Multiple sequence alignment - TraesCS6B01G240500

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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 TraesCS6B01G240500 chr6B 100.000 9865 0 0 1 9865 422315792 422325656 0.000000e+00 18218.0
1 TraesCS6B01G240500 chr6B 88.889 108 11 1 9171 9277 520852322 520852429 2.240000e-26 132.0
2 TraesCS6B01G240500 chr6D 96.008 4609 92 30 4559 9122 269700998 269705559 0.000000e+00 7408.0
3 TraesCS6B01G240500 chr6D 96.161 3048 90 10 607 3629 269696718 269699763 0.000000e+00 4955.0
4 TraesCS6B01G240500 chr6D 93.307 747 43 5 9070 9813 269705552 269706294 0.000000e+00 1096.0
5 TraesCS6B01G240500 chr6D 92.248 645 19 6 3618 4243 269699881 269700513 0.000000e+00 885.0
6 TraesCS6B01G240500 chr6D 93.538 325 11 7 4242 4563 269700637 269700954 8.970000e-130 475.0
7 TraesCS6B01G240500 chr6D 85.795 176 16 3 3233 3408 380449183 380449349 2.830000e-40 178.0
8 TraesCS6B01G240500 chr6D 89.815 108 10 1 9171 9277 79857211 79857104 4.810000e-28 137.0
9 TraesCS6B01G240500 chr6A 95.112 3764 84 31 4559 8267 383963829 383967547 0.000000e+00 5840.0
10 TraesCS6B01G240500 chr6A 93.556 2126 81 18 676 2772 383959685 383961783 0.000000e+00 3116.0
11 TraesCS6B01G240500 chr6A 93.505 970 31 12 3618 4563 383962824 383963785 0.000000e+00 1413.0
12 TraesCS6B01G240500 chr6A 95.262 781 21 9 8261 9028 383967835 383968612 0.000000e+00 1223.0
13 TraesCS6B01G240500 chr6A 92.520 869 40 6 2765 3629 383961858 383962705 0.000000e+00 1221.0
14 TraesCS6B01G240500 chr6A 90.707 721 53 7 9147 9865 383969929 383970637 0.000000e+00 948.0
15 TraesCS6B01G240500 chr6A 89.836 610 51 9 3 606 579139969 579140573 0.000000e+00 773.0
16 TraesCS6B01G240500 chr6A 90.278 144 3 2 660 793 383944412 383944554 2.830000e-40 178.0
17 TraesCS6B01G240500 chr6A 80.349 229 32 8 9359 9578 604874725 604874949 2.850000e-35 161.0
18 TraesCS6B01G240500 chr6A 87.037 108 13 1 9171 9277 603185176 603185283 4.840000e-23 121.0
19 TraesCS6B01G240500 chr5A 88.411 604 51 10 3 604 461735042 461735628 0.000000e+00 710.0
20 TraesCS6B01G240500 chr5A 89.714 350 30 4 7351 7700 170840095 170840438 9.090000e-120 442.0
21 TraesCS6B01G240500 chr5A 81.446 415 49 17 3017 3408 343049905 343050314 2.070000e-81 315.0
22 TraesCS6B01G240500 chr5A 91.279 172 13 2 5351 5521 320214235 320214405 5.960000e-57 233.0
23 TraesCS6B01G240500 chr1B 98.715 389 4 1 1 389 8770420 8770033 0.000000e+00 689.0
24 TraesCS6B01G240500 chr1B 82.670 427 37 20 3024 3426 240488578 240488991 2.640000e-90 344.0
25 TraesCS6B01G240500 chr1B 95.755 212 7 2 385 594 8769953 8769742 3.410000e-89 340.0
26 TraesCS6B01G240500 chr1B 81.087 423 47 23 3017 3416 656376475 656376063 3.460000e-79 307.0
27 TraesCS6B01G240500 chr1B 93.210 162 11 0 5360 5521 436689151 436688990 1.280000e-58 239.0
28 TraesCS6B01G240500 chr2B 98.458 389 5 1 1 389 767913892 767913505 0.000000e+00 684.0
29 TraesCS6B01G240500 chr2B 85.442 419 38 9 3016 3416 112468279 112467866 1.980000e-111 414.0
30 TraesCS6B01G240500 chr2B 95.575 226 8 2 385 608 767913426 767913201 2.620000e-95 361.0
31 TraesCS6B01G240500 chr2B 83.532 419 32 21 3019 3408 297436201 297436611 3.390000e-94 357.0
32 TraesCS6B01G240500 chr2B 92.638 163 9 3 5360 5521 366017519 366017679 2.140000e-56 231.0
33 TraesCS6B01G240500 chr2B 84.716 229 23 7 389 606 722348947 722349174 1.670000e-52 219.0
