Multiple sequence alignment - TraesCS5B01G533300

Loading Multiple Alignment...

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 TraesCS5B01G533300 chr5B 100.000 2372 0 0 1 2372 690169360 690171731 0.000000e+00 4381
1 TraesCS5B01G533300 chr5B 86.486 111 8 3 1734 1843 690220879 690220983 5.360000e-22 115
2 TraesCS5B01G533300 chr5B 93.846 65 4 0 1734 1798 690220799 690220863 5.400000e-17 99
3 TraesCS5B01G533300 chr5D 87.117 1141 63 39 708 1798 547048946 547050052 0.000000e+00 1216
4 TraesCS5B01G533300 chr4A 83.490 1387 92 56 490 1791 621794028 621792694 0.000000e+00 1166
5 TraesCS5B01G533300 chr4A 91.176 510 36 3 1 503 621796146 621795639 0.000000e+00 684
6 TraesCS5B01G533300 chr2D 92.898 521 35 2 1850 2369 297180670 297180151 0.000000e+00 756
7 TraesCS5B01G533300 chr2D 92.337 522 36 4 1850 2369 634075403 634075922 0.000000e+00 739
8 TraesCS5B01G533300 chr1D 91.221 524 40 6 1850 2369 107545145 107544624 0.000000e+00 708
9 TraesCS5B01G533300 chr3A 90.421 522 46 4 1850 2369 568244001 568244520 0.000000e+00 684
10 TraesCS5B01G533300 chrUn 90.230 522 46 5 1850 2369 77774378 77774896 0.000000e+00 676
11 TraesCS5B01G533300 chr7B 88.952 525 52 3 1850 2369 729231536 729232059 0.000000e+00 643
12 TraesCS5B01G533300 chr2A 89.060 521 54 3 1850 2369 19922763 19923281 0.000000e+00 643
13 TraesCS5B01G533300 chr5A 89.147 516 52 3 1855 2369 691792796 691792284 7.150000e-180 640
14 TraesCS5B01G533300 chr6B 88.697 522 55 4 1850 2369 716582844 716582325 3.330000e-178 634
15 TraesCS5B01G533300 chr4B 79.310 203 34 8 404 603 5828398 5828595 4.110000e-28 135


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 TraesCS5B01G533300 chr5B 690169360 690171731 2371 False 4381 4381 100.000 1 2372 1 chr5B.!!$F1 2371
1 TraesCS5B01G533300 chr5D 547048946 547050052 1106 False 1216 1216 87.117 708 1798 1 chr5D.!!$F1 1090
2 TraesCS5B01G533300 chr4A 621792694 621796146 3452 True 925 1166 87.333 1 1791 2 chr4A.!!$R1 1790
3 TraesCS5B01G533300 chr2D 297180151 297180670 519 True 756 756 92.898 1850 2369 1 chr2D.!!$R1 519
4 TraesCS5B01G533300 chr2D 634075403 634075922 519 False 739 739 92.337 1850 2369 1 chr2D.!!$F1 519
5 TraesCS5B01G533300 chr1D 107544624 107545145 521 True 708 708 91.221 1850 2369 1 chr1D.!!$R1 519
6 TraesCS5B01G533300 chr3A 568244001 568244520 519 False 684 684 90.421 1850 2369 1 chr3A.!!$F1 519
7 TraesCS5B01G533300 chrUn 77774378 77774896 518 False 676 676 90.230 1850 2369 1 chrUn.!!$F1 519
8 TraesCS5B01G533300 chr7B 729231536 729232059 523 False 643 643 88.952 1850 2369 1 chr7B.!!$F1 519
9 TraesCS5B01G533300 chr2A 19922763 19923281 518 False 643 643 89.060 1850 2369 1 chr2A.!!$F1 519
10 TraesCS5B01G533300 chr5A 691792284 691792796 512 True 640 640 89.147 1855 2369 1 chr5A.!!$R1 514
11 TraesCS5B01G533300 chr6B 716582325 716582844 519 True 634 634 88.697 1850 2369 1 chr6B.!!$R1 519

