Multiple sequence alignment - TraesCS6A01G164100

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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 TraesCS6A01G164100 chr6A 100.000 2928 0 0 560 3487 162033439 162036366 0.000000e+00 5408
1 TraesCS6A01G164100 chr6A 100.000 169 0 0 1 169 162032880 162033048 2.610000e-81 313
2 TraesCS6A01G164100 chr6B 92.895 2857 127 38 564 3386 216468186 216471000 0.000000e+00 4082
3 TraesCS6A01G164100 chr6B 88.235 170 13 3 1 169 216466661 216466824 2.750000e-46 196
4 TraesCS6A01G164100 chr6D 95.017 2348 82 14 564 2895 122730113 122732441 0.000000e+00 3655
5 TraesCS6A01G164100 chrUn 98.798 416 5 0 1369 1784 476947789 476948204 0.000000e+00 741
6 TraesCS6A01G164100 chrUn 94.286 105 6 0 3381 3485 334966781 334966677 1.000000e-35 161
7 TraesCS6A01G164100 chrUn 93.519 108 7 0 3378 3485 355809739 355809846 1.000000e-35 161
8 TraesCS6A01G164100 chr3A 97.087 103 3 0 3385 3487 745267491 745267593 1.290000e-39 174
9 TraesCS6A01G164100 chr3A 96.154 104 4 0 3384 3487 241447411 241447308 1.660000e-38 171
10 TraesCS6A01G164100 chr4B 94.393 107 6 0 3379 3485 8657668 8657562 7.740000e-37 165
11 TraesCS6A01G164100 chr1D 94.393 107 6 0 3379 3485 116998741 116998847 7.740000e-37 165
12 TraesCS6A01G164100 chr1B 94.340 106 6 0 3380 3485 264417430 264417535 2.780000e-36 163
13 TraesCS6A01G164100 chr1B 94.286 105 6 0 3381 3485 491723418 491723314 1.000000e-35 161
14 TraesCS6A01G164100 chr1A 94.286 105 6 0 3383 3487 513367025 513366921 1.000000e-35 161


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 TraesCS6A01G164100 chr6A 162032880 162036366 3486 False 2860.5 5408 100.000 1 3487 2 chr6A.!!$F1 3486
1 TraesCS6A01G164100 chr6B 216466661 216471000 4339 False 2139.0 4082 90.565 1 3386 2 chr6B.!!$F1 3385
2 TraesCS6A01G164100 chr6D 122730113 122732441 2328 False 3655.0 3655 95.017 564 2895 1 chr6D.!!$F1 2331

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
81 82 0.689412 ACTAGCTGGCTCCTCCCTTC 60.689 60.0 0.0 0.0 0.0 3.46 F
1087 2067 0.105709 CCTCCTCCTCCTCTTCCTCC 60.106 65.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1853 2842 1.066787 CCCGTCTTGGAGAAGAAGTCC 60.067 57.143 0.0 0.0 40.00 3.85 R
2494 3490 0.459585 TACAGAATGCGGGCGAGTTC 60.460 55.000 0.0 0.0 42.53 3.01 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
24 25 1.792367 GCTTTCACCCGAAAATTGTGC 59.208 47.619 0.00 0.00 40.57 4.57
29 30 2.490115 TCACCCGAAAATTGTGCATACC 59.510 45.455 0.00 0.00 0.00 2.73
30 31 2.230025 CACCCGAAAATTGTGCATACCA 59.770 45.455 0.00 0.00 0.00 3.25
32 33 3.249917 CCCGAAAATTGTGCATACCAAC 58.750 45.455 0.00 0.00 0.00 3.77
50 51 5.496556 ACCAACTATCAAAATCATCGGTCA 58.503 37.500 0.00 0.00 0.00 4.02
69 70 5.618863 CGGTCATAGCAATCTCTACTAGCTG 60.619 48.000 0.00 0.00 36.80 4.24
81 82 0.689412 ACTAGCTGGCTCCTCCCTTC 60.689 60.000 0.00 0.00 0.00 3.46
82 83 1.743321 CTAGCTGGCTCCTCCCTTCG 61.743 65.000 0.00 0.00 0.00 3.79
83 84 4.847444 GCTGGCTCCTCCCTTCGC 62.847 72.222 0.00 0.00 0.00 4.70
84 85 4.168291 CTGGCTCCTCCCTTCGCC 62.168 72.222 0.00 0.00 42.78 5.54
86 87 3.483869 GGCTCCTCCCTTCGCCAT 61.484 66.667 0.00 0.00 42.06 4.40
87 88 2.110006 GCTCCTCCCTTCGCCATC 59.890 66.667 0.00 0.00 0.00 3.51
91 92 1.115930 TCCTCCCTTCGCCATCTAGC 61.116 60.000 0.00 0.00 0.00 3.42
