Multiple sequence alignment - TraesCS2B01G102000

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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 TraesCS2B01G102000 chr2B 100.000 2603 0 0 1 2603 63093360 63095962 0.000000e+00 4807.0
1 TraesCS2B01G102000 chr2B 95.816 741 28 1 1862 2599 67554519 67553779 0.000000e+00 1194.0
2 TraesCS2B01G102000 chr2D 90.629 1782 121 25 1 1757 36750138 36751898 0.000000e+00 2324.0
3 TraesCS2B01G102000 chr2D 81.429 350 34 15 2253 2599 32555804 32555483 9.240000e-65 257.0
4 TraesCS2B01G102000 chr2D 94.737 38 0 2 1853 1890 125926161 125926196 1.010000e-04 58.4
5 TraesCS2B01G102000 chr2D 90.476 42 3 1 1849 1890 112341952 112341992 1.000000e-03 54.7
6 TraesCS2B01G102000 chr2A 90.077 1683 118 29 1 1651 41102407 41104072 0.000000e+00 2137.0
7 TraesCS2B01G102000 chr2A 98.026 152 2 1 1701 1852 41104079 41104229 1.990000e-66 263.0
8 TraesCS2B01G102000 chr3D 85.797 345 48 1 2256 2599 552739254 552738910 5.290000e-97 364.0
9 TraesCS2B01G102000 chr6D 87.640 89 10 1 2253 2340 426371264 426371176 4.580000e-18 102.0
10 TraesCS2B01G102000 chr6B 88.679 53 3 3 1851 1902 604707218 604707268 7.780000e-06 62.1
11 TraesCS2B01G102000 chr5B 74.843 159 28 10 1855 2007 618150791 618150639 7.780000e-06 62.1
12 TraesCS2B01G102000 chr7B 86.538 52 6 1 1851 1902 733701261 733701311 3.620000e-04 56.5


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 TraesCS2B01G102000 chr2B 63093360 63095962 2602 False 4807 4807 100.0000 1 2603 1 chr2B.!!$F1 2602
1 TraesCS2B01G102000 chr2B 67553779 67554519 740 True 1194 1194 95.8160 1862 2599 1 chr2B.!!$R1 737
2 TraesCS2B01G102000 chr2D 36750138 36751898 1760 False 2324 2324 90.6290 1 1757 1 chr2D.!!$F1 1756
3 TraesCS2B01G102000 chr2A 41102407 41104229 1822 False 1200 2137 94.0515 1 1852 2 chr2A.!!$F1 1851

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
671 685 0.036294 GGGGACGAAAAGGGAGTCAG 60.036 60.0 0.0 0.0 36.68 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2052 2086 0.468226 TGGAAAAGTCGTGGAGCTGT 59.532 50.0 0.0 0.0 0.0 4.4 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
41 48 0.392706 CCAAAGAAAGTGGGGGTTGC 59.607 55.000 0.00 0.00 32.03 4.17
66 73 4.051922 CCCTTGTTCGCTATTGCTACTAG 58.948 47.826 0.00 2.48 36.97 2.57
75 82 0.815734 ATTGCTACTAGTGGCGACGT 59.184 50.000 22.17 6.05 40.17 4.34
85 92 0.094730 GTGGCGACGTCAATTGCTAC 59.905 55.000 17.16 14.37 33.83 3.58
111 118 1.303888 CATGGCCAAGCTGTGACCT 60.304 57.895 10.96 0.00 0.00 3.85
