Multiple sequence alignment - TraesCS7D01G141000

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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 TraesCS7D01G141000 chr7D 100.000 4921 0 0 1 4921 89945959 89941039 0.000000e+00 9088
1 TraesCS7D01G141000 chr7D 96.154 546 19 1 1 544 528098823 528099368 0.000000e+00 891
2 TraesCS7D01G141000 chr7D 86.630 546 71 1 1 544 442170908 442170363 1.960000e-168 603
3 TraesCS7D01G141000 chr7D 94.388 392 19 2 541 932 528100403 528100791 2.530000e-167 599
4 TraesCS7D01G141000 chr7B 89.784 2594 183 28 1672 4208 41046993 41044425 0.000000e+00 3247
5 TraesCS7D01G141000 chr7B 89.806 775 48 11 938 1687 41054542 41053774 0.000000e+00 965
6 TraesCS7D01G141000 chr7B 91.099 191 15 2 4731 4921 41044414 41044226 1.760000e-64 257
7 TraesCS7D01G141000 chr7A 96.353 1755 50 5 1655 3406 91507800 91506057 0.000000e+00 2874
8 TraesCS7D01G141000 chr7A 89.545 220 16 4 3996 4208 91506054 91505835 6.280000e-69 272
9 TraesCS7D01G141000 chr7A 95.890 73 3 0 1574 1646 91507790 91507862 8.650000e-23 119
10 TraesCS7D01G141000 chr2B 85.410 1926 222 35 962 2848 185769850 185771755 0.000000e+00 1945
11 TraesCS7D01G141000 chr2B 85.864 573 61 12 2288 2848 186317527 186316963 4.240000e-165 592
12 TraesCS7D01G141000 chr2B 87.449 494 54 5 1801 2291 186363513 186363025 3.330000e-156 562
13 TraesCS7D01G141000 chr2B 83.904 584 74 10 962 1527 186375524 186374943 1.560000e-149 540
14 TraesCS7D01G141000 chr2B 84.439 437 55 8 3145 3576 185771771 185772199 7.620000e-113 418
15 TraesCS7D01G141000 chr2B 83.957 187 27 1 1610 1793 186371039 186370853 5.060000e-40 176
16 TraesCS7D01G141000 chr2A 84.371 1702 220 31 962 2637 139509144 139510825 0.000000e+00 1628
17 TraesCS7D01G141000 chr2D 83.871 1674 204 34 962 2602 131765378 131767018 0.000000e+00 1535
18 TraesCS7D01G141000 chr2D 84.764 571 72 4 3643 4208 131773701 131774261 4.300000e-155 558
19 TraesCS7D01G141000 chr2D 83.971 418 55 12 2586 2998 131772345 131772755 1.660000e-104 390
20 TraesCS7D01G141000 chr2D 82.671 277 45 2 3714 3987 132699230 132699506 4.920000e-60 243
21 TraesCS7D01G141000 chr2D 80.153 262 50 2 3710 3970 132295628 132295888 1.400000e-45 195
22 TraesCS7D01G141000 chr5A 95.421 546 23 1 1 544 30031053 30031598 0.000000e+00 869
23 TraesCS7D01G141000 chr5A 93.053 547 35 3 1 544 491577603 491578149 0.000000e+00 797
24 TraesCS7D01G141000 chr5A 92.628 529 37 2 18 544 8170100 8170628 0.000000e+00 760
25 TraesCS7D01G141000 chr5A 91.026 546 46 2 1 544 463605561 463606105 0.000000e+00 734
26 TraesCS7D01G141000 chr5A 94.792 384 20 0 541 924 30055463 30055846 2.530000e-167 599
27 TraesCS7D01G141000 chr5A 92.208 385 29 1 541 924 491579185 491579569 1.200000e-150 544
28 TraesCS7D01G141000 chr5A 91.406 384 33 0 541 924 8171589 8171972 1.210000e-145 527
29 TraesCS7D01G141000 chr5A 88.953 344 37 1 541 883 463607139 463607482 1.640000e-114 424
30 TraesCS7D01G141000 chr3A 93.956 546 31 2 1 544 641877715 641878260 0.000000e+00 824
31 TraesCS7D01G141000 chr3A 90.874 515 27 11 4226 4730 548624379 548623875 0.000000e+00 673
32 TraesCS7D01G141000 chr3A 91.906 383 31 0 542 924 641879297 641879679 2.020000e-148 536
33 TraesCS7D01G141000 chr3A 78.229 542 112 6 1 538 729177884 729178423 4.720000e-90 342
34 TraesCS7D01G141000 chr1D 92.277 505 25 6 4230 4730 343741840 343741346 0.000000e+00 704
