Multiple sequence alignment - TraesCS2D01G310300

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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 TraesCS2D01G310300 chr2D 100.000 3384 0 0 1001 4384 398507072 398510455 0.000000e+00 6250
1 TraesCS2D01G310300 chr2D 94.689 1111 50 7 2778 3886 111146339 111145236 0.000000e+00 1716
2 TraesCS2D01G310300 chr2D 100.000 576 0 0 1 576 398506072 398506647 0.000000e+00 1064
3 TraesCS2D01G310300 chr2B 87.782 1596 113 46 1010 2560 471437019 471435461 0.000000e+00 1792
4 TraesCS2D01G310300 chr2B 89.239 381 23 7 200 576 471437400 471437034 1.110000e-125 460
5 TraesCS2D01G310300 chr2B 87.399 373 40 4 3886 4251 471435271 471434899 5.240000e-114 422
6 TraesCS2D01G310300 chr2B 89.313 131 9 3 1 126 339992155 339992285 4.540000e-35 159
7 TraesCS2D01G310300 chr6D 95.418 1113 39 7 2778 3886 58444215 58443111 0.000000e+00 1762
8 TraesCS2D01G310300 chr6D 94.737 1121 50 4 2777 3889 47350325 47351444 0.000000e+00 1735
9 TraesCS2D01G310300 chr3D 95.148 1113 45 7 2778 3886 608917425 608916318 0.000000e+00 1748
10 TraesCS2D01G310300 chr3D 94.350 1115 53 7 2777 3886 112578900 112580009 0.000000e+00 1701
11 TraesCS2D01G310300 chr3D 94.521 73 1 2 4312 4382 343272659 343272730 4.640000e-20 110
12 TraesCS2D01G310300 chr5B 94.718 1117 49 4 2779 3886 448102975 448101860 0.000000e+00 1727
13 TraesCS2D01G310300 chr7D 94.689 1111 53 6 2778 3885 97945137 97944030 0.000000e+00 1720
14 TraesCS2D01G310300 chr7D 93.421 76 2 2 4311 4384 154913543 154913469 4.640000e-20 110
15 TraesCS2D01G310300 chr7D 93.421 76 2 2 4311 4384 286816541 286816615 4.640000e-20 110
16 TraesCS2D01G310300 chr6A 94.281 1119 53 8 2778 3886 603623583 603624700 0.000000e+00 1701
17 TraesCS2D01G310300 chr1D 94.439 1115 45 12 2778 3886 393529353 393530456 0.000000e+00 1700
18 TraesCS2D01G310300 chr2A 92.751 1145 44 16 1675 2780 535738700 535739844 0.000000e+00 1618
19 TraesCS2D01G310300 chr2A 93.225 679 30 7 1003 1675 535737952 535738620 0.000000e+00 985
20 TraesCS2D01G310300 chr2A 94.508 437 10 1 3886 4322 535739843 535740265 0.000000e+00 662
21 TraesCS2D01G310300 chr2A 91.494 435 18 12 146 576 535737512 535737931 8.170000e-162 580
22 TraesCS2D01G310300 chr2A 87.582 153 12 3 2 147 535737229 535737381 2.100000e-38 171
23 TraesCS2D01G310300 chr2A 87.970 133 10 3 1 127 154412443 154412575 7.590000e-33 152
24 TraesCS2D01G310300 chr2A 87.050 139 8 8 7 137 276170144 276170008 9.820000e-32 148
25 TraesCS2D01G310300 chr4B 89.474 133 8 4 1 127 441086199 441086067 3.510000e-36 163
26 TraesCS2D01G310300 chr4B 94.521 73 1 2 4312 4382 201553814 201553743 4.640000e-20 110
27 TraesCS2D01G310300 chr3B 87.500 136 11 3 1 130 507886004 507885869 7.590000e-33 152
28 TraesCS2D01G310300 chr3A 87.970 133 10 3 1 127 702494629 702494497 7.590000e-33 152
29 TraesCS2D01G310300 chr3A 92.208 77 3 2 4308 4382 395414817 395414892 6.000000e-19 106
30 TraesCS2D01G310300 chr1A 87.970 133 10 4 1 127 12309228 12309360 7.590000e-33 152
31 TraesCS2D01G310300 chr1A 92.208 77 2 3 4311 4384 292350004 292350079 6.000000e-19 106
32 TraesCS2D01G310300 chr1A 92.208 77 2 3 4311 4384 322092804 322092879 6.000000e-19 106
33 TraesCS2D01G310300 chr7A 86.014 143 12 7 1 136 643101177 643101318 3.530000e-31 147
