Multiple sequence alignment - TraesCS1D01G119800

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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 TraesCS1D01G119800 chr1D 100.000 3442 0 0 1 3442 116776186 116779627 0.000000e+00 6357
1 TraesCS1D01G119800 chr1D 94.681 94 2 2 28 118 324732983 324733076 3.580000e-30 143
2 TraesCS1D01G119800 chr1B 95.616 2190 56 18 1239 3397 178720654 178722834 0.000000e+00 3476
3 TraesCS1D01G119800 chr1B 90.812 1121 45 30 114 1192 178719553 178720657 0.000000e+00 1447
4 TraesCS1D01G119800 chr1B 87.500 120 12 2 2 118 504098999 504098880 5.990000e-28 135
5 TraesCS1D01G119800 chr1A 96.259 2058 48 15 907 2952 127831898 127833938 0.000000e+00 3347
6 TraesCS1D01G119800 chr1A 92.564 511 20 7 114 621 127831052 127831547 0.000000e+00 717
7 TraesCS1D01G119800 chr1A 93.382 408 17 4 2935 3333 127838259 127838665 2.290000e-166 595
8 TraesCS1D01G119800 chr1A 91.923 260 20 1 631 889 127831589 127831848 2.520000e-96 363
9 TraesCS1D01G119800 chr2A 87.124 233 28 2 2159 2390 37099892 37099661 2.630000e-66 263
10 TraesCS1D01G119800 chr4D 91.736 121 7 3 1 118 74082402 74082282 7.640000e-37 165
11 TraesCS1D01G119800 chr5D 90.476 126 7 3 1 122 315924696 315924572 9.890000e-36 161
12 TraesCS1D01G119800 chr3B 89.431 123 13 0 1 123 28323183 28323061 4.600000e-34 156
13 TraesCS1D01G119800 chr7D 89.076 119 11 2 1 118 312452061 312452178 2.770000e-31 147
14 TraesCS1D01G119800 chr7B 88.136 118 13 1 1 117 185628416 185628299 4.630000e-29 139
15 TraesCS1D01G119800 chr2B 87.395 119 14 1 1 118 405282397 405282279 5.990000e-28 135
16 TraesCS1D01G119800 chr6A 85.039 127 13 5 1 122 146012047 146011922 1.300000e-24 124


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 TraesCS1D01G119800 chr1D 116776186 116779627 3441 False 6357.000000 6357 100.000 1 3442 1 chr1D.!!$F1 3441
1 TraesCS1D01G119800 chr1B 178719553 178722834 3281 False 2461.500000 3476 93.214 114 3397 2 chr1B.!!$F1 3283
2 TraesCS1D01G119800 chr1A 127831052 127833938 2886 False 1475.666667 3347 93.582 114 2952 3 chr1A.!!$F2 2838

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
23 24 0.104144 TCCTCCTCCACCCCTGAAAA 60.104 55.0 0.0 0.0 0.00 2.29 F
1201 1277 0.244994 CTCAACACTCCCTCTCCGTG 59.755 60.0 0.0 0.0 34.92 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1319 1395 1.153147 GCCAGTCGGGGAGGAATTC 60.153 63.158 0.0 0.0 37.04 2.17 R
3178 3289 1.076850 TAGCCCCACGTCATCGGTA 60.077 57.895 0.0 0.0 41.85 4.02 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
17 18 3.695825 TCCCTCCTCCTCCACCCC 61.696 72.222 0.00 0.00 0.00 4.95
18 19 3.700350 CCCTCCTCCTCCACCCCT 61.700 72.222 0.00 0.00 0.00 4.79
19 20 2.366167 CCTCCTCCTCCACCCCTG 60.366 72.222 0.00 0.00 0.00 4.45
20 21 2.780693 CTCCTCCTCCACCCCTGA 59.219 66.667 0.00 0.00 0.00 3.86
21 22 1.081092 CTCCTCCTCCACCCCTGAA 59.919 63.158 0.00 0.00 0.00 3.02
22 23 0.547712 CTCCTCCTCCACCCCTGAAA 60.548 60.000 0.00 0.00 0.00 2.69
23 24 0.104144 TCCTCCTCCACCCCTGAAAA 60.104 55.000 0.00 0.00 0.00 2.29
