Multiple sequence alignment - TraesCS7A01G307400

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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 TraesCS7A01G307400 chr7A 100.000 6755 0 0 1 6755 434733010 434739764 0.000000e+00 12475.0
1 TraesCS7A01G307400 chr7A 73.820 466 73 34 110 539 76972286 76972738 9.130000e-29 139.0
2 TraesCS7A01G307400 chr7A 74.636 343 64 16 446 783 436848842 436849166 5.500000e-26 130.0
3 TraesCS7A01G307400 chr7A 84.483 116 18 0 42 157 78500964 78501079 1.540000e-21 115.0
4 TraesCS7A01G307400 chr7A 82.787 122 18 3 3519 3638 85209406 85209286 9.270000e-19 106.0
5 TraesCS7A01G307400 chr7A 86.316 95 11 1 3526 3620 159698839 159698747 1.200000e-17 102.0
6 TraesCS7A01G307400 chr7A 84.091 88 9 5 116 199 434733086 434733172 5.620000e-11 80.5
7 TraesCS7A01G307400 chr7A 84.270 89 7 6 77 163 434733125 434733208 5.620000e-11 80.5
8 TraesCS7A01G307400 chr7D 96.694 6050 150 29 739 6755 386352805 386358837 0.000000e+00 10019.0
9 TraesCS7A01G307400 chr7D 84.150 347 22 12 41 386 386352465 386352779 8.510000e-79 305.0
10 TraesCS7A01G307400 chr7D 83.962 106 13 3 3526 3629 141360089 141359986 1.550000e-16 99.0
11 TraesCS7A01G307400 chr7D 100.000 38 0 0 2 39 386352397 386352434 3.380000e-08 71.3
12 TraesCS7A01G307400 chr7B 91.997 2824 154 35 40 2823 380505706 380508497 0.000000e+00 3897.0
13 TraesCS7A01G307400 chr7B 93.858 2198 103 17 3622 5811 380509627 380511800 0.000000e+00 3282.0
14 TraesCS7A01G307400 chr7B 91.989 749 49 7 5980 6723 380536708 380537450 0.000000e+00 1040.0
15 TraesCS7A01G307400 chr7B 94.246 643 25 5 2822 3455 380508566 380509205 0.000000e+00 972.0
16 TraesCS7A01G307400 chr7B 85.965 171 16 4 5807 5976 380511828 380511991 6.960000e-40 176.0
17 TraesCS7A01G307400 chr7B 81.356 118 17 3 40 156 663112472 663112585 2.590000e-14 91.6
18 TraesCS7A01G307400 chr1D 80.045 441 53 22 359 780 235581659 235581235 1.840000e-75 294.0
19 TraesCS7A01G307400 chr1D 74.148 704 109 39 131 784 347302549 347303229 2.450000e-54 224.0
20 TraesCS7A01G307400 chr4A 78.638 426 78 8 348 773 596829170 596829582 3.100000e-68 270.0
21 TraesCS7A01G307400 chr4A 77.200 250 34 7 56 305 596828863 596829089 2.560000e-24 124.0
22 TraesCS7A01G307400 chr3A 74.711 779 107 55 40 783 635539776 635539053 1.440000e-66 265.0
23 TraesCS7A01G307400 chr4D 76.128 532 64 33 40 550 7470784 7470295 3.170000e-53 220.0
24 TraesCS7A01G307400 chr1A 79.279 333 48 9 387 710 163377299 163377619 5.310000e-51 213.0
25 TraesCS7A01G307400 chr2A 80.632 253 33 7 401 645 167945647 167945403 1.500000e-41 182.0
26 TraesCS7A01G307400 chr2A 80.986 142 15 8 154 283 592816163 592816304 1.200000e-17 102.0
27 TraesCS7A01G307400 chr2A 83.333 102 17 0 191 292 22195438 22195337 2.010000e-15 95.3
28 TraesCS7A01G307400 chr2D 75.926 432 56 28 359 781 631169070 631169462 1.940000e-40 178.0
29 TraesCS7A01G307400 chr2D 72.658 790 110 61 41 783 621451705 621450975 1.510000e-36 165.0
30 TraesCS7A01G307400 chr2D 72.849 744 103 49 113 783 650236105 650236822 5.420000e-36 163.0
