Multiple sequence alignment - TraesCS7A01G037400

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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 TraesCS7A01G037400 chr7A 100.000 4074 0 0 1 4074 16728356 16732429 0.000000e+00 7524.0
1 TraesCS7A01G037400 chr4A 86.377 3127 312 50 903 3956 716965016 716961931 0.000000e+00 3310.0
2 TraesCS7A01G037400 chr4A 87.057 1553 165 18 1684 3212 123767951 123766411 0.000000e+00 1722.0
3 TraesCS7A01G037400 chr4A 91.519 849 53 13 3058 3894 716960951 716960110 0.000000e+00 1151.0
4 TraesCS7A01G037400 chr4A 82.587 201 29 5 3870 4065 716961957 716961758 5.410000e-39 172.0
5 TraesCS7A01G037400 chr4A 82.212 208 14 6 3868 4074 716960069 716959884 1.520000e-34 158.0
6 TraesCS7A01G037400 chr1D 89.489 2331 212 14 903 3212 334043039 334040721 0.000000e+00 2916.0
7 TraesCS7A01G037400 chr1D 93.023 43 1 2 3525 3566 348017954 348017913 1.220000e-05 62.1
8 TraesCS7A01G037400 chr1A 88.844 2250 221 15 985 3212 431979034 431976793 0.000000e+00 2737.0
9 TraesCS7A01G037400 chr1A 95.294 85 4 0 903 987 431980323 431980239 7.100000e-28 135.0
10 TraesCS7A01G037400 chr7D 88.616 1669 156 18 710 2348 17424446 17426110 0.000000e+00 1999.0
11 TraesCS7A01G037400 chr7D 92.346 810 61 1 2344 3152 17427425 17428234 0.000000e+00 1151.0
12 TraesCS7A01G037400 chr7D 92.227 669 42 8 35 701 180796307 180795647 0.000000e+00 939.0
13 TraesCS7A01G037400 chr7D 91.154 667 56 2 35 701 241380378 241381041 0.000000e+00 902.0
14 TraesCS7A01G037400 chr6A 85.820 945 117 8 978 1915 121659015 121659949 0.000000e+00 987.0
15 TraesCS7A01G037400 chr6A 84.930 929 113 15 999 1915 121871007 121871920 0.000000e+00 915.0
16 TraesCS7A01G037400 chr6D 85.805 944 113 7 978 1915 101202176 101203104 0.000000e+00 981.0
17 TraesCS7A01G037400 chr6D 84.832 923 113 12 999 1915 101212212 101213113 0.000000e+00 904.0
18 TraesCS7A01G037400 chr6D 81.766 872 148 10 2231 3095 101203304 101204171 0.000000e+00 719.0
19 TraesCS7A01G037400 chr6D 80.915 634 119 2 2451 3083 100567617 100566985 2.190000e-137 499.0
20 TraesCS7A01G037400 chr6D 85.246 61 7 2 3505 3565 459816532 459816474 1.220000e-05 62.1
21 TraesCS7A01G037400 chr6D 92.683 41 3 0 3525 3565 218386768 218386728 4.400000e-05 60.2
22 TraesCS7A01G037400 chr6B 85.381 944 117 8 978 1915 185100001 185100929 0.000000e+00 959.0
23 TraesCS7A01G037400 chr6B 84.449 926 120 10 999 1915 185110529 185111439 0.000000e+00 891.0
24 TraesCS7A01G037400 chr6B 82.069 870 146 10 2231 3094 185101124 185101989 0.000000e+00 734.0
25 TraesCS7A01G037400 chr6B 83.168 808 129 7 2296 3097 185112524 185113330 0.000000e+00 732.0
26 TraesCS7A01G037400 chr6B 79.370 635 129 2 2450 3083 184705823 184705190 2.890000e-121 446.0
27 TraesCS7A01G037400 chr6B 95.238 42 2 0 3525 3566 632527299 632527258 2.630000e-07 67.6
28 TraesCS7A01G037400 chr2D 92.192 666 51 1 35 700 55761893 55761229 0.000000e+00 941.0
29 TraesCS7A01G037400 chr2D 91.154 667 53 5 35 701 131420402 131419742 0.000000e+00 900.0
30 TraesCS7A01G037400 chr2D 90.855 667 55 5 35 701 556197555 556198215 0.000000e+00 889.0
31 TraesCS7A01G037400 chr2B 91.304 667 55 3 35 701 588025349 588026012 0.000000e+00 907.0
32 TraesCS7A01G037400 chr2A 90.560 678 61 3 35 711 712361308 712360633 0.000000e+00 894.0
33 TraesCS7A01G037400 chr2A 90.868 668 54 6 35 701 233170224 233170885 0.000000e+00 889.0
