Multiple sequence alignment - TraesCS4A01G219500

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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 TraesCS4A01G219500 chr4A 100.000 4878 0 0 1 4878 521811354 521816231 0.000000e+00 9009.0
1 TraesCS4A01G219500 chr4A 83.022 589 50 23 1020 1606 564728015 564727475 5.670000e-134 488.0
2 TraesCS4A01G219500 chr4D 95.543 3096 91 17 1806 4876 69646715 69649788 0.000000e+00 4909.0
3 TraesCS4A01G219500 chr4D 91.113 1429 74 29 390 1802 69645278 69646669 0.000000e+00 1886.0
4 TraesCS4A01G219500 chr4D 94.524 347 19 0 1 347 69644924 69645270 2.000000e-148 536.0
5 TraesCS4A01G219500 chr4D 84.211 152 19 2 4732 4878 69650802 69650953 5.090000e-30 143.0
6 TraesCS4A01G219500 chr4B 93.037 3131 132 35 1806 4878 103004500 103007602 0.000000e+00 4495.0
7 TraesCS4A01G219500 chr4B 91.033 1829 106 32 1 1809 103002673 103004463 0.000000e+00 2416.0
8 TraesCS4A01G219500 chr4B 83.108 148 20 1 4736 4878 103008422 103008569 3.960000e-26 130.0
9 TraesCS4A01G219500 chr3D 96.114 1750 58 6 2070 3816 567166156 567164414 0.000000e+00 2846.0
10 TraesCS4A01G219500 chr1D 93.672 1691 67 19 2131 3816 26569462 26567807 0.000000e+00 2494.0
11 TraesCS4A01G219500 chr7B 80.309 777 135 13 3103 3866 732087197 732087968 5.480000e-159 571.0
12 TraesCS4A01G219500 chr7B 80.051 777 136 14 3103 3866 731961441 731962211 4.260000e-155 558.0
13 TraesCS4A01G219500 chr7B 74.449 227 42 5 495 716 671710483 671710698 3.130000e-12 84.2
14 TraesCS4A01G219500 chrUn 80.180 777 136 13 3103 3866 88429641 88430412 2.550000e-157 566.0
15 TraesCS4A01G219500 chrUn 80.180 777 136 13 3103 3866 160383506 160384277 2.550000e-157 566.0
16 TraesCS4A01G219500 chrUn 80.157 766 134 13 3103 3855 347939929 347940689 1.530000e-154 556.0
17 TraesCS4A01G219500 chr7A 86.458 192 15 5 1119 1310 692500390 692500570 2.980000e-47 200.0
18 TraesCS4A01G219500 chr2B 78.175 252 38 6 496 740 457346066 457345825 1.420000e-30 145.0
19 TraesCS4A01G219500 chr5A 92.683 82 6 0 4796 4877 698349726 698349645 8.580000e-23 119.0
20 TraesCS4A01G219500 chr6D 90.000 90 8 1 4783 4872 54081284 54081196 1.110000e-21 115.0
21 TraesCS4A01G219500 chr6B 90.000 90 8 1 4783 4872 116824538 116824450 1.110000e-21 115.0
22 TraesCS4A01G219500 chr6B 90.000 90 8 1 4783 4872 117124272 117124360 1.110000e-21 115.0
