Multiple sequence alignment - TraesCS6A01G197600

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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 TraesCS6A01G197600 chr6A 100.000 4392 0 0 1 4392 298324293 298328684 0.000000e+00 8111
1 TraesCS6A01G197600 chr6A 91.270 1638 129 13 2764 4392 99394969 99396601 0.000000e+00 2220
2 TraesCS6A01G197600 chr6A 91.843 993 72 7 2764 3749 130454434 130453444 0.000000e+00 1376
3 TraesCS6A01G197600 chr7D 94.156 2755 119 9 1 2733 59692455 59689721 0.000000e+00 4157
4 TraesCS6A01G197600 chr7D 95.378 649 28 1 3744 4392 41185104 41184458 0.000000e+00 1031
5 TraesCS6A01G197600 chr7D 95.194 645 28 3 3748 4392 146081296 146080655 0.000000e+00 1016
6 TraesCS6A01G197600 chr7D 93.173 542 34 2 378 917 79046620 79046080 0.000000e+00 793
7 TraesCS6A01G197600 chr3D 93.994 2764 126 15 1 2733 482588018 482590772 0.000000e+00 4148
8 TraesCS6A01G197600 chr3D 91.726 991 75 7 2764 3749 611027065 611028053 0.000000e+00 1369
9 TraesCS6A01G197600 chr3D 95.814 645 24 2 3748 4392 258012874 258012233 0.000000e+00 1038
10 TraesCS6A01G197600 chr6D 93.725 2757 139 12 1 2733 343522013 343524759 0.000000e+00 4102
11 TraesCS6A01G197600 chr6D 90.634 1025 84 11 3372 4392 105278087 105277071 0.000000e+00 1351
12 TraesCS6A01G197600 chr6D 95.349 645 28 2 3748 4392 123758334 123758976 0.000000e+00 1024
13 TraesCS6A01G197600 chr6D 94.313 211 12 0 279 489 58461852 58461642 1.520000e-84 324
14 TraesCS6A01G197600 chr6D 90.769 195 17 1 52 246 154199221 154199414 4.360000e-65 259
15 TraesCS6A01G197600 chr5D 93.396 2756 148 16 1 2733 170710878 170713622 0.000000e+00 4050
16 TraesCS6A01G197600 chr5D 91.200 250 18 3 1 246 254079758 254080007 1.960000e-88 337
17 TraesCS6A01G197600 chr5D 91.818 220 14 1 2518 2733 254080885 254081104 1.980000e-78 303
18 TraesCS6A01G197600 chr2D 93.435 2757 125 17 1 2733 621171015 621168291 0.000000e+00 4037
19 TraesCS6A01G197600 chr2D 95.201 646 27 4 3748 4392 551369106 551368464 0.000000e+00 1018
20 TraesCS6A01G197600 chr5B 94.926 1892 86 7 850 2733 658347010 658348899 0.000000e+00 2953
21 TraesCS6A01G197600 chr5B 91.970 934 58 2 1 917 290877393 290878326 0.000000e+00 1293
22 TraesCS6A01G197600 chr5B 92.308 754 41 2 1 737 658346252 658347005 0.000000e+00 1055
23 TraesCS6A01G197600 chr5B 91.143 621 40 1 1 606 481734404 481735024 0.000000e+00 828
24 TraesCS6A01G197600 chr5B 89.636 357 22 1 1 342 17593366 17593722 1.450000e-119 440
25 TraesCS6A01G197600 chr6B 94.503 1892 91 8 850 2733 651661139 651659253 0.000000e+00 2905
26 TraesCS6A01G197600 chr6B 91.006 934 67 6 1 917 396296136 396297069 0.000000e+00 1243
27 TraesCS6A01G197600 chr6B 92.042 754 43 2 1 737 651661897 651661144 0.000000e+00 1044
28 TraesCS6A01G197600 chr6B 91.584 606 45 4 1 606 245117198 245116599 0.000000e+00 832
29 TraesCS6A01G197600 chr1B 94.447 1891 96 6 850 2733 149121727 149119839 0.000000e+00 2902
30 TraesCS6A01G197600 chr1B 94.242 1893 95 8 850 2733 198113642 198111755 0.000000e+00 2880
