Multiple sequence alignment - TraesCS2A01G042800

Loading Multiple Alignment...

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 TraesCS2A01G042800 chr2A 100.000 3546 0 0 1 3546 17117069 17120614 0.000000e+00 6549.0
1 TraesCS2A01G042800 chr2A 78.993 1271 217 28 1191 2452 19471834 19473063 0.000000e+00 822.0
2 TraesCS2A01G042800 chr2A 76.946 1349 254 38 1139 2457 711855954 711857275 0.000000e+00 715.0
3 TraesCS2A01G042800 chr2A 85.437 103 8 4 1057 1154 19471732 19471832 2.250000e-17 100.0
4 TraesCS2A01G042800 chr2A 91.111 45 4 0 2563 2607 701007362 701007406 1.060000e-05 62.1
5 TraesCS2A01G042800 chr2B 90.979 1818 124 17 666 2456 27009644 27011448 0.000000e+00 2412.0
6 TraesCS2A01G042800 chr2B 94.562 662 35 1 2 662 796904993 796904332 0.000000e+00 1022.0
7 TraesCS2A01G042800 chr2B 80.000 1410 217 36 1062 2456 26925243 26926602 0.000000e+00 981.0
8 TraesCS2A01G042800 chr2B 76.929 1413 258 49 1078 2457 687634073 687635450 0.000000e+00 741.0
9 TraesCS2A01G042800 chr2B 95.312 384 18 0 276 659 25577304 25576921 8.420000e-171 610.0
10 TraesCS2A01G042800 chr2B 89.499 419 40 3 2993 3410 63045763 63046178 8.720000e-146 527.0
11 TraesCS2A01G042800 chr2B 93.559 295 13 3 2197 2490 26929970 26930259 5.440000e-118 435.0
12 TraesCS2A01G042800 chr2B 94.762 210 11 0 1113 1322 26929766 26929975 9.490000e-86 327.0
13 TraesCS2A01G042800 chr2B 83.391 289 13 14 699 968 26929494 26929766 5.920000e-58 235.0
14 TraesCS2A01G042800 chr2D 90.680 1749 109 22 770 2490 14970318 14972040 0.000000e+00 2278.0
15 TraesCS2A01G042800 chr2D 77.054 1412 258 44 1078 2457 572404259 572405636 0.000000e+00 752.0
16 TraesCS2A01G042800 chr2D 83.740 369 45 7 1057 1422 18325659 18326015 5.670000e-88 335.0
17 TraesCS2A01G042800 chr2D 97.436 39 1 0 1914 1952 13434973 13434935 2.280000e-07 67.6
18 TraesCS2A01G042800 chr3A 93.886 965 58 1 2563 3527 19781212 19782175 0.000000e+00 1454.0
19 TraesCS2A01G042800 chr3A 78.524 1369 208 54 1153 2506 13363472 13364769 0.000000e+00 821.0
20 TraesCS2A01G042800 chr7B 83.006 1424 168 40 1064 2459 712766774 712768151 0.000000e+00 1221.0
21 TraesCS2A01G042800 chr7B 90.548 529 44 5 2563 3086 320268274 320268801 0.000000e+00 695.0
22 TraesCS2A01G042800 chr3D 95.000 660 31 2 2 660 571178970 571178312 0.000000e+00 1035.0
23 TraesCS2A01G042800 chr3D 79.824 1477 214 35 1057 2506 7023346 7021927 0.000000e+00 1000.0
24 TraesCS2A01G042800 chr1D 94.260 662 36 2 2 663 439137369 439138028 0.000000e+00 1011.0
25 TraesCS2A01G042800 chr1D 74.523 1048 197 40 1459 2462 476249211 476248190 3.320000e-105 392.0
26 TraesCS2A01G042800 chr1D 82.639 144 17 4 3269 3410 423060630 423060767 1.730000e-23 121.0
27 TraesCS2A01G042800 chr3B 93.303 657 41 3 5 659 823964725 823964070 0.000000e+00 966.0
28 TraesCS2A01G042800 chr3B 85.238 210 29 2 2248 2456 8521866 8521658 7.710000e-52 215.0
29 TraesCS2A01G042800 chr3B 87.324 142 18 0 3269 3410 736470511 736470370 2.830000e-36 163.0
30 TraesCS2A01G042800 chr5B 90.141 639 60 3 2 639 514006300 514005664 0.000000e+00 828.0
31 TraesCS2A01G042800 chr5B 85.211 284 35 6 2912 3193 360404022 360404300 5.790000e-73 285.0
32 TraesCS2A01G042800 chr6A 91.058 548 47 2 132 679 465235107 465234562 0.000000e+00 739.0
33 TraesCS2A01G042800 chr1A 91.667 528 39 4 2563 3086 412784469 412783943 0.000000e+00 726.0
34 TraesCS2A01G042800 chr1A 89.362 47 5 0 2561 2607 506496910 506496864 3.820000e-05 60.2
35 TraesCS2A01G042800 chr6B 91.288 528 41 5 2563 3086 412163755 412164281 0.000000e+00 715.0
