Multiple sequence alignment - TraesCS7B01G218600

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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 TraesCS7B01G218600 chr7B 100.000 4615 0 0 1 4615 405972492 405967878 0.000000e+00 8523.0
1 TraesCS7B01G218600 chr7B 90.568 3117 147 70 1563 4612 427885582 427882546 0.000000e+00 3991.0
2 TraesCS7B01G218600 chr7B 95.132 493 16 1 975 1467 427886228 427885744 0.000000e+00 771.0
3 TraesCS7B01G218600 chr7B 85.833 120 5 7 1 120 427886326 427886219 2.920000e-22 117.0
4 TraesCS7B01G218600 chr7B 98.182 55 1 0 4296 4350 405968139 405968085 3.800000e-16 97.1
5 TraesCS7B01G218600 chr7B 98.182 55 1 0 4354 4408 405968197 405968143 3.800000e-16 97.1
6 TraesCS7B01G218600 chr7B 92.857 56 4 0 1466 1521 427885703 427885648 1.060000e-11 82.4
7 TraesCS7B01G218600 chr7A 91.797 2682 137 24 975 3594 475208144 475205484 0.000000e+00 3657.0
8 TraesCS7B01G218600 chr7A 89.120 864 85 9 126 985 703810505 703809647 0.000000e+00 1066.0
9 TraesCS7B01G218600 chr7A 89.606 279 12 9 4350 4612 475204824 475204547 5.720000e-89 339.0
10 TraesCS7B01G218600 chr7A 82.031 128 7 6 3763 3874 475205386 475205259 1.370000e-15 95.3
11 TraesCS7B01G218600 chr7A 93.750 48 3 0 2045 2092 572872156 572872109 6.400000e-09 73.1
12 TraesCS7B01G218600 chr7D 95.612 1504 58 7 2093 3592 413545576 413544077 0.000000e+00 2405.0
13 TraesCS7B01G218600 chr7D 90.714 1163 46 17 975 2093 413546787 413545643 0.000000e+00 1493.0
14 TraesCS7B01G218600 chr7D 90.168 834 78 4 146 977 580496648 580495817 0.000000e+00 1083.0
15 TraesCS7B01G218600 chr7D 86.842 418 14 21 4215 4615 413535617 413535224 3.300000e-116 429.0
16 TraesCS7B01G218600 chr7D 77.098 441 31 32 3763 4159 413543984 413543570 1.690000e-44 191.0
17 TraesCS7B01G218600 chr7D 90.164 122 9 3 1 120 413547007 413546887 6.180000e-34 156.0
18 TraesCS7B01G218600 chr2B 93.373 830 49 3 146 974 291374227 291373403 0.000000e+00 1223.0
19 TraesCS7B01G218600 chr2B 91.215 831 69 3 146 974 799436608 799435780 0.000000e+00 1127.0
20 TraesCS7B01G218600 chr3D 92.437 833 60 3 143 974 257649781 257650611 0.000000e+00 1186.0
21 TraesCS7B01G218600 chr3D 90.767 834 69 6 141 971 613317209 613316381 0.000000e+00 1107.0
22 TraesCS7B01G218600 chr6B 91.576 831 66 3 146 974 153659406 153658578 0.000000e+00 1144.0
23 TraesCS7B01G218600 chr6B 91.576 831 62 7 146 974 153740678 153739854 0.000000e+00 1140.0
24 TraesCS7B01G218600 chr6B 95.652 46 2 0 2049 2094 678773715 678773760 1.780000e-09 75.0
25 TraesCS7B01G218600 chr4B 90.843 830 71 5 146 974 173513292 173512467 0.000000e+00 1107.0
26 TraesCS7B01G218600 chr5B 95.918 49 2 0 2048 2096 176590631 176590583 3.830000e-11 80.5
27 TraesCS7B01G218600 chr5D 95.652 46 2 0 2048 2093 164606039 164605994 1.780000e-09 75.0
28 TraesCS7B01G218600 chr3A 94.000 50 2 1 2047 2096 733410255 733410303 1.780000e-09 75.0
29 TraesCS7B01G218600 chr2D 95.556 45 2 0 2048 2092 371786912 371786868 6.400000e-09 73.1
