Multiple sequence alignment - TraesCS1B01G011800

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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 TraesCS1B01G011800 chr1B 100.000 5332 0 0 1 5332 5695043 5700374 0.000000e+00 9847.0
1 TraesCS1B01G011800 chr1B 88.027 5053 541 29 1 5034 6060593 6065600 0.000000e+00 5921.0
2 TraesCS1B01G011800 chr1B 88.394 4360 425 46 25 4337 6487595 6483270 0.000000e+00 5173.0
3 TraesCS1B01G011800 chr1B 86.813 4383 495 47 25 4367 7256816 7252477 0.000000e+00 4815.0
4 TraesCS1B01G011800 chr1B 86.639 4094 502 32 1 4072 629652844 629656914 0.000000e+00 4488.0
5 TraesCS1B01G011800 chr1B 89.340 2955 308 5 1 2950 6281268 6284220 0.000000e+00 3705.0
6 TraesCS1B01G011800 chr1B 84.536 3117 418 40 2 3103 22714373 22711306 0.000000e+00 3027.0
7 TraesCS1B01G011800 chr1B 84.860 2074 271 28 1 2061 5986060 5988103 0.000000e+00 2050.0
8 TraesCS1B01G011800 chr1B 86.922 1277 130 16 3649 4906 6284914 6286172 0.000000e+00 1399.0
9 TraesCS1B01G011800 chr1B 84.326 1327 176 19 25 1345 29951367 29950067 0.000000e+00 1269.0
10 TraesCS1B01G011800 chr1B 88.264 1031 94 7 3325 4337 5757563 5758584 0.000000e+00 1208.0
11 TraesCS1B01G011800 chr1B 86.497 1022 83 20 4069 5074 629661883 629662865 0.000000e+00 1072.0
12 TraesCS1B01G011800 chr1B 87.134 785 70 12 4383 5164 7698167 7697411 0.000000e+00 861.0
13 TraesCS1B01G011800 chr1B 89.862 434 40 3 4641 5074 22666219 22665790 6.030000e-154 555.0
14 TraesCS1B01G011800 chr1B 83.919 541 67 15 4736 5272 7345149 7345673 2.870000e-137 499.0
15 TraesCS1B01G011800 chr1B 88.424 406 31 6 4091 4481 7341332 7341736 4.830000e-130 475.0
16 TraesCS1B01G011800 chr1B 79.305 604 91 13 1 593 6405036 6405616 5.010000e-105 392.0
17 TraesCS1B01G011800 chr1B 94.444 126 5 2 4514 4638 6483134 6483010 5.450000e-45 193.0
18 TraesCS1B01G011800 chr1B 84.416 154 9 6 4704 4857 6482990 6482852 2.590000e-28 137.0
19 TraesCS1B01G011800 chr1B 95.238 84 4 0 4771 4854 5758949 5759032 3.350000e-27 134.0
20 TraesCS1B01G011800 chr1B 88.889 90 9 1 5076 5164 629662963 629663052 5.650000e-20 110.0
21 TraesCS1B01G011800 chr1B 96.610 59 2 0 5274 5332 7697295 7697237 1.220000e-16 99.0
22 TraesCS1B01G011800 chr1D 89.262 4135 390 31 289 4388 77380 73265 0.000000e+00 5127.0
23 TraesCS1B01G011800 chr1D 88.007 4119 451 24 1 4112 5135089 5131007 0.000000e+00 4830.0
24 TraesCS1B01G011800 chr1D 86.895 2686 289 32 1987 4661 3972948 3970315 0.000000e+00 2952.0
25 TraesCS1B01G011800 chr1D 84.699 1098 122 23 3295 4366 4217849 4216772 0.000000e+00 1055.0
26 TraesCS1B01G011800 chr1D 87.666 827 93 8 3335 4160 4236195 4235377 0.000000e+00 953.0
27 TraesCS1B01G011800 chr1D 98.305 59 1 0 5274 5332 4762522 4762464 2.630000e-18 104.0
28 TraesCS1B01G011800 chr1D 85.870 92 12 1 5072 5162 4201143 4201052 4.400000e-16 97.1
29 TraesCS1B01G011800 chr1D 87.342 79 7 1 4977 5055 4202679 4202604 2.650000e-13 87.9
30 TraesCS1B01G011800 chr1D 94.643 56 2 1 5110 5164 4762769 4762714 9.510000e-13 86.1
31 TraesCS1B01G011800 chr1A 88.297 4110 429 30 25 4112 6341108 6337029 0.000000e+00 4878.0
