Multiple sequence alignment - TraesCS2B01G004200

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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 TraesCS2B01G004200 chr2B 100.000 4514 0 0 1 4514 2234561 2239074 0.000000e+00 8336.0
1 TraesCS2B01G004200 chr2B 96.148 3531 101 15 988 4514 2503987 2500488 0.000000e+00 5734.0
2 TraesCS2B01G004200 chr2B 85.050 1699 200 33 1878 3540 2219179 2220859 0.000000e+00 1681.0
3 TraesCS2B01G004200 chr2B 80.062 1615 242 46 1935 3516 2527649 2526082 0.000000e+00 1125.0
4 TraesCS2B01G004200 chr2B 79.603 1662 255 50 1928 3528 2346241 2344603 0.000000e+00 1114.0
5 TraesCS2B01G004200 chr2B 86.214 972 105 18 1878 2835 2512853 2511897 0.000000e+00 1026.0
6 TraesCS2B01G004200 chr2B 80.474 1393 209 32 2148 3516 2131345 2132698 0.000000e+00 1007.0
7 TraesCS2B01G004200 chr2B 92.105 608 36 1 1 596 2504872 2504265 0.000000e+00 846.0
8 TraesCS2B01G004200 chr2B 87.000 600 66 6 2950 3540 2511804 2511208 0.000000e+00 665.0
9 TraesCS2B01G004200 chr2B 85.374 588 72 11 3937 4514 361902961 361902378 8.360000e-167 597.0
10 TraesCS2B01G004200 chr2B 99.257 269 2 0 651 919 2504261 2503993 1.890000e-133 486.0
11 TraesCS2B01G004200 chr2B 87.936 373 44 1 1469 1840 2218390 2218762 5.360000e-119 438.0
12 TraesCS2B01G004200 chr2B 87.193 367 43 3 1474 1836 2346949 2346583 9.030000e-112 414.0
13 TraesCS2B01G004200 chr2B 88.426 216 16 8 967 1175 2136129 2136342 7.500000e-63 252.0
14 TraesCS2B01G004200 chr2B 81.343 268 47 3 191 456 215925390 215925124 9.830000e-52 215.0
15 TraesCS2B01G004200 chr2B 89.697 165 12 5 978 1139 2523635 2523473 5.920000e-49 206.0
16 TraesCS2B01G004200 chr2B 76.923 377 55 24 852 1197 2348025 2347650 7.710000e-43 185.0
17 TraesCS2B01G004200 chr2B 78.716 296 33 16 932 1197 2407492 2407197 2.160000e-38 171.0
18 TraesCS2B01G004200 chr2B 83.146 178 30 0 283 460 8230803 8230626 3.610000e-36 163.0
19 TraesCS2B01G004200 chr2B 79.343 213 35 8 189 396 401281729 401281937 1.690000e-29 141.0
20 TraesCS2B01G004200 chr2D 95.645 1952 70 11 1878 3821 7073843 7071899 0.000000e+00 3120.0
21 TraesCS2B01G004200 chr2D 86.675 1696 176 27 1878 3540 7086960 7085282 0.000000e+00 1834.0
22 TraesCS2B01G004200 chr2D 92.152 1236 45 20 651 1876 7075155 7073962 0.000000e+00 1698.0
23 TraesCS2B01G004200 chr2D 80.387 1652 247 44 1928 3541 7091648 7090036 0.000000e+00 1184.0
24 TraesCS2B01G004200 chr2D 80.134 1641 235 46 1928 3515 7064772 7066374 0.000000e+00 1140.0
25 TraesCS2B01G004200 chr2D 81.090 1486 215 38 2071 3540 7002277 7003712 0.000000e+00 1127.0
26 TraesCS2B01G004200 chr2D 87.255 408 52 0 1469 1876 7087487 7087080 2.460000e-127 466.0
27 TraesCS2B01G004200 chr2D 87.017 362 44 1 1498 1859 7001661 7002019 5.440000e-109 405.0
28 TraesCS2B01G004200 chr2D 87.050 278 27 8 973 1243 7088041 7087766 5.670000e-79 305.0
29 TraesCS2B01G004200 chr2D 81.111 270 34 10 941 1197 7093073 7092808 2.750000e-47 200.0
