Multiple sequence alignment - TraesCS1B01G459800

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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 TraesCS1B01G459800 chr1B 100.000 3781 0 0 1 3781 673783661 673787441 0.000000e+00 6983
1 TraesCS1B01G459800 chr1B 84.094 767 116 5 2031 2794 673750584 673751347 0.000000e+00 736
2 TraesCS1B01G459800 chr1B 90.972 288 22 3 1039 1324 673748439 673748724 5.920000e-103 385
3 TraesCS1B01G459800 chr1D 89.080 2271 142 49 1546 3781 483529051 483531250 0.000000e+00 2723
4 TraesCS1B01G459800 chr1D 89.456 607 41 15 733 1321 483527934 483528535 0.000000e+00 745
5 TraesCS1B01G459800 chr1D 87.814 279 22 7 1045 1323 483520906 483521172 2.190000e-82 316
6 TraesCS1B01G459800 chr1D 81.499 427 36 18 4 408 483526851 483527256 1.020000e-80 311
7 TraesCS1B01G459800 chr1D 94.872 195 8 2 1340 1533 483528587 483528780 1.710000e-78 303
8 TraesCS1B01G459800 chr1D 85.890 163 22 1 1042 1204 483518446 483518607 5.020000e-39 172
9 TraesCS1B01G459800 chr1A 90.369 2004 105 43 1546 3517 580445318 580447265 0.000000e+00 2551
10 TraesCS1B01G459800 chr1A 85.075 1005 78 42 554 1530 580444208 580445168 0.000000e+00 959
11 TraesCS1B01G459800 chr1A 85.569 887 93 18 1687 2571 580448485 580449338 0.000000e+00 896
12 TraesCS1B01G459800 chr1A 82.920 767 125 6 2031 2794 580435847 580436610 0.000000e+00 686
13 TraesCS1B01G459800 chr1A 91.367 278 20 3 1044 1319 580433996 580434271 9.910000e-101 377
14 TraesCS1B01G459800 chr1A 86.471 170 17 3 1042 1207 580426659 580426826 8.340000e-42 182
15 TraesCS1B01G459800 chr1A 86.232 138 11 2 420 556 580444012 580444142 3.940000e-30 143
16 TraesCS1B01G459800 chr6B 92.453 265 17 3 3515 3777 688594584 688594847 3.570000e-100 375
17 TraesCS1B01G459800 chr3B 90.391 281 25 2 3499 3777 206273065 206273345 5.970000e-98 368
18 TraesCS1B01G459800 chr3B 86.975 238 28 3 1083 1319 406871821 406871586 8.050000e-67 265
19 TraesCS1B01G459800 chr7D 91.321 265 22 1 3515 3778 621266972 621266708 9.980000e-96 361
20 TraesCS1B01G459800 chr3D 90.545 275 23 3 3505 3777 536423565 536423838 9.980000e-96 361
21 TraesCS1B01G459800 chr3D 86.555 238 29 3 1083 1319 313100080 313100315 3.750000e-65 259
22 TraesCS1B01G459800 chr3A 91.045 268 21 3 3515 3780 12408996 12408730 3.590000e-95 359
23 TraesCS1B01G459800 chr3A 90.672 268 21 4 3515 3779 465820750 465820484 1.670000e-93 353
24 TraesCS1B01G459800 chr4D 90.706 269 24 1 3510 3777 416431862 416431594 1.290000e-94 357
25 TraesCS1B01G459800 chr6D 90.943 265 23 1 3514 3777 94757180 94757444 4.650000e-94 355


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 TraesCS1B01G459800 chr1B 673783661 673787441 3780 False 6983.00 6983 100.00000 1 3781 1 chr1B.!!$F1 3780
1 TraesCS1B01G459800 chr1B 673748439 673751347 2908 False 560.50 736 87.53300 1039 2794 2 chr1B.!!$F2 1755
2 TraesCS1B01G459800 chr1D 483526851 483531250 4399 False 1020.50 2723 88.72675 4 3781 4 chr1D.!!$F2 3777
3 TraesCS1B01G459800 chr1D 483518446 483521172 2726 False 244.00 316 86.85200 1042 1323 2 chr1D.!!$F1 281
4 TraesCS1B01G459800 chr1A 580444012 580449338 5326 False 1137.25 2551 86.81125 420 3517 4 chr1A.!!$F3 3097