30 TraesCS7B01G218600 chr3B 100.000 28 0 0 1466 1493 23942508 23942535 8.000000e-03 52.8


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 TraesCS7B01G218600 chr7B 405967878 405972492 4614 True 8523.000000 8523 100.000000 1 4615 1 chr7B.!!$R1 4614
1 TraesCS7B01G218600 chr7B 427882546 427886326 3780 True 1240.350000 3991 91.097500 1 4612 4 chr7B.!!$R3 4611
2 TraesCS7B01G218600 chr7A 475204547 475208144 3597 True 1363.766667 3657 87.811333 975 4612 3 chr7A.!!$R3 3637
3 TraesCS7B01G218600 chr7A 703809647 703810505 858 True 1066.000000 1066 89.120000 126 985 1 chr7A.!!$R2 859
4 TraesCS7B01G218600 chr7D 580495817 580496648 831 True 1083.000000 1083 90.168000 146 977 1 chr7D.!!$R2 831
5 TraesCS7B01G218600 chr7D 413543570 413547007 3437 True 1061.250000 2405 88.397000 1 4159 4 chr7D.!!$R3 4158
6 TraesCS7B01G218600 chr2B 291373403 291374227 824 True 1223.000000 1223 93.373000 146 974 1 chr2B.!!$R1 828
7 TraesCS7B01G218600 chr2B 799435780 799436608 828 True 1127.000000 1127 91.215000 146 974 1 chr2B.!!$R2 828
8 TraesCS7B01G218600 chr3D 257649781 257650611 830 False 1186.000000 1186 92.437000 143 974 1 chr3D.!!$F1 831
9 TraesCS7B01G218600 chr3D 613316381 613317209 828 True 1107.000000 1107 90.767000 141 971 1 chr3D.!!$R1 830
10 TraesCS7B01G218600 chr6B 153658578 153659406 828 True 1144.000000 1144 91.576000 146 974 1 chr6B.!!$R1 828
11 TraesCS7B01G218600 chr6B 153739854 153740678 824 True 1140.000000 1140 91.576000 146 974 1 chr6B.!!$R2 828
12 TraesCS7B01G218600 chr4B 173512467 173513292 825 True 1107.000000 1107 90.843000 146 974 1 chr4B.!!$R1 828

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
960 1083 0.107410 AACATGTCACACGTGTGGGT 60.107 50.000 39.88 29.82 46.74 4.51 F
1511 1710 0.038251 GTCCACACGATCTGCTGTGA 60.038 55.000 13.72 0.00 40.28 3.58 F
1515 1714 0.528017 ACACGATCTGCTGTGACGAT 59.472 50.000 5.60 0.00 39.38 3.73 F
2024 2267 1.152649 CTTGCCTGGGGGAGGATAAT 58.847 55.000 0.00 0.00 46.33 1.28 F
3176 3499 1.335142 GCACGACTTCTTCAGAGACGT 60.335 52.381 0.00 0.00 37.12 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2053 2296 3.267483 CGACACTTATTTTGGGACGGAT 58.733 45.455 0.00 0.00 0.00 4.18 R
3176 3499 1.826054 CCCACCAAACCGAGCAACA 60.826 57.895 0.00 0.00 0.00 3.33 R
3357 3680 3.240134 GACCGGGCTTGCAGAGACA 62.240 63.158 6.32 0.00 33.80 3.41 R
3549 3877 0.238817 GAGCGGATCGAACGATAGCT 59.761 55.000 26.44 26.44 44.99 3.32 R
4086 4609 0.251742 CACCCCTCCTGCAAATCCAA 60.252 55.000 0.00 0.00 0.00 3.53 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
25 26 5.571285 ACTCCCAATTAAGAGAAGTTTCCC 58.429 41.667 10.13 0.00 34.13 3.97
59 60 6.759497 AAAAGTATCCATACAAAGTGCTCC 57.241 37.500 0.00 0.00 35.74 4.70
66 67 5.185454 TCCATACAAAGTGCTCCATACAAG 58.815 41.667 0.00 0.00 0.00 3.16
184 297 0.182775 GTGTGGTGGGAGTGAAACCT 59.817 55.000 0.00 0.00 37.80 3.50
192 305 0.251341 GGAGTGAAACCTGCCCACAT 60.251 55.000 0.00 0.00 37.80 3.21
