Multiple sequence alignment - TraesCS4A01G258600

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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 TraesCS4A01G258600 chr4A 100.000 3560 0 0 1 3560 571211794 571215353 0.000000e+00 6575.0
1 TraesCS4A01G258600 chr4A 84.507 426 31 20 2377 2792 571220875 571221275 4.310000e-104 388.0
2 TraesCS4A01G258600 chr4A 85.185 135 18 1 2108 2240 571220543 571220677 1.720000e-28 137.0
3 TraesCS4A01G258600 chr4A 84.722 72 8 2 3465 3536 534047005 534047073 6.380000e-08 69.4
4 TraesCS4A01G258600 chr4D 89.946 1850 108 37 425 2240 31435101 31436906 0.000000e+00 2314.0
5 TraesCS4A01G258600 chr4D 95.597 1272 48 3 2290 3560 31437033 31438297 0.000000e+00 2032.0
6 TraesCS4A01G258600 chr4D 87.406 397 29 11 77 462 31434709 31435095 1.520000e-118 436.0
7 TraesCS4A01G258600 chr4D 85.158 411 31 14 2427 2837 31443600 31443980 9.260000e-106 394.0
8 TraesCS4A01G258600 chr4D 84.951 206 22 5 2968 3165 31444163 31444367 2.170000e-47 200.0
9 TraesCS4A01G258600 chr4D 85.185 135 18 1 2108 2240 31443208 31443342 1.720000e-28 137.0
10 TraesCS4A01G258600 chr4B 86.441 1003 77 26 446 1402 44953528 44952539 0.000000e+00 1044.0
11 TraesCS4A01G258600 chr4B 85.904 830 63 21 1437 2240 44952541 44951740 0.000000e+00 835.0
12 TraesCS4A01G258600 chr4B 91.211 512 33 9 2308 2811 44951611 44951104 0.000000e+00 686.0
13 TraesCS4A01G258600 chr4B 85.792 366 13 13 77 429 44953926 44953587 5.650000e-93 351.0
14 TraesCS4A01G258600 chr5B 85.021 474 51 11 2380 2845 633115098 633114637 6.960000e-127 464.0
15 TraesCS4A01G258600 chr5B 83.784 481 54 12 2377 2845 625233179 625233647 5.460000e-118 435.0
16 TraesCS4A01G258600 chr5B 83.784 481 54 12 2377 2845 628832698 628833166 5.460000e-118 435.0
17 TraesCS4A01G258600 chr5B 95.500 200 5 3 2471 2668 600187331 600187528 2.060000e-82 316.0
18 TraesCS4A01G258600 chr5D 84.696 477 53 10 2377 2845 501520438 501520902 3.240000e-125 459.0
19 TraesCS4A01G258600 chr5D 95.122 41 0 2 3464 3503 259528205 259528166 2.970000e-06 63.9
20 TraesCS4A01G258600 chrUn 83.784 481 54 12 2377 2845 310639539 310640007 5.460000e-118 435.0
21 TraesCS4A01G258600 chr7D 88.525 61 6 1 3476 3535 576198147 576198087 4.930000e-09 73.1
22 TraesCS4A01G258600 chr6A 95.238 42 0 2 3465 3505 158047896 158047856 8.250000e-07 65.8
23 TraesCS4A01G258600 chr3A 91.489 47 3 1 3460 3506 36757266 36757221 2.970000e-06 63.9
24 TraesCS4A01G258600 chr2D 86.207 58 5 1 3477 3531 49394746 49394803 3.840000e-05 60.2
25 TraesCS4A01G258600 chr2D 91.111 45 3 1 3465 3509 620551040 620551083 3.840000e-05 60.2
26 TraesCS4A01G258600 chr2B 89.130 46 4 1 3461 3505 706696943 706696988 4.960000e-04 56.5


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 TraesCS4A01G258600 chr4A 571211794 571215353 3559 False 6575.000000 6575 100.000 1 3560 1 chr4A.!!$F2 3559
1 TraesCS4A01G258600 chr4A 571220543 571221275 732 False 262.500000 388 84.846 2108 2792 2 chr4A.!!$F3 684
2 TraesCS4A01G258600 chr4D 31434709 31438297 3588 False 1594.000000 2314 90.983 77 3560 3 chr4D.!!$F1 3483
3 TraesCS4A01G258600 chr4D 31443208 31444367 1159 False 243.666667 394 85.098 2108 3165 3 chr4D.!!$F2 1057
4 TraesCS4A01G258600 chr4B 44951104 44953926 2822 True 729.000000 1044 87.337 77 2811 4 chr4B.!!$R1 2734

