Multiple sequence alignment - TraesCS6D01G293800

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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 TraesCS6D01G293800 chr6D 100.000 3643 0 0 1 3643 404591365 404595007 0.000000e+00 6728.0
1 TraesCS6D01G293800 chr6D 80.674 564 81 9 1 537 262746830 262746268 2.620000e-111 412.0
2 TraesCS6D01G293800 chr6D 80.354 565 80 14 1 537 68087802 68088363 2.040000e-107 399.0
3 TraesCS6D01G293800 chr6D 94.545 165 8 1 3232 3395 229430891 229431055 1.680000e-63 254.0
4 TraesCS6D01G293800 chr6D 89.744 78 8 0 3055 3132 72021808 72021731 2.310000e-17 100.0
5 TraesCS6D01G293800 chr6D 84.810 79 8 1 3054 3128 464768222 464768300 3.900000e-10 76.8
6 TraesCS6D01G293800 chr6A 86.329 2092 175 55 1 2042 551086203 551088233 0.000000e+00 2176.0
7 TraesCS6D01G293800 chr6A 92.424 924 50 11 2546 3463 551089281 551090190 0.000000e+00 1301.0
8 TraesCS6D01G293800 chr6A 94.094 508 17 6 2042 2544 551088423 551088922 0.000000e+00 760.0
9 TraesCS6D01G293800 chr6A 95.395 152 7 0 3448 3599 551090209 551090360 3.630000e-60 243.0
10 TraesCS6D01G293800 chr6A 91.026 78 7 0 3055 3132 88767667 88767590 4.980000e-19 106.0
11 TraesCS6D01G293800 chr6B 93.608 1189 44 10 2042 3220 606963585 606964751 0.000000e+00 1746.0
12 TraesCS6D01G293800 chr6B 85.889 900 43 29 647 1501 606961879 606962739 0.000000e+00 881.0
13 TraesCS6D01G293800 chr6B 90.359 529 29 13 1497 2007 606962867 606963391 0.000000e+00 675.0
14 TraesCS6D01G293800 chr6B 80.031 641 98 20 1 622 606838318 606838947 7.180000e-122 448.0
15 TraesCS6D01G293800 chr6B 95.385 260 8 2 3388 3643 606965146 606965405 9.410000e-111 411.0
16 TraesCS6D01G293800 chr6B 80.034 591 83 17 1 562 662144656 662145240 4.380000e-109 405.0
17 TraesCS6D01G293800 chr2A 80.475 589 85 18 8 571 617430017 617429434 1.210000e-114 424.0
18 TraesCS6D01G293800 chr3D 80.135 594 94 13 1 571 407210368 407209776 4.350000e-114 422.0
19 TraesCS6D01G293800 chr3D 94.643 168 6 2 3231 3395 486424786 486424953 1.300000e-64 257.0
20 TraesCS6D01G293800 chrUn 80.071 562 84 10 1 535 33187254 33187814 3.410000e-105 392.0
21 TraesCS6D01G293800 chr5D 81.458 480 82 5 94 572 481954991 481955464 1.590000e-103 387.0
22 TraesCS6D01G293800 chr5D 80.952 504 78 12 1 488 495020642 495020141 2.050000e-102 383.0
23 TraesCS6D01G293800 chr5D 78.024 587 86 26 1 560 551088936 551089506 2.710000e-86 329.0
24 TraesCS6D01G293800 chr7B 79.381 582 89 13 9 560 678903975 678904555 7.380000e-102 381.0
25 TraesCS6D01G293800 chr7B 91.620 179 13 2 3216 3392 123945202 123945380 2.810000e-61 246.0
26 TraesCS6D01G293800 chr7B 88.372 86 9 1 9 93 679095318 679095403 6.440000e-18 102.0
27 TraesCS6D01G293800 chr1D 80.855 491 74 18 87 571 232139689 232140165 5.750000e-98 368.0
28 TraesCS6D01G293800 chr3A 81.422 436 54 13 1 410 31668661 31669095 7.540000e-87 331.0
29 TraesCS6D01G293800 chr2B 77.837 564 90 24 1 538 164627397 164626843 2.110000e-82 316.0
30 TraesCS6D01G293800 chr2B 93.491 169 10 1 3232 3399 255572378 255572210 2.170000e-62 250.0
31 TraesCS6D01G293800 chr7A 76.283 565 101 15 1 533 239189487 239188924 1.670000e-68 270.0
