Multiple sequence alignment - TraesCS3A01G221300

Loading Multiple Alignment...

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 TraesCS3A01G221300 chr3A 100.000 2525 0 0 1 2525 410246583 410249107 0.000000e+00 4663.0
1 TraesCS3A01G221300 chr3A 90.765 1646 141 6 57 1691 410233246 410234891 0.000000e+00 2187.0
2 TraesCS3A01G221300 chr3A 93.021 874 54 5 1656 2525 410234891 410235761 0.000000e+00 1269.0
3 TraesCS3A01G221300 chr3A 76.129 775 119 50 47 790 423435150 423435889 1.860000e-91 346.0
4 TraesCS3A01G221300 chr3A 87.365 277 29 6 2252 2525 456030979 456031252 1.890000e-81 313.0
5 TraesCS3A01G221300 chr3A 75.584 385 70 16 1719 2089 502392926 502393300 4.320000e-38 169.0
6 TraesCS3A01G221300 chr3A 88.971 136 14 1 1115 1250 332131610 332131744 1.550000e-37 167.0
7 TraesCS3A01G221300 chr3A 87.591 137 16 1 1115 1251 258704893 258704758 9.350000e-35 158.0
8 TraesCS3A01G221300 chr3A 85.926 135 18 1 1115 1249 332141470 332141603 2.620000e-30 143.0
9 TraesCS3A01G221300 chr3A 78.571 140 23 7 1776 1911 333277079 333277215 4.480000e-13 86.1
10 TraesCS3A01G221300 chr3A 79.762 84 16 1 1372 1454 675286946 675286863 2.710000e-05 60.2
11 TraesCS3A01G221300 chr5B 81.972 710 95 27 1 698 205797269 205797957 2.820000e-159 571.0
12 TraesCS3A01G221300 chr3B 83.770 573 63 23 128 684 239019141 239019699 1.340000e-142 516.0
13 TraesCS3A01G221300 chr3B 83.566 572 66 21 128 684 239027273 239027831 6.230000e-141 510.0
14 TraesCS3A01G221300 chr3B 77.273 440 68 28 286 709 712372671 712373094 1.950000e-56 230.0
15 TraesCS3A01G221300 chr3B 75.556 315 57 15 1782 2090 616471280 616470980 1.220000e-28 137.0
16 TraesCS3A01G221300 chr4D 80.791 708 90 30 1844 2525 191323145 191322458 1.730000e-141 512.0
17 TraesCS3A01G221300 chr4D 79.858 705 101 26 1844 2525 191304282 191303596 6.320000e-131 477.0
18 TraesCS3A01G221300 chr4D 75.181 415 74 19 1696 2091 41201448 41201852 4.320000e-38 169.0
19 TraesCS3A01G221300 chr4D 85.256 156 10 5 1115 1268 239119486 239119630 5.630000e-32 148.0
20 TraesCS3A01G221300 chr6B 81.231 666 93 28 1 652 113042336 113042983 2.240000e-140 508.0
21 TraesCS3A01G221300 chr6B 76.291 755 123 43 47 760 100400396 100401135 4.000000e-93 351.0
22 TraesCS3A01G221300 chr6B 83.673 147 20 3 1311 1454 331121786 331121931 4.380000e-28 135.0
23 TraesCS3A01G221300 chr3D 82.010 617 93 16 47 652 356760957 356760348 2.240000e-140 508.0
24 TraesCS3A01G221300 chr3D 83.274 562 75 19 101 651 356727563 356727010 1.350000e-137 499.0
25 TraesCS3A01G221300 chr3D 75.644 776 123 51 1 749 146534952 146534216 2.420000e-85 326.0
26 TraesCS3A01G221300 chr3D 79.710 414 58 17 1806 2205 164918757 164919158 2.470000e-70 276.0
27 TraesCS3A01G221300 chr3D 78.632 351 62 10 1753 2095 254210363 254210708 1.180000e-53 220.0
28 TraesCS3A01G221300 chr7B 80.301 665 101 26 1 652 300976668 300976021 2.270000e-130 475.0
29 TraesCS3A01G221300 chr7B 79.549 665 105 28 1 652 300984322 300983676 1.780000e-121 446.0
30 TraesCS3A01G221300 chr7B 86.335 161 20 1 1820 1980 207844552 207844394 9.280000e-40 174.0
31 TraesCS3A01G221300 chr7B 97.059 34 1 0 1732 1765 582761228 582761261 9.760000e-05 58.4