5 TraesCS1B01G459800 chr1A 580433996 580436610 2614 False 531.50 686 87.14350 1044 2794 2 chr1A.!!$F2 1750

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
608 1044 0.041684 CCTCCCTTTCCCCTGCAAAT 59.958 55.0 0.0 0.0 0.00 2.32 F
752 1197 0.532862 ACAGTCCAGCAAGAACACGG 60.533 55.0 0.0 0.0 0.00 4.94 F
1892 4690 0.033642 TATGTGCAAACACCGACCGA 59.966 50.0 0.0 0.0 46.86 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1891 4689 0.044161 GTAACGCACGCACGATCATC 60.044 55.0 4.54 0.0 36.70 2.92 R
2453 5255 0.107017 CCAGGTTCCGCCATGAGAAT 60.107 55.0 0.00 0.0 40.61 2.40 R
3187 5996 0.321298 GTCTTTTGCCCCTGCGTAGA 60.321 55.0 0.53 0.0 41.78 2.59 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 2.872858 GTTTTCTACTCCCATCCGATGC 59.127 50.000 2.53 0.00 0.00 3.91
40 41 2.329267 TCTACTCCCATCCGATGCATT 58.671 47.619 0.00 0.00 0.00 3.56
45 46 4.473444 ACTCCCATCCGATGCATTTTAAT 58.527 39.130 0.00 0.00 0.00 1.40
58 59 7.463119 CGATGCATTTTAATTTGTCGCTGATTT 60.463 33.333 0.00 0.00 0.00 2.17
104 105 6.808008 AATCATCGACAATTGATATGGACC 57.192 37.500 13.59 0.00 32.40 4.46
105 106 5.289083 TCATCGACAATTGATATGGACCA 57.711 39.130 13.59 0.00 0.00 4.02
106 107 5.679601 TCATCGACAATTGATATGGACCAA 58.320 37.500 13.59 0.00 0.00 3.67
108 109 4.450976 TCGACAATTGATATGGACCAAGG 58.549 43.478 13.59 0.00 0.00 3.61
151 152 6.081356 ACCAAATCACCCTAAAATTTCAGGA 58.919 36.000 9.16 0.00 33.42 3.86
162 163 7.540745 CCCTAAAATTTCAGGATTACACAAACG 59.459 37.037 9.16 0.00 33.42 3.60
179 180 6.128282 ACACAAACGTTAATTGCCAGAGATAG 60.128 38.462 0.00 0.00 0.00 2.08
180 181 6.092122 CACAAACGTTAATTGCCAGAGATAGA 59.908 38.462 0.00 0.00 0.00 1.98
181 182 6.313905 ACAAACGTTAATTGCCAGAGATAGAG 59.686 38.462 0.00 0.00 0.00 2.43
182 183 5.854010 ACGTTAATTGCCAGAGATAGAGA 57.146 39.130 0.00 0.00 0.00 3.10
192 193 7.652524 TGCCAGAGATAGAGATTACCATATC 57.347 40.000 0.00 0.00 0.00 1.63
193 194 6.609212 TGCCAGAGATAGAGATTACCATATCC 59.391 42.308 0.00 0.00 0.00 2.59
242 243 4.974645 ATGCGTTGAAGAATATCCCCTA 57.025 40.909 0.00 0.00 0.00 3.53
248 249 5.765182 CGTTGAAGAATATCCCCTAAATGCT 59.235 40.000 0.00 0.00 0.00 3.79
289 311 6.909909 ACACTTTTGGTAGCTACTAAAATGC 58.090 36.000 34.37 15.31 42.83 3.56
299 321 6.995511 AGCTACTAAAATGCCGATAAACAA 57.004 33.333 0.00 0.00 0.00 2.83
347 369 7.217200 AGCATTCATTTACGTCAGTATACCAT 58.783 34.615 0.00 0.00 32.12 3.55
349 371 9.151471 GCATTCATTTACGTCAGTATACCATAT 57.849 33.333 0.00 0.00 32.12 1.78
390 412 3.289836 CAACTCATGCATATCCCACCAA 58.710 45.455 0.00 0.00 0.00 3.67
408 430 6.483974 CCCACCAAATGCGTGTATTTATACTA 59.516 38.462 1.95 0.00 34.41 1.82
409 431 7.349711 CCACCAAATGCGTGTATTTATACTAC 58.650 38.462 1.95 0.00 34.41 2.73
412 780 9.252962 ACCAAATGCGTGTATTTATACTACTAC 57.747 33.333 1.95 0.00 34.41 2.73
426 794 9.845740 TTTATACTACTACTTGTACGTATGGGA 57.154 33.333 0.00 0.00 32.77 4.37
427 795 7.976135 ATACTACTACTTGTACGTATGGGAG 57.024 40.000 0.00 0.93 31.10 4.30
456 824 3.234630 TTGTCGTCTTGCTCCCCGG 62.235 63.158 0.00 0.00 0.00 5.73
473 841 2.506472 GTCCCGGAGAGGATTGGC 59.494 66.667 0.73 0.00 45.00 4.52
474 842 2.768344 TCCCGGAGAGGATTGGCC 60.768 66.667 0.73 0.00 45.00 5.36