32 TraesCS6D01G293800 chr7D 95.783 166 5 1 3232 3395 235502568 235502403 2.160000e-67 267.0
33 TraesCS6D01G293800 chr3B 91.848 184 12 3 3224 3406 252358614 252358433 1.680000e-63 254.0
34 TraesCS6D01G293800 chr3B 85.366 82 8 1 3055 3132 637059475 637059394 8.380000e-12 82.4
35 TraesCS6D01G293800 chr2D 94.545 165 8 1 3231 3394 445733670 445733834 1.680000e-63 254.0
36 TraesCS6D01G293800 chr4B 94.012 167 9 1 3229 3394 483266376 483266542 6.040000e-63 252.0
37 TraesCS6D01G293800 chr5A 86.486 74 5 2 3055 3123 333742865 333742938 3.900000e-10 76.8
38 TraesCS6D01G293800 chr1A 84.337 83 8 2 3055 3132 587861394 587861312 3.900000e-10 76.8
39 TraesCS6D01G293800 chr1B 81.720 93 11 3 3056 3142 571427503 571427595 5.050000e-09 73.1


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 TraesCS6D01G293800 chr6D 404591365 404595007 3642 False 6728.00 6728 100.00000 1 3643 1 chr6D.!!$F3 3642
1 TraesCS6D01G293800 chr6D 262746268 262746830 562 True 412.00 412 80.67400 1 537 1 chr6D.!!$R2 536
2 TraesCS6D01G293800 chr6D 68087802 68088363 561 False 399.00 399 80.35400 1 537 1 chr6D.!!$F1 536
3 TraesCS6D01G293800 chr6A 551086203 551090360 4157 False 1120.00 2176 92.06050 1 3599 4 chr6A.!!$F1 3598
4 TraesCS6D01G293800 chr6B 606961879 606965405 3526 False 928.25 1746 91.31025 647 3643 4 chr6B.!!$F3 2996
5 TraesCS6D01G293800 chr6B 606838318 606838947 629 False 448.00 448 80.03100 1 622 1 chr6B.!!$F1 621
6 TraesCS6D01G293800 chr6B 662144656 662145240 584 False 405.00 405 80.03400 1 562 1 chr6B.!!$F2 561
7 TraesCS6D01G293800 chr2A 617429434 617430017 583 True 424.00 424 80.47500 8 571 1 chr2A.!!$R1 563
8 TraesCS6D01G293800 chr3D 407209776 407210368 592 True 422.00 422 80.13500 1 571 1 chr3D.!!$R1 570
9 TraesCS6D01G293800 chrUn 33187254 33187814 560 False 392.00 392 80.07100 1 535 1 chrUn.!!$F1 534
10 TraesCS6D01G293800 chr5D 495020141 495020642 501 True 383.00 383 80.95200 1 488 1 chr5D.!!$R1 487
11 TraesCS6D01G293800 chr5D 551088936 551089506 570 False 329.00 329 78.02400 1 560 1 chr5D.!!$F2 559
12 TraesCS6D01G293800 chr7B 678903975 678904555 580 False 381.00 381 79.38100 9 560 1 chr7B.!!$F2 551
13 TraesCS6D01G293800 chr2B 164626843 164627397 554 True 316.00 316 77.83700 1 538 1 chr2B.!!$R1 537
14 TraesCS6D01G293800 chr7A 239188924 239189487 563 True 270.00 270 76.28300 1 533 1 chr7A.!!$R1 532

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
889 994 0.035439 AGCCCACGAAATCCAACGAT 60.035 50.0 0.0 0.0 0.0 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2651 3500 0.038526 ACGCAGACTCTTGTAACCCG 60.039 55.0 0.0 0.0 0.0 5.28 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
140 177 6.477033 CGACGACTTCTTGAAGATGGAATAAT 59.523 38.462 16.21 0.00 0.00 1.28
280 347 4.668576 TCTTCGTTCGTCTACGTATGTT 57.331 40.909 0.00 0.00 42.01 2.71
328 408 1.153549 GCTTCTCTTCATCGGCGGT 60.154 57.895 7.21 0.00 0.00 5.68
333 413 0.174845 CTCTTCATCGGCGGTGGTTA 59.825 55.000 21.45 5.36 0.00 2.85
347 427 2.147958 GTGGTTATTGTTCTGGTGCGA 58.852 47.619 0.00 0.00 0.00 5.10
357 437 0.613572 TCTGGTGCGATGGTCCTACA 60.614 55.000 0.00 0.00 0.00 2.74
385 465 6.732154 CCTTAATACGATGACTTTCCGACTA 58.268 40.000 0.00 0.00 0.00 2.59
