Multiple sequence alignment - TraesCS4B01G206800

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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 TraesCS4B01G206800 chr4B 100.000 3370 0 0 1 3370 440045072 440048441 0.000000e+00 6224
1 TraesCS4B01G206800 chr4D 95.231 2705 47 13 596 3245 356561447 356564124 0.000000e+00 4205
2 TraesCS4B01G206800 chr4D 93.293 492 16 3 122 602 356560788 356561273 0.000000e+00 710
3 TraesCS4B01G206800 chr4D 96.203 79 3 0 1 79 356560702 356560780 2.730000e-26 130
4 TraesCS4B01G206800 chr4A 94.201 2811 65 32 492 3245 108873429 108870660 0.000000e+00 4198
5 TraesCS4B01G206800 chr3D 88.830 188 21 0 1441 1628 610544050 610544237 7.270000e-57 231
6 TraesCS4B01G206800 chr3D 87.195 164 21 0 1450 1613 613806079 613805916 1.600000e-43 187
7 TraesCS4B01G206800 chr3B 88.830 188 21 0 1441 1628 828111450 828111637 7.270000e-57 231
8 TraesCS4B01G206800 chr3B 84.848 198 30 0 1434 1631 675649883 675650080 2.050000e-47 200
9 TraesCS4B01G206800 chr3B 91.129 124 5 2 3241 3364 426312071 426312188 2.690000e-36 163
10 TraesCS4B01G206800 chr3B 89.922 129 7 2 3242 3370 383706803 383706925 9.680000e-36 161
11 TraesCS4B01G206800 chr3A 88.298 188 22 0 1441 1628 744879520 744879707 3.380000e-55 226
12 TraesCS4B01G206800 chr3A 84.264 197 31 0 1450 1646 750298743 750298547 3.430000e-45 193
13 TraesCS4B01G206800 chr3A 86.331 139 12 3 3233 3370 607110033 607110165 9.750000e-31 145
14 TraesCS4B01G206800 chr6A 86.628 172 19 4 1475 1644 520355733 520355564 1.600000e-43 187
15 TraesCS4B01G206800 chr2B 93.750 128 1 2 3243 3370 36841569 36841689 5.740000e-43 185
16 TraesCS4B01G206800 chr7B 90.909 132 5 3 3240 3370 55858344 55858469 1.610000e-38 171
17 TraesCS4B01G206800 chr7B 88.281 128 9 2 3243 3370 108491028 108491149 7.530000e-32 148
18 TraesCS4B01G206800 chr7B 88.281 128 9 2 3243 3370 646052792 646052671 7.530000e-32 148
19 TraesCS4B01G206800 chr6B 90.698 129 6 2 3242 3370 136800323 136800201 2.080000e-37 167
20 TraesCS4B01G206800 chr6B 87.597 129 10 2 3242 3370 714074679 714074557 9.750000e-31 145


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 TraesCS4B01G206800 chr4B 440045072 440048441 3369 False 6224.000000 6224 100.000 1 3370 1 chr4B.!!$F1 3369
1 TraesCS4B01G206800 chr4D 356560702 356564124 3422 False 1681.666667 4205 94.909 1 3245 3 chr4D.!!$F1 3244
2 TraesCS4B01G206800 chr4A 108870660 108873429 2769 True 4198.000000 4198 94.201 492 3245 1 chr4A.!!$R1 2753

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
36 37 0.179936 AGCTGCCTAATCTGACCAGC 59.820 55.0 0.0 2.94 46.82 4.85 F
1085 1312 0.041833 CCTCCCTCTCCAAGTCTCCA 59.958 60.0 0.0 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1724 1963 0.249073 GCATAGATGACGCGACACCT 60.249 55.0 15.93 13.05 0.0 4.0 R
2577 2840 0.246635 GACACGTACCACAGGCAGAT 59.753 55.0 0.00 0.00 0.0 2.9 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
36 37 0.179936 AGCTGCCTAATCTGACCAGC 59.820 55.000 0.00 2.94 46.82 4.85
61 62 2.048597 GCGACGATGTCACCCACA 60.049 61.111 0.00 0.00 40.18 4.17
79 80 1.007479 ACATCAACCCCATCAGCCAAT 59.993 47.619 0.00 0.00 0.00 3.16
80 81 1.684983 CATCAACCCCATCAGCCAATC 59.315 52.381 0.00 0.00 0.00 2.67
