Multiple sequence alignment - TraesCS6B01G158400

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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 TraesCS6B01G158400 chr6B 100.000 2897 0 0 1 2897 160905884 160902988 0.000000e+00 5350
1 TraesCS6B01G158400 chr6B 89.411 2172 212 13 743 2897 160663427 160661257 0.000000e+00 2721
2 TraesCS6B01G158400 chr6B 93.333 585 36 2 1 582 160664010 160663426 0.000000e+00 861
3 TraesCS6B01G158400 chr6B 97.041 169 5 0 576 744 606434022 606433854 4.720000e-73 285
4 TraesCS6B01G158400 chr6B 89.604 202 16 3 383 582 159990253 159990055 4.790000e-63 252
5 TraesCS6B01G158400 chr6B 83.333 216 24 8 375 582 160664974 160664763 3.810000e-44 189
6 TraesCS6B01G158400 chr6A 96.207 2162 75 3 743 2897 101865617 101863456 0.000000e+00 3531
7 TraesCS6B01G158400 chr6A 89.207 2168 220 9 743 2897 101548410 101546244 0.000000e+00 2695
8 TraesCS6B01G158400 chr6A 88.492 2181 218 23 743 2897 101562894 101560721 0.000000e+00 2606
9 TraesCS6B01G158400 chr6A 87.533 1909 227 6 999 2897 101844965 101843058 0.000000e+00 2196
10 TraesCS6B01G158400 chr6A 95.704 582 22 2 1 582 101866194 101865616 0.000000e+00 933
11 TraesCS6B01G158400 chr6A 92.321 586 31 7 1 582 101548984 101548409 0.000000e+00 821
12 TraesCS6B01G158400 chr6A 90.374 187 10 3 401 582 101563076 101562893 3.730000e-59 239
13 TraesCS6B01G158400 chr6D 89.250 2186 219 11 727 2897 84218389 84216205 0.000000e+00 2721
14 TraesCS6B01G158400 chr6D 88.645 2184 217 22 743 2897 84232079 84229898 0.000000e+00 2630
15 TraesCS6B01G158400 chr6D 88.623 2171 227 13 743 2897 84474272 84472106 0.000000e+00 2623
16 TraesCS6B01G158400 chr6D 85.455 2152 259 42 783 2897 84620233 84618099 0.000000e+00 2191
17 TraesCS6B01G158400 chr6D 85.514 2002 250 26 925 2897 85608141 85610131 0.000000e+00 2054
18 TraesCS6B01G158400 chr6D 85.845 1971 234 24 950 2897 84653918 84651970 0.000000e+00 2052
19 TraesCS6B01G158400 chr6D 84.094 1905 238 24 1045 2897 84661507 84659616 0.000000e+00 1779
20 TraesCS6B01G158400 chr6D 93.522 602 26 7 1 598 84219029 84218437 0.000000e+00 883
21 TraesCS6B01G158400 chr6D 92.650 585 34 5 1 582 84474849 84474271 0.000000e+00 833
22 TraesCS6B01G158400 chr6D 81.714 525 47 22 80 582 84232575 84232078 2.710000e-105 392
23 TraesCS6B01G158400 chr5B 100.000 165 0 0 580 744 497454798 497454962 3.630000e-79 305
24 TraesCS6B01G158400 chr5B 98.193 166 3 0 579 744 514075786 514075621 1.020000e-74 291
25 TraesCS6B01G158400 chr5B 97.605 167 3 1 579 744 221204314 221204148 4.720000e-73 285
26 TraesCS6B01G158400 chr5B 97.006 167 4 1 581 746 93472265 93472099 2.200000e-71 279
27 TraesCS6B01G158400 chr5B 95.429 175 7 1 581 754 700231594 700231420 7.910000e-71 278
28 TraesCS6B01G158400 chr1B 98.214 168 2 1 577 744 662537068 662536902 2.820000e-75 292
29 TraesCS6B01G158400 chr4A 96.552 174 5 1 574 746 690408922 690409095 1.310000e-73 287
30 TraesCS6B01G158400 chr2B 98.171 164 3 0 581 744 548626817 548626654 1.310000e-73 287


