Multiple sequence alignment - TraesCS7A01G207200

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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 TraesCS7A01G207200 chr7A 100.000 2735 0 0 1 2735 169955429 169952695 0.000000e+00 5051.0
1 TraesCS7A01G207200 chr7A 90.909 726 37 15 760 1456 631954991 631954266 0.000000e+00 948.0
2 TraesCS7A01G207200 chr7A 83.616 1062 89 36 760 1758 138982205 138983244 0.000000e+00 918.0
3 TraesCS7A01G207200 chr7A 89.238 669 35 16 814 1456 630436345 630437002 0.000000e+00 802.0
4 TraesCS7A01G207200 chr7A 85.325 661 50 20 96 749 594449748 594450368 8.260000e-180 640.0
5 TraesCS7A01G207200 chr7A 91.081 370 21 5 362 729 628647720 628648079 8.800000e-135 490.0
6 TraesCS7A01G207200 chr7A 86.911 382 41 5 2223 2600 628522992 628523368 1.170000e-113 420.0
7 TraesCS7A01G207200 chr7A 94.340 265 15 0 1494 1758 631954267 631954003 9.120000e-110 407.0
8 TraesCS7A01G207200 chr7A 93.089 246 17 0 1513 1758 630437030 630437275 7.200000e-96 361.0
9 TraesCS7A01G207200 chr7A 91.620 179 15 0 1753 1931 138983297 138983475 5.850000e-62 248.0
10 TraesCS7A01G207200 chr7A 80.851 282 39 12 2275 2548 627230005 627229731 9.930000e-50 207.0
11 TraesCS7A01G207200 chr7A 90.164 122 8 2 158 275 628647549 628647670 3.650000e-34 156.0
12 TraesCS7A01G207200 chr7A 80.124 161 10 5 1 160 628647360 628647499 1.730000e-17 100.0
13 TraesCS7A01G207200 chr7A 97.297 37 1 0 2083 2119 628653241 628653277 2.270000e-06 63.9
14 TraesCS7A01G207200 chr7D 89.932 1023 70 12 760 1758 548089294 548088281 0.000000e+00 1288.0
15 TraesCS7A01G207200 chr7D 89.709 962 65 11 825 1758 548095918 548094963 0.000000e+00 1197.0
16 TraesCS7A01G207200 chr7D 88.042 669 32 14 96 749 545653035 545653670 0.000000e+00 749.0
17 TraesCS7A01G207200 chr7D 87.576 660 54 16 96 749 518775256 518775893 0.000000e+00 739.0
18 TraesCS7A01G207200 chr7D 91.106 416 29 5 2321 2735 546780846 546781254 8.560000e-155 556.0
19 TraesCS7A01G207200 chr7D 92.737 179 13 0 1753 1931 139084521 139084699 2.700000e-65 259.0
20 TraesCS7A01G207200 chr7D 92.045 176 14 0 1756 1931 548094928 548094753 5.850000e-62 248.0
21 TraesCS7A01G207200 chr7D 91.124 169 14 1 2120 2288 546780681 546780848 7.620000e-56 228.0
22 TraesCS7A01G207200 chr7D 100.000 35 0 0 760 794 548095946 548095912 6.320000e-07 65.8
23 TraesCS7A01G207200 chr7D 97.222 36 1 0 2084 2119 518777568 518777603 8.180000e-06 62.1
24 TraesCS7A01G207200 chr7B 90.149 1005 52 29 776 1758 589916276 589917255 0.000000e+00 1264.0
25 TraesCS7A01G207200 chr7B 90.041 974 68 6 811 1758 591577023 591577993 0.000000e+00 1234.0
26 TraesCS7A01G207200 chr7B 88.420 1019 62 12 790 1758 591073342 591072330 0.000000e+00 1177.0
27 TraesCS7A01G207200 chr7B 87.037 1026 81 26 760 1758 591279450 591278450 0.000000e+00 1110.0
