Multiple sequence alignment - TraesCS4A01G196300

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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 TraesCS4A01G196300 chr4A 100.000 4178 0 0 1 4178 478303737 478299560 0.000000e+00 7716.0
1 TraesCS4A01G196300 chr4A 94.281 1224 30 16 549 1746 478340498 478339289 0.000000e+00 1836.0
2 TraesCS4A01G196300 chr4A 84.676 1018 82 34 703 1689 478220000 478219026 0.000000e+00 948.0
3 TraesCS4A01G196300 chr4A 88.496 791 63 10 2676 3464 478338863 478338099 0.000000e+00 931.0
4 TraesCS4A01G196300 chr4A 96.607 501 17 0 2152 2652 62547530 62547030 0.000000e+00 832.0
5 TraesCS4A01G196300 chr4A 82.569 327 14 11 1852 2147 478339165 478338851 8.970000e-62 248.0
6 TraesCS4A01G196300 chr4A 86.395 147 10 6 552 688 478220198 478220052 7.230000e-33 152.0
7 TraesCS4A01G196300 chr4B 89.211 1344 74 34 430 1747 139471694 139472992 0.000000e+00 1613.0
8 TraesCS4A01G196300 chr4B 89.137 1344 75 34 430 1747 139510142 139511440 0.000000e+00 1607.0
9 TraesCS4A01G196300 chr4B 87.871 1245 60 43 549 1747 139398649 139399848 0.000000e+00 1378.0
10 TraesCS4A01G196300 chr4B 91.446 830 54 6 2674 3494 139473439 139474260 0.000000e+00 1123.0
11 TraesCS4A01G196300 chr4B 91.205 830 56 6 2674 3494 139400295 139401116 0.000000e+00 1112.0
12 TraesCS4A01G196300 chr4B 93.003 686 43 4 3495 4178 80841369 80840687 0.000000e+00 996.0
13 TraesCS4A01G196300 chr4B 87.252 808 76 12 2676 3466 139516268 139517065 0.000000e+00 896.0
14 TraesCS4A01G196300 chr4B 93.864 440 26 1 2674 3113 139532236 139532674 0.000000e+00 662.0
15 TraesCS4A01G196300 chr4B 88.212 509 32 12 1187 1694 139511506 139511987 2.160000e-162 582.0
16 TraesCS4A01G196300 chr4B 91.294 402 35 0 2779 3180 139545947 139546348 2.200000e-152 549.0
17 TraesCS4A01G196300 chr4B 91.293 379 25 1 3124 3494 139533719 139534097 1.040000e-140 510.0
18 TraesCS4A01G196300 chr4B 86.280 379 26 10 1745 2104 139399896 139400267 5.070000e-104 388.0
19 TraesCS4A01G196300 chr4B 86.280 379 26 10 1745 2104 139473040 139473411 5.070000e-104 388.0
20 TraesCS4A01G196300 chr4B 86.994 346 12 6 112 432 139509559 139509896 3.970000e-95 359.0
21 TraesCS4A01G196300 chr4B 86.705 346 13 6 112 432 139471111 139471448 1.850000e-93 353.0
22 TraesCS4A01G196300 chr4B 93.780 209 12 1 1939 2147 139516073 139516280 3.140000e-81 313.0
23 TraesCS4A01G196300 chr4B 93.814 194 11 1 24 216 139531194 139531387 1.470000e-74 291.0
24 TraesCS4A01G196300 chr4B 88.235 238 15 3 359 583 139528880 139529117 5.320000e-69 272.0
25 TraesCS4A01G196300 chr4B 87.556 225 11 2 1939 2147 139532027 139532250 1.160000e-60 244.0
26 TraesCS4A01G196300 chr4B 85.263 190 12 6 1753 1941 139515755 139515929 9.230000e-42 182.0
27 TraesCS4A01G196300 chr4B 80.469 128 13 7 1939 2065 139545659 139545775 2.070000e-13 87.9
28 TraesCS4A01G196300 chr4D 93.388 847 26 15 864 1687 97508470 97509309 0.000000e+00 1227.0
29 TraesCS4A01G196300 chr4D 89.505 1010 36 20 10 966 97604259 97605251 0.000000e+00 1214.0
