Multiple sequence alignment - TraesCS4A01G200400

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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 TraesCS4A01G200400 chr4A 100.000 3193 0 0 1 3193 489082272 489085464 0.000000e+00 5897.0
1 TraesCS4A01G200400 chr4A 94.196 672 36 3 1 670 489065812 489066482 0.000000e+00 1022.0
2 TraesCS4A01G200400 chr4A 89.879 662 61 6 13 670 286869257 286869916 0.000000e+00 846.0
3 TraesCS4A01G200400 chr4A 89.728 662 62 6 13 670 286861205 286861864 0.000000e+00 841.0
4 TraesCS4A01G200400 chr4A 86.314 643 74 7 2553 3193 690146461 690147091 0.000000e+00 688.0
5 TraesCS4A01G200400 chr4D 96.057 1750 45 8 670 2395 93347400 93345651 0.000000e+00 2828.0
6 TraesCS4A01G200400 chr4B 94.585 1736 56 14 723 2446 131167975 131166266 0.000000e+00 2651.0
7 TraesCS4A01G200400 chr6A 93.016 673 43 4 1 670 312797112 312797783 0.000000e+00 979.0
8 TraesCS4A01G200400 chr6A 92.239 670 48 4 1 667 262278760 262279428 0.000000e+00 946.0
9 TraesCS4A01G200400 chr6A 88.589 666 64 11 12 670 568526940 568526280 0.000000e+00 798.0
10 TraesCS4A01G200400 chr6A 83.844 588 80 9 2610 3193 59825702 59826278 2.170000e-151 545.0
11 TraesCS4A01G200400 chr3A 89.164 646 63 7 26 666 226942881 226943524 0.000000e+00 798.0
12 TraesCS4A01G200400 chr7A 87.856 667 71 9 4 666 36105184 36104524 0.000000e+00 774.0
13 TraesCS4A01G200400 chr7A 87.798 672 69 12 1 666 316067424 316066760 0.000000e+00 774.0
14 TraesCS4A01G200400 chr7B 86.244 647 70 11 2553 3193 24413758 24414391 0.000000e+00 684.0
15 TraesCS4A01G200400 chr7B 85.317 647 76 12 2553 3193 742229017 742229650 0.000000e+00 651.0
16 TraesCS4A01G200400 chr7B 84.175 594 72 11 2611 3193 63626318 63626900 1.000000e-154 556.0
17 TraesCS4A01G200400 chr7B 96.970 33 1 0 2545 2577 725314760 725314792 4.450000e-04 56.5
18 TraesCS4A01G200400 chr7D 86.159 643 72 11 2553 3193 39020634 39020007 0.000000e+00 678.0
19 TraesCS4A01G200400 chr7D 93.023 43 1 2 2536 2577 625370896 625370937 9.560000e-06 62.1
20 TraesCS4A01G200400 chr1A 84.603 643 85 8 2553 3193 518086579 518085949 7.520000e-176 627.0
21 TraesCS4A01G200400 chr3D 84.409 635 73 15 2565 3193 497807781 497808395 4.560000e-168 601.0
22 TraesCS4A01G200400 chr2D 87.500 496 49 8 2700 3193 608513651 608513167 7.730000e-156 560.0
23 TraesCS4A01G200400 chr2D 82.529 601 89 7 2596 3193 110022695 110022108 6.110000e-142 514.0
24 TraesCS4A01G200400 chrUn 100.000 33 0 0 2545 2577 87733821 87733789 9.560000e-06 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 TraesCS4A01G200400 chr4A 489082272 489085464 3192 False 5897 5897 100.000 1 3193 1 chr4A.!!$F4 3192
1 TraesCS4A01G200400 chr4A 489065812 489066482 670 False 1022 1022 94.196 1 670 1 chr4A.!!$F3 669
2 TraesCS4A01G200400 chr4A 286869257 286869916 659 False 846 846 89.879 13 670 1 chr4A.!!$F2 657
3 TraesCS4A01G200400 chr4A 286861205 286861864 659 False 841 841 89.728 13 670 1 chr4A.!!$F1 657
4 TraesCS4A01G200400 chr4A 690146461 690147091 630 False 688 688 86.314 2553 3193 1 chr4A.!!$F5 640
5 TraesCS4A01G200400 chr4D 93345651 93347400 1749 True 2828 2828 96.057 670 2395 1 chr4D.!!$R1 1725
6 TraesCS4A01G200400 chr4B 131166266 131167975 1709 True 2651 2651 94.585 723 2446 1 chr4B.!!$R1 1723
7 TraesCS4A01G200400 chr6A 312797112 312797783 671 False 979 979 93.016 1 670 1 chr6A.!!$F3 669
