Multiple sequence alignment - TraesCS7D01G448700

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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 TraesCS7D01G448700 chr7D 100.000 3152 0 0 1 3152 568372543 568369392 0.000000e+00 5821.0
1 TraesCS7D01G448700 chr7B 94.161 1610 67 4 837 2423 623951497 623949892 0.000000e+00 2427.0
2 TraesCS7D01G448700 chr7B 89.786 842 47 16 1 837 623955251 623954444 0.000000e+00 1042.0
3 TraesCS7D01G448700 chr7B 88.199 644 16 8 2543 3150 623949884 623949265 0.000000e+00 713.0
4 TraesCS7D01G448700 chr7A 94.649 1551 54 3 936 2457 657024889 657023339 0.000000e+00 2377.0
5 TraesCS7D01G448700 chr7A 92.033 979 38 12 2 955 657025863 657024900 0.000000e+00 1339.0
6 TraesCS7D01G448700 chr7A 98.227 282 5 0 2543 2824 657023337 657023056 7.850000e-136 494.0
7 TraesCS7D01G448700 chr7A 91.286 241 12 5 2918 3150 123426636 123426397 1.410000e-83 320.0
8 TraesCS7D01G448700 chr7A 100.000 36 0 0 2881 2916 123426696 123426661 2.030000e-07 67.6
9 TraesCS7D01G448700 chr7A 86.885 61 1 2 3085 3138 657023058 657022998 9.440000e-06 62.1
10 TraesCS7D01G448700 chr6B 83.309 1354 179 21 838 2152 13819096 13817751 0.000000e+00 1205.0
11 TraesCS7D01G448700 chr6B 79.544 1183 211 24 982 2147 14340441 14341609 0.000000e+00 815.0
12 TraesCS7D01G448700 chr6B 77.517 1192 233 30 984 2152 39326125 39327304 0.000000e+00 684.0
13 TraesCS7D01G448700 chr6B 76.772 1171 245 25 997 2152 15751004 15749846 5.740000e-177 630.0
14 TraesCS7D01G448700 chr6B 75.897 1199 242 43 984 2152 14323508 14324689 1.270000e-158 569.0
15 TraesCS7D01G448700 chr6B 90.071 423 30 7 392 804 13819607 13819187 3.580000e-149 538.0
16 TraesCS7D01G448700 chr6B 75.499 751 168 13 1408 2150 52573771 52573029 1.390000e-93 353.0
17 TraesCS7D01G448700 chr6B 83.453 278 36 6 1 276 13832948 13832679 1.880000e-62 250.0
18 TraesCS7D01G448700 chr6B 86.607 224 20 4 2923 3138 14360517 14360296 4.060000e-59 239.0
19 TraesCS7D01G448700 chr6B 84.615 169 24 2 1972 2139 178881752 178881585 1.940000e-37 167.0
20 TraesCS7D01G448700 chr6B 82.738 168 28 1 2290 2456 21459784 21459951 7.040000e-32 148.0
21 TraesCS7D01G448700 chr6B 83.553 152 25 0 1973 2124 670582037 670581886 3.280000e-30 143.0
22 TraesCS7D01G448700 chr6B 81.081 148 28 0 2290 2437 28472531 28472678 5.520000e-23 119.0
23 TraesCS7D01G448700 chr6D 81.924 1206 184 30 970 2152 7901239 7902433 0.000000e+00 989.0
24 TraesCS7D01G448700 chr6D 82.308 1040 153 12 1118 2152 7404832 7403819 0.000000e+00 872.0
25 TraesCS7D01G448700 chr6D 76.572 1097 234 18 1070 2152 15344766 15343679 5.860000e-162 580.0
26 TraesCS7D01G448700 chr6D 81.503 692 106 13 965 1650 7728433 7729108 1.650000e-152 549.0
27 TraesCS7D01G448700 chr6D 77.551 637 125 13 1520 2147 7729142 7729769 4.970000e-98 368.0
28 TraesCS7D01G448700 chr6D 78.593 654 56 29 2540 3138 7963118 7963742 3.870000e-94 355.0
