Multiple sequence alignment - TraesCS4B01G060800

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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 TraesCS4B01G060800 chr4B 100.000 3573 0 0 1 3573 52864251 52860679 0.000000e+00 6599.0
1 TraesCS4B01G060800 chr4B 91.016 2126 145 15 675 2761 472887481 472885363 0.000000e+00 2826.0
2 TraesCS4B01G060800 chr4B 97.171 813 21 2 2762 3573 52851399 52850588 0.000000e+00 1373.0
3 TraesCS4B01G060800 chr4B 96.196 815 29 2 2761 3573 6962939 6963753 0.000000e+00 1332.0
4 TraesCS4B01G060800 chr4B 94.142 478 10 2 34 510 53075067 53075527 0.000000e+00 712.0
5 TraesCS4B01G060800 chr5B 92.103 2102 134 19 677 2761 620016108 620014022 0.000000e+00 2933.0
6 TraesCS4B01G060800 chr5B 91.048 2100 153 22 677 2761 478602963 478600884 0.000000e+00 2804.0
7 TraesCS4B01G060800 chr5B 96.182 812 31 0 2762 3573 124300326 124299515 0.000000e+00 1328.0
8 TraesCS4B01G060800 chr7B 91.811 2027 143 15 706 2721 701285848 701283834 0.000000e+00 2802.0
9 TraesCS4B01G060800 chr7B 96.310 813 29 1 2762 3573 502357523 502358335 0.000000e+00 1334.0
10 TraesCS4B01G060800 chr7B 96.182 812 31 0 2762 3573 596649504 596650315 0.000000e+00 1328.0
11 TraesCS4B01G060800 chr6B 90.699 2118 134 25 677 2761 646705067 646702980 0.000000e+00 2761.0
12 TraesCS4B01G060800 chr6B 91.335 1962 148 16 677 2628 29406321 29408270 0.000000e+00 2662.0
13 TraesCS4B01G060800 chr6B 89.303 2066 191 20 677 2733 545609492 545607448 0.000000e+00 2564.0
14 TraesCS4B01G060800 chr6B 91.023 1593 73 14 1198 2761 47872193 47870642 0.000000e+00 2085.0
15 TraesCS4B01G060800 chr6B 96.569 816 25 2 2759 3573 14276990 14276177 0.000000e+00 1349.0
16 TraesCS4B01G060800 chr6B 96.429 812 29 0 2762 3573 479526165 479525354 0.000000e+00 1339.0
17 TraesCS4B01G060800 chr6B 96.429 812 28 1 2762 3573 532441934 532441124 0.000000e+00 1338.0
18 TraesCS4B01G060800 chr6B 96.078 816 30 2 2759 3573 532447155 532446341 0.000000e+00 1328.0
19 TraesCS4B01G060800 chr1B 90.959 1991 163 10 677 2657 684866545 684864562 0.000000e+00 2663.0
20 TraesCS4B01G060800 chr1B 93.624 596 26 10 83 673 321702308 321701720 0.000000e+00 880.0
21 TraesCS4B01G060800 chr6A 89.497 2066 182 14 677 2721 601153029 601150978 0.000000e+00 2580.0
22 TraesCS4B01G060800 chr6D 88.650 2097 209 18 674 2761 473050816 473052892 0.000000e+00 2527.0
23 TraesCS4B01G060800 chr6D 95.745 47 1 1 1 47 377341705 377341750 1.380000e-09 75.0
24 TraesCS4B01G060800 chr6D 95.652 46 0 2 1 45 299191298 299191254 4.950000e-09 73.1
25 TraesCS4B01G060800 chr6D 95.556 45 0 2 1 44 199210377 199210420 1.780000e-08 71.3
26 TraesCS4B01G060800 chr3B 92.790 638 43 3 37 672 273552320 273551684 0.000000e+00 920.0
27 TraesCS4B01G060800 chr3B 88.506 174 20 0 2588 2761 166154941 166155114 1.010000e-50 211.0
28 TraesCS4B01G060800 chr3B 85.000 180 21 3 2588 2761 159572632 159572453 1.020000e-40 178.0
29 TraesCS4B01G060800 chr3B 95.556 45 0 2 1 44 42122587 42122630 1.780000e-08 71.3
30 TraesCS4B01G060800 chr2A 89.971 339 28 4 338 673 776206735 776206400 1.970000e-117 433.0
31 TraesCS4B01G060800 chr2A 90.826 218 19 1 37 254 330485989 330485773 1.250000e-74 291.0
32 TraesCS4B01G060800 chr2A 90.367 218 20 1 37 254 454871475 454871259 5.840000e-73 285.0
33 TraesCS4B01G060800 chr2D 92.202 218 15 1 37 254 437710680 437710465 1.250000e-79 307.0
34 TraesCS4B01G060800 chr7A 91.403 221 18 1 34 254 149504438 149504657 5.800000e-78 302.0
35 TraesCS4B01G060800 chr7A 89.474 152 12 3 2614 2761 130235015 130235166 4.710000e-44 189.0
