Multiple sequence alignment - TraesCS2D01G302900

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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 TraesCS2D01G302900 chr2D 100.000 4709 0 0 1 4709 386585407 386580699 0.000000e+00 8696.0
1 TraesCS2D01G302900 chr2D 85.276 163 22 2 1784 1945 388825595 388825756 2.910000e-37 167.0
2 TraesCS2D01G302900 chr2B 96.018 2461 63 11 1794 4253 457682820 457680394 0.000000e+00 3969.0
3 TraesCS2D01G302900 chr2B 93.569 933 35 9 849 1757 457683754 457682823 0.000000e+00 1367.0
4 TraesCS2D01G302900 chr2B 90.098 818 54 15 1 805 457684561 457683758 0.000000e+00 1037.0
5 TraesCS2D01G302900 chr2B 93.697 238 10 4 4254 4488 457680360 457680125 7.500000e-93 351.0
6 TraesCS2D01G302900 chr2B 93.197 147 6 2 4566 4709 457678572 457678427 3.690000e-51 213.0
7 TraesCS2D01G302900 chr2B 87.719 114 12 2 1784 1896 460817445 460817557 1.060000e-26 132.0
8 TraesCS2D01G302900 chr2A 95.874 1551 41 11 2765 4300 522841268 522839726 0.000000e+00 2488.0
9 TraesCS2D01G302900 chr2A 91.730 1717 86 27 1 1687 522844117 522842427 0.000000e+00 2333.0
10 TraesCS2D01G302900 chr2A 96.739 1012 23 5 1756 2767 522842430 522841429 0.000000e+00 1677.0
11 TraesCS2D01G302900 chr2A 78.884 251 34 12 1056 1288 769191319 769191070 8.160000e-33 152.0
12 TraesCS2D01G302900 chr2A 87.719 114 12 2 1784 1896 525610806 525610918 1.060000e-26 132.0
13 TraesCS2D01G302900 chr2A 100.000 33 0 0 4294 4326 522824780 522824748 1.410000e-05 62.1
14 TraesCS2D01G302900 chr7A 80.083 241 37 9 1056 1285 409248044 409248284 8.100000e-38 169.0
15 TraesCS2D01G302900 chrUn 80.380 158 14 3 1734 1874 479229879 479230036 2.320000e-18 104.0
16 TraesCS2D01G302900 chr4D 80.380 158 14 3 1734 1874 371139924 371140081 2.320000e-18 104.0
17 TraesCS2D01G302900 chr4B 80.380 158 14 3 1734 1874 456385519 456385676 2.320000e-18 104.0
18 TraesCS2D01G302900 chr4A 79.878 164 16 3 1734 1880 92736478 92736315 2.320000e-18 104.0
19 TraesCS2D01G302900 chr3B 100.000 28 0 0 1941 1968 636455853 636455826 9.000000e-03 52.8


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 TraesCS2D01G302900 chr2D 386580699 386585407 4708 True 8696.0 8696 100.0000 1 4709 1 chr2D.!!$R1 4708
1 TraesCS2D01G302900 chr2B 457678427 457684561 6134 True 1387.4 3969 93.3158 1 4709 5 chr2B.!!$R1 4708
2 TraesCS2D01G302900 chr2A 522839726 522844117 4391 True 2166.0 2488 94.7810 1 4300 3 chr2A.!!$R3 4299

