Multiple sequence alignment - TraesCS2D01G378300

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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 TraesCS2D01G378300 chr2D 100.000 5476 0 0 1 5476 482660984 482666459 0.000000e+00 10113.0
1 TraesCS2D01G378300 chr2D 87.059 170 21 1 1489 1658 302250082 302250250 2.010000e-44 191.0
2 TraesCS2D01G378300 chr2D 87.417 151 19 0 1500 1650 554431938 554432088 2.030000e-39 174.0
3 TraesCS2D01G378300 chr2D 86.145 166 12 6 1494 1650 46297772 46297609 9.430000e-38 169.0
4 TraesCS2D01G378300 chr2A 93.403 5154 215 56 4 5065 625024149 625029269 0.000000e+00 7518.0
5 TraesCS2D01G378300 chr2A 90.308 227 18 2 5206 5431 625029476 625029699 1.490000e-75 294.0
6 TraesCS2D01G378300 chr2A 94.000 50 2 1 5426 5475 1456355 1456403 2.120000e-09 75.0
7 TraesCS2D01G378300 chr2B 93.374 4875 216 34 131 4943 566623447 566628276 0.000000e+00 7114.0
8 TraesCS2D01G378300 chr2B 85.345 232 19 8 4956 5187 566628318 566628534 5.520000e-55 226.0
9 TraesCS2D01G378300 chr2B 92.126 127 10 0 5305 5431 566631147 566631273 4.360000e-41 180.0
10 TraesCS2D01G378300 chr6D 85.253 217 24 6 309 524 298911548 298911339 3.320000e-52 217.0
11 TraesCS2D01G378300 chr5A 88.050 159 19 0 1492 1650 339743158 339743000 7.240000e-44 189.0
12 TraesCS2D01G378300 chr5A 91.667 60 1 2 5420 5476 152641172 152641114 4.550000e-11 80.5
13 TraesCS2D01G378300 chr7A 87.662 154 19 0 1499 1652 238551388 238551541 4.360000e-41 180.0
14 TraesCS2D01G378300 chr7A 86.517 89 8 4 1660 1745 667224802 667224715 1.620000e-15 95.3
15 TraesCS2D01G378300 chr6B 84.516 155 24 0 1498 1652 471136001 471135847 2.640000e-33 154.0
16 TraesCS2D01G378300 chr6B 92.308 52 3 1 5425 5476 456599673 456599723 7.610000e-09 73.1
17 TraesCS2D01G378300 chr1A 87.218 133 16 1 1517 1648 494438587 494438455 3.420000e-32 150.0
18 TraesCS2D01G378300 chr1A 91.011 89 7 1 1657 1744 154576781 154576869 9.640000e-23 119.0
19 TraesCS2D01G378300 chr1D 91.011 89 7 1 1657 1744 138347207 138347295 9.640000e-23 119.0
20 TraesCS2D01G378300 chr1D 90.909 55 3 2 5421 5475 289408785 289408837 7.610000e-09 73.1
21 TraesCS2D01G378300 chr7D 88.764 89 9 1 1656 1743 99461788 99461876 2.090000e-19 108.0
22 TraesCS2D01G378300 chr1B 88.372 86 9 1 1657 1741 156850359 156850444 9.700000e-18 102.0
23 TraesCS2D01G378300 chr1B 87.640 89 10 1 1657 1744 212748973 212748885 9.700000e-18 102.0
24 TraesCS2D01G378300 chr4B 84.884 86 12 1 1651 1735 416642524 416642609 9.770000e-13 86.1
25 TraesCS2D01G378300 chr4D 89.394 66 4 3 5413 5476 5768091 5768027 4.550000e-11 80.5
26 TraesCS2D01G378300 chr4A 94.118 51 2 1 5426 5476 552461608 552461657 5.880000e-10 76.8
27 TraesCS2D01G378300 chr3B 92.453 53 2 2 5425 5476 773703406 773703457 2.120000e-09 75.0
28 TraesCS2D01G378300 chr3A 91.228 57 2 3 5420 5476 586642515 586642462 2.120000e-09 75.0
29 TraesCS2D01G378300 chr3A 95.556 45 1 1 5432 5476 692507820 692507777 2.740000e-08 71.3


