Multiple sequence alignment - TraesCS2B01G201300

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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 TraesCS2B01G201300 chr2B 100.000 2017 0 0 650 2666 180545881 180547897 0.000000e+00 3725.0
1 TraesCS2B01G201300 chr2B 100.000 258 0 0 1 258 180545232 180545489 6.680000e-131 477.0
2 TraesCS2B01G201300 chr2B 76.730 679 126 20 1025 1678 180539921 180540592 1.520000e-92 350.0
3 TraesCS2B01G201300 chr2D 92.874 842 50 7 965 1800 126958554 126959391 0.000000e+00 1214.0
4 TraesCS2B01G201300 chr2D 81.452 620 54 28 2054 2649 126966070 126966652 4.050000e-123 451.0
5 TraesCS2B01G201300 chr2D 76.618 680 126 23 1025 1678 126946654 126947326 7.070000e-91 344.0
6 TraesCS2B01G201300 chr2D 94.860 214 11 0 6 219 126952784 126952997 4.250000e-88 335.0
7 TraesCS2B01G201300 chr2D 91.163 215 16 1 701 912 126953440 126953654 3.360000e-74 289.0
8 TraesCS2B01G201300 chr2D 86.408 206 16 7 1805 2007 126965538 126965734 5.780000e-52 215.0
9 TraesCS2B01G201300 chr2A 93.462 673 41 1 987 1656 133484869 133485541 0.000000e+00 996.0
10 TraesCS2B01G201300 chr2A 84.006 694 72 14 1853 2520 133488648 133489328 4.840000e-177 630.0
11 TraesCS2B01G201300 chr2A 75.806 682 129 23 1025 1678 133473118 133473791 1.990000e-81 313.0
12 TraesCS2B01G201300 chr2A 90.850 153 14 0 1658 1810 133488492 133488644 3.480000e-49 206.0
13 TraesCS2B01G201300 chr2A 82.427 239 19 8 1 238 133483852 133484068 1.260000e-43 187.0
14 TraesCS2B01G201300 chr2A 86.325 117 16 0 796 912 133484283 133484399 7.750000e-26 128.0
15 TraesCS2B01G201300 chr7B 73.199 694 148 23 1936 2600 384649855 384650539 1.610000e-52 217.0
16 TraesCS2B01G201300 chr5A 73.639 588 119 18 2039 2596 651862137 651861556 7.530000e-46 195.0
17 TraesCS2B01G201300 chr4A 73.504 585 116 25 2031 2585 613501620 613501045 4.530000e-43 185.0
18 TraesCS2B01G201300 chrUn 86.713 143 17 2 756 897 48427550 48427691 9.880000e-35 158.0
19 TraesCS2B01G201300 chr5D 72.878 483 95 19 2132 2585 552909167 552908692 1.660000e-27 134.0
20 TraesCS2B01G201300 chr5D 75.130 193 47 1 2399 2591 393638402 393638593 3.660000e-14 89.8
21 TraesCS2B01G201300 chr6D 74.317 183 33 12 2204 2378 154379786 154379610 6.160000e-07 65.8


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 TraesCS2B01G201300 chr2B 180545232 180547897 2665 False 2101.0 3725 100.0000 1 2666 2 chr2B.!!$F2 2665
1 TraesCS2B01G201300 chr2B 180539921 180540592 671 False 350.0 350 76.7300 1025 1678 1 chr2B.!!$F1 653
2 TraesCS2B01G201300 chr2D 126958554 126959391 837 False 1214.0 1214 92.8740 965 1800 1 chr2D.!!$F2 835
3 TraesCS2B01G201300 chr2D 126946654 126947326 672 False 344.0 344 76.6180 1025 1678 1 chr2D.!!$F1 653
4 TraesCS2B01G201300 chr2D 126965538 126966652 1114 False 333.0 451 83.9300 1805 2649 2 chr2D.!!$F4 844