36 TraesCS2A01G042800 chr6B 90.926 529 42 5 2563 3086 106477067 106476540 0.000000e+00 706.0
37 TraesCS2A01G042800 chr4A 93.061 490 33 1 171 659 725932599 725933088 0.000000e+00 715.0
38 TraesCS2A01G042800 chr4B 93.446 473 31 0 1 473 148924599 148924127 0.000000e+00 702.0
39 TraesCS2A01G042800 chr4B 92.737 358 26 0 21 378 530015101 530015458 5.250000e-143 518.0
40 TraesCS2A01G042800 chr4B 74.919 925 183 31 1257 2170 627812810 627811924 9.290000e-101 377.0
41 TraesCS2A01G042800 chr1B 73.871 1439 269 61 1072 2453 603604433 603605821 3.200000e-130 475.0
42 TraesCS2A01G042800 chr7A 93.980 299 18 0 1 299 519564997 519565295 1.500000e-123 453.0
43 TraesCS2A01G042800 chr7A 82.022 267 45 3 2870 3136 731694439 731694702 1.280000e-54 224.0
44 TraesCS2A01G042800 chr7A 86.014 143 19 1 3269 3410 733693425 733693567 6.130000e-33 152.0
45 TraesCS2A01G042800 chr7A 85.915 142 18 1 3267 3406 116014164 116014305 2.210000e-32 150.0
46 TraesCS2A01G042800 chr7D 84.383 397 56 5 2870 3265 634562940 634562549 5.550000e-103 385.0
47 TraesCS2A01G042800 chr4D 86.620 142 19 0 3269 3410 426646885 426646744 1.320000e-34 158.0
48 TraesCS2A01G042800 chr5D 96.875 32 1 0 2563 2594 342510164 342510133 2.000000e-03 54.7


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 TraesCS2A01G042800 chr2A 17117069 17120614 3545 False 6549.0 6549 100.000 1 3546 1 chr2A.!!$F1 3545
1 TraesCS2A01G042800 chr2A 711855954 711857275 1321 False 715.0 715 76.946 1139 2457 1 chr2A.!!$F3 1318
2 TraesCS2A01G042800 chr2A 19471732 19473063 1331 False 461.0 822 82.215 1057 2452 2 chr2A.!!$F4 1395
3 TraesCS2A01G042800 chr2B 27009644 27011448 1804 False 2412.0 2412 90.979 666 2456 1 chr2B.!!$F1 1790
4 TraesCS2A01G042800 chr2B 796904332 796904993 661 True 1022.0 1022 94.562 2 662 1 chr2B.!!$R2 660
5 TraesCS2A01G042800 chr2B 687634073 687635450 1377 False 741.0 741 76.929 1078 2457 1 chr2B.!!$F3 1379
6 TraesCS2A01G042800 chr2B 26925243 26930259 5016 False 494.5 981 87.928 699 2490 4 chr2B.!!$F4 1791
7 TraesCS2A01G042800 chr2D 14970318 14972040 1722 False 2278.0 2278 90.680 770 2490 1 chr2D.!!$F1 1720
8 TraesCS2A01G042800 chr2D 572404259 572405636 1377 False 752.0 752 77.054 1078 2457 1 chr2D.!!$F3 1379
9 TraesCS2A01G042800 chr3A 19781212 19782175 963 False 1454.0 1454 93.886 2563 3527 1 chr3A.!!$F2 964
10 TraesCS2A01G042800 chr3A 13363472 13364769 1297 False 821.0 821 78.524 1153 2506 1 chr3A.!!$F1 1353
11 TraesCS2A01G042800 chr7B 712766774 712768151 1377 False 1221.0 1221 83.006 1064 2459 1 chr7B.!!$F2 1395
12 TraesCS2A01G042800 chr7B 320268274 320268801 527 False 695.0 695 90.548 2563 3086 1 chr7B.!!$F1 523
13 TraesCS2A01G042800 chr3D 571178312 571178970 658 True 1035.0 1035 95.000 2 660 1 chr3D.!!$R2 658
14 TraesCS2A01G042800 chr3D 7021927 7023346 1419 True 1000.0 1000 79.824 1057 2506 1 chr3D.!!$R1 1449
15 TraesCS2A01G042800 chr1D 439137369 439138028 659 False 1011.0 1011 94.260 2 663 1 chr1D.!!$F2 661
16 TraesCS2A01G042800 chr1D 476248190 476249211 1021 True 392.0 392 74.523 1459 2462 1 chr1D.!!$R1 1003
17 TraesCS2A01G042800 chr3B 823964070 823964725 655 True 966.0 966 93.303 5 659 1 chr3B.!!$R3 654
18 TraesCS2A01G042800 chr5B 514005664 514006300 636 True 828.0 828 90.141 2 639 1 chr5B.!!$R1 637
19 TraesCS2A01G042800 chr6A 465234562 465235107 545 True 739.0 739 91.058 132 679 1 chr6A.!!$R1 547
20 TraesCS2A01G042800 chr1A 412783943 412784469 526 True 726.0 726 91.667 2563 3086 1 chr1A.!!$R1 523