476 844 2.190578 CCGGAGAGGATTGGCCAC 59.809 66.667 3.88 0.00 45.00 5.01
563 999 2.359967 GCTCCTTGGGTAGCTCCGT 61.360 63.158 0.00 0.00 35.80 4.69
564 1000 1.817209 CTCCTTGGGTAGCTCCGTC 59.183 63.158 0.00 0.00 37.00 4.79
595 1031 3.449918 CTTCTTCTTCTTCCTCCTCCCT 58.550 50.000 0.00 0.00 0.00 4.20
597 1033 3.875571 TCTTCTTCTTCCTCCTCCCTTT 58.124 45.455 0.00 0.00 0.00 3.11
599 1035 2.552367 TCTTCTTCCTCCTCCCTTTCC 58.448 52.381 0.00 0.00 0.00 3.13
600 1036 1.562008 CTTCTTCCTCCTCCCTTTCCC 59.438 57.143 0.00 0.00 0.00 3.97
601 1037 0.253207 TCTTCCTCCTCCCTTTCCCC 60.253 60.000 0.00 0.00 0.00 4.81
602 1038 0.253394 CTTCCTCCTCCCTTTCCCCT 60.253 60.000 0.00 0.00 0.00 4.79
603 1039 0.550147 TTCCTCCTCCCTTTCCCCTG 60.550 60.000 0.00 0.00 0.00 4.45
604 1040 2.684499 CCTCCTCCCTTTCCCCTGC 61.684 68.421 0.00 0.00 0.00 4.85
607 1043 1.071314 TCCTCCCTTTCCCCTGCAAA 61.071 55.000 0.00 0.00 0.00 3.68
608 1044 0.041684 CCTCCCTTTCCCCTGCAAAT 59.958 55.000 0.00 0.00 0.00 2.32
610 1046 1.551883 CTCCCTTTCCCCTGCAAATTG 59.448 52.381 0.00 0.00 0.00 2.32
613 1049 1.066645 CCTTTCCCCTGCAAATTGAGC 60.067 52.381 0.00 0.00 0.00 4.26
635 1071 4.246458 CGAGAAAAGTAAACAGGAGAGGG 58.754 47.826 0.00 0.00 0.00 4.30
693 1129 1.153489 CTGCCTGTCCGGATCTGTG 60.153 63.158 7.81 0.00 33.16 3.66
695 1131 2.660064 GCCTGTCCGGATCTGTGGT 61.660 63.158 7.81 0.00 33.16 4.16
698 1134 1.341531 CCTGTCCGGATCTGTGGTATC 59.658 57.143 7.81 0.00 33.16 2.24
699 1135 1.341531 CTGTCCGGATCTGTGGTATCC 59.658 57.143 7.81 0.00 39.71 2.59
701 1137 0.826256 TCCGGATCTGTGGTATCCCG 60.826 60.000 0.00 0.00 39.92 5.14
703 1139 1.006102 GGATCTGTGGTATCCCGCG 60.006 63.158 0.00 0.00 44.67 6.46
708 1144 3.845259 GTGGTATCCCGCGGCTCA 61.845 66.667 22.85 9.80 0.00 4.26
709 1145 3.078196 TGGTATCCCGCGGCTCAA 61.078 61.111 22.85 4.72 0.00 3.02
710 1146 2.588034 GGTATCCCGCGGCTCAAC 60.588 66.667 22.85 14.36 0.00 3.18
711 1147 2.960129 GTATCCCGCGGCTCAACG 60.960 66.667 22.85 4.77 0.00 4.10
752 1197 0.532862 ACAGTCCAGCAAGAACACGG 60.533 55.000 0.00 0.00 0.00 4.94
754 1199 1.070786 GTCCAGCAAGAACACGGGA 59.929 57.895 0.00 0.00 0.00 5.14
774 1219 2.428171 GAGGGCAAATTAATCTGCAGCA 59.572 45.455 15.38 0.00 40.46 4.41
778 1223 4.142182 GGGCAAATTAATCTGCAGCAAGTA 60.142 41.667 15.38 0.00 40.46 2.24
823 1268 4.025401 CGCGCCATTAATCCCGCC 62.025 66.667 18.30 6.30 43.16 6.13
845 1291 1.552792 CACACCTTCCTTCTCCTCCTC 59.447 57.143 0.00 0.00 0.00 3.71
846 1292 1.199615 CACCTTCCTTCTCCTCCTCC 58.800 60.000 0.00 0.00 0.00 4.30
892 1349 2.967615 GCCTAATCTGACGCCGCC 60.968 66.667 0.00 0.00 0.00 6.13
924 1389 4.452733 GTCTTGACCGGCGGGGAG 62.453 72.222 31.78 22.84 39.97 4.30
978 1447 2.435059 GACAGCCCGTTCCTGCTC 60.435 66.667 0.00 0.00 35.12 4.26
1034 1518 4.867599 CTACGACGGGAAGCCGGC 62.868 72.222 21.89 21.89 37.94 6.13
1336 3149 4.324974 GGTACGCACGTTGCTTTAATTA 57.675 40.909 0.00 0.00 42.25 1.40
1337 3150 4.900664 GGTACGCACGTTGCTTTAATTAT 58.099 39.130 0.00 0.00 42.25 1.28
1353 3168 7.569226 GCTTTAATTATTGCCATTAATGCGGTG 60.569 37.037 10.11 0.00 37.44 4.94
1380 3269 7.979444 AATAATCGTGGACCAAGTATAATGG 57.021 36.000 7.33 4.62 43.84 3.16
