Multiple sequence alignment - TraesCS7A01G308700

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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 TraesCS7A01G308700 chr7A 100.000 4595 0 0 1 4595 436880293 436884887 0.000000e+00 8486.0
1 TraesCS7A01G308700 chr7D 92.756 2333 111 26 881 3193 386844452 386846746 0.000000e+00 3319.0
2 TraesCS7A01G308700 chr7D 91.194 670 42 9 3279 3935 386846894 386847559 0.000000e+00 894.0
3 TraesCS7A01G308700 chr7D 88.028 568 25 17 3927 4474 386847583 386848127 2.330000e-177 632.0
4 TraesCS7A01G308700 chr7D 93.684 95 6 0 4501 4595 386848124 386848218 4.790000e-30 143.0
5 TraesCS7A01G308700 chr7B 91.341 2275 152 25 987 3240 382130456 382132706 0.000000e+00 3068.0
6 TraesCS7A01G308700 chr7B 86.357 1356 73 46 3279 4595 382132780 382134062 0.000000e+00 1376.0
7 TraesCS7A01G308700 chr6A 95.568 880 38 1 1 879 536794476 536795355 0.000000e+00 1408.0
8 TraesCS7A01G308700 chr6A 95.568 880 38 1 1 879 536798076 536798955 0.000000e+00 1408.0
9 TraesCS7A01G308700 chr6A 95.568 880 38 1 1 879 536801661 536802540 0.000000e+00 1408.0
10 TraesCS7A01G308700 chr6A 93.878 49 2 1 3426 3473 409430681 409430729 6.380000e-09 73.1
11 TraesCS7A01G308700 chr6D 92.559 887 65 1 1 886 450270309 450271195 0.000000e+00 1271.0
12 TraesCS7A01G308700 chrUn 90.271 884 82 4 4 885 109004655 109003774 0.000000e+00 1153.0
13 TraesCS7A01G308700 chrUn 89.078 879 91 5 1 877 87299734 87298859 0.000000e+00 1086.0
14 TraesCS7A01G308700 chr1D 89.294 878 93 1 1 878 83812530 83811654 0.000000e+00 1099.0
15 TraesCS7A01G308700 chr1D 90.385 52 4 1 3426 3476 438878642 438878693 2.970000e-07 67.6
16 TraesCS7A01G308700 chr1D 90.385 52 4 1 3426 3476 438941669 438941720 2.970000e-07 67.6
17 TraesCS7A01G308700 chr6B 88.562 883 97 4 1 880 12387432 12388313 0.000000e+00 1068.0
18 TraesCS7A01G308700 chr6B 88.068 880 103 2 1 878 22754105 22754984 0.000000e+00 1042.0
19 TraesCS7A01G308700 chr6B 93.878 49 2 1 3426 3473 471675181 471675229 6.380000e-09 73.1
20 TraesCS7A01G308700 chr4B 100.000 36 0 0 3438 3473 550397087 550397052 2.970000e-07 67.6
21 TraesCS7A01G308700 chr2D 97.368 38 1 0 3439 3476 114223041 114223078 1.070000e-06 65.8
22 TraesCS7A01G308700 chr4D 92.857 42 3 0 3438 3479 499225915 499225956 1.380000e-05 62.1


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 TraesCS7A01G308700 chr7A 436880293 436884887 4594 False 8486 8486 100.0000 1 4595 1 chr7A.!!$F1 4594
1 TraesCS7A01G308700 chr7D 386844452 386848218 3766 False 1247 3319 91.4155 881 4595 4 chr7D.!!$F1 3714
2 TraesCS7A01G308700 chr7B 382130456 382134062 3606 False 2222 3068 88.8490 987 4595 2 chr7B.!!$F1 3608
3 TraesCS7A01G308700 chr6A 536794476 536802540 8064 False 1408 1408 95.5680 1 879 3 chr6A.!!$F2 878
4 TraesCS7A01G308700 chr6D 450270309 450271195 886 False 1271 1271 92.5590 1 886 1 chr6D.!!$F1 885
5 TraesCS7A01G308700 chrUn 109003774 109004655 881 True 1153 1153 90.2710 4 885 1 chrUn.!!$R2 881
6 TraesCS7A01G308700 chrUn 87298859 87299734 875 True 1086 1086 89.0780 1 877 1 chrUn.!!$R1 876
7 TraesCS7A01G308700 chr1D 83811654 83812530 876 True 1099 1099 89.2940 1 878 1 chr1D.!!$R1 877
8 TraesCS7A01G308700 chr6B 12387432 12388313 881 False 1068 1068 88.5620 1 880 1 chr6B.!!$F1 879
9 TraesCS7A01G308700 chr6B 22754105 22754984 879 False 1042 1042 88.0680 1 878 1 chr6B.!!$F2 877

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
972 977 0.317479 ACGGTGTAGACCTGAGTTGC 59.683 55.0 7.56 0.00 40.58 4.17 F
