Multiple sequence alignment - TraesCS2A01G134300

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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 TraesCS2A01G134300 chr2A 100.000 4468 0 0 1 4468 80620759 80616292 0.000000e+00 8251.0
1 TraesCS2A01G134300 chr2D 90.653 3691 238 55 824 4468 80039219 80035590 0.000000e+00 4806.0
2 TraesCS2A01G134300 chr2D 86.716 813 41 25 1 781 80040006 80039229 0.000000e+00 841.0
3 TraesCS2A01G134300 chr2B 93.463 1958 100 21 2522 4466 131584623 131582681 0.000000e+00 2881.0
4 TraesCS2A01G134300 chr2B 85.967 2601 183 80 3 2526 131587146 131584651 0.000000e+00 2614.0
5 TraesCS2A01G134300 chr2B 90.429 700 41 14 1071 1767 338730051 338729375 0.000000e+00 898.0
6 TraesCS2A01G134300 chr3A 78.587 2349 333 89 1588 3845 1621340 1623609 0.000000e+00 1395.0
7 TraesCS2A01G134300 chrUn 80.059 2051 262 82 1599 3567 270454337 270452352 0.000000e+00 1386.0
8 TraesCS2A01G134300 chrUn 80.059 2051 262 82 1599 3567 270462601 270460616 0.000000e+00 1386.0
9 TraesCS2A01G134300 chrUn 80.059 2051 262 82 1599 3567 280683196 280681211 0.000000e+00 1386.0
10 TraesCS2A01G134300 chrUn 87.209 172 20 2 1058 1228 270454985 270454815 1.270000e-45 195.0
11 TraesCS2A01G134300 chrUn 88.889 99 5 2 4371 4468 168654469 168654376 2.820000e-22 117.0
12 TraesCS2A01G134300 chr3B 79.718 1346 193 42 2520 3845 3260249 3258964 0.000000e+00 900.0
13 TraesCS2A01G134300 chr3B 90.000 700 46 12 1071 1767 395708411 395707733 0.000000e+00 883.0
14 TraesCS2A01G134300 chr3B 80.410 975 133 35 1599 2526 3261241 3260278 0.000000e+00 689.0
15 TraesCS2A01G134300 chr3B 89.071 183 17 2 1049 1228 3261908 3261726 1.620000e-54 224.0
16 TraesCS2A01G134300 chr3B 88.406 69 2 2 4371 4438 35688798 35688861 1.330000e-10 78.7
17 TraesCS2A01G134300 chr3D 83.266 992 120 26 2520 3495 2449542 2448581 0.000000e+00 870.0
18 TraesCS2A01G134300 chr3D 78.974 975 142 35 1603 2526 2450533 2449571 1.370000e-169 606.0
19 TraesCS2A01G134300 chr3D 88.372 172 18 2 1058 1228 2451162 2450992 5.860000e-49 206.0
20 TraesCS2A01G134300 chr5A 90.328 641 38 12 1071 1708 698851609 698852228 0.000000e+00 819.0
21 TraesCS2A01G134300 chr5A 90.177 621 37 12 1091 1708 690644679 690644080 0.000000e+00 787.0
22 TraesCS2A01G134300 chr5D 89.423 104 5 2 4366 4468 489745713 489745811 4.690000e-25 126.0
23 TraesCS2A01G134300 chr7B 88.462 104 6 2 4366 4468 193200034 193199936 2.180000e-23 121.0
24 TraesCS2A01G134300 chr4B 88.462 104 6 3 4366 4468 614205372 614205470 2.180000e-23 121.0
25 TraesCS2A01G134300 chr4D 88.542 96 5 2 4371 4465 200716318 200716408 1.310000e-20 111.0


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 TraesCS2A01G134300 chr2A 80616292 80620759 4467 True 8251.000000 8251 100.000000 1 4468 1 chr2A.!!$R1 4467
1 TraesCS2A01G134300 chr2D 80035590 80040006 4416 True 2823.500000 4806 88.684500 1 4468 2 chr2D.!!$R1 4467
2 TraesCS2A01G134300 chr2B 131582681 131587146 4465 True 2747.500000 2881 89.715000 3 4466 2 chr2B.!!$R2 4463
3 TraesCS2A01G134300 chr2B 338729375 338730051 676 True 898.000000 898 90.429000 1071 1767 1 chr2B.!!$R1 696
4 TraesCS2A01G134300 chr3A 1621340 1623609 2269 False 1395.000000 1395 78.587000 1588 3845 1 chr3A.!!$F1 2257
5 TraesCS2A01G134300 chrUn 270460616 270462601 1985 True 1386.000000 1386 80.059000 1599 3567 1 chrUn.!!$R2 1968