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
169 175 0.093026 CGATCGCAACGTTGAGTTCC 59.907 55.0 31.62 18.41 42.02 3.62 F
1608 1743 0.238817 TGGCAACCACGTTAAATCGC 59.761 50.0 0.00 0.00 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1904 2053 0.383231 CAAGAAATCCGGATGCCTGC 59.617 55.0 19.95 0.07 0.00 4.85 R
2916 3288 0.323725 GCCCAAGGCTCCATTCAGAA 60.324 55.0 0.00 0.00 46.69 3.02 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
42 43 8.839310 ACTATTATTCTCTGTATTGCCATGAC 57.161 34.615 0.00 0.00 0.00 3.06
43 44 8.432013 ACTATTATTCTCTGTATTGCCATGACA 58.568 33.333 0.00 0.00 0.00 3.58
44 45 9.445878 CTATTATTCTCTGTATTGCCATGACAT 57.554 33.333 0.00 0.00 0.00 3.06
46 47 9.970553 ATTATTCTCTGTATTGCCATGACATAT 57.029 29.630 0.00 0.00 0.00 1.78
47 48 7.683437 ATTCTCTGTATTGCCATGACATATG 57.317 36.000 0.00 0.00 0.00 1.78
48 49 6.423776 TCTCTGTATTGCCATGACATATGA 57.576 37.500 10.38 0.00 0.00 2.15
49 50 7.012661 TCTCTGTATTGCCATGACATATGAT 57.987 36.000 10.38 0.00 0.00 2.45
50 51 6.877322 TCTCTGTATTGCCATGACATATGATG 59.123 38.462 10.38 3.54 0.00 3.07
51 52 6.771573 TCTGTATTGCCATGACATATGATGA 58.228 36.000 10.38 0.00 0.00 2.92
52 53 7.225725 TCTGTATTGCCATGACATATGATGAA 58.774 34.615 10.38 0.00 0.00 2.57
53 54 7.886446 TCTGTATTGCCATGACATATGATGAAT 59.114 33.333 10.38 3.70 0.00 2.57
54 55 8.047413 TGTATTGCCATGACATATGATGAATC 57.953 34.615 10.38 0.00 0.00 2.52
55 56 7.666388 TGTATTGCCATGACATATGATGAATCA 59.334 33.333 10.38 2.37 41.70 2.57
57 58 7.533289 TTGCCATGACATATGATGAATCATT 57.467 32.000 10.38 0.00 44.70 2.57
58 59 7.533289 TGCCATGACATATGATGAATCATTT 57.467 32.000 10.38 1.11 44.70 2.32
59 60 7.375053 TGCCATGACATATGATGAATCATTTG 58.625 34.615 10.38 17.13 44.70 2.32
60 61 7.231722 TGCCATGACATATGATGAATCATTTGA 59.768 33.333 22.55 8.38 44.70 2.69
61 62 8.085909 GCCATGACATATGATGAATCATTTGAA 58.914 33.333 22.55 14.07 44.70 2.69
62 63 9.974980 CCATGACATATGATGAATCATTTGAAA 57.025 29.630 22.55 13.83 44.70 2.69
118 124 3.600157 AGGGAGATAGATAGAGATGCCCA 59.400 47.826 0.00 0.00 35.50 5.36
129 135 1.226379 GATGCCCATCACGTTTGCG 60.226 57.895 3.48 0.00 44.93 4.85
169 175 0.093026 CGATCGCAACGTTGAGTTCC 59.907 55.000 31.62 18.41 42.02 3.62
170 176 1.144969 GATCGCAACGTTGAGTTCCA 58.855 50.000 31.62 12.78 42.02 3.53
241 250 2.380410 CCTCAAAACCGAGTCGCCG 61.380 63.158 7.12 0.00 0.00 6.46
405 414 1.210478 CCCACACATCTTGACCCCTAG 59.790 57.143 0.00 0.00 0.00 3.02
429 476 0.802222 CGGTCACGCGATCACATCTT 60.802 55.000 15.93 0.00 0.00 2.40
497 587 3.952628 CTTCCCTCGCGTGAACCCC 62.953 68.421 10.21 0.00 0.00 4.95
581 671 0.318445 CTCTGCAAAAGCCAGCACAC 60.318 55.000 0.00 0.00 36.62 3.82
590 680 4.671549 CCAGCACACACGCAAGCG 62.672 66.667 13.50 13.50 46.03 4.68
661 774 0.792640 ATGAGACGCAAGAAGCAACG 59.207 50.000 0.00 0.00 46.13 4.10
762 876 3.785499 GTCGAAACGGGAAGCCGC 61.785 66.667 0.00 0.00 36.58 6.53
927 1046 1.528129 CACCACAAGCTTTCTCCTCC 58.472 55.000 0.00 0.00 0.00 4.30
937 1056 2.748641 TTTCTCCTCCCTCGGCTGGT 62.749 60.000 0.00 0.00 0.00 4.00
953 1072 0.252284 TGGTTGGGTTGGTTGGTTGT 60.252 50.000 0.00 0.00 0.00 3.32
954 1073 1.006758 TGGTTGGGTTGGTTGGTTGTA 59.993 47.619 0.00 0.00 0.00 2.41
955 1074 1.684450 GGTTGGGTTGGTTGGTTGTAG 59.316 52.381 0.00 0.00 0.00 2.74
