Multiple sequence alignment - TraesCS6A01G240100

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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 TraesCS6A01G240100 chr6A 100.000 3181 0 0 1 3181 450109385 450106205 0.000000e+00 5875.0
1 TraesCS6A01G240100 chr6D 92.086 2641 105 42 1 2613 313189288 313186724 0.000000e+00 3624.0
2 TraesCS6A01G240100 chr6D 80.488 492 83 11 2696 3181 110985221 110984737 6.480000e-97 364.0
3 TraesCS6A01G240100 chr6B 90.489 2639 114 55 4 2613 513134552 513137082 0.000000e+00 3356.0
4 TraesCS6A01G240100 chr6B 77.913 575 106 19 2612 3181 182354206 182354764 3.930000e-89 339.0
5 TraesCS6A01G240100 chr6B 76.240 484 92 10 2700 3181 601311670 601312132 5.300000e-58 235.0
6 TraesCS6A01G240100 chr2B 80.967 662 101 20 1495 2148 576744900 576744256 4.740000e-138 501.0
7 TraesCS6A01G240100 chr2B 96.825 63 2 0 1270 1332 768651575 768651637 4.340000e-19 106.0
8 TraesCS6A01G240100 chr2A 80.539 668 102 23 1492 2148 637223051 637222401 3.690000e-134 488.0
9 TraesCS6A01G240100 chr4B 93.082 318 22 0 1015 1332 27404958 27404641 1.730000e-127 466.0
10 TraesCS6A01G240100 chr1B 83.368 487 68 4 2708 3181 626760564 626761050 3.770000e-119 438.0
11 TraesCS6A01G240100 chr1B 81.279 219 38 3 1150 1368 364919506 364919291 1.170000e-39 174.0
12 TraesCS6A01G240100 chr1B 89.231 65 7 0 1850 1914 539547535 539547471 7.310000e-12 82.4
13 TraesCS6A01G240100 chr1D 78.534 573 106 15 2610 3179 472335440 472335998 8.390000e-96 361.0
14 TraesCS6A01G240100 chr1D 77.523 436 85 10 1484 1917 249560541 249560965 1.890000e-62 250.0
15 TraesCS6A01G240100 chr1D 80.822 219 39 3 1150 1368 249560225 249560440 5.460000e-38 169.0
16 TraesCS6A01G240100 chr1D 89.231 65 7 0 1850 1914 401667225 401667161 7.310000e-12 82.4
17 TraesCS6A01G240100 chr5B 79.837 491 78 16 2696 3181 491882713 491883187 3.930000e-89 339.0
18 TraesCS6A01G240100 chr7D 83.929 336 47 7 2848 3180 118822348 118822017 6.620000e-82 315.0
19 TraesCS6A01G240100 chr4D 77.193 513 89 16 2685 3181 49801432 49801932 1.120000e-69 274.0
20 TraesCS6A01G240100 chr1A 78.161 435 82 10 1485 1917 319320525 319320948 6.770000e-67 265.0
21 TraesCS6A01G240100 chr1A 89.231 65 7 0 1850 1914 497504520 497504456 7.310000e-12 82.4
22 TraesCS6A01G240100 chr4A 80.531 339 57 8 2848 3181 38700210 38700544 5.270000e-63 252.0
23 TraesCS6A01G240100 chr4A 93.798 129 8 0 1204 1332 21864824 21864952 9.000000e-46 195.0
24 TraesCS6A01G240100 chr5A 96.899 129 4 0 1204 1332 645412949 645412821 1.920000e-52 217.0
25 TraesCS6A01G240100 chr7A 96.124 129 5 0 1204 1332 83536322 83536450 8.940000e-51 211.0
26 TraesCS6A01G240100 chr7B 74.155 503 102 21 2615 3101 428473841 428474331 1.950000e-42 183.0


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 TraesCS6A01G240100 chr6A 450106205 450109385 3180 True 5875.0 5875 100.0000 1 3181 1 chr6A.!!$R1 3180
1 TraesCS6A01G240100 chr6D 313186724 313189288 2564 True 3624.0 3624 92.0860 1 2613 1 chr6D.!!$R2 2612
2 TraesCS6A01G240100 chr6B 513134552 513137082 2530 False 3356.0 3356 90.4890 4 2613 1 chr6B.!!$F2 2609
3 TraesCS6A01G240100 chr6B 182354206 182354764 558 False 339.0 339 77.9130 2612 3181 1 chr6B.!!$F1 569
4 TraesCS6A01G240100 chr2B 576744256 576744900 644 True 501.0 501 80.9670 1495 2148 1 chr2B.!!$R1 653
5 TraesCS6A01G240100 chr2A 637222401 637223051 650 True 488.0 488 80.5390 1492 2148 1 chr2A.!!$R1 656
6 TraesCS6A01G240100 chr1D 472335440 472335998 558 False 361.0 361 78.5340 2610 3179 1 chr1D.!!$F1 569
