Multiple sequence alignment - TraesCS4B01G380900

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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 TraesCS4B01G380900 chr4B 100.000 7961 0 0 1 7961 660873274 660881234 0.000000e+00 14702.0
1 TraesCS4B01G380900 chr4B 98.183 7044 113 13 517 7554 660904037 660911071 0.000000e+00 12285.0
2 TraesCS4B01G380900 chr4B 94.467 2494 119 12 517 3002 660929336 660931818 0.000000e+00 3823.0
3 TraesCS4B01G380900 chr4B 89.675 1385 116 15 6073 7439 660935438 660936813 0.000000e+00 1740.0
4 TraesCS4B01G380900 chr4B 88.666 1447 134 19 4650 6071 660933875 660935316 0.000000e+00 1736.0
5 TraesCS4B01G380900 chr4B 91.651 527 44 0 4094 4620 660933352 660933878 0.000000e+00 730.0
6 TraesCS4B01G380900 chr4B 85.843 332 35 2 7563 7883 668872979 668872649 7.650000e-90 342.0
7 TraesCS4B01G380900 chr4B 86.525 282 25 7 3544 3817 660932911 660933187 1.680000e-76 298.0
8 TraesCS4B01G380900 chr4B 89.815 216 18 3 3126 3340 660931817 660932029 2.830000e-69 274.0
9 TraesCS4B01G380900 chr4B 79.003 381 73 6 4199 4577 660953836 660954211 3.690000e-63 254.0
10 TraesCS4B01G380900 chr4B 92.466 146 9 2 7818 7961 668872600 668872455 2.910000e-49 207.0
11 TraesCS4B01G380900 chr5A 91.778 3515 225 38 4094 7554 701301444 701297940 0.000000e+00 4831.0
12 TraesCS4B01G380900 chr5A 89.116 1516 123 31 1842 3343 701303536 701302049 0.000000e+00 1847.0
13 TraesCS4B01G380900 chr5A 91.165 498 33 5 3555 4043 701301960 701301465 0.000000e+00 665.0
14 TraesCS4B01G380900 chr5A 95.694 418 7 1 7555 7961 565687787 565688204 0.000000e+00 662.0
15 TraesCS4B01G380900 chr5A 83.908 696 76 19 862 1553 701304891 701304228 4.050000e-177 632.0
16 TraesCS4B01G380900 chr5A 85.843 332 35 2 7563 7883 513703296 513703626 7.650000e-90 342.0
17 TraesCS4B01G380900 chr5A 84.940 332 38 2 7563 7883 335712770 335712440 7.700000e-85 326.0
18 TraesCS4B01G380900 chr5A 75.628 677 122 23 5190 5834 701865785 701866450 6.040000e-76 296.0
19 TraesCS4B01G380900 chr5A 75.369 678 122 23 5190 5834 701779562 701780227 1.310000e-72 285.0
20 TraesCS4B01G380900 chr5A 79.572 421 61 16 2195 2603 701776226 701776633 2.190000e-70 278.0
21 TraesCS4B01G380900 chr5A 79.896 383 66 10 4199 4577 701378362 701378737 3.660000e-68 270.0
22 TraesCS4B01G380900 chr5A 93.642 173 8 2 2187 2359 701085197 701085366 1.030000e-63 255.0
23 TraesCS4B01G380900 chr5A 84.733 262 16 11 1132 1371 701079849 701080108 2.870000e-59 241.0
24 TraesCS4B01G380900 chr5A 80.488 287 26 16 1922 2199 701082803 701083068 8.150000e-45 193.0
25 TraesCS4B01G380900 chr5A 82.301 226 37 2 1598 1822 701304016 701303793 8.150000e-45 193.0
26 TraesCS4B01G380900 chr5A 85.227 176 12 5 779 953 701079400 701079562 1.370000e-37 169.0
27 TraesCS4B01G380900 chr5A 95.604 91 4 0 779 869 701305012 701304922 6.440000e-31 147.0
28 TraesCS4B01G380900 chr5A 94.595 37 2 0 985 1021 701079814 701079850 3.100000e-04 58.4
29 TraesCS4B01G380900 chrUn 92.792 3177 188 14 4094 7249 111025550 111028706 0.000000e+00 4560.0
30 TraesCS4B01G380900 chrUn 87.475 1964 161 47 1639 3545 111023010 111024945 0.000000e+00 2185.0
31 TraesCS4B01G380900 chrUn 100.000 402 0 0 2628 3029 478540852 478540451 0.000000e+00 743.0
32 TraesCS4B01G380900 chrUn 97.052 407 1 1 7555 7961 48293509 48293904 0.000000e+00 675.0
33 TraesCS4B01G380900 chrUn 84.291 592 54 24 862 1447 111022192 111022750 7.030000e-150 542.0
34 TraesCS4B01G380900 chrUn 90.238 420 27 7 7555 7961 452911321 452910903 3.270000e-148 536.0
