Multiple sequence alignment - TraesCS1A01G059200

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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 TraesCS1A01G059200 chr1A 100.000 3734 0 0 1 3734 39895819 39892086 0.000000e+00 6896
1 TraesCS1A01G059200 chr1D 93.075 2758 119 26 994 3734 40797945 40795243 0.000000e+00 3969
2 TraesCS1A01G059200 chr1D 84.475 438 38 12 1 419 40798969 40798543 4.490000e-109 405
3 TraesCS1A01G059200 chr1D 84.342 281 25 5 701 964 40798292 40798014 1.330000e-64 257
4 TraesCS1A01G059200 chr1D 93.210 162 11 0 543 704 77381678 77381517 4.820000e-59 239
5 TraesCS1A01G059200 chr1D 91.228 171 14 1 543 712 178466467 178466297 8.070000e-57 231
6 TraesCS1A01G059200 chr1B 93.954 1836 80 15 983 2800 60255805 60257627 0.000000e+00 2747
7 TraesCS1A01G059200 chr1B 86.414 898 84 21 2846 3734 60131202 60130334 0.000000e+00 948
8 TraesCS1A01G059200 chr1B 87.481 655 68 7 3080 3730 60273053 60273697 0.000000e+00 743
9 TraesCS1A01G059200 chr1B 89.234 548 50 7 1 544 60252696 60253238 0.000000e+00 676
10 TraesCS1A01G059200 chr1B 85.150 633 71 12 3101 3727 60165926 60165311 8.800000e-176 627
11 TraesCS1A01G059200 chr1B 87.500 528 55 5 3205 3730 60129124 60128606 1.920000e-167 599
12 TraesCS1A01G059200 chr1B 88.945 398 30 9 2399 2794 60194076 60193691 2.610000e-131 479
13 TraesCS1A01G059200 chr1B 84.511 368 24 16 2534 2885 60272560 60272910 2.150000e-87 333
14 TraesCS1A01G059200 chr1B 84.969 326 37 5 3404 3729 60193349 60193036 1.670000e-83 320
15 TraesCS1A01G059200 chr3D 82.602 661 93 17 1171 1830 605568923 605568284 7.000000e-157 564
16 TraesCS1A01G059200 chr3D 85.663 279 29 5 979 1249 605490959 605490684 2.200000e-72 283
17 TraesCS1A01G059200 chr3D 93.210 162 11 0 543 704 165471235 165471396 4.820000e-59 239
18 TraesCS1A01G059200 chr3D 85.646 209 18 4 1053 1249 605510719 605510511 3.780000e-50 209
19 TraesCS1A01G059200 chr3A 83.153 463 76 2 1285 1747 738726496 738726956 4.460000e-114 422
20 TraesCS1A01G059200 chr3A 80.000 275 25 15 984 1232 738726244 738726514 3.830000e-40 176
21 TraesCS1A01G059200 chr6B 93.210 162 11 0 543 704 211161640 211161479 4.820000e-59 239
22 TraesCS1A01G059200 chr2A 92.216 167 13 0 543 709 522841269 522841435 1.730000e-58 237
23 TraesCS1A01G059200 chr2D 91.228 171 15 0 543 713 426427962 426427792 2.240000e-57 233
24 TraesCS1A01G059200 chr2D 85.437 103 12 3 2934 3034 376821217 376821116 1.830000e-18 104
25 TraesCS1A01G059200 chr6A 90.805 174 15 1 536 708 153669707 153669880 8.070000e-57 231
26 TraesCS1A01G059200 chr5D 91.176 170 14 1 536 704 25039975 25040144 2.900000e-56 230
27 TraesCS1A01G059200 chr4A 91.566 166 14 0 543 708 732790029 732790194 2.900000e-56 230


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 TraesCS1A01G059200 chr1A 39892086 39895819 3733 True 6896.000000 6896 100.000000 1 3734 1 chr1A.!!$R1 3733
1 TraesCS1A01G059200 chr1D 40795243 40798969 3726 True 1543.666667 3969 87.297333 1 3734 3 chr1D.!!$R3 3733
2 TraesCS1A01G059200 chr1B 60252696 60257627 4931 False 1711.500000 2747 91.594000 1 2800 2 chr1B.!!$F1 2799
3 TraesCS1A01G059200 chr1B 60128606 60131202 2596 True 773.500000 948 86.957000 2846 3734 2 chr1B.!!$R2 888
4 TraesCS1A01G059200 chr1B 60165311 60165926 615 True 627.000000 627 85.150000 3101 3727 1 chr1B.!!$R1 626
5 TraesCS1A01G059200 chr1B 60272560 60273697 1137 False 538.000000 743 85.996000 2534 3730 2 chr1B.!!$F2 1196
