Multiple sequence alignment - TraesCS3D01G109400

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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 TraesCS3D01G109400 chr3D 100.000 6963 0 0 1 6963 63248572 63241610 0.000000e+00 12859
1 TraesCS3D01G109400 chr3D 87.850 214 25 1 1228 1441 65279474 65279686 4.170000e-62 250
2 TraesCS3D01G109400 chr3A 94.146 4646 170 40 1 4575 72299560 72294946 0.000000e+00 6979
3 TraesCS3D01G109400 chr3A 95.368 993 32 11 5593 6584 72294113 72293134 0.000000e+00 1567
4 TraesCS3D01G109400 chr3A 95.173 808 28 5 4758 5561 72294907 72294107 0.000000e+00 1266
5 TraesCS3D01G109400 chr3A 93.093 333 20 3 6600 6931 72293147 72292817 1.050000e-132 484
6 TraesCS3D01G109400 chr3B 92.748 3861 174 39 37 3829 102600569 102596747 0.000000e+00 5481
7 TraesCS3D01G109400 chr3B 93.902 2509 82 25 4100 6584 102596395 102593934 0.000000e+00 3720
8 TraesCS3D01G109400 chr3B 89.516 372 29 4 6601 6963 102593946 102593576 4.920000e-126 462
9 TraesCS3D01G109400 chr3B 85.900 461 29 15 3681 4108 102596898 102596441 6.360000e-125 459
10 TraesCS3D01G109400 chr2D 88.889 216 23 1 1226 1441 213033053 213033267 1.490000e-66 265
11 TraesCS3D01G109400 chr1D 87.907 215 25 1 1226 1440 200308381 200308594 1.160000e-62 252
12 TraesCS3D01G109400 chr6D 87.558 217 26 1 1226 1442 104996294 104996079 4.170000e-62 250
13 TraesCS3D01G109400 chr7D 87.500 216 26 1 1226 1441 210973665 210973879 1.500000e-61 248
14 TraesCS3D01G109400 chr7D 85.153 229 26 4 2062 2286 471557083 471557307 1.950000e-55 228
15 TraesCS3D01G109400 chr7D 78.571 308 49 9 1965 2271 243741269 243741560 3.320000e-43 187
16 TraesCS3D01G109400 chr6A 87.097 217 27 1 1225 1441 315944785 315945000 1.940000e-60 244
17 TraesCS3D01G109400 chr6A 77.170 311 53 8 1963 2271 111164809 111165103 1.550000e-36 165
18 TraesCS3D01G109400 chr4D 87.097 217 27 1 1226 1442 13437734 13437519 1.940000e-60 244
19 TraesCS3D01G109400 chr7B 85.153 229 26 4 2062 2286 495338137 495338361 1.950000e-55 228
20 TraesCS3D01G109400 chr7A 84.914 232 27 4 2062 2289 526132376 526132149 1.950000e-55 228
21 TraesCS3D01G109400 chr1A 77.273 308 52 6 1966 2271 80871100 80870809 1.550000e-36 165
22 TraesCS3D01G109400 chr5D 92.135 89 7 0 2182 2270 319917776 319917688 7.330000e-25 126


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 TraesCS3D01G109400 chr3D 63241610 63248572 6962 True 12859.0 12859 100.0000 1 6963 1 chr3D.!!$R1 6962
1 TraesCS3D01G109400 chr3A 72292817 72299560 6743 True 2574.0 6979 94.4450 1 6931 4 chr3A.!!$R1 6930
2 TraesCS3D01G109400 chr3B 102593576 102600569 6993 True 2530.5 5481 90.5165 37 6963 4 chr3B.!!$R1 6926

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
637 662 0.322008 AAAGCGAGAGAAGCCAAGGG 60.322 55.000 0.00 0.00 34.64 3.95 F
844 869 2.732619 CCTCCAACTCTACCCGCCC 61.733 68.421 0.00 0.00 0.00 6.13 F
1421 1454 4.129380 GCATATGCTACACACATCCTGAA 58.871 43.478 20.64 0.00 38.21 3.02 F
2669 2702 0.294887 GCAGATCACGCGAAAGTACG 59.705 55.000 15.93 0.00 0.00 3.67 F
