Multiple sequence alignment - TraesCS6D01G032700

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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 TraesCS6D01G032700 chr6D 100.000 3214 0 0 1 3214 13761785 13764998 0.000000e+00 5936.0
1 TraesCS6D01G032700 chr6A 92.997 2456 98 37 788 3214 4420634 4418224 0.000000e+00 3515.0
2 TraesCS6D01G032700 chr6A 93.519 1759 72 18 788 2528 4362352 4360618 0.000000e+00 2579.0
3 TraesCS6D01G032700 chr6A 93.458 1758 75 16 788 2528 4241957 4240223 0.000000e+00 2573.0
4 TraesCS6D01G032700 chr6A 93.231 1758 79 17 788 2528 4291753 4290019 0.000000e+00 2551.0
5 TraesCS6D01G032700 chr6A 96.333 709 19 3 2513 3214 4290004 4289296 0.000000e+00 1158.0
6 TraesCS6D01G032700 chr6A 96.333 709 19 3 2513 3214 4360603 4359895 0.000000e+00 1158.0
7 TraesCS6D01G032700 chr6A 96.192 709 20 3 2513 3214 4240208 4239500 0.000000e+00 1153.0
8 TraesCS6D01G032700 chr6A 85.294 646 69 18 1 632 5123839 5124472 0.000000e+00 643.0
9 TraesCS6D01G032700 chr6A 84.045 539 68 11 1 530 4421361 4420832 1.330000e-138 503.0
10 TraesCS6D01G032700 chr6A 83.799 537 73 9 1 530 4292461 4291932 6.190000e-137 497.0
11 TraesCS6D01G032700 chr6A 83.426 537 75 9 1 530 4242684 4242155 1.340000e-133 486.0
12 TraesCS6D01G032700 chr6A 83.488 539 71 11 1 530 4363079 4362550 1.340000e-133 486.0
13 TraesCS6D01G032700 chrUn 93.800 1758 69 16 788 2528 62401302 62403036 0.000000e+00 2606.0
14 TraesCS6D01G032700 chrUn 93.743 1758 70 16 788 2528 62529034 62530768 0.000000e+00 2601.0
15 TraesCS6D01G032700 chrUn 93.515 1758 74 16 788 2528 62457004 62458738 0.000000e+00 2579.0
16 TraesCS6D01G032700 chrUn 93.383 1738 76 15 807 2528 62585442 62587156 0.000000e+00 2536.0
17 TraesCS6D01G032700 chrUn 93.463 1178 43 10 788 1948 62340341 62341501 0.000000e+00 1718.0
18 TraesCS6D01G032700 chrUn 92.069 870 36 9 788 1641 431610430 431609578 0.000000e+00 1194.0
19 TraesCS6D01G032700 chrUn 96.333 709 19 3 2513 3214 62458752 62459460 0.000000e+00 1158.0
20 TraesCS6D01G032700 chrUn 96.333 709 19 3 2513 3214 62530783 62531491 0.000000e+00 1158.0
21 TraesCS6D01G032700 chrUn 96.333 709 19 3 2513 3214 62587171 62587879 0.000000e+00 1158.0
22 TraesCS6D01G032700 chrUn 96.051 709 21 3 2513 3214 62342070 62342778 0.000000e+00 1147.0
23 TraesCS6D01G032700 chrUn 96.296 702 19 3 2513 3207 439042683 439041982 0.000000e+00 1146.0
24 TraesCS6D01G032700 chrUn 95.628 709 23 4 2513 3214 62403051 62403758 0.000000e+00 1131.0
25 TraesCS6D01G032700 chrUn 83.859 539 69 11 1 530 62528307 62528836 6.190000e-137 497.0
26 TraesCS6D01G032700 chrUn 83.426 537 75 9 1 530 62339614 62340143 1.340000e-133 486.0
27 TraesCS6D01G032700 chrUn 83.302 539 72 13 1 530 62456277 62456806 6.240000e-132 481.0
28 TraesCS6D01G032700 chrUn 82.931 539 74 11 1 530 62584715 62585244 1.350000e-128 470.0
29 TraesCS6D01G032700 chr6B 90.343 1781 114 27 788 2526 9765167 9766931 0.000000e+00 2283.0
