Multiple sequence alignment - TraesCS3D01G395400

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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 TraesCS3D01G395400 chr3D 100.000 2738 0 0 1 2738 511203153 511200416 0.000000e+00 5057.0
1 TraesCS3D01G395400 chr3D 80.676 1273 183 36 270 1510 511294091 511292850 0.000000e+00 929.0
2 TraesCS3D01G395400 chr3D 84.442 932 126 12 588 1510 511129336 511128415 0.000000e+00 900.0
3 TraesCS3D01G395400 chr3D 93.091 550 25 8 1 540 511129879 511129333 0.000000e+00 793.0
4 TraesCS3D01G395400 chr3D 80.583 1030 169 21 515 1534 511321687 511320679 0.000000e+00 765.0
5 TraesCS3D01G395400 chr3D 81.296 941 144 21 614 1531 511181573 511180642 0.000000e+00 734.0
6 TraesCS3D01G395400 chr3D 88.909 550 43 9 1 540 511267129 511266588 0.000000e+00 662.0
7 TraesCS3D01G395400 chr3D 85.851 523 53 11 1540 2056 511261440 511260933 1.120000e-148 536.0
8 TraesCS3D01G395400 chr3D 84.436 559 54 21 1596 2134 511180322 511179777 1.120000e-143 520.0
9 TraesCS3D01G395400 chr3D 80.412 582 71 17 1540 2113 511128319 511127773 1.180000e-108 403.0
10 TraesCS3D01G395400 chr3D 81.679 524 55 14 1540 2059 511265570 511265084 5.490000e-107 398.0
11 TraesCS3D01G395400 chr3D 94.355 248 10 4 588 831 511266591 511266344 7.160000e-101 377.0
12 TraesCS3D01G395400 chr3D 86.850 327 38 3 1540 1864 511292757 511292434 7.210000e-96 361.0
13 TraesCS3D01G395400 chr3D 86.364 330 36 9 1540 1864 511320610 511320285 4.340000e-93 351.0
14 TraesCS3D01G395400 chr3D 82.660 421 33 16 2317 2713 511319938 511319534 1.210000e-88 337.0
15 TraesCS3D01G395400 chr3D 81.481 432 38 17 2317 2724 511291503 511291090 1.580000e-82 316.0
16 TraesCS3D01G395400 chr3D 83.929 224 19 6 2491 2713 511260447 511260240 5.980000e-47 198.0
17 TraesCS3D01G395400 chr3D 77.635 389 40 20 2367 2734 511264821 511264459 2.780000e-45 193.0
18 TraesCS3D01G395400 chr3D 96.296 81 2 1 815 894 511266331 511266251 6.150000e-27 132.0
19 TraesCS3D01G395400 chr3A 81.134 1288 179 38 264 1525 647444739 647443490 0.000000e+00 974.0
20 TraesCS3D01G395400 chr3A 80.000 805 126 23 745 1525 647388861 647388068 1.840000e-156 562.0
21 TraesCS3D01G395400 chr3A 82.812 640 90 17 909 1534 647448367 647447734 3.080000e-154 555.0
22 TraesCS3D01G395400 chr3A 87.579 475 51 6 1540 2011 647358282 647357813 6.670000e-151 544.0
23 TraesCS3D01G395400 chr3A 79.745 627 114 9 916 1534 647358972 647358351 2.500000e-120 442.0
24 TraesCS3D01G395400 chr3A 82.166 471 79 3 1000 1467 647351163 647350695 1.530000e-107 399.0
25 TraesCS3D01G395400 chr3A 85.714 329 29 6 1540 1864 647270229 647269915 5.650000e-87 331.0
26 TraesCS3D01G395400 chr3A 80.556 432 42 17 2317 2724 647269569 647269156 7.410000e-76 294.0
27 TraesCS3D01G395400 chr3A 85.043 234 22 4 2491 2724 647387119 647386899 2.740000e-55 226.0
28 TraesCS3D01G395400 chr3A 83.190 232 36 2 1000 1228 647276921 647276690 2.760000e-50 209.0
29 TraesCS3D01G395400 chr3A 77.635 389 41 18 2367 2734 647353030 647352667 7.740000e-46 195.0
30 TraesCS3D01G395400 chr3A 94.118 51 3 0 2417 2467 647387216 647387166 8.130000e-11 78.7
31 TraesCS3D01G395400 chr3B 81.091 1301 171 48 270 1534 672777650 672776389 0.000000e+00 970.0
32 TraesCS3D01G395400 chr3B 82.051 819 78 21 1517 2299 672744151 672743366 3.850000e-178 634.0
33 TraesCS3D01G395400 chr3B 87.643 437 48 4 1579 2012 672655234 672654801 1.130000e-138 503.0
34 TraesCS3D01G395400 chr3B 81.913 481 50 13 1540 2012 672654080 672653629 3.330000e-99 372.0