24 25 0.777446 CCTCCTCCACCCCTGAAAAA 59.223 55.000 0.00 0.00 0.00 1.94
25 26 1.547901 CCTCCTCCACCCCTGAAAAAC 60.548 57.143 0.00 0.00 0.00 2.43
26 27 1.144913 CTCCTCCACCCCTGAAAAACA 59.855 52.381 0.00 0.00 0.00 2.83
27 28 1.786441 TCCTCCACCCCTGAAAAACAT 59.214 47.619 0.00 0.00 0.00 2.71
28 29 2.171003 CCTCCACCCCTGAAAAACATC 58.829 52.381 0.00 0.00 0.00 3.06
29 30 2.490718 CCTCCACCCCTGAAAAACATCA 60.491 50.000 0.00 0.00 0.00 3.07
30 31 3.434309 CTCCACCCCTGAAAAACATCAT 58.566 45.455 0.00 0.00 0.00 2.45
31 32 3.430453 TCCACCCCTGAAAAACATCATC 58.570 45.455 0.00 0.00 0.00 2.92
32 33 3.075882 TCCACCCCTGAAAAACATCATCT 59.924 43.478 0.00 0.00 0.00 2.90
33 34 3.445096 CCACCCCTGAAAAACATCATCTC 59.555 47.826 0.00 0.00 0.00 2.75
34 35 4.338879 CACCCCTGAAAAACATCATCTCT 58.661 43.478 0.00 0.00 0.00 3.10
35 36 4.768968 CACCCCTGAAAAACATCATCTCTT 59.231 41.667 0.00 0.00 0.00 2.85
36 37 5.244626 CACCCCTGAAAAACATCATCTCTTT 59.755 40.000 0.00 0.00 0.00 2.52
37 38 5.478332 ACCCCTGAAAAACATCATCTCTTTC 59.522 40.000 0.00 0.00 0.00 2.62
38 39 5.713861 CCCCTGAAAAACATCATCTCTTTCT 59.286 40.000 0.00 0.00 0.00 2.52
39 40 6.210185 CCCCTGAAAAACATCATCTCTTTCTT 59.790 38.462 0.00 0.00 0.00 2.52
40 41 7.088905 CCCTGAAAAACATCATCTCTTTCTTG 58.911 38.462 0.00 0.00 0.00 3.02
41 42 7.040201 CCCTGAAAAACATCATCTCTTTCTTGA 60.040 37.037 0.00 0.00 0.00 3.02
42 43 8.521176 CCTGAAAAACATCATCTCTTTCTTGAT 58.479 33.333 0.00 0.00 0.00 2.57
43 44 9.557338 CTGAAAAACATCATCTCTTTCTTGATC 57.443 33.333 0.00 0.00 0.00 2.92
44 45 9.070179 TGAAAAACATCATCTCTTTCTTGATCA 57.930 29.630 0.00 0.00 0.00 2.92
45 46 9.339492 GAAAAACATCATCTCTTTCTTGATCAC 57.661 33.333 0.00 0.00 0.00 3.06
46 47 8.632906 AAAACATCATCTCTTTCTTGATCACT 57.367 30.769 0.00 0.00 0.00 3.41
47 48 8.632906 AAACATCATCTCTTTCTTGATCACTT 57.367 30.769 0.00 0.00 0.00 3.16
48 49 7.612668 ACATCATCTCTTTCTTGATCACTTG 57.387 36.000 0.00 0.00 0.00 3.16
49 50 7.392418 ACATCATCTCTTTCTTGATCACTTGA 58.608 34.615 0.00 0.00 0.00 3.02
50 51 8.047911 ACATCATCTCTTTCTTGATCACTTGAT 58.952 33.333 0.00 0.00 37.51 2.57
66 67 7.658179 TCACTTGATCACAATTCTGTAACTC 57.342 36.000 0.00 0.00 35.37 3.01
67 68 7.445121 TCACTTGATCACAATTCTGTAACTCT 58.555 34.615 0.00 0.00 35.37 3.24
68 69 7.600375 TCACTTGATCACAATTCTGTAACTCTC 59.400 37.037 0.00 0.00 35.37 3.20
69 70 6.876257 ACTTGATCACAATTCTGTAACTCTCC 59.124 38.462 0.00 0.00 35.37 3.71
70 71 5.734720 TGATCACAATTCTGTAACTCTCCC 58.265 41.667 0.00 0.00 33.22 4.30
71 72 4.553330 TCACAATTCTGTAACTCTCCCC 57.447 45.455 0.00 0.00 33.22 4.81
72 73 4.168101 TCACAATTCTGTAACTCTCCCCT 58.832 43.478 0.00 0.00 33.22 4.79
73 74 4.020218 TCACAATTCTGTAACTCTCCCCTG 60.020 45.833 0.00 0.00 33.22 4.45
74 75 3.274288 CAATTCTGTAACTCTCCCCTGC 58.726 50.000 0.00 0.00 0.00 4.85
75 76 2.327325 TTCTGTAACTCTCCCCTGCT 57.673 50.000 0.00 0.00 0.00 4.24
76 77 3.468071 TTCTGTAACTCTCCCCTGCTA 57.532 47.619 0.00 0.00 0.00 3.49
77 78 3.468071 TCTGTAACTCTCCCCTGCTAA 57.532 47.619 0.00 0.00 0.00 3.09
78 79 3.366396 TCTGTAACTCTCCCCTGCTAAG 58.634 50.000 0.00 0.00 0.00 2.18
