Multiple sequence alignment - TraesCS6B01G374100

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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 TraesCS6B01G374100 chr6B 100.000 2652 0 0 1 2652 646945222 646947873 0.000000e+00 4898.0
1 TraesCS6B01G374100 chr6B 84.821 784 69 20 1192 1953 647386884 647387639 0.000000e+00 743.0
2 TraesCS6B01G374100 chr6B 88.258 511 29 8 1357 1864 647359435 647359917 1.370000e-162 582.0
3 TraesCS6B01G374100 chr6B 90.741 378 27 4 1366 1738 647364991 647365365 5.100000e-137 497.0
4 TraesCS6B01G374100 chr6B 84.842 442 52 9 1426 1864 647357551 647357980 5.240000e-117 431.0
5 TraesCS6B01G374100 chr6B 93.493 292 14 3 2001 2290 647387652 647387940 1.890000e-116 429.0
6 TraesCS6B01G374100 chr6B 92.593 243 15 3 2411 2652 647388008 647388248 1.950000e-91 346.0
7 TraesCS6B01G374100 chr6B 83.290 389 35 12 1900 2272 647271949 647272323 5.470000e-87 331.0
8 TraesCS6B01G374100 chr6B 77.474 586 65 29 1723 2260 647146928 647147494 3.340000e-74 289.0
9 TraesCS6B01G374100 chr6B 81.533 287 53 0 1578 1864 647056074 647056360 1.230000e-58 237.0
10 TraesCS6B01G374100 chr6B 90.789 152 13 1 2405 2556 647365401 647365551 4.480000e-48 202.0
11 TraesCS6B01G374100 chr6B 81.857 237 38 3 2416 2651 647358554 647358786 7.490000e-46 195.0
12 TraesCS6B01G374100 chr6B 81.356 236 39 3 2416 2650 647360431 647360662 1.250000e-43 187.0
13 TraesCS6B01G374100 chr6B 94.595 74 4 0 2187 2260 647437347 647437420 6.000000e-22 115.0
14 TraesCS6B01G374100 chr6B 96.429 56 2 0 2187 2242 646953708 646953763 2.810000e-15 93.5
15 TraesCS6B01G374100 chr6B 100.000 28 0 0 2457 2484 646794213 646794186 5.000000e-03 52.8
16 TraesCS6B01G374100 chr6A 90.824 1275 65 25 616 1864 574567646 574568894 0.000000e+00 1659.0
17 TraesCS6B01G374100 chr6A 85.208 987 77 23 896 1864 574587278 574588213 0.000000e+00 950.0
18 TraesCS6B01G374100 chr6A 87.424 493 36 10 1 490 574567177 574567646 6.460000e-151 544.0
19 TraesCS6B01G374100 chr6A 82.343 572 73 16 1401 1955 574669900 574670460 3.090000e-129 472.0
20 TraesCS6B01G374100 chr6A 83.453 417 62 4 1426 1837 574633361 574633775 5.360000e-102 381.0
21 TraesCS6B01G374100 chr6A 77.347 671 88 31 989 1652 574695475 574696088 3.270000e-89 339.0
22 TraesCS6B01G374100 chr6A 90.141 213 21 0 1440 1652 574691880 574692092 7.230000e-71 278.0
23 TraesCS6B01G374100 chr6A 78.829 222 22 3 1040 1261 574691515 574691711 2.770000e-25 126.0
24 TraesCS6B01G374100 chr6A 90.541 74 7 0 2187 2260 574634097 574634170 6.040000e-17 99.0
25 TraesCS6B01G374100 chr6A 97.727 44 1 0 2187 2230 574588592 574588635 2.830000e-10 76.8
26 TraesCS6B01G374100 chr6A 91.071 56 5 0 2187 2242 574670573 574670628 2.830000e-10 76.8
27 TraesCS6B01G374100 chr6A 96.875 32 0 1 258 289 340290259 340290289 5.000000e-03 52.8
28 TraesCS6B01G374100 chr6D 88.281 1152 61 30 744 1864 429383104 429384212 0.000000e+00 1312.0
29 TraesCS6B01G374100 chr6D 91.549 213 18 0 1440 1652 429492182 429492394 7.180000e-76 294.0
30 TraesCS6B01G374100 chr6D 78.458 506 49 31 1605 2052 429388985 429389488 2.600000e-70 276.0
31 TraesCS6B01G374100 chr6D 84.393 173 7 8 1900 2052 429384291 429384463 4.570000e-33 152.0
32 TraesCS6B01G374100 chr6D 91.011 89 8 0 1173 1261 429491940 429492028 1.290000e-23 121.0
33 TraesCS6B01G374100 chr6D 91.071 56 4 1 2187 2242 429479382 429479436 1.020000e-09 75.0
34 TraesCS6B01G374100 chr7D 100.000 31 0 0 2457 2487 11682481 11682451 1.030000e-04 58.4