112 119 1.303888 ATGGCCAAGCTGTGACCTG 60.304 57.895 10.96 0.00 0.00 4.00
113 120 2.072874 ATGGCCAAGCTGTGACCTGT 62.073 55.000 10.96 0.00 0.00 4.00
117 124 2.281070 AAGCTGTGACCTGTGGCG 60.281 61.111 0.00 0.00 0.00 5.69
147 154 5.757886 ACAATTTGTTGTAACTGTCATCGG 58.242 37.500 0.00 0.00 32.60 4.18
154 161 4.217754 TGTAACTGTCATCGGTTTTTGC 57.782 40.909 0.00 0.00 42.38 3.68
161 168 0.179174 CATCGGTTTTTGCTACGGCC 60.179 55.000 0.00 0.00 37.74 6.13
167 174 3.961838 TTTTGCTACGGCCGGCGAT 62.962 57.895 31.76 13.78 37.74 4.58
187 194 5.004726 GCGATGAAATTTGCTACAACCATTC 59.995 40.000 0.00 0.00 0.00 2.67
213 220 0.038892 GAAGCTACAACCCACGACGA 60.039 55.000 0.00 0.00 0.00 4.20
214 221 0.606604 AAGCTACAACCCACGACGAT 59.393 50.000 0.00 0.00 0.00 3.73
215 222 0.108804 AGCTACAACCCACGACGATG 60.109 55.000 0.00 0.00 0.00 3.84
216 223 1.082117 GCTACAACCCACGACGATGG 61.082 60.000 0.00 5.65 39.71 3.51
227 237 1.012234 GACGATGGCGACGATTTGC 60.012 57.895 0.00 0.00 41.64 3.68
234 244 1.663643 TGGCGACGATTTGCTACAATC 59.336 47.619 0.00 0.00 31.91 2.67
262 272 0.373716 CTTTTGCTATGACCGCCGAC 59.626 55.000 0.00 0.00 0.00 4.79
263 273 1.022451 TTTTGCTATGACCGCCGACC 61.022 55.000 0.00 0.00 0.00 4.79
277 287 2.324860 GCCGACCAAATTTGCTACAAC 58.675 47.619 12.92 0.00 0.00 3.32
278 288 2.287909 GCCGACCAAATTTGCTACAACA 60.288 45.455 12.92 0.00 0.00 3.33
288 298 6.484818 AATTTGCTACAACAATTTCATGGC 57.515 33.333 0.00 0.00 0.00 4.40
292 302 3.792956 GCTACAACAATTTCATGGCGATG 59.207 43.478 1.66 1.66 0.00 3.84
293 303 3.235157 ACAACAATTTCATGGCGATGG 57.765 42.857 8.98 0.00 0.00 3.51
311 321 1.702491 GGCCGATGGTAGTTGTTCGC 61.702 60.000 0.00 0.00 0.00 4.70
312 322 1.995991 CCGATGGTAGTTGTTCGCG 59.004 57.895 0.00 0.00 0.00 5.87
313 323 1.418342 CCGATGGTAGTTGTTCGCGG 61.418 60.000 6.13 0.00 0.00 6.46
320 330 1.987770 GTAGTTGTTCGCGGAAATCGA 59.012 47.619 6.13 0.00 42.43 3.59
328 338 0.247695 CGCGGAAATCGAGGAAAAGC 60.248 55.000 0.00 0.00 42.43 3.51
330 340 2.277084 GCGGAAATCGAGGAAAAGCTA 58.723 47.619 0.00 0.00 42.43 3.32
344 354 1.878953 AAGCTACAACTGTTGACGGG 58.121 50.000 26.00 13.08 0.00 5.28
377 387 2.167861 GCAACGACGAGGATGGAGC 61.168 63.158 0.00 0.00 0.00 4.70
395 405 1.215647 CGGAGACTTCCTGGAACGG 59.784 63.158 4.68 0.00 41.67 4.44
407 417 4.054825 GAACGGCCGACGGTGGTA 62.055 66.667 35.90 0.00 46.88 3.25
411 421 3.142838 GGCCGACGGTGGTAGCTA 61.143 66.667 16.73 0.00 0.00 3.32
413 423 2.703798 GCCGACGGTGGTAGCTACA 61.704 63.158 24.75 8.87 0.00 2.74