5 TraesCS2B01G201300 chr2D 126952784 126953654 870 False 312.0 335 93.0115 6 912 2 chr2D.!!$F3 906
6 TraesCS2B01G201300 chr2A 133483852 133489328 5476 False 429.4 996 87.4140 1 2520 5 chr2A.!!$F2 2519
7 TraesCS2B01G201300 chr2A 133473118 133473791 673 False 313.0 313 75.8060 1025 1678 1 chr2A.!!$F1 653
8 TraesCS2B01G201300 chr7B 384649855 384650539 684 False 217.0 217 73.1990 1936 2600 1 chr7B.!!$F1 664

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
783 811 0.104487 TAACTGGCGAACGTTCACCA 59.896 50.0 30.49 30.49 37.08 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 5559 0.326264 ACAAGGAGCGGATGAAGCTT 59.674 50.0 0.0 0.0 46.13 3.74 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
97 99 1.183549 TCCCAAGAAGAGCCGACTAC 58.816 55.000 0.00 0.00 0.00 2.73
99 101 1.550976 CCCAAGAAGAGCCGACTACTT 59.449 52.381 0.00 0.00 0.00 2.24
102 104 0.533032 AGAAGAGCCGACTACTTGCC 59.467 55.000 0.00 0.00 0.00 4.52
109 111 1.369091 CCGACTACTTGCCATGCACC 61.369 60.000 0.00 0.00 38.71 5.01
114 116 1.888512 CTACTTGCCATGCACCAAAGT 59.111 47.619 9.88 9.88 38.71 2.66
123 125 1.021202 TGCACCAAAGTTGAAGACGG 58.979 50.000 0.00 0.00 0.00 4.79
128 130 2.604174 AAAGTTGAAGACGGCGGCG 61.604 57.895 31.06 31.06 0.00 6.46
184 186 4.971125 GCCTCATACGGGAGCGGC 62.971 72.222 0.00 0.00 33.47 6.53
193 195 2.262303 CGGGAGCGGCCTAGAGTAG 61.262 68.421 0.00 0.00 36.66 2.57
238 240 1.524863 CTGAGGTTGACCGGTCGAGT 61.525 60.000 28.70 17.34 42.08 4.18
239 241 1.080705 GAGGTTGACCGGTCGAGTG 60.081 63.158 28.70 0.00 42.08 3.51
240 242 1.521450 GAGGTTGACCGGTCGAGTGA 61.521 60.000 28.70 8.90 42.08 3.41
241 243 1.111116 AGGTTGACCGGTCGAGTGAA 61.111 55.000 28.70 14.77 42.08 3.18
242 244 0.942884 GGTTGACCGGTCGAGTGAAC 60.943 60.000 28.70 24.26 31.50 3.18
243 245 0.249155 GTTGACCGGTCGAGTGAACA 60.249 55.000 28.70 7.20 32.43 3.18
244 246 0.677288 TTGACCGGTCGAGTGAACAT 59.323 50.000 28.70 0.00 0.00 2.71
245 247 1.536940 TGACCGGTCGAGTGAACATA 58.463 50.000 28.70 4.91 0.00 2.29
246 248 2.097036 TGACCGGTCGAGTGAACATAT 58.903 47.619 28.70 0.00 0.00 1.78
247 249 3.281158 TGACCGGTCGAGTGAACATATA 58.719 45.455 28.70 4.13 0.00 0.86
249 251 5.065235 TGACCGGTCGAGTGAACATATATA 58.935 41.667 28.70 2.96 0.00 0.86
250 252 5.180680 TGACCGGTCGAGTGAACATATATAG 59.819 44.000 28.70 0.00 0.00 1.31
251 253 4.458295 ACCGGTCGAGTGAACATATATAGG 59.542 45.833 0.00 0.00 0.00 2.57
252 254 4.142447 CCGGTCGAGTGAACATATATAGGG 60.142 50.000 0.00 0.00 0.00 3.53
253 255 4.698780 CGGTCGAGTGAACATATATAGGGA 59.301 45.833 0.00 0.00 0.00 4.20
256 258 5.125739 GTCGAGTGAACATATATAGGGAGGG 59.874 48.000 0.00 0.00 0.00 4.30
707 735 2.676471 GCAGGCGGTTCCATTGGT 60.676 61.111 1.86 0.00 37.29 3.67
711 739 0.402504 AGGCGGTTCCATTGGTTGTA 59.597 50.000 1.86 0.00 37.29 2.41
719 747 5.234752 GGTTCCATTGGTTGTAAATCCAAC 58.765 41.667 1.86 0.00 44.80 3.77
