Multiple sequence alignment - TraesCS7D01G074100

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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 TraesCS7D01G074100 chr7D 100.000 2386 0 0 1 2386 43385527 43383142 0.000000e+00 4407.0
1 TraesCS7D01G074100 chr7D 84.759 1555 132 47 3 1509 43431052 43429555 0.000000e+00 1461.0
2 TraesCS7D01G074100 chr7D 82.763 760 68 24 1591 2315 43424952 43424221 9.370000e-174 619.0
3 TraesCS7D01G074100 chr7A 86.663 1642 134 26 712 2299 45602973 45601363 0.000000e+00 1740.0
4 TraesCS7D01G074100 chr7A 86.131 1644 142 27 712 2299 45574272 45572659 0.000000e+00 1694.0
5 TraesCS7D01G074100 chr7A 86.131 1644 142 27 712 2299 45593962 45592349 0.000000e+00 1694.0
6 TraesCS7D01G074100 chr7A 88.848 816 55 16 713 1509 43439448 43438650 0.000000e+00 970.0
7 TraesCS7D01G074100 chr7A 88.848 816 55 16 713 1509 43458124 43457326 0.000000e+00 970.0
8 TraesCS7D01G074100 chr7A 84.081 936 86 28 1452 2349 45071387 45070477 0.000000e+00 845.0
9 TraesCS7D01G074100 chr7A 85.425 741 89 13 83 822 44885723 44885001 0.000000e+00 752.0
10 TraesCS7D01G074100 chr7A 89.445 559 46 6 1132 1683 45185987 45185435 0.000000e+00 693.0
11 TraesCS7D01G074100 chr7A 85.863 672 55 12 1452 2088 45024533 45023867 0.000000e+00 678.0
12 TraesCS7D01G074100 chr7A 84.257 686 84 17 83 764 45021965 45021300 0.000000e+00 647.0
13 TraesCS7D01G074100 chr7A 84.111 686 85 17 83 764 45068782 45068117 2.000000e-180 641.0
14 TraesCS7D01G074100 chr7A 82.472 793 72 25 1591 2349 43417298 43416539 1.200000e-177 632.0
15 TraesCS7D01G074100 chr7A 87.196 453 37 12 621 1059 45186568 45186123 1.650000e-136 496.0
16 TraesCS7D01G074100 chr7A 87.147 389 26 10 1408 1791 44942440 44942071 1.020000e-113 420.0
17 TraesCS7D01G074100 chr7A 87.812 361 34 4 9 364 45610550 45610195 4.750000e-112 414.0
18 TraesCS7D01G074100 chr7A 85.864 382 39 9 3 380 43440434 43440064 2.220000e-105 392.0
19 TraesCS7D01G074100 chr7A 84.689 418 36 9 1698 2089 44859445 44859030 2.220000e-105 392.0
20 TraesCS7D01G074100 chr7A 85.586 333 20 12 1411 1737 44910669 44910359 8.230000e-85 324.0
21 TraesCS7D01G074100 chr7A 89.516 248 23 1 815 1059 44884948 44884701 6.400000e-81 311.0
22 TraesCS7D01G074100 chr7A 89.024 246 18 4 448 685 45594353 45594109 1.790000e-76 296.0
23 TraesCS7D01G074100 chr7A 88.618 246 19 4 448 685 45574663 45574419 8.340000e-75 291.0
24 TraesCS7D01G074100 chr7A 88.211 246 20 4 448 685 43439903 43439659 3.880000e-73 285.0
25 TraesCS7D01G074100 chr7A 86.992 246 23 4 448 685 45603363 45603119 3.910000e-68 268.0
26 TraesCS7D01G074100 chr7A 87.310 197 17 3 496 685 43458471 43458276 3.990000e-53 219.0
27 TraesCS7D01G074100 chr7A 77.869 122 22 4 2268 2384 680338478 680338357 1.180000e-08 71.3
28 TraesCS7D01G074100 chr4A 95.415 916 30 7 211 1118 651639155 651638244 0.000000e+00 1448.0
29 TraesCS7D01G074100 chr4A 91.373 765 48 9 1111 1867 651637819 651637065 0.000000e+00 1031.0