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
611 616 0.732571 GATTCTTGCCGGAAATCGCA 59.267 50.000 5.05 0.0 37.59 5.10 F
1396 1456 0.460284 CCCTAGTGATGTGGTGCGAC 60.460 60.000 0.00 0.0 0.00 5.19 F
2819 3042 0.458260 TGAGGCTAGTAAATGCGCGA 59.542 50.000 12.10 0.0 0.00 5.87 F
2982 3205 3.372206 ACTCAGATGCAAATTCTACGCAC 59.628 43.478 0.00 0.0 38.73 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1891 1951 0.037046 GGCAGCCCATGTTTCTTTGG 60.037 55.0 0.00 0.0 0.00 3.28 R
3005 3228 0.673333 ATCACGGTTCGCATGAGCAA 60.673 50.0 0.00 0.0 42.27 3.91 R
3680 3903 0.036010 ATGAACCCGTCTTGGCTGAG 60.036 55.0 0.00 0.0 35.87 3.35 R
3825 4048 0.784778 CTGACAGAGAAACGGCGAAC 59.215 55.0 16.62 4.1 0.00 3.95 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
290 293 9.995003 ACCTATTTTGAATTTAGCATTTTGTGA 57.005 25.926 0.00 0.0 0.00 3.58
318 321 4.672587 AAGCTGTCACTTCACTTGACTA 57.327 40.909 4.27 0.0 43.30 2.59
346 349 4.024387 TGTTTCGTGTTACTCCATTTGCTC 60.024 41.667 0.00 0.0 0.00 4.26
506 511 0.944386 TGACGCCTCTTTTGCACTTC 59.056 50.000 0.00 0.0 0.00 3.01
549 554 7.882791 TGTCAGATAATGATTGTGTAGTTTGGT 59.117 33.333 0.00 0.0 40.92 3.67
550 555 9.378551 GTCAGATAATGATTGTGTAGTTTGGTA 57.621 33.333 0.00 0.0 40.92 3.25
551 556 9.378551 TCAGATAATGATTGTGTAGTTTGGTAC 57.621 33.333 0.00 0.0 31.12 3.34
552 557 9.383519 CAGATAATGATTGTGTAGTTTGGTACT 57.616 33.333 0.00 0.0 41.04 2.73
553 558 9.601217 AGATAATGATTGTGTAGTTTGGTACTC 57.399 33.333 0.00 0.0 38.33 2.59
554 559 8.732746 ATAATGATTGTGTAGTTTGGTACTCC 57.267 34.615 0.00 0.0 38.33 3.85
611 616 0.732571 GATTCTTGCCGGAAATCGCA 59.267 50.000 5.05 0.0 37.59 5.10
643 648 1.717937 CAAGATGGCGAAAGAGGCG 59.282 57.895 0.00 0.0 39.82 5.52
651 656 1.017387 GCGAAAGAGGCGGATTCAAT 58.983 50.000 0.00 0.0 0.00 2.57
658 663 3.539604 AGAGGCGGATTCAATCTTTCAG 58.460 45.455 0.00 0.0 0.00 3.02
663 668 3.242673 GCGGATTCAATCTTTCAGCTCTG 60.243 47.826 0.00 0.0 0.00 3.35
668 673 7.361201 CGGATTCAATCTTTCAGCTCTGTTTAA 60.361 37.037 0.00 0.0 0.00 1.52
690 695 4.093472 TGTTTGTGTGGTGGTATAAGCT 57.907 40.909 0.00 0.0 0.00 3.74
714 723 2.032030 CACTTCGGCTTGGTACTTGTTG 60.032 50.000 0.00 0.0 0.00 3.33
724 733 5.446143 TTGGTACTTGTTGGCTTATGTTG 57.554 39.130 0.00 0.0 0.00 3.33
738 747 6.883756 TGGCTTATGTTGTACTGATGATGAAA 59.116 34.615 0.00 0.0 0.00 2.69
805 819 6.166279 CAAGTGAGGTAAAACATGAGAGCTA 58.834 40.000 0.00 0.0 0.00 3.32