737 765 6.249035 TCCAACGGTTCAAATAGAATTGAC 57.751 37.500 0.00 0.00 38.95 3.18
743 771 5.793457 CGGTTCAAATAGAATTGACCGAAAC 59.207 40.000 17.88 3.86 45.82 2.78
746 774 7.308348 GGTTCAAATAGAATTGACCGAAACTGA 60.308 37.037 0.00 0.00 38.95 3.41
771 799 5.632244 TTTTTCCGGAAATAGTAACTGGC 57.368 39.130 29.37 0.00 0.00 4.85
772 800 2.589798 TCCGGAAATAGTAACTGGCG 57.410 50.000 0.00 0.00 0.00 5.69
773 801 2.101783 TCCGGAAATAGTAACTGGCGA 58.898 47.619 0.00 0.00 0.00 5.54
774 802 2.496871 TCCGGAAATAGTAACTGGCGAA 59.503 45.455 0.00 0.00 0.00 4.70
775 803 2.606272 CCGGAAATAGTAACTGGCGAAC 59.394 50.000 0.00 0.00 0.00 3.95
776 804 2.280708 CGGAAATAGTAACTGGCGAACG 59.719 50.000 0.00 0.00 0.00 3.95
777 805 3.256558 GGAAATAGTAACTGGCGAACGT 58.743 45.455 0.00 0.00 0.00 3.99
778 806 3.681417 GGAAATAGTAACTGGCGAACGTT 59.319 43.478 0.00 0.00 0.00 3.99
779 807 4.201656 GGAAATAGTAACTGGCGAACGTTC 60.202 45.833 18.47 18.47 0.00 3.95
780 808 3.581024 ATAGTAACTGGCGAACGTTCA 57.419 42.857 26.71 8.47 0.00 3.18
781 809 1.494824 AGTAACTGGCGAACGTTCAC 58.505 50.000 26.71 17.89 0.00 3.18
782 810 0.509929 GTAACTGGCGAACGTTCACC 59.490 55.000 25.14 25.14 0.00 4.02
783 811 0.104487 TAACTGGCGAACGTTCACCA 59.896 50.000 30.49 30.49 37.08 4.17
785 813 2.280524 TGGCGAACGTTCACCAGG 60.281 61.111 29.41 13.81 34.66 4.45
786 814 3.047877 GGCGAACGTTCACCAGGG 61.048 66.667 26.51 11.62 29.86 4.45
787 815 2.029964 GCGAACGTTCACCAGGGA 59.970 61.111 26.71 0.00 0.00 4.20
788 816 2.027625 GCGAACGTTCACCAGGGAG 61.028 63.158 26.71 9.79 0.00 4.30
789 817 2.027625 CGAACGTTCACCAGGGAGC 61.028 63.158 26.71 0.00 0.00 4.70
790 818 1.070786 GAACGTTCACCAGGGAGCA 59.929 57.895 23.12 0.00 0.00 4.26
791 819 0.534203 GAACGTTCACCAGGGAGCAA 60.534 55.000 23.12 0.00 0.00 3.91
792 820 0.818040 AACGTTCACCAGGGAGCAAC 60.818 55.000 0.00 0.00 0.00 4.17
793 821 1.071471 CGTTCACCAGGGAGCAACT 59.929 57.895 0.00 0.00 0.00 3.16
794 822 1.230635 CGTTCACCAGGGAGCAACTG 61.231 60.000 0.00 0.00 35.74 3.16
795 823 1.228245 TTCACCAGGGAGCAACTGC 60.228 57.895 0.00 0.00 42.49 4.40
796 824 2.674380 CACCAGGGAGCAACTGCC 60.674 66.667 0.00 0.00 42.52 4.85
797 825 3.177884 ACCAGGGAGCAACTGCCA 61.178 61.111 7.92 0.00 44.71 4.92
798 826 2.360852 CCAGGGAGCAACTGCCAG 60.361 66.667 7.92 0.00 44.71 4.85
799 827 3.060615 CAGGGAGCAACTGCCAGC 61.061 66.667 7.92 0.00 44.71 4.85
800 828 4.357279 AGGGAGCAACTGCCAGCC 62.357 66.667 7.92 0.00 44.71 4.85
801 829 4.666253 GGGAGCAACTGCCAGCCA 62.666 66.667 0.00 0.00 41.77 4.75
802 830 2.598394 GGAGCAACTGCCAGCCAA 60.598 61.111 0.00 0.00 43.38 4.52
803 831 2.633509 GGAGCAACTGCCAGCCAAG 61.634 63.158 0.00 0.00 43.38 3.61
820 848 3.603365 GGCCTAAACTGCCGCATT 58.397 55.556 0.00 0.00 39.48 3.56
823 851 1.266989 GGCCTAAACTGCCGCATTATC 59.733 52.381 0.00 0.00 39.48 1.75
