Multiple sequence alignment - TraesCS6D01G065800

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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 TraesCS6D01G065800 chr6D 100.000 3080 0 0 1 3080 32246695 32243616 0.000000e+00 5688.0
1 TraesCS6D01G065800 chr6D 80.651 522 95 5 2561 3078 31966037 31965518 1.720000e-107 399.0
2 TraesCS6D01G065800 chr6D 79.468 526 101 5 2557 3080 31991432 31990912 1.750000e-97 366.0
3 TraesCS6D01G065800 chr6D 91.525 59 4 1 95 153 32246475 32246418 2.550000e-11 80.5
4 TraesCS6D01G065800 chr6D 91.525 59 4 1 221 278 32246601 32246543 2.550000e-11 80.5
5 TraesCS6D01G065800 chr6B 93.999 1633 72 11 705 2328 67732796 67731181 0.000000e+00 2449.0
6 TraesCS6D01G065800 chr6B 94.289 1576 70 10 762 2328 67692603 67691039 0.000000e+00 2394.0
7 TraesCS6D01G065800 chr6B 95.767 756 28 2 2327 3080 67690779 67690026 0.000000e+00 1216.0
8 TraesCS6D01G065800 chr6B 95.695 604 24 1 2327 2928 67730921 67730318 0.000000e+00 970.0
9 TraesCS6D01G065800 chr6B 90.935 353 28 3 242 590 67733800 67733448 3.590000e-129 472.0
10 TraesCS6D01G065800 chr6B 79.846 521 99 6 2561 3078 67683322 67682805 2.900000e-100 375.0
11 TraesCS6D01G065800 chr6B 85.924 341 34 7 407 734 67692936 67692597 4.890000e-93 351.0
12 TraesCS6D01G065800 chr6B 78.667 525 107 3 2557 3080 67679712 67679192 8.180000e-91 344.0
13 TraesCS6D01G065800 chr6B 97.382 191 5 0 2890 3080 67730100 67729910 2.960000e-85 326.0
14 TraesCS6D01G065800 chr6B 94.118 187 8 3 1 186 67814340 67814156 6.500000e-72 281.0
15 TraesCS6D01G065800 chr6B 88.649 185 20 1 42 226 67693476 67693293 1.110000e-54 224.0
16 TraesCS6D01G065800 chr6B 95.122 41 2 0 113 153 67733804 67733764 7.130000e-07 65.8
17 TraesCS6D01G065800 chr6B 100.000 34 0 0 1 34 67693502 67693469 2.560000e-06 63.9
18 TraesCS6D01G065800 chr6A 94.246 869 39 7 2214 3080 36531389 36530530 0.000000e+00 1317.0
19 TraesCS6D01G065800 chr6A 78.932 337 64 4 2561 2892 36520737 36520403 4.000000e-54 222.0
20 TraesCS6D01G065800 chr7B 100.000 31 0 0 1242 1272 668356674 668356644 1.190000e-04 58.4
21 TraesCS6D01G065800 chr7B 96.970 33 1 0 1243 1275 665511887 665511855 4.290000e-04 56.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G065800 chr6D 32243616 32246695 3079 True 1949.666667 5688 94.3500 1 3080 3 chr6D.!!$R3 3079
1 TraesCS6D01G065800 chr6D 31965518 31966037 519 True 399.000000 399 80.6510 2561 3078 1 chr6D.!!$R1 517
2 TraesCS6D01G065800 chr6D 31990912 31991432 520 True 366.000000 366 79.4680 2557 3080 1 chr6D.!!$R2 523
3 TraesCS6D01G065800 chr6B 67729910 67733804 3894 True 856.560000 2449 94.6266 113 3080 5 chr6B.!!$R4 2967
4 TraesCS6D01G065800 chr6B 67690026 67693502 3476 True 849.780000 2394 92.9258 1 3080 5 chr6B.!!$R3 3079
5 TraesCS6D01G065800 chr6B 67679192 67683322 4130 True 359.500000 375 79.2565 2557 3080 2 chr6B.!!$R2 523
6 TraesCS6D01G065800 chr6A 36530530 36531389 859 True 1317.000000 1317 94.2460 2214 3080 1 chr6A.!!$R2 866

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
966 1752 0.107456 CTCCTCCATCAACCCATCGG 59.893 60.0 0.0 0.0 0.0 4.18 F