806 820 6.360370 AGTGAGGTAAAACATGAGAGCTAA 57.640 37.500 0.00 0.0 0.00 3.09
807 821 6.769512 AGTGAGGTAAAACATGAGAGCTAAA 58.230 36.000 0.00 0.0 0.00 1.85
810 824 7.173390 GTGAGGTAAAACATGAGAGCTAAAGTT 59.827 37.037 0.00 0.0 0.00 2.66
811 825 7.173218 TGAGGTAAAACATGAGAGCTAAAGTTG 59.827 37.037 0.00 0.0 0.00 3.16
818 840 9.555727 AAACATGAGAGCTAAAGTTGTACTAAA 57.444 29.630 0.00 0.0 0.00 1.85
819 841 9.726438 AACATGAGAGCTAAAGTTGTACTAAAT 57.274 29.630 0.00 0.0 0.00 1.40
825 847 6.395629 AGCTAAAGTTGTACTAAATCTGCGA 58.604 36.000 0.00 0.0 0.00 5.10
833 855 8.440833 AGTTGTACTAAATCTGCGACAATTAAC 58.559 33.333 0.00 0.0 0.00 2.01
880 902 2.511600 GGCGTTGCAGCGGACTAT 60.512 61.111 24.49 0.0 38.18 2.12
904 930 3.621558 GGCCTAACAAATTGCTCCTACT 58.378 45.455 0.00 0.0 0.00 2.57
911 937 6.899393 AACAAATTGCTCCTACTCATTTCA 57.101 33.333 0.00 0.0 0.00 2.69
1170 1212 2.373707 CCTTCCCCTCCTCCTGCTG 61.374 68.421 0.00 0.0 0.00 4.41
1331 1382 4.208686 CGCTCCCGAGGTACTGCC 62.209 72.222 0.00 0.0 41.55 4.85
1380 1440 3.117474 TGCTACTGCTATCACTAGTCCCT 60.117 47.826 0.00 0.0 40.48 4.20
1383 1443 4.799715 ACTGCTATCACTAGTCCCTAGT 57.200 45.455 0.00 0.0 46.75 2.57
1396 1456 0.460284 CCCTAGTGATGTGGTGCGAC 60.460 60.000 0.00 0.0 0.00 5.19
1415 1475 3.306166 CGACTTGAGTTGTTTCGACTGTT 59.694 43.478 0.00 0.0 0.00 3.16
1683 1743 8.109634 ACTATATGGAAGAACAGAAATTGGTGT 58.890 33.333 0.00 0.0 0.00 4.16
1891 1951 3.960102 TGGCATCCCAACCAATTAAGATC 59.040 43.478 0.00 0.0 38.46 2.75
1903 1963 8.928733 CAACCAATTAAGATCCAAAGAAACATG 58.071 33.333 0.00 0.0 0.00 3.21
1949 2009 2.197324 TTGGCACCAACCAGACCC 59.803 61.111 0.00 0.0 41.82 4.46
1950 2010 2.694920 TTGGCACCAACCAGACCCA 61.695 57.895 0.00 0.0 41.82 4.51
1951 2011 2.282462 GGCACCAACCAGACCCAG 60.282 66.667 0.00 0.0 0.00 4.45
1952 2012 2.829384 GGCACCAACCAGACCCAGA 61.829 63.158 0.00 0.0 0.00 3.86
1953 2013 1.600916 GCACCAACCAGACCCAGAC 60.601 63.158 0.00 0.0 0.00 3.51
1954 2014 1.073199 CACCAACCAGACCCAGACC 59.927 63.158 0.00 0.0 0.00 3.85
2010 2070 9.713713 GTTTCTTTCTTGACCTTAACTAGATCT 57.286 33.333 0.00 0.0 0.00 2.75
2065 2125 1.986882 AAGCAGGGAACTTTGGAGTG 58.013 50.000 0.00 0.0 40.21 3.51
2174 2234 3.577848 TCATGGTTGCCAAAGTAAATGCT 59.422 39.130 0.00 0.0 36.95 3.79
2239 2299 3.382546 GTGTTCCGCCCATAACTAGTCTA 59.617 47.826 0.00 0.0 0.00 2.59
2329 2389 8.179509 TCCCTACTCTAATGCTCTTTATACAC 57.820 38.462 0.00 0.0 0.00 2.90