30 TraesCS6D01G032700 chr6B 92.079 101 8 0 426 526 9360900 9361000 3.340000e-30 143.0
31 TraesCS6D01G032700 chr6B 90.323 62 0 2 698 759 9361104 9361159 3.440000e-10 76.8


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 TraesCS6D01G032700 chr6D 13761785 13764998 3213 False 5936.000000 5936 100.000000 1 3214 1 chr6D.!!$F1 3213
1 TraesCS6D01G032700 chr6A 4418224 4421361 3137 True 2009.000000 3515 88.521000 1 3214 2 chr6A.!!$R4 3213
2 TraesCS6D01G032700 chr6A 4359895 4363079 3184 True 1407.666667 2579 91.113333 1 3214 3 chr6A.!!$R3 3213
3 TraesCS6D01G032700 chr6A 4239500 4242684 3184 True 1404.000000 2573 91.025333 1 3214 3 chr6A.!!$R1 3213
4 TraesCS6D01G032700 chr6A 4289296 4292461 3165 True 1402.000000 2551 91.121000 1 3214 3 chr6A.!!$R2 3213
5 TraesCS6D01G032700 chr6A 5123839 5124472 633 False 643.000000 643 85.294000 1 632 1 chr6A.!!$F1 631
6 TraesCS6D01G032700 chrUn 62401302 62403758 2456 False 1868.500000 2606 94.714000 788 3214 2 chrUn.!!$F2 2426
7 TraesCS6D01G032700 chrUn 62528307 62531491 3184 False 1418.666667 2601 91.311667 1 3214 3 chrUn.!!$F4 3213
8 TraesCS6D01G032700 chrUn 62456277 62459460 3183 False 1406.000000 2579 91.050000 1 3214 3 chrUn.!!$F3 3213
9 TraesCS6D01G032700 chrUn 62584715 62587879 3164 False 1388.000000 2536 90.882333 1 3214 3 chrUn.!!$F5 3213
10 TraesCS6D01G032700 chrUn 431609578 431610430 852 True 1194.000000 1194 92.069000 788 1641 1 chrUn.!!$R1 853
11 TraesCS6D01G032700 chrUn 439041982 439042683 701 True 1146.000000 1146 96.296000 2513 3207 1 chrUn.!!$R2 694
12 TraesCS6D01G032700 chrUn 62339614 62342778 3164 False 1117.000000 1718 90.980000 1 3214 3 chrUn.!!$F1 3213
13 TraesCS6D01G032700 chr6B 9765167 9766931 1764 False 2283.000000 2283 90.343000 788 2526 1 chr6B.!!$F1 1738

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
973 1030 0.032615 CCCTGTACTGAGCTCCCTCT 60.033 60.0 12.15 0.0 38.93 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2551 2678 0.611714 GCGGTCAGTCCTTTCCCTTA 59.388 55.0 0.0 0.0 0.0 2.69 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
39 40 3.165160 ATCCATCTACGGCGCCCAC 62.165 63.158 23.46 0.00 0.00 4.61
52 53 3.849951 CCCACCCATCCTCCGTCG 61.850 72.222 0.00 0.00 0.00 5.12
55 56 1.436336 CACCCATCCTCCGTCGTAC 59.564 63.158 0.00 0.00 0.00 3.67
57 58 0.548031 ACCCATCCTCCGTCGTACTA 59.452 55.000 0.00 0.00 0.00 1.82
87 88 1.412710 TCTTTCAATAGCCGCGATCCT 59.587 47.619 8.23 3.05 0.00 3.24
91 92 1.006102 AATAGCCGCGATCCTTCCG 60.006 57.895 8.23 0.00 0.00 4.30
101 102 2.674461 GATCCTTCCGCCGTCGTACC 62.674 65.000 0.00 0.00 0.00 3.34
153 154 2.287584 TGGGATTGGAACCTGAAGGAT 58.712 47.619 2.62 0.00 38.94 3.24
168 169 1.153147 GGATCCCACCTTCTTCGGC 60.153 63.158 0.00 0.00 0.00 5.54
191 192 3.933332 GCAGTAAATTAGGCACTTCTCGT 59.067 43.478 0.00 0.00 41.75 4.18
196 197 2.060326 TTAGGCACTTCTCGTTGACG 57.940 50.000 0.00 0.00 41.75 4.35
201 202 0.874175 CACTTCTCGTTGACGGTGCA 60.874 55.000 3.48 0.00 40.29 4.57
