Multiple sequence alignment - TraesCS3D01G216400

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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 TraesCS3D01G216400 chr3D 100.000 3753 0 0 1 3753 293608758 293612510 0.000000e+00 6931.0
1 TraesCS3D01G216400 chr3B 94.395 2926 78 22 856 3753 387183288 387186155 0.000000e+00 4416.0
2 TraesCS3D01G216400 chr3B 92.032 866 64 5 1 865 387182225 387183086 0.000000e+00 1212.0
3 TraesCS3D01G216400 chr6A 91.667 132 11 0 44 175 334589628 334589497 2.300000e-42 183.0
4 TraesCS3D01G216400 chr6B 87.500 152 18 1 44 195 480240663 480240813 1.390000e-39 174.0
5 TraesCS3D01G216400 chr6B 87.692 65 8 0 379 443 673855551 673855487 4.020000e-10 76.8
6 TraesCS3D01G216400 chr5D 88.194 144 17 0 52 195 406819668 406819525 4.980000e-39 172.0
7 TraesCS3D01G216400 chr5D 88.194 144 15 1 52 195 27484771 27484630 1.790000e-38 171.0
8 TraesCS3D01G216400 chr5D 84.106 151 24 0 1117 1267 58677822 58677972 3.020000e-31 147.0
9 TraesCS3D01G216400 chr5D 84.821 112 17 0 1117 1228 58947094 58947205 3.060000e-21 113.0
10 TraesCS3D01G216400 chr5D 79.470 151 28 3 1117 1266 58659227 58659375 1.840000e-18 104.0
11 TraesCS3D01G216400 chr4D 88.194 144 17 0 52 195 118428995 118428852 4.980000e-39 172.0
12 TraesCS3D01G216400 chr4D 76.953 256 44 13 1023 1276 93612662 93612420 8.460000e-27 132.0
13 TraesCS3D01G216400 chr7D 86.842 152 20 0 44 195 221305016 221305167 1.790000e-38 171.0
14 TraesCS3D01G216400 chr4B 87.013 154 17 3 44 195 142720431 142720279 1.790000e-38 171.0
15 TraesCS3D01G216400 chr1D 88.194 144 16 1 52 195 325693629 325693487 1.790000e-38 171.0
16 TraesCS3D01G216400 chr5B 82.192 146 26 0 1121 1266 63632076 63632221 3.940000e-25 126.0
17 TraesCS3D01G216400 chr5B 79.866 149 28 2 1120 1267 72631215 72631068 1.430000e-19 108.0
18 TraesCS3D01G216400 chr4A 78.947 190 34 6 1081 1270 488249107 488249290 1.420000e-24 124.0
19 TraesCS3D01G216400 chr3A 81.250 128 22 2 335 461 710799004 710798878 6.630000e-18 102.0
20 TraesCS3D01G216400 chr6D 76.974 152 33 2 1120 1270 380576959 380576809 6.680000e-13 86.1
21 TraesCS3D01G216400 chr7B 87.097 62 8 0 379 440 242667035 242666974 1.870000e-08 71.3
22 TraesCS3D01G216400 chr1B 87.097 62 8 0 379 440 11863598 11863537 1.870000e-08 71.3
23 TraesCS3D01G216400 chr2B 85.484 62 9 0 379 440 614307244 614307183 8.700000e-07 65.8
24 TraesCS3D01G216400 chr2B 85.484 62 9 0 379 440 614412672 614412611 8.700000e-07 65.8


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 TraesCS3D01G216400 chr3D 293608758 293612510 3752 False 6931 6931 100.0000 1 3753 1 chr3D.!!$F1 3752
1 TraesCS3D01G216400 chr3B 387182225 387186155 3930 False 2814 4416 93.2135 1 3753 2 chr3B.!!$F1 3752

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
362 364 0.107268 TGGCGATCACCATCCATCTG 59.893 55.0 0.0 0.0 33.75 2.90 F
659 661 0.112412 TTGAGAGGAAACAAGGGGGC 59.888 55.0 0.0 0.0 0.00 5.80 F
836 838 0.383231 GAAATCATCTTGCTGGGCCG 59.617 55.0 0.0 0.0 0.00 6.13 F
2207 2421 0.674895 AGTGCGCAAAGAGGCTAAGG 60.675 55.0 14.0 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2207 2421 0.107945 CTGAGGAAGGTAGGCAGCAC 60.108 60.0 0.00 0.00 0.00 4.40 R
2334 2553 0.179100 ATCAGATCAACCAGACGGCG 60.179 55.0 4.80 4.80 34.57 6.46 R
2447 2666 0.239347 GTGTGTGACTGCAGGCATTC 59.761 55.0 28.33 21.29 0.00 2.67 R