36 TraesCS4B01G060800 chr7A 95.556 45 0 2 1 44 82512353 82512310 1.780000e-08 71.3
37 TraesCS4B01G060800 chr7A 95.455 44 2 0 1 44 663591555 663591598 1.780000e-08 71.3
38 TraesCS4B01G060800 chr5A 91.204 216 18 1 37 252 7518687 7518473 3.490000e-75 292.0
39 TraesCS4B01G060800 chr1A 90.783 217 19 1 37 253 465684756 465684541 4.510000e-74 289.0
40 TraesCS4B01G060800 chr2B 85.311 177 18 6 2591 2761 749852620 749852794 3.670000e-40 176.0
41 TraesCS4B01G060800 chr4D 97.674 43 0 1 1 42 423945349 423945307 4.950000e-09 73.1
42 TraesCS4B01G060800 chr5D 92.308 52 1 3 1 50 469062782 469062732 1.780000e-08 71.3
43 TraesCS4B01G060800 chrUn 92.157 51 1 3 1 48 3346433 3346383 6.400000e-08 69.4


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 TraesCS4B01G060800 chr4B 52860679 52864251 3572 True 6599 6599 100.000 1 3573 1 chr4B.!!$R2 3572
1 TraesCS4B01G060800 chr4B 472885363 472887481 2118 True 2826 2826 91.016 675 2761 1 chr4B.!!$R3 2086
2 TraesCS4B01G060800 chr4B 52850588 52851399 811 True 1373 1373 97.171 2762 3573 1 chr4B.!!$R1 811
3 TraesCS4B01G060800 chr4B 6962939 6963753 814 False 1332 1332 96.196 2761 3573 1 chr4B.!!$F1 812
4 TraesCS4B01G060800 chr5B 620014022 620016108 2086 True 2933 2933 92.103 677 2761 1 chr5B.!!$R3 2084
5 TraesCS4B01G060800 chr5B 478600884 478602963 2079 True 2804 2804 91.048 677 2761 1 chr5B.!!$R2 2084
6 TraesCS4B01G060800 chr5B 124299515 124300326 811 True 1328 1328 96.182 2762 3573 1 chr5B.!!$R1 811
7 TraesCS4B01G060800 chr7B 701283834 701285848 2014 True 2802 2802 91.811 706 2721 1 chr7B.!!$R1 2015
8 TraesCS4B01G060800 chr7B 502357523 502358335 812 False 1334 1334 96.310 2762 3573 1 chr7B.!!$F1 811
9 TraesCS4B01G060800 chr7B 596649504 596650315 811 False 1328 1328 96.182 2762 3573 1 chr7B.!!$F2 811
10 TraesCS4B01G060800 chr6B 646702980 646705067 2087 True 2761 2761 90.699 677 2761 1 chr6B.!!$R7 2084
11 TraesCS4B01G060800 chr6B 29406321 29408270 1949 False 2662 2662 91.335 677 2628 1 chr6B.!!$F1 1951
12 TraesCS4B01G060800 chr6B 545607448 545609492 2044 True 2564 2564 89.303 677 2733 1 chr6B.!!$R6 2056
13 TraesCS4B01G060800 chr6B 47870642 47872193 1551 True 2085 2085 91.023 1198 2761 1 chr6B.!!$R2 1563
14 TraesCS4B01G060800 chr6B 14276177 14276990 813 True 1349 1349 96.569 2759 3573 1 chr6B.!!$R1 814
15 TraesCS4B01G060800 chr6B 479525354 479526165 811 True 1339 1339 96.429 2762 3573 1 chr6B.!!$R3 811
16 TraesCS4B01G060800 chr6B 532441124 532441934 810 True 1338 1338 96.429 2762 3573 1 chr6B.!!$R4 811
17 TraesCS4B01G060800 chr6B 532446341 532447155 814 True 1328 1328 96.078 2759 3573 1 chr6B.!!$R5 814
18 TraesCS4B01G060800 chr1B 684864562 684866545 1983 True 2663 2663 90.959 677 2657 1 chr1B.!!$R2 1980
19 TraesCS4B01G060800 chr1B 321701720 321702308 588 True 880 880 93.624 83 673 1 chr1B.!!$R1 590
20 TraesCS4B01G060800 chr6A 601150978 601153029 2051 True 2580 2580 89.497 677 2721 1 chr6A.!!$R1 2044
21 TraesCS4B01G060800 chr6D 473050816 473052892 2076 False 2527 2527 88.650 674 2761 1 chr6D.!!$F3 2087
22 TraesCS4B01G060800 chr3B 273551684 273552320 636 True 920 920 92.790 37 672 1 chr3B.!!$R2 635

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
906 911 0.111446 CTCCTCTCCGCCTCCTATGA 59.889 60.0 0.0 0.0 0.00 2.15 F
2121 2170 0.172127 TTGAGCAACAAACGCAAGCA 59.828 45.0 0.0 0.0 35.39 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2420 2514 1.077212 CCATGCCCACCTTCCTCTG 60.077 63.158 0.0 0.0 0.00 3.35 R
2945 3138 0.316204 CGTAAGTGACCGTGAAGGGT 59.684 55.000 0.0 0.0 46.96 4.34 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