30 TraesCS7D01G074100 chr4A 86.626 815 65 18 724 1509 651986141 651985342 0.000000e+00 861.0
31 TraesCS7D01G074100 chr4A 81.356 708 87 23 1610 2314 651837229 651836564 3.490000e-148 534.0
32 TraesCS7D01G074100 chr4A 93.388 121 8 0 1 121 651639286 651639166 1.880000e-41 180.0
33 TraesCS7D01G074100 chr1D 80.795 151 23 5 2241 2386 489752075 489752224 1.940000e-21 113.0
34 TraesCS7D01G074100 chr4B 79.866 149 24 5 2243 2386 640288412 640288559 1.170000e-18 104.0
35 TraesCS7D01G074100 chr5A 91.304 69 5 1 2243 2311 381686355 381686422 2.530000e-15 93.5
36 TraesCS7D01G074100 chr2B 93.443 61 3 1 2255 2315 98301461 98301402 3.270000e-14 89.8
37 TraesCS7D01G074100 chr6A 88.571 70 7 1 2243 2311 464539611 464539542 1.520000e-12 84.2


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 TraesCS7D01G074100 chr7D 43383142 43385527 2385 True 4407.000000 4407 100.0000 1 2386 1 chr7D.!!$R1 2385
1 TraesCS7D01G074100 chr7D 43429555 43431052 1497 True 1461.000000 1461 84.7590 3 1509 1 chr7D.!!$R3 1506
2 TraesCS7D01G074100 chr7D 43424221 43424952 731 True 619.000000 619 82.7630 1591 2315 1 chr7D.!!$R2 724
3 TraesCS7D01G074100 chr7A 45601363 45603363 2000 True 1004.000000 1740 86.8275 448 2299 2 chr7A.!!$R15 1851
4 TraesCS7D01G074100 chr7A 45592349 45594353 2004 True 995.000000 1694 87.5775 448 2299 2 chr7A.!!$R14 1851
5 TraesCS7D01G074100 chr7A 45572659 45574663 2004 True 992.500000 1694 87.3745 448 2299 2 chr7A.!!$R13 1851
6 TraesCS7D01G074100 chr7A 45068117 45071387 3270 True 743.000000 845 84.0960 83 2349 2 chr7A.!!$R11 2266
7 TraesCS7D01G074100 chr7A 45021300 45024533 3233 True 662.500000 678 85.0600 83 2088 2 chr7A.!!$R10 2005
8 TraesCS7D01G074100 chr7A 43416539 43417298 759 True 632.000000 632 82.4720 1591 2349 1 chr7A.!!$R1 758
9 TraesCS7D01G074100 chr7A 43457326 43458471 1145 True 594.500000 970 88.0790 496 1509 2 chr7A.!!$R8 1013
10 TraesCS7D01G074100 chr7A 45185435 45186568 1133 True 594.500000 693 88.3205 621 1683 2 chr7A.!!$R12 1062
11 TraesCS7D01G074100 chr7A 43438650 43440434 1784 True 549.000000 970 87.6410 3 1509 3 chr7A.!!$R7 1506
12 TraesCS7D01G074100 chr7A 44884701 44885723 1022 True 531.500000 752 87.4705 83 1059 2 chr7A.!!$R9 976
13 TraesCS7D01G074100 chr4A 651637065 651639286 2221 True 886.333333 1448 93.3920 1 1867 3 chr4A.!!$R3 1866
14 TraesCS7D01G074100 chr4A 651985342 651986141 799 True 861.000000 861 86.6260 724 1509 1 chr4A.!!$R2 785
15 TraesCS7D01G074100 chr4A 651836564 651837229 665 True 534.000000 534 81.3560 1610 2314 1 chr4A.!!$R1 704

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
105 2630 0.183492 TTGCCTCAACCTTGCTCTGT 59.817 50.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1939 5404 0.39034 CTCACGGCTGCACTATGTGT 60.39 55.0 0.5 0.0 35.75 3.72 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
28 29 4.161565 ACCGGAAGAAGATGCACTGTATAA 59.838 41.667 9.46 0.00 0.00 0.98
44 45 6.527722 CACTGTATAACATGGTGAAAATGTGC 59.472 38.462 0.00 0.00 38.27 4.57