34 TraesCS7A01G037400 chr2A 91.111 45 4 0 3518 3562 653675007 653675051 1.220000e-05 62.1
35 TraesCS7A01G037400 chr7B 90.705 667 58 3 35 701 465126818 465126156 0.000000e+00 885.0
36 TraesCS7A01G037400 chr7B 92.857 42 3 0 3525 3566 494735449 494735490 1.220000e-05 62.1
37 TraesCS7A01G037400 chr5B 97.368 38 1 0 3525 3562 447575571 447575608 9.450000e-07 65.8


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 TraesCS7A01G037400 chr7A 16728356 16732429 4073 False 7524.00 7524 100.00000 1 4074 1 chr7A.!!$F1 4073
1 TraesCS7A01G037400 chr4A 123766411 123767951 1540 True 1722.00 1722 87.05700 1684 3212 1 chr4A.!!$R1 1528
2 TraesCS7A01G037400 chr4A 716959884 716965016 5132 True 1197.75 3310 85.67375 903 4074 4 chr4A.!!$R2 3171
3 TraesCS7A01G037400 chr1D 334040721 334043039 2318 True 2916.00 2916 89.48900 903 3212 1 chr1D.!!$R1 2309
4 TraesCS7A01G037400 chr1A 431976793 431980323 3530 True 1436.00 2737 92.06900 903 3212 2 chr1A.!!$R1 2309
5 TraesCS7A01G037400 chr7D 17424446 17428234 3788 False 1575.00 1999 90.48100 710 3152 2 chr7D.!!$F2 2442
6 TraesCS7A01G037400 chr7D 180795647 180796307 660 True 939.00 939 92.22700 35 701 1 chr7D.!!$R1 666
7 TraesCS7A01G037400 chr7D 241380378 241381041 663 False 902.00 902 91.15400 35 701 1 chr7D.!!$F1 666
8 TraesCS7A01G037400 chr6A 121659015 121659949 934 False 987.00 987 85.82000 978 1915 1 chr6A.!!$F1 937
9 TraesCS7A01G037400 chr6A 121871007 121871920 913 False 915.00 915 84.93000 999 1915 1 chr6A.!!$F2 916
10 TraesCS7A01G037400 chr6D 101212212 101213113 901 False 904.00 904 84.83200 999 1915 1 chr6D.!!$F1 916
11 TraesCS7A01G037400 chr6D 101202176 101204171 1995 False 850.00 981 83.78550 978 3095 2 chr6D.!!$F2 2117
12 TraesCS7A01G037400 chr6D 100566985 100567617 632 True 499.00 499 80.91500 2451 3083 1 chr6D.!!$R1 632
13 TraesCS7A01G037400 chr6B 185100001 185101989 1988 False 846.50 959 83.72500 978 3094 2 chr6B.!!$F1 2116
14 TraesCS7A01G037400 chr6B 185110529 185113330 2801 False 811.50 891 83.80850 999 3097 2 chr6B.!!$F2 2098
15 TraesCS7A01G037400 chr6B 184705190 184705823 633 True 446.00 446 79.37000 2450 3083 1 chr6B.!!$R1 633
16 TraesCS7A01G037400 chr2D 55761229 55761893 664 True 941.00 941 92.19200 35 700 1 chr2D.!!$R1 665
17 TraesCS7A01G037400 chr2D 131419742 131420402 660 True 900.00 900 91.15400 35 701 1 chr2D.!!$R2 666
18 TraesCS7A01G037400 chr2D 556197555 556198215 660 False 889.00 889 90.85500 35 701 1 chr2D.!!$F1 666
19 TraesCS7A01G037400 chr2B 588025349 588026012 663 False 907.00 907 91.30400 35 701 1 chr2B.!!$F1 666
20 TraesCS7A01G037400 chr2A 712360633 712361308 675 True 894.00 894 90.56000 35 711 1 chr2A.!!$R1 676
21 TraesCS7A01G037400 chr2A 233170224 233170885 661 False 889.00 889 90.86800 35 701 1 chr2A.!!$F1 666
22 TraesCS7A01G037400 chr7B 465126156 465126818 662 True 885.00 885 90.70500 35 701 1 chr7B.!!$R1 666

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
579 584 0.105862 TCCCATACCCGTACCCTCTG 60.106 60.000 0.0 0.0 0.00 3.35 F
1594 2832 0.400594 CGGGGAAAGGTTCAAGAGGT 59.599 55.000 0.0 0.0 0.00 3.85 F
1753 2991 1.135139 GCTTCGAGCTCATGGAGTACA 59.865 52.381 15.4 0.0 38.45 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2526 6051 0.179129 CTTCCGCATCACATTTGGGC 60.179 55.0 0.0 0.0 0.0 5.36 R
2641 6166 0.813184 CTGGATGAAGCCGCATTGTT 59.187 50.0 0.0 0.0 0.0 2.83 R