31 TraesCS7A01G307400 chr2D 78.846 260 32 14 40 299 605383948 605383712 3.260000e-33 154.0
32 TraesCS7A01G307400 chr2D 86.735 98 13 0 3523 3620 564920656 564920753 7.160000e-20 110.0
33 TraesCS7A01G307400 chr3B 79.336 271 40 8 402 664 481317773 481318035 6.960000e-40 176.0
34 TraesCS7A01G307400 chr3B 74.654 434 67 24 359 783 160685973 160686372 1.170000e-32 152.0
35 TraesCS7A01G307400 chr3B 85.841 113 12 2 40 152 180273859 180273967 4.280000e-22 117.0
36 TraesCS7A01G307400 chr3B 85.366 82 11 1 116 196 180273893 180273974 4.340000e-12 84.2
37 TraesCS7A01G307400 chr3B 80.952 105 12 2 430 534 447002509 447002605 7.260000e-10 76.8
38 TraesCS7A01G307400 chr3D 79.365 252 29 10 40 291 496370168 496369940 9.070000e-34 156.0
39 TraesCS7A01G307400 chr3D 86.420 81 11 0 225 305 532763730 532763650 9.330000e-14 89.8
40 TraesCS7A01G307400 chr5A 75.287 348 61 4 321 651 437023696 437024035 7.060000e-30 143.0
41 TraesCS7A01G307400 chr5A 81.633 98 14 4 3525 3620 429513002 429512907 2.020000e-10 78.7
42 TraesCS7A01G307400 chr5D 75.445 281 42 11 401 669 106685500 106685765 1.990000e-20 111.0
43 TraesCS7A01G307400 chr6B 85.577 104 11 4 3520 3620 530560358 530560460 9.270000e-19 106.0
44 TraesCS7A01G307400 chr1B 89.610 77 8 0 318 394 662210108 662210184 1.550000e-16 99.0
45 TraesCS7A01G307400 chr1B 77.419 124 20 5 404 527 645533109 645533224 4.370000e-07 67.6
46 TraesCS7A01G307400 chrUn 83.495 103 13 2 3526 3626 70193293 70193193 7.210000e-15 93.5
47 TraesCS7A01G307400 chr2B 84.211 95 11 3 3526 3620 622914013 622914103 9.330000e-14 89.8


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 TraesCS7A01G307400 chr7A 434733010 434739764 6754 False 12475.00 12475 100.000000 1 6755 1 chr7A.!!$F3 6754
1 TraesCS7A01G307400 chr7D 386352397 386358837 6440 False 3465.10 10019 93.614667 2 6755 3 chr7D.!!$F1 6753
2 TraesCS7A01G307400 chr7B 380505706 380511991 6285 False 2081.75 3897 91.516500 40 5976 4 chr7B.!!$F3 5936
3 TraesCS7A01G307400 chr7B 380536708 380537450 742 False 1040.00 1040 91.989000 5980 6723 1 chr7B.!!$F1 743
4 TraesCS7A01G307400 chr1D 347302549 347303229 680 False 224.00 224 74.148000 131 784 1 chr1D.!!$F1 653
5 TraesCS7A01G307400 chr3A 635539053 635539776 723 True 265.00 265 74.711000 40 783 1 chr3A.!!$R1 743

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
182 213 0.178861 AACCCATCCACCACCTCTCT 60.179 55.000 0.00 0.0 0.00 3.10 F
339 413 0.415429 AGGCAGAGGAGGAAGAGGAA 59.585 55.000 0.00 0.0 0.00 3.36 F
1381 1510 0.036164 ATGGCGTTAGGTTCAGCACA 59.964 50.000 0.00 0.0 0.00 4.57 F
1382 1511 0.036164 TGGCGTTAGGTTCAGCACAT 59.964 50.000 0.00 0.0 0.00 3.21 F
2841 3064 0.615827 AGCAAGAAAAGGGGCCATCC 60.616 55.000 4.39 0.0 0.00 3.51 F
3675 4257 3.576078 TGCTTTCTCCCTTTTGACTGA 57.424 42.857 0.00 0.0 0.00 3.41 F
5055 5645 1.609072 GCAGAAACCCTCAACAAGGTC 59.391 52.381 0.00 0.0 44.56 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1077 1204 0.672401 GCTTGTTCGGATCGGTTCCA 60.672 55.000 5.97 0.0 45.78 3.53 R
2241 2382 0.984230 TTCCTGCCCTGTAGTTGAGG 59.016 55.000 0.00 0.0 0.00 3.86 R
