Multiple sequence alignment - TraesCS3B01G504200

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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 TraesCS3B01G504200 chr3B 100.000 3553 0 0 3932 7484 748614429 748617981 0.000000e+00 6562.0
1 TraesCS3B01G504200 chr3B 100.000 2144 0 0 1504 3647 748612001 748614144 0.000000e+00 3960.0
2 TraesCS3B01G504200 chr3B 100.000 1298 0 0 1 1298 748610498 748611795 0.000000e+00 2398.0
3 TraesCS3B01G504200 chr3B 80.996 2510 372 61 4078 6533 748453109 748455567 0.000000e+00 1895.0
4 TraesCS3B01G504200 chr3B 78.396 2444 398 75 4183 6568 747834474 747836845 0.000000e+00 1469.0
5 TraesCS3B01G504200 chr3B 78.305 2443 402 73 4183 6568 747851001 747853372 0.000000e+00 1458.0
6 TraesCS3B01G504200 chr3B 78.223 2443 404 73 4183 6568 747821998 747824369 0.000000e+00 1447.0
7 TraesCS3B01G504200 chr3B 78.223 2443 404 71 4183 6568 747838526 747840897 0.000000e+00 1447.0
8 TraesCS3B01G504200 chr3B 82.467 827 109 16 473 1287 748450284 748451086 0.000000e+00 691.0
9 TraesCS3B01G504200 chr3B 81.553 721 103 15 473 1185 748410733 748411431 1.090000e-157 568.0
10 TraesCS3B01G504200 chr3B 90.491 326 25 4 6512 6833 748455575 748455898 6.940000e-115 425.0
11 TraesCS3B01G504200 chr3B 83.168 404 54 11 2603 3002 748412676 748413069 2.570000e-94 357.0
12 TraesCS3B01G504200 chr3B 79.124 388 30 18 7127 7472 748457647 748458025 3.520000e-53 220.0
13 TraesCS3B01G504200 chr3B 78.448 232 45 4 4867 5097 718266966 718266739 6.050000e-31 147.0
14 TraesCS3B01G504200 chr3A 94.745 3368 140 23 3932 7290 697373377 697376716 0.000000e+00 5204.0
15 TraesCS3B01G504200 chr3A 93.606 2174 90 16 1512 3645 697371096 697373260 0.000000e+00 3199.0
16 TraesCS3B01G504200 chr3A 81.148 2822 400 70 4079 6833 697276852 697279608 0.000000e+00 2143.0
17 TraesCS3B01G504200 chr3A 93.904 853 47 2 447 1298 697370043 697370891 0.000000e+00 1282.0
18 TraesCS3B01G504200 chr3A 94.655 449 22 2 1 448 697368897 697369344 0.000000e+00 695.0
19 TraesCS3B01G504200 chr3A 85.000 380 22 13 7127 7472 697280610 697280988 3.320000e-93 353.0
20 TraesCS3B01G504200 chr3A 97.938 194 2 2 7289 7481 697376744 697376936 1.200000e-87 335.0
21 TraesCS3B01G504200 chr3A 81.557 244 38 7 4858 5097 678391481 678391241 2.130000e-45 195.0
22 TraesCS3B01G504200 chr3A 77.714 350 50 9 378 727 697275134 697275455 9.910000e-44 189.0
23 TraesCS3B01G504200 chr3D 90.179 2016 179 13 5200 7208 561444149 561446152 0.000000e+00 2608.0
24 TraesCS3B01G504200 chr3D 95.364 151 4 1 7337 7484 561446670 561446820 3.490000e-58 237.0
25 TraesCS3B01G504200 chr3D 83.058 242 37 4 4858 5097 542266677 542266438 4.550000e-52 217.0
26 TraesCS3B01G504200 chr3D 80.894 246 42 5 4858 5100 542230645 542230402 9.910000e-44 189.0
27 TraesCS3B01G504200 chr3D 93.220 59 3 1 7280 7337 561446168 561446226 1.340000e-12 86.1
28 TraesCS3B01G504200 chr3D 100.000 30 0 0 7228 7257 561378602 561378631 1.000000e-03 56.5
29 TraesCS3B01G504200 chr6D 78.448 2487 410 72 4074 6488 427482782 427485214 0.000000e+00 1507.0
30 TraesCS3B01G504200 chrUn 78.620 2044 370 41 4662 6662 108321537 108323556 0.000000e+00 1291.0
31 TraesCS3B01G504200 chrUn 82.916 1317 205 15 5258 6568 331495101 331496403 0.000000e+00 1168.0
