Multiple sequence alignment - TraesCS4D01G253800

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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 TraesCS4D01G253800 chr4D 100.000 3128 0 0 1 3128 422547524 422550651 0.000000e+00 5777
1 TraesCS4D01G253800 chr4A 93.430 1994 98 20 744 2726 41920507 41918536 0.000000e+00 2926
2 TraesCS4D01G253800 chr4A 96.471 340 12 0 2789 3128 41918080 41917741 2.110000e-156 562
3 TraesCS4D01G253800 chr4B 93.906 1526 81 8 799 2317 519403689 519405209 0.000000e+00 2292
4 TraesCS4D01G253800 chr4B 89.066 814 44 10 2317 3128 519405331 519406101 0.000000e+00 968
5 TraesCS4D01G253800 chr7D 94.411 662 35 2 1 660 75958030 75958691 0.000000e+00 1016
6 TraesCS4D01G253800 chr7D 93.062 663 41 4 1 660 410554181 410554841 0.000000e+00 965
7 TraesCS4D01G253800 chr5D 93.958 662 38 2 1 660 168013592 168014253 0.000000e+00 1000
8 TraesCS4D01G253800 chr5D 92.900 662 41 5 1 661 76210914 76211570 0.000000e+00 957
9 TraesCS4D01G253800 chr2D 93.051 662 41 4 1 661 77419320 77418663 0.000000e+00 963
10 TraesCS4D01G253800 chr2D 78.182 385 70 11 981 1355 24878051 24878431 1.880000e-57 233
11 TraesCS4D01G253800 chr1B 92.911 663 39 5 1 659 395802211 395802869 0.000000e+00 957
12 TraesCS4D01G253800 chr6B 92.760 663 43 5 1 659 660107759 660108420 0.000000e+00 953
13 TraesCS4D01G253800 chr6B 87.903 372 44 1 988 1358 576269349 576268978 1.330000e-118 436
14 TraesCS4D01G253800 chrUn 92.609 663 45 4 1 660 369789569 369790230 0.000000e+00 950
15 TraesCS4D01G253800 chr3D 92.738 661 43 4 1 660 480059717 480059061 0.000000e+00 950
16 TraesCS4D01G253800 chr5B 91.350 474 27 3 226 688 467368224 467367754 1.220000e-178 636
17 TraesCS4D01G253800 chr6A 90.349 373 33 3 988 1358 530252937 530252566 1.300000e-133 486
18 TraesCS4D01G253800 chr6D 89.785 372 37 1 988 1358 385787092 385786721 2.820000e-130 475
19 TraesCS4D01G253800 chr6D 73.071 635 145 23 1498 2120 470030670 470030050 5.290000e-48 202
20 TraesCS4D01G253800 chr2A 78.552 373 70 7 991 1355 27277239 27276869 1.450000e-58 237
21 TraesCS4D01G253800 chr2A 77.922 385 71 11 981 1355 27127084 27126704 8.730000e-56 228
22 TraesCS4D01G253800 chr2B 77.865 384 74 8 981 1355 39978559 39978178 8.730000e-56 228
23 TraesCS4D01G253800 chr2B 71.181 635 135 37 1504 2103 39978037 39977416 7.090000e-22 115