235 236 1.685421 GAGGAGCAGCAGAGGGAGT 60.685 63.158 0.00 0.00 0.00 3.85
340 341 2.436646 CTCACACGGACCATGCCC 60.437 66.667 0.00 0.00 0.00 5.36
343 344 4.722700 ACACGGACCATGCCCAGC 62.723 66.667 0.00 0.00 0.00 4.85
382 411 1.336755 GTTCTTGTTTCGTGCCCATGT 59.663 47.619 0.00 0.00 0.00 3.21
404 433 3.499737 GTCGCGGTTGGCCATCTG 61.500 66.667 17.07 17.07 38.94 2.90
407 436 3.818787 GCGGTTGGCCATCTGCAG 61.819 66.667 33.40 7.63 43.89 4.41
408 437 3.136123 CGGTTGGCCATCTGCAGG 61.136 66.667 15.13 0.00 43.89 4.85
428 457 3.423154 CCGGCGTCCTTGCAGTTC 61.423 66.667 6.01 0.00 36.28 3.01
482 515 3.921119 TGTAGTCCAAACGTCACGTAT 57.079 42.857 1.57 0.00 39.99 3.06
545 578 4.955774 GGGTCGCGTCACGTTGGT 62.956 66.667 5.77 0.00 44.19 3.67
591 625 0.872388 GGCAACGTCTGTACCCTTTG 59.128 55.000 0.00 0.00 0.00 2.77
593 627 2.548493 GGCAACGTCTGTACCCTTTGTA 60.548 50.000 0.00 0.00 0.00 2.41
626 660 7.848128 ACGAGGAGATAATCAAGAAAAGGTTA 58.152 34.615 0.00 0.00 0.00 2.85
639 673 6.165659 AGAAAAGGTTATCGTTTCATCGTG 57.834 37.500 6.66 0.00 43.24 4.35
640 674 4.336532 AAAGGTTATCGTTTCATCGTGC 57.663 40.909 0.00 0.00 0.00 5.34
657 700 1.519455 GCAGCTACGAGTCGCCAAT 60.519 57.895 13.59 0.00 0.00 3.16
659 702 0.179137 CAGCTACGAGTCGCCAATCA 60.179 55.000 13.59 0.00 0.00 2.57
668 711 1.135083 AGTCGCCAATCACCGAAGTAG 60.135 52.381 0.00 0.00 35.00 2.57
677 720 5.465051 CAATCACCGAAGTAGATCGATCAT 58.535 41.667 26.47 14.08 45.48 2.45
683 726 5.049336 ACCGAAGTAGATCGATCATGTACTG 60.049 44.000 26.47 14.90 45.48 2.74
685 728 5.560953 CGAAGTAGATCGATCATGTACTGCA 60.561 44.000 26.47 0.00 45.48 4.41
686 729 5.774498 AGTAGATCGATCATGTACTGCAA 57.226 39.130 26.47 0.00 39.57 4.08
693 736 3.185188 CGATCATGTACTGCAATAGCCAC 59.815 47.826 0.00 0.00 41.13 5.01
696 739 0.107897 TGTACTGCAATAGCCACCCG 60.108 55.000 0.00 0.00 41.13 5.28
699 742 0.255890 ACTGCAATAGCCACCCGATT 59.744 50.000 0.00 0.00 41.13 3.34
701 744 2.092646 ACTGCAATAGCCACCCGATTAA 60.093 45.455 0.00 0.00 41.13 1.40
702 745 2.549754 CTGCAATAGCCACCCGATTAAG 59.450 50.000 0.00 0.00 41.13 1.85
703 746 1.266989 GCAATAGCCACCCGATTAAGC 59.733 52.381 0.00 0.00 33.58 3.09
704 747 2.851195 CAATAGCCACCCGATTAAGCT 58.149 47.619 0.00 0.00 37.58 3.74
705 748 2.549754 CAATAGCCACCCGATTAAGCTG 59.450 50.000 0.00 0.00 35.03 4.24
706 749 0.179056 TAGCCACCCGATTAAGCTGC 60.179 55.000 0.00 0.00 35.03 5.25
707 750 2.481471 GCCACCCGATTAAGCTGCC 61.481 63.158 0.00 0.00 0.00 4.85
708 751 1.224592 CCACCCGATTAAGCTGCCT 59.775 57.895 0.00 0.00 0.00 4.75
709 752 1.097547 CCACCCGATTAAGCTGCCTG 61.098 60.000 0.00 0.00 0.00 4.85
710 753 1.452108 ACCCGATTAAGCTGCCTGC 60.452 57.895 0.00 0.00 43.29 4.85
738 781 0.250295 TTGTTCGGCTAGCTTGCACT 60.250 50.000 21.53 0.00 34.04 4.40
740 783 0.166814 GTTCGGCTAGCTTGCACTTG 59.833 55.000 21.53 8.30 34.04 3.16
752 795 2.241880 GCACTTGCACGTACGTGGT 61.242 57.895 40.17 29.52 45.49 4.16
758 801 2.649034 CACGTACGTGGTGCTCCT 59.351 61.111 35.09 1.70 42.00 3.69
759 802 1.443872 CACGTACGTGGTGCTCCTC 60.444 63.158 35.09 1.30 42.00 3.71
