Multiple sequence alignment - TraesCS3D01G217200

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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 TraesCS3D01G217200 chr3D 100.000 5126 0 0 1 5126 295136029 295141154 0.000000e+00 9467.0
1 TraesCS3D01G217200 chr3D 92.920 113 8 0 1 113 414780587 414780699 1.140000e-36 165.0
2 TraesCS3D01G217200 chr3D 91.228 114 10 0 1 114 272490146 272490259 6.870000e-34 156.0
3 TraesCS3D01G217200 chr3B 95.819 3444 79 18 898 4289 389256050 389259480 0.000000e+00 5502.0
4 TraesCS3D01G217200 chr3B 92.047 767 51 6 1 766 389255281 389256038 0.000000e+00 1070.0
5 TraesCS3D01G217200 chr3B 93.794 709 19 9 4433 5123 389259809 389260510 0.000000e+00 1042.0
6 TraesCS3D01G217200 chr3B 98.182 55 1 0 4378 4432 389259574 389259628 4.220000e-16 97.1
7 TraesCS3D01G217200 chr3B 97.561 41 1 0 818 858 84445374 84445334 2.560000e-08 71.3
8 TraesCS3D01G217200 chr3A 97.120 1910 32 5 2189 4077 392779365 392781272 0.000000e+00 3201.0
9 TraesCS3D01G217200 chr3A 93.722 1784 73 12 444 2193 392777486 392779264 0.000000e+00 2638.0
10 TraesCS3D01G217200 chr3A 92.195 410 25 2 1 410 392777089 392777491 1.600000e-159 573.0
11 TraesCS3D01G217200 chr3A 93.725 255 7 2 4875 5126 392799604 392799852 1.740000e-99 374.0
12 TraesCS3D01G217200 chr3A 84.507 142 12 8 735 867 697244686 697244826 1.160000e-26 132.0
13 TraesCS3D01G217200 chr3A 82.143 140 19 5 4478 4614 392781826 392781962 1.170000e-21 115.0
14 TraesCS3D01G217200 chr5A 94.828 116 6 0 1 116 353866097 353865982 1.130000e-41 182.0
15 TraesCS3D01G217200 chr5D 92.035 113 9 0 1 113 373723236 373723348 5.310000e-35 159.0
16 TraesCS3D01G217200 chr5D 91.892 111 9 0 1 111 476293979 476293869 6.870000e-34 156.0
17 TraesCS3D01G217200 chr5D 88.421 95 7 4 714 807 521371562 521371653 1.510000e-20 111.0
18 TraesCS3D01G217200 chr5B 91.379 116 10 0 1 116 300326617 300326732 5.310000e-35 159.0
19 TraesCS3D01G217200 chr5B 88.288 111 9 4 1232 1340 16405992 16405884 4.170000e-26 130.0
20 TraesCS3D01G217200 chr4D 88.889 126 12 2 1 125 36582276 36582152 2.470000e-33 154.0
21 TraesCS3D01G217200 chr7D 87.500 128 15 1 1 128 181999338 181999212 4.140000e-31 147.0
22 TraesCS3D01G217200 chr7D 88.889 108 8 4 1232 1337 66071721 66071826 4.170000e-26 130.0
23 TraesCS3D01G217200 chr7D 95.556 45 2 0 820 864 600971895 600971939 7.120000e-09 73.1
24 TraesCS3D01G217200 chr4B 85.915 142 10 9 735 867 188176814 188176954 5.350000e-30 143.0
25 TraesCS3D01G217200 chr4B 91.463 82 4 3 735 813 28147645 28147564 5.430000e-20 110.0
