Multiple sequence alignment - TraesCS7D01G512200

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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 TraesCS7D01G512200 chr7D 100.000 4404 0 0 1 4404 613874395 613869992 0.000000e+00 8133.0
1 TraesCS7D01G512200 chr7D 83.459 133 12 9 3644 3774 38641466 38641590 1.000000e-21 115.0
2 TraesCS7D01G512200 chr7A 94.564 3495 123 28 204 3640 705691204 705687719 0.000000e+00 5339.0
3 TraesCS7D01G512200 chr7A 87.331 592 67 5 1821 2407 2542787 2543375 0.000000e+00 671.0
4 TraesCS7D01G512200 chr7A 87.162 592 68 5 1821 2407 67565467 67566055 0.000000e+00 665.0
5 TraesCS7D01G512200 chr7A 92.051 390 21 5 4015 4404 705687488 705687109 1.390000e-149 540.0
6 TraesCS7D01G512200 chr7A 88.421 380 31 7 4028 4404 34789057 34788688 3.130000e-121 446.0
7 TraesCS7D01G512200 chr7A 87.854 247 11 5 3758 3990 705687724 705687483 5.610000e-69 272.0
8 TraesCS7D01G512200 chr7B 92.712 3554 161 41 148 3624 705257657 705254125 0.000000e+00 5038.0
9 TraesCS7D01G512200 chr7B 88.538 602 36 18 3818 4404 705254035 705253452 0.000000e+00 699.0
10 TraesCS7D01G512200 chr6D 88.401 569 55 8 1844 2407 331238593 331239155 0.000000e+00 675.0
11 TraesCS7D01G512200 chr6D 85.149 303 43 2 2418 2719 331239349 331239650 4.280000e-80 309.0
12 TraesCS7D01G512200 chr6D 90.076 131 13 0 2754 2884 331239656 331239786 2.110000e-38 171.0
13 TraesCS7D01G512200 chr6D 87.500 128 8 8 3640 3764 462028484 462028362 1.650000e-29 141.0
14 TraesCS7D01G512200 chr6D 87.931 116 10 4 3646 3761 382346870 382346981 2.760000e-27 134.0
15 TraesCS7D01G512200 chr6D 85.950 121 10 7 3642 3760 462028366 462028481 5.980000e-24 122.0
16 TraesCS7D01G512200 chr4A 87.162 592 68 5 1821 2407 12666786 12666198 0.000000e+00 665.0
17 TraesCS7D01G512200 chr1A 87.162 592 68 5 1821 2407 502835060 502834472 0.000000e+00 665.0
18 TraesCS7D01G512200 chr1A 83.682 478 57 13 1116 1592 362620539 362620996 8.750000e-117 431.0
19 TraesCS7D01G512200 chr1A 80.899 356 41 7 1631 1959 362620999 362621354 5.650000e-64 255.0
20 TraesCS7D01G512200 chr3A 86.824 592 70 7 1821 2407 141553419 141554007 0.000000e+00 654.0
21 TraesCS7D01G512200 chr3B 86.824 592 69 6 1821 2407 492109320 492108733 0.000000e+00 652.0
22 TraesCS7D01G512200 chr6A 85.458 612 76 7 1116 1719 36490616 36491222 3.740000e-175 625.0
23 TraesCS7D01G512200 chr2D 81.672 622 67 21 1365 1959 429498906 429499507 1.430000e-129 473.0
24 TraesCS7D01G512200 chr2D 88.235 119 8 5 3645 3761 627911187 627911301 2.140000e-28 137.0
25 TraesCS7D01G512200 chr2D 88.136 118 8 6 3643 3758 627911300 627911187 7.680000e-28 135.0
26 TraesCS7D01G512200 chr5B 89.076 119 6 4 3642 3760 344615930 344615819 1.650000e-29 141.0
27 TraesCS7D01G512200 chr6B 86.777 121 10 6 3643 3762 106468656 106468771 3.570000e-26 130.0
28 TraesCS7D01G512200 chr6B 100.000 31 0 0 75 105 213393403 213393373 1.710000e-04 58.4
29 TraesCS7D01G512200 chr6B 91.892 37 3 0 65 101 32716530 32716566 8.000000e-03 52.8
30 TraesCS7D01G512200 chr2B 82.857 140 13 9 3643 3775 25018791 25018656 1.000000e-21 115.0
31 TraesCS7D01G512200 chr5D 96.970 33 0 1 74 106 495020108 495020077 2.000000e-03 54.7


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 TraesCS7D01G512200 chr7D 613869992 613874395 4403 True 8133.000000 8133 100.000000 1 4404 1 chr7D.!!$R1 4403