760 803 1.602888 ACGTACGTGGTGCTCCTCT 60.603 57.895 22.14 0.00 34.23 3.69
761 804 1.136984 CGTACGTGGTGCTCCTCTC 59.863 63.158 7.22 0.00 34.23 3.20
762 805 1.511768 GTACGTGGTGCTCCTCTCC 59.488 63.158 6.34 0.00 34.23 3.71
765 808 2.985456 GTGGTGCTCCTCTCCTGG 59.015 66.667 6.34 0.00 34.23 4.45
768 811 2.664081 GGTGCTCCTCTCCTGGGTG 61.664 68.421 0.00 0.00 0.00 4.61
769 812 1.915769 GTGCTCCTCTCCTGGGTGT 60.916 63.158 0.00 0.00 0.00 4.16
770 813 1.152030 TGCTCCTCTCCTGGGTGTT 60.152 57.895 0.00 0.00 0.00 3.32
771 814 0.768221 TGCTCCTCTCCTGGGTGTTT 60.768 55.000 0.00 0.00 0.00 2.83
773 816 1.352083 CTCCTCTCCTGGGTGTTTGA 58.648 55.000 0.00 0.00 0.00 2.69
774 817 1.912043 CTCCTCTCCTGGGTGTTTGAT 59.088 52.381 0.00 0.00 0.00 2.57
775 818 1.909302 TCCTCTCCTGGGTGTTTGATC 59.091 52.381 0.00 0.00 0.00 2.92
776 819 1.912043 CCTCTCCTGGGTGTTTGATCT 59.088 52.381 0.00 0.00 0.00 2.75
777 820 3.107601 CCTCTCCTGGGTGTTTGATCTA 58.892 50.000 0.00 0.00 0.00 1.98
778 821 3.713764 CCTCTCCTGGGTGTTTGATCTAT 59.286 47.826 0.00 0.00 0.00 1.98
779 822 4.202305 CCTCTCCTGGGTGTTTGATCTATC 60.202 50.000 0.00 0.00 0.00 2.08
780 823 4.624913 TCTCCTGGGTGTTTGATCTATCT 58.375 43.478 0.00 0.00 0.00 1.98
781 824 5.777449 TCTCCTGGGTGTTTGATCTATCTA 58.223 41.667 0.00 0.00 0.00 1.98
782 825 6.385443 TCTCCTGGGTGTTTGATCTATCTAT 58.615 40.000 0.00 0.00 0.00 1.98
783 826 6.846505 TCTCCTGGGTGTTTGATCTATCTATT 59.153 38.462 0.00 0.00 0.00 1.73
784 827 6.830912 TCCTGGGTGTTTGATCTATCTATTG 58.169 40.000 0.00 0.00 0.00 1.90
785 828 5.471456 CCTGGGTGTTTGATCTATCTATTGC 59.529 44.000 0.00 0.00 0.00 3.56
786 829 6.252599 TGGGTGTTTGATCTATCTATTGCT 57.747 37.500 0.00 0.00 0.00 3.91
787 830 7.373617 TGGGTGTTTGATCTATCTATTGCTA 57.626 36.000 0.00 0.00 0.00 3.49
788 831 7.217200 TGGGTGTTTGATCTATCTATTGCTAC 58.783 38.462 0.00 0.00 0.00 3.58
789 832 6.366332 GGGTGTTTGATCTATCTATTGCTACG 59.634 42.308 0.00 0.00 0.00 3.51
790 833 6.924060 GGTGTTTGATCTATCTATTGCTACGT 59.076 38.462 0.00 0.00 0.00 3.57
791 834 8.080417 GGTGTTTGATCTATCTATTGCTACGTA 58.920 37.037 0.00 0.00 0.00 3.57
861 904 1.982958 ACGGAAACCCAAGTCATACCT 59.017 47.619 0.00 0.00 0.00 3.08
930 985 6.175471 TCATCTGGGCTAATTATACAGCATG 58.825 40.000 0.66 0.00 46.00 4.06
937 992 5.178797 GCTAATTATACAGCATGGATCGGT 58.821 41.667 0.00 0.00 29.66 4.69
973 1030 0.032615 CCCTGTACTGAGCTCCCTCT 60.033 60.000 12.15 0.00 38.93 3.69
987 1046 2.566724 CTCCCTCTTAGAGCCATCCATC 59.433 54.545 3.26 0.00 0.00 3.51
1139 1219 4.428922 CACGTGCGTGGACATGCG 62.429 66.667 15.98 1.59 45.93 4.73
1248 1337 0.686441 TGATCTACCAGTCCCACGGG 60.686 60.000 0.00 0.00 39.46 5.28
1438 1527 1.415200 GAGTCTCACCCTACCATCCC 58.585 60.000 0.00 0.00 0.00 3.85
1469 1558 1.804601 CCAAGAACGACTGGGGTAAC 58.195 55.000 0.00 0.00 36.09 2.50
1547 1637 2.947652 CCAAGTGGTCAAGGCATATCTG 59.052 50.000 0.00 0.00 0.00 2.90
1563 1653 5.456265 CATATCTGGAGATGTCACAGTACG 58.544 45.833 0.00 0.00 36.05 3.67