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 TraesCS2D01G378300 chr2D 482660984 482666459 5475 False 10113.000000 10113 100.000000 1 5476 1 chr2D.!!$F2 5475
1 TraesCS2D01G378300 chr2A 625024149 625029699 5550 False 3906.000000 7518 91.855500 4 5431 2 chr2A.!!$F2 5427
2 TraesCS2D01G378300 chr2B 566623447 566631273 7826 False 2506.666667 7114 90.281667 131 5431 3 chr2B.!!$F1 5300

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
977 1000 0.037232 AAAGGAAGAAGACGAGGCGG 60.037 55.000 0.0 0.0 0.00 6.13 F
1050 1073 2.158755 ACCTCGCAATCCTTTATCCCTG 60.159 50.000 0.0 0.0 0.00 4.45 F
1594 1640 2.361789 ACACACTAAAACGTGCCTGTT 58.638 42.857 0.0 0.0 38.45 3.16 F
2879 2937 2.467566 AGTACGGCCGAAACATCTTT 57.532 45.000 35.9 8.5 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2866 2924 2.927553 ATCAGCAAAGATGTTTCGGC 57.072 45.000 0.00 0.00 0.00 5.54 R
2879 2937 6.489700 TCTGAAATGGTTACAGAAAATCAGCA 59.510 34.615 0.00 0.00 37.66 4.41 R
3234 3292 0.032403 TGCCATTTGAAGTGCAGCAC 59.968 50.000 18.55 18.55 34.10 4.40 R
4529 4614 0.384725 CTGCAACTCTGAAAACCGCG 60.385 55.000 0.00 0.00 0.00 6.46 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
28 29 1.808945 GTGTGGCATCTTCTGAAGTGG 59.191 52.381 16.43 11.00 0.00 4.00
29 30 0.807496 GTGGCATCTTCTGAAGTGGC 59.193 55.000 25.16 25.16 36.43 5.01
30 31 0.694771 TGGCATCTTCTGAAGTGGCT 59.305 50.000 28.39 10.99 36.65 4.75
31 32 1.339438 TGGCATCTTCTGAAGTGGCTC 60.339 52.381 28.39 20.53 36.65 4.70
32 33 1.005340 GCATCTTCTGAAGTGGCTCG 58.995 55.000 16.43 2.68 0.00 5.03
81 87 9.530633 GAACTAATACGGACTAGAATGACAAAT 57.469 33.333 0.00 0.00 0.00 2.32
102 117 1.532523 TTTCATCACCATTCTGCGCA 58.467 45.000 10.98 10.98 0.00 6.09
120 135 3.058224 GCGCAAACCTATCATAACCCATC 60.058 47.826 0.30 0.00 0.00 3.51
129 144 9.438163 AACCTATCATAACCCATCATGAATTTT 57.562 29.630 0.00 0.00 34.96 1.82
147 162 5.869753 ATTTTGTACACTGAGATCACAGC 57.130 39.130 18.71 4.60 41.06 4.40
172 187 6.397217 AGCACCCCTAATAAACTCCTAAAA 57.603 37.500 0.00 0.00 0.00 1.52
249 264 2.743636 ACAACTCTGCGCTAAAGCTA 57.256 45.000 9.73 0.00 39.32 3.32
266 281 2.761208 AGCTACTACTTCACCGAAGCAT 59.239 45.455 3.67 0.00 42.79 3.79
270 285 5.008415 GCTACTACTTCACCGAAGCATACTA 59.992 44.000 3.67 0.00 42.79 1.82
296 311 1.641123 CCGCTAAATTCGTGGGCGTT 61.641 55.000 0.00 0.00 43.57 4.84
308 323 0.542805 TGGGCGTTGGGTAGTATTCC 59.457 55.000 0.00 0.00 0.00 3.01
644 659 3.495629 GCTATGGTGATCTTCTCATGGCA 60.496 47.826 15.46 0.00 41.58 4.92
647 668 4.776435 TGGTGATCTTCTCATGGCAATA 57.224 40.909 0.00 0.00 35.97 1.90
674 695 1.529438 TGTTCGGTCAAATGAGTTCGC 59.471 47.619 0.00 0.00 0.00 4.70
722 744 4.379221 GACGGTCGTCGAGGAATG 57.621 61.111 9.78 7.77 42.43 2.67
723 745 1.226603 GACGGTCGTCGAGGAATGG 60.227 63.158 9.78 4.73 42.43 3.16
724 746 2.104331 CGGTCGTCGAGGAATGGG 59.896 66.667 9.78 0.00 42.43 4.00
725 747 2.202892 GGTCGTCGAGGAATGGGC 60.203 66.667 9.78 0.00 0.00 5.36
726 748 2.202892 GTCGTCGAGGAATGGGCC 60.203 66.667 9.78 0.00 0.00 5.80
858 880 2.630098 TGTGACAGAAGAGGAGTTGGAG 59.370 50.000 0.00 0.00 0.00 3.86
977 1000 0.037232 AAAGGAAGAAGACGAGGCGG 60.037 55.000 0.00 0.00 0.00 6.13