7 TraesCS6A01G240100 chr1D 249560225 249560965 740 False 209.5 250 79.1725 1150 1917 2 chr1D.!!$F2 767
8 TraesCS6A01G240100 chr4D 49801432 49801932 500 False 274.0 274 77.1930 2685 3181 1 chr4D.!!$F1 496

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
182 185 0.037697 ATCGACAGCGCAGTAAACCA 60.038 50.0 11.47 0.00 37.46 3.67 F
271 300 0.040157 CTTTTGCAGCGCAGTAAGCA 60.040 50.0 11.47 8.86 46.13 3.91 F
341 370 0.108138 CCACAACTCGGACATCTCCC 60.108 60.0 0.00 0.00 31.93 4.30 F
664 693 0.187361 CAGGGGAGGAGGAGGAGTAG 59.813 65.0 0.00 0.00 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1430 1464 0.034896 AACTCCATTGCCTCGTTCGT 59.965 50.000 0.0 0.0 0.00 3.85 R
1432 1466 1.734465 CAGAACTCCATTGCCTCGTTC 59.266 52.381 0.0 0.0 35.44 3.95 R
1444 1478 2.125350 CGCTCCAGCCAGAACTCC 60.125 66.667 0.0 0.0 37.91 3.85 R
2559 2618 0.537143 ACGTGCATCCAAAGCTCCAA 60.537 50.000 0.0 0.0 0.00 3.53 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
41 42 6.796705 AATTTTAACAGAGTAGTCGTTGGG 57.203 37.500 14.20 0.00 0.00 4.12
87 88 1.678101 AGTGCTCCACTGTGAAAAAGC 59.322 47.619 9.86 12.33 43.63 3.51
89 90 1.677576 TGCTCCACTGTGAAAAAGCAG 59.322 47.619 9.86 0.00 35.02 4.24
95 98 4.037923 TCCACTGTGAAAAAGCAGAAATCC 59.962 41.667 9.86 0.00 36.62 3.01
107 110 3.521126 AGCAGAAATCCATGGACAGTAGT 59.479 43.478 18.99 0.00 0.00 2.73
108 111 4.716784 AGCAGAAATCCATGGACAGTAGTA 59.283 41.667 18.99 0.00 0.00 1.82
109 112 4.811557 GCAGAAATCCATGGACAGTAGTAC 59.188 45.833 18.99 3.21 0.00 2.73
110 113 5.043903 CAGAAATCCATGGACAGTAGTACG 58.956 45.833 18.99 0.00 0.00 3.67
117 120 3.339253 TGGACAGTAGTACGTAGCAGA 57.661 47.619 0.00 0.00 0.00 4.26
138 141 0.185901 TCTGCATTAATCCAGGGGCC 59.814 55.000 6.55 0.00 0.00 5.80
139 142 1.152777 TGCATTAATCCAGGGGCCG 60.153 57.895 0.00 0.00 0.00 6.13
163 166 1.743623 CGGGTGCGCAGTAAATCCA 60.744 57.895 12.22 0.00 0.00 3.41
172 175 1.258982 GCAGTAAATCCATCGACAGCG 59.741 52.381 0.00 0.00 39.35 5.18
173 176 1.258982 CAGTAAATCCATCGACAGCGC 59.741 52.381 0.00 0.00 37.46 5.92
174 177 1.134818 AGTAAATCCATCGACAGCGCA 60.135 47.619 11.47 0.00 37.46 6.09
175 178 1.258982 GTAAATCCATCGACAGCGCAG 59.741 52.381 11.47 3.33 37.46 5.18
176 179 0.391661 AAATCCATCGACAGCGCAGT 60.392 50.000 11.47 8.04 37.46 4.40
178 181 0.459899 ATCCATCGACAGCGCAGTAA 59.540 50.000 11.47 0.00 37.46 2.24
179 182 0.245266 TCCATCGACAGCGCAGTAAA 59.755 50.000 11.47 0.00 37.46 2.01
180 183 0.370273 CCATCGACAGCGCAGTAAAC 59.630 55.000 11.47 0.00 37.46 2.01
182 185 0.037697 ATCGACAGCGCAGTAAACCA 60.038 50.000 11.47 0.00 37.46 3.67
183 186 0.666274 TCGACAGCGCAGTAAACCAG 60.666 55.000 11.47 0.00 37.46 4.00
184 187 0.944311 CGACAGCGCAGTAAACCAGT 60.944 55.000 11.47 0.00 0.00 4.00
185 188 1.667756 CGACAGCGCAGTAAACCAGTA 60.668 52.381 11.47 0.00 0.00 2.74
186 189 1.993370 GACAGCGCAGTAAACCAGTAG 59.007 52.381 11.47 0.00 0.00 2.57
187 190 1.343465 ACAGCGCAGTAAACCAGTAGT 59.657 47.619 11.47 0.00 0.00 2.73
238 267 3.692998 CGCACAACGGCATGTAAAT 57.307 47.368 0.00 0.00 38.44 1.40
239 268 1.258427 CGCACAACGGCATGTAAATG 58.742 50.000 0.00 0.00 38.44 2.32
240 269 1.400888 CGCACAACGGCATGTAAATGT 60.401 47.619 0.00 0.00 38.44 2.71
241 270 2.159639 CGCACAACGGCATGTAAATGTA 60.160 45.455 0.00 0.00 38.44 2.29
242 271 3.168193 GCACAACGGCATGTAAATGTAC 58.832 45.455 0.00 0.00 30.84 2.90
271 300 0.040157 CTTTTGCAGCGCAGTAAGCA 60.040 50.000 11.47 8.86 46.13 3.91
282 311 2.027625 AGTAAGCAAGCACGTCCGC 61.028 57.895 0.00 0.00 0.00 5.54