34 TraesCS2D01G310300 chr7B 94.521 73 1 2 4312 4382 35985763 35985692 4.640000e-20 110
35 TraesCS2D01G310300 chr7B 94.521 73 1 2 4312 4382 128925650 128925579 4.640000e-20 110


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 TraesCS2D01G310300 chr2D 398506072 398510455 4383 False 3657.000000 6250 100.000 1 4384 2 chr2D.!!$F1 4383
1 TraesCS2D01G310300 chr2D 111145236 111146339 1103 True 1716.000000 1716 94.689 2778 3886 1 chr2D.!!$R1 1108
2 TraesCS2D01G310300 chr2B 471434899 471437400 2501 True 891.333333 1792 88.140 200 4251 3 chr2B.!!$R1 4051
3 TraesCS2D01G310300 chr6D 58443111 58444215 1104 True 1762.000000 1762 95.418 2778 3886 1 chr6D.!!$R1 1108
4 TraesCS2D01G310300 chr6D 47350325 47351444 1119 False 1735.000000 1735 94.737 2777 3889 1 chr6D.!!$F1 1112
5 TraesCS2D01G310300 chr3D 608916318 608917425 1107 True 1748.000000 1748 95.148 2778 3886 1 chr3D.!!$R1 1108
6 TraesCS2D01G310300 chr3D 112578900 112580009 1109 False 1701.000000 1701 94.350 2777 3886 1 chr3D.!!$F1 1109
7 TraesCS2D01G310300 chr5B 448101860 448102975 1115 True 1727.000000 1727 94.718 2779 3886 1 chr5B.!!$R1 1107
8 TraesCS2D01G310300 chr7D 97944030 97945137 1107 True 1720.000000 1720 94.689 2778 3885 1 chr7D.!!$R1 1107
9 TraesCS2D01G310300 chr6A 603623583 603624700 1117 False 1701.000000 1701 94.281 2778 3886 1 chr6A.!!$F1 1108
10 TraesCS2D01G310300 chr1D 393529353 393530456 1103 False 1700.000000 1700 94.439 2778 3886 1 chr1D.!!$F1 1108
11 TraesCS2D01G310300 chr2A 535737229 535740265 3036 False 803.200000 1618 91.912 2 4322 5 chr2A.!!$F2 4320

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
110 117 0.653636 ATATTAACCGGCGTTGCACG 59.346 50.000 6.01 4.61 45.88 5.34 F
1102 1260 0.108138 GTCGGTGCTGGATTACTGCT 60.108 55.000 0.00 0.00 43.66 4.24 F
1210 1372 0.176680 CGTTGACATCTGGCTAGGCT 59.823 55.000 18.18 0.00 0.00 4.58 F
1858 2142 0.734253 CGTCACGGAAAGAGCAGAGG 60.734 60.000 0.00 0.00 0.00 3.69 F
2503 2790 1.202806 TGAGGCCTTTGGTCAGAACAG 60.203 52.381 6.77 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1759 2033 0.811915 GGTAGCTCAGAGTTCTCGCA 59.188 55.000 0.0 0.0 0.00 5.10 R
2503 2790 1.580132 CGCAAATTAGTCACGGCGC 60.580 57.895 6.9 0.0 37.96 6.53 R
2929 3272 2.036217 TCGTTGTATGAAAGGGTGACGT 59.964 45.455 0.0 0.0 0.00 4.34 R
3244 3591 0.029700 TCAAGAACGCTCGACAACGA 59.970 50.000 4.9 0.0 46.56 3.85 R
3589 3936 0.257328 TTTGCCACCACAACTGAGGA 59.743 50.000 0.0 0.0 0.00 3.71 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
110 117 0.653636 ATATTAACCGGCGTTGCACG 59.346 50.000 6.01 4.61 45.88 5.34
124 131 3.538828 CGTTGCACGTGCGTATTTACTAG 60.539 47.826 33.22 12.51 45.83 2.57
144 151 7.045126 ACTAGTAGATGAGAAATAGCACACC 57.955 40.000 3.59 0.00 0.00 4.16
306 446 0.954449 TCGATCGACGGCCCTAGATC 60.954 60.000 15.15 12.70 42.82 2.75
547 691 1.794701 CATGGGACGCGATGACTAATG 59.205 52.381 15.93 3.29 0.00 1.90
549 693 1.222115 GGGACGCGATGACTAATGCC 61.222 60.000 15.93 0.00 0.00 4.40
566 711 3.721706 CACCCCCTGGCTCTGTCC 61.722 72.222 0.00 0.00 33.59 4.02
1025 1183 3.003378 CGCCTTCTTTCGTTTTCTTCCTT 59.997 43.478 0.00 0.00 0.00 3.36
1029 1187 5.049336 CCTTCTTTCGTTTTCTTCCTTCTCC 60.049 44.000 0.00 0.00 0.00 3.71
1031 1189 2.450609 TCGTTTTCTTCCTTCTCCCG 57.549 50.000 0.00 0.00 0.00 5.14