35 TraesCS7D01G141000 chr1D 91.194 511 23 11 4229 4729 435273336 435272838 0.000000e+00 675
36 TraesCS7D01G141000 chr1D 91.089 505 29 8 4228 4729 388775806 388776297 0.000000e+00 669
37 TraesCS7D01G141000 chr6D 90.680 515 27 9 4226 4730 361141644 361141141 0.000000e+00 665
38 TraesCS7D01G141000 chr3D 90.448 513 30 8 4227 4729 431103409 431103912 0.000000e+00 658
39 TraesCS7D01G141000 chr5B 90.291 515 26 11 4226 4730 433397533 433397033 0.000000e+00 652
40 TraesCS7D01G141000 chr1A 90.116 516 29 9 4226 4730 482687559 482687055 0.000000e+00 651
41 TraesCS7D01G141000 chr6A 89.194 509 39 7 4226 4730 172658596 172658100 5.410000e-174 621
42 TraesCS7D01G141000 chr4A 91.223 376 31 2 550 924 688819987 688819613 1.220000e-140 510
43 TraesCS7D01G141000 chr4A 91.223 376 31 2 550 924 688832746 688832372 1.220000e-140 510
44 TraesCS7D01G141000 chr4B 79.208 505 99 6 1 501 168190572 168191074 3.650000e-91 346
45 TraesCS7D01G141000 chr4B 82.597 362 56 6 559 916 420104816 420104458 3.700000e-81 313


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 TraesCS7D01G141000 chr7D 89941039 89945959 4920 True 9088.0 9088 100.0000 1 4921 1 chr7D.!!$R1 4920
1 TraesCS7D01G141000 chr7D 528098823 528100791 1968 False 745.0 891 95.2710 1 932 2 chr7D.!!$F1 931
2 TraesCS7D01G141000 chr7D 442170363 442170908 545 True 603.0 603 86.6300 1 544 1 chr7D.!!$R2 543
3 TraesCS7D01G141000 chr7B 41044226 41046993 2767 True 1752.0 3247 90.4415 1672 4921 2 chr7B.!!$R2 3249
4 TraesCS7D01G141000 chr7B 41053774 41054542 768 True 965.0 965 89.8060 938 1687 1 chr7B.!!$R1 749
5 TraesCS7D01G141000 chr7A 91505835 91507800 1965 True 1573.0 2874 92.9490 1655 4208 2 chr7A.!!$R1 2553
6 TraesCS7D01G141000 chr2B 185769850 185772199 2349 False 1181.5 1945 84.9245 962 3576 2 chr2B.!!$F1 2614
7 TraesCS7D01G141000 chr2B 186316963 186317527 564 True 592.0 592 85.8640 2288 2848 1 chr2B.!!$R1 560
8 TraesCS7D01G141000 chr2B 186370853 186375524 4671 True 358.0 540 83.9305 962 1793 2 chr2B.!!$R3 831
9 TraesCS7D01G141000 chr2A 139509144 139510825 1681 False 1628.0 1628 84.3710 962 2637 1 chr2A.!!$F1 1675
10 TraesCS7D01G141000 chr2D 131765378 131767018 1640 False 1535.0 1535 83.8710 962 2602 1 chr2D.!!$F1 1640
11 TraesCS7D01G141000 chr2D 131772345 131774261 1916 False 474.0 558 84.3675 2586 4208 2 chr2D.!!$F4 1622
12 TraesCS7D01G141000 chr5A 30031053 30031598 545 False 869.0 869 95.4210 1 544 1 chr5A.!!$F1 543
13 TraesCS7D01G141000 chr5A 491577603 491579569 1966 False 670.5 797 92.6305 1 924 2 chr5A.!!$F5 923
14 TraesCS7D01G141000 chr5A 8170100 8171972 1872 False 643.5 760 92.0170 18 924 2 chr5A.!!$F3 906
15 TraesCS7D01G141000 chr5A 463605561 463607482 1921 False 579.0 734 89.9895 1 883 2 chr5A.!!$F4 882
16 TraesCS7D01G141000 chr3A 641877715 641879679 1964 False 680.0 824 92.9310 1 924 2 chr3A.!!$F2 923
17 TraesCS7D01G141000 chr3A 548623875 548624379 504 True 673.0 673 90.8740 4226 4730 1 chr3A.!!$R1 504
18 TraesCS7D01G141000 chr3A 729177884 729178423 539 False 342.0 342 78.2290 1 538 1 chr3A.!!$F1 537
19 TraesCS7D01G141000 chr6D 361141141 361141644 503 True 665.0 665 90.6800 4226 4730 1 chr6D.!!$R1 504
20 TraesCS7D01G141000 chr3D 431103409 431103912 503 False 658.0 658 90.4480 4227 4729 1 chr3D.!!$F1 502
21 TraesCS7D01G141000 chr5B 433397033 433397533 500 True 652.0 652 90.2910 4226 4730 1 chr5B.!!$R1 504