30 TraesCS2B01G004200 chr2A 84.888 1972 225 35 1879 3811 5484960 5483023 0.000000e+00 1923.0
31 TraesCS2B01G004200 chr2A 80.346 1562 238 40 2010 3541 5527648 5526126 0.000000e+00 1120.0
32 TraesCS2B01G004200 chr2A 79.975 1588 224 59 1974 3526 5310467 5311995 0.000000e+00 1085.0
33 TraesCS2B01G004200 chr2A 80.160 1497 230 40 2071 3540 5189963 5191419 0.000000e+00 1057.0
34 TraesCS2B01G004200 chr2A 85.035 715 82 9 3821 4514 424915407 424916117 0.000000e+00 704.0
35 TraesCS2B01G004200 chr2A 88.725 408 46 0 1469 1876 5485486 5485079 2.420000e-137 499.0
36 TraesCS2B01G004200 chr2A 88.643 361 38 1 1498 1858 5189284 5189641 1.930000e-118 436.0
37 TraesCS2B01G004200 chr2A 88.081 344 40 1 1498 1840 5309613 5309956 1.510000e-109 407.0
38 TraesCS2B01G004200 chr2A 83.333 252 24 11 993 1227 5486853 5486603 2.730000e-52 217.0
39 TraesCS2B01G004200 chr2A 79.795 292 28 23 932 1194 5188015 5188304 2.770000e-42 183.0
40 TraesCS2B01G004200 chr2A 88.000 50 6 0 671 720 497452461 497452412 4.880000e-05 60.2
41 TraesCS2B01G004200 chr1D 91.667 696 32 11 3821 4514 420992734 420993405 0.000000e+00 941.0
42 TraesCS2B01G004200 chr1D 89.286 84 6 2 1359 1442 458142915 458142835 7.990000e-18 102.0
43 TraesCS2B01G004200 chr1D 89.744 78 6 1 1359 1436 458142856 458142931 1.030000e-16 99.0
44 TraesCS2B01G004200 chr4D 91.367 695 36 10 3821 4514 221139674 221139003 0.000000e+00 929.0
45 TraesCS2B01G004200 chr4D 90.909 176 12 3 3821 3996 184309754 184309583 2.720000e-57 233.0
46 TraesCS2B01G004200 chr3B 90.704 710 26 12 3821 4514 750419279 750419964 0.000000e+00 909.0
47 TraesCS2B01G004200 chr3B 88.158 76 9 0 1361 1436 748463069 748462994 1.730000e-14 91.6
48 TraesCS2B01G004200 chr6D 90.127 709 31 11 3821 4514 408621413 408620729 0.000000e+00 885.0
49 TraesCS2B01G004200 chr6D 89.155 710 37 15 3821 4514 227940982 227941667 0.000000e+00 848.0
50 TraesCS2B01G004200 chr6B 89.170 711 55 7 3821 4514 37487466 37486761 0.000000e+00 867.0
51 TraesCS2B01G004200 chr4B 89.437 710 33 13 3821 4512 362256874 362257559 0.000000e+00 857.0
52 TraesCS2B01G004200 chrUn 87.989 716 40 18 3821 4514 329799467 329798776 0.000000e+00 804.0
53 TraesCS2B01G004200 chr5A 86.592 716 70 19 3821 4514 307062947 307063658 0.000000e+00 767.0
54 TraesCS2B01G004200 chr1B 88.845 511 38 6 3822 4315 644779419 644778911 1.070000e-170 610.0
55 TraesCS2B01G004200 chr1B 80.392 714 113 18 3821 4511 287373609 287374318 6.690000e-143 518.0
56 TraesCS2B01G004200 chr1B 85.430 151 21 1 189 338 187060707 187060557 6.050000e-34 156.0
57 TraesCS2B01G004200 chr7D 86.230 443 51 9 3920 4356 545826699 545827137 5.290000e-129 472.0
58 TraesCS2B01G004200 chr7D 76.744 215 28 16 189 399 633444216 633444020 2.870000e-17 100.0
59 TraesCS2B01G004200 chr7D 76.744 215 28 16 189 399 633458956 633458760 2.870000e-17 100.0