434 444 1.362224 AAGCATGACTAGTGGGGTGT 58.638 50.000 0.00 0.00 0.00 4.16
441 451 1.479323 GACTAGTGGGGTGTTGCGATA 59.521 52.381 0.00 0.00 0.00 2.92
460 470 1.827789 GCCAGGTGCTCAAACCACA 60.828 57.895 0.00 0.00 43.20 4.17
464 474 1.750778 CAGGTGCTCAAACCACAAACT 59.249 47.619 0.00 0.00 43.20 2.66
481 491 3.239464 TGGTGGCAAGCAGAGACA 58.761 55.556 0.00 0.00 0.00 3.41
482 492 1.071987 TGGTGGCAAGCAGAGACAG 59.928 57.895 0.00 0.00 0.00 3.51
506 516 2.585791 TTATGCGATGGTGCTGCCGA 62.586 55.000 0.00 0.00 41.21 5.54
557 571 1.409427 GTGGAGTACCGATGAAGGAGG 59.591 57.143 0.00 0.00 39.42 4.30
562 576 1.549170 GTACCGATGAAGGAGGTGTGT 59.451 52.381 0.00 0.00 38.90 3.72
575 589 0.041312 GGTGTGTTGCGTGTGATGAC 60.041 55.000 0.00 0.00 0.00 3.06
580 594 1.202521 TGTTGCGTGTGATGACTCTGT 60.203 47.619 0.00 0.00 0.00 3.41
611 625 3.214697 TGTGCTTGTTGTTGTGACTTG 57.785 42.857 0.00 0.00 0.00 3.16
615 629 1.408702 CTTGTTGTTGTGACTTGGGGG 59.591 52.381 0.00 0.00 0.00 5.40
616 630 1.040339 TGTTGTTGTGACTTGGGGGC 61.040 55.000 0.00 0.00 0.00 5.80
617 631 1.040339 GTTGTTGTGACTTGGGGGCA 61.040 55.000 0.00 0.00 0.00 5.36
618 632 0.754957 TTGTTGTGACTTGGGGGCAG 60.755 55.000 0.00 0.00 30.92 4.85
619 633 1.150536 GTTGTGACTTGGGGGCAGA 59.849 57.895 0.00 0.00 30.92 4.26
620 634 0.467290 GTTGTGACTTGGGGGCAGAA 60.467 55.000 0.00 0.00 33.54 3.02
671 685 0.036294 GGGGACGAAAAGGGAGTCAG 60.036 60.000 0.00 0.00 36.68 3.51
743 757 0.476771 AGTTGGACCGGTTGATTGGT 59.523 50.000 9.42 0.00 42.42 3.67
753 767 3.888930 CCGGTTGATTGGTGCCTATTTAT 59.111 43.478 0.00 0.00 0.00 1.40
754 768 4.340950 CCGGTTGATTGGTGCCTATTTATT 59.659 41.667 0.00 0.00 0.00 1.40
757 771 6.507023 GGTTGATTGGTGCCTATTTATTGAG 58.493 40.000 0.00 0.00 0.00 3.02
761 777 8.359875 TGATTGGTGCCTATTTATTGAGAAAA 57.640 30.769 0.00 0.00 0.00 2.29
793 809 8.531530 CAATCTTTTCAAAACGAAAACGATCTT 58.468 29.630 0.00 0.00 46.33 2.40
796 812 9.377383 TCTTTTCAAAACGAAAACGATCTTATC 57.623 29.630 0.00 0.00 46.33 1.75
798 814 9.672086 TTTTCAAAACGAAAACGATCTTATCAT 57.328 25.926 0.00 0.00 46.33 2.45
801 817 9.914923 TCAAAACGAAAACGATCTTATCATATG 57.085 29.630 0.00 0.00 0.00 1.78
802 818 9.158364 CAAAACGAAAACGATCTTATCATATGG 57.842 33.333 2.13 0.00 0.00 2.74
803 819 6.467723 ACGAAAACGATCTTATCATATGGC 57.532 37.500 2.13 0.00 0.00 4.40
804 820 5.118664 ACGAAAACGATCTTATCATATGGCG 59.881 40.000 2.13 0.00 0.00 5.69
805 821 5.444613 CGAAAACGATCTTATCATATGGCGG 60.445 44.000 2.13 0.00 0.00 6.13
806 822 3.526931 ACGATCTTATCATATGGCGGG 57.473 47.619 2.13 0.00 0.00 6.13