35 TraesCS3D01G395400 chr3B 79.740 385 39 15 2352 2713 672636141 672635773 2.720000e-60 243.0
36 TraesCS3D01G395400 chr3B 78.182 385 43 17 2352 2713 672646399 672646033 9.940000e-50 207.0
37 TraesCS3D01G395400 chr3B 75.388 516 58 28 2158 2649 672654659 672654189 4.660000e-43 185.0
38 TraesCS3D01G395400 chr3B 92.063 63 4 1 1951 2012 672764090 672764028 1.350000e-13 87.9
39 TraesCS3D01G395400 chr3B 95.833 48 2 0 2420 2467 672760266 672760219 8.130000e-11 78.7


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 TraesCS3D01G395400 chr3D 511200416 511203153 2737 True 5057.000000 5057 100.000000 1 2738 1 chr3D.!!$R1 2737
1 TraesCS3D01G395400 chr3D 511127773 511129879 2106 True 698.666667 900 85.981667 1 2113 3 chr3D.!!$R2 2112
2 TraesCS3D01G395400 chr3D 511179777 511181573 1796 True 627.000000 734 82.866000 614 2134 2 chr3D.!!$R3 1520
3 TraesCS3D01G395400 chr3D 511291090 511294091 3001 True 535.333333 929 83.002333 270 2724 3 chr3D.!!$R5 2454
4 TraesCS3D01G395400 chr3D 511319534 511321687 2153 True 484.333333 765 83.202333 515 2713 3 chr3D.!!$R6 2198
5 TraesCS3D01G395400 chr3D 511260240 511267129 6889 True 356.571429 662 86.950571 1 2734 7 chr3D.!!$R4 2733
6 TraesCS3D01G395400 chr3A 647443490 647448367 4877 True 764.500000 974 81.973000 264 1534 2 chr3A.!!$R6 1270
7 TraesCS3D01G395400 chr3A 647357813 647358972 1159 True 493.000000 544 83.662000 916 2011 2 chr3A.!!$R4 1095
8 TraesCS3D01G395400 chr3A 647269156 647270229 1073 True 312.500000 331 83.135000 1540 2724 2 chr3A.!!$R2 1184
9 TraesCS3D01G395400 chr3A 647350695 647353030 2335 True 297.000000 399 79.900500 1000 2734 2 chr3A.!!$R3 1734
10 TraesCS3D01G395400 chr3A 647386899 647388861 1962 True 288.900000 562 86.387000 745 2724 3 chr3A.!!$R5 1979
11 TraesCS3D01G395400 chr3B 672776389 672777650 1261 True 970.000000 970 81.091000 270 1534 1 chr3B.!!$R4 1264
12 TraesCS3D01G395400 chr3B 672743366 672744151 785 True 634.000000 634 82.051000 1517 2299 1 chr3B.!!$R3 782
13 TraesCS3D01G395400 chr3B 672653629 672655234 1605 True 353.333333 503 81.648000 1540 2649 3 chr3B.!!$R5 1109

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
997 1088 0.100325 TTGTTTGCACTCCACGCTTG 59.9 50.0 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2578 10864 0.034186 CAAGCCCTGGAGCCATTACA 60.034 55.0 0.0 0.0 0.0 2.41 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
37 38 0.467290 ACTGCAAATTCACCCGGTGT 60.467 50.000 17.32 0.00 34.79 4.16
51 52 3.906660 GGTGTGACCGTGAGATCAA 57.093 52.632 0.00 0.00 33.62 2.57
137 138 5.005394 CGTTCCTCCGTGACAACTAATTATG 59.995 44.000 0.00 0.00 0.00 1.90
286 296 1.539065 CCCGGAGTAGCATCACATCAC 60.539 57.143 0.73 0.00 0.00 3.06
400 421 1.859302 AGGAGTGGGAGAAGCACTAG 58.141 55.000 0.00 0.00 0.00 2.57
413 434 6.183360 GGAGAAGCACTAGTACCTTTACTCTC 60.183 46.154 15.87 13.41 39.43 3.20
448 469 0.525668 GCCTGTCACATACGTCCTCG 60.526 60.000 0.00 0.00 43.34 4.63
469 490 7.877097 TCCTCGTAAATACTACTCCTAGATGAC 59.123 40.741 0.00 0.00 0.00 3.06
540 565 1.179814 ACTGGTGACCGGTGAGTCTC 61.180 60.000 16.71 0.00 42.23 3.36
547 572 4.244326 CGGTGAGTCTCCGGAGAT 57.756 61.111 35.64 23.81 43.68 2.75
551 576 0.747852 GTGAGTCTCCGGAGATTCCC 59.252 60.000 38.93 30.55 41.71 3.97
552 577 0.631753 TGAGTCTCCGGAGATTCCCT 59.368 55.000 38.93 30.09 41.71 4.20
553 578 1.036707 GAGTCTCCGGAGATTCCCTG 58.963 60.000 35.24 10.85 37.98 4.45
574 603 2.301346 GAATGGGGACTATTGGCAGTG 58.699 52.381 0.00 0.00 0.00 3.66