1409 3298 4.624024 GTGAATGATGTGCTGTTTTGGATG 59.376 41.667 0.00 0.00 0.00 3.51
1531 3421 2.795329 CAACTGCCTCCAGGTAAACAT 58.205 47.619 0.00 0.00 43.53 2.71
1532 3422 3.872240 GCAACTGCCTCCAGGTAAACATA 60.872 47.826 0.00 0.00 43.53 2.29
1534 3424 3.182152 ACTGCCTCCAGGTAAACATACT 58.818 45.455 0.00 0.00 43.53 2.12
1536 3426 2.504175 TGCCTCCAGGTAAACATACTCC 59.496 50.000 0.00 0.00 37.57 3.85
1539 3429 4.202233 GCCTCCAGGTAAACATACTCCTAC 60.202 50.000 0.00 0.00 37.57 3.18
1542 3432 6.070424 CCTCCAGGTAAACATACTCCTACAAA 60.070 42.308 0.00 0.00 0.00 2.83
1545 3435 7.675195 TCCAGGTAAACATACTCCTACAAAGTA 59.325 37.037 0.00 0.00 33.94 2.24
1546 3436 7.763071 CCAGGTAAACATACTCCTACAAAGTAC 59.237 40.741 0.00 0.00 32.30 2.73
1547 3437 8.308931 CAGGTAAACATACTCCTACAAAGTACA 58.691 37.037 0.00 0.00 32.30 2.90
1548 3438 8.873144 AGGTAAACATACTCCTACAAAGTACAA 58.127 33.333 0.00 0.00 32.30 2.41
1566 4039 4.535526 ACAATAAAATGGTGGCAGGAAC 57.464 40.909 0.00 0.00 0.00 3.62
1656 4147 2.749076 TGATATGTCTGTTGCACCTTGC 59.251 45.455 0.00 0.00 45.29 4.01
1659 4150 1.102809 TGTCTGTTGCACCTTGCCTG 61.103 55.000 0.00 0.00 44.23 4.85
1890 4688 0.519961 GGTATGTGCAAACACCGACC 59.480 55.000 0.00 0.00 46.86 4.79
1891 4689 0.165079 GTATGTGCAAACACCGACCG 59.835 55.000 0.00 0.00 46.86 4.79
1892 4690 0.033642 TATGTGCAAACACCGACCGA 59.966 50.000 0.00 0.00 46.86 4.69
1906 4704 3.976375 CCGATGATCGTGCGTGCG 61.976 66.667 14.27 0.00 38.40 5.34
1908 4706 2.788176 CGATGATCGTGCGTGCGTT 61.788 57.895 6.68 0.00 34.72 4.84
1911 4709 0.734597 ATGATCGTGCGTGCGTTACA 60.735 50.000 0.00 0.00 0.00 2.41
1915 4713 1.203065 CGTGCGTGCGTTACATGTT 59.797 52.632 2.30 0.00 37.62 2.71
1916 4714 0.383737 CGTGCGTGCGTTACATGTTT 60.384 50.000 2.30 0.00 37.62 2.83
1917 4715 1.136584 CGTGCGTGCGTTACATGTTTA 60.137 47.619 2.30 0.00 37.62 2.01
1943 4741 6.088016 ACGTCTATGTTGTACTTGGTGTTA 57.912 37.500 0.00 0.00 0.00 2.41
2114 4916 2.692709 TCCTCTCCATCTCCATCCTC 57.307 55.000 0.00 0.00 0.00 3.71
2435 5237 1.452108 CATGGAGAAAGGGTCGGCC 60.452 63.158 0.00 0.00 0.00 6.13
2621 5423 2.343101 CCCGTCGTCATGTACAACATT 58.657 47.619 0.00 0.00 36.53 2.71
2785 5587 5.530171 GTGACCATGTCATCAGCTGAATTAT 59.470 40.000 22.50 10.14 44.63 1.28
2806 5608 7.561021 TTATTTTCTTGCCGCATATGTAGAA 57.439 32.000 4.29 0.00 0.00 2.10
2864 5668 1.276989 CAGGTAAAGTAGGCCGGTCAA 59.723 52.381 9.71 0.00 0.00 3.18
2876 5680 0.609131 CCGGTCAAAGCCCATCAACT 60.609 55.000 0.00 0.00 0.00 3.16
2950 5754 1.138069 TGTCTGAGCAACACCGAAAGA 59.862 47.619 0.00 0.00 0.00 2.52
2958 5762 3.004734 AGCAACACCGAAAGAAATTCTGG 59.995 43.478 0.00 0.00 37.57 3.86
2964 5768 7.787725 ACACCGAAAGAAATTCTGGTATATC 57.212 36.000 0.00 0.00 40.53 1.63
3045 5851 6.024552 TCAGCAAATAACCTAAAAAGGCAG 57.975 37.500 0.00 0.00 0.00 4.85
3048 5854 4.994217 GCAAATAACCTAAAAAGGCAGCAA 59.006 37.500 0.00 0.00 0.00 3.91
3063 5869 2.420022 GCAGCAAATCACGTGGTTCTAT 59.580 45.455 15.69 0.26 0.00 1.98
3064 5870 3.119849 GCAGCAAATCACGTGGTTCTATT 60.120 43.478 15.69 3.94 0.00 1.73
3065 5871 4.615912 GCAGCAAATCACGTGGTTCTATTT 60.616 41.667 15.69 10.24 0.00 1.40
3066 5872 5.460646 CAGCAAATCACGTGGTTCTATTTT 58.539 37.500 15.69 0.00 0.00 1.82