956 1075 1.067974 GTTGGGTTGGTTGGTTGTAGC 59.932 52.381 0.00 0.00 0.00 3.58
959 1078 1.542987 GGGTTGGTTGGTTGTAGCGTA 60.543 52.381 0.00 0.00 0.00 4.42
960 1079 1.802365 GGTTGGTTGGTTGTAGCGTAG 59.198 52.381 0.00 0.00 0.00 3.51
975 1094 1.305201 CGTAGCCTCTGTCCTCTCTC 58.695 60.000 0.00 0.00 0.00 3.20
976 1095 1.687563 GTAGCCTCTGTCCTCTCTCC 58.312 60.000 0.00 0.00 0.00 3.71
977 1096 1.214424 GTAGCCTCTGTCCTCTCTCCT 59.786 57.143 0.00 0.00 0.00 3.69
979 1098 0.258774 GCCTCTGTCCTCTCTCCTCT 59.741 60.000 0.00 0.00 0.00 3.69
980 1099 1.750682 GCCTCTGTCCTCTCTCCTCTC 60.751 61.905 0.00 0.00 0.00 3.20
1015 1144 1.127343 GGTGATGGAGAGGAAGGAGG 58.873 60.000 0.00 0.00 0.00 4.30
1033 1162 2.812619 GGCGGGGAGAAGATGGAGG 61.813 68.421 0.00 0.00 0.00 4.30
1162 1297 1.203523 AGGACTACTTCAAGCAGCTCG 59.796 52.381 0.00 0.00 0.00 5.03
1163 1298 1.634702 GACTACTTCAAGCAGCTCGG 58.365 55.000 0.00 0.00 0.00 4.63
1165 1300 0.532573 CTACTTCAAGCAGCTCGGGA 59.467 55.000 0.00 0.00 0.00 5.14
1204 1339 1.421268 ACTGGGACTGCATCAAGAACA 59.579 47.619 0.00 0.00 0.00 3.18
1276 1411 2.367512 CTCCTTCCCCTCCCCCTG 60.368 72.222 0.00 0.00 0.00 4.45
1333 1468 4.253685 TGCCTTGTTCTACTTCTATGCAC 58.746 43.478 0.00 0.00 0.00 4.57
1336 1471 4.563184 CCTTGTTCTACTTCTATGCACGTC 59.437 45.833 0.00 0.00 0.00 4.34
1367 1502 0.808847 GTTCGATCTTGGCCCGTACC 60.809 60.000 0.00 0.00 0.00 3.34
1373 1508 3.324108 TTGGCCCGTACCTGTCCC 61.324 66.667 0.00 0.00 0.00 4.46
1402 1537 4.197522 CGCTAGATCGTGCGTCTC 57.802 61.111 21.35 0.00 46.09 3.36
1407 1542 2.319011 TAGATCGTGCGTCTCGTGCC 62.319 60.000 0.00 0.00 0.00 5.01
1413 1548 4.849329 GCGTCTCGTGCCGGTAGG 62.849 72.222 1.90 4.11 41.62 3.18
1422 1557 0.457035 GTGCCGGTAGGAACACGATA 59.543 55.000 1.90 0.00 45.91 2.92
1423 1558 0.742505 TGCCGGTAGGAACACGATAG 59.257 55.000 1.90 0.00 41.02 2.08
1425 1560 1.683943 CCGGTAGGAACACGATAGGA 58.316 55.000 0.00 0.00 41.02 2.94
1516 1651 2.349438 CGTGCTGTTACGAAATGTTGCT 60.349 45.455 0.00 0.00 46.46 3.91
1520 1655 4.151689 TGCTGTTACGAAATGTTGCTACTC 59.848 41.667 0.00 0.00 0.00 2.59
1573 1708 2.159531 TGCATGTTCTTGTAGCAATCGC 60.160 45.455 0.00 0.00 38.99 4.58
1608 1743 0.238817 TGGCAACCACGTTAAATCGC 59.761 50.000 0.00 0.00 0.00 4.58
1629 1764 4.620803 CGCAAGGGAGTTAGTGTAGATGTT 60.621 45.833 0.00 0.00 0.00 2.71
1789 1932 3.119291 CAGTGTGGATGAAGTAGCGATC 58.881 50.000 0.00 0.00 0.00 3.69
1802 1945 4.663444 CGATCCGCAGATCCTTCC 57.337 61.111 4.33 0.00 45.32 3.46
1803 1946 1.372251 CGATCCGCAGATCCTTCCG 60.372 63.158 4.33 0.00 45.32 4.30
1832 1977 0.617535 TTTCCCCTCGAGCATCTGGA 60.618 55.000 6.99 4.43 0.00 3.86
1863 2008 7.548196 TTTCTAAGATTGTTATGCTTACCGG 57.452 36.000 0.00 0.00 0.00 5.28
1870 2015 2.685897 TGTTATGCTTACCGGCAATTCC 59.314 45.455 0.00 0.00 45.68 3.01
1875 2020 1.132453 GCTTACCGGCAATTCCTTGTC 59.868 52.381 0.00 0.00 34.69 3.18
1897 2046 6.150318 GTCCGATATATATAGGTGGCGATTG 58.850 44.000 18.25 0.00 31.35 2.67
1904 2053 0.249120 TAGGTGGCGATTGACCTGTG 59.751 55.000 3.85 0.00 42.80 3.66
1933 2082 5.097742 TCCGGATTTCTTGATTCTTGCTA 57.902 39.130 0.00 0.00 0.00 3.49
2007 2179 9.039870 CAGTCTCTGTCCATGTAGATTTATTTC 57.960 37.037 0.00 0.00 0.00 2.17
2008 2180 8.986991 AGTCTCTGTCCATGTAGATTTATTTCT 58.013 33.333 0.00 0.00 0.00 2.52