603 632 4.724399 TGGTATGTCTTTCTTCCTTGCAA 58.276 39.130 0.00 0.00 0.00 4.08
624 653 4.853924 AACTTGTGGCAAATACTTCCAG 57.146 40.909 0.00 0.00 0.00 3.86
951 1027 2.224523 TGGTCAGGTGACACTGGAATTC 60.225 50.000 12.09 0.00 46.47 2.17
980 1064 0.108424 AGCTTCTAGCCGAGCAGTTG 60.108 55.000 12.89 0.00 43.77 3.16
981 1065 0.390472 GCTTCTAGCCGAGCAGTTGT 60.390 55.000 7.45 0.00 34.48 3.32
984 1068 1.795768 TCTAGCCGAGCAGTTGTTTG 58.204 50.000 0.00 0.00 0.00 2.93
997 1088 0.100325 TTGTTTGCACTCCACGCTTG 59.900 50.000 0.00 0.00 0.00 4.01
998 1089 0.746204 TGTTTGCACTCCACGCTTGA 60.746 50.000 0.00 0.00 0.00 3.02
999 1090 0.040958 GTTTGCACTCCACGCTTGAG 60.041 55.000 0.00 0.00 35.92 3.02
1000 1091 0.179059 TTTGCACTCCACGCTTGAGA 60.179 50.000 3.73 0.00 33.95 3.27
1001 1092 0.035317 TTGCACTCCACGCTTGAGAT 59.965 50.000 3.73 0.00 33.95 2.75
1002 1093 0.671472 TGCACTCCACGCTTGAGATG 60.671 55.000 3.73 0.89 33.95 2.90
1003 1094 1.364626 GCACTCCACGCTTGAGATGG 61.365 60.000 3.73 0.00 33.95 3.51
1008 1877 1.364626 CCACGCTTGAGATGGCTGAC 61.365 60.000 0.00 0.00 0.00 3.51
1019 1888 2.101582 AGATGGCTGACGATACCAAGTC 59.898 50.000 0.00 0.00 36.94 3.01
1023 1892 1.207329 GCTGACGATACCAAGTCCCTT 59.793 52.381 0.00 0.00 36.61 3.95
1024 1893 2.429610 GCTGACGATACCAAGTCCCTTA 59.570 50.000 0.00 0.00 36.61 2.69
1053 1922 0.829333 TCCTCTTGAGCAGCTCATCC 59.171 55.000 25.94 0.00 40.39 3.51
1072 1941 5.598005 TCATCCTTGTGTTTTGGTTCTGAAT 59.402 36.000 0.00 0.00 0.00 2.57
1082 1951 7.337942 GTGTTTTGGTTCTGAATCTGATATCCT 59.662 37.037 1.90 0.00 0.00 3.24
1091 1960 4.040095 TGAATCTGATATCCTGTGCCTGAG 59.960 45.833 0.00 0.00 0.00 3.35
1096 1967 2.254152 TATCCTGTGCCTGAGGTCTT 57.746 50.000 0.00 0.00 31.85 3.01
1161 2032 6.240089 CCTCATGGATCTTTGAATATCCCAGA 60.240 42.308 5.89 3.82 40.91 3.86
1178 2052 2.039084 CCAGAGAGGGTTACATATGCCC 59.961 54.545 1.58 5.69 42.64 5.36
1207 2081 3.588511 TGGAATGCTGGCACCCCA 61.589 61.111 11.78 11.78 39.32 4.96
1228 2102 1.889829 ACGAGAACAGGGTTCTCTCTG 59.110 52.381 27.10 18.27 41.98 3.35
1232 2106 1.070758 GAACAGGGTTCTCTCTGTGCA 59.929 52.381 1.40 0.00 42.67 4.57
1237 2111 1.134551 GGGTTCTCTCTGTGCATCTCC 60.135 57.143 0.00 0.00 0.00 3.71
1238 2112 1.552337 GGTTCTCTCTGTGCATCTCCA 59.448 52.381 0.00 0.00 0.00 3.86
1258 2132 2.054799 ACAACCTAGGACTTCAAGGCA 58.945 47.619 17.98 0.00 33.42 4.75
1263 2137 3.274288 CCTAGGACTTCAAGGCACATTC 58.726 50.000 1.05 0.00 0.00 2.67
1272 2146 2.440980 GGCACATTCCCTCAGGGC 60.441 66.667 4.08 0.00 43.94 5.19
1279 2153 0.919710 ATTCCCTCAGGGCCTACAAC 59.080 55.000 4.08 0.00 43.94 3.32
1287 2161 1.818674 CAGGGCCTACAACATTGTTCC 59.181 52.381 5.28 0.00 42.35 3.62
1297 2171 1.549203 ACATTGTTCCAGCATGACCC 58.451 50.000 0.00 0.00 39.69 4.46
1335 2209 9.844257 TCAAATAACAATTTTTCAGGACCAATT 57.156 25.926 0.00 0.00 0.00 2.32
1355 2232 1.483004 TCCCGATATTTCACGGCTGAA 59.517 47.619 0.00 0.00 46.59 3.02
1356 2233 2.104111 TCCCGATATTTCACGGCTGAAT 59.896 45.455 0.00 0.00 46.59 2.57
1380 2257 5.954752 TCCATACCTGACATATCTGGATCTC 59.045 44.000 3.62 0.00 44.77 2.75
1391 2268 8.637196 ACATATCTGGATCTCTCGTACAATAA 57.363 34.615 0.00 0.00 0.00 1.40
1402 2279 6.866770 TCTCTCGTACAATAACTTTTCAGGTG 59.133 38.462 0.00 0.00 0.00 4.00
1403 2280 6.751157 TCTCGTACAATAACTTTTCAGGTGA 58.249 36.000 0.00 0.00 0.00 4.02
1420 2297 3.639094 AGGTGAAATCCCAGAGAGTATCG 59.361 47.826 0.00 0.00 42.67 2.92
1421 2298 3.385111 GGTGAAATCCCAGAGAGTATCGT 59.615 47.826 0.00 0.00 42.67 3.73
1426 2303 7.711339 GTGAAATCCCAGAGAGTATCGTAAATT 59.289 37.037 0.00 0.00 42.67 1.82
