Multiple sequence alignment - TraesCS7D01G048800

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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 TraesCS7D01G048800 chr7D 100.000 3692 0 0 1 3692 25184666 25188357 0.000000e+00 6818.0
1 TraesCS7D01G048800 chrUn 93.765 2085 83 18 956 2996 327953157 327955238 0.000000e+00 3086.0
2 TraesCS7D01G048800 chrUn 93.717 2085 84 18 956 2996 326025942 326028023 0.000000e+00 3081.0
3 TraesCS7D01G048800 chrUn 93.282 1682 74 16 1353 2996 339887036 339888716 0.000000e+00 2444.0
4 TraesCS7D01G048800 chrUn 92.590 1417 66 16 1618 2996 349955731 349957146 0.000000e+00 1999.0
5 TraesCS7D01G048800 chrUn 95.506 801 35 1 2196 2996 387894895 387894096 0.000000e+00 1279.0
6 TraesCS7D01G048800 chrUn 89.022 501 35 8 3138 3623 326028019 326028514 1.470000e-168 603.0
7 TraesCS7D01G048800 chrUn 89.022 501 35 8 3138 3623 327955234 327955729 1.470000e-168 603.0
8 TraesCS7D01G048800 chrUn 89.022 501 35 8 3138 3623 339888712 339889207 1.470000e-168 603.0
9 TraesCS7D01G048800 chrUn 89.022 501 35 8 3138 3623 349957142 349957637 1.470000e-168 603.0
10 TraesCS7D01G048800 chrUn 89.022 501 35 8 3138 3623 387894100 387893605 1.470000e-168 603.0
11 TraesCS7D01G048800 chr7A 90.205 1562 104 12 2034 3572 26027464 26028999 0.000000e+00 1991.0
12 TraesCS7D01G048800 chr7A 96.644 1043 29 3 917 1957 26026386 26027424 0.000000e+00 1727.0
13 TraesCS7D01G048800 chr7A 87.671 730 36 22 1 694 26025421 26026132 0.000000e+00 800.0
14 TraesCS7D01G048800 chr7A 96.407 167 6 0 691 857 115807521 115807687 3.630000e-70 276.0
15 TraesCS7D01G048800 chr7A 89.677 155 13 2 3501 3654 26029002 26029154 1.050000e-45 195.0
16 TraesCS7D01G048800 chr1D 95.930 172 7 0 689 860 238940384 238940213 2.810000e-71 279.0
17 TraesCS7D01G048800 chr1D 76.812 207 29 15 437 633 443416370 443416567 8.440000e-17 99.0
18 TraesCS7D01G048800 chr6D 96.407 167 6 0 693 859 270587371 270587537 3.630000e-70 276.0
19 TraesCS7D01G048800 chr6D 95.858 169 7 0 692 860 392896974 392897142 1.310000e-69 274.0
20 TraesCS7D01G048800 chr3D 95.376 173 8 0 686 858 304588272 304588100 3.630000e-70 276.0
21 TraesCS7D01G048800 chr3D 91.192 193 13 4 668 858 610353577 610353387 3.660000e-65 259.0
22 TraesCS7D01G048800 chr5D 94.857 175 9 0 689 863 274578180 274578006 1.310000e-69 274.0
23 TraesCS7D01G048800 chr5D 89.583 48 2 2 560 604 308022778 308022731 1.430000e-04 58.4
24 TraesCS7D01G048800 chr4D 95.858 169 7 0 691 859 75782219 75782051 1.310000e-69 274.0
25 TraesCS7D01G048800 chr4D 83.562 73 5 5 538 604 2970981 2971052 1.110000e-05 62.1
26 TraesCS7D01G048800 chr3B 93.855 179 11 0 686 864 571752518 571752696 1.690000e-68 270.0
27 TraesCS7D01G048800 chr3B 83.636 110 8 6 487 593 122012842 122012740 1.090000e-15 95.3
28 TraesCS7D01G048800 chr3B 79.114 158 16 12 440 593 122081740 122081596 3.930000e-15 93.5
29 TraesCS7D01G048800 chr4A 77.778 171 26 9 446 610 513345161 513344997 1.090000e-15 95.3
30 TraesCS7D01G048800 chr6A 81.720 93 11 6 503 593 2945349 2945261 5.110000e-09 73.1
31 TraesCS7D01G048800 chr6A 80.682 88 14 2 523 610 17771622 17771706 8.560000e-07 65.8


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 TraesCS7D01G048800 chr7D 25184666 25188357 3691 False 6818.00 6818 100.00000 1 3692 1 chr7D.!!$F1 3691
1 TraesCS7D01G048800 chrUn 327953157 327955729 2572 False 1844.50 3086 91.39350 956 3623 2 chrUn.!!$F2 2667
2 TraesCS7D01G048800 chrUn 326025942 326028514 2572 False 1842.00 3081 91.36950 956 3623 2 chrUn.!!$F1 2667