807 823 2.205074 CGATCTTATCATATGGCGGGC 58.795 52.381 2.13 0.00 0.00 6.13
808 824 2.418609 CGATCTTATCATATGGCGGGCA 60.419 50.000 6.74 6.74 0.00 5.36
809 825 3.742327 CGATCTTATCATATGGCGGGCAT 60.742 47.826 21.24 21.24 0.00 4.40
810 826 4.501400 CGATCTTATCATATGGCGGGCATA 60.501 45.833 24.07 24.07 0.00 3.14
840 865 3.835378 AACAAAATACTTTACGGCCGG 57.165 42.857 31.76 14.36 0.00 6.13
849 874 3.887335 TTACGGCCGGTTGGAGTGC 62.887 63.158 31.76 0.00 37.49 4.40
873 899 6.989169 GCATATCTCAACCAGATTACAACTCT 59.011 38.462 0.00 0.00 38.95 3.24
874 900 7.497249 GCATATCTCAACCAGATTACAACTCTT 59.503 37.037 0.00 0.00 38.95 2.85
910 936 5.698545 GGTCTCTTATACCAATCTCATGCAC 59.301 44.000 0.00 0.00 36.96 4.57
942 968 6.117488 TCGTCTCTTCCAAACCTAAACTTTT 58.883 36.000 0.00 0.00 0.00 2.27
946 972 6.037830 TCTCTTCCAAACCTAAACTTTTGTCG 59.962 38.462 0.00 0.00 31.86 4.35
983 1009 0.179268 AATACGTCGCGTGCGTTTTC 60.179 50.000 28.30 3.30 41.39 2.29
990 1016 1.727335 TCGCGTGCGTTTTCATCAATA 59.273 42.857 14.47 0.00 40.74 1.90
1320 1352 2.417379 CGACAAGGAGAACATCGTCCAT 60.417 50.000 0.00 0.00 35.02 3.41
1387 1419 4.057428 GGCCGTCACACTCGCTCT 62.057 66.667 0.00 0.00 0.00 4.09
1518 1550 2.426023 GTCCGGTGCAAGGTCACT 59.574 61.111 0.00 0.00 37.16 3.41
1530 1562 0.674534 AGGTCACTGTCGTCCAGAAC 59.325 55.000 10.98 8.44 44.49 3.01
1657 1691 3.120580 CGCATTGTTGGGAGAAAATTTGC 60.121 43.478 0.00 0.00 38.00 3.68
1661 1695 7.041107 GCATTGTTGGGAGAAAATTTGCTATA 58.959 34.615 0.00 0.00 0.00 1.31
1689 1723 8.617809 GTTAACTAATTCCTGTTGTTTCACTCA 58.382 33.333 0.00 0.00 0.00 3.41
1697 1731 4.452455 CCTGTTGTTTCACTCATACCAGTC 59.548 45.833 0.00 0.00 0.00 3.51
1787 1821 0.838608 TCGGTCTACCTCCTCTCTCC 59.161 60.000 0.00 0.00 0.00 3.71
1791 1825 0.254154 TCTACCTCCTCTCTCCCCCA 60.254 60.000 0.00 0.00 0.00 4.96
1852 1886 6.127980 GCCCCTTTCATGTTTCTTAGTTCTAC 60.128 42.308 0.00 0.00 0.00 2.59
1853 1887 6.092259 CCCCTTTCATGTTTCTTAGTTCTACG 59.908 42.308 0.00 0.00 0.00 3.51
1854 1888 6.092259 CCCTTTCATGTTTCTTAGTTCTACGG 59.908 42.308 0.00 0.00 0.00 4.02
1855 1889 6.872020 CCTTTCATGTTTCTTAGTTCTACGGA 59.128 38.462 0.00 0.00 0.00 4.69
1856 1890 7.386848 CCTTTCATGTTTCTTAGTTCTACGGAA 59.613 37.037 0.00 0.00 0.00 4.30
1857 1891 8.665643 TTTCATGTTTCTTAGTTCTACGGAAA 57.334 30.769 0.00 0.00 32.81 3.13
1858 1892 8.665643 TTCATGTTTCTTAGTTCTACGGAAAA 57.334 30.769 0.00 0.00 32.81 2.29
1859 1893 8.665643 TCATGTTTCTTAGTTCTACGGAAAAA 57.334 30.769 0.00 0.00 32.81 1.94
