Multiple sequence alignment - TraesCS3A01G002700

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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 TraesCS3A01G002700 chr3A 100.000 2432 0 0 1 2432 1592227 1594658 0.000000e+00 4492.0
1 TraesCS3A01G002700 chr3A 86.160 513 32 12 1091 1590 1574667 1575153 3.580000e-143 518.0
2 TraesCS3A01G002700 chr3A 85.230 501 43 16 325 824 1574029 1574499 1.010000e-133 486.0
3 TraesCS3A01G002700 chr3A 76.615 650 78 43 908 1526 1514142 1514748 8.510000e-75 291.0
4 TraesCS3A01G002700 chr3A 75.000 668 93 39 836 1474 1519189 1519811 8.690000e-60 241.0
5 TraesCS3A01G002700 chr3A 98.361 61 1 0 1091 1151 1574573 1574633 9.190000e-20 108.0
6 TraesCS3A01G002700 chr3A 85.000 80 7 2 749 828 1513993 1514067 2.590000e-10 76.8
7 TraesCS3A01G002700 chr3A 87.234 47 4 2 1716 1761 455036326 455036371 4.000000e-03 52.8
8 TraesCS3A01G002700 chrUn 87.192 1460 111 30 2 1454 32261235 32262625 0.000000e+00 1591.0
9 TraesCS3A01G002700 chrUn 84.256 1156 79 42 348 1484 307092877 307093948 0.000000e+00 1031.0
10 TraesCS3A01G002700 chrUn 88.626 677 36 11 827 1498 34183679 34184319 0.000000e+00 785.0
11 TraesCS3A01G002700 chrUn 86.257 553 44 16 1580 2125 307094069 307094596 2.710000e-159 571.0
12 TraesCS3A01G002700 chrUn 77.993 877 81 60 615 1447 32250475 32251283 4.770000e-122 448.0
13 TraesCS3A01G002700 chrUn 76.445 934 104 58 615 1481 34500027 34499143 1.350000e-107 399.0
14 TraesCS3A01G002700 chrUn 75.248 808 87 67 646 1391 34498223 34497467 1.840000e-71 279.0
15 TraesCS3A01G002700 chrUn 88.261 230 12 8 2063 2279 477972078 477971851 6.670000e-66 261.0
16 TraesCS3A01G002700 chrUn 96.250 80 2 1 1443 1521 307093970 307094049 1.960000e-26 130.0
17 TraesCS3A01G002700 chr3D 81.614 1425 149 59 223 1610 2526990 2525642 0.000000e+00 1075.0
18 TraesCS3A01G002700 chr3D 87.904 835 59 18 822 1644 2462433 2461629 0.000000e+00 944.0
19 TraesCS3A01G002700 chr3D 86.207 406 28 11 2048 2432 2461490 2461092 4.840000e-112 414.0
20 TraesCS3A01G002700 chr3D 75.810 926 116 47 615 1475 2533726 2532844 1.060000e-98 370.0
21 TraesCS3A01G002700 chr3D 75.711 914 114 54 649 1521 2465945 2465099 2.300000e-95 359.0
22 TraesCS3A01G002700 chr3D 76.364 715 97 43 836 1524 2469735 2469067 3.900000e-83 318.0


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 TraesCS3A01G002700 chr3A 1592227 1594658 2431 False 4492.000000 4492 100.0000 1 2432 1 chr3A.!!$F2 2431