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 TraesCS4D01G253800 chr4D 422547524 422550651 3127 False 5777 5777 100.0000 1 3128 1 chr4D.!!$F1 3127
1 TraesCS4D01G253800 chr4A 41917741 41920507 2766 True 1744 2926 94.9505 744 3128 2 chr4A.!!$R1 2384
2 TraesCS4D01G253800 chr4B 519403689 519406101 2412 False 1630 2292 91.4860 799 3128 2 chr4B.!!$F1 2329
3 TraesCS4D01G253800 chr7D 75958030 75958691 661 False 1016 1016 94.4110 1 660 1 chr7D.!!$F1 659
4 TraesCS4D01G253800 chr7D 410554181 410554841 660 False 965 965 93.0620 1 660 1 chr7D.!!$F2 659
5 TraesCS4D01G253800 chr5D 168013592 168014253 661 False 1000 1000 93.9580 1 660 1 chr5D.!!$F2 659
6 TraesCS4D01G253800 chr5D 76210914 76211570 656 False 957 957 92.9000 1 661 1 chr5D.!!$F1 660
7 TraesCS4D01G253800 chr2D 77418663 77419320 657 True 963 963 93.0510 1 661 1 chr2D.!!$R1 660
8 TraesCS4D01G253800 chr1B 395802211 395802869 658 False 957 957 92.9110 1 659 1 chr1B.!!$F1 658
9 TraesCS4D01G253800 chr6B 660107759 660108420 661 False 953 953 92.7600 1 659 1 chr6B.!!$F1 658
10 TraesCS4D01G253800 chrUn 369789569 369790230 661 False 950 950 92.6090 1 660 1 chrUn.!!$F1 659
11 TraesCS4D01G253800 chr3D 480059061 480059717 656 True 950 950 92.7380 1 660 1 chr3D.!!$R1 659
12 TraesCS4D01G253800 chr6D 470030050 470030670 620 True 202 202 73.0710 1498 2120 1 chr6D.!!$R2 622

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
726 741 0.44231 TTGATACGCAACGCTCTTGC 59.558 50.0 6.01 6.01 41.71 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2630 2789 1.195115 TCTCTCATGGCCACCTGTAC 58.805 55.0 8.16 0.0 0.0 2.9 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 3.358111 TTCACCATTAAATCCCTCGCA 57.642 42.857 0.00 0.00 0.00 5.10
178 186 6.152492 TGAAGTTGCCATAATATGTTTCAGCA 59.848 34.615 0.00 0.00 0.00 4.41
386 395 8.726068 TCGCAATGATCTACAAACTAAAATTGA 58.274 29.630 0.00 0.00 0.00 2.57
435 444 9.109393 CACTATGGCAACTATAGTGTAAACATT 57.891 33.333 17.94 0.00 44.60 2.71
643 658 5.022122 TGGCAAAATAAATGGTGATGGAGA 58.978 37.500 0.00 0.00 0.00 3.71
651 666 0.830023 TGGTGATGGAGACGTGTGGA 60.830 55.000 0.00 0.00 0.00 4.02
679 694 3.243226 CGTGTGGACGTTAGTTTTTCC 57.757 47.619 0.00 0.00 40.91 3.13
680 695 2.347846 CGTGTGGACGTTAGTTTTTCCG 60.348 50.000 0.00 0.00 40.91 4.30
681 696 2.609002 GTGTGGACGTTAGTTTTTCCGT 59.391 45.455 0.00 0.00 36.04 4.69
682 697 3.063861 GTGTGGACGTTAGTTTTTCCGTT 59.936 43.478 0.00 0.00 33.03 4.44
683 698 3.309410 TGTGGACGTTAGTTTTTCCGTTC 59.691 43.478 0.00 0.00 33.03 3.95