214 327 2.354704 GCCCTATAACACACAGACTGCA 60.355 50.000 1.25 0.00 0.00 4.41
216 329 4.517285 CCCTATAACACACAGACTGCATT 58.483 43.478 1.25 0.00 0.00 3.56
315 430 3.188460 CCGATTGAACATCCGTTTTCACT 59.812 43.478 0.00 0.00 34.75 3.41
324 439 9.226606 TGAACATCCGTTTTCACTATTAAATCT 57.773 29.630 0.00 0.00 34.75 2.40
414 532 4.525996 AGTTGCCATGTCTATTGCACATA 58.474 39.130 0.00 0.00 34.99 2.29
445 563 2.286772 GGTGTTTACACTGAAGTTGCCG 60.287 50.000 12.32 0.00 45.73 5.69
541 660 7.902920 ATTAGACTTGCCATGAACCATAAAT 57.097 32.000 0.00 0.00 0.00 1.40
583 702 3.684305 GCACTTAAAATTGCCATGGTTCC 59.316 43.478 14.67 0.00 32.21 3.62
716 837 8.255206 CCCTATGACAACTACAGTGTAAACATA 58.745 37.037 4.21 8.66 0.00 2.29
876 999 7.851387 TTTAAGCCGAAAACCAAAAAGATTT 57.149 28.000 0.00 0.00 0.00 2.17
888 1011 6.789262 ACCAAAAAGATTTCTGCTGATATCG 58.211 36.000 14.99 5.91 36.31 2.92
920 1043 7.933577 TCACATGTGGCAAAATAAATGGTAAAA 59.066 29.630 25.16 0.00 0.00 1.52
921 1044 8.562892 CACATGTGGCAAAATAAATGGTAAAAA 58.437 29.630 18.51 0.00 0.00 1.94
960 1083 0.107410 AACATGTCACACGTGTGGGT 60.107 50.000 39.88 29.82 46.74 4.51
1107 1255 2.917227 TCACGCCTCAGTGCCTCA 60.917 61.111 0.00 0.00 41.61 3.86
1108 1256 2.740055 CACGCCTCAGTGCCTCAC 60.740 66.667 0.00 0.00 35.17 3.51
1109 1257 2.919856 ACGCCTCAGTGCCTCACT 60.920 61.111 0.00 0.00 46.51 3.41
1348 1504 7.646314 CAAGGTGATTTCCTATGCTTGAATAG 58.354 38.462 0.00 0.00 36.74 1.73
1511 1710 0.038251 GTCCACACGATCTGCTGTGA 60.038 55.000 13.72 0.00 40.28 3.58
1515 1714 0.528017 ACACGATCTGCTGTGACGAT 59.472 50.000 5.60 0.00 39.38 3.73
1549 1771 7.556275 AGATTGTTTTCTCTCTGTTTGTTGGTA 59.444 33.333 0.00 0.00 0.00 3.25
1634 1858 4.628074 ACTACGAACTAGAGCAAGCAAAA 58.372 39.130 0.00 0.00 0.00 2.44
1635 1859 3.879932 ACGAACTAGAGCAAGCAAAAC 57.120 42.857 0.00 0.00 0.00 2.43
1637 1861 3.002348 ACGAACTAGAGCAAGCAAAACAC 59.998 43.478 0.00 0.00 0.00 3.32
1872 2107 7.356680 AGTGATTCATTGATTCCCCTTCATAA 58.643 34.615 6.19 0.00 0.00 1.90
1965 2207 6.130298 TGAATTATAGTTCGGCCACAATTG 57.870 37.500 2.24 3.24 0.00 2.32
2024 2267 1.152649 CTTGCCTGGGGGAGGATAAT 58.847 55.000 0.00 0.00 46.33 1.28
2025 2268 1.500736 CTTGCCTGGGGGAGGATAATT 59.499 52.381 0.00 0.00 46.33 1.40
2026 2269 1.619298 TGCCTGGGGGAGGATAATTT 58.381 50.000 0.00 0.00 46.33 1.82
2027 2270 1.936631 TGCCTGGGGGAGGATAATTTT 59.063 47.619 0.00 0.00 46.33 1.82
2028 2271 2.317594 TGCCTGGGGGAGGATAATTTTT 59.682 45.455 0.00 0.00 46.33 1.94
2188 2498 6.063496 ACCCTCTCCCTCTTATTTTGTAAC 57.937 41.667 0.00 0.00 0.00 2.50
2349 2660 7.859325 ATGCTGTTTCGTAAGGTAATATGTT 57.141 32.000 0.00 0.00 38.47 2.71
2350 2661 7.067532 TGCTGTTTCGTAAGGTAATATGTTG 57.932 36.000 0.00 0.00 38.47 3.33
2351 2662 5.963586 GCTGTTTCGTAAGGTAATATGTTGC 59.036 40.000 0.00 0.00 38.47 4.17
2352 2663 6.402766 GCTGTTTCGTAAGGTAATATGTTGCA 60.403 38.462 0.00 0.00 38.47 4.08
2353 2664 7.618502 TGTTTCGTAAGGTAATATGTTGCAT 57.381 32.000 0.00 0.00 38.47 3.96
