Multiple sequence alignment - TraesCS3B01G057200

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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 TraesCS3B01G057200 chr3B 100.000 4595 0 0 1 4595 29851441 29856035 0.000000e+00 8486.0
1 TraesCS3B01G057200 chr3B 90.308 1981 153 12 2477 4420 29781902 29783880 0.000000e+00 2558.0
2 TraesCS3B01G057200 chr3B 87.855 2009 211 24 2086 4083 75523626 75521640 0.000000e+00 2327.0
3 TraesCS3B01G057200 chr3B 89.762 1807 163 16 2509 4305 30244133 30245927 0.000000e+00 2292.0
4 TraesCS3B01G057200 chr3B 87.705 2009 184 29 2440 4416 30517248 30519225 0.000000e+00 2283.0
5 TraesCS3B01G057200 chr3B 91.662 1619 125 7 2477 4089 30207290 30208904 0.000000e+00 2233.0
6 TraesCS3B01G057200 chr3B 86.909 1818 136 41 312 2090 29732032 29733786 0.000000e+00 1945.0
7 TraesCS3B01G057200 chr3B 91.232 479 31 3 878 1356 75524960 75524493 3.880000e-180 641.0
8 TraesCS3B01G057200 chr3B 84.416 693 48 16 1411 2093 75524322 75523680 1.090000e-175 627.0
9 TraesCS3B01G057200 chr3B 82.083 720 97 17 3859 4551 29629814 29630528 1.840000e-163 586.0
10 TraesCS3B01G057200 chr3B 85.646 418 35 8 465 882 75528135 75527743 2.560000e-112 416.0
11 TraesCS3B01G057200 chr3B 93.985 266 16 0 4330 4595 30247036 30247301 1.990000e-108 403.0
12 TraesCS3B01G057200 chr3B 87.421 318 25 3 2086 2401 29733846 29734150 7.310000e-93 351.0
13 TraesCS3B01G057200 chr3B 76.117 649 122 19 502 1126 30529260 30529899 4.460000e-80 309.0
14 TraesCS3B01G057200 chr3B 84.641 306 26 13 3 294 29731122 29731420 7.520000e-73 285.0
15 TraesCS3B01G057200 chr3B 76.099 364 64 16 1465 1821 30376359 30376706 7.910000e-38 169.0
16 TraesCS3B01G057200 chr7B 87.904 2166 198 30 2409 4523 64321500 64323652 0.000000e+00 2490.0
17 TraesCS3B01G057200 chr3D 88.103 2135 179 34 2338 4448 18801120 18803203 0.000000e+00 2466.0
18 TraesCS3B01G057200 chr3D 91.315 1589 128 7 2338 3922 18908487 18910069 0.000000e+00 2161.0
19 TraesCS3B01G057200 chr3D 90.681 955 65 10 469 1411 18950591 18951533 0.000000e+00 1249.0
20 TraesCS3B01G057200 chr3D 90.701 699 45 14 1411 2092 18951562 18952257 0.000000e+00 913.0
21 TraesCS3B01G057200 chr3D 83.602 372 45 9 3828 4190 18953893 18954257 7.370000e-88 335.0
22 TraesCS3B01G057200 chr3D 89.474 209 21 1 4102 4309 18910251 18910459 3.530000e-66 263.0
23 TraesCS3B01G057200 chr3D 81.470 313 40 11 4227 4523 18954454 18954764 1.650000e-59 241.0
24 TraesCS3B01G057200 chr3D 83.984 256 24 7 2086 2336 18952313 18952556 3.580000e-56 230.0
25 TraesCS3B01G057200 chr3D 79.692 325 47 13 1623 1940 18908182 18908494 2.780000e-52 217.0
26 TraesCS3B01G057200 chr3D 100.000 30 0 0 4561 4590 18803295 18803324 6.420000e-04 56.5
27 TraesCS3B01G057200 chr7D 90.996 1577 133 6 2479 4052 105686153 105687723 0.000000e+00 2117.0
28 TraesCS3B01G057200 chr7D 79.310 232 31 16 2085 2305 87489484 87489259 3.700000e-31 147.0