23 TraesCS4A01G219500 chr5B 90.000 90 8 1 4783 4872 43908598 43908510 1.110000e-21 115.0
24 TraesCS4A01G219500 chr2A 77.619 210 27 11 496 699 744446311 744446506 5.160000e-20 110.0


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 TraesCS4A01G219500 chr4A 521811354 521816231 4877 False 9009.0 9009 100.000000 1 4878 1 chr4A.!!$F1 4877
1 TraesCS4A01G219500 chr4A 564727475 564728015 540 True 488.0 488 83.022000 1020 1606 1 chr4A.!!$R1 586
2 TraesCS4A01G219500 chr4D 69644924 69650953 6029 False 1868.5 4909 91.347750 1 4878 4 chr4D.!!$F1 4877
3 TraesCS4A01G219500 chr4B 103002673 103008569 5896 False 2347.0 4495 89.059333 1 4878 3 chr4B.!!$F1 4877
4 TraesCS4A01G219500 chr3D 567164414 567166156 1742 True 2846.0 2846 96.114000 2070 3816 1 chr3D.!!$R1 1746
5 TraesCS4A01G219500 chr1D 26567807 26569462 1655 True 2494.0 2494 93.672000 2131 3816 1 chr1D.!!$R1 1685
6 TraesCS4A01G219500 chr7B 732087197 732087968 771 False 571.0 571 80.309000 3103 3866 1 chr7B.!!$F3 763
7 TraesCS4A01G219500 chr7B 731961441 731962211 770 False 558.0 558 80.051000 3103 3866 1 chr7B.!!$F2 763
8 TraesCS4A01G219500 chrUn 88429641 88430412 771 False 566.0 566 80.180000 3103 3866 1 chrUn.!!$F1 763
9 TraesCS4A01G219500 chrUn 160383506 160384277 771 False 566.0 566 80.180000 3103 3866 1 chrUn.!!$F2 763
10 TraesCS4A01G219500 chrUn 347939929 347940689 760 False 556.0 556 80.157000 3103 3855 1 chrUn.!!$F3 752

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
673 679 0.100325 TAAATTTGCCATCTGCGCGG 59.900 50.000 10.86 10.86 45.60 6.46 F
1640 1663 2.033141 GACCTCAGCTGGCTGCAA 59.967 61.111 18.84 5.30 45.94 4.08 F
1943 2014 0.251922 ATGTGGAATGCAGGCCTTGT 60.252 50.000 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 1995 0.251922 ACAAGGCCTGCATTCCACAT 60.252 50.0 5.69 0.0 0.00 3.21 R
3375 3468 0.761187 AGCAAAGAGGCAGACTGACA 59.239 50.0 11.83 0.0 35.83 3.58 R
3906 4009 0.307760 CAGCCAGTGTTTGAACGGAC 59.692 55.0 0.00 0.0 0.00 4.79 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
36 39 0.515127 TGGTGCGCATAAACGTCTTG 59.485 50.000 15.91 0.00 34.88 3.02
43 46 3.772932 CGCATAAACGTCTTGTACCCTA 58.227 45.455 0.00 0.00 0.00 3.53
44 47 3.795101 CGCATAAACGTCTTGTACCCTAG 59.205 47.826 0.00 0.00 0.00 3.02
60 63 5.806654 ACCCTAGAAAATGTTGTGCAAAT 57.193 34.783 0.00 0.00 0.00 2.32
87 90 1.902508 CAGGCTTGTCCCTCTTAGTCA 59.097 52.381 0.00 0.00 31.24 3.41