26 TraesCS3D01G217200 chr6B 88.889 108 8 4 1232 1337 675803944 675804049 4.170000e-26 130.0
27 TraesCS3D01G217200 chr6B 93.103 87 5 1 1255 1340 713229621 713229535 5.390000e-25 126.0
28 TraesCS3D01G217200 chr6B 92.857 84 5 1 1255 1337 676793118 676793201 2.510000e-23 121.0
29 TraesCS3D01G217200 chr6A 92.857 84 5 1 1255 1337 463741342 463741425 2.510000e-23 121.0
30 TraesCS3D01G217200 chr6A 100.000 30 0 0 345 374 581103351 581103380 7.170000e-04 56.5
31 TraesCS3D01G217200 chr2A 87.037 108 10 4 1232 1337 765080009 765080114 9.020000e-23 119.0
32 TraesCS3D01G217200 chr2A 91.026 78 6 1 731 807 68155819 68155896 2.520000e-18 104.0
33 TraesCS3D01G217200 chr1B 90.000 80 7 1 729 807 56752385 56752464 9.080000e-18 102.0
34 TraesCS3D01G217200 chr6D 81.890 127 15 7 736 857 34582459 34582582 3.270000e-17 100.0
35 TraesCS3D01G217200 chr6D 84.848 99 10 5 712 807 354905706 354905802 1.520000e-15 95.3
36 TraesCS3D01G217200 chr6D 91.837 49 3 1 819 867 374820242 374820195 3.310000e-07 67.6
37 TraesCS3D01G217200 chrUn 95.455 44 1 1 820 863 477580615 477580657 9.210000e-08 69.4
38 TraesCS3D01G217200 chr7B 81.481 81 8 4 774 854 611935230 611935157 5.540000e-05 60.2


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 TraesCS3D01G217200 chr3D 295136029 295141154 5125 False 9467.000 9467 100.0000 1 5126 1 chr3D.!!$F2 5125
1 TraesCS3D01G217200 chr3B 389255281 389260510 5229 False 1927.775 5502 94.9605 1 5123 4 chr3B.!!$F1 5122
2 TraesCS3D01G217200 chr3A 392777089 392781962 4873 False 1631.750 3201 91.2950 1 4614 4 chr3A.!!$F3 4613

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
417 418 0.250858 TGGTCCATGTTGTGAGGCAG 60.251 55.000 0.00 0.0 0.00 4.85 F
550 552 0.251742 AGCTTATTGGGGTTGCTGCA 60.252 50.000 0.00 0.0 32.32 4.41 F
1980 1999 1.068748 GTCCTGCTGAACATGCTTGTG 60.069 52.381 5.94 0.0 35.83 3.33 F
3105 3276 0.394488 TGACCAACTCGGCAAACCAA 60.394 50.000 0.00 0.0 39.03 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 2128 0.039074 CGCCTAATCAGCCCTCGTAG 60.039 60.00 0.00 0.0 0.00 3.51 R
2520 2675 3.003482 GCAAACAAATGAAAATGCTGGCA 59.997 39.13 0.00 0.0 0.00 4.92 R
3536 3710 0.041839 CACAACTGCTGCGTCTTCAC 60.042 55.00 0.00 0.0 0.00 3.18 R
4916 5484 0.038166 ATTTGGCCTGCGAGAAGGAA 59.962 50.00 3.32 0.0 40.02 3.36 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
185 186 9.755804 CATTCTAGTCTGCTTAGTTTCATATCA 57.244 33.333 0.00 0.00 0.00 2.15
339 340 7.224753 TGCATCTTCAAGATAATTTACTCCGTC 59.775 37.037 0.00 0.00 32.12 4.79
380 381 3.780850 ACCCCCTCTAGTCGATTTTTGAT 59.219 43.478 0.00 0.00 0.00 2.57
417 418 0.250858 TGGTCCATGTTGTGAGGCAG 60.251 55.000 0.00 0.00 0.00 4.85