6 TraesCS2A01G134300 chrUn 280681211 280683196 1985 True 1386.000000 1386 80.059000 1599 3567 1 chrUn.!!$R3 1968
7 TraesCS2A01G134300 chrUn 270452352 270454985 2633 True 790.500000 1386 83.634000 1058 3567 2 chrUn.!!$R4 2509
8 TraesCS2A01G134300 chr3B 395707733 395708411 678 True 883.000000 883 90.000000 1071 1767 1 chr3B.!!$R1 696
9 TraesCS2A01G134300 chr3B 3258964 3261908 2944 True 604.333333 900 83.066333 1049 3845 3 chr3B.!!$R2 2796
10 TraesCS2A01G134300 chr3D 2448581 2451162 2581 True 560.666667 870 83.537333 1058 3495 3 chr3D.!!$R1 2437
11 TraesCS2A01G134300 chr5A 698851609 698852228 619 False 819.000000 819 90.328000 1071 1708 1 chr5A.!!$F1 637
12 TraesCS2A01G134300 chr5A 690644080 690644679 599 True 787.000000 787 90.177000 1091 1708 1 chr5A.!!$R1 617

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
783 845 0.308068 ACGTCGCATCATAGTCGAGG 59.692 55.0 0.00 0.0 41.86 4.63 F
1644 1930 0.476771 GGACTGGGAAGGTGAACCAA 59.523 55.0 1.62 0.0 38.89 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1791 2116 0.179468 TAGAGGTTTGCATACGGGGC 59.821 55.0 1.02 0.0 0.00 5.80 R
3496 3938 0.179009 AAGCTGGAGCAAGTGAGCAA 60.179 50.0 0.65 0.0 45.16 3.91 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
48 49 3.957535 CAGCGAATGCATCCCGGC 61.958 66.667 18.84 11.74 46.23 6.13
57 58 2.276116 GCATCCCGGCGGAGAGATA 61.276 63.158 30.79 5.48 43.12 1.98
69 74 1.266446 GGAGAGATAGGGCGTACGTTC 59.734 57.143 17.90 9.53 0.00 3.95
138 143 1.003223 CCAAAACCGACGACAGGAAAC 60.003 52.381 0.00 0.00 0.00 2.78
139 144 1.003223 CAAAACCGACGACAGGAAACC 60.003 52.381 0.00 0.00 0.00 3.27
140 145 0.533531 AAACCGACGACAGGAAACCC 60.534 55.000 0.00 0.00 0.00 4.11
142 147 2.431942 CGACGACAGGAAACCCGG 60.432 66.667 0.00 0.00 0.00 5.73
260 273 4.400251 GGAAACGAAAGGGTTTATTAGGGG 59.600 45.833 0.00 0.00 40.05 4.79
333 346 1.131303 ACCACCATTCCACCGGAGAA 61.131 55.000 9.46 11.67 31.21 2.87
368 387 2.194271 CGCACGTTATCTTCTCTTCCC 58.806 52.381 0.00 0.00 0.00 3.97
416 435 2.691526 CCTAGGTACGTGTGCTAATCCA 59.308 50.000 0.00 0.00 0.00 3.41
417 436 3.321111 CCTAGGTACGTGTGCTAATCCAT 59.679 47.826 0.00 0.00 0.00 3.41
430 453 5.879223 GTGCTAATCCATCCCATCTTATCTG 59.121 44.000 0.00 0.00 0.00 2.90
439 472 4.129380 TCCCATCTTATCTGATTGTTGCG 58.871 43.478 0.00 0.00 0.00 4.85
509 542 2.421952 TAGGTACTAGGTAGGCACCGTG 60.422 54.545 0.00 0.00 45.49 4.94
560 622 3.452627 CCAGCTGAACCAGGAGTAACTAT 59.547 47.826 17.39 0.00 31.21 2.12
561 623 4.649674 CCAGCTGAACCAGGAGTAACTATA 59.350 45.833 17.39 0.00 31.21 1.31
565 627 5.681695 GCTGAACCAGGAGTAACTATACACC 60.682 48.000 0.00 0.00 41.54 4.16
612 674 2.642254 AAGTGTAGCGCGTGCCCTA 61.642 57.895 19.02 0.81 44.31 3.53
615 677 2.106332 GTAGCGCGTGCCCTACAT 59.894 61.111 19.02 0.00 44.31 2.29
639 701 0.834687 TCACTCCCTTGCCTTACCGT 60.835 55.000 0.00 0.00 0.00 4.83
640 702 0.899720 CACTCCCTTGCCTTACCGTA 59.100 55.000 0.00 0.00 0.00 4.02
641 703 0.900421 ACTCCCTTGCCTTACCGTAC 59.100 55.000 0.00 0.00 0.00 3.67
642 704 1.192428 CTCCCTTGCCTTACCGTACT 58.808 55.000 0.00 0.00 0.00 2.73
643 705 2.291800 ACTCCCTTGCCTTACCGTACTA 60.292 50.000 0.00 0.00 0.00 1.82
681 743 4.657824 CCTGTCACCGTCGCCGTT 62.658 66.667 0.00 0.00 0.00 4.44
682 744 3.403057 CTGTCACCGTCGCCGTTG 61.403 66.667 0.00 0.00 0.00 4.10
743 805 2.838202 ACCACTGATAGTAACACCTGGG 59.162 50.000 0.00 0.00 0.00 4.45
783 845 0.308068 ACGTCGCATCATAGTCGAGG 59.692 55.000 0.00 0.00 41.86 4.63
