Multiple sequence alignment - TraesCS5D01G277200

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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 TraesCS5D01G277200 chr5D 100.000 3986 0 0 1 3986 379345127 379341142 0.000000e+00 7361.0
1 TraesCS5D01G277200 chr5D 89.552 134 11 3 997 1130 379257439 379257309 2.460000e-37 167.0
2 TraesCS5D01G277200 chr5D 75.477 367 72 15 1011 1371 379229736 379229382 3.190000e-36 163.0
3 TraesCS5D01G277200 chr5D 91.071 112 10 0 1019 1130 379387305 379387194 6.900000e-33 152.0
4 TraesCS5D01G277200 chr5D 90.351 114 11 0 1019 1132 379133828 379133715 2.480000e-32 150.0
5 TraesCS5D01G277200 chr5D 91.262 103 9 0 1028 1130 379220075 379219973 1.490000e-29 141.0
6 TraesCS5D01G277200 chr5A 93.585 1403 73 10 2015 3417 480041675 480040290 0.000000e+00 2076.0
7 TraesCS5D01G277200 chr5A 91.301 1345 62 27 696 2011 480043044 480041726 0.000000e+00 1784.0
8 TraesCS5D01G277200 chr5A 91.622 561 38 8 3433 3986 439396380 439395822 0.000000e+00 767.0
9 TraesCS5D01G277200 chr5A 91.250 560 39 9 3433 3985 439427905 439427349 0.000000e+00 754.0
10 TraesCS5D01G277200 chr5A 90.391 281 22 3 1 281 439828705 439828430 8.140000e-97 364.0
11 TraesCS5D01G277200 chr5A 75.588 340 65 16 1028 1358 479397629 479397299 6.900000e-33 152.0
12 TraesCS5D01G277200 chr5A 88.136 118 14 0 1017 1134 479408740 479408623 1.490000e-29 141.0
13 TraesCS5D01G277200 chr5B 93.573 1198 69 7 2016 3210 455272674 455271482 0.000000e+00 1779.0
14 TraesCS5D01G277200 chr5B 93.761 1138 63 6 2076 3210 455269774 455268642 0.000000e+00 1701.0
15 TraesCS5D01G277200 chr5B 93.497 1138 66 6 2076 3210 455271194 455270062 0.000000e+00 1685.0
16 TraesCS5D01G277200 chr5B 85.810 1487 115 44 549 1961 455274214 455272750 0.000000e+00 1489.0
17 TraesCS5D01G277200 chr5B 92.999 957 59 7 2257 3210 455267628 455266677 0.000000e+00 1389.0
18 TraesCS5D01G277200 chr5B 96.296 189 7 0 2076 2264 455268354 455268166 1.080000e-80 311.0
19 TraesCS5D01G277200 chr5B 79.808 416 58 18 997 1401 455166772 455166372 3.030000e-71 279.0
20 TraesCS5D01G277200 chr5B 89.423 208 16 4 3206 3413 455258511 455258310 1.420000e-64 257.0
21 TraesCS5D01G277200 chr5B 74.696 411 88 12 2506 2913 75033600 75033997 6.850000e-38 169.0
22 TraesCS5D01G277200 chr5B 90.179 112 11 0 1019 1130 455294741 455294630 3.210000e-31 147.0
23 TraesCS5D01G277200 chr7D 95.745 517 17 4 1 515 630515996 630516509 0.000000e+00 828.0
24 TraesCS5D01G277200 chr7D 90.227 573 38 6 3432 3986 161536504 161535932 0.000000e+00 732.0
25 TraesCS5D01G277200 chr7D 97.297 37 1 0 554 590 60434528 60434492 3.330000e-06 63.9
26 TraesCS5D01G277200 chr7B 95.728 515 19 2 3 516 743492202 743492714 0.000000e+00 826.0
27 TraesCS5D01G277200 chr7B 95.122 41 2 0 483 523 735927720 735927760 9.250000e-07 65.8
28 TraesCS5D01G277200 chr7B 94.595 37 0 2 486 520 675006984 675006948 5.560000e-04 56.5
29 TraesCS5D01G277200 chr6D 93.642 519 16 6 1 515 44818113 44818618 0.000000e+00 760.0
30 TraesCS5D01G277200 chr6D 88.693 283 23 6 1 279 431171031 431171308 1.770000e-88 337.0
31 TraesCS5D01G277200 chr6D 92.683 41 3 0 554 594 387047237 387047197 4.300000e-05 60.2
32 TraesCS5D01G277200 chr6D 92.683 41 3 0 554 594 452542126 452542086 4.300000e-05 60.2
33 TraesCS5D01G277200 chr6A 93.064 519 17 7 1 515 514044065 514043562 0.000000e+00 741.0
34 TraesCS5D01G277200 chr6A 89.753 566 44 10 3433 3986 30652518 30651955 0.000000e+00 712.0
35 TraesCS5D01G277200 chr6A 92.683 41 3 0 554 594 502244328 502244288 4.300000e-05 60.2
36 TraesCS5D01G277200 chr2A 90.459 566 38 12 3434 3986 699518693 699519255 0.000000e+00 732.0
