Multiple sequence alignment - TraesCS4D01G089600

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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 TraesCS4D01G089600 chr4D 100.000 3563 0 0 1 3563 65077077 65073515 0.000000e+00 6580
1 TraesCS4D01G089600 chr4D 93.617 658 39 3 2909 3563 83024762 83024105 0.000000e+00 979
2 TraesCS4D01G089600 chr4A 89.653 2938 200 44 4 2907 530939425 530936558 0.000000e+00 3646
3 TraesCS4D01G089600 chr4A 76.531 490 93 12 1034 1522 531247130 531247598 7.640000e-62 248
4 TraesCS4D01G089600 chr4A 80.899 178 29 5 115 289 474937596 474937421 6.200000e-28 135
5 TraesCS4D01G089600 chr4B 95.879 1626 46 10 1226 2848 95374311 95372704 0.000000e+00 2612
6 TraesCS4D01G089600 chr4B 83.691 1165 101 40 69 1200 95375410 95374302 0.000000e+00 1016
7 TraesCS4D01G089600 chr5D 96.505 658 20 3 2909 3563 434681043 434681700 0.000000e+00 1085
8 TraesCS4D01G089600 chr5D 93.797 661 38 3 2906 3563 553625364 553624704 0.000000e+00 990
9 TraesCS4D01G089600 chr5D 93.343 661 41 3 2906 3563 389487324 389487984 0.000000e+00 974
10 TraesCS4D01G089600 chr5D 82.174 230 27 10 69 287 459761151 459761377 6.070000e-43 185
11 TraesCS4D01G089600 chr5D 81.416 226 29 7 69 284 459753012 459753234 4.730000e-39 172
12 TraesCS4D01G089600 chr1A 94.179 670 36 3 2897 3563 30298169 30298838 0.000000e+00 1018
13 TraesCS4D01G089600 chrUn 94.402 661 33 4 2906 3563 28297064 28296405 0.000000e+00 1013
14 TraesCS4D01G089600 chrUn 78.914 1252 220 29 1221 2445 12633140 12631906 0.000000e+00 809
15 TraesCS4D01G089600 chr5B 93.646 661 38 4 2906 3563 70467479 70468138 0.000000e+00 985
16 TraesCS4D01G089600 chr5B 85.185 135 14 5 162 293 273158453 273158584 2.230000e-27 134
17 TraesCS4D01G089600 chr7D 93.636 660 37 4 2906 3562 425440576 425439919 0.000000e+00 981
18 TraesCS4D01G089600 chr1D 93.617 658 38 4 2909 3563 143357396 143358052 0.000000e+00 979
19 TraesCS4D01G089600 chr1D 79.279 777 146 9 1776 2540 382743046 382742273 2.440000e-146 529
20 TraesCS4D01G089600 chr1D 80.723 166 25 3 128 287 401286287 401286123 4.830000e-24 122
21 TraesCS4D01G089600 chr2D 79.669 1328 225 33 1244 2541 11045482 11046794 0.000000e+00 915
22 TraesCS4D01G089600 chr2D 75.410 244 60 0 1285 1528 155477376 155477133 6.250000e-23 119
23 TraesCS4D01G089600 chr2B 77.878 1546 264 46 1026 2542 17366299 17364803 0.000000e+00 889
24 TraesCS4D01G089600 chr7B 77.419 1550 268 49 1027 2542 78244573 78243072 0.000000e+00 848
25 TraesCS4D01G089600 chr7B 81.250 144 19 5 148 289 266573706 266573569 3.760000e-20 110
26 TraesCS4D01G089600 chr2A 80.853 914 149 19 1642 2542 11910504 11909604 0.000000e+00 695
