Multiple sequence alignment - TraesCS5A01G122500

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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 TraesCS5A01G122500 chr5A 100.000 2441 0 0 1 2441 267793484 267795924 0.000000e+00 4508.0
1 TraesCS5A01G122500 chr5A 94.103 2357 134 4 1 2354 267785046 267787400 0.000000e+00 3578.0
2 TraesCS5A01G122500 chr5A 92.057 768 61 0 670 1437 441797717 441798484 0.000000e+00 1081.0
3 TraesCS5A01G122500 chr5A 91.731 774 61 1 670 1443 441789757 441790527 0.000000e+00 1072.0
4 TraesCS5A01G122500 chr5A 88.542 192 22 0 1587 1778 265267257 265267066 1.460000e-57 233.0
5 TraesCS5A01G122500 chr5A 89.189 185 16 4 1587 1769 265250490 265250308 6.790000e-56 228.0
6 TraesCS5A01G122500 chr5A 96.591 88 3 0 2354 2441 267749812 267749899 1.960000e-31 147.0
7 TraesCS5A01G122500 chr5A 92.000 100 7 1 2343 2441 235248255 235248156 3.270000e-29 139.0
8 TraesCS5A01G122500 chr5A 91.489 94 7 1 1583 1676 441798494 441798586 7.080000e-26 128.0
9 TraesCS5A01G122500 chr5A 77.586 116 18 7 1553 1664 104756807 104756918 2.030000e-06 63.9
10 TraesCS5A01G122500 chr6A 87.200 1711 174 26 1 1674 37773035 37771333 0.000000e+00 1905.0
11 TraesCS5A01G122500 chr6A 94.178 584 34 0 1093 1676 37715128 37714545 0.000000e+00 891.0
12 TraesCS5A01G122500 chr6A 88.235 680 62 15 1 670 259854460 259855131 0.000000e+00 797.0
13 TraesCS5A01G122500 chr6A 77.047 623 88 39 1755 2354 357144840 357144250 8.480000e-80 307.0
14 TraesCS5A01G122500 chr6A 76.726 623 90 36 1755 2354 357136888 357136298 1.840000e-76 296.0
15 TraesCS5A01G122500 chr6A 76.358 626 91 39 1753 2354 357152839 357152247 1.430000e-72 283.0
16 TraesCS5A01G122500 chr6A 91.379 58 5 0 1619 1676 70821076 70821133 2.010000e-11 80.5
17 TraesCS5A01G122500 chr4A 88.880 1250 123 15 1 1241 302606811 302608053 0.000000e+00 1524.0
18 TraesCS5A01G122500 chr4A 88.010 1251 134 15 1 1241 302614716 302615960 0.000000e+00 1465.0
19 TraesCS5A01G122500 chr4A 87.690 1251 137 16 1 1241 366967657 366968900 0.000000e+00 1441.0
20 TraesCS5A01G122500 chr4A 87.228 689 73 12 1 681 47997313 47996632 0.000000e+00 771.0
21 TraesCS5A01G122500 chr4A 86.522 690 75 16 1 681 47989201 47988521 0.000000e+00 743.0
22 TraesCS5A01G122500 chr4A 96.758 401 11 2 1955 2354 443312888 443313287 0.000000e+00 667.0
23 TraesCS5A01G122500 chr4A 83.832 167 16 8 1822 1985 66087039 66087197 5.440000e-32 148.0
24 TraesCS5A01G122500 chr4A 83.735 166 16 8 1822 1984 66103827 66103984 1.960000e-31 147.0
25 TraesCS5A01G122500 chr4A 89.167 120 10 3 1462 1578 278300852 278300733 1.960000e-31 147.0
26 TraesCS5A01G122500 chr4A 85.271 129 16 3 1453 1578 278309789 278309661 1.970000e-26 130.0
27 TraesCS5A01G122500 chr7A 92.308 1027 79 0 649 1675 30233072 30232046 0.000000e+00 1459.0
28 TraesCS5A01G122500 chr7A 90.040 502 35 11 1859 2354 492314694 492315186 9.520000e-179 636.0
29 TraesCS5A01G122500 chr7A 95.214 397 19 0 1958 2354 403212025 403211629 1.590000e-176 628.0
30 TraesCS5A01G122500 chr7A 91.379 116 9 1 1569 1684 89489138 89489024 9.040000e-35 158.0
31 TraesCS5A01G122500 chr7A 94.828 58 3 0 1619 1676 271107809 271107752 9.290000e-15 91.6
