Multiple sequence alignment - TraesCS2A01G363100

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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 TraesCS2A01G363100 chr2A 100.000 5075 0 0 1 5075 607518661 607513587 0.000000e+00 9372.0
1 TraesCS2A01G363100 chr2A 95.752 918 34 2 4160 5075 610178457 610177543 0.000000e+00 1474.0
2 TraesCS2A01G363100 chr2A 93.142 452 24 2 871 1322 610209991 610209547 0.000000e+00 656.0
3 TraesCS2A01G363100 chr2A 94.074 405 22 2 1 403 610210884 610210480 9.340000e-172 614.0
4 TraesCS2A01G363100 chr2A 86.424 302 35 4 1 297 607598358 607598058 4.900000e-85 326.0
5 TraesCS2A01G363100 chr2A 88.670 203 23 0 2146 2348 607516414 607516212 1.090000e-61 248.0
6 TraesCS2A01G363100 chr2A 88.670 203 23 0 2248 2450 607516516 607516314 1.090000e-61 248.0
7 TraesCS2A01G363100 chr2A 81.720 279 28 11 460 719 607597717 607597443 1.430000e-50 211.0
8 TraesCS2A01G363100 chr2A 91.566 83 7 0 316 398 607597904 607597822 1.150000e-21 115.0
9 TraesCS2A01G363100 chr2A 86.408 103 9 4 4006 4105 610124634 610124534 1.930000e-19 108.0
10 TraesCS2A01G363100 chr2A 88.710 62 7 0 3875 3936 81088620 81088559 5.450000e-10 76.8
11 TraesCS2A01G363100 chr2D 92.342 4492 209 56 688 5075 462245438 462240978 0.000000e+00 6264.0
12 TraesCS2A01G363100 chr2D 91.781 657 42 8 1 654 462246071 462245424 0.000000e+00 904.0
13 TraesCS2A01G363100 chr2D 83.436 652 95 7 4424 5075 131641673 131642311 1.220000e-165 593.0
14 TraesCS2A01G363100 chr2D 86.174 311 40 1 1 308 462784914 462784604 2.930000e-87 333.0
15 TraesCS2A01G363100 chr2D 81.443 388 37 16 460 828 462784263 462783892 8.320000e-73 285.0
16 TraesCS2A01G363100 chr2D 90.323 124 12 0 2327 2450 462243847 462243724 4.070000e-36 163.0
17 TraesCS2A01G363100 chr2D 91.860 86 7 0 309 394 462784455 462784370 2.480000e-23 121.0
18 TraesCS2A01G363100 chr2B 91.758 2451 115 30 622 3020 545158308 545155893 0.000000e+00 3326.0
19 TraesCS2A01G363100 chr2B 91.357 1400 60 21 3009 4386 545155732 545154372 0.000000e+00 1858.0
20 TraesCS2A01G363100 chr2B 95.204 834 32 2 4247 5075 545154134 545153304 0.000000e+00 1312.0
21 TraesCS2A01G363100 chr2B 91.552 580 35 6 1 577 545158873 545158305 0.000000e+00 787.0
22 TraesCS2A01G363100 chr2B 82.946 387 32 18 460 828 545226680 545226310 8.200000e-83 318.0
23 TraesCS2A01G363100 chr2B 83.387 313 38 6 1 308 545227326 545227023 1.390000e-70 278.0
24 TraesCS2A01G363100 chr2B 91.411 163 14 0 2288 2450 545156717 545156555 1.840000e-54 224.0
25 TraesCS2A01G363100 chr2B 87.097 93 10 2 4136 4226 724551015 724550923 2.500000e-18 104.0
26 TraesCS2A01G363100 chr2B 85.437 103 10 4 4006 4105 544999334 544999234 8.990000e-18 102.0
27 TraesCS2A01G363100 chr1A 85.952 662 86 4 4416 5075 246127767 246128423 0.000000e+00 701.0
28 TraesCS2A01G363100 chr1A 86.735 98 11 1 4132 4227 587861405 587861308 1.930000e-19 108.0
29 TraesCS2A01G363100 chr1B 85.843 664 83 7 4416 5075 275554860 275554204 0.000000e+00 695.0
30 TraesCS2A01G363100 chr1B 85.865 665 81 9 4416 5075 275673482 275672826 0.000000e+00 695.0