27 TraesCS4D01G089600 chr3A 76.992 778 149 24 1756 2515 32415706 32416471 5.500000e-113 418
28 TraesCS4D01G089600 chr3A 78.761 226 39 6 69 287 521573737 521573960 3.710000e-30 143
29 TraesCS4D01G089600 chr1B 81.169 154 18 9 194 337 659722858 659723010 2.910000e-21 113


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 TraesCS4D01G089600 chr4D 65073515 65077077 3562 True 6580 6580 100.000 1 3563 1 chr4D.!!$R1 3562
1 TraesCS4D01G089600 chr4D 83024105 83024762 657 True 979 979 93.617 2909 3563 1 chr4D.!!$R2 654
2 TraesCS4D01G089600 chr4A 530936558 530939425 2867 True 3646 3646 89.653 4 2907 1 chr4A.!!$R2 2903
3 TraesCS4D01G089600 chr4B 95372704 95375410 2706 True 1814 2612 89.785 69 2848 2 chr4B.!!$R1 2779
4 TraesCS4D01G089600 chr5D 434681043 434681700 657 False 1085 1085 96.505 2909 3563 1 chr5D.!!$F2 654
5 TraesCS4D01G089600 chr5D 553624704 553625364 660 True 990 990 93.797 2906 3563 1 chr5D.!!$R1 657
6 TraesCS4D01G089600 chr5D 389487324 389487984 660 False 974 974 93.343 2906 3563 1 chr5D.!!$F1 657
7 TraesCS4D01G089600 chr1A 30298169 30298838 669 False 1018 1018 94.179 2897 3563 1 chr1A.!!$F1 666
8 TraesCS4D01G089600 chrUn 28296405 28297064 659 True 1013 1013 94.402 2906 3563 1 chrUn.!!$R2 657
9 TraesCS4D01G089600 chrUn 12631906 12633140 1234 True 809 809 78.914 1221 2445 1 chrUn.!!$R1 1224
10 TraesCS4D01G089600 chr5B 70467479 70468138 659 False 985 985 93.646 2906 3563 1 chr5B.!!$F1 657
11 TraesCS4D01G089600 chr7D 425439919 425440576 657 True 981 981 93.636 2906 3562 1 chr7D.!!$R1 656
12 TraesCS4D01G089600 chr1D 143357396 143358052 656 False 979 979 93.617 2909 3563 1 chr1D.!!$F1 654
13 TraesCS4D01G089600 chr1D 382742273 382743046 773 True 529 529 79.279 1776 2540 1 chr1D.!!$R1 764
14 TraesCS4D01G089600 chr2D 11045482 11046794 1312 False 915 915 79.669 1244 2541 1 chr2D.!!$F1 1297
15 TraesCS4D01G089600 chr2B 17364803 17366299 1496 True 889 889 77.878 1026 2542 1 chr2B.!!$R1 1516
16 TraesCS4D01G089600 chr7B 78243072 78244573 1501 True 848 848 77.419 1027 2542 1 chr7B.!!$R1 1515
17 TraesCS4D01G089600 chr2A 11909604 11910504 900 True 695 695 80.853 1642 2542 1 chr2A.!!$R1 900
18 TraesCS4D01G089600 chr3A 32415706 32416471 765 False 418 418 76.992 1756 2515 1 chr3A.!!$F1 759

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
136 140 0.684535 TCGCCTGAGTGGATGAACAA 59.315 50.0 0.0 0.0 38.35 2.83 F
977 1016 0.743701 AGATTGAAGCAGCTCGCCTG 60.744 55.0 0.0 0.0 44.04 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1119 1158 0.033366 AAACAGTTCCAAATGCGCCC 59.967 50.0 4.18 0.0 0.0 6.13 R
2701 2803 0.179192 CGTCCATTCCATGTTGCACG 60.179 55.0 0.00 0.0 0.0 5.34 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