21 TraesCS2A01G042800 chr6B 412163755 412164281 526 False 715.0 715 91.288 2563 3086 1 chr6B.!!$F1 523
22 TraesCS2A01G042800 chr6B 106476540 106477067 527 True 706.0 706 90.926 2563 3086 1 chr6B.!!$R1 523
23 TraesCS2A01G042800 chr4B 627811924 627812810 886 True 377.0 377 74.919 1257 2170 1 chr4B.!!$R2 913
24 TraesCS2A01G042800 chr1B 603604433 603605821 1388 False 475.0 475 73.871 1072 2453 1 chr1B.!!$F1 1381

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
360 362 0.109226 GGCACTGACGTGGAGTACTC 60.109 60.0 14.87 14.87 41.51 2.59 F
361 363 0.454620 GCACTGACGTGGAGTACTCG 60.455 60.0 16.56 8.76 41.51 4.18 F
1352 1415 0.248289 ACCGGGGAACAATACTGACG 59.752 55.0 6.32 0.00 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1333 1387 0.248289 CGTCAGTATTGTTCCCCGGT 59.752 55.0 0.0 0.0 0.00 5.28 R
1859 2052 0.311790 TTCGCCTTTGCTTTGAGCTG 59.688 50.0 0.0 0.0 42.97 4.24 R
2546 6426 0.323725 GGCCCAGATGGAAAGCAAGA 60.324 55.0 0.0 0.0 37.39 3.02 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
181 183 0.543277 TCCCCGTCGACTTCTAGCTA 59.457 55.000 14.70 0.00 0.00 3.32
273 275 1.480212 TTCCGCACTGAGACATGGGT 61.480 55.000 0.00 0.00 0.00 4.51
304 306 1.799544 GGTCGTGACGGTGGTTTAAT 58.200 50.000 4.70 0.00 0.00 1.40
360 362 0.109226 GGCACTGACGTGGAGTACTC 60.109 60.000 14.87 14.87 41.51 2.59
361 363 0.454620 GCACTGACGTGGAGTACTCG 60.455 60.000 16.56 8.76 41.51 4.18
519 522 4.379290 GCTACGGAAGAACTCGACTTAGTT 60.379 45.833 0.00 0.00 42.36 2.24
554 557 8.519799 AATTTCATATCTTGTAATGGTTCGGT 57.480 30.769 0.00 0.00 0.00 4.69
696 699 7.495055 AGCTGAAACTGAAACTCAAAATTCAT 58.505 30.769 0.00 0.00 35.20 2.57
831 844 1.271840 CCGGTTGAGATTGAGGGGGA 61.272 60.000 0.00 0.00 0.00 4.81
833 846 1.212935 CGGTTGAGATTGAGGGGGAAT 59.787 52.381 0.00 0.00 0.00 3.01
835 848 3.713003 GGTTGAGATTGAGGGGGAATTT 58.287 45.455 0.00 0.00 0.00 1.82
934 966 4.581077 TCTGATCTGATCCGACATCAAG 57.419 45.455 14.71 3.53 0.00 3.02
985 1018 8.940012 AATCATCATATAAATAGAGGGGGAGT 57.060 34.615 0.00 0.00 0.00 3.85
988 1021 8.186985 TCATCATATAAATAGAGGGGGAGTTCT 58.813 37.037 0.00 0.00 0.00 3.01
1004 1037 3.445008 AGTTCTAGAGGCCAATCACAGA 58.555 45.455 5.01 0.00 0.00 3.41
1006 1039 4.081198 AGTTCTAGAGGCCAATCACAGAAG 60.081 45.833 5.01 0.00 0.00 2.85
1012 1045 5.189180 AGAGGCCAATCACAGAAGATTAAC 58.811 41.667 5.01 0.00 36.13 2.01
1015 1048 4.142381 GGCCAATCACAGAAGATTAACCAC 60.142 45.833 0.00 0.00 36.13 4.16
1026 1060 6.881602 CAGAAGATTAACCACCTTCTTAGCTT 59.118 38.462 0.00 0.00 42.65 3.74
1027 1061 8.041323 CAGAAGATTAACCACCTTCTTAGCTTA 58.959 37.037 0.00 0.00 42.65 3.09
1028 1062 8.041919 AGAAGATTAACCACCTTCTTAGCTTAC 58.958 37.037 0.00 0.00 42.65 2.34
1029 1063 7.497773 AGATTAACCACCTTCTTAGCTTACT 57.502 36.000 0.00 0.00 0.00 2.24
1030 1064 7.331791 AGATTAACCACCTTCTTAGCTTACTG 58.668 38.462 0.00 0.00 0.00 2.74
1031 1065 3.336138 ACCACCTTCTTAGCTTACTGC 57.664 47.619 0.00 0.00 43.29 4.40
1195 1240 2.808933 CGCCTTGGAGTACAACCAGAAA 60.809 50.000 10.76 0.00 38.70 2.52
1231 1276 2.370445 CCCTCCCGCCACAGAAGAT 61.370 63.158 0.00 0.00 0.00 2.40
1346 1409 1.003812 CCTTCACACCGGGGAACAATA 59.996 52.381 12.96 0.00 0.00 1.90
1352 1415 0.248289 ACCGGGGAACAATACTGACG 59.752 55.000 6.32 0.00 0.00 4.35
1513 1619 4.100084 CTGGACGGGCTGCATGGA 62.100 66.667 0.50 0.00 0.00 3.41
1591 1697 1.138036 CGGTGTCTTCGTCGGCATA 59.862 57.895 0.00 0.00 0.00 3.14
1661 1767 2.415010 CCTGGTCCGAGATCAGCG 59.585 66.667 8.24 0.00 39.27 5.18
1893 2086 1.004277 GCGAACGCCGAGATCTATGG 61.004 60.000 8.03 8.78 41.76 2.74
1894 2087 1.004277 CGAACGCCGAGATCTATGGC 61.004 60.000 22.76 22.76 45.39 4.40