31 TraesCS6A01G197600 chr1B 91.756 934 60 2 1 917 92077542 92078475 0.000000e+00 1282
32 TraesCS6A01G197600 chr1B 91.910 754 43 3 1 737 198114399 198113647 0.000000e+00 1038
33 TraesCS6A01G197600 chr1B 90.584 754 54 7 1 737 149122485 149121732 0.000000e+00 983
34 TraesCS6A01G197600 chr1B 88.136 354 27 4 1 339 472253990 472254343 1.470000e-109 407
35 TraesCS6A01G197600 chr1D 88.984 1643 154 23 2764 4392 120804799 120803170 0.000000e+00 2006
36 TraesCS6A01G197600 chr1D 90.400 250 20 3 1 246 425079755 425080004 4.240000e-85 326
37 TraesCS6A01G197600 chr1D 93.213 221 9 4 2518 2733 425081220 425081439 1.970000e-83 320
38 TraesCS6A01G197600 chr1D 89.712 243 18 4 9 246 38867046 38867286 1.980000e-78 303
39 TraesCS6A01G197600 chr1D 87.698 252 25 4 1 246 24463259 24463008 5.560000e-74 289
40 TraesCS6A01G197600 chr1D 87.251 251 26 5 1 246 24484340 24484091 9.300000e-72 281
41 TraesCS6A01G197600 chr2A 90.211 1328 120 8 2764 4083 699396989 699395664 0.000000e+00 1724
42 TraesCS6A01G197600 chr7A 91.843 993 73 7 2764 3749 667903524 667904515 0.000000e+00 1378
43 TraesCS6A01G197600 chr7A 91.641 993 75 8 2764 3752 429306476 429305488 0.000000e+00 1367
44 TraesCS6A01G197600 chr4D 91.972 984 73 6 2773 3752 446501331 446500350 0.000000e+00 1375
45 TraesCS6A01G197600 chr3A 91.558 995 77 7 2764 3752 399674595 399673602 0.000000e+00 1365
46 TraesCS6A01G197600 chr1A 92.827 934 49 3 1 917 365221314 365222246 0.000000e+00 1338
47 TraesCS6A01G197600 chr3B 93.039 747 49 2 1 744 226329883 226329137 0.000000e+00 1088
48 TraesCS6A01G197600 chr2B 94.375 640 34 1 280 917 86849696 86849057 0.000000e+00 981
49 TraesCS6A01G197600 chrUn 89.372 621 51 8 1 606 66128371 66128991 0.000000e+00 767


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 TraesCS6A01G197600 chr6A 298324293 298328684 4391 False 8111.0 8111 100.0000 1 4392 1 chr6A.!!$F2 4391
1 TraesCS6A01G197600 chr6A 99394969 99396601 1632 False 2220.0 2220 91.2700 2764 4392 1 chr6A.!!$F1 1628
2 TraesCS6A01G197600 chr6A 130453444 130454434 990 True 1376.0 1376 91.8430 2764 3749 1 chr6A.!!$R1 985
3 TraesCS6A01G197600 chr7D 59689721 59692455 2734 True 4157.0 4157 94.1560 1 2733 1 chr7D.!!$R2 2732
4 TraesCS6A01G197600 chr7D 41184458 41185104 646 True 1031.0 1031 95.3780 3744 4392 1 chr7D.!!$R1 648
5 TraesCS6A01G197600 chr7D 146080655 146081296 641 True 1016.0 1016 95.1940 3748 4392 1 chr7D.!!$R4 644
6 TraesCS6A01G197600 chr7D 79046080 79046620 540 True 793.0 793 93.1730 378 917 1 chr7D.!!$R3 539
7 TraesCS6A01G197600 chr3D 482588018 482590772 2754 False 4148.0 4148 93.9940 1 2733 1 chr3D.!!$F1 2732
8 TraesCS6A01G197600 chr3D 611027065 611028053 988 False 1369.0 1369 91.7260 2764 3749 1 chr3D.!!$F2 985
9 TraesCS6A01G197600 chr3D 258012233 258012874 641 True 1038.0 1038 95.8140 3748 4392 1 chr3D.!!$R1 644
10 TraesCS6A01G197600 chr6D 343522013 343524759 2746 False 4102.0 4102 93.7250 1 2733 1 chr6D.!!$F3 2732