2350 2410 2.224450 CGGGGTCCCTATTGAATACACC 60.224 54.545 8.15 0.0 0.00 4.16
2500 2560 2.595750 TCGGTTTTGGGGTCAATGAT 57.404 45.000 0.00 0.0 32.28 2.45
2504 2564 3.613910 CGGTTTTGGGGTCAATGATTCAC 60.614 47.826 0.00 0.0 32.28 3.18
2718 2778 6.884472 TTCCCTCCTTATGTCTAACATTCA 57.116 37.500 0.00 0.0 39.88 2.57
2760 2820 9.567776 TTGAATCTGAGTGGTAATTTGACTAAA 57.432 29.630 0.00 0.0 0.00 1.85
2769 2992 9.216117 AGTGGTAATTTGACTAAACATGTAGAC 57.784 33.333 0.00 0.0 0.00 2.59
2815 3038 6.294176 CCCATGTTTATGAGGCTAGTAAATGC 60.294 42.308 6.97 0.0 36.36 3.56
2819 3042 0.458260 TGAGGCTAGTAAATGCGCGA 59.542 50.000 12.10 0.0 0.00 5.87
2857 3080 6.017440 CACAGGACGTTTCTTGGAAGATTTTA 60.017 38.462 0.00 0.0 33.06 1.52
2982 3205 3.372206 ACTCAGATGCAAATTCTACGCAC 59.628 43.478 0.00 0.0 38.73 5.34
2992 3215 5.390613 CAAATTCTACGCACCTGGTAAAAG 58.609 41.667 0.00 0.0 0.00 2.27
3004 3227 5.359860 CACCTGGTAAAAGTTTTGAGGTCTT 59.640 40.000 18.60 3.6 29.69 3.01
3005 3228 5.955959 ACCTGGTAAAAGTTTTGAGGTCTTT 59.044 36.000 16.87 0.0 33.61 2.52
3232 3455 6.873605 CACCTTTAGTGTATCACTGTTCATCA 59.126 38.462 11.92 0.0 45.01 3.07
3235 3458 5.659440 TAGTGTATCACTGTTCATCAGCA 57.341 39.130 11.92 0.0 45.01 4.41
3435 3658 7.730067 TTTATAGTTCGTCATGTCGTGTAAG 57.270 36.000 11.96 0.0 0.00 2.34
3496 3719 3.983044 AGTTAGAAGAAGGCGACCAAT 57.017 42.857 0.00 0.0 0.00 3.16
3564 3787 6.884280 ACAATAAAGAAGAAAGTCAGTGGG 57.116 37.500 0.00 0.0 0.00 4.61
3661 3884 4.494484 TCTCGGTGTCATGATGTACTTTG 58.506 43.478 0.00 0.0 0.00 2.77
3680 3903 1.141657 TGCTGGCCAAGATGATACTCC 59.858 52.381 7.01 0.0 0.00 3.85
3681 3904 1.419387 GCTGGCCAAGATGATACTCCT 59.581 52.381 7.01 0.0 0.00 3.69
3682 3905 2.549778 GCTGGCCAAGATGATACTCCTC 60.550 54.545 7.01 0.0 0.00 3.71
3740 3963 6.647334 TGCATGAAAAGAAGGTTATCAACA 57.353 33.333 0.00 0.0 0.00 3.33
3753 3976 4.876679 GGTTATCAACAAGGAGTTCTAGCC 59.123 45.833 0.00 0.0 38.74 3.93
3825 4048 4.037923 AGGTTTTAGTGGTTGCTTGTGATG 59.962 41.667 0.00 0.0 0.00 3.07
4088 4311 5.210715 GCTCTGTTCTTCATTTTGTCACTG 58.789 41.667 0.00 0.0 0.00 3.66
4116 4339 2.162408 GCCCTTCTGTCCAGATTTTTCG 59.838 50.000 0.00 0.0 37.29 3.46
4253 4497 8.896722 AATAGATATGTACTCCCTCCGTAAAT 57.103 34.615 0.00 0.0 0.00 1.40
4269 4528 9.490379 CCTCCGTAAATGCTCTTATATTTTACT 57.510 33.333 0.00 0.0 0.00 2.24
4324 4583 4.471904 TGACGATGCAGAATAAGAACCT 57.528 40.909 0.00 0.0 0.00 3.50