404 487 7.972277 TCCGACTATCTACTACAACAATGTTTC 59.028 37.037 0.00 0.00 41.05 2.78
411 494 1.786937 ACAACAATGTTTCCCTGGCA 58.213 45.000 0.00 0.00 35.91 4.92
481 564 6.457392 CGAATACTTGTAGTCGTTGCTAGGTA 60.457 42.308 18.45 0.00 33.54 3.08
510 593 4.503007 CGGACGTGGATGTAATTCTTACTG 59.497 45.833 0.00 0.00 37.06 2.74
546 630 4.345859 ACTACCTTGACAACCGATGAAA 57.654 40.909 0.00 0.00 0.00 2.69
547 631 4.315803 ACTACCTTGACAACCGATGAAAG 58.684 43.478 0.00 0.00 0.00 2.62
548 632 3.485463 ACCTTGACAACCGATGAAAGA 57.515 42.857 0.00 0.00 31.88 2.52
549 633 4.021102 ACCTTGACAACCGATGAAAGAT 57.979 40.909 0.00 0.00 31.88 2.40
551 635 4.002982 CCTTGACAACCGATGAAAGATCA 58.997 43.478 0.00 0.00 40.57 2.92
556 640 5.939883 TGACAACCGATGAAAGATCAGAAAT 59.060 36.000 0.00 0.00 39.39 2.17
563 647 8.025445 ACCGATGAAAGATCAGAAATTTTCTTG 58.975 33.333 8.95 5.76 39.39 3.02
564 648 8.239314 CCGATGAAAGATCAGAAATTTTCTTGA 58.761 33.333 8.95 10.34 39.39 3.02
583 669 9.487790 TTTCTTGAAAGAAACTCACATTTTGTT 57.512 25.926 12.99 0.00 46.80 2.83
584 670 8.687824 TCTTGAAAGAAACTCACATTTTGTTC 57.312 30.769 0.00 0.00 30.73 3.18
600 687 6.978024 TTTTGTTCGTGAAAATAATGGTCG 57.022 33.333 0.00 0.00 0.00 4.79
628 715 8.780846 ATTAGACATAAAAATACGACACACCA 57.219 30.769 0.00 0.00 0.00 4.17
661 751 0.804989 GGTTACACACCATGCTGCTC 59.195 55.000 0.00 0.00 46.42 4.26
704 795 3.523157 TGGGTGATGACTTGTATCCACAT 59.477 43.478 0.00 0.00 33.76 3.21
734 825 2.438434 CCGCCAAGGCCCAACTAG 60.438 66.667 5.34 0.00 37.98 2.57
770 861 0.250124 TCGGGCGTGTCAAATTCTGT 60.250 50.000 0.00 0.00 0.00 3.41
782 873 4.821805 GTCAAATTCTGTTCCAGTCTTCCA 59.178 41.667 0.00 0.00 32.61 3.53
783 874 5.299279 GTCAAATTCTGTTCCAGTCTTCCAA 59.701 40.000 0.00 0.00 32.61 3.53
792 883 4.829064 TCCAGTCTTCCAAACGAAAATG 57.171 40.909 0.00 0.00 0.00 2.32
793 884 3.568007 TCCAGTCTTCCAAACGAAAATGG 59.432 43.478 0.00 0.00 38.09 3.16
794 885 3.317993 CCAGTCTTCCAAACGAAAATGGT 59.682 43.478 0.00 0.00 37.94 3.55
795 886 4.202111 CCAGTCTTCCAAACGAAAATGGTT 60.202 41.667 0.00 0.00 37.94 3.67
796 887 5.348164 CAGTCTTCCAAACGAAAATGGTTT 58.652 37.500 0.00 0.00 38.07 3.27
797 888 5.810074 CAGTCTTCCAAACGAAAATGGTTTT 59.190 36.000 0.00 0.00 35.53 2.43
798 889 6.312672 CAGTCTTCCAAACGAAAATGGTTTTT 59.687 34.615 0.00 0.00 35.53 1.94
889 994 0.035439 AGCCCACGAAATCCAACGAT 60.035 50.000 0.00 0.00 0.00 3.73
898 1003 2.496899 AATCCAACGATTGCCAGACT 57.503 45.000 0.00 0.00 37.33 3.24
966 1092 4.483243 GCGGCGAAGGAATCCCCA 62.483 66.667 12.98 0.00 37.41 4.96
1209 1351 2.866523 TAGGGGGCGGATCGTGTTCT 62.867 60.000 0.00 0.00 0.00 3.01
1240 1382 1.078143 GCTGGCAATCGAGTCCCTT 60.078 57.895 0.00 0.00 0.00 3.95
1252 1394 3.564225 TCGAGTCCCTTTTCTTTTTCTGC 59.436 43.478 0.00 0.00 0.00 4.26
1256 1398 2.965147 TCCCTTTTCTTTTTCTGCTGGG 59.035 45.455 0.00 0.00 0.00 4.45
1261 1403 3.297134 TTCTTTTTCTGCTGGGTGAGT 57.703 42.857 0.00 0.00 0.00 3.41
1264 1406 3.632145 TCTTTTTCTGCTGGGTGAGTTTC 59.368 43.478 0.00 0.00 0.00 2.78
1265 1407 3.297134 TTTTCTGCTGGGTGAGTTTCT 57.703 42.857 0.00 0.00 0.00 2.52
1266 1408 2.550830 TTCTGCTGGGTGAGTTTCTC 57.449 50.000 0.00 0.00 0.00 2.87
1267 1409 1.423584 TCTGCTGGGTGAGTTTCTCA 58.576 50.000 0.00 0.00 38.25 3.27
