Multiple sequence alignment - TraesCS4D01G026000

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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 TraesCS4D01G026000 chr4D 100.000 2828 0 0 1 2828 11166112 11163285 0.000000e+00 5223
1 TraesCS4D01G026000 chr4D 80.100 1005 151 29 826 1788 11115823 11114826 0.000000e+00 704
2 TraesCS4D01G026000 chr4D 79.502 1044 171 24 755 1783 431674252 431673237 0.000000e+00 702
3 TraesCS4D01G026000 chr4D 78.571 1050 181 24 755 1794 431620890 431619875 0.000000e+00 652
4 TraesCS4D01G026000 chr4D 78.495 1023 176 17 791 1783 10828993 10830001 5.140000e-177 630
5 TraesCS4D01G026000 chr4D 78.006 1023 181 17 791 1783 10811224 10812232 1.120000e-168 603
6 TraesCS4D01G026000 chr4D 80.990 626 84 22 826 1419 11133091 11132469 5.520000e-127 464
7 TraesCS4D01G026000 chr4D 86.552 290 34 5 2502 2789 212032177 212031891 5.880000e-82 315
8 TraesCS4D01G026000 chr4D 86.552 290 34 5 2502 2789 222210883 222210597 5.880000e-82 315
9 TraesCS4D01G026000 chr4D 81.851 281 28 6 2021 2280 467190396 467190674 6.140000e-52 215
10 TraesCS4D01G026000 chr4B 91.234 2042 128 20 3 2034 21159182 21157182 0.000000e+00 2732
11 TraesCS4D01G026000 chr4B 81.965 865 138 11 932 1786 21153424 21152568 0.000000e+00 717
12 TraesCS4D01G026000 chr4B 81.734 865 140 11 932 1786 21151763 21150907 0.000000e+00 706
13 TraesCS4D01G026000 chr4B 90.476 294 25 2 2180 2473 21157117 21156827 4.420000e-103 385
14 TraesCS4D01G026000 chr4B 80.162 494 55 22 1817 2277 641425344 641424861 2.100000e-86 329
15 TraesCS4D01G026000 chr4B 77.509 289 34 15 2018 2277 70575385 70575671 8.170000e-31 145
16 TraesCS4D01G026000 chr4A 91.314 1324 79 12 789 2099 591244685 591245985 0.000000e+00 1775
17 TraesCS4D01G026000 chr4A 92.580 283 17 2 2192 2473 591247069 591247348 1.220000e-108 403
18 TraesCS4D01G026000 chr4A 87.814 279 18 6 2472 2737 591247428 591247703 2.120000e-81 313
19 TraesCS4D01G026000 chr4A 87.500 128 8 6 2155 2280 577217476 577217355 1.060000e-29 141
20 TraesCS4D01G026000 chr4A 85.593 118 9 6 631 743 591244185 591244299 1.780000e-22 117
21 TraesCS4D01G026000 chrUn 81.713 1039 156 18 755 1786 256114634 256115645 0.000000e+00 835
22 TraesCS4D01G026000 chrUn 81.713 1039 156 18 755 1786 390478455 390479466 0.000000e+00 835
23 TraesCS4D01G026000 chr5B 81.713 1039 156 18 755 1786 660880372 660879361 0.000000e+00 835
24 TraesCS4D01G026000 chr5B 81.382 1042 160 16 755 1786 660926321 660925304 0.000000e+00 819
25 TraesCS4D01G026000 chr5B 82.746 284 24 14 2021 2282 592312301 592312021 2.190000e-56 230
26 TraesCS4D01G026000 chr5B 80.783 281 32 8 2021 2280 115420643 115420922 1.720000e-47 200
27 TraesCS4D01G026000 chr2D 90.370 270 21 5 2516 2781 126681578 126681310 1.610000e-92 350
28 TraesCS4D01G026000 chr2D 88.489 278 28 4 2502 2778 268200238 268200512 1.620000e-87 333
29 TraesCS4D01G026000 chr2D 87.981 208 20 2 1817 2024 120561291 120561493 1.010000e-59 241
30 TraesCS4D01G026000 chr6B 89.011 273 26 4 2516 2785 684141386 684141115 4.510000e-88 335
31 TraesCS4D01G026000 chr6B 80.822 292 33 13 2007 2277 652122490 652122779 1.030000e-49 207
32 TraesCS4D01G026000 chr3B 87.719 285 30 5 2502 2784 244451911 244452192 7.550000e-86 327
33 TraesCS4D01G026000 chr3B 81.655 278 30 14 2020 2277 607429236 607429512 7.940000e-51 211
34 TraesCS4D01G026000 chr3B 88.393 112 9 3 2180 2291 458011291 458011184 6.360000e-27 132
35 TraesCS4D01G026000 chr2B 87.589 282 30 5 2504 2783 36267671 36267949 3.510000e-84 322
