Multiple sequence alignment - TraesCS4D01G144700

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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 TraesCS4D01G144700 chr4D 100.000 3788 0 0 1 3788 133467898 133471685 0.000000e+00 6996
1 TraesCS4D01G144700 chr6A 92.966 3028 142 20 793 3788 74907086 74904098 0.000000e+00 4346
2 TraesCS4D01G144700 chr6A 88.263 213 11 8 201 399 74972597 74972385 3.780000e-60 243
3 TraesCS4D01G144700 chr6A 90.909 132 8 1 573 700 74907242 74907111 1.400000e-39 174
4 TraesCS4D01G144700 chr6D 92.719 2321 98 22 883 3150 58856861 58854559 0.000000e+00 3284
5 TraesCS4D01G144700 chr6D 92.044 641 30 4 3148 3788 58842867 58842248 0.000000e+00 881
6 TraesCS4D01G144700 chr6B 94.828 2030 67 10 795 2790 132432651 132430626 0.000000e+00 3133
7 TraesCS4D01G144700 chr6B 91.377 835 47 9 2958 3788 132422842 132422029 0.000000e+00 1120
8 TraesCS4D01G144700 chr6B 84.634 423 27 14 1 399 132433451 132433043 1.650000e-103 387
9 TraesCS4D01G144700 chr6B 89.247 186 11 3 520 700 132432856 132432675 1.370000e-54 224
10 TraesCS4D01G144700 chr6B 94.565 92 5 0 712 803 55994004 55994095 3.940000e-30 143
11 TraesCS4D01G144700 chr6B 93.548 93 6 0 712 804 367268597 367268689 5.100000e-29 139
12 TraesCS4D01G144700 chr4A 90.696 1967 109 24 1840 3788 428164103 428162193 0.000000e+00 2551
13 TraesCS4D01G144700 chr4A 95.278 720 23 5 865 1578 428259774 428259060 0.000000e+00 1131
14 TraesCS4D01G144700 chr4A 95.956 272 11 0 1574 1845 428253791 428253520 3.470000e-120 442
15 TraesCS4D01G144700 chr4A 88.011 367 18 9 2 357 428263456 428263105 9.790000e-111 411
16 TraesCS4D01G144700 chr4A 88.393 224 12 5 487 701 428260118 428259900 1.350000e-64 257
17 TraesCS4D01G144700 chr4B 91.102 708 50 10 2897 3601 161604401 161603704 0.000000e+00 946
18 TraesCS4D01G144700 chr4B 95.540 426 19 0 2269 2694 161620195 161619770 0.000000e+00 682
19 TraesCS4D01G144700 chr4B 87.943 423 27 7 1 399 161622458 161622036 9.520000e-131 477
20 TraesCS4D01G144700 chr4B 92.386 197 14 1 3591 3786 161563106 161562910 2.880000e-71 279
21 TraesCS4D01G144700 chr4B 85.467 289 12 8 795 1081 161621271 161621011 1.340000e-69 274
22 TraesCS4D01G144700 chr4B 87.619 210 16 3 2692 2891 161619497 161619288 6.330000e-58 235
23 TraesCS4D01G144700 chr5B 82.632 737 114 10 1991 2714 622605437 622606172 1.150000e-179 640
24 TraesCS4D01G144700 chr3B 81.593 766 112 21 1964 2704 620454967 620454206 1.160000e-169 606
25 TraesCS4D01G144700 chr3B 89.720 107 10 1 710 816 819011622 819011517 6.600000e-28 135
26 TraesCS4D01G144700 chr3A 81.486 767 117 16 1966 2709 609687790 609687026 1.160000e-169 606
27 TraesCS4D01G144700 chr3D 81.462 766 113 21 1964 2704 466679144 466678383 5.410000e-168 601
28 TraesCS4D01G144700 chr3D 93.814 97 4 2 703 797 37369106 37369010 1.100000e-30 145
29 TraesCS4D01G144700 chr5A 92.381 105 5 3 702 804 306880983 306880880 3.050000e-31 147
30 TraesCS4D01G144700 chr2D 94.737 95 1 4 707 801 457410259 457410349 1.100000e-30 145
31 TraesCS4D01G144700 chr2D 93.617 94 6 0 712 805 650216403 650216496 1.420000e-29 141
32 TraesCS4D01G144700 chr1A 91.089 101 8 1 705 804 168394377 168394477 6.600000e-28 135
33 TraesCS4D01G144700 chr2A 90.291 103 8 2 705 806 127212323 127212222 2.370000e-27 134


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 TraesCS4D01G144700 chr4D 133467898 133471685 3787 False 6996.000000 6996 100.000000 1 3788 1 chr4D.!!$F1 3787