1431 1889 0.250513 ACACCTGCTCGAGGAATTCC 59.749 55.0 17.31 17.31 46.33 3.01 F
3223 5190 0.395586 TTGAATGGCATCCTTCCCCG 60.396 55.0 0.00 0.00 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2120 4046 2.431782 AGGCACATTTCAGCACAAGTTT 59.568 40.909 0.00 0.0 0.00 2.66 R
3267 5234 0.031857 TGCAAAAACATCCCGTGCTG 59.968 50.000 0.00 0.0 36.18 4.41 R
4269 6380 0.322816 TTCATCTTGCTCCAGGTGCC 60.323 55.000 11.07 0.0 0.00 5.01 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
73 74 3.801293 TGCGTTAATTTACTGTTCGCAC 58.199 40.909 5.29 0.00 45.25 5.34
99 101 1.148273 AGTTCTGGGACAAAGCGCA 59.852 52.632 11.47 0.00 38.70 6.09
336 339 4.753107 TGTACCTAAACAGCAAGCTACAAC 59.247 41.667 0.00 0.00 0.00 3.32
344 347 1.134367 AGCAAGCTACAACGCTATCGA 59.866 47.619 0.00 0.00 39.86 3.59
459 462 2.358737 CCGCTCCCAGACAACACC 60.359 66.667 0.00 0.00 0.00 4.16
645 648 1.595382 GTCGCTCTGTTGTGGCACT 60.595 57.895 19.83 0.00 0.00 4.40
695 699 8.281212 AGCGGATAGTTTTCATTCTTTTGTAT 57.719 30.769 0.00 0.00 0.00 2.29
815 819 2.846827 AGTTTCCTGGTTAGCAGCCTAT 59.153 45.455 5.83 0.00 0.00 2.57
865 870 6.970484 TGTTTGAATAAAGCTCAGAAGTTCC 58.030 36.000 0.00 0.00 0.00 3.62
869 874 6.475504 TGAATAAAGCTCAGAAGTTCCATGA 58.524 36.000 0.00 0.00 0.00 3.07
958 963 1.312371 CCCAGCCCACATAAACGGTG 61.312 60.000 0.00 0.00 36.03 4.94
965 970 2.235402 CCCACATAAACGGTGTAGACCT 59.765 50.000 7.56 0.00 40.58 3.85
972 977 0.317479 ACGGTGTAGACCTGAGTTGC 59.683 55.000 7.56 0.00 40.58 4.17
974 979 1.816835 CGGTGTAGACCTGAGTTGCTA 59.183 52.381 7.56 0.00 40.58 3.49
977 982 3.258622 GGTGTAGACCTGAGTTGCTAGTT 59.741 47.826 0.76 0.00 39.47 2.24
979 984 3.190744 TGTAGACCTGAGTTGCTAGTTCG 59.809 47.826 0.00 0.00 0.00 3.95
980 985 2.515854 AGACCTGAGTTGCTAGTTCGA 58.484 47.619 0.00 0.00 0.00 3.71
982 987 1.272769 ACCTGAGTTGCTAGTTCGACC 59.727 52.381 0.00 0.00 0.00 4.79
983 988 1.546476 CCTGAGTTGCTAGTTCGACCT 59.454 52.381 0.00 0.00 0.00 3.85
984 989 2.416162 CCTGAGTTGCTAGTTCGACCTC 60.416 54.545 0.00 0.00 0.00 3.85
985 990 1.199327 TGAGTTGCTAGTTCGACCTCG 59.801 52.381 0.00 0.00 41.45 4.63
1012 1365 0.977395 AGAGTCCCGGAAGAAACAGG 59.023 55.000 0.73 0.00 0.00 4.00
1015 1368 1.462627 TCCCGGAAGAAACAGGGGT 60.463 57.895 0.73 0.00 43.65 4.95
1016 1369 1.063654 TCCCGGAAGAAACAGGGGTT 61.064 55.000 0.73 0.00 43.65 4.11
1017 1370 0.608308 CCCGGAAGAAACAGGGGTTC 60.608 60.000 0.73 0.00 40.65 3.62
1018 1371 0.608308 CCGGAAGAAACAGGGGTTCC 60.608 60.000 0.00 0.00 35.82 3.62
1052 1405 2.046292 GGAGGAAGAAGAGGGATCAGG 58.954 57.143 0.00 0.00 0.00 3.86
1431 1889 0.250513 ACACCTGCTCGAGGAATTCC 59.749 55.000 17.31 17.31 46.33 3.01
1496 2323 2.629617 ACCCTGATTCAAAACCTGCAAG 59.370 45.455 0.00 0.00 0.00 4.01
1540 2789 4.326826 TCCTGATTCCAAACACAGATGTC 58.673 43.478 0.00 0.00 38.45 3.06
1569 2818 7.806690 TCTCTTCTGTGAATGAATTTAAACCG 58.193 34.615 0.00 0.00 0.00 4.44
1597 3522 4.952335 CCCTCCTAAATTGCACTCTCAAAT 59.048 41.667 0.00 0.00 0.00 2.32
1646 3571 9.199982 CATGTTGCAATCCATTATCCTAAATTC 57.800 33.333 0.59 0.00 0.00 2.17
1669 3594 7.867305 TCGGTCAATATAAAACAATAAGGCA 57.133 32.000 0.00 0.00 0.00 4.75
1725 3651 6.739331 AAGAATGAGGGTATAGTTCCTGAG 57.261 41.667 0.00 0.00 32.74 3.35
1747 3673 1.089920 CTAGCAGGGCATGTTGTGTC 58.910 55.000 0.00 0.00 0.00 3.67
1872 3798 1.270625 CCGTTGCTGGTAGAGTGGAAA 60.271 52.381 0.00 0.00 0.00 3.13
1897 3823 9.814899 AATTTGTCTGTTTTATCATTTGTGTCA 57.185 25.926 0.00 0.00 0.00 3.58
1979 3905 5.207354 TGATCAGCATACTTCTCCTCTCTT 58.793 41.667 0.00 0.00 0.00 2.85
