Multiple sequence alignment - TraesCS5D01G147200

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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 TraesCS5D01G147200 chr5D 100.000 2687 0 0 1 2687 233690229 233687543 0.000000e+00 4963.0
1 TraesCS5D01G147200 chr5D 81.418 522 89 7 2166 2682 341685435 341684917 1.150000e-113 420.0
2 TraesCS5D01G147200 chr5D 80.608 526 94 8 2166 2686 212570785 212570263 1.500000e-107 399.0
3 TraesCS5D01G147200 chr5D 80.488 123 14 8 499 614 476942347 476942228 4.770000e-13 86.1
4 TraesCS5D01G147200 chr5A 89.929 2125 156 21 588 2687 321051544 321053635 0.000000e+00 2686.0
5 TraesCS5D01G147200 chr5A 89.091 330 18 8 184 498 321051219 321051545 6.970000e-106 394.0
6 TraesCS5D01G147200 chr5B 92.888 1406 50 14 596 2001 271181596 271182951 0.000000e+00 1997.0
7 TraesCS5D01G147200 chr5B 84.286 700 106 3 1986 2685 271189540 271190235 0.000000e+00 680.0
8 TraesCS5D01G147200 chr5B 84.551 479 32 16 30 498 271180823 271181269 1.140000e-118 436.0
9 TraesCS5D01G147200 chr6D 79.630 648 119 9 2045 2687 155243861 155244500 1.130000e-123 453.0
10 TraesCS5D01G147200 chr3B 80.868 507 92 5 2184 2687 154827899 154828403 6.970000e-106 394.0
11 TraesCS5D01G147200 chr3B 91.209 91 7 1 500 589 141861513 141861423 3.630000e-24 122.0
12 TraesCS5D01G147200 chr3B 90.110 91 8 1 500 589 141861423 141861513 1.690000e-22 117.0
13 TraesCS5D01G147200 chr2D 77.523 654 139 8 2038 2686 95182658 95182008 1.170000e-103 387.0
14 TraesCS5D01G147200 chr2D 84.906 106 7 7 496 592 2310700 2310805 6.120000e-17 99.0
15 TraesCS5D01G147200 chr1A 79.496 556 97 10 2125 2670 535293543 535294091 1.950000e-101 379.0
16 TraesCS5D01G147200 chr7D 78.333 600 117 12 2094 2686 28687895 28687302 2.530000e-100 375.0
17 TraesCS5D01G147200 chr7D 78.636 220 43 4 2040 2257 620128076 620127859 2.790000e-30 143.0
18 TraesCS5D01G147200 chr7D 77.293 229 43 9 2035 2258 186517344 186517120 2.810000e-25 126.0
19 TraesCS5D01G147200 chr7D 75.355 211 47 5 2038 2246 34486031 34485824 2.200000e-16 97.1
20 TraesCS5D01G147200 chr7D 77.439 164 34 3 2042 2204 467515980 467516141 7.920000e-16 95.3
21 TraesCS5D01G147200 chr4D 79.188 591 70 33 1077 1639 102534320 102533755 7.070000e-96 361.0
22 TraesCS5D01G147200 chr4D 86.000 100 7 5 497 589 375134919 375135018 1.700000e-17 100.0
23 TraesCS5D01G147200 chr4B 78.849 591 72 33 1077 1639 147066781 147066216 1.530000e-92 350.0
24 TraesCS5D01G147200 chr4B 72.443 352 72 20 2038 2379 167332940 167333276 3.680000e-14 89.8
25 TraesCS5D01G147200 chr3D 88.172 93 8 2 500 589 92122349 92122257 1.020000e-19 108.0
26 TraesCS5D01G147200 chr3D 87.097 93 9 2 500 589 92122257 92122349 4.730000e-18 102.0
27 TraesCS5D01G147200 chr6A 85.294 102 7 6 496 589 539706783 539706682 6.120000e-17 99.0
28 TraesCS5D01G147200 chr2B 83.486 109 10 6 493 593 743698084 743697976 7.920000e-16 95.3


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 TraesCS5D01G147200 chr5D 233687543 233690229 2686 True 4963.0 4963 100.0000 1 2687 1 chr5D.!!$R2 2686
