Multiple sequence alignment - TraesCS7D01G401700

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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 TraesCS7D01G401700 chr7D 100.000 4054 0 0 1 4054 518776542 518780595 0.000000e+00 7487.0
1 TraesCS7D01G401700 chr7D 93.432 2101 121 7 413 2499 545654205 545656302 0.000000e+00 3099.0
2 TraesCS7D01G401700 chr7D 86.801 1485 191 3 1019 2499 545660102 545661585 0.000000e+00 1652.0
3 TraesCS7D01G401700 chr7D 86.281 1487 199 3 1017 2499 546129865 546128380 0.000000e+00 1611.0
4 TraesCS7D01G401700 chr7D 96.226 318 12 0 2641 2958 545656295 545656612 4.640000e-144 521.0
5 TraesCS7D01G401700 chr7D 94.340 318 18 0 2641 2958 545661578 545661895 4.710000e-134 488.0
6 TraesCS7D01G401700 chr7D 92.835 321 23 0 2641 2961 546128387 546128067 2.210000e-127 466.0
7 TraesCS7D01G401700 chr7D 100.000 39 0 0 3192 3230 518779696 518779734 5.620000e-09 73.1
8 TraesCS7D01G401700 chr7D 100.000 39 0 0 3155 3193 518779733 518779771 5.620000e-09 73.1
9 TraesCS7D01G401700 chr7A 96.590 2317 47 8 195 2499 594451763 594454059 0.000000e+00 3812.0
10 TraesCS7D01G401700 chr7A 93.102 2102 126 9 413 2499 628652620 628654717 0.000000e+00 3061.0
11 TraesCS7D01G401700 chr7A 85.926 1485 204 3 1019 2499 628867192 628865709 0.000000e+00 1580.0
12 TraesCS7D01G401700 chr7A 96.671 841 17 3 3224 4054 594458838 594459677 0.000000e+00 1387.0
13 TraesCS7D01G401700 chr7A 97.826 552 6 3 2641 3191 594454052 594454598 0.000000e+00 948.0
14 TraesCS7D01G401700 chr7A 98.113 318 6 0 2641 2958 628654710 628655027 4.580000e-154 555.0
15 TraesCS7D01G401700 chr7A 92.835 321 23 0 2641 2961 628865716 628865396 2.210000e-127 466.0
16 TraesCS7D01G401700 chr7A 89.137 313 34 0 2649 2961 169951418 169951106 1.370000e-104 390.0
17 TraesCS7D01G401700 chr7A 97.778 45 1 0 3193 3237 594454563 594454607 1.210000e-10 78.7
18 TraesCS7D01G401700 chr7B 90.898 2516 169 18 4 2498 589938946 589941422 0.000000e+00 3323.0
19 TraesCS7D01G401700 chr7B 85.724 1506 210 3 998 2499 590107498 590105994 0.000000e+00 1585.0
20 TraesCS7D01G401700 chr7B 85.464 1486 202 11 1016 2494 589899221 589900699 0.000000e+00 1535.0
21 TraesCS7D01G401700 chr7B 93.772 867 43 8 3193 4054 552115481 552116341 0.000000e+00 1291.0
22 TraesCS7D01G401700 chr7B 90.826 327 30 0 2641 2967 590106001 590105675 4.810000e-119 438.0
23 TraesCS7D01G401700 chr7B 89.032 310 34 0 2649 2958 589900705 589901014 6.360000e-103 385.0
24 TraesCS7D01G401700 chr7B 89.121 239 12 7 2965 3193 552115284 552115518 6.630000e-73 285.0
25 TraesCS7D01G401700 chr7B 84.091 132 20 1 3703 3834 552009707 552009837 4.250000e-25 126.0
26 TraesCS7D01G401700 chr7B 95.455 44 2 0 970 1013 589917947 589917990 2.020000e-08 71.3
27 TraesCS7D01G401700 chr6A 95.620 137 6 0 1 137 158242741 158242605 1.900000e-53 220.0
28 TraesCS7D01G401700 chr6B 94.891 137 7 0 1 137 216634234 216634370 8.830000e-52 215.0
29 TraesCS7D01G401700 chr6D 93.431 137 8 1 1 137 122992402 122992537 6.870000e-48 202.0
30 TraesCS7D01G401700 chr6D 84.507 142 19 3 2499 2639 308589893 308590032 1.970000e-28 137.0
31 TraesCS7D01G401700 chr2D 85.000 140 7 4 1 137 412474079 412474207 3.290000e-26 130.0
32 TraesCS7D01G401700 chr2B 92.473 93 4 2 48 137 485895226 485895318 3.290000e-26 130.0
33 TraesCS7D01G401700 chr5D 89.855 69 7 0 931 999 42079680 42079612 5.580000e-14 89.8


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 TraesCS7D01G401700 chr7D 518776542 518780595 4053 False 2544.4 7487 100.00000 1 4054 3 chr7D.!!$F1 4053
1 TraesCS7D01G401700 chr7D 545654205 545661895 7690 False 1440.0 3099 92.69975 413 2958 4 chr7D.!!$F2 2545