46 47 7.093814 ACTGTATAACATGGTGAAAATGTGCAT 60.094 33.333 0.00 0.00 38.27 3.96
48 49 8.093307 TGTATAACATGGTGAAAATGTGCATTT 58.907 29.630 4.48 4.48 42.35 2.32
50 51 4.958509 ACATGGTGAAAATGTGCATTTCA 58.041 34.783 9.38 9.38 39.88 2.69
51 52 5.366460 ACATGGTGAAAATGTGCATTTCAA 58.634 33.333 13.97 2.65 39.88 2.69
52 53 5.821470 ACATGGTGAAAATGTGCATTTCAAA 59.179 32.000 13.97 7.62 39.88 2.69
53 54 6.318144 ACATGGTGAAAATGTGCATTTCAAAA 59.682 30.769 13.97 7.33 39.88 2.44
54 55 6.748333 TGGTGAAAATGTGCATTTCAAAAA 57.252 29.167 13.97 2.76 39.88 1.94
56 57 7.194278 TGGTGAAAATGTGCATTTCAAAAATG 58.806 30.769 13.97 7.82 39.88 2.32
57 58 7.066645 TGGTGAAAATGTGCATTTCAAAAATGA 59.933 29.630 13.97 0.00 39.88 2.57
58 59 7.588488 GGTGAAAATGTGCATTTCAAAAATGAG 59.412 33.333 13.97 0.00 39.88 2.90
59 60 8.336806 GTGAAAATGTGCATTTCAAAAATGAGA 58.663 29.630 13.97 0.00 39.88 3.27
60 61 8.890718 TGAAAATGTGCATTTCAAAAATGAGAA 58.109 25.926 14.82 1.59 39.88 2.87
62 63 8.665643 AAATGTGCATTTCAAAAATGAGAAGA 57.334 26.923 14.82 1.18 36.34 2.87
63 64 7.884816 ATGTGCATTTCAAAAATGAGAAGAG 57.115 32.000 14.82 0.00 0.00 2.85
64 65 6.218019 TGTGCATTTCAAAAATGAGAAGAGG 58.782 36.000 14.82 0.00 0.00 3.69
65 66 6.183360 TGTGCATTTCAAAAATGAGAAGAGGT 60.183 34.615 14.82 0.00 0.00 3.85
66 67 7.014134 TGTGCATTTCAAAAATGAGAAGAGGTA 59.986 33.333 14.82 0.00 0.00 3.08
67 68 8.031277 GTGCATTTCAAAAATGAGAAGAGGTAT 58.969 33.333 14.82 0.00 0.00 2.73
68 69 8.030692 TGCATTTCAAAAATGAGAAGAGGTATG 58.969 33.333 14.82 0.00 0.00 2.39
70 71 7.466746 TTTCAAAAATGAGAAGAGGTATGGG 57.533 36.000 0.00 0.00 0.00 4.00
71 72 5.509498 TCAAAAATGAGAAGAGGTATGGGG 58.491 41.667 0.00 0.00 0.00 4.96
72 73 5.015178 TCAAAAATGAGAAGAGGTATGGGGT 59.985 40.000 0.00 0.00 0.00 4.95
73 74 5.536497 AAAATGAGAAGAGGTATGGGGTT 57.464 39.130 0.00 0.00 0.00 4.11
74 75 4.779993 AATGAGAAGAGGTATGGGGTTC 57.220 45.455 0.00 0.00 0.00 3.62
76 77 3.107601 TGAGAAGAGGTATGGGGTTCAG 58.892 50.000 0.00 0.00 0.00 3.02
77 78 3.245984 TGAGAAGAGGTATGGGGTTCAGA 60.246 47.826 0.00 0.00 0.00 3.27
78 79 3.379452 AGAAGAGGTATGGGGTTCAGAG 58.621 50.000 0.00 0.00 0.00 3.35
79 80 3.012959 AGAAGAGGTATGGGGTTCAGAGA 59.987 47.826 0.00 0.00 0.00 3.10
80 81 3.715648 AGAGGTATGGGGTTCAGAGAT 57.284 47.619 0.00 0.00 0.00 2.75
81 82 4.834406 AGAGGTATGGGGTTCAGAGATA 57.166 45.455 0.00 0.00 0.00 1.98
105 2630 0.183492 TTGCCTCAACCTTGCTCTGT 59.817 50.000 0.00 0.00 0.00 3.41
127 2652 6.126568 GTTTGCTAAACAAGAGTGGTAACA 57.873 37.500 6.82 0.00 42.34 2.41
179 2704 8.885722 GCTATAGTGCTACGAGAAAGATACTAT 58.114 37.037 0.84 0.00 33.85 2.12
184 2709 6.858993 GTGCTACGAGAAAGATACTATCCTTG 59.141 42.308 0.00 0.00 0.00 3.61
193 2718 4.145807 AGATACTATCCTTGTGGAGACCG 58.854 47.826 0.00 0.00 46.91 4.79
199 2724 1.202604 TCCTTGTGGAGACCGTTTGAC 60.203 52.381 0.00 0.00 37.46 3.18
200 2725 1.226746 CTTGTGGAGACCGTTTGACC 58.773 55.000 0.00 0.00 0.00 4.02
310 2846 9.110502 GTCGATGATGGTCACAGTATAGATATA 57.889 37.037 0.00 0.00 0.00 0.86