4328 4587 5.918608 ACGATGCAGAATAAGAACCTATGT 58.081 37.500 0.00 0.0 0.00 2.29
4431 4690 0.109412 GCAGCCAAGTCTGAATGCAC 60.109 55.000 0.00 0.0 36.19 4.57
4432 4691 1.241165 CAGCCAAGTCTGAATGCACA 58.759 50.000 0.00 0.0 36.19 4.57
4438 4697 4.084223 GCCAAGTCTGAATGCACATTTTTG 60.084 41.667 0.00 0.0 0.00 2.44
4441 4700 6.037391 CCAAGTCTGAATGCACATTTTTGTTT 59.963 34.615 0.00 0.0 0.00 2.83
4491 4932 5.606348 TTTTGCCTTAACATGTCCTGTTT 57.394 34.783 0.00 0.0 45.98 2.83
4524 4968 2.485266 AGCTTGTTTTGTGCGGTAAC 57.515 45.000 0.00 0.0 0.00 2.50
4529 4973 1.026584 GTTTTGTGCGGTAACCCACT 58.973 50.000 0.00 0.0 33.26 4.00
4533 4977 0.250124 TGTGCGGTAACCCACTTCTG 60.250 55.000 0.00 0.0 33.26 3.02
4557 5001 1.604879 AGGCTCGTCTGCTCTGTGA 60.605 57.895 0.00 0.0 0.00 3.58
4558 5002 1.181741 AGGCTCGTCTGCTCTGTGAA 61.182 55.000 0.00 0.0 0.00 3.18
4566 5010 1.829849 TCTGCTCTGTGAAGCTATGCT 59.170 47.619 0.00 0.0 42.94 3.79
4575 5019 4.566004 TGTGAAGCTATGCTCGTTACTTT 58.434 39.130 0.00 0.0 38.25 2.66
4576 5020 4.625742 TGTGAAGCTATGCTCGTTACTTTC 59.374 41.667 0.00 0.0 38.25 2.62
4577 5021 4.033014 GTGAAGCTATGCTCGTTACTTTCC 59.967 45.833 0.00 0.0 38.25 3.13
4578 5022 3.180891 AGCTATGCTCGTTACTTTCCC 57.819 47.619 0.00 0.0 30.62 3.97
4614 6355 3.143728 GCTCGTTACTTGGAAGGGAAAA 58.856 45.455 0.00 0.0 0.00 2.29
4633 6374 4.635769 TCCATGTGGCGTGGATTC 57.364 55.556 6.01 0.0 43.70 2.52
4643 6384 1.272781 GCGTGGATTCTCTGACTTCG 58.727 55.000 0.00 0.0 0.00 3.79
4655 6396 2.364324 TCTGACTTCGTACAGCCAAGTT 59.636 45.455 0.00 0.0 34.57 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
318 321 6.385649 AATGGAGTAACACGAAACAACAAT 57.614 33.333 0.00 0.00 0.00 2.71
549 554 6.426937 GCAATTTTCGCCAGATAATAGGAGTA 59.573 38.462 0.00 0.00 29.84 2.59
550 555 5.239525 GCAATTTTCGCCAGATAATAGGAGT 59.760 40.000 0.00 0.00 29.84 3.85
551 556 5.471456 AGCAATTTTCGCCAGATAATAGGAG 59.529 40.000 0.00 0.00 29.84 3.69
552 557 5.376625 AGCAATTTTCGCCAGATAATAGGA 58.623 37.500 0.00 0.00 29.84 2.94
553 558 5.239306 TGAGCAATTTTCGCCAGATAATAGG 59.761 40.000 0.00 0.00 29.84 2.57
554 559 6.304356 TGAGCAATTTTCGCCAGATAATAG 57.696 37.500 0.00 0.00 29.84 1.73
611 616 4.685628 CGCCATCTTGCAATTTTACACTTT 59.314 37.500 0.00 0.00 0.00 2.66
643 648 5.893897 AACAGAGCTGAAAGATTGAATCC 57.106 39.130 4.21 0.00 34.07 3.01
651 656 7.148086 ACACAAACATTAAACAGAGCTGAAAGA 60.148 33.333 4.21 0.00 34.07 2.52