1396 1539 1.212688 TGCCCCATCACACCATTCTAG 59.787 52.381 0.00 0.00 0.00 2.43
1397 1540 1.212935 GCCCCATCACACCATTCTAGT 59.787 52.381 0.00 0.00 0.00 2.57
1398 1541 2.438021 GCCCCATCACACCATTCTAGTA 59.562 50.000 0.00 0.00 0.00 1.82
1399 1542 3.744530 GCCCCATCACACCATTCTAGTAC 60.745 52.174 0.00 0.00 0.00 2.73
1400 1543 3.711704 CCCCATCACACCATTCTAGTACT 59.288 47.826 0.00 0.00 0.00 2.73
1401 1544 4.443457 CCCCATCACACCATTCTAGTACTG 60.443 50.000 5.39 0.00 0.00 2.74
1402 1545 4.122776 CCATCACACCATTCTAGTACTGC 58.877 47.826 5.39 0.00 0.00 4.40
1403 1546 4.383010 CCATCACACCATTCTAGTACTGCA 60.383 45.833 5.39 0.00 0.00 4.41
1404 1547 5.363101 CATCACACCATTCTAGTACTGCAT 58.637 41.667 5.39 0.00 0.00 3.96
1405 1548 4.758688 TCACACCATTCTAGTACTGCATG 58.241 43.478 5.39 4.84 0.00 4.06
1406 1549 4.222810 TCACACCATTCTAGTACTGCATGT 59.777 41.667 5.39 0.00 0.00 3.21
1418 1561 1.970640 ACTGCATGTTTTTCCCCTTCC 59.029 47.619 0.00 0.00 0.00 3.46
1467 1610 2.222729 CGGAAATCGCTTACCTGAAACG 60.223 50.000 0.00 0.00 0.00 3.60
1527 1802 7.497925 ACTTTAACCTAGAAACTCTGCTTTG 57.502 36.000 0.00 0.00 0.00 2.77
1547 1822 4.023739 TGATTCTTTTGCTCATCATGCG 57.976 40.909 0.00 0.00 0.00 4.73
1618 1908 8.406297 GTGGAAATGACCAATCTACTATTTTCC 58.594 37.037 0.00 0.00 41.87 3.13
1694 1984 4.818546 AGATTTCAGGACATTAATGAGGCG 59.181 41.667 22.16 7.72 0.00 5.52
1723 2013 3.189702 GGTGCGCTTTGGTAGTTGATAAA 59.810 43.478 9.73 0.00 0.00 1.40
1724 2014 4.320641 GGTGCGCTTTGGTAGTTGATAAAA 60.321 41.667 9.73 0.00 0.00 1.52
1726 2016 5.511729 GTGCGCTTTGGTAGTTGATAAAATC 59.488 40.000 9.73 0.00 0.00 2.17
1910 2201 2.939103 ACTAATGCGCAAGAGTTCATCC 59.061 45.455 17.11 0.00 43.02 3.51
1922 2213 4.023980 AGAGTTCATCCACGAGTAATCCA 58.976 43.478 0.00 0.00 0.00 3.41
1923 2214 4.113354 GAGTTCATCCACGAGTAATCCAC 58.887 47.826 0.00 0.00 0.00 4.02
1924 2215 3.769844 AGTTCATCCACGAGTAATCCACT 59.230 43.478 0.00 0.00 41.47 4.00
1925 2216 4.954202 AGTTCATCCACGAGTAATCCACTA 59.046 41.667 0.00 0.00 37.72 2.74
1926 2217 5.421056 AGTTCATCCACGAGTAATCCACTAA 59.579 40.000 0.00 0.00 37.72 2.24
1927 2218 6.098409 AGTTCATCCACGAGTAATCCACTAAT 59.902 38.462 0.00 0.00 37.72 1.73
1928 2219 6.085555 TCATCCACGAGTAATCCACTAATC 57.914 41.667 0.00 0.00 37.72 1.75
1929 2220 4.931661 TCCACGAGTAATCCACTAATCC 57.068 45.455 0.00 0.00 37.72 3.01
1941 2232 6.699575 ATCCACTAATCCTAAACATTGCAC 57.300 37.500 0.00 0.00 0.00 4.57
2019 2316 1.823169 TTGCGGTACCTGGTGGAGTC 61.823 60.000 10.23 0.00 37.04 3.36
2024 2321 1.829849 GGTACCTGGTGGAGTCTTACC 59.170 57.143 10.23 2.22 37.48 2.85
2100 2587 5.300286 GGCCATCAAACTATGCACTTAGATT 59.700 40.000 0.00 0.00 0.00 2.40
2190 2677 3.499737 GGAGGTTGGTCGCATGCG 61.500 66.667 33.61 33.61 41.35 4.73
2380 2868 4.785346 AGGATGATACATCAGGTGCTTT 57.215 40.909 12.66 0.00 40.64 3.51
2523 3015 1.618143 CCACCCACCCCTCACCATA 60.618 63.158 0.00 0.00 0.00 2.74
2651 3500 1.070758 TCTGTGTGGTGAGCTTTCTCC 59.929 52.381 0.00 0.00 38.58 3.71
2655 3504 1.841556 TGGTGAGCTTTCTCCGGGT 60.842 57.895 0.00 0.00 38.58 5.28
2717 3566 6.370718 GTGTGTAGTTGTAAAATCCCACCTAG 59.629 42.308 0.00 0.00 28.66 3.02
2942 3798 0.454600 CATTGAGTGTGGCTGGATGC 59.545 55.000 0.00 0.00 41.94 3.91