1860 1894 8.553696 TCATGTTTCTTAGTTCTACGGAAAAAC 58.446 33.333 0.00 0.00 32.81 2.43
1867 1901 4.625028 AGTTCTACGGAAAAACTAACGCT 58.375 39.130 0.00 0.00 31.68 5.07
1902 1936 3.128589 AGTTTTGCACTTCATTCACACGT 59.871 39.130 0.00 0.00 27.32 4.49
1913 1947 1.348538 TTCACACGTGCTAATCGCCG 61.349 55.000 17.22 0.00 38.05 6.46
1940 1974 6.795098 ATTTGTAGTGCACGAATCTTACAA 57.205 33.333 18.04 18.04 36.66 2.41
2037 2071 0.600782 ACTTAACGCTTTCGCCCGAA 60.601 50.000 0.00 0.00 39.84 4.30
2063 2097 0.900182 ATCCACTCACAGCTCCACGA 60.900 55.000 0.00 0.00 0.00 4.35
2082 2116 2.817839 CGACTTTTCCAACCCATTCCCT 60.818 50.000 0.00 0.00 0.00 4.20
2139 2176 2.434884 CACTGCAATCTCCGCCGT 60.435 61.111 0.00 0.00 0.00 5.68
2156 2193 1.134694 GTGCGGATTTGAAGGCGAC 59.865 57.895 0.00 0.00 0.00 5.19
2191 2228 1.562672 ATGCGGGAGTAGGCAAAGGT 61.563 55.000 0.00 0.00 43.26 3.50
2258 2295 4.864334 CTCCGCATGGTGGGCCTC 62.864 72.222 4.53 0.00 36.30 4.70
2286 2323 4.735132 TCCGCTTCGCCGAGGTTG 62.735 66.667 0.00 0.00 0.00 3.77
2312 2349 3.712907 GGCCGGTTCCTACTGCCA 61.713 66.667 1.90 0.00 40.00 4.92
2498 2535 1.136305 CCGTTGACGACAGGGATATGT 59.864 52.381 4.91 0.00 43.02 2.29
2563 2600 0.237498 TAGCCGATCTACATCACGCG 59.763 55.000 3.53 3.53 31.80 6.01
2596 2633 2.031919 ATGGAACCGCAACTCGCA 59.968 55.556 0.00 0.00 42.60 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.119684 GTTGCAACCCCCACTTTCTT 58.880 50.000 19.15 0.00 0.00 2.52
41 48 2.262572 GCAATAGCGAACAAGGGTTG 57.737 50.000 0.00 0.00 37.36 3.77
66 73 0.094730 GTAGCAATTGACGTCGCCAC 59.905 55.000 10.34 3.55 0.00 5.01
75 82 5.327616 CCATGAATGGTTGTAGCAATTGA 57.672 39.130 10.34 0.00 43.05 2.57
98 105 2.263741 GCCACAGGTCACAGCTTGG 61.264 63.158 0.00 0.00 31.61 3.61
99 106 2.610694 CGCCACAGGTCACAGCTTG 61.611 63.158 0.00 0.00 0.00 4.01
111 118 1.336440 CAAATTGTTGTCTCCGCCACA 59.664 47.619 0.00 0.00 0.00 4.17
112 119 1.336755 ACAAATTGTTGTCTCCGCCAC 59.663 47.619 0.00 0.00 45.00 5.01
113 120 1.686355 ACAAATTGTTGTCTCCGCCA 58.314 45.000 0.00 0.00 45.00 5.69
132 139 4.336993 AGCAAAAACCGATGACAGTTACAA 59.663 37.500 0.00 0.00 0.00 2.41
139 146 1.801771 CCGTAGCAAAAACCGATGACA 59.198 47.619 0.00 0.00 0.00 3.58
143 150 1.641123 CGGCCGTAGCAAAAACCGAT 61.641 55.000 19.50 0.00 43.19 4.18
147 154 2.126618 GCCGGCCGTAGCAAAAAC 60.127 61.111 26.12 0.00 42.56 2.43
154 161 1.157870 AATTTCATCGCCGGCCGTAG 61.158 55.000 26.12 17.58 38.35 3.51
161 168 2.823196 TGTAGCAAATTTCATCGCCG 57.177 45.000 0.00 0.00 0.00 6.46