27 28 9.241317 TCTAAACGCTCTTATATTTCTTTACGG 57.759 33.333 0.00 0.00 0.00 4.02
28 29 9.241317 CTAAACGCTCTTATATTTCTTTACGGA 57.759 33.333 0.00 0.00 0.00 4.69
29 30 7.695869 AACGCTCTTATATTTCTTTACGGAG 57.304 36.000 0.00 0.00 0.00 4.63
30 31 6.214399 ACGCTCTTATATTTCTTTACGGAGG 58.786 40.000 0.00 0.00 0.00 4.30
31 32 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
32 33 6.516194 CGCTCTTATATTTCTTTACGGAGGGA 60.516 42.308 0.00 0.00 34.63 4.20
33 34 6.869388 GCTCTTATATTTCTTTACGGAGGGAG 59.131 42.308 0.00 0.00 0.00 4.30
34 35 7.471679 GCTCTTATATTTCTTTACGGAGGGAGT 60.472 40.741 0.00 0.00 0.00 3.85
35 36 7.949434 TCTTATATTTCTTTACGGAGGGAGTC 58.051 38.462 0.00 0.00 0.00 3.36
136 137 8.046107 AGGAATTTCTGGAGTAAAATGAGAGAG 58.954 37.037 0.00 0.00 0.00 3.20
174 175 2.041755 GGGATTTGGAGGAAGTGACCTT 59.958 50.000 0.00 0.00 40.73 3.50
175 176 3.084786 GGATTTGGAGGAAGTGACCTTG 58.915 50.000 0.00 0.00 40.73 3.61
463 464 2.829458 GAGGACGTCGAGGAGGGG 60.829 72.222 12.85 0.00 0.00 4.79
464 465 4.444081 AGGACGTCGAGGAGGGGG 62.444 72.222 12.85 0.00 0.00 5.40
472 473 3.157949 GAGGAGGGGGCGAGGAAG 61.158 72.222 0.00 0.00 0.00 3.46
481 482 4.135153 GCGAGGAAGCGAGCTGGA 62.135 66.667 0.00 0.00 0.00 3.86
482 483 2.103934 CGAGGAAGCGAGCTGGAG 59.896 66.667 0.00 0.00 0.00 3.86
483 484 2.498726 GAGGAAGCGAGCTGGAGG 59.501 66.667 0.00 0.00 0.00 4.30
484 485 2.038007 AGGAAGCGAGCTGGAGGA 59.962 61.111 0.00 0.00 0.00 3.71
485 486 2.015227 GAGGAAGCGAGCTGGAGGAG 62.015 65.000 0.00 0.00 0.00 3.69
486 487 2.498726 GAAGCGAGCTGGAGGAGG 59.501 66.667 0.00 0.00 0.00 4.30
487 488 2.038007 AAGCGAGCTGGAGGAGGA 59.962 61.111 0.00 0.00 0.00 3.71
488 489 2.015227 GAAGCGAGCTGGAGGAGGAG 62.015 65.000 0.00 0.00 0.00 3.69
489 490 3.535962 GCGAGCTGGAGGAGGAGG 61.536 72.222 0.00 0.00 0.00 4.30
490 491 2.837291 CGAGCTGGAGGAGGAGGG 60.837 72.222 0.00 0.00 0.00 4.30
491 492 2.445654 GAGCTGGAGGAGGAGGGG 60.446 72.222 0.00 0.00 0.00 4.79
492 493 4.101077 AGCTGGAGGAGGAGGGGG 62.101 72.222 0.00 0.00 0.00 5.40
502 503 4.554036 GGAGGGGGCGCACTGATC 62.554 72.222 11.69 5.06 0.00 2.92
503 504 3.474570 GAGGGGGCGCACTGATCT 61.475 66.667 11.69 1.87 0.00 2.75
504 505 3.746949 GAGGGGGCGCACTGATCTG 62.747 68.421 11.69 0.00 0.00 2.90
505 506 4.101448 GGGGGCGCACTGATCTGT 62.101 66.667 10.74 0.00 0.00 3.41
506 507 2.821366 GGGGCGCACTGATCTGTG 60.821 66.667 24.08 24.08 40.62 3.66
507 508 2.265739 GGGCGCACTGATCTGTGA 59.734 61.111 30.31 0.00 40.12 3.58
508 509 1.812922 GGGCGCACTGATCTGTGAG 60.813 63.158 30.31 27.66 40.12 3.51
509 510 1.812922 GGCGCACTGATCTGTGAGG 60.813 63.158 30.31 22.16 40.12 3.86
510 511 1.812922 GCGCACTGATCTGTGAGGG 60.813 63.158 30.31 20.16 40.12 4.30
511 512 1.153489 CGCACTGATCTGTGAGGGG 60.153 63.158 30.31 15.00 40.12 4.79
512 513 1.607801 CGCACTGATCTGTGAGGGGA 61.608 60.000 30.31 0.00 40.12 4.81
513 514 0.177604 GCACTGATCTGTGAGGGGAG 59.822 60.000 30.31 8.00 40.12 4.30
514 515 0.829333 CACTGATCTGTGAGGGGAGG 59.171 60.000 24.09 0.00 40.12 4.30
515 516 0.326048 ACTGATCTGTGAGGGGAGGG 60.326 60.000 4.21 0.00 0.00 4.30
516 517 1.003442 TGATCTGTGAGGGGAGGGG 59.997 63.158 0.00 0.00 0.00 4.79
517 518 1.003573 GATCTGTGAGGGGAGGGGT 59.996 63.158 0.00 0.00 0.00 4.95
518 519 0.264955 GATCTGTGAGGGGAGGGGTA 59.735 60.000 0.00 0.00 0.00 3.69
519 520 0.266152 ATCTGTGAGGGGAGGGGTAG 59.734 60.000 0.00 0.00 0.00 3.18
520 521 1.383248 CTGTGAGGGGAGGGGTAGG 60.383 68.421 0.00 0.00 0.00 3.18
521 522 2.040779 GTGAGGGGAGGGGTAGGG 60.041 72.222 0.00 0.00 0.00 3.53
