Multiple sequence alignment - TraesCS5A01G491900

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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 TraesCS5A01G491900 chr5A 100.000 2835 0 0 1 2835 660835432 660838266 0.000000e+00 5236.0
1 TraesCS5A01G491900 chr5A 93.214 280 19 0 1181 1460 502528695 502528416 2.030000e-111 412.0
2 TraesCS5A01G491900 chr4D 84.928 2070 115 73 1 1927 481885021 481883006 0.000000e+00 1912.0
3 TraesCS5A01G491900 chr4D 83.088 816 61 31 1945 2748 481883017 481882267 0.000000e+00 671.0
4 TraesCS5A01G491900 chr4D 93.286 283 19 0 1181 1463 211482126 211481844 4.370000e-113 418.0
5 TraesCS5A01G491900 chr4B 83.648 1957 121 82 587 2445 611321521 611319666 0.000000e+00 1657.0
6 TraesCS5A01G491900 chr4B 84.499 529 34 11 1 487 611401923 611401401 1.980000e-131 479.0
7 TraesCS5A01G491900 chr4B 85.373 335 27 9 2427 2751 611319645 611319323 7.570000e-86 327.0
8 TraesCS5A01G491900 chr4B 84.706 85 5 4 2606 2690 541243959 541243883 8.420000e-11 78.7
9 TraesCS5A01G491900 chr1B 91.011 356 29 1 1121 1473 665253068 665252713 7.110000e-131 477.0
10 TraesCS5A01G491900 chr5D 93.571 280 18 0 1181 1460 498728551 498728830 4.370000e-113 418.0
11 TraesCS5A01G491900 chr5D 85.366 82 4 4 2610 2690 495490159 495490085 8.420000e-11 78.7
12 TraesCS5A01G491900 chr7A 92.058 277 22 0 1187 1463 676070042 676069766 9.520000e-105 390.0
13 TraesCS5A01G491900 chr6B 88.489 278 20 5 1186 1463 716387819 716387554 2.720000e-85 326.0
14 TraesCS5A01G491900 chr2B 88.214 280 21 5 1181 1460 638526559 638526826 9.800000e-85 324.0
15 TraesCS5A01G491900 chr3D 84.706 85 5 2 2606 2690 447983660 447983584 8.420000e-11 78.7
16 TraesCS5A01G491900 chr3B 100.000 28 0 0 745 772 631611580 631611553 5.000000e-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 TraesCS5A01G491900 chr5A 660835432 660838266 2834 False 5236.0 5236 100.0000 1 2835 1 chr5A.!!$F1 2834
1 TraesCS5A01G491900 chr4D 481882267 481885021 2754 True 1291.5 1912 84.0080 1 2748 2 chr4D.!!$R2 2747
2 TraesCS5A01G491900 chr4B 611319323 611321521 2198 True 992.0 1657 84.5105 587 2751 2 chr4B.!!$R3 2164
3 TraesCS5A01G491900 chr4B 611401401 611401923 522 True 479.0 479 84.4990 1 487 1 chr4B.!!$R2 486


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
621 719 0.036732 TCTTGCACACCACCCTCATC 59.963 55.0 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2212 2413 0.169009 GTCCGCAAAATCTCCACTGC 59.831 55.0 0.0 0.0 0.0 4.4 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
39 40 2.586079 CGTGCTATCAGCCGGTGG 60.586 66.667 1.90 0.00 41.51 4.61
42 43 0.882042 GTGCTATCAGCCGGTGGATG 60.882 60.000 17.06 6.11 41.51 3.51
44 45 0.882042 GCTATCAGCCGGTGGATGTG 60.882 60.000 17.06 11.74 40.37 3.21
58 59 2.159184 TGGATGTGACGATCAGCTTCTC 60.159 50.000 0.00 0.00 0.00 2.87
72 73 2.452295 CTTCTCTGTGAAGCAGCTGA 57.548 50.000 20.43 0.00 44.62 4.26
99 104 4.451629 AAATTACTCCGCGAGAGAGAAA 57.548 40.909 25.01 17.13 46.50 2.52
137 152 1.936547 GAGATTTCAGACGGTGATGGC 59.063 52.381 0.00 0.00 34.17 4.40
209 254 1.966451 GCCTGAAACTGGACACCGG 60.966 63.158 0.00 0.00 35.68 5.28
228 273 0.185416 GTCGAGTCCCAGGGATAGGA 59.815 60.000 12.84 6.34 32.73 2.94
262 307 1.078426 AATCGTGGGAAAGGAGGCG 60.078 57.895 0.00 0.00 0.00 5.52
313 358 3.737172 CTTTTGGGACGGCGGCAG 61.737 66.667 17.61 0.00 0.00 4.85
437 482 2.136196 CTCGGCGGATAGGACAGAGC 62.136 65.000 7.21 0.00 0.00 4.09
