Multiple sequence alignment - TraesCS2A01G298800

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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 TraesCS2A01G298800 chr2A 100.000 3159 0 0 556 3714 514745794 514748952 0.000000e+00 5834
1 TraesCS2A01G298800 chr2A 100.000 250 0 0 1 250 514745239 514745488 2.610000e-126 462
2 TraesCS2A01G298800 chr2B 94.647 2690 93 23 577 3233 450757804 450760475 0.000000e+00 4122
3 TraesCS2A01G298800 chr2B 93.381 423 23 3 3276 3695 450760410 450760830 4.070000e-174 621
4 TraesCS2A01G298800 chr2B 80.645 279 17 9 1 250 450757385 450757655 8.190000e-42 182
5 TraesCS2A01G298800 chr2D 94.346 2034 74 19 1232 3229 379720514 379722542 0.000000e+00 3081
6 TraesCS2A01G298800 chr2D 90.409 636 36 17 556 1186 379718868 379719483 0.000000e+00 813
7 TraesCS2A01G298800 chr2D 93.439 442 23 3 3276 3714 379722482 379722920 0.000000e+00 651
8 TraesCS2A01G298800 chr2D 89.032 155 12 3 1 155 379707285 379707434 1.760000e-43 187


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 TraesCS2A01G298800 chr2A 514745239 514748952 3713 False 3148.000000 5834 100.000000 1 3714 2 chr2A.!!$F1 3713
1 TraesCS2A01G298800 chr2B 450757385 450760830 3445 False 1641.666667 4122 89.557667 1 3695 3 chr2B.!!$F1 3694
2 TraesCS2A01G298800 chr2D 379718868 379722920 4052 False 1515.000000 3081 92.731333 556 3714 3 chr2D.!!$F2 3158

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
155 162 0.469144 ACCAAACCATCCGCAAACCT 60.469 50.0 0.0 0.0 0.00 3.50 F
1098 1136 0.174617 CCTCCTCTGCTCGTTCCTTC 59.825 60.0 0.0 0.0 0.00 3.46 F
1127 1165 0.179073 CAGAATGATCCGCTCCGGTT 60.179 55.0 0.0 0.0 43.92 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 3102 0.106918 TATGGCGTTAGGGGGCAAAG 60.107 55.000 0.00 0.00 43.55 2.77 R
2129 3175 0.737219 GGTGCCTGATGATCAGCAAC 59.263 55.000 15.55 16.01 42.98 4.17 R
2753 3809 4.985538 ACGACACCAACCAATGTAAAAA 57.014 36.364 0.00 0.00 0.00 1.94 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
26 27 6.830873 AAGCAAAAGCATAAGACAGAAGAT 57.169 33.333 0.00 0.00 0.00 2.40
27 28 6.830873 AGCAAAAGCATAAGACAGAAGATT 57.169 33.333 0.00 0.00 0.00 2.40
47 48 3.427425 CGTGATTCGGCGCCCAAA 61.427 61.111 23.46 16.45 35.71 3.28
48 49 2.178273 GTGATTCGGCGCCCAAAC 59.822 61.111 23.46 14.62 0.00 2.93
49 50 2.033448 TGATTCGGCGCCCAAACT 59.967 55.556 23.46 0.00 0.00 2.66
50 51 2.331893 TGATTCGGCGCCCAAACTG 61.332 57.895 23.46 5.48 0.00 3.16
51 52 3.683587 GATTCGGCGCCCAAACTGC 62.684 63.158 23.46 2.09 0.00 4.40
74 75 6.152661 TGCAGACCAGAAACCCTAAAAATATG 59.847 38.462 0.00 0.00 0.00 1.78
75 76 6.405842 GCAGACCAGAAACCCTAAAAATATGG 60.406 42.308 0.00 0.00 0.00 2.74
76 77 6.663523 CAGACCAGAAACCCTAAAAATATGGT 59.336 38.462 0.00 0.00 41.06 3.55
77 78 7.832187 CAGACCAGAAACCCTAAAAATATGGTA 59.168 37.037 0.00 0.00 38.58 3.25
78 79 8.566109 AGACCAGAAACCCTAAAAATATGGTAT 58.434 33.333 0.00 0.00 38.58 2.73
88 89 5.860648 AAAAATATGGTATCCCCCGATCT 57.139 39.130 0.00 0.00 0.00 2.75
97 98 1.144057 CCCCCGATCTCTCCAAACG 59.856 63.158 0.00 0.00 0.00 3.60
99 100 0.535335 CCCCGATCTCTCCAAACGAA 59.465 55.000 0.00 0.00 0.00 3.85
137 144 1.187087 AATCACAGGGAGTCGAGGAC 58.813 55.000 0.00 0.00 0.00 3.85
146 153 1.405661 GGAGTCGAGGACCAAACCATC 60.406 57.143 0.00 0.00 32.18 3.51
147 154 0.613777 AGTCGAGGACCAAACCATCC 59.386 55.000 0.00 0.00 32.18 3.51
149 156 2.106683 CGAGGACCAAACCATCCGC 61.107 63.158 0.00 0.00 40.20 5.54
155 162 0.469144 ACCAAACCATCCGCAAACCT 60.469 50.000 0.00 0.00 0.00 3.50
156 163 0.678950 CCAAACCATCCGCAAACCTT 59.321 50.000 0.00 0.00 0.00 3.50