1378 2164 0.319040 CGGTAGAGCCCATGTGATCG 60.319 60.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1912 2698 0.327924 ATCAACTTCCCGCCATCACA 59.672 50.000 0.00 0.0 0.00 3.58 R
2800 3849 1.796459 GGCATGAAAGTTTTGCTGCTG 59.204 47.619 11.12 0.0 36.62 4.41 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
34 35 7.826690 TGTTGGCAAAAGATAGTTTATTCCTC 58.173 34.615 0.00 0.00 0.00 3.71
35 36 7.450014 TGTTGGCAAAAGATAGTTTATTCCTCA 59.550 33.333 0.00 0.00 0.00 3.86
36 37 8.303876 GTTGGCAAAAGATAGTTTATTCCTCAA 58.696 33.333 0.00 0.00 0.00 3.02
37 38 7.826690 TGGCAAAAGATAGTTTATTCCTCAAC 58.173 34.615 0.00 0.00 0.00 3.18
38 39 6.967199 GGCAAAAGATAGTTTATTCCTCAACG 59.033 38.462 0.00 0.00 0.00 4.10
39 40 6.469275 GCAAAAGATAGTTTATTCCTCAACGC 59.531 38.462 0.00 0.00 0.00 4.84
40 41 5.968387 AAGATAGTTTATTCCTCAACGCG 57.032 39.130 3.53 3.53 0.00 6.01
41 42 5.007385 AGATAGTTTATTCCTCAACGCGT 57.993 39.130 5.58 5.58 0.00 6.01
42 43 5.416947 AGATAGTTTATTCCTCAACGCGTT 58.583 37.500 20.79 20.79 0.00 4.84
43 44 6.567050 AGATAGTTTATTCCTCAACGCGTTA 58.433 36.000 26.11 9.29 0.00 3.18
44 45 7.208080 AGATAGTTTATTCCTCAACGCGTTAT 58.792 34.615 26.11 16.42 0.00 1.89
45 46 5.713822 AGTTTATTCCTCAACGCGTTATC 57.286 39.130 26.11 5.65 0.00 1.75
46 47 4.569564 AGTTTATTCCTCAACGCGTTATCC 59.430 41.667 26.11 6.07 0.00 2.59
47 48 1.949465 ATTCCTCAACGCGTTATCCC 58.051 50.000 26.11 0.00 0.00 3.85
48 49 0.899720 TTCCTCAACGCGTTATCCCT 59.100 50.000 26.11 0.00 0.00 4.20
49 50 0.174845 TCCTCAACGCGTTATCCCTG 59.825 55.000 26.11 12.41 0.00 4.45
60 61 2.292794 TTATCCCTGCCGTGAGACGC 62.293 60.000 0.00 0.00 40.91 5.19
69 70 0.589708 CCGTGAGACGCCGTATATGA 59.410 55.000 0.00 0.00 40.91 2.15
71 72 2.242564 CGTGAGACGCCGTATATGATG 58.757 52.381 0.00 0.00 33.65 3.07
72 73 1.986378 GTGAGACGCCGTATATGATGC 59.014 52.381 0.00 0.00 0.00 3.91
91 92 1.545759 CCAGCGTACACATGTACTCG 58.454 55.000 17.68 8.65 46.43 4.18
103 104 4.564372 CACATGTACTCGGCAGATATATGC 59.436 45.833 13.99 13.99 45.74 3.14
150 151 3.499048 CTTATAGCTATGCCGTGTACCG 58.501 50.000 16.77 0.00 0.00 4.02
152 153 0.664761 TAGCTATGCCGTGTACCGAC 59.335 55.000 5.46 0.00 39.56 4.79
155 156 0.736636 CTATGCCGTGTACCGACAGA 59.263 55.000 5.46 0.00 39.56 3.41
186 187 2.634940 GGCTTAGATCTATGACAGGGCA 59.365 50.000 17.50 0.00 0.00 5.36
189 190 4.524714 GCTTAGATCTATGACAGGGCAGTA 59.475 45.833 17.50 0.00 0.00 2.74
195 196 0.902984 ATGACAGGGCAGTACCGACA 60.903 55.000 0.00 0.00 40.62 4.35
202 203 1.153745 GCAGTACCGACAGAGCTGG 60.154 63.158 0.00 0.00 34.19 4.85
203 204 1.595993 GCAGTACCGACAGAGCTGGA 61.596 60.000 0.00 0.00 34.19 3.86
204 205 0.453793 CAGTACCGACAGAGCTGGAG 59.546 60.000 0.00 0.00 34.19 3.86
205 206 0.328592 AGTACCGACAGAGCTGGAGA 59.671 55.000 0.00 0.00 34.19 3.71
206 207 1.174783 GTACCGACAGAGCTGGAGAA 58.825 55.000 0.00 0.00 34.19 2.87
207 208 1.133407 GTACCGACAGAGCTGGAGAAG 59.867 57.143 0.00 0.00 34.19 2.85
208 209 0.540830 ACCGACAGAGCTGGAGAAGT 60.541 55.000 0.00 0.00 34.19 3.01
209 210 0.108898 CCGACAGAGCTGGAGAAGTG 60.109 60.000 0.00 0.00 34.19 3.16
210 211 0.735632 CGACAGAGCTGGAGAAGTGC 60.736 60.000 0.00 0.00 34.19 4.40
211 212 0.607620 GACAGAGCTGGAGAAGTGCT 59.392 55.000 0.00 0.00 40.02 4.40