3 TraesCS7D01G048800 chrUn 339887036 339889207 2171 False 1523.50 2444 91.15200 1353 3623 2 chrUn.!!$F3 2270
4 TraesCS7D01G048800 chrUn 349955731 349957637 1906 False 1301.00 1999 90.80600 1618 3623 2 chrUn.!!$F4 2005
5 TraesCS7D01G048800 chrUn 387893605 387894895 1290 True 941.00 1279 92.26400 2196 3623 2 chrUn.!!$R1 1427
6 TraesCS7D01G048800 chr7A 26025421 26029154 3733 False 1178.25 1991 91.04925 1 3654 4 chr7A.!!$F2 3653

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
288 298 0.319040 ACTGTAGCTGAGCGTGTGTG 60.319 55.000 0.0 0.0 0.00 3.82 F
812 935 0.539518 CATCCGTATGTGGTGGTCCA 59.460 55.000 0.0 0.0 42.05 4.02 F
813 936 1.140852 CATCCGTATGTGGTGGTCCAT 59.859 52.381 0.0 0.0 46.20 3.41 F
814 937 1.281419 TCCGTATGTGGTGGTCCATT 58.719 50.000 0.0 0.0 46.20 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2247 2415 0.539051 AGGCTTCATTCAGGAGACCG 59.461 55.000 0.0 0.0 0.00 4.79 R
2352 2520 1.079503 CTGCTGTTTCCGCTAGTTCC 58.920 55.000 0.0 0.0 0.00 3.62 R
2457 2625 1.136961 TCCATACCTGGGCAACACCA 61.137 55.000 0.0 0.0 43.34 4.17 R
2790 2958 1.407258 TGCCACCTTTTTGAAGAACCG 59.593 47.619 0.0 0.0 0.00 4.44 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
50 51 8.526147 GCCTGAAATTAGGTATGCATAATCATT 58.474 33.333 8.28 2.29 40.11 2.57
51 52 9.850628 CCTGAAATTAGGTATGCATAATCATTG 57.149 33.333 8.28 0.00 31.30 2.82
57 58 5.319453 AGGTATGCATAATCATTGTCAGGG 58.681 41.667 8.28 0.00 0.00 4.45
60 61 2.689471 TGCATAATCATTGTCAGGGTGC 59.311 45.455 0.00 0.00 0.00 5.01
96 98 3.095347 TTTTTGGGGCGTTGTGGGC 62.095 57.895 0.00 0.00 0.00 5.36
118 120 4.668289 CTTTTTCACGCTAAGTTGTGGTT 58.332 39.130 0.00 0.00 36.74 3.67
161 169 6.377429 TGCTTTTTCGGTATAGAGAGAGAGAA 59.623 38.462 0.00 0.00 0.00 2.87
171 179 6.926630 ATAGAGAGAGAGAAAGTTGTGGTT 57.073 37.500 0.00 0.00 0.00 3.67
196 205 5.671493 TCTCTTAAGGGCTATTTTCTTCGG 58.329 41.667 1.85 0.00 0.00 4.30
223 233 5.897050 GCTATATGTAGCCCATACTGAGAC 58.103 45.833 10.20 0.00 46.14 3.36
224 234 5.449314 GCTATATGTAGCCCATACTGAGACG 60.449 48.000 10.20 0.00 46.14 4.18
225 235 0.744874 TGTAGCCCATACTGAGACGC 59.255 55.000 0.00 0.00 35.24 5.19
226 236 0.744874 GTAGCCCATACTGAGACGCA 59.255 55.000 0.00 0.00 0.00 5.24
227 237 1.136305 GTAGCCCATACTGAGACGCAA 59.864 52.381 0.00 0.00 0.00 4.85
228 238 0.833287 AGCCCATACTGAGACGCAAT 59.167 50.000 0.00 0.00 0.00 3.56
229 239 2.039418 AGCCCATACTGAGACGCAATA 58.961 47.619 0.00 0.00 0.00 1.90
282 292 1.137086 ACCCAATACTGTAGCTGAGCG 59.863 52.381 0.00 0.00 0.00 5.03
288 298 0.319040 ACTGTAGCTGAGCGTGTGTG 60.319 55.000 0.00 0.00 0.00 3.82
360 385 4.873827 GGTTTCCTTTGGGTTTTCTTGTTC 59.126 41.667 0.00 0.00 0.00 3.18
361 386 5.483811 GTTTCCTTTGGGTTTTCTTGTTCA 58.516 37.500 0.00 0.00 0.00 3.18
366 391 6.821160 TCCTTTGGGTTTTCTTGTTCATTTTC 59.179 34.615 0.00 0.00 0.00 2.29
391 425 6.937886 TTTTTCTTCGGTTTTCTTTGTGTC 57.062 33.333 0.00 0.00 0.00 3.67
400 434 4.566759 GGTTTTCTTTGTGTCTTTCTTGGC 59.433 41.667 0.00 0.00 0.00 4.52
639 675 9.033481 ACTTGAAATACATGTGTTGACATTTTG 57.967 29.630 9.11 3.39 41.12 2.44
640 676 8.939201 TTGAAATACATGTGTTGACATTTTGT 57.061 26.923 9.11 0.00 41.12 2.83
641 677 8.350238 TGAAATACATGTGTTGACATTTTGTG 57.650 30.769 9.11 0.00 41.12 3.33
642 678 8.193438 TGAAATACATGTGTTGACATTTTGTGA 58.807 29.630 9.11 0.00 41.12 3.58
644 680 9.545105 AAATACATGTGTTGACATTTTGTGAAT 57.455 25.926 9.11 0.00 41.12 2.57
647 683 8.523523 ACATGTGTTGACATTTTGTGAATATG 57.476 30.769 0.00 0.00 41.12 1.78
648 684 8.143193 ACATGTGTTGACATTTTGTGAATATGT 58.857 29.630 0.00 0.00 41.12 2.29
649 685 7.927305 TGTGTTGACATTTTGTGAATATGTG 57.073 32.000 0.00 0.00 32.94 3.21