1994 3920 5.258841 TCCTCTCTTAGGTTGTAATCGTGA 58.741 41.667 0.00 0.00 46.62 4.35
2062 3988 3.910568 TCATGTGATAGTGTCATGCCA 57.089 42.857 0.00 0.00 39.48 4.92
2158 4084 6.268825 TGTGCCTCTAGTTACTACTTTCAG 57.731 41.667 0.00 0.00 35.78 3.02
2288 4216 5.470098 TCAAGAACTTCAGGTATGTTTCAGC 59.530 40.000 0.00 0.00 0.00 4.26
2297 4225 2.159627 GGTATGTTTCAGCTTCACGGTG 59.840 50.000 0.56 0.56 42.42 4.94
2321 4250 7.967854 GTGTCAGTATCAGAGTATATGATCAGC 59.032 40.741 0.09 0.00 38.36 4.26
2369 4298 5.009631 AGTTACACAAGGAATTATGCAGCA 58.990 37.500 0.00 0.00 0.00 4.41
2575 4515 5.011090 TGTGGTCTCATTGTATCTGCTAC 57.989 43.478 0.00 0.00 0.00 3.58
2719 4662 6.982141 TGAAGACTAGTAATGAACGTTTGTGT 59.018 34.615 0.46 0.00 0.00 3.72
2721 4664 7.404139 AGACTAGTAATGAACGTTTGTGTTC 57.596 36.000 0.46 0.00 46.63 3.18
2722 4665 7.208080 AGACTAGTAATGAACGTTTGTGTTCT 58.792 34.615 0.46 0.48 46.59 3.01
2774 4722 8.561212 TGCTTGATGTTACAAGTTTATAACGTT 58.439 29.630 5.88 5.88 45.98 3.99
2818 4766 8.560903 AGGACAAAATTAGTTCCTCCTGATATT 58.439 33.333 0.00 0.00 0.00 1.28
2865 4813 0.677288 TACCCGATTACCCATCAGCG 59.323 55.000 0.00 0.00 0.00 5.18
2870 4818 2.480419 CCGATTACCCATCAGCGAATTC 59.520 50.000 0.00 0.00 0.00 2.17
2882 4833 5.309323 TCAGCGAATTCTTGTTTTATGGG 57.691 39.130 3.52 0.00 0.00 4.00
2900 4851 1.070601 GGGTTGTCTTGGCAAATGCTT 59.929 47.619 0.00 0.00 41.70 3.91
2902 4853 3.244044 GGGTTGTCTTGGCAAATGCTTAA 60.244 43.478 0.00 1.03 41.70 1.85
3072 5023 6.367422 GCACTTCTTATCATGGTATAGCTGAC 59.633 42.308 0.00 0.00 0.00 3.51
3119 5073 2.821969 CCTTCCACAGAACTGGAATTGG 59.178 50.000 6.76 5.07 47.00 3.16
3154 5108 7.986085 AGTGTTGTTTAATGAAGCTACAGAT 57.014 32.000 0.00 0.00 33.61 2.90
3212 5179 9.480053 AATATTATGCATGTAAGTTTGAATGGC 57.520 29.630 10.16 0.00 0.00 4.40
3219 5186 5.643379 TGTAAGTTTGAATGGCATCCTTC 57.357 39.130 0.00 0.00 0.00 3.46
3220 5187 4.462483 TGTAAGTTTGAATGGCATCCTTCC 59.538 41.667 0.00 0.00 0.00 3.46
3221 5188 2.460669 AGTTTGAATGGCATCCTTCCC 58.539 47.619 0.00 0.00 0.00 3.97
3223 5190 0.395586 TTGAATGGCATCCTTCCCCG 60.396 55.000 0.00 0.00 0.00 5.73
3235 5202 5.188359 GCATCCTTCCCCGGTATATTAGTAA 59.812 44.000 0.00 0.00 0.00 2.24
3242 5209 8.954834 TTCCCCGGTATATTAGTAAACTATCA 57.045 34.615 0.00 0.00 0.00 2.15
3244 5211 8.806146 TCCCCGGTATATTAGTAAACTATCAAC 58.194 37.037 0.00 0.00 0.00 3.18
3245 5212 8.037166 CCCCGGTATATTAGTAAACTATCAACC 58.963 40.741 0.00 0.00 0.00 3.77
3246 5213 8.587608 CCCGGTATATTAGTAAACTATCAACCA 58.412 37.037 0.00 0.00 0.00 3.67
3272 5239 6.478344 TCAATTGGTTATTGTGTTTTCAGCAC 59.522 34.615 5.42 0.00 43.41 4.40
3277 5244 1.686355 TTGTGTTTTCAGCACGGGAT 58.314 45.000 0.00 0.00 39.53 3.85
3278 5245 0.950836 TGTGTTTTCAGCACGGGATG 59.049 50.000 0.00 0.00 39.53 3.51
3279 5246 0.951558 GTGTTTTCAGCACGGGATGT 59.048 50.000 1.39 0.00 0.00 3.06
3283 5250 3.118956 TGTTTTCAGCACGGGATGTTTTT 60.119 39.130 1.39 0.00 0.00 1.94
3285 5252 0.313672 TCAGCACGGGATGTTTTTGC 59.686 50.000 1.39 0.00 0.00 3.68
3286 5253 0.031857 CAGCACGGGATGTTTTTGCA 59.968 50.000 0.00 0.00 35.57 4.08
3287 5254 0.968405 AGCACGGGATGTTTTTGCAT 59.032 45.000 0.00 0.00 35.57 3.96
3288 5255 2.094803 CAGCACGGGATGTTTTTGCATA 60.095 45.455 0.00 0.00 35.57 3.14
3290 5257 2.529151 CACGGGATGTTTTTGCATAGC 58.471 47.619 0.00 0.00 0.00 2.97
3292 5259 1.750778 CGGGATGTTTTTGCATAGCCT 59.249 47.619 0.00 0.00 0.00 4.58
3296 5263 5.623368 CGGGATGTTTTTGCATAGCCTAAAA 60.623 40.000 0.00 0.00 0.00 1.52