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 TraesCS6B01G158400 chr6B 160902988 160905884 2896 True 5350.0 5350 100.000000 1 2897 1 chr6B.!!$R2 2896
1 TraesCS6B01G158400 chr6B 160661257 160664974 3717 True 1257.0 2721 88.692333 1 2897 3 chr6B.!!$R4 2896
2 TraesCS6B01G158400 chr6A 101863456 101866194 2738 True 2232.0 3531 95.955500 1 2897 2 chr6A.!!$R4 2896
3 TraesCS6B01G158400 chr6A 101843058 101844965 1907 True 2196.0 2196 87.533000 999 2897 1 chr6A.!!$R1 1898
4 TraesCS6B01G158400 chr6A 101546244 101548984 2740 True 1758.0 2695 90.764000 1 2897 2 chr6A.!!$R2 2896
5 TraesCS6B01G158400 chr6A 101560721 101563076 2355 True 1422.5 2606 89.433000 401 2897 2 chr6A.!!$R3 2496
6 TraesCS6B01G158400 chr6D 84618099 84620233 2134 True 2191.0 2191 85.455000 783 2897 1 chr6D.!!$R1 2114
7 TraesCS6B01G158400 chr6D 85608141 85610131 1990 False 2054.0 2054 85.514000 925 2897 1 chr6D.!!$F1 1972
8 TraesCS6B01G158400 chr6D 84651970 84653918 1948 True 2052.0 2052 85.845000 950 2897 1 chr6D.!!$R2 1947
9 TraesCS6B01G158400 chr6D 84216205 84219029 2824 True 1802.0 2721 91.386000 1 2897 2 chr6D.!!$R4 2896
10 TraesCS6B01G158400 chr6D 84659616 84661507 1891 True 1779.0 1779 84.094000 1045 2897 1 chr6D.!!$R3 1852
11 TraesCS6B01G158400 chr6D 84472106 84474849 2743 True 1728.0 2623 90.636500 1 2897 2 chr6D.!!$R6 2896
12 TraesCS6B01G158400 chr6D 84229898 84232575 2677 True 1511.0 2630 85.179500 80 2897 2 chr6D.!!$R5 2817

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
358 1367 0.252103 GTAGAGGAGACCACCACCCA 60.252 60.0 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2104 3180 0.110486 AAATGGTTGGCCGACAGTCT 59.89 50.0 24.82 3.38 37.67 3.24 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
95 1063 3.274288 GGAACTAACAGGAAGCATGAGG 58.726 50.000 0.00 0.00 0.00 3.86
100 1072 5.006386 ACTAACAGGAAGCATGAGGAAAAG 58.994 41.667 0.00 0.00 0.00 2.27
171 1148 1.657751 GCTGGCGGAAAATGACCTCC 61.658 60.000 0.00 0.00 33.38 4.30
203 1180 8.459635 CAATTATTGAGCAGAATATCTCCCATG 58.540 37.037 0.00 0.00 0.00 3.66
317 1325 1.233285 GCCCTCATTAGCTCATGCCG 61.233 60.000 2.83 0.00 40.80 5.69
358 1367 0.252103 GTAGAGGAGACCACCACCCA 60.252 60.000 0.00 0.00 0.00 4.51
395 1404 0.928922 CTATGCACTCTTGAGCAGCG 59.071 55.000 0.00 0.00 42.55 5.18
464 1474 6.374417 ACCTTAGTCTCTTCAGGCATTTAA 57.626 37.500 0.00 0.00 0.00 1.52
592 1609 5.424573 AGCTTTATAAACTACTCCCTCCGTT 59.575 40.000 0.00 0.00 0.00 4.44
593 1610 5.752472 GCTTTATAAACTACTCCCTCCGTTC 59.248 44.000 0.00 0.00 0.00 3.95
595 1612 2.322339 AAACTACTCCCTCCGTTCCT 57.678 50.000 0.00 0.00 0.00 3.36
596 1613 3.463048 AAACTACTCCCTCCGTTCCTA 57.537 47.619 0.00 0.00 0.00 2.94
600 1617 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
602 1619 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
603 1620 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
605 1622 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
607 1624 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
