Multiple sequence alignment - TraesCS7D01G154600

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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 TraesCS7D01G154600 chr7D 100.000 4218 0 0 1 4218 102757133 102752916 0.000000e+00 7790.0
1 TraesCS7D01G154600 chr7D 75.096 783 165 26 1333 2102 102738809 102738044 5.220000e-89 339.0
2 TraesCS7D01G154600 chr7D 81.667 120 18 4 3356 3473 189169912 189169795 3.470000e-16 97.1
3 TraesCS7D01G154600 chr7A 95.328 2440 101 5 809 3244 107603744 107601314 0.000000e+00 3862.0
4 TraesCS7D01G154600 chr7A 78.125 1920 359 48 943 2831 106995248 106993359 0.000000e+00 1162.0
5 TraesCS7D01G154600 chr7A 82.465 1152 191 9 1704 2847 106294619 106293471 0.000000e+00 998.0
6 TraesCS7D01G154600 chr7A 79.984 1229 206 30 1631 2831 107322288 107321072 0.000000e+00 870.0
7 TraesCS7D01G154600 chr7A 86.264 546 43 13 3238 3753 107601227 107600684 7.920000e-157 564.0
8 TraesCS7D01G154600 chr7A 88.328 317 28 3 3878 4194 107599861 107599554 5.150000e-99 372.0
9 TraesCS7D01G154600 chr7A 81.739 115 19 1 3376 3490 2395155 2395043 1.250000e-15 95.3
10 TraesCS7D01G154600 chr7A 81.739 115 19 1 3376 3490 2456255 2456143 1.250000e-15 95.3
11 TraesCS7D01G154600 chr7A 78.065 155 30 4 3320 3472 194809595 194809747 1.250000e-15 95.3
12 TraesCS7D01G154600 chr3A 96.315 787 28 1 1 786 735334258 735335044 0.000000e+00 1291.0
13 TraesCS7D01G154600 chr7B 78.928 1922 338 51 951 2831 60497010 60495115 0.000000e+00 1243.0
14 TraesCS7D01G154600 chr7B 78.678 1876 324 58 991 2819 60605463 60603617 0.000000e+00 1179.0
15 TraesCS7D01G154600 chr7B 78.047 1895 347 48 962 2806 60566504 60564629 0.000000e+00 1131.0
16 TraesCS7D01G154600 chr7B 77.686 1936 351 57 943 2831 60092601 60090700 0.000000e+00 1107.0
17 TraesCS7D01G154600 chr7B 82.986 1152 185 8 1704 2847 60030689 60029541 0.000000e+00 1031.0
18 TraesCS7D01G154600 chr7B 76.756 1893 362 58 986 2844 59668425 59666577 0.000000e+00 987.0
19 TraesCS7D01G154600 chr7B 72.888 1527 334 65 995 2489 61055727 61054249 1.790000e-123 453.0
20 TraesCS7D01G154600 chr7B 90.179 224 14 5 3995 4218 61063903 61063688 6.900000e-73 285.0
21 TraesCS7D01G154600 chr4B 92.875 786 54 2 1 785 428453176 428452392 0.000000e+00 1140.0
22 TraesCS7D01G154600 chrUn 82.133 1097 183 10 1760 2847 91513104 91514196 0.000000e+00 928.0
23 TraesCS7D01G154600 chrUn 96.318 516 19 0 1 516 232194256 232193741 0.000000e+00 848.0
24 TraesCS7D01G154600 chr5B 82.172 746 132 1 5 750 631633049 631633793 1.280000e-179 640.0
25 TraesCS7D01G154600 chr5D 82.086 748 129 4 5 750 502783242 502782498 5.950000e-178 634.0
26 TraesCS7D01G154600 chr1A 85.353 553 63 5 4 555 572329705 572330240 1.320000e-154 556.0
27 TraesCS7D01G154600 chr1D 78.453 181 33 5 3308 3485 479672316 479672493 3.450000e-21 113.0
28 TraesCS7D01G154600 chr3B 81.818 132 19 5 3356 3485 195352738 195352610 5.770000e-19 106.0
29 TraesCS7D01G154600 chr6B 78.235 170 30 7 3308 3473 617769304 617769470 7.460000e-18 102.0
30 TraesCS7D01G154600 chr1B 76.667 180 37 5 3308 3485 122918045 122917869 1.250000e-15 95.3


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 TraesCS7D01G154600 chr7D 102752916 102757133 4217 True 7790.000000 7790 100.000000 1 4218 1 chr7D.!!$R2 4217
1 TraesCS7D01G154600 chr7D 102738044 102738809 765 True 339.000000 339 75.096000 1333 2102 1 chr7D.!!$R1 769
2 TraesCS7D01G154600 chr7A 107599554 107603744 4190 True 1599.333333 3862 89.973333 809 4194 3 chr7A.!!$R6 3385
3 TraesCS7D01G154600 chr7A 106993359 106995248 1889 True 1162.000000 1162 78.125000 943 2831 1 chr7A.!!$R4 1888