60 TraesCS2B01G004200 chr4A 85.448 268 35 4 191 456 34247406 34247141 4.450000e-70 276.0
61 TraesCS2B01G004200 chr4A 86.747 83 7 1 1358 1436 590661835 590661753 6.220000e-14 89.8
62 TraesCS2B01G004200 chr6A 84.328 268 39 3 191 456 212222507 212222773 4.480000e-65 259.0
63 TraesCS2B01G004200 chr6A 82.593 270 30 8 188 455 582924337 582924591 5.880000e-54 222.0
64 TraesCS2B01G004200 chr1A 84.337 249 36 3 210 456 23023139 23023386 1.620000e-59 241.0
65 TraesCS2B01G004200 chr1A 81.768 181 31 2 277 456 50287193 50287014 2.810000e-32 150.0
66 TraesCS2B01G004200 chr5D 89.041 73 8 0 1359 1431 332041713 332041785 1.730000e-14 91.6
67 TraesCS2B01G004200 chr5D 85.542 83 9 3 1365 1445 80707320 80707401 2.890000e-12 84.2
68 TraesCS2B01G004200 chr5B 86.747 83 8 2 1365 1445 89636086 89636167 6.220000e-14 89.8
69 TraesCS2B01G004200 chr7A 100.000 30 0 0 691 720 628964662 628964633 6.310000e-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 TraesCS2B01G004200 chr2B 2234561 2239074 4513 False 8336.000000 8336 100.000000 1 4514 1 chr2B.!!$F1 4513
1 TraesCS2B01G004200 chr2B 2500488 2504872 4384 True 2355.333333 5734 95.836667 1 4514 3 chr2B.!!$R6 4513
2 TraesCS2B01G004200 chr2B 2218390 2220859 2469 False 1059.500000 1681 86.493000 1469 3540 2 chr2B.!!$F4 2071
3 TraesCS2B01G004200 chr2B 2511208 2512853 1645 True 845.500000 1026 86.607000 1878 3540 2 chr2B.!!$R7 1662
4 TraesCS2B01G004200 chr2B 2523473 2527649 4176 True 665.500000 1125 84.879500 978 3516 2 chr2B.!!$R8 2538
5 TraesCS2B01G004200 chr2B 2131345 2136342 4997 False 629.500000 1007 84.450000 967 3516 2 chr2B.!!$F3 2549
6 TraesCS2B01G004200 chr2B 361902378 361902961 583 True 597.000000 597 85.374000 3937 4514 1 chr2B.!!$R4 577
7 TraesCS2B01G004200 chr2B 2344603 2348025 3422 True 571.000000 1114 81.239667 852 3528 3 chr2B.!!$R5 2676
8 TraesCS2B01G004200 chr2D 7071899 7075155 3256 True 2409.000000 3120 93.898500 651 3821 2 chr2D.!!$R1 3170
9 TraesCS2B01G004200 chr2D 7064772 7066374 1602 False 1140.000000 1140 80.134000 1928 3515 1 chr2D.!!$F1 1587
10 TraesCS2B01G004200 chr2D 7085282 7093073 7791 True 797.800000 1834 84.495600 941 3541 5 chr2D.!!$R2 2600
11 TraesCS2B01G004200 chr2D 7001661 7003712 2051 False 766.000000 1127 84.053500 1498 3540 2 chr2D.!!$F2 2042
12 TraesCS2B01G004200 chr2A 5526126 5527648 1522 True 1120.000000 1120 80.346000 2010 3541 1 chr2A.!!$R1 1531
13 TraesCS2B01G004200 chr2A 5483023 5486853 3830 True 879.666667 1923 85.648667 993 3811 3 chr2A.!!$R3 2818
14 TraesCS2B01G004200 chr2A 5309613 5311995 2382 False 746.000000 1085 84.028000 1498 3526 2 chr2A.!!$F3 2028
15 TraesCS2B01G004200 chr2A 424915407 424916117 710 False 704.000000 704 85.035000 3821 4514 1 chr2A.!!$F1 693
16 TraesCS2B01G004200 chr2A 5188015 5191419 3404 False 558.666667 1057 82.866000 932 3540 3 chr2A.!!$F2 2608