3080 3936 8.159229 ACTCCCTCTGTAAACAAATATAAGGT 57.841 34.615 0.00 0.00 0.00 3.50
3081 3937 9.275572 ACTCCCTCTGTAAACAAATATAAGGTA 57.724 33.333 0.00 0.00 0.00 3.08
3172 4035 1.886886 TTGGTCGCCAAGTAACTTCC 58.113 50.000 7.15 0.00 38.75 3.46
3173 4036 0.320073 TGGTCGCCAAGTAACTTCCG 60.320 55.000 0.00 0.00 0.00 4.30
3174 4037 0.037975 GGTCGCCAAGTAACTTCCGA 60.038 55.000 0.00 0.00 0.00 4.55
3175 4038 1.606224 GGTCGCCAAGTAACTTCCGAA 60.606 52.381 0.00 0.00 30.25 4.30
3176 4039 1.725164 GTCGCCAAGTAACTTCCGAAG 59.275 52.381 6.59 6.59 30.25 3.79
3177 4040 1.342174 TCGCCAAGTAACTTCCGAAGT 59.658 47.619 8.03 8.03 45.46 3.01
3237 4481 7.769220 TCAGTTTTCTCTTACCTAATACTCCG 58.231 38.462 0.00 0.00 0.00 4.63
3246 4490 2.305009 CCTAATACTCCGTCCGTTCCT 58.695 52.381 0.00 0.00 0.00 3.36
3251 4495 6.207417 CCTAATACTCCGTCCGTTCCTAAATA 59.793 42.308 0.00 0.00 0.00 1.40
3261 4505 7.042925 CCGTCCGTTCCTAAATATAAGTCTTTG 60.043 40.741 0.00 0.00 0.00 2.77
3262 4506 7.042925 CGTCCGTTCCTAAATATAAGTCTTTGG 60.043 40.741 0.00 0.00 0.00 3.28
3275 4519 9.829507 ATATAAGTCTTTGGAGAGATTTCACTG 57.170 33.333 0.00 0.00 31.07 3.66
3276 4520 5.559148 AGTCTTTGGAGAGATTTCACTGT 57.441 39.130 0.00 0.00 31.07 3.55
3280 4525 3.969287 TGGAGAGATTTCACTGTGGAG 57.031 47.619 8.11 0.00 0.00 3.86
3287 4532 6.868622 AGAGATTTCACTGTGGAGTACATAC 58.131 40.000 8.11 0.00 38.92 2.39
3298 4543 4.034048 GTGGAGTACATACGGAGCAAAATG 59.966 45.833 0.00 0.00 0.00 2.32
3300 4545 4.508124 GGAGTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
3341 4587 8.877808 AATGCATCTATATACATCCGTATGTG 57.122 34.615 3.56 0.00 45.99 3.21
3344 4590 7.093509 TGCATCTATATACATCCGTATGTGGTT 60.094 37.037 3.56 0.00 45.99 3.67
3345 4591 7.435488 GCATCTATATACATCCGTATGTGGTTC 59.565 40.741 3.56 0.00 45.99 3.62
3346 4592 8.466798 CATCTATATACATCCGTATGTGGTTCA 58.533 37.037 3.56 0.00 45.99 3.18
3347 4593 8.589701 TCTATATACATCCGTATGTGGTTCAT 57.410 34.615 3.56 0.00 45.99 2.57
3348 4594 9.689501 TCTATATACATCCGTATGTGGTTCATA 57.310 33.333 3.56 0.00 45.99 2.15
3356 4604 7.490962 TCCGTATGTGGTTCATAATGAAATC 57.509 36.000 0.00 0.00 38.22 2.17
3366 4614 9.958180 TGGTTCATAATGAAATCTCTACAAAGA 57.042 29.630 0.00 0.00 38.22 2.52
3392 4640 5.271598 TGTATTTAGGAACGGAGGGAGTAA 58.728 41.667 0.00 0.00 0.00 2.24
3540 4822 7.814264 AATTATCTAAGCACCAAAGATGAGG 57.186 36.000 0.00 0.00 32.39 3.86
3564 4846 3.874400 CTCGCATTGGAGCAGATAAAG 57.126 47.619 0.00 0.00 0.00 1.85
3574 4856 5.253330 TGGAGCAGATAAAGTTTACAAGGG 58.747 41.667 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
140 177 0.033011 GAGGCTAGACAGGGAGGACA 60.033 60.000 0.00 0.00 0.00 4.02
237 279 5.468072 AGATCGGATCCATCGAAGAAAAATG 59.532 40.000 13.41 0.00 43.58 2.32
238 280 5.615289 AGATCGGATCCATCGAAGAAAAAT 58.385 37.500 13.41 0.00 43.58 1.82
280 347 0.478072 AGGATCCAACCTGCACACAA 59.522 50.000 15.82 0.00 39.01 3.33
328 408 2.552599 TCGCACCAGAACAATAACCA 57.447 45.000 0.00 0.00 0.00 3.67
333 413 1.453155 GACCATCGCACCAGAACAAT 58.547 50.000 0.00 0.00 0.00 2.71
357 437 4.444449 GGAAAGTCATCGTATTAAGGCCCT 60.444 45.833 0.00 0.00 0.00 5.19
367 447 6.286758 AGTAGATAGTCGGAAAGTCATCGTA 58.713 40.000 0.00 0.00 0.00 3.43