2748 2901 0.179073 ATCTCACTGGGCGTGTATGC 60.179 55.000 0.00 0.0 44.16 3.14 R
2905 3129 1.192428 AGATACGGTTCCAGGGTCAC 58.808 55.000 0.00 0.0 0.00 3.67 R
4565 5149 1.271054 ACCTCGAGCAAACTGAGCAAT 60.271 47.619 6.99 0.0 0.00 3.56 R
5306 5896 0.924090 GGACAACATCTCGCATCGAC 59.076 55.000 0.00 0.0 0.00 4.20 R
6474 7101 1.063616 CTCATCGTCGGCTTCTCGTTA 59.936 52.381 0.00 0.0 0.00 3.18 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
53 83 1.299976 GTGACCCGAGGCCAAATCT 59.700 57.895 5.01 0.00 0.00 2.40
69 99 4.881850 CCAAATCTGGCTATTTAAGTCGGT 59.118 41.667 0.00 0.00 37.47 4.69
101 132 0.341961 ACCCTAGCCACATCCACCTA 59.658 55.000 0.00 0.00 0.00 3.08
152 183 2.120718 ACCACCTCTCTCCCGCTT 59.879 61.111 0.00 0.00 0.00 4.68
157 188 3.452786 CTCTCTCCCGCTTCGCCA 61.453 66.667 0.00 0.00 0.00 5.69
158 189 3.423162 CTCTCTCCCGCTTCGCCAG 62.423 68.421 0.00 0.00 0.00 4.85
172 203 3.727258 CCAGCCCGAACCCATCCA 61.727 66.667 0.00 0.00 0.00 3.41
173 204 2.438434 CAGCCCGAACCCATCCAC 60.438 66.667 0.00 0.00 0.00 4.02
174 205 3.728373 AGCCCGAACCCATCCACC 61.728 66.667 0.00 0.00 0.00 4.61
175 206 4.041762 GCCCGAACCCATCCACCA 62.042 66.667 0.00 0.00 0.00 4.17
176 207 2.045340 CCCGAACCCATCCACCAC 60.045 66.667 0.00 0.00 0.00 4.16
177 208 2.045340 CCGAACCCATCCACCACC 60.045 66.667 0.00 0.00 0.00 4.61
178 209 2.602676 CCGAACCCATCCACCACCT 61.603 63.158 0.00 0.00 0.00 4.00
179 210 1.078426 CGAACCCATCCACCACCTC 60.078 63.158 0.00 0.00 0.00 3.85
180 211 1.553690 CGAACCCATCCACCACCTCT 61.554 60.000 0.00 0.00 0.00 3.69
181 212 0.253327 GAACCCATCCACCACCTCTC 59.747 60.000 0.00 0.00 0.00 3.20
182 213 0.178861 AACCCATCCACCACCTCTCT 60.179 55.000 0.00 0.00 0.00 3.10
183 214 0.618968 ACCCATCCACCACCTCTCTC 60.619 60.000 0.00 0.00 0.00 3.20
184 215 1.341156 CCCATCCACCACCTCTCTCC 61.341 65.000 0.00 0.00 0.00 3.71
185 216 1.341156 CCATCCACCACCTCTCTCCC 61.341 65.000 0.00 0.00 0.00 4.30
186 217 1.381872 ATCCACCACCTCTCTCCCG 60.382 63.158 0.00 0.00 0.00 5.14
187 218 3.775654 CCACCACCTCTCTCCCGC 61.776 72.222 0.00 0.00 0.00 6.13
188 219 2.681778 CACCACCTCTCTCCCGCT 60.682 66.667 0.00 0.00 0.00 5.52
189 220 2.363147 ACCACCTCTCTCCCGCTC 60.363 66.667 0.00 0.00 0.00 5.03
252 284 1.226974 GCTATGCTCACGCCGAAGA 60.227 57.895 0.00 0.00 34.43 2.87
339 413 0.415429 AGGCAGAGGAGGAAGAGGAA 59.585 55.000 0.00 0.00 0.00 3.36
342 416 1.625818 GCAGAGGAGGAAGAGGAACAA 59.374 52.381 0.00 0.00 0.00 2.83
433 531 3.957435 ATGGAGGACGTGGAGGCGA 62.957 63.158 0.00 0.00 35.59 5.54
492 590 2.407340 AGGGTATCCTGGAGTCCATC 57.593 55.000 13.56 1.45 42.98 3.51
493 591 0.969894 GGGTATCCTGGAGTCCATCG 59.030 60.000 13.56 6.18 30.82 3.84
516 622 2.386811 TCCATCCAGGATGAGGCCTATA 59.613 50.000 28.79 0.00 43.07 1.31
534 640 2.057137 TATGGAGGCCAATTGACAGC 57.943 50.000 5.01 1.43 36.95 4.40
539 645 2.097825 GAGGCCAATTGACAGCTCATT 58.902 47.619 5.01 0.00 0.00 2.57
561 682 1.594293 CAGGAACACCGACACGCTT 60.594 57.895 0.00 0.00 0.00 4.68
585 706 1.393603 ATGAGATCGAAGCGGAGACA 58.606 50.000 0.00 0.00 0.00 3.41