17 TraesCS2B01G004200 chr1D 420992734 420993405 671 False 941.000000 941 91.667000 3821 4514 1 chr1D.!!$F1 693
18 TraesCS2B01G004200 chr4D 221139003 221139674 671 True 929.000000 929 91.367000 3821 4514 1 chr4D.!!$R2 693
19 TraesCS2B01G004200 chr3B 750419279 750419964 685 False 909.000000 909 90.704000 3821 4514 1 chr3B.!!$F1 693
20 TraesCS2B01G004200 chr6D 408620729 408621413 684 True 885.000000 885 90.127000 3821 4514 1 chr6D.!!$R1 693
21 TraesCS2B01G004200 chr6D 227940982 227941667 685 False 848.000000 848 89.155000 3821 4514 1 chr6D.!!$F1 693
22 TraesCS2B01G004200 chr6B 37486761 37487466 705 True 867.000000 867 89.170000 3821 4514 1 chr6B.!!$R1 693
23 TraesCS2B01G004200 chr4B 362256874 362257559 685 False 857.000000 857 89.437000 3821 4512 1 chr4B.!!$F1 691
24 TraesCS2B01G004200 chrUn 329798776 329799467 691 True 804.000000 804 87.989000 3821 4514 1 chrUn.!!$R1 693
25 TraesCS2B01G004200 chr5A 307062947 307063658 711 False 767.000000 767 86.592000 3821 4514 1 chr5A.!!$F1 693
26 TraesCS2B01G004200 chr1B 644778911 644779419 508 True 610.000000 610 88.845000 3822 4315 1 chr1B.!!$R2 493
27 TraesCS2B01G004200 chr1B 287373609 287374318 709 False 518.000000 518 80.392000 3821 4511 1 chr1B.!!$F1 690

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
184 197 0.109132 GATTGCACGCCCTCTTTTGG 60.109 55.000 0.00 0.0 0.00 3.28 F
930 947 0.321671 CTTCTTGCTGAGACCCCGAA 59.678 55.000 0.00 0.0 33.02 4.30 F
1651 3406 3.838271 GCTCGACATCCTCGGCCA 61.838 66.667 2.24 0.0 43.16 5.36 F
3214 5760 1.899437 GATGTTCGGAGGAGGTGGCA 61.899 60.000 0.00 0.0 0.00 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1651 3406 1.891919 ACGGCAGCGATGTTGTTGT 60.892 52.632 1.22 0.0 0.0 3.32 R
1752 3507 2.220761 GCATGAAGGCGTCGATCTC 58.779 57.895 0.00 0.0 0.0 2.75 R
3387 5945 0.642156 TGCCTTCCTCCTCCCATCTA 59.358 55.000 0.00 0.0 0.0 1.98 R
4027 12482 1.403679 GCACAAGGTAAATATGGCGCA 59.596 47.619 10.83 0.0 0.0 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
27 28 6.786461 AGTGGAGATGGAGATGAAGATTATCA 59.214 38.462 0.00 0.00 0.00 2.15
47 48 4.903054 TCAAACTGCATGTGATTCTCTCT 58.097 39.130 0.00 0.00 0.00 3.10
79 92 9.497030 CGCTGAGTATTATTACTAGCAATCTAG 57.503 37.037 17.06 0.00 46.06 2.43
168 181 0.546122 TTATGGCCGTGCTGAGGATT 59.454 50.000 8.05 0.00 0.00 3.01
169 182 0.179048 TATGGCCGTGCTGAGGATTG 60.179 55.000 8.05 0.00 0.00 2.67
170 183 3.512516 GGCCGTGCTGAGGATTGC 61.513 66.667 0.00 0.00 0.00 3.56
171 184 2.747460 GCCGTGCTGAGGATTGCA 60.747 61.111 0.00 0.00 36.79 4.08
184 197 0.109132 GATTGCACGCCCTCTTTTGG 60.109 55.000 0.00 0.00 0.00 3.28
209 222 1.568504 AGGCTGGTCGTAATGGAGAA 58.431 50.000 0.00 0.00 0.00 2.87
217 230 6.531948 GCTGGTCGTAATGGAGAATATCATAC 59.468 42.308 0.00 0.00 0.00 2.39
326 339 6.915544 ATTGTCTTGCATGACACATAGTAG 57.084 37.500 29.16 1.17 45.32 2.57
348 361 9.828039 AGTAGCACATCATGTAATATGATATGG 57.172 33.333 9.42 2.03 36.69 2.74