684 699 3.557185 GTGGACGTTAGTTTTTCCGTTCT 59.443 43.478 0.00 0.00 33.03 3.01
685 700 4.034394 GTGGACGTTAGTTTTTCCGTTCTT 59.966 41.667 0.00 0.00 33.03 2.52
686 701 4.635324 TGGACGTTAGTTTTTCCGTTCTTT 59.365 37.500 0.00 0.00 33.03 2.52
687 702 5.123661 TGGACGTTAGTTTTTCCGTTCTTTT 59.876 36.000 0.00 0.00 33.03 2.27
688 703 6.029607 GGACGTTAGTTTTTCCGTTCTTTTT 58.970 36.000 0.00 0.00 33.03 1.94
689 704 7.148340 TGGACGTTAGTTTTTCCGTTCTTTTTA 60.148 33.333 0.00 0.00 33.03 1.52
690 705 7.374228 GGACGTTAGTTTTTCCGTTCTTTTTAG 59.626 37.037 0.00 0.00 33.03 1.85
691 706 6.688385 ACGTTAGTTTTTCCGTTCTTTTTAGC 59.312 34.615 0.00 0.00 0.00 3.09
692 707 6.908820 CGTTAGTTTTTCCGTTCTTTTTAGCT 59.091 34.615 0.00 0.00 0.00 3.32
693 708 7.097168 CGTTAGTTTTTCCGTTCTTTTTAGCTG 60.097 37.037 0.00 0.00 0.00 4.24
694 709 6.203808 AGTTTTTCCGTTCTTTTTAGCTGT 57.796 33.333 0.00 0.00 0.00 4.40
695 710 6.263344 AGTTTTTCCGTTCTTTTTAGCTGTC 58.737 36.000 0.00 0.00 0.00 3.51
696 711 6.095021 AGTTTTTCCGTTCTTTTTAGCTGTCT 59.905 34.615 0.00 0.00 0.00 3.41
697 712 5.418310 TTTCCGTTCTTTTTAGCTGTCTG 57.582 39.130 0.00 0.00 0.00 3.51
698 713 2.806244 TCCGTTCTTTTTAGCTGTCTGC 59.194 45.455 0.00 0.00 43.29 4.26
699 714 2.548057 CCGTTCTTTTTAGCTGTCTGCA 59.452 45.455 0.00 0.00 45.94 4.41
700 715 3.545633 CGTTCTTTTTAGCTGTCTGCAC 58.454 45.455 0.00 0.00 45.94 4.57
701 716 3.002246 CGTTCTTTTTAGCTGTCTGCACA 59.998 43.478 0.00 0.00 45.94 4.57
702 717 4.495679 CGTTCTTTTTAGCTGTCTGCACAA 60.496 41.667 0.00 0.00 45.94 3.33
703 718 5.523369 GTTCTTTTTAGCTGTCTGCACAAT 58.477 37.500 0.00 0.00 45.94 2.71
704 719 5.112220 TCTTTTTAGCTGTCTGCACAATG 57.888 39.130 0.00 0.00 45.94 2.82
705 720 2.995466 TTTAGCTGTCTGCACAATGC 57.005 45.000 0.00 0.00 45.94 3.56
725 740 2.145053 GTTGATACGCAACGCTCTTG 57.855 50.000 0.00 0.00 46.50 3.02
726 741 0.442310 TTGATACGCAACGCTCTTGC 59.558 50.000 6.01 6.01 41.71 4.01
738 753 2.300623 GCTCTTGCGTATATTTGCGG 57.699 50.000 0.00 0.00 0.00 5.69
739 754 1.864711 GCTCTTGCGTATATTTGCGGA 59.135 47.619 0.00 0.00 0.00 5.54
740 755 2.096713 GCTCTTGCGTATATTTGCGGAG 60.097 50.000 12.72 12.72 36.96 4.63
741 756 3.123804 CTCTTGCGTATATTTGCGGAGT 58.876 45.455 0.00 0.00 32.28 3.85
742 757 2.863740 TCTTGCGTATATTTGCGGAGTG 59.136 45.455 0.00 0.00 32.28 3.51
753 768 5.705609 ATTTGCGGAGTGAAAAGTATTGT 57.294 34.783 0.00 0.00 0.00 2.71
761 777 1.883275 TGAAAAGTATTGTGGTGGCCG 59.117 47.619 0.00 0.00 0.00 6.13