29 TraesCS7D01G448700 chr6A 81.541 1181 167 21 842 1995 7224885 7223729 0.000000e+00 926.0
30 TraesCS7D01G448700 chr6A 80.083 1205 190 32 970 2152 8174948 8176124 0.000000e+00 850.0
31 TraesCS7D01G448700 chr6A 86.777 484 47 9 317 791 7225541 7225066 1.000000e-144 523.0
32 TraesCS7D01G448700 chr6A 82.368 397 45 11 2540 2914 8176202 8176595 3.920000e-84 322.0
33 TraesCS7D01G448700 chr6A 95.522 134 6 0 2918 3051 572389319 572389186 6.850000e-52 215.0
34 TraesCS7D01G448700 chr6A 84.354 147 21 2 2288 2432 7294896 7294750 3.280000e-30 143.0
35 TraesCS7D01G448700 chr6A 81.290 155 29 0 2290 2444 16630071 16630225 3.300000e-25 126.0
36 TraesCS7D01G448700 chr6A 100.000 36 0 0 2881 2916 572389379 572389344 2.030000e-07 67.6
37 TraesCS7D01G448700 chr5D 98.837 86 1 0 2456 2541 492288233 492288318 1.510000e-33 154.0
38 TraesCS7D01G448700 chr5D 96.667 90 2 1 2454 2542 485753373 485753462 7.040000e-32 148.0
39 TraesCS7D01G448700 chr5D 93.069 101 6 1 2456 2555 276292518 276292418 2.530000e-31 147.0
40 TraesCS7D01G448700 chr5D 86.179 123 15 2 2290 2411 524578602 524578723 7.090000e-27 132.0
41 TraesCS7D01G448700 chr5B 93.137 102 7 0 2442 2543 533571345 533571446 1.960000e-32 150.0
42 TraesCS7D01G448700 chr5A 95.745 94 3 1 2449 2541 309680169 309680262 1.960000e-32 150.0
43 TraesCS7D01G448700 chr5A 85.366 123 16 2 2290 2411 650825628 650825749 3.300000e-25 126.0
44 TraesCS7D01G448700 chr4D 97.701 87 2 0 2455 2541 379169331 379169417 1.960000e-32 150.0
45 TraesCS7D01G448700 chr4A 93.204 103 6 1 2456 2557 674557906 674557804 1.960000e-32 150.0
46 TraesCS7D01G448700 chr1B 94.000 100 5 1 2456 2554 133188941 133188842 1.960000e-32 150.0
47 TraesCS7D01G448700 chr1B 83.333 168 23 4 2288 2453 630650604 630650768 1.960000e-32 150.0
48 TraesCS7D01G448700 chr1B 94.737 95 5 0 2456 2550 608052565 608052471 7.040000e-32 148.0
49 TraesCS7D01G448700 chrUn 100.000 34 0 0 2991 3024 24973575 24973608 2.620000e-06 63.9


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 TraesCS7D01G448700 chr7D 568369392 568372543 3151 True 5821.000 5821 100.000000 1 3152 1 chr7D.!!$R1 3151
1 TraesCS7D01G448700 chr7B 623949265 623955251 5986 True 1394.000 2427 90.715333 1 3150 3 chr7B.!!$R1 3149
2 TraesCS7D01G448700 chr7A 657022998 657025863 2865 True 1068.025 2377 92.948500 2 3138 4 chr7A.!!$R2 3136
3 TraesCS7D01G448700 chr6B 13817751 13819607 1856 True 871.500 1205 86.690000 392 2152 2 chr6B.!!$R7 1760
4 TraesCS7D01G448700 chr6B 14340441 14341609 1168 False 815.000 815 79.544000 982 2147 1 chr6B.!!$F2 1165
5 TraesCS7D01G448700 chr6B 39326125 39327304 1179 False 684.000 684 77.517000 984 2152 1 chr6B.!!$F5 1168
6 TraesCS7D01G448700 chr6B 15749846 15751004 1158 True 630.000 630 76.772000 997 2152 1 chr6B.!!$R3 1155