349 362 9.605275 GTAGCACATCATGTAATATGATATGGT 57.395 33.333 14.65 14.65 43.38 3.55
382 395 8.099364 TGTGATACTCAACCATTTCTTTCTTC 57.901 34.615 0.00 0.00 0.00 2.87
447 460 7.604164 GCATGCATAATACTACCTGTGATACTT 59.396 37.037 14.21 0.00 0.00 2.24
469 482 5.531122 TCCATTACGGACAATCTTAGAGG 57.469 43.478 0.00 0.00 39.64 3.69
472 485 4.996788 TTACGGACAATCTTAGAGGGAC 57.003 45.455 0.00 0.00 0.00 4.46
478 491 5.508153 CGGACAATCTTAGAGGGACTACATG 60.508 48.000 0.00 0.00 41.55 3.21
532 545 9.751542 AGAGAATTAATGGTGAGTATTAAGACG 57.248 33.333 0.00 0.00 34.54 4.18
603 616 9.693739 TGAACAACCAGATTTATACCAATATGT 57.306 29.630 0.00 0.00 0.00 2.29
669 682 7.828508 AAATCTGAATGGCTGATATTGCTTA 57.171 32.000 2.47 0.00 34.50 3.09
880 896 2.612493 GGCTCCACCCCTGCCTAAA 61.612 63.158 0.00 0.00 43.05 1.85
925 942 2.565841 ACAACACTTCTTGCTGAGACC 58.434 47.619 0.00 0.00 33.02 3.85
926 943 1.876156 CAACACTTCTTGCTGAGACCC 59.124 52.381 0.00 0.00 33.02 4.46
927 944 0.398318 ACACTTCTTGCTGAGACCCC 59.602 55.000 0.00 0.00 33.02 4.95
930 947 0.321671 CTTCTTGCTGAGACCCCGAA 59.678 55.000 0.00 0.00 33.02 4.30
1651 3406 3.838271 GCTCGACATCCTCGGCCA 61.838 66.667 2.24 0.00 43.16 5.36
2048 4417 8.285394 GCCAACACATATCACATAATCTTACTG 58.715 37.037 0.00 0.00 0.00 2.74
2732 5192 7.066887 ACACACACAAAAATGATGTCAGAGTAA 59.933 33.333 0.00 0.00 0.00 2.24
2942 5462 5.574891 AAGTTTATTCATGCGGCATTACA 57.425 34.783 13.81 0.01 0.00 2.41
3138 5681 5.872070 CCACAACAGAGGAAGTTCTAATCTC 59.128 44.000 2.25 0.99 0.00 2.75
3214 5760 1.899437 GATGTTCGGAGGAGGTGGCA 61.899 60.000 0.00 0.00 0.00 4.92
3387 5945 4.944619 TCTCACTCAGTCTTGATGTTGT 57.055 40.909 0.00 0.00 31.68 3.32
3448 10764 2.843545 GGGTGGAAGCTCCCAACA 59.156 61.111 10.12 0.00 45.65 3.33
3473 10789 5.992217 GGCTACATATCCGAGTTCAAGATTT 59.008 40.000 0.00 0.00 0.00 2.17
3474 10790 6.483640 GGCTACATATCCGAGTTCAAGATTTT 59.516 38.462 0.00 0.00 0.00 1.82
3504 10824 2.031769 TGCAGCATACATTTCGCATAGC 60.032 45.455 0.00 0.00 0.00 2.97
3555 10878 5.654209 TGATGAGAGCTTGACACTAGTGTAT 59.346 40.000 27.98 14.39 45.05 2.29
3739 11157 5.909621 AGAAGATAACAAACATGCAGCAT 57.090 34.783 0.52 0.52 0.00 3.79
3899 11347 3.685756 GGTGCGCCACTAGTAACAAATAA 59.314 43.478 12.58 0.00 34.40 1.40
3906 12261 7.255001 GCGCCACTAGTAACAAATAATAATGGT 60.255 37.037 0.00 0.00 34.73 3.55
3996 12451 2.677836 CACAAGTGCGCCATTACTATGT 59.322 45.455 4.18 6.31 0.00 2.29
3997 12452 3.126858 CACAAGTGCGCCATTACTATGTT 59.873 43.478 4.18 0.00 0.00 2.71
3998 12453 3.374058 ACAAGTGCGCCATTACTATGTTC 59.626 43.478 4.18 0.00 0.00 3.18
3999 12454 3.260475 AGTGCGCCATTACTATGTTCA 57.740 42.857 4.18 0.00 0.00 3.18
4001 12456 2.675844 GTGCGCCATTACTATGTTCACA 59.324 45.455 4.18 0.00 0.00 3.58
4004 12459 3.374058 GCGCCATTACTATGTTCACAAGT 59.626 43.478 0.00 0.00 0.00 3.16
4006 12461 4.662145 GCCATTACTATGTTCACAAGTGC 58.338 43.478 0.00 0.00 0.00 4.40