29 TraesCS3B01G057200 chr3A 90.365 1588 141 10 2509 4088 26481456 26483039 0.000000e+00 2074.0
30 TraesCS3B01G057200 chr3A 90.903 1539 124 14 2440 3965 26261463 26262998 0.000000e+00 2052.0
31 TraesCS3B01G057200 chr3A 89.681 1599 113 24 507 2090 26425365 26426926 0.000000e+00 1991.0
32 TraesCS3B01G057200 chr3A 88.715 319 29 5 121 437 26425011 26425324 2.590000e-102 383.0
33 TraesCS3B01G057200 chr3A 86.792 318 27 4 2086 2401 26426986 26427290 1.580000e-89 340.0
34 TraesCS3B01G057200 chr3A 78.744 414 67 14 1495 1893 26010223 26009816 1.640000e-64 257.0
35 TraesCS3B01G057200 chr3A 85.600 250 29 5 4085 4331 26483069 26483314 5.900000e-64 255.0
36 TraesCS3B01G057200 chr3A 79.936 314 40 12 4227 4518 26429482 26429794 4.660000e-50 209.0
37 TraesCS3B01G057200 chr3A 94.118 102 6 0 1 102 26424922 26425023 6.160000e-34 156.0
38 TraesCS3B01G057200 chr3A 92.632 95 7 0 3994 4088 26262998 26263092 2.230000e-28 137.0
39 TraesCS3B01G057200 chr4A 76.266 316 57 13 1588 1889 744032520 744032209 7.960000e-33 152.0
40 TraesCS3B01G057200 chr4A 82.099 162 21 7 2105 2261 691806806 691806648 1.040000e-26 132.0
41 TraesCS3B01G057200 chr2B 78.472 144 24 6 2105 2243 781104927 781105068 2.280000e-13 87.9


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 TraesCS3B01G057200 chr3B 29851441 29856035 4594 False 8486.000000 8486 100.000000 1 4595 1 chr3B.!!$F3 4594
1 TraesCS3B01G057200 chr3B 29781902 29783880 1978 False 2558.000000 2558 90.308000 2477 4420 1 chr3B.!!$F2 1943
2 TraesCS3B01G057200 chr3B 30517248 30519225 1977 False 2283.000000 2283 87.705000 2440 4416 1 chr3B.!!$F6 1976
3 TraesCS3B01G057200 chr3B 30207290 30208904 1614 False 2233.000000 2233 91.662000 2477 4089 1 chr3B.!!$F4 1612
4 TraesCS3B01G057200 chr3B 30244133 30247301 3168 False 1347.500000 2292 91.873500 2509 4595 2 chr3B.!!$F9 2086
5 TraesCS3B01G057200 chr3B 75521640 75528135 6495 True 1002.750000 2327 87.287250 465 4083 4 chr3B.!!$R1 3618
6 TraesCS3B01G057200 chr3B 29731122 29734150 3028 False 860.333333 1945 86.323667 3 2401 3 chr3B.!!$F8 2398
7 TraesCS3B01G057200 chr3B 29629814 29630528 714 False 586.000000 586 82.083000 3859 4551 1 chr3B.!!$F1 692
8 TraesCS3B01G057200 chr3B 30529260 30529899 639 False 309.000000 309 76.117000 502 1126 1 chr3B.!!$F7 624
9 TraesCS3B01G057200 chr7B 64321500 64323652 2152 False 2490.000000 2490 87.904000 2409 4523 1 chr7B.!!$F1 2114
10 TraesCS3B01G057200 chr3D 18801120 18803324 2204 False 1261.250000 2466 94.051500 2338 4590 2 chr3D.!!$F1 2252
11 TraesCS3B01G057200 chr3D 18908182 18910459 2277 False 880.333333 2161 86.827000 1623 4309 3 chr3D.!!$F2 2686
12 TraesCS3B01G057200 chr3D 18950591 18954764 4173 False 593.600000 1249 86.087600 469 4523 5 chr3D.!!$F3 4054
13 TraesCS3B01G057200 chr7D 105686153 105687723 1570 False 2117.000000 2117 90.996000 2479 4052 1 chr7D.!!$F1 1573
14 TraesCS3B01G057200 chr3A 26481456 26483314 1858 False 1164.500000 2074 87.982500 2509 4331 2 chr3A.!!$F3 1822