1 TraesCS4D01G144700 chr6A 74904098 74907242 3144 True 2260.000000 4346 91.937500 573 3788 2 chr6A.!!$R2 3215
2 TraesCS4D01G144700 chr6D 58854559 58856861 2302 True 3284.000000 3284 92.719000 883 3150 1 chr6D.!!$R2 2267
3 TraesCS4D01G144700 chr6D 58842248 58842867 619 True 881.000000 881 92.044000 3148 3788 1 chr6D.!!$R1 640
4 TraesCS4D01G144700 chr6B 132430626 132433451 2825 True 1248.000000 3133 89.569667 1 2790 3 chr6B.!!$R2 2789
5 TraesCS4D01G144700 chr6B 132422029 132422842 813 True 1120.000000 1120 91.377000 2958 3788 1 chr6B.!!$R1 830
6 TraesCS4D01G144700 chr4A 428162193 428164103 1910 True 2551.000000 2551 90.696000 1840 3788 1 chr4A.!!$R1 1948
7 TraesCS4D01G144700 chr4A 428259060 428263456 4396 True 599.666667 1131 90.560667 2 1578 3 chr4A.!!$R3 1576
8 TraesCS4D01G144700 chr4B 161603704 161604401 697 True 946.000000 946 91.102000 2897 3601 1 chr4B.!!$R2 704
9 TraesCS4D01G144700 chr4B 161619288 161622458 3170 True 417.000000 682 89.142250 1 2891 4 chr4B.!!$R3 2890
10 TraesCS4D01G144700 chr5B 622605437 622606172 735 False 640.000000 640 82.632000 1991 2714 1 chr5B.!!$F1 723
11 TraesCS4D01G144700 chr3B 620454206 620454967 761 True 606.000000 606 81.593000 1964 2704 1 chr3B.!!$R1 740
12 TraesCS4D01G144700 chr3A 609687026 609687790 764 True 606.000000 606 81.486000 1966 2709 1 chr3A.!!$R1 743
13 TraesCS4D01G144700 chr3D 466678383 466679144 761 True 601.000000 601 81.462000 1964 2704 1 chr3D.!!$R2 740

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
413 2040 0.174845 ATCGTATCGTGTGGGTGGTG 59.825 55.0 0.0 0.0 0.0 4.17 F
1554 4947 0.182061 TCTACCTCGCCATCTACGGT 59.818 55.0 0.0 0.0 0.0 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1997 5441 0.240945 CGGGTTGAACATGTGCTTCC 59.759 55.0 5.18 7.29 0.00 3.46 R
3096 7560 0.317479 CGGACGAGTCACTTCCCTTT 59.683 55.0 5.55 0.00 33.98 3.11 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
72 73 5.126061 AGTCCATGAAGATATGTGGCAAAAC 59.874 40.000 0.00 0.00 0.00 2.43
73 74 5.015515 TCCATGAAGATATGTGGCAAAACA 58.984 37.500 0.00 0.00 0.00 2.83
75 76 5.808540 CCATGAAGATATGTGGCAAAACAAG 59.191 40.000 0.00 0.00 32.81 3.16
80 83 7.984050 TGAAGATATGTGGCAAAACAAGAAAAA 59.016 29.630 0.00 0.00 32.81 1.94
85 88 7.913674 ATGTGGCAAAACAAGAAAAAGTTAA 57.086 28.000 0.00 0.00 32.81 2.01
115 126 3.499737 GACCAGCACCCGCGATTG 61.500 66.667 8.23 4.89 45.49 2.67
127 138 1.920762 GCGATTGCTGCGAGTAGAC 59.079 57.895 0.00 0.00 38.39 2.59
132 143 0.450583 TTGCTGCGAGTAGACGTAGG 59.549 55.000 0.00 0.00 43.79 3.18
172 191 1.135689 CCAGAAACTTGTACGCATGCC 60.136 52.381 13.15 0.00 0.00 4.40
206 225 1.270358 ACTCACTGAAGAAACGGAGGC 60.270 52.381 0.00 0.00 0.00 4.70
251 270 4.556592 TGTAGCCGGTTAGGTTAATTGT 57.443 40.909 1.90 0.00 43.70 2.71
252 271 4.909001 TGTAGCCGGTTAGGTTAATTGTT 58.091 39.130 1.90 0.00 43.70 2.83
253 272 6.047511 TGTAGCCGGTTAGGTTAATTGTTA 57.952 37.500 1.90 0.00 43.70 2.41
254 273 6.108015 TGTAGCCGGTTAGGTTAATTGTTAG 58.892 40.000 1.90 0.00 43.70 2.34
255 274 5.425196 AGCCGGTTAGGTTAATTGTTAGA 57.575 39.130 1.90 0.00 43.70 2.10
256 275 5.997843 AGCCGGTTAGGTTAATTGTTAGAT 58.002 37.500 1.90 0.00 43.70 1.98
257 276 5.820947 AGCCGGTTAGGTTAATTGTTAGATG 59.179 40.000 1.90 0.00 43.70 2.90
258 277 5.587443 GCCGGTTAGGTTAATTGTTAGATGT 59.413 40.000 1.90 0.00 43.70 3.06
259 278 6.238293 GCCGGTTAGGTTAATTGTTAGATGTC 60.238 42.308 1.90 0.00 43.70 3.06