979 1002 2.184579 GAAGAAGACGAGGCGGGG 59.815 66.667 0.00 0.00 0.00 5.73
1050 1073 2.158755 ACCTCGCAATCCTTTATCCCTG 60.159 50.000 0.00 0.00 0.00 4.45
1358 1403 4.508124 CAGGATTACGCATGAAACTAGGAC 59.492 45.833 0.00 0.00 0.00 3.85
1373 1418 4.315803 ACTAGGACGACAGTGAAAAATGG 58.684 43.478 0.00 0.00 0.00 3.16
1549 1595 9.473007 TGTTTTGGATATTTCAATATGGACTGA 57.527 29.630 0.00 0.00 31.96 3.41
1594 1640 2.361789 ACACACTAAAACGTGCCTGTT 58.638 42.857 0.00 0.00 38.45 3.16
1601 1647 5.049680 CACTAAAACGTGCCTGTTTACATCT 60.050 40.000 4.10 0.00 41.01 2.90
1691 1738 9.384682 CGTACCAAAATATAAGACGTTTTTGTT 57.615 29.630 15.79 7.73 37.36 2.83
1699 1746 9.620660 AATATAAGACGTTTTTGTTGGCTAAAG 57.379 29.630 0.00 0.00 0.00 1.85
1850 1897 5.356426 TCGACTCTGTTGTCATTTCTGAAA 58.644 37.500 5.15 5.15 36.82 2.69
2047 2095 7.556733 TTTTTGGACAGAAAGTGTTATACGT 57.443 32.000 0.00 0.00 40.56 3.57
2072 2120 5.901552 AGTTTGGTGTGATTGTTTAACTGG 58.098 37.500 0.00 0.00 0.00 4.00
2078 2126 4.522789 GTGTGATTGTTTAACTGGTGGGAT 59.477 41.667 0.00 0.00 0.00 3.85
2096 2144 8.493607 TGGTGGGATATGTTACATATCATATGG 58.506 37.037 33.02 0.00 37.37 2.74
2277 2326 9.823647 AGTACTGGAATGTTACTTTCATGATAG 57.176 33.333 11.18 11.18 0.00 2.08
2475 2524 3.312697 TCTTGATACTCTGATGGACGACG 59.687 47.826 0.00 0.00 0.00 5.12
2634 2686 7.333423 TGCTGTTATTCGTTAGCAATAAGAGTT 59.667 33.333 10.42 0.00 42.60 3.01
2666 2718 6.974622 GGATAATGTGTGTCATTTCCATGAAC 59.025 38.462 0.00 0.00 43.33 3.18
2866 2924 4.715527 AAGTTTCTAGCAGGTAGTACGG 57.284 45.455 6.54 0.00 0.00 4.02
2879 2937 2.467566 AGTACGGCCGAAACATCTTT 57.532 45.000 35.90 8.50 0.00 2.52
3104 3162 3.812053 GCTACATCATCGATGCCTCTTTT 59.188 43.478 20.81 3.08 43.15 2.27
3234 3292 2.164219 AGGTGCGGATTTAACTTGCATG 59.836 45.455 0.00 0.00 37.93 4.06
3289 3348 2.907910 ATCTTCTGTTCACATTGCGC 57.092 45.000 0.00 0.00 0.00 6.09
3299 3358 4.504461 TGTTCACATTGCGCGTTTAATTTT 59.496 33.333 8.43 0.00 0.00 1.82
3332 3391 7.095774 GCTTACTCAAAGATAAAACGACTGTCA 60.096 37.037 8.73 0.00 37.38 3.58
3406 3465 9.859427 TCAAAATGAACATATTTGTCCAGATTC 57.141 29.630 14.94 0.00 34.06 2.52
3427 3486 1.417517 TCTGCCTGAAAACTGAGCTGA 59.582 47.619 0.00 0.00 0.00 4.26
3655 3714 6.891908 ACTCAAGGAAAGGTACATATTTGCAT 59.108 34.615 10.16 0.00 0.00 3.96
3965 4045 7.450014 TGGCTGATTTTATCAAGGTTTCTTACA 59.550 33.333 0.00 0.00 39.11 2.41
3988 4068 5.699097 TTTGACCTGTAACTGTAAATGCC 57.301 39.130 0.00 0.00 0.00 4.40
3993 4073 4.781087 ACCTGTAACTGTAAATGCCTCCTA 59.219 41.667 0.00 0.00 0.00 2.94
4000 4080 5.201243 ACTGTAAATGCCTCCTATTTTCCC 58.799 41.667 0.00 0.00 0.00 3.97
4002 4082 5.200483 TGTAAATGCCTCCTATTTTCCCAG 58.800 41.667 0.00 0.00 0.00 4.45
4009 4089 4.324331 GCCTCCTATTTTCCCAGTTACTGT 60.324 45.833 11.68 0.00 0.00 3.55
4074 4154 1.270571 GCCCAGCTGAGCTAAGATACC 60.271 57.143 17.39 0.00 36.40 2.73
4217 4297 4.377897 ACGAGAAGTTTTTACTCACCCAG 58.622 43.478 0.00 0.00 0.00 4.45
4352 4432 2.094182 ACGCGACACAGTCCTAAATGAT 60.094 45.455 15.93 0.00 0.00 2.45
