Multiple sequence alignment - TraesCS2D01G104300

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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 TraesCS2D01G104300 chr2D 100.000 4307 0 0 1 4307 56231861 56236167 0.000000e+00 7954.0
1 TraesCS2D01G104300 chr2A 93.011 2790 137 24 972 3731 57838568 57841329 0.000000e+00 4019.0
2 TraesCS2D01G104300 chr2A 84.165 802 53 25 148 932 57837831 57838575 0.000000e+00 710.0
3 TraesCS2D01G104300 chr2A 87.681 276 30 4 3766 4038 57841950 57842224 6.950000e-83 318.0
4 TraesCS2D01G104300 chr2A 84.436 257 24 9 4059 4307 57842447 57842695 5.570000e-59 239.0
5 TraesCS2D01G104300 chr2B 92.783 2494 139 20 1456 3921 88976823 88979303 0.000000e+00 3570.0
6 TraesCS2D01G104300 chr2B 85.332 934 62 33 1 913 88975354 88976233 0.000000e+00 896.0
7 TraesCS2D01G104300 chr2B 87.931 464 28 10 972 1407 88976245 88976708 4.940000e-144 521.0
8 TraesCS2D01G104300 chr2B 97.260 73 2 0 1389 1461 88976720 88976792 1.630000e-24 124.0
9 TraesCS2D01G104300 chr6B 80.940 766 118 12 2006 2751 635019590 635020347 8.030000e-162 580.0
10 TraesCS2D01G104300 chr7D 84.100 522 50 19 2660 3179 225675727 225676217 1.400000e-129 473.0
11 TraesCS2D01G104300 chr7D 87.814 279 25 2 2007 2276 637569283 637569561 6.950000e-83 318.0
12 TraesCS2D01G104300 chr7D 87.925 265 25 4 2915 3179 637569742 637569999 5.410000e-79 305.0
13 TraesCS2D01G104300 chr7D 86.170 282 30 2 2003 2275 225675443 225675724 3.260000e-76 296.0
14 TraesCS2D01G104300 chr7D 100.000 57 0 0 2660 2716 637569563 637569619 5.890000e-19 106.0
15 TraesCS2D01G104300 chr7D 80.952 126 11 9 3183 3297 225826422 225826545 2.130000e-13 87.9
16 TraesCS2D01G104300 chr4D 83.877 521 39 21 2660 3175 143563518 143563038 5.080000e-124 455.0
17 TraesCS2D01G104300 chr4D 88.693 283 23 3 2003 2276 143563802 143563520 1.920000e-88 337.0
18 TraesCS2D01G104300 chr7A 85.342 307 20 1 2771 3077 728230692 728230973 1.170000e-75 294.0
19 TraesCS2D01G104300 chr7A 94.595 111 6 0 2166 2276 728230515 728230625 5.730000e-39 172.0
20 TraesCS2D01G104300 chr7A 94.595 111 6 0 2166 2276 728459241 728459131 5.730000e-39 172.0
21 TraesCS2D01G104300 chr7A 100.000 57 0 0 2660 2716 728230627 728230683 5.890000e-19 106.0
22 TraesCS2D01G104300 chr7A 100.000 57 0 0 2660 2716 728459129 728459073 5.890000e-19 106.0
23 TraesCS2D01G104300 chr7A 90.909 55 5 0 2775 2829 728459059 728459005 1.660000e-09 75.0


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 TraesCS2D01G104300 chr2D 56231861 56236167 4306 False 7954.00 7954 100.00000 1 4307 1 chr2D.!!$F1 4306
1 TraesCS2D01G104300 chr2A 57837831 57842695 4864 False 1321.50 4019 87.32325 148 4307 4 chr2A.!!$F1 4159
2 TraesCS2D01G104300 chr2B 88975354 88979303 3949 False 1277.75 3570 90.82650 1 3921 4 chr2B.!!$F1 3920
3 TraesCS2D01G104300 chr6B 635019590 635020347 757 False 580.00 580 80.94000 2006 2751 1 chr6B.!!$F1 745
4 TraesCS2D01G104300 chr7D 225675443 225676217 774 False 384.50 473 85.13500 2003 3179 2 chr7D.!!$F2 1176
5 TraesCS2D01G104300 chr7D 637569283 637569999 716 False 243.00 318 91.91300 2007 3179 3 chr7D.!!$F3 1172
6 TraesCS2D01G104300 chr4D 143563038 143563802 764 True 396.00 455 86.28500 2003 3175 2 chr4D.!!$R1 1172

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
962 1001 0.248336 GGCACGATCACACGATACGA 60.248 55.0 0.0 0.0 37.03 3.43 F