11 TraesCS6A01G197600 chr6D 105277071 105278087 1016 True 1351.0 1351 90.6340 3372 4392 1 chr6D.!!$R2 1020
12 TraesCS6A01G197600 chr6D 123758334 123758976 642 False 1024.0 1024 95.3490 3748 4392 1 chr6D.!!$F1 644
13 TraesCS6A01G197600 chr5D 170710878 170713622 2744 False 4050.0 4050 93.3960 1 2733 1 chr5D.!!$F1 2732
14 TraesCS6A01G197600 chr5D 254079758 254081104 1346 False 320.0 337 91.5090 1 2733 2 chr5D.!!$F2 2732
15 TraesCS6A01G197600 chr2D 621168291 621171015 2724 True 4037.0 4037 93.4350 1 2733 1 chr2D.!!$R2 2732
16 TraesCS6A01G197600 chr2D 551368464 551369106 642 True 1018.0 1018 95.2010 3748 4392 1 chr2D.!!$R1 644
17 TraesCS6A01G197600 chr5B 658346252 658348899 2647 False 2004.0 2953 93.6170 1 2733 2 chr5B.!!$F4 2732
18 TraesCS6A01G197600 chr5B 290877393 290878326 933 False 1293.0 1293 91.9700 1 917 1 chr5B.!!$F2 916
19 TraesCS6A01G197600 chr5B 481734404 481735024 620 False 828.0 828 91.1430 1 606 1 chr5B.!!$F3 605
20 TraesCS6A01G197600 chr6B 651659253 651661897 2644 True 1974.5 2905 93.2725 1 2733 2 chr6B.!!$R2 2732
21 TraesCS6A01G197600 chr6B 396296136 396297069 933 False 1243.0 1243 91.0060 1 917 1 chr6B.!!$F1 916
22 TraesCS6A01G197600 chr6B 245116599 245117198 599 True 832.0 832 91.5840 1 606 1 chr6B.!!$R1 605
23 TraesCS6A01G197600 chr1B 198111755 198114399 2644 True 1959.0 2880 93.0760 1 2733 2 chr1B.!!$R2 2732
24 TraesCS6A01G197600 chr1B 149119839 149122485 2646 True 1942.5 2902 92.5155 1 2733 2 chr1B.!!$R1 2732
25 TraesCS6A01G197600 chr1B 92077542 92078475 933 False 1282.0 1282 91.7560 1 917 1 chr1B.!!$F1 916
26 TraesCS6A01G197600 chr1D 120803170 120804799 1629 True 2006.0 2006 88.9840 2764 4392 1 chr1D.!!$R3 1628
27 TraesCS6A01G197600 chr1D 425079755 425081439 1684 False 323.0 326 91.8065 1 2733 2 chr1D.!!$F2 2732
28 TraesCS6A01G197600 chr2A 699395664 699396989 1325 True 1724.0 1724 90.2110 2764 4083 1 chr2A.!!$R1 1319
29 TraesCS6A01G197600 chr7A 667903524 667904515 991 False 1378.0 1378 91.8430 2764 3749 1 chr7A.!!$F1 985
30 TraesCS6A01G197600 chr7A 429305488 429306476 988 True 1367.0 1367 91.6410 2764 3752 1 chr7A.!!$R1 988
31 TraesCS6A01G197600 chr4D 446500350 446501331 981 True 1375.0 1375 91.9720 2773 3752 1 chr4D.!!$R1 979
32 TraesCS6A01G197600 chr3A 399673602 399674595 993 True 1365.0 1365 91.5580 2764 3752 1 chr3A.!!$R1 988
33 TraesCS6A01G197600 chr1A 365221314 365222246 932 False 1338.0 1338 92.8270 1 917 1 chr1A.!!$F1 916
34 TraesCS6A01G197600 chr3B 226329137 226329883 746 True 1088.0 1088 93.0390 1 744 1 chr3B.!!$R1 743
35 TraesCS6A01G197600 chr2B 86849057 86849696 639 True 981.0 981 94.3750 280 917 1 chr2B.!!$R1 637
36 TraesCS6A01G197600 chrUn 66128371 66128991 620 False 767.0 767 89.3720 1 606 1 chrUn.!!$F1 605

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
88 93 0.249531 ACACACACGCACGTTGGATA 60.250 50.000 0.0 0.0 0.00 2.59 F
1182 1215 1.066303 CTAGCTCCTCAATCGCTTCGT 59.934 52.381 0.0 0.0 35.33 3.85 F