1050 1208 0.536260 GTCTGCCTGTCTGCATCTCT 59.464 55.000 0.00 0.00 41.16 3.10
1052 1210 0.528033 CTGCCTGTCTGCATCTCTCG 60.528 60.000 0.00 0.00 41.16 4.04
1063 1221 1.845266 CATCTCTCGGTCCATGAACG 58.155 55.000 0.00 0.00 44.86 3.95
1074 1232 1.402613 TCCATGAACGAGCGATCGTAA 59.597 47.619 30.35 20.76 46.41 3.18
1078 1236 1.652124 TGAACGAGCGATCGTAAAAGC 59.348 47.619 30.35 16.03 46.41 3.51
1080 1238 0.172803 ACGAGCGATCGTAAAAGCCT 59.827 50.000 29.12 0.00 45.19 4.58
1095 1253 3.461773 CCTCGGTCGGTGCTGGAT 61.462 66.667 0.00 0.00 0.00 3.41
1096 1254 2.579201 CTCGGTCGGTGCTGGATT 59.421 61.111 0.00 0.00 0.00 3.01
1102 1260 0.108138 GTCGGTGCTGGATTACTGCT 60.108 55.000 0.00 0.00 43.66 4.24
1104 1262 1.091771 CGGTGCTGGATTACTGCTGG 61.092 60.000 0.00 0.00 43.66 4.85
1106 1264 1.089920 GTGCTGGATTACTGCTGGTG 58.910 55.000 0.00 0.00 43.66 4.17
1115 1273 4.101119 GGATTACTGCTGGTGGTGTATACT 59.899 45.833 4.17 0.00 0.00 2.12
1148 1306 2.941720 CCAGGAAAAGATGCTAGCTGAC 59.058 50.000 17.23 7.24 0.00 3.51
1207 1369 5.856126 TTTTTACGTTGACATCTGGCTAG 57.144 39.130 0.00 0.00 0.00 3.42
1208 1370 3.520290 TTACGTTGACATCTGGCTAGG 57.480 47.619 0.00 0.00 0.00 3.02
1209 1371 0.108138 ACGTTGACATCTGGCTAGGC 60.108 55.000 9.85 9.85 0.00 3.93
1210 1372 0.176680 CGTTGACATCTGGCTAGGCT 59.823 55.000 18.18 0.00 0.00 4.58
1211 1373 1.409064 CGTTGACATCTGGCTAGGCTA 59.591 52.381 18.18 6.12 0.00 3.93
1225 1387 2.160822 AGGCTATGCATGTGATCGTC 57.839 50.000 10.16 0.00 0.00 4.20
1232 1394 5.741510 GCTATGCATGTGATCGTCTATCTAC 59.258 44.000 10.16 0.00 35.45 2.59
1244 1406 3.546670 CGTCTATCTACTTTTGTCGGTGC 59.453 47.826 0.00 0.00 0.00 5.01
1267 1429 4.496895 CGTACGTACCTTGCTTACATACAC 59.503 45.833 19.67 0.00 0.00 2.90
1417 1605 8.527810 GGATTCTTTCCCAGATACTAGATGTAG 58.472 40.741 0.00 0.00 38.75 2.74
1418 1606 9.084533 GATTCTTTCCCAGATACTAGATGTAGT 57.915 37.037 7.77 7.77 42.49 2.73
1452 1643 3.655615 TGTGTTAGTTGGGAACTGGTT 57.344 42.857 0.00 0.00 42.84 3.67
1644 1838 5.435820 AGCTAGGTATACACGTAAAGCTC 57.564 43.478 5.01 0.00 31.85 4.09
1691 1965 1.914634 ACTAGCTCGATTGCTTCACG 58.085 50.000 4.33 0.00 43.74 4.35
1697 1971 1.510623 CGATTGCTTCACGTGCTGC 60.511 57.895 20.41 20.41 0.00 5.25
1767 2047 4.039151 TCTGATCTGATTCTGCGAGAAC 57.961 45.455 0.00 0.00 37.00 3.01
1858 2142 0.734253 CGTCACGGAAAGAGCAGAGG 60.734 60.000 0.00 0.00 0.00 3.69
1957 2243 1.446907 CTGATCAACAGTGGCCTCAC 58.553 55.000 3.32 0.00 43.93 3.51
1979 2265 1.811266 CAACGCATCTACGCCAGCT 60.811 57.895 0.00 0.00 36.19 4.24
2033 2319 4.719369 GCCGGAAGCACGTCGTCT 62.719 66.667 5.05 0.00 42.97 4.18
2346 2632 8.672815 ACTTGTAGATAACTAGTACGTCCTTTC 58.327 37.037 0.00 0.00 41.54 2.62
2417 2704 1.941377 TGCCCATCAATTGAAGCCTT 58.059 45.000 13.09 0.00 0.00 4.35
2503 2790 1.202806 TGAGGCCTTTGGTCAGAACAG 60.203 52.381 6.77 0.00 0.00 3.16
2568 2855 9.976255 TTGCTATATTAACACGAAACATTGTAC 57.024 29.630 0.00 0.00 0.00 2.90
2658 2987 1.427020 GCTTCGAGCACCTGATTGC 59.573 57.895 2.53 0.00 41.89 3.56
2661 2992 1.536766 CTTCGAGCACCTGATTGCAAA 59.463 47.619 1.71 0.00 45.62 3.68
2662 2993 1.603456 TCGAGCACCTGATTGCAAAA 58.397 45.000 1.71 0.00 45.62 2.44
2666 2997 3.365820 CGAGCACCTGATTGCAAAATTTC 59.634 43.478 1.71 0.00 45.62 2.17