1 TraesCS5D01G147200 chr5D 341684917 341685435 518 True 420.0 420 81.4180 2166 2682 1 chr5D.!!$R3 516
2 TraesCS5D01G147200 chr5D 212570263 212570785 522 True 399.0 399 80.6080 2166 2686 1 chr5D.!!$R1 520
3 TraesCS5D01G147200 chr5A 321051219 321053635 2416 False 1540.0 2686 89.5100 184 2687 2 chr5A.!!$F1 2503
4 TraesCS5D01G147200 chr5B 271180823 271182951 2128 False 1216.5 1997 88.7195 30 2001 2 chr5B.!!$F2 1971
5 TraesCS5D01G147200 chr5B 271189540 271190235 695 False 680.0 680 84.2860 1986 2685 1 chr5B.!!$F1 699
6 TraesCS5D01G147200 chr6D 155243861 155244500 639 False 453.0 453 79.6300 2045 2687 1 chr6D.!!$F1 642
7 TraesCS5D01G147200 chr3B 154827899 154828403 504 False 394.0 394 80.8680 2184 2687 1 chr3B.!!$F2 503
8 TraesCS5D01G147200 chr2D 95182008 95182658 650 True 387.0 387 77.5230 2038 2686 1 chr2D.!!$R1 648
9 TraesCS5D01G147200 chr1A 535293543 535294091 548 False 379.0 379 79.4960 2125 2670 1 chr1A.!!$F1 545
10 TraesCS5D01G147200 chr7D 28687302 28687895 593 True 375.0 375 78.3330 2094 2686 1 chr7D.!!$R1 592
11 TraesCS5D01G147200 chr4D 102533755 102534320 565 True 361.0 361 79.1880 1077 1639 1 chr4D.!!$R1 562
12 TraesCS5D01G147200 chr4B 147066216 147066781 565 True 350.0 350 78.8490 1077 1639 1 chr4B.!!$R1 562

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
170 175 0.036388 TGCGATGTTTGAGGACCCTC 60.036 55.0 9.08 9.08 43.01 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2043 2368 0.391263 GAGGGTCGGCGTTGAAGATT 60.391 55.0 6.85 0.0 0.0 2.4 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
24 25 7.915293 ATTCACGAGTTATATCACCAAAACA 57.085 32.000 0.00 0.00 0.00 2.83
25 26 6.715344 TCACGAGTTATATCACCAAAACAC 57.285 37.500 0.00 0.00 0.00 3.32
26 27 6.224584 TCACGAGTTATATCACCAAAACACA 58.775 36.000 0.00 0.00 0.00 3.72
27 28 6.876789 TCACGAGTTATATCACCAAAACACAT 59.123 34.615 0.00 0.00 0.00 3.21
28 29 7.389330 TCACGAGTTATATCACCAAAACACATT 59.611 33.333 0.00 0.00 0.00 2.71
48 49 9.625747 ACACATTTTTATTTCCCTCAAAACAAT 57.374 25.926 0.00 0.00 0.00 2.71
57 58 5.319043 TCCCTCAAAACAATACTCCAGTT 57.681 39.130 0.00 0.00 0.00 3.16
117 118 6.096705 TGCGAATTTAATCAGGACATGGAATT 59.903 34.615 0.00 0.00 0.00 2.17
155 160 1.792367 GCTATTCGTACATGCATGCGA 59.208 47.619 26.53 23.30 0.00 5.10
156 161 2.413112 GCTATTCGTACATGCATGCGAT 59.587 45.455 26.53 17.52 33.27 4.58
157 162 2.955607 ATTCGTACATGCATGCGATG 57.044 45.000 26.53 18.82 33.27 3.84
158 163 1.650825 TTCGTACATGCATGCGATGT 58.349 45.000 26.53 27.23 37.75 3.06
159 164 1.650825 TCGTACATGCATGCGATGTT 58.349 45.000 28.44 18.02 35.62 2.71
160 165 2.006169 TCGTACATGCATGCGATGTTT 58.994 42.857 28.44 15.16 35.62 2.83
161 166 2.103388 CGTACATGCATGCGATGTTTG 58.897 47.619 28.44 20.73 35.62 2.93
162 167 2.222999 CGTACATGCATGCGATGTTTGA 60.223 45.455 28.44 15.78 35.62 2.69
163 168 2.554806 ACATGCATGCGATGTTTGAG 57.445 45.000 26.53 0.00 29.39 3.02
164 169 1.133598 ACATGCATGCGATGTTTGAGG 59.866 47.619 26.53 5.46 29.39 3.86
165 170 1.402613 CATGCATGCGATGTTTGAGGA 59.597 47.619 14.93 0.00 0.00 3.71