28 TraesCS7A01G207200 chr7B 86.257 1026 89 26 760 1758 591228321 591227321 0.000000e+00 1066.0
29 TraesCS7A01G207200 chr7B 90.767 704 45 10 790 1485 591159658 591158967 0.000000e+00 922.0
30 TraesCS7A01G207200 chr7B 92.176 524 21 6 96 604 589937525 589938043 0.000000e+00 723.0
31 TraesCS7A01G207200 chr7B 83.117 616 48 13 2120 2735 589897947 589898506 6.760000e-141 510.0
32 TraesCS7A01G207200 chr7B 93.846 325 15 1 1757 2081 589917291 589917610 4.090000e-133 484.0
33 TraesCS7A01G207200 chr7B 94.142 239 14 0 1520 1758 591147724 591147486 5.570000e-97 364.0
34 TraesCS7A01G207200 chr7B 80.000 295 41 14 2270 2556 588821502 588821218 4.620000e-48 202.0
35 TraesCS7A01G207200 chr7B 89.262 149 9 2 601 749 589938112 589938253 2.160000e-41 180.0
36 TraesCS7A01G207200 chr7B 89.928 139 14 0 1756 1894 591147451 591147313 2.160000e-41 180.0
37 TraesCS7A01G207200 chr7B 88.489 139 16 0 1756 1894 591227286 591227148 4.680000e-38 169.0
38 TraesCS7A01G207200 chr7B 88.489 139 16 0 1756 1894 591278415 591278277 4.680000e-38 169.0
39 TraesCS7A01G207200 chr7B 95.000 100 1 2 1756 1851 591072295 591072196 1.310000e-33 154.0
40 TraesCS7A01G207200 chr7B 95.745 47 2 0 1932 1978 589938878 589938924 2.920000e-10 76.8
41 TraesCS7A01G207200 chr7B 97.297 37 1 0 2083 2119 589939946 589939982 2.270000e-06 63.9
42 TraesCS7A01G207200 chr6A 88.557 769 41 18 1 742 158244197 158243449 0.000000e+00 889.0
43 TraesCS7A01G207200 chr6A 95.455 88 4 0 1997 2084 158242190 158242103 1.020000e-29 141.0
44 TraesCS7A01G207200 chr6D 87.922 770 46 13 1 743 122990942 122991691 0.000000e+00 863.0
45 TraesCS7A01G207200 chr6D 92.500 320 24 0 418 737 122982241 122982560 2.480000e-125 459.0
46 TraesCS7A01G207200 chr6D 87.255 204 10 7 246 435 122982029 122982230 4.590000e-53 219.0
47 TraesCS7A01G207200 chr6D 81.439 264 29 6 1 250 122980825 122981082 5.970000e-47 198.0
48 TraesCS7A01G207200 chr6D 94.521 73 4 0 1984 2056 122992977 122993049 2.230000e-21 113.0
49 TraesCS7A01G207200 chr6D 92.105 38 3 0 2043 2080 122993060 122993097 1.000000e-03 54.7
50 TraesCS7A01G207200 chr6B 87.466 734 46 12 1 707 216632995 216633709 0.000000e+00 804.0
51 TraesCS7A01G207200 chr5D 90.265 339 26 4 2223 2558 331839621 331839955 1.160000e-118 436.0
52 TraesCS7A01G207200 chr5D 81.505 465 58 17 288 741 331839117 331839564 9.310000e-95 357.0
53 TraesCS7A01G207200 chr5D 83.102 361 28 23 219 562 42080292 42079948 5.730000e-77 298.0
54 TraesCS7A01G207200 chr5D 80.000 295 41 14 2270 2556 289419063 289418779 4.620000e-48 202.0
55 TraesCS7A01G207200 chr5A 80.217 369 44 15 219 572 30650524 30650170 1.630000e-62 250.0
56 TraesCS7A01G207200 chr1B 89.691 194 19 1 2225 2417 398966613 398966806 2.100000e-61 246.0