2668 2999 5.619757 CGAGCACCTGATTGCAAAATTTCTA 60.620 40.000 1.71 0.00 45.62 2.10
2669 3000 6.290294 AGCACCTGATTGCAAAATTTCTAT 57.710 33.333 1.71 0.00 45.62 1.98
2729 3064 6.953101 TCTTGTGATACCAGGCAATAGTTTA 58.047 36.000 0.00 0.00 0.00 2.01
2730 3065 7.047891 TCTTGTGATACCAGGCAATAGTTTAG 58.952 38.462 0.00 0.00 0.00 1.85
2731 3066 5.680619 TGTGATACCAGGCAATAGTTTAGG 58.319 41.667 0.00 0.00 0.00 2.69
2741 3080 6.430000 CAGGCAATAGTTTAGGTGTTTACAGT 59.570 38.462 0.00 0.00 0.00 3.55
2788 3127 5.474578 TGATAACATGCATCTCTACTCCC 57.525 43.478 0.00 0.00 0.00 4.30
2929 3272 5.359576 CCCCCACTTCATCGATTTATTTTCA 59.640 40.000 0.00 0.00 0.00 2.69
2943 3286 6.642707 TTTATTTTCACGTCACCCTTTCAT 57.357 33.333 0.00 0.00 0.00 2.57
3244 3591 6.393897 TGTATATGATCTTCCCTTCCCTCTT 58.606 40.000 0.00 0.00 0.00 2.85
3589 3936 7.224557 GCTGGCCGATTTACATGAAATTAATTT 59.775 33.333 13.24 13.24 37.90 1.82
3746 4111 1.286553 GAGAGGGGGAGAGAGAGTGAA 59.713 57.143 0.00 0.00 0.00 3.18
4003 4377 0.249826 TGCGACAGTGTCAAGCATGA 60.250 50.000 22.66 1.37 32.43 3.07
4109 4484 9.034800 ACAACTTATTTGATATGTTCCCACATT 57.965 29.630 0.00 0.00 40.28 2.71
4151 4527 6.294731 GGTCTTCCTGCTTGAAACATGTAATT 60.295 38.462 0.00 0.00 0.00 1.40
4196 4572 9.908152 GTTTTGTAAGCAGAAAATAGGTAATGT 57.092 29.630 0.00 0.00 30.51 2.71
4203 4579 6.882678 AGCAGAAAATAGGTAATGTTAACCGT 59.117 34.615 2.48 0.00 42.15 4.83
4204 4580 7.065443 AGCAGAAAATAGGTAATGTTAACCGTC 59.935 37.037 2.48 0.00 42.15 4.79
4205 4581 7.396419 CAGAAAATAGGTAATGTTAACCGTCG 58.604 38.462 2.48 0.00 42.15 5.12
4332 4711 9.991906 GTATGTAGATGCATACTAGGGTTTAAA 57.008 33.333 12.20 0.00 44.57 1.52
4333 4712 8.904099 ATGTAGATGCATACTAGGGTTTAAAC 57.096 34.615 9.98 9.98 0.00 2.01
4334 4713 8.086143 TGTAGATGCATACTAGGGTTTAAACT 57.914 34.615 17.50 1.96 0.00 2.66
4335 4714 8.545472 TGTAGATGCATACTAGGGTTTAAACTT 58.455 33.333 17.50 9.23 0.00 2.66
4336 4715 9.392259 GTAGATGCATACTAGGGTTTAAACTTT 57.608 33.333 17.50 8.90 0.00 2.66
4337 4716 8.879427 AGATGCATACTAGGGTTTAAACTTTT 57.121 30.769 17.50 6.65 0.00 2.27
4338 4717 8.739972 AGATGCATACTAGGGTTTAAACTTTTG 58.260 33.333 17.50 9.58 0.00 2.44
4339 4718 7.826918 TGCATACTAGGGTTTAAACTTTTGT 57.173 32.000 17.50 13.97 0.00 2.83
4340 4719 7.878036 TGCATACTAGGGTTTAAACTTTTGTC 58.122 34.615 17.50 0.27 0.00 3.18
4341 4720 7.502895 TGCATACTAGGGTTTAAACTTTTGTCA 59.497 33.333 17.50 5.91 0.00 3.58
4342 4721 7.806487 GCATACTAGGGTTTAAACTTTTGTCAC 59.194 37.037 17.50 0.00 0.00 3.67
4343 4722 9.063615 CATACTAGGGTTTAAACTTTTGTCACT 57.936 33.333 17.50 0.00 0.00 3.41
4344 4723 7.563888 ACTAGGGTTTAAACTTTTGTCACTC 57.436 36.000 17.50 0.00 0.00 3.51
4345 4724 7.344134 ACTAGGGTTTAAACTTTTGTCACTCT 58.656 34.615 17.50 0.00 0.00 3.24
4346 4725 8.488668 ACTAGGGTTTAAACTTTTGTCACTCTA 58.511 33.333 17.50 0.00 0.00 2.43
4347 4726 7.803279 AGGGTTTAAACTTTTGTCACTCTAG 57.197 36.000 17.50 0.00 0.00 2.43
4348 4727 6.262496 AGGGTTTAAACTTTTGTCACTCTAGC 59.738 38.462 17.50 0.00 0.00 3.42
4349 4728 6.038936 GGGTTTAAACTTTTGTCACTCTAGCA 59.961 38.462 17.50 0.00 0.00 3.49
4350 4729 7.415877 GGGTTTAAACTTTTGTCACTCTAGCAA 60.416 37.037 17.50 0.00 0.00 3.91
4351 4730 7.431376 GGTTTAAACTTTTGTCACTCTAGCAAC 59.569 37.037 17.50 0.00 0.00 4.17
4352 4731 5.500645 AAACTTTTGTCACTCTAGCAACC 57.499 39.130 0.00 0.00 0.00 3.77