35 TraesCS4B01G380900 chrUn 89.078 412 29 3 7555 7955 79244794 79244388 1.540000e-136 497.0
36 TraesCS4B01G380900 chrUn 90.678 354 23 8 3699 4043 111025177 111025529 5.630000e-126 462.0
37 TraesCS4B01G380900 chrUn 89.531 277 27 2 7687 7961 355960177 355960453 4.570000e-92 350.0
38 TraesCS4B01G380900 chrUn 83.090 343 23 24 7243 7551 111030403 111030744 6.080000e-71 279.0
39 TraesCS4B01G380900 chrUn 80.541 370 63 8 4210 4577 111135508 111135870 7.870000e-70 276.0
40 TraesCS4B01G380900 chrUn 78.974 390 73 8 4191 4577 111053212 111053595 2.850000e-64 257.0
41 TraesCS4B01G380900 chrUn 78.421 380 77 4 4199 4577 110995378 110995753 7.980000e-60 243.0
42 TraesCS4B01G380900 chrUn 82.353 272 33 7 7555 7825 89804150 89804407 1.040000e-53 222.0
43 TraesCS4B01G380900 chrUn 95.604 91 4 0 779 869 111022070 111022160 6.440000e-31 147.0
44 TraesCS4B01G380900 chrUn 84.354 147 15 5 2472 2612 479411591 479411735 3.870000e-28 137.0
45 TraesCS4B01G380900 chr3A 99.263 407 3 0 7555 7961 721022939 721022533 0.000000e+00 736.0
46 TraesCS4B01G380900 chr3A 96.651 418 3 1 7555 7961 720986020 720985603 0.000000e+00 684.0
47 TraesCS4B01G380900 chr3A 95.943 419 5 2 7555 7961 217959892 217960310 0.000000e+00 669.0
48 TraesCS4B01G380900 chr3A 95.823 407 17 0 7555 7961 726715860 726715454 0.000000e+00 658.0
49 TraesCS4B01G380900 chr2A 99.263 407 3 0 7555 7961 41759890 41759484 0.000000e+00 736.0
50 TraesCS4B01G380900 chr2A 90.465 409 36 3 7555 7961 730608688 730608281 3.270000e-148 536.0
51 TraesCS4B01G380900 chr2A 89.681 407 30 4 7555 7961 17499218 17498824 7.130000e-140 508.0
52 TraesCS4B01G380900 chr2A 85.843 332 35 3 7563 7883 750961861 750961531 7.650000e-90 342.0
53 TraesCS4B01G380900 chr2A 94.444 90 3 2 3809 3897 632952998 632952910 3.870000e-28 137.0
54 TraesCS4B01G380900 chr7B 98.522 406 6 0 7556 7961 714304554 714304149 0.000000e+00 717.0
55 TraesCS4B01G380900 chr7A 98.034 407 7 1 7555 7961 718436742 718437147 0.000000e+00 706.0
56 TraesCS4B01G380900 chr7A 96.814 408 1 2 7555 7961 692048586 692048190 0.000000e+00 671.0
57 TraesCS4B01G380900 chr7A 95.261 422 8 2 7551 7961 48003060 48002640 0.000000e+00 658.0
58 TraesCS4B01G380900 chr7A 95.455 330 4 1 7555 7873 186397626 186397955 4.260000e-142 516.0
59 TraesCS4B01G380900 chr6A 93.052 403 17 2 7559 7961 72976293 72975902 5.360000e-161 579.0
60 TraesCS4B01G380900 chr6A 90.686 408 37 1 7554 7961 23193397 23193803 7.030000e-150 542.0
61 TraesCS4B01G380900 chr6A 78.657 670 101 27 106 764 457076614 457075976 2.670000e-109 407.0
62 TraesCS4B01G380900 chr6A 85.843 332 35 2 7563 7883 3636232 3635902 7.650000e-90 342.0
63 TraesCS4B01G380900 chr6A 91.781 146 10 2 7818 7961 3635853 3635708 1.350000e-47 202.0
64 TraesCS4B01G380900 chr6A 93.846 65 4 0 7819 7883 3635909 3635845 1.830000e-16 99.0
65 TraesCS4B01G380900 chr6A 90.625 64 6 0 4031 4094 26954770 26954833 1.420000e-12 86.1
66 TraesCS4B01G380900 chr6B 91.190 420 23 4 7555 7961 714429603 714429185 6.980000e-155 558.0
67 TraesCS4B01G380900 chr7D 85.907 518 57 14 3 509 119561180 119561692 9.090000e-149 538.0
68 TraesCS4B01G380900 chr7D 84.109 516 70 12 3 508 50711128 50711641 9.290000e-134 488.0
69 TraesCS4B01G380900 chr7D 79.270 685 93 29 90 764 431340030 431339385 4.410000e-117 433.0
70 TraesCS4B01G380900 chr4D 85.171 526 58 16 3 509 475196979 475197503 9.150000e-144 521.0
71 TraesCS4B01G380900 chr3D 84.393 519 66 15 3 509 591714984 591714469 5.550000e-136 496.0