31 TraesCS2A01G363100 chr1B 85.693 664 84 7 4416 5075 275359916 275359260 0.000000e+00 689.0
32 TraesCS2A01G363100 chr1B 85.542 664 85 7 4416 5075 275459906 275459250 0.000000e+00 684.0
33 TraesCS2A01G363100 chr1B 91.011 89 6 1 4143 4229 480972935 480973023 8.930000e-23 119.0
34 TraesCS2A01G363100 chr1D 91.954 87 5 1 4143 4227 358222637 358222551 2.480000e-23 121.0
35 TraesCS2A01G363100 chr3D 89.888 89 7 2 4140 4226 85447040 85447128 4.150000e-21 113.0
36 TraesCS2A01G363100 chr3B 88.764 89 8 2 4140 4226 135685001 135685089 1.930000e-19 108.0
37 TraesCS2A01G363100 chr6B 91.892 74 4 2 105 178 121782525 121782596 8.990000e-18 102.0
38 TraesCS2A01G363100 chr6D 92.754 69 4 1 110 178 292399130 292399063 1.160000e-16 99.0
39 TraesCS2A01G363100 chr4D 92.754 69 4 1 110 178 432949008 432948941 1.160000e-16 99.0


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 TraesCS2A01G363100 chr2A 607513587 607518661 5074 True 3289.333333 9372 92.446667 1 5075 3 chr2A.!!$R4 5074
1 TraesCS2A01G363100 chr2A 610177543 610178457 914 True 1474.000000 1474 95.752000 4160 5075 1 chr2A.!!$R3 915
2 TraesCS2A01G363100 chr2A 610209547 610210884 1337 True 635.000000 656 93.608000 1 1322 2 chr2A.!!$R6 1321
3 TraesCS2A01G363100 chr2A 607597443 607598358 915 True 217.333333 326 86.570000 1 719 3 chr2A.!!$R5 718
4 TraesCS2A01G363100 chr2D 462240978 462246071 5093 True 2443.666667 6264 91.482000 1 5075 3 chr2D.!!$R1 5074
5 TraesCS2A01G363100 chr2D 131641673 131642311 638 False 593.000000 593 83.436000 4424 5075 1 chr2D.!!$F1 651
6 TraesCS2A01G363100 chr2D 462783892 462784914 1022 True 246.333333 333 86.492333 1 828 3 chr2D.!!$R2 827
7 TraesCS2A01G363100 chr2B 545153304 545158873 5569 True 1501.400000 3326 92.256400 1 5075 5 chr2B.!!$R3 5074
8 TraesCS2A01G363100 chr2B 545226310 545227326 1016 True 298.000000 318 83.166500 1 828 2 chr2B.!!$R4 827
9 TraesCS2A01G363100 chr1A 246127767 246128423 656 False 701.000000 701 85.952000 4416 5075 1 chr1A.!!$F1 659
10 TraesCS2A01G363100 chr1B 275554204 275554860 656 True 695.000000 695 85.843000 4416 5075 1 chr1B.!!$R3 659
11 TraesCS2A01G363100 chr1B 275672826 275673482 656 True 695.000000 695 85.865000 4416 5075 1 chr1B.!!$R4 659
12 TraesCS2A01G363100 chr1B 275359260 275359916 656 True 689.000000 689 85.693000 4416 5075 1 chr1B.!!$R1 659
13 TraesCS2A01G363100 chr1B 275459250 275459906 656 True 684.000000 684 85.542000 4416 5075 1 chr1B.!!$R2 659

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
597 975 0.034896 TGGCTTCAAGGGAACGAGTC 59.965 55.0 0.00 0.0 0.00 3.36 F
1612 2193 0.034198 TAAGTAGCACTGGCAACGCA 59.966 50.0 10.09 0.0 44.61 5.24 F
1870 2451 0.168128 CAGCGAATTCCACCGGAAAC 59.832 55.0 9.46 0.0 45.41 2.78 F
3418 4201 0.250166 AAGGCTACCGTGTTCACCAC 60.250 55.0 0.00 0.0 40.89 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1703 2284 1.002544 CGCTTTCCCCATATCCTCCTC 59.997 57.143 0.0 0.0 0.00 3.71 R
3418 4201 0.107312 CCTCCATCACCTCAAGGCTG 60.107 60.000 0.0 0.0 39.32 4.85 R
3689 4475 0.449388 GGTACTCGGTGAGGTACGTG 59.551 60.000 0.0 0.0 39.13 4.49 R