591 712 1.153765 CGAAGCGGAGACAGATGCA 60.154 57.895 0.00 0.00 0.00 3.96
670 791 1.686325 GCCGGGCAAGGAGATAGTGA 61.686 60.000 15.62 0.00 0.00 3.41
760 881 9.748708 GTTTGCATGCTTTTATATGGATCTAAA 57.251 29.630 20.33 1.93 0.00 1.85
784 905 2.076189 TCTAGTATGGGGTATCCGGGT 58.924 52.381 0.00 0.00 38.76 5.28
785 906 3.268146 TCTAGTATGGGGTATCCGGGTA 58.732 50.000 0.00 0.00 38.76 3.69
822 944 1.633432 AGGGATCGGATTTGTTGTCCA 59.367 47.619 0.00 0.00 35.41 4.02
825 947 2.358898 GGATCGGATTTGTTGTCCATGG 59.641 50.000 4.97 4.97 35.41 3.66
827 949 2.870175 TCGGATTTGTTGTCCATGGTT 58.130 42.857 12.58 0.00 35.41 3.67
858 980 2.663808 TGCATTTGAAACTCATGCACG 58.336 42.857 1.95 0.00 37.44 5.34
875 998 2.421073 GCACGATTACAAAACTACCCCC 59.579 50.000 0.00 0.00 0.00 5.40
925 1049 5.131142 TCCTGACCTGTCTTTTCTCTTCTTT 59.869 40.000 0.00 0.00 0.00 2.52
930 1057 6.427441 ACCTGTCTTTTCTCTTCTTTTTCCT 58.573 36.000 0.00 0.00 0.00 3.36
963 1090 5.376854 TTGCTTTATTCTCAACAGGAAGC 57.623 39.130 0.00 0.00 38.69 3.86
1151 1278 1.115467 CATTCAGGTAGTCCGCTCCT 58.885 55.000 0.00 0.00 39.05 3.69
1164 1291 4.282703 AGTCCGCTCCTGTAAGTTTCTTTA 59.717 41.667 0.00 0.00 0.00 1.85
1165 1292 4.992951 GTCCGCTCCTGTAAGTTTCTTTAA 59.007 41.667 0.00 0.00 0.00 1.52
1166 1293 5.642491 GTCCGCTCCTGTAAGTTTCTTTAAT 59.358 40.000 0.00 0.00 0.00 1.40
1167 1294 6.815142 GTCCGCTCCTGTAAGTTTCTTTAATA 59.185 38.462 0.00 0.00 0.00 0.98
1378 1507 4.428615 TTTTAATGGCGTTAGGTTCAGC 57.571 40.909 0.00 0.00 0.00 4.26
1380 1509 1.165270 AATGGCGTTAGGTTCAGCAC 58.835 50.000 0.00 0.00 0.00 4.40
1381 1510 0.036164 ATGGCGTTAGGTTCAGCACA 59.964 50.000 0.00 0.00 0.00 4.57
1382 1511 0.036164 TGGCGTTAGGTTCAGCACAT 59.964 50.000 0.00 0.00 0.00 3.21
1509 1650 4.957684 ATCCCCCAAATCTTAGTACTCG 57.042 45.455 0.00 0.00 0.00 4.18
1549 1690 3.743567 AAACTACTGTAGAGAGTCGCG 57.256 47.619 21.01 0.00 0.00 5.87
2077 2218 4.568592 GGGGTTTCTGAAGGTCTGATCATT 60.569 45.833 0.00 0.00 0.00 2.57
2191 2332 1.213182 AGTAGCTCGAGGAGGTCATCA 59.787 52.381 15.58 0.00 40.94 3.07
2241 2382 0.668706 ACATGTGCAGAGCTGTCGAC 60.669 55.000 9.11 9.11 0.00 4.20
2376 2517 4.189231 GCGTACAAGTATGTTCCCTTGAT 58.811 43.478 6.41 0.00 40.36 2.57
2396 2541 7.992033 CCTTGATCTTTCTCTATTCTCATGGTT 59.008 37.037 0.00 0.00 0.00 3.67
2513 2658 5.003804 GGTTCTAAAATGAAGCTCCTGTCA 58.996 41.667 0.00 0.00 40.19 3.58
2515 2660 6.823689 GGTTCTAAAATGAAGCTCCTGTCATA 59.176 38.462 0.00 0.00 40.19 2.15
2659 2812 6.378280 ACTGGAGAAAATAATGATGGTTGGTC 59.622 38.462 0.00 0.00 0.00 4.02
2664 2817 8.877864 AGAAAATAATGATGGTTGGTCTGTAA 57.122 30.769 0.00 0.00 0.00 2.41
2685 2838 8.389779 TGTAATAGAAAGAGAAAATGCACACA 57.610 30.769 0.00 0.00 0.00 3.72
2689 2842 9.598517 AATAGAAAGAGAAAATGCACACAAAAA 57.401 25.926 0.00 0.00 0.00 1.94
2748 2901 5.178797 AGTGAAGGATAGGAAAACATGTCG 58.821 41.667 0.00 0.00 0.00 4.35
2834 3057 8.360390 GGACCATAAATATTAGCAAGAAAAGGG 58.640 37.037 0.00 0.00 0.00 3.95
2841 3064 0.615827 AGCAAGAAAAGGGGCCATCC 60.616 55.000 4.39 0.00 0.00 3.51
3256 3481 3.773119 AGGTCTTACTTCTTGGGCGATTA 59.227 43.478 0.00 0.00 0.00 1.75