1902 2101 1.202568 CGAGATCTATGGCACCAGCAA 60.203 52.381 0.00 0.00 44.61 3.91
1903 2102 2.549563 CGAGATCTATGGCACCAGCAAT 60.550 50.000 0.00 0.00 44.61 3.56
1976 2190 4.316823 TGACCCGAGCCAGGAGGT 62.317 66.667 0.00 0.00 37.19 3.85
2017 2239 1.354506 GTACGTCATCCTCGTCGGG 59.645 63.158 0.00 0.00 41.72 5.14
2124 2349 3.412408 GGAGAGGGGGCTGGGTTC 61.412 72.222 0.00 0.00 0.00 3.62
2347 6227 1.696832 GAGCGAACAAGATGGACGGC 61.697 60.000 0.00 0.00 0.00 5.68
2458 6338 0.969149 ACGAGGAGTTCATGAGCACA 59.031 50.000 12.41 0.00 0.00 4.57
2459 6339 1.067283 ACGAGGAGTTCATGAGCACAG 60.067 52.381 12.41 4.02 0.00 3.66
2460 6340 1.067283 CGAGGAGTTCATGAGCACAGT 60.067 52.381 12.41 0.00 0.00 3.55
2461 6341 2.344950 GAGGAGTTCATGAGCACAGTG 58.655 52.381 12.41 0.00 0.00 3.66
2462 6342 1.973515 AGGAGTTCATGAGCACAGTGA 59.026 47.619 12.41 0.00 0.00 3.41
2463 6343 2.072298 GGAGTTCATGAGCACAGTGAC 58.928 52.381 12.41 0.00 0.00 3.67
2470 6350 2.355126 AGCACAGTGACGTGAGCG 60.355 61.111 4.15 0.00 38.86 5.03
2493 6373 0.948623 CCACAGCGTGACCGATCAAA 60.949 55.000 9.75 0.00 36.31 2.69
2497 6377 0.317160 AGCGTGACCGATCAAACAGA 59.683 50.000 0.00 0.00 36.31 3.41
2506 6386 7.033791 GTGACCGATCAAACAGATTCTTACTA 58.966 38.462 0.00 0.00 37.00 1.82
2507 6387 7.221067 GTGACCGATCAAACAGATTCTTACTAG 59.779 40.741 0.00 0.00 37.00 2.57
2508 6388 7.093902 TGACCGATCAAACAGATTCTTACTAGT 60.094 37.037 0.00 0.00 37.00 2.57
2509 6389 7.036220 ACCGATCAAACAGATTCTTACTAGTG 58.964 38.462 5.39 0.00 37.00 2.74
2510 6390 7.036220 CCGATCAAACAGATTCTTACTAGTGT 58.964 38.462 5.39 0.00 37.00 3.55
2511 6391 7.221067 CCGATCAAACAGATTCTTACTAGTGTC 59.779 40.741 5.39 0.00 37.00 3.67
2512 6392 7.971168 CGATCAAACAGATTCTTACTAGTGTCT 59.029 37.037 5.39 0.00 37.00 3.41
2515 6395 9.298250 TCAAACAGATTCTTACTAGTGTCTAGT 57.702 33.333 5.39 12.91 0.00 2.57
2516 6396 9.347934 CAAACAGATTCTTACTAGTGTCTAGTG 57.652 37.037 16.60 4.46 0.00 2.74
2517 6397 7.633193 ACAGATTCTTACTAGTGTCTAGTGG 57.367 40.000 16.60 10.68 0.00 4.00
2518 6398 7.176490 ACAGATTCTTACTAGTGTCTAGTGGT 58.824 38.462 16.60 0.00 0.00 4.16
2519 6399 7.121463 ACAGATTCTTACTAGTGTCTAGTGGTG 59.879 40.741 16.60 8.59 0.00 4.17
2520 6400 5.640189 TTCTTACTAGTGTCTAGTGGTGC 57.360 43.478 16.60 0.00 0.00 5.01
2521 6401 4.659115 TCTTACTAGTGTCTAGTGGTGCA 58.341 43.478 16.60 0.00 0.00 4.57
2522 6402 5.262009 TCTTACTAGTGTCTAGTGGTGCAT 58.738 41.667 16.60 0.00 0.00 3.96
2523 6403 5.357314 TCTTACTAGTGTCTAGTGGTGCATC 59.643 44.000 16.60 0.00 0.00 3.91
2524 6404 3.431415 ACTAGTGTCTAGTGGTGCATCA 58.569 45.455 0.00 0.00 0.00 3.07
2525 6405 3.445450 ACTAGTGTCTAGTGGTGCATCAG 59.555 47.826 0.00 0.00 0.00 2.90
2526 6406 2.251818 AGTGTCTAGTGGTGCATCAGT 58.748 47.619 12.88 12.88 0.00 3.41
2527 6407 2.634940 AGTGTCTAGTGGTGCATCAGTT 59.365 45.455 13.62 0.34 0.00 3.16
2528 6408 3.832490 AGTGTCTAGTGGTGCATCAGTTA 59.168 43.478 13.62 1.67 0.00 2.24
2529 6409 4.081972 AGTGTCTAGTGGTGCATCAGTTAG 60.082 45.833 13.62 11.88 0.00 2.34
2530 6410 3.190874 GTCTAGTGGTGCATCAGTTAGC 58.809 50.000 13.62 5.16 0.00 3.09
2531 6411 3.099905 TCTAGTGGTGCATCAGTTAGCT 58.900 45.455 13.62 2.12 0.00 3.32
2532 6412 4.098044 GTCTAGTGGTGCATCAGTTAGCTA 59.902 45.833 13.62 3.32 0.00 3.32
2533 6413 3.252974 AGTGGTGCATCAGTTAGCTAC 57.747 47.619 0.00 0.00 0.00 3.58
2534 6414 2.567169 AGTGGTGCATCAGTTAGCTACA 59.433 45.455 0.00 0.00 0.00 2.74
2535 6415 3.198635 AGTGGTGCATCAGTTAGCTACAT 59.801 43.478 0.00 0.00 0.00 2.29
2536 6416 3.310774 GTGGTGCATCAGTTAGCTACATG 59.689 47.826 0.00 0.00 0.00 3.21