157 164 1.336795 CCAAACCATCCGCAAACCTTC 60.337 52.381 0.00 0.00 0.00 3.46
158 165 0.596082 AAACCATCCGCAAACCTTCG 59.404 50.000 0.00 0.00 0.00 3.79
161 179 2.033448 ATCCGCAAACCTTCGCCA 59.967 55.556 0.00 0.00 0.00 5.69
175 193 3.313526 CCTTCGCCATCACAAGAATTAGG 59.686 47.826 0.00 0.00 0.00 2.69
195 213 4.779475 CCAGTCGGCAGTCTGTTT 57.221 55.556 9.81 0.00 32.79 2.83
197 215 1.284982 CCAGTCGGCAGTCTGTTTCG 61.285 60.000 9.81 4.14 32.79 3.46
199 217 2.733218 TCGGCAGTCTGTTTCGCG 60.733 61.111 0.00 0.00 0.00 5.87
200 218 4.430423 CGGCAGTCTGTTTCGCGC 62.430 66.667 0.00 0.00 0.00 6.86
201 219 3.345808 GGCAGTCTGTTTCGCGCA 61.346 61.111 8.75 0.00 0.00 6.09
589 619 2.896854 CCATGGGCCACACGATCG 60.897 66.667 9.28 14.88 0.00 3.69
623 653 4.765273 TCAACCAAAGCCTTTTCTTTTCC 58.235 39.130 0.00 0.00 34.31 3.13
624 654 3.452755 ACCAAAGCCTTTTCTTTTCCG 57.547 42.857 0.00 0.00 34.31 4.30
628 658 0.591659 AGCCTTTTCTTTTCCGCGAC 59.408 50.000 8.23 0.00 0.00 5.19
724 756 3.934962 GCAGGATCTCGGCCCCTC 61.935 72.222 0.00 0.00 0.00 4.30
725 757 3.237741 CAGGATCTCGGCCCCTCC 61.238 72.222 0.00 0.00 0.00 4.30
726 758 3.443479 AGGATCTCGGCCCCTCCT 61.443 66.667 0.00 0.08 33.23 3.69
764 797 3.330720 CCACACTCCCACTCCCCC 61.331 72.222 0.00 0.00 0.00 5.40
765 798 2.529136 CACACTCCCACTCCCCCA 60.529 66.667 0.00 0.00 0.00 4.96
1098 1136 0.174617 CCTCCTCTGCTCGTTCCTTC 59.825 60.000 0.00 0.00 0.00 3.46
1127 1165 0.179073 CAGAATGATCCGCTCCGGTT 60.179 55.000 0.00 0.00 43.92 4.44
1128 1166 1.743772 CAGAATGATCCGCTCCGGTTT 60.744 52.381 0.00 0.00 43.92 3.27
1129 1167 3.880592 CAGAATGATCCGCTCCGGTTTG 61.881 54.545 0.00 0.00 43.92 2.93
1146 1184 2.606717 TTGTGTAGCGTAGAGACACG 57.393 50.000 0.00 0.00 44.22 4.49
1255 2286 3.270027 TCCTGTAGGTGCAAATTCATCG 58.730 45.455 0.00 0.00 36.34 3.84
1274 2305 2.028203 TCGATGAATCTGGTTGAGTGCA 60.028 45.455 0.00 0.00 0.00 4.57
1303 2335 1.474478 GATCTGCTTCCACTCTCACGA 59.526 52.381 0.00 0.00 0.00 4.35
1315 2347 2.490115 ACTCTCACGAACACTCTCATCC 59.510 50.000 0.00 0.00 0.00 3.51
1365 2398 2.597520 GACTTTGAGTACGGTGCTCTC 58.402 52.381 23.54 11.45 34.30 3.20
1437 2470 1.982073 GCAACTATGGCGTGCACTCC 61.982 60.000 19.17 19.17 0.00 3.85
1518 2551 7.338710 AGGATGAATATTGGGGATACATTACG 58.661 38.462 0.00 0.00 39.74 3.18
1530 2563 1.519408 ACATTACGAACTGTGGCACC 58.481 50.000 16.26 0.00 0.00 5.01
1681 2725 3.006323 GGATCTTGTATGCCTCTCGTGAT 59.994 47.826 0.00 0.00 0.00 3.06
1684 2728 3.447229 TCTTGTATGCCTCTCGTGATTCA 59.553 43.478 0.00 0.00 0.00 2.57
1693 2737 3.486043 CCTCTCGTGATTCACACTACTCG 60.486 52.174 16.61 1.30 46.24 4.18
1840 2884 3.928727 AATGTCAACATTGGTGAGCTG 57.071 42.857 4.21 0.00 44.22 4.24
1854 2898 4.080919 TGGTGAGCTGCATACACTCTTTAT 60.081 41.667 18.28 0.00 35.28 1.40
1856 2900 6.049149 GGTGAGCTGCATACACTCTTTATTA 58.951 40.000 18.28 0.00 35.28 0.98
1901 2945 3.118884 TGATCGGGCTGTAAACCTAACTC 60.119 47.826 0.00 0.00 0.00 3.01
2009 3053 7.208080 AGGATCGGTTTTATATACACTGTGAC 58.792 38.462 15.86 0.00 0.00 3.67
2058 3102 5.585047 CCATTTGTTAAGCAGGTACCTCTAC 59.415 44.000 12.84 4.60 0.00 2.59
2105 3151 6.455513 GGTTGCTTCTTTTGACACATTGTTTC 60.456 38.462 0.00 0.00 0.00 2.78
2540 3586 1.584380 GCAGCTTGCTTGTGAGGGAG 61.584 60.000 0.00 0.00 40.96 4.30
2708 3754 4.122776 CTGTCTTTGTACTCTGCACAAGT 58.877 43.478 2.76 2.76 37.22 3.16
2753 3809 7.566760 CTCTCTGTGAGTGATACTTGAGTAT 57.433 40.000 3.40 3.40 39.52 2.12
2754 3810 7.946381 TCTCTGTGAGTGATACTTGAGTATT 57.054 36.000 5.22 0.00 40.99 1.89
2873 3946 3.403277 GCACGGTAGCATGCTGAG 58.597 61.111 30.42 21.32 38.84 3.35