6 TraesCS1A01G059200 chr1B 60193036 60194076 1040 True 399.500000 479 86.957000 2399 3729 2 chr1B.!!$R3 1330
7 TraesCS1A01G059200 chr3D 605568284 605568923 639 True 564.000000 564 82.602000 1171 1830 1 chr3D.!!$R3 659
8 TraesCS1A01G059200 chr3A 738726244 738726956 712 False 299.000000 422 81.576500 984 1747 2 chr3A.!!$F1 763

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
59 70 0.036732 TGAAGCAAGGTCCAGCGAAT 59.963 50.0 0.0 0.0 35.48 3.34 F
62 73 0.036732 AGCAAGGTCCAGCGAATGAA 59.963 50.0 0.0 0.0 35.48 2.57 F
899 3182 0.100682 CCCGTGTGGACTCATCTACG 59.899 60.0 0.0 0.0 39.13 3.51 F
2659 5136 0.674534 GGGAGCCGATACACCAGTAG 59.325 60.0 0.0 0.0 32.86 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 4314 0.829602 ATGATGAGGAGGCCGACGAT 60.830 55.000 0.0 0.0 0.0 3.73 R
1839 4316 1.006805 GATGATGAGGAGGCCGACG 60.007 63.158 0.0 0.0 0.0 5.12 R
2691 5168 0.037590 CGTCTTTCCCATGTTCCCCA 59.962 55.000 0.0 0.0 0.0 4.96 R
3619 7992 1.133598 CTCCGAGTGTACAATGCCGTA 59.866 52.381 0.0 0.0 0.0 4.02 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
30 31 4.699735 TGATGCAATACCACCTACAACAAG 59.300 41.667 0.00 0.00 0.00 3.16
59 70 0.036732 TGAAGCAAGGTCCAGCGAAT 59.963 50.000 0.00 0.00 35.48 3.34
62 73 0.036732 AGCAAGGTCCAGCGAATGAA 59.963 50.000 0.00 0.00 35.48 2.57
63 74 0.449388 GCAAGGTCCAGCGAATGAAG 59.551 55.000 0.00 0.00 0.00 3.02
64 75 1.945819 GCAAGGTCCAGCGAATGAAGA 60.946 52.381 0.00 0.00 0.00 2.87
65 76 2.426522 CAAGGTCCAGCGAATGAAGAA 58.573 47.619 0.00 0.00 0.00 2.52
66 77 2.393271 AGGTCCAGCGAATGAAGAAG 57.607 50.000 0.00 0.00 0.00 2.85
67 78 1.065854 AGGTCCAGCGAATGAAGAAGG 60.066 52.381 0.00 0.00 0.00 3.46
68 79 0.729690 GTCCAGCGAATGAAGAAGGC 59.270 55.000 0.00 0.00 0.00 4.35
69 80 0.324614 TCCAGCGAATGAAGAAGGCA 59.675 50.000 0.00 0.00 0.00 4.75
70 81 1.167851 CCAGCGAATGAAGAAGGCAA 58.832 50.000 0.00 0.00 0.00 4.52
90 101 4.864247 GCAAGGCCAACACACATTATAAAG 59.136 41.667 5.01 0.00 0.00 1.85
100 111 5.584649 ACACACATTATAAAGGTCATGGTCG 59.415 40.000 0.00 0.00 0.00 4.79
121 132 3.364366 CGTCATCTTCCAAAGCAACACTC 60.364 47.826 0.00 0.00 0.00 3.51
134 145 7.346695 CAAAGCAACACTCCAAAAACATATTG 58.653 34.615 0.00 0.00 0.00 1.90
173 187 6.096705 AGGAGATATCCACTCATCGATGAATC 59.903 42.308 27.09 23.30 36.18 2.52
174 188 5.970612 GAGATATCCACTCATCGATGAATCG 59.029 44.000 27.09 18.46 41.15 3.34
193 207 2.497675 TCGATACTTTGGCAGCTTCTCT 59.502 45.455 0.00 0.00 0.00 3.10
203 217 1.440708 CAGCTTCTCTGAGGCACTTG 58.559 55.000 4.59 0.00 45.72 3.16
245 259 4.390264 AGAGAAAGCAACCTTGTCCTAAC 58.610 43.478 0.00 0.00 0.00 2.34
247 261 3.138468 AGAAAGCAACCTTGTCCTAACCT 59.862 43.478 0.00 0.00 0.00 3.50
324 348 6.258160 CACGTTCCCAATTGAAGAATACATC 58.742 40.000 7.12 0.00 0.00 3.06
343 367 9.471702 AATACATCAAAGATGATTTGAAGGAGT 57.528 29.630 13.46 6.70 43.89 3.85
347 371 5.707298 TCAAAGATGATTTGAAGGAGTGTCC 59.293 40.000 0.73 0.00 35.69 4.02
348 372 7.748513 ATCAAAGATGATTTGAAGGAGTGTCCT 60.749 37.037 7.08 0.00 46.13 3.85
357 387 1.566211 AGGAGTGTCCTCATCCACTG 58.434 55.000 0.00 0.00 45.66 3.66
427 457 7.248743 ACTGCAAACAATACTTACCCTACTA 57.751 36.000 0.00 0.00 0.00 1.82
444 474 8.159229 ACCCTACTATAAACAACTCTCCATTT 57.841 34.615 0.00 0.00 0.00 2.32
445 475 9.275572 ACCCTACTATAAACAACTCTCCATTTA 57.724 33.333 0.00 0.00 0.00 1.40
480 510 9.541143 AAAAGGATTGTAAAAACTGTACCATTG 57.459 29.630 0.00 0.00 0.00 2.82
481 511 7.833285 AGGATTGTAAAAACTGTACCATTGT 57.167 32.000 0.00 0.00 0.00 2.71
482 512 7.657336 AGGATTGTAAAAACTGTACCATTGTG 58.343 34.615 0.00 0.00 0.00 3.33