522 523 3.373846 TGAGGGGAGGGGTAGGGG 61.374 72.222 0.00 0.00 0.00 4.79
523 524 3.040814 GAGGGGAGGGGTAGGGGA 61.041 72.222 0.00 0.00 0.00 4.81
524 525 3.043404 AGGGGAGGGGTAGGGGAG 61.043 72.222 0.00 0.00 0.00 4.30
525 526 3.040814 GGGGAGGGGTAGGGGAGA 61.041 72.222 0.00 0.00 0.00 3.71
526 527 2.615773 GGGAGGGGTAGGGGAGAG 59.384 72.222 0.00 0.00 0.00 3.20
527 528 2.615773 GGAGGGGTAGGGGAGAGG 59.384 72.222 0.00 0.00 0.00 3.69
528 529 2.615773 GAGGGGTAGGGGAGAGGG 59.384 72.222 0.00 0.00 0.00 4.30
529 530 2.019272 GAGGGGTAGGGGAGAGGGA 61.019 68.421 0.00 0.00 0.00 4.20
530 531 2.021652 AGGGGTAGGGGAGAGGGAG 61.022 68.421 0.00 0.00 0.00 4.30
531 532 2.019272 GGGGTAGGGGAGAGGGAGA 61.019 68.421 0.00 0.00 0.00 3.71
532 533 1.544703 GGGTAGGGGAGAGGGAGAG 59.455 68.421 0.00 0.00 0.00 3.20
533 534 1.544703 GGTAGGGGAGAGGGAGAGG 59.455 68.421 0.00 0.00 0.00 3.69
534 535 1.544703 GTAGGGGAGAGGGAGAGGG 59.455 68.421 0.00 0.00 0.00 4.30
535 536 2.404750 TAGGGGAGAGGGAGAGGGC 61.405 68.421 0.00 0.00 0.00 5.19
537 538 4.467107 GGGAGAGGGAGAGGGCGT 62.467 72.222 0.00 0.00 0.00 5.68
538 539 2.601868 GGAGAGGGAGAGGGCGTA 59.398 66.667 0.00 0.00 0.00 4.42
539 540 1.529713 GGAGAGGGAGAGGGCGTAG 60.530 68.421 0.00 0.00 0.00 3.51
540 541 1.529713 GAGAGGGAGAGGGCGTAGG 60.530 68.421 0.00 0.00 0.00 3.18
551 552 4.849329 GCGTAGGCCGACGAGGTG 62.849 72.222 37.82 12.63 45.82 4.00
552 553 3.437795 CGTAGGCCGACGAGGTGT 61.438 66.667 31.70 0.00 45.82 4.16
553 554 2.181021 GTAGGCCGACGAGGTGTG 59.819 66.667 0.00 0.00 43.70 3.82
554 555 2.034532 TAGGCCGACGAGGTGTGA 59.965 61.111 0.00 0.00 43.70 3.58
555 556 2.044555 TAGGCCGACGAGGTGTGAG 61.045 63.158 0.00 0.00 43.70 3.51
556 557 4.436998 GGCCGACGAGGTGTGAGG 62.437 72.222 0.00 0.00 43.70 3.86
557 558 4.436998 GCCGACGAGGTGTGAGGG 62.437 72.222 0.00 0.00 43.70 4.30
558 559 2.675423 CCGACGAGGTGTGAGGGA 60.675 66.667 0.00 0.00 34.51 4.20
559 560 2.701780 CCGACGAGGTGTGAGGGAG 61.702 68.421 0.00 0.00 34.51 4.30
560 561 1.674651 CGACGAGGTGTGAGGGAGA 60.675 63.158 0.00 0.00 0.00 3.71
561 562 1.884444 GACGAGGTGTGAGGGAGAC 59.116 63.158 0.00 0.00 0.00 3.36
562 563 1.924320 GACGAGGTGTGAGGGAGACG 61.924 65.000 0.00 0.00 0.00 4.18
563 564 1.674651 CGAGGTGTGAGGGAGACGA 60.675 63.158 0.00 0.00 0.00 4.20
564 565 1.649390 CGAGGTGTGAGGGAGACGAG 61.649 65.000 0.00 0.00 0.00 4.18
565 566 1.304547 AGGTGTGAGGGAGACGAGG 60.305 63.158 0.00 0.00 0.00 4.63
566 567 2.574399 GTGTGAGGGAGACGAGGC 59.426 66.667 0.00 0.00 0.00 4.70
567 568 3.062466 TGTGAGGGAGACGAGGCG 61.062 66.667 0.00 0.00 0.00 5.52
568 569 3.827898 GTGAGGGAGACGAGGCGG 61.828 72.222 0.00 0.00 0.00 6.13
569 570 4.361971 TGAGGGAGACGAGGCGGT 62.362 66.667 0.00 0.00 0.00 5.68
570 571 3.827898 GAGGGAGACGAGGCGGTG 61.828 72.222 0.00 0.00 0.00 4.94
573 574 3.692406 GGAGACGAGGCGGTGGTT 61.692 66.667 0.00 0.00 0.00 3.67
574 575 2.432628 GAGACGAGGCGGTGGTTG 60.433 66.667 0.00 0.00 0.00 3.77
575 576 3.934391 GAGACGAGGCGGTGGTTGG 62.934 68.421 0.00 0.00 0.00 3.77
639 640 3.162202 GGGAACGAGTAGGTTTAGCTC 57.838 52.381 0.00 0.00 0.00 4.09
644 645 1.825077 GAGTAGGTTTAGCTCGACGC 58.175 55.000 0.00 0.00 39.57 5.19
645 646 0.455005 AGTAGGTTTAGCTCGACGCC 59.545 55.000 0.00 0.00 40.39 5.68
646 647 0.455005 GTAGGTTTAGCTCGACGCCT 59.545 55.000 0.00 0.00 40.39 5.52
647 648 0.737219 TAGGTTTAGCTCGACGCCTC 59.263 55.000 0.00 0.00 40.39 4.70
648 649 1.872679 GGTTTAGCTCGACGCCTCG 60.873 63.158 0.00 0.00 41.65 4.63
649 650 1.136147 GTTTAGCTCGACGCCTCGA 59.864 57.895 7.57 7.57 46.85 4.04
650 651 1.132780 GTTTAGCTCGACGCCTCGAC 61.133 60.000 3.56 2.39 44.14 4.20