3295 3536 0.105593 CAGCACATCCGGTAGAGCAT 59.894 55.0 16.91 0.00 0.00 3.79 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
30 31 4.025313 GCTTAGATTTCTCAGCGGAATCAC 60.025 45.833 0.00 0.00 34.08 3.06
41 42 2.202866 GGAATCACTCCGCCAGAGA 58.797 57.895 5.45 0.00 46.50 3.10
48 49 2.373335 ACTCCGCCAGAGAGTGATAT 57.627 50.000 5.45 0.00 46.50 1.63
50 51 0.676184 TCCGCCAGAGAGTGATATGC 59.324 55.000 0.00 0.00 0.00 3.14
68 69 8.033038 GTGATATGCCTCCAACGTATCTATAAA 58.967 37.037 0.00 0.00 37.08 1.40
70 71 9.601217 GATATGCCTCCAACGTATCTATAAATT 57.399 33.333 0.00 0.00 34.54 1.82
75 76 9.874215 GCCTCCAACGTATCTATAAATTTTTAC 57.126 33.333 0.00 0.00 0.00 2.01
162 163 6.670902 TGGACTAACCTATTAACTTAGTGCCT 59.329 38.462 6.02 0.00 37.78 4.75
164 165 6.885922 ACTAACCTATTAACTTAGTGCCTGG 58.114 40.000 0.00 0.00 31.01 4.45
178 179 2.669569 CTGGTGCCAGTTCCCGTG 60.670 66.667 9.96 0.00 39.10 4.94
185 186 2.644992 CAGTTCCCGTGCTTTGCC 59.355 61.111 0.00 0.00 0.00 4.52
204 205 5.112129 TGCCTATTTCTTTAACCCTCTCC 57.888 43.478 0.00 0.00 0.00 3.71
205 206 4.538490 TGCCTATTTCTTTAACCCTCTCCA 59.462 41.667 0.00 0.00 0.00 3.86
206 207 5.126779 GCCTATTTCTTTAACCCTCTCCAG 58.873 45.833 0.00 0.00 0.00 3.86
207 208 5.339282 GCCTATTTCTTTAACCCTCTCCAGT 60.339 44.000 0.00 0.00 0.00 4.00
208 209 6.350103 CCTATTTCTTTAACCCTCTCCAGTC 58.650 44.000 0.00 0.00 0.00 3.51
211 212 2.158066 TCTTTAACCCTCTCCAGTCCCA 60.158 50.000 0.00 0.00 0.00 4.37
226 228 0.830648 TCCCATAGGCAGAAGAACCG 59.169 55.000 0.00 0.00 0.00 4.44
237 239 3.380637 GCAGAAGAACCGGAGAGTATACA 59.619 47.826 9.46 0.00 0.00 2.29
248 250 6.183360 ACCGGAGAGTATACAGATTTTCTTCC 60.183 42.308 9.46 2.00 0.00 3.46
249 251 5.915758 CGGAGAGTATACAGATTTTCTTCCG 59.084 44.000 5.50 9.05 0.00 4.30
351 353 1.995066 ATGTGGACCCTGGCGATCA 60.995 57.895 0.00 0.00 0.00 2.92
362 364 0.107268 TGGCGATCACCATCCATCTG 59.893 55.000 0.00 0.00 33.75 2.90
373 375 1.482182 CATCCATCTGGTGACTTCCGA 59.518 52.381 0.00 0.00 36.34 4.55
420 422 5.191426 CCACATCATCCAAGTCTTCTTCAT 58.809 41.667 0.00 0.00 0.00 2.57
440 442 5.271598 TCATGCAACCCTAATTCCTTCATT 58.728 37.500 0.00 0.00 0.00 2.57
443 445 7.564660 TCATGCAACCCTAATTCCTTCATTAAT 59.435 33.333 0.00 0.00 0.00 1.40
452 454 9.135189 CCTAATTCCTTCATTAATGATTCCACA 57.865 33.333 18.61 2.25 36.56 4.17
456 458 5.239306 TCCTTCATTAATGATTCCACATCGC 59.761 40.000 18.61 0.00 36.56 4.58
464 466 2.289631 TGATTCCACATCGCTGACTGTT 60.290 45.455 0.00 0.00 0.00 3.16
465 467 1.511850 TTCCACATCGCTGACTGTTG 58.488 50.000 0.00 0.00 0.00 3.33
478 480 0.949105 ACTGTTGTTGATCCCGACGC 60.949 55.000 0.00 0.00 0.00 5.19
479 481 0.670546 CTGTTGTTGATCCCGACGCT 60.671 55.000 0.00 0.00 0.00 5.07
504 506 1.375908 GACGCAGAACCTGATGGCA 60.376 57.895 0.00 0.00 36.63 4.92
524 526 1.625818 ACGCTCTTCTCCATCTGGTTT 59.374 47.619 0.00 0.00 36.34 3.27
586 588 1.739667 CACGTCATAGCCCCGATGA 59.260 57.895 0.00 0.00 0.00 2.92
601 603 0.175989 GATGAGTCCCGACCAAGACC 59.824 60.000 0.00 0.00 33.29 3.85
613 615 3.000819 AAGACCGGGTGGCGATCA 61.001 61.111 3.30 0.00 39.70 2.92
635 637 2.867109 AGGATCACCCTGTTTCAGTG 57.133 50.000 0.00 0.00 45.61 3.66
636 638 2.057922 AGGATCACCCTGTTTCAGTGT 58.942 47.619 0.00 0.00 45.61 3.55
659 661 0.112412 TTGAGAGGAAACAAGGGGGC 59.888 55.000 0.00 0.00 0.00 5.80
667 669 3.521765 AACAAGGGGGCAATGGCGA 62.522 57.895 0.00 0.00 42.47 5.54
691 693 0.868177 GAAGAAGCGAGCTCTACGGC 60.868 60.000 12.85 7.72 0.00 5.68