3351 8784 1.032114 GGGGGAGAACCGAAGCATTG 61.032 60.0 0.0 0.0 41.6 2.82 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
20 21 3.609103 CTGCGTAATGTGCTTAATCCC 57.391 47.619 0.00 0.00 0.00 3.85
21 22 2.942376 CTGCGTAATGTGCTTAATCCCA 59.058 45.455 0.00 0.00 0.00 4.37
22 23 2.680841 TGCGTAATGTGCTTAATCCCAC 59.319 45.455 0.00 0.00 0.00 4.61
23 24 2.032924 GCGTAATGTGCTTAATCCCACC 59.967 50.000 0.00 0.00 0.00 4.61
24 25 2.616842 CGTAATGTGCTTAATCCCACCC 59.383 50.000 0.00 0.00 0.00 4.61
25 26 2.917713 AATGTGCTTAATCCCACCCA 57.082 45.000 0.00 0.00 0.00 4.51
26 27 3.403228 AATGTGCTTAATCCCACCCAT 57.597 42.857 0.00 0.00 0.00 4.00
27 28 2.435372 TGTGCTTAATCCCACCCATC 57.565 50.000 0.00 0.00 0.00 3.51
28 29 1.638070 TGTGCTTAATCCCACCCATCA 59.362 47.619 0.00 0.00 0.00 3.07
29 30 2.301346 GTGCTTAATCCCACCCATCAG 58.699 52.381 0.00 0.00 0.00 2.90
30 31 1.322442 GCTTAATCCCACCCATCAGC 58.678 55.000 0.00 0.00 0.00 4.26
31 32 1.986882 CTTAATCCCACCCATCAGCC 58.013 55.000 0.00 0.00 0.00 4.85
32 33 0.555769 TTAATCCCACCCATCAGCCC 59.444 55.000 0.00 0.00 0.00 5.19
33 34 1.360393 TAATCCCACCCATCAGCCCC 61.360 60.000 0.00 0.00 0.00 5.80
121 122 6.581122 ACTTACCTATCACCCATACCCATAT 58.419 40.000 0.00 0.00 0.00 1.78
137 138 4.828829 CCCATATCCGTCAAGGGTATAAC 58.171 47.826 0.00 0.00 44.38 1.89
219 221 5.685511 GCGTTTACAACACATCAATTGAGTT 59.314 36.000 14.54 9.73 39.36 3.01
358 362 9.894439 GTGACACATAAAAATGTTAAACAACAC 57.106 29.630 0.00 0.00 35.22 3.32
468 472 6.673154 AAAGTTTTTACCTAGCGCGATTAT 57.327 33.333 12.10 0.00 0.00 1.28
495 500 9.807921 GAGGGGAAAATTGATACATTAGGATAA 57.192 33.333 0.00 0.00 0.00 1.75
554 559 2.748647 GTACGCGGGCATGGGTTT 60.749 61.111 12.47 0.00 36.35 3.27
579 584 0.105862 TCCCATACCCGTACCCTCTG 60.106 60.000 0.00 0.00 0.00 3.35
605 610 3.938963 CCGATGGGTATGATATTTTCCCG 59.061 47.826 0.00 0.00 40.86 5.14
611 616 8.950007 ATGGGTATGATATTTTCCCGTTTAAT 57.050 30.769 0.00 0.00 40.86 1.40
620 625 8.770010 ATATTTTCCCGTTTAATTACCCATGA 57.230 30.769 0.00 0.00 0.00 3.07
703 709 1.692411 GGTACCCATTGCCATCCTTC 58.308 55.000 0.00 0.00 0.00 3.46
704 710 1.064017 GGTACCCATTGCCATCCTTCA 60.064 52.381 0.00 0.00 0.00 3.02
705 711 2.301346 GTACCCATTGCCATCCTTCAG 58.699 52.381 0.00 0.00 0.00 3.02
707 713 1.397390 CCCATTGCCATCCTTCAGCC 61.397 60.000 0.00 0.00 0.00 4.85
745 751 9.021807 CCTATTAATTACTAACCTCGGATCAGA 57.978 37.037 0.00 0.00 0.00 3.27
749 755 9.595823 TTAATTACTAACCTCGGATCAGAAAAG 57.404 33.333 0.00 0.00 0.00 2.27
750 756 6.600882 TTACTAACCTCGGATCAGAAAAGT 57.399 37.500 0.00 1.57 0.00 2.66
792 802 3.648339 AATTTGATTGTGCGTCAGCTT 57.352 38.095 0.00 0.00 45.42 3.74
797 807 1.532868 GATTGTGCGTCAGCTTGTTCT 59.467 47.619 0.00 0.00 45.42 3.01
816 826 2.037251 TCTGTAACACTTGTGCTCTCCC 59.963 50.000 0.10 0.00 0.00 4.30
823 833 0.901124 CTTGTGCTCTCCCTACAGCT 59.099 55.000 0.00 0.00 36.53 4.24
1053 2279 0.415429 TGGCTCTCCTCCTTCCTCTT 59.585 55.000 0.00 0.00 0.00 2.85
1072 2304 4.302455 TCTTCTTCTCTTCAAGCTCAACG 58.698 43.478 0.00 0.00 0.00 4.10
1178 2410 2.672651 CAACCCGCTCATGCACCA 60.673 61.111 0.00 0.00 39.64 4.17
1233 2465 2.093235 GCCTCTCATGTACCTCAAGCTT 60.093 50.000 0.00 0.00 0.00 3.74
1288 2520 2.418777 CTGCCCGCGAGATCATGA 59.581 61.111 8.23 0.00 0.00 3.07
1387 2625 2.316586 CCCTATGGCCCCTTGTGGT 61.317 63.158 0.00 0.00 0.00 4.16
1423 2661 1.952990 TCTGCATCCTAGAGCTTCTCG 59.047 52.381 0.00 0.00 35.36 4.04