4 TraesCS7D01G154600 chr7A 106293471 106294619 1148 True 998.000000 998 82.465000 1704 2847 1 chr7A.!!$R3 1143
5 TraesCS7D01G154600 chr7A 107321072 107322288 1216 True 870.000000 870 79.984000 1631 2831 1 chr7A.!!$R5 1200
6 TraesCS7D01G154600 chr3A 735334258 735335044 786 False 1291.000000 1291 96.315000 1 786 1 chr3A.!!$F1 785
7 TraesCS7D01G154600 chr7B 60495115 60497010 1895 True 1243.000000 1243 78.928000 951 2831 1 chr7B.!!$R4 1880
8 TraesCS7D01G154600 chr7B 60603617 60605463 1846 True 1179.000000 1179 78.678000 991 2819 1 chr7B.!!$R6 1828
9 TraesCS7D01G154600 chr7B 60564629 60566504 1875 True 1131.000000 1131 78.047000 962 2806 1 chr7B.!!$R5 1844
10 TraesCS7D01G154600 chr7B 60090700 60092601 1901 True 1107.000000 1107 77.686000 943 2831 1 chr7B.!!$R3 1888
11 TraesCS7D01G154600 chr7B 60029541 60030689 1148 True 1031.000000 1031 82.986000 1704 2847 1 chr7B.!!$R2 1143
12 TraesCS7D01G154600 chr7B 59666577 59668425 1848 True 987.000000 987 76.756000 986 2844 1 chr7B.!!$R1 1858
13 TraesCS7D01G154600 chr7B 61054249 61055727 1478 True 453.000000 453 72.888000 995 2489 1 chr7B.!!$R7 1494
14 TraesCS7D01G154600 chr4B 428452392 428453176 784 True 1140.000000 1140 92.875000 1 785 1 chr4B.!!$R1 784
15 TraesCS7D01G154600 chrUn 91513104 91514196 1092 False 928.000000 928 82.133000 1760 2847 1 chrUn.!!$F1 1087
16 TraesCS7D01G154600 chrUn 232193741 232194256 515 True 848.000000 848 96.318000 1 516 1 chrUn.!!$R1 515
17 TraesCS7D01G154600 chr5B 631633049 631633793 744 False 640.000000 640 82.172000 5 750 1 chr5B.!!$F1 745
18 TraesCS7D01G154600 chr5D 502782498 502783242 744 True 634.000000 634 82.086000 5 750 1 chr5D.!!$R1 745
19 TraesCS7D01G154600 chr1A 572329705 572330240 535 False 556.000000 556 85.353000 4 555 1 chr1A.!!$F1 551

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
801 804 0.031616 AAAGTGGGGGTTTTCCAGCA 60.032 50.0 0.00 0.0 42.91 4.41 F
802 805 0.190815 AAGTGGGGGTTTTCCAGCAT 59.809 50.0 0.00 0.0 42.91 3.79 F
806 809 0.251787 GGGGGTTTTCCAGCATGACT 60.252 55.0 0.00 0.0 39.69 3.41 F
849 852 0.323087 ACCGCCAATTAGGTTCACCC 60.323 55.0 0.00 0.0 37.49 4.61 F
899 902 0.725784 CGAATTCACCACACGCTTGC 60.726 55.0 6.22 0.0 0.00 4.01 F
2862 2967 0.106149 ACACTCTTCGTGACCAACCC 59.894 55.0 0.00 0.0 46.81 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2715 2817 0.610174 TGAGAGGCGCAGAATCACTT 59.390 50.00 10.83 0.00 0.00 3.16 R
2787 2889 5.806654 TCACAATGCCTATCAGTAGCATA 57.193 39.13 0.00 0.00 30.07 3.14 R
2818 2920 5.376625 TCTAGAGGTGTTGCTTTTGTCATT 58.623 37.50 0.00 0.00 0.00 2.57 R
2848 2950 0.889186 CCAAGGGGTTGGTCACGAAG 60.889 60.00 0.00 0.00 37.32 3.79 R
2906 3011 2.030185 CGTATCGAATGGGAATCCTCGT 60.030 50.00 8.86 1.18 33.87 4.18 R
4185 5117 0.033366 TGTGTACGTGCATGCACTCT 59.967 50.00 39.46 28.72 44.16 3.24 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
173 174 8.494433 TGGATAGAAGTAGCCTGTTTATCAATT 58.506 33.333 0.00 0.00 35.54 2.32
283 285 2.393768 GCTCTGACGGGCACATGTG 61.394 63.158 21.83 21.83 0.00 3.21
402 404 4.094830 ACGAAAGTGTTTTCCCCTACAT 57.905 40.909 0.00 0.00 46.97 2.29
415 417 4.340617 TCCCCTACATTGTGGAAATTCAC 58.659 43.478 1.15 0.00 38.09 3.18
566 568 3.453679 GGCGTCGCCTCTTCCTCT 61.454 66.667 28.98 0.00 46.69 3.69
581 583 7.108847 CCTCTTCCTCTGATATGTCAAGTTTT 58.891 38.462 0.00 0.00 33.05 2.43
786 789 2.036387 CAAGGGGTTTTCCGGAAAAGT 58.964 47.619 36.51 21.16 40.53 2.66
787 790 1.699730 AGGGGTTTTCCGGAAAAGTG 58.300 50.000 36.51 0.00 40.53 3.16
788 791 0.677288 GGGGTTTTCCGGAAAAGTGG 59.323 55.000 36.51 0.00 40.53 4.00
789 792 0.677288 GGGTTTTCCGGAAAAGTGGG 59.323 55.000 36.51 0.00 40.53 4.61