419 3080 1.470890 CGTGAACAGTTGGGTGTTTGT 59.529 47.619 0.00 0.00 40.83 2.83
437 3098 2.471818 TGTCTTAGCGCGTGTTAAACA 58.528 42.857 8.43 10.35 0.00 2.83
484 3145 0.817013 TGATGCTTTGATTTCCCCGC 59.183 50.000 0.00 0.00 0.00 6.13
486 3147 0.614415 ATGCTTTGATTTCCCCGCCA 60.614 50.000 0.00 0.00 0.00 5.69
710 3568 3.826524 TGGTGCTCCTTAATTGTGTGAA 58.173 40.909 6.34 0.00 34.23 3.18
793 3662 4.678256 TGCCACCCTTAATTACATTCCAA 58.322 39.130 0.00 0.00 0.00 3.53
794 3663 4.464597 TGCCACCCTTAATTACATTCCAAC 59.535 41.667 0.00 0.00 0.00 3.77
795 3664 4.142026 GCCACCCTTAATTACATTCCAACC 60.142 45.833 0.00 0.00 0.00 3.77
796 3665 4.404394 CCACCCTTAATTACATTCCAACCC 59.596 45.833 0.00 0.00 0.00 4.11
884 3819 3.632145 AGGCCCGTTCTTTGCATTATAAG 59.368 43.478 0.00 0.00 0.00 1.73
917 3855 1.517257 CACTTAGCTCGTCCGGCAG 60.517 63.158 0.00 0.00 0.00 4.85
944 3885 3.012518 AGCTGAATACACATTCCAGCAC 58.987 45.455 13.98 0.00 42.05 4.40
1082 4074 4.022242 AGGCAGATCTACGTGCGTTATTAT 60.022 41.667 1.66 0.00 40.82 1.28
1098 4091 8.963130 TGCGTTATTATTTTCAACTTTCAAGTG 58.037 29.630 0.00 0.00 39.66 3.16
1118 4113 8.783093 TCAAGTGACAAACTGGAGTAAAATATG 58.217 33.333 0.00 0.00 39.81 1.78
1126 4553 8.822855 CAAACTGGAGTAAAATATGTATACGCA 58.177 33.333 0.00 0.00 0.00 5.24
1186 4617 2.264794 GGCGACGAAGGTGGTGAT 59.735 61.111 0.00 0.00 0.00 3.06
1417 4848 1.302752 TGACGCTGCTGCATCCTTT 60.303 52.632 16.29 0.00 39.64 3.11
1502 4942 8.821894 CCTTCACTGTTACTCTCAAATAATAGC 58.178 37.037 0.00 0.00 0.00 2.97
1509 4949 7.769044 TGTTACTCTCAAATAATAGCCCTGTTC 59.231 37.037 0.00 0.00 0.00 3.18
1551 4998 6.591834 CGAGAGTTGTTCAACAGAAATCCTAT 59.408 38.462 16.31 0.00 0.00 2.57
1587 5034 5.296531 GGCAGTTGTTCCAAAATCACATTTT 59.703 36.000 0.00 0.00 42.81 1.82
1588 5035 6.183360 GGCAGTTGTTCCAAAATCACATTTTT 60.183 34.615 0.00 0.00 40.27 1.94
1657 5109 2.103736 GTGCCGAGCGTAGGGTAC 59.896 66.667 0.00 0.00 0.00 3.34
1672 5124 5.220931 CGTAGGGTACACCAATGAGTACTAC 60.221 48.000 12.94 9.09 43.89 2.73
1673 5125 4.944177 AGGGTACACCAATGAGTACTACT 58.056 43.478 12.94 9.92 43.89 2.57
1674 5126 4.954826 AGGGTACACCAATGAGTACTACTC 59.045 45.833 9.04 9.04 43.21 2.59
1787 5242 5.659048 AGATTTGTCTTGAGTCAAACGTC 57.341 39.130 7.06 7.94 36.30 4.34
1799 5254 6.711579 TGAGTCAAACGTCTTTATGTTTCAC 58.288 36.000 0.00 0.00 41.79 3.18
1816 5271 6.690530 TGTTTCACAGATCCATGAAAATTCC 58.309 36.000 18.67 10.30 44.24 3.01
1887 5352 9.877178 TTTTATAATGATTACATTTTTGCGGGT 57.123 25.926 0.00 0.00 43.17 5.28
1939 5404 2.227865 GACGCAGCAAGGGTGAAAATAA 59.772 45.455 3.66 0.00 44.33 1.40
1945 5410 5.336372 GCAGCAAGGGTGAAAATAACACATA 60.336 40.000 0.00 0.00 39.65 2.29
1962 5452 1.961180 ATAGTGCAGCCGTGAGACCC 61.961 60.000 0.00 0.00 0.00 4.46
2004 5495 4.961511 TGTCCGTGGTGAGTGCGC 62.962 66.667 0.00 0.00 0.00 6.09
2075 5570 1.999735 CGAGCGCAAATCTAACTTGGA 59.000 47.619 11.47 0.00 0.00 3.53
2082 5577 5.147162 CGCAAATCTAACTTGGAACAGAAC 58.853 41.667 0.00 0.00 42.39 3.01
2118 5613 0.528901 CGTCCACCAGTTCGTCAACA 60.529 55.000 0.00 0.00 34.60 3.33