81 82 1.002069 TCAACCCCATCAGCCAATCT 58.998 50.000 0.00 0.00 0.00 2.40
82 83 1.064463 TCAACCCCATCAGCCAATCTC 60.064 52.381 0.00 0.00 0.00 2.75
83 84 1.064166 CAACCCCATCAGCCAATCTCT 60.064 52.381 0.00 0.00 0.00 3.10
84 85 0.549950 ACCCCATCAGCCAATCTCTG 59.450 55.000 0.00 0.00 0.00 3.35
94 95 2.267174 CCAATCTCTGGTAGGCCATG 57.733 55.000 5.01 0.00 45.05 3.66
95 96 1.602311 CAATCTCTGGTAGGCCATGC 58.398 55.000 5.01 0.00 45.05 4.06
96 97 1.134007 CAATCTCTGGTAGGCCATGCA 60.134 52.381 5.01 0.00 45.05 3.96
97 98 1.442773 ATCTCTGGTAGGCCATGCAT 58.557 50.000 5.01 0.00 45.05 3.96
98 99 0.761187 TCTCTGGTAGGCCATGCATC 59.239 55.000 5.01 0.00 45.05 3.91
99 100 0.763652 CTCTGGTAGGCCATGCATCT 59.236 55.000 5.01 0.00 45.05 2.90
100 101 0.471191 TCTGGTAGGCCATGCATCTG 59.529 55.000 5.01 0.00 45.05 2.90
101 102 0.182061 CTGGTAGGCCATGCATCTGT 59.818 55.000 5.01 0.00 45.05 3.41
102 103 0.625316 TGGTAGGCCATGCATCTGTT 59.375 50.000 5.01 0.00 40.46 3.16
103 104 1.312815 GGTAGGCCATGCATCTGTTC 58.687 55.000 5.01 0.00 34.09 3.18
104 105 1.133976 GGTAGGCCATGCATCTGTTCT 60.134 52.381 5.01 0.00 34.09 3.01
105 106 2.104792 GGTAGGCCATGCATCTGTTCTA 59.895 50.000 5.01 0.00 34.09 2.10
106 107 2.634815 AGGCCATGCATCTGTTCTAG 57.365 50.000 5.01 0.00 0.00 2.43
107 108 1.842562 AGGCCATGCATCTGTTCTAGT 59.157 47.619 5.01 0.00 0.00 2.57
108 109 2.240667 AGGCCATGCATCTGTTCTAGTT 59.759 45.455 5.01 0.00 0.00 2.24
109 110 3.455910 AGGCCATGCATCTGTTCTAGTTA 59.544 43.478 5.01 0.00 0.00 2.24
110 111 4.080356 AGGCCATGCATCTGTTCTAGTTAA 60.080 41.667 5.01 0.00 0.00 2.01
111 112 4.823989 GGCCATGCATCTGTTCTAGTTAAT 59.176 41.667 0.00 0.00 0.00 1.40
112 113 5.049129 GGCCATGCATCTGTTCTAGTTAATC 60.049 44.000 0.00 0.00 0.00 1.75
113 114 5.762218 GCCATGCATCTGTTCTAGTTAATCT 59.238 40.000 0.00 0.00 0.00 2.40
114 115 6.261826 GCCATGCATCTGTTCTAGTTAATCTT 59.738 38.462 0.00 0.00 0.00 2.40
115 116 7.637229 CCATGCATCTGTTCTAGTTAATCTTG 58.363 38.462 0.00 0.00 0.00 3.02
116 117 7.496920 CCATGCATCTGTTCTAGTTAATCTTGA 59.503 37.037 0.00 0.00 0.00 3.02
117 118 8.549548 CATGCATCTGTTCTAGTTAATCTTGAG 58.450 37.037 0.00 0.00 30.58 3.02
118 119 6.536582 TGCATCTGTTCTAGTTAATCTTGAGC 59.463 38.462 0.00 0.00 32.19 4.26
119 120 6.018343 GCATCTGTTCTAGTTAATCTTGAGCC 60.018 42.308 0.00 0.00 31.04 4.70
120 121 5.978814 TCTGTTCTAGTTAATCTTGAGCCC 58.021 41.667 0.00 0.00 31.04 5.19
131 132 3.751767 TTGAGCCCAAGAACTGCAT 57.248 47.368 0.00 0.00 0.00 3.96
231 232 2.097680 AATTGGCTCCCATTTTTGCG 57.902 45.000 0.00 0.00 31.53 4.85
262 263 4.747931 GCATAATAGGTGACAGAAGCCCAT 60.748 45.833 0.00 0.00 0.00 4.00
264 265 4.423625 AATAGGTGACAGAAGCCCATAC 57.576 45.455 0.00 0.00 0.00 2.39
266 267 1.556911 AGGTGACAGAAGCCCATACTG 59.443 52.381 0.00 0.00 37.62 2.74
279 280 2.636830 CCATACTGAGGTGGCTTCAAG 58.363 52.381 0.00 0.00 0.00 3.02
366 378 2.712087 TGTACAAAAGGCTTCCCTGGTA 59.288 45.455 0.00 0.00 41.90 3.25
367 379 2.287977 ACAAAAGGCTTCCCTGGTAC 57.712 50.000 0.00 0.00 41.90 3.34
368 380 1.165270 CAAAAGGCTTCCCTGGTACG 58.835 55.000 0.00 0.00 41.90 3.67
369 381 0.769247 AAAAGGCTTCCCTGGTACGT 59.231 50.000 0.00 0.00 41.90 3.57
370 382 1.648116 AAAGGCTTCCCTGGTACGTA 58.352 50.000 0.00 0.00 41.90 3.57