8 TraesCS4A01G200400 chr6A 262278760 262279428 668 False 946 946 92.239 1 667 1 chr6A.!!$F2 666
9 TraesCS4A01G200400 chr6A 568526280 568526940 660 True 798 798 88.589 12 670 1 chr6A.!!$R1 658
10 TraesCS4A01G200400 chr6A 59825702 59826278 576 False 545 545 83.844 2610 3193 1 chr6A.!!$F1 583
11 TraesCS4A01G200400 chr3A 226942881 226943524 643 False 798 798 89.164 26 666 1 chr3A.!!$F1 640
12 TraesCS4A01G200400 chr7A 36104524 36105184 660 True 774 774 87.856 4 666 1 chr7A.!!$R1 662
13 TraesCS4A01G200400 chr7A 316066760 316067424 664 True 774 774 87.798 1 666 1 chr7A.!!$R2 665
14 TraesCS4A01G200400 chr7B 24413758 24414391 633 False 684 684 86.244 2553 3193 1 chr7B.!!$F1 640
15 TraesCS4A01G200400 chr7B 742229017 742229650 633 False 651 651 85.317 2553 3193 1 chr7B.!!$F4 640
16 TraesCS4A01G200400 chr7B 63626318 63626900 582 False 556 556 84.175 2611 3193 1 chr7B.!!$F2 582
17 TraesCS4A01G200400 chr7D 39020007 39020634 627 True 678 678 86.159 2553 3193 1 chr7D.!!$R1 640
18 TraesCS4A01G200400 chr1A 518085949 518086579 630 True 627 627 84.603 2553 3193 1 chr1A.!!$R1 640
19 TraesCS4A01G200400 chr3D 497807781 497808395 614 False 601 601 84.409 2565 3193 1 chr3D.!!$F1 628
20 TraesCS4A01G200400 chr2D 110022108 110022695 587 True 514 514 82.529 2596 3193 1 chr2D.!!$R1 597

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
443 450 0.179200 CGAAGAACATTTTCCGGCCG 60.179 55.000 21.04 21.04 31.28 6.13 F
674 685 1.302192 GGGCGTCACAGCACCTTAA 60.302 57.895 0.00 0.00 39.27 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1337 1364 0.895530 GACCGATGGAGGTGAGAACA 59.104 55.0 0.0 0.0 46.09 3.18 R
2489 2530 0.517316 GCTTCACCTTGTTGCGTAGG 59.483 55.0 0.0 0.0 37.56 3.18 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
66 69 7.909485 AAAATAGTTAGGGAGTCCGAATAGA 57.091 36.000 2.26 0.00 38.33 1.98
67 70 7.909485 AAATAGTTAGGGAGTCCGAATAGAA 57.091 36.000 2.26 0.00 38.33 2.10
262 267 2.926329 AGAGAAGAGAAGAGAGGGAGGT 59.074 50.000 0.00 0.00 0.00 3.85
269 274 2.829458 GAGAGGGAGGTCCGACGG 60.829 72.222 7.84 7.84 41.52 4.79
278 283 2.029964 GTCCGACGGCTGTTTCCA 59.970 61.111 9.66 0.00 0.00 3.53
406 413 6.028146 TCTACACTAAAATAAGACCGCACA 57.972 37.500 0.00 0.00 0.00 4.57
425 432 2.360801 ACACCAACTTTCAACCCATTCG 59.639 45.455 0.00 0.00 0.00 3.34
443 450 0.179200 CGAAGAACATTTTCCGGCCG 60.179 55.000 21.04 21.04 31.28 6.13
575 585 5.242838 ACATGATGATGCAATGCACATGATA 59.757 36.000 30.27 16.37 43.04 2.15
621 632 3.195396 ACAAATGACAAGGCAACAACAGT 59.805 39.130 0.00 0.00 41.41 3.55
674 685 1.302192 GGGCGTCACAGCACCTTAA 60.302 57.895 0.00 0.00 39.27 1.85
686 697 4.154195 ACAGCACCTTAAATCATTGTCGTC 59.846 41.667 0.00 0.00 0.00 4.20
803 829 8.491958 GGAAATAGAACTACTCCTATTTTGGGA 58.508 37.037 0.00 0.00 42.39 4.37
810 836 8.581253 AACTACTCCTATTTTGGGAAATCAAG 57.419 34.615 0.00 0.00 36.82 3.02
901 928 2.597217 CCCAGCTCGGTTTTGCCA 60.597 61.111 0.00 0.00 36.97 4.92
941 968 2.026301 GGCTTCGATCGACCCTCG 59.974 66.667 19.26 5.32 42.10 4.63
1337 1364 2.181021 GGCGTCGATGACTCCGTT 59.819 61.111 9.31 0.00 27.57 4.44
1676 1703 1.139095 GGACCAGACCATCGACGTC 59.861 63.158 5.18 5.18 0.00 4.34
1991 2018 2.969016 CGTCTGCTGCTCAGGTCT 59.031 61.111 0.00 0.00 43.06 3.85
1993 2020 1.871126 CGTCTGCTGCTCAGGTCTGA 61.871 60.000 0.00 0.45 43.06 3.27
1997 2024 2.125753 CTGCTCAGGTCTGACGGC 60.126 66.667 1.07 1.38 35.46 5.68