32 TraesCS5A01G122500 chr7A 94.643 56 3 0 1621 1676 271491802 271491857 1.200000e-13 87.9
33 TraesCS5A01G122500 chr7A 81.522 92 13 4 1905 1994 320957432 320957521 3.370000e-09 73.1
34 TraesCS5A01G122500 chr7A 93.333 45 0 3 1617 1660 248121230 248121272 2.030000e-06 63.9
35 TraesCS5A01G122500 chr2A 92.912 776 53 2 670 1444 156226653 156225879 0.000000e+00 1127.0
36 TraesCS5A01G122500 chr2A 85.814 1001 121 19 1 989 204728705 204727714 0.000000e+00 1042.0
37 TraesCS5A01G122500 chr2A 96.250 400 13 2 1955 2354 335750883 335750486 0.000000e+00 654.0
38 TraesCS5A01G122500 chr2A 95.980 398 14 2 1958 2354 431625958 431625562 0.000000e+00 645.0
39 TraesCS5A01G122500 chr2A 95.729 398 15 2 1958 2354 431642567 431642171 7.360000e-180 640.0
40 TraesCS5A01G122500 chr2A 95.604 91 3 1 2351 2441 226367739 226367828 7.030000e-31 145.0
41 TraesCS5A01G122500 chr2A 90.090 111 10 1 1565 1675 156225894 156225785 2.530000e-30 143.0
42 TraesCS5A01G122500 chr2A 100.000 35 0 0 1848 1882 581109286 581109252 5.630000e-07 65.8
43 TraesCS5A01G122500 chr1A 86.988 684 74 13 1 675 55426325 55425648 0.000000e+00 756.0
44 TraesCS5A01G122500 chr1A 95.477 398 16 2 1958 2354 157935328 157934932 3.420000e-178 634.0
45 TraesCS5A01G122500 chr1A 94.681 94 4 1 2349 2441 139542001 139542094 7.030000e-31 145.0
46 TraesCS5A01G122500 chr3A 95.477 398 16 2 1958 2354 362192969 362193365 3.420000e-178 634.0
47 TraesCS5A01G122500 chr3A 77.492 622 83 39 1754 2351 626415159 626415747 1.090000e-83 320.0
48 TraesCS5A01G122500 chr3A 76.748 615 86 38 1753 2344 626412274 626411694 8.540000e-75 291.0
49 TraesCS5A01G122500 chr3A 87.500 192 24 0 1587 1778 294453330 294453521 3.160000e-54 222.0
50 TraesCS5A01G122500 chr3A 81.522 92 13 4 1905 1994 320476875 320476964 3.370000e-09 73.1
51 TraesCS5A01G122500 chr3A 88.525 61 5 2 1935 1994 359522593 359522534 3.370000e-09 73.1
52 TraesCS5A01G122500 chr3A 88.525 61 5 2 1935 1994 359552603 359552544 3.370000e-09 73.1
53 TraesCS5A01G122500 chr7B 97.727 88 2 0 2354 2441 743496520 743496433 4.200000e-33 152.0
54 TraesCS5A01G122500 chr4D 97.701 87 2 0 2355 2441 175064294 175064380 1.510000e-32 150.0
55 TraesCS5A01G122500 chr5B 95.652 92 3 1 2350 2441 611566305 611566395 1.960000e-31 147.0
56 TraesCS5A01G122500 chr4B 97.647 85 2 0 2357 2441 427516299 427516215 1.960000e-31 147.0
57 TraesCS5A01G122500 chr4B 92.000 100 5 2 2343 2441 383138196 383138099 1.180000e-28 137.0


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 TraesCS5A01G122500 chr5A 267793484 267795924 2440 False 4508.0 4508 100.000 1 2441 1 chr5A.!!$F4 2440
1 TraesCS5A01G122500 chr5A 267785046 267787400 2354 False 3578.0 3578 94.103 1 2354 1 chr5A.!!$F3 2353
2 TraesCS5A01G122500 chr5A 441789757 441790527 770 False 1072.0 1072 91.731 670 1443 1 chr5A.!!$F5 773
3 TraesCS5A01G122500 chr5A 441797717 441798586 869 False 604.5 1081 91.773 670 1676 2 chr5A.!!$F6 1006
4 TraesCS5A01G122500 chr6A 37771333 37773035 1702 True 1905.0 1905 87.200 1 1674 1 chr6A.!!$R2 1673
5 TraesCS5A01G122500 chr6A 37714545 37715128 583 True 891.0 891 94.178 1093 1676 1 chr6A.!!$R1 583