22 TraesCS7D01G141000 chr1A 482687055 482687559 504 True 651.0 651 90.1160 4226 4730 1 chr1A.!!$R1 504
23 TraesCS7D01G141000 chr4B 168190572 168191074 502 False 346.0 346 79.2080 1 501 1 chr4B.!!$F1 500

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
531 535 0.179034 GCACTATTCTGGAGGCAGGG 60.179 60.000 0.00 0.00 0.00 4.45 F
703 1746 0.459585 GGCACGTCGGCTTCTTATGA 60.460 55.000 0.00 0.00 37.17 2.15 F
1615 6523 0.459934 GCGAGCTCATCTCAACAGCT 60.460 55.000 15.40 0.00 46.42 4.24 F
1618 6526 0.740164 AGCTCATCTCAACAGCTGCG 60.740 55.000 15.27 5.38 42.07 5.18 F
1625 6533 1.201414 TCTCAACAGCTGCGATTCGTA 59.799 47.619 15.27 1.85 0.00 3.43 F
2283 7224 1.273886 ACGGAGAGAGAAGGCAGTTTC 59.726 52.381 0.00 0.00 0.00 2.78 F
3514 8862 1.055040 TTGGCCATTTGGAACTTGGG 58.945 50.000 6.09 0.00 37.39 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1786 6699 0.661552 CATCTGCCCGCAAGATCTTG 59.338 55.000 27.82 27.82 43.14 3.02 R
2117 7030 5.890424 TTCCGGGAAATGTAGAATGAAAC 57.110 39.130 7.09 0.00 0.00 2.78 R
3345 8693 0.674581 TGCTGACATCTTTCGCCAGG 60.675 55.000 0.00 0.00 0.00 4.45 R
3424 8772 0.882927 CCTTCTGCGACGGTTCCAAA 60.883 55.000 0.00 0.00 0.00 3.28 R
3425 8773 1.301401 CCTTCTGCGACGGTTCCAA 60.301 57.895 0.00 0.00 0.00 3.53 R
3637 8986 0.036483 ACATGTCACGGCTGCACATA 60.036 50.000 9.78 0.00 0.00 2.29 R
4804 10172 1.430632 GTCAGCGCCCATTGACATG 59.569 57.895 19.24 2.18 42.47 3.21 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
50 51 3.567164 CCAGGCAGCGAATCAAAGATATT 59.433 43.478 0.00 0.00 0.00 1.28
177 178 4.352298 GGGAAAGGATAAGAGGATGGATGT 59.648 45.833 0.00 0.00 0.00 3.06
198 201 0.598065 GAAATTTGTCAGCGGCAGGT 59.402 50.000 1.45 0.00 0.00 4.00
396 399 1.226311 AGAATTTGGGAGGGCTAGGG 58.774 55.000 0.00 0.00 0.00 3.53
531 535 0.179034 GCACTATTCTGGAGGCAGGG 60.179 60.000 0.00 0.00 0.00 4.45
552 1595 1.961277 GGGGCCGCACTCATATTCG 60.961 63.158 16.21 0.00 0.00 3.34
703 1746 0.459585 GGCACGTCGGCTTCTTATGA 60.460 55.000 0.00 0.00 37.17 2.15
714 1757 4.083643 CGGCTTCTTATGATGCAATAGTGG 60.084 45.833 15.52 0.00 42.84 4.00
834 1878 3.760035 CGCTGGGTACTGGTCGCT 61.760 66.667 0.00 0.00 0.00 4.93
874 1918 2.611971 CCGGAGATCTTGTTTTCGTCCA 60.612 50.000 0.00 0.00 0.00 4.02
887 1931 5.821470 TGTTTTCGTCCATGTAAACCTTGTA 59.179 36.000 0.00 0.00 31.25 2.41
916 1960 2.517650 TAAAAGCTTTGCGGGTTTGG 57.482 45.000 13.54 0.00 37.07 3.28
924 1968 3.398406 CTTTGCGGGTTTGGCTAAAAAT 58.602 40.909 0.00 0.00 0.00 1.82
925 1969 3.477210 TTGCGGGTTTGGCTAAAAATT 57.523 38.095 0.00 0.00 0.00 1.82
927 1971 4.602340 TGCGGGTTTGGCTAAAAATTAA 57.398 36.364 0.00 0.00 0.00 1.40
928 1972 4.957296 TGCGGGTTTGGCTAAAAATTAAA 58.043 34.783 0.00 0.00 0.00 1.52
929 1973 4.750598 TGCGGGTTTGGCTAAAAATTAAAC 59.249 37.500 0.00 0.00 0.00 2.01
930 1974 4.152759 GCGGGTTTGGCTAAAAATTAAACC 59.847 41.667 0.00 0.00 45.86 3.27
931 1975 5.543714 CGGGTTTGGCTAAAAATTAAACCT 58.456 37.500 13.70 0.00 45.86 3.50
932 1976 5.407084 CGGGTTTGGCTAAAAATTAAACCTG 59.593 40.000 13.70 11.86 45.86 4.00
933 1977 6.292923 GGGTTTGGCTAAAAATTAAACCTGT 58.707 36.000 13.70 0.00 45.86 4.00
934 1978 6.425721 GGGTTTGGCTAAAAATTAAACCTGTC 59.574 38.462 13.70 0.00 45.86 3.51
935 1979 7.214381 GGTTTGGCTAAAAATTAAACCTGTCT 58.786 34.615 0.00 0.00 44.17 3.41
936 1980 8.361889 GGTTTGGCTAAAAATTAAACCTGTCTA 58.638 33.333 0.00 0.00 44.17 2.59
976 2025 0.909623 AATTCTACTCCACACCCCCG 59.090 55.000 0.00 0.00 0.00 5.73