34 TraesCS6B01G240500 chr3B 98.201 389 5 1 1 389 810548867 810548481 0.000000e+00 678.0
35 TraesCS6B01G240500 chr3B 84.536 679 77 17 6610 7284 54498204 54498858 0.000000e+00 647.0
36 TraesCS6B01G240500 chr3B 85.128 390 38 6 1 389 71876863 71876493 2.010000e-101 381.0
37 TraesCS6B01G240500 chr3B 94.915 236 10 2 385 618 810548377 810548142 1.570000e-97 368.0
38 TraesCS6B01G240500 chr3B 89.151 212 17 3 5047 5252 445200777 445200566 9.830000e-65 259.0
39 TraesCS6B01G240500 chr3B 88.991 218 12 6 5041 5252 727477448 727477237 9.830000e-65 259.0
40 TraesCS6B01G240500 chr3B 84.080 201 26 4 5353 5548 571752518 571752717 1.310000e-43 189.0
41 TraesCS6B01G240500 chr3B 86.607 112 14 1 9167 9277 78608742 78608631 1.350000e-23 122.0
42 TraesCS6B01G240500 chr3B 86.735 98 12 1 9171 9267 145259187 145259090 3.770000e-19 108.0
43 TraesCS6B01G240500 chr3B 79.592 98 19 1 507 603 806765993 806766090 1.780000e-07 69.4
44 TraesCS6B01G240500 chr3D 83.602 683 71 19 6610 7284 31841752 31842401 3.940000e-168 603.0
45 TraesCS6B01G240500 chr3D 80.179 782 99 36 5517 6275 31840812 31841560 1.460000e-147 534.0
46 TraesCS6B01G240500 chr3D 89.970 329 31 2 7373 7700 182651653 182651326 3.290000e-114 424.0
47 TraesCS6B01G240500 chr3D 88.338 343 37 3 7361 7700 466287143 466287485 9.220000e-110 409.0
48 TraesCS6B01G240500 chr3D 86.411 287 37 2 9579 9865 348919993 348920277 7.440000e-81 313.0
49 TraesCS6B01G240500 chr3D 90.566 212 14 1 5047 5252 602056156 602055945 9.760000e-70 276.0
50 TraesCS6B01G240500 chr3D 92.727 165 12 0 5360 5524 87926000 87926164 1.280000e-58 239.0
51 TraesCS6B01G240500 chr5B 84.615 611 82 10 1 604 545289520 545288915 1.830000e-166 597.0
52 TraesCS6B01G240500 chr5B 87.834 337 33 7 7370 7700 596937612 596937946 1.200000e-103 388.0
53 TraesCS6B01G240500 chr2A 84.177 632 57 15 1 607 631786703 631787316 3.090000e-159 573.0
54 TraesCS6B01G240500 chr2A 86.159 289 37 2 9577 9865 14239410 14239695 9.620000e-80 309.0
55 TraesCS6B01G240500 chr2A 89.610 231 22 2 378 606 95948718 95948948 9.690000e-75 292.0
56 TraesCS6B01G240500 chr2A 85.473 296 21 14 3017 3291 270466569 270466863 1.250000e-73 289.0
57 TraesCS6B01G240500 chr2A 92.638 163 12 0 5359 5521 184561316 184561154 1.660000e-57 235.0
58 TraesCS6B01G240500 chr7A 89.460 389 33 7 3 389 469014468 469014850 1.490000e-132 484.0
59 TraesCS6B01G240500 chr1D 89.231 325 31 1 7376 7700 194674522 194674202 4.290000e-108 403.0
60 TraesCS6B01G240500 chr1D 87.857 280 33 1 9577 9856 364629397 364629675 2.660000e-85 327.0
61 TraesCS6B01G240500 chr7D 88.623 334 25 7 7375 7708 493569894 493569574 2.580000e-105 394.0
62 TraesCS6B01G240500 chr3A 79.066 621 95 30 1 606 61451064 61451664 2.580000e-105 394.0
63 TraesCS6B01G240500 chr3A 87.870 338 30 7 7366 7700 289106493 289106822 4.320000e-103 387.0
64 TraesCS6B01G240500 chr3A 86.760 287 34 3 9579 9865 72184878 72185160 5.750000e-82 316.0
65 TraesCS6B01G240500 chr3A 86.713 286 35 2 9580 9865 526853833 526854115 2.070000e-81 315.0
66 TraesCS6B01G240500 chr3A 91.329 173 13 2 5351 5522 585298151 585297980 1.660000e-57 235.0
67 TraesCS6B01G240500 chr4A 84.018 438 35 15 3017 3426 14355865 14355435 1.200000e-103 388.0
68 TraesCS6B01G240500 chr4A 98.333 60 1 0 1 60 707254704 707254645 1.360000e-18 106.0
69 TraesCS6B01G240500 chr7B 87.197 289 35 2 9577 9865 185031646 185031932 2.660000e-85 327.0
70 TraesCS6B01G240500 chr7B 92.925 212 8 3 5047 5252 445020177 445020387 1.610000e-77 302.0