790 793 0.677288 GGTTTTCCGGAAAAGTGGGG 59.323 55.000 36.51 0.00 40.53 4.96
791 794 0.677288 GTTTTCCGGAAAAGTGGGGG 59.323 55.000 36.51 0.00 40.53 5.40
792 795 0.262285 TTTTCCGGAAAAGTGGGGGT 59.738 50.000 33.30 0.00 35.57 4.95
793 796 0.262285 TTTCCGGAAAAGTGGGGGTT 59.738 50.000 27.12 0.00 0.00 4.11
794 797 0.262285 TTCCGGAAAAGTGGGGGTTT 59.738 50.000 16.28 0.00 0.00 3.27
795 798 0.262285 TCCGGAAAAGTGGGGGTTTT 59.738 50.000 0.00 0.00 0.00 2.43
796 799 0.677288 CCGGAAAAGTGGGGGTTTTC 59.323 55.000 0.00 0.00 41.33 2.29
800 803 1.070134 GAAAAGTGGGGGTTTTCCAGC 59.930 52.381 0.00 0.00 42.91 4.85
801 804 0.031616 AAAGTGGGGGTTTTCCAGCA 60.032 50.000 0.00 0.00 42.91 4.41
802 805 0.190815 AAGTGGGGGTTTTCCAGCAT 59.809 50.000 0.00 0.00 42.91 3.79
803 806 0.542702 AGTGGGGGTTTTCCAGCATG 60.543 55.000 0.00 0.00 42.91 4.06
804 807 0.541764 GTGGGGGTTTTCCAGCATGA 60.542 55.000 0.00 0.00 39.69 3.07
805 808 0.541764 TGGGGGTTTTCCAGCATGAC 60.542 55.000 0.00 0.00 39.69 3.06
806 809 0.251787 GGGGGTTTTCCAGCATGACT 60.252 55.000 0.00 0.00 39.69 3.41
807 810 0.890683 GGGGTTTTCCAGCATGACTG 59.109 55.000 0.00 3.35 46.77 3.51
846 849 1.612199 GGTGACCGCCAATTAGGTTCA 60.612 52.381 0.00 0.25 41.51 3.18
849 852 0.323087 ACCGCCAATTAGGTTCACCC 60.323 55.000 0.00 0.00 37.49 4.61
866 869 8.068733 AGGTTCACCCTAGAGAAATACTATCTT 58.931 37.037 0.00 0.00 43.87 2.40
896 899 3.253955 GCGAATTCACCACACGCT 58.746 55.556 6.22 0.00 44.67 5.07
899 902 0.725784 CGAATTCACCACACGCTTGC 60.726 55.000 6.22 0.00 0.00 4.01
925 928 1.795286 CTCACTTGGACGTGAAGCTTC 59.205 52.381 19.89 19.89 42.80 3.86
937 940 4.561606 ACGTGAAGCTTCGATACAATACAC 59.438 41.667 21.11 9.36 0.00 2.90
938 941 4.798907 CGTGAAGCTTCGATACAATACACT 59.201 41.667 21.11 0.00 0.00 3.55
940 943 6.140895 CGTGAAGCTTCGATACAATACACTAG 59.859 42.308 21.11 0.00 0.00 2.57
984 990 9.897744 CTAATTGTTTCTAGAACATGCTTTTGA 57.102 29.630 4.18 0.00 0.00 2.69
990 996 4.766373 TCTAGAACATGCTTTTGATTGGCA 59.234 37.500 0.00 0.00 40.32 4.92
992 998 4.901868 AGAACATGCTTTTGATTGGCAAT 58.098 34.783 13.54 13.54 39.46 3.56
1040 1046 2.432146 CCGAGGACCTCATCAAGAATGA 59.568 50.000 21.49 0.00 42.21 2.57
1134 1143 6.540189 AGAACAACCATATTCCATTTCTCTCG 59.460 38.462 0.00 0.00 0.00 4.04
1155 1170 5.746284 TCGTACAACATTTCCCCAATATCA 58.254 37.500 0.00 0.00 0.00 2.15
1160 1175 3.565307 ACATTTCCCCAATATCATGCGT 58.435 40.909 0.00 0.00 0.00 5.24
1762 1810 1.165270 CCGAGGATGAACCAAACACC 58.835 55.000 0.00 0.00 42.04 4.16
2011 2070 9.403110 GATGCCTTATCAATGTATCATTGTTTC 57.597 33.333 17.93 4.57 35.78 2.78
2053 2116 8.055181 TGATAACATAATTTTCTGGCTCTTCCT 58.945 33.333 0.00 0.00 35.26 3.36
2055 2118 9.920946 ATAACATAATTTTCTGGCTCTTCCTTA 57.079 29.630 0.00 0.00 35.26 2.69
2310 2379 8.979574 CAGTGAAAGTAGGTTAAGAAACTACAG 58.020 37.037 15.00 0.00 35.81 2.74
2389 2458 0.961753 CCATCGTCGATGAGATCCCA 59.038 55.000 31.82 0.00 42.09 4.37
2527 2601 6.628919 TTCATGATTACTCCATGATGCTTG 57.371 37.500 0.00 0.00 46.57 4.01
2754 2856 3.007506 TCACATTACAAAGCTTCTCCGGA 59.992 43.478 2.93 2.93 0.00 5.14
2787 2889 5.246981 TCACTGGATCCATTTCAACTCTT 57.753 39.130 16.63 0.00 0.00 2.85
2818 2920 6.714810 ACTGATAGGCATTGTGAAGTTGTTTA 59.285 34.615 0.00 0.00 0.00 2.01
2848 2950 3.996480 AGCAACACCTCTAGAAACACTC 58.004 45.455 0.00 0.00 0.00 3.51
2852 2954 4.506886 ACACCTCTAGAAACACTCTTCG 57.493 45.455 0.00 0.00 35.41 3.79
2862 2967 0.106149 ACACTCTTCGTGACCAACCC 59.894 55.000 0.00 0.00 46.81 4.11
2966 3071 1.599797 CCGACCCTGACCAACAACC 60.600 63.158 0.00 0.00 0.00 3.77
2972 3077 1.512926 CCTGACCAACAACCTCTTCG 58.487 55.000 0.00 0.00 0.00 3.79