4353 4732 3.477530 ACTTTTGTCACTCTAGCAACCC 58.522 45.455 0.00 0.00 0.00 4.11
4354 4733 3.118038 ACTTTTGTCACTCTAGCAACCCA 60.118 43.478 0.00 0.00 0.00 4.51
4355 4734 3.788227 TTTGTCACTCTAGCAACCCAT 57.212 42.857 0.00 0.00 0.00 4.00
4356 4735 3.334583 TTGTCACTCTAGCAACCCATC 57.665 47.619 0.00 0.00 0.00 3.51
4357 4736 2.256306 TGTCACTCTAGCAACCCATCA 58.744 47.619 0.00 0.00 0.00 3.07
4358 4737 2.840038 TGTCACTCTAGCAACCCATCAT 59.160 45.455 0.00 0.00 0.00 2.45
4359 4738 3.118629 TGTCACTCTAGCAACCCATCATC 60.119 47.826 0.00 0.00 0.00 2.92
4360 4739 3.133721 GTCACTCTAGCAACCCATCATCT 59.866 47.826 0.00 0.00 0.00 2.90
4361 4740 4.342378 GTCACTCTAGCAACCCATCATCTA 59.658 45.833 0.00 0.00 0.00 1.98
4362 4741 4.962362 TCACTCTAGCAACCCATCATCTAA 59.038 41.667 0.00 0.00 0.00 2.10
4363 4742 5.604231 TCACTCTAGCAACCCATCATCTAAT 59.396 40.000 0.00 0.00 0.00 1.73
4364 4743 6.782494 TCACTCTAGCAACCCATCATCTAATA 59.218 38.462 0.00 0.00 0.00 0.98
4365 4744 7.290014 TCACTCTAGCAACCCATCATCTAATAA 59.710 37.037 0.00 0.00 0.00 1.40
4366 4745 7.386299 CACTCTAGCAACCCATCATCTAATAAC 59.614 40.741 0.00 0.00 0.00 1.89
4367 4746 7.291182 ACTCTAGCAACCCATCATCTAATAACT 59.709 37.037 0.00 0.00 0.00 2.24
4368 4747 8.721133 TCTAGCAACCCATCATCTAATAACTA 57.279 34.615 0.00 0.00 0.00 2.24
4369 4748 8.585881 TCTAGCAACCCATCATCTAATAACTAC 58.414 37.037 0.00 0.00 0.00 2.73
4370 4749 7.380423 AGCAACCCATCATCTAATAACTACT 57.620 36.000 0.00 0.00 0.00 2.57
4371 4750 7.445945 AGCAACCCATCATCTAATAACTACTC 58.554 38.462 0.00 0.00 0.00 2.59
4372 4751 6.651225 GCAACCCATCATCTAATAACTACTCC 59.349 42.308 0.00 0.00 0.00 3.85
4373 4752 7.689313 GCAACCCATCATCTAATAACTACTCCA 60.689 40.741 0.00 0.00 0.00 3.86
4374 4753 7.304497 ACCCATCATCTAATAACTACTCCAC 57.696 40.000 0.00 0.00 0.00 4.02
4375 4754 6.844388 ACCCATCATCTAATAACTACTCCACA 59.156 38.462 0.00 0.00 0.00 4.17
4376 4755 7.347222 ACCCATCATCTAATAACTACTCCACAA 59.653 37.037 0.00 0.00 0.00 3.33
4377 4756 8.378565 CCCATCATCTAATAACTACTCCACAAT 58.621 37.037 0.00 0.00 0.00 2.71
4378 4757 9.212641 CCATCATCTAATAACTACTCCACAATG 57.787 37.037 0.00 0.00 0.00 2.82
4379 4758 8.715998 CATCATCTAATAACTACTCCACAATGC 58.284 37.037 0.00 0.00 0.00 3.56
4380 4759 7.791029 TCATCTAATAACTACTCCACAATGCA 58.209 34.615 0.00 0.00 0.00 3.96
4381 4760 8.432013 TCATCTAATAACTACTCCACAATGCAT 58.568 33.333 0.00 0.00 0.00 3.96
4382 4761 8.715998 CATCTAATAACTACTCCACAATGCATC 58.284 37.037 0.00 0.00 0.00 3.91
4383 4762 7.217200 TCTAATAACTACTCCACAATGCATCC 58.783 38.462 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 59 3.659786 TGCACGTGGATATTAGGTATGC 58.340 45.455 18.88 0.00 0.00 3.14
110 117 9.680315 ATTTCTCATCTACTAGTAAATACGCAC 57.320 33.333 3.76 0.00 0.00 5.34
124 131 4.141711 TGGGGTGTGCTATTTCTCATCTAC 60.142 45.833 0.00 0.00 0.00 2.59
138 145 3.572255 TGTAGATTTTTCTTGGGGTGTGC 59.428 43.478 0.00 0.00 0.00 4.57
141 148 4.082125 AGCTGTAGATTTTTCTTGGGGTG 58.918 43.478 0.00 0.00 0.00 4.61
144 151 3.507233 TGCAGCTGTAGATTTTTCTTGGG 59.493 43.478 16.64 0.00 0.00 4.12
306 446 1.595489 GCATTGTTAATCGCAGCGGAG 60.595 52.381 16.42 0.00 0.00 4.63
472 613 0.553333 GGAGGGGATGGAAAGGAAGG 59.447 60.000 0.00 0.00 0.00 3.46
473 614 1.213926 CAGGAGGGGATGGAAAGGAAG 59.786 57.143 0.00 0.00 0.00 3.46