4400 4480 1.196808 CCCATGTTCGTTTCGGAAGTG 59.803 52.381 0.00 0.00 0.00 3.16
4480 4560 0.315382 GCGAAATCTGAATGACCGCG 60.315 55.000 0.00 0.00 33.95 6.46
4481 4561 0.315382 CGAAATCTGAATGACCGCGC 60.315 55.000 0.00 0.00 0.00 6.86
4486 4566 3.459378 CTGAATGACCGCGCATGCC 62.459 63.158 13.15 3.98 38.08 4.40
4632 4730 1.067582 CTCGTAGGGTCGCCATTCC 59.932 63.158 0.00 0.00 0.00 3.01
4642 4740 3.496870 GGGTCGCCATTCCATCTTTCTAT 60.497 47.826 0.00 0.00 0.00 1.98
4694 4792 4.260170 GAGTGGATGCTTTGTCTTCAGAT 58.740 43.478 0.00 0.00 0.00 2.90
4714 4812 5.919707 CAGATCTTCCTGAATCATACACGAG 59.080 44.000 0.00 0.00 36.29 4.18
4737 4835 1.408422 GAAAACCAACACGATGCTGC 58.592 50.000 0.00 0.00 0.00 5.25
4744 4842 1.129251 CAACACGATGCTGCTACTTGG 59.871 52.381 0.00 0.00 0.00 3.61
4771 4869 3.012518 GGCTGCATCTGTTTGACTATGT 58.987 45.455 0.50 0.00 0.00 2.29
4773 4871 3.438087 GCTGCATCTGTTTGACTATGTGT 59.562 43.478 0.00 0.00 0.00 3.72
4776 4874 4.821260 TGCATCTGTTTGACTATGTGTTGT 59.179 37.500 0.00 0.00 0.00 3.32
4786 4884 5.165676 TGACTATGTGTTGTCGTATGGTTC 58.834 41.667 0.00 0.00 36.10 3.62
4846 4946 2.804572 CGGCATCTCGATTCCAAGTGAT 60.805 50.000 0.00 0.00 0.00 3.06
4879 4979 0.654683 CTTAGTCAAGATGCTGCCGC 59.345 55.000 0.00 0.00 33.20 6.53
4946 5046 6.642950 CGAAGCCATCTTTATTCTGTACTAGG 59.357 42.308 0.00 0.00 31.48 3.02
4947 5047 7.439108 AAGCCATCTTTATTCTGTACTAGGT 57.561 36.000 0.00 0.00 0.00 3.08
4948 5048 7.439108 AGCCATCTTTATTCTGTACTAGGTT 57.561 36.000 0.00 0.00 0.00 3.50
4950 5050 8.329502 AGCCATCTTTATTCTGTACTAGGTTTT 58.670 33.333 0.00 0.00 0.00 2.43
4953 5053 7.916914 TCTTTATTCTGTACTAGGTTTTGGC 57.083 36.000 0.00 0.00 0.00 4.52
4954 5054 6.592607 TCTTTATTCTGTACTAGGTTTTGGCG 59.407 38.462 0.00 0.00 0.00 5.69
4973 5102 2.734670 CGTAGTCACCACGAGTTGAAA 58.265 47.619 0.00 0.00 41.91 2.69
4981 5110 4.020573 TCACCACGAGTTGAAATATCCTGT 60.021 41.667 0.00 0.00 0.00 4.00
4982 5111 5.186215 TCACCACGAGTTGAAATATCCTGTA 59.814 40.000 0.00 0.00 0.00 2.74
4983 5112 5.520288 CACCACGAGTTGAAATATCCTGTAG 59.480 44.000 0.00 0.00 0.00 2.74
4996 5125 4.732672 ATCCTGTAGTCGGGTTAACTTC 57.267 45.455 5.42 0.00 40.77 3.01
5022 5151 0.249155 TTGAGTGAACCACGTCGTCC 60.249 55.000 0.00 0.00 39.64 4.79
5027 5156 1.361271 GAACCACGTCGTCCACTCA 59.639 57.895 0.00 0.00 0.00 3.41
5029 5158 0.319555 AACCACGTCGTCCACTCATG 60.320 55.000 0.00 0.00 0.00 3.07
5078 5207 2.520741 GGCTCCTCCTCCTCCTCG 60.521 72.222 0.00 0.00 0.00 4.63
5124 5253 1.746470 CGAAGGGGTGGTTTGGTATC 58.254 55.000 0.00 0.00 0.00 2.24
5132 5261 0.322098 TGGTTTGGTATCCAGCGTGG 60.322 55.000 0.00 0.00 39.43 4.94
5151 5280 3.716195 TGACCGGTCCATGGCTGG 61.716 66.667 31.19 24.43 44.64 4.85
5190 5319 4.616181 AAAAATATCTGCCGAAAGTCCG 57.384 40.909 0.00 0.00 0.00 4.79
5198 5327 2.646719 CGAAAGTCCGTCGGTCCA 59.353 61.111 11.88 0.00 34.85 4.02
5199 5328 1.214589 CGAAAGTCCGTCGGTCCAT 59.785 57.895 11.88 0.00 34.85 3.41
5200 5329 1.076533 CGAAAGTCCGTCGGTCCATG 61.077 60.000 11.88 0.00 34.85 3.66
5201 5330 0.739813 GAAAGTCCGTCGGTCCATGG 60.740 60.000 11.88 4.97 0.00 3.66