6 TraesCS5A01G122500 chr6A 259854460 259855131 671 False 797.0 797 88.235 1 670 1 chr6A.!!$F2 669
7 TraesCS5A01G122500 chr6A 357144250 357144840 590 True 307.0 307 77.047 1755 2354 1 chr6A.!!$R4 599
8 TraesCS5A01G122500 chr6A 357136298 357136888 590 True 296.0 296 76.726 1755 2354 1 chr6A.!!$R3 599
9 TraesCS5A01G122500 chr6A 357152247 357152839 592 True 283.0 283 76.358 1753 2354 1 chr6A.!!$R5 601
10 TraesCS5A01G122500 chr4A 302606811 302608053 1242 False 1524.0 1524 88.880 1 1241 1 chr4A.!!$F3 1240
11 TraesCS5A01G122500 chr4A 302614716 302615960 1244 False 1465.0 1465 88.010 1 1241 1 chr4A.!!$F4 1240
12 TraesCS5A01G122500 chr4A 366967657 366968900 1243 False 1441.0 1441 87.690 1 1241 1 chr4A.!!$F5 1240
13 TraesCS5A01G122500 chr4A 47996632 47997313 681 True 771.0 771 87.228 1 681 1 chr4A.!!$R2 680
14 TraesCS5A01G122500 chr4A 47988521 47989201 680 True 743.0 743 86.522 1 681 1 chr4A.!!$R1 680
15 TraesCS5A01G122500 chr7A 30232046 30233072 1026 True 1459.0 1459 92.308 649 1675 1 chr7A.!!$R1 1026
16 TraesCS5A01G122500 chr2A 204727714 204728705 991 True 1042.0 1042 85.814 1 989 1 chr2A.!!$R1 988
17 TraesCS5A01G122500 chr2A 156225785 156226653 868 True 635.0 1127 91.501 670 1675 2 chr2A.!!$R6 1005
18 TraesCS5A01G122500 chr1A 55425648 55426325 677 True 756.0 756 86.988 1 675 1 chr1A.!!$R1 674
19 TraesCS5A01G122500 chr3A 626415159 626415747 588 False 320.0 320 77.492 1754 2351 1 chr3A.!!$F4 597
20 TraesCS5A01G122500 chr3A 626411694 626412274 580 True 291.0 291 76.748 1753 2344 1 chr3A.!!$R3 591

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
353 368 0.036306 GAAAGAAAGGGTGCCTCGGA 59.964 55.0 0.0 0.0 30.89 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 1873 0.725133 TCCCATCTCTCCTTTCCCCT 59.275 55.0 0.0 0.0 0.0 4.79 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
91 92 8.362639 TCTCGTTTAGGTACCCATCAATATTAC 58.637 37.037 8.74 0.00 0.00 1.89
151 154 8.573035 TGAAAAACTACCTATTTAGGCAAGTTG 58.427 33.333 18.52 0.00 45.10 3.16
162 165 0.968405 GGCAAGTTGAAATGAGGCCA 59.032 50.000 5.01 0.00 39.66 5.36
349 364 0.178961 GGTGGAAAGAAAGGGTGCCT 60.179 55.000 0.00 0.00 33.87 4.75
353 368 0.036306 GAAAGAAAGGGTGCCTCGGA 59.964 55.000 0.00 0.00 30.89 4.55
445 462 0.597637 AAGTGACGGAAGCGTGTCAG 60.598 55.000 4.07 0.00 45.08 3.51
471 488 0.107848 GTGGGGTGATCCTGGTTACG 60.108 60.000 0.00 0.00 35.33 3.18
502 519 1.280746 GTCGACGACGGTGACAAGA 59.719 57.895 12.94 0.00 40.21 3.02
635 654 1.774254 TGCATTATCGGAGGGGTTCAT 59.226 47.619 0.00 0.00 0.00 2.57
654 673 1.252215 TGTTCGATGCGGTGTAGGGA 61.252 55.000 0.00 0.00 0.00 4.20
707 756 3.244579 ACGTTCTTAGTCGCACAAGTTTC 59.755 43.478 0.00 0.00 0.00 2.78
737 786 2.741211 GGGTCACGGCGAGAAACC 60.741 66.667 16.62 13.71 0.00 3.27
739 788 1.301479 GGTCACGGCGAGAAACCTT 60.301 57.895 16.62 0.00 0.00 3.50
818 867 4.205587 AGGGTAGTTGTTCTCGTATCGAT 58.794 43.478 2.16 2.16 34.61 3.59
887 936 3.693085 CCTCGTAGAACTAGTACTTGGCA 59.307 47.826 0.00 0.00 34.09 4.92
927 976 3.703001 AAGGAGTTCACGATGATGGTT 57.297 42.857 0.00 0.00 0.00 3.67
1053 1102 2.029290 ACGGTACTTGTCAGGTCATCAC 60.029 50.000 0.00 0.00 0.00 3.06