2009 2181 9.039870 GTCTCTGTCCATGTAGATTTATTTCTG 57.960 37.037 0.00 0.00 0.00 3.02
2010 2182 7.712639 TCTCTGTCCATGTAGATTTATTTCTGC 59.287 37.037 0.00 0.00 0.00 4.26
2011 2183 7.568349 TCTGTCCATGTAGATTTATTTCTGCT 58.432 34.615 0.00 0.00 30.56 4.24
2012 2184 7.496920 TCTGTCCATGTAGATTTATTTCTGCTG 59.503 37.037 0.00 0.00 30.56 4.41
2013 2185 6.543465 TGTCCATGTAGATTTATTTCTGCTGG 59.457 38.462 0.00 0.00 32.87 4.85
2014 2186 6.767902 GTCCATGTAGATTTATTTCTGCTGGA 59.232 38.462 0.00 0.00 35.48 3.86
2015 2187 6.994496 TCCATGTAGATTTATTTCTGCTGGAG 59.006 38.462 0.00 0.00 34.29 3.86
2016 2188 6.994496 CCATGTAGATTTATTTCTGCTGGAGA 59.006 38.462 0.00 0.00 33.11 3.71
2017 2189 7.664731 CCATGTAGATTTATTTCTGCTGGAGAT 59.335 37.037 0.00 0.00 33.11 2.75
2018 2190 9.064706 CATGTAGATTTATTTCTGCTGGAGATT 57.935 33.333 0.00 0.00 30.56 2.40
2019 2191 8.442632 TGTAGATTTATTTCTGCTGGAGATTG 57.557 34.615 0.00 0.00 30.56 2.67
2020 2192 8.049117 TGTAGATTTATTTCTGCTGGAGATTGT 58.951 33.333 0.00 0.00 30.56 2.71
2021 2193 7.565323 AGATTTATTTCTGCTGGAGATTGTC 57.435 36.000 0.00 0.00 0.00 3.18
2022 2194 7.344913 AGATTTATTTCTGCTGGAGATTGTCT 58.655 34.615 0.00 0.00 0.00 3.41
2023 2195 7.833183 AGATTTATTTCTGCTGGAGATTGTCTT 59.167 33.333 0.00 0.00 0.00 3.01
2032 2204 4.615452 GCTGGAGATTGTCTTTTGCAAGAG 60.615 45.833 10.67 10.67 39.86 2.85
2052 2224 3.195661 AGTTCGTCCTGTGTTCAGAAAC 58.804 45.455 0.00 0.00 43.76 2.78
2071 2245 6.151648 CAGAAACTTATTCTTGGAATCCAGCA 59.848 38.462 0.86 0.00 33.81 4.41
2123 2297 2.269172 GAGAAAGCTTGCCGTACTACC 58.731 52.381 0.00 0.00 0.00 3.18
2133 2307 2.229543 TGCCGTACTACCTGTTACAGTG 59.770 50.000 11.68 5.56 0.00 3.66
2145 2319 4.389374 CTGTTACAGTGACCCACATTTCT 58.611 43.478 3.88 0.00 36.74 2.52
2170 2346 4.380973 GCTCTGATGCTGTGTTGTAGTAGA 60.381 45.833 0.00 0.00 0.00 2.59
2201 2377 6.990349 TGTTCTAAATGATAAGGATCCGTTCC 59.010 38.462 5.22 0.00 45.85 3.62
2214 2390 1.067846 TCCGTTCCGACTTCAGTCATG 60.068 52.381 7.71 0.00 44.99 3.07
2222 2398 2.032894 CGACTTCAGTCATGCGTTGTTT 60.033 45.455 7.71 0.00 44.99 2.83
2236 2412 5.507077 TGCGTTGTTTGATTCTGTTCTTAC 58.493 37.500 0.00 0.00 0.00 2.34
2267 2547 6.649155 TGCCATCTATTGTAGTTTCTTGCTA 58.351 36.000 0.00 0.00 0.00 3.49
2328 2633 1.544724 TTTCCCAATTCCGAAGCCTG 58.455 50.000 0.00 0.00 0.00 4.85
2349 2656 3.196254 TGTCTGCTGCTATGTTCTGATGA 59.804 43.478 0.00 0.00 0.00 2.92
2360 2667 8.645110 TGCTATGTTCTGATGAATCTGAATAGA 58.355 33.333 13.58 8.93 43.44 1.98
2392 2702 3.264947 TGGAATCTGAATTCTGACAGCG 58.735 45.455 16.26 0.00 40.99 5.18
2513 2823 3.787001 GGCCAAGGAGGAGACCCG 61.787 72.222 0.00 0.00 41.22 5.28
2657 2971 7.881775 TCAGCCTAAGAGTTTTTCTTTTTCT 57.118 32.000 0.00 0.00 43.68 2.52
2706 3020 1.098050 ATGGTTTGCCTGAGCGATTC 58.902 50.000 0.00 0.00 44.31 2.52
2742 3058 3.243569 CCGTTCCTAGCTGTGGATCTTAG 60.244 52.174 10.48 2.73 33.09 2.18
2786 3102 0.030101 CGGTGCGTTTTGGTGACATT 59.970 50.000 0.00 0.00 42.32 2.71
2820 3136 4.323417 TCACCTATGCTTCATTTTGTCGT 58.677 39.130 0.00 0.00 0.00 4.34
2913 3285 2.224314 GCACTAAACTGGCTGAGTGTTC 59.776 50.000 11.49 0.00 41.14 3.18
2914 3286 2.808543 CACTAAACTGGCTGAGTGTTCC 59.191 50.000 0.00 0.00 35.61 3.62
2915 3287 2.069273 CTAAACTGGCTGAGTGTTCCG 58.931 52.381 0.00 0.00 34.02 4.30
2916 3288 0.180406 AAACTGGCTGAGTGTTCCGT 59.820 50.000 0.00 0.00 34.02 4.69