37 TraesCS5D01G277200 chr2A 90.335 538 40 8 3456 3986 155776882 155776350 0.000000e+00 695.0
38 TraesCS5D01G277200 chr2A 95.789 95 4 0 425 519 763912738 763912644 1.920000e-33 154.0
39 TraesCS5D01G277200 chr3B 90.681 558 39 8 3433 3986 436837474 436836926 0.000000e+00 730.0
40 TraesCS5D01G277200 chr3B 97.059 34 1 0 483 516 706496016 706496049 1.550000e-04 58.4
41 TraesCS5D01G277200 chr6B 90.340 559 42 9 3433 3986 28739491 28738940 0.000000e+00 723.0
42 TraesCS5D01G277200 chr6B 89.964 558 42 9 3433 3986 90976478 90977025 0.000000e+00 708.0
43 TraesCS5D01G277200 chr6B 95.455 66 3 0 625 690 207926442 207926377 5.450000e-19 106.0
44 TraesCS5D01G277200 chr1D 91.459 281 19 3 1 281 453087613 453087888 8.080000e-102 381.0
45 TraesCS5D01G277200 chr1D 90.580 276 22 2 6 281 25460601 25460872 2.930000e-96 363.0
46 TraesCS5D01G277200 chr1A 78.360 573 110 14 2505 3073 586722718 586722156 3.790000e-95 359.0
47 TraesCS5D01G277200 chr1A 92.308 104 8 0 1031 1134 586720495 586720392 8.920000e-32 148.0
48 TraesCS5D01G277200 chr1A 87.356 87 10 1 1008 1093 586725862 586725776 9.120000e-17 99.0
49 TraesCS5D01G277200 chr4D 89.324 281 25 2 1 281 23954506 23954231 8.200000e-92 348.0
50 TraesCS5D01G277200 chr4D 93.939 66 4 0 625 690 108628597 108628662 2.530000e-17 100.0
51 TraesCS5D01G277200 chr4D 92.424 66 5 0 625 690 280179786 280179721 1.180000e-15 95.3
52 TraesCS5D01G277200 chr4D 92.683 41 3 0 554 594 65935224 65935184 4.300000e-05 60.2
53 TraesCS5D01G277200 chr4D 97.143 35 1 0 560 594 302003473 302003439 4.300000e-05 60.2
54 TraesCS5D01G277200 chr2B 96.970 66 2 0 625 690 51645246 51645311 1.170000e-20 111.0
55 TraesCS5D01G277200 chr4B 92.424 66 5 0 625 690 411629654 411629589 1.180000e-15 95.3
56 TraesCS5D01G277200 chr7A 93.220 59 4 0 630 688 360082290 360082232 1.970000e-13 87.9
57 TraesCS5D01G277200 chr7A 92.683 41 3 0 554 594 532704960 532705000 4.300000e-05 60.2
58 TraesCS5D01G277200 chr3A 93.220 59 4 0 630 688 750523967 750523909 1.970000e-13 87.9
59 TraesCS5D01G277200 chr3A 87.302 63 8 0 625 687 23210121 23210183 5.530000e-09 73.1
60 TraesCS5D01G277200 chr3A 91.111 45 4 0 553 597 59816590 59816546 1.200000e-05 62.1
61 TraesCS5D01G277200 chr1B 91.803 61 5 0 626 686 269316713 269316653 7.100000e-13 86.1
62 TraesCS5D01G277200 chr4A 92.857 42 3 0 553 594 529631062 529631103 1.200000e-05 62.1


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 TraesCS5D01G277200 chr5D 379341142 379345127 3985 True 7361.000000 7361 100.000 1 3986 1 chr5D.!!$R5 3985
1 TraesCS5D01G277200 chr5A 480040290 480043044 2754 True 1930.000000 2076 92.443 696 3417 2 chr5A.!!$R6 2721
2 TraesCS5D01G277200 chr5A 439395822 439396380 558 True 767.000000 767 91.622 3433 3986 1 chr5A.!!$R1 553
3 TraesCS5D01G277200 chr5A 439427349 439427905 556 True 754.000000 754 91.250 3433 3985 1 chr5A.!!$R2 552
4 TraesCS5D01G277200 chr5B 455266677 455274214 7537 True 1392.333333 1779 92.656 549 3210 6 chr5B.!!$R4 2661
5 TraesCS5D01G277200 chr7D 630515996 630516509 513 False 828.000000 828 95.745 1 515 1 chr7D.!!$F1 514
6 TraesCS5D01G277200 chr7D 161535932 161536504 572 True 732.000000 732 90.227 3432 3986 1 chr7D.!!$R2 554
7 TraesCS5D01G277200 chr7B 743492202 743492714 512 False 826.000000 826 95.728 3 516 1 chr7B.!!$F2 513
8 TraesCS5D01G277200 chr6D 44818113 44818618 505 False 760.000000 760 93.642 1 515 1 chr6D.!!$F1 514
9 TraesCS5D01G277200 chr6A 514043562 514044065 503 True 741.000000 741 93.064 1 515 1 chr6A.!!$R3 514
10 TraesCS5D01G277200 chr6A 30651955 30652518 563 True 712.000000 712 89.753 3433 3986 1 chr6A.!!$R1 553
11 TraesCS5D01G277200 chr2A 699518693 699519255 562 False 732.000000 732 90.459 3434 3986 1 chr2A.!!$F1 552