700 702 2.261671 CTCTACGGCGGTGCAGTT 59.738 61.111 13.24 0.00 38.09 3.16
716 718 5.429915 TGCAGTTGCCTTCGAGAGAATGA 62.430 47.826 1.06 0.00 43.80 2.57
727 729 4.491676 TCGAGAGAATGAAAACCCTAACG 58.508 43.478 0.00 0.00 37.03 3.18
760 762 0.451783 GGCAGGGACAAGCGTATTTG 59.548 55.000 0.00 0.00 32.45 2.32
826 828 3.703001 ACAGGTTCACGGAAATCATCT 57.297 42.857 0.00 0.00 0.00 2.90
836 838 0.383231 GAAATCATCTTGCTGGGCCG 59.617 55.000 0.00 0.00 0.00 6.13
845 847 2.172483 TTGCTGGGCCGAGAAGAGAC 62.172 60.000 20.35 0.00 0.00 3.36
846 848 2.650116 GCTGGGCCGAGAAGAGACA 61.650 63.158 20.35 0.00 0.00 3.41
854 856 1.480137 CCGAGAAGAGACATTGCTCCT 59.520 52.381 0.00 0.00 35.49 3.69
908 1121 5.821516 ACATCCTTGTACAAAACGACAAA 57.178 34.783 10.03 0.00 35.24 2.83
935 1148 2.408241 CCGTCTCTCCGTCTCCACC 61.408 68.421 0.00 0.00 0.00 4.61
936 1149 1.674651 CGTCTCTCCGTCTCCACCA 60.675 63.158 0.00 0.00 0.00 4.17
937 1150 1.241990 CGTCTCTCCGTCTCCACCAA 61.242 60.000 0.00 0.00 0.00 3.67
948 1161 1.152030 TCCACCAACTGCTCCCTCT 60.152 57.895 0.00 0.00 0.00 3.69
1036 1249 3.677648 GCATCATGCGGGCCATCC 61.678 66.667 4.39 0.00 31.71 3.51
1304 1517 4.434938 CGAAGCCGACGACGACGA 62.435 66.667 20.63 0.00 42.66 4.20
1401 1614 4.699522 GGACCCTTCCGCTGCGTT 62.700 66.667 21.59 0.00 29.98 4.84
1485 1698 2.262915 CTCTTCGCCGCCAAGTCT 59.737 61.111 0.00 0.00 0.00 3.24
1623 1836 0.796312 CGGACACAAATGACCTTCCG 59.204 55.000 0.00 0.00 38.39 4.30
1650 1863 2.030562 CACGTCTTCCCGCACCTT 59.969 61.111 0.00 0.00 0.00 3.50
1695 1908 2.675317 CGACATCAAGACCAAGGACCTC 60.675 54.545 0.00 0.00 0.00 3.85
1704 1917 2.603776 AAGGACCTCGACCGCCTT 60.604 61.111 0.00 2.89 35.98 4.35
2020 2234 3.634283 GTCATCGAGGTTAGCTAGCTTC 58.366 50.000 24.88 13.34 33.94 3.86
2021 2235 2.290916 TCATCGAGGTTAGCTAGCTTCG 59.709 50.000 28.32 28.32 33.94 3.79
2156 2370 1.156736 CACGACCACCATTCCAAGTC 58.843 55.000 0.00 0.00 0.00 3.01
2170 2384 1.649664 CAAGTCTCAAGATCCTGGCG 58.350 55.000 0.00 0.00 0.00 5.69
2207 2421 0.674895 AGTGCGCAAAGAGGCTAAGG 60.675 55.000 14.00 0.00 0.00 2.69
2245 2459 1.281867 AGATGCTTCCCCAATGTCGAA 59.718 47.619 0.00 0.00 0.00 3.71
2275 2489 5.300034 GCATGTCATGGTGAGATTCCATTTA 59.700 40.000 14.64 0.00 42.92 1.40
2332 2551 9.330063 TCAACTTATTATCTGATGATTGTGTCC 57.670 33.333 0.00 0.00 34.32 4.02
2334 2553 6.425114 ACTTATTATCTGATGATTGTGTCCGC 59.575 38.462 0.00 0.00 34.32 5.54
2337 2556 2.040213 CTGATGATTGTGTCCGCGCC 62.040 60.000 0.00 0.00 0.00 6.53
2447 2666 1.224069 GCATGATGTCGGACCCATCG 61.224 60.000 5.55 5.92 41.28 3.84
2527 2746 0.680061 AGGTCGTGTTCCTCAGGTTC 59.320 55.000 0.00 0.00 34.10 3.62
2531 2750 1.002250 CGTGTTCCTCAGGTTCGTCG 61.002 60.000 0.00 0.00 0.00 5.12
2659 2878 2.505777 CGTGCCAGCAGAGACTCG 60.506 66.667 0.00 0.00 0.00 4.18
2801 3020 6.309009 GCTGATATGTTTCGATCGTGATACAT 59.691 38.462 15.94 19.38 41.41 2.29
2809 3028 3.059166 CGATCGTGATACATCATTGCCA 58.941 45.455 7.03 0.00 39.30 4.92
2823 3042 6.592607 ACATCATTGCCATTTCTTTTGCTAAG 59.407 34.615 0.00 0.00 0.00 2.18
2826 3045 5.720371 TTGCCATTTCTTTTGCTAAGCTA 57.280 34.783 0.00 0.00 0.00 3.32
2853 3072 8.440021 CAACATACTTTGCTTGTTTGAGTATC 57.560 34.615 0.00 0.00 32.74 2.24
2854 3073 6.831769 ACATACTTTGCTTGTTTGAGTATCG 58.168 36.000 0.00 0.00 38.61 2.92
2855 3074 4.147219 ACTTTGCTTGTTTGAGTATCGC 57.853 40.909 0.00 0.00 38.61 4.58
2856 3075 3.058224 ACTTTGCTTGTTTGAGTATCGCC 60.058 43.478 0.00 0.00 38.61 5.54