483 513 7.286775 AGGATTGTAAAAACTGTACCATTGTGT 59.713 33.333 0.00 0.00 0.00 3.72
484 514 7.923878 GGATTGTAAAAACTGTACCATTGTGTT 59.076 33.333 0.00 0.00 0.00 3.32
485 515 8.865590 ATTGTAAAAACTGTACCATTGTGTTC 57.134 30.769 0.00 0.00 0.00 3.18
486 516 7.392494 TGTAAAAACTGTACCATTGTGTTCA 57.608 32.000 0.00 0.00 0.00 3.18
487 517 8.001881 TGTAAAAACTGTACCATTGTGTTCAT 57.998 30.769 0.00 0.00 0.00 2.57
488 518 8.132362 TGTAAAAACTGTACCATTGTGTTCATC 58.868 33.333 0.00 0.00 0.00 2.92
489 519 6.707440 AAAACTGTACCATTGTGTTCATCA 57.293 33.333 0.00 0.00 0.00 3.07
490 520 6.899393 AAACTGTACCATTGTGTTCATCAT 57.101 33.333 0.00 0.00 0.00 2.45
491 521 7.994425 AAACTGTACCATTGTGTTCATCATA 57.006 32.000 0.00 0.00 0.00 2.15
492 522 7.615582 AACTGTACCATTGTGTTCATCATAG 57.384 36.000 0.00 0.00 0.00 2.23
493 523 5.586243 ACTGTACCATTGTGTTCATCATAGC 59.414 40.000 0.00 0.00 0.00 2.97
494 524 5.744171 TGTACCATTGTGTTCATCATAGCT 58.256 37.500 0.00 0.00 0.00 3.32
495 525 5.817296 TGTACCATTGTGTTCATCATAGCTC 59.183 40.000 0.00 0.00 0.00 4.09
496 526 5.108187 ACCATTGTGTTCATCATAGCTCT 57.892 39.130 0.00 0.00 0.00 4.09
497 527 4.880120 ACCATTGTGTTCATCATAGCTCTG 59.120 41.667 0.00 0.00 0.00 3.35
498 528 5.121105 CCATTGTGTTCATCATAGCTCTGA 58.879 41.667 4.05 4.05 0.00 3.27
499 529 5.587443 CCATTGTGTTCATCATAGCTCTGAA 59.413 40.000 5.83 1.77 0.00 3.02
500 530 6.094464 CCATTGTGTTCATCATAGCTCTGAAA 59.906 38.462 5.83 0.00 31.21 2.69
501 531 6.732531 TTGTGTTCATCATAGCTCTGAAAG 57.267 37.500 5.83 2.61 31.21 2.62
502 532 6.041423 TGTGTTCATCATAGCTCTGAAAGA 57.959 37.500 5.83 4.90 43.69 2.52
503 533 6.647229 TGTGTTCATCATAGCTCTGAAAGAT 58.353 36.000 5.83 0.00 45.62 2.40
504 534 6.537660 TGTGTTCATCATAGCTCTGAAAGATG 59.462 38.462 5.83 0.00 45.62 2.90
505 535 6.018098 GTGTTCATCATAGCTCTGAAAGATGG 60.018 42.308 5.83 0.00 45.62 3.51
506 536 6.126968 TGTTCATCATAGCTCTGAAAGATGGA 60.127 38.462 5.83 0.00 45.62 3.41
507 537 6.490241 TCATCATAGCTCTGAAAGATGGAA 57.510 37.500 5.83 0.00 45.62 3.53
508 538 6.892485 TCATCATAGCTCTGAAAGATGGAAA 58.108 36.000 5.83 0.00 45.62 3.13
509 539 7.341030 TCATCATAGCTCTGAAAGATGGAAAA 58.659 34.615 5.83 0.00 45.62 2.29
510 540 6.992063 TCATAGCTCTGAAAGATGGAAAAC 57.008 37.500 0.00 0.00 45.62 2.43
511 541 6.715280 TCATAGCTCTGAAAGATGGAAAACT 58.285 36.000 0.00 0.00 45.62 2.66
512 542 7.170965 TCATAGCTCTGAAAGATGGAAAACTT 58.829 34.615 0.00 0.00 45.62 2.66
513 543 5.702349 AGCTCTGAAAGATGGAAAACTTG 57.298 39.130 0.00 0.00 45.62 3.16
514 544 4.022503 AGCTCTGAAAGATGGAAAACTTGC 60.023 41.667 0.00 0.00 45.62 4.01
515 545 4.261741 GCTCTGAAAGATGGAAAACTTGCA 60.262 41.667 0.00 0.00 45.62 4.08
516 546 5.566230 GCTCTGAAAGATGGAAAACTTGCAT 60.566 40.000 0.00 0.00 45.62 3.96
517 547 5.775686 TCTGAAAGATGGAAAACTTGCATG 58.224 37.500 0.00 0.00 42.07 4.06
518 548 5.302568 TCTGAAAGATGGAAAACTTGCATGT 59.697 36.000 0.00 0.00 42.07 3.21
519 549 6.489700 TCTGAAAGATGGAAAACTTGCATGTA 59.510 34.615 5.56 0.00 42.07 2.29
520 550 7.177216 TCTGAAAGATGGAAAACTTGCATGTAT 59.823 33.333 5.56 0.00 42.07 2.29
521 551 8.347004 TGAAAGATGGAAAACTTGCATGTATA 57.653 30.769 5.56 0.00 42.07 1.47
522 552 8.970020 TGAAAGATGGAAAACTTGCATGTATAT 58.030 29.630 5.56 0.00 42.07 0.86
523 553 9.455847 GAAAGATGGAAAACTTGCATGTATATC 57.544 33.333 5.56 5.00 42.07 1.63
524 554 8.523915 AAGATGGAAAACTTGCATGTATATCA 57.476 30.769 5.56 3.90 42.07 2.15
525 555 8.523915 AGATGGAAAACTTGCATGTATATCAA 57.476 30.769 5.56 0.00 42.07 2.57