2537 6417 3.055167 TGGTGCATCAGTTAGCTACATGT 60.055 43.478 2.69 2.69 0.00 3.21
2538 6418 3.310774 GGTGCATCAGTTAGCTACATGTG 59.689 47.826 9.11 0.00 0.00 3.21
2539 6419 3.310774 GTGCATCAGTTAGCTACATGTGG 59.689 47.826 9.11 6.75 0.00 4.17
2540 6420 2.874701 GCATCAGTTAGCTACATGTGGG 59.125 50.000 9.11 2.29 0.00 4.61
2541 6421 3.432186 GCATCAGTTAGCTACATGTGGGA 60.432 47.826 9.11 0.00 0.00 4.37
2542 6422 4.744867 GCATCAGTTAGCTACATGTGGGAT 60.745 45.833 9.11 2.53 0.00 3.85
2543 6423 5.511373 GCATCAGTTAGCTACATGTGGGATA 60.511 44.000 9.11 1.49 0.00 2.59
2544 6424 6.524734 CATCAGTTAGCTACATGTGGGATAA 58.475 40.000 9.11 7.83 0.00 1.75
2545 6425 6.553953 TCAGTTAGCTACATGTGGGATAAA 57.446 37.500 9.11 0.00 0.00 1.40
2546 6426 7.136822 TCAGTTAGCTACATGTGGGATAAAT 57.863 36.000 9.11 7.15 0.00 1.40
2547 6427 7.217200 TCAGTTAGCTACATGTGGGATAAATC 58.783 38.462 9.11 0.85 0.00 2.17
2548 6428 7.071196 TCAGTTAGCTACATGTGGGATAAATCT 59.929 37.037 9.11 0.00 0.00 2.40
2549 6429 7.716998 CAGTTAGCTACATGTGGGATAAATCTT 59.283 37.037 9.11 0.00 0.00 2.40
2550 6430 7.716998 AGTTAGCTACATGTGGGATAAATCTTG 59.283 37.037 9.11 0.00 0.00 3.02
2551 6431 4.823989 AGCTACATGTGGGATAAATCTTGC 59.176 41.667 9.11 0.00 0.00 4.01
2552 6432 4.823989 GCTACATGTGGGATAAATCTTGCT 59.176 41.667 9.11 0.00 0.00 3.91
2553 6433 5.300286 GCTACATGTGGGATAAATCTTGCTT 59.700 40.000 9.11 0.00 0.00 3.91
2554 6434 6.183360 GCTACATGTGGGATAAATCTTGCTTT 60.183 38.462 9.11 0.00 0.00 3.51
2555 6435 6.212888 ACATGTGGGATAAATCTTGCTTTC 57.787 37.500 0.00 0.00 0.00 2.62
2556 6436 5.127682 ACATGTGGGATAAATCTTGCTTTCC 59.872 40.000 0.00 0.00 0.00 3.13
2557 6437 4.671831 TGTGGGATAAATCTTGCTTTCCA 58.328 39.130 0.00 0.00 0.00 3.53
2558 6438 5.271598 TGTGGGATAAATCTTGCTTTCCAT 58.728 37.500 0.00 0.00 0.00 3.41
2559 6439 5.360714 TGTGGGATAAATCTTGCTTTCCATC 59.639 40.000 0.00 0.00 0.00 3.51
2560 6440 5.595952 GTGGGATAAATCTTGCTTTCCATCT 59.404 40.000 0.00 0.00 0.00 2.90
2561 6441 5.595542 TGGGATAAATCTTGCTTTCCATCTG 59.404 40.000 0.00 0.00 0.00 2.90
2633 6515 2.761195 GCCGTTCGATTTGGGCTCC 61.761 63.158 8.71 0.00 42.29 4.70
2691 6574 1.938585 TCATCTTCAACCTCCGTCCT 58.061 50.000 0.00 0.00 0.00 3.85
2705 6588 1.821061 CGTCCTCACAAGCCTCCACT 61.821 60.000 0.00 0.00 0.00 4.00
2707 6590 0.178921 TCCTCACAAGCCTCCACTCT 60.179 55.000 0.00 0.00 0.00 3.24
2909 6796 6.151985 TGCTTCAGTTGAAACTTTTTCCACTA 59.848 34.615 5.37 0.00 37.08 2.74
2916 6803 9.936759 AGTTGAAACTTTTTCCACTATTTGAAA 57.063 25.926 4.10 0.00 35.21 2.69
3097 6986 1.005037 TTGCAGCTTCGACGTCCAT 60.005 52.632 10.58 0.00 0.00 3.41
3112 7001 2.180017 CATGCTTGCAACCTCGCC 59.820 61.111 0.00 0.00 0.00 5.54
3124 7013 2.578178 CTCGCCGTCGAAGAGCAG 60.578 66.667 0.00 0.00 44.98 4.24
3126 7015 2.578178 CGCCGTCGAAGAGCAGAG 60.578 66.667 0.00 0.00 36.95 3.35
3127 7016 2.569134 GCCGTCGAAGAGCAGAGT 59.431 61.111 0.00 0.00 36.95 3.24
3132 7021 0.456995 GTCGAAGAGCAGAGTTCCCG 60.457 60.000 0.00 0.00 36.95 5.14
3266 7155 2.548493 GGTTGGTTGCAGCATTTGTCAT 60.548 45.455 2.05 0.00 0.00 3.06
3267 7156 3.132925 GTTGGTTGCAGCATTTGTCATT 58.867 40.909 2.05 0.00 0.00 2.57
3269 7158 1.461897 GGTTGCAGCATTTGTCATTGC 59.538 47.619 2.05 1.04 39.17 3.56
3337 7226 0.105760 TGCAACATCAGGGGGTGTTT 60.106 50.000 0.00 0.00 36.48 2.83
3353 7242 3.159104 TTTCCCTTGGTGCCCCCAG 62.159 63.158 0.00 0.00 46.31 4.45
3357 7246 3.970410 CTTGGTGCCCCCAGCTCA 61.970 66.667 0.00 0.00 46.31 4.26
3387 7276 1.209261 TCGATCTTGTAAGCCATGGCA 59.791 47.619 37.18 16.60 44.88 4.92