2572 3063 0.394625 GGAGTAGGAGGACGAGCAGT 60.395 60.000 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1189 1222 0.734309 CGCCAGACTTGCATTGCATA 59.266 50.000 12.95 2.96 38.76 3.14 R
2689 3180 0.258774 AGGTTGTTGTCTGCCACCTT 59.741 50.000 0.00 0.00 0.00 3.50 R
4062 4580 2.019984 CATCCCCAAGCTTAGTTGCTC 58.980 52.381 0.00 0.00 43.24 4.26 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
77 82 3.935872 CCCACACGCACACACACG 61.936 66.667 0.00 0.00 0.00 4.49
88 93 0.249531 ACACACACGCACGTTGGATA 60.250 50.000 0.00 0.00 0.00 2.59
100 105 3.381590 CACGTTGGATACCATCTCTCTCA 59.618 47.826 0.00 0.00 31.53 3.27
182 187 3.710722 CACCGCCCAGCTCTCCTT 61.711 66.667 0.00 0.00 0.00 3.36
184 189 3.080121 CCGCCCAGCTCTCCTTCT 61.080 66.667 0.00 0.00 0.00 2.85
250 255 3.965026 CTCGCCCAGGAGAGTCCCA 62.965 68.421 9.11 0.00 37.19 4.37
323 343 3.474570 GCAGACCTCGCCTCCCAT 61.475 66.667 0.00 0.00 0.00 4.00
712 743 4.571250 GTCATCGAGACGCCACAA 57.429 55.556 0.00 0.00 37.53 3.33
816 849 3.897239 TGTGGGATGTTGTCTCAGTTTT 58.103 40.909 0.00 0.00 38.21 2.43
889 922 1.352017 TCTGATGGTCATGGTGTGCTT 59.648 47.619 0.00 0.00 0.00 3.91
890 923 2.571202 TCTGATGGTCATGGTGTGCTTA 59.429 45.455 0.00 0.00 0.00 3.09
1169 1202 6.874288 AAATGACATTCATTAGCTAGCTCC 57.126 37.500 23.26 1.26 45.57 4.70
1182 1215 1.066303 CTAGCTCCTCAATCGCTTCGT 59.934 52.381 0.00 0.00 35.33 3.85
1189 1222 5.258456 TCCTCAATCGCTTCGTATTAAGT 57.742 39.130 0.00 0.00 0.00 2.24
1203 1236 6.943981 TCGTATTAAGTATGCAATGCAAGTC 58.056 36.000 13.45 5.79 43.62 3.01
1214 1247 2.820037 GCAAGTCTGGCGGGCTAC 60.820 66.667 0.00 0.00 0.00 3.58
1215 1248 2.125106 CAAGTCTGGCGGGCTACC 60.125 66.667 0.00 0.00 0.00 3.18
1312 1345 4.699522 GTGGGACGAAGCGGGCTT 62.700 66.667 5.45 5.45 39.23 4.35
1409 1449 1.993948 GTTTAGAGGAGGCCCCGGT 60.994 63.158 0.00 0.00 40.87 5.28
1431 1471 1.958205 GTCGAGCTGCTGTTGCTGT 60.958 57.895 7.01 0.00 41.30 4.40
1471 1511 2.685017 TCAGGATGGTCGCAGCCT 60.685 61.111 0.00 0.00 36.16 4.58
1489 1529 2.814336 GCCTTTCAAGATTCTCAACGGT 59.186 45.455 0.00 0.00 0.00 4.83
1492 1532 3.485463 TTCAAGATTCTCAACGGTGGT 57.515 42.857 0.00 0.00 0.00 4.16
1671 1878 8.213489 TGTAGGAGTATTTGGCAATGGATATA 57.787 34.615 0.00 0.00 0.00 0.86
2033 2242 7.545265 TGAATTTGGTTGCTGCTATTCATTTAC 59.455 33.333 0.00 0.00 29.76 2.01
2034 2243 4.981806 TGGTTGCTGCTATTCATTTACC 57.018 40.909 0.00 0.00 0.00 2.85
2193 2404 7.164122 TGATCATCTACTTTTGCCTATCATCC 58.836 38.462 0.00 0.00 0.00 3.51
2228 2439 3.738982 TCCATGAAAGTGACACGTGATT 58.261 40.909 25.01 8.34 0.00 2.57
2294 2712 3.244735 TGGCAGAAGTTATGGTTGTGCTA 60.245 43.478 0.00 0.00 42.35 3.49
2374 2860 3.090037 CCACGGTTCCTTCTCTTAGAGA 58.910 50.000 8.00 8.00 36.86 3.10
2390 2876 7.558081 TCTCTTAGAGATGTACTTGTACAGCAT 59.442 37.037 24.63 17.11 38.69 3.79
2410 2896 1.721691 TGTTTTGGATTGGGAGGGGAT 59.278 47.619 0.00 0.00 0.00 3.85
2424 2910 3.139211 GGAGGGGATAATGCTCTTCCTTT 59.861 47.826 0.00 0.00 0.00 3.11
2425 2911 4.140536 GAGGGGATAATGCTCTTCCTTTG 58.859 47.826 0.00 0.00 0.00 2.77