2172 2199 3.888930 GCGAAGGATGATGGGGATAAAAA 59.111 43.478 0.00 0.00 0.00 1.94
2266 2296 1.000385 CATCAGGCTCTCGTCAGATCC 60.000 57.143 0.00 0.00 35.40 3.36
2303 2333 5.708948 CTCCGTCATAGAAATCTCTGATCC 58.291 45.833 2.37 0.00 32.79 3.36
2411 2452 8.931385 ATACTAAAGCTGTGCCAATTAATTTG 57.069 30.769 0.00 0.00 34.93 2.32
2428 2469 9.927668 AATTAATTTGGATTGAAACAGTACTGG 57.072 29.630 26.12 9.07 34.19 4.00
2431 2472 8.650143 AATTTGGATTGAAACAGTACTGGTAT 57.350 30.769 26.12 11.01 34.19 2.73
2446 2487 8.142551 CAGTACTGGTATAGTTTTATCAGTCCC 58.857 40.741 15.49 0.00 40.89 4.46
2447 2488 7.842743 AGTACTGGTATAGTTTTATCAGTCCCA 59.157 37.037 0.00 0.00 40.89 4.37
2448 2489 7.691993 ACTGGTATAGTTTTATCAGTCCCAT 57.308 36.000 0.00 0.00 35.67 4.00
2449 2490 7.509546 ACTGGTATAGTTTTATCAGTCCCATG 58.490 38.462 0.00 0.00 35.67 3.66
2450 2491 6.837312 TGGTATAGTTTTATCAGTCCCATGG 58.163 40.000 4.14 4.14 0.00 3.66
2451 2492 5.705905 GGTATAGTTTTATCAGTCCCATGGC 59.294 44.000 6.09 0.00 0.00 4.40
2452 2493 5.653255 ATAGTTTTATCAGTCCCATGGCT 57.347 39.130 6.09 0.00 0.00 4.75
2453 2494 3.624777 AGTTTTATCAGTCCCATGGCTG 58.375 45.455 6.09 9.72 0.00 4.85
2454 2495 2.057137 TTTATCAGTCCCATGGCTGC 57.943 50.000 6.09 0.00 33.09 5.25
2455 2496 0.918258 TTATCAGTCCCATGGCTGCA 59.082 50.000 6.09 0.58 33.09 4.41
2456 2497 0.918258 TATCAGTCCCATGGCTGCAA 59.082 50.000 6.09 0.00 33.09 4.08
2457 2498 0.682209 ATCAGTCCCATGGCTGCAAC 60.682 55.000 6.09 0.00 33.09 4.17
2458 2499 1.604308 CAGTCCCATGGCTGCAACA 60.604 57.895 6.09 0.00 0.00 3.33
2459 2500 0.968901 CAGTCCCATGGCTGCAACAT 60.969 55.000 6.09 0.00 0.00 2.71
2460 2501 0.625316 AGTCCCATGGCTGCAACATA 59.375 50.000 6.09 0.00 0.00 2.29
2461 2502 1.027357 GTCCCATGGCTGCAACATAG 58.973 55.000 6.09 0.00 0.00 2.23
2462 2503 0.918258 TCCCATGGCTGCAACATAGA 59.082 50.000 6.09 2.17 0.00 1.98
2463 2504 1.027357 CCCATGGCTGCAACATAGAC 58.973 55.000 6.09 0.00 0.00 2.59
2464 2505 1.682702 CCCATGGCTGCAACATAGACA 60.683 52.381 6.09 0.00 37.63 3.41
2465 2506 2.304092 CCATGGCTGCAACATAGACAT 58.696 47.619 0.00 0.00 44.59 3.06
2467 2508 1.097232 TGGCTGCAACATAGACATGC 58.903 50.000 0.50 0.00 40.45 4.06
2468 2509 1.340308 TGGCTGCAACATAGACATGCT 60.340 47.619 0.50 0.00 40.66 3.79
2469 2510 1.747355 GGCTGCAACATAGACATGCTT 59.253 47.619 0.50 0.00 40.66 3.91
2470 2511 2.165030 GGCTGCAACATAGACATGCTTT 59.835 45.455 0.50 0.00 40.66 3.51
2471 2512 3.176708 GCTGCAACATAGACATGCTTTG 58.823 45.455 0.00 0.00 40.66 2.77
2472 2513 3.766151 CTGCAACATAGACATGCTTTGG 58.234 45.455 0.00 0.00 40.66 3.28
2473 2514 3.156293 TGCAACATAGACATGCTTTGGT 58.844 40.909 0.00 0.00 40.66 3.67
2474 2515 4.331108 TGCAACATAGACATGCTTTGGTA 58.669 39.130 0.00 0.00 40.66 3.25
2475 2516 4.395854 TGCAACATAGACATGCTTTGGTAG 59.604 41.667 0.00 0.00 40.66 3.18
2476 2517 4.396166 GCAACATAGACATGCTTTGGTAGT 59.604 41.667 0.00 0.00 37.12 2.73
2477 2518 5.674569 GCAACATAGACATGCTTTGGTAGTG 60.675 44.000 0.00 0.00 37.12 2.74
2478 2519 5.165961 ACATAGACATGCTTTGGTAGTGT 57.834 39.130 0.00 0.00 35.39 3.55
2479 2520 6.294361 ACATAGACATGCTTTGGTAGTGTA 57.706 37.500 0.00 0.00 35.39 2.90
2480 2521 6.106673 ACATAGACATGCTTTGGTAGTGTAC 58.893 40.000 0.00 0.00 35.39 2.90
2481 2522 4.617253 AGACATGCTTTGGTAGTGTACA 57.383 40.909 0.00 0.00 0.00 2.90
2482 2523 4.315803 AGACATGCTTTGGTAGTGTACAC 58.684 43.478 18.56 18.56 0.00 2.90
2483 2524 4.040461 AGACATGCTTTGGTAGTGTACACT 59.960 41.667 30.13 30.13 45.02 3.55