1913 2049 0.175073 GGTACGGTTAGTGCTCCCAG 59.825 60.0 0.0 0.0 35.67 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 2092 0.944311 TTTCAGTCTCGGCTTCACGC 60.944 55.0 0.0 0.0 38.13 5.34 R
3851 4660 0.179084 TGATGGTCGGGCGAAAGATC 60.179 55.0 0.0 0.0 0.00 2.75 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
107 108 4.662961 CGCGACCAGTCACCAGCA 62.663 66.667 0.00 0.00 0.00 4.41
108 109 3.044305 GCGACCAGTCACCAGCAC 61.044 66.667 0.00 0.00 0.00 4.40
109 110 2.734723 CGACCAGTCACCAGCACG 60.735 66.667 0.00 0.00 0.00 5.34
110 111 2.734591 GACCAGTCACCAGCACGA 59.265 61.111 0.00 0.00 0.00 4.35
113 114 1.293179 CCAGTCACCAGCACGATCA 59.707 57.895 0.00 0.00 0.00 2.92
121 122 4.063967 AGCACGATCACCGCGGAA 62.064 61.111 35.90 20.33 43.32 4.30
342 357 1.275291 GGTCGTCCCTGTCATTGAAGA 59.725 52.381 0.00 0.00 0.00 2.87
379 400 3.157949 CCCGCCTCCTTCCTCCTC 61.158 72.222 0.00 0.00 0.00 3.71
380 401 3.157949 CCGCCTCCTTCCTCCTCC 61.158 72.222 0.00 0.00 0.00 4.30
381 402 3.532155 CGCCTCCTTCCTCCTCCG 61.532 72.222 0.00 0.00 0.00 4.63
382 403 2.364448 GCCTCCTTCCTCCTCCGT 60.364 66.667 0.00 0.00 0.00 4.69
383 404 2.428085 GCCTCCTTCCTCCTCCGTC 61.428 68.421 0.00 0.00 0.00 4.79
384 405 1.758906 CCTCCTTCCTCCTCCGTCC 60.759 68.421 0.00 0.00 0.00 4.79
385 406 1.308326 CTCCTTCCTCCTCCGTCCT 59.692 63.158 0.00 0.00 0.00 3.85
386 407 0.753848 CTCCTTCCTCCTCCGTCCTC 60.754 65.000 0.00 0.00 0.00 3.71
387 408 2.122167 CCTTCCTCCTCCGTCCTCG 61.122 68.421 0.00 0.00 0.00 4.63
388 409 1.378778 CTTCCTCCTCCGTCCTCGT 60.379 63.158 0.00 0.00 35.01 4.18
520 548 2.338620 CAACAGGGACGCGTCTCA 59.661 61.111 38.15 0.00 30.85 3.27
562 597 2.094700 CGTACTACAAGAAGCAGAGCCA 60.095 50.000 0.00 0.00 0.00 4.75
588 623 1.213013 CTGTCCGGTCTGAACTCCG 59.787 63.158 0.00 0.00 45.42 4.63
595 630 1.784525 GGTCTGAACTCCGAACAGTG 58.215 55.000 0.00 0.00 33.93 3.66
672 707 2.516460 TAGGAGAGGCGGCTCGAC 60.516 66.667 30.50 25.94 35.74 4.20
673 708 3.339738 TAGGAGAGGCGGCTCGACA 62.340 63.158 30.50 15.91 37.34 4.35
674 709 4.200283 GGAGAGGCGGCTCGACAG 62.200 72.222 30.50 0.00 37.34 3.51
811 850 1.536073 TAGCTGTGCTCGAGTGCCTT 61.536 55.000 15.13 2.31 40.44 4.35
845 884 2.293399 CCTCCTTTCCGGAAACAACAAG 59.707 50.000 25.67 14.45 42.53 3.16
860 899 5.169836 ACAACAAGTTGGACGAAGAAATC 57.830 39.130 16.45 0.00 44.45 2.17
899 938 4.143030 ACGATTTCATGCTTTCTTCTGTCG 60.143 41.667 0.00 0.00 0.00 4.35
908 947 3.175240 CTTCTGTCGACGCAGGCG 61.175 66.667 12.71 12.71 46.03 5.52
924 963 0.451783 GGCGGCGACTTTGATTGATT 59.548 50.000 12.98 0.00 0.00 2.57
928 967 2.789092 CGGCGACTTTGATTGATTGAGC 60.789 50.000 0.00 0.00 0.00 4.26
932 971 4.512657 CGACTTTGATTGATTGAGCGATC 58.487 43.478 0.00 0.00 0.00 3.69
933 972 4.512657 GACTTTGATTGATTGAGCGATCG 58.487 43.478 11.69 11.69 32.39 3.69
934 973 4.183865 ACTTTGATTGATTGAGCGATCGA 58.816 39.130 21.57 0.00 32.39 3.59
935 974 4.033358 ACTTTGATTGATTGAGCGATCGAC 59.967 41.667 21.57 12.41 32.39 4.20
936 975 2.119457 TGATTGATTGAGCGATCGACG 58.881 47.619 21.57 0.00 45.66 5.12
937 976 1.453524 GATTGATTGAGCGATCGACGG 59.546 52.381 21.57 0.00 42.83 4.79
938 977 1.145759 TTGATTGAGCGATCGACGGC 61.146 55.000 21.57 0.00 42.83 5.68
939 978 2.639926 GATTGAGCGATCGACGGCG 61.640 63.158 21.57 2.87 42.83 6.46
957 996 4.429212 CCGGGCACGATCACACGA 62.429 66.667 11.66 0.00 44.60 4.35
958 997 2.202743 CGGGCACGATCACACGAT 60.203 61.111 0.00 0.00 44.60 3.73
959 998 1.065109 CGGGCACGATCACACGATA 59.935 57.895 0.00 0.00 44.60 2.92