34 35 5.647225 TGTTTAGGACTAACGGTTTTGTTGT 59.353 36.000 0.00 0.00 33.32 3.32
35 36 6.150809 TGTTTAGGACTAACGGTTTTGTTGTT 59.849 34.615 0.00 0.00 33.32 2.83
40 41 6.319405 AGGACTAACGGTTTTGTTGTTATTGT 59.681 34.615 0.00 0.00 33.32 2.71
53 54 3.334691 TGTTATTGTTCTTGCCTCTCGG 58.665 45.455 0.00 0.00 0.00 4.63
96 98 3.703052 AGGATGGAACATCCTTGAAATGC 59.297 43.478 21.83 0.00 45.78 3.56
103 107 5.471456 GGAACATCCTTGAAATGCGATCTAT 59.529 40.000 0.00 0.00 32.53 1.98
136 140 0.684535 TCGCCTGAGTGGATGAACAA 59.315 50.000 0.00 0.00 38.35 2.83
141 145 3.496130 GCCTGAGTGGATGAACAATATCG 59.504 47.826 0.00 0.00 38.35 2.92
198 202 2.936498 ACCCTCATTTCAGCGTATTTCG 59.064 45.455 0.00 0.00 43.12 3.46
201 205 3.865745 CCTCATTTCAGCGTATTTCGTCT 59.134 43.478 0.00 0.00 42.13 4.18
344 355 7.135591 TCCAAAAGGGATTTTCAGACAATTT 57.864 32.000 0.00 0.00 42.15 1.82
347 358 8.344831 CCAAAAGGGATTTTCAGACAATTTTTC 58.655 33.333 0.00 0.00 40.01 2.29
382 393 6.410942 AATAGAAGAGGCAAAGTTTTTGCT 57.589 33.333 21.54 10.87 44.36 3.91
409 439 3.513750 AAGCCTTGCCCCTGACACC 62.514 63.158 0.00 0.00 0.00 4.16
549 579 8.019669 GCGATGCTGACATGATTTTATATTCTT 58.980 33.333 0.00 0.00 36.35 2.52
567 597 4.085357 TCTTATTAGTGGGCGCATCATT 57.915 40.909 10.83 6.48 0.00 2.57
622 652 2.681706 CATCATAGGCTAGACCGCTTG 58.318 52.381 0.00 0.00 46.52 4.01
647 678 2.622942 TCAAGTCAACACATTCTTGCCC 59.377 45.455 0.00 0.00 37.68 5.36
700 731 4.698201 TCATATAAATCCACCCGAAGCA 57.302 40.909 0.00 0.00 0.00 3.91
707 738 2.644992 CACCCGAAGCAAGCAACC 59.355 61.111 0.00 0.00 0.00 3.77
742 779 2.259917 TCTTCTCACAAGCCTCATCCA 58.740 47.619 0.00 0.00 0.00 3.41
748 785 1.608590 CACAAGCCTCATCCACGTTTT 59.391 47.619 0.00 0.00 0.00 2.43
754 791 2.604614 GCCTCATCCACGTTTTGTTGTC 60.605 50.000 0.00 0.00 0.00 3.18
793 830 2.162681 GAGAATCACCCCCAAGTGTTG 58.837 52.381 0.00 0.00 38.91 3.33
808 845 4.278975 AGTGTTGGATCTTCTTCAGGTC 57.721 45.455 0.00 0.00 30.66 3.85
812 849 4.249661 GTTGGATCTTCTTCAGGTCAGTC 58.750 47.826 0.00 0.00 33.65 3.51
818 855 5.373812 TCTTCTTCAGGTCAGTCCTTTTT 57.626 39.130 0.00 0.00 45.67 1.94
824 861 4.000988 TCAGGTCAGTCCTTTTTAATCGC 58.999 43.478 0.00 0.00 45.67 4.58
846 883 5.165911 CGAAGCTGCATATTTTCAGATGT 57.834 39.130 1.02 0.00 32.26 3.06
847 884 5.575957 CGAAGCTGCATATTTTCAGATGTT 58.424 37.500 1.02 0.00 32.26 2.71
848 885 5.680229 CGAAGCTGCATATTTTCAGATGTTC 59.320 40.000 1.02 0.00 32.26 3.18
849 886 6.457934 CGAAGCTGCATATTTTCAGATGTTCT 60.458 38.462 1.02 0.00 32.26 3.01
850 887 6.770746 AGCTGCATATTTTCAGATGTTCTT 57.229 33.333 1.02 0.00 32.26 2.52
851 888 6.561614 AGCTGCATATTTTCAGATGTTCTTG 58.438 36.000 1.02 0.00 32.26 3.02