438 483 2.737830 GGCGGATAGGACAGAGCC 59.262 66.667 0.00 0.00 37.61 4.70
459 506 0.171231 GCCAACTTTGATTCCGAGGC 59.829 55.000 0.00 0.00 0.00 4.70
460 507 0.447801 CCAACTTTGATTCCGAGGCG 59.552 55.000 0.00 0.00 0.00 5.52
461 508 1.438651 CAACTTTGATTCCGAGGCGA 58.561 50.000 0.00 0.00 0.00 5.54
462 509 1.128692 CAACTTTGATTCCGAGGCGAC 59.871 52.381 0.00 0.00 0.00 5.19
512 579 1.618861 GATCGCGATCGGGAATACTG 58.381 55.000 34.15 6.36 40.40 2.74
515 582 0.997226 CGCGATCGGGAATACTGACG 60.997 60.000 26.36 8.15 37.28 4.35
522 589 1.535437 CGGGAATACTGACGGTACTGC 60.535 57.143 0.23 0.00 32.72 4.40
542 609 1.792301 GGATGATGGATGCGATGCG 59.208 57.895 0.00 0.00 0.00 4.73
544 611 1.150827 GATGATGGATGCGATGCGAA 58.849 50.000 0.00 0.00 0.00 4.70
550 622 0.040958 GGATGCGATGCGAAATCCAC 60.041 55.000 13.60 0.00 39.63 4.02
600 685 2.571216 CCAGACACGGACGGACCTT 61.571 63.158 0.00 0.00 36.31 3.50
603 688 2.732658 ACACGGACGGACCTTGTC 59.267 61.111 2.98 0.00 46.04 3.18
604 689 1.831286 ACACGGACGGACCTTGTCT 60.831 57.895 2.98 0.00 46.04 3.41
617 714 0.466189 CTTGTCTTGCACACCACCCT 60.466 55.000 0.00 0.00 33.41 4.34
619 717 1.148273 GTCTTGCACACCACCCTCA 59.852 57.895 0.00 0.00 0.00 3.86
620 718 0.250901 GTCTTGCACACCACCCTCAT 60.251 55.000 0.00 0.00 0.00 2.90
621 719 0.036732 TCTTGCACACCACCCTCATC 59.963 55.000 0.00 0.00 0.00 2.92
622 720 0.250858 CTTGCACACCACCCTCATCA 60.251 55.000 0.00 0.00 0.00 3.07
623 721 0.405198 TTGCACACCACCCTCATCAT 59.595 50.000 0.00 0.00 0.00 2.45
624 722 0.322726 TGCACACCACCCTCATCATG 60.323 55.000 0.00 0.00 0.00 3.07
633 731 1.425066 ACCCTCATCATGGTGTTGTGT 59.575 47.619 5.73 0.00 32.36 3.72
933 1076 7.277981 ACGTGGAGAGCAGTAAATAAATACAAG 59.722 37.037 0.00 0.00 0.00 3.16
1085 1233 3.157949 CTCTCCTTCCTCCGCCCC 61.158 72.222 0.00 0.00 0.00 5.80
1126 1274 2.026945 GAGGAGCAGACCAGCTAGCC 62.027 65.000 12.13 0.00 46.75 3.93
1127 1275 2.105930 GAGCAGACCAGCTAGCCG 59.894 66.667 12.13 0.00 46.75 5.52
1128 1276 4.154347 AGCAGACCAGCTAGCCGC 62.154 66.667 12.13 4.96 44.50 6.53
1491 1663 4.637489 CCGGCCGAGCGATGAGAG 62.637 72.222 30.73 0.44 0.00 3.20
1492 1664 3.893763 CGGCCGAGCGATGAGAGT 61.894 66.667 24.07 0.00 0.00 3.24
1493 1665 2.279120 GGCCGAGCGATGAGAGTG 60.279 66.667 0.00 0.00 0.00 3.51
1494 1666 2.775856 GGCCGAGCGATGAGAGTGA 61.776 63.158 0.00 0.00 0.00 3.41
1495 1667 1.299014 GCCGAGCGATGAGAGTGAG 60.299 63.158 0.00 0.00 0.00 3.51
1498 1670 0.729690 CGAGCGATGAGAGTGAGACA 59.270 55.000 0.00 0.00 0.00 3.41
1576 1748 1.938577 CGATTCTTGATCCTGGCTGTG 59.061 52.381 0.00 0.00 0.00 3.66
1580 1752 3.726557 TCTTGATCCTGGCTGTGAATT 57.273 42.857 0.00 0.00 0.00 2.17
1584 1756 4.508551 TGATCCTGGCTGTGAATTACAT 57.491 40.909 0.00 0.00 38.92 2.29
1591 1763 5.416952 CCTGGCTGTGAATTACATCTTCTTT 59.583 40.000 0.00 0.00 38.92 2.52
1693 1873 7.348201 GTTTAAGATGATCGGAATGTAAGCAG 58.652 38.462 0.00 0.00 0.00 4.24
1719 1899 1.589993 CGCTACCTCAGTGCCGATG 60.590 63.158 0.00 0.00 0.00 3.84
1720 1900 1.816537 GCTACCTCAGTGCCGATGA 59.183 57.895 0.00 0.00 0.00 2.92
1721 1901 0.249238 GCTACCTCAGTGCCGATGAG 60.249 60.000 3.57 3.57 43.15 2.90
1723 1903 2.298610 CTACCTCAGTGCCGATGAGTA 58.701 52.381 8.55 2.55 42.18 2.59
1763 1955 5.794894 CCCGCAGATTAGTTGGATAAGTAT 58.205 41.667 0.00 0.00 0.00 2.12
1764 1956 5.869888 CCCGCAGATTAGTTGGATAAGTATC 59.130 44.000 0.00 0.00 0.00 2.24
1765 1957 5.573282 CCGCAGATTAGTTGGATAAGTATCG 59.427 44.000 0.00 0.00 33.52 2.92
1766 1958 6.150318 CGCAGATTAGTTGGATAAGTATCGT 58.850 40.000 0.00 0.00 33.52 3.73