2 TraesCS7D01G401700 chr7D 546128067 546129865 1798 True 1038.5 1611 89.55800 1017 2961 2 chr7D.!!$R1 1944
3 TraesCS7D01G401700 chr7A 628652620 628655027 2407 False 1808.0 3061 95.60750 413 2958 2 chr7A.!!$F3 2545
4 TraesCS7D01G401700 chr7A 594451763 594454607 2844 False 1612.9 3812 97.39800 195 3237 3 chr7A.!!$F2 3042
5 TraesCS7D01G401700 chr7A 594458838 594459677 839 False 1387.0 1387 96.67100 3224 4054 1 chr7A.!!$F1 830
6 TraesCS7D01G401700 chr7A 628865396 628867192 1796 True 1023.0 1580 89.38050 1019 2961 2 chr7A.!!$R2 1942
7 TraesCS7D01G401700 chr7B 589938946 589941422 2476 False 3323.0 3323 90.89800 4 2498 1 chr7B.!!$F3 2494
8 TraesCS7D01G401700 chr7B 590105675 590107498 1823 True 1011.5 1585 88.27500 998 2967 2 chr7B.!!$R1 1969
9 TraesCS7D01G401700 chr7B 589899221 589901014 1793 False 960.0 1535 87.24800 1016 2958 2 chr7B.!!$F5 1942
10 TraesCS7D01G401700 chr7B 552115284 552116341 1057 False 788.0 1291 91.44650 2965 4054 2 chr7B.!!$F4 1089

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
179 180 0.872388 CGAACTTTGGAACCCTTCGG 59.128 55.0 0.00 0.00 32.06 4.30 F
829 847 0.896940 AGGTGCCAAGCCATTGAGTG 60.897 55.0 0.00 0.00 38.83 3.51 F
2516 2542 0.584054 GCGAAATTGCTGAGCGTACG 60.584 55.0 11.84 11.84 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1649 1667 0.031178 GTGGCCAACTTTGAGCACTG 59.969 55.000 7.24 0.0 0.00 3.66 R
2569 2595 0.865111 CGTCAACAGCCGTTTGATCA 59.135 50.000 0.00 0.0 31.13 2.92 R
3498 4774 1.541588 GGGAAACTTGCTTGCTACCAG 59.458 52.381 0.00 0.0 0.00 4.00 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
77 78 5.059833 AGACAGTTTCTGAACTCCACAATC 58.940 41.667 3.70 0.00 44.14 2.67
88 89 3.350833 ACTCCACAATCTCAATTGCCTC 58.649 45.455 0.00 0.00 45.16 4.70
97 98 1.750399 CAATTGCCTCCCAGACCCG 60.750 63.158 0.00 0.00 0.00 5.28
132 133 1.135083 GCAAGCGCACTACTTCTCCTA 60.135 52.381 11.47 0.00 38.36 2.94
138 139 3.364062 CGCACTACTTCTCCTATTGTCG 58.636 50.000 0.00 0.00 0.00 4.35
160 161 2.006772 CGGAGTGCCAGCGTTTATC 58.993 57.895 0.00 0.00 0.00 1.75
175 176 3.749609 CGTTTATCGAACTTTGGAACCCT 59.250 43.478 0.00 0.00 42.86 4.34
177 178 5.616204 CGTTTATCGAACTTTGGAACCCTTC 60.616 44.000 0.00 0.00 42.86 3.46
179 180 0.872388 CGAACTTTGGAACCCTTCGG 59.128 55.000 0.00 0.00 32.06 4.30
193 194 3.309436 TTCGGGTGGTGGAGCATCG 62.309 63.158 0.00 0.00 34.37 3.84
248 249 3.258123 CCACGGTTTCAATCCATTTTCCT 59.742 43.478 0.00 0.00 0.00 3.36
423 429 2.751259 CCCAGATTGAAGTGTGTCCATG 59.249 50.000 0.00 0.00 0.00 3.66
575 593 1.481901 TACTTACCCAGCAACCCGCA 61.482 55.000 0.00 0.00 46.13 5.69
639 657 7.795431 ATTTTATCAATTGCAGTTGTACACG 57.205 32.000 19.91 0.00 0.00 4.49
796 814 3.623060 AGCTACCTATTTGCACATGTTCG 59.377 43.478 0.00 0.00 0.00 3.95
813 831 5.217978 TGTTCGTCCAGTTTACATAAGGT 57.782 39.130 0.00 0.00 0.00 3.50
817 835 3.681593 GTCCAGTTTACATAAGGTGCCA 58.318 45.455 0.00 0.00 0.00 4.92
829 847 0.896940 AGGTGCCAAGCCATTGAGTG 60.897 55.000 0.00 0.00 38.83 3.51
879 897 5.938125 TCCTCATGGCTTCAGTACTAAAAAC 59.062 40.000 0.00 0.00 0.00 2.43
1013 1031 4.934356 AGTTTATCCATGCCTTTCCTTGA 58.066 39.130 0.00 0.00 0.00 3.02
1556 1574 8.783660 ACAGGACAAATACCATCTTCTATCTA 57.216 34.615 0.00 0.00 0.00 1.98
1649 1667 1.012841 GGCAGTTGCTCTATGCTGAC 58.987 55.000 3.88 0.00 43.37 3.51
1679 1697 2.983512 TTGGCCACAACAACCTTGT 58.016 47.368 3.88 0.00 44.72 3.16
1763 1782 8.796649 AACAATGGTTTGCAAGGAGTTCTTGG 62.797 42.308 13.22 0.00 42.71 3.61
2293 2319 8.631797 CCATACCACATGATGAAACATTTGATA 58.368 33.333 0.00 0.00 31.94 2.15
2300 2326 9.426837 ACATGATGAAACATTTGATAGTTTTGG 57.573 29.630 0.00 0.00 38.01 3.28
2499 2525 2.897969 ACTTACAGGGGATATACCAGCG 59.102 50.000 6.25 0.00 41.20 5.18