91 94 2.613223 GCTTGTCCCTCTTAGTCACACC 60.613 54.545 0.00 0.00 0.00 4.16
205 208 2.913590 GTCTCTCCGTGTTAGTTTACGC 59.086 50.000 0.00 0.00 38.87 4.42
296 300 9.034800 AGAAAATGCAAGGAAAATTATCCACTA 57.965 29.630 0.00 0.00 42.27 2.74
307 311 2.812836 TATCCACTAGTCCACACGGA 57.187 50.000 0.00 0.00 39.79 4.69
362 366 8.370266 TGTACCTTTACTCCTTTAGCATCTTA 57.630 34.615 0.00 0.00 0.00 2.10
368 372 5.483685 ACTCCTTTAGCATCTTACACACA 57.516 39.130 0.00 0.00 0.00 3.72
385 389 6.329838 ACACACAAATTTTCATGTTTGACG 57.670 33.333 12.08 6.42 38.39 4.35
386 390 5.866633 ACACACAAATTTTCATGTTTGACGT 59.133 32.000 12.08 0.00 38.39 4.34
462 466 9.683651 CAGTGTGTGTATTTTTGTATGTATACG 57.316 33.333 0.00 0.00 36.06 3.06
465 469 6.842282 GTGTGTATTTTTGTATGTATACGGCG 59.158 38.462 4.80 4.80 36.06 6.46
466 470 6.534436 TGTGTATTTTTGTATGTATACGGCGT 59.466 34.615 19.64 19.64 36.06 5.68
473 477 3.636300 TGTATGTATACGGCGTAGGGTTT 59.364 43.478 25.01 10.49 36.06 3.27
509 513 3.755378 GGCAGATTGAATATCCAGCGAAT 59.245 43.478 0.00 0.00 0.00 3.34
520 524 6.949352 ATATCCAGCGAATGTCAGATTTTT 57.051 33.333 0.00 0.00 0.00 1.94
576 580 2.408271 TGTTAGCTGAGGATGGCAAG 57.592 50.000 0.00 0.00 0.00 4.01
600 606 6.604795 AGTTTAGTTGATGCATAGCAAATCCT 59.395 34.615 0.00 0.00 43.62 3.24
611 617 5.066893 GCATAGCAAATCCTCATCAGTTCAA 59.933 40.000 0.00 0.00 0.00 2.69
648 654 3.342719 TGCCAGAAAATTATCGTGCTCA 58.657 40.909 0.00 0.00 0.00 4.26
673 679 0.100325 TAAATTTGCCATCTGCGCGG 59.900 50.000 10.86 10.86 45.60 6.46
685 691 3.980646 TCTGCGCGGCAATATAAATTT 57.019 38.095 12.58 0.00 38.41 1.82
687 693 2.979813 CTGCGCGGCAATATAAATTTCC 59.020 45.455 8.83 0.00 38.41 3.13
1204 1215 3.944015 CTGATCAGATTGGGTTGGTTCTC 59.056 47.826 18.34 0.00 0.00 2.87
1387 1405 4.279420 GCACAAAGTCCAAGAATCCTCTTT 59.721 41.667 0.00 0.00 40.05 2.52
1408 1426 3.819368 TGACTTTTGCTCCATGAACTGA 58.181 40.909 0.00 0.00 0.00 3.41
1414 1432 5.596836 TTTGCTCCATGAACTGACTTTTT 57.403 34.783 0.00 0.00 0.00 1.94
1474 1497 3.395941 AGGGATCCACTGAACTGTTTTCT 59.604 43.478 15.23 0.00 0.00 2.52
1501 1524 7.707624 TTGCATCCTCTGTTTATTTTCTCAT 57.292 32.000 0.00 0.00 0.00 2.90
1502 1525 7.325660 TGCATCCTCTGTTTATTTTCTCATC 57.674 36.000 0.00 0.00 0.00 2.92
1503 1526 6.885918 TGCATCCTCTGTTTATTTTCTCATCA 59.114 34.615 0.00 0.00 0.00 3.07
