC 59.993 47.826 5.50 0.00 0.00 3.51
222 223 3.618507 GCAGGAGTATACATCAGCCATCC 60.619 52.174 5.50 0.61 0.00 3.51
223 224 2.828520 AGGAGTATACATCAGCCATCCG 59.171 50.000 5.50 0.00 0.00 4.18
224 225 2.093973 GGAGTATACATCAGCCATCCGG 60.094 54.545 5.50 0.00 0.00 5.14
225 226 2.826128 GAGTATACATCAGCCATCCGGA 59.174 50.000 6.61 6.61 0.00 5.14
226 227 3.239449 AGTATACATCAGCCATCCGGAA 58.761 45.455 9.01 0.00 0.00 4.30
227 228 2.847327 ATACATCAGCCATCCGGAAG 57.153 50.000 9.01 3.04 0.00 3.46
228 229 0.106708 TACATCAGCCATCCGGAAGC 59.893 55.000 19.44 19.44 0.00 3.86
229 230 1.895707 CATCAGCCATCCGGAAGCC 60.896 63.158 22.41 2.63 0.00 4.35
230 231 3.125376 ATCAGCCATCCGGAAGCCC 62.125 63.158 22.41 6.81 0.00 5.19
231 232 3.801997 CAGCCATCCGGAAGCCCT 61.802 66.667 22.41 8.86 0.00 5.19
232 233 3.801997 AGCCATCCGGAAGCCCTG 61.802 66.667 22.41 10.27 0.00 4.45
233 234 3.797353 GCCATCCGGAAGCCCTGA 61.797 66.667 9.01 0.00 0.00 3.86
234 235 2.998097 CCATCCGGAAGCCCTGAA 59.002 61.111 9.01 0.00 0.00 3.02
235 236 1.302949 CCATCCGGAAGCCCTGAAA 59.697 57.895 9.01 0.00 0.00 2.69
236 237 0.749454 CCATCCGGAAGCCCTGAAAG 60.749 60.000 9.01 0.00 0.00 2.62
237 238 0.253044 CATCCGGAAGCCCTGAAAGA 59.747 55.000 9.01 0.00 34.07 2.52
238 239 0.253327 ATCCGGAAGCCCTGAAAGAC 59.747 55.000 9.01 0.00 34.07 3.01
239 240 1.125093 TCCGGAAGCCCTGAAAGACA 61.125 55.000 0.00 0.00 34.07 3.41
240 241 0.250727 CCGGAAGCCCTGAAAGACAA 60.251 55.000 0.00 0.00 34.07 3.18
241 242 1.604604 CGGAAGCCCTGAAAGACAAA 58.395 50.000 0.00 0.00 34.07 2.83
242 243 1.537202 CGGAAGCCCTGAAAGACAAAG 59.463 52.381 0.00 0.00 34.07 2.77
243 244 2.810400 CGGAAGCCCTGAAAGACAAAGA 60.810 50.000 0.00 0.00 34.07 2.52
244 245 2.554462 GGAAGCCCTGAAAGACAAAGAC 59.446 50.000 0.00 0.00 34.07 3.01
245 246 3.481453 GAAGCCCTGAAAGACAAAGACT 58.519 45.455 0.00 0.00 34.07 3.24
246 247 3.584733 AGCCCTGAAAGACAAAGACTT 57.415 42.857 0.00 0.00 34.07 3.01
247 248 3.481453 AGCCCTGAAAGACAAAGACTTC 58.519 45.455 0.00 0.00 34.07 3.01
248 249 3.117888 AGCCCTGAAAGACAAAGACTTCA 60.118 43.478 0.00 0.00 34.07 3.02
249 250 3.632145 GCCCTGAAAGACAAAGACTTCAA 59.368 43.478 0.00 0.00 34.07 2.69
250 251 4.279420 GCCCTGAAAGACAAAGACTTCAAT 59.721 41.667 0.00 0.00 34.07 2.57
251 252 5.473504 GCCCTGAAAGACAAAGACTTCAATA 59.526 40.000 0.00 0.00 34.07 1.90