2985 3090 4.273148 ACCTCTTCGTGAAGTTAGCAAT 57.727 40.909 9.29 0.00 39.38 3.56
2997 3102 7.315142 GTGAAGTTAGCAATGATGATTTCCAA 58.685 34.615 0.00 0.00 0.00 3.53
3006 3111 3.420893 TGATGATTTCCAAGGTGTCCAC 58.579 45.455 0.00 0.00 0.00 4.02
3029 3134 1.689258 GGAAGGTGGAAATGATGGGGG 60.689 57.143 0.00 0.00 0.00 5.40
3033 3138 1.001503 TGGAAATGATGGGGGTGCC 59.998 57.895 0.00 0.00 0.00 5.01
3092 3197 0.250234 TCTATGCCTGCAGGACACAC 59.750 55.000 37.21 18.40 37.39 3.82
3124 3229 5.361427 AGATGAGCAATGTCTGAGATGAAG 58.639 41.667 0.00 0.00 0.00 3.02
3160 3265 7.505248 AGATGCTCATGAGTACTTCTCTTATCA 59.495 37.037 23.38 8.68 43.13 2.15
3277 3477 4.946157 CCATTTCTAGTTGGTGCAGAATCT 59.054 41.667 0.00 0.00 0.00 2.40
3331 3539 2.309613 TGGGTCATTGATTAGGCATGC 58.690 47.619 9.90 9.90 0.00 4.06
3332 3540 2.309613 GGGTCATTGATTAGGCATGCA 58.690 47.619 21.36 0.00 0.00 3.96
3333 3541 2.694628 GGGTCATTGATTAGGCATGCAA 59.305 45.455 21.36 6.46 0.00 4.08
3352 3560 3.747193 CAATTGTGCAACGTGACTATCC 58.253 45.455 0.00 0.00 42.39 2.59
3353 3561 2.535012 TTGTGCAACGTGACTATCCA 57.465 45.000 0.00 0.00 42.39 3.41
3389 3597 2.566833 TTGACAGGTGATCCACAAGG 57.433 50.000 0.00 0.00 35.86 3.61
3426 3634 4.824479 TGAGGATCAAGCTTGATGTGTA 57.176 40.909 39.54 22.69 45.97 2.90
3427 3635 5.164620 TGAGGATCAAGCTTGATGTGTAA 57.835 39.130 39.54 21.09 45.97 2.41
3429 3637 5.819379 TGAGGATCAAGCTTGATGTGTAATC 59.181 40.000 39.54 25.81 45.97 1.75
3442 3650 5.481824 TGATGTGTAATCTGAACACTCCTCT 59.518 40.000 12.39 0.00 45.95 3.69
3469 3677 9.280174 AGATAAAATCTTGGTACTCGTCAAAAA 57.720 29.630 0.00 0.00 35.76 1.94
3504 3712 1.143684 AGGCTTGTTGTGTGGTGAGAT 59.856 47.619 0.00 0.00 0.00 2.75
3514 3722 4.377021 TGTGTGGTGAGATTACACTTCAC 58.623 43.478 0.00 1.56 43.73 3.18
3565 3773 7.656707 AAAATTGTGTGCATCCTTAATTGAC 57.343 32.000 0.00 0.00 0.00 3.18
3574 3782 3.247006 TCCTTAATTGACGCAGAGACC 57.753 47.619 0.00 0.00 0.00 3.85
3597 3805 5.751028 CCGGAAAGTGAAATTAAGCAAACAA 59.249 36.000 0.00 0.00 0.00 2.83
3621 3830 0.250727 TTGGCTCACTGGTTAGGCAC 60.251 55.000 10.03 0.00 46.61 5.01
3641 3868 4.825085 GCACCATCCGGATTTAATTCCTAA 59.175 41.667 16.19 3.31 35.59 2.69
3643 3870 6.015434 GCACCATCCGGATTTAATTCCTAAAT 60.015 38.462 16.19 3.16 41.93 1.40
3650 3877 8.691797 TCCGGATTTAATTCCTAAATTTGAAGG 58.308 33.333 0.00 0.40 39.79 3.46
3662 3889 6.322201 CCTAAATTTGAAGGGTGATGCATAGT 59.678 38.462 0.00 0.00 0.00 2.12
3663 3890 6.610075 AAATTTGAAGGGTGATGCATAGTT 57.390 33.333 0.00 0.00 0.00 2.24
3706 3934 6.488006 GGATCAAGCTTAATGTATGGTGTGAT 59.512 38.462 0.00 0.00 0.00 3.06
3710 3938 5.994250 AGCTTAATGTATGGTGTGATCACT 58.006 37.500 25.55 8.87 43.41 3.41
3711 3939 5.819379 AGCTTAATGTATGGTGTGATCACTG 59.181 40.000 25.55 2.80 43.41 3.66
3712 3940 5.586243 GCTTAATGTATGGTGTGATCACTGT 59.414 40.000 25.55 11.66 43.41 3.55
3757 4403 1.223187 ACAAGGTTACAACTTCGCCG 58.777 50.000 0.00 0.00 0.00 6.46
3758 4404 1.223187 CAAGGTTACAACTTCGCCGT 58.777 50.000 0.00 0.00 0.00 5.68
3761 4407 2.680577 AGGTTACAACTTCGCCGTTAG 58.319 47.619 0.00 0.00 0.00 2.34
3767 4413 2.199236 CAACTTCGCCGTTAGATACCC 58.801 52.381 0.00 0.00 0.00 3.69
3779 4425 1.789523 AGATACCCTTGCCGCTAGAA 58.210 50.000 3.16 0.00 0.00 2.10
3780 4426 2.116238 AGATACCCTTGCCGCTAGAAA 58.884 47.619 3.16 0.00 0.00 2.52
3806 4452 5.713807 AGAACTATTTCCGTACTCCCCTAT 58.286 41.667 0.00 0.00 31.28 2.57
3808 4454 3.577415 ACTATTTCCGTACTCCCCTATGC 59.423 47.826 0.00 0.00 0.00 3.14
3810 4456 0.031917 TTCCGTACTCCCCTATGCCA 60.032 55.000 0.00 0.00 0.00 4.92
3815 4461 1.204941 GTACTCCCCTATGCCATAGCG 59.795 57.143 6.18 0.00 44.31 4.26
3824 4470 2.566833 ATGCCATAGCGAGCCATTTA 57.433 45.000 0.00 0.00 44.31 1.40