549 693 3.721706 GGACAGAGCCAGGGGGTG 61.722 72.222 0.00 0.00 36.17 4.61
1000 1145 2.143925 AGAAAACGAAAGAAGGCGGAG 58.856 47.619 0.00 0.00 0.00 4.63
1001 1146 2.249844 AGAAAACGAAAGAAGGCGGA 57.750 45.000 0.00 0.00 0.00 5.54
1002 1147 2.350484 GGAAGAAAACGAAAGAAGGCGG 60.350 50.000 0.00 0.00 0.00 6.13
1003 1148 2.548480 AGGAAGAAAACGAAAGAAGGCG 59.452 45.455 0.00 0.00 0.00 5.52
1004 1149 4.276183 AGAAGGAAGAAAACGAAAGAAGGC 59.724 41.667 0.00 0.00 0.00 4.35
1005 1150 5.049336 GGAGAAGGAAGAAAACGAAAGAAGG 60.049 44.000 0.00 0.00 0.00 3.46
1006 1151 5.049336 GGGAGAAGGAAGAAAACGAAAGAAG 60.049 44.000 0.00 0.00 0.00 2.85
1007 1152 4.820173 GGGAGAAGGAAGAAAACGAAAGAA 59.180 41.667 0.00 0.00 0.00 2.52
1008 1153 4.386711 GGGAGAAGGAAGAAAACGAAAGA 58.613 43.478 0.00 0.00 0.00 2.52
1014 1159 3.067833 CAGACGGGAGAAGGAAGAAAAC 58.932 50.000 0.00 0.00 0.00 2.43
1025 1183 1.979155 CAGACAGGCAGACGGGAGA 60.979 63.158 0.00 0.00 0.00 3.71
1050 1208 1.663379 ATCGCTCGTTCATGGACCGA 61.663 55.000 6.46 6.46 0.00 4.69
1052 1210 1.209275 CGATCGCTCGTTCATGGACC 61.209 60.000 0.26 0.00 40.07 4.46
1063 1221 0.847035 CGAGGCTTTTACGATCGCTC 59.153 55.000 16.60 10.56 0.00 5.03
1074 1232 3.626924 AGCACCGACCGAGGCTTT 61.627 61.111 0.00 0.00 31.34 3.51
1078 1236 1.672854 TAATCCAGCACCGACCGAGG 61.673 60.000 0.00 0.00 37.30 4.63
1080 1238 0.968901 AGTAATCCAGCACCGACCGA 60.969 55.000 0.00 0.00 0.00 4.69
1095 1253 5.394883 GCTTAGTATACACCACCAGCAGTAA 60.395 44.000 5.50 0.00 0.00 2.24
1096 1254 4.098960 GCTTAGTATACACCACCAGCAGTA 59.901 45.833 5.50 0.00 0.00 2.74
1102 1260 5.670485 CATCAAGCTTAGTATACACCACCA 58.330 41.667 5.50 0.00 0.00 4.17
1104 1262 4.511826 GGCATCAAGCTTAGTATACACCAC 59.488 45.833 5.50 0.00 44.79 4.16
1106 1264 4.065789 GGGCATCAAGCTTAGTATACACC 58.934 47.826 5.50 0.00 44.79 4.16
1115 1273 2.897271 TTTCCTGGGCATCAAGCTTA 57.103 45.000 0.00 0.00 44.79 3.09
1207 1369 2.160822 AGACGATCACATGCATAGCC 57.839 50.000 0.00 0.00 0.00 3.93
1208 1370 4.742417 AGATAGACGATCACATGCATAGC 58.258 43.478 0.00 0.00 36.98 2.97
1209 1371 7.082700 AGTAGATAGACGATCACATGCATAG 57.917 40.000 0.00 0.00 36.98 2.23
1210 1372 7.454260 AAGTAGATAGACGATCACATGCATA 57.546 36.000 0.00 0.00 36.98 3.14
1211 1373 5.973899 AGTAGATAGACGATCACATGCAT 57.026 39.130 0.00 0.00 36.98 3.96
1225 1387 3.508762 ACGCACCGACAAAAGTAGATAG 58.491 45.455 0.00 0.00 0.00 2.08
1232 1394 1.123038 GTACGTACGCACCGACAAAAG 59.877 52.381 16.72 0.00 0.00 2.27
1244 1406 4.496895 GTGTATGTAAGCAAGGTACGTACG 59.503 45.833 18.98 15.01 42.83 3.67
1267 1429 1.081242 GCTTTCGCCCACATGTGTG 60.081 57.895 23.79 14.60 45.23 3.82
1370 1558 6.167061 TCCCTAACTATATAGGCAGGACAT 57.833 41.667 23.75 0.00 41.03 3.06
1371 1559 5.610429 TCCCTAACTATATAGGCAGGACA 57.390 43.478 23.75 12.83 41.03 4.02
1372 1560 6.898521 AGAATCCCTAACTATATAGGCAGGAC 59.101 42.308 23.75 15.26 41.03 3.85
1373 1561 7.057732 AGAATCCCTAACTATATAGGCAGGA 57.942 40.000 23.75 18.36 41.03 3.86
1375 1563 8.261522 GGAAAGAATCCCTAACTATATAGGCAG 58.738 40.741 14.25 9.66 43.00 4.85
1376 1564 8.147244 GGAAAGAATCCCTAACTATATAGGCA 57.853 38.462 14.25 0.58 43.00 4.75
1417 1605 7.810759 CCAACTAACACAACCATTACCAATTAC 59.189 37.037 0.00 0.00 0.00 1.89
1418 1606 7.039644 CCCAACTAACACAACCATTACCAATTA 60.040 37.037 0.00 0.00 0.00 1.40