3427 3659 5.321102 ACAGTAATTACTTGGGCACATTCA 58.679 37.500 15.60 0.00 33.46 2.57
3562 4144 7.973944 GTCCTAATTAAATGTTGCTGGTTTAGG 59.026 37.037 0.00 0.00 36.22 2.69
3598 4180 4.530710 AAGTTGTACTAATCCAGCGACA 57.469 40.909 0.00 0.00 0.00 4.35
3611 4193 6.992063 ATCCAGCGACAATTAATATGGATC 57.008 37.500 0.00 0.00 41.11 3.36
3613 4195 4.093408 CCAGCGACAATTAATATGGATCGG 59.907 45.833 0.00 0.00 0.00 4.18
3620 4202 4.762289 ATTAATATGGATCGGAGGGAGC 57.238 45.455 0.00 0.00 0.00 4.70
3674 4256 3.822735 TGATGCTTTCTCCCTTTTGACTG 59.177 43.478 0.00 0.00 0.00 3.51
3675 4257 3.576078 TGCTTTCTCCCTTTTGACTGA 57.424 42.857 0.00 0.00 0.00 3.41
3676 4258 4.104383 TGCTTTCTCCCTTTTGACTGAT 57.896 40.909 0.00 0.00 0.00 2.90
3677 4259 5.241403 TGCTTTCTCCCTTTTGACTGATA 57.759 39.130 0.00 0.00 0.00 2.15
3678 4260 5.248640 TGCTTTCTCCCTTTTGACTGATAG 58.751 41.667 0.00 0.00 0.00 2.08
3679 4261 5.221925 TGCTTTCTCCCTTTTGACTGATAGT 60.222 40.000 0.00 0.00 0.00 2.12
3962 4545 6.542821 TGGGATTTGAGGGTAAATATAGCTG 58.457 40.000 0.00 0.00 30.78 4.24
4054 4637 7.814587 TCATGATCCATGATGTAATACGAAGAC 59.185 37.037 5.61 0.00 44.60 3.01
4295 4878 8.630917 GCACCTCTGTATTCTTAACTCATACTA 58.369 37.037 0.00 0.00 0.00 1.82
4307 4891 4.650754 ACTCATACTACCGACATTGGTC 57.349 45.455 0.00 0.00 42.62 4.02
4407 4991 6.500589 TTTGTTCCTTATCTCAGATAGGGG 57.499 41.667 20.15 14.02 0.00 4.79
4466 5050 8.414778 GTCTAGAAGCATAACCAATGTAGTAGT 58.585 37.037 0.00 0.00 37.93 2.73
4565 5149 7.364232 GCCTAAGCTTATAAGGAGATATGAGCA 60.364 40.741 16.52 0.00 43.58 4.26
5055 5645 1.609072 GCAGAAACCCTCAACAAGGTC 59.391 52.381 0.00 0.00 44.56 3.85
5087 5677 4.350368 TGTTGAGCTTGTAAGGATGTCA 57.650 40.909 0.00 0.00 0.00 3.58
5147 5737 7.338710 ACACTATGGTTGTAAATGCTGACTAT 58.661 34.615 0.00 0.00 0.00 2.12
5306 5896 2.506438 GTCTCCCGAAAGCGACCG 60.506 66.667 0.00 0.00 40.82 4.79
5344 5934 3.717294 GGCACTGATCCGGGTGGT 61.717 66.667 0.00 0.00 36.30 4.16
5384 5974 2.105993 CAGGAATCATCATGGCAGGAGA 59.894 50.000 8.21 5.92 33.78 3.71
5435 6025 2.106338 TGTTGACCTTGAGGCATCAGAA 59.894 45.455 0.00 0.00 39.32 3.02
5526 6116 6.801862 CGTCTGATGGAAACTAACCAAAATTC 59.198 38.462 0.00 0.00 40.93 2.17
5796 6386 5.725110 CACTAGATGATGTGCTGGTTTAC 57.275 43.478 0.00 0.00 0.00 2.01
5848 6470 3.225104 AGCAAAGATCTTCTGTTTGGCA 58.775 40.909 8.78 0.00 38.29 4.92
5915 6537 3.119209 TGCATAGCGAAAATGGAAATGCA 60.119 39.130 3.15 3.15 44.16 3.96
5978 6602 5.929992 ACTATCAGACAAAATTCGTTCGGAA 59.070 36.000 0.00 0.00 39.42 4.30
6010 6634 7.982354 ACTACTTTGAGCTATTTGATACCACTC 59.018 37.037 0.00 0.00 0.00 3.51
6096 6720 4.318263 GCATTCACAACAAAACAGTGATGC 60.318 41.667 0.00 0.00 41.42 3.91
6145 6769 2.330231 TGCGCAACTTTGATACAAGC 57.670 45.000 8.16 0.00 0.00 4.01
6474 7101 3.988678 ATGGCCCCAGCAAGCAGT 61.989 61.111 0.00 0.00 42.56 4.40
6498 7125 1.139734 GAAGCCGACGATGAGAGCA 59.860 57.895 0.00 0.00 0.00 4.26
6506 7133 3.497118 CGACGATGAGAGCAATCCTATC 58.503 50.000 0.00 0.00 32.38 2.08
6670 7297 2.945008 TCTCTGGCTTAATGAAATGGCG 59.055 45.455 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.198236 GACGTTCGTCGGACCACCA 62.198 63.158 9.50 0.00 44.69 4.17