12 TraesCS5D01G277200 chr2A 155776350 155776882 532 True 695.000000 695 90.335 3456 3986 1 chr2A.!!$R1 530
13 TraesCS5D01G277200 chr3B 436836926 436837474 548 True 730.000000 730 90.681 3433 3986 1 chr3B.!!$R1 553
14 TraesCS5D01G277200 chr6B 28738940 28739491 551 True 723.000000 723 90.340 3433 3986 1 chr6B.!!$R1 553
15 TraesCS5D01G277200 chr6B 90976478 90977025 547 False 708.000000 708 89.964 3433 3986 1 chr6B.!!$F1 553
16 TraesCS5D01G277200 chr1A 586720392 586725862 5470 True 202.000000 359 86.008 1008 3073 3 chr1A.!!$R1 2065

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
517 524 0.249363 GCACGGGCTAAGCTAGTACC 60.249 60.0 0.00 0.0 36.96 3.34 F
1208 1281 0.031585 TAATCTTCCGGGTCGATGCG 59.968 55.0 0.00 0.0 0.00 4.73 F
2605 7405 0.106469 TTGTACAACAAGGCAGGGCA 60.106 50.0 3.59 0.0 32.34 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2151 4069 1.094785 GTATTGACCGCCACATGCTT 58.905 50.0 0.0 0.0 38.05 3.91 R
2813 7622 0.599204 TTCCGAAGTGACTCCAACGC 60.599 55.0 0.0 0.0 0.00 4.84 R
3698 11376 0.380378 AGATGAGCGAGCGAGAAGAC 59.620 55.0 0.0 0.0 0.00 3.01 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
159 165 9.232473 ACATTATCTCGATGTATAGCTGAAGTA 57.768 33.333 0.00 0.00 36.04 2.24
211 217 3.772932 AGGTTCATGCACATTATTTGCG 58.227 40.909 0.00 0.00 43.34 4.85
389 396 5.523916 GGTCGCAATGTGTATTTCTCTATGT 59.476 40.000 0.00 0.00 0.00 2.29
398 405 7.556844 TGTGTATTTCTCTATGTCTCTTTCCC 58.443 38.462 0.00 0.00 0.00 3.97
516 523 0.594284 CGCACGGGCTAAGCTAGTAC 60.594 60.000 8.62 0.00 38.10 2.73
517 524 0.249363 GCACGGGCTAAGCTAGTACC 60.249 60.000 0.00 0.00 36.96 3.34
518 525 1.108776 CACGGGCTAAGCTAGTACCA 58.891 55.000 0.00 0.00 0.00 3.25
519 526 1.687123 CACGGGCTAAGCTAGTACCAT 59.313 52.381 0.00 0.00 0.00 3.55
520 527 1.962100 ACGGGCTAAGCTAGTACCATC 59.038 52.381 0.00 0.00 0.00 3.51
521 528 2.240279 CGGGCTAAGCTAGTACCATCT 58.760 52.381 0.00 0.00 0.00 2.90
522 529 3.181436 ACGGGCTAAGCTAGTACCATCTA 60.181 47.826 0.00 0.00 0.00 1.98
523 530 3.440872 CGGGCTAAGCTAGTACCATCTAG 59.559 52.174 0.00 0.00 40.01 2.43
530 537 3.290308 CTAGTACCATCTAGCCAAGCG 57.710 52.381 0.00 0.00 32.42 4.68
531 538 1.486211 AGTACCATCTAGCCAAGCGT 58.514 50.000 0.00 0.00 0.00 5.07
532 539 2.662866 AGTACCATCTAGCCAAGCGTA 58.337 47.619 0.00 0.00 0.00 4.42
533 540 3.028850 AGTACCATCTAGCCAAGCGTAA 58.971 45.455 0.00 0.00 0.00 3.18
534 541 2.604046 ACCATCTAGCCAAGCGTAAG 57.396 50.000 0.00 0.00 43.44 2.34
535 542 1.831736 ACCATCTAGCCAAGCGTAAGT 59.168 47.619 0.00 0.00 41.68 2.24
536 543 2.236395 ACCATCTAGCCAAGCGTAAGTT 59.764 45.455 0.00 0.00 41.68 2.66
537 544 3.270877 CCATCTAGCCAAGCGTAAGTTT 58.729 45.455 0.00 0.00 43.49 2.66
538 545 3.309954 CCATCTAGCCAAGCGTAAGTTTC 59.690 47.826 0.00 0.00 39.40 2.78
539 546 3.955650 TCTAGCCAAGCGTAAGTTTCT 57.044 42.857 0.00 0.00 39.40 2.52
540 547 3.585862 TCTAGCCAAGCGTAAGTTTCTG 58.414 45.455 0.00 0.00 39.40 3.02
541 548 2.543777 AGCCAAGCGTAAGTTTCTGA 57.456 45.000 0.00 0.00 39.40 3.27
542 549 2.143925 AGCCAAGCGTAAGTTTCTGAC 58.856 47.619 0.00 0.00 39.40 3.51
543 550 1.871039 GCCAAGCGTAAGTTTCTGACA 59.129 47.619 0.00 0.00 39.40 3.58
544 551 2.289547 GCCAAGCGTAAGTTTCTGACAA 59.710 45.455 0.00 0.00 39.40 3.18
545 552 3.242936 GCCAAGCGTAAGTTTCTGACAAA 60.243 43.478 0.00 0.00 39.40 2.83
546 553 4.556699 GCCAAGCGTAAGTTTCTGACAAAT 60.557 41.667 0.00 0.00 39.40 2.32
547 554 4.911610 CCAAGCGTAAGTTTCTGACAAATG 59.088 41.667 0.00 0.00 39.40 2.32
552 559 5.334879 GCGTAAGTTTCTGACAAATGATGGT 60.335 40.000 0.00 0.00 41.68 3.55
556 563 5.874093 AGTTTCTGACAAATGATGGTCTCT 58.126 37.500 0.00 0.00 35.11 3.10