341 370 0.108138 CCACAACTCGGACATCTCCC 60.108 60.000 0.00 0.00 31.93 4.30
390 419 1.224003 ACTTGCCCTGGGATCCCATT 61.224 55.000 33.89 9.44 46.15 3.16
398 427 1.690352 CTGGGATCCCATTGGAAATGC 59.310 52.381 33.89 1.29 45.98 3.56
461 490 3.670377 GCCACTTGGTGCCGGTTC 61.670 66.667 1.90 0.00 37.57 3.62
547 576 5.556915 ACAGATGGAAATACCTGTCGAAAA 58.443 37.500 0.00 0.00 35.15 2.29
548 577 6.001460 ACAGATGGAAATACCTGTCGAAAAA 58.999 36.000 0.00 0.00 35.15 1.94
552 581 9.238368 AGATGGAAATACCTGTCGAAAAATTAA 57.762 29.630 0.00 0.00 39.86 1.40
554 583 7.822658 TGGAAATACCTGTCGAAAAATTAAGG 58.177 34.615 0.00 0.00 39.86 2.69
556 585 7.121611 GGAAATACCTGTCGAAAAATTAAGGGA 59.878 37.037 0.00 0.00 35.41 4.20
559 588 4.202535 ACCTGTCGAAAAATTAAGGGACCT 60.203 41.667 0.00 0.00 0.00 3.85
560 589 4.395231 CCTGTCGAAAAATTAAGGGACCTC 59.605 45.833 0.00 0.00 0.00 3.85
615 644 9.846248 AGGAATTCGAGAATGTTTTCTTAATTG 57.154 29.630 0.00 0.00 42.34 2.32
656 685 1.271054 CGATAAATGCAGGGGAGGAGG 60.271 57.143 0.00 0.00 0.00 4.30
659 688 1.284841 AAATGCAGGGGAGGAGGAGG 61.285 60.000 0.00 0.00 0.00 4.30
661 690 2.445654 GCAGGGGAGGAGGAGGAG 60.446 72.222 0.00 0.00 0.00 3.69
664 693 0.187361 CAGGGGAGGAGGAGGAGTAG 59.813 65.000 0.00 0.00 0.00 2.57
667 696 0.757561 GGGAGGAGGAGGAGTAGTGC 60.758 65.000 0.00 0.00 0.00 4.40
703 735 4.385405 AGGACTGCACAGAGGCGC 62.385 66.667 0.00 0.00 36.28 6.53
719 751 1.133253 CGCCACACATCTCAAAGCG 59.867 57.895 0.00 0.00 35.82 4.68
726 758 0.392193 ACATCTCAAAGCGGCCTGAG 60.392 55.000 18.78 18.78 40.42 3.35
740 772 1.084370 CCTGAGCCTTCCTTTACGCG 61.084 60.000 3.53 3.53 0.00 6.01
776 808 0.394192 CCCACTCAACTGACAGCTCA 59.606 55.000 1.25 0.00 0.00 4.26
804 836 4.003788 AACGGACTCCAGTGCCCG 62.004 66.667 5.52 5.52 46.65 6.13
876 908 3.619038 CAGAGAGAAAAATACGCACTCCC 59.381 47.826 0.00 0.00 0.00 4.30
925 959 3.571590 AGCCTTCTCGATCTATTCCAGT 58.428 45.455 0.00 0.00 0.00 4.00
926 960 4.730966 AGCCTTCTCGATCTATTCCAGTA 58.269 43.478 0.00 0.00 0.00 2.74
927 961 4.764823 AGCCTTCTCGATCTATTCCAGTAG 59.235 45.833 0.00 0.00 0.00 2.57
928 962 4.617298 GCCTTCTCGATCTATTCCAGTAGC 60.617 50.000 0.00 0.00 0.00 3.58
1427 1461 2.692709 TGGTCAACCCATCCACATTT 57.307 45.000 0.00 0.00 38.72 2.32
1430 1464 3.332187 TGGTCAACCCATCCACATTTCTA 59.668 43.478 0.00 0.00 38.72 2.10
1432 1466 3.374058 GTCAACCCATCCACATTTCTACG 59.626 47.826 0.00 0.00 0.00 3.51
1444 1478 3.370978 ACATTTCTACGAACGAGGCAATG 59.629 43.478 0.14 7.76 0.00 2.82
1517 1561 0.038892 TCTTGGTGTTCGAGTACGCC 60.039 55.000 12.06 12.06 46.55 5.68
1973 2024 2.266055 GTGGTCAGCGAGGGGAAG 59.734 66.667 0.00 0.00 0.00 3.46
2185 2239 4.094830 AGATGGTGGTTTCGTAAAGGTT 57.905 40.909 0.00 0.00 0.00 3.50
2186 2240 4.466827 AGATGGTGGTTTCGTAAAGGTTT 58.533 39.130 0.00 0.00 0.00 3.27
2187 2241 5.623169 AGATGGTGGTTTCGTAAAGGTTTA 58.377 37.500 0.00 0.00 0.00 2.01
2233 2288 1.216930 AGGTAGGGCACACAACCTTTT 59.783 47.619 2.03 0.00 39.32 2.27
2234 2289 1.611977 GGTAGGGCACACAACCTTTTC 59.388 52.381 0.00 0.00 38.30 2.29
2248 2304 8.311109 ACACAACCTTTTCTCACTTTGTTATTT 58.689 29.630 0.00 0.00 0.00 1.40
2249 2305 9.796120 CACAACCTTTTCTCACTTTGTTATTTA 57.204 29.630 0.00 0.00 0.00 1.40
2280 2337 6.665992 AGTGGATCAGTTAGTAGTTGAACA 57.334 37.500 0.00 0.00 0.00 3.18
2281 2338 7.062749 AGTGGATCAGTTAGTAGTTGAACAA 57.937 36.000 0.00 0.00 0.00 2.83
2282 2339 7.680730 AGTGGATCAGTTAGTAGTTGAACAAT 58.319 34.615 0.00 0.00 0.00 2.71
2283 2340 7.819900 AGTGGATCAGTTAGTAGTTGAACAATC 59.180 37.037 0.00 0.00 0.00 2.67