3826 4472 3.694043 TGCCATAGCGAGCCATTTATA 57.306 42.857 0.00 0.00 44.31 0.98
3843 4489 9.691362 GCCATTTATAGTTGAAAAACAGAAGAA 57.309 29.630 0.00 0.00 0.00 2.52
3850 4496 6.744112 AGTTGAAAAACAGAAGAAACACACA 58.256 32.000 0.00 0.00 0.00 3.72
3851 4497 6.640907 AGTTGAAAAACAGAAGAAACACACAC 59.359 34.615 0.00 0.00 0.00 3.82
3852 4498 6.078202 TGAAAAACAGAAGAAACACACACA 57.922 33.333 0.00 0.00 0.00 3.72
3853 4499 5.918011 TGAAAAACAGAAGAAACACACACAC 59.082 36.000 0.00 0.00 0.00 3.82
3854 4500 5.446143 AAAACAGAAGAAACACACACACA 57.554 34.783 0.00 0.00 0.00 3.72
3866 4512 1.876799 ACACACACACTCTCTCTCTCG 59.123 52.381 0.00 0.00 0.00 4.04
3880 4526 5.069648 TCTCTCTCTCGCATCAACCAATATT 59.930 40.000 0.00 0.00 0.00 1.28
3905 4837 7.744087 TCTAATGTGTCAAAATGTGCTACTT 57.256 32.000 0.00 0.00 0.00 2.24
3906 4838 7.806690 TCTAATGTGTCAAAATGTGCTACTTC 58.193 34.615 0.00 0.00 0.00 3.01
3909 4841 4.515191 TGTGTCAAAATGTGCTACTTCCTC 59.485 41.667 0.00 0.00 0.00 3.71
3914 4846 5.470098 TCAAAATGTGCTACTTCCTCTGTTC 59.530 40.000 0.00 0.00 0.00 3.18
3916 4848 2.609747 TGTGCTACTTCCTCTGTTCCT 58.390 47.619 0.00 0.00 0.00 3.36
3918 4850 4.157246 TGTGCTACTTCCTCTGTTCCTAA 58.843 43.478 0.00 0.00 0.00 2.69
3923 4855 7.988028 GTGCTACTTCCTCTGTTCCTAAAATAT 59.012 37.037 0.00 0.00 0.00 1.28
3925 4857 9.478768 GCTACTTCCTCTGTTCCTAAAATATAC 57.521 37.037 0.00 0.00 0.00 1.47
3989 4921 6.234177 AGATATTTATTTTGAGAGCGGAGGG 58.766 40.000 0.00 0.00 0.00 4.30
3990 4922 3.992943 TTTATTTTGAGAGCGGAGGGA 57.007 42.857 0.00 0.00 0.00 4.20
4013 4945 7.013369 GGGAGTAGATTATTTGACCATTCAACC 59.987 40.741 0.00 0.00 41.64 3.77
4018 4950 6.432783 AGATTATTTGACCATTCAACCGTCAA 59.567 34.615 0.00 0.00 41.64 3.18
4033 4965 1.593209 TCAACTGTGTCGCGGGAAC 60.593 57.895 6.13 5.84 0.00 3.62
4045 4977 4.934989 GGGAACCGGCTAGTTCAG 57.065 61.111 17.32 0.00 46.52 3.02
4046 4978 2.283824 GGGAACCGGCTAGTTCAGA 58.716 57.895 17.32 0.00 46.52 3.27
4047 4979 0.108281 GGGAACCGGCTAGTTCAGAC 60.108 60.000 17.32 6.86 46.52 3.51
4119 5051 3.976793 GCTAGCATAGGTACACGTACA 57.023 47.619 10.63 0.00 39.70 2.90
4130 5062 1.809619 CACGTACATCCCCGCTGTG 60.810 63.158 0.00 0.00 0.00 3.66
4131 5063 1.980232 ACGTACATCCCCGCTGTGA 60.980 57.895 0.00 0.00 0.00 3.58
4133 5065 0.390603 CGTACATCCCCGCTGTGAAA 60.391 55.000 0.00 0.00 0.00 2.69
4137 5069 1.338769 ACATCCCCGCTGTGAAAGTAC 60.339 52.381 0.00 0.00 0.00 2.73
4143 5075 1.335597 CCGCTGTGAAAGTACGAGTGA 60.336 52.381 0.00 0.00 0.00 3.41
4185 5117 7.446319 ACAGTACTAATATATGCAGTACGACCA 59.554 37.037 21.14 0.00 45.96 4.02
4191 5123 0.108615 ATGCAGTACGACCAGAGTGC 60.109 55.000 0.00 0.00 0.00 4.40
4194 5126 1.633561 CAGTACGACCAGAGTGCATG 58.366 55.000 0.00 0.00 0.00 4.06
4195 5127 0.108615 AGTACGACCAGAGTGCATGC 60.109 55.000 11.82 11.82 0.00 4.06
4196 5128 0.389817 GTACGACCAGAGTGCATGCA 60.390 55.000 18.46 18.46 0.00 3.96
4197 5129 0.389817 TACGACCAGAGTGCATGCAC 60.390 55.000 37.87 37.87 46.50 4.57
4206 5138 2.234613 GTGCATGCACGTACACAGT 58.765 52.632 33.20 0.00 37.19 3.55
4207 5139 0.586319 GTGCATGCACGTACACAGTT 59.414 50.000 33.20 0.00 37.19 3.16
4208 5140 1.002900 GTGCATGCACGTACACAGTTT 60.003 47.619 33.20 0.00 37.19 2.66
4209 5141 1.003008 TGCATGCACGTACACAGTTTG 60.003 47.619 18.46 0.00 0.00 2.93
4210 5142 1.262950 GCATGCACGTACACAGTTTGA 59.737 47.619 14.21 0.00 0.00 2.69
4211 5143 2.903678 CATGCACGTACACAGTTTGAC 58.096 47.619 0.00 0.00 0.00 3.18
4212 5144 2.303163 TGCACGTACACAGTTTGACT 57.697 45.000 0.00 0.00 0.00 3.41
4213 5145 2.623535 TGCACGTACACAGTTTGACTT 58.376 42.857 0.00 0.00 0.00 3.01
4214 5146 2.350192 TGCACGTACACAGTTTGACTTG 59.650 45.455 0.00 0.00 0.00 3.16