2434 2920 2.037772 TGCTCTTCCTTTGGTCTCTGTC 59.962 50.000 0.00 0.00 0.00 3.51
2538 3029 4.813027 CATGCCATTCAACTAACTTGCTT 58.187 39.130 0.00 0.00 0.00 3.91
2572 3063 0.394625 GGAGTAGGAGGACGAGCAGT 60.395 60.000 0.00 0.00 0.00 4.40
2585 3076 1.938577 CGAGCAGTAGCAGCAAATCAT 59.061 47.619 0.00 0.00 45.49 2.45
2646 3137 1.030457 GATGGCATGAAGAAGGCTGG 58.970 55.000 3.81 0.00 0.00 4.85
2651 3142 1.883638 GCATGAAGAAGGCTGGTGACA 60.884 52.381 0.00 0.00 39.59 3.58
2659 3150 1.136828 AGGCTGGTGACAACAACCTA 58.863 50.000 13.93 0.00 42.06 3.08
2693 3184 5.567423 GCATTTAGAGATGGCAAACAAAGGT 60.567 40.000 0.00 0.00 0.00 3.50
2733 3228 0.774491 ACCCACCTCCCTTGCCTTTA 60.774 55.000 0.00 0.00 0.00 1.85
2734 3229 0.034089 CCCACCTCCCTTGCCTTTAG 60.034 60.000 0.00 0.00 0.00 1.85
2735 3230 0.698818 CCACCTCCCTTGCCTTTAGT 59.301 55.000 0.00 0.00 0.00 2.24
2736 3231 1.075536 CCACCTCCCTTGCCTTTAGTT 59.924 52.381 0.00 0.00 0.00 2.24
2737 3232 2.307686 CCACCTCCCTTGCCTTTAGTTA 59.692 50.000 0.00 0.00 0.00 2.24
2738 3233 3.053619 CCACCTCCCTTGCCTTTAGTTAT 60.054 47.826 0.00 0.00 0.00 1.89
2739 3234 4.165372 CCACCTCCCTTGCCTTTAGTTATA 59.835 45.833 0.00 0.00 0.00 0.98
2740 3235 5.339695 CCACCTCCCTTGCCTTTAGTTATAA 60.340 44.000 0.00 0.00 0.00 0.98
2741 3236 5.823045 CACCTCCCTTGCCTTTAGTTATAAG 59.177 44.000 0.00 0.00 0.00 1.73
2742 3237 5.104067 ACCTCCCTTGCCTTTAGTTATAAGG 60.104 44.000 0.00 0.00 44.09 2.69
2751 3246 6.771188 CCTTTAGTTATAAGGCGTCTCATG 57.229 41.667 0.00 0.00 36.08 3.07
2752 3247 6.513180 CCTTTAGTTATAAGGCGTCTCATGA 58.487 40.000 0.00 0.00 36.08 3.07
2753 3248 6.984474 CCTTTAGTTATAAGGCGTCTCATGAA 59.016 38.462 0.00 0.00 36.08 2.57
2754 3249 7.494625 CCTTTAGTTATAAGGCGTCTCATGAAA 59.505 37.037 0.00 0.00 36.08 2.69
2755 3250 8.780846 TTTAGTTATAAGGCGTCTCATGAAAA 57.219 30.769 0.00 0.00 0.00 2.29
2756 3251 8.958119 TTAGTTATAAGGCGTCTCATGAAAAT 57.042 30.769 0.00 0.00 0.00 1.82
2757 3252 7.865706 AGTTATAAGGCGTCTCATGAAAATT 57.134 32.000 0.00 0.00 0.00 1.82
2758 3253 8.958119 AGTTATAAGGCGTCTCATGAAAATTA 57.042 30.769 0.00 0.00 0.00 1.40
2759 3254 9.561069 AGTTATAAGGCGTCTCATGAAAATTAT 57.439 29.630 0.00 0.00 0.00 1.28
2760 3255 9.599322 GTTATAAGGCGTCTCATGAAAATTATG 57.401 33.333 0.00 0.00 0.00 1.90
2761 3256 9.554395 TTATAAGGCGTCTCATGAAAATTATGA 57.446 29.630 0.00 0.00 33.76 2.15
2762 3257 6.757897 AAGGCGTCTCATGAAAATTATGAA 57.242 33.333 0.00 0.00 34.41 2.57
2763 3258 6.757897 AGGCGTCTCATGAAAATTATGAAA 57.242 33.333 0.00 0.00 34.41 2.69
2764 3259 7.156876 AGGCGTCTCATGAAAATTATGAAAA 57.843 32.000 0.00 0.00 34.41 2.29
2765 3260 7.775120 AGGCGTCTCATGAAAATTATGAAAAT 58.225 30.769 0.00 0.00 34.41 1.82
2766 3261 8.253113 AGGCGTCTCATGAAAATTATGAAAATT 58.747 29.630 0.00 0.00 34.41 1.82
2767 3262 8.323140 GGCGTCTCATGAAAATTATGAAAATTG 58.677 33.333 0.00 0.00 34.41 2.32
2768 3263 8.863049 GCGTCTCATGAAAATTATGAAAATTGT 58.137 29.630 0.00 0.00 34.41 2.71
2902 3397 8.034215 TGATGAAAGCTTTTGAAGAAAAGTTGA 58.966 29.630 14.05 0.00 46.77 3.18
3024 3519 6.212791 TGGGTGCTAGTGTTTCTACTATTCTT 59.787 38.462 0.00 0.00 33.04 2.52