3067 5873 5.343058 CAGCAAATCACGTGGTTCTATTTTG 59.657 40.000 15.69 9.35 0.00 2.44
3068 5874 5.009610 AGCAAATCACGTGGTTCTATTTTGT 59.990 36.000 15.69 0.00 0.00 2.83
3181 5987 8.890718 GCTAAGCATCATAATATCACATCACAT 58.109 33.333 0.00 0.00 0.00 3.21
3205 6014 0.618458 ATCTACGCAGGGGCAAAAGA 59.382 50.000 0.00 0.00 41.24 2.52
3234 6043 2.805671 CCAGTTGCAGACAATAACGACA 59.194 45.455 0.00 0.00 38.27 4.35
3235 6044 3.436704 CCAGTTGCAGACAATAACGACAT 59.563 43.478 0.00 0.00 38.27 3.06
3236 6045 4.397382 CAGTTGCAGACAATAACGACATG 58.603 43.478 0.00 0.00 38.27 3.21
3237 6046 4.152223 CAGTTGCAGACAATAACGACATGA 59.848 41.667 0.00 0.00 38.27 3.07
3238 6047 4.754618 AGTTGCAGACAATAACGACATGAA 59.245 37.500 0.00 0.00 38.27 2.57
3239 6048 5.412594 AGTTGCAGACAATAACGACATGAAT 59.587 36.000 0.00 0.00 38.27 2.57
3240 6049 5.469373 TGCAGACAATAACGACATGAATC 57.531 39.130 0.00 0.00 0.00 2.52
3356 6184 0.323725 ACTCATGGCGCCCTGATTTT 60.324 50.000 30.87 17.34 0.00 1.82
3357 6185 0.101759 CTCATGGCGCCCTGATTTTG 59.898 55.000 30.87 17.56 0.00 2.44
3358 6186 1.519898 CATGGCGCCCTGATTTTGC 60.520 57.895 25.69 0.00 0.00 3.68
3478 6309 8.419076 AATATGTTTTGATGAAAATTACCGCC 57.581 30.769 0.00 0.00 33.63 6.13
3482 6314 6.201806 TGTTTTGATGAAAATTACCGCCAAAG 59.798 34.615 0.00 0.00 33.63 2.77
3554 6386 5.881923 AAGAGTGTACTTCCAACTTGGTA 57.118 39.130 7.72 0.00 39.03 3.25
3594 7422 3.791973 AAATTTGACCGAGTTTGTGCA 57.208 38.095 0.00 0.00 0.00 4.57
3608 7436 9.729023 CCGAGTTTGTGCAAAAATATATCAATA 57.271 29.630 5.11 0.00 31.33 1.90
3679 7508 8.874744 AATCTAATGCTACTATTTGATGGCAT 57.125 30.769 0.00 0.00 41.30 4.40
3768 7905 3.121738 AGTACACCCTTTCAAAGACGG 57.878 47.619 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.230455 AGAAAACATGTGAATTGGGGGAA 58.770 39.130 0.00 0.00 0.00 3.97
45 46 6.854496 ACTTTGTACTAAATCAGCGACAAA 57.146 33.333 0.00 0.00 39.38 2.83
79 80 7.936301 TGGTCCATATCAATTGTCGATGATTTA 59.064 33.333 5.13 0.00 37.46 1.40
80 81 6.772233 TGGTCCATATCAATTGTCGATGATTT 59.228 34.615 5.13 0.00 37.46 2.17
91 92 3.618120 CCCCCTTGGTCCATATCAATT 57.382 47.619 0.00 0.00 0.00 2.32
112 113 8.410912 GGGTGATTTGGTTATGATTAAACTACC 58.589 37.037 0.00 0.00 0.00 3.18
123 124 9.369904 CTGAAATTTTAGGGTGATTTGGTTATG 57.630 33.333 2.06 0.00 0.00 1.90
128 129 6.603940 TCCTGAAATTTTAGGGTGATTTGG 57.396 37.500 24.45 1.72 34.76 3.28
151 152 6.205853 TCTCTGGCAATTAACGTTTGTGTAAT 59.794 34.615 5.91 0.00 0.00 1.89
162 163 8.150945 TGGTAATCTCTATCTCTGGCAATTAAC 58.849 37.037 0.00 0.00 0.00 2.01
179 180 8.910351 AAGCTTACAAAGGATATGGTAATCTC 57.090 34.615 0.00 0.00 0.00 2.75
225 226 7.001073 AGAGCATTTAGGGGATATTCTTCAAC 58.999 38.462 0.00 0.00 0.00 3.18
229 230 7.399674 AGAAGAGCATTTAGGGGATATTCTT 57.600 36.000 0.00 0.00 0.00 2.52
287 309 2.029200 TGTCCTACGTTGTTTATCGGCA 60.029 45.455 0.00 0.00 0.00 5.69
289 311 3.061697 GCTTGTCCTACGTTGTTTATCGG 59.938 47.826 0.00 0.00 0.00 4.18
299 321 2.550208 CCTTTCTTGGCTTGTCCTACGT 60.550 50.000 0.00 0.00 35.26 3.57
353 375 7.148255 TGCATGAGTTGTTTCTCGCTATTTATT 60.148 33.333 0.00 0.00 37.28 1.40
363 385 4.883585 TGGGATATGCATGAGTTGTTTCTC 59.116 41.667 10.16 0.00 35.28 2.87
