Multiple sequence alignment - TraesCS5A01G073200

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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 TraesCS5A01G073200 chr5A 100.000 3287 0 0 1 3287 85254227 85257513 0.000000e+00 6071.0
1 TraesCS5A01G073200 chr5A 85.000 120 16 2 546 665 85172109 85172226 1.600000e-23 121.0
2 TraesCS5A01G073200 chr5D 93.002 2015 85 18 554 2534 91552240 91554232 0.000000e+00 2889.0
3 TraesCS5A01G073200 chr5D 96.709 547 17 1 1 546 508313968 508313422 0.000000e+00 909.0
4 TraesCS5A01G073200 chr5D 96.709 547 15 3 1 545 110935661 110935116 0.000000e+00 907.0
5 TraesCS5A01G073200 chr5D 91.414 198 12 1 3015 3212 91554955 91555147 1.940000e-67 267.0
6 TraesCS5A01G073200 chr5D 88.462 182 14 2 2654 2835 91554319 91554493 2.570000e-51 213.0
7 TraesCS5A01G073200 chr5D 81.818 121 19 3 546 665 91411727 91411845 7.510000e-17 99.0
8 TraesCS5A01G073200 chr5B 93.580 1729 67 17 649 2369 96850330 96852022 0.000000e+00 2538.0
9 TraesCS5A01G073200 chr5B 92.308 273 16 1 3015 3287 96852894 96853161 1.850000e-102 383.0
10 TraesCS5A01G073200 chr5B 94.702 151 5 3 546 693 96850196 96850346 7.090000e-57 231.0
11 TraesCS5A01G073200 chr5B 89.011 182 13 2 2654 2835 96852252 96852426 5.520000e-53 219.0
12 TraesCS5A01G073200 chr5B 90.756 119 7 1 2420 2534 96852047 96852165 4.390000e-34 156.0
13 TraesCS5A01G073200 chr5B 93.878 49 2 1 2618 2666 96852185 96852232 4.550000e-09 73.1
14 TraesCS5A01G073200 chr2D 96.886 546 16 1 1 545 73105560 73105015 0.000000e+00 913.0
15 TraesCS5A01G073200 chr2D 96.703 546 17 1 1 545 563724230 563723685 0.000000e+00 907.0
16 TraesCS5A01G073200 chr2D 96.533 548 18 1 1 547 231237635 231237088 0.000000e+00 905.0
17 TraesCS5A01G073200 chr2D 100.000 29 0 0 2014 2042 533166294 533166322 2.000000e-03 54.7
18 TraesCS5A01G073200 chr6D 96.881 545 16 1 3 546 174469729 174470273 0.000000e+00 911.0
19 TraesCS5A01G073200 chr7D 96.709 547 17 1 1 546 235562763 235563309 0.000000e+00 909.0
20 TraesCS5A01G073200 chr7D 96.703 546 17 1 1 545 321034310 321034855 0.000000e+00 907.0
21 TraesCS5A01G073200 chr1D 96.703 546 17 1 1 545 363785251 363784706 0.000000e+00 907.0
22 TraesCS5A01G073200 chr2B 87.097 62 6 2 559 619 44900913 44900853 5.890000e-08 69.4
23 TraesCS5A01G073200 chr2B 100.000 29 0 0 2014 2042 632989201 632989229 2.000000e-03 54.7
24 TraesCS5A01G073200 chr2A 85.075 67 6 3 556 620 30278553 30278617 7.610000e-07 65.8
25 TraesCS5A01G073200 chr2A 92.500 40 3 0 2003 2042 677547133 677547172 1.270000e-04 58.4


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 TraesCS5A01G073200 chr5A 85254227 85257513 3286 False 6071.000000 6071 100.000000 1 3287 1 chr5A.!!$F2 3286
1 TraesCS5A01G073200 chr5D 91552240 91555147 2907 False 1123.000000 2889 90.959333 554 3212 3 chr5D.!!$F2 2658
2 TraesCS5A01G073200 chr5D 508313422 508313968 546 True 909.000000 909 96.709000 1 546 1 chr5D.!!$R2 545
3 TraesCS5A01G073200 chr5D 110935116 110935661 545 True 907.000000 907 96.709000 1 545 1 chr5D.!!$R1 544
4 TraesCS5A01G073200 chr5B 96850196 96853161 2965 False 600.016667 2538 92.372500 546 3287 6 chr5B.!!$F1 2741
5 TraesCS5A01G073200 chr2D 73105015 73105560 545 True 913.000000 913 96.886000 1 545 1 chr2D.!!$R1 544
6 TraesCS5A01G073200 chr2D 563723685 563724230 545 True 907.000000 907 96.703000 1 545 1 chr2D.!!$R3 544
7 TraesCS5A01G073200 chr2D 231237088 231237635 547 True 905.000000 905 96.533000 1 547 1 chr2D.!!$R2 546
8 TraesCS5A01G073200 chr6D 174469729 174470273 544 False 911.000000 911 96.881000 3 546 1 chr6D.!!$F1 543