1528 1551 7.221452 CAGTTCTTTCAGGATTTGTTTGTTCAG 59.779 37.037 0.00 0.00 0.00 3.02
1640 1663 2.033141 GACCTCAGCTGGCTGCAA 59.967 61.111 18.84 5.30 45.94 4.08
1700 1723 9.181805 CACTACACCTCAATGTTATATCTTACG 57.818 37.037 0.00 0.00 33.85 3.18
1701 1724 8.910944 ACTACACCTCAATGTTATATCTTACGT 58.089 33.333 0.00 0.00 33.85 3.57
1704 1727 8.139989 ACACCTCAATGTTATATCTTACGTACC 58.860 37.037 0.00 0.00 0.00 3.34
1705 1728 8.358148 CACCTCAATGTTATATCTTACGTACCT 58.642 37.037 0.00 0.00 0.00 3.08
1771 1794 4.655963 TCATAGCTTTTCTTTCTGCCACT 58.344 39.130 0.00 0.00 0.00 4.00
1781 1804 8.691661 TTTTCTTTCTGCCACTAGATTTAGTT 57.308 30.769 0.00 0.00 38.05 2.24
1924 1995 6.069673 TGGCTTAATTCTAGTCCCAGATTTGA 60.070 38.462 0.00 0.00 0.00 2.69
1943 2014 0.251922 ATGTGGAATGCAGGCCTTGT 60.252 50.000 0.00 0.00 0.00 3.16
2257 2328 5.659463 TGCCAATTTATGTTACATTGCCTC 58.341 37.500 2.23 0.00 0.00 4.70
2259 2330 5.678616 GCCAATTTATGTTACATTGCCTCGT 60.679 40.000 2.23 0.00 0.00 4.18
2262 2333 8.134895 CCAATTTATGTTACATTGCCTCGTTAT 58.865 33.333 2.23 0.00 0.00 1.89
2291 2362 7.486870 GTGTTTTAGTTCCGTTCTTGATGTTTT 59.513 33.333 0.00 0.00 0.00 2.43
2542 2618 0.756294 CCCATGGCTCGTACCACATA 59.244 55.000 6.09 0.00 44.17 2.29
2559 2635 5.775686 CCACATATGGGTAAGAATGCATTG 58.224 41.667 18.59 0.40 43.04 2.82
2683 2765 3.716353 AGTGACATGGCATGGACCTAATA 59.284 43.478 29.49 6.20 33.60 0.98
2698 2780 5.047306 GGACCTAATAAAATGGCCCTATTGC 60.047 44.000 0.00 0.00 0.00 3.56
2763 2845 7.177392 AGCTATCCTTATCTTTTTGTGCTTTGT 59.823 33.333 0.00 0.00 0.00 2.83
2781 2863 5.801380 CTTTGTAGCTACAGGAGGGTAAAA 58.199 41.667 24.79 12.92 37.52 1.52
2822 2906 4.176271 TGACAACTCAGTGATAATGCTCG 58.824 43.478 0.00 0.00 0.00 5.03
2867 2951 8.517878 CCTGTTGAATGTTTTCAGTCTATCATT 58.482 33.333 0.00 0.00 44.07 2.57
2868 2952 9.338291 CTGTTGAATGTTTTCAGTCTATCATTG 57.662 33.333 0.00 0.00 44.07 2.82
2947 3031 7.914871 GGGTAAAAACTTTAGCGTCTTAAAACA 59.085 33.333 3.13 0.00 0.00 2.83
2953 3037 9.659830 AAACTTTAGCGTCTTAAAACATGTTAG 57.340 29.630 12.39 6.00 0.00 2.34
3009 3102 2.744202 CACCTGAACTGAATGCCTGTAC 59.256 50.000 0.00 0.00 0.00 2.90
3010 3103 2.290323 ACCTGAACTGAATGCCTGTACC 60.290 50.000 0.00 0.00 0.00 3.34
3011 3104 2.026822 CCTGAACTGAATGCCTGTACCT 60.027 50.000 0.00 0.00 0.00 3.08
3012 3105 3.560025 CCTGAACTGAATGCCTGTACCTT 60.560 47.826 0.00 0.00 0.00 3.50