2119 5614 1.658994 GTCCACCAGTTCGTCAACAA 58.341 50.000 0.00 0.00 34.60 2.83
2120 5615 2.011222 GTCCACCAGTTCGTCAACAAA 58.989 47.619 0.00 0.00 34.60 2.83
2121 5616 2.616842 GTCCACCAGTTCGTCAACAAAT 59.383 45.455 0.00 0.00 34.60 2.32
2122 5617 2.616376 TCCACCAGTTCGTCAACAAATG 59.384 45.455 0.00 0.00 34.60 2.32
2123 5618 2.287547 CCACCAGTTCGTCAACAAATGG 60.288 50.000 0.00 0.00 34.60 3.16
2124 5619 2.616376 CACCAGTTCGTCAACAAATGGA 59.384 45.455 7.21 0.00 34.60 3.41
2125 5620 3.066064 CACCAGTTCGTCAACAAATGGAA 59.934 43.478 7.21 0.00 34.60 3.53
2126 5621 3.888930 ACCAGTTCGTCAACAAATGGAAT 59.111 39.130 7.21 0.00 34.60 3.01
2127 5622 4.340950 ACCAGTTCGTCAACAAATGGAATT 59.659 37.500 7.21 0.00 38.98 2.17
2128 5623 4.917415 CCAGTTCGTCAACAAATGGAATTC 59.083 41.667 0.00 0.00 33.67 2.17
2129 5624 4.917415 CAGTTCGTCAACAAATGGAATTCC 59.083 41.667 18.17 18.17 33.67 3.01
2130 5625 4.022329 AGTTCGTCAACAAATGGAATTCCC 60.022 41.667 21.90 4.57 33.67 3.97
2131 5626 4.261825 GTTCGTCAACAAATGGAATTCCCA 60.262 41.667 21.90 10.28 39.86 4.37
2132 5627 5.737635 GTTCGTCAACAAATGGAATTCCCAA 60.738 40.000 21.90 4.35 39.38 4.12
2133 5628 7.711661 GTTCGTCAACAAATGGAATTCCCAAC 61.712 42.308 21.90 7.18 39.38 3.77
2134 5629 9.965369 GTTCGTCAACAAATGGAATTCCCAACA 62.965 40.741 21.90 3.15 39.38 3.33
2148 5643 0.457035 CCAACAAATCGGCATGGGAG 59.543 55.000 0.00 0.00 0.00 4.30
2167 5662 6.409704 TGGGAGATTTGTCTTTCACTATCAG 58.590 40.000 0.00 0.00 0.00 2.90
2190 5685 2.223340 GCATTCAATTGCCTGTAGTCGG 60.223 50.000 0.00 0.00 36.60 4.79
2196 5691 3.488090 GCCTGTAGTCGGCGCAAC 61.488 66.667 10.83 6.93 37.87 4.17
2228 5723 1.203052 CCATCTTTCTTGCGCACCAAT 59.797 47.619 11.12 0.00 31.91 3.16
2229 5724 2.256174 CATCTTTCTTGCGCACCAATG 58.744 47.619 11.12 8.31 31.91 2.82
2287 5782 4.078571 TGGTTAGGAGGACAGTGATATCCT 60.079 45.833 15.62 15.62 42.89 3.24
2315 5810 3.581332 CACCAGGGTTTAAGTCCTAGACA 59.419 47.826 0.00 0.00 34.60 3.41
2317 5812 4.470304 ACCAGGGTTTAAGTCCTAGACATC 59.530 45.833 0.00 0.00 34.60 3.06
2318 5813 4.441634 CCAGGGTTTAAGTCCTAGACATCG 60.442 50.000 0.00 0.00 34.60 3.84
2319 5814 3.705072 AGGGTTTAAGTCCTAGACATCGG 59.295 47.826 0.00 0.00 34.60 4.18
2320 5815 3.450096 GGGTTTAAGTCCTAGACATCGGT 59.550 47.826 0.00 0.00 34.60 4.69
2321 5816 4.430908 GGTTTAAGTCCTAGACATCGGTG 58.569 47.826 0.00 0.00 34.60 4.94
2323 5818 1.853963 AAGTCCTAGACATCGGTGCT 58.146 50.000 0.00 0.00 34.60 4.40
2326 5824 1.335496 GTCCTAGACATCGGTGCTCTC 59.665 57.143 0.00 0.00 32.09 3.20
2346 5844 7.229306 TGCTCTCGCATATTCTGGATTTATTTT 59.771 33.333 0.00 0.00 42.25 1.82
2349 5847 9.778741 TCTCGCATATTCTGGATTTATTTTAGT 57.221 29.630 0.00 0.00 0.00 2.24
2351 5849 9.778741 TCGCATATTCTGGATTTATTTTAGTCT 57.221 29.630 0.00 0.00 0.00 3.24
2358 5856 8.732746 TCTGGATTTATTTTAGTCTTACCAGC 57.267 34.615 0.00 0.00 40.31 4.85
2359 5857 8.325787 TCTGGATTTATTTTAGTCTTACCAGCA 58.674 33.333 0.00 0.00 40.31 4.41
