Multiple sequence alignment - TraesCS1D01G052700

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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 TraesCS1D01G052700 chr1D 100.000 3742 0 0 1 3742 33637663 33641404 0.000000e+00 6911.0
1 TraesCS1D01G052700 chr1A 88.481 2587 160 54 118 2621 32259312 32261843 0.000000e+00 3000.0
2 TraesCS1D01G052700 chr1A 84.500 1071 105 27 2704 3742 32261917 32262958 0.000000e+00 1002.0
3 TraesCS1D01G052700 chr1A 94.910 334 14 2 3409 3742 32306123 32306453 1.540000e-143 520.0
4 TraesCS1D01G052700 chr1A 86.230 305 26 4 3313 3602 32272734 32273037 2.170000e-82 316.0
5 TraesCS1D01G052700 chr1A 95.726 117 5 0 5 121 32259171 32259287 4.930000e-44 189.0
6 TraesCS1D01G052700 chr1A 94.000 50 2 1 2880 2928 32264138 32264187 1.440000e-09 75.0
7 TraesCS1D01G052700 chr1B 88.688 2325 158 57 341 2605 51104853 51107132 0.000000e+00 2739.0
8 TraesCS1D01G052700 chr1B 86.011 1058 95 18 2704 3742 51141239 51142262 0.000000e+00 1085.0
9 TraesCS1D01G052700 chr1B 85.322 1056 93 21 2704 3742 51107213 51108223 0.000000e+00 1035.0
10 TraesCS1D01G052700 chr1B 84.195 696 80 11 3063 3742 51135343 51136024 0.000000e+00 649.0
11 TraesCS1D01G052700 chr1B 85.714 476 53 11 2158 2621 51113053 51113525 4.340000e-134 488.0
12 TraesCS1D01G052700 chr1B 87.088 364 22 9 2704 3065 51113599 51113939 4.530000e-104 388.0
13 TraesCS1D01G052700 chr1B 89.035 228 18 4 118 343 51104595 51104817 3.680000e-70 276.0
14 TraesCS1D01G052700 chr1B 89.500 200 19 2 2422 2621 51140968 51141165 6.200000e-63 252.0
15 TraesCS1D01G052700 chr1B 89.167 120 10 3 3 120 51104450 51104568 3.010000e-31 147.0
16 TraesCS1D01G052700 chr1B 90.476 63 2 2 2158 2216 51140853 51140915 3.100000e-11 80.5
17 TraesCS1D01G052700 chr6D 79.940 663 97 29 1988 2628 3726998 3727646 4.410000e-124 455.0
18 TraesCS1D01G052700 chr6D 76.952 807 135 36 1994 2771 3714110 3714894 2.690000e-111 412.0
19 TraesCS1D01G052700 chr6D 80.247 567 80 26 1984 2532 3740063 3740615 7.530000e-107 398.0
20 TraesCS1D01G052700 chr6D 83.473 357 41 10 1628 1977 3739612 3739957 2.170000e-82 316.0
21 TraesCS1D01G052700 chr6D 83.146 356 49 8 1628 1982 4721956 4721611 7.800000e-82 315.0
22 TraesCS1D01G052700 chr6D 82.192 365 42 16 1635 1993 3713605 3713952 3.660000e-75 292.0
23 TraesCS1D01G052700 chr6D 81.308 321 47 10 2221 2533 3764097 3764412 8.030000e-62 248.0
24 TraesCS1D01G052700 chr6D 82.990 194 21 4 714 903 3725744 3725929 8.310000e-37 165.0
25 TraesCS1D01G052700 chr6D 79.355 155 20 3 2450 2601 3766658 3766803 8.550000e-17 99.0
26 TraesCS1D01G052700 chrUn 77.200 807 133 36 1994 2771 306429324 306430108 1.240000e-114 424.0
27 TraesCS1D01G052700 chrUn 82.192 365 43 17 1635 1993 306428817 306429165 1.020000e-75 294.0
28 TraesCS1D01G052700 chr6A 79.469 565 91 21 1984 2531 3747022 3746466 9.810000e-101 377.0
29 TraesCS1D01G052700 chr6A 77.126 682 107 29 1986 2646 3772962 3772309 2.140000e-92 350.0
30 TraesCS1D01G052700 chr6A 84.807 362 37 10 1628 1982 3747473 3747123 7.690000e-92 348.0
31 TraesCS1D01G052700 chr6A 84.530 362 45 8 1623 1982 3773465 3773113 7.690000e-92 348.0
32 TraesCS1D01G052700 chr6A 80.570 386 67 7 1771 2152 601472861 601473242 1.310000e-74 291.0
33 TraesCS1D01G052700 chr6B 79.574 563 77 27 1986 2531 9035581 9036122 5.900000e-98 368.0
34 TraesCS1D01G052700 chr6B 79.038 582 86 25 1984 2538 9080357 9080929 2.120000e-97 366.0