260 279 6.259387 CCGGTTAGGTTAATTGTTAGATGTCC 59.741 42.308 0.00 0.00 34.51 4.02
261 280 7.046033 CGGTTAGGTTAATTGTTAGATGTCCT 58.954 38.462 0.00 0.00 0.00 3.85
262 281 7.224167 CGGTTAGGTTAATTGTTAGATGTCCTC 59.776 40.741 0.00 0.00 0.00 3.71
301 332 2.342279 CTGCCAGAAACGACCGGA 59.658 61.111 9.46 0.00 0.00 5.14
318 357 1.963747 GGAACGCGAAATTGTCAAGG 58.036 50.000 15.93 0.00 0.00 3.61
336 375 0.616111 GGGTGAGAGGGCTGAGAAGA 60.616 60.000 0.00 0.00 0.00 2.87
338 377 0.823460 GTGAGAGGGCTGAGAAGAGG 59.177 60.000 0.00 0.00 0.00 3.69
347 387 3.008049 GGGCTGAGAAGAGGTTCAGTTTA 59.992 47.826 3.74 0.00 42.17 2.01
348 388 3.997681 GGCTGAGAAGAGGTTCAGTTTAC 59.002 47.826 3.74 0.00 42.17 2.01
349 389 4.262678 GGCTGAGAAGAGGTTCAGTTTACT 60.263 45.833 3.74 0.00 42.17 2.24
350 390 4.688413 GCTGAGAAGAGGTTCAGTTTACTG 59.312 45.833 3.47 3.47 42.17 2.74
380 2007 7.481275 AATGTTGTTAGCTTTTCCATTGTTG 57.519 32.000 0.00 0.00 0.00 3.33
388 2015 4.060205 GCTTTTCCATTGTTGTTGCTGAT 58.940 39.130 0.00 0.00 0.00 2.90
399 2026 5.901552 TGTTGTTGCTGATCATCTATCGTA 58.098 37.500 0.00 0.00 37.42 3.43
401 2028 6.642540 TGTTGTTGCTGATCATCTATCGTATC 59.357 38.462 0.00 0.00 37.42 2.24
402 2029 5.393962 TGTTGCTGATCATCTATCGTATCG 58.606 41.667 0.00 0.00 37.42 2.92
403 2030 5.048713 TGTTGCTGATCATCTATCGTATCGT 60.049 40.000 0.00 0.00 37.42 3.73
404 2031 4.974591 TGCTGATCATCTATCGTATCGTG 58.025 43.478 0.00 0.00 37.42 4.35
405 2032 4.455877 TGCTGATCATCTATCGTATCGTGT 59.544 41.667 0.00 0.00 37.42 4.49
406 2033 4.790651 GCTGATCATCTATCGTATCGTGTG 59.209 45.833 0.00 0.00 37.42 3.82
407 2034 5.296813 TGATCATCTATCGTATCGTGTGG 57.703 43.478 0.00 0.00 37.42 4.17
408 2035 4.156008 TGATCATCTATCGTATCGTGTGGG 59.844 45.833 0.00 0.00 37.42 4.61
409 2036 3.483421 TCATCTATCGTATCGTGTGGGT 58.517 45.455 0.00 0.00 0.00 4.51
410 2037 3.252458 TCATCTATCGTATCGTGTGGGTG 59.748 47.826 0.00 0.00 0.00 4.61
411 2038 1.951602 TCTATCGTATCGTGTGGGTGG 59.048 52.381 0.00 0.00 0.00 4.61
412 2039 1.679680 CTATCGTATCGTGTGGGTGGT 59.320 52.381 0.00 0.00 0.00 4.16
413 2040 0.174845 ATCGTATCGTGTGGGTGGTG 59.825 55.000 0.00 0.00 0.00 4.17
414 2041 0.894642 TCGTATCGTGTGGGTGGTGA 60.895 55.000 0.00 0.00 0.00 4.02
415 2042 0.457853 CGTATCGTGTGGGTGGTGAG 60.458 60.000 0.00 0.00 0.00 3.51
416 2043 0.892755 GTATCGTGTGGGTGGTGAGA 59.107 55.000 0.00 0.00 0.00 3.27
417 2044 1.274167 GTATCGTGTGGGTGGTGAGAA 59.726 52.381 0.00 0.00 0.00 2.87
418 2045 0.984230 ATCGTGTGGGTGGTGAGAAT 59.016 50.000 0.00 0.00 0.00 2.40
419 2046 0.762418 TCGTGTGGGTGGTGAGAATT 59.238 50.000 0.00 0.00 0.00 2.17
420 2047 1.142060 TCGTGTGGGTGGTGAGAATTT 59.858 47.619 0.00 0.00 0.00 1.82
421 2048 2.369203 TCGTGTGGGTGGTGAGAATTTA 59.631 45.455 0.00 0.00 0.00 1.40
422 2049 2.482721 CGTGTGGGTGGTGAGAATTTAC 59.517 50.000 0.00 0.00 0.00 2.01
423 2050 3.482436 GTGTGGGTGGTGAGAATTTACA 58.518 45.455 0.00 0.00 0.00 2.41
426 2053 4.142038 GTGGGTGGTGAGAATTTACAAGT 58.858 43.478 0.00 0.00 0.00 3.16
448 2079 3.876198 CGCCGGATCGCCTTTTGG 61.876 66.667 5.05 0.00 44.18 3.28
461 2125 1.152567 TTTTGGGGGTGTCTGCCTG 60.153 57.895 0.00 0.00 0.00 4.85
473 2137 4.451435 GGTGTCTGCCTGTCTTTACTTAAC 59.549 45.833 0.00 0.00 0.00 2.01
474 2138 5.054477 GTGTCTGCCTGTCTTTACTTAACA 58.946 41.667 0.00 0.00 0.00 2.41
475 2139 5.701290 GTGTCTGCCTGTCTTTACTTAACAT 59.299 40.000 0.00 0.00 0.00 2.71
476 2140 5.700832 TGTCTGCCTGTCTTTACTTAACATG 59.299 40.000 0.00 0.00 0.00 3.21