35 TraesCS6B01G374100 chr7D 100.000 28 0 0 128 155 235828227 235828200 5.000000e-03 52.8
36 TraesCS6B01G374100 chr4A 100.000 28 0 0 2457 2484 724245628 724245655 5.000000e-03 52.8


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 TraesCS6B01G374100 chr6B 646945222 646947873 2651 False 4898.000000 4898 100.000000 1 2652 1 chr6B.!!$F1 2651
1 TraesCS6B01G374100 chr6B 647386884 647388248 1364 False 506.000000 743 90.302333 1192 2652 3 chr6B.!!$F9 1460
2 TraesCS6B01G374100 chr6B 647364991 647365551 560 False 349.500000 497 90.765000 1366 2556 2 chr6B.!!$F8 1190
3 TraesCS6B01G374100 chr6B 647357551 647360662 3111 False 348.750000 582 84.078250 1357 2651 4 chr6B.!!$F7 1294
4 TraesCS6B01G374100 chr6B 647146928 647147494 566 False 289.000000 289 77.474000 1723 2260 1 chr6B.!!$F4 537
5 TraesCS6B01G374100 chr6A 574567177 574568894 1717 False 1101.500000 1659 89.124000 1 1864 2 chr6A.!!$F2 1863
6 TraesCS6B01G374100 chr6A 574587278 574588635 1357 False 513.400000 950 91.467500 896 2230 2 chr6A.!!$F3 1334
7 TraesCS6B01G374100 chr6A 574669900 574670628 728 False 274.400000 472 86.707000 1401 2242 2 chr6A.!!$F5 841
8 TraesCS6B01G374100 chr6A 574691515 574696088 4573 False 247.666667 339 82.105667 989 1652 3 chr6A.!!$F6 663
9 TraesCS6B01G374100 chr6A 574633361 574634170 809 False 240.000000 381 86.997000 1426 2260 2 chr6A.!!$F4 834
10 TraesCS6B01G374100 chr6D 429383104 429384463 1359 False 732.000000 1312 86.337000 744 2052 2 chr6D.!!$F3 1308
11 TraesCS6B01G374100 chr6D 429388985 429389488 503 False 276.000000 276 78.458000 1605 2052 1 chr6D.!!$F1 447

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
574 577 0.033504 GACAAGAGGGAGTGCGTGAA 59.966 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2373 3299 0.040067 GCAAAAGCAACTCCGAGTGG 60.04 55.0 0.65 0.0 0.0 4.0 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
61 62 8.638685 ATGTTTGTGAGTTTGAGAAATCTTTG 57.361 30.769 0.00 0.00 31.42 2.77
62 63 6.531240 TGTTTGTGAGTTTGAGAAATCTTTGC 59.469 34.615 0.00 0.00 31.42 3.68
63 64 5.833406 TGTGAGTTTGAGAAATCTTTGCA 57.167 34.783 0.00 0.00 31.42 4.08
64 65 6.206395 TGTGAGTTTGAGAAATCTTTGCAA 57.794 33.333 0.00 0.00 31.42 4.08
65 66 6.808829 TGTGAGTTTGAGAAATCTTTGCAAT 58.191 32.000 0.00 0.00 31.42 3.56
66 67 6.698329 TGTGAGTTTGAGAAATCTTTGCAATG 59.302 34.615 0.00 2.27 31.42 2.82
67 68 6.698766 GTGAGTTTGAGAAATCTTTGCAATGT 59.301 34.615 11.67 0.00 31.42 2.71
69 70 7.765360 TGAGTTTGAGAAATCTTTGCAATGTTT 59.235 29.630 11.67 10.97 31.42 2.83
70 71 8.496707 AGTTTGAGAAATCTTTGCAATGTTTT 57.503 26.923 16.82 16.82 0.00 2.43
71 72 8.949177 AGTTTGAGAAATCTTTGCAATGTTTTT 58.051 25.926 17.52 14.86 0.00 1.94
107 108 7.611467 TGCAATTCTCTATGTGTCCACTAATTT 59.389 33.333 0.00 0.00 0.00 1.82
114 115 7.907389 TCTATGTGTCCACTAATTTGAGAAGT 58.093 34.615 0.00 0.00 0.00 3.01
120 121 6.998074 TGTCCACTAATTTGAGAAGTGTTCAT 59.002 34.615 4.95 0.00 39.17 2.57
128 129 8.812513 AATTTGAGAAGTGTTCATGGATATGA 57.187 30.769 0.00 0.00 41.44 2.15
310 311 8.244113 AGATGGTTCTCGGATTAATTTGTTTTC 58.756 33.333 0.00 0.00 0.00 2.29
314 315 7.275560 GGTTCTCGGATTAATTTGTTTTCATGG 59.724 37.037 0.00 0.00 0.00 3.66
355 356 6.841443 AATTGAAAATGTTCACATTGCGAA 57.159 29.167 5.94 0.64 45.06 4.70
492 495 3.057315 GCAGCAAGAAAACCATGCTAGAA 60.057 43.478 0.00 0.00 46.84 2.10
493 496 4.730657 CAGCAAGAAAACCATGCTAGAAG 58.269 43.478 0.00 0.00 46.84 2.85
508 511 3.812609 GCTAGAAGCATTTAGAAGCCTCC 59.187 47.826 0.00 0.00 41.89 4.30
509 512 4.684485 GCTAGAAGCATTTAGAAGCCTCCA 60.684 45.833 0.00 0.00 41.89 3.86