30 TraesCS4A01G196300 chr4D 92.883 829 51 1 2674 3494 97760771 97759943 0.000000e+00 1197.0
31 TraesCS4A01G196300 chr4D 89.364 959 36 20 10 916 97717688 97718632 0.000000e+00 1146.0
32 TraesCS4A01G196300 chr4D 94.937 711 19 9 990 1687 97605241 97605947 0.000000e+00 1098.0
33 TraesCS4A01G196300 chr4D 93.875 702 23 6 990 1685 97720614 97721301 0.000000e+00 1040.0
34 TraesCS4A01G196300 chr4D 89.114 790 72 9 2676 3464 97509910 97510686 0.000000e+00 970.0
35 TraesCS4A01G196300 chr4D 85.054 1017 72 38 708 1689 97957633 97958604 0.000000e+00 963.0
36 TraesCS4A01G196300 chr4D 88.608 790 76 8 2676 3464 97606564 97607340 0.000000e+00 948.0
37 TraesCS4A01G196300 chr4D 91.045 402 36 0 2779 3180 97959266 97959667 1.020000e-150 544.0
38 TraesCS4A01G196300 chr4D 83.033 389 17 14 1793 2147 97509549 97509922 1.460000e-79 307.0
39 TraesCS4A01G196300 chr4D 89.333 225 8 3 1939 2147 97760981 97760757 6.880000e-68 268.0
40 TraesCS4A01G196300 chr4D 80.750 400 25 16 1793 2147 97606184 97606576 8.910000e-67 265.0
41 TraesCS4A01G196300 chr4D 84.585 253 18 10 549 784 97508188 97508436 9.030000e-57 231.0
42 TraesCS4A01G196300 chr4D 77.803 446 32 25 101 483 97956908 97957349 3.270000e-51 213.0
43 TraesCS4A01G196300 chr4D 94.828 58 3 0 1939 1996 97958928 97958985 1.600000e-14 91.6
44 TraesCS4A01G196300 chr3D 93.713 684 38 4 3495 4176 213100275 213099595 0.000000e+00 1020.0
45 TraesCS4A01G196300 chr1D 93.314 688 40 5 3492 4176 389873250 389872566 0.000000e+00 1011.0
46 TraesCS4A01G196300 chr1D 93.304 687 41 4 3494 4178 136987954 136988637 0.000000e+00 1009.0
47 TraesCS4A01G196300 chr1D 95.210 501 24 0 2152 2652 388964874 388965374 0.000000e+00 793.0
48 TraesCS4A01G196300 chr7D 93.149 686 42 4 3495 4178 408361653 408362335 0.000000e+00 1002.0
49 TraesCS4A01G196300 chr7D 92.857 686 43 5 3495 4178 194237189 194237870 0.000000e+00 990.0
50 TraesCS4A01G196300 chr2D 93.003 686 43 4 3495 4178 87279163 87279845 0.000000e+00 996.0
51 TraesCS4A01G196300 chr7B 92.993 685 40 7 3495 4176 103297983 103297304 0.000000e+00 992.0
52 TraesCS4A01G196300 chr5D 92.857 686 44 4 3495 4178 327539148 327538466 0.000000e+00 990.0
53 TraesCS4A01G196300 chr5D 78.780 377 76 4 1042 1416 230505177 230505551 2.490000e-62 250.0
54 TraesCS4A01G196300 chr1A 97.405 501 13 0 2152 2652 543651838 543651338 0.000000e+00 854.0
55 TraesCS4A01G196300 chr7A 97.006 501 15 0 2152 2652 193116749 193117249 0.000000e+00 843.0
56 TraesCS4A01G196300 chr7A 96.464 509 17 1 2144 2652 669735888 669735381 0.000000e+00 839.0
57 TraesCS4A01G196300 chr7A 96.607 501 17 0 2152 2652 513204231 513204731 0.000000e+00 832.0
58 TraesCS4A01G196300 chr3A 97.006 501 15 0 2152 2652 502504919 502504419 0.000000e+00 843.0
59 TraesCS4A01G196300 chr3A 96.208 501 16 1 2152 2652 648371263 648371760 0.000000e+00 817.0
60 TraesCS4A01G196300 chr3B 95.409 501 23 0 2152 2652 228753732 228753232 0.000000e+00 798.0
61 TraesCS4A01G196300 chrUn 86.705 346 13 6 112 432 403948094 403947757 1.850000e-93 353.0