4007 12462 4.727734 GCCATTACTATGTTCACAAGTGCG 60.728 45.833 0.00 0.00 0.00 5.34
4008 12463 4.334443 CATTACTATGTTCACAAGTGCGC 58.666 43.478 0.00 0.00 0.00 6.09
4009 12464 1.156736 ACTATGTTCACAAGTGCGCC 58.843 50.000 4.18 0.00 0.00 6.53
4010 12465 1.155889 CTATGTTCACAAGTGCGCCA 58.844 50.000 4.18 0.00 0.00 5.69
4011 12466 1.739466 CTATGTTCACAAGTGCGCCAT 59.261 47.619 4.18 0.00 0.00 4.40
4012 12467 0.961019 ATGTTCACAAGTGCGCCATT 59.039 45.000 4.18 0.00 0.00 3.16
4013 12468 1.598882 TGTTCACAAGTGCGCCATTA 58.401 45.000 4.18 0.00 0.00 1.90
4014 12469 1.265635 TGTTCACAAGTGCGCCATTAC 59.734 47.619 4.18 0.00 0.00 1.89
4015 12470 1.535462 GTTCACAAGTGCGCCATTACT 59.465 47.619 4.18 0.00 0.00 2.24
4016 12471 2.739913 GTTCACAAGTGCGCCATTACTA 59.260 45.455 4.18 0.00 0.00 1.82
4017 12472 3.260475 TCACAAGTGCGCCATTACTAT 57.740 42.857 4.18 0.00 0.00 2.12
4018 12473 2.935849 TCACAAGTGCGCCATTACTATG 59.064 45.455 4.18 4.30 0.00 2.23
4019 12474 2.677836 CACAAGTGCGCCATTACTATGT 59.322 45.455 4.18 6.31 0.00 2.29
4020 12475 2.936498 ACAAGTGCGCCATTACTATGTC 59.064 45.455 4.18 0.00 0.00 3.06
4021 12476 2.240493 AGTGCGCCATTACTATGTCC 57.760 50.000 4.18 0.00 0.00 4.02
4022 12477 1.484653 AGTGCGCCATTACTATGTCCA 59.515 47.619 4.18 0.00 0.00 4.02
4023 12478 1.597663 GTGCGCCATTACTATGTCCAC 59.402 52.381 4.18 0.00 0.00 4.02
4024 12479 1.208293 TGCGCCATTACTATGTCCACA 59.792 47.619 4.18 0.00 0.00 4.17
4025 12480 2.285083 GCGCCATTACTATGTCCACAA 58.715 47.619 0.00 0.00 0.00 3.33
4026 12481 2.680841 GCGCCATTACTATGTCCACAAA 59.319 45.455 0.00 0.00 0.00 2.83
4027 12482 3.315191 GCGCCATTACTATGTCCACAAAT 59.685 43.478 0.00 0.00 0.00 2.32
4028 12483 4.789481 GCGCCATTACTATGTCCACAAATG 60.789 45.833 0.00 0.00 0.00 2.32
4029 12484 4.610945 GCCATTACTATGTCCACAAATGC 58.389 43.478 0.00 0.00 0.00 3.56
4404 14321 9.988815 ATCATCTAAACTACCATCACATAGAAC 57.011 33.333 0.00 0.00 0.00 3.01
4468 14736 2.092914 GTCTTCATCCGGTTCCTCCAAT 60.093 50.000 0.00 0.00 35.57 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 7.750229 TTAAAGAGAGAATCACATGCAGTTT 57.250 32.000 0.00 0.00 37.82 2.66
79 92 8.412608 TCAACGATTAAGAAGAGAATCACATC 57.587 34.615 0.00 0.00 37.82 3.06
126 139 6.566079 AGGAGAGAAATGTATGTGGATTGA 57.434 37.500 0.00 0.00 0.00 2.57
127 140 8.781196 CATAAGGAGAGAAATGTATGTGGATTG 58.219 37.037 0.00 0.00 0.00 2.67
132 145 5.471456 GGCCATAAGGAGAGAAATGTATGTG 59.529 44.000 0.00 0.00 36.89 3.21
168 181 3.294493 GCCAAAAGAGGGCGTGCA 61.294 61.111 0.00 0.00 42.39 4.57
184 197 1.792949 CATTACGACCAGCCTAATCGC 59.207 52.381 0.00 0.00 39.47 4.58
307 320 4.183865 GTGCTACTATGTGTCATGCAAGA 58.816 43.478 0.00 0.00 33.71 3.02
396 409 6.463472 CCAACTAGGCAATAGTGATGAGATGA 60.463 42.308 0.00 0.00 44.26 2.92
423 436 8.314751 GGAAGTATCACAGGTAGTATTATGCAT 58.685 37.037 3.79 3.79 0.00 3.96
469 482 2.988010 TCCATGCAGTCATGTAGTCC 57.012 50.000 0.00 0.00 46.64 3.85
472 485 4.259356 CCCATATCCATGCAGTCATGTAG 58.741 47.826 0.00 0.00 46.64 2.74