32 TraesCS3B01G504200 chrUn 84.000 100 13 3 3535 3634 108320731 108320827 8.000000e-15 93.5
33 TraesCS3B01G504200 chr6B 81.447 1590 262 19 4916 6488 643264141 643265714 0.000000e+00 1271.0
34 TraesCS3B01G504200 chr5A 78.374 2067 367 49 4662 6679 705844264 705842229 0.000000e+00 1267.0
35 TraesCS3B01G504200 chr5D 78.756 1817 344 32 4925 6719 355203672 355205468 0.000000e+00 1179.0


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 TraesCS3B01G504200 chr3B 748610498 748617981 7483 False 4306.666667 6562 100.000000 1 7484 3 chr3B.!!$F6 7483
1 TraesCS3B01G504200 chr3B 747834474 747840897 6423 False 1458.000000 1469 78.309500 4183 6568 2 chr3B.!!$F3 2385
2 TraesCS3B01G504200 chr3B 747851001 747853372 2371 False 1458.000000 1458 78.305000 4183 6568 1 chr3B.!!$F2 2385
3 TraesCS3B01G504200 chr3B 747821998 747824369 2371 False 1447.000000 1447 78.223000 4183 6568 1 chr3B.!!$F1 2385
4 TraesCS3B01G504200 chr3B 748450284 748458025 7741 False 807.750000 1895 83.269500 473 7472 4 chr3B.!!$F5 6999
5 TraesCS3B01G504200 chr3B 748410733 748413069 2336 False 462.500000 568 82.360500 473 3002 2 chr3B.!!$F4 2529
6 TraesCS3B01G504200 chr3A 697368897 697376936 8039 False 2143.000000 5204 94.969600 1 7481 5 chr3A.!!$F2 7480
7 TraesCS3B01G504200 chr3A 697275134 697280988 5854 False 895.000000 2143 81.287333 378 7472 3 chr3A.!!$F1 7094
8 TraesCS3B01G504200 chr3D 561444149 561446820 2671 False 977.033333 2608 92.921000 5200 7484 3 chr3D.!!$F2 2284
9 TraesCS3B01G504200 chr6D 427482782 427485214 2432 False 1507.000000 1507 78.448000 4074 6488 1 chr6D.!!$F1 2414
10 TraesCS3B01G504200 chrUn 331495101 331496403 1302 False 1168.000000 1168 82.916000 5258 6568 1 chrUn.!!$F1 1310
11 TraesCS3B01G504200 chrUn 108320731 108323556 2825 False 692.250000 1291 81.310000 3535 6662 2 chrUn.!!$F2 3127
12 TraesCS3B01G504200 chr6B 643264141 643265714 1573 False 1271.000000 1271 81.447000 4916 6488 1 chr6B.!!$F1 1572
13 TraesCS3B01G504200 chr5A 705842229 705844264 2035 True 1267.000000 1267 78.374000 4662 6679 1 chr5A.!!$R1 2017
14 TraesCS3B01G504200 chr5D 355203672 355205468 1796 False 1179.000000 1179 78.756000 4925 6719 1 chr5D.!!$F1 1794

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
53 54 1.205417 CCTGGCATTTCACAACATCCC 59.795 52.381 0.00 0.00 0.00 3.85 F
742 1449 2.700371 TGATGTCTGCACCGGAATAGAT 59.300 45.455 9.46 0.00 0.00 1.98 F
1671 2389 1.379642 CGAAAATGCTGGAGGGGAGC 61.380 60.000 0.00 0.00 36.95 4.70 F
3185 3993 0.110644 GATCGATTCATTTCGGCGCC 60.111 55.000 19.07 19.07 39.56 6.53 F
3251 4059 0.452987 CGGATTTGATGGCCACACAG 59.547 55.000 8.16 0.00 0.00 3.66 F
5047 6022 1.009829 GTGGTGCGGCTCTATTTGAG 58.990 55.000 0.00 0.00 45.33 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1027 1740 1.008538 GCTTGTCAAAGGTGTGCCG 60.009 57.895 0.00 0.0 40.50 5.69 R
2288 3025 3.034721 AGCAATGCATTTTGGTCACTG 57.965 42.857 9.83 0.0 32.06 3.66 R
3361 4169 0.037605 AGTTTTCCTAGCCGTCGTGG 60.038 55.000 0.00 0.0 42.50 4.94 R
5151 6130 2.221749 CCCGTGATGCACTAATCGAATG 59.778 50.000 0.00 0.0 31.34 2.67 R
5294 6291 1.454479 CATCCACCCATGACCTGCC 60.454 63.158 0.00 0.0 0.00 4.85 R
6968 8947 0.884704 GCAACAGAAACTCCGCTCCA 60.885 55.000 0.00 0.0 0.00 3.86 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