511 514 4.666512 AGAAGCATTTAGAAGCCTCCAAA 58.333 39.130 0.00 0.00 0.00 3.28
512 515 5.079643 AGAAGCATTTAGAAGCCTCCAAAA 58.920 37.500 0.00 0.00 0.00 2.44
513 516 4.790765 AGCATTTAGAAGCCTCCAAAAC 57.209 40.909 0.00 0.00 0.00 2.43
514 517 3.511540 AGCATTTAGAAGCCTCCAAAACC 59.488 43.478 0.00 0.00 0.00 3.27
515 518 3.673323 GCATTTAGAAGCCTCCAAAACCG 60.673 47.826 0.00 0.00 0.00 4.44
516 519 2.194201 TTAGAAGCCTCCAAAACCGG 57.806 50.000 0.00 0.00 0.00 5.28
517 520 1.354101 TAGAAGCCTCCAAAACCGGA 58.646 50.000 9.46 0.00 0.00 5.14
518 521 0.698818 AGAAGCCTCCAAAACCGGAT 59.301 50.000 9.46 0.00 33.56 4.18
519 522 0.811281 GAAGCCTCCAAAACCGGATG 59.189 55.000 9.46 3.78 33.56 3.51
521 524 2.710902 GCCTCCAAAACCGGATGCC 61.711 63.158 9.46 0.00 39.90 4.40
523 526 1.032114 CCTCCAAAACCGGATGCCTC 61.032 60.000 9.46 0.00 33.56 4.70
524 527 1.001393 TCCAAAACCGGATGCCTCC 60.001 57.895 9.46 0.00 38.29 4.30
525 528 2.052104 CCAAAACCGGATGCCTCCC 61.052 63.158 9.46 0.00 38.45 4.30
526 529 1.000896 CAAAACCGGATGCCTCCCT 60.001 57.895 9.46 0.00 38.45 4.20
527 530 1.000896 AAAACCGGATGCCTCCCTG 60.001 57.895 9.46 0.00 38.45 4.45
528 531 2.499303 AAAACCGGATGCCTCCCTGG 62.499 60.000 9.46 1.59 38.45 4.45
537 540 4.625800 CCTCCCTGGCTTCGAAAG 57.374 61.111 0.00 0.00 0.00 2.62
546 549 2.781300 CTTCGAAAGCTGCGAGCC 59.219 61.111 11.14 0.00 43.77 4.70
547 550 3.076296 CTTCGAAAGCTGCGAGCCG 62.076 63.158 11.14 0.00 43.77 5.52
565 568 4.069232 CGCTGCCGACAAGAGGGA 62.069 66.667 0.00 0.00 36.29 4.20
567 570 3.382111 CTGCCGACAAGAGGGAGT 58.618 61.111 0.00 0.00 41.55 3.85
568 571 1.079543 CTGCCGACAAGAGGGAGTG 60.080 63.158 0.00 0.00 41.55 3.51
570 573 2.125912 CCGACAAGAGGGAGTGCG 60.126 66.667 0.00 0.00 0.00 5.34
572 575 1.734477 CGACAAGAGGGAGTGCGTG 60.734 63.158 0.00 0.00 0.00 5.34
574 577 0.033504 GACAAGAGGGAGTGCGTGAA 59.966 55.000 0.00 0.00 0.00 3.18
575 578 0.034059 ACAAGAGGGAGTGCGTGAAG 59.966 55.000 0.00 0.00 0.00 3.02
576 579 0.034059 CAAGAGGGAGTGCGTGAAGT 59.966 55.000 0.00 0.00 0.00 3.01
577 580 0.759346 AAGAGGGAGTGCGTGAAGTT 59.241 50.000 0.00 0.00 0.00 2.66
578 581 1.629043 AGAGGGAGTGCGTGAAGTTA 58.371 50.000 0.00 0.00 0.00 2.24
579 582 1.968493 AGAGGGAGTGCGTGAAGTTAA 59.032 47.619 0.00 0.00 0.00 2.01
580 583 2.367567 AGAGGGAGTGCGTGAAGTTAAA 59.632 45.455 0.00 0.00 0.00 1.52
584 587 3.065648 GGGAGTGCGTGAAGTTAAAAACA 59.934 43.478 0.00 0.00 0.00 2.83
586 589 5.278604 GGAGTGCGTGAAGTTAAAAACAAT 58.721 37.500 0.00 0.00 0.00 2.71
587 590 6.432107 GGAGTGCGTGAAGTTAAAAACAATA 58.568 36.000 0.00 0.00 0.00 1.90
589 592 6.435428 AGTGCGTGAAGTTAAAAACAATAGG 58.565 36.000 0.00 0.00 0.00 2.57
591 594 6.913673 GTGCGTGAAGTTAAAAACAATAGGAA 59.086 34.615 0.00 0.00 0.00 3.36
593 596 6.087687 GCGTGAAGTTAAAAACAATAGGAAGC 59.912 38.462 0.00 0.00 0.00 3.86
594 597 6.302313 CGTGAAGTTAAAAACAATAGGAAGCG 59.698 38.462 0.00 0.00 0.00 4.68
595 598 6.581166 GTGAAGTTAAAAACAATAGGAAGCGG 59.419 38.462 0.00 0.00 0.00 5.52
596 599 5.055642 AGTTAAAAACAATAGGAAGCGGC 57.944 39.130 0.00 0.00 0.00 6.53
598 601 0.170339 AAAACAATAGGAAGCGGCGC 59.830 50.000 26.86 26.86 0.00 6.53
601 604 1.893808 CAATAGGAAGCGGCGCCAT 60.894 57.895 30.40 18.82 0.00 4.40
602 605 1.893808 AATAGGAAGCGGCGCCATG 60.894 57.895 30.40 12.69 0.00 3.66
603 606 2.324014 AATAGGAAGCGGCGCCATGA 62.324 55.000 30.40 11.09 0.00 3.07
604 607 2.721971 ATAGGAAGCGGCGCCATGAG 62.722 60.000 30.40 11.41 0.00 2.90
623 626 1.730064 AGCGATGAATACAAAACGCGT 59.270 42.857 5.58 5.58 44.35 6.01