213 214 4.492955 GAGCTGGAGAAGTGCTCG 57.507 61.111 0.00 0.00 44.91 5.03
214 215 1.153667 GAGCTGGAGAAGTGCTCGG 60.154 63.158 0.00 0.00 44.91 4.63
215 216 2.817396 GCTGGAGAAGTGCTCGGC 60.817 66.667 0.00 0.00 44.91 5.54
216 217 2.977178 CTGGAGAAGTGCTCGGCT 59.023 61.111 0.00 0.00 44.91 5.52
217 218 1.294780 CTGGAGAAGTGCTCGGCTT 59.705 57.895 0.00 0.00 44.91 4.35
218 219 0.532573 CTGGAGAAGTGCTCGGCTTA 59.467 55.000 0.00 0.00 44.91 3.09
219 220 1.137872 CTGGAGAAGTGCTCGGCTTAT 59.862 52.381 0.00 0.00 44.91 1.73
220 221 2.362397 CTGGAGAAGTGCTCGGCTTATA 59.638 50.000 0.00 0.00 44.91 0.98
221 222 2.362397 TGGAGAAGTGCTCGGCTTATAG 59.638 50.000 0.00 0.00 44.91 1.31
222 223 2.623889 GGAGAAGTGCTCGGCTTATAGA 59.376 50.000 0.00 0.00 44.91 1.98
223 224 3.257127 GGAGAAGTGCTCGGCTTATAGAT 59.743 47.826 0.00 0.00 44.91 1.98
224 225 4.459685 GGAGAAGTGCTCGGCTTATAGATA 59.540 45.833 0.00 0.00 44.91 1.98
225 226 5.126384 GGAGAAGTGCTCGGCTTATAGATAT 59.874 44.000 0.00 0.00 44.91 1.63
226 227 6.319152 GGAGAAGTGCTCGGCTTATAGATATA 59.681 42.308 0.00 0.00 44.91 0.86
227 228 7.013846 GGAGAAGTGCTCGGCTTATAGATATAT 59.986 40.741 0.00 0.00 44.91 0.86
228 229 7.711846 AGAAGTGCTCGGCTTATAGATATATG 58.288 38.462 0.00 0.00 0.00 1.78
229 230 5.837437 AGTGCTCGGCTTATAGATATATGC 58.163 41.667 8.50 8.50 38.12 3.14
235 236 4.693283 GGCTTATAGATATATGCCGTGCA 58.307 43.478 16.56 1.01 44.37 4.57
236 237 4.747108 GGCTTATAGATATATGCCGTGCAG 59.253 45.833 16.56 0.00 44.37 4.41
237 238 5.451937 GGCTTATAGATATATGCCGTGCAGA 60.452 44.000 16.56 0.56 44.37 4.26
238 239 5.689514 GCTTATAGATATATGCCGTGCAGAG 59.310 44.000 4.90 0.00 43.65 3.35
239 240 2.376808 AGATATATGCCGTGCAGAGC 57.623 50.000 4.90 0.84 43.65 4.09
240 241 1.620323 AGATATATGCCGTGCAGAGCA 59.380 47.619 12.62 12.62 43.65 4.26
274 275 3.251571 GCTTATAGCTATGCCGTGTACC 58.748 50.000 16.77 0.00 38.45 3.34
275 276 3.305813 GCTTATAGCTATGCCGTGTACCA 60.306 47.826 16.77 0.00 38.45 3.25
365 366 1.278985 ACTGCCGTCTCCATTTGATGA 59.721 47.619 0.00 0.00 0.00 2.92
371 374 2.673893 CGTCTCCATTTGATGACCGTCA 60.674 50.000 3.10 3.10 0.00 4.35
372 375 3.535561 GTCTCCATTTGATGACCGTCAT 58.464 45.455 14.01 14.01 40.34 3.06
388 391 4.457603 ACCGTCATAGTGCTTTATTTTGCA 59.542 37.500 0.00 0.00 36.79 4.08
398 401 6.823182 AGTGCTTTATTTTGCAAAGAACCTTT 59.177 30.769 12.41 0.00 40.91 3.11
427 646 2.597510 GGCAAAGTGGAAGCCGGT 60.598 61.111 1.90 0.00 38.86 5.28
432 651 2.640581 AAAGTGGAAGCCGGTTGCCT 62.641 55.000 17.51 0.00 42.71 4.75
465 684 4.095590 GCTTACAGCCCTTTGCCA 57.904 55.556 0.00 0.00 42.71 4.92
492 711 0.903236 GTAAGCCGAGAAGGGGAAGT 59.097 55.000 0.00 0.00 41.48 3.01
517 737 0.179121 CAACACTCGGCATACGGCTA 60.179 55.000 0.00 0.00 44.45 3.93
541 762 2.505405 GAGTTCAAGGTTTCCTCCACC 58.495 52.381 0.00 0.00 30.89 4.61
579 802 3.302221 CGGCGTATTACGATTTTCCTGTG 60.302 47.826 19.86 0.00 46.05 3.66
581 804 4.493545 GGCGTATTACGATTTTCCTGTGTG 60.494 45.833 19.86 0.00 46.05 3.82
582 805 4.092383 GCGTATTACGATTTTCCTGTGTGT 59.908 41.667 19.86 0.00 46.05 3.72
590 1358 4.690748 CGATTTTCCTGTGTGTGTAGTGAT 59.309 41.667 0.00 0.00 0.00 3.06
592 1360 3.401033 TTCCTGTGTGTGTAGTGATGG 57.599 47.619 0.00 0.00 0.00 3.51