92 93 1.369321 CTCCCTTCGCCATCTAGCC 59.631 63.158 0.00 0.00 0.00 3.93
103 104 1.617850 CCATCTAGCCGCTGAGAGAAT 59.382 52.381 2.16 0.00 0.00 2.40
115 116 4.331108 GCTGAGAGAATCCAAGAACCTTT 58.669 43.478 0.00 0.00 33.66 3.11
116 117 4.155644 GCTGAGAGAATCCAAGAACCTTTG 59.844 45.833 0.00 0.00 33.66 2.77
132 134 2.224042 CCTTTGGTGCCCTTGAGAAAAC 60.224 50.000 0.00 0.00 0.00 2.43
164 166 2.514824 GAGGACCTTGCATCCCGC 60.515 66.667 0.00 0.00 36.86 6.13
622 1593 6.294508 CCCCACTATTTGTTTGACTAACCAAG 60.295 42.308 0.00 0.00 35.81 3.61
636 1610 2.916702 ACCAAGCATAGCGATGATGA 57.083 45.000 11.36 0.00 34.73 2.92
637 1611 3.413846 ACCAAGCATAGCGATGATGAT 57.586 42.857 11.36 0.00 34.73 2.45
638 1612 3.072211 ACCAAGCATAGCGATGATGATG 58.928 45.455 11.36 0.38 34.73 3.07
784 1764 1.542030 AGAAGGTACAGACACAGAGCG 59.458 52.381 0.00 0.00 0.00 5.03
785 1765 1.269998 GAAGGTACAGACACAGAGCGT 59.730 52.381 0.00 0.00 0.00 5.07
819 1799 2.803670 GCGCTGTACGTCGCTTGA 60.804 61.111 19.85 0.00 46.92 3.02
868 1848 4.472701 TGGATCCGCCAGTAACCT 57.527 55.556 7.39 0.00 43.33 3.50
874 1854 2.509336 CGCCAGTAACCTCGCCTG 60.509 66.667 0.00 0.00 0.00 4.85
1080 2060 2.063378 CCACAGCCTCCTCCTCCTC 61.063 68.421 0.00 0.00 0.00 3.71
1081 2061 1.001503 CACAGCCTCCTCCTCCTCT 59.998 63.158 0.00 0.00 0.00 3.69
1082 2062 0.617249 CACAGCCTCCTCCTCCTCTT 60.617 60.000 0.00 0.00 0.00 2.85
1083 2063 0.325203 ACAGCCTCCTCCTCCTCTTC 60.325 60.000 0.00 0.00 0.00 2.87
1084 2064 1.048160 CAGCCTCCTCCTCCTCTTCC 61.048 65.000 0.00 0.00 0.00 3.46
1085 2065 1.228215 AGCCTCCTCCTCCTCTTCCT 61.228 60.000 0.00 0.00 0.00 3.36
1086 2066 0.759060 GCCTCCTCCTCCTCTTCCTC 60.759 65.000 0.00 0.00 0.00 3.71
1087 2067 0.105709 CCTCCTCCTCCTCTTCCTCC 60.106 65.000 0.00 0.00 0.00 4.30
1088 2068 0.933700 CTCCTCCTCCTCTTCCTCCT 59.066 60.000 0.00 0.00 0.00 3.69
1101 2081 2.997315 CTCCTCCAGTCGCCACCA 60.997 66.667 0.00 0.00 0.00 4.17
1102 2082 3.302347 CTCCTCCAGTCGCCACCAC 62.302 68.421 0.00 0.00 0.00 4.16
1103 2083 4.742201 CCTCCAGTCGCCACCACG 62.742 72.222 0.00 0.00 0.00 4.94
1104 2084 3.991051 CTCCAGTCGCCACCACGT 61.991 66.667 0.00 0.00 0.00 4.49
1105 2085 4.293648 TCCAGTCGCCACCACGTG 62.294 66.667 9.08 9.08 0.00 4.49
1358 2347 2.357034 GTCGCGGCTTTCCACTCA 60.357 61.111 1.90 0.00 0.00 3.41
1397 2386 4.217159 AACTACGGCCGGATCGCC 62.217 66.667 31.76 0.00 46.13 5.54
1617 2606 4.764771 TGCGGCCCTACTACCCGT 62.765 66.667 0.00 0.00 43.70 5.28
1622 2611 2.779033 GCCCTACTACCCGTCCACG 61.779 68.421 0.00 0.00 39.44 4.94
1649 2638 3.846180 GCCATCATCGTGGGCAAT 58.154 55.556 0.00 0.00 46.92 3.56
1784 2773 2.030562 CACTCGGAGGCGGTGTTT 59.969 61.111 10.23 0.00 0.00 2.83
1853 2842 1.153549 GTACCTGAAGCCGCTCCTG 60.154 63.158 0.00 0.00 0.00 3.86
2267 3256 4.097361 GACCTCAAGACCGGCCCC 62.097 72.222 0.00 0.00 0.00 5.80
2342 3331 2.361737 GGCTTCAAGGGCCTCACC 60.362 66.667 6.46 0.00 45.57 4.02
2489 3485 3.667166 GCAAGCCTGCGTTTACTTAGAAC 60.667 47.826 0.00 0.00 39.20 3.01
2494 3490 3.432252 CCTGCGTTTACTTAGAACACCAG 59.568 47.826 0.00 0.00 0.00 4.00
2529 3525 5.621197 TTCTGTAAATTCCACCACGATTG 57.379 39.130 0.00 0.00 0.00 2.67
2650 3652 2.064762 CGTGCTTCTTCAGAGTTCAGG 58.935 52.381 0.00 0.00 0.00 3.86
2668 3671 1.202976 AGGGAGCTGCTTTCACAACAT 60.203 47.619 2.53 0.00 0.00 2.71