167 174 5.798125 TGGAATGGTTGTAGCAAATTTCA 57.202 34.783 0.00 0.00 0.00 2.69
187 194 1.376609 GGGTTGTAGCTTCGCCATGG 61.377 60.000 7.63 7.63 0.00 3.66
194 201 0.038892 TCGTCGTGGGTTGTAGCTTC 60.039 55.000 0.00 0.00 0.00 3.86
202 209 3.687102 TCGCCATCGTCGTGGGTT 61.687 61.111 13.41 0.00 39.73 4.11
207 214 1.153901 AAATCGTCGCCATCGTCGT 60.154 52.632 4.60 0.00 44.86 4.34
213 220 1.732941 TTGTAGCAAATCGTCGCCAT 58.267 45.000 0.00 0.00 0.00 4.40
214 221 1.663643 GATTGTAGCAAATCGTCGCCA 59.336 47.619 0.00 0.00 0.00 5.69
215 222 2.368980 GATTGTAGCAAATCGTCGCC 57.631 50.000 0.00 0.00 0.00 5.54
227 237 3.785505 GCAAAAGCCGATGACGATTGTAG 60.786 47.826 0.00 0.00 42.66 2.74
234 244 1.933181 TCATAGCAAAAGCCGATGACG 59.067 47.619 0.00 0.00 39.43 4.35
237 247 1.003545 CGGTCATAGCAAAAGCCGATG 60.004 52.381 3.49 0.00 41.45 3.84
238 248 1.299541 CGGTCATAGCAAAAGCCGAT 58.700 50.000 3.49 0.00 41.45 4.18
262 272 7.299586 CCATGAAATTGTTGTAGCAAATTTGG 58.700 34.615 19.47 2.11 31.63 3.28
263 273 6.797995 GCCATGAAATTGTTGTAGCAAATTTG 59.202 34.615 14.03 14.03 31.63 2.32
288 298 0.179084 ACAACTACCATCGGCCATCG 60.179 55.000 2.24 0.00 40.90 3.84
292 302 1.702491 GCGAACAACTACCATCGGCC 61.702 60.000 0.00 0.00 35.91 6.13
293 303 1.713830 GCGAACAACTACCATCGGC 59.286 57.895 0.00 0.00 35.91 5.54
297 307 2.172851 TTTCCGCGAACAACTACCAT 57.827 45.000 8.23 0.00 0.00 3.55
299 309 1.060122 CGATTTCCGCGAACAACTACC 59.940 52.381 8.23 0.00 0.00 3.18
311 321 3.259064 TGTAGCTTTTCCTCGATTTCCG 58.741 45.455 0.00 0.00 40.25 4.30
312 322 4.695928 AGTTGTAGCTTTTCCTCGATTTCC 59.304 41.667 0.00 0.00 0.00 3.13
313 323 5.179555 ACAGTTGTAGCTTTTCCTCGATTTC 59.820 40.000 0.00 0.00 0.00 2.17
320 330 3.560068 CGTCAACAGTTGTAGCTTTTCCT 59.440 43.478 13.14 0.00 0.00 3.36
328 338 1.289109 CGCCCCGTCAACAGTTGTAG 61.289 60.000 13.14 8.22 0.00 2.74
330 340 2.590575 CGCCCCGTCAACAGTTGT 60.591 61.111 13.14 0.00 0.00 3.32
344 354 4.704833 TGCCACTGAAGCTCCGCC 62.705 66.667 0.00 0.00 0.00 6.13
355 365 1.079819 CATCCTCGTCGTTGCCACT 60.080 57.895 0.00 0.00 0.00 4.00
357 367 2.225791 CTCCATCCTCGTCGTTGCCA 62.226 60.000 0.00 0.00 0.00 4.92
361 371 2.490217 CGCTCCATCCTCGTCGTT 59.510 61.111 0.00 0.00 0.00 3.85
395 405 2.012902 ATGTAGCTACCACCGTCGGC 62.013 60.000 21.01 0.00 0.00 5.54
409 419 4.345257 ACCCCACTAGTCATGCTTATGTAG 59.655 45.833 0.00 0.00 0.00 2.74
411 421 3.115390 ACCCCACTAGTCATGCTTATGT 58.885 45.455 0.00 0.00 0.00 2.29
413 423 3.115390 ACACCCCACTAGTCATGCTTAT 58.885 45.455 0.00 0.00 0.00 1.73