1429 2306 5.914033 TCCCAGAGAGTATCGTAAATTTGG 58.086 41.667 0.00 0.00 42.67 3.28
1430 2307 5.659525 TCCCAGAGAGTATCGTAAATTTGGA 59.340 40.000 0.00 0.00 42.67 3.53
1485 2362 0.109532 TCAGCGGTCAAATTCCACCA 59.890 50.000 6.58 0.00 32.33 4.17
1525 2468 5.526846 ACTCGGTTAACCACGTTCAATTTTA 59.473 36.000 24.14 0.00 35.14 1.52
1529 2472 6.511444 CGGTTAACCACGTTCAATTTTACTGA 60.511 38.462 24.14 0.00 35.14 3.41
1530 2473 6.634035 GGTTAACCACGTTCAATTTTACTGAC 59.366 38.462 20.12 0.00 35.64 3.51
1535 2478 4.973663 CACGTTCAATTTTACTGACAACCC 59.026 41.667 0.00 0.00 0.00 4.11
1538 2481 6.037098 CGTTCAATTTTACTGACAACCCAAA 58.963 36.000 0.00 0.00 0.00 3.28
1547 2490 1.134848 TGACAACCCAAAGCTTTGTGC 60.135 47.619 31.67 20.31 43.29 4.57
1558 2501 0.874390 GCTTTGTGCTTCACCGATGA 59.126 50.000 0.00 0.00 38.95 2.92
1563 2506 2.076100 TGTGCTTCACCGATGAATGAC 58.924 47.619 0.00 0.00 43.92 3.06
1571 2515 1.889105 CGATGAATGACTGCCCCCG 60.889 63.158 0.00 0.00 0.00 5.73
1580 2524 4.082523 CTGCCCCCGCTCGAGAAA 62.083 66.667 18.75 0.00 35.36 2.52
1591 2538 2.286950 CGCTCGAGAAAGAGATGGAGAG 60.287 54.545 18.75 0.00 40.57 3.20
1594 2743 1.403679 CGAGAAAGAGATGGAGAGCGT 59.596 52.381 0.00 0.00 0.00 5.07
1632 2781 1.367840 GCTCAACGACCAGTCCAGT 59.632 57.895 0.00 0.00 0.00 4.00
1744 9181 3.187842 CGTCGTCCGGATATGATTCACTA 59.812 47.826 7.81 0.00 0.00 2.74
1745 9182 4.474113 GTCGTCCGGATATGATTCACTAC 58.526 47.826 7.81 0.00 0.00 2.73
1767 9204 6.817765 ACTTGTTCTGAAACTTTGTCTGAA 57.182 33.333 0.00 0.00 36.30 3.02
1768 9205 7.214467 ACTTGTTCTGAAACTTTGTCTGAAA 57.786 32.000 0.00 0.00 35.53 2.69
1769 9206 7.657336 ACTTGTTCTGAAACTTTGTCTGAAAA 58.343 30.769 0.00 0.00 35.53 2.29
1770 9207 8.141268 ACTTGTTCTGAAACTTTGTCTGAAAAA 58.859 29.630 0.00 0.00 35.53 1.94
1809 9249 0.880278 TGAGCACTTCCGACAGCAAC 60.880 55.000 0.00 0.00 0.00 4.17
1853 9331 7.837505 TGCAGTAACGATTATCTTAATTCACG 58.162 34.615 0.00 0.00 0.00 4.35
1861 9339 8.648097 ACGATTATCTTAATTCACGTGATATGC 58.352 33.333 20.80 1.59 0.00 3.14
1982 9485 2.159379 GCCGGCATTTCTAAAGGAACAG 60.159 50.000 24.80 0.00 33.13 3.16
1990 9495 6.239036 GCATTTCTAAAGGAACAGAACAAGGT 60.239 38.462 0.00 0.00 33.13 3.50
1998 9508 0.608640 ACAGAACAAGGTAGCTCCGG 59.391 55.000 0.00 0.00 41.99 5.14
2011 9521 2.833631 GCTCCGGCTAGCCTATAAAA 57.166 50.000 30.55 8.98 36.45 1.52
2012 9522 3.336138 GCTCCGGCTAGCCTATAAAAT 57.664 47.619 30.55 0.00 36.45 1.82
2013 9523 4.467198 GCTCCGGCTAGCCTATAAAATA 57.533 45.455 30.55 6.62 36.45 1.40
2034 9547 3.923017 ATAAAACTCTGCACTTGTGCC 57.077 42.857 21.01 5.89 0.00 5.01
2044 9557 0.100325 CACTTGTGCCGTGCTTTTCA 59.900 50.000 0.00 0.00 0.00 2.69
2059 9572 2.323999 TTTCACCCCATTTCCATGCT 57.676 45.000 0.00 0.00 0.00 3.79
2076 9589 2.106566 TGCTTTTGCCCTTCTTGAACA 58.893 42.857 0.00 0.00 46.87 3.18
2156 9685 1.883084 GCCGACCAAGCTGGATACG 60.883 63.158 8.91 10.10 40.96 3.06
2222 10354 0.952497 CGTGTGCCATCAACAGAGCT 60.952 55.000 0.00 0.00 0.00 4.09
2253 10385 2.058798 TGTGTAAGCTCGCTTCTTTCG 58.941 47.619 7.52 0.00 37.47 3.46
2265 10397 3.040795 GCTTCTTTCGGTTTCGTTTTCC 58.959 45.455 0.00 0.00 37.69 3.13
2303 10436 2.120909 GCATGGATGGGGTTCGTGG 61.121 63.158 0.00 0.00 0.00 4.94
2307 10440 2.750237 GATGGGGTTCGTGGTGGC 60.750 66.667 0.00 0.00 0.00 5.01
2310 10443 4.360405 GGGGTTCGTGGTGGCCAT 62.360 66.667 9.72 0.00 35.28 4.40
2311 10444 2.750237 GGGTTCGTGGTGGCCATC 60.750 66.667 9.72 9.78 35.28 3.51
2312 10445 2.351276 GGTTCGTGGTGGCCATCT 59.649 61.111 18.94 0.00 35.28 2.90