1419 1607 6.239458 CCCAACTAACACAACCATTACCAATT 60.239 38.462 0.00 0.00 0.00 2.32
1423 1611 4.400120 TCCCAACTAACACAACCATTACC 58.600 43.478 0.00 0.00 0.00 2.85
1452 1643 2.498078 GGGCGAAATGATTACCCCAAAA 59.502 45.455 0.00 0.00 34.23 2.44
1644 1838 1.308998 ACCAGTCTTTTCCTTGCGTG 58.691 50.000 0.00 0.00 0.00 5.34
1691 1965 5.742446 CGAAAAAGGATATCTTAGCAGCAC 58.258 41.667 2.05 0.00 34.78 4.40
1697 1971 7.857885 GGATTGTTGCGAAAAAGGATATCTTAG 59.142 37.037 2.05 0.00 34.78 2.18
1759 2033 0.811915 GGTAGCTCAGAGTTCTCGCA 59.188 55.000 0.00 0.00 0.00 5.10
1858 2142 4.762251 GCTACCATGGAATTTGATACCTCC 59.238 45.833 21.47 0.00 0.00 4.30
1957 2243 2.020016 GCGTAGATGCGTTGCACG 59.980 61.111 0.00 4.61 43.04 5.34
1970 2256 1.153842 CATGTCGTCAGCTGGCGTA 60.154 57.895 36.80 27.34 44.53 4.42
1979 2265 2.885113 CCGCTCTCCATGTCGTCA 59.115 61.111 0.00 0.00 0.00 4.35
2322 2608 7.831193 AGGAAAGGACGTACTAGTTATCTACAA 59.169 37.037 0.00 0.00 0.00 2.41
2346 2632 7.118971 TCACAAAATCCAAAAGAACAAACAAGG 59.881 33.333 0.00 0.00 0.00 3.61
2417 2704 2.504367 GAAAAGCAGCAGGTACCTTCA 58.496 47.619 13.15 0.00 0.00 3.02
2503 2790 1.580132 CGCAAATTAGTCACGGCGC 60.580 57.895 6.90 0.00 37.96 6.53
2598 2927 8.250332 GCCCTGTGTATTGAAGAAATTAAATGA 58.750 33.333 0.00 0.00 0.00 2.57
2612 2941 3.118261 ACCATAGTGAGCCCTGTGTATTG 60.118 47.826 0.00 0.00 0.00 1.90
2645 2974 4.563061 AGAAATTTTGCAATCAGGTGCTC 58.437 39.130 0.00 0.00 45.17 4.26
2729 3064 7.283580 TGTTTTATGTAGCAACTGTAAACACCT 59.716 33.333 0.00 0.00 31.26 4.00
2730 3065 7.419204 TGTTTTATGTAGCAACTGTAAACACC 58.581 34.615 0.00 0.00 31.26 4.16
2731 3066 8.901748 CATGTTTTATGTAGCAACTGTAAACAC 58.098 33.333 0.00 0.00 35.03 3.32
2741 3080 3.829026 TGGGTGCATGTTTTATGTAGCAA 59.171 39.130 8.86 0.00 34.58 3.91
2788 3127 4.319333 GCGAGACTATCAATTGCTCCATTG 60.319 45.833 0.00 0.00 0.00 2.82
2798 3137 3.452627 ACCCTGAAAGCGAGACTATCAAT 59.547 43.478 0.00 0.00 0.00 2.57
2802 3141 3.983044 AAACCCTGAAAGCGAGACTAT 57.017 42.857 0.00 0.00 0.00 2.12
2919 3262 6.642707 TGAAAGGGTGACGTGAAAATAAAT 57.357 33.333 0.00 0.00 0.00 1.40
2929 3272 2.036217 TCGTTGTATGAAAGGGTGACGT 59.964 45.455 0.00 0.00 0.00 4.34
2960 3303 9.167311 GTCAGTATGGAAAGTTCTGATATGTTT 57.833 33.333 0.00 0.00 37.46 2.83
2965 3308 5.105513 TGCGTCAGTATGGAAAGTTCTGATA 60.106 40.000 0.00 0.00 37.46 2.15
2983 3329 9.642327 TTCTACATTACTAAATAACTTGCGTCA 57.358 29.630 0.00 0.00 0.00 4.35
3099 3445 7.652909 TGTGATTGAGCGATTTTTCTGAAAATT 59.347 29.630 15.63 12.28 43.61 1.82
3244 3591 0.029700 TCAAGAACGCTCGACAACGA 59.970 50.000 4.90 0.00 46.56 3.85
3589 3936 0.257328 TTTGCCACCACAACTGAGGA 59.743 50.000 0.00 0.00 0.00 3.71
3746 4111 2.007636 ACTCTCTCTCCCTCCCTCTTT 58.992 52.381 0.00 0.00 0.00 2.52
3798 4170 7.277174 TCTCATACATATCAAGTGACATCGT 57.723 36.000 0.00 0.00 0.00 3.73
3870 4242 3.007506 TCAAATGACTAGAAGAACGCCCA 59.992 43.478 0.00 0.00 0.00 5.36
4090 4465 5.278463 GCGCTAATGTGGGAACATATCAAAT 60.278 40.000 0.00 0.00 41.82 2.32
4098 4473 1.553248 ACTAGCGCTAATGTGGGAACA 59.447 47.619 19.37 0.00 38.70 3.18
4196 4572 3.665745 AGGCTAAAGAACGACGGTTAA 57.334 42.857 0.00 0.00 36.24 2.01
4200 4576 1.730612 GGAAAGGCTAAAGAACGACGG 59.269 52.381 0.00 0.00 0.00 4.79
4203 4579 4.618920 AAGAGGAAAGGCTAAAGAACGA 57.381 40.909 0.00 0.00 0.00 3.85