32 TraesCS1B01G011800 chr1A 88.111 3869 403 39 1 3848 5505860 5502028 0.000000e+00 4543.0
33 TraesCS1B01G011800 chr1A 82.466 2863 434 37 1 2830 4550044 4552871 0.000000e+00 2444.0
34 TraesCS1B01G011800 chr1A 84.693 2071 277 20 1 2061 4497890 4499930 0.000000e+00 2032.0
35 TraesCS1B01G011800 chr1A 88.703 1496 148 11 2629 4112 4500504 4501990 0.000000e+00 1807.0
36 TraesCS1B01G011800 chr1A 88.604 1404 142 13 2663 4049 4504746 4506148 0.000000e+00 1690.0
37 TraesCS1B01G011800 chr1A 86.413 1472 133 27 3589 5037 6294905 6293478 0.000000e+00 1548.0
38 TraesCS1B01G011800 chr1A 85.124 1452 190 17 1 1442 6012399 6010964 0.000000e+00 1461.0


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 TraesCS1B01G011800 chr1B 5695043 5700374 5331 False 9847.000000 9847 100.000000 1 5332 1 chr1B.!!$F1 5331
1 TraesCS1B01G011800 chr1B 6060593 6065600 5007 False 5921.000000 5921 88.027000 1 5034 1 chr1B.!!$F3 5033
2 TraesCS1B01G011800 chr1B 7252477 7256816 4339 True 4815.000000 4815 86.813000 25 4367 1 chr1B.!!$R1 4342
3 TraesCS1B01G011800 chr1B 629652844 629656914 4070 False 4488.000000 4488 86.639000 1 4072 1 chr1B.!!$F5 4071
4 TraesCS1B01G011800 chr1B 22711306 22714373 3067 True 3027.000000 3027 84.536000 2 3103 1 chr1B.!!$R3 3101
5 TraesCS1B01G011800 chr1B 6281268 6286172 4904 False 2552.000000 3705 88.131000 1 4906 2 chr1B.!!$F7 4905
6 TraesCS1B01G011800 chr1B 5986060 5988103 2043 False 2050.000000 2050 84.860000 1 2061 1 chr1B.!!$F2 2060
7 TraesCS1B01G011800 chr1B 6482852 6487595 4743 True 1834.333333 5173 89.084667 25 4857 3 chr1B.!!$R5 4832
8 TraesCS1B01G011800 chr1B 29950067 29951367 1300 True 1269.000000 1269 84.326000 25 1345 1 chr1B.!!$R4 1320
9 TraesCS1B01G011800 chr1B 5757563 5759032 1469 False 671.000000 1208 91.751000 3325 4854 2 chr1B.!!$F6 1529
10 TraesCS1B01G011800 chr1B 629661883 629663052 1169 False 591.000000 1072 87.693000 4069 5164 2 chr1B.!!$F9 1095
11 TraesCS1B01G011800 chr1B 7341332 7345673 4341 False 487.000000 499 86.171500 4091 5272 2 chr1B.!!$F8 1181
12 TraesCS1B01G011800 chr1B 7697237 7698167 930 True 480.000000 861 91.872000 4383 5332 2 chr1B.!!$R6 949
13 TraesCS1B01G011800 chr1B 6405036 6405616 580 False 392.000000 392 79.305000 1 593 1 chr1B.!!$F4 592
14 TraesCS1B01G011800 chr1D 73265 77380 4115 True 5127.000000 5127 89.262000 289 4388 1 chr1D.!!$R1 4099
15 TraesCS1B01G011800 chr1D 5131007 5135089 4082 True 4830.000000 4830 88.007000 1 4112 1 chr1D.!!$R5 4111
16 TraesCS1B01G011800 chr1D 3970315 3972948 2633 True 2952.000000 2952 86.895000 1987 4661 1 chr1D.!!$R2 2674
17 TraesCS1B01G011800 chr1D 4216772 4217849 1077 True 1055.000000 1055 84.699000 3295 4366 1 chr1D.!!$R3 1071
18 TraesCS1B01G011800 chr1D 4235377 4236195 818 True 953.000000 953 87.666000 3335 4160 1 chr1D.!!$R4 825
19 TraesCS1B01G011800 chr1A 6337029 6341108 4079 True 4878.000000 4878 88.297000 25 4112 1 chr1A.!!$R4 4087
20 TraesCS1B01G011800 chr1A 5502028 5505860 3832 True 4543.000000 4543 88.111000 1 3848 1 chr1A.!!$R1 3847