3405 3444 0.898320 CCACGTCCTTCCTGATCAGT 59.102 55.000 21.11 0.00 0.00 3.41 F
4881 5075 0.598419 GTGGGAAAGCTGCAAGTTGC 60.598 55.000 21.17 21.17 45.29 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 1967 0.035317 TCACACCTGCTCATGACCAC 59.965 55.000 0.0 0.0 0.00 4.16 R
1936 1969 0.035317 TGTCACACCTGCTCATGACC 59.965 55.000 0.0 0.0 40.63 4.02 R
3336 3375 0.108585 GGTGAGGCTGTTGTTCCTGA 59.891 55.000 0.0 0.0 31.71 3.86 R
4456 4646 0.102844 TCTTTTGCTGGTGCTGTTGC 59.897 50.000 0.0 0.0 40.48 4.17 R
5370 5564 0.310854 GAAAGAACAAGTGCCCCGTG 59.689 55.000 0.0 0.0 0.00 4.94 R
6195 6390 3.215642 GCACAACAATGCCTTTCCC 57.784 52.632 0.0 0.0 39.86 3.97 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
25 26 1.065053 TGTTAATGGGGTCGTCCATGG 60.065 52.381 4.97 4.97 46.05 3.66
68 69 2.277084 AGTTGAGGTGTGTTGAACGAC 58.723 47.619 0.00 0.00 0.00 4.34
102 103 4.084171 CGTGAATGTTATGCTCAGCTATGG 60.084 45.833 0.00 0.00 0.00 2.74
194 203 1.468565 CCGTTTGAGATGCATGGCAAG 60.469 52.381 2.46 0.00 43.62 4.01
396 409 3.055530 TCTTGCCTTTTGCTTTTGGTTGA 60.056 39.130 0.00 0.00 42.00 3.18
402 415 6.375455 TGCCTTTTGCTTTTGGTTGATTTTAA 59.625 30.769 0.00 0.00 42.00 1.52
462 475 4.801147 ACATACATGCATCAACGCTAAG 57.199 40.909 0.00 0.00 0.00 2.18
503 516 1.012086 GTGCACTGTCATCGCATCAT 58.988 50.000 10.32 0.00 38.07 2.45
530 543 2.292794 TACAGCGAGCCGTTCCCATC 62.293 60.000 0.00 0.00 0.00 3.51
533 546 2.750888 GCGAGCCGTTCCCATCAAC 61.751 63.158 0.00 0.00 0.00 3.18
599 620 1.844357 GTGTATGCTGCGTACTACGTG 59.156 52.381 26.93 5.20 44.73 4.49
600 621 1.469703 TGTATGCTGCGTACTACGTGT 59.530 47.619 26.93 0.00 44.73 4.49
601 622 2.677337 TGTATGCTGCGTACTACGTGTA 59.323 45.455 26.93 7.53 44.73 2.90
615 640 1.340211 ACGTGTAGGGTGAGAGAGGAG 60.340 57.143 0.00 0.00 0.00 3.69
632 657 1.364721 GAGGAAAAGCGAGAGAAGCC 58.635 55.000 0.00 0.00 34.64 4.35
637 662 0.322008 AAAGCGAGAGAAGCCAAGGG 60.322 55.000 0.00 0.00 34.64 3.95
844 869 2.732619 CCTCCAACTCTACCCGCCC 61.733 68.421 0.00 0.00 0.00 6.13
1237 1270 7.807907 GCATATAGTTTTGATGGAATTAACCGG 59.192 37.037 0.00 0.00 0.00 5.28
1421 1454 4.129380 GCATATGCTACACACATCCTGAA 58.871 43.478 20.64 0.00 38.21 3.02
1442 1475 5.104693 TGAAAAACTTCCAGGTGAGACACTA 60.105 40.000 0.00 0.00 34.40 2.74
1483 1516 4.785301 ACAACTATGCTAGCCATGAACAT 58.215 39.130 13.29 0.00 35.34 2.71
1846 1879 6.332735 ACCTTTTACATGCCTTCTCTTTTC 57.667 37.500 0.00 0.00 0.00 2.29
1926 1959 6.090898 ACGTGCTCATACTGACTGTTAATTTC 59.909 38.462 0.00 0.00 0.00 2.17
1934 1967 6.492007 ACTGACTGTTAATTTCTGCATCTG 57.508 37.500 0.00 0.00 0.00 2.90
1935 1968 6.000219 ACTGACTGTTAATTTCTGCATCTGT 59.000 36.000 0.00 0.00 0.00 3.41
1936 1969 6.072838 ACTGACTGTTAATTTCTGCATCTGTG 60.073 38.462 0.00 0.00 0.00 3.66
2108 2141 1.077501 CCGACCAGTGATGGCCAAT 60.078 57.895 10.96 0.00 0.00 3.16
2249 2282 3.519930 GAGGGGGAGCTCGTCGTC 61.520 72.222 7.83 9.43 0.00 4.20
2312 2345 2.680352 GCCTCCTCAGACCGTGGA 60.680 66.667 0.00 0.00 35.92 4.02