371 383 0.900421 AAGGCTTCCCTGGTACGTAC 59.100 55.000 17.56 17.56 41.90 3.67
391 403 2.028658 ACATGAGCGATGAGACACTGTT 60.029 45.455 0.00 0.00 35.80 3.16
393 405 1.341209 TGAGCGATGAGACACTGTTGT 59.659 47.619 0.00 0.00 39.32 3.32
531 543 3.055819 TCTCCACAATGCTGGAAGAGTAC 60.056 47.826 6.15 0.00 39.97 2.73
623 815 4.840680 TCTCTCTCAAACATTCTTCCCAGA 59.159 41.667 0.00 0.00 0.00 3.86
714 906 1.280998 CCCGCCCTTTCTCTTTCCTAA 59.719 52.381 0.00 0.00 0.00 2.69
956 1183 1.755200 AAAGCTGGAGTTAAGGGGGA 58.245 50.000 0.00 0.00 0.00 4.81
957 1184 1.290134 AAGCTGGAGTTAAGGGGGAG 58.710 55.000 0.00 0.00 0.00 4.30
958 1185 0.417841 AGCTGGAGTTAAGGGGGAGA 59.582 55.000 0.00 0.00 0.00 3.71
1018 1245 1.918293 ATGGTGTTCCCTCCAGCGA 60.918 57.895 0.00 0.00 37.63 4.93
1078 1305 2.575921 ACATGATCCTCCCTCTCCAA 57.424 50.000 0.00 0.00 0.00 3.53
1079 1306 2.406559 ACATGATCCTCCCTCTCCAAG 58.593 52.381 0.00 0.00 0.00 3.61
1080 1307 2.293452 ACATGATCCTCCCTCTCCAAGT 60.293 50.000 0.00 0.00 0.00 3.16
1081 1308 2.166907 TGATCCTCCCTCTCCAAGTC 57.833 55.000 0.00 0.00 0.00 3.01
1082 1309 1.648568 TGATCCTCCCTCTCCAAGTCT 59.351 52.381 0.00 0.00 0.00 3.24
1083 1310 2.316108 GATCCTCCCTCTCCAAGTCTC 58.684 57.143 0.00 0.00 0.00 3.36
1084 1311 0.336737 TCCTCCCTCTCCAAGTCTCC 59.663 60.000 0.00 0.00 0.00 3.71
1085 1312 0.041833 CCTCCCTCTCCAAGTCTCCA 59.958 60.000 0.00 0.00 0.00 3.86
1094 1321 1.550524 TCCAAGTCTCCATGTCCTTCG 59.449 52.381 0.00 0.00 0.00 3.79
1098 1325 3.533606 AGTCTCCATGTCCTTCGATTG 57.466 47.619 0.00 0.00 0.00 2.67
1195 1422 7.220875 GGCAAAATTAAAGTAGCTTAGCATGAC 59.779 37.037 7.07 1.22 0.00 3.06
2152 2394 0.393537 GGGCAGTCTAGTGCAAGCAT 60.394 55.000 11.65 0.00 45.93 3.79
2510 2765 0.249784 CGCTGCTAGCTCATGATGGT 60.250 55.000 17.23 0.00 39.60 3.55
2511 2766 1.510776 GCTGCTAGCTCATGATGGTC 58.489 55.000 17.23 0.00 38.45 4.02
2512 2767 1.070445 GCTGCTAGCTCATGATGGTCT 59.930 52.381 17.23 0.00 38.45 3.85
2513 2768 2.298446 GCTGCTAGCTCATGATGGTCTA 59.702 50.000 17.23 0.00 38.45 2.59
2514 2769 3.244009 GCTGCTAGCTCATGATGGTCTAA 60.244 47.826 17.23 0.00 38.45 2.10
2515 2770 4.558178 CTGCTAGCTCATGATGGTCTAAG 58.442 47.826 17.23 0.00 0.00 2.18
2516 2771 3.244009 TGCTAGCTCATGATGGTCTAAGC 60.244 47.826 17.23 3.71 0.00 3.09
2517 2772 2.926778 AGCTCATGATGGTCTAAGCC 57.073 50.000 0.00 0.00 0.00 4.35
2577 2840 5.582665 GGTTAACACTTTTGCACCATTTTGA 59.417 36.000 8.10 0.00 0.00 2.69
2587 2855 2.673043 GCACCATTTTGATCTGCCTGTG 60.673 50.000 0.00 0.00 0.00 3.66
2637 2905 8.865978 CCTTTAAAAACCTTTTCACACTTACAC 58.134 33.333 0.00 0.00 0.00 2.90
2986 3274 7.823745 AACCATTACCATAATCCATGAAGTC 57.176 36.000 0.00 0.00 36.69 3.01
3058 3346 3.838244 TCTCATATTTCCCCAGTTCCG 57.162 47.619 0.00 0.00 0.00 4.30
3248 3537 9.661954 TCTCCCATATTATTGAGATATACTCCC 57.338 37.037 0.00 0.00 44.34 4.30
3249 3538 9.667607 CTCCCATATTATTGAGATATACTCCCT 57.332 37.037 0.00 0.00 44.34 4.20
3250 3539 9.661954 TCCCATATTATTGAGATATACTCCCTC 57.338 37.037 0.00 0.00 44.34 4.30
3251 3540 8.875168 CCCATATTATTGAGATATACTCCCTCC 58.125 40.741 0.00 0.00 44.34 4.30
3252 3541 8.580720 CCATATTATTGAGATATACTCCCTCCG 58.419 40.741 0.00 0.00 44.34 4.63