2682 3685 3.563808 TCACAACATAAACTTCAAGCGCT 59.436 39.130 2.64 2.64 0.00 5.92
2742 3746 6.455647 TCATCGTGTCATTTTCTCTACTTGT 58.544 36.000 0.00 0.00 0.00 3.16
2891 3896 3.058293 TCACAAGTTAAGGATTGCTTGCG 60.058 43.478 0.02 0.00 42.22 4.85
2950 3955 1.675641 AGTTGTCCAAGGCGATGGC 60.676 57.895 7.42 0.00 40.46 4.40
2956 3961 0.546122 TCCAAGGCGATGGCTAACAT 59.454 50.000 7.42 0.00 44.18 2.71
2980 3985 5.016051 TGAGATCCTTCTGTTCTGCATAC 57.984 43.478 0.00 0.00 30.30 2.39
2983 3988 3.334583 TCCTTCTGTTCTGCATACCAC 57.665 47.619 0.00 0.00 0.00 4.16
2999 4004 2.571212 ACCACAGCGATGAACTGAAAA 58.429 42.857 8.12 0.00 38.55 2.29
3024 4029 3.872511 TCATCGCAATGGCAAGAATTT 57.127 38.095 0.00 0.00 41.24 1.82
3025 4030 3.513662 TCATCGCAATGGCAAGAATTTG 58.486 40.909 0.00 0.00 41.24 2.32
3050 4055 3.261580 CAGTGCAATACATGTCTCCGAA 58.738 45.455 0.00 0.00 0.00 4.30
3055 4060 3.770666 CAATACATGTCTCCGAACGAGT 58.229 45.455 0.00 0.00 39.84 4.18
3060 4065 0.591659 TGTCTCCGAACGAGTGACTG 59.408 55.000 0.00 0.00 39.84 3.51
3062 4067 1.266175 GTCTCCGAACGAGTGACTGAA 59.734 52.381 0.00 0.00 39.84 3.02
3092 4121 2.415491 GGAAAGCAAATACGAACAGGGC 60.415 50.000 0.00 0.00 0.00 5.19
3100 4129 5.282510 CAAATACGAACAGGGCTAGTAGAG 58.717 45.833 0.00 0.00 0.00 2.43
3113 4142 6.272792 AGGGCTAGTAGAGTAGCAGTAGATTA 59.727 42.308 16.29 0.00 46.29 1.75
3114 4143 6.596497 GGGCTAGTAGAGTAGCAGTAGATTAG 59.404 46.154 16.29 0.00 46.29 1.73
3115 4144 7.388437 GGCTAGTAGAGTAGCAGTAGATTAGA 58.612 42.308 16.29 0.00 46.29 2.10
3123 4152 8.052748 AGAGTAGCAGTAGATTAGATAGATGGG 58.947 40.741 0.00 0.00 0.00 4.00
3124 4153 7.122715 AGTAGCAGTAGATTAGATAGATGGGG 58.877 42.308 0.00 0.00 0.00 4.96
3125 4154 5.909760 AGCAGTAGATTAGATAGATGGGGT 58.090 41.667 0.00 0.00 0.00 4.95
3126 4155 5.719085 AGCAGTAGATTAGATAGATGGGGTG 59.281 44.000 0.00 0.00 0.00 4.61
3127 4156 5.717178 GCAGTAGATTAGATAGATGGGGTGA 59.283 44.000 0.00 0.00 0.00 4.02
3128 4157 6.211584 GCAGTAGATTAGATAGATGGGGTGAA 59.788 42.308 0.00 0.00 0.00 3.18
3129 4158 7.093112 GCAGTAGATTAGATAGATGGGGTGAAT 60.093 40.741 0.00 0.00 0.00 2.57
3130 4159 8.474025 CAGTAGATTAGATAGATGGGGTGAATC 58.526 40.741 0.00 0.00 0.00 2.52
3131 4160 8.405850 AGTAGATTAGATAGATGGGGTGAATCT 58.594 37.037 0.00 0.00 38.03 2.40
3132 4161 7.493499 AGATTAGATAGATGGGGTGAATCTG 57.507 40.000 0.00 0.00 35.92 2.90
3133 4162 6.443206 AGATTAGATAGATGGGGTGAATCTGG 59.557 42.308 0.00 0.00 35.92 3.86
3134 4163 2.641815 AGATAGATGGGGTGAATCTGGC 59.358 50.000 0.00 0.00 35.92 4.85
3135 4164 0.758734 TAGATGGGGTGAATCTGGCG 59.241 55.000 0.00 0.00 35.92 5.69
3136 4165 1.224592 GATGGGGTGAATCTGGCGT 59.775 57.895 0.00 0.00 0.00 5.68
3137 4166 1.077501 ATGGGGTGAATCTGGCGTG 60.078 57.895 0.00 0.00 0.00 5.34
3138 4167 1.852157 ATGGGGTGAATCTGGCGTGT 61.852 55.000 0.00 0.00 0.00 4.49
3139 4168 2.040544 GGGGTGAATCTGGCGTGTG 61.041 63.158 0.00 0.00 0.00 3.82
3140 4169 1.302511 GGGTGAATCTGGCGTGTGT 60.303 57.895 0.00 0.00 0.00 3.72
3141 4170 1.577328 GGGTGAATCTGGCGTGTGTG 61.577 60.000 0.00 0.00 0.00 3.82
3142 4171 0.884704 GGTGAATCTGGCGTGTGTGT 60.885 55.000 0.00 0.00 0.00 3.72
3156 4185 1.148310 GTGTGTGGTCGAGTGATTGG 58.852 55.000 0.00 0.00 0.00 3.16
3167 4196 2.076863 GAGTGATTGGGGTTCTTCGTG 58.923 52.381 0.00 0.00 0.00 4.35