2562 2595 6.968335 GGTAACTAGACATTCTTTCGTCTCTC 59.032 42.308 0.00 0.00 41.52 3.20
2564 2597 3.495670 AGACATTCTTTCGTCTCTCCG 57.504 47.619 0.00 0.00 38.03 4.63
2570 2603 0.521659 CTTTCGTCTCTCCGTCTCGC 60.522 60.000 0.00 0.00 0.00 5.03
2573 2606 2.486042 GTCTCTCCGTCTCGCCAC 59.514 66.667 0.00 0.00 0.00 5.01
2578 2611 3.052620 CTCCGTCTCGCCACATCGT 62.053 63.158 0.00 0.00 0.00 3.73
2579 2612 2.126071 CCGTCTCGCCACATCGTT 60.126 61.111 0.00 0.00 0.00 3.85
2596 2629 5.581085 ACATCGTTGGTTTGCTTAGATCTAC 59.419 40.000 0.67 0.00 0.00 2.59
2603 2636 6.631016 TGGTTTGCTTAGATCTACACTACTG 58.369 40.000 0.67 0.00 0.00 2.74
2608 2641 6.971602 TGCTTAGATCTACACTACTGTATGC 58.028 40.000 0.67 0.00 32.21 3.14
2612 2645 5.317808 AGATCTACACTACTGTATGCCGAT 58.682 41.667 0.00 0.00 32.21 4.18
2669 2702 0.294887 GCAGATCACGCGAAAGTACG 59.705 55.000 15.93 0.00 0.00 3.67
2672 2705 0.912528 GATCACGCGAAAGTACGGTC 59.087 55.000 15.93 0.00 0.00 4.79
2740 2775 3.546670 GCTACAGTTTCGAGTTACGGATG 59.453 47.826 0.00 0.00 42.82 3.51
2766 2803 2.233922 AGATCGATGGTTTCTGTTCGGT 59.766 45.455 0.54 0.00 32.67 4.69
2767 2804 2.536761 TCGATGGTTTCTGTTCGGTT 57.463 45.000 0.00 0.00 32.67 4.44
2768 2805 3.663995 TCGATGGTTTCTGTTCGGTTA 57.336 42.857 0.00 0.00 32.67 2.85
2769 2806 3.581755 TCGATGGTTTCTGTTCGGTTAG 58.418 45.455 0.00 0.00 32.67 2.34
2770 2807 3.006110 TCGATGGTTTCTGTTCGGTTAGT 59.994 43.478 0.00 0.00 32.67 2.24
2861 2898 2.979814 TTGTGTGTAGGATCGATGGG 57.020 50.000 0.54 0.00 0.00 4.00
3120 3157 4.756084 AGATTTCCAGAAAGCTCAAACG 57.244 40.909 5.11 0.00 42.67 3.60
3187 3224 7.396055 AGTGAGATATAAAGGAGACTAGCCATC 59.604 40.741 0.00 0.00 42.68 3.51
3255 3294 9.121517 GATATACATTTTCGGCATTCATTTCTG 57.878 33.333 0.00 0.00 0.00 3.02
3281 3320 3.343941 TGAACAGGTTGGTATAGGTGC 57.656 47.619 0.00 0.00 0.00 5.01
3282 3321 2.910319 TGAACAGGTTGGTATAGGTGCT 59.090 45.455 0.00 0.00 0.00 4.40
3285 3324 3.115390 ACAGGTTGGTATAGGTGCTGAT 58.885 45.455 0.00 0.00 0.00 2.90
3345 3384 1.971167 GCATGCCGGTCAGGAACAA 60.971 57.895 6.36 0.00 45.00 2.83
3400 3439 2.583441 CCTGCCACGTCCTTCCTGA 61.583 63.158 0.00 0.00 0.00 3.86
3405 3444 0.898320 CCACGTCCTTCCTGATCAGT 59.102 55.000 21.11 0.00 0.00 3.41
3441 3480 1.517257 CTCAGCTACAGTTCCGCCG 60.517 63.158 0.00 0.00 0.00 6.46
3468 3507 1.856012 GCACACTTCTGTCGTGCTC 59.144 57.895 6.50 0.00 42.37 4.26
3736 3822 5.102313 GCTTGCTAACAACTGAAAAACACT 58.898 37.500 0.00 0.00 0.00 3.55
3821 3908 2.821437 TCTCAAGCTAGGTTGGCTAGT 58.179 47.619 29.13 0.00 39.30 2.57
3831 3918 6.781014 AGCTAGGTTGGCTAGTGTATATACAA 59.219 38.462 17.07 2.24 38.36 2.41
3833 3920 7.760340 GCTAGGTTGGCTAGTGTATATACAATC 59.240 40.741 18.42 7.18 38.04 2.67
3834 3921 7.857404 AGGTTGGCTAGTGTATATACAATCT 57.143 36.000 18.42 13.72 38.04 2.40
3835 3922 8.951614 AGGTTGGCTAGTGTATATACAATCTA 57.048 34.615 18.42 14.08 38.04 1.98
3836 3923 9.026121 AGGTTGGCTAGTGTATATACAATCTAG 57.974 37.037 23.73 23.73 38.04 2.43
3889 4006 7.591426 GTCATAACTAGTCCTTTTGTTTTGCAG 59.409 37.037 0.00 0.00 0.00 4.41