2500 2526 2.984435 TACAGGGGATATACCAGCGA 57.016 50.000 6.25 0.00 41.20 4.93
2501 2527 2.097110 ACAGGGGATATACCAGCGAA 57.903 50.000 6.25 0.00 41.20 4.70
2502 2528 2.404559 ACAGGGGATATACCAGCGAAA 58.595 47.619 6.25 0.00 41.20 3.46
2503 2529 2.979678 ACAGGGGATATACCAGCGAAAT 59.020 45.455 6.25 0.00 41.20 2.17
2504 2530 3.394606 ACAGGGGATATACCAGCGAAATT 59.605 43.478 6.25 0.00 41.20 1.82
2505 2531 3.753272 CAGGGGATATACCAGCGAAATTG 59.247 47.826 6.25 0.00 41.20 2.32
2506 2532 2.488153 GGGGATATACCAGCGAAATTGC 59.512 50.000 6.25 0.00 41.20 3.56
2513 2539 3.972227 AGCGAAATTGCTGAGCGT 58.028 50.000 0.00 0.00 45.28 5.07
2514 2540 3.137484 AGCGAAATTGCTGAGCGTA 57.863 47.368 0.00 0.00 45.28 4.42
2515 2541 0.721718 AGCGAAATTGCTGAGCGTAC 59.278 50.000 0.00 0.00 45.28 3.67
2516 2542 0.584054 GCGAAATTGCTGAGCGTACG 60.584 55.000 11.84 11.84 0.00 3.67
2517 2543 0.989164 CGAAATTGCTGAGCGTACGA 59.011 50.000 21.65 0.00 0.00 3.43
2518 2544 1.588404 CGAAATTGCTGAGCGTACGAT 59.412 47.619 21.65 14.36 0.00 3.73
2519 2545 2.595188 CGAAATTGCTGAGCGTACGATG 60.595 50.000 21.65 2.41 0.00 3.84
2520 2546 2.293677 AATTGCTGAGCGTACGATGA 57.706 45.000 21.65 5.81 0.00 2.92
2521 2547 2.293677 ATTGCTGAGCGTACGATGAA 57.706 45.000 21.65 1.96 0.00 2.57
2522 2548 2.293677 TTGCTGAGCGTACGATGAAT 57.706 45.000 21.65 0.00 0.00 2.57
2523 2549 3.430333 TTGCTGAGCGTACGATGAATA 57.570 42.857 21.65 0.00 0.00 1.75
2524 2550 3.000082 TGCTGAGCGTACGATGAATAG 58.000 47.619 21.65 9.20 0.00 1.73
2525 2551 2.357952 TGCTGAGCGTACGATGAATAGT 59.642 45.455 21.65 0.00 0.00 2.12
2526 2552 2.721603 GCTGAGCGTACGATGAATAGTG 59.278 50.000 21.65 0.00 0.00 2.74
2527 2553 3.792459 GCTGAGCGTACGATGAATAGTGT 60.792 47.826 21.65 0.00 0.00 3.55
2528 2554 3.691498 TGAGCGTACGATGAATAGTGTG 58.309 45.455 21.65 0.00 0.00 3.82
2529 2555 3.128068 TGAGCGTACGATGAATAGTGTGT 59.872 43.478 21.65 0.00 0.00 3.72
2530 2556 4.333372 TGAGCGTACGATGAATAGTGTGTA 59.667 41.667 21.65 0.00 0.00 2.90
2531 2557 4.595116 AGCGTACGATGAATAGTGTGTAC 58.405 43.478 21.65 0.00 0.00 2.90
2536 2562 7.675270 GTACGATGAATAGTGTGTACGATTT 57.325 36.000 0.00 0.00 33.13 2.17
2537 2563 8.112099 GTACGATGAATAGTGTGTACGATTTT 57.888 34.615 0.00 0.00 33.13 1.82
2538 2564 7.218145 ACGATGAATAGTGTGTACGATTTTC 57.782 36.000 0.00 0.00 33.13 2.29
2539 2565 6.020916 ACGATGAATAGTGTGTACGATTTTCG 60.021 38.462 0.00 12.85 46.93 3.46
2554 2580 6.727569 CGATTTTCGTACGACATGATCTAA 57.272 37.500 19.36 3.90 34.72 2.10
2555 2581 6.561039 CGATTTTCGTACGACATGATCTAAC 58.439 40.000 19.36 0.00 34.72 2.34
2556 2582 6.414109 CGATTTTCGTACGACATGATCTAACT 59.586 38.462 19.36 0.90 34.72 2.24
2557 2583 7.356557 CGATTTTCGTACGACATGATCTAACTC 60.357 40.741 19.36 9.49 34.72 3.01
2558 2584 4.448363 TCGTACGACATGATCTAACTCG 57.552 45.455 15.28 0.00 0.00 4.18
2559 2585 3.867493 TCGTACGACATGATCTAACTCGT 59.133 43.478 15.28 5.02 40.51 4.18
2560 2586 4.026228 TCGTACGACATGATCTAACTCGTC 60.026 45.833 15.28 1.91 38.48 4.20
2561 2587 3.694535 ACGACATGATCTAACTCGTCC 57.305 47.619 0.00 0.00 32.22 4.79
2562 2588 3.014623 ACGACATGATCTAACTCGTCCA 58.985 45.455 0.00 0.00 32.22 4.02
2563 2589 3.632604 ACGACATGATCTAACTCGTCCAT 59.367 43.478 0.00 0.00 32.22 3.41
2564 2590 4.222886 CGACATGATCTAACTCGTCCATC 58.777 47.826 0.00 0.00 0.00 3.51
2565 2591 4.551388 GACATGATCTAACTCGTCCATCC 58.449 47.826 0.00 0.00 0.00 3.51
2566 2592 3.960755 ACATGATCTAACTCGTCCATCCA 59.039 43.478 0.00 0.00 0.00 3.41
2567 2593 4.405680 ACATGATCTAACTCGTCCATCCAA 59.594 41.667 0.00 0.00 0.00 3.53
2568 2594 5.070981 ACATGATCTAACTCGTCCATCCAAT 59.929 40.000 0.00 0.00 0.00 3.16
2569 2595 5.614324 TGATCTAACTCGTCCATCCAATT 57.386 39.130 0.00 0.00 0.00 2.32
2570 2596 5.359756 TGATCTAACTCGTCCATCCAATTG 58.640 41.667 0.00 0.00 0.00 2.32