40 41 5.193728 TCCTAAATTCTAACTTCCCTGGCAT 59.806 40.000 0.00 0.00 0.00 4.40
45 46 3.686016 TCTAACTTCCCTGGCATTTCAC 58.314 45.455 0.00 0.00 0.00 3.18
53 54 1.205417 CCTGGCATTTCACAACATCCC 59.795 52.381 0.00 0.00 0.00 3.85
172 173 9.793259 GTAATCTTATTCTTGGTGATAATGGGA 57.207 33.333 0.00 0.00 0.00 4.37
190 191 4.335416 TGGGAAAATCTGGTCAATCTGAC 58.665 43.478 0.00 0.00 46.23 3.51
191 192 4.043310 TGGGAAAATCTGGTCAATCTGACT 59.957 41.667 6.74 0.00 46.19 3.41
210 211 6.940298 TCTGACTACCTTTTTGGATTTACCTG 59.060 38.462 0.00 0.00 39.71 4.00
213 214 7.393234 TGACTACCTTTTTGGATTTACCTGATG 59.607 37.037 0.00 0.00 39.71 3.07
226 227 5.732331 TTACCTGATGATTTTCCTCCCAT 57.268 39.130 0.00 0.00 0.00 4.00
363 365 7.881142 TGGTGTATATTATTTGTGCATTAGCC 58.119 34.615 0.00 0.00 41.13 3.93
378 380 5.106869 TGCATTAGCCTACAGTTTTGTTACG 60.107 40.000 0.00 0.00 41.13 3.18
391 393 5.346822 AGTTTTGTTACGAAGTGCTATACGG 59.653 40.000 0.00 0.00 45.73 4.02
407 409 6.153510 TGCTATACGGATTTCATGCTAGAGAT 59.846 38.462 0.00 0.00 0.00 2.75
471 1173 7.149307 GGTAGAATTATTGCTCTCCTCTACAC 58.851 42.308 8.20 0.00 36.89 2.90
474 1176 7.271511 AGAATTATTGCTCTCCTCTACACTTG 58.728 38.462 0.00 0.00 0.00 3.16
525 1227 9.846248 ATTGAATGAAGTGTGCTTAACTAATTC 57.154 29.630 11.32 11.32 34.61 2.17
661 1367 3.700038 CTGGTACCTCAGGTAGTAACTGG 59.300 52.174 15.25 2.68 39.02 4.00
699 1405 3.051081 AGAGCTAGCCAAGACTTGTTG 57.949 47.619 12.13 1.04 0.00 3.33
711 1418 9.686683 AGCCAAGACTTGTTGTTATTAAGATAT 57.313 29.630 14.03 0.00 0.00 1.63
733 1440 2.751166 AGTAGTGTGATGTCTGCACC 57.249 50.000 0.00 0.00 35.43 5.01
742 1449 2.700371 TGATGTCTGCACCGGAATAGAT 59.300 45.455 9.46 0.00 0.00 1.98
803 1511 5.036737 GTCCAATGTGTTTGTGAGTCAAAG 58.963 41.667 0.00 0.00 45.15 2.77
909 1618 5.991933 TGGCTGGATGTTTTGCTTTTATA 57.008 34.783 0.00 0.00 0.00 0.98
1027 1740 1.477553 ACCATGATGACACATTGGCC 58.522 50.000 0.00 0.00 0.00 5.36
1031 1744 2.035469 ATGACACATTGGCCGGCA 59.965 55.556 30.85 9.36 0.00 5.69
1032 1745 2.270297 GATGACACATTGGCCGGCAC 62.270 60.000 30.85 18.39 0.00 5.01
1042 1755 2.904866 GCCGGCACACCTTTGACA 60.905 61.111 24.80 0.00 0.00 3.58
1044 1757 1.654220 CCGGCACACCTTTGACAAG 59.346 57.895 0.00 0.00 0.00 3.16
1058 1772 6.861055 ACCTTTGACAAGCATGTATTTAAACG 59.139 34.615 0.00 0.00 40.74 3.60
1067 1781 9.502145 CAAGCATGTATTTAAACGTGTTGATAT 57.498 29.630 0.00 0.00 38.41 1.63
1147 1861 8.734386 AGTTCAAAATTCTTACTTATCTGGCAG 58.266 33.333 8.58 8.58 0.00 4.85
1166 1880 3.305539 GCAGTTCACCTCATGCATTTGAA 60.306 43.478 0.00 0.98 38.54 2.69
1287 2001 4.164843 TCTAGGTGATAATGGGCAAACC 57.835 45.455 0.00 0.00 40.81 3.27
1288 2002 4.447762 ATCTAGGTGATAATGGGCAAACCC 60.448 45.833 0.00 0.00 44.84 4.11
1523 2237 3.658351 GCTACGCATAAAGTGGTCAAG 57.342 47.619 0.00 0.00 0.00 3.02
1527 2241 3.596214 ACGCATAAAGTGGTCAAGTAGG 58.404 45.455 0.00 0.00 0.00 3.18
1534 2248 7.418025 GCATAAAGTGGTCAAGTAGGTAGAGAT 60.418 40.741 0.00 0.00 0.00 2.75
1535 2249 6.936968 AAAGTGGTCAAGTAGGTAGAGATT 57.063 37.500 0.00 0.00 0.00 2.40
1536 2250 5.923733 AGTGGTCAAGTAGGTAGAGATTG 57.076 43.478 0.00 0.00 0.00 2.67
1671 2389 1.379642 CGAAAATGCTGGAGGGGAGC 61.380 60.000 0.00 0.00 36.95 4.70
1720 2438 8.419076 TTTCTTCTTGCTTTTTAATGTGTTCC 57.581 30.769 0.00 0.00 0.00 3.62