528 530 1.202964 TGTTACGAGAGGTGGAGGACA 60.203 52.381 0.00 0.00 0.00 4.02
531 533 0.469331 ACGAGAGGTGGAGGACAACA 60.469 55.000 0.00 0.00 40.07 3.33
536 538 1.623811 GAGGTGGAGGACAACAGCTTA 59.376 52.381 0.00 0.00 44.58 3.09
544 546 2.110011 AGGACAACAGCTTATTGGGGTT 59.890 45.455 11.29 0.00 0.00 4.11
550 552 0.251742 AGCTTATTGGGGTTGCTGCA 60.252 50.000 0.00 0.00 32.32 4.41
607 609 5.911752 TGCTGTTGTGTTGACCAATTTAAT 58.088 33.333 0.00 0.00 0.00 1.40
608 610 6.344500 TGCTGTTGTGTTGACCAATTTAATT 58.656 32.000 0.00 0.00 0.00 1.40
634 636 6.719370 ACATATGGTACCAATCAAACAACTGT 59.281 34.615 20.76 7.36 0.00 3.55
659 661 6.758416 TCAAGTCAGAAATCAATAGGATGACG 59.242 38.462 0.00 0.00 36.02 4.35
670 672 1.788258 AGGATGACGCATAATGCTCG 58.212 50.000 0.00 0.00 42.25 5.03
741 748 6.054295 ACGAGTTTAGATATGACGTACTCCT 58.946 40.000 0.00 0.00 0.00 3.69
745 752 6.832384 AGTTTAGATATGACGTACTCCTTCCA 59.168 38.462 0.00 0.00 0.00 3.53
756 763 6.338937 ACGTACTCCTTCCATCTCAAAATAC 58.661 40.000 0.00 0.00 0.00 1.89
766 773 7.827819 TCCATCTCAAAATACGTGTCTTAAG 57.172 36.000 0.00 0.00 0.00 1.85
847 857 4.517453 TGAAACACTTATTTTGGGACGGAG 59.483 41.667 0.00 0.00 0.00 4.63
849 859 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
869 879 4.650131 AGGGAGTAGTATGTTAGAGTTGCC 59.350 45.833 0.00 0.00 0.00 4.52
908 918 6.038271 AGAGTTGCTTTAAACATCGTTCTGTT 59.962 34.615 0.00 0.00 41.01 3.16
925 935 5.160607 TCTGTTATCCAAACACACCCTAG 57.839 43.478 0.00 0.00 0.00 3.02
954 964 2.427506 GTTGTCAGTGTGATCCCTTCC 58.572 52.381 0.00 0.00 0.00 3.46
1207 1226 3.827898 CTCCTCCGCGACTCCACC 61.828 72.222 8.23 0.00 0.00 4.61
1465 1484 2.164338 GTCTCCGAACTCTTCCACTCT 58.836 52.381 0.00 0.00 0.00 3.24
1626 1645 3.345808 GAGCGTGCGCAACTCCAA 61.346 61.111 24.32 0.00 44.88 3.53
1726 1745 1.597027 CACTTTCCTCGCCGGTGTT 60.597 57.895 16.01 0.00 0.00 3.32
1729 1748 1.153127 TTTCCTCGCCGGTGTTGTT 60.153 52.632 16.01 0.00 0.00 2.83
1980 1999 1.068748 GTCCTGCTGAACATGCTTGTG 60.069 52.381 5.94 0.00 35.83 3.33
2101 2140 2.519771 TTAAGGACTACGAGGGCTGA 57.480 50.000 0.00 0.00 0.00 4.26
2310 2463 3.899052 ACTTGGGATGGAATTTGCATG 57.101 42.857 8.23 0.00 0.00 4.06
2326 2479 1.470285 GCATGCCATCTTTGCGATGTT 60.470 47.619 6.36 0.00 46.56 2.71
2460 2613 4.177165 TGCTCAATTGCTACCATGTTTG 57.823 40.909 0.00 0.00 0.00 2.93
2520 2675 9.178758 CTAGTCCCTTGCTAATGAATTAAGTTT 57.821 33.333 0.00 0.00 0.00 2.66
2544 2699 4.320641 GCCAGCATTTTCATTTGTTTGCAT 60.321 37.500 0.00 0.00 32.66 3.96
2601 2756 7.658575 GTCTATCTTCGTATAGTGACTCCTTCT 59.341 40.741 0.00 0.00 32.31 2.85