916 938 2.691526 CTGTATAACCAGCCGTCACCTA 59.308 50.000 0.00 0.00 0.00 3.08
1009 1031 0.179054 GCAGCAGCTGATGGAGATCA 60.179 55.000 31.37 0.00 37.07 2.92
1013 1035 1.407851 GCAGCTGATGGAGATCACCAA 60.408 52.381 20.43 0.00 43.47 3.67
1032 1054 2.821366 GTCGACCTCCGCGGACTA 60.821 66.667 27.28 3.73 38.37 2.59
1036 1058 1.451747 GACCTCCGCGGACTAGAGT 60.452 63.158 27.28 16.34 36.31 3.24
1045 1067 3.217743 GACTAGAGTCCGGCGGGG 61.218 72.222 27.98 11.62 39.07 5.73
1286 1308 4.421479 CGTGCGCCTCTCCGAAGT 62.421 66.667 4.18 0.00 0.00 3.01
1358 1380 1.131928 AACCCCGCCTTCTGGTAACT 61.132 55.000 0.00 0.00 35.27 2.24
1379 1401 0.681175 AGCAGTGCCCACCATTTTTC 59.319 50.000 12.58 0.00 0.00 2.29
1383 1405 3.420893 CAGTGCCCACCATTTTTCTCTA 58.579 45.455 0.00 0.00 0.00 2.43
1384 1406 3.826157 CAGTGCCCACCATTTTTCTCTAA 59.174 43.478 0.00 0.00 0.00 2.10
1393 1416 3.062234 CCATTTTTCTCTAAGTCCGTCGC 59.938 47.826 0.00 0.00 0.00 5.19
1424 1447 2.168106 GTGCATCCATTTTGGCATGGTA 59.832 45.455 5.57 0.00 43.94 3.25
1438 1461 2.708671 TGGTATGCCCATGGTGACT 58.291 52.632 11.73 0.00 38.72 3.41
1447 1471 0.950555 CCATGGTGACTGTGTCCGTG 60.951 60.000 2.57 11.01 37.81 4.94
1477 1501 0.526954 GACACGATTATGTCCGCGGT 60.527 55.000 27.15 8.80 42.74 5.68
1496 1520 1.000506 GTCAAGAACGTGTGGGAGCTA 59.999 52.381 0.00 0.00 0.00 3.32
1784 1808 3.414700 GGCGAGCTGTTCACGGTG 61.415 66.667 0.56 0.56 0.00 4.94
2018 2052 1.076906 ACCCTCTGCTGTACCGTCT 59.923 57.895 0.00 0.00 0.00 4.18
2112 2146 0.836400 TCTGTGGGGTGGAGAAGGAC 60.836 60.000 0.00 0.00 0.00 3.85
2117 2152 0.976073 GGGGTGGAGAAGGACGATCA 60.976 60.000 0.00 0.00 0.00 2.92
2198 2233 0.597568 CACCATTCTGAAGCCGCAAA 59.402 50.000 0.00 0.00 0.00 3.68
2205 2240 1.066215 TCTGAAGCCGCAAATGCTAGA 60.066 47.619 3.63 0.00 38.34 2.43
2219 2254 7.119116 CGCAAATGCTAGATTACCCATGTAATA 59.881 37.037 3.63 0.00 41.87 0.98
2245 2280 3.512680 CGACACCATTCTGAAGTCCTAC 58.487 50.000 0.00 0.00 0.00 3.18
2409 2566 3.724732 ATTTGCTTGCCCCATTTCAAT 57.275 38.095 0.00 0.00 0.00 2.57
2416 2573 3.056588 TGCCCCATTTCAATTTTGAGC 57.943 42.857 0.00 0.00 38.61 4.26
2422 2579 6.584488 CCCCATTTCAATTTTGAGCATATGA 58.416 36.000 6.97 0.00 38.61 2.15
2567 2724 3.194861 CATTCCGGTCACACGTTGATAT 58.805 45.455 0.00 0.00 36.32 1.63
2622 2781 1.240641 TGCAACCGAAATGGCACGAT 61.241 50.000 0.00 0.00 43.94 3.73
2630 2789 3.302221 CCGAAATGGCACGATTAACTACG 60.302 47.826 0.00 0.00 0.00 3.51