2484 2525 4.714632 ACATGCTTTGGTAGTGTACACTT 58.285 39.130 32.15 16.83 42.54 3.16
2485 2526 4.515191 ACATGCTTTGGTAGTGTACACTTG 59.485 41.667 32.15 21.95 42.54 3.16
2486 2527 4.145365 TGCTTTGGTAGTGTACACTTGT 57.855 40.909 32.15 12.46 42.54 3.16
2487 2528 5.279255 TGCTTTGGTAGTGTACACTTGTA 57.721 39.130 32.15 13.27 42.54 2.41
2488 2529 5.860611 TGCTTTGGTAGTGTACACTTGTAT 58.139 37.500 32.15 11.70 42.54 2.29
2489 2530 5.929992 TGCTTTGGTAGTGTACACTTGTATC 59.070 40.000 32.15 16.30 42.54 2.24
2490 2531 5.350640 GCTTTGGTAGTGTACACTTGTATCC 59.649 44.000 32.15 23.51 42.54 2.59
2491 2532 6.675413 TTTGGTAGTGTACACTTGTATCCT 57.325 37.500 32.15 9.47 42.54 3.24
2492 2533 7.578189 GCTTTGGTAGTGTACACTTGTATCCTA 60.578 40.741 32.15 18.99 42.54 2.94
2493 2534 6.764308 TGGTAGTGTACACTTGTATCCTAC 57.236 41.667 32.15 20.56 42.54 3.18
2494 2535 5.355071 TGGTAGTGTACACTTGTATCCTACG 59.645 44.000 32.15 0.00 42.54 3.51
2495 2536 4.367386 AGTGTACACTTGTATCCTACGC 57.633 45.455 22.95 0.00 38.83 4.42
2496 2537 3.760151 AGTGTACACTTGTATCCTACGCA 59.240 43.478 22.95 0.00 38.83 5.24
2497 2538 4.219070 AGTGTACACTTGTATCCTACGCAA 59.781 41.667 22.95 0.00 38.83 4.85
2498 2539 4.325472 GTGTACACTTGTATCCTACGCAAC 59.675 45.833 18.92 0.00 32.54 4.17
2499 2540 3.671008 ACACTTGTATCCTACGCAACA 57.329 42.857 0.00 0.00 0.00 3.33
2500 2541 3.997762 ACACTTGTATCCTACGCAACAA 58.002 40.909 0.00 0.00 0.00 2.83
2503 2544 3.596214 CTTGTATCCTACGCAACAAGGT 58.404 45.455 6.23 0.00 43.17 3.50
2504 2545 2.967362 TGTATCCTACGCAACAAGGTG 58.033 47.619 0.00 0.00 34.30 4.00
2505 2546 2.563620 TGTATCCTACGCAACAAGGTGA 59.436 45.455 0.00 0.00 34.30 4.02
2506 2547 2.851263 ATCCTACGCAACAAGGTGAA 57.149 45.000 0.00 0.00 34.30 3.18
2507 2548 2.163818 TCCTACGCAACAAGGTGAAG 57.836 50.000 0.00 0.00 34.30 3.02
2508 2549 0.517316 CCTACGCAACAAGGTGAAGC 59.483 55.000 0.00 0.00 0.00 3.86
2509 2550 1.225855 CTACGCAACAAGGTGAAGCA 58.774 50.000 0.00 0.00 0.00 3.91
2510 2551 1.601903 CTACGCAACAAGGTGAAGCAA 59.398 47.619 0.00 0.00 0.00 3.91
2511 2552 0.814457 ACGCAACAAGGTGAAGCAAA 59.186 45.000 0.00 0.00 0.00 3.68
2512 2553 1.203523 ACGCAACAAGGTGAAGCAAAA 59.796 42.857 0.00 0.00 0.00 2.44
2513 2554 2.266554 CGCAACAAGGTGAAGCAAAAA 58.733 42.857 0.00 0.00 0.00 1.94
2531 2572 4.563140 AAAAAGATACGGCTAGGGTTCA 57.437 40.909 0.00 0.00 0.00 3.18
2532 2573 3.821421 AAAGATACGGCTAGGGTTCAG 57.179 47.619 0.00 0.00 0.00 3.02
2533 2574 2.456073 AGATACGGCTAGGGTTCAGT 57.544 50.000 0.00 0.00 0.00 3.41
2534 2575 3.589951 AGATACGGCTAGGGTTCAGTA 57.410 47.619 0.00 0.00 0.00 2.74
2535 2576 3.488363 AGATACGGCTAGGGTTCAGTAG 58.512 50.000 0.00 0.00 0.00 2.57
2536 2577 3.137913 AGATACGGCTAGGGTTCAGTAGA 59.862 47.826 0.00 0.00 0.00 2.59
2537 2578 2.226962 ACGGCTAGGGTTCAGTAGAA 57.773 50.000 0.00 0.00 0.00 2.10
2538 2579 2.532843 ACGGCTAGGGTTCAGTAGAAA 58.467 47.619 0.00 0.00 35.08 2.52
2539 2580 2.496470 ACGGCTAGGGTTCAGTAGAAAG 59.504 50.000 0.00 0.00 35.08 2.62
2540 2581 2.159085 CGGCTAGGGTTCAGTAGAAAGG 60.159 54.545 0.00 0.00 35.08 3.11
2541 2582 2.420269 GGCTAGGGTTCAGTAGAAAGGC 60.420 54.545 0.00 0.00 35.08 4.35
2542 2583 2.236395 GCTAGGGTTCAGTAGAAAGGCA 59.764 50.000 0.00 0.00 35.08 4.75
2543 2584 3.118223 GCTAGGGTTCAGTAGAAAGGCAT 60.118 47.826 0.00 0.00 35.08 4.40
2544 2585 3.356529 AGGGTTCAGTAGAAAGGCATG 57.643 47.619 0.00 0.00 35.08 4.06
2545 2586 2.644798 AGGGTTCAGTAGAAAGGCATGT 59.355 45.455 0.00 0.00 35.08 3.21