1767 1959 7.303261 CGCAGATTAGTTGGATAAGTATCGTA 58.697 38.462 0.00 0.00 33.52 3.43
1768 1960 7.270793 CGCAGATTAGTTGGATAAGTATCGTAC 59.729 40.741 0.00 0.00 33.52 3.67
1769 1961 8.298140 GCAGATTAGTTGGATAAGTATCGTACT 58.702 37.037 0.00 8.25 41.73 2.73
1770 1962 9.828852 CAGATTAGTTGGATAAGTATCGTACTC 57.171 37.037 7.04 0.00 38.26 2.59
1771 1963 9.012161 AGATTAGTTGGATAAGTATCGTACTCC 57.988 37.037 7.04 0.00 38.26 3.85
1866 2064 4.566987 ACGTGGTAAATTCTCCTTCTCAC 58.433 43.478 0.00 0.00 0.00 3.51
1896 2094 0.969149 AGTGGCTGACAGTGATTCGA 59.031 50.000 3.99 0.00 0.00 3.71
1927 2125 0.178950 ACAGTCCACTCAGGCTCAGA 60.179 55.000 0.00 0.00 37.29 3.27
1928 2126 0.531657 CAGTCCACTCAGGCTCAGAG 59.468 60.000 0.00 0.00 39.04 3.35
1929 2127 0.614415 AGTCCACTCAGGCTCAGAGG 60.614 60.000 0.00 0.00 37.43 3.69
1930 2128 0.902516 GTCCACTCAGGCTCAGAGGT 60.903 60.000 1.29 0.00 37.43 3.85
1931 2129 0.178921 TCCACTCAGGCTCAGAGGTT 60.179 55.000 1.29 0.00 37.43 3.50
1932 2130 0.689623 CCACTCAGGCTCAGAGGTTT 59.310 55.000 0.00 0.00 37.43 3.27
1933 2131 1.072965 CCACTCAGGCTCAGAGGTTTT 59.927 52.381 0.00 0.00 37.43 2.43
1934 2132 2.487986 CCACTCAGGCTCAGAGGTTTTT 60.488 50.000 0.00 0.00 37.43 1.94
1955 2153 4.637483 TTTTTGAAACACTCAGGCTCAG 57.363 40.909 0.00 0.00 34.81 3.35
2032 2230 8.336080 CGATTCTGAAGTATTTTTAGGTTAGCC 58.664 37.037 0.00 0.00 0.00 3.93
2039 2237 7.334844 AGTATTTTTAGGTTAGCCTGCATTC 57.665 36.000 8.65 0.00 46.47 2.67
2040 2238 5.598416 ATTTTTAGGTTAGCCTGCATTCC 57.402 39.130 8.65 0.00 46.47 3.01
2041 2239 2.729028 TTAGGTTAGCCTGCATTCCC 57.271 50.000 8.65 0.00 46.47 3.97
2055 2253 1.208535 CATTCCCTAACCCGTGCTACA 59.791 52.381 0.00 0.00 0.00 2.74
2093 2291 1.298667 GCCGGGAAAGAAGCTGGTA 59.701 57.895 2.18 0.00 0.00 3.25
2094 2292 0.744771 GCCGGGAAAGAAGCTGGTAG 60.745 60.000 2.18 0.00 0.00 3.18
2095 2293 0.613777 CCGGGAAAGAAGCTGGTAGT 59.386 55.000 0.00 0.00 0.00 2.73
2096 2294 1.829222 CCGGGAAAGAAGCTGGTAGTA 59.171 52.381 0.00 0.00 0.00 1.82
2097 2295 2.434702 CCGGGAAAGAAGCTGGTAGTAT 59.565 50.000 0.00 0.00 0.00 2.12
2098 2296 3.118371 CCGGGAAAGAAGCTGGTAGTATT 60.118 47.826 0.00 0.00 0.00 1.89
2099 2297 4.100498 CCGGGAAAGAAGCTGGTAGTATTA 59.900 45.833 0.00 0.00 0.00 0.98
2146 2347 3.642705 TCATGGCTTAATGACGATCGAG 58.357 45.455 24.34 8.58 31.58 4.04
2171 2372 3.537471 CATGTACGCATGTGGCATG 57.463 52.632 22.46 22.46 45.48 4.06
2211 2412 1.999634 GCCTCCCCCATGTACTGCAT 62.000 60.000 0.00 0.00 38.60 3.96
2267 2468 1.562575 GGCAACTGTTGTACCGTCGG 61.563 60.000 20.57 10.48 0.00 4.79
2274 2475 0.509929 GTTGTACCGTCGGCTTCAAC 59.490 55.000 21.78 21.78 0.00 3.18
2310 2522 1.226802 CCGGCGTCAGTGAGAGATG 60.227 63.158 6.01 0.00 0.00 2.90
2311 2523 1.226802 CGGCGTCAGTGAGAGATGG 60.227 63.158 0.00 0.00 0.00 3.51
2322 2534 3.768757 AGTGAGAGATGGACTTGGAGAAG 59.231 47.826 0.00 0.00 35.07 2.85
2337 2549 1.738099 GAAGTCGTGCGTGGCTCAT 60.738 57.895 0.00 0.00 0.00 2.90
2342 2554 2.870372 GTGCGTGGCTCATTGTCC 59.130 61.111 0.00 0.00 0.00 4.02
2347 2559 1.374252 GTGGCTCATTGTCCGACGT 60.374 57.895 0.00 0.00 0.00 4.34
2433 2687 1.213013 CGGTCGTGGGAGAGAAGTG 59.787 63.158 0.00 0.00 0.00 3.16
2493 2747 0.316204 TGGTCGAAAACGAGAGGACC 59.684 55.000 1.68 1.68 45.75 4.46
2496 2750 0.890542 TCGAAAACGAGAGGACCGGA 60.891 55.000 9.46 0.00 0.00 5.14
2504 2758 1.604604 GAGAGGACCGGAGATGAGAG 58.395 60.000 9.46 0.00 0.00 3.20
2516 2782 3.490348 GAGATGAGAGGAGAAGAGGAGG 58.510 54.545 0.00 0.00 0.00 4.30