852 889 5.231568 GCTGCATATTTTCAGATGTTCTTGC 59.768 40.000 0.00 0.00 32.26 4.01
853 890 6.270156 TGCATATTTTCAGATGTTCTTGCA 57.730 33.333 0.00 0.00 34.33 4.08
854 891 6.689554 TGCATATTTTCAGATGTTCTTGCAA 58.310 32.000 0.00 0.00 33.85 4.08
855 892 7.324935 TGCATATTTTCAGATGTTCTTGCAAT 58.675 30.769 0.00 0.00 33.85 3.56
856 893 8.468399 TGCATATTTTCAGATGTTCTTGCAATA 58.532 29.630 0.00 0.00 33.85 1.90
857 894 9.304731 GCATATTTTCAGATGTTCTTGCAATAA 57.695 29.630 0.00 0.00 0.00 1.40
859 896 9.807649 ATATTTTCAGATGTTCTTGCAATAACC 57.192 29.630 20.98 9.66 0.00 2.85
860 897 6.647334 TTTCAGATGTTCTTGCAATAACCA 57.353 33.333 20.98 11.86 0.00 3.67
861 898 6.839124 TTCAGATGTTCTTGCAATAACCAT 57.161 33.333 20.98 15.15 0.00 3.55
862 899 6.198650 TCAGATGTTCTTGCAATAACCATG 57.801 37.500 20.98 16.66 0.00 3.66
882 919 5.068198 CCATGTATGCTGCTTAGTTTCCAAT 59.932 40.000 0.00 0.00 0.00 3.16
906 943 3.475566 TCCATGTATGCCTAGTCTTGC 57.524 47.619 0.00 0.00 0.00 4.01
907 944 2.771372 TCCATGTATGCCTAGTCTTGCA 59.229 45.455 0.00 0.00 42.52 4.08
930 967 9.588096 TGCATACTTAGATCTGTCCTTCTATAA 57.412 33.333 5.18 0.00 0.00 0.98
956 995 4.575645 TGCATATGAATTTCTGACGATGCA 59.424 37.500 6.97 14.45 44.41 3.96
960 999 7.148523 GCATATGAATTTCTGACGATGCATAGA 60.149 37.037 14.19 3.14 38.60 1.98
973 1012 2.207590 TGCATAGATTGAAGCAGCTCG 58.792 47.619 0.00 0.00 32.48 5.03
977 1016 0.743701 AGATTGAAGCAGCTCGCCTG 60.744 55.000 0.00 0.00 44.04 4.85
1062 1101 2.614057 CACATTACCGAAGAATCTGCCC 59.386 50.000 0.00 0.00 0.00 5.36
1148 1187 8.779303 CGCATTTGGAACTGTTTATATGGTATA 58.221 33.333 0.00 0.00 0.00 1.47
1171 1210 5.912149 TGGTCATTCCTCTGCCTTTATAT 57.088 39.130 0.00 0.00 37.07 0.86
1200 1260 4.222114 CCTTCGCATGAGTTTCTGAAAAC 58.778 43.478 4.09 3.37 44.24 2.43
1201 1261 4.261155 CCTTCGCATGAGTTTCTGAAAACA 60.261 41.667 4.09 8.75 45.94 2.83
1202 1262 4.209452 TCGCATGAGTTTCTGAAAACAC 57.791 40.909 4.09 0.67 45.94 3.32
1204 1264 4.335315 TCGCATGAGTTTCTGAAAACACTT 59.665 37.500 4.09 0.00 45.94 3.16
1205 1265 4.672413 CGCATGAGTTTCTGAAAACACTTC 59.328 41.667 4.09 0.00 45.94 3.01
1206 1266 5.504665 CGCATGAGTTTCTGAAAACACTTCT 60.505 40.000 4.09 0.00 45.94 2.85
1207 1267 5.684626 GCATGAGTTTCTGAAAACACTTCTG 59.315 40.000 4.09 5.34 45.94 3.02
1208 1268 6.458751 GCATGAGTTTCTGAAAACACTTCTGA 60.459 38.462 4.09 0.00 45.94 3.27
1209 1269 7.475015 CATGAGTTTCTGAAAACACTTCTGAA 58.525 34.615 4.09 3.54 45.94 3.02
1210 1270 7.447374 TGAGTTTCTGAAAACACTTCTGAAA 57.553 32.000 4.09 12.64 45.94 2.69
1351 1411 4.129878 GTTTGCTAACGAGGTTCAGAAC 57.870 45.455 4.52 4.52 0.00 3.01
1402 1462 0.317479 AGTTGGTCGGCTACTGTCAC 59.683 55.000 0.00 0.00 0.00 3.67