15 TraesCS3B01G057200 chr3A 26261463 26263092 1629 False 1094.500000 2052 91.767500 2440 4088 2 chr3A.!!$F1 1648
16 TraesCS3B01G057200 chr3A 26424922 26429794 4872 False 615.800000 1991 87.848400 1 4518 5 chr3A.!!$F2 4517

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
862 1538 0.179000 GATGGACTCACCTTGCCGAT 59.821 55.000 0.00 0.0 39.86 4.18 F
2027 5634 1.467342 GACCGTGCATGAACTTTACCC 59.533 52.381 7.72 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2284 5974 0.390860 CCCCTTATCTGAGCTGTCCG 59.609 60.000 0.00 0.0 0.00 4.79 R
3954 7922 2.038033 TGTTCTGTAACTTAGGGCGCTT 59.962 45.455 9.23 0.0 36.51 4.68 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
27 28 3.117813 CAGAGGGAGTACTAGCTAGGTGT 60.118 52.174 24.35 8.12 0.00 4.16
70 71 6.780944 CGCAGCAATTTTATTCACTAAGAC 57.219 37.500 0.00 0.00 0.00 3.01
89 112 3.679980 AGACGATCAAACCATCAGTTTCG 59.320 43.478 0.00 0.00 45.85 3.46
90 113 3.399330 ACGATCAAACCATCAGTTTCGT 58.601 40.909 0.00 0.00 45.85 3.85
106 129 3.819564 TTCGTACAAGCTGGAGCATAT 57.180 42.857 0.00 0.00 45.16 1.78
107 130 4.929819 TTCGTACAAGCTGGAGCATATA 57.070 40.909 0.00 0.00 45.16 0.86
108 131 4.505313 TCGTACAAGCTGGAGCATATAG 57.495 45.455 0.00 0.00 45.16 1.31
109 132 3.889538 TCGTACAAGCTGGAGCATATAGT 59.110 43.478 0.00 0.00 45.16 2.12
110 133 4.341235 TCGTACAAGCTGGAGCATATAGTT 59.659 41.667 0.00 0.00 45.16 2.24
111 134 4.445718 CGTACAAGCTGGAGCATATAGTTG 59.554 45.833 0.00 0.00 45.16 3.16
112 135 4.760530 ACAAGCTGGAGCATATAGTTGA 57.239 40.909 0.00 0.00 45.16 3.18
113 136 5.102953 ACAAGCTGGAGCATATAGTTGAA 57.897 39.130 0.00 0.00 45.16 2.69
114 137 5.500234 ACAAGCTGGAGCATATAGTTGAAA 58.500 37.500 0.00 0.00 45.16 2.69
115 138 5.355350 ACAAGCTGGAGCATATAGTTGAAAC 59.645 40.000 0.00 0.00 45.16 2.78
127 150 9.677567 GCATATAGTTGAAACTTGAAAACAAGA 57.322 29.630 15.32 0.00 40.37 3.02
155 178 9.399403 GGAGTGATAAAAGAATTTCTCAACAAC 57.601 33.333 0.00 0.00 37.28 3.32
167 190 9.636965 GAATTTCTCAACAACAAAAATAAGTGC 57.363 29.630 0.00 0.00 0.00 4.40
210 233 1.135112 GGTCAATGCCGGTGGAAAATC 60.135 52.381 1.90 0.00 0.00 2.17
211 234 0.808125 TCAATGCCGGTGGAAAATCG 59.192 50.000 1.90 0.00 0.00 3.34
236 259 7.537306 CGAAACGATACTTTGACCAAAATGATT 59.463 33.333 0.00 0.00 0.00 2.57
280 303 6.889722 TCATCCCAAAGTTCATAACTAAAGGG 59.110 38.462 13.71 13.71 41.91 3.95
295 901 5.497474 ACTAAAGGGCAACGATACTTTGAT 58.503 37.500 0.00 0.00 35.11 2.57
339 956 1.589803 AGCCGCGTTAACAAGTCTTT 58.410 45.000 4.92 0.00 0.00 2.52
353 970 6.927294 ACAAGTCTTTCAACTCCTTGTTAG 57.073 37.500 0.00 0.00 42.09 2.34
361 978 2.481289 ACTCCTTGTTAGCTTCCAGC 57.519 50.000 0.00 0.00 42.84 4.85
363 980 1.003580 CTCCTTGTTAGCTTCCAGCCA 59.996 52.381 0.00 0.00 43.77 4.75
374 991 2.966516 GCTTCCAGCCACCTACTACTAT 59.033 50.000 0.00 0.00 34.48 2.12
377 994 5.509332 GCTTCCAGCCACCTACTACTATTAC 60.509 48.000 0.00 0.00 34.48 1.89