3173 4202 1.161563 TGGGGTTCTTCGTGTTTCGC 61.162 55.000 0.00 0.00 39.67 4.70
3206 4235 0.322997 TGCAAAGTTGGGTATCCGGG 60.323 55.000 0.00 0.00 35.24 5.73
3207 4236 0.034863 GCAAAGTTGGGTATCCGGGA 60.035 55.000 0.00 0.00 35.24 5.14
3210 4239 2.752903 CAAAGTTGGGTATCCGGGAAAG 59.247 50.000 0.00 0.00 35.24 2.62
3211 4240 1.961133 AGTTGGGTATCCGGGAAAGA 58.039 50.000 0.00 0.00 35.24 2.52
3212 4241 2.271777 AGTTGGGTATCCGGGAAAGAA 58.728 47.619 0.00 0.00 35.24 2.52
3213 4242 2.238898 AGTTGGGTATCCGGGAAAGAAG 59.761 50.000 0.00 0.00 35.24 2.85
3214 4243 2.237893 GTTGGGTATCCGGGAAAGAAGA 59.762 50.000 0.00 0.00 35.24 2.87
3215 4244 2.553464 TGGGTATCCGGGAAAGAAGAA 58.447 47.619 0.00 0.00 35.24 2.52
3228 4257 5.765182 GGGAAAGAAGAAGATTGAACACTCA 59.235 40.000 0.00 0.00 0.00 3.41
3282 4311 1.771073 CTTTGTCGTTGCGCTGTCCA 61.771 55.000 9.73 0.00 0.00 4.02
3306 4335 5.544176 ACTCACTTTCTATGAACTTCCCAGA 59.456 40.000 0.00 0.00 0.00 3.86
3315 4344 5.886960 ATGAACTTCCCAGAATTTTCTCG 57.113 39.130 0.00 0.00 34.74 4.04
3340 4369 2.264813 GCACCTTTCTATTCGTACGCA 58.735 47.619 11.24 0.00 0.00 5.24
3341 4370 2.864343 GCACCTTTCTATTCGTACGCAT 59.136 45.455 11.24 8.21 0.00 4.73
3342 4371 3.302480 GCACCTTTCTATTCGTACGCATG 60.302 47.826 11.24 0.84 0.00 4.06
3376 4405 3.620488 GGTCAGGTTCCATTATTGCTGA 58.380 45.455 0.00 0.00 0.00 4.26
3377 4406 3.378427 GGTCAGGTTCCATTATTGCTGAC 59.622 47.826 0.00 0.00 37.97 3.51
3387 4416 3.591196 TTATTGCTGACAACAATGGCC 57.409 42.857 13.20 0.00 38.99 5.36
3388 4417 0.609662 ATTGCTGACAACAATGGCCC 59.390 50.000 0.00 0.00 38.99 5.80
3389 4418 0.469705 TTGCTGACAACAATGGCCCT 60.470 50.000 0.00 0.00 31.48 5.19
3390 4419 1.180456 TGCTGACAACAATGGCCCTG 61.180 55.000 0.00 0.00 31.48 4.45
3391 4420 1.181098 GCTGACAACAATGGCCCTGT 61.181 55.000 0.00 0.00 31.48 4.00
3392 4421 1.331214 CTGACAACAATGGCCCTGTT 58.669 50.000 13.24 13.24 37.49 3.16
3393 4422 1.688197 CTGACAACAATGGCCCTGTTT 59.312 47.619 15.75 9.03 34.80 2.83
3394 4423 1.411977 TGACAACAATGGCCCTGTTTG 59.588 47.619 15.75 13.53 34.80 2.93
3395 4424 0.758123 ACAACAATGGCCCTGTTTGG 59.242 50.000 15.75 9.65 34.80 3.28
3396 4425 1.047002 CAACAATGGCCCTGTTTGGA 58.953 50.000 15.75 0.00 34.80 3.53
3397 4426 1.624813 CAACAATGGCCCTGTTTGGAT 59.375 47.619 15.75 0.00 34.80 3.41
3398 4427 2.830923 CAACAATGGCCCTGTTTGGATA 59.169 45.455 15.75 0.00 34.80 2.59
3399 4428 2.456577 ACAATGGCCCTGTTTGGATAC 58.543 47.619 0.00 0.00 38.35 2.24
3400 4429 2.042979 ACAATGGCCCTGTTTGGATACT 59.957 45.455 0.00 0.00 38.35 2.12
3401 4430 2.689983 CAATGGCCCTGTTTGGATACTC 59.310 50.000 0.00 0.00 38.35 2.59
3402 4431 1.668826 TGGCCCTGTTTGGATACTCT 58.331 50.000 0.00 0.00 38.35 3.24
3403 4432 2.840511 TGGCCCTGTTTGGATACTCTA 58.159 47.619 0.00 0.00 38.35 2.43
3404 4433 3.186283 TGGCCCTGTTTGGATACTCTAA 58.814 45.455 0.00 0.00 38.35 2.10
3405 4434 3.054655 TGGCCCTGTTTGGATACTCTAAC 60.055 47.826 0.00 0.00 38.35 2.34
3406 4435 3.200165 GGCCCTGTTTGGATACTCTAACT 59.800 47.826 0.00 0.00 38.35 2.24
3407 4436 4.443621 GCCCTGTTTGGATACTCTAACTC 58.556 47.826 0.00 0.00 38.35 3.01
3408 4437 4.081087 GCCCTGTTTGGATACTCTAACTCA 60.081 45.833 0.00 0.00 38.35 3.41
3409 4438 5.665459 CCCTGTTTGGATACTCTAACTCAG 58.335 45.833 0.00 0.00 38.35 3.35