21 TraesCS1B01G011800 chr1A 4550044 4552871 2827 False 2444.000000 2444 82.466000 1 2830 1 chr1A.!!$F1 2829
22 TraesCS1B01G011800 chr1A 4497890 4506148 8258 False 1843.000000 2032 87.333333 1 4112 3 chr1A.!!$F2 4111
23 TraesCS1B01G011800 chr1A 6293478 6294905 1427 True 1548.000000 1548 86.413000 3589 5037 1 chr1A.!!$R3 1448
24 TraesCS1B01G011800 chr1A 6010964 6012399 1435 True 1461.000000 1461 85.124000 1 1442 1 chr1A.!!$R2 1441

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
808 827 0.035630 AGGTCTGTCTTCAGCATGGC 60.036 55.0 0.00 0.00 41.10 4.40 F
2544 2816 0.035725 TTCAGAGATGGGCTGCAGTG 60.036 55.0 16.64 2.78 33.45 3.66 F
3260 3800 0.114168 AGGAGTCAGCACCTGAGAGT 59.886 55.0 0.00 0.00 41.46 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2736 3008 0.324943 CTTCGACCACACCCCATCTT 59.675 55.0 0.0 0.00 0.00 2.40 R
3882 4428 0.178301 GGGAAGCTAGGGTACTGCAC 59.822 60.0 0.0 0.00 0.00 4.57 R
4712 6315 0.385974 CTGCGGCACAGTTAAGTTGC 60.386 55.0 0.0 8.21 41.86 4.17 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
23 24 2.876091 TGAAACGCAGACTTCCTATCG 58.124 47.619 0.00 0.00 0.00 2.92
223 224 6.834168 TTTGATGTGATAAAACTCTTCCCC 57.166 37.500 0.00 0.00 0.00 4.81
241 242 0.655733 CCACTCACAACCGTGTTGTC 59.344 55.000 16.37 0.00 44.02 3.18
245 246 1.257936 CTCACAACCGTGTTGTCTTCG 59.742 52.381 16.37 8.34 44.02 3.79
246 247 1.003851 CACAACCGTGTTGTCTTCGT 58.996 50.000 16.37 0.00 38.41 3.85
250 251 1.567504 ACCGTGTTGTCTTCGTTCAG 58.432 50.000 0.00 0.00 0.00 3.02
323 324 1.404391 CAGAGATGCATGACTTTGGGC 59.596 52.381 2.46 0.00 0.00 5.36
337 338 0.112995 TTGGGCTGAGGCAGACATTT 59.887 50.000 8.68 0.00 42.18 2.32
397 401 4.020543 AGGAGTGGAGACAGACAGATTAC 58.979 47.826 0.00 0.00 44.46 1.89
416 420 1.001520 ACGTCATCATCGACCCACAAA 59.998 47.619 0.00 0.00 31.91 2.83
418 422 2.094258 CGTCATCATCGACCCACAAAAG 59.906 50.000 0.00 0.00 31.91 2.27
439 443 0.622136 TTGCCAGCAGATCCAGACAT 59.378 50.000 0.00 0.00 0.00 3.06
593 606 5.452078 AATTCAGAAGCATTTTCCGTTGA 57.548 34.783 0.00 0.00 0.00 3.18
727 740 1.896660 GAAACTGGTCAGCGGGCAA 60.897 57.895 0.00 0.00 0.00 4.52
769 788 5.306678 GGATGATGTCTGGAATAGAGAGGTT 59.693 44.000 0.00 0.00 35.70 3.50
808 827 0.035630 AGGTCTGTCTTCAGCATGGC 60.036 55.000 0.00 0.00 41.10 4.40
809 828 0.321919 GGTCTGTCTTCAGCATGGCA 60.322 55.000 0.00 0.00 41.10 4.92
812 831 1.978712 CTGTCTTCAGCATGGCAGCG 61.979 60.000 0.00 0.00 40.15 5.18
823 842 4.394712 GGCAGCGTGGGTAGTGCT 62.395 66.667 0.00 0.00 40.16 4.40
872 891 3.577848 AGTTGCTGAAATTATGGGTGCAA 59.422 39.130 0.00 0.00 36.74 4.08
873 892 3.591196 TGCTGAAATTATGGGTGCAAC 57.409 42.857 0.00 0.00 0.00 4.17
905 927 7.972277 CCTACAATCTCAATGTTTTGAAGGATG 59.028 37.037 0.00 0.00 41.22 3.51
1003 1026 3.603532 TGGTGAGATTGTGAAGAGATGC 58.396 45.455 0.00 0.00 0.00 3.91
1055 1085 4.954202 TGGATCTGTACTTCGTACCAAGAT 59.046 41.667 7.27 6.68 38.14 2.40
1194 1224 3.861689 GCTTTGCTTTCTGTGCCATATTC 59.138 43.478 0.00 0.00 0.00 1.75
1219 1249 6.461509 CCCCAAGGATTACAAGATTAATGTGC 60.462 42.308 0.00 0.00 33.47 4.57
1223 1253 7.798596 AGGATTACAAGATTAATGTGCAGAG 57.201 36.000 0.00 0.00 32.27 3.35