378 995 5.399052 TCCAGCCACCTACTACTATTACT 57.601 43.478 0.00 0.00 0.00 2.24
379 996 6.520021 TCCAGCCACCTACTACTATTACTA 57.480 41.667 0.00 0.00 0.00 1.82
419 1057 2.032550 GGATCCATTTCACGTCATGCAG 59.967 50.000 6.95 0.00 0.00 4.41
459 1113 1.208293 CTCACCCTCCTTTCTAGCACC 59.792 57.143 0.00 0.00 0.00 5.01
495 1149 2.743928 CTGTCGTCCTGCAAGCCC 60.744 66.667 0.00 0.00 0.00 5.19
496 1150 3.535629 CTGTCGTCCTGCAAGCCCA 62.536 63.158 0.00 0.00 0.00 5.36
578 1232 3.554692 CGGCTACAGCGCTTTCCG 61.555 66.667 7.50 14.55 43.26 4.30
654 1330 5.010933 TCTCCTACGAAGACAACTCATTCT 58.989 41.667 0.00 0.00 0.00 2.40
685 1361 1.202734 CCCCGACATCTCCTACTACGA 60.203 57.143 0.00 0.00 0.00 3.43
849 1525 4.094684 CGAACTGCTCGGATGGAC 57.905 61.111 0.00 0.00 44.20 4.02
862 1538 0.179000 GATGGACTCACCTTGCCGAT 59.821 55.000 0.00 0.00 39.86 4.18
890 4353 2.053865 ATTCACATGGCTTGCCGGG 61.054 57.895 2.18 4.15 0.00 5.73
891 4354 4.738998 TCACATGGCTTGCCGGGG 62.739 66.667 2.18 3.22 0.00 5.73
1139 4603 1.471287 CGTGTCTCCGTCCAACATCTA 59.529 52.381 0.00 0.00 0.00 1.98
1164 4628 4.089636 GGTAAGCTTCGCACGTATAATAGC 59.910 45.833 0.00 0.00 0.00 2.97
1302 4766 5.046231 AGGAGATTTACAGGAGAAGTGAACC 60.046 44.000 0.00 0.00 0.00 3.62
1316 4780 3.813443 AGTGAACCCATCATGCATCTAC 58.187 45.455 0.00 0.00 40.97 2.59
1351 4815 8.673626 TTACTACACTGCGTACTAAAATGTAC 57.326 34.615 0.00 0.00 39.35 2.90
1375 4922 3.828451 ACTAACTAGTGCAACCGGTCTAA 59.172 43.478 8.04 0.00 37.80 2.10
1401 4952 3.896888 TGTACCCTACTCTTCGGTTTTGA 59.103 43.478 0.00 0.00 0.00 2.69
1458 5038 6.586751 GTTCATTGCAATGTCATTGAAACAG 58.413 36.000 32.67 18.20 40.45 3.16
1463 5043 4.100529 GCAATGTCATTGAAACAGATCCG 58.899 43.478 26.36 0.00 42.83 4.18
1498 5078 9.632638 ACAGTTTATGCAATCTCTTATATTGGT 57.367 29.630 0.00 0.00 35.34 3.67
1587 5167 7.229506 ACATAGTTGCTCAGTTAAAAGAAAGCT 59.770 33.333 0.00 0.00 0.00 3.74
1594 5174 6.361748 GCTCAGTTAAAAGAAAGCTCATGTTG 59.638 38.462 0.00 0.00 0.00 3.33
1595 5175 7.333528 TCAGTTAAAAGAAAGCTCATGTTGT 57.666 32.000 0.00 0.00 0.00 3.32
1596 5176 8.445275 TCAGTTAAAAGAAAGCTCATGTTGTA 57.555 30.769 0.00 0.00 0.00 2.41
1597 5177 9.066892 TCAGTTAAAAGAAAGCTCATGTTGTAT 57.933 29.630 0.00 0.00 0.00 2.29
1603 5186 9.598517 AAAAGAAAGCTCATGTTGTATTTTTCA 57.401 25.926 0.00 0.00 0.00 2.69
1621 5204 8.697846 ATTTTTCATCACTATCTTGCAATGTG 57.302 30.769 0.00 7.56 0.00 3.21
1924 5522 9.986833 TTATCATGTCTGTAATCGTTGAAATTG 57.013 29.630 0.00 0.00 0.00 2.32
1925 5523 7.433708 TCATGTCTGTAATCGTTGAAATTGT 57.566 32.000 0.00 0.00 0.00 2.71
1994 5598 4.451900 CACCCACTTATCCAACCATCTAC 58.548 47.826 0.00 0.00 0.00 2.59
2027 5634 1.467342 GACCGTGCATGAACTTTACCC 59.533 52.381 7.72 0.00 0.00 3.69
2032 5640 4.226761 CGTGCATGAACTTTACCCTTTTC 58.773 43.478 0.00 0.00 0.00 2.29
2033 5641 4.556233 GTGCATGAACTTTACCCTTTTCC 58.444 43.478 0.00 0.00 0.00 3.13
2171 5845 7.433719 CGAAATTTTTCACACATTGTAGTTCCA 59.566 33.333 4.12 0.00 37.01 3.53