36 TraesCS4D01G026000 chr2B 81.533 287 28 10 2016 2280 450333823 450333540 2.210000e-51 213
37 TraesCS4D01G026000 chr7D 87.063 286 31 6 2504 2786 228407477 228407195 4.550000e-83 318
38 TraesCS4D01G026000 chr7D 87.864 206 21 1 1817 2022 37000854 37000653 3.640000e-59 239
39 TraesCS4D01G026000 chr3D 87.544 281 28 6 2503 2781 14382739 14383014 4.550000e-83 318
40 TraesCS4D01G026000 chr2A 79.276 497 61 21 1817 2279 722516490 722516002 2.740000e-80 309
41 TraesCS4D01G026000 chr2A 82.867 286 25 14 2014 2277 39930249 39930532 4.710000e-58 235
42 TraesCS4D01G026000 chr2A 81.495 281 29 12 2020 2279 710664460 710664182 2.850000e-50 209
43 TraesCS4D01G026000 chr7B 83.039 283 40 6 1853 2133 594403578 594403302 1.680000e-62 250
44 TraesCS4D01G026000 chr6A 83.895 267 33 7 1853 2116 615124871 615124612 2.180000e-61 246
45 TraesCS4D01G026000 chr5D 86.957 207 23 1 1817 2023 260866186 260866388 2.190000e-56 230
46 TraesCS4D01G026000 chr5D 87.255 204 21 4 1818 2021 560223897 560224095 7.880000e-56 228
47 TraesCS4D01G026000 chr1B 81.979 283 28 13 2018 2279 521740457 521740737 4.740000e-53 219
48 TraesCS4D01G026000 chr7A 79.197 274 32 13 2026 2277 66452242 66452512 1.740000e-37 167
49 TraesCS4D01G026000 chr1D 92.000 100 7 1 2180 2279 439031676 439031774 3.800000e-29 139


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 TraesCS4D01G026000 chr4D 11163285 11166112 2827 True 5223 5223 100.00000 1 2828 1 chr4D.!!$R3 2827
1 TraesCS4D01G026000 chr4D 11114826 11115823 997 True 704 704 80.10000 826 1788 1 chr4D.!!$R1 962
2 TraesCS4D01G026000 chr4D 431673237 431674252 1015 True 702 702 79.50200 755 1783 1 chr4D.!!$R7 1028
3 TraesCS4D01G026000 chr4D 431619875 431620890 1015 True 652 652 78.57100 755 1794 1 chr4D.!!$R6 1039
4 TraesCS4D01G026000 chr4D 10828993 10830001 1008 False 630 630 78.49500 791 1783 1 chr4D.!!$F2 992
5 TraesCS4D01G026000 chr4D 10811224 10812232 1008 False 603 603 78.00600 791 1783 1 chr4D.!!$F1 992
6 TraesCS4D01G026000 chr4D 11132469 11133091 622 True 464 464 80.99000 826 1419 1 chr4D.!!$R2 593
7 TraesCS4D01G026000 chr4B 21150907 21159182 8275 True 1135 2732 86.35225 3 2473 4 chr4B.!!$R2 2470
8 TraesCS4D01G026000 chr4A 591244185 591247703 3518 False 652 1775 89.32525 631 2737 4 chr4A.!!$F1 2106
9 TraesCS4D01G026000 chrUn 256114634 256115645 1011 False 835 835 81.71300 755 1786 1 chrUn.!!$F1 1031
10 TraesCS4D01G026000 chrUn 390478455 390479466 1011 False 835 835 81.71300 755 1786 1 chrUn.!!$F2 1031
11 TraesCS4D01G026000 chr5B 660879361 660880372 1011 True 835 835 81.71300 755 1786 1 chr5B.!!$R2 1031
12 TraesCS4D01G026000 chr5B 660925304 660926321 1017 True 819 819 81.38200 755 1786 1 chr5B.!!$R3 1031

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
279 280 0.032540 GGGTTCGGTTGACTACACGT 59.967 55.0 0.00 0.00 0.00 4.49 F
606 613 0.108329 TTAGACGTAGGCTTGCAGGC 60.108 55.0 13.24 13.24 41.73 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1562 6825 0.391597 AAAGGCGGACTTGAAGACGA 59.608 50.0 15.53 0.0 39.96 4.20 R
2443 8737 0.378257 CGATATGTTGCTGGTGTGCC 59.622 55.0 0.00 0.0 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
18 19 2.109799 CGCCTAGGACATGCCCTG 59.890 66.667 14.75 0.78 37.10 4.45
21 22 2.377810 CCTAGGACATGCCCTGCCA 61.378 63.158 11.39 0.00 37.10 4.92
73 74 1.676967 CTGCCAGCAAACTCCTCCC 60.677 63.158 0.00 0.00 0.00 4.30
86 87 2.587777 ACTCCTCCCTCCTGTGATCTTA 59.412 50.000 0.00 0.00 0.00 2.10
88 89 4.230455 CTCCTCCCTCCTGTGATCTTATT 58.770 47.826 0.00 0.00 0.00 1.40
94 95 3.633986 CCTCCTGTGATCTTATTTTGGCC 59.366 47.826 0.00 0.00 0.00 5.36