3253 3542 9.137459 CATATTATTGAGATATACTCCCTCCGT 57.863 37.037 0.00 0.00 44.34 4.69
3254 3543 7.648039 ATTATTGAGATATACTCCCTCCGTC 57.352 40.000 0.00 0.00 44.34 4.79
3255 3544 3.436577 TGAGATATACTCCCTCCGTCC 57.563 52.381 0.00 0.00 44.34 4.79
3256 3545 2.290134 TGAGATATACTCCCTCCGTCCG 60.290 54.545 0.00 0.00 44.34 4.79
3257 3546 1.004511 AGATATACTCCCTCCGTCCGG 59.995 57.143 0.00 0.00 0.00 5.14
3258 3547 1.004044 GATATACTCCCTCCGTCCGGA 59.996 57.143 0.00 0.00 42.90 5.14
3259 3548 0.846015 TATACTCCCTCCGTCCGGAA 59.154 55.000 5.23 0.00 44.66 4.30
3260 3549 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
3261 3550 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
3262 3551 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
3263 3552 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
3264 3553 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
3265 3554 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
3266 3555 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
3267 3556 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
3268 3557 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
3269 3558 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
3270 3559 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
3271 3560 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
3272 3561 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
3273 3562 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
3274 3563 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
3275 3564 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
3276 3565 6.084277 GTCCGGAAATACTTGTCATCAAAAC 58.916 40.000 5.23 0.00 32.87 2.43
3277 3566 5.086058 CCGGAAATACTTGTCATCAAAACG 58.914 41.667 0.00 0.00 32.87 3.60
3278 3567 5.106869 CCGGAAATACTTGTCATCAAAACGA 60.107 40.000 0.00 0.00 32.87 3.85
3279 3568 6.367421 CGGAAATACTTGTCATCAAAACGAA 58.633 36.000 0.00 0.00 32.87 3.85
3280 3569 7.021196 CGGAAATACTTGTCATCAAAACGAAT 58.979 34.615 0.00 0.00 32.87 3.34
3281 3570 8.172484 CGGAAATACTTGTCATCAAAACGAATA 58.828 33.333 0.00 0.00 32.87 1.75
3282 3571 9.834628 GGAAATACTTGTCATCAAAACGAATAA 57.165 29.630 0.00 0.00 32.87 1.40
3287 3576 8.378172 ACTTGTCATCAAAACGAATAAAGAGA 57.622 30.769 0.00 0.00 32.87 3.10
3288 3577 8.499162 ACTTGTCATCAAAACGAATAAAGAGAG 58.501 33.333 0.00 0.00 32.87 3.20
3289 3578 8.601845 TTGTCATCAAAACGAATAAAGAGAGA 57.398 30.769 0.00 0.00 0.00 3.10
3290 3579 8.777865 TGTCATCAAAACGAATAAAGAGAGAT 57.222 30.769 0.00 0.00 0.00 2.75
3291 3580 8.659491 TGTCATCAAAACGAATAAAGAGAGATG 58.341 33.333 0.00 0.00 0.00 2.90
3292 3581 8.660373 GTCATCAAAACGAATAAAGAGAGATGT 58.340 33.333 0.00 0.00 33.02 3.06
3293 3582 9.869757 TCATCAAAACGAATAAAGAGAGATGTA 57.130 29.630 0.00 0.00 33.02 2.29
3302 3591 9.536558 CGAATAAAGAGAGATGTATCTAGAACG 57.463 37.037 0.00 0.00 37.25 3.95
3303 3592 9.834628 GAATAAAGAGAGATGTATCTAGAACGG 57.165 37.037 0.00 0.00 37.25 4.44
3304 3593 9.575868 AATAAAGAGAGATGTATCTAGAACGGA 57.424 33.333 0.00 0.00 37.25 4.69
3305 3594 7.883391 AAAGAGAGATGTATCTAGAACGGAA 57.117 36.000 0.00 0.00 37.25 4.30
3306 3595 7.883391 AAGAGAGATGTATCTAGAACGGAAA 57.117 36.000 0.00 0.00 37.25 3.13
3307 3596 8.472007 AAGAGAGATGTATCTAGAACGGAAAT 57.528 34.615 0.00 0.00 37.25 2.17