477 2141 5.122396 GTCTGCCTGTCTTTACTTAACATGG 59.878 44.000 0.00 0.00 0.00 3.66
478 2142 5.012664 TCTGCCTGTCTTTACTTAACATGGA 59.987 40.000 0.00 0.00 0.00 3.41
481 2145 7.047891 TGCCTGTCTTTACTTAACATGGATAG 58.952 38.462 0.00 0.00 0.00 2.08
485 3428 8.718102 TGTCTTTACTTAACATGGATAGAAGC 57.282 34.615 0.00 0.00 0.00 3.86
493 3436 8.709308 ACTTAACATGGATAGAAGCAGATTACT 58.291 33.333 0.00 0.00 0.00 2.24
506 3449 4.002982 GCAGATTACTGGACATGTGAACA 58.997 43.478 1.15 0.00 43.62 3.18
510 3453 6.818142 CAGATTACTGGACATGTGAACACATA 59.182 38.462 18.04 4.46 43.35 2.29
641 3665 9.803315 GGGTTTATGAAAAGAAAATCATAGGTC 57.197 33.333 0.00 0.00 39.12 3.85
683 3742 6.054295 CCCACAGAGAGAAGATTAATCCTTG 58.946 44.000 11.92 2.02 0.00 3.61
714 4060 3.676291 ATTGCCGGCAAAAACAATACT 57.324 38.095 42.74 22.31 39.55 2.12
715 4061 2.715737 TGCCGGCAAAAACAATACTC 57.284 45.000 30.74 0.00 0.00 2.59
716 4062 1.271102 TGCCGGCAAAAACAATACTCC 59.729 47.619 30.74 0.00 0.00 3.85
717 4063 1.403647 GCCGGCAAAAACAATACTCCC 60.404 52.381 24.80 0.00 0.00 4.30
718 4064 2.167662 CCGGCAAAAACAATACTCCCT 58.832 47.619 0.00 0.00 0.00 4.20
719 4065 2.163613 CCGGCAAAAACAATACTCCCTC 59.836 50.000 0.00 0.00 0.00 4.30
720 4066 3.081804 CGGCAAAAACAATACTCCCTCT 58.918 45.455 0.00 0.00 0.00 3.69
721 4067 4.258543 CGGCAAAAACAATACTCCCTCTA 58.741 43.478 0.00 0.00 0.00 2.43
722 4068 4.881850 CGGCAAAAACAATACTCCCTCTAT 59.118 41.667 0.00 0.00 0.00 1.98
723 4069 6.053005 CGGCAAAAACAATACTCCCTCTATA 58.947 40.000 0.00 0.00 0.00 1.31
724 4070 6.540914 CGGCAAAAACAATACTCCCTCTATAA 59.459 38.462 0.00 0.00 0.00 0.98
725 4071 7.066525 CGGCAAAAACAATACTCCCTCTATAAA 59.933 37.037 0.00 0.00 0.00 1.40
726 4072 8.188799 GGCAAAAACAATACTCCCTCTATAAAC 58.811 37.037 0.00 0.00 0.00 2.01
727 4073 8.957466 GCAAAAACAATACTCCCTCTATAAACT 58.043 33.333 0.00 0.00 0.00 2.66
757 4103 7.721286 AAGAGTGTTTAGATCACTGTTTCAG 57.279 36.000 3.29 0.00 43.46 3.02
758 4104 6.821388 AGAGTGTTTAGATCACTGTTTCAGT 58.179 36.000 3.29 0.00 46.51 3.41
772 4118 6.821388 ACTGTTTCAGTGATCTAAACACTCT 58.179 36.000 4.37 0.00 43.63 3.24
773 4119 7.275920 ACTGTTTCAGTGATCTAAACACTCTT 58.724 34.615 4.37 0.00 43.63 2.85
774 4120 8.421784 ACTGTTTCAGTGATCTAAACACTCTTA 58.578 33.333 4.37 0.00 43.63 2.10
775 4121 9.429359 CTGTTTCAGTGATCTAAACACTCTTAT 57.571 33.333 4.37 0.00 45.15 1.73
790 4136 9.813446 AAACACTCTTATATTAGTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
791 4137 7.949434 ACACTCTTATATTAGTTTACGGAGGG 58.051 38.462 0.00 0.00 0.00 4.30
792 4138 7.781693 ACACTCTTATATTAGTTTACGGAGGGA 59.218 37.037 0.00 0.00 0.00 4.20
818 4164 6.662414 AGTAATCAAATCGCTCGAAAATCA 57.338 33.333 0.00 0.00 0.00 2.57
958 4344 2.730672 CGCACCAACTCTACTGCGC 61.731 63.158 0.00 0.00 45.19 6.09
975 4364 3.145551 CCCGTACGTGGAGGAGGG 61.146 72.222 15.21 1.28 38.46 4.30
1101 4494 3.803082 CGGTGGTTCATGGCGCTG 61.803 66.667 7.64 0.00 0.00 5.18
1323 4716 1.069765 CATGAACCTCGCCGGCTAT 59.930 57.895 26.68 5.35 35.61 2.97
1458 4851 0.319900 TCACCTGCGTCAAGAGCTTC 60.320 55.000 0.00 0.00 35.28 3.86
1554 4947 0.182061 TCTACCTCGCCATCTACGGT 59.818 55.000 0.00 0.00 0.00 4.83
1671 5085 1.399440 CCTAGACGAAACGACGATGGA 59.601 52.381 0.00 0.00 37.03 3.41
1698 5112 4.865905 TCTTCTGCTTCCTCTACATCTCT 58.134 43.478 0.00 0.00 0.00 3.10
1734 5148 4.213482 TCCTACATACTCGTGATGATCGTG 59.787 45.833 0.00 0.00 0.00 4.35