5202 5331 2.798148 AAAGTCCGTCGGTCCATGGC 62.798 60.000 11.88 1.78 0.00 4.40
5222 5469 1.548269 CTGGGCCGAGAGAGGATATTC 59.452 57.143 9.58 0.00 0.00 1.75
5250 5497 1.668101 AAAACGTCAGGCCCGCAAAA 61.668 50.000 0.00 0.00 0.00 2.44
5279 5526 4.938080 AGTCTATGCTAAGACCAATCACG 58.062 43.478 13.35 0.00 45.86 4.35
5309 7936 4.465305 TCTCTGGCCTAACAAGTTAGTACC 59.535 45.833 16.34 16.40 40.59 3.34
5419 8046 5.644644 GTGGAAATTTATTCAGTCCAGCAG 58.355 41.667 0.00 0.00 39.02 4.24
5432 8059 2.872408 CAGCAGGTGGGTGGTAATG 58.128 57.895 0.00 0.00 41.32 1.90
5433 8060 0.038166 CAGCAGGTGGGTGGTAATGT 59.962 55.000 0.00 0.00 41.32 2.71
5434 8061 0.777446 AGCAGGTGGGTGGTAATGTT 59.223 50.000 0.00 0.00 0.00 2.71
5435 8062 0.887933 GCAGGTGGGTGGTAATGTTG 59.112 55.000 0.00 0.00 0.00 3.33
5436 8063 1.544724 CAGGTGGGTGGTAATGTTGG 58.455 55.000 0.00 0.00 0.00 3.77
5437 8064 1.074727 CAGGTGGGTGGTAATGTTGGA 59.925 52.381 0.00 0.00 0.00 3.53
5438 8065 1.783979 AGGTGGGTGGTAATGTTGGAA 59.216 47.619 0.00 0.00 0.00 3.53
5439 8066 2.178106 AGGTGGGTGGTAATGTTGGAAA 59.822 45.455 0.00 0.00 0.00 3.13
5440 8067 2.966516 GGTGGGTGGTAATGTTGGAAAA 59.033 45.455 0.00 0.00 0.00 2.29
5441 8068 3.580895 GGTGGGTGGTAATGTTGGAAAAT 59.419 43.478 0.00 0.00 0.00 1.82
5442 8069 4.773149 GGTGGGTGGTAATGTTGGAAAATA 59.227 41.667 0.00 0.00 0.00 1.40
5443 8070 5.423931 GGTGGGTGGTAATGTTGGAAAATAT 59.576 40.000 0.00 0.00 0.00 1.28
5444 8071 6.337356 GTGGGTGGTAATGTTGGAAAATATG 58.663 40.000 0.00 0.00 0.00 1.78
5445 8072 6.153680 GTGGGTGGTAATGTTGGAAAATATGA 59.846 38.462 0.00 0.00 0.00 2.15
5446 8073 6.153680 TGGGTGGTAATGTTGGAAAATATGAC 59.846 38.462 0.00 0.00 0.00 3.06
5447 8074 6.406512 GGGTGGTAATGTTGGAAAATATGACC 60.407 42.308 0.00 0.00 30.50 4.02
5448 8075 6.379988 GGTGGTAATGTTGGAAAATATGACCT 59.620 38.462 4.06 0.00 30.94 3.85
5449 8076 7.558444 GGTGGTAATGTTGGAAAATATGACCTA 59.442 37.037 4.06 0.00 30.94 3.08
5450 8077 8.962679 GTGGTAATGTTGGAAAATATGACCTAA 58.037 33.333 4.06 0.00 30.94 2.69
5451 8078 9.535170 TGGTAATGTTGGAAAATATGACCTAAA 57.465 29.630 4.06 0.00 30.94 1.85
5454 8081 6.524101 TGTTGGAAAATATGACCTAAAGGC 57.476 37.500 0.00 0.00 39.32 4.35
5455 8082 6.013379 TGTTGGAAAATATGACCTAAAGGCA 58.987 36.000 0.00 0.00 39.32 4.75
5456 8083 6.495181 TGTTGGAAAATATGACCTAAAGGCAA 59.505 34.615 0.00 0.00 39.32 4.52
5457 8084 7.180051 TGTTGGAAAATATGACCTAAAGGCAAT 59.820 33.333 0.00 0.00 39.32 3.56
5458 8085 8.691797 GTTGGAAAATATGACCTAAAGGCAATA 58.308 33.333 0.00 0.00 39.32 1.90
5459 8086 8.830915 TGGAAAATATGACCTAAAGGCAATAA 57.169 30.769 0.00 0.00 39.32 1.40
5460 8087 9.432982 TGGAAAATATGACCTAAAGGCAATAAT 57.567 29.630 0.00 0.00 39.32 1.28
5468 8095 8.602472 TGACCTAAAGGCAATAATAAAATGGT 57.398 30.769 0.00 0.00 39.32 3.55
5469 8096 9.041354 TGACCTAAAGGCAATAATAAAATGGTT 57.959 29.630 0.00 0.00 39.32 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.937620 TCAGAAGATGCCACACTACAAATC 59.062 41.667 0.00 0.00 0.00 2.17
1 2 4.910195 TCAGAAGATGCCACACTACAAAT 58.090 39.130 0.00 0.00 0.00 2.32