2284 2341 6.811665 TGGATCAGTTAGTAGTTGAACAATCG 59.188 38.462 0.00 0.00 0.00 3.34
2285 2342 7.033791 GGATCAGTTAGTAGTTGAACAATCGA 58.966 38.462 0.00 0.00 0.00 3.59
2286 2343 7.221067 GGATCAGTTAGTAGTTGAACAATCGAG 59.779 40.741 0.00 0.00 0.00 4.04
2287 2344 6.978338 TCAGTTAGTAGTTGAACAATCGAGT 58.022 36.000 0.00 0.00 0.00 4.18
2288 2345 7.082602 TCAGTTAGTAGTTGAACAATCGAGTC 58.917 38.462 0.00 0.00 0.00 3.36
2289 2346 6.308282 CAGTTAGTAGTTGAACAATCGAGTCC 59.692 42.308 0.00 0.00 0.00 3.85
2290 2347 4.189639 AGTAGTTGAACAATCGAGTCCC 57.810 45.455 0.00 0.00 0.00 4.46
2329 2386 2.757099 GGATGGGGTTGCAGGCAG 60.757 66.667 0.00 0.00 0.00 4.85
2368 2425 3.644884 AATCCGCCTGTAGATCTTACG 57.355 47.619 0.00 0.00 0.00 3.18
2476 2534 5.048434 AGTTTACTGCTGAGGAAATCAAAGC 60.048 40.000 0.00 0.00 34.38 3.51
2555 2614 6.016360 CCATGGTCAGAAATGTTGTTTACTCA 60.016 38.462 2.57 0.00 0.00 3.41
2556 2615 7.309377 CCATGGTCAGAAATGTTGTTTACTCAT 60.309 37.037 2.57 0.00 0.00 2.90
2558 2617 6.998074 TGGTCAGAAATGTTGTTTACTCATCT 59.002 34.615 0.00 0.00 0.00 2.90
2559 2618 7.502226 TGGTCAGAAATGTTGTTTACTCATCTT 59.498 33.333 0.00 0.00 0.00 2.40
2560 2619 8.352942 GGTCAGAAATGTTGTTTACTCATCTTT 58.647 33.333 0.00 0.00 0.00 2.52
2561 2620 9.173939 GTCAGAAATGTTGTTTACTCATCTTTG 57.826 33.333 0.00 0.00 0.00 2.77
2562 2621 8.352201 TCAGAAATGTTGTTTACTCATCTTTGG 58.648 33.333 0.00 0.00 0.00 3.28
2563 2622 8.352201 CAGAAATGTTGTTTACTCATCTTTGGA 58.648 33.333 0.00 0.00 0.00 3.53
2564 2623 8.571336 AGAAATGTTGTTTACTCATCTTTGGAG 58.429 33.333 0.00 0.00 38.36 3.86
2565 2624 5.689383 TGTTGTTTACTCATCTTTGGAGC 57.311 39.130 0.00 0.00 35.79 4.70
2566 2625 5.376625 TGTTGTTTACTCATCTTTGGAGCT 58.623 37.500 0.00 0.00 35.79 4.09
2632 2691 2.805546 GAGCATCTACGGCCACGA 59.194 61.111 2.24 0.00 44.60 4.35
2636 2695 1.441729 CATCTACGGCCACGATGGT 59.558 57.895 14.84 1.61 44.60 3.55
2644 2703 0.679640 GGCCACGATGGTCAAATCCA 60.680 55.000 0.00 0.00 42.98 3.41
2645 2704 0.734889 GCCACGATGGTCAAATCCAG 59.265 55.000 0.00 0.00 40.46 3.86
2646 2705 1.950484 GCCACGATGGTCAAATCCAGT 60.950 52.381 0.00 0.00 40.46 4.00
2659 2718 1.201429 ATCCAGTCCCTCAAACGCCT 61.201 55.000 0.00 0.00 0.00 5.52
2662 2721 2.281484 GTCCCTCAAACGCCTGCA 60.281 61.111 0.00 0.00 0.00 4.41
2675 2734 2.034879 CCTGCAGACGCGTTTGGAT 61.035 57.895 28.24 4.12 42.97 3.41
2683 2742 3.253955 GCGTTTGGATGCGTCTGT 58.746 55.556 5.77 0.00 0.00 3.41
2693 2752 0.610174 ATGCGTCTGTGGACACTGAT 59.390 50.000 13.81 0.00 42.21 2.90
2694 2753 0.392706 TGCGTCTGTGGACACTGATT 59.607 50.000 13.81 0.00 42.21 2.57
2708 2767 1.340991 ACTGATTGGGCACGCCTTATT 60.341 47.619 8.20 0.00 36.10 1.40
2710 2769 1.476085 TGATTGGGCACGCCTTATTTG 59.524 47.619 8.20 0.00 36.10 2.32
2714 2773 0.108851 GGGCACGCCTTATTTGTTGG 60.109 55.000 8.20 0.00 36.10 3.77
2718 2777 2.327568 CACGCCTTATTTGTTGGCTTG 58.672 47.619 0.00 0.00 44.09 4.01
2724 2783 4.805219 CCTTATTTGTTGGCTTGTACACC 58.195 43.478 0.00 0.00 0.00 4.16
2727 2786 0.107116 TTGTTGGCTTGTACACCCGT 60.107 50.000 0.00 0.00 0.00 5.28
2732 2791 1.370064 GCTTGTACACCCGTGTCCT 59.630 57.895 3.23 0.00 43.74 3.85
2741 2800 2.168521 ACACCCGTGTCCTTCATATCTG 59.831 50.000 0.00 0.00 40.24 2.90
2753 2812 7.890127 TGTCCTTCATATCTGAAACCTCAAAAT 59.110 33.333 0.00 0.00 40.78 1.82
2775 2835 5.550232 TCATACAAAGCATGCAACACTAG 57.450 39.130 21.98 4.88 0.00 2.57
2777 2837 2.862541 ACAAAGCATGCAACACTAGGA 58.137 42.857 21.98 0.00 0.00 2.94
2804 2865 4.166246 AGATCATCACATGCAGTCCATT 57.834 40.909 0.00 0.00 29.71 3.16