1546 1608 4.755266 ATACTACCCGACTCAAATTGCT 57.245 40.909 0.00 0.00 0.00 3.91
2027 2109 7.822334 CAGAATGTTGTTGGGTCATAGTAAGTA 59.178 37.037 0.00 0.00 0.00 2.24
2053 2135 4.385447 CCACAAACTGCGATAATGTTTTGG 59.615 41.667 0.00 0.00 32.42 3.28
2436 2538 3.053395 ACCCATTGTTAGATGCAGATGGT 60.053 43.478 0.00 0.00 33.79 3.55
2523 2625 7.637511 AGAGACCATCCATAGAAACAATTCTT 58.362 34.615 0.00 0.00 43.43 2.52
2567 2669 7.035004 TGTGCATCCATAAGAAACTAAAATGC 58.965 34.615 0.00 0.00 37.94 3.56
2589 2691 2.937469 TGCCAGGTATGCAATTTTCG 57.063 45.000 0.00 0.00 35.40 3.46
2593 2695 2.223572 CCAGGTATGCAATTTTCGCTCC 60.224 50.000 0.00 0.00 0.00 4.70
2612 2714 5.914635 CGCTCCGTTATAAACCGACTTATTA 59.085 40.000 0.00 0.00 0.00 0.98
2623 2725 7.624360 AAACCGACTTATTATGCATTTCAGA 57.376 32.000 3.54 0.00 0.00 3.27
2701 2803 1.748493 TGGGTTTTGTTCAGCAGACAC 59.252 47.619 0.00 0.00 0.00 3.67
2708 2810 0.316196 GTTCAGCAGACACGTGCAAC 60.316 55.000 17.22 7.68 46.60 4.17
2733 2835 6.911250 TGGAATGGACGCTCTCTATTATTA 57.089 37.500 0.00 0.00 30.45 0.98
2796 2898 6.916440 TGTACTATGTACGTCATTGTGAAGT 58.084 36.000 17.89 11.98 41.15 3.01
2848 2950 5.008712 TGCTACGTACTCCACATATCTCTTG 59.991 44.000 0.00 0.00 0.00 3.02
3100 3205 2.174349 GGAGCAAAAGACGCTGCG 59.826 61.111 21.91 21.91 43.51 5.18
3102 3207 2.591715 AGCAAAAGACGCTGCGGT 60.592 55.556 26.95 11.85 43.51 5.68
3122 3227 2.819595 CACGAAGACCCGCCATGG 60.820 66.667 7.63 7.63 37.55 3.66
3269 3374 1.061546 GGTACACCAAAGGGACCAGA 58.938 55.000 0.00 0.00 38.05 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.719778 AAACCGTTAGTCCTAAACAAGTTAG 57.280 36.000 0.00 0.00 39.25 2.34
5 6 7.552330 ACAAAACCGTTAGTCCTAAACAAGTTA 59.448 33.333 0.00 0.00 0.00 2.24
6 7 6.375174 ACAAAACCGTTAGTCCTAAACAAGTT 59.625 34.615 0.00 0.00 0.00 2.66
7 8 5.882000 ACAAAACCGTTAGTCCTAAACAAGT 59.118 36.000 0.00 0.00 0.00 3.16
8 9 6.367686 ACAAAACCGTTAGTCCTAAACAAG 57.632 37.500 0.00 0.00 0.00 3.16
9 10 6.150809 ACAACAAAACCGTTAGTCCTAAACAA 59.849 34.615 0.00 0.00 0.00 2.83
10 11 5.647225 ACAACAAAACCGTTAGTCCTAAACA 59.353 36.000 0.00 0.00 0.00 2.83
11 12 6.122850 ACAACAAAACCGTTAGTCCTAAAC 57.877 37.500 0.00 0.00 0.00 2.01
23 24 5.276631 GGCAAGAACAATAACAACAAAACCG 60.277 40.000 0.00 0.00 0.00 4.44
26 27 6.872920 AGAGGCAAGAACAATAACAACAAAA 58.127 32.000 0.00 0.00 0.00 2.44
56 57 2.104792 TCCTGAAATTCGGCCTCCATAG 59.895 50.000 0.00 0.00 0.00 2.23
57 58 2.123589 TCCTGAAATTCGGCCTCCATA 58.876 47.619 0.00 0.00 0.00 2.74
109 113 0.534412 CCACTCAGGCGATGACTTCT 59.466 55.000 0.00 0.00 33.22 2.85
110 114 0.532573 TCCACTCAGGCGATGACTTC 59.467 55.000 0.00 0.00 37.29 3.01
118 122 1.742761 ATTGTTCATCCACTCAGGCG 58.257 50.000 0.00 0.00 37.29 5.52