797 859 1.519455 CGAGGCGGTCCATCAGAAC 60.519 63.158 0.00 0.00 33.74 3.01
810 872 3.118775 CCATCAGAACCGTGACCAAGATA 60.119 47.826 0.00 0.00 0.00 1.98
822 884 1.134098 ACCAAGATACCAAGATGCGGG 60.134 52.381 0.00 0.00 0.00 6.13
840 902 2.528797 GTTGCGATCGTGACAACCT 58.471 52.632 19.98 0.00 38.15 3.50
892 954 1.082496 GCAGTGCAGCGAAGACAAC 60.082 57.895 11.09 0.00 0.00 3.32
895 957 0.882042 AGTGCAGCGAAGACAACCAG 60.882 55.000 0.00 0.00 0.00 4.00
921 983 1.344191 ATCCAGCAGGAGCCTCCTTC 61.344 60.000 11.57 6.38 46.91 3.46
923 985 2.690510 AGCAGGAGCCTCCTTCCC 60.691 66.667 11.57 2.50 46.91 3.97
924 986 2.690510 GCAGGAGCCTCCTTCCCT 60.691 66.667 11.57 0.00 46.91 4.20
954 1053 4.379243 AAGGCAGGGCTCGTGTCG 62.379 66.667 0.00 0.00 0.00 4.35
990 1089 1.535444 TTCCTCCTTCCTCGGTGCA 60.535 57.895 0.00 0.00 0.00 4.57
1006 1105 2.981302 CACGGGCAGACATGAGGA 59.019 61.111 0.00 0.00 0.00 3.71
1035 1134 1.004080 ACTGCTGCTGCTGGTAGTG 60.004 57.895 22.83 5.90 41.57 2.74
1038 1137 1.219124 GCTGCTGCTGGTAGTGCTA 59.781 57.895 8.53 0.00 36.03 3.49
1044 1143 2.112898 GCTGGTAGTGCTAGCGGTA 58.887 57.895 10.77 0.58 41.75 4.02
1046 1145 1.390565 CTGGTAGTGCTAGCGGTAGT 58.609 55.000 21.77 6.04 35.74 2.73
1047 1146 1.065701 CTGGTAGTGCTAGCGGTAGTG 59.934 57.143 21.77 0.00 35.74 2.74
1309 1561 4.781087 ACCATAGGTACAAGGTGTGTGTAT 59.219 41.667 0.00 0.00 41.89 2.29
1344 1599 3.118482 ACAATCCTCCTGACTGCTATGTG 60.118 47.826 0.00 0.00 0.00 3.21
1348 1603 3.327757 TCCTCCTGACTGCTATGTGTTTT 59.672 43.478 0.00 0.00 0.00 2.43
1350 1606 4.564406 CCTCCTGACTGCTATGTGTTTTCT 60.564 45.833 0.00 0.00 0.00 2.52
1351 1607 4.569943 TCCTGACTGCTATGTGTTTTCTC 58.430 43.478 0.00 0.00 0.00 2.87
1352 1608 4.284490 TCCTGACTGCTATGTGTTTTCTCT 59.716 41.667 0.00 0.00 0.00 3.10
1353 1609 4.999950 CCTGACTGCTATGTGTTTTCTCTT 59.000 41.667 0.00 0.00 0.00 2.85
1354 1610 5.121454 CCTGACTGCTATGTGTTTTCTCTTC 59.879 44.000 0.00 0.00 0.00 2.87
1355 1611 5.858381 TGACTGCTATGTGTTTTCTCTTCT 58.142 37.500 0.00 0.00 0.00 2.85
1500 1783 5.163099 CCAGGATTTTCCCAGGTATATGTGA 60.163 44.000 0.00 0.00 37.19 3.58
1501 1784 5.765182 CAGGATTTTCCCAGGTATATGTGAC 59.235 44.000 0.00 0.00 37.19 3.67
1502 1785 5.431731 AGGATTTTCCCAGGTATATGTGACA 59.568 40.000 0.00 0.00 37.19 3.58
1503 1786 6.103205 AGGATTTTCCCAGGTATATGTGACAT 59.897 38.462 2.65 2.65 37.19 3.06
1504 1787 6.207417 GGATTTTCCCAGGTATATGTGACATG 59.793 42.308 8.61 0.00 0.00 3.21
1507 1790 4.037222 TCCCAGGTATATGTGACATGTGT 58.963 43.478 8.61 0.00 0.00 3.72
1508 1791 4.129380 CCCAGGTATATGTGACATGTGTG 58.871 47.826 8.61 1.76 0.00 3.82
1509 1792 4.384098 CCCAGGTATATGTGACATGTGTGT 60.384 45.833 8.61 0.00 42.49 3.72
1519 1802 2.550830 ACATGTGTGTCCTGAACTCC 57.449 50.000 0.00 0.00 31.41 3.85
1520 1803 2.050144 ACATGTGTGTCCTGAACTCCT 58.950 47.619 0.00 0.00 31.41 3.69
1521 1804 2.224378 ACATGTGTGTCCTGAACTCCTG 60.224 50.000 0.00 0.00 31.41 3.86
1522 1805 1.788229 TGTGTGTCCTGAACTCCTGA 58.212 50.000 0.00 0.00 0.00 3.86
1523 1806 2.329267 TGTGTGTCCTGAACTCCTGAT 58.671 47.619 0.00 0.00 0.00 2.90
1524 1807 2.300152 TGTGTGTCCTGAACTCCTGATC 59.700 50.000 0.00 0.00 0.00 2.92
1535 1818 3.491766 ACTCCTGATCCCTCCAACTAA 57.508 47.619 0.00 0.00 0.00 2.24
1540 1823 3.274288 CTGATCCCTCCAACTAAAGCAC 58.726 50.000 0.00 0.00 0.00 4.40
1561 1844 5.633182 GCACTTTGCTAATTTTCGATCCAAA 59.367 36.000 0.00 0.00 40.96 3.28
1644 1930 0.476771 GGACTGGGAAGGTGAACCAA 59.523 55.000 1.62 0.00 38.89 3.67