252 253 6.151817 GCCCTGAAAGACAAAGACTTCAATAT 59.848 38.462 0.00 0.00 34.07 1.28
284 285 6.060028 TGTTGACTGAATAGAACAAGTTGC 57.940 37.500 1.81 0.00 0.00 4.17
290 291 5.769662 ACTGAATAGAACAAGTTGCCATTCA 59.230 36.000 1.81 11.14 31.94 2.57
296 297 4.276926 AGAACAAGTTGCCATTCAAGAGAC 59.723 41.667 1.81 0.00 34.91 3.36
311 312 1.133407 AGAGACGGACAAGAAGCGATC 59.867 52.381 0.00 0.00 0.00 3.69
357 358 1.809567 GACCTGGCCAGCAACCTTTG 61.810 60.000 28.39 13.38 0.00 2.77
385 386 0.321671 ACTCCCTCCGTTCACACATG 59.678 55.000 0.00 0.00 0.00 3.21
387 388 1.548719 CTCCCTCCGTTCACACATGTA 59.451 52.381 0.00 0.00 0.00 2.29
398 399 5.624900 CGTTCACACATGTAAGATGTTTTGG 59.375 40.000 0.00 0.00 0.00 3.28
440 441 9.476202 CTATATACGGAATGAAATGAGTGAACA 57.524 33.333 0.00 0.00 0.00 3.18
456 457 5.034152 AGTGAACAAACACACTAAAATGCG 58.966 37.500 0.00 0.00 44.06 4.73
475 477 8.846943 AAATGCGTCTATATACATCCAAATCA 57.153 30.769 0.00 0.00 0.00 2.57
476 478 8.846943 AATGCGTCTATATACATCCAAATCAA 57.153 30.769 0.00 0.00 0.00 2.57
477 479 8.846943 ATGCGTCTATATACATCCAAATCAAA 57.153 30.769 0.00 0.00 0.00 2.69
517 519 8.902540 TCCATATTAATTGTCGCTGATTTAGT 57.097 30.769 0.00 0.00 0.00 2.24
643 650 4.211920 TGGAAGTTTGAAACAAGTAGGGG 58.788 43.478 11.02 0.00 0.00 4.79
644 651 4.212716 GGAAGTTTGAAACAAGTAGGGGT 58.787 43.478 11.02 0.00 0.00 4.95
645 652 5.104024 TGGAAGTTTGAAACAAGTAGGGGTA 60.104 40.000 11.02 0.00 0.00 3.69
646 653 6.008331 GGAAGTTTGAAACAAGTAGGGGTAT 58.992 40.000 11.02 0.00 0.00 2.73
647 654 6.072119 GGAAGTTTGAAACAAGTAGGGGTATG 60.072 42.308 11.02 0.00 0.00 2.39
716 724 3.175594 AGTGGCCCAAATTGAATGATGT 58.824 40.909 0.00 0.00 0.00 3.06
754 763 8.598041 GGACCTTATTTCAGGAGTATACATCAT 58.402 37.037 5.50 0.00 37.39 2.45
851 861 4.160252 ACTGGTTGACAAACAAGAGCAAAT 59.840 37.500 7.45 0.00 39.41 2.32
1161 1213 0.537143 TCACCTGCGGCTTCAACAAT 60.537 50.000 0.00 0.00 0.00 2.71
1172 1224 4.201950 CGGCTTCAACAATATTTCTGGGAG 60.202 45.833 0.00 0.00 0.00 4.30
1270 1322 0.686441 CGTGTACTCCTGGGGATCCA 60.686 60.000 15.23 0.00 41.58 3.41
1271 1323 1.807814 GTGTACTCCTGGGGATCCAT 58.192 55.000 15.23 0.00 43.11 3.41
1491 1550 8.621532 ATCAGAACATTACTTCTGCTACAAAA 57.378 30.769 4.37 0.00 44.73 2.44
1710 1769 7.411486 TTTCCTTGGAAGTGACAATTTAACA 57.589 32.000 2.16 0.00 0.00 2.41
2145 2214 3.070603 AGGAAGTGGAAGTTGCTTTCCG 61.071 50.000 18.35 0.00 46.45 4.30