2571 2597 5.128663 TGATCTAACTCGTCCATCCAATTGA 59.871 40.000 7.12 0.00 0.00 2.57
2572 2598 5.614324 TCTAACTCGTCCATCCAATTGAT 57.386 39.130 7.12 0.00 0.00 2.57
2573 2599 5.601662 TCTAACTCGTCCATCCAATTGATC 58.398 41.667 7.12 0.00 0.00 2.92
2574 2600 3.912496 ACTCGTCCATCCAATTGATCA 57.088 42.857 7.12 0.00 0.00 2.92
2575 2601 4.220693 ACTCGTCCATCCAATTGATCAA 57.779 40.909 11.26 11.26 0.00 2.57
2576 2602 4.588899 ACTCGTCCATCCAATTGATCAAA 58.411 39.130 13.09 0.00 0.00 2.69
2577 2603 4.396166 ACTCGTCCATCCAATTGATCAAAC 59.604 41.667 13.09 2.42 0.00 2.93
2578 2604 3.373748 TCGTCCATCCAATTGATCAAACG 59.626 43.478 13.09 14.52 33.89 3.60
2579 2605 3.487376 CGTCCATCCAATTGATCAAACGG 60.487 47.826 13.09 15.30 31.20 4.44
2580 2606 2.426738 TCCATCCAATTGATCAAACGGC 59.573 45.455 13.09 0.00 0.00 5.68
2581 2607 2.428171 CCATCCAATTGATCAAACGGCT 59.572 45.455 13.09 4.70 0.00 5.52
2582 2608 3.441163 CATCCAATTGATCAAACGGCTG 58.559 45.455 13.09 13.05 0.00 4.85
2583 2609 2.513753 TCCAATTGATCAAACGGCTGT 58.486 42.857 13.09 0.00 0.00 4.40
2584 2610 2.890311 TCCAATTGATCAAACGGCTGTT 59.110 40.909 13.09 4.68 40.98 3.16
2585 2611 2.988493 CCAATTGATCAAACGGCTGTTG 59.012 45.455 12.68 10.11 38.62 3.33
2586 2612 3.305267 CCAATTGATCAAACGGCTGTTGA 60.305 43.478 12.68 11.85 38.62 3.18
2587 2613 3.559238 ATTGATCAAACGGCTGTTGAC 57.441 42.857 12.68 4.73 38.62 3.18
2629 2655 3.771245 CGAAATTCGTCGTACGTGTAG 57.229 47.619 16.05 5.51 43.14 2.74
2630 2656 2.037066 CGAAATTCGTCGTACGTGTAGC 60.037 50.000 16.05 1.30 43.14 3.58
2631 2657 2.617250 AATTCGTCGTACGTGTAGCA 57.383 45.000 16.05 0.00 43.14 3.49
2632 2658 2.169663 ATTCGTCGTACGTGTAGCAG 57.830 50.000 16.05 0.65 43.14 4.24
2633 2659 0.867746 TTCGTCGTACGTGTAGCAGT 59.132 50.000 16.05 0.00 43.14 4.40
2634 2660 0.867746 TCGTCGTACGTGTAGCAGTT 59.132 50.000 16.05 0.00 43.14 3.16
2635 2661 1.136252 TCGTCGTACGTGTAGCAGTTC 60.136 52.381 16.05 0.00 43.14 3.01
2636 2662 1.136141 CGTCGTACGTGTAGCAGTTCT 60.136 52.381 16.05 0.00 36.74 3.01
2637 2663 2.503871 GTCGTACGTGTAGCAGTTCTC 58.496 52.381 16.05 0.00 0.00 2.87
2638 2664 2.096069 GTCGTACGTGTAGCAGTTCTCA 60.096 50.000 16.05 0.00 0.00 3.27
2639 2665 2.096069 TCGTACGTGTAGCAGTTCTCAC 60.096 50.000 16.05 0.00 0.00 3.51
2640 2666 2.350102 CGTACGTGTAGCAGTTCTCACA 60.350 50.000 7.22 0.00 0.00 3.58
2641 2667 3.669824 CGTACGTGTAGCAGTTCTCACAT 60.670 47.826 7.22 0.00 0.00 3.21
2642 2668 4.436451 CGTACGTGTAGCAGTTCTCACATA 60.436 45.833 7.22 0.00 0.00 2.29
2643 2669 3.834610 ACGTGTAGCAGTTCTCACATAC 58.165 45.455 0.00 0.00 0.00 2.39
2644 2670 3.179830 CGTGTAGCAGTTCTCACATACC 58.820 50.000 0.00 0.00 0.00 2.73
2645 2671 3.366985 CGTGTAGCAGTTCTCACATACCA 60.367 47.826 0.00 0.00 0.00 3.25
2646 2672 4.177026 GTGTAGCAGTTCTCACATACCAG 58.823 47.826 0.00 0.00 0.00 4.00
2647 2673 2.393271 AGCAGTTCTCACATACCAGC 57.607 50.000 0.00 0.00 0.00 4.85
2983 3009 4.028490 CAGCCTGGTAACCCGGCA 62.028 66.667 21.14 0.00 46.45 5.69
3156 3387 0.670162 CATCCAAAGGCCCATAAGCG 59.330 55.000 0.00 0.00 0.00 4.68
3157 3388 0.258774 ATCCAAAGGCCCATAAGCGT 59.741 50.000 0.00 0.00 0.00 5.07
3158 3389 0.393808 TCCAAAGGCCCATAAGCGTC 60.394 55.000 0.00 0.00 0.00 5.19
3159 3390 0.679640 CCAAAGGCCCATAAGCGTCA 60.680 55.000 0.00 0.00 0.00 4.35
3160 3391 0.734889 CAAAGGCCCATAAGCGTCAG 59.265 55.000 0.00 0.00 0.00 3.51
3163 3394 2.472909 GGCCCATAAGCGTCAGTGC 61.473 63.158 0.00 0.00 0.00 4.40
3167 3398 1.002366 CCATAAGCGTCAGTGCACTC 58.998 55.000 18.64 5.86 37.31 3.51
3171 3402 0.319728 AAGCGTCAGTGCACTCAGAT 59.680 50.000 18.64 7.05 37.31 2.90
3172 3403 0.319728 AGCGTCAGTGCACTCAGATT 59.680 50.000 18.64 0.00 37.31 2.40