136 140 5.354234 CCTGAGGCTTTTTAACACACGATAT 59.646 40.000 0.00 0.00 0.00 1.63
141 145 4.649088 AACCTGAGGCTTTTTAACACAC 57.351 40.909 0.00 0.00 0.00 3.82
300 306 2.515523 CCGAGCTTCATGGGCCAG 60.516 66.667 13.78 4.37 0.00 4.85
301 307 4.802051 GCCGAGCTTCATGGGCCA 62.802 66.667 9.61 9.61 38.06 5.36
366 377 5.351189 TCTTTTGAAGCAAAAACTTTGCCTC 59.649 36.000 17.99 15.56 45.98 4.70
382 393 1.416030 GGGGCAAGGCTTTCTTTTGAA 59.584 47.619 0.00 0.00 36.52 2.69
409 439 0.789753 CGTGTCTCTGTCAGTACGCG 60.790 60.000 20.94 20.94 39.15 6.01
567 597 6.317642 TGATGTCTTTCCGTGAAGAAGAAAAA 59.682 34.615 0.00 0.00 37.40 1.94
572 602 3.124297 GCTGATGTCTTTCCGTGAAGAAG 59.876 47.826 0.00 0.00 37.40 2.85
573 603 3.067106 GCTGATGTCTTTCCGTGAAGAA 58.933 45.455 0.00 0.00 37.40 2.52
574 604 2.688507 GCTGATGTCTTTCCGTGAAGA 58.311 47.619 0.00 0.00 33.44 2.87
575 605 1.391485 CGCTGATGTCTTTCCGTGAAG 59.609 52.381 0.00 0.00 0.00 3.02
579 609 0.603569 ACTCGCTGATGTCTTTCCGT 59.396 50.000 0.00 0.00 0.00 4.69
581 611 2.266554 CTCACTCGCTGATGTCTTTCC 58.733 52.381 0.00 0.00 0.00 3.13
622 652 4.555511 GCAAGAATGTGTTGACTTGACTCC 60.556 45.833 0.00 0.00 41.16 3.85
636 666 3.737172 GCGCGTGGGCAAGAATGT 61.737 61.111 8.43 0.00 39.92 2.71
647 678 2.013483 GATCTGGATCGAGCGCGTG 61.013 63.158 10.30 0.00 38.98 5.34
700 731 1.799258 CGCTTCCTTGCTGGTTGCTT 61.799 55.000 11.36 0.00 43.37 3.91
707 738 2.821307 GAAGAATCGCTTCCTTGCTG 57.179 50.000 0.00 0.00 45.90 4.41
742 779 1.329599 GCGAAGAGGACAACAAAACGT 59.670 47.619 0.00 0.00 0.00 3.99
748 785 0.601046 CAGCTGCGAAGAGGACAACA 60.601 55.000 0.00 0.00 0.00 3.33
793 830 3.535280 GGACTGACCTGAAGAAGATCC 57.465 52.381 0.00 0.00 35.41 3.36
808 845 3.125316 AGCTTCGCGATTAAAAAGGACTG 59.875 43.478 10.88 0.00 0.00 3.51
812 849 2.177173 GCAGCTTCGCGATTAAAAAGG 58.823 47.619 10.88 0.00 0.00 3.11
818 855 4.272261 TGAAAATATGCAGCTTCGCGATTA 59.728 37.500 10.88 0.00 33.35 1.75
824 861 5.165911 ACATCTGAAAATATGCAGCTTCG 57.834 39.130 0.00 0.00 32.27 3.79
830 867 6.270156 TGCAAGAACATCTGAAAATATGCA 57.730 33.333 0.00 0.00 37.70 3.96
836 873 7.048629 TGGTTATTGCAAGAACATCTGAAAA 57.951 32.000 31.44 9.15 32.02 2.29
837 874 6.647334 TGGTTATTGCAAGAACATCTGAAA 57.353 33.333 31.44 10.31 32.02 2.69
838 875 6.209192 ACATGGTTATTGCAAGAACATCTGAA 59.791 34.615 31.44 14.07 32.02 3.02
839 876 5.711506 ACATGGTTATTGCAAGAACATCTGA 59.288 36.000 31.44 14.24 32.02 3.27
840 877 5.957798 ACATGGTTATTGCAAGAACATCTG 58.042 37.500 31.44 25.66 32.02 2.90
841 878 7.682741 GCATACATGGTTATTGCAAGAACATCT 60.683 37.037 31.44 16.38 32.02 2.90
842 879 6.418819 GCATACATGGTTATTGCAAGAACATC 59.581 38.462 31.44 19.03 32.02 3.06