1846 5260 4.672251 TCCGGCAGGAGTACTACC 57.328 61.111 0.00 2.33 42.75 3.18
1847 5261 1.693034 TCCGGCAGGAGTACTACCA 59.307 57.895 0.00 0.00 42.75 3.25
1848 5262 0.682209 TCCGGCAGGAGTACTACCAC 60.682 60.000 0.00 0.00 42.75 4.16
1869 5283 5.163602 CCACTACTACTACTGGCTCAAGAAG 60.164 48.000 0.00 0.00 0.00 2.85
1934 5363 1.009389 GTGACCGTCGAGAAGCCAAG 61.009 60.000 0.00 0.00 0.00 3.61
1950 5379 2.313172 AAGCGCTCAAGTCGTGCAG 61.313 57.895 12.06 0.00 40.20 4.41
1997 5441 2.359107 TTGCCTCGGCTCTTGCTG 60.359 61.111 9.65 0.00 46.48 4.41
2083 5527 0.607489 GGACATGCTGGTGCTGTTCT 60.607 55.000 0.00 0.00 40.48 3.01
2613 6789 0.179134 GGGAGTCGTTCCTCATCGTG 60.179 60.000 8.28 0.00 45.98 4.35
2783 7234 0.663568 CACGAGTCGAGTCAACACCC 60.664 60.000 21.50 0.00 0.00 4.61
2823 7275 2.290134 ACCTGTACTGCTAGACTCACGA 60.290 50.000 0.00 0.00 0.00 4.35
2879 7340 9.617523 TGAGCAAATCTAAGTCAAATGATATGA 57.382 29.630 0.00 0.00 0.00 2.15
2935 7397 7.332430 TGAAAAATTTGCATGGATCTTCACATC 59.668 33.333 0.00 0.00 0.00 3.06
2974 7436 4.076394 ACATCGGCTAAGGCTTGTTTAAA 58.924 39.130 10.69 0.00 38.73 1.52
3013 7477 2.578683 ACAAATCATGTTCCCCGCC 58.421 52.632 0.00 0.00 40.06 6.13
3207 7673 4.820897 TGCTCTATGTTTGATCTTCGTGT 58.179 39.130 0.00 0.00 0.00 4.49
3208 7674 5.237815 TGCTCTATGTTTGATCTTCGTGTT 58.762 37.500 0.00 0.00 0.00 3.32
3209 7675 5.700832 TGCTCTATGTTTGATCTTCGTGTTT 59.299 36.000 0.00 0.00 0.00 2.83
3210 7676 6.204688 TGCTCTATGTTTGATCTTCGTGTTTT 59.795 34.615 0.00 0.00 0.00 2.43
3438 7905 1.444553 GGCGAGTGTCTTGGTCGAG 60.445 63.158 0.00 0.00 35.70 4.04
3446 7913 3.128349 GTGTCTTGGTCGAGCTAAAACA 58.872 45.455 16.64 12.07 0.00 2.83
3472 7939 2.624838 CAGTCCAAGGAATGTTTGCTGT 59.375 45.455 8.32 0.00 35.75 4.40
3473 7940 3.068590 CAGTCCAAGGAATGTTTGCTGTT 59.931 43.478 8.32 0.00 35.75 3.16
3528 8005 8.844441 TTTCGTTTGAATTTTGATAGACGTTT 57.156 26.923 0.00 0.00 33.20 3.60
3610 8090 6.992063 AGTTTGACTATGTAGGAAAGCATG 57.008 37.500 0.00 0.00 0.00 4.06
3615 8095 6.806751 TGACTATGTAGGAAAGCATGTACTC 58.193 40.000 0.00 0.00 0.00 2.59
3628 8108 6.422776 AGCATGTACTCCAACGAATTTAAG 57.577 37.500 0.00 0.00 0.00 1.85
3676 8156 9.825972 CGTAACTCTTATGTCATTTGATTTTGT 57.174 29.630 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.874701 CCTCCCTGCATATTTCAGTTCG 59.125 50.000 0.00 0.00 0.00 3.95
72 73 7.361286 CCAGCTAGGCTAGTTAACTTTTTCTTG 60.361 40.741 21.92 8.70 36.40 3.02
73 74 6.655425 CCAGCTAGGCTAGTTAACTTTTTCTT 59.345 38.462 21.92 0.38 36.40 2.52
75 76 6.092396 GTCCAGCTAGGCTAGTTAACTTTTTC 59.908 42.308 21.92 1.97 36.40 2.29
80 83 3.032459 GGTCCAGCTAGGCTAGTTAACT 58.968 50.000 21.92 13.68 36.40 2.24
85 88 3.215671 CTGGTCCAGCTAGGCTAGT 57.784 57.895 21.92 7.06 36.40 2.57
115 126 0.248134 CACCTACGTCTACTCGCAGC 60.248 60.000 0.00 0.00 0.00 5.25
120 131 1.747709 TCTGGCACCTACGTCTACTC 58.252 55.000 0.00 0.00 0.00 2.59
127 138 6.761099 AAGAGTATATATCTGGCACCTACG 57.239 41.667 0.00 0.00 0.00 3.51
132 143 7.704578 TCTGGTAAGAGTATATATCTGGCAC 57.295 40.000 0.00 0.00 0.00 5.01
172 191 2.816087 CAGTGAGTGGACCAAATCAAGG 59.184 50.000 11.31 4.61 0.00 3.61
251 270 5.425217 TGGTGATTAGCAAGAGGACATCTAA 59.575 40.000 0.00 0.00 37.23 2.10
252 271 4.962362 TGGTGATTAGCAAGAGGACATCTA 59.038 41.667 0.00 0.00 37.23 1.98
253 272 3.776969 TGGTGATTAGCAAGAGGACATCT 59.223 43.478 0.00 0.00 41.27 2.90
254 273 4.142609 TGGTGATTAGCAAGAGGACATC 57.857 45.455 0.00 0.00 0.00 3.06
255 274 4.164796 TCATGGTGATTAGCAAGAGGACAT 59.835 41.667 0.00 0.00 37.91 3.06