2675 2830 0.531657 CGCCCCTGATGCAATTTGAA 59.468 50.000 0.00 0.00 0.00 2.69
2791 2947 5.695816 GTGAGAGATGTCCTTTATGATGCTC 59.304 44.000 0.00 0.00 0.00 4.26
2850 3006 6.705302 TGAAGTTGATCAAGCTGATAGTTCT 58.295 36.000 8.80 0.00 37.20 3.01
3105 3276 0.394488 TGACCAACTCGGCAAACCAA 60.394 50.000 0.00 0.00 39.03 3.67
3205 3376 9.146984 GTGCTTGTTATTGTGTTGTATAGAGTA 57.853 33.333 0.00 0.00 0.00 2.59
3528 3702 4.396357 TGGCATAAGGAAAAGGAAGGAA 57.604 40.909 0.00 0.00 0.00 3.36
3536 3710 4.411013 AGGAAAAGGAAGGAATGTGGAAG 58.589 43.478 0.00 0.00 0.00 3.46
3636 3810 1.141019 CAATGGCATGAGCAGTGGC 59.859 57.895 0.00 3.18 44.61 5.01
3731 3905 6.211584 ACTCACTAATGCTTACTTGAGGAGAA 59.788 38.462 9.15 0.00 35.76 2.87
3857 4039 1.764723 TGGTTCCTGCTCGATGATGAT 59.235 47.619 0.00 0.00 0.00 2.45
3958 4140 0.516001 GCGTGATGCCATGAGCTATG 59.484 55.000 0.00 0.00 44.23 2.23
4103 4313 7.385267 TGGCTACCTTTTAGTTCGTAATTACA 58.615 34.615 15.67 0.56 0.00 2.41
4112 4322 7.795482 TTAGTTCGTAATTACAATGGATGGG 57.205 36.000 15.67 0.00 0.00 4.00
4126 4336 1.473258 GATGGGTATTGTGCCTTGCA 58.527 50.000 0.00 0.00 35.60 4.08
4127 4337 2.034124 GATGGGTATTGTGCCTTGCAT 58.966 47.619 0.00 0.00 41.91 3.96
4131 4341 3.072184 TGGGTATTGTGCCTTGCATTTTT 59.928 39.130 0.00 0.00 41.91 1.94
4238 4535 5.221441 GGTTCAACATAGGCACTTTCCTTTT 60.221 40.000 0.00 0.00 41.75 2.27
4264 4561 9.541143 TCTCTCTGAAAACAAAACAAAACTTTT 57.459 25.926 0.00 0.00 0.00 2.27
4267 4564 7.866729 TCTGAAAACAAAACAAAACTTTTCCC 58.133 30.769 0.00 0.00 32.27 3.97
4326 4625 8.593679 TGAGATCTAGTTTTAAAGGTCATGTCA 58.406 33.333 0.00 0.00 0.00 3.58
4327 4626 8.779354 AGATCTAGTTTTAAAGGTCATGTCAC 57.221 34.615 0.00 0.00 0.00 3.67
4328 4627 7.545965 AGATCTAGTTTTAAAGGTCATGTCACG 59.454 37.037 0.00 0.00 0.00 4.35
4333 4632 4.610605 TTAAAGGTCATGTCACGAGGAA 57.389 40.909 0.00 0.00 0.00 3.36
4353 4652 3.800826 ACAGTGGGTGAAAGTGGAC 57.199 52.632 0.00 0.00 0.00 4.02
4370 4674 2.896685 TGGACTTTGATTTGGCCGATTT 59.103 40.909 0.00 0.00 0.00 2.17
4375 4679 5.848406 ACTTTGATTTGGCCGATTTGTTTA 58.152 33.333 0.00 0.00 0.00 2.01
4491 5041 0.623723 TACCCTTGGGTGAAGATGCC 59.376 55.000 20.78 0.00 32.82 4.40
4501 5053 4.165950 TGGGTGAAGATGCCTGTATATGTT 59.834 41.667 0.00 0.00 0.00 2.71
4702 5257 8.724229 TCATGTTCTAGAGTGAAAATTGTCATG 58.276 33.333 0.61 0.00 30.76 3.07
4710 5265 8.902540 AGAGTGAAAATTGTCATGTAGTGTAA 57.097 30.769 0.61 0.00 0.00 2.41
4757 5312 1.804748 TGCTATGCGTACGATCGAGAT 59.195 47.619 24.34 1.27 0.00 2.75
4809 5364 8.679100 CGTGAAATGTATATTGGGGTTAAAAGA 58.321 33.333 0.00 0.00 0.00 2.52