650 686 7.487484 TGTGTTGACATTTTGTGAATATGTGT 58.513 30.769 0.00 0.00 32.94 3.72
651 687 8.624776 TGTGTTGACATTTTGTGAATATGTGTA 58.375 29.630 0.00 0.00 32.94 2.90
704 763 8.302515 TCGACTTATTTTATACTCCCTCTGTT 57.697 34.615 0.00 0.00 0.00 3.16
706 765 8.414778 CGACTTATTTTATACTCCCTCTGTTCT 58.585 37.037 0.00 0.00 0.00 3.01
718 841 8.794335 ACTCCCTCTGTTCTTAAATATTTGTC 57.206 34.615 11.05 0.00 0.00 3.18
739 862 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
750 873 8.589338 AGAGATTTCAACAAGTGACTACATACT 58.411 33.333 0.00 0.00 35.39 2.12
763 886 6.591834 GTGACTACATACTGAGCAAAATGAGT 59.408 38.462 0.00 0.00 0.00 3.41
773 896 6.148480 ACTGAGCAAAATGAGTGAATCTACAC 59.852 38.462 0.00 0.00 40.60 2.90
807 930 7.153217 TGTCTATATACATCCGTATGTGGTG 57.847 40.000 3.56 0.00 45.99 4.17
808 931 6.152154 TGTCTATATACATCCGTATGTGGTGG 59.848 42.308 3.56 0.00 45.99 4.61
810 933 3.746045 ATACATCCGTATGTGGTGGTC 57.254 47.619 3.56 0.00 45.99 4.02
811 934 0.539986 ACATCCGTATGTGGTGGTCC 59.460 55.000 0.00 0.00 44.79 4.46
812 935 0.539518 CATCCGTATGTGGTGGTCCA 59.460 55.000 0.00 0.00 42.05 4.02
813 936 1.140852 CATCCGTATGTGGTGGTCCAT 59.859 52.381 0.00 0.00 46.20 3.41
814 937 1.281419 TCCGTATGTGGTGGTCCATT 58.719 50.000 0.00 0.00 46.20 3.16
815 938 1.631388 TCCGTATGTGGTGGTCCATTT 59.369 47.619 0.00 0.00 46.20 2.32
824 947 4.082125 GTGGTGGTCCATTTGAAATCTCT 58.918 43.478 0.00 0.00 46.20 3.10
826 949 5.710099 GTGGTGGTCCATTTGAAATCTCTAA 59.290 40.000 0.00 0.00 46.20 2.10
832 955 9.142014 TGGTCCATTTGAAATCTCTAAAAAGAA 57.858 29.630 0.00 0.00 0.00 2.52
833 956 9.981114 GGTCCATTTGAAATCTCTAAAAAGAAA 57.019 29.630 0.00 0.00 0.00 2.52
852 975 9.923143 AAAAGAAAAATATTTAGAAACGGAGGG 57.077 29.630 0.01 0.00 0.00 4.30
853 976 8.873186 AAGAAAAATATTTAGAAACGGAGGGA 57.127 30.769 0.01 0.00 0.00 4.20
854 977 8.507524 AGAAAAATATTTAGAAACGGAGGGAG 57.492 34.615 0.01 0.00 0.00 4.30
855 978 8.107729 AGAAAAATATTTAGAAACGGAGGGAGT 58.892 33.333 0.01 0.00 0.00 3.85
856 979 9.387257 GAAAAATATTTAGAAACGGAGGGAGTA 57.613 33.333 0.01 0.00 0.00 2.59
858 981 9.916360 AAAATATTTAGAAACGGAGGGAGTATT 57.084 29.630 0.01 0.00 0.00 1.89
862 985 8.728337 ATTTAGAAACGGAGGGAGTATTAAAC 57.272 34.615 0.00 0.00 0.00 2.01
864 987 8.593945 TTAGAAACGGAGGGAGTATTAAACTA 57.406 34.615 0.00 0.00 39.07 2.24
865 988 7.486407 AGAAACGGAGGGAGTATTAAACTAA 57.514 36.000 0.00 0.00 39.07 2.24
866 989 7.910584 AGAAACGGAGGGAGTATTAAACTAAA 58.089 34.615 0.00 0.00 39.07 1.85
867 990 8.039538 AGAAACGGAGGGAGTATTAAACTAAAG 58.960 37.037 0.00 0.00 39.07 1.85
868 991 6.864151 ACGGAGGGAGTATTAAACTAAAGT 57.136 37.500 0.00 0.00 39.07 2.66
869 992 7.250032 ACGGAGGGAGTATTAAACTAAAGTT 57.750 36.000 0.00 0.00 39.07 2.66
870 993 8.366359 ACGGAGGGAGTATTAAACTAAAGTTA 57.634 34.615 0.00 0.00 39.07 2.24
871 994 8.473219 ACGGAGGGAGTATTAAACTAAAGTTAG 58.527 37.037 0.00 0.00 39.07 2.34
872 995 8.473219 CGGAGGGAGTATTAAACTAAAGTTAGT 58.527 37.037 0.00 0.00 45.43 2.24
891 1014 9.836076 AAGTTAGTACAAAAAGTTGAGTCAAAC 57.164 29.630 7.25 2.37 38.20 2.93
892 1015 8.173130 AGTTAGTACAAAAAGTTGAGTCAAACG 58.827 33.333 7.25 0.00 38.20 3.60
893 1016 6.730960 AGTACAAAAAGTTGAGTCAAACGA 57.269 33.333 7.25 0.00 38.20 3.85
894 1017 7.136289 AGTACAAAAAGTTGAGTCAAACGAA 57.864 32.000 7.25 0.00 38.20 3.85
895 1018 7.241376 AGTACAAAAAGTTGAGTCAAACGAAG 58.759 34.615 7.25 0.00 38.20 3.79
896 1019 6.249035 ACAAAAAGTTGAGTCAAACGAAGA 57.751 33.333 7.25 0.00 38.20 2.87
897 1020 6.314784 ACAAAAAGTTGAGTCAAACGAAGAG 58.685 36.000 7.25 0.00 38.20 2.85