166 171 0.804364 TGCATGCGATGTTTGAGGAC 59.196 50.000 14.09 0.00 0.00 3.85
167 172 0.099436 GCATGCGATGTTTGAGGACC 59.901 55.000 0.00 0.00 0.00 4.46
168 173 0.734889 CATGCGATGTTTGAGGACCC 59.265 55.000 0.00 0.00 0.00 4.46
169 174 0.620556 ATGCGATGTTTGAGGACCCT 59.379 50.000 0.00 0.00 0.00 4.34
170 175 0.036388 TGCGATGTTTGAGGACCCTC 60.036 55.000 9.08 9.08 43.01 4.30
171 176 0.250513 GCGATGTTTGAGGACCCTCT 59.749 55.000 16.25 0.00 43.12 3.69
172 177 1.339151 GCGATGTTTGAGGACCCTCTT 60.339 52.381 16.25 0.00 43.12 2.85
173 178 2.876079 GCGATGTTTGAGGACCCTCTTT 60.876 50.000 16.25 0.00 43.12 2.52
174 179 3.412386 CGATGTTTGAGGACCCTCTTTT 58.588 45.455 16.25 0.00 43.12 2.27
175 180 3.821033 CGATGTTTGAGGACCCTCTTTTT 59.179 43.478 16.25 0.00 43.12 1.94
396 413 0.883370 GCCCGTCCACGATTTATCCC 60.883 60.000 0.00 0.00 43.02 3.85
403 420 2.969950 TCCACGATTTATCCCGATTCCT 59.030 45.455 0.00 0.00 0.00 3.36
405 422 3.067106 CACGATTTATCCCGATTCCTGG 58.933 50.000 0.00 0.00 0.00 4.45
438 456 3.914426 AGCCCGTCATTCATATATCCC 57.086 47.619 0.00 0.00 0.00 3.85
445 463 6.351711 CCGTCATTCATATATCCCATGACAT 58.648 40.000 19.32 0.00 42.59 3.06
448 466 7.713942 CGTCATTCATATATCCCATGACATCAT 59.286 37.037 19.32 0.00 42.59 2.45
452 470 8.797350 TTCATATATCCCATGACATCATCAAC 57.203 34.615 0.00 0.00 41.93 3.18
453 471 7.920227 TCATATATCCCATGACATCATCAACA 58.080 34.615 0.00 0.00 41.93 3.33
454 472 8.384718 TCATATATCCCATGACATCATCAACAA 58.615 33.333 0.00 0.00 41.93 2.83
455 473 9.016438 CATATATCCCATGACATCATCAACAAA 57.984 33.333 0.00 0.00 41.93 2.83
456 474 9.763837 ATATATCCCATGACATCATCAACAAAT 57.236 29.630 0.00 0.00 41.93 2.32
457 475 5.840243 TCCCATGACATCATCAACAAATC 57.160 39.130 0.00 0.00 41.93 2.17
458 476 4.336153 TCCCATGACATCATCAACAAATCG 59.664 41.667 0.00 0.00 41.93 3.34
459 477 4.498513 CCCATGACATCATCAACAAATCGG 60.499 45.833 0.00 0.00 41.93 4.18
460 478 4.336153 CCATGACATCATCAACAAATCGGA 59.664 41.667 0.00 0.00 41.93 4.55
462 480 5.956068 TGACATCATCAACAAATCGGAAA 57.044 34.783 0.00 0.00 33.02 3.13
464 482 6.324042 TGACATCATCAACAAATCGGAAATG 58.676 36.000 0.00 0.00 33.02 2.32
465 483 6.072008 TGACATCATCAACAAATCGGAAATGT 60.072 34.615 0.00 0.00 33.02 2.71
466 484 6.690530 ACATCATCAACAAATCGGAAATGTT 58.309 32.000 6.09 6.09 37.76 2.71
468 486 8.469200 ACATCATCAACAAATCGGAAATGTTAT 58.531 29.630 10.28 1.02 35.63 1.89
473 491 8.287439 TCAACAAATCGGAAATGTTATATGGT 57.713 30.769 10.28 0.00 35.63 3.55
476 494 8.287439 ACAAATCGGAAATGTTATATGGTGAA 57.713 30.769 0.00 0.00 0.00 3.18
488 506 7.747888 TGTTATATGGTGAAAGATTTGTCGTG 58.252 34.615 0.00 0.00 0.00 4.35
498 516 8.067784 GTGAAAGATTTGTCGTGTCTTTGATAA 58.932 33.333 4.51 0.00 41.01 1.75
499 517 8.783093 TGAAAGATTTGTCGTGTCTTTGATAAT 58.217 29.630 4.51 0.00 41.01 1.28
502 520 9.436957 AAGATTTGTCGTGTCTTTGATAATACT 57.563 29.630 0.00 0.00 0.00 2.12
503 521 9.088512 AGATTTGTCGTGTCTTTGATAATACTC 57.911 33.333 0.00 0.00 0.00 2.59
504 522 7.591006 TTTGTCGTGTCTTTGATAATACTCC 57.409 36.000 0.00 0.00 0.00 3.85
505 523 5.337554 TGTCGTGTCTTTGATAATACTCCG 58.662 41.667 0.00 0.00 0.00 4.63