1730 2049 1.227205 CCTAGGCAAGCAGCTCTCG 60.227 63.158 0.00 0.00 44.79 4.04
1791 2116 7.272244 TGTATATAATGGTGGATTAGGCATCG 58.728 38.462 0.00 0.00 31.73 3.84
1859 2184 1.144936 GCAGTACCTAGGCTGGCTG 59.855 63.158 14.70 12.67 33.62 4.85
1887 2212 5.346822 CCAAAGATTGTGTAAGCATTTCAGC 59.653 40.000 0.00 0.00 0.00 4.26
1888 2213 5.710513 AAGATTGTGTAAGCATTTCAGCA 57.289 34.783 0.00 0.00 36.85 4.41
1889 2214 5.909621 AGATTGTGTAAGCATTTCAGCAT 57.090 34.783 0.00 0.00 36.85 3.79
1890 2215 6.276832 AGATTGTGTAAGCATTTCAGCATT 57.723 33.333 0.00 0.00 36.85 3.56
1891 2216 6.694447 AGATTGTGTAAGCATTTCAGCATTT 58.306 32.000 0.00 0.00 36.85 2.32
1892 2217 6.810182 AGATTGTGTAAGCATTTCAGCATTTC 59.190 34.615 0.00 0.00 36.85 2.17
1893 2218 5.450592 TGTGTAAGCATTTCAGCATTTCA 57.549 34.783 0.00 0.00 36.85 2.69
1894 2219 5.463286 TGTGTAAGCATTTCAGCATTTCAG 58.537 37.500 0.00 0.00 36.85 3.02
1930 2263 1.718396 TTCAGAGCTGAATGTGAGCG 58.282 50.000 8.76 0.00 43.90 5.03
1943 2277 0.867746 GTGAGCGTGTCTTTGATGCA 59.132 50.000 0.00 0.00 0.00 3.96
1952 2296 4.540824 GTGTCTTTGATGCAGTTTCCTTC 58.459 43.478 0.00 0.00 0.00 3.46
1953 2297 4.276926 GTGTCTTTGATGCAGTTTCCTTCT 59.723 41.667 0.00 0.00 0.00 2.85
1954 2298 4.889409 TGTCTTTGATGCAGTTTCCTTCTT 59.111 37.500 0.00 0.00 0.00 2.52
1955 2299 5.360714 TGTCTTTGATGCAGTTTCCTTCTTT 59.639 36.000 0.00 0.00 0.00 2.52
1956 2300 6.127366 TGTCTTTGATGCAGTTTCCTTCTTTT 60.127 34.615 0.00 0.00 0.00 2.27
1957 2301 6.758416 GTCTTTGATGCAGTTTCCTTCTTTTT 59.242 34.615 0.00 0.00 0.00 1.94
2036 2380 2.104963 AGACAGGGTGAAGAACTGGTTC 59.895 50.000 5.43 5.43 39.78 3.62
2219 2563 3.946558 ACCGTGAGAAGTATCAGGTAGAC 59.053 47.826 0.00 0.00 34.11 2.59
2220 2564 4.200874 CCGTGAGAAGTATCAGGTAGACT 58.799 47.826 0.00 0.00 34.11 3.24
2456 2836 4.625225 AACCCATTTCACCCAGGATAAT 57.375 40.909 0.00 0.00 0.00 1.28
2457 2837 4.625225 ACCCATTTCACCCAGGATAATT 57.375 40.909 0.00 0.00 0.00 1.40
2458 2838 4.959080 ACCCATTTCACCCAGGATAATTT 58.041 39.130 0.00 0.00 0.00 1.82
2517 2897 2.404215 CCACCAACTGTCACTACTTCG 58.596 52.381 0.00 0.00 0.00 3.79
2540 2956 0.623723 GCAGGTTCCTTGACCCCATA 59.376 55.000 0.00 0.00 40.73 2.74
2613 3029 2.811317 GCTTCAGTGCCGACGAGG 60.811 66.667 0.00 0.00 44.97 4.63
2690 3106 3.411517 ATGAAGGACCCTGGGGCG 61.412 66.667 18.88 0.00 39.32 6.13
2755 3171 3.376546 GGATTTGTCTGTGAGATCTTGCC 59.623 47.826 0.00 0.00 0.00 4.52
2781 3200 3.582647 TCACTCCAAATCCTTCTGCTGTA 59.417 43.478 0.00 0.00 0.00 2.74
2782 3201 4.225942 TCACTCCAAATCCTTCTGCTGTAT 59.774 41.667 0.00 0.00 0.00 2.29
2783 3202 5.425217 TCACTCCAAATCCTTCTGCTGTATA 59.575 40.000 0.00 0.00 0.00 1.47
2784 3203 5.525378 CACTCCAAATCCTTCTGCTGTATAC 59.475 44.000 0.00 0.00 0.00 1.47
2785 3204 5.426833 ACTCCAAATCCTTCTGCTGTATACT 59.573 40.000 4.17 0.00 0.00 2.12
2786 3205 6.069963 ACTCCAAATCCTTCTGCTGTATACTT 60.070 38.462 4.17 0.00 0.00 2.24
2789 3208 7.769044 TCCAAATCCTTCTGCTGTATACTTTAC 59.231 37.037 4.17 0.00 0.00 2.01
2790 3209 7.552687 CCAAATCCTTCTGCTGTATACTTTACA 59.447 37.037 4.17 0.00 0.00 2.41
2794 3220 9.686683 ATCCTTCTGCTGTATACTTTACATTTT 57.313 29.630 4.17 0.00 0.00 1.82
2814 3240 6.505044 TTTTTCAGATCCTCATGATGTGTG 57.495 37.500 0.00 0.00 43.47 3.82
2819 3245 1.812235 TCCTCATGATGTGTGTGTGC 58.188 50.000 0.00 0.00 0.00 4.57
2868 3294 0.319211 TTGGACCTCGTGTAAGTGCG 60.319 55.000 0.00 0.00 0.00 5.34
2869 3295 1.288127 GGACCTCGTGTAAGTGCGT 59.712 57.895 0.00 0.00 0.00 5.24