960 999 1.206745 CGGGCACGATCACACGATAC 61.207 60.000 0.00 0.00 44.60 2.24
961 1000 1.206745 GGGCACGATCACACGATACG 61.207 60.000 0.00 0.00 37.03 3.06
962 1001 0.248336 GGCACGATCACACGATACGA 60.248 55.000 0.00 0.00 37.03 3.43
963 1002 1.113253 GCACGATCACACGATACGAG 58.887 55.000 0.00 0.00 37.03 4.18
964 1003 1.531264 GCACGATCACACGATACGAGT 60.531 52.381 0.00 0.00 37.03 4.18
965 1004 2.101878 CACGATCACACGATACGAGTG 58.898 52.381 13.48 13.48 46.37 3.51
966 1005 1.113253 CGATCACACGATACGAGTGC 58.887 55.000 14.49 3.95 45.11 4.40
967 1006 1.113253 GATCACACGATACGAGTGCG 58.887 55.000 14.49 0.00 45.11 5.34
968 1007 0.866061 ATCACACGATACGAGTGCGC 60.866 55.000 14.49 0.00 45.11 6.09
969 1008 2.202570 ACACGATACGAGTGCGCC 60.203 61.111 4.18 0.00 42.94 6.53
970 1009 3.312504 CACGATACGAGTGCGCCG 61.313 66.667 4.18 3.44 42.48 6.46
973 1012 4.899687 GATACGAGTGCGCCGCGA 62.900 66.667 23.45 11.06 42.48 5.87
974 1013 4.907034 ATACGAGTGCGCCGCGAG 62.907 66.667 23.45 1.54 42.48 5.03
991 1030 1.743996 GAGTGATGTTCTTGGGCCTC 58.256 55.000 4.53 0.00 0.00 4.70
1127 1178 2.158755 CCAGCCTCCGAGGTAAATTCAT 60.159 50.000 16.09 0.00 37.80 2.57
1129 1180 2.505819 AGCCTCCGAGGTAAATTCATGT 59.494 45.455 16.09 0.00 37.80 3.21
1130 1181 2.872858 GCCTCCGAGGTAAATTCATGTC 59.127 50.000 16.09 0.00 37.80 3.06
1178 1245 0.380378 CCATGTAATTTGTCGCGGGG 59.620 55.000 6.13 0.00 0.00 5.73
1189 1256 2.824041 CGCGGGGTTCTGATTGGG 60.824 66.667 0.00 0.00 0.00 4.12
1198 1265 3.305131 GGGTTCTGATTGGGTTTCGTTTC 60.305 47.826 0.00 0.00 0.00 2.78
1510 1643 2.512515 GGAGTGCCGATCAGGTGC 60.513 66.667 0.00 0.00 43.70 5.01
1514 1647 1.672356 GTGCCGATCAGGTGCAAGT 60.672 57.895 0.00 0.00 43.70 3.16
1796 1929 0.616111 AGGAAGCATCACTCCTCGGT 60.616 55.000 0.00 0.00 0.00 4.69
1862 1998 0.324738 AGTGCCGATCAGGAGGAAGA 60.325 55.000 7.64 0.00 45.00 2.87
1869 2005 2.402564 GATCAGGAGGAAGATGGTGGA 58.597 52.381 0.00 0.00 0.00 4.02
1870 2006 1.573108 TCAGGAGGAAGATGGTGGAC 58.427 55.000 0.00 0.00 0.00 4.02
1871 2007 0.543749 CAGGAGGAAGATGGTGGACC 59.456 60.000 0.00 0.00 0.00 4.46
1897 2033 4.475444 CTCGCAGGGGGAGGGGTA 62.475 72.222 2.66 0.00 38.66 3.69
1902 2038 3.619030 AGGGGGAGGGGTACGGTT 61.619 66.667 0.00 0.00 0.00 4.44
1913 2049 0.175073 GGTACGGTTAGTGCTCCCAG 59.825 60.000 0.00 0.00 35.67 4.45
1956 2092 2.726351 GCGAGGTTCAGAGAGGGGG 61.726 68.421 0.00 0.00 0.00 5.40
2283 2441 3.499737 CCAAGGACACCATCGCGC 61.500 66.667 0.00 0.00 0.00 6.86
2522 2680 3.561213 CAGCTGCTGCGATCACGG 61.561 66.667 17.73 0.00 45.42 4.94
2524 2682 3.558411 GCTGCTGCGATCACGGTC 61.558 66.667 0.00 0.00 40.15 4.79
2525 2683 2.125952 CTGCTGCGATCACGGTCA 60.126 61.111 0.00 0.00 40.15 4.02
2526 2684 2.432456 TGCTGCGATCACGGTCAC 60.432 61.111 0.00 0.00 40.15 3.67
2528 2686 2.880879 CTGCGATCACGGTCACGG 60.881 66.667 0.00 0.00 46.48 4.94
2931 3120 2.580867 GCGAGCAGCTACTCCACG 60.581 66.667 8.41 0.00 44.04 4.94
3183 3378 2.115291 GGGGAAAGGCATCTGCGTC 61.115 63.158 0.00 0.00 43.26 5.19
3186 3381 1.696832 GGAAAGGCATCTGCGTCGAC 61.697 60.000 5.18 5.18 43.26 4.20
3311 3506 0.678395 ATCAGGATCAGGTAGCAGCG 59.322 55.000 0.00 0.00 0.00 5.18
3336 3537 2.608546 GAGCTCGGCTCGTCGTATATAT 59.391 50.000 9.63 0.00 45.85 0.86
3337 3538 3.790091 AGCTCGGCTCGTCGTATATATA 58.210 45.455 0.00 0.00 30.62 0.86
3338 3539 3.555139 AGCTCGGCTCGTCGTATATATAC 59.445 47.826 12.18 12.18 30.62 1.47