444 454 1.750778 AGTTTGTGGTTTGAGCACCTG 59.249 47.619 7.68 0.00 45.33 4.00
457 467 0.249155 CTGCTTGCCACCAGTTTGTG 60.249 55.000 0.00 0.00 35.98 3.33
460 470 0.183492 TCTCTGCTTGCCACCAGTTT 59.817 50.000 0.00 0.00 0.00 2.66
464 474 1.071987 CTGTCTCTGCTTGCCACCA 59.928 57.895 0.00 0.00 0.00 4.17
480 490 1.523711 ACCATCGCATAACGCCCTG 60.524 57.895 0.00 0.00 43.23 4.45
481 491 1.523711 CACCATCGCATAACGCCCT 60.524 57.895 0.00 0.00 43.23 5.19
482 492 3.022287 CACCATCGCATAACGCCC 58.978 61.111 0.00 0.00 43.23 6.13
537 548 1.409427 CCTCCTTCATCGGTACTCCAC 59.591 57.143 0.00 0.00 0.00 4.02
557 571 0.937304 AGTCATCACACGCAACACAC 59.063 50.000 0.00 0.00 0.00 3.82
562 576 2.238942 AACAGAGTCATCACACGCAA 57.761 45.000 0.00 0.00 0.00 4.85
575 589 5.065731 ACAAGCACAAGAAGAGAAAACAGAG 59.934 40.000 0.00 0.00 0.00 3.35
580 594 5.643379 ACAACAAGCACAAGAAGAGAAAA 57.357 34.783 0.00 0.00 0.00 2.29
611 625 1.931007 ATCCTTCTGCTTCTGCCCCC 61.931 60.000 0.00 0.00 38.71 5.40
615 629 3.401182 CATCCTATCCTTCTGCTTCTGC 58.599 50.000 0.00 0.00 40.20 4.26
616 630 3.181457 TGCATCCTATCCTTCTGCTTCTG 60.181 47.826 0.00 0.00 34.02 3.02
617 631 3.044156 TGCATCCTATCCTTCTGCTTCT 58.956 45.455 0.00 0.00 34.02 2.85
618 632 3.482156 TGCATCCTATCCTTCTGCTTC 57.518 47.619 0.00 0.00 34.02 3.86
619 633 3.498121 CCATGCATCCTATCCTTCTGCTT 60.498 47.826 0.00 0.00 34.02 3.91
620 634 2.040012 CCATGCATCCTATCCTTCTGCT 59.960 50.000 0.00 0.00 34.02 4.24
671 685 0.036577 CATCTCCCAGCCATCGGATC 60.037 60.000 0.00 0.00 0.00 3.36
782 798 5.163854 CCCGCCATATGATAAGATCGTTTTC 60.164 44.000 3.65 0.00 0.00 2.29
793 809 2.418060 CGTGTATGCCCGCCATATGATA 60.418 50.000 3.65 0.00 38.60 2.15
796 812 1.298157 CCGTGTATGCCCGCCATATG 61.298 60.000 0.00 0.00 38.60 1.78
798 814 2.134933 TCCGTGTATGCCCGCCATA 61.135 57.895 0.00 0.00 35.34 2.74
801 817 3.961838 TTGTCCGTGTATGCCCGCC 62.962 63.158 0.00 0.00 0.00 6.13
802 818 1.579084 TTTTGTCCGTGTATGCCCGC 61.579 55.000 0.00 0.00 0.00 6.13
803 819 0.167251 GTTTTGTCCGTGTATGCCCG 59.833 55.000 0.00 0.00 0.00 6.13
804 820 1.240256 TGTTTTGTCCGTGTATGCCC 58.760 50.000 0.00 0.00 0.00 5.36
805 821 3.357166 TTTGTTTTGTCCGTGTATGCC 57.643 42.857 0.00 0.00 0.00 4.40
806 822 6.146898 AGTATTTTGTTTTGTCCGTGTATGC 58.853 36.000 0.00 0.00 0.00 3.14
807 823 8.568732 AAAGTATTTTGTTTTGTCCGTGTATG 57.431 30.769 0.00 0.00 31.62 2.39
808 824 9.667989 GTAAAGTATTTTGTTTTGTCCGTGTAT 57.332 29.630 0.00 0.00 40.09 2.29
809 825 7.850003 CGTAAAGTATTTTGTTTTGTCCGTGTA 59.150 33.333 0.00 0.00 40.09 2.90