32 TraesCS3A01G221300 chr7D 90.461 304 27 2 1450 1751 360474179 360473876 1.410000e-107 399.0
33 TraesCS3A01G221300 chr7D 83.582 134 20 2 1844 1977 360473839 360473708 9.480000e-25 124.0
34 TraesCS3A01G221300 chr2B 76.548 759 121 43 57 790 193778279 193777553 1.850000e-96 363.0
35 TraesCS3A01G221300 chr2B 76.282 156 25 10 1965 2116 366011726 366011579 3.480000e-09 73.1
36 TraesCS3A01G221300 chr2A 80.370 433 62 19 2103 2525 310297856 310297437 8.770000e-80 307.0
37 TraesCS3A01G221300 chr2A 82.222 270 36 10 1936 2205 273918936 273918679 3.270000e-54 222.0
38 TraesCS3A01G221300 chr2A 85.946 185 25 1 1450 1633 216320969 216320785 1.980000e-46 196.0
39 TraesCS3A01G221300 chr2A 87.681 138 16 1 1493 1629 224395513 224395376 2.600000e-35 159.0
40 TraesCS3A01G221300 chr2A 83.824 136 21 1 1115 1250 233616389 233616523 7.330000e-26 128.0
41 TraesCS3A01G221300 chr2A 76.423 246 43 14 1853 2094 469074510 469074276 4.410000e-23 119.0
42 TraesCS3A01G221300 chr2A 87.805 82 10 0 752 833 352386599 352386680 2.070000e-16 97.1
43 TraesCS3A01G221300 chr2A 78.571 140 23 7 1776 1911 326750 326886 4.480000e-13 86.1
44 TraesCS3A01G221300 chr1A 80.046 431 68 14 2103 2525 179773878 179774298 1.130000e-78 303.0
45 TraesCS3A01G221300 chr1A 84.385 301 41 5 2228 2525 179984427 179984130 8.840000e-75 291.0
46 TraesCS3A01G221300 chr1A 89.781 137 14 0 1114 1250 302862579 302862443 2.580000e-40 176.0
47 TraesCS3A01G221300 chr1A 86.538 156 21 0 877 1032 141258914 141259069 3.340000e-39 172.0
48 TraesCS3A01G221300 chr1A 89.051 137 15 0 1114 1250 302870642 302870506 1.200000e-38 171.0
49 TraesCS3A01G221300 chr1A 84.694 98 7 6 1363 1454 208397128 208397033 9.620000e-15 91.6
50 TraesCS3A01G221300 chr2D 83.923 311 44 6 2212 2519 69423405 69423712 2.460000e-75 292.0
51 TraesCS3A01G221300 chr5D 78.555 429 75 16 2106 2525 47678421 47678001 1.490000e-67 267.0
52 TraesCS3A01G221300 chr5D 79.827 347 57 12 2185 2525 47685549 47685210 9.030000e-60 241.0
53 TraesCS3A01G221300 chr1B 78.082 438 72 20 1820 2241 508292574 508292145 3.220000e-64 255.0
54 TraesCS3A01G221300 chr1B 75.676 481 84 23 1777 2241 530008319 530008782 2.550000e-50 209.0
55 TraesCS3A01G221300 chr1B 78.549 317 58 9 1928 2241 530016509 530016818 1.530000e-47 200.0
56 TraesCS3A01G221300 chrUn 92.614 176 13 0 1576 1751 92433944 92433769 1.160000e-63 254.0
57 TraesCS3A01G221300 chr7A 82.079 279 41 8 1965 2241 252474241 252474512 1.950000e-56 230.0
58 TraesCS3A01G221300 chr7A 86.628 172 18 4 1459 1629 325548469 325548302 4.290000e-43 185.0
59 TraesCS3A01G221300 chr7A 75.862 145 27 7 1953 2095 309719017 309718879 1.620000e-07 67.6
60 TraesCS3A01G221300 chr7A 86.667 60 6 2 702 760 552281952 552282010 5.830000e-07 65.8
61 TraesCS3A01G221300 chr4A 87.500 176 21 1 1459 1633 166507264 166507089 4.260000e-48 202.0
62 TraesCS3A01G221300 chr4A 87.500 136 16 1 1115 1250 347530056 347530190 3.360000e-34 156.0
63 TraesCS3A01G221300 chr4A 89.157 83 8 1 747 829 357613141 357613222 4.440000e-18 102.0
64 TraesCS3A01G221300 chr4A 89.157 83 8 1 747 829 357621129 357621210 4.440000e-18 102.0
65 TraesCS3A01G221300 chr4A 85.714 91 7 4 1363 1453 248259519 248259603 9.620000e-15 91.6