557 564 5.704515 AGTTTCTGACAAATGATGGTCTCTG 59.295 40.000 0.00 0.00 35.11 3.35
561 568 5.424573 TCTGACAAATGATGGTCTCTGATCT 59.575 40.000 0.00 0.00 35.11 2.75
583 590 5.975344 TCTATATTAGTTGTCGCTCAAACGG 59.025 40.000 0.00 0.00 37.81 4.44
590 597 3.786516 TGTCGCTCAAACGGATGTATA 57.213 42.857 0.00 0.00 0.00 1.47
594 601 5.009310 TGTCGCTCAAACGGATGTATATAGT 59.991 40.000 0.00 0.00 0.00 2.12
596 603 7.094506 TGTCGCTCAAACGGATGTATATAGTAT 60.095 37.037 0.00 0.00 0.00 2.12
597 604 8.393366 GTCGCTCAAACGGATGTATATAGTATA 58.607 37.037 0.00 0.00 0.00 1.47
607 614 9.383462 CGGATGTATATAGTATATCGCTCAAAC 57.617 37.037 5.92 0.00 0.00 2.93
609 616 9.383462 GATGTATATAGTATATCGCTCAAACGG 57.617 37.037 5.92 0.00 0.00 4.44
619 626 4.224715 TCGCTCAAACGGATGTATCTAG 57.775 45.455 0.00 0.00 0.00 2.43
620 627 2.726760 CGCTCAAACGGATGTATCTAGC 59.273 50.000 0.00 0.00 0.00 3.42
647 654 4.611782 CGCTAAAACGGATGTATCTAGACG 59.388 45.833 0.00 0.00 0.00 4.18
651 658 7.806960 GCTAAAACGGATGTATCTAGACGTATT 59.193 37.037 0.00 0.00 33.85 1.89
654 661 7.507733 AACGGATGTATCTAGACGTATTTCT 57.492 36.000 0.00 0.00 33.85 2.52
658 665 6.583050 GGATGTATCTAGACGTATTTCTGTGC 59.417 42.308 0.00 0.00 0.00 4.57
669 676 6.448006 ACGTATTTCTGTGCTAGATACATCC 58.552 40.000 0.00 0.00 34.80 3.51
670 677 6.265649 ACGTATTTCTGTGCTAGATACATCCT 59.734 38.462 0.00 0.00 34.80 3.24
691 698 7.766219 TCCTTTTGAGCGACAACTAATATAC 57.234 36.000 0.00 0.00 38.29 1.47
694 709 7.306051 CCTTTTGAGCGACAACTAATATACGAG 60.306 40.741 0.00 0.00 38.29 4.18
698 713 7.031372 TGAGCGACAACTAATATACGAGTTTT 58.969 34.615 0.00 0.00 33.60 2.43
716 731 9.909043 ACGAGTTTTTATTTTTGCACATTTTAC 57.091 25.926 0.00 0.00 0.00 2.01
789 810 1.558233 AAACCAAAAACGGGTCACCA 58.442 45.000 0.00 0.00 37.77 4.17
792 813 0.383949 CCAAAAACGGGTCACCAGTG 59.616 55.000 0.00 0.00 36.13 3.66
817 842 5.356426 GGTTTTTCAAACAATGCCTACACT 58.644 37.500 2.00 0.00 0.00 3.55
821 846 3.146066 TCAAACAATGCCTACACTGGAC 58.854 45.455 0.00 0.00 0.00 4.02
824 849 4.568072 AACAATGCCTACACTGGACATA 57.432 40.909 0.00 0.00 0.00 2.29
841 866 5.764686 TGGACATATCATCGGAAATCTTTGG 59.235 40.000 0.00 0.00 0.00 3.28
842 867 5.765182 GGACATATCATCGGAAATCTTTGGT 59.235 40.000 0.00 0.00 0.00 3.67
928 963 4.636249 GACAGAGAGTCAAGAATGGTTGT 58.364 43.478 0.00 0.00 46.77 3.32
929 964 4.636249 ACAGAGAGTCAAGAATGGTTGTC 58.364 43.478 0.00 0.00 0.00 3.18
933 980 3.392616 AGAGTCAAGAATGGTTGTCCTGT 59.607 43.478 0.00 0.00 34.23 4.00
948 995 3.985279 TGTCCTGTGAAACGATAACGAAG 59.015 43.478 0.00 0.00 42.39 3.79
969 1016 0.462225 CTCTCGCGTCCTCTCACCTA 60.462 60.000 5.77 0.00 0.00 3.08
971 1018 1.002990 TCGCGTCCTCTCACCTACA 60.003 57.895 5.77 0.00 0.00 2.74
1130 1180 4.183686 CGTCCGCGACCCACGTAT 62.184 66.667 8.23 0.00 44.60 3.06
1131 1181 2.581409 GTCCGCGACCCACGTATG 60.581 66.667 8.23 0.00 44.60 2.39
1132 1182 4.501714 TCCGCGACCCACGTATGC 62.502 66.667 8.23 0.00 44.60 3.14
1133 1183 4.805231 CCGCGACCCACGTATGCA 62.805 66.667 8.23 0.00 44.60 3.96
1134 1184 2.811747 CGCGACCCACGTATGCAA 60.812 61.111 0.00 0.00 44.60 4.08
1135 1185 2.171079 CGCGACCCACGTATGCAAT 61.171 57.895 0.00 0.00 44.60 3.56
1148 1198 1.120184 ATGCAATGCAACCACCACCA 61.120 50.000 13.45 0.00 43.62 4.17
1154 1204 2.127232 GCAACCACCACCAACAGCT 61.127 57.895 0.00 0.00 0.00 4.24
1208 1281 0.031585 TAATCTTCCGGGTCGATGCG 59.968 55.000 0.00 0.00 0.00 4.73
1354 1427 1.079127 CGAGGGCGTCTTCCATGTT 60.079 57.895 5.58 0.00 0.00 2.71
1372 1445 4.101448 GCCACTCCAGTGCCCGAT 62.101 66.667 0.76 0.00 44.34 4.18
1625 2612 5.371526 TGTCAAGATGCTTTTCTTCTCAGT 58.628 37.500 0.00 0.00 33.69 3.41
1626 2613 5.824624 TGTCAAGATGCTTTTCTTCTCAGTT 59.175 36.000 0.00 0.00 33.69 3.16