4204 4580 6.986904 ATTAAGAGGAAAGGCTAAAGAACG 57.013 37.500 0.00 0.00 0.00 3.95
4283 4662 5.880332 ACTTTTACTGAGCTTTCTGACACAA 59.120 36.000 0.00 0.00 0.00 3.33
4322 4701 7.443272 GCTAGAGTGACAAAAGTTTAAACCCTA 59.557 37.037 14.72 1.56 0.00 3.53
4323 4702 6.262496 GCTAGAGTGACAAAAGTTTAAACCCT 59.738 38.462 14.72 0.00 0.00 4.34
4324 4703 6.038936 TGCTAGAGTGACAAAAGTTTAAACCC 59.961 38.462 14.72 0.00 0.00 4.11
4325 4704 7.023197 TGCTAGAGTGACAAAAGTTTAAACC 57.977 36.000 14.72 0.00 0.00 3.27
4326 4705 7.431376 GGTTGCTAGAGTGACAAAAGTTTAAAC 59.569 37.037 10.47 10.47 0.00 2.01
4327 4706 7.415877 GGGTTGCTAGAGTGACAAAAGTTTAAA 60.416 37.037 0.00 0.00 0.00 1.52
4328 4707 6.038936 GGGTTGCTAGAGTGACAAAAGTTTAA 59.961 38.462 0.00 0.00 0.00 1.52
4329 4708 5.529800 GGGTTGCTAGAGTGACAAAAGTTTA 59.470 40.000 0.00 0.00 0.00 2.01
4330 4709 4.338400 GGGTTGCTAGAGTGACAAAAGTTT 59.662 41.667 0.00 0.00 0.00 2.66
4331 4710 3.883489 GGGTTGCTAGAGTGACAAAAGTT 59.117 43.478 0.00 0.00 0.00 2.66
4332 4711 3.118038 TGGGTTGCTAGAGTGACAAAAGT 60.118 43.478 0.00 0.00 0.00 2.66
4333 4712 3.476552 TGGGTTGCTAGAGTGACAAAAG 58.523 45.455 0.00 0.00 0.00 2.27
4334 4713 3.569194 TGGGTTGCTAGAGTGACAAAA 57.431 42.857 0.00 0.00 0.00 2.44
4335 4714 3.072330 TGATGGGTTGCTAGAGTGACAAA 59.928 43.478 0.00 0.00 0.00 2.83
4336 4715 2.637382 TGATGGGTTGCTAGAGTGACAA 59.363 45.455 0.00 0.00 0.00 3.18
4337 4716 2.256306 TGATGGGTTGCTAGAGTGACA 58.744 47.619 0.00 0.00 0.00 3.58
4338 4717 3.133721 AGATGATGGGTTGCTAGAGTGAC 59.866 47.826 0.00 0.00 0.00 3.67
4339 4718 3.378512 AGATGATGGGTTGCTAGAGTGA 58.621 45.455 0.00 0.00 0.00 3.41
4340 4719 3.834489 AGATGATGGGTTGCTAGAGTG 57.166 47.619 0.00 0.00 0.00 3.51
4341 4720 7.291182 AGTTATTAGATGATGGGTTGCTAGAGT 59.709 37.037 0.00 0.00 0.00 3.24
4342 4721 7.675062 AGTTATTAGATGATGGGTTGCTAGAG 58.325 38.462 0.00 0.00 0.00 2.43
4343 4722 7.618019 AGTTATTAGATGATGGGTTGCTAGA 57.382 36.000 0.00 0.00 0.00 2.43
4344 4723 8.589338 AGTAGTTATTAGATGATGGGTTGCTAG 58.411 37.037 0.00 0.00 0.00 3.42
4345 4724 8.492415 AGTAGTTATTAGATGATGGGTTGCTA 57.508 34.615 0.00 0.00 0.00 3.49
4346 4725 7.380423 AGTAGTTATTAGATGATGGGTTGCT 57.620 36.000 0.00 0.00 0.00 3.91
4347 4726 6.651225 GGAGTAGTTATTAGATGATGGGTTGC 59.349 42.308 0.00 0.00 0.00 4.17
4348 4727 7.657761 GTGGAGTAGTTATTAGATGATGGGTTG 59.342 40.741 0.00 0.00 0.00 3.77
4349 4728 7.347222 TGTGGAGTAGTTATTAGATGATGGGTT 59.653 37.037 0.00 0.00 0.00 4.11
4350 4729 6.844388 TGTGGAGTAGTTATTAGATGATGGGT 59.156 38.462 0.00 0.00 0.00 4.51
4351 4730 7.303182 TGTGGAGTAGTTATTAGATGATGGG 57.697 40.000 0.00 0.00 0.00 4.00
4352 4731 9.212641 CATTGTGGAGTAGTTATTAGATGATGG 57.787 37.037 0.00 0.00 0.00 3.51
4353 4732 8.715998 GCATTGTGGAGTAGTTATTAGATGATG 58.284 37.037 0.00 0.00 0.00 3.07
4354 4733 8.432013 TGCATTGTGGAGTAGTTATTAGATGAT 58.568 33.333 0.00 0.00 0.00 2.45
4355 4734 7.791029 TGCATTGTGGAGTAGTTATTAGATGA 58.209 34.615 0.00 0.00 0.00 2.92
4356 4735 8.613060 ATGCATTGTGGAGTAGTTATTAGATG 57.387 34.615 0.00 0.00 0.00 2.90
4357 4736 7.880195 GGATGCATTGTGGAGTAGTTATTAGAT 59.120 37.037 0.00 0.00 0.00 1.98
4358 4737 7.217200 GGATGCATTGTGGAGTAGTTATTAGA 58.783 38.462 0.00 0.00 0.00 2.10
4359 4738 7.426929 GGATGCATTGTGGAGTAGTTATTAG 57.573 40.000 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.