9 TraesCS5A01G073200 chr7D 235562763 235563309 546 False 909.000000 909 96.709000 1 546 1 chr7D.!!$F1 545
10 TraesCS5A01G073200 chr7D 321034310 321034855 545 False 907.000000 907 96.703000 1 545 1 chr7D.!!$F2 544
11 TraesCS5A01G073200 chr1D 363784706 363785251 545 True 907.000000 907 96.703000 1 545 1 chr1D.!!$R1 544

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
376 377 0.034767 ACTAGTCATGTCGGTCCGGA 60.035 55.0 12.29 0.0 0.0 5.14 F
754 790 0.175760 TAACCGGATGCTGCTGAGTC 59.824 55.0 9.46 0.0 0.0 3.36 F
936 993 0.729116 CGCATTCCACTTTCGCATCT 59.271 50.0 0.00 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1622 1694 0.031616 GGACACCTCCTCCTCCTCAT 60.032 60.0 0.00 0.0 33.07 2.90 R
1676 1748 0.107897 TTGCGTGTGAGTCCACTTGT 60.108 50.0 9.24 0.0 43.55 3.16 R
2856 3117 0.530744 ATCGGCGACTACAAGCAAGA 59.469 50.0 13.76 0.0 34.54 3.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 3.156288 TGAGCCATAGTAGTCCGCTAT 57.844 47.619 0.00 0.00 0.00 2.97
150 151 1.227853 GAACACTTGACTGGCCGGT 60.228 57.895 19.82 19.82 0.00 5.28
239 240 1.397672 CTAGCCTGCTACAGCTCAGA 58.602 55.000 2.44 0.00 42.66 3.27
350 351 3.395639 CGTAAGTTAGTGCCACTTTGGA 58.604 45.455 1.02 0.00 40.96 3.53
376 377 0.034767 ACTAGTCATGTCGGTCCGGA 60.035 55.000 12.29 0.00 0.00 5.14
466 467 2.652530 GTAAGGCGACACCCGTGA 59.347 61.111 0.96 0.00 40.58 4.35
557 559 1.000052 TCCTGACAATGCGACACGTTA 60.000 47.619 0.00 0.00 0.00 3.18
704 738 1.273986 TGGGCTGCAGCATCTCCTAA 61.274 55.000 37.63 13.57 44.36 2.69
719 753 4.832492 TCTCCTAATCCTGGGCTTTAGAT 58.168 43.478 11.23 0.00 0.00 1.98
754 790 0.175760 TAACCGGATGCTGCTGAGTC 59.824 55.000 9.46 0.00 0.00 3.36
782 819 2.575532 CTCTTCTGTTGTTTCCAGGCA 58.424 47.619 0.00 0.00 0.00 4.75
833 870 2.045242 TCCCTCCTCCACGAGACG 60.045 66.667 0.00 0.00 30.97 4.18
884 940 2.060980 GCCCACCTCGACCATCTCT 61.061 63.158 0.00 0.00 0.00 3.10
925 982 1.397672 CTCTCTCTCCTCGCATTCCA 58.602 55.000 0.00 0.00 0.00 3.53
928 985 1.480137 CTCTCTCCTCGCATTCCACTT 59.520 52.381 0.00 0.00 0.00 3.16
936 993 0.729116 CGCATTCCACTTTCGCATCT 59.271 50.000 0.00 0.00 0.00 2.90
956 1013 2.159382 TCATCCGCTGATATCGCTACA 58.841 47.619 14.57 2.82 0.00 2.74
989 1046 4.075793 CTCCTCCCTCCCCACCGA 62.076 72.222 0.00 0.00 0.00 4.69
1113 1173 4.961511 AAGTGCGTCGCGAAGGCA 62.962 61.111 26.38 26.38 46.01 4.75
1180 1240 2.820197 CAAACCCTACAAGGCTTCTTCC 59.180 50.000 0.00 0.00 32.73 3.46
1200 1260 2.240667 CCTCATTGACAAGGAGACCCAT 59.759 50.000 27.01 0.00 41.61 4.00
1213 1273 1.961180 GACCCATAGGCAGCGTGTCT 61.961 60.000 0.00 0.00 35.80 3.41
1259 1319 2.725008 GCCTCTCCAGATCGACCG 59.275 66.667 0.00 0.00 0.00 4.79
1351 1411 1.151668 CCTCTTCGAGCACAAACTGG 58.848 55.000 0.00 0.00 0.00 4.00
1386 1446 8.638873 CCATATAATCTATTGGGCTATGTCGTA 58.361 37.037 0.00 0.00 0.00 3.43
1396 1456 1.497991 CTATGTCGTATGCAACCCCG 58.502 55.000 0.00 0.00 0.00 5.73
1458 1518 2.343101 CTTCCGTTGTATCTTCGGCAA 58.657 47.619 0.00 0.00 43.35 4.52
1467 1527 1.256812 ATCTTCGGCAACCCAAAAGG 58.743 50.000 0.00 0.00 43.78 3.11
1615 1687 1.292941 TGAGGAGGAGGAGGAGGAGG 61.293 65.000 0.00 0.00 0.00 4.30
1616 1688 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1617 1689 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1618 1690 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1619 1691 2.018086 AGGAGGAGGAGGAGGAGGG 61.018 68.421 0.00 0.00 0.00 4.30
1620 1692 2.123033 GAGGAGGAGGAGGAGGGC 60.123 72.222 0.00 0.00 0.00 5.19
1621 1693 4.150454 AGGAGGAGGAGGAGGGCG 62.150 72.222 0.00 0.00 0.00 6.13