256 275 3.519107 TCATGGTGATTAGCAAGAGGACA 59.481 43.478 0.00 0.00 37.91 4.02
257 276 4.125703 CTCATGGTGATTAGCAAGAGGAC 58.874 47.826 12.55 0.00 42.98 3.85
258 277 3.432749 GCTCATGGTGATTAGCAAGAGGA 60.433 47.826 19.37 4.48 45.35 3.71
259 278 2.877168 GCTCATGGTGATTAGCAAGAGG 59.123 50.000 19.37 5.82 45.35 3.69
260 279 3.806380 AGCTCATGGTGATTAGCAAGAG 58.194 45.455 15.21 15.21 46.96 2.85
261 280 3.920231 AGCTCATGGTGATTAGCAAGA 57.080 42.857 4.82 0.00 37.91 3.02
262 281 3.497640 GCTAGCTCATGGTGATTAGCAAG 59.502 47.826 7.70 0.00 38.37 4.01
301 332 1.001815 CACCCTTGACAATTTCGCGTT 60.002 47.619 5.77 0.00 0.00 4.84
310 345 0.768221 AGCCCTCTCACCCTTGACAA 60.768 55.000 0.00 0.00 0.00 3.18
314 349 0.906756 TCTCAGCCCTCTCACCCTTG 60.907 60.000 0.00 0.00 0.00 3.61
316 351 0.617249 CTTCTCAGCCCTCTCACCCT 60.617 60.000 0.00 0.00 0.00 4.34
318 357 0.823460 CTCTTCTCAGCCCTCTCACC 59.177 60.000 0.00 0.00 0.00 4.02
347 387 8.135529 GGAAAAGCTAACAACATTTAGTTCAGT 58.864 33.333 0.00 0.00 38.74 3.41
348 388 8.134895 TGGAAAAGCTAACAACATTTAGTTCAG 58.865 33.333 0.00 0.00 38.74 3.02
349 389 8.001881 TGGAAAAGCTAACAACATTTAGTTCA 57.998 30.769 0.00 0.00 38.74 3.18
350 390 9.476202 AATGGAAAAGCTAACAACATTTAGTTC 57.524 29.630 0.00 0.00 38.74 3.01
351 391 9.260002 CAATGGAAAAGCTAACAACATTTAGTT 57.740 29.630 0.00 0.00 42.42 2.24
380 2007 5.284897 CACGATACGATAGATGATCAGCAAC 59.715 44.000 14.38 3.06 41.38 4.17
388 2015 3.252458 CACCCACACGATACGATAGATGA 59.748 47.826 0.00 0.00 41.38 2.92
399 2026 0.984230 ATTCTCACCACCCACACGAT 59.016 50.000 0.00 0.00 0.00 3.73
401 2028 1.604604 AAATTCTCACCACCCACACG 58.395 50.000 0.00 0.00 0.00 4.49
402 2029 3.482436 TGTAAATTCTCACCACCCACAC 58.518 45.455 0.00 0.00 0.00 3.82
403 2030 3.866703 TGTAAATTCTCACCACCCACA 57.133 42.857 0.00 0.00 0.00 4.17
404 2031 4.142038 ACTTGTAAATTCTCACCACCCAC 58.858 43.478 0.00 0.00 0.00 4.61
405 2032 4.394729 GACTTGTAAATTCTCACCACCCA 58.605 43.478 0.00 0.00 0.00 4.51
406 2033 3.756963 GGACTTGTAAATTCTCACCACCC 59.243 47.826 0.00 0.00 0.00 4.61
407 2034 3.756963 GGGACTTGTAAATTCTCACCACC 59.243 47.826 0.00 0.00 0.00 4.61
408 2035 4.652822 AGGGACTTGTAAATTCTCACCAC 58.347 43.478 0.00 0.00 27.25 4.16
409 2036 4.562757 CGAGGGACTTGTAAATTCTCACCA 60.563 45.833 0.00 0.00 41.55 4.17
410 2037 3.933332 CGAGGGACTTGTAAATTCTCACC 59.067 47.826 0.00 0.00 41.55 4.02
411 2038 3.371285 GCGAGGGACTTGTAAATTCTCAC 59.629 47.826 0.00 0.00 43.14 3.51
412 2039 3.596214 GCGAGGGACTTGTAAATTCTCA 58.404 45.455 0.00 0.00 43.14 3.27
413 2040 2.937149 GGCGAGGGACTTGTAAATTCTC 59.063 50.000 0.00 0.00 43.14 2.87
414 2041 2.677037 CGGCGAGGGACTTGTAAATTCT 60.677 50.000 0.00 0.00 43.14 2.40
415 2042 1.664151 CGGCGAGGGACTTGTAAATTC 59.336 52.381 0.00 0.00 43.14 2.17
416 2043 1.677820 CCGGCGAGGGACTTGTAAATT 60.678 52.381 9.30 0.00 43.14 1.82
417 2044 0.107848 CCGGCGAGGGACTTGTAAAT 60.108 55.000 9.30 0.00 43.14 1.40
418 2045 1.186917 TCCGGCGAGGGACTTGTAAA 61.187 55.000 9.30 0.00 43.14 2.01
419 2046 0.974010 ATCCGGCGAGGGACTTGTAA 60.974 55.000 9.30 0.00 43.14 2.41
420 2047 1.380785 ATCCGGCGAGGGACTTGTA 60.381 57.895 9.30 0.00 43.14 2.41
421 2048 2.683933 ATCCGGCGAGGGACTTGT 60.684 61.111 9.30 0.00 43.14 3.16
422 2049 2.107141 GATCCGGCGAGGGACTTG 59.893 66.667 9.30 0.00 41.55 3.16
423 2050 3.528370 CGATCCGGCGAGGGACTT 61.528 66.667 9.30 0.00 41.55 3.01
448 2079 0.690762 TAAAGACAGGCAGACACCCC 59.309 55.000 0.00 0.00 0.00 4.95