526 556 9.139734 AGATGGAAAACTTGCATGTATATCAAT 57.860 29.630 5.56 4.20 42.07 2.57
527 557 9.188588 GATGGAAAACTTGCATGTATATCAATG 57.811 33.333 5.56 0.00 42.07 2.82
528 558 8.065473 TGGAAAACTTGCATGTATATCAATGT 57.935 30.769 5.56 0.00 0.00 2.71
529 559 9.183368 TGGAAAACTTGCATGTATATCAATGTA 57.817 29.630 5.56 0.00 0.00 2.29
546 576 7.819521 TCAATGTATAGATTCATGGATCCCT 57.180 36.000 10.58 0.00 0.00 4.20
547 577 7.855375 TCAATGTATAGATTCATGGATCCCTC 58.145 38.462 10.58 0.46 0.00 4.30
548 578 7.681598 TCAATGTATAGATTCATGGATCCCTCT 59.318 37.037 10.58 6.25 0.00 3.69
549 579 6.864151 TGTATAGATTCATGGATCCCTCTG 57.136 41.667 10.58 4.49 0.00 3.35
550 580 6.565036 TGTATAGATTCATGGATCCCTCTGA 58.435 40.000 10.58 6.97 0.00 3.27
551 581 7.194761 TGTATAGATTCATGGATCCCTCTGAT 58.805 38.462 10.58 0.00 36.01 2.90
587 617 9.787532 TTGTCTTTCTAGAAATTTCAACAAGTG 57.212 29.630 18.02 2.79 30.65 3.16
591 621 9.443283 CTTTCTAGAAATTTCAACAAGTGACTG 57.557 33.333 18.02 0.00 35.39 3.51
598 628 3.378911 TCAACAAGTGACTGCATACGA 57.621 42.857 0.00 0.00 0.00 3.43
603 633 2.455674 AGTGACTGCATACGAAGCAA 57.544 45.000 0.00 0.00 42.17 3.91
663 693 5.364778 CATCCGGATGTGGTAGTCAATTTA 58.635 41.667 32.39 0.00 34.23 1.40
699 729 6.301169 AGACAAATAGTTAGGAACAGAGGG 57.699 41.667 0.00 0.00 0.00 4.30
726 878 3.868757 TGTCAAGATAGACGGTCCTTG 57.131 47.619 15.31 15.31 41.41 3.61
727 879 2.094182 TGTCAAGATAGACGGTCCTTGC 60.094 50.000 16.17 12.90 41.41 4.01
728 880 2.166664 GTCAAGATAGACGGTCCTTGCT 59.833 50.000 16.17 3.56 36.77 3.91
729 881 2.166459 TCAAGATAGACGGTCCTTGCTG 59.834 50.000 16.17 5.99 36.77 4.41
730 882 2.145397 AGATAGACGGTCCTTGCTGA 57.855 50.000 4.14 0.00 0.00 4.26
732 884 2.025155 GATAGACGGTCCTTGCTGAGA 58.975 52.381 4.14 0.00 0.00 3.27
773 1046 7.831193 AGTCAACATAGAATTAGCAAATCTGGT 59.169 33.333 0.00 0.00 37.06 4.00
774 1047 8.125448 GTCAACATAGAATTAGCAAATCTGGTC 58.875 37.037 0.00 0.00 34.40 4.02
775 1048 7.283127 TCAACATAGAATTAGCAAATCTGGTCC 59.717 37.037 0.00 0.00 34.40 4.46
788 1062 9.528489 AGCAAATCTGGTCCTAGTAATTTAAAA 57.472 29.630 0.00 0.00 0.00 1.52
797 1071 7.416326 GGTCCTAGTAATTTAAAAGGCATGGTG 60.416 40.741 0.00 0.00 0.00 4.17
822 3096 4.431416 AGTTTACCACATCCTTCACACA 57.569 40.909 0.00 0.00 0.00 3.72
878 3161 1.771255 AGATTTGGAATCTCCTCCCCG 59.229 52.381 0.00 0.00 37.46 5.73
895 3178 2.125106 GCCCCGTGTGGACTCATC 60.125 66.667 0.00 0.00 37.49 2.92
896 3179 2.660064 GCCCCGTGTGGACTCATCT 61.660 63.158 0.00 0.00 37.49 2.90
899 3182 0.100682 CCCGTGTGGACTCATCTACG 59.899 60.000 0.00 0.00 39.13 3.51
901 3184 1.202154 CCGTGTGGACTCATCTACGTC 60.202 57.143 0.00 0.00 39.13 4.34
905 3188 3.440872 GTGTGGACTCATCTACGTCTCTT 59.559 47.826 0.00 0.00 39.13 2.85
906 3189 3.440522 TGTGGACTCATCTACGTCTCTTG 59.559 47.826 0.00 0.00 39.13 3.02
907 3190 3.017442 TGGACTCATCTACGTCTCTTGG 58.983 50.000 0.00 0.00 0.00 3.61
914 3197 2.005960 CTACGTCTCTTGGCCCCTCG 62.006 65.000 0.00 0.00 0.00 4.63
983 3303 1.737008 GCCAGACGAACGAACTCCC 60.737 63.158 0.14 0.00 0.00 4.30
1536 4013 3.200165 TCGTCTTCCTCCTCATCTCTGTA 59.800 47.826 0.00 0.00 0.00 2.74
1837 4314 4.116328 CGACCTTCTGGCTCGCGA 62.116 66.667 9.26 9.26 36.63 5.87
1839 4316 1.590259 GACCTTCTGGCTCGCGATC 60.590 63.158 10.36 4.94 36.63 3.69
2031 4508 2.436646 CACCGCATCCAGTCCACC 60.437 66.667 0.00 0.00 0.00 4.61
2433 4910 2.127869 GTGATGATGATGCGCGCG 60.128 61.111 28.44 28.44 0.00 6.86
2613 5090 1.568025 GTTTGGTTGTCGTCCTCGC 59.432 57.895 0.00 0.00 36.96 5.03
2631 5108 4.636435 CGGAAAGTGGGTGGCGGT 62.636 66.667 0.00 0.00 0.00 5.68