7 TraesCS7D01G448700 chr6B 14323508 14324689 1181 False 569.000 569 75.897000 984 2152 1 chr6B.!!$F1 1168
8 TraesCS7D01G448700 chr6B 52573029 52573771 742 True 353.000 353 75.499000 1408 2150 1 chr6B.!!$R4 742
9 TraesCS7D01G448700 chr6D 7901239 7902433 1194 False 989.000 989 81.924000 970 2152 1 chr6D.!!$F1 1182
10 TraesCS7D01G448700 chr6D 7403819 7404832 1013 True 872.000 872 82.308000 1118 2152 1 chr6D.!!$R1 1034
11 TraesCS7D01G448700 chr6D 15343679 15344766 1087 True 580.000 580 76.572000 1070 2152 1 chr6D.!!$R2 1082
12 TraesCS7D01G448700 chr6D 7728433 7729769 1336 False 458.500 549 79.527000 965 2147 2 chr6D.!!$F3 1182
13 TraesCS7D01G448700 chr6D 7963118 7963742 624 False 355.000 355 78.593000 2540 3138 1 chr6D.!!$F2 598
14 TraesCS7D01G448700 chr6A 7223729 7225541 1812 True 724.500 926 84.159000 317 1995 2 chr6A.!!$R2 1678
15 TraesCS7D01G448700 chr6A 8174948 8176595 1647 False 586.000 850 81.225500 970 2914 2 chr6A.!!$F2 1944

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
816 875 2.871096 TTAGCAACGGGACTTCCATT 57.129 45.0 0.0 0.00 37.91 3.16 F
1134 4229 0.592148 GATTCGCCGTCGAGGAGTAT 59.408 55.0 6.7 1.93 46.34 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2030 5295 1.081840 GCAAACACCTTCTCGCTGC 60.082 57.895 0.0 0.0 0.00 5.25 R
2526 5814 3.056465 CACAGAAGTACTCCCTCAGTTCC 60.056 52.174 0.0 0.0 36.43 3.62 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
142 143 3.623510 GGCTACCTGACAGAACTTTATGC 59.376 47.826 3.32 0.00 0.00 3.14
163 164 6.811253 TGCCGTCATCAAACTAATTAAACT 57.189 33.333 0.00 0.00 0.00 2.66
168 169 7.081349 CGTCATCAAACTAATTAAACTGCCAA 58.919 34.615 0.00 0.00 0.00 4.52
293 294 7.689299 TGCCATAGCATTATTAATGGACTAGT 58.311 34.615 16.22 0.00 46.52 2.57
341 342 9.288124 CGCTTCATCACAATTTTTGTTATCATA 57.712 29.630 0.00 0.00 43.23 2.15
745 761 4.692155 CACTTTGAAAATGGGGCTTCAATC 59.308 41.667 0.47 0.00 40.31 2.67
785 803 8.414003 GTCAATACTTTTTCCCTTTGAGAAGTT 58.586 33.333 0.00 0.00 34.75 2.66
791 809 9.642343 ACTTTTTCCCTTTGAGAAGTTAATACT 57.358 29.630 0.00 0.00 31.16 2.12
816 875 2.871096 TTAGCAACGGGACTTCCATT 57.129 45.000 0.00 0.00 37.91 3.16
817 876 2.871096 TAGCAACGGGACTTCCATTT 57.129 45.000 0.00 0.00 37.91 2.32
1134 4229 0.592148 GATTCGCCGTCGAGGAGTAT 59.408 55.000 6.70 1.93 46.34 2.12
1191 4286 2.116125 AAGGCCTCCGCAAAGCTT 59.884 55.556 5.23 0.00 36.38 3.74
1215 4310 1.076044 CCTCAAATCCCCCGCCAAT 60.076 57.895 0.00 0.00 0.00 3.16
1216 4311 1.394266 CCTCAAATCCCCCGCCAATG 61.394 60.000 0.00 0.00 0.00 2.82
1746 5011 0.820871 GTGAGGAGAAGATCGCCACT 59.179 55.000 3.00 0.00 38.94 4.00
1750 5015 3.706594 TGAGGAGAAGATCGCCACTAAAT 59.293 43.478 3.00 0.00 38.94 1.40
1817 5082 2.072874 ATTGCTGTGTCCAGGTGGCT 62.073 55.000 0.00 0.00 39.22 4.75
1867 5132 1.373497 CAGCGCAAGTCCGACTTCT 60.373 57.895 11.47 3.19 36.03 2.85