461 2125 8.718102 TGCTTCTATCCATGTTAAGTAAAGAC 57.282 34.615 0.00 0.00 0.00 3.01
473 2137 5.931146 GTCCAGTAATCTGCTTCTATCCATG 59.069 44.000 0.00 0.00 40.09 3.66
474 2138 5.604231 TGTCCAGTAATCTGCTTCTATCCAT 59.396 40.000 0.00 0.00 40.09 3.41
475 2139 4.962362 TGTCCAGTAATCTGCTTCTATCCA 59.038 41.667 0.00 0.00 40.09 3.41
476 2140 5.537300 TGTCCAGTAATCTGCTTCTATCC 57.463 43.478 0.00 0.00 40.09 2.59
477 2141 6.423302 CACATGTCCAGTAATCTGCTTCTATC 59.577 42.308 0.00 0.00 40.09 2.08
478 2142 6.098838 TCACATGTCCAGTAATCTGCTTCTAT 59.901 38.462 0.00 0.00 40.09 1.98
481 2145 4.507710 TCACATGTCCAGTAATCTGCTTC 58.492 43.478 0.00 0.00 40.09 3.86
485 3428 4.996758 TGTGTTCACATGTCCAGTAATCTG 59.003 41.667 0.00 0.00 41.01 2.90
493 3436 4.661222 ACCAATATGTGTTCACATGTCCA 58.339 39.130 23.33 8.24 0.00 4.02
637 3661 1.889530 GCCGGCAACAGACTAGACCT 61.890 60.000 24.80 0.00 0.00 3.85
641 3665 1.153549 GAGGCCGGCAACAGACTAG 60.154 63.158 30.85 0.00 0.00 2.57
642 3666 2.656069 GGAGGCCGGCAACAGACTA 61.656 63.158 30.85 0.00 0.00 2.59
665 3724 7.335422 TCAACTTGCAAGGATTAATCTTCTCTC 59.665 37.037 29.18 0.00 0.00 3.20
683 3742 1.135141 TGCCGGCAATAATCAACTTGC 60.135 47.619 30.74 0.00 45.46 4.01
731 4077 9.429359 CTGAAACAGTGATCTAAACACTCTTAT 57.571 33.333 0.00 0.00 45.15 1.73
732 4078 8.421784 ACTGAAACAGTGATCTAAACACTCTTA 58.578 33.333 0.00 0.00 43.63 2.10
733 4079 7.275920 ACTGAAACAGTGATCTAAACACTCTT 58.724 34.615 0.00 0.00 43.63 2.85
734 4080 6.821388 ACTGAAACAGTGATCTAAACACTCT 58.179 36.000 0.00 0.00 43.63 3.24
748 4094 6.821388 AGAGTGTTTAGATCACTGAAACAGT 58.179 36.000 16.40 16.40 46.51 3.55
749 4095 7.721286 AAGAGTGTTTAGATCACTGAAACAG 57.279 36.000 12.65 0.00 44.68 3.16
764 4110 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
765 4111 8.419442 CCCTCCGTAAACTAATATAAGAGTGTT 58.581 37.037 0.00 0.00 0.00 3.32
766 4112 7.781693 TCCCTCCGTAAACTAATATAAGAGTGT 59.218 37.037 0.00 0.00 0.00 3.55
767 4113 8.174733 TCCCTCCGTAAACTAATATAAGAGTG 57.825 38.462 0.00 0.00 0.00 3.51
768 4114 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
769 4115 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
770 4116 9.512588 CTACTCCCTCCGTAAACTAATATAAGA 57.487 37.037 0.00 0.00 0.00 2.10
771 4117 9.294614 ACTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
774 4120 9.819754 ATTACTACTCCCTCCGTAAACTAATAT 57.180 33.333 0.00 0.00 0.00 1.28
775 4121 9.289782 GATTACTACTCCCTCCGTAAACTAATA 57.710 37.037 0.00 0.00 0.00 0.98
776 4122 7.781693 TGATTACTACTCCCTCCGTAAACTAAT 59.218 37.037 0.00 0.00 0.00 1.73
777 4123 7.118723 TGATTACTACTCCCTCCGTAAACTAA 58.881 38.462 0.00 0.00 0.00 2.24
778 4124 6.662755 TGATTACTACTCCCTCCGTAAACTA 58.337 40.000 0.00 0.00 0.00 2.24
779 4125 5.513233 TGATTACTACTCCCTCCGTAAACT 58.487 41.667 0.00 0.00 0.00 2.66
780 4126 5.841957 TGATTACTACTCCCTCCGTAAAC 57.158 43.478 0.00 0.00 0.00 2.01
781 4127 6.855763 TTTGATTACTACTCCCTCCGTAAA 57.144 37.500 0.00 0.00 0.00 2.01
782 4128 6.238842 CGATTTGATTACTACTCCCTCCGTAA 60.239 42.308 0.00 0.00 0.00 3.18
783 4129 5.240183 CGATTTGATTACTACTCCCTCCGTA 59.760 44.000 0.00 0.00 0.00 4.02
784 4130 4.037684 CGATTTGATTACTACTCCCTCCGT 59.962 45.833 0.00 0.00 0.00 4.69
785 4131 4.547532 CGATTTGATTACTACTCCCTCCG 58.452 47.826 0.00 0.00 0.00 4.63
786 4132 4.039366 AGCGATTTGATTACTACTCCCTCC 59.961 45.833 0.00 0.00 0.00 4.30
787 4133 5.203060 AGCGATTTGATTACTACTCCCTC 57.797 43.478 0.00 0.00 0.00 4.30