79 80 1.831736 TGTAACTCTCCCCTGCTAAGC 59.168 52.381 0.00 0.00 0.00 3.09
80 81 1.139256 GTAACTCTCCCCTGCTAAGCC 59.861 57.143 0.00 0.00 0.00 4.35
81 82 0.547712 AACTCTCCCCTGCTAAGCCA 60.548 55.000 0.00 0.00 0.00 4.75
82 83 0.547712 ACTCTCCCCTGCTAAGCCAA 60.548 55.000 0.00 0.00 0.00 4.52
83 84 0.842635 CTCTCCCCTGCTAAGCCAAT 59.157 55.000 0.00 0.00 0.00 3.16
84 85 0.548031 TCTCCCCTGCTAAGCCAATG 59.452 55.000 0.00 0.00 0.00 2.82
85 86 0.548031 CTCCCCTGCTAAGCCAATGA 59.452 55.000 0.00 0.00 0.00 2.57
86 87 0.998928 TCCCCTGCTAAGCCAATGAA 59.001 50.000 0.00 0.00 0.00 2.57
87 88 1.357420 TCCCCTGCTAAGCCAATGAAA 59.643 47.619 0.00 0.00 0.00 2.69
88 89 2.178580 CCCCTGCTAAGCCAATGAAAA 58.821 47.619 0.00 0.00 0.00 2.29
89 90 2.167075 CCCCTGCTAAGCCAATGAAAAG 59.833 50.000 0.00 0.00 0.00 2.27
90 91 2.417787 CCCTGCTAAGCCAATGAAAAGC 60.418 50.000 0.00 0.00 0.00 3.51
91 92 2.417787 CCTGCTAAGCCAATGAAAAGCC 60.418 50.000 0.00 0.00 0.00 4.35
92 93 2.231964 CTGCTAAGCCAATGAAAAGCCA 59.768 45.455 0.00 0.00 0.00 4.75
93 94 2.231964 TGCTAAGCCAATGAAAAGCCAG 59.768 45.455 0.00 0.00 0.00 4.85
94 95 2.884827 CTAAGCCAATGAAAAGCCAGC 58.115 47.619 0.00 0.00 0.00 4.85
95 96 1.050204 AAGCCAATGAAAAGCCAGCA 58.950 45.000 0.00 0.00 0.00 4.41
96 97 1.050204 AGCCAATGAAAAGCCAGCAA 58.950 45.000 0.00 0.00 0.00 3.91
97 98 1.001633 AGCCAATGAAAAGCCAGCAAG 59.998 47.619 0.00 0.00 0.00 4.01
98 99 1.435577 CCAATGAAAAGCCAGCAAGC 58.564 50.000 0.00 0.00 0.00 4.01
99 100 1.435577 CAATGAAAAGCCAGCAAGCC 58.564 50.000 0.00 0.00 0.00 4.35
100 101 1.001633 CAATGAAAAGCCAGCAAGCCT 59.998 47.619 0.00 0.00 0.00 4.58
101 102 0.606604 ATGAAAAGCCAGCAAGCCTG 59.393 50.000 0.00 0.00 41.41 4.85
112 113 4.789012 CAGCAAGCCTGGATCTTAAAAA 57.211 40.909 0.00 0.00 37.93 1.94
135 136 2.717639 AAGCAACATTCCCGCTCTAT 57.282 45.000 0.00 0.00 34.11 1.98
165 166 4.506255 CCCCCTTCCACCATCCGC 62.506 72.222 0.00 0.00 0.00 5.54
400 401 2.202756 AGACCGGATCGCTTTCGC 60.203 61.111 9.46 0.00 35.26 4.70
409 410 2.185310 ATCGCTTTCGCTTGGTCCCT 62.185 55.000 0.00 0.00 35.26 4.20
410 411 1.966451 CGCTTTCGCTTGGTCCCTT 60.966 57.895 0.00 0.00 0.00 3.95
435 437 4.760220 GGCCTTCCCTCCCTCCCA 62.760 72.222 0.00 0.00 0.00 4.37
437 439 2.692741 CCTTCCCTCCCTCCCACC 60.693 72.222 0.00 0.00 0.00 4.61
438 440 2.124996 CTTCCCTCCCTCCCACCA 59.875 66.667 0.00 0.00 0.00 4.17
447 449 4.329545 CTCCCACCACCACCACCG 62.330 72.222 0.00 0.00 0.00 4.94
532 542 1.609555 CGCTACAGGGGTCTCTATCAC 59.390 57.143 0.00 0.00 0.00 3.06
533 543 2.667470 GCTACAGGGGTCTCTATCACA 58.333 52.381 0.00 0.00 0.00 3.58
534 544 3.031736 GCTACAGGGGTCTCTATCACAA 58.968 50.000 0.00 0.00 0.00 3.33
535 545 3.643792 GCTACAGGGGTCTCTATCACAAT 59.356 47.826 0.00 0.00 0.00 2.71
536 546 4.101741 GCTACAGGGGTCTCTATCACAATT 59.898 45.833 0.00 0.00 0.00 2.32
537 547 4.762289 ACAGGGGTCTCTATCACAATTC 57.238 45.455 0.00 0.00 0.00 2.17
539 549 3.455910 CAGGGGTCTCTATCACAATTCCA 59.544 47.826 0.00 0.00 0.00 3.53
540 550 3.456277 AGGGGTCTCTATCACAATTCCAC 59.544 47.826 0.00 0.00 0.00 4.02