651 652 2.262471 TTTAGCTCGACGCCTCGACC 62.262 60.000 3.56 0.00 44.14 4.79
702 703 2.824041 CCACCAGCCGCGCTAAAT 60.824 61.111 5.56 0.00 36.40 1.40
799 804 1.858458 GTGCGCGCTATAATGAGTTGA 59.142 47.619 33.29 3.26 0.00 3.18
906 911 0.111446 CTCCTCTCCGCCTCCTATGA 59.889 60.000 0.00 0.00 0.00 2.15
915 924 3.900892 CTCCTATGACCCGCGCGT 61.901 66.667 29.95 11.62 0.00 6.01
918 927 4.873129 CTATGACCCGCGCGTGCT 62.873 66.667 29.95 10.20 39.65 4.40
1111 1138 2.742372 GCCGCAGATGACCACGTT 60.742 61.111 0.00 0.00 0.00 3.99
1323 1356 4.680237 CACTCGTTGAGCCGGCCA 62.680 66.667 26.15 18.56 32.04 5.36
1499 1542 1.783979 ACTATGGGTGTTGGGTCCAAA 59.216 47.619 3.74 0.00 37.70 3.28
1509 1552 2.993220 GTTGGGTCCAAAAATTCGCATC 59.007 45.455 3.74 0.00 37.70 3.91
1543 1586 2.616960 TGACATCCATTTCGAAGACCG 58.383 47.619 0.00 0.00 34.32 4.79
1587 1630 4.373116 AGGGCATTGTCGACGCGT 62.373 61.111 13.85 13.85 0.00 6.01
1698 1741 5.303078 GGAGGTGATCAAAGTAGAGATGCTA 59.697 44.000 0.00 0.00 0.00 3.49
1731 1776 6.602179 CGAATGAAAGAACACTTTGATGCTA 58.398 36.000 0.00 0.00 34.54 3.49
1853 1898 4.715534 TGACAAGATTAACCCAAGTGGA 57.284 40.909 0.00 0.00 37.39 4.02
1948 1997 9.477484 TGCTAACTTGTTTTGTTTTTCTTGTAA 57.523 25.926 0.00 0.00 0.00 2.41
2011 2060 4.202716 ACAACCAAGAAGGGGAAGATCAAT 60.203 41.667 0.00 0.00 43.89 2.57
2029 2078 7.865820 AGATCAATAAAGGAAGGATCTTCACA 58.134 34.615 9.48 0.00 41.26 3.58
2121 2170 0.172127 TTGAGCAACAAACGCAAGCA 59.828 45.000 0.00 0.00 35.39 3.91
2290 2342 4.813809 AGAGGAAAGGAGATGATGAGCTA 58.186 43.478 0.00 0.00 0.00 3.32
2367 2419 1.856629 ATGGCAAGGAACCAAGATGG 58.143 50.000 0.00 0.00 45.02 3.51
2420 2514 0.813821 GAGGAAAGTGGCATTGGAGC 59.186 55.000 0.00 0.00 0.00 4.70
2443 2537 1.691219 GAAGGTGGGCATGGAGGAA 59.309 57.895 0.00 0.00 0.00 3.36
2510 2604 4.022935 ACACATCTTTGTTCAATGATGCGT 60.023 37.500 26.47 23.03 39.68 5.24
2749 2942 2.134287 ACCATCCGACGCTATGGCT 61.134 57.895 21.02 10.25 45.53 4.75
2847 3040 6.608610 CGTAAGTATTTCCCTCAGTTTTTGG 58.391 40.000 0.00 0.00 0.00 3.28
2945 3138 2.980568 ACGCGATTAGGGATTGTCAAA 58.019 42.857 15.93 0.00 36.53 2.69
3169 3365 9.174166 GTATTCTACAGTGGGTGAACAAATTAT 57.826 33.333 0.00 0.00 0.00 1.28
3295 3491 8.798402 GCATCTACTACTATTACTCCACTCATT 58.202 37.037 0.00 0.00 0.00 2.57
3417 3616 7.898636 TGATAAAAACCCCATCTTGTTATCCTT 59.101 33.333 0.00 0.00 0.00 3.36
3448 3647 2.465860 TACAATACGTGCCTTGCTGT 57.534 45.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.241317 CCGTAAAGAAATATAAGAGCGTTTAGA 57.759 33.333 0.00 0.00 0.00 2.10
2 3 9.241317 TCCGTAAAGAAATATAAGAGCGTTTAG 57.759 33.333 0.00 0.00 0.00 1.85
3 4 9.241317 CTCCGTAAAGAAATATAAGAGCGTTTA 57.759 33.333 0.00 0.00 0.00 2.01
4 5 7.224167 CCTCCGTAAAGAAATATAAGAGCGTTT 59.776 37.037 0.00 0.00 0.00 3.60
5 6 6.700520 CCTCCGTAAAGAAATATAAGAGCGTT 59.299 38.462 0.00 0.00 0.00 4.84
6 7 6.214399 CCTCCGTAAAGAAATATAAGAGCGT 58.786 40.000 0.00 0.00 0.00 5.07
7 8 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
8 9 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
9 10 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
10 11 7.562454 TGACTCCCTCCGTAAAGAAATATAAGA 59.438 37.037 0.00 0.00 0.00 2.10
11 12 7.723324 TGACTCCCTCCGTAAAGAAATATAAG 58.277 38.462 0.00 0.00 0.00 1.73
12 13 7.664552 TGACTCCCTCCGTAAAGAAATATAA 57.335 36.000 0.00 0.00 0.00 0.98
13 14 7.850935 ATGACTCCCTCCGTAAAGAAATATA 57.149 36.000 0.00 0.00 0.00 0.86
14 15 6.749036 ATGACTCCCTCCGTAAAGAAATAT 57.251 37.500 0.00 0.00 0.00 1.28
15 16 6.555463 AATGACTCCCTCCGTAAAGAAATA 57.445 37.500 0.00 0.00 0.00 1.40