3297 5264 6.348498 GGGATGTTTTTGCATAGCCTAAAAT 58.652 36.000 0.00 0.00 0.00 1.82
3299 5266 7.653311 GGGATGTTTTTGCATAGCCTAAAATAG 59.347 37.037 0.00 0.00 0.00 1.73
3300 5267 8.197439 GGATGTTTTTGCATAGCCTAAAATAGT 58.803 33.333 0.00 0.00 0.00 2.12
3302 5269 8.116651 TGTTTTTGCATAGCCTAAAATAGTGA 57.883 30.769 0.00 0.00 0.00 3.41
3303 5270 8.580720 TGTTTTTGCATAGCCTAAAATAGTGAA 58.419 29.630 0.00 0.00 0.00 3.18
3307 5335 8.662781 TTGCATAGCCTAAAATAGTGAAGTAG 57.337 34.615 0.00 0.00 0.00 2.57
3313 5341 6.927294 CCTAAAATAGTGAAGTAGGCCTTG 57.073 41.667 12.58 0.00 32.03 3.61
3318 5346 6.869206 AATAGTGAAGTAGGCCTTGAGTTA 57.131 37.500 12.58 0.00 32.03 2.24
3354 5382 1.748879 TGCCATTTCAGGTAGCCGC 60.749 57.895 0.00 0.00 0.00 6.53
3430 5458 8.365399 TGTACAAGTCTCTAAAATGTCTTGTG 57.635 34.615 15.46 0.00 43.04 3.33
3490 5519 6.274579 GGAGTAGTTCCTAATGTCTTACAGC 58.725 44.000 0.00 0.00 43.16 4.40
3628 5659 9.601810 ACCCTGAAATAGTTTAAAGAATCCTTT 57.398 29.630 0.00 0.00 44.26 3.11
3648 5679 1.072489 TGCGTGGATTGGTCTGGTAAA 59.928 47.619 0.00 0.00 0.00 2.01
3649 5680 2.156098 GCGTGGATTGGTCTGGTAAAA 58.844 47.619 0.00 0.00 0.00 1.52
3650 5681 2.161609 GCGTGGATTGGTCTGGTAAAAG 59.838 50.000 0.00 0.00 0.00 2.27
3684 5715 8.398665 GGGTAACTGAAATGATATTTCACTGTC 58.601 37.037 11.71 5.21 34.96 3.51
3722 5757 4.040095 GGATGGACATCTCATGATCACTCA 59.960 45.833 11.67 0.00 37.92 3.41
3845 5880 4.929808 TCTTATTTTCTCGGCTTCAGTGAC 59.070 41.667 0.00 0.00 0.00 3.67
3894 5933 1.630369 TGCCTAGACCTGCAATGAAGT 59.370 47.619 0.00 0.00 33.87 3.01
3895 5934 2.040278 TGCCTAGACCTGCAATGAAGTT 59.960 45.455 0.00 0.00 33.87 2.66
3900 5950 5.352569 CCTAGACCTGCAATGAAGTTAAGTG 59.647 44.000 0.00 0.00 0.00 3.16
3964 6046 0.250209 GGCGGCATGAGATGAGATGT 60.250 55.000 3.07 0.00 0.00 3.06
3966 6048 1.809271 GCGGCATGAGATGAGATGTGT 60.809 52.381 0.00 0.00 0.00 3.72
3967 6049 1.865340 CGGCATGAGATGAGATGTGTG 59.135 52.381 0.00 0.00 0.00 3.82
4070 6166 3.499737 GCGTTCATGGCCACCGAG 61.500 66.667 8.16 0.00 0.00 4.63
4133 6229 4.221422 GTGCCCTGGATCGCGCTA 62.221 66.667 5.56 0.00 32.74 4.26
4250 6361 5.046910 GCAGCAGCAAAACTATGAGTAAA 57.953 39.130 0.00 0.00 41.58 2.01
4266 6377 7.608308 ATGAGTAAATCAAGAGCTGAAGAAC 57.392 36.000 0.00 0.00 42.53 3.01
4269 6380 7.118825 TGAGTAAATCAAGAGCTGAAGAACATG 59.881 37.037 0.00 0.00 37.67 3.21
4271 6382 2.430465 TCAAGAGCTGAAGAACATGGC 58.570 47.619 0.00 0.00 0.00 4.40
4272 6383 2.156917 CAAGAGCTGAAGAACATGGCA 58.843 47.619 0.00 0.00 0.00 4.92
4273 6384 1.818642 AGAGCTGAAGAACATGGCAC 58.181 50.000 0.00 0.00 0.00 5.01
4277 6388 1.171308 CTGAAGAACATGGCACCTGG 58.829 55.000 0.00 0.00 0.00 4.45
4278 6389 0.770499 TGAAGAACATGGCACCTGGA 59.230 50.000 0.00 0.00 0.00 3.86
4279 6390 1.271543 TGAAGAACATGGCACCTGGAG 60.272 52.381 0.00 0.00 0.00 3.86
4280 6391 0.610232 AAGAACATGGCACCTGGAGC 60.610 55.000 7.65 7.65 0.00 4.70
4281 6392 1.303561 GAACATGGCACCTGGAGCA 60.304 57.895 17.81 4.76 0.00 4.26
4282 6393 0.895100 GAACATGGCACCTGGAGCAA 60.895 55.000 17.81 7.09 0.00 3.91
4285 6396 0.395311 CATGGCACCTGGAGCAAGAT 60.395 55.000 17.81 3.88 0.00 2.40
4286 6397 0.395311 ATGGCACCTGGAGCAAGATG 60.395 55.000 17.81 0.00 0.00 2.90
4287 6398 1.300963 GGCACCTGGAGCAAGATGA 59.699 57.895 17.81 0.00 0.00 2.92
4288 6399 0.322816 GGCACCTGGAGCAAGATGAA 60.323 55.000 17.81 0.00 0.00 2.57
4289 6400 1.093159 GCACCTGGAGCAAGATGAAG 58.907 55.000 11.41 0.00 0.00 3.02
4290 6401 1.339438 GCACCTGGAGCAAGATGAAGA 60.339 52.381 11.41 0.00 0.00 2.87
4291 6402 2.683152 GCACCTGGAGCAAGATGAAGAT 60.683 50.000 11.41 0.00 0.00 2.40