541 551 3.433740 GGGGTCTCTATCACAATTCCACC 60.434 52.174 0.00 0.00 0.00 4.61
542 552 3.458189 GGTCTCTATCACAATTCCACCG 58.542 50.000 0.00 0.00 0.00 4.94
543 553 2.866762 GTCTCTATCACAATTCCACCGC 59.133 50.000 0.00 0.00 0.00 5.68
544 554 2.158957 TCTCTATCACAATTCCACCGCC 60.159 50.000 0.00 0.00 0.00 6.13
545 555 0.937304 CTATCACAATTCCACCGCCG 59.063 55.000 0.00 0.00 0.00 6.46
546 556 1.092921 TATCACAATTCCACCGCCGC 61.093 55.000 0.00 0.00 0.00 6.53
547 557 3.361158 CACAATTCCACCGCCGCA 61.361 61.111 0.00 0.00 0.00 5.69
548 558 2.361104 ACAATTCCACCGCCGCAT 60.361 55.556 0.00 0.00 0.00 4.73
578 588 0.460284 CCACATTCCCTTCCTCGTCG 60.460 60.000 0.00 0.00 0.00 5.12
621 631 3.637229 AGAGATTTATTTCGCCTCGGAGA 59.363 43.478 6.58 0.00 0.00 3.71
835 878 2.357034 GCAGCGTTCTCCACCGAA 60.357 61.111 0.00 0.00 0.00 4.30
941 1017 7.993821 ATTATGTCGACTTGTTAGATCTGTG 57.006 36.000 17.92 0.00 0.00 3.66
942 1018 3.575630 TGTCGACTTGTTAGATCTGTGC 58.424 45.455 17.92 0.00 0.00 4.57
1011 1087 2.755876 AGCGAGATGAGGGCGTCA 60.756 61.111 12.80 12.80 40.38 4.35
1018 1094 1.227380 ATGAGGGCGTCATCTTCGC 60.227 57.895 16.45 1.63 42.80 4.70
1092 1168 3.074999 GCTCTGCTCCGTCTCCCTG 62.075 68.421 0.00 0.00 0.00 4.45
1199 1275 0.814457 CTCTCAACACTCCCTCTCCG 59.186 60.000 0.00 0.00 0.00 4.63
1201 1277 0.244994 CTCAACACTCCCTCTCCGTG 59.755 60.000 0.00 0.00 34.92 4.94
1216 1292 1.403679 TCCGTGTTTCTGTTTTGCCAG 59.596 47.619 0.00 0.00 0.00 4.85
1217 1293 1.535860 CCGTGTTTCTGTTTTGCCAGG 60.536 52.381 0.00 0.00 33.14 4.45
1231 1307 1.077265 CCAGGGGCTTCCATGTTGT 59.923 57.895 0.00 0.00 40.47 3.32
1257 1333 2.349297 ACTCGTCTGGATGTTTCGTC 57.651 50.000 0.00 0.00 0.00 4.20
1287 1363 1.333308 CACAAATCACACGGACTTGCA 59.667 47.619 0.00 0.00 0.00 4.08
1419 1496 2.260434 GTTCCTGCGCTCCGTGTA 59.740 61.111 9.73 0.00 0.00 2.90
1887 1967 1.378646 GGGGGTACTTTGAGCCTGC 60.379 63.158 0.00 0.00 37.16 4.85
2043 2124 3.682292 GACATGTGGGGCCGTCTCC 62.682 68.421 1.15 0.00 0.00 3.71
2047 2128 2.046217 GTGGGGCCGTCTCCTTTC 60.046 66.667 0.00 0.00 0.00 2.62
2106 2187 4.980805 GCGTGGACGAGGGTTGCA 62.981 66.667 2.73 0.00 43.02 4.08
2677 2776 1.363744 GTGATCCGGAGCTGTCTTTG 58.636 55.000 22.18 0.00 0.00 2.77
2891 2993 3.800280 GCTCGTGTAGCCTAGTGCAGG 62.800 61.905 6.07 0.00 46.25 4.85
2936 3038 3.192844 TGTAGCCTACTGTAGCAAGTGTC 59.807 47.826 9.35 0.00 0.00 3.67
2952 3054 2.028476 AGTGTCGCCTGTAAATGTGCTA 60.028 45.455 0.00 0.00 0.00 3.49
3006 3108 1.134907 ACCGTGTGAGTCGTGTTTTCT 60.135 47.619 0.00 0.00 0.00 2.52
3051 3153 3.434319 GCATGGGTCTGTGTGCGG 61.434 66.667 0.00 0.00 0.00 5.69
3106 3217 4.887071 TGATGGGTACATTAATTGGACTGC 59.113 41.667 0.00 0.00 39.36 4.40
3107 3218 4.308526 TGGGTACATTAATTGGACTGCA 57.691 40.909 0.00 0.00 39.36 4.41
3125 3236 2.038426 TGCAATGTCCTTTTCTCTCGGA 59.962 45.455 0.00 0.00 0.00 4.55
3259 3370 1.741145 TCCTCGATCGTGATTCGTGAA 59.259 47.619 18.20 0.00 40.80 3.18
3263 3374 1.522676 CGATCGTGATTCGTGAATGGG 59.477 52.381 7.03 0.00 40.80 4.00
3276 3387 0.037046 GAATGGGTTGCTGCCTTTGG 60.037 55.000 0.00 0.00 0.00 3.28