3013 3106 4.323485 CCTGAACTGAATGCCTGTACCTTA 60.323 45.833 0.00 0.00 0.00 2.69
3054 3147 6.033091 CCGTGTCAACAGAAAGTTTTGTAAAC 59.967 38.462 0.00 0.00 38.74 2.01
3222 3315 3.863142 AGTACCTACACCTACTTTGCG 57.137 47.619 0.00 0.00 0.00 4.85
3228 3321 1.602323 CACCTACTTTGCGGCCCAA 60.602 57.895 0.00 0.00 0.00 4.12
3375 3468 6.648725 GCAAGTCACTTAAAGAAGTCTCAGAT 59.351 38.462 0.00 0.00 44.39 2.90
3429 3522 7.388776 CAGAAGGTATTCAAATCTGTGTCAGAA 59.611 37.037 3.58 0.00 39.77 3.02
3631 3729 4.796110 ATATGGGAATGTGTGCTTAGGT 57.204 40.909 0.00 0.00 0.00 3.08
3968 4071 6.092748 GTGCCATCCAAATAAAAGTACTGTG 58.907 40.000 0.00 0.00 0.00 3.66
4089 4196 7.199167 TCTCCTCCTGTTCATAATGAAATGA 57.801 36.000 0.00 0.00 38.22 2.57
4194 4302 4.274421 CAGAACTGAATGCTGCACATAG 57.726 45.455 3.57 5.90 38.34 2.23
4197 4305 2.362736 ACTGAATGCTGCACATAGTGG 58.637 47.619 3.57 0.00 38.34 4.00
4231 4342 3.667497 ATCATACCTGCACATACCGAG 57.333 47.619 0.00 0.00 0.00 4.63
4236 4347 2.594131 ACCTGCACATACCGAGCTATA 58.406 47.619 0.00 0.00 31.61 1.31
4287 4410 0.534877 AGGAATTGCACGTGCTGACA 60.535 50.000 37.59 20.95 42.66 3.58
4757 4887 9.807921 AGAAAAGGGAGAATGTTTCTAAATACA 57.192 29.630 0.00 0.00 40.87 2.29
4812 4948 3.871594 GCAACTATCTAACTGAATGCCGT 59.128 43.478 0.00 0.00 0.00 5.68
4821 4958 2.413837 ACTGAATGCCGTTACTGTCAC 58.586 47.619 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 29 7.444299 ACATTTTCTAGGGTACAAGACGTTTA 58.556 34.615 0.00 0.00 0.00 2.01
28 31 5.861727 ACATTTTCTAGGGTACAAGACGTT 58.138 37.500 0.00 0.00 0.00 3.99
36 39 5.699097 TTGCACAACATTTTCTAGGGTAC 57.301 39.130 0.00 0.00 0.00 3.34
43 46 8.715191 TGTCTAAAATTTGCACAACATTTTCT 57.285 26.923 14.09 2.67 33.28 2.52
44 47 8.063630 CCTGTCTAAAATTTGCACAACATTTTC 58.936 33.333 14.09 6.69 33.28 2.29
78 81 1.347707 TGGCCTTGGTGTGACTAAGAG 59.652 52.381 3.32 0.00 38.76 2.85
87 90 4.898861 TCTCTTTTTAAATGGCCTTGGTGT 59.101 37.500 3.32 0.00 0.00 4.16
91 94 6.748132 TCACTTCTCTTTTTAAATGGCCTTG 58.252 36.000 3.32 0.00 0.00 3.61
147 150 2.417933 CAGACCATCACTTGCTTGTAGC 59.582 50.000 0.00 0.00 42.82 3.58
205 208 4.768659 GACTTGAGTTGCTATCATGTCG 57.231 45.455 12.84 0.00 40.10 4.35
296 300 3.818773 CTGGTTTTAATTCCGTGTGGACT 59.181 43.478 0.00 0.00 46.45 3.85
347 351 6.801539 TTTGTGTGTAAGATGCTAAAGGAG 57.198 37.500 0.00 0.00 0.00 3.69
348 352 7.759489 AATTTGTGTGTAAGATGCTAAAGGA 57.241 32.000 0.00 0.00 0.00 3.36