478 491 1.070758 ACGACCCATATCCATGCAGTC 59.929 52.381 0.00 0.00 33.67 3.51
532 545 7.251994 TGTATTGTTTTGTCAACACCAACTAC 58.748 34.615 0.00 0.00 0.00 2.73
634 647 9.625747 TCAGCCATTCAGATTTTGTATTACATA 57.374 29.630 0.00 0.00 0.00 2.29
635 648 8.523915 TCAGCCATTCAGATTTTGTATTACAT 57.476 30.769 0.00 0.00 0.00 2.29
636 649 7.936496 TCAGCCATTCAGATTTTGTATTACA 57.064 32.000 0.00 0.00 0.00 2.41
639 652 9.976511 CAATATCAGCCATTCAGATTTTGTATT 57.023 29.630 0.00 0.00 30.66 1.89
640 653 8.086522 GCAATATCAGCCATTCAGATTTTGTAT 58.913 33.333 0.00 0.00 34.52 2.29
641 654 7.286087 AGCAATATCAGCCATTCAGATTTTGTA 59.714 33.333 0.00 0.00 34.52 2.41
642 655 6.097839 AGCAATATCAGCCATTCAGATTTTGT 59.902 34.615 0.00 0.00 34.52 2.83
643 656 6.513180 AGCAATATCAGCCATTCAGATTTTG 58.487 36.000 0.00 0.00 34.86 2.44
644 657 6.726490 AGCAATATCAGCCATTCAGATTTT 57.274 33.333 0.00 0.00 0.00 1.82
645 658 6.726490 AAGCAATATCAGCCATTCAGATTT 57.274 33.333 0.00 0.00 0.00 2.17
646 659 7.229308 TCTAAGCAATATCAGCCATTCAGATT 58.771 34.615 0.00 0.00 0.00 2.40
647 660 6.776744 TCTAAGCAATATCAGCCATTCAGAT 58.223 36.000 0.00 0.00 0.00 2.90
648 661 6.178607 TCTAAGCAATATCAGCCATTCAGA 57.821 37.500 0.00 0.00 0.00 3.27
649 662 6.093771 GGATCTAAGCAATATCAGCCATTCAG 59.906 42.308 0.00 0.00 0.00 3.02
669 682 1.707427 AGCAAGAGTTGGGTTGGATCT 59.293 47.619 0.00 0.00 0.00 2.75
880 896 2.547218 GGTTGTGTGTGTACTGGACGAT 60.547 50.000 0.00 0.00 0.00 3.73
927 944 4.821589 GAGGCCGGGCAGAGTTCG 62.822 72.222 31.59 0.00 0.00 3.95
930 947 3.710722 CAAGAGGCCGGGCAGAGT 61.711 66.667 31.59 9.41 0.00 3.24
1651 3406 1.891919 ACGGCAGCGATGTTGTTGT 60.892 52.632 1.22 0.00 0.00 3.32
1752 3507 2.220761 GCATGAAGGCGTCGATCTC 58.779 57.895 0.00 0.00 0.00 2.75
2048 4417 4.054671 GTCAGTCAGCTACAATATGAGCC 58.945 47.826 0.00 0.00 39.65 4.70
2502 4916 5.124776 TCCCGCAAGAACAATATCGATTTTT 59.875 36.000 1.71 0.00 43.02 1.94
2594 5041 3.067883 TCAAGATGCTCTCTCTGGATTCG 59.932 47.826 0.00 0.00 31.03 3.34
2926 5417 5.663456 AGAAATTTGTAATGCCGCATGAAT 58.337 33.333 6.63 3.08 0.00 2.57
2942 5462 9.320295 TGGAATGACATACCCTAAAAGAAATTT 57.680 29.630 0.00 0.00 34.92 1.82
3138 5681 6.372659 CCTGTATATTTATAGTGGGCAGCAAG 59.627 42.308 0.00 0.00 0.00 4.01
3214 5760 2.677228 CTTTCCGGGGCACATCCT 59.323 61.111 0.00 0.00 34.39 3.24
3286 5832 2.544267 GAGTCACAAAAGGAACAGACCG 59.456 50.000 0.00 0.00 34.73 4.79
3374 5932 4.163078 CCTCCCATCTACAACATCAAGACT 59.837 45.833 0.00 0.00 0.00 3.24
3387 5945 0.642156 TGCCTTCCTCCTCCCATCTA 59.358 55.000 0.00 0.00 0.00 1.98
3448 10764 4.215908 TCTTGAACTCGGATATGTAGCCT 58.784 43.478 0.00 0.00 0.00 4.58
3473 10789 6.238184 CGAAATGTATGCTGCAAGATCAGTAA 60.238 38.462 6.36 0.00 36.49 2.24
3474 10790 5.234972 CGAAATGTATGCTGCAAGATCAGTA 59.765 40.000 6.36 0.00 36.49 2.74
3504 10824 5.416326 CCCGTCTAGGTCCTATCAATCTAAG 59.584 48.000 0.00 0.00 38.74 2.18