1 TraesCS7D01G512200 chr7A 705687109 705691204 4095 True 2050.333333 5339 91.489667 204 4404 3 chr7A.!!$R2 4200
2 TraesCS7D01G512200 chr7A 2542787 2543375 588 False 671.000000 671 87.331000 1821 2407 1 chr7A.!!$F1 586
3 TraesCS7D01G512200 chr7A 67565467 67566055 588 False 665.000000 665 87.162000 1821 2407 1 chr7A.!!$F2 586
4 TraesCS7D01G512200 chr7B 705253452 705257657 4205 True 2868.500000 5038 90.625000 148 4404 2 chr7B.!!$R1 4256
5 TraesCS7D01G512200 chr6D 331238593 331239786 1193 False 385.000000 675 87.875333 1844 2884 3 chr6D.!!$F3 1040
6 TraesCS7D01G512200 chr4A 12666198 12666786 588 True 665.000000 665 87.162000 1821 2407 1 chr4A.!!$R1 586
7 TraesCS7D01G512200 chr1A 502834472 502835060 588 True 665.000000 665 87.162000 1821 2407 1 chr1A.!!$R1 586
8 TraesCS7D01G512200 chr1A 362620539 362621354 815 False 343.000000 431 82.290500 1116 1959 2 chr1A.!!$F1 843
9 TraesCS7D01G512200 chr3A 141553419 141554007 588 False 654.000000 654 86.824000 1821 2407 1 chr3A.!!$F1 586
10 TraesCS7D01G512200 chr3B 492108733 492109320 587 True 652.000000 652 86.824000 1821 2407 1 chr3B.!!$R1 586
11 TraesCS7D01G512200 chr6A 36490616 36491222 606 False 625.000000 625 85.458000 1116 1719 1 chr6A.!!$F1 603
12 TraesCS7D01G512200 chr2D 429498906 429499507 601 False 473.000000 473 81.672000 1365 1959 1 chr2D.!!$F1 594

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
123 124 0.112995 TCCCCTAATCCATGCCATGC 59.887 55.0 0.00 0.0 0.00 4.06 F
124 125 0.178955 CCCCTAATCCATGCCATGCA 60.179 55.0 0.00 0.0 44.86 3.96 F
1206 1277 0.464036 GGGATGTGTGGATAGCGACA 59.536 55.0 0.00 0.0 0.00 4.35 F
1875 1987 0.953727 GATATGGCGCTGATTTGGCA 59.046 50.0 7.64 0.0 45.22 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 1574 0.603569 CCCCGACGGATCCTTCATAG 59.396 60.000 17.49 6.09 0.00 2.23 R
1966 2078 1.438743 TGGAATCCCAAAATCCCCCAA 59.561 47.619 0.00 0.00 40.09 4.12 R
3033 3336 0.178992 TTTGCCAGGGAAGGTCACAG 60.179 55.000 0.00 0.00 0.00 3.66 R
3638 3957 0.115745 AGGAACGGAGGGAGTACCAA 59.884 55.000 0.00 0.00 43.89 3.67 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
40 41 9.747898 TCAACCAGTATAAATACAATCAAACCT 57.252 29.630 3.13 0.00 35.74 3.50
58 59 7.485810 TCAAACCTAAGTTTCACTAAAAAGGC 58.514 34.615 0.00 0.00 44.47 4.35
59 60 7.122948 TCAAACCTAAGTTTCACTAAAAAGGCA 59.877 33.333 0.00 0.00 44.47 4.75
60 61 7.412853 AACCTAAGTTTCACTAAAAAGGCAA 57.587 32.000 0.00 0.00 29.61 4.52
61 62 7.412853 ACCTAAGTTTCACTAAAAAGGCAAA 57.587 32.000 0.00 0.00 30.03 3.68
62 63 7.842982 ACCTAAGTTTCACTAAAAAGGCAAAA 58.157 30.769 0.00 0.00 30.03 2.44
63 64 8.315482 ACCTAAGTTTCACTAAAAAGGCAAAAA 58.685 29.630 0.00 0.00 30.03 1.94
64 65 9.325198 CCTAAGTTTCACTAAAAAGGCAAAAAT 57.675 29.630 0.00 0.00 0.00 1.82
81 82 9.200817 AGGCAAAAATTATACCATATTGACAGT 57.799 29.630 0.00 0.00 0.00 3.55
82 83 9.816354 GGCAAAAATTATACCATATTGACAGTT 57.184 29.630 0.00 0.00 0.00 3.16
94 95 9.499479 ACCATATTGACAGTTGATGAATAGATC 57.501 33.333 0.00 0.00 0.00 2.75
95 96 8.654215 CCATATTGACAGTTGATGAATAGATCG 58.346 37.037 0.00 0.00 0.00 3.69
96 97 8.654215 CATATTGACAGTTGATGAATAGATCGG 58.346 37.037 0.00 0.00 0.00 4.18
97 98 5.852282 TGACAGTTGATGAATAGATCGGA 57.148 39.130 0.00 0.00 0.00 4.55
98 99 6.220726 TGACAGTTGATGAATAGATCGGAA 57.779 37.500 0.00 0.00 0.00 4.30