607 1375 9.209175 GTGTAGTGATGGATGGAGTAATATTTC 57.791 37.037 0.00 0.00 0.00 2.17
611 1379 6.710744 GTGATGGATGGAGTAATATTTCCGTT 59.289 38.462 2.99 0.00 36.22 4.44
621 1389 7.331193 GGAGTAATATTTCCGTTCGATATTGCT 59.669 37.037 11.87 11.87 39.64 3.91
622 1390 8.603242 AGTAATATTTCCGTTCGATATTGCTT 57.397 30.769 0.00 0.00 36.15 3.91
623 1391 8.709646 AGTAATATTTCCGTTCGATATTGCTTC 58.290 33.333 0.00 0.00 36.15 3.86
643 1419 4.736126 TCATGAAAGCGGTCTCATCTTA 57.264 40.909 0.00 0.00 29.69 2.10
644 1420 5.084818 TCATGAAAGCGGTCTCATCTTAA 57.915 39.130 0.00 0.00 29.69 1.85
649 1425 0.539986 GCGGTCTCATCTTAACCCCA 59.460 55.000 0.00 0.00 0.00 4.96
658 1435 6.768381 GTCTCATCTTAACCCCAGGATAAAAG 59.232 42.308 0.00 0.00 0.00 2.27
669 1446 3.379372 CCAGGATAAAAGGTGCTCACATG 59.621 47.826 2.21 0.00 0.00 3.21
670 1447 3.019564 AGGATAAAAGGTGCTCACATGC 58.980 45.455 2.21 0.00 0.00 4.06
692 1469 5.183522 TGCTGCATGTTTCATGAATTCTGTA 59.816 36.000 9.40 5.75 0.00 2.74
718 1495 7.444629 ACAAGTACAACTACAAGTATCTCGA 57.555 36.000 0.00 0.00 0.00 4.04
778 1555 5.447279 CGGGTAAACTACAAGCAGCTAATTG 60.447 44.000 0.00 8.20 0.00 2.32
779 1556 5.646360 GGGTAAACTACAAGCAGCTAATTGA 59.354 40.000 15.05 1.31 0.00 2.57
780 1557 6.150474 GGGTAAACTACAAGCAGCTAATTGAA 59.850 38.462 15.05 0.00 0.00 2.69
795 1573 6.264067 AGCTAATTGAATTGCTTACCATCTCC 59.736 38.462 0.00 0.00 30.96 3.71
796 1574 5.505173 AATTGAATTGCTTACCATCTCCG 57.495 39.130 0.00 0.00 0.00 4.63
841 1620 4.026062 CCAATCCAATACGTGTACACATCG 60.026 45.833 24.98 14.15 0.00 3.84
850 1629 3.172050 CGTGTACACATCGAAGAGGAAG 58.828 50.000 24.98 0.81 43.16 3.46
856 1635 5.255710 ACACATCGAAGAGGAAGTCTATG 57.744 43.478 0.00 0.00 43.16 2.23
861 1640 6.038825 ACATCGAAGAGGAAGTCTATGTACAG 59.961 42.308 0.33 0.00 43.16 2.74
921 1702 0.605319 TTACGCCAAGCCCTCAACTG 60.605 55.000 0.00 0.00 0.00 3.16
926 1707 2.224281 CGCCAAGCCCTCAACTGATATA 60.224 50.000 0.00 0.00 0.00 0.86
927 1708 3.557898 CGCCAAGCCCTCAACTGATATAT 60.558 47.826 0.00 0.00 0.00 0.86
930 1711 5.624159 CCAAGCCCTCAACTGATATATTCA 58.376 41.667 0.00 0.00 0.00 2.57
944 1725 6.751157 TGATATATTCAACGTACGGGTCAAT 58.249 36.000 21.06 13.45 0.00 2.57
949 1730 1.997606 CAACGTACGGGTCAATTCCTC 59.002 52.381 21.06 0.00 0.00 3.71
954 1735 0.546747 ACGGGTCAATTCCTCCTCCA 60.547 55.000 0.00 0.00 0.00 3.86
955 1736 0.839946 CGGGTCAATTCCTCCTCCAT 59.160 55.000 0.00 0.00 0.00 3.41
956 1737 1.202698 CGGGTCAATTCCTCCTCCATC 60.203 57.143 0.00 0.00 0.00 3.51
963 1749 1.985622 TTCCTCCTCCATCAACCCAT 58.014 50.000 0.00 0.00 0.00 4.00
966 1752 0.107456 CTCCTCCATCAACCCATCGG 59.893 60.000 0.00 0.00 0.00 4.18
967 1753 1.526917 CCTCCATCAACCCATCGGC 60.527 63.158 0.00 0.00 0.00 5.54
978 1764 2.741985 CATCGGCCGTTCTGCACA 60.742 61.111 27.15 2.48 0.00 4.57
979 1765 2.434884 ATCGGCCGTTCTGCACAG 60.435 61.111 27.15 0.00 0.00 3.66
980 1766 3.958147 ATCGGCCGTTCTGCACAGG 62.958 63.158 27.15 0.00 0.00 4.00
981 1767 4.680237 CGGCCGTTCTGCACAGGA 62.680 66.667 19.50 0.00 0.00 3.86
982 1768 2.281484 GGCCGTTCTGCACAGGAA 60.281 61.111 0.00 0.00 0.00 3.36
983 1769 2.617274 GGCCGTTCTGCACAGGAAC 61.617 63.158 7.14 7.14 39.49 3.62