2380 2458 9.871238 AGTACTTGTACTTGTATGTATTCTTGG 57.129 33.333 7.55 0.00 0.00 3.61
2995 3081 3.270027 GACTTTGGCCTTGCAAAACTTT 58.730 40.909 3.32 0.00 27.77 2.66
3315 3405 2.474526 CCAGTTCGATAACTTGCAAGCG 60.475 50.000 26.27 20.18 43.60 4.68
3402 3492 5.335897 GGAAAATGTTGTGCAGATGCTTCTA 60.336 40.000 6.35 0.00 42.66 2.10
3458 3548 1.949525 CAGTATGCATGCTACCAACCC 59.050 52.381 17.42 0.00 0.00 4.11
3492 3583 9.302345 AGAGTTTGATGTTTGATATAGTACACG 57.698 33.333 0.00 0.00 0.00 4.49
3549 3647 9.708222 CTATGATGTGTTAGAAATAAAGTGCAC 57.292 33.333 9.40 9.40 0.00 4.57
3550 3648 7.503521 TGATGTGTTAGAAATAAAGTGCACA 57.496 32.000 21.04 0.00 39.44 4.57
3574 3672 7.826252 ACATCACTTTGCATAAGTAGATTCTGT 59.174 33.333 12.06 10.55 0.00 3.41
3665 3763 2.741878 CGAGTTGGTGTCCTGTTGAGTT 60.742 50.000 0.00 0.00 0.00 3.01
3703 3801 3.291101 TTGGCCGCCGAGTCAGTAC 62.291 63.158 4.58 0.00 0.00 2.73
3704 3802 3.450115 GGCCGCCGAGTCAGTACT 61.450 66.667 0.00 0.00 39.21 2.73
3733 3831 3.797256 GCACTAGCCTTGTAACTGATACG 59.203 47.826 0.00 0.00 34.10 3.06
3838 3936 5.047021 AGTTTCTGTGCATGTCTAGCTTCTA 60.047 40.000 0.00 0.00 0.00 2.10
3916 4014 2.880890 AGCTTCATGCACGAAAGACTTT 59.119 40.909 0.00 0.00 45.94 2.66
3929 4027 4.745125 CGAAAGACTTTTCAGCTAGTCACA 59.255 41.667 15.10 0.00 42.27 3.58
3963 4061 4.327357 GGTGTATCAGTGACTTGATCAACG 59.673 45.833 3.38 3.82 39.72 4.10
3989 4087 2.224606 CGGGCTCAATGCTAACATGAT 58.775 47.619 0.00 0.00 42.39 2.45
4012 4110 4.023279 TGTGTGTCCATGTAAATCAACTGC 60.023 41.667 0.00 0.00 0.00 4.40
4083 4181 3.808174 GTCTCCTCTAACGTTTGTGCTTT 59.192 43.478 5.91 0.00 0.00 3.51
4084 4182 3.807622 TCTCCTCTAACGTTTGTGCTTTG 59.192 43.478 5.91 0.00 0.00 2.77
4087 4185 4.451096 TCCTCTAACGTTTGTGCTTTGATC 59.549 41.667 5.91 0.00 0.00 2.92
4131 4230 0.494551 TTAGGACCCTGGACCCTTGA 59.505 55.000 11.21 0.80 0.00 3.02
4255 4354 2.093447 ACTAAAGGGGATCAGCAAGACG 60.093 50.000 0.00 0.00 0.00 4.18
4256 4355 0.693049 AAAGGGGATCAGCAAGACGT 59.307 50.000 0.00 0.00 0.00 4.34
4257 4356 0.250513 AAGGGGATCAGCAAGACGTC 59.749 55.000 7.70 7.70 0.00 4.34
4258 4357 0.616111 AGGGGATCAGCAAGACGTCT 60.616 55.000 13.58 13.58 0.00 4.18
4277 4376 1.347707 CTGTCTACTCCTGTTGGCCAA 59.652 52.381 16.05 16.05 0.00 4.52
4288 4387 1.227823 TTGGCCAACACGAGGTCAG 60.228 57.895 16.05 0.00 42.55 3.51