3173 3404 0.718343 GCGTCAGTGCACTCAGATTC 59.282 55.000 18.64 4.81 34.15 2.52
3174 3405 1.354040 CGTCAGTGCACTCAGATTCC 58.646 55.000 18.64 0.00 0.00 3.01
3175 3406 1.337167 CGTCAGTGCACTCAGATTCCA 60.337 52.381 18.64 0.00 0.00 3.53
3176 3407 2.771089 GTCAGTGCACTCAGATTCCAA 58.229 47.619 18.64 0.00 0.00 3.53
3177 3408 2.740981 GTCAGTGCACTCAGATTCCAAG 59.259 50.000 18.64 1.33 0.00 3.61
3178 3409 2.634453 TCAGTGCACTCAGATTCCAAGA 59.366 45.455 18.64 4.08 0.00 3.02
3179 3410 3.262660 TCAGTGCACTCAGATTCCAAGAT 59.737 43.478 18.64 0.00 0.00 2.40
3181 3412 4.569966 CAGTGCACTCAGATTCCAAGATAC 59.430 45.833 18.64 0.00 0.00 2.24
3183 3414 4.569966 GTGCACTCAGATTCCAAGATACTG 59.430 45.833 10.32 0.00 0.00 2.74
3184 3415 4.125703 GCACTCAGATTCCAAGATACTGG 58.874 47.826 0.00 0.00 37.87 4.00
3185 3416 4.125703 CACTCAGATTCCAAGATACTGGC 58.874 47.826 0.00 0.00 36.32 4.85
3186 3417 3.776969 ACTCAGATTCCAAGATACTGGCA 59.223 43.478 0.00 0.00 36.32 4.92
3188 3419 4.517285 TCAGATTCCAAGATACTGGCAAC 58.483 43.478 0.00 0.00 36.32 4.17
3292 3523 2.161855 CGAGATCTGCTCTATGAGGCT 58.838 52.381 0.00 0.00 41.66 4.58
3490 4766 6.656270 TGAGCTGTAATGTTCATCAATCAACT 59.344 34.615 0.00 0.00 0.00 3.16
3920 6220 8.037758 TCTTCAGCTAAGAAAATAGACAAGGAG 58.962 37.037 0.00 0.00 41.35 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 4.934602 GTCTCTGCCCAAGAATGCTATATC 59.065 45.833 0.00 0.00 33.37 1.63
35 36 4.349048 TGTCTCTGCCCAAGAATGCTATAT 59.651 41.667 0.00 0.00 33.37 0.86
46 47 1.768275 TCAGAAACTGTCTCTGCCCAA 59.232 47.619 6.26 0.00 40.18 4.12
77 78 0.394899 GGGTCTGGGAGGCAATTGAG 60.395 60.000 10.34 0.00 0.00 3.02
88 89 1.087771 GCGATGTTAACGGGTCTGGG 61.088 60.000 0.26 0.00 0.00 4.45
97 98 2.509870 GCTTGCTTCTGCGATGTTAAC 58.490 47.619 0.00 0.00 43.34 2.01
132 133 4.778143 GCACTCCGCCCCGACAAT 62.778 66.667 0.00 0.00 32.94 2.71
151 152 3.187842 GGTTCCAAAGTTCGATAAACGCT 59.812 43.478 0.00 0.00 43.02 5.07
156 157 3.998341 CGAAGGGTTCCAAAGTTCGATAA 59.002 43.478 0.00 0.00 41.96 1.75
157 158 3.592059 CGAAGGGTTCCAAAGTTCGATA 58.408 45.455 0.00 0.00 41.96 2.92
175 176 2.668632 GATGCTCCACCACCCGAA 59.331 61.111 0.00 0.00 0.00 4.30
177 178 4.082523 ACGATGCTCCACCACCCG 62.083 66.667 0.00 0.00 0.00 5.28
179 180 2.034879 CACACGATGCTCCACCACC 61.035 63.158 0.00 0.00 0.00 4.61
181 182 2.347114 CCACACGATGCTCCACCA 59.653 61.111 0.00 0.00 0.00 4.17
182 183 1.741770 GACCACACGATGCTCCACC 60.742 63.158 0.00 0.00 0.00 4.61
183 184 2.094659 CGACCACACGATGCTCCAC 61.095 63.158 0.00 0.00 35.09 4.02
184 185 2.212900 CTCGACCACACGATGCTCCA 62.213 60.000 0.00 0.00 41.39 3.86
185 186 1.517257 CTCGACCACACGATGCTCC 60.517 63.158 0.00 0.00 41.39 4.70
186 187 1.073216 CACTCGACCACACGATGCTC 61.073 60.000 0.00 0.00 41.39 4.26
193 194 2.665185 GGCACCACTCGACCACAC 60.665 66.667 0.00 0.00 0.00 3.82
423 429 1.610673 TGGAGAGAGCCCTGGTGAC 60.611 63.158 0.00 0.00 0.00 3.67
575 593 9.661954 TTGAGAGAAGGATACCTACAAGAATAT 57.338 33.333 0.00 0.00 31.13 1.28
624 642 0.536233 TGGGCGTGTACAACTGCAAT 60.536 50.000 15.34 0.00 32.26 3.56
631 649 1.671845 GTTGAAACTGGGCGTGTACAA 59.328 47.619 0.00 0.00 0.00 2.41
632 650 1.134340 AGTTGAAACTGGGCGTGTACA 60.134 47.619 0.00 0.00 37.98 2.90
633 651 1.589803 AGTTGAAACTGGGCGTGTAC 58.410 50.000 0.00 0.00 37.98 2.90
639 657 1.953686 TGCAAGTAGTTGAAACTGGGC 59.046 47.619 14.64 5.00 40.07 5.36
796 814 3.681593 TGGCACCTTATGTAAACTGGAC 58.318 45.455 0.00 0.00 0.00 4.02
813 831 3.368822 GCACTCAATGGCTTGGCA 58.631 55.556 0.00 0.00 32.95 4.92
829 847 2.107204 AGGAATAGGATGATGGTGTGGC 59.893 50.000 0.00 0.00 0.00 5.01
879 897 2.614057 CAATACTAAAAGCCGCCTGAGG 59.386 50.000 0.00 0.00 0.00 3.86
1013 1031 2.282745 GGAGGCCAGCAGCAAGTT 60.283 61.111 5.01 0.00 46.50 2.66