385 465 6.180472 CCAGGGAAACATTGTTGTAGTAGAT 58.820 40.000 2.13 0.00 34.06 1.98
404 487 4.087892 CCCTCGTCAGTGCCAGGG 62.088 72.222 6.51 6.51 39.90 4.45
481 564 2.408271 TACATCCACGTCCGTAGACT 57.592 50.000 0.00 0.00 41.16 3.24
539 623 9.616634 TTCAAGAAAATTTCTGATCTTTCATCG 57.383 29.630 9.21 0.00 40.59 3.84
563 647 6.745450 TCACGAACAAAATGTGAGTTTCTTTC 59.255 34.615 0.00 0.00 37.69 2.62
564 648 6.616947 TCACGAACAAAATGTGAGTTTCTTT 58.383 32.000 0.00 0.00 37.69 2.52
567 653 6.862944 TTTCACGAACAAAATGTGAGTTTC 57.137 33.333 0.00 0.00 42.93 2.78
583 669 8.385111 GTCTAATTTCGACCATTATTTTCACGA 58.615 33.333 0.00 0.00 0.00 4.35
584 670 8.172484 TGTCTAATTTCGACCATTATTTTCACG 58.828 33.333 0.00 0.00 0.00 4.35
661 751 3.497103 TGTGATTGAGCCCATATCCAG 57.503 47.619 0.00 0.00 0.00 3.86
770 861 4.037446 CCATTTTCGTTTGGAAGACTGGAA 59.963 41.667 0.00 0.00 35.70 3.53
797 888 7.656948 TCCTACCGATTTTCGTTCTTCTAAAAA 59.343 33.333 0.00 0.00 38.40 1.94
798 889 7.153985 TCCTACCGATTTTCGTTCTTCTAAAA 58.846 34.615 0.00 0.00 38.40 1.52
799 890 6.690530 TCCTACCGATTTTCGTTCTTCTAAA 58.309 36.000 0.00 0.00 38.40 1.85
800 891 6.151648 TCTCCTACCGATTTTCGTTCTTCTAA 59.848 38.462 0.00 0.00 38.40 2.10
801 892 5.649395 TCTCCTACCGATTTTCGTTCTTCTA 59.351 40.000 0.00 0.00 38.40 2.10
802 893 4.461781 TCTCCTACCGATTTTCGTTCTTCT 59.538 41.667 0.00 0.00 38.40 2.85
803 894 4.562000 GTCTCCTACCGATTTTCGTTCTTC 59.438 45.833 0.00 0.00 38.40 2.87
804 895 4.492611 GTCTCCTACCGATTTTCGTTCTT 58.507 43.478 0.00 0.00 38.40 2.52
805 896 3.427233 CGTCTCCTACCGATTTTCGTTCT 60.427 47.826 0.00 0.00 38.40 3.01
806 897 2.850647 CGTCTCCTACCGATTTTCGTTC 59.149 50.000 0.00 0.00 38.40 3.95
818 909 5.895216 TTTTTCTTTTCGTCGTCTCCTAC 57.105 39.130 0.00 0.00 0.00 3.18
1114 1240 1.067416 CGGCGGATGAATCGAAGGA 59.933 57.895 0.00 0.00 0.00 3.36
1159 1285 2.524569 AATCCAACAACCCAAAAGCG 57.475 45.000 0.00 0.00 0.00 4.68
1160 1286 3.684305 GCATAATCCAACAACCCAAAAGC 59.316 43.478 0.00 0.00 0.00 3.51
1161 1287 3.925913 CGCATAATCCAACAACCCAAAAG 59.074 43.478 0.00 0.00 0.00 2.27
1165 1304 2.208132 ACGCATAATCCAACAACCCA 57.792 45.000 0.00 0.00 0.00 4.51
1209 1351 1.114119 TGCCAGCAACAGCATTCCAA 61.114 50.000 0.00 0.00 33.08 3.53
1240 1382 3.631250 ACTCACCCAGCAGAAAAAGAAA 58.369 40.909 0.00 0.00 0.00 2.52
1264 1406 2.278857 CGCGAATCTCCCCGTGAG 60.279 66.667 0.00 0.00 42.90 3.51
1265 1407 4.508128 GCGCGAATCTCCCCGTGA 62.508 66.667 12.10 0.00 38.42 4.35
1272 1414 3.918220 CCTGCACGCGCGAATCTC 61.918 66.667 39.36 19.16 42.97 2.75
1273 1415 3.723235 ATCCTGCACGCGCGAATCT 62.723 57.895 39.36 11.73 42.97 2.40
1274 1416 1.487452 TAATCCTGCACGCGCGAATC 61.487 55.000 39.36 23.50 42.97 2.52
1276 1418 2.125872 TAATCCTGCACGCGCGAA 60.126 55.556 39.36 20.09 42.97 4.70
1278 1420 1.587876 TAGTAATCCTGCACGCGCG 60.588 57.895 30.96 30.96 42.97 6.86
1279 1421 0.804544 TGTAGTAATCCTGCACGCGC 60.805 55.000 5.73 0.00 39.24 6.86
1396 1539 3.056821 GGAAGGGGAAAAACATGCAGTAC 60.057 47.826 0.00 0.00 0.00 2.73
1397 1540 3.161866 GGAAGGGGAAAAACATGCAGTA 58.838 45.455 0.00 0.00 0.00 2.74
1398 1541 1.970640 GGAAGGGGAAAAACATGCAGT 59.029 47.619 0.00 0.00 0.00 4.40
1399 1542 2.250924 AGGAAGGGGAAAAACATGCAG 58.749 47.619 0.00 0.00 0.00 4.41