2546 2587 3.074538 AGGGTTCAGTAGAAAGGCATGTT 59.925 43.478 0.00 0.00 35.08 2.71
2547 2588 3.826729 GGGTTCAGTAGAAAGGCATGTTT 59.173 43.478 0.00 0.00 35.08 2.83
2548 2589 4.082733 GGGTTCAGTAGAAAGGCATGTTTC 60.083 45.833 0.00 0.00 35.08 2.78
2549 2590 4.082733 GGTTCAGTAGAAAGGCATGTTTCC 60.083 45.833 5.43 0.00 37.16 3.13
2550 2591 4.640771 TCAGTAGAAAGGCATGTTTCCT 57.359 40.909 5.43 0.00 37.16 3.36
2551 2592 4.579869 TCAGTAGAAAGGCATGTTTCCTC 58.420 43.478 5.43 0.96 37.16 3.71
2567 2608 1.079503 CCTCTTTGGCTAGCGACAAC 58.920 55.000 9.00 0.00 38.04 3.32
2582 2625 3.633116 AACAACCCTAGCCGCCGT 61.633 61.111 0.00 0.00 0.00 5.68
2591 2634 1.658686 CTAGCCGCCGTCAAGAGAGT 61.659 60.000 0.00 0.00 0.00 3.24
2596 2639 1.009389 CGCCGTCAAGAGAGTCAACC 61.009 60.000 0.00 0.00 0.00 3.77
2642 2685 1.030488 CCTCCGCTGACGACCTCTTA 61.030 60.000 0.00 0.00 43.93 2.10
2693 2741 2.672188 CGTGTGTGCGGATTGTTTTA 57.328 45.000 0.00 0.00 0.00 1.52
2694 2742 2.303537 CGTGTGTGCGGATTGTTTTAC 58.696 47.619 0.00 0.00 0.00 2.01
2719 2768 6.610425 CCTTTAGGTTTTAGAGCCCTAGTAGA 59.390 42.308 0.00 0.00 32.64 2.59
2808 2863 8.637196 AATAAAGAAGGTTCGGATTTTTCTCT 57.363 30.769 0.00 0.00 0.00 3.10
2811 2866 3.073274 AGGTTCGGATTTTTCTCTGGG 57.927 47.619 0.00 0.00 0.00 4.45
2846 2902 5.539955 TCTCTATGGTCGATGATGGATTTGA 59.460 40.000 0.00 0.00 0.00 2.69
2951 3007 2.390599 GCATTTGCTCCAGCGTCGA 61.391 57.895 0.00 0.00 45.83 4.20
2953 3009 1.005037 ATTTGCTCCAGCGTCGACA 60.005 52.632 17.16 0.00 45.83 4.35
2975 3031 2.180276 GGAGCTTGAGAGGTAGTCCAA 58.820 52.381 0.00 0.00 32.79 3.53
3041 3097 1.944024 GAACGTGTGTTGGGTTCATGA 59.056 47.619 0.00 0.00 38.78 3.07
3049 3105 3.511146 GTGTTGGGTTCATGATTGATGGT 59.489 43.478 0.00 0.00 32.26 3.55
3052 3108 3.777087 TGGGTTCATGATTGATGGTTGT 58.223 40.909 0.00 0.00 32.26 3.32
3165 3224 1.234821 TCAACGACAATGGCTTCACC 58.765 50.000 0.00 0.00 39.84 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 69 5.163733 ACGTCTACAAAACATCACCGTTTTT 60.164 36.000 0.00 0.00 44.61 1.94
126 130 3.918328 ATTGTCCCGGACCGACCCT 62.918 63.158 17.49 0.00 34.64 4.34
269 274 6.818145 CGTTTTTCGGTCTCTGGAAACAGC 62.818 50.000 0.00 0.00 46.26 4.40
278 283 0.670162 TCGGACGTTTTTCGGTCTCT 59.330 50.000 0.00 0.00 44.69 3.10
306 311 7.379750 GTTAAACTATAGCAGCAGTATAGCCT 58.620 38.462 0.00 0.87 34.89 4.58
406 413 2.938838 TCGAATGGGTTGAAAGTTGGT 58.061 42.857 0.00 0.00 0.00 3.67
425 432 0.879090 ACGGCCGGAAAATGTTCTTC 59.121 50.000 31.76 0.00 33.92 2.87
575 585 4.019919 GCGTGTTGCATCTTATCATGTT 57.980 40.909 0.00 0.00 45.45 2.71
599 610 3.195396 ACTGTTGTTGCCTTGTCATTTGT 59.805 39.130 0.00 0.00 0.00 2.83
621 632 0.981183 AGGTGTCCGCCAGTTATTCA 59.019 50.000 0.00 0.00 0.00 2.57
632 643 1.300931 CCGATATGCCAGGTGTCCG 60.301 63.158 0.00 0.00 0.00 4.79
645 656 2.903855 GACGCCCCGAGACCGATA 60.904 66.667 0.00 0.00 38.22 2.92
674 685 7.382488 CCATATTCGAAGTAGACGACAATGATT 59.618 37.037 3.35 0.00 39.46 2.57
713 724 1.401018 GGGACGTTTGCCAAATCTTCG 60.401 52.381 0.00 0.00 32.04 3.79
825 852 5.564550 AGCTAACCTGCAGGGATATAATTG 58.435 41.667 35.42 16.17 40.27 2.32
1095 1122 2.042259 TGCGTACGGGTCGATGAGT 61.042 57.895 18.39 0.00 0.00 3.41
1337 1364 0.895530 GACCGATGGAGGTGAGAACA 59.104 55.000 0.00 0.00 46.09 3.18
1706 1733 2.049063 GTGAAGTCGCGCTGTCCT 60.049 61.111 5.56 0.00 0.00 3.85
1991 2018 3.078196 TTATGCTCCGGGCCGTCA 61.078 61.111 26.32 19.14 40.92 4.35