2526 2792 3.772572 GGAGAAGAGGAGGAGTAGCTTTT 59.227 47.826 0.00 0.00 0.00 2.27
2559 2825 0.745845 CCATGGGACGCTTCTCTTGG 60.746 60.000 10.17 10.17 40.30 3.61
2581 2847 0.594796 CTGCAAACGGACAAACCTGC 60.595 55.000 0.00 0.00 37.70 4.85
2640 2906 3.876198 CCGCGCCGCTGCTTTTAT 61.876 61.111 7.78 0.00 34.43 1.40
2641 2907 2.648724 CGCGCCGCTGCTTTTATG 60.649 61.111 7.78 0.00 34.43 1.90
2642 2908 2.485122 GCGCCGCTGCTTTTATGT 59.515 55.556 0.00 0.00 34.43 2.29
2643 2909 1.719117 GCGCCGCTGCTTTTATGTA 59.281 52.632 0.00 0.00 34.43 2.29
2644 2910 0.098025 GCGCCGCTGCTTTTATGTAA 59.902 50.000 0.00 0.00 34.43 2.41
2645 2911 1.856014 GCGCCGCTGCTTTTATGTAAG 60.856 52.381 0.00 0.00 34.43 2.34
2648 2914 3.543460 CGCCGCTGCTTTTATGTAAGTAC 60.543 47.826 0.00 0.00 34.43 2.73
2666 2932 1.558741 ACGTACGTGTTTTTCGAGCA 58.441 45.000 22.14 0.00 0.00 4.26
2685 2951 0.965439 AGATACGCTGCTGGATCCTC 59.035 55.000 14.23 5.46 0.00 3.71
2686 2952 0.387878 GATACGCTGCTGGATCCTCG 60.388 60.000 14.23 10.71 0.00 4.63
2687 2953 2.427540 ATACGCTGCTGGATCCTCGC 62.428 60.000 14.23 15.68 0.00 5.03
2748 3014 2.135933 GAGAGTTGTTTGACCGTCCAG 58.864 52.381 0.00 0.00 0.00 3.86
2761 3027 1.263217 CCGTCCAGGTTTCAGTTTTCG 59.737 52.381 0.00 0.00 34.51 3.46
2762 3028 1.333791 CGTCCAGGTTTCAGTTTTCGC 60.334 52.381 0.00 0.00 0.00 4.70
2763 3029 1.001706 GTCCAGGTTTCAGTTTTCGCC 60.002 52.381 0.00 0.00 0.00 5.54
2764 3030 1.133915 TCCAGGTTTCAGTTTTCGCCT 60.134 47.619 0.00 0.00 0.00 5.52
2765 3031 1.681264 CCAGGTTTCAGTTTTCGCCTT 59.319 47.619 0.00 0.00 0.00 4.35
2766 3032 2.287608 CCAGGTTTCAGTTTTCGCCTTC 60.288 50.000 0.00 0.00 0.00 3.46
2767 3033 1.954382 AGGTTTCAGTTTTCGCCTTCC 59.046 47.619 0.00 0.00 0.00 3.46
2768 3034 1.954382 GGTTTCAGTTTTCGCCTTCCT 59.046 47.619 0.00 0.00 0.00 3.36
2769 3035 2.361119 GGTTTCAGTTTTCGCCTTCCTT 59.639 45.455 0.00 0.00 0.00 3.36
2770 3036 3.566742 GGTTTCAGTTTTCGCCTTCCTTA 59.433 43.478 0.00 0.00 0.00 2.69
2771 3037 4.037089 GGTTTCAGTTTTCGCCTTCCTTAA 59.963 41.667 0.00 0.00 0.00 1.85
2772 3038 5.278808 GGTTTCAGTTTTCGCCTTCCTTAAT 60.279 40.000 0.00 0.00 0.00 1.40
2773 3039 6.213677 GTTTCAGTTTTCGCCTTCCTTAATT 58.786 36.000 0.00 0.00 0.00 1.40
2774 3040 6.399639 TTCAGTTTTCGCCTTCCTTAATTT 57.600 33.333 0.00 0.00 0.00 1.82
2775 3041 6.009115 TCAGTTTTCGCCTTCCTTAATTTC 57.991 37.500 0.00 0.00 0.00 2.17
2776 3042 5.768164 TCAGTTTTCGCCTTCCTTAATTTCT 59.232 36.000 0.00 0.00 0.00 2.52
2777 3043 6.264518 TCAGTTTTCGCCTTCCTTAATTTCTT 59.735 34.615 0.00 0.00 0.00 2.52
2778 3044 6.582672 CAGTTTTCGCCTTCCTTAATTTCTTC 59.417 38.462 0.00 0.00 0.00 2.87
2779 3045 6.490381 AGTTTTCGCCTTCCTTAATTTCTTCT 59.510 34.615 0.00 0.00 0.00 2.85
2780 3046 6.894339 TTTCGCCTTCCTTAATTTCTTCTT 57.106 33.333 0.00 0.00 0.00 2.52
2781 3047 6.894339 TTCGCCTTCCTTAATTTCTTCTTT 57.106 33.333 0.00 0.00 0.00 2.52
2782 3048 6.894339 TCGCCTTCCTTAATTTCTTCTTTT 57.106 33.333 0.00 0.00 0.00 2.27
2783 3049 7.284919 TCGCCTTCCTTAATTTCTTCTTTTT 57.715 32.000 0.00 0.00 0.00 1.94
2784 3050 8.398878 TCGCCTTCCTTAATTTCTTCTTTTTA 57.601 30.769 0.00 0.00 0.00 1.52
2785 3051 8.852135 TCGCCTTCCTTAATTTCTTCTTTTTAA 58.148 29.630 0.00 0.00 0.00 1.52
2786 3052 9.471084 CGCCTTCCTTAATTTCTTCTTTTTAAA 57.529 29.630 0.00 0.00 0.00 1.52
2791 3057 9.758651 TCCTTAATTTCTTCTTTTTAAAGTGGC 57.241 29.630 2.44 0.00 37.31 5.01
2792 3058 9.541143 CCTTAATTTCTTCTTTTTAAAGTGGCA 57.459 29.630 2.44 0.00 37.31 4.92