3333 3444 3.976701 ATCAAAGCGGGCGGTCTGG 62.977 63.158 0.00 0.00 0.00 3.86
3342 3453 3.866582 GCGGTCTGGGCCATAGCT 61.867 66.667 17.51 0.00 39.73 3.32
3357 3474 1.644509 TAGCTGGACTGCCTCTCAAA 58.355 50.000 0.00 0.00 34.31 2.69
3358 3475 0.324285 AGCTGGACTGCCTCTCAAAG 59.676 55.000 0.00 0.00 34.31 2.77
3371 3488 2.991580 TCTCAAAGGGAGGGAGAAAGT 58.008 47.619 0.00 0.00 44.19 2.66
3375 3492 4.435137 TCAAAGGGAGGGAGAAAGTATCA 58.565 43.478 0.00 0.00 0.00 2.15
3406 3523 4.935885 GAAAGTTTCGTGCTCTCATGAT 57.064 40.909 0.00 0.00 37.99 2.45
3408 3525 5.786401 AAAGTTTCGTGCTCTCATGATAC 57.214 39.130 0.00 0.00 39.16 2.24
3409 3526 4.456280 AGTTTCGTGCTCTCATGATACA 57.544 40.909 0.00 0.00 40.42 2.29
3410 3527 4.820897 AGTTTCGTGCTCTCATGATACAA 58.179 39.130 0.00 0.00 40.42 2.41
3411 3528 4.867047 AGTTTCGTGCTCTCATGATACAAG 59.133 41.667 0.00 0.00 40.42 3.16
3412 3529 4.718940 TTCGTGCTCTCATGATACAAGA 57.281 40.909 0.00 0.14 37.99 3.02
3413 3530 4.033990 TCGTGCTCTCATGATACAAGAC 57.966 45.455 0.00 0.00 33.54 3.01
3414 3531 2.786027 CGTGCTCTCATGATACAAGACG 59.214 50.000 0.00 0.00 0.00 4.18
3415 3532 3.487544 CGTGCTCTCATGATACAAGACGA 60.488 47.826 0.00 0.00 0.00 4.20
3416 3533 3.794028 GTGCTCTCATGATACAAGACGAC 59.206 47.826 0.00 0.00 0.00 4.34
3417 3534 3.039405 GCTCTCATGATACAAGACGACG 58.961 50.000 0.00 0.00 0.00 5.12
3418 3535 3.487711 GCTCTCATGATACAAGACGACGT 60.488 47.826 0.00 0.00 0.00 4.34
3419 3536 4.016113 TCTCATGATACAAGACGACGTG 57.984 45.455 4.58 0.00 0.00 4.49
3420 3537 3.108881 CTCATGATACAAGACGACGTGG 58.891 50.000 4.58 0.00 0.00 4.94
3421 3538 2.159296 TCATGATACAAGACGACGTGGG 60.159 50.000 4.58 0.00 0.00 4.61
3422 3539 1.250328 TGATACAAGACGACGTGGGT 58.750 50.000 4.58 2.95 0.00 4.51
3423 3540 1.200716 TGATACAAGACGACGTGGGTC 59.799 52.381 4.58 5.38 39.89 4.46
3435 3552 2.373540 CGTGGGTCGTTGGATCTAAA 57.626 50.000 0.00 0.00 34.52 1.85
3436 3553 2.690786 CGTGGGTCGTTGGATCTAAAA 58.309 47.619 0.00 0.00 34.52 1.52
3437 3554 3.267483 CGTGGGTCGTTGGATCTAAAAT 58.733 45.455 0.00 0.00 34.52 1.82
3438 3555 3.687698 CGTGGGTCGTTGGATCTAAAATT 59.312 43.478 0.00 0.00 34.52 1.82
3439 3556 4.201783 CGTGGGTCGTTGGATCTAAAATTC 60.202 45.833 0.00 0.00 34.52 2.17
3440 3557 4.698304 GTGGGTCGTTGGATCTAAAATTCA 59.302 41.667 0.00 0.00 0.00 2.57
3441 3558 5.182380 GTGGGTCGTTGGATCTAAAATTCAA 59.818 40.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.695825 GGGGTGGAGGAGGAGGGA 61.696 72.222 0.00 0.00 0.00 4.20
1 2 3.700350 AGGGGTGGAGGAGGAGGG 61.700 72.222 0.00 0.00 0.00 4.30
3 4 0.547712 TTTCAGGGGTGGAGGAGGAG 60.548 60.000 0.00 0.00 0.00 3.69
4 5 0.104144 TTTTCAGGGGTGGAGGAGGA 60.104 55.000 0.00 0.00 0.00 3.71
5 6 0.777446 TTTTTCAGGGGTGGAGGAGG 59.223 55.000 0.00 0.00 0.00 4.30
6 7 1.144913 TGTTTTTCAGGGGTGGAGGAG 59.855 52.381 0.00 0.00 0.00 3.69
7 8 1.227249 TGTTTTTCAGGGGTGGAGGA 58.773 50.000 0.00 0.00 0.00 3.71
8 9 2.171003 GATGTTTTTCAGGGGTGGAGG 58.829 52.381 0.00 0.00 0.00 4.30
9 10 2.875296 TGATGTTTTTCAGGGGTGGAG 58.125 47.619 0.00 0.00 0.00 3.86