72 TraesCS4B01G380900 chr3D 84.333 517 63 13 3 506 504420124 504420635 2.580000e-134 490.0
73 TraesCS4B01G380900 chr3D 88.808 411 29 2 7551 7961 556046939 556047332 9.290000e-134 488.0
74 TraesCS4B01G380900 chr1D 84.405 513 67 12 3 504 247134209 247133699 7.180000e-135 492.0
75 TraesCS4B01G380900 chr1D 77.851 456 65 15 320 764 471285331 471285761 4.770000e-62 250.0
76 TraesCS4B01G380900 chr6D 84.139 517 67 14 3 509 59026053 59025542 3.340000e-133 486.0
77 TraesCS4B01G380900 chr6D 84.069 521 65 16 3 509 423361076 423361592 3.340000e-133 486.0
78 TraesCS4B01G380900 chr6D 95.455 88 2 2 3811 3897 403969210 403969124 1.080000e-28 139.0
79 TraesCS4B01G380900 chr5D 83.977 518 71 12 3 509 478460156 478459640 3.340000e-133 486.0
80 TraesCS4B01G380900 chr5D 95.455 88 2 2 3811 3897 339760790 339760876 1.080000e-28 139.0
81 TraesCS4B01G380900 chr3B 77.875 800 111 34 3 765 617959713 617958943 3.410000e-118 436.0
82 TraesCS4B01G380900 chr3B 76.957 447 61 25 2178 2612 827683221 827682805 4.840000e-52 217.0
83 TraesCS4B01G380900 chr3B 76.734 447 62 25 2178 2612 827139051 827138635 2.250000e-50 211.0
84 TraesCS4B01G380900 chr3B 91.837 98 6 2 3808 3903 113917057 113917154 1.390000e-27 135.0
85 TraesCS4B01G380900 chr1A 82.353 272 33 7 7555 7825 292588003 292588260 1.040000e-53 222.0
86 TraesCS4B01G380900 chr1B 77.011 435 62 22 338 764 634930641 634930237 1.740000e-51 215.0
87 TraesCS4B01G380900 chr1B 76.498 434 66 21 338 764 634862176 634861772 3.770000e-48 204.0
88 TraesCS4B01G380900 chr1B 85.714 126 9 7 3807 3926 541468129 541468007 3.020000e-24 124.0
89 TraesCS4B01G380900 chr4A 80.469 256 39 9 515 764 709846725 709846475 1.360000e-42 185.0
90 TraesCS4B01G380900 chr2D 96.512 86 2 1 3813 3897 128890637 128890722 3.000000e-29 141.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G380900 chr4B 660873274 660881234 7960 False 14702.000000 14702 100.000000 1 7961 1 chr4B.!!$F1 7960
1 TraesCS4B01G380900 chr4B 660904037 660911071 7034 False 12285.000000 12285 98.183000 517 7554 1 chr4B.!!$F2 7037
2 TraesCS4B01G380900 chr4B 660929336 660936813 7477 False 1433.500000 3823 90.133167 517 7439 6 chr4B.!!$F4 6922
3 TraesCS4B01G380900 chr4B 668872455 668872979 524 True 274.500000 342 89.154500 7563 7961 2 chr4B.!!$R1 398
4 TraesCS4B01G380900 chr5A 701297940 701305012 7072 True 1385.833333 4831 88.978667 779 7554 6 chr5A.!!$R2 6775
5 TraesCS4B01G380900 chr5A 701865785 701866450 665 False 296.000000 296 75.628000 5190 5834 1 chr5A.!!$F4 644
6 TraesCS4B01G380900 chr5A 701776226 701780227 4001 False 281.500000 285 77.470500 2195 5834 2 chr5A.!!$F6 3639
7 TraesCS4B01G380900 chrUn 111022070 111030744 8674 False 1362.500000 4560 88.988333 779 7551 6 chrUn.!!$F8 6772
8 TraesCS4B01G380900 chr6A 457075976 457076614 638 True 407.000000 407 78.657000 106 764 1 chr6A.!!$R2 658
9 TraesCS4B01G380900 chr6A 3635708 3636232 524 True 214.333333 342 90.490000 7563 7961 3 chr6A.!!$R3 398
10 TraesCS4B01G380900 chr7D 119561180 119561692 512 False 538.000000 538 85.907000 3 509 1 chr7D.!!$F2 506
11 TraesCS4B01G380900 chr7D 50711128 50711641 513 False 488.000000 488 84.109000 3 508 1 chr7D.!!$F1 505
12 TraesCS4B01G380900 chr7D 431339385 431340030 645 True 433.000000 433 79.270000 90 764 1 chr7D.!!$R1 674
13 TraesCS4B01G380900 chr4D 475196979 475197503 524 False 521.000000 521 85.171000 3 509 1 chr4D.!!$F1 506