3308 3597 9.575868 AAGAGAGATGTATCTAGAACGGAAATA 57.424 33.333 0.00 0.00 37.25 1.40
3309 3598 9.747898 AGAGAGATGTATCTAGAACGGAAATAT 57.252 33.333 0.00 0.00 37.25 1.28
3310 3599 9.781834 GAGAGATGTATCTAGAACGGAAATATG 57.218 37.037 0.00 0.00 37.25 1.78
3311 3600 9.303116 AGAGATGTATCTAGAACGGAAATATGT 57.697 33.333 0.00 0.00 37.25 2.29
3312 3601 9.562583 GAGATGTATCTAGAACGGAAATATGTC 57.437 37.037 0.00 0.00 37.25 3.06
3313 3602 9.303116 AGATGTATCTAGAACGGAAATATGTCT 57.697 33.333 0.00 0.00 34.85 3.41
3316 3605 9.346005 TGTATCTAGAACGGAAATATGTCTACA 57.654 33.333 0.00 0.00 0.00 2.74
3320 3609 9.346005 TCTAGAACGGAAATATGTCTACATACA 57.654 33.333 4.98 0.00 41.15 2.29
3323 3612 8.088981 AGAACGGAAATATGTCTACATACATCC 58.911 37.037 17.91 17.91 41.15 3.51
3324 3613 6.698380 ACGGAAATATGTCTACATACATCCC 58.302 40.000 20.04 12.47 41.15 3.85
3325 3614 6.106673 CGGAAATATGTCTACATACATCCCC 58.893 44.000 20.04 11.33 41.15 4.81
3326 3615 6.070767 CGGAAATATGTCTACATACATCCCCT 60.071 42.308 20.04 0.00 41.15 4.79
3327 3616 7.527196 CGGAAATATGTCTACATACATCCCCTT 60.527 40.741 20.04 4.66 41.15 3.95
3328 3617 8.164070 GGAAATATGTCTACATACATCCCCTTT 58.836 37.037 17.45 8.86 41.15 3.11
3329 3618 9.574516 GAAATATGTCTACATACATCCCCTTTT 57.425 33.333 4.98 0.56 41.15 2.27
3330 3619 9.936329 AAATATGTCTACATACATCCCCTTTTT 57.064 29.630 4.98 0.00 41.15 1.94
3334 3623 8.331931 TGTCTACATACATCCCCTTTTTATCT 57.668 34.615 0.00 0.00 0.00 1.98
3335 3624 9.442062 TGTCTACATACATCCCCTTTTTATCTA 57.558 33.333 0.00 0.00 0.00 1.98
3362 3651 8.741101 TTTGATTTGATGACAAGTATTTTCGG 57.259 30.769 0.00 0.00 37.32 4.30
3363 3652 7.680442 TGATTTGATGACAAGTATTTTCGGA 57.320 32.000 0.00 0.00 37.32 4.55
3364 3653 7.526608 TGATTTGATGACAAGTATTTTCGGAC 58.473 34.615 0.00 0.00 37.32 4.79
3365 3654 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
3366 3655 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
3367 3656 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
3368 3657 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
3369 3658 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.718904 TGACATCGTCGCGGATTTTG 59.281 50.000 6.13 0.57 34.95 2.44
61 62 1.572415 AGATTGGCTGATGGGGTTGAT 59.428 47.619 0.00 0.00 0.00 2.57
65 66 0.549950 CAGAGATTGGCTGATGGGGT 59.450 55.000 0.00 0.00 35.39 4.95
84 85 1.133976 AGAACAGATGCATGGCCTACC 60.134 52.381 2.46 0.00 0.00 3.18
85 86 2.338577 AGAACAGATGCATGGCCTAC 57.661 50.000 2.46 0.00 0.00 3.18
86 87 3.041211 ACTAGAACAGATGCATGGCCTA 58.959 45.455 2.46 1.28 0.00 3.93
87 88 1.842562 ACTAGAACAGATGCATGGCCT 59.157 47.619 2.46 0.00 0.00 5.19
88 89 2.338577 ACTAGAACAGATGCATGGCC 57.661 50.000 2.46 0.00 0.00 5.36
89 90 5.762218 AGATTAACTAGAACAGATGCATGGC 59.238 40.000 2.46 0.00 0.00 4.40
90 91 7.496920 TCAAGATTAACTAGAACAGATGCATGG 59.503 37.037 2.46 0.00 0.00 3.66
91 92 8.429493 TCAAGATTAACTAGAACAGATGCATG 57.571 34.615 2.46 0.00 0.00 4.06
92 93 7.226325 GCTCAAGATTAACTAGAACAGATGCAT 59.774 37.037 0.00 0.00 0.00 3.96
93 94 6.536582 GCTCAAGATTAACTAGAACAGATGCA 59.463 38.462 0.00 0.00 0.00 3.96
94 95 6.018343 GGCTCAAGATTAACTAGAACAGATGC 60.018 42.308 0.00 0.00 0.00 3.91