507 525 5.454877 GTCGTGTCTTTGATAATACTCCGTC 59.545 44.000 0.00 0.00 0.00 4.79
508 526 4.738740 CGTGTCTTTGATAATACTCCGTCC 59.261 45.833 0.00 0.00 0.00 4.79
509 527 4.738740 GTGTCTTTGATAATACTCCGTCCG 59.261 45.833 0.00 0.00 0.00 4.79
511 529 4.974888 GTCTTTGATAATACTCCGTCCGTC 59.025 45.833 0.00 0.00 0.00 4.79
512 530 3.996150 TTGATAATACTCCGTCCGTCC 57.004 47.619 0.00 0.00 0.00 4.79
513 531 2.233271 TGATAATACTCCGTCCGTCCC 58.767 52.381 0.00 0.00 0.00 4.46
514 532 2.233271 GATAATACTCCGTCCGTCCCA 58.767 52.381 0.00 0.00 0.00 4.37
515 533 2.142356 TAATACTCCGTCCGTCCCAA 57.858 50.000 0.00 0.00 0.00 4.12
516 534 1.269012 AATACTCCGTCCGTCCCAAA 58.731 50.000 0.00 0.00 0.00 3.28
517 535 1.269012 ATACTCCGTCCGTCCCAAAA 58.731 50.000 0.00 0.00 0.00 2.44
518 536 1.269012 TACTCCGTCCGTCCCAAAAT 58.731 50.000 0.00 0.00 0.00 1.82
521 539 2.277084 CTCCGTCCGTCCCAAAATAAG 58.723 52.381 0.00 0.00 0.00 1.73
522 540 1.624813 TCCGTCCGTCCCAAAATAAGT 59.375 47.619 0.00 0.00 0.00 2.24
523 541 1.735571 CCGTCCGTCCCAAAATAAGTG 59.264 52.381 0.00 0.00 0.00 3.16
524 542 2.419667 CGTCCGTCCCAAAATAAGTGT 58.580 47.619 0.00 0.00 0.00 3.55
525 543 2.414138 CGTCCGTCCCAAAATAAGTGTC 59.586 50.000 0.00 0.00 0.00 3.67
526 544 3.671716 GTCCGTCCCAAAATAAGTGTCT 58.328 45.455 0.00 0.00 0.00 3.41
527 545 3.683340 GTCCGTCCCAAAATAAGTGTCTC 59.317 47.826 0.00 0.00 0.00 3.36
528 546 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
529 547 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
530 548 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
531 549 4.755123 CGTCCCAAAATAAGTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
533 551 6.238648 CGTCCCAAAATAAGTGTCTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
535 553 8.793592 GTCCCAAAATAAGTGTCTCAACTTTAT 58.206 33.333 0.00 0.00 40.77 1.40
582 798 7.660208 AGTTGACACACTTATTTTAAGACGGAT 59.340 33.333 1.47 0.00 0.00 4.18
602 849 6.040878 CGGATGGAGTAGTTTCGTTATTTCT 58.959 40.000 0.00 0.00 0.00 2.52
610 857 9.583765 GAGTAGTTTCGTTATTTCTATGTCCTT 57.416 33.333 0.00 0.00 0.00 3.36
688 947 0.944311 GCAACTGCCGAGACGAAGAA 60.944 55.000 0.00 0.00 34.31 2.52
689 948 1.497991 CAACTGCCGAGACGAAGAAA 58.502 50.000 0.00 0.00 0.00 2.52
690 949 1.457303 CAACTGCCGAGACGAAGAAAG 59.543 52.381 0.00 0.00 0.00 2.62
924 1193 2.112190 CTCTCCTCCAACCTCCTAACC 58.888 57.143 0.00 0.00 0.00 2.85
925 1194 0.824759 CTCCTCCAACCTCCTAACCG 59.175 60.000 0.00 0.00 0.00 4.44
926 1195 1.221021 CCTCCAACCTCCTAACCGC 59.779 63.158 0.00 0.00 0.00 5.68
927 1196 1.550130 CCTCCAACCTCCTAACCGCA 61.550 60.000 0.00 0.00 0.00 5.69
928 1197 0.323629 CTCCAACCTCCTAACCGCAA 59.676 55.000 0.00 0.00 0.00 4.85
929 1198 0.323629 TCCAACCTCCTAACCGCAAG 59.676 55.000 0.00 0.00 0.00 4.01
930 1199 1.305930 CCAACCTCCTAACCGCAAGC 61.306 60.000 0.00 0.00 0.00 4.01
931 1200 0.605319 CAACCTCCTAACCGCAAGCA 60.605 55.000 0.00 0.00 0.00 3.91
932 1201 0.605589 AACCTCCTAACCGCAAGCAC 60.606 55.000 0.00 0.00 0.00 4.40
933 1202 2.100631 CCTCCTAACCGCAAGCACG 61.101 63.158 0.00 0.00 0.00 5.34