2030 5295 4.639310 AGACTACTACGGTATGGTCTTGTG 59.361 45.833 10.10 0.00 32.87 3.33
2253 5518 2.802719 GGATTGCTCAAAGGTAACCCA 58.197 47.619 0.00 0.00 37.17 4.51
2274 5539 5.334879 CCCAAGCTATTATACAATCGCCAAC 60.335 44.000 0.00 0.00 34.25 3.77
2436 5724 5.116983 GGTGCGACAAAGTTTTCATTATGTG 59.883 40.000 0.00 0.00 0.00 3.21
2458 5746 8.834004 TGTGTGGTAAGATAGTAATTCCTACT 57.166 34.615 0.00 0.00 43.58 2.57
2459 5747 8.910944 TGTGTGGTAAGATAGTAATTCCTACTC 58.089 37.037 0.00 0.00 40.21 2.59
2460 5748 8.358895 GTGTGGTAAGATAGTAATTCCTACTCC 58.641 40.741 0.00 0.00 40.21 3.85
2461 5749 7.508296 TGTGGTAAGATAGTAATTCCTACTCCC 59.492 40.741 0.00 0.00 40.21 4.30
2462 5750 7.729431 GTGGTAAGATAGTAATTCCTACTCCCT 59.271 40.741 0.00 0.00 40.21 4.20
2463 5751 7.949006 TGGTAAGATAGTAATTCCTACTCCCTC 59.051 40.741 0.00 0.00 40.21 4.30
2464 5752 7.396907 GGTAAGATAGTAATTCCTACTCCCTCC 59.603 44.444 0.00 0.00 40.21 4.30
2465 5753 5.572252 AGATAGTAATTCCTACTCCCTCCG 58.428 45.833 0.00 0.00 40.21 4.63
2466 5754 3.684408 AGTAATTCCTACTCCCTCCGT 57.316 47.619 0.00 0.00 35.90 4.69
2467 5755 3.991683 AGTAATTCCTACTCCCTCCGTT 58.008 45.455 0.00 0.00 35.90 4.44
2468 5756 3.959449 AGTAATTCCTACTCCCTCCGTTC 59.041 47.826 0.00 0.00 35.90 3.95
2469 5757 1.790818 ATTCCTACTCCCTCCGTTCC 58.209 55.000 0.00 0.00 0.00 3.62
2470 5758 0.410663 TTCCTACTCCCTCCGTTCCA 59.589 55.000 0.00 0.00 0.00 3.53
2471 5759 0.635009 TCCTACTCCCTCCGTTCCAT 59.365 55.000 0.00 0.00 0.00 3.41
2472 5760 1.854939 TCCTACTCCCTCCGTTCCATA 59.145 52.381 0.00 0.00 0.00 2.74
2473 5761 2.449730 TCCTACTCCCTCCGTTCCATAT 59.550 50.000 0.00 0.00 0.00 1.78
2474 5762 3.116862 TCCTACTCCCTCCGTTCCATATT 60.117 47.826 0.00 0.00 0.00 1.28
2475 5763 4.106825 TCCTACTCCCTCCGTTCCATATTA 59.893 45.833 0.00 0.00 0.00 0.98
2476 5764 4.220163 CCTACTCCCTCCGTTCCATATTAC 59.780 50.000 0.00 0.00 0.00 1.89
2477 5765 3.924922 ACTCCCTCCGTTCCATATTACT 58.075 45.455 0.00 0.00 0.00 2.24
2478 5766 4.296056 ACTCCCTCCGTTCCATATTACTT 58.704 43.478 0.00 0.00 0.00 2.24
2479 5767 4.101119 ACTCCCTCCGTTCCATATTACTTG 59.899 45.833 0.00 0.00 0.00 3.16
2480 5768 4.035112 TCCCTCCGTTCCATATTACTTGT 58.965 43.478 0.00 0.00 0.00 3.16
2481 5769 4.100498 TCCCTCCGTTCCATATTACTTGTC 59.900 45.833 0.00 0.00 0.00 3.18
2482 5770 4.049186 CCTCCGTTCCATATTACTTGTCG 58.951 47.826 0.00 0.00 0.00 4.35
2483 5771 3.450578 TCCGTTCCATATTACTTGTCGC 58.549 45.455 0.00 0.00 0.00 5.19
2484 5772 3.131577 TCCGTTCCATATTACTTGTCGCT 59.868 43.478 0.00 0.00 0.00 4.93
2485 5773 3.245284 CCGTTCCATATTACTTGTCGCTG 59.755 47.826 0.00 0.00 0.00 5.18
2486 5774 4.109766 CGTTCCATATTACTTGTCGCTGA 58.890 43.478 0.00 0.00 0.00 4.26
2487 5775 4.745125 CGTTCCATATTACTTGTCGCTGAT 59.255 41.667 0.00 0.00 0.00 2.90
2488 5776 5.234329 CGTTCCATATTACTTGTCGCTGATT 59.766 40.000 0.00 0.00 0.00 2.57
2489 5777 6.238103 CGTTCCATATTACTTGTCGCTGATTT 60.238 38.462 0.00 0.00 0.00 2.17