3056 3551 0.727398 GATGTGCTTGGTCTTACCGC 59.273 55.000 0.00 0.00 42.58 5.68
3057 3552 0.676782 ATGTGCTTGGTCTTACCGCC 60.677 55.000 0.00 0.00 42.58 6.13
3115 3610 9.706691 CGGATTCTACTATTAAAAAGCCTATGA 57.293 33.333 0.00 0.00 0.00 2.15
3208 3705 4.561500 TTGGAATCCGTCTTGTCCAATA 57.438 40.909 0.00 0.00 43.54 1.90
3216 3713 5.556915 TCCGTCTTGTCCAATAATTCTTGT 58.443 37.500 3.23 0.00 0.00 3.16
3328 3825 7.659652 ACACTTCACTAGAACAAGAATTAGC 57.340 36.000 0.00 0.00 0.00 3.09
3358 3856 3.493334 TGAATCAATCATGAGGGCATCC 58.507 45.455 0.09 0.00 39.39 3.51
3398 3896 9.793259 ACAAAGATGACAAAACTTAGATCCTTA 57.207 29.630 0.00 0.00 0.00 2.69
3557 4061 7.602644 TGTGTTTTAATTAGTGTTTGTGCCAAA 59.397 29.630 0.00 0.00 0.00 3.28
3583 4088 3.282885 CCTTTAGGATCTTCTTGGGTGC 58.717 50.000 0.00 0.00 37.39 5.01
3586 4091 4.755266 TTAGGATCTTCTTGGGTGCTAC 57.245 45.455 0.00 0.00 0.00 3.58
3628 4134 0.229500 CAAAAACTTTTGCGCTCGCC 59.771 50.000 9.73 0.00 40.76 5.54
3799 4314 6.038603 GTGTGCTTATTTTGATGGCTCTATGA 59.961 38.462 0.00 0.00 0.00 2.15
3957 4475 8.442384 GTTTTGTTGAGTTTTGTGTGATTGAAT 58.558 29.630 0.00 0.00 0.00 2.57
4000 4518 7.361457 TCTTACGATGGATGAAGGAATAAGT 57.639 36.000 0.00 0.00 0.00 2.24
4062 4580 6.148480 CCCAAGATATTATCCAAAAGAGAGCG 59.852 42.308 0.00 0.00 0.00 5.03
4083 4602 1.635487 AGCAACTAAGCTTGGGGATGA 59.365 47.619 14.86 0.00 43.70 2.92
4146 4666 9.793245 CGGTATTTTACTCGAAGCTATATTTTG 57.207 33.333 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 82 2.101582 AGAGAGATGGTATCCAACGTGC 59.898 50.000 0.00 0.00 36.95 5.34
88 93 3.117701 TCGAGGAAGATGAGAGAGATGGT 60.118 47.826 0.00 0.00 0.00 3.55
100 105 2.969262 GAGAAAGGGGATCGAGGAAGAT 59.031 50.000 0.00 0.00 0.00 2.40
201 206 1.305297 TCGGTGGAGATGGTGAGCT 60.305 57.895 0.00 0.00 0.00 4.09
250 255 2.529744 GCCTTGGTGGTGAGGAGGT 61.530 63.158 0.00 0.00 38.35 3.85
425 454 2.203938 TCCCACTCCTCCGCCTTT 60.204 61.111 0.00 0.00 0.00 3.11
670 700 3.311110 GAGTCTCCACCACCCGCA 61.311 66.667 0.00 0.00 0.00 5.69
712 743 0.178973 GGGGCTAACACTTGTTGGGT 60.179 55.000 4.82 0.00 38.90 4.51
816 849 5.836821 AATCTAGTCTACTCATCGCACAA 57.163 39.130 0.00 0.00 0.00 3.33
889 922 4.069304 ACGCTGAACTTAACCTGCAAATA 58.931 39.130 0.00 0.00 0.00 1.40
890 923 2.884639 ACGCTGAACTTAACCTGCAAAT 59.115 40.909 0.00 0.00 0.00 2.32
943 976 2.338984 GTCGTCCGAGTGCAACCT 59.661 61.111 0.00 0.00 37.80 3.50
1071 1104 1.374758 CGCGAAGGCTTTCTGGAGT 60.375 57.895 0.00 0.00 36.88 3.85
1169 1202 6.143919 TGCATACTTAATACGAAGCGATTGAG 59.856 38.462 0.00 0.00 0.00 3.02
1182 1215 6.238731 GCCAGACTTGCATTGCATACTTAATA 60.239 38.462 12.95 0.00 38.76 0.98
1189 1222 0.734309 CGCCAGACTTGCATTGCATA 59.266 50.000 12.95 2.96 38.76 3.14
1214 1247 9.241317 CATTTGTACTACTATGTTAGTAACCGG 57.759 37.037 10.51 0.00 40.49 5.28
1215 1248 9.793252 ACATTTGTACTACTATGTTAGTAACCG 57.207 33.333 10.51 2.16 40.49 4.44
1312 1345 1.203187 AGTAGGAGGAGTGCAAGTGGA 60.203 52.381 0.00 0.00 0.00 4.02