35 TraesCS1D01G052700 chr6B 76.958 664 110 30 1986 2631 9059345 9059983 4.630000e-89 339.0
36 TraesCS1D01G052700 chr6B 82.906 351 46 9 1635 1982 9058855 9059194 1.690000e-78 303.0
37 TraesCS1D01G052700 chr6B 81.918 365 53 9 1620 1982 9035078 9035431 2.830000e-76 296.0
38 TraesCS1D01G052700 chr3D 98.936 94 1 0 1919 2012 569547413 569547506 6.430000e-38 169.0


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 TraesCS1D01G052700 chr1D 33637663 33641404 3741 False 6911.00 6911 100.000000 1 3742 1 chr1D.!!$F1 3741
1 TraesCS1D01G052700 chr1A 32259171 32264187 5016 False 1066.50 3000 90.676750 5 3742 4 chr1A.!!$F3 3737
2 TraesCS1D01G052700 chr1B 51104450 51108223 3773 False 1049.25 2739 88.053000 3 3742 4 chr1B.!!$F2 3739
3 TraesCS1D01G052700 chr1B 51135343 51136024 681 False 649.00 649 84.195000 3063 3742 1 chr1B.!!$F1 679
4 TraesCS1D01G052700 chr1B 51140853 51142262 1409 False 472.50 1085 88.662333 2158 3742 3 chr1B.!!$F4 1584
5 TraesCS1D01G052700 chr1B 51113053 51113939 886 False 438.00 488 86.401000 2158 3065 2 chr1B.!!$F3 907
6 TraesCS1D01G052700 chr6D 3739612 3740615 1003 False 357.00 398 81.860000 1628 2532 2 chr6D.!!$F3 904
7 TraesCS1D01G052700 chr6D 3713605 3714894 1289 False 352.00 412 79.572000 1635 2771 2 chr6D.!!$F1 1136
8 TraesCS1D01G052700 chr6D 3725744 3727646 1902 False 310.00 455 81.465000 714 2628 2 chr6D.!!$F2 1914
9 TraesCS1D01G052700 chrUn 306428817 306430108 1291 False 359.00 424 79.696000 1635 2771 2 chrUn.!!$F1 1136
10 TraesCS1D01G052700 chr6A 3746466 3747473 1007 True 362.50 377 82.138000 1628 2531 2 chr6A.!!$R1 903
11 TraesCS1D01G052700 chr6A 3772309 3773465 1156 True 349.00 350 80.828000 1623 2646 2 chr6A.!!$R2 1023
12 TraesCS1D01G052700 chr6B 9080357 9080929 572 False 366.00 366 79.038000 1984 2538 1 chr6B.!!$F1 554
13 TraesCS1D01G052700 chr6B 9035078 9036122 1044 False 332.00 368 80.746000 1620 2531 2 chr6B.!!$F2 911
14 TraesCS1D01G052700 chr6B 9058855 9059983 1128 False 321.00 339 79.932000 1635 2631 2 chr6B.!!$F3 996

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
496 603 0.252467 AGCTCTCTGCCTTGTAGGGT 60.252 55.0 0.00 0.0 44.23 4.34 F
770 886 0.391130 ACACGCGATAAGGCATGTGT 60.391 50.0 15.93 0.0 38.01 3.72 F
1313 1541 0.539986 ATCGGCGTATTGTTCCAGGT 59.460 50.0 6.85 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1860 2161 0.039074 GCAGCGCGTAGTAGATCCAT 60.039 55.0 8.43 0.0 0.00 3.41 R
2565 3153 0.249699 ATGTTGACAACGTGCTCGGA 60.250 50.0 12.26 0.0 41.85 4.55 R
3199 3831 0.027979 CAATAATGCCACGGCTGTCG 59.972 55.0 9.92 0.0 45.88 4.35 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
64 67 5.124457 AGAGTACAAAACTATGCAGCATTGG 59.876 40.000 14.58 9.68 39.07 3.16
65 68 3.598019 ACAAAACTATGCAGCATTGGG 57.402 42.857 14.58 7.14 0.00 4.12
166 226 4.513318 AGCTGAGTCAAGCAACTTTCTTAC 59.487 41.667 14.37 0.00 46.08 2.34
168 228 4.689071 TGAGTCAAGCAACTTTCTTACGA 58.311 39.130 0.00 0.00 0.00 3.43
173 233 7.480810 AGTCAAGCAACTTTCTTACGATTTTT 58.519 30.769 0.00 0.00 0.00 1.94
224 284 2.677875 CCCACAAGCCAGAAGCCC 60.678 66.667 0.00 0.00 45.47 5.19
233 293 0.962855 GCCAGAAGCCCTTCCAAGAC 60.963 60.000 4.49 0.00 40.33 3.01
353 455 2.052237 CTTCGTGTGTGCAACGGC 60.052 61.111 9.37 0.00 42.39 5.68
362 464 3.513438 TGCAACGGCGCAACAAGT 61.513 55.556 10.83 0.00 45.35 3.16