1 TraesCS3A01G002700 chr3A 1574029 1575153 1124 False 370.666667 518 89.9170 325 1590 3 chr3A.!!$F5 1265
2 TraesCS3A01G002700 chr3A 1519189 1519811 622 False 241.000000 241 75.0000 836 1474 1 chr3A.!!$F1 638
3 TraesCS3A01G002700 chrUn 32261235 32262625 1390 False 1591.000000 1591 87.1920 2 1454 1 chrUn.!!$F2 1452
4 TraesCS3A01G002700 chrUn 34183679 34184319 640 False 785.000000 785 88.6260 827 1498 1 chrUn.!!$F3 671
5 TraesCS3A01G002700 chrUn 307092877 307094596 1719 False 577.333333 1031 88.9210 348 2125 3 chrUn.!!$F4 1777
6 TraesCS3A01G002700 chrUn 32250475 32251283 808 False 448.000000 448 77.9930 615 1447 1 chrUn.!!$F1 832
7 TraesCS3A01G002700 chrUn 34497467 34500027 2560 True 339.000000 399 75.8465 615 1481 2 chrUn.!!$R2 866
8 TraesCS3A01G002700 chr3D 2525642 2526990 1348 True 1075.000000 1075 81.6140 223 1610 1 chr3D.!!$R1 1387
9 TraesCS3A01G002700 chr3D 2461092 2469735 8643 True 508.750000 944 81.5465 649 2432 4 chr3D.!!$R3 1783
10 TraesCS3A01G002700 chr3D 2532844 2533726 882 True 370.000000 370 75.8100 615 1475 1 chr3D.!!$R2 860

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
685 3837 0.039256 TGCGGTTTTGCTCAATCTGC 60.039 50.0 10.15 10.15 35.36 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2015 8818 0.179 ATCGACATGGAAGTCCTGGC 59.821 55.0 0.0 0.0 35.07 4.85 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
37 38 6.959639 TGAATCAGTGGAAATAATTAGCCC 57.040 37.500 0.00 0.00 0.00 5.19
47 48 5.602561 GGAAATAATTAGCCCTTTCCCATGT 59.397 40.000 13.85 0.00 40.38 3.21
48 49 6.462909 GGAAATAATTAGCCCTTTCCCATGTG 60.463 42.308 13.85 0.00 40.38 3.21
123 126 8.934825 GGTTCATGTTTGCAAATATGTTATTGT 58.065 29.630 34.02 8.32 38.28 2.71
128 131 9.872721 ATGTTTGCAAATATGTTATTGTGATCA 57.127 25.926 19.23 5.65 0.00 2.92
130 133 8.594687 GTTTGCAAATATGTTATTGTGATCACC 58.405 33.333 22.85 7.69 0.00 4.02
132 135 8.744568 TGCAAATATGTTATTGTGATCACCTA 57.255 30.769 22.85 11.47 0.00 3.08
187 190 2.828520 TGTTGCAAAAGTTCAAGGGTCA 59.171 40.909 0.00 0.00 0.00 4.02
189 192 4.081198 TGTTGCAAAAGTTCAAGGGTCATT 60.081 37.500 0.00 0.00 0.00 2.57
193 196 4.202151 GCAAAAGTTCAAGGGTCATTGACT 60.202 41.667 16.02 0.00 38.87 3.41
194 197 5.284079 CAAAAGTTCAAGGGTCATTGACTG 58.716 41.667 16.02 7.37 38.87 3.51
213 216 8.696410 TTGACTGACAATTCCAAAAAGTAAAC 57.304 30.769 0.00 0.00 33.18 2.01
248 252 2.195956 GCCATAGCCCCCAACCTC 59.804 66.667 0.00 0.00 0.00 3.85