898 1021 6.148811 ACAAAAAGTTGAGTCAAACGAAGAGA 59.851 34.615 7.25 0.00 38.20 3.10
899 1022 5.975410 AAAGTTGAGTCAAACGAAGAGAG 57.025 39.130 7.25 0.00 35.13 3.20
900 1023 4.657436 AGTTGAGTCAAACGAAGAGAGT 57.343 40.909 7.25 0.00 35.13 3.24
901 1024 5.769484 AGTTGAGTCAAACGAAGAGAGTA 57.231 39.130 7.25 0.00 35.13 2.59
902 1025 5.764131 AGTTGAGTCAAACGAAGAGAGTAG 58.236 41.667 7.25 0.00 35.13 2.57
903 1026 5.299782 AGTTGAGTCAAACGAAGAGAGTAGT 59.700 40.000 7.25 0.00 35.13 2.73
904 1027 6.485984 AGTTGAGTCAAACGAAGAGAGTAGTA 59.514 38.462 7.25 0.00 35.13 1.82
905 1028 7.175293 AGTTGAGTCAAACGAAGAGAGTAGTAT 59.825 37.037 7.25 0.00 35.13 2.12
906 1029 8.449397 GTTGAGTCAAACGAAGAGAGTAGTATA 58.551 37.037 7.25 0.00 0.00 1.47
907 1030 8.734218 TGAGTCAAACGAAGAGAGTAGTATAT 57.266 34.615 0.00 0.00 0.00 0.86
908 1031 9.828039 TGAGTCAAACGAAGAGAGTAGTATATA 57.172 33.333 0.00 0.00 0.00 0.86
973 1098 2.507407 TACACTTGGATGGGCCTTTC 57.493 50.000 4.53 0.00 37.63 2.62
999 1126 3.334751 CGCAGCGTGGTTCGTTCA 61.335 61.111 6.65 0.00 42.13 3.18
1773 1903 2.322355 ATGCACTGCTGGAGATGTAC 57.678 50.000 2.24 0.00 0.00 2.90
1869 1999 4.712829 TGGAACTCAATGATCATGGCATTT 59.287 37.500 9.46 0.00 33.93 2.32
1955 2085 8.110860 TCTTCCTTGAATTGTATTTCACTTCC 57.889 34.615 0.00 0.00 35.42 3.46
1956 2086 7.944554 TCTTCCTTGAATTGTATTTCACTTCCT 59.055 33.333 0.00 0.00 35.42 3.36
1958 2088 8.477419 TCCTTGAATTGTATTTCACTTCCTTT 57.523 30.769 0.00 0.00 35.42 3.11
1959 2089 8.576442 TCCTTGAATTGTATTTCACTTCCTTTC 58.424 33.333 0.00 0.00 35.42 2.62
1960 2090 8.359642 CCTTGAATTGTATTTCACTTCCTTTCA 58.640 33.333 0.00 0.00 35.42 2.69
1961 2091 9.748708 CTTGAATTGTATTTCACTTCCTTTCAA 57.251 29.630 0.00 0.00 35.42 2.69
2016 2165 9.911788 AGATTTAGTGATTGGTGACATTAGAAT 57.088 29.630 0.00 0.00 42.32 2.40
2032 2181 9.586150 GACATTAGAATCACATAGCAAATTACG 57.414 33.333 0.00 0.00 0.00 3.18
2034 2183 9.586150 CATTAGAATCACATAGCAAATTACGTC 57.414 33.333 0.00 0.00 0.00 4.34
2045 2213 6.170675 AGCAAATTACGTCATTTCTCACTC 57.829 37.500 4.74 0.00 0.00 3.51
2159 2327 3.084786 GAGGTTTGGTGGATGAAGGAAG 58.915 50.000 0.00 0.00 0.00 3.46
2184 2352 1.558756 CTCTTCAACTCCATGGAGGCT 59.441 52.381 38.54 25.54 45.88 4.58
2238 2406 2.290832 TGGTTGCATGGTTGATCTGCTA 60.291 45.455 5.60 0.00 36.84 3.49
2247 2415 2.280457 GATCTGCTAGGGCGTGCC 60.280 66.667 1.16 1.16 42.25 5.01
2307 2475 4.681978 GTGGAGCCTGACGCCGTT 62.682 66.667 0.00 0.00 42.11 4.44
2319 2487 2.908015 GCCGTTATCTGGGGAGCA 59.092 61.111 0.00 0.00 0.00 4.26
2406 2574 2.031258 TTCTCGAGCCACAAAACACA 57.969 45.000 7.81 0.00 0.00 3.72
2439 2607 4.808895 GTGATCCTGTCAAACATATACGCA 59.191 41.667 0.00 0.00 38.90 5.24
2457 2625 2.301346 GCATCGTCTGGAAAATGGGAT 58.699 47.619 0.00 0.00 0.00 3.85
2655 2823 7.487822 TGTCAGACTAGAAAATGAGGAAGAT 57.512 36.000 1.31 0.00 0.00 2.40
2658 2826 6.070596 TCAGACTAGAAAATGAGGAAGATGCA 60.071 38.462 0.00 0.00 0.00 3.96
2685 2853 3.580458 AGCTGTTTCTGTCACCTGTAGAT 59.420 43.478 0.00 0.00 0.00 1.98
2757 2925 1.538047 TTGCCCATGAACTTCTCTGC 58.462 50.000 0.00 0.00 0.00 4.26
2786 2954 5.384336 TCTTCCAAGTCAAATTGATGTGGA 58.616 37.500 20.05 20.05 39.15 4.02
2790 2958 4.687483 CCAAGTCAAATTGATGTGGAAAGC 59.313 41.667 17.82 0.00 36.07 3.51
2792 2960 3.057315 AGTCAAATTGATGTGGAAAGCGG 60.057 43.478 0.00 0.00 0.00 5.52
2799 2967 2.151202 GATGTGGAAAGCGGTTCTTCA 58.849 47.619 0.00 0.00 36.40 3.02
2833 3001 3.056322 ACAGAAGGAATGCCAAATCAAGC 60.056 43.478 0.00 0.00 36.29 4.01
2834 3002 2.165030 AGAAGGAATGCCAAATCAAGCG 59.835 45.455 0.00 0.00 36.29 4.68
2839 3007 1.538047 ATGCCAAATCAAGCGAGTGT 58.462 45.000 0.00 0.00 0.00 3.55