2313 10446 1.600107 GGTTCGTGGTGGCCATCTA 59.400 57.895 18.94 2.15 35.28 1.98
2314 10447 0.180406 GGTTCGTGGTGGCCATCTAT 59.820 55.000 18.94 0.00 35.28 1.98
2315 10448 1.414919 GGTTCGTGGTGGCCATCTATA 59.585 52.381 18.94 0.00 35.28 1.31
2316 10449 2.480845 GTTCGTGGTGGCCATCTATAC 58.519 52.381 18.94 6.19 35.28 1.47
2343 10476 2.203294 GGTTTGTGTCCCGTGCCT 60.203 61.111 0.00 0.00 0.00 4.75
2350 10487 0.753262 GTGTCCCGTGCCTATGATCT 59.247 55.000 0.00 0.00 0.00 2.75
2363 10613 6.094186 GTGCCTATGATCTATCTATGTCGACA 59.906 42.308 22.48 22.48 0.00 4.35
2382 10632 1.001641 GCTTGTCAGCCAGGGATGT 60.002 57.895 3.19 0.00 40.61 3.06
2393 10643 1.283029 CCAGGGATGTCAAGGATGTGT 59.717 52.381 0.00 0.00 0.00 3.72
2402 10652 5.482163 TGTCAAGGATGTGTAGAATGTCA 57.518 39.130 0.00 0.00 0.00 3.58
2406 10656 4.207891 AGGATGTGTAGAATGTCACACC 57.792 45.455 2.69 4.96 45.26 4.16
2411 10662 5.493133 TGTGTAGAATGTCACACCAAAAC 57.507 39.130 2.69 0.00 43.54 2.43
2413 10664 5.163703 TGTGTAGAATGTCACACCAAAACAC 60.164 40.000 2.69 5.66 43.54 3.32
2415 10666 4.637483 AGAATGTCACACCAAAACACAG 57.363 40.909 0.00 0.00 0.00 3.66
2467 10730 0.184933 ACCTGCTGCCTTTGTTGGTA 59.815 50.000 0.00 0.00 0.00 3.25
2468 10731 1.327303 CCTGCTGCCTTTGTTGGTAA 58.673 50.000 0.00 0.00 0.00 2.85
2469 10732 1.000274 CCTGCTGCCTTTGTTGGTAAC 60.000 52.381 0.00 0.00 0.00 2.50
2486 10749 5.977635 TGGTAACAGAGGATGTGTAGAATG 58.022 41.667 0.00 0.00 44.43 2.67
2489 10775 5.489792 AACAGAGGATGTGTAGAATGTGT 57.510 39.130 0.00 0.00 44.43 3.72
2503 10789 3.632145 AGAATGTGTGTGTCCAAAAGGAC 59.368 43.478 7.69 7.69 39.16 3.85
2527 10813 2.350772 GCTTGTGTACATTCTGGTGTGC 60.351 50.000 0.00 0.00 35.59 4.57
2531 10817 4.646572 TGTGTACATTCTGGTGTGCATTA 58.353 39.130 0.00 0.00 44.46 1.90
2532 10818 4.454161 TGTGTACATTCTGGTGTGCATTAC 59.546 41.667 0.00 0.00 44.46 1.89
2558 10844 5.246981 TGTCTCCTGGATTCAAACAAGAT 57.753 39.130 0.00 0.00 0.00 2.40
2613 10899 1.280421 GCTTGAGGGAACTGATGAGGT 59.720 52.381 0.00 0.00 44.43 3.85
2672 10958 7.201496 CGGTATATCAACGGGAAATAGTAATGC 60.201 40.741 0.00 0.00 0.00 3.56
2705 11336 3.599343 TGTCAATTTGATCCCTCGACTG 58.401 45.455 1.78 0.00 0.00 3.51
2713 11344 4.655762 TGATCCCTCGACTGTTGATTAG 57.344 45.455 0.00 0.00 0.00 1.73
2724 11355 6.708949 TCGACTGTTGATTAGCCTTAGTTTTT 59.291 34.615 0.00 0.00 0.00 1.94
2726 11357 8.169268 CGACTGTTGATTAGCCTTAGTTTTTAG 58.831 37.037 0.00 0.00 0.00 1.85
2727 11358 9.216117 GACTGTTGATTAGCCTTAGTTTTTAGA 57.784 33.333 0.00 0.00 0.00 2.10
2728 11359 9.000486 ACTGTTGATTAGCCTTAGTTTTTAGAC 58.000 33.333 0.00 0.00 0.00 2.59
2730 11361 8.161425 TGTTGATTAGCCTTAGTTTTTAGACCT 58.839 33.333 0.00 0.00 0.00 3.85
2731 11362 8.666573 GTTGATTAGCCTTAGTTTTTAGACCTC 58.333 37.037 0.00 0.00 0.00 3.85
2732 11363 7.913789 TGATTAGCCTTAGTTTTTAGACCTCA 58.086 34.615 0.00 0.00 0.00 3.86
2733 11364 8.041323 TGATTAGCCTTAGTTTTTAGACCTCAG 58.959 37.037 0.00 0.00 0.00 3.35
2734 11365 4.580868 AGCCTTAGTTTTTAGACCTCAGC 58.419 43.478 0.00 0.00 0.00 4.26
2735 11366 4.287326 AGCCTTAGTTTTTAGACCTCAGCT 59.713 41.667 0.00 0.00 0.00 4.24
2736 11367 4.393371 GCCTTAGTTTTTAGACCTCAGCTG 59.607 45.833 7.63 7.63 0.00 4.24
2737 11368 4.393371 CCTTAGTTTTTAGACCTCAGCTGC 59.607 45.833 9.47 0.00 0.00 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 3.554960 CCAGAACTTTGATCTCACGGTCA 60.555 47.826 0.00 0.00 0.00 4.02
51 52 0.037447 GAGCCCTCTTGCCAGAACTT 59.963 55.000 0.00 0.00 0.00 2.66
98 99 0.580104 GAACGTGTGTCGGGAGTTTG 59.420 55.000 0.00 0.00 44.69 2.93
137 138 1.509004 GTGAGTCTCCAGTCTCGGC 59.491 63.158 0.00 0.00 33.83 5.54