2354 2665 8.719560 TGTTTCGTAAGGTAATATGTTGCATA 57.280 30.769 0.00 0.00 38.47 3.14
2355 2666 9.332502 TGTTTCGTAAGGTAATATGTTGCATAT 57.667 29.630 0.00 0.00 38.47 1.78
2700 3023 8.515414 CAGTGAATATAGTTGATGAGGACGATA 58.485 37.037 0.00 0.00 0.00 2.92
2785 3108 4.907457 CCCTCAAGTTGGCACACT 57.093 55.556 2.34 0.00 39.29 3.55
2934 3257 2.838736 TCAAGAAAGCTCGAACTTGCT 58.161 42.857 3.03 3.03 37.11 3.91
2944 3267 3.248602 GCTCGAACTTGCTCTTCTGAAAA 59.751 43.478 0.00 0.00 0.00 2.29
3176 3499 1.335142 GCACGACTTCTTCAGAGACGT 60.335 52.381 0.00 0.00 37.12 4.34
3296 3619 3.396276 TGGTCTCCCTTACAATGAACCAA 59.604 43.478 0.00 0.00 0.00 3.67
3357 3680 8.854117 GGAGAAAATTAATCCATGCTATTGACT 58.146 33.333 0.00 0.00 33.08 3.41
3564 3893 7.409465 AAATTAGAAAGCTATCGTTCGATCC 57.591 36.000 10.97 4.66 36.12 3.36
3578 3907 3.793797 TCGATCCGCTCTGTGAAATAA 57.206 42.857 0.00 0.00 0.00 1.40
3659 3994 2.385361 GTAAACGTCGACGCTGCG 59.615 61.111 35.92 21.91 44.43 5.18
3900 4258 2.096980 CCTACAATCGTCGAGCTGTACA 59.903 50.000 13.29 0.00 0.00 2.90
3903 4261 2.120232 CAATCGTCGAGCTGTACATCC 58.880 52.381 0.00 0.00 0.00 3.51
3970 4443 2.178764 AGGGGTCTCTCTGCTCATATCA 59.821 50.000 0.00 0.00 0.00 2.15
3993 4479 3.175594 ACCGAGAACCCTACAATTGGTA 58.824 45.455 10.83 0.00 33.52 3.25
3994 4480 3.778629 ACCGAGAACCCTACAATTGGTAT 59.221 43.478 10.83 0.00 33.52 2.73
3995 4481 4.141779 ACCGAGAACCCTACAATTGGTATC 60.142 45.833 10.83 0.00 33.52 2.24
3996 4482 4.101119 CCGAGAACCCTACAATTGGTATCT 59.899 45.833 10.83 4.50 33.52 1.98
3997 4483 5.303589 CCGAGAACCCTACAATTGGTATCTA 59.696 44.000 10.83 0.00 33.52 1.98
3998 4484 6.448006 CGAGAACCCTACAATTGGTATCTAG 58.552 44.000 10.83 1.89 33.52 2.43
3999 4485 6.264744 CGAGAACCCTACAATTGGTATCTAGA 59.735 42.308 10.83 0.00 33.52 2.43
4027 4550 2.097680 TCCGACCGTAAAATTCCACC 57.902 50.000 0.00 0.00 0.00 4.61
4071 4594 7.595502 TGTTTCGGTAATATTTCGTGCAAAATT 59.404 29.630 1.86 0.00 31.50 1.82
4086 4609 5.414765 GTGCAAAATTACTAGCTAGGTTGGT 59.585 40.000 24.35 6.75 0.00 3.67
4095 4618 2.171003 AGCTAGGTTGGTTGGATTTGC 58.829 47.619 0.00 0.00 0.00 3.68
4103 4626 0.972471 GGTTGGATTTGCAGGAGGGG 60.972 60.000 0.00 0.00 0.00 4.79
4125 4650 2.370445 ATAGCACGGCAAGCCCTCT 61.370 57.895 5.34 2.86 0.00 3.69
4163 4701 3.136123 CACCGCAATGGGGCAGAG 61.136 66.667 16.73 0.43 44.64 3.35
4195 4733 3.118454 CGGTGCCGCTCACGAAAT 61.118 61.111 0.00 0.00 46.56 2.17
4196 4734 1.807981 CGGTGCCGCTCACGAAATA 60.808 57.895 0.00 0.00 46.56 1.40
4197 4735 1.713830 GGTGCCGCTCACGAAATAC 59.286 57.895 0.00 0.00 46.56 1.89
4198 4736 2.020836 GGTGCCGCTCACGAAATACG 62.021 60.000 0.00 0.00 46.56 3.06
4213 4751 6.021055 CGAAATACGTACAATTCAGTGGAG 57.979 41.667 0.00 0.00 37.22 3.86
4290 4828 4.704833 GCTGAGCGCCTTGTCCCA 62.705 66.667 2.29 0.00 0.00 4.37
4291 4829 2.270205 CTGAGCGCCTTGTCCCAT 59.730 61.111 2.29 0.00 0.00 4.00
4292 4830 2.046023 TGAGCGCCTTGTCCCATG 60.046 61.111 2.29 0.00 0.00 3.66
4294 4832 3.329542 GAGCGCCTTGTCCCATGGA 62.330 63.158 15.22 0.00 31.33 3.41