843 880 6.097270 AGCATACATGGTTATTGCAAGAACAT 59.903 34.615 31.44 20.92 34.35 2.71
844 881 5.418524 AGCATACATGGTTATTGCAAGAACA 59.581 36.000 31.44 19.73 34.35 3.18
845 882 5.745294 CAGCATACATGGTTATTGCAAGAAC 59.255 40.000 25.14 25.14 36.17 3.01
846 883 5.679382 GCAGCATACATGGTTATTGCAAGAA 60.679 40.000 4.94 3.20 36.17 2.52
847 884 4.202040 GCAGCATACATGGTTATTGCAAGA 60.202 41.667 4.94 0.00 36.17 3.02
848 885 4.046462 GCAGCATACATGGTTATTGCAAG 58.954 43.478 4.94 0.00 36.17 4.01
849 886 3.700539 AGCAGCATACATGGTTATTGCAA 59.299 39.130 0.00 0.00 36.17 4.08
850 887 3.289836 AGCAGCATACATGGTTATTGCA 58.710 40.909 13.65 0.00 36.17 4.08
851 888 3.996150 AGCAGCATACATGGTTATTGC 57.004 42.857 0.00 1.59 36.17 3.56
852 889 6.624352 ACTAAGCAGCATACATGGTTATTG 57.376 37.500 0.00 0.00 39.23 1.90
853 890 7.201821 GGAAACTAAGCAGCATACATGGTTATT 60.202 37.037 0.00 0.00 39.23 1.40
854 891 6.263168 GGAAACTAAGCAGCATACATGGTTAT 59.737 38.462 0.00 0.00 39.23 1.89
855 892 5.588648 GGAAACTAAGCAGCATACATGGTTA 59.411 40.000 0.00 0.00 39.06 2.85
856 893 4.399303 GGAAACTAAGCAGCATACATGGTT 59.601 41.667 0.00 0.00 41.06 3.67
857 894 3.947834 GGAAACTAAGCAGCATACATGGT 59.052 43.478 0.00 0.00 39.42 3.55
858 895 3.947196 TGGAAACTAAGCAGCATACATGG 59.053 43.478 0.00 0.00 0.00 3.66
859 896 5.565592 TTGGAAACTAAGCAGCATACATG 57.434 39.130 0.00 0.00 0.00 3.21
860 897 7.282585 TCTATTGGAAACTAAGCAGCATACAT 58.717 34.615 0.00 0.00 0.00 2.29
861 898 6.649155 TCTATTGGAAACTAAGCAGCATACA 58.351 36.000 0.00 0.00 0.00 2.29
862 899 7.095017 GGATCTATTGGAAACTAAGCAGCATAC 60.095 40.741 0.00 0.00 0.00 2.39
882 919 5.047021 GCAAGACTAGGCATACATGGATCTA 60.047 44.000 0.00 0.00 0.00 1.98
930 967 4.769688 TCGTCAGAAATTCATATGCACCT 58.230 39.130 0.00 0.00 0.00 4.00
933 970 4.575645 TGCATCGTCAGAAATTCATATGCA 59.424 37.500 12.94 12.94 44.33 3.96
939 976 6.762661 TCAATCTATGCATCGTCAGAAATTCA 59.237 34.615 0.19 0.00 0.00 2.57
956 995 1.415659 AGGCGAGCTGCTTCAATCTAT 59.584 47.619 2.53 0.00 45.43 1.98
960 999 0.321919 TTCAGGCGAGCTGCTTCAAT 60.322 50.000 2.53 0.00 45.43 2.57
973 1012 1.408702 TGGTTGAACAAGCTTTCAGGC 59.591 47.619 15.77 0.00 36.84 4.85
977 1016 4.836125 TCTGATGGTTGAACAAGCTTTC 57.164 40.909 15.77 12.91 39.38 2.62
1018 1057 3.659089 GAACGCTCGGCTGGCCTAA 62.659 63.158 3.32 0.00 0.00 2.69
1019 1058 4.143333 GAACGCTCGGCTGGCCTA 62.143 66.667 3.32 0.00 0.00 3.93
1023 1062 2.507992 CTCAGAACGCTCGGCTGG 60.508 66.667 12.14 0.00 0.00 4.85
1062 1101 6.347725 CGGTGATGGTTTTCAGAAAGTCTAAG 60.348 42.308 0.00 0.00 0.00 2.18
1119 1158 0.033366 AAACAGTTCCAAATGCGCCC 59.967 50.000 4.18 0.00 0.00 6.13
1148 1187 4.803329 ATAAAGGCAGAGGAATGACCAT 57.197 40.909 0.00 0.00 42.04 3.55