1807 1901 2.248835 GGTTCCCACACCACGAACG 61.249 63.158 0.00 0.00 37.38 3.95
1853 1948 3.770040 CGGGTCGGGATGTGCTCA 61.770 66.667 0.00 0.00 0.00 4.26
1959 2054 6.863126 GTGATCAACATGACGGAGAAAATTTT 59.137 34.615 2.28 2.28 0.00 1.82
2015 2110 1.666872 CCGACGAACCCAGTCCAAC 60.667 63.158 0.00 0.00 35.33 3.77
2033 2128 5.003804 TCCAACTCAAGCTAATCTGGTTTC 58.996 41.667 0.00 0.00 0.00 2.78
2041 2136 2.194271 CTAATCTGGTTTCGGCGAGAC 58.806 52.381 20.95 20.95 0.00 3.36
2045 2140 2.257676 GGTTTCGGCGAGACGAGT 59.742 61.111 21.98 0.00 44.47 4.18
2048 2143 3.909258 TTTCGGCGAGACGAGTGGC 62.909 63.158 10.46 0.00 44.47 5.01
2100 2195 3.695606 GGCTCGACCTGCAGTCCA 61.696 66.667 13.81 0.00 43.08 4.02
2101 2196 2.581354 GCTCGACCTGCAGTCCAT 59.419 61.111 13.81 0.00 43.08 3.41
2102 2197 1.520342 GCTCGACCTGCAGTCCATC 60.520 63.158 13.81 3.82 43.08 3.51
2190 2285 1.029681 GAGTTTGACGGCTTGGGTTT 58.970 50.000 0.00 0.00 0.00 3.27
2200 2295 2.223923 CGGCTTGGGTTTCAACATTCAA 60.224 45.455 0.00 0.00 0.00 2.69
2234 2329 7.885297 TGTGATTAATTCTTTCAGGTTCTTGG 58.115 34.615 0.00 0.00 0.00 3.61
2271 2366 9.890629 ACTTCATTATCAACTATAGAAGCACAA 57.109 29.630 6.78 0.00 35.61 3.33
2338 2433 9.651913 TTTATTTGCCAATTAGTGAGGAAATTC 57.348 29.630 6.13 0.00 33.61 2.17
2403 2498 3.122297 TGTACTTGTGCAAGCATTTTGC 58.878 40.909 11.43 5.00 45.46 3.68
2550 2677 0.248907 CGTTGGATGTCGTCGCCTAT 60.249 55.000 0.00 0.00 0.00 2.57
2551 2678 1.801395 CGTTGGATGTCGTCGCCTATT 60.801 52.381 0.00 0.00 0.00 1.73
2571 2698 2.046217 GGGAAAGGACTGACCGCC 60.046 66.667 0.00 0.00 44.74 6.13
2713 2845 8.685427 TGGTTTATGATGACAATTCCATGTTAG 58.315 33.333 0.00 0.00 32.57 2.34
2881 3013 9.726232 CCAGAAAATCATATATTTCACACTGTG 57.274 33.333 6.19 6.19 37.87 3.66
2976 3108 9.740710 AACATAATGCTATAAAGTATTCCCTCC 57.259 33.333 0.00 0.00 38.72 4.30
3067 3199 7.867305 TTTGTATGGTGTTCTCAACAAAGTA 57.133 32.000 0.00 0.00 44.84 2.24
3068 3200 7.867305 TTGTATGGTGTTCTCAACAAAGTAA 57.133 32.000 0.00 0.00 44.84 2.24
3096 3228 1.344763 AGAGACGCCTATTATGGTGCC 59.655 52.381 0.00 0.00 41.02 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 1.236628 CTAGTACGACGGAGGATGGG 58.763 60.000 0.00 0.00 0.00 4.00
87 88 2.491152 GATGGTACGACGGCGGAA 59.509 61.111 18.49 0.00 43.17 4.30
91 92 1.660575 CATCGGATGGTACGACGGC 60.661 63.158 10.18 0.00 43.78 5.68
101 102 2.793585 GCAACATGCAGTTCATCGGATG 60.794 50.000 11.79 11.79 44.26 3.51
123 124 0.112995 TCCAATCCCAAGCAAGCTGT 59.887 50.000 0.00 0.00 0.00 4.40
153 154 4.388499 GCGCCGAAGAAGGTGGGA 62.388 66.667 0.00 0.00 41.84 4.37
155 156 2.501223 TACTGCGCCGAAGAAGGTGG 62.501 60.000 4.18 0.00 41.84 4.61
163 164 1.011333 GCCTAATTTACTGCGCCGAA 58.989 50.000 4.18 0.00 0.00 4.30
168 169 3.000322 CGAGAAGTGCCTAATTTACTGCG 60.000 47.826 0.00 0.00 0.00 5.18
201 202 1.908793 CTCTCACCTGTGGACCGGT 60.909 63.158 6.92 6.92 0.00 5.28
340 341 4.135153 CTCCCCGACGACCTGCTG 62.135 72.222 0.00 0.00 0.00 4.41
343 344 4.436998 GTGCTCCCCGACGACCTG 62.437 72.222 0.00 0.00 0.00 4.00