71 TraesCS6B01G240500 chr7B 86.740 181 19 4 3247 3426 293159510 293159686 7.820000e-46 196.0
72 TraesCS6B01G240500 chr7B 81.776 214 30 8 397 606 34053977 34053769 4.740000e-38 171.0
73 TraesCS6B01G240500 chr2D 86.552 290 23 8 3017 3291 238157916 238158204 1.240000e-78 305.0
74 TraesCS6B01G240500 chr2D 91.765 170 9 5 5360 5527 296364209 296364043 2.140000e-56 231.0
75 TraesCS6B01G240500 chr2D 81.633 245 18 12 3017 3258 426424812 426425032 2.830000e-40 178.0
76 TraesCS6B01G240500 chr2D 82.915 199 31 2 409 604 72592653 72592455 1.020000e-39 176.0
77 TraesCS6B01G240500 chr2D 87.500 112 12 2 9171 9280 617338703 617338814 2.890000e-25 128.0
78 TraesCS6B01G240500 chr2D 87.963 108 12 1 9171 9277 586772169 586772062 1.040000e-24 126.0
79 TraesCS6B01G240500 chrUn 85.911 291 33 7 9577 9865 215330203 215329919 4.480000e-78 303.0
80 TraesCS6B01G240500 chrUn 89.372 207 15 2 5052 5252 17183985 17183780 4.570000e-63 254.0
81 TraesCS6B01G240500 chrUn 89.048 210 16 2 5049 5252 423412861 423413069 4.570000e-63 254.0
82 TraesCS6B01G240500 chr4B 90.094 212 15 1 5047 5252 450474530 450474741 4.540000e-68 270.0
83 TraesCS6B01G240500 chr4B 89.767 215 13 4 5047 5252 189811823 189812037 5.870000e-67 267.0
84 TraesCS6B01G240500 chr4B 84.324 185 25 1 3242 3426 206801776 206801596 2.830000e-40 178.0
85 TraesCS6B01G240500 chr1A 91.176 136 8 2 3291 3426 222350483 222350614 2.190000e-41 182.0


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 TraesCS6B01G240500 chr6B 422315792 422325656 9864 False 18218.0 18218 100.000000 1 9865 1 chr6B.!!$F1 9864
1 TraesCS6B01G240500 chr6D 269696718 269706294 9576 False 2963.8 7408 94.252400 607 9813 5 chr6D.!!$F2 9206
2 TraesCS6B01G240500 chr6A 383959685 383970637 10952 False 2293.5 5840 93.443667 676 9865 6 chr6A.!!$F5 9189
3 TraesCS6B01G240500 chr6A 579139969 579140573 604 False 773.0 773 89.836000 3 606 1 chr6A.!!$F2 603
4 TraesCS6B01G240500 chr5A 461735042 461735628 586 False 710.0 710 88.411000 3 604 1 chr5A.!!$F4 601
5 TraesCS6B01G240500 chr1B 8769742 8770420 678 True 514.5 689 97.235000 1 594 2 chr1B.!!$R3 593
6 TraesCS6B01G240500 chr2B 767913201 767913892 691 True 522.5 684 97.016500 1 608 2 chr2B.!!$R2 607
7 TraesCS6B01G240500 chr3B 54498204 54498858 654 False 647.0 647 84.536000 6610 7284 1 chr3B.!!$F1 674
8 TraesCS6B01G240500 chr3B 810548142 810548867 725 True 523.0 678 96.558000 1 618 2 chr3B.!!$R6 617
9 TraesCS6B01G240500 chr3D 31840812 31842401 1589 False 568.5 603 81.890500 5517 7284 2 chr3D.!!$F4 1767
10 TraesCS6B01G240500 chr5B 545288915 545289520 605 True 597.0 597 84.615000 1 604 1 chr5B.!!$R1 603
11 TraesCS6B01G240500 chr2A 631786703 631787316 613 False 573.0 573 84.177000 1 607 1 chr2A.!!$F4 606
12 TraesCS6B01G240500 chr3A 61451064 61451664 600 False 394.0 394 79.066000 1 606 1 chr3A.!!$F1 605

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
622 760 0.036105 TCCGCTGTGAGTAGTACCGA 60.036 55.000 0.00 0.0 0.00 4.69 F
1274 1442 0.253044 GCAGCTACACCAAGATGGGA 59.747 55.000 0.87 0.0 43.37 4.37 F
2070 2242 0.321996 GTGTCCTGGGGAAGACTGAC 59.678 60.000 0.00 0.0 31.38 3.51 F
3046 3309 0.969409 GCTTTCCAGGCTTGCTCCAT 60.969 55.000 0.00 0.0 0.00 3.41 F
3996 4414 0.322456 TTGAGAACCCGGCAGATTGG 60.322 55.000 0.00 0.0 0.00 3.16 F
5097 5701 0.168128 CAATTCCGAGAAACGCCACC 59.832 55.000 0.00 0.0 41.07 4.61 F