3340 3541 4.550447 GCTCGGCTCGTCGTATATATACTG 60.550 50.000 18.46 12.74 0.00 2.74
3341 3542 4.498241 TCGGCTCGTCGTATATATACTGT 58.502 43.478 18.46 0.00 0.00 3.55
3343 3544 5.745769 TCGGCTCGTCGTATATATACTGTAG 59.254 44.000 18.46 11.94 0.00 2.74
3525 3728 6.935167 TGTTGCAGAAATGTAGATACTCAGA 58.065 36.000 0.00 0.00 0.00 3.27
3536 3739 4.935352 AGATACTCAGACTCTCAATGCC 57.065 45.455 0.00 0.00 0.00 4.40
3543 3746 3.447229 TCAGACTCTCAATGCCGTGATTA 59.553 43.478 0.00 0.00 0.00 1.75
3545 3748 4.210746 CAGACTCTCAATGCCGTGATTATG 59.789 45.833 0.00 0.00 0.00 1.90
3557 3772 5.013079 TGCCGTGATTATGAGGATAAGGAAT 59.987 40.000 0.00 0.00 0.00 3.01
3622 3837 8.902806 ACAGTTCTAAAATCAAGTTCATGTTCA 58.097 29.630 0.00 0.00 0.00 3.18
3627 3842 9.195411 TCTAAAATCAAGTTCATGTTCATTTGC 57.805 29.630 0.00 0.00 0.00 3.68
3632 3847 6.671190 TCAAGTTCATGTTCATTTGCTACTG 58.329 36.000 0.00 0.00 0.00 2.74
3678 3894 5.220970 CGTTGCCACGGGATAATAGAAAAAT 60.221 40.000 1.68 0.00 43.16 1.82
3768 4577 9.880157 CAAATATGGATTTTGGACATCTTTCTT 57.120 29.630 0.00 0.00 32.73 2.52
3772 4581 6.077322 TGGATTTTGGACATCTTTCTTCCTT 58.923 36.000 0.00 0.00 0.00 3.36
3782 4591 5.045942 ACATCTTTCTTCCTTCTTCTCCTCC 60.046 44.000 0.00 0.00 0.00 4.30
3828 4637 1.795768 CCTTTGCTCTAGCGTTGTCA 58.204 50.000 0.00 0.00 45.83 3.58
3837 4646 4.272018 GCTCTAGCGTTGTCATCATTTCAT 59.728 41.667 0.00 0.00 0.00 2.57
3842 4651 6.441093 AGCGTTGTCATCATTTCATTACAT 57.559 33.333 0.00 0.00 0.00 2.29
3847 4656 9.773328 CGTTGTCATCATTTCATTACATAAGTT 57.227 29.630 0.00 0.00 0.00 2.66
3851 4660 9.507280 GTCATCATTTCATTACATAAGTTGGTG 57.493 33.333 0.00 0.00 0.00 4.17
3871 4680 0.251916 ATCTTTCGCCCGACCATCAA 59.748 50.000 0.00 0.00 0.00 2.57
3929 4738 5.522460 TGAAATAATCCTCACGAATCCGAAC 59.478 40.000 0.00 0.00 39.50 3.95
3950 4759 3.802139 ACGAGCGATTGTTGTATGTATGG 59.198 43.478 0.00 0.00 0.00 2.74
3965 4774 8.675705 TGTATGTATGGTTTACAGATGGAATG 57.324 34.615 0.00 0.00 0.00 2.67
3971 4780 4.764823 TGGTTTACAGATGGAATGGTTGTC 59.235 41.667 0.00 0.00 0.00 3.18
3993 4802 4.519350 TCGCCTACTCACCTATAATGACAG 59.481 45.833 0.00 0.00 0.00 3.51
3994 4803 4.321304 CGCCTACTCACCTATAATGACAGG 60.321 50.000 0.00 0.00 37.97 4.00
3995 4804 4.021016 GCCTACTCACCTATAATGACAGGG 60.021 50.000 9.53 0.00 36.15 4.45
3999 4808 5.155161 ACTCACCTATAATGACAGGGCATA 58.845 41.667 0.00 0.00 36.15 3.14
4015 4825 7.889469 ACAGGGCATAGCATATTAAATTTCTG 58.111 34.615 0.00 0.00 0.00 3.02
4018 4828 9.979897 AGGGCATAGCATATTAAATTTCTGATA 57.020 29.630 0.00 0.00 0.00 2.15
4044 5057 5.450826 GCAATATGAAAGATGCACATGGTGA 60.451 40.000 0.00 0.00 38.63 4.02
4052 5065 3.827876 AGATGCACATGGTGAAATGACAA 59.172 39.130 0.00 0.00 35.23 3.18
4053 5066 4.281435 AGATGCACATGGTGAAATGACAAA 59.719 37.500 0.00 0.00 35.23 2.83
4054 5067 4.397481 TGCACATGGTGAAATGACAAAA 57.603 36.364 0.00 0.00 35.23 2.44
4055 5068 4.763073 TGCACATGGTGAAATGACAAAAA 58.237 34.783 0.00 0.00 35.23 1.94
4081 5094 8.641498 AATTGTCTTGACTCCAACAAAGATAT 57.359 30.769 2.35 0.00 0.00 1.63
4086 5099 9.220767 GTCTTGACTCCAACAAAGATATAGTTT 57.779 33.333 0.00 0.00 0.00 2.66
4091 5104 9.827411 GACTCCAACAAAGATATAGTTTGAAAC 57.173 33.333 14.21 0.00 38.13 2.78
4094 5107 8.296713 TCCAACAAAGATATAGTTTGAAACTGC 58.703 33.333 20.06 7.27 42.84 4.40
4095 5108 8.081633 CCAACAAAGATATAGTTTGAAACTGCA 58.918 33.333 20.06 8.19 42.84 4.41
4096 5109 9.462174 CAACAAAGATATAGTTTGAAACTGCAA 57.538 29.630 20.06 6.12 42.84 4.08