2659 5136 0.674534 GGGAGCCGATACACCAGTAG 59.325 60.000 0.00 0.00 32.86 2.57
2660 5137 1.400737 GGAGCCGATACACCAGTAGT 58.599 55.000 0.00 0.00 32.86 2.73
2661 5138 2.579873 GGAGCCGATACACCAGTAGTA 58.420 52.381 0.00 0.00 32.86 1.82
2662 5139 2.954318 GGAGCCGATACACCAGTAGTAA 59.046 50.000 0.00 0.00 32.86 2.24
2706 5183 1.274712 GCAATGGGGAACATGGGAAA 58.725 50.000 0.00 0.00 40.44 3.13
2736 5213 4.398358 TCTCACGTGGAATTGTCCTAGTAG 59.602 45.833 17.00 0.00 45.22 2.57
2739 5221 3.119101 ACGTGGAATTGTCCTAGTAGCAG 60.119 47.826 0.00 0.00 45.22 4.24
2759 5248 6.443876 GCAGTTTTCATTTTCTGCTTGTAG 57.556 37.500 8.46 0.00 46.35 2.74
2821 5316 6.154021 AGGACTAGACTCGGTGCTAAATTAAA 59.846 38.462 0.00 0.00 32.60 1.52
2822 5317 6.815142 GGACTAGACTCGGTGCTAAATTAAAA 59.185 38.462 0.00 0.00 0.00 1.52
2823 5318 7.332678 GGACTAGACTCGGTGCTAAATTAAAAA 59.667 37.037 0.00 0.00 0.00 1.94
2824 5319 8.788325 ACTAGACTCGGTGCTAAATTAAAAAT 57.212 30.769 0.00 0.00 0.00 1.82
2825 5320 9.880157 ACTAGACTCGGTGCTAAATTAAAAATA 57.120 29.630 0.00 0.00 0.00 1.40
2963 5487 5.080969 TGGTCCCTCGTATTAAGTTTCAG 57.919 43.478 0.00 0.00 0.00 3.02
3070 5715 8.670135 CAACCTATGTTAATGAACCGTCAAATA 58.330 33.333 0.00 0.00 33.06 1.40
3075 5720 6.904498 TGTTAATGAACCGTCAAATACCTTG 58.096 36.000 0.00 0.00 37.30 3.61
3113 5758 8.502738 ACTGGTAATATCTCATTGGGTATTTGT 58.497 33.333 0.00 0.00 0.00 2.83
3120 5767 7.738437 ATCTCATTGGGTATTTGTGGATTTT 57.262 32.000 0.00 0.00 0.00 1.82
3121 5768 7.552050 TCTCATTGGGTATTTGTGGATTTTT 57.448 32.000 0.00 0.00 0.00 1.94
3122 5769 7.610865 TCTCATTGGGTATTTGTGGATTTTTC 58.389 34.615 0.00 0.00 0.00 2.29
3135 5782 4.211164 GTGGATTTTTCTTTTTGCCCTTCG 59.789 41.667 0.00 0.00 0.00 3.79
3151 5799 5.184096 TGCCCTTCGCATTTGTCTATTTTTA 59.816 36.000 0.00 0.00 44.64 1.52
3165 5813 9.575868 TTGTCTATTTTTATACAAACACCCTCA 57.424 29.630 0.00 0.00 0.00 3.86
3286 7653 4.256920 GGCCATTACTCATCGAGCATAAT 58.743 43.478 0.00 0.00 32.04 1.28
3349 7716 2.892640 CGAACTGCCGAGATGGGA 59.107 61.111 0.00 0.00 38.63 4.37
3421 7789 4.499183 ACAAGCTATTGGAGAAGACTTCG 58.501 43.478 9.53 0.00 40.97 3.79
3451 7819 1.069765 CGTCACCACTGCTGGAAGT 59.930 57.895 0.00 0.00 40.55 3.01
3465 7833 1.014564 GGAAGTTCTGAAGCGACGGG 61.015 60.000 2.25 0.00 0.00 5.28
3523 7895 1.349688 ACCTACAACTTCATCCGGCAA 59.650 47.619 0.00 0.00 0.00 4.52
3540 7912 1.079127 AAATCAGTGTCTCCCGCCG 60.079 57.895 0.00 0.00 0.00 6.46
3614 7987 3.827898 CGACGGAGGAGAGGTGGC 61.828 72.222 0.00 0.00 0.00 5.01
3615 7988 3.827898 GACGGAGGAGAGGTGGCG 61.828 72.222 0.00 0.00 0.00 5.69
3618 7991 3.775654 GGAGGAGAGGTGGCGGTG 61.776 72.222 0.00 0.00 0.00 4.94
3619 7992 2.997897 GAGGAGAGGTGGCGGTGT 60.998 66.667 0.00 0.00 0.00 4.16
3683 8056 4.781934 AGAGGAACGATTATGGAAAAGGG 58.218 43.478 0.00 0.00 0.00 3.95
3688 8061 3.642141 ACGATTATGGAAAAGGGCCAAT 58.358 40.909 6.18 0.00 39.21 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.218417 TGGACCTTGCTTCATTTTTAGCTC 59.782 41.667 0.00 0.00 38.22 4.09
67 78 4.448537 TTATAATGTGTGTTGGCCTTGC 57.551 40.909 3.32 0.00 0.00 4.01
68 79 5.047377 ACCTTTATAATGTGTGTTGGCCTTG 60.047 40.000 3.32 0.00 0.00 3.61
69 80 5.083821 ACCTTTATAATGTGTGTTGGCCTT 58.916 37.500 3.32 0.00 0.00 4.35
70 81 4.672899 ACCTTTATAATGTGTGTTGGCCT 58.327 39.130 3.32 0.00 0.00 5.19
85 96 5.359194 AAGATGACGACCATGACCTTTAT 57.641 39.130 0.00 0.00 35.17 1.40
90 101 1.207089 TGGAAGATGACGACCATGACC 59.793 52.381 0.00 0.00 35.17 4.02