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
972 2649 0.305313 CTCGATCGGAGAACCTCGAC 59.695 60.0 16.41 0.0 46.23 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1942 3691 0.326927 AATGTCCCACTACAACGGGG 59.673 55.0 0.0 0.0 43.29 5.73 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
21 22 4.360951 TTTCTGGTGGATTCCTACGTTT 57.639 40.909 3.95 0.00 0.00 3.60
24 25 3.056107 TCTGGTGGATTCCTACGTTTCTG 60.056 47.826 3.95 0.00 0.00 3.02
25 26 2.007608 GGTGGATTCCTACGTTTCTGC 58.992 52.381 3.95 0.00 0.00 4.26
31 32 4.879545 GGATTCCTACGTTTCTGCCAAATA 59.120 41.667 0.00 0.00 0.00 1.40
42 43 5.356882 TTCTGCCAAATAGTCGAAACTTG 57.643 39.130 0.00 0.00 36.92 3.16
70 71 1.090728 GGGCTTAGCAGCTCTTTGAC 58.909 55.000 6.53 0.00 44.19 3.18
72 73 1.673033 GGCTTAGCAGCTCTTTGACGA 60.673 52.381 6.53 0.00 46.44 4.20
92 93 2.111384 AGCGATAAGGAAGCTCCAGAA 58.889 47.619 5.21 0.00 39.61 3.02
118 119 5.004922 AGCTTGTTTTGATTTCAAACCGA 57.995 34.783 5.26 0.00 44.56 4.69
121 122 6.538381 AGCTTGTTTTGATTTCAAACCGATTT 59.462 30.769 5.26 0.00 44.56 2.17
151 152 4.497300 GGCTGAATTTGTGTGTTATGCAT 58.503 39.130 3.79 3.79 0.00 3.96
160 161 4.049869 TGTGTGTTATGCATGCTTGTTTG 58.950 39.130 20.33 0.00 0.00 2.93
170 171 4.022503 TGCATGCTTGTTTGTGCATTACTA 60.023 37.500 20.33 0.00 46.29 1.82
301 308 4.927049 AGCTCAAGAAGATGAAAATGGGA 58.073 39.130 0.00 0.00 0.00 4.37
360 367 3.136763 AGTGGATAAGCTGATGATTGCG 58.863 45.455 0.00 0.00 0.00 4.85
376 383 3.847671 TTGCGGTGGATTGTGGATATA 57.152 42.857 0.00 0.00 0.00 0.86
380 387 3.119849 GCGGTGGATTGTGGATATATTGC 60.120 47.826 0.00 0.00 0.00 3.56
381 388 3.440173 CGGTGGATTGTGGATATATTGCC 59.560 47.826 0.00 0.00 0.00 4.52
398 405 1.340502 TGCCTTGTCTGTGTTTGGACA 60.341 47.619 0.00 0.00 40.17 4.02
420 427 2.668250 TGGACTACACATTTGACGTCG 58.332 47.619 11.62 0.00 0.00 5.12
442 450 5.242615 TCGGATTTTTGACCATGACAAATCA 59.757 36.000 15.03 8.50 39.83 2.57
444 452 6.423302 CGGATTTTTGACCATGACAAATCAAA 59.577 34.615 15.03 10.20 38.69 2.69
445 453 7.118101 CGGATTTTTGACCATGACAAATCAAAT 59.882 33.333 15.03 12.54 39.94 2.32
495 503 6.861065 TCAAGAATGACAAGGTTAGTTGAC 57.139 37.500 0.00 0.00 0.00 3.18
503 511 1.726853 AGGTTAGTTGACGAGCATGC 58.273 50.000 10.51 10.51 0.00 4.06
540 2172 8.191446 TCGGTTCATTTGTTTGTCAGAAAATTA 58.809 29.630 0.00 0.00 0.00 1.40
541 2173 8.265998 CGGTTCATTTGTTTGTCAGAAAATTAC 58.734 33.333 0.00 0.00 0.00 1.89
545 2177 7.433719 TCATTTGTTTGTCAGAAAATTACCGTG 59.566 33.333 0.00 0.00 0.00 4.94
555 2188 3.444703 AAATTACCGTGCTTGCAAACA 57.555 38.095 0.00 0.00 0.00 2.83
559 2192 2.307934 ACCGTGCTTGCAAACAAAAT 57.692 40.000 3.67 0.00 34.74 1.82
576 2209 7.669438 AACAAAATTTGCTATCATCGAATCG 57.331 32.000 5.52 0.00 0.00 3.34
608 2242 9.767228 AATTGTCATGAAAAACATCAGATTCAA 57.233 25.926 1.55 0.00 37.07 2.69