66 TraesCS3A01G221300 chr4A 93.220 59 4 0 1738 1796 370358557 370358499 1.240000e-13 87.9
67 TraesCS3A01G221300 chr4A 95.349 43 2 0 1753 1795 393416975 393417017 4.510000e-08 69.4
68 TraesCS3A01G221300 chr4A 81.176 85 13 3 1372 1454 526176640 526176723 5.830000e-07 65.8
69 TraesCS3A01G221300 chr4A 100.000 30 0 0 1372 1401 526208833 526208862 3.510000e-04 56.5
70 TraesCS3A01G221300 chr6A 82.581 155 24 3 1115 1267 240638544 240638391 1.580000e-27 134.0
71 TraesCS3A01G221300 chr6A 90.526 95 6 1 1312 1403 303769365 303769271 3.410000e-24 122.0
72 TraesCS3A01G221300 chr6A 87.952 83 9 1 747 829 322600017 322600098 2.070000e-16 97.1
73 TraesCS3A01G221300 chr6A 86.747 83 10 1 747 829 322607971 322608052 9.620000e-15 91.6
74 TraesCS3A01G221300 chr6A 72.022 361 79 19 1812 2166 244508728 244509072 1.240000e-13 87.9
75 TraesCS3A01G221300 chr6A 100.000 30 0 0 1698 1727 325824640 325824611 3.510000e-04 56.5
76 TraesCS3A01G221300 chr5A 87.952 83 9 1 747 829 169131919 169131838 2.070000e-16 97.1
77 TraesCS3A01G221300 chr1D 88.889 54 5 1 1372 1424 340375182 340375235 5.830000e-07 65.8


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 TraesCS3A01G221300 chr3A 410246583 410249107 2524 False 4663 4663 100.000 1 2525 1 chr3A.!!$F4 2524
1 TraesCS3A01G221300 chr3A 410233246 410235761 2515 False 1728 2187 91.893 57 2525 2 chr3A.!!$F8 2468
2 TraesCS3A01G221300 chr3A 423435150 423435889 739 False 346 346 76.129 47 790 1 chr3A.!!$F5 743
3 TraesCS3A01G221300 chr5B 205797269 205797957 688 False 571 571 81.972 1 698 1 chr5B.!!$F1 697
4 TraesCS3A01G221300 chr3B 239019141 239019699 558 False 516 516 83.770 128 684 1 chr3B.!!$F1 556
5 TraesCS3A01G221300 chr3B 239027273 239027831 558 False 510 510 83.566 128 684 1 chr3B.!!$F2 556
6 TraesCS3A01G221300 chr4D 191322458 191323145 687 True 512 512 80.791 1844 2525 1 chr4D.!!$R2 681
7 TraesCS3A01G221300 chr4D 191303596 191304282 686 True 477 477 79.858 1844 2525 1 chr4D.!!$R1 681
8 TraesCS3A01G221300 chr6B 113042336 113042983 647 False 508 508 81.231 1 652 1 chr6B.!!$F2 651
9 TraesCS3A01G221300 chr6B 100400396 100401135 739 False 351 351 76.291 47 760 1 chr6B.!!$F1 713
10 TraesCS3A01G221300 chr3D 356760348 356760957 609 True 508 508 82.010 47 652 1 chr3D.!!$R3 605
11 TraesCS3A01G221300 chr3D 356727010 356727563 553 True 499 499 83.274 101 651 1 chr3D.!!$R2 550
12 TraesCS3A01G221300 chr3D 146534216 146534952 736 True 326 326 75.644 1 749 1 chr3D.!!$R1 748
13 TraesCS3A01G221300 chr7B 300976021 300976668 647 True 475 475 80.301 1 652 1 chr7B.!!$R2 651
14 TraesCS3A01G221300 chr7B 300983676 300984322 646 True 446 446 79.549 1 652 1 chr7B.!!$R3 651
15 TraesCS3A01G221300 chr2B 193777553 193778279 726 True 363 363 76.548 57 790 1 chr2B.!!$R1 733


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
63 64 0.037326 GTTGTGATGCCTCGAGACCA 60.037 55.0 15.71 11.11 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1693 1814 0.193574 TCCAAGGTCTTCAGGGGTCT 59.806 55.0 0.0 0.0 0.0 3.85 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
51 52 3.646162 TGTAAGTGGAGGAGTGTTGTGAT 59.354 43.478 0.00 0.00 0.00 3.06