1627 2614 6.319658 TGTCAAGATGCTTTTCTTCTCAGTTT 59.680 34.615 0.00 0.00 33.69 2.66
1689 2727 7.710676 TCAGAAAACTCTCTGCTTCTATAGT 57.289 36.000 0.00 0.00 42.25 2.12
1690 2728 8.809468 TCAGAAAACTCTCTGCTTCTATAGTA 57.191 34.615 0.00 0.00 42.25 1.82
2003 3721 2.358898 CCAGGATTAAAATCTGCCACCG 59.641 50.000 2.91 0.00 35.73 4.94
2011 3839 3.855689 AAATCTGCCACCGAAATCTTG 57.144 42.857 0.00 0.00 0.00 3.02
2151 4069 0.536460 GGTTTTCGGCCCTCTGTTGA 60.536 55.000 0.00 0.00 0.00 3.18
2329 4290 4.751767 TTCCTTCCATTTTGCTGTTGTT 57.248 36.364 0.00 0.00 0.00 2.83
2330 4291 4.057406 TCCTTCCATTTTGCTGTTGTTG 57.943 40.909 0.00 0.00 0.00 3.33
2335 4296 4.180057 TCCATTTTGCTGTTGTTGTTGTC 58.820 39.130 0.00 0.00 0.00 3.18
2409 4370 5.639931 GGAGCTCCTCGGCTTTTATATTAAG 59.360 44.000 26.25 0.00 43.20 1.85
2448 4409 5.048991 GCCTCGGTTTTAATGAAGTTCAGAA 60.049 40.000 11.91 5.39 0.00 3.02
2463 5844 9.801873 TGAAGTTCAGAAAATGACCTTTTAAAG 57.198 29.630 0.08 0.00 40.44 1.85
2605 7405 0.106469 TTGTACAACAAGGCAGGGCA 60.106 50.000 3.59 0.00 32.34 5.36
2606 7406 0.537143 TGTACAACAAGGCAGGGCAG 60.537 55.000 0.00 0.00 0.00 4.85
2657 7457 5.394553 CCAAATGGACCTAAAGGATTTGCTC 60.395 44.000 2.23 0.00 36.43 4.26
2664 7464 2.947448 AAAGGATTTGCTCGCAATCC 57.053 45.000 17.66 17.66 36.60 3.01
2728 7528 5.767269 AGTGTCATAGCATCAAGACTATCG 58.233 41.667 0.00 0.00 32.41 2.92
2754 7559 7.056006 ACACCATGTCATAGCTTGATTATCAA 58.944 34.615 7.46 7.46 36.54 2.57
2813 7622 5.450965 GCAGGATGGTTGATGTGGATTTTAG 60.451 44.000 0.00 0.00 35.86 1.85
2901 7710 5.352016 ACTCGCAGATAGTATCGAATCCTAC 59.648 44.000 4.48 0.00 33.89 3.18
2961 7770 1.421268 TGCCGGCTTCCATTCATCTAT 59.579 47.619 29.70 0.00 0.00 1.98
3168 7977 2.246789 GTCAAGAGAAAGCGAGACTCG 58.753 52.381 20.56 20.56 43.89 4.18
3207 8016 5.021033 AGCAGTGACTCCAGATTTATGAG 57.979 43.478 0.00 0.00 0.00 2.90
3242 8051 5.181748 GTCCAAGTGCTGATATGAAAGTCT 58.818 41.667 0.00 0.00 0.00 3.24
3308 9825 7.496920 TGATATGGCTCTTATGTCAAACTCAAG 59.503 37.037 0.00 0.00 0.00 3.02
3310 9827 5.240891 TGGCTCTTATGTCAAACTCAAGAG 58.759 41.667 12.79 12.79 43.23 2.85
3311 9828 5.012046 TGGCTCTTATGTCAAACTCAAGAGA 59.988 40.000 17.70 3.74 43.09 3.10
3312 9829 5.934625 GGCTCTTATGTCAAACTCAAGAGAA 59.065 40.000 17.70 0.00 43.09 2.87
3313 9830 6.091986 GGCTCTTATGTCAAACTCAAGAGAAG 59.908 42.308 17.70 0.00 43.09 2.85
3314 9831 6.091986 GCTCTTATGTCAAACTCAAGAGAAGG 59.908 42.308 17.70 0.00 43.09 3.46
3315 9832 7.067496 TCTTATGTCAAACTCAAGAGAAGGT 57.933 36.000 3.73 0.00 0.00 3.50
3317 9834 8.647796 TCTTATGTCAAACTCAAGAGAAGGTTA 58.352 33.333 3.73 0.00 0.00 2.85
3319 9836 9.793259 TTATGTCAAACTCAAGAGAAGGTTATT 57.207 29.630 3.73 0.00 0.00 1.40
3321 9838 8.519799 TGTCAAACTCAAGAGAAGGTTATTTT 57.480 30.769 3.73 0.00 0.00 1.82
3343 9860 5.432885 TTTTCTCTGTCGGAAAACAATCC 57.567 39.130 0.00 0.00 37.63 3.01
3344 9861 3.762407 TCTCTGTCGGAAAACAATCCA 57.238 42.857 0.00 0.00 39.61 3.41
3345 9862 3.664107 TCTCTGTCGGAAAACAATCCAG 58.336 45.455 0.00 0.00 39.61 3.86
3346 9863 2.151202 TCTGTCGGAAAACAATCCAGC 58.849 47.619 0.00 0.00 39.61 4.85
3347 9864 2.154462 CTGTCGGAAAACAATCCAGCT 58.846 47.619 0.00 0.00 39.61 4.24
3348 9865 2.554032 CTGTCGGAAAACAATCCAGCTT 59.446 45.455 0.00 0.00 39.61 3.74
3349 9866 2.552315 TGTCGGAAAACAATCCAGCTTC 59.448 45.455 0.00 0.00 39.61 3.86
3350 9867 2.814336 GTCGGAAAACAATCCAGCTTCT 59.186 45.455 0.00 0.00 39.61 2.85
3351 9868 3.253432 GTCGGAAAACAATCCAGCTTCTT 59.747 43.478 0.00 0.00 39.61 2.52
3356 9873 6.512297 GGAAAACAATCCAGCTTCTTTACAA 58.488 36.000 0.00 0.00 39.42 2.41
3427 9944 9.477484 TTTAGATTATTAACGAGCATCTCTTCC 57.523 33.333 0.00 0.00 0.00 3.46