634 637 4.322101 ACAAAACGCGTTATGTCTCATC 57.678 40.909 26.87 0.00 0.00 2.92
639 642 4.365899 ACGCGTTATGTCTCATCAACTA 57.634 40.909 5.58 0.00 0.00 2.24
642 645 5.061808 ACGCGTTATGTCTCATCAACTAAAC 59.938 40.000 5.58 0.00 0.00 2.01
643 646 5.481472 GCGTTATGTCTCATCAACTAAACG 58.519 41.667 0.00 0.00 37.92 3.60
644 647 5.287752 GCGTTATGTCTCATCAACTAAACGA 59.712 40.000 13.53 0.00 37.50 3.85
739 750 4.760530 ATCCAGAACAGCAGCAGTATTA 57.239 40.909 0.00 0.00 0.00 0.98
740 751 4.760530 TCCAGAACAGCAGCAGTATTAT 57.239 40.909 0.00 0.00 0.00 1.28
741 752 5.102953 TCCAGAACAGCAGCAGTATTATT 57.897 39.130 0.00 0.00 0.00 1.40
847 858 2.041891 TCTCGAACCTTCTTCCTCCTCT 59.958 50.000 0.00 0.00 0.00 3.69
921 933 1.043816 TCCAATCCATCGAGCTCTCC 58.956 55.000 12.85 0.00 0.00 3.71
974 986 2.108976 CACCCACACACAGCGAGT 59.891 61.111 0.00 0.00 0.00 4.18
1199 1233 4.530857 CATCGTGGAGACCCCCGC 62.531 72.222 0.00 0.00 0.00 6.13
1316 1370 4.421479 AACTCGTCGGCTCGGCAG 62.421 66.667 0.00 0.00 0.00 4.85
1360 1420 3.009140 CGCGCGCTCTGAATGAAT 58.991 55.556 30.48 0.00 0.00 2.57
1659 2204 1.951130 CCATCGCCTGATCGTTCGG 60.951 63.158 0.00 0.00 30.49 4.30
1794 2385 3.998672 TTCGTGGTCTGGCCGGAC 61.999 66.667 33.19 33.19 41.21 4.79
1807 2408 1.440060 CCGGACATTAGGCGTGCTA 59.560 57.895 0.00 0.00 0.00 3.49
1831 2432 3.010420 TGTGGTCGTGTTTTGTGAATCA 58.990 40.909 0.00 0.00 0.00 2.57
1843 2445 3.497297 TGTGAATCATGCTGTGAATGC 57.503 42.857 0.00 0.00 40.97 3.56
1847 2449 2.554806 ATCATGCTGTGAATGCAACG 57.445 45.000 0.00 0.00 44.01 4.10
1871 2501 3.197766 TGGAGCACGAATTGTATCTTCCT 59.802 43.478 0.00 0.00 0.00 3.36
1879 2515 4.026475 CGAATTGTATCTTCCTCGCTTGAC 60.026 45.833 0.00 0.00 0.00 3.18
1980 2689 1.067565 TGCACGATCTGTCAACTCCTC 60.068 52.381 0.00 0.00 0.00 3.71
1983 2692 1.821753 ACGATCTGTCAACTCCTCTGG 59.178 52.381 0.00 0.00 0.00 3.86
2108 2911 1.312815 GATGCCCATGTGCTCCTTAC 58.687 55.000 0.86 0.00 0.00 2.34
2116 2919 3.201290 CATGTGCTCCTTACATCAGGAC 58.799 50.000 0.00 0.00 38.11 3.85
2150 2955 8.165239 ACAGAACAACAAGACTAAATGCATAA 57.835 30.769 0.00 0.00 0.00 1.90
2252 3082 6.418057 AACATGGTTGTTGGTTCACATTAT 57.582 33.333 0.00 0.00 44.36 1.28
2281 3150 4.935808 AGTGTTCTTCTATTTAACGCCAGG 59.064 41.667 0.00 0.00 34.87 4.45
2286 3201 6.045072 TCTTCTATTTAACGCCAGGAAAGA 57.955 37.500 0.00 0.00 0.00 2.52
2299 3215 1.657751 GGAAAGATGGGCCGAGCAAC 61.658 60.000 5.60 0.00 0.00 4.17
2331 3257 3.660621 GCTTCACAGCCACCACTC 58.339 61.111 0.00 0.00 40.61 3.51
2332 3258 1.072159 GCTTCACAGCCACCACTCT 59.928 57.895 0.00 0.00 40.61 3.24
2333 3259 0.952984 GCTTCACAGCCACCACTCTC 60.953 60.000 0.00 0.00 40.61 3.20
2334 3260 0.683973 CTTCACAGCCACCACTCTCT 59.316 55.000 0.00 0.00 0.00 3.10
2335 3261 0.681733 TTCACAGCCACCACTCTCTC 59.318 55.000 0.00 0.00 0.00 3.20
2336 3262 0.178950 TCACAGCCACCACTCTCTCT 60.179 55.000 0.00 0.00 0.00 3.10
2337 3263 0.246086 CACAGCCACCACTCTCTCTC 59.754 60.000 0.00 0.00 0.00 3.20
2338 3264 0.114168 ACAGCCACCACTCTCTCTCT 59.886 55.000 0.00 0.00 0.00 3.10
2339 3265 0.817013 CAGCCACCACTCTCTCTCTC 59.183 60.000 0.00 0.00 0.00 3.20
2340 3266 0.704076 AGCCACCACTCTCTCTCTCT 59.296 55.000 0.00 0.00 0.00 3.10
2341 3267 1.102978 GCCACCACTCTCTCTCTCTC 58.897 60.000 0.00 0.00 0.00 3.20
2342 3268 1.340991 GCCACCACTCTCTCTCTCTCT 60.341 57.143 0.00 0.00 0.00 3.10
2343 3269 2.643551 CCACCACTCTCTCTCTCTCTC 58.356 57.143 0.00 0.00 0.00 3.20
2344 3270 2.239654 CCACCACTCTCTCTCTCTCTCT 59.760 54.545 0.00 0.00 0.00 3.10
2345 3271 3.535561 CACCACTCTCTCTCTCTCTCTC 58.464 54.545 0.00 0.00 0.00 3.20