2917 3289 0.180406 AACTGGCTGAGTGTTCCGTT 59.820 50.000 0.00 0.00 34.02 4.44
2931 3303 0.984230 TCCGTTCTGAATGGAGCCTT 59.016 50.000 24.01 0.00 41.59 4.35
3006 3397 5.587443 TCATCACATTCTCCTGCTATGTTTG 59.413 40.000 0.00 0.00 30.45 2.93
3017 3408 7.336931 TCTCCTGCTATGTTTGAAATTAACCTC 59.663 37.037 0.00 0.00 0.00 3.85
3212 3611 7.589954 AGAAACACAAACGTACAATAGCAAATC 59.410 33.333 0.00 0.00 0.00 2.17
3228 3627 8.969260 ATAGCAAATCTGTGAAATGTCTATGA 57.031 30.769 0.00 0.00 0.00 2.15
3266 3665 9.366216 AGTCTTTTTCAACATGGTTAAAAGTTC 57.634 29.630 19.67 15.61 37.20 3.01
3287 3686 4.139038 TCGTATTCTATGATGGTCCGTCA 58.861 43.478 16.26 16.26 33.71 4.35
3299 3698 5.534654 TGATGGTCCGTCAAGAAAAAGATTT 59.465 36.000 11.60 0.00 0.00 2.17
3308 3707 9.113876 CCGTCAAGAAAAAGATTTGTAATGTAC 57.886 33.333 0.00 0.00 0.00 2.90
3353 3752 0.827507 GTGGGGCATGTGTTTGGACT 60.828 55.000 0.00 0.00 0.00 3.85
3359 3758 1.877637 CATGTGTTTGGACTCGACCA 58.122 50.000 0.00 0.00 38.24 4.02
3398 3797 3.188460 CAGTATGTAAATGCCCGTATGCC 59.812 47.826 0.00 0.00 0.00 4.40
3423 3822 3.942829 TCAAACACCTAGGCATGAGAAG 58.057 45.455 9.30 0.00 0.00 2.85
3446 3845 3.452755 TCAGGCTATTGTCCATACACG 57.547 47.619 0.00 0.00 34.61 4.49
3510 3909 5.060506 TGACGTTTTGGTAGTTCATGTCAT 58.939 37.500 0.00 0.00 0.00 3.06
3528 3927 5.909477 TGTCATACATTTAGGAACGTAGGG 58.091 41.667 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 9.929180 GTCATGGCAATACAGAGAATAATAGTA 57.071 33.333 0.00 0.00 0.00 1.82
17 18 8.432013 TGTCATGGCAATACAGAGAATAATAGT 58.568 33.333 0.00 0.00 0.00 2.12
18 19 8.837788 TGTCATGGCAATACAGAGAATAATAG 57.162 34.615 0.00 0.00 0.00 1.73
20 21 9.970553 ATATGTCATGGCAATACAGAGAATAAT 57.029 29.630 3.01 0.00 0.00 1.28
21 22 9.223099 CATATGTCATGGCAATACAGAGAATAA 57.777 33.333 3.01 0.00 0.00 1.40
22 23 8.596293 TCATATGTCATGGCAATACAGAGAATA 58.404 33.333 3.01 0.00 0.00 1.75
23 24 7.455891 TCATATGTCATGGCAATACAGAGAAT 58.544 34.615 3.01 0.00 0.00 2.40
24 25 6.829849 TCATATGTCATGGCAATACAGAGAA 58.170 36.000 3.01 0.00 0.00 2.87
25 26 6.423776 TCATATGTCATGGCAATACAGAGA 57.576 37.500 3.01 6.07 0.00 3.10
26 27 6.877322 TCATCATATGTCATGGCAATACAGAG 59.123 38.462 3.01 0.00 0.00 3.35
27 28 6.771573 TCATCATATGTCATGGCAATACAGA 58.228 36.000 3.01 6.85 0.00 3.41
28 29 7.443259 TTCATCATATGTCATGGCAATACAG 57.557 36.000 3.01 0.00 0.00 2.74
29 30 7.666388 TGATTCATCATATGTCATGGCAATACA 59.334 33.333 3.01 7.60 0.00 2.29
30 31 8.047413 TGATTCATCATATGTCATGGCAATAC 57.953 34.615 3.01 0.00 0.00 1.89
31 32 8.817092 ATGATTCATCATATGTCATGGCAATA 57.183 30.769 3.01 0.00 45.17 1.90
32 33 7.718334 ATGATTCATCATATGTCATGGCAAT 57.282 32.000 3.01 0.00 45.17 3.56
33 34 7.533289 AATGATTCATCATATGTCATGGCAA 57.467 32.000 3.01 0.00 46.22 4.52
34 35 7.231722 TCAAATGATTCATCATATGTCATGGCA 59.768 33.333 0.60 0.60 46.22 4.92
35 36 7.599171 TCAAATGATTCATCATATGTCATGGC 58.401 34.615 1.90 0.00 46.22 4.40
36 37 9.974980 TTTCAAATGATTCATCATATGTCATGG 57.025 29.630 1.90 1.76 46.22 3.66
118 124 3.634568 TTTTGAATCCGCAAACGTGAT 57.365 38.095 0.00 0.00 37.48 3.06
147 153 2.716828 CTCAACGTTGCGATCGCGT 61.717 57.895 32.64 22.47 45.51 6.01
148 154 2.018670 CTCAACGTTGCGATCGCG 59.981 61.111 32.64 21.81 45.51 5.87
149 155 0.516524 GAACTCAACGTTGCGATCGC 60.517 55.000 32.48 32.48 42.35 4.58