4720 5920 1.134699 TCTCGTCATTCTGATGGTGGC 60.135 52.381 0.0 0.0 34.27 5.01 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
58 64 6.373216 ACACAAACACATACAGTAACTGTTGT 59.627 34.615 2.69 0.00 42.59 3.32
71 77 6.857964 CAGTAACTGTTGTGCAAATAGGAAAG 59.142 38.462 2.69 0.00 0.00 2.62
87 93 2.479560 GGAAAGGAAACACAGCACACAC 60.480 50.000 0.00 0.00 0.00 3.82
201 208 0.251253 TCATCACTGTTGCCATGCCA 60.251 50.000 0.00 0.00 0.00 4.92
214 221 2.327568 CCATGCCAACGTCATTTCAAC 58.672 47.619 0.00 0.00 0.00 3.18
215 222 2.030007 CCATGCCAACGTCATTTCAACT 60.030 45.455 0.00 0.00 0.00 3.16
239 248 9.209175 ACTAGACAATCAAACATAACAAGACTC 57.791 33.333 0.00 0.00 0.00 3.36
243 252 7.865707 ACAATCAAACATAACAAGACTCTCAC 58.134 34.615 0.00 0.00 0.00 3.51
323 483 3.505293 ACTACAACGACTCAGTCCCTTAC 59.495 47.826 0.00 0.00 0.00 2.34
415 575 0.719465 CGTGCACAACCCTACGAATC 59.281 55.000 18.64 0.00 38.72 2.52
477 686 7.764443 TCCTAGTACATGCTAGAACAAATCAAC 59.236 37.037 8.49 0.00 40.54 3.18
492 702 6.668323 ACAAATCAACAACAGTAGCATGTAC 58.332 36.000 0.00 0.00 31.70 2.90
506 882 5.089970 AGCATGTACATGTAAGAGCTTGA 57.910 39.130 31.10 0.00 40.80 3.02
597 975 0.034896 TGGCTTCAAGGGAACGAGTC 59.965 55.000 0.00 0.00 0.00 3.36
660 1038 0.245266 TGACGAAGCGCTACCAATCA 59.755 50.000 12.05 8.04 0.00 2.57
661 1039 1.337354 TGACGAAGCGCTACCAATCAA 60.337 47.619 12.05 0.00 0.00 2.57
663 1041 2.351726 GACGAAGCGCTACCAATCAAAT 59.648 45.455 12.05 0.00 0.00 2.32
664 1042 2.351726 ACGAAGCGCTACCAATCAAATC 59.648 45.455 12.05 0.00 0.00 2.17
665 1043 2.351418 CGAAGCGCTACCAATCAAATCA 59.649 45.455 12.05 0.00 0.00 2.57
666 1044 3.181511 CGAAGCGCTACCAATCAAATCAA 60.182 43.478 12.05 0.00 0.00 2.57
857 1293 0.955428 CCATGGTGGACACACTTCGG 60.955 60.000 2.57 0.00 46.85 4.30
872 1413 4.016706 CGGAAAGGTGGCGGAGGT 62.017 66.667 0.00 0.00 0.00 3.85
873 1414 2.046217 GGAAAGGTGGCGGAGGTC 60.046 66.667 0.00 0.00 0.00 3.85
874 1415 2.747686 GAAAGGTGGCGGAGGTCA 59.252 61.111 0.00 0.00 0.00 4.02
875 1416 1.072505 GAAAGGTGGCGGAGGTCAA 59.927 57.895 0.00 0.00 0.00 3.18
876 1417 0.322546 GAAAGGTGGCGGAGGTCAAT 60.323 55.000 0.00 0.00 0.00 2.57
883 1434 0.526211 GGCGGAGGTCAATTTGGAAC 59.474 55.000 0.00 0.00 0.00 3.62
889 1440 0.109919 GGTCAATTTGGAACGGCGAC 60.110 55.000 16.62 7.14 0.00 5.19
981 1532 0.245813 GAACGAACCCTAGGAAGCGT 59.754 55.000 11.48 13.29 0.00 5.07
983 1534 1.810030 CGAACCCTAGGAAGCGTGC 60.810 63.158 11.48 0.00 0.00 5.34
988 1539 1.300233 CCTAGGAAGCGTGCGATCC 60.300 63.158 1.05 10.55 0.00 3.36
1070 1621 0.034477 CCAACTGGCCCTTAACGGAT 60.034 55.000 0.00 0.00 33.16 4.18
1326 1883 2.695970 CCTCCTCCTCCTCCCTCGT 61.696 68.421 0.00 0.00 0.00 4.18
1423 1980 1.137825 CTGCTTCTCCGTCGTCCTC 59.862 63.158 0.00 0.00 0.00 3.71
1559 2116 4.099170 CGACGTCGCCGAGGAAGT 62.099 66.667 26.59 0.00 37.88 3.01
1580 2137 4.675303 CTCCTCCCCACCCACCCA 62.675 72.222 0.00 0.00 0.00 4.51
1603 2160 7.275920 CCATTTCTCCTAATGTAAGTAGCACT 58.724 38.462 0.00 0.00 32.12 4.40
1609 2190 4.332819 CCTAATGTAAGTAGCACTGGCAAC 59.667 45.833 0.00 0.00 44.61 4.17
1612 2193 0.034198 TAAGTAGCACTGGCAACGCA 59.966 50.000 10.09 0.00 44.61 5.24
1658 2239 3.005554 CAGAGCAACAACTCGGATGATT 58.994 45.455 0.00 0.00 41.77 2.57