1379 1419 6.407202 GCCTCCTCTAAACAAGACTGAAATA 58.593 40.000 0.00 0.00 0.00 1.40
1409 1449 4.299547 AACAGCAGCTCGACGCCA 62.300 61.111 0.00 0.00 40.39 5.69
1431 1471 4.201679 CCGACGTCGCTATGCCCA 62.202 66.667 31.73 0.00 38.18 5.36
1471 1511 3.563808 CACCACCGTTGAGAATCTTGAAA 59.436 43.478 0.00 0.00 34.92 2.69
1489 1529 3.381983 ATCAGCGCCGAGACACCA 61.382 61.111 2.29 0.00 0.00 4.17
1492 1532 4.819761 GCCATCAGCGCCGAGACA 62.820 66.667 2.29 0.00 0.00 3.41
1520 1560 2.369257 CTGTACCCGCCGATGCTCAT 62.369 60.000 0.00 0.00 34.43 2.90
1956 2165 1.644509 ATAGCTGGACGCCCATCATA 58.355 50.000 0.00 0.00 42.59 2.15
1989 2198 5.789710 ATTCAACGGTACTACCAAAATCG 57.210 39.130 6.06 0.00 38.47 3.34
2033 2242 6.484643 CACATTATCCAACTCCTTCACATAGG 59.515 42.308 0.00 0.00 36.59 2.57
2034 2243 6.017605 GCACATTATCCAACTCCTTCACATAG 60.018 42.308 0.00 0.00 0.00 2.23
2193 2404 6.639686 CACTTTCATGGAAAACATCAGAAGTG 59.360 38.462 0.00 0.00 40.46 3.16
2228 2439 6.463995 TCAGCTAAAGAAAAGCAAAGGAAA 57.536 33.333 0.00 0.00 42.62 3.13
2265 2627 2.821969 CCATAACTTCTGCCAAGCAAGT 59.178 45.455 0.00 0.00 38.41 3.16
2374 2860 5.767665 TCCAAAACATGCTGTACAAGTACAT 59.232 36.000 12.95 0.00 44.15 2.29
2390 2876 1.162505 TCCCCTCCCAATCCAAAACA 58.837 50.000 0.00 0.00 0.00 2.83
2410 2896 4.287067 ACAGAGACCAAAGGAAGAGCATTA 59.713 41.667 0.00 0.00 0.00 1.90
2424 2910 2.223971 GGTTTGACTTCGACAGAGACCA 60.224 50.000 0.00 0.00 0.00 4.02
2425 2911 2.405172 GGTTTGACTTCGACAGAGACC 58.595 52.381 0.00 0.00 0.00 3.85
2434 2920 1.133025 GCATGGATGGGTTTGACTTCG 59.867 52.381 0.00 0.00 0.00 3.79
2490 2977 6.798476 CACGATAAAACTGCAAGGCATATATG 59.202 38.462 8.45 8.45 38.13 1.78
2585 3076 1.971505 GCACCCCGTCATCATCAGGA 61.972 60.000 0.00 0.00 0.00 3.86
2646 3137 3.470645 ACAGGTCTAGGTTGTTGTCAC 57.529 47.619 0.00 0.00 0.00 3.67
2651 3142 1.493022 TGCCAACAGGTCTAGGTTGTT 59.507 47.619 8.26 5.57 42.09 2.83
2659 3150 4.521146 CATCTCTAAATGCCAACAGGTCT 58.479 43.478 0.00 0.00 0.00 3.85
2689 3180 0.258774 AGGTTGTTGTCTGCCACCTT 59.741 50.000 0.00 0.00 0.00 3.50
2693 3184 0.465460 GTCCAGGTTGTTGTCTGCCA 60.465 55.000 0.00 0.00 0.00 4.92
2733 3228 7.865706 AATTTTCATGAGACGCCTTATAACT 57.134 32.000 0.00 0.00 0.00 2.24
2734 3229 9.599322 CATAATTTTCATGAGACGCCTTATAAC 57.401 33.333 0.00 0.00 0.00 1.89
2735 3230 9.554395 TCATAATTTTCATGAGACGCCTTATAA 57.446 29.630 0.00 0.00 0.00 0.98
2736 3231 9.554395 TTCATAATTTTCATGAGACGCCTTATA 57.446 29.630 0.00 0.00 34.07 0.98
2737 3232 8.450578 TTCATAATTTTCATGAGACGCCTTAT 57.549 30.769 0.00 0.00 34.07 1.73
2738 3233 7.857734 TTCATAATTTTCATGAGACGCCTTA 57.142 32.000 0.00 0.00 34.07 2.69
2739 3234 6.757897 TTCATAATTTTCATGAGACGCCTT 57.242 33.333 0.00 0.00 34.07 4.35
2740 3235 6.757897 TTTCATAATTTTCATGAGACGCCT 57.242 33.333 0.00 0.00 34.07 5.52
2741 3236 7.992180 ATTTTCATAATTTTCATGAGACGCC 57.008 32.000 0.00 0.00 34.07 5.68
2742 3237 8.863049 ACAATTTTCATAATTTTCATGAGACGC 58.137 29.630 0.00 0.00 34.07 5.19
2756 3251 9.905713 AGGAGCAACTATCTACAATTTTCATAA 57.094 29.630 0.00 0.00 0.00 1.90