95 96 6.481644 GGGCTCAAGATTAACTAGAACAGATG 59.518 42.308 0.00 0.00 0.00 2.90
96 97 6.156949 TGGGCTCAAGATTAACTAGAACAGAT 59.843 38.462 0.00 0.00 0.00 2.90
97 98 5.483937 TGGGCTCAAGATTAACTAGAACAGA 59.516 40.000 0.00 0.00 0.00 3.41
98 99 5.734720 TGGGCTCAAGATTAACTAGAACAG 58.265 41.667 0.00 0.00 0.00 3.16
99 100 5.755409 TGGGCTCAAGATTAACTAGAACA 57.245 39.130 0.00 0.00 0.00 3.18
113 114 1.538047 GATGCAGTTCTTGGGCTCAA 58.462 50.000 0.00 0.00 0.00 3.02
114 115 0.674581 CGATGCAGTTCTTGGGCTCA 60.675 55.000 0.00 0.00 0.00 4.26
115 116 0.391661 TCGATGCAGTTCTTGGGCTC 60.392 55.000 0.00 0.00 0.00 4.70
116 117 0.036732 TTCGATGCAGTTCTTGGGCT 59.963 50.000 0.00 0.00 0.00 5.19
117 118 0.449388 CTTCGATGCAGTTCTTGGGC 59.551 55.000 0.00 0.00 0.00 5.36
118 119 2.099141 TCTTCGATGCAGTTCTTGGG 57.901 50.000 0.00 0.00 0.00 4.12
119 120 3.669023 GCTTTCTTCGATGCAGTTCTTGG 60.669 47.826 0.00 0.00 0.00 3.61
120 121 3.058708 TGCTTTCTTCGATGCAGTTCTTG 60.059 43.478 0.00 0.00 0.00 3.02
131 132 4.188462 TCTGTTCAACTTGCTTTCTTCGA 58.812 39.130 0.00 0.00 0.00 3.71
146 147 3.554934 AGCTCAATGTGGTTTCTGTTCA 58.445 40.909 0.00 0.00 0.00 3.18
231 232 0.859232 CACCTATTATGCGACGTGCC 59.141 55.000 0.00 0.00 45.60 5.01
238 239 2.802816 GGCTTCTGTCACCTATTATGCG 59.197 50.000 0.00 0.00 0.00 4.73
262 263 1.902508 CTCCTTGAAGCCACCTCAGTA 59.097 52.381 0.00 0.00 0.00 2.74
264 265 0.035630 CCTCCTTGAAGCCACCTCAG 60.036 60.000 0.00 0.00 0.00 3.35
266 267 1.377856 GCCTCCTTGAAGCCACCTC 60.378 63.158 0.00 0.00 0.00 3.85
279 280 4.946478 TTATTCTAGCTCTTGAGCCTCC 57.054 45.455 17.78 0.00 34.90 4.30
293 305 5.179368 GCTTGCGCCTATGATGTTTATTCTA 59.821 40.000 4.18 0.00 0.00 2.10
304 316 1.300931 GATCCGCTTGCGCCTATGA 60.301 57.895 4.18 1.54 0.00 2.15
366 378 1.743394 TGTCTCATCGCTCATGTACGT 59.257 47.619 9.34 0.00 33.66 3.57
367 379 2.112522 GTGTCTCATCGCTCATGTACG 58.887 52.381 4.13 4.13 33.66 3.67
368 380 3.111838 CAGTGTCTCATCGCTCATGTAC 58.888 50.000 0.00 0.00 33.66 2.90
369 381 2.755103 ACAGTGTCTCATCGCTCATGTA 59.245 45.455 0.00 0.00 33.66 2.29
370 382 1.547820 ACAGTGTCTCATCGCTCATGT 59.452 47.619 0.00 0.00 33.66 3.21
371 383 2.290531 ACAGTGTCTCATCGCTCATG 57.709 50.000 0.00 0.00 0.00 3.07
391 403 1.064017 AGTGGGGAGTCTTTTGCAACA 60.064 47.619 0.00 0.00 0.00 3.33
393 405 3.806949 ATAGTGGGGAGTCTTTTGCAA 57.193 42.857 0.00 0.00 0.00 4.08
623 815 5.669164 TTTCTAGTTTTTGCTTTGTGGGT 57.331 34.783 0.00 0.00 0.00 4.51
714 906 0.634465 GAGGGGGAGGAGAGAGAAGT 59.366 60.000 0.00 0.00 0.00 3.01
956 1183 8.109634 GTGGATATATTTCCTCTCTCTCTCTCT 58.890 40.741 12.72 0.00 36.68 3.10
957 1184 7.339466 GGTGGATATATTTCCTCTCTCTCTCTC 59.661 44.444 12.72 0.00 36.68 3.20
958 1185 7.182060 GGTGGATATATTTCCTCTCTCTCTCT 58.818 42.308 12.72 0.00 36.68 3.10
1018 1245 0.969894 GGCGGATCTAGGTATGCAGT 59.030 55.000 0.00 0.00 0.00 4.40
1078 1305 2.834549 ACAATCGAAGGACATGGAGACT 59.165 45.455 0.00 0.00 0.00 3.24
1079 1306 3.190874 GACAATCGAAGGACATGGAGAC 58.809 50.000 0.00 0.00 0.00 3.36
1080 1307 2.159240 CGACAATCGAAGGACATGGAGA 60.159 50.000 0.00 0.00 43.74 3.71
1081 1308 2.196749 CGACAATCGAAGGACATGGAG 58.803 52.381 0.00 0.00 43.74 3.86
1082 1309 1.739035 GCGACAATCGAAGGACATGGA 60.739 52.381 1.69 0.00 43.74 3.41