99 100 6.276091 TGACAGTTGATGAATAGATCGGAAG 58.724 40.000 0.00 0.00 0.00 3.46
100 101 6.127338 TGACAGTTGATGAATAGATCGGAAGT 60.127 38.462 0.00 0.00 0.00 3.01
101 102 7.068226 TGACAGTTGATGAATAGATCGGAAGTA 59.932 37.037 0.00 0.00 0.00 2.24
102 103 7.957002 ACAGTTGATGAATAGATCGGAAGTAT 58.043 34.615 0.00 0.00 0.00 2.12
103 104 8.424918 ACAGTTGATGAATAGATCGGAAGTATT 58.575 33.333 0.00 0.00 0.00 1.89
104 105 9.265901 CAGTTGATGAATAGATCGGAAGTATTT 57.734 33.333 0.00 0.00 0.00 1.40
105 106 9.482627 AGTTGATGAATAGATCGGAAGTATTTC 57.517 33.333 0.00 0.00 0.00 2.17
118 119 4.767409 GGAAGTATTTCCCCTAATCCATGC 59.233 45.833 5.71 0.00 46.03 4.06
119 120 4.388577 AGTATTTCCCCTAATCCATGCC 57.611 45.455 0.00 0.00 0.00 4.40
120 121 3.726859 AGTATTTCCCCTAATCCATGCCA 59.273 43.478 0.00 0.00 0.00 4.92
121 122 3.929245 ATTTCCCCTAATCCATGCCAT 57.071 42.857 0.00 0.00 0.00 4.40
122 123 2.681319 TTCCCCTAATCCATGCCATG 57.319 50.000 0.00 0.00 0.00 3.66
123 124 0.112995 TCCCCTAATCCATGCCATGC 59.887 55.000 0.00 0.00 0.00 4.06
124 125 0.178955 CCCCTAATCCATGCCATGCA 60.179 55.000 0.00 0.00 44.86 3.96
125 126 1.707106 CCCTAATCCATGCCATGCAA 58.293 50.000 0.00 0.00 43.62 4.08
126 127 2.040939 CCCTAATCCATGCCATGCAAA 58.959 47.619 0.00 0.00 43.62 3.68
127 128 2.435069 CCCTAATCCATGCCATGCAAAA 59.565 45.455 0.00 0.00 43.62 2.44
128 129 3.118334 CCCTAATCCATGCCATGCAAAAA 60.118 43.478 0.00 0.00 43.62 1.94
336 346 2.066999 CCCCTCTTTCCCCTCCTCG 61.067 68.421 0.00 0.00 0.00 4.63
337 347 2.736826 CCCTCTTTCCCCTCCTCGC 61.737 68.421 0.00 0.00 0.00 5.03
338 348 1.990060 CCTCTTTCCCCTCCTCGCA 60.990 63.158 0.00 0.00 0.00 5.10
352 379 3.953775 CGCACCACCCAACCTCCT 61.954 66.667 0.00 0.00 0.00 3.69
466 499 6.861065 TTAGTACTTTCTTGACCAAGCAAG 57.139 37.500 16.62 16.62 43.86 4.01
702 745 2.755103 GCCGGATTCTTGATTTTGTCCT 59.245 45.455 5.05 0.00 0.00 3.85
713 756 2.673775 TTTTGTCCTTGATCCAGGCA 57.326 45.000 8.01 6.88 33.35 4.75
769 833 4.545823 TCTTACGGTTTTTGAGCTTGTG 57.454 40.909 0.00 0.00 0.00 3.33
842 906 1.886542 CCCCCAGTTTTACAGTTGAGC 59.113 52.381 0.00 0.00 0.00 4.26
853 917 6.795098 TTTACAGTTGAGCGTAAATGTCAT 57.205 33.333 11.29 0.00 39.31 3.06
872 936 5.425217 TGTCATAGCAGGGATCTTGTTTCTA 59.575 40.000 0.00 0.00 0.00 2.10
929 993 9.645059 CAAGAGATTATTGTTGACTAGTGAGAA 57.355 33.333 0.00 0.00 0.00 2.87
1016 1087 6.515832 AGAAACCAATGGTGAATTTTCTGAC 58.484 36.000 13.70 0.00 35.34 3.51
1206 1277 0.464036 GGGATGTGTGGATAGCGACA 59.536 55.000 0.00 0.00 0.00 4.35
1484 1564 5.419788 TCATGGATTTTCAGCTTTGCATAGT 59.580 36.000 6.03 0.00 0.00 2.12
1494 1574 5.122869 TCAGCTTTGCATAGTGATGAAGTTC 59.877 40.000 6.03 0.00 34.73 3.01
1606 1687 8.081633 TCCACAGTTTTGAACATATTTGATGTC 58.918 33.333 0.00 0.00 0.00 3.06
1652 1735 8.762426 CGGCTTATCTTAAGAATACAGTTTACC 58.238 37.037 9.71 0.35 0.00 2.85
1653 1736 9.609346 GGCTTATCTTAAGAATACAGTTTACCA 57.391 33.333 9.71 0.00 0.00 3.25
1750 1844 6.261118 GTGTTGATTGATTAACTGGCAGATC 58.739 40.000 23.66 14.27 0.00 2.75
1775 1869 3.712016 TTATCACCTTAGTGCAGGCAA 57.288 42.857 0.00 0.00 44.16 4.52
1778 1872 2.161855 TCACCTTAGTGCAGGCAAATG 58.838 47.619 0.00 0.00 44.16 2.32
1818 1913 6.132791 AGAATGCTTATGATGCTCTGTTTG 57.867 37.500 0.00 0.00 0.00 2.93
1875 1987 0.953727 GATATGGCGCTGATTTGGCA 59.046 50.000 7.64 0.00 45.22 4.92
1950 2062 6.894103 AGCCTTGTAATTTTCTCCTTGATGAT 59.106 34.615 0.00 0.00 0.00 2.45