3428 9945 6.459923 AGATTATTAACGAGCATCTCTTCCC 58.540 40.000 0.00 0.00 0.00 3.97
3429 9946 2.579207 TTAACGAGCATCTCTTCCCG 57.421 50.000 0.00 0.00 0.00 5.14
3430 9947 1.471119 TAACGAGCATCTCTTCCCGT 58.529 50.000 0.00 0.00 0.00 5.28
3437 9954 1.002251 GCATCTCTTCCCGTCGAGTAG 60.002 57.143 0.00 0.00 0.00 2.57
3577 10175 2.161012 GGGCCGCTTTAAGTGAGTTTAC 59.839 50.000 7.14 0.00 0.00 2.01
3675 11353 1.968493 TCGGTCCTAGCAGTCAAAAGT 59.032 47.619 0.00 0.00 0.00 2.66
3698 11376 4.081862 TGTGAACCGTTACTCCTTATCCAG 60.082 45.833 0.00 0.00 0.00 3.86
3702 11380 4.351127 ACCGTTACTCCTTATCCAGTCTT 58.649 43.478 0.00 0.00 0.00 3.01
3840 11898 3.646787 AGCACATGAGCTCAGCTTT 57.353 47.368 22.96 1.51 42.18 3.51
3942 12006 8.243426 TCTTTTCAAATTATGGACCAAATCTCG 58.757 33.333 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
211 217 8.499162 GTTAACATGATAGAGTTCATACATGGC 58.501 37.037 0.00 0.00 39.20 4.40
248 254 1.227674 CCATTAGCCGAGGGAGTGC 60.228 63.158 0.00 0.00 0.00 4.40
389 396 7.235935 TGTAGAAAGATAAACGGGAAAGAGA 57.764 36.000 0.00 0.00 0.00 3.10
398 405 7.980099 AGAACCCTGTATGTAGAAAGATAAACG 59.020 37.037 0.00 0.00 0.00 3.60
516 523 2.604046 ACTTACGCTTGGCTAGATGG 57.396 50.000 0.00 0.00 0.00 3.51
517 524 4.033358 CAGAAACTTACGCTTGGCTAGATG 59.967 45.833 0.00 0.00 0.00 2.90
518 525 4.081642 TCAGAAACTTACGCTTGGCTAGAT 60.082 41.667 0.00 0.00 0.00 1.98
519 526 3.257375 TCAGAAACTTACGCTTGGCTAGA 59.743 43.478 0.00 0.00 0.00 2.43
520 527 3.368236 GTCAGAAACTTACGCTTGGCTAG 59.632 47.826 0.00 0.00 0.00 3.42
521 528 3.243941 TGTCAGAAACTTACGCTTGGCTA 60.244 43.478 0.00 0.00 0.00 3.93
522 529 2.143925 GTCAGAAACTTACGCTTGGCT 58.856 47.619 0.00 0.00 0.00 4.75
523 530 1.871039 TGTCAGAAACTTACGCTTGGC 59.129 47.619 0.00 0.00 0.00 4.52
524 531 4.545823 TTTGTCAGAAACTTACGCTTGG 57.454 40.909 0.00 0.00 0.00 3.61
525 532 5.747565 TCATTTGTCAGAAACTTACGCTTG 58.252 37.500 0.00 0.00 0.00 4.01
526 533 6.373779 CATCATTTGTCAGAAACTTACGCTT 58.626 36.000 0.00 0.00 0.00 4.68
527 534 5.106555 CCATCATTTGTCAGAAACTTACGCT 60.107 40.000 0.00 0.00 0.00 5.07
528 535 5.088739 CCATCATTTGTCAGAAACTTACGC 58.911 41.667 0.00 0.00 0.00 4.42
529 536 6.147821 AGACCATCATTTGTCAGAAACTTACG 59.852 38.462 0.00 0.00 33.89 3.18
530 537 7.389053 AGAGACCATCATTTGTCAGAAACTTAC 59.611 37.037 0.00 0.00 33.89 2.34
531 538 7.388776 CAGAGACCATCATTTGTCAGAAACTTA 59.611 37.037 0.00 0.00 33.89 2.24
532 539 6.206243 CAGAGACCATCATTTGTCAGAAACTT 59.794 38.462 0.00 0.00 33.89 2.66
533 540 5.704515 CAGAGACCATCATTTGTCAGAAACT 59.295 40.000 0.00 0.00 33.89 2.66
534 541 5.702670 TCAGAGACCATCATTTGTCAGAAAC 59.297 40.000 0.00 0.00 33.89 2.78
535 542 5.868454 TCAGAGACCATCATTTGTCAGAAA 58.132 37.500 0.00 0.00 33.89 2.52
536 543 5.488262 TCAGAGACCATCATTTGTCAGAA 57.512 39.130 0.00 0.00 33.89 3.02
537 544 5.424573 AGATCAGAGACCATCATTTGTCAGA 59.575 40.000 0.00 0.00 33.89 3.27
538 545 5.672503 AGATCAGAGACCATCATTTGTCAG 58.327 41.667 0.00 0.00 33.89 3.51
539 546 5.688814 AGATCAGAGACCATCATTTGTCA 57.311 39.130 0.00 0.00 33.89 3.58
540 547 9.941325 AATATAGATCAGAGACCATCATTTGTC 57.059 33.333 0.00 0.00 0.00 3.18
546 553 9.593565 ACAACTAATATAGATCAGAGACCATCA 57.406 33.333 0.00 0.00 0.00 3.07
552 559 7.661847 TGAGCGACAACTAATATAGATCAGAGA 59.338 37.037 0.00 0.00 0.00 3.10
556 563 7.378728 CGTTTGAGCGACAACTAATATAGATCA 59.621 37.037 0.00 0.00 38.29 2.92
557 564 7.148950 CCGTTTGAGCGACAACTAATATAGATC 60.149 40.741 0.00 0.00 38.29 2.75
561 568 5.893687 TCCGTTTGAGCGACAACTAATATA 58.106 37.500 0.00 0.00 38.29 0.86
583 590 9.383462 CCGTTTGAGCGATATACTATATACATC 57.617 37.037 0.00 0.00 0.00 3.06
590 597 6.268825 ACATCCGTTTGAGCGATATACTAT 57.731 37.500 0.00 0.00 0.00 2.12