1458 1512 3.701205 TGTGTTGCTGTGACTATGGAT 57.299 42.857 0.00 0.00 0.00 3.41
1459 1513 4.817318 TGTGTTGCTGTGACTATGGATA 57.183 40.909 0.00 0.00 0.00 2.59
1529 1583 9.667107 TTTATCATGTAAAGGAACAGAAGGTAG 57.333 33.333 0.00 0.00 31.70 3.18
1582 1636 3.130869 TGCCATTCAAACACTGATATGCC 59.869 43.478 0.00 0.00 32.78 4.40
1584 1638 4.381825 GCCATTCAAACACTGATATGCCAA 60.382 41.667 0.00 0.00 32.78 4.52
1804 1858 6.940867 GGACCTTTCCTACTGTTGTTATCTTT 59.059 38.462 0.00 0.00 39.13 2.52
1828 1882 2.919229 CGACTTCCAATGCAAATGAAGC 59.081 45.455 17.43 11.62 38.17 3.86
1868 1922 3.448660 CACCTCTACACTCATGGATGTCA 59.551 47.826 6.09 0.00 0.00 3.58
1921 1975 1.329256 ACTCACTAACCTGCAGACGT 58.671 50.000 17.39 1.80 0.00 4.34
2302 2463 5.048083 CCAAAACTGAAGGTGCTTATGCTAA 60.048 40.000 1.96 0.00 40.48 3.09
2303 2464 6.350445 CCAAAACTGAAGGTGCTTATGCTAAT 60.350 38.462 1.96 0.00 40.48 1.73
2472 2744 5.014202 GGTCAAGGTGGTTATACATTGGTT 58.986 41.667 0.00 0.00 41.29 3.67
2537 2809 1.474855 GGAGAGCTTTCAGAGATGGGC 60.475 57.143 6.59 0.00 0.00 5.36
2544 2816 0.035725 TTCAGAGATGGGCTGCAGTG 60.036 55.000 16.64 2.78 33.45 3.66
2565 2837 3.322254 TGGAAGAGACTCAAGGAGAACAC 59.678 47.826 5.02 0.00 33.32 3.32
2569 2841 5.652994 AGAGACTCAAGGAGAACACATAC 57.347 43.478 5.02 0.00 33.32 2.39
2619 2891 2.293122 TGAGAAATGCCCAAAGTTGACG 59.707 45.455 0.00 0.00 0.00 4.35
2719 2991 5.741673 GCCTTAAAGGTGCTCAAAATGGAAA 60.742 40.000 0.00 0.00 37.80 3.13
2728 3000 3.742882 GCTCAAAATGGAAAACTTGGAGC 59.257 43.478 0.00 0.00 0.00 4.70
2736 3008 2.100087 GGAAAACTTGGAGCGGTTTCAA 59.900 45.455 0.00 0.00 35.02 2.69
2747 3019 1.616159 CGGTTTCAAAGATGGGGTGT 58.384 50.000 0.00 0.00 0.00 4.16
2748 3020 1.269448 CGGTTTCAAAGATGGGGTGTG 59.731 52.381 0.00 0.00 0.00 3.82
2757 3029 2.536997 GATGGGGTGTGGTCGAAGGG 62.537 65.000 0.00 0.00 0.00 3.95
2796 3077 6.873076 AGCTTGAGAAACTATCAGTTCAGAAG 59.127 38.462 0.00 0.00 37.47 2.85
2802 3284 2.237392 ACTATCAGTTCAGAAGTGCCCC 59.763 50.000 12.62 0.00 0.00 5.80
2820 3302 4.415179 TGCCCCAAGATGATAGATTTACCA 59.585 41.667 0.00 0.00 0.00 3.25
2841 3323 1.604278 GAGGCACCAAAACTCAGTGTC 59.396 52.381 0.00 0.00 36.37 3.67
2845 3327 3.630312 GGCACCAAAACTCAGTGTCTTAA 59.370 43.478 0.00 0.00 33.37 1.85
2882 3364 2.032675 GGCAAGAGATCTCCGATTTTGC 59.967 50.000 26.64 26.64 35.99 3.68
2895 3377 8.908786 TCTCCGATTTTGCAGATAGATATTTT 57.091 30.769 0.00 0.00 0.00 1.82
2922 3404 9.246670 TCTTCATTGACCAAACTGATATTGAAT 57.753 29.630 0.00 0.00 0.00 2.57
2998 3538 2.154462 ACAGCAAGGAGAAATGGAACG 58.846 47.619 0.00 0.00 0.00 3.95
3018 3558 3.195825 ACGAGAAATCCCCTCTTACAGTG 59.804 47.826 0.00 0.00 0.00 3.66
3123 3663 6.604396 TGGAAATTGATAGATGTGATGTGCTT 59.396 34.615 0.00 0.00 0.00 3.91
3185 3725 7.331026 TCCTTGAGGACATTAGTGATTACAAG 58.669 38.462 0.00 0.00 39.78 3.16
3260 3800 0.114168 AGGAGTCAGCACCTGAGAGT 59.886 55.000 0.00 0.00 41.46 3.24
3625 4165 1.152830 GGTGGGCTCCAGAAACCAA 59.847 57.895 0.00 0.00 32.34 3.67
3655 4195 2.503356 ACCTCCATAAGCAGAAGTCCTG 59.497 50.000 0.00 0.00 45.67 3.86
3674 4214 2.753043 CATGCCAGAGCCACCACC 60.753 66.667 0.00 0.00 38.69 4.61