1208 2264 1.302511 CCACCACCAGAAACCTCCG 60.303 63.158 0.00 0.00 0.00 4.63
1209 2265 1.302511 CACCACCAGAAACCTCCGG 60.303 63.158 0.00 0.00 0.00 5.14
1239 2295 0.531974 CGTCATGGGATACAACGGGG 60.532 60.000 0.00 0.00 39.74 5.73
1287 2343 0.687427 TCCAGATCTCATCCCGCACA 60.687 55.000 0.00 0.00 0.00 4.57
1314 2370 1.555075 TCTTTTCCCCAGACATCCTCG 59.445 52.381 0.00 0.00 0.00 4.63
1329 2385 0.671251 CCTCGACCTCTACATGGAGC 59.329 60.000 0.00 0.00 32.43 4.70
1332 2388 1.064685 TCGACCTCTACATGGAGCTGA 60.065 52.381 0.00 0.00 32.43 4.26
1334 2390 2.363680 CGACCTCTACATGGAGCTGATT 59.636 50.000 0.00 0.00 32.43 2.57
1459 2526 3.866651 CAAGGAGATTGTCGTCTGGAAT 58.133 45.455 0.00 0.00 33.95 3.01
1552 2628 8.727100 TGATAGGTATCCACAGAGACAATAAT 57.273 34.615 0.00 0.00 35.87 1.28
1615 6523 0.459934 GCGAGCTCATCTCAACAGCT 60.460 55.000 15.40 0.00 46.42 4.24
1618 6526 0.740164 AGCTCATCTCAACAGCTGCG 60.740 55.000 15.27 5.38 42.07 5.18
1625 6533 1.201414 TCTCAACAGCTGCGATTCGTA 59.799 47.619 15.27 1.85 0.00 3.43
1732 6642 9.941325 CTCAGATTTGATTTAGATAGGCATAGT 57.059 33.333 0.00 0.00 31.68 2.12
1769 6682 5.491982 AGATGCCGGATTTGAGGTATTATC 58.508 41.667 5.05 0.00 32.98 1.75
2117 7030 3.496130 CAGAAGTTTCTACACTGCAGGTG 59.504 47.826 19.93 15.72 42.68 4.00
2275 7216 5.766150 ATTGTCATCTACGGAGAGAGAAG 57.234 43.478 2.53 0.00 34.35 2.85
2283 7224 1.273886 ACGGAGAGAGAAGGCAGTTTC 59.726 52.381 0.00 0.00 0.00 2.78
2350 7291 8.460831 AATCTGGCAAAATCGTTAAAATACAC 57.539 30.769 0.00 0.00 0.00 2.90
2725 7676 6.769512 TGCAAGTCTAACTGTAATCCTTTCT 58.230 36.000 0.00 0.00 0.00 2.52
2948 7912 5.184340 ACTGACTTAGTGTGTGTGAGTAC 57.816 43.478 0.00 0.00 38.49 2.73
3345 8693 4.129148 GGTGGCATCCCCAGACCC 62.129 72.222 0.00 0.00 46.54 4.46
3382 8730 2.753452 AGCATCATGTTTCCTGCTTCAG 59.247 45.455 0.00 0.00 42.03 3.02
3407 8755 2.052690 TAGGAGCGGCAGGAGACAC 61.053 63.158 1.45 0.00 0.00 3.67
3424 8772 2.667536 CTGTTGCAGCTGCCTCGT 60.668 61.111 34.64 0.00 41.18 4.18
3425 8773 2.203195 TGTTGCAGCTGCCTCGTT 60.203 55.556 34.64 0.00 41.18 3.85
3435 8783 1.566018 CTGCCTCGTTTGGAACCGTC 61.566 60.000 0.00 0.00 0.00 4.79
3438 8786 1.952133 CTCGTTTGGAACCGTCGCA 60.952 57.895 0.00 0.00 0.00 5.10
3453 8801 2.159226 CGTCGCAGAAGGAGGTAAGATT 60.159 50.000 0.00 0.00 39.69 2.40
3454 8802 3.066342 CGTCGCAGAAGGAGGTAAGATTA 59.934 47.826 0.00 0.00 39.69 1.75
3455 8803 4.261656 CGTCGCAGAAGGAGGTAAGATTAT 60.262 45.833 0.00 0.00 39.69 1.28
3456 8804 5.048921 CGTCGCAGAAGGAGGTAAGATTATA 60.049 44.000 0.00 0.00 39.69 0.98
3457 8805 6.151004 GTCGCAGAAGGAGGTAAGATTATAC 58.849 44.000 0.00 0.00 39.69 1.47
3458 8806 6.016108 GTCGCAGAAGGAGGTAAGATTATACT 60.016 42.308 0.00 0.00 39.69 2.12
3459 8807 6.550108 TCGCAGAAGGAGGTAAGATTATACTT 59.450 38.462 0.00 0.00 0.00 2.24
3460 8808 7.722728 TCGCAGAAGGAGGTAAGATTATACTTA 59.277 37.037 0.00 0.00 0.00 2.24
3507 8855 3.763360 CAGTTAGACATTGGCCATTTGGA 59.237 43.478 6.09 0.00 37.39 3.53
3514 8862 1.055040 TTGGCCATTTGGAACTTGGG 58.945 50.000 6.09 0.00 37.39 4.12
3555 8903 5.025453 AGATTTGTGGGTTTCCATTAGCAT 58.975 37.500 0.00 0.00 46.09 3.79
3615 8963 5.225129 GCACGTTTGCTAATAACTCATTTCG 59.775 40.000 0.00 0.00 46.17 3.46
3617 8965 7.449827 CACGTTTGCTAATAACTCATTTCGTA 58.550 34.615 0.00 0.00 0.00 3.43
3633 8981 7.890763 TCATTTCGTAGAAAGTTTGCAAAAAC 58.109 30.769 14.67 2.88 45.90 2.43
3637 8986 5.099575 CGTAGAAAGTTTGCAAAAACCTGT 58.900 37.500 14.67 1.69 33.28 4.00