621 2255 6.832384 ACATCAGATTCAACATGCCTAGAAAT 59.168 34.615 0.00 0.00 0.00 2.17
622 2256 6.932356 TCAGATTCAACATGCCTAGAAATC 57.068 37.500 0.00 0.00 0.00 2.17
623 2257 6.656902 TCAGATTCAACATGCCTAGAAATCT 58.343 36.000 0.00 0.00 0.00 2.40
624 2258 6.541278 TCAGATTCAACATGCCTAGAAATCTG 59.459 38.462 18.30 18.30 32.83 2.90
625 2259 6.541278 CAGATTCAACATGCCTAGAAATCTGA 59.459 38.462 18.98 0.00 33.04 3.27
626 2260 7.228906 CAGATTCAACATGCCTAGAAATCTGAT 59.771 37.037 18.98 0.00 33.04 2.90
627 2261 8.435187 AGATTCAACATGCCTAGAAATCTGATA 58.565 33.333 0.00 0.00 0.00 2.15
628 2262 9.228949 GATTCAACATGCCTAGAAATCTGATAT 57.771 33.333 0.00 0.00 0.00 1.63
630 2264 8.387190 TCAACATGCCTAGAAATCTGATATTG 57.613 34.615 0.00 0.00 0.00 1.90
631 2265 7.446319 TCAACATGCCTAGAAATCTGATATTGG 59.554 37.037 0.00 0.00 0.00 3.16
632 2266 7.083062 ACATGCCTAGAAATCTGATATTGGA 57.917 36.000 0.00 0.00 0.00 3.53
633 2267 7.696981 ACATGCCTAGAAATCTGATATTGGAT 58.303 34.615 0.00 0.00 0.00 3.41
648 2310 8.568676 TGATATTGGATTTTTAGTGTTTCCGA 57.431 30.769 0.00 0.00 0.00 4.55
649 2311 9.184523 TGATATTGGATTTTTAGTGTTTCCGAT 57.815 29.630 0.00 0.00 35.30 4.18
675 2337 2.040544 GGACGTGGAATGGGTGCTG 61.041 63.158 0.00 0.00 0.00 4.41
677 2339 1.577328 GACGTGGAATGGGTGCTGTG 61.577 60.000 0.00 0.00 0.00 3.66
711 2373 2.748461 TTCACGCGGAAACAAGAAAG 57.252 45.000 12.47 0.00 30.98 2.62
740 2405 0.320160 AACTAAACAGGGACGGCGAC 60.320 55.000 16.62 7.58 0.00 5.19
875 2540 1.828595 TCCCGTGGCACGCATATATAT 59.171 47.619 33.15 0.00 40.91 0.86
876 2541 3.025262 TCCCGTGGCACGCATATATATA 58.975 45.455 33.15 7.77 40.91 0.86
877 2542 3.639561 TCCCGTGGCACGCATATATATAT 59.360 43.478 33.15 0.00 40.91 0.86
878 2543 4.828387 TCCCGTGGCACGCATATATATATA 59.172 41.667 33.15 4.92 40.91 0.86
941 2606 3.470567 GCCGACGACGCAGACTTG 61.471 66.667 0.64 0.00 38.29 3.16
971 2648 1.437772 GCTCGATCGGAGAACCTCGA 61.438 60.000 16.41 1.31 46.23 4.04
972 2649 0.305313 CTCGATCGGAGAACCTCGAC 59.695 60.000 16.41 0.00 46.23 4.20
973 2650 1.011019 CGATCGGAGAACCTCGACG 60.011 63.158 7.38 0.00 43.58 5.12
974 2651 1.703438 CGATCGGAGAACCTCGACGT 61.703 60.000 7.38 0.00 43.58 4.34
975 2652 1.293924 GATCGGAGAACCTCGACGTA 58.706 55.000 0.00 0.00 43.58 3.57
976 2653 1.004079 GATCGGAGAACCTCGACGTAC 60.004 57.143 0.00 0.00 43.58 3.67
977 2654 1.059994 CGGAGAACCTCGACGTACG 59.940 63.158 15.01 15.01 44.09 3.67
978 2655 1.630244 CGGAGAACCTCGACGTACGT 61.630 60.000 23.04 23.04 43.13 3.57
990 2679 2.758840 GTACGTACGTGCGTGTGC 59.241 61.111 36.35 23.35 45.33 4.57
1386 3078 4.743955 GCCTTCTAATTAAGCTCCGTCCAT 60.744 45.833 0.00 0.00 0.00 3.41
1399 3091 3.576861 TCCGTCCATGGAGATCAACTAT 58.423 45.455 16.81 0.00 33.05 2.12
1405 3101 2.910688 TGGAGATCAACTATTCCGGC 57.089 50.000 0.00 0.00 32.27 6.13
1407 3103 1.068741 GGAGATCAACTATTCCGGCGT 59.931 52.381 6.01 0.00 0.00 5.68