1993 2020 4.547367 GCTTATGCTCCGGGCCGT 62.547 66.667 26.32 8.37 40.92 5.68
2172 2199 2.829023 TCAGGATTCCCCGTTCTTACT 58.171 47.619 0.00 0.00 40.87 2.24
2266 2296 2.100418 TGACGGAGCAAGAGATCAGATG 59.900 50.000 0.00 0.00 0.00 2.90
2303 2333 6.818142 TCAACAACATATGTATCACTCCACAG 59.182 38.462 9.21 0.00 42.99 3.66
2355 2396 1.979809 TTGGATGGAGGGTGTGGTAT 58.020 50.000 0.00 0.00 0.00 2.73
2407 2448 9.396022 CTATACCAGTACTGTTTCAATCCAAAT 57.604 33.333 21.18 0.00 0.00 2.32
2411 2452 8.788325 AAACTATACCAGTACTGTTTCAATCC 57.212 34.615 21.18 0.00 36.04 3.01
2420 2461 8.142551 GGGACTGATAAAACTATACCAGTACTG 58.857 40.741 16.34 16.34 36.04 2.74
2422 2463 8.015185 TGGGACTGATAAAACTATACCAGTAC 57.985 38.462 0.00 0.00 36.04 2.73
2426 2467 6.690460 GCCATGGGACTGATAAAACTATACCA 60.690 42.308 15.13 0.00 0.00 3.25
2427 2468 5.705905 GCCATGGGACTGATAAAACTATACC 59.294 44.000 15.13 0.00 0.00 2.73
2428 2469 6.428159 CAGCCATGGGACTGATAAAACTATAC 59.572 42.308 15.13 0.00 35.90 1.47
2431 2472 4.780815 CAGCCATGGGACTGATAAAACTA 58.219 43.478 15.13 0.00 35.90 2.24
2446 2487 2.543031 GCATGTCTATGTTGCAGCCATG 60.543 50.000 10.80 10.80 36.65 3.66
2447 2488 1.679680 GCATGTCTATGTTGCAGCCAT 59.320 47.619 0.00 2.08 36.65 4.40
2448 2489 1.097232 GCATGTCTATGTTGCAGCCA 58.903 50.000 0.00 0.00 36.65 4.75
2449 2490 1.386533 AGCATGTCTATGTTGCAGCC 58.613 50.000 0.00 0.00 38.84 4.85
2450 2491 3.176708 CAAAGCATGTCTATGTTGCAGC 58.823 45.455 0.00 0.00 38.84 5.25
2451 2492 3.192001 ACCAAAGCATGTCTATGTTGCAG 59.808 43.478 0.00 0.00 38.84 4.41
2452 2493 3.156293 ACCAAAGCATGTCTATGTTGCA 58.844 40.909 0.00 0.00 38.84 4.08
2453 2494 3.855689 ACCAAAGCATGTCTATGTTGC 57.144 42.857 0.00 0.00 36.65 4.17
2454 2495 5.412594 ACACTACCAAAGCATGTCTATGTTG 59.587 40.000 0.00 0.00 36.65 3.33
2455 2496 5.560724 ACACTACCAAAGCATGTCTATGTT 58.439 37.500 0.00 0.00 36.65 2.71
2456 2497 5.165961 ACACTACCAAAGCATGTCTATGT 57.834 39.130 0.00 0.00 36.65 2.29
2457 2498 6.036083 GTGTACACTACCAAAGCATGTCTATG 59.964 42.308 18.92 0.00 37.36 2.23
2458 2499 6.070767 AGTGTACACTACCAAAGCATGTCTAT 60.071 38.462 26.91 0.00 40.43 1.98
2459 2500 5.245301 AGTGTACACTACCAAAGCATGTCTA 59.755 40.000 26.91 0.00 40.43 2.59
2460 2501 4.040461 AGTGTACACTACCAAAGCATGTCT 59.960 41.667 26.91 0.00 40.43 3.41
2461 2502 4.315803 AGTGTACACTACCAAAGCATGTC 58.684 43.478 26.91 0.00 40.43 3.06
2462 2503 4.351874 AGTGTACACTACCAAAGCATGT 57.648 40.909 26.91 0.00 40.43 3.21
2463 2504 4.515191 ACAAGTGTACACTACCAAAGCATG 59.485 41.667 28.13 20.11 41.58 4.06
2464 2505 4.714632 ACAAGTGTACACTACCAAAGCAT 58.285 39.130 28.13 7.08 41.58 3.79
2465 2506 4.145365 ACAAGTGTACACTACCAAAGCA 57.855 40.909 28.13 0.00 41.58 3.91
2466 2507 5.350640 GGATACAAGTGTACACTACCAAAGC 59.649 44.000 28.13 14.39 41.58 3.51
2467 2508 6.698380 AGGATACAAGTGTACACTACCAAAG 58.302 40.000 28.13 15.53 41.58 2.77
2468 2509 6.675413 AGGATACAAGTGTACACTACCAAA 57.325 37.500 28.13 12.85 41.58 3.28
2469 2510 6.127925 CGTAGGATACAAGTGTACACTACCAA 60.128 42.308 28.13 14.52 43.24 3.67
2470 2511 5.355071 CGTAGGATACAAGTGTACACTACCA 59.645 44.000 28.13 15.91 43.24 3.25
2471 2512 5.731686 GCGTAGGATACAAGTGTACACTACC 60.732 48.000 28.13 22.55 43.24 3.18
2472 2513 5.163723 TGCGTAGGATACAAGTGTACACTAC 60.164 44.000 28.13 17.97 43.24 2.73
2473 2514 4.943093 TGCGTAGGATACAAGTGTACACTA 59.057 41.667 28.13 13.96 43.24 2.74