1060 1109 2.510613 TGTCAGGTCATCACGTAGACA 58.489 47.619 14.40 0.00 36.50 3.41
1065 1114 5.526479 GTCAGGTCATCACGTAGACATACTA 59.474 44.000 14.40 0.00 36.50 1.82
1090 1139 3.110178 GGAACTTGTCGCGTCCCG 61.110 66.667 5.77 0.00 38.61 5.14
1522 1571 2.679716 GGTGGAGCTGGCCTGAAT 59.320 61.111 14.77 0.04 0.00 2.57
1660 1709 3.141488 GGCGCGAGGAAGGAGAGA 61.141 66.667 12.10 0.00 0.00 3.10
1692 1741 2.033448 GGCATGACGGTGGTGGAA 59.967 61.111 0.00 0.00 0.00 3.53
1694 1743 2.690778 GCATGACGGTGGTGGAAGC 61.691 63.158 0.00 0.00 0.00 3.86
1695 1744 1.302431 CATGACGGTGGTGGAAGCA 60.302 57.895 0.00 0.00 45.41 3.91
1722 1771 1.469335 GGAAGGAGACGTGGGTGTCA 61.469 60.000 0.00 0.00 41.41 3.58
1735 1784 1.678970 GTGTCAGGCCATGGGGTTC 60.679 63.158 15.13 0.00 36.17 3.62
1736 1785 2.159490 TGTCAGGCCATGGGGTTCA 61.159 57.895 15.13 0.00 36.17 3.18
1761 1810 2.024022 CGAAGAGAGCGCGAGGAG 59.976 66.667 12.10 0.00 0.00 3.69
1790 1839 1.271163 GGAGATCGATCGGGAGAGAGT 60.271 57.143 19.33 0.00 45.48 3.24
1792 1841 0.878416 GATCGATCGGGAGAGAGTGG 59.122 60.000 16.41 0.00 45.48 4.00
1914 1963 2.776526 AATGGATGGGCCGGCCTA 60.777 61.111 42.70 39.29 40.66 3.93
1949 1998 4.659172 TGGGCTGGCGGGAAGTTG 62.659 66.667 0.00 0.00 0.00 3.16
1996 2081 1.950484 GCTGGCCTAAAGCTGCAGTTA 60.950 52.381 16.64 6.10 43.05 2.24
2008 2093 7.986085 AAAGCTGCAGTTATCTTTTCTCTAA 57.014 32.000 16.64 0.00 0.00 2.10
2111 2201 4.836736 CCCTGAATTCATGCCCTATTTGAT 59.163 41.667 8.96 0.00 0.00 2.57
2308 2400 4.450976 GGAAAAGGTCACTTGCCAAAATT 58.549 39.130 0.00 0.00 36.93 1.82
2322 2414 9.665719 ACTTGCCAAAATTAAAGAAAGAAGAAA 57.334 25.926 0.00 0.00 0.00 2.52
2359 2451 4.784177 TGATGCATGATCATACACAAGGT 58.216 39.130 10.85 0.00 36.06 3.50
2360 2452 5.927819 TGATGCATGATCATACACAAGGTA 58.072 37.500 10.85 0.00 36.06 3.08
2361 2453 5.993441 TGATGCATGATCATACACAAGGTAG 59.007 40.000 10.85 0.00 36.06 3.18
2362 2454 5.357742 TGCATGATCATACACAAGGTAGT 57.642 39.130 8.15 0.00 34.92 2.73
2363 2455 5.359756 TGCATGATCATACACAAGGTAGTC 58.640 41.667 8.15 0.00 34.92 2.59
2364 2456 5.104982 TGCATGATCATACACAAGGTAGTCA 60.105 40.000 8.15 0.00 34.92 3.41
2365 2457 5.464722 GCATGATCATACACAAGGTAGTCAG 59.535 44.000 8.15 0.00 34.92 3.51
2366 2458 6.683861 GCATGATCATACACAAGGTAGTCAGA 60.684 42.308 8.15 0.00 34.92 3.27
2367 2459 6.456795 TGATCATACACAAGGTAGTCAGAG 57.543 41.667 0.00 0.00 34.92 3.35
2368 2460 5.952347 TGATCATACACAAGGTAGTCAGAGT 59.048 40.000 0.00 0.00 34.92 3.24
2369 2461 5.899120 TCATACACAAGGTAGTCAGAGTC 57.101 43.478 0.00 0.00 34.92 3.36
2370 2462 4.395231 TCATACACAAGGTAGTCAGAGTCG 59.605 45.833 0.00 0.00 34.92 4.18
2371 2463 1.887198 ACACAAGGTAGTCAGAGTCGG 59.113 52.381 0.00 0.00 0.00 4.79
2372 2464 1.202582 CACAAGGTAGTCAGAGTCGGG 59.797 57.143 0.00 0.00 0.00 5.14
2373 2465 1.075050 ACAAGGTAGTCAGAGTCGGGA 59.925 52.381 0.00 0.00 0.00 5.14
2374 2466 2.291670 ACAAGGTAGTCAGAGTCGGGAT 60.292 50.000 0.00 0.00 0.00 3.85
2375 2467 2.761208 CAAGGTAGTCAGAGTCGGGATT 59.239 50.000 0.00 0.00 0.00 3.01
2376 2468 2.657143 AGGTAGTCAGAGTCGGGATTC 58.343 52.381 0.00 0.00 0.00 2.52
2377 2469 1.334243 GGTAGTCAGAGTCGGGATTCG 59.666 57.143 0.00 0.00 40.90 3.34