16 17 5.437191 AATGACTCCCTCCGTAAAGAAAT 57.563 39.130 0.00 0.00 0.00 2.17
17 18 4.903045 AATGACTCCCTCCGTAAAGAAA 57.097 40.909 0.00 0.00 0.00 2.52
18 19 4.903045 AAATGACTCCCTCCGTAAAGAA 57.097 40.909 0.00 0.00 0.00 2.52
19 20 4.773674 TGTAAATGACTCCCTCCGTAAAGA 59.226 41.667 0.00 0.00 0.00 2.52
20 21 5.080969 TGTAAATGACTCCCTCCGTAAAG 57.919 43.478 0.00 0.00 0.00 1.85
21 22 5.486735 TTGTAAATGACTCCCTCCGTAAA 57.513 39.130 0.00 0.00 0.00 2.01
22 23 5.012354 ACTTTGTAAATGACTCCCTCCGTAA 59.988 40.000 0.00 0.00 0.00 3.18
23 24 4.529377 ACTTTGTAAATGACTCCCTCCGTA 59.471 41.667 0.00 0.00 0.00 4.02
24 25 3.326880 ACTTTGTAAATGACTCCCTCCGT 59.673 43.478 0.00 0.00 0.00 4.69
25 26 3.684788 CACTTTGTAAATGACTCCCTCCG 59.315 47.826 0.00 0.00 0.00 4.63
26 27 4.010349 CCACTTTGTAAATGACTCCCTCC 58.990 47.826 0.00 0.00 0.00 4.30
27 28 4.652822 ACCACTTTGTAAATGACTCCCTC 58.347 43.478 0.00 0.00 0.00 4.30
28 29 4.351111 AGACCACTTTGTAAATGACTCCCT 59.649 41.667 0.00 0.00 0.00 4.20
29 30 4.652822 AGACCACTTTGTAAATGACTCCC 58.347 43.478 0.00 0.00 0.00 4.30
30 31 6.369065 CAGTAGACCACTTTGTAAATGACTCC 59.631 42.308 0.00 0.00 34.26 3.85
31 32 6.128526 GCAGTAGACCACTTTGTAAATGACTC 60.129 42.308 0.00 0.00 34.26 3.36
32 33 5.701290 GCAGTAGACCACTTTGTAAATGACT 59.299 40.000 0.00 0.00 34.26 3.41
33 34 5.468746 TGCAGTAGACCACTTTGTAAATGAC 59.531 40.000 0.00 0.00 34.26 3.06
34 35 5.468746 GTGCAGTAGACCACTTTGTAAATGA 59.531 40.000 0.00 0.00 34.26 2.57
35 36 5.470098 AGTGCAGTAGACCACTTTGTAAATG 59.530 40.000 0.00 0.00 39.11 2.32
158 159 1.699634 CCTCAAGGTCACTTCCTCCAA 59.300 52.381 0.00 0.00 36.74 3.53
194 195 3.676049 CGCTCATCTACAAGGCTACAACA 60.676 47.826 0.00 0.00 0.00 3.33
311 312 2.515071 GCGGCCTGGAGGATCAGAT 61.515 63.158 0.00 0.00 36.93 2.90
352 353 2.994995 AGCCCCGTCATCGTCACA 60.995 61.111 0.00 0.00 35.01 3.58
445 446 3.203412 CCCTCCTCGACGTCCTCG 61.203 72.222 10.58 0.00 44.44 4.63
446 447 2.829458 CCCCTCCTCGACGTCCTC 60.829 72.222 10.58 0.00 0.00 3.71
447 448 4.444081 CCCCCTCCTCGACGTCCT 62.444 72.222 10.58 0.00 0.00 3.85
455 456 3.157949 CTTCCTCGCCCCCTCCTC 61.158 72.222 0.00 0.00 0.00 3.71
464 465 4.135153 TCCAGCTCGCTTCCTCGC 62.135 66.667 0.00 0.00 0.00 5.03
465 466 2.103934 CTCCAGCTCGCTTCCTCG 59.896 66.667 0.00 0.00 0.00 4.63
466 467 2.015227 CTCCTCCAGCTCGCTTCCTC 62.015 65.000 0.00 0.00 0.00 3.71
467 468 2.038007 TCCTCCAGCTCGCTTCCT 59.962 61.111 0.00 0.00 0.00 3.36
468 469 2.498726 CTCCTCCAGCTCGCTTCC 59.501 66.667 0.00 0.00 0.00 3.46
469 470 2.015227 CTCCTCCTCCAGCTCGCTTC 62.015 65.000 0.00 0.00 0.00 3.86
470 471 2.038007 TCCTCCTCCAGCTCGCTT 59.962 61.111 0.00 0.00 0.00 4.68
471 472 2.441901 CTCCTCCTCCAGCTCGCT 60.442 66.667 0.00 0.00 0.00 4.93
472 473 3.535962 CCTCCTCCTCCAGCTCGC 61.536 72.222 0.00 0.00 0.00 5.03
473 474 2.837291 CCCTCCTCCTCCAGCTCG 60.837 72.222 0.00 0.00 0.00 5.03
474 475 2.445654 CCCCTCCTCCTCCAGCTC 60.446 72.222 0.00 0.00 0.00 4.09
475 476 4.101077 CCCCCTCCTCCTCCAGCT 62.101 72.222 0.00 0.00 0.00 4.24
485 486 4.554036 GATCAGTGCGCCCCCTCC 62.554 72.222 4.18 0.00 0.00 4.30
486 487 3.474570 AGATCAGTGCGCCCCCTC 61.475 66.667 4.18 0.00 0.00 4.30
487 488 3.790437 CAGATCAGTGCGCCCCCT 61.790 66.667 4.18 0.00 0.00 4.79
488 489 4.101448 ACAGATCAGTGCGCCCCC 62.101 66.667 4.18 0.00 0.00 5.40
489 490 2.821366 CACAGATCAGTGCGCCCC 60.821 66.667 4.18 0.00 32.04 5.80
490 491 1.812922 CTCACAGATCAGTGCGCCC 60.813 63.158 13.08 0.00 39.35 6.13
491 492 1.812922 CCTCACAGATCAGTGCGCC 60.813 63.158 13.08 0.00 39.35 6.53