2805 2866 5.300411 AGATCATCACATGCAGTCCATTA 57.700 39.130 0.00 0.00 29.71 1.90
2809 2870 5.303165 TCATCACATGCAGTCCATTAGATC 58.697 41.667 0.00 0.00 29.71 2.75
2810 2871 4.758773 TCACATGCAGTCCATTAGATCA 57.241 40.909 0.00 0.00 29.71 2.92
2811 2872 4.445453 TCACATGCAGTCCATTAGATCAC 58.555 43.478 0.00 0.00 29.71 3.06
2812 2873 3.562973 CACATGCAGTCCATTAGATCACC 59.437 47.826 0.00 0.00 29.71 4.02
2813 2874 3.200605 ACATGCAGTCCATTAGATCACCA 59.799 43.478 0.00 0.00 29.71 4.17
2814 2875 4.141321 ACATGCAGTCCATTAGATCACCAT 60.141 41.667 0.00 0.00 29.71 3.55
2815 2876 4.508551 TGCAGTCCATTAGATCACCATT 57.491 40.909 0.00 0.00 0.00 3.16
2816 2877 4.858850 TGCAGTCCATTAGATCACCATTT 58.141 39.130 0.00 0.00 0.00 2.32
2817 2878 4.883585 TGCAGTCCATTAGATCACCATTTC 59.116 41.667 0.00 0.00 0.00 2.17
2818 2879 4.883585 GCAGTCCATTAGATCACCATTTCA 59.116 41.667 0.00 0.00 0.00 2.69
2820 2881 6.293845 GCAGTCCATTAGATCACCATTTCATC 60.294 42.308 0.00 0.00 0.00 2.92
2835 2896 2.099141 TCATCGCTGGACAAAAGGAG 57.901 50.000 0.00 0.00 0.00 3.69
2843 2904 4.261801 GCTGGACAAAAGGAGCATAGTTA 58.738 43.478 0.00 0.00 0.00 2.24
2844 2905 4.333926 GCTGGACAAAAGGAGCATAGTTAG 59.666 45.833 0.00 0.00 0.00 2.34
2856 2917 5.363939 GAGCATAGTTAGTTGGAGCTCAAT 58.636 41.667 17.19 0.00 44.60 2.57
2861 2922 0.901827 TAGTTGGAGCTCAATGGCGA 59.098 50.000 17.19 0.00 37.73 5.54
2865 2926 0.250684 TGGAGCTCAATGGCGAACAA 60.251 50.000 17.19 0.00 37.29 2.83
2873 2934 3.661944 TCAATGGCGAACAATGCAAATT 58.338 36.364 0.00 0.00 29.85 1.82
2881 2942 6.033341 GGCGAACAATGCAAATTCATACTAA 58.967 36.000 0.00 0.00 0.00 2.24
2916 2990 0.618458 TAAGCACAAGGGCGAAGGAT 59.382 50.000 0.00 0.00 39.27 3.24
2942 3016 2.214376 AATCACCATTTCCAAGCCGA 57.786 45.000 0.00 0.00 0.00 5.54
2943 3017 2.214376 ATCACCATTTCCAAGCCGAA 57.786 45.000 0.00 0.00 0.00 4.30
2945 3019 2.524306 TCACCATTTCCAAGCCGAAAT 58.476 42.857 0.00 0.00 41.98 2.17
2959 3033 0.252197 CGAAATCTTCCCCTTCCGGT 59.748 55.000 0.00 0.00 0.00 5.28
2961 3035 1.280998 GAAATCTTCCCCTTCCGGTCA 59.719 52.381 0.00 0.00 0.00 4.02
2963 3037 1.596496 ATCTTCCCCTTCCGGTCATT 58.404 50.000 0.00 0.00 0.00 2.57
2987 3061 2.360475 GCTGTGCCCCTCCTTCAC 60.360 66.667 0.00 0.00 0.00 3.18
2990 3064 2.397413 CTGTGCCCCTCCTTCACGTT 62.397 60.000 0.00 0.00 33.69 3.99
3010 3084 3.680786 CGTCGGTGTGAGGAGGCA 61.681 66.667 0.00 0.00 34.34 4.75
3014 3088 2.426023 GGTGTGAGGAGGCACGTT 59.574 61.111 0.00 0.00 41.63 3.99
3015 3089 1.961277 GGTGTGAGGAGGCACGTTG 60.961 63.158 0.00 0.00 41.63 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.694037 GCCCAACGACTACTCTGTTAAAAT 59.306 41.667 0.00 0.00 0.00 1.82
28 29 0.824759 ATCCTGCCCAACGACTACTC 59.175 55.000 0.00 0.00 0.00 2.59
87 88 5.043903 CGTACTACTGTCCATGGATTTCTG 58.956 45.833 19.62 11.61 0.00 3.02
89 90 5.007385 ACGTACTACTGTCCATGGATTTC 57.993 43.478 19.62 5.73 0.00 2.17
95 98 3.626217 TCTGCTACGTACTACTGTCCATG 59.374 47.826 0.00 0.00 0.00 3.66
146 149 0.663153 GATGGATTTACTGCGCACCC 59.337 55.000 5.66 1.46 0.00 4.61
163 166 0.037697 TGGTTTACTGCGCTGTCGAT 60.038 50.000 23.87 1.50 38.10 3.59
182 185 3.975479 ACCCACTAGCCAGATACTACT 57.025 47.619 0.00 0.00 0.00 2.57
183 186 3.958798 TGAACCCACTAGCCAGATACTAC 59.041 47.826 0.00 0.00 0.00 2.73
184 187 3.958798 GTGAACCCACTAGCCAGATACTA 59.041 47.826 0.00 0.00 40.10 1.82
185 188 2.766828 GTGAACCCACTAGCCAGATACT 59.233 50.000 0.00 0.00 40.10 2.12
186 189 2.500098 TGTGAACCCACTAGCCAGATAC 59.500 50.000 0.00 0.00 43.55 2.24
187 190 2.766263 CTGTGAACCCACTAGCCAGATA 59.234 50.000 0.00 0.00 43.55 1.98