2887 3106 4.142026 TGGCAAGAGCGCTTATTTAGACTA 60.142 41.667 13.26 0.00 43.41 2.59
2888 3107 4.991687 GGCAAGAGCGCTTATTTAGACTAT 59.008 41.667 13.26 0.00 43.41 2.12
2970 3189 2.939103 GGTCAGTAGTCCATGCAATGTC 59.061 50.000 0.00 0.00 44.81 3.06
2973 3192 2.941064 CAGTAGTCCATGCAATGTCTGG 59.059 50.000 0.00 0.00 44.81 3.86
3018 3237 4.039004 TGGCTAAATTGCAGACATTTGTGT 59.961 37.500 5.31 0.00 34.04 3.72
3032 3251 6.919662 AGACATTTGTGTGTTTCATGTGATTC 59.080 34.615 0.00 0.00 31.16 2.52
3064 3283 6.086222 CCATTTTCTCGTGAATTCGTTTCAT 58.914 36.000 0.02 0.00 45.77 2.57
3065 3284 6.582295 CCATTTTCTCGTGAATTCGTTTCATT 59.418 34.615 0.02 0.00 45.77 2.57
3066 3285 7.114811 CCATTTTCTCGTGAATTCGTTTCATTT 59.885 33.333 0.02 0.00 45.77 2.32
3067 3286 7.979115 TTTTCTCGTGAATTCGTTTCATTTT 57.021 28.000 0.02 0.00 45.77 1.82
3068 3287 6.968004 TTCTCGTGAATTCGTTTCATTTTG 57.032 33.333 0.04 0.50 45.77 2.44
3080 3299 4.520078 GTTTCATTTTGTGTGCTGCATTG 58.480 39.130 5.27 0.00 0.00 2.82
3083 3302 3.556365 TCATTTTGTGTGCTGCATTGTTG 59.444 39.130 5.27 0.00 0.00 3.33
3094 3313 3.059461 GCTGCATTGTTGGTTGAAATGTG 60.059 43.478 0.00 0.00 34.48 3.21
3109 3328 9.744468 GGTTGAAATGTGTTACTGTATTTCTTT 57.256 29.630 11.92 0.84 39.23 2.52
3227 3468 6.833342 TGTATCGATCATGTGATTTGTCAG 57.167 37.500 0.00 0.00 34.37 3.51
3240 3481 7.592938 TGTGATTTGTCAGTTTGTGATTATCC 58.407 34.615 0.00 0.00 37.56 2.59
3246 3487 0.315869 GTTTGTGATTATCCGCGGCG 60.316 55.000 23.51 16.78 0.00 6.46
3262 3503 2.983930 GCGTTTGGTATTGCCGGCA 61.984 57.895 29.03 29.03 41.21 5.69
3272 3513 4.022416 TGGTATTGCCGGCATTTAATGATC 60.022 41.667 33.25 12.08 41.21 2.92
3295 3536 5.879777 TCGAATTGAAGAATGAAGGTGCATA 59.120 36.000 0.00 0.00 0.00 3.14
3302 3543 5.557576 AGAATGAAGGTGCATATGCTCTA 57.442 39.130 27.13 11.65 42.66 2.43
3376 3617 5.627499 TGAACTTATGTTGAAGGTGCATC 57.373 39.130 0.00 0.00 36.39 3.91
3377 3618 4.458989 TGAACTTATGTTGAAGGTGCATCC 59.541 41.667 0.00 0.00 36.39 3.51
3378 3619 3.009723 ACTTATGTTGAAGGTGCATCCG 58.990 45.455 0.00 0.00 41.99 4.18
3379 3620 2.779755 TATGTTGAAGGTGCATCCGT 57.220 45.000 0.00 0.00 41.99 4.69
3380 3621 1.167851 ATGTTGAAGGTGCATCCGTG 58.832 50.000 0.00 0.00 41.99 4.94
3399 3640 3.527533 GTGCATGTAGTCACCGGAATTA 58.472 45.455 9.46 0.00 0.00 1.40
3433 3674 1.202405 GGTGTTGCCACTGAAAGGTTG 60.202 52.381 0.00 0.00 41.53 3.77
3440 3681 1.876156 CCACTGAAAGGTTGAGCTGAC 59.124 52.381 0.00 0.00 39.30 3.51
3454 3695 1.202651 AGCTGACGGCACAAACTAGTT 60.203 47.619 9.39 1.12 44.79 2.24
3463 3704 2.964768 GCACAAACTAGTTCGCTTTTCG 59.035 45.455 8.95 0.00 40.15 3.46
3464 3705 3.545426 GCACAAACTAGTTCGCTTTTCGT 60.545 43.478 8.95 0.00 39.67 3.85
3478 3719 7.203525 TCGCTTTTCGTTAATTGCAATAATG 57.796 32.000 13.39 12.16 39.67 1.90
3507 3748 4.037446 TGTTGATTCCTTCCGTTTTTGGAG 59.963 41.667 0.00 0.00 39.72 3.86
3512 3753 4.376225 TCCTTCCGTTTTTGGAGGTAAT 57.624 40.909 0.00 0.00 39.72 1.89
3523 3764 6.435430 TTTTGGAGGTAATCATGAATCGTG 57.565 37.500 0.00 0.00 0.00 4.35
3540 3781 8.568732 TGAATCGTGTTAATTCCTTTTGTTTC 57.431 30.769 0.00 0.00 33.13 2.78
3561 3802 3.907474 TCTGGAAGTAACCATGAAGGTGA 59.093 43.478 0.00 0.00 43.20 4.02
3598 3839 3.636300 TGAGTGTTGCTGGCTTATTTGTT 59.364 39.130 0.00 0.00 0.00 2.83
3628 3869 3.897325 TCGATAGTGTATGCGATTGACC 58.103 45.455 0.00 0.00 37.40 4.02
3647 3888 4.148128 ACCTGAGGTCATAGAGCAAATG 57.852 45.455 0.00 0.00 31.89 2.32