1400 1543 2.397044 AGGAAGGGGAAAAACATGCA 57.603 45.000 0.00 0.00 0.00 3.96
1401 1544 4.820897 CTTTAGGAAGGGGAAAAACATGC 58.179 43.478 0.00 0.00 0.00 4.06
1402 1545 4.618227 CGCTTTAGGAAGGGGAAAAACATG 60.618 45.833 0.00 0.00 40.91 3.21
1403 1546 3.509967 CGCTTTAGGAAGGGGAAAAACAT 59.490 43.478 0.00 0.00 40.91 2.71
1404 1547 2.888414 CGCTTTAGGAAGGGGAAAAACA 59.112 45.455 0.00 0.00 40.91 2.83
1405 1548 2.889045 ACGCTTTAGGAAGGGGAAAAAC 59.111 45.455 7.89 0.00 46.77 2.43
1406 1549 2.888414 CACGCTTTAGGAAGGGGAAAAA 59.112 45.455 7.89 0.00 46.77 1.94
1418 1561 1.144969 TTTCAGACCGCACGCTTTAG 58.855 50.000 0.00 0.00 0.00 1.85
1467 1610 9.250624 GAGATTGTAACTACTGACATCAATACC 57.749 37.037 0.00 0.00 0.00 2.73
1519 1794 5.242171 TGATGAGCAAAAGAATCAAAGCAGA 59.758 36.000 0.00 0.00 0.00 4.26
1527 1802 4.033684 GTCGCATGATGAGCAAAAGAATC 58.966 43.478 0.00 0.00 0.00 2.52
1593 1868 7.559897 GGGAAAATAGTAGATTGGTCATTTCCA 59.440 37.037 13.54 0.00 43.07 3.53
1596 1871 7.561356 CAGGGGAAAATAGTAGATTGGTCATTT 59.439 37.037 0.00 0.00 0.00 2.32
1597 1872 7.062957 CAGGGGAAAATAGTAGATTGGTCATT 58.937 38.462 0.00 0.00 0.00 2.57
1598 1873 6.160459 ACAGGGGAAAATAGTAGATTGGTCAT 59.840 38.462 0.00 0.00 0.00 3.06
1618 1908 0.625849 AGGGTGCCATTTCTACAGGG 59.374 55.000 0.00 0.00 0.00 4.45
1694 1984 1.170290 ACCAAAGCGCACCTTGGTAC 61.170 55.000 29.30 0.00 34.96 3.34
1723 2013 5.762179 TGAACATGAGGGTACTGAAGATT 57.238 39.130 0.00 0.00 0.00 2.40
1724 2014 5.249393 AGTTGAACATGAGGGTACTGAAGAT 59.751 40.000 0.00 0.00 0.00 2.40
1726 2016 4.899502 AGTTGAACATGAGGGTACTGAAG 58.100 43.478 0.00 0.00 0.00 3.02
1910 2201 7.262772 TGTTTAGGATTAGTGGATTACTCGTG 58.737 38.462 0.00 0.00 40.89 4.35
1922 2213 6.127647 CCATGTGTGCAATGTTTAGGATTAGT 60.128 38.462 0.00 0.00 0.00 2.24
1923 2214 6.267817 CCATGTGTGCAATGTTTAGGATTAG 58.732 40.000 0.00 0.00 0.00 1.73
1924 2215 5.126869 CCCATGTGTGCAATGTTTAGGATTA 59.873 40.000 0.00 0.00 0.00 1.75
1925 2216 4.081531 CCCATGTGTGCAATGTTTAGGATT 60.082 41.667 0.00 0.00 0.00 3.01
1926 2217 3.448301 CCCATGTGTGCAATGTTTAGGAT 59.552 43.478 0.00 0.00 0.00 3.24
1927 2218 2.824936 CCCATGTGTGCAATGTTTAGGA 59.175 45.455 0.00 0.00 0.00 2.94
1928 2219 2.674747 GCCCATGTGTGCAATGTTTAGG 60.675 50.000 0.00 0.00 0.00 2.69
1929 2220 2.029200 TGCCCATGTGTGCAATGTTTAG 60.029 45.455 0.00 0.00 33.87 1.85
1941 2232 1.619827 ACCAAATGAACTGCCCATGTG 59.380 47.619 0.00 0.00 0.00 3.21
2019 2316 8.627208 AAATCTTATGGCAGTCATATGGTAAG 57.373 34.615 2.13 0.00 38.08 2.34
2024 2321 6.094603 GCCCTAAATCTTATGGCAGTCATATG 59.905 42.308 0.00 0.00 41.76 1.78
2074 2561 3.931907 AGTGCATAGTTTGATGGCCTA 57.068 42.857 3.32 0.00 0.00 3.93
2295 2782 3.184379 TCGTGAAAGAACATTCTTCAGCG 59.816 43.478 7.32 11.12 46.22 5.18
2299 2786 5.034554 TGCATCGTGAAAGAACATTCTTC 57.965 39.130 7.32 2.96 46.22 2.87
2380 2868 8.077991 GTCAAAAACAAGAGATGTCATGAATGA 58.922 33.333 1.69 0.00 42.99 2.57
2523 3015 1.336755 GAAGATTTGCGTGTGGTGGTT 59.663 47.619 0.00 0.00 0.00 3.67
2633 3482 0.249868 CGGAGAAAGCTCACCACACA 60.250 55.000 0.00 0.00 43.14 3.72
2651 3500 0.038526 ACGCAGACTCTTGTAACCCG 60.039 55.000 0.00 0.00 0.00 5.28
2655 3504 4.733850 CACATAGACGCAGACTCTTGTAA 58.266 43.478 0.00 0.00 32.98 2.41