1622 1694 4.144727 GGAGGAGGAGGAGGGCGA 62.145 72.222 0.00 0.00 0.00 5.54
1623 1695 2.200092 GAGGAGGAGGAGGGCGAT 59.800 66.667 0.00 0.00 0.00 4.58
1624 1696 2.123077 AGGAGGAGGAGGGCGATG 60.123 66.667 0.00 0.00 0.00 3.84
1625 1697 2.123251 GGAGGAGGAGGGCGATGA 60.123 66.667 0.00 0.00 0.00 2.92
1626 1698 2.206536 GGAGGAGGAGGGCGATGAG 61.207 68.421 0.00 0.00 0.00 2.90
1627 1699 2.123077 AGGAGGAGGGCGATGAGG 60.123 66.667 0.00 0.00 0.00 3.86
1628 1700 2.123251 GGAGGAGGGCGATGAGGA 60.123 66.667 0.00 0.00 0.00 3.71
1629 1701 2.206536 GGAGGAGGGCGATGAGGAG 61.207 68.421 0.00 0.00 0.00 3.69
1630 1702 2.123077 AGGAGGGCGATGAGGAGG 60.123 66.667 0.00 0.00 0.00 4.30
1631 1703 2.123251 GGAGGGCGATGAGGAGGA 60.123 66.667 0.00 0.00 0.00 3.71
1632 1704 2.206536 GGAGGGCGATGAGGAGGAG 61.207 68.421 0.00 0.00 0.00 3.69
1633 1705 2.123077 AGGGCGATGAGGAGGAGG 60.123 66.667 0.00 0.00 0.00 4.30
1634 1706 2.123251 GGGCGATGAGGAGGAGGA 60.123 66.667 0.00 0.00 0.00 3.71
1635 1707 2.206536 GGGCGATGAGGAGGAGGAG 61.207 68.421 0.00 0.00 0.00 3.69
1636 1708 2.206536 GGCGATGAGGAGGAGGAGG 61.207 68.421 0.00 0.00 0.00 4.30
1676 1748 2.568062 ACGTCTACTCCTCTGAGACTGA 59.432 50.000 6.17 0.00 41.42 3.41
2048 2120 1.933853 GCATAGTGTGAGCTTTACGGG 59.066 52.381 0.00 0.00 0.00 5.28
2139 2211 6.047870 TGGAAATGTGGTTTTCATTGTTCAG 58.952 36.000 0.00 0.00 37.34 3.02
2155 2227 3.181449 TGTTCAGGATTGGAACCGAAAGA 60.181 43.478 0.00 0.00 43.05 2.52
2171 2243 8.539770 AACCGAAAGATGATATCATATCACAC 57.460 34.615 18.19 7.40 36.57 3.82
2191 2263 3.859961 CACGGACAATAAGCTAGTGAGTG 59.140 47.826 0.00 0.00 0.00 3.51
2196 2268 6.757010 CGGACAATAAGCTAGTGAGTGTTATT 59.243 38.462 0.00 0.00 30.24 1.40
2236 2308 6.543100 TGATGCTTCAGATATGCATGTTGTAA 59.457 34.615 10.16 0.00 46.03 2.41
2273 2345 4.436998 CGAGTCACCGGCACTCCC 62.437 72.222 22.54 5.87 37.58 4.30
2305 2377 4.661993 TGAATGTGTTGCGTTCATCTAC 57.338 40.909 0.00 0.00 45.27 2.59
2306 2378 4.061596 TGAATGTGTTGCGTTCATCTACA 58.938 39.130 0.00 0.00 45.27 2.74
2313 2385 3.934457 TGCGTTCATCTACACAGAAGA 57.066 42.857 0.00 0.00 33.50 2.87
2342 2414 8.821894 GCAACTTGGTTAGATCTAGTAGAATTG 58.178 37.037 3.45 6.92 0.00 2.32
2343 2415 9.319143 CAACTTGGTTAGATCTAGTAGAATTGG 57.681 37.037 3.45 0.00 0.00 3.16
2383 2461 7.467344 CCATGGTTGGATGTATCCTTCTCATG 61.467 46.154 2.57 16.16 46.92 3.07
2393 2471 2.795329 TCCTTCTCATGCTTTTGGTCC 58.205 47.619 0.00 0.00 0.00 4.46
2401 2479 5.183713 TCTCATGCTTTTGGTCCAAGTAATG 59.816 40.000 4.09 8.05 0.00 1.90
2448 2526 6.538945 TGTCAGGTAGTTTCATGTATGCTA 57.461 37.500 0.00 0.00 0.00 3.49
2454 2532 9.416794 CAGGTAGTTTCATGTATGCTAGATTAG 57.583 37.037 0.00 0.00 0.00 1.73
2486 2564 6.471146 TGTTGCCCAAGTTGCATATAATTTT 58.529 32.000 0.00 0.00 38.76 1.82
2510 2593 7.213216 TGAAGTGTTAATGCTTCAAATGCTA 57.787 32.000 16.98 0.00 45.33 3.49
2511 2594 7.829725 TGAAGTGTTAATGCTTCAAATGCTAT 58.170 30.769 16.98 0.00 45.33 2.97
2525 2608 8.806429 TTCAAATGCTATCTTTTATGTCTCCA 57.194 30.769 0.00 0.00 0.00 3.86
2530 2613 7.974482 TGCTATCTTTTATGTCTCCATGATG 57.026 36.000 0.00 0.00 32.29 3.07
2562 2645 7.754851 TTGTCTTACATTACTCCTTTTTCCC 57.245 36.000 0.00 0.00 0.00 3.97
2563 2646 7.086685 TGTCTTACATTACTCCTTTTTCCCT 57.913 36.000 0.00 0.00 0.00 4.20
2564 2647 6.940298 TGTCTTACATTACTCCTTTTTCCCTG 59.060 38.462 0.00 0.00 0.00 4.45
2565 2648 6.374613 GTCTTACATTACTCCTTTTTCCCTGG 59.625 42.308 0.00 0.00 0.00 4.45
2566 2649 3.431415 ACATTACTCCTTTTTCCCTGGC 58.569 45.455 0.00 0.00 0.00 4.85
2567 2650 2.597578 TTACTCCTTTTTCCCTGGCC 57.402 50.000 0.00 0.00 0.00 5.36