4097 5110 9.683069 AACAAAGATATAGTTTGAAACTGCAAG 57.317 29.630 20.06 5.10 42.84 4.01
4098 5111 9.066892 ACAAAGATATAGTTTGAAACTGCAAGA 57.933 29.630 20.06 0.26 42.84 3.02
4099 5112 9.897744 CAAAGATATAGTTTGAAACTGCAAGAA 57.102 29.630 20.06 0.00 42.84 2.52
4101 5114 9.899226 AAGATATAGTTTGAAACTGCAAGAAAC 57.101 29.630 20.06 4.40 42.84 2.78
4114 5127 4.493547 TGCAAGAAACCAAGAAACACAAG 58.506 39.130 0.00 0.00 0.00 3.16
4122 5135 4.093743 ACCAAGAAACACAAGGGAAAAGT 58.906 39.130 0.00 0.00 0.00 2.66
4135 5150 8.023128 CACAAGGGAAAAGTTGTATACATGAAG 58.977 37.037 6.36 0.00 35.10 3.02
4139 5154 9.014297 AGGGAAAAGTTGTATACATGAAGAAAG 57.986 33.333 6.36 0.00 0.00 2.62
4166 5181 7.745620 ACTAAAACAAGGATCTGGTTAACTG 57.254 36.000 5.42 0.00 26.14 3.16
4169 5184 7.654022 AAAACAAGGATCTGGTTAACTGAAA 57.346 32.000 5.42 0.00 26.14 2.69
4171 5186 7.839680 AACAAGGATCTGGTTAACTGAAATT 57.160 32.000 5.42 0.00 0.00 1.82
4181 5199 8.221944 TCTGGTTAACTGAAATTTCCTTCCTTA 58.778 33.333 15.48 1.88 0.00 2.69
4203 5222 4.829064 AACTTCTTTAGTTTCGCATGCA 57.171 36.364 19.57 1.73 44.73 3.96
4229 5248 4.614555 TTGCTACATAAGGTGATTTGCG 57.385 40.909 0.00 0.00 0.00 4.85
4287 5308 6.781138 TGAAACAATAATCATGGTTACTCGC 58.219 36.000 0.00 0.00 27.57 5.03
4296 5317 2.851263 TGGTTACTCGCTTGAACCAT 57.149 45.000 1.63 0.00 45.95 3.55
4299 5320 2.415512 GGTTACTCGCTTGAACCATGTC 59.584 50.000 0.00 0.00 41.93 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.030297 AGCTGGGAGGAGACCATCAT 60.030 55.000 0.00 0.00 37.38 2.45
43 44 3.168604 CGCTCACTGTCGCTGTCG 61.169 66.667 0.00 0.00 0.00 4.35
91 92 3.044305 GTGCTGGTGACTGGTCGC 61.044 66.667 5.80 5.80 39.26 5.19
92 93 2.492449 ATCGTGCTGGTGACTGGTCG 62.492 60.000 0.00 0.00 0.00 4.79
94 95 1.293498 GATCGTGCTGGTGACTGGT 59.707 57.895 0.00 0.00 0.00 4.00
97 98 1.293498 GGTGATCGTGCTGGTGACT 59.707 57.895 0.00 0.00 0.00 3.41
98 99 2.094659 CGGTGATCGTGCTGGTGAC 61.095 63.158 0.00 0.00 0.00 3.67
99 100 2.261361 CGGTGATCGTGCTGGTGA 59.739 61.111 0.00 0.00 0.00 4.02
100 101 3.490759 GCGGTGATCGTGCTGGTG 61.491 66.667 0.00 0.00 41.72 4.17
103 104 4.794439 TCCGCGGTGATCGTGCTG 62.794 66.667 27.15 0.00 46.91 4.41
104 105 3.583276 TTTCCGCGGTGATCGTGCT 62.583 57.895 27.15 0.00 46.91 4.40
105 106 2.563086 CTTTTCCGCGGTGATCGTGC 62.563 60.000 27.15 0.00 46.91 5.34
107 108 1.740296 CCTTTTCCGCGGTGATCGT 60.740 57.895 27.15 0.00 41.72 3.73
108 109 3.089784 CCTTTTCCGCGGTGATCG 58.910 61.111 27.15 10.89 42.76 3.69
109 110 2.791927 GCCTTTTCCGCGGTGATC 59.208 61.111 27.15 7.07 0.00 2.92
110 111 3.124921 CGCCTTTTCCGCGGTGAT 61.125 61.111 27.15 0.00 45.80 3.06
118 119 3.500642 GCCGCTCTCGCCTTTTCC 61.501 66.667 0.00 0.00 0.00 3.13
288 289 2.038269 GGATTTGGCGTTGGCGAGA 61.038 57.895 0.00 0.00 41.24 4.04
582 617 1.227853 GGGTGCACTGTTCGGAGTT 60.228 57.895 17.98 0.00 0.00 3.01
588 623 3.712881 GTCGCGGGTGCACTGTTC 61.713 66.667 17.98 0.00 42.97 3.18
655 690 2.516460 GTCGAGCCGCCTCTCCTA 60.516 66.667 0.00 0.00 35.90 2.94
676 711 1.265454 TTCTTCTTCCTCCGGCCCTC 61.265 60.000 0.00 0.00 0.00 4.30
677 712 1.229529 TTCTTCTTCCTCCGGCCCT 60.230 57.895 0.00 0.00 0.00 5.19
678 713 1.222113 CTTCTTCTTCCTCCGGCCC 59.778 63.158 0.00 0.00 0.00 5.80
679 714 0.613777 TTCTTCTTCTTCCTCCGGCC 59.386 55.000 0.00 0.00 0.00 6.13
680 715 2.009542 GCTTCTTCTTCTTCCTCCGGC 61.010 57.143 0.00 0.00 0.00 6.13
681 716 1.552792 AGCTTCTTCTTCTTCCTCCGG 59.447 52.381 0.00 0.00 0.00 5.14