658 663 4.739716 CACCACACAAACATTAAACAGAGC 59.260 41.667 0.00 0.00 0.00 4.09
663 668 7.327518 GCTTATACCACCACACAAACATTAAAC 59.672 37.037 0.00 0.00 0.00 2.01
668 673 4.662278 AGCTTATACCACCACACAAACAT 58.338 39.130 0.00 0.00 0.00 2.71
690 695 0.107831 AGTACCAAGCCGAAGTGCAA 59.892 50.000 0.00 0.00 0.00 4.08
714 723 6.925610 TTCATCATCAGTACAACATAAGCC 57.074 37.500 0.00 0.00 0.00 4.35
768 782 7.531857 TTACCTCACTTGCCAATTGAATTAA 57.468 32.000 7.12 0.00 0.00 1.40
781 795 4.999950 AGCTCTCATGTTTTACCTCACTTG 59.000 41.667 0.00 0.00 0.00 3.16
805 819 6.854496 TTGTCGCAGATTTAGTACAACTTT 57.146 33.333 0.00 0.00 40.67 2.66
806 820 7.435068 AATTGTCGCAGATTTAGTACAACTT 57.565 32.000 0.00 0.00 40.67 2.66
807 821 8.440833 GTTAATTGTCGCAGATTTAGTACAACT 58.559 33.333 0.00 0.00 40.67 3.16
810 824 8.440059 CAAGTTAATTGTCGCAGATTTAGTACA 58.560 33.333 0.00 0.00 40.67 2.90
811 825 7.903431 CCAAGTTAATTGTCGCAGATTTAGTAC 59.097 37.037 0.00 0.00 40.67 2.73
818 840 5.163622 CCAATCCAAGTTAATTGTCGCAGAT 60.164 40.000 8.53 0.00 40.67 2.90
819 841 4.155826 CCAATCCAAGTTAATTGTCGCAGA 59.844 41.667 8.53 0.00 37.17 4.26
825 847 5.222337 ACTCCCTCCAATCCAAGTTAATTGT 60.222 40.000 8.53 0.00 37.17 2.71
833 855 3.713764 ACATCTACTCCCTCCAATCCAAG 59.286 47.826 0.00 0.00 0.00 3.61
880 902 1.555967 GAGCAATTTGTTAGGCCCCA 58.444 50.000 0.00 0.00 0.00 4.96
956 985 1.134694 GAGGGACGCAAATTCGCAC 59.865 57.895 0.00 0.00 0.00 5.34
987 1016 5.419542 GAAAAGTTCATTTATGCCCCTTCC 58.580 41.667 0.00 0.00 0.00 3.46
1331 1382 2.202623 GTGTGAGGCCGAGTAGCG 60.203 66.667 0.00 0.00 40.47 4.26
1380 1440 1.616374 TCAAGTCGCACCACATCACTA 59.384 47.619 0.00 0.00 0.00 2.74
1383 1443 0.392706 ACTCAAGTCGCACCACATCA 59.607 50.000 0.00 0.00 0.00 3.07
1390 1450 1.591158 TCGAAACAACTCAAGTCGCAC 59.409 47.619 0.00 0.00 0.00 5.34
1396 1456 4.857871 TGAACAGTCGAAACAACTCAAG 57.142 40.909 0.00 0.00 0.00 3.02
1415 1475 1.672363 GCATCTCAATTCGCACCATGA 59.328 47.619 0.00 0.00 0.00 3.07
1591 1651 3.306166 CACTTAACATTTAGGTCGCCTCG 59.694 47.826 1.46 0.00 34.61 4.63
1662 1722 5.183904 GCTACACCAATTTCTGTTCTTCCAT 59.816 40.000 0.00 0.00 0.00 3.41
1683 1743 0.397941 AGAAGGCTTGTGTGCAGCTA 59.602 50.000 3.46 0.00 34.04 3.32
1697 1757 4.637977 GGTAGGCTGAAAAGATCAAGAAGG 59.362 45.833 0.00 0.00 37.67 3.46
1891 1951 0.037046 GGCAGCCCATGTTTCTTTGG 60.037 55.000 0.00 0.00 0.00 3.28
1945 2005 2.203938 TGGGTCTGGGTCTGGGTC 60.204 66.667 0.00 0.00 0.00 4.46