2794 3060 7.463469 AATTTCTTCTTTTTAAAGTGGCACG 57.537 32.000 12.71 0.00 37.31 5.34
2795 3061 4.561735 TCTTCTTTTTAAAGTGGCACGG 57.438 40.909 12.71 0.00 37.31 4.94
2796 3062 4.200874 TCTTCTTTTTAAAGTGGCACGGA 58.799 39.130 12.71 0.00 37.31 4.69
2797 3063 3.974871 TCTTTTTAAAGTGGCACGGAC 57.025 42.857 12.71 0.00 37.31 4.79
2798 3064 2.288458 TCTTTTTAAAGTGGCACGGACG 59.712 45.455 12.71 0.00 37.31 4.79
2799 3065 1.666054 TTTTAAAGTGGCACGGACGT 58.334 45.000 12.71 0.00 0.00 4.34
2800 3066 2.522836 TTTAAAGTGGCACGGACGTA 57.477 45.000 12.71 0.00 0.00 3.57
2801 3067 2.522836 TTAAAGTGGCACGGACGTAA 57.477 45.000 12.71 4.90 0.00 3.18
2802 3068 8.148962 TCTTTTTAAAGTGGCACGGACGTAAG 62.149 42.308 12.71 12.82 39.37 2.34
2830 3096 9.398170 ACGATTTTATGATGAAAACTTGACTTG 57.602 29.630 0.00 0.00 31.35 3.16
2831 3097 9.611284 CGATTTTATGATGAAAACTTGACTTGA 57.389 29.630 0.00 0.00 31.35 3.02
2834 3100 9.734620 TTTTATGATGAAAACTTGACTTGACAG 57.265 29.630 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 0.528466 CTGATAGCACGACCGCACAT 60.528 55.000 0.00 0.00 0.00 3.21
39 40 3.435105 AGAGAAGCTGATCGTCACATC 57.565 47.619 0.00 0.00 0.00 3.06
72 73 2.232941 TCTCGCGGAGTAATTTTGTCCT 59.767 45.455 6.13 0.00 0.00 3.85
137 152 0.099968 CAGCATCCGCACCTTGATTG 59.900 55.000 0.00 0.00 42.27 2.67
166 199 0.500178 CGATACTCGCACATGCTTCG 59.500 55.000 1.82 0.00 39.32 3.79
172 205 2.398498 GCAAGATCGATACTCGCACAT 58.602 47.619 0.00 0.00 40.21 3.21
191 224 1.966451 CCGGTGTCCAGTTTCAGGC 60.966 63.158 0.00 0.00 0.00 4.85
209 254 0.185416 TCCTATCCCTGGGACTCGAC 59.815 60.000 19.82 0.00 32.98 4.20
228 273 1.267806 CGATTCTGGCTGCAACAAACT 59.732 47.619 0.50 0.00 0.00 2.66
262 307 1.812922 CGCATGTGCTCCTCTCCAC 60.813 63.158 3.25 0.00 39.32 4.02
316 361 1.597742 ACATAAGTGGCGATCCATGC 58.402 50.000 0.00 0.00 45.62 4.06
317 362 3.002656 GTCAACATAAGTGGCGATCCATG 59.997 47.826 0.00 0.00 45.62 3.66
318 363 3.118261 AGTCAACATAAGTGGCGATCCAT 60.118 43.478 0.00 0.00 45.62 3.41
359 404 7.408756 TTGTCATGGGAATATTTTCTTCAGG 57.591 36.000 0.00 0.00 32.16 3.86
360 405 7.485913 CGTTTGTCATGGGAATATTTTCTTCAG 59.514 37.037 0.00 0.00 32.16 3.02
437 482 0.958382 TCGGAATCAAAGTTGGCCGG 60.958 55.000 15.62 0.00 37.89 6.13
438 483 0.447801 CTCGGAATCAAAGTTGGCCG 59.552 55.000 0.00 11.88 38.31 6.13
459 506 1.846541 AAACAAAAACCATGGCGTCG 58.153 45.000 13.04 0.00 0.00 5.12
460 507 2.933260 ACAAAACAAAAACCATGGCGTC 59.067 40.909 13.04 0.00 0.00 5.19
461 508 2.979240 ACAAAACAAAAACCATGGCGT 58.021 38.095 13.04 0.00 0.00 5.68
462 509 4.094212 CAAACAAAACAAAAACCATGGCG 58.906 39.130 13.04 0.00 0.00 5.69
467 515 7.065563 CCTCATCATCAAACAAAACAAAAACCA 59.934 33.333 0.00 0.00 0.00 3.67
515 582 0.687354 ATCCATCATCCGGCAGTACC 59.313 55.000 0.00 0.00 0.00 3.34
522 589 1.642037 GCATCGCATCCATCATCCGG 61.642 60.000 0.00 0.00 0.00 5.14
542 609 0.716108 CTCGTGCGTCTGTGGATTTC 59.284 55.000 0.00 0.00 0.00 2.17
544 611 1.738099 GCTCGTGCGTCTGTGGATT 60.738 57.895 0.00 0.00 0.00 3.01
550 622 3.756677 CGTGTGCTCGTGCGTCTG 61.757 66.667 4.84 0.00 43.34 3.51
579 664 1.526575 GGTCCGTCCGTGTCTGGTTA 61.527 60.000 0.00 0.00 0.00 2.85
600 685 1.148273 GAGGGTGGTGTGCAAGACA 59.852 57.895 0.00 0.00 0.00 3.41
602 687 0.036732 GATGAGGGTGGTGTGCAAGA 59.963 55.000 0.00 0.00 0.00 3.02
603 688 0.250858 TGATGAGGGTGGTGTGCAAG 60.251 55.000 0.00 0.00 0.00 4.01
604 689 0.405198 ATGATGAGGGTGGTGTGCAA 59.595 50.000 0.00 0.00 0.00 4.08
617 714 1.423161 TCCCACACAACACCATGATGA 59.577 47.619 0.00 0.00 0.00 2.92