1737 2455 5.694910 TGTGTTCCAACTCTAAAATCGAGTC 59.305 40.000 0.00 0.00 40.65 3.36
1783 2501 7.434307 AGAAATTTCATTTGCGATATCTTGCAG 59.566 33.333 19.99 0.00 42.72 4.41
1785 2503 2.944349 TCATTTGCGATATCTTGCAGCA 59.056 40.909 0.34 0.00 42.72 4.41
1845 2563 8.017418 TCTACAATTGATTTCCTTGTGGTTTT 57.983 30.769 13.59 0.00 34.26 2.43
1928 2661 3.885297 GGGATAAGTGATGGTGATGTTGG 59.115 47.826 0.00 0.00 0.00 3.77
2253 2990 1.398692 ATTTGTGTTTGCACCGTCCT 58.601 45.000 0.00 0.00 44.65 3.85
2288 3025 0.463620 TGGTTTTGCTTTCAGGGCAC 59.536 50.000 0.00 0.00 39.55 5.01
2490 3227 6.069673 AGGTGATGAAGATACATTGGGTAACA 60.070 38.462 0.00 0.00 35.14 2.41
2665 3457 1.089112 GCACGCCCCTTTACGTATTT 58.911 50.000 0.00 0.00 41.32 1.40
2714 3506 5.555017 AGCATTTCATGAGTGTAGACTTGT 58.445 37.500 10.66 0.00 30.16 3.16
2716 3508 5.625251 CATTTCATGAGTGTAGACTTGTGC 58.375 41.667 0.00 0.00 30.16 4.57
2848 3640 4.528596 CCTCCCTCAAAGTACTCAAAGAGA 59.471 45.833 12.64 0.84 33.32 3.10
2867 3659 4.525100 AGAGACTGTGAAGGAGTAGAAACC 59.475 45.833 0.00 0.00 0.00 3.27
2878 3670 3.864003 GGAGTAGAAACCGAGTGTATTGC 59.136 47.826 0.00 0.00 0.00 3.56
2967 3762 8.801715 TTCTTCAGTTCTTGTGCATTTAAATC 57.198 30.769 0.00 0.00 0.00 2.17
3013 3808 4.300189 TGAGGATGTTGGTTTTGAAACG 57.700 40.909 0.95 0.00 39.77 3.60
3041 3836 3.181487 ACAAATCACACCAAGAGCAACAC 60.181 43.478 0.00 0.00 0.00 3.32
3056 3851 4.798152 CACGTACGTGCAAAGCTG 57.202 55.556 32.93 9.58 39.39 4.24
3084 3892 3.904136 ACAAGCACACAAGCTATGAAC 57.096 42.857 4.95 0.00 45.89 3.18
3086 3894 3.251729 ACAAGCACACAAGCTATGAACAG 59.748 43.478 4.95 0.00 45.89 3.16
3185 3993 0.110644 GATCGATTCATTTCGGCGCC 60.111 55.000 19.07 19.07 39.56 6.53
3217 4025 3.757493 ACTCCTACCTAACTTGACGACAG 59.243 47.826 0.00 0.00 0.00 3.51
3230 4038 4.584327 TGACGACAGAAAACTCAGATCA 57.416 40.909 0.00 0.00 0.00 2.92
3251 4059 0.452987 CGGATTTGATGGCCACACAG 59.547 55.000 8.16 0.00 0.00 3.66
3270 4078 4.268687 CTCGTGTGGAGCCTGTTC 57.731 61.111 0.00 0.00 35.63 3.18
3361 4169 8.265055 ACTAGGCTAGTCTAGATATCTCATGAC 58.735 40.741 32.94 15.10 39.14 3.06
3363 4171 6.012069 AGGCTAGTCTAGATATCTCATGACCA 60.012 42.308 20.43 12.22 30.84 4.02
3364 4172 6.094881 GGCTAGTCTAGATATCTCATGACCAC 59.905 46.154 20.43 13.96 30.84 4.16
3367 4175 5.703592 AGTCTAGATATCTCATGACCACGAC 59.296 44.000 20.43 10.98 30.84 4.34
3368 4176 3.906014 AGATATCTCATGACCACGACG 57.094 47.619 0.00 0.00 0.00 5.12
3520 4368 9.853555 ATACACATAAGAATTCAAAATTTGCGA 57.146 25.926 8.44 0.00 0.00 5.10
3580 4428 7.677892 AGATATAGTGTACAGTCGGAGTGATA 58.322 38.462 19.25 6.06 0.00 2.15
3609 4457 4.281182 AGAGTTCGGAAAGAAGTAGAAGCA 59.719 41.667 0.00 0.00 42.26 3.91
3645 4493 5.884232 TGCTGAATACTGAAGAAAGATGCAT 59.116 36.000 0.00 0.00 0.00 3.96
3958 4806 7.856145 AGAATAACATGCAAGTTAGGAAGAG 57.144 36.000 18.33 0.00 37.39 2.85
4070 4919 7.675619 AGAATATCAAACTCACCCCAAGAAATT 59.324 33.333 0.00 0.00 0.00 1.82
4126 4999 3.680777 AAACTGAGGGGGTCAAGAAAA 57.319 42.857 0.00 0.00 33.60 2.29
4127 5000 2.658807 ACTGAGGGGGTCAAGAAAAC 57.341 50.000 0.00 0.00 33.60 2.43
4130 5003 3.295973 CTGAGGGGGTCAAGAAAACAAA 58.704 45.455 0.00 0.00 33.60 2.83
4292 5165 6.882610 TTGCTAGAAATATGTAATGCCTGG 57.117 37.500 0.00 0.00 0.00 4.45