2173 5847 8.647143 AATTTTTCACACATTGTAGTTCCAAG 57.353 30.769 0.00 0.00 0.00 3.61
2190 5865 5.381174 TCCAAGATTTTGTTGATCTGCAG 57.619 39.130 7.63 7.63 34.24 4.41
2198 5873 4.548451 TTGTTGATCTGCAGAGTCTGAT 57.452 40.909 24.55 8.43 32.44 2.90
2202 5877 3.363627 TGATCTGCAGAGTCTGATGTCT 58.636 45.455 24.55 0.03 32.44 3.41
2208 5883 5.476254 TCTGCAGAGTCTGATGTCTATATGG 59.524 44.000 24.55 0.00 32.44 2.74
2245 5935 7.539436 AGAGAAACAAAAAGAGAAACTTCCAC 58.461 34.615 0.00 0.00 37.93 4.02
2284 5974 4.872691 AGTAGCACACATCAAAGCAGTATC 59.127 41.667 0.00 0.00 0.00 2.24
2329 6019 2.029380 GTGCGCCTGGGTTTAGAAAAAT 60.029 45.455 4.18 0.00 0.00 1.82
2460 6383 7.601508 GGAAGGAGAAATTTAAACTACTGACGA 59.398 37.037 0.00 0.00 0.00 4.20
2578 6519 8.344831 TCTTTGCATGTATTTATGTGCTGATAC 58.655 33.333 0.00 0.00 38.37 2.24
2597 6538 3.163616 ACGGCATAGAAAGGGGAAAAA 57.836 42.857 0.00 0.00 0.00 1.94
2715 6656 5.717078 ACACGTACTCAGAGGTAATGAAA 57.283 39.130 1.53 0.00 0.00 2.69
2718 6659 7.159372 ACACGTACTCAGAGGTAATGAAAATT 58.841 34.615 1.53 0.00 0.00 1.82
2918 6859 5.660460 CTTATATGGGTTTTGTTTGGAGGC 58.340 41.667 0.00 0.00 0.00 4.70
2976 6918 5.019785 ACGGTTCCTTGGATAAGTACATC 57.980 43.478 0.00 0.00 31.80 3.06
3277 7219 2.498078 GGGGTGGTTTCAACAAAGTCAA 59.502 45.455 0.00 0.00 30.63 3.18
3313 7255 4.602107 TGGAATGATGCTTTTGGAGATGA 58.398 39.130 0.00 0.00 0.00 2.92
3331 7273 6.043706 GGAGATGATTGGAGGAAGGAGAAATA 59.956 42.308 0.00 0.00 0.00 1.40
3332 7274 6.836242 AGATGATTGGAGGAAGGAGAAATAC 58.164 40.000 0.00 0.00 0.00 1.89
3341 7283 7.728083 TGGAGGAAGGAGAAATACAAAATCAAA 59.272 33.333 0.00 0.00 0.00 2.69
3611 7553 8.853077 TTGCTGTAAGATATTCTCCCATATTG 57.147 34.615 0.00 0.00 34.07 1.90
3668 7619 5.878332 TGCAATAACTTGACCTACATGTG 57.122 39.130 9.11 0.00 37.05 3.21
3712 7663 4.689812 GCTCAGCTCACAATATGGATGTAG 59.310 45.833 0.00 0.00 0.00 2.74
3954 7922 1.065926 AGTCAAGAGCATCCGCATGAA 60.066 47.619 0.00 0.00 42.27 2.57
3970 7967 2.843401 TGAAAGCGCCCTAAGTTACA 57.157 45.000 2.29 0.00 0.00 2.41
3973 7970 3.244284 TGAAAGCGCCCTAAGTTACAGAA 60.244 43.478 2.29 0.00 0.00 3.02
3987 7986 9.706691 CTAAGTTACAGAACACAGAAGGAATAA 57.293 33.333 0.00 0.00 38.10 1.40
3991 7990 9.612620 GTTACAGAACACAGAAGGAATAAAATG 57.387 33.333 0.00 0.00 35.48 2.32
4109 8284 5.892160 ATTTCAGAATCCGGATGCATATG 57.108 39.130 24.87 14.01 0.00 1.78
4161 8345 7.088905 CCATTCATAGCAAGCAGATTAAATCC 58.911 38.462 0.00 0.00 0.00 3.01
4186 8512 1.553248 AGCGGAAGGTGCATACTTACA 59.447 47.619 14.41 0.00 42.35 2.41
4205 8531 4.180377 ACATGGTCCTCTCCGTAGATTA 57.820 45.455 0.00 0.00 0.00 1.75
4213 8539 5.944599 GTCCTCTCCGTAGATTATATCCACA 59.055 44.000 0.00 0.00 0.00 4.17
4247 8592 2.110213 TGCCTTTCCTTGACGCGT 59.890 55.556 13.85 13.85 0.00 6.01
4248 8593 0.947180 GTGCCTTTCCTTGACGCGTA 60.947 55.000 13.97 0.00 0.00 4.42
4309 9581 3.972276 CTCTCCCTCCGCTAGCGC 61.972 72.222 31.35 0.00 38.24 5.92
4426 9899 4.592192 CGGAGATCCACGCGCCAT 62.592 66.667 5.73 0.00 35.14 4.40