2490 5778 7.042992 CGTTCCATATTACTTGTCGCTGATTTA 60.043 37.037 0.00 0.00 0.00 1.40
2491 5779 7.946655 TCCATATTACTTGTCGCTGATTTAG 57.053 36.000 0.00 0.00 0.00 1.85
2492 5780 7.497595 TCCATATTACTTGTCGCTGATTTAGT 58.502 34.615 0.00 0.00 0.00 2.24
2493 5781 8.635328 TCCATATTACTTGTCGCTGATTTAGTA 58.365 33.333 0.00 0.00 0.00 1.82
2494 5782 8.700644 CCATATTACTTGTCGCTGATTTAGTAC 58.299 37.037 0.00 0.00 0.00 2.73
2495 5783 9.244799 CATATTACTTGTCGCTGATTTAGTACA 57.755 33.333 0.00 0.00 0.00 2.90
2496 5784 9.811995 ATATTACTTGTCGCTGATTTAGTACAA 57.188 29.630 0.00 0.00 34.99 2.41
2497 5785 5.840940 ACTTGTCGCTGATTTAGTACAAC 57.159 39.130 0.00 0.00 33.64 3.32
2498 5786 5.539048 ACTTGTCGCTGATTTAGTACAACT 58.461 37.500 0.00 0.00 33.64 3.16
2499 5787 5.989777 ACTTGTCGCTGATTTAGTACAACTT 59.010 36.000 0.00 0.00 33.64 2.66
2500 5788 6.482308 ACTTGTCGCTGATTTAGTACAACTTT 59.518 34.615 0.00 0.00 33.64 2.66
2501 5789 6.223138 TGTCGCTGATTTAGTACAACTTTG 57.777 37.500 0.00 0.00 0.00 2.77
2502 5790 5.756347 TGTCGCTGATTTAGTACAACTTTGT 59.244 36.000 0.00 0.00 44.86 2.83
2503 5791 6.924612 TGTCGCTGATTTAGTACAACTTTGTA 59.075 34.615 0.00 0.00 42.35 2.41
2516 5804 6.224420 ACAACTTTGTACTAAATCAGCGAC 57.776 37.500 0.00 0.00 40.16 5.19
2517 5805 5.756347 ACAACTTTGTACTAAATCAGCGACA 59.244 36.000 0.00 0.00 40.16 4.35
2518 5806 6.259167 ACAACTTTGTACTAAATCAGCGACAA 59.741 34.615 0.00 0.00 40.16 3.18
2519 5807 6.467723 ACTTTGTACTAAATCAGCGACAAG 57.532 37.500 0.00 0.00 35.77 3.16
2520 5808 5.989777 ACTTTGTACTAAATCAGCGACAAGT 59.010 36.000 0.00 0.00 35.77 3.16
2521 5809 7.149973 ACTTTGTACTAAATCAGCGACAAGTA 58.850 34.615 0.00 0.00 35.77 2.24
2522 5810 7.654520 ACTTTGTACTAAATCAGCGACAAGTAA 59.345 33.333 0.00 0.00 35.77 2.24
2523 5811 8.542497 TTTGTACTAAATCAGCGACAAGTAAT 57.458 30.769 0.00 0.00 35.77 1.89
2524 5812 9.642327 TTTGTACTAAATCAGCGACAAGTAATA 57.358 29.630 0.00 0.00 35.77 0.98
2525 5813 9.811995 TTGTACTAAATCAGCGACAAGTAATAT 57.188 29.630 0.00 0.00 31.65 1.28
2526 5814 9.244799 TGTACTAAATCAGCGACAAGTAATATG 57.755 33.333 0.00 0.00 0.00 1.78
2527 5815 7.715265 ACTAAATCAGCGACAAGTAATATGG 57.285 36.000 0.00 0.00 0.00 2.74
2528 5816 7.497595 ACTAAATCAGCGACAAGTAATATGGA 58.502 34.615 0.00 0.00 0.00 3.41
2529 5817 7.985184 ACTAAATCAGCGACAAGTAATATGGAA 59.015 33.333 0.00 0.00 0.00 3.53
2530 5818 6.604735 AATCAGCGACAAGTAATATGGAAC 57.395 37.500 0.00 0.00 0.00 3.62
2531 5819 5.339008 TCAGCGACAAGTAATATGGAACT 57.661 39.130 0.00 0.00 0.00 3.01
2532 5820 5.109210 TCAGCGACAAGTAATATGGAACTG 58.891 41.667 0.00 0.00 0.00 3.16
2533 5821 5.105513 TCAGCGACAAGTAATATGGAACTGA 60.106 40.000 0.00 0.00 0.00 3.41
2534 5822 5.233050 CAGCGACAAGTAATATGGAACTGAG 59.767 44.000 0.00 0.00 0.00 3.35
2535 5823 4.508124 GCGACAAGTAATATGGAACTGAGG 59.492 45.833 0.00 0.00 0.00 3.86
2536 5824 5.050490 CGACAAGTAATATGGAACTGAGGG 58.950 45.833 0.00 0.00 0.00 4.30