1739 2320 3.142393 CGCAGGGTCCCCTCTATG 58.858 66.667 3.51 0.00 46.28 2.23
1773 2354 3.031495 GATCAGCGGATCGGACGA 58.969 61.111 11.15 0.00 40.50 4.20
1870 2451 0.168128 CAGCGAATTCCACCGGAAAC 59.832 55.000 9.46 0.00 45.41 2.78
1888 2472 4.996434 CCCATCATCGGCGCTCCC 62.996 72.222 7.64 0.00 0.00 4.30
2030 2614 4.842292 CAGCGCTGCCATCTAGAA 57.158 55.556 26.68 0.00 0.00 2.10
2037 2621 2.016393 CTGCCATCTAGAACGCCGGA 62.016 60.000 5.05 0.00 0.00 5.14
2103 2687 4.436448 GCACAAGCAGCGCTCGAC 62.436 66.667 7.13 0.00 38.25 4.20
2142 2726 1.918293 TCCACCCGATGCAGGAAGT 60.918 57.895 0.00 0.00 0.00 3.01
2169 2753 4.059459 CGACAACAGCGACGGCAC 62.059 66.667 0.00 0.00 43.41 5.01
2170 2754 3.712881 GACAACAGCGACGGCACC 61.713 66.667 0.00 0.00 43.41 5.01
2214 2798 1.845809 GCGAACACCAGAGTTGCCAG 61.846 60.000 0.00 0.00 0.00 4.85
2219 2827 4.335647 CCAGAGTTGCCAGCGGGT 62.336 66.667 4.36 0.00 36.17 5.28
2230 2838 3.884774 AGCGGGTCAGGCAACCAA 61.885 61.111 10.72 0.00 41.40 3.67
2232 2840 3.353836 CGGGTCAGGCAACCAACG 61.354 66.667 10.72 3.11 41.40 4.10
2248 2856 3.612681 CGGGTGGTGTGGACGTCT 61.613 66.667 16.46 0.00 0.00 4.18
2249 2857 2.030562 GGGTGGTGTGGACGTCTG 59.969 66.667 16.46 0.00 0.00 3.51
2372 2980 2.261361 CCGACCACAGCGATGACA 59.739 61.111 8.12 0.00 0.00 3.58
2527 3135 3.003763 AGGGAGGAGAACCACGCC 61.004 66.667 0.00 0.00 39.65 5.68
2668 3276 1.202615 TGCATGCATCCTCTGACTAGC 60.203 52.381 18.46 0.00 0.00 3.42
2669 3277 1.070445 GCATGCATCCTCTGACTAGCT 59.930 52.381 14.21 0.00 0.00 3.32
2670 3278 2.485124 GCATGCATCCTCTGACTAGCTT 60.485 50.000 14.21 0.00 0.00 3.74
2671 3279 3.391965 CATGCATCCTCTGACTAGCTTC 58.608 50.000 0.00 0.00 0.00 3.86
2676 3284 4.141959 GCATCCTCTGACTAGCTTCTTCTT 60.142 45.833 0.00 0.00 0.00 2.52
2677 3285 5.350633 CATCCTCTGACTAGCTTCTTCTTG 58.649 45.833 0.00 0.00 0.00 3.02
2682 3290 5.960113 TCTGACTAGCTTCTTCTTGTCATC 58.040 41.667 0.00 0.00 43.81 2.92
2702 3310 1.913403 CGCAAATGTTCCGAGCAATTC 59.087 47.619 0.00 0.00 0.00 2.17
2711 3319 4.192317 GTTCCGAGCAATTCCATTAGAGT 58.808 43.478 0.00 0.00 0.00 3.24
2796 3404 1.267574 ATTTCCTGGAGAGGCTGCGA 61.268 55.000 0.00 0.00 39.57 5.10
2820 3428 2.820197 CCAGAGGATCATATTCGTCGGA 59.180 50.000 0.00 0.00 37.82 4.55
2874 3482 4.783621 TGCACTCTCCGCCATGGC 62.784 66.667 27.67 27.67 37.80 4.40
2981 3589 1.279496 ACTGGCTGCCTCACTGAATA 58.721 50.000 21.03 0.00 0.00 1.75
2982 3590 1.209019 ACTGGCTGCCTCACTGAATAG 59.791 52.381 21.03 7.76 0.00 1.73
2983 3591 1.209019 CTGGCTGCCTCACTGAATAGT 59.791 52.381 21.03 0.00 37.75 2.12
3053 3833 6.809630 AAGAGAAACTTGGTAGAATCTTGC 57.190 37.500 0.00 0.00 37.45 4.01
3286 4066 4.124238 CAAAGACGTCAAAAGGGTCTGTA 58.876 43.478 19.50 0.00 40.67 2.74
3287 4067 4.618920 AAGACGTCAAAAGGGTCTGTAT 57.381 40.909 19.50 0.00 40.67 2.29
3288 4068 3.926616 AGACGTCAAAAGGGTCTGTATG 58.073 45.455 19.50 0.00 39.43 2.39
3289 4069 3.323979 AGACGTCAAAAGGGTCTGTATGT 59.676 43.478 19.50 0.00 39.43 2.29
3319 4099 1.296715 CACTTCCCCCAGAACTCCG 59.703 63.158 0.00 0.00 0.00 4.63
3372 4155 5.581126 TTACATCCTGATTGGTGAAATGC 57.419 39.130 0.00 0.00 37.07 3.56