3899 4016 7.835634 CCTTTTGTTTTGCAGTTAAAAGGTA 57.164 32.000 23.96 0.02 46.12 3.08
3948 4065 8.169977 ACCAGCCTATGTAAAATGATATTGTG 57.830 34.615 0.00 0.00 0.00 3.33
4087 4204 1.273048 TGGTGGAAGATGCATTGCAAC 59.727 47.619 16.46 13.33 43.62 4.17
4097 4214 7.551035 AAGATGCATTGCAACTTTTTACAAA 57.449 28.000 23.67 0.00 46.57 2.83
4199 4373 4.635765 GCATAGCATGAGAAACCACTTGTA 59.364 41.667 0.00 0.00 0.00 2.41
4299 4473 9.825972 AATGTTTGTTTCATCTAACGATGTTAG 57.174 29.630 9.83 9.83 45.76 2.34
4313 4487 3.623060 CGATGTTAGTGCAATACCAGCTT 59.377 43.478 5.48 0.00 0.00 3.74
4324 4498 9.184523 AGTGCAATACCAGCTTATTTGTTTATA 57.815 29.630 0.00 0.00 0.00 0.98
4456 4646 2.099592 ACCACAGAACATGCAACAACAG 59.900 45.455 0.00 0.00 0.00 3.16
4579 4769 8.519526 CATTACTTGTATTTGTTTTGCCTCCTA 58.480 33.333 0.00 0.00 0.00 2.94
4595 4785 4.442706 CCTCCTATGCGTGTATGAAAACT 58.557 43.478 0.00 0.00 0.00 2.66
4698 4888 7.217200 TCTTATAATGGAAATCGAAGAGGGTG 58.783 38.462 0.00 0.00 43.63 4.61
4771 4961 1.556451 ACCTATGAGCTGCATGTGACA 59.444 47.619 1.02 0.00 37.87 3.58
4881 5075 0.598419 GTGGGAAAGCTGCAAGTTGC 60.598 55.000 21.17 21.17 45.29 4.17
5260 5454 5.240891 TGCTTTCATCACCATATAGCTAGC 58.759 41.667 6.62 6.62 0.00 3.42
5312 5506 0.825840 CCCGGCCTTCTTGTTTTCCA 60.826 55.000 0.00 0.00 0.00 3.53
5314 5508 1.604604 CGGCCTTCTTGTTTTCCAGA 58.395 50.000 0.00 0.00 0.00 3.86
5315 5509 1.266989 CGGCCTTCTTGTTTTCCAGAC 59.733 52.381 0.00 0.00 0.00 3.51
5316 5510 2.587522 GGCCTTCTTGTTTTCCAGACT 58.412 47.619 0.00 0.00 0.00 3.24
5317 5511 3.751518 GGCCTTCTTGTTTTCCAGACTA 58.248 45.455 0.00 0.00 0.00 2.59
5346 5540 8.041323 ACATGTCCTAGAGTTGTTTACCATTAG 58.959 37.037 0.00 0.00 0.00 1.73
5375 5569 3.314080 TGAAAAGAGCAAAGTAACACGGG 59.686 43.478 0.00 0.00 0.00 5.28
5395 5589 3.481453 GGGCACTTGTTCTTTCTCTCTT 58.519 45.455 0.00 0.00 0.00 2.85
5464 5658 6.183360 TGCATGGCATTTGTTATCATTGATCT 60.183 34.615 1.55 0.00 31.71 2.75
5640 5834 7.195839 ACAGAACAAACTGCTTTCTTATCTC 57.804 36.000 0.00 0.00 41.06 2.75
5663 5857 0.108138 ACGTGTAATCCAGCTCTGCC 60.108 55.000 0.00 0.00 0.00 4.85
5692 5886 9.436957 GTATCTTTTCTCACTTGAACCTTGATA 57.563 33.333 0.00 0.00 0.00 2.15
5716 5911 7.814264 ATCTTCTGGAGCTTAAATGTTATGG 57.186 36.000 0.00 0.00 0.00 2.74
5788 5983 3.200605 TCCACTGACATGCATGTATCCTT 59.799 43.478 31.45 8.74 41.95 3.36
5802 5997 7.093333 TGCATGTATCCTTCTCTCTTTCAAGTA 60.093 37.037 0.00 0.00 0.00 2.24
5844 6039 1.000060 CAATGTTGCACTTCACTGGGG 60.000 52.381 0.00 0.00 0.00 4.96
6007 6202 5.105146 ACCAGATTAAACAAAAGCAACCACA 60.105 36.000 0.00 0.00 0.00 4.17
6043 6238 3.812882 GCTAGTATGGTCTCTCCCTCCTC 60.813 56.522 0.00 0.00 34.77 3.71
6195 6390 0.905337 AGAGGAGGAGAACGGTTGGG 60.905 60.000 0.00 0.00 0.00 4.12
6361 6557 9.205916 GTAATACTGTTTGCATGTACATTAACG 57.794 33.333 5.37 9.53 0.00 3.18
6365 6561 5.822278 TGTTTGCATGTACATTAACGTTGT 58.178 33.333 11.99 3.51 0.00 3.32
6408 6605 5.355910 ACGCCTTCTTTTTCTTTTAGTGACA 59.644 36.000 0.00 0.00 0.00 3.58