349 353 8.816640 AAAATTTGTGTGTAAGATGCTAAAGG 57.183 30.769 0.00 0.00 0.00 3.11
350 354 9.462174 TGAAAATTTGTGTGTAAGATGCTAAAG 57.538 29.630 0.00 0.00 0.00 1.85
351 355 9.979578 ATGAAAATTTGTGTGTAAGATGCTAAA 57.020 25.926 0.00 0.00 0.00 1.85
352 356 9.409312 CATGAAAATTTGTGTGTAAGATGCTAA 57.591 29.630 0.00 0.00 0.00 3.09
353 357 8.575589 ACATGAAAATTTGTGTGTAAGATGCTA 58.424 29.630 0.00 0.00 0.00 3.49
354 358 7.436118 ACATGAAAATTTGTGTGTAAGATGCT 58.564 30.769 0.00 0.00 0.00 3.79
362 366 5.866633 ACGTCAAACATGAAAATTTGTGTGT 59.133 32.000 0.00 0.00 37.16 3.72
438 442 7.637132 GCCGTATACATACAAAAATACACACAC 59.363 37.037 3.32 0.00 32.87 3.82
451 455 2.862541 ACCCTACGCCGTATACATACA 58.137 47.619 0.00 0.00 32.87 2.29
456 460 1.211743 GCAAACCCTACGCCGTATAC 58.788 55.000 0.00 0.00 0.00 1.47
462 466 0.679960 ATTCAGGCAAACCCTACGCC 60.680 55.000 0.00 0.00 44.09 5.68
465 469 4.864704 TGAAAATTCAGGCAAACCCTAC 57.135 40.909 0.00 0.00 44.09 3.18
491 495 5.698089 TCTGACATTCGCTGGATATTCAATC 59.302 40.000 0.00 0.00 0.00 2.67
549 553 7.233632 TGCCATCCTCAGCTAACATAATTTAT 58.766 34.615 0.00 0.00 0.00 1.40
576 580 6.799512 AGGATTTGCTATGCATCAACTAAAC 58.200 36.000 0.19 0.00 38.76 2.01
623 629 5.537188 AGCACGATAATTTTCTGGCAAAAA 58.463 33.333 9.06 9.06 32.99 1.94
629 635 5.739752 TGATGAGCACGATAATTTTCTGG 57.260 39.130 0.00 0.00 0.00 3.86
639 645 5.335127 GCAAATTTAGTTGATGAGCACGAT 58.665 37.500 0.00 0.00 0.00 3.73
640 646 4.379394 GGCAAATTTAGTTGATGAGCACGA 60.379 41.667 0.00 0.00 0.00 4.35
648 654 4.675510 CGCAGATGGCAAATTTAGTTGAT 58.324 39.130 0.00 0.00 45.17 2.57
673 679 8.474006 ACGTTTTTCCTGGAAATTTATATTGC 57.526 30.769 21.70 5.01 31.34 3.56
685 691 3.223435 TGGCAAATACGTTTTTCCTGGA 58.777 40.909 15.33 0.00 0.00 3.86
687 693 3.367630 GCATGGCAAATACGTTTTTCCTG 59.632 43.478 15.33 12.78 0.00 3.86
910 921 1.444383 TGAACAGCTGTCGCGCTAG 60.444 57.895 21.95 2.69 42.32 3.42
974 985 2.677848 GGGAGGGAAGAAGGTGGC 59.322 66.667 0.00 0.00 0.00 5.01
977 988 1.083141 GGAGGGGAGGGAAGAAGGT 59.917 63.158 0.00 0.00 0.00 3.50
978 989 1.694525 GGGAGGGGAGGGAAGAAGG 60.695 68.421 0.00 0.00 0.00 3.46
980 991 2.040606 CGGGAGGGGAGGGAAGAA 59.959 66.667 0.00 0.00 0.00 2.52
1204 1215 0.687354 CAGAACCCGGGGATATCCTG 59.313 60.000 27.92 17.02 41.69 3.86
1332 1350 0.303493 CGGGATTAACATCAACGCCG 59.697 55.000 0.00 0.00 0.00 6.46