934 1203 2.740714 CTCCTAACCGCAAGCACGC 61.741 63.158 0.00 0.00 0.00 5.34
935 1204 3.799755 CCTAACCGCAAGCACGCC 61.800 66.667 0.00 0.00 0.00 5.68
936 1205 4.147322 CTAACCGCAAGCACGCCG 62.147 66.667 0.00 0.00 0.00 6.46
947 1216 4.592192 CACGCCGGCCAGATCGAT 62.592 66.667 23.46 0.00 0.00 3.59
948 1217 4.286320 ACGCCGGCCAGATCGATC 62.286 66.667 23.46 17.91 0.00 3.69
983 1278 3.004944 GCGAGCCAAGCTAACTATCTACT 59.995 47.826 0.00 0.00 39.88 2.57
984 1279 4.789784 CGAGCCAAGCTAACTATCTACTC 58.210 47.826 0.00 0.00 39.88 2.59
985 1280 4.611807 CGAGCCAAGCTAACTATCTACTCG 60.612 50.000 0.00 0.00 39.88 4.18
986 1281 4.208746 AGCCAAGCTAACTATCTACTCGT 58.791 43.478 0.00 0.00 36.99 4.18
987 1282 5.374921 AGCCAAGCTAACTATCTACTCGTA 58.625 41.667 0.00 0.00 36.99 3.43
988 1283 5.239087 AGCCAAGCTAACTATCTACTCGTAC 59.761 44.000 0.00 0.00 36.99 3.67
995 1290 6.364706 GCTAACTATCTACTCGTACGAGCTAA 59.635 42.308 38.10 25.59 45.54 3.09
1069 1364 3.878519 GAGCCGTCGTCGAGGAGG 61.879 72.222 18.26 18.26 39.71 4.30
1189 1484 3.857854 GCTACGGCTCGTCGTCGA 61.858 66.667 0.00 4.42 45.36 4.20
1281 1576 0.913451 AGATCAAGCTGAGCCTGGGT 60.913 55.000 0.00 0.00 32.25 4.51
1347 1648 3.780173 GCCAAGCCGCTCCTCTCT 61.780 66.667 0.00 0.00 0.00 3.10
1470 1789 2.117156 CGTCGTGGAGGGGTCGTAT 61.117 63.158 0.00 0.00 0.00 3.06
1860 2185 6.976636 AGTAGCAAAGCAGAAGAGTAATTC 57.023 37.500 0.00 0.00 0.00 2.17
1930 2255 5.776208 TGCCTTAGGAATCGGTGTATATACA 59.224 40.000 11.62 11.62 0.00 2.29
1966 2291 4.847198 ACTTGTGTTCATGGATGATGCTA 58.153 39.130 0.00 0.00 36.56 3.49
2043 2368 1.750018 TCGCCGATCGTGTAAGGGA 60.750 57.895 15.09 9.03 39.67 4.20
2151 2478 0.179142 TTCACGACACGGTTCGAACA 60.179 50.000 28.24 2.83 41.78 3.18
2233 2562 2.520458 CCTGCTTCCAACCACCCA 59.480 61.111 0.00 0.00 0.00 4.51
2300 2634 1.526686 CCAGCTGCCCGCATTCATA 60.527 57.895 8.66 0.00 42.61 2.15
2312 2646 4.816385 CCCGCATTCATATTGTTGTAGAGT 59.184 41.667 0.00 0.00 0.00 3.24
2334 2668 1.741401 CCGCTCCGCATTGAAGACA 60.741 57.895 0.00 0.00 0.00 3.41
2338 2672 1.446907 CTCCGCATTGAAGACAGCTT 58.553 50.000 0.00 0.00 36.96 3.74
2352 2686 2.263540 GCTTAGGGTGGACGCGAA 59.736 61.111 15.93 0.00 0.00 4.70
2421 2755 2.705220 CGACGCGTCTCCGATGTA 59.295 61.111 33.94 0.00 35.63 2.29
2463 2797 1.213013 GCGTGACTGGACGAGATGT 59.787 57.895 5.77 0.00 42.10 3.06
2465 2799 1.073216 CGTGACTGGACGAGATGTGC 61.073 60.000 0.00 0.00 42.10 4.57
2479 2813 4.159321 CGAGATGTGCCAGATATCTACCAT 59.841 45.833 4.54 5.27 32.89 3.55
2482 2816 2.705127 TGTGCCAGATATCTACCATGCA 59.295 45.455 4.54 6.90 0.00 3.96
2483 2817 3.328637 TGTGCCAGATATCTACCATGCAT 59.671 43.478 4.54 0.00 0.00 3.96
2490 2824 6.072838 CCAGATATCTACCATGCATGTTCAAC 60.073 42.308 24.58 8.62 0.00 3.18
2546 2881 1.370064 CCGACCGAGAAACCCACTT 59.630 57.895 0.00 0.00 0.00 3.16
2553 2892 0.883370 GAGAAACCCACTTCGGCGTT 60.883 55.000 6.85 0.00 31.65 4.84
2613 2953 1.202256 GCTATTTAAAGGCGGCCACAC 60.202 52.381 23.09 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.389330 TGTGTTTTGGTGATATAACTCGTGAAT 59.611 33.333 0.00 0.00 0.00 2.57