53 83 3.255725 CACGAACCGACTTAAATAGCCA 58.744 45.455 0.00 0.00 0.00 4.75
69 99 1.152074 TAGGGTTGGGGGACACGAA 60.152 57.895 0.00 0.00 0.00 3.85
157 188 3.728373 GGTGGATGGGTTCGGGCT 61.728 66.667 0.00 0.00 0.00 5.19
158 189 4.041762 TGGTGGATGGGTTCGGGC 62.042 66.667 0.00 0.00 0.00 6.13
159 190 2.045340 GTGGTGGATGGGTTCGGG 60.045 66.667 0.00 0.00 0.00 5.14
161 192 1.078426 GAGGTGGTGGATGGGTTCG 60.078 63.158 0.00 0.00 0.00 3.95
162 193 0.253327 GAGAGGTGGTGGATGGGTTC 59.747 60.000 0.00 0.00 0.00 3.62
163 194 0.178861 AGAGAGGTGGTGGATGGGTT 60.179 55.000 0.00 0.00 0.00 4.11
164 195 0.618968 GAGAGAGGTGGTGGATGGGT 60.619 60.000 0.00 0.00 0.00 4.51
166 197 1.341156 GGGAGAGAGGTGGTGGATGG 61.341 65.000 0.00 0.00 0.00 3.51
167 198 1.680522 CGGGAGAGAGGTGGTGGATG 61.681 65.000 0.00 0.00 0.00 3.51
168 199 1.381872 CGGGAGAGAGGTGGTGGAT 60.382 63.158 0.00 0.00 0.00 3.41
169 200 2.037367 CGGGAGAGAGGTGGTGGA 59.963 66.667 0.00 0.00 0.00 4.02
170 201 3.775654 GCGGGAGAGAGGTGGTGG 61.776 72.222 0.00 0.00 0.00 4.61
171 202 2.681778 AGCGGGAGAGAGGTGGTG 60.682 66.667 0.00 0.00 0.00 4.17
172 203 2.363147 GAGCGGGAGAGAGGTGGT 60.363 66.667 0.00 0.00 0.00 4.16
173 204 3.151022 GGAGCGGGAGAGAGGTGG 61.151 72.222 0.00 0.00 0.00 4.61
174 205 3.522731 CGGAGCGGGAGAGAGGTG 61.523 72.222 0.00 0.00 0.00 4.00
213 245 4.288626 AGCATAGGTGGTCTTCTTTTACCA 59.711 41.667 0.00 0.00 43.47 3.25
216 248 6.055588 GCATAGCATAGGTGGTCTTCTTTTA 58.944 40.000 0.00 0.00 37.28 1.52
252 284 0.694771 TGCTCAATCTGGAACTGGCT 59.305 50.000 0.00 0.00 0.00 4.75
298 330 4.489795 CTGCGATGCGTGCGACAC 62.490 66.667 0.00 0.00 34.24 3.67
319 393 0.032615 TCCTCTTCCTCCTCTGCCTC 60.033 60.000 0.00 0.00 0.00 4.70
339 413 3.883744 CTTCGGAGCCGGCTGTTGT 62.884 63.158 38.41 10.09 40.25 3.32
477 575 1.480683 GGACCGATGGACTCCAGGATA 60.481 57.143 9.84 0.00 36.75 2.59
486 584 1.048724 TCCTGGATGGACCGATGGAC 61.049 60.000 0.00 0.00 40.56 4.02
487 585 1.313129 TCCTGGATGGACCGATGGA 59.687 57.895 0.00 0.00 40.56 3.41
488 586 3.970332 TCCTGGATGGACCGATGG 58.030 61.111 0.00 0.00 40.56 3.51
516 622 0.333993 AGCTGTCAATTGGCCTCCAT 59.666 50.000 7.75 0.00 31.53 3.41
527 633 0.674581 CCTGCCGAATGAGCTGTCAA 60.675 55.000 0.00 0.00 35.88 3.18
528 634 1.078918 CCTGCCGAATGAGCTGTCA 60.079 57.895 0.00 0.00 37.02 3.58
534 640 2.471255 GGTGTTCCTGCCGAATGAG 58.529 57.895 0.00 0.00 31.67 2.90
561 682 3.119137 TCTCCGCTTCGATCTCATTGAAA 60.119 43.478 0.00 0.00 32.50 2.69
591 712 2.042537 TCCTCCGCATCTGCCTCT 60.043 61.111 0.00 0.00 37.91 3.69
634 755 1.451936 GCTCCGAATACATGGGCCT 59.548 57.895 4.53 0.00 0.00 5.19
635 756 1.600916 GGCTCCGAATACATGGGCC 60.601 63.158 0.00 0.00 35.43 5.80
670 791 3.947834 CCCTAATCTTCGCCAGAAATGTT 59.052 43.478 0.00 0.00 35.71 2.71
714 835 9.225436 TGCAAACAATAGAATTCATGTACTACA 57.775 29.630 8.44 4.64 0.00 2.74
729 850 9.701098 ATCCATATAAAAGCATGCAAACAATAG 57.299 29.630 21.98 3.83 0.00 1.73
760 881 4.158015 CCGGATACCCCATACTAGAAACT 58.842 47.826 0.00 0.00 34.14 2.66