3385 4168 1.881973 TGAAATGCTTGTGACAGGCTC 59.118 47.619 20.34 10.42 37.36 4.70
3412 4195 4.546829 TTATCAAGAAGGCTACCGTGTT 57.453 40.909 0.00 0.00 0.00 3.32
3418 4201 0.250166 AAGGCTACCGTGTTCACCAC 60.250 55.000 0.00 0.00 40.89 4.16
3466 4249 3.064324 GCACTGACCACATGGGCC 61.064 66.667 0.00 0.00 44.80 5.80
3575 4361 1.493022 ACCGCCACCACAACCATATAT 59.507 47.619 0.00 0.00 0.00 0.86
3577 4363 3.136809 ACCGCCACCACAACCATATATTA 59.863 43.478 0.00 0.00 0.00 0.98
3578 4364 3.751175 CCGCCACCACAACCATATATTAG 59.249 47.826 0.00 0.00 0.00 1.73
3579 4365 3.751175 CGCCACCACAACCATATATTAGG 59.249 47.826 0.00 0.00 0.00 2.69
3580 4366 3.506067 GCCACCACAACCATATATTAGGC 59.494 47.826 0.00 0.00 0.00 3.93
3590 4376 5.027460 ACCATATATTAGGCCATCGGTACA 58.973 41.667 5.01 0.00 0.00 2.90
3662 4448 1.840650 CTCGGGAGGGAGATGCCAT 60.841 63.158 0.00 0.00 38.95 4.40
3689 4475 1.217882 CCGAGCCGATATTCAACCAC 58.782 55.000 0.00 0.00 0.00 4.16
3744 4530 0.908198 ACTGGAGAAGGTCATGAGCC 59.092 55.000 20.92 12.97 0.00 4.70
3960 4746 1.228675 CTCCAGGCAGGCAAAGGTT 60.229 57.895 0.00 0.00 37.29 3.50
4032 4820 2.546162 GCTTGCGAGGGGTAGATAAGAC 60.546 54.545 2.37 0.00 0.00 3.01
4048 4836 8.954350 GTAGATAAGACTTACAGGTAGTTCACA 58.046 37.037 0.00 0.00 0.00 3.58
4083 4871 7.331026 TCTGTGATTAGAGGTGGATAAACTTG 58.669 38.462 0.00 0.00 0.00 3.16
4107 4895 3.379372 AGGAAATCATGCATTCAGTTCGG 59.621 43.478 0.00 0.00 0.00 4.30
4109 4897 4.380867 GGAAATCATGCATTCAGTTCGGTT 60.381 41.667 0.00 0.00 0.00 4.44
4110 4898 4.361451 AATCATGCATTCAGTTCGGTTC 57.639 40.909 0.00 0.00 0.00 3.62
4111 4899 3.057969 TCATGCATTCAGTTCGGTTCT 57.942 42.857 0.00 0.00 0.00 3.01
4112 4900 2.743664 TCATGCATTCAGTTCGGTTCTG 59.256 45.455 0.00 0.00 0.00 3.02
4113 4901 2.254546 TGCATTCAGTTCGGTTCTGT 57.745 45.000 0.00 0.00 34.86 3.41
4114 4902 1.872952 TGCATTCAGTTCGGTTCTGTG 59.127 47.619 0.00 0.00 34.86 3.66
4115 4903 2.143122 GCATTCAGTTCGGTTCTGTGA 58.857 47.619 0.00 0.00 34.86 3.58
4116 4904 2.744202 GCATTCAGTTCGGTTCTGTGAT 59.256 45.455 0.00 0.00 34.86 3.06
4146 4952 4.056050 CGGCGGCATTTTAGATACTACTT 58.944 43.478 10.53 0.00 0.00 2.24
4244 5065 7.118390 GGCAGTACTTCACATAGCATAATAAGG 59.882 40.741 0.00 0.00 0.00 2.69
4284 5105 6.387041 AGTCGGATAACATTAGTCGATTCA 57.613 37.500 0.00 0.00 0.00 2.57
4289 5110 7.009815 TCGGATAACATTAGTCGATTCACAAAC 59.990 37.037 0.00 0.00 0.00 2.93
4303 5124 6.073276 CGATTCACAAACAGTTGGACAGATTA 60.073 38.462 0.00 0.00 39.22 1.75
4304 5125 7.519809 CGATTCACAAACAGTTGGACAGATTAA 60.520 37.037 0.00 0.00 39.22 1.40
4305 5126 7.581213 TTCACAAACAGTTGGACAGATTAAT 57.419 32.000 0.00 0.00 39.22 1.40
4357 5178 2.222007 GCAAACCACATGCAAGACAA 57.778 45.000 0.00 0.00 43.29 3.18
4387 5208 7.068103 CAGATAAAATTGGGCAACAGGTACATA 59.932 37.037 0.00 0.00 39.74 2.29
4477 5677 8.428063 CAAACATGTCCTTCTAAGAGGATATCT 58.572 37.037 0.00 0.00 46.94 1.98
4632 5832 4.177026 CCAGACTGTGAGTATGCTTGTAC 58.823 47.826 0.93 0.00 36.19 2.90
4638 5838 4.816392 TGTGAGTATGCTTGTACGACAAT 58.184 39.130 0.00 0.00 37.48 2.71
4721 5921 1.438814 CCCATTGGCATTTCTCCGC 59.561 57.895 0.00 0.00 0.00 5.54