2757 3252 9.905713 AAGGAGCAACTATCTACAATTTTCATA 57.094 29.630 0.00 0.00 0.00 2.15
2758 3253 8.680903 CAAGGAGCAACTATCTACAATTTTCAT 58.319 33.333 0.00 0.00 0.00 2.57
2759 3254 7.882791 TCAAGGAGCAACTATCTACAATTTTCA 59.117 33.333 0.00 0.00 0.00 2.69
2760 3255 8.268850 TCAAGGAGCAACTATCTACAATTTTC 57.731 34.615 0.00 0.00 0.00 2.29
2761 3256 8.814038 ATCAAGGAGCAACTATCTACAATTTT 57.186 30.769 0.00 0.00 0.00 1.82
2762 3257 8.680903 CAATCAAGGAGCAACTATCTACAATTT 58.319 33.333 0.00 0.00 0.00 1.82
2763 3258 8.049117 TCAATCAAGGAGCAACTATCTACAATT 58.951 33.333 0.00 0.00 0.00 2.32
2764 3259 7.568349 TCAATCAAGGAGCAACTATCTACAAT 58.432 34.615 0.00 0.00 0.00 2.71
2765 3260 6.946340 TCAATCAAGGAGCAACTATCTACAA 58.054 36.000 0.00 0.00 0.00 2.41
2766 3261 6.544928 TCAATCAAGGAGCAACTATCTACA 57.455 37.500 0.00 0.00 0.00 2.74
2767 3262 7.497249 ACAATCAATCAAGGAGCAACTATCTAC 59.503 37.037 0.00 0.00 0.00 2.59
2768 3263 7.568349 ACAATCAATCAAGGAGCAACTATCTA 58.432 34.615 0.00 0.00 0.00 1.98
2769 3264 6.421485 ACAATCAATCAAGGAGCAACTATCT 58.579 36.000 0.00 0.00 0.00 1.98
2781 3276 8.980610 TGCAACAAAGAAATACAATCAATCAAG 58.019 29.630 0.00 0.00 0.00 3.02
2920 3415 6.834969 TCCCATTCATCATGCAATTTTCTAGA 59.165 34.615 0.00 0.00 0.00 2.43
2995 3490 6.368779 AGTAGAAACACTAGCACCCAAATA 57.631 37.500 0.00 0.00 0.00 1.40
3024 3519 9.407380 AGACCAAGCACATCACATAAATATTTA 57.593 29.630 10.27 10.27 0.00 1.40
3029 3524 6.095440 GGTAAGACCAAGCACATCACATAAAT 59.905 38.462 0.00 0.00 38.42 1.40
3056 3551 7.960738 GCAAATTCAAAGAACATGATTCAATGG 59.039 33.333 0.00 0.00 31.46 3.16
3057 3552 8.499967 TGCAAATTCAAAGAACATGATTCAATG 58.500 29.630 0.00 3.73 0.00 2.82
3137 3634 7.167924 TGAGCACATAATTCCTATTTGCAAA 57.832 32.000 15.44 15.44 43.40 3.68
3190 3687 6.927294 AGAATTATTGGACAAGACGGATTC 57.073 37.500 0.00 0.00 0.00 2.52
3208 3705 7.593644 GTGCATAAAAACGGTCTAACAAGAATT 59.406 33.333 0.00 0.00 0.00 2.17
3216 3713 6.655848 ACCAATAGTGCATAAAAACGGTCTAA 59.344 34.615 0.00 0.00 0.00 2.10
3244 3741 6.455360 TTGCCTTCTTTCATATCAATCACC 57.545 37.500 0.00 0.00 0.00 4.02
3291 3788 3.000727 GTGAAGTGTTCCATACCCTTCG 58.999 50.000 0.00 0.00 42.21 3.79
3311 3808 4.288626 TGGTGGGCTAATTCTTGTTCTAGT 59.711 41.667 0.00 0.00 0.00 2.57
3328 3825 5.417894 CCTCATGATTGATTCATATGGTGGG 59.582 44.000 2.13 0.00 43.40 4.61
3358 3856 6.758416 TGTCATCTTTGTTTCGAGATCCATAG 59.242 38.462 0.00 0.00 30.43 2.23
3473 3972 8.447053 GCTAACACTCAAGAATAGGAAGAAAAG 58.553 37.037 0.00 0.00 0.00 2.27
3557 4061 5.433381 ACCCAAGAAGATCCTAAAGGCTTAT 59.567 40.000 0.00 0.00 34.44 1.73
3753 4268 4.035017 ACAACGCAAAGAAAACAGAATCG 58.965 39.130 0.00 0.00 0.00 3.34
3799 4314 9.211485 CTATGGCAAAAACTCATCAAAGAAAAT 57.789 29.630 0.00 0.00 0.00 1.82
3957 4475 6.975772 CGTAAGATCACCCAAAACTTGAAAAA 59.024 34.615 0.00 0.00 43.02 1.94
4062 4580 2.019984 CATCCCCAAGCTTAGTTGCTC 58.980 52.381 0.00 0.00 43.24 4.26
4215 4735 5.763204 AGCAAGGAATCGAGACTTAAAACAA 59.237 36.000 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.