1428 2666 2.775856 CCTAGAGCTTCTCGGCGCA 61.776 63.158 10.83 0.00 35.36 6.09
1482 2720 2.104859 CGAGGTCAGCCGACTCGTA 61.105 63.158 11.43 0.00 42.21 3.43
1486 2724 2.360726 TCAGCCGACTCGTAGCCA 60.361 61.111 0.00 0.00 0.00 4.75
1523 2761 2.401766 CCATGGAGCCTGTGAACGC 61.402 63.158 5.56 0.00 0.00 4.84
1556 2794 0.462047 GCCGTCCTCATCACCGATTT 60.462 55.000 0.00 0.00 0.00 2.17
1594 2832 0.400594 CGGGGAAAGGTTCAAGAGGT 59.599 55.000 0.00 0.00 0.00 3.85
1753 2991 1.135139 GCTTCGAGCTCATGGAGTACA 59.865 52.381 15.40 0.00 38.45 2.90
1767 3005 3.262420 GGAGTACACGATCAAGCAACAT 58.738 45.455 0.00 0.00 0.00 2.71
1807 3045 2.425592 CCTCGGTGAACAGTGCCA 59.574 61.111 0.00 0.00 0.00 4.92
1840 3084 3.412879 GACCTAGTGGACGCGCTCC 62.413 68.421 17.43 17.43 39.97 4.70
1869 3113 1.604378 CAAGGAAGGTGGCCTCGAT 59.396 57.895 3.32 0.00 33.76 3.59
1941 3198 4.263683 ACAATTTCTTAGCTTCTGCCTCCT 60.264 41.667 0.00 0.00 40.80 3.69
1960 3421 6.342111 CCTCCTCTCTTCAAGTTGTTATACC 58.658 44.000 2.11 0.00 0.00 2.73
2022 3710 7.535139 TGAAATTCGAATGGTTTGGAGATTAC 58.465 34.615 12.25 0.00 0.00 1.89
2038 3726 3.840666 AGATTACTCACCAGTCACCACAT 59.159 43.478 0.00 0.00 33.62 3.21
2051 3739 1.448540 CCACATCCACCTCGCAGTC 60.449 63.158 0.00 0.00 0.00 3.51
2052 3740 1.807165 CACATCCACCTCGCAGTCG 60.807 63.158 0.00 0.00 0.00 4.18
2227 4420 2.632987 AACTTTGGAGTAGTTGCCGT 57.367 45.000 0.00 0.00 34.68 5.68
2234 4428 3.395639 TGGAGTAGTTGCCGTAAAACAG 58.604 45.455 0.00 0.00 0.00 3.16
2241 4435 3.697542 AGTTGCCGTAAAACAGAAAGGTT 59.302 39.130 0.00 0.00 0.00 3.50
2283 4477 4.058817 AGTAGTTAGCAAGACACAAGTGC 58.941 43.478 0.00 0.00 38.59 4.40
2294 4490 4.327680 AGACACAAGTGCCTCTTAATTCC 58.672 43.478 0.00 0.00 34.66 3.01
2373 5894 4.461431 TGTTACTCGAGGATTTGCTACTGA 59.539 41.667 18.41 0.00 0.00 3.41
2418 5942 6.029346 ACAATCCAAAACTGCCAAGAATAG 57.971 37.500 0.00 0.00 0.00 1.73
2426 5950 3.610911 ACTGCCAAGAATAGGTAGCAAC 58.389 45.455 0.00 0.00 41.91 4.17
2526 6051 2.552031 CATGTCAGAGCTCATGAGGTG 58.448 52.381 30.99 17.76 42.52 4.00
2590 6115 2.356227 CCTCCAAGGAAAGCCTAAGGTC 60.356 54.545 0.00 0.00 46.28 3.85
2641 6166 2.493675 CCTCAGACTCGTCATCAAGGAA 59.506 50.000 0.00 0.00 0.00 3.36
2648 6173 3.189287 ACTCGTCATCAAGGAAACAATGC 59.811 43.478 0.00 0.00 0.00 3.56
2893 6418 2.825836 CGAAGGATGTGCCCTGGC 60.826 66.667 0.00 0.00 36.49 4.85
2962 6487 1.079543 CCACTTCGACTGGGAGCTG 60.080 63.158 0.00 0.00 0.00 4.24
2967 6492 1.841302 TTCGACTGGGAGCTGCCAAT 61.841 55.000 28.21 19.78 38.95 3.16
3004 6529 1.839994 GGGATGGACATGACAGAGGAA 59.160 52.381 0.00 0.00 0.00 3.36
3099 6624 3.357021 CACTTGCATTGATATGTCACGC 58.643 45.455 6.20 6.20 34.90 5.34
3100 6625 3.064408 CACTTGCATTGATATGTCACGCT 59.936 43.478 12.44 0.00 35.21 5.07
3128 6653 6.374565 TCTTAAGTACGAGTGCCTTCTATC 57.625 41.667 1.63 0.00 0.00 2.08
3143 6668 5.394663 GCCTTCTATCTCTTTGTCTAGTGCA 60.395 44.000 0.00 0.00 0.00 4.57
3192 6720 6.887376 TTACATCACTTCAAGATAAGCGTC 57.113 37.500 0.00 0.00 0.00 5.19
3202 6730 5.271625 TCAAGATAAGCGTCGAGTTATGTC 58.728 41.667 0.00 0.00 0.00 3.06
3204 6732 4.849883 AGATAAGCGTCGAGTTATGTCTG 58.150 43.478 0.00 0.00 0.00 3.51
3231 8664 7.704578 AGTATCAAGTATGTGTGTGACTAGT 57.295 36.000 0.00 0.00 0.00 2.57
3263 8696 5.762179 TTCCTATGAAGTGGAGTGAACAT 57.238 39.130 0.00 0.00 33.46 2.71
3287 8720 4.633565 GCCTCTTCAATAAAGGACTGTGAG 59.366 45.833 0.00 0.00 35.54 3.51