2537 5825 5.163447 CGACAAGTAATATGGAACTGAGGGA 60.163 44.000 0.00 0.00 0.00 4.20
2538 5826 6.240549 ACAAGTAATATGGAACTGAGGGAG 57.759 41.667 0.00 0.00 0.00 4.30
2541 5829 6.980416 AGTAATATGGAACTGAGGGAGTAC 57.020 41.667 0.00 0.00 33.09 2.73
2815 6128 3.746492 GCCTAGCAATGTTCCGTTATAGG 59.254 47.826 0.00 0.00 33.24 2.57
2952 6311 3.327172 AGAAGATGATGGCCTCTGGTATG 59.673 47.826 3.32 0.00 0.00 2.39
2984 6343 2.159198 GGCATGCTAGTTTGGTCATTGG 60.159 50.000 18.92 0.00 0.00 3.16
3034 6397 7.665690 AGATTCATGAGTACTGATATGTCCAC 58.334 38.462 0.00 0.00 0.00 4.02
3036 6399 4.278419 TCATGAGTACTGATATGTCCACGG 59.722 45.833 0.00 0.00 0.00 4.94
3109 6473 5.461526 GGGAACTATTTTGAACTTGCTGAC 58.538 41.667 0.00 0.00 0.00 3.51
3150 6522 3.056821 GGAGGCAGTTAATTTTGACCCAC 60.057 47.826 0.00 0.00 0.00 4.61
3151 6523 3.826729 GAGGCAGTTAATTTTGACCCACT 59.173 43.478 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 107 4.898861 TCAGGTAGCCAATTTCACCTTTTT 59.101 37.500 0.00 0.00 39.40 1.94
107 108 4.280929 GTCAGGTAGCCAATTTCACCTTTT 59.719 41.667 0.00 0.00 39.40 2.27
108 109 3.826729 GTCAGGTAGCCAATTTCACCTTT 59.173 43.478 0.00 0.00 39.40 3.11
109 110 3.181434 TGTCAGGTAGCCAATTTCACCTT 60.181 43.478 0.00 0.00 39.40 3.50
110 111 2.375174 TGTCAGGTAGCCAATTTCACCT 59.625 45.455 0.00 0.00 42.17 4.00
111 112 2.749621 CTGTCAGGTAGCCAATTTCACC 59.250 50.000 0.00 0.00 0.00 4.02
112 113 3.674997 TCTGTCAGGTAGCCAATTTCAC 58.325 45.455 0.00 0.00 0.00 3.18
142 143 6.027749 GGCAGTTTAATTAGTTTGATGACGG 58.972 40.000 0.00 0.00 0.00 4.79
163 164 2.295909 GCACTAACTTCATTGGTTGGCA 59.704 45.455 0.00 0.00 27.49 4.92
168 169 5.186198 GGTCATAGCACTAACTTCATTGGT 58.814 41.667 0.00 0.00 30.84 3.67
293 294 9.906660 AAGCGTCTTAATTGTGATGAAAAATAA 57.093 25.926 6.08 0.00 0.00 1.40
297 298 6.964908 TGAAGCGTCTTAATTGTGATGAAAA 58.035 32.000 0.31 0.00 0.00 2.29
315 316 7.565450 TGATAACAAAAATTGTGATGAAGCG 57.435 32.000 0.00 0.00 44.59 4.68
507 510 6.910433 GTCATCGTCAAAACTTAACAACACAT 59.090 34.615 0.00 0.00 0.00 3.21
1134 4229 3.680786 CCGCAGGTGTCGACCAGA 61.681 66.667 14.12 0.00 45.98 3.86
1191 4286 1.858739 CGGGGGATTTGAGGTGGGAA 61.859 60.000 0.00 0.00 0.00 3.97
1746 5011 6.009589 TGCCTTCTTCAAGTGATCCAATTTA 58.990 36.000 0.00 0.00 0.00 1.40
1750 5015 3.507162 TGCCTTCTTCAAGTGATCCAA 57.493 42.857 0.00 0.00 0.00 3.53
1817 5082 1.209261 TGGACAAACTCAGCACACTCA 59.791 47.619 0.00 0.00 0.00 3.41
1867 5132 1.622607 AATCCCACCTCCGCGATGAA 61.623 55.000 8.23 0.00 0.00 2.57
2030 5295 1.081840 GCAAACACCTTCTCGCTGC 60.082 57.895 0.00 0.00 0.00 5.25
2253 5518 6.765989 TGAAGTTGGCGATTGTATAATAGCTT 59.234 34.615 14.95 3.93 42.40 3.74
2274 5539 7.754111 CCTTGTGAGGACCTTCTCAGTGAAG 62.754 52.000 0.00 5.38 46.74 3.02
2436 5724 7.729431 AGGGAGTAGGAATTACTATCTTACCAC 59.271 40.741 0.00 0.00 42.69 4.16