2717 3566 6.359480 AGTACTGTGCTAAACTTTGTGAAC 57.641 37.500 0.00 0.00 0.00 3.18
2799 3655 2.146342 CCTGCAACCTACAACAGACAG 58.854 52.381 0.00 0.00 31.67 3.51
2942 3798 5.390613 CGGTAAACAGTAAGCATTTTCTGG 58.609 41.667 0.00 0.00 34.68 3.86
3023 3879 6.824958 AGGAAAATACTAATGCCAGGACTA 57.175 37.500 0.00 0.00 0.00 2.59
3124 3980 5.769662 CACTCCTATAAGATGCTCTCACTCT 59.230 44.000 0.00 0.00 0.00 3.24
3132 3988 6.126652 ACCAATTGTCACTCCTATAAGATGCT 60.127 38.462 4.43 0.00 0.00 3.79
3133 3989 6.058183 ACCAATTGTCACTCCTATAAGATGC 58.942 40.000 4.43 0.00 0.00 3.91
3134 3990 6.422100 CGACCAATTGTCACTCCTATAAGATG 59.578 42.308 4.43 0.00 44.71 2.90
3171 4034 4.253685 TCTCCAAGCAAAAGATACTTCGG 58.746 43.478 0.00 0.00 0.00 4.30
3172 4035 5.862924 TTCTCCAAGCAAAAGATACTTCG 57.137 39.130 0.00 0.00 0.00 3.79
3173 4036 6.529477 GCATTTCTCCAAGCAAAAGATACTTC 59.471 38.462 0.00 0.00 0.00 3.01
3174 4037 6.210185 AGCATTTCTCCAAGCAAAAGATACTT 59.790 34.615 0.00 0.00 0.00 2.24
3175 4038 5.713861 AGCATTTCTCCAAGCAAAAGATACT 59.286 36.000 0.00 0.00 0.00 2.12
3176 4039 5.958955 AGCATTTCTCCAAGCAAAAGATAC 58.041 37.500 0.00 0.00 0.00 2.24
3177 4040 5.711506 TGAGCATTTCTCCAAGCAAAAGATA 59.288 36.000 0.00 0.00 41.18 1.98
3237 4481 7.983484 TCCAAAGACTTATATTTAGGAACGGAC 59.017 37.037 0.00 0.00 0.00 4.79
3251 4495 7.605691 CACAGTGAAATCTCTCCAAAGACTTAT 59.394 37.037 0.00 0.00 0.00 1.73
3261 4505 3.971245 ACTCCACAGTGAAATCTCTCC 57.029 47.619 0.62 0.00 0.00 3.71
3262 4506 5.392767 TGTACTCCACAGTGAAATCTCTC 57.607 43.478 0.62 0.00 33.62 3.20
3273 4517 1.749063 TGCTCCGTATGTACTCCACAG 59.251 52.381 0.00 0.00 41.51 3.66
3275 4519 2.953466 TTGCTCCGTATGTACTCCAC 57.047 50.000 0.00 0.00 0.00 4.02
3276 4520 3.965379 TTTTGCTCCGTATGTACTCCA 57.035 42.857 0.00 0.00 0.00 3.86
3280 4525 4.868171 TCACTCATTTTGCTCCGTATGTAC 59.132 41.667 0.00 0.00 0.00 2.90
3287 4532 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
3298 4543 8.887717 AGATGCATTTTAAGTGTAGATTCACTC 58.112 33.333 0.00 0.00 46.25 3.51
3317 4563 7.069950 ACCACATACGGATGTATATAGATGCAT 59.930 37.037 14.23 0.00 44.82 3.96
3319 4565 6.806751 ACCACATACGGATGTATATAGATGC 58.193 40.000 14.23 0.00 44.82 3.91
3320 4566 8.466798 TGAACCACATACGGATGTATATAGATG 58.533 37.037 14.23 0.00 44.82 2.90
3321 4567 8.589701 TGAACCACATACGGATGTATATAGAT 57.410 34.615 14.23 0.00 44.82 1.98
3326 4572 8.808092 TCATTATGAACCACATACGGATGTATA 58.192 33.333 14.23 4.47 44.82 1.47
3333 4579 7.442364 AGAGATTTCATTATGAACCACATACGG 59.558 37.037 7.19 0.00 40.62 4.02
3361 4609 6.092259 CCTCCGTTCCTAAATACAAGTCTTTG 59.908 42.308 0.00 0.00 40.24 2.77
3366 4614 4.098894 TCCCTCCGTTCCTAAATACAAGT 58.901 43.478 0.00 0.00 0.00 3.16
3370 4618 5.859205 TTACTCCCTCCGTTCCTAAATAC 57.141 43.478 0.00 0.00 0.00 1.89
3392 4640 8.571336 GCTTCAGAATAATAAGCACCAATGTAT 58.429 33.333 0.00 0.00 43.98 2.29
3533 4815 2.074948 AATGCGAGCCCCCTCATCT 61.075 57.895 0.00 0.00 38.00 2.90
3564 4846 4.082245 CACATCATCAACCCCCTTGTAAAC 60.082 45.833 0.00 0.00 0.00 2.01
3574 4856 5.564550 AGAATATAGCCACATCATCAACCC 58.435 41.667 0.00 0.00 0.00 4.11


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

AutoCloner maintained by Alex Coulton.