3288 8721 5.181748 CCTCTTCAATAAAGGACTGTGAGG 58.818 45.833 0.00 0.00 35.54 3.86
3295 8728 1.680338 AAGGACTGTGAGGTGTTTGC 58.320 50.000 0.00 0.00 0.00 3.68
3384 8817 2.272146 CCCCCTCCACCATGTTCG 59.728 66.667 0.00 0.00 0.00 3.95
3401 8834 3.311322 TGTTCGTTCGCTGATTTGTTTCT 59.689 39.130 0.00 0.00 0.00 2.52
3408 8841 3.629855 TCGCTGATTTGTTTCTGTCCAAA 59.370 39.130 0.00 0.00 35.25 3.28
3410 8843 3.730715 GCTGATTTGTTTCTGTCCAAACG 59.269 43.478 0.00 0.00 38.85 3.60
3418 8851 6.210287 TGTTTCTGTCCAAACGGTTTTTAT 57.790 33.333 2.79 0.00 38.85 1.40
3472 8907 7.912250 CCATGCACTACTCAATCAACTTAATTC 59.088 37.037 0.00 0.00 0.00 2.17
3474 8909 8.565896 TGCACTACTCAATCAACTTAATTCAT 57.434 30.769 0.00 0.00 0.00 2.57
3508 8943 6.150976 TGCACCAATTCCATCTTAACTTACTG 59.849 38.462 0.00 0.00 0.00 2.74
3510 8945 7.094377 GCACCAATTCCATCTTAACTTACTGAA 60.094 37.037 0.00 0.00 0.00 3.02
3511 8946 8.792633 CACCAATTCCATCTTAACTTACTGAAA 58.207 33.333 0.00 0.00 0.00 2.69
3582 9021 4.620589 AACATGGGCATGATTTGTTGAA 57.379 36.364 0.00 0.00 41.20 2.69
3592 9031 7.964011 GGGCATGATTTGTTGAACATTTATTTG 59.036 33.333 0.00 0.00 0.00 2.32
3670 9109 1.169577 TGCAACGAACGGGCATTATT 58.830 45.000 10.58 0.00 31.58 1.40
3680 9119 8.836268 ACGAACGGGCATTATTCTATTAAATA 57.164 30.769 0.00 0.00 0.00 1.40
3732 9174 6.597832 ACACATATCATAGCCTAGAGAACC 57.402 41.667 0.00 0.00 0.00 3.62
3782 9224 7.538303 TTTCTTTGAGCAATGTTTTTCTTCC 57.462 32.000 0.00 0.00 0.00 3.46
3783 9225 6.469782 TCTTTGAGCAATGTTTTTCTTCCT 57.530 33.333 0.00 0.00 0.00 3.36
3786 9228 3.960102 TGAGCAATGTTTTTCTTCCTGGT 59.040 39.130 0.00 0.00 0.00 4.00
3789 9231 5.744171 AGCAATGTTTTTCTTCCTGGTTTT 58.256 33.333 0.00 0.00 0.00 2.43
3912 9423 6.855914 TCATTTTAAGACGCATGAACACTTTC 59.144 34.615 0.00 0.00 0.00 2.62
3934 9445 6.449635 TCACTACAAGTGTTGAGCATTTTT 57.550 33.333 6.93 0.00 46.03 1.94
3949 9460 9.878667 TTGAGCATTTTTCAAATACATGATGAT 57.121 25.926 0.00 0.00 31.98 2.45
3989 9500 8.939929 ACATGATGAATAACTCTTAATATGCGG 58.060 33.333 0.00 0.00 0.00 5.69
3990 9501 8.939929 CATGATGAATAACTCTTAATATGCGGT 58.060 33.333 0.00 0.00 0.00 5.68
3991 9502 8.310406 TGATGAATAACTCTTAATATGCGGTG 57.690 34.615 0.00 0.00 0.00 4.94
3992 9503 8.147704 TGATGAATAACTCTTAATATGCGGTGA 58.852 33.333 0.00 0.00 0.00 4.02
3993 9504 8.902540 ATGAATAACTCTTAATATGCGGTGAA 57.097 30.769 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.942376 TGGGATTAAGCACATTACGCAG 59.058 45.455 0.00 0.00 0.00 5.18
1 2 2.680841 GTGGGATTAAGCACATTACGCA 59.319 45.455 0.00 0.00 0.00 5.24
2 3 2.032924 GGTGGGATTAAGCACATTACGC 59.967 50.000 0.00 0.00 0.00 4.42
3 4 2.616842 GGGTGGGATTAAGCACATTACG 59.383 50.000 0.00 0.00 0.00 3.18
4 5 3.626930 TGGGTGGGATTAAGCACATTAC 58.373 45.455 0.00 0.00 0.00 1.89
5 6 4.079500 TGATGGGTGGGATTAAGCACATTA 60.080 41.667 0.00 0.00 0.00 1.90
6 7 2.917713 TGGGTGGGATTAAGCACATT 57.082 45.000 0.00 0.00 0.00 2.71
7 8 2.244510 TGATGGGTGGGATTAAGCACAT 59.755 45.455 0.00 0.00 0.00 3.21
8 9 1.638070 TGATGGGTGGGATTAAGCACA 59.362 47.619 0.00 0.00 0.00 4.57
9 10 2.301346 CTGATGGGTGGGATTAAGCAC 58.699 52.381 0.00 0.00 0.00 4.40
10 11 1.410083 GCTGATGGGTGGGATTAAGCA 60.410 52.381 0.00 0.00 0.00 3.91
11 12 1.322442 GCTGATGGGTGGGATTAAGC 58.678 55.000 0.00 0.00 0.00 3.09
12 13 1.479389 GGGCTGATGGGTGGGATTAAG 60.479 57.143 0.00 0.00 0.00 1.85
13 14 0.555769 GGGCTGATGGGTGGGATTAA 59.444 55.000 0.00 0.00 0.00 1.40