4215 5147 2.605818 GCACGTACACAGTTTGACTTGA 59.394 45.455 0.00 0.00 0.00 3.02
4216 5148 3.247648 GCACGTACACAGTTTGACTTGAT 59.752 43.478 0.00 0.00 0.00 2.57
4217 5149 4.260620 GCACGTACACAGTTTGACTTGATT 60.261 41.667 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
283 285 8.633075 TGTGATTTTGTCTGAATTTGAAGAAC 57.367 30.769 0.00 0.00 0.00 3.01
402 404 2.785357 AAGGGGGTGAATTTCCACAA 57.215 45.000 5.46 0.00 38.74 3.33
566 568 4.631377 CAGCTCGGAAAACTTGACATATCA 59.369 41.667 0.00 0.00 0.00 2.15
581 583 2.826287 CTCGAGGAGCAGCTCGGA 60.826 66.667 16.47 11.95 42.61 4.55
604 606 1.463214 TCCCCCAAGTCTGCAAGGA 60.463 57.895 0.00 0.00 0.00 3.36
786 789 0.541764 GTCATGCTGGAAAACCCCCA 60.542 55.000 0.00 0.00 0.00 4.96
787 790 0.251787 AGTCATGCTGGAAAACCCCC 60.252 55.000 0.00 0.00 0.00 5.40
788 791 0.890683 CAGTCATGCTGGAAAACCCC 59.109 55.000 8.70 0.00 41.42 4.95
830 833 0.323087 GGGTGAACCTAATTGGCGGT 60.323 55.000 0.00 0.00 40.22 5.68
846 849 8.425703 GCTTGAAAGATAGTATTTCTCTAGGGT 58.574 37.037 0.00 0.00 37.51 4.34
849 852 8.138712 ACGGCTTGAAAGATAGTATTTCTCTAG 58.861 37.037 0.00 0.00 37.51 2.43
850 853 8.008513 ACGGCTTGAAAGATAGTATTTCTCTA 57.991 34.615 0.00 0.00 37.51 2.43
866 869 2.809119 TGAATTCGCTTAACGGCTTGAA 59.191 40.909 0.04 0.00 43.89 2.69
896 899 2.538790 TCCAAGTGAGGGACTGCAA 58.461 52.632 0.00 0.00 41.55 4.08
915 918 4.798907 AGTGTATTGTATCGAAGCTTCACG 59.201 41.667 25.47 13.84 0.00 4.35
925 928 9.745880 AATTGGTCTAACTAGTGTATTGTATCG 57.254 33.333 0.00 0.00 0.00 2.92
984 990 3.401182 ACGCATCACAAAAATTGCCAAT 58.599 36.364 0.00 0.00 0.00 3.16
990 996 4.370917 AGCTCAAACGCATCACAAAAATT 58.629 34.783 0.00 0.00 0.00 1.82
992 998 3.435105 AGCTCAAACGCATCACAAAAA 57.565 38.095 0.00 0.00 0.00 1.94
1040 1046 1.180029 GATGATGGCTTGCACTTGGT 58.820 50.000 0.00 0.00 0.00 3.67
1134 1143 6.215845 GCATGATATTGGGGAAATGTTGTAC 58.784 40.000 0.00 0.00 0.00 2.90
1155 1170 1.002430 TCTTCAAGCCAGAAGACGCAT 59.998 47.619 12.87 0.00 46.62 4.73
1203 1218 9.525409 CTTGATCCAAATGTAAATCCAATCTTC 57.475 33.333 0.00 0.00 0.00 2.87
1762 1810 6.686630 TGGCTTTACAAATGTCCAACTAATG 58.313 36.000 0.00 0.00 0.00 1.90
2053 2116 6.877322 GGCTTCTAATACTTTGACCTGTGTAA 59.123 38.462 0.00 0.00 0.00 2.41
2055 2118 5.246307 GGCTTCTAATACTTTGACCTGTGT 58.754 41.667 0.00 0.00 0.00 3.72
2310 2379 5.517770 GCAACATCATATTCTTCTTTGGTGC 59.482 40.000 0.00 0.00 38.89 5.01
2518 2591 5.475719 CCAAGAATGAAACACAAGCATCAT 58.524 37.500 0.00 0.00 34.11 2.45
2521 2594 3.896888 TCCCAAGAATGAAACACAAGCAT 59.103 39.130 0.00 0.00 0.00 3.79
2527 2601 6.486993 AGAAAGTACTCCCAAGAATGAAACAC 59.513 38.462 0.00 0.00 0.00 3.32
2715 2817 0.610174 TGAGAGGCGCAGAATCACTT 59.390 50.000 10.83 0.00 0.00 3.16
2787 2889 5.806654 TCACAATGCCTATCAGTAGCATA 57.193 39.130 0.00 0.00 30.07 3.14
2818 2920 5.376625 TCTAGAGGTGTTGCTTTTGTCATT 58.623 37.500 0.00 0.00 0.00 2.57
2848 2950 0.889186 CCAAGGGGTTGGTCACGAAG 60.889 60.000 0.00 0.00 37.32 3.79
2862 2967 2.715046 TCATTGCTAGCTTCACCAAGG 58.285 47.619 17.23 2.30 0.00 3.61
2906 3011 2.030185 CGTATCGAATGGGAATCCTCGT 60.030 50.000 8.86 1.18 33.87 4.18
2966 3071 5.578336 TCATCATTGCTAACTTCACGAAGAG 59.422 40.000 13.60 2.85 40.79 2.85
2972 3077 6.855836 TGGAAATCATCATTGCTAACTTCAC 58.144 36.000 0.00 0.00 0.00 3.18
2985 3090 3.420893 GTGGACACCTTGGAAATCATCA 58.579 45.455 0.00 0.00 0.00 3.07
3006 3111 1.392589 CATCATTTCCACCTTCCCGG 58.607 55.000 0.00 0.00 39.35 5.73
3029 3134 1.602311 CATTAGATCAGGCTGGGCAC 58.398 55.000 15.73 4.02 0.00 5.01
3033 3138 1.419012 TGCTCCATTAGATCAGGCTGG 59.581 52.381 15.73 0.00 0.00 4.85