4289 4388 1.978455 TTGGCCAACACGAGGTCAGT 61.978 55.000 16.05 0.00 42.55 3.41
4310 4409 3.589881 GGTGGCGCTCATGCATCC 61.590 66.667 7.64 0.00 39.64 3.51
4311 4410 3.589881 GTGGCGCTCATGCATCCC 61.590 66.667 7.64 0.00 39.64 3.85
4312 4411 3.800833 TGGCGCTCATGCATCCCT 61.801 61.111 7.64 0.00 39.64 4.20
4315 4414 1.963338 GCGCTCATGCATCCCTACC 60.963 63.158 0.00 0.00 39.64 3.18
4316 4415 1.750930 CGCTCATGCATCCCTACCT 59.249 57.895 0.00 0.00 39.64 3.08
4317 4416 0.320247 CGCTCATGCATCCCTACCTC 60.320 60.000 0.00 0.00 39.64 3.85
4318 4417 1.055040 GCTCATGCATCCCTACCTCT 58.945 55.000 0.00 0.00 39.41 3.69
4319 4418 1.419387 GCTCATGCATCCCTACCTCTT 59.581 52.381 0.00 0.00 39.41 2.85
4320 4419 2.549778 GCTCATGCATCCCTACCTCTTC 60.550 54.545 0.00 0.00 39.41 2.87
4321 4420 2.038295 CTCATGCATCCCTACCTCTTCC 59.962 54.545 0.00 0.00 0.00 3.46
4322 4421 1.072965 CATGCATCCCTACCTCTTCCC 59.927 57.143 0.00 0.00 0.00 3.97
4323 4422 0.343372 TGCATCCCTACCTCTTCCCT 59.657 55.000 0.00 0.00 0.00 4.20
4324 4423 0.761802 GCATCCCTACCTCTTCCCTG 59.238 60.000 0.00 0.00 0.00 4.45
4325 4424 0.761802 CATCCCTACCTCTTCCCTGC 59.238 60.000 0.00 0.00 0.00 4.85
4326 4425 0.343372 ATCCCTACCTCTTCCCTGCA 59.657 55.000 0.00 0.00 0.00 4.41
4327 4426 0.325671 TCCCTACCTCTTCCCTGCAG 60.326 60.000 6.78 6.78 0.00 4.41
4328 4427 1.524482 CCTACCTCTTCCCTGCAGC 59.476 63.158 8.66 0.00 0.00 5.25
4329 4428 1.267574 CCTACCTCTTCCCTGCAGCA 61.268 60.000 8.66 0.00 0.00 4.41
4330 4429 0.835941 CTACCTCTTCCCTGCAGCAT 59.164 55.000 8.66 0.00 0.00 3.79
4331 4430 0.833287 TACCTCTTCCCTGCAGCATC 59.167 55.000 8.66 0.00 0.00 3.91
4332 4431 0.913451 ACCTCTTCCCTGCAGCATCT 60.913 55.000 8.66 0.00 0.00 2.90
4333 4432 0.179051 CCTCTTCCCTGCAGCATCTC 60.179 60.000 8.66 0.00 0.00 2.75
4334 4433 0.179051 CTCTTCCCTGCAGCATCTCC 60.179 60.000 8.66 0.00 0.00 3.71
4335 4434 0.911045 TCTTCCCTGCAGCATCTCCA 60.911 55.000 8.66 0.00 0.00 3.86
4336 4435 0.747283 CTTCCCTGCAGCATCTCCAC 60.747 60.000 8.66 0.00 0.00 4.02
4337 4436 2.124403 CCCTGCAGCATCTCCACC 60.124 66.667 8.66 0.00 0.00 4.61
4338 4437 2.672908 CCTGCAGCATCTCCACCA 59.327 61.111 8.66 0.00 0.00 4.17
4339 4438 1.748122 CCTGCAGCATCTCCACCAC 60.748 63.158 8.66 0.00 0.00 4.16
4340 4439 1.748122 CTGCAGCATCTCCACCACC 60.748 63.158 0.00 0.00 0.00 4.61
4341 4440 2.821366 GCAGCATCTCCACCACCG 60.821 66.667 0.00 0.00 0.00 4.94