984 1770 1.891919 GCCGTTCTGCACAGGAACA 60.892 57.895 15.22 0.00 41.99 3.18
993 1779 2.590575 ACAGGAACAACGCCACCG 60.591 61.111 0.00 0.00 41.14 4.94
1283 2069 0.605319 GACGGCAATGTTGTCAGGGA 60.605 55.000 0.00 0.00 31.86 4.20
1378 2164 0.319040 CGGTAGAGCCCATGTGATCG 60.319 60.000 0.00 0.00 0.00 3.69
1401 2187 2.283173 GCCAAAGGGGAGGTGGTG 60.283 66.667 0.00 0.00 40.01 4.17
1424 2210 1.067846 GGACTGCCCGAAACCAAAATC 60.068 52.381 0.00 0.00 0.00 2.17
1426 2212 0.732538 CTGCCCGAAACCAAAATCGC 60.733 55.000 0.00 0.00 37.73 4.58
1429 2215 1.671556 GCCCGAAACCAAAATCGCAAT 60.672 47.619 0.00 0.00 37.73 3.56
1430 2216 2.682836 CCCGAAACCAAAATCGCAATT 58.317 42.857 0.00 0.00 37.73 2.32
1431 2217 2.411409 CCCGAAACCAAAATCGCAATTG 59.589 45.455 0.00 0.00 37.73 2.32
1457 2243 0.874175 GTCTTTGGTTTTGGCCGTGC 60.874 55.000 0.00 0.00 0.00 5.34
1460 2246 1.323271 TTTGGTTTTGGCCGTGCTGA 61.323 50.000 0.00 0.00 0.00 4.26
1467 2253 2.045926 GGCCGTGCTGAACCATCT 60.046 61.111 0.00 0.00 0.00 2.90
1485 2271 1.071699 TCTGGCAAGTACAAGGTGGTC 59.928 52.381 0.00 0.00 0.00 4.02
1501 2287 1.228154 GTCCGCCTCTTGTTGGGTT 60.228 57.895 0.00 0.00 0.00 4.11
1508 2294 1.675552 CTCTTGTTGGGTTGGTCGTT 58.324 50.000 0.00 0.00 0.00 3.85
1539 2325 1.378250 CCTGACGGTAGGAGACGGT 60.378 63.158 1.25 0.00 43.78 4.83
1786 2572 3.486841 CGAACTCAATGGCTGTTTTTGTG 59.513 43.478 0.00 0.00 0.00 3.33
1802 2588 1.678970 GTGTGGTTCATCTGGGGGC 60.679 63.158 0.00 0.00 0.00 5.80
1813 2599 3.006133 TGGGGGCGCACATGACTA 61.006 61.111 13.89 0.00 0.00 2.59
2088 2874 0.754472 TCCGGCCCTAGTTTAATCCG 59.246 55.000 0.00 0.00 36.90 4.18
2099 2885 7.495055 CCCTAGTTTAATCCGCTCTACTTTTA 58.505 38.462 0.00 0.00 0.00 1.52
2100 2886 8.148999 CCCTAGTTTAATCCGCTCTACTTTTAT 58.851 37.037 0.00 0.00 0.00 1.40
2178 2964 2.508891 CGGACTCGTCGCTCAATGC 61.509 63.158 0.00 0.00 38.57 3.56
2183 2969 1.424493 CTCGTCGCTCAATGCCTTCC 61.424 60.000 0.00 0.00 38.78 3.46
2242 3028 0.590732 GCAGAGTGTATGCATTGCGC 60.591 55.000 3.54 0.00 43.31 6.09
2271 3057 7.976175 ACATACATATGTGTAGATATCGGCTTG 59.024 37.037 18.81 0.72 44.66 4.01
2320 3106 8.825745 GCTTTTTCATTGATGGTCAAACTTAAA 58.174 29.630 0.00 0.00 40.12 1.52
2800 3849 4.867608 GGTAGCTTGTCATCTTCAAGAGAC 59.132 45.833 9.40 9.05 43.17 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.808958 CGGCAGGGATAACGCGTTG 61.809 63.158 33.40 17.99 0.00 4.10
35 36 2.510691 CGGCAGGGATAACGCGTT 60.511 61.111 29.27 29.27 0.00 4.84
36 37 3.766691 ACGGCAGGGATAACGCGT 61.767 61.111 5.58 5.58 0.00 6.01
37 38 3.261951 CACGGCAGGGATAACGCG 61.262 66.667 3.53 3.53 0.00 6.01
38 39 1.883084 CTCACGGCAGGGATAACGC 60.883 63.158 0.00 0.00 0.00 4.84
39 40 0.527817 GTCTCACGGCAGGGATAACG 60.528 60.000 0.00 0.00 0.00 3.18
40 41 0.527817 CGTCTCACGGCAGGGATAAC 60.528 60.000 0.00 0.00 38.08 1.89
41 42 1.813859 CGTCTCACGGCAGGGATAA 59.186 57.895 0.00 0.00 38.08 1.75
42 43 2.782222 GCGTCTCACGGCAGGGATA 61.782 63.158 0.00 0.00 42.82 2.59
43 44 4.148825 GCGTCTCACGGCAGGGAT 62.149 66.667 0.00 0.00 42.82 3.85
60 61 2.259618 GTACGCTGGCATCATATACGG 58.740 52.381 0.00 0.00 0.00 4.02
69 70 1.651987 GTACATGTGTACGCTGGCAT 58.348 50.000 9.11 0.00 41.06 4.40