2883 3956 2.719739 AGCATGCTGAGCTTTATGTGT 58.280 42.857 21.98 0.00 39.87 3.72
2908 3981 6.268566 TGTATTCATCGTCTGTCTTCATCTG 58.731 40.000 0.00 0.00 0.00 2.90
2915 3988 3.923461 CGTCTGTCTTCATCTGTTCTTCC 59.077 47.826 0.00 0.00 0.00 3.46
2997 4070 4.201714 CGGCATGCCATATTCGTAACATAG 60.202 45.833 34.93 9.99 35.37 2.23
3178 4251 7.666623 TGTTTTTCTTGAGAAATAATGGGTCC 58.333 34.615 6.98 0.00 42.83 4.46
3222 4295 6.426646 AGAGTCTTAACACAGAAACATCCT 57.573 37.500 0.00 0.00 0.00 3.24
3223 4296 6.831976 AGAGTCTTAACACAGAAACATCCTT 58.168 36.000 0.00 0.00 0.00 3.36
3224 4297 7.283329 AGAGTCTTAACACAGAAACATCCTTT 58.717 34.615 0.00 0.00 0.00 3.11
3225 4298 7.227512 AGAGTCTTAACACAGAAACATCCTTTG 59.772 37.037 0.00 0.00 0.00 2.77
3226 4299 5.915196 GTCTTAACACAGAAACATCCTTTGC 59.085 40.000 0.00 0.00 0.00 3.68
3227 4300 5.592282 TCTTAACACAGAAACATCCTTTGCA 59.408 36.000 0.00 0.00 0.00 4.08
3228 4301 3.715628 ACACAGAAACATCCTTTGCAC 57.284 42.857 0.00 0.00 0.00 4.57
3229 4302 3.290710 ACACAGAAACATCCTTTGCACT 58.709 40.909 0.00 0.00 0.00 4.40
3230 4303 3.701040 ACACAGAAACATCCTTTGCACTT 59.299 39.130 0.00 0.00 0.00 3.16
3231 4304 4.887071 ACACAGAAACATCCTTTGCACTTA 59.113 37.500 0.00 0.00 0.00 2.24
3232 4305 5.536161 ACACAGAAACATCCTTTGCACTTAT 59.464 36.000 0.00 0.00 0.00 1.73
3233 4306 6.088824 CACAGAAACATCCTTTGCACTTATC 58.911 40.000 0.00 0.00 0.00 1.75
3234 4307 5.183904 ACAGAAACATCCTTTGCACTTATCC 59.816 40.000 0.00 0.00 0.00 2.59
3235 4308 5.416952 CAGAAACATCCTTTGCACTTATCCT 59.583 40.000 0.00 0.00 0.00 3.24
3236 4309 6.599244 CAGAAACATCCTTTGCACTTATCCTA 59.401 38.462 0.00 0.00 0.00 2.94
3237 4310 6.599638 AGAAACATCCTTTGCACTTATCCTAC 59.400 38.462 0.00 0.00 0.00 3.18
3238 4311 5.435686 ACATCCTTTGCACTTATCCTACA 57.564 39.130 0.00 0.00 0.00 2.74
3239 4312 6.006275 ACATCCTTTGCACTTATCCTACAT 57.994 37.500 0.00 0.00 0.00 2.29
3240 4313 6.426587 ACATCCTTTGCACTTATCCTACATT 58.573 36.000 0.00 0.00 0.00 2.71
3241 4314 6.543831 ACATCCTTTGCACTTATCCTACATTC 59.456 38.462 0.00 0.00 0.00 2.67
3242 4315 5.116180 TCCTTTGCACTTATCCTACATTCG 58.884 41.667 0.00 0.00 0.00 3.34
3243 4316 4.260784 CCTTTGCACTTATCCTACATTCGC 60.261 45.833 0.00 0.00 0.00 4.70
3244 4317 2.469826 TGCACTTATCCTACATTCGCG 58.530 47.619 0.00 0.00 0.00 5.87
3245 4318 2.159156 TGCACTTATCCTACATTCGCGT 60.159 45.455 5.77 0.00 0.00 6.01
3246 4319 2.864343 GCACTTATCCTACATTCGCGTT 59.136 45.455 5.77 0.00 0.00 4.84
3247 4320 3.060473 GCACTTATCCTACATTCGCGTTC 60.060 47.826 5.77 0.00 0.00 3.95
3248 4321 4.360563 CACTTATCCTACATTCGCGTTCT 58.639 43.478 5.77 0.00 0.00 3.01
3249 4322 4.207224 CACTTATCCTACATTCGCGTTCTG 59.793 45.833 5.77 4.84 0.00 3.02
3250 4323 2.225068 ATCCTACATTCGCGTTCTGG 57.775 50.000 5.77 2.62 0.00 3.86
3251 4324 0.459585 TCCTACATTCGCGTTCTGGC 60.460 55.000 5.77 0.00 0.00 4.85
3252 4325 0.739462 CCTACATTCGCGTTCTGGCA 60.739 55.000 5.77 0.00 0.00 4.92
3253 4326 0.647410 CTACATTCGCGTTCTGGCAG 59.353 55.000 8.58 8.58 0.00 4.85
3254 4327 0.245266 TACATTCGCGTTCTGGCAGA 59.755 50.000 14.43 14.43 0.00 4.26
3255 4328 0.391661 ACATTCGCGTTCTGGCAGAT 60.392 50.000 19.50 0.00 0.00 2.90
3256 4329 0.729116 CATTCGCGTTCTGGCAGATT 59.271 50.000 19.50 0.00 0.00 2.40
3257 4330 0.729116 ATTCGCGTTCTGGCAGATTG 59.271 50.000 19.50 14.57 0.00 2.67
3258 4331 0.602638 TTCGCGTTCTGGCAGATTGT 60.603 50.000 19.50 0.00 0.00 2.71
3259 4332 1.133253 CGCGTTCTGGCAGATTGTG 59.867 57.895 19.50 15.83 0.00 3.33
3260 4333 1.503542 GCGTTCTGGCAGATTGTGG 59.496 57.895 19.50 7.17 0.00 4.17
3261 4334 1.237285 GCGTTCTGGCAGATTGTGGT 61.237 55.000 19.50 0.00 0.00 4.16