3680 9029 6.747280 GTGGTTGAATCATTTATTCTTGTCGG 59.253 38.462 0.00 0.00 43.83 4.79
3731 9080 5.923733 ACAGAGTTCAAGGAATCGATACT 57.076 39.130 0.00 0.00 0.00 2.12
3749 9098 2.281484 GGTCTTGTGCCAAGCCGA 60.281 61.111 9.35 0.00 0.00 5.54
3793 9142 8.777865 ATTGACGTGATATTCAAGAAAGAGAA 57.222 30.769 0.00 0.00 35.25 2.87
3827 9176 0.598065 AACTTAGCAAAGCTTGGGCG 59.402 50.000 15.30 6.49 44.37 6.13
3838 9187 0.316841 GCTTGGGCGAAATGGTTTCA 59.683 50.000 3.66 0.00 39.63 2.69
3842 9191 1.243902 GGGCGAAATGGTTTCACAGA 58.756 50.000 3.66 0.00 39.63 3.41
3846 9195 4.082463 GGGCGAAATGGTTTCACAGAAATA 60.082 41.667 3.66 0.00 39.63 1.40
3860 9209 5.470098 TCACAGAAATAGTGTTCCAGAAAGC 59.530 40.000 0.00 0.00 38.16 3.51
3914 9263 2.100605 AGTTAACACAGCAGCTAGGC 57.899 50.000 8.61 0.00 0.00 3.93
3918 9267 1.772819 AACACAGCAGCTAGGCACCT 61.773 55.000 0.00 0.00 35.83 4.00
3924 9273 0.393537 GCAGCTAGGCACCTGATTGT 60.394 55.000 0.00 0.00 0.00 2.71
3941 9290 3.420397 GTCTGTTCCTACAGGCGAC 57.580 57.895 5.55 0.00 46.08 5.19
3965 9314 3.654806 AGCTAGGTGGCATAAATCTGGAT 59.345 43.478 0.00 0.00 34.17 3.41
4015 9365 5.382303 CGTGAATGTTAACCACTTGTCATC 58.618 41.667 2.48 0.00 0.00 2.92
4085 9437 2.417933 CTGCCTCATGAACTGTGCTTAC 59.582 50.000 0.00 0.00 0.00 2.34
4110 9462 6.121776 TCTTCTGAGCCTTGGTTGTTTATA 57.878 37.500 0.00 0.00 0.00 0.98
4129 9481 8.402472 TGTTTATAAACTTTTATCTGGCGATGG 58.598 33.333 24.81 0.00 39.59 3.51
4140 9495 0.251121 TGGCGATGGTTTGGTGATGT 60.251 50.000 0.00 0.00 0.00 3.06
4208 9564 4.890088 TGCCAACTAAGTACAAGTAGGTG 58.110 43.478 8.56 8.56 35.23 4.00
4209 9565 4.589798 TGCCAACTAAGTACAAGTAGGTGA 59.410 41.667 14.54 0.00 37.23 4.02
4211 9567 5.581085 GCCAACTAAGTACAAGTAGGTGATG 59.419 44.000 14.54 4.17 37.23 3.07
4212 9568 6.573680 GCCAACTAAGTACAAGTAGGTGATGA 60.574 42.308 14.54 0.00 37.23 2.92
4213 9569 7.383687 CCAACTAAGTACAAGTAGGTGATGAA 58.616 38.462 14.54 0.00 37.23 2.57
4214 9570 7.545965 CCAACTAAGTACAAGTAGGTGATGAAG 59.454 40.741 14.54 0.00 37.23 3.02
4215 9571 6.631962 ACTAAGTACAAGTAGGTGATGAAGC 58.368 40.000 0.00 0.00 0.00 3.86
4216 9572 5.483685 AAGTACAAGTAGGTGATGAAGCA 57.516 39.130 0.00 0.00 0.00 3.91
4218 9574 6.054860 AGTACAAGTAGGTGATGAAGCATT 57.945 37.500 0.00 0.00 0.00 3.56
4219 9575 5.877012 AGTACAAGTAGGTGATGAAGCATTG 59.123 40.000 0.00 0.00 0.00 2.82
4220 9576 4.655963 ACAAGTAGGTGATGAAGCATTGT 58.344 39.130 0.00 0.00 0.00 2.71
4221 9577 5.804639 ACAAGTAGGTGATGAAGCATTGTA 58.195 37.500 0.00 0.00 31.83 2.41
4222 9578 6.418101 ACAAGTAGGTGATGAAGCATTGTAT 58.582 36.000 0.00 0.00 31.83 2.29
4223 9579 6.886459 ACAAGTAGGTGATGAAGCATTGTATT 59.114 34.615 0.00 0.00 31.83 1.89
4224 9580 7.066284 ACAAGTAGGTGATGAAGCATTGTATTC 59.934 37.037 0.00 0.00 31.83 1.75
4275 9632 0.322816 GGTGATGATGGTGTGCCTGT 60.323 55.000 0.00 0.00 35.27 4.00
4276 9633 1.089920 GTGATGATGGTGTGCCTGTC 58.910 55.000 0.00 0.00 35.27 3.51
4277 9634 0.691904 TGATGATGGTGTGCCTGTCA 59.308 50.000 0.00 0.00 35.64 3.58
4278 9635 1.282738 TGATGATGGTGTGCCTGTCAT 59.717 47.619 0.00 0.00 40.71 3.06
4279 9636 1.945394 GATGATGGTGTGCCTGTCATC 59.055 52.381 12.83 12.83 43.32 2.92
4280 9637 0.035152 TGATGGTGTGCCTGTCATCC 60.035 55.000 0.00 0.00 36.21 3.51
4281 9638 0.254178 GATGGTGTGCCTGTCATCCT 59.746 55.000 0.00 0.00 35.27 3.24
4282 9639 0.034767 ATGGTGTGCCTGTCATCCTG 60.035 55.000 0.00 0.00 35.27 3.86
4283 9640 1.376466 GGTGTGCCTGTCATCCTGT 59.624 57.895 0.00 0.00 0.00 4.00