3410 7299 0.529337 CTGCATGTGAGCTCGTAGGG 60.529 60.000 9.64 0.00 34.99 3.53
3439 7328 0.744414 CATCCTGAATCGCCGGTTGT 60.744 55.000 1.90 0.00 0.00 3.32
3449 7338 2.656069 GCCGGTTGTAGCTCTGGGA 61.656 63.158 1.90 0.00 0.00 4.37
3484 7373 0.394565 GGAAGACATGGCCGCTAGAT 59.605 55.000 0.00 0.00 0.00 1.98
3527 7416 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
3528 7417 4.078922 AGAGAGAGAGAGAGAGAGAGAGGA 60.079 50.000 0.00 0.00 0.00 3.71
3529 7418 4.624913 AGAGAGAGAGAGAGAGAGAGGAA 58.375 47.826 0.00 0.00 0.00 3.36
3530 7419 5.222870 AGAGAGAGAGAGAGAGAGAGGAAT 58.777 45.833 0.00 0.00 0.00 3.01
3531 7420 5.306678 AGAGAGAGAGAGAGAGAGAGGAATC 59.693 48.000 0.00 0.00 0.00 2.52
3532 7421 5.222870 AGAGAGAGAGAGAGAGAGGAATCT 58.777 45.833 0.00 0.00 0.00 2.40
3533 7422 5.071519 AGAGAGAGAGAGAGAGAGGAATCTG 59.928 48.000 0.00 0.00 0.00 2.90
3534 7423 4.103785 AGAGAGAGAGAGAGAGGAATCTGG 59.896 50.000 0.00 0.00 0.00 3.86
3535 7424 3.788142 AGAGAGAGAGAGAGGAATCTGGT 59.212 47.826 0.00 0.00 0.00 4.00
3536 7425 3.885297 GAGAGAGAGAGAGGAATCTGGTG 59.115 52.174 0.00 0.00 0.00 4.17
3537 7426 2.362077 GAGAGAGAGAGGAATCTGGTGC 59.638 54.545 0.00 0.00 0.00 5.01
3538 7427 2.024080 AGAGAGAGAGGAATCTGGTGCT 60.024 50.000 0.00 0.00 0.00 4.40
3539 7428 2.362077 GAGAGAGAGGAATCTGGTGCTC 59.638 54.545 0.00 0.00 36.30 4.26
3540 7429 2.106566 GAGAGAGGAATCTGGTGCTCA 58.893 52.381 0.00 0.00 38.37 4.26
3541 7430 1.830477 AGAGAGGAATCTGGTGCTCAC 59.170 52.381 0.00 0.00 38.37 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
287 289 2.136728 CACATTAAACCACCGTCACGA 58.863 47.619 0.00 0.00 0.00 4.35
361 363 0.778815 CATTCGATAGTCGCCTTCGC 59.221 55.000 0.00 0.00 40.21 4.70
457 460 3.369400 ACTCGTCGCTGCTGAGCT 61.369 61.111 5.83 0.00 43.77 4.09
554 557 4.759693 AGTACAAAACGAAGGCAATCATGA 59.240 37.500 0.00 0.00 0.00 3.07
595 598 3.419264 TGCGATGCATACAACCATTTC 57.581 42.857 0.00 0.00 31.71 2.17
619 622 2.411765 AAAACCCCCGACCTCTGCAG 62.412 60.000 7.63 7.63 0.00 4.41
659 662 9.222916 GTTTCAGTTTCAGCTAAGTTTAACTTC 57.777 33.333 14.03 1.07 39.51 3.01
664 667 8.500753 TTGAGTTTCAGTTTCAGCTAAGTTTA 57.499 30.769 0.00 0.00 0.00 2.01
727 730 0.835276 ATGTGCTCCAGCTCTATGCA 59.165 50.000 0.00 0.00 45.94 3.96
903 935 8.421002 TGTCGGATCAGATCAGATATGTTAAAA 58.579 33.333 15.36 0.00 35.98 1.52
934 966 5.119931 TCAGCACCAAATTGTACATCAAC 57.880 39.130 0.00 0.00 38.97 3.18
980 1013 2.119495 TGATTGGCCTCTAGAACTCCC 58.881 52.381 3.32 0.00 0.00 4.30
982 1015 3.449018 TCTGTGATTGGCCTCTAGAACTC 59.551 47.826 3.32 0.00 0.00 3.01
983 1016 3.445008 TCTGTGATTGGCCTCTAGAACT 58.555 45.455 3.32 0.00 0.00 3.01
984 1017 3.895232 TCTGTGATTGGCCTCTAGAAC 57.105 47.619 3.32 0.00 0.00 3.01
985 1018 4.096681 TCTTCTGTGATTGGCCTCTAGAA 58.903 43.478 3.32 7.97 0.00 2.10
988 1021 6.349300 GTTAATCTTCTGTGATTGGCCTCTA 58.651 40.000 3.32 0.00 37.27 2.43
1004 1037 7.824779 CAGTAAGCTAAGAAGGTGGTTAATCTT 59.175 37.037 0.00 0.00 36.24 2.40
1006 1039 6.037281 GCAGTAAGCTAAGAAGGTGGTTAATC 59.963 42.308 0.00 0.00 41.15 1.75
1012 1045 2.271800 CGCAGTAAGCTAAGAAGGTGG 58.728 52.381 0.00 0.00 42.61 4.61
1032 1066 3.305177 TTTCGGCTGCGGGGAGTAC 62.305 63.158 7.38 0.00 0.00 2.73
1033 1067 2.998480 TTTCGGCTGCGGGGAGTA 60.998 61.111 7.38 0.00 0.00 2.59
1231 1276 1.911766 GTGTCCCCGTCCTTCTCCA 60.912 63.158 0.00 0.00 0.00 3.86
1324 1378 2.852075 TTCCCCGGTGTGAAGGCT 60.852 61.111 0.00 0.00 0.00 4.58
1328 1382 1.700739 AGTATTGTTCCCCGGTGTGAA 59.299 47.619 0.00 0.00 0.00 3.18
1333 1387 0.248289 CGTCAGTATTGTTCCCCGGT 59.752 55.000 0.00 0.00 0.00 5.28