3262 4335 0.518636 CGTTCTGGCAGATTGTGGTG 59.481 55.000 19.50 0.00 0.00 4.17
3263 4336 1.609208 GTTCTGGCAGATTGTGGTGT 58.391 50.000 19.50 0.00 0.00 4.16
3264 4337 1.956477 GTTCTGGCAGATTGTGGTGTT 59.044 47.619 19.50 0.00 0.00 3.32
3265 4338 3.146066 GTTCTGGCAGATTGTGGTGTTA 58.854 45.455 19.50 0.00 0.00 2.41
3266 4339 3.500448 TCTGGCAGATTGTGGTGTTAA 57.500 42.857 14.43 0.00 0.00 2.01
3267 4340 4.032960 TCTGGCAGATTGTGGTGTTAAT 57.967 40.909 14.43 0.00 0.00 1.40
3268 4341 3.758023 TCTGGCAGATTGTGGTGTTAATG 59.242 43.478 14.43 0.00 0.00 1.90
3269 4342 3.758023 CTGGCAGATTGTGGTGTTAATGA 59.242 43.478 9.42 0.00 0.00 2.57
3270 4343 3.505680 TGGCAGATTGTGGTGTTAATGAC 59.494 43.478 0.00 0.00 0.00 3.06
3271 4344 3.758554 GGCAGATTGTGGTGTTAATGACT 59.241 43.478 0.00 0.00 0.00 3.41
3272 4345 4.142600 GGCAGATTGTGGTGTTAATGACTC 60.143 45.833 0.00 0.00 0.00 3.36
3273 4346 4.455533 GCAGATTGTGGTGTTAATGACTCA 59.544 41.667 0.00 0.00 0.00 3.41
3274 4347 5.124457 GCAGATTGTGGTGTTAATGACTCAT 59.876 40.000 0.00 0.00 0.00 2.90
3275 4348 6.316140 GCAGATTGTGGTGTTAATGACTCATA 59.684 38.462 0.00 0.00 0.00 2.15
3276 4349 7.148255 GCAGATTGTGGTGTTAATGACTCATAA 60.148 37.037 0.00 0.00 0.00 1.90
3277 4350 8.393366 CAGATTGTGGTGTTAATGACTCATAAG 58.607 37.037 0.00 0.00 0.00 1.73
3278 4351 8.321353 AGATTGTGGTGTTAATGACTCATAAGA 58.679 33.333 0.00 0.00 0.00 2.10
3279 4352 8.862325 ATTGTGGTGTTAATGACTCATAAGAA 57.138 30.769 0.00 0.00 0.00 2.52
3280 4353 8.862325 TTGTGGTGTTAATGACTCATAAGAAT 57.138 30.769 0.00 0.00 0.00 2.40
3281 4354 8.267620 TGTGGTGTTAATGACTCATAAGAATG 57.732 34.615 0.00 0.00 0.00 2.67
3282 4355 7.336679 TGTGGTGTTAATGACTCATAAGAATGG 59.663 37.037 0.00 0.00 33.61 3.16
3283 4356 6.828273 TGGTGTTAATGACTCATAAGAATGGG 59.172 38.462 0.00 0.00 39.71 4.00
3292 4365 6.319048 ACTCATAAGAATGGGTCAATGACT 57.681 37.500 13.53 0.00 43.70 3.41
3293 4366 6.352516 ACTCATAAGAATGGGTCAATGACTC 58.647 40.000 13.53 10.13 43.70 3.36
3294 4367 6.070021 ACTCATAAGAATGGGTCAATGACTCA 60.070 38.462 19.14 19.14 43.70 3.41
3304 4377 7.147958 TGGGTCAATGACTCATAATAATCCA 57.852 36.000 12.59 4.30 38.21 3.41
3305 4378 7.226441 TGGGTCAATGACTCATAATAATCCAG 58.774 38.462 12.59 0.00 38.21 3.86
3306 4379 7.072328 TGGGTCAATGACTCATAATAATCCAGA 59.928 37.037 12.59 0.00 38.21 3.86
3307 4380 7.939039 GGGTCAATGACTCATAATAATCCAGAA 59.061 37.037 13.53 0.00 32.50 3.02
3308 4381 8.997323 GGTCAATGACTCATAATAATCCAGAAG 58.003 37.037 13.53 0.00 32.47 2.85
3309 4382 9.770097 GTCAATGACTCATAATAATCCAGAAGA 57.230 33.333 6.07 0.00 0.00 2.87
3310 4383 9.993454 TCAATGACTCATAATAATCCAGAAGAG 57.007 33.333 0.00 0.00 0.00 2.85
3311 4384 9.775854 CAATGACTCATAATAATCCAGAAGAGT 57.224 33.333 0.00 0.00 37.76 3.24
3312 4385 9.995003 AATGACTCATAATAATCCAGAAGAGTC 57.005 33.333 11.19 11.19 46.58 3.36
3313 4386 8.774546 TGACTCATAATAATCCAGAAGAGTCT 57.225 34.615 16.97 0.00 46.55 3.24
3314 4387 9.206690 TGACTCATAATAATCCAGAAGAGTCTT 57.793 33.333 4.68 4.68 46.55 3.01
3319 4392 9.495572 CATAATAATCCAGAAGAGTCTTAACCC 57.504 37.037 5.09 0.00 28.78 4.11
3320 4393 7.510675 AATAATCCAGAAGAGTCTTAACCCA 57.489 36.000 5.09 0.00 28.78 4.51
3321 4394 5.428184 AATCCAGAAGAGTCTTAACCCAG 57.572 43.478 5.09 0.00 28.78 4.45
3322 4395 4.127918 TCCAGAAGAGTCTTAACCCAGA 57.872 45.455 5.09 0.00 28.78 3.86
3323 4396 4.489737 TCCAGAAGAGTCTTAACCCAGAA 58.510 43.478 5.09 0.00 28.78 3.02
3324 4397 4.905456 TCCAGAAGAGTCTTAACCCAGAAA 59.095 41.667 5.09 0.00 28.78 2.52
3325 4398 4.998033 CCAGAAGAGTCTTAACCCAGAAAC 59.002 45.833 5.09 0.00 28.78 2.78
3326 4399 5.454755 CCAGAAGAGTCTTAACCCAGAAACA 60.455 44.000 5.09 0.00 28.78 2.83