4292 6403 3.432749 GCACCTGGAGCAAGATGAAGATA 60.433 47.826 11.41 0.00 0.00 1.98
4293 6404 4.774124 CACCTGGAGCAAGATGAAGATAA 58.226 43.478 0.00 0.00 0.00 1.75
4294 6405 4.815308 CACCTGGAGCAAGATGAAGATAAG 59.185 45.833 0.00 0.00 0.00 1.73
4295 6406 3.814283 CCTGGAGCAAGATGAAGATAAGC 59.186 47.826 0.00 0.00 0.00 3.09
4296 6407 4.444591 CCTGGAGCAAGATGAAGATAAGCT 60.445 45.833 0.00 0.00 0.00 3.74
4297 6408 4.449131 TGGAGCAAGATGAAGATAAGCTG 58.551 43.478 0.00 0.00 0.00 4.24
4300 6411 5.356291 AGCAAGATGAAGATAAGCTGTCT 57.644 39.130 0.00 0.00 0.00 3.41
4313 6424 2.533916 AGCTGTCTGTCAGGAGAATGA 58.466 47.619 0.00 0.00 43.78 2.57
4371 6482 1.464687 CGCTGAAAGAATTCGCCACAG 60.465 52.381 15.28 15.28 38.46 3.66
4372 6483 1.806542 GCTGAAAGAATTCGCCACAGA 59.193 47.619 20.29 0.00 38.46 3.41
4373 6484 2.159599 GCTGAAAGAATTCGCCACAGAG 60.160 50.000 20.29 6.75 38.46 3.35
4374 6485 3.329386 CTGAAAGAATTCGCCACAGAGA 58.671 45.455 14.80 0.00 38.46 3.10
4400 6511 8.188799 AGAACAATCGATCGATGTTAGAAACTA 58.811 33.333 29.99 0.00 34.70 2.24
4401 6512 7.681125 ACAATCGATCGATGTTAGAAACTAC 57.319 36.000 29.99 0.00 34.70 2.73
4402 6513 7.255569 ACAATCGATCGATGTTAGAAACTACA 58.744 34.615 29.99 0.00 34.70 2.74
4403 6514 7.432545 ACAATCGATCGATGTTAGAAACTACAG 59.567 37.037 29.99 4.33 34.70 2.74
4404 6515 6.432607 TCGATCGATGTTAGAAACTACAGT 57.567 37.500 15.15 0.00 0.00 3.55
4478 7505 2.474816 CCACGGAATTCGGAGAATCTC 58.525 52.381 18.83 0.71 45.90 2.75
4480 7507 2.022195 ACGGAATTCGGAGAATCTCGA 58.978 47.619 18.83 2.71 45.90 4.04
4481 7508 2.033550 ACGGAATTCGGAGAATCTCGAG 59.966 50.000 18.83 5.93 45.90 4.04
4482 7509 2.399448 GGAATTCGGAGAATCTCGAGC 58.601 52.381 7.81 0.00 45.90 5.03
4483 7510 2.223829 GGAATTCGGAGAATCTCGAGCA 60.224 50.000 7.81 0.00 45.90 4.26
4484 7511 3.448686 GAATTCGGAGAATCTCGAGCAA 58.551 45.455 7.81 0.00 45.90 3.91
4516 7543 4.059511 GCAGATGAGATTGAGGAGTGATG 58.940 47.826 0.00 0.00 0.00 3.07
4540 8912 2.662857 TGAGTGCAGTGCGTCAGC 60.663 61.111 14.34 6.12 45.41 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 1.444553 GTCCCAGAACTGTCTCGCG 60.445 63.158 0.00 0.00 28.78 5.87
99 101 2.107204 AGCTTGATGTCCAGAACAAGGT 59.893 45.455 0.00 0.00 42.37 3.50
254 257 2.758979 AGTTCACCGGATCGTACTTCAT 59.241 45.455 9.46 0.00 0.00 2.57
255 258 2.163010 GAGTTCACCGGATCGTACTTCA 59.837 50.000 9.46 0.00 0.00 3.02
336 339 1.491670 CCAACCATGTCTCGATAGCG 58.508 55.000 0.00 0.00 39.35 4.26
607 610 2.031919 TTGCGGCGAGTGTTCCAT 59.968 55.556 12.98 0.00 0.00 3.41
695 699 5.733676 TGCAGATCTACTAACATGCTGAAA 58.266 37.500 0.00 0.00 34.80 2.69
789 793 1.695242 TGCTAACCAGGAAACTCGGAA 59.305 47.619 0.00 0.00 40.21 4.30
824 828 3.527720 AACAAAAGTGTTCGCTGGGCG 62.528 52.381 5.52 5.52 45.00 6.13
905 910 2.419990 CCGTAATCACATTCCAGCCTCA 60.420 50.000 0.00 0.00 0.00 3.86
958 963 3.439476 TCGAACTAGCAACTCAGGTCTAC 59.561 47.826 0.00 0.00 0.00 2.59
965 970 1.199327 CGAGGTCGAACTAGCAACTCA 59.801 52.381 1.02 0.00 43.02 3.41
972 977 1.015868 GAGGTCCGAGGTCGAACTAG 58.984 60.000 1.02 2.30 43.02 2.57
974 979 1.678300 GGAGGTCCGAGGTCGAACT 60.678 63.158 0.34 0.34 43.02 3.01
977 982 2.045242 CTGGAGGTCCGAGGTCGA 60.045 66.667 0.00 0.00 43.02 4.20
979 984 1.000646 ACTCTGGAGGTCCGAGGTC 60.001 63.158 16.89 0.00 39.37 3.85
980 985 1.000646 GACTCTGGAGGTCCGAGGT 60.001 63.158 16.89 5.46 39.37 3.85
982 987 3.927501 GGACTCTGGAGGTCCGAG 58.072 66.667 13.16 13.16 42.84 4.63
1012 1365 0.179070 GATCTTCTGCCTCGGAACCC 60.179 60.000 0.00 0.00 0.00 4.11