2346 3272 3.198635 CACCACTCTCTCTCTCTCTCTCT 59.801 52.174 0.00 0.00 0.00 3.10
2347 3273 3.452627 ACCACTCTCTCTCTCTCTCTCTC 59.547 52.174 0.00 0.00 0.00 3.20
2348 3274 3.708631 CCACTCTCTCTCTCTCTCTCTCT 59.291 52.174 0.00 0.00 0.00 3.10
2349 3275 4.202202 CCACTCTCTCTCTCTCTCTCTCTC 60.202 54.167 0.00 0.00 0.00 3.20
2350 3276 4.403752 CACTCTCTCTCTCTCTCTCTCTCA 59.596 50.000 0.00 0.00 0.00 3.27
2351 3277 5.026121 ACTCTCTCTCTCTCTCTCTCTCAA 58.974 45.833 0.00 0.00 0.00 3.02
2352 3278 5.485353 ACTCTCTCTCTCTCTCTCTCTCAAA 59.515 44.000 0.00 0.00 0.00 2.69
2353 3279 6.013379 ACTCTCTCTCTCTCTCTCTCTCAAAA 60.013 42.308 0.00 0.00 0.00 2.44
2354 3280 6.778821 TCTCTCTCTCTCTCTCTCTCAAAAA 58.221 40.000 0.00 0.00 0.00 1.94
2378 3304 3.660621 GCTTCACAGCCACCACTC 58.339 61.111 0.00 0.00 40.61 3.51
2379 3305 2.320587 GCTTCACAGCCACCACTCG 61.321 63.158 0.00 0.00 40.61 4.18
2380 3306 1.669115 CTTCACAGCCACCACTCGG 60.669 63.158 0.00 0.00 38.77 4.63
2381 3307 2.099652 CTTCACAGCCACCACTCGGA 62.100 60.000 0.00 0.00 35.59 4.55
2382 3308 2.047844 CACAGCCACCACTCGGAG 60.048 66.667 2.83 2.83 35.59 4.63
2383 3309 2.524394 ACAGCCACCACTCGGAGT 60.524 61.111 4.45 4.45 35.59 3.85
2384 3310 2.140792 ACAGCCACCACTCGGAGTT 61.141 57.895 8.18 0.00 35.59 3.01
2385 3311 1.669115 CAGCCACCACTCGGAGTTG 60.669 63.158 8.18 7.86 35.59 3.16
2386 3312 3.050275 GCCACCACTCGGAGTTGC 61.050 66.667 8.18 5.52 35.59 4.17
2387 3313 2.743718 CCACCACTCGGAGTTGCT 59.256 61.111 8.18 0.00 35.59 3.91
2388 3314 1.071471 CCACCACTCGGAGTTGCTT 59.929 57.895 8.18 0.00 35.59 3.91
2389 3315 0.535102 CCACCACTCGGAGTTGCTTT 60.535 55.000 8.18 0.00 35.59 3.51
2390 3316 1.308998 CACCACTCGGAGTTGCTTTT 58.691 50.000 8.18 0.00 35.59 2.27
2391 3317 1.002468 CACCACTCGGAGTTGCTTTTG 60.002 52.381 8.18 0.00 35.59 2.44
2392 3318 2.682469 ACCACTCGGAGTTGCTTTTGC 61.682 52.381 8.18 0.00 40.30 3.68
2393 3319 4.968103 ACCACTCGGAGTTGCTTTTGCT 62.968 50.000 8.18 0.00 40.45 3.91
2404 3330 2.412421 GCTTTTGCTTCAGTCACCTG 57.588 50.000 0.00 0.00 43.35 4.00
2405 3331 1.949525 GCTTTTGCTTCAGTCACCTGA 59.050 47.619 0.00 0.00 43.05 3.86
2406 3332 2.031333 GCTTTTGCTTCAGTCACCTGAG 60.031 50.000 0.00 0.00 41.52 3.35
2407 3333 4.548105 GCTTTTGCTTCAGTCACCTGAGT 61.548 47.826 0.00 0.00 41.52 3.41
2408 3334 5.989430 GCTTTTGCTTCAGTCACCTGAGTT 61.989 45.833 0.00 0.00 41.52 3.01
2409 3335 7.933558 GCTTTTGCTTCAGTCACCTGAGTTG 62.934 48.000 0.00 0.00 41.52 3.16
2493 3830 3.237268 AGCATCGGGATCTCTTAGTCT 57.763 47.619 0.00 0.00 0.00 3.24
2538 3875 7.790027 AGTGATTTGACTAGCATACTCTTGAT 58.210 34.615 0.00 0.00 0.00 2.57
2563 3900 2.588027 TTAGTGCAACGTGACACTGA 57.412 45.000 25.85 18.55 46.31 3.41
2591 3928 6.697641 AGTAGGTTTGGTTCCATCTTAAGA 57.302 37.500 7.82 7.82 0.00 2.10
2626 5423 1.748493 GTCTCCTGCTCTCACGATCTT 59.252 52.381 0.00 0.00 0.00 2.40
2643 6102 6.422701 CACGATCTTCTAGTTGTTGTTGGTAA 59.577 38.462 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 7.599998 GTGGACACATAGAGAATTGCAATTTTT 59.400 33.333 24.81 16.36 0.00 1.94
76 77 7.039504 AGTGGACACATAGAGAATTGCAATTTT 60.040 33.333 24.81 19.75 0.00 1.82
77 78 6.435277 AGTGGACACATAGAGAATTGCAATTT 59.565 34.615 24.81 14.80 0.00 1.82
78 79 5.948162 AGTGGACACATAGAGAATTGCAATT 59.052 36.000 24.33 24.33 0.00 2.32
79 80 5.503927 AGTGGACACATAGAGAATTGCAAT 58.496 37.500 5.99 5.99 0.00 3.56
90 91 7.604164 ACACTTCTCAAATTAGTGGACACATAG 59.396 37.037 9.51 0.00 42.70 2.23
92 93 6.299141 ACACTTCTCAAATTAGTGGACACAT 58.701 36.000 9.51 0.00 42.70 3.21