833 861 3.664107 TGCCGCATTATCTTGATCCTAC 58.336 45.455 0.00 0.00 0.00 3.18
838 866 4.376413 CGCATTATCTTGATCCTACGTTGC 60.376 45.833 0.00 0.00 0.00 4.17
843 871 3.937814 TCTTGATCCTACGTTGCATGTT 58.062 40.909 0.00 0.00 0.00 2.71
845 873 1.737236 TGATCCTACGTTGCATGTTGC 59.263 47.619 0.00 0.00 45.29 4.17
897 925 1.787012 CCATGGCAGTTCTGCAAAAC 58.213 50.000 23.23 0.00 36.33 2.43
917 1030 0.255890 GGCCAGCCAGTTTCCTGATA 59.744 55.000 3.12 0.00 41.50 2.15
945 1058 4.862574 GGCGATTCCAATAAAACAAACTCC 59.137 41.667 0.00 0.00 34.01 3.85
970 1388 1.735376 GCCGGCTAGAGTGGATCGAA 61.735 60.000 22.15 0.00 0.00 3.71
971 1389 0.962489 CCGGCTAGAGTGGATCGAAT 59.038 55.000 0.00 0.00 0.00 3.34
972 1390 1.068194 CCGGCTAGAGTGGATCGAATC 60.068 57.143 0.00 0.00 0.00 2.52
990 1413 1.700955 TCCTCAGATAGGGTTACGCC 58.299 55.000 0.00 0.00 46.55 5.68
994 1417 0.956633 CAGATAGGGTTACGCCGCTA 59.043 55.000 0.00 0.00 38.44 4.26
1015 1438 2.436646 CCATGTCGGCGCCTCTTT 60.437 61.111 26.68 3.66 0.00 2.52
1029 1452 1.699634 CCTCTTTTGGACAGAGACCCA 59.300 52.381 0.00 0.00 40.39 4.51
1035 1458 2.300967 GGACAGAGACCCATGCCCA 61.301 63.158 0.00 0.00 0.00 5.36
1146 1569 2.819595 AATGGCGCGCGAATCAGT 60.820 55.556 37.18 23.24 0.00 3.41
1475 1901 3.055719 CAACTTGGCCACGGCGAT 61.056 61.111 16.62 0.00 43.06 4.58
1548 2409 2.359011 GGGGGTAGCTGGTTTGGG 59.641 66.667 0.00 0.00 0.00 4.12
1554 2415 1.230017 TAGCTGGTTTGGGGGCCTA 60.230 57.895 0.84 0.00 0.00 3.93
1579 2443 2.355615 GGCAAGGAGAAGGAGAAGAAGG 60.356 54.545 0.00 0.00 0.00 3.46
1738 5551 3.315191 CACTCGGTTTCAGGAAAATGTGT 59.685 43.478 0.00 0.00 31.33 3.72
1746 5559 7.262048 GGTTTCAGGAAAATGTGTTGTCTTTA 58.738 34.615 0.00 0.00 31.33 1.85
1752 5565 7.168135 CAGGAAAATGTGTTGTCTTTAAGCTTC 59.832 37.037 0.00 0.00 0.00 3.86
1758 5571 3.188460 TGTTGTCTTTAAGCTTCATCCGC 59.812 43.478 0.00 0.00 0.00 5.54
1772 5585 1.740025 CATCCGCTCCTTGTTTCTTCC 59.260 52.381 0.00 0.00 0.00 3.46
1774 5587 1.351017 TCCGCTCCTTGTTTCTTCCAT 59.649 47.619 0.00 0.00 0.00 3.41
1788 5601 2.373836 TCTTCCATTTTCACGGGAGGAA 59.626 45.455 6.02 6.02 34.33 3.36
1805 5618 1.268032 GGAAGTGGCAATTATCGCGTG 60.268 52.381 5.77 0.00 0.00 5.34
1840 5653 3.645286 GCAGGTTCGTGCGGTTTA 58.355 55.556 1.90 0.00 32.74 2.01
1841 5654 1.495951 GCAGGTTCGTGCGGTTTAG 59.504 57.895 1.90 0.00 32.74 1.85
1842 5655 1.226030 GCAGGTTCGTGCGGTTTAGT 61.226 55.000 1.90 0.00 32.74 2.24
1843 5656 0.788391 CAGGTTCGTGCGGTTTAGTC 59.212 55.000 0.00 0.00 0.00 2.59
1844 5657 0.390124 AGGTTCGTGCGGTTTAGTCA 59.610 50.000 0.00 0.00 0.00 3.41
1845 5658 1.001633 AGGTTCGTGCGGTTTAGTCAT 59.998 47.619 0.00 0.00 0.00 3.06
1846 5659 1.127951 GGTTCGTGCGGTTTAGTCATG 59.872 52.381 0.00 0.00 0.00 3.07
1847 5660 0.793861 TTCGTGCGGTTTAGTCATGC 59.206 50.000 0.00 0.00 0.00 4.06
1850 5663 1.156736 GTGCGGTTTAGTCATGCTGT 58.843 50.000 0.00 0.00 0.00 4.40