286 296 6.222389 TGACATTGGGCAAAAACATTAGAAG 58.778 36.000 0.00 0.00 0.00 2.85
372 388 4.954826 GCTTCTCCCACTCCTAACTACTAA 59.045 45.833 0.00 0.00 0.00 2.24
400 421 4.676849 ACTTCGTCGAGAGTAAAGGTAC 57.323 45.455 7.89 0.00 0.00 3.34
413 434 1.459592 CAGGCAGGTAAAACTTCGTCG 59.540 52.381 0.00 0.00 0.00 5.12
469 490 2.439409 TGTGGAACTGATGCCATCAAG 58.561 47.619 9.00 5.81 39.11 3.02
519 544 1.152525 ACTCACCGGTCACCAGTCT 60.153 57.895 2.59 0.00 0.00 3.24
540 565 0.109342 CCATTCCAGGGAATCTCCGG 59.891 60.000 10.57 5.78 42.30 5.14
551 576 1.215173 TGCCAATAGTCCCCATTCCAG 59.785 52.381 0.00 0.00 0.00 3.86
552 577 1.215173 CTGCCAATAGTCCCCATTCCA 59.785 52.381 0.00 0.00 0.00 3.53
553 578 1.215423 ACTGCCAATAGTCCCCATTCC 59.785 52.381 0.00 0.00 0.00 3.01
574 603 3.004752 AGAAAGACATACCATGTGCCC 57.995 47.619 0.00 0.00 45.03 5.36
581 610 4.365514 TGCAAGGAAGAAAGACATACCA 57.634 40.909 0.00 0.00 0.00 3.25
603 632 3.573967 CCTGGAAGTATTTGCCACAAGTT 59.426 43.478 0.00 0.00 0.00 2.66
624 653 5.163612 GCCAAATCCTGAAGTCTTATTGACC 60.164 44.000 0.00 0.00 46.46 4.02
980 1064 0.040958 CTCAAGCGTGGAGTGCAAAC 60.041 55.000 0.00 0.00 33.85 2.93
981 1065 0.179059 TCTCAAGCGTGGAGTGCAAA 60.179 50.000 0.00 0.00 34.04 3.68
984 1068 1.364626 CCATCTCAAGCGTGGAGTGC 61.365 60.000 0.00 0.00 34.94 4.40
997 1088 2.101582 ACTTGGTATCGTCAGCCATCTC 59.898 50.000 0.00 0.00 31.71 2.75
998 1089 2.101582 GACTTGGTATCGTCAGCCATCT 59.898 50.000 0.00 0.00 31.71 2.90
999 1090 2.474816 GACTTGGTATCGTCAGCCATC 58.525 52.381 0.00 0.00 31.71 3.51
1000 1091 1.139058 GGACTTGGTATCGTCAGCCAT 59.861 52.381 0.00 0.00 31.71 4.40
1001 1092 0.535335 GGACTTGGTATCGTCAGCCA 59.465 55.000 0.00 0.00 31.88 4.75
1002 1093 0.179081 GGGACTTGGTATCGTCAGCC 60.179 60.000 0.00 0.00 31.88 4.85
1003 1094 0.824759 AGGGACTTGGTATCGTCAGC 59.175 55.000 0.00 0.00 27.25 4.26
1053 1922 6.135290 TCAGATTCAGAACCAAAACACAAG 57.865 37.500 0.00 0.00 0.00 3.16
1072 1941 2.323599 CCTCAGGCACAGGATATCAGA 58.676 52.381 4.83 0.00 31.91 3.27
1082 1951 0.106769 TTGCAAAGACCTCAGGCACA 60.107 50.000 0.00 0.00 33.66 4.57
1091 1960 3.988379 TCACTGATTGTTGCAAAGACC 57.012 42.857 0.00 0.00 0.00 3.85
1096 1967 4.082081 GGGATCAATCACTGATTGTTGCAA 60.082 41.667 24.72 10.83 45.23 4.08
1178 2052 3.119029 CCAGCATTCCACACCAATAAAGG 60.119 47.826 0.00 0.00 0.00 3.11
1228 2102 1.555075 TCCTAGGTTGTGGAGATGCAC 59.445 52.381 9.08 0.00 0.00 4.57
1232 2106 3.791320 TGAAGTCCTAGGTTGTGGAGAT 58.209 45.455 9.08 0.00 32.36 2.75
1237 2111 2.224523 TGCCTTGAAGTCCTAGGTTGTG 60.225 50.000 9.08 0.00 39.55 3.33
1238 2112 2.054799 TGCCTTGAAGTCCTAGGTTGT 58.945 47.619 9.08 0.00 39.55 3.32
1263 2137 4.283230 ACAATGTTGTAGGCCCTGAGGG 62.283 54.545 14.80 14.80 42.39 4.30
1272 2146 3.758023 TCATGCTGGAACAATGTTGTAGG 59.242 43.478 2.20 0.00 41.31 3.18
1279 2153 1.203052 GTGGGTCATGCTGGAACAATG 59.797 52.381 0.00 0.00 38.70 2.82
1287 2161 1.377725 GTCCAGGTGGGTCATGCTG 60.378 63.158 0.00 0.00 38.11 4.41
1297 2171 3.750371 TGTTATTTGACAGGTCCAGGTG 58.250 45.455 0.00 0.00 0.00 4.00
1335 2209 1.116308 TCAGCCGTGAAATATCGGGA 58.884 50.000 5.78 0.00 45.85 5.14
1341 2218 4.102524 AGGTATGGATTCAGCCGTGAAATA 59.897 41.667 0.00 0.00 45.88 1.40
1355 2232 6.510296 AGATCCAGATATGTCAGGTATGGAT 58.490 40.000 13.39 13.39 46.13 3.41
1356 2233 5.908590 AGATCCAGATATGTCAGGTATGGA 58.091 41.667 6.18 6.18 39.52 3.41
1380 2257 7.416154 TTCACCTGAAAAGTTATTGTACGAG 57.584 36.000 0.00 0.00 0.00 4.18
1391 2268 4.104738 TCTCTGGGATTTCACCTGAAAAGT 59.895 41.667 4.61 0.00 45.81 2.66