2378 2470 1.334243 GTAGTCAGAGTCGGGATTCGG 59.666 57.143 0.00 0.00 39.77 4.30
2379 2471 0.034380 AGTCAGAGTCGGGATTCGGA 60.034 55.000 0.00 0.00 39.77 4.55
2380 2472 0.382515 GTCAGAGTCGGGATTCGGAG 59.617 60.000 0.00 0.00 39.77 4.63
2381 2473 0.034380 TCAGAGTCGGGATTCGGAGT 60.034 55.000 0.00 0.00 39.77 3.85
2382 2474 0.382515 CAGAGTCGGGATTCGGAGTC 59.617 60.000 8.09 8.09 40.72 3.36
2383 2475 1.096386 AGAGTCGGGATTCGGAGTCG 61.096 60.000 10.00 0.00 43.34 4.18
2384 2476 2.061182 GAGTCGGGATTCGGAGTCGG 62.061 65.000 0.92 0.00 39.77 4.79
2385 2477 2.117156 GTCGGGATTCGGAGTCGGA 61.117 63.158 0.00 0.00 39.77 4.55
2386 2478 1.152819 TCGGGATTCGGAGTCGGAT 60.153 57.895 0.69 0.00 37.30 4.18
2391 2483 2.708386 GATTCGGAGTCGGATCGATT 57.292 50.000 0.00 0.00 40.99 3.34
2392 2484 3.014604 GATTCGGAGTCGGATCGATTT 57.985 47.619 0.00 0.00 40.99 2.17
2393 2485 2.953466 TTCGGAGTCGGATCGATTTT 57.047 45.000 0.00 0.00 38.42 1.82
2394 2486 2.486951 TCGGAGTCGGATCGATTTTC 57.513 50.000 0.00 0.00 38.42 2.29
2395 2487 1.066605 TCGGAGTCGGATCGATTTTCC 59.933 52.381 0.00 0.00 38.42 3.13
2396 2488 1.067212 CGGAGTCGGATCGATTTTCCT 59.933 52.381 0.00 0.00 38.42 3.36
2397 2489 2.481449 CGGAGTCGGATCGATTTTCCTT 60.481 50.000 0.00 0.00 38.42 3.36
2398 2490 3.243301 CGGAGTCGGATCGATTTTCCTTA 60.243 47.826 0.00 0.00 38.42 2.69
2399 2491 4.299978 GGAGTCGGATCGATTTTCCTTAG 58.700 47.826 0.00 0.00 38.42 2.18
2400 2492 4.037684 GGAGTCGGATCGATTTTCCTTAGA 59.962 45.833 0.00 0.00 38.42 2.10
2401 2493 4.934515 AGTCGGATCGATTTTCCTTAGAC 58.065 43.478 0.00 0.91 38.42 2.59
2402 2494 4.401519 AGTCGGATCGATTTTCCTTAGACA 59.598 41.667 0.00 0.00 38.42 3.41
2403 2495 4.740695 GTCGGATCGATTTTCCTTAGACAG 59.259 45.833 0.00 0.00 38.42 3.51
2404 2496 4.643334 TCGGATCGATTTTCCTTAGACAGA 59.357 41.667 0.00 0.00 0.00 3.41
2405 2497 5.126545 TCGGATCGATTTTCCTTAGACAGAA 59.873 40.000 0.00 0.00 0.00 3.02
2406 2498 5.986135 CGGATCGATTTTCCTTAGACAGAAT 59.014 40.000 0.00 0.00 0.00 2.40
2407 2499 6.144724 CGGATCGATTTTCCTTAGACAGAATC 59.855 42.308 0.00 0.00 0.00 2.52
2408 2500 6.144724 GGATCGATTTTCCTTAGACAGAATCG 59.855 42.308 0.00 9.30 0.00 3.34
2409 2501 6.203808 TCGATTTTCCTTAGACAGAATCGA 57.796 37.500 13.05 13.05 34.98 3.59
2410 2502 6.627243 TCGATTTTCCTTAGACAGAATCGAA 58.373 36.000 14.26 2.01 34.54 3.71
2411 2503 7.094631 TCGATTTTCCTTAGACAGAATCGAAA 58.905 34.615 14.26 0.00 34.54 3.46
2412 2504 7.063074 TCGATTTTCCTTAGACAGAATCGAAAC 59.937 37.037 14.26 0.00 34.54 2.78
2413 2505 6.462073 TTTTCCTTAGACAGAATCGAAACG 57.538 37.500 0.00 0.00 0.00 3.60
2414 2506 4.778534 TCCTTAGACAGAATCGAAACGT 57.221 40.909 0.00 0.00 0.00 3.99
2415 2507 5.885230 TCCTTAGACAGAATCGAAACGTA 57.115 39.130 0.00 0.00 0.00 3.57
2416 2508 5.877031 TCCTTAGACAGAATCGAAACGTAG 58.123 41.667 0.00 0.00 0.00 3.51
2418 2510 6.595326 TCCTTAGACAGAATCGAAACGTAGTA 59.405 38.462 0.00 0.00 45.00 1.82
2419 2511 7.281774 TCCTTAGACAGAATCGAAACGTAGTAT 59.718 37.037 0.00 0.00 45.00 2.12
2420 2512 7.587028 CCTTAGACAGAATCGAAACGTAGTATC 59.413 40.741 0.00 0.00 45.00 2.24
2421 2513 5.499935 AGACAGAATCGAAACGTAGTATCG 58.500 41.667 0.00 0.00 45.00 2.92
2422 2514 5.292834 AGACAGAATCGAAACGTAGTATCGA 59.707 40.000 14.96 14.96 45.00 3.59