4733 5933 0.911769 TTCTCCGCCACCATCAGAAT 59.088 50.000 0.00 0.00 0.00 2.40
4734 5934 0.178767 TCTCCGCCACCATCAGAATG 59.821 55.000 0.00 0.00 37.54 2.67
4782 5985 3.705072 CTGGATAGGGAGTCCGTAACTTT 59.295 47.826 15.28 0.00 38.74 2.66
4784 5987 3.069300 GGATAGGGAGTCCGTAACTTTCC 59.931 52.174 15.28 13.20 38.74 3.13
4939 6142 0.179020 TGTTGCTGGAGAAGGTGGTG 60.179 55.000 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 64 4.261994 GCTGTGTTTCCTTTCCTATTTGCA 60.262 41.667 0.00 0.00 0.00 4.08
71 77 1.405105 ACATGTGTGTGCTGTGTTTCC 59.595 47.619 0.00 0.00 37.14 3.13
201 208 7.490962 TTGATTGTCTAGTTGAAATGACGTT 57.509 32.000 0.00 0.00 32.64 3.99
214 221 9.429359 AGAGTCTTGTTATGTTTGATTGTCTAG 57.571 33.333 0.00 0.00 0.00 2.43
215 222 9.424319 GAGAGTCTTGTTATGTTTGATTGTCTA 57.576 33.333 0.00 0.00 0.00 2.59
323 483 5.633927 TGATCGCTTGATTCAAAGAACATG 58.366 37.500 0.01 0.00 30.70 3.21
439 605 5.106673 GCATGTACTAGGAACAAGGTCAAAC 60.107 44.000 4.51 0.00 0.00 2.93
477 686 6.237942 GCTCTTACATGTACATGCTACTGTTG 60.238 42.308 31.19 16.46 42.39 3.33
492 702 1.003116 GGCGCATCAAGCTCTTACATG 60.003 52.381 10.83 0.00 42.61 3.21
560 938 3.132824 AGCCACATCATCTCGTTGTATCA 59.867 43.478 0.00 0.00 0.00 2.15
660 1038 1.528161 GGGTTTCGTCGTCGTTGATTT 59.472 47.619 1.33 0.00 38.33 2.17
661 1039 1.142474 GGGTTTCGTCGTCGTTGATT 58.858 50.000 1.33 0.00 38.33 2.57
663 1041 0.318107 GAGGGTTTCGTCGTCGTTGA 60.318 55.000 1.33 0.00 38.33 3.18
664 1042 1.602877 CGAGGGTTTCGTCGTCGTTG 61.603 60.000 1.33 0.00 44.27 4.10
665 1043 1.370900 CGAGGGTTTCGTCGTCGTT 60.371 57.895 1.33 0.00 44.27 3.85
666 1044 2.253452 CGAGGGTTTCGTCGTCGT 59.747 61.111 1.33 0.00 44.27 4.34
686 1104 1.227639 AGATCTACCCGTCGTCATCG 58.772 55.000 0.00 0.00 38.55 3.84
743 1172 1.130561 GCCAACAAGTAATGCTCGACC 59.869 52.381 0.00 0.00 0.00 4.79
851 1287 2.032071 CCGCCACCTTTCCGAAGT 59.968 61.111 0.00 0.00 0.00 3.01
852 1288 1.741770 CTCCGCCACCTTTCCGAAG 60.742 63.158 0.00 0.00 0.00 3.79
853 1289 2.345991 CTCCGCCACCTTTCCGAA 59.654 61.111 0.00 0.00 0.00 4.30
857 1293 0.322546 ATTGACCTCCGCCACCTTTC 60.323 55.000 0.00 0.00 0.00 2.62
872 1413 1.863491 CGTCGCCGTTCCAAATTGA 59.137 52.632 0.00 0.00 0.00 2.57
873 1414 4.433102 CGTCGCCGTTCCAAATTG 57.567 55.556 0.00 0.00 0.00 2.32
889 1440 1.809619 ACCCGAATGTCGCATCACG 60.810 57.895 0.00 10.04 45.62 4.35
891 1442 1.449423 CCACCCGAATGTCGCATCA 60.449 57.895 0.00 0.00 38.82 3.07
922 1473 2.034305 CCCAGCCCGCGTATATATAGAC 59.966 54.545 4.92 0.00 0.00 2.59
1059 1610 7.122204 AGTTTATGGAGAAAAATCCGTTAAGGG 59.878 37.037 7.93 7.93 42.77 3.95
1062 1613 8.726988 CAGAGTTTATGGAGAAAAATCCGTTAA 58.273 33.333 0.00 0.00 42.77 2.01
1070 1621 5.707298 CAGGCTCAGAGTTTATGGAGAAAAA 59.293 40.000 0.00 0.00 0.00 1.94
1423 1980 1.202154 ACGTAGAAGAAGGCGATCACG 60.202 52.381 0.00 0.00 42.93 4.35
1563 2120 3.970363 ATGGGTGGGTGGGGAGGAG 62.970 68.421 0.00 0.00 0.00 3.69
1576 2133 6.157994 TGCTACTTACATTAGGAGAAATGGGT 59.842 38.462 2.05 1.24 40.48 4.51
1580 2137 7.275920 CCAGTGCTACTTACATTAGGAGAAAT 58.724 38.462 0.00 0.00 0.00 2.17
1702 2283 1.352687 GCTTTCCCCATATCCTCCTCC 59.647 57.143 0.00 0.00 0.00 4.30