3410 4439 5.187967 CCCTGTTTGGATACTCTAACTCAGT 59.812 44.000 0.00 0.00 38.35 3.41
3411 4440 6.295916 CCCTGTTTGGATACTCTAACTCAGTT 60.296 42.308 0.00 0.00 38.35 3.16
3412 4441 7.093465 CCCTGTTTGGATACTCTAACTCAGTTA 60.093 40.741 0.00 0.00 38.35 2.24
3413 4442 8.311836 CCTGTTTGGATACTCTAACTCAGTTAA 58.688 37.037 0.00 0.00 38.35 2.01
3414 4443 9.706691 CTGTTTGGATACTCTAACTCAGTTAAA 57.293 33.333 0.00 0.00 37.61 1.52
3415 4444 9.706691 TGTTTGGATACTCTAACTCAGTTAAAG 57.293 33.333 0.00 0.00 37.61 1.85
3416 4445 9.708092 GTTTGGATACTCTAACTCAGTTAAAGT 57.292 33.333 8.61 8.61 34.31 2.66
3459 4488 9.599056 ACCCTAAACTAACTCTAAACTAACTCT 57.401 33.333 0.00 0.00 0.00 3.24
3464 4493 8.647256 AACTAACTCTAAACTAACTCTAGCCA 57.353 34.615 0.00 0.00 0.00 4.75
3465 4494 8.647256 ACTAACTCTAAACTAACTCTAGCCAA 57.353 34.615 0.00 0.00 0.00 4.52
3466 4495 9.086758 ACTAACTCTAAACTAACTCTAGCCAAA 57.913 33.333 0.00 0.00 0.00 3.28
3467 4496 9.924650 CTAACTCTAAACTAACTCTAGCCAAAA 57.075 33.333 0.00 0.00 0.00 2.44
3469 4498 8.834749 ACTCTAAACTAACTCTAGCCAAAAAG 57.165 34.615 0.00 0.00 0.00 2.27
3470 4499 7.878644 ACTCTAAACTAACTCTAGCCAAAAAGG 59.121 37.037 0.00 0.00 41.84 3.11
3471 4500 7.742767 TCTAAACTAACTCTAGCCAAAAAGGT 58.257 34.615 0.00 0.00 40.61 3.50
3472 4501 6.635030 AAACTAACTCTAGCCAAAAAGGTG 57.365 37.500 0.00 0.00 40.61 4.00
3473 4502 5.306114 ACTAACTCTAGCCAAAAAGGTGT 57.694 39.130 0.00 0.00 40.61 4.16
3474 4503 5.691896 ACTAACTCTAGCCAAAAAGGTGTT 58.308 37.500 0.00 0.00 40.61 3.32
3475 4504 6.127101 ACTAACTCTAGCCAAAAAGGTGTTT 58.873 36.000 0.00 0.00 40.61 2.83
3476 4505 4.918810 ACTCTAGCCAAAAAGGTGTTTG 57.081 40.909 0.00 0.00 40.61 2.93
3483 4512 3.191078 CAAAAAGGTGTTTGGATGGCA 57.809 42.857 0.00 0.00 35.29 4.92
3484 4513 3.132925 CAAAAAGGTGTTTGGATGGCAG 58.867 45.455 0.00 0.00 35.29 4.85
3485 4514 2.380064 AAAGGTGTTTGGATGGCAGA 57.620 45.000 0.00 0.00 0.00 4.26
3486 4515 1.915141 AAGGTGTTTGGATGGCAGAG 58.085 50.000 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.226523 TGACCGATGATTTTGATAGTTGGTATG 59.773 37.037 0.00 0.00 0.00 2.39
29 30 7.041848 TGCTATGACCGATGATTTTGATAGTTG 60.042 37.037 0.00 0.00 0.00 3.16
30 31 6.992123 TGCTATGACCGATGATTTTGATAGTT 59.008 34.615 0.00 0.00 0.00 2.24
32 33 7.425577 TTGCTATGACCGATGATTTTGATAG 57.574 36.000 0.00 0.00 0.00 2.08
50 51 4.415596 AGCCAGCTAGTAGAGATTGCTAT 58.584 43.478 0.00 0.00 40.55 2.97
82 83 1.006337 CTCTCAGCGGCTAGATGGC 60.006 63.158 0.26 0.00 36.78 4.40
83 84 1.035923 TTCTCTCAGCGGCTAGATGG 58.964 55.000 0.26 0.00 36.78 3.51
84 85 2.352617 GGATTCTCTCAGCGGCTAGATG 60.353 54.545 0.26 0.00 37.65 2.90
85 86 1.892474 GGATTCTCTCAGCGGCTAGAT 59.108 52.381 0.26 0.00 0.00 1.98
86 87 1.323412 GGATTCTCTCAGCGGCTAGA 58.677 55.000 0.26 0.00 0.00 2.43
87 88 1.035923 TGGATTCTCTCAGCGGCTAG 58.964 55.000 0.26 0.00 0.00 3.42
91 92 2.275318 GTTCTTGGATTCTCTCAGCGG 58.725 52.381 0.00 0.00 0.00 5.52
92 93 2.093764 AGGTTCTTGGATTCTCTCAGCG 60.094 50.000 0.00 0.00 0.00 5.18
132 134 2.093235 GGTCCTCATTCTCCTTCTGGTG 60.093 54.545 0.00 0.00 34.23 4.17
568 1537 3.149981 GACTTGGAAAAGAACCCTCCTG 58.850 50.000 0.00 0.00 0.00 3.86
622 1593 5.636965 ACTTAGAACATCATCATCGCTATGC 59.363 40.000 0.00 0.00 32.76 3.14
784 1764 1.670406 CCCTGCTCTGTGTCTGCAC 60.670 63.158 0.00 0.00 45.44 4.57