1387 1405 3.565482 GTCAGTTCATGGAGCAAAAGTCA 59.435 43.478 0.00 0.00 0.00 3.41
1474 1497 7.014134 TGAGAAAATAAACAGAGGATGCAAACA 59.986 33.333 0.00 0.00 0.00 2.83
1501 1524 6.773976 ACAAACAAATCCTGAAAGAACTGA 57.226 33.333 0.00 0.00 34.07 3.41
1502 1525 7.035004 TGAACAAACAAATCCTGAAAGAACTG 58.965 34.615 0.00 0.00 34.07 3.16
1503 1526 7.122650 TCTGAACAAACAAATCCTGAAAGAACT 59.877 33.333 0.00 0.00 34.07 3.01
1528 1551 3.182372 GCAGAAACGGCACAGAAAATTTC 59.818 43.478 0.00 0.00 0.00 2.17
1574 1597 2.614331 TTGGCCGGGTCCCCAATA 60.614 61.111 2.18 0.00 36.25 1.90
1680 1703 8.474710 AGGTACGTAAGATATAACATTGAGGT 57.525 34.615 0.00 0.00 43.62 3.85
1700 1723 4.669197 CGTGCAACTCAAGCAATTAGGTAC 60.669 45.833 0.00 0.00 44.64 3.34
1701 1724 3.435327 CGTGCAACTCAAGCAATTAGGTA 59.565 43.478 0.00 0.00 44.64 3.08
1702 1725 2.226437 CGTGCAACTCAAGCAATTAGGT 59.774 45.455 0.00 0.00 44.64 3.08
1703 1726 2.414559 CCGTGCAACTCAAGCAATTAGG 60.415 50.000 0.00 0.00 44.64 2.69
1704 1727 2.483877 TCCGTGCAACTCAAGCAATTAG 59.516 45.455 0.00 0.00 44.64 1.73
1705 1728 2.483877 CTCCGTGCAACTCAAGCAATTA 59.516 45.455 0.00 0.00 44.64 1.40
1771 1794 9.877178 GAGAGACCAATTCTTGAACTAAATCTA 57.123 33.333 0.00 0.00 33.22 1.98
1781 1804 5.070981 ACACAGAAGAGAGACCAATTCTTGA 59.929 40.000 0.00 0.00 33.22 3.02
1924 1995 0.251922 ACAAGGCCTGCATTCCACAT 60.252 50.000 5.69 0.00 0.00 3.21
2257 2328 5.347012 ACGGAACTAAAACACCAATAACG 57.653 39.130 0.00 0.00 0.00 3.18
2259 2330 7.282675 TCAAGAACGGAACTAAAACACCAATAA 59.717 33.333 0.00 0.00 0.00 1.40
2262 2333 4.942483 TCAAGAACGGAACTAAAACACCAA 59.058 37.500 0.00 0.00 0.00 3.67
2291 2362 4.456911 CCACAGCTGAAAAGAGAAGCAATA 59.543 41.667 23.35 0.00 39.47 1.90
2542 2618 7.178274 TGTTAAGAACAATGCATTCTTACCCAT 59.822 33.333 16.81 0.00 44.46 4.00
2632 2714 8.814931 TGATCAAGAAATCAACCAAATACCAAT 58.185 29.630 0.00 0.00 32.80 3.16
2638 2720 6.268387 ACTGGTGATCAAGAAATCAACCAAAT 59.732 34.615 0.00 0.00 41.74 2.32
2683 2765 3.582208 TGTTTCAGCAATAGGGCCATTTT 59.418 39.130 6.18 0.00 0.00 1.82
2698 2780 7.499438 TTTTTACGTTGTCATGTTGTTTCAG 57.501 32.000 0.00 0.00 0.00 3.02
2734 2816 6.319911 AGCACAAAAAGATAAGGATAGCTTCC 59.680 38.462 0.00 0.00 45.85 3.46
2781 2863 8.199449 AGTTGTCATGTGAAGTTGATGATTTTT 58.801 29.630 0.00 0.00 0.00 1.94
2947 3031 6.603940 AAAAGAGAGAGTCTGAGCTAACAT 57.396 37.500 0.00 0.00 34.84 2.71