103 104 0.172803 GCTTTTCCAGCTCTGCATGG 59.827 55.000 0.00 0.00 46.27 3.66
150 151 1.935327 AAGCCGAGTACCGCTCTGTC 61.935 60.000 0.63 0.00 41.98 3.51
152 153 0.029567 CTAAGCCGAGTACCGCTCTG 59.970 60.000 0.63 0.00 41.98 3.35
155 156 0.953003 GATCTAAGCCGAGTACCGCT 59.047 55.000 0.00 0.00 36.84 5.52
186 187 0.328592 TCTCCAGCTCTGTCGGTACT 59.671 55.000 0.00 0.00 0.00 2.73
189 190 0.540830 ACTTCTCCAGCTCTGTCGGT 60.541 55.000 0.00 0.00 0.00 4.69
202 203 3.992260 TCTATAAGCCGAGCACTTCTC 57.008 47.619 0.00 0.00 38.47 2.87
203 204 7.683222 GCATATATCTATAAGCCGAGCACTTCT 60.683 40.741 0.00 0.00 29.32 2.85
204 205 6.419413 GCATATATCTATAAGCCGAGCACTTC 59.581 42.308 0.00 0.00 29.32 3.01
205 206 6.276847 GCATATATCTATAAGCCGAGCACTT 58.723 40.000 0.00 0.00 29.32 3.16
206 207 5.221342 GGCATATATCTATAAGCCGAGCACT 60.221 44.000 7.50 0.00 41.41 4.40
207 208 4.985409 GGCATATATCTATAAGCCGAGCAC 59.015 45.833 7.50 0.00 41.41 4.40
208 209 5.201713 GGCATATATCTATAAGCCGAGCA 57.798 43.478 7.50 0.00 41.41 4.26
213 214 4.693283 TGCACGGCATATATCTATAAGCC 58.307 43.478 11.65 11.65 45.03 4.35
214 215 5.592054 TCTGCACGGCATATATCTATAAGC 58.408 41.667 0.00 0.00 38.13 3.09
215 216 5.689514 GCTCTGCACGGCATATATCTATAAG 59.310 44.000 0.00 0.00 38.13 1.73
216 217 5.127031 TGCTCTGCACGGCATATATCTATAA 59.873 40.000 4.91 0.00 38.13 0.98
217 218 4.644685 TGCTCTGCACGGCATATATCTATA 59.355 41.667 4.91 0.00 38.13 1.31
218 219 3.448660 TGCTCTGCACGGCATATATCTAT 59.551 43.478 4.91 0.00 38.13 1.98
219 220 2.825532 TGCTCTGCACGGCATATATCTA 59.174 45.455 4.91 0.00 38.13 1.98
220 221 1.620323 TGCTCTGCACGGCATATATCT 59.380 47.619 4.91 0.00 38.13 1.98
221 222 1.998315 CTGCTCTGCACGGCATATATC 59.002 52.381 8.94 0.00 38.13 1.63
222 223 1.620323 TCTGCTCTGCACGGCATATAT 59.380 47.619 8.94 0.00 38.13 0.86
223 224 1.039856 TCTGCTCTGCACGGCATATA 58.960 50.000 8.94 0.00 38.13 0.86
224 225 0.178767 TTCTGCTCTGCACGGCATAT 59.821 50.000 8.94 0.00 38.13 1.78
225 226 0.036483 TTTCTGCTCTGCACGGCATA 60.036 50.000 8.94 0.63 38.13 3.14
226 227 0.890542 TTTTCTGCTCTGCACGGCAT 60.891 50.000 8.94 0.00 38.13 4.40
227 228 1.100463 TTTTTCTGCTCTGCACGGCA 61.100 50.000 8.31 8.31 33.79 5.69
228 229 0.661483 GTTTTTCTGCTCTGCACGGC 60.661 55.000 0.00 0.00 33.79 5.68
229 230 0.384725 CGTTTTTCTGCTCTGCACGG 60.385 55.000 0.00 0.00 33.79 4.94
230 231 0.993746 GCGTTTTTCTGCTCTGCACG 60.994 55.000 0.00 0.00 33.79 5.34
231 232 0.308993 AGCGTTTTTCTGCTCTGCAC 59.691 50.000 0.00 0.00 36.53 4.57
232 233 2.706636 AGCGTTTTTCTGCTCTGCA 58.293 47.368 0.00 0.00 36.53 4.41
237 238 1.166531 AAGCCGAGCGTTTTTCTGCT 61.167 50.000 0.00 0.00 45.90 4.24
238 239 0.515564 TAAGCCGAGCGTTTTTCTGC 59.484 50.000 0.00 0.00 0.00 4.26
239 240 3.544244 GCTATAAGCCGAGCGTTTTTCTG 60.544 47.826 0.00 0.00 34.48 3.02
240 241 2.608090 GCTATAAGCCGAGCGTTTTTCT 59.392 45.455 0.00 0.00 34.48 2.52
316 317 2.053627 GCATGTTTGTAAGCTGTGTGC 58.946 47.619 0.00 0.00 43.29 4.57
347 348 1.678728 GGTCATCAAATGGAGACGGCA 60.679 52.381 0.00 0.00 31.93 5.69
365 366 4.457603 TGCAAAATAAAGCACTATGACGGT 59.542 37.500 0.00 0.00 35.51 4.83
371 374 7.670364 AGGTTCTTTGCAAAATAAAGCACTAT 58.330 30.769 22.28 8.12 41.05 2.12