619 717 1.881925 CGTCCCACACAACACCATGAT 60.882 52.381 0.00 0.00 0.00 2.45
620 718 0.533978 CGTCCCACACAACACCATGA 60.534 55.000 0.00 0.00 0.00 3.07
621 719 1.948508 CGTCCCACACAACACCATG 59.051 57.895 0.00 0.00 0.00 3.66
622 720 1.896660 GCGTCCCACACAACACCAT 60.897 57.895 0.00 0.00 0.00 3.55
623 721 2.515057 GCGTCCCACACAACACCA 60.515 61.111 0.00 0.00 0.00 4.17
624 722 1.852067 GATGCGTCCCACACAACACC 61.852 60.000 0.00 0.00 0.00 4.16
633 731 4.429212 CGTGTCGGATGCGTCCCA 62.429 66.667 19.51 9.54 41.83 4.37
761 863 3.905678 CTAGGACCAGAGGCGGCG 61.906 72.222 0.51 0.51 0.00 6.46
762 864 3.541713 CCTAGGACCAGAGGCGGC 61.542 72.222 1.05 0.00 0.00 6.53
763 865 0.976073 TTTCCTAGGACCAGAGGCGG 60.976 60.000 12.22 0.00 32.40 6.13
888 1026 4.136250 GGAATTAACCCGAGCCCG 57.864 61.111 0.00 0.00 0.00 6.13
933 1076 0.038526 TCCTTCTCTTTCACGACGCC 60.039 55.000 0.00 0.00 0.00 5.68
1099 1247 1.300542 GTCTGCTCCTCCTATGCGC 60.301 63.158 0.00 0.00 0.00 6.09
1128 1276 4.005472 GCCATTGCGATCGAGGCG 62.005 66.667 21.57 3.57 35.42 5.52
1491 1663 1.478510 AGATGGGATCGTGTGTCTCAC 59.521 52.381 0.00 0.00 43.03 3.51
1492 1664 1.751351 GAGATGGGATCGTGTGTCTCA 59.249 52.381 0.00 0.00 33.93 3.27
1493 1665 1.268794 CGAGATGGGATCGTGTGTCTC 60.269 57.143 0.00 0.00 35.48 3.36
1494 1666 0.741326 CGAGATGGGATCGTGTGTCT 59.259 55.000 0.00 0.00 35.48 3.41
1495 1667 0.249073 CCGAGATGGGATCGTGTGTC 60.249 60.000 0.00 0.00 38.50 3.67
1498 1670 2.021068 CTGCCGAGATGGGATCGTGT 62.021 60.000 0.00 0.00 37.50 4.49
1525 1697 0.390340 AACACTGATCGATGCGTGCT 60.390 50.000 18.53 8.17 0.00 4.40
1576 1748 8.105135 CGAGAGAAACGAAAGAAGATGTAATTC 58.895 37.037 0.00 0.00 0.00 2.17
1580 1752 5.048224 ACCGAGAGAAACGAAAGAAGATGTA 60.048 40.000 0.00 0.00 0.00 2.29
1584 1756 3.608707 CGACCGAGAGAAACGAAAGAAGA 60.609 47.826 0.00 0.00 0.00 2.87
1591 1763 1.081641 GTGCGACCGAGAGAAACGA 60.082 57.895 0.00 0.00 0.00 3.85
1693 1873 2.047274 TGAGGTAGCGGCAACTGC 60.047 61.111 1.45 0.00 41.14 4.40
1765 1957 2.900122 TTGCACGTACGTAGGAGTAC 57.100 50.000 22.34 5.40 42.48 2.73
1766 1958 4.439305 AAATTGCACGTACGTAGGAGTA 57.561 40.909 22.34 10.54 0.00 2.59
1767 1959 3.308438 AAATTGCACGTACGTAGGAGT 57.692 42.857 22.34 10.64 0.00 3.85
1768 1960 4.084223 ACAAAAATTGCACGTACGTAGGAG 60.084 41.667 22.34 14.50 0.00 3.69
1769 1961 3.808726 ACAAAAATTGCACGTACGTAGGA 59.191 39.130 22.34 13.76 0.00 2.94
1770 1962 3.903644 CACAAAAATTGCACGTACGTAGG 59.096 43.478 22.34 11.14 0.00 3.18
1771 1963 4.520078 ACACAAAAATTGCACGTACGTAG 58.480 39.130 22.34 16.04 0.00 3.51
1866 2064 0.964700 TCAGCCACTCACTCAGTCTG 59.035 55.000 0.00 0.00 30.26 3.51
1896 2094 0.900182 TGGACTGTCTGACTGCCGAT 60.900 55.000 13.73 0.00 0.00 4.18
1934 2132 4.016444 ACTGAGCCTGAGTGTTTCAAAAA 58.984 39.130 0.00 0.00 34.81 1.94
1935 2133 3.620488 ACTGAGCCTGAGTGTTTCAAAA 58.380 40.909 0.00 0.00 34.81 2.44
1936 2134 3.281727 ACTGAGCCTGAGTGTTTCAAA 57.718 42.857 0.00 0.00 34.81 2.69
1937 2135 3.281727 AACTGAGCCTGAGTGTTTCAA 57.718 42.857 0.00 0.00 34.81 2.69
1938 2136 4.040339 TCATAACTGAGCCTGAGTGTTTCA 59.960 41.667 0.00 0.00 0.00 2.69
1939 2137 4.390297 GTCATAACTGAGCCTGAGTGTTTC 59.610 45.833 0.00 0.00 30.18 2.78
1940 2138 4.040952 AGTCATAACTGAGCCTGAGTGTTT 59.959 41.667 0.00 0.00 33.32 2.83
1941 2139 3.580458 AGTCATAACTGAGCCTGAGTGTT 59.420 43.478 0.00 0.00 33.32 3.32
1942 2140 3.169099 AGTCATAACTGAGCCTGAGTGT 58.831 45.455 0.00 0.00 33.32 3.55
1943 2141 3.883830 AGTCATAACTGAGCCTGAGTG 57.116 47.619 0.00 0.00 33.32 3.51