398 500 5.047306 TGTGGTGACTGATAACTCCTAACTG 60.047 44.000 0.00 0.00 0.00 3.16
399 501 5.047235 GTGGTGACTGATAACTCCTAACTGT 60.047 44.000 0.00 0.00 0.00 3.55
400 502 6.152323 GTGGTGACTGATAACTCCTAACTGTA 59.848 42.308 0.00 0.00 0.00 2.74
401 503 6.377429 TGGTGACTGATAACTCCTAACTGTAG 59.623 42.308 0.00 0.00 0.00 2.74
402 504 6.267070 GTGACTGATAACTCCTAACTGTAGC 58.733 44.000 0.00 0.00 0.00 3.58
403 505 6.095720 GTGACTGATAACTCCTAACTGTAGCT 59.904 42.308 0.00 0.00 0.00 3.32
458 565 3.181487 GCATGTGATCCTTAATTTGCGGT 60.181 43.478 0.00 0.00 0.00 5.68
496 603 0.252467 AGCTCTCTGCCTTGTAGGGT 60.252 55.000 0.00 0.00 44.23 4.34
580 689 0.758734 TCCACGCATTATGGAGGGAG 59.241 55.000 0.00 0.00 41.47 4.30
606 715 3.367087 CGAGAGGAAAAGTGTACCGACAT 60.367 47.826 0.00 0.00 38.04 3.06
661 770 2.785713 TGTCCTTTGTTTAAAGCGGC 57.214 45.000 0.00 0.00 41.55 6.53
770 886 0.391130 ACACGCGATAAGGCATGTGT 60.391 50.000 15.93 0.00 38.01 3.72
820 936 4.039973 TCCCAGCACTATATAAACCCTTCG 59.960 45.833 0.00 0.00 0.00 3.79
821 937 4.039973 CCCAGCACTATATAAACCCTTCGA 59.960 45.833 0.00 0.00 0.00 3.71
925 1099 3.394645 AGCCCAACTATTACCCTAGCTT 58.605 45.455 0.00 0.00 0.00 3.74
934 1108 3.622166 TTACCCTAGCTTGCTTGGTAC 57.378 47.619 18.60 0.00 31.56 3.34
954 1130 2.295885 CAACCATCTCATTGCTCTCCC 58.704 52.381 0.00 0.00 0.00 4.30
963 1139 2.309755 TCATTGCTCTCCCCATCAACTT 59.690 45.455 0.00 0.00 0.00 2.66
966 1142 1.918262 TGCTCTCCCCATCAACTTGAT 59.082 47.619 0.00 0.00 37.65 2.57
1005 1181 3.893326 AATTAAGGTCTTGCAATGGGC 57.107 42.857 0.00 0.00 45.13 5.36
1023 1199 1.220206 CGGCCTCTCTGTTCAGCAT 59.780 57.895 0.00 0.00 0.00 3.79
1178 1361 3.936564 TGGTTTGCCAAAATTAGCATCC 58.063 40.909 0.00 5.96 42.83 3.51
1179 1362 3.326006 TGGTTTGCCAAAATTAGCATCCA 59.674 39.130 13.35 13.35 42.83 3.41
1180 1363 4.202398 TGGTTTGCCAAAATTAGCATCCAA 60.202 37.500 14.24 0.97 42.83 3.53
1182 1393 5.237048 GTTTGCCAAAATTAGCATCCAAGA 58.763 37.500 0.00 0.00 39.11 3.02
1249 1477 4.071423 GGGTTGCATGCCAAAAGTAAAAT 58.929 39.130 16.68 0.00 34.68 1.82
1300 1528 2.435234 TTTTGTCCCCGATCGGCG 60.435 61.111 29.12 21.04 40.47 6.46
1308 1536 1.219522 CCCCGATCGGCGTATTGTTC 61.220 60.000 29.12 0.00 38.67 3.18
1313 1541 0.539986 ATCGGCGTATTGTTCCAGGT 59.460 50.000 6.85 0.00 0.00 4.00
1394 1622 4.003648 AGTTCATTCGTCATTGGAGGAAC 58.996 43.478 2.39 0.00 46.94 3.62
1395 1623 3.694043 TCATTCGTCATTGGAGGAACA 57.306 42.857 2.39 0.00 46.94 3.18
1398 1626 0.677288 TCGTCATTGGAGGAACACGT 59.323 50.000 0.00 0.00 35.16 4.49
1399 1627 1.887854 TCGTCATTGGAGGAACACGTA 59.112 47.619 0.00 0.00 35.16 3.57
1400 1628 1.990563 CGTCATTGGAGGAACACGTAC 59.009 52.381 0.00 0.00 0.00 3.67
1401 1629 2.344025 GTCATTGGAGGAACACGTACC 58.656 52.381 0.00 0.00 0.00 3.34
1414 1642 2.025418 CGTACCTGGTGACGGCAAC 61.025 63.158 10.23 0.00 35.43 4.17
1423 1651 0.741915 GTGACGGCAACCAAAAAGGA 59.258 50.000 0.00 0.00 41.22 3.36
1430 1658 4.126437 CGGCAACCAAAAAGGAAGAAAAT 58.874 39.130 0.00 0.00 41.22 1.82
1512 1741 1.617755 GCGTGTGTGACATCTCACCG 61.618 60.000 10.66 13.08 45.68 4.94
1616 1850 6.963242 ACTGTCGTATGTAATGTAACGTACTG 59.037 38.462 0.00 0.00 38.95 2.74
1700 1939 0.814457 AGCCTCTCGATCACACTCAC 59.186 55.000 0.00 0.00 0.00 3.51
1729 2010 5.049398 TCGTGTTTCTCTCTCTAGCTTTC 57.951 43.478 0.00 0.00 0.00 2.62
1741 2026 4.348168 TCTCTAGCTTTCCTTGTTGGTCTT 59.652 41.667 0.00 0.00 37.07 3.01
1763 2048 2.228103 TCTCGTCTGACTACGTGCAAAT 59.772 45.455 6.21 0.00 43.31 2.32