57 TraesCS7A01G207200 chr1B 80.921 304 49 7 2256 2556 398839088 398838791 5.890000e-57 231.0
58 TraesCS7A01G207200 chrUn 80.000 295 41 14 2270 2556 479833318 479833034 4.620000e-48 202.0


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 TraesCS7A01G207200 chr7A 169952695 169955429 2734 True 5051.000000 5051 100.000000 1 2735 1 chr7A.!!$R1 2734
1 TraesCS7A01G207200 chr7A 631954003 631954991 988 True 677.500000 948 92.624500 760 1758 2 chr7A.!!$R3 998
2 TraesCS7A01G207200 chr7A 594449748 594450368 620 False 640.000000 640 85.325000 96 749 1 chr7A.!!$F1 653
3 TraesCS7A01G207200 chr7A 138982205 138983475 1270 False 583.000000 918 87.618000 760 1931 2 chr7A.!!$F4 1171
4 TraesCS7A01G207200 chr7A 630436345 630437275 930 False 581.500000 802 91.163500 814 1758 2 chr7A.!!$F6 944
5 TraesCS7A01G207200 chr7A 628647360 628648079 719 False 248.666667 490 87.123000 1 729 3 chr7A.!!$F5 728
6 TraesCS7A01G207200 chr7D 548088281 548089294 1013 True 1288.000000 1288 89.932000 760 1758 1 chr7D.!!$R1 998
7 TraesCS7A01G207200 chr7D 545653035 545653670 635 False 749.000000 749 88.042000 96 749 1 chr7D.!!$F2 653
8 TraesCS7A01G207200 chr7D 548094753 548095946 1193 True 503.600000 1197 93.918000 760 1931 3 chr7D.!!$R2 1171
9 TraesCS7A01G207200 chr7D 518775256 518777603 2347 False 400.550000 739 92.399000 96 2119 2 chr7D.!!$F3 2023
10 TraesCS7A01G207200 chr7D 546780681 546781254 573 False 392.000000 556 91.115000 2120 2735 2 chr7D.!!$F4 615
11 TraesCS7A01G207200 chr7B 591577023 591577993 970 False 1234.000000 1234 90.041000 811 1758 1 chr7B.!!$F2 947
12 TraesCS7A01G207200 chr7B 591158967 591159658 691 True 922.000000 922 90.767000 790 1485 1 chr7B.!!$R2 695
13 TraesCS7A01G207200 chr7B 589916276 589917610 1334 False 874.000000 1264 91.997500 776 2081 2 chr7B.!!$F3 1305
14 TraesCS7A01G207200 chr7B 591072196 591073342 1146 True 665.500000 1177 91.710000 790 1851 2 chr7B.!!$R3 1061
15 TraesCS7A01G207200 chr7B 591278277 591279450 1173 True 639.500000 1110 87.763000 760 1894 2 chr7B.!!$R6 1134
16 TraesCS7A01G207200 chr7B 591227148 591228321 1173 True 617.500000 1066 87.373000 760 1894 2 chr7B.!!$R5 1134
17 TraesCS7A01G207200 chr7B 589897947 589898506 559 False 510.000000 510 83.117000 2120 2735 1 chr7B.!!$F1 615
18 TraesCS7A01G207200 chr7B 589937525 589939982 2457 False 260.925000 723 93.620000 96 2119 4 chr7B.!!$F4 2023
19 TraesCS7A01G207200 chr6A 158242103 158244197 2094 True 515.000000 889 92.006000 1 2084 2 chr6A.!!$R1 2083
20 TraesCS7A01G207200 chr6D 122990942 122993097 2155 False 343.566667 863 91.516000 1 2080 3 chr6D.!!$F2 2079
21 TraesCS7A01G207200 chr6D 122980825 122982560 1735 False 292.000000 459 87.064667 1 737 3 chr6D.!!$F1 736
22 TraesCS7A01G207200 chr6B 216632995 216633709 714 False 804.000000 804 87.466000 1 707 1 chr6B.!!$F1 706