150 156 0.093026 GGAACTCAACGTTGCGATCG 59.907 55.000 24.02 11.69 35.56 3.69
157 163 2.140717 GGATTCGTGGAACTCAACGTT 58.859 47.619 6.53 0.00 38.91 3.99
169 175 4.812476 TGGCGCTCCGGATTCGTG 62.812 66.667 21.99 12.09 34.14 4.35
170 176 4.077184 TTGGCGCTCCGGATTCGT 62.077 61.111 21.99 0.00 34.14 3.85
185 191 1.457346 GGTGGAAGATGCTCTGGTTG 58.543 55.000 0.00 0.00 0.00 3.77
201 207 2.137523 GCAGTGCAATCTTTTTGGGTG 58.862 47.619 11.09 0.00 0.00 4.61
241 250 1.146358 CGGATCGAACGGAAGCTTCC 61.146 60.000 32.12 32.12 44.05 3.46
273 282 0.806492 GGTTTGGAGCGTCCGATCTC 60.806 60.000 4.87 0.00 40.17 2.75
317 326 1.062525 GTACGTACCGCCGGTAGTG 59.937 63.158 17.86 14.71 39.02 2.74
318 327 0.958382 TTGTACGTACCGCCGGTAGT 60.958 55.000 17.86 17.94 39.02 2.73
319 328 0.523335 GTTGTACGTACCGCCGGTAG 60.523 60.000 17.86 13.11 39.02 3.18
320 329 1.504446 GTTGTACGTACCGCCGGTA 59.496 57.895 22.43 12.92 37.09 4.02
321 330 2.258286 GTTGTACGTACCGCCGGT 59.742 61.111 22.43 15.63 40.16 5.28
322 331 2.506881 GGTTGTACGTACCGCCGG 60.507 66.667 22.43 0.00 0.00 6.13
323 332 2.506881 GGGTTGTACGTACCGCCG 60.507 66.667 22.43 0.00 36.49 6.46
324 333 1.446618 CAGGGTTGTACGTACCGCC 60.447 63.158 22.43 21.47 36.49 6.13
325 334 2.096442 GCAGGGTTGTACGTACCGC 61.096 63.158 22.43 15.48 36.49 5.68
326 335 1.802715 CGCAGGGTTGTACGTACCG 60.803 63.158 22.43 12.75 36.49 4.02
327 336 2.096442 GCGCAGGGTTGTACGTACC 61.096 63.158 22.43 10.39 34.82 3.34
328 337 1.080298 AGCGCAGGGTTGTACGTAC 60.080 57.895 18.90 18.90 0.00 3.67
329 338 1.080366 CAGCGCAGGGTTGTACGTA 60.080 57.895 11.47 0.00 0.00 3.57
330 339 2.357034 CAGCGCAGGGTTGTACGT 60.357 61.111 11.47 0.00 0.00 3.57
331 340 3.788766 GCAGCGCAGGGTTGTACG 61.789 66.667 11.47 0.00 0.00 3.67
405 414 4.867599 GATCGCGTGACCGGGTCC 62.868 72.222 23.81 14.00 46.13 4.46
429 476 1.472878 CAGCGAAGTAGTAGCAGGTGA 59.527 52.381 0.00 0.00 0.00 4.02
466 556 4.452733 GGAAGGCTGCTACCGCGT 62.453 66.667 4.92 0.00 39.65 6.01
468 558 3.741830 GAGGGAAGGCTGCTACCGC 62.742 68.421 0.00 0.00 33.69 5.68
470 560 2.501610 CGAGGGAAGGCTGCTACC 59.498 66.667 0.00 0.71 0.00 3.18
497 587 3.827784 CGAGCGGAGTTTGCGACG 61.828 66.667 0.00 0.00 37.44 5.12
772 886 3.746949 CTCCGCCTCCCACTGATGC 62.747 68.421 0.00 0.00 0.00 3.91
774 888 2.765807 CCTCCGCCTCCCACTGAT 60.766 66.667 0.00 0.00 0.00 2.90
833 947 2.315386 ACGAAAGAAAGCCGCGGAC 61.315 57.895 33.48 20.78 0.00 4.79
913 1032 0.107945 CCGAGGGAGGAGAAAGCTTG 60.108 60.000 0.00 0.00 0.00 4.01
927 1046 2.672996 CAACCCAACCAGCCGAGG 60.673 66.667 0.00 0.00 0.00 4.63
937 1056 1.404843 GCTACAACCAACCAACCCAA 58.595 50.000 0.00 0.00 0.00 4.12
953 1072 0.547075 AGAGGACAGAGGCTACGCTA 59.453 55.000 0.00 0.00 0.00 4.26
954 1073 0.750182 GAGAGGACAGAGGCTACGCT 60.750 60.000 0.00 0.00 0.00 5.07
955 1074 0.750182 AGAGAGGACAGAGGCTACGC 60.750 60.000 0.00 0.00 0.00 4.42
956 1075 1.305201 GAGAGAGGACAGAGGCTACG 58.695 60.000 0.00 0.00 0.00 3.51
959 1078 0.258774 GAGGAGAGAGGACAGAGGCT 59.741 60.000 0.00 0.00 0.00 4.58
960 1079 0.258774 AGAGGAGAGAGGACAGAGGC 59.741 60.000 0.00 0.00 0.00 4.70
961 1080 1.475034 CGAGAGGAGAGAGGACAGAGG 60.475 61.905 0.00 0.00 0.00 3.69
962 1081 1.953559 CGAGAGGAGAGAGGACAGAG 58.046 60.000 0.00 0.00 0.00 3.35
976 1095 3.823330 CGACCGAACCCCCGAGAG 61.823 72.222 0.00 0.00 0.00 3.20