106 107 0.321653 TTTTGGCCCTCTCGCTTCTC 60.322 55.000 0.00 0.00 0.00 2.87
110 111 2.492090 CCCTCTCGCTTCTCCACG 59.508 66.667 0.00 0.00 0.00 4.94
111 112 2.202676 CCTCTCGCTTCTCCACGC 60.203 66.667 0.00 0.00 0.00 5.34
112 113 2.568612 CTCTCGCTTCTCCACGCA 59.431 61.111 0.00 0.00 0.00 5.24
193 194 3.056107 CCGGGTGTATCGTCCATATGAAT 60.056 47.826 3.65 0.00 0.00 2.57
249 250 2.502130 TGTACCATGACATTCGCCCTTA 59.498 45.455 0.00 0.00 0.00 2.69
278 279 1.005294 CGGGTTCGGTTGACTACACG 61.005 60.000 0.00 0.00 0.00 4.49
279 280 0.032540 GGGTTCGGTTGACTACACGT 59.967 55.000 0.00 0.00 0.00 4.49
322 323 0.456995 GTCCTCTTCGAACTCGCTGG 60.457 60.000 0.00 0.00 39.60 4.85
353 354 2.156098 AGAGTCGACAGTCTCAAGGAC 58.844 52.381 19.50 0.00 44.80 3.85
360 361 4.891566 GTCTCAAGGACGATGCGT 57.108 55.556 0.00 0.00 45.10 5.24
369 370 3.207354 ACGATGCGTCCCCTACTG 58.793 61.111 0.00 0.00 33.69 2.74
370 371 2.417516 CGATGCGTCCCCTACTGG 59.582 66.667 0.00 0.00 0.00 4.00
371 372 2.109181 GATGCGTCCCCTACTGGC 59.891 66.667 0.00 0.00 0.00 4.85
372 373 3.462199 GATGCGTCCCCTACTGGCC 62.462 68.421 0.00 0.00 0.00 5.36
379 380 3.782443 CCCTACTGGCCCCGTGAC 61.782 72.222 0.00 0.00 0.00 3.67
380 381 3.000819 CCTACTGGCCCCGTGACA 61.001 66.667 0.00 0.00 0.00 3.58
391 392 4.680237 CGTGACAAGCGAGGCCCA 62.680 66.667 0.00 0.00 0.00 5.36
422 423 2.345760 GCCTGTGTCATGGGGCTTG 61.346 63.158 0.00 0.00 41.20 4.01
508 515 6.539464 AGTTGTATACGGTTGTGTTCTTTCAA 59.461 34.615 0.00 0.00 0.00 2.69
509 516 6.289745 TGTATACGGTTGTGTTCTTTCAAC 57.710 37.500 0.00 0.00 41.88 3.18
565 572 1.062886 AGGTCCAGAGGTGCAGCTATA 60.063 52.381 20.22 0.00 0.00 1.31
568 575 2.630098 GTCCAGAGGTGCAGCTATATGA 59.370 50.000 20.22 12.74 0.00 2.15
577 584 1.337260 GCAGCTATATGACCCGACAGG 60.337 57.143 0.00 0.00 43.78 4.00
606 613 0.108329 TTAGACGTAGGCTTGCAGGC 60.108 55.000 13.24 13.24 41.73 4.85
607 614 1.254975 TAGACGTAGGCTTGCAGGCA 61.255 55.000 23.28 0.00 44.19 4.75
608 615 2.358737 ACGTAGGCTTGCAGGCAC 60.359 61.111 23.28 11.98 44.19 5.01
609 616 2.358615 CGTAGGCTTGCAGGCACA 60.359 61.111 23.28 6.30 44.19 4.57
632 639 1.016130 AGCATTCCAGCGAACAGACG 61.016 55.000 0.00 0.00 40.15 4.18
633 640 1.291877 GCATTCCAGCGAACAGACGT 61.292 55.000 0.00 0.00 35.59 4.34
634 641 1.990799 CATTCCAGCGAACAGACGTA 58.009 50.000 0.00 0.00 35.59 3.57
635 642 1.654105 CATTCCAGCGAACAGACGTAC 59.346 52.381 0.00 0.00 35.59 3.67
653 660 2.124011 ACGAAACTGAAACGCTCGTA 57.876 45.000 0.00 0.00 40.69 3.43
662 669 1.796459 GAAACGCTCGTAGCCTTTTCA 59.204 47.619 15.74 0.00 38.56 2.69
677 684 4.199310 CCTTTTCATTCATTCCTAGGCGA 58.801 43.478 2.96 0.00 0.00 5.54
681 688 1.417890 CATTCATTCCTAGGCGACCCT 59.582 52.381 2.96 0.00 45.61 4.34
787 823 7.329588 TGAGATCAAACAGTAGTTAGCGATA 57.670 36.000 0.00 0.00 36.84 2.92
807 1158 6.446318 CGATATAATTGATTGGTTTGTGGGG 58.554 40.000 0.00 0.00 0.00 4.96
810 1161 2.166907 TTGATTGGTTTGTGGGGTGT 57.833 45.000 0.00 0.00 0.00 4.16
815 1166 1.214217 TGGTTTGTGGGGTGTAGACA 58.786 50.000 0.00 0.00 0.00 3.41
839 1190 7.998383 ACATCACATGGATAATTAGTTTGGCTA 59.002 33.333 0.00 0.00 33.95 3.93
904 1261 2.039624 TCTCCTGGCCTCTCACCC 59.960 66.667 3.32 0.00 0.00 4.61
924 1299 3.758554 CCCTAATGCTAATTTGGATCCCG 59.241 47.826 9.90 0.00 40.07 5.14
965 1356 4.080469 ACAATCTCTCCTCCTACGTACTGA 60.080 45.833 0.00 0.00 0.00 3.41
973 1364 3.582780 CTCCTACGTACTGAACAAACCC 58.417 50.000 0.00 0.00 0.00 4.11
988 1383 1.039856 AACCCACCAATGCAAGACAC 58.960 50.000 0.00 0.00 0.00 3.67
1158 1553 0.465460 TTGAGAAGGCCAACAACGCT 60.465 50.000 5.01 0.00 0.00 5.07