62 TraesCS4A01G196300 chrUn 86.705 346 13 6 112 432 460039660 460039323 1.850000e-93 353.0
63 TraesCS4A01G196300 chr5A 76.911 654 107 30 1060 1679 326058235 326057592 8.660000e-87 331.0


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 TraesCS4A01G196300 chr4A 478299560 478303737 4177 True 7716.000000 7716 100.000000 1 4178 1 chr4A.!!$R2 4177
1 TraesCS4A01G196300 chr4A 478338099 478340498 2399 True 1005.000000 1836 88.448667 549 3464 3 chr4A.!!$R4 2915
2 TraesCS4A01G196300 chr4A 62547030 62547530 500 True 832.000000 832 96.607000 2152 2652 1 chr4A.!!$R1 500
3 TraesCS4A01G196300 chr4A 478219026 478220198 1172 True 550.000000 948 85.535500 552 1689 2 chr4A.!!$R3 1137
4 TraesCS4A01G196300 chr4B 80840687 80841369 682 True 996.000000 996 93.003000 3495 4178 1 chr4B.!!$R1 683
5 TraesCS4A01G196300 chr4B 139398649 139401116 2467 False 959.333333 1378 88.452000 549 3494 3 chr4B.!!$F1 2945
6 TraesCS4A01G196300 chr4B 139471111 139474260 3149 False 869.250000 1613 88.410500 112 3494 4 chr4B.!!$F2 3382
7 TraesCS4A01G196300 chr4B 139509559 139517065 7506 False 656.500000 1607 88.439667 112 3466 6 chr4B.!!$F3 3354
8 TraesCS4A01G196300 chr4B 139528880 139534097 5217 False 395.800000 662 90.952400 24 3494 5 chr4B.!!$F4 3470
9 TraesCS4A01G196300 chr4B 139545659 139546348 689 False 318.450000 549 85.881500 1939 3180 2 chr4B.!!$F5 1241
10 TraesCS4A01G196300 chr4D 97717688 97721301 3613 False 1093.000000 1146 91.619500 10 1685 2 chr4D.!!$F3 1675
11 TraesCS4A01G196300 chr4D 97604259 97607340 3081 False 881.250000 1214 88.450000 10 3464 4 chr4D.!!$F2 3454
12 TraesCS4A01G196300 chr4D 97759943 97760981 1038 True 732.500000 1197 91.108000 1939 3494 2 chr4D.!!$R1 1555
13 TraesCS4A01G196300 chr4D 97508188 97510686 2498 False 683.750000 1227 87.530000 549 3464 4 chr4D.!!$F1 2915
14 TraesCS4A01G196300 chr4D 97956908 97959667 2759 False 452.900000 963 87.182500 101 3180 4 chr4D.!!$F4 3079
15 TraesCS4A01G196300 chr3D 213099595 213100275 680 True 1020.000000 1020 93.713000 3495 4176 1 chr3D.!!$R1 681
16 TraesCS4A01G196300 chr1D 389872566 389873250 684 True 1011.000000 1011 93.314000 3492 4176 1 chr1D.!!$R1 684
17 TraesCS4A01G196300 chr1D 136987954 136988637 683 False 1009.000000 1009 93.304000 3494 4178 1 chr1D.!!$F1 684
18 TraesCS4A01G196300 chr1D 388964874 388965374 500 False 793.000000 793 95.210000 2152 2652 1 chr1D.!!$F2 500
19 TraesCS4A01G196300 chr7D 408361653 408362335 682 False 1002.000000 1002 93.149000 3495 4178 1 chr7D.!!$F2 683
20 TraesCS4A01G196300 chr7D 194237189 194237870 681 False 990.000000 990 92.857000 3495 4178 1 chr7D.!!$F1 683
21 TraesCS4A01G196300 chr2D 87279163 87279845 682 False 996.000000 996 93.003000 3495 4178 1 chr2D.!!$F1 683
22 TraesCS4A01G196300 chr7B 103297304 103297983 679 True 992.000000 992 92.993000 3495 4176 1 chr7B.!!$R1 681
23 TraesCS4A01G196300 chr5D 327538466 327539148 682 True 990.000000 990 92.857000 3495 4178 1 chr5D.!!$R1 683