785 1765 2.745698 CCCTGCTCTGTGTCTGCA 59.254 61.111 0.00 0.00 35.30 4.41
786 1766 2.745492 GCCCTGCTCTGTGTCTGC 60.745 66.667 0.00 0.00 0.00 4.26
787 1767 2.433838 CGCCCTGCTCTGTGTCTG 60.434 66.667 0.00 0.00 0.00 3.51
788 1768 4.385405 GCGCCCTGCTCTGTGTCT 62.385 66.667 0.00 0.00 41.73 3.41
816 1796 1.202639 TCTCTTGCGTTGCTTCCTCAA 60.203 47.619 0.00 0.00 0.00 3.02
817 1797 0.392706 TCTCTTGCGTTGCTTCCTCA 59.607 50.000 0.00 0.00 0.00 3.86
819 1799 0.603975 GGTCTCTTGCGTTGCTTCCT 60.604 55.000 0.00 0.00 0.00 3.36
868 1848 3.062466 CCGAGAGTGGTCAGGCGA 61.062 66.667 0.00 0.00 0.00 5.54
874 1854 1.733399 GACGTTGCCGAGAGTGGTC 60.733 63.158 0.00 0.00 37.88 4.02
930 1910 1.537562 CCGCGGTTACTTACTCCATCC 60.538 57.143 19.50 0.00 0.00 3.51
1080 2060 1.984570 TGGCGACTGGAGGAGGAAG 60.985 63.158 0.00 0.00 0.00 3.46
1081 2061 2.119611 TGGCGACTGGAGGAGGAA 59.880 61.111 0.00 0.00 0.00 3.36
1082 2062 2.680352 GTGGCGACTGGAGGAGGA 60.680 66.667 0.00 0.00 0.00 3.71
1083 2063 3.775654 GGTGGCGACTGGAGGAGG 61.776 72.222 0.00 0.00 0.00 4.30
1084 2064 2.997315 TGGTGGCGACTGGAGGAG 60.997 66.667 0.00 0.00 0.00 3.69
1085 2065 3.311110 GTGGTGGCGACTGGAGGA 61.311 66.667 0.00 0.00 0.00 3.71
1086 2066 4.742201 CGTGGTGGCGACTGGAGG 62.742 72.222 0.00 0.00 0.00 4.30
1087 2067 3.991051 ACGTGGTGGCGACTGGAG 61.991 66.667 0.00 0.00 35.59 3.86
1088 2068 4.293648 CACGTGGTGGCGACTGGA 62.294 66.667 7.95 0.00 35.59 3.86
1260 2240 4.193893 TGATCAGGCGGGGGCATG 62.194 66.667 0.00 0.00 0.00 4.06
1273 2253 2.802774 GCAACAGAGAGGCTAGCTGATC 60.803 54.545 15.72 10.54 33.94 2.92
1622 2611 3.245948 GATGATGGCCACGATGCGC 62.246 63.158 8.16 0.00 0.00 6.09
1853 2842 1.066787 CCCGTCTTGGAGAAGAAGTCC 60.067 57.143 0.00 0.00 40.00 3.85
2342 3331 0.748367 TGATGGAGGAGGACGACGAG 60.748 60.000 0.00 0.00 0.00 4.18
2381 3370 3.507009 AGGAGCGTCGCCGAGTAC 61.507 66.667 14.86 0.00 35.63 2.73
2489 3485 3.958147 ATGCGGGCGAGTTCTGGTG 62.958 63.158 0.00 0.00 0.00 4.17
2494 3490 0.459585 TACAGAATGCGGGCGAGTTC 60.460 55.000 0.00 0.00 42.53 3.01
2650 3652 4.022849 AGTTTATGTTGTGAAAGCAGCTCC 60.023 41.667 0.00 0.00 0.00 4.70
2668 3671 4.911514 AAAAAGGAGCGCTTGAAGTTTA 57.088 36.364 13.26 0.00 0.00 2.01
2742 3746 3.678806 CGGAAGGAACAAGATTCCATCGA 60.679 47.826 8.35 0.00 42.20 3.59
2795 3799 5.066117 GCAGAGATGCCATATTCCATACATG 59.934 44.000 0.00 0.00 0.00 3.21
2899 3904 1.275291 TGAAGGTCACGATGGGTTCTC 59.725 52.381 0.00 0.00 0.00 2.87
2950 3955 7.413877 GCAGAACAGAAGGATCTCAAATGTTAG 60.414 40.741 0.00 0.00 32.03 2.34
2956 3961 4.356405 TGCAGAACAGAAGGATCTCAAA 57.644 40.909 0.00 0.00 32.03 2.69
2980 3985 2.549754 ACTTTTCAGTTCATCGCTGTGG 59.450 45.455 0.00 0.00 35.60 4.17
2983 3988 5.273170 TGAAAACTTTTCAGTTCATCGCTG 58.727 37.500 12.12 0.00 42.89 5.18
2999 4004 2.557924 TCTTGCCATTGCGATGAAAACT 59.442 40.909 15.98 0.00 41.78 2.66
3026 4031 3.181517 CGGAGACATGTATTGCACTGTTG 60.182 47.826 0.00 0.00 0.00 3.33
3027 4032 3.002791 CGGAGACATGTATTGCACTGTT 58.997 45.455 0.00 0.00 0.00 3.16
3028 4033 2.233676 TCGGAGACATGTATTGCACTGT 59.766 45.455 0.00 0.00 0.00 3.55
3029 4034 2.892374 TCGGAGACATGTATTGCACTG 58.108 47.619 0.00 0.00 0.00 3.66
3030 4035 3.262420 GTTCGGAGACATGTATTGCACT 58.738 45.455 0.00 0.00 34.32 4.40
3031 4036 2.029244 CGTTCGGAGACATGTATTGCAC 59.971 50.000 0.00 0.00 34.32 4.57