810 826 6.687958 CGTAAAGTATTTTGTTTTGTCCGTGT 59.312 34.615 0.00 0.00 40.09 4.49
840 865 3.609853 TGGTTGAGATATGCACTCCAAC 58.390 45.455 16.09 16.09 33.95 3.77
849 874 8.954950 AAGAGTTGTAATCTGGTTGAGATATG 57.045 34.615 0.00 0.00 40.89 1.78
873 899 0.690762 AGAGACCAAGCCCGCTTAAA 59.309 50.000 0.77 0.00 34.50 1.52
874 900 0.690762 AAGAGACCAAGCCCGCTTAA 59.309 50.000 0.77 0.00 34.50 1.85
942 968 6.673154 TTCTATTCTACAATCGACTCGACA 57.327 37.500 2.53 0.00 39.18 4.35
946 972 7.474948 CGACGTATTCTATTCTACAATCGACTC 59.525 40.741 0.00 0.00 32.22 3.36
983 1009 8.112016 AGATGGCATCTTTCTCAATATTGATG 57.888 34.615 24.01 13.16 35.76 3.07
1320 1352 4.778415 GCGAACTCGAGCTCGGCA 62.778 66.667 32.28 16.52 43.02 5.69
1353 1385 1.305219 GCCACTTTATCAGCGTGCCA 61.305 55.000 0.00 0.00 0.00 4.92
1518 1550 1.069090 GGCACAGTTCTGGACGACA 59.931 57.895 4.82 0.00 0.00 4.35
1527 1559 1.515521 CCCCTTTGACGGCACAGTTC 61.516 60.000 3.27 0.00 0.00 3.01
1530 1562 1.966451 GTCCCCTTTGACGGCACAG 60.966 63.158 0.00 0.00 0.00 3.66
1661 1695 7.281549 AGTGAAACAACAGGAATTAGTTAACGT 59.718 33.333 0.00 0.00 41.43 3.99
1791 1825 2.905880 CCGACTAGACCGCCCGAT 60.906 66.667 0.00 0.00 0.00 4.18
1852 1886 2.658224 CGTGTGAGCGTTAGTTTTTCCG 60.658 50.000 0.00 0.00 0.00 4.30
1853 1887 2.286025 ACGTGTGAGCGTTAGTTTTTCC 59.714 45.455 0.00 0.00 43.04 3.13
1854 1888 3.242188 ACACGTGTGAGCGTTAGTTTTTC 60.242 43.478 22.71 0.00 43.83 2.29
1855 1889 2.674357 ACACGTGTGAGCGTTAGTTTTT 59.326 40.909 22.71 0.00 43.83 1.94
1856 1890 2.273557 ACACGTGTGAGCGTTAGTTTT 58.726 42.857 22.71 0.00 43.83 2.43
1857 1891 1.930567 ACACGTGTGAGCGTTAGTTT 58.069 45.000 22.71 0.00 43.83 2.66
1858 1892 3.654178 ACACGTGTGAGCGTTAGTT 57.346 47.368 22.71 0.00 43.83 2.24
1913 1947 5.283060 AGATTCGTGCACTACAAATCAAC 57.717 39.130 16.19 0.00 0.00 3.18
1940 1974 2.066999 GGAGACCCCGGCTGATTCT 61.067 63.158 0.00 0.00 0.00 2.40
2052 2086 0.468226 TGGAAAAGTCGTGGAGCTGT 59.532 50.000 0.00 0.00 0.00 4.40
2063 2097 3.239449 GAAGGGAATGGGTTGGAAAAGT 58.761 45.455 0.00 0.00 0.00 2.66
2082 2116 2.231380 GGAGAAGGCAGTGGGGGAA 61.231 63.158 0.00 0.00 0.00 3.97
2139 2176 1.003839 AGTCGCCTTCAAATCCGCA 60.004 52.632 0.00 0.00 0.00 5.69
2286 2323 4.735358 GAACCGGCCTCCCCAACC 62.735 72.222 0.00 0.00 0.00 3.77
2299 2336 1.379527 CGGAAATGGCAGTAGGAACC 58.620 55.000 0.00 0.00 0.00 3.62
2563 2600 1.970114 CATGGCCATCTGATCCGGC 60.970 63.158 17.61 9.84 45.47 6.13


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

AutoCloner maintained by Alex Coulton.