14 15 1.360393 GGGGCTGATGGGTGGGATTA 61.360 60.000 0.00 0.00 0.00 1.75
15 16 2.704424 GGGGCTGATGGGTGGGATT 61.704 63.158 0.00 0.00 0.00 3.01
16 17 3.105928 GGGGCTGATGGGTGGGAT 61.106 66.667 0.00 0.00 0.00 3.85
19 20 3.492353 ATCGGGGCTGATGGGTGG 61.492 66.667 0.00 0.00 0.00 4.61
20 21 2.203252 CATCGGGGCTGATGGGTG 60.203 66.667 10.99 0.00 41.63 4.61
121 122 5.247862 GGAAAAAGTTATACCCTTGACGGA 58.752 41.667 0.00 0.00 33.16 4.69
137 138 2.089201 GGTGACGGGTATGGGAAAAAG 58.911 52.381 0.00 0.00 0.00 2.27
367 371 9.033481 GTGTACGCCTATGTGTTGTTATTTATA 57.967 33.333 0.00 0.00 36.42 0.98
446 450 5.813672 TCATAATCGCGCTAGGTAAAAACTT 59.186 36.000 5.56 0.00 0.00 2.66
468 472 7.219601 TCCTAATGTATCAATTTTCCCCTCA 57.780 36.000 0.00 0.00 0.00 3.86
501 506 9.703892 CATCTAAAATGTTGACAAATGGGTTTA 57.296 29.630 0.00 0.00 0.00 2.01
509 514 7.825331 TGTACCCATCTAAAATGTTGACAAA 57.175 32.000 0.00 0.00 0.00 2.83
554 559 3.175594 GGGTACGGGTATGGGATCATAA 58.824 50.000 0.00 0.00 37.58 1.90
611 616 7.242359 TGGGAAGAAAATTTACTCATGGGTAA 58.758 34.615 14.34 14.34 0.00 2.85
620 625 7.837689 GGTAAGGGTATGGGAAGAAAATTTACT 59.162 37.037 0.00 0.00 0.00 2.24
630 636 5.487845 CCTATTAGGGTAAGGGTATGGGAAG 59.512 48.000 1.37 0.00 0.00 3.46
631 637 5.417755 CCTATTAGGGTAAGGGTATGGGAA 58.582 45.833 1.37 0.00 0.00 3.97
701 707 1.374252 GCTTTCGTCTCCGGCTGAA 60.374 57.895 0.00 0.00 33.95 3.02
703 709 1.945354 TAGGCTTTCGTCTCCGGCTG 61.945 60.000 0.00 0.00 34.01 4.85
704 710 1.043673 ATAGGCTTTCGTCTCCGGCT 61.044 55.000 0.00 0.00 36.23 5.52
705 711 0.179081 AATAGGCTTTCGTCTCCGGC 60.179 55.000 0.00 0.00 33.95 6.13
707 713 6.214399 AGTAATTAATAGGCTTTCGTCTCCG 58.786 40.000 0.00 0.00 0.00 4.63
728 734 5.950549 AGACTTTTCTGATCCGAGGTTAGTA 59.049 40.000 0.00 0.00 0.00 1.82
733 739 4.382147 GCTAAGACTTTTCTGATCCGAGGT 60.382 45.833 0.00 0.00 29.98 3.85
770 776 3.311106 AGCTGACGCACAATCAAATTTG 58.689 40.909 12.15 12.15 39.10 2.32
792 802 4.119862 GAGAGCACAAGTGTTACAGAACA 58.880 43.478 1.79 0.00 43.41 3.18
797 807 2.047061 AGGGAGAGCACAAGTGTTACA 58.953 47.619 1.79 0.00 0.00 2.41
865 877 7.614583 CACCCGGAGTAGAAAATCCTATATCTA 59.385 40.741 0.73 0.00 33.12 1.98
866 878 6.437793 CACCCGGAGTAGAAAATCCTATATCT 59.562 42.308 0.73 0.00 33.12 1.98
869 881 5.461327 ACACCCGGAGTAGAAAATCCTATA 58.539 41.667 0.73 0.00 33.12 1.31
872 884 2.547990 ACACCCGGAGTAGAAAATCCT 58.452 47.619 0.73 0.00 33.12 3.24
1053 2279 2.289072 CCCGTTGAGCTTGAAGAGAAGA 60.289 50.000 0.00 0.00 0.00 2.87
1072 2304 3.282920 GCCGCTGCTATGCTTCCC 61.283 66.667 0.00 0.00 33.53 3.97
1131 2363 0.462581 GATGAAGGCTGCCGATGACA 60.463 55.000 13.96 10.41 0.00 3.58
1178 2410 2.501128 CGAGGTCGGCCATGACAT 59.499 61.111 9.71 5.44 40.72 3.06
1378 2616 2.674380 GAGCTGCCACCACAAGGG 60.674 66.667 0.00 0.00 44.81 3.95
1413 2651 4.785512 CGTGCGCCGAGAAGCTCT 62.786 66.667 4.18 0.00 39.56 4.09
1471 2709 3.450115 GGTGGCTACGAGTCGGCT 61.450 66.667 18.30 0.00 0.00 5.52
1515 2753 4.639171 TGCTCGCTCGCGTTCACA 62.639 61.111 5.77 3.15 40.74 3.58
1523 2761 2.276868 CGGCAATTTGCTCGCTCG 60.277 61.111 20.06 11.26 44.28 5.03
1753 2991 2.625737 CTCCTCATGTTGCTTGATCGT 58.374 47.619 0.00 0.00 0.00 3.73
1767 3005 3.005539 GTGGCCCTCTGCTCCTCA 61.006 66.667 0.00 0.00 40.92 3.86
1796 3034 0.770499 TTCCTCCATGGCACTGTTCA 59.230 50.000 6.96 0.00 35.26 3.18
1801 3039 0.252881 TCTCCTTCCTCCATGGCACT 60.253 55.000 6.96 0.00 35.26 4.40