1764 2049 2.987149 CTCGTCTGACTACGTGCAAATT 59.013 45.455 6.21 0.00 43.31 1.82
1768 2068 4.432503 CGTCTGACTACGTGCAAATTACAC 60.433 45.833 6.21 2.20 38.07 2.90
1827 2128 2.046892 CAGGGCTTCCAGTCGGTG 60.047 66.667 0.00 0.00 0.00 4.94
2004 2475 0.984230 TCTTCACCGCCAAGATCCTT 59.016 50.000 0.00 0.00 0.00 3.36
2239 2757 2.113860 ATATGCAGCGTCTTGTGGTT 57.886 45.000 0.00 0.00 0.00 3.67
2245 2763 2.530497 GCGTCTTGTGGTTCGCACA 61.530 57.895 0.00 0.00 46.40 4.57
2374 2897 4.218417 AGCAACACAAACAGAACAAACTCT 59.782 37.500 0.00 0.00 0.00 3.24
2388 2911 7.708752 CAGAACAAACTCTTCACTCTACTTTCT 59.291 37.037 0.00 0.00 0.00 2.52
2389 2912 7.923878 AGAACAAACTCTTCACTCTACTTTCTC 59.076 37.037 0.00 0.00 0.00 2.87
2390 2913 7.113658 ACAAACTCTTCACTCTACTTTCTCA 57.886 36.000 0.00 0.00 0.00 3.27
2393 2916 4.083003 ACTCTTCACTCTACTTTCTCAGCG 60.083 45.833 0.00 0.00 0.00 5.18
2394 2917 3.191581 TCTTCACTCTACTTTCTCAGCGG 59.808 47.826 0.00 0.00 0.00 5.52
2397 2920 2.096248 ACTCTACTTTCTCAGCGGAGG 58.904 52.381 14.13 0.60 41.69 4.30
2399 2922 3.280295 CTCTACTTTCTCAGCGGAGGTA 58.720 50.000 14.13 7.52 41.69 3.08
2400 2923 3.015327 TCTACTTTCTCAGCGGAGGTAC 58.985 50.000 14.13 0.00 41.69 3.34
2401 2924 1.629043 ACTTTCTCAGCGGAGGTACA 58.371 50.000 14.13 0.00 41.69 2.90
2402 2925 1.968493 ACTTTCTCAGCGGAGGTACAA 59.032 47.619 14.13 0.00 41.69 2.41
2403 2926 2.367567 ACTTTCTCAGCGGAGGTACAAA 59.632 45.455 14.13 6.20 41.69 2.83
2411 2934 1.272769 GCGGAGGTACAAACTGACTCT 59.727 52.381 0.00 0.00 0.00 3.24
2416 2942 5.471257 GGAGGTACAAACTGACTCTAACTG 58.529 45.833 0.00 0.00 0.00 3.16
2562 3150 2.742372 ACGATGGTGCCGTCAAGC 60.742 61.111 10.65 0.00 34.97 4.01
2565 3153 4.329545 ATGGTGCCGTCAAGCCGT 62.330 61.111 0.00 0.00 0.00 5.68
2633 3221 2.417339 TCGAGCTCAACACACACTAC 57.583 50.000 15.40 0.00 0.00 2.73
2642 3230 0.672342 ACACACACTACCCTGTCGAC 59.328 55.000 9.11 9.11 0.00 4.20
2646 3234 1.183676 ACACTACCCTGTCGACCCAC 61.184 60.000 14.12 0.00 0.00 4.61
2647 3235 1.608627 ACTACCCTGTCGACCCACC 60.609 63.158 14.12 0.00 0.00 4.61
2742 3348 1.751351 CCCATGTCGAGCAAGTCTAGA 59.249 52.381 0.00 0.00 0.00 2.43
2794 3404 2.431454 TGTCGTGCATCCAAATAAGCA 58.569 42.857 0.00 0.00 34.10 3.91
2811 3421 1.728490 GCAATGACGGGGATCAAGCC 61.728 60.000 0.00 0.00 31.23 4.35
2812 3422 0.394216 CAATGACGGGGATCAAGCCA 60.394 55.000 0.00 0.00 30.82 4.75
2813 3423 0.552848 AATGACGGGGATCAAGCCAT 59.447 50.000 0.00 0.00 30.82 4.40
2814 3424 0.179009 ATGACGGGGATCAAGCCATG 60.179 55.000 0.00 0.00 30.82 3.66
2815 3425 1.271127 TGACGGGGATCAAGCCATGA 61.271 55.000 0.00 0.00 43.67 3.07
2816 3426 0.815615 GACGGGGATCAAGCCATGAC 60.816 60.000 0.00 0.00 41.93 3.06
2817 3427 1.889105 CGGGGATCAAGCCATGACG 60.889 63.158 0.00 0.00 41.93 4.35
2818 3428 1.526917 GGGGATCAAGCCATGACGG 60.527 63.158 0.00 0.00 41.93 4.79
2819 3429 1.526917 GGGATCAAGCCATGACGGG 60.527 63.158 0.00 0.00 41.93 5.28
2820 3430 1.526917 GGATCAAGCCATGACGGGG 60.527 63.158 0.00 0.00 41.93 5.73
2821 3431 1.526887 GATCAAGCCATGACGGGGA 59.473 57.895 0.00 0.00 41.93 4.81
2822 3432 0.109342 GATCAAGCCATGACGGGGAT 59.891 55.000 0.00 0.00 41.93 3.85
2823 3433 0.109342 ATCAAGCCATGACGGGGATC 59.891 55.000 0.00 0.00 41.93 3.36
2824 3434 1.889105 CAAGCCATGACGGGGATCG 60.889 63.158 0.00 0.00 45.88 3.69
2825 3435 2.063979 AAGCCATGACGGGGATCGA 61.064 57.895 0.00 0.00 42.43 3.59