1156 1174 0.971386 CCTTCCCATTTGCAGCAGTT 59.029 50.000 0.00 0.00 0.00 3.16
1556 1574 2.158871 GCAAATGATGGGGCATTGATGT 60.159 45.455 0.00 0.00 38.42 3.06
1649 1667 0.031178 GTGGCCAACTTTGAGCACTG 59.969 55.000 7.24 0.00 0.00 3.66
2293 2319 6.434340 GTCAATACCTGAAGATTCCCAAAACT 59.566 38.462 0.00 0.00 35.22 2.66
2300 2326 6.931840 GTCTATGGTCAATACCTGAAGATTCC 59.068 42.308 0.00 0.00 46.91 3.01
2325 2351 1.451207 TCCGGTCAATGGGCAATCG 60.451 57.895 0.00 0.00 0.00 3.34
2499 2525 2.603110 TCATCGTACGCTCAGCAATTTC 59.397 45.455 11.24 0.00 0.00 2.17
2500 2526 2.616960 TCATCGTACGCTCAGCAATTT 58.383 42.857 11.24 0.00 0.00 1.82
2501 2527 2.293677 TCATCGTACGCTCAGCAATT 57.706 45.000 11.24 0.00 0.00 2.32
2502 2528 2.293677 TTCATCGTACGCTCAGCAAT 57.706 45.000 11.24 0.00 0.00 3.56
2503 2529 2.293677 ATTCATCGTACGCTCAGCAA 57.706 45.000 11.24 0.00 0.00 3.91
2504 2530 2.357952 ACTATTCATCGTACGCTCAGCA 59.642 45.455 11.24 0.00 0.00 4.41
2505 2531 2.721603 CACTATTCATCGTACGCTCAGC 59.278 50.000 11.24 0.00 0.00 4.26
2506 2532 3.726235 CACACTATTCATCGTACGCTCAG 59.274 47.826 11.24 4.20 0.00 3.35
2507 2533 3.128068 ACACACTATTCATCGTACGCTCA 59.872 43.478 11.24 0.00 0.00 4.26
2508 2534 3.692576 ACACACTATTCATCGTACGCTC 58.307 45.455 11.24 0.00 0.00 5.03
2509 2535 3.777465 ACACACTATTCATCGTACGCT 57.223 42.857 11.24 0.00 0.00 5.07
2510 2536 3.416674 CGTACACACTATTCATCGTACGC 59.583 47.826 11.24 0.00 43.58 4.42
2512 2538 7.675270 AAATCGTACACACTATTCATCGTAC 57.325 36.000 0.00 0.00 0.00 3.67
2513 2539 7.164662 CGAAAATCGTACACACTATTCATCGTA 59.835 37.037 0.00 0.00 34.72 3.43
2514 2540 6.020916 CGAAAATCGTACACACTATTCATCGT 60.021 38.462 0.00 0.00 34.72 3.73
2515 2541 6.337152 CGAAAATCGTACACACTATTCATCG 58.663 40.000 0.00 0.00 34.72 3.84
2531 2557 6.414109 AGTTAGATCATGTCGTACGAAAATCG 59.586 38.462 21.39 8.00 46.93 3.34
2532 2558 7.356557 CGAGTTAGATCATGTCGTACGAAAATC 60.357 40.741 21.39 15.11 0.00 2.17
2533 2559 6.414109 CGAGTTAGATCATGTCGTACGAAAAT 59.586 38.462 21.39 13.93 0.00 1.82
2534 2560 5.735892 CGAGTTAGATCATGTCGTACGAAAA 59.264 40.000 21.39 12.05 0.00 2.29
2535 2561 5.163824 ACGAGTTAGATCATGTCGTACGAAA 60.164 40.000 21.39 16.34 41.82 3.46
2536 2562 4.330894 ACGAGTTAGATCATGTCGTACGAA 59.669 41.667 21.39 10.90 41.82 3.85
2537 2563 3.867493 ACGAGTTAGATCATGTCGTACGA 59.133 43.478 15.28 15.28 41.82 3.43
2538 2564 4.193021 ACGAGTTAGATCATGTCGTACG 57.807 45.455 9.53 9.53 41.82 3.67
2539 2565 4.034858 TGGACGAGTTAGATCATGTCGTAC 59.965 45.833 12.64 12.64 43.55 3.67
2540 2566 4.193865 TGGACGAGTTAGATCATGTCGTA 58.806 43.478 11.02 0.00 43.55 3.43
2541 2567 3.014623 TGGACGAGTTAGATCATGTCGT 58.985 45.455 10.89 10.89 46.02 4.34
2542 2568 3.692791 TGGACGAGTTAGATCATGTCG 57.307 47.619 0.00 0.26 36.71 4.35
2543 2569 4.038042 TGGATGGACGAGTTAGATCATGTC 59.962 45.833 0.00 0.00 0.00 3.06
2544 2570 3.960755 TGGATGGACGAGTTAGATCATGT 59.039 43.478 0.00 0.00 0.00 3.21
2545 2571 4.590850 TGGATGGACGAGTTAGATCATG 57.409 45.455 0.00 0.00 0.00 3.07
2546 2572 5.815233 ATTGGATGGACGAGTTAGATCAT 57.185 39.130 0.00 0.00 0.00 2.45
2547 2573 5.128663 TCAATTGGATGGACGAGTTAGATCA 59.871 40.000 5.42 0.00 0.00 2.92
2548 2574 5.601662 TCAATTGGATGGACGAGTTAGATC 58.398 41.667 5.42 0.00 0.00 2.75
2549 2575 5.614324 TCAATTGGATGGACGAGTTAGAT 57.386 39.130 5.42 0.00 0.00 1.98
2550 2576 5.128663 TGATCAATTGGATGGACGAGTTAGA 59.871 40.000 5.42 0.00 36.00 2.10
2551 2577 5.359756 TGATCAATTGGATGGACGAGTTAG 58.640 41.667 5.42 0.00 36.00 2.34
2552 2578 5.351948 TGATCAATTGGATGGACGAGTTA 57.648 39.130 5.42 0.00 36.00 2.24
2553 2579 4.220693 TGATCAATTGGATGGACGAGTT 57.779 40.909 5.42 0.00 36.00 3.01
2554 2580 3.912496 TGATCAATTGGATGGACGAGT 57.088 42.857 5.42 0.00 36.00 4.18