411 440 3.423154 GAACTGCAAGGACGCCGG 61.423 66.667 0.00 0.00 39.30 6.13
412 441 1.961277 AAGAACTGCAAGGACGCCG 60.961 57.895 0.00 0.00 39.30 6.46
413 442 1.576421 CAAGAACTGCAAGGACGCC 59.424 57.895 0.00 0.00 39.30 5.68
426 455 3.198409 ACATAGATCGGCATGCAAGAA 57.802 42.857 21.36 3.98 0.00 2.52
427 456 2.916702 ACATAGATCGGCATGCAAGA 57.083 45.000 21.36 18.22 0.00 3.02
428 457 3.657634 ACTACATAGATCGGCATGCAAG 58.342 45.455 21.36 13.07 0.00 4.01
468 501 3.498927 AGGACTATACGTGACGTTTGG 57.501 47.619 18.28 13.44 41.54 3.28
469 502 5.475273 TCTAGGACTATACGTGACGTTTG 57.525 43.478 18.28 9.46 41.54 2.93
482 515 8.554870 TCCAGTTTACAACTCTATCTAGGACTA 58.445 37.037 0.00 0.00 40.46 2.59
595 629 6.536731 TCTTGATTATCTCCTCGTACGTAC 57.463 41.667 15.90 15.90 0.00 3.67
596 630 7.558161 TTTCTTGATTATCTCCTCGTACGTA 57.442 36.000 16.05 0.00 0.00 3.57
597 631 6.446781 TTTCTTGATTATCTCCTCGTACGT 57.553 37.500 16.05 0.00 0.00 3.57
598 632 6.418226 CCTTTTCTTGATTATCTCCTCGTACG 59.582 42.308 9.53 9.53 0.00 3.67
599 633 7.266400 ACCTTTTCTTGATTATCTCCTCGTAC 58.734 38.462 0.00 0.00 0.00 3.67
600 634 7.419711 ACCTTTTCTTGATTATCTCCTCGTA 57.580 36.000 0.00 0.00 0.00 3.43
602 636 8.894768 ATAACCTTTTCTTGATTATCTCCTCG 57.105 34.615 0.00 0.00 0.00 4.63
603 637 8.983724 CGATAACCTTTTCTTGATTATCTCCTC 58.016 37.037 0.00 0.00 32.46 3.71
604 638 8.487028 ACGATAACCTTTTCTTGATTATCTCCT 58.513 33.333 0.00 0.00 32.46 3.69
605 639 8.664211 ACGATAACCTTTTCTTGATTATCTCC 57.336 34.615 0.00 0.00 32.46 3.71
617 651 4.786575 GCACGATGAAACGATAACCTTTTC 59.213 41.667 0.00 0.00 37.03 2.29
626 660 1.927174 GTAGCTGCACGATGAAACGAT 59.073 47.619 1.02 0.00 37.03 3.73
639 673 1.483424 GATTGGCGACTCGTAGCTGC 61.483 60.000 0.00 0.00 0.00 5.25
640 674 0.179137 TGATTGGCGACTCGTAGCTG 60.179 55.000 0.00 0.00 0.00 4.24
657 700 3.883489 ACATGATCGATCTACTTCGGTGA 59.117 43.478 25.02 2.17 39.56 4.02
659 702 5.049336 CAGTACATGATCGATCTACTTCGGT 60.049 44.000 25.02 14.12 39.56 4.69
668 711 4.328440 GGCTATTGCAGTACATGATCGATC 59.672 45.833 18.72 18.72 41.91 3.69
677 720 0.107897 CGGGTGGCTATTGCAGTACA 60.108 55.000 0.66 0.00 41.91 2.90
683 726 1.266989 GCTTAATCGGGTGGCTATTGC 59.733 52.381 0.00 0.00 38.76 3.56
685 728 2.851195 CAGCTTAATCGGGTGGCTATT 58.149 47.619 0.00 0.00 0.00 1.73
686 729 1.543429 GCAGCTTAATCGGGTGGCTAT 60.543 52.381 0.00 0.00 33.43 2.97
693 736 3.425422 GCAGGCAGCTTAATCGGG 58.575 61.111 0.00 0.00 41.15 5.14
706 749 1.288127 GAACAAGCAGCCAAGCAGG 59.712 57.895 0.00 0.00 41.84 4.85
707 750 1.081641 CGAACAAGCAGCCAAGCAG 60.082 57.895 0.00 0.00 36.85 4.24
708 751 2.554636 CCGAACAAGCAGCCAAGCA 61.555 57.895 0.00 0.00 36.85 3.91
709 752 2.256461 CCGAACAAGCAGCCAAGC 59.744 61.111 0.00 0.00 0.00 4.01
710 753 0.955428 TAGCCGAACAAGCAGCCAAG 60.955 55.000 0.00 0.00 0.00 3.61
711 754 0.955428 CTAGCCGAACAAGCAGCCAA 60.955 55.000 0.00 0.00 0.00 4.52
712 755 1.375908 CTAGCCGAACAAGCAGCCA 60.376 57.895 0.00 0.00 0.00 4.75
713 756 2.754995 GCTAGCCGAACAAGCAGCC 61.755 63.158 2.29 0.00 36.26 4.85