1947 2007 2.122729 TCTGGGTCTGGGTCTGGG 59.877 66.667 0.00 0.00 0.00 4.45
1948 2008 2.294078 GGTCTGGGTCTGGGTCTGG 61.294 68.421 0.00 0.00 0.00 3.86
1949 2009 2.294078 GGGTCTGGGTCTGGGTCTG 61.294 68.421 0.00 0.00 0.00 3.51
1950 2010 2.122954 GGGTCTGGGTCTGGGTCT 59.877 66.667 0.00 0.00 0.00 3.85
1951 2011 0.326238 TATGGGTCTGGGTCTGGGTC 60.326 60.000 0.00 0.00 0.00 4.46
1952 2012 0.326618 CTATGGGTCTGGGTCTGGGT 60.327 60.000 0.00 0.00 0.00 4.51
1953 2013 1.056700 CCTATGGGTCTGGGTCTGGG 61.057 65.000 0.00 0.00 0.00 4.45
1954 2014 0.326618 ACCTATGGGTCTGGGTCTGG 60.327 60.000 0.00 0.00 43.38 3.86
2065 2125 6.207025 TCAGTCTTAAGTCCTACAAGACAGAC 59.793 42.308 17.28 7.31 46.85 3.51
2174 2234 2.703536 TCCAAGCTTCCTGTACTTGTCA 59.296 45.455 0.00 0.00 39.30 3.58
2239 2299 8.486210 TGATAGCATGTACAAATCTCTAAACCT 58.514 33.333 0.00 0.00 0.00 3.50
2329 2389 2.224450 GGTGTATTCAATAGGGACCCCG 60.224 54.545 7.00 0.00 41.95 5.73
2350 2410 1.884235 AGTCAGCTTTCCTTGAACCG 58.116 50.000 0.00 0.00 0.00 4.44
2500 2560 5.104402 TCCTCCATATTCAGCAATCAGTGAA 60.104 40.000 0.00 0.00 37.10 3.18
2504 2564 6.704289 TTTTCCTCCATATTCAGCAATCAG 57.296 37.500 0.00 0.00 0.00 2.90
2712 2772 8.506168 TCAAGAAACTAGAAACTGTTGAATGT 57.494 30.769 0.00 0.00 0.00 2.71
2713 2773 9.956720 ATTCAAGAAACTAGAAACTGTTGAATG 57.043 29.630 15.37 0.00 40.26 2.67
2718 2778 8.964476 TCAGATTCAAGAAACTAGAAACTGTT 57.036 30.769 0.00 0.00 40.70 3.16
2788 3011 6.763715 TTACTAGCCTCATAAACATGGGAT 57.236 37.500 0.00 0.00 0.00 3.85
2794 3017 4.272504 GCGCATTTACTAGCCTCATAAACA 59.727 41.667 0.30 0.00 0.00 2.83
2815 3038 1.790043 TGTGTACACAACAAGATCGCG 59.210 47.619 26.07 0.00 40.63 5.87
2819 3042 3.181469 ACGTCCTGTGTACACAACAAGAT 60.181 43.478 27.66 10.65 40.63 2.40
2969 3192 5.048991 ACTTTTACCAGGTGCGTAGAATTTG 60.049 40.000 0.76 0.00 0.00 2.32
2982 3205 6.465439 AAAGACCTCAAAACTTTTACCAGG 57.535 37.500 0.00 0.00 31.11 4.45
2992 3215 3.737774 GCATGAGCAAAAGACCTCAAAAC 59.262 43.478 0.00 0.00 41.04 2.43
3004 3227 0.882484 TCACGGTTCGCATGAGCAAA 60.882 50.000 0.00 0.00 42.27 3.68
3005 3228 0.673333 ATCACGGTTCGCATGAGCAA 60.673 50.000 0.00 0.00 42.27 3.91
3179 3402 0.835941 AGGATGCTGGTAGCTGGAAG 59.164 55.000 0.00 0.00 42.97 3.46
3260 3483 5.597182 AGGACTAAACATATCGCTTCTACCA 59.403 40.000 0.00 0.00 0.00 3.25
3496 3719 4.882559 AGGAATTGGCTTAATTGGGATGA 58.117 39.130 4.58 0.00 39.06 2.92