23 TraesCS7A01G207200 chr5D 331839117 331839955 838 False 396.500000 436 85.885000 288 2558 2 chr5D.!!$F1 2270

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
517 1591 0.390340 GTGTCATCCGCAGCTTCTCA 60.390 55.0 0.00 0.0 0.00 3.27 F
1490 2711 0.525668 GTCGATTCTGGCATCGTCGT 60.526 55.0 8.63 0.0 45.28 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1493 2714 0.036010 CTTGCTGATTCCCACGGTCT 60.036 55.0 0.0 0.0 0.0 3.85 R
2637 5539 0.109532 TTGATGCTCGGTTGGGTTGA 59.890 50.0 0.0 0.0 0.0 3.18 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 3.726557 AGCATGTTTCCTGAATCCTGA 57.273 42.857 0.00 0.00 0.00 3.86
33 34 4.246712 AGCATGTTTCCTGAATCCTGAT 57.753 40.909 0.00 0.00 0.00 2.90
34 35 3.952323 AGCATGTTTCCTGAATCCTGATG 59.048 43.478 0.00 0.00 0.00 3.07
35 36 3.490419 GCATGTTTCCTGAATCCTGATGC 60.490 47.826 0.00 0.00 0.00 3.91
43 48 3.756963 CCTGAATCCTGATGCATACATGG 59.243 47.826 0.00 0.00 36.35 3.66
72 91 2.928801 ACCAACAGCTCATGTGTACA 57.071 45.000 0.00 0.00 43.00 2.90
73 92 2.771089 ACCAACAGCTCATGTGTACAG 58.229 47.619 0.00 0.00 43.00 2.74
76 95 0.686789 ACAGCTCATGTGTACAGGCA 59.313 50.000 0.00 0.00 41.91 4.75
77 96 1.072173 ACAGCTCATGTGTACAGGCAA 59.928 47.619 0.00 0.00 41.91 4.52
78 97 2.290514 ACAGCTCATGTGTACAGGCAAT 60.291 45.455 0.00 0.00 41.91 3.56
79 98 2.751259 CAGCTCATGTGTACAGGCAATT 59.249 45.455 0.00 0.00 0.00 2.32
80 99 3.940852 CAGCTCATGTGTACAGGCAATTA 59.059 43.478 0.00 0.00 0.00 1.40
81 100 3.941483 AGCTCATGTGTACAGGCAATTAC 59.059 43.478 0.00 0.00 0.00 1.89
82 101 3.689161 GCTCATGTGTACAGGCAATTACA 59.311 43.478 0.00 0.00 0.00 2.41
83 102 4.437390 GCTCATGTGTACAGGCAATTACAC 60.437 45.833 13.41 13.41 45.60 2.90
84 103 4.905429 TCATGTGTACAGGCAATTACACT 58.095 39.130 18.30 6.96 45.60 3.55
85 104 4.694982 TCATGTGTACAGGCAATTACACTG 59.305 41.667 18.30 14.72 45.60 3.66
86 105 4.344359 TGTGTACAGGCAATTACACTGA 57.656 40.909 18.30 3.41 45.60 3.41
87 106 4.905429 TGTGTACAGGCAATTACACTGAT 58.095 39.130 18.30 0.00 45.60 2.90
88 107 4.935205 TGTGTACAGGCAATTACACTGATC 59.065 41.667 18.30 0.00 45.60 2.92
89 108 4.332819 GTGTACAGGCAATTACACTGATCC 59.667 45.833 13.15 0.00 43.18 3.36
90 109 3.719268 ACAGGCAATTACACTGATCCA 57.281 42.857 9.40 0.00 36.17 3.41
91 110 4.032960 ACAGGCAATTACACTGATCCAA 57.967 40.909 9.40 0.00 36.17 3.53
92 111 4.406456 ACAGGCAATTACACTGATCCAAA 58.594 39.130 9.40 0.00 36.17 3.28
93 112 4.218417 ACAGGCAATTACACTGATCCAAAC 59.782 41.667 9.40 0.00 36.17 2.93
94 113 4.218200 CAGGCAATTACACTGATCCAAACA 59.782 41.667 0.00 0.00 34.21 2.83
142 162 8.801715 AATTTTGTTCAGTACAATTGCTGTAG 57.198 30.769 5.05 0.00 45.72 2.74
175 249 9.874205 ACCACTTTCATTTAATTAACATGGATG 57.126 29.630 14.77 9.21 0.00 3.51