251 255 1.697754 CATAGCCCCCAACCTCCCT 60.698 63.158 0.00 0.00 0.00 4.20
260 264 1.106285 CCAACCTCCCTAGCAATTGC 58.894 55.000 23.05 23.05 42.49 3.56
269 273 1.133790 CCTAGCAATTGCAGTTCTGGC 59.866 52.381 30.89 1.63 45.16 4.85
272 276 0.319405 GCAATTGCAGTTCTGGCCTT 59.681 50.000 25.36 0.00 41.59 4.35
282 286 1.340889 GTTCTGGCCTTTGTCATGCAA 59.659 47.619 3.32 0.00 34.87 4.08
284 288 2.037901 TCTGGCCTTTGTCATGCAAAA 58.962 42.857 3.32 5.07 45.35 2.44
288 292 3.386078 TGGCCTTTGTCATGCAAAAAGTA 59.614 39.130 3.32 2.86 45.35 2.24
296 300 4.517075 TGTCATGCAAAAAGTAATGACCGA 59.483 37.500 9.62 0.00 45.36 4.69
298 302 6.372937 TGTCATGCAAAAAGTAATGACCGATA 59.627 34.615 9.62 0.00 45.36 2.92
301 305 5.933790 TGCAAAAAGTAATGACCGATACAC 58.066 37.500 0.00 0.00 0.00 2.90
310 314 2.761559 TGACCGATACACACAACCTTG 58.238 47.619 0.00 0.00 0.00 3.61
313 317 2.158726 ACCGATACACACAACCTTGGTT 60.159 45.455 0.00 0.00 0.00 3.67
319 323 1.949525 CACACAACCTTGGTTGAGAGG 59.050 52.381 31.71 20.94 37.72 3.69
322 326 1.843851 ACAACCTTGGTTGAGAGGTGA 59.156 47.619 31.71 0.00 45.32 4.02
323 327 2.443255 ACAACCTTGGTTGAGAGGTGAT 59.557 45.455 31.71 10.10 45.32 3.06
329 333 1.351017 TGGTTGAGAGGTGATGGAACC 59.649 52.381 0.00 0.00 40.85 3.62
333 337 0.984230 GAGAGGTGATGGAACCCACA 59.016 55.000 0.00 0.00 41.54 4.17
339 343 1.135960 TGATGGAACCCACAGTCACA 58.864 50.000 0.00 0.00 35.80 3.58
346 350 2.750350 CCACAGTCACACCCTCCC 59.250 66.667 0.00 0.00 0.00 4.30
398 402 0.105453 ATCACCGGCATCCTCTAGGT 60.105 55.000 0.00 0.00 36.34 3.08
404 408 1.543802 CGGCATCCTCTAGGTCATCTC 59.456 57.143 0.00 0.00 36.34 2.75
422 426 1.986378 CTCGAAGATCCGTCACAACAC 59.014 52.381 0.00 0.00 33.89 3.32
439 443 7.331193 GTCACAACACGGTAAATTCTTAGAGAT 59.669 37.037 0.00 0.00 0.00 2.75
440 444 7.876068 TCACAACACGGTAAATTCTTAGAGATT 59.124 33.333 0.00 0.00 0.00 2.40
442 446 9.148104 ACAACACGGTAAATTCTTAGAGATTAC 57.852 33.333 9.37 9.37 0.00 1.89
444 448 7.844009 ACACGGTAAATTCTTAGAGATTACCA 58.156 34.615 24.61 0.00 43.57 3.25
446 450 7.980099 CACGGTAAATTCTTAGAGATTACCAGT 59.020 37.037 24.61 21.10 43.57 4.00
519 523 5.324409 TGATTTGTTGCTACTCCCAATCTT 58.676 37.500 0.00 0.00 0.00 2.40
532 536 7.693969 ACTCCCAATCTTTTTGTCAATCTAG 57.306 36.000 0.00 0.00 0.00 2.43
553 561 4.254492 AGCCTCGAGACTTGGATTTAAAC 58.746 43.478 15.71 0.00 0.00 2.01
596 605 1.003718 CGAACCTCACAACCCCCTC 60.004 63.158 0.00 0.00 0.00 4.30
601 610 1.573857 ACCTCACAACCCCCTCTTTTT 59.426 47.619 0.00 0.00 0.00 1.94