100 111 3.057946 GGAGTGTTGCTTTGGAAGATGAC 60.058 47.826 0.00 0.00 0.00 3.06
173 187 2.606725 CAGAGAAGCTGCCAAAGTATCG 59.393 50.000 0.00 0.00 37.90 2.92
174 188 3.866651 TCAGAGAAGCTGCCAAAGTATC 58.133 45.455 0.00 0.00 44.52 2.24
193 207 2.565391 TCCGTCTAATTCAAGTGCCTCA 59.435 45.455 0.00 0.00 0.00 3.86
203 217 9.751542 TTTCTCTCTCAATAATCCGTCTAATTC 57.248 33.333 0.00 0.00 0.00 2.17
245 259 5.712004 TGAACATGTGATTAATGTTGCAGG 58.288 37.500 0.00 0.00 45.81 4.85
247 261 8.302438 TGTAATGAACATGTGATTAATGTTGCA 58.698 29.630 0.00 5.54 45.81 4.08
324 348 5.709164 AGGACACTCCTTCAAATCATCTTTG 59.291 40.000 0.00 0.00 46.91 2.77
343 367 2.905736 TGATTCACAGTGGATGAGGACA 59.094 45.455 0.00 0.00 0.00 4.02
347 371 8.900781 AGAATTTATTGATTCACAGTGGATGAG 58.099 33.333 0.00 0.00 38.27 2.90
348 372 8.812513 AGAATTTATTGATTCACAGTGGATGA 57.187 30.769 0.00 0.00 38.27 2.92
350 374 8.812513 TGAGAATTTATTGATTCACAGTGGAT 57.187 30.769 0.00 0.00 38.27 3.41
357 387 8.937634 ATTTGGCTGAGAATTTATTGATTCAC 57.062 30.769 1.07 0.00 38.27 3.18
417 447 8.849543 ATGGAGAGTTGTTTATAGTAGGGTAA 57.150 34.615 0.00 0.00 0.00 2.85
477 507 7.108194 TCTTTCAGAGCTATGATGAACACAAT 58.892 34.615 12.63 0.00 32.91 2.71
479 509 6.041423 TCTTTCAGAGCTATGATGAACACA 57.959 37.500 12.63 0.00 32.91 3.72
480 510 6.018098 CCATCTTTCAGAGCTATGATGAACAC 60.018 42.308 12.63 0.00 34.86 3.32
481 511 6.053650 CCATCTTTCAGAGCTATGATGAACA 58.946 40.000 12.63 0.00 34.86 3.18
482 512 6.286758 TCCATCTTTCAGAGCTATGATGAAC 58.713 40.000 12.63 0.00 34.86 3.18
483 513 6.490241 TCCATCTTTCAGAGCTATGATGAA 57.510 37.500 12.63 3.53 34.86 2.57
484 514 6.490241 TTCCATCTTTCAGAGCTATGATGA 57.510 37.500 12.63 13.57 34.86 2.92
485 515 7.282675 AGTTTTCCATCTTTCAGAGCTATGATG 59.717 37.037 12.63 7.27 0.00 3.07
486 516 7.344913 AGTTTTCCATCTTTCAGAGCTATGAT 58.655 34.615 12.63 0.00 0.00 2.45
487 517 6.715280 AGTTTTCCATCTTTCAGAGCTATGA 58.285 36.000 7.02 7.02 0.00 2.15
488 518 6.998968 AGTTTTCCATCTTTCAGAGCTATG 57.001 37.500 0.69 0.69 0.00 2.23
489 519 6.127786 GCAAGTTTTCCATCTTTCAGAGCTAT 60.128 38.462 0.00 0.00 0.00 2.97
490 520 5.182001 GCAAGTTTTCCATCTTTCAGAGCTA 59.818 40.000 0.00 0.00 0.00 3.32
491 521 4.022503 GCAAGTTTTCCATCTTTCAGAGCT 60.023 41.667 0.00 0.00 0.00 4.09
492 522 4.233005 GCAAGTTTTCCATCTTTCAGAGC 58.767 43.478 0.00 0.00 0.00 4.09
493 523 5.443185 TGCAAGTTTTCCATCTTTCAGAG 57.557 39.130 0.00 0.00 0.00 3.35
494 524 5.302568 ACATGCAAGTTTTCCATCTTTCAGA 59.697 36.000 0.00 0.00 0.00 3.27
495 525 5.535333 ACATGCAAGTTTTCCATCTTTCAG 58.465 37.500 0.00 0.00 0.00 3.02
496 526 5.534207 ACATGCAAGTTTTCCATCTTTCA 57.466 34.783 0.00 0.00 0.00 2.69
497 527 9.455847 GATATACATGCAAGTTTTCCATCTTTC 57.544 33.333 0.00 0.00 0.00 2.62
498 528 8.970020 TGATATACATGCAAGTTTTCCATCTTT 58.030 29.630 0.00 0.00 0.00 2.52
499 529 8.523915 TGATATACATGCAAGTTTTCCATCTT 57.476 30.769 0.00 0.00 0.00 2.40
500 530 8.523915 TTGATATACATGCAAGTTTTCCATCT 57.476 30.769 0.00 0.00 0.00 2.90
501 531 9.188588 CATTGATATACATGCAAGTTTTCCATC 57.811 33.333 0.00 0.00 0.00 3.51
502 532 8.698210 ACATTGATATACATGCAAGTTTTCCAT 58.302 29.630 0.00 0.00 0.00 3.41
503 533 8.065473 ACATTGATATACATGCAAGTTTTCCA 57.935 30.769 0.00 0.00 0.00 3.53
520 550 9.511404 AGGGATCCATGAATCTATACATTGATA 57.489 33.333 15.23 0.00 31.96 2.15
521 551 8.403292 AGGGATCCATGAATCTATACATTGAT 57.597 34.615 15.23 0.00 33.61 2.57
522 552 7.681598 AGAGGGATCCATGAATCTATACATTGA 59.318 37.037 15.23 0.00 0.00 2.57
523 553 7.769507 CAGAGGGATCCATGAATCTATACATTG 59.230 40.741 15.23 0.00 0.00 2.82