1018 1371 1.103987 TCCTCCGATCTTCTGCCTCG 61.104 60.000 0.00 0.00 0.00 4.63
1052 1405 0.866427 CTGCGAGATGATGTCCATGC 59.134 55.000 0.00 0.00 35.17 4.06
1496 2323 6.208204 AGGATGATGAATTAGTTGCTAATGCC 59.792 38.462 2.60 0.00 36.85 4.40
1540 2789 2.662006 TCATTCACAGAAGAGAGGCG 57.338 50.000 0.00 0.00 0.00 5.52
1569 2818 5.196695 AGAGTGCAATTTAGGAGGGAAATC 58.803 41.667 0.00 0.00 0.00 2.17
1622 3547 7.424803 CGAATTTAGGATAATGGATTGCAACA 58.575 34.615 0.00 0.00 0.00 3.33
1669 3594 7.977818 TCACAGCATATTCTGGGTCTAATAAT 58.022 34.615 4.48 0.00 38.58 1.28
1676 3601 8.621532 TTATTAATCACAGCATATTCTGGGTC 57.378 34.615 4.48 0.00 38.58 4.46
1705 3630 6.684538 AGTACTCAGGAACTATACCCTCATT 58.315 40.000 0.00 0.00 36.02 2.57
1710 3635 5.383476 TGCTAGTACTCAGGAACTATACCC 58.617 45.833 0.00 0.00 36.02 3.69
1725 3651 2.009774 CACAACATGCCCTGCTAGTAC 58.990 52.381 0.00 0.00 0.00 2.73
1747 3673 6.209361 CCAATATATCGATATCACGGACCTG 58.791 44.000 20.95 8.12 0.00 4.00
1872 3798 9.985730 ATGACACAAATGATAAAACAGACAAAT 57.014 25.926 0.00 0.00 0.00 2.32
1897 3823 6.037720 CGCTATACTATGTGCTCTAGCTGTAT 59.962 42.308 0.00 6.86 42.66 2.29
1994 3920 9.751542 CGTGGAAGACAAAGAGAGTATAATTAT 57.248 33.333 2.97 2.97 0.00 1.28
2120 4046 2.431782 AGGCACATTTCAGCACAAGTTT 59.568 40.909 0.00 0.00 0.00 2.66
2288 4216 3.191581 ACTCTGATACTGACACCGTGAAG 59.808 47.826 5.28 5.07 0.00 3.02
2297 4225 7.065204 TCGCTGATCATATACTCTGATACTGAC 59.935 40.741 0.00 0.00 33.56 3.51
2321 4250 6.730960 TTTTGGTAAGTTAGCCTATGTTCG 57.269 37.500 9.51 0.00 0.00 3.95
2369 4298 2.498885 GCCCTTTGATTCAGAAATGCCT 59.501 45.455 0.00 0.00 0.00 4.75
2610 4551 4.523943 AGGAGAAAGCATAACATTTGCACA 59.476 37.500 0.00 0.00 42.62 4.57
2719 4662 8.460428 TGCTTTTCTTCGGTTTAACTTTAAGAA 58.540 29.630 0.00 12.37 32.67 2.52
2721 4664 8.126700 TCTGCTTTTCTTCGGTTTAACTTTAAG 58.873 33.333 0.00 0.00 0.00 1.85
2722 4665 7.987649 TCTGCTTTTCTTCGGTTTAACTTTAA 58.012 30.769 0.00 0.00 0.00 1.52
2805 4753 8.297470 CATTTTCTGGAAAATATCAGGAGGAA 57.703 34.615 17.39 0.00 46.01 3.36
2865 4813 7.384932 CCAAGACAACCCATAAAACAAGAATTC 59.615 37.037 0.00 0.00 0.00 2.17
2870 4818 4.202202 TGCCAAGACAACCCATAAAACAAG 60.202 41.667 0.00 0.00 0.00 3.16
2882 4833 4.367450 TGTTAAGCATTTGCCAAGACAAC 58.633 39.130 0.00 0.00 43.38 3.32
2900 4851 4.401202 TGGATCTTAGACGATGCACTGTTA 59.599 41.667 0.00 0.00 36.92 2.41
2902 4853 2.760650 TGGATCTTAGACGATGCACTGT 59.239 45.455 0.00 0.00 36.92 3.55
2994 4945 3.507162 TGTTTCTGAAGCTCCAATCCA 57.493 42.857 5.84 0.00 0.00 3.41
3092 5046 3.138283 TCCAGTTCTGTGGAAGGAACAAT 59.862 43.478 8.24 0.00 44.01 2.71
3102 5056 2.226437 CGTTCCAATTCCAGTTCTGTGG 59.774 50.000 0.00 0.82 39.19 4.17
3119 5073 3.497297 AAACAACACTTCAACCCGTTC 57.503 42.857 0.00 0.00 0.00 3.95
3154 5108 9.733556 TCTGGCTTCTTCAAATTTATACAGTTA 57.266 29.630 0.00 0.00 0.00 2.24
3189 5143 6.876155 TGCCATTCAAACTTACATGCATAAT 58.124 32.000 0.00 0.00 0.00 1.28
3207 5174 0.991355 TACCGGGGAAGGATGCCATT 60.991 55.000 6.32 0.00 32.29 3.16
3212 5179 6.862469 TTACTAATATACCGGGGAAGGATG 57.138 41.667 6.32 0.00 34.73 3.51
3219 5186 8.037166 GGTTGATAGTTTACTAATATACCGGGG 58.963 40.741 6.32 0.00 31.39 5.73
3220 5187 8.587608 TGGTTGATAGTTTACTAATATACCGGG 58.412 37.037 6.32 0.00 31.39 5.73
3245 5212 7.171167 TGCTGAAAACACAATAACCAATTGATG 59.829 33.333 7.12 0.72 46.81 3.07
3246 5213 7.171337 GTGCTGAAAACACAATAACCAATTGAT 59.829 33.333 7.12 0.00 46.81 2.57
3247 5214 6.478344 GTGCTGAAAACACAATAACCAATTGA 59.522 34.615 7.12 0.00 46.81 2.57