1407 1805 1.589993 CGAGTCGCTCCGCATCATT 60.590 57.895 0.00 0.00 0.00 2.57
1462 1869 2.291043 GGCGAGGAAGTCAAGGGGA 61.291 63.158 0.00 0.00 0.00 4.81
1562 6825 2.504367 CCCAATCAAGGACAAGTTCGT 58.496 47.619 0.00 0.00 0.00 3.85
1633 6896 2.925724 CATACGGGGGCTACAAATTCA 58.074 47.619 0.00 0.00 0.00 2.57
1722 6985 0.467290 TTTTGGCCTTTGAGTCCGCT 60.467 50.000 3.32 0.00 0.00 5.52
1723 6986 0.467290 TTTGGCCTTTGAGTCCGCTT 60.467 50.000 3.32 0.00 0.00 4.68
1789 7052 4.335647 CTCCCACTGCCGCCACTT 62.336 66.667 0.00 0.00 0.00 3.16
1794 7057 4.988598 ACTGCCGCCACTTCCACG 62.989 66.667 0.00 0.00 0.00 4.94
1813 7088 1.668151 GCAACCGTCACTCCCACTC 60.668 63.158 0.00 0.00 0.00 3.51
1815 7090 1.152312 AACCGTCACTCCCACTCCT 60.152 57.895 0.00 0.00 0.00 3.69
1838 7113 7.121759 TCCTGAGAAATCATAAGAAAAGGCTTG 59.878 37.037 0.00 0.00 0.00 4.01
1843 7118 8.518702 AGAAATCATAAGAAAAGGCTTGTCTTC 58.481 33.333 30.86 17.63 33.70 2.87
1844 7119 8.414629 AAATCATAAGAAAAGGCTTGTCTTCT 57.585 30.769 30.86 21.01 33.70 2.85
1845 7120 9.520515 AAATCATAAGAAAAGGCTTGTCTTCTA 57.479 29.630 30.86 18.16 33.70 2.10
1846 7121 9.692325 AATCATAAGAAAAGGCTTGTCTTCTAT 57.308 29.630 30.86 19.43 33.70 1.98
1847 7122 9.692325 ATCATAAGAAAAGGCTTGTCTTCTATT 57.308 29.630 30.86 13.70 33.70 1.73
1922 7197 6.546428 AGCTAGTTGTTGAAGATAAGGCTA 57.454 37.500 0.00 0.00 0.00 3.93
2024 7299 6.499106 TCAATCATTGTAGATGCCCTTAGA 57.501 37.500 0.00 0.00 0.00 2.10
2037 7312 4.960938 TGCCCTTAGAGCATGTACAATAG 58.039 43.478 0.00 0.00 34.69 1.73
2040 7315 5.823045 GCCCTTAGAGCATGTACAATAGTTT 59.177 40.000 0.00 0.00 0.00 2.66
2076 7351 6.220930 TGACACGTAGGATAAATAATGAGGC 58.779 40.000 0.00 0.00 0.00 4.70
2084 7359 5.073144 AGGATAAATAATGAGGCGGAGGAAA 59.927 40.000 0.00 0.00 0.00 3.13
2099 7374 5.817816 GCGGAGGAAAGAGAAATCATAAGAA 59.182 40.000 0.00 0.00 0.00 2.52
2102 7377 8.897752 CGGAGGAAAGAGAAATCATAAGAAAAT 58.102 33.333 0.00 0.00 0.00 1.82
2150 7425 8.607459 AGAAGACAATTGATATTTCTTAGCACG 58.393 33.333 13.59 0.00 29.39 5.34
2154 7437 4.875544 TTGATATTTCTTAGCACGCACC 57.124 40.909 0.00 0.00 0.00 5.01
2159 7442 6.710295 TGATATTTCTTAGCACGCACCATATT 59.290 34.615 0.00 0.00 0.00 1.28
2164 7447 6.745159 TCTTAGCACGCACCATATTTTTAA 57.255 33.333 0.00 0.00 0.00 1.52
2170 7453 7.767261 AGCACGCACCATATTTTTAAGAATAA 58.233 30.769 2.84 0.00 0.00 1.40
2286 8579 3.872696 TGTACATGCCCTTATCACACAG 58.127 45.455 0.00 0.00 0.00 3.66
2288 8581 1.004628 ACATGCCCTTATCACACAGCA 59.995 47.619 0.00 0.00 34.28 4.41
2311 8604 7.559845 GCAAACTGCATTTAAAAATTGACGTA 58.440 30.769 0.00 0.00 44.26 3.57
2321 8614 9.634163 ATTTAAAAATTGACGTAGAACCAATCC 57.366 29.630 0.00 0.00 30.93 3.01
2322 8615 6.894339 AAAAATTGACGTAGAACCAATCCT 57.106 33.333 0.00 0.00 30.93 3.24
2323 8616 7.989416 AAAAATTGACGTAGAACCAATCCTA 57.011 32.000 0.00 0.00 30.93 2.94
2379 8672 1.285950 GGGGAGTCGCTGCAAAAAC 59.714 57.895 7.19 0.00 0.00 2.43
2387 8680 1.950630 GCTGCAAAAACGCCCACAG 60.951 57.895 0.00 0.00 0.00 3.66
2443 8737 0.385473 GTTTTGGACATGCACGGTCG 60.385 55.000 12.65 0.00 36.12 4.79
2456 8750 3.660111 GGTCGGCACACCAGCAAC 61.660 66.667 0.00 0.00 36.32 4.17
2500 8875 2.276740 GAGCCAAGGGTGGGGATG 59.723 66.667 0.00 0.00 46.09 3.51
2513 8888 1.149401 GGGATGGCTAAGGCTGACC 59.851 63.158 0.00 0.00 38.73 4.02
2514 8889 1.635817 GGGATGGCTAAGGCTGACCA 61.636 60.000 5.94 5.94 39.06 4.02
2535 8910 4.632153 CACATAGTGGTGGTATCTTAGCC 58.368 47.826 0.00 0.00 35.13 3.93
2536 8911 3.321111 ACATAGTGGTGGTATCTTAGCCG 59.679 47.826 0.00 0.00 0.00 5.52
2538 8913 0.532196 GTGGTGGTATCTTAGCCGGC 60.532 60.000 21.89 21.89 0.00 6.13