55 56 0.326264 GGAGGAGTGTTGTGATGCCT 59.674 55.000 0.00 0.00 0.00 4.75
63 64 0.037326 GTTGTGATGCCTCGAGACCA 60.037 55.000 15.71 11.11 0.00 4.02
80 81 0.962356 CCAACGCTCCAGATGCCTTT 60.962 55.000 0.00 0.00 0.00 3.11
100 101 3.696281 TCATGTTTTGTGTGTCAGCTG 57.304 42.857 7.63 7.63 0.00 4.24
101 102 3.016031 TCATGTTTTGTGTGTCAGCTGT 58.984 40.909 14.67 0.00 0.00 4.40
102 103 2.917701 TGTTTTGTGTGTCAGCTGTG 57.082 45.000 14.67 0.00 0.00 3.66
103 104 2.158559 TGTTTTGTGTGTCAGCTGTGT 58.841 42.857 14.67 0.00 0.00 3.72
105 106 3.753797 TGTTTTGTGTGTCAGCTGTGTTA 59.246 39.130 14.67 0.00 0.00 2.41
162 166 3.383185 TGCATTGCATCATGTCATCATGT 59.617 39.130 7.38 0.00 41.79 3.21
174 191 7.031226 CATGTCATCATGTAACCCCTTTTAG 57.969 40.000 0.00 0.00 44.37 1.85
283 314 7.633018 AGTCTCCCAATATTATTAAGGAGCA 57.367 36.000 20.26 12.08 40.60 4.26
344 380 4.871557 CACACTTGCAAATAATTCCCATGG 59.128 41.667 4.14 4.14 0.00 3.66
350 386 4.718774 TGCAAATAATTCCCATGGCCTTTA 59.281 37.500 6.09 3.65 0.00 1.85
353 389 7.071698 TGCAAATAATTCCCATGGCCTTTATAA 59.928 33.333 6.09 0.00 0.00 0.98
364 400 6.258507 CCATGGCCTTTATAATTCAAGTTTGC 59.741 38.462 3.32 0.00 0.00 3.68
409 446 6.901081 TCTTATCTCATTTATCGAGGCTCA 57.099 37.500 15.95 2.07 0.00 4.26
520 566 2.717639 ACAATCATGCCCACTCCTAC 57.282 50.000 0.00 0.00 0.00 3.18
526 572 2.642311 TCATGCCCACTCCTACTTTTCA 59.358 45.455 0.00 0.00 0.00 2.69
546 593 3.190327 TCATGGACCGTGCACATTTTTAG 59.810 43.478 18.64 1.48 0.00 1.85
608 669 3.686916 ACCCTCTCTTTCTTTTCCTCG 57.313 47.619 0.00 0.00 0.00 4.63
619 681 6.591834 TCTTTCTTTTCCTCGCTCTATTTCTG 59.408 38.462 0.00 0.00 0.00 3.02
630 695 5.807520 TCGCTCTATTTCTGTTCTGCTAAAG 59.192 40.000 0.00 0.00 0.00 1.85
633 698 7.148573 CGCTCTATTTCTGTTCTGCTAAAGAAA 60.149 37.037 0.00 0.00 46.51 2.52
658 726 2.515057 GAGAGAGAGAGCCGGCGA 60.515 66.667 23.20 0.00 0.00 5.54
694 762 3.637273 GACCAACCAGACCGGCCT 61.637 66.667 0.00 0.00 39.03 5.19
733 807 2.966915 ACATATAACCCTAGCCCGACA 58.033 47.619 0.00 0.00 0.00 4.35
760 837 3.181413 CCCATCTCTCCAATCTCTCCCTA 60.181 52.174 0.00 0.00 0.00 3.53
763 840 4.396357 TCTCTCCAATCTCTCCCTATCC 57.604 50.000 0.00 0.00 0.00 2.59
830 907 0.397816 ATCCCCTCCTCTCGAACCTG 60.398 60.000 0.00 0.00 0.00 4.00
833 910 1.684049 CCTCCTCTCGAACCTGCCT 60.684 63.158 0.00 0.00 0.00 4.75
856 933 2.812499 GTCATCGCCGCCCTTCTA 59.188 61.111 0.00 0.00 0.00 2.10
908 985 3.009115 TTCCTCCCCCAGCCTTCG 61.009 66.667 0.00 0.00 0.00 3.79
915 992 2.657237 CCCAGCCTTCGTCGTCTT 59.343 61.111 0.00 0.00 0.00 3.01
919 996 0.523966 CAGCCTTCGTCGTCTTCTCT 59.476 55.000 0.00 0.00 0.00 3.10
926 1003 1.935436 GTCGTCTTCTCTAGCGCGC 60.935 63.158 26.66 26.66 0.00 6.86
942 1019 2.520741 GCCGCTAGAGAGGAGCCT 60.521 66.667 3.17 0.00 37.14 4.58
943 1020 2.855514 GCCGCTAGAGAGGAGCCTG 61.856 68.421 3.17 0.00 37.14 4.85
1048 1125 2.273449 CTGCCCCACACCATCTCC 59.727 66.667 0.00 0.00 0.00 3.71
1059 1136 1.066587 CCATCTCCGTCTTCCTCGC 59.933 63.158 0.00 0.00 0.00 5.03
1061 1138 2.482333 ATCTCCGTCTTCCTCGCCG 61.482 63.158 0.00 0.00 0.00 6.46
1088 1171 3.546543 CCAATCCGGCGGCTCCTA 61.547 66.667 23.83 3.23 0.00 2.94
1117 1200 1.140052 TGGAAGTCGCAAGGAACTCAA 59.860 47.619 0.00 0.00 38.49 3.02