3010 3103 7.387673 TGACACGGAATGCAAATCCTATATAAG 59.612 37.037 17.08 5.20 34.66 1.73
3011 3104 7.220740 TGACACGGAATGCAAATCCTATATAA 58.779 34.615 17.08 0.16 34.66 0.98
3012 3105 6.764379 TGACACGGAATGCAAATCCTATATA 58.236 36.000 17.08 2.11 34.66 0.86
3013 3106 5.620206 TGACACGGAATGCAAATCCTATAT 58.380 37.500 17.08 3.41 34.66 0.86
3024 3117 2.290641 ACTTTCTGTTGACACGGAATGC 59.709 45.455 8.85 0.00 45.89 3.56
3222 3315 0.902516 TTGCTTGGTATGGTTGGGCC 60.903 55.000 0.00 0.00 37.90 5.80
3228 3321 3.569701 CAGAAACAGTTGCTTGGTATGGT 59.430 43.478 0.00 0.00 0.00 3.55
3375 3468 0.761187 AGCAAAGAGGCAGACTGACA 59.239 50.000 11.83 0.00 35.83 3.58
3429 3522 5.235186 CAGTGACTTGAAATCGTTCTTGACT 59.765 40.000 0.00 0.00 34.60 3.41
3631 3729 1.070134 GCAGCCGTACCATCAAGGATA 59.930 52.381 0.00 0.00 41.22 2.59
3883 3986 7.286316 GGACAGGTTAATGATTTGGATCTGATT 59.714 37.037 0.00 0.00 33.28 2.57
3892 3995 5.621197 TGAACGGACAGGTTAATGATTTG 57.379 39.130 0.00 0.00 0.00 2.32
3906 4009 0.307760 CAGCCAGTGTTTGAACGGAC 59.692 55.000 0.00 0.00 0.00 4.79
3968 4071 6.594159 AGGCTCATGTTAATACACTACAACAC 59.406 38.462 0.00 0.00 37.03 3.32
4194 4302 8.548721 CAGGTATGATTTATTTAAGTCGTCCAC 58.451 37.037 0.00 0.00 0.00 4.02
4197 4305 8.062448 GTGCAGGTATGATTTATTTAAGTCGTC 58.938 37.037 0.00 0.00 0.00 4.20
4231 4342 4.686191 ATGCAGGATAGCTCCATATAGC 57.314 45.455 0.00 0.00 44.79 2.97
4236 4347 4.103785 ACAGTTAATGCAGGATAGCTCCAT 59.896 41.667 0.00 0.00 44.79 3.41
4287 4410 9.811995 TTGCGTTCAATGTTAGAAGTAGTATAT 57.188 29.630 0.00 0.00 0.00 0.86
4444 4568 2.807967 GCATGCGCCATCAGATAGTTTA 59.192 45.455 4.18 0.00 0.00 2.01
4447 4571 0.395686 AGCATGCGCCATCAGATAGT 59.604 50.000 13.01 0.00 39.83 2.12
4683 4810 8.660373 GGCTCACATTATAAAGATATACAGTGC 58.340 37.037 0.00 0.00 33.36 4.40
4707 4834 5.470098 TGTCATTTTCTACTCTCAGTTTGGC 59.530 40.000 0.00 0.00 0.00 4.52
4714 4841 6.936900 CCCTTTTCTGTCATTTTCTACTCTCA 59.063 38.462 0.00 0.00 0.00 3.27
4756 4886 8.593492 TGTATCTCACCTCGAATAATTCATTG 57.407 34.615 0.00 0.00 0.00 2.82
4757 4887 9.265901 CTTGTATCTCACCTCGAATAATTCATT 57.734 33.333 0.00 0.00 0.00 2.57
4812 4948 6.597562 ACAGACTTTATTTGGGTGACAGTAA 58.402 36.000 0.00 0.00 0.00 2.24
4821 4958 8.718734 GTTAAGACAGTACAGACTTTATTTGGG 58.281 37.037 8.13 0.00 31.73 4.12


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

AutoCloner maintained by Alex Coulton.