492 493 1.812922 CCCTCACAGATCAGTGCGC 60.813 63.158 13.08 0.00 39.35 6.09
493 494 1.153489 CCCCTCACAGATCAGTGCG 60.153 63.158 13.08 7.28 39.35 5.34
494 495 0.177604 CTCCCCTCACAGATCAGTGC 59.822 60.000 13.08 0.00 39.35 4.40
495 496 0.829333 CCTCCCCTCACAGATCAGTG 59.171 60.000 11.79 11.79 40.85 3.66
496 497 0.326048 CCCTCCCCTCACAGATCAGT 60.326 60.000 0.00 0.00 0.00 3.41
497 498 1.053264 CCCCTCCCCTCACAGATCAG 61.053 65.000 0.00 0.00 0.00 2.90
498 499 1.003442 CCCCTCCCCTCACAGATCA 59.997 63.158 0.00 0.00 0.00 2.92
499 500 0.264955 TACCCCTCCCCTCACAGATC 59.735 60.000 0.00 0.00 0.00 2.75
500 501 0.266152 CTACCCCTCCCCTCACAGAT 59.734 60.000 0.00 0.00 0.00 2.90
501 502 1.704082 CTACCCCTCCCCTCACAGA 59.296 63.158 0.00 0.00 0.00 3.41
502 503 1.383248 CCTACCCCTCCCCTCACAG 60.383 68.421 0.00 0.00 0.00 3.66
503 504 2.784984 CCTACCCCTCCCCTCACA 59.215 66.667 0.00 0.00 0.00 3.58
504 505 2.040779 CCCTACCCCTCCCCTCAC 60.041 72.222 0.00 0.00 0.00 3.51
505 506 3.373846 CCCCTACCCCTCCCCTCA 61.374 72.222 0.00 0.00 0.00 3.86
506 507 3.040814 TCCCCTACCCCTCCCCTC 61.041 72.222 0.00 0.00 0.00 4.30
507 508 3.043404 CTCCCCTACCCCTCCCCT 61.043 72.222 0.00 0.00 0.00 4.79
508 509 3.040814 TCTCCCCTACCCCTCCCC 61.041 72.222 0.00 0.00 0.00 4.81
509 510 2.615773 CTCTCCCCTACCCCTCCC 59.384 72.222 0.00 0.00 0.00 4.30
510 511 2.615773 CCTCTCCCCTACCCCTCC 59.384 72.222 0.00 0.00 0.00 4.30
511 512 2.019272 TCCCTCTCCCCTACCCCTC 61.019 68.421 0.00 0.00 0.00 4.30
512 513 2.021652 CTCCCTCTCCCCTACCCCT 61.022 68.421 0.00 0.00 0.00 4.79
513 514 2.019272 TCTCCCTCTCCCCTACCCC 61.019 68.421 0.00 0.00 0.00 4.95
514 515 1.544703 CTCTCCCTCTCCCCTACCC 59.455 68.421 0.00 0.00 0.00 3.69
515 516 1.544703 CCTCTCCCTCTCCCCTACC 59.455 68.421 0.00 0.00 0.00 3.18
516 517 1.544703 CCCTCTCCCTCTCCCCTAC 59.455 68.421 0.00 0.00 0.00 3.18
517 518 2.404750 GCCCTCTCCCTCTCCCCTA 61.405 68.421 0.00 0.00 0.00 3.53
518 519 3.773154 GCCCTCTCCCTCTCCCCT 61.773 72.222 0.00 0.00 0.00 4.79
520 521 2.987355 CTACGCCCTCTCCCTCTCCC 62.987 70.000 0.00 0.00 0.00 4.30
521 522 1.529713 CTACGCCCTCTCCCTCTCC 60.530 68.421 0.00 0.00 0.00 3.71
522 523 1.529713 CCTACGCCCTCTCCCTCTC 60.530 68.421 0.00 0.00 0.00 3.20
523 524 2.604152 CCTACGCCCTCTCCCTCT 59.396 66.667 0.00 0.00 0.00 3.69
524 525 3.228017 GCCTACGCCCTCTCCCTC 61.228 72.222 0.00 0.00 0.00 4.30
534 535 4.849329 CACCTCGTCGGCCTACGC 62.849 72.222 23.98 0.00 42.56 4.42
535 536 3.437795 ACACCTCGTCGGCCTACG 61.438 66.667 22.93 22.93 44.19 3.51
536 537 2.181021 CACACCTCGTCGGCCTAC 59.819 66.667 0.00 0.00 35.61 3.18
537 538 2.034532 TCACACCTCGTCGGCCTA 59.965 61.111 0.00 0.00 35.61 3.93
538 539 3.374402 CTCACACCTCGTCGGCCT 61.374 66.667 0.00 0.00 35.61 5.19
539 540 4.436998 CCTCACACCTCGTCGGCC 62.437 72.222 0.00 0.00 35.61 6.13
540 541 4.436998 CCCTCACACCTCGTCGGC 62.437 72.222 0.00 0.00 35.61 5.54
541 542 2.675423 TCCCTCACACCTCGTCGG 60.675 66.667 0.00 0.00 39.35 4.79
542 543 1.674651 TCTCCCTCACACCTCGTCG 60.675 63.158 0.00 0.00 0.00 5.12
543 544 1.884444 GTCTCCCTCACACCTCGTC 59.116 63.158 0.00 0.00 0.00 4.20
544 545 1.972223 CGTCTCCCTCACACCTCGT 60.972 63.158 0.00 0.00 0.00 4.18
545 546 1.649390 CTCGTCTCCCTCACACCTCG 61.649 65.000 0.00 0.00 0.00 4.63
546 547 1.316706 CCTCGTCTCCCTCACACCTC 61.317 65.000 0.00 0.00 0.00 3.85
547 548 1.304547 CCTCGTCTCCCTCACACCT 60.305 63.158 0.00 0.00 0.00 4.00
548 549 3.007973 GCCTCGTCTCCCTCACACC 62.008 68.421 0.00 0.00 0.00 4.16
549 550 2.574399 GCCTCGTCTCCCTCACAC 59.426 66.667 0.00 0.00 0.00 3.82
550 551 3.062466 CGCCTCGTCTCCCTCACA 61.062 66.667 0.00 0.00 0.00 3.58