4296 4834 2.989639 CGCCTTGTCCCATGGAGA 59.010 61.111 15.22 6.02 32.06 3.71
4297 4835 1.450312 CGCCTTGTCCCATGGAGAC 60.450 63.158 15.22 18.62 32.06 3.36
4300 4838 1.264749 CCTTGTCCCATGGAGACCGA 61.265 60.000 22.90 14.35 33.09 4.69
4302 4840 1.884075 TTGTCCCATGGAGACCGACG 61.884 60.000 22.90 3.06 33.09 5.12
4303 4841 2.036731 TCCCATGGAGACCGACGT 59.963 61.111 15.22 0.00 0.00 4.34
4304 4842 2.050350 TCCCATGGAGACCGACGTC 61.050 63.158 15.22 5.18 39.50 4.34
4305 4843 2.348104 CCCATGGAGACCGACGTCA 61.348 63.158 15.22 0.00 41.87 4.35
4306 4844 1.153823 CCATGGAGACCGACGTCAC 60.154 63.158 17.16 6.33 41.87 3.67
4307 4845 1.153823 CATGGAGACCGACGTCACC 60.154 63.158 17.16 10.49 46.70 4.02
4309 4847 3.285371 GGAGACCGACGTCACCAT 58.715 61.111 17.16 0.00 46.03 3.55
4310 4848 1.153823 GGAGACCGACGTCACCATG 60.154 63.158 17.16 0.00 46.03 3.66
4312 4850 1.592400 GAGACCGACGTCACCATGGA 61.592 60.000 21.47 0.00 41.87 3.41
4313 4851 1.153823 GACCGACGTCACCATGGAG 60.154 63.158 21.47 11.61 38.99 3.86
4314 4852 1.592400 GACCGACGTCACCATGGAGA 61.592 60.000 21.47 14.37 38.99 3.71
4315 4853 1.153823 CCGACGTCACCATGGAGAC 60.154 63.158 27.07 27.07 33.46 3.36
4317 4855 1.153823 GACGTCACCATGGAGACCG 60.154 63.158 29.51 25.58 33.26 4.79
4319 4857 2.125106 GTCACCATGGAGACCGGC 60.125 66.667 26.73 6.43 31.18 6.13
4320 4858 2.606213 TCACCATGGAGACCGGCA 60.606 61.111 21.47 0.00 0.00 5.69
4321 4859 1.995066 TCACCATGGAGACCGGCAT 60.995 57.895 21.47 0.00 0.00 4.40
4322 4860 1.820906 CACCATGGAGACCGGCATG 60.821 63.158 21.47 7.12 0.00 4.06
4323 4861 2.300967 ACCATGGAGACCGGCATGT 61.301 57.895 21.47 4.73 0.00 3.21
4324 4862 1.524621 CCATGGAGACCGGCATGTC 60.525 63.158 5.56 0.76 35.43 3.06
4325 4863 1.884464 CATGGAGACCGGCATGTCG 60.884 63.158 13.99 13.99 40.26 4.35
4326 4864 2.359169 ATGGAGACCGGCATGTCGT 61.359 57.895 19.75 6.74 40.26 4.34
4327 4865 2.202756 GGAGACCGGCATGTCGTC 60.203 66.667 19.75 15.48 40.26 4.20
4328 4866 2.579787 GAGACCGGCATGTCGTCG 60.580 66.667 19.75 6.70 44.31 5.12
4347 4885 2.819595 CGACCCGCCCATCACAAG 60.820 66.667 0.00 0.00 0.00 3.16
4348 4886 2.351276 GACCCGCCCATCACAAGT 59.649 61.111 0.00 0.00 0.00 3.16
4386 4924 2.579787 GAGACCGGCATGTCGTCG 60.580 66.667 19.75 6.70 44.31 5.12
4407 4945 1.745489 GACCCGCCCATCACAAGTC 60.745 63.158 0.00 0.00 0.00 3.01
4408 4946 2.438434 CCCGCCCATCACAAGTCC 60.438 66.667 0.00 0.00 0.00 3.85
4409 4947 2.350895 CCGCCCATCACAAGTCCA 59.649 61.111 0.00 0.00 0.00 4.02
4410 4948 1.746615 CCGCCCATCACAAGTCCAG 60.747 63.158 0.00 0.00 0.00 3.86
4411 4949 1.746615 CGCCCATCACAAGTCCAGG 60.747 63.158 0.00 0.00 0.00 4.45
4412 4950 1.380302 GCCCATCACAAGTCCAGGT 59.620 57.895 0.00 0.00 0.00 4.00
4413 4951 0.618458 GCCCATCACAAGTCCAGGTA 59.382 55.000 0.00 0.00 0.00 3.08
4415 4953 1.065418 CCCATCACAAGTCCAGGTACC 60.065 57.143 2.73 2.73 0.00 3.34
4416 4954 1.909302 CCATCACAAGTCCAGGTACCT 59.091 52.381 9.21 9.21 0.00 3.08
4494 5042 3.490759 GGGCTGCGTCACGACATG 61.491 66.667 0.00 0.00 0.00 3.21