3032 4037 2.094442 TCGTTCGGAGACATGTATTGCA 60.094 45.455 0.00 0.00 34.32 4.08
3033 4038 2.535984 CTCGTTCGGAGACATGTATTGC 59.464 50.000 0.00 0.00 46.23 3.56
3034 4039 3.547868 CACTCGTTCGGAGACATGTATTG 59.452 47.826 0.00 0.00 46.23 1.90
3035 4040 3.442625 TCACTCGTTCGGAGACATGTATT 59.557 43.478 0.00 0.00 46.23 1.89
3038 4043 1.068472 GTCACTCGTTCGGAGACATGT 60.068 52.381 0.00 0.00 46.23 3.21
3068 4092 4.022329 CCCTGTTCGTATTTGCTTTCCTTT 60.022 41.667 0.00 0.00 0.00 3.11
3069 4093 3.506067 CCCTGTTCGTATTTGCTTTCCTT 59.494 43.478 0.00 0.00 0.00 3.36
3084 4108 3.288964 TGCTACTCTACTAGCCCTGTTC 58.711 50.000 0.00 0.00 38.77 3.18
3089 4118 4.354893 TCTACTGCTACTCTACTAGCCC 57.645 50.000 0.00 0.00 38.77 5.19
3100 4129 6.893005 ACCCCATCTATCTAATCTACTGCTAC 59.107 42.308 0.00 0.00 0.00 3.58
3113 4142 2.641815 GCCAGATTCACCCCATCTATCT 59.358 50.000 0.00 0.00 29.36 1.98
3114 4143 2.613977 CGCCAGATTCACCCCATCTATC 60.614 54.545 0.00 0.00 29.36 2.08
3115 4144 1.349026 CGCCAGATTCACCCCATCTAT 59.651 52.381 0.00 0.00 29.36 1.98
3123 4152 0.884704 ACACACACGCCAGATTCACC 60.885 55.000 0.00 0.00 0.00 4.02
3124 4153 0.235665 CACACACACGCCAGATTCAC 59.764 55.000 0.00 0.00 0.00 3.18
3125 4154 0.884259 CCACACACACGCCAGATTCA 60.884 55.000 0.00 0.00 0.00 2.57
3126 4155 0.884704 ACCACACACACGCCAGATTC 60.885 55.000 0.00 0.00 0.00 2.52
3127 4156 0.884704 GACCACACACACGCCAGATT 60.885 55.000 0.00 0.00 0.00 2.40
3128 4157 1.301716 GACCACACACACGCCAGAT 60.302 57.895 0.00 0.00 0.00 2.90
3129 4158 2.108157 GACCACACACACGCCAGA 59.892 61.111 0.00 0.00 0.00 3.86
3130 4159 3.337889 CGACCACACACACGCCAG 61.338 66.667 0.00 0.00 0.00 4.85
3131 4160 3.783478 CTCGACCACACACACGCCA 62.783 63.158 0.00 0.00 0.00 5.69
3132 4161 3.036084 CTCGACCACACACACGCC 61.036 66.667 0.00 0.00 0.00 5.68
3133 4162 2.279252 ACTCGACCACACACACGC 60.279 61.111 0.00 0.00 0.00 5.34
3134 4163 0.318699 ATCACTCGACCACACACACG 60.319 55.000 0.00 0.00 0.00 4.49
3135 4164 1.526887 CAATCACTCGACCACACACAC 59.473 52.381 0.00 0.00 0.00 3.82
3136 4165 1.540146 CCAATCACTCGACCACACACA 60.540 52.381 0.00 0.00 0.00 3.72
3137 4166 1.148310 CCAATCACTCGACCACACAC 58.852 55.000 0.00 0.00 0.00 3.82
3138 4167 0.034756 CCCAATCACTCGACCACACA 59.965 55.000 0.00 0.00 0.00 3.72
3139 4168 0.673644 CCCCAATCACTCGACCACAC 60.674 60.000 0.00 0.00 0.00 3.82
3140 4169 1.125093 ACCCCAATCACTCGACCACA 61.125 55.000 0.00 0.00 0.00 4.17
3141 4170 0.036306 AACCCCAATCACTCGACCAC 59.964 55.000 0.00 0.00 0.00 4.16
3142 4171 0.323629 GAACCCCAATCACTCGACCA 59.676 55.000 0.00 0.00 0.00 4.02
3156 4185 0.942252 AAGCGAAACACGAAGAACCC 59.058 50.000 0.00 0.00 45.77 4.11
3167 4196 3.814945 CACAAGGATCAGAAAGCGAAAC 58.185 45.455 0.00 0.00 0.00 2.78
3173 4202 4.843220 ACTTTGCACAAGGATCAGAAAG 57.157 40.909 11.59 0.00 0.00 2.62
3206 4235 6.201044 TCGTGAGTGTTCAATCTTCTTCTTTC 59.799 38.462 2.21 0.00 34.49 2.62
3207 4236 6.049149 TCGTGAGTGTTCAATCTTCTTCTTT 58.951 36.000 2.21 0.00 34.49 2.52
3210 4239 5.463724 AGTTCGTGAGTGTTCAATCTTCTTC 59.536 40.000 2.21 0.00 34.49 2.87
3211 4240 5.360591 AGTTCGTGAGTGTTCAATCTTCTT 58.639 37.500 2.21 0.00 34.49 2.52
3212 4241 4.950050 AGTTCGTGAGTGTTCAATCTTCT 58.050 39.130 2.21 0.00 34.49 2.85
3213 4242 4.143514 CGAGTTCGTGAGTGTTCAATCTTC 60.144 45.833 2.21 0.00 34.49 2.87