4369 9726 5.957771 ATAAAAGATACCTGCACCTCTCA 57.042 39.130 0.00 0.00 0.00 3.27
4409 9766 1.757118 CTTGCCTCCTTCATCGTCCTA 59.243 52.381 0.00 0.00 0.00 2.94
4414 9771 3.070302 GCCTCCTTCATCGTCCTAATCTT 59.930 47.826 0.00 0.00 0.00 2.40
4416 9773 4.342378 CCTCCTTCATCGTCCTAATCTTCA 59.658 45.833 0.00 0.00 0.00 3.02
4502 9869 2.597340 CGTCCATCCCCATGCCTT 59.403 61.111 0.00 0.00 0.00 4.35
4540 9907 1.532078 TCACCACCACGCTCCACTA 60.532 57.895 0.00 0.00 0.00 2.74
4566 9933 6.439487 TCCTCACCTTATCTCTCATCTTTCT 58.561 40.000 0.00 0.00 0.00 2.52
4655 10023 2.779430 ACATGGGATTACTCCTGCATGA 59.221 45.455 18.85 0.00 40.74 3.07
4773 10141 3.521531 TGTGGGTGATGAAGCTATTGGTA 59.478 43.478 0.00 0.00 0.00 3.25
4779 10147 5.067674 GGTGATGAAGCTATTGGTAATTGCA 59.932 40.000 9.81 0.00 41.19 4.08
4780 10148 6.239120 GGTGATGAAGCTATTGGTAATTGCAT 60.239 38.462 9.81 0.00 41.19 3.96
4787 10155 6.799512 AGCTATTGGTAATTGCATTTGTCTC 58.200 36.000 4.11 0.00 41.19 3.36
4788 10156 6.377996 AGCTATTGGTAATTGCATTTGTCTCA 59.622 34.615 4.11 0.00 41.19 3.27
4804 10172 3.561310 TGTCTCAGTCACTTGATTGTTGC 59.439 43.478 2.10 0.00 34.01 4.17
4811 10179 4.338964 AGTCACTTGATTGTTGCATGTCAA 59.661 37.500 0.00 0.00 0.00 3.18
4821 10189 2.409055 GCATGTCAATGGGCGCTGA 61.409 57.895 7.64 0.00 34.09 4.26
4826 10194 3.803082 CAATGGGCGCTGACGGTG 61.803 66.667 7.64 0.00 40.57 4.94
4848 10216 7.040478 CGGTGTGTCAATTATCATGGGAAATAT 60.040 37.037 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 1.881973 GACTCATTCTGCACAGCCAAA 59.118 47.619 0.00 0.00 0.00 3.28
177 178 2.083774 CCTGCCGCTGACAAATTTCTA 58.916 47.619 0.00 0.00 0.00 2.10
198 201 9.174166 GCCACAGATTTTATAAGAACCTCTTTA 57.826 33.333 0.00 0.00 37.89 1.85
276 279 8.837788 TTATGGTTGATGTTATGCTCTCATAG 57.162 34.615 0.00 0.00 36.60 2.23
278 281 6.713903 CCTTATGGTTGATGTTATGCTCTCAT 59.286 38.462 0.00 0.00 36.73 2.90
396 399 2.491675 AAATCTCAAGGTCCCGGAAC 57.508 50.000 0.73 0.00 0.00 3.62
531 535 0.751643 AATATGAGTGCGGCCCCAAC 60.752 55.000 0.00 0.00 0.00 3.77
552 1595 3.322254 ACCTCAGGGTCATCGATATTGTC 59.678 47.826 0.00 0.00 43.38 3.18
566 1609 0.396811 ACGTCTCCAAAACCTCAGGG 59.603 55.000 0.00 0.00 38.88 4.45
656 1699 4.326826 TGATTGCCTCTACCACTTTCTTG 58.673 43.478 0.00 0.00 0.00 3.02
698 1741 8.759481 TTATTTCACCCACTATTGCATCATAA 57.241 30.769 0.00 0.00 0.00 1.90
703 1746 6.543831 GTCTCTTATTTCACCCACTATTGCAT 59.456 38.462 0.00 0.00 0.00 3.96
714 1757 3.528597 AGCTCGGTCTCTTATTTCACC 57.471 47.619 0.00 0.00 0.00 4.02
874 1918 4.354893 TCACCCGTTACAAGGTTTACAT 57.645 40.909 0.00 0.00 32.72 2.29
887 1931 3.649073 GCAAAGCTTTTATTCACCCGTT 58.351 40.909 9.53 0.00 0.00 4.44
916 1960 8.950403 CTGTGTAGACAGGTTTAATTTTTAGC 57.050 34.615 12.14 0.00 45.26 3.09
931 1975 6.971726 TTTTTAGGAGAGACTGTGTAGACA 57.028 37.500 0.00 0.00 0.00 3.41
958 2002 1.623542 GCGGGGGTGTGGAGTAGAAT 61.624 60.000 0.00 0.00 0.00 2.40
959 2003 2.288025 GCGGGGGTGTGGAGTAGAA 61.288 63.158 0.00 0.00 0.00 2.10
976 2025 2.094659 CGTCGACTGGATGTGGTGC 61.095 63.158 14.70 0.00 0.00 5.01
1208 2264 3.148279 ATGACGAGGCCGAGGACC 61.148 66.667 0.00 0.00 39.50 4.46
1209 2265 2.105128 CATGACGAGGCCGAGGAC 59.895 66.667 0.00 0.00 39.50 3.85
1239 2295 0.390472 CTGGACCTGAAGAACGGCTC 60.390 60.000 0.00 0.00 0.00 4.70
1287 2343 1.954382 GTCTGGGGAAAAGAAACGCTT 59.046 47.619 0.00 0.00 38.88 4.68
1299 2355 1.381327 GGTCGAGGATGTCTGGGGA 60.381 63.158 0.00 0.00 0.00 4.81