2872 3298 1.862827 GACCTCGTGTAAGTGCGTTTT 59.137 47.619 0.00 0.00 0.00 2.43
2873 3299 3.052036 GACCTCGTGTAAGTGCGTTTTA 58.948 45.455 0.00 0.00 0.00 1.52
2876 3302 3.054878 CTCGTGTAAGTGCGTTTTAGGT 58.945 45.455 0.00 0.00 0.00 3.08
2884 3311 7.532884 GTGTAAGTGCGTTTTAGGTTTATCTTG 59.467 37.037 0.00 0.00 0.00 3.02
3143 3582 8.840833 AAACAACAAATTGAAACTTAGGTGTT 57.159 26.923 0.00 0.00 39.30 3.32
3383 3823 1.143969 CCCGTTTCGGCATCGTCTAC 61.144 60.000 2.41 0.00 46.86 2.59
3449 3889 3.181451 TGTGGTTCAAGAACATGCTCTCT 60.181 43.478 14.25 0.00 42.85 3.10
3484 3924 3.054139 AGCTAGGATTGCAAACAGGATCA 60.054 43.478 1.71 0.00 0.00 2.92
3496 3938 1.293458 ACAGGATCAGGGAGGATCAGT 59.707 52.381 5.63 1.26 44.38 3.41
3497 3939 2.293452 ACAGGATCAGGGAGGATCAGTT 60.293 50.000 5.63 0.00 44.38 3.16
3498 3940 2.104451 CAGGATCAGGGAGGATCAGTTG 59.896 54.545 5.63 0.00 44.38 3.16
3499 3941 1.202746 GGATCAGGGAGGATCAGTTGC 60.203 57.143 5.63 0.00 44.38 4.17
3500 3942 1.767681 GATCAGGGAGGATCAGTTGCT 59.232 52.381 0.00 0.00 42.58 3.91
3501 3943 1.198713 TCAGGGAGGATCAGTTGCTC 58.801 55.000 0.00 0.00 41.82 4.26
3502 3944 0.907486 CAGGGAGGATCAGTTGCTCA 59.093 55.000 2.74 0.00 44.19 4.26
3503 3945 0.908198 AGGGAGGATCAGTTGCTCAC 59.092 55.000 2.74 0.00 46.09 3.51
3577 4028 8.691661 AGCACCTCAGAATTTTAAGAAACTTA 57.308 30.769 0.00 0.00 0.00 2.24
3629 4083 6.169557 TGCCCGCCCTTATATATAATACAG 57.830 41.667 5.64 0.00 0.00 2.74
3723 4181 7.593825 AGGTAAACTGAAGCACATGAAATAAC 58.406 34.615 0.00 0.00 0.00 1.89
3729 4187 7.310664 ACTGAAGCACATGAAATAACTGAATG 58.689 34.615 0.00 0.00 0.00 2.67
3765 4224 5.281693 TGAGACAATTTCAACAGCATACG 57.718 39.130 0.00 0.00 0.00 3.06
3801 4260 2.223433 GGAAAGCCAGATGAGCAATTCG 60.223 50.000 0.00 0.00 32.35 3.34
3957 4426 8.504815 TCATGAAACTGCTATCTATACGACTAC 58.495 37.037 0.00 0.00 0.00 2.73
4093 4562 1.448985 TCGATTAAACAGCAGGTGCC 58.551 50.000 0.00 0.00 43.38 5.01
4175 4646 2.858344 CCAACTCCTTCGCTATAACACG 59.142 50.000 0.00 0.00 0.00 4.49
4194 4665 4.000988 CACGGCTTACTTAACTTCACCAT 58.999 43.478 0.00 0.00 0.00 3.55
4375 4848 2.093021 AGGTTGCCACAAAATTTGCAGT 60.093 40.909 5.52 0.00 34.81 4.40
4389 4862 1.388547 TGCAGTGTTCAGGGTTCAAC 58.611 50.000 0.00 0.00 0.00 3.18
4462 4935 9.076596 GGACAAGTTAATCAGATTTAACATTGC 57.923 33.333 0.00 6.99 42.11 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.550524 TGGGTGGAGAGATCTTCGTTG 59.449 52.381 0.00 0.00 0.00 4.10
16 17 1.145819 GCTGCTGGGTGGAGAGATC 59.854 63.158 0.00 0.00 36.08 2.75
48 49 0.883814 ACGTACGCCCTATCTCTCCG 60.884 60.000 16.72 0.00 0.00 4.63
238 243 4.400251 CCCCCTAATAAACCCTTTCGTTTC 59.600 45.833 0.00 0.00 37.20 2.78
368 387 4.155733 TATGGGCGCCACGACAGG 62.156 66.667 30.85 0.00 36.10 4.00
416 435 4.758674 CGCAACAATCAGATAAGATGGGAT 59.241 41.667 4.94 0.00 0.00 3.85
417 436 4.129380 CGCAACAATCAGATAAGATGGGA 58.871 43.478 4.94 0.00 0.00 4.37
439 472 1.194772 GTTGGACTTGAACTGCGCTAC 59.805 52.381 9.73 0.00 0.00 3.58
486 519 2.225467 GGTGCCTACCTAGTACCTACG 58.775 57.143 0.00 0.00 43.97 3.51
491 524 1.467920 ACACGGTGCCTACCTAGTAC 58.532 55.000 8.30 0.00 45.22 2.73
492 525 2.643551 GTACACGGTGCCTACCTAGTA 58.356 52.381 8.30 0.00 45.22 1.82
493 526 1.467920 GTACACGGTGCCTACCTAGT 58.532 55.000 8.30 0.00 45.22 2.57
494 527 0.379669 CGTACACGGTGCCTACCTAG 59.620 60.000 8.30 0.00 45.22 3.02
496 529 0.322456 TACGTACACGGTGCCTACCT 60.322 55.000 8.30 0.00 45.22 3.08