4549 5097 2.863153 GTGGCACATGACACGAGC 59.137 61.111 13.86 0.00 45.07 5.03
4550 5098 1.669115 GTGGCACATGACACGAGCT 60.669 57.895 13.86 0.00 45.07 4.09
4554 5110 1.639298 GCACATGACACGAGCTTCCC 61.639 60.000 0.00 0.00 0.00 3.97
4598 5155 2.405143 CAGATCGCGACTGGGAGTA 58.595 57.895 22.80 0.00 40.74 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 3.585289 TCCCTTGTATGGAGCACTTTGTA 59.415 43.478 0.00 0.00 0.00 2.41
50 51 3.624777 CATCCCTTGTATGGAGCACTTT 58.375 45.455 0.00 0.00 34.80 2.66
59 60 1.270305 ACGATCGCCATCCCTTGTATG 60.270 52.381 16.60 0.00 0.00 2.39
66 67 1.134560 GGTATCTACGATCGCCATCCC 59.865 57.143 16.60 4.78 0.00 3.85
144 257 1.666872 GTGGGCGTTAGCGTTGTCT 60.667 57.895 0.00 0.00 46.35 3.41
184 297 0.922626 TGTTATAGGGCATGTGGGCA 59.077 50.000 0.00 0.00 45.66 5.36
192 305 2.354704 GCAGTCTGTGTGTTATAGGGCA 60.355 50.000 0.93 0.00 0.00 5.36
214 327 1.001048 GCATGCATGCGGTGACATAAT 60.001 47.619 33.99 1.66 44.67 1.28
216 329 2.024117 GCATGCATGCGGTGACATA 58.976 52.632 33.99 0.00 44.67 2.29
518 637 7.716799 AATTTATGGTTCATGGCAAGTCTAA 57.283 32.000 0.00 0.00 0.00 2.10
716 837 2.725221 TTTGCCCAAAAGTTGCCATT 57.275 40.000 0.00 0.00 0.00 3.16
848 970 8.943909 TCTTTTTGGTTTTCGGCTTAAAAATA 57.056 26.923 0.00 0.00 30.53 1.40
876 999 3.443681 TGTGAACAGACGATATCAGCAGA 59.556 43.478 3.12 0.00 0.00 4.26
888 1011 3.435105 TTTTGCCACATGTGAACAGAC 57.565 42.857 27.46 9.28 0.00 3.51
920 1043 1.497991 CACATCGTCCACACGTCTTT 58.502 50.000 0.00 0.00 46.76 2.52
921 1044 0.944311 GCACATCGTCCACACGTCTT 60.944 55.000 0.00 0.00 46.76 3.01
932 1055 1.264020 GTGTGACATGTTGCACATCGT 59.736 47.619 19.72 0.00 45.59 3.73
947 1070 0.825410 ACTAACACCCACACGTGTGA 59.175 50.000 42.33 24.27 46.19 3.58
1057 1205 2.484651 TCGTTGACAGTAGAGTGAGCTC 59.515 50.000 6.82 6.82 41.94 4.09
1107 1255 2.051256 CGTGACGCGTGAGACAGT 60.051 61.111 20.70 0.00 35.54 3.55
1108 1256 3.461982 GCGTGACGCGTGAGACAG 61.462 66.667 20.70 8.12 44.55 3.51
1511 1710 0.391661 AACAATCTGCTCGCCATCGT 60.392 50.000 0.00 0.00 36.96 3.73
1515 1714 1.806542 GAGAAAACAATCTGCTCGCCA 59.193 47.619 0.00 0.00 0.00 5.69
1549 1771 1.762370 CCAAACAAGCCAGGGTTCTTT 59.238 47.619 0.00 0.00 0.00 2.52
1634 1858 9.131791 ACTTCATGTCTTTTATTTAACTGGTGT 57.868 29.630 0.00 0.00 0.00 4.16
1635 1859 9.965824 AACTTCATGTCTTTTATTTAACTGGTG 57.034 29.630 0.00 0.00 0.00 4.17
1970 2212 6.954944 TCTTACAACAAAAGATCAACGGAAG 58.045 36.000 0.00 0.00 0.00 3.46
2053 2296 3.267483 CGACACTTATTTTGGGACGGAT 58.733 45.455 0.00 0.00 0.00 4.18
2188 2498 4.848357 AGTCACCTACAATTTCATCCAGG 58.152 43.478 0.00 0.00 0.00 4.45
2700 3023 6.128007 CGCTGTTTCTTGACTATAACCCAATT 60.128 38.462 0.00 0.00 0.00 2.32
2776 3099 4.523083 AGAACTTAACTTGAGTGTGCCAA 58.477 39.130 0.00 0.00 0.00 4.52
2785 3108 7.871463 GGCTAACTTGTCTAGAACTTAACTTGA 59.129 37.037 0.00 0.00 0.00 3.02
2905 3228 5.663795 TCGAGCTTTCTTGATATTGATGC 57.336 39.130 0.00 0.00 0.00 3.91