1301 2357 0.396417 AGAGGTCGAGGATGTCTGGG 60.396 60.000 0.00 0.00 0.00 4.45
1314 2370 3.494048 CCAATCAGCTCCATGTAGAGGTC 60.494 52.174 1.24 0.00 42.56 3.85
1410 2477 3.567579 ATTGGTGGGACGGCCACAG 62.568 63.158 11.00 0.00 39.66 3.66
1455 2522 3.747976 AAAGCACGGCGCCATTCC 61.748 61.111 28.98 11.33 44.04 3.01
1456 2523 2.504681 CAAAGCACGGCGCCATTC 60.505 61.111 28.98 14.05 44.04 2.67
1501 2568 2.989639 CTCGAGTGGCAATCCCCA 59.010 61.111 9.62 0.00 0.00 4.96
1615 6523 5.861787 CAGGTCATACATATTACGAATCGCA 59.138 40.000 1.15 0.00 0.00 5.10
1618 6526 7.061905 CGGTTCAGGTCATACATATTACGAATC 59.938 40.741 0.00 0.00 0.00 2.52
1625 6533 4.202326 GGGACGGTTCAGGTCATACATATT 60.202 45.833 0.00 0.00 36.12 1.28
1657 6565 3.130340 CCCAATAAACAGAATCCCCAACG 59.870 47.826 0.00 0.00 0.00 4.10
1732 6642 6.769134 TCCGGCATCTCGATATTAAATAGA 57.231 37.500 0.00 0.00 0.00 1.98
1786 6699 0.661552 CATCTGCCCGCAAGATCTTG 59.338 55.000 27.82 27.82 43.14 3.02
2117 7030 5.890424 TTCCGGGAAATGTAGAATGAAAC 57.110 39.130 7.09 0.00 0.00 2.78
2948 7912 2.094752 CCGGCTGGTTAGGAATGTTTTG 60.095 50.000 2.29 0.00 0.00 2.44
2982 7960 0.828022 TACCAACAGGTATGGCCGAG 59.172 55.000 0.00 0.00 41.89 4.63
3345 8693 0.674581 TGCTGACATCTTTCGCCAGG 60.675 55.000 0.00 0.00 0.00 4.45
3382 8730 3.075005 TGCCGCTCCTACTCCCAC 61.075 66.667 0.00 0.00 0.00 4.61
3407 8755 1.789078 AAACGAGGCAGCTGCAACAG 61.789 55.000 37.63 26.32 44.36 3.16
3424 8772 0.882927 CCTTCTGCGACGGTTCCAAA 60.883 55.000 0.00 0.00 0.00 3.28
3425 8773 1.301401 CCTTCTGCGACGGTTCCAA 60.301 57.895 0.00 0.00 0.00 3.53
3435 8783 6.334102 AGTATAATCTTACCTCCTTCTGCG 57.666 41.667 0.00 0.00 0.00 5.18
3482 8830 2.489938 TGGCCAATGTCTAACTGGTC 57.510 50.000 0.61 0.00 35.31 4.02
3531 8879 4.837860 TGCTAATGGAAACCCACAAATCTT 59.162 37.500 0.00 0.00 36.36 2.40
3555 8903 9.066892 GGTGCAATCATTCTACATTAAGGATAA 57.933 33.333 0.00 0.00 28.05 1.75
3615 8963 7.704899 ACATACAGGTTTTTGCAAACTTTCTAC 59.295 33.333 12.39 3.64 41.92 2.59
3617 8965 6.534793 CACATACAGGTTTTTGCAAACTTTCT 59.465 34.615 12.39 4.64 41.92 2.52
3633 8981 1.079197 TCACGGCTGCACATACAGG 60.079 57.895 0.50 0.00 38.16 4.00
3637 8986 0.036483 ACATGTCACGGCTGCACATA 60.036 50.000 9.78 0.00 0.00 2.29
3680 9029 2.953466 TGTCTAACGTATCTGTGGGC 57.047 50.000 0.00 0.00 0.00 5.36
3749 9098 5.462398 GTCAATTCGAGTTTGTGTCAGTACT 59.538 40.000 9.24 0.00 0.00 2.73
3793 9142 5.869579 TGCTAAGTTTTGATCTTGTCTCCT 58.130 37.500 0.00 0.00 0.00 3.69
3827 9176 7.595130 GGAACACTATTTCTGTGAAACCATTTC 59.405 37.037 0.00 0.00 38.65 2.17
3838 9187 5.376625 TGCTTTCTGGAACACTATTTCTGT 58.623 37.500 0.00 0.00 0.00 3.41
3842 9191 5.068987 TGCTTTGCTTTCTGGAACACTATTT 59.931 36.000 0.00 0.00 0.00 1.40
3846 9195 2.360165 CTGCTTTGCTTTCTGGAACACT 59.640 45.455 0.00 0.00 0.00 3.55
3860 9209 0.820891 AGTGTGGGCAGTCTGCTTTG 60.821 55.000 23.68 0.00 44.28 2.77
3914 9263 4.271696 TGTAGGAACAGACAATCAGGTG 57.728 45.455 0.00 0.00 0.00 4.00
3941 9290 3.062763 CAGATTTATGCCACCTAGCTCG 58.937 50.000 0.00 0.00 0.00 5.03
3965 9314 0.472471 ACGGAAGTTCTTCCTTGGCA 59.528 50.000 23.55 0.00 46.40 4.92
3969 9318 5.236282 GCTTAACTACGGAAGTTCTTCCTT 58.764 41.667 23.55 18.68 45.64 3.36
3986 9335 5.352643 AGTGGTTAACATTCACGCTTAAC 57.647 39.130 8.10 0.00 36.60 2.01
3987 9336 5.297278 ACAAGTGGTTAACATTCACGCTTAA 59.703 36.000 8.10 0.00 36.60 1.85
3990 9339 3.211045 ACAAGTGGTTAACATTCACGCT 58.789 40.909 8.10 0.00 36.60 5.07