1083 1310 0.652592 GCGACAATCGAAGGACATGG 59.347 55.000 1.69 0.00 43.74 3.66
1084 1311 1.590238 GAGCGACAATCGAAGGACATG 59.410 52.381 1.69 0.00 43.74 3.21
1085 1312 1.799181 CGAGCGACAATCGAAGGACAT 60.799 52.381 1.69 0.00 43.74 3.06
1094 1321 1.584308 GCTCTACAACGAGCGACAATC 59.416 52.381 0.00 0.00 45.91 2.67
1224 1451 4.835284 AGAAAGGAGGAGAGAATTGTCC 57.165 45.455 0.00 0.00 37.02 4.02
1637 1876 4.741781 CGCTTGTTTCGGCGGCAG 62.742 66.667 10.53 0.00 46.42 4.85
1681 1920 0.252881 AGATGGCTTGGAGGAGGACA 60.253 55.000 0.00 0.00 0.00 4.02
1724 1963 0.249073 GCATAGATGACGCGACACCT 60.249 55.000 15.93 13.05 0.00 4.00
1729 1968 0.673437 TGATGGCATAGATGACGCGA 59.327 50.000 15.93 0.00 39.17 5.87
2510 2765 3.136896 TCCCCTACCTTAGAGGCTTAGA 58.863 50.000 0.00 0.00 39.63 2.10
2511 2766 3.614568 TCCCCTACCTTAGAGGCTTAG 57.385 52.381 0.00 0.00 39.63 2.18
2512 2767 4.078219 TGAATCCCCTACCTTAGAGGCTTA 60.078 45.833 0.00 0.00 39.63 3.09
2513 2768 3.311402 TGAATCCCCTACCTTAGAGGCTT 60.311 47.826 0.00 0.00 39.63 4.35
2514 2769 2.250273 TGAATCCCCTACCTTAGAGGCT 59.750 50.000 0.00 0.00 39.63 4.58
2515 2770 2.690840 TGAATCCCCTACCTTAGAGGC 58.309 52.381 0.00 0.00 39.63 4.70
2516 2771 4.299485 ACTTGAATCCCCTACCTTAGAGG 58.701 47.826 0.00 0.00 42.49 3.69
2517 2772 5.959583 AACTTGAATCCCCTACCTTAGAG 57.040 43.478 0.00 0.00 0.00 2.43
2577 2840 0.246635 GACACGTACCACAGGCAGAT 59.753 55.000 0.00 0.00 0.00 2.90
2587 2855 6.421801 GGTATATAACACAATGGACACGTACC 59.578 42.308 4.30 4.30 0.00 3.34
2798 3081 6.977502 CACTGATGAAACTAGTACAGATGGAG 59.022 42.308 15.51 7.41 0.00 3.86
2924 3212 6.155247 AGGAAGAGTCTAGGACTAGGAAAA 57.845 41.667 6.52 0.00 43.53 2.29
3046 3334 1.952621 AGAGATTCGGAACTGGGGAA 58.047 50.000 0.00 0.00 0.00 3.97
3052 3340 4.225267 ACCCATGTTTAGAGATTCGGAACT 59.775 41.667 0.00 0.00 0.00 3.01
3160 3449 1.985473 AGCAGCAACCATCACAAAGA 58.015 45.000 0.00 0.00 0.00 2.52
3245 3534 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
3246 3535 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3247 3536 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
3248 3537 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
3249 3538 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
3250 3539 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
3251 3540 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
3252 3541 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
3253 3542 5.106869 CGTTTTGATGACAAGTATTTCCGGA 60.107 40.000 0.00 0.00 37.32 5.14
3254 3543 5.086058 CGTTTTGATGACAAGTATTTCCGG 58.914 41.667 0.00 0.00 37.32 5.14
3255 3544 5.922546 TCGTTTTGATGACAAGTATTTCCG 58.077 37.500 0.00 0.00 37.32 4.30
3256 3545 9.834628 TTATTCGTTTTGATGACAAGTATTTCC 57.165 29.630 0.00 0.00 37.32 3.13
3261 3550 9.483916 TCTCTTTATTCGTTTTGATGACAAGTA 57.516 29.630 0.00 0.00 37.32 2.24
3262 3551 8.378172 TCTCTTTATTCGTTTTGATGACAAGT 57.622 30.769 0.00 0.00 37.32 3.16
3263 3552 8.712363 TCTCTCTTTATTCGTTTTGATGACAAG 58.288 33.333 0.00 0.00 37.32 3.16
3264 3553 8.601845 TCTCTCTTTATTCGTTTTGATGACAA 57.398 30.769 0.00 0.00 0.00 3.18
3265 3554 8.659491 CATCTCTCTTTATTCGTTTTGATGACA 58.341 33.333 0.00 0.00 32.05 3.58
3266 3555 8.660373 ACATCTCTCTTTATTCGTTTTGATGAC 58.340 33.333 0.00 0.00 33.85 3.06