373 395 2.629137 GCATTTGGTGGGATATGCATGA 59.371 45.455 10.16 0.00 42.18 3.07
377 399 1.032014 ACGCATTTGGTGGGATATGC 58.968 50.000 0.00 0.00 43.02 3.14
408 430 4.397417 GTGACTCCCATACGTACAAGTAGT 59.603 45.833 0.00 0.00 0.00 2.73
409 431 4.201990 GGTGACTCCCATACGTACAAGTAG 60.202 50.000 0.00 0.00 0.00 2.57
412 780 2.494471 TGGTGACTCCCATACGTACAAG 59.506 50.000 0.00 0.00 34.77 3.16
425 793 1.859080 GACGACAACACTTGGTGACTC 59.141 52.381 0.07 0.00 36.96 3.36
426 794 1.480954 AGACGACAACACTTGGTGACT 59.519 47.619 0.07 0.00 36.96 3.41
427 795 1.935933 AGACGACAACACTTGGTGAC 58.064 50.000 0.07 0.00 36.96 3.67
456 824 2.506472 GCCAATCCTCTCCGGGAC 59.494 66.667 0.00 0.00 38.30 4.46
474 842 4.342378 CCCATATCTATCTATCCACCGGTG 59.658 50.000 28.26 28.26 0.00 4.94
476 844 3.322254 GCCCATATCTATCTATCCACCGG 59.678 52.174 0.00 0.00 0.00 5.28
485 853 5.245751 CACAACTCTCTGCCCATATCTATCT 59.754 44.000 0.00 0.00 0.00 1.98
548 916 1.033574 CTAGACGGAGCTACCCAAGG 58.966 60.000 0.00 0.00 34.64 3.61
549 917 1.765230 ACTAGACGGAGCTACCCAAG 58.235 55.000 0.00 0.00 34.64 3.61
563 999 6.555360 AGGAAGAAGAAGAAGGTCAAACTAGA 59.445 38.462 0.00 0.00 0.00 2.43
564 1000 6.764379 AGGAAGAAGAAGAAGGTCAAACTAG 58.236 40.000 0.00 0.00 0.00 2.57
595 1031 0.602562 CGCTCAATTTGCAGGGGAAA 59.397 50.000 0.00 0.00 0.00 3.13
597 1033 0.677731 CTCGCTCAATTTGCAGGGGA 60.678 55.000 10.63 7.64 0.00 4.81
599 1035 1.167851 TTCTCGCTCAATTTGCAGGG 58.832 50.000 0.00 0.00 0.00 4.45
600 1036 2.995466 TTTCTCGCTCAATTTGCAGG 57.005 45.000 0.00 0.00 0.00 4.85
601 1037 3.893720 ACTTTTCTCGCTCAATTTGCAG 58.106 40.909 0.00 0.00 0.00 4.41
602 1038 3.988379 ACTTTTCTCGCTCAATTTGCA 57.012 38.095 0.00 0.00 0.00 4.08
603 1039 5.685511 TGTTTACTTTTCTCGCTCAATTTGC 59.314 36.000 0.00 0.00 0.00 3.68
604 1040 6.360681 CCTGTTTACTTTTCTCGCTCAATTTG 59.639 38.462 0.00 0.00 0.00 2.32
607 1043 5.305585 TCCTGTTTACTTTTCTCGCTCAAT 58.694 37.500 0.00 0.00 0.00 2.57
608 1044 4.699637 TCCTGTTTACTTTTCTCGCTCAA 58.300 39.130 0.00 0.00 0.00 3.02
610 1046 4.557205 TCTCCTGTTTACTTTTCTCGCTC 58.443 43.478 0.00 0.00 0.00 5.03
613 1049 4.246458 CCCTCTCCTGTTTACTTTTCTCG 58.754 47.826 0.00 0.00 0.00 4.04
695 1131 4.215742 CCGTTGAGCCGCGGGATA 62.216 66.667 29.38 0.00 43.85 2.59
708 1144 1.750399 GATCATGTGGCCTGCCGTT 60.750 57.895 3.32 0.00 39.42 4.44
709 1145 2.124570 GATCATGTGGCCTGCCGT 60.125 61.111 3.32 0.00 39.42 5.68
710 1146 2.903855 GGATCATGTGGCCTGCCG 60.904 66.667 3.32 0.00 39.42 5.69
711 1147 1.826921 CTGGATCATGTGGCCTGCC 60.827 63.158 3.32 0.00 0.00 4.85
712 1148 2.487532 GCTGGATCATGTGGCCTGC 61.488 63.158 3.32 13.68 39.01 4.85
714 1150 2.005266 AGGCTGGATCATGTGGCCT 61.005 57.895 3.32 11.54 46.95 5.19
715 1151 0.536006 GTAGGCTGGATCATGTGGCC 60.536 60.000 0.00 0.00 42.74 5.36
716 1152 0.181114 TGTAGGCTGGATCATGTGGC 59.819 55.000 0.00 0.00 0.00 5.01
752 1197 2.223900 GCTGCAGATTAATTTGCCCTCC 60.224 50.000 23.78 9.15 39.54 4.30
754 1199 2.459644 TGCTGCAGATTAATTTGCCCT 58.540 42.857 23.78 0.00 39.54 5.19
774 1219 2.359531 GAGATCGTGGCTGCTACTACTT 59.640 50.000 14.29 0.00 0.00 2.24
778 1223 1.395826 GGGAGATCGTGGCTGCTACT 61.396 60.000 14.29 0.00 0.00 2.57