24 TraesCS4A01G196300 chr1A 543651338 543651838 500 True 854.000000 854 97.405000 2152 2652 1 chr1A.!!$R1 500
25 TraesCS4A01G196300 chr7A 193116749 193117249 500 False 843.000000 843 97.006000 2152 2652 1 chr7A.!!$F1 500
26 TraesCS4A01G196300 chr7A 669735381 669735888 507 True 839.000000 839 96.464000 2144 2652 1 chr7A.!!$R1 508
27 TraesCS4A01G196300 chr7A 513204231 513204731 500 False 832.000000 832 96.607000 2152 2652 1 chr7A.!!$F2 500
28 TraesCS4A01G196300 chr3A 502504419 502504919 500 True 843.000000 843 97.006000 2152 2652 1 chr3A.!!$R1 500
29 TraesCS4A01G196300 chr3B 228753232 228753732 500 True 798.000000 798 95.409000 2152 2652 1 chr3B.!!$R1 500
30 TraesCS4A01G196300 chr5A 326057592 326058235 643 True 331.000000 331 76.911000 1060 1679 1 chr5A.!!$R1 619

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
784 1453 0.541764 TTGGTGAAGACAATGGGGGC 60.542 55.000 0.00 0.0 0.0 5.80 F
786 1455 0.681243 GGTGAAGACAATGGGGGCTC 60.681 60.000 0.00 0.0 0.0 4.70 F
2257 11205 1.065491 ACGGCATGGCAATTACTCTCA 60.065 47.619 20.37 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2435 11383 0.036306 GGACCGACATGTGAAACCCT 59.964 55.0 1.15 0.00 34.36 4.34 R
2665 11613 0.245539 TTAGCACTACGTCCAGTGGC 59.754 55.0 17.81 11.13 45.03 5.01 R
3195 13186 1.240641 ACATCGGAATTGTTGGCGCA 61.241 50.0 10.83 0.00 0.00 6.09 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
55 56 0.664761 TGCGGTACTATACGGTCAGC 59.335 55.000 0.00 0.00 0.00 4.26
95 96 2.622436 ACGGACCTACTCTACGTACAC 58.378 52.381 0.00 0.00 35.85 2.90
96 97 1.936547 CGGACCTACTCTACGTACACC 59.063 57.143 0.00 0.00 0.00 4.16
174 188 2.821378 TCAGGTTGAATTGTCCATGCTG 59.179 45.455 0.00 0.00 0.00 4.41
335 379 6.493116 AGAAAAATCATCATCTCGTTCATGC 58.507 36.000 0.00 0.00 0.00 4.06
352 396 1.299926 GCTCATGTACCGGTAGGCG 60.300 63.158 16.41 6.14 42.76 5.52
442 760 4.530710 AGGCGTGTTAATGTACTCTTCA 57.469 40.909 0.00 0.00 0.00 3.02
505 823 5.627499 TTAGCACGCTGATGATTTTCTTT 57.373 34.783 0.72 0.00 0.00 2.52
661 1292 1.468054 GGCATGCAGCTTTTTCTACCG 60.468 52.381 21.36 0.00 44.79 4.02
776 1445 2.523440 ACCGGAGTTGGTGAAGACA 58.477 52.632 9.46 0.00 41.85 3.41
781 1450 2.162681 GGAGTTGGTGAAGACAATGGG 58.837 52.381 0.00 0.00 0.00 4.00
782 1451 2.162681 GAGTTGGTGAAGACAATGGGG 58.837 52.381 0.00 0.00 0.00 4.96
783 1452 1.203050 AGTTGGTGAAGACAATGGGGG 60.203 52.381 0.00 0.00 0.00 5.40
784 1453 0.541764 TTGGTGAAGACAATGGGGGC 60.542 55.000 0.00 0.00 0.00 5.80
786 1455 0.681243 GGTGAAGACAATGGGGGCTC 60.681 60.000 0.00 0.00 0.00 4.70
787 1456 0.681243 GTGAAGACAATGGGGGCTCC 60.681 60.000 0.00 0.00 0.00 4.70
1428 5197 6.868339 TCTTCGTAAGTATCCATACATGCATG 59.132 38.462 25.09 25.09 35.74 4.06
1429 5198 4.929211 TCGTAAGTATCCATACATGCATGC 59.071 41.667 26.53 11.82 35.74 4.06
1431 5200 5.352293 CGTAAGTATCCATACATGCATGCAT 59.648 40.000 27.46 27.46 35.74 3.96
1702 5714 9.447040 GGTAGTACATACATACATATACGCATG 57.553 37.037 2.06 0.00 35.96 4.06
1712 5732 5.381174 ACATATACGCATGTACACGGTAT 57.619 39.130 15.47 15.47 37.37 2.73