2558 8933 2.808202 GCATCATGCACTCGGGAATAGT 60.808 50.000 4.20 0.00 44.26 2.12
2571 8946 5.056480 TCGGGAATAGTAAACATGCTGATG 58.944 41.667 0.00 0.00 35.49 3.07
2593 8968 6.114187 TGTGGCAGAGAATTAAAGAAGAGA 57.886 37.500 0.00 0.00 0.00 3.10
2604 8979 8.977412 AGAATTAAAGAAGAGAGAGAGGGTTAG 58.023 37.037 0.00 0.00 0.00 2.34
2606 8981 7.948034 TTAAAGAAGAGAGAGAGGGTTAGAG 57.052 40.000 0.00 0.00 0.00 2.43
2615 8990 6.066032 AGAGAGAGGGTTAGAGTAACATAGC 58.934 44.000 0.00 0.00 40.39 2.97
2631 9006 8.894731 AGTAACATAGCTAGATACCGTATCATG 58.105 37.037 18.67 14.67 37.65 3.07
2639 9025 7.545965 AGCTAGATACCGTATCATGTTAAATGC 59.454 37.037 18.67 9.55 37.65 3.56
2663 9049 6.479990 GCTATGCTACTTTGTGTCATACATGA 59.520 38.462 0.00 0.00 39.48 3.07
2778 9165 8.770010 ATATAATACTCCCCACTATGAGTAGC 57.230 38.462 5.70 0.00 44.72 3.58
2779 9166 2.089600 ACTCCCCACTATGAGTAGCC 57.910 55.000 0.00 0.00 39.96 3.93
2780 9167 1.576272 ACTCCCCACTATGAGTAGCCT 59.424 52.381 0.00 0.00 39.96 4.58
2782 9169 3.206866 ACTCCCCACTATGAGTAGCCTAA 59.793 47.826 0.00 0.00 39.96 2.69
2783 9170 3.829601 CTCCCCACTATGAGTAGCCTAAG 59.170 52.174 0.00 0.00 0.00 2.18
2784 9171 2.900546 CCCCACTATGAGTAGCCTAAGG 59.099 54.545 0.00 0.00 0.00 2.69
2795 9182 4.904466 CCTAAGGCACGTACGCTT 57.096 55.556 16.72 13.10 0.00 4.68
2797 9184 1.553308 CCTAAGGCACGTACGCTTAC 58.447 55.000 16.72 3.34 0.00 2.34
2798 9185 1.553308 CTAAGGCACGTACGCTTACC 58.447 55.000 16.72 11.59 0.00 2.85
2800 9187 1.176527 AAGGCACGTACGCTTACCTA 58.823 50.000 16.72 0.00 0.00 3.08
2801 9188 0.453390 AGGCACGTACGCTTACCTAC 59.547 55.000 16.72 0.00 0.00 3.18
2802 9189 0.526310 GGCACGTACGCTTACCTACC 60.526 60.000 16.72 1.53 0.00 3.18
2803 9190 0.453390 GCACGTACGCTTACCTACCT 59.547 55.000 16.72 0.00 0.00 3.08
2805 9192 1.098050 ACGTACGCTTACCTACCTGG 58.902 55.000 16.72 0.00 42.93 4.45
2806 9193 0.248784 CGTACGCTTACCTACCTGGC 60.249 60.000 0.52 0.00 40.22 4.85
2807 9194 0.819582 GTACGCTTACCTACCTGGCA 59.180 55.000 0.00 0.00 40.22 4.92
2810 9197 2.112998 ACGCTTACCTACCTGGCAATA 58.887 47.619 0.00 0.00 40.22 1.90
2811 9198 2.704065 ACGCTTACCTACCTGGCAATAT 59.296 45.455 0.00 0.00 40.22 1.28
2812 9199 3.244112 ACGCTTACCTACCTGGCAATATC 60.244 47.826 0.00 0.00 40.22 1.63
2814 9201 3.326747 CTTACCTACCTGGCAATATCGC 58.673 50.000 0.00 0.00 40.22 4.58
2816 9203 1.291877 CCTACCTGGCAATATCGCGC 61.292 60.000 0.00 0.00 0.00 6.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.164269 AGGGCATGTCCTAGGCGG 61.164 66.667 19.81 0.00 36.83 6.13
18 19 4.864334 CCTCCGCCCTGATGTGGC 62.864 72.222 0.00 0.00 45.70 5.01
62 63 1.352083 TCACAGGAGGGAGGAGTTTG 58.648 55.000 0.00 0.00 0.00 2.93
73 74 3.633986 GGGCCAAAATAAGATCACAGGAG 59.366 47.826 4.39 0.00 0.00 3.69
86 87 0.329596 AGAAGCGAGAGGGCCAAAAT 59.670 50.000 6.18 0.00 0.00 1.82
88 89 1.296715 GAGAAGCGAGAGGGCCAAA 59.703 57.895 6.18 0.00 0.00 3.28
94 95 2.202676 GCGTGGAGAAGCGAGAGG 60.203 66.667 0.00 0.00 0.00 3.69
106 107 4.025401 GGTCGTTTGGCTGCGTGG 62.025 66.667 0.00 0.00 0.00 4.94
110 111 3.365265 CAGGGGTCGTTTGGCTGC 61.365 66.667 0.00 0.00 0.00 5.25
111 112 2.463589 TAGCAGGGGTCGTTTGGCTG 62.464 60.000 0.00 0.00 33.10 4.85
112 113 2.221299 TAGCAGGGGTCGTTTGGCT 61.221 57.895 0.00 0.00 35.50 4.75
249 250 1.258445 ACCGAACCCGAGAAGCAGAT 61.258 55.000 0.00 0.00 38.22 2.90
278 279 1.537202 CTCCTGCTGCTTGGTTTACAC 59.463 52.381 0.00 0.00 0.00 2.90
279 280 1.545428 CCTCCTGCTGCTTGGTTTACA 60.545 52.381 0.00 0.00 0.00 2.41
307 308 1.080501 CTGCCAGCGAGTTCGAAGA 60.081 57.895 5.60 0.00 43.02 2.87
322 323 2.105930 CGACTCTAGGCCAGCTGC 59.894 66.667 8.66 3.68 40.16 5.25