1870 5683 3.188460 TGTTCTTGCACGGATTTAGCTTC 59.812 43.478 0.00 0.00 0.00 3.86
1884 5697 6.747739 GGATTTAGCTTCGTTTTTCCATTCTC 59.252 38.462 0.00 0.00 0.00 2.87
1924 5739 7.639945 ACAGAGTTAAGTTTGTGACTTTATGC 58.360 34.615 5.71 0.00 46.34 3.14
1981 5797 4.511527 TCCTCAATCTCAGCTTCACAATC 58.488 43.478 0.00 0.00 0.00 2.67
1988 5804 4.965814 TCTCAGCTTCACAATCTTCACTT 58.034 39.130 0.00 0.00 0.00 3.16
1989 5805 6.101650 TCTCAGCTTCACAATCTTCACTTA 57.898 37.500 0.00 0.00 0.00 2.24
2016 6140 3.563223 TCCTACTAATAGCCTCAACGCT 58.437 45.455 0.00 0.00 43.09 5.07
2023 6147 1.254975 TAGCCTCAACGCTGTAGCCA 61.255 55.000 0.00 0.00 40.08 4.75
2037 6161 4.858692 GCTGTAGCCAATTATGTGTTGTTG 59.141 41.667 0.00 0.00 34.31 3.33
2107 6235 3.433513 AGTTATCCTAGAACCGTTCGC 57.566 47.619 5.62 0.00 34.02 4.70
2156 6284 5.485620 GGGTAGTATTCAAGACCGACTTTT 58.514 41.667 0.00 0.00 36.61 2.27
2174 6302 9.724839 CCGACTTTTAAAAGACTTGTGATAAAA 57.275 29.630 29.97 0.00 39.31 1.52
2197 6333 3.429547 CCAAATGGTCGTTGTTCCAACAA 60.430 43.478 7.76 0.55 45.88 2.83
2251 6388 3.769536 ACGCGAATGGATCCAAAATTTC 58.230 40.909 20.67 16.43 0.00 2.17
2270 6407 7.876936 AATTTCGTCACTAGAGGTAGTATGA 57.123 36.000 0.00 0.00 37.40 2.15
2313 6454 9.383519 GGACATAGATCATTACTTTCTGACAAA 57.616 33.333 0.00 0.00 0.00 2.83
2342 6483 1.613630 CTACACCAGGCTGACCCCT 60.614 63.158 17.94 0.00 36.11 4.79
2347 6493 1.303643 CCAGGCTGACCCCTTCAAC 60.304 63.158 17.94 0.00 36.11 3.18
2454 6634 7.338440 TCTTTATCTTGCAATATGTCGATCG 57.662 36.000 9.36 9.36 0.00 3.69
2463 6643 5.176774 TGCAATATGTCGATCGTACAATTCC 59.823 40.000 15.94 10.56 0.00 3.01
2591 6771 3.412386 TGGTTTAGAGAAGCCAAAGAGC 58.588 45.455 0.00 0.00 42.43 4.09
2616 6796 1.881973 CGAAGTGGCATGGAATATGGG 59.118 52.381 0.00 0.00 0.00 4.00
2624 6804 0.110486 ATGGAATATGGGGTGTCGGC 59.890 55.000 0.00 0.00 0.00 5.54
2644 6824 2.755103 GCCCAAGAAATTAGGTGGACTG 59.245 50.000 3.39 0.00 32.54 3.51
2649 6829 3.474920 AGAAATTAGGTGGACTGGGGAT 58.525 45.455 0.00 0.00 0.00 3.85
2650 6830 3.459969 AGAAATTAGGTGGACTGGGGATC 59.540 47.826 0.00 0.00 0.00 3.36
2651 6831 1.821088 ATTAGGTGGACTGGGGATCC 58.179 55.000 1.92 1.92 36.70 3.36
2655 6835 4.679500 TGGACTGGGGATCCACAA 57.321 55.556 19.55 0.00 41.47 3.33
2656 6836 2.074967 TGGACTGGGGATCCACAAC 58.925 57.895 19.55 14.66 41.47 3.32
2657 6837 0.475632 TGGACTGGGGATCCACAACT 60.476 55.000 19.55 5.77 41.47 3.16
2658 6838 0.698818 GGACTGGGGATCCACAACTT 59.301 55.000 19.55 5.02 38.32 2.66
2659 6839 1.075536 GGACTGGGGATCCACAACTTT 59.924 52.381 19.55 2.17 38.32 2.66
2660 6840 2.490902 GGACTGGGGATCCACAACTTTT 60.491 50.000 19.55 0.00 38.32 2.27
2661 6841 3.230976 GACTGGGGATCCACAACTTTTT 58.769 45.455 19.55 0.00 38.32 1.94
2663 6843 3.117131 ACTGGGGATCCACAACTTTTTCT 60.117 43.478 19.55 0.00 38.32 2.52
2664 6844 3.496331 TGGGGATCCACAACTTTTTCTC 58.504 45.455 16.35 0.00 38.32 2.87