6227 6868 1.207329 GCCCTGAGGTTAGTACACTGG 59.793 57.143 0.00 0.0 34.57 4.00 F
6914 7563 3.244770 TGTCTGGGGGTTCAACTATGTTC 60.245 47.826 0.00 0.0 0.00 3.18 F
7648 8312 1.682257 GAGCTTCTGGAGGCCTGTT 59.318 57.895 12.00 0.0 33.44 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1651 1823 0.898320 CTGGGTCACACCTGAGGTAG 59.102 60.000 2.59 0.00 38.64 3.18 R
2585 2764 0.970937 TGGCCTCTACGGTTCTCTGG 60.971 60.000 3.32 0.00 34.25 3.86 R
3914 4332 1.370064 CGAAGGAAACCCACCGACT 59.630 57.895 0.00 0.00 0.00 4.18 R
4591 5186 0.266152 GGATGGAAGGGAGAGGGAGA 59.734 60.000 0.00 0.00 0.00 3.71 R
5782 6413 3.217626 ACCTTCAGCTGAGAACAAAAGG 58.782 45.455 21.56 21.56 38.19 3.11 R
6984 7633 0.247736 GCATCTCCACCAAGTCGAGT 59.752 55.000 0.00 0.00 0.00 4.18 R
7333 7994 1.206745 ATCGCGTAATCACTTCGGCG 61.207 55.000 5.77 0.00 0.00 6.46 R
8360 9330 0.740737 ACTCTGCTTTTGTGTGGCAC 59.259 50.000 11.55 11.55 34.56 5.01 R
9094 10122 0.108138 CCACGGACTGATCCCTTGTC 60.108 60.000 0.00 0.00 42.83 3.18 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
364 385 2.805657 GCAATACGAGTATTTCCCCGCT 60.806 50.000 5.81 0.00 33.79 5.52
459 595 0.112412 AAATCCCGGGTTTGAGCTGT 59.888 50.000 22.86 0.00 0.00 4.40
515 652 5.703730 AGGTTTAAAATAGACCGGGATCA 57.296 39.130 6.32 0.00 38.48 2.92
540 677 2.948979 AGTTCGGTGTGCTGATTTCAAA 59.051 40.909 0.00 0.00 0.00 2.69
541 678 3.380004 AGTTCGGTGTGCTGATTTCAAAA 59.620 39.130 0.00 0.00 0.00 2.44
571 709 7.833285 AAGTCAGGGTTTGATTTAGCTTTTA 57.167 32.000 0.00 0.00 38.29 1.52
622 760 0.036105 TCCGCTGTGAGTAGTACCGA 60.036 55.000 0.00 0.00 0.00 4.69
807 952 0.908198 ACAAACCCAGGCAAAGCAAA 59.092 45.000 0.00 0.00 0.00 3.68
897 1052 3.515901 TCCCTTCTTCTCCAAGCTTCTAC 59.484 47.826 0.00 0.00 0.00 2.59
907 1062 0.719623 AAGCTTCTACTCCCCTCCCT 59.280 55.000 0.00 0.00 0.00 4.20
1274 1442 0.253044 GCAGCTACACCAAGATGGGA 59.747 55.000 0.87 0.00 43.37 4.37
1515 1686 2.685850 GGGTACCGACTAAACTGCAT 57.314 50.000 5.65 0.00 40.86 3.96
1533 1705 4.239304 TGCATTGCTGAATGTTGATGTTC 58.761 39.130 10.49 0.00 41.09 3.18
1571 1743 3.120546 CGTGTGTTCATGTGTGATCTTCC 60.121 47.826 0.00 0.00 33.56 3.46
1596 1768 7.148423 CCTTAATTTGGGCTGAAAATTAACTGC 60.148 37.037 15.50 0.00 41.28 4.40
1651 1823 2.144730 TGGCAGCAATGCATTTTCAAC 58.855 42.857 9.83 1.28 36.33 3.18
1771 1943 0.798776 CGTTCAATGTGCCTGGTCTC 59.201 55.000 0.00 0.00 0.00 3.36
1932 2104 7.881142 AGTTTTACTGCTGTATTGCACATTTA 58.119 30.769 4.12 0.00 38.12 1.40
1973 2145 5.464069 AGTGGTTCCCTTTTCAATTACCTT 58.536 37.500 0.00 0.00 0.00 3.50
2070 2242 0.321996 GTGTCCTGGGGAAGACTGAC 59.678 60.000 0.00 0.00 31.38 3.51
2183 2362 6.433766 CAGATTTTGGCTGCTATAGTTTAGC 58.566 40.000 13.84 13.84 40.76 3.09
2266 2445 5.541953 ACTTAAACCCGGATATGTACCTC 57.458 43.478 0.73 0.00 0.00 3.85
2307 2486 1.331214 CTGCCACAAGGTCCACAATT 58.669 50.000 0.00 0.00 37.19 2.32
2448 2627 9.262358 GTTAATACCACTGAATCTGGTAATCTC 57.738 37.037 5.63 0.00 45.42 2.75
2773 3034 4.581409 AGAGACGGAGAAATAGGAAGTAGC 59.419 45.833 0.00 0.00 0.00 3.58
2831 3092 8.567948 CACTGTTACAAACTTGAATTATGAGGT 58.432 33.333 0.00 0.00 0.00 3.85
2832 3093 8.567948 ACTGTTACAAACTTGAATTATGAGGTG 58.432 33.333 0.00 0.00 0.00 4.00
3046 3309 0.969409 GCTTTCCAGGCTTGCTCCAT 60.969 55.000 0.00 0.00 0.00 3.41
3135 3398 2.036256 GGTGCCCAGGAGCATTGT 59.964 61.111 5.96 0.00 46.24 2.71
3435 3698 6.128282 TGACTCGTAATTCTTGGATGCTTTTC 60.128 38.462 0.00 0.00 0.00 2.29