551 552 3.827898 CCGCCTCGTCTCCCTCAC 61.828 72.222 0.00 0.00 0.00 3.51
552 553 4.361971 ACCGCCTCGTCTCCCTCA 62.362 66.667 0.00 0.00 0.00 3.86
553 554 3.827898 CACCGCCTCGTCTCCCTC 61.828 72.222 0.00 0.00 0.00 4.30
556 557 3.692406 AACCACCGCCTCGTCTCC 61.692 66.667 0.00 0.00 0.00 3.71
557 558 2.432628 CAACCACCGCCTCGTCTC 60.433 66.667 0.00 0.00 0.00 3.36
558 559 4.003788 CCAACCACCGCCTCGTCT 62.004 66.667 0.00 0.00 0.00 4.18
617 618 1.474077 GCTAAACCTACTCGTTCCCGA 59.526 52.381 0.00 0.00 41.73 5.14
618 619 1.475682 AGCTAAACCTACTCGTTCCCG 59.524 52.381 0.00 0.00 0.00 5.14
619 620 2.479219 CGAGCTAAACCTACTCGTTCCC 60.479 54.545 3.61 0.00 46.19 3.97
620 621 2.795117 CGAGCTAAACCTACTCGTTCC 58.205 52.381 3.61 0.00 46.19 3.62
625 626 1.825077 GCGTCGAGCTAAACCTACTC 58.175 55.000 0.00 0.00 44.04 2.59
641 642 4.816984 ATCGAGGGGTCGAGGCGT 62.817 66.667 3.65 0.00 45.70 5.68
642 643 4.271816 CATCGAGGGGTCGAGGCG 62.272 72.222 3.65 0.00 45.70 5.52
643 644 3.917760 CCATCGAGGGGTCGAGGC 61.918 72.222 8.61 0.00 45.70 4.70
668 669 3.072915 TGGTGGAGATGCTCTGAGAAAAA 59.927 43.478 9.28 0.00 0.00 1.94
669 670 2.639347 TGGTGGAGATGCTCTGAGAAAA 59.361 45.455 9.28 0.00 0.00 2.29
670 671 2.235650 CTGGTGGAGATGCTCTGAGAAA 59.764 50.000 9.28 0.00 0.00 2.52
671 672 1.829849 CTGGTGGAGATGCTCTGAGAA 59.170 52.381 9.28 0.00 0.00 2.87
672 673 1.482954 CTGGTGGAGATGCTCTGAGA 58.517 55.000 9.28 0.00 0.00 3.27
688 689 1.279840 GCTAATTTAGCGCGGCTGG 59.720 57.895 12.39 0.00 42.62 4.85
780 785 2.127251 CTCAACTCATTATAGCGCGCA 58.873 47.619 35.10 19.76 0.00 6.09
1009 1036 4.137872 CCGCGCTAGGGTTTCCGA 62.138 66.667 5.56 0.00 38.33 4.55
1337 1370 0.671251 GGGGCATTTCGTCAAACACA 59.329 50.000 0.00 0.00 0.00 3.72
1499 1542 2.161609 GGTTTGAGACCGATGCGAATTT 59.838 45.455 0.00 0.00 39.00 1.82
1509 1552 6.835320 AATGGATGTCATTGGTTTGAGACCG 61.835 44.000 0.00 0.00 43.85 4.79
1543 1586 1.605712 CCTCGTCCACCTCAAACTCAC 60.606 57.143 0.00 0.00 0.00 3.51
1587 1630 2.107041 TTGCCCGCTCTTCCTTTCGA 62.107 55.000 0.00 0.00 0.00 3.71
1698 1741 2.230130 TCTTTCATTCGCCCCCAATT 57.770 45.000 0.00 0.00 0.00 2.32
1731 1776 2.616842 GGTCAATTCCACTCACGTTGTT 59.383 45.455 0.00 0.00 0.00 2.83
1853 1898 7.989741 CCACTTACTCTATCATCCTCATTTGTT 59.010 37.037 0.00 0.00 0.00 2.83
1948 1997 6.815641 TGAACAAGTTTTGTGCAATGTTGTAT 59.184 30.769 0.16 0.84 46.01 2.29
2011 2060 4.949856 GGCAATGTGAAGATCCTTCCTTTA 59.050 41.667 4.48 0.00 0.00 1.85
2029 2078 4.275810 ACACTTCATAGCAATGAGGCAAT 58.724 39.130 0.00 0.00 42.97 3.56
2121 2170 8.033038 CCTCATCATCATTCAACTCAATTGTTT 58.967 33.333 5.13 0.00 39.54 2.83
2367 2419 3.708220 CTTCTCTCCTCGGCCGCAC 62.708 68.421 23.51 0.00 0.00 5.34
2420 2514 1.077212 CCATGCCCACCTTCCTCTG 60.077 63.158 0.00 0.00 0.00 3.35
2443 2537 3.074412 CCATTCCAACAACTTAGCTCGT 58.926 45.455 0.00 0.00 0.00 4.18
2510 2604 5.420739 GGGCAAGGTTGACATATTCCTTTTA 59.579 40.000 0.00 0.00 38.18 1.52
2734 2927 2.029666 GCAGCCATAGCGTCGGAT 59.970 61.111 0.00 0.00 46.67 4.18
2749 2942 2.679342 GGTAGCACCTCCCATGGCA 61.679 63.158 6.09 0.00 34.73 4.92
2847 3040 4.236527 ACTGGATTGATACCTTGGTTCC 57.763 45.455 0.00 0.00 0.00 3.62
2945 3138 0.316204 CGTAAGTGACCGTGAAGGGT 59.684 55.000 0.00 0.00 46.96 4.34
3169 3365 7.031372 GCTCAATTCTATCAATTGCTCAACAA 58.969 34.615 0.00 0.00 44.01 2.83
3214 3410 6.254373 GTGATGCCTATACACATGATCATACG 59.746 42.308 8.15 4.95 35.06 3.06
3295 3491 1.048160 TGCATCCTGGATAGCGGTCA 61.048 55.000 9.27 0.00 0.00 4.02
3417 3616 4.438065 GCACGTATTGTATTGTTGCCATCA 60.438 41.667 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.