1954 2152 1.618837 AGCACCGTGTCAGTCATAACT 59.381 47.619 0.00 0.00 35.60 2.24
1955 2153 2.080286 AGCACCGTGTCAGTCATAAC 57.920 50.000 0.00 0.00 0.00 1.89
2025 2223 2.298610 GTTAGGGAATGCAGGCTAACC 58.701 52.381 0.00 0.00 0.00 2.85
2026 2224 2.298610 GGTTAGGGAATGCAGGCTAAC 58.701 52.381 0.00 0.00 0.00 2.34
2032 2230 1.376609 GCACGGGTTAGGGAATGCAG 61.377 60.000 0.00 0.00 33.27 4.41
2039 2237 1.153429 GCTGTAGCACGGGTTAGGG 60.153 63.158 0.00 0.00 41.59 3.53
2040 2238 1.108776 TAGCTGTAGCACGGGTTAGG 58.891 55.000 6.65 0.00 45.16 2.69
2041 2239 1.202382 GGTAGCTGTAGCACGGGTTAG 60.202 57.143 6.65 0.00 45.16 2.34
2055 2253 2.606519 TGGCGTTCTGGGGTAGCT 60.607 61.111 0.00 0.00 0.00 3.32
2138 2339 2.123251 ATGGGGGAGCTCGATCGT 60.123 61.111 15.94 0.00 0.00 3.73
2146 2347 2.510906 ATGCGTACATGGGGGAGC 59.489 61.111 0.00 0.00 34.35 4.70
2165 2366 1.031571 GGAAGACGGATTGCATGCCA 61.032 55.000 16.68 4.04 0.00 4.92
2166 2367 1.031571 TGGAAGACGGATTGCATGCC 61.032 55.000 16.68 0.00 0.00 4.40
2167 2368 0.379669 CTGGAAGACGGATTGCATGC 59.620 55.000 11.82 11.82 34.07 4.06
2168 2369 2.028420 TCTGGAAGACGGATTGCATG 57.972 50.000 0.00 0.00 38.67 4.06
2211 2412 0.250684 TCCGCAAAATCTCCACTGCA 60.251 50.000 0.00 0.00 34.39 4.41
2212 2413 0.169009 GTCCGCAAAATCTCCACTGC 59.831 55.000 0.00 0.00 0.00 4.40
2213 2414 0.443869 CGTCCGCAAAATCTCCACTG 59.556 55.000 0.00 0.00 0.00 3.66
2214 2415 1.298859 GCGTCCGCAAAATCTCCACT 61.299 55.000 6.82 0.00 41.49 4.00
2215 2416 1.134694 GCGTCCGCAAAATCTCCAC 59.865 57.895 6.82 0.00 41.49 4.02
2260 2461 1.671054 CATGGTTGAAGCCGACGGT 60.671 57.895 16.73 0.00 0.00 4.83
2261 2462 3.039202 GCATGGTTGAAGCCGACGG 62.039 63.158 10.29 10.29 0.00 4.79
2267 2468 2.126346 GCCGTGCATGGTTGAAGC 60.126 61.111 25.67 6.82 0.00 3.86
2322 2534 2.227968 GACAATGAGCCACGCACGAC 62.228 60.000 0.00 0.00 0.00 4.34
2337 2549 1.067974 ACTGACATTGACGTCGGACAA 59.932 47.619 11.62 0.00 43.75 3.18
2342 2554 0.386858 ACCGACTGACATTGACGTCG 60.387 55.000 11.62 18.20 46.21 5.12
2347 2559 0.455464 CGCGTACCGACTGACATTGA 60.455 55.000 0.00 0.00 40.02 2.57
2493 2747 2.158682 TCCTCTTCTCCTCTCATCTCCG 60.159 54.545 0.00 0.00 0.00 4.63
2496 2750 3.130450 TCCTCCTCTTCTCCTCTCATCT 58.870 50.000 0.00 0.00 0.00 2.90
2504 2758 2.748209 AGCTACTCCTCCTCTTCTCC 57.252 55.000 0.00 0.00 0.00 3.71
2516 2782 1.003108 GAGCCTCGCAAAAGCTACTC 58.997 55.000 0.00 0.00 36.87 2.59
2526 2792 3.381983 ATGGACGTGAGCCTCGCA 61.382 61.111 6.04 0.00 0.00 5.10
2549 2815 0.670162 TTTGCAGCACCAAGAGAAGC 59.330 50.000 0.00 0.00 0.00 3.86
2559 2825 0.869880 GGTTTGTCCGTTTGCAGCAC 60.870 55.000 0.00 0.00 0.00 4.40
2581 2847 1.825285 CGATCGCGGCCAGATTCTTG 61.825 60.000 6.13 0.82 0.00 3.02
2638 2904 7.072647 TCGAAAAACACGTACGTACTTACATA 58.927 34.615 22.34 1.51 0.00 2.29
2639 2905 5.912396 TCGAAAAACACGTACGTACTTACAT 59.088 36.000 22.34 4.32 0.00 2.29
2640 2906 5.267009 TCGAAAAACACGTACGTACTTACA 58.733 37.500 22.34 0.00 0.00 2.41
2641 2907 5.660674 GCTCGAAAAACACGTACGTACTTAC 60.661 44.000 22.34 12.75 0.00 2.34
2642 2908 4.378616 GCTCGAAAAACACGTACGTACTTA 59.621 41.667 22.34 1.62 0.00 2.24
2643 2909 3.180387 GCTCGAAAAACACGTACGTACTT 59.820 43.478 22.34 14.05 0.00 2.24
2644 2910 2.721090 GCTCGAAAAACACGTACGTACT 59.279 45.455 22.34 8.16 0.00 2.73
2645 2911 2.467305 TGCTCGAAAAACACGTACGTAC 59.533 45.455 22.34 15.90 0.00 3.67
2648 2914 1.782569 TCTGCTCGAAAAACACGTACG 59.217 47.619 15.01 15.01 0.00 3.67