10 11 3.075882 AGATGATGTTTTTCAGGGGTGGA 59.924 43.478 0.00 0.00 0.00 4.02
11 12 3.434309 AGATGATGTTTTTCAGGGGTGG 58.566 45.455 0.00 0.00 0.00 4.61
12 13 4.338879 AGAGATGATGTTTTTCAGGGGTG 58.661 43.478 0.00 0.00 0.00 4.61
13 14 4.664688 AGAGATGATGTTTTTCAGGGGT 57.335 40.909 0.00 0.00 0.00 4.95
14 15 5.713861 AGAAAGAGATGATGTTTTTCAGGGG 59.286 40.000 8.03 0.00 31.83 4.79
15 16 6.830873 AGAAAGAGATGATGTTTTTCAGGG 57.169 37.500 8.03 0.00 31.83 4.45
16 17 7.879070 TCAAGAAAGAGATGATGTTTTTCAGG 58.121 34.615 8.03 0.98 31.83 3.86
17 18 9.557338 GATCAAGAAAGAGATGATGTTTTTCAG 57.443 33.333 8.03 1.59 34.10 3.02
18 19 9.070179 TGATCAAGAAAGAGATGATGTTTTTCA 57.930 29.630 8.03 0.00 34.10 2.69
19 20 9.339492 GTGATCAAGAAAGAGATGATGTTTTTC 57.661 33.333 0.00 0.00 34.10 2.29
20 21 9.075678 AGTGATCAAGAAAGAGATGATGTTTTT 57.924 29.630 0.00 0.00 34.10 1.94
21 22 8.632906 AGTGATCAAGAAAGAGATGATGTTTT 57.367 30.769 0.00 0.00 34.10 2.43
22 23 8.512956 CAAGTGATCAAGAAAGAGATGATGTTT 58.487 33.333 0.00 0.00 34.10 2.83
23 24 7.881751 TCAAGTGATCAAGAAAGAGATGATGTT 59.118 33.333 0.00 0.00 34.10 2.71
24 25 7.392418 TCAAGTGATCAAGAAAGAGATGATGT 58.608 34.615 0.00 0.00 34.10 3.06
25 26 7.845066 TCAAGTGATCAAGAAAGAGATGATG 57.155 36.000 0.00 0.00 34.10 3.07
41 42 8.099537 AGAGTTACAGAATTGTGATCAAGTGAT 58.900 33.333 9.96 0.00 38.23 3.06
42 43 7.445121 AGAGTTACAGAATTGTGATCAAGTGA 58.555 34.615 9.96 0.00 38.23 3.41
43 44 7.148507 GGAGAGTTACAGAATTGTGATCAAGTG 60.149 40.741 9.96 0.00 38.23 3.16
44 45 6.876257 GGAGAGTTACAGAATTGTGATCAAGT 59.124 38.462 9.96 3.44 38.23 3.16
45 46 6.314896 GGGAGAGTTACAGAATTGTGATCAAG 59.685 42.308 9.96 0.00 38.23 3.02
46 47 6.173339 GGGAGAGTTACAGAATTGTGATCAA 58.827 40.000 9.96 0.00 38.23 2.57
47 48 5.338381 GGGGAGAGTTACAGAATTGTGATCA 60.338 44.000 9.96 0.00 38.23 2.92
48 49 5.104735 AGGGGAGAGTTACAGAATTGTGATC 60.105 44.000 9.96 2.25 38.23 2.92
49 50 4.785376 AGGGGAGAGTTACAGAATTGTGAT 59.215 41.667 9.96 0.00 38.23 3.06
50 51 4.020218 CAGGGGAGAGTTACAGAATTGTGA 60.020 45.833 9.96 0.00 38.23 3.58
51 52 4.256920 CAGGGGAGAGTTACAGAATTGTG 58.743 47.826 0.13 0.13 38.23 3.33
52 53 3.307762 GCAGGGGAGAGTTACAGAATTGT 60.308 47.826 0.00 0.00 41.39 2.71
53 54 3.054802 AGCAGGGGAGAGTTACAGAATTG 60.055 47.826 0.00 0.00 0.00 2.32
54 55 3.185455 AGCAGGGGAGAGTTACAGAATT 58.815 45.455 0.00 0.00 0.00 2.17
55 56 2.839228 AGCAGGGGAGAGTTACAGAAT 58.161 47.619 0.00 0.00 0.00 2.40
56 57 2.327325 AGCAGGGGAGAGTTACAGAA 57.673 50.000 0.00 0.00 0.00 3.02
57 58 3.366396 CTTAGCAGGGGAGAGTTACAGA 58.634 50.000 0.00 0.00 0.00 3.41
58 59 2.159028 GCTTAGCAGGGGAGAGTTACAG 60.159 54.545 0.00 0.00 0.00 2.74
59 60 1.831736 GCTTAGCAGGGGAGAGTTACA 59.168 52.381 0.00 0.00 0.00 2.41
60 61 1.139256 GGCTTAGCAGGGGAGAGTTAC 59.861 57.143 6.53 0.00 0.00 2.50
61 62 1.273609 TGGCTTAGCAGGGGAGAGTTA 60.274 52.381 6.53 0.00 0.00 2.24
62 63 0.547712 TGGCTTAGCAGGGGAGAGTT 60.548 55.000 6.53 0.00 0.00 3.01
63 64 0.547712 TTGGCTTAGCAGGGGAGAGT 60.548 55.000 6.53 0.00 0.00 3.24
64 65 0.842635 ATTGGCTTAGCAGGGGAGAG 59.157 55.000 6.53 0.00 0.00 3.20