1591 1697 1.738099 GACAGCGTGGTTGAGCGAT 60.738 57.895 0.00 0.00 38.61 4.58
1666 1775 4.373116 ATGTCGGCGCCGTCACTT 62.373 61.111 42.40 30.50 39.81 3.16
1859 2052 0.311790 TTCGCCTTTGCTTTGAGCTG 59.688 50.000 0.00 0.00 42.97 4.24
1890 2083 3.454573 CGCCATTGCTGGTGCCAT 61.455 61.111 0.00 0.00 45.59 4.40
1895 2088 2.672996 GGTGACGCCATTGCTGGT 60.673 61.111 0.00 0.00 45.10 4.00
1896 2089 2.672651 TGGTGACGCCATTGCTGG 60.673 61.111 2.83 0.00 43.61 4.85
1908 2119 0.608130 CAACGAGGAGATGGTGGTGA 59.392 55.000 0.00 0.00 0.00 4.02
1976 2190 4.947147 GCTGTGGTCCGGTGCCAA 62.947 66.667 19.11 10.60 37.81 4.52
2144 2369 4.097361 GAAGGACCCCACCGCTCC 62.097 72.222 0.00 0.00 34.73 4.70
2347 6227 4.986587 TCGAACACCGTCGCCGTG 62.987 66.667 0.74 0.74 40.88 4.94
2437 6317 0.532573 TGCTCATGAACTCCTCGTCC 59.467 55.000 0.00 0.00 0.00 4.79
2493 6373 7.121463 CACCACTAGACACTAGTAAGAATCTGT 59.879 40.741 10.46 0.00 0.00 3.41
2497 6377 5.715279 TGCACCACTAGACACTAGTAAGAAT 59.285 40.000 10.46 0.00 0.00 2.40
2506 6386 2.251818 ACTGATGCACCACTAGACACT 58.748 47.619 0.00 0.00 0.00 3.55
2507 6387 2.751166 ACTGATGCACCACTAGACAC 57.249 50.000 0.00 0.00 0.00 3.67
2508 6388 3.368427 GCTAACTGATGCACCACTAGACA 60.368 47.826 0.00 0.00 0.00 3.41
2509 6389 3.118956 AGCTAACTGATGCACCACTAGAC 60.119 47.826 0.00 0.00 0.00 2.59
2510 6390 3.099905 AGCTAACTGATGCACCACTAGA 58.900 45.455 0.00 0.00 0.00 2.43
2511 6391 3.533606 AGCTAACTGATGCACCACTAG 57.466 47.619 0.00 0.00 0.00 2.57
2512 6392 3.767131 TGTAGCTAACTGATGCACCACTA 59.233 43.478 0.00 0.00 0.00 2.74
2513 6393 2.567169 TGTAGCTAACTGATGCACCACT 59.433 45.455 0.00 0.00 0.00 4.00
2514 6394 2.972625 TGTAGCTAACTGATGCACCAC 58.027 47.619 0.00 0.00 0.00 4.16
2515 6395 3.055167 ACATGTAGCTAACTGATGCACCA 60.055 43.478 0.00 0.00 27.89 4.17
2516 6396 3.310774 CACATGTAGCTAACTGATGCACC 59.689 47.826 0.00 0.00 27.89 5.01
2517 6397 3.310774 CCACATGTAGCTAACTGATGCAC 59.689 47.826 0.00 0.00 27.89 4.57
2518 6398 3.534554 CCACATGTAGCTAACTGATGCA 58.465 45.455 0.00 0.00 0.00 3.96
2519 6399 2.874701 CCCACATGTAGCTAACTGATGC 59.125 50.000 0.00 0.00 0.00 3.91
2520 6400 4.406648 TCCCACATGTAGCTAACTGATG 57.593 45.455 0.00 6.36 0.00 3.07
2521 6401 6.747414 TTATCCCACATGTAGCTAACTGAT 57.253 37.500 0.00 0.00 0.00 2.90
2522 6402 6.553953 TTTATCCCACATGTAGCTAACTGA 57.446 37.500 0.00 0.00 0.00 3.41
2523 6403 7.220030 AGATTTATCCCACATGTAGCTAACTG 58.780 38.462 0.00 0.00 0.00 3.16
2524 6404 7.380423 AGATTTATCCCACATGTAGCTAACT 57.620 36.000 0.00 0.00 0.00 2.24
2525 6405 7.520614 GCAAGATTTATCCCACATGTAGCTAAC 60.521 40.741 0.00 0.00 0.00 2.34
2526 6406 6.486657 GCAAGATTTATCCCACATGTAGCTAA 59.513 38.462 0.00 0.00 0.00 3.09
2527 6407 5.997746 GCAAGATTTATCCCACATGTAGCTA 59.002 40.000 0.00 0.00 0.00 3.32
2528 6408 4.823989 GCAAGATTTATCCCACATGTAGCT 59.176 41.667 0.00 0.00 0.00 3.32
2529 6409 4.823989 AGCAAGATTTATCCCACATGTAGC 59.176 41.667 0.00 0.00 0.00 3.58
2530 6410 6.949352 AAGCAAGATTTATCCCACATGTAG 57.051 37.500 0.00 0.00 0.00 2.74
2531 6411 6.321181 GGAAAGCAAGATTTATCCCACATGTA 59.679 38.462 0.00 0.00 0.00 2.29
2532 6412 5.127682 GGAAAGCAAGATTTATCCCACATGT 59.872 40.000 0.00 0.00 0.00 3.21
2533 6413 5.127519 TGGAAAGCAAGATTTATCCCACATG 59.872 40.000 0.00 0.00 0.00 3.21
2534 6414 5.271598 TGGAAAGCAAGATTTATCCCACAT 58.728 37.500 0.00 0.00 0.00 3.21
2535 6415 4.671831 TGGAAAGCAAGATTTATCCCACA 58.328 39.130 0.00 0.00 0.00 4.17
2536 6416 5.595952 AGATGGAAAGCAAGATTTATCCCAC 59.404 40.000 0.00 0.00 0.00 4.61
2537 6417 5.595542 CAGATGGAAAGCAAGATTTATCCCA 59.404 40.000 0.00 0.00 0.00 4.37