3676 4216 3.574074 ATGCCAGAGCCACCACCAC 62.574 63.158 0.00 0.00 38.69 4.16
3776 4322 3.062466 TGGGACTCTCCGTCTGCG 61.062 66.667 0.00 0.00 42.44 5.18
3882 4428 5.335504 GCTGGAAGTCCTTGATCTTCAAAAG 60.336 44.000 0.00 0.00 40.98 2.27
3894 4440 4.967084 TCTTCAAAAGTGCAGTACCCTA 57.033 40.909 0.00 0.00 0.00 3.53
3897 4443 2.637872 TCAAAAGTGCAGTACCCTAGCT 59.362 45.455 0.00 0.00 0.00 3.32
3937 4483 4.036852 CGCAAGTATACATGTCTCTCTGGA 59.963 45.833 0.00 0.00 0.00 3.86
4011 4560 0.613853 AGCAACTGGGCAGCATTGAT 60.614 50.000 0.00 0.00 35.83 2.57
4015 4564 1.028330 ACTGGGCAGCATTGATGACG 61.028 55.000 6.01 0.00 0.00 4.35
4017 4566 0.745486 TGGGCAGCATTGATGACGAG 60.745 55.000 6.01 0.00 0.00 4.18
4055 4604 3.256631 GCCCATTATGAAGGTATGCTTGG 59.743 47.826 0.00 0.00 0.00 3.61
4168 4722 9.887406 GTTTGTTCTCCATTATTTTACTTTCGA 57.113 29.630 0.00 0.00 0.00 3.71
4211 4796 1.028130 TTGTTCTGACGCCATTTGCA 58.972 45.000 0.00 0.00 41.33 4.08
4338 4938 2.795329 CCATGCAGGAGTAAACAGGTT 58.205 47.619 0.00 0.00 41.22 3.50
4367 5030 3.297134 TGTAGAAAGGGCATGGATTCC 57.703 47.619 0.00 0.00 0.00 3.01
4368 5031 2.580322 TGTAGAAAGGGCATGGATTCCA 59.420 45.455 8.08 8.08 38.19 3.53
4535 5460 5.506686 TGTGTGTCTGTGAGCTATCTATC 57.493 43.478 0.00 0.00 0.00 2.08
4570 5496 6.035542 TGTTTTTGCTTTGCTTAGTTAACTGC 59.964 34.615 18.56 14.00 0.00 4.40
4588 5515 3.006537 ACTGCGAAGACACTAGCCTTTAA 59.993 43.478 0.00 0.00 0.00 1.52
4635 5716 5.022021 GTGGCTTTTATCTGTCGATTTTCG 58.978 41.667 0.00 0.00 42.10 3.46
4650 5731 0.759959 TTTCGTGGTTGACAGGCCTA 59.240 50.000 3.98 0.00 35.01 3.93
4665 5746 1.683385 GGCCTAATCCCTGATTGTTGC 59.317 52.381 0.00 0.49 33.95 4.17
4666 5747 2.659428 GCCTAATCCCTGATTGTTGCT 58.341 47.619 0.00 0.00 33.95 3.91
4667 5748 2.620585 GCCTAATCCCTGATTGTTGCTC 59.379 50.000 0.00 0.00 33.95 4.26
4668 5749 3.686691 GCCTAATCCCTGATTGTTGCTCT 60.687 47.826 0.00 0.00 33.95 4.09
4697 6297 1.070445 CTGCTCTGCTAGGGGAATGAG 59.930 57.143 0.00 0.00 0.00 2.90
4702 6302 1.211457 CTGCTAGGGGAATGAGCTGTT 59.789 52.381 0.00 0.00 37.12 3.16
4712 6315 4.201990 GGGAATGAGCTGTTATTGCTTCTG 60.202 45.833 0.00 0.00 41.30 3.02
4795 8639 3.782244 GCTGCTTGGCGTCGAGTG 61.782 66.667 6.07 0.68 0.00 3.51
4854 8698 4.008330 CTCATCTTGATCTGGTTTGCTGT 58.992 43.478 0.00 0.00 0.00 4.40
4857 8701 3.554934 TCTTGATCTGGTTTGCTGTTGT 58.445 40.909 0.00 0.00 0.00 3.32
4984 10098 2.737252 GCTCCGTTAAACTCTGACCTTG 59.263 50.000 0.00 0.00 0.00 3.61
5015 11643 7.665559 TGTTATTAAAGATTCAGACACTTGCCT 59.334 33.333 0.00 0.00 0.00 4.75
5016 11644 6.749923 ATTAAAGATTCAGACACTTGCCTC 57.250 37.500 0.00 0.00 0.00 4.70
5074 11702 8.382405 TGCCATATATATTTCTAGTTTCAGCCA 58.618 33.333 0.00 0.00 0.00 4.75
5081 11805 8.773033 ATATTTCTAGTTTCAGCCATTTCCAT 57.227 30.769 0.00 0.00 0.00 3.41
5096 11820 6.514048 GCCATTTCCATATCAAGTACAAGCTC 60.514 42.308 0.00 0.00 0.00 4.09
5168 11893 8.942669 CGCAAGTTTTACAGACATATAAAACA 57.057 30.769 17.29 0.00 46.59 2.83
5169 11894 9.554724 CGCAAGTTTTACAGACATATAAAACAT 57.445 29.630 17.29 6.86 46.59 2.71
5210 11970 6.927294 ATATACAGTTAAGCAGCAGTTTCC 57.073 37.500 0.00 0.00 0.00 3.13