4432 9905 1.222115 GATCCACGCGCCATAAGACC 61.222 60.000 5.73 0.00 0.00 3.85
4442 9915 4.217159 ATAAGACCCCGCGGCGAC 62.217 66.667 25.92 12.67 0.00 5.19
4467 9940 4.443266 GCTCTTCTCTGCGCCGGT 62.443 66.667 4.18 0.00 0.00 5.28
4541 10034 1.532794 GAATTGGGGGCACACACCA 60.533 57.895 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.124861 ACACCTAGCTAGTACTCCCTCT 58.875 50.000 19.31 0.00 0.00 3.69
27 28 1.069204 GCCGAAGCATGTGATCCTAGA 59.931 52.381 0.00 0.00 39.53 2.43
70 71 4.387559 TGTACGAAACTGATGGTTTGATCG 59.612 41.667 0.00 0.00 46.77 3.69
89 112 5.601662 TCAACTATATGCTCCAGCTTGTAC 58.398 41.667 0.00 0.00 42.66 2.90
90 113 5.869649 TCAACTATATGCTCCAGCTTGTA 57.130 39.130 0.00 0.00 42.66 2.41
127 150 9.300681 TGTTGAGAAATTCTTTTATCACTCCAT 57.699 29.630 0.00 0.00 41.43 3.41
155 178 5.630680 GGTGTCACATCTGCACTTATTTTTG 59.369 40.000 5.12 0.00 33.96 2.44
160 183 3.603532 CAGGTGTCACATCTGCACTTAT 58.396 45.455 4.77 0.00 35.75 1.73
162 185 1.888215 CAGGTGTCACATCTGCACTT 58.112 50.000 4.77 0.00 35.75 3.16
163 186 3.620061 CAGGTGTCACATCTGCACT 57.380 52.632 4.77 0.00 35.75 4.40
167 190 0.604511 TGCTGCAGGTGTCACATCTG 60.605 55.000 14.29 14.29 44.62 2.90
210 233 6.367421 TCATTTTGGTCAAAGTATCGTTTCG 58.633 36.000 0.00 0.00 0.00 3.46
211 234 8.742554 AATCATTTTGGTCAAAGTATCGTTTC 57.257 30.769 0.00 0.00 0.00 2.78
236 259 8.988060 TGGGATGACTATACAAAATCTTGAGTA 58.012 33.333 0.00 0.00 36.33 2.59
295 901 0.534877 ATTGCTGCACCAGTTCACGA 60.535 50.000 0.00 0.00 33.43 4.35
300 906 3.191371 GCTTAGTTATTGCTGCACCAGTT 59.809 43.478 0.00 0.00 33.43 3.16
339 956 4.008074 CTGGAAGCTAACAAGGAGTTGA 57.992 45.455 0.00 0.00 41.50 3.18
374 991 9.889388 TCCATCTCCTAGTAGTAGTAGTAGTAA 57.111 37.037 15.39 5.57 32.18 2.24
377 994 8.480501 GGATCCATCTCCTAGTAGTAGTAGTAG 58.519 44.444 6.95 11.24 33.42 2.57
378 995 7.960290 TGGATCCATCTCCTAGTAGTAGTAGTA 59.040 40.741 11.44 0.00 36.20 1.82
379 996 6.793482 TGGATCCATCTCCTAGTAGTAGTAGT 59.207 42.308 11.44 0.00 36.20 2.73
419 1057 1.505353 GTGAGCAGAACATGGCAGC 59.495 57.895 0.00 0.00 0.00 5.25
477 1131 2.031163 GGCTTGCAGGACGACAGT 59.969 61.111 0.00 0.00 0.00 3.55
553 1207 3.191539 GCTGTAGCCGCACTCTGC 61.192 66.667 0.00 0.00 40.69 4.26
578 1232 0.536006 GCCATCTATGCACCTGACCC 60.536 60.000 0.00 0.00 0.00 4.46
685 1361 1.202639 TGAGCTCGGTGTCACAAATGT 60.203 47.619 9.64 0.00 0.00 2.71
833 1509 0.532573 TGAGTCCATCCGAGCAGTTC 59.467 55.000 0.00 0.00 0.00 3.01
849 1525 0.321564 TTGGACATCGGCAAGGTGAG 60.322 55.000 0.00 0.00 34.34 3.51
862 1538 2.161855 GCCATGTGAATGAGTTGGACA 58.838 47.619 0.00 0.00 0.00 4.02
900 4363 1.256812 GACTCCATTGGTTGTTGGGG 58.743 55.000 1.86 0.00 39.54 4.96
938 4401 2.300967 ACCGGCATCATGGACACCT 61.301 57.895 0.00 0.00 0.00 4.00
1164 4628 0.311165 AACTCACTGTCGGTCTGTCG 59.689 55.000 0.00 0.00 0.00 4.35
1165 4629 2.128035 CAAACTCACTGTCGGTCTGTC 58.872 52.381 0.00 0.00 0.00 3.51