743 786 1.136984 GAGAGGAGCACCACGTACG 59.863 63.158 15.01 15.01 38.94 3.67
744 787 0.966370 AGGAGAGGAGCACCACGTAC 60.966 60.000 2.07 0.00 38.94 3.67
745 788 0.965866 CAGGAGAGGAGCACCACGTA 60.966 60.000 2.07 0.00 38.94 3.57
747 790 2.575993 CAGGAGAGGAGCACCACG 59.424 66.667 2.07 0.00 38.94 4.94
748 791 2.664081 CCCAGGAGAGGAGCACCAC 61.664 68.421 2.07 0.00 38.94 4.16
750 793 2.284995 ACCCAGGAGAGGAGCACC 60.285 66.667 0.00 0.00 0.00 5.01
752 795 0.768221 AAACACCCAGGAGAGGAGCA 60.768 55.000 0.00 0.00 0.00 4.26
754 797 1.352083 TCAAACACCCAGGAGAGGAG 58.648 55.000 0.00 0.00 0.00 3.69
755 798 1.909302 GATCAAACACCCAGGAGAGGA 59.091 52.381 0.00 0.00 0.00 3.71
756 799 1.912043 AGATCAAACACCCAGGAGAGG 59.088 52.381 0.00 0.00 0.00 3.69
758 801 4.624913 AGATAGATCAAACACCCAGGAGA 58.375 43.478 0.00 0.00 0.00 3.71
759 802 6.678568 ATAGATAGATCAAACACCCAGGAG 57.321 41.667 0.00 0.00 0.00 3.69
760 803 6.688922 GCAATAGATAGATCAAACACCCAGGA 60.689 42.308 0.00 0.00 0.00 3.86
761 804 5.471456 GCAATAGATAGATCAAACACCCAGG 59.529 44.000 0.00 0.00 0.00 4.45
762 805 6.294473 AGCAATAGATAGATCAAACACCCAG 58.706 40.000 0.00 0.00 0.00 4.45
765 808 6.924060 ACGTAGCAATAGATAGATCAAACACC 59.076 38.462 0.00 0.00 0.00 4.16
768 811 7.270793 CCGTACGTAGCAATAGATAGATCAAAC 59.729 40.741 15.21 0.00 0.00 2.93
769 812 7.173735 TCCGTACGTAGCAATAGATAGATCAAA 59.826 37.037 15.21 0.00 0.00 2.69
770 813 6.652062 TCCGTACGTAGCAATAGATAGATCAA 59.348 38.462 15.21 0.00 0.00 2.57
771 814 6.091849 GTCCGTACGTAGCAATAGATAGATCA 59.908 42.308 15.21 0.00 0.00 2.92
773 816 6.171921 AGTCCGTACGTAGCAATAGATAGAT 58.828 40.000 15.21 0.00 0.00 1.98
774 817 5.545588 AGTCCGTACGTAGCAATAGATAGA 58.454 41.667 15.21 0.00 0.00 1.98
775 818 5.444350 CGAGTCCGTACGTAGCAATAGATAG 60.444 48.000 15.21 0.00 0.00 2.08
776 819 4.386954 CGAGTCCGTACGTAGCAATAGATA 59.613 45.833 15.21 0.00 0.00 1.98
777 820 3.186001 CGAGTCCGTACGTAGCAATAGAT 59.814 47.826 15.21 0.00 0.00 1.98
778 821 2.541346 CGAGTCCGTACGTAGCAATAGA 59.459 50.000 15.21 0.00 0.00 1.98
779 822 2.541346 TCGAGTCCGTACGTAGCAATAG 59.459 50.000 15.21 0.00 37.05 1.73
780 823 2.549926 TCGAGTCCGTACGTAGCAATA 58.450 47.619 15.21 0.00 37.05 1.90
781 824 1.372582 TCGAGTCCGTACGTAGCAAT 58.627 50.000 15.21 0.00 37.05 3.56
782 825 1.328680 GATCGAGTCCGTACGTAGCAA 59.671 52.381 15.21 0.00 37.05 3.91
783 826 0.933097 GATCGAGTCCGTACGTAGCA 59.067 55.000 15.21 0.00 37.05 3.49
784 827 0.111354 CGATCGAGTCCGTACGTAGC 60.111 60.000 10.26 3.73 37.05 3.58
785 828 0.506080 CCGATCGAGTCCGTACGTAG 59.494 60.000 18.66 0.00 37.05 3.51
786 829 0.875908 CCCGATCGAGTCCGTACGTA 60.876 60.000 18.66 0.00 37.05 3.57
787 830 2.176273 CCCGATCGAGTCCGTACGT 61.176 63.158 18.66 0.00 37.05 3.57
788 831 1.884464 TCCCGATCGAGTCCGTACG 60.884 63.158 18.66 8.69 37.05 3.67
789 832 1.645997 GTCCCGATCGAGTCCGTAC 59.354 63.158 18.66 0.00 37.05 3.67
790 833 1.884464 CGTCCCGATCGAGTCCGTA 60.884 63.158 18.66 0.00 37.05 4.02