308 1338 1.929230 TGTCACGTCGCAGAGAAAAA 58.071 45.000 0.00 0.00 36.95 1.94
355 1386 9.979270 GTGTTTACTTCACTGAATATCTGAATG 57.021 33.333 0.00 0.00 33.59 2.67
356 1387 9.725019 TGTTTACTTCACTGAATATCTGAATGT 57.275 29.630 0.00 0.00 0.00 2.71
413 1458 7.734924 TGCCTGATACATAATCTGAATTCAC 57.265 36.000 3.38 0.00 36.01 3.18
447 1520 5.960113 TCAATCAATTACAACGGGAAATGG 58.040 37.500 0.00 0.00 0.00 3.16
517 1591 0.390340 GTGTCATCCGCAGCTTCTCA 60.390 55.000 0.00 0.00 0.00 3.27
530 1604 1.566211 CTTCTCAGCTCCCTTCCTCA 58.434 55.000 0.00 0.00 0.00 3.86
563 1638 1.145738 AGGAGTGCCCATTTTGACACT 59.854 47.619 0.00 0.00 45.66 3.55
566 1641 2.508526 AGTGCCCATTTTGACACTCTC 58.491 47.619 0.00 0.00 39.04 3.20
615 1762 8.680903 AGAATAATCAATACTTCAAAGTGGCAG 58.319 33.333 5.66 0.00 40.07 4.85
716 1864 5.712152 ATACTTCAAAACTTCCAGCAAGG 57.288 39.130 0.00 0.00 36.26 3.61
729 1877 2.032550 CCAGCAAGGCATTCAGAATACG 59.967 50.000 0.00 0.00 0.00 3.06
749 1907 2.048222 CCATCGCGGTCAGTGTGT 60.048 61.111 6.13 0.00 0.00 3.72
751 1909 1.372872 CATCGCGGTCAGTGTGTCA 60.373 57.895 6.13 0.00 0.00 3.58
753 1911 2.765250 ATCGCGGTCAGTGTGTCACC 62.765 60.000 6.13 0.00 34.49 4.02
755 1913 2.415843 CGGTCAGTGTGTCACCGT 59.584 61.111 11.86 0.00 46.58 4.83
756 1914 1.949133 CGGTCAGTGTGTCACCGTG 60.949 63.158 11.86 0.00 46.58 4.94
869 2030 1.424493 CGAATTGGAGTGGAGCTCGC 61.424 60.000 7.83 3.05 45.03 5.03
911 2078 8.632906 ACTTATATAAGCGTACTACATCCACT 57.367 34.615 20.24 0.00 36.79 4.00
970 2179 2.615262 CTACCCCGCGAGACAAGAGC 62.615 65.000 8.23 0.00 0.00 4.09
971 2180 4.069232 CCCCGCGAGACAAGAGCA 62.069 66.667 8.23 0.00 0.00 4.26
972 2181 2.811317 CCCGCGAGACAAGAGCAC 60.811 66.667 8.23 0.00 0.00 4.40
973 2182 2.811317 CCGCGAGACAAGAGCACC 60.811 66.667 8.23 0.00 0.00 5.01
976 2185 2.029844 GCGAGACAAGAGCACCACC 61.030 63.158 0.00 0.00 0.00 4.61
1378 2599 2.046285 TCGATGCAGGACGAGCTCA 61.046 57.895 15.40 0.00 34.49 4.26
1459 2680 3.260483 CCGTCGATCAGCAGCAGC 61.260 66.667 0.00 0.00 42.56 5.25
1460 2681 2.507769 CGTCGATCAGCAGCAGCA 60.508 61.111 3.17 0.00 45.49 4.41
1461 2682 2.096442 CGTCGATCAGCAGCAGCAA 61.096 57.895 3.17 0.00 45.49 3.91
1472 2693 0.952497 CAGCAGCAACATGTCTCCGT 60.952 55.000 0.00 0.00 0.00 4.69
1481 2702 1.135139 ACATGTCTCCGTCGATTCTGG 59.865 52.381 0.00 0.00 0.00 3.86
1487 2708 1.226974 CCGTCGATTCTGGCATCGT 60.227 57.895 8.63 0.00 45.28 3.73
1489 2710 1.532343 CGTCGATTCTGGCATCGTCG 61.532 60.000 12.48 12.48 46.26 5.12
1490 2711 0.525668 GTCGATTCTGGCATCGTCGT 60.526 55.000 8.63 0.00 45.28 4.34
1493 2714 1.640428 GATTCTGGCATCGTCGTGAA 58.360 50.000 0.00 0.00 0.00 3.18
1807 4671 1.986698 CTGTAATGCAGTTGCTTGCC 58.013 50.000 5.62 0.00 43.43 4.52
1855 4731 6.774656 AGGAAGTTGATGAATTGAAAGTGAGT 59.225 34.615 0.00 0.00 0.00 3.41