2861 3029 1.447643 GCACTACCTGGGCATCGAT 59.552 57.895 0.00 0.00 46.29 3.59
2938 3106 0.737715 GATGCACAGACCACCGAGAC 60.738 60.000 0.00 0.00 0.00 3.36
2983 3151 6.575244 TCAAGATACATCCCAACAAGGTAT 57.425 37.500 0.00 0.00 34.66 2.73
3015 3183 8.731275 TCTTGAATAATGAAATCCACATACGT 57.269 30.769 0.00 0.00 0.00 3.57
3023 3191 5.301555 TGAAATCCACATACGTGAACTGAA 58.698 37.500 0.00 0.00 46.80 3.02
3028 3196 5.487433 TCCACATACGTGAACTGAAATGAT 58.513 37.500 0.00 0.00 46.80 2.45
3059 3227 7.840342 ATGAGCAAAGAGTACAGAAACATAG 57.160 36.000 0.00 0.00 0.00 2.23
3060 3228 6.993079 TGAGCAAAGAGTACAGAAACATAGA 58.007 36.000 0.00 0.00 0.00 1.98
3061 3229 7.615403 TGAGCAAAGAGTACAGAAACATAGAT 58.385 34.615 0.00 0.00 0.00 1.98
3062 3230 8.749354 TGAGCAAAGAGTACAGAAACATAGATA 58.251 33.333 0.00 0.00 0.00 1.98
3063 3231 9.587772 GAGCAAAGAGTACAGAAACATAGATAA 57.412 33.333 0.00 0.00 0.00 1.75
3064 3232 9.593134 AGCAAAGAGTACAGAAACATAGATAAG 57.407 33.333 0.00 0.00 0.00 1.73
3065 3233 9.372369 GCAAAGAGTACAGAAACATAGATAAGT 57.628 33.333 0.00 0.00 0.00 2.24
3084 3252 8.375506 AGATAAGTAAATGAGTTGTGTTGAGGA 58.624 33.333 0.00 0.00 0.00 3.71
3122 3290 0.388134 CTGTGTGCTTCATTGCTGCC 60.388 55.000 0.00 0.00 0.00 4.85
3133 3301 4.155063 TCATTGCTGCCACACTATGTAT 57.845 40.909 0.00 0.00 0.00 2.29
3136 3304 2.016318 TGCTGCCACACTATGTATTGC 58.984 47.619 0.00 0.00 0.00 3.56
3171 3339 0.113190 AGCCAACCCTCTTTTCCCTG 59.887 55.000 0.00 0.00 0.00 4.45
3243 3411 5.222631 CGAGGTGAATTTTCCCAAAAGAAG 58.777 41.667 0.00 0.00 33.22 2.85
3253 3421 2.754552 TCCCAAAAGAAGATCATTGCCG 59.245 45.455 0.00 0.00 0.00 5.69
3261 3429 0.035152 AGATCATTGCCGGTTGCTCA 60.035 50.000 1.90 0.00 42.00 4.26
3272 3440 3.052082 TTGCTCAGAAGGCGCTGC 61.052 61.111 7.64 0.00 35.86 5.25
3445 3641 7.892778 TGTGTTCGATTGCAGTTTATTACTA 57.107 32.000 0.00 0.00 34.56 1.82
3520 3716 2.309528 TGTTTATAGCTCCCGTGCAG 57.690 50.000 0.00 0.00 34.99 4.41
3587 3857 5.373812 AAATCTACGGTGGAATCTTGGAT 57.626 39.130 0.00 0.00 0.00 3.41
3636 3911 6.809630 AATGTCTAGAACTTTCTTTCCTGC 57.190 37.500 0.00 0.00 38.70 4.85
3664 3939 6.932356 CACAACATGCCAATCTCTAGTTAT 57.068 37.500 0.00 0.00 0.00 1.89
3665 3940 7.325660 CACAACATGCCAATCTCTAGTTATT 57.674 36.000 0.00 0.00 0.00 1.40
3666 3941 7.765307 CACAACATGCCAATCTCTAGTTATTT 58.235 34.615 0.00 0.00 0.00 1.40
3667 3942 8.246180 CACAACATGCCAATCTCTAGTTATTTT 58.754 33.333 0.00 0.00 0.00 1.82
3668 3943 8.806146 ACAACATGCCAATCTCTAGTTATTTTT 58.194 29.630 0.00 0.00 0.00 1.94
3688 3963 5.359194 TTTTGGGGTTTTGCTAAATGTCA 57.641 34.783 0.00 0.00 0.00 3.58
3689 3964 5.559148 TTTGGGGTTTTGCTAAATGTCAT 57.441 34.783 0.00 0.00 0.00 3.06
3690 3965 4.533919 TGGGGTTTTGCTAAATGTCATG 57.466 40.909 0.00 0.00 0.00 3.07
3691 3966 3.900601 TGGGGTTTTGCTAAATGTCATGT 59.099 39.130 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 1.340889 GCAAAAATGAGCACCCTGACA 59.659 47.619 0.00 0.00 0.00 3.58
51 52 1.615392 AGCAAAAATGAGCACCCTGAC 59.385 47.619 0.00 0.00 0.00 3.51
57 58 5.723492 AAAACAAGAGCAAAAATGAGCAC 57.277 34.783 0.00 0.00 0.00 4.40
87 89 1.206115 GCGTGAAAAAGCCCACAACG 61.206 55.000 0.00 0.00 33.13 4.10
96 98 4.287238 ACCACAACTTAGCGTGAAAAAG 57.713 40.909 4.24 0.00 35.02 2.27
138 140 8.463607 ACTTTCTCTCTCTCTATACCGAAAAAG 58.536 37.037 0.00 0.00 0.00 2.27
145 147 6.378848 ACCACAACTTTCTCTCTCTCTATACC 59.621 42.308 0.00 0.00 0.00 2.73
146 148 7.399245 ACCACAACTTTCTCTCTCTCTATAC 57.601 40.000 0.00 0.00 0.00 1.47
149 151 6.732896 AAACCACAACTTTCTCTCTCTCTA 57.267 37.500 0.00 0.00 0.00 2.43
161 169 4.341235 GCCCTTAAGAGAAAACCACAACTT 59.659 41.667 3.36 0.00 0.00 2.66