2360 5858 8.506168 TGGATTTATTTTAGTCTTACCAGCAG 57.494 34.615 0.00 0.00 0.00 4.24
2361 5859 7.556275 TGGATTTATTTTAGTCTTACCAGCAGG 59.444 37.037 0.00 0.00 42.21 4.85
2362 5860 7.013369 GGATTTATTTTAGTCTTACCAGCAGGG 59.987 40.741 0.00 0.00 44.81 4.45
2374 5872 3.357079 GCAGGGTGCGTTCAGTGG 61.357 66.667 0.00 0.00 31.71 4.00
2375 5873 2.669569 CAGGGTGCGTTCAGTGGG 60.670 66.667 0.00 0.00 0.00 4.61
2376 5874 2.847234 AGGGTGCGTTCAGTGGGA 60.847 61.111 0.00 0.00 0.00 4.37
2377 5875 2.358737 GGGTGCGTTCAGTGGGAG 60.359 66.667 0.00 0.00 0.00 4.30
2378 5876 2.358737 GGTGCGTTCAGTGGGAGG 60.359 66.667 0.00 0.00 0.00 4.30
2379 5877 2.741092 GTGCGTTCAGTGGGAGGA 59.259 61.111 0.00 0.00 0.00 3.71
2380 5878 1.374758 GTGCGTTCAGTGGGAGGAG 60.375 63.158 0.00 0.00 0.00 3.69
2381 5879 1.533033 TGCGTTCAGTGGGAGGAGA 60.533 57.895 0.00 0.00 0.00 3.71
2382 5880 1.079750 GCGTTCAGTGGGAGGAGAC 60.080 63.158 0.00 0.00 0.00 3.36
2383 5881 1.213013 CGTTCAGTGGGAGGAGACG 59.787 63.158 0.00 0.00 0.00 4.18
2384 5882 1.524863 CGTTCAGTGGGAGGAGACGT 61.525 60.000 0.00 0.00 0.00 4.34
2385 5883 0.680061 GTTCAGTGGGAGGAGACGTT 59.320 55.000 0.00 0.00 0.00 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.958509 TGAAATGCACATTTTCACCATGT 58.041 34.783 9.38 0.00 40.77 3.21
44 45 7.977853 CCCATACCTCTTCTCATTTTTGAAATG 59.022 37.037 6.99 6.99 0.00 2.32
46 47 6.437162 CCCCATACCTCTTCTCATTTTTGAAA 59.563 38.462 0.00 0.00 0.00 2.69
48 49 5.015178 ACCCCATACCTCTTCTCATTTTTGA 59.985 40.000 0.00 0.00 0.00 2.69
50 51 5.536497 ACCCCATACCTCTTCTCATTTTT 57.464 39.130 0.00 0.00 0.00 1.94
51 52 5.015178 TGAACCCCATACCTCTTCTCATTTT 59.985 40.000 0.00 0.00 0.00 1.82
52 53 4.540099 TGAACCCCATACCTCTTCTCATTT 59.460 41.667 0.00 0.00 0.00 2.32
53 54 4.111577 TGAACCCCATACCTCTTCTCATT 58.888 43.478 0.00 0.00 0.00 2.57
54 55 3.713764 CTGAACCCCATACCTCTTCTCAT 59.286 47.826 0.00 0.00 0.00 2.90
56 57 3.375699 TCTGAACCCCATACCTCTTCTC 58.624 50.000 0.00 0.00 0.00 2.87
57 58 3.012959 TCTCTGAACCCCATACCTCTTCT 59.987 47.826 0.00 0.00 0.00 2.85
58 59 3.375699 TCTCTGAACCCCATACCTCTTC 58.624 50.000 0.00 0.00 0.00 2.87
59 60 3.491766 TCTCTGAACCCCATACCTCTT 57.508 47.619 0.00 0.00 0.00 2.85
60 61 3.715648 ATCTCTGAACCCCATACCTCT 57.284 47.619 0.00 0.00 0.00 3.69
62 63 5.977533 TGTATATCTCTGAACCCCATACCT 58.022 41.667 0.00 0.00 0.00 3.08
63 64 6.875972 ATGTATATCTCTGAACCCCATACC 57.124 41.667 0.00 0.00 0.00 2.73
64 65 6.595716 GCAATGTATATCTCTGAACCCCATAC 59.404 42.308 0.00 0.00 0.00 2.39
65 66 6.296432 GGCAATGTATATCTCTGAACCCCATA 60.296 42.308 0.00 0.00 0.00 2.74
66 67 5.515534 GGCAATGTATATCTCTGAACCCCAT 60.516 44.000 0.00 0.00 0.00 4.00
67 68 4.202461 GGCAATGTATATCTCTGAACCCCA 60.202 45.833 0.00 0.00 0.00 4.96
68 69 4.042187 AGGCAATGTATATCTCTGAACCCC 59.958 45.833 0.00 0.00 0.00 4.95
70 71 5.858381 TGAGGCAATGTATATCTCTGAACC 58.142 41.667 0.00 0.00 0.00 3.62
71 72 6.203723 GGTTGAGGCAATGTATATCTCTGAAC 59.796 42.308 0.00 0.00 0.00 3.18
72 73 6.100279 AGGTTGAGGCAATGTATATCTCTGAA 59.900 38.462 0.00 0.00 0.00 3.02