1862 4738 5.418310 TGAATTGAAAGTGAGTTTCGGTC 57.582 39.130 8.11 5.92 46.76 4.79
2113 5013 2.327325 TCTTTGCCTCTCCTACCAGT 57.673 50.000 0.00 0.00 0.00 4.00
2128 5028 2.927028 ACCAGTTCCTGTTACACCAAC 58.073 47.619 0.00 0.00 37.67 3.77
2139 5039 5.181690 TGTTACACCAACAAGATTGCTTC 57.818 39.130 0.00 0.00 44.20 3.86
2185 5085 6.152661 TGACTGTTGTTGTTCAGGAGAAAAAT 59.847 34.615 0.00 0.00 33.70 1.82
2186 5086 7.338196 TGACTGTTGTTGTTCAGGAGAAAAATA 59.662 33.333 0.00 0.00 33.70 1.40
2194 5094 9.508567 GTTGTTCAGGAGAAAAATAAGATATGC 57.491 33.333 0.00 0.00 33.70 3.14
2207 5107 0.179150 GATATGCGCGCTCCCTCTAG 60.179 60.000 33.29 0.00 0.00 2.43
2236 5136 7.948513 AGTTTACATCGAATTTATTTGTCGC 57.051 32.000 0.00 0.00 34.80 5.19
2355 5255 5.562506 ATTTCATGTCACATTGCAGAGAG 57.437 39.130 0.00 0.00 0.00 3.20
2389 5289 5.452078 ACAACAATGGTGTTTACTCCATG 57.548 39.130 15.09 11.96 46.01 3.66
2433 5333 2.780010 AGATCCACTGGATTACAAGGGG 59.220 50.000 12.09 0.00 43.27 4.79
2435 5335 2.196595 TCCACTGGATTACAAGGGGAG 58.803 52.381 0.00 0.00 29.88 4.30
2449 5349 1.492176 AGGGGAGTACAATGCCTGATG 59.508 52.381 0.00 0.00 0.00 3.07
2471 5371 5.737860 TGCATCATCTGAATTCACAGTACT 58.262 37.500 3.38 0.00 38.79 2.73
2472 5372 6.877236 TGCATCATCTGAATTCACAGTACTA 58.123 36.000 3.38 0.00 38.79 1.82
2473 5373 7.503549 TGCATCATCTGAATTCACAGTACTAT 58.496 34.615 3.38 0.00 38.79 2.12
2542 5444 2.722094 TCACAGGTGTTGCAGTTTCTT 58.278 42.857 0.00 0.00 0.00 2.52
2558 5460 5.936956 CAGTTTCTTCTCTGCCTCTGTAATT 59.063 40.000 0.00 0.00 0.00 1.40
2600 5502 3.023832 AGCAACACTAACAAAGCCAACT 58.976 40.909 0.00 0.00 0.00 3.16
2612 5514 2.103042 GCCAACTAGAGGCGTGCTG 61.103 63.158 13.65 0.00 43.15 4.41
2613 5515 1.591703 CCAACTAGAGGCGTGCTGA 59.408 57.895 0.00 0.00 0.00 4.26
2637 5539 4.397417 GCAGAGAACCTAAACAGCATCAAT 59.603 41.667 0.00 0.00 0.00 2.57
2693 5595 0.811915 GTGCGGAGTAGAGCAAGAGA 59.188 55.000 0.00 0.00 45.61 3.10
2694 5596 1.098869 TGCGGAGTAGAGCAAGAGAG 58.901 55.000 0.00 0.00 40.78 3.20
2695 5597 0.248866 GCGGAGTAGAGCAAGAGAGC 60.249 60.000 0.00 0.00 0.00 4.09
2718 5623 2.607442 TAGCAGCACAGGGGAGCA 60.607 61.111 0.00 0.00 32.55 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 6.579666 GGTAACAATGATCCATGTATGCAT 57.420 37.500 3.79 3.79 35.32 3.96
72 91 4.406456 TGTTTGGATCAGTGTAATTGCCT 58.594 39.130 0.00 0.00 0.00 4.75
73 92 4.782019 TGTTTGGATCAGTGTAATTGCC 57.218 40.909 0.00 0.00 0.00 4.52
76 95 8.585471 ATTCAGATGTTTGGATCAGTGTAATT 57.415 30.769 0.00 0.00 0.00 1.40
77 96 8.585471 AATTCAGATGTTTGGATCAGTGTAAT 57.415 30.769 0.00 0.00 0.00 1.89
78 97 8.408043 AAATTCAGATGTTTGGATCAGTGTAA 57.592 30.769 0.00 0.00 0.00 2.41
79 98 8.298854 CAAAATTCAGATGTTTGGATCAGTGTA 58.701 33.333 0.00 0.00 0.00 2.90
80 99 6.906157 AAATTCAGATGTTTGGATCAGTGT 57.094 33.333 0.00 0.00 0.00 3.55