1807 3045 1.022903 AGGTCCTCTCCTTCCTCCAT 58.977 55.000 0.00 0.00 33.52 3.41
1840 3084 1.482593 ACCTTCCTTGCGTATCCTCAG 59.517 52.381 0.00 0.00 0.00 3.35
1869 3113 1.367346 TTCCCATGGTAAGAGGCACA 58.633 50.000 11.73 0.00 0.00 4.57
1917 3161 5.045578 AGGAGGCAGAAGCTAAGAAATTGTA 60.046 40.000 0.00 0.00 41.70 2.41
1941 3198 5.938125 GCCAAGGTATAACAACTTGAAGAGA 59.062 40.000 0.00 0.00 43.13 3.10
2004 3692 4.332819 GGTGAGTAATCTCCAAACCATTCG 59.667 45.833 6.41 0.00 39.75 3.34
2010 3698 4.691216 GTGACTGGTGAGTAATCTCCAAAC 59.309 45.833 14.26 11.30 39.75 2.93
2022 3710 0.686789 TGGATGTGGTGACTGGTGAG 59.313 55.000 0.00 0.00 0.00 3.51
2093 4255 3.809234 TCAATCACGAAATGAACTTGCG 58.191 40.909 0.00 0.00 41.93 4.85
2095 4257 7.060289 CACTGAATCAATCACGAAATGAACTTG 59.940 37.037 0.00 0.00 41.93 3.16
2141 4317 8.885494 TTTGGTTTGACTCAAATTATGAAAGG 57.115 30.769 7.47 0.00 37.67 3.11
2190 4383 9.308318 TCCAAAGTTTTAAAATACTTGAACTGC 57.692 29.630 3.52 0.00 34.95 4.40
2211 4404 4.197750 TGTTTTACGGCAACTACTCCAAA 58.802 39.130 0.00 0.00 0.00 3.28
2212 4405 3.806380 TGTTTTACGGCAACTACTCCAA 58.194 40.909 0.00 0.00 0.00 3.53
2223 4416 5.428496 ACTTAACCTTTCTGTTTTACGGC 57.572 39.130 0.00 0.00 0.00 5.68
2256 4450 6.041069 ACTTGTGTCTTGCTAACTACTCTCTT 59.959 38.462 0.00 0.00 0.00 2.85
2348 5869 4.705507 AGTAGCAAATCCTCGAGTAACAGA 59.294 41.667 12.31 0.83 0.00 3.41
2351 5872 4.995124 TCAGTAGCAAATCCTCGAGTAAC 58.005 43.478 12.31 0.00 0.00 2.50
2355 5876 6.686630 AGATATTCAGTAGCAAATCCTCGAG 58.313 40.000 5.13 5.13 0.00 4.04
2373 5894 5.072193 TGTCACCCATATGCAGTGAGATATT 59.928 40.000 20.85 0.00 40.98 1.28
2418 5942 5.643379 TGATGAAATTTGGAGTTGCTACC 57.357 39.130 0.00 0.00 0.00 3.18
2426 5950 8.385111 CAATTTCCGATTTGATGAAATTTGGAG 58.615 33.333 10.74 0.36 42.83 3.86
2526 6051 0.179129 CTTCCGCATCACATTTGGGC 60.179 55.000 0.00 0.00 0.00 5.36
2590 6115 2.967599 TGATCAAGTCATCCTCGGTG 57.032 50.000 0.00 0.00 0.00 4.94
2641 6166 0.813184 CTGGATGAAGCCGCATTGTT 59.187 50.000 0.00 0.00 0.00 2.83
2648 6173 2.437180 TGCAGCTGGATGAAGCCG 60.437 61.111 17.12 0.00 44.68 5.52
2893 6418 1.679680 CTAGCCTGGGCAAACATCATG 59.320 52.381 14.39 0.00 44.88 3.07
2905 6430 1.069823 ACAATCTCGATGCTAGCCTGG 59.930 52.381 13.29 3.69 0.00 4.45
2962 6487 1.931635 TTGGTTTCACCCCTATTGGC 58.068 50.000 0.00 0.00 37.50 4.52
2967 6492 2.074579 TCCCATTTGGTTTCACCCCTA 58.925 47.619 0.00 0.00 37.50 3.53
2987 6512 3.372349 CCCATTTCCTCTGTCATGTCCAT 60.372 47.826 0.00 0.00 0.00 3.41
3099 6624 7.760340 AGAAGGCACTCGTACTTAAGATTTTAG 59.240 37.037 10.09 2.65 38.49 1.85
3100 6625 7.609056 AGAAGGCACTCGTACTTAAGATTTTA 58.391 34.615 10.09 0.00 38.49 1.52
3114 6639 4.109050 GACAAAGAGATAGAAGGCACTCG 58.891 47.826 0.00 0.00 38.49 4.18
3176 6704 3.851976 ACTCGACGCTTATCTTGAAGT 57.148 42.857 0.00 0.00 0.00 3.01
3184 6712 3.630769 TCCAGACATAACTCGACGCTTAT 59.369 43.478 0.00 0.00 0.00 1.73
3192 6720 6.565234 ACTTGATACTTCCAGACATAACTCG 58.435 40.000 0.00 0.00 0.00 4.18
3202 6730 6.311445 GTCACACACATACTTGATACTTCCAG 59.689 42.308 0.00 0.00 0.00 3.86
3204 6732 6.398918 AGTCACACACATACTTGATACTTCC 58.601 40.000 0.00 0.00 0.00 3.46
3263 8696 4.041567 TCACAGTCCTTTATTGAAGAGGCA 59.958 41.667 0.00 0.00 37.57 4.75
3337 8770 1.868469 GCATTGTGCTGGCAGAAAAA 58.132 45.000 20.86 10.24 40.96 1.94
3351 8784 1.032114 GGGGGAGAACCGAAGCATTG 61.032 60.000 0.00 0.00 41.60 2.82