2826 3436 2.029666 GCCATGACGGGGATCGAG 59.970 66.667 0.00 0.00 42.43 4.04
2827 3437 2.029666 CCATGACGGGGATCGAGC 59.970 66.667 0.00 0.00 42.43 5.03
2844 3454 1.806542 GAGCAAACAAGCGATGGAGAA 59.193 47.619 0.00 0.00 40.15 2.87
2845 3455 2.421424 GAGCAAACAAGCGATGGAGAAT 59.579 45.455 0.00 0.00 40.15 2.40
2846 3456 2.163010 AGCAAACAAGCGATGGAGAATG 59.837 45.455 0.00 0.00 40.15 2.67
2847 3457 2.523015 CAAACAAGCGATGGAGAATGC 58.477 47.619 0.00 0.00 0.00 3.56
2878 3499 1.743431 GCATGGGGCCTTGTAAATTGC 60.743 52.381 0.84 0.00 36.11 3.56
2959 3586 7.062956 CGTTGCAAAGGGTTCTTATTTTATTCC 59.937 37.037 0.00 0.00 32.01 3.01
3027 3656 6.183361 GGTCTTATTATAAGGAACCAGCAGGA 60.183 42.308 14.34 0.00 38.69 3.86
3034 3663 1.078848 GAACCAGCAGGATGAGCGT 60.079 57.895 0.35 0.00 39.69 5.07
3178 3810 3.634397 TGATTGCCCTTAGGAAGTCTG 57.366 47.619 0.00 0.00 33.47 3.51
3179 3811 2.912956 TGATTGCCCTTAGGAAGTCTGT 59.087 45.455 0.00 0.00 33.47 3.41
3180 3812 4.101114 TGATTGCCCTTAGGAAGTCTGTA 58.899 43.478 0.00 0.00 33.47 2.74
3181 3813 4.162320 TGATTGCCCTTAGGAAGTCTGTAG 59.838 45.833 0.00 0.00 33.47 2.74
3199 3831 8.204836 AGTCTGTAGTATGGGATTGTTGATAAC 58.795 37.037 0.00 0.00 0.00 1.89
3232 3865 7.271653 CGTGGCATTATTGTTACGTTGTTAATT 59.728 33.333 0.00 0.00 33.01 1.40
3246 3879 7.528307 ACGTTGTTAATTGTGTAAACACTTGA 58.472 30.769 13.95 1.73 46.55 3.02
3286 3919 1.687123 CGGATCTAACTAGTGGGGTGG 59.313 57.143 0.00 0.00 0.00 4.61
3300 3933 1.304282 GGTGGTGTGATGGCATCCT 59.696 57.895 23.92 0.00 0.00 3.24
3326 3960 0.753867 TCGAGTTTGTAGGTGTGGCA 59.246 50.000 0.00 0.00 0.00 4.92
3328 3962 1.732259 CGAGTTTGTAGGTGTGGCATC 59.268 52.381 0.00 0.00 0.00 3.91
3329 3963 2.778299 GAGTTTGTAGGTGTGGCATCA 58.222 47.619 0.00 0.00 0.00 3.07
3332 3966 3.081061 GTTTGTAGGTGTGGCATCATGA 58.919 45.455 0.00 0.00 0.00 3.07
3335 3969 3.281158 TGTAGGTGTGGCATCATGATTG 58.719 45.455 5.16 3.21 0.00 2.67
3337 3971 3.650281 AGGTGTGGCATCATGATTGTA 57.350 42.857 5.16 0.00 0.00 2.41
3359 3993 9.522804 TTGTAGGTTGTTTGATGTATGTTTTTC 57.477 29.630 0.00 0.00 0.00 2.29
3362 3996 5.404066 GGTTGTTTGATGTATGTTTTTCCCG 59.596 40.000 0.00 0.00 0.00 5.14
3365 3999 5.158494 GTTTGATGTATGTTTTTCCCGGAC 58.842 41.667 0.73 0.00 0.00 4.79
3373 4007 7.173722 TGTATGTTTTTCCCGGACCTTTATTA 58.826 34.615 0.73 0.00 0.00 0.98
3379 4013 9.357652 GTTTTTCCCGGACCTTTATTAAATAAC 57.642 33.333 0.73 0.00 0.00 1.89
3380 4014 8.647256 TTTTCCCGGACCTTTATTAAATAACA 57.353 30.769 0.73 0.00 0.00 2.41
3385 4019 8.570488 CCCGGACCTTTATTAAATAACATAACC 58.430 37.037 0.73 0.00 0.00 2.85
3441 4075 3.746045 GGGGTTTCAACCTCTTTTTCC 57.254 47.619 8.63 0.00 46.40 3.13
3469 4119 5.666462 CATCAAATTGATCATGGGCTTTGA 58.334 37.500 5.36 14.66 34.28 2.69
3473 4123 0.627451 TGATCATGGGCTTTGAGGCT 59.373 50.000 0.00 0.00 41.09 4.58
3484 4134 3.194329 GGCTTTGAGGCTTAGAGCAAAAT 59.806 43.478 20.82 0.00 44.75 1.82
3586 4237 1.581223 ACTTTAGGGACCCACTAGCC 58.419 55.000 14.60 0.00 0.00 3.93
3588 4239 2.127708 CTTTAGGGACCCACTAGCCAT 58.872 52.381 14.60 0.00 0.00 4.40
3590 4241 0.105142 TAGGGACCCACTAGCCATCC 60.105 60.000 14.60 0.00 0.00 3.51
3620 4272 1.203162 TCACCATGCATTTTCCCCACT 60.203 47.619 0.00 0.00 0.00 4.00
3662 4314 3.951563 TTTTAGCTATGACATGGCCCT 57.048 42.857 19.07 5.55 37.49 5.19
3724 4376 7.813645 ACAAGAACCGATGGTAATACTTTTTC 58.186 34.615 0.00 0.00 33.12 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.762745 AGAAAGGCGTTCAACGTACAT 58.237 42.857 12.40 0.00 44.73 2.29