2538 6418 5.010415 CCAGATGGAAAGCAAGATTTATCCC 59.990 44.000 0.00 0.00 37.39 3.85
2539 6419 5.010415 CCCAGATGGAAAGCAAGATTTATCC 59.990 44.000 0.00 0.00 37.39 2.59
2540 6420 5.508657 GCCCAGATGGAAAGCAAGATTTATC 60.509 44.000 0.00 0.00 37.39 1.75
2541 6421 4.343239 GCCCAGATGGAAAGCAAGATTTAT 59.657 41.667 0.00 0.00 37.39 1.40
2542 6422 3.701040 GCCCAGATGGAAAGCAAGATTTA 59.299 43.478 0.00 0.00 37.39 1.40
2543 6423 2.498885 GCCCAGATGGAAAGCAAGATTT 59.501 45.455 0.00 0.00 37.39 2.17
2544 6424 2.105766 GCCCAGATGGAAAGCAAGATT 58.894 47.619 0.00 0.00 37.39 2.40
2545 6425 1.687368 GGCCCAGATGGAAAGCAAGAT 60.687 52.381 0.00 0.00 37.39 2.40
2546 6426 0.323725 GGCCCAGATGGAAAGCAAGA 60.324 55.000 0.00 0.00 37.39 3.02
2547 6427 0.612732 TGGCCCAGATGGAAAGCAAG 60.613 55.000 0.00 0.00 37.39 4.01
2548 6428 0.612732 CTGGCCCAGATGGAAAGCAA 60.613 55.000 4.15 0.00 37.39 3.91
2549 6429 1.000521 CTGGCCCAGATGGAAAGCA 60.001 57.895 4.15 0.00 37.39 3.91
2550 6430 2.421399 GCTGGCCCAGATGGAAAGC 61.421 63.158 16.85 2.79 37.06 3.51
2551 6431 1.000521 TGCTGGCCCAGATGGAAAG 60.001 57.895 16.85 0.00 37.39 2.62
2552 6432 1.304381 GTGCTGGCCCAGATGGAAA 60.304 57.895 16.85 0.00 37.39 3.13
2553 6433 2.202236 GAGTGCTGGCCCAGATGGAA 62.202 60.000 16.85 0.00 37.39 3.53
2554 6434 2.611800 AGTGCTGGCCCAGATGGA 60.612 61.111 16.85 0.00 37.39 3.41
2555 6435 2.124403 GAGTGCTGGCCCAGATGG 60.124 66.667 16.85 0.00 32.44 3.51
2556 6436 1.451567 CAGAGTGCTGGCCCAGATG 60.452 63.158 16.85 0.36 38.51 2.90
2557 6437 2.996395 CAGAGTGCTGGCCCAGAT 59.004 61.111 16.85 0.00 38.51 2.90
2558 6438 4.025858 GCAGAGTGCTGGCCCAGA 62.026 66.667 16.85 0.00 42.53 3.86
2584 6464 2.340328 GGCCGAAAATTCAGCCGGT 61.340 57.895 1.90 0.00 40.58 5.28
2633 6515 1.202568 TGCCAGATCTGACGGCTATTG 60.203 52.381 24.62 4.93 46.39 1.90
2691 6574 1.372683 GCAGAGTGGAGGCTTGTGA 59.627 57.895 0.00 0.00 0.00 3.58
2705 6588 4.980805 AAAACGGAGGCGCGCAGA 62.981 61.111 34.42 0.00 0.00 4.26
2738 6621 4.361971 ACAGGGAGAGGACGCGGA 62.362 66.667 12.47 0.00 0.00 5.54
2784 6667 1.744368 CGAACGACGAGGGGAGAGA 60.744 63.158 0.00 0.00 45.77 3.10
2890 6777 9.936759 TTTCAAATAGTGGAAAAAGTTTCAACT 57.063 25.926 13.77 13.77 42.04 3.16
2926 6813 6.657541 ACCATAGAAAAAGCTTCAATCGGTAA 59.342 34.615 0.00 0.00 0.00 2.85
2929 6816 5.567138 ACCATAGAAAAAGCTTCAATCGG 57.433 39.130 0.00 0.00 0.00 4.18
3097 6986 4.927782 ACGGCGAGGTTGCAAGCA 62.928 61.111 28.75 0.00 36.28 3.91
3112 7001 0.456995 GGGAACTCTGCTCTTCGACG 60.457 60.000 0.00 0.00 0.00 5.12
3124 7013 4.410400 CAGGGGCCACGGGAACTC 62.410 72.222 4.39 0.00 0.00 3.01
3126 7015 4.280019 AACAGGGGCCACGGGAAC 62.280 66.667 10.79 0.00 0.00 3.62
3127 7016 4.278513 CAACAGGGGCCACGGGAA 62.279 66.667 10.79 0.00 0.00 3.97
3198 7087 1.204312 GTCGCACGAAGCTTCAACC 59.796 57.895 25.47 11.45 42.61 3.77
3286 7175 1.737793 GGAAAGCTACAACCGATGTGG 59.262 52.381 4.34 2.76 43.77 4.17
3290 7179 2.354805 GGTCTGGAAAGCTACAACCGAT 60.355 50.000 0.00 0.00 0.00 4.18
3353 7242 1.736586 ATCGAGGTGGACGATGAGC 59.263 57.895 0.00 0.00 46.35 4.26
3387 7276 2.271497 GAGCTCACATGCAGGGCT 59.729 61.111 12.52 12.52 35.86 5.19
3394 7283 4.427394 GCCCTACGAGCTCACATG 57.573 61.111 15.40 0.00 0.00 3.21
3410 7299 1.327764 GATTCAGGATGTTCGAACCGC 59.672 52.381 24.78 16.01 37.40 5.68
3439 7328 1.703513 TCGGCTACTATCCCAGAGCTA 59.296 52.381 0.00 0.00 35.23 3.32
3449 7338 3.071167 GTCTTCCCCAAATCGGCTACTAT 59.929 47.826 0.00 0.00 0.00 2.12
3484 7373 3.506398 TCTCTCCACAACATCACCTACA 58.494 45.455 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.