73 74 5.604231 AGGTTGAGGCAATGTATATCTCTGA 59.396 40.000 0.00 0.00 0.00 3.27
74 75 5.862845 AGGTTGAGGCAATGTATATCTCTG 58.137 41.667 0.00 0.00 0.00 3.35
76 77 5.049129 GCAAGGTTGAGGCAATGTATATCTC 60.049 44.000 0.00 0.00 0.00 2.75
77 78 4.823989 GCAAGGTTGAGGCAATGTATATCT 59.176 41.667 0.00 0.00 0.00 1.98
78 79 4.823989 AGCAAGGTTGAGGCAATGTATATC 59.176 41.667 0.00 0.00 0.00 1.63
79 80 4.796606 AGCAAGGTTGAGGCAATGTATAT 58.203 39.130 0.00 0.00 0.00 0.86
80 81 4.080356 AGAGCAAGGTTGAGGCAATGTATA 60.080 41.667 0.00 0.00 0.00 1.47
81 82 3.019564 GAGCAAGGTTGAGGCAATGTAT 58.980 45.455 0.00 0.00 0.00 2.29
105 2630 6.761099 TTGTTACCACTCTTGTTTAGCAAA 57.239 33.333 0.00 0.00 36.53 3.68
141 2666 7.012989 TCGTAGCACTATAGCACAAAGAGAATA 59.987 37.037 0.00 0.00 36.85 1.75
179 2704 1.124780 TCAAACGGTCTCCACAAGGA 58.875 50.000 0.00 0.00 43.21 3.36
184 2709 2.315386 GCGGTCAAACGGTCTCCAC 61.315 63.158 0.00 0.00 0.00 4.02
387 3008 6.594159 CCCAACTGTTCACGATTCTAGTTATT 59.406 38.462 0.00 0.00 0.00 1.40
492 3153 8.261522 TGTATATTGTGCACACTACATTTAGGA 58.738 33.333 21.56 0.00 0.00 2.94
793 3662 4.265856 ACTTCTCAAAAAGAAAGGGGGT 57.734 40.909 0.00 0.00 43.39 4.95
794 3663 6.918067 AATACTTCTCAAAAAGAAAGGGGG 57.082 37.500 0.00 0.00 43.39 5.40
795 3664 8.404107 TGTAATACTTCTCAAAAAGAAAGGGG 57.596 34.615 0.00 0.00 43.39 4.79
917 3855 4.580167 TGGAATGTGTATTCAGCTAATGGC 59.420 41.667 0.00 0.00 43.62 4.40
937 3878 1.272490 CGAAGGTTACTGAGTGCTGGA 59.728 52.381 0.00 0.00 0.00 3.86
944 3885 2.685897 AGAGCTAGCGAAGGTTACTGAG 59.314 50.000 9.55 0.00 40.68 3.35
1082 4074 6.644592 CCAGTTTGTCACTTGAAAGTTGAAAA 59.355 34.615 0.00 0.00 37.08 2.29
1126 4553 3.610114 GCACACAAAGAAATCAGCACGAT 60.610 43.478 0.00 0.00 35.12 3.73
1422 4853 6.640907 TCGTCGTCAACATATCATTATTCAGG 59.359 38.462 0.00 0.00 0.00 3.86
1501 4941 2.185004 ACACATGTACAGAACAGGGC 57.815 50.000 0.00 0.00 44.20 5.19
1502 4942 6.435428 GTTTTAACACATGTACAGAACAGGG 58.565 40.000 0.00 0.00 44.20 4.45
1509 4949 6.764877 ACTCTCGTTTTAACACATGTACAG 57.235 37.500 0.00 0.00 0.00 2.74
1657 5109 4.282496 AGGAGGAGTAGTACTCATTGGTG 58.718 47.826 27.41 0.00 46.79 4.17
1767 5222 6.436843 AAAGACGTTTGACTCAAGACAAAT 57.563 33.333 10.06 0.00 40.50 2.32
1799 5254 8.857098 ACATTATCAGGAATTTTCATGGATCTG 58.143 33.333 5.25 2.46 39.29 2.90
1907 5372 4.707840 CTGCGTCGTTGCGTGCTG 62.708 66.667 0.00 5.87 37.81 4.41
1913 5378 4.389576 CCCTTGCTGCGTCGTTGC 62.390 66.667 0.00 0.00 0.00 4.17
1939 5404 0.390340 CTCACGGCTGCACTATGTGT 60.390 55.000 0.50 0.00 35.75 3.72
1945 5410 4.008933 GGGTCTCACGGCTGCACT 62.009 66.667 0.50 0.00 0.00 4.40
1962 5452 7.910162 CACTTCGAATTTAAGGTGATACCATTG 59.090 37.037 0.00 0.00 41.95 2.82
2004 5495 4.380233 GGAGATGAACCAAAGACAGCATTG 60.380 45.833 0.00 0.00 0.00 2.82
2075 5570 2.191109 ACGGCCCAACGTTCTGTT 59.809 55.556 0.00 0.00 46.25 3.16
2098 5593 0.529119 GTTGACGAACTGGTGGACGT 60.529 55.000 0.00 0.00 41.57 4.34
2105 5600 3.980646 TTCCATTTGTTGACGAACTGG 57.019 42.857 0.00 0.00 32.79 4.00