65 66 0.548031 CATTGGCTTAGCAGGGGAGA 59.452 55.000 6.53 0.00 0.00 3.71
66 67 0.548031 TCATTGGCTTAGCAGGGGAG 59.452 55.000 6.53 0.00 0.00 4.30
67 68 0.998928 TTCATTGGCTTAGCAGGGGA 59.001 50.000 6.53 0.00 0.00 4.81
68 69 1.851304 TTTCATTGGCTTAGCAGGGG 58.149 50.000 6.53 0.00 0.00 4.79
69 70 2.417787 GCTTTTCATTGGCTTAGCAGGG 60.418 50.000 6.53 0.00 0.00 4.45
70 71 2.417787 GGCTTTTCATTGGCTTAGCAGG 60.418 50.000 6.53 0.00 0.00 4.85
71 72 2.231964 TGGCTTTTCATTGGCTTAGCAG 59.768 45.455 6.53 0.00 0.00 4.24
72 73 2.231964 CTGGCTTTTCATTGGCTTAGCA 59.768 45.455 6.53 0.00 0.00 3.49
73 74 2.884827 CTGGCTTTTCATTGGCTTAGC 58.115 47.619 0.00 0.00 0.00 3.09
74 75 2.231964 TGCTGGCTTTTCATTGGCTTAG 59.768 45.455 0.00 0.00 0.00 2.18
75 76 2.246469 TGCTGGCTTTTCATTGGCTTA 58.754 42.857 0.00 0.00 0.00 3.09
76 77 1.050204 TGCTGGCTTTTCATTGGCTT 58.950 45.000 0.00 0.00 0.00 4.35
77 78 1.001633 CTTGCTGGCTTTTCATTGGCT 59.998 47.619 0.00 0.00 0.00 4.75
78 79 1.435577 CTTGCTGGCTTTTCATTGGC 58.564 50.000 0.00 0.00 0.00 4.52
79 80 1.435577 GCTTGCTGGCTTTTCATTGG 58.564 50.000 0.00 0.00 0.00 3.16
80 81 1.435577 GGCTTGCTGGCTTTTCATTG 58.564 50.000 1.99 0.00 38.32 2.82
81 82 3.921257 GGCTTGCTGGCTTTTCATT 57.079 47.368 1.99 0.00 38.32 2.57
89 90 0.107017 TAAGATCCAGGCTTGCTGGC 60.107 55.000 2.79 0.00 41.53 4.85
90 91 2.425143 TTAAGATCCAGGCTTGCTGG 57.575 50.000 1.27 1.27 43.06 4.85
91 92 4.789012 TTTTTAAGATCCAGGCTTGCTG 57.211 40.909 0.00 0.00 0.00 4.41
135 136 2.510613 GAAGGGGGTTCGTGAATTCAA 58.489 47.619 10.35 0.00 0.00 2.69
165 166 0.321298 AATCGTTTGGACTGGGACGG 60.321 55.000 0.00 0.00 42.99 4.79
343 344 0.550914 AAAAGTGTGTCCTGCTGGGA 59.449 50.000 10.07 2.15 42.77 4.37
423 424 4.348495 GGTGGTGGGAGGGAGGGA 62.348 72.222 0.00 0.00 0.00 4.20
509 519 0.395311 TAGAGACCCCTGTAGCGTGG 60.395 60.000 0.00 0.00 0.00 4.94
532 542 2.102749 CATGCGGCGGTGGAATTG 59.897 61.111 9.78 0.00 0.00 2.32
533 543 3.825611 GCATGCGGCGGTGGAATT 61.826 61.111 9.78 0.00 0.00 2.17
545 555 4.197498 GTGGGTGATGCGGCATGC 62.197 66.667 21.98 9.90 46.70 4.06
546 556 1.669049 AATGTGGGTGATGCGGCATG 61.669 55.000 21.98 0.00 0.00 4.06
547 557 1.380246 AATGTGGGTGATGCGGCAT 60.380 52.632 16.65 16.65 0.00 4.40
548 558 2.035469 AATGTGGGTGATGCGGCA 59.965 55.556 4.58 4.58 0.00 5.69
891 935 3.782042 GCAAGTAGCGTTCTCCCG 58.218 61.111 0.00 0.00 0.00 5.14
941 1017 0.460284 ACATGGAGATCAACGACGGC 60.460 55.000 0.00 0.00 0.00 5.68
942 1018 2.010145 AACATGGAGATCAACGACGG 57.990 50.000 0.00 0.00 0.00 4.79
1199 1275 1.202521 CCCCTGGCAAAACAGAAACAC 60.203 52.381 0.00 0.00 40.97 3.32
1201 1277 3.986970 CCCCTGGCAAAACAGAAAC 57.013 52.632 0.00 0.00 40.97 2.78
1216 1292 2.238898 AGTACTACAACATGGAAGCCCC 59.761 50.000 0.00 0.00 0.00 5.80
1217 1293 3.629142 AGTACTACAACATGGAAGCCC 57.371 47.619 0.00 0.00 0.00 5.19
1231 1307 5.292834 CGAAACATCCAGACGAGTAGTACTA 59.707 44.000 1.88 0.00 0.00 1.82
1257 1333 4.681025 CCGTGTGATTTGTGAATGGAAAAG 59.319 41.667 0.00 0.00 0.00 2.27
1287 1363 3.615496 CGTACGAGGGTTCAAATCGAAAT 59.385 43.478 10.44 0.00 39.66 2.17