264 265 9.927668 ACCATCTTTGAATTCGTGAATATTTTT 57.072 25.926 0.04 0.00 0.00 1.94
276 277 6.442513 AATCCGAGAACCATCTTTGAATTC 57.557 37.500 0.00 0.00 35.54 2.17
288 289 7.275560 CCATGAAAACAAATTAATCCGAGAACC 59.724 37.037 0.00 0.00 0.00 3.62
336 337 6.648502 ACATTTTCGCAATGTGAACATTTTC 58.351 32.000 8.93 1.47 43.48 2.29
343 344 5.105063 TCACAAACATTTTCGCAATGTGAA 58.895 33.333 4.98 4.98 41.70 3.18
346 347 6.601741 AATTCACAAACATTTTCGCAATGT 57.398 29.167 6.91 6.91 42.19 2.71
347 348 7.124471 TCAAATTCACAAACATTTTCGCAATG 58.876 30.769 5.80 5.80 0.00 2.82
350 351 6.653273 TTCAAATTCACAAACATTTTCGCA 57.347 29.167 0.00 0.00 0.00 5.10
492 495 3.511540 GGTTTTGGAGGCTTCTAAATGCT 59.488 43.478 8.17 0.00 34.33 3.79
493 496 3.673323 CGGTTTTGGAGGCTTCTAAATGC 60.673 47.826 8.17 5.03 34.33 3.56
496 499 2.106857 TCCGGTTTTGGAGGCTTCTAAA 59.893 45.455 3.13 3.13 32.69 1.85
498 501 1.354101 TCCGGTTTTGGAGGCTTCTA 58.646 50.000 0.00 0.00 33.05 2.10
499 502 0.698818 ATCCGGTTTTGGAGGCTTCT 59.301 50.000 0.00 0.00 42.45 2.85
500 503 0.811281 CATCCGGTTTTGGAGGCTTC 59.189 55.000 0.00 0.00 42.45 3.86
502 505 4.743018 CATCCGGTTTTGGAGGCT 57.257 55.556 0.00 0.00 42.45 4.58
504 507 1.000896 AGGCATCCGGTTTTGGAGG 60.001 57.895 0.00 0.00 42.45 4.30
505 508 1.032114 GGAGGCATCCGGTTTTGGAG 61.032 60.000 0.00 0.00 42.45 3.86
529 532 2.781300 GGCTCGCAGCTTTCGAAG 59.219 61.111 8.88 5.25 41.99 3.79
530 533 3.112075 CGGCTCGCAGCTTTCGAA 61.112 61.111 8.88 0.00 41.99 3.71
549 552 2.125350 CTCCCTCTTGTCGGCAGC 60.125 66.667 0.00 0.00 0.00 5.25
550 553 1.079543 CACTCCCTCTTGTCGGCAG 60.080 63.158 0.00 0.00 0.00 4.85
551 554 3.059982 CACTCCCTCTTGTCGGCA 58.940 61.111 0.00 0.00 0.00 5.69
553 556 2.125912 CGCACTCCCTCTTGTCGG 60.126 66.667 0.00 0.00 0.00 4.79
554 557 1.734477 CACGCACTCCCTCTTGTCG 60.734 63.158 0.00 0.00 0.00 4.35
555 558 0.033504 TTCACGCACTCCCTCTTGTC 59.966 55.000 0.00 0.00 0.00 3.18
556 559 0.034059 CTTCACGCACTCCCTCTTGT 59.966 55.000 0.00 0.00 0.00 3.16
558 561 0.759346 AACTTCACGCACTCCCTCTT 59.241 50.000 0.00 0.00 0.00 2.85
559 562 1.629043 TAACTTCACGCACTCCCTCT 58.371 50.000 0.00 0.00 0.00 3.69
560 563 2.450609 TTAACTTCACGCACTCCCTC 57.549 50.000 0.00 0.00 0.00 4.30
561 564 2.922740 TTTAACTTCACGCACTCCCT 57.077 45.000 0.00 0.00 0.00 4.20
562 565 3.065648 TGTTTTTAACTTCACGCACTCCC 59.934 43.478 0.00 0.00 0.00 4.30
563 566 4.281525 TGTTTTTAACTTCACGCACTCC 57.718 40.909 0.00 0.00 0.00 3.85
565 568 6.261381 TCCTATTGTTTTTAACTTCACGCACT 59.739 34.615 0.00 0.00 0.00 4.40
566 569 6.432107 TCCTATTGTTTTTAACTTCACGCAC 58.568 36.000 0.00 0.00 0.00 5.34
567 570 6.621316 TCCTATTGTTTTTAACTTCACGCA 57.379 33.333 0.00 0.00 0.00 5.24
568 571 6.087687 GCTTCCTATTGTTTTTAACTTCACGC 59.912 38.462 0.00 0.00 0.00 5.34
570 573 6.581166 CCGCTTCCTATTGTTTTTAACTTCAC 59.419 38.462 0.00 0.00 0.00 3.18
572 575 5.571741 GCCGCTTCCTATTGTTTTTAACTTC 59.428 40.000 0.00 0.00 0.00 3.01
574 577 4.379082 CGCCGCTTCCTATTGTTTTTAACT 60.379 41.667 0.00 0.00 0.00 2.24
575 578 3.849708 CGCCGCTTCCTATTGTTTTTAAC 59.150 43.478 0.00 0.00 0.00 2.01
576 579 3.671164 GCGCCGCTTCCTATTGTTTTTAA 60.671 43.478 0.00 0.00 0.00 1.52
577 580 2.159490 GCGCCGCTTCCTATTGTTTTTA 60.159 45.455 0.00 0.00 0.00 1.52
578 581 1.402325 GCGCCGCTTCCTATTGTTTTT 60.402 47.619 0.00 0.00 0.00 1.94
579 582 0.170339 GCGCCGCTTCCTATTGTTTT 59.830 50.000 0.00 0.00 0.00 2.43
580 583 1.654023 GGCGCCGCTTCCTATTGTTT 61.654 55.000 12.58 0.00 0.00 2.83
584 587 1.893808 CATGGCGCCGCTTCCTATT 60.894 57.895 23.90 0.00 0.00 1.73