1729 5749 3.903644 CGGTATATGCAAAATAAACCGCG 59.096 43.478 0.00 0.00 41.48 6.46
1789 10169 5.932303 GCACTCTCAGGTAGTACAATTTTGA 59.068 40.000 2.06 0.00 0.00 2.69
1797 10283 7.230510 TCAGGTAGTACAATTTTGAAGTTGCAT 59.769 33.333 2.06 0.00 0.00 3.96
1820 10306 7.148755 GCATTCTGAACCAACATAATTTGTCAC 60.149 37.037 0.00 0.00 37.68 3.67
1838 10560 5.250200 TGTCACGGCCAAGTAATATTTTCT 58.750 37.500 2.24 0.00 0.00 2.52
1841 10563 7.088272 GTCACGGCCAAGTAATATTTTCTTTT 58.912 34.615 2.24 0.00 0.00 2.27
1880 10602 9.952188 AAGCAAGTTAAAATTCTTTGACTACTC 57.048 29.630 0.00 0.00 39.68 2.59
1885 10607 7.603024 AGTTAAAATTCTTTGACTACTCTCCCG 59.397 37.037 0.00 0.00 39.03 5.14
1904 10626 6.155565 TCTCCCGGACTGTTAATTTCTCAATA 59.844 38.462 0.73 0.00 0.00 1.90
1908 10630 6.480320 CCGGACTGTTAATTTCTCAATAGAGG 59.520 42.308 0.00 0.00 42.34 3.69
2038 10942 6.427853 CAGGTGATGAGTTACAAAGTTGATCA 59.572 38.462 0.00 0.00 0.00 2.92
2106 11044 4.116961 TGTAAGACTGGACAACGTCAAAG 58.883 43.478 0.00 0.00 33.68 2.77
2132 11080 5.654650 ACATTGTTCCTTGGTCACTTAAACA 59.345 36.000 0.00 0.00 0.00 2.83
2133 11081 6.323739 ACATTGTTCCTTGGTCACTTAAACAT 59.676 34.615 0.00 0.00 0.00 2.71
2134 11082 5.766150 TGTTCCTTGGTCACTTAAACATG 57.234 39.130 0.00 0.00 0.00 3.21
2135 11083 5.197451 TGTTCCTTGGTCACTTAAACATGT 58.803 37.500 0.00 0.00 0.00 3.21
2136 11084 6.358178 TGTTCCTTGGTCACTTAAACATGTA 58.642 36.000 0.00 0.00 0.00 2.29
2137 11085 6.485313 TGTTCCTTGGTCACTTAAACATGTAG 59.515 38.462 0.00 0.00 0.00 2.74
2138 11086 6.182507 TCCTTGGTCACTTAAACATGTAGT 57.817 37.500 0.00 0.00 0.00 2.73
2139 11087 5.995282 TCCTTGGTCACTTAAACATGTAGTG 59.005 40.000 17.59 17.59 40.42 2.74
2140 11088 5.334879 CCTTGGTCACTTAAACATGTAGTGC 60.335 44.000 18.51 14.16 39.24 4.40
2141 11089 4.968259 TGGTCACTTAAACATGTAGTGCT 58.032 39.130 18.51 0.00 39.24 4.40
2142 11090 6.104146 TGGTCACTTAAACATGTAGTGCTA 57.896 37.500 18.51 11.04 39.24 3.49
2143 11091 6.526526 TGGTCACTTAAACATGTAGTGCTAA 58.473 36.000 18.51 6.84 39.24 3.09
2144 11092 7.165485 TGGTCACTTAAACATGTAGTGCTAAT 58.835 34.615 18.51 0.00 39.24 1.73
2145 11093 7.663905 TGGTCACTTAAACATGTAGTGCTAATT 59.336 33.333 18.51 2.03 39.24 1.40
2146 11094 9.158233 GGTCACTTAAACATGTAGTGCTAATTA 57.842 33.333 18.51 1.14 39.24 1.40
2200 11148 6.910191 TGCCTCATCCATTAAATAAGAGGAA 58.090 36.000 9.57 0.00 42.87 3.36
2257 11205 1.065491 ACGGCATGGCAATTACTCTCA 60.065 47.619 20.37 0.00 0.00 3.27
2394 11342 5.162075 CGTTTCTCTCGTTCCAAATAGTCT 58.838 41.667 0.00 0.00 0.00 3.24
2435 11383 1.540267 GAGGCCATCGCTCGTCTATTA 59.460 52.381 5.01 0.00 34.44 0.98
2443 11391 3.018856 TCGCTCGTCTATTAGGGTTTCA 58.981 45.455 0.00 0.00 0.00 2.69
2541 11489 3.888930 ACCAAACTTGTCAATGACCGATT 59.111 39.130 11.24 0.65 0.00 3.34
2606 11554 2.343101 CCCGATTCTTGCTCACGTTTA 58.657 47.619 0.00 0.00 0.00 2.01
2658 11606 3.578272 GCCGCACCAACGTCACAA 61.578 61.111 0.00 0.00 0.00 3.33
2659 11607 2.326550 CCGCACCAACGTCACAAC 59.673 61.111 0.00 0.00 0.00 3.32