1143 1226 1.695597 CTGGCCCTCATCCCCTTCT 60.696 63.158 0.00 0.00 0.00 2.85
1147 1230 1.056700 GCCCTCATCCCCTTCTGCTA 61.057 60.000 0.00 0.00 0.00 3.49
1152 1235 0.107703 CATCCCCTTCTGCTAACGCA 60.108 55.000 0.00 0.00 45.60 5.24
1168 1251 1.073897 GCAGTTCTGCCCAAGGTCT 59.926 57.895 13.11 0.00 0.00 3.85
1179 1262 1.457346 CCAAGGTCTGGCAAGATCAC 58.543 55.000 3.65 0.00 38.76 3.06
1180 1263 1.271543 CCAAGGTCTGGCAAGATCACA 60.272 52.381 3.65 0.00 38.76 3.58
1190 1273 1.945387 CAAGATCACAGGTGGATCCG 58.055 55.000 7.39 0.00 41.64 4.18
1209 1292 4.088351 TCCCCTCGCATCTCCCCA 62.088 66.667 0.00 0.00 0.00 4.96
1213 1296 2.105128 CTCGCATCTCCCCACGTC 59.895 66.667 0.00 0.00 0.00 4.34
1272 1355 2.667536 CTGCAGCAGGCTGTCGTT 60.668 61.111 21.19 0.00 45.24 3.85
1273 1356 2.962827 CTGCAGCAGGCTGTCGTTG 61.963 63.158 21.19 10.64 45.24 4.10
1283 1366 0.593128 GCTGTCGTTGCACCTTCATT 59.407 50.000 0.00 0.00 0.00 2.57
1284 1367 1.001378 GCTGTCGTTGCACCTTCATTT 60.001 47.619 0.00 0.00 0.00 2.32
1293 1376 1.002366 CACCTTCATTTCTCGAGCCG 58.998 55.000 7.81 0.00 0.00 5.52
1302 1385 4.896829 CTCGAGCCGCCCCTCCTA 62.897 72.222 0.00 0.00 0.00 2.94
1310 1393 2.291043 CGCCCCTCCTACCAGTTGT 61.291 63.158 0.00 0.00 0.00 3.32
1312 1395 0.322546 GCCCCTCCTACCAGTTGTTG 60.323 60.000 0.00 0.00 0.00 3.33
1320 1403 2.069273 CTACCAGTTGTTGCTTCTCCG 58.931 52.381 0.00 0.00 0.00 4.63
1322 1405 1.205064 CAGTTGTTGCTTCTCCGCG 59.795 57.895 0.00 0.00 0.00 6.46
1355 1438 1.299926 GTCGTTGTCACCACGAGCT 60.300 57.895 3.99 0.00 36.53 4.09
1357 1440 1.007271 CGTTGTCACCACGAGCTCT 60.007 57.895 12.85 0.00 0.00 4.09
1362 1445 2.740055 CACCACGAGCTCTGTGCC 60.740 66.667 24.24 0.00 44.23 5.01
1396 1482 2.224159 ACCACCATCGCCTCCTTGT 61.224 57.895 0.00 0.00 0.00 3.16
1397 1483 1.002134 CCACCATCGCCTCCTTGTT 60.002 57.895 0.00 0.00 0.00 2.83
1407 1493 2.203480 TCCTTGTTGCTGCCCACC 60.203 61.111 0.00 0.00 0.00 4.61
1408 1494 2.203538 CCTTGTTGCTGCCCACCT 60.204 61.111 0.00 0.00 0.00 4.00
1428 1514 2.203480 GGCCCTGGTGTTGCTTCA 60.203 61.111 0.00 0.00 0.00 3.02
1433 1519 1.962807 CCCTGGTGTTGCTTCATTTCA 59.037 47.619 0.00 0.00 0.00 2.69
1446 1532 4.699257 GCTTCATTTCAGACCATCAAGACT 59.301 41.667 0.00 0.00 0.00 3.24
1456 1542 2.158623 ACCATCAAGACTGGCAAGAACA 60.159 45.455 0.00 0.00 37.27 3.18
1469 1555 3.751698 GGCAAGAACACCTTCGTAGATTT 59.248 43.478 0.00 0.00 35.04 2.17
1478 1564 4.693566 CACCTTCGTAGATTTGCCAAGTAA 59.306 41.667 0.00 0.00 35.04 2.24
1498 1584 0.036388 CCACACCGGCAAGACTACAT 60.036 55.000 0.00 0.00 0.00 2.29
1517 1603 5.654603 ACATGGACGTTCAATCTACTACA 57.345 39.130 0.00 0.00 0.00 2.74
1519 1605 5.867716 ACATGGACGTTCAATCTACTACAAC 59.132 40.000 0.00 0.00 0.00 3.32
1523 1609 7.604549 TGGACGTTCAATCTACTACAACATTA 58.395 34.615 0.00 0.00 0.00 1.90
1550 1636 2.132762 CAGGTCGACTACGTTTTGCTT 58.867 47.619 16.46 0.00 40.69 3.91
1558 1644 1.196127 CTACGTTTTGCTTCCCCGTTC 59.804 52.381 0.00 0.00 33.32 3.95
1565 1651 1.221021 GCTTCCCCGTTCGGAATCT 59.779 57.895 13.08 0.00 41.12 2.40
1599 1685 3.740115 AGACCACATTGACACCAAGTAC 58.260 45.455 0.00 0.00 35.48 2.73
1602 1688 4.134563 ACCACATTGACACCAAGTACTTC 58.865 43.478 4.77 0.00 35.48 3.01