171 179 6.598064 CCGAAGAAAATAGCCCTTAAGAGAAA 59.402 38.462 3.36 0.00 0.00 2.52
220 230 0.595053 CGGCGAGATGTATTGCGTCT 60.595 55.000 0.00 0.00 45.56 4.18
221 231 0.594028 TCGGCGAGATGTATTGCGTC 60.594 55.000 4.99 0.00 0.00 5.19
222 232 0.870307 GTCGGCGAGATGTATTGCGT 60.870 55.000 11.20 0.00 0.00 5.24
223 233 0.869880 TGTCGGCGAGATGTATTGCG 60.870 55.000 11.20 0.00 0.00 4.85
224 234 0.855349 CTGTCGGCGAGATGTATTGC 59.145 55.000 11.20 0.00 0.00 3.56
225 235 0.855349 GCTGTCGGCGAGATGTATTG 59.145 55.000 11.20 0.00 0.00 1.90
226 236 3.274393 GCTGTCGGCGAGATGTATT 57.726 52.632 11.20 0.00 0.00 1.89
267 277 1.819288 ACACACGCTCAGCTACAGTAT 59.181 47.619 0.00 0.00 0.00 2.12
282 292 3.612423 GTGAAAGCAGGAAAAACACACAC 59.388 43.478 0.00 0.00 0.00 3.82
288 298 7.827819 AAAACTAAGTGAAAGCAGGAAAAAC 57.172 32.000 0.00 0.00 0.00 2.43
334 359 5.045213 ACAAGAAAACCCAAAGGAAACCATT 60.045 36.000 0.00 0.00 36.73 3.16
342 367 6.823182 AGAAAATGAACAAGAAAACCCAAAGG 59.177 34.615 0.00 0.00 40.04 3.11
376 410 4.798387 CCAAGAAAGACACAAAGAAAACCG 59.202 41.667 0.00 0.00 0.00 4.44
390 424 1.133915 ACCGGTGAAAGCCAAGAAAGA 60.134 47.619 6.12 0.00 0.00 2.52
391 425 1.318576 ACCGGTGAAAGCCAAGAAAG 58.681 50.000 6.12 0.00 0.00 2.62
425 460 6.019398 TGTGTACGAAAAGTAGATGTGTGTTG 60.019 38.462 0.00 0.00 35.72 3.33
610 646 8.801715 ATGTCAACACATGTATTTCAAGTTTC 57.198 30.769 0.00 0.00 42.05 2.78
617 653 8.572828 TCACAAAATGTCAACACATGTATTTC 57.427 30.769 0.00 0.00 42.89 2.17
714 837 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
715 838 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
718 841 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
722 845 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
731 854 5.010617 TGCTCAGTATGTAGTCACTTGTTGA 59.989 40.000 0.00 0.00 37.40 3.18
735 858 6.785488 TTTTGCTCAGTATGTAGTCACTTG 57.215 37.500 0.00 0.00 37.40 3.16
736 859 7.161404 TCATTTTGCTCAGTATGTAGTCACTT 58.839 34.615 0.00 0.00 37.40 3.16
737 860 6.701340 TCATTTTGCTCAGTATGTAGTCACT 58.299 36.000 0.00 0.00 37.40 3.41
739 862 6.591448 CACTCATTTTGCTCAGTATGTAGTCA 59.409 38.462 0.00 0.00 37.40 3.41
750 873 6.233434 AGTGTAGATTCACTCATTTTGCTCA 58.767 36.000 0.00 0.00 44.07 4.26
780 903 8.900781 ACCACATACGGATGTATATAGACATAC 58.099 37.037 14.23 12.39 44.82 2.39
804 927 6.834168 TTTAGAGATTTCAAATGGACCACC 57.166 37.500 0.00 0.00 0.00 4.61
807 930 9.981114 TTTCTTTTTAGAGATTTCAAATGGACC 57.019 29.630 0.00 0.00 0.00 4.46
826 949 9.923143 CCCTCCGTTTCTAAATATTTTTCTTTT 57.077 29.630 5.91 0.00 0.00 2.27
832 955 9.916360 AATACTCCCTCCGTTTCTAAATATTTT 57.084 29.630 5.91 0.00 0.00 1.82
843 966 7.683578 ACTTTAGTTTAATACTCCCTCCGTTT 58.316 34.615 0.00 0.00 38.33 3.60
846 969 8.473219 ACTAACTTTAGTTTAATACTCCCTCCG 58.527 37.037 0.00 0.00 40.96 4.63
865 988 9.836076 GTTTGACTCAACTTTTTGTACTAACTT 57.164 29.630 0.00 0.00 34.02 2.66
866 989 8.173130 CGTTTGACTCAACTTTTTGTACTAACT 58.827 33.333 0.00 0.00 34.02 2.24
867 990 8.170553 TCGTTTGACTCAACTTTTTGTACTAAC 58.829 33.333 0.00 0.00 34.02 2.34
868 991 8.254178 TCGTTTGACTCAACTTTTTGTACTAA 57.746 30.769 0.00 0.00 34.02 2.24
869 992 7.830940 TCGTTTGACTCAACTTTTTGTACTA 57.169 32.000 0.00 0.00 34.02 1.82
870 993 6.730960 TCGTTTGACTCAACTTTTTGTACT 57.269 33.333 0.00 0.00 34.02 2.73
871 994 7.238571 TCTTCGTTTGACTCAACTTTTTGTAC 58.761 34.615 0.00 0.00 34.02 2.90
872 995 7.332430 TCTCTTCGTTTGACTCAACTTTTTGTA 59.668 33.333 0.00 0.00 34.02 2.41
873 996 6.148811 TCTCTTCGTTTGACTCAACTTTTTGT 59.851 34.615 0.00 0.00 34.02 2.83
874 997 6.542852 TCTCTTCGTTTGACTCAACTTTTTG 58.457 36.000 0.00 0.00 0.00 2.44