2714 2873 3.696051 TGCCTTAGCCTGCAAAAGAATAG 59.304 43.478 5.99 0.00 38.69 1.73
2735 2894 2.551938 GGGGATCTAGAGCAAATCAGCC 60.552 54.545 10.68 0.00 34.23 4.85
2742 2901 7.067494 GGATCTAGAGCAAATCAGCCTTTTAAA 59.933 37.037 10.68 0.00 34.23 1.52
2746 2905 3.903714 AGCAAATCAGCCTTTTAAACCCT 59.096 39.130 0.00 0.00 34.23 4.34
2750 2909 6.039270 GCAAATCAGCCTTTTAAACCCTTTTT 59.961 34.615 0.00 0.00 0.00 1.94
2752 2911 5.284861 TCAGCCTTTTAAACCCTTTTTCC 57.715 39.130 0.00 0.00 0.00 3.13
2754 2913 4.102524 CAGCCTTTTAAACCCTTTTTCCCT 59.897 41.667 0.00 0.00 0.00 4.20
2755 2914 4.102524 AGCCTTTTAAACCCTTTTTCCCTG 59.897 41.667 0.00 0.00 0.00 4.45
2802 3354 6.474751 GCTTCCATCTTATGTTGAAATGAAGC 59.525 38.462 0.00 0.00 33.39 3.86
2803 3355 6.455360 TCCATCTTATGTTGAAATGAAGCC 57.545 37.500 0.00 0.00 0.00 4.35
2846 3398 4.505324 TCGAGGTCTTTGAGGAGAGATA 57.495 45.455 0.00 0.00 0.00 1.98
2907 3459 4.260620 CCCGAACTGTACAGTCACAAAAAG 60.261 45.833 28.04 12.74 41.58 2.27
2946 3498 3.236816 CATGTAACAGCCAAAGAAAGCG 58.763 45.455 0.00 0.00 0.00 4.68
2967 3519 2.526432 GGGAGAGCGGATATCACCTTA 58.474 52.381 4.83 0.00 0.00 2.69
2976 3528 3.643763 GGATATCACCTTACGCTCACTG 58.356 50.000 4.83 0.00 0.00 3.66
3009 3561 5.241064 CCTGATGGCCTTCAGATTTGAATAG 59.759 44.000 37.67 20.38 44.88 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 6.459710 GGGATTTAATGGTGAAAACGGATCTC 60.460 42.308 0.00 0.00 0.00 2.75
121 128 4.684877 TCATGGCAATTCATGTGCAATAC 58.315 39.130 8.81 0.00 44.07 1.89
318 327 6.486056 TGGCAATTCCAGTACTTTAACCATA 58.514 36.000 0.00 0.00 40.72 2.74
361 370 8.788813 GTCAATTTTAGTTTGTAGATCATTGCG 58.211 33.333 0.00 0.00 0.00 4.85
386 395 6.423604 GTGCTTAAACTAAAATTGCCATGTGT 59.576 34.615 0.00 0.00 0.00 3.72
397 406 7.519032 AGTTGCCATAGTGCTTAAACTAAAA 57.481 32.000 0.00 0.00 36.28 1.52
435 444 2.300956 TTTGCCCAGAAGTTGCCATA 57.699 45.000 0.00 0.00 0.00 2.74
643 658 2.733218 CGCACATCGTCCACACGT 60.733 61.111 0.00 0.00 46.76 4.49
661 676 2.903798 ACGGAAAAACTAACGTCCACA 58.096 42.857 0.00 0.00 33.92 4.17
662 677 3.557185 AGAACGGAAAAACTAACGTCCAC 59.443 43.478 0.00 0.00 38.79 4.02
663 678 3.795877 AGAACGGAAAAACTAACGTCCA 58.204 40.909 0.00 0.00 38.79 4.02
664 679 4.801147 AAGAACGGAAAAACTAACGTCC 57.199 40.909 0.00 0.00 38.79 4.79
665 680 7.097289 GCTAAAAAGAACGGAAAAACTAACGTC 60.097 37.037 0.00 0.00 38.79 4.34
666 681 6.688385 GCTAAAAAGAACGGAAAAACTAACGT 59.312 34.615 0.00 0.00 41.88 3.99