1966 2078 2.793288 TGATCATGACCATGCTGTGT 57.207 45.000 0.00 0.00 38.65 3.72
2001 2113 1.631405 TTCCATCCTTGCTGTTTGGG 58.369 50.000 0.00 0.00 0.00 4.12
2357 2474 9.640963 GTAACATGCTAAAACTCTCTTCTTCTA 57.359 33.333 0.00 0.00 0.00 2.10
2659 2962 1.162800 GCATGGAGGATGGAGAACGC 61.163 60.000 0.00 0.00 31.99 4.84
2719 3022 1.257743 CTCTGAAGGTCCGTTCCTCA 58.742 55.000 0.00 0.00 36.74 3.86
2720 3023 1.203523 CTCTGAAGGTCCGTTCCTCAG 59.796 57.143 12.02 12.02 36.74 3.35
2866 3169 3.931907 TTGATAGGAATGGACACCCTG 57.068 47.619 0.00 0.00 0.00 4.45
2932 3235 1.909700 TGGGACAATTTGTGAGGCTC 58.090 50.000 7.79 7.79 31.92 4.70
2989 3292 1.715993 GAAAGAGAGGCGGAGTGTTC 58.284 55.000 0.00 0.00 0.00 3.18
3033 3336 0.942962 CTCTCGAATGGATGCCTTGC 59.057 55.000 0.00 0.00 0.00 4.01
3130 3433 2.357034 TTCGACAAGTGCGAGGGC 60.357 61.111 0.00 0.00 39.14 5.19
3190 3493 0.036010 CGGTGAGGCCTCTGTTCATT 60.036 55.000 32.28 0.00 34.25 2.57
3232 3535 4.938226 GCTATGAAGCTAGGTGTCTTTGTT 59.062 41.667 0.00 0.00 45.85 2.83
3280 3583 2.493907 GAAAGGTCGCCAGCGTCTCT 62.494 60.000 12.32 5.45 40.74 3.10
3335 3638 2.401583 AGAAGTGCACAACAGTGTCA 57.598 45.000 21.04 0.00 35.07 3.58
3377 3680 0.697010 CGTCGCAAACATGCTTTTCG 59.303 50.000 0.00 0.00 0.00 3.46
3422 3725 5.277297 GGGTAAAACTGCAAAAGCAATGTTC 60.277 40.000 0.00 0.00 0.00 3.18
3425 3728 0.785979 CTGCAAAAGCAATGTTCGGC 59.214 50.000 0.00 0.00 0.00 5.54
3427 3730 1.616872 GCAAAAGCAATGTTCGGCGG 61.617 55.000 7.21 0.00 34.54 6.13
3429 3732 0.240945 AAAAGCAATGTTCGGCGGAG 59.759 50.000 7.21 0.00 34.54 4.63
3615 3934 4.623932 TGCAACTACATGAGGTTCTCTT 57.376 40.909 0.00 0.00 0.00 2.85
3626 3945 3.760151 TGAGGTTCTCTTTTCATGCATGG 59.240 43.478 25.97 10.42 0.00 3.66
3634 3953 3.444742 TCTTTTCATGCATGGCTAGTTGG 59.555 43.478 25.97 8.92 0.00 3.77
3635 3954 2.512692 TTCATGCATGGCTAGTTGGT 57.487 45.000 25.97 0.00 0.00 3.67
3636 3955 3.643199 TTCATGCATGGCTAGTTGGTA 57.357 42.857 25.97 0.00 0.00 3.25
3637 3956 3.198409 TCATGCATGGCTAGTTGGTAG 57.802 47.619 25.97 0.00 0.00 3.18
3638 3957 2.505407 TCATGCATGGCTAGTTGGTAGT 59.495 45.455 25.97 0.00 0.00 2.73
3639 3958 3.054434 TCATGCATGGCTAGTTGGTAGTT 60.054 43.478 25.97 0.00 0.00 2.24
3640 3959 2.710377 TGCATGGCTAGTTGGTAGTTG 58.290 47.619 0.00 0.00 0.00 3.16
3641 3960 2.017049 GCATGGCTAGTTGGTAGTTGG 58.983 52.381 0.00 0.00 0.00 3.77
3642 3961 2.618045 GCATGGCTAGTTGGTAGTTGGT 60.618 50.000 0.00 0.00 0.00 3.67
3643 3962 3.370103 GCATGGCTAGTTGGTAGTTGGTA 60.370 47.826 0.00 0.00 0.00 3.25
3644 3963 3.967332 TGGCTAGTTGGTAGTTGGTAC 57.033 47.619 0.00 0.00 0.00 3.34
3645 3964 3.513517 TGGCTAGTTGGTAGTTGGTACT 58.486 45.455 0.00 0.00 38.44 2.73
3646 3965 3.512724 TGGCTAGTTGGTAGTTGGTACTC 59.487 47.826 0.00 0.00 35.78 2.59
3647 3966 3.118847 GGCTAGTTGGTAGTTGGTACTCC 60.119 52.174 0.00 0.00 35.78 3.85
3648 3967 3.118847 GCTAGTTGGTAGTTGGTACTCCC 60.119 52.174 0.00 0.00 35.78 4.30
3649 3968 3.271153 AGTTGGTAGTTGGTACTCCCT 57.729 47.619 0.00 0.00 31.88 4.20
3650 3969 3.171528 AGTTGGTAGTTGGTACTCCCTC 58.828 50.000 0.00 0.00 31.88 4.30
3651 3970 2.235650 GTTGGTAGTTGGTACTCCCTCC 59.764 54.545 0.00 0.00 31.88 4.30
3652 3971 1.109609 GGTAGTTGGTACTCCCTCCG 58.890 60.000 0.00 0.00 35.78 4.63
3653 3972 1.618074 GGTAGTTGGTACTCCCTCCGT 60.618 57.143 0.00 0.00 35.78 4.69