676 3828 0.948678 TAGTTCAGGTGCGGTTTTGC 59.051 50.000 0.00 0.00 0.00 3.68
677 3829 0.751643 AGTTCAGGTGCGGTTTTGCT 60.752 50.000 0.00 0.00 35.36 3.91
678 3830 0.317854 GTTCAGGTGCGGTTTTGCTC 60.318 55.000 0.00 0.00 35.36 4.26
679 3831 0.749818 TTCAGGTGCGGTTTTGCTCA 60.750 50.000 0.00 0.00 35.36 4.26
680 3832 0.749818 TCAGGTGCGGTTTTGCTCAA 60.750 50.000 0.00 0.00 35.36 3.02
681 3833 0.314935 CAGGTGCGGTTTTGCTCAAT 59.685 50.000 0.00 0.00 35.36 2.57
682 3834 0.598065 AGGTGCGGTTTTGCTCAATC 59.402 50.000 0.00 0.00 35.36 2.67
683 3835 0.598065 GGTGCGGTTTTGCTCAATCT 59.402 50.000 0.00 0.00 35.36 2.40
684 3836 1.666888 GGTGCGGTTTTGCTCAATCTG 60.667 52.381 0.00 0.00 35.36 2.90
685 3837 0.039256 TGCGGTTTTGCTCAATCTGC 60.039 50.000 10.15 10.15 35.36 4.26
686 3838 0.242017 GCGGTTTTGCTCAATCTGCT 59.758 50.000 9.94 0.00 0.00 4.24
687 3839 1.336240 GCGGTTTTGCTCAATCTGCTT 60.336 47.619 9.94 0.00 0.00 3.91
688 3840 2.863704 GCGGTTTTGCTCAATCTGCTTT 60.864 45.455 9.94 0.00 0.00 3.51
689 3841 3.383761 CGGTTTTGCTCAATCTGCTTTT 58.616 40.909 0.00 0.00 0.00 2.27
690 3842 3.182972 CGGTTTTGCTCAATCTGCTTTTG 59.817 43.478 0.00 0.00 0.00 2.44
737 3893 4.604843 TCAACAAAGCACGATGATGATC 57.395 40.909 0.00 0.00 0.00 2.92
1537 8325 2.156117 GTGTGCGCTAAACGTAATCACA 59.844 45.455 9.73 0.00 46.11 3.58
1567 8355 7.255491 TCGTCCTGTACTGTACATATACTTG 57.745 40.000 19.99 7.48 38.15 3.16
1574 8362 6.819649 TGTACTGTACATATACTTGGGTTTGC 59.180 38.462 16.26 0.00 32.89 3.68
1592 8386 5.186198 GTTTGCACTACATATGGTCTTCCT 58.814 41.667 7.80 0.00 34.23 3.36
1628 8422 9.891828 AAGTTTTTCTTTTCTTTTGCGAAAAAT 57.108 22.222 0.72 0.00 42.16 1.82
1786 8584 3.005554 CACATCAGCTCCAAGGTTACTG 58.994 50.000 0.00 0.00 0.00 2.74
1791 8589 3.070018 CAGCTCCAAGGTTACTGACAAG 58.930 50.000 0.00 0.00 0.00 3.16
1875 8678 3.732721 GTGATCAAGTTGTGCAGCTTTTC 59.267 43.478 0.00 1.39 29.11 2.29
1892 8695 4.687483 GCTTTTCTTTCCATGGTCATTGTG 59.313 41.667 12.58 0.00 0.00 3.33
1894 8697 6.477053 TTTTCTTTCCATGGTCATTGTGAA 57.523 33.333 12.58 5.48 0.00 3.18
1895 8698 6.477053 TTTCTTTCCATGGTCATTGTGAAA 57.523 33.333 12.58 10.66 0.00 2.69
1897 8700 5.139727 TCTTTCCATGGTCATTGTGAAACT 58.860 37.500 12.58 0.00 38.04 2.66
1898 8701 4.852134 TTCCATGGTCATTGTGAAACTG 57.148 40.909 12.58 0.00 38.04 3.16
1899 8702 3.156293 TCCATGGTCATTGTGAAACTGG 58.844 45.455 12.58 0.00 38.04 4.00
1900 8703 3.156293 CCATGGTCATTGTGAAACTGGA 58.844 45.455 2.57 0.00 38.04 3.86