682 717 2.615869 CAGCTTCTTCTTCTTCCTCCG 58.384 52.381 0.00 0.00 0.00 4.63
683 718 2.289945 TGCAGCTTCTTCTTCTTCCTCC 60.290 50.000 0.00 0.00 0.00 4.30
689 724 2.425539 GCTCTTGCAGCTTCTTCTTCT 58.574 47.619 0.00 0.00 45.83 2.85
761 796 2.350522 CACTCACCTCAAAATCTCCCG 58.649 52.381 0.00 0.00 0.00 5.14
811 850 2.723530 AAGGAGGAAGAACAGGAGGA 57.276 50.000 0.00 0.00 0.00 3.71
845 884 1.136057 GCACCGATTTCTTCGTCCAAC 60.136 52.381 0.00 0.00 46.65 3.77
860 899 2.175811 GTTAGCGCTTTGGCACCG 59.824 61.111 18.68 0.00 38.60 4.94
883 922 1.201855 GCGTCGACAGAAGAAAGCATG 60.202 52.381 17.16 0.00 0.00 4.06
908 947 2.789092 CGCTCAATCAATCAAAGTCGCC 60.789 50.000 0.00 0.00 0.00 5.54
913 952 4.512657 GTCGATCGCTCAATCAATCAAAG 58.487 43.478 11.09 0.00 0.00 2.77
940 979 2.344521 TATCGTGTGATCGTGCCCGG 62.345 60.000 0.00 0.00 35.99 5.73
941 980 1.065109 TATCGTGTGATCGTGCCCG 59.935 57.895 0.00 0.00 35.99 6.13
942 981 1.206745 CGTATCGTGTGATCGTGCCC 61.207 60.000 0.00 0.00 35.99 5.36
943 982 0.248336 TCGTATCGTGTGATCGTGCC 60.248 55.000 0.00 0.00 35.99 5.01
944 983 1.113253 CTCGTATCGTGTGATCGTGC 58.887 55.000 0.00 0.00 35.99 5.34
945 984 2.453650 ACTCGTATCGTGTGATCGTG 57.546 50.000 0.00 0.00 35.99 4.35
952 991 2.202570 GGCGCACTCGTATCGTGT 60.203 61.111 10.83 0.00 38.14 4.49
953 992 3.312504 CGGCGCACTCGTATCGTG 61.313 66.667 10.83 0.00 38.14 4.35
956 995 4.899687 TCGCGGCGCACTCGTATC 62.900 66.667 32.61 0.00 38.14 2.24
957 996 4.907034 CTCGCGGCGCACTCGTAT 62.907 66.667 32.61 0.00 38.14 3.06
965 1004 4.210304 GAACATCACTCGCGGCGC 62.210 66.667 24.21 24.21 0.00 6.53
966 1005 2.094659 AAGAACATCACTCGCGGCG 61.095 57.895 17.70 17.70 0.00 6.46
967 1006 1.421485 CAAGAACATCACTCGCGGC 59.579 57.895 6.13 0.00 0.00 6.53
968 1007 1.361668 CCCAAGAACATCACTCGCGG 61.362 60.000 6.13 0.00 0.00 6.46
969 1008 1.970917 GCCCAAGAACATCACTCGCG 61.971 60.000 0.00 0.00 0.00 5.87
970 1009 1.648467 GGCCCAAGAACATCACTCGC 61.648 60.000 0.00 0.00 0.00 5.03
971 1010 0.036010 AGGCCCAAGAACATCACTCG 60.036 55.000 0.00 0.00 0.00 4.18
972 1011 1.680249 GGAGGCCCAAGAACATCACTC 60.680 57.143 0.00 0.00 0.00 3.51
973 1012 0.329596 GGAGGCCCAAGAACATCACT 59.670 55.000 0.00 0.00 0.00 3.41
974 1013 0.329596 AGGAGGCCCAAGAACATCAC 59.670 55.000 0.00 0.00 33.88 3.06
975 1014 0.620556 GAGGAGGCCCAAGAACATCA 59.379 55.000 0.00 0.00 33.88 3.07
976 1015 0.462759 CGAGGAGGCCCAAGAACATC 60.463 60.000 0.00 0.00 33.88 3.06
977 1016 1.604378 CGAGGAGGCCCAAGAACAT 59.396 57.895 0.00 0.00 33.88 2.71
978 1017 2.592993 CCGAGGAGGCCCAAGAACA 61.593 63.158 0.00 0.00 33.88 3.18
979 1018 2.269241 CCGAGGAGGCCCAAGAAC 59.731 66.667 0.00 0.00 33.88 3.01
991 1030 2.356793 GATCGCCATGAGCCGAGG 60.357 66.667 0.00 0.00 38.78 4.63
1178 1245 3.002965 ACGAAACGAAACCCAATCAGAAC 59.997 43.478 0.00 0.00 0.00 3.01
1189 1256 1.525804 GCGCAACCACGAAACGAAAC 61.526 55.000 0.30 0.00 34.06 2.78
1198 1265 4.306471 TTTCGCTGCGCAACCACG 62.306 61.111 18.65 13.38 0.00 4.94
1272 1339 2.752238 CGAGGAGACGGCAGGACT 60.752 66.667 0.00 0.00 0.00 3.85
1461 1558 1.545706 GCCCCTTCCTCTCAACGACT 61.546 60.000 0.00 0.00 0.00 4.18
1510 1643 1.311859 TGAGAACTGCCAGCAACTTG 58.688 50.000 0.00 0.00 0.00 3.16
1514 1647 1.165907 CGGTTGAGAACTGCCAGCAA 61.166 55.000 0.00 0.00 0.00 3.91
1569 1702 2.507324 GAAGACGGAGCGGCACTC 60.507 66.667 1.45 0.00 45.45 3.51
1672 1805 1.605058 CGAACATCAGGAGTCGGGGT 61.605 60.000 0.00 0.00 0.00 4.95