5212 11972 3.142174 ACAGTTAAGCAGCAGTTTCCTC 58.858 45.455 0.00 0.00 0.00 3.71
5240 12029 0.938008 GATGGTTAAGTAGCAGCCGC 59.062 55.000 0.00 0.00 37.73 6.53
5259 12048 1.475403 CAGGTATCAGTCAGTCCGGT 58.525 55.000 0.00 0.00 0.00 5.28
5260 12049 2.651455 CAGGTATCAGTCAGTCCGGTA 58.349 52.381 0.00 0.00 0.00 4.02
5262 12051 2.241685 AGGTATCAGTCAGTCCGGTACT 59.758 50.000 0.00 0.30 39.81 2.73
5267 12056 2.035449 TCAGTCAGTCCGGTACTTGTTG 59.965 50.000 0.00 2.40 35.76 3.33
5310 12099 1.197264 CTCTGCTCTGCTGCAAAACTC 59.803 52.381 3.02 0.00 42.83 3.01
5312 12101 0.949397 TGCTCTGCTGCAAAACTCTG 59.051 50.000 3.02 0.00 40.29 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 0.888619 TCAGTGATGACGTCCAGGAC 59.111 55.000 14.12 9.92 0.00 3.85
241 242 3.190874 GCTACCCATTCTCTGAACGAAG 58.809 50.000 0.00 0.00 0.00 3.79
245 246 2.680339 GCTTGCTACCCATTCTCTGAAC 59.320 50.000 0.00 0.00 0.00 3.18
246 247 2.573462 AGCTTGCTACCCATTCTCTGAA 59.427 45.455 0.00 0.00 0.00 3.02
250 251 3.772060 CAAAGCTTGCTACCCATTCTC 57.228 47.619 0.00 0.00 0.00 2.87
323 324 2.624838 ACACCAAAAATGTCTGCCTCAG 59.375 45.455 0.00 0.00 0.00 3.35
337 338 4.072131 GCCTCAACTGATTAGACACCAAA 58.928 43.478 0.00 0.00 0.00 3.28
346 347 2.637382 TGGTGTCTGCCTCAACTGATTA 59.363 45.455 0.00 0.00 0.00 1.75
385 389 4.335594 TCGATGATGACGTAATCTGTCTGT 59.664 41.667 14.13 0.00 37.26 3.41
397 401 1.720805 TTTGTGGGTCGATGATGACG 58.279 50.000 0.00 0.00 39.83 4.35
416 420 1.562942 TCTGGATCTGCTGGCAATCTT 59.437 47.619 13.16 0.00 0.00 2.40
418 422 1.307097 GTCTGGATCTGCTGGCAATC 58.693 55.000 0.00 3.60 0.00 2.67
465 469 4.351874 TTGCTAGCTTCACCAAGTAGTT 57.648 40.909 17.23 0.00 31.45 2.24
593 606 1.882989 GAGACGCAGACCCAGAGCTT 61.883 60.000 0.00 0.00 0.00 3.74
769 788 3.308402 CCTTCAGCCTTTCCCACTTATGA 60.308 47.826 0.00 0.00 0.00 2.15
809 828 2.040009 AACACAGCACTACCCACGCT 62.040 55.000 0.00 0.00 36.10 5.07
812 831 1.226746 GTCAACACAGCACTACCCAC 58.773 55.000 0.00 0.00 0.00 4.61
872 891 9.003658 CAAAACATTGAGATTGTAGGTTCTAGT 57.996 33.333 0.00 0.00 0.00 2.57
873 892 9.219603 TCAAAACATTGAGATTGTAGGTTCTAG 57.780 33.333 0.00 0.00 0.00 2.43
919 941 9.890352 GAACTGAATGCTCTATCCAAAATAATC 57.110 33.333 0.00 0.00 0.00 1.75
926 948 5.423290 TCTCTGAACTGAATGCTCTATCCAA 59.577 40.000 0.00 0.00 0.00 3.53
1003 1026 0.460987 CAGCTAAAGGAGAGCCACGG 60.461 60.000 0.00 0.00 41.06 4.94
1055 1085 1.339055 CCTTCCATTCTTCCACGCTGA 60.339 52.381 0.00 0.00 0.00 4.26
1194 1224 6.461509 GCACATTAATCTTGTAATCCTTGGGG 60.462 42.308 0.00 0.00 0.00 4.96
1458 1512 4.278170 CCAAGCCACTCAATTTCACTTGTA 59.722 41.667 0.00 0.00 33.00 2.41
1459 1513 3.068590 CCAAGCCACTCAATTTCACTTGT 59.931 43.478 0.00 0.00 33.00 3.16
1557 1611 2.655090 TCAGTGTTTGAATGGCAGGA 57.345 45.000 0.00 0.00 31.34 3.86
1582 1636 4.808077 ATGAGCTTCGCATATGACTTTG 57.192 40.909 6.97 0.00 0.00 2.77
1584 1638 4.445453 TCAATGAGCTTCGCATATGACTT 58.555 39.130 6.97 0.00 0.00 3.01
1804 1858 5.449041 GCTTCATTTGCATTGGAAGTCGATA 60.449 40.000 17.62 0.00 39.10 2.92
1868 1922 2.617532 GGAGGCATGCTCTTCAACTTCT 60.618 50.000 18.92 1.11 0.00 2.85