372 375 7.049799 AGGTTCTTTGCAAAATAAAGCACTA 57.950 32.000 22.28 0.00 41.05 2.74
388 391 4.995487 CCGAGTGCTAAGTAAAGGTTCTTT 59.005 41.667 0.00 0.00 0.00 2.52
426 645 2.603173 CGAGAGCTTTTTCACAGGCAAC 60.603 50.000 0.00 0.00 0.00 4.17
427 646 1.603802 CGAGAGCTTTTTCACAGGCAA 59.396 47.619 0.00 0.00 0.00 4.52
465 684 2.615493 CCTTCTCGGCTTACACCATGTT 60.615 50.000 0.00 0.00 0.00 2.71
517 737 2.486727 GGAGGAAACCTTGAACTCGGTT 60.487 50.000 0.00 0.00 45.01 4.44
521 741 2.505405 GGTGGAGGAAACCTTGAACTC 58.495 52.381 0.00 0.00 31.76 3.01
525 745 0.685097 CTCGGTGGAGGAAACCTTGA 59.315 55.000 0.00 0.00 36.61 3.02
579 802 3.895232 ACTCCATCCATCACTACACAC 57.105 47.619 0.00 0.00 0.00 3.82
581 804 9.209175 GAAATATTACTCCATCCATCACTACAC 57.791 37.037 0.00 0.00 0.00 2.90
582 805 8.375506 GGAAATATTACTCCATCCATCACTACA 58.624 37.037 1.87 0.00 0.00 2.74
590 1358 5.069383 TCGAACGGAAATATTACTCCATCCA 59.931 40.000 6.92 0.00 0.00 3.41
592 1360 8.928270 ATATCGAACGGAAATATTACTCCATC 57.072 34.615 6.92 3.90 0.00 3.51
607 1375 4.794248 TTCATGAAGCAATATCGAACGG 57.206 40.909 3.38 0.00 0.00 4.44
621 1389 3.616956 AGATGAGACCGCTTTCATGAA 57.383 42.857 3.38 3.38 34.33 2.57
622 1390 3.616956 AAGATGAGACCGCTTTCATGA 57.383 42.857 0.00 0.00 34.33 3.07
623 1391 4.034510 GGTTAAGATGAGACCGCTTTCATG 59.965 45.833 0.00 0.00 34.33 3.07
632 1408 2.478292 TCCTGGGGTTAAGATGAGACC 58.522 52.381 0.00 0.00 0.00 3.85
643 1419 1.716503 AGCACCTTTTATCCTGGGGTT 59.283 47.619 0.00 0.00 0.00 4.11
644 1420 1.285078 GAGCACCTTTTATCCTGGGGT 59.715 52.381 0.00 0.00 0.00 4.95
649 1425 3.019564 GCATGTGAGCACCTTTTATCCT 58.980 45.455 0.00 0.00 0.00 3.24
658 1435 1.138883 CATGCAGCATGTGAGCACC 59.861 57.895 25.12 0.00 41.60 5.01
669 1446 4.491676 ACAGAATTCATGAAACATGCAGC 58.508 39.130 13.09 0.00 0.00 5.25
670 1447 8.400186 TGTATACAGAATTCATGAAACATGCAG 58.600 33.333 13.09 2.06 0.00 4.41
692 1469 9.170734 TCGAGATACTTGTAGTTGTACTTGTAT 57.829 33.333 0.00 0.00 34.25 2.29
725 1502 8.996024 AAAACAAATGCTTGTAGTTGTACTTT 57.004 26.923 5.15 1.75 45.25 2.66
726 1503 8.996024 AAAAACAAATGCTTGTAGTTGTACTT 57.004 26.923 5.15 0.87 45.25 2.24
778 1555 4.438744 CCAAACGGAGATGGTAAGCAATTC 60.439 45.833 0.00 0.00 34.39 2.17
779 1556 3.443681 CCAAACGGAGATGGTAAGCAATT 59.556 43.478 0.00 0.00 34.39 2.32
780 1557 3.016736 CCAAACGGAGATGGTAAGCAAT 58.983 45.455 0.00 0.00 34.39 3.56
795 1573 6.073657 TGGACTCGTATTTTACTTTCCAAACG 60.074 38.462 0.00 0.00 30.40 3.60
796 1574 7.193377 TGGACTCGTATTTTACTTTCCAAAC 57.807 36.000 0.00 0.00 30.40 2.93
841 1620 5.585445 TCGTCTGTACATAGACTTCCTCTTC 59.415 44.000 12.02 0.00 43.82 2.87
850 1629 4.698583 AGGTGTTCGTCTGTACATAGAC 57.301 45.455 0.00 0.07 42.83 2.59
856 1635 1.529865 GGCAAAGGTGTTCGTCTGTAC 59.470 52.381 0.00 0.00 0.00 2.90
861 1640 2.613506 CGGGGCAAAGGTGTTCGTC 61.614 63.158 0.00 0.00 0.00 4.20
921 1702 7.148689 GGAATTGACCCGTACGTTGAATATATC 60.149 40.741 15.21 2.08 0.00 1.63
926 1707 3.004862 GGAATTGACCCGTACGTTGAAT 58.995 45.455 15.21 3.84 0.00 2.57
927 1708 2.037511 AGGAATTGACCCGTACGTTGAA 59.962 45.455 15.21 1.36 0.00 2.69
930 1711 1.066645 GGAGGAATTGACCCGTACGTT 60.067 52.381 15.21 0.00 0.00 3.99
944 1725 1.846439 GATGGGTTGATGGAGGAGGAA 59.154 52.381 0.00 0.00 0.00 3.36