4421 5311 6.044637 TGGATGGGAATATCATCATGTTCTCA 59.955 38.462 0.00 0.00 42.85 3.27
4492 5396 3.727726 TGAAAAGCGTCATGAAGAGACA 58.272 40.909 13.18 2.28 35.77 3.41
4523 5451 6.374333 ACTGTGTTTCACCACCATTATACATC 59.626 38.462 0.00 0.00 34.35 3.06
4527 5455 7.066887 GTGTTTCACCACCATTATACATCATGA 59.933 37.037 0.00 0.00 0.00 3.07
4550 5479 6.147656 TGACATGTAACAAAGCTAGATGTGTG 59.852 38.462 4.17 0.00 34.42 3.82
4700 5630 7.919690 TCTCAAATAGCATTTGGAGAATAACG 58.080 34.615 16.44 0.00 0.00 3.18
4747 5681 9.992910 TCATCGATTTAGTTCTCATTCAATTTG 57.007 29.630 0.00 0.00 0.00 2.32
4773 5710 4.489737 TCTCTTGTTTCTGGGGAAGTAGA 58.510 43.478 0.00 0.00 32.61 2.59
4937 5912 8.034215 TCCATTATACTTTTGTGCAGGATTTTG 58.966 33.333 0.00 0.00 0.00 2.44
4950 5925 5.769662 TGCAGGATTTTGTACAAGAGATGTT 59.230 36.000 8.56 0.00 43.63 2.71
4972 5947 6.486657 TGTTTGAGAAGGACGAGAAAATCAAT 59.513 34.615 0.00 0.00 0.00 2.57
5034 6009 8.511604 AATATGGCTATTATAAGATGTGGTGC 57.488 34.615 0.00 0.00 0.00 5.01
5047 6022 1.009829 GTGGTGCGGCTCTATTTGAG 58.990 55.000 0.00 0.00 45.33 3.02
5099 6077 7.284034 CCATGGATAAGGCACCTTATGATATTC 59.716 40.741 23.45 10.78 45.88 1.75
5151 6130 7.014711 TGGATGGTGATCTCTCTGTATTAGTTC 59.985 40.741 0.00 0.00 0.00 3.01
5222 6211 5.943416 CCATCAGGTACTTTGTGGTTTGATA 59.057 40.000 0.00 0.00 34.60 2.15
5293 6290 8.306038 AGAACATTGCAATATGTGTACATTTGT 58.694 29.630 12.53 0.00 38.69 2.83
5294 6291 7.815398 ACATTGCAATATGTGTACATTTGTG 57.185 32.000 12.53 0.00 37.36 3.33
5308 6305 0.827089 TTTGTGGCAGGTCATGGGTG 60.827 55.000 0.00 0.00 0.00 4.61
5434 6432 4.459390 TTGGATTGCAACCATGATGAAG 57.541 40.909 17.71 0.00 37.26 3.02
5443 6441 6.063404 TGCAACCATGATGAAGATATGCTTA 58.937 36.000 0.00 0.00 36.83 3.09
5487 6485 3.688049 AACCTGCCCAATTATAGCCTT 57.312 42.857 0.00 0.00 0.00 4.35
5492 6490 4.154942 CTGCCCAATTATAGCCTTCCATT 58.845 43.478 0.00 0.00 0.00 3.16
5565 6563 5.258456 TCTACTACGAAAATGTGGCTAGG 57.742 43.478 0.00 0.00 0.00 3.02
5574 6572 4.162690 GTGGCTAGGGCTCCCACG 62.163 72.222 7.82 0.00 39.56 4.94
5904 6902 9.035607 AGTATTCAAAAGTATGTCATCGATCAC 57.964 33.333 0.00 0.00 0.00 3.06
6009 7007 0.106217 CAAAGGACCACACAAGGGGT 60.106 55.000 0.00 0.00 40.96 4.95
6502 7508 6.485830 AGTAGCCTAATCATTGCAGTTCTA 57.514 37.500 0.00 0.00 0.00 2.10
6688 7734 3.379452 AGACTATTCTTGGTCCCCTCAG 58.621 50.000 0.00 0.00 34.05 3.35
6709 7756 7.716998 CCTCAGCTATTTCAGAGCCTAATTTTA 59.283 37.037 0.00 0.00 41.06 1.52
6926 8905 6.374578 GCAGTAGAACAGATTGTTTTCTTCC 58.625 40.000 0.00 0.00 41.28 3.46
6928 8907 7.387948 GCAGTAGAACAGATTGTTTTCTTCCTA 59.612 37.037 0.00 0.00 41.28 2.94
6968 8947 4.941263 TCCGAACATAATTTTGCTAGCTGT 59.059 37.500 17.23 7.00 0.00 4.40
7030 9012 2.477104 TCCAGATGCAGTGGAGGATA 57.523 50.000 15.14 0.00 39.28 2.59
7131 10371 4.001017 CAAAATATTTTGCCGCGCATTT 57.999 36.364 24.00 0.00 40.76 2.32
7142 10382 2.476320 GCGCATTTCTGCTCCTCCC 61.476 63.158 0.30 0.00 46.65 4.30
7269 12090 5.337009 GCAAATGGATGATCTGTTGGTTCTT 60.337 40.000 0.00 0.00 0.00 2.52
7325 12250 2.238942 TGGCAGCTCATATTACCACG 57.761 50.000 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.963515 GTTGTGAAATGCCAGGGAAGT 59.036 47.619 0.00 0.00 0.00 3.01
40 41 5.261209 CAACTCAAAGGGATGTTGTGAAA 57.739 39.130 0.00 0.00 36.15 2.69