4391 4490 4.792804 GGACCCTGCTGCTGCTCC 62.793 72.222 17.00 11.07 40.48 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 3.108289 CAGCGGTGCAGACAGACG 61.108 66.667 0.00 0.00 0.00 4.18
44 45 2.029844 GGACTTCAGCGGTGCAGAC 61.030 63.158 20.85 14.18 0.00 3.51
45 46 1.830587 ATGGACTTCAGCGGTGCAGA 61.831 55.000 20.85 0.00 38.32 4.26
46 47 0.108186 TATGGACTTCAGCGGTGCAG 60.108 55.000 12.74 12.74 38.32 4.41
47 48 0.541392 ATATGGACTTCAGCGGTGCA 59.459 50.000 10.38 1.63 39.17 4.57
48 49 0.940126 CATATGGACTTCAGCGGTGC 59.060 55.000 10.38 0.00 0.00 5.01
49 50 2.315925 ACATATGGACTTCAGCGGTG 57.684 50.000 8.67 8.67 0.00 4.94
50 51 2.632377 CAACATATGGACTTCAGCGGT 58.368 47.619 7.80 0.00 0.00 5.68
51 52 1.331756 GCAACATATGGACTTCAGCGG 59.668 52.381 7.80 0.00 0.00 5.52
52 53 1.331756 GGCAACATATGGACTTCAGCG 59.668 52.381 7.80 0.00 0.00 5.18
91 92 1.725641 TCAACAGTTGGCTGCTATCG 58.274 50.000 13.52 0.00 46.30 2.92
99 100 7.617041 AGTCTCTATTATTTCAACAGTTGGC 57.383 36.000 13.52 0.00 0.00 4.52
118 119 4.006319 AGCTGGCAAGTGAAATAAGTCTC 58.994 43.478 0.00 0.00 0.00 3.36
144 145 1.266175 GCTTCAGCCAATCATCCATCG 59.734 52.381 0.00 0.00 34.31 3.84
158 159 3.867771 GAGCCACTCGTGCTTCAG 58.132 61.111 0.00 0.00 39.69 3.02
188 189 7.938140 TGTATACTCCTGCAATAAAGCTTTT 57.062 32.000 18.47 2.49 34.99 2.27
190 191 7.282585 TGATGTATACTCCTGCAATAAAGCTT 58.717 34.615 4.17 0.00 34.99 3.74
196 197 4.592778 TGGCTGATGTATACTCCTGCAATA 59.407 41.667 19.71 9.43 0.00 1.90
212 213 2.512896 GGCTTCCGGATGGCTGAT 59.487 61.111 29.81 0.00 34.14 2.90
213 214 3.797353 GGGCTTCCGGATGGCTGA 61.797 66.667 33.46 7.44 34.14 4.26
214 215 3.801997 AGGGCTTCCGGATGGCTG 61.802 66.667 33.46 12.63 35.17 4.85
215 216 3.801997 CAGGGCTTCCGGATGGCT 61.802 66.667 33.46 21.19 35.17 4.75
216 217 2.837031 TTTCAGGGCTTCCGGATGGC 62.837 60.000 29.42 29.42 34.80 4.40
217 218 0.749454 CTTTCAGGGCTTCCGGATGG 60.749 60.000 18.22 9.71 34.80 3.51
218 219 0.253044 TCTTTCAGGGCTTCCGGATG 59.747 55.000 4.15 9.44 34.80 3.51
219 220 0.253327 GTCTTTCAGGGCTTCCGGAT 59.747 55.000 4.15 0.00 34.80 4.18
220 221 1.125093 TGTCTTTCAGGGCTTCCGGA 61.125 55.000 0.00 0.00 35.17 5.14
221 222 0.250727 TTGTCTTTCAGGGCTTCCGG 60.251 55.000 0.00 0.00 35.17 5.14
222 223 1.537202 CTTTGTCTTTCAGGGCTTCCG 59.463 52.381 0.00 0.00 35.17 4.30