1703 2284 1.002544 CGCTTTCCCCATATCCTCCTC 59.997 57.143 0.00 0.00 0.00 3.71
1704 2285 1.059913 CGCTTTCCCCATATCCTCCT 58.940 55.000 0.00 0.00 0.00 3.69
1870 2451 4.996434 GGAGCGCCGATGATGGGG 62.996 72.222 2.29 0.00 44.36 4.96
1888 2472 2.725008 GAGTCCGAGGGCTCATCG 59.275 66.667 18.03 2.83 39.86 3.84
1944 2528 4.496183 CGTTTCGATCTTCCTTACTCGAAG 59.504 45.833 6.38 0.00 46.80 3.79
2037 2621 1.205893 GTCTGTCCTCCTTTCGCTGAT 59.794 52.381 0.00 0.00 0.00 2.90
2103 2687 2.837371 GAACTCCTTCCGTCGCCTGG 62.837 65.000 0.00 0.00 0.00 4.45
2142 2726 3.932580 CTGTTGTCGGCGGCAGCTA 62.933 63.158 27.47 13.84 44.37 3.32
2206 2790 4.335647 CCTGACCCGCTGGCAACT 62.336 66.667 0.00 0.00 33.59 3.16
2214 2798 3.670377 GTTGGTTGCCTGACCCGC 61.670 66.667 0.00 0.00 39.01 6.13
2219 2827 2.203280 CACCCGTTGGTTGCCTGA 60.203 61.111 0.00 0.00 44.75 3.86
2230 2838 3.920196 GACGTCCACACCACCCGT 61.920 66.667 3.51 0.00 0.00 5.28
2232 2840 2.030562 CAGACGTCCACACCACCC 59.969 66.667 13.01 0.00 0.00 4.61
2368 2976 4.927782 GTGCCAGTGCCGGTGTCA 62.928 66.667 1.90 0.00 36.33 3.58
2488 3096 2.046892 CACCTCCCGCTGAACAGG 60.047 66.667 3.99 0.00 0.00 4.00
2668 3276 5.039480 ACATTTGCGATGACAAGAAGAAG 57.961 39.130 6.86 0.00 0.00 2.85
2669 3277 5.437289 AACATTTGCGATGACAAGAAGAA 57.563 34.783 6.86 0.00 0.00 2.52
2670 3278 4.083324 GGAACATTTGCGATGACAAGAAGA 60.083 41.667 6.86 0.00 0.00 2.87
2671 3279 4.161333 GGAACATTTGCGATGACAAGAAG 58.839 43.478 6.86 0.00 0.00 2.85
2682 3290 1.913403 GAATTGCTCGGAACATTTGCG 59.087 47.619 0.00 0.00 46.40 4.85
2711 3319 6.978338 ACTTAAGTTTCGATCACAGAGTGTA 58.022 36.000 1.12 0.00 34.79 2.90
2796 3404 2.564947 GACGAATATGATCCTCTGGCCT 59.435 50.000 3.32 0.00 0.00 5.19
2820 3428 1.664965 GTTGCGGTTCAGCGAGTCT 60.665 57.895 1.86 0.00 40.67 3.24
2874 3482 2.218759 CACGTTCTTCTTGTTCCTGACG 59.781 50.000 0.00 0.00 0.00 4.35
3286 4066 4.261801 GGGAAGTGTTGCACTATACACAT 58.738 43.478 18.85 9.12 44.62 3.21
3287 4067 3.558321 GGGGAAGTGTTGCACTATACACA 60.558 47.826 18.85 2.50 44.62 3.72
3288 4068 3.007635 GGGGAAGTGTTGCACTATACAC 58.992 50.000 10.74 10.74 44.62 2.90
3289 4069 2.026636 GGGGGAAGTGTTGCACTATACA 60.027 50.000 1.97 0.00 44.62 2.29
3319 4099 0.179051 AGCAGATCAGCTTAGCCTGC 60.179 55.000 20.18 20.18 43.70 4.85
3324 4107 3.465742 TTGGCTAGCAGATCAGCTTAG 57.534 47.619 18.45 13.42 43.70 2.18
3372 4155 6.108687 TGATAATAGTTGAGCCTGTCACAAG 58.891 40.000 0.00 0.00 33.71 3.16
3385 4168 6.201044 CACGGTAGCCTTCTTGATAATAGTTG 59.799 42.308 0.00 0.00 0.00 3.16
3412 4195 3.986054 ACCTCAAGGCTGTGGTGA 58.014 55.556 5.68 0.00 45.60 4.02
3418 4201 0.107312 CCTCCATCACCTCAAGGCTG 60.107 60.000 0.00 0.00 39.32 4.85
3466 4249 4.935205 TCTATGTTCTTGTCGACCCATTTG 59.065 41.667 14.12 4.90 0.00 2.32
3575 4361 6.182507 AGATTAATTGTACCGATGGCCTAA 57.817 37.500 3.32 0.00 0.00 2.69
3577 4363 4.706842 AGATTAATTGTACCGATGGCCT 57.293 40.909 3.32 0.00 0.00 5.19
3578 4364 5.995897 AGTAAGATTAATTGTACCGATGGCC 59.004 40.000 0.00 0.00 0.00 5.36
3579 4365 6.929606 AGAGTAAGATTAATTGTACCGATGGC 59.070 38.462 0.00 0.00 0.00 4.40
3580 4366 8.141909 TGAGAGTAAGATTAATTGTACCGATGG 58.858 37.037 0.00 0.00 0.00 3.51