524 554 7.681598 TCAGAGGGATCCATGAATCTATACATT 59.318 37.037 15.23 0.00 0.00 2.71
525 555 7.194761 TCAGAGGGATCCATGAATCTATACAT 58.805 38.462 15.23 0.00 0.00 2.29
526 556 6.565036 TCAGAGGGATCCATGAATCTATACA 58.435 40.000 15.23 0.00 0.00 2.29
527 557 7.673641 ATCAGAGGGATCCATGAATCTATAC 57.326 40.000 15.23 0.00 0.00 1.47
528 558 7.911130 GATCAGAGGGATCCATGAATCTATA 57.089 40.000 15.23 1.44 45.58 1.31
529 559 6.811634 GATCAGAGGGATCCATGAATCTAT 57.188 41.667 15.23 0.00 45.58 1.98
541 571 7.589993 AGACAAATAATTTGGATCAGAGGGAT 58.410 34.615 0.00 0.00 44.81 3.85
542 572 6.973642 AGACAAATAATTTGGATCAGAGGGA 58.026 36.000 0.00 0.00 44.81 4.20
543 573 7.651027 AAGACAAATAATTTGGATCAGAGGG 57.349 36.000 0.00 0.00 44.81 4.30
544 574 8.964772 AGAAAGACAAATAATTTGGATCAGAGG 58.035 33.333 0.00 0.00 44.81 3.69
574 604 5.238432 TCGTATGCAGTCACTTGTTGAAATT 59.762 36.000 0.00 0.00 35.39 1.82
587 617 4.142816 ACTCATTTTGCTTCGTATGCAGTC 60.143 41.667 0.00 0.00 41.71 3.51
591 621 4.340894 TCACTCATTTTGCTTCGTATGC 57.659 40.909 0.00 0.00 0.00 3.14
644 674 7.985476 AGATTTTAAATTGACTACCACATCCG 58.015 34.615 0.00 0.00 0.00 4.18
674 704 7.017254 TCCCTCTGTTCCTAACTATTTGTCTTT 59.983 37.037 0.00 0.00 0.00 2.52
685 715 6.051179 ACATTTACTCCCTCTGTTCCTAAC 57.949 41.667 0.00 0.00 0.00 2.34
694 724 6.039941 CGTCTATCTTGACATTTACTCCCTCT 59.960 42.308 0.00 0.00 36.82 3.69
695 725 6.210078 CGTCTATCTTGACATTTACTCCCTC 58.790 44.000 0.00 0.00 36.82 4.30
696 726 5.069251 CCGTCTATCTTGACATTTACTCCCT 59.931 44.000 0.00 0.00 36.82 4.20
699 729 5.978322 GGACCGTCTATCTTGACATTTACTC 59.022 44.000 0.00 0.00 36.82 2.59
726 878 9.973450 TTGACTGAGTATTAGATAAATCTCAGC 57.027 33.333 22.66 18.50 43.99 4.26
754 1027 8.268878 ACTAGGACCAGATTTGCTAATTCTAT 57.731 34.615 0.00 0.00 0.00 1.98
773 1046 7.338449 GTCACCATGCCTTTTAAATTACTAGGA 59.662 37.037 7.01 0.00 0.00 2.94
774 1047 7.339466 AGTCACCATGCCTTTTAAATTACTAGG 59.661 37.037 0.00 0.00 0.00 3.02
775 1048 8.281212 AGTCACCATGCCTTTTAAATTACTAG 57.719 34.615 0.00 0.00 0.00 2.57
788 1062 2.910319 TGGTAAACTAGTCACCATGCCT 59.090 45.455 20.19 0.00 37.42 4.75
797 1071 5.638234 GTGTGAAGGATGTGGTAAACTAGTC 59.362 44.000 0.00 0.00 0.00 2.59
878 3161 1.327690 TAGATGAGTCCACACGGGGC 61.328 60.000 0.00 0.00 43.70 5.80
889 3172 1.751924 GGCCAAGAGACGTAGATGAGT 59.248 52.381 0.00 0.00 0.00 3.41
891 3174 1.112113 GGGCCAAGAGACGTAGATGA 58.888 55.000 4.39 0.00 0.00 2.92
892 3175 0.105039 GGGGCCAAGAGACGTAGATG 59.895 60.000 4.39 0.00 0.00 2.90
893 3176 0.032017 AGGGGCCAAGAGACGTAGAT 60.032 55.000 4.39 0.00 0.00 1.98
895 3178 1.817209 GAGGGGCCAAGAGACGTAG 59.183 63.158 4.39 0.00 0.00 3.51
896 3179 2.050350 CGAGGGGCCAAGAGACGTA 61.050 63.158 4.39 0.00 0.00 3.57
899 3182 3.706373 TGCGAGGGGCCAAGAGAC 61.706 66.667 4.39 0.00 42.61 3.36
901 3184 4.785453 GGTGCGAGGGGCCAAGAG 62.785 72.222 4.39 0.00 42.61 2.85
914 3197 2.617274 GGGTCAAACGCTGAGGTGC 61.617 63.158 0.00 0.00 33.60 5.01
964 3254 2.087009 GGAGTTCGTTCGTCTGGCG 61.087 63.158 0.00 0.00 43.01 5.69
977 3297 4.988598 CGTGTGGCTGCGGGAGTT 62.989 66.667 0.00 0.00 0.00 3.01
1125 3589 2.434774 GTGGTGAAGGTGGTCCCC 59.565 66.667 0.00 0.00 0.00 4.81
1564 4041 2.124570 CACGGGCTTGGGGATGAG 60.125 66.667 0.00 0.00 0.00 2.90
1629 4106 2.360852 CCCTGGTTGCTCTGCAGG 60.361 66.667 15.13 5.82 40.61 4.85
1837 4314 0.829602 ATGATGAGGAGGCCGACGAT 60.830 55.000 0.00 0.00 0.00 3.73
1839 4316 1.006805 GATGATGAGGAGGCCGACG 60.007 63.158 0.00 0.00 0.00 5.12