667 682 6.908820 AGCTAAAAAGAACGGAAAAACTAACG 59.091 34.615 0.00 0.00 0.00 3.18
668 683 7.699391 ACAGCTAAAAAGAACGGAAAAACTAAC 59.301 33.333 0.00 0.00 0.00 2.34
669 684 7.764331 ACAGCTAAAAAGAACGGAAAAACTAA 58.236 30.769 0.00 0.00 0.00 2.24
670 685 7.281549 AGACAGCTAAAAAGAACGGAAAAACTA 59.718 33.333 0.00 0.00 0.00 2.24
671 686 6.095021 AGACAGCTAAAAAGAACGGAAAAACT 59.905 34.615 0.00 0.00 0.00 2.66
672 687 6.196538 CAGACAGCTAAAAAGAACGGAAAAAC 59.803 38.462 0.00 0.00 0.00 2.43
673 688 6.262601 CAGACAGCTAAAAAGAACGGAAAAA 58.737 36.000 0.00 0.00 0.00 1.94
674 689 5.732247 GCAGACAGCTAAAAAGAACGGAAAA 60.732 40.000 0.00 0.00 41.15 2.29
675 690 4.261031 GCAGACAGCTAAAAAGAACGGAAA 60.261 41.667 0.00 0.00 41.15 3.13
676 691 3.250040 GCAGACAGCTAAAAAGAACGGAA 59.750 43.478 0.00 0.00 41.15 4.30
677 692 2.806244 GCAGACAGCTAAAAAGAACGGA 59.194 45.455 0.00 0.00 41.15 4.69
678 693 2.548057 TGCAGACAGCTAAAAAGAACGG 59.452 45.455 0.00 0.00 45.94 4.44
679 694 3.002246 TGTGCAGACAGCTAAAAAGAACG 59.998 43.478 0.00 0.00 45.94 3.95
680 695 4.552166 TGTGCAGACAGCTAAAAAGAAC 57.448 40.909 0.00 0.00 45.94 3.01
681 696 5.522456 CATTGTGCAGACAGCTAAAAAGAA 58.478 37.500 0.00 0.00 45.94 2.52
682 697 4.557296 GCATTGTGCAGACAGCTAAAAAGA 60.557 41.667 0.00 0.00 44.26 2.52
683 698 3.671928 GCATTGTGCAGACAGCTAAAAAG 59.328 43.478 0.00 0.00 44.26 2.27
684 699 3.641648 GCATTGTGCAGACAGCTAAAAA 58.358 40.909 0.00 0.00 44.26 1.94
685 700 2.350676 CGCATTGTGCAGACAGCTAAAA 60.351 45.455 2.63 0.00 45.36 1.52
686 701 1.197492 CGCATTGTGCAGACAGCTAAA 59.803 47.619 2.63 0.00 45.36 1.85
687 702 0.798159 CGCATTGTGCAGACAGCTAA 59.202 50.000 2.63 0.00 45.36 3.09
688 703 0.320683 ACGCATTGTGCAGACAGCTA 60.321 50.000 2.63 0.00 45.36 3.32
689 704 1.168407 AACGCATTGTGCAGACAGCT 61.168 50.000 2.63 0.00 45.36 4.24
690 705 1.000233 CAACGCATTGTGCAGACAGC 61.000 55.000 2.63 0.00 45.36 4.40
691 706 0.587768 TCAACGCATTGTGCAGACAG 59.412 50.000 2.63 0.00 45.36 3.51
692 707 1.237533 ATCAACGCATTGTGCAGACA 58.762 45.000 2.63 0.00 45.36 3.41
693 708 2.774007 GTATCAACGCATTGTGCAGAC 58.226 47.619 2.63 0.00 45.36 3.51
694 709 1.393196 CGTATCAACGCATTGTGCAGA 59.607 47.619 2.63 0.00 45.36 4.26
695 710 1.801618 CGTATCAACGCATTGTGCAG 58.198 50.000 2.63 0.00 45.36 4.41
696 711 3.965677 CGTATCAACGCATTGTGCA 57.034 47.368 2.63 0.00 45.36 4.57
707 722 0.442310 GCAAGAGCGTTGCGTATCAA 59.558 50.000 10.54 0.00 35.58 2.57