232 261 8.776470 GCAAAAGGTAAGTACAGTACATTTACA 58.224 33.333 18.04 0.00 35.15 2.41
233 262 8.776470 TGCAAAAGGTAAGTACAGTACATTTAC 58.224 33.333 13.37 12.43 35.15 2.01
234 263 8.905660 TGCAAAAGGTAAGTACAGTACATTTA 57.094 30.769 13.37 1.32 35.15 1.40
235 264 7.521585 GCTGCAAAAGGTAAGTACAGTACATTT 60.522 37.037 13.37 11.39 37.12 2.32
236 265 6.072673 GCTGCAAAAGGTAAGTACAGTACATT 60.073 38.462 13.37 6.99 0.00 2.71
237 266 5.411669 GCTGCAAAAGGTAAGTACAGTACAT 59.588 40.000 13.37 3.51 0.00 2.29
238 267 4.753107 GCTGCAAAAGGTAAGTACAGTACA 59.247 41.667 13.37 0.00 0.00 2.90
239 268 4.143179 CGCTGCAAAAGGTAAGTACAGTAC 60.143 45.833 2.05 2.05 0.00 2.73
240 269 3.991773 CGCTGCAAAAGGTAAGTACAGTA 59.008 43.478 0.00 0.00 0.00 2.74
241 270 2.806244 CGCTGCAAAAGGTAAGTACAGT 59.194 45.455 0.00 0.00 0.00 3.55
242 271 2.412847 GCGCTGCAAAAGGTAAGTACAG 60.413 50.000 0.00 0.00 0.00 2.74
271 300 1.222115 GACTTTCAGCGGACGTGCTT 61.222 55.000 5.27 0.00 44.46 3.91
282 311 3.428045 GCCAATGGGAATTCGACTTTCAG 60.428 47.826 0.00 0.00 35.59 3.02
341 370 8.746052 TTATGGTACTGTATGAAATCCCAAAG 57.254 34.615 0.00 0.00 0.00 2.77
352 381 3.717707 AGTGCGCTTATGGTACTGTATG 58.282 45.455 9.73 0.00 0.00 2.39
390 419 6.705381 CCTGTTTCATTAACAAAGCATTTCCA 59.295 34.615 0.00 0.00 45.69 3.53
398 427 7.116233 GTGTAATGGCCTGTTTCATTAACAAAG 59.884 37.037 3.32 0.00 45.69 2.77
461 490 4.824166 CGTGACGTCCTACCGGCG 62.824 72.222 14.12 0.00 39.23 6.46
554 583 4.459089 GTGCAGCGAGGGAGGTCC 62.459 72.222 0.00 0.00 0.00 4.46
559 588 3.071206 GAGAGGTGCAGCGAGGGA 61.071 66.667 10.78 0.00 0.00 4.20
560 589 2.947532 TTGAGAGGTGCAGCGAGGG 61.948 63.158 10.78 0.00 0.00 4.30
656 685 3.057876 CCTATCGTCATGCACTACTCCTC 60.058 52.174 0.00 0.00 0.00 3.71
659 688 3.566322 ACTCCTATCGTCATGCACTACTC 59.434 47.826 0.00 0.00 0.00 2.59
661 690 3.633235 CACTCCTATCGTCATGCACTAC 58.367 50.000 0.00 0.00 0.00 2.73
664 693 1.212616 GCACTCCTATCGTCATGCAC 58.787 55.000 0.00 0.00 33.27 4.57
667 696 0.249031 TGCGCACTCCTATCGTCATG 60.249 55.000 5.66 0.00 0.00 3.07
693 725 2.359107 ATGTGTGGCGCCTCTGTG 60.359 61.111 29.70 0.00 0.00 3.66
694 726 2.046892 GATGTGTGGCGCCTCTGT 60.047 61.111 29.70 13.84 0.00 3.41
703 735 1.503542 GCCGCTTTGAGATGTGTGG 59.496 57.895 0.00 0.00 0.00 4.17
726 758 0.523335 CATTGCGCGTAAAGGAAGGC 60.523 55.000 14.95 0.00 0.00 4.35
731 763 3.546020 CCACTAATCATTGCGCGTAAAGG 60.546 47.826 14.95 9.63 0.00 3.11
740 772 1.322442 GGGGCTCCACTAATCATTGC 58.678 55.000 0.00 0.00 0.00 3.56
776 808 4.641989 ACTGGAGTCCGTTGTTATATACGT 59.358 41.667 4.30 0.00 36.09 3.57
804 836 2.675423 GGGGCCGGGTCAAAGAAC 60.675 66.667 2.18 0.00 0.00 3.01
876 908 0.512952 GTCGCTGTTGTTGCTAGGTG 59.487 55.000 0.00 0.00 0.00 4.00
925 959 4.456222 GTCGTTGATGGAGATAGCTAGCTA 59.544 45.833 26.09 26.09 0.00 3.32
926 960 3.254657 GTCGTTGATGGAGATAGCTAGCT 59.745 47.826 23.12 23.12 0.00 3.32
927 961 3.570559 GTCGTTGATGGAGATAGCTAGC 58.429 50.000 6.62 6.62 0.00 3.42
928 962 3.816091 CGTCGTTGATGGAGATAGCTAG 58.184 50.000 0.00 0.00 0.00 3.42
998 1032 4.114997 CGCACCCGGGCAACATTC 62.115 66.667 24.08 0.41 39.74 2.67
1209 1243 0.670546 CCAGGTACACGGTGCTGAAG 60.671 60.000 8.30 0.00 0.00 3.02
1427 1461 1.134367 CTCCATTGCCTCGTTCGTAGA 59.866 52.381 0.00 0.00 0.00 2.59
1430 1464 0.034896 AACTCCATTGCCTCGTTCGT 59.965 50.000 0.00 0.00 0.00 3.85
1432 1466 1.734465 CAGAACTCCATTGCCTCGTTC 59.266 52.381 0.00 0.00 35.44 3.95
1444 1478 2.125350 CGCTCCAGCCAGAACTCC 60.125 66.667 0.00 0.00 37.91 3.85