560 622 1.606994 CGTGCTAGCTTTGGTGGTGTA 60.607 52.381 17.23 0.00 0.00 2.90
561 623 0.884704 CGTGCTAGCTTTGGTGGTGT 60.885 55.000 17.23 0.00 0.00 4.16
565 627 1.915614 CTGCCGTGCTAGCTTTGGTG 61.916 60.000 17.23 8.34 0.00 4.17
612 674 2.578021 AGGCAAGGGAGTGAATGTATGT 59.422 45.455 0.00 0.00 0.00 2.29
615 677 3.054655 GGTAAGGCAAGGGAGTGAATGTA 60.055 47.826 0.00 0.00 0.00 2.29
680 742 1.153066 TCCAAGCCACTGAACGCAA 60.153 52.632 0.00 0.00 0.00 4.85
681 743 1.597854 CTCCAAGCCACTGAACGCA 60.598 57.895 0.00 0.00 0.00 5.24
682 744 2.970974 GCTCCAAGCCACTGAACGC 61.971 63.158 0.00 0.00 34.48 4.84
683 745 3.257933 GCTCCAAGCCACTGAACG 58.742 61.111 0.00 0.00 34.48 3.95
743 805 0.166814 GCCTTGATGCTGACACGTTC 59.833 55.000 0.00 0.00 0.00 3.95
797 859 3.198068 CATCTTGGTATCTTGGTCACGG 58.802 50.000 0.00 0.00 0.00 4.94
810 872 2.819984 ATCGCAACCCGCATCTTGGT 62.820 55.000 0.00 0.00 42.60 3.67
822 884 0.865769 AAGGTTGTCACGATCGCAAC 59.134 50.000 21.57 21.57 41.02 4.17
840 902 1.841663 GCAGCTCGGTTCGAAGCAAA 61.842 55.000 25.46 12.76 34.74 3.68
892 954 1.833630 TCCTGCTGGATTACTGACTGG 59.166 52.381 8.48 0.00 37.46 4.00
895 957 1.474143 GGCTCCTGCTGGATTACTGAC 60.474 57.143 13.33 0.00 42.29 3.51
917 979 1.772453 TCCGGGCTTTATAAGGGAAGG 59.228 52.381 0.00 0.00 0.00 3.46
918 980 3.477530 CTTCCGGGCTTTATAAGGGAAG 58.522 50.000 0.00 12.67 43.01 3.46
919 981 2.173996 CCTTCCGGGCTTTATAAGGGAA 59.826 50.000 0.00 1.55 34.35 3.97
921 983 2.271944 CCTTCCGGGCTTTATAAGGG 57.728 55.000 0.00 0.00 34.35 3.95
954 1053 3.471806 GGAGGGAGGAAGGACGGC 61.472 72.222 0.00 0.00 0.00 5.68
960 1059 0.341609 AGGAGGAAGGAGGGAGGAAG 59.658 60.000 0.00 0.00 0.00 3.46
990 1089 2.660064 GGTCCTCATGTCTGCCCGT 61.660 63.158 0.00 0.00 0.00 5.28
1021 1120 0.809241 GCTAGCACTACCAGCAGCAG 60.809 60.000 10.63 0.00 36.68 4.24
1027 1126 1.065701 CACTACCGCTAGCACTACCAG 59.934 57.143 16.45 5.00 0.00 4.00
1309 1561 7.987458 GTCAGGAGGATTGTTCATTCAGTATAA 59.013 37.037 0.00 0.00 0.00 0.98
1344 1599 5.125578 ACCAAGAAACACCAGAAGAGAAAAC 59.874 40.000 0.00 0.00 0.00 2.43
1348 1603 3.433598 CCACCAAGAAACACCAGAAGAGA 60.434 47.826 0.00 0.00 0.00 3.10
1350 1606 2.241176 ACCACCAAGAAACACCAGAAGA 59.759 45.455 0.00 0.00 0.00 2.87
1351 1607 2.358898 CACCACCAAGAAACACCAGAAG 59.641 50.000 0.00 0.00 0.00 2.85
1352 1608 2.291282 ACACCACCAAGAAACACCAGAA 60.291 45.455 0.00 0.00 0.00 3.02
1353 1609 1.283613 ACACCACCAAGAAACACCAGA 59.716 47.619 0.00 0.00 0.00 3.86
1354 1610 1.676006 GACACCACCAAGAAACACCAG 59.324 52.381 0.00 0.00 0.00 4.00
1355 1611 1.683629 GGACACCACCAAGAAACACCA 60.684 52.381 0.00 0.00 0.00 4.17
1500 1783 2.050144 AGGAGTTCAGGACACACATGT 58.950 47.619 0.00 0.00 43.71 3.21
1501 1784 2.037641 TCAGGAGTTCAGGACACACATG 59.962 50.000 0.00 0.00 0.00 3.21
1502 1785 2.329267 TCAGGAGTTCAGGACACACAT 58.671 47.619 0.00 0.00 0.00 3.21
1503 1786 1.788229 TCAGGAGTTCAGGACACACA 58.212 50.000 0.00 0.00 0.00 3.72
1504 1787 2.354203 GGATCAGGAGTTCAGGACACAC 60.354 54.545 0.00 0.00 0.00 3.82
1507 1790 1.079490 AGGGATCAGGAGTTCAGGACA 59.921 52.381 0.00 0.00 0.00 4.02
1508 1791 1.760029 GAGGGATCAGGAGTTCAGGAC 59.240 57.143 0.00 0.00 0.00 3.85
1509 1792 1.343478 GGAGGGATCAGGAGTTCAGGA 60.343 57.143 0.00 0.00 0.00 3.86
1513 1796 2.192263 AGTTGGAGGGATCAGGAGTTC 58.808 52.381 0.00 0.00 0.00 3.01
1514 1797 2.350863 AGTTGGAGGGATCAGGAGTT 57.649 50.000 0.00 0.00 0.00 3.01