4840 5395 7.565398 ACATATAGGCTGTTTCCTTTCTCTCTA 59.435 37.037 0.00 0.00 37.66 2.43
4912 5480 4.966247 TGGTCACTGCCCACTCTA 57.034 55.556 0.00 0.00 0.00 2.43
4915 5483 0.533032 GGTCACTGCCCACTCTACTC 59.467 60.000 0.00 0.00 0.00 2.59
4916 5484 1.551452 GTCACTGCCCACTCTACTCT 58.449 55.000 0.00 0.00 0.00 3.24
4917 5485 1.896465 GTCACTGCCCACTCTACTCTT 59.104 52.381 0.00 0.00 0.00 2.85
4982 5550 1.146263 CCCATTCTCCTACCACCGC 59.854 63.158 0.00 0.00 0.00 5.68
5099 5667 3.267860 CAAGCCGATGAGCTCCGC 61.268 66.667 12.15 7.64 44.11 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
185 186 9.968870 GATAAACGATAGAGGAACATCTAAGTT 57.031 33.333 11.61 11.61 37.84 2.66
312 313 7.716998 ACGGAGTAAATTATCTTGAAGATGCAT 59.283 33.333 17.50 0.00 41.94 3.96
333 334 4.839668 ATAGGAGATTTCTTCGACGGAG 57.160 45.455 0.00 0.00 0.00 4.63
339 340 4.816925 GGGGTTGAATAGGAGATTTCTTCG 59.183 45.833 0.00 0.00 0.00 3.79
380 381 5.843969 TGGACCATATTGCAGAACTATAGGA 59.156 40.000 4.43 0.00 0.00 2.94
399 400 0.250901 ACTGCCTCACAACATGGACC 60.251 55.000 0.00 0.00 0.00 4.46
417 418 1.202510 TGCAACATGGCCTCACAAAAC 60.203 47.619 3.32 0.00 0.00 2.43
528 530 1.895131 CAGCAACCCCAATAAGCTGTT 59.105 47.619 0.00 0.00 45.57 3.16
531 533 0.251742 TGCAGCAACCCCAATAAGCT 60.252 50.000 0.00 0.00 35.63 3.74
536 538 0.322322 CACATTGCAGCAACCCCAAT 59.678 50.000 10.85 0.00 0.00 3.16
544 546 1.348696 TCCTCTCTTCACATTGCAGCA 59.651 47.619 0.00 0.00 0.00 4.41
550 552 3.307059 CCCTTCGTTCCTCTCTTCACATT 60.307 47.826 0.00 0.00 0.00 2.71
607 609 8.735315 CAGTTGTTTGATTGGTACCATATGTAA 58.265 33.333 17.17 0.00 0.00 2.41
608 610 7.885922 ACAGTTGTTTGATTGGTACCATATGTA 59.114 33.333 17.17 0.00 0.00 2.29
617 619 5.883115 TGACTTGACAGTTGTTTGATTGGTA 59.117 36.000 0.00 0.00 31.22 3.25
634 636 6.758416 CGTCATCCTATTGATTTCTGACTTGA 59.242 38.462 0.00 0.00 0.00 3.02
700 702 9.884465 CTAAACTCGTCAAAATCTTCTCAAAAT 57.116 29.630 0.00 0.00 0.00 1.82
718 725 6.542574 AGGAGTACGTCATATCTAAACTCG 57.457 41.667 0.00 0.00 34.17 4.18
741 748 7.876068 ACTTAAGACACGTATTTTGAGATGGAA 59.124 33.333 10.09 0.00 0.00 3.53
745 752 9.924650 ACTAACTTAAGACACGTATTTTGAGAT 57.075 29.630 10.09 0.00 0.00 2.75
756 763 8.123445 ACAAAGTTGTACTAACTTAAGACACG 57.877 34.615 10.09 0.00 39.36 4.49
815 823 9.981114 CCCAAAATAAGTGTTTCAACTTTATCT 57.019 29.630 0.00 0.00 40.77 1.98
817 825 9.758651 GTCCCAAAATAAGTGTTTCAACTTTAT 57.241 29.630 0.00 0.00 40.77 1.40
818 826 7.916450 CGTCCCAAAATAAGTGTTTCAACTTTA 59.084 33.333 0.00 0.00 40.77 1.85
827 837 3.418047 CCTCCGTCCCAAAATAAGTGTT 58.582 45.455 0.00 0.00 0.00 3.32
831 841 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