2455 5743 5.070823 AGTAATATGGAACGGAGGGAGTA 57.929 43.478 0.00 0.00 0.00 2.59
2456 5744 3.924922 AGTAATATGGAACGGAGGGAGT 58.075 45.455 0.00 0.00 0.00 3.85
2457 5745 4.101119 ACAAGTAATATGGAACGGAGGGAG 59.899 45.833 0.00 0.00 0.00 4.30
2458 5746 4.035112 ACAAGTAATATGGAACGGAGGGA 58.965 43.478 0.00 0.00 0.00 4.20
2459 5747 4.377897 GACAAGTAATATGGAACGGAGGG 58.622 47.826 0.00 0.00 0.00 4.30
2460 5748 4.049186 CGACAAGTAATATGGAACGGAGG 58.951 47.826 0.00 0.00 0.00 4.30
2461 5749 3.489785 GCGACAAGTAATATGGAACGGAG 59.510 47.826 0.00 0.00 0.00 4.63
2462 5750 3.131577 AGCGACAAGTAATATGGAACGGA 59.868 43.478 0.00 0.00 0.00 4.69
2463 5751 3.245284 CAGCGACAAGTAATATGGAACGG 59.755 47.826 0.00 0.00 0.00 4.44
2464 5752 4.109766 TCAGCGACAAGTAATATGGAACG 58.890 43.478 0.00 0.00 0.00 3.95
2465 5753 6.604735 AATCAGCGACAAGTAATATGGAAC 57.395 37.500 0.00 0.00 0.00 3.62
2466 5754 7.985184 ACTAAATCAGCGACAAGTAATATGGAA 59.015 33.333 0.00 0.00 0.00 3.53
2467 5755 7.497595 ACTAAATCAGCGACAAGTAATATGGA 58.502 34.615 0.00 0.00 0.00 3.41
2468 5756 7.715265 ACTAAATCAGCGACAAGTAATATGG 57.285 36.000 0.00 0.00 0.00 2.74
2469 5757 9.244799 TGTACTAAATCAGCGACAAGTAATATG 57.755 33.333 0.00 0.00 0.00 1.78
2470 5758 9.811995 TTGTACTAAATCAGCGACAAGTAATAT 57.188 29.630 0.00 0.00 31.65 1.28
2471 5759 9.079833 GTTGTACTAAATCAGCGACAAGTAATA 57.920 33.333 0.00 0.00 35.28 0.98
2472 5760 7.817962 AGTTGTACTAAATCAGCGACAAGTAAT 59.182 33.333 0.00 0.00 36.22 1.89
2473 5761 7.149973 AGTTGTACTAAATCAGCGACAAGTAA 58.850 34.615 0.00 0.00 36.22 2.24
2474 5762 6.684686 AGTTGTACTAAATCAGCGACAAGTA 58.315 36.000 0.00 0.00 36.22 2.24
2475 5763 5.539048 AGTTGTACTAAATCAGCGACAAGT 58.461 37.500 0.00 0.00 35.28 3.16
2476 5764 6.467723 AAGTTGTACTAAATCAGCGACAAG 57.532 37.500 0.00 0.00 35.28 3.16
2477 5765 6.259167 ACAAAGTTGTACTAAATCAGCGACAA 59.741 34.615 0.00 0.00 40.16 3.18
2478 5766 5.756347 ACAAAGTTGTACTAAATCAGCGACA 59.244 36.000 0.00 0.00 40.16 4.35
2479 5767 6.224420 ACAAAGTTGTACTAAATCAGCGAC 57.776 37.500 0.00 0.00 40.16 5.19
2492 5780 6.924612 TGTCGCTGATTTAGTACAAAGTTGTA 59.075 34.615 0.00 0.00 42.35 2.41
2493 5781 5.756347 TGTCGCTGATTTAGTACAAAGTTGT 59.244 36.000 1.75 1.75 44.86 3.32
2494 5782 6.223138 TGTCGCTGATTTAGTACAAAGTTG 57.777 37.500 0.00 0.00 0.00 3.16
2495 5783 6.482308 ACTTGTCGCTGATTTAGTACAAAGTT 59.518 34.615 0.00 0.00 35.46 2.66
2496 5784 5.989777 ACTTGTCGCTGATTTAGTACAAAGT 59.010 36.000 0.00 0.00 35.46 2.66
2497 5785 6.467723 ACTTGTCGCTGATTTAGTACAAAG 57.532 37.500 0.00 0.00 35.46 2.77
2498 5786 7.949903 TTACTTGTCGCTGATTTAGTACAAA 57.050 32.000 0.00 0.00 35.46 2.83
2499 5787 9.811995 ATATTACTTGTCGCTGATTTAGTACAA 57.188 29.630 0.00 0.00 34.99 2.41
2500 5788 9.244799 CATATTACTTGTCGCTGATTTAGTACA 57.755 33.333 0.00 0.00 0.00 2.90
2501 5789 8.700644 CCATATTACTTGTCGCTGATTTAGTAC 58.299 37.037 0.00 0.00 0.00 2.73