2908 3231 6.402550 GCAAGTTCGAGCTTTCTTGATATTGA 60.403 38.462 12.23 0.00 39.39 2.57
3176 3499 1.826054 CCCACCAAACCGAGCAACA 60.826 57.895 0.00 0.00 0.00 3.33
3296 3619 4.530875 CAATAAGGCCCATCTCTTTCAGT 58.469 43.478 0.00 0.00 0.00 3.41
3357 3680 3.240134 GACCGGGCTTGCAGAGACA 62.240 63.158 6.32 0.00 33.80 3.41
3402 3725 5.418310 ACATCTAACAAACCGAAACACAG 57.582 39.130 0.00 0.00 0.00 3.66
3549 3877 0.238817 GAGCGGATCGAACGATAGCT 59.761 55.000 26.44 26.44 44.99 3.32
3564 3893 5.295292 ACAATGGATCTTATTTCACAGAGCG 59.705 40.000 0.00 0.00 0.00 5.03
3578 3907 4.184629 GCGAGTGTTCTTACAATGGATCT 58.815 43.478 0.00 0.00 35.69 2.75
3676 4011 2.510238 CAGTAGCTGCACCGGAGC 60.510 66.667 17.78 17.78 36.65 4.70
3900 4258 0.558220 TCGGTGGAGAGATGAGGGAT 59.442 55.000 0.00 0.00 0.00 3.85
3903 4261 1.739049 GCTCGGTGGAGAGATGAGG 59.261 63.158 0.00 0.00 43.27 3.86
3970 4443 3.778629 ACCAATTGTAGGGTTCTCGGTAT 59.221 43.478 4.43 0.00 32.12 2.73
3993 4479 1.002684 GTCGGATCGTGCGTTCTAGAT 60.003 52.381 0.00 0.00 31.47 1.98
3994 4480 0.376152 GTCGGATCGTGCGTTCTAGA 59.624 55.000 0.00 0.00 31.47 2.43
3995 4481 0.591741 GGTCGGATCGTGCGTTCTAG 60.592 60.000 3.23 0.00 31.47 2.43
3996 4482 1.430632 GGTCGGATCGTGCGTTCTA 59.569 57.895 3.23 0.00 31.47 2.10
3997 4483 2.181021 GGTCGGATCGTGCGTTCT 59.819 61.111 3.23 0.00 31.47 3.01
3998 4484 2.582202 TACGGTCGGATCGTGCGTTC 62.582 60.000 25.35 0.00 41.24 3.95
3999 4485 2.198906 TTACGGTCGGATCGTGCGTT 62.199 55.000 25.35 1.09 41.24 4.84
4027 4550 0.714994 CAAAATTTGCACCCATCGCG 59.285 50.000 0.00 0.00 0.00 5.87
4071 4594 5.741011 CAAATCCAACCAACCTAGCTAGTA 58.259 41.667 19.31 0.00 0.00 1.82
4086 4609 0.251742 CACCCCTCCTGCAAATCCAA 60.252 55.000 0.00 0.00 0.00 3.53
4095 4618 3.323622 TGCTATGCACCCCTCCTG 58.676 61.111 0.00 0.00 31.71 3.86
4109 4632 4.711949 CAGAGGGCTTGCCGTGCT 62.712 66.667 11.78 6.12 0.00 4.40
4116 4639 2.528743 CGTATGCGCAGAGGGCTTG 61.529 63.158 18.32 0.00 42.10 4.01
4181 4719 3.775314 CGTATTTCGTGAGCGGCA 58.225 55.556 1.45 0.00 38.89 5.69
4190 4728 5.500290 GCTCCACTGAATTGTACGTATTTCG 60.500 44.000 0.00 3.22 46.00 3.46
4191 4729 5.581085 AGCTCCACTGAATTGTACGTATTTC 59.419 40.000 0.00 3.92 0.00 2.17
4192 4730 5.488341 AGCTCCACTGAATTGTACGTATTT 58.512 37.500 0.00 0.00 0.00 1.40
4193 4731 5.086104 AGCTCCACTGAATTGTACGTATT 57.914 39.130 0.00 0.00 0.00 1.89
4194 4732 4.441634 GGAGCTCCACTGAATTGTACGTAT 60.442 45.833 28.43 0.00 35.64 3.06
4195 4733 3.119245 GGAGCTCCACTGAATTGTACGTA 60.119 47.826 28.43 0.00 35.64 3.57
4196 4734 2.353803 GGAGCTCCACTGAATTGTACGT 60.354 50.000 28.43 0.00 35.64 3.57
4197 4735 2.271800 GGAGCTCCACTGAATTGTACG 58.728 52.381 28.43 0.00 35.64 3.67
4198 4736 2.271800 CGGAGCTCCACTGAATTGTAC 58.728 52.381 31.67 0.53 35.14 2.90
4199 4737 2.672961 CGGAGCTCCACTGAATTGTA 57.327 50.000 31.67 0.00 35.14 2.41
4200 4738 3.540211 CGGAGCTCCACTGAATTGT 57.460 52.632 31.67 0.00 35.14 2.71
4227 4765 4.521010 GCTTCAAATTTGCTTGCTCAAAC 58.479 39.130 13.54 0.00 38.58 2.93