14 TraesCS4B01G380900 chr3D 591714469 591714984 515 True 496.000000 496 84.393000 3 509 1 chr3D.!!$R1 506
15 TraesCS4B01G380900 chr3D 504420124 504420635 511 False 490.000000 490 84.333000 3 506 1 chr3D.!!$F1 503
16 TraesCS4B01G380900 chr1D 247133699 247134209 510 True 492.000000 492 84.405000 3 504 1 chr1D.!!$R1 501
17 TraesCS4B01G380900 chr6D 59025542 59026053 511 True 486.000000 486 84.139000 3 509 1 chr6D.!!$R1 506
18 TraesCS4B01G380900 chr6D 423361076 423361592 516 False 486.000000 486 84.069000 3 509 1 chr6D.!!$F1 506
19 TraesCS4B01G380900 chr5D 478459640 478460156 516 True 486.000000 486 83.977000 3 509 1 chr5D.!!$R1 506
20 TraesCS4B01G380900 chr3B 617958943 617959713 770 True 436.000000 436 77.875000 3 765 1 chr3B.!!$R1 762

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
515 608 0.111266 CAGAAAACACGTTCTCGCGG 60.111 55.000 6.13 0.0 41.18 6.46 F
516 609 0.249155 AGAAAACACGTTCTCGCGGA 60.249 50.000 6.13 0.0 41.18 5.54 F
765 871 0.319641 GAAGGAGCGTTCGTCAACCT 60.320 55.000 0.00 0.0 0.00 3.50 F
1943 2524 0.037697 TGTTCGTCGCAAGGTGCTAT 60.038 50.000 0.00 0.0 42.25 2.97 F
2307 2905 0.320050 TGTATGGAGACGTTGCTGCA 59.680 50.000 0.00 0.0 40.57 4.41 F
4007 5888 0.396811 AACTGTAGCAGTGTCCACCC 59.603 55.000 2.31 0.0 44.62 4.61 F
4722 6687 1.040646 CGGCCAACCTGCTCTATCTA 58.959 55.000 2.24 0.0 0.00 1.98 F
4724 6689 1.269831 GGCCAACCTGCTCTATCTACG 60.270 57.143 0.00 0.0 0.00 3.51 F
5691 7768 0.804989 CCCTCAATGTGCGGAAGAAC 59.195 55.000 0.00 0.0 41.28 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1790 2131 0.383949 GCGTGGTTTCTTTTCTGGCA 59.616 50.000 0.00 0.00 0.00 4.92 R
1825 2166 1.142465 CTGATCAGGTATTGGGCTGCT 59.858 52.381 15.38 0.00 0.00 4.24 R
2514 3116 2.196776 AGCACTGCAGCAACCCTT 59.803 55.556 15.27 0.00 36.85 3.95 R
3437 4971 1.701847 GTATGGCAGGGATGAGGTGAT 59.298 52.381 0.00 0.00 0.00 3.06 R
4134 6017 4.037446 ACGCTTTAATTTCCTGCAGTTCAA 59.963 37.500 13.81 2.33 0.00 2.69 R
5517 7587 0.179936 CTGATCCCTGAGCCACCTTC 59.820 60.000 0.00 0.00 0.00 3.46 R
5691 7768 4.446371 AGGTCGATAAGATTGCCTTTGAG 58.554 43.478 0.00 0.00 36.34 3.02 R
6849 9064 4.321718 TGTCTTCTTCAGCCATCTTCTTG 58.678 43.478 0.00 0.00 0.00 3.02 R
7731 11698 0.662619 TGCGCTGCTATATTTGTGGC 59.337 50.000 9.73 0.00 0.00 5.01 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
70 75 1.029681 AAAACCAAACCGAGAGCACC 58.970 50.000 0.00 0.00 0.00 5.01
99 107 0.320697 CTTTCCGAAAGAGGGACGGT 59.679 55.000 14.72 0.00 45.71 4.83
100 108 0.760572 TTTCCGAAAGAGGGACGGTT 59.239 50.000 0.00 0.00 45.71 4.44
102 110 2.033194 CCGAAAGAGGGACGGTTGC 61.033 63.158 0.00 0.00 41.47 4.17
140 148 2.636412 CCGTGCCTCTCGTGGAAGA 61.636 63.158 0.00 0.00 0.00 2.87
144 152 1.801178 GTGCCTCTCGTGGAAGAAAAG 59.199 52.381 0.00 0.00 0.00 2.27
150 159 1.082104 CGTGGAAGAAAAGCCGTGC 60.082 57.895 0.00 0.00 0.00 5.34
168 179 1.087501 GCCTCTCGCGGAAGAAAAAT 58.912 50.000 6.13 0.00 0.00 1.82
174 195 6.457799 GCCTCTCGCGGAAGAAAAATAAAATA 60.458 38.462 6.13 0.00 0.00 1.40
258 284 2.338620 GGAAGCAAAACCGTGCCC 59.661 61.111 0.00 0.00 46.14 5.36
361 395 1.593196 CTCTCGTGGAAGCAAAACCA 58.407 50.000 0.00 0.00 0.00 3.67
482 574 1.209128 CAAAACTGTGACTCTCGCGT 58.791 50.000 5.77 0.00 0.00 6.01
489 581 2.911723 CTGTGACTCTCGCGTAAGAAAG 59.088 50.000 5.77 0.00 43.02 2.62
513 606 2.732001 AACAGAAAACACGTTCTCGC 57.268 45.000 0.00 0.00 41.18 5.03
514 607 0.575390 ACAGAAAACACGTTCTCGCG 59.425 50.000 0.00 0.00 41.18 5.87
515 608 0.111266 CAGAAAACACGTTCTCGCGG 60.111 55.000 6.13 0.00 41.18 6.46