2665 6845 2.826128 GGGGATCCACAACTTTTTCTCC 59.174 50.000 15.23 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.567615 AGTCATTAAGCACCGGACTTCT 59.432 45.455 9.46 1.41 35.41 2.85
79 81 1.187087 AGTAGTCGGCTCTTCTTGGG 58.813 55.000 0.00 0.00 0.00 4.12
94 96 1.888512 ACTTTGGTGCATGGCAAGTAG 59.111 47.619 0.00 0.00 41.47 2.57
97 99 1.068895 TCAACTTTGGTGCATGGCAAG 59.931 47.619 0.00 0.00 41.47 4.01
99 101 1.068895 CTTCAACTTTGGTGCATGGCA 59.931 47.619 0.00 0.00 35.60 4.92
102 104 2.605338 CCGTCTTCAACTTTGGTGCATG 60.605 50.000 0.00 0.00 0.00 4.06
109 111 1.082104 GCCGCCGTCTTCAACTTTG 60.082 57.895 0.00 0.00 0.00 2.77
150 152 2.182537 CCTTGCCATCGCCTTTGC 59.817 61.111 0.00 0.00 0.00 3.68
151 153 2.182537 GCCTTGCCATCGCCTTTG 59.817 61.111 0.00 0.00 0.00 2.77
173 175 1.699054 TACTCTAGGCCGCTCCCGTA 61.699 60.000 0.00 0.00 34.51 4.02
175 177 2.203308 TACTCTAGGCCGCTCCCG 60.203 66.667 0.00 0.00 34.51 5.14
177 179 0.467659 TTCCTACTCTAGGCCGCTCC 60.468 60.000 0.00 0.00 45.82 4.70
193 195 1.408822 CCTTCACCAGGGCATAGTTCC 60.409 57.143 0.00 0.00 39.39 3.62
194 196 2.044123 CCTTCACCAGGGCATAGTTC 57.956 55.000 0.00 0.00 39.39 3.01
707 735 7.747155 TCTATTTGAACCGTTGGATTTACAA 57.253 32.000 0.00 0.00 0.00 2.41
711 739 7.812669 GTCAATTCTATTTGAACCGTTGGATTT 59.187 33.333 0.00 0.00 37.36 2.17
719 747 5.539582 TTCGGTCAATTCTATTTGAACCG 57.460 39.130 15.59 15.59 43.60 4.44
753 781 2.101783 TCGCCAGTTACTATTTCCGGA 58.898 47.619 0.00 0.00 0.00 5.14
756 784 3.256558 ACGTTCGCCAGTTACTATTTCC 58.743 45.455 0.00 0.00 0.00 3.13
757 785 4.386652 TGAACGTTCGCCAGTTACTATTTC 59.613 41.667 22.48 0.00 0.00 2.17
758 786 4.151157 GTGAACGTTCGCCAGTTACTATTT 59.849 41.667 27.45 0.00 0.00 1.40
761 789 2.664916 GTGAACGTTCGCCAGTTACTA 58.335 47.619 27.45 2.14 0.00 1.82
762 790 1.494824 GTGAACGTTCGCCAGTTACT 58.505 50.000 27.45 0.00 0.00 2.24
770 798 2.027625 CTCCCTGGTGAACGTTCGC 61.028 63.158 29.23 29.23 36.98 4.70
771 799 2.027625 GCTCCCTGGTGAACGTTCG 61.028 63.158 22.48 8.70 0.00 3.95
772 800 0.534203 TTGCTCCCTGGTGAACGTTC 60.534 55.000 21.42 21.42 0.00 3.95
773 801 0.818040 GTTGCTCCCTGGTGAACGTT 60.818 55.000 0.00 0.00 0.00 3.99
774 802 1.227853 GTTGCTCCCTGGTGAACGT 60.228 57.895 0.00 0.00 0.00 3.99
775 803 1.071471 AGTTGCTCCCTGGTGAACG 59.929 57.895 0.00 0.00 0.00 3.95
776 804 1.518903 GCAGTTGCTCCCTGGTGAAC 61.519 60.000 0.00 0.00 38.21 3.18
777 805 1.228245 GCAGTTGCTCCCTGGTGAA 60.228 57.895 0.00 0.00 38.21 3.18
778 806 2.431683 GCAGTTGCTCCCTGGTGA 59.568 61.111 0.00 0.00 38.21 4.02
779 807 2.674380 GGCAGTTGCTCCCTGGTG 60.674 66.667 3.88 0.00 41.70 4.17
780 808 3.177884 TGGCAGTTGCTCCCTGGT 61.178 61.111 3.88 0.00 41.70 4.00
781 809 2.360852 CTGGCAGTTGCTCCCTGG 60.361 66.667 6.28 0.00 41.70 4.45
782 810 3.060615 GCTGGCAGTTGCTCCCTG 61.061 66.667 17.16 0.00 41.70 4.45