2568 2651 0.702316 TACTCCTTTTTCCCTGGCCC 59.298 55.000 0.00 0.00 0.00 5.80
2569 2652 1.074296 ACTCCTTTTTCCCTGGCCCT 61.074 55.000 0.00 0.00 0.00 5.19
2570 2653 0.999712 CTCCTTTTTCCCTGGCCCTA 59.000 55.000 0.00 0.00 0.00 3.53
2571 2654 1.570979 CTCCTTTTTCCCTGGCCCTAT 59.429 52.381 0.00 0.00 0.00 2.57
2572 2655 2.007636 TCCTTTTTCCCTGGCCCTATT 58.992 47.619 0.00 0.00 0.00 1.73
2573 2656 3.203059 TCCTTTTTCCCTGGCCCTATTA 58.797 45.455 0.00 0.00 0.00 0.98
2574 2657 3.204382 TCCTTTTTCCCTGGCCCTATTAG 59.796 47.826 0.00 0.00 0.00 1.73
2575 2658 3.052869 CCTTTTTCCCTGGCCCTATTAGT 60.053 47.826 0.00 0.00 0.00 2.24
2576 2659 3.662759 TTTTCCCTGGCCCTATTAGTG 57.337 47.619 0.00 0.00 0.00 2.74
2577 2660 2.579624 TTCCCTGGCCCTATTAGTGA 57.420 50.000 0.00 0.00 0.00 3.41
2578 2661 2.103153 TCCCTGGCCCTATTAGTGAG 57.897 55.000 0.00 0.00 0.00 3.51
2579 2662 1.294068 TCCCTGGCCCTATTAGTGAGT 59.706 52.381 0.00 0.00 0.00 3.41
2580 2663 2.520980 TCCCTGGCCCTATTAGTGAGTA 59.479 50.000 0.00 0.00 0.00 2.59
2581 2664 2.633481 CCCTGGCCCTATTAGTGAGTAC 59.367 54.545 0.00 0.00 0.00 2.73
2582 2665 3.577919 CCTGGCCCTATTAGTGAGTACT 58.422 50.000 0.00 0.00 40.99 2.73
2583 2666 4.448787 CCCTGGCCCTATTAGTGAGTACTA 60.449 50.000 0.00 0.00 38.36 1.82
2591 2674 7.068470 GCCCTATTAGTGAGTACTAACTGACTT 59.932 40.741 21.55 3.64 46.53 3.01
2592 2675 8.968969 CCCTATTAGTGAGTACTAACTGACTTT 58.031 37.037 21.55 2.97 46.53 2.66
2616 2699 7.504924 TTTTGTTCCTAAAGACCTGTGTATG 57.495 36.000 0.00 0.00 0.00 2.39
2668 2782 8.620116 TGTTTATATGTGATGTATGTGATGGG 57.380 34.615 0.00 0.00 0.00 4.00
2674 2788 6.245890 TGTGATGTATGTGATGGGAATACA 57.754 37.500 0.00 0.00 40.16 2.29
2685 2799 6.828273 TGTGATGGGAATACATAAACTGAAGG 59.172 38.462 0.00 0.00 0.00 3.46
2689 2803 6.964464 TGGGAATACATAAACTGAAGGCTTA 58.036 36.000 0.00 0.00 0.00 3.09
2700 2814 5.824904 ACTGAAGGCTTACATTAATGCTG 57.175 39.130 15.48 6.92 0.00 4.41
2747 2861 5.726793 AGGACAATAGGTTCCTAGTTGATGT 59.273 40.000 18.45 12.10 0.00 3.06
2770 2884 6.721668 TGTTGGTTACATGATATTGGTTTCCA 59.278 34.615 0.00 0.00 0.00 3.53
2783 2897 2.164624 TGGTTTCCACACCAAGTTTTCG 59.835 45.455 0.00 0.00 44.30 3.46
2787 2901 2.920524 TCCACACCAAGTTTTCGCTTA 58.079 42.857 0.00 0.00 0.00 3.09
2797 2911 5.335127 CAAGTTTTCGCTTATATGCTGCTT 58.665 37.500 8.77 0.00 0.00 3.91
2856 3117 1.069823 CATACTTCGCCCAGAGCAGAT 59.930 52.381 0.00 0.00 44.04 2.90
2872 3133 1.929836 CAGATCTTGCTTGTAGTCGCC 59.070 52.381 0.00 0.00 0.00 5.54
2902 3163 1.474143 GGCCTAGTTTAGCAGAGCTGG 60.474 57.143 0.00 0.00 40.10 4.85
2909 3170 3.774216 AGTTTAGCAGAGCTGGAGAAGAT 59.226 43.478 0.00 0.00 40.10 2.40
2910 3171 4.959210 AGTTTAGCAGAGCTGGAGAAGATA 59.041 41.667 0.00 0.00 40.10 1.98
2916 3177 5.010922 AGCAGAGCTGGAGAAGATAACTATG 59.989 44.000 0.00 0.00 37.57 2.23
2944 3205 4.046938 TCTCGCTGACACCAAATAGATC 57.953 45.455 0.00 0.00 0.00 2.75
2946 3207 4.046938 TCGCTGACACCAAATAGATCTC 57.953 45.455 0.00 0.00 0.00 2.75
2960 3221 7.041780 CCAAATAGATCTCTTGGTTCCGTATTG 60.042 40.741 21.01 2.91 35.80 1.90
2962 3223 5.269505 AGATCTCTTGGTTCCGTATTGAG 57.730 43.478 0.00 0.00 0.00 3.02
2989 3250 5.582665 GGAACTGGCTATTAACTCTTGACAG 59.417 44.000 0.00 0.00 0.00 3.51
2998 3259 8.119226 GCTATTAACTCTTGACAGCATTGTAAG 58.881 37.037 0.00 0.00 37.76 2.34
3008 3271 6.567959 TGACAGCATTGTAAGATCTAGAGTG 58.432 40.000 0.00 0.00 37.76 3.51
3021 3425 5.591067 AGATCTAGAGTGTGGTACTAACTGC 59.409 44.000 0.00 0.00 40.53 4.40
3045 3449 2.816087 CAATGCTCAAGCCTACTGTTGT 59.184 45.455 0.00 0.00 41.18 3.32