2555 2581 4.494690 CGTTTGATCAATTGGATGGACGAG 60.495 45.833 16.20 0.00 36.00 4.18
2556 2582 3.373748 CGTTTGATCAATTGGATGGACGA 59.626 43.478 16.20 0.00 36.00 4.20
2557 2583 3.487376 CCGTTTGATCAATTGGATGGACG 60.487 47.826 17.44 16.11 36.00 4.79
2558 2584 3.734902 GCCGTTTGATCAATTGGATGGAC 60.735 47.826 23.63 10.52 36.00 4.02
2559 2585 2.426738 GCCGTTTGATCAATTGGATGGA 59.573 45.455 23.63 0.04 36.00 3.41
2560 2586 2.428171 AGCCGTTTGATCAATTGGATGG 59.572 45.455 23.63 17.38 36.00 3.51
2561 2587 3.119388 ACAGCCGTTTGATCAATTGGATG 60.119 43.478 28.93 28.93 37.37 3.51
2562 2588 3.091545 ACAGCCGTTTGATCAATTGGAT 58.908 40.909 23.63 17.50 39.53 3.41
2563 2589 2.513753 ACAGCCGTTTGATCAATTGGA 58.486 42.857 23.63 2.44 0.00 3.53
2564 2590 2.988493 CAACAGCCGTTTGATCAATTGG 59.012 45.455 17.84 17.84 31.13 3.16
2565 2591 3.670055 GTCAACAGCCGTTTGATCAATTG 59.330 43.478 9.40 8.96 31.13 2.32
2566 2592 3.609175 CGTCAACAGCCGTTTGATCAATT 60.609 43.478 9.40 0.00 31.13 2.32
2567 2593 2.095768 CGTCAACAGCCGTTTGATCAAT 60.096 45.455 9.40 0.00 31.13 2.57
2568 2594 1.262950 CGTCAACAGCCGTTTGATCAA 59.737 47.619 3.38 3.38 31.13 2.57
2569 2595 0.865111 CGTCAACAGCCGTTTGATCA 59.135 50.000 0.00 0.00 31.13 2.92
2570 2596 1.144969 TCGTCAACAGCCGTTTGATC 58.855 50.000 0.00 0.00 31.13 2.92
2571 2597 1.808411 ATCGTCAACAGCCGTTTGAT 58.192 45.000 0.00 0.00 31.13 2.57
2572 2598 1.262950 CAATCGTCAACAGCCGTTTGA 59.737 47.619 0.00 0.00 36.41 2.69
2573 2599 1.002900 ACAATCGTCAACAGCCGTTTG 60.003 47.619 0.00 0.00 38.84 2.93
2574 2600 1.263217 GACAATCGTCAACAGCCGTTT 59.737 47.619 0.00 0.00 42.13 3.60
2575 2601 0.865769 GACAATCGTCAACAGCCGTT 59.134 50.000 0.00 0.00 42.13 4.44
2576 2602 1.282248 CGACAATCGTCAACAGCCGT 61.282 55.000 0.00 0.00 42.74 5.68
2577 2603 1.416049 CGACAATCGTCAACAGCCG 59.584 57.895 0.00 0.00 42.74 5.52
2609 2635 2.037066 GCTACACGTACGACGAATTTCG 60.037 50.000 24.41 16.84 46.05 3.46
2610 2636 2.910482 TGCTACACGTACGACGAATTTC 59.090 45.455 24.41 3.67 46.05 2.17
2611 2637 2.912967 CTGCTACACGTACGACGAATTT 59.087 45.455 24.41 0.00 46.05 1.82
2612 2638 2.095567 ACTGCTACACGTACGACGAATT 60.096 45.455 24.41 0.00 46.05 2.17
2613 2639 1.466167 ACTGCTACACGTACGACGAAT 59.534 47.619 24.41 4.57 46.05 3.34
2614 2640 0.867746 ACTGCTACACGTACGACGAA 59.132 50.000 24.41 3.26 46.05 3.85
2615 2641 0.867746 AACTGCTACACGTACGACGA 59.132 50.000 24.41 4.92 46.05 4.20
2617 2643 2.096069 TGAGAACTGCTACACGTACGAC 60.096 50.000 24.41 6.19 0.00 4.34
2618 2644 2.096069 GTGAGAACTGCTACACGTACGA 60.096 50.000 24.41 0.00 0.00 3.43
2619 2645 2.240040 GTGAGAACTGCTACACGTACG 58.760 52.381 15.01 15.01 0.00 3.67
2620 2646 3.278367 TGTGAGAACTGCTACACGTAC 57.722 47.619 0.00 0.00 36.25 3.67
2621 2647 4.142534 GGTATGTGAGAACTGCTACACGTA 60.143 45.833 0.00 0.00 36.25 3.57
2622 2648 3.367087 GGTATGTGAGAACTGCTACACGT 60.367 47.826 0.00 0.00 36.25 4.49
2623 2649 3.179830 GGTATGTGAGAACTGCTACACG 58.820 50.000 0.00 0.00 36.25 4.49
2624 2650 4.177026 CTGGTATGTGAGAACTGCTACAC 58.823 47.826 0.00 0.00 0.00 2.90
2625 2651 3.368427 GCTGGTATGTGAGAACTGCTACA 60.368 47.826 0.00 0.00 0.00 2.74
2626 2652 3.118956 AGCTGGTATGTGAGAACTGCTAC 60.119 47.826 0.00 0.00 0.00 3.58
2627 2653 3.099905 AGCTGGTATGTGAGAACTGCTA 58.900 45.455 0.00 0.00 0.00 3.49
2628 2654 1.905215 AGCTGGTATGTGAGAACTGCT 59.095 47.619 0.00 0.00 0.00 4.24
2629 2655 2.005451 CAGCTGGTATGTGAGAACTGC 58.995 52.381 5.57 0.00 0.00 4.40
2630 2656 2.005451 GCAGCTGGTATGTGAGAACTG 58.995 52.381 17.12 0.00 0.00 3.16
2631 2657 1.625315 TGCAGCTGGTATGTGAGAACT 59.375 47.619 17.12 0.00 0.00 3.01
2632 2658 2.099141 TGCAGCTGGTATGTGAGAAC 57.901 50.000 17.12 0.00 0.00 3.01
2633 2659 3.011818 CAATGCAGCTGGTATGTGAGAA 58.988 45.455 17.12 0.00 0.00 2.87