3327 4400 6.234177 CAGAAGAGTCTTAACCCAGAAACAT 58.766 40.000 5.09 0.00 28.78 2.71
3328 4401 6.370166 CAGAAGAGTCTTAACCCAGAAACATC 59.630 42.308 5.09 0.00 28.78 3.06
3499 4574 2.359900 CTACCACTAGCAGCAAAAGGG 58.640 52.381 0.00 0.00 0.00 3.95
3503 4578 3.245264 ACCACTAGCAGCAAAAGGGTAAT 60.245 43.478 0.00 0.00 0.00 1.89
3504 4579 3.378427 CCACTAGCAGCAAAAGGGTAATC 59.622 47.826 0.00 0.00 0.00 1.75
3522 4597 8.452868 AGGGTAATCTCTATCTGTCAGATACTT 58.547 37.037 17.07 11.10 36.20 2.24
3548 4623 1.371558 GTCAGAACCTCTTGGCCGT 59.628 57.895 0.00 0.00 36.63 5.68
3598 4673 6.013379 TCTGGATTCAACCTATTTCTGTCAGT 60.013 38.462 0.00 0.00 0.00 3.41
3602 4677 4.973168 TCAACCTATTTCTGTCAGTTGCT 58.027 39.130 0.00 0.00 35.67 3.91
3620 4695 1.117994 CTGGAGTGCATCTAGAGGCA 58.882 55.000 27.07 27.07 46.53 4.75
3698 4777 3.792515 AGAGCTACTTAAGTTGACCCCT 58.207 45.455 19.37 7.73 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 1.338020 GGGTTTCTGGTCTGCAGTTTG 59.662 52.381 14.67 3.17 0.00 2.93
47 48 1.729586 TAGGGTTTCTGGTCTGCAGT 58.270 50.000 14.67 0.00 0.00 4.40
48 49 2.859165 TTAGGGTTTCTGGTCTGCAG 57.141 50.000 7.63 7.63 0.00 4.41
49 50 3.586470 TTTTAGGGTTTCTGGTCTGCA 57.414 42.857 0.00 0.00 0.00 4.41
50 51 6.405842 CCATATTTTTAGGGTTTCTGGTCTGC 60.406 42.308 0.00 0.00 0.00 4.26
51 52 6.663523 ACCATATTTTTAGGGTTTCTGGTCTG 59.336 38.462 0.00 0.00 28.45 3.51
52 53 6.800890 ACCATATTTTTAGGGTTTCTGGTCT 58.199 36.000 0.00 0.00 28.45 3.85
75 76 2.011122 TTGGAGAGATCGGGGGATAC 57.989 55.000 0.00 0.00 0.00 2.24
76 77 2.326428 GTTTGGAGAGATCGGGGGATA 58.674 52.381 0.00 0.00 0.00 2.59
77 78 1.132500 GTTTGGAGAGATCGGGGGAT 58.868 55.000 0.00 0.00 0.00 3.85
78 79 1.327690 CGTTTGGAGAGATCGGGGGA 61.328 60.000 0.00 0.00 0.00 4.81
88 89 3.541632 GCATTAGGGATTCGTTTGGAGA 58.458 45.455 0.00 0.00 0.00 3.71
97 98 5.505181 TTATCTCTGGGCATTAGGGATTC 57.495 43.478 3.81 0.00 36.74 2.52
99 100 5.045286 GTGATTATCTCTGGGCATTAGGGAT 60.045 44.000 3.94 3.94 38.80 3.85
137 144 0.678950 AAGGTTTGCGGATGGTTTGG 59.321 50.000 0.00 0.00 0.00 3.28
146 153 2.331893 TGATGGCGAAGGTTTGCGG 61.332 57.895 0.00 0.00 38.49 5.69
147 154 1.154225 GTGATGGCGAAGGTTTGCG 60.154 57.895 0.00 0.00 38.49 4.85
149 156 1.879380 TCTTGTGATGGCGAAGGTTTG 59.121 47.619 0.00 0.00 0.00 2.93
155 162 3.278574 CCCTAATTCTTGTGATGGCGAA 58.721 45.455 0.00 0.00 0.00 4.70
156 163 2.421388 CCCCTAATTCTTGTGATGGCGA 60.421 50.000 0.00 0.00 0.00 5.54
157 164 1.949525 CCCCTAATTCTTGTGATGGCG 59.050 52.381 0.00 0.00 0.00 5.69
158 165 1.683385 GCCCCTAATTCTTGTGATGGC 59.317 52.381 0.00 0.00 0.00 4.40
161 179 2.582636 ACTGGCCCCTAATTCTTGTGAT 59.417 45.455 0.00 0.00 0.00 3.06
193 211 0.665068 TTAGTCGAAGCTGCGCGAAA 60.665 50.000 12.10 10.38 38.36 3.46
194 212 0.665068 TTTAGTCGAAGCTGCGCGAA 60.665 50.000 12.10 0.00 38.36 4.70
195 213 0.665068 TTTTAGTCGAAGCTGCGCGA 60.665 50.000 12.10 14.73 0.00 5.87
197 215 1.529826 CCATTTTAGTCGAAGCTGCGC 60.530 52.381 10.01 0.00 0.00 6.09
199 217 4.346129 CATTCCATTTTAGTCGAAGCTGC 58.654 43.478 0.00 0.00 0.00 5.25
200 218 4.346129 GCATTCCATTTTAGTCGAAGCTG 58.654 43.478 0.00 0.00 0.00 4.24
201 219 3.063997 CGCATTCCATTTTAGTCGAAGCT 59.936 43.478 0.00 0.00 0.00 3.74
573 603 3.576356 GCGATCGTGTGGCCCATG 61.576 66.667 17.81 3.45 0.00 3.66
578 608 3.545481 CTGTCGCGATCGTGTGGC 61.545 66.667 26.40 17.92 36.96 5.01
589 619 1.523154 TTGGTTGATTGGCCTGTCGC 61.523 55.000 3.32 0.00 0.00 5.19
721 753 3.687828 AAGGCGGAGGAGGAGGAGG 62.688 68.421 0.00 0.00 0.00 4.30
722 754 2.042435 AAGGCGGAGGAGGAGGAG 60.042 66.667 0.00 0.00 0.00 3.69