784 905 1.342555 CTCAAACGTCCGCGAACATA 58.657 50.000 8.23 0.00 42.00 2.29
785 906 1.289109 CCTCAAACGTCCGCGAACAT 61.289 55.000 8.23 0.00 42.00 2.71
858 980 3.021695 GGCTGGGGGTAGTTTTGTAATC 58.978 50.000 0.00 0.00 0.00 1.75
875 998 1.636003 AGGAGAAAAAGGTAGGGGCTG 59.364 52.381 0.00 0.00 0.00 4.85
925 1049 4.817318 AAGCAAACAAAACAGGAGGAAA 57.183 36.364 0.00 0.00 0.00 3.13
930 1057 7.106439 TGAGAATAAAGCAAACAAAACAGGA 57.894 32.000 0.00 0.00 0.00 3.86
963 1090 4.407496 AAGACGACTTTCGAGAGTGTAG 57.593 45.455 14.11 7.23 43.74 2.74
1077 1204 0.672401 GCTTGTTCGGATCGGTTCCA 60.672 55.000 5.97 0.00 45.78 3.53
1081 1208 2.813908 GCGCTTGTTCGGATCGGT 60.814 61.111 0.00 0.00 0.00 4.69
1164 1291 9.942850 AATCCAAAATCAAGAAACCGAATTATT 57.057 25.926 0.00 0.00 0.00 1.40
1165 1292 9.369904 CAATCCAAAATCAAGAAACCGAATTAT 57.630 29.630 0.00 0.00 0.00 1.28
1166 1293 7.816995 CCAATCCAAAATCAAGAAACCGAATTA 59.183 33.333 0.00 0.00 0.00 1.40
1167 1294 6.650390 CCAATCCAAAATCAAGAAACCGAATT 59.350 34.615 0.00 0.00 0.00 2.17
1378 1507 3.362986 CGTCAACTTCCACTTCGAATGTG 60.363 47.826 16.20 16.20 35.39 3.21
1380 1509 2.411547 GCGTCAACTTCCACTTCGAATG 60.412 50.000 0.00 0.00 0.00 2.67
1381 1510 1.798813 GCGTCAACTTCCACTTCGAAT 59.201 47.619 0.00 0.00 0.00 3.34
1382 1511 1.214367 GCGTCAACTTCCACTTCGAA 58.786 50.000 0.00 0.00 0.00 3.71
1549 1690 6.094048 TGCTATGAAACAACTGAAGAATAGCC 59.906 38.462 8.41 0.00 40.18 3.93
2030 2171 4.402616 TCATTCTCCCCCAATTCAGTTT 57.597 40.909 0.00 0.00 0.00 2.66
2191 2332 2.426023 GCGCGGATGGGGATAGTT 59.574 61.111 8.83 0.00 0.00 2.24
2241 2382 0.984230 TTCCTGCCCTGTAGTTGAGG 59.016 55.000 0.00 0.00 0.00 3.86
2376 2517 6.053632 TGCAACCATGAGAATAGAGAAAGA 57.946 37.500 0.00 0.00 0.00 2.52
2513 2658 6.217693 AGTCCAAAAGAGGATAACCAACCTAT 59.782 38.462 0.00 0.00 40.42 2.57
2515 2660 4.354087 AGTCCAAAAGAGGATAACCAACCT 59.646 41.667 0.00 0.00 40.42 3.50
2622 2775 0.914417 TCTCCAGTTCCCACCATCCC 60.914 60.000 0.00 0.00 0.00 3.85
2659 2812 8.506437 TGTGTGCATTTTCTCTTTCTATTACAG 58.494 33.333 0.00 0.00 0.00 2.74
2689 2842 9.707957 TCTCTCTAAAGAAGATCAGGTAGAATT 57.292 33.333 0.00 0.00 32.41 2.17
2709 2862 4.217550 CCTTCACTCTCGTTTCTTCTCTCT 59.782 45.833 0.00 0.00 0.00 3.10
2722 2875 6.410540 ACATGTTTTCCTATCCTTCACTCTC 58.589 40.000 0.00 0.00 0.00 3.20
2723 2876 6.380079 ACATGTTTTCCTATCCTTCACTCT 57.620 37.500 0.00 0.00 0.00 3.24
2748 2901 0.179073 ATCTCACTGGGCGTGTATGC 60.179 55.000 0.00 0.00 44.16 3.14
2834 3057 4.998051 TGATTTTCCCTATTAGGATGGCC 58.002 43.478 11.52 0.00 37.67 5.36
2905 3129 1.192428 AGATACGGTTCCAGGGTCAC 58.808 55.000 0.00 0.00 0.00 3.67
3196 3421 1.708341 AATTACCAGGCATGCCCATC 58.292 50.000 33.14 8.47 36.58 3.51
3379 3611 7.675962 AAGGAGTGTTATTACAAATACGCAA 57.324 32.000 0.00 0.00 35.69 4.85
3427 3659 5.124457 CAGAGTTATGGTAGCAACAAAGCAT 59.876 40.000 0.00 0.00 37.56 3.79
3598 4180 4.536090 TGCTCCCTCCGATCCATATTAATT 59.464 41.667 0.00 0.00 0.00 1.40
3611 4193 2.431057 ACTGTAATTACTGCTCCCTCCG 59.569 50.000 19.14 0.00 0.00 4.63
3613 4195 5.112686 CAAGACTGTAATTACTGCTCCCTC 58.887 45.833 19.14 10.74 0.00 4.30