3046 3450 1.882912 TGCTCAAGCCTACTGTTGTG 58.117 50.000 0.00 0.00 41.18 3.33
3047 3451 1.416030 TGCTCAAGCCTACTGTTGTGA 59.584 47.619 0.00 0.00 41.18 3.58
3048 3452 2.072298 GCTCAAGCCTACTGTTGTGAG 58.928 52.381 4.72 4.72 36.43 3.51
3049 3453 2.072298 CTCAAGCCTACTGTTGTGAGC 58.928 52.381 0.00 0.00 0.00 4.26
3088 3492 4.202315 ACCTGTCTTATGCAACACACTGTA 60.202 41.667 0.00 0.00 0.00 2.74
3090 3494 5.163824 CCTGTCTTATGCAACACACTGTATG 60.164 44.000 0.00 0.00 0.00 2.39
3095 3499 3.980646 TGCAACACACTGTATGTTTCC 57.019 42.857 0.94 0.00 40.64 3.13
3110 3514 7.254852 TGTATGTTTCCTTCTGTGTTTTGTTC 58.745 34.615 0.00 0.00 0.00 3.18
3123 3527 6.804677 TGTGTTTTGTTCAGCATATGTCTTT 58.195 32.000 4.29 0.00 0.00 2.52
3187 3591 4.556697 TCAGCCTTTCATGATCCTACCTA 58.443 43.478 0.00 0.00 0.00 3.08
3212 3616 8.766994 ATGCCAGGATACATTAACTTAACATT 57.233 30.769 0.00 0.00 41.41 2.71
3214 3618 9.337396 TGCCAGGATACATTAACTTAACATTAG 57.663 33.333 0.00 0.00 41.41 1.73
3253 3657 4.516321 GGAGTTTTTCAGGCATTTTTGCAT 59.484 37.500 0.00 0.00 36.33 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.309296 CCCATAAGAGAGGCTACCAAGA 58.691 50.000 0.00 0.00 0.00 3.02
150 151 4.929211 CACAGGAACGAAGTGAATCACATA 59.071 41.667 16.38 0.00 45.00 2.29
239 240 0.831307 GCTAACAGGACTCCGGGAAT 59.169 55.000 0.00 0.00 0.00 3.01
371 372 3.844640 TCCATATGACAGAGAATCCGGA 58.155 45.455 6.61 6.61 33.66 5.14
376 377 5.624052 CGCTAGCATCCATATGACAGAGAAT 60.624 44.000 16.45 0.00 34.84 2.40
466 467 0.249398 GGCCTCACACACGGTATTCT 59.751 55.000 0.00 0.00 0.00 2.40
624 627 6.778834 AATTGTCATGGCAGATTCATAACA 57.221 33.333 0.00 0.00 0.00 2.41
704 738 3.674477 AGAGGAATCTAAAGCCCAGGAT 58.326 45.455 0.00 0.00 0.00 3.24
737 773 1.620739 ATGACTCAGCAGCATCCGGT 61.621 55.000 0.00 0.00 0.00 5.28
754 790 5.159209 GGAAACAACAGAAGAGCATTCATG 58.841 41.667 4.71 0.00 0.00 3.07
782 819 2.929043 AGGGAAAGAAATGGAGGATGGT 59.071 45.455 0.00 0.00 0.00 3.55
907 963 1.107114 GTGGAATGCGAGGAGAGAGA 58.893 55.000 0.00 0.00 0.00 3.10
908 964 1.110442 AGTGGAATGCGAGGAGAGAG 58.890 55.000 0.00 0.00 0.00 3.20
909 965 1.561643 AAGTGGAATGCGAGGAGAGA 58.438 50.000 0.00 0.00 0.00 3.10
936 993 2.095212 GTGTAGCGATATCAGCGGATGA 60.095 50.000 9.82 0.00 43.70 2.92
1180 1240 3.641434 ATGGGTCTCCTTGTCAATGAG 57.359 47.619 10.68 10.68 0.00 2.90
1213 1273 5.247862 TCTATCAAGCAGATTTGTGAAGCA 58.752 37.500 0.00 0.00 38.19 3.91
1259 1319 2.011540 CTTCAGGAAGGCGAGGTTAC 57.988 55.000 1.01 0.00 34.87 2.50
1366 1426 5.178797 GCATACGACATAGCCCAATAGATT 58.821 41.667 0.00 0.00 0.00 2.40
1368 1428 3.576550 TGCATACGACATAGCCCAATAGA 59.423 43.478 0.00 0.00 0.00 1.98
1386 1446 4.652131 TTCGTGGCGGGGTTGCAT 62.652 61.111 0.00 0.00 36.28 3.96
1458 1518 4.966168 ACCAAATAGTTGAACCTTTTGGGT 59.034 37.500 28.32 15.68 46.75 4.51
1467 1527 6.921307 ACGGATCAAAAACCAAATAGTTGAAC 59.079 34.615 4.10 0.00 36.83 3.18
1469 1529 6.294286 GGACGGATCAAAAACCAAATAGTTGA 60.294 38.462 4.10 0.00 36.83 3.18
1615 1687 2.206536 CCTCCTCCTCATCGCCCTC 61.207 68.421 0.00 0.00 0.00 4.30
1616 1688 2.123077 CCTCCTCCTCATCGCCCT 60.123 66.667 0.00 0.00 0.00 5.19
1617 1689 2.123251 TCCTCCTCCTCATCGCCC 60.123 66.667 0.00 0.00 0.00 6.13
1618 1690 2.206536 CCTCCTCCTCCTCATCGCC 61.207 68.421 0.00 0.00 0.00 5.54
1619 1691 1.456705 ACCTCCTCCTCCTCATCGC 60.457 63.158 0.00 0.00 0.00 4.58
1620 1692 0.396417 ACACCTCCTCCTCCTCATCG 60.396 60.000 0.00 0.00 0.00 3.84
1621 1693 1.408969 GACACCTCCTCCTCCTCATC 58.591 60.000 0.00 0.00 0.00 2.92
1622 1694 0.031616 GGACACCTCCTCCTCCTCAT 60.032 60.000 0.00 0.00 33.07 2.90
1623 1695 1.388531 GGACACCTCCTCCTCCTCA 59.611 63.158 0.00 0.00 33.07 3.86