1427 3123 4.111016 CCAGCTGCATGCACGTGG 62.111 66.667 23.04 23.04 45.94 4.94
1428 3124 4.111016 CAGCTGCATGCACGTGGG 62.111 66.667 18.46 8.01 45.94 4.61
1473 3180 0.943359 CGGCTCATCGCTCTTCCATC 60.943 60.000 0.00 0.00 39.13 3.51
1476 3205 1.202627 GCTCATCGCTCTTCCATCCTT 60.203 52.381 0.00 0.00 35.14 3.36
1490 3219 2.100584 CCATCCTTTCTCTCTCTCCGTG 59.899 54.545 0.00 0.00 0.00 4.94
1513 3242 6.521133 GTGTATATGTATCTAACCACGTACGC 59.479 42.308 16.72 0.00 0.00 4.42
1532 3270 1.372582 CTGGCATGCACGACACTATT 58.627 50.000 21.36 0.00 0.00 1.73
1542 3280 3.306166 GCACGACACTATTAAACTGCGAT 59.694 43.478 0.00 0.00 0.00 4.58
1579 3317 3.353836 GACCGTGGTGCGTGCAAT 61.354 61.111 0.00 0.00 39.32 3.56
1581 3319 1.366111 GACCGTGGTGCGTGCAATAT 61.366 55.000 0.00 0.00 39.32 1.28
1582 3320 0.108089 ACCGTGGTGCGTGCAATATA 60.108 50.000 0.00 0.00 39.32 0.86
1583 3321 0.581529 CCGTGGTGCGTGCAATATAG 59.418 55.000 0.00 0.00 39.32 1.31
1597 3335 7.545965 GCGTGCAATATAGTATAGTTCTCCAAT 59.454 37.037 0.00 0.00 0.00 3.16
1632 3370 7.281774 CCATGCTAATCTCATTGTAAGTTCAGT 59.718 37.037 0.00 0.00 0.00 3.41
1633 3371 7.601073 TGCTAATCTCATTGTAAGTTCAGTG 57.399 36.000 0.00 0.00 0.00 3.66
1636 3374 6.882610 AATCTCATTGTAAGTTCAGTGCAA 57.117 33.333 0.00 0.00 0.00 4.08
1742 3484 6.007677 GTCGCTGATTTAGTACAAAGTTTCG 58.992 40.000 0.00 0.00 0.00 3.46
1743 3485 5.119588 TCGCTGATTTAGTACAAAGTTTCGG 59.880 40.000 0.00 0.00 0.00 4.30
1744 3486 5.628134 GCTGATTTAGTACAAAGTTTCGGG 58.372 41.667 0.00 0.00 0.00 5.14
1746 3488 5.867330 TGATTTAGTACAAAGTTTCGGGGA 58.133 37.500 0.00 0.00 0.00 4.81
1757 3499 5.340439 AAGTTTCGGGGAGAGTATTACAG 57.660 43.478 0.00 0.00 0.00 2.74
1798 3540 0.955178 TGCAGCCGCTAGATAGAGAC 59.045 55.000 0.00 0.00 39.64 3.36
1799 3541 1.243902 GCAGCCGCTAGATAGAGACT 58.756 55.000 0.00 0.00 34.30 3.24
1800 3542 2.224548 TGCAGCCGCTAGATAGAGACTA 60.225 50.000 0.00 0.00 39.64 2.59
1801 3543 2.418628 GCAGCCGCTAGATAGAGACTAG 59.581 54.545 0.00 0.00 39.92 2.57
1823 3565 4.553756 CAGAATGCCTGAATGTCTGATG 57.446 45.455 0.00 0.00 45.78 3.07
1824 3566 3.945921 CAGAATGCCTGAATGTCTGATGT 59.054 43.478 0.00 0.00 45.78 3.06
1825 3567 4.035324 CAGAATGCCTGAATGTCTGATGTC 59.965 45.833 0.00 0.00 45.78 3.06
1826 3568 2.408271 TGCCTGAATGTCTGATGTCC 57.592 50.000 0.00 0.00 0.00 4.02
1827 3569 1.629861 TGCCTGAATGTCTGATGTCCA 59.370 47.619 0.00 0.00 0.00 4.02
1828 3570 2.240414 TGCCTGAATGTCTGATGTCCAT 59.760 45.455 0.00 0.00 0.00 3.41
1829 3571 3.455543 TGCCTGAATGTCTGATGTCCATA 59.544 43.478 0.00 0.00 0.00 2.74
1830 3572 4.103627 TGCCTGAATGTCTGATGTCCATAT 59.896 41.667 0.00 0.00 0.00 1.78
1831 3573 5.307716 TGCCTGAATGTCTGATGTCCATATA 59.692 40.000 0.00 0.00 0.00 0.86
1832 3574 6.183361 TGCCTGAATGTCTGATGTCCATATAA 60.183 38.462 0.00 0.00 0.00 0.98
1833 3575 6.712095 GCCTGAATGTCTGATGTCCATATAAA 59.288 38.462 0.00 0.00 0.00 1.40