223 224 2.554462 GTCTTTGTCTTTCAGGGCTTCC 59.446 50.000 0.00 0.00 0.00 3.46
224 225 3.481453 AGTCTTTGTCTTTCAGGGCTTC 58.519 45.455 0.00 0.00 0.00 3.86
225 226 3.584733 AGTCTTTGTCTTTCAGGGCTT 57.415 42.857 0.00 0.00 0.00 4.35
226 227 3.117888 TGAAGTCTTTGTCTTTCAGGGCT 60.118 43.478 0.00 0.00 0.00 5.19
227 228 3.214328 TGAAGTCTTTGTCTTTCAGGGC 58.786 45.455 0.00 0.00 0.00 5.19
228 229 7.693969 ATATTGAAGTCTTTGTCTTTCAGGG 57.306 36.000 0.00 0.00 0.00 4.45
229 230 9.442047 ACTATATTGAAGTCTTTGTCTTTCAGG 57.558 33.333 0.00 0.00 0.00 3.86
252 253 9.554395 TGTTCTATTCAGTCAACAATTCAACTA 57.446 29.630 0.00 0.00 0.00 2.24
270 271 6.716628 TCTCTTGAATGGCAACTTGTTCTATT 59.283 34.615 0.00 0.00 37.61 1.73
272 273 5.470098 GTCTCTTGAATGGCAACTTGTTCTA 59.530 40.000 0.00 0.00 37.61 2.10
284 285 3.319137 TCTTGTCCGTCTCTTGAATGG 57.681 47.619 0.00 0.00 0.00 3.16
290 291 0.959553 TCGCTTCTTGTCCGTCTCTT 59.040 50.000 0.00 0.00 0.00 2.85
296 297 0.098905 TCTCGATCGCTTCTTGTCCG 59.901 55.000 11.09 0.00 0.00 4.79
311 312 6.146837 ACATTTCTTCATGTCACTTTCTCTCG 59.853 38.462 0.00 0.00 31.26 4.04
319 320 4.074970 GGTCCACATTTCTTCATGTCACT 58.925 43.478 0.00 0.00 35.03 3.41
330 331 1.598701 GCTGGCCAGGTCCACATTTC 61.599 60.000 33.46 9.38 31.74 2.17
357 358 3.703052 TGAACGGAGGGAGTATTTCCTAC 59.297 47.826 0.00 0.00 45.98 3.18
387 388 9.699410 TCCATACTGAAATATCCAAAACATCTT 57.301 29.630 0.00 0.00 0.00 2.40
422 423 6.198966 GTGTGTTTGTTCACTCATTTCATTCC 59.801 38.462 0.00 0.00 38.90 3.01
440 441 9.373603 TGTATATAGACGCATTTTAGTGTGTTT 57.626 29.630 0.00 0.00 42.45 2.83
517 519 8.645730 TGTCGTTGATTTAGTACAACTTTGTA 57.354 30.769 0.00 0.00 42.53 2.41
551 553 4.735369 AGATGTTCTACTCCATCCGATCT 58.265 43.478 0.00 0.00 38.57 2.75
688 695 1.276989 CAATTTGGGCCACTCATTGCT 59.723 47.619 5.23 0.00 0.00 3.91
716 724 3.491766 ATAAGGTCCAGACTCCCAAGA 57.508 47.619 0.00 0.00 0.00 3.02
851 861 5.055265 TGTCCTTTTGTTGAGGGTGATAA 57.945 39.130 0.00 0.00 34.93 1.75
907 919 6.615726 AGGAACCAACTAGAGGAAGCAATATA 59.384 38.462 11.98 0.00 0.00 0.86
1161 1213 1.906574 ACGAAGGCACTCCCAGAAATA 59.093 47.619 0.00 0.00 38.49 1.40
1172 1224 4.215613 ACCAAATAGAGAAAACGAAGGCAC 59.784 41.667 0.00 0.00 0.00 5.01
1270 1322 4.741837 GCCATCCGCATATAGCATGACTAT 60.742 45.833 0.00 5.92 46.13 2.12
1271 1323 3.430790 GCCATCCGCATATAGCATGACTA 60.431 47.826 0.00 0.00 46.13 2.59