81 100 6.090358 GCAAAATTCAGATGTTTGGATCAGTG 59.910 38.462 0.00 0.00 33.72 3.66
82 101 6.161381 GCAAAATTCAGATGTTTGGATCAGT 58.839 36.000 0.00 0.00 33.72 3.41
83 102 6.160684 TGCAAAATTCAGATGTTTGGATCAG 58.839 36.000 0.00 0.00 33.72 2.90
84 103 6.099159 TGCAAAATTCAGATGTTTGGATCA 57.901 33.333 0.00 0.00 33.72 2.92
85 104 6.647895 AGTTGCAAAATTCAGATGTTTGGATC 59.352 34.615 0.00 5.27 33.43 3.36
86 105 6.425721 CAGTTGCAAAATTCAGATGTTTGGAT 59.574 34.615 0.00 0.00 33.43 3.41
87 106 5.754406 CAGTTGCAAAATTCAGATGTTTGGA 59.246 36.000 0.00 3.46 33.72 3.53
88 107 5.559417 GCAGTTGCAAAATTCAGATGTTTGG 60.559 40.000 0.00 0.00 41.59 3.28
89 108 5.235616 AGCAGTTGCAAAATTCAGATGTTTG 59.764 36.000 0.00 3.06 45.16 2.93
90 109 5.235616 CAGCAGTTGCAAAATTCAGATGTTT 59.764 36.000 0.00 0.00 45.16 2.83
91 110 4.748102 CAGCAGTTGCAAAATTCAGATGTT 59.252 37.500 0.00 0.00 45.16 2.71
92 111 4.304110 CAGCAGTTGCAAAATTCAGATGT 58.696 39.130 0.00 0.00 45.16 3.06
93 112 4.903638 CAGCAGTTGCAAAATTCAGATG 57.096 40.909 0.00 0.00 45.16 2.90
142 162 9.076596 GTTAATTAAATGAAAGTGGTCTGCATC 57.923 33.333 0.00 0.00 0.00 3.91
175 249 7.827819 TGTACTGAATATGTTAACTCAGTGC 57.172 36.000 26.45 25.37 46.09 4.40
270 1299 6.092748 GTGACATGTGGTTTGATTTGATACC 58.907 40.000 1.15 0.00 0.00 2.73
308 1338 5.041287 CACCATCGTCGTCAAGTATGTATT 58.959 41.667 0.00 0.00 0.00 1.89
309 1339 4.097437 ACACCATCGTCGTCAAGTATGTAT 59.903 41.667 0.00 0.00 0.00 2.29
325 1355 8.607459 CAGATATTCAGTGAAGTAAACACCATC 58.393 37.037 11.91 3.34 38.82 3.51
355 1386 7.963532 TCCCTTCTAATCCAGTGAATATGTAC 58.036 38.462 0.00 0.00 0.00 2.90
356 1387 8.561536 TTCCCTTCTAATCCAGTGAATATGTA 57.438 34.615 0.00 0.00 0.00 2.29
413 1458 8.891928 CGTTGTAATTGATTGAAGTTGTTACTG 58.108 33.333 0.00 0.00 34.01 2.74
447 1520 1.032014 ACACCTGTGAATGTTGCCAC 58.968 50.000 3.94 0.00 0.00 5.01
517 1591 0.619832 TCTGCATGAGGAAGGGAGCT 60.620 55.000 0.00 0.00 0.00 4.09
530 1604 2.641305 GCACTCCTGATTTCTCTGCAT 58.359 47.619 0.00 0.00 0.00 3.96
563 1638 3.599343 CTTGGTCATGTCATTTCCGAGA 58.401 45.455 11.97 0.00 32.97 4.04
566 1641 2.679837 CTCCTTGGTCATGTCATTTCCG 59.320 50.000 0.00 0.00 0.00 4.30
716 1864 2.156504 CGATGGCTCGTATTCTGAATGC 59.843 50.000 13.01 10.53 40.07 3.56
729 1877 2.887568 CACTGACCGCGATGGCTC 60.888 66.667 8.23 0.00 43.94 4.70
753 1911 3.629491 GATGTGTTGCGCGTCCACG 62.629 63.158 8.43 0.00 43.27 4.94
754 1912 2.173382 GATGTGTTGCGCGTCCAC 59.827 61.111 8.43 12.66 0.00 4.02
755 1913 3.047280 GGATGTGTTGCGCGTCCA 61.047 61.111 8.43 0.00 46.05 4.02
756 1914 2.742372 AGGATGTGTTGCGCGTCC 60.742 61.111 8.43 11.73 46.84 4.79
869 2030 7.741027 ATATAAGTTCTGATGATGTGCAAGG 57.259 36.000 0.00 0.00 0.00 3.61
911 2078 5.487433 TCAAGGAAAGCGATGAATTCTGTA 58.513 37.500 7.05 0.00 0.00 2.74
971 2180 4.719369 GAACGCGAGCTCGGTGGT 62.719 66.667 35.10 21.71 40.23 4.16