3648 3889 3.776969 ACCTGAGGTCATAGAGCAAATGA 59.223 43.478 0.00 0.00 31.89 2.57
3649 3890 4.141756 ACCTGAGGTCATAGAGCAAATGAG 60.142 45.833 0.00 0.00 34.12 2.90
3650 3891 4.378774 CTGAGGTCATAGAGCAAATGAGG 58.621 47.826 0.00 0.00 34.12 3.86
3651 3892 3.137533 GAGGTCATAGAGCAAATGAGGC 58.862 50.000 0.00 0.00 34.12 4.70
3652 3893 2.776536 AGGTCATAGAGCAAATGAGGCT 59.223 45.455 0.00 0.00 46.07 4.58
3658 3899 3.149899 AGCAAATGAGGCTCGAGTG 57.850 52.632 15.13 8.27 36.81 3.51
3659 3900 1.023513 AGCAAATGAGGCTCGAGTGC 61.024 55.000 21.61 21.61 36.81 4.40
3660 3901 1.712081 CAAATGAGGCTCGAGTGCG 59.288 57.895 15.13 0.00 39.35 5.34
3661 3902 0.737367 CAAATGAGGCTCGAGTGCGA 60.737 55.000 15.13 0.00 45.71 5.10
3662 3903 0.176680 AAATGAGGCTCGAGTGCGAT 59.823 50.000 15.13 0.00 46.80 4.58
3663 3904 0.176680 AATGAGGCTCGAGTGCGATT 59.823 50.000 15.13 5.30 46.80 3.34
3664 3905 0.176680 ATGAGGCTCGAGTGCGATTT 59.823 50.000 15.13 0.00 46.80 2.17
3665 3906 0.815095 TGAGGCTCGAGTGCGATTTA 59.185 50.000 15.13 0.00 46.80 1.40
3666 3907 1.203758 TGAGGCTCGAGTGCGATTTAA 59.796 47.619 15.13 0.00 46.80 1.52
3667 3908 2.159099 TGAGGCTCGAGTGCGATTTAAT 60.159 45.455 15.13 0.00 46.80 1.40
3668 3909 2.866762 GAGGCTCGAGTGCGATTTAATT 59.133 45.455 15.13 0.00 46.80 1.40
3680 3921 5.799936 GTGCGATTTAATTTGCTGCTTCTTA 59.200 36.000 10.21 0.00 0.00 2.10
3701 3942 7.999679 TCTTAATCACTAAAATGATTGCCTGG 58.000 34.615 10.51 0.00 46.44 4.45
3708 3949 2.028561 AATGATTGCCTGGTTTGGGT 57.971 45.000 0.00 0.00 0.00 4.51
3713 3954 1.280457 TTGCCTGGTTTGGGTTTTGT 58.720 45.000 0.00 0.00 0.00 2.83
3714 3955 2.160721 TGCCTGGTTTGGGTTTTGTA 57.839 45.000 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.936547 CCGCTGAGAAATCTAAGCCAC 59.063 52.381 13.10 0.00 45.76 5.01
11 12 3.431486 GGAGTGATTCCGCTGAGAAATCT 60.431 47.826 0.00 0.00 35.91 2.40
30 31 1.336702 GCATATCACTCTCTGGCGGAG 60.337 57.143 17.47 17.47 43.12 4.63
36 37 3.726607 GTTGGAGGCATATCACTCTCTG 58.273 50.000 3.85 0.00 34.22 3.35
40 41 2.604046 ACGTTGGAGGCATATCACTC 57.396 50.000 0.00 0.00 0.00 3.51
41 42 3.898123 AGATACGTTGGAGGCATATCACT 59.102 43.478 0.00 0.00 0.00 3.41
48 49 8.514330 AAAAATTTATAGATACGTTGGAGGCA 57.486 30.769 0.00 0.00 0.00 4.75
96 97 8.696043 AAGGCATATAAAGCATACAAGATTGA 57.304 30.769 0.00 0.00 0.00 2.57
162 163 4.947147 GCACGGGAACTGGCACCA 62.947 66.667 0.00 0.00 40.47 4.17
164 165 2.193536 AAAGCACGGGAACTGGCAC 61.194 57.895 0.00 0.00 40.47 5.01
178 179 5.419155 AGAGGGTTAAAGAAATAGGCAAAGC 59.581 40.000 0.00 0.00 0.00 3.51
185 186 6.350103 GGACTGGAGAGGGTTAAAGAAATAG 58.650 44.000 0.00 0.00 0.00 1.73
204 205 2.420687 GGTTCTTCTGCCTATGGGACTG 60.421 54.545 0.00 0.00 33.58 3.51
205 206 1.840635 GGTTCTTCTGCCTATGGGACT 59.159 52.381 0.00 0.00 33.58 3.85
206 207 1.473434 CGGTTCTTCTGCCTATGGGAC 60.473 57.143 0.00 0.00 33.58 4.46
207 208 0.830648 CGGTTCTTCTGCCTATGGGA 59.169 55.000 0.00 0.00 33.58 4.37
208 209 0.179045 CCGGTTCTTCTGCCTATGGG 60.179 60.000 0.00 0.00 0.00 4.00
211 212 2.035632 CTCTCCGGTTCTTCTGCCTAT 58.964 52.381 0.00 0.00 0.00 2.57
226 228 7.040473 TCGGAAGAAAATCTGTATACTCTCC 57.960 40.000 4.17 1.56 37.03 3.71
237 239 1.290134 AGGCCCTCGGAAGAAAATCT 58.710 50.000 0.00 0.00 41.32 2.40
248 250 3.545703 AGATGTGAAATTTAGGCCCTCG 58.454 45.455 0.00 0.00 0.00 4.63
249 251 3.561725 CGAGATGTGAAATTTAGGCCCTC 59.438 47.826 0.00 0.00 0.00 4.30