3654 3973 2.174360 GTAGTTGGTACTCCCTCCGTT 58.826 52.381 0.00 0.00 35.78 4.44
3655 3974 1.264295 AGTTGGTACTCCCTCCGTTC 58.736 55.000 0.00 0.00 0.00 3.95
3656 3975 0.248565 GTTGGTACTCCCTCCGTTCC 59.751 60.000 0.00 0.00 0.00 3.62
3657 3976 0.115745 TTGGTACTCCCTCCGTTCCT 59.884 55.000 0.00 0.00 0.00 3.36
3658 3977 1.002069 TGGTACTCCCTCCGTTCCTA 58.998 55.000 0.00 0.00 0.00 2.94
3659 3978 1.358787 TGGTACTCCCTCCGTTCCTAA 59.641 52.381 0.00 0.00 0.00 2.69
3660 3979 2.225343 TGGTACTCCCTCCGTTCCTAAA 60.225 50.000 0.00 0.00 0.00 1.85
3661 3980 3.036819 GGTACTCCCTCCGTTCCTAAAT 58.963 50.000 0.00 0.00 0.00 1.40
3662 3981 4.218312 GGTACTCCCTCCGTTCCTAAATA 58.782 47.826 0.00 0.00 0.00 1.40
3663 3982 4.837298 GGTACTCCCTCCGTTCCTAAATAT 59.163 45.833 0.00 0.00 0.00 1.28
3664 3983 6.012745 GGTACTCCCTCCGTTCCTAAATATA 58.987 44.000 0.00 0.00 0.00 0.86
3665 3984 6.494835 GGTACTCCCTCCGTTCCTAAATATAA 59.505 42.308 0.00 0.00 0.00 0.98
3666 3985 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3667 3986 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3668 3987 6.614496 ACTCCCTCCGTTCCTAAATATAAGTT 59.386 38.462 0.00 0.00 0.00 2.66
3669 3988 7.126879 ACTCCCTCCGTTCCTAAATATAAGTTT 59.873 37.037 0.00 0.00 0.00 2.66
3670 3989 7.864770 TCCCTCCGTTCCTAAATATAAGTTTT 58.135 34.615 0.00 0.00 0.00 2.43
3671 3990 8.330993 TCCCTCCGTTCCTAAATATAAGTTTTT 58.669 33.333 0.00 0.00 0.00 1.94
3754 4073 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
3755 4074 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
3756 4075 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
3784 4115 6.992715 AGTTTACAGCTACTTCATGTTTCTGT 59.007 34.615 0.00 0.00 40.48 3.41
3796 4127 8.403236 ACTTCATGTTTCTGTAAACTTACCAAC 58.597 33.333 0.00 0.13 44.44 3.77
3899 4259 9.838339 ATCTAAACCTTTCAGAATACAGGTATG 57.162 33.333 5.57 1.06 38.80 2.39
3932 4294 8.920509 AAAGTTGTATACACCAAAAACTGAAC 57.079 30.769 4.68 0.00 0.00 3.18
3935 4297 7.227910 AGTTGTATACACCAAAAACTGAACGAT 59.772 33.333 4.68 0.00 0.00 3.73
3988 4350 3.944015 CCTCCATTGCAAAACCAAAACAA 59.056 39.130 1.71 0.00 0.00 2.83
4033 4395 5.820423 TCAGTAACAAATACACACAGCAACT 59.180 36.000 0.00 0.00 36.94 3.16
4055 4417 3.342377 GGAGCCTTTCTCAGCTACTTT 57.658 47.619 0.00 0.00 43.70 2.66
4073 4435 7.345914 AGCTACTTTCTGTTTCCAGTATCCTAT 59.654 37.037 0.00 0.00 39.82 2.57
4074 4436 8.639761 GCTACTTTCTGTTTCCAGTATCCTATA 58.360 37.037 0.00 0.00 39.82 1.31
4102 4464 2.373169 TGAAGAACAGTGGATGCTTCCT 59.627 45.455 18.67 0.00 43.07 3.36
4129 4491 1.219393 CGAAGGGAAGCTCCAGGAC 59.781 63.158 0.00 0.00 38.64 3.85
4141 4504 2.383855 CTCCAGGACTCCCACTAGAAG 58.616 57.143 0.00 0.00 33.88 2.85
4168 4531 2.507324 GAGCCTTGCGTCGAGGAC 60.507 66.667 9.75 0.95 37.20 3.85
4322 4685 5.362556 AACCTGCATATCGATGTAAATGC 57.637 39.130 19.44 19.44 43.92 3.56
4324 4687 3.752747 CCTGCATATCGATGTAAATGCCA 59.247 43.478 22.05 12.61 43.19 4.92
4326 4689 5.106038 CCTGCATATCGATGTAAATGCCATT 60.106 40.000 22.05 0.00 43.19 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 9.200817 ACTGTCAATATGGTATAATTTTTGCCT 57.799 29.630 0.00 0.00 0.00 4.75
56 57 9.816354 AACTGTCAATATGGTATAATTTTTGCC 57.184 29.630 0.00 0.00 0.00 4.52
68 69 9.499479 GATCTATTCATCAACTGTCAATATGGT 57.501 33.333 0.00 0.00 0.00 3.55
69 70 8.654215 CGATCTATTCATCAACTGTCAATATGG 58.346 37.037 0.00 0.00 0.00 2.74