1252 2473 0.179040 TCCGTGGAAACCAACAGGTC 60.179 55.000 0.00 0.00 34.18 3.85
1378 2599 2.584391 GGGCGTCTCTGACCTTGGT 61.584 63.158 0.00 0.00 32.64 3.67
1459 2680 2.600420 CAGAATCGACGGAGACATGTTG 59.400 50.000 0.00 0.00 0.00 3.33
1460 2681 2.417379 CCAGAATCGACGGAGACATGTT 60.417 50.000 0.00 0.00 0.00 2.71
1461 2682 1.135139 CCAGAATCGACGGAGACATGT 59.865 52.381 0.00 0.00 0.00 3.21
1481 2702 1.443872 ACGGTCTTCACGACGATGC 60.444 57.895 0.00 0.00 43.79 3.91
1487 2708 0.245539 GATTCCCACGGTCTTCACGA 59.754 55.000 0.00 0.00 34.93 4.35
1489 2710 1.726853 CTGATTCCCACGGTCTTCAC 58.273 55.000 0.00 0.00 0.00 3.18
1490 2711 0.036388 GCTGATTCCCACGGTCTTCA 60.036 55.000 0.00 0.00 0.00 3.02
1493 2714 0.036010 CTTGCTGATTCCCACGGTCT 60.036 55.000 0.00 0.00 0.00 3.85
1582 4348 2.859165 TCTTGGTAACCTTGGCAGAG 57.141 50.000 0.00 0.00 0.00 3.35
1807 4671 6.419116 CCTTCGATCATGTACATAACAGACAG 59.581 42.308 8.32 6.82 42.70 3.51
1862 4738 6.961359 TGAACATGTCGGTAGATTTGTAAG 57.039 37.500 0.00 0.00 0.00 2.34
2015 4891 5.419788 TCCATTGCATGCTAAATTCTTCAGT 59.580 36.000 20.33 0.00 0.00 3.41
2128 5028 2.071540 TCGAGCACAGAAGCAATCTTG 58.928 47.619 0.00 0.00 35.73 3.02
2139 5039 1.528586 CTTGGAACAGTTCGAGCACAG 59.471 52.381 7.22 0.00 42.39 3.66
2185 5085 0.243907 GAGGGAGCGCGCATATCTTA 59.756 55.000 35.10 0.00 0.00 2.10
2186 5086 1.005630 GAGGGAGCGCGCATATCTT 60.006 57.895 35.10 11.72 0.00 2.40
2194 5094 1.281899 CTTTTTCTAGAGGGAGCGCG 58.718 55.000 0.00 0.00 0.00 6.86
2236 5136 1.547372 CTTTTTGGTGCCCTCCTGATG 59.453 52.381 0.00 0.00 0.00 3.07
2449 5349 7.959689 ATAGTACTGTGAATTCAGATGATGC 57.040 36.000 8.80 0.42 38.63 3.91
2471 5371 9.513906 TGAGTTGATTTTGAATGAGGTTGTATA 57.486 29.630 0.00 0.00 0.00 1.47
2472 5372 8.408043 TGAGTTGATTTTGAATGAGGTTGTAT 57.592 30.769 0.00 0.00 0.00 2.29
2473 5373 7.815840 TGAGTTGATTTTGAATGAGGTTGTA 57.184 32.000 0.00 0.00 0.00 2.41
2509 5411 0.518636 CCTGTGAATGCTGTCAACGG 59.481 55.000 0.00 0.00 0.00 4.44
2542 5444 3.703556 CCTCAGAATTACAGAGGCAGAGA 59.296 47.826 7.21 0.00 43.42 3.10
2558 5460 1.000955 GTTGCTCTCGGTTTCCTCAGA 59.999 52.381 0.00 0.00 0.00 3.27
2600 5502 1.661498 CTCTGCTCAGCACGCCTCTA 61.661 60.000 0.00 0.00 33.79 2.43
2608 5510 2.368548 TGTTTAGGTTCTCTGCTCAGCA 59.631 45.455 0.00 0.00 36.92 4.41
2612 5514 3.045601 TGCTGTTTAGGTTCTCTGCTC 57.954 47.619 0.00 0.00 0.00 4.26
2613 5515 3.008375 TGATGCTGTTTAGGTTCTCTGCT 59.992 43.478 0.00 0.00 0.00 4.24
2637 5539 0.109532 TTGATGCTCGGTTGGGTTGA 59.890 50.000 0.00 0.00 0.00 3.18
2678 5580 1.202405 GCTGCTCTCTTGCTCTACTCC 60.202 57.143 0.00 0.00 0.00 3.85
2695 5597 1.744368 CCCTGTGCTGCTACTGCTG 60.744 63.158 0.00 0.00 40.48 4.41


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

AutoCloner maintained by Alex Coulton.