1921 1975 1.039068 CCTGCCACAAACCATGTCAA 58.961 50.000 0.00 0.00 41.46 3.18
1999 2155 7.706100 TCTCTATCTGACGTAGCTCTAGATA 57.294 40.000 0.00 0.00 31.19 1.98
2302 2463 7.501559 CCATCTCTCAAAATCCAACAGATGTAT 59.498 37.037 0.00 0.00 35.85 2.29
2303 2464 6.825213 CCATCTCTCAAAATCCAACAGATGTA 59.175 38.462 0.00 0.00 35.85 2.29
2452 2613 5.047377 AGCAAACCAATGTATAACCACCTTG 60.047 40.000 0.00 0.00 0.00 3.61
2537 2809 2.612471 CCTTGAGTCTCTTCCACTGCAG 60.612 54.545 13.48 13.48 0.00 4.41
2544 2816 3.322254 TGTGTTCTCCTTGAGTCTCTTCC 59.678 47.826 0.65 0.00 0.00 3.46
2565 2837 4.020218 TCCTCCAGACAAGGAAACAGTATG 60.020 45.833 0.00 0.00 39.99 2.39
2619 2891 0.676782 ATGGTGCTTCAGGTAACGCC 60.677 55.000 0.00 0.00 46.39 5.68
2719 2991 2.650322 TCTTTGAAACCGCTCCAAGTT 58.350 42.857 0.00 0.00 0.00 2.66
2728 3000 1.269448 CACACCCCATCTTTGAAACCG 59.731 52.381 0.00 0.00 0.00 4.44
2736 3008 0.324943 CTTCGACCACACCCCATCTT 59.675 55.000 0.00 0.00 0.00 2.40
2747 3019 2.500229 GAAACAATGTCCCTTCGACCA 58.500 47.619 0.00 0.00 41.18 4.02
2748 3020 1.810755 GGAAACAATGTCCCTTCGACC 59.189 52.381 0.00 0.00 41.18 4.79
2757 3029 4.067896 TCTCAAGCTGAGGAAACAATGTC 58.932 43.478 11.63 0.00 44.39 3.06
2796 3077 4.762251 GGTAAATCTATCATCTTGGGGCAC 59.238 45.833 0.00 0.00 0.00 5.01
2802 3284 6.426328 GTGCCTCTGGTAAATCTATCATCTTG 59.574 42.308 0.00 0.00 0.00 3.02
2820 3302 1.212935 ACACTGAGTTTTGGTGCCTCT 59.787 47.619 0.00 0.00 34.70 3.69
2845 3327 8.829373 ATCTCTTGCCTACCATCTTTAATTTT 57.171 30.769 0.00 0.00 0.00 1.82
2859 3341 4.697514 CAAAATCGGAGATCTCTTGCCTA 58.302 43.478 21.81 0.00 45.12 3.93
2861 3343 2.032675 GCAAAATCGGAGATCTCTTGCC 59.967 50.000 25.26 10.72 45.12 4.52
2895 3377 8.634335 TCAATATCAGTTTGGTCAATGAAGAA 57.366 30.769 0.00 0.00 0.00 2.52
2917 3399 8.735315 TGTTGTTTCTGTGTTTTCTAGATTCAA 58.265 29.630 0.00 0.00 0.00 2.69
2922 3404 7.768582 TCTGATGTTGTTTCTGTGTTTTCTAGA 59.231 33.333 0.00 0.00 0.00 2.43
2998 3538 5.363939 CATCACTGTAAGAGGGGATTTCTC 58.636 45.833 0.00 0.00 37.43 2.87
3018 3558 2.251409 TGCAGCATCTTAGCTCCATC 57.749 50.000 0.00 0.00 44.54 3.51
3123 3663 0.397941 CTTTCTCTGGCCAGTGGACA 59.602 55.000 31.58 19.17 39.14 4.02
3185 3725 1.442769 TCCAGTCAGATTTTCGCAGC 58.557 50.000 0.00 0.00 0.00 5.25
3260 3800 5.808366 TTCTAAGCAAAGAGACTCCAGAA 57.192 39.130 0.00 0.00 0.00 3.02
3625 4165 4.777896 TCTGCTTATGGAGGTAGTGACTTT 59.222 41.667 0.00 0.00 32.15 2.66
3655 4195 2.042831 GTGGTGGCTCTGGCATGAC 61.043 63.158 0.00 0.00 40.92 3.06
3776 4322 0.321122 CAGTCTCTTGAGGGGTGCAC 60.321 60.000 8.80 8.80 0.00 4.57
3882 4428 0.178301 GGGAAGCTAGGGTACTGCAC 59.822 60.000 0.00 0.00 0.00 4.57
3894 4440 1.222936 CTCATTCGGCAGGGAAGCT 59.777 57.895 0.00 0.00 34.17 3.74
3897 4443 2.272146 GGCTCATTCGGCAGGGAA 59.728 61.111 0.00 0.00 0.00 3.97
3937 4483 3.956848 GGGCAGCCTCTAATTTCAAGATT 59.043 43.478 12.43 0.00 0.00 2.40
4011 4560 5.399858 GCATCTAGTTCTTTGTACTCGTCA 58.600 41.667 0.00 0.00 0.00 4.35
4015 4564 5.086104 TGGGCATCTAGTTCTTTGTACTC 57.914 43.478 0.00 0.00 0.00 2.59
4017 4566 7.715249 TCATAATGGGCATCTAGTTCTTTGTAC 59.285 37.037 0.00 0.00 0.00 2.90