1319 1395 1.153147 GCCAGTCGGGGAGGAATTC 60.153 63.158 0.00 0.00 37.04 2.17
1419 1496 5.070685 GGGATCTTAACAAACACCTGAACT 58.929 41.667 0.00 0.00 0.00 3.01
2043 2124 2.671177 CGTCCGTGCCTGCAGAAAG 61.671 63.158 17.39 5.29 0.00 2.62
2106 2187 2.990479 GATGTCCTCCTTGCCGGT 59.010 61.111 1.90 0.00 0.00 5.28
2677 2776 4.382541 CCCCCTTCCTTGCCCCAC 62.383 72.222 0.00 0.00 0.00 4.61
2936 3038 1.594862 GAGCTAGCACATTTACAGGCG 59.405 52.381 18.83 0.00 0.00 5.52
2968 3070 4.505217 CACGCGGCTGTCATTCGC 62.505 66.667 12.47 9.14 45.15 4.70
2969 3071 2.809174 TCACGCGGCTGTCATTCG 60.809 61.111 12.47 0.00 0.00 3.34
3017 3119 1.743252 GCACAAAGGAGGCGAGAGG 60.743 63.158 0.00 0.00 0.00 3.69
3021 3123 1.675310 CCATGCACAAAGGAGGCGA 60.675 57.895 0.00 0.00 0.00 5.54
3023 3125 1.598701 GACCCATGCACAAAGGAGGC 61.599 60.000 0.00 0.00 0.00 4.70
3051 3153 2.419673 TCGAATCACACATTGCATGTCC 59.580 45.455 0.00 0.00 42.70 4.02
3073 3175 2.063979 TACCCATCACAGAGCCCCG 61.064 63.158 0.00 0.00 0.00 5.73
3106 3217 4.697352 ACATTCCGAGAGAAAAGGACATTG 59.303 41.667 0.00 0.00 38.21 2.82
3107 3218 4.697352 CACATTCCGAGAGAAAAGGACATT 59.303 41.667 0.00 0.00 38.21 2.71
3125 3236 1.325355 GCTATGGAGCCATGCACATT 58.675 50.000 12.18 0.00 43.49 2.71
3178 3289 1.076850 TAGCCCCACGTCATCGGTA 60.077 57.895 0.00 0.00 41.85 4.02
3259 3370 1.152269 ACCAAAGGCAGCAACCCAT 60.152 52.632 0.00 0.00 0.00 4.00
3263 3374 1.809567 CTGGGACCAAAGGCAGCAAC 61.810 60.000 0.00 0.00 0.00 4.17
3316 3427 4.697756 CCAGACCGCCCGCTTTGA 62.698 66.667 0.00 0.00 0.00 2.69
3339 3450 0.324285 CTTTGAGAGGCAGTCCAGCT 59.676 55.000 0.00 0.00 33.74 4.24
3341 3452 0.035630 CCCTTTGAGAGGCAGTCCAG 60.036 60.000 0.00 0.00 44.85 3.86
3342 3453 0.473694 TCCCTTTGAGAGGCAGTCCA 60.474 55.000 0.00 0.00 44.85 4.02
3357 3474 2.319438 ACCTGATACTTTCTCCCTCCCT 59.681 50.000 0.00 0.00 0.00 4.20
3358 3475 2.436173 CACCTGATACTTTCTCCCTCCC 59.564 54.545 0.00 0.00 0.00 4.30
3359 3476 3.375699 TCACCTGATACTTTCTCCCTCC 58.624 50.000 0.00 0.00 0.00 4.30
3388 3505 4.456280 TGTATCATGAGAGCACGAAACT 57.544 40.909 0.09 0.00 0.00 2.66
3392 3509 3.487544 CGTCTTGTATCATGAGAGCACGA 60.488 47.826 0.09 0.69 0.00 4.35
3397 3514 4.031691 CACGTCGTCTTGTATCATGAGAG 58.968 47.826 0.09 0.00 0.00 3.20
3398 3515 3.181500 CCACGTCGTCTTGTATCATGAGA 60.181 47.826 0.09 0.00 0.00 3.27
3399 3516 3.108881 CCACGTCGTCTTGTATCATGAG 58.891 50.000 0.09 0.00 0.00 2.90
3400 3517 2.159296 CCCACGTCGTCTTGTATCATGA 60.159 50.000 0.00 0.00 0.00 3.07
3401 3518 2.193447 CCCACGTCGTCTTGTATCATG 58.807 52.381 0.00 0.00 0.00 3.07
3402 3519 1.822990 ACCCACGTCGTCTTGTATCAT 59.177 47.619 0.00 0.00 0.00 2.45
3403 3520 1.200716 GACCCACGTCGTCTTGTATCA 59.799 52.381 0.00 0.00 0.00 2.15
3404 3521 1.905449 GACCCACGTCGTCTTGTATC 58.095 55.000 0.00 0.00 0.00 2.24
3417 3534 4.698304 TGAATTTTAGATCCAACGACCCAC 59.302 41.667 0.00 0.00 0.00 4.61
3418 3535 4.912586 TGAATTTTAGATCCAACGACCCA 58.087 39.130 0.00 0.00 0.00 4.51
3419 3536 5.890424 TTGAATTTTAGATCCAACGACCC 57.110 39.130 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.