1766 1899 4.742201 GCTTCCTCGCTGGCGTGA 62.742 66.667 16.72 11.10 40.74 4.35
1811 1944 1.258445 ATGCCCCTTCTTCTCGACGT 61.258 55.000 0.00 0.00 0.00 4.34
1862 1998 2.298661 GGTTCGGAGGGTCCACCAT 61.299 63.158 4.45 0.00 43.89 3.55
1897 2033 2.663196 GCTGGGAGCACTAACCGT 59.337 61.111 0.00 0.00 41.89 4.83
1956 2092 0.944311 TTTCAGTCTCGGCTTCACGC 60.944 55.000 0.00 0.00 38.13 5.34
1969 2105 3.036084 CGCGGCGTCAGTTTCAGT 61.036 61.111 15.36 0.00 0.00 3.41
2292 2450 2.045926 CCTTCTTGCCTGGGACGG 60.046 66.667 0.00 0.00 0.00 4.79
2522 2680 4.008933 ACTCAGGCCTGCCGTGAC 62.009 66.667 28.91 0.00 41.95 3.67
2769 2958 2.409651 GAGTAGGAGAGCACGGCG 59.590 66.667 4.80 4.80 0.00 6.46
2931 3120 4.500116 GGCTGCTCGTCCTCCGTC 62.500 72.222 0.00 0.00 37.94 4.79
3183 3378 4.394078 TCGCCGGTGAAGTCGTCG 62.394 66.667 17.09 0.00 0.00 5.12
3186 3381 4.394078 TCGTCGCCGGTGAAGTCG 62.394 66.667 26.58 22.06 33.95 4.18
3337 3538 9.832445 TGAACTGAAACTATCTTTTTCTACAGT 57.168 29.630 0.00 0.00 34.58 3.55
3340 3541 8.231161 GCCTGAACTGAAACTATCTTTTTCTAC 58.769 37.037 0.00 0.00 34.58 2.59
3341 3542 7.117812 CGCCTGAACTGAAACTATCTTTTTCTA 59.882 37.037 0.00 0.00 34.58 2.10
3343 3544 6.073222 TCGCCTGAACTGAAACTATCTTTTTC 60.073 38.462 0.00 0.00 34.16 2.29
3525 3728 4.375272 CTCATAATCACGGCATTGAGAGT 58.625 43.478 0.00 0.00 34.00 3.24
3543 3746 7.181845 GGACCTGAAGATATTCCTTATCCTCAT 59.818 40.741 0.00 0.00 37.22 2.90
3545 3748 6.728632 AGGACCTGAAGATATTCCTTATCCTC 59.271 42.308 0.00 0.00 37.96 3.71
3627 3842 7.316640 ACAGACATTCAGCTAGTTAACAGTAG 58.683 38.462 8.61 3.05 0.00 2.57
3632 3847 6.091437 ACGTACAGACATTCAGCTAGTTAAC 58.909 40.000 0.00 0.00 0.00 2.01
3692 3908 8.800370 ACACATGTTTCCAAATTAAAACCTTT 57.200 26.923 0.00 0.00 35.07 3.11
3707 3923 7.962373 TGAATAATCGTCATGAACACATGTTTC 59.038 33.333 0.00 4.79 41.24 2.78
3736 4545 8.821686 ATGTCCAAAATCCATATTTGTCACTA 57.178 30.769 0.00 0.00 35.46 2.74
3746 4555 7.413446 AGGAAGAAAGATGTCCAAAATCCATA 58.587 34.615 0.00 0.00 33.57 2.74
3747 4556 6.259123 AGGAAGAAAGATGTCCAAAATCCAT 58.741 36.000 0.00 0.00 33.57 3.41
3748 4557 5.644188 AGGAAGAAAGATGTCCAAAATCCA 58.356 37.500 0.00 0.00 33.57 3.41
3749 4558 6.435591 AGAAGGAAGAAAGATGTCCAAAATCC 59.564 38.462 0.00 0.00 33.57 3.01
3750 4559 7.459795 AGAAGGAAGAAAGATGTCCAAAATC 57.540 36.000 0.00 0.00 33.57 2.17
3754 4563 6.192970 AGAAGAAGGAAGAAAGATGTCCAA 57.807 37.500 0.00 0.00 33.57 3.53
3756 4565 5.045942 AGGAGAAGAAGGAAGAAAGATGTCC 60.046 44.000 0.00 0.00 0.00 4.02
3768 4577 1.001760 CCGGGGAGGAGAAGAAGGA 59.998 63.158 0.00 0.00 45.00 3.36
3769 4578 2.736826 GCCGGGGAGGAGAAGAAGG 61.737 68.421 2.18 0.00 45.00 3.46
3772 4581 4.005978 TGGCCGGGGAGGAGAAGA 62.006 66.667 2.18 0.00 45.00 2.87
3782 4591 3.482232 GATGATGGAGGTGGCCGGG 62.482 68.421 2.18 0.00 0.00 5.73
3837 4646 5.353123 GGCGAAAGATCACCAACTTATGTAA 59.647 40.000 0.00 0.00 0.00 2.41
3842 4651 2.706890 GGGCGAAAGATCACCAACTTA 58.293 47.619 0.00 0.00 28.73 2.24
3847 4656 1.079405 GTCGGGCGAAAGATCACCA 60.079 57.895 0.00 0.00 28.73 4.17
3851 4660 0.179084 TGATGGTCGGGCGAAAGATC 60.179 55.000 0.00 0.00 0.00 2.75
3871 4680 9.062524 GTTAAAATTTTAGAAAAGGTGCCCATT 57.937 29.630 10.40 0.00 0.00 3.16
3901 4710 5.817816 GGATTCGTGAGGATTATTTCACAGT 59.182 40.000 10.04 0.00 42.94 3.55
3904 4713 5.047847 TCGGATTCGTGAGGATTATTTCAC 58.952 41.667 0.00 2.15 40.16 3.18
3910 4719 2.684374 TCGTTCGGATTCGTGAGGATTA 59.316 45.455 0.00 0.00 37.69 1.75