1 2 6.706716 TGTGTTTTGGTGATATAACTCGTGAA 59.293 34.615 0.00 0.00 0.00 3.18
2 3 6.224584 TGTGTTTTGGTGATATAACTCGTGA 58.775 36.000 0.00 0.00 0.00 4.35
3 4 6.474819 TGTGTTTTGGTGATATAACTCGTG 57.525 37.500 0.00 0.00 0.00 4.35
4 5 7.681939 AATGTGTTTTGGTGATATAACTCGT 57.318 32.000 0.00 0.00 0.00 4.18
5 6 8.964420 AAAATGTGTTTTGGTGATATAACTCG 57.036 30.769 0.00 0.00 36.24 4.18
12 13 9.495572 GGGAAATAAAAATGTGTTTTGGTGATA 57.504 29.630 0.00 0.00 37.59 2.15
13 14 8.217111 AGGGAAATAAAAATGTGTTTTGGTGAT 58.783 29.630 0.00 0.00 37.59 3.06
14 15 7.569240 AGGGAAATAAAAATGTGTTTTGGTGA 58.431 30.769 0.00 0.00 37.59 4.02
15 16 7.497249 TGAGGGAAATAAAAATGTGTTTTGGTG 59.503 33.333 0.00 0.00 37.59 4.17
16 17 7.569240 TGAGGGAAATAAAAATGTGTTTTGGT 58.431 30.769 0.00 0.00 37.59 3.67
17 18 8.443953 TTGAGGGAAATAAAAATGTGTTTTGG 57.556 30.769 0.00 0.00 37.59 3.28
20 21 9.454859 TGTTTTGAGGGAAATAAAAATGTGTTT 57.545 25.926 0.00 0.00 0.00 2.83
21 22 9.454859 TTGTTTTGAGGGAAATAAAAATGTGTT 57.545 25.926 0.00 0.00 0.00 3.32
22 23 9.625747 ATTGTTTTGAGGGAAATAAAAATGTGT 57.374 25.926 0.00 0.00 0.00 3.72
27 28 9.990360 GGAGTATTGTTTTGAGGGAAATAAAAA 57.010 29.630 0.00 0.00 0.00 1.94
28 29 9.148879 TGGAGTATTGTTTTGAGGGAAATAAAA 57.851 29.630 0.00 0.00 0.00 1.52
48 49 8.475639 GGAGTCATAGTTTAATCAACTGGAGTA 58.524 37.037 0.00 0.00 45.98 2.59
49 50 7.331791 GGAGTCATAGTTTAATCAACTGGAGT 58.668 38.462 0.00 0.00 45.98 3.85
50 51 6.763610 GGGAGTCATAGTTTAATCAACTGGAG 59.236 42.308 0.00 0.00 45.98 3.86
51 52 6.443849 AGGGAGTCATAGTTTAATCAACTGGA 59.556 38.462 0.00 0.00 45.98 3.86
52 53 6.653989 AGGGAGTCATAGTTTAATCAACTGG 58.346 40.000 0.00 0.00 45.98 4.00
57 58 9.661954 AATCTAGAGGGAGTCATAGTTTAATCA 57.338 33.333 0.00 0.00 0.00 2.57
92 93 4.522114 TCCATGTCCTGATTAAATTCGCA 58.478 39.130 0.00 0.00 0.00 5.10
108 109 2.033236 CGTGCGCGTATAAATTCCATGT 60.033 45.455 12.43 0.00 0.00 3.21
109 110 2.559872 CGTGCGCGTATAAATTCCATG 58.440 47.619 12.43 0.00 0.00 3.66
142 147 3.357021 CTCAAACATCGCATGCATGTAC 58.643 45.455 26.79 11.10 33.12 2.90
173 178 6.133356 AGGGTCCTCAAACATTCTGTAAAAA 58.867 36.000 0.00 0.00 0.00 1.94
174 179 5.701224 AGGGTCCTCAAACATTCTGTAAAA 58.299 37.500 0.00 0.00 0.00 1.52
175 180 5.319043 AGGGTCCTCAAACATTCTGTAAA 57.681 39.130 0.00 0.00 0.00 2.01
176 181 4.993705 AGGGTCCTCAAACATTCTGTAA 57.006 40.909 0.00 0.00 0.00 2.41
177 182 4.651778 CAAGGGTCCTCAAACATTCTGTA 58.348 43.478 0.00 0.00 0.00 2.74
178 183 3.490348 CAAGGGTCCTCAAACATTCTGT 58.510 45.455 0.00 0.00 0.00 3.41
179 184 2.229784 GCAAGGGTCCTCAAACATTCTG 59.770 50.000 0.00 0.00 0.00 3.02
180 185 2.108952 AGCAAGGGTCCTCAAACATTCT 59.891 45.455 0.00 0.00 0.00 2.40
181 186 2.519013 AGCAAGGGTCCTCAAACATTC 58.481 47.619 0.00 0.00 0.00 2.67
182 187 2.683211 AGCAAGGGTCCTCAAACATT 57.317 45.000 0.00 0.00 0.00 2.71
248 253 4.855715 AGTCGTAGTGATATGGTCCATG 57.144 45.455 15.10 0.00 0.00 3.66
396 413 2.281070 CGGGGCATCCAGGAATCG 60.281 66.667 0.00 0.00 34.36 3.34
438 456 5.488645 TCCGATTTGTTGATGATGTCATG 57.511 39.130 0.00 0.00 36.54 3.07