70 71 8.654215 CCGATCTATTCATCAACTGTCAATATG 58.346 37.037 0.00 0.00 0.00 1.78
71 72 8.588472 TCCGATCTATTCATCAACTGTCAATAT 58.412 33.333 0.00 0.00 0.00 1.28
72 73 7.951591 TCCGATCTATTCATCAACTGTCAATA 58.048 34.615 0.00 0.00 0.00 1.90
73 74 6.820335 TCCGATCTATTCATCAACTGTCAAT 58.180 36.000 0.00 0.00 0.00 2.57
74 75 6.220726 TCCGATCTATTCATCAACTGTCAA 57.779 37.500 0.00 0.00 0.00 3.18
75 76 5.852282 TCCGATCTATTCATCAACTGTCA 57.148 39.130 0.00 0.00 0.00 3.58
76 77 6.276847 ACTTCCGATCTATTCATCAACTGTC 58.723 40.000 0.00 0.00 0.00 3.51
77 78 6.227298 ACTTCCGATCTATTCATCAACTGT 57.773 37.500 0.00 0.00 0.00 3.55
78 79 8.824159 AATACTTCCGATCTATTCATCAACTG 57.176 34.615 0.00 0.00 0.00 3.16
79 80 9.482627 GAAATACTTCCGATCTATTCATCAACT 57.517 33.333 0.00 0.00 0.00 3.16
80 81 8.713271 GGAAATACTTCCGATCTATTCATCAAC 58.287 37.037 0.00 0.00 41.89 3.18
81 82 8.833231 GGAAATACTTCCGATCTATTCATCAA 57.167 34.615 0.00 0.00 41.89 2.57
96 97 4.767409 GGCATGGATTAGGGGAAATACTTC 59.233 45.833 0.00 0.00 0.00 3.01
97 98 4.169856 TGGCATGGATTAGGGGAAATACTT 59.830 41.667 0.00 0.00 0.00 2.24
98 99 3.726859 TGGCATGGATTAGGGGAAATACT 59.273 43.478 0.00 0.00 0.00 2.12
99 100 4.112634 TGGCATGGATTAGGGGAAATAC 57.887 45.455 0.00 0.00 0.00 1.89
100 101 4.676109 CATGGCATGGATTAGGGGAAATA 58.324 43.478 19.80 0.00 0.00 1.40
101 102 3.513517 CATGGCATGGATTAGGGGAAAT 58.486 45.455 19.80 0.00 0.00 2.17
102 103 2.961510 CATGGCATGGATTAGGGGAAA 58.038 47.619 19.80 0.00 0.00 3.13
103 104 1.481055 GCATGGCATGGATTAGGGGAA 60.481 52.381 27.48 0.00 0.00 3.97
104 105 0.112995 GCATGGCATGGATTAGGGGA 59.887 55.000 27.48 0.00 0.00 4.81
105 106 0.178955 TGCATGGCATGGATTAGGGG 60.179 55.000 27.48 0.36 31.71 4.79
106 107 1.707106 TTGCATGGCATGGATTAGGG 58.293 50.000 27.48 1.12 38.76 3.53
107 108 3.823281 TTTTGCATGGCATGGATTAGG 57.177 42.857 27.48 1.89 38.76 2.69
336 346 2.282462 CAGGAGGTTGGGTGGTGC 60.282 66.667 0.00 0.00 0.00 5.01
337 347 1.228245 CACAGGAGGTTGGGTGGTG 60.228 63.158 0.00 0.00 0.00 4.17
338 348 3.133365 GCACAGGAGGTTGGGTGGT 62.133 63.158 0.00 0.00 0.00 4.16
443 476 6.861065 CTTGCTTGGTCAAGAAAGTACTAA 57.139 37.500 18.69 0.00 45.08 2.24
456 489 0.109132 CGAATTGGGCTTGCTTGGTC 60.109 55.000 0.00 0.00 0.00 4.02
466 499 3.810896 GGTGTCGGCGAATTGGGC 61.811 66.667 12.92 3.77 0.00 5.36
558 596 5.250313 AGAATCTTGAATCCACAGAAGGAGT 59.750 40.000 0.00 0.00 41.90 3.85
559 597 5.743117 AGAATCTTGAATCCACAGAAGGAG 58.257 41.667 0.00 0.00 41.90 3.69
560 598 5.338708 GGAGAATCTTGAATCCACAGAAGGA 60.339 44.000 0.00 0.00 37.41 3.36
561 599 4.880696 GGAGAATCTTGAATCCACAGAAGG 59.119 45.833 0.00 0.00 33.73 3.46
713 756 2.594592 GCACAGGTCAACGGCCTT 60.595 61.111 0.00 0.00 33.31 4.35
842 906 4.887748 AGATCCCTGCTATGACATTTACG 58.112 43.478 0.00 0.00 0.00 3.18
853 917 5.248477 ACAACTAGAAACAAGATCCCTGCTA 59.752 40.000 0.00 0.00 0.00 3.49
872 936 1.544314 GCAGCTCAAGGGAGAACAACT 60.544 52.381 0.00 0.00 44.26 3.16
920 984 5.777732 AGCTGGGAGGTTATATTCTCACTAG 59.222 44.000 6.64 0.00 34.69 2.57
929 993 7.394144 AATCTTGTAAGCTGGGAGGTTATAT 57.606 36.000 0.00 0.00 39.91 0.86
932 996 5.514500 AAATCTTGTAAGCTGGGAGGTTA 57.486 39.130 0.00 0.00 37.16 2.85
935 999 3.445096 CCAAAATCTTGTAAGCTGGGAGG 59.555 47.826 0.00 0.00 0.00 4.30
1194 1265 0.739813 GGTGGTGTGTCGCTATCCAC 60.740 60.000 13.53 13.53 45.17 4.02
1206 1277 1.908793 CTCCGTCCTCTGGTGGTGT 60.909 63.158 0.00 0.00 0.00 4.16