3249 5216 5.461737 CGTGCTGAAAACACAATAACCAATT 59.538 36.000 0.00 0.00 37.93 2.32
3250 5217 4.981674 CGTGCTGAAAACACAATAACCAAT 59.018 37.500 0.00 0.00 37.93 3.16
3251 5218 4.355437 CGTGCTGAAAACACAATAACCAA 58.645 39.130 0.00 0.00 37.93 3.67
3252 5219 3.243234 CCGTGCTGAAAACACAATAACCA 60.243 43.478 0.00 0.00 37.93 3.67
3253 5220 3.305110 CCGTGCTGAAAACACAATAACC 58.695 45.455 0.00 0.00 37.93 2.85
3267 5234 0.031857 TGCAAAAACATCCCGTGCTG 59.968 50.000 0.00 0.00 36.18 4.41
3272 5239 1.750778 AGGCTATGCAAAAACATCCCG 59.249 47.619 0.00 0.00 30.72 5.14
3277 5244 8.116651 TCACTATTTTAGGCTATGCAAAAACA 57.883 30.769 0.00 0.00 31.43 2.83
3278 5245 8.980143 TTCACTATTTTAGGCTATGCAAAAAC 57.020 30.769 0.00 0.00 31.43 2.43
3279 5246 8.802267 ACTTCACTATTTTAGGCTATGCAAAAA 58.198 29.630 0.00 0.00 32.53 1.94
3283 5250 7.217200 CCTACTTCACTATTTTAGGCTATGCA 58.783 38.462 0.00 0.00 0.00 3.96
3290 5257 6.650120 TCAAGGCCTACTTCACTATTTTAGG 58.350 40.000 5.16 0.00 37.29 2.69
3292 5259 7.253905 ACTCAAGGCCTACTTCACTATTTTA 57.746 36.000 5.16 0.00 37.29 1.52
3296 5263 6.440965 AGTTAACTCAAGGCCTACTTCACTAT 59.559 38.462 5.16 0.00 37.29 2.12
3297 5264 5.778750 AGTTAACTCAAGGCCTACTTCACTA 59.221 40.000 5.16 0.00 37.29 2.74
3299 5266 4.895961 AGTTAACTCAAGGCCTACTTCAC 58.104 43.478 5.16 0.00 37.29 3.18
3300 5267 4.020485 GGAGTTAACTCAAGGCCTACTTCA 60.020 45.833 31.30 0.00 44.60 3.02
3302 5269 3.263681 GGGAGTTAACTCAAGGCCTACTT 59.736 47.826 31.30 0.00 44.60 2.24
3303 5270 2.838813 GGGAGTTAACTCAAGGCCTACT 59.161 50.000 31.30 3.03 44.60 2.57
3307 5335 2.808906 ATGGGAGTTAACTCAAGGCC 57.191 50.000 31.30 23.86 44.60 5.19
3309 5337 6.840780 ATTTGAATGGGAGTTAACTCAAGG 57.159 37.500 31.30 0.00 44.60 3.61
3313 5341 6.366061 GCACAAATTTGAATGGGAGTTAACTC 59.634 38.462 24.73 24.73 42.14 3.01
3318 5346 3.390639 TGGCACAAATTTGAATGGGAGTT 59.609 39.130 24.64 0.00 31.92 3.01
3401 5429 9.832445 AAGACATTTTAGAGACTTGTACAAGAA 57.168 29.630 36.14 20.76 40.79 2.52
3430 5458 9.455847 CAAATATAAGACATTTTAGAGGCTTGC 57.544 33.333 0.00 0.00 0.00 4.01
3490 5519 4.245660 TGTCGACAAATCTAGCTTGGAAG 58.754 43.478 17.62 0.00 0.00 3.46
3626 5657 0.179004 ACCAGACCAATCCACGCAAA 60.179 50.000 0.00 0.00 0.00 3.68
3628 5659 0.687920 TTACCAGACCAATCCACGCA 59.312 50.000 0.00 0.00 0.00 5.24
3648 5679 4.513406 TTTCAGTTACCCTGGTGAACTT 57.487 40.909 7.53 0.00 41.83 2.66
3649 5680 4.104102 TCATTTCAGTTACCCTGGTGAACT 59.896 41.667 0.00 4.99 41.83 3.01
3650 5681 4.394729 TCATTTCAGTTACCCTGGTGAAC 58.605 43.478 0.00 0.00 41.83 3.18
3680 5711 5.296283 CCATCCTATGCTCTTTCTTTGACAG 59.704 44.000 0.00 0.00 0.00 3.51
3684 5715 5.188434 TGTCCATCCTATGCTCTTTCTTTG 58.812 41.667 0.00 0.00 0.00 2.77
3691 5722 3.854437 TGAGATGTCCATCCTATGCTCT 58.146 45.455 3.70 0.00 38.58 4.09
3692 5723 4.222366 TCATGAGATGTCCATCCTATGCTC 59.778 45.833 12.78 0.00 38.58 4.26
3722 5757 3.754965 TCAGGCATAGCTTCAGTGTTTT 58.245 40.909 0.00 0.00 0.00 2.43
3860 5899 1.672881 CTAGGCACTTGCAAGTATGCC 59.327 52.381 36.43 36.43 46.76 4.40
3894 5933 4.038763 TCTGACCGCTTCTTTCTCACTTAA 59.961 41.667 0.00 0.00 0.00 1.85
3895 5934 3.572682 TCTGACCGCTTCTTTCTCACTTA 59.427 43.478 0.00 0.00 0.00 2.24
3900 5950 3.186119 CTCATCTGACCGCTTCTTTCTC 58.814 50.000 0.00 0.00 0.00 2.87
3964 6046 0.249120 CGACCCCAGTAAGCATCACA 59.751 55.000 0.00 0.00 0.00 3.58
3966 6048 0.907704 ACCGACCCCAGTAAGCATCA 60.908 55.000 0.00 0.00 0.00 3.07
3967 6049 0.462047 CACCGACCCCAGTAAGCATC 60.462 60.000 0.00 0.00 0.00 3.91
4250 6361 3.015327 GCCATGTTCTTCAGCTCTTGAT 58.985 45.455 0.00 0.00 35.27 2.57