586 589 3.445518 CTCATGGCGCCGCTTCCTA 62.446 63.158 23.90 1.41 0.00 2.94
587 590 4.845580 CTCATGGCGCCGCTTCCT 62.846 66.667 23.90 0.00 0.00 3.36
598 601 4.274069 CGTTTTGTATTCATCGCTCATGG 58.726 43.478 0.00 0.00 32.64 3.66
601 604 2.222707 CGCGTTTTGTATTCATCGCTCA 60.223 45.455 0.00 0.00 41.17 4.26
602 605 2.222729 ACGCGTTTTGTATTCATCGCTC 60.223 45.455 5.58 0.00 41.17 5.03
603 606 1.730064 ACGCGTTTTGTATTCATCGCT 59.270 42.857 5.58 0.00 41.17 4.93
604 607 2.153680 ACGCGTTTTGTATTCATCGC 57.846 45.000 5.58 0.00 40.19 4.58
605 608 5.252583 ACATAACGCGTTTTGTATTCATCG 58.747 37.500 35.77 15.18 33.97 3.84
606 609 6.475207 AGACATAACGCGTTTTGTATTCATC 58.525 36.000 36.35 25.84 35.45 2.92
607 610 6.091577 TGAGACATAACGCGTTTTGTATTCAT 59.908 34.615 36.35 23.64 35.45 2.57
609 612 5.849858 TGAGACATAACGCGTTTTGTATTC 58.150 37.500 36.35 32.86 35.45 1.75
610 613 5.849357 TGAGACATAACGCGTTTTGTATT 57.151 34.783 36.35 28.99 35.45 1.89
611 614 5.579119 TGATGAGACATAACGCGTTTTGTAT 59.421 36.000 36.35 34.40 35.45 2.29
613 616 3.743911 TGATGAGACATAACGCGTTTTGT 59.256 39.130 36.72 36.72 37.43 2.83
614 617 4.320667 TGATGAGACATAACGCGTTTTG 57.679 40.909 31.78 31.78 0.00 2.44
615 618 4.451096 AGTTGATGAGACATAACGCGTTTT 59.549 37.500 31.50 20.19 0.00 2.43
696 706 3.418744 AACACGGGCCGTTTTGTGC 62.419 57.895 32.12 0.00 38.32 4.57
739 750 5.050126 TGTACGAGACTGATCTAGGGAAT 57.950 43.478 0.00 0.00 34.34 3.01
740 751 4.452825 CTGTACGAGACTGATCTAGGGAA 58.547 47.826 0.00 0.00 34.34 3.97
741 752 3.744846 GCTGTACGAGACTGATCTAGGGA 60.745 52.174 0.00 0.00 34.34 4.20
847 858 3.536434 AGGGAGAGGGAGTGGTATAAAGA 59.464 47.826 0.00 0.00 0.00 2.52
921 933 1.078759 GGATGGTGCGAGTCGACTTG 61.079 60.000 25.82 25.82 0.00 3.16
974 986 1.626825 CTTCCTTCCTCGGGTTGGTTA 59.373 52.381 0.00 0.00 0.00 2.85
1199 1233 2.202756 GCAGGAAGGCGTACTCGG 60.203 66.667 0.00 0.00 37.56 4.63
1360 1420 0.902048 CCTCCAGAGTCACCTGCTCA 60.902 60.000 0.00 0.00 35.55 4.26
1438 1979 4.377760 TCCTCCTCCCGCTTCCGT 62.378 66.667 0.00 0.00 0.00 4.69
1794 2385 1.665679 CCACAACTAGCACGCCTAATG 59.334 52.381 0.00 0.00 0.00 1.90
1801 2402 0.596600 ACACGACCACAACTAGCACG 60.597 55.000 0.00 0.00 0.00 5.34
1807 2408 2.428491 TCACAAAACACGACCACAACT 58.572 42.857 0.00 0.00 0.00 3.16
1831 2432 1.133598 CCATCGTTGCATTCACAGCAT 59.866 47.619 0.00 0.00 42.33 3.79
1843 2445 1.464608 ACAATTCGTGCTCCATCGTTG 59.535 47.619 0.00 0.00 0.00 4.10
1847 2449 4.212214 GGAAGATACAATTCGTGCTCCATC 59.788 45.833 0.00 0.00 0.00 3.51
1871 2501 2.390599 GCTGCATTCGGTCAAGCGA 61.391 57.895 0.00 0.00 0.00 4.93
1980 2689 1.191535 TGATAGACCGTGGAACCCAG 58.808 55.000 0.00 0.00 32.34 4.45
1983 2692 5.878669 AGTTAATTTGATAGACCGTGGAACC 59.121 40.000 0.00 0.00 0.00 3.62
2038 2786 9.271828 AGTTTCTTTCAATTCACTTTGTTTTGT 57.728 25.926 0.00 0.00 0.00 2.83
2071 2843 6.189859 GGGCATCCCTCATAAATCATAATCA 58.810 40.000 0.00 0.00 41.34 2.57
2108 2911 7.905604 TGTTCTGTACATTTTAGTCCTGATG 57.094 36.000 0.00 0.00 0.00 3.07
2252 3082 6.694411 GCGTTAAATAGAAGAACACTCGGATA 59.306 38.462 0.00 0.00 0.00 2.59
2281 3150 1.803289 GTTGCTCGGCCCATCTTTC 59.197 57.895 0.00 0.00 0.00 2.62
2286 3201 2.298158 CTACTCGTTGCTCGGCCCAT 62.298 60.000 0.00 0.00 40.32 4.00
2299 3215 1.813178 TGAAGCTGTGGACTCTACTCG 59.187 52.381 0.00 0.00 0.00 4.18
2327 3253 4.403752 TGAGAGAGAGAGAGAGAGAGAGTG 59.596 50.000 0.00 0.00 0.00 3.51
2328 3254 4.614475 TGAGAGAGAGAGAGAGAGAGAGT 58.386 47.826 0.00 0.00 0.00 3.24
2329 3255 5.604758 TTGAGAGAGAGAGAGAGAGAGAG 57.395 47.826 0.00 0.00 0.00 3.20