708 723 2.078226 GCAAGAGCGTTGCGTATCA 58.922 52.632 10.54 0.00 35.58 2.15
709 724 4.955238 GCAAGAGCGTTGCGTATC 57.045 55.556 10.54 0.00 35.58 2.24
719 734 1.864711 TCCGCAAATATACGCAAGAGC 59.135 47.619 0.00 0.00 43.62 4.09
720 735 3.060272 CACTCCGCAAATATACGCAAGAG 60.060 47.826 9.85 9.85 43.62 2.85
721 736 2.863740 CACTCCGCAAATATACGCAAGA 59.136 45.455 0.00 0.00 43.62 3.02
723 738 2.894902 TCACTCCGCAAATATACGCAA 58.105 42.857 0.00 0.00 0.00 4.85
724 739 2.588027 TCACTCCGCAAATATACGCA 57.412 45.000 0.00 0.00 0.00 5.24
725 740 3.936902 TTTCACTCCGCAAATATACGC 57.063 42.857 0.00 0.00 0.00 4.42
726 741 5.464965 ACTTTTCACTCCGCAAATATACG 57.535 39.130 0.00 0.00 0.00 3.06
727 742 8.395633 ACAATACTTTTCACTCCGCAAATATAC 58.604 33.333 0.00 0.00 0.00 1.47
728 743 8.394877 CACAATACTTTTCACTCCGCAAATATA 58.605 33.333 0.00 0.00 0.00 0.86
729 744 7.250569 CACAATACTTTTCACTCCGCAAATAT 58.749 34.615 0.00 0.00 0.00 1.28
730 745 6.348950 CCACAATACTTTTCACTCCGCAAATA 60.349 38.462 0.00 0.00 0.00 1.40
731 746 5.460646 CACAATACTTTTCACTCCGCAAAT 58.539 37.500 0.00 0.00 0.00 2.32
732 747 4.261405 CCACAATACTTTTCACTCCGCAAA 60.261 41.667 0.00 0.00 0.00 3.68
733 748 3.252215 CCACAATACTTTTCACTCCGCAA 59.748 43.478 0.00 0.00 0.00 4.85
734 749 2.811431 CCACAATACTTTTCACTCCGCA 59.189 45.455 0.00 0.00 0.00 5.69
735 750 2.812011 ACCACAATACTTTTCACTCCGC 59.188 45.455 0.00 0.00 0.00 5.54
736 751 3.188460 CCACCACAATACTTTTCACTCCG 59.812 47.826 0.00 0.00 0.00 4.63
737 752 3.057526 GCCACCACAATACTTTTCACTCC 60.058 47.826 0.00 0.00 0.00 3.85
738 753 3.057526 GGCCACCACAATACTTTTCACTC 60.058 47.826 0.00 0.00 0.00 3.51
739 754 2.890945 GGCCACCACAATACTTTTCACT 59.109 45.455 0.00 0.00 0.00 3.41
740 755 2.351350 CGGCCACCACAATACTTTTCAC 60.351 50.000 2.24 0.00 0.00 3.18
741 756 1.883275 CGGCCACCACAATACTTTTCA 59.117 47.619 2.24 0.00 0.00 2.69
742 757 1.402325 GCGGCCACCACAATACTTTTC 60.402 52.381 2.24 0.00 0.00 2.29
839 855 0.528466 TCATCATGCGACGCTCTTCC 60.528 55.000 22.08 0.00 0.00 3.46
916 938 4.286297 TCTTGGTTTGTTCGATGGAGAT 57.714 40.909 0.00 0.00 0.00 2.75
1160 1182 1.958205 GCGAAGATCTCCGGCATGG 60.958 63.158 2.74 0.00 40.09 3.66
1338 1360 0.251033 GTTACCAGAAGGCGGGGTTT 60.251 55.000 0.00 0.00 39.06 3.27
1358 1380 2.008242 AAAATGGTGGGCACTGCTTA 57.992 45.000 0.00 0.00 0.00 3.09
1379 1401 1.583967 CTGCGCGACGGACTTAGAG 60.584 63.158 12.10 0.00 0.00 2.43