1624 1696 1.382009 GGGACACCTCCTCCTCCTC 60.382 68.421 0.00 0.00 36.68 3.71
1625 1697 2.781406 GGGACACCTCCTCCTCCT 59.219 66.667 0.00 0.00 36.68 3.69
1626 1698 2.760385 CGGGACACCTCCTCCTCC 60.760 72.222 0.00 0.00 36.68 4.30
1627 1699 2.760385 CCGGGACACCTCCTCCTC 60.760 72.222 0.00 0.00 36.68 3.71
1628 1700 3.273654 TCCGGGACACCTCCTCCT 61.274 66.667 0.00 0.00 36.68 3.69
1629 1701 3.075641 GTCCGGGACACCTCCTCC 61.076 72.222 22.10 0.00 36.68 4.30
1630 1702 3.450115 CGTCCGGGACACCTCCTC 61.450 72.222 25.80 0.00 36.68 3.71
1631 1703 4.296729 ACGTCCGGGACACCTCCT 62.297 66.667 25.80 0.00 36.68 3.69
1632 1704 3.756727 GACGTCCGGGACACCTCC 61.757 72.222 25.80 6.73 35.50 4.30
1633 1705 2.987547 TGACGTCCGGGACACCTC 60.988 66.667 25.80 16.44 32.09 3.85
1634 1706 2.989824 CTGACGTCCGGGACACCT 60.990 66.667 25.80 8.25 32.09 4.00
1635 1707 3.300765 ACTGACGTCCGGGACACC 61.301 66.667 25.80 16.55 32.09 4.16
1636 1708 2.049433 CACTGACGTCCGGGACAC 60.049 66.667 25.80 18.54 32.09 3.67
1676 1748 0.107897 TTGCGTGTGAGTCCACTTGT 60.108 50.000 9.24 0.00 43.55 3.16
1711 1783 1.104577 TTGTTCCGGCCACTTTGGAC 61.105 55.000 2.24 0.00 44.03 4.02
1922 1994 1.543944 CCCTTGGGATTGGGCAACAC 61.544 60.000 0.00 0.00 36.61 3.32
2048 2120 3.123790 GCGTCTCTTTTCTCTAAACAGCC 59.876 47.826 0.00 0.00 0.00 4.85
2139 2211 5.997746 TGATATCATCTTTCGGTTCCAATCC 59.002 40.000 0.00 0.00 0.00 3.01
2155 2227 9.591792 CTTATTGTCCGTGTGATATGATATCAT 57.408 33.333 21.50 21.50 40.22 2.45
2171 2243 4.111375 ACACTCACTAGCTTATTGTCCG 57.889 45.455 0.00 0.00 0.00 4.79
2224 2296 5.951747 AGGGAACATAAGTTACAACATGCAT 59.048 36.000 0.00 0.00 40.54 3.96
2236 2308 3.581332 TCGGAGAAACAGGGAACATAAGT 59.419 43.478 0.00 0.00 0.00 2.24
2271 2343 2.746269 CACATTCAGTGCTTGTTTGGG 58.254 47.619 0.00 0.00 42.15 4.12
2292 2364 4.251543 TCTTCTGTGTAGATGAACGCAA 57.748 40.909 0.00 0.00 39.25 4.85
2298 2370 6.782082 AGTTGCTATCTTCTGTGTAGATGA 57.218 37.500 0.00 0.00 40.22 2.92
2305 2377 6.166279 TCTAACCAAGTTGCTATCTTCTGTG 58.834 40.000 0.00 0.00 0.00 3.66
2306 2378 6.360370 TCTAACCAAGTTGCTATCTTCTGT 57.640 37.500 0.00 0.00 0.00 3.41
2313 2385 8.998277 TCTACTAGATCTAACCAAGTTGCTAT 57.002 34.615 3.57 0.00 0.00 2.97
2342 2414 5.129368 ACCATGGGCATAATATATCACCC 57.871 43.478 18.09 0.00 37.88 4.61
2343 2415 5.360714 CCAACCATGGGCATAATATATCACC 59.639 44.000 18.09 0.00 43.51 4.02
2393 2471 1.888512 ACTGCCTTGCACCATTACTTG 59.111 47.619 0.00 0.00 33.79 3.16
2401 2479 0.819259 TGTCTCAACTGCCTTGCACC 60.819 55.000 0.00 0.00 33.79 5.01
2448 2526 6.891908 ACTTGGGCAACATCATTTACTAATCT 59.108 34.615 0.00 0.00 39.74 2.40
2454 2532 3.679502 GCAACTTGGGCAACATCATTTAC 59.320 43.478 0.00 0.00 39.74 2.01
2536 2619 8.803235 GGGAAAAAGGAGTAATGTAAGACAATT 58.197 33.333 0.00 0.00 0.00 2.32
2537 2620 8.170730 AGGGAAAAAGGAGTAATGTAAGACAAT 58.829 33.333 0.00 0.00 0.00 2.71
2539 2622 6.940298 CAGGGAAAAAGGAGTAATGTAAGACA 59.060 38.462 0.00 0.00 0.00 3.41
2540 2623 6.374613 CCAGGGAAAAAGGAGTAATGTAAGAC 59.625 42.308 0.00 0.00 0.00 3.01
2541 2624 6.481643 CCAGGGAAAAAGGAGTAATGTAAGA 58.518 40.000 0.00 0.00 0.00 2.10
2542 2625 5.125578 GCCAGGGAAAAAGGAGTAATGTAAG 59.874 44.000 0.00 0.00 0.00 2.34
2543 2626 5.014202 GCCAGGGAAAAAGGAGTAATGTAA 58.986 41.667 0.00 0.00 0.00 2.41
2544 2627 4.569015 GGCCAGGGAAAAAGGAGTAATGTA 60.569 45.833 0.00 0.00 0.00 2.29
2545 2628 3.431415 GCCAGGGAAAAAGGAGTAATGT 58.569 45.455 0.00 0.00 0.00 2.71
2546 2629 2.760650 GGCCAGGGAAAAAGGAGTAATG 59.239 50.000 0.00 0.00 0.00 1.90