1609 1695 2.230750 GACACCAAGTACTTCTACCGCT 59.769 50.000 4.77 0.00 0.00 5.52
1664 1750 0.528924 TTCCATGACGTCCACTACCG 59.471 55.000 14.12 0.00 0.00 4.02
1670 1756 1.294659 GACGTCCACTACCGTCGTCT 61.295 60.000 3.51 0.00 43.22 4.18
1678 1764 1.475682 ACTACCGTCGTCTTGGGATTC 59.524 52.381 0.00 0.00 0.00 2.52
1693 1814 4.584874 TGGGATTCGACAAGCTCAATAAA 58.415 39.130 0.00 0.00 0.00 1.40
1716 1837 1.635487 CCCCTGAAGACCTTGGATTCA 59.365 52.381 10.07 10.07 0.00 2.57
1730 1851 2.242196 TGGATTCATCAAGTTCCCCTCC 59.758 50.000 0.00 0.00 0.00 4.30
1736 1857 2.603776 AAGTTCCCCTCCGTCGCT 60.604 61.111 0.00 0.00 0.00 4.93
1737 1858 2.943978 AAGTTCCCCTCCGTCGCTG 61.944 63.158 0.00 0.00 0.00 5.18
1751 1872 2.606308 CGTCGCTGTGTACCACTACTTT 60.606 50.000 0.00 0.00 35.11 2.66
1764 1885 1.200948 ACTACTTTCACTACCGTCGCC 59.799 52.381 0.00 0.00 0.00 5.54
1788 1909 5.120519 CGAGGACCGATAGTATCACTACTTC 59.879 48.000 10.71 4.09 38.68 3.01
1789 1910 5.938279 AGGACCGATAGTATCACTACTTCA 58.062 41.667 10.71 0.00 39.04 3.02
1793 1914 7.443575 GGACCGATAGTATCACTACTTCAACTA 59.556 40.741 10.71 0.00 39.04 2.24
1795 1916 7.042187 ACCGATAGTATCACTACTTCAACTACG 60.042 40.741 10.71 0.00 39.04 3.51
1797 1918 5.892160 AGTATCACTACTTCAACTACGCA 57.108 39.130 0.00 0.00 34.42 5.24
1798 1919 5.638783 AGTATCACTACTTCAACTACGCAC 58.361 41.667 0.00 0.00 34.42 5.34
1799 1920 4.785511 ATCACTACTTCAACTACGCACT 57.214 40.909 0.00 0.00 0.00 4.40
1800 1921 3.897325 TCACTACTTCAACTACGCACTG 58.103 45.455 0.00 0.00 0.00 3.66
1866 1987 1.862827 GCTACAAAGGTATAACCGCCG 59.137 52.381 0.00 0.00 44.90 6.46
1869 1990 1.826720 ACAAAGGTATAACCGCCGAGA 59.173 47.619 0.00 0.00 44.90 4.04
1903 2026 7.770433 CCGTGGATGAATGGATATTATGTATGT 59.230 37.037 0.00 0.00 0.00 2.29
1936 2069 2.222213 CCGAATTGTAAGTTGCACGTCA 59.778 45.455 0.00 0.00 0.00 4.35
2009 2143 2.621407 CCCCACCATCACTAGCATGTTT 60.621 50.000 0.00 0.00 0.00 2.83
2045 2179 0.179043 TGCTCTGTTGCACCGGTTTA 60.179 50.000 2.97 0.00 38.12 2.01
2050 2184 2.550606 TCTGTTGCACCGGTTTATCAAC 59.449 45.455 22.05 22.05 37.94 3.18
2099 2233 3.617045 CGTGGCACCATTTCCATTTTCAT 60.617 43.478 12.86 0.00 34.47 2.57
2101 2235 3.581770 TGGCACCATTTCCATTTTCATCA 59.418 39.130 0.00 0.00 0.00 3.07
2145 2279 3.047735 CCGTGGCACCTTTTTCCC 58.952 61.111 12.86 0.00 0.00 3.97
2323 2459 1.202382 ACTAATCAACCGTAGCTCCGC 60.202 52.381 0.00 0.00 0.00 5.54
2328 2464 1.202371 TCAACCGTAGCTCCGCATTAG 60.202 52.381 0.00 0.00 0.00 1.73
2333 2469 3.057456 ACCGTAGCTCCGCATTAGATAAG 60.057 47.826 0.00 0.00 0.00 1.73
2376 2512 9.590451 CTTGGAAAAATGCATAGATTAACATGT 57.410 29.630 0.00 0.00 0.00 3.21
2379 2515 8.819974 GGAAAAATGCATAGATTAACATGTTGG 58.180 33.333 21.42 3.23 0.00 3.77
2457 2594 1.511850 TCGAAATATGCGCATGAGGG 58.488 50.000 32.48 16.90 0.00 4.30
2463 2600 2.418368 TATGCGCATGAGGGTTTTCT 57.582 45.000 32.48 4.93 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.396478 TCCACTTACAAGAGATCTCGTCTG 59.604 45.833 16.97 16.63 37.29 3.51
16 17 4.590918 TCCACTTACAAGAGATCTCGTCT 58.409 43.478 16.97 4.37 40.81 4.18
51 52 3.282745 GAGCGTTGGTCTCGAGGCA 62.283 63.158 20.37 1.91 39.83 4.75
55 56 0.965866 ATCTGGAGCGTTGGTCTCGA 60.966 55.000 0.00 0.00 0.00 4.04