2502 5790 8.635328 TCCATATTACTTGTCGCTGATTTAGTA 58.365 33.333 0.00 0.00 0.00 1.82
2503 5791 7.497595 TCCATATTACTTGTCGCTGATTTAGT 58.502 34.615 0.00 0.00 0.00 2.24
2504 5792 7.946655 TCCATATTACTTGTCGCTGATTTAG 57.053 36.000 0.00 0.00 0.00 1.85
2505 5793 7.985184 AGTTCCATATTACTTGTCGCTGATTTA 59.015 33.333 0.00 0.00 0.00 1.40
2506 5794 6.823689 AGTTCCATATTACTTGTCGCTGATTT 59.176 34.615 0.00 0.00 0.00 2.17
2507 5795 6.258727 CAGTTCCATATTACTTGTCGCTGATT 59.741 38.462 0.00 0.00 0.00 2.57
2508 5796 5.755375 CAGTTCCATATTACTTGTCGCTGAT 59.245 40.000 0.00 0.00 0.00 2.90
2509 5797 5.105513 TCAGTTCCATATTACTTGTCGCTGA 60.106 40.000 0.00 0.00 0.00 4.26
2510 5798 5.109210 TCAGTTCCATATTACTTGTCGCTG 58.891 41.667 0.00 0.00 0.00 5.18
2511 5799 5.339008 TCAGTTCCATATTACTTGTCGCT 57.661 39.130 0.00 0.00 0.00 4.93
2512 5800 4.508124 CCTCAGTTCCATATTACTTGTCGC 59.492 45.833 0.00 0.00 0.00 5.19
2513 5801 5.050490 CCCTCAGTTCCATATTACTTGTCG 58.950 45.833 0.00 0.00 0.00 4.35
2514 5802 6.127026 ACTCCCTCAGTTCCATATTACTTGTC 60.127 42.308 0.00 0.00 26.56 3.18
2515 5803 5.726793 ACTCCCTCAGTTCCATATTACTTGT 59.273 40.000 0.00 0.00 26.56 3.16
2516 5804 6.240549 ACTCCCTCAGTTCCATATTACTTG 57.759 41.667 0.00 0.00 26.56 3.16
2517 5805 7.133483 AGTACTCCCTCAGTTCCATATTACTT 58.867 38.462 0.00 0.00 36.43 2.24
2518 5806 6.684538 AGTACTCCCTCAGTTCCATATTACT 58.315 40.000 0.00 0.00 36.43 2.24
2519 5807 6.980416 AGTACTCCCTCAGTTCCATATTAC 57.020 41.667 0.00 0.00 36.43 1.89
2520 5808 7.287927 CAGAAGTACTCCCTCAGTTCCATATTA 59.712 40.741 0.00 0.00 36.43 0.98
2521 5809 6.098982 CAGAAGTACTCCCTCAGTTCCATATT 59.901 42.308 0.00 0.00 36.43 1.28
2522 5810 5.600484 CAGAAGTACTCCCTCAGTTCCATAT 59.400 44.000 0.00 0.00 36.43 1.78
2523 5811 4.956700 CAGAAGTACTCCCTCAGTTCCATA 59.043 45.833 0.00 0.00 36.43 2.74
2524 5812 3.772025 CAGAAGTACTCCCTCAGTTCCAT 59.228 47.826 0.00 0.00 36.43 3.41
2525 5813 3.165875 CAGAAGTACTCCCTCAGTTCCA 58.834 50.000 0.00 0.00 36.43 3.53
2526 5814 3.056465 CACAGAAGTACTCCCTCAGTTCC 60.056 52.174 0.00 0.00 36.43 3.62
2527 5815 3.574826 ACACAGAAGTACTCCCTCAGTTC 59.425 47.826 0.00 0.00 36.43 3.01
2528 5816 3.577919 ACACAGAAGTACTCCCTCAGTT 58.422 45.455 0.00 0.00 36.43 3.16
2529 5817 3.246416 ACACAGAAGTACTCCCTCAGT 57.754 47.619 0.00 0.00 39.41 3.41
2530 5818 4.705337 GTACACAGAAGTACTCCCTCAG 57.295 50.000 0.00 0.00 40.85 3.35
2538 5826 4.626172 GCTAGGCAAAGTACACAGAAGTAC 59.374 45.833 0.00 0.00 43.61 2.73
2541 5829 3.681897 CAGCTAGGCAAAGTACACAGAAG 59.318 47.826 0.00 0.00 0.00 2.85
2952 6311 3.480470 ACTAGCATGCCACATTCATACC 58.520 45.455 15.66 0.00 0.00 2.73
3034 6397 8.323140 GTCATTCAAAGAAATTTTATGATGCCG 58.677 33.333 0.00 0.00 0.00 5.69
3109 6473 3.977427 TCCTCGGATTGATCAACATACG 58.023 45.455 11.07 8.87 0.00 3.06


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

AutoCloner maintained by Alex Coulton.