1834 3576 7.094890 GCCTGAATGTCTGATGTCCATATAAAG 60.095 40.741 0.00 0.00 0.00 1.85
1835 3577 8.152898 CCTGAATGTCTGATGTCCATATAAAGA 58.847 37.037 0.00 0.00 0.00 2.52
1836 3578 8.893219 TGAATGTCTGATGTCCATATAAAGAC 57.107 34.615 0.00 0.00 34.52 3.01
1837 3579 8.708378 TGAATGTCTGATGTCCATATAAAGACT 58.292 33.333 6.96 0.00 34.91 3.24
1840 3582 7.661968 TGTCTGATGTCCATATAAAGACTAGC 58.338 38.462 6.96 0.00 34.91 3.42
1841 3583 7.287696 TGTCTGATGTCCATATAAAGACTAGCA 59.712 37.037 6.96 3.09 34.91 3.49
1842 3584 7.812191 GTCTGATGTCCATATAAAGACTAGCAG 59.188 40.741 6.96 9.98 33.15 4.24
1843 3585 7.725844 TCTGATGTCCATATAAAGACTAGCAGA 59.274 37.037 14.52 14.52 35.85 4.26
1844 3586 8.250143 TGATGTCCATATAAAGACTAGCAGAA 57.750 34.615 6.96 0.00 34.02 3.02
1845 3587 8.874156 TGATGTCCATATAAAGACTAGCAGAAT 58.126 33.333 6.96 0.00 34.02 2.40
1846 3588 9.149225 GATGTCCATATAAAGACTAGCAGAATG 57.851 37.037 6.96 0.00 34.64 2.67
1905 3650 0.949397 CCATCCCACGATGCATCTTG 59.051 55.000 22.75 22.75 44.00 3.02
1942 3691 2.361230 CCCCTTCCCGCTTGGTTC 60.361 66.667 0.00 0.00 34.77 3.62
1953 3702 0.250597 GCTTGGTTCCCCGTTGTAGT 60.251 55.000 0.00 0.00 0.00 2.73
1973 3722 2.338809 TGGGACATTTCTCACTGGAGT 58.661 47.619 0.00 0.00 42.05 3.85
1997 3746 7.123547 AGTCAGTTCCTTTAAAACCAAATGACA 59.876 33.333 22.70 0.00 33.74 3.58
2003 3752 6.553100 TCCTTTAAAACCAAATGACATCCACT 59.447 34.615 0.00 0.00 0.00 4.00
2014 3763 4.271696 TGACATCCACTTCATCTTCGTT 57.728 40.909 0.00 0.00 0.00 3.85
2100 3850 7.990917 ACACATACTATTGACACAAAACAACA 58.009 30.769 0.00 0.00 0.00 3.33
2209 3960 6.499106 TTCCTAGTCATCAATATGCTCCAA 57.501 37.500 0.00 0.00 32.76 3.53
2215 3966 4.274459 GTCATCAATATGCTCCAACTCCAC 59.726 45.833 0.00 0.00 32.76 4.02
2257 4009 6.657541 TGCTAAAGGGATAATTGTCGTTCTTT 59.342 34.615 15.37 15.37 0.00 2.52
2357 4109 3.170791 TCAACGCCTCATCATCTTCTC 57.829 47.619 0.00 0.00 0.00 2.87
2369 4121 7.233144 CCTCATCATCTTCTCTCTCATTCCTTA 59.767 40.741 0.00 0.00 0.00 2.69
2370 4122 7.950512 TCATCATCTTCTCTCTCATTCCTTAC 58.049 38.462 0.00 0.00 0.00 2.34
2371 4123 7.784073 TCATCATCTTCTCTCTCATTCCTTACT 59.216 37.037 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.901868 ACTATTTGGCAGAAACGTAGGAA 58.098 39.130 0.00 0.00 0.00 3.36
16 17 3.034721 TCGACTATTTGGCAGAAACGT 57.965 42.857 0.00 0.00 0.00 3.99
17 18 4.084013 AGTTTCGACTATTTGGCAGAAACG 60.084 41.667 15.89 7.31 44.23 3.60
21 22 3.188460 GCAAGTTTCGACTATTTGGCAGA 59.812 43.478 0.00 0.00 0.00 4.26
24 25 3.552604 TGCAAGTTTCGACTATTTGGC 57.447 42.857 0.00 0.00 0.00 4.52
25 26 6.420604 ACAATTTGCAAGTTTCGACTATTTGG 59.579 34.615 4.19 0.00 0.00 3.28
31 32 3.490761 CCCACAATTTGCAAGTTTCGACT 60.491 43.478 4.19 0.00 0.00 4.18
42 43 2.000429 CTGCTAAGCCCACAATTTGC 58.000 50.000 0.00 0.00 0.00 3.68
72 73 1.781786 TCTGGAGCTTCCTTATCGCT 58.218 50.000 0.00 0.00 37.46 4.93