783 811 4.357279 GGCTGGCAGTTGCTCCCT 62.357 66.667 17.16 0.00 41.70 4.20
784 812 4.666253 TGGCTGGCAGTTGCTCCC 62.666 66.667 17.16 7.99 41.70 4.30
785 813 2.598394 TTGGCTGGCAGTTGCTCC 60.598 61.111 17.16 8.75 41.70 4.70
786 814 2.633509 CCTTGGCTGGCAGTTGCTC 61.634 63.158 17.16 0.00 41.70 4.26
787 815 2.599578 CCTTGGCTGGCAGTTGCT 60.600 61.111 17.16 0.00 41.70 3.91
795 823 1.598701 GCAGTTTAGGCCTTGGCTGG 61.599 60.000 12.58 0.00 39.30 4.85
796 824 1.885871 GCAGTTTAGGCCTTGGCTG 59.114 57.895 12.58 17.40 39.30 4.85
797 825 4.423231 GCAGTTTAGGCCTTGGCT 57.577 55.556 12.58 3.32 42.39 4.75
810 838 2.105477 AGGATCAAGATAATGCGGCAGT 59.895 45.455 9.25 8.81 0.00 4.40
816 844 4.511454 TGCAACGTAGGATCAAGATAATGC 59.489 41.667 0.00 0.00 0.00 3.56
820 848 5.276461 ACATGCAACGTAGGATCAAGATA 57.724 39.130 0.00 0.00 0.00 1.98
823 851 3.728864 GCAACATGCAACGTAGGATCAAG 60.729 47.826 0.00 0.00 44.26 3.02
838 866 4.986034 AGTGTGAAAATGTCATGCAACATG 59.014 37.500 4.81 1.05 39.76 3.21
843 871 4.915158 TTGAGTGTGAAAATGTCATGCA 57.085 36.364 0.00 0.00 38.90 3.96
853 881 8.825745 GGCATTTCTTTAATTTTGAGTGTGAAA 58.174 29.630 0.00 0.00 0.00 2.69
889 917 3.562779 CTGGCTGGCCGTTTTGCAG 62.563 63.158 7.14 0.00 39.42 4.41
945 1058 1.065928 CACTCTAGCCGGCGGTTAG 59.934 63.158 35.22 35.22 37.76 2.34
972 1390 0.314302 CGGCGTAACCCTATCTGAGG 59.686 60.000 0.00 0.00 46.25 3.86
973 1391 0.318784 GCGGCGTAACCCTATCTGAG 60.319 60.000 9.37 0.00 33.26 3.35
1015 1438 1.685224 GGCATGGGTCTCTGTCCAA 59.315 57.895 0.00 0.00 36.54 3.53
1035 1458 0.316522 CATCCTCGATGATGCGGTCT 59.683 55.000 16.24 0.00 42.09 3.85
1554 2415 1.573108 TCTCCTTCTCCTTGCCGAAT 58.427 50.000 0.00 0.00 0.00 3.34
1567 2428 1.298014 CGCTGGCCTTCTTCTCCTT 59.702 57.895 3.32 0.00 0.00 3.36
1685 5498 3.450457 AGACCAGAGAGCAGTCCAATTAG 59.550 47.826 0.00 0.00 0.00 1.73
1738 5551 3.674997 AGCGGATGAAGCTTAAAGACAA 58.325 40.909 0.00 0.00 43.24 3.18
1746 5559 0.326264 ACAAGGAGCGGATGAAGCTT 59.674 50.000 0.00 0.00 46.13 3.74
1752 5565 1.740025 GGAAGAAACAAGGAGCGGATG 59.260 52.381 0.00 0.00 0.00 3.51
1758 5571 5.215160 CGTGAAAATGGAAGAAACAAGGAG 58.785 41.667 0.00 0.00 0.00 3.69
1772 5585 1.812571 CCACTTCCTCCCGTGAAAATG 59.187 52.381 0.00 0.00 33.04 2.32
1774 5587 0.536460 GCCACTTCCTCCCGTGAAAA 60.536 55.000 0.00 0.00 33.04 2.29
1788 5601 0.744414 AGCACGCGATAATTGCCACT 60.744 50.000 15.93 0.00 36.91 4.00
1805 5618 2.010817 CTCGCCGTGCAACAAAAGC 61.011 57.895 0.00 0.00 35.74 3.51
1843 5656 0.806868 ATCCGTGCAAGAACAGCATG 59.193 50.000 0.00 0.00 44.79 4.06
1844 5657 1.538047 AATCCGTGCAAGAACAGCAT 58.462 45.000 0.00 0.00 44.79 3.79
1845 5658 1.317613 AAATCCGTGCAAGAACAGCA 58.682 45.000 0.00 0.00 40.19 4.41
1846 5659 2.729156 GCTAAATCCGTGCAAGAACAGC 60.729 50.000 0.00 2.66 0.00 4.40
1847 5660 2.744202 AGCTAAATCCGTGCAAGAACAG 59.256 45.455 0.00 0.00 0.00 3.16