6410 6607 5.681543 GCCTTCTTTTTCTTTTAGTGACACG 59.318 40.000 0.00 0.00 0.00 4.49
6488 6685 5.609423 TCACATTCCAAATTGTTTCCAAGG 58.391 37.500 0.00 0.00 33.17 3.61
6575 6778 7.801716 ATTTTATTTTAGCGCTCCAGACATA 57.198 32.000 16.34 0.05 0.00 2.29
6576 6779 7.801716 TTTTATTTTAGCGCTCCAGACATAT 57.198 32.000 16.34 0.00 0.00 1.78
6577 6780 8.896320 TTTTATTTTAGCGCTCCAGACATATA 57.104 30.769 16.34 0.00 0.00 0.86
6578 6781 7.884816 TTATTTTAGCGCTCCAGACATATAC 57.115 36.000 16.34 0.00 0.00 1.47
6579 6782 4.929819 TTTAGCGCTCCAGACATATACA 57.070 40.909 16.34 0.00 0.00 2.29
6580 6783 4.929819 TTAGCGCTCCAGACATATACAA 57.070 40.909 16.34 0.00 0.00 2.41
6581 6784 5.468540 TTAGCGCTCCAGACATATACAAT 57.531 39.130 16.34 0.00 0.00 2.71
6582 6785 6.584185 TTAGCGCTCCAGACATATACAATA 57.416 37.500 16.34 0.00 0.00 1.90
6583 6786 5.667539 AGCGCTCCAGACATATACAATAT 57.332 39.130 2.64 0.00 0.00 1.28
6584 6787 5.655488 AGCGCTCCAGACATATACAATATC 58.345 41.667 2.64 0.00 0.00 1.63
6585 6788 5.420421 AGCGCTCCAGACATATACAATATCT 59.580 40.000 2.64 0.00 0.00 1.98
6586 6789 6.071108 AGCGCTCCAGACATATACAATATCTT 60.071 38.462 2.64 0.00 0.00 2.40
6587 6790 6.254589 GCGCTCCAGACATATACAATATCTTC 59.745 42.308 0.00 0.00 0.00 2.87
6588 6791 6.470556 CGCTCCAGACATATACAATATCTTCG 59.529 42.308 0.00 0.00 0.00 3.79
6589 6792 6.254589 GCTCCAGACATATACAATATCTTCGC 59.745 42.308 0.00 0.00 0.00 4.70
6590 6793 7.227049 TCCAGACATATACAATATCTTCGCA 57.773 36.000 0.00 0.00 0.00 5.10
6591 6794 7.666623 TCCAGACATATACAATATCTTCGCAA 58.333 34.615 0.00 0.00 0.00 4.85
6592 6795 8.147704 TCCAGACATATACAATATCTTCGCAAA 58.852 33.333 0.00 0.00 0.00 3.68
6593 6796 8.773645 CCAGACATATACAATATCTTCGCAAAA 58.226 33.333 0.00 0.00 0.00 2.44
6646 6849 3.120199 ACTTACTGCTGCACGCTAATTTG 60.120 43.478 0.00 0.00 40.11 2.32
6687 6890 9.128404 TCTACTCTCTACACTAAAAACTGTTCA 57.872 33.333 0.00 0.00 0.00 3.18
6699 6902 6.528537 AAAAACTGTTCATATGCATAGCCA 57.471 33.333 12.79 5.13 0.00 4.75
6706 6909 5.651576 TGTTCATATGCATAGCCACAAAAGA 59.348 36.000 12.79 0.00 0.00 2.52
6708 6911 4.580167 TCATATGCATAGCCACAAAAGACC 59.420 41.667 12.79 0.00 0.00 3.85
6715 6918 5.569413 CATAGCCACAAAAGACCGTTAATC 58.431 41.667 0.00 0.00 0.00 1.75
6782 6985 5.656859 AGGATTGGTCAAAAGGTATTTAGCC 59.343 40.000 0.00 0.00 0.00 3.93
6940 7153 4.703897 ACTAACACTGCTTTGCTCTGTTA 58.296 39.130 10.11 10.11 33.44 2.41
6949 7162 8.834465 CACTGCTTTGCTCTGTTATAATCTAAT 58.166 33.333 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 3.432252 CACCTAACCAACATTCTGACGAC 59.568 47.826 0.00 0.00 0.00 4.34
194 203 2.187163 GCTCAACGAGGGGTAGCC 59.813 66.667 1.07 1.07 0.00 3.93
396 409 4.524328 AGCAAGCTAAGCTGGTGTTAAAAT 59.476 37.500 12.33 0.00 41.61 1.82
402 415 2.427506 GTTAGCAAGCTAAGCTGGTGT 58.572 47.619 20.40 0.43 43.33 4.16
503 516 4.543692 GAACGGCTCGCTGTAATATAAGA 58.456 43.478 3.47 0.00 34.70 2.10
599 620 2.830651 TTCCTCCTCTCTCACCCTAC 57.169 55.000 0.00 0.00 0.00 3.18
600 621 3.714144 CTTTTCCTCCTCTCTCACCCTA 58.286 50.000 0.00 0.00 0.00 3.53