3500 3763 5.823570 TGAAAACCAAGTGAGAATTCCGTAA 59.176 36.000 0.65 0.00 0.00 3.18
3773 4170 9.826574 TTCTGTGTACCCTATAAATGAACATAC 57.173 33.333 0.00 0.00 0.00 2.39
3914 4332 9.280174 CTCCTTTGTCTTATTACACCAAGTTAA 57.720 33.333 0.00 0.00 0.00 2.01
3995 4413 0.804989 GTTGAGAACCCGGCAGATTG 59.195 55.000 0.00 0.00 0.00 2.67
3996 4414 0.322456 TTGAGAACCCGGCAGATTGG 60.322 55.000 0.00 0.00 0.00 3.16
4002 4420 1.895707 CCCGGCAGATTGGCTCATC 60.896 63.158 0.00 0.00 41.25 2.92
4007 4425 1.541889 GGCAGATTGGCTCATCGATGA 60.542 52.381 25.80 25.80 40.14 2.92
4106 4525 5.529430 TGAGCAATTAAGTTCGAGTTGGAAA 59.471 36.000 0.00 0.00 0.00 3.13
4277 4821 2.481952 GTCACAACAGCAGTCCTTCATC 59.518 50.000 0.00 0.00 0.00 2.92
4278 4822 2.104622 TCACAACAGCAGTCCTTCATCA 59.895 45.455 0.00 0.00 0.00 3.07
4289 4834 5.218139 CAGTCCTTCATCAGCTTTGTTTTC 58.782 41.667 0.00 0.00 0.00 2.29
4336 4881 6.206634 TGTTATCCGTTTTGCTTTCAGATTCT 59.793 34.615 0.00 0.00 0.00 2.40
4345 4890 6.377327 TTGCTTTCAGATTCTCGAACTTTT 57.623 33.333 0.00 0.00 0.00 2.27
4393 4938 4.895297 CCCAACTAAACCTGCATCCATATT 59.105 41.667 0.00 0.00 0.00 1.28
4394 4939 6.068010 CCCAACTAAACCTGCATCCATATTA 58.932 40.000 0.00 0.00 0.00 0.98
4405 4950 8.825774 ACCTGCATCCATATTATATGTCTGTAA 58.174 33.333 10.83 1.99 0.00 2.41
4422 4967 2.303175 GTAAAAACCTGGTCCAGTGCA 58.697 47.619 17.85 0.00 0.00 4.57
4423 4968 2.086610 AAAAACCTGGTCCAGTGCAT 57.913 45.000 17.85 0.00 0.00 3.96
4431 4976 2.756760 CTGGTCCAGTGCATATGCTTTT 59.243 45.455 27.13 10.79 42.66 2.27
4499 5044 0.890542 GGTCTGGCATGTTGAGTGCA 60.891 55.000 0.00 0.00 44.25 4.57
4591 5186 6.183347 AGCTTACTAGATGTTTGCAAATCCT 58.817 36.000 16.21 14.24 0.00 3.24
4619 5214 1.203376 TCCCTTCCATCCAGTGTGGTA 60.203 52.381 0.06 0.00 39.03 3.25
4674 5276 9.439500 ACAGAATATTTGCATATTTTGTTGCTT 57.561 25.926 9.35 0.00 43.37 3.91
4685 5287 7.622672 GCATATTTTGTTGCTTCATCCACTTTG 60.623 37.037 0.00 0.00 35.95 2.77
5015 5618 8.270744 AGCAGGAAGTGATAAAATAGTTCTGAT 58.729 33.333 0.00 0.00 0.00 2.90
5068 5672 9.791801 AAAAGGTTAATTTGATAAATGCCACTT 57.208 25.926 0.00 0.00 0.00 3.16
5097 5701 0.168128 CAATTCCGAGAAACGCCACC 59.832 55.000 0.00 0.00 41.07 4.61
5269 5896 4.635223 TCCAAGACAGACTGAAACTCATG 58.365 43.478 10.08 0.00 0.00 3.07
5372 6000 5.769162 GTCATATAGAGTACTCCCTCCGTTT 59.231 44.000 19.38 0.74 31.53 3.60
5782 6413 6.546403 AGGTCTTTGTAGAAAAGAAGTTTCCC 59.454 38.462 2.27 0.00 45.91 3.97
6021 6659 6.521151 AGTCTGCTCTAAATCATTTTTGGG 57.479 37.500 0.00 0.00 0.00 4.12
6037 6675 4.605640 TTTGGGAAGAAGCAATCCAAAG 57.394 40.909 0.00 0.00 41.02 2.77
6227 6868 1.207329 GCCCTGAGGTTAGTACACTGG 59.793 57.143 0.00 0.00 34.57 4.00
6246 6894 4.038883 ACTGGTGTAGTTACTTCTGTGGTC 59.961 45.833 0.00 0.00 35.67 4.02
6367 7015 8.750298 TGTTTCATAAGTTCAGGGTTTGTTTTA 58.250 29.630 0.00 0.00 0.00 1.52
6468 7116 7.722949 AATGGTAAACTTGACATCATGGATT 57.277 32.000 0.00 0.00 0.00 3.01
6800 7448 3.805066 TCATCCCCAATTGACACAAGA 57.195 42.857 7.12 0.00 0.00 3.02
6914 7563 3.244770 TGTCTGGGGGTTCAACTATGTTC 60.245 47.826 0.00 0.00 0.00 3.18
7333 7994 5.103290 TCACTTCAAAATGGTACTTTCGC 57.897 39.130 0.00 0.00 0.00 4.70
7363 8024 7.204496 AGTGATTACGCGATTAGATAGAACT 57.796 36.000 15.93 0.00 0.00 3.01
7387 8049 5.112686 ACAACAACAACACAACAACAAAGT 58.887 33.333 0.00 0.00 0.00 2.66
7407 8069 7.039293 ACAAAGTCTTTAGTCCCAAACAAGTTT 60.039 33.333 0.00 0.00 0.00 2.66