45 46 3.315191 ACGAACAACTCAAAGGGATGTTG 59.685 43.478 0.00 0.00 43.55 3.33
53 54 4.783450 GCAGTCTCAACGAACAACTCAAAG 60.783 45.833 0.00 0.00 0.00 2.77
190 191 7.938140 TCATCAGGTAAATCCAAAAAGGTAG 57.062 36.000 0.00 0.00 39.02 3.18
191 192 8.893563 AATCATCAGGTAAATCCAAAAAGGTA 57.106 30.769 0.00 0.00 39.02 3.08
210 211 7.310052 GGGCTATTTTATGGGAGGAAAATCATC 60.310 40.741 0.00 0.00 36.77 2.92
213 214 6.015095 CAGGGCTATTTTATGGGAGGAAAATC 60.015 42.308 0.00 0.00 36.77 2.17
283 284 3.011708 AGGGATGGCTAATTGGTTGAAGT 59.988 43.478 0.00 0.00 0.00 3.01
284 285 3.635591 AGGGATGGCTAATTGGTTGAAG 58.364 45.455 0.00 0.00 0.00 3.02
339 341 8.110860 AGGCTAATGCACAAATAATATACACC 57.889 34.615 0.00 0.00 41.91 4.16
363 365 5.652744 AGCACTTCGTAACAAAACTGTAG 57.347 39.130 0.00 0.00 0.00 2.74
378 380 4.752101 AGCATGAAATCCGTATAGCACTTC 59.248 41.667 0.00 0.00 0.00 3.01
391 393 9.234384 CACAATTGAAATCTCTAGCATGAAATC 57.766 33.333 13.59 0.00 0.00 2.17
407 409 9.878667 ATCATTTGCAAGATATCACAATTGAAA 57.121 25.926 21.45 10.97 36.54 2.69
440 442 5.116084 AGAGCAATAATTCTACCCTGCAA 57.884 39.130 0.00 0.00 32.21 4.08
471 1173 7.908230 TGAAAGCAAACAATTAGAAAAGCAAG 58.092 30.769 0.00 0.00 0.00 4.01
508 1210 5.003804 CCTGTGGAATTAGTTAAGCACACT 58.996 41.667 0.00 0.00 0.00 3.55
525 1227 0.323629 TCGTTCCTAAAGCCCTGTGG 59.676 55.000 0.00 0.00 0.00 4.17
661 1367 9.756461 GCTAGCTCTTGTACTTAAATACAAAAC 57.244 33.333 7.70 3.85 42.88 2.43
711 1418 4.036380 CGGTGCAGACATCACACTACTATA 59.964 45.833 0.00 0.00 36.22 1.31
712 1419 3.181486 CGGTGCAGACATCACACTACTAT 60.181 47.826 0.00 0.00 36.22 2.12
713 1420 2.163613 CGGTGCAGACATCACACTACTA 59.836 50.000 0.00 0.00 36.22 1.82
714 1421 1.067565 CGGTGCAGACATCACACTACT 60.068 52.381 0.00 0.00 36.22 2.57
768 1475 5.452078 ACACATTGGACATAACAACAAGG 57.548 39.130 0.00 0.00 0.00 3.61
803 1511 4.373156 AGTCAACTATGGGCCCATATTC 57.627 45.455 38.83 26.01 38.13 1.75
871 1580 8.754080 ACATCCAGCCATTAATATACTACTCTC 58.246 37.037 0.00 0.00 0.00 3.20
1008 1721 1.477553 GGCCAATGTGTCATCATGGT 58.522 50.000 0.00 0.00 0.00 3.55
1027 1740 1.008538 GCTTGTCAAAGGTGTGCCG 60.009 57.895 0.00 0.00 40.50 5.69
1031 1744 5.789643 AAATACATGCTTGTCAAAGGTGT 57.210 34.783 8.74 0.00 37.28 4.16
1032 1745 7.148983 CGTTTAAATACATGCTTGTCAAAGGTG 60.149 37.037 8.74 0.00 37.28 4.00
1044 1757 9.716507 AGAATATCAACACGTTTAAATACATGC 57.283 29.630 0.00 0.00 0.00 4.06
1121 1835 8.635765 TGCCAGATAAGTAAGAATTTTGAACT 57.364 30.769 0.00 0.00 0.00 3.01
1124 1838 8.635765 AACTGCCAGATAAGTAAGAATTTTGA 57.364 30.769 0.00 0.00 0.00 2.69
1147 1861 4.510038 AGTTCAAATGCATGAGGTGAAC 57.490 40.909 24.36 24.36 45.37 3.18
1191 1905 7.099266 TGCATCAAATGGATAAACAAGGTAG 57.901 36.000 0.00 0.00 33.95 3.18
1504 2218 4.804139 CCTACTTGACCACTTTATGCGTAG 59.196 45.833 0.00 0.00 0.00 3.51
1518 2232 6.406065 GGAAGGACAATCTCTACCTACTTGAC 60.406 46.154 0.00 0.00 32.06 3.18
1523 2237 6.127793 TGTAGGAAGGACAATCTCTACCTAC 58.872 44.000 0.00 0.00 44.78 3.18
1527 2241 5.813157 GCTTTGTAGGAAGGACAATCTCTAC 59.187 44.000 0.00 0.00 36.71 2.59
1534 2248 3.326588 TGCTAGCTTTGTAGGAAGGACAA 59.673 43.478 17.23 0.00 35.03 3.18
1535 2249 2.903784 TGCTAGCTTTGTAGGAAGGACA 59.096 45.455 17.23 0.00 0.00 4.02