2660 11608 2.326550 CGCACCAACGTCACAACC 59.673 61.111 0.00 0.00 0.00 3.77
2661 11609 2.177580 CGCACCAACGTCACAACCT 61.178 57.895 0.00 0.00 0.00 3.50
2662 11610 1.355210 GCACCAACGTCACAACCTG 59.645 57.895 0.00 0.00 0.00 4.00
2663 11611 2.021722 CACCAACGTCACAACCTGG 58.978 57.895 0.00 0.00 33.15 4.45
2664 11612 1.822186 ACCAACGTCACAACCTGGC 60.822 57.895 0.09 0.00 31.03 4.85
2669 11617 3.660111 GTCACAACCTGGCGCCAC 61.660 66.667 29.03 9.73 0.00 5.01
2670 11618 3.872603 TCACAACCTGGCGCCACT 61.873 61.111 29.03 11.09 0.00 4.00
2671 11619 3.663176 CACAACCTGGCGCCACTG 61.663 66.667 29.03 24.17 0.00 3.66
2672 11620 4.954970 ACAACCTGGCGCCACTGG 62.955 66.667 29.03 28.58 35.76 4.00
2732 11681 5.059404 ACCGATCAATGGAATGACAAAAC 57.941 39.130 0.00 0.00 30.82 2.43
3036 11987 0.178995 TCTTCAATGGTGGTGCTGCA 60.179 50.000 0.00 0.00 0.00 4.41
3117 12068 2.381275 GGGAATGATCAAGATGGGGGAT 59.619 50.000 0.00 0.00 0.00 3.85
3195 13186 6.502158 TCAACTAAGATTCTTCTCCCCTTTCT 59.498 38.462 1.27 0.00 0.00 2.52
3321 13346 1.187567 AATCTGCCCCTTTGTGCCAC 61.188 55.000 0.00 0.00 0.00 5.01
3351 13376 1.098050 GAACTGGACATGGATGCACC 58.902 55.000 0.00 0.00 39.54 5.01
3388 13413 2.223782 TGCAAAGTGAGATGTGGCAAAC 60.224 45.455 0.00 0.00 0.00 2.93
3431 13457 3.667360 GCAGTGGCAAATCCTGAAATTT 58.333 40.909 6.99 0.00 40.72 1.82
3476 13502 4.072131 TCAAATGCCACAGTCTTTACCTC 58.928 43.478 0.00 0.00 0.00 3.85
3512 13538 9.827198 TTGATAAATGAAGGAAATATGCCCTAT 57.173 29.630 0.00 0.00 31.36 2.57
3648 13675 7.781548 ACAAAACATCGTGTCTTTAGTAAGT 57.218 32.000 0.00 0.00 32.98 2.24
3658 13685 7.277539 TCGTGTCTTTAGTAAGTCTCTACTAGC 59.722 40.741 0.00 0.00 36.11 3.42
3672 13699 6.873076 GTCTCTACTAGCCTAGCTCGTTAATA 59.127 42.308 0.00 0.00 40.44 0.98
3771 13800 2.193127 TGGACAAGACCCATCCGTTAT 58.807 47.619 0.00 0.00 35.06 1.89
3790 13819 9.725019 TCCGTTATCTTAGCATAATGATCATTT 57.275 29.630 25.26 10.58 29.76 2.32
3990 14020 5.661458 GAGATTAGGATTTGTCACTCCGAA 58.339 41.667 0.00 0.46 36.62 4.30
4053 14083 6.403866 TCATAAGAAGCCTTTCAAGCAAAA 57.596 33.333 0.00 0.00 35.70 2.44
4147 14178 2.412421 GGTATGTGGATACCGACGAC 57.588 55.000 0.00 0.00 43.81 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 8.672823 ACTCTTACCTTCTTCACGTTTTATTT 57.327 30.769 0.00 0.00 0.00 1.40
10 11 9.939802 ATATTACTCTTACCTTCTTCACGTTTT 57.060 29.630 0.00 0.00 0.00 2.43
11 12 9.367444 CATATTACTCTTACCTTCTTCACGTTT 57.633 33.333 0.00 0.00 0.00 3.60
13 14 6.979238 GCATATTACTCTTACCTTCTTCACGT 59.021 38.462 0.00 0.00 0.00 4.49
14 15 6.142480 CGCATATTACTCTTACCTTCTTCACG 59.858 42.308 0.00 0.00 0.00 4.35
55 56 6.144080 GTCCGTATGTGAAAAAGATCTATCCG 59.856 42.308 0.00 0.00 0.00 4.18
95 96 2.816087 AGCAAATTCTATAGCATGGCGG 59.184 45.455 0.00 0.00 0.00 6.13
96 97 3.499537 TCAGCAAATTCTATAGCATGGCG 59.500 43.478 0.00 0.00 0.00 5.69
406 475 9.950680 ATTAACACGCCTATGATTTCTTAATTG 57.049 29.630 0.00 0.00 0.00 2.32
422 492 4.630069 ACATGAAGAGTACATTAACACGCC 59.370 41.667 0.00 0.00 0.00 5.68
442 760 0.823356 AAGGCGACACTTTGGCACAT 60.823 50.000 0.00 0.00 39.30 3.21