3929 4738 3.802139 ACCATACATACAACAATCGCTCG 59.198 43.478 0.00 0.00 0.00 5.03
3950 4759 4.671766 GCGACAACCATTCCATCTGTAAAC 60.672 45.833 0.00 0.00 0.00 2.01
3965 4774 1.180029 TAGGTGAGTAGGCGACAACC 58.820 55.000 12.62 12.62 37.33 3.77
3971 4780 4.321304 CCTGTCATTATAGGTGAGTAGGCG 60.321 50.000 0.00 0.00 29.69 5.52
4015 4825 7.488150 CCATGTGCATCTTTCATATTGCATATC 59.512 37.037 4.60 0.00 45.80 1.63
4018 4828 5.069914 ACCATGTGCATCTTTCATATTGCAT 59.930 36.000 1.12 0.00 45.80 3.96
4021 4831 6.139048 TCACCATGTGCATCTTTCATATTG 57.861 37.500 0.00 0.00 32.98 1.90
4024 4834 6.377712 TCATTTCACCATGTGCATCTTTCATA 59.622 34.615 0.00 0.00 32.98 2.15
4025 4835 5.186215 TCATTTCACCATGTGCATCTTTCAT 59.814 36.000 0.00 0.00 32.98 2.57
4026 4836 4.523558 TCATTTCACCATGTGCATCTTTCA 59.476 37.500 0.00 0.00 32.98 2.69
4027 4837 4.860907 GTCATTTCACCATGTGCATCTTTC 59.139 41.667 0.00 0.00 32.98 2.62
4028 4838 4.281435 TGTCATTTCACCATGTGCATCTTT 59.719 37.500 0.00 0.00 32.98 2.52
4053 5066 7.610865 TCTTTGTTGGAGTCAAGACAATTTTT 58.389 30.769 2.72 0.00 32.92 1.94
4054 5067 7.169158 TCTTTGTTGGAGTCAAGACAATTTT 57.831 32.000 2.72 0.00 32.92 1.82
4055 5068 6.773976 TCTTTGTTGGAGTCAAGACAATTT 57.226 33.333 2.72 0.00 32.92 1.82
4056 5069 6.966534 ATCTTTGTTGGAGTCAAGACAATT 57.033 33.333 2.72 0.00 32.92 2.32
4057 5070 9.388506 CTATATCTTTGTTGGAGTCAAGACAAT 57.611 33.333 2.72 1.33 32.92 2.71
4060 5073 8.779354 AACTATATCTTTGTTGGAGTCAAGAC 57.221 34.615 0.00 0.00 32.92 3.01
4081 5094 5.906113 TGGTTTCTTGCAGTTTCAAACTA 57.094 34.783 1.43 0.00 40.46 2.24
4086 5099 5.167845 GTTTCTTGGTTTCTTGCAGTTTCA 58.832 37.500 0.00 0.00 0.00 2.69
4091 5104 4.108699 TGTGTTTCTTGGTTTCTTGCAG 57.891 40.909 0.00 0.00 0.00 4.41
4094 5107 4.159506 TCCCTTGTGTTTCTTGGTTTCTTG 59.840 41.667 0.00 0.00 0.00 3.02
4095 5108 4.349365 TCCCTTGTGTTTCTTGGTTTCTT 58.651 39.130 0.00 0.00 0.00 2.52
4096 5109 3.976015 TCCCTTGTGTTTCTTGGTTTCT 58.024 40.909 0.00 0.00 0.00 2.52
4097 5110 4.729227 TTCCCTTGTGTTTCTTGGTTTC 57.271 40.909 0.00 0.00 0.00 2.78
4098 5111 5.012664 ACTTTTCCCTTGTGTTTCTTGGTTT 59.987 36.000 0.00 0.00 0.00 3.27
4099 5112 4.530553 ACTTTTCCCTTGTGTTTCTTGGTT 59.469 37.500 0.00 0.00 0.00 3.67
4100 5113 4.093743 ACTTTTCCCTTGTGTTTCTTGGT 58.906 39.130 0.00 0.00 0.00 3.67
4101 5114 4.736126 ACTTTTCCCTTGTGTTTCTTGG 57.264 40.909 0.00 0.00 0.00 3.61
4114 5127 9.010029 TCTTTCTTCATGTATACAACTTTTCCC 57.990 33.333 10.14 0.00 0.00 3.97
4135 5150 7.941919 ACCAGATCCTTGTTTTAGTTTCTTTC 58.058 34.615 0.00 0.00 0.00 2.62
4139 5154 8.847196 AGTTAACCAGATCCTTGTTTTAGTTTC 58.153 33.333 0.88 0.00 0.00 2.78
4141 5156 7.996644 TCAGTTAACCAGATCCTTGTTTTAGTT 59.003 33.333 0.88 0.00 0.00 2.24
4152 5167 7.363007 GGAAGGAAATTTCAGTTAACCAGATCC 60.363 40.741 19.49 5.19 0.00 3.36
4187 5205 3.266541 TGTGTGCATGCGAAACTAAAG 57.733 42.857 14.09 0.00 0.00 1.85
4203 5222 6.625740 GCAAATCACCTTATGTAGCAATGTGT 60.626 38.462 0.00 0.00 0.00 3.72
4212 5231 6.517605 TGTATAGCGCAAATCACCTTATGTA 58.482 36.000 11.47 0.00 0.00 2.29
4215 5234 6.935741 TTTGTATAGCGCAAATCACCTTAT 57.064 33.333 11.47 0.00 31.74 1.73
4229 5248 9.450807 CAGGTGCTACATTTAAATTTGTATAGC 57.549 33.333 0.00 4.21 31.23 2.97
4263 5284 6.597672 AGCGAGTAACCATGATTATTGTTTCA 59.402 34.615 0.00 0.00 0.00 2.69
4285 5306 1.026718 GGAGGGACATGGTTCAAGCG 61.027 60.000 0.00 0.00 0.00 4.68
4287 5308 2.814805 ATGGAGGGACATGGTTCAAG 57.185 50.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.