63 64 0.036732 TGAAAGGCATCTGGAGCGTT 59.963 50.000 0.00 0.00 41.30 4.84
80 81 3.016031 ACAGCTGACACACAAAACATGA 58.984 40.909 23.35 0.00 0.00 3.07
316 348 6.040955 TGGGAATTATTTGCAAGTGTGTTACA 59.959 34.615 4.47 0.00 0.00 2.41
344 380 5.116180 GGGGCAAACTTGAATTATAAAGGC 58.884 41.667 0.00 0.00 0.00 4.35
409 446 8.314021 GGTCCAAAAATGTTGAGAATTTAGGAT 58.686 33.333 0.00 0.00 35.52 3.24
520 566 0.950836 TGTGCACGGTCCATGAAAAG 59.049 50.000 13.13 0.00 0.00 2.27
526 572 2.491693 CCTAAAAATGTGCACGGTCCAT 59.508 45.455 13.13 0.00 0.00 3.41
546 593 2.372264 GGGTTTATTTTCCCGGACTCC 58.628 52.381 0.73 0.00 33.97 3.85
608 669 7.602517 TTCTTTAGCAGAACAGAAATAGAGC 57.397 36.000 0.00 0.00 36.51 4.09
619 681 9.267084 CTCTCCCTTATATTTCTTTAGCAGAAC 57.733 37.037 0.00 0.00 41.56 3.01
630 695 5.105917 CGGCTCTCTCTCTCCCTTATATTTC 60.106 48.000 0.00 0.00 0.00 2.17
633 698 3.308832 CCGGCTCTCTCTCTCCCTTATAT 60.309 52.174 0.00 0.00 0.00 0.86
636 701 0.183971 CCGGCTCTCTCTCTCCCTTA 59.816 60.000 0.00 0.00 0.00 2.69
637 702 1.076339 CCGGCTCTCTCTCTCCCTT 60.076 63.158 0.00 0.00 0.00 3.95
664 732 1.774217 TTGGTCAGGCCCAAGAGGT 60.774 57.895 0.00 0.00 39.56 3.85
694 762 1.562475 GTTAGGTGGGCCTGTGGAATA 59.438 52.381 4.53 0.00 46.47 1.75
715 783 3.537795 TCTGTCGGGCTAGGGTTATAT 57.462 47.619 0.00 0.00 0.00 0.86
733 807 3.144509 AGAGATTGGAGAGATGGGGATCT 59.855 47.826 0.00 0.00 0.00 2.75
777 854 2.727544 CCTTTTGTGTGGGTGGCG 59.272 61.111 0.00 0.00 0.00 5.69
785 862 2.978010 CGCCTCCGCCTTTTGTGT 60.978 61.111 0.00 0.00 0.00 3.72
802 879 3.551407 GGAGGGGATCGAGGCCAC 61.551 72.222 5.01 0.00 0.00 5.01
908 985 1.935436 GCGCGCTAGAGAAGACGAC 60.935 63.158 26.67 0.00 0.00 4.34
926 1003 2.855514 GCAGGCTCCTCTCTAGCGG 61.856 68.421 0.00 0.00 41.03 5.52
949 1026 2.750637 GGAGCTCTGACGTCGGGA 60.751 66.667 23.78 16.22 0.00 5.14
1008 1085 4.111016 TGTAGGGTCGTCAGCGCG 62.111 66.667 0.00 0.00 38.14 6.86
1021 1098 3.390521 TGGGGCAGCGACCTGTAG 61.391 66.667 6.35 0.00 41.26 2.74
1073 1156 3.547513 GGTAGGAGCCGCCGGATT 61.548 66.667 7.68 0.00 43.43 3.01
1082 1165 3.541713 CCAGGGCGAGGTAGGAGC 61.542 72.222 0.00 0.00 0.00 4.70
1088 1171 3.382832 CGACTTCCAGGGCGAGGT 61.383 66.667 0.00 0.00 0.00 3.85
1152 1235 1.763770 CCAGACCTTGGGCAGAACT 59.236 57.895 0.00 0.00 43.75 3.01
1168 1251 0.994247 ATCCACCTGTGATCTTGCCA 59.006 50.000 0.00 0.00 0.00 4.92
1172 1255 0.833287 CCGGATCCACCTGTGATCTT 59.167 55.000 13.41 0.00 36.31 2.40
1261 1344 1.845809 GAAGGTGCAACGACAGCCTG 61.846 60.000 0.00 0.00 38.85 4.85
1268 1351 1.798223 CGAGAAATGAAGGTGCAACGA 59.202 47.619 0.00 0.00 38.12 3.85
1271 1354 1.806542 GCTCGAGAAATGAAGGTGCAA 59.193 47.619 18.75 0.00 0.00 4.08
1272 1355 1.442769 GCTCGAGAAATGAAGGTGCA 58.557 50.000 18.75 0.00 0.00 4.57
1273 1356 0.729690 GGCTCGAGAAATGAAGGTGC 59.270 55.000 18.75 0.00 0.00 5.01
1293 1376 0.322546 CAACAACTGGTAGGAGGGGC 60.323 60.000 0.00 0.00 0.00 5.80
1300 1383 2.069273 CGGAGAAGCAACAACTGGTAG 58.931 52.381 0.00 0.00 33.58 3.18
1302 1385 1.166531 GCGGAGAAGCAACAACTGGT 61.167 55.000 0.00 0.00 37.35 4.00
1355 1438 2.033141 GCAGGAAGCAGGCACAGA 59.967 61.111 0.00 0.00 44.79 3.41
1407 1493 2.674380 GCAACACCAGGGCCTCAG 60.674 66.667 0.95 0.00 0.00 3.35