2 3 3.737774 ACTAAGAAAGGCGTTCAACGTAC 59.262 43.478 12.40 5.22 44.73 3.67
3 4 3.981211 ACTAAGAAAGGCGTTCAACGTA 58.019 40.909 12.40 0.00 44.73 3.57
9 10 7.036829 AGAGATTTAGACTAAGAAAGGCGTTC 58.963 38.462 4.93 4.93 38.81 3.95
233 293 2.356793 GCTCGCCTCCATGATCCG 60.357 66.667 0.00 0.00 0.00 4.18
244 304 3.741476 CAGTGCCCTTTGCTCGCC 61.741 66.667 0.00 0.00 42.00 5.54
359 461 1.305201 CCACACGGTTACTTGCACTT 58.695 50.000 0.00 0.00 0.00 3.16
362 464 0.178301 TCACCACACGGTTACTTGCA 59.822 50.000 0.00 0.00 46.31 4.08
374 476 5.047306 CAGTTAGGAGTTATCAGTCACCACA 60.047 44.000 0.00 0.00 0.00 4.17
398 500 2.354805 CCAGTGTCCAAACCCTAGCTAC 60.355 54.545 0.00 0.00 0.00 3.58
399 501 1.906574 CCAGTGTCCAAACCCTAGCTA 59.093 52.381 0.00 0.00 0.00 3.32
400 502 0.693049 CCAGTGTCCAAACCCTAGCT 59.307 55.000 0.00 0.00 0.00 3.32
401 503 0.400594 ACCAGTGTCCAAACCCTAGC 59.599 55.000 0.00 0.00 0.00 3.42
402 504 1.978580 AGACCAGTGTCCAAACCCTAG 59.021 52.381 0.00 0.00 42.81 3.02
403 505 1.975680 GAGACCAGTGTCCAAACCCTA 59.024 52.381 0.00 0.00 42.81 3.53
516 623 4.072839 ACTTCAAGTTAACAGGCTTAGGC 58.927 43.478 8.61 0.00 37.82 3.93
521 628 5.057149 CAGTACACTTCAAGTTAACAGGCT 58.943 41.667 8.61 0.00 0.00 4.58
523 630 4.814234 TGCAGTACACTTCAAGTTAACAGG 59.186 41.667 8.61 0.00 0.00 4.00
525 632 6.935741 ATTGCAGTACACTTCAAGTTAACA 57.064 33.333 8.61 0.00 33.01 2.41
580 689 2.479275 GGTACACTTTTCCTCTCGCAAC 59.521 50.000 0.00 0.00 0.00 4.17
606 715 1.350684 TGCATGACACAAAGCTCCCTA 59.649 47.619 0.00 0.00 0.00 3.53
845 961 5.790593 CTTACTACCTGAGGTTGTTGCTTA 58.209 41.667 22.84 2.87 38.39 3.09
859 975 2.541466 AGAACTGCCAGCTTACTACCT 58.459 47.619 0.00 0.00 0.00 3.08
860 976 3.055747 AGAAGAACTGCCAGCTTACTACC 60.056 47.826 0.00 0.00 0.00 3.18
875 991 4.398319 TGGTTGAATGGGAAGAGAAGAAC 58.602 43.478 0.00 0.00 0.00 3.01
934 1108 2.295885 GGGAGAGCAATGAGATGGTTG 58.704 52.381 0.00 0.00 0.00 3.77
963 1139 8.893219 AATTAGCTATGAATTTGAGACGATCA 57.107 30.769 0.00 0.00 35.62 2.92
966 1142 9.261180 CCTTAATTAGCTATGAATTTGAGACGA 57.739 33.333 0.00 0.00 0.00 4.20
1005 1181 0.809241 GATGCTGAACAGAGAGGCCG 60.809 60.000 5.97 0.00 0.00 6.13
1023 1199 1.681076 GAAGGTAAAGGCCCACGGA 59.319 57.895 0.00 0.00 0.00 4.69
1175 1358 6.732896 CTACCACAAGTAGGTATCTTGGAT 57.267 41.667 9.82 0.00 44.19 3.41
1249 1477 4.619760 CACTACGTCGCAACAAGAGAAATA 59.380 41.667 0.00 0.00 0.00 1.40
1282 1510 3.184206 GCCGATCGGGGACAAAAC 58.816 61.111 33.98 12.15 35.78 2.43
1313 1541 0.328926 AAGAAATTAACGGCGGGGGA 59.671 50.000 13.24 0.00 0.00 4.81
1394 1622 2.431942 GCCGTCACCAGGTACGTG 60.432 66.667 8.61 8.61 37.40 4.49
1395 1623 2.500714 TTGCCGTCACCAGGTACGT 61.501 57.895 15.92 0.00 37.40 3.57
1398 1626 1.697082 TTGGTTGCCGTCACCAGGTA 61.697 55.000 0.00 0.00 34.72 3.08
1399 1627 2.559922 TTTGGTTGCCGTCACCAGGT 62.560 55.000 0.00 0.00 34.72 4.00
1400 1628 1.388065 TTTTGGTTGCCGTCACCAGG 61.388 55.000 0.00 0.00 34.72 4.45
1401 1629 0.457851 TTTTTGGTTGCCGTCACCAG 59.542 50.000 0.00 0.00 34.72 4.00
1414 1642 9.382275 TCTTTCTTTCATTTTCTTCCTTTTTGG 57.618 29.630 0.00 0.00 37.10 3.28
1430 1658 7.724061 AGCCCTTTAGTTTACATCTTTCTTTCA 59.276 33.333 0.00 0.00 0.00 2.69
1474 1703 5.050490 CACGCTACACCATAAGATAAAGCT 58.950 41.667 0.00 0.00 0.00 3.74
1476 1705 5.810587 ACACACGCTACACCATAAGATAAAG 59.189 40.000 0.00 0.00 0.00 1.85