362 364 2.804090 GCGTCGTCGGAAGTCACC 60.804 66.667 3.90 0.00 37.56 4.02
366 368 3.745803 GGAGGCGTCGTCGGAAGT 61.746 66.667 3.90 0.00 37.56 3.01
370 372 3.398353 GAGAAGGAGGCGTCGTCGG 62.398 68.421 3.90 0.00 37.56 4.79
373 375 0.965866 TGATGAGAAGGAGGCGTCGT 60.966 55.000 0.00 0.00 0.00 4.34
420 422 6.894654 TCATTAATGAAGGAATTAGGGTTGCA 59.105 34.615 15.82 0.00 33.08 4.08
440 442 4.122046 CAGTCAGCGATGTGGAATCATTA 58.878 43.478 0.00 0.00 0.00 1.90
443 445 1.276138 ACAGTCAGCGATGTGGAATCA 59.724 47.619 0.00 0.00 0.00 2.57
452 454 2.350522 GGATCAACAACAGTCAGCGAT 58.649 47.619 0.00 0.00 0.00 4.58
456 458 2.069273 GTCGGGATCAACAACAGTCAG 58.931 52.381 0.00 0.00 0.00 3.51
464 466 0.389817 CTTCAGCGTCGGGATCAACA 60.390 55.000 0.00 0.00 0.00 3.33
465 467 1.696832 GCTTCAGCGTCGGGATCAAC 61.697 60.000 0.00 0.00 0.00 3.18
478 480 2.383527 GGTTCTGCGTCCGCTTCAG 61.384 63.158 13.31 2.28 42.51 3.02
479 481 2.357034 GGTTCTGCGTCCGCTTCA 60.357 61.111 13.31 0.00 42.51 3.02
491 493 1.078848 GAGCGTGCCATCAGGTTCT 60.079 57.895 0.00 0.00 36.06 3.01
504 506 1.270907 AACCAGATGGAGAAGAGCGT 58.729 50.000 5.72 0.00 38.94 5.07
524 526 2.498941 CGCTCCAATCGGGCTAGGA 61.499 63.158 0.00 0.00 36.21 2.94
567 569 1.300931 CATCGGGGCTATGACGTGG 60.301 63.158 0.00 0.00 0.00 4.94
574 576 1.908793 CGGGACTCATCGGGGCTAT 60.909 63.158 0.00 0.00 0.00 2.97
586 588 2.995574 CCGGTCTTGGTCGGGACT 60.996 66.667 0.00 0.00 42.32 3.85
601 603 2.593468 ATCCTTGTGATCGCCACCCG 62.593 60.000 3.31 0.00 45.09 5.28
626 628 5.034852 TCCTCTCAATTCACACTGAAACA 57.965 39.130 0.00 0.00 40.12 2.83
635 637 3.507622 CCCCTTGTTTCCTCTCAATTCAC 59.492 47.826 0.00 0.00 0.00 3.18
636 638 3.500289 CCCCCTTGTTTCCTCTCAATTCA 60.500 47.826 0.00 0.00 0.00 2.57
659 661 1.089920 CTTCTTCCCTGTCGCCATTG 58.910 55.000 0.00 0.00 0.00 2.82
667 669 0.902516 AGAGCTCGCTTCTTCCCTGT 60.903 55.000 8.37 0.00 0.00 4.00
700 702 3.074412 GGTTTTCATTCTCTCGAAGGCA 58.926 45.455 0.00 0.00 31.33 4.75
705 707 4.219070 TCGTTAGGGTTTTCATTCTCTCGA 59.781 41.667 0.00 0.00 0.00 4.04
727 729 1.141858 CCCTGCCAATAGTTCCCTCTC 59.858 57.143 0.00 0.00 0.00 3.20
813 815 1.402968 CCCAGCAAGATGATTTCCGTG 59.597 52.381 0.00 0.00 0.00 4.94
826 828 1.913262 TCTCTTCTCGGCCCAGCAA 60.913 57.895 0.00 0.00 0.00 3.91
836 838 2.425312 TCGAGGAGCAATGTCTCTTCTC 59.575 50.000 12.18 7.52 37.14 2.87
845 847 0.933097 CCGAATGTCGAGGAGCAATG 59.067 55.000 0.00 0.00 43.74 2.82
846 848 0.811616 GCCGAATGTCGAGGAGCAAT 60.812 55.000 0.00 0.00 43.74 3.56
854 856 4.467084 GGCTGGGCCGAATGTCGA 62.467 66.667 0.00 0.00 43.74 4.20
935 1148 1.204467 GAGTGAGAGAGGGAGCAGTTG 59.796 57.143 0.00 0.00 0.00 3.16
936 1149 1.555967 GAGTGAGAGAGGGAGCAGTT 58.444 55.000 0.00 0.00 0.00 3.16
937 1150 0.324275 GGAGTGAGAGAGGGAGCAGT 60.324 60.000 0.00 0.00 0.00 4.40
948 1161 2.900546 GAGAGGGTTTTCAGGAGTGAGA 59.099 50.000 0.00 0.00 32.98 3.27
995 1208 2.108514 ATGGTTGCTGGCATCGTCG 61.109 57.895 0.00 0.00 0.00 5.12
1089 1302 2.581354 CAGGTGGAGGAGAAGGCG 59.419 66.667 0.00 0.00 0.00 5.52
1401 1614 2.425592 CAAGCCGTGGTGAGGTGA 59.574 61.111 0.00 0.00 0.00 4.02
1695 1908 2.383527 GCACTGAAGAAGGCGGTCG 61.384 63.158 0.00 0.00 0.00 4.79
1704 1917 3.240134 GACGGGGCTGCACTGAAGA 62.240 63.158 19.31 0.00 0.00 2.87
1974 2187 1.066422 GCCGATCTCGAGCACATGA 59.934 57.895 7.81 0.00 43.02 3.07
2020 2234 7.553881 ACATGATAAGTCCATTAAAGGAACG 57.446 36.000 0.00 0.00 39.92 3.95