2423 2515 5.499935 ACAGAATCGAAACGTAGTATCGAG 58.500 41.667 16.81 8.91 45.00 4.04
2424 2516 5.064452 ACAGAATCGAAACGTAGTATCGAGT 59.936 40.000 16.81 15.07 45.00 4.18
2425 2517 5.616383 CAGAATCGAAACGTAGTATCGAGTC 59.384 44.000 23.53 23.53 45.00 3.36
2426 2518 3.559530 TCGAAACGTAGTATCGAGTCG 57.440 47.619 6.09 6.09 45.00 4.18
2427 2519 2.923655 TCGAAACGTAGTATCGAGTCGT 59.076 45.455 13.12 2.64 45.00 4.34
2428 2520 3.018246 CGAAACGTAGTATCGAGTCGTG 58.982 50.000 13.12 0.00 45.00 4.35
2429 2521 3.349176 GAAACGTAGTATCGAGTCGTGG 58.651 50.000 13.12 0.00 45.00 4.94
2430 2522 2.299993 ACGTAGTATCGAGTCGTGGA 57.700 50.000 13.12 0.00 41.94 4.02
2431 2523 2.621338 ACGTAGTATCGAGTCGTGGAA 58.379 47.619 13.12 0.00 41.94 3.53
2432 2524 3.201290 ACGTAGTATCGAGTCGTGGAAT 58.799 45.455 13.12 0.79 41.94 3.01
2433 2525 3.247173 ACGTAGTATCGAGTCGTGGAATC 59.753 47.826 13.12 0.51 41.94 2.52
2434 2526 6.065858 ACGTAGTATCGAGTCGTGGAATCG 62.066 50.000 13.12 8.95 45.52 3.34
2440 2532 2.873133 GAGTCGTGGAATCGAGGATT 57.127 50.000 0.00 0.00 40.52 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
151 154 6.454795 TGTTTGTTATTTCTGGCCTCATTTC 58.545 36.000 3.32 0.00 0.00 2.17
353 368 2.614057 GGCATCATTTTCGGATTCGTCT 59.386 45.455 0.00 0.00 37.69 4.18
445 462 1.133976 CAGGATCACCCCACCATCTTC 60.134 57.143 0.00 0.00 36.73 2.87
502 519 1.734388 GCACGTTGCCCCTCTTTTGT 61.734 55.000 0.00 0.00 37.42 2.83
635 654 1.216977 CCCTACACCGCATCGAACA 59.783 57.895 0.00 0.00 0.00 3.18
654 673 1.724018 CGTCGCGAGAACGTCTACTTT 60.724 52.381 10.24 0.00 45.01 2.66
707 756 1.469251 CGTGACCCTGAACATCTACGG 60.469 57.143 0.00 0.00 0.00 4.02
739 788 1.471287 CTCGAAGACACCATGGACGTA 59.529 52.381 21.47 0.00 0.00 3.57
818 867 1.883275 CCAAAATCGCCAAGTACCACA 59.117 47.619 0.00 0.00 0.00 4.17
856 905 1.272769 AGTTCTACGAGGACTGCCAAC 59.727 52.381 0.00 0.00 36.29 3.77
887 936 8.041323 ACTCCTTTCGAAACATGTATCACTAAT 58.959 33.333 6.47 0.00 0.00 1.73
927 976 1.546923 TCGGATCACTAAGTTTCGGCA 59.453 47.619 0.00 0.00 0.00 5.69
977 1026 4.597507 TCTCCAAGGATTTCACCAAGTACT 59.402 41.667 0.00 0.00 0.00 2.73
1053 1102 6.424509 AGTTCCTCTTCGATAGTATGTCTACG 59.575 42.308 0.00 0.00 32.82 3.51
1060 1109 5.505985 GCGACAAGTTCCTCTTCGATAGTAT 60.506 44.000 0.00 0.00 33.63 2.12
1065 1114 1.732732 CGCGACAAGTTCCTCTTCGAT 60.733 52.381 0.00 0.00 33.63 3.59
1226 1275 2.836360 CTGCATCCACCATGGCCC 60.836 66.667 13.04 0.00 37.47 5.80
1294 1343 1.897137 CCTGCATCATGCCGCTCAT 60.897 57.895 7.30 0.00 44.23 2.90
1522 1571 2.449518 TGCCTCCTCCACCACCAA 60.450 61.111 0.00 0.00 0.00 3.67
1559 1608 1.824329 CTCGCGCCTCCTTCTCCTA 60.824 63.158 0.00 0.00 0.00 2.94
1702 1751 2.168666 GACACCCACGTCTCCTTCCC 62.169 65.000 0.00 0.00 32.92 3.97
1703 1752 1.292541 GACACCCACGTCTCCTTCC 59.707 63.158 0.00 0.00 32.92 3.46
1711 1760 3.249189 ATGGCCTGACACCCACGT 61.249 61.111 3.32 0.00 33.17 4.49
1712 1761 2.747460 CATGGCCTGACACCCACG 60.747 66.667 3.32 0.00 33.17 4.94
1714 1763 3.660571 CCCATGGCCTGACACCCA 61.661 66.667 6.09 0.00 35.21 4.51
1722 1771 4.066139 GCCTGAACCCCATGGCCT 62.066 66.667 6.09 0.00 39.49 5.19