977 1096 4.666253 ACGACCGAACCCCCGAGA 62.666 66.667 0.00 0.00 0.00 4.04
1015 1144 2.812619 CCTCCATCTTCTCCCCGCC 61.813 68.421 0.00 0.00 0.00 6.13
1033 1162 4.083862 GTCGCCCACCTCCACCTC 62.084 72.222 0.00 0.00 0.00 3.85
1163 1298 4.980805 TGTCGGCGCTGGTGTTCC 62.981 66.667 17.88 0.00 0.00 3.62
1251 1386 3.787001 GGGGAAGGAGGAGGCGTG 61.787 72.222 0.00 0.00 0.00 5.34
1276 1411 1.766864 GTTAGGAGGAGGGGAGGGC 60.767 68.421 0.00 0.00 0.00 5.19
1278 1413 2.134933 GCGTTAGGAGGAGGGGAGG 61.135 68.421 0.00 0.00 0.00 4.30
1280 1415 1.684734 GTGCGTTAGGAGGAGGGGA 60.685 63.158 0.00 0.00 0.00 4.81
1283 1418 2.202756 GCGTGCGTTAGGAGGAGG 60.203 66.667 0.00 0.00 0.00 4.30
1284 1419 2.579787 CGCGTGCGTTAGGAGGAG 60.580 66.667 6.00 0.00 34.35 3.69
1310 1445 4.331168 GTGCATAGAAGTAGAACAAGGCAG 59.669 45.833 0.00 0.00 0.00 4.85
1367 1502 3.655810 GAGCAGAGGCACGGGACAG 62.656 68.421 0.00 0.00 44.61 3.51
1407 1542 3.568853 AGATTCCTATCGTGTTCCTACCG 59.431 47.826 0.00 0.00 35.85 4.02
1413 1548 4.039366 AGGGCTAAGATTCCTATCGTGTTC 59.961 45.833 0.00 0.00 35.85 3.18
1422 1557 1.139853 CGCAAGAGGGCTAAGATTCCT 59.860 52.381 0.00 0.00 43.02 3.36
1423 1558 1.587547 CGCAAGAGGGCTAAGATTCC 58.412 55.000 0.00 0.00 43.02 3.01
1425 1560 1.204146 TCCGCAAGAGGGCTAAGATT 58.796 50.000 0.00 0.00 43.02 2.40
1516 1651 2.707257 ACAAAGGGGGAAACGAAGAGTA 59.293 45.455 0.00 0.00 0.00 2.59
1520 1655 1.611977 GGAACAAAGGGGGAAACGAAG 59.388 52.381 0.00 0.00 0.00 3.79
1573 1708 5.221422 TGGTTGCCAGGAAAATAAAACAGAG 60.221 40.000 0.00 0.00 0.00 3.35
1608 1743 4.631813 GCAACATCTACACTAACTCCCTTG 59.368 45.833 0.00 0.00 0.00 3.61
1792 1935 5.567138 AAAAATAAGTGCGGAAGGATCTG 57.433 39.130 0.00 0.00 34.87 2.90
1861 2006 1.948104 TATCGGACAAGGAATTGCCG 58.052 50.000 13.82 13.82 43.43 5.69
1863 2008 8.204836 ACCTATATATATCGGACAAGGAATTGC 58.795 37.037 17.85 0.00 0.00 3.56
1870 2015 5.298527 TCGCCACCTATATATATCGGACAAG 59.701 44.000 17.85 8.15 0.00 3.16
1875 2020 6.150318 GTCAATCGCCACCTATATATATCGG 58.850 44.000 10.94 10.94 0.00 4.18
1904 2053 0.383231 CAAGAAATCCGGATGCCTGC 59.617 55.000 19.95 0.07 0.00 4.85
1933 2082 2.597455 CAAGGTCACCCCAACTTTGAT 58.403 47.619 0.00 0.00 36.20 2.57
2007 2179 2.555325 TGCAAAAGACAATCTCCAGCAG 59.445 45.455 0.00 0.00 0.00 4.24
2008 2180 2.585330 TGCAAAAGACAATCTCCAGCA 58.415 42.857 0.00 0.00 0.00 4.41
2009 2181 3.254166 TCTTGCAAAAGACAATCTCCAGC 59.746 43.478 0.00 0.00 0.00 4.85
2010 2182 4.518211 ACTCTTGCAAAAGACAATCTCCAG 59.482 41.667 6.82 0.00 0.00 3.86
2011 2183 4.464008 ACTCTTGCAAAAGACAATCTCCA 58.536 39.130 6.82 0.00 0.00 3.86
2012 2184 5.444663 AACTCTTGCAAAAGACAATCTCC 57.555 39.130 6.82 0.00 0.00 3.71
2013 2185 5.142962 CGAACTCTTGCAAAAGACAATCTC 58.857 41.667 6.82 0.00 0.00 2.75
2014 2186 4.576463 ACGAACTCTTGCAAAAGACAATCT 59.424 37.500 6.82 0.00 0.00 2.40
2015 2187 4.848757 ACGAACTCTTGCAAAAGACAATC 58.151 39.130 6.82 0.00 0.00 2.67
2016 2188 4.261197 GGACGAACTCTTGCAAAAGACAAT 60.261 41.667 6.82 0.00 0.00 2.71
2017 2189 3.064820 GGACGAACTCTTGCAAAAGACAA 59.935 43.478 6.82 0.00 0.00 3.18
2018 2190 2.612212 GGACGAACTCTTGCAAAAGACA 59.388 45.455 6.82 0.00 0.00 3.41
2019 2191 2.872858 AGGACGAACTCTTGCAAAAGAC 59.127 45.455 6.82 0.00 0.00 3.01
2020 2192 2.872245 CAGGACGAACTCTTGCAAAAGA 59.128 45.455 6.82 0.00 0.00 2.52