2140 2354 2.859165 TGAGACTTGGAATGGTGGTC 57.141 50.000 0.00 0.00 0.00 4.02
2156 2370 2.555199 CCTTAACGCCAGGATCTTGAG 58.445 52.381 6.37 2.72 32.41 3.02
2170 2384 2.161609 CACTCCAAATCGCACCCTTAAC 59.838 50.000 0.00 0.00 0.00 2.01
2207 2421 0.107945 CTGAGGAAGGTAGGCAGCAC 60.108 60.000 0.00 0.00 0.00 4.40
2275 2489 8.462016 GTGTAAAATGCTAAATGAGGAGATTGT 58.538 33.333 0.00 0.00 0.00 2.71
2285 2499 6.176975 TGAGACGGTGTAAAATGCTAAATG 57.823 37.500 0.00 0.00 0.00 2.32
2332 2551 3.554692 GATCAACCAGACGGCGCG 61.555 66.667 6.90 0.00 34.57 6.86
2334 2553 0.179100 ATCAGATCAACCAGACGGCG 60.179 55.000 4.80 4.80 34.57 6.46
2337 2556 2.932614 GTTGGATCAGATCAACCAGACG 59.067 50.000 12.66 0.00 37.77 4.18
2447 2666 0.239347 GTGTGTGACTGCAGGCATTC 59.761 55.000 28.33 21.29 0.00 2.67
2527 2746 1.154131 CTGTGCTCTCTCCACGACG 60.154 63.158 0.00 0.00 36.01 5.12
2531 2750 0.607620 AGAAGCTGTGCTCTCTCCAC 59.392 55.000 0.00 0.00 38.25 4.02
2659 2878 3.174375 GCGCACCAAGATTGAGAATTTC 58.826 45.455 0.30 0.00 0.00 2.17
2801 3020 4.931002 GCTTAGCAAAAGAAATGGCAATGA 59.069 37.500 0.00 0.00 0.00 2.57
2855 3074 1.596477 GCTCTTGCCAGCGGATAGG 60.596 63.158 0.00 0.00 0.00 2.57
2856 3075 4.040068 GCTCTTGCCAGCGGATAG 57.960 61.111 0.00 0.00 0.00 2.08
2874 3093 9.061435 AGCCAAGAATTCATAGTCTAAATAAGC 57.939 33.333 8.44 0.00 0.00 3.09
2887 3106 7.899973 AGACAAAACATAAGCCAAGAATTCAT 58.100 30.769 8.44 0.00 0.00 2.57
2888 3107 7.288810 AGACAAAACATAAGCCAAGAATTCA 57.711 32.000 8.44 0.00 0.00 2.57
2951 3170 3.369787 CCAGACATTGCATGGACTACTGA 60.370 47.826 0.00 0.00 36.09 3.41
2970 3189 2.359900 GGTACAATTCAGCAGGACCAG 58.640 52.381 0.00 0.00 0.00 4.00
2973 3192 2.488153 GTTGGGTACAATTCAGCAGGAC 59.512 50.000 0.00 0.00 39.13 3.85
3018 3237 3.004629 GGCACACAGAATCACATGAAACA 59.995 43.478 0.00 0.00 0.00 2.83
3032 3251 1.069022 CACGAGAAAATGGGCACACAG 60.069 52.381 0.00 0.00 0.00 3.66
3064 3283 2.277969 CCAACAATGCAGCACACAAAA 58.722 42.857 0.00 0.00 0.00 2.44
3065 3284 1.206610 ACCAACAATGCAGCACACAAA 59.793 42.857 0.00 0.00 0.00 2.83
3066 3285 0.822811 ACCAACAATGCAGCACACAA 59.177 45.000 0.00 0.00 0.00 3.33
3067 3286 0.822811 AACCAACAATGCAGCACACA 59.177 45.000 0.00 0.00 0.00 3.72
3068 3287 1.202394 TCAACCAACAATGCAGCACAC 60.202 47.619 0.00 0.00 0.00 3.82
3080 3299 8.865590 AAATACAGTAACACATTTCAACCAAC 57.134 30.769 0.00 0.00 0.00 3.77
3083 3302 9.744468 AAAGAAATACAGTAACACATTTCAACC 57.256 29.630 7.99 0.00 39.01 3.77
3094 3313 6.073440 TCGGCACAAGAAAGAAATACAGTAAC 60.073 38.462 0.00 0.00 0.00 2.50
3109 3328 2.829720 ACCTGTACTAATCGGCACAAGA 59.170 45.455 0.00 0.00 0.00 3.02
3162 3384 9.489084 CAATGGATCATCATTGCAGAAAATTAT 57.511 29.630 10.52 0.00 44.70 1.28
3211 3452 6.638096 TCACAAACTGACAAATCACATGAT 57.362 33.333 0.00 0.00 36.07 2.45
3227 3468 0.315869 CGCCGCGGATAATCACAAAC 60.316 55.000 33.48 4.93 0.00 2.93
3240 3481 2.575789 GCAATACCAAACGCCGCG 60.576 61.111 12.14 12.14 0.00 6.46
3246 3487 2.378445 AAATGCCGGCAATACCAAAC 57.622 45.000 36.33 0.00 39.03 2.93
3272 3513 4.424061 TGCACCTTCATTCTTCAATTCG 57.576 40.909 0.00 0.00 0.00 3.34
3295 3536 0.105593 CAGCACATCCGGTAGAGCAT 59.894 55.000 16.91 0.00 0.00 3.79
3302 3543 1.078426 GGCTTACAGCACATCCGGT 60.078 57.895 0.00 0.00 44.75 5.28
3329 3570 4.024218 CAGCTCAACCTTTCAGTCTTTCAG 60.024 45.833 0.00 0.00 0.00 3.02
3330 3571 3.879295 CAGCTCAACCTTTCAGTCTTTCA 59.121 43.478 0.00 0.00 0.00 2.69