2547 2630 2.292257 GGGCCAGGGAAAAAGGAGTAAT 60.292 50.000 4.39 0.00 0.00 1.89
2548 2631 1.076513 GGGCCAGGGAAAAAGGAGTAA 59.923 52.381 4.39 0.00 0.00 2.24
2550 2633 1.074296 AGGGCCAGGGAAAAAGGAGT 61.074 55.000 6.18 0.00 0.00 3.85
2552 2635 1.693799 ATAGGGCCAGGGAAAAAGGA 58.306 50.000 6.18 0.00 0.00 3.36
2553 2636 2.550277 AATAGGGCCAGGGAAAAAGG 57.450 50.000 6.18 0.00 0.00 3.11
2554 2637 3.954258 CACTAATAGGGCCAGGGAAAAAG 59.046 47.826 6.18 0.00 0.00 2.27
2555 2638 3.594232 TCACTAATAGGGCCAGGGAAAAA 59.406 43.478 6.18 0.00 0.00 1.94
2556 2639 3.194620 TCACTAATAGGGCCAGGGAAAA 58.805 45.455 6.18 0.00 0.00 2.29
2557 2640 2.777692 CTCACTAATAGGGCCAGGGAAA 59.222 50.000 6.18 0.00 0.00 3.13
2558 2641 2.293586 ACTCACTAATAGGGCCAGGGAA 60.294 50.000 6.18 0.00 0.00 3.97
2559 2642 1.294068 ACTCACTAATAGGGCCAGGGA 59.706 52.381 6.18 0.00 0.00 4.20
2560 2643 1.807814 ACTCACTAATAGGGCCAGGG 58.192 55.000 6.18 0.00 0.00 4.45
2561 2644 3.577919 AGTACTCACTAATAGGGCCAGG 58.422 50.000 6.18 0.00 31.45 4.45
2562 2645 5.834204 AGTTAGTACTCACTAATAGGGCCAG 59.166 44.000 7.97 0.00 46.32 4.85
2563 2646 5.597182 CAGTTAGTACTCACTAATAGGGCCA 59.403 44.000 9.36 0.00 46.32 5.36
2564 2647 5.832060 TCAGTTAGTACTCACTAATAGGGCC 59.168 44.000 9.36 0.00 46.32 5.80
2565 2648 6.546772 AGTCAGTTAGTACTCACTAATAGGGC 59.453 42.308 9.36 0.00 46.32 5.19
2566 2649 8.522542 AAGTCAGTTAGTACTCACTAATAGGG 57.477 38.462 9.36 0.00 46.32 3.53
2591 2674 7.558444 ACATACACAGGTCTTTAGGAACAAAAA 59.442 33.333 0.00 0.00 33.21 1.94
2592 2675 7.057894 ACATACACAGGTCTTTAGGAACAAAA 58.942 34.615 0.00 0.00 33.21 2.44
2593 2676 6.597562 ACATACACAGGTCTTTAGGAACAAA 58.402 36.000 0.00 0.00 33.21 2.83
2594 2677 6.182507 ACATACACAGGTCTTTAGGAACAA 57.817 37.500 0.00 0.00 33.21 2.83
2595 2678 5.818678 ACATACACAGGTCTTTAGGAACA 57.181 39.130 0.00 0.00 33.21 3.18
2596 2679 7.227910 TCAAAACATACACAGGTCTTTAGGAAC 59.772 37.037 0.00 0.00 0.00 3.62
2597 2680 7.284074 TCAAAACATACACAGGTCTTTAGGAA 58.716 34.615 0.00 0.00 0.00 3.36
2598 2681 6.833041 TCAAAACATACACAGGTCTTTAGGA 58.167 36.000 0.00 0.00 0.00 2.94
2599 2682 6.934645 TCTCAAAACATACACAGGTCTTTAGG 59.065 38.462 0.00 0.00 0.00 2.69
2600 2683 7.962964 TCTCAAAACATACACAGGTCTTTAG 57.037 36.000 0.00 0.00 0.00 1.85
2601 2684 8.208224 TCTTCTCAAAACATACACAGGTCTTTA 58.792 33.333 0.00 0.00 0.00 1.85
2602 2685 7.054124 TCTTCTCAAAACATACACAGGTCTTT 58.946 34.615 0.00 0.00 0.00 2.52
2603 2686 6.591935 TCTTCTCAAAACATACACAGGTCTT 58.408 36.000 0.00 0.00 0.00 3.01
2604 2687 6.174720 TCTTCTCAAAACATACACAGGTCT 57.825 37.500 0.00 0.00 0.00 3.85
2605 2688 6.483640 AGTTCTTCTCAAAACATACACAGGTC 59.516 38.462 0.00 0.00 0.00 3.85
2606 2689 6.357367 AGTTCTTCTCAAAACATACACAGGT 58.643 36.000 0.00 0.00 0.00 4.00
2607 2690 6.867662 AGTTCTTCTCAAAACATACACAGG 57.132 37.500 0.00 0.00 0.00 4.00
2608 2691 7.134815 CCAAGTTCTTCTCAAAACATACACAG 58.865 38.462 0.00 0.00 0.00 3.66
2609 2692 6.601613 ACCAAGTTCTTCTCAAAACATACACA 59.398 34.615 0.00 0.00 0.00 3.72
2610 2693 7.027778 ACCAAGTTCTTCTCAAAACATACAC 57.972 36.000 0.00 0.00 0.00 2.90
2611 2694 6.262273 GGACCAAGTTCTTCTCAAAACATACA 59.738 38.462 0.00 0.00 0.00 2.29
2612 2695 6.486993 AGGACCAAGTTCTTCTCAAAACATAC 59.513 38.462 0.00 0.00 0.00 2.39
2613 2696 6.486657 CAGGACCAAGTTCTTCTCAAAACATA 59.513 38.462 0.00 0.00 0.00 2.29
2614 2697 5.300286 CAGGACCAAGTTCTTCTCAAAACAT 59.700 40.000 0.00 0.00 0.00 2.71
2615 2698 4.640201 CAGGACCAAGTTCTTCTCAAAACA 59.360 41.667 0.00 0.00 0.00 2.83
2616 2699 4.881850 TCAGGACCAAGTTCTTCTCAAAAC 59.118 41.667 0.00 0.00 0.00 2.43