1491 1550 8.714906 ACAAGTAACCTATTAGCAGATACCAAT 58.285 33.333 0.00 0.00 0.00 3.16
1710 1769 1.065418 CCCCAGTCAGTCGCCTTAAAT 60.065 52.381 0.00 0.00 0.00 1.40
2141 2210 0.754472 AACAAGGGACGACTTCGGAA 59.246 50.000 3.30 0.00 44.95 4.30
2145 2214 1.226746 CACCAACAAGGGACGACTTC 58.773 55.000 0.00 0.00 43.89 3.01
2177 2246 2.262637 AGATAGAACGACCCAAACCCA 58.737 47.619 0.00 0.00 0.00 4.51
2380 2458 3.871594 ACCTCTACACAAAATATCGCTGC 59.128 43.478 0.00 0.00 0.00 5.25
2995 3081 5.512942 TTATTGGATCCACCTCTGTTCAA 57.487 39.130 15.91 0.00 39.86 2.69
3172 3259 1.614413 GACTGTCTCCACTTCCTCGTT 59.386 52.381 0.00 0.00 0.00 3.85
3315 3405 1.674962 GCCAGCTTGACCATCATTCTC 59.325 52.381 0.00 0.00 0.00 2.87
3492 3583 5.418840 TGTTTTGGATCCAAGAATAAGCTCC 59.581 40.000 25.69 8.81 37.24 4.70
3549 3647 8.206325 ACAGAATCTACTTATGCAAAGTGATG 57.794 34.615 18.57 12.89 28.76 3.07
3550 3648 7.223582 CGACAGAATCTACTTATGCAAAGTGAT 59.776 37.037 18.57 15.87 28.76 3.06
3574 3672 1.468914 CTCGATCAGACACTTGGACGA 59.531 52.381 0.00 0.00 0.00 4.20
3611 3709 6.696411 TCTGGACGAAATGCCAAAATAAAAT 58.304 32.000 0.00 0.00 32.95 1.82
3665 3763 3.893326 ACACATCTATACAGCAGCACA 57.107 42.857 0.00 0.00 0.00 4.57
3703 3801 3.601443 ACAAGGCTAGTGCTTACTGAG 57.399 47.619 0.00 0.00 39.59 3.35
3704 3802 4.527038 AGTTACAAGGCTAGTGCTTACTGA 59.473 41.667 0.00 0.00 39.59 3.41
3705 3803 4.627467 CAGTTACAAGGCTAGTGCTTACTG 59.373 45.833 0.00 0.00 39.59 2.74
3706 3804 4.527038 TCAGTTACAAGGCTAGTGCTTACT 59.473 41.667 0.00 0.00 39.59 2.24
3707 3805 4.817517 TCAGTTACAAGGCTAGTGCTTAC 58.182 43.478 0.00 0.00 39.59 2.34
3708 3806 5.677319 ATCAGTTACAAGGCTAGTGCTTA 57.323 39.130 0.00 0.00 39.59 3.09
3709 3807 4.559862 ATCAGTTACAAGGCTAGTGCTT 57.440 40.909 0.00 0.00 39.59 3.91
3733 3831 9.095065 TCTGTCTCTTTTTACTTTATTATCGGC 57.905 33.333 0.00 0.00 0.00 5.54
3794 3892 6.655078 AACTGGCTAACAAACAGATTGATT 57.345 33.333 0.00 0.00 41.85 2.57
3838 3936 5.255443 AGTTATTTTGGTGGGAAGGACCTAT 59.745 40.000 0.00 0.00 38.98 2.57
3916 4014 0.108186 CCCGCATGTGACTAGCTGAA 60.108 55.000 8.11 0.00 0.00 3.02
3929 4027 1.337384 TGATACACCAGAGCCCGCAT 61.337 55.000 0.00 0.00 0.00 4.73
3979 4077 3.691118 ACATGGACACACATCATGTTAGC 59.309 43.478 0.00 0.00 46.20 3.09
3989 4087 4.023279 GCAGTTGATTTACATGGACACACA 60.023 41.667 0.00 0.00 0.00 3.72