3331 3572 4.130118 TCAGCTCAACCTTTCAGTCTTTC 58.870 43.478 0.00 0.00 0.00 2.62
3332 3573 4.156455 TCAGCTCAACCTTTCAGTCTTT 57.844 40.909 0.00 0.00 0.00 2.52
3333 3574 3.845781 TCAGCTCAACCTTTCAGTCTT 57.154 42.857 0.00 0.00 0.00 3.01
3334 3575 3.326006 TCATCAGCTCAACCTTTCAGTCT 59.674 43.478 0.00 0.00 0.00 3.24
3335 3576 3.668447 TCATCAGCTCAACCTTTCAGTC 58.332 45.455 0.00 0.00 0.00 3.51
3336 3577 3.777106 TCATCAGCTCAACCTTTCAGT 57.223 42.857 0.00 0.00 0.00 3.41
3376 3617 1.809619 CCGGTGACTACATGCACGG 60.810 63.158 0.00 0.00 35.91 4.94
3377 3618 0.389296 TTCCGGTGACTACATGCACG 60.389 55.000 0.00 0.00 35.91 5.34
3378 3619 2.024176 ATTCCGGTGACTACATGCAC 57.976 50.000 0.00 0.00 0.00 4.57
3379 3620 2.779755 AATTCCGGTGACTACATGCA 57.220 45.000 0.00 0.00 0.00 3.96
3380 3621 4.873827 TCTTTAATTCCGGTGACTACATGC 59.126 41.667 0.00 0.00 0.00 4.06
3382 3623 6.708285 AGTTCTTTAATTCCGGTGACTACAT 58.292 36.000 0.00 0.00 0.00 2.29
3383 3624 6.105397 AGTTCTTTAATTCCGGTGACTACA 57.895 37.500 0.00 0.00 0.00 2.74
3399 3640 4.944048 GGCAACACCAACATAAGTTCTTT 58.056 39.130 0.00 0.00 38.86 2.52
3433 3674 1.071605 CTAGTTTGTGCCGTCAGCTC 58.928 55.000 0.00 0.00 44.23 4.09
3440 3681 0.865769 AAGCGAACTAGTTTGTGCCG 59.134 50.000 21.42 15.07 0.00 5.69
3454 3695 7.024171 TCATTATTGCAATTAACGAAAAGCGA 58.976 30.769 18.75 2.47 44.57 4.93
3507 3748 8.154649 AGGAATTAACACGATTCATGATTACC 57.845 34.615 0.00 0.00 35.66 2.85
3512 3753 7.881142 ACAAAAGGAATTAACACGATTCATGA 58.119 30.769 0.00 0.00 35.66 3.07
3535 3776 5.070001 CCTTCATGGTTACTTCCAGAAACA 58.930 41.667 0.00 0.00 41.05 2.83
3598 3839 4.260579 CGCATACACTATCGAATTTTGGCA 60.261 41.667 0.00 0.00 0.00 4.92
3608 3849 3.670523 CAGGTCAATCGCATACACTATCG 59.329 47.826 0.00 0.00 0.00 2.92
3628 3869 4.378774 CCTCATTTGCTCTATGACCTCAG 58.621 47.826 0.00 0.00 0.00 3.35
3643 3884 1.591703 TCGCACTCGAGCCTCATTT 59.408 52.632 13.61 0.00 40.21 2.32
3644 3885 3.288484 TCGCACTCGAGCCTCATT 58.712 55.556 13.61 0.00 40.21 2.57
3653 3894 2.527487 GCAGCAAATTAAATCGCACTCG 59.473 45.455 0.00 0.00 0.00 4.18
3654 3895 3.762779 AGCAGCAAATTAAATCGCACTC 58.237 40.909 0.00 0.00 0.00 3.51
3655 3896 3.855689 AGCAGCAAATTAAATCGCACT 57.144 38.095 0.00 0.00 0.00 4.40
3656 3897 4.168760 AGAAGCAGCAAATTAAATCGCAC 58.831 39.130 0.00 0.00 0.00 5.34
3657 3898 4.439305 AGAAGCAGCAAATTAAATCGCA 57.561 36.364 0.00 0.00 0.00 5.10
3658 3899 6.869421 TTAAGAAGCAGCAAATTAAATCGC 57.131 33.333 0.00 0.00 0.00 4.58
3659 3900 8.526681 GTGATTAAGAAGCAGCAAATTAAATCG 58.473 33.333 0.00 0.00 0.00 3.34
3660 3901 9.578439 AGTGATTAAGAAGCAGCAAATTAAATC 57.422 29.630 0.00 0.00 0.00 2.17
3665 3906 9.933723 ATTTTAGTGATTAAGAAGCAGCAAATT 57.066 25.926 0.00 0.00 0.00 1.82
3666 3907 9.362539 CATTTTAGTGATTAAGAAGCAGCAAAT 57.637 29.630 0.00 0.00 0.00 2.32
3667 3908 8.575589 TCATTTTAGTGATTAAGAAGCAGCAAA 58.424 29.630 0.00 0.00 0.00 3.68
3668 3909 8.109705 TCATTTTAGTGATTAAGAAGCAGCAA 57.890 30.769 0.00 0.00 0.00 3.91
3680 3921 6.610075 AACCAGGCAATCATTTTAGTGATT 57.390 33.333 0.00 0.00 46.77 2.57
3701 3942 7.317390 CCTAACCACATATACAAAACCCAAAC 58.683 38.462 0.00 0.00 0.00 2.93
3713 3954 8.739039 GCATCAATTTATGCCTAACCACATATA 58.261 33.333 12.69 0.00 45.31 0.86
3714 3955 7.605449 GCATCAATTTATGCCTAACCACATAT 58.395 34.615 12.69 0.00 45.31 1.78


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

AutoCloner maintained by Alex Coulton.