3781 11200 0.905357 ACCCAAGACTCTCAATCCCG 59.095 55.000 0.00 0.00 0.00 5.14
3856 11276 4.142026 ACCTGTAGTGCGTCATTAATAGCA 60.142 41.667 7.94 7.94 37.26 3.49
3899 11347 0.552848 CCCCAGAGGTGCACCATTAT 59.447 55.000 36.39 17.30 38.89 1.28
3921 12276 7.670140 CACCACTATTATCTGGGATACTAGTGA 59.330 40.741 27.50 0.00 46.96 3.41
3996 12451 1.890876 AGTAATGGCGCACTTGTGAA 58.109 45.000 10.83 0.00 0.00 3.18
3997 12452 2.753055 TAGTAATGGCGCACTTGTGA 57.247 45.000 10.83 0.00 0.00 3.58
3998 12453 2.677836 ACATAGTAATGGCGCACTTGTG 59.322 45.455 10.83 9.11 37.43 3.33
3999 12454 2.936498 GACATAGTAATGGCGCACTTGT 59.064 45.455 10.83 10.78 37.43 3.16
4001 12456 2.093181 TGGACATAGTAATGGCGCACTT 60.093 45.455 10.83 4.06 42.67 3.16
4004 12459 1.208293 TGTGGACATAGTAATGGCGCA 59.792 47.619 10.83 0.00 42.67 6.09
4006 12461 4.789481 GCATTTGTGGACATAGTAATGGCG 60.789 45.833 0.00 0.00 42.67 5.69
4007 12462 4.610945 GCATTTGTGGACATAGTAATGGC 58.389 43.478 0.00 0.00 40.80 4.40
4008 12463 4.789481 GCGCATTTGTGGACATAGTAATGG 60.789 45.833 0.30 0.00 37.43 3.16
4009 12464 4.282068 GCGCATTTGTGGACATAGTAATG 58.718 43.478 0.30 0.00 39.17 1.90
4010 12465 3.315191 GGCGCATTTGTGGACATAGTAAT 59.685 43.478 10.83 0.00 0.00 1.89
4011 12466 2.680841 GGCGCATTTGTGGACATAGTAA 59.319 45.455 10.83 0.00 0.00 2.24
4012 12467 2.285083 GGCGCATTTGTGGACATAGTA 58.715 47.619 10.83 0.00 0.00 1.82
4013 12468 1.094785 GGCGCATTTGTGGACATAGT 58.905 50.000 10.83 0.00 0.00 2.12
4014 12469 1.093972 TGGCGCATTTGTGGACATAG 58.906 50.000 10.83 0.00 0.00 2.23
4015 12470 1.761449 ATGGCGCATTTGTGGACATA 58.239 45.000 10.83 0.00 0.00 2.29
4016 12471 1.761449 TATGGCGCATTTGTGGACAT 58.239 45.000 10.83 2.16 0.00 3.06
4017 12472 1.761449 ATATGGCGCATTTGTGGACA 58.239 45.000 10.83 0.00 0.00 4.02
4018 12473 2.869233 AATATGGCGCATTTGTGGAC 57.131 45.000 10.83 0.00 0.00 4.02
4019 12474 3.067461 GGTAAATATGGCGCATTTGTGGA 59.933 43.478 10.83 0.00 0.00 4.02
4020 12475 3.068024 AGGTAAATATGGCGCATTTGTGG 59.932 43.478 10.83 0.00 0.00 4.17
4021 12476 4.305989 AGGTAAATATGGCGCATTTGTG 57.694 40.909 10.83 0.00 0.00 3.33
4022 12477 4.159506 ACAAGGTAAATATGGCGCATTTGT 59.840 37.500 10.83 4.16 0.00 2.83
4023 12478 4.503734 CACAAGGTAAATATGGCGCATTTG 59.496 41.667 10.83 3.57 0.00 2.32
4024 12479 4.681744 CACAAGGTAAATATGGCGCATTT 58.318 39.130 10.83 9.64 0.00 2.32
4025 12480 3.490761 GCACAAGGTAAATATGGCGCATT 60.491 43.478 10.83 0.00 0.00 3.56
4026 12481 2.034558 GCACAAGGTAAATATGGCGCAT 59.965 45.455 10.83 3.40 0.00 4.73
4027 12482 1.403679 GCACAAGGTAAATATGGCGCA 59.596 47.619 10.83 0.00 0.00 6.09
4028 12483 1.676006 AGCACAAGGTAAATATGGCGC 59.324 47.619 0.00 0.00 0.00 6.53
4029 12484 3.002656 CAGAGCACAAGGTAAATATGGCG 59.997 47.826 0.00 0.00 0.00 5.69
4404 14321 2.163390 CGTGATGACCGCAGCTCTG 61.163 63.158 0.00 0.00 0.00 3.35
4468 14736 2.693017 GGGAGAGAGGAGGGAGCA 59.307 66.667 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.