601 622 2.545810 CTTTTCCTCCTCTCTCACCCT 58.454 52.381 0.00 0.00 0.00 4.34
615 640 1.466558 CTTGGCTTCTCTCGCTTTTCC 59.533 52.381 0.00 0.00 0.00 3.13
844 869 4.452733 GTGAGCGAACCGAGGGGG 62.453 72.222 0.00 0.00 43.62 5.40
866 891 3.241678 CGAAAATACGGCGAGAAACTGAG 60.242 47.826 16.62 0.00 0.00 3.35
903 928 2.851235 CAGAATTCAGAACGCGAGAGAG 59.149 50.000 15.93 0.00 0.00 3.20
1237 1270 3.304928 CCAATCCTTCTTGCAGTTGACAC 60.305 47.826 0.00 0.00 0.00 3.67
1319 1352 1.463214 TTCCCTCACCTTGGCCTCA 60.463 57.895 3.32 0.00 0.00 3.86
1421 1454 3.933861 AGTGTCTCACCTGGAAGTTTT 57.066 42.857 0.00 0.00 34.49 2.43
1442 1475 3.491342 TGTCTAGCTAGCCATCTCGAAT 58.509 45.455 16.35 0.00 0.00 3.34
1668 1701 3.100671 GTGGAGAACACCAGGAGTAGAT 58.899 50.000 0.00 0.00 44.49 1.98
1846 1879 1.068055 GCAGATGCAACAAACCTCTGG 60.068 52.381 11.96 0.00 41.59 3.86
1926 1959 1.015109 GCTCATGACCACAGATGCAG 58.985 55.000 0.00 0.00 0.00 4.41
1934 1967 0.035317 TCACACCTGCTCATGACCAC 59.965 55.000 0.00 0.00 0.00 4.16
1935 1968 0.035317 GTCACACCTGCTCATGACCA 59.965 55.000 0.00 0.00 36.31 4.02
1936 1969 0.035317 TGTCACACCTGCTCATGACC 59.965 55.000 0.00 0.00 40.63 4.02
2057 2090 4.316823 TGCCACCTCGTCTCCCCT 62.317 66.667 0.00 0.00 0.00 4.79
2198 2231 1.033574 GGTCTCCGAGATGGTACTGG 58.966 60.000 0.33 0.00 39.52 4.00
2249 2282 3.181516 GCGTTTGGTAGAAGATCTTGCAG 60.182 47.826 14.00 0.00 0.00 4.41
2420 2453 1.611592 GGTACGACGTTGCCGACAAG 61.612 60.000 5.50 0.00 36.16 3.16
2429 2462 4.060038 CCAGCCGGGTACGACGTT 62.060 66.667 5.47 0.00 44.60 3.99
2562 2595 2.126071 AACGATGTGGCGAGACGG 60.126 61.111 0.00 0.00 34.83 4.79
2564 2597 0.949105 AACCAACGATGTGGCGAGAC 60.949 55.000 0.00 0.00 43.00 3.36
2570 2603 2.811431 TCTAAGCAAACCAACGATGTGG 59.189 45.455 0.00 0.00 44.92 4.17
2573 2606 5.580691 TGTAGATCTAAGCAAACCAACGATG 59.419 40.000 3.40 0.00 0.00 3.84
2578 2611 7.097192 CAGTAGTGTAGATCTAAGCAAACCAA 58.903 38.462 3.40 0.00 0.00 3.67
2579 2612 6.210784 ACAGTAGTGTAGATCTAAGCAAACCA 59.789 38.462 3.40 0.00 34.05 3.67
2596 2629 5.568685 AGCTATATCGGCATACAGTAGTG 57.431 43.478 0.00 0.00 0.00 2.74
2669 2702 2.047179 GGACCAACCGAGCAGACC 60.047 66.667 0.00 0.00 0.00 3.85
2740 2775 5.681982 CGAACAGAAACCATCGATCTACTAC 59.318 44.000 0.00 0.00 37.48 2.73
2769 2806 4.400844 CGCGATCGACAGGCAACTAAAC 62.401 54.545 21.57 0.00 42.10 2.01
2770 2807 2.322860 CGCGATCGACAGGCAACTAAA 61.323 52.381 21.57 0.00 42.10 1.85
2843 2880 0.464036 GCCCATCGATCCTACACACA 59.536 55.000 0.00 0.00 0.00 3.72
2844 2881 0.753262 AGCCCATCGATCCTACACAC 59.247 55.000 0.00 0.00 0.00 3.82
3120 3157 2.351418 TCAGTTATGCTGTTACATGCGC 59.649 45.455 0.00 0.00 45.23 6.09
3221 3260 9.647797 AATGCCGAAAATGTATATCTTCGTATA 57.352 29.630 7.09 0.00 39.14 1.47
3223 3262 7.654116 TGAATGCCGAAAATGTATATCTTCGTA 59.346 33.333 7.09 0.00 39.14 3.43
3224 3263 6.481976 TGAATGCCGAAAATGTATATCTTCGT 59.518 34.615 7.09 0.00 39.14 3.85
3225 3264 6.887368 TGAATGCCGAAAATGTATATCTTCG 58.113 36.000 1.30 1.30 40.18 3.79