516 609 0.249155 AGAAAACACGTTCTCGCGGA 60.249 50.000 6.13 0.00 41.18 5.54
517 610 0.578211 GAAAACACGTTCTCGCGGAA 59.422 50.000 6.13 6.05 41.18 4.30
518 611 1.004715 GAAAACACGTTCTCGCGGAAA 60.005 47.619 6.13 0.00 41.18 3.13
519 612 1.008329 AAACACGTTCTCGCGGAAAA 58.992 45.000 6.13 0.00 41.18 2.29
520 613 0.580104 AACACGTTCTCGCGGAAAAG 59.420 50.000 6.13 6.02 41.18 2.27
521 614 0.249155 ACACGTTCTCGCGGAAAAGA 60.249 50.000 6.13 0.00 41.18 2.52
522 615 0.856641 CACGTTCTCGCGGAAAAGAA 59.143 50.000 6.13 4.88 41.18 2.52
523 616 1.259507 CACGTTCTCGCGGAAAAGAAA 59.740 47.619 6.13 0.00 41.18 2.52
524 617 1.259770 ACGTTCTCGCGGAAAAGAAAC 59.740 47.619 6.13 2.52 41.18 2.78
525 618 1.525619 CGTTCTCGCGGAAAAGAAACT 59.474 47.619 6.13 0.00 35.51 2.66
526 619 2.409879 CGTTCTCGCGGAAAAGAAACTC 60.410 50.000 6.13 0.00 35.51 3.01
527 620 1.415374 TCTCGCGGAAAAGAAACTCG 58.585 50.000 6.13 0.00 0.00 4.18
534 627 4.099824 GCGGAAAAGAAACTCGTTTTTCA 58.900 39.130 12.09 0.00 40.70 2.69
584 680 6.783708 TTTTTCCAAAAGCTAAGGAAGACA 57.216 33.333 12.48 0.00 41.97 3.41
603 699 2.488937 ACAAGTGGAAAACCGAAACGTT 59.511 40.909 0.00 0.00 0.00 3.99
613 710 3.198409 ACCGAAACGTTAAGAAACCCT 57.802 42.857 0.00 0.00 31.46 4.34
743 849 0.949105 CGCTGGTCGTTGTAAGGCTT 60.949 55.000 4.58 4.58 0.00 4.35
765 871 0.319641 GAAGGAGCGTTCGTCAACCT 60.320 55.000 0.00 0.00 0.00 3.50
839 949 0.827507 GCAGGGAGCCCACTGAAAAA 60.828 55.000 0.00 0.00 36.86 1.94
850 960 4.881273 GCCCACTGAAAAAGATTTTTGGTT 59.119 37.500 7.96 0.00 40.21 3.67
1387 1537 2.073816 CCTTGTACCATCACGTTGGAC 58.926 52.381 13.22 7.41 39.25 4.02
1408 1558 2.815158 TCCTTTTGGATTTGGGGCTAC 58.185 47.619 0.00 0.00 45.19 3.58
1505 1657 2.540383 TCTGAGGTCCATACACTGCTT 58.460 47.619 0.00 0.00 0.00 3.91
1674 2014 6.035112 GCCTTTTAGACGAGATTTCACTACAG 59.965 42.308 0.00 0.00 0.00 2.74
1790 2131 5.893897 TTTGAAATTTTGCTTGCCAAAGT 57.106 30.435 0.00 0.00 43.77 2.66
1806 2147 3.118811 CCAAAGTGCCAGAAAAGAAACCA 60.119 43.478 0.00 0.00 0.00 3.67
1825 2166 1.240641 ACGCCATTTTCCATCACGCA 61.241 50.000 0.00 0.00 0.00 5.24
1835 2413 2.044650 ATCACGCAGCAGCCCAAT 60.045 55.556 0.00 0.00 37.52 3.16
1840 2418 2.475466 CGCAGCAGCCCAATACCTG 61.475 63.158 0.00 0.00 37.52 4.00
1862 2440 7.446013 ACCTGATCAGTAAACCATCGTTTAAAA 59.554 33.333 21.11 0.00 44.12 1.52
1925 2506 3.616956 TCTGGTGTCTTAGATGGCTTG 57.383 47.619 0.00 0.00 0.00 4.01
1933 2514 1.324736 CTTAGATGGCTTGTTCGTCGC 59.675 52.381 0.00 0.00 0.00 5.19
1941 2522 1.498865 CTTGTTCGTCGCAAGGTGCT 61.499 55.000 5.08 0.00 42.25 4.40
1943 2524 0.037697 TGTTCGTCGCAAGGTGCTAT 60.038 50.000 0.00 0.00 42.25 2.97
2207 2797 8.630917 TGGCTTGTATTCTAACTATGAGACTAC 58.369 37.037 0.00 0.00 32.49 2.73
2307 2905 0.320050 TGTATGGAGACGTTGCTGCA 59.680 50.000 0.00 0.00 40.57 4.41
2514 3116 5.069318 TCTATGCACCAGAAAACATGTTGA 58.931 37.500 12.82 0.00 0.00 3.18
2626 3232 9.747898 TTAGATGTAGGATGTTGGTTTATGTTT 57.252 29.630 0.00 0.00 0.00 2.83
3368 4898 4.091453 AGACGCCAAATTTTTATGTCGG 57.909 40.909 0.00 0.00 0.00 4.79
3437 4971 7.989947 AATCTAGGGGATCAACAAGTAGTTA 57.010 36.000 0.00 0.00 34.22 2.24
3840 5720 8.616799 ACTCCCTCTGAAAGAAATATAAGAGT 57.383 34.615 0.00 0.00 46.34 3.24
4007 5888 0.396811 AACTGTAGCAGTGTCCACCC 59.603 55.000 2.31 0.00 44.62 4.61
4072 5955 7.090953 TCCGTTCACTTTTGTATGTCTTTTT 57.909 32.000 0.00 0.00 0.00 1.94
4097 5980 6.296026 AGACAACTCAAAATAGGCTGTGTTA 58.704 36.000 0.00 0.00 30.39 2.41
4134 6017 9.783081 ATAAATTCTTCTTTTGTTCAATTGGCT 57.217 25.926 5.42 0.00 0.00 4.75