2474 2515 3.760151 TGCGTAGGATACAAGTGTACACT 59.240 43.478 22.95 22.95 43.24 3.55
2475 2516 4.100707 TGCGTAGGATACAAGTGTACAC 57.899 45.455 18.56 18.56 43.24 2.90
2476 2517 4.022155 TGTTGCGTAGGATACAAGTGTACA 60.022 41.667 0.00 0.00 43.24 2.90
2477 2518 4.487948 TGTTGCGTAGGATACAAGTGTAC 58.512 43.478 0.00 0.00 43.24 2.90
2478 2519 4.787260 TGTTGCGTAGGATACAAGTGTA 57.213 40.909 0.00 0.00 43.24 2.90
2479 2520 3.671008 TGTTGCGTAGGATACAAGTGT 57.329 42.857 0.00 0.00 43.24 3.55
2480 2521 3.370978 CCTTGTTGCGTAGGATACAAGTG 59.629 47.826 19.62 12.31 43.24 3.16
2481 2522 3.007614 ACCTTGTTGCGTAGGATACAAGT 59.992 43.478 19.62 11.00 43.24 3.16
2482 2523 3.370978 CACCTTGTTGCGTAGGATACAAG 59.629 47.826 16.69 16.69 43.24 3.16
2483 2524 3.007074 TCACCTTGTTGCGTAGGATACAA 59.993 43.478 0.00 0.00 43.24 2.41
2484 2525 2.563620 TCACCTTGTTGCGTAGGATACA 59.436 45.455 0.00 0.00 43.24 2.29
2485 2526 3.241067 TCACCTTGTTGCGTAGGATAC 57.759 47.619 0.00 0.00 38.50 2.24
2486 2527 3.857052 CTTCACCTTGTTGCGTAGGATA 58.143 45.455 0.00 0.00 35.45 2.59
2487 2528 2.699954 CTTCACCTTGTTGCGTAGGAT 58.300 47.619 0.00 0.00 35.45 3.24
2488 2529 1.876416 GCTTCACCTTGTTGCGTAGGA 60.876 52.381 0.00 0.00 35.45 2.94
2489 2530 0.517316 GCTTCACCTTGTTGCGTAGG 59.483 55.000 0.00 0.00 37.56 3.18
2490 2531 1.225855 TGCTTCACCTTGTTGCGTAG 58.774 50.000 0.00 0.00 0.00 3.51
2491 2532 1.669604 TTGCTTCACCTTGTTGCGTA 58.330 45.000 0.00 0.00 0.00 4.42
2492 2533 0.814457 TTTGCTTCACCTTGTTGCGT 59.186 45.000 0.00 0.00 0.00 5.24
2493 2534 1.919918 TTTTGCTTCACCTTGTTGCG 58.080 45.000 0.00 0.00 0.00 4.85
2510 2551 4.019591 ACTGAACCCTAGCCGTATCTTTTT 60.020 41.667 0.00 0.00 0.00 1.94
2511 2552 3.518303 ACTGAACCCTAGCCGTATCTTTT 59.482 43.478 0.00 0.00 0.00 2.27
2512 2553 3.105283 ACTGAACCCTAGCCGTATCTTT 58.895 45.455 0.00 0.00 0.00 2.52
2513 2554 2.748388 ACTGAACCCTAGCCGTATCTT 58.252 47.619 0.00 0.00 0.00 2.40
2514 2555 2.456073 ACTGAACCCTAGCCGTATCT 57.544 50.000 0.00 0.00 0.00 1.98
2515 2556 3.484407 TCTACTGAACCCTAGCCGTATC 58.516 50.000 0.00 0.00 0.00 2.24
2516 2557 3.589951 TCTACTGAACCCTAGCCGTAT 57.410 47.619 0.00 0.00 0.00 3.06
2517 2558 3.370840 TTCTACTGAACCCTAGCCGTA 57.629 47.619 0.00 0.00 0.00 4.02
2518 2559 2.226962 TTCTACTGAACCCTAGCCGT 57.773 50.000 0.00 0.00 0.00 5.68
2519 2560 2.159085 CCTTTCTACTGAACCCTAGCCG 60.159 54.545 0.00 0.00 31.02 5.52
2520 2561 2.420269 GCCTTTCTACTGAACCCTAGCC 60.420 54.545 0.00 0.00 31.02 3.93
2521 2562 2.236395 TGCCTTTCTACTGAACCCTAGC 59.764 50.000 0.00 0.00 31.02 3.42
2522 2563 4.080863 ACATGCCTTTCTACTGAACCCTAG 60.081 45.833 0.00 0.00 31.02 3.02
2523 2564 3.844211 ACATGCCTTTCTACTGAACCCTA 59.156 43.478 0.00 0.00 31.02 3.53
2524 2565 2.644798 ACATGCCTTTCTACTGAACCCT 59.355 45.455 0.00 0.00 31.02 4.34
2525 2566 3.073274 ACATGCCTTTCTACTGAACCC 57.927 47.619 0.00 0.00 31.02 4.11
2526 2567 4.082733 GGAAACATGCCTTTCTACTGAACC 60.083 45.833 8.27 0.00 31.76 3.62
2527 2568 4.762251 AGGAAACATGCCTTTCTACTGAAC 59.238 41.667 8.27 0.00 31.76 3.18
2528 2569 4.985538 AGGAAACATGCCTTTCTACTGAA 58.014 39.130 8.27 0.00 31.76 3.02
2529 2570 4.287067 AGAGGAAACATGCCTTTCTACTGA 59.713 41.667 8.27 0.00 35.44 3.41
2530 2571 4.583871 AGAGGAAACATGCCTTTCTACTG 58.416 43.478 8.27 0.00 35.44 2.74
2531 2572 4.917906 AGAGGAAACATGCCTTTCTACT 57.082 40.909 8.27 5.93 35.44 2.57
2532 2573 5.335976 CCAAAGAGGAAACATGCCTTTCTAC 60.336 44.000 8.27 4.26 41.22 2.59