3226 3265 9.683069 AAATGAATGCCGAAAATGTATATCTTC 57.317 29.630 0.00 0.00 0.00 2.87
3227 3266 9.683069 GAAATGAATGCCGAAAATGTATATCTT 57.317 29.630 0.00 0.00 0.00 2.40
3228 3267 9.071276 AGAAATGAATGCCGAAAATGTATATCT 57.929 29.630 0.00 0.00 0.00 1.98
3229 3268 9.121517 CAGAAATGAATGCCGAAAATGTATATC 57.878 33.333 0.00 0.00 0.00 1.63
3230 3269 8.632679 ACAGAAATGAATGCCGAAAATGTATAT 58.367 29.630 0.00 0.00 0.00 0.86
3231 3270 7.914871 CACAGAAATGAATGCCGAAAATGTATA 59.085 33.333 0.00 0.00 0.00 1.47
3234 3273 4.925054 CACAGAAATGAATGCCGAAAATGT 59.075 37.500 0.00 0.00 0.00 2.71
3248 3287 4.637483 ACCTGTTCAACACACAGAAATG 57.363 40.909 1.54 0.00 43.90 2.32
3255 3294 4.454504 CCTATACCAACCTGTTCAACACAC 59.545 45.833 0.00 0.00 0.00 3.82
3281 3320 2.021068 ATCGGACGGCACCTGATCAG 62.021 60.000 16.24 16.24 0.00 2.90
3282 3321 2.016393 GATCGGACGGCACCTGATCA 62.016 60.000 15.80 0.00 38.50 2.92
3285 3324 2.678580 TGATCGGACGGCACCTGA 60.679 61.111 0.00 0.00 0.00 3.86
3336 3375 0.108585 GGTGAGGCTGTTGTTCCTGA 59.891 55.000 0.00 0.00 31.71 3.86
3391 3430 1.794714 GGCCTACTGATCAGGAAGGA 58.205 55.000 34.04 14.03 37.70 3.36
3400 3439 1.673808 GGGTTCGTCGGCCTACTGAT 61.674 60.000 5.79 0.00 32.57 2.90
3405 3444 2.364579 ATGGGGTTCGTCGGCCTA 60.365 61.111 0.00 0.00 0.00 3.93
3441 3480 2.050985 GAAGTGTGCTGCAACGGC 60.051 61.111 2.77 0.00 41.68 5.68
3468 3507 2.092681 CACGTGAAACTGATCATGGTCG 59.907 50.000 10.90 0.00 40.02 4.79
3624 3681 5.447846 GTGAATAAACACATGCGTTCATACG 59.552 40.000 0.00 0.00 43.59 3.06
3954 4071 8.877864 TCTATGAAACAATCTACCCATGTTTT 57.122 30.769 4.80 0.00 44.72 2.43
4014 4131 2.192664 ATGTGTGCCGTACCATGAAA 57.807 45.000 0.00 0.00 0.00 2.69
4299 4473 9.965824 ATATAAACAAATAAGCTGGTATTGCAC 57.034 29.630 0.00 0.00 0.00 4.57
4324 4498 8.437575 TGACTTAACTGAAAACTTAGGAAGGAT 58.562 33.333 0.00 0.00 0.00 3.24
4456 4646 0.102844 TCTTTTGCTGGTGCTGTTGC 59.897 50.000 0.00 0.00 40.48 4.17
4579 4769 7.609760 TTCTTATCAGTTTTCATACACGCAT 57.390 32.000 0.00 0.00 0.00 4.73
4616 4806 5.461078 ACATCATCGCTGGTACGTTAATTAC 59.539 40.000 0.00 0.00 0.00 1.89
4617 4807 5.460748 CACATCATCGCTGGTACGTTAATTA 59.539 40.000 0.00 0.00 0.00 1.40
4618 4808 4.270084 CACATCATCGCTGGTACGTTAATT 59.730 41.667 0.00 0.00 0.00 1.40
4619 4809 3.802139 CACATCATCGCTGGTACGTTAAT 59.198 43.478 0.00 0.00 0.00 1.40
4620 4810 3.183754 CACATCATCGCTGGTACGTTAA 58.816 45.455 0.00 0.00 0.00 2.01
4621 4811 2.804647 CACATCATCGCTGGTACGTTA 58.195 47.619 0.00 0.00 0.00 3.18
4622 4812 1.640428 CACATCATCGCTGGTACGTT 58.360 50.000 0.00 0.00 0.00 3.99
4623 4813 0.806102 GCACATCATCGCTGGTACGT 60.806 55.000 0.00 0.00 0.00 3.57
4624 4814 0.528466 AGCACATCATCGCTGGTACG 60.528 55.000 0.00 0.00 37.02 3.67
4625 4815 2.509052 TAGCACATCATCGCTGGTAC 57.491 50.000 0.00 0.00 39.30 3.34
4626 4816 4.220602 ACATATAGCACATCATCGCTGGTA 59.779 41.667 0.00 0.00 39.30 3.25
4627 4817 3.007290 ACATATAGCACATCATCGCTGGT 59.993 43.478 0.00 0.00 39.30 4.00
4628 4818 3.593096 ACATATAGCACATCATCGCTGG 58.407 45.455 0.00 0.00 39.30 4.85