1484 1564 5.363868 ACGGATCCTTCATAGAACTTCATCA 59.636 40.000 10.75 0.00 0.00 3.07
1494 1574 0.603569 CCCCGACGGATCCTTCATAG 59.396 60.000 17.49 6.09 0.00 2.23
1606 1687 3.551890 CCGACGAACATTCAGTATTCAGG 59.448 47.826 0.00 0.00 0.00 3.86
1750 1844 4.811557 GCCTGCACTAAGGTGATAAACTAG 59.188 45.833 0.00 0.00 45.61 2.57
1775 1869 7.600065 CATTCTCAAAAGTCAACAGGATCATT 58.400 34.615 0.00 0.00 0.00 2.57
1778 1872 5.182760 AGCATTCTCAAAAGTCAACAGGATC 59.817 40.000 0.00 0.00 0.00 3.36
1875 1987 1.835267 TAGGTCCAGCACACCACGT 60.835 57.895 0.00 0.00 36.23 4.49
1950 2062 1.536940 CCAACACAGCATGGTCATGA 58.463 50.000 14.43 0.00 43.62 3.07
1966 2078 1.438743 TGGAATCCCAAAATCCCCCAA 59.561 47.619 0.00 0.00 40.09 4.12
2001 2113 4.043200 GGGTTTGGCAGCGACAGC 62.043 66.667 0.00 0.00 45.58 4.40
2409 2527 9.374711 AGAAAACAAATTTAGGGAAGAACCATA 57.625 29.630 0.00 0.00 41.20 2.74
2659 2962 5.749620 ACTCGTACAAGAATGTAGCTATCG 58.250 41.667 0.00 0.00 42.54 2.92
2702 3005 0.390472 GCTGAGGAACGGACCTTCAG 60.390 60.000 16.69 16.69 40.73 3.02
2719 3022 1.915769 GGTCACCCTCTCCACTGCT 60.916 63.158 0.00 0.00 0.00 4.24
2720 3023 0.614979 TAGGTCACCCTCTCCACTGC 60.615 60.000 0.00 0.00 41.45 4.40
2866 3169 4.352298 AGATCTGAATATTCCCCCTTCCAC 59.648 45.833 12.90 0.00 0.00 4.02
2912 3215 2.225091 TGAGCCTCACAAATTGTCCCAT 60.225 45.455 0.00 0.00 0.00 4.00
2932 3235 2.814336 GGGGCTTGAAGTGTTAGTTCTG 59.186 50.000 0.00 0.00 0.00 3.02
2994 3297 5.449107 GAGTATCTGTGAAATACGGCCTA 57.551 43.478 0.00 0.00 35.26 3.93
3033 3336 0.178992 TTTGCCAGGGAAGGTCACAG 60.179 55.000 0.00 0.00 0.00 3.66
3130 3433 3.123621 GGTGCTCATACTTCTTCACAACG 59.876 47.826 0.00 0.00 0.00 4.10
3190 3493 4.301072 AGCAGTAAAGAAACCTATGGCA 57.699 40.909 0.00 0.00 0.00 4.92
3232 3535 0.322816 GCCTTGTGATGCTCTTCCCA 60.323 55.000 0.00 0.00 0.00 4.37
3280 3583 1.383109 AGGATCGGCACCCTGATCA 60.383 57.895 12.91 0.00 42.19 2.92
3425 3728 3.075148 TCGAGATATACTTCAGGCTCCG 58.925 50.000 0.00 0.00 0.00 4.63
3427 3730 5.888691 TGATCGAGATATACTTCAGGCTC 57.111 43.478 0.00 0.00 0.00 4.70
3429 3732 4.803088 GCATGATCGAGATATACTTCAGGC 59.197 45.833 0.00 2.78 34.94 4.85
3542 3853 1.303888 CAGTTGGGCTCAGGCATGT 60.304 57.895 0.00 0.00 40.87 3.21
3615 3934 2.806434 ACCAACTAGCCATGCATGAAA 58.194 42.857 28.31 11.36 0.00 2.69
3626 3945 4.120792 GGAGTACCAACTACCAACTAGC 57.879 50.000 0.00 0.00 35.56 3.42
3634 3953 1.844687 ACGGAGGGAGTACCAACTAC 58.155 55.000 0.00 0.00 43.89 2.73
3635 3954 2.450476 GAACGGAGGGAGTACCAACTA 58.550 52.381 0.00 0.00 43.89 2.24
3636 3955 1.264295 GAACGGAGGGAGTACCAACT 58.736 55.000 0.00 0.00 43.89 3.16
3637 3956 0.248565 GGAACGGAGGGAGTACCAAC 59.751 60.000 0.00 0.00 43.89 3.77
3638 3957 0.115745 AGGAACGGAGGGAGTACCAA 59.884 55.000 0.00 0.00 43.89 3.67
3639 3958 1.002069 TAGGAACGGAGGGAGTACCA 58.998 55.000 0.00 0.00 43.89 3.25
3640 3959 2.149973 TTAGGAACGGAGGGAGTACC 57.850 55.000 0.00 0.00 40.67 3.34
3641 3960 7.232330 ACTTATATTTAGGAACGGAGGGAGTAC 59.768 40.741 0.00 0.00 0.00 2.73
3642 3961 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
3643 3962 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
3644 3963 6.667558 ACTTATATTTAGGAACGGAGGGAG 57.332 41.667 0.00 0.00 0.00 4.30
3645 3964 7.441903 AAACTTATATTTAGGAACGGAGGGA 57.558 36.000 0.00 0.00 0.00 4.20