353 354 2.417516 CCAGTAGGGGACGCATCG 59.582 66.667 0.00 0.00 0.00 3.84
355 356 3.480133 GGCCAGTAGGGGACGCAT 61.480 66.667 0.00 0.00 37.04 4.73
362 363 3.782443 GTCACGGGGCCAGTAGGG 61.782 72.222 9.55 0.00 40.85 3.53
363 364 2.521958 CTTGTCACGGGGCCAGTAGG 62.522 65.000 9.55 0.00 38.23 3.18
365 366 3.065306 CTTGTCACGGGGCCAGTA 58.935 61.111 9.55 0.00 0.00 2.74
366 367 4.643387 GCTTGTCACGGGGCCAGT 62.643 66.667 4.39 4.01 0.00 4.00
374 375 4.680237 TGGGCCTCGCTTGTCACG 62.680 66.667 4.53 0.00 0.00 4.35
375 376 2.167398 TACTGGGCCTCGCTTGTCAC 62.167 60.000 4.53 0.00 0.00 3.67
376 377 1.888436 CTACTGGGCCTCGCTTGTCA 61.888 60.000 4.53 0.00 0.00 3.58
377 378 1.153549 CTACTGGGCCTCGCTTGTC 60.154 63.158 4.53 0.00 0.00 3.18
378 379 2.982130 CTACTGGGCCTCGCTTGT 59.018 61.111 4.53 0.00 0.00 3.16
379 380 2.512515 GCTACTGGGCCTCGCTTG 60.513 66.667 4.53 0.00 0.00 4.01
402 403 4.365111 GCCCCATGACACAGGCCA 62.365 66.667 5.01 0.00 39.60 5.36
422 423 2.865343 TAATCCTCTCGAAGCGGAAC 57.135 50.000 1.68 0.00 0.00 3.62
461 468 2.668457 CAGAAAACGAATCCCTGACGAG 59.332 50.000 0.00 0.00 0.00 4.18
508 515 2.254651 GCTCGTGTCGACTTCCGT 59.745 61.111 17.92 0.00 39.75 4.69
509 516 2.081212 GTGCTCGTGTCGACTTCCG 61.081 63.158 17.92 15.60 40.25 4.30
577 584 6.487103 CAAGCCTACGTCTAAATCAAATTCC 58.513 40.000 0.00 0.00 0.00 3.01
578 585 5.965918 GCAAGCCTACGTCTAAATCAAATTC 59.034 40.000 0.00 0.00 0.00 2.17
589 596 2.266055 GCCTGCAAGCCTACGTCT 59.734 61.111 0.00 0.00 0.00 4.18
606 613 1.655484 TCGCTGGAATGCTATGTGTG 58.345 50.000 0.00 0.00 0.00 3.82
607 614 2.009774 GTTCGCTGGAATGCTATGTGT 58.990 47.619 0.00 0.00 34.05 3.72
608 615 2.009051 TGTTCGCTGGAATGCTATGTG 58.991 47.619 0.00 0.00 34.05 3.21
609 616 2.093500 TCTGTTCGCTGGAATGCTATGT 60.093 45.455 0.00 0.00 34.05 2.29
632 639 1.783140 ACGAGCGTTTCAGTTTCGTAC 59.217 47.619 0.00 0.00 42.05 3.67
633 640 2.124011 ACGAGCGTTTCAGTTTCGTA 57.876 45.000 0.00 0.00 42.05 3.43
634 641 2.049228 CTACGAGCGTTTCAGTTTCGT 58.951 47.619 0.00 3.31 45.30 3.85
635 642 1.201672 GCTACGAGCGTTTCAGTTTCG 60.202 52.381 0.00 0.00 37.31 3.46
653 660 3.956848 GCCTAGGAATGAATGAAAAGGCT 59.043 43.478 14.75 0.00 43.88 4.58
662 669 1.807814 AGGGTCGCCTAGGAATGAAT 58.192 50.000 14.75 0.00 0.00 2.57
755 791 7.200434 ACTACTGTTTGATCTCATGGGTAAT 57.800 36.000 0.00 0.00 0.00 1.89
787 823 4.843516 ACACCCCACAAACCAATCAATTAT 59.156 37.500 0.00 0.00 0.00 1.28
807 1158 9.547753 AACTAATTATCCATGTGATGTCTACAC 57.452 33.333 6.87 0.00 38.55 2.90
810 1161 9.559732 CCAAACTAATTATCCATGTGATGTCTA 57.440 33.333 6.87 0.00 34.76 2.59
815 1166 8.995027 TTAGCCAAACTAATTATCCATGTGAT 57.005 30.769 0.00 0.00 35.89 3.06
904 1261 3.820467 TGCGGGATCCAAATTAGCATTAG 59.180 43.478 15.23 0.00 0.00 1.73
924 1299 0.593128 GTGGTGTGGTGTGAAGATGC 59.407 55.000 0.00 0.00 0.00 3.91
965 1356 2.114616 TCTTGCATTGGTGGGTTTGTT 58.885 42.857 0.00 0.00 0.00 2.83
973 1364 1.229428 ACTCGTGTCTTGCATTGGTG 58.771 50.000 0.00 0.00 0.00 4.17
988 1383 1.129251 CACTGCCATTGTTGCTACTCG 59.871 52.381 0.00 0.00 0.00 4.18
1063 1458 0.453950 GCTTCGACAGCGTACGAGAA 60.454 55.000 21.65 13.60 39.29 2.87
1158 1553 3.294493 GCCACAGCCGCCTTGAAA 61.294 61.111 0.00 0.00 0.00 2.69
1407 1805 3.329542 GACCTCAAGGATGCCGGCA 62.330 63.158 34.80 34.80 38.94 5.69
1462 1869 3.518998 CTCGTCGGCAGGGATCGT 61.519 66.667 0.00 0.00 0.00 3.73
1562 6825 0.391597 AAAGGCGGACTTGAAGACGA 59.608 50.000 15.53 0.00 39.96 4.20
1722 6985 1.945819 GCGAGGATGGTCTTGCTCAAA 60.946 52.381 0.00 0.00 40.20 2.69
1723 6986 0.391661 GCGAGGATGGTCTTGCTCAA 60.392 55.000 0.00 0.00 40.20 3.02