594 601 6.510879 AGATACATCCGTTTGAGCGATATA 57.489 37.500 0.00 0.00 0.00 0.86
596 603 4.848562 AGATACATCCGTTTGAGCGATA 57.151 40.909 0.00 0.00 0.00 2.92
597 604 3.735237 AGATACATCCGTTTGAGCGAT 57.265 42.857 0.00 0.00 0.00 4.58
607 614 1.970447 GCGTCTGCTAGATACATCCG 58.030 55.000 0.00 0.00 38.39 4.18
619 626 1.076332 ACATCCGTTTTAGCGTCTGC 58.924 50.000 0.00 0.00 43.24 4.26
620 627 4.360563 AGATACATCCGTTTTAGCGTCTG 58.639 43.478 0.00 0.00 0.00 3.51
647 654 8.894768 AAAGGATGTATCTAGCACAGAAATAC 57.105 34.615 3.80 0.00 36.67 1.89
651 658 6.946340 TCAAAAGGATGTATCTAGCACAGAA 58.054 36.000 3.80 0.00 36.67 3.02
654 661 5.118990 GCTCAAAAGGATGTATCTAGCACA 58.881 41.667 0.22 0.22 0.00 4.57
658 665 5.592054 TGTCGCTCAAAAGGATGTATCTAG 58.408 41.667 0.00 0.00 0.00 2.43
669 676 7.220300 ACTCGTATATTAGTTGTCGCTCAAAAG 59.780 37.037 0.00 0.00 37.81 2.27
670 677 7.031372 ACTCGTATATTAGTTGTCGCTCAAAA 58.969 34.615 0.00 0.00 37.81 2.44
707 722 9.360093 TGGTTGTTTAGACAAAAGTAAAATGTG 57.640 29.630 0.00 0.00 46.62 3.21
715 730 4.460034 ACCGTTGGTTGTTTAGACAAAAGT 59.540 37.500 0.00 0.00 46.62 2.66
716 731 4.989044 ACCGTTGGTTGTTTAGACAAAAG 58.011 39.130 0.00 0.00 46.62 2.27
776 793 2.184167 CGCACTGGTGACCCGTTTT 61.184 57.895 0.00 0.00 0.00 2.43
789 810 2.607180 GCATTGTTTGAAAAACCGCACT 59.393 40.909 0.71 0.00 0.00 4.40
792 813 2.209273 AGGCATTGTTTGAAAAACCGC 58.791 42.857 0.71 1.61 0.00 5.68
804 825 4.164030 TGATATGTCCAGTGTAGGCATTGT 59.836 41.667 0.00 0.00 31.37 2.71
817 842 5.764686 CCAAAGATTTCCGATGATATGTCCA 59.235 40.000 0.00 0.00 0.00 4.02
821 846 6.128172 GGCTACCAAAGATTTCCGATGATATG 60.128 42.308 0.00 0.00 0.00 1.78
824 849 4.137543 GGCTACCAAAGATTTCCGATGAT 58.862 43.478 0.00 0.00 0.00 2.45
925 960 3.979948 TCGTTATCGTTTCACAGGACAA 58.020 40.909 0.00 0.00 38.33 3.18
926 961 3.646611 TCGTTATCGTTTCACAGGACA 57.353 42.857 0.00 0.00 38.33 4.02
928 963 4.022589 AGTCTTCGTTATCGTTTCACAGGA 60.023 41.667 0.00 0.00 38.33 3.86
929 964 4.235360 AGTCTTCGTTATCGTTTCACAGG 58.765 43.478 0.00 0.00 38.33 4.00
933 980 4.400845 CGAGAGTCTTCGTTATCGTTTCA 58.599 43.478 0.00 0.00 38.33 2.69
948 995 1.426223 GTGAGAGGACGCGAGAGTC 59.574 63.158 15.93 0.00 40.25 3.36
969 1016 4.160439 TGTTCAGAGTTCAGAGTTCAGTGT 59.840 41.667 0.00 0.00 0.00 3.55
971 1018 5.112686 GTTGTTCAGAGTTCAGAGTTCAGT 58.887 41.667 0.00 0.00 0.00 3.41
1130 1180 1.332889 TTGGTGGTGGTTGCATTGCA 61.333 50.000 7.38 7.38 36.47 4.08
1131 1181 0.879839 GTTGGTGGTGGTTGCATTGC 60.880 55.000 0.46 0.46 0.00 3.56
1132 1182 0.463204 TGTTGGTGGTGGTTGCATTG 59.537 50.000 0.00 0.00 0.00 2.82
1133 1183 0.752054 CTGTTGGTGGTGGTTGCATT 59.248 50.000 0.00 0.00 0.00 3.56
1134 1184 1.747325 GCTGTTGGTGGTGGTTGCAT 61.747 55.000 0.00 0.00 0.00 3.96
1135 1185 2.422231 GCTGTTGGTGGTGGTTGCA 61.422 57.895 0.00 0.00 0.00 4.08
1148 1198 2.031163 GTCGTCAGGGCAGCTGTT 59.969 61.111 16.64 0.00 0.00 3.16
1208 1281 1.967319 TCACCTGCAAGAGAAACCAC 58.033 50.000 0.00 0.00 34.07 4.16
1689 2727 7.011499 TCAGTAATAACAGCAGAAGGGTTTA 57.989 36.000 0.00 0.00 0.00 2.01
1690 2728 5.876357 TCAGTAATAACAGCAGAAGGGTTT 58.124 37.500 0.00 0.00 0.00 3.27
1729 3445 4.654915 TCCATCATCTCTTTCTGCACAAA 58.345 39.130 0.00 0.00 0.00 2.83
2011 3839 7.384660 TCTGCCAACACAAACATGAATAATTTC 59.615 33.333 0.00 0.00 0.00 2.17
2151 4069 1.094785 GTATTGACCGCCACATGCTT 58.905 50.000 0.00 0.00 38.05 3.91
2329 4290 1.487452 GCTGCACTTCGACGACAACA 61.487 55.000 0.00 0.00 0.00 3.33
2330 4291 1.201825 GCTGCACTTCGACGACAAC 59.798 57.895 0.00 0.00 0.00 3.32
2335 4296 2.724708 GCTCTGCTGCACTTCGACG 61.725 63.158 0.00 0.00 0.00 5.12
2409 4370 3.130693 ACCGAGGCTGTCTTAATACACTC 59.869 47.826 0.00 3.02 0.00 3.51