2330 3256 6.373005 TTTTGAGAGAGAGAGAGAGAGAGA 57.627 41.667 0.00 0.00 0.00 3.10
2361 3287 2.320587 CGAGTGGTGGCTGTGAAGC 61.321 63.158 0.00 0.00 0.00 3.86
2362 3288 1.669115 CCGAGTGGTGGCTGTGAAG 60.669 63.158 0.00 0.00 0.00 3.02
2363 3289 2.099652 CTCCGAGTGGTGGCTGTGAA 62.100 60.000 0.00 0.00 36.30 3.18
2364 3290 2.523168 TCCGAGTGGTGGCTGTGA 60.523 61.111 0.00 0.00 36.30 3.58
2365 3291 2.047844 CTCCGAGTGGTGGCTGTG 60.048 66.667 0.00 0.00 36.30 3.66
2366 3292 2.140792 AACTCCGAGTGGTGGCTGT 61.141 57.895 0.65 0.00 36.30 4.40
2367 3293 1.669115 CAACTCCGAGTGGTGGCTG 60.669 63.158 0.65 0.00 36.30 4.85
2368 3294 2.743718 CAACTCCGAGTGGTGGCT 59.256 61.111 0.65 0.00 36.30 4.75
2369 3295 3.050275 GCAACTCCGAGTGGTGGC 61.050 66.667 0.65 0.70 36.30 5.01
2370 3296 0.535102 AAAGCAACTCCGAGTGGTGG 60.535 55.000 0.65 0.00 36.30 4.61
2371 3297 1.002468 CAAAAGCAACTCCGAGTGGTG 60.002 52.381 0.65 0.00 36.30 4.17
2372 3298 1.308998 CAAAAGCAACTCCGAGTGGT 58.691 50.000 0.65 0.00 36.30 4.16
2373 3299 0.040067 GCAAAAGCAACTCCGAGTGG 60.040 55.000 0.65 0.00 0.00 4.00
2374 3300 0.947244 AGCAAAAGCAACTCCGAGTG 59.053 50.000 0.65 0.00 0.00 3.51
2375 3301 1.604278 GAAGCAAAAGCAACTCCGAGT 59.396 47.619 0.00 0.00 0.00 4.18
2376 3302 1.603802 TGAAGCAAAAGCAACTCCGAG 59.396 47.619 0.00 0.00 0.00 4.63
2377 3303 1.603802 CTGAAGCAAAAGCAACTCCGA 59.396 47.619 0.00 0.00 0.00 4.55
2378 3304 1.334869 ACTGAAGCAAAAGCAACTCCG 59.665 47.619 0.00 0.00 0.00 4.63
2379 3305 2.358898 TGACTGAAGCAAAAGCAACTCC 59.641 45.455 0.00 0.00 0.00 3.85
2380 3306 3.366719 GTGACTGAAGCAAAAGCAACTC 58.633 45.455 0.00 0.00 0.00 3.01
2381 3307 2.099756 GGTGACTGAAGCAAAAGCAACT 59.900 45.455 0.00 0.00 0.00 3.16
2382 3308 2.099756 AGGTGACTGAAGCAAAAGCAAC 59.900 45.455 0.00 0.00 41.13 4.17
2383 3309 2.378038 AGGTGACTGAAGCAAAAGCAA 58.622 42.857 0.00 0.00 41.13 3.91
2384 3310 2.057137 AGGTGACTGAAGCAAAAGCA 57.943 45.000 0.00 0.00 41.13 3.91
2396 3322 1.678101 GCAAAAGCAACTCAGGTGACT 59.322 47.619 0.00 0.00 46.44 3.41
2397 3323 1.678101 AGCAAAAGCAACTCAGGTGAC 59.322 47.619 0.00 0.00 0.00 3.67
2398 3324 2.057137 AGCAAAAGCAACTCAGGTGA 57.943 45.000 0.00 0.00 0.00 4.02
2399 3325 2.099592 TGAAGCAAAAGCAACTCAGGTG 59.900 45.455 0.00 0.00 0.00 4.00
2400 3326 2.099756 GTGAAGCAAAAGCAACTCAGGT 59.900 45.455 0.00 0.00 0.00 4.00
2401 3327 2.099592 TGTGAAGCAAAAGCAACTCAGG 59.900 45.455 0.00 0.00 0.00 3.86
2402 3328 3.181493 ACTGTGAAGCAAAAGCAACTCAG 60.181 43.478 0.00 0.00 0.00 3.35
2403 3329 2.754552 ACTGTGAAGCAAAAGCAACTCA 59.245 40.909 0.00 0.00 0.00 3.41
2404 3330 3.181497 TGACTGTGAAGCAAAAGCAACTC 60.181 43.478 0.00 0.00 0.00 3.01
2405 3331 2.754552 TGACTGTGAAGCAAAAGCAACT 59.245 40.909 0.00 0.00 0.00 3.16
2406 3332 2.854185 GTGACTGTGAAGCAAAAGCAAC 59.146 45.455 0.00 0.00 0.00 4.17
2407 3333 2.159254 GGTGACTGTGAAGCAAAAGCAA 60.159 45.455 0.00 0.00 0.00 3.91
2408 3334 1.405105 GGTGACTGTGAAGCAAAAGCA 59.595 47.619 0.00 0.00 0.00 3.91
2409 3335 1.678101 AGGTGACTGTGAAGCAAAAGC 59.322 47.619 0.00 0.00 41.13 3.51
2424 3350 1.761449 TGCAAAAGCAACTCAGGTGA 58.239 45.000 0.00 0.00 0.00 4.02
2493 3830 4.464951 CACTAGGACACACCCACATACTTA 59.535 45.833 0.00 0.00 40.05 2.24
2538 3875 4.812091 AGTGTCACGTTGCACTAAAATACA 59.188 37.500 17.17 0.00 43.30 2.29
2563 3900 6.388619 AGATGGAACCAAACCTACTATGTT 57.611 37.500 0.00 0.00 0.00 2.71
2626 5423 7.506114 AGAGATGTTTACCAACAACAACTAGA 58.494 34.615 0.00 0.00 46.17 2.43


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

AutoCloner maintained by Alex Coulton.