949 1730 1.526917 GCCGATGGGTTGATGGAGG 60.527 63.158 0.00 0.00 34.97 4.30
954 1735 1.451387 GAACGGCCGATGGGTTGAT 60.451 57.895 35.90 1.64 34.97 2.57
955 1736 2.046700 GAACGGCCGATGGGTTGA 60.047 61.111 35.90 0.00 34.97 3.18
956 1737 2.046314 AGAACGGCCGATGGGTTG 60.046 61.111 35.90 0.00 34.97 3.77
963 1749 4.680237 CCTGTGCAGAACGGCCGA 62.680 66.667 35.90 4.54 33.36 5.54
966 1752 1.444119 TTGTTCCTGTGCAGAACGGC 61.444 55.000 11.39 0.00 33.36 5.68
967 1753 0.307760 GTTGTTCCTGTGCAGAACGG 59.692 55.000 11.39 0.00 34.63 4.44
1009 1795 4.025401 GCGTTTGGGTGACAGCGG 62.025 66.667 0.00 0.00 32.46 5.52
1010 1796 4.025401 GGCGTTTGGGTGACAGCG 62.025 66.667 0.00 0.00 34.11 5.18
1017 1803 3.591835 CAACAGCGGCGTTTGGGT 61.592 61.111 9.37 0.00 0.00 4.51
1283 2069 0.536006 GCCGCCTATGCCTTTCATCT 60.536 55.000 0.00 0.00 36.63 2.90
1368 2154 1.592669 GGCGAGGTCGATCACATGG 60.593 63.158 2.94 0.00 43.02 3.66
1378 2164 2.269241 CTCCCCTTTGGCGAGGTC 59.731 66.667 6.06 0.00 34.88 3.85
1401 2187 2.671963 GGTTTCGGGCAGTCCACC 60.672 66.667 0.00 0.00 34.36 4.61
1424 2210 0.317770 AAAGACGTGGTGCAATTGCG 60.318 50.000 24.58 12.76 45.83 4.85
1426 2212 1.769733 CCAAAGACGTGGTGCAATTG 58.230 50.000 0.00 0.00 33.63 2.32
1457 2243 3.057969 TGTACTTGCCAGATGGTTCAG 57.942 47.619 0.00 0.00 37.57 3.02
1460 2246 2.108250 ACCTTGTACTTGCCAGATGGTT 59.892 45.455 0.00 0.00 37.57 3.67
1467 2253 0.109723 GGACCACCTTGTACTTGCCA 59.890 55.000 0.00 0.00 0.00 4.92
1485 2271 2.268076 CCAACCCAACAAGAGGCGG 61.268 63.158 0.00 0.00 0.00 6.13
1501 2287 0.603707 ACCTCGTAGTCGAACGACCA 60.604 55.000 20.97 7.50 46.29 4.02
1508 2294 0.738762 CGTCAGGACCTCGTAGTCGA 60.739 60.000 0.00 0.00 44.12 4.20
1786 2572 2.438434 CGCCCCCAGATGAACCAC 60.438 66.667 0.00 0.00 0.00 4.16
1802 2588 3.030668 TGAGCCATATAGTCATGTGCG 57.969 47.619 0.00 0.00 31.42 5.34
1813 2599 3.580022 TCTGATTCGGTCATGAGCCATAT 59.420 43.478 18.81 9.60 35.97 1.78
1912 2698 0.327924 ATCAACTTCCCGCCATCACA 59.672 50.000 0.00 0.00 0.00 3.58
2088 2874 6.918022 ACACAAAAGCACAATAAAAGTAGAGC 59.082 34.615 0.00 0.00 0.00 4.09
2135 2921 2.226712 ATCATGCACACGCGTTGACG 62.227 55.000 10.22 0.00 42.97 4.35
2178 2964 9.163899 GTAAGAACTAATAGGAAAACAGGAAGG 57.836 37.037 0.00 0.00 0.00 3.46
2242 3028 8.595533 GCCGATATCTACACATATGTATGTTTG 58.404 37.037 8.32 0.00 43.99 2.93
2250 3036 5.578336 CACCAAGCCGATATCTACACATATG 59.422 44.000 0.00 0.00 0.00 1.78
2251 3037 5.246203 ACACCAAGCCGATATCTACACATAT 59.754 40.000 0.34 0.00 0.00 1.78
2252 3038 4.587262 ACACCAAGCCGATATCTACACATA 59.413 41.667 0.34 0.00 0.00 2.29
2253 3039 3.388024 ACACCAAGCCGATATCTACACAT 59.612 43.478 0.34 0.00 0.00 3.21
2271 3057 6.149474 AGCAAGATAACAACATCTACAACACC 59.851 38.462 0.00 0.00 34.08 4.16
2338 3385 2.293677 TTGGAGATCACCAACGATCG 57.706 50.000 19.34 14.88 45.39 3.69
2538 3587 2.224314 TGCTCATCTAGATAGACACGCG 59.776 50.000 3.53 3.53 34.72 6.01
2689 3738 4.109050 TGAAAATTTCTGTTGCAACCGAC 58.891 39.130 26.14 12.51 0.00 4.79
2800 3849 1.796459 GGCATGAAAGTTTTGCTGCTG 59.204 47.619 11.12 0.00 36.62 4.41


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

AutoCloner maintained by Alex Coulton.