1536 2250 3.263261 GTGCTAGCTTTGTAGGAAGGAC 58.737 50.000 17.23 0.00 0.00 3.85
1629 2347 6.371548 TCGCATGAAGACAATAAGCTAAAGTT 59.628 34.615 0.00 0.00 0.00 2.66
1737 2455 4.348656 TCTAGCACGAAACAAGTATAGCG 58.651 43.478 0.00 0.00 0.00 4.26
1783 2501 5.476614 TCTATCATGCACTATCACATCTGC 58.523 41.667 0.00 0.00 0.00 4.26
1845 2563 8.777865 AGAAAACACGAATCAATATTGAGAGA 57.222 30.769 21.97 0.76 41.08 3.10
1868 2586 6.178324 TCACGATCACTCCTCTTAGTTAAGA 58.822 40.000 0.00 1.95 39.82 2.10
2253 2990 5.768317 CAAAACCAAAAGCCTCGATTAGAA 58.232 37.500 0.00 0.00 0.00 2.10
2288 3025 3.034721 AGCAATGCATTTTGGTCACTG 57.965 42.857 9.83 0.00 32.06 3.66
2295 3032 7.124347 ACAGTAATTCAAGCAATGCATTTTG 57.876 32.000 9.83 13.00 0.00 2.44
2393 3130 7.673180 TCTCTTGTGCATGATACATATGATCA 58.327 34.615 10.38 13.76 37.70 2.92
2541 3278 3.686241 TCACCATTCGAGCTCTCAAAATG 59.314 43.478 12.85 14.54 34.65 2.32
2714 3506 3.321396 TCAGGTGCTCAAATTTCATTGCA 59.679 39.130 0.00 0.00 0.00 4.08
2716 3508 7.429636 AAAATCAGGTGCTCAAATTTCATTG 57.570 32.000 0.00 0.00 0.00 2.82
2848 3640 3.228453 TCGGTTTCTACTCCTTCACAGT 58.772 45.455 0.00 0.00 0.00 3.55
2867 3659 1.800586 AGCAACACAGCAATACACTCG 59.199 47.619 0.00 0.00 36.85 4.18
2878 3670 7.172757 GTCAAAATTACAAACAAGCAACACAG 58.827 34.615 0.00 0.00 0.00 3.66
2967 3762 8.916654 CAAGTCACATGTCTTGTAGTAACTAAG 58.083 37.037 15.72 0.00 36.57 2.18
3013 3808 4.293415 CTCTTGGTGTGATTTGTTCAAGC 58.707 43.478 0.00 0.00 35.70 4.01
3041 3836 1.841663 AAGCCAGCTTTGCACGTACG 61.842 55.000 15.01 15.01 31.29 3.67
3056 3851 2.195922 CTTGTGTGCTTGTTTGAAGCC 58.804 47.619 4.05 0.00 42.36 4.35
3084 3892 6.374565 AACACGTATTCCTACTAGCTACTG 57.625 41.667 0.00 0.00 0.00 2.74
3086 3894 6.558909 ACAAACACGTATTCCTACTAGCTAC 58.441 40.000 0.00 0.00 0.00 3.58
3142 3950 5.593909 CGATCCAATCTAGATCTAGCTCCAT 59.406 44.000 22.81 9.88 38.39 3.41
3152 3960 6.765915 TGAATCGATCGATCCAATCTAGAT 57.234 37.500 29.48 10.97 33.08 1.98
3217 4025 6.241207 TCAAATCCGTTGATCTGAGTTTTC 57.759 37.500 0.00 0.00 41.47 2.29
3230 4038 0.887933 GTGTGGCCATCAAATCCGTT 59.112 50.000 9.72 0.00 0.00 4.44
3293 4101 3.142951 CCTTGTAAACATCAACCCGTGA 58.857 45.455 0.00 0.00 41.67 4.35
3294 4102 2.227865 CCCTTGTAAACATCAACCCGTG 59.772 50.000 0.00 0.00 0.00 4.94
3295 4103 2.510613 CCCTTGTAAACATCAACCCGT 58.489 47.619 0.00 0.00 0.00 5.28
3296 4104 1.816224 CCCCTTGTAAACATCAACCCG 59.184 52.381 0.00 0.00 0.00 5.28
3350 4158 1.000163 GCCGTCGTGGTCATGAGATAT 60.000 52.381 0.00 0.00 41.21 1.63
3361 4169 0.037605 AGTTTTCCTAGCCGTCGTGG 60.038 55.000 0.00 0.00 42.50 4.94
3363 4171 3.446516 AGATTAGTTTTCCTAGCCGTCGT 59.553 43.478 0.00 0.00 0.00 4.34
3364 4172 4.043037 AGATTAGTTTTCCTAGCCGTCG 57.957 45.455 0.00 0.00 0.00 5.12
3367 4175 5.753921 CACCTAAGATTAGTTTTCCTAGCCG 59.246 44.000 0.00 0.00 0.00 5.52
3368 4176 6.056236 CCACCTAAGATTAGTTTTCCTAGCC 58.944 44.000 0.00 0.00 0.00 3.93
3580 4428 5.476091 ACTTCTTTCCGAACTCTTCTCAT 57.524 39.130 0.00 0.00 0.00 2.90
3945 4793 6.994221 TGAAGACCTTACTCTTCCTAACTTG 58.006 40.000 6.50 0.00 43.90 3.16
3947 4795 7.800300 ATTGAAGACCTTACTCTTCCTAACT 57.200 36.000 6.50 0.00 43.90 2.24
4126 4999 5.695851 ATTCAACTCTCGCTGAATTTTGT 57.304 34.783 0.00 0.00 38.79 2.83
4127 5000 6.024049 GGTATTCAACTCTCGCTGAATTTTG 58.976 40.000 2.90 0.00 41.41 2.44