2 3 4.350368 TCAGAAGATGCCACACTACAAA 57.650 40.909 0.00 0.00 0.00 2.83
81 87 2.295629 TGCGCAGAATGGTGATGAAAAA 59.704 40.909 5.66 0.00 35.86 1.94
102 117 9.438163 AAATTCATGATGGGTTATGATAGGTTT 57.562 29.630 0.00 0.00 33.68 3.27
120 135 7.809665 TGTGATCTCAGTGTACAAAATTCATG 58.190 34.615 0.00 0.00 0.00 3.07
129 144 2.159382 TCGCTGTGATCTCAGTGTACA 58.841 47.619 28.19 13.69 43.68 2.90
147 162 2.434702 AGGAGTTTATTAGGGGTGCTCG 59.565 50.000 0.00 0.00 0.00 5.03
172 187 3.285484 CAAGGAGGATGTTGCTGCTTAT 58.715 45.455 0.00 0.00 43.89 1.73
217 232 3.221771 CAGAGTTGTTTGGGGTTGATGA 58.778 45.455 0.00 0.00 0.00 2.92
218 233 2.288395 GCAGAGTTGTTTGGGGTTGATG 60.288 50.000 0.00 0.00 0.00 3.07
219 234 1.963515 GCAGAGTTGTTTGGGGTTGAT 59.036 47.619 0.00 0.00 0.00 2.57
249 264 5.909621 TTAGTATGCTTCGGTGAAGTAGT 57.090 39.130 8.23 0.58 41.27 2.73
266 281 6.919662 CCACGAATTTAGCGGTAGATTTAGTA 59.080 38.462 11.20 0.00 0.00 1.82
270 285 3.875134 CCCACGAATTTAGCGGTAGATTT 59.125 43.478 11.20 0.00 0.00 2.17
296 311 1.910671 AGGTTTGCGGAATACTACCCA 59.089 47.619 4.80 0.00 0.00 4.51
308 323 2.097038 CAGCTCCTCGAGGTTTGCG 61.097 63.158 30.17 21.26 38.40 4.85
384 399 2.126071 AAGTCCATCCGCGACACG 60.126 61.111 8.23 0.00 43.15 4.49
588 603 3.492311 GATCCCGAGCAGCTCCGAC 62.492 68.421 17.16 4.41 0.00 4.79
644 659 6.406370 TCATTTGACCGAACACATCTCTATT 58.594 36.000 0.00 0.00 0.00 1.73
647 668 4.248859 CTCATTTGACCGAACACATCTCT 58.751 43.478 0.00 0.00 0.00 3.10
674 695 0.944386 CGTGACAAGTCCAAACTGGG 59.056 55.000 0.00 0.00 38.32 4.45
1258 1286 6.938596 ACTAGTAACCACAAGGGAAAATGTAC 59.061 38.462 0.00 0.00 41.15 2.90
1358 1403 5.098893 TGAAAACACCATTTTTCACTGTCG 58.901 37.500 6.88 0.00 45.99 4.35
1386 1431 7.072961 TGCTAGAGGGGAAATCTAATCTGATTT 59.927 37.037 8.38 2.62 45.83 2.17
1549 1595 5.547465 TGTTCACTCATTTCAGTCCGTATT 58.453 37.500 0.00 0.00 0.00 1.89
1618 1664 5.753438 TCCGTTCACAGATATAAGATGTTGC 59.247 40.000 0.00 0.00 0.00 4.17
1619 1665 6.422100 CCTCCGTTCACAGATATAAGATGTTG 59.578 42.308 0.00 0.00 0.00 3.33
1632 1678 1.893801 AGTTACTCCCTCCGTTCACAG 59.106 52.381 0.00 0.00 0.00 3.66
2041 2089 7.966246 AACAATCACACCAAACTAACGTATA 57.034 32.000 0.00 0.00 0.00 1.47
2042 2090 6.870971 AACAATCACACCAAACTAACGTAT 57.129 33.333 0.00 0.00 0.00 3.06
2047 2095 7.122948 ACCAGTTAAACAATCACACCAAACTAA 59.877 33.333 0.00 0.00 0.00 2.24
2072 2120 7.445402 GGCCATATGATATGTAACATATCCCAC 59.555 40.741 11.20 0.24 37.53 4.61
2078 2126 8.390143 ACAAAGGGCCATATGATATGTAACATA 58.610 33.333 6.18 0.00 34.27 2.29
2380 2429 9.710900 AAAAACTTGTTCAAGAAAGAATCAACT 57.289 25.926 17.75 0.00 0.00 3.16
2526 2575 5.057149 AGTGCTCGGAATTTGGTATATGTC 58.943 41.667 0.00 0.00 0.00 3.06
2634 2686 7.362834 GGAAATGACACACATTATCCAATGACA 60.363 37.037 4.46 0.00 46.90 3.58
2666 2718 8.644318 TTTAAGTATCTAGAAAGCGGCTAAAG 57.356 34.615 1.35 0.00 0.00 1.85
2709 2761 4.832266 AGGTACCATGTTTGCTCATCAAAA 59.168 37.500 15.94 0.00 45.35 2.44
2866 2924 2.927553 ATCAGCAAAGATGTTTCGGC 57.072 45.000 0.00 0.00 0.00 5.54
2879 2937 6.489700 TCTGAAATGGTTACAGAAAATCAGCA 59.510 34.615 0.00 0.00 37.66 4.41