3590 4376 9.868277 GGATCGATCATGAGAGTAAGATTAATT 57.132 33.333 25.93 0.00 0.00 1.40
3647 4433 1.204113 CCCTATGGCATCTCCCTCCC 61.204 65.000 1.65 0.00 0.00 4.30
3662 4448 0.697079 ATATCGGCTCGGTCTCCCTA 59.303 55.000 0.00 0.00 0.00 3.53
3689 4475 0.449388 GGTACTCGGTGAGGTACGTG 59.551 60.000 0.00 0.00 39.13 4.49
3723 4509 2.159028 GGCTCATGACCTTCTCCAGTAC 60.159 54.545 0.00 0.00 0.00 2.73
3744 4530 0.833287 ATCACAGGGGTCTTCATCCG 59.167 55.000 0.00 0.00 0.00 4.18
3914 4700 1.332997 GCATACAGCAGCTCATTCCAC 59.667 52.381 0.00 0.00 44.79 4.02
3960 4746 4.358310 ACCATCCTATCATAGTCTCCAGGA 59.642 45.833 0.00 0.00 36.66 3.86
3999 4785 4.137543 CCCTCGCAAGCTATAAAAAGGAT 58.862 43.478 0.00 0.00 37.18 3.24
4016 4803 4.519730 CCTGTAAGTCTTATCTACCCCTCG 59.480 50.000 0.00 0.00 0.00 4.63
4032 4820 5.176958 CCGAACTTTGTGAACTACCTGTAAG 59.823 44.000 0.00 0.00 0.00 2.34
4048 4836 5.221661 ACCTCTAATCACAGAACCGAACTTT 60.222 40.000 0.00 0.00 0.00 2.66
4083 4871 3.795623 ACTGAATGCATGATTTCCTGC 57.204 42.857 0.00 1.41 38.87 4.85
4105 4893 2.159572 CCGCCTTTAAATCACAGAACCG 60.160 50.000 0.00 0.00 0.00 4.44
4107 4895 2.727916 CGCCGCCTTTAAATCACAGAAC 60.728 50.000 0.00 0.00 0.00 3.01
4109 4897 1.083489 CGCCGCCTTTAAATCACAGA 58.917 50.000 0.00 0.00 0.00 3.41
4110 4898 0.098728 CCGCCGCCTTTAAATCACAG 59.901 55.000 0.00 0.00 0.00 3.66
4111 4899 1.928706 GCCGCCGCCTTTAAATCACA 61.929 55.000 0.00 0.00 0.00 3.58
4112 4900 1.226575 GCCGCCGCCTTTAAATCAC 60.227 57.895 0.00 0.00 0.00 3.06
4113 4901 1.034838 ATGCCGCCGCCTTTAAATCA 61.035 50.000 0.00 0.00 0.00 2.57
4114 4902 0.102300 AATGCCGCCGCCTTTAAATC 59.898 50.000 0.00 0.00 0.00 2.17
4115 4903 0.534873 AAATGCCGCCGCCTTTAAAT 59.465 45.000 0.00 0.00 31.90 1.40
4116 4904 0.318762 AAAATGCCGCCGCCTTTAAA 59.681 45.000 1.27 0.00 32.42 1.52
4206 5025 6.094061 GTGAAGTACTGCCTCTGTAAACTAG 58.906 44.000 0.00 0.00 0.00 2.57
4284 5105 8.691661 AGTTATTAATCTGTCCAACTGTTTGT 57.308 30.769 0.00 0.00 0.00 2.83
4289 5110 9.529325 TCGATTAGTTATTAATCTGTCCAACTG 57.471 33.333 8.62 0.00 43.61 3.16
4314 5135 7.596248 TGCAAAACTGCAGAATTATTTCTCTTC 59.404 33.333 23.35 0.00 40.28 2.87
4357 5178 5.997129 CCTGTTGCCCAATTTTATCTGTTTT 59.003 36.000 0.00 0.00 0.00 2.43
4477 5677 3.141398 CCAACTTGCTAAGCACAAGAGA 58.859 45.455 10.26 0.00 45.99 3.10
4624 5824 2.068519 CTGCAGATTGTCGTACAAGCA 58.931 47.619 8.42 12.54 46.06 3.91
4632 5832 1.446907 AGAAAGCCTGCAGATTGTCG 58.553 50.000 17.39 0.00 0.00 4.35
4638 5838 2.645838 ACTTGAAGAAAGCCTGCAGA 57.354 45.000 17.39 0.00 39.76 4.26
4720 5920 1.134699 TCTCGTCATTCTGATGGTGGC 60.135 52.381 0.00 0.00 34.27 5.01
4721 5921 2.967599 TCTCGTCATTCTGATGGTGG 57.032 50.000 0.00 0.00 34.27 4.61
4722 5922 4.436332 TGATTCTCGTCATTCTGATGGTG 58.564 43.478 0.00 0.00 34.27 4.17
4733 5933 3.186702 TGTGTTGGTTGATTCTCGTCA 57.813 42.857 0.00 0.00 0.00 4.35
4734 5934 3.560068 AGTTGTGTTGGTTGATTCTCGTC 59.440 43.478 0.00 0.00 0.00 4.20
4933 6136 2.556622 CCATGAAGGTTTACACACCACC 59.443 50.000 0.00 0.00 39.62 4.61


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

AutoCloner maintained by Alex Coulton.