2533 2574 4.766891 CCAAAGAGGAAACATGCCTTTCTA 59.233 41.667 8.27 0.00 41.22 2.10
2534 2575 3.575687 CCAAAGAGGAAACATGCCTTTCT 59.424 43.478 8.27 0.00 41.22 2.52
2535 2576 3.862264 GCCAAAGAGGAAACATGCCTTTC 60.862 47.826 0.00 0.00 41.22 2.62
2536 2577 2.037641 GCCAAAGAGGAAACATGCCTTT 59.962 45.455 0.00 0.00 41.22 3.11
2537 2578 1.620323 GCCAAAGAGGAAACATGCCTT 59.380 47.619 0.00 0.00 41.22 4.35
2538 2579 1.203100 AGCCAAAGAGGAAACATGCCT 60.203 47.619 0.00 0.00 41.22 4.75
2539 2580 1.260544 AGCCAAAGAGGAAACATGCC 58.739 50.000 0.00 0.00 41.22 4.40
2540 2581 2.159324 GCTAGCCAAAGAGGAAACATGC 60.159 50.000 2.29 0.00 41.22 4.06
2541 2582 2.096496 CGCTAGCCAAAGAGGAAACATG 59.904 50.000 9.66 0.00 41.22 3.21
2542 2583 2.027192 TCGCTAGCCAAAGAGGAAACAT 60.027 45.455 9.66 0.00 41.22 2.71
2543 2584 1.346395 TCGCTAGCCAAAGAGGAAACA 59.654 47.619 9.66 0.00 41.22 2.83
2544 2585 1.732809 GTCGCTAGCCAAAGAGGAAAC 59.267 52.381 9.66 0.00 41.22 2.78
2545 2586 1.346395 TGTCGCTAGCCAAAGAGGAAA 59.654 47.619 9.66 0.00 41.22 3.13
2546 2587 0.973632 TGTCGCTAGCCAAAGAGGAA 59.026 50.000 9.66 0.00 41.22 3.36
2547 2588 0.973632 TTGTCGCTAGCCAAAGAGGA 59.026 50.000 9.66 0.00 41.22 3.71
2548 2589 1.079503 GTTGTCGCTAGCCAAAGAGG 58.920 55.000 9.66 0.00 41.84 3.69
2549 2590 1.795768 TGTTGTCGCTAGCCAAAGAG 58.204 50.000 9.66 0.00 0.00 2.85
2550 2591 1.871039 GTTGTTGTCGCTAGCCAAAGA 59.129 47.619 9.66 0.00 0.00 2.52
2551 2592 1.069227 GGTTGTTGTCGCTAGCCAAAG 60.069 52.381 9.66 0.00 0.00 2.77
2567 2608 3.599285 TTGACGGCGGCTAGGGTTG 62.599 63.158 16.45 0.00 0.00 3.77
2622 2665 3.827898 GAGGTCGTCAGCGGAGGG 61.828 72.222 6.71 0.00 38.89 4.30
2642 2685 3.054503 CCCTCACCGTCGACGACT 61.055 66.667 37.65 19.94 43.02 4.18
2678 2725 4.216687 CCTAAAGGTAAAACAATCCGCACA 59.783 41.667 0.00 0.00 0.00 4.57
2694 2742 5.695424 ACTAGGGCTCTAAAACCTAAAGG 57.305 43.478 0.00 0.00 36.49 3.11
2719 2768 3.937079 GTCGGACGATCCAAAAACCTAAT 59.063 43.478 0.00 0.00 35.91 1.73
2768 2822 0.874175 TTATTCAGCATCGCCGTCGG 60.874 55.000 6.99 6.99 36.13 4.79
2769 2823 0.927537 TTTATTCAGCATCGCCGTCG 59.072 50.000 0.00 0.00 0.00 5.12
2770 2824 2.201732 TCTTTATTCAGCATCGCCGTC 58.798 47.619 0.00 0.00 0.00 4.79
2771 2825 2.309528 TCTTTATTCAGCATCGCCGT 57.690 45.000 0.00 0.00 0.00 5.68
2772 2826 2.032549 CCTTCTTTATTCAGCATCGCCG 60.033 50.000 0.00 0.00 0.00 6.46
2773 2827 2.945668 ACCTTCTTTATTCAGCATCGCC 59.054 45.455 0.00 0.00 0.00 5.54
2808 2863 1.991339 TAGAGACGATCGCCTCCCCA 61.991 60.000 25.23 10.31 0.00 4.96
2811 2866 0.523966 CCATAGAGACGATCGCCTCC 59.476 60.000 25.23 9.78 0.00 4.30
2846 2902 1.541233 CCGCTTGAACAGACTGGTTCT 60.541 52.381 7.51 0.00 45.74 3.01
2935 2991 0.391661 ATGTCGACGCTGGAGCAAAT 60.392 50.000 11.62 0.00 42.21 2.32
2951 3007 2.763448 GACTACCTCTCAAGCTCCATGT 59.237 50.000 0.00 0.00 0.00 3.21
2953 3009 2.292521 TGGACTACCTCTCAAGCTCCAT 60.293 50.000 0.00 0.00 37.04 3.41
2975 3031 0.463295 CCACAATCTGCATCCGCTCT 60.463 55.000 0.00 0.00 39.64 4.09
3002 3058 1.201647 TCCGTCTTTCAGATGTCGTCC 59.798 52.381 0.00 0.00 29.27 4.79
3041 3097 6.322201 GGAAATCATACCTGACAACCATCAAT 59.678 38.462 0.00 0.00 33.22 2.57
3049 3105 5.626809 CGAAGGAGGAAATCATACCTGACAA 60.627 44.000 0.00 0.00 36.57 3.18
3052 3108 4.672587 CGAAGGAGGAAATCATACCTGA 57.327 45.455 0.00 0.00 36.57 3.86


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

AutoCloner maintained by Alex Coulton.