87 88 7.596494 TGAAATCAAAACAAGCTCTATTCTGG 58.404 34.615 0.00 0.00 0.00 3.86
118 119 4.019174 ACAAATTCAGCCGGAGATCAAAT 58.981 39.130 5.05 0.00 0.00 2.32
121 122 2.290260 ACACAAATTCAGCCGGAGATCA 60.290 45.455 5.05 0.00 0.00 2.92
123 124 2.086869 CACACAAATTCAGCCGGAGAT 58.913 47.619 5.05 0.00 0.00 2.75
126 127 1.686355 AACACACAAATTCAGCCGGA 58.314 45.000 5.05 0.00 0.00 5.14
127 128 3.500982 CATAACACACAAATTCAGCCGG 58.499 45.455 0.00 0.00 0.00 6.13
151 152 3.057596 GCCTAGTAATGCACAAACAAGCA 60.058 43.478 0.00 0.00 45.92 3.91
283 284 5.156355 CGTGTTCCCATTTTCATCTTCTTG 58.844 41.667 0.00 0.00 0.00 3.02
301 308 2.567615 AGTCTTCTTCCATAGCCGTGTT 59.432 45.455 0.00 0.00 0.00 3.32
360 367 4.666512 AGGCAATATATCCACAATCCACC 58.333 43.478 0.00 0.00 0.00 4.61
376 383 2.362077 GTCCAAACACAGACAAGGCAAT 59.638 45.455 0.00 0.00 33.08 3.56
380 387 3.243501 CCAATGTCCAAACACAGACAAGG 60.244 47.826 0.00 0.00 45.54 3.61
381 388 3.631686 TCCAATGTCCAAACACAGACAAG 59.368 43.478 0.00 0.00 45.54 3.16
398 405 3.678072 CGACGTCAAATGTGTAGTCCAAT 59.322 43.478 17.16 0.00 32.51 3.16
420 427 7.727331 TTTGATTTGTCATGGTCAAAAATCC 57.273 32.000 16.37 9.64 37.56 3.01
476 484 4.143094 GCTCGTCAACTAACCTTGTCATTC 60.143 45.833 0.00 0.00 0.00 2.67
477 485 3.746492 GCTCGTCAACTAACCTTGTCATT 59.254 43.478 0.00 0.00 0.00 2.57
495 503 1.148157 AGACGGATTTCGCATGCTCG 61.148 55.000 17.13 11.60 43.89 5.03
540 2172 2.307934 ATTTTGTTTGCAAGCACGGT 57.692 40.000 16.13 1.74 35.82 4.83
541 2173 3.352652 CAAATTTTGTTTGCAAGCACGG 58.647 40.909 16.13 0.00 35.82 4.94
603 2237 9.584008 AATATCAGATTTCTAGGCATGTTGAAT 57.416 29.630 0.00 0.00 0.00 2.57
608 2242 7.083062 TCCAATATCAGATTTCTAGGCATGT 57.917 36.000 0.00 0.00 0.00 3.21
621 2255 8.673711 CGGAAACACTAAAAATCCAATATCAGA 58.326 33.333 0.00 0.00 0.00 3.27
622 2256 8.673711 TCGGAAACACTAAAAATCCAATATCAG 58.326 33.333 0.00 0.00 0.00 2.90
623 2257 8.568676 TCGGAAACACTAAAAATCCAATATCA 57.431 30.769 0.00 0.00 0.00 2.15
633 2267 9.504708 TCCTGTAATAATCGGAAACACTAAAAA 57.495 29.630 0.00 0.00 0.00 1.94
648 2310 4.165372 ACCCATTCCACGTCCTGTAATAAT 59.835 41.667 0.00 0.00 0.00 1.28
649 2311 3.520317 ACCCATTCCACGTCCTGTAATAA 59.480 43.478 0.00 0.00 0.00 1.40
651 2313 1.913419 ACCCATTCCACGTCCTGTAAT 59.087 47.619 0.00 0.00 0.00 1.89
655 2317 2.040544 GCACCCATTCCACGTCCTG 61.041 63.158 0.00 0.00 0.00 3.86
675 2337 6.299604 CGCGTGAATATATCTTGGAAATCAC 58.700 40.000 0.00 0.00 34.19 3.06
677 2339 5.637810 TCCGCGTGAATATATCTTGGAAATC 59.362 40.000 4.92 0.00 0.00 2.17
711 2373 7.248437 CCGTCCCTGTTTAGTTTTTCATATTC 58.752 38.462 0.00 0.00 0.00 1.75
805 2470 3.359523 GGTTTGAACCGGGCGGAC 61.360 66.667 6.32 0.00 39.66 4.79
814 2479 2.322830 GGGCGGACGAGGTTTGAAC 61.323 63.158 0.00 0.00 0.00 3.18
854 2519 0.037326 ATATATGCGTGCCACGGGAG 60.037 55.000 20.07 0.00 42.82 4.30
924 2589 3.470567 CAAGTCTGCGTCGTCGGC 61.471 66.667 3.90 0.00 37.56 5.54