4722 6687 1.040646 CGGCCAACCTGCTCTATCTA 58.959 55.000 2.24 0.00 0.00 1.98
4724 6689 1.269831 GGCCAACCTGCTCTATCTACG 60.270 57.143 0.00 0.00 0.00 3.51
4930 6901 6.352137 CCATCTCCATGTTGGGATTCGATATA 60.352 42.308 0.00 0.00 38.32 0.86
5691 7768 0.804989 CCCTCAATGTGCGGAAGAAC 59.195 55.000 0.00 0.00 41.28 3.01
6338 8538 5.410355 AGTGGCATTGACATAAAATTGCT 57.590 34.783 0.00 0.00 0.00 3.91
6340 8540 3.933955 TGGCATTGACATAAAATTGCTGC 59.066 39.130 0.00 0.00 0.00 5.25
6849 9064 2.941720 GGTGTTGATGAAGGAGCAGATC 59.058 50.000 0.00 0.00 0.00 2.75
6991 9206 4.025040 TCAAAGCTGATGAATGGTCAGT 57.975 40.909 0.17 0.00 43.86 3.41
7554 11510 1.978617 CACCCATCACCCTTGCCAC 60.979 63.158 0.00 0.00 0.00 5.01
7555 11511 2.162906 ACCCATCACCCTTGCCACT 61.163 57.895 0.00 0.00 0.00 4.00
7556 11512 1.679977 CCCATCACCCTTGCCACTG 60.680 63.158 0.00 0.00 0.00 3.66
7557 11513 1.075482 CCATCACCCTTGCCACTGT 59.925 57.895 0.00 0.00 0.00 3.55
7558 11514 1.246056 CCATCACCCTTGCCACTGTG 61.246 60.000 0.00 0.00 0.00 3.66
7559 11515 0.538057 CATCACCCTTGCCACTGTGT 60.538 55.000 7.08 0.00 0.00 3.72
7560 11516 0.185901 ATCACCCTTGCCACTGTGTT 59.814 50.000 7.08 0.00 0.00 3.32
7561 11517 0.033601 TCACCCTTGCCACTGTGTTT 60.034 50.000 7.08 0.00 0.00 2.83
7652 11608 3.669557 CGGCAAAATCTCGGACGAAATTT 60.670 43.478 0.54 0.54 34.22 1.82
7708 11675 2.535934 CGAAATTCGGCCGAAATTCA 57.464 45.000 43.90 28.18 41.53 2.57
7714 11681 2.697431 TCGGCCGAAATTCAAACAAG 57.303 45.000 28.99 0.00 0.00 3.16
7716 11683 2.817258 TCGGCCGAAATTCAAACAAGAT 59.183 40.909 28.99 0.00 0.00 2.40
7719 11686 4.143347 CGGCCGAAATTCAAACAAGATTTG 60.143 41.667 24.07 0.00 0.00 2.32
7732 11699 8.825745 TCAAACAAGATTTGAAATAAAACAGGC 58.174 29.630 0.00 0.00 35.69 4.85
7735 11702 6.705825 ACAAGATTTGAAATAAAACAGGCCAC 59.294 34.615 5.01 0.00 0.00 5.01
7739 11706 7.938490 AGATTTGAAATAAAACAGGCCACAAAT 59.062 29.630 5.01 0.00 37.86 2.32
7743 11710 9.868277 TTGAAATAAAACAGGCCACAAATATAG 57.132 29.630 5.01 0.00 0.00 1.31
7748 11715 1.265095 CAGGCCACAAATATAGCAGCG 59.735 52.381 5.01 0.00 0.00 5.18
7780 11747 8.638685 CCATCAGGTTTGATCATGTAAATTTC 57.361 34.615 0.00 0.00 42.12 2.17
7804 11771 7.749666 TCAGCAAATAAGCTCTAGGGATTAAT 58.250 34.615 4.08 0.00 44.54 1.40
7812 11779 7.809546 AAGCTCTAGGGATTAATAAAACTGC 57.190 36.000 0.00 0.00 0.00 4.40
7851 11932 7.377766 ACAGGCACACATTAGTTATAAAGTG 57.622 36.000 2.76 2.76 43.15 3.16
7857 11938 6.038271 CACACATTAGTTATAAAGTGGCCTCC 59.962 42.308 3.32 0.00 42.28 4.30
7873 11955 3.562609 GGCCTCCAACATAACCCTTAACA 60.563 47.826 0.00 0.00 0.00 2.41
7879 11961 5.074115 CCAACATAACCCTTAACAGTCCAA 58.926 41.667 0.00 0.00 0.00 3.53
7909 11991 4.256110 TCAACCATCACAGCATAGTTCAG 58.744 43.478 0.00 0.00 0.00 3.02
7924 12006 7.707035 AGCATAGTTCAGAGTTTAAATAGTCCG 59.293 37.037 0.00 0.00 0.00 4.79
7935 12017 2.685850 AATAGTCCGGTACAGCCAAC 57.314 50.000 0.00 0.00 36.97 3.77
7946 12029 4.386711 GGTACAGCCAACAGACTTAAAGT 58.613 43.478 0.00 0.00 37.17 2.66
7951 12034 7.668525 ACAGCCAACAGACTTAAAGTATTAC 57.331 36.000 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.124466 TCGTCAAAACCTATCAACATGCG 59.876 43.478 0.00 0.00 0.00 4.73
1 2 4.678509 TCGTCAAAACCTATCAACATGC 57.321 40.909 0.00 0.00 0.00 4.06
80 88 0.320697 ACCGTCCCTCTTTCGGAAAG 59.679 55.000 21.64 21.64 46.05 2.62
94 102 2.125512 ATGAGAGGCGCAACCGTC 60.126 61.111 10.83 0.00 46.52 4.79
99 107 1.739466 GTGATTTCATGAGAGGCGCAA 59.261 47.619 10.83 0.00 0.00 4.85