2021 2193 2.614057 ACAGGACGAACTCTTGCAAAAG 59.386 45.455 0.00 0.00 28.63 2.27
2022 2194 2.354510 CACAGGACGAACTCTTGCAAAA 59.645 45.455 0.00 0.00 28.63 2.44
2023 2195 1.939934 CACAGGACGAACTCTTGCAAA 59.060 47.619 0.00 0.00 28.63 3.68
2032 2204 3.195661 AGTTTCTGAACACAGGACGAAC 58.804 45.455 0.00 0.00 38.26 3.95
2090 2264 5.278169 GCAAGCTTTCTCAAGAGATCACAAA 60.278 40.000 0.00 0.00 37.29 2.83
2123 2297 4.389374 AGAAATGTGGGTCACTGTAACAG 58.611 43.478 0.00 0.00 35.11 3.16
2133 2307 2.783135 TCAGAGCAAGAAATGTGGGTC 58.217 47.619 0.00 0.00 0.00 4.46
2145 2319 1.971481 ACAACACAGCATCAGAGCAA 58.029 45.000 0.00 0.00 36.85 3.91
2214 2390 5.507077 TGTAAGAACAGAATCAAACAACGC 58.493 37.500 0.00 0.00 0.00 4.84
2236 2412 4.639334 ACTACAATAGATGGCATCAGCTG 58.361 43.478 27.93 21.38 40.22 4.24
2267 2547 9.372369 GAGTTAACAGAGCAAATACAGAAGTAT 57.628 33.333 8.61 0.00 42.66 2.12
2328 2633 3.790091 TCATCAGAACATAGCAGCAGAC 58.210 45.455 0.00 0.00 0.00 3.51
2388 2698 7.611717 TCAGAGAACAGTAGCAGATTCGCTG 62.612 48.000 9.44 9.44 45.08 5.18
2392 2702 4.507388 GCATCAGAGAACAGTAGCAGATTC 59.493 45.833 0.00 0.00 0.00 2.52
2657 2971 1.416401 AGGCGAACAGAAGGACAAAGA 59.584 47.619 0.00 0.00 0.00 2.52
2706 3020 0.725117 GAACGGGTCTTACAATGCGG 59.275 55.000 0.00 0.00 0.00 5.69
2786 3102 5.435686 AGCATAGGTGATAGGACAAACAA 57.564 39.130 0.00 0.00 0.00 2.83
2913 3285 1.089920 CAAGGCTCCATTCAGAACGG 58.910 55.000 0.00 0.00 0.00 4.44
2914 3286 1.089920 CCAAGGCTCCATTCAGAACG 58.910 55.000 0.00 0.00 0.00 3.95
2915 3287 1.467920 CCCAAGGCTCCATTCAGAAC 58.532 55.000 0.00 0.00 0.00 3.01
2916 3288 0.323725 GCCCAAGGCTCCATTCAGAA 60.324 55.000 0.00 0.00 46.69 3.02
2917 3289 1.304282 GCCCAAGGCTCCATTCAGA 59.696 57.895 0.00 0.00 46.69 3.27
2931 3303 1.619654 CATTGTCAGTCCAAAGCCCA 58.380 50.000 0.00 0.00 0.00 5.36
3006 3397 7.908601 CCACGCTTAATAGTTGAGGTTAATTTC 59.091 37.037 0.00 0.00 0.00 2.17
3017 3408 2.702592 TCCCCCACGCTTAATAGTTG 57.297 50.000 0.00 0.00 0.00 3.16
3212 3611 8.183104 TCTACCCTATCATAGACATTTCACAG 57.817 38.462 0.00 0.00 0.00 3.66
3261 3660 5.068723 ACGGACCATCATAGAATACGAACTT 59.931 40.000 0.00 0.00 0.00 2.66
3266 3665 4.499037 TGACGGACCATCATAGAATACG 57.501 45.455 0.00 0.00 0.00 3.06
3287 3686 9.063615 AGGACGTACATTACAAATCTTTTTCTT 57.936 29.630 0.00 0.00 0.00 2.52
3299 3698 6.289834 TCCTTTTTGAAGGACGTACATTACA 58.710 36.000 0.00 0.00 43.68 2.41
3308 3707 0.517316 CGGCTCCTTTTTGAAGGACG 59.483 55.000 3.84 4.22 43.68 4.79
3334 3733 0.827507 AGTCCAAACACATGCCCCAC 60.828 55.000 0.00 0.00 0.00 4.61
3375 3774 4.062293 GCATACGGGCATTTACATACTGA 58.938 43.478 0.00 0.00 0.00 3.41
3398 3797 2.026641 CATGCCTAGGTGTTTGATGGG 58.973 52.381 11.31 0.00 0.00 4.00
3423 3822 4.449068 CGTGTATGGACAATAGCCTGAATC 59.551 45.833 0.00 0.00 37.31 2.52
3437 3836 3.845259 GGGCCGAGCGTGTATGGA 61.845 66.667 0.00 0.00 0.00 3.41
3446 3845 2.040009 TAGCTACCATTGGGCCGAGC 62.040 60.000 7.78 9.88 37.75 5.03
3505 3904 5.657745 TCCCTACGTTCCTAAATGTATGACA 59.342 40.000 0.00 0.00 36.52 3.58
3510 3909 6.186957 TGTACTCCCTACGTTCCTAAATGTA 58.813 40.000 0.00 0.00 36.11 2.29
3528 3927 2.484264 GTGAGGCAACACCAATGTACTC 59.516 50.000 0.00 0.00 43.14 2.59


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

AutoCloner maintained by Alex Coulton.