1735 1784 1.803519 GCTCTCTTCGTCGTGCCTG 60.804 63.158 0.00 0.00 0.00 4.85
1736 1785 2.569134 GCTCTCTTCGTCGTGCCT 59.431 61.111 0.00 0.00 0.00 4.75
1740 1789 3.369860 CTCGCGCTCTCTTCGTCGT 62.370 63.158 5.56 0.00 0.00 4.34
1761 1810 1.834188 GATCGATCTCCCTCTCTCCC 58.166 60.000 18.29 0.00 0.00 4.30
1824 1873 0.725133 TCCCATCTCTCCTTTCCCCT 59.275 55.000 0.00 0.00 0.00 4.79
1828 1877 1.346068 CCCGATCCCATCTCTCCTTTC 59.654 57.143 0.00 0.00 0.00 2.62
1942 1991 1.915983 CCTCCCTAGGCCAACTTCC 59.084 63.158 5.01 0.00 35.64 3.46
2041 2129 2.735259 ACACCTCTCCTTTTCCCCTA 57.265 50.000 0.00 0.00 0.00 3.53
2111 2201 9.771534 CCTCTAAAAATGTCCAAACCAATTTTA 57.228 29.630 0.00 0.00 0.00 1.52
2308 2400 7.072581 ACCTCCTCCTTCTTTCTTCTTTCTTTA 59.927 37.037 0.00 0.00 0.00 1.85
2322 2414 1.767681 GCATCATCACCTCCTCCTTCT 59.232 52.381 0.00 0.00 0.00 2.85
2354 2446 1.835494 TCCCGACTCTGACTACCTTG 58.165 55.000 0.00 0.00 0.00 3.61
2355 2447 2.830651 ATCCCGACTCTGACTACCTT 57.169 50.000 0.00 0.00 0.00 3.50
2356 2448 2.657143 GAATCCCGACTCTGACTACCT 58.343 52.381 0.00 0.00 0.00 3.08
2357 2449 1.334243 CGAATCCCGACTCTGACTACC 59.666 57.143 0.00 0.00 41.76 3.18
2358 2450 1.334243 CCGAATCCCGACTCTGACTAC 59.666 57.143 0.00 0.00 41.76 2.73
2359 2451 1.211212 TCCGAATCCCGACTCTGACTA 59.789 52.381 0.00 0.00 41.76 2.59
2360 2452 0.034380 TCCGAATCCCGACTCTGACT 60.034 55.000 0.00 0.00 41.76 3.41
2361 2453 0.382515 CTCCGAATCCCGACTCTGAC 59.617 60.000 0.00 0.00 41.76 3.51
2362 2454 0.034380 ACTCCGAATCCCGACTCTGA 60.034 55.000 0.00 0.00 41.76 3.27
2363 2455 0.382515 GACTCCGAATCCCGACTCTG 59.617 60.000 0.00 0.00 41.76 3.35
2364 2456 1.096386 CGACTCCGAATCCCGACTCT 61.096 60.000 0.00 0.00 41.76 3.24
2365 2457 1.355916 CGACTCCGAATCCCGACTC 59.644 63.158 0.00 0.00 41.76 3.36
2366 2458 2.119655 CCGACTCCGAATCCCGACT 61.120 63.158 0.00 0.00 41.76 4.18
2367 2459 1.453762 ATCCGACTCCGAATCCCGAC 61.454 60.000 0.00 0.00 41.76 4.79
2368 2460 1.152819 ATCCGACTCCGAATCCCGA 60.153 57.895 0.00 0.00 41.76 5.14
2369 2461 1.286260 GATCCGACTCCGAATCCCG 59.714 63.158 0.00 0.00 38.22 5.14
2370 2462 1.170919 TCGATCCGACTCCGAATCCC 61.171 60.000 0.00 0.00 38.22 3.85
2371 2463 0.882474 ATCGATCCGACTCCGAATCC 59.118 55.000 0.00 0.00 39.18 3.01
2372 2464 2.708386 AATCGATCCGACTCCGAATC 57.292 50.000 0.00 0.00 39.18 2.52
2373 2465 3.381949 GAAAATCGATCCGACTCCGAAT 58.618 45.455 0.00 0.00 39.18 3.34
2374 2466 2.480759 GGAAAATCGATCCGACTCCGAA 60.481 50.000 0.00 0.00 39.18 4.30
2375 2467 1.066605 GGAAAATCGATCCGACTCCGA 59.933 52.381 0.00 0.00 39.18 4.55
2376 2468 1.067212 AGGAAAATCGATCCGACTCCG 59.933 52.381 0.00 0.00 42.03 4.63
2377 2469 2.892784 AGGAAAATCGATCCGACTCC 57.107 50.000 0.00 0.84 42.03 3.85
2378 2470 4.977347 GTCTAAGGAAAATCGATCCGACTC 59.023 45.833 0.00 0.00 42.03 3.36
2379 2471 4.401519 TGTCTAAGGAAAATCGATCCGACT 59.598 41.667 0.00 0.00 42.03 4.18
2380 2472 4.679662 TGTCTAAGGAAAATCGATCCGAC 58.320 43.478 0.00 1.01 42.03 4.79
2381 2473 4.643334 TCTGTCTAAGGAAAATCGATCCGA 59.357 41.667 0.00 0.00 42.03 4.55
2382 2474 4.933330 TCTGTCTAAGGAAAATCGATCCG 58.067 43.478 0.00 0.00 42.03 4.18
2383 2475 6.144724 CGATTCTGTCTAAGGAAAATCGATCC 59.855 42.308 0.00 0.00 44.89 3.36