3991 9340 3.002862 TGACAAGTGGTTAACATTCACGC 59.997 43.478 8.10 0.00 36.60 5.34
4015 9365 2.306341 AAGGCATGAGTCATCAGTCG 57.694 50.000 1.56 0.00 39.29 4.18
4085 9437 2.856222 ACAACCAAGGCTCAGAAGAAG 58.144 47.619 0.00 0.00 0.00 2.85
4110 9462 5.469479 CAAACCATCGCCAGATAAAAGTTT 58.531 37.500 0.00 0.00 34.85 2.66
4140 9495 7.817418 AAGTTGAGAAACTAGCAAAATGGTA 57.183 32.000 0.00 0.00 31.72 3.25
4188 9544 6.931838 TCATCACCTACTTGTACTTAGTTGG 58.068 40.000 19.47 19.47 42.07 3.77
4209 9565 9.217278 GTAGAGATGATGAATACAATGCTTCAT 57.783 33.333 10.26 10.26 43.07 2.57
4211 9567 8.830201 AGTAGAGATGATGAATACAATGCTTC 57.170 34.615 0.00 0.00 0.00 3.86
4212 9568 8.649591 AGAGTAGAGATGATGAATACAATGCTT 58.350 33.333 0.00 0.00 0.00 3.91
4213 9569 8.192743 AGAGTAGAGATGATGAATACAATGCT 57.807 34.615 0.00 0.00 0.00 3.79
4214 9570 8.830201 AAGAGTAGAGATGATGAATACAATGC 57.170 34.615 0.00 0.00 0.00 3.56
4275 9632 8.807118 GGTCTATATTACAAGATGACAGGATGA 58.193 37.037 0.00 0.00 39.69 2.92
4276 9633 7.757173 CGGTCTATATTACAAGATGACAGGATG 59.243 40.741 0.00 0.00 46.00 3.51
4277 9634 7.451877 ACGGTCTATATTACAAGATGACAGGAT 59.548 37.037 0.00 0.00 0.00 3.24
4278 9635 6.776116 ACGGTCTATATTACAAGATGACAGGA 59.224 38.462 0.00 0.00 0.00 3.86
4279 9636 6.982852 ACGGTCTATATTACAAGATGACAGG 58.017 40.000 0.00 0.00 0.00 4.00
4280 9637 7.085116 GGACGGTCTATATTACAAGATGACAG 58.915 42.308 8.23 0.00 0.00 3.51
4281 9638 6.293790 CGGACGGTCTATATTACAAGATGACA 60.294 42.308 8.23 0.00 0.00 3.58
4282 9639 6.072838 TCGGACGGTCTATATTACAAGATGAC 60.073 42.308 8.23 0.00 0.00 3.06
4283 9640 5.999600 TCGGACGGTCTATATTACAAGATGA 59.000 40.000 8.23 0.00 0.00 2.92
4348 9705 4.081087 GGTGAGAGGTGCAGGTATCTTTTA 60.081 45.833 0.00 0.00 0.00 1.52
4359 9716 2.105649 TGTAAATGTGGTGAGAGGTGCA 59.894 45.455 0.00 0.00 0.00 4.57
4369 9726 1.960689 GGCCTTGTGTGTAAATGTGGT 59.039 47.619 0.00 0.00 0.00 4.16
4397 9754 6.183360 GGTTGTTGAAGATTAGGACGATGAAG 60.183 42.308 0.00 0.00 0.00 3.02
4481 9848 4.935495 CATGGGGATGGACGGCGG 62.935 72.222 13.24 0.00 0.00 6.13
4540 9907 5.402054 AGATGAGAGATAAGGTGAGGAGT 57.598 43.478 0.00 0.00 0.00 3.85
4579 9946 6.623486 TCGAAAAACTGGTATCTCGACAATA 58.377 36.000 0.00 0.00 30.94 1.90
4626 9994 6.096846 GCAGGAGTAATCCCATGTGTAAAAAT 59.903 38.462 5.39 0.00 0.00 1.82
4686 10054 2.950975 TGCACGGAACATCAATATGCAT 59.049 40.909 3.79 3.79 36.50 3.96
4735 10103 8.472413 CATCACCCACAAGAAGATCAAAATAAT 58.528 33.333 0.00 0.00 0.00 1.28
4742 10110 4.582869 CTTCATCACCCACAAGAAGATCA 58.417 43.478 0.00 0.00 38.30 2.92
4773 10141 5.300034 TCAAGTGACTGAGACAAATGCAATT 59.700 36.000 0.00 0.00 38.98 2.32
4779 10147 6.732154 CAACAATCAAGTGACTGAGACAAAT 58.268 36.000 0.00 0.00 0.00 2.32
4780 10148 5.449041 GCAACAATCAAGTGACTGAGACAAA 60.449 40.000 0.00 0.00 0.00 2.83
4787 10155 4.224433 GACATGCAACAATCAAGTGACTG 58.776 43.478 0.00 0.00 0.00 3.51
4788 10156 3.884693 TGACATGCAACAATCAAGTGACT 59.115 39.130 0.00 0.00 0.00 3.41
4804 10172 1.430632 GTCAGCGCCCATTGACATG 59.569 57.895 19.24 2.18 42.47 3.21
4821 10189 3.054728 TCCCATGATAATTGACACACCGT 60.055 43.478 0.00 0.00 0.00 4.83
4848 10216 8.039603 ACTTCGCAGATGATGTAATAACAAAA 57.960 30.769 0.00 0.00 35.94 2.44
4855 10223 4.813161 CCAGAACTTCGCAGATGATGTAAT 59.187 41.667 0.00 0.00 35.04 1.89
4863 10231 3.902881 AGATTCCAGAACTTCGCAGAT 57.097 42.857 0.00 0.00 35.04 2.90


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

AutoCloner maintained by Alex Coulton.