839 849 1.133544 ACATACTACTCCCTCCGTCCC 60.134 57.143 0.00 0.00 0.00 4.46
840 850 2.361643 ACATACTACTCCCTCCGTCC 57.638 55.000 0.00 0.00 0.00 4.79
847 857 4.946445 GGCAACTCTAACATACTACTCCC 58.054 47.826 0.00 0.00 0.00 4.30
877 887 6.149474 ACGATGTTTAAAGCAACTCTAGCATT 59.851 34.615 0.00 0.00 0.00 3.56
878 888 5.643777 ACGATGTTTAAAGCAACTCTAGCAT 59.356 36.000 0.00 0.00 0.00 3.79
879 889 4.994852 ACGATGTTTAAAGCAACTCTAGCA 59.005 37.500 0.00 0.00 0.00 3.49
880 890 5.532025 ACGATGTTTAAAGCAACTCTAGC 57.468 39.130 0.00 0.00 0.00 3.42
881 891 7.095607 ACAGAACGATGTTTAAAGCAACTCTAG 60.096 37.037 0.00 0.00 0.00 2.43
882 892 6.704493 ACAGAACGATGTTTAAAGCAACTCTA 59.296 34.615 0.00 0.00 0.00 2.43
883 893 5.527582 ACAGAACGATGTTTAAAGCAACTCT 59.472 36.000 0.00 0.00 0.00 3.24
884 894 5.748592 ACAGAACGATGTTTAAAGCAACTC 58.251 37.500 0.00 0.00 0.00 3.01
908 918 2.238646 CCAGCTAGGGTGTGTTTGGATA 59.761 50.000 0.00 0.00 0.00 2.59
925 935 4.643387 ACTGACAACCGGGCCAGC 62.643 66.667 6.32 0.00 0.00 4.85
954 964 5.105595 GGTTTGAAGAAGAAAGATGGGATGG 60.106 44.000 0.00 0.00 0.00 3.51
1980 1999 3.553095 AACAGGCAGCGGAGGGTTC 62.553 63.158 0.00 0.00 0.00 3.62
2089 2128 0.039074 CGCCTAATCAGCCCTCGTAG 60.039 60.000 0.00 0.00 0.00 3.51
2326 2479 5.105187 CCACAGATCAGACTTCATCCAGTTA 60.105 44.000 0.00 0.00 0.00 2.24
2460 2613 5.348164 ACAACAGTTTGTGGTCAAATAAGC 58.652 37.500 0.00 0.00 44.66 3.09
2520 2675 3.003482 GCAAACAAATGAAAATGCTGGCA 59.997 39.130 0.00 0.00 0.00 4.92
2601 2756 4.791411 GCACAGTAAACGCAAGGAATTGAA 60.791 41.667 0.00 0.00 46.39 2.69
2791 2947 7.002879 AGGAATGAATAATCCACCAAGATCAG 58.997 38.462 0.00 0.00 38.23 2.90
2850 3006 7.106439 TCTTGACACAAAAATAGGCAAAAGA 57.894 32.000 0.00 0.00 0.00 2.52
3105 3276 3.641434 AGCTTGAGGTGTGATAGCAAT 57.359 42.857 0.00 0.00 34.37 3.56
3205 3376 4.718961 AGAAACCATGTACAACTTCAGCT 58.281 39.130 0.00 0.00 0.00 4.24
3369 3543 4.222114 GCTTGTCAATGAAGAAAAGGTCG 58.778 43.478 0.00 0.00 34.15 4.79
3528 3702 1.800805 CTGCGTCTTCACTTCCACAT 58.199 50.000 0.00 0.00 0.00 3.21
3536 3710 0.041839 CACAACTGCTGCGTCTTCAC 60.042 55.000 0.00 0.00 0.00 3.18
3636 3810 1.900351 TGGATTCTCCACCTCGCTG 59.100 57.895 0.00 0.00 42.67 5.18
3666 3840 3.329386 TCAAGCTGTTTCTTCCATCTCG 58.671 45.455 0.00 0.00 0.00 4.04
3731 3905 4.511826 GTCCAGTGAACTCTTCAAAACGAT 59.488 41.667 0.00 0.00 42.15 3.73
3857 4039 1.610624 GGAACCCGCTTCAACTCATCA 60.611 52.381 0.00 0.00 0.00 3.07
3958 4140 9.669353 CTAATTGCATATAACAAGGAACATGAC 57.331 33.333 0.00 0.00 0.00 3.06
4103 4313 3.033184 CAAGGCACAATACCCATCCATT 58.967 45.455 0.00 0.00 0.00 3.16