1480 1709 3.194755 TCACACACGCTACACCATAAGAT 59.805 43.478 0.00 0.00 0.00 2.40
1512 1741 2.615912 CAGCTTTCAGTAATGGCTAGCC 59.384 50.000 27.71 27.71 0.00 3.93
1616 1850 1.282875 GGAAGCAAAGTGGCACGTC 59.717 57.895 12.71 2.79 35.83 4.34
1700 1939 4.804108 AGAGAGAGAAACACGATGTTGAG 58.196 43.478 4.51 0.00 40.14 3.02
1729 2010 2.802816 CAGACGAGAAAGACCAACAAGG 59.197 50.000 0.00 0.00 45.67 3.61
1741 2026 1.232119 TGCACGTAGTCAGACGAGAA 58.768 50.000 2.55 0.00 45.82 2.87
1860 2161 0.039074 GCAGCGCGTAGTAGATCCAT 60.039 55.000 8.43 0.00 0.00 3.41
2004 2475 1.155390 ACCCACGTTCAGGAGGAGA 59.845 57.895 3.12 0.00 0.00 3.71
2091 2562 3.665675 GAAGCCGACGCAGACCCAT 62.666 63.158 0.00 0.00 37.52 4.00
2245 2763 1.079819 CATGAACTCCACGCTCCGT 60.080 57.895 0.00 0.00 42.36 4.69
2374 2897 3.154710 TCCGCTGAGAAAGTAGAGTGAA 58.845 45.455 0.00 0.00 0.00 3.18
2388 2911 1.000506 GTCAGTTTGTACCTCCGCTGA 59.999 52.381 0.00 0.00 0.00 4.26
2389 2912 1.000955 AGTCAGTTTGTACCTCCGCTG 59.999 52.381 0.00 0.00 0.00 5.18
2390 2913 1.272769 GAGTCAGTTTGTACCTCCGCT 59.727 52.381 0.00 0.00 0.00 5.52
2393 2916 5.010820 ACAGTTAGAGTCAGTTTGTACCTCC 59.989 44.000 0.00 0.00 0.00 4.30
2394 2917 6.086785 ACAGTTAGAGTCAGTTTGTACCTC 57.913 41.667 0.00 0.00 0.00 3.85
2397 2920 8.421673 AAAGAACAGTTAGAGTCAGTTTGTAC 57.578 34.615 0.00 0.00 0.00 2.90
2399 2922 7.606456 TCAAAAGAACAGTTAGAGTCAGTTTGT 59.394 33.333 0.00 0.00 0.00 2.83
2400 2923 7.974675 TCAAAAGAACAGTTAGAGTCAGTTTG 58.025 34.615 0.00 0.00 0.00 2.93
2401 2924 8.738645 ATCAAAAGAACAGTTAGAGTCAGTTT 57.261 30.769 0.00 0.00 0.00 2.66
2402 2925 8.738645 AATCAAAAGAACAGTTAGAGTCAGTT 57.261 30.769 0.00 0.00 0.00 3.16
2403 2926 8.616076 CAAATCAAAAGAACAGTTAGAGTCAGT 58.384 33.333 0.00 0.00 0.00 3.41
2411 2934 6.147864 AGCTGCAAATCAAAAGAACAGTTA 57.852 33.333 1.02 0.00 0.00 2.24
2416 2942 3.742882 GGGAAGCTGCAAATCAAAAGAAC 59.257 43.478 1.02 0.00 0.00 3.01
2562 3150 3.103911 GACAACGTGCTCGGACGG 61.104 66.667 15.07 1.30 43.84 4.79
2565 3153 0.249699 ATGTTGACAACGTGCTCGGA 60.250 50.000 12.26 0.00 41.85 4.55
2606 3194 2.125552 TTGAGCTCGATGGCGGTG 60.126 61.111 9.64 0.00 38.28 4.94
2607 3195 2.125512 GTTGAGCTCGATGGCGGT 60.126 61.111 7.00 0.00 38.28 5.68
2646 3234 2.278857 CTCCTTCATCGACGGCGG 60.279 66.667 12.58 0.00 38.28 6.13
2647 3235 2.278857 CCTCCTTCATCGACGGCG 60.279 66.667 2.87 2.87 39.35 6.46
2649 3237 2.797278 CCCCCTCCTTCATCGACGG 61.797 68.421 0.00 0.00 0.00 4.79
2650 3238 2.815308 CCCCCTCCTTCATCGACG 59.185 66.667 0.00 0.00 0.00 5.12
2701 3289 2.175878 TGCCTTGTCAAGCTTCTCTC 57.824 50.000 7.09 0.00 0.00 3.20
2702 3290 2.225467 GTTGCCTTGTCAAGCTTCTCT 58.775 47.619 7.09 0.00 0.00 3.10
2794 3404 0.552848 ATGGCTTGATCCCCGTCATT 59.447 50.000 0.00 0.00 0.00 2.57
2811 3421 0.461870 TTTGCTCGATCCCCGTCATG 60.462 55.000 0.00 0.00 39.75 3.07
2812 3422 0.462047 GTTTGCTCGATCCCCGTCAT 60.462 55.000 0.00 0.00 39.75 3.06
2813 3423 1.079405 GTTTGCTCGATCCCCGTCA 60.079 57.895 0.00 0.00 39.75 4.35
2814 3424 0.672401 TTGTTTGCTCGATCCCCGTC 60.672 55.000 0.00 0.00 39.75 4.79
2815 3425 0.673644 CTTGTTTGCTCGATCCCCGT 60.674 55.000 0.00 0.00 39.75 5.28
2816 3426 1.982073 GCTTGTTTGCTCGATCCCCG 61.982 60.000 0.00 0.00 40.25 5.73
2817 3427 1.803289 GCTTGTTTGCTCGATCCCC 59.197 57.895 0.00 0.00 0.00 4.81
2818 3428 1.019278 TCGCTTGTTTGCTCGATCCC 61.019 55.000 0.00 0.00 0.00 3.85
2819 3429 1.009829 ATCGCTTGTTTGCTCGATCC 58.990 50.000 0.00 0.00 37.09 3.36