3646 3965 8.515695 AAAAACTTATATTTAGGAACGGAGGG 57.484 34.615 0.00 0.00 0.00 4.30
3728 4047 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
3729 4048 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
3730 4049 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
3731 4050 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
3732 4051 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
3733 4052 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
3734 4053 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3735 4054 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3736 4055 7.300658 ACTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
3737 4056 6.856757 ACTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
3738 4057 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
3739 4058 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
3740 4059 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
3741 4060 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
3742 4061 3.463048 AACTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
3743 4062 3.463048 AAACTACTCCCTCCGTTCCTA 57.537 47.619 0.00 0.00 0.00 2.94
3744 4063 2.322339 AAACTACTCCCTCCGTTCCT 57.678 50.000 0.00 0.00 0.00 3.36
3745 4064 2.827921 TGTAAACTACTCCCTCCGTTCC 59.172 50.000 0.00 0.00 0.00 3.62
3746 4065 3.675502 GCTGTAAACTACTCCCTCCGTTC 60.676 52.174 0.00 0.00 0.00 3.95
3747 4066 2.233186 GCTGTAAACTACTCCCTCCGTT 59.767 50.000 0.00 0.00 0.00 4.44
3748 4067 1.823610 GCTGTAAACTACTCCCTCCGT 59.176 52.381 0.00 0.00 0.00 4.69
3749 4068 2.100989 AGCTGTAAACTACTCCCTCCG 58.899 52.381 0.00 0.00 0.00 4.63
3750 4069 4.279982 AGTAGCTGTAAACTACTCCCTCC 58.720 47.826 0.00 0.00 45.65 4.30
3784 4115 7.562454 CTTCTTGTGAAGGTTGGTAAGTTTA 57.438 36.000 0.00 0.00 44.33 2.01
3859 4206 9.614792 GAAAGGTTTAGATTGTACTACCATGAT 57.385 33.333 0.00 0.00 0.00 2.45
3860 4207 8.598916 TGAAAGGTTTAGATTGTACTACCATGA 58.401 33.333 0.00 0.00 0.00 3.07
3861 4208 8.786826 TGAAAGGTTTAGATTGTACTACCATG 57.213 34.615 0.00 0.00 0.00 3.66
3862 4209 8.822805 TCTGAAAGGTTTAGATTGTACTACCAT 58.177 33.333 0.00 0.00 0.00 3.55
3864 4211 9.668497 ATTCTGAAAGGTTTAGATTGTACTACC 57.332 33.333 0.00 0.00 0.00 3.18
3899 4259 6.978343 TGGTGTATACAACTTTCAGCATAC 57.022 37.500 21.18 0.00 33.92 2.39
3904 4266 8.402472 TCAGTTTTTGGTGTATACAACTTTCAG 58.598 33.333 21.18 6.31 33.92 3.02
3932 4294 4.541973 TCCATTCCCATCTCATGTATCG 57.458 45.455 0.00 0.00 0.00 2.92
3935 4297 4.225942 GCCTATCCATTCCCATCTCATGTA 59.774 45.833 0.00 0.00 0.00 2.29
3988 4350 7.555965 ACTGAAAATGCAACTTTTAGAGGTTT 58.444 30.769 17.85 0.00 0.00 3.27
4033 4395 3.390175 AGTAGCTGAGAAAGGCTCCTA 57.610 47.619 0.00 0.00 43.26 2.94
4102 4464 3.385111 GGAGCTTCCCTTCGAGAATAGAA 59.615 47.826 0.00 0.00 0.00 2.10
4129 4491 1.403679 CAGCTCGACTTCTAGTGGGAG 59.596 57.143 0.00 0.00 31.91 4.30
4141 4504 3.184683 CAAGGCTCGCAGCTCGAC 61.185 66.667 7.85 3.16 43.16 4.20
4168 4531 1.078918 TGGATCAGGCAGTTGCTCG 60.079 57.895 3.88 0.00 41.70 5.03
4322 4685 4.202202 TGTGCCCTTCTGTTTTAACAATGG 60.202 41.667 0.00 0.33 38.66 3.16
4324 4687 5.105146 TGTTGTGCCCTTCTGTTTTAACAAT 60.105 36.000 0.00 0.00 38.66 2.71
4326 4689 3.764434 TGTTGTGCCCTTCTGTTTTAACA 59.236 39.130 0.00 0.00 37.37 2.41


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

AutoCloner maintained by Alex Coulton.