100 108 1.338960 TGTGATTTCATGAGAGGCGCA 60.339 47.619 10.83 0.00 0.00 6.09
102 110 2.096496 GGTTGTGATTTCATGAGAGGCG 59.904 50.000 0.00 0.00 0.00 5.52
140 148 3.050275 GCGAGAGGCACGGCTTTT 61.050 61.111 0.00 0.00 42.87 2.27
150 159 4.939509 TTTATTTTTCTTCCGCGAGAGG 57.060 40.909 8.23 3.76 0.00 3.69
210 236 1.493311 GTTGTGCTTTCGCGAGAGG 59.507 57.895 25.84 13.55 43.69 3.69
307 340 4.039357 CGAGAGGCACGACCGTGT 62.039 66.667 21.38 5.02 46.90 4.49
332 365 0.108804 TCCACGAGAGGCACGATTTC 60.109 55.000 0.00 0.00 34.70 2.17
333 366 0.320374 TTCCACGAGAGGCACGATTT 59.680 50.000 0.00 0.00 34.70 2.17
336 369 2.962569 CTTCCACGAGAGGCACGA 59.037 61.111 0.00 0.00 34.70 4.35
361 395 5.581126 TTTTTATCTTCCGCAAGATGCAT 57.419 34.783 11.96 0.00 46.99 3.96
442 485 0.605319 TTCCGCAAGAGGCACGATTT 60.605 50.000 0.00 0.00 45.17 2.17
445 488 2.048222 CTTCCGCAAGAGGCACGA 60.048 61.111 0.00 0.00 45.17 4.35
505 598 1.525619 AGTTTCTTTTCCGCGAGAACG 59.474 47.619 8.23 0.00 42.93 3.95
509 602 1.137513 ACGAGTTTCTTTTCCGCGAG 58.862 50.000 8.23 0.00 0.00 5.03
510 603 1.574134 AACGAGTTTCTTTTCCGCGA 58.426 45.000 8.23 0.00 0.00 5.87
511 604 2.378507 AAACGAGTTTCTTTTCCGCG 57.621 45.000 0.00 0.00 0.00 6.46
512 605 4.027945 GTGAAAAACGAGTTTCTTTTCCGC 60.028 41.667 13.85 0.00 37.97 5.54
513 606 5.600262 GTGAAAAACGAGTTTCTTTTCCG 57.400 39.130 13.85 0.00 37.97 4.30
527 620 9.484326 AAAAAGACATATTTTTGCGTGAAAAAC 57.516 25.926 8.72 0.00 44.44 2.43
534 627 7.867445 AATCGAAAAAGACATATTTTTGCGT 57.133 28.000 10.02 0.00 43.62 5.24
584 680 4.635324 TCTTAACGTTTCGGTTTTCCACTT 59.365 37.500 5.91 0.00 40.70 3.16
737 843 2.113243 AACGCTCCTTCGGAAGCCTT 62.113 55.000 12.29 0.00 0.00 4.35
743 849 1.798234 TTGACGAACGCTCCTTCGGA 61.798 55.000 10.16 0.00 46.00 4.55
773 879 5.860648 TCCCCTAATTTGAAGAAAGGTCT 57.139 39.130 0.00 0.00 34.72 3.85
774 880 6.127338 CCATTCCCCTAATTTGAAGAAAGGTC 60.127 42.308 0.00 0.00 0.00 3.85
775 881 5.721480 CCATTCCCCTAATTTGAAGAAAGGT 59.279 40.000 0.00 0.00 0.00 3.50
839 949 7.777440 TGGGCTTATTTTTCAAACCAAAAATCT 59.223 29.630 7.07 0.00 42.43 2.40
850 960 4.219115 TCCACTGTGGGCTTATTTTTCAA 58.781 39.130 25.67 0.00 38.32 2.69
1093 1243 4.353437 GACGACACCTCCGGCGTT 62.353 66.667 6.01 0.00 37.07 4.84
1197 1347 3.592814 CGATGAGGGCCGTCGCTA 61.593 66.667 19.99 3.65 45.81 4.26
1387 1537 1.942776 AGCCCCAAATCCAAAAGGAG 58.057 50.000 0.00 0.00 0.00 3.69
1505 1657 9.147732 TGCAATCCTCTTCAGTATCTAATTAGA 57.852 33.333 17.32 17.32 36.65 2.10
1674 2014 1.343506 AGCCGTCGAAATTACGTCAC 58.656 50.000 0.00 0.00 38.67 3.67
1790 2131 0.383949 GCGTGGTTTCTTTTCTGGCA 59.616 50.000 0.00 0.00 0.00 4.92
1806 2147 1.240641 TGCGTGATGGAAAATGGCGT 61.241 50.000 0.00 0.00 0.00 5.68
1825 2166 1.142465 CTGATCAGGTATTGGGCTGCT 59.858 52.381 15.38 0.00 0.00 4.24
1835 2413 5.670792 AACGATGGTTTACTGATCAGGTA 57.329 39.130 26.08 13.14 30.42 3.08
1840 2418 7.539710 GGGTTTTTAAACGATGGTTTACTGATC 59.460 37.037 12.03 2.70 45.63 2.92
1862 2440 4.401657 CTGGCTAGGGCTAGGGTT 57.598 61.111 0.00 0.00 42.29 4.11
1941 2522 3.620427 TTAGAGGCCTCGTTGCAAATA 57.380 42.857 26.95 8.53 34.09 1.40
1943 2524 2.290008 TGATTAGAGGCCTCGTTGCAAA 60.290 45.455 26.95 14.97 34.09 3.68
2207 2797 7.621428 ATGATTAGTGATCCAAAAGTGTCAG 57.379 36.000 0.00 0.00 33.60 3.51
2514 3116 2.196776 AGCACTGCAGCAACCCTT 59.803 55.556 15.27 0.00 36.85 3.95
3368 4898 5.826208 TCCTTGTTTTTCTCAGAAGGGTTAC 59.174 40.000 0.00 0.00 34.97 2.50
3437 4971 1.701847 GTATGGCAGGGATGAGGTGAT 59.298 52.381 0.00 0.00 0.00 3.06