875 998 6.371825 ACTCTCTTCGTTTGACTCAACTTTTT 59.628 34.615 0.00 0.00 0.00 1.94
876 999 5.875359 ACTCTCTTCGTTTGACTCAACTTTT 59.125 36.000 0.00 0.00 0.00 2.27
877 1000 5.420409 ACTCTCTTCGTTTGACTCAACTTT 58.580 37.500 0.00 0.00 0.00 2.66
878 1001 5.012328 ACTCTCTTCGTTTGACTCAACTT 57.988 39.130 0.00 0.00 0.00 2.66
879 1002 4.657436 ACTCTCTTCGTTTGACTCAACT 57.343 40.909 0.00 0.00 0.00 3.16
880 1003 5.521544 ACTACTCTCTTCGTTTGACTCAAC 58.478 41.667 0.00 0.00 0.00 3.18
881 1004 5.769484 ACTACTCTCTTCGTTTGACTCAA 57.231 39.130 0.00 0.00 0.00 3.02
882 1005 8.734218 ATATACTACTCTCTTCGTTTGACTCA 57.266 34.615 0.00 0.00 0.00 3.41
900 1023 9.767228 GCCTTCTCTCTCGATGTATATATACTA 57.233 37.037 20.80 9.98 34.41 1.82
901 1024 7.717875 GGCCTTCTCTCTCGATGTATATATACT 59.282 40.741 20.80 8.90 34.41 2.12
902 1025 7.307514 CGGCCTTCTCTCTCGATGTATATATAC 60.308 44.444 14.86 14.86 0.00 1.47
903 1026 6.706716 CGGCCTTCTCTCTCGATGTATATATA 59.293 42.308 0.00 0.00 0.00 0.86
904 1027 5.529430 CGGCCTTCTCTCTCGATGTATATAT 59.471 44.000 0.00 0.00 0.00 0.86
905 1028 4.876679 CGGCCTTCTCTCTCGATGTATATA 59.123 45.833 0.00 0.00 0.00 0.86
906 1029 3.692101 CGGCCTTCTCTCTCGATGTATAT 59.308 47.826 0.00 0.00 0.00 0.86
907 1030 3.075148 CGGCCTTCTCTCTCGATGTATA 58.925 50.000 0.00 0.00 0.00 1.47
908 1031 1.883275 CGGCCTTCTCTCTCGATGTAT 59.117 52.381 0.00 0.00 0.00 2.29
909 1032 1.309950 CGGCCTTCTCTCTCGATGTA 58.690 55.000 0.00 0.00 0.00 2.29
910 1033 2.010582 GCGGCCTTCTCTCTCGATGT 62.011 60.000 0.00 0.00 0.00 3.06
911 1034 1.299773 GCGGCCTTCTCTCTCGATG 60.300 63.158 0.00 0.00 0.00 3.84
912 1035 1.454847 AGCGGCCTTCTCTCTCGAT 60.455 57.895 0.00 0.00 0.00 3.59
913 1036 2.044848 AGCGGCCTTCTCTCTCGA 60.045 61.111 0.00 0.00 0.00 4.04
914 1037 2.103934 CAGCGGCCTTCTCTCTCG 59.896 66.667 0.00 0.00 0.00 4.04
915 1038 2.498726 CCAGCGGCCTTCTCTCTC 59.501 66.667 0.00 0.00 0.00 3.20
999 1126 1.604378 CCGCCTCACTTCCTCCATT 59.396 57.895 0.00 0.00 0.00 3.16
1494 1624 0.762418 TTTCCCCGAACAGCTTCTCA 59.238 50.000 0.00 0.00 0.00 3.27
1680 1810 4.559063 CTCCCCAGCTCCATGGCG 62.559 72.222 6.96 0.71 39.17 5.69
1949 2079 4.121317 TGCAAGCAAATTGAAAGGAAGTG 58.879 39.130 0.00 0.00 41.83 3.16
1953 2083 4.768583 ACTTTGCAAGCAAATTGAAAGGA 58.231 34.783 19.25 0.00 43.78 3.36
1959 2089 9.332301 CCAAATAATAACTTTGCAAGCAAATTG 57.668 29.630 19.25 16.41 43.78 2.32
1960 2090 9.065798 ACCAAATAATAACTTTGCAAGCAAATT 57.934 25.926 19.25 12.00 43.78 1.82
1961 2091 8.620116 ACCAAATAATAACTTTGCAAGCAAAT 57.380 26.923 19.25 9.35 43.78 2.32
1963 2093 7.930865 AGAACCAAATAATAACTTTGCAAGCAA 59.069 29.630 2.89 2.89 33.27 3.91
1964 2094 7.441017 AGAACCAAATAATAACTTTGCAAGCA 58.559 30.769 0.00 0.00 33.27 3.91
1965 2095 7.889589 AGAACCAAATAATAACTTTGCAAGC 57.110 32.000 0.00 0.00 33.27 4.01
2012 2161 7.792374 ATGACGTAATTTGCTATGTGATTCT 57.208 32.000 0.00 0.00 0.00 2.40
2013 2162 8.841444 AAATGACGTAATTTGCTATGTGATTC 57.159 30.769 10.20 0.00 28.31 2.52
2016 2165 7.333174 TGAGAAATGACGTAATTTGCTATGTGA 59.667 33.333 15.80 0.00 29.89 3.58
2032 2181 5.300752 TCAAGTTCCAGAGTGAGAAATGAC 58.699 41.667 0.00 0.00 0.00 3.06
2034 2183 6.654161 AGATTCAAGTTCCAGAGTGAGAAATG 59.346 38.462 0.00 0.00 0.00 2.32
2045 2213 9.831737 CACAGTAAAATAAGATTCAAGTTCCAG 57.168 33.333 0.00 0.00 0.00 3.86
2159 2327 2.501723 TCCATGGAGTTGAAGAGTAGCC 59.498 50.000 11.44 0.00 0.00 3.93
2184 2352 8.528643 TCGATTCTTGGAGTAAGACTAAATTCA 58.471 33.333 0.00 0.00 44.84 2.57
2247 2415 0.539051 AGGCTTCATTCAGGAGACCG 59.461 55.000 0.00 0.00 0.00 4.79