1901 8704 3.057315 CCATGGTCATTGTGAAACTGGAC 60.057 47.826 2.57 0.00 38.04 4.02
1902 8705 2.217750 TGGTCATTGTGAAACTGGACG 58.782 47.619 0.00 0.00 38.04 4.79
1903 8706 2.218603 GGTCATTGTGAAACTGGACGT 58.781 47.619 0.00 0.00 38.04 4.34
1904 8707 2.616842 GGTCATTGTGAAACTGGACGTT 59.383 45.455 0.00 0.00 38.04 3.99
1905 8708 3.548014 GGTCATTGTGAAACTGGACGTTG 60.548 47.826 0.00 0.00 38.04 4.10
1906 8709 3.064820 GTCATTGTGAAACTGGACGTTGT 59.935 43.478 0.00 0.00 38.04 3.32
1907 8710 3.064682 TCATTGTGAAACTGGACGTTGTG 59.935 43.478 0.00 0.00 38.04 3.33
1908 8711 2.102070 TGTGAAACTGGACGTTGTGT 57.898 45.000 0.00 0.00 38.04 3.72
1911 8714 2.160813 GTGAAACTGGACGTTGTGTTGT 59.839 45.455 0.00 0.00 35.61 3.32
1912 8715 2.160615 TGAAACTGGACGTTGTGTTGTG 59.839 45.455 0.00 0.00 35.61 3.33
1945 8748 3.620821 GGTTGTTGGTTTGATGGTTTGTG 59.379 43.478 0.00 0.00 0.00 3.33
1948 8751 3.118956 TGTTGGTTTGATGGTTTGTGTCC 60.119 43.478 0.00 0.00 0.00 4.02
1951 8754 2.542824 GGTTTGATGGTTTGTGTCCGTG 60.543 50.000 0.00 0.00 0.00 4.94
1961 8764 0.389296 TGTGTCCGTGGTAATCTGCG 60.389 55.000 0.00 0.00 0.00 5.18
1962 8765 1.447140 TGTCCGTGGTAATCTGCGC 60.447 57.895 0.00 0.00 0.00 6.09
1978 8781 1.277440 CGCGTGGTTGGTTGTGTAC 59.723 57.895 0.00 0.00 0.00 2.90
1995 8798 2.027561 TGTACCTATCAAGCGCTTTGGT 60.028 45.455 22.51 24.97 37.39 3.67
1996 8799 2.200373 ACCTATCAAGCGCTTTGGTT 57.800 45.000 22.51 8.08 39.32 3.67
1998 8801 3.007635 ACCTATCAAGCGCTTTGGTTAC 58.992 45.455 22.51 0.00 36.29 2.50
2125 8929 7.016361 ACTTTTATCTGCGTGTCCATATTTC 57.984 36.000 0.00 0.00 0.00 2.17
2133 9054 2.745152 CGTGTCCATATTTCTCCCCACC 60.745 54.545 0.00 0.00 0.00 4.61
2148 9374 4.406456 TCCCCACCATACATTATGCATTC 58.594 43.478 3.54 0.00 34.85 2.67
2149 9375 3.511146 CCCCACCATACATTATGCATTCC 59.489 47.826 3.54 0.00 34.85 3.01
2190 9417 5.936187 ATATATGCACTCAGGAGGATCAG 57.064 43.478 0.83 0.00 36.25 2.90
2270 9734 6.208644 AGTGTAACAGTCAAATGAAATGCAC 58.791 36.000 0.00 0.00 41.43 4.57
2281 9746 1.173913 GAAATGCACGGCCCTTAAGT 58.826 50.000 0.00 0.00 0.00 2.24
2291 9756 2.742589 CGGCCCTTAAGTCTTTTCTCAC 59.257 50.000 0.00 0.00 0.00 3.51
2293 9758 3.753797 GGCCCTTAAGTCTTTTCTCACTG 59.246 47.826 0.97 0.00 0.00 3.66
2294 9759 4.505039 GGCCCTTAAGTCTTTTCTCACTGA 60.505 45.833 0.97 0.00 0.00 3.41
2295 9760 4.452795 GCCCTTAAGTCTTTTCTCACTGAC 59.547 45.833 0.97 0.00 0.00 3.51
2296 9761 5.743422 GCCCTTAAGTCTTTTCTCACTGACT 60.743 44.000 0.97 0.00 40.95 3.41