1992 2043 2.776370 TACGCGTCTCCCAACCTCCT 62.776 60.000 18.63 0.00 0.00 3.69
2185 2239 6.676943 GCATTTACACCCTACGTACGTACTAA 60.677 42.308 23.60 6.22 0.00 2.24
2186 2240 5.220777 GCATTTACACCCTACGTACGTACTA 60.221 44.000 23.60 6.61 0.00 1.82
2187 2241 4.438744 GCATTTACACCCTACGTACGTACT 60.439 45.833 23.60 12.43 0.00 2.73
2251 2307 9.470399 TCAACTACTAACTGATCCACTTATACA 57.530 33.333 0.00 0.00 0.00 2.29
2254 2310 8.812972 TGTTCAACTACTAACTGATCCACTTAT 58.187 33.333 0.00 0.00 0.00 1.73
2255 2311 8.185506 TGTTCAACTACTAACTGATCCACTTA 57.814 34.615 0.00 0.00 0.00 2.24
2259 2315 6.811665 CGATTGTTCAACTACTAACTGATCCA 59.188 38.462 0.00 0.00 0.00 3.41
2280 2337 4.758165 ACAAAAATTGTACGGGACTCGATT 59.242 37.500 0.00 0.00 43.27 3.34
2281 2338 4.153475 CACAAAAATTGTACGGGACTCGAT 59.847 41.667 0.00 0.00 43.23 3.59
2282 2339 3.495377 CACAAAAATTGTACGGGACTCGA 59.505 43.478 0.00 0.00 43.23 4.04
2283 2340 3.495377 TCACAAAAATTGTACGGGACTCG 59.505 43.478 0.00 0.00 43.23 4.18
2284 2341 5.048991 ACATCACAAAAATTGTACGGGACTC 60.049 40.000 0.00 0.00 43.23 3.36
2285 2342 4.825085 ACATCACAAAAATTGTACGGGACT 59.175 37.500 0.00 0.00 43.23 3.85
2286 2343 5.116069 ACATCACAAAAATTGTACGGGAC 57.884 39.130 0.00 0.00 43.23 4.46
2287 2344 4.822350 TGACATCACAAAAATTGTACGGGA 59.178 37.500 0.00 0.00 43.23 5.14
2288 2345 5.114785 TGACATCACAAAAATTGTACGGG 57.885 39.130 0.00 0.00 43.23 5.28
2289 2346 5.572511 CCATGACATCACAAAAATTGTACGG 59.427 40.000 0.00 0.00 43.23 4.02
2290 2347 6.377780 TCCATGACATCACAAAAATTGTACG 58.622 36.000 0.00 0.00 43.23 3.67
2329 2386 5.228665 GGATTAGATTAACGAGCCACTACC 58.771 45.833 0.00 0.00 0.00 3.18
2340 2397 6.926313 AGATCTACAGGCGGATTAGATTAAC 58.074 40.000 0.00 0.00 33.57 2.01
2476 2534 0.597637 CGGGATCCGTTGAAGATCGG 60.598 60.000 5.45 0.00 46.93 4.18
2555 2614 2.494870 GTGCATCCAAAGCTCCAAAGAT 59.505 45.455 0.00 0.00 0.00 2.40
2556 2615 1.888512 GTGCATCCAAAGCTCCAAAGA 59.111 47.619 0.00 0.00 0.00 2.52
2558 2617 0.597568 CGTGCATCCAAAGCTCCAAA 59.402 50.000 0.00 0.00 0.00 3.28
2559 2618 0.537143 ACGTGCATCCAAAGCTCCAA 60.537 50.000 0.00 0.00 0.00 3.53
2560 2619 0.955428 GACGTGCATCCAAAGCTCCA 60.955 55.000 0.00 0.00 0.00 3.86
2561 2620 1.648467 GGACGTGCATCCAAAGCTCC 61.648 60.000 0.63 0.00 38.77 4.70
2562 2621 0.955428 TGGACGTGCATCCAAAGCTC 60.955 55.000 5.33 0.00 46.08 4.09
2563 2622 1.073025 TGGACGTGCATCCAAAGCT 59.927 52.632 5.33 0.00 46.08 3.74
2564 2623 3.667087 TGGACGTGCATCCAAAGC 58.333 55.556 5.33 0.00 46.08 3.51
2607 2666 2.558795 GGCCGTAGATGCTCTTAGATCA 59.441 50.000 0.00 0.00 0.00 2.92
2625 2684 0.679640 TGGATTTGACCATCGTGGCC 60.680 55.000 0.00 0.00 42.67 5.36
2631 2690 2.239654 TGAGGGACTGGATTTGACCATC 59.760 50.000 0.00 0.00 41.55 3.51
2632 2691 2.278245 TGAGGGACTGGATTTGACCAT 58.722 47.619 0.00 0.00 41.55 3.55
2636 2695 2.778299 CGTTTGAGGGACTGGATTTGA 58.222 47.619 0.00 0.00 41.55 2.69
2645 2704 2.281484 TGCAGGCGTTTGAGGGAC 60.281 61.111 0.00 0.00 0.00 4.46
2646 2705 2.032528 CTGCAGGCGTTTGAGGGA 59.967 61.111 5.57 0.00 0.00 4.20
2659 2718 2.965147 GCATCCAAACGCGTCTGCA 61.965 57.895 14.44 0.00 42.97 4.41
2669 2728 0.107643 TGTCCACAGACGCATCCAAA 59.892 50.000 0.00 0.00 46.74 3.28
2670 2729 1.751563 TGTCCACAGACGCATCCAA 59.248 52.632 0.00 0.00 46.74 3.53
2671 2730 3.465701 TGTCCACAGACGCATCCA 58.534 55.556 0.00 0.00 46.74 3.41
2681 2740 0.537143 GTGCCCAATCAGTGTCCACA 60.537 55.000 0.00 0.00 0.00 4.17
2683 2742 1.302431 CGTGCCCAATCAGTGTCCA 60.302 57.895 0.00 0.00 0.00 4.02
2693 2752 1.000283 CAACAAATAAGGCGTGCCCAA 60.000 47.619 7.39 0.00 36.58 4.12