3058 3163 1.000607 CATAGAGCCATTGTGCATGCC 60.001 52.381 16.68 7.25 0.00 4.40
3092 3197 5.235401 CAGACATTGCTCATCTCAATCTGAG 59.765 44.000 0.00 0.00 45.59 3.35
3160 3265 9.976511 GATATTGATTGTGGACATTGATTCAAT 57.023 29.630 6.06 6.06 34.04 2.57
3240 3346 7.745620 ACTAGAAATGGACACAACCTTTTAG 57.254 36.000 0.00 0.00 37.40 1.85
3254 3454 4.946157 AGATTCTGCACCAACTAGAAATGG 59.054 41.667 0.00 4.57 42.60 3.16
3277 3477 3.801307 GGAAGGGAGTTTTACTTCCCA 57.199 47.619 11.82 0.00 45.48 4.37
3306 3506 2.949963 GCCTAATCAATGACCCAAGGCA 60.950 50.000 16.98 0.00 45.81 4.75
3331 3539 3.188254 TGGATAGTCACGTTGCACAATTG 59.812 43.478 3.24 3.24 0.00 2.32
3332 3540 3.407698 TGGATAGTCACGTTGCACAATT 58.592 40.909 0.00 0.00 0.00 2.32
3333 3541 3.002791 CTGGATAGTCACGTTGCACAAT 58.997 45.455 0.00 0.00 0.00 2.71
3343 3551 8.561738 TTTAAGAATTGAACCTGGATAGTCAC 57.438 34.615 0.00 0.00 0.00 3.67
3352 3560 8.143835 ACCTGTCAATTTTAAGAATTGAACCTG 58.856 33.333 18.80 13.85 45.06 4.00
3353 3561 8.143835 CACCTGTCAATTTTAAGAATTGAACCT 58.856 33.333 18.80 7.22 45.06 3.50
3389 3597 6.546484 TGATCCTCAATAAATGGGAAGATCC 58.454 40.000 0.00 0.00 33.73 3.36
3391 3599 6.492772 GCTTGATCCTCAATAAATGGGAAGAT 59.507 38.462 0.00 0.00 35.59 2.40
3393 3601 5.832060 AGCTTGATCCTCAATAAATGGGAAG 59.168 40.000 0.00 0.00 35.59 3.46
3396 3604 5.595542 TCAAGCTTGATCCTCAATAAATGGG 59.404 40.000 25.16 0.00 35.59 4.00
3415 3623 5.163814 GGAGTGTTCAGATTACACATCAAGC 60.164 44.000 7.90 0.00 46.42 4.01
3427 3635 9.432982 AGATTTTATCTAGAGGAGTGTTCAGAT 57.567 33.333 0.00 0.00 38.00 2.90
3429 3637 9.311916 CAAGATTTTATCTAGAGGAGTGTTCAG 57.688 37.037 0.00 0.00 39.08 3.02
3442 3650 9.932207 TTTTGACGAGTACCAAGATTTTATCTA 57.068 29.630 0.00 0.00 39.08 1.98
3469 3677 6.098266 ACAACAAGCCTGGTCTTTAAAGATTT 59.902 34.615 20.41 6.68 37.39 2.17
3470 3678 5.598417 ACAACAAGCCTGGTCTTTAAAGATT 59.402 36.000 20.41 7.35 37.39 2.40
3543 3751 5.401550 CGTCAATTAAGGATGCACACAATT 58.598 37.500 0.00 0.00 0.00 2.32
3544 3752 4.675146 GCGTCAATTAAGGATGCACACAAT 60.675 41.667 15.52 0.00 44.67 2.71
3545 3753 3.365868 GCGTCAATTAAGGATGCACACAA 60.366 43.478 15.52 0.00 44.67 3.33
3547 3755 2.785679 GCGTCAATTAAGGATGCACAC 58.214 47.619 15.52 0.00 44.67 3.82
3565 3773 0.319555 TTCACTTTCCGGTCTCTGCG 60.320 55.000 0.00 0.00 0.00 5.18
3574 3782 6.820470 TTGTTTGCTTAATTTCACTTTCCG 57.180 33.333 0.00 0.00 0.00 4.30
3621 3830 8.637986 TCAAATTTAGGAATTAAATCCGGATGG 58.362 33.333 19.95 0.00 44.60 3.51
3624 3851 8.691797 CCTTCAAATTTAGGAATTAAATCCGGA 58.308 33.333 6.61 6.61 44.60 5.14
3641 3868 6.610075 AAACTATGCATCACCCTTCAAATT 57.390 33.333 0.19 0.00 0.00 1.82
3643 3870 6.418057 AAAAACTATGCATCACCCTTCAAA 57.582 33.333 0.19 0.00 0.00 2.69
3668 3896 6.872585 AAGCTTGATCCCCAATAAATGAAA 57.127 33.333 0.00 0.00 33.68 2.69
3680 3908 5.009010 CACACCATACATTAAGCTTGATCCC 59.991 44.000 9.86 0.00 0.00 3.85
3688 3916 5.586243 ACAGTGATCACACCATACATTAAGC 59.414 40.000 27.02 0.00 46.99 3.09
3736 3964 2.032426 CGGCGAAGTTGTAACCTTGTTT 59.968 45.455 0.00 0.00 0.00 2.83
3753 3981 0.878961 GGCAAGGGTATCTAACGGCG 60.879 60.000 4.80 4.80 0.00 6.46
3757 4403 2.626743 TCTAGCGGCAAGGGTATCTAAC 59.373 50.000 1.45 0.00 0.00 2.34
3758 4404 2.953453 TCTAGCGGCAAGGGTATCTAA 58.047 47.619 1.45 0.00 0.00 2.10
3761 4407 2.614829 TTTCTAGCGGCAAGGGTATC 57.385 50.000 1.45 0.00 0.00 2.24
3779 4425 5.942236 GGGGAGTACGGAAATAGTTCTTTTT 59.058 40.000 2.56 0.00 33.92 1.94
3780 4426 5.250082 AGGGGAGTACGGAAATAGTTCTTTT 59.750 40.000 2.56 0.00 33.92 2.27
3794 4440 1.204941 GCTATGGCATAGGGGAGTACG 59.795 57.143 30.19 8.18 38.54 3.67
3795 4441 1.204941 CGCTATGGCATAGGGGAGTAC 59.795 57.143 32.63 16.43 40.82 2.73