957 2622 1.012841 GTACGTCGAGGTTCTCCGAT 58.987 55.000 16.86 0.00 37.14 4.18
958 2623 1.354337 CGTACGTCGAGGTTCTCCGA 61.354 60.000 16.86 0.00 42.86 4.55
973 2650 2.010286 TGCACACGCACGTACGTAC 61.010 57.895 22.34 15.19 46.34 3.67
974 2651 2.330745 TGCACACGCACGTACGTA 59.669 55.556 22.34 0.00 46.34 3.57
1040 2729 4.405671 GCAGGAGGAGCAGCAGCA 62.406 66.667 3.17 0.00 45.49 4.41
1113 2805 4.176752 GCCACCGGGGTCAGGATC 62.177 72.222 6.32 0.00 39.65 3.36
1386 3078 1.068588 CGCCGGAATAGTTGATCTCCA 59.931 52.381 5.05 0.00 0.00 3.86
1473 3180 5.533154 ACATATACACGGAGAGAGAGAAAGG 59.467 44.000 0.00 0.00 0.00 3.11
1476 3205 7.681679 AGATACATATACACGGAGAGAGAGAA 58.318 38.462 0.00 0.00 0.00 2.87
1490 3219 6.740002 CAGCGTACGTGGTTAGATACATATAC 59.260 42.308 17.90 0.00 0.00 1.47
1513 3242 1.372582 AATAGTGTCGTGCATGCCAG 58.627 50.000 16.68 9.29 0.00 4.85
1542 3280 8.822855 CACGGTCATTAATTTACTTGTATGCTA 58.177 33.333 0.00 0.00 0.00 3.49
1550 3288 4.142773 CGCACCACGGTCATTAATTTACTT 60.143 41.667 0.00 0.00 38.44 2.24
1581 3319 9.847224 GGGAAAATTCATTGGAGAACTATACTA 57.153 33.333 0.00 0.00 0.00 1.82
1582 3320 8.336235 TGGGAAAATTCATTGGAGAACTATACT 58.664 33.333 0.00 0.00 0.00 2.12
1583 3321 8.519799 TGGGAAAATTCATTGGAGAACTATAC 57.480 34.615 0.00 0.00 0.00 1.47
1597 3335 7.124599 ACAATGAGATTAGCATGGGAAAATTCA 59.875 33.333 0.00 0.00 0.00 2.57
1632 3370 3.817647 AGGCAAACAAAAACAAAGTTGCA 59.182 34.783 8.29 0.00 0.00 4.08
1633 3371 4.418013 AGGCAAACAAAAACAAAGTTGC 57.582 36.364 0.00 0.00 0.00 4.17
1636 3374 4.935205 GGAGAAGGCAAACAAAAACAAAGT 59.065 37.500 0.00 0.00 0.00 2.66
1698 3439 9.450807 CAGCGACGATGATTAATCATATATACA 57.549 33.333 26.97 1.54 46.84 2.29
1718 3460 6.007677 CGAAACTTTGTACTAAATCAGCGAC 58.992 40.000 0.00 0.00 0.00 5.19
1719 3461 5.119588 CCGAAACTTTGTACTAAATCAGCGA 59.880 40.000 0.00 0.00 0.00 4.93
1720 3462 5.313623 CCGAAACTTTGTACTAAATCAGCG 58.686 41.667 0.00 0.00 0.00 5.18
1721 3463 5.391629 CCCCGAAACTTTGTACTAAATCAGC 60.392 44.000 0.00 0.00 0.00 4.26
1742 3484 9.847224 TTTGAAATAATCTGTAATACTCTCCCC 57.153 33.333 0.00 0.00 0.00 4.81
1798 3540 3.560481 CAGACATTCAGGCATTCTGCTAG 59.440 47.826 0.00 0.00 44.28 3.42
1799 3541 3.198417 TCAGACATTCAGGCATTCTGCTA 59.802 43.478 0.00 0.00 44.28 3.49
1800 3542 2.026542 TCAGACATTCAGGCATTCTGCT 60.027 45.455 0.00 0.00 44.28 4.24
1801 3543 2.362736 TCAGACATTCAGGCATTCTGC 58.637 47.619 0.00 0.00 43.06 4.26
1802 3544 3.945921 ACATCAGACATTCAGGCATTCTG 59.054 43.478 0.00 0.00 44.68 3.02
1803 3545 4.197750 GACATCAGACATTCAGGCATTCT 58.802 43.478 0.00 0.00 0.00 2.40
1804 3546 3.314635 GGACATCAGACATTCAGGCATTC 59.685 47.826 0.00 0.00 0.00 2.67
1805 3547 3.285484 GGACATCAGACATTCAGGCATT 58.715 45.455 0.00 0.00 0.00 3.56
1806 3548 2.240414 TGGACATCAGACATTCAGGCAT 59.760 45.455 0.00 0.00 0.00 4.40
1807 3549 1.629861 TGGACATCAGACATTCAGGCA 59.370 47.619 0.00 0.00 0.00 4.75