7478 8140 6.015350 GGTTCTGGTACATGAATAGCTAGCTA 60.015 42.308 26.09 26.09 38.20 3.32
7634 8298 2.060383 TCCGCTATGCACTGGAGCT 61.060 57.895 9.31 0.00 33.91 4.09
7648 8312 1.682257 GAGCTTCTGGAGGCCTGTT 59.318 57.895 12.00 0.00 33.44 3.16
7716 8380 9.091784 TCTCTTCAATCGTTGATAGAAAATCAG 57.908 33.333 2.09 0.00 39.84 2.90
7928 8599 5.095490 CGGAATTAAGGAAAATCTGTGCAC 58.905 41.667 10.75 10.75 0.00 4.57
8050 8721 4.633547 ACCCACCGGTGTCTACTT 57.366 55.556 31.80 7.38 42.48 2.24
8179 8851 5.395214 GGGGCAAATTTTAATCTCGACCAAT 60.395 40.000 0.00 0.00 0.00 3.16
8298 9268 6.712095 AGTGAAGCATCTTTACTGTGATTTGA 59.288 34.615 3.64 0.00 0.00 2.69
8311 9281 5.924254 ACTGTGATTTGATTTGACTTGCATG 59.076 36.000 0.00 0.00 0.00 4.06
8320 9290 6.614160 TGATTTGACTTGCATGTTCAGTATG 58.386 36.000 6.70 0.00 37.54 2.39
8325 9295 5.122711 TGACTTGCATGTTCAGTATGTGATG 59.877 40.000 6.70 0.00 37.40 3.07
8360 9330 5.406780 GTCATATTTCTATCTCCAACAGGCG 59.593 44.000 0.00 0.00 0.00 5.52
8612 9582 6.072728 AGCGTGCACATAGAGATAAACAAAAA 60.073 34.615 18.64 0.00 0.00 1.94
8663 9639 1.351017 CATATGTAGAATGGGGCCGGT 59.649 52.381 1.90 0.00 0.00 5.28
8859 9842 7.715249 CCGATTTTCTGGATAGTGGAAGATTTA 59.285 37.037 0.00 0.00 0.00 1.40
9037 10065 0.179145 CACCGTTTAGAGTCGCCGAT 60.179 55.000 0.00 0.00 0.00 4.18
9094 10122 3.057969 TGCTCCCGCATTTATCTATGG 57.942 47.619 0.00 0.00 42.25 2.74
9268 11457 9.483916 TCTAAAATGTCTTACAGAAATGAACGA 57.516 29.630 0.00 0.00 0.00 3.85
9283 11472 4.931661 TGAACGAAGGGAGTATATGTCC 57.068 45.455 0.00 0.00 0.00 4.02
9292 11481 5.071370 AGGGAGTATATGTCCGTCAGTAAG 58.929 45.833 1.01 0.00 34.56 2.34
9345 11535 1.227380 GATCGCCGGATCACAAGCT 60.227 57.895 5.05 0.00 46.81 3.74
9591 11783 1.967319 TCTGCCTTCAAGGACAACAC 58.033 50.000 7.98 0.00 37.67 3.32
9637 11829 4.434857 GCGATCTTCACCTTCTTTTCTTCG 60.435 45.833 0.00 0.00 0.00 3.79
9644 11836 6.340962 TCACCTTCTTTTCTTCGAGTATCA 57.659 37.500 0.00 0.00 33.17 2.15
9656 11848 5.533154 TCTTCGAGTATCATCTTCTTCTCCC 59.467 44.000 0.00 0.00 33.17 4.30
9747 11939 4.792068 TCCATCAACAGTTTGAACCTCTT 58.208 39.130 0.00 0.00 45.01 2.85
9752 11944 1.141053 ACAGTTTGAACCTCTTCGCCT 59.859 47.619 0.00 0.00 0.00 5.52
9858 12050 1.961277 CGCCACACCTTCTCGCTTT 60.961 57.895 0.00 0.00 0.00 3.51
9859 12051 1.507141 CGCCACACCTTCTCGCTTTT 61.507 55.000 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
364 385 2.230508 AGTGAATCGAACTTGCGACCTA 59.769 45.455 0.00 0.00 43.79 3.08
459 595 2.821378 CAAACAGGGATTGCTGATGTGA 59.179 45.455 0.00 0.00 0.00 3.58
515 652 4.142271 TGAAATCAGCACACCGAACTTTTT 60.142 37.500 0.00 0.00 0.00 1.94
540 677 9.489084 GCTAAATCAAACCCTGACTTTTAATTT 57.511 29.630 0.00 0.00 36.69 1.82
541 678 8.870116 AGCTAAATCAAACCCTGACTTTTAATT 58.130 29.630 0.00 0.00 36.69 1.40
622 760 3.331889 TGCCTTTCCTTCTCCTCAATCTT 59.668 43.478 0.00 0.00 0.00 2.40
807 952 1.695114 GCTTGGCTTTGGGTTTGGGT 61.695 55.000 0.00 0.00 0.00 4.51
835 980 1.490574 ACCTGGAGCGAGATTAGCTT 58.509 50.000 0.00 0.00 46.13 3.74
897 1052 3.151022 GCGAGACAGGGAGGGGAG 61.151 72.222 0.00 0.00 0.00 4.30
907 1062 3.800863 GGTCGAGAGCGCGAGACA 61.801 66.667 12.10 0.00 41.49 3.41
972 1127 4.814294 CCACCGACCGGCACTAGC 62.814 72.222 8.55 0.00 39.32 3.42
1027 1192 3.762247 CGGCGGGAGGAAACGGTA 61.762 66.667 0.00 0.00 0.00 4.02
1274 1442 3.659089 CTCCACGTTCCCGGCGAAT 62.659 63.158 9.30 0.00 38.78 3.34
1515 1686 3.305539 GCCAGAACATCAACATTCAGCAA 60.306 43.478 0.00 0.00 0.00 3.91