1515 1798 3.491766 TTAGTTGGAGGGATCAGGAGT 57.508 47.619 0.00 0.00 0.00 3.85
1516 1799 3.432890 GCTTTAGTTGGAGGGATCAGGAG 60.433 52.174 0.00 0.00 0.00 3.69
1517 1800 2.505819 GCTTTAGTTGGAGGGATCAGGA 59.494 50.000 0.00 0.00 0.00 3.86
1518 1801 2.239654 TGCTTTAGTTGGAGGGATCAGG 59.760 50.000 0.00 0.00 0.00 3.86
1519 1802 3.054802 AGTGCTTTAGTTGGAGGGATCAG 60.055 47.826 0.00 0.00 0.00 2.90
1520 1803 2.912956 AGTGCTTTAGTTGGAGGGATCA 59.087 45.455 0.00 0.00 0.00 2.92
1521 1804 3.636153 AGTGCTTTAGTTGGAGGGATC 57.364 47.619 0.00 0.00 0.00 3.36
1522 1805 4.082125 CAAAGTGCTTTAGTTGGAGGGAT 58.918 43.478 0.00 0.00 0.00 3.85
1523 1806 3.486383 CAAAGTGCTTTAGTTGGAGGGA 58.514 45.455 0.00 0.00 0.00 4.20
1524 1807 2.029918 GCAAAGTGCTTTAGTTGGAGGG 60.030 50.000 0.00 0.00 40.96 4.30
1582 1866 7.050970 ACACAACTCTACATCAGAAACTACA 57.949 36.000 0.00 0.00 31.12 2.74
1644 1930 4.737578 TGTTGTAGTAGTCCACTCCTTCT 58.262 43.478 0.00 0.00 38.80 2.85
1791 2116 0.179468 TAGAGGTTTGCATACGGGGC 59.821 55.000 1.02 0.00 0.00 5.80
1859 2184 2.819608 TGCTTACACAATCTTTGGGCTC 59.180 45.455 0.00 0.00 37.68 4.70
1918 2251 2.802247 TCAAAGACACGCTCACATTCAG 59.198 45.455 0.00 0.00 0.00 3.02
1924 2257 0.867746 TGCATCAAAGACACGCTCAC 59.132 50.000 0.00 0.00 0.00 3.51
1926 2259 1.151668 ACTGCATCAAAGACACGCTC 58.848 50.000 0.00 0.00 0.00 5.03
1930 2263 4.276926 AGAAGGAAACTGCATCAAAGACAC 59.723 41.667 0.00 0.00 42.68 3.67
1954 2298 4.398673 ACGCGCCCCTTTTATATACAAAAA 59.601 37.500 5.73 0.00 0.00 1.94
1955 2299 3.946558 ACGCGCCCCTTTTATATACAAAA 59.053 39.130 5.73 0.00 0.00 2.44
1956 2300 3.543665 ACGCGCCCCTTTTATATACAAA 58.456 40.909 5.73 0.00 0.00 2.83
1957 2301 3.196939 ACGCGCCCCTTTTATATACAA 57.803 42.857 5.73 0.00 0.00 2.41
1958 2302 2.914695 ACGCGCCCCTTTTATATACA 57.085 45.000 5.73 0.00 0.00 2.29
1959 2303 3.850740 GCAAACGCGCCCCTTTTATATAC 60.851 47.826 5.73 0.00 0.00 1.47
1960 2304 2.291190 GCAAACGCGCCCCTTTTATATA 59.709 45.455 5.73 0.00 0.00 0.86
1961 2305 1.066454 GCAAACGCGCCCCTTTTATAT 59.934 47.619 5.73 0.00 0.00 0.86
2036 2380 1.738099 CCTCGGCTCGTTGAAGGTG 60.738 63.158 0.00 0.00 0.00 4.00
2075 2419 2.827051 CGCATGGAGGCCATTGTCG 61.827 63.158 5.01 0.00 42.23 4.35
2105 2449 2.987547 CCTGCAGGGCACTTGGTG 60.988 66.667 26.14 0.00 33.79 4.17
2106 2450 3.177884 TCCTGCAGGGCACTTGGT 61.178 61.111 32.23 0.00 33.79 3.67
2138 2482 2.461110 CGTGGCAATGTACGGCTCC 61.461 63.158 0.00 0.00 36.71 4.70
2194 2538 6.933521 GTCTACCTGATACTTCTCACGGTATA 59.066 42.308 0.00 0.00 32.96 1.47
2266 2620 1.815003 CAAATTCACTCCTGGGCACTC 59.185 52.381 0.00 0.00 0.00 3.51
2458 2838 5.394115 GCAACCTGAACTTCTGAAGGAAAAA 60.394 40.000 20.61 2.16 33.07 1.94
2463 2843 2.575532 TGCAACCTGAACTTCTGAAGG 58.424 47.619 20.61 6.58 35.82 3.46
2478 2858 1.235724 GGTAGACCCTGTGTTGCAAC 58.764 55.000 22.83 22.83 0.00 4.17
2517 2897 0.673985 GGGTCAAGGAACCTGCAAAC 59.326 55.000 0.00 0.00 36.31 2.93
2549 2965 1.547820 AGCATCGACGATGGATAGCAT 59.452 47.619 32.61 10.40 40.10 3.79
2550 2966 0.961753 AGCATCGACGATGGATAGCA 59.038 50.000 32.61 0.00 40.10 3.49
2613 3029 1.000396 AGCCTTTCACCATCCTGGC 60.000 57.895 0.00 0.00 42.67 4.85
2690 3106 4.309950 ACCGGCGTCTGGTTCCAC 62.310 66.667 6.01 0.00 35.82 4.02
2755 3171 3.350833 CAGAAGGATTTGGAGTGAAGGG 58.649 50.000 0.00 0.00 0.00 3.95
2782 3201 9.958180 TCATGAGGATCTGAAAAATGTAAAGTA 57.042 29.630 0.00 0.00 34.92 2.24
2783 3202 8.868522 TCATGAGGATCTGAAAAATGTAAAGT 57.131 30.769 0.00 0.00 34.92 2.66