4055 4604 2.605366 GCAAAGATAGAAGGACGTGCTC 59.395 50.000 10.99 4.17 0.00 4.26
4338 4938 2.109128 TGCCCTTTCTACATGGTTTCCA 59.891 45.455 0.00 0.00 38.19 3.53
4367 5030 6.671190 TCTTGTACATTGTTCAGAGCAATTG 58.329 36.000 9.65 0.00 34.68 2.32
4368 5031 6.882610 TCTTGTACATTGTTCAGAGCAATT 57.117 33.333 9.65 5.20 34.68 2.32
4470 5135 1.207089 CTACTGAACCGGGCAGATTCA 59.793 52.381 27.04 16.60 36.86 2.57
4535 5460 6.546395 AGCAAAGCAAAAACAGATAGATACG 58.454 36.000 0.00 0.00 0.00 3.06
4570 5496 6.147164 TGAACAATTAAAGGCTAGTGTCTTCG 59.853 38.462 0.00 0.00 37.09 3.79
4635 5716 1.682087 GGGATTAGGCCTGTCAACCAC 60.682 57.143 17.99 0.00 0.00 4.16
4650 5731 4.018597 AGAGAAGAGCAACAATCAGGGATT 60.019 41.667 0.00 0.00 31.86 3.01
4665 5746 1.470285 GCAGAGCAGAGCAGAGAAGAG 60.470 57.143 0.00 0.00 0.00 2.85
4666 5747 0.531657 GCAGAGCAGAGCAGAGAAGA 59.468 55.000 0.00 0.00 0.00 2.87
4667 5748 0.533491 AGCAGAGCAGAGCAGAGAAG 59.467 55.000 0.00 0.00 0.00 2.85
4668 5749 1.750206 CTAGCAGAGCAGAGCAGAGAA 59.250 52.381 0.00 0.00 0.00 2.87
4712 6315 0.385974 CTGCGGCACAGTTAAGTTGC 60.386 55.000 0.00 8.21 41.86 4.17
4778 8622 3.782244 CACTCGACGCCAAGCAGC 61.782 66.667 0.00 0.00 0.00 5.25
4795 8639 5.558818 AGGATGTTGATTCAGATATGCTCC 58.441 41.667 0.00 0.00 0.00 4.70
4854 8698 0.756294 TTCCTCGCTTGACTGGACAA 59.244 50.000 0.00 0.00 0.00 3.18
4857 8701 0.756294 TGTTTCCTCGCTTGACTGGA 59.244 50.000 0.00 0.00 0.00 3.86
4960 10074 2.338500 GTCAGAGTTTAACGGAGCAGG 58.662 52.381 0.00 0.00 0.00 4.85
5007 10729 3.368236 GCTTCTACTAAACGAGGCAAGTG 59.632 47.826 0.00 0.00 33.09 3.16
5015 11643 2.532843 ACCCCAGCTTCTACTAAACGA 58.467 47.619 0.00 0.00 0.00 3.85
5016 11644 3.446516 AGTACCCCAGCTTCTACTAAACG 59.553 47.826 0.00 0.00 0.00 3.60
5060 11688 7.345691 TGATATGGAAATGGCTGAAACTAGAA 58.654 34.615 0.00 0.00 0.00 2.10
5074 11702 5.760253 CCGAGCTTGTACTTGATATGGAAAT 59.240 40.000 0.00 0.00 0.00 2.17
5081 11805 4.755411 CCTTTCCGAGCTTGTACTTGATA 58.245 43.478 0.00 0.00 0.00 2.15
5096 11820 0.613777 AGACCACCTAAGCCTTTCCG 59.386 55.000 0.00 0.00 0.00 4.30
5106 11830 3.071023 CCAGAAAGTTCACAGACCACCTA 59.929 47.826 0.00 0.00 0.00 3.08
5210 11970 5.175856 GCTACTTAACCATCTTACATGCGAG 59.824 44.000 0.00 0.00 0.00 5.03
5212 11972 4.808895 TGCTACTTAACCATCTTACATGCG 59.191 41.667 0.00 0.00 0.00 4.73
5240 12029 1.475403 ACCGGACTGACTGATACCTG 58.525 55.000 9.46 0.00 0.00 4.00
5245 12034 2.526432 ACAAGTACCGGACTGACTGAT 58.474 47.619 9.46 0.00 38.87 2.90
5254 12043 1.979308 TCCCATTCAACAAGTACCGGA 59.021 47.619 9.46 0.00 0.00 5.14
5259 12048 4.020573 ACTGTCGATCCCATTCAACAAGTA 60.021 41.667 0.00 0.00 0.00 2.24
5260 12049 3.244561 ACTGTCGATCCCATTCAACAAGT 60.245 43.478 0.00 0.00 0.00 3.16
5262 12051 3.417069 ACTGTCGATCCCATTCAACAA 57.583 42.857 0.00 0.00 0.00 2.83
5267 12056 4.731773 GCAATTCAACTGTCGATCCCATTC 60.732 45.833 0.00 0.00 0.00 2.67
5310 12099 0.179020 TCCTCCACAGGCAAACACAG 60.179 55.000 0.00 0.00 40.12 3.66
5312 12101 1.620822 ATTCCTCCACAGGCAAACAC 58.379 50.000 0.00 0.00 40.12 3.32


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

AutoCloner maintained by Alex Coulton.