1571 1743 7.603784 AGCAGTTAATTTTCAGCCCAAATTAAG 59.396 33.333 14.06 8.20 42.57 1.85
1596 1768 1.140852 TGTCCCAGTTGTCAACCTGAG 59.859 52.381 12.17 1.91 0.00 3.35
1651 1823 0.898320 CTGGGTCACACCTGAGGTAG 59.102 60.000 2.59 0.00 38.64 3.18
1932 2104 4.142227 ACCACTATAAATCTTGCTCGTCGT 60.142 41.667 0.00 0.00 0.00 4.34
1973 2145 5.895636 ACATTGACAGAACAGAACAAACA 57.104 34.783 0.00 0.00 0.00 2.83
2266 2445 6.402550 GCAGCATATAACCTACAATTCCATCG 60.403 42.308 0.00 0.00 0.00 3.84
2448 2627 1.759299 CCCTGGGGCATGGACAATG 60.759 63.158 4.27 0.00 39.49 2.82
2585 2764 0.970937 TGGCCTCTACGGTTCTCTGG 60.971 60.000 3.32 0.00 34.25 3.86
2831 3092 2.230992 GCACATGCAGGGTGTTTAATCA 59.769 45.455 18.98 0.00 41.59 2.57
2832 3093 2.879826 GCACATGCAGGGTGTTTAATC 58.120 47.619 18.98 2.10 41.59 1.75
3046 3309 2.678934 AGGTGAGGCGGCTCGTTA 60.679 61.111 30.84 13.70 0.00 3.18
3135 3398 4.742649 AGCGGAGGGAGAGCGTCA 62.743 66.667 0.00 0.00 35.78 4.35
3288 3551 8.845413 ACAGTACTCGACTAATAATACCTAGG 57.155 38.462 7.41 7.41 35.64 3.02
3435 3698 7.043258 TCACGCGTTTATAATATACACCAACAG 60.043 37.037 10.22 0.00 0.00 3.16
3476 3739 4.204012 ACGGAATTCTCACTTGGTTTTCA 58.796 39.130 5.23 0.00 0.00 2.69
3493 3756 5.591067 AGTGTGGTGAAATTTTCTTACGGAA 59.409 36.000 10.33 0.00 0.00 4.30
3885 4303 3.621715 GGTGTAATAAGACAAAGGAGCGG 59.378 47.826 0.00 0.00 0.00 5.52
3914 4332 1.370064 CGAAGGAAACCCACCGACT 59.630 57.895 0.00 0.00 0.00 4.18
4082 4501 4.637276 TCCAACTCGAACTTAATTGCTCA 58.363 39.130 0.00 0.00 0.00 4.26
4106 4525 3.131933 CAGTCCATTCGATCCTCTTCTGT 59.868 47.826 0.00 0.00 0.00 3.41
4277 4821 9.199982 ACAGAAAATATGATGAAAACAAAGCTG 57.800 29.630 0.00 0.00 0.00 4.24
4278 4822 9.415544 GACAGAAAATATGATGAAAACAAAGCT 57.584 29.630 0.00 0.00 0.00 3.74
4301 4846 6.150307 AGCAAAACGGATAACATATGTTGACA 59.850 34.615 27.62 11.23 38.90 3.58
4336 4881 6.409524 TTCTCTACCTTACCAAAAGTTCGA 57.590 37.500 0.00 0.00 0.00 3.71
4345 4890 7.008941 GGATAGGTGTATTCTCTACCTTACCA 58.991 42.308 0.00 0.00 41.93 3.25
4393 4938 7.037873 ACTGGACCAGGTTTTTACAGACATATA 60.038 37.037 25.34 0.00 35.51 0.86
4394 4939 6.134535 TGGACCAGGTTTTTACAGACATAT 57.865 37.500 0.00 0.00 0.00 1.78
4405 4950 2.969821 TATGCACTGGACCAGGTTTT 57.030 45.000 25.34 10.00 35.51 2.43
4422 4967 6.097356 CACTGTCATTTCAGCAAAAGCATAT 58.903 36.000 0.00 0.00 38.84 1.78
4423 4968 5.463286 CACTGTCATTTCAGCAAAAGCATA 58.537 37.500 0.00 0.00 38.84 3.14
4431 4976 1.001048 GCAAGCACTGTCATTTCAGCA 60.001 47.619 0.00 0.00 38.84 4.41
4591 5186 0.266152 GGATGGAAGGGAGAGGGAGA 59.734 60.000 0.00 0.00 0.00 3.71
4619 5214 8.929260 TCAGGAATGCATGATTGTTAGATTAT 57.071 30.769 0.00 0.00 28.45 1.28
4674 5276 2.361757 CACAAACTGCCAAAGTGGATGA 59.638 45.455 0.00 0.00 40.96 2.92
5015 5618 3.333804 TGCGCATGACTGAGAACATTAA 58.666 40.909 5.66 0.00 0.00 1.40
5045 5649 8.133024 TCAAGTGGCATTTATCAAATTAACCT 57.867 30.769 0.00 0.00 0.00 3.50
5068 5672 3.348647 TCTCGGAATTGCCAGAATTCA 57.651 42.857 8.44 0.00 38.15 2.57
5097 5701 6.075467 GCATTTTTCAAAGTTTGGAAATTGCG 60.075 34.615 32.72 19.64 46.60 4.85
5211 5837 5.470845 AATTCTGGCGATTTAGAGAAACG 57.529 39.130 0.00 0.00 0.00 3.60
5269 5896 7.125792 TCCTTAGTCCAAGATGAGGATAAAC 57.874 40.000 0.00 0.00 37.52 2.01
5491 6120 6.127253 CCCTCCGTTCCTAAATACAAGTCTTA 60.127 42.308 0.00 0.00 0.00 2.10
5782 6413 3.217626 ACCTTCAGCTGAGAACAAAAGG 58.782 45.455 21.56 21.56 38.19 3.11
6021 6659 5.695851 TGTTCTCTTTGGATTGCTTCTTC 57.304 39.130 0.00 0.00 0.00 2.87