1794 7057 2.668550 GTGGGAGTGACGGTTGCC 60.669 66.667 0.00 0.00 0.00 4.52
1800 7075 0.609406 TCTCAGGAGTGGGAGTGACG 60.609 60.000 0.00 0.00 32.93 4.35
1802 7077 2.398754 TTTCTCAGGAGTGGGAGTGA 57.601 50.000 0.00 0.00 33.50 3.41
1813 7088 7.094032 ACAAGCCTTTTCTTATGATTTCTCAGG 60.094 37.037 0.00 0.00 34.12 3.86
1815 7090 7.667219 AGACAAGCCTTTTCTTATGATTTCTCA 59.333 33.333 0.00 0.00 35.41 3.27
1854 7129 8.306038 AGACATATTGTGCTAAGAGATCATCTC 58.694 37.037 6.55 6.55 43.70 2.75
1855 7130 8.192743 AGACATATTGTGCTAAGAGATCATCT 57.807 34.615 0.00 0.00 41.27 2.90
1856 7131 8.087136 TGAGACATATTGTGCTAAGAGATCATC 58.913 37.037 0.00 0.00 0.00 2.92
1857 7132 7.960262 TGAGACATATTGTGCTAAGAGATCAT 58.040 34.615 0.00 0.00 0.00 2.45
1858 7133 7.352079 TGAGACATATTGTGCTAAGAGATCA 57.648 36.000 0.00 0.00 0.00 2.92
1859 7134 9.920133 TTATGAGACATATTGTGCTAAGAGATC 57.080 33.333 0.00 0.00 0.00 2.75
1895 7170 8.049721 AGCCTTATCTTCAACAACTAGCTATTT 58.950 33.333 0.00 0.00 0.00 1.40
1900 7175 7.042335 TCTTAGCCTTATCTTCAACAACTAGC 58.958 38.462 0.00 0.00 0.00 3.42
1907 7182 9.438228 GGGTTATATCTTAGCCTTATCTTCAAC 57.562 37.037 0.00 0.00 0.00 3.18
1918 7193 6.037172 CGCATACAATGGGTTATATCTTAGCC 59.963 42.308 0.00 0.00 38.30 3.93
1991 7266 8.834465 GCATCTACAATGATTGATAAGACAGTT 58.166 33.333 12.80 0.00 0.00 3.16
2015 7290 3.931907 ATTGTACATGCTCTAAGGGCA 57.068 42.857 0.00 0.00 44.05 5.36
2036 7311 9.367444 CCTACGTGTCATTCTTAAGATAAAACT 57.633 33.333 5.89 0.00 0.00 2.66
2037 7312 9.362539 TCCTACGTGTCATTCTTAAGATAAAAC 57.637 33.333 5.89 3.78 0.00 2.43
2054 7329 5.227908 CGCCTCATTATTTATCCTACGTGT 58.772 41.667 0.00 0.00 0.00 4.49
2076 7351 7.849804 TTTCTTATGATTTCTCTTTCCTCCG 57.150 36.000 0.00 0.00 0.00 4.63
2122 7397 9.896645 TGCTAAGAAATATCAATTGTCTTCTCT 57.103 29.630 10.54 4.52 31.19 3.10
2123 7398 9.928236 GTGCTAAGAAATATCAATTGTCTTCTC 57.072 33.333 10.54 6.10 31.19 2.87
2124 7399 8.607459 CGTGCTAAGAAATATCAATTGTCTTCT 58.393 33.333 10.54 8.97 31.19 2.85
2125 7400 7.374491 GCGTGCTAAGAAATATCAATTGTCTTC 59.626 37.037 10.54 7.25 31.19 2.87
2126 7401 7.148255 TGCGTGCTAAGAAATATCAATTGTCTT 60.148 33.333 5.13 9.11 32.33 3.01
2127 7402 6.316140 TGCGTGCTAAGAAATATCAATTGTCT 59.684 34.615 5.13 0.00 0.00 3.41
2128 7403 6.412072 GTGCGTGCTAAGAAATATCAATTGTC 59.588 38.462 5.13 0.00 0.00 3.18
2129 7404 6.258160 GTGCGTGCTAAGAAATATCAATTGT 58.742 36.000 5.13 0.00 0.00 2.71
2130 7405 5.682862 GGTGCGTGCTAAGAAATATCAATTG 59.317 40.000 0.00 0.00 0.00 2.32
2131 7406 5.356751 TGGTGCGTGCTAAGAAATATCAATT 59.643 36.000 0.00 0.00 0.00 2.32
2132 7407 4.881273 TGGTGCGTGCTAAGAAATATCAAT 59.119 37.500 0.00 0.00 0.00 2.57
2133 7408 4.257731 TGGTGCGTGCTAAGAAATATCAA 58.742 39.130 0.00 0.00 0.00 2.57
2134 7409 3.867857 TGGTGCGTGCTAAGAAATATCA 58.132 40.909 0.00 0.00 0.00 2.15
2135 7410 6.727824 ATATGGTGCGTGCTAAGAAATATC 57.272 37.500 0.00 0.00 0.00 1.63
2136 7411 7.510549 AAATATGGTGCGTGCTAAGAAATAT 57.489 32.000 0.00 0.00 0.00 1.28
2137 7412 6.935741 AAATATGGTGCGTGCTAAGAAATA 57.064 33.333 0.00 0.00 0.00 1.40
2213 8506 9.911788 AAGTCTTGTATGTAATTTGGAGATGAT 57.088 29.630 0.00 0.00 0.00 2.45
2286 8579 6.418141 ACGTCAATTTTTAAATGCAGTTTGC 58.582 32.000 4.05 0.00 45.29 3.68
2288 8581 9.522804 TTCTACGTCAATTTTTAAATGCAGTTT 57.477 25.926 4.05 2.06 0.00 2.66
2297 8590 8.398878 AGGATTGGTTCTACGTCAATTTTTAA 57.601 30.769 0.00 0.00 32.05 1.52
2304 8597 4.439057 GCATAGGATTGGTTCTACGTCAA 58.561 43.478 0.00 0.00 0.00 3.18
2311 8604 2.582636 ACCTTGGCATAGGATTGGTTCT 59.417 45.455 18.54 0.00 38.73 3.01
2321 8614 1.715585 CGCGAACACCTTGGCATAG 59.284 57.895 0.00 0.00 30.79 2.23