3267 3556 8.777865 ACATCTCTCTTTATTCGTTTTGATGA 57.222 30.769 0.00 0.00 33.85 2.92
3276 3565 9.536558 CGTTCTAGATACATCTCTCTTTATTCG 57.463 37.037 0.00 0.00 38.32 3.34
3277 3566 9.834628 CCGTTCTAGATACATCTCTCTTTATTC 57.165 37.037 0.00 0.00 38.32 1.75
3278 3567 9.575868 TCCGTTCTAGATACATCTCTCTTTATT 57.424 33.333 0.00 0.00 38.32 1.40
3279 3568 9.575868 TTCCGTTCTAGATACATCTCTCTTTAT 57.424 33.333 0.00 0.00 38.32 1.40
3280 3569 8.975663 TTCCGTTCTAGATACATCTCTCTTTA 57.024 34.615 0.00 0.00 38.32 1.85
3281 3570 7.883391 TTCCGTTCTAGATACATCTCTCTTT 57.117 36.000 0.00 0.00 38.32 2.52
3282 3571 7.883391 TTTCCGTTCTAGATACATCTCTCTT 57.117 36.000 0.00 0.00 38.32 2.85
3283 3572 9.747898 ATATTTCCGTTCTAGATACATCTCTCT 57.252 33.333 0.00 0.00 38.32 3.10
3284 3573 9.781834 CATATTTCCGTTCTAGATACATCTCTC 57.218 37.037 0.00 0.00 38.32 3.20
3285 3574 9.303116 ACATATTTCCGTTCTAGATACATCTCT 57.697 33.333 0.00 0.00 38.32 3.10
3286 3575 9.562583 GACATATTTCCGTTCTAGATACATCTC 57.437 37.037 0.00 0.00 38.32 2.75
3287 3576 9.303116 AGACATATTTCCGTTCTAGATACATCT 57.697 33.333 0.00 0.00 40.86 2.90
3290 3579 9.346005 TGTAGACATATTTCCGTTCTAGATACA 57.654 33.333 0.00 0.00 0.00 2.29
3294 3583 9.346005 TGTATGTAGACATATTTCCGTTCTAGA 57.654 33.333 5.69 0.00 40.53 2.43
3297 3586 8.088981 GGATGTATGTAGACATATTTCCGTTCT 58.911 37.037 5.69 0.00 40.18 3.01
3298 3587 7.331193 GGGATGTATGTAGACATATTTCCGTTC 59.669 40.741 18.27 8.70 40.18 3.95
3299 3588 7.159372 GGGATGTATGTAGACATATTTCCGTT 58.841 38.462 18.27 0.00 40.18 4.44
3300 3589 6.295688 GGGGATGTATGTAGACATATTTCCGT 60.296 42.308 18.27 5.61 40.18 4.69
3301 3590 6.070767 AGGGGATGTATGTAGACATATTTCCG 60.071 42.308 18.27 0.00 40.18 4.30
3302 3591 7.259088 AGGGGATGTATGTAGACATATTTCC 57.741 40.000 17.44 17.44 40.18 3.13
3303 3592 9.574516 AAAAGGGGATGTATGTAGACATATTTC 57.425 33.333 5.69 6.11 40.18 2.17
3304 3593 9.936329 AAAAAGGGGATGTATGTAGACATATTT 57.064 29.630 5.69 0.00 40.18 1.40
3308 3597 8.949421 AGATAAAAAGGGGATGTATGTAGACAT 58.051 33.333 0.08 0.08 42.82 3.06
3309 3598 8.331931 AGATAAAAAGGGGATGTATGTAGACA 57.668 34.615 0.00 0.00 0.00 3.41
3336 3625 9.190858 CCGAAAATACTTGTCATCAAATCAAAA 57.809 29.630 0.00 0.00 32.87 2.44
3337 3626 8.572185 TCCGAAAATACTTGTCATCAAATCAAA 58.428 29.630 0.00 0.00 32.87 2.69
3338 3627 8.020819 GTCCGAAAATACTTGTCATCAAATCAA 58.979 33.333 0.00 0.00 32.87 2.57
3339 3628 7.526608 GTCCGAAAATACTTGTCATCAAATCA 58.473 34.615 0.00 0.00 32.87 2.57
3340 3629 6.682863 CGTCCGAAAATACTTGTCATCAAATC 59.317 38.462 0.00 0.00 32.87 2.17
3341 3630 6.403200 CCGTCCGAAAATACTTGTCATCAAAT 60.403 38.462 0.00 0.00 32.87 2.32
3342 3631 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
3343 3632 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
3344 3633 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
3345 3634 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
3346 3635 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
3347 3636 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
3348 3637 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
3349 3638 2.968675 CCTCCGTCCGAAAATACTTGT 58.031 47.619 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.