1166 4630 1.754803 TCAAACTCACTGTCGGTCTGT 59.245 47.619 0.00 0.00 0.00 3.41
1167 4631 2.128035 GTCAAACTCACTGTCGGTCTG 58.872 52.381 0.00 0.00 0.00 3.51
1168 4632 1.068741 GGTCAAACTCACTGTCGGTCT 59.931 52.381 0.00 0.00 0.00 3.85
1169 4633 1.068741 AGGTCAAACTCACTGTCGGTC 59.931 52.381 0.00 0.00 0.00 4.79
1170 4634 1.120530 AGGTCAAACTCACTGTCGGT 58.879 50.000 0.00 0.00 0.00 4.69
1171 4635 1.202533 ACAGGTCAAACTCACTGTCGG 60.203 52.381 0.00 0.00 39.84 4.79
1206 4670 3.983741 TGCCAAAATTGAACTAAACCGG 58.016 40.909 0.00 0.00 0.00 5.28
1302 4766 1.878088 GCAGGTGTAGATGCATGATGG 59.122 52.381 2.46 0.00 42.11 3.51
1316 4780 3.551890 CGCAGTGTAGTAATTAGCAGGTG 59.448 47.826 0.00 0.00 0.00 4.00
1351 4815 3.442977 AGACCGGTTGCACTAGTTAGTAG 59.557 47.826 9.42 0.00 34.13 2.57
1365 4912 3.447950 AGGGTACAGAATTAGACCGGTT 58.552 45.455 9.42 0.87 32.38 4.44
1375 4922 3.978610 ACCGAAGAGTAGGGTACAGAAT 58.021 45.455 0.00 0.00 30.76 2.40
1401 4952 1.959985 TCCACATTTTTCACGGTGCAT 59.040 42.857 2.51 0.00 0.00 3.96
1458 5038 8.083462 TGCATAAACTGTGAATTATACGGATC 57.917 34.615 7.86 0.00 0.00 3.36
1546 5126 6.931281 AGCAACTATGTCGCTCAAATATACAT 59.069 34.615 0.00 0.00 35.16 2.29
1572 5152 9.683069 AATACAACATGAGCTTTCTTTTAACTG 57.317 29.630 0.00 0.00 0.00 3.16
1594 5174 9.793252 ACATTGCAAGATAGTGATGAAAAATAC 57.207 29.630 4.94 0.00 0.00 1.89
1595 5175 9.791820 CACATTGCAAGATAGTGATGAAAAATA 57.208 29.630 15.05 0.00 32.14 1.40
1596 5176 8.308931 ACACATTGCAAGATAGTGATGAAAAAT 58.691 29.630 22.66 3.71 34.47 1.82
1597 5177 7.660112 ACACATTGCAAGATAGTGATGAAAAA 58.340 30.769 22.66 0.00 34.47 1.94
1743 5331 6.017192 TCCTCTCGCTACCTGGAATATAATT 58.983 40.000 0.00 0.00 0.00 1.40
1929 5527 6.484977 GTCACAACCTTCTCTTCAGATTTTCT 59.515 38.462 0.00 0.00 0.00 2.52
1930 5528 6.484977 AGTCACAACCTTCTCTTCAGATTTTC 59.515 38.462 0.00 0.00 0.00 2.29
1977 5581 5.648092 GCAACAAGTAGATGGTTGGATAAGT 59.352 40.000 0.00 0.00 41.57 2.24
1994 5598 1.741993 CACGGTCGAAAAGCAACAAG 58.258 50.000 0.00 0.00 0.00 3.16
2066 5674 7.532682 TTATTTTGTTGACCTGCAAACTTTC 57.467 32.000 1.05 0.00 38.44 2.62
2126 5798 4.210724 TCGTATTCTTTTGGTCCCGAAT 57.789 40.909 0.00 0.00 0.00 3.34
2130 5802 7.654116 TGAAAAATTTCGTATTCTTTTGGTCCC 59.346 33.333 0.00 0.00 40.01 4.46
2145 5817 7.433719 TGGAACTACAATGTGTGAAAAATTTCG 59.566 33.333 0.00 0.00 40.01 3.46
2171 5845 6.002704 AGACTCTGCAGATCAACAAAATCTT 58.997 36.000 18.63 0.00 31.05 2.40
2173 5847 5.410746 TCAGACTCTGCAGATCAACAAAATC 59.589 40.000 18.63 4.26 0.00 2.17
2190 5865 8.948631 TGAAAAACCATATAGACATCAGACTC 57.051 34.615 0.00 0.00 0.00 3.36
2198 5873 9.958180 TCTCTCAAATGAAAAACCATATAGACA 57.042 29.630 0.00 0.00 0.00 3.41
2227 5902 6.359480 ACTACGTGGAAGTTTCTCTTTTTG 57.641 37.500 5.70 0.00 36.40 2.44
2245 5935 6.522510 GTGTGCTACTCAACTAACTTACTACG 59.477 42.308 0.00 0.00 0.00 3.51
2284 5974 0.390860 CCCCTTATCTGAGCTGTCCG 59.609 60.000 0.00 0.00 0.00 4.79
2379 6070 7.178274 ACAGACTAATTGCCATAAATTGACCAA 59.822 33.333 0.00 0.00 32.16 3.67