2384 2476 6.918569 TCGATTCTGTCTAAGGAAAATCGATC 59.081 38.462 12.39 0.00 45.36 3.69
2385 2477 6.806751 TCGATTCTGTCTAAGGAAAATCGAT 58.193 36.000 12.39 0.00 45.36 3.59
2386 2478 6.203808 TCGATTCTGTCTAAGGAAAATCGA 57.796 37.500 12.39 12.39 46.95 3.59
2387 2479 6.887376 TTCGATTCTGTCTAAGGAAAATCG 57.113 37.500 8.54 8.54 44.00 3.34
2388 2480 7.148623 ACGTTTCGATTCTGTCTAAGGAAAATC 60.149 37.037 0.00 0.00 0.00 2.17
2389 2481 6.649557 ACGTTTCGATTCTGTCTAAGGAAAAT 59.350 34.615 0.00 0.00 0.00 1.82
2390 2482 5.987347 ACGTTTCGATTCTGTCTAAGGAAAA 59.013 36.000 0.00 0.00 0.00 2.29
2391 2483 5.535333 ACGTTTCGATTCTGTCTAAGGAAA 58.465 37.500 0.00 0.00 0.00 3.13
2392 2484 5.130292 ACGTTTCGATTCTGTCTAAGGAA 57.870 39.130 0.00 0.00 0.00 3.36
2393 2485 4.778534 ACGTTTCGATTCTGTCTAAGGA 57.221 40.909 0.00 0.00 0.00 3.36
2394 2486 5.638783 ACTACGTTTCGATTCTGTCTAAGG 58.361 41.667 0.00 0.00 0.00 2.69
2395 2487 7.318439 CGATACTACGTTTCGATTCTGTCTAAG 59.682 40.741 0.00 0.00 38.79 2.18
2396 2488 7.010460 TCGATACTACGTTTCGATTCTGTCTAA 59.990 37.037 0.00 0.00 39.99 2.10
2397 2489 6.476706 TCGATACTACGTTTCGATTCTGTCTA 59.523 38.462 0.00 0.00 39.99 2.59
2398 2490 5.292834 TCGATACTACGTTTCGATTCTGTCT 59.707 40.000 0.00 0.00 39.99 3.41
2399 2491 5.496387 TCGATACTACGTTTCGATTCTGTC 58.504 41.667 0.00 0.00 39.99 3.51
2400 2492 5.064452 ACTCGATACTACGTTTCGATTCTGT 59.936 40.000 9.32 3.04 42.71 3.41
2401 2493 5.499935 ACTCGATACTACGTTTCGATTCTG 58.500 41.667 9.32 2.55 42.71 3.02
2402 2494 5.556006 CGACTCGATACTACGTTTCGATTCT 60.556 44.000 17.56 4.68 42.71 2.40
2403 2495 4.602333 CGACTCGATACTACGTTTCGATTC 59.398 45.833 9.32 11.47 42.71 2.52
2404 2496 4.033358 ACGACTCGATACTACGTTTCGATT 59.967 41.667 5.20 5.10 42.71 3.34
2405 2497 3.553511 ACGACTCGATACTACGTTTCGAT 59.446 43.478 5.20 2.36 42.71 3.59
2406 2498 2.923655 ACGACTCGATACTACGTTTCGA 59.076 45.455 5.20 2.80 41.82 3.71
2407 2499 3.018246 CACGACTCGATACTACGTTTCG 58.982 50.000 5.20 0.00 40.88 3.46
2408 2500 3.062639 TCCACGACTCGATACTACGTTTC 59.937 47.826 5.20 0.00 35.05 2.78
2409 2501 3.002791 TCCACGACTCGATACTACGTTT 58.997 45.455 5.20 0.00 35.05 3.60
2410 2502 2.621338 TCCACGACTCGATACTACGTT 58.379 47.619 5.20 0.00 35.05 3.99
2411 2503 2.299993 TCCACGACTCGATACTACGT 57.700 50.000 5.20 0.00 37.68 3.57
2412 2504 3.661162 CGATTCCACGACTCGATACTACG 60.661 52.174 5.20 1.08 36.98 3.51
2413 2505 3.492383 TCGATTCCACGACTCGATACTAC 59.508 47.826 5.20 0.00 38.45 2.73
2414 2506 3.721035 TCGATTCCACGACTCGATACTA 58.279 45.455 5.20 0.00 38.45 1.82
2415 2507 2.544686 CTCGATTCCACGACTCGATACT 59.455 50.000 5.20 0.00 41.41 2.12
2416 2508 2.349627 CCTCGATTCCACGACTCGATAC 60.350 54.545 5.20 0.00 41.41 2.24
2417 2509 1.871676 CCTCGATTCCACGACTCGATA 59.128 52.381 5.20 0.00 41.41 2.92
2418 2510 0.663688 CCTCGATTCCACGACTCGAT 59.336 55.000 5.20 0.00 41.41 3.59
2419 2511 0.392060 TCCTCGATTCCACGACTCGA 60.392 55.000 5.20 4.39 40.40 4.04
2420 2512 0.663688 ATCCTCGATTCCACGACTCG 59.336 55.000 0.00 0.00 37.37 4.18
2421 2513 2.873133 AATCCTCGATTCCACGACTC 57.127 50.000 0.00 0.00 37.37 3.36


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

AutoCloner maintained by Alex Coulton.