2322 8615 2.395360 GCGCGAACACCTTGGCATA 61.395 57.895 12.10 0.00 30.79 3.14
2323 8616 3.737172 GCGCGAACACCTTGGCAT 61.737 61.111 12.10 0.00 30.79 4.40
2419 8713 2.414559 CCGTGCATGTCCAAAACAGATC 60.415 50.000 4.96 0.00 42.37 2.75
2443 8737 0.378257 CGATATGTTGCTGGTGTGCC 59.622 55.000 0.00 0.00 0.00 5.01
2456 8750 4.555313 GCCACCAACACATGAATCGATATG 60.555 45.833 0.00 2.07 0.00 1.78
2500 8875 1.486726 ACTATGTGGTCAGCCTTAGCC 59.513 52.381 0.00 0.00 41.25 3.93
2513 8888 4.632153 GGCTAAGATACCACCACTATGTG 58.368 47.826 0.00 0.00 35.98 3.21
2514 8889 3.321111 CGGCTAAGATACCACCACTATGT 59.679 47.826 0.00 0.00 0.00 2.29
2535 8910 3.274586 CCCGAGTGCATGATGCCG 61.275 66.667 15.70 11.07 44.23 5.69
2536 8911 0.820891 ATTCCCGAGTGCATGATGCC 60.821 55.000 15.70 6.37 44.23 4.40
2538 8913 3.117491 ACTATTCCCGAGTGCATGATG 57.883 47.619 0.00 0.00 0.00 3.07
2550 8925 5.009010 CCACATCAGCATGTTTACTATTCCC 59.991 44.000 0.00 0.00 40.66 3.97
2558 8933 3.011818 CTCTGCCACATCAGCATGTTTA 58.988 45.455 0.00 0.00 40.66 2.01
2571 8946 6.402222 TCTCTCTTCTTTAATTCTCTGCCAC 58.598 40.000 0.00 0.00 0.00 5.01
2593 8968 6.020881 AGCTATGTTACTCTAACCCTCTCT 57.979 41.667 0.00 0.00 37.88 3.10
2604 8979 8.489990 TGATACGGTATCTAGCTATGTTACTC 57.510 38.462 24.27 0.00 36.17 2.59
2606 8981 8.675504 ACATGATACGGTATCTAGCTATGTTAC 58.324 37.037 24.27 0.00 36.17 2.50
2615 8990 8.988064 AGCATTTAACATGATACGGTATCTAG 57.012 34.615 24.27 19.00 36.17 2.43
2631 9006 7.526608 TGACACAAAGTAGCATAGCATTTAAC 58.473 34.615 0.00 0.00 0.00 2.01
2753 9140 7.785506 GGCTACTCATAGTGGGGAGTATTATAT 59.214 40.741 0.00 0.00 43.51 0.86
2756 9143 5.076039 AGGCTACTCATAGTGGGGAGTATTA 59.924 44.000 0.00 0.00 43.51 0.98
2757 9144 4.140663 AGGCTACTCATAGTGGGGAGTATT 60.141 45.833 0.00 0.00 43.51 1.89
2760 9147 1.576272 AGGCTACTCATAGTGGGGAGT 59.424 52.381 0.00 0.00 45.72 3.85
2761 9148 2.390225 AGGCTACTCATAGTGGGGAG 57.610 55.000 0.00 0.00 37.18 4.30
2763 9150 2.900546 CCTTAGGCTACTCATAGTGGGG 59.099 54.545 0.00 0.00 0.00 4.96
2764 9151 2.300437 GCCTTAGGCTACTCATAGTGGG 59.700 54.545 17.16 0.00 46.69 4.61
2765 9152 3.669251 GCCTTAGGCTACTCATAGTGG 57.331 52.381 17.16 0.00 46.69 4.00
2778 9165 1.553308 GTAAGCGTACGTGCCTTAGG 58.447 55.000 17.90 0.00 34.65 2.69
2779 9166 1.133790 AGGTAAGCGTACGTGCCTTAG 59.866 52.381 17.90 0.00 37.06 2.18
2780 9167 1.176527 AGGTAAGCGTACGTGCCTTA 58.823 50.000 17.90 12.73 37.06 2.69
2782 9169 0.453390 GTAGGTAAGCGTACGTGCCT 59.547 55.000 17.90 17.56 42.61 4.75
2783 9170 0.526310 GGTAGGTAAGCGTACGTGCC 60.526 60.000 19.72 19.72 41.57 5.01
2784 9171 0.453390 AGGTAGGTAAGCGTACGTGC 59.547 55.000 17.90 12.49 36.97 5.34
2785 9172 1.202222 CCAGGTAGGTAAGCGTACGTG 60.202 57.143 17.90 2.68 44.55 4.49
2786 9173 1.098050 CCAGGTAGGTAAGCGTACGT 58.902 55.000 17.90 9.83 36.97 3.57
2787 9174 0.248784 GCCAGGTAGGTAAGCGTACG 60.249 60.000 11.84 11.84 40.61 3.67
2789 9176 1.559368 TTGCCAGGTAGGTAAGCGTA 58.441 50.000 0.00 0.00 37.04 4.42
2790 9177 0.909623 ATTGCCAGGTAGGTAAGCGT 59.090 50.000 0.00 0.00 45.58 5.07
2791 9178 2.902705 TATTGCCAGGTAGGTAAGCG 57.097 50.000 0.00 0.00 45.58 4.68
2792 9179 3.326747 CGATATTGCCAGGTAGGTAAGC 58.673 50.000 0.00 0.00 45.58 3.09
2793 9180 3.326747 GCGATATTGCCAGGTAGGTAAG 58.673 50.000 3.25 0.00 45.58 2.34
2795 9182 1.271379 CGCGATATTGCCAGGTAGGTA 59.729 52.381 0.00 0.00 40.61 3.08
2797 9184 1.291877 GCGCGATATTGCCAGGTAGG 61.292 60.000 12.10 0.00 41.84 3.18
2798 9185 2.153913 GCGCGATATTGCCAGGTAG 58.846 57.895 12.10 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.