2784 3203 9.731819 CATCATGAGGATCTGAAAAATGTAAAG 57.268 33.333 0.00 0.00 32.57 1.85
2785 3204 9.246670 ACATCATGAGGATCTGAAAAATGTAAA 57.753 29.630 15.42 0.00 32.57 2.01
2786 3205 8.680001 CACATCATGAGGATCTGAAAAATGTAA 58.320 33.333 15.42 0.00 32.57 2.41
2789 3208 6.972901 CACACATCATGAGGATCTGAAAAATG 59.027 38.462 15.42 0.03 32.57 2.32
2790 3209 6.662234 ACACACATCATGAGGATCTGAAAAAT 59.338 34.615 15.42 0.00 32.57 1.82
2794 3220 4.019950 ACACACACATCATGAGGATCTGAA 60.020 41.667 15.42 0.00 32.57 3.02
2819 3245 3.057315 ACCATTTCGTTCATCTGCAAAGG 60.057 43.478 0.00 0.00 0.00 3.11
3066 3497 5.607477 TCATCAGTACCGTTTTCAGAAAGT 58.393 37.500 0.00 0.00 0.00 2.66
3130 3569 6.431198 TGTCAGTGAAAACACCTAAGTTTC 57.569 37.500 0.00 0.00 40.60 2.78
3131 3570 6.127730 CCTTGTCAGTGAAAACACCTAAGTTT 60.128 38.462 0.00 0.00 43.13 2.66
3138 3577 4.421058 GTTTCCTTGTCAGTGAAAACACC 58.579 43.478 10.96 0.00 30.47 4.16
3139 3578 4.095610 CGTTTCCTTGTCAGTGAAAACAC 58.904 43.478 14.56 0.00 30.47 3.32
3140 3579 4.004314 TCGTTTCCTTGTCAGTGAAAACA 58.996 39.130 14.56 0.00 30.47 2.83
3141 3580 4.609691 TCGTTTCCTTGTCAGTGAAAAC 57.390 40.909 0.00 0.69 30.47 2.43
3143 3582 4.878971 TCATTCGTTTCCTTGTCAGTGAAA 59.121 37.500 0.00 0.00 0.00 2.69
3150 3589 5.942872 ACATTGATCATTCGTTTCCTTGTC 58.057 37.500 0.00 0.00 0.00 3.18
3239 3679 2.879646 GTCTCTGTAGTACCGGATCCTG 59.120 54.545 9.46 5.80 0.00 3.86
3311 3751 3.710209 AGCAGAGACCAAGCAAAGTAT 57.290 42.857 0.00 0.00 0.00 2.12
3449 3889 4.534647 ATCCTAGCTCCTCTTCTTCTCA 57.465 45.455 0.00 0.00 0.00 3.27
3484 3924 0.908198 GTGAGCAACTGATCCTCCCT 59.092 55.000 0.00 0.00 0.00 4.20
3496 3938 0.179009 AAGCTGGAGCAAGTGAGCAA 60.179 50.000 0.65 0.00 45.16 3.91
3497 3939 0.179009 AAAGCTGGAGCAAGTGAGCA 60.179 50.000 0.65 0.00 45.16 4.26
3498 3940 0.520847 GAAAGCTGGAGCAAGTGAGC 59.479 55.000 0.65 0.00 45.16 4.26
3499 3941 1.805345 CTGAAAGCTGGAGCAAGTGAG 59.195 52.381 0.65 0.00 45.16 3.51
3500 3942 1.417517 TCTGAAAGCTGGAGCAAGTGA 59.582 47.619 0.65 0.00 45.16 3.41
3501 3943 1.888215 TCTGAAAGCTGGAGCAAGTG 58.112 50.000 0.65 0.00 45.16 3.16
3502 3944 2.645838 TTCTGAAAGCTGGAGCAAGT 57.354 45.000 0.65 0.00 45.16 3.16
3503 3945 5.633830 TTTATTCTGAAAGCTGGAGCAAG 57.366 39.130 0.65 0.00 45.16 4.01
3577 4028 6.880529 CCACAATCTCAATGGCCTTTTATTTT 59.119 34.615 3.32 0.00 0.00 1.82
3612 4063 8.768397 TGCTTCCCACTGTATTATATATAAGGG 58.232 37.037 14.83 14.83 0.00 3.95
3629 4083 2.508526 AGACATGTCTTTGCTTCCCAC 58.491 47.619 22.89 0.00 36.31 4.61
3801 4260 0.825840 TTGGGGTACTGGTTTGCAGC 60.826 55.000 0.00 0.00 0.00 5.25
3862 4331 5.631026 GCAAGAAGCACGAGAAATAATTGA 58.369 37.500 0.00 0.00 44.79 2.57
3929 4398 8.240682 AGTCGTATAGATAGCAGTTTCATGATC 58.759 37.037 0.00 0.00 0.00 2.92
3957 4426 7.230027 AGCTCTTGGATAGAAAGATAAATGGG 58.770 38.462 0.00 0.00 33.34 4.00
4043 4512 0.605589 CTAGCCTCCCCGCAGATAAG 59.394 60.000 0.00 0.00 0.00 1.73
4175 4646 6.569179 TGAAATGGTGAAGTTAAGTAAGCC 57.431 37.500 0.00 0.00 0.00 4.35
4229 4700 3.643320 TCCCAGGCTTCTCATGTATACTG 59.357 47.826 4.17 0.58 0.00 2.74
4323 4796 1.207089 CGATCAACTTGGTAGCCCAGA 59.793 52.381 0.00 0.00 43.15 3.86
4375 4848 3.499563 CCCCATTAGTTGAACCCTGAACA 60.500 47.826 0.00 0.00 0.00 3.18
4389 4862 4.664688 ATAATCCTGGAAGCCCCATTAG 57.335 45.455 0.00 0.00 45.57 1.73
4405 4878 5.982516 CACTCACAGCCTCAGTTCTATAATC 59.017 44.000 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.