1408 1494 2.697147 GAAGCAACACCAGGGCCTCA 62.697 60.000 0.95 0.00 0.00 3.86
1428 1514 3.245016 TGCCAGTCTTGATGGTCTGAAAT 60.245 43.478 0.00 0.00 40.17 2.17
1433 1519 1.980765 TCTTGCCAGTCTTGATGGTCT 59.019 47.619 0.00 0.00 40.17 3.85
1446 1532 1.689813 TCTACGAAGGTGTTCTTGCCA 59.310 47.619 0.00 0.00 35.50 4.92
1456 1542 3.418684 ACTTGGCAAATCTACGAAGGT 57.581 42.857 0.00 0.00 0.00 3.50
1469 1555 1.228003 CCGGTGTGGTTACTTGGCA 60.228 57.895 0.00 0.00 0.00 4.92
1478 1564 1.370064 GTAGTCTTGCCGGTGTGGT 59.630 57.895 1.90 0.00 41.21 4.16
1498 1584 5.456548 TGTTGTAGTAGATTGAACGTCCA 57.543 39.130 0.00 0.00 0.00 4.02
1517 1603 4.720530 GTCGACCTGACGTTTTAATGTT 57.279 40.909 3.51 0.00 37.96 2.71
1530 1616 1.779569 AGCAAAACGTAGTCGACCTG 58.220 50.000 13.01 4.76 45.00 4.00
1550 1636 0.978151 TTGAAGATTCCGAACGGGGA 59.022 50.000 13.29 3.34 36.01 4.81
1558 1644 2.953466 TCGGGTACTTGAAGATTCCG 57.047 50.000 14.65 14.65 37.61 4.30
1565 1651 2.040939 TGTGGTCTTCGGGTACTTGAA 58.959 47.619 0.00 0.00 0.00 2.69
1609 1695 2.882137 GGTCTTGGTGATTCCGAAAACA 59.118 45.455 0.00 0.00 39.52 2.83
1670 1756 2.559698 TTGAGCTTGTCGAATCCCAA 57.440 45.000 0.00 0.00 0.00 4.12
1678 1764 2.678336 GGGGTCTTTATTGAGCTTGTCG 59.322 50.000 0.00 0.00 35.11 4.35
1693 1814 0.193574 TCCAAGGTCTTCAGGGGTCT 59.806 55.000 0.00 0.00 0.00 3.85
1716 1837 1.898154 CGACGGAGGGGAACTTGAT 59.102 57.895 0.00 0.00 0.00 2.57
1764 1885 4.567971 AGTAGTGATACTATCGGTCCTCG 58.432 47.826 0.00 0.00 32.65 4.63
1788 1909 3.575630 AGATGTACACAGTGCGTAGTTG 58.424 45.455 0.00 0.00 0.00 3.16
1789 1910 3.936372 AGATGTACACAGTGCGTAGTT 57.064 42.857 0.00 0.00 0.00 2.24
1831 1952 1.202440 TGTAGCGTGTGTTTTCGGAGT 60.202 47.619 0.00 0.00 0.00 3.85
1936 2069 1.741770 GCACGGTCAAGCGAGGAAT 60.742 57.895 8.77 0.00 0.00 3.01
1998 2132 1.676014 GGAGGTGCGAAACATGCTAGT 60.676 52.381 0.00 0.00 0.00 2.57
2009 2143 1.741401 CAAGAATGCGGAGGTGCGA 60.741 57.895 0.00 0.00 37.81 5.10
2045 2179 1.144057 GATCCGGTGGCTCGTTGAT 59.856 57.895 0.00 0.00 0.00 2.57
2050 2184 2.355126 CGATGATCCGGTGGCTCG 60.355 66.667 0.00 3.00 0.00 5.03
2099 2233 1.602323 GGAAATGGTGCCACGGTGA 60.602 57.895 10.28 0.00 0.00 4.02
2101 2235 0.541764 AATGGAAATGGTGCCACGGT 60.542 50.000 0.00 0.00 36.92 4.83
2183 2317 6.376581 TGGGTGCAATTTTCTGAAAAATGTTT 59.623 30.769 24.14 11.51 42.82 2.83
2188 2322 4.637977 GGTTGGGTGCAATTTTCTGAAAAA 59.362 37.500 18.43 0.60 38.66 1.94
2195 2329 3.399440 TCATGGTTGGGTGCAATTTTC 57.601 42.857 0.00 0.00 0.00 2.29
2376 2512 6.283694 TGTTAAACATGCAAAGTAATGCCAA 58.716 32.000 0.00 0.00 45.83 4.52
2379 2515 7.382218 AGAGTTGTTAAACATGCAAAGTAATGC 59.618 33.333 0.00 0.00 41.60 3.56
2422 2559 8.921670 GCATATTTCGAATTGGTTACAGTTTTT 58.078 29.630 0.00 0.00 0.00 1.94
2428 2565 4.095036 TGCGCATATTTCGAATTGGTTACA 59.905 37.500 5.66 0.00 0.00 2.41
2432 2569 3.314913 TCATGCGCATATTTCGAATTGGT 59.685 39.130 24.84 0.00 0.00 3.67
2434 2571 3.910170 CCTCATGCGCATATTTCGAATTG 59.090 43.478 24.84 8.38 0.00 2.32
2463 2600 6.037098 CCGGAAACAACAAACAACAATTCTA 58.963 36.000 0.00 0.00 0.00 2.10



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

AutoCloner maintained by Alex Coulton.