791 834 3.200593 CGTCCCGATCGAGTCCGT 61.201 66.667 18.66 0.00 37.05 4.69
907 962 5.356190 CCATGCTGTATAATTAGCCCAGATG 59.644 44.000 11.11 10.66 39.15 2.90
973 1030 0.681733 GCCTCGATGGATGGCTCTAA 59.318 55.000 5.43 0.00 43.05 2.10
987 1046 2.969238 GCCATGGTCGATGCCTCG 60.969 66.667 14.67 4.89 46.41 4.63
1063 1131 1.717937 CAATGTCCACTAGCGCTGC 59.282 57.895 22.90 3.63 0.00 5.25
1066 1134 2.703409 CGCAATGTCCACTAGCGC 59.297 61.111 0.00 0.00 41.95 5.92
1139 1219 1.813753 TATTCCTTGACGCGGCAGC 60.814 57.895 17.30 0.00 40.74 5.25
1140 1220 0.739462 TGTATTCCTTGACGCGGCAG 60.739 55.000 17.30 9.80 0.00 4.85
1141 1221 0.107897 ATGTATTCCTTGACGCGGCA 60.108 50.000 12.71 12.71 0.00 5.69
1142 1222 0.582005 GATGTATTCCTTGACGCGGC 59.418 55.000 12.47 8.67 0.00 6.53
1438 1527 0.310854 GTTCTTGGGAACGCCTGTTG 59.689 55.000 0.00 0.00 41.70 3.33
1469 1558 1.618861 CACGGACGAGCAAGACTAAG 58.381 55.000 0.00 0.00 0.00 2.18
1514 1604 1.213537 CACTTGGAAATGCCGGCAG 59.786 57.895 35.36 21.15 40.66 4.85
1515 1605 2.274645 CCACTTGGAAATGCCGGCA 61.275 57.895 34.80 34.80 40.66 5.69
1547 1637 0.525668 CGCCGTACTGTGACATCTCC 60.526 60.000 0.00 0.00 0.00 3.71
1807 1901 4.893424 TGTTGCTAGAAGTTTTGGTGTC 57.107 40.909 0.00 0.00 0.00 3.67
2015 2110 2.352960 GCCGAAACCAGATTAGCTTGAG 59.647 50.000 0.00 0.00 0.00 3.02
2041 2136 3.939837 ATGAGCACGGTGCCACTCG 62.940 63.158 28.14 0.00 46.52 4.18
2045 2140 3.690280 TCGATGAGCACGGTGCCA 61.690 61.111 28.14 24.06 46.52 4.92
2048 2143 0.737367 ATGTGTCGATGAGCACGGTG 60.737 55.000 3.15 3.15 38.36 4.94
2100 2195 2.848694 ACCACCTCACAATCTCCATGAT 59.151 45.455 0.00 0.00 36.89 2.45
2101 2196 2.269023 ACCACCTCACAATCTCCATGA 58.731 47.619 0.00 0.00 0.00 3.07
2102 2197 2.795231 ACCACCTCACAATCTCCATG 57.205 50.000 0.00 0.00 0.00 3.66
2111 2206 2.054021 TGATCCAAGAACCACCTCACA 58.946 47.619 0.00 0.00 0.00 3.58
2147 2242 6.846505 TCATCTCATAGGGGATATTATGGGTC 59.153 42.308 0.00 0.00 31.21 4.46
2190 2285 6.631971 TCACAAAGTGCTATTGAATGTTGA 57.368 33.333 4.15 0.00 32.98 3.18
2221 2316 4.141274 TGAGAATGGACCAAGAACCTGAAA 60.141 41.667 0.00 0.00 0.00 2.69
2234 2329 8.273780 AGTTGATAATGAAGTTGAGAATGGAC 57.726 34.615 0.00 0.00 0.00 4.02
2370 2465 7.624344 GCTTGCACAAGTACAGATAAAACTAGG 60.624 40.741 11.77 0.00 40.45 3.02
2550 2677 1.002773 GCGGTCAGTCCTTTCCCTTAA 59.997 52.381 0.00 0.00 0.00 1.85
2551 2678 0.611714 GCGGTCAGTCCTTTCCCTTA 59.388 55.000 0.00 0.00 0.00 2.69
2878 3010 8.744652 TCTTTTGAAAACAAAGGATAACTCACA 58.255 29.630 0.00 0.00 32.86 3.58
2972 3104 2.612212 CGAAATAACATTGGGACGGAGG 59.388 50.000 0.00 0.00 0.00 4.30
2976 3108 2.634600 TCCCGAAATAACATTGGGACG 58.365 47.619 0.00 0.00 43.85 4.79
3032 3164 7.930217 AGAACACCATACAAATCATATTTCGG 58.070 34.615 0.00 0.00 0.00 4.30
3067 3199 4.744795 AATAGGCGTCTCTGTCTCATTT 57.255 40.909 0.00 0.00 0.00 2.32
3068 3200 5.279206 CCATAATAGGCGTCTCTGTCTCATT 60.279 44.000 0.00 0.00 0.00 2.57
3096 3228 0.460284 AGTATTGTGAAGGCCGCTCG 60.460 55.000 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.