2304 9769 7.106239 AGTCTTTTCTCACTGACTTTGAAAGA 58.894 34.615 12.53 0.00 36.50 2.52
2384 9856 2.461110 GCCAAGCCGTACGACCATG 61.461 63.158 18.76 10.16 0.00 3.66
2392 9864 0.526954 CGTACGACCATGTGTAGCCC 60.527 60.000 10.44 0.00 0.00 5.19
2400 9872 3.031417 ATGTGTAGCCCCTGCGGAC 62.031 63.158 0.00 0.00 44.33 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.822185 GGCTAATTATTTCCACTGATTCAATTT 57.178 29.630 0.00 0.00 0.00 1.82
13 14 7.125391 AGGGCTAATTATTTCCACTGATTCAA 58.875 34.615 0.00 0.00 0.00 2.69
24 25 6.515832 CACATGGGAAAGGGCTAATTATTTC 58.484 40.000 0.00 2.07 0.00 2.17
37 38 0.527113 TGCAATCGCACATGGGAAAG 59.473 50.000 0.00 0.42 45.36 2.62
48 49 3.500982 ACACACAACAATATGCAATCGC 58.499 40.909 0.00 0.00 39.24 4.58
62 65 4.256110 CATGCATAGGAAGAGACACACAA 58.744 43.478 0.00 0.00 0.00 3.33
63 66 3.369787 CCATGCATAGGAAGAGACACACA 60.370 47.826 0.00 0.00 0.00 3.72
162 165 5.066593 ACCCTTGAACTTTTGCAACAAAAA 58.933 33.333 0.00 0.00 0.00 1.94
163 166 4.646572 ACCCTTGAACTTTTGCAACAAAA 58.353 34.783 0.00 5.47 0.00 2.44
173 176 4.792068 TCAGTCAATGACCCTTGAACTTT 58.208 39.130 10.12 0.00 36.92 2.66
189 192 7.831753 TGTTTACTTTTTGGAATTGTCAGTCA 58.168 30.769 0.00 0.00 0.00 3.41
231 234 2.195956 GAGGTTGGGGGCTATGGC 59.804 66.667 0.00 0.00 37.82 4.40
236 239 2.042930 CTAGGGAGGTTGGGGGCT 59.957 66.667 0.00 0.00 0.00 5.19
248 252 1.747355 CCAGAACTGCAATTGCTAGGG 59.253 52.381 29.37 17.79 42.66 3.53
251 255 1.176527 GGCCAGAACTGCAATTGCTA 58.823 50.000 29.37 15.63 42.66 3.49
260 264 1.068055 GCATGACAAAGGCCAGAACTG 60.068 52.381 5.01 0.00 0.00 3.16
272 276 5.009110 TCGGTCATTACTTTTTGCATGACAA 59.991 36.000 13.20 0.00 44.97 3.18
282 286 6.072893 GGTTGTGTGTATCGGTCATTACTTTT 60.073 38.462 0.00 0.00 0.00 2.27
284 288 4.933400 GGTTGTGTGTATCGGTCATTACTT 59.067 41.667 0.00 0.00 0.00 2.24
288 292 3.695830 AGGTTGTGTGTATCGGTCATT 57.304 42.857 0.00 0.00 0.00 2.57
310 314 1.340114 GGGTTCCATCACCTCTCAACC 60.340 57.143 0.00 0.00 36.97 3.77
313 317 0.984230 GTGGGTTCCATCACCTCTCA 59.016 55.000 0.00 0.00 35.28 3.27
319 323 1.202758 TGTGACTGTGGGTTCCATCAC 60.203 52.381 10.55 10.55 35.28 3.06
322 326 0.110486 GGTGTGACTGTGGGTTCCAT 59.890 55.000 0.00 0.00 35.28 3.41
323 327 1.529796 GGTGTGACTGTGGGTTCCA 59.470 57.895 0.00 0.00 0.00 3.53
329 333 2.750350 GGGAGGGTGTGACTGTGG 59.250 66.667 0.00 0.00 0.00 4.17
346 350 1.848886 AACTTTGGAGGGGTAGGGCG 61.849 60.000 0.00 0.00 0.00 6.13