788 4134 4.261656 CGAGCGATTTGATTACTACTCCCT 60.262 45.833 0.00 0.00 0.00 4.20
789 4135 3.982058 CGAGCGATTTGATTACTACTCCC 59.018 47.826 0.00 0.00 0.00 4.30
790 4136 4.856664 TCGAGCGATTTGATTACTACTCC 58.143 43.478 0.00 0.00 0.00 3.85
791 4137 6.807708 TTTCGAGCGATTTGATTACTACTC 57.192 37.500 0.00 0.00 0.00 2.59
792 4138 7.491372 TGATTTTCGAGCGATTTGATTACTACT 59.509 33.333 0.00 0.00 0.00 2.57
835 4181 2.479837 TGAAACTGGAACGTAGTGCTG 58.520 47.619 0.00 0.00 45.00 4.41
836 4182 2.902705 TGAAACTGGAACGTAGTGCT 57.097 45.000 0.00 0.00 45.00 4.40
837 4183 5.600908 TTAATGAAACTGGAACGTAGTGC 57.399 39.130 0.00 0.00 45.00 4.40
840 4186 7.201530 GGTCAGATTAATGAAACTGGAACGTAG 60.202 40.741 0.48 0.00 0.00 3.51
896 4272 5.475220 TGTTGGTTTGGTTATGATGATTCGT 59.525 36.000 0.00 0.00 0.00 3.85
939 4322 4.675404 GCAGTAGAGTTGGTGCGT 57.325 55.556 0.00 0.00 0.00 5.24
958 4344 3.145551 CCCTCCTCCACGTACGGG 61.146 72.222 21.06 16.64 0.00 5.28
975 4364 4.893424 TTAATATTGGCGCCAAGAAGAC 57.107 40.909 41.38 8.62 39.47 3.01
1101 4494 4.479993 AGGATGAGCAGGCACGCC 62.480 66.667 0.00 0.00 0.00 5.68
1150 4543 2.102553 GAGCGCCGTGGAGTAGAC 59.897 66.667 2.29 0.00 0.00 2.59
1323 4716 1.101635 CGGCGAGGTAGACCATGAGA 61.102 60.000 0.00 0.00 38.89 3.27
1554 4947 1.911766 GGACTTGGAGTCGTCCCCA 60.912 63.158 4.74 0.00 45.96 4.96
1608 5001 2.416432 GGGGAGGAAGACGACGGAG 61.416 68.421 0.00 0.00 0.00 4.63
1671 5085 3.580458 TGTAGAGGAAGCAGAAGAAAGCT 59.420 43.478 0.00 0.00 44.31 3.74
1734 5148 1.744741 GCTGCTCTGCTTCTGGACC 60.745 63.158 0.00 0.00 0.00 4.46
1846 5260 5.648526 TCTTCTTGAGCCAGTAGTAGTAGTG 59.351 44.000 5.54 5.54 0.00 2.74
1847 5261 5.817784 TCTTCTTGAGCCAGTAGTAGTAGT 58.182 41.667 0.00 0.00 0.00 2.73
1848 5262 6.116806 TCTCTTCTTGAGCCAGTAGTAGTAG 58.883 44.000 0.00 0.00 42.38 2.57
1934 5363 3.782244 CCTGCACGACTTGAGCGC 61.782 66.667 0.00 0.00 36.92 5.92
1961 5390 4.736896 AAGAAGACGGCGGCGGAC 62.737 66.667 35.05 26.34 0.00 4.79
1997 5441 0.240945 CGGGTTGAACATGTGCTTCC 59.759 55.000 5.18 7.29 0.00 3.46
2317 6475 1.170919 GCGAGGGCGATGAGTAGGTA 61.171 60.000 0.00 0.00 40.82 3.08
2434 6592 1.213537 GCGTGGCGTAGTACCTCAA 59.786 57.895 0.00 0.00 0.00 3.02
2783 7234 5.390613 CAGGTTTTATGCTTCCTGTTTACG 58.609 41.667 0.00 0.00 41.51 3.18
2823 7275 5.684550 GTCAATTGAGACCTAAAACCGTT 57.315 39.130 8.80 0.00 32.36 4.44
2910 7372 7.332430 TGATGTGAAGATCCATGCAAATTTTTC 59.668 33.333 0.00 0.00 0.00 2.29
2935 7397 4.864806 CCGATGTTATATTCGTGGGATCTG 59.135 45.833 0.00 0.00 33.60 2.90
3096 7560 0.317479 CGGACGAGTCACTTCCCTTT 59.683 55.000 5.55 0.00 33.98 3.11
3166 7632 2.912987 ATCACTCCCGACTCCCCGAG 62.913 65.000 0.00 0.00 35.52 4.63
3167 7633 2.992576 ATCACTCCCGACTCCCCGA 61.993 63.158 0.00 0.00 0.00 5.14
3419 7886 2.805353 CGACCAAGACACTCGCCG 60.805 66.667 0.00 0.00 0.00 6.46
3438 7905 1.234615 TGGACTGCGCCTGTTTTAGC 61.235 55.000 4.18 0.00 0.00 3.09
3446 7913 1.377725 CATTCCTTGGACTGCGCCT 60.378 57.895 4.18 0.00 0.00 5.52
3472 7939 7.236847 TGTCCTTTTCTATTCCTTGTCCTCTAA 59.763 37.037 0.00 0.00 0.00 2.10
3473 7940 6.729100 TGTCCTTTTCTATTCCTTGTCCTCTA 59.271 38.462 0.00 0.00 0.00 2.43
3610 8090 9.934190 TTTGTAAACTTAAATTCGTTGGAGTAC 57.066 29.630 0.00 0.00 0.00 2.73
3641 8121 7.827819 TGACATAAGAGTTACGAGATTTTGG 57.172 36.000 0.00 0.00 0.00 3.28
3676 8156 5.468746 AGAAAAATCAACACGAATCTCCGAA 59.531 36.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.