4294 4832 1.595993 CTCCATGGTGACGTCGGTCT 61.596 60.000 12.58 0.00 43.79 3.85
4296 4834 1.605451 TCTCCATGGTGACGTCGGT 60.605 57.895 12.58 0.00 0.00 4.69
4297 4835 1.153823 GTCTCCATGGTGACGTCGG 60.154 63.158 26.46 5.55 0.00 4.79
4300 4838 2.646175 CCGGTCTCCATGGTGACGT 61.646 63.158 30.74 0.00 38.91 4.34
4302 4840 2.125106 GCCGGTCTCCATGGTGAC 60.125 66.667 30.49 30.49 37.75 3.67
4303 4841 1.995066 ATGCCGGTCTCCATGGTGA 60.995 57.895 12.58 12.54 0.00 4.02
4304 4842 1.820906 CATGCCGGTCTCCATGGTG 60.821 63.158 12.58 9.91 36.16 4.17
4305 4843 2.257409 GACATGCCGGTCTCCATGGT 62.257 60.000 19.77 8.80 42.31 3.55
4306 4844 1.524621 GACATGCCGGTCTCCATGG 60.525 63.158 19.77 4.97 42.31 3.66
4307 4845 1.884464 CGACATGCCGGTCTCCATG 60.884 63.158 15.68 15.68 43.34 3.66
4308 4846 2.298158 GACGACATGCCGGTCTCCAT 62.298 60.000 6.33 0.00 35.63 3.41
4309 4847 2.994995 ACGACATGCCGGTCTCCA 60.995 61.111 6.33 0.00 35.63 3.86
4310 4848 2.202756 GACGACATGCCGGTCTCC 60.203 66.667 6.33 0.00 35.63 3.71
4312 4850 4.129737 CCGACGACATGCCGGTCT 62.130 66.667 6.33 0.00 38.55 3.85
4330 4868 2.819595 CTTGTGATGGGCGGGTCG 60.820 66.667 0.00 0.00 0.00 4.79
4331 4869 1.745489 GACTTGTGATGGGCGGGTC 60.745 63.158 0.00 0.00 0.00 4.46
4332 4870 2.351276 GACTTGTGATGGGCGGGT 59.649 61.111 0.00 0.00 0.00 5.28
4333 4871 2.819595 CGACTTGTGATGGGCGGG 60.820 66.667 0.00 0.00 0.00 6.13
4334 4872 2.819595 CCGACTTGTGATGGGCGG 60.820 66.667 0.00 0.00 0.00 6.13
4335 4873 3.499737 GCCGACTTGTGATGGGCG 61.500 66.667 0.00 0.00 33.58 6.13
4336 4874 3.499737 CGCCGACTTGTGATGGGC 61.500 66.667 0.00 0.00 40.36 5.36
4337 4875 2.100631 GTCGCCGACTTGTGATGGG 61.101 63.158 10.56 0.00 0.00 4.00
4338 4876 2.100631 GGTCGCCGACTTGTGATGG 61.101 63.158 17.76 0.00 32.47 3.51
4339 4877 3.474806 GGTCGCCGACTTGTGATG 58.525 61.111 17.76 0.00 32.47 3.07
4395 4933 1.065418 GGTACCTGGACTTGTGATGGG 60.065 57.143 4.06 0.00 0.00 4.00
4407 4945 3.528370 CGAGGCGGAGGTACCTGG 61.528 72.222 22.10 12.30 36.05 4.45
4408 4946 4.208686 GCGAGGCGGAGGTACCTG 62.209 72.222 22.10 7.07 36.05 4.00
4411 4949 3.766691 TTGGCGAGGCGGAGGTAC 61.767 66.667 0.00 0.00 0.00 3.34
4412 4950 3.766691 GTTGGCGAGGCGGAGGTA 61.767 66.667 0.00 0.00 0.00 3.08
4415 4953 3.423154 GTTGTTGGCGAGGCGGAG 61.423 66.667 0.00 0.00 0.00 4.63
4416 4954 3.758973 TTGTTGTTGGCGAGGCGGA 62.759 57.895 0.00 0.00 0.00 5.54
4475 5019 3.315142 ATGTCGTGACGCAGCCCAT 62.315 57.895 0.00 0.00 0.00 4.00
4489 5037 1.170442 CCAACGGTTAACCCCATGTC 58.830 55.000 19.09 0.00 0.00 3.06
4494 5042 1.202794 TCTGTTCCAACGGTTAACCCC 60.203 52.381 19.09 0.00 36.65 4.95
4540 5088 2.583441 CCCTGGGAAGCTCGTGTCA 61.583 63.158 7.01 0.00 0.00 3.58
4548 5096 2.107141 CGTCGATCCCTGGGAAGC 59.893 66.667 21.42 13.88 34.34 3.86
4549 5097 2.107141 GCGTCGATCCCTGGGAAG 59.893 66.667 21.42 16.77 34.34 3.46
4550 5098 3.467226 GGCGTCGATCCCTGGGAA 61.467 66.667 21.42 0.00 34.34 3.97


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

AutoCloner maintained by Alex Coulton.