4130 5003 4.872691 CAGGTATTCAACTCTCGCTGAATT 59.127 41.667 2.90 0.00 41.41 2.17
4270 5143 6.186420 TCCAGGCATTACATATTTCTAGCA 57.814 37.500 0.00 0.00 0.00 3.49
4292 5165 4.911514 TGCTTTCCCTACTTGTTGTTTC 57.088 40.909 0.00 0.00 0.00 2.78
4421 5311 5.361571 TGATAAGGCAAATGCATGTCTTCAT 59.638 36.000 10.32 4.03 41.19 2.57
4473 5377 4.380531 TCTTGTCTCTTCATGACGCTTTT 58.619 39.130 0.00 0.00 37.26 2.27
4492 5396 3.214328 GGTGGTGAAACACAGTCATCTT 58.786 45.455 0.19 0.00 43.08 2.40
4523 5451 7.148356 ACACATCTAGCTTTGTTACATGTCATG 60.148 37.037 11.41 11.41 0.00 3.07
4527 5455 5.106555 GCACACATCTAGCTTTGTTACATGT 60.107 40.000 2.69 2.69 0.00 3.21
4550 5479 3.686016 TGGACTGGAATAAACTGAAGGC 58.314 45.455 0.00 0.00 0.00 4.35
4688 5618 5.011738 AGGAACTCAACTCGTTATTCTCCAA 59.988 40.000 0.00 0.00 0.00 3.53
4700 5630 9.922305 CGATGAAATAATTTAGGAACTCAACTC 57.078 33.333 0.00 0.00 41.75 3.01
4738 5672 9.101655 CCAGAAACAAGAGAAAACAAATTGAAT 57.898 29.630 0.00 0.00 0.00 2.57
4747 5681 4.645136 ACTTCCCCAGAAACAAGAGAAAAC 59.355 41.667 0.00 0.00 0.00 2.43
4912 5887 7.818930 ACAAAATCCTGCACAAAAGTATAATGG 59.181 33.333 0.00 0.00 0.00 3.16
4937 5912 5.346281 CGTCCTTCTCAAACATCTCTTGTAC 59.654 44.000 0.00 0.00 37.68 2.90
4950 5925 6.710295 TGAATTGATTTTCTCGTCCTTCTCAA 59.290 34.615 0.00 0.00 0.00 3.02
5034 6009 3.743396 GGCAATAGTCTCAAATAGAGCCG 59.257 47.826 0.00 0.00 44.35 5.52
5099 6077 8.960591 ACACCTAGGAATGTTTAATCAGAAATG 58.039 33.333 17.98 0.00 0.00 2.32
5113 6092 2.505407 TCACCATCCACACCTAGGAATG 59.495 50.000 17.98 12.71 38.93 2.67
5114 6093 2.845659 TCACCATCCACACCTAGGAAT 58.154 47.619 17.98 0.00 38.93 3.01
5151 6130 2.221749 CCCGTGATGCACTAATCGAATG 59.778 50.000 0.00 0.00 31.34 2.67
5293 6290 1.930133 ATCCACCCATGACCTGCCA 60.930 57.895 0.00 0.00 0.00 4.92
5294 6291 1.454479 CATCCACCCATGACCTGCC 60.454 63.158 0.00 0.00 0.00 4.85
5308 6305 3.065925 CCTCCAAAAGAATCGAAGCATCC 59.934 47.826 0.00 0.00 0.00 3.51
5434 6432 7.899973 ACCATTGGATTTGGAATAAGCATATC 58.100 34.615 10.37 0.00 37.69 1.63
5487 6485 4.069312 TCTGGTCACCCTAACTAATGGA 57.931 45.455 0.00 0.00 0.00 3.41
5492 6490 3.839323 TCCTTCTGGTCACCCTAACTA 57.161 47.619 0.00 0.00 34.23 2.24
5565 6563 2.189521 CATACACCCGTGGGAGCC 59.810 66.667 13.01 0.00 38.96 4.70
5904 6902 5.455392 CAGACAAGATTGTACCTTTTGCAG 58.545 41.667 0.00 0.00 42.43 4.41
5950 6948 6.365970 TTCAATCTCTTGAGGCTCTAACTT 57.634 37.500 16.72 0.00 42.19 2.66
5955 6953 6.742082 GCAGATATTCAATCTCTTGAGGCTCT 60.742 42.308 16.72 0.00 42.19 4.09
6009 7007 3.379057 TGTATCTATTTGTGTCGCCGAGA 59.621 43.478 0.00 0.00 0.00 4.04
6709 7756 4.969359 ACTAAATGTACTCCCTGCCTGTAT 59.031 41.667 0.00 0.00 0.00 2.29
6947 8926 5.030295 CCACAGCTAGCAAAATTATGTTCG 58.970 41.667 18.83 0.00 0.00 3.95
6968 8947 0.884704 GCAACAGAAACTCCGCTCCA 60.885 55.000 0.00 0.00 0.00 3.86
7017 8997 2.035961 GCGTCTTATATCCTCCACTGCA 59.964 50.000 0.00 0.00 0.00 4.41
7030 9012 1.670811 CCCTGAATTTGCGCGTCTTAT 59.329 47.619 8.43 0.00 0.00 1.73
7131 10371 3.003173 CCAACGGGGAGGAGCAGA 61.003 66.667 0.00 0.00 40.01 4.26
7142 10382 2.045926 CCAGGAGGCTTCCAACGG 60.046 66.667 18.32 10.44 46.64 4.44
7325 12250 8.915871 TTGAATTTGTTAATATGAGCTGCTTC 57.084 30.769 2.53 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.