2666 2932 0.965439 GAGGATCCAGCAGCGTATCT 59.035 55.000 15.82 0.00 0.00 1.98
2724 2990 0.784778 CGGTCAAACAACTCTCTCGC 59.215 55.000 0.00 0.00 0.00 5.03
2727 2993 1.760613 TGGACGGTCAAACAACTCTCT 59.239 47.619 10.76 0.00 0.00 3.10
2730 2996 1.226746 CCTGGACGGTCAAACAACTC 58.773 55.000 10.76 0.00 0.00 3.01
2748 3014 1.954382 AGGAAGGCGAAAACTGAAACC 59.046 47.619 0.00 0.00 0.00 3.27
2751 3017 6.264518 AGAAATTAAGGAAGGCGAAAACTGAA 59.735 34.615 0.00 0.00 0.00 3.02
2752 3018 5.768164 AGAAATTAAGGAAGGCGAAAACTGA 59.232 36.000 0.00 0.00 0.00 3.41
2753 3019 6.013842 AGAAATTAAGGAAGGCGAAAACTG 57.986 37.500 0.00 0.00 0.00 3.16
2754 3020 6.490381 AGAAGAAATTAAGGAAGGCGAAAACT 59.510 34.615 0.00 0.00 0.00 2.66
2755 3021 6.678878 AGAAGAAATTAAGGAAGGCGAAAAC 58.321 36.000 0.00 0.00 0.00 2.43
2756 3022 6.894339 AGAAGAAATTAAGGAAGGCGAAAA 57.106 33.333 0.00 0.00 0.00 2.29
2757 3023 6.894339 AAGAAGAAATTAAGGAAGGCGAAA 57.106 33.333 0.00 0.00 0.00 3.46
2758 3024 6.894339 AAAGAAGAAATTAAGGAAGGCGAA 57.106 33.333 0.00 0.00 0.00 4.70
2759 3025 6.894339 AAAAGAAGAAATTAAGGAAGGCGA 57.106 33.333 0.00 0.00 0.00 5.54
2760 3026 9.471084 TTTAAAAAGAAGAAATTAAGGAAGGCG 57.529 29.630 0.00 0.00 0.00 5.52
2765 3031 9.758651 GCCACTTTAAAAAGAAGAAATTAAGGA 57.241 29.630 9.37 0.00 39.31 3.36
2766 3032 9.541143 TGCCACTTTAAAAAGAAGAAATTAAGG 57.459 29.630 9.37 0.00 39.31 2.69
2768 3034 9.026074 CGTGCCACTTTAAAAAGAAGAAATTAA 57.974 29.630 9.37 0.00 39.31 1.40
2769 3035 7.650104 CCGTGCCACTTTAAAAAGAAGAAATTA 59.350 33.333 9.37 0.00 39.31 1.40
2770 3036 6.478673 CCGTGCCACTTTAAAAAGAAGAAATT 59.521 34.615 9.37 0.00 39.31 1.82
2771 3037 5.983118 CCGTGCCACTTTAAAAAGAAGAAAT 59.017 36.000 9.37 0.00 39.31 2.17
2772 3038 5.125739 TCCGTGCCACTTTAAAAAGAAGAAA 59.874 36.000 9.37 0.00 39.31 2.52
2773 3039 4.641094 TCCGTGCCACTTTAAAAAGAAGAA 59.359 37.500 9.37 0.00 39.31 2.52
2774 3040 4.035909 GTCCGTGCCACTTTAAAAAGAAGA 59.964 41.667 9.37 0.00 39.31 2.87
2775 3041 4.287720 GTCCGTGCCACTTTAAAAAGAAG 58.712 43.478 9.37 1.66 39.31 2.85
2776 3042 3.242804 CGTCCGTGCCACTTTAAAAAGAA 60.243 43.478 9.37 0.00 39.31 2.52
2777 3043 2.288458 CGTCCGTGCCACTTTAAAAAGA 59.712 45.455 9.37 0.00 39.31 2.52
2778 3044 2.032426 ACGTCCGTGCCACTTTAAAAAG 59.968 45.455 0.90 0.90 41.73 2.27
2779 3045 2.015587 ACGTCCGTGCCACTTTAAAAA 58.984 42.857 0.00 0.00 0.00 1.94
2780 3046 1.666054 ACGTCCGTGCCACTTTAAAA 58.334 45.000 0.00 0.00 0.00 1.52
2781 3047 2.522836 TACGTCCGTGCCACTTTAAA 57.477 45.000 1.98 0.00 0.00 1.52
2782 3048 2.224018 ACTTACGTCCGTGCCACTTTAA 60.224 45.455 1.98 0.00 0.00 1.52
2783 3049 1.340889 ACTTACGTCCGTGCCACTTTA 59.659 47.619 1.98 0.00 0.00 1.85
2784 3050 0.105408 ACTTACGTCCGTGCCACTTT 59.895 50.000 1.98 0.00 0.00 2.66
2785 3051 0.961019 TACTTACGTCCGTGCCACTT 59.039 50.000 1.98 0.00 0.00 3.16
2786 3052 0.242017 GTACTTACGTCCGTGCCACT 59.758 55.000 1.98 0.00 0.00 4.00
2787 3053 1.067199 CGTACTTACGTCCGTGCCAC 61.067 60.000 1.98 0.00 44.13 5.01
2788 3054 1.209898 CGTACTTACGTCCGTGCCA 59.790 57.895 1.98 0.00 44.13 4.92
2789 3055 4.062183 CGTACTTACGTCCGTGCC 57.938 61.111 1.98 0.00 44.13 5.01
2804 3070 9.398170 CAAGTCAAGTTTTCATCATAAAATCGT 57.602 29.630 0.00 0.00 31.43 3.73
2805 3071 9.611284 TCAAGTCAAGTTTTCATCATAAAATCG 57.389 29.630 0.00 0.00 31.43 3.34
2808 3074 9.734620 CTGTCAAGTCAAGTTTTCATCATAAAA 57.265 29.630 0.00 0.00 0.00 1.52



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

AutoCloner maintained by Alex Coulton.