4266 6377 0.395311 ATCTTGCTCCAGGTGCCATG 60.395 55.000 11.07 1.67 0.00 3.66
4269 6380 0.322816 TTCATCTTGCTCCAGGTGCC 60.323 55.000 11.07 0.00 0.00 5.01
4271 6382 2.775911 TCTTCATCTTGCTCCAGGTG 57.224 50.000 0.00 0.00 0.00 4.00
4272 6383 4.685575 GCTTATCTTCATCTTGCTCCAGGT 60.686 45.833 0.00 0.00 0.00 4.00
4273 6384 3.814283 GCTTATCTTCATCTTGCTCCAGG 59.186 47.826 0.00 0.00 0.00 4.45
4277 6388 5.234757 CAGACAGCTTATCTTCATCTTGCTC 59.765 44.000 0.00 0.00 0.00 4.26
4278 6389 5.117584 CAGACAGCTTATCTTCATCTTGCT 58.882 41.667 0.00 0.00 0.00 3.91
4279 6390 4.874966 ACAGACAGCTTATCTTCATCTTGC 59.125 41.667 0.00 0.00 0.00 4.01
4280 6391 6.104665 TGACAGACAGCTTATCTTCATCTTG 58.895 40.000 0.00 0.00 0.00 3.02
4281 6392 6.291648 TGACAGACAGCTTATCTTCATCTT 57.708 37.500 0.00 0.00 0.00 2.40
4282 6393 5.163426 CCTGACAGACAGCTTATCTTCATCT 60.163 44.000 3.32 0.00 44.52 2.90
4285 6396 4.089361 TCCTGACAGACAGCTTATCTTCA 58.911 43.478 3.32 3.15 44.52 3.02
4286 6397 4.400884 TCTCCTGACAGACAGCTTATCTTC 59.599 45.833 3.32 0.00 44.52 2.87
4287 6398 4.348486 TCTCCTGACAGACAGCTTATCTT 58.652 43.478 3.32 0.00 44.52 2.40
4288 6399 3.974719 TCTCCTGACAGACAGCTTATCT 58.025 45.455 3.32 0.00 44.52 1.98
4289 6400 4.727507 TTCTCCTGACAGACAGCTTATC 57.272 45.455 3.32 0.00 44.52 1.75
4290 6401 4.713814 TCATTCTCCTGACAGACAGCTTAT 59.286 41.667 3.32 0.00 44.52 1.73
4291 6402 4.081972 GTCATTCTCCTGACAGACAGCTTA 60.082 45.833 3.32 0.00 44.03 3.09
4292 6403 2.902486 TCATTCTCCTGACAGACAGCTT 59.098 45.455 3.32 0.00 44.52 3.74
4293 6404 2.233431 GTCATTCTCCTGACAGACAGCT 59.767 50.000 3.32 0.00 44.03 4.24
4294 6405 2.233431 AGTCATTCTCCTGACAGACAGC 59.767 50.000 3.32 0.00 46.45 4.40
4295 6406 3.763360 AGAGTCATTCTCCTGACAGACAG 59.237 47.826 3.32 0.00 46.45 3.51
4296 6407 3.761218 GAGAGTCATTCTCCTGACAGACA 59.239 47.826 3.32 0.00 46.45 3.41
4297 6408 4.370364 GAGAGTCATTCTCCTGACAGAC 57.630 50.000 3.32 0.00 46.45 3.51
4313 6424 2.042464 TCAGCAGAAACAGGTGAGAGT 58.958 47.619 0.00 0.00 38.45 3.24
4371 6482 6.431278 TCTAACATCGATCGATTGTTCTCTC 58.569 40.000 30.95 0.00 32.51 3.20
4372 6483 6.378710 TCTAACATCGATCGATTGTTCTCT 57.621 37.500 30.95 19.46 32.51 3.10
4373 6484 7.221067 AGTTTCTAACATCGATCGATTGTTCTC 59.779 37.037 30.95 21.93 32.51 2.87
4374 6485 7.036220 AGTTTCTAACATCGATCGATTGTTCT 58.964 34.615 30.95 23.39 32.51 3.01
4400 6511 8.364142 GCTTGGTCTCTGATCTATTTATACTGT 58.636 37.037 0.00 0.00 0.00 3.55
4401 6512 8.363390 TGCTTGGTCTCTGATCTATTTATACTG 58.637 37.037 0.00 0.00 0.00 2.74
4402 6513 8.484214 TGCTTGGTCTCTGATCTATTTATACT 57.516 34.615 0.00 0.00 0.00 2.12
4403 6514 8.364142 ACTGCTTGGTCTCTGATCTATTTATAC 58.636 37.037 0.00 0.00 0.00 1.47
4404 6515 8.484214 ACTGCTTGGTCTCTGATCTATTTATA 57.516 34.615 0.00 0.00 0.00 0.98
4478 7505 0.725686 CTGCATCCTCAACTTGCTCG 59.274 55.000 0.00 0.00 37.28 5.03
4480 7507 2.026542 TCATCTGCATCCTCAACTTGCT 60.027 45.455 0.00 0.00 37.28 3.91
4481 7508 2.355132 CTCATCTGCATCCTCAACTTGC 59.645 50.000 0.00 0.00 36.91 4.01
4482 7509 3.870274 TCTCATCTGCATCCTCAACTTG 58.130 45.455 0.00 0.00 0.00 3.16
4483 7510 4.774660 ATCTCATCTGCATCCTCAACTT 57.225 40.909 0.00 0.00 0.00 2.66
4484 7511 4.163649 TCAATCTCATCTGCATCCTCAACT 59.836 41.667 0.00 0.00 0.00 3.16
4516 7543 2.027625 GCACTGCACTCACGGTACC 61.028 63.158 0.16 0.16 0.00 3.34
4570 8942 1.599797 GGGTTCAACCACCGTCAGG 60.600 63.158 9.35 0.00 41.02 3.86


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

AutoCloner maintained by Alex Coulton.