723 755 2.042843 GAAGGCGGAGGAGGAGGA 60.043 66.667 0.00 0.00 0.00 3.71
724 756 2.042435 AGAAGGCGGAGGAGGAGG 60.042 66.667 0.00 0.00 0.00 4.30
725 757 2.131067 GGAGAAGGCGGAGGAGGAG 61.131 68.421 0.00 0.00 0.00 3.69
726 758 2.042843 GGAGAAGGCGGAGGAGGA 60.043 66.667 0.00 0.00 0.00 3.71
764 797 1.677633 GTCGGGGGTGGTTGGAATG 60.678 63.158 0.00 0.00 0.00 2.67
765 798 2.761160 GTCGGGGGTGGTTGGAAT 59.239 61.111 0.00 0.00 0.00 3.01
1098 1136 0.299895 GATCATTCTGCACTGCGTCG 59.700 55.000 0.00 0.00 0.00 5.12
1127 1165 1.198408 CCGTGTCTCTACGCTACACAA 59.802 52.381 0.00 0.00 42.87 3.33
1128 1166 0.800631 CCGTGTCTCTACGCTACACA 59.199 55.000 0.00 0.00 42.87 3.72
1129 1167 0.801251 ACCGTGTCTCTACGCTACAC 59.199 55.000 0.00 0.00 42.44 2.90
1130 1168 0.800631 CACCGTGTCTCTACGCTACA 59.199 55.000 0.00 0.00 42.44 2.74
1131 1169 1.081892 TCACCGTGTCTCTACGCTAC 58.918 55.000 0.00 0.00 42.44 3.58
1146 1184 1.867363 ATATCGGGGCTAGGATCACC 58.133 55.000 0.00 0.00 0.00 4.02
1255 2286 4.088823 GTTGCACTCAACCAGATTCATC 57.911 45.455 0.00 0.00 45.15 2.92
1274 2305 1.160137 GGAAGCAGATCAGTTGCGTT 58.840 50.000 0.00 0.00 45.98 4.84
1276 2307 0.445436 GTGGAAGCAGATCAGTTGCG 59.555 55.000 0.00 0.00 45.98 4.85
1303 2335 2.549754 CAAGCAAACGGATGAGAGTGTT 59.450 45.455 0.00 0.00 0.00 3.32
1315 2347 1.084289 GGGTAGCCTACAAGCAAACG 58.916 55.000 2.95 0.00 34.23 3.60
1365 2398 2.033757 AAGTGCTGCAGCTGGGAG 59.966 61.111 36.61 8.04 42.66 4.30
1437 2470 0.670162 CACCCACTTCAAACTGCCTG 59.330 55.000 0.00 0.00 0.00 4.85
1518 2551 0.534203 TTCCTTCGGTGCCACAGTTC 60.534 55.000 0.00 0.00 0.00 3.01
1530 2563 2.042686 TCCCATGCAGATTTCCTTCG 57.957 50.000 0.00 0.00 0.00 3.79
1693 2737 0.944386 TTCTCGCTGCTTTGAACACC 59.056 50.000 0.00 0.00 0.00 4.16
1840 2884 7.072177 TGCAAGTGTAATAAAGAGTGTATGC 57.928 36.000 0.00 0.00 0.00 3.14
1901 2945 4.256920 CAGTTGTCCCTACATCAAGGAAG 58.743 47.826 0.00 0.00 39.15 3.46
2009 3053 0.249868 TCAGACCAAACAGAGCACCG 60.250 55.000 0.00 0.00 0.00 4.94
2058 3102 0.106918 TATGGCGTTAGGGGGCAAAG 60.107 55.000 0.00 0.00 43.55 2.77
2129 3175 0.737219 GGTGCCTGATGATCAGCAAC 59.263 55.000 15.55 16.01 42.98 4.17
2365 3411 8.656806 TGAACTTCCTTCTGAAAACCTCTATAA 58.343 33.333 0.00 0.00 31.06 0.98
2753 3809 4.985538 ACGACACCAACCAATGTAAAAA 57.014 36.364 0.00 0.00 0.00 1.94
2754 3810 6.636562 AATACGACACCAACCAATGTAAAA 57.363 33.333 0.00 0.00 0.00 1.52
2873 3946 6.901887 CAGACGATGAATACAACACATAAAGC 59.098 38.462 0.00 0.00 0.00 3.51
2883 3956 6.753744 CAGATGAAGACAGACGATGAATACAA 59.246 38.462 0.00 0.00 0.00 2.41
2908 3981 6.072112 TGCACAGAACTTTATTGGAAGAAC 57.928 37.500 0.00 0.00 0.00 3.01
2915 3988 7.878477 ACATCATTTGCACAGAACTTTATTG 57.122 32.000 0.00 0.00 0.00 1.90
2997 4070 7.646130 TGCTATACTTTGTAAAACAACACAAGC 59.354 33.333 0.00 0.53 37.90 4.01
3178 4251 7.499292 ACTCTTCTGGATTCTTATGAGTCATG 58.501 38.462 16.15 0.00 31.51 3.07
3222 4295 3.308595 CGCGAATGTAGGATAAGTGCAAA 59.691 43.478 0.00 0.00 0.00 3.68
3223 4296 2.863740 CGCGAATGTAGGATAAGTGCAA 59.136 45.455 0.00 0.00 0.00 4.08
3224 4297 2.159156 ACGCGAATGTAGGATAAGTGCA 60.159 45.455 15.93 0.00 0.00 4.57
3225 4298 2.470821 ACGCGAATGTAGGATAAGTGC 58.529 47.619 15.93 0.00 0.00 4.40
3226 4299 4.207224 CAGAACGCGAATGTAGGATAAGTG 59.793 45.833 15.93 0.00 0.00 3.16
3227 4300 4.360563 CAGAACGCGAATGTAGGATAAGT 58.639 43.478 15.93 0.00 0.00 2.24
3228 4301 3.736252 CCAGAACGCGAATGTAGGATAAG 59.264 47.826 15.93 0.00 0.00 1.73
3229 4302 3.713288 CCAGAACGCGAATGTAGGATAA 58.287 45.455 15.93 0.00 0.00 1.75
3230 4303 2.545113 GCCAGAACGCGAATGTAGGATA 60.545 50.000 15.93 0.00 0.00 2.59