4629 4819 5.379827 CAAACATATAGCACATCATCGCTG 58.620 41.667 0.00 0.00 39.30 5.18
4630 4820 4.083643 GCAAACATATAGCACATCATCGCT 60.084 41.667 0.00 0.00 42.34 4.93
4631 4821 4.153986 GCAAACATATAGCACATCATCGC 58.846 43.478 0.00 0.00 0.00 4.58
4632 4822 4.150451 TCGCAAACATATAGCACATCATCG 59.850 41.667 0.00 0.00 0.00 3.84
4633 4823 5.178252 ACTCGCAAACATATAGCACATCATC 59.822 40.000 0.00 0.00 0.00 2.92
4771 4961 5.178061 GCTTAGCTTAAACCATGCCAAAAT 58.822 37.500 0.00 0.00 0.00 1.82
4977 5171 1.348036 AGGCCTTGTTCCACAGTACTC 59.652 52.381 0.00 0.00 0.00 2.59
5229 5423 2.886523 TGGTGATGAAAGCAGGAAAGTG 59.113 45.455 0.00 0.00 24.12 3.16
5260 5454 4.201724 CGGAGTAAAAGCTCTCATTTTCGG 60.202 45.833 2.90 0.00 35.89 4.30
5312 5506 6.723339 ACAACTCTAGGACATGTAGTAGTCT 58.277 40.000 0.00 0.00 35.18 3.24
5314 5508 7.778185 AAACAACTCTAGGACATGTAGTAGT 57.222 36.000 0.00 0.00 0.00 2.73
5315 5509 8.189460 GGTAAACAACTCTAGGACATGTAGTAG 58.811 40.741 0.00 2.83 0.00 2.57
5316 5510 7.670979 TGGTAAACAACTCTAGGACATGTAGTA 59.329 37.037 0.00 0.00 0.00 1.82
5317 5511 6.495872 TGGTAAACAACTCTAGGACATGTAGT 59.504 38.462 0.00 0.00 0.00 2.73
5370 5564 0.310854 GAAAGAACAAGTGCCCCGTG 59.689 55.000 0.00 0.00 0.00 4.94
5375 5569 5.506686 AAAAGAGAGAAAGAACAAGTGCC 57.493 39.130 0.00 0.00 0.00 5.01
5395 5589 5.720371 ATGTGAATCGGTTCATGGAAAAA 57.280 34.783 15.35 0.00 45.46 1.94
5464 5658 5.266733 ACTGTAGTAGGACAAAACGAACA 57.733 39.130 0.00 0.00 0.00 3.18
5640 5834 1.478510 AGAGCTGGATTACACGTGAGG 59.521 52.381 25.01 0.00 0.00 3.86
5663 5857 7.678947 AGGTTCAAGTGAGAAAAGATACATG 57.321 36.000 0.00 0.00 0.00 3.21
5692 5886 7.349598 ACCATAACATTTAAGCTCCAGAAGAT 58.650 34.615 0.00 0.00 0.00 2.40
5716 5911 6.591834 GTGCATATATGGATCCAACTGTCTAC 59.408 42.308 20.67 10.06 0.00 2.59
5758 5953 5.419788 ACATGCATGTCAGTGGATACAAAAT 59.580 36.000 26.61 0.00 43.74 1.82
5788 5983 4.333690 AGCTACGGTACTTGAAAGAGAGA 58.666 43.478 0.00 0.00 0.00 3.10
5802 5997 5.245531 TGATTCAAATGAGAAAGCTACGGT 58.754 37.500 0.00 0.00 0.00 4.83
5844 6039 5.350365 GGAAAAGTGGTCAAAAAGGAACAAC 59.650 40.000 0.00 0.00 36.00 3.32
6007 6202 6.436890 ACCATACTAGCTAGAGAAAGAGGTT 58.563 40.000 27.45 3.13 0.00 3.50
6043 6238 5.175126 CCAAGAAAGCAGTACCGTATATTCG 59.825 44.000 0.00 0.00 0.00 3.34
6195 6390 3.215642 GCACAACAATGCCTTTCCC 57.784 52.632 0.00 0.00 39.86 3.97
6595 6798 9.378551 ACGACATACATATTGTACATGTCTTTT 57.621 29.630 17.05 3.85 41.06 2.27
6596 6799 8.942338 ACGACATACATATTGTACATGTCTTT 57.058 30.769 17.05 5.70 41.06 2.52
6646 6849 5.010213 AGAGAGTAGAGTTCAGTTCACAACC 59.990 44.000 0.00 0.00 0.00 3.77
6687 6890 3.565482 CGGTCTTTTGTGGCTATGCATAT 59.435 43.478 6.92 0.00 0.00 1.78
6699 6902 9.457436 ACTAATAATGGATTAACGGTCTTTTGT 57.543 29.630 0.00 0.00 29.39 2.83
6706 6909 8.911918 TGCAATACTAATAATGGATTAACGGT 57.088 30.769 0.00 0.00 29.39 4.83
6875 7088 8.573566 TTTCTTTTTGAATGGGGTTATGGGACA 61.574 37.037 0.00 0.00 37.34 4.02


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

AutoCloner maintained by Alex Coulton.