2820 3430 1.267732 CCATCGCTTGTTTGCTCGATC 60.268 52.381 0.00 0.00 39.33 3.69
2821 3431 0.729116 CCATCGCTTGTTTGCTCGAT 59.271 50.000 0.00 0.00 41.66 3.59
2822 3432 0.320334 TCCATCGCTTGTTTGCTCGA 60.320 50.000 0.00 0.00 35.34 4.04
2823 3433 0.095935 CTCCATCGCTTGTTTGCTCG 59.904 55.000 0.00 0.00 0.00 5.03
2824 3434 1.442769 TCTCCATCGCTTGTTTGCTC 58.557 50.000 0.00 0.00 0.00 4.26
2825 3435 1.896220 TTCTCCATCGCTTGTTTGCT 58.104 45.000 0.00 0.00 0.00 3.91
2826 3436 2.523015 CATTCTCCATCGCTTGTTTGC 58.477 47.619 0.00 0.00 0.00 3.68
2827 3437 2.095110 TGCATTCTCCATCGCTTGTTTG 60.095 45.455 0.00 0.00 0.00 2.93
2878 3499 4.183865 TGGAGCATCGACAGTAGAAATTG 58.816 43.478 0.00 0.00 34.37 2.32
2959 3586 5.765176 TGGATACACTAATGAATACGACCG 58.235 41.667 0.00 0.00 46.17 4.79
3015 3642 1.817099 CGCTCATCCTGCTGGTTCC 60.817 63.158 9.73 0.00 34.23 3.62
3027 3656 3.819564 TTTACATCTAGCCACGCTCAT 57.180 42.857 0.00 0.00 40.44 2.90
3138 3770 9.941664 GCAATCATGTTATCATAATGGCTATAC 57.058 33.333 0.00 0.00 32.47 1.47
3153 3785 5.191722 AGACTTCCTAAGGGCAATCATGTTA 59.808 40.000 0.00 0.00 0.00 2.41
3178 3810 6.982141 TGTCGTTATCAACAATCCCATACTAC 59.018 38.462 0.00 0.00 0.00 2.73
3179 3811 7.114866 TGTCGTTATCAACAATCCCATACTA 57.885 36.000 0.00 0.00 0.00 1.82
3180 3812 5.984725 TGTCGTTATCAACAATCCCATACT 58.015 37.500 0.00 0.00 0.00 2.12
3181 3813 5.277345 GCTGTCGTTATCAACAATCCCATAC 60.277 44.000 0.00 0.00 0.00 2.39
3199 3831 0.027979 CAATAATGCCACGGCTGTCG 59.972 55.000 9.92 0.00 45.88 4.35
3232 3865 5.764487 TTGATGCATCAAGTGTTTACACA 57.236 34.783 33.08 11.18 42.48 3.72
3286 3919 3.815133 ATGGAGGATGCCATCACAC 57.185 52.632 7.06 0.00 45.36 3.82
3300 3933 3.513912 ACACCTACAAACTCGATGATGGA 59.486 43.478 0.00 0.00 0.00 3.41
3326 3960 7.707624 ACATCAAACAACCTACAATCATGAT 57.292 32.000 1.18 1.18 0.00 2.45
3328 3962 8.461222 ACATACATCAAACAACCTACAATCATG 58.539 33.333 0.00 0.00 0.00 3.07
3329 3963 8.579850 ACATACATCAAACAACCTACAATCAT 57.420 30.769 0.00 0.00 0.00 2.45
3335 3969 7.597369 GGGAAAAACATACATCAAACAACCTAC 59.403 37.037 0.00 0.00 0.00 3.18
3337 3971 6.521162 GGGAAAAACATACATCAAACAACCT 58.479 36.000 0.00 0.00 0.00 3.50
3359 3993 8.570488 GGTTATGTTATTTAATAAAGGTCCGGG 58.430 37.037 0.00 0.00 0.00 5.73
3379 4013 6.814644 AGATGCACACAATCATTTTGGTTATG 59.185 34.615 0.00 0.00 0.00 1.90
3380 4014 6.938507 AGATGCACACAATCATTTTGGTTAT 58.061 32.000 0.00 0.00 0.00 1.89
3385 4019 7.179927 TCAAAAGATGCACACAATCATTTTG 57.820 32.000 0.00 2.61 0.00 2.44
3388 4022 6.961359 CATCAAAAGATGCACACAATCATT 57.039 33.333 0.00 0.00 0.00 2.57
3441 4075 4.213270 GCCCATGATCAATTTGATGCATTG 59.787 41.667 16.41 13.32 37.20 2.82
3469 4119 4.768968 ACACATTGATTTTGCTCTAAGCCT 59.231 37.500 0.00 0.00 41.51 4.58
3473 4123 6.671190 CACTGACACATTGATTTTGCTCTAA 58.329 36.000 0.00 0.00 0.00 2.10
3484 4134 6.149308 CCTATTTTGTAGCACTGACACATTGA 59.851 38.462 0.00 0.00 0.00 2.57
3600 4251 1.203162 AGTGGGGAAAATGCATGGTGA 60.203 47.619 0.00 0.00 0.00 4.02
3601 4252 1.066716 CAGTGGGGAAAATGCATGGTG 60.067 52.381 0.00 0.00 0.00 4.17
3602 4253 1.203162 TCAGTGGGGAAAATGCATGGT 60.203 47.619 0.00 0.00 0.00 3.55
3620 4272 1.075601 AAGAGCAGGGGGATGTTTCA 58.924 50.000 0.00 0.00 0.00 2.69
3662 4314 6.207025 GTCTAGAGGAATCTTCACCGCTATAA 59.793 42.308 0.00 0.00 37.76 0.98


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

AutoCloner maintained by Alex Coulton.