445 463 9.949174 CATATAACATTTCCGATTTGTTGATGA 57.051 29.630 6.69 0.00 33.90 2.92
448 466 8.187480 CACCATATAACATTTCCGATTTGTTGA 58.813 33.333 6.69 0.00 35.37 3.18
452 470 9.236691 CTTTCACCATATAACATTTCCGATTTG 57.763 33.333 0.00 0.00 0.00 2.32
453 471 9.184523 TCTTTCACCATATAACATTTCCGATTT 57.815 29.630 0.00 0.00 0.00 2.17
454 472 8.746052 TCTTTCACCATATAACATTTCCGATT 57.254 30.769 0.00 0.00 0.00 3.34
455 473 8.924511 ATCTTTCACCATATAACATTTCCGAT 57.075 30.769 0.00 0.00 0.00 4.18
456 474 8.746052 AATCTTTCACCATATAACATTTCCGA 57.254 30.769 0.00 0.00 0.00 4.55
457 475 9.236691 CAAATCTTTCACCATATAACATTTCCG 57.763 33.333 0.00 0.00 0.00 4.30
460 478 9.787532 CGACAAATCTTTCACCATATAACATTT 57.212 29.630 0.00 0.00 0.00 2.32
462 480 8.397906 CACGACAAATCTTTCACCATATAACAT 58.602 33.333 0.00 0.00 0.00 2.71
464 482 7.748847 ACACGACAAATCTTTCACCATATAAC 58.251 34.615 0.00 0.00 0.00 1.89
465 483 7.822334 AGACACGACAAATCTTTCACCATATAA 59.178 33.333 0.00 0.00 0.00 0.98
466 484 7.327975 AGACACGACAAATCTTTCACCATATA 58.672 34.615 0.00 0.00 0.00 0.86
468 486 5.547465 AGACACGACAAATCTTTCACCATA 58.453 37.500 0.00 0.00 0.00 2.74
470 488 3.804036 AGACACGACAAATCTTTCACCA 58.196 40.909 0.00 0.00 0.00 4.17
473 491 6.618287 ATCAAAGACACGACAAATCTTTCA 57.382 33.333 0.00 0.00 39.98 2.69
476 494 9.436957 AGTATTATCAAAGACACGACAAATCTT 57.563 29.630 0.00 0.00 34.11 2.40
501 519 2.277084 CTTATTTTGGGACGGACGGAG 58.723 52.381 0.00 0.00 0.00 4.63
502 520 1.624813 ACTTATTTTGGGACGGACGGA 59.375 47.619 0.00 0.00 0.00 4.69
503 521 1.735571 CACTTATTTTGGGACGGACGG 59.264 52.381 0.00 0.00 0.00 4.79
504 522 2.414138 GACACTTATTTTGGGACGGACG 59.586 50.000 0.00 0.00 0.00 4.79
505 523 3.671716 AGACACTTATTTTGGGACGGAC 58.328 45.455 0.00 0.00 0.00 4.79
507 525 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
508 526 4.755123 AGTTGAGACACTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
509 527 6.635030 AAGTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
555 573 7.496591 TCCGTCTTAAAATAAGTGTGTCAACTT 59.503 33.333 0.00 0.00 42.89 2.66
556 574 6.987992 TCCGTCTTAAAATAAGTGTGTCAACT 59.012 34.615 0.00 0.00 0.00 3.16
557 575 7.181143 TCCGTCTTAAAATAAGTGTGTCAAC 57.819 36.000 0.00 0.00 0.00 3.18
558 576 7.094975 CCATCCGTCTTAAAATAAGTGTGTCAA 60.095 37.037 0.00 0.00 0.00 3.18
559 577 6.370442 CCATCCGTCTTAAAATAAGTGTGTCA 59.630 38.462 0.00 0.00 0.00 3.58
563 581 6.708285 ACTCCATCCGTCTTAAAATAAGTGT 58.292 36.000 0.00 0.00 0.00 3.55
564 582 7.980099 ACTACTCCATCCGTCTTAAAATAAGTG 59.020 37.037 0.00 0.00 0.00 3.16
566 584 8.943909 AACTACTCCATCCGTCTTAAAATAAG 57.056 34.615 0.00 0.00 0.00 1.73
567 585 9.374838 GAAACTACTCCATCCGTCTTAAAATAA 57.625 33.333 0.00 0.00 0.00 1.40
569 587 6.534079 CGAAACTACTCCATCCGTCTTAAAAT 59.466 38.462 0.00 0.00 0.00 1.82
570 588 5.865552 CGAAACTACTCCATCCGTCTTAAAA 59.134 40.000 0.00 0.00 0.00 1.52
571 589 5.047802 ACGAAACTACTCCATCCGTCTTAAA 60.048 40.000 0.00 0.00 0.00 1.52
573 591 4.012374 ACGAAACTACTCCATCCGTCTTA 58.988 43.478 0.00 0.00 0.00 2.10
576 594 2.935481 ACGAAACTACTCCATCCGTC 57.065 50.000 0.00 0.00 0.00 4.79