1171 1210 4.338118 AGAAACTCATGCGAAGGTGAAAAA 59.662 37.500 0.00 0.00 0.00 1.94
1209 1269 4.706035 TCAGCAAACATTGGCATCTTTTT 58.294 34.783 0.00 0.00 0.00 1.94
1210 1270 4.339872 TCAGCAAACATTGGCATCTTTT 57.660 36.364 0.00 0.00 0.00 2.27
1330 1390 3.558418 TGTTCTGAACCTCGTTAGCAAAC 59.442 43.478 17.26 0.00 0.00 2.93
1351 1411 9.037058 ACATTTTCATGGTGGAGAGCCATAATG 62.037 40.741 12.83 12.83 44.25 1.90
1402 1462 3.792124 GCACCACTTTCTTTTGACCTTCG 60.792 47.826 0.00 0.00 0.00 3.79
1660 1737 7.805071 CCTTTCAGTACAATAGCAAGTTCTTTG 59.195 37.037 0.00 0.00 39.88 2.77
2027 2109 3.674997 ACATTATCGCAGTTTGTGGTCT 58.325 40.909 0.00 0.00 0.00 3.85
2053 2135 7.023197 TGCAGTTTACTTTAAGACAAAGGAC 57.977 36.000 0.00 0.00 0.00 3.85
2296 2385 9.696917 CATGAGCTTTTAAAGTTTAGTTTCCAT 57.303 29.630 6.57 0.00 0.00 3.41
2523 2625 2.288579 ACATCGTCCGTTTAGCTTGTCA 60.289 45.455 0.00 0.00 0.00 3.58
2567 2669 3.460103 GAAAATTGCATACCTGGCATGG 58.540 45.455 8.92 0.00 41.58 3.66
2589 2691 7.620806 GCATAATAAGTCGGTTTATAACGGAGC 60.621 40.741 0.00 0.00 40.72 4.70
2593 2695 9.872757 AAATGCATAATAAGTCGGTTTATAACG 57.127 29.630 0.00 0.00 0.00 3.18
2612 2714 5.138276 AGGTTATCAGCATCTGAAATGCAT 58.862 37.500 12.12 0.00 44.04 3.96
2701 2803 0.179192 CGTCCATTCCATGTTGCACG 60.179 55.000 0.00 0.00 0.00 5.34
2708 2810 3.674528 ATAGAGAGCGTCCATTCCATG 57.325 47.619 0.00 0.00 0.00 3.66
2770 2872 8.680001 ACTTCACAATGACGTACATAGTACATA 58.320 33.333 7.93 0.00 38.38 2.29
2771 2873 7.544622 ACTTCACAATGACGTACATAGTACAT 58.455 34.615 7.93 0.00 38.38 2.29
2772 2874 6.916440 ACTTCACAATGACGTACATAGTACA 58.084 36.000 7.93 0.00 38.38 2.90
2773 2875 7.249147 AGACTTCACAATGACGTACATAGTAC 58.751 38.462 0.00 0.00 38.38 2.73
2774 2876 7.387119 AGACTTCACAATGACGTACATAGTA 57.613 36.000 0.00 0.00 38.38 1.82
2775 2877 6.268825 AGACTTCACAATGACGTACATAGT 57.731 37.500 0.00 0.00 38.38 2.12
2776 2878 8.858003 AATAGACTTCACAATGACGTACATAG 57.142 34.615 0.00 0.00 38.38 2.23
2848 2950 9.362151 TGGAGAATAAAAATATCCATTACCACC 57.638 33.333 0.00 0.00 35.16 4.61
2884 2986 8.902806 TCTTAACTGAAATTGAACAGACAACAT 58.097 29.630 12.37 0.00 37.54 2.71
2885 2987 8.275015 TCTTAACTGAAATTGAACAGACAACA 57.725 30.769 12.37 0.00 37.54 3.33
2886 2988 9.567848 TTTCTTAACTGAAATTGAACAGACAAC 57.432 29.630 12.37 0.00 37.54 3.32
2999 3101 1.076412 TTGTCTTGCTGTGCCCCAA 60.076 52.632 0.00 0.00 0.00 4.12
3078 3183 0.321122 AGCGTCTTTTGCTCCTCCTG 60.321 55.000 0.00 0.00 38.62 3.86
3269 3374 1.679977 TCGCGCTAGGTACCCTTGT 60.680 57.895 8.74 0.00 34.61 3.16
3290 3395 1.668151 CTAGGCGCGCCCCTATTTC 60.668 63.158 44.47 19.17 36.88 2.17


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

AutoCloner maintained by Alex Coulton.