3104 3162 1.412079 ACATCAGCTGGCACCAAAAA 58.588 45.000 15.13 0.00 0.00 1.94
3234 3292 0.032403 TGCCATTTGAAGTGCAGCAC 59.968 50.000 18.55 18.55 34.10 4.40
3289 3348 5.934921 AGTAAGCCCTCGAAAAATTAAACG 58.065 37.500 0.00 0.00 0.00 3.60
3299 3358 5.670792 TTATCTTTGAGTAAGCCCTCGAA 57.329 39.130 0.00 0.00 34.44 3.71
3332 3391 3.261643 TCATATAACCATCAGGCGCAGAT 59.738 43.478 10.83 9.49 39.06 2.90
3406 3465 1.805345 CAGCTCAGTTTTCAGGCAGAG 59.195 52.381 0.00 0.00 0.00 3.35
3427 3486 7.772292 ACAAGCAATAAGATATCACTGTGATGT 59.228 33.333 28.67 23.69 37.70 3.06
3965 4045 6.010219 AGGCATTTACAGTTACAGGTCAAAT 58.990 36.000 0.00 0.00 0.00 2.32
3988 4068 9.543783 GTATTACAGTAACTGGGAAAATAGGAG 57.456 37.037 0.00 0.00 35.51 3.69
4031 4111 1.518903 AAACCTTTCCGCTCTGCAGC 61.519 55.000 9.47 0.00 42.96 5.25
4074 4154 5.344884 GTTAGGGAACAGAAGATCTTCTCG 58.655 45.833 30.93 26.07 46.13 4.04
4098 4178 5.432645 GCTTCCTGCTTCTTCTATTAACCT 58.567 41.667 0.00 0.00 38.95 3.50
4140 4220 1.460273 GGGCTCAAAACCCTGCGAAA 61.460 55.000 0.00 0.00 44.68 3.46
4165 4245 1.621992 AGACCTCAGCTCTTCGACAA 58.378 50.000 0.00 0.00 0.00 3.18
4217 4297 0.863144 TGTACGCCTTGTCGCTTTTC 59.137 50.000 0.00 0.00 0.00 2.29
4271 4351 4.599500 ACCAGCCACCCCCTCAGT 62.599 66.667 0.00 0.00 0.00 3.41
4334 4414 2.609459 GGCATCATTTAGGACTGTGTCG 59.391 50.000 0.00 0.00 32.65 4.35
4352 4432 2.632028 GCTCTCCATCTTCTGATAGGCA 59.368 50.000 0.00 0.00 0.00 4.75
4480 4560 2.899339 GCTCTTCCTCCGGCATGC 60.899 66.667 9.90 9.90 0.00 4.06
4481 4561 1.817099 GTGCTCTTCCTCCGGCATG 60.817 63.158 0.00 0.00 37.05 4.06
4486 4566 1.153939 CGACAGTGCTCTTCCTCCG 60.154 63.158 0.00 0.00 0.00 4.63
4529 4614 0.384725 CTGCAACTCTGAAAACCGCG 60.385 55.000 0.00 0.00 0.00 6.46
4593 4690 6.019152 CGAGTGACGAAAGACAAAAGAAAAA 58.981 36.000 0.00 0.00 45.77 1.94
4632 4730 5.873712 ACACTGCACTGAAGATAGAAAGATG 59.126 40.000 0.00 0.00 0.00 2.90
4642 4740 5.047377 TGTCATACATACACTGCACTGAAGA 60.047 40.000 0.00 0.00 0.00 2.87
4694 4792 5.221322 CCATCTCGTGTATGATTCAGGAAGA 60.221 44.000 0.00 0.00 31.09 2.87
4737 4835 0.615331 TGCAGCCTCCTTCCAAGTAG 59.385 55.000 0.00 0.00 0.00 2.57
4744 4842 1.471684 CAAACAGATGCAGCCTCCTTC 59.528 52.381 0.00 0.00 0.00 3.46
4776 4874 1.730121 GCACGAAGTCGAACCATACGA 60.730 52.381 7.87 0.00 41.61 3.43
4786 4884 1.901173 CACGATACGCACGAAGTCG 59.099 57.895 0.00 0.00 41.61 4.18
4791 4889 2.277057 CTCGCACGATACGCACGA 60.277 61.111 0.00 0.00 36.43 4.35
4846 4946 0.613260 ACTAAGATGCGGCAGTTCCA 59.387 50.000 9.25 0.00 34.01 3.53
4879 4979 2.219445 CGCGTGATTATGTCATCCACTG 59.781 50.000 0.00 0.00 39.48 3.66
4932 5032 5.797051 ACGCCAAAACCTAGTACAGAATAA 58.203 37.500 0.00 0.00 0.00 1.40
4943 5043 2.460757 GGTGACTACGCCAAAACCTA 57.539 50.000 0.00 0.00 45.14 3.08
4953 5053 2.410785 TTCAACTCGTGGTGACTACG 57.589 50.000 15.53 15.53 42.56 3.51
4954 5054 5.519206 GGATATTTCAACTCGTGGTGACTAC 59.481 44.000 4.39 0.00 0.00 2.73
4973 5102 5.303845 GGAAGTTAACCCGACTACAGGATAT 59.696 44.000 0.88 0.00 0.00 1.63