661 1292 5.273944 AGCTCGTGAAAAATGAACAGTTTC 58.726 37.500 0.98 4.37 32.92 2.78
781 1450 3.201707 ATCATCATGCCCGGAGCCC 62.202 63.158 0.73 0.00 42.71 5.19
782 1451 1.970114 CATCATCATGCCCGGAGCC 60.970 63.158 0.73 0.00 42.71 4.70
783 1452 3.664495 CATCATCATGCCCGGAGC 58.336 61.111 0.73 5.29 44.14 4.70
1263 4845 2.357034 GGCGTGGCGTTCTTCTCA 60.357 61.111 0.00 0.00 0.00 3.27
1429 5198 9.069082 AGTACTAACTACCTAAGCATGACTATG 57.931 37.037 0.00 0.00 32.84 2.23
1431 5200 8.051535 ACAGTACTAACTACCTAAGCATGACTA 58.948 37.037 0.00 0.00 33.48 2.59
1648 5660 1.407437 GCGACCATGTCTTTCTGGGAT 60.407 52.381 0.00 0.00 36.82 3.85
1695 5707 3.004524 TGCATATACCGTGTACATGCGTA 59.995 43.478 16.94 12.80 43.84 4.42
1697 5709 2.399448 TGCATATACCGTGTACATGCG 58.601 47.619 16.94 4.20 43.84 4.73
1698 5710 4.804608 TTTGCATATACCGTGTACATGC 57.195 40.909 15.89 15.89 41.81 4.06
1702 5714 6.847289 CGGTTTATTTTGCATATACCGTGTAC 59.153 38.462 15.51 0.00 41.16 2.90
1712 5732 1.130749 ACGCGCGGTTTATTTTGCATA 59.869 42.857 35.22 0.00 0.00 3.14
1751 10131 8.813643 ACCTGAGAGTGCGTAATTATTTATAC 57.186 34.615 0.00 0.00 0.00 1.47
1789 10169 4.942761 ATGTTGGTTCAGAATGCAACTT 57.057 36.364 0.00 0.00 37.45 2.66
1797 10283 6.434596 CGTGACAAATTATGTTGGTTCAGAA 58.565 36.000 0.00 0.00 44.12 3.02
1880 10602 4.202245 TGAGAAATTAACAGTCCGGGAG 57.798 45.455 0.00 0.00 0.00 4.30
1885 10607 6.018669 CGCCTCTATTGAGAAATTAACAGTCC 60.019 42.308 5.68 0.00 42.73 3.85
2038 10942 7.182206 AGGTTAGGTCAGTGGTAATTAGTCATT 59.818 37.037 0.00 0.00 0.00 2.57
2106 11044 4.918810 AAGTGACCAAGGAACAATGTTC 57.081 40.909 17.16 17.16 0.00 3.18
2141 11089 9.505995 GCCTCCGTTTCGAAAAATTAATAATTA 57.494 29.630 13.10 0.00 0.00 1.40
2142 11090 8.030106 TGCCTCCGTTTCGAAAAATTAATAATT 58.970 29.630 13.10 0.00 0.00 1.40
2143 11091 7.540299 TGCCTCCGTTTCGAAAAATTAATAAT 58.460 30.769 13.10 0.00 0.00 1.28
2144 11092 6.910995 TGCCTCCGTTTCGAAAAATTAATAA 58.089 32.000 13.10 0.00 0.00 1.40
2145 11093 6.497785 TGCCTCCGTTTCGAAAAATTAATA 57.502 33.333 13.10 0.00 0.00 0.98
2146 11094 5.379732 TGCCTCCGTTTCGAAAAATTAAT 57.620 34.783 13.10 0.00 0.00 1.40
2147 11095 4.832590 TGCCTCCGTTTCGAAAAATTAA 57.167 36.364 13.10 0.00 0.00 1.40
2148 11096 4.832590 TTGCCTCCGTTTCGAAAAATTA 57.167 36.364 13.10 0.00 0.00 1.40
2149 11097 3.719173 TTGCCTCCGTTTCGAAAAATT 57.281 38.095 13.10 0.00 0.00 1.82
2150 11098 3.719173 TTTGCCTCCGTTTCGAAAAAT 57.281 38.095 13.10 0.00 0.00 1.82
2222 11170 3.047280 CGTGTTGCAAGGGCGCTA 61.047 61.111 7.64 0.00 45.35 4.26
2257 11205 7.891498 AAGAAACTAGGGTGTTTTGTTGTAT 57.109 32.000 0.00 0.00 39.86 2.29
2394 11342 1.751351 CCTCACCATGCTCGTCTCTTA 59.249 52.381 0.00 0.00 0.00 2.10
2435 11383 0.036306 GGACCGACATGTGAAACCCT 59.964 55.000 1.15 0.00 34.36 4.34
2443 11391 2.574369 TGGGATAAAAGGACCGACATGT 59.426 45.455 0.00 0.00 0.00 3.21
2541 11489 1.487976 CTTCTCCATTAGGCTCTGGCA 59.512 52.381 10.42 0.00 40.87 4.92
2652 11600 3.660111 GTGGCGCCAGGTTGTGAC 61.660 66.667 33.73 12.14 0.00 3.67