582 798 7.977853 GGACATAGAAATAACGAAACTACTCCA 59.022 37.037 0.00 0.00 0.00 3.86
688 947 6.697019 CGACAACAATGGACATTTTCTTTCTT 59.303 34.615 0.00 0.00 0.00 2.52
689 948 6.039270 TCGACAACAATGGACATTTTCTTTCT 59.961 34.615 0.00 0.00 0.00 2.52
690 949 6.205784 TCGACAACAATGGACATTTTCTTTC 58.794 36.000 0.00 0.00 0.00 2.62
738 1007 5.995897 AGGCGTGACTACTTTTCAGTTTATT 59.004 36.000 0.00 0.00 34.06 1.40
930 1199 4.592192 ATCGATCTGGCCGGCGTG 62.592 66.667 22.54 15.82 0.00 5.34
931 1200 4.286320 GATCGATCTGGCCGGCGT 62.286 66.667 22.54 6.11 0.00 5.68
939 1208 3.905705 GAGGGGCGCGATCGATCTG 62.906 68.421 21.57 16.35 38.10 2.90
940 1209 3.675563 GAGGGGCGCGATCGATCT 61.676 66.667 21.57 7.53 38.10 2.75
941 1210 3.618710 GAGAGGGGCGCGATCGATC 62.619 68.421 21.57 15.68 38.10 3.69
942 1211 3.675563 GAGAGGGGCGCGATCGAT 61.676 66.667 21.57 0.00 38.10 3.59
983 1278 0.248336 CATGCCGTTAGCTCGTACGA 60.248 55.000 18.41 18.41 44.23 3.43
984 1279 1.206745 CCATGCCGTTAGCTCGTACG 61.207 60.000 9.53 9.53 44.23 3.67
985 1280 1.488261 GCCATGCCGTTAGCTCGTAC 61.488 60.000 0.00 0.00 44.23 3.67
986 1281 1.227147 GCCATGCCGTTAGCTCGTA 60.227 57.895 0.00 0.00 44.23 3.43
987 1282 2.511600 GCCATGCCGTTAGCTCGT 60.512 61.111 0.00 0.00 44.23 4.18
988 1283 1.643868 TTTGCCATGCCGTTAGCTCG 61.644 55.000 0.00 0.00 44.23 5.03
995 1290 3.683937 GCACCTTTGCCATGCCGT 61.684 61.111 0.00 0.00 43.66 5.68
1281 1576 4.270153 ACCCAGTGCTCCCCCAGA 62.270 66.667 0.00 0.00 0.00 3.86
1752 2077 0.875059 CCCTTGCGAAGAACCTTGTC 59.125 55.000 0.00 0.00 0.00 3.18
1860 2185 7.732664 AGCTTTGCTTTCTAAATTTAAATGCG 58.267 30.769 0.39 0.00 33.89 4.73
1878 2203 2.109126 CCAGCCTCCGTAGCTTTGC 61.109 63.158 0.00 0.00 38.95 3.68
1930 2255 2.171448 ACACAAGTTTCAGAGGCTGACT 59.829 45.455 0.00 0.00 40.46 3.41
2043 2368 0.391263 GAGGGTCGGCGTTGAAGATT 60.391 55.000 6.85 0.00 0.00 2.40
2111 2438 4.537135 ACTGATACAGAATCACGTTGGT 57.463 40.909 5.76 0.00 39.77 3.67
2151 2478 7.889469 TGTCTACGGTTTACTGAAGAAAGTAT 58.111 34.615 0.00 0.00 32.78 2.12
2233 2562 2.526110 GAGGTTTTGGGTGGGCCT 59.474 61.111 4.53 0.00 34.45 5.19
2300 2634 1.156736 GCGGTGCACTCTACAACAAT 58.843 50.000 17.98 0.00 0.00 2.71
2334 2668 2.280552 TTCGCGTCCACCCTAAGCT 61.281 57.895 5.77 0.00 0.00 3.74
2338 2672 1.303888 AGAGTTCGCGTCCACCCTA 60.304 57.895 5.77 0.00 0.00 3.53
2421 2755 0.244450 CCGGCATTGAACAAGCACAT 59.756 50.000 0.00 0.00 0.00 3.21
2463 2797 3.328637 ACATGCATGGTAGATATCTGGCA 59.671 43.478 29.41 15.50 0.00 4.92
2465 2799 5.554070 TGAACATGCATGGTAGATATCTGG 58.446 41.667 29.41 0.88 0.00 3.86
2479 2813 1.535028 GGACATGACGTTGAACATGCA 59.465 47.619 13.24 0.00 45.03 3.96
2482 2816 2.066262 GACGGACATGACGTTGAACAT 58.934 47.619 18.10 0.00 45.68 2.71
2483 2817 1.493772 GACGGACATGACGTTGAACA 58.506 50.000 18.10 0.00 45.68 3.18
2490 2824 1.206745 GCATACGGACGGACATGACG 61.207 60.000 0.00 6.35 37.36 4.35
2553 2892 1.227793 TCCAGTGTGTCAATGCGCA 60.228 52.632 14.96 14.96 0.00 6.09
2613 2953 0.396695 TGGAGTAGAGTTAGCCGGGG 60.397 60.000 2.18 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.