3231 4304 1.806623 GCCAGAACGCGAATGTAGGAT 60.807 52.381 15.93 0.00 0.00 3.24
3232 4305 0.459585 GCCAGAACGCGAATGTAGGA 60.460 55.000 15.93 0.00 0.00 2.94
3233 4306 0.739462 TGCCAGAACGCGAATGTAGG 60.739 55.000 15.93 7.95 0.00 3.18
3234 4307 0.647410 CTGCCAGAACGCGAATGTAG 59.353 55.000 15.93 5.25 0.00 2.74
3235 4308 0.245266 TCTGCCAGAACGCGAATGTA 59.755 50.000 15.93 0.00 0.00 2.29
3236 4309 0.391661 ATCTGCCAGAACGCGAATGT 60.392 50.000 15.93 0.00 0.00 2.71
3237 4310 0.729116 AATCTGCCAGAACGCGAATG 59.271 50.000 15.93 8.14 0.00 2.67
3238 4311 0.729116 CAATCTGCCAGAACGCGAAT 59.271 50.000 15.93 0.00 0.00 3.34
3239 4312 0.602638 ACAATCTGCCAGAACGCGAA 60.603 50.000 15.93 0.00 0.00 4.70
3240 4313 1.005037 ACAATCTGCCAGAACGCGA 60.005 52.632 15.93 0.00 0.00 5.87
3241 4314 1.133253 CACAATCTGCCAGAACGCG 59.867 57.895 3.53 3.53 0.00 6.01
3242 4315 1.237285 ACCACAATCTGCCAGAACGC 61.237 55.000 0.00 0.00 0.00 4.84
3243 4316 0.518636 CACCACAATCTGCCAGAACG 59.481 55.000 0.00 0.00 0.00 3.95
3244 4317 1.609208 ACACCACAATCTGCCAGAAC 58.391 50.000 0.00 0.00 0.00 3.01
3245 4318 2.363306 AACACCACAATCTGCCAGAA 57.637 45.000 0.00 0.00 0.00 3.02
3246 4319 3.500448 TTAACACCACAATCTGCCAGA 57.500 42.857 0.00 0.00 0.00 3.86
3247 4320 3.758023 TCATTAACACCACAATCTGCCAG 59.242 43.478 0.00 0.00 0.00 4.85
3248 4321 3.505680 GTCATTAACACCACAATCTGCCA 59.494 43.478 0.00 0.00 0.00 4.92
3249 4322 3.758554 AGTCATTAACACCACAATCTGCC 59.241 43.478 0.00 0.00 0.00 4.85
3250 4323 4.455533 TGAGTCATTAACACCACAATCTGC 59.544 41.667 0.00 0.00 0.00 4.26
3251 4324 6.748333 ATGAGTCATTAACACCACAATCTG 57.252 37.500 0.00 0.00 0.00 2.90
3252 4325 8.321353 TCTTATGAGTCATTAACACCACAATCT 58.679 33.333 11.68 0.00 0.00 2.40
3253 4326 8.492673 TCTTATGAGTCATTAACACCACAATC 57.507 34.615 11.68 0.00 0.00 2.67
3254 4327 8.862325 TTCTTATGAGTCATTAACACCACAAT 57.138 30.769 11.68 0.00 0.00 2.71
3255 4328 8.729756 CATTCTTATGAGTCATTAACACCACAA 58.270 33.333 11.68 0.00 33.37 3.33
3256 4329 7.336679 CCATTCTTATGAGTCATTAACACCACA 59.663 37.037 11.68 0.00 33.37 4.17
3257 4330 7.201732 CCCATTCTTATGAGTCATTAACACCAC 60.202 40.741 11.68 0.00 33.37 4.16
3258 4331 6.828273 CCCATTCTTATGAGTCATTAACACCA 59.172 38.462 11.68 0.00 33.37 4.17
3259 4332 6.828785 ACCCATTCTTATGAGTCATTAACACC 59.171 38.462 11.68 0.00 33.37 4.16
3260 4333 7.552687 TGACCCATTCTTATGAGTCATTAACAC 59.447 37.037 11.68 0.00 42.43 3.32
3261 4334 7.629157 TGACCCATTCTTATGAGTCATTAACA 58.371 34.615 11.68 0.00 42.43 2.41
3262 4335 8.506168 TTGACCCATTCTTATGAGTCATTAAC 57.494 34.615 11.68 0.00 45.33 2.01
3263 4336 9.123902 CATTGACCCATTCTTATGAGTCATTAA 57.876 33.333 11.68 4.46 45.33 1.40
3264 4337 8.493607 TCATTGACCCATTCTTATGAGTCATTA 58.506 33.333 11.68 0.60 45.33 1.90
3265 4338 7.284034 GTCATTGACCCATTCTTATGAGTCATT 59.716 37.037 11.68 0.00 45.33 2.57
3266 4339 6.769822 GTCATTGACCCATTCTTATGAGTCAT 59.230 38.462 11.12 11.12 45.33 3.06
3267 4340 6.070021 AGTCATTGACCCATTCTTATGAGTCA 60.070 38.462 13.14 0.00 44.65 3.41
3268 4341 6.352516 AGTCATTGACCCATTCTTATGAGTC 58.647 40.000 13.14 0.00 39.29 3.36
3269 4342 6.070021 TGAGTCATTGACCCATTCTTATGAGT 60.070 38.462 13.14 0.00 34.75 3.41
3270 4343 6.351711 TGAGTCATTGACCCATTCTTATGAG 58.648 40.000 13.14 0.00 31.26 2.90
3271 4344 6.312141 TGAGTCATTGACCCATTCTTATGA 57.688 37.500 13.14 0.00 31.26 2.15
3272 4345 8.681486 TTATGAGTCATTGACCCATTCTTATG 57.319 34.615 17.50 0.00 33.31 1.90
3275 4348 9.872684 ATTATTATGAGTCATTGACCCATTCTT 57.127 29.630 17.50 7.89 33.31 2.52
3276 4349 9.512588 GATTATTATGAGTCATTGACCCATTCT 57.487 33.333 17.50 9.07 33.31 2.40