1402 2279 8.552034 CAAATTTACGATACTCTCTGGGATTTC 58.448 37.037 0.00 0.00 0.00 2.17
1403 2280 7.499232 CCAAATTTACGATACTCTCTGGGATTT 59.501 37.037 0.00 0.00 0.00 2.17
1421 2298 9.919416 TGAGGACATTCAGATATTCCAAATTTA 57.081 29.630 0.00 0.00 0.00 1.40
1426 2303 6.069440 AGGTTGAGGACATTCAGATATTCCAA 60.069 38.462 0.00 0.00 0.00 3.53
1429 2306 5.994668 GGAGGTTGAGGACATTCAGATATTC 59.005 44.000 0.00 0.00 0.00 1.75
1430 2307 5.429762 TGGAGGTTGAGGACATTCAGATATT 59.570 40.000 0.00 0.00 0.00 1.28
1485 2362 4.000988 ACCGAGTAAGCAAATCGAATTGT 58.999 39.130 14.40 0.00 38.72 2.71
1525 2468 2.166254 CACAAAGCTTTGGGTTGTCAGT 59.834 45.455 35.65 14.39 42.34 3.41
1529 2472 3.758715 GCACAAAGCTTTGGGTTGT 57.241 47.368 35.27 17.69 43.39 3.32
1547 2490 1.667724 GGCAGTCATTCATCGGTGAAG 59.332 52.381 17.41 9.10 46.75 3.02
1555 2498 2.124151 GCGGGGGCAGTCATTCAT 60.124 61.111 0.00 0.00 0.00 2.57
1558 2501 4.473520 CGAGCGGGGGCAGTCATT 62.474 66.667 0.00 0.00 0.00 2.57
1563 2506 4.082523 TTTCTCGAGCGGGGGCAG 62.083 66.667 7.81 0.00 0.00 4.85
1571 2515 2.543653 GCTCTCCATCTCTTTCTCGAGC 60.544 54.545 7.81 0.00 36.32 5.03
1580 2524 2.039818 TCGTAACGCTCTCCATCTCT 57.960 50.000 0.00 0.00 0.00 3.10
1591 2538 1.348594 GCAGCCTGATTCGTAACGC 59.651 57.895 0.00 0.00 0.00 4.84
1594 2743 1.675714 CCTGTGCAGCCTGATTCGTAA 60.676 52.381 0.00 0.00 0.00 3.18
1744 9181 6.817765 TTCAGACAAAGTTTCAGAACAAGT 57.182 33.333 0.00 0.00 38.26 3.16
1745 9182 8.519492 TTTTTCAGACAAAGTTTCAGAACAAG 57.481 30.769 0.00 0.00 38.26 3.16
1767 9204 1.005450 TGGCCTCCGGAAGCTATTTTT 59.995 47.619 23.85 0.00 0.00 1.94
1768 9205 0.623723 TGGCCTCCGGAAGCTATTTT 59.376 50.000 23.85 0.00 0.00 1.82
1769 9206 0.623723 TTGGCCTCCGGAAGCTATTT 59.376 50.000 23.85 0.00 0.00 1.40
1770 9207 0.623723 TTTGGCCTCCGGAAGCTATT 59.376 50.000 23.85 0.00 0.00 1.73
1825 9267 7.985184 TGAATTAAGATAATCGTTACTGCAGGT 59.015 33.333 19.93 6.35 0.00 4.00
1853 9331 1.034356 TTGCCAGGCATGCATATCAC 58.966 50.000 17.09 0.00 38.76 3.06
1861 9339 0.171903 GTTGCTAGTTGCCAGGCATG 59.828 55.000 17.09 7.40 38.76 4.06
1881 9361 1.668751 ATGTATTAACAAGCACCGGCG 59.331 47.619 0.00 0.00 40.67 6.46
1933 9433 4.585879 ACATAACTAATCACGGCCAGTTT 58.414 39.130 8.98 2.08 33.47 2.66
1982 9485 4.203618 GCCGGAGCTACCTTGTTC 57.796 61.111 5.05 0.00 36.31 3.18
2044 9557 1.003464 GCAAAAGCATGGAAATGGGGT 59.997 47.619 0.00 0.00 0.00 4.95
2059 9572 3.740764 GCATGTGTTCAAGAAGGGCAAAA 60.741 43.478 0.00 0.00 0.00 2.44
2076 9589 0.535335 AAGACGACCGGTATGCATGT 59.465 50.000 7.34 0.00 0.00 3.21
2173 9722 2.606587 AACCCCGGCATCAAGAGCT 61.607 57.895 0.00 0.00 0.00 4.09
2222 10354 4.791411 GCGAGCTTACACAAAAACCAATCA 60.791 41.667 0.00 0.00 0.00 2.57
2265 10397 2.360165 GCACCAGGCTCTCCAAATAATG 59.640 50.000 0.00 0.00 40.25 1.90
2283 10416 1.378514 ACGAACCCCATCCATGCAC 60.379 57.895 0.00 0.00 0.00 4.57
2303 10436 3.643792 AGTCAGGAAGTATAGATGGCCAC 59.356 47.826 8.16 1.58 0.00 5.01
2307 10440 5.878406 AACCAGTCAGGAAGTATAGATGG 57.122 43.478 0.00 0.00 41.22 3.51
2309 10442 6.213600 ACACAAACCAGTCAGGAAGTATAGAT 59.786 38.462 0.00 0.00 41.22 1.98
2310 10443 5.542635 ACACAAACCAGTCAGGAAGTATAGA 59.457 40.000 0.00 0.00 41.22 1.98
2311 10444 5.794894 ACACAAACCAGTCAGGAAGTATAG 58.205 41.667 0.00 0.00 41.22 1.31
2312 10445 5.279809 GGACACAAACCAGTCAGGAAGTATA 60.280 44.000 0.00 0.00 41.22 1.47
2313 10446 4.505039 GGACACAAACCAGTCAGGAAGTAT 60.505 45.833 0.00 0.00 41.22 2.12
2314 10447 3.181458 GGACACAAACCAGTCAGGAAGTA 60.181 47.826 0.00 0.00 41.22 2.24