3384 8817 3.003275 TGGACAGAAACAAATCAGCGAAC 59.997 43.478 0.00 0.00 0.00 3.95
3410 8843 8.481974 AAAAATATGTGGCGGTAATAAAAACC 57.518 30.769 0.00 0.00 0.00 3.27
3436 8871 1.496444 TAGTGCATGGGGAAGGTGCA 61.496 55.000 0.00 0.00 0.00 4.57
3472 8907 5.732633 TGGAATTGGTGCAAAAGGATAATG 58.267 37.500 0.00 0.00 0.00 1.90
3474 8909 5.721000 AGATGGAATTGGTGCAAAAGGATAA 59.279 36.000 0.00 0.00 0.00 1.75
3476 8911 4.098894 AGATGGAATTGGTGCAAAAGGAT 58.901 39.130 0.00 0.00 0.00 3.24
3477 8912 3.509442 AGATGGAATTGGTGCAAAAGGA 58.491 40.909 0.00 0.00 0.00 3.36
3563 9002 3.927854 TGTTCAACAAATCATGCCCATG 58.072 40.909 1.86 1.86 40.09 3.66
3564 9003 4.829872 ATGTTCAACAAATCATGCCCAT 57.170 36.364 0.00 0.00 0.00 4.00
3565 9004 4.620589 AATGTTCAACAAATCATGCCCA 57.379 36.364 0.00 0.00 0.00 5.36
3582 9021 8.811994 ACCCTTATTAGTTGTGCAAATAAATGT 58.188 29.630 8.54 0.00 35.02 2.71
3592 9031 8.515695 AATTTACCTACCCTTATTAGTTGTGC 57.484 34.615 0.00 0.00 0.00 4.57
3711 9153 7.863901 AAAGGTTCTCTAGGCTATGATATGT 57.136 36.000 0.00 0.00 0.00 2.29
3789 9231 8.608844 ACACAATAACAAAACAAACTGGAAAA 57.391 26.923 0.00 0.00 0.00 2.29
3791 9233 8.608844 AAACACAATAACAAAACAAACTGGAA 57.391 26.923 0.00 0.00 0.00 3.53
3877 9388 4.085261 GCGTCTTAAAATGATCATCGCGTA 60.085 41.667 16.60 2.75 32.68 4.42
3879 9390 3.210539 GCGTCTTAAAATGATCATCGCG 58.789 45.455 16.60 0.00 32.68 5.87
3963 9474 8.939929 CCGCATATTAAGAGTTATTCATCATGT 58.060 33.333 0.00 0.00 0.00 3.21
3964 9475 8.939929 ACCGCATATTAAGAGTTATTCATCATG 58.060 33.333 0.00 0.00 0.00 3.07
3965 9476 8.939929 CACCGCATATTAAGAGTTATTCATCAT 58.060 33.333 0.00 0.00 0.00 2.45
3966 9477 8.147704 TCACCGCATATTAAGAGTTATTCATCA 58.852 33.333 0.00 0.00 0.00 3.07
3968 9479 8.774586 GTTCACCGCATATTAAGAGTTATTCAT 58.225 33.333 0.00 0.00 0.00 2.57
3969 9480 7.766738 TGTTCACCGCATATTAAGAGTTATTCA 59.233 33.333 0.00 0.00 0.00 2.57
3970 9481 8.138365 TGTTCACCGCATATTAAGAGTTATTC 57.862 34.615 0.00 0.00 0.00 1.75
3971 9482 8.677148 ATGTTCACCGCATATTAAGAGTTATT 57.323 30.769 0.00 0.00 0.00 1.40
3972 9483 8.677148 AATGTTCACCGCATATTAAGAGTTAT 57.323 30.769 0.00 0.00 0.00 1.89
3973 9484 8.500753 AAATGTTCACCGCATATTAAGAGTTA 57.499 30.769 0.00 0.00 0.00 2.24
3974 9485 7.391148 AAATGTTCACCGCATATTAAGAGTT 57.609 32.000 0.00 0.00 0.00 3.01
3975 9486 7.391148 AAAATGTTCACCGCATATTAAGAGT 57.609 32.000 0.00 0.00 0.00 3.24
3976 9487 9.950680 ATAAAAATGTTCACCGCATATTAAGAG 57.049 29.630 0.00 0.00 0.00 2.85
3977 9488 9.729023 CATAAAAATGTTCACCGCATATTAAGA 57.271 29.630 0.00 0.00 0.00 2.10
3978 9489 9.729023 TCATAAAAATGTTCACCGCATATTAAG 57.271 29.630 0.00 0.00 0.00 1.85
3979 9490 9.729023 CTCATAAAAATGTTCACCGCATATTAA 57.271 29.630 0.00 0.00 0.00 1.40
3980 9491 7.860373 GCTCATAAAAATGTTCACCGCATATTA 59.140 33.333 0.00 0.00 0.00 0.98
3981 9492 6.697019 GCTCATAAAAATGTTCACCGCATATT 59.303 34.615 0.00 0.00 0.00 1.28
3982 9493 6.183360 TGCTCATAAAAATGTTCACCGCATAT 60.183 34.615 0.00 0.00 0.00 1.78
3983 9494 5.124617 TGCTCATAAAAATGTTCACCGCATA 59.875 36.000 0.00 0.00 0.00 3.14
3984 9495 4.082300 TGCTCATAAAAATGTTCACCGCAT 60.082 37.500 0.00 0.00 0.00 4.73
3985 9496 3.254411 TGCTCATAAAAATGTTCACCGCA 59.746 39.130 0.00 0.00 0.00 5.69
3986 9497 3.832276 TGCTCATAAAAATGTTCACCGC 58.168 40.909 0.00 0.00 0.00 5.68
3987 9498 6.949578 AAATGCTCATAAAAATGTTCACCG 57.050 33.333 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.