3806 4452 2.566833 ATAAATGGCTCGCTATGGCA 57.433 45.000 0.74 0.00 43.90 4.92
3808 4454 5.237815 TCAACTATAAATGGCTCGCTATGG 58.762 41.667 0.00 0.00 0.00 2.74
3810 4456 7.801716 TTTTCAACTATAAATGGCTCGCTAT 57.198 32.000 0.00 0.00 0.00 2.97
3815 4461 9.346725 CTTCTGTTTTTCAACTATAAATGGCTC 57.653 33.333 0.00 0.00 33.58 4.70
3824 4470 8.519526 TGTGTGTTTCTTCTGTTTTTCAACTAT 58.480 29.630 0.00 0.00 33.58 2.12
3826 4472 6.640907 GTGTGTGTTTCTTCTGTTTTTCAACT 59.359 34.615 0.00 0.00 33.58 3.16
3843 4489 3.027412 AGAGAGAGAGTGTGTGTGTGTT 58.973 45.455 0.00 0.00 0.00 3.32
3846 4492 1.876799 CGAGAGAGAGAGTGTGTGTGT 59.123 52.381 0.00 0.00 0.00 3.72
3848 4494 0.878416 GCGAGAGAGAGAGTGTGTGT 59.122 55.000 0.00 0.00 0.00 3.72
3850 4496 1.742831 GATGCGAGAGAGAGAGTGTGT 59.257 52.381 0.00 0.00 0.00 3.72
3851 4497 1.742268 TGATGCGAGAGAGAGAGTGTG 59.258 52.381 0.00 0.00 0.00 3.82
3852 4498 2.121291 TGATGCGAGAGAGAGAGTGT 57.879 50.000 0.00 0.00 0.00 3.55
3853 4499 2.479389 GGTTGATGCGAGAGAGAGAGTG 60.479 54.545 0.00 0.00 0.00 3.51
3854 4500 1.748493 GGTTGATGCGAGAGAGAGAGT 59.252 52.381 0.00 0.00 0.00 3.24
3866 4512 8.190122 TGACACATTAGAAATATTGGTTGATGC 58.810 33.333 0.00 0.00 0.00 3.91
3880 4526 7.744087 AGTAGCACATTTTGACACATTAGAA 57.256 32.000 0.00 0.00 0.00 2.10
3968 4900 5.130477 ACTCCCTCCGCTCTCAAAATAAATA 59.870 40.000 0.00 0.00 0.00 1.40
3970 4902 3.263425 ACTCCCTCCGCTCTCAAAATAAA 59.737 43.478 0.00 0.00 0.00 1.40
3983 4915 4.344102 TGGTCAAATAATCTACTCCCTCCG 59.656 45.833 0.00 0.00 0.00 4.63
3985 4917 7.509546 TGAATGGTCAAATAATCTACTCCCTC 58.490 38.462 0.00 0.00 0.00 4.30
3986 4918 7.451731 TGAATGGTCAAATAATCTACTCCCT 57.548 36.000 0.00 0.00 0.00 4.20
3989 4921 7.280205 ACGGTTGAATGGTCAAATAATCTACTC 59.720 37.037 0.00 0.00 45.29 2.59
3990 4922 7.110155 ACGGTTGAATGGTCAAATAATCTACT 58.890 34.615 0.00 0.00 45.29 2.57
4013 4945 3.403057 CCCGCGACACAGTTGACG 61.403 66.667 8.23 0.00 42.76 4.35
4018 4950 4.657824 CGGTTCCCGCGACACAGT 62.658 66.667 8.23 0.00 41.17 3.55
4033 4965 1.819288 TCTGAAGTCTGAACTAGCCGG 59.181 52.381 0.00 0.00 33.48 6.13
4041 4973 5.012893 TCTGATAGTGCTCTGAAGTCTGAA 58.987 41.667 0.00 0.00 0.00 3.02
4042 4974 4.593956 TCTGATAGTGCTCTGAAGTCTGA 58.406 43.478 0.00 0.00 0.00 3.27
4043 4975 4.979943 TCTGATAGTGCTCTGAAGTCTG 57.020 45.455 0.00 0.00 0.00 3.51
4044 4976 4.142182 GCTTCTGATAGTGCTCTGAAGTCT 60.142 45.833 16.43 0.00 45.57 3.24
4045 4977 4.111916 GCTTCTGATAGTGCTCTGAAGTC 58.888 47.826 16.43 9.05 45.57 3.01
4046 4978 3.768757 AGCTTCTGATAGTGCTCTGAAGT 59.231 43.478 16.43 6.15 45.57 3.01
4047 4979 4.389890 AGCTTCTGATAGTGCTCTGAAG 57.610 45.455 12.95 12.95 46.10 3.02
4119 5051 0.108329 CGTACTTTCACAGCGGGGAT 60.108 55.000 0.00 0.00 0.00 3.85
4130 5062 5.171337 TCGTTTTACGTTCACTCGTACTTTC 59.829 40.000 0.00 0.00 44.18 2.62
4131 5063 5.034152 TCGTTTTACGTTCACTCGTACTTT 58.966 37.500 0.00 0.00 44.18 2.66
4133 5065 3.968724 GTCGTTTTACGTTCACTCGTACT 59.031 43.478 0.00 0.00 44.18 2.73
4137 5069 2.785477 ACAGTCGTTTTACGTTCACTCG 59.215 45.455 0.00 0.00 43.14 4.18
4143 5075 5.821204 AGTACTGTACAGTCGTTTTACGTT 58.179 37.500 31.11 6.09 43.14 3.99
4152 5084 8.504815 ACTGCATATATTAGTACTGTACAGTCG 58.495 37.037 31.11 5.34 42.54 4.18
4180 5112 2.733671 CGTGCATGCACTCTGGTCG 61.734 63.158 39.46 25.43 44.16 4.79
4185 5117 0.033366 TGTGTACGTGCATGCACTCT 59.967 50.000 39.46 28.72 44.16 3.24
4191 5123 2.543848 AGTCAAACTGTGTACGTGCATG 59.456 45.455 10.21 3.82 0.00 4.06
4194 5126 2.605818 TCAAGTCAAACTGTGTACGTGC 59.394 45.455 0.00 0.00 0.00 5.34
4195 5127 5.403897 AATCAAGTCAAACTGTGTACGTG 57.596 39.130 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.