3214 4243 3.736252 CGAGTTCGTGAGTGTTCAATCTT 59.264 43.478 2.21 0.00 34.49 2.40
3215 4244 3.004419 TCGAGTTCGTGAGTGTTCAATCT 59.996 43.478 1.07 0.00 40.80 2.40
3228 4257 0.667792 GCCTCTGCTTTCGAGTTCGT 60.668 55.000 1.07 0.00 36.10 3.85
3282 4311 5.544176 TCTGGGAAGTTCATAGAAAGTGAGT 59.456 40.000 5.01 0.00 0.00 3.41
3306 4335 0.321653 AGGTGCGAGGCGAGAAAATT 60.322 50.000 0.00 0.00 0.00 1.82
3315 4344 0.931005 CGAATAGAAAGGTGCGAGGC 59.069 55.000 0.00 0.00 0.00 4.70
3357 4386 4.299586 TGTCAGCAATAATGGAACCTGA 57.700 40.909 0.00 0.00 0.00 3.86
3359 4388 4.406456 TGTTGTCAGCAATAATGGAACCT 58.594 39.130 0.00 0.00 36.92 3.50
3376 4405 0.758123 CCAAACAGGGCCATTGTTGT 59.242 50.000 21.34 11.42 38.67 3.32
3377 4406 1.047002 TCCAAACAGGGCCATTGTTG 58.953 50.000 21.34 12.85 38.67 3.33
3386 4415 5.187967 ACTGAGTTAGAGTATCCAAACAGGG 59.812 44.000 0.00 0.00 34.84 4.45
3387 4416 6.287589 ACTGAGTTAGAGTATCCAAACAGG 57.712 41.667 0.00 0.00 34.84 4.00
3388 4417 9.706691 TTTAACTGAGTTAGAGTATCCAAACAG 57.293 33.333 5.10 0.00 34.84 3.16
3389 4418 9.706691 CTTTAACTGAGTTAGAGTATCCAAACA 57.293 33.333 13.13 0.00 34.84 2.83
3390 4419 9.708092 ACTTTAACTGAGTTAGAGTATCCAAAC 57.292 33.333 22.36 0.00 40.18 2.93
3433 4462 9.599056 AGAGTTAGTTTAGAGTTAGTTTAGGGT 57.401 33.333 0.00 0.00 0.00 4.34
3438 4467 9.086758 TGGCTAGAGTTAGTTTAGAGTTAGTTT 57.913 33.333 0.00 0.00 0.00 2.66
3439 4468 8.647256 TGGCTAGAGTTAGTTTAGAGTTAGTT 57.353 34.615 0.00 0.00 0.00 2.24
3440 4469 8.647256 TTGGCTAGAGTTAGTTTAGAGTTAGT 57.353 34.615 0.00 0.00 0.00 2.24
3441 4470 9.924650 TTTTGGCTAGAGTTAGTTTAGAGTTAG 57.075 33.333 0.00 0.00 0.00 2.34
3443 4472 9.274206 CTTTTTGGCTAGAGTTAGTTTAGAGTT 57.726 33.333 0.00 0.00 0.00 3.01
3444 4473 7.878644 CCTTTTTGGCTAGAGTTAGTTTAGAGT 59.121 37.037 0.00 0.00 0.00 3.24
3445 4474 7.878644 ACCTTTTTGGCTAGAGTTAGTTTAGAG 59.121 37.037 0.00 0.00 40.22 2.43
3446 4475 7.660208 CACCTTTTTGGCTAGAGTTAGTTTAGA 59.340 37.037 0.00 0.00 40.22 2.10
3447 4476 7.444487 ACACCTTTTTGGCTAGAGTTAGTTTAG 59.556 37.037 0.00 0.00 40.22 1.85
3448 4477 7.284820 ACACCTTTTTGGCTAGAGTTAGTTTA 58.715 34.615 0.00 0.00 40.22 2.01
3449 4478 6.127101 ACACCTTTTTGGCTAGAGTTAGTTT 58.873 36.000 0.00 0.00 40.22 2.66
3450 4479 5.691896 ACACCTTTTTGGCTAGAGTTAGTT 58.308 37.500 0.00 0.00 40.22 2.24
3451 4480 5.306114 ACACCTTTTTGGCTAGAGTTAGT 57.694 39.130 0.00 0.00 40.22 2.24
3452 4481 6.438763 CAAACACCTTTTTGGCTAGAGTTAG 58.561 40.000 0.00 0.00 40.22 2.34
3453 4482 5.300792 CCAAACACCTTTTTGGCTAGAGTTA 59.699 40.000 1.81 0.00 46.92 2.24
3454 4483 4.099419 CCAAACACCTTTTTGGCTAGAGTT 59.901 41.667 1.81 0.00 46.92 3.01
3455 4484 3.636764 CCAAACACCTTTTTGGCTAGAGT 59.363 43.478 1.81 0.00 46.92 3.24
3456 4485 4.243007 CCAAACACCTTTTTGGCTAGAG 57.757 45.455 1.81 0.00 46.92 2.43
3463 4492 3.132925 CTGCCATCCAAACACCTTTTTG 58.867 45.455 0.00 0.00 36.40 2.44
3464 4493 3.037549 TCTGCCATCCAAACACCTTTTT 58.962 40.909 0.00 0.00 0.00 1.94
3465 4494 2.629617 CTCTGCCATCCAAACACCTTTT 59.370 45.455 0.00 0.00 0.00 2.27
3466 4495 2.242043 CTCTGCCATCCAAACACCTTT 58.758 47.619 0.00 0.00 0.00 3.11
3467 4496 1.915141 CTCTGCCATCCAAACACCTT 58.085 50.000 0.00 0.00 0.00 3.50
3468 4497 3.658398 CTCTGCCATCCAAACACCT 57.342 52.632 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.