2597 6538 5.385198 TCTTGCAAAGGAGAAACCATAGTT 58.615 37.500 0.00 0.00 46.24 2.24
2642 6583 3.997021 CACTATCATGGCCTCGTAATTCC 59.003 47.826 3.32 0.00 0.00 3.01
2715 6656 4.688879 TGATTGTTGCGAGAAGACGTAATT 59.311 37.500 0.00 0.00 39.57 1.40
2718 6659 3.242518 CTGATTGTTGCGAGAAGACGTA 58.757 45.455 0.00 0.00 35.59 3.57
2918 6859 9.416794 ACTCATATATAAGAGCTCGTTTTGATG 57.583 33.333 7.67 9.51 35.28 3.07
2976 6918 4.891992 TTCTTTGGGGTTCTCTGAGTAG 57.108 45.455 4.32 0.00 0.00 2.57
3313 7255 7.895429 TGATTTTGTATTTCTCCTTCCTCCAAT 59.105 33.333 0.00 0.00 0.00 3.16
3331 7273 7.330900 TGGATTTTGCAACATTTGATTTTGT 57.669 28.000 0.00 0.00 0.00 2.83
3332 7274 6.361214 GCTGGATTTTGCAACATTTGATTTTG 59.639 34.615 0.00 0.00 0.00 2.44
3341 7283 3.383620 TTTCGCTGGATTTTGCAACAT 57.616 38.095 0.00 0.00 0.00 2.71
3611 7553 6.103330 TGCCTAGAAAAACAAAGGAACAAAC 58.897 36.000 0.00 0.00 0.00 2.93
3642 7586 8.124823 CACATGTAGGTCAAGTTATTGCATAAG 58.875 37.037 0.00 0.00 36.30 1.73
3668 7619 4.874966 AGCTTTCACTGCAATGAGAGATAC 59.125 41.667 18.74 2.25 33.63 2.24
3712 7663 5.580297 CAGATCTGGTAGAGCTTGAACTTTC 59.420 44.000 15.38 0.00 37.81 2.62
3954 7922 2.038033 TGTTCTGTAACTTAGGGCGCTT 59.962 45.455 9.23 0.00 36.51 4.68
3959 7927 5.011738 TCCTTCTGTGTTCTGTAACTTAGGG 59.988 44.000 0.00 0.00 36.51 3.53
3973 7970 9.739276 TGAGAATACATTTTATTCCTTCTGTGT 57.261 29.630 0.05 0.00 35.19 3.72
3987 7986 9.683069 GAACACAAAACTCATGAGAATACATTT 57.317 29.630 29.27 14.41 0.00 2.32
3991 7990 7.202016 TGGAACACAAAACTCATGAGAATAC 57.798 36.000 29.27 9.48 0.00 1.89
3998 8084 3.798337 GCAGTTGGAACACAAAACTCATG 59.202 43.478 0.00 0.00 41.58 3.07
4068 8201 6.764379 TGAAATATTCAGTTTTGGGGGAAAC 58.236 36.000 0.00 0.00 39.28 2.78
4100 8275 8.146479 TCACAATGTTTAGACTCATATGCATC 57.854 34.615 0.19 0.00 0.00 3.91
4161 8345 0.107703 TATGCACCTTCCGCTTCCAG 60.108 55.000 0.00 0.00 0.00 3.86
4175 8359 3.388024 GGAGAGGACCATGTAAGTATGCA 59.612 47.826 0.00 0.00 0.00 3.96
4186 8512 6.130569 GGATATAATCTACGGAGAGGACCAT 58.869 44.000 2.53 0.00 34.35 3.55
4205 8531 3.809832 GCGCTACTTGATTGTGTGGATAT 59.190 43.478 0.00 0.00 0.00 1.63
4213 8539 1.635663 GCACGGCGCTACTTGATTGT 61.636 55.000 6.90 0.00 37.77 2.71
4233 8578 1.279527 TGCGTACGCGTCAAGGAAAG 61.280 55.000 32.65 0.00 45.51 2.62
4315 9587 2.819595 GAGAAGCGGCGCAATCCA 60.820 61.111 35.02 0.00 0.00 3.41
4318 9590 1.210155 GTTTGAGAAGCGGCGCAAT 59.790 52.632 35.02 22.58 0.00 3.56
4409 9853 2.693250 TTATGGCGCGTGGATCTCCG 62.693 60.000 8.43 0.00 39.43 4.63
4412 9856 0.249489 GTCTTATGGCGCGTGGATCT 60.249 55.000 8.43 0.00 0.00 2.75
4442 9915 1.221293 CAGAGAAGAGCCTGGCCTG 59.779 63.158 16.57 10.46 0.00 4.85
4519 10000 4.374584 TGTGCCCCCAATTCCCCG 62.375 66.667 0.00 0.00 0.00 5.73
4541 10034 2.920645 CGACGTGGACTGTCTGGCT 61.921 63.158 7.85 0.00 34.17 4.75


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

AutoCloner maintained by Alex Coulton.