2694 2753 0.600557 CAACAAATAAGGCGTGCCCA 59.399 50.000 7.39 0.00 36.58 5.36
2714 2773 0.250166 AAGGACACGGGTGTACAAGC 60.250 55.000 16.04 0.00 46.74 4.01
2718 2777 3.383825 AGATATGAAGGACACGGGTGTAC 59.616 47.826 0.00 6.04 45.05 2.90
2724 2783 3.871594 GGTTTCAGATATGAAGGACACGG 59.128 47.826 2.58 0.00 0.00 4.94
2727 2786 6.373005 TTGAGGTTTCAGATATGAAGGACA 57.627 37.500 2.58 1.01 34.15 4.02
2741 2800 7.412237 GCATGCTTTGTATGATTTTGAGGTTTC 60.412 37.037 11.37 0.00 0.00 2.78
2753 2812 4.395854 CCTAGTGTTGCATGCTTTGTATGA 59.604 41.667 20.33 0.00 0.00 2.15
2757 2817 2.862541 TCCTAGTGTTGCATGCTTTGT 58.137 42.857 20.33 2.35 0.00 2.83
2782 2842 3.639672 TGGACTGCATGTGATGATCTT 57.360 42.857 0.00 0.00 0.00 2.40
2784 2844 5.303165 TCTAATGGACTGCATGTGATGATC 58.697 41.667 0.00 0.00 0.00 2.92
2787 2847 5.049612 GTGATCTAATGGACTGCATGTGATG 60.050 44.000 0.00 0.00 0.00 3.07
2792 2852 3.812262 TGGTGATCTAATGGACTGCATG 58.188 45.455 0.00 0.00 0.00 4.06
2794 2854 4.508551 AATGGTGATCTAATGGACTGCA 57.491 40.909 0.00 0.00 0.00 4.41
2800 2861 4.758674 AGCGATGAAATGGTGATCTAATGG 59.241 41.667 0.00 0.00 0.00 3.16
2804 2865 3.387699 TCCAGCGATGAAATGGTGATCTA 59.612 43.478 0.06 0.00 35.69 1.98
2805 2866 2.171237 TCCAGCGATGAAATGGTGATCT 59.829 45.455 0.06 0.00 35.69 2.75
2809 2870 1.452110 TGTCCAGCGATGAAATGGTG 58.548 50.000 0.06 0.00 35.51 4.17
2810 2871 2.198827 TTGTCCAGCGATGAAATGGT 57.801 45.000 0.06 0.00 35.51 3.55
2811 2872 3.504863 CTTTTGTCCAGCGATGAAATGG 58.495 45.455 0.06 0.00 35.30 3.16
2812 2873 3.191162 TCCTTTTGTCCAGCGATGAAATG 59.809 43.478 0.06 0.00 0.00 2.32
2813 2874 3.420893 TCCTTTTGTCCAGCGATGAAAT 58.579 40.909 0.06 0.00 0.00 2.17
2814 2875 2.813754 CTCCTTTTGTCCAGCGATGAAA 59.186 45.455 0.06 0.00 0.00 2.69
2815 2876 2.426522 CTCCTTTTGTCCAGCGATGAA 58.573 47.619 0.06 0.00 0.00 2.57
2816 2877 1.945819 GCTCCTTTTGTCCAGCGATGA 60.946 52.381 0.06 0.00 0.00 2.92
2817 2878 0.449388 GCTCCTTTTGTCCAGCGATG 59.551 55.000 0.00 0.00 0.00 3.84
2818 2879 0.036732 TGCTCCTTTTGTCCAGCGAT 59.963 50.000 0.00 0.00 34.39 4.58
2820 2881 1.667724 CTATGCTCCTTTTGTCCAGCG 59.332 52.381 0.00 0.00 34.39 5.18
2835 2896 4.274459 CCATTGAGCTCCAACTAACTATGC 59.726 45.833 12.15 0.00 37.63 3.14
2843 2904 0.036732 TTCGCCATTGAGCTCCAACT 59.963 50.000 12.15 0.00 37.63 3.16
2844 2905 0.169009 GTTCGCCATTGAGCTCCAAC 59.831 55.000 12.15 0.00 37.63 3.77
2856 2917 2.808523 TGAATTTGCATTGTTCGCCA 57.191 40.000 0.00 0.00 0.00 5.69
2886 2959 8.453238 TCGCCCTTGTGCTTATATTTTAATTA 57.547 30.769 0.00 0.00 0.00 1.40
2889 2962 6.183360 CCTTCGCCCTTGTGCTTATATTTTAA 60.183 38.462 0.00 0.00 0.00 1.52
2900 2974 2.409870 CCATCCTTCGCCCTTGTGC 61.410 63.158 0.00 0.00 0.00 4.57
2903 2977 1.153086 CCTCCATCCTTCGCCCTTG 60.153 63.158 0.00 0.00 0.00 3.61
2906 2980 0.183731 ATTTCCTCCATCCTTCGCCC 59.816 55.000 0.00 0.00 0.00 6.13
2908 2982 1.943340 GTGATTTCCTCCATCCTTCGC 59.057 52.381 0.00 0.00 0.00 4.70
2909 2983 2.092968 TGGTGATTTCCTCCATCCTTCG 60.093 50.000 0.00 0.00 33.79 3.79
2936 3010 1.341089 GGAAGGGGAAGATTTCGGCTT 60.341 52.381 0.00 0.00 0.00 4.35
2937 3011 0.256177 GGAAGGGGAAGATTTCGGCT 59.744 55.000 0.00 0.00 0.00 5.52
2990 3064 3.680786 CTCCTCACACCGACGCCA 61.681 66.667 0.00 0.00 0.00 5.69
2999 3073 1.069090 GACAACGTGCCTCCTCACA 59.931 57.895 0.00 0.00 36.80 3.58
3014 3088 1.901948 ACCTCCAGCTTCGACGACA 60.902 57.895 0.00 0.00 0.00 4.35
3015 3089 1.444553 CACCTCCAGCTTCGACGAC 60.445 63.158 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.