823 1268 0.615850 GAGGAGAAGGAAGGTGTGGG 59.384 60.000 0.00 0.00 0.00 4.61
897 1354 0.028242 CGGTCAAGACTCTCGATCGG 59.972 60.000 16.41 6.26 29.70 4.18
924 1389 1.069258 GTTCGGATCCATCGACCCC 59.931 63.158 13.41 0.00 36.30 4.95
962 1431 2.925170 AGAGCAGGAACGGGCTGT 60.925 61.111 0.00 0.00 43.27 4.40
1324 2741 7.793427 CGCATTAATGGCAATAATTAAAGCAAC 59.207 33.333 17.02 0.00 41.12 4.17
1332 3145 4.100808 ACCACCGCATTAATGGCAATAATT 59.899 37.500 17.02 0.00 36.96 1.40
1336 3149 1.484038 ACCACCGCATTAATGGCAAT 58.516 45.000 17.02 0.00 36.96 3.56
1337 3150 2.130272 TACCACCGCATTAATGGCAA 57.870 45.000 17.02 0.00 36.96 4.52
1353 3168 8.932791 CATTATACTTGGTCCACGATTATTACC 58.067 37.037 1.66 0.00 0.00 2.85
1380 3269 2.404789 CACATCATTCACGCCGCC 59.595 61.111 0.00 0.00 0.00 6.13
1409 3298 2.754375 CCTACCCACACCACACCC 59.246 66.667 0.00 0.00 0.00 4.61
1532 3422 9.010029 CACCATTTTATTGTACTTTGTAGGAGT 57.990 33.333 0.00 0.00 0.00 3.85
1534 3424 7.094118 GCCACCATTTTATTGTACTTTGTAGGA 60.094 37.037 0.00 0.00 0.00 2.94
1536 3426 7.598278 TGCCACCATTTTATTGTACTTTGTAG 58.402 34.615 0.00 0.00 0.00 2.74
1539 3429 5.868801 CCTGCCACCATTTTATTGTACTTTG 59.131 40.000 0.00 0.00 0.00 2.77
1542 3432 4.929479 TCCTGCCACCATTTTATTGTACT 58.071 39.130 0.00 0.00 0.00 2.73
1545 3435 3.900601 TGTTCCTGCCACCATTTTATTGT 59.099 39.130 0.00 0.00 0.00 2.71
1546 3436 4.220382 TCTGTTCCTGCCACCATTTTATTG 59.780 41.667 0.00 0.00 0.00 1.90
1547 3437 4.415596 TCTGTTCCTGCCACCATTTTATT 58.584 39.130 0.00 0.00 0.00 1.40
1548 3438 4.046286 TCTGTTCCTGCCACCATTTTAT 57.954 40.909 0.00 0.00 0.00 1.40
1551 3441 2.450476 GATCTGTTCCTGCCACCATTT 58.550 47.619 0.00 0.00 0.00 2.32
1566 4039 3.607422 TGTGCTTTTTCACACGATCTG 57.393 42.857 0.00 0.00 41.57 2.90
1656 4147 3.113322 CGTTGATATGTACACGTCCAGG 58.887 50.000 0.00 0.00 0.00 4.45
1659 4150 3.789756 CACTCGTTGATATGTACACGTCC 59.210 47.826 0.00 0.00 0.00 4.79
1890 4688 1.468340 TAACGCACGCACGATCATCG 61.468 55.000 5.22 5.22 46.93 3.84
1891 4689 0.044161 GTAACGCACGCACGATCATC 60.044 55.000 4.54 0.00 36.70 2.92
1892 4690 0.734597 TGTAACGCACGCACGATCAT 60.735 50.000 4.54 0.00 36.70 2.45
1915 4713 8.306038 ACACCAAGTACAACATAGACGTAATAA 58.694 33.333 0.00 0.00 0.00 1.40
1916 4714 7.829725 ACACCAAGTACAACATAGACGTAATA 58.170 34.615 0.00 0.00 0.00 0.98
1917 4715 6.694447 ACACCAAGTACAACATAGACGTAAT 58.306 36.000 0.00 0.00 0.00 1.89
1943 4741 8.980481 TTCTTCTTCCTAGTTCTTTTTCATGT 57.020 30.769 0.00 0.00 0.00 3.21
1974 4776 7.873719 TGACCAAGTCTATCTCAAACAAAAA 57.126 32.000 0.00 0.00 33.15 1.94
1975 4777 7.873719 TTGACCAAGTCTATCTCAAACAAAA 57.126 32.000 0.00 0.00 33.15 2.44
1977 4779 7.453393 AGATTGACCAAGTCTATCTCAAACAA 58.547 34.615 13.57 0.00 46.25 2.83
1985 4787 8.855110 TCAGATCTAAGATTGACCAAGTCTATC 58.145 37.037 10.06 10.06 42.17 2.08
1986 4788 8.774546 TCAGATCTAAGATTGACCAAGTCTAT 57.225 34.615 0.00 0.00 33.15 1.98
1987 4789 8.595362 TTCAGATCTAAGATTGACCAAGTCTA 57.405 34.615 0.00 0.00 33.15 2.59
1988 4790 7.487822 TTCAGATCTAAGATTGACCAAGTCT 57.512 36.000 0.00 0.00 33.15 3.24
1989 4791 8.729805 AATTCAGATCTAAGATTGACCAAGTC 57.270 34.615 0.00 0.00 0.00 3.01