2448 4409 8.706322 AGGATGTGTACTTTAAAAGGTCATTT 57.294 30.769 0.00 0.00 0.00 2.32
2479 5860 9.214957 TCGGACATATGATGGAATTACATTTAC 57.785 33.333 10.38 0.00 33.60 2.01
2605 7405 6.207221 CAGTGAGCATATGTATCTCTCAGACT 59.793 42.308 9.44 3.55 34.84 3.24
2606 7406 6.380995 CAGTGAGCATATGTATCTCTCAGAC 58.619 44.000 9.44 1.73 34.84 3.51
2657 7457 1.376543 ACATGCTCTTCAGGATTGCG 58.623 50.000 0.00 0.00 0.00 4.85
2664 7464 2.697751 AGCTAGGGTACATGCTCTTCAG 59.302 50.000 0.00 0.00 0.00 3.02
2728 7528 7.227314 TTGATAATCAAGCTATGACATGGTGTC 59.773 37.037 0.00 3.22 41.93 3.67
2813 7622 0.599204 TTCCGAAGTGACTCCAACGC 60.599 55.000 0.00 0.00 0.00 4.84
2961 7770 1.367471 CTGGATAGGCGGCATTCGA 59.633 57.895 13.08 3.67 42.43 3.71
3168 7977 2.167487 CTGCTTTGAGAGTACTCCTCCC 59.833 54.545 19.38 7.17 41.47 4.30
3225 8034 9.190858 CTCATTACTAGACTTTCATATCAGCAC 57.809 37.037 0.00 0.00 0.00 4.40
3321 9838 4.884744 TGGATTGTTTTCCGACAGAGAAAA 59.115 37.500 0.00 0.00 40.08 2.29
3323 9840 4.065088 CTGGATTGTTTTCCGACAGAGAA 58.935 43.478 0.00 0.00 38.74 2.87
3329 9846 2.814336 AGAAGCTGGATTGTTTTCCGAC 59.186 45.455 0.00 0.00 38.74 4.79
3332 9849 6.084326 TGTAAAGAAGCTGGATTGTTTTCC 57.916 37.500 0.00 0.00 36.24 3.13
3333 9850 9.129209 GTATTGTAAAGAAGCTGGATTGTTTTC 57.871 33.333 0.00 0.00 29.50 2.29
3334 9851 8.860088 AGTATTGTAAAGAAGCTGGATTGTTTT 58.140 29.630 0.00 0.00 29.50 2.43
3335 9852 8.409358 AGTATTGTAAAGAAGCTGGATTGTTT 57.591 30.769 0.00 0.05 31.40 2.83
3336 9853 9.515226 TTAGTATTGTAAAGAAGCTGGATTGTT 57.485 29.630 0.00 0.00 0.00 2.83
3338 9855 9.383519 TCTTAGTATTGTAAAGAAGCTGGATTG 57.616 33.333 0.00 0.00 0.00 2.67
3414 9931 1.298713 CGACGGGAAGAGATGCTCG 60.299 63.158 0.00 0.00 35.36 5.03
3417 9934 1.002251 CTACTCGACGGGAAGAGATGC 60.002 57.143 0.00 0.00 37.87 3.91
3418 9935 2.562635 TCTACTCGACGGGAAGAGATG 58.437 52.381 0.00 0.00 37.87 2.90
3419 9936 3.495434 ATCTACTCGACGGGAAGAGAT 57.505 47.619 0.00 3.72 37.87 2.75
3420 9937 2.943690 CAATCTACTCGACGGGAAGAGA 59.056 50.000 0.00 1.15 37.87 3.10
3421 9938 2.541999 GCAATCTACTCGACGGGAAGAG 60.542 54.545 0.00 0.00 40.16 2.85
3422 9939 1.404391 GCAATCTACTCGACGGGAAGA 59.596 52.381 0.00 0.00 0.00 2.87
3423 9940 1.134367 TGCAATCTACTCGACGGGAAG 59.866 52.381 0.00 0.00 0.00 3.46
3424 9941 1.179152 TGCAATCTACTCGACGGGAA 58.821 50.000 0.00 0.00 0.00 3.97
3425 9942 1.399714 ATGCAATCTACTCGACGGGA 58.600 50.000 0.00 0.00 0.00 5.14
3426 9943 3.364889 TTATGCAATCTACTCGACGGG 57.635 47.619 0.00 0.00 0.00 5.28
3427 9944 4.025979 GGTTTTATGCAATCTACTCGACGG 60.026 45.833 0.00 0.00 0.00 4.79
3428 9945 4.565166 TGGTTTTATGCAATCTACTCGACG 59.435 41.667 0.00 0.00 0.00 5.12
3429 9946 5.220605 GGTGGTTTTATGCAATCTACTCGAC 60.221 44.000 0.00 0.00 0.00 4.20
3430 9947 4.873827 GGTGGTTTTATGCAATCTACTCGA 59.126 41.667 0.00 0.00 0.00 4.04
3437 9954 5.537188 TCAAAGTGGTGGTTTTATGCAATC 58.463 37.500 0.00 0.00 0.00 2.67
3563 10082 5.929992 CCCATCTGTCGTAAACTCACTTAAA 59.070 40.000 0.00 0.00 0.00 1.52
3577 10175 3.622060 AAACGGGCCCCATCTGTCG 62.622 63.158 18.66 3.86 0.00 4.35
3675 11353 3.833650 TGGATAAGGAGTAACGGTTCACA 59.166 43.478 0.00 0.00 0.00 3.58
3698 11376 0.380378 AGATGAGCGAGCGAGAAGAC 59.620 55.000 0.00 0.00 0.00 3.01
3702 11380 1.494766 CGAGAGATGAGCGAGCGAGA 61.495 60.000 0.00 0.00 0.00 4.04
3772 11830 2.347114 CTCCACGACACCATGGCA 59.653 61.111 13.04 0.00 35.81 4.92
3824 11882 1.392853 GTCGAAAGCTGAGCTCATGTG 59.607 52.381 18.63 7.01 38.25 3.21
3840 11898 0.457166 CTTAATGGTGCCGTCGTCGA 60.457 55.000 2.98 0.00 39.71 4.20
3942 12006 1.815003 CTGGAGTGCAAAGGAATGACC 59.185 52.381 0.00 0.00 39.35 4.02


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

AutoCloner maintained by Alex Coulton.