2652 2735 8.846943 TTATGTATTCCCATCACATACATCAC 57.153 34.615 7.19 0.00 41.27 3.06
2674 2788 8.408601 CAGCATTAATGTAAGCCTTCAGTTTAT 58.591 33.333 16.61 0.00 0.00 1.40
2685 2799 4.501921 GCAGCTTTCAGCATTAATGTAAGC 59.498 41.667 23.76 23.76 45.56 3.09
2689 2803 3.094572 AGGCAGCTTTCAGCATTAATGT 58.905 40.909 16.61 1.42 45.56 2.71
2700 2814 5.438761 TCAAAAGAAACTAGGCAGCTTTC 57.561 39.130 0.00 0.00 0.00 2.62
2747 2861 6.721668 TGTGGAAACCAATATCATGTAACCAA 59.278 34.615 0.00 0.00 34.18 3.67
2770 2884 4.700213 AGCATATAAGCGAAAACTTGGTGT 59.300 37.500 0.00 0.00 40.15 4.16
2777 2891 7.734538 TTTTAAGCAGCATATAAGCGAAAAC 57.265 32.000 0.00 0.00 40.15 2.43
2778 2892 8.925161 ATTTTTAAGCAGCATATAAGCGAAAA 57.075 26.923 0.00 0.00 40.15 2.29
2838 3099 0.747255 GATCTGCTCTGGGCGAAGTA 59.253 55.000 0.00 0.00 45.43 2.24
2843 3104 4.121691 CAAGATCTGCTCTGGGCG 57.878 61.111 0.00 0.00 45.43 6.13
2856 3117 0.530744 ATCGGCGACTACAAGCAAGA 59.469 50.000 13.76 0.00 34.54 3.02
2872 3133 1.024579 AAACTAGGCCCACGCAATCG 61.025 55.000 0.00 0.00 42.43 3.34
2879 3140 1.744114 GCTCTGCTAAACTAGGCCCAC 60.744 57.143 0.00 0.00 0.00 4.61
2884 3145 3.027412 TCTCCAGCTCTGCTAAACTAGG 58.973 50.000 0.00 0.00 36.40 3.02
2909 3170 5.414765 TGTCAGCGAGAAGAGAACATAGTTA 59.585 40.000 0.00 0.00 0.00 2.24
2910 3171 4.218635 TGTCAGCGAGAAGAGAACATAGTT 59.781 41.667 0.00 0.00 0.00 2.24
2916 3177 1.000163 TGGTGTCAGCGAGAAGAGAAC 60.000 52.381 0.00 0.00 0.00 3.01
2924 3185 4.047822 GAGATCTATTTGGTGTCAGCGAG 58.952 47.826 0.00 0.00 0.00 5.03
2944 3205 4.122776 CCATCTCAATACGGAACCAAGAG 58.877 47.826 0.00 0.00 0.00 2.85
2946 3207 4.137116 TCCATCTCAATACGGAACCAAG 57.863 45.455 0.00 0.00 0.00 3.61
2955 3216 7.934120 AGTTAATAGCCAGTTCCATCTCAATAC 59.066 37.037 0.00 0.00 0.00 1.89
2960 3221 6.168270 AGAGTTAATAGCCAGTTCCATCTC 57.832 41.667 0.00 0.00 0.00 2.75
2962 3223 6.258947 GTCAAGAGTTAATAGCCAGTTCCATC 59.741 42.308 0.00 0.00 0.00 3.51
2989 3250 5.665459 ACCACACTCTAGATCTTACAATGC 58.335 41.667 0.00 0.00 0.00 3.56
2998 3259 5.357314 TGCAGTTAGTACCACACTCTAGATC 59.643 44.000 0.00 0.00 38.80 2.75
3021 3425 2.816087 ACAGTAGGCTTGAGCATTGTTG 59.184 45.455 5.24 0.67 44.36 3.33
3032 3436 2.704572 GATGCTCACAACAGTAGGCTT 58.295 47.619 0.00 0.00 0.00 4.35
3037 3441 1.067142 GGTCCGATGCTCACAACAGTA 60.067 52.381 0.00 0.00 0.00 2.74
3045 3449 2.668632 GTTGGGGTCCGATGCTCA 59.331 61.111 0.00 0.00 0.00 4.26
3046 3450 1.335132 TAGGTTGGGGTCCGATGCTC 61.335 60.000 0.00 0.00 0.00 4.26
3047 3451 1.306654 TAGGTTGGGGTCCGATGCT 60.307 57.895 0.00 0.00 0.00 3.79
3048 3452 1.153229 GTAGGTTGGGGTCCGATGC 60.153 63.158 0.00 0.00 0.00 3.91
3049 3453 0.981277 AGGTAGGTTGGGGTCCGATG 60.981 60.000 0.00 0.00 0.00 3.84
3088 3492 6.279513 TGAACAAAACACAGAAGGAAACAT 57.720 33.333 0.00 0.00 0.00 2.71
3090 3494 4.562789 GCTGAACAAAACACAGAAGGAAAC 59.437 41.667 0.00 0.00 34.07 2.78
3095 3499 6.441274 ACATATGCTGAACAAAACACAGAAG 58.559 36.000 1.58 0.00 34.07 2.85
3110 3514 4.510711 CCTAGTGCAGAAAGACATATGCTG 59.489 45.833 1.58 2.84 39.42 4.41
3123 3527 2.251818 AGCTTGAAGACCTAGTGCAGA 58.748 47.619 0.00 0.00 0.00 4.26
3187 3591 8.766994 AATGTTAAGTTAATGTATCCTGGCAT 57.233 30.769 0.00 0.00 0.00 4.40
3212 3616 3.157881 CTCCATGAAGGCCGATCTACTA 58.842 50.000 12.08 0.00 37.29 1.82
3214 3618 1.689273 ACTCCATGAAGGCCGATCTAC 59.311 52.381 12.08 0.00 37.29 2.59
3217 3621 2.044123 AAACTCCATGAAGGCCGATC 57.956 50.000 0.00 0.00 37.29 3.69
3219 3623 2.159382 GAAAAACTCCATGAAGGCCGA 58.841 47.619 0.00 0.00 37.29 5.54


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

AutoCloner maintained by Alex Coulton.