4052 4150 2.094130 CGTTAGAGGAGACTTTGTCCCC 60.094 54.545 0.00 0.00 44.43 4.81
4114 4213 0.916358 CATCAAGGGTCCAGGGTCCT 60.916 60.000 1.69 0.00 0.00 3.85
4131 4230 1.929494 TCCCCCTTCTATTTGTGGCAT 59.071 47.619 0.00 0.00 0.00 4.40
4164 4263 7.009179 ACCCATGTATGTATCTGTATTCCAG 57.991 40.000 0.00 0.00 42.97 3.86
4255 4354 1.066787 GGCCAACAGGAGTAGACAGAC 60.067 57.143 0.00 0.00 0.00 3.51
4256 4355 1.267121 GGCCAACAGGAGTAGACAGA 58.733 55.000 0.00 0.00 0.00 3.41
4257 4356 0.976641 TGGCCAACAGGAGTAGACAG 59.023 55.000 0.61 0.00 0.00 3.51
4258 4357 1.071699 GTTGGCCAACAGGAGTAGACA 59.928 52.381 37.95 1.78 40.84 3.41
4277 4376 2.134287 ACCAGCACTGACCTCGTGT 61.134 57.895 0.00 0.00 34.91 4.49
4288 4387 3.807538 CATGAGCGCCACCAGCAC 61.808 66.667 2.29 0.00 44.04 4.40
4310 4409 1.267574 TGCTGCAGGGAAGAGGTAGG 61.268 60.000 17.12 0.00 0.00 3.18
4311 4410 0.835941 ATGCTGCAGGGAAGAGGTAG 59.164 55.000 17.12 0.00 0.00 3.18
4312 4411 0.833287 GATGCTGCAGGGAAGAGGTA 59.167 55.000 17.12 0.00 0.00 3.08
4315 4414 0.179051 GGAGATGCTGCAGGGAAGAG 60.179 60.000 17.12 0.00 0.00 2.85
4316 4415 0.911045 TGGAGATGCTGCAGGGAAGA 60.911 55.000 17.12 0.00 0.00 2.87
4317 4416 0.747283 GTGGAGATGCTGCAGGGAAG 60.747 60.000 17.12 0.00 31.31 3.46
4318 4417 1.300963 GTGGAGATGCTGCAGGGAA 59.699 57.895 17.12 0.00 31.31 3.97
4319 4418 2.673200 GGTGGAGATGCTGCAGGGA 61.673 63.158 17.12 0.00 31.31 4.20
4320 4419 2.124403 GGTGGAGATGCTGCAGGG 60.124 66.667 17.12 0.00 31.31 4.45
4321 4420 1.748122 GTGGTGGAGATGCTGCAGG 60.748 63.158 17.12 0.00 31.31 4.85
4322 4421 1.748122 GGTGGTGGAGATGCTGCAG 60.748 63.158 10.11 10.11 31.31 4.41
4323 4422 2.352422 GGTGGTGGAGATGCTGCA 59.648 61.111 4.13 4.13 0.00 4.41
4324 4423 2.821366 CGGTGGTGGAGATGCTGC 60.821 66.667 0.00 0.00 0.00 5.25
4325 4424 2.124983 CCGGTGGTGGAGATGCTG 60.125 66.667 0.00 0.00 0.00 4.41
4326 4425 4.101448 GCCGGTGGTGGAGATGCT 62.101 66.667 1.90 0.00 0.00 3.79
4327 4426 4.101448 AGCCGGTGGTGGAGATGC 62.101 66.667 1.90 0.00 0.00 3.91
4328 4427 2.124983 CAGCCGGTGGTGGAGATG 60.125 66.667 1.90 0.00 36.33 2.90
4329 4428 4.101448 GCAGCCGGTGGTGGAGAT 62.101 66.667 1.90 0.00 40.37 2.75
4391 4490 1.402456 GGTGTAGCCGCGGTGATATAG 60.402 57.143 28.70 0.00 0.00 1.31


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

AutoCloner maintained by Alex Coulton.