2634 2660 2.236893 TCAATGCAGCTGGTATGTGAGA 59.763 45.455 17.12 0.00 0.00 3.27
2635 2661 2.353889 GTCAATGCAGCTGGTATGTGAG 59.646 50.000 17.12 0.00 0.00 3.51
2636 2662 2.290197 TGTCAATGCAGCTGGTATGTGA 60.290 45.455 17.12 5.70 0.00 3.58
2637 2663 2.086094 TGTCAATGCAGCTGGTATGTG 58.914 47.619 17.12 3.75 0.00 3.21
2638 2664 2.495155 TGTCAATGCAGCTGGTATGT 57.505 45.000 17.12 0.00 0.00 2.29
2639 2665 3.441222 TCTTTGTCAATGCAGCTGGTATG 59.559 43.478 17.12 0.00 0.00 2.39
2640 2666 3.689347 TCTTTGTCAATGCAGCTGGTAT 58.311 40.909 17.12 0.00 0.00 2.73
2641 2667 3.138884 TCTTTGTCAATGCAGCTGGTA 57.861 42.857 17.12 0.00 0.00 3.25
2642 2668 1.985473 TCTTTGTCAATGCAGCTGGT 58.015 45.000 17.12 0.00 0.00 4.00
2643 2669 2.876091 CATCTTTGTCAATGCAGCTGG 58.124 47.619 17.12 0.00 0.00 4.85
2644 2670 2.259618 GCATCTTTGTCAATGCAGCTG 58.740 47.619 10.11 10.11 45.97 4.24
2645 2671 2.649331 GCATCTTTGTCAATGCAGCT 57.351 45.000 5.03 0.00 45.97 4.24
2983 3009 9.087424 GACAAAGAAGTTTAAAATGCAGTTTCT 57.913 29.630 16.40 4.42 0.00 2.52
3156 3387 2.462456 TGGAATCTGAGTGCACTGAC 57.538 50.000 27.27 11.73 0.00 3.51
3157 3388 2.634453 TCTTGGAATCTGAGTGCACTGA 59.366 45.455 27.27 16.42 0.00 3.41
3158 3389 3.049708 TCTTGGAATCTGAGTGCACTG 57.950 47.619 27.27 11.39 0.00 3.66
3159 3390 3.996921 ATCTTGGAATCTGAGTGCACT 57.003 42.857 21.88 21.88 0.00 4.40
3160 3391 4.569966 CAGTATCTTGGAATCTGAGTGCAC 59.430 45.833 9.40 9.40 0.00 4.57
3163 3394 4.125703 GCCAGTATCTTGGAATCTGAGTG 58.874 47.826 0.00 0.00 40.87 3.51
3167 3398 4.264253 TGTTGCCAGTATCTTGGAATCTG 58.736 43.478 0.00 0.00 40.87 2.90
3171 3402 2.754552 GCATGTTGCCAGTATCTTGGAA 59.245 45.455 0.00 0.00 40.87 3.53
3172 3403 2.368439 GCATGTTGCCAGTATCTTGGA 58.632 47.619 0.00 0.00 40.87 3.53
3173 3404 1.064505 CGCATGTTGCCAGTATCTTGG 59.935 52.381 0.00 0.00 41.12 3.61
3174 3405 1.739466 ACGCATGTTGCCAGTATCTTG 59.261 47.619 0.00 0.00 41.12 3.02
3175 3406 2.009774 GACGCATGTTGCCAGTATCTT 58.990 47.619 0.00 0.00 41.12 2.40
3176 3407 1.066215 TGACGCATGTTGCCAGTATCT 60.066 47.619 0.00 0.00 41.12 1.98
3177 3408 1.328680 CTGACGCATGTTGCCAGTATC 59.671 52.381 0.00 0.00 41.12 2.24
3178 3409 1.339055 ACTGACGCATGTTGCCAGTAT 60.339 47.619 7.14 0.00 41.69 2.12
3179 3410 0.034756 ACTGACGCATGTTGCCAGTA 59.965 50.000 7.14 0.00 41.69 2.74
3181 3412 1.208358 CACTGACGCATGTTGCCAG 59.792 57.895 0.00 0.00 41.12 4.85
3183 3414 2.126734 GCACTGACGCATGTTGCC 60.127 61.111 0.00 0.00 41.12 4.52
3184 3415 1.727022 GTGCACTGACGCATGTTGC 60.727 57.895 10.32 0.00 45.26 4.17
3185 3416 0.110509 GAGTGCACTGACGCATGTTG 60.111 55.000 27.27 0.00 45.26 3.33
3186 3417 0.532640 TGAGTGCACTGACGCATGTT 60.533 50.000 27.27 0.00 45.26 2.71
3188 3419 0.668401 TCTGAGTGCACTGACGCATG 60.668 55.000 27.27 3.26 45.26 4.06
3189 3420 0.248565 ATCTGAGTGCACTGACGCAT 59.751 50.000 27.27 5.82 45.26 4.73
3190 3421 0.033920 AATCTGAGTGCACTGACGCA 59.966 50.000 27.27 14.98 40.32 5.24
3191 3422 0.718343 GAATCTGAGTGCACTGACGC 59.282 55.000 27.27 10.48 0.00 5.19
3292 3523 2.418777 CGCCATGATCGCCTCTCA 59.581 61.111 0.00 0.00 0.00 3.27
3483 4759 7.281100 GCTTGCTACCAGTTATCTAAGTTGATT 59.719 37.037 0.00 0.00 0.00 2.57
3490 4766 6.049955 ACTTGCTTGCTACCAGTTATCTAA 57.950 37.500 0.00 0.00 0.00 2.10
3498 4774 1.541588 GGGAAACTTGCTTGCTACCAG 59.458 52.381 0.00 0.00 0.00 4.00
3800 5076 4.343239 GCTTCAAATGGCTGAGGGAATATT 59.657 41.667 0.00 0.00 0.00 1.28
3836 5112 6.892310 AAAATTTCAGTTTGACTGTGAAGC 57.108 33.333 7.85 0.00 46.03 3.86
3870 5146 7.775561 AGACAGGAATTCCTATTAACATGTTCC 59.224 37.037 26.61 6.05 46.65 3.62
3985 7072 2.106566 CTCCTCTAGCTTGCTTCCTCA 58.893 52.381 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.