2169 4646 3.459063 CCCTCGAACTCCCCCGTC 61.459 72.222 0.00 0.00 0.00 4.79
2253 4730 0.168348 ACTCGATGAAGACCGTGACG 59.832 55.000 0.00 0.00 0.00 4.35
2256 4733 0.168348 ACGACTCGATGAAGACCGTG 59.832 55.000 5.20 0.00 31.73 4.94
2433 4910 4.394712 CAGTCCACCTCCGCCACC 62.395 72.222 0.00 0.00 0.00 4.61
2596 5073 4.036977 GCGAGGACGACAACCAAA 57.963 55.556 0.00 0.00 42.66 3.28
2641 5118 1.400737 ACTACTGGTGTATCGGCTCC 58.599 55.000 0.00 0.00 0.00 4.70
2659 5136 2.480419 CACTGCCACTGTTGCTACTTAC 59.520 50.000 5.42 0.00 0.00 2.34
2660 5137 2.766313 CACTGCCACTGTTGCTACTTA 58.234 47.619 5.42 0.00 0.00 2.24
2661 5138 1.597742 CACTGCCACTGTTGCTACTT 58.402 50.000 5.42 0.00 0.00 2.24
2662 5139 0.886490 GCACTGCCACTGTTGCTACT 60.886 55.000 5.42 0.00 0.00 2.57
2691 5168 0.037590 CGTCTTTCCCATGTTCCCCA 59.962 55.000 0.00 0.00 0.00 4.96
2821 5316 5.010617 AGTTTCAGGTTTGGCGTCATTATTT 59.989 36.000 0.00 0.00 0.00 1.40
2822 5317 4.522789 AGTTTCAGGTTTGGCGTCATTATT 59.477 37.500 0.00 0.00 0.00 1.40
2823 5318 4.079253 AGTTTCAGGTTTGGCGTCATTAT 58.921 39.130 0.00 0.00 0.00 1.28
2824 5319 3.252215 CAGTTTCAGGTTTGGCGTCATTA 59.748 43.478 0.00 0.00 0.00 1.90
2825 5320 2.034558 CAGTTTCAGGTTTGGCGTCATT 59.965 45.455 0.00 0.00 0.00 2.57
2826 5321 1.608590 CAGTTTCAGGTTTGGCGTCAT 59.391 47.619 0.00 0.00 0.00 3.06
2941 5465 4.773674 TCTGAAACTTAATACGAGGGACCA 59.226 41.667 0.00 0.00 0.00 4.02
2994 5639 3.489047 ACATTTTGAATGCGTTTTGACGG 59.511 39.130 0.00 0.00 0.00 4.79
2996 5641 5.888412 AGACATTTTGAATGCGTTTTGAC 57.112 34.783 0.00 0.00 0.00 3.18
3070 5715 1.971357 CAGTAGGACACAGGTCAAGGT 59.029 52.381 0.00 0.00 46.17 3.50
3075 5720 5.834204 AGATATTACCAGTAGGACACAGGTC 59.166 44.000 0.00 0.00 43.15 3.85
3113 5758 4.376146 CGAAGGGCAAAAAGAAAAATCCA 58.624 39.130 0.00 0.00 0.00 3.41
3151 5799 4.675063 ATTTCCCTGAGGGTGTTTGTAT 57.325 40.909 18.83 0.00 44.74 2.29
3183 5833 2.019984 GACTCCCATGGACTTCAATGC 58.980 52.381 15.22 0.00 0.00 3.56
3195 5845 1.866015 TGAAGATGGTCGACTCCCAT 58.134 50.000 16.46 10.77 45.37 4.00
3253 7620 0.534873 GTAATGGCCCGCATGGTTTT 59.465 50.000 0.00 0.00 36.04 2.43
3263 7630 0.106708 TGCTCGATGAGTAATGGCCC 59.893 55.000 0.00 0.00 31.39 5.80
3286 7653 4.019681 AGGGTGTATTTTTCTGGTCGATCA 60.020 41.667 0.00 0.00 0.00 2.92
3294 7661 3.826157 TGGCTCAAGGGTGTATTTTTCTG 59.174 43.478 0.00 0.00 0.00 3.02
3295 7662 4.112634 TGGCTCAAGGGTGTATTTTTCT 57.887 40.909 0.00 0.00 0.00 2.52
3339 7706 0.033228 GCAGAGTCATCCCATCTCGG 59.967 60.000 0.00 0.00 33.96 4.63
3349 7716 3.865745 CGAATAAGGTTTCGCAGAGTCAT 59.134 43.478 0.00 0.00 41.61 3.06
3421 7789 2.251642 GGTGACGGTGGCACTCAAC 61.252 63.158 18.45 13.21 36.53 3.18
3451 7819 1.959226 GTTGCCCGTCGCTTCAGAA 60.959 57.895 0.00 0.00 38.78 3.02
3465 7833 3.124806 GCTCTTAGGTAGGTTTTCGTTGC 59.875 47.826 0.00 0.00 0.00 4.17
3523 7895 2.579201 CGGCGGGAGACACTGATT 59.421 61.111 0.00 0.00 38.29 2.57
3540 7912 3.982241 GCTTGCTGGTGTGGGTGC 61.982 66.667 0.00 0.00 0.00 5.01
3601 7974 3.775654 CACCGCCACCTCTCCTCC 61.776 72.222 0.00 0.00 0.00 4.30
3614 7987 3.125200 TGTACAATGCCGTACACCG 57.875 52.632 0.00 0.00 45.18 4.94
3618 7991 1.135315 TCCGAGTGTACAATGCCGTAC 60.135 52.381 0.00 0.00 41.78 3.67
3619 7992 1.133598 CTCCGAGTGTACAATGCCGTA 59.866 52.381 0.00 0.00 0.00 4.02
3683 8056 4.248691 ACAGAAAGCAGAAAGAATTGGC 57.751 40.909 0.00 0.00 0.00 4.52
3688 8061 5.123186 TCGTTCAAACAGAAAGCAGAAAGAA 59.877 36.000 0.00 0.00 38.13 2.52


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

AutoCloner maintained by Alex Coulton.