4996 5125 1.333619 CGTGGTTCACTCAAACTTGGG 59.666 52.381 0.00 0.00 31.34 4.12
5022 5151 1.738365 CGCTCTGGAAGACCATGAGTG 60.738 57.143 0.00 0.00 45.87 3.51
5027 5156 2.185350 CGCGCTCTGGAAGACCAT 59.815 61.111 5.56 0.00 45.87 3.55
5029 5158 2.507324 GTCGCGCTCTGGAAGACC 60.507 66.667 5.56 0.00 38.67 3.85
5067 5196 0.681564 GAACTCTGCGAGGAGGAGGA 60.682 60.000 9.75 0.00 38.98 3.71
5068 5197 0.682855 AGAACTCTGCGAGGAGGAGG 60.683 60.000 9.75 0.00 38.98 4.30
5069 5198 0.738389 GAGAACTCTGCGAGGAGGAG 59.262 60.000 9.75 0.00 39.94 3.69
5070 5199 1.027255 CGAGAACTCTGCGAGGAGGA 61.027 60.000 9.75 0.00 37.63 3.71
5071 5200 1.431440 CGAGAACTCTGCGAGGAGG 59.569 63.158 9.75 0.00 37.63 4.30
5072 5201 1.226547 GCGAGAACTCTGCGAGGAG 60.227 63.158 9.75 5.33 39.09 3.69
5073 5202 2.878429 GCGAGAACTCTGCGAGGA 59.122 61.111 9.75 0.00 33.35 3.71
5074 5203 2.578178 CGCGAGAACTCTGCGAGG 60.578 66.667 24.22 6.49 46.81 4.63
5078 5207 0.387367 TTGTCTCGCGAGAACTCTGC 60.387 55.000 38.20 24.88 41.32 4.26
5092 5221 1.674057 CCTTCGGTCTGGCTTGTCT 59.326 57.895 0.00 0.00 0.00 3.41
5093 5222 1.376037 CCCTTCGGTCTGGCTTGTC 60.376 63.158 0.00 0.00 0.00 3.18
5112 5241 0.802494 CACGCTGGATACCAAACCAC 59.198 55.000 0.00 0.00 30.80 4.16
5113 5242 0.322098 CCACGCTGGATACCAAACCA 60.322 55.000 0.00 0.00 40.96 3.67
5114 5243 1.029947 CCCACGCTGGATACCAAACC 61.030 60.000 5.71 0.00 40.96 3.27
5115 5244 0.322187 ACCCACGCTGGATACCAAAC 60.322 55.000 5.71 0.00 40.96 2.93
5116 5245 0.322098 CACCCACGCTGGATACCAAA 60.322 55.000 5.71 0.00 40.96 3.28
5117 5246 1.195442 TCACCCACGCTGGATACCAA 61.195 55.000 5.71 0.00 40.96 3.67
5120 5249 1.153429 GGTCACCCACGCTGGATAC 60.153 63.158 5.71 0.13 40.96 2.24
5132 5261 3.717294 AGCCATGGACCGGTCACC 61.717 66.667 34.40 20.63 0.00 4.02
5187 5316 3.770040 CAGCCATGGACCGACGGA 61.770 66.667 23.38 0.00 0.00 4.69
5201 5330 0.902516 ATATCCTCTCTCGGCCCAGC 60.903 60.000 0.00 0.00 0.00 4.85
5202 5331 1.548269 GAATATCCTCTCTCGGCCCAG 59.452 57.143 0.00 0.00 0.00 4.45
5250 5497 4.467795 TGGTCTTAGCATAGACTCTTTGCT 59.532 41.667 22.66 22.66 46.84 3.91
5279 5526 2.514803 TGTTAGGCCAGAGAAAAAGCC 58.485 47.619 5.01 0.00 46.13 4.35
5309 7936 8.511321 GTGATACTAGTGATCATCAAGTAGGAG 58.489 40.741 5.39 0.00 35.81 3.69
5385 8012 9.289303 CTGAATAAATTTCCACCTTATTCGTTG 57.711 33.333 0.00 0.00 41.67 4.10
5396 8023 5.393461 CCTGCTGGACTGAATAAATTTCCAC 60.393 44.000 2.92 0.00 32.79 4.02
5419 8046 2.296073 TTCCAACATTACCACCCACC 57.704 50.000 0.00 0.00 0.00 4.61
5431 8058 6.013379 TGCCTTTAGGTCATATTTTCCAACA 58.987 36.000 0.00 0.00 37.57 3.33
5432 8059 6.524101 TGCCTTTAGGTCATATTTTCCAAC 57.476 37.500 0.00 0.00 37.57 3.77
5433 8060 7.732222 ATTGCCTTTAGGTCATATTTTCCAA 57.268 32.000 0.00 0.00 37.57 3.53
5434 8061 8.830915 TTATTGCCTTTAGGTCATATTTTCCA 57.169 30.769 0.00 0.00 37.57 3.53
5442 8069 9.212593 ACCATTTTATTATTGCCTTTAGGTCAT 57.787 29.630 0.00 0.00 37.57 3.06
5443 8070 8.602472 ACCATTTTATTATTGCCTTTAGGTCA 57.398 30.769 0.00 0.00 37.57 4.02


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

AutoCloner maintained by Alex Coulton.