1990 4792 9.525826 AAAATTCAGATCTAAGATTGACCAAGT 57.474 29.630 0.00 0.00 0.00 3.16
2177 4979 1.604378 CGCCTTCACCATCTTCCCT 59.396 57.895 0.00 0.00 0.00 4.20
2447 5249 1.301244 CCGCCATGAGAATCTCCCG 60.301 63.158 7.91 5.44 34.92 5.14
2453 5255 0.107017 CCAGGTTCCGCCATGAGAAT 60.107 55.000 0.00 0.00 40.61 2.40
2785 5587 4.697828 TGTTCTACATATGCGGCAAGAAAA 59.302 37.500 13.83 7.66 0.00 2.29
2829 5631 9.871238 CTACTTTACCTGAGCTATAACAAGAAA 57.129 33.333 0.00 0.00 0.00 2.52
2864 5668 3.569701 CAGTTTGTGTAGTTGATGGGCTT 59.430 43.478 0.00 0.00 0.00 4.35
2958 5762 8.438676 AGCCAATTACAGAAACACAGATATAC 57.561 34.615 0.00 0.00 0.00 1.47
2964 5768 5.437289 TTGAGCCAATTACAGAAACACAG 57.563 39.130 0.00 0.00 0.00 3.66
3045 5851 5.219633 ACAAAATAGAACCACGTGATTTGC 58.780 37.500 19.30 0.00 31.52 3.68
3048 5854 7.762159 ACAAAAACAAAATAGAACCACGTGATT 59.238 29.630 19.30 5.75 0.00 2.57
3181 5987 1.220749 GCCCCTGCGTAGATTGTGA 59.779 57.895 0.53 0.00 0.00 3.58
3187 5996 0.321298 GTCTTTTGCCCCTGCGTAGA 60.321 55.000 0.53 0.00 41.78 2.59
3213 6022 2.805671 TGTCGTTATTGTCTGCAACTGG 59.194 45.455 0.00 0.00 37.44 4.00
3216 6025 4.661993 TCATGTCGTTATTGTCTGCAAC 57.338 40.909 0.00 0.00 37.44 4.17
3234 6043 5.650703 TGCAGTGAAGTTCATCATGATTCAT 59.349 36.000 9.18 0.00 30.84 2.57
3235 6044 5.005094 TGCAGTGAAGTTCATCATGATTCA 58.995 37.500 9.18 4.99 0.00 2.57
3236 6045 5.106436 TGTGCAGTGAAGTTCATCATGATTC 60.106 40.000 9.18 2.10 0.00 2.52
3237 6046 4.763279 TGTGCAGTGAAGTTCATCATGATT 59.237 37.500 9.18 0.00 0.00 2.57
3238 6047 4.329392 TGTGCAGTGAAGTTCATCATGAT 58.671 39.130 9.18 1.18 0.00 2.45
3239 6048 3.742385 TGTGCAGTGAAGTTCATCATGA 58.258 40.909 9.18 0.00 0.00 3.07
3240 6049 4.696899 ATGTGCAGTGAAGTTCATCATG 57.303 40.909 9.18 9.66 0.00 3.07
3333 6154 2.041922 AGGGCGCCATGAGTCCTA 60.042 61.111 30.85 0.00 0.00 2.94
3334 6155 3.790437 CAGGGCGCCATGAGTCCT 61.790 66.667 36.51 14.80 0.00 3.85
3356 6184 6.595772 AAATATTGCTTTTGTGTTTTCGCA 57.404 29.167 0.00 0.00 38.65 5.10
3357 6185 7.122550 TCAAAATATTGCTTTTGTGTTTTCGC 58.877 30.769 8.28 0.00 43.43 4.70
3358 6186 9.483062 TTTCAAAATATTGCTTTTGTGTTTTCG 57.517 25.926 8.28 0.00 43.43 3.46
3457 6288 5.201713 TGGCGGTAATTTTCATCAAAACA 57.798 34.783 0.00 0.00 34.24 2.83
3464 6295 5.913137 TGATCTTTGGCGGTAATTTTCAT 57.087 34.783 0.00 0.00 0.00 2.57
3471 6302 6.119536 AGAAATACATGATCTTTGGCGGTAA 58.880 36.000 0.00 0.00 0.00 2.85
3476 6307 6.484643 TGAGCTAGAAATACATGATCTTTGGC 59.515 38.462 0.00 3.95 0.00 4.52
3478 6309 8.016229 GCATGAGCTAGAAATACATGATCTTTG 58.984 37.037 12.15 0.00 40.13 2.77
3482 6314 6.649973 AGTGCATGAGCTAGAAATACATGATC 59.350 38.462 12.15 5.29 42.74 2.92
3554 6386 8.534496 CAAATTTTGAGATATTTTGACCCTCCT 58.466 33.333 2.88 0.00 30.69 3.69
3722 7859 8.879342 TTCAACTTTGTTGAAAAGTCAGAAAA 57.121 26.923 19.44 0.00 39.36 2.29
3724 7861 8.141268 ACTTTCAACTTTGTTGAAAAGTCAGAA 58.859 29.630 27.35 15.58 44.67 3.02
3726 7863 7.873739 ACTTTCAACTTTGTTGAAAAGTCAG 57.126 32.000 27.35 20.98 44.67 3.51
3736 7873 6.599356 AAAGGGTGTACTTTCAACTTTGTT 57.401 33.333 0.00 0.00 35.92 2.83
3763 7900 4.759893 GGTGTACTCCCTCCGTCT 57.240 61.111 2.33 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.