1850 5663 2.415168 CGAAGCTAAATCCGTGCAAGAA 59.585 45.455 0.00 0.00 0.00 2.52
1870 5683 2.480419 AGAGTGCGAGAATGGAAAAACG 59.520 45.455 0.00 0.00 0.00 3.60
1884 5697 2.289274 ACTCTGTATCATCGAGAGTGCG 59.711 50.000 0.00 0.00 43.83 5.34
1921 5736 7.573710 TGTATGTTGGATTCTAAAGTAGGCAT 58.426 34.615 0.00 0.00 0.00 4.40
1924 5739 7.435488 CGTCTGTATGTTGGATTCTAAAGTAGG 59.565 40.741 0.00 0.00 0.00 3.18
1988 5804 7.977853 CGTTGAGGCTATTAGTAGGAACTTTTA 59.022 37.037 0.00 0.00 41.75 1.52
1989 5805 6.817140 CGTTGAGGCTATTAGTAGGAACTTTT 59.183 38.462 0.00 0.00 41.75 2.27
2007 5823 1.453155 AATTGGCTACAGCGTTGAGG 58.547 50.000 6.16 0.00 43.26 3.86
2016 6140 4.219507 CCCAACAACACATAATTGGCTACA 59.780 41.667 0.00 0.00 40.30 2.74
2023 6147 3.197549 GGATGGCCCAACAACACATAATT 59.802 43.478 0.00 0.00 34.14 1.40
2080 6204 6.448207 ACGGTTCTAGGATAACTACTCAAC 57.552 41.667 0.00 0.00 0.00 3.18
2107 6235 3.183574 TCACGTTTTTCTAGTGCATGTCG 59.816 43.478 0.00 0.00 35.97 4.35
2156 6284 9.757227 CCATTTGGTTTTATCACAAGTCTTTTA 57.243 29.630 0.00 0.00 0.00 1.52
2174 6302 2.060050 TGGAACAACGACCATTTGGT 57.940 45.000 0.83 0.83 45.18 3.67
2205 6341 9.750125 GTCATAACTCAAAGAAACCTTTCATTT 57.250 29.630 0.78 0.00 39.61 2.32
2226 6363 2.900716 TTGGATCCATTCGCGTCATA 57.099 45.000 17.06 0.00 0.00 2.15
2251 6388 7.153315 TGATAGTCATACTACCTCTAGTGACG 58.847 42.308 0.00 0.00 33.79 4.35
2287 6424 8.948631 TTGTCAGAAAGTAATGATCTATGTCC 57.051 34.615 0.00 0.00 0.00 4.02
2314 6455 6.602009 GGTCAGCCTGGTGTAGTAATATTTTT 59.398 38.462 0.00 0.00 0.00 1.94
2315 6456 6.120220 GGTCAGCCTGGTGTAGTAATATTTT 58.880 40.000 0.00 0.00 0.00 1.82
2319 6460 3.036091 GGGTCAGCCTGGTGTAGTAATA 58.964 50.000 0.00 0.00 34.45 0.98
2321 6462 1.272807 GGGTCAGCCTGGTGTAGTAA 58.727 55.000 0.00 0.00 34.45 2.24
2322 6463 0.616679 GGGGTCAGCCTGGTGTAGTA 60.617 60.000 0.00 0.00 34.45 1.82
2328 6469 1.774217 TTGAAGGGGTCAGCCTGGT 60.774 57.895 0.00 0.00 37.61 4.00
2334 6475 7.461182 TGTTAAATAATGTTGAAGGGGTCAG 57.539 36.000 0.00 0.00 37.61 3.51
2463 6643 9.831737 CCTTGTTCAAGTCATGTTCTATAAAAG 57.168 33.333 10.93 0.00 0.00 2.27
2483 6663 2.814336 GTTTCAGATTCCTCGCCTTGTT 59.186 45.455 0.00 0.00 0.00 2.83
2561 6741 9.747898 TTTGGCTTCTCTAAACCAGAATAATTA 57.252 29.630 0.00 0.00 32.51 1.40
2566 6746 5.880901 TCTTTGGCTTCTCTAAACCAGAAT 58.119 37.500 0.00 0.00 32.51 2.40
2597 6777 2.242043 CCCCATATTCCATGCCACTTC 58.758 52.381 0.00 0.00 0.00 3.01
2609 6789 2.923837 GGGCCGACACCCCATATT 59.076 61.111 0.00 0.00 45.00 1.28
2616 6796 1.743394 CTAATTTCTTGGGCCGACACC 59.257 52.381 0.00 0.00 0.00 4.16
2624 6804 3.356290 CCAGTCCACCTAATTTCTTGGG 58.644 50.000 0.00 0.00 38.88 4.12
2630 6810 2.514160 GGATCCCCAGTCCACCTAATTT 59.486 50.000 0.00 0.00 35.76 1.82
2644 6824 2.826128 GGAGAAAAAGTTGTGGATCCCC 59.174 50.000 9.90 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.