1808 3550 2.408271 TGGACATCAGACATTCAGGC 57.592 50.000 0.00 0.00 0.00 4.85
1809 3551 8.152898 TCTTTATATGGACATCAGACATTCAGG 58.847 37.037 0.00 0.00 0.00 3.86
1810 3552 8.986847 GTCTTTATATGGACATCAGACATTCAG 58.013 37.037 0.00 0.00 33.19 3.02
1811 3553 8.708378 AGTCTTTATATGGACATCAGACATTCA 58.292 33.333 12.49 0.00 35.18 2.57
1814 3556 8.310382 GCTAGTCTTTATATGGACATCAGACAT 58.690 37.037 12.49 0.00 35.18 3.06
1815 3557 7.287696 TGCTAGTCTTTATATGGACATCAGACA 59.712 37.037 12.49 0.00 35.18 3.41
1816 3558 7.661968 TGCTAGTCTTTATATGGACATCAGAC 58.338 38.462 7.88 0.00 35.18 3.51
1817 3559 7.725844 TCTGCTAGTCTTTATATGGACATCAGA 59.274 37.037 13.47 13.47 34.94 3.27
1818 3560 7.890515 TCTGCTAGTCTTTATATGGACATCAG 58.109 38.462 7.88 9.77 35.18 2.90
1819 3561 7.839680 TCTGCTAGTCTTTATATGGACATCA 57.160 36.000 7.88 3.22 35.18 3.07
1820 3562 9.149225 CATTCTGCTAGTCTTTATATGGACATC 57.851 37.037 7.88 0.00 35.18 3.06
1821 3563 7.605691 GCATTCTGCTAGTCTTTATATGGACAT 59.394 37.037 7.88 0.00 40.96 3.06
1822 3564 6.931281 GCATTCTGCTAGTCTTTATATGGACA 59.069 38.462 7.88 0.00 40.96 4.02
1823 3565 7.357951 GCATTCTGCTAGTCTTTATATGGAC 57.642 40.000 0.00 0.00 40.96 4.02
1838 3580 8.306038 TGTTAAAAATAACATGAGCATTCTGCT 58.694 29.630 0.00 0.35 44.50 4.24
1839 3581 8.464770 TGTTAAAAATAACATGAGCATTCTGC 57.535 30.769 0.00 0.00 38.08 4.26
1843 3585 9.086336 CCGATTGTTAAAAATAACATGAGCATT 57.914 29.630 0.00 0.00 39.39 3.56
1844 3586 7.706179 CCCGATTGTTAAAAATAACATGAGCAT 59.294 33.333 0.00 0.00 39.39 3.79
1845 3587 7.032580 CCCGATTGTTAAAAATAACATGAGCA 58.967 34.615 0.00 0.00 39.39 4.26
1846 3588 7.033185 ACCCGATTGTTAAAAATAACATGAGC 58.967 34.615 0.00 0.00 39.39 4.26
1847 3589 7.700656 GGACCCGATTGTTAAAAATAACATGAG 59.299 37.037 0.00 0.00 39.39 2.90
1848 3590 7.176865 TGGACCCGATTGTTAAAAATAACATGA 59.823 33.333 0.00 0.00 39.39 3.07
1860 3602 2.932855 TGTGTTGGACCCGATTGTTA 57.067 45.000 0.00 0.00 0.00 2.41
1905 3650 1.613925 GAGGTTCCAACAGAAAAGGGC 59.386 52.381 0.00 0.00 35.85 5.19
1942 3691 0.326927 AATGTCCCACTACAACGGGG 59.673 55.000 0.00 0.00 43.29 5.73
1953 3702 2.303022 GACTCCAGTGAGAAATGTCCCA 59.697 50.000 0.00 0.00 41.42 4.37
1973 3722 7.411486 TGTCATTTGGTTTTAAAGGAACTGA 57.589 32.000 0.00 0.00 40.86 3.41
1997 3746 2.744202 GCACAACGAAGATGAAGTGGAT 59.256 45.455 0.00 0.00 33.32 3.41
2003 3752 2.292845 TGCAATGCACAACGAAGATGAA 59.707 40.909 2.72 0.00 33.32 2.57
2014 3763 0.604073 CATCCCTGTTGCAATGCACA 59.396 50.000 7.72 8.81 38.71 4.57
2178 3929 8.598924 GCATATTGATGACTAGGAATATGTTCG 58.401 37.037 0.00 0.00 39.44 3.95
2209 3960 0.838987 AATGGTACGTGGGGTGGAGT 60.839 55.000 0.00 0.00 0.00 3.85
2215 3966 0.738389 GCAATGAATGGTACGTGGGG 59.262 55.000 0.00 0.00 0.00 4.96
2257 4009 1.002087 GCAGGGAAGGACGAGAAAGAA 59.998 52.381 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.