4072 5955 5.865085 ACACAGCCTATTTTGAGTTGTCTA 58.135 37.500 0.00 0.00 0.00 2.59
4132 6015 4.386954 GCTTTAATTTCCTGCAGTTCAAGC 59.613 41.667 13.81 14.11 0.00 4.01
4134 6017 4.037446 ACGCTTTAATTTCCTGCAGTTCAA 59.963 37.500 13.81 2.33 0.00 2.69
4724 6689 4.083862 GGAGGTCCACGGCTCCAC 62.084 72.222 0.00 0.00 36.11 4.02
4782 6747 5.948842 AGTATGTACCCAAAAAGACCAACT 58.051 37.500 0.00 0.00 0.00 3.16
5042 7038 5.133941 AGCGTTATTCCTCTCAGTGAGATA 58.866 41.667 22.90 11.74 45.39 1.98
5517 7587 0.179936 CTGATCCCTGAGCCACCTTC 59.820 60.000 0.00 0.00 0.00 3.46
5691 7768 4.446371 AGGTCGATAAGATTGCCTTTGAG 58.554 43.478 0.00 0.00 36.34 3.02
6849 9064 4.321718 TGTCTTCTTCAGCCATCTTCTTG 58.678 43.478 0.00 0.00 0.00 3.02
7430 11353 0.877649 CAATGTCTCGGCGAGATGGG 60.878 60.000 38.36 24.59 40.98 4.00
7554 11510 5.347364 ACACAAACCGAAAATCAAAACACAG 59.653 36.000 0.00 0.00 0.00 3.66
7555 11511 5.230942 ACACAAACCGAAAATCAAAACACA 58.769 33.333 0.00 0.00 0.00 3.72
7556 11512 5.771602 ACACAAACCGAAAATCAAAACAC 57.228 34.783 0.00 0.00 0.00 3.32
7557 11513 6.787085 AAACACAAACCGAAAATCAAAACA 57.213 29.167 0.00 0.00 0.00 2.83
7621 11577 5.859648 GTCCGAGATTTTGCCGAAAAATTTA 59.140 36.000 9.29 0.00 46.29 1.40
7625 11581 2.350007 CGTCCGAGATTTTGCCGAAAAA 60.350 45.455 0.00 0.00 41.88 1.94
7626 11582 1.195900 CGTCCGAGATTTTGCCGAAAA 59.804 47.619 0.00 0.00 35.52 2.29
7627 11583 0.793861 CGTCCGAGATTTTGCCGAAA 59.206 50.000 0.00 0.00 0.00 3.46
7652 11608 9.310716 GGCCAAATTTTCAAATTTTGATTTTGA 57.689 25.926 25.38 9.10 43.91 2.69
7707 11674 8.069574 GGCCTGTTTTATTTCAAATCTTGTTTG 58.930 33.333 0.00 0.00 0.00 2.93
7708 11675 7.772757 TGGCCTGTTTTATTTCAAATCTTGTTT 59.227 29.630 3.32 0.00 0.00 2.83
7714 11681 7.489574 TTTGTGGCCTGTTTTATTTCAAATC 57.510 32.000 3.32 0.00 0.00 2.17
7719 11686 7.978975 TGCTATATTTGTGGCCTGTTTTATTTC 59.021 33.333 3.32 0.00 0.00 2.17
7728 11695 1.265095 CGCTGCTATATTTGTGGCCTG 59.735 52.381 3.32 0.00 0.00 4.85
7731 11698 0.662619 TGCGCTGCTATATTTGTGGC 59.337 50.000 9.73 0.00 0.00 5.01
7732 11699 2.097304 TGTTGCGCTGCTATATTTGTGG 59.903 45.455 9.73 0.00 0.00 4.17
7735 11702 3.108144 GGTTGTTGCGCTGCTATATTTG 58.892 45.455 9.73 0.00 0.00 2.32
7739 11706 1.939934 GATGGTTGTTGCGCTGCTATA 59.060 47.619 9.73 0.00 0.00 1.31
7743 11710 1.443194 CTGATGGTTGTTGCGCTGC 60.443 57.895 9.73 1.25 0.00 5.25
7765 11732 9.304731 GCTTATTTGCTGAAATTTACATGATCA 57.695 29.630 0.00 0.00 33.63 2.92
7772 11739 8.131731 CCCTAGAGCTTATTTGCTGAAATTTAC 58.868 37.037 0.00 0.00 44.17 2.01
7777 11744 5.435686 TCCCTAGAGCTTATTTGCTGAAA 57.564 39.130 0.00 0.00 44.17 2.69
7780 11747 7.992754 ATTAATCCCTAGAGCTTATTTGCTG 57.007 36.000 0.00 0.00 44.17 4.41
7804 11771 6.488344 TGTTATGTTGGACAGATGCAGTTTTA 59.512 34.615 0.00 0.00 0.00 1.52
7809 11776 3.376234 CCTGTTATGTTGGACAGATGCAG 59.624 47.826 5.15 0.00 44.65 4.41
7812 11779 3.127548 GTGCCTGTTATGTTGGACAGATG 59.872 47.826 5.15 0.00 44.65 2.90
7851 11932 3.021695 GTTAAGGGTTATGTTGGAGGCC 58.978 50.000 0.00 0.00 0.00 5.19
7857 11938 5.533154 TGTTGGACTGTTAAGGGTTATGTTG 59.467 40.000 0.00 0.00 0.00 3.33
7873 11955 3.576078 TGGTTGAACTGATGTTGGACT 57.424 42.857 0.00 0.00 36.39 3.85
7879 11961 2.816087 GCTGTGATGGTTGAACTGATGT 59.184 45.455 0.00 0.00 0.00 3.06
7909 11991 4.807834 GGCTGTACCGGACTATTTAAACTC 59.192 45.833 9.46 0.00 0.00 3.01
7924 12006 4.386711 ACTTTAAGTCTGTTGGCTGTACC 58.613 43.478 0.00 0.00 39.84 3.34


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

AutoCloner maintained by Alex Coulton.