4131 4341 2.158682 TGCAAGCTCTGGTAGGACAAAA 60.159 45.455 0.00 0.00 0.00 2.44
4138 4348 3.507233 TGGATTTTTGCAAGCTCTGGTAG 59.493 43.478 0.00 0.00 0.00 3.18
4238 4535 9.541143 AAAAGTTTTGTTTTGTTTTCAGAGAGA 57.459 25.926 0.00 0.00 0.00 3.10
4264 4561 3.066190 CGACAGCCACCTACGGGA 61.066 66.667 0.00 0.00 36.25 5.14
4267 4564 3.411418 ATCGCGACAGCCACCTACG 62.411 63.158 12.93 0.00 41.18 3.51
4310 4609 4.963373 TCCTCGTGACATGACCTTTAAAA 58.037 39.130 0.00 0.00 0.00 1.52
4314 4613 2.104111 TGTTCCTCGTGACATGACCTTT 59.896 45.455 0.00 0.00 0.00 3.11
4318 4617 2.061773 CTGTGTTCCTCGTGACATGAC 58.938 52.381 0.00 0.00 0.00 3.06
4326 4625 1.046472 TCACCCACTGTGTTCCTCGT 61.046 55.000 7.08 0.00 45.61 4.18
4327 4626 0.105964 TTCACCCACTGTGTTCCTCG 59.894 55.000 7.08 0.00 45.61 4.63
4328 4627 2.222027 CTTTCACCCACTGTGTTCCTC 58.778 52.381 7.08 0.00 45.61 3.71
4333 4632 0.916086 TCCACTTTCACCCACTGTGT 59.084 50.000 7.08 0.00 45.61 3.72
4353 4652 6.777526 TTAAACAAATCGGCCAAATCAAAG 57.222 33.333 2.24 0.00 0.00 2.77
4396 4700 4.632688 GCACCATGCAAAGCTATTTTTGAT 59.367 37.500 0.00 0.00 44.26 2.57
4491 5041 5.753438 ACTACGGCACATGAAACATATACAG 59.247 40.000 0.00 0.00 0.00 2.74
4501 5053 3.869187 CGCACTACGGCACATGAA 58.131 55.556 0.00 0.00 38.44 2.57
4590 5144 4.749245 AATGCTAAAAACTGACGTCTGG 57.251 40.909 23.96 15.55 0.00 3.86
4702 5257 5.195379 CAGCACGACAAGTTTTTACACTAC 58.805 41.667 0.00 0.00 0.00 2.73
4710 5265 0.248621 GCTGCAGCACGACAAGTTTT 60.249 50.000 33.36 0.00 41.59 2.43
4757 5312 0.899720 AAAATCTGAGGTACGCCGGA 59.100 50.000 5.05 0.00 40.50 5.14
4817 5372 7.973048 TTAGAGAGAAAGGAAACAGCCTATA 57.027 36.000 0.00 0.00 37.26 1.31
4819 5374 6.681729 TTTAGAGAGAAAGGAAACAGCCTA 57.318 37.500 0.00 0.00 37.26 3.93
4821 5376 6.635030 TTTTTAGAGAGAAAGGAAACAGCC 57.365 37.500 0.00 0.00 0.00 4.85
4910 5478 1.202359 GCCTGCGAGAAGGAAGAGTAG 60.202 57.143 0.16 0.00 40.02 2.57
4911 5479 0.818296 GCCTGCGAGAAGGAAGAGTA 59.182 55.000 0.16 0.00 40.02 2.59
4912 5480 1.594310 GCCTGCGAGAAGGAAGAGT 59.406 57.895 0.16 0.00 40.02 3.24
4915 5483 0.606401 TTTGGCCTGCGAGAAGGAAG 60.606 55.000 3.32 0.00 40.02 3.46
4916 5484 0.038166 ATTTGGCCTGCGAGAAGGAA 59.962 50.000 3.32 0.00 40.02 3.36
4917 5485 0.038166 AATTTGGCCTGCGAGAAGGA 59.962 50.000 3.32 0.00 40.02 3.36
4982 5550 3.827898 GGTGACGAGGGAGGAGCG 61.828 72.222 0.00 0.00 0.00 5.03
5030 5598 3.929948 GGAGAAGAATGCGCCGCG 61.930 66.667 8.83 8.83 0.00 6.46
5031 5599 2.041366 GAAGGAGAAGAATGCGCCGC 62.041 60.000 4.18 0.00 0.00 6.53


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

AutoCloner maintained by Alex Coulton.