3564 3787 1.923356 TGAAACCCATGAAGGAAGGC 58.077 50.000 0.00 0.00 41.22 4.35
3661 3884 1.419387 AGGAGTATCATCTTGGCCAGC 59.581 52.381 5.11 0.00 36.25 4.85
3680 3903 0.036010 ATGAACCCGTCTTGGCTGAG 60.036 55.000 0.00 0.00 35.87 3.35
3681 3904 0.321564 CATGAACCCGTCTTGGCTGA 60.322 55.000 0.00 0.00 35.87 4.26
3682 3905 0.321564 TCATGAACCCGTCTTGGCTG 60.322 55.000 0.00 0.00 35.87 4.85
3740 3963 0.688087 CCTCCGGGCTAGAACTCCTT 60.688 60.000 0.00 0.00 0.00 3.36
3753 3976 1.520787 GTGGCAATACGACCTCCGG 60.521 63.158 0.00 0.00 43.93 5.14
3825 4048 0.784778 CTGACAGAGAAACGGCGAAC 59.215 55.000 16.62 4.10 0.00 3.95
3981 4204 8.816894 CAGAGTATGATACACCATATAACCCTT 58.183 37.037 5.28 0.00 32.33 3.95
4088 4311 1.674651 GGACAGAAGGGCCCGTTTC 60.675 63.158 18.44 16.21 0.00 2.78
4116 4339 6.399986 GCTGAAGAGTTGACAAAACAAACAAC 60.400 38.462 0.00 0.00 41.61 3.32
4253 4497 7.676683 ACTCCCTCAGTAAAATATAAGAGCA 57.323 36.000 0.00 0.00 31.37 4.26
4269 4528 6.575244 ACATGGATGTTTAATACTCCCTCA 57.425 37.500 0.00 0.00 37.90 3.86
4324 4583 5.105392 GCCCATTCCATTCAACAGAAACATA 60.105 40.000 0.00 0.00 0.00 2.29
4328 4587 3.237746 TGCCCATTCCATTCAACAGAAA 58.762 40.909 0.00 0.00 0.00 2.52
4421 4680 4.272991 GGCAAACAAAAATGTGCATTCAGA 59.727 37.500 0.00 0.00 38.78 3.27
4431 4690 8.364129 AGTACATGTTAAGGCAAACAAAAATG 57.636 30.769 2.30 6.16 42.33 2.32
4432 4691 8.421002 AGAGTACATGTTAAGGCAAACAAAAAT 58.579 29.630 2.30 0.00 42.33 1.82
4438 4697 5.941948 ACAGAGTACATGTTAAGGCAAAC 57.058 39.130 2.30 0.00 0.00 2.93
4441 4700 5.472137 GGAAAACAGAGTACATGTTAAGGCA 59.528 40.000 14.59 0.00 39.91 4.75
4491 4932 2.047061 ACAAGCTTACAGACAGGACCA 58.953 47.619 0.00 0.00 0.00 4.02
4524 4968 2.673523 CCTGGGCTCAGAAGTGGG 59.326 66.667 17.43 0.00 43.49 4.61
4546 4990 1.829849 AGCATAGCTTCACAGAGCAGA 59.170 47.619 0.00 0.00 45.12 4.26
4547 4991 2.203401 GAGCATAGCTTCACAGAGCAG 58.797 52.381 0.00 0.00 45.12 4.24
4548 4992 1.470458 CGAGCATAGCTTCACAGAGCA 60.470 52.381 0.00 0.00 45.12 4.26
4549 4993 1.207390 CGAGCATAGCTTCACAGAGC 58.793 55.000 0.00 0.00 39.88 4.09
4557 5001 3.197983 AGGGAAAGTAACGAGCATAGCTT 59.802 43.478 0.00 0.00 39.88 3.74
4558 5002 2.766828 AGGGAAAGTAACGAGCATAGCT 59.233 45.455 0.00 0.00 43.88 3.32
4633 6374 2.029828 ACTTGGCTGTACGAAGTCAGAG 60.030 50.000 0.00 0.00 43.04 3.35


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

AutoCloner maintained by Alex Coulton.