6076 6714 7.659652 AAATTCCTGAAACAAACACGAAAAA 57.340 28.000 0.00 0.00 0.00 1.94
6077 6715 8.758633 TTAAATTCCTGAAACAAACACGAAAA 57.241 26.923 0.00 0.00 0.00 2.29
6078 6716 8.934507 ATTAAATTCCTGAAACAAACACGAAA 57.065 26.923 0.00 0.00 0.00 3.46
6227 6868 5.449107 TGAGACCACAGAAGTAACTACAC 57.551 43.478 0.00 0.00 0.00 2.90
6246 6894 7.856145 AAGACAAGCCTAAATAAGACATGAG 57.144 36.000 0.00 0.00 0.00 2.90
6309 6957 5.146010 ACTTCAAAGTGGTTTTTGCTGAA 57.854 34.783 0.00 0.00 37.98 3.02
6335 6983 3.691609 CCTGAACTTATGAAACAGGCTCC 59.308 47.826 0.00 0.00 40.90 4.70
6367 7015 4.083271 GGTGCTAAAACTTTCAAGCGATCT 60.083 41.667 0.00 0.00 37.80 2.75
6800 7448 6.786122 TGTACAAACCTTATAAAGAGCCCTT 58.214 36.000 0.00 0.00 0.00 3.95
6914 7563 6.404074 GCTGTAATCTTCTGTGGAAATCCTTG 60.404 42.308 0.44 0.00 36.82 3.61
6984 7633 0.247736 GCATCTCCACCAAGTCGAGT 59.752 55.000 0.00 0.00 0.00 4.18
7333 7994 1.206745 ATCGCGTAATCACTTCGGCG 61.207 55.000 5.77 0.00 0.00 6.46
7363 8024 6.273825 ACTTTGTTGTTGTGTTGTTGTTGTA 58.726 32.000 0.00 0.00 0.00 2.41
7387 8049 5.845391 CCAAACTTGTTTGGGACTAAAGA 57.155 39.130 28.23 0.00 45.86 2.52
7407 8069 1.831736 GTTTCAGCTCTAGCCTACCCA 59.168 52.381 0.00 0.00 43.38 4.51
7582 8244 2.937149 GCTAAAAATGTCGAGAGGGGTC 59.063 50.000 0.00 0.00 0.00 4.46
7634 8298 1.434188 TTCAGAACAGGCCTCCAGAA 58.566 50.000 0.00 0.86 0.00 3.02
7648 8312 4.079844 TGAGATGGTTTGGGCATATTCAGA 60.080 41.667 0.00 0.00 0.00 3.27
7916 8587 5.008619 TGTGTTTGATGTGCACAGATTTT 57.991 34.783 25.84 7.75 38.09 1.82
7928 8599 5.163622 GGGGAGTTCATGTATGTGTTTGATG 60.164 44.000 0.00 0.00 0.00 3.07
8050 8721 1.682740 CATACATGCTGGCCACATCA 58.317 50.000 15.32 8.57 0.00 3.07
8159 8831 9.229784 CAGATCATTGGTCGAGATTAAAATTTG 57.770 33.333 0.00 0.00 0.00 2.32
8179 8851 5.434408 ACTTTTGATGCATAGCTCAGATCA 58.566 37.500 0.00 0.00 0.00 2.92
8298 9268 6.207221 TCACATACTGAACATGCAAGTCAAAT 59.793 34.615 0.00 0.00 0.00 2.32
8311 9281 7.545965 ACAGTTAGCTTACATCACATACTGAAC 59.454 37.037 5.55 0.00 35.62 3.18
8320 9290 9.319143 AGAAATATGACAGTTAGCTTACATCAC 57.681 33.333 10.80 1.22 0.00 3.06
8360 9330 0.740737 ACTCTGCTTTTGTGTGGCAC 59.259 50.000 11.55 11.55 34.56 5.01
8646 9622 1.420138 CTAACCGGCCCCATTCTACAT 59.580 52.381 0.00 0.00 0.00 2.29
8663 9639 2.878406 GTTCTCCTGTTTGCTGCACTAA 59.122 45.455 0.00 0.00 0.00 2.24
8859 9842 4.034858 GCATCATGATCACGATGTCAACTT 59.965 41.667 27.26 0.00 40.93 2.66
8920 9903 4.942483 GCCAGGGAGAATCATCATGATTAG 59.058 45.833 13.09 0.00 46.20 1.73
9094 10122 0.108138 CCACGGACTGATCCCTTGTC 60.108 60.000 0.00 0.00 42.83 3.18
9258 11447 6.424207 GGACATATACTCCCTTCGTTCATTTC 59.576 42.308 0.00 0.00 0.00 2.17
9268 11457 3.912248 ACTGACGGACATATACTCCCTT 58.088 45.455 0.00 0.00 0.00 3.95
9283 11472 7.883229 AAATTTTAAATTGCCCTTACTGACG 57.117 32.000 3.51 0.00 0.00 4.35
9407 11599 2.186826 GCACAAACTGCCGGACTGT 61.187 57.895 5.05 3.87 40.42 3.55
9508 11700 1.820866 AAGGAGGCAGAGGAGGAGGT 61.821 60.000 0.00 0.00 0.00 3.85
9637 11829 4.145807 TCGGGGAGAAGAAGATGATACTC 58.854 47.826 0.00 0.00 0.00 2.59
9644 11836 1.415659 CATGCTCGGGGAGAAGAAGAT 59.584 52.381 0.00 0.00 0.00 2.40
9656 11848 0.813210 GAGAAGAAGGCCATGCTCGG 60.813 60.000 5.01 0.00 0.00 4.63
9717 11909 1.296392 CTGTTGATGGAGGCGACCA 59.704 57.895 8.68 8.68 44.41 4.02
9818 12010 3.452474 GTCAAGATGATGGAGAGGTTCG 58.548 50.000 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.