1424 1447 0.322816 GACACAGTCACCATGGGCAT 60.323 55.000 18.09 0.00 32.09 4.40
1466 1490 0.457166 CGTTCTTGACCGCGGACATA 60.457 55.000 35.90 20.03 0.00 2.29
1467 1491 1.736645 CGTTCTTGACCGCGGACAT 60.737 57.895 35.90 10.08 0.00 3.06
1468 1492 2.355363 CGTTCTTGACCGCGGACA 60.355 61.111 35.90 30.66 0.00 4.02
1477 1501 1.000506 GTAGCTCCCACACGTTCTTGA 59.999 52.381 0.00 0.00 0.00 3.02
1496 1520 4.664677 GTCTCCACCGTGCGCTGT 62.665 66.667 9.73 0.00 0.00 4.40
1799 1833 1.363744 CAAAGAAAGGAGAGCGCGAT 58.636 50.000 12.10 1.23 0.00 4.58
1887 1921 2.029964 GTCCTCACGCGGTGGAAA 59.970 61.111 12.47 0.00 40.67 3.13
2018 2052 2.566570 TAGCCGTCGTTGGTGCAGA 61.567 57.895 0.00 0.00 0.00 4.26
2112 2146 2.251869 TGACTTACGAACGGTGATCG 57.748 50.000 0.95 0.95 45.47 3.69
2117 2152 1.338973 TGAGCTTGACTTACGAACGGT 59.661 47.619 0.00 0.00 0.00 4.83
2198 2233 7.495934 GCGATTATTACATGGGTAATCTAGCAT 59.504 37.037 17.40 0.00 44.88 3.79
2219 2254 2.002586 CTTCAGAATGGTGTCGCGATT 58.997 47.619 14.06 0.56 36.16 3.34
2245 2280 6.670927 GCGATTTGAGTAAAGTTCAGTAGCAG 60.671 42.308 0.00 0.00 0.00 4.24
2396 2553 2.371179 TGCTCAAAATTGAAATGGGGCA 59.629 40.909 0.00 0.06 36.64 5.36
2409 2566 7.868906 TGAAGTGATCATCATATGCTCAAAA 57.131 32.000 0.00 0.00 37.19 2.44
2567 2724 5.047448 GCCATCTAGCTCATCTGTAATCTGA 60.047 44.000 0.00 0.00 0.00 3.27
2622 2781 2.246469 TGGCCACCTGTACGTAGTTAA 58.754 47.619 0.00 0.00 37.78 2.01
2630 2789 1.195115 TCTCTCATGGCCACCTGTAC 58.805 55.000 8.16 0.00 0.00 2.90
2714 2873 2.551938 GGCTGATTTGCTCTAGATCCCC 60.552 54.545 0.00 0.00 0.00 4.81
2735 2894 8.746052 ATTTTCAGGGAAAAAGGGTTTAAAAG 57.254 30.769 8.06 0.00 43.32 2.27
2752 2911 3.142174 GAGCGGATCCCTTATTTTCAGG 58.858 50.000 6.06 0.00 0.00 3.86
2754 2913 3.208747 GGAGCGGATCCCTTATTTTCA 57.791 47.619 6.06 0.00 43.01 2.69
2802 3354 0.109597 GTGAAAGGCTGACAATGCGG 60.110 55.000 0.00 0.00 0.00 5.69
2803 3355 0.877071 AGTGAAAGGCTGACAATGCG 59.123 50.000 0.00 0.00 0.00 4.73
2946 3498 0.543174 AGGTGATATCCGCTCTCCCC 60.543 60.000 0.00 0.00 0.00 4.81
2967 3519 0.038159 GGAGCAAGTACAGTGAGCGT 60.038 55.000 0.00 0.00 0.00 5.07
2976 3528 0.543749 AGGCCATCAGGAGCAAGTAC 59.456 55.000 5.01 0.00 36.89 2.73
3009 3561 0.675633 ATTTGCAGTTGGGCAGACAC 59.324 50.000 0.00 0.00 45.88 3.67
3051 3603 3.490761 GCTACAAGGTCTCTGATCTCAGC 60.491 52.174 2.21 0.00 43.46 4.26


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

AutoCloner maintained by Alex Coulton.