2118 5613 4.831107 CCGATTTGTTGGGAATTCCATTT 58.169 39.130 25.67 3.18 46.52 2.32
2119 5614 3.369366 GCCGATTTGTTGGGAATTCCATT 60.369 43.478 25.67 1.52 46.52 3.16
2120 5615 2.168313 GCCGATTTGTTGGGAATTCCAT 59.832 45.455 25.67 9.54 46.52 3.41
2121 5616 1.548269 GCCGATTTGTTGGGAATTCCA 59.452 47.619 25.67 9.48 45.43 3.53
2122 5617 1.548269 TGCCGATTTGTTGGGAATTCC 59.452 47.619 16.74 16.74 0.00 3.01
2123 5618 3.189285 CATGCCGATTTGTTGGGAATTC 58.811 45.455 0.00 0.00 0.00 2.17
2124 5619 2.093553 CCATGCCGATTTGTTGGGAATT 60.094 45.455 0.00 0.00 0.00 2.17
2125 5620 1.481772 CCATGCCGATTTGTTGGGAAT 59.518 47.619 0.00 0.00 0.00 3.01
2126 5621 0.894141 CCATGCCGATTTGTTGGGAA 59.106 50.000 0.00 0.00 0.00 3.97
2127 5622 2.577490 CCATGCCGATTTGTTGGGA 58.423 52.632 0.00 0.00 0.00 4.37
2128 5623 0.969917 TCCCATGCCGATTTGTTGGG 60.970 55.000 0.00 0.00 46.99 4.12
2129 5624 0.457035 CTCCCATGCCGATTTGTTGG 59.543 55.000 0.00 0.00 0.00 3.77
2130 5625 1.462616 TCTCCCATGCCGATTTGTTG 58.537 50.000 0.00 0.00 0.00 3.33
2131 5626 2.442236 ATCTCCCATGCCGATTTGTT 57.558 45.000 0.00 0.00 0.00 2.83
2132 5627 2.428171 CAAATCTCCCATGCCGATTTGT 59.572 45.455 21.75 3.17 44.25 2.83
2133 5628 3.088194 CAAATCTCCCATGCCGATTTG 57.912 47.619 19.12 19.12 44.03 2.32
2134 5629 2.689983 GACAAATCTCCCATGCCGATTT 59.310 45.455 8.42 8.42 37.73 2.17
2196 5691 1.033746 AAAGATGGCACCTGGCGATG 61.034 55.000 0.00 0.00 41.41 3.84
2248 5743 6.716284 TCCTAACCATACAATCACATGTTGA 58.284 36.000 0.00 0.00 39.11 3.18
2253 5748 5.428457 TGTCCTCCTAACCATACAATCACAT 59.572 40.000 0.00 0.00 0.00 3.21
2262 5757 6.017192 GGATATCACTGTCCTCCTAACCATA 58.983 44.000 4.83 0.00 30.28 2.74
2303 5798 2.950309 GAGCACCGATGTCTAGGACTTA 59.050 50.000 0.00 0.00 33.15 2.24
2323 5818 9.778741 ACTAAAATAAATCCAGAATATGCGAGA 57.221 29.630 0.00 0.00 0.00 4.04
2354 5852 3.052082 CTGAACGCACCCTGCTGG 61.052 66.667 1.89 1.89 42.25 4.85
2355 5853 2.281070 ACTGAACGCACCCTGCTG 60.281 61.111 0.00 0.00 42.25 4.41
2356 5854 2.281070 CACTGAACGCACCCTGCT 60.281 61.111 0.00 0.00 42.25 4.24
2357 5855 3.357079 CCACTGAACGCACCCTGC 61.357 66.667 0.00 0.00 40.69 4.85
2358 5856 2.669569 CCCACTGAACGCACCCTG 60.670 66.667 0.00 0.00 0.00 4.45
2359 5857 2.847234 TCCCACTGAACGCACCCT 60.847 61.111 0.00 0.00 0.00 4.34
2360 5858 2.358737 CTCCCACTGAACGCACCC 60.359 66.667 0.00 0.00 0.00 4.61
2361 5859 2.358737 CCTCCCACTGAACGCACC 60.359 66.667 0.00 0.00 0.00 5.01
2362 5860 1.374758 CTCCTCCCACTGAACGCAC 60.375 63.158 0.00 0.00 0.00 5.34
2363 5861 1.533033 TCTCCTCCCACTGAACGCA 60.533 57.895 0.00 0.00 0.00 5.24
2364 5862 1.079750 GTCTCCTCCCACTGAACGC 60.080 63.158 0.00 0.00 0.00 4.84
2365 5863 1.213013 CGTCTCCTCCCACTGAACG 59.787 63.158 0.00 0.00 0.00 3.95
2366 5864 0.680061 AACGTCTCCTCCCACTGAAC 59.320 55.000 0.00 0.00 0.00 3.18
2367 5865 3.143010 AACGTCTCCTCCCACTGAA 57.857 52.632 0.00 0.00 0.00 3.02
2368 5866 4.945645 AACGTCTCCTCCCACTGA 57.054 55.556 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.