2315 10448 2.421529 GGACACAAACCAGTCAGGAAGT 60.422 50.000 0.00 0.00 41.22 3.01
2316 10449 2.222027 GGACACAAACCAGTCAGGAAG 58.778 52.381 0.00 0.00 41.22 3.46
2343 10476 7.391833 ACAAGCTGTCGACATAGATAGATCATA 59.608 37.037 20.40 0.00 32.04 2.15
2382 10632 5.237815 GTGTGACATTCTACACATCCTTGA 58.762 41.667 0.00 0.00 46.20 3.02
2393 10643 5.432645 TCTGTGTTTTGGTGTGACATTCTA 58.567 37.500 0.00 0.00 0.00 2.10
2402 10652 3.297134 ACATCCTCTGTGTTTTGGTGT 57.703 42.857 0.00 0.00 36.48 4.16
2413 10664 5.114780 CCACTTCATTCTACACATCCTCTG 58.885 45.833 0.00 0.00 0.00 3.35
2415 10666 3.873952 GCCACTTCATTCTACACATCCTC 59.126 47.826 0.00 0.00 0.00 3.71
2424 10680 4.774124 CATTCTCCTGCCACTTCATTCTA 58.226 43.478 0.00 0.00 0.00 2.10
2433 10689 1.001641 AGGTGCATTCTCCTGCCAC 60.002 57.895 0.00 0.00 41.58 5.01
2467 10730 5.221722 ACACACATTCTACACATCCTCTGTT 60.222 40.000 0.00 0.00 35.29 3.16
2468 10731 4.284490 ACACACATTCTACACATCCTCTGT 59.716 41.667 0.00 0.00 39.20 3.41
2469 10732 4.628766 CACACACATTCTACACATCCTCTG 59.371 45.833 0.00 0.00 0.00 3.35
2470 10733 4.284490 ACACACACATTCTACACATCCTCT 59.716 41.667 0.00 0.00 0.00 3.69
2471 10734 4.569943 ACACACACATTCTACACATCCTC 58.430 43.478 0.00 0.00 0.00 3.71
2472 10735 4.563580 GGACACACACATTCTACACATCCT 60.564 45.833 0.00 0.00 0.00 3.24
2473 10736 3.684788 GGACACACACATTCTACACATCC 59.315 47.826 0.00 0.00 0.00 3.51
2474 10737 4.314961 TGGACACACACATTCTACACATC 58.685 43.478 0.00 0.00 0.00 3.06
2475 10738 4.350368 TGGACACACACATTCTACACAT 57.650 40.909 0.00 0.00 0.00 3.21
2476 10739 3.828875 TGGACACACACATTCTACACA 57.171 42.857 0.00 0.00 0.00 3.72
2477 10740 5.493133 TTTTGGACACACACATTCTACAC 57.507 39.130 0.00 0.00 0.00 2.90
2480 10743 5.042463 TCCTTTTGGACACACACATTCTA 57.958 39.130 0.00 0.00 45.19 2.10
2481 10744 3.897239 TCCTTTTGGACACACACATTCT 58.103 40.909 0.00 0.00 45.19 2.40
2503 10789 2.413112 CACCAGAATGTACACAAGCTCG 59.587 50.000 0.00 0.00 0.00 5.03
2527 10813 7.395190 TTGAATCCAGGAGACATTTGTAATG 57.605 36.000 0.00 0.00 0.00 1.90
2531 10817 5.139727 TGTTTGAATCCAGGAGACATTTGT 58.860 37.500 0.00 0.00 0.00 2.83
2532 10818 5.710513 TGTTTGAATCCAGGAGACATTTG 57.289 39.130 0.00 0.00 0.00 2.32
2565 10851 5.452636 GGAGCCATTACAGGTTTCACAAAAA 60.453 40.000 0.00 0.00 0.00 1.94
2567 10853 3.572255 GGAGCCATTACAGGTTTCACAAA 59.428 43.478 0.00 0.00 0.00 2.83
2569 10855 2.107378 TGGAGCCATTACAGGTTTCACA 59.893 45.455 0.00 0.00 0.00 3.58
2571 10857 2.290896 CCTGGAGCCATTACAGGTTTCA 60.291 50.000 0.00 0.00 45.21 2.69
2572 10858 2.369394 CCTGGAGCCATTACAGGTTTC 58.631 52.381 0.00 0.00 45.21 2.78
2573 10859 2.514458 CCTGGAGCCATTACAGGTTT 57.486 50.000 0.00 0.00 45.21 3.27
2577 10863 0.257039 AAGCCCTGGAGCCATTACAG 59.743 55.000 0.00 0.00 0.00 2.74
2578 10864 0.034186 CAAGCCCTGGAGCCATTACA 60.034 55.000 0.00 0.00 0.00 2.41
2579 10865 0.255890 TCAAGCCCTGGAGCCATTAC 59.744 55.000 0.00 0.00 0.00 1.89
2580 10866 0.548031 CTCAAGCCCTGGAGCCATTA 59.452 55.000 0.00 0.00 0.00 1.90
2613 10899 9.624697 GTAAAGCATGAACAAGATCACATAAAA 57.375 29.630 0.00 0.00 30.82 1.52
2652 10938 5.189928 TGTGCATTACTATTTCCCGTTGAT 58.810 37.500 0.00 0.00 0.00 2.57
2653 10939 4.580868 TGTGCATTACTATTTCCCGTTGA 58.419 39.130 0.00 0.00 0.00 3.18
2701 11332 9.216117 TCTAAAAACTAAGGCTAATCAACAGTC 57.784 33.333 0.00 0.00 0.00 3.51
2705 11336 8.563123 AGGTCTAAAAACTAAGGCTAATCAAC 57.437 34.615 0.00 0.00 0.00 3.18
2713 11344 4.393371 CAGCTGAGGTCTAAAAACTAAGGC 59.607 45.833 8.42 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.