3277 4350 8.734386 GGATTATTATGAGTCATTGACCCATTC 58.266 37.037 17.50 9.48 33.31 2.67
3278 4351 8.226810 TGGATTATTATGAGTCATTGACCCATT 58.773 33.333 17.50 5.18 33.31 3.16
3279 4352 7.758609 TGGATTATTATGAGTCATTGACCCAT 58.241 34.615 16.66 16.66 35.33 4.00
3280 4353 7.072328 TCTGGATTATTATGAGTCATTGACCCA 59.928 37.037 11.68 8.36 32.18 4.51
3281 4354 7.453393 TCTGGATTATTATGAGTCATTGACCC 58.547 38.462 11.68 1.98 32.18 4.46
3282 4355 8.908786 TTCTGGATTATTATGAGTCATTGACC 57.091 34.615 11.68 7.54 32.18 4.02
3283 4356 9.770097 TCTTCTGGATTATTATGAGTCATTGAC 57.230 33.333 11.68 8.82 0.00 3.18
3284 4357 9.993454 CTCTTCTGGATTATTATGAGTCATTGA 57.007 33.333 11.68 1.00 0.00 2.57
3285 4358 9.775854 ACTCTTCTGGATTATTATGAGTCATTG 57.224 33.333 11.68 0.00 0.00 2.82
3286 4359 9.995003 GACTCTTCTGGATTATTATGAGTCATT 57.005 33.333 11.68 0.00 44.73 2.57
3287 4360 9.378504 AGACTCTTCTGGATTATTATGAGTCAT 57.621 33.333 11.12 11.12 46.55 3.06
3288 4361 8.774546 AGACTCTTCTGGATTATTATGAGTCA 57.225 34.615 17.99 0.00 46.55 3.41
3293 4366 9.495572 GGGTTAAGACTCTTCTGGATTATTATG 57.504 37.037 0.00 0.00 29.98 1.90
3294 4367 9.225682 TGGGTTAAGACTCTTCTGGATTATTAT 57.774 33.333 0.00 0.00 29.98 1.28
3295 4368 8.618240 TGGGTTAAGACTCTTCTGGATTATTA 57.382 34.615 0.00 0.00 29.98 0.98
3296 4369 7.403231 TCTGGGTTAAGACTCTTCTGGATTATT 59.597 37.037 0.00 0.00 29.98 1.40
3297 4370 6.903534 TCTGGGTTAAGACTCTTCTGGATTAT 59.096 38.462 0.00 0.00 29.98 1.28
3298 4371 6.261435 TCTGGGTTAAGACTCTTCTGGATTA 58.739 40.000 0.00 0.00 29.98 1.75
3299 4372 5.094387 TCTGGGTTAAGACTCTTCTGGATT 58.906 41.667 0.00 0.00 29.98 3.01
3300 4373 4.689062 TCTGGGTTAAGACTCTTCTGGAT 58.311 43.478 0.00 0.00 29.98 3.41
3301 4374 4.127918 TCTGGGTTAAGACTCTTCTGGA 57.872 45.455 0.00 0.00 29.98 3.86
3302 4375 4.891992 TTCTGGGTTAAGACTCTTCTGG 57.108 45.455 0.00 0.00 29.98 3.86
3303 4376 5.611374 TGTTTCTGGGTTAAGACTCTTCTG 58.389 41.667 0.00 0.00 29.98 3.02
3304 4377 5.888982 TGTTTCTGGGTTAAGACTCTTCT 57.111 39.130 0.00 0.00 0.00 2.85
3305 4378 5.644206 GGATGTTTCTGGGTTAAGACTCTTC 59.356 44.000 0.00 0.00 0.00 2.87
3306 4379 5.310857 AGGATGTTTCTGGGTTAAGACTCTT 59.689 40.000 0.00 0.00 0.00 2.85
3307 4380 4.846940 AGGATGTTTCTGGGTTAAGACTCT 59.153 41.667 0.00 0.00 0.00 3.24
3308 4381 5.167303 AGGATGTTTCTGGGTTAAGACTC 57.833 43.478 0.00 0.00 0.00 3.36
3309 4382 5.584551 AAGGATGTTTCTGGGTTAAGACT 57.415 39.130 0.00 0.00 0.00 3.24
3310 4383 5.564848 GCAAAGGATGTTTCTGGGTTAAGAC 60.565 44.000 0.00 0.00 0.00 3.01
3311 4384 4.522789 GCAAAGGATGTTTCTGGGTTAAGA 59.477 41.667 0.00 0.00 0.00 2.10
3312 4385 4.280677 TGCAAAGGATGTTTCTGGGTTAAG 59.719 41.667 0.00 0.00 0.00 1.85
3313 4386 4.038642 GTGCAAAGGATGTTTCTGGGTTAA 59.961 41.667 0.00 0.00 0.00 2.01
3314 4387 3.572255 GTGCAAAGGATGTTTCTGGGTTA 59.428 43.478 0.00 0.00 0.00 2.85
3315 4388 2.365293 GTGCAAAGGATGTTTCTGGGTT 59.635 45.455 0.00 0.00 0.00 4.11
3316 4389 1.963515 GTGCAAAGGATGTTTCTGGGT 59.036 47.619 0.00 0.00 0.00 4.51
3317 4390 1.962807 TGTGCAAAGGATGTTTCTGGG 59.037 47.619 0.00 0.00 0.00 4.45
3318 4391 3.947910 ATGTGCAAAGGATGTTTCTGG 57.052 42.857 0.00 0.00 0.00 3.86
3345 4418 9.991906 AGTGCACTTTAGATAGTTAAGTGTTAA 57.008 29.630 15.25 1.08 46.48 2.01
3410 4485 1.511850 CACAATCTGCCAGAACACGA 58.488 50.000 0.00 0.00 0.00 4.35
3491 4566 6.349300 TGACAGATAGAGATTACCCTTTTGC 58.651 40.000 0.00 0.00 0.00 3.68
3548 4623 9.534565 GATATAAAGATAGATGCGGCATTTAGA 57.465 33.333 17.78 8.85 0.00 2.10
3602 4677 1.483827 CTTGCCTCTAGATGCACTCCA 59.516 52.381 20.65 7.01 37.18 3.86


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

AutoCloner maintained by Alex Coulton.