398 402 2.365582 TGTGACGGATCTTCGAGATGA 58.634 47.619 0.00 0.00 34.53 2.92
404 408 0.708370 CGTGTTGTGACGGATCTTCG 59.292 55.000 0.00 0.00 35.65 3.79
422 426 8.818057 CAACTGGTAATCTCTAAGAATTTACCG 58.182 37.037 14.39 12.38 42.99 4.02
426 430 8.383175 TGGTCAACTGGTAATCTCTAAGAATTT 58.617 33.333 0.00 0.00 0.00 1.82
439 443 0.475044 GGGTGGTGGTCAACTGGTAA 59.525 55.000 0.00 0.00 32.53 2.85
440 444 0.400815 AGGGTGGTGGTCAACTGGTA 60.401 55.000 0.00 0.00 32.53 3.25
442 446 1.073199 GAGGGTGGTGGTCAACTGG 59.927 63.158 0.00 0.00 32.53 4.00
444 448 3.148084 CGAGGGTGGTGGTCAACT 58.852 61.111 0.00 0.00 32.53 3.16
446 450 3.948719 GGCGAGGGTGGTGGTCAA 61.949 66.667 0.00 0.00 0.00 3.18
474 478 1.289109 ACCTTGGCGTCGATGTTTCG 61.289 55.000 6.48 0.00 46.87 3.46
519 523 4.220821 AGTCTCGAGGCTAGATTGACAAAA 59.779 41.667 20.10 0.00 0.00 2.44
532 536 4.254492 AGTTTAAATCCAAGTCTCGAGGC 58.746 43.478 9.58 9.58 0.00 4.70
601 610 8.893563 ATCAAGGGATTACTGATTTTACCAAA 57.106 30.769 0.00 0.00 0.00 3.28
602 611 7.282224 CGATCAAGGGATTACTGATTTTACCAA 59.718 37.037 0.00 0.00 32.67 3.67
604 613 6.204882 CCGATCAAGGGATTACTGATTTTACC 59.795 42.308 0.00 0.00 32.67 2.85
605 614 7.190920 CCGATCAAGGGATTACTGATTTTAC 57.809 40.000 0.00 0.00 32.67 2.01
676 3828 4.279169 TGGAAAGGTCAAAAGCAGATTGAG 59.721 41.667 0.00 0.00 37.46 3.02
677 3829 4.037923 GTGGAAAGGTCAAAAGCAGATTGA 59.962 41.667 0.00 0.00 34.56 2.57
678 3830 4.202141 TGTGGAAAGGTCAAAAGCAGATTG 60.202 41.667 0.00 0.00 0.00 2.67
679 3831 3.960102 TGTGGAAAGGTCAAAAGCAGATT 59.040 39.130 0.00 0.00 0.00 2.40
680 3832 3.565307 TGTGGAAAGGTCAAAAGCAGAT 58.435 40.909 0.00 0.00 0.00 2.90
681 3833 3.011566 TGTGGAAAGGTCAAAAGCAGA 57.988 42.857 0.00 0.00 0.00 4.26
682 3834 3.799281 TTGTGGAAAGGTCAAAAGCAG 57.201 42.857 0.00 0.00 0.00 4.24
683 3835 4.502962 CTTTTGTGGAAAGGTCAAAAGCA 58.497 39.130 13.79 0.00 45.40 3.91
689 3841 9.581289 TCTTTATATTCTTTTGTGGAAAGGTCA 57.419 29.630 0.00 0.00 44.00 4.02
706 3858 8.892723 TCATCGTGCTTTGTTGATCTTTATATT 58.107 29.630 0.00 0.00 0.00 1.28
707 3859 8.437360 TCATCGTGCTTTGTTGATCTTTATAT 57.563 30.769 0.00 0.00 0.00 0.86
737 3893 1.800586 CAGAGGTGGTGATTGTTGTCG 59.199 52.381 0.00 0.00 0.00 4.35
743 3899 1.278985 TGGCTACAGAGGTGGTGATTG 59.721 52.381 0.00 0.00 0.00 2.67
1537 8325 3.570975 TGTACAGTACAGGACGAACATGT 59.429 43.478 9.51 0.00 45.55 3.21
1567 8355 3.886123 AGACCATATGTAGTGCAAACCC 58.114 45.455 1.24 0.00 0.00 4.11