2352 2520 1.079503 CTGCTGTTTCCGCTAGTTCC 58.920 55.000 0.00 0.00 0.00 3.62
2406 2574 3.184628 TGACAGGATCACCAGATTTCCT 58.815 45.455 0.00 0.00 38.94 3.36
2439 2607 2.242196 ACCATCCCATTTTCCAGACGAT 59.758 45.455 0.00 0.00 0.00 3.73
2457 2625 1.136961 TCCATACCTGGGCAACACCA 61.137 55.000 0.00 0.00 43.34 4.17
2478 2646 5.825593 TGTGGTCTTTCTCCTTGAGTAAT 57.174 39.130 0.00 0.00 0.00 1.89
2635 2803 6.155910 TCTGCATCTTCCTCATTTTCTAGTCT 59.844 38.462 0.00 0.00 0.00 3.24
2655 2823 2.042686 ACAGAAACAGCTGTTCTGCA 57.957 45.000 34.39 0.00 46.42 4.41
2751 2919 3.439154 ACTTGGAAGATCAGAGCAGAGA 58.561 45.455 0.00 0.00 0.00 3.10
2757 2925 7.120873 ACATCAATTTGACTTGGAAGATCAGAG 59.879 37.037 0.15 0.00 0.00 3.35
2786 2954 3.430236 CCACCTTTTTGAAGAACCGCTTT 60.430 43.478 0.00 0.00 36.83 3.51
2790 2958 1.407258 TGCCACCTTTTTGAAGAACCG 59.593 47.619 0.00 0.00 0.00 4.44
2792 2960 3.855858 TGTTGCCACCTTTTTGAAGAAC 58.144 40.909 0.00 0.00 0.00 3.01
2799 2967 2.745968 TCCTTCTGTTGCCACCTTTTT 58.254 42.857 0.00 0.00 0.00 1.94
2839 3007 0.830648 GATGCCCAGGTAGTGCTACA 59.169 55.000 10.98 0.00 37.78 2.74
2847 3015 2.365617 GAGAAGAATCGATGCCCAGGTA 59.634 50.000 0.00 0.00 0.00 3.08
2861 3029 8.043113 TGATTTATAGCAGCAAGAAGAGAAGAA 58.957 33.333 0.00 0.00 0.00 2.52
2938 3106 6.718388 TGAAATTATATGCTTCGTCTGCAAG 58.282 36.000 4.23 0.00 44.01 4.01
2993 3161 8.394877 GTTCACGTATGTGGATTTCATTATTCA 58.605 33.333 15.02 0.00 46.42 2.57
3015 3183 9.230122 TGCTCATTTACTTATCATTTCAGTTCA 57.770 29.630 0.00 0.00 0.00 3.18
3028 3196 9.772973 TTTCTGTACTCTTTGCTCATTTACTTA 57.227 29.630 0.00 0.00 0.00 2.24
3059 3227 8.547967 TCCTCAACACAACTCATTTACTTATC 57.452 34.615 0.00 0.00 0.00 1.75
3084 3252 8.840321 GCACACAGACTCAACCAAATTATATAT 58.160 33.333 0.00 0.00 0.00 0.86
3122 3290 4.542662 GCTCAAGGCAATACATAGTGTG 57.457 45.455 0.00 0.00 41.35 3.82
3136 3304 2.186384 CTCCGCCTCTGCTCAAGG 59.814 66.667 0.00 0.00 36.95 3.61
3171 3339 1.799544 CCAAATGCCAAAGCTCCAAC 58.200 50.000 0.00 0.00 40.80 3.77
3213 3381 1.908066 AAAATTCACCTCGGCGTCGC 61.908 55.000 9.22 9.22 36.13 5.19
3228 3396 6.175471 GGCAATGATCTTCTTTTGGGAAAAT 58.825 36.000 0.00 0.00 0.00 1.82
3253 3421 2.359230 AGCGCCTTCTGAGCAACC 60.359 61.111 2.29 0.00 0.00 3.77
3272 3440 0.737715 GCAGGTCAACCTCTACGCAG 60.738 60.000 0.00 0.00 46.65 5.18
3320 3516 1.218047 GATCACTGGTGGCGCTACA 59.782 57.895 25.79 12.20 0.00 2.74
3359 3555 1.967319 AACGAGATGCACCTTGTTGT 58.033 45.000 13.32 0.00 38.85 3.32
3408 3604 0.895530 GAACACATCAGGAGGGACGA 59.104 55.000 0.00 0.00 0.00 4.20
3560 3830 4.514401 AGATTCCACCGTAGATTTTGACC 58.486 43.478 0.00 0.00 0.00 4.02
3561 3831 5.163754 CCAAGATTCCACCGTAGATTTTGAC 60.164 44.000 0.00 0.00 0.00 3.18
3566 3836 6.688073 ATATCCAAGATTCCACCGTAGATT 57.312 37.500 0.00 0.00 0.00 2.40
3572 3842 3.251729 CAGCAATATCCAAGATTCCACCG 59.748 47.826 0.00 0.00 0.00 4.94
3574 3844 5.841957 AACAGCAATATCCAAGATTCCAC 57.158 39.130 0.00 0.00 0.00 4.02
3624 3899 0.519077 GTGCCGAGCAGGAAAGAAAG 59.481 55.000 2.12 0.00 45.00 2.62
3626 3901 0.179032 TTGTGCCGAGCAGGAAAGAA 60.179 50.000 2.12 0.00 45.00 2.52
3665 3940 5.745227 TGACATTTAGCAAAACCCCAAAAA 58.255 33.333 0.00 0.00 0.00 1.94
3666 3941 5.359194 TGACATTTAGCAAAACCCCAAAA 57.641 34.783 0.00 0.00 0.00 2.44
3667 3942 5.163258 ACATGACATTTAGCAAAACCCCAAA 60.163 36.000 0.00 0.00 0.00 3.28
3668 3943 4.346418 ACATGACATTTAGCAAAACCCCAA 59.654 37.500 0.00 0.00 0.00 4.12
3669 3944 3.900601 ACATGACATTTAGCAAAACCCCA 59.099 39.130 0.00 0.00 0.00 4.96
3670 3945 4.535526 ACATGACATTTAGCAAAACCCC 57.464 40.909 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.