3620 4202 8.882736 TGATGTATTGCAAGACTGTAATTACTG 58.117 33.333 23.50 17.99 38.61 2.74
3677 4259 8.294577 GGTTATTTTACCGAGTGATCAAAAACT 58.705 33.333 0.00 0.00 0.00 2.66
3678 4260 8.077386 TGGTTATTTTACCGAGTGATCAAAAAC 58.923 33.333 0.00 0.00 41.28 2.43
3679 4261 8.077386 GTGGTTATTTTACCGAGTGATCAAAAA 58.923 33.333 0.00 0.00 41.28 1.94
3841 4424 4.098501 TGTGATACTCTGGCTGTAGATGTG 59.901 45.833 0.00 0.00 0.00 3.21
3962 4545 2.421529 CCAACCCCCTAGCAACATCTAC 60.422 54.545 0.00 0.00 0.00 2.59
4054 4637 9.167311 ACTAAAGTTAAGCCAGATGAAGTAATG 57.833 33.333 0.00 0.00 0.00 1.90
4163 4746 8.858003 ACTATGACAAATTACAGAGATGTACG 57.142 34.615 0.00 0.00 0.00 3.67
4249 4832 6.491403 AGGTGCAAACTGAGAGACAAATAATT 59.509 34.615 0.00 0.00 0.00 1.40
4307 4891 5.605534 AGCTGTATGCAGGATAAAGTACAG 58.394 41.667 13.03 13.14 45.94 2.74
4466 5050 8.856153 TTTCTTTGGCATATTCAGTAAGTACA 57.144 30.769 0.00 0.00 0.00 2.90
4493 5077 5.600696 AGCAAAGAATGTTCCGTGATTTTT 58.399 33.333 0.00 0.00 0.00 1.94
4494 5078 5.200368 AGCAAAGAATGTTCCGTGATTTT 57.800 34.783 0.00 0.00 0.00 1.82
4495 5079 4.853924 AGCAAAGAATGTTCCGTGATTT 57.146 36.364 0.00 0.00 0.00 2.17
4496 5080 4.853924 AAGCAAAGAATGTTCCGTGATT 57.146 36.364 0.00 0.00 0.00 2.57
4497 5081 5.957842 TTAAGCAAAGAATGTTCCGTGAT 57.042 34.783 0.00 0.00 0.00 3.06
4565 5149 1.271054 ACCTCGAGCAAACTGAGCAAT 60.271 47.619 6.99 0.00 0.00 3.56
4631 5216 7.388437 AGAAAAAGCAATAATGAGCAAATCCA 58.612 30.769 0.00 0.00 0.00 3.41
4719 5304 8.386606 GCTTAAACACATATCAGAAGACTCTTG 58.613 37.037 0.00 0.00 0.00 3.02
5055 5645 8.562892 CCTTACAAGCTCAACATATTCCATTAG 58.437 37.037 0.00 0.00 0.00 1.73
5087 5677 9.271828 CTAAATTCTGCAACAAAAATAAAGGGT 57.728 29.630 0.00 0.00 0.00 4.34
5147 5737 4.698780 GCAGCCTGATCATAGATTGCATTA 59.301 41.667 0.00 0.00 31.51 1.90
5306 5896 0.924090 GGACAACATCTCGCATCGAC 59.076 55.000 0.00 0.00 0.00 4.20
5344 5934 1.727511 GCTGCTGTGGCTGTGTTTCA 61.728 55.000 0.00 0.00 39.19 2.69
5384 5974 3.637273 GTCCTGCCCGGTGGAAGT 61.637 66.667 9.27 0.00 35.14 3.01
5435 6025 2.040939 CCAGAGGCAGATGACTGATCT 58.959 52.381 0.00 0.00 46.03 2.75
5595 6185 3.264193 AGTTCCATGCTTGATCAGGTACA 59.736 43.478 6.70 0.00 0.00 2.90
5796 6386 3.119708 GCAAGGCAGTTGTATGAAAGGAG 60.120 47.826 0.54 0.00 38.55 3.69
5848 6470 6.206243 CACTGATCTGTGATTCAACCTTCTTT 59.794 38.462 24.09 0.00 40.12 2.52
5915 6537 9.651913 AAGCACCGAATCAAAATTATAAACATT 57.348 25.926 0.00 0.00 0.00 2.71
5978 6602 6.640518 TCAAATAGCTCAAAGTAGTCCGAAT 58.359 36.000 0.00 0.00 0.00 3.34
6096 6720 8.418662 AGGAATATGATTGTGGTTTGATTGATG 58.581 33.333 0.00 0.00 0.00 3.07
6189 6813 1.673920 TCTTTCAGTTTGTGGTTCGGC 59.326 47.619 0.00 0.00 0.00 5.54
6474 7101 1.063616 CTCATCGTCGGCTTCTCGTTA 59.936 52.381 0.00 0.00 0.00 3.18
6498 7125 6.548622 CCATTGTTGGATGTTCTGATAGGATT 59.451 38.462 0.00 0.00 46.92 3.01
6506 7133 7.257722 GGTAATAACCATTGTTGGATGTTCTG 58.742 38.462 0.00 0.00 46.92 3.02
6670 7297 2.094234 AGAACACACAAAAGGGTTGCAC 60.094 45.455 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.