2653 11601 3.872603 AGTGGCGCCAGGTTGTGA 61.873 61.111 33.73 0.61 0.00 3.58
2654 11602 3.663176 CAGTGGCGCCAGGTTGTG 61.663 66.667 33.73 18.18 0.00 3.33
2655 11603 4.954970 CCAGTGGCGCCAGGTTGT 62.955 66.667 33.73 9.58 0.00 3.32
2656 11604 4.641645 TCCAGTGGCGCCAGGTTG 62.642 66.667 33.73 26.60 0.00 3.77
2657 11605 4.643387 GTCCAGTGGCGCCAGGTT 62.643 66.667 33.73 16.41 0.00 3.50
2660 11608 3.989698 CTACGTCCAGTGGCGCCAG 62.990 68.421 33.73 20.03 0.00 4.85
2661 11609 4.063967 CTACGTCCAGTGGCGCCA 62.064 66.667 29.03 29.03 0.00 5.69
2662 11610 4.065281 ACTACGTCCAGTGGCGCC 62.065 66.667 22.73 22.73 34.33 6.53
2663 11611 2.809601 CACTACGTCCAGTGGCGC 60.810 66.667 21.05 0.00 41.88 6.53
2664 11612 1.929806 TAGCACTACGTCCAGTGGCG 61.930 60.000 17.81 19.97 45.03 5.69
2665 11613 0.245539 TTAGCACTACGTCCAGTGGC 59.754 55.000 17.81 11.13 45.03 5.01
2666 11614 2.961526 ATTAGCACTACGTCCAGTGG 57.038 50.000 17.81 1.40 45.03 4.00
2668 11616 4.275810 TCCTAATTAGCACTACGTCCAGT 58.724 43.478 6.99 0.00 0.00 4.00
2669 11617 4.913335 TCCTAATTAGCACTACGTCCAG 57.087 45.455 6.99 0.00 0.00 3.86
2670 11618 5.186409 ACTTTCCTAATTAGCACTACGTCCA 59.814 40.000 6.99 0.00 0.00 4.02
2671 11619 5.658468 ACTTTCCTAATTAGCACTACGTCC 58.342 41.667 6.99 0.00 0.00 4.79
2672 11620 6.035758 CCAACTTTCCTAATTAGCACTACGTC 59.964 42.308 6.99 0.00 0.00 4.34
2732 11681 6.149474 AGTTATTACCTGTTTTGCAGCTACTG 59.851 38.462 0.00 0.00 43.71 2.74
2761 11712 4.281435 TGGAACACAAGTTATACCGTCAGA 59.719 41.667 0.00 0.00 38.30 3.27
2938 11889 1.735559 CGAAGACGGTCGGGGTTTC 60.736 63.158 1.89 0.06 37.37 2.78
3000 11951 1.679305 GAGCTCCTGGTCCGAGTGA 60.679 63.158 0.87 0.00 34.87 3.41
3117 12068 1.391933 ATCCTGTCAGCGGCGTGATA 61.392 55.000 9.37 8.59 0.00 2.15
3195 13186 1.240641 ACATCGGAATTGTTGGCGCA 61.241 50.000 10.83 0.00 0.00 6.09
3221 13212 9.985730 GGGAAAATTATCATGAATTCAAGCATA 57.014 29.630 13.09 6.28 0.00 3.14
3303 13327 1.607467 GTGGCACAAAGGGGCAGAT 60.607 57.895 13.86 0.00 44.16 2.90
3304 13328 2.203480 GTGGCACAAAGGGGCAGA 60.203 61.111 13.86 0.00 44.16 4.26
3351 13376 2.420628 TGCACTTTGATCTTTTGCCG 57.579 45.000 0.00 0.00 31.94 5.69
3361 13386 3.316029 CCACATCTCACTTTGCACTTTGA 59.684 43.478 0.00 0.00 0.00 2.69
3431 13457 5.836024 TCTTTAGCCCCTCTTTACTTGAA 57.164 39.130 0.00 0.00 0.00 2.69
3476 13502 3.173668 TCATTTATCAACTCGTCGGGG 57.826 47.619 0.00 0.00 0.00 5.73
3639 13666 7.804147 AGCTAGGCTAGTAGAGACTTACTAAA 58.196 38.462 21.92 0.00 43.14 1.85
3640 13667 7.377696 AGCTAGGCTAGTAGAGACTTACTAA 57.622 40.000 21.92 0.00 43.14 2.24
3648 13675 3.842007 AACGAGCTAGGCTAGTAGAGA 57.158 47.619 21.92 0.00 43.16 3.10
3658 13685 7.787725 AACCATCTTTTATTAACGAGCTAGG 57.212 36.000 0.00 0.00 0.00 3.02
3864 13894 3.205784 AGCACATAAGGCATTCCTCTC 57.794 47.619 0.00 0.00 43.40 3.20
4009 14039 1.702401 TGTGCATTACCAAGAGGACCA 59.298 47.619 0.00 0.00 38.69 4.02
4012 14042 3.998913 TGATGTGCATTACCAAGAGGA 57.001 42.857 0.00 0.00 38.69 3.71


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

AutoCloner maintained by Alex Coulton.