1574 8362 5.596361 AGACAGAGGAAGACCATATGTAGTG 59.404 44.000 1.24 0.00 38.94 2.74
1592 8386 6.113411 AGAAAAGAAAAACTTCGGAGACAGA 58.887 36.000 0.00 0.00 37.93 3.41
1747 8541 7.439157 TGATGTGAAAAAGACCTTGATGTAG 57.561 36.000 0.00 0.00 0.00 2.74
1756 8554 3.149196 TGGAGCTGATGTGAAAAAGACC 58.851 45.455 0.00 0.00 0.00 3.85
1757 8555 4.320788 CCTTGGAGCTGATGTGAAAAAGAC 60.321 45.833 0.00 0.00 0.00 3.01
1820 8618 6.481313 TCTCAATCTTTCCTCTTGCGAATATG 59.519 38.462 0.00 0.00 0.00 1.78
1833 8631 6.254281 TCACGGATTTTTCTCAATCTTTCC 57.746 37.500 0.00 0.00 34.12 3.13
1841 8639 5.530915 ACAACTTGATCACGGATTTTTCTCA 59.469 36.000 4.03 0.00 0.00 3.27
1842 8640 5.853282 CACAACTTGATCACGGATTTTTCTC 59.147 40.000 4.03 0.00 0.00 2.87
1843 8641 5.762045 CACAACTTGATCACGGATTTTTCT 58.238 37.500 4.03 0.00 0.00 2.52
1844 8642 4.382754 GCACAACTTGATCACGGATTTTTC 59.617 41.667 4.03 0.00 0.00 2.29
1875 8678 5.224888 CAGTTTCACAATGACCATGGAAAG 58.775 41.667 21.47 5.83 0.00 2.62
1892 8695 2.160813 ACACAACACAACGTCCAGTTTC 59.839 45.455 0.00 0.00 42.02 2.78
1894 8697 1.816074 ACACAACACAACGTCCAGTT 58.184 45.000 0.00 0.00 45.45 3.16
1895 8698 1.816074 AACACAACACAACGTCCAGT 58.184 45.000 0.00 0.00 0.00 4.00
1897 8700 3.644884 AAAAACACAACACAACGTCCA 57.355 38.095 0.00 0.00 0.00 4.02
1945 8748 2.514013 CGCGCAGATTACCACGGAC 61.514 63.158 8.75 0.00 0.00 4.79
1948 8751 2.695055 CACGCGCAGATTACCACG 59.305 61.111 5.73 0.00 0.00 4.94
1951 8754 1.423845 CAACCACGCGCAGATTACC 59.576 57.895 5.73 0.00 0.00 2.85
1978 8781 2.030457 CGTAACCAAAGCGCTTGATAGG 59.970 50.000 25.80 23.50 37.17 2.57
2015 8818 0.179000 ATCGACATGGAAGTCCTGGC 59.821 55.000 0.00 0.00 35.07 4.85
2125 8929 3.507162 TGCATAATGTATGGTGGGGAG 57.493 47.619 0.00 0.00 36.68 4.30
2185 9412 4.887748 TGAGACAACCTGAAGAACTGATC 58.112 43.478 0.00 0.00 0.00 2.92
2190 9417 2.805099 CAGCTGAGACAACCTGAAGAAC 59.195 50.000 8.42 0.00 0.00 3.01
2222 9449 8.283291 ACTCGTTAACTTTCTTCTTGCTAATTG 58.717 33.333 3.71 0.00 0.00 2.32
2270 9734 2.742589 GTGAGAAAAGACTTAAGGGCCG 59.257 50.000 7.53 0.00 0.00 6.13
2281 9746 7.921786 TTCTTTCAAAGTCAGTGAGAAAAGA 57.078 32.000 0.00 2.57 0.00 2.52
2304 9769 7.196331 GCTGTACATGTGAAGAAAAGTCTTTT 58.804 34.615 10.38 10.38 44.42 2.27
2368 9840 0.669318 ACACATGGTCGTACGGCTTG 60.669 55.000 20.62 18.83 0.00 4.01
2400 9872 2.682893 GCATCTTGCGGTCCAGTAG 58.317 57.895 0.00 0.00 31.71 2.57


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

AutoCloner maintained by Alex Coulton.