610 1627 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
612 1629 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
613 1630 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
614 1631 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
627 1644 9.573166 TTTGTCTTTCTAGAGATTTCAAATGGA 57.427 29.630 0.00 0.00 0.00 3.41
628 1645 8.553459 TGTCTTTCTAGAGATTTCAAATGGAC 57.447 34.615 0.00 0.00 0.00 4.02
630 1647 8.663911 GTCTTTCTAGAGATTTCAAATGGACTG 58.336 37.037 0.00 0.00 0.00 3.51
631 1648 6.992063 TTCTAGAGATTTCAAATGGACTGC 57.008 37.500 0.00 0.00 0.00 4.40
633 1650 5.877012 TCTAGAGATTTCAAATGGACTGCAC 59.123 40.000 0.00 0.00 0.00 4.57
635 1652 5.014858 AGAGATTTCAAATGGACTGCACAT 58.985 37.500 0.00 0.00 0.00 3.21
638 1655 4.418013 TTTCAAATGGACTGCACATACG 57.582 40.909 0.00 0.00 0.00 3.06
640 1657 2.027653 TCAAATGGACTGCACATACGGA 60.028 45.455 0.00 0.00 0.00 4.69
642 1659 2.245159 ATGGACTGCACATACGGATG 57.755 50.000 5.94 5.94 39.16 3.51
644 1661 2.104170 TGGACTGCACATACGGATGTA 58.896 47.619 14.23 0.00 44.82 2.29
645 1662 2.698274 TGGACTGCACATACGGATGTAT 59.302 45.455 14.23 0.00 44.82 2.29
646 1663 3.892588 TGGACTGCACATACGGATGTATA 59.107 43.478 14.23 4.41 44.82 1.47
649 1666 6.127730 TGGACTGCACATACGGATGTATATAG 60.128 42.308 14.23 11.40 44.82 1.31
650 1667 6.095021 GGACTGCACATACGGATGTATATAGA 59.905 42.308 14.23 0.00 44.82 1.98
651 1668 6.853720 ACTGCACATACGGATGTATATAGAC 58.146 40.000 14.23 0.00 44.82 2.59
652 1669 6.433093 ACTGCACATACGGATGTATATAGACA 59.567 38.462 14.23 2.07 44.82 3.41
653 1670 7.122799 ACTGCACATACGGATGTATATAGACAT 59.877 37.037 14.23 12.70 44.82 3.06
654 1671 8.514330 TGCACATACGGATGTATATAGACATA 57.486 34.615 14.23 0.00 44.82 2.29
655 1672 9.131791 TGCACATACGGATGTATATAGACATAT 57.868 33.333 14.23 5.08 44.82 1.78
656 1673 9.967346 GCACATACGGATGTATATAGACATATT 57.033 33.333 14.23 3.62 44.82 1.28
686 1703 9.214953 GAGTATAAATTCACTCATTTTGCTTCG 57.785 33.333 8.98 0.00 40.74 3.79
687 1704 8.730680 AGTATAAATTCACTCATTTTGCTTCGT 58.269 29.630 0.00 0.00 0.00 3.85
688 1705 9.982291 GTATAAATTCACTCATTTTGCTTCGTA 57.018 29.630 0.00 0.00 0.00 3.43
690 1707 7.801547 AAATTCACTCATTTTGCTTCGTATG 57.198 32.000 0.00 0.00 0.00 2.39
691 1708 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
692 1709 7.609760 ATTCACTCATTTTGCTTCGTATGTA 57.390 32.000 0.00 0.00 0.00 2.29
693 1710 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
694 1711 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
695 1712 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
696 1713 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
697 1714 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
698 1715 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
699 1716 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
700 1717 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
701 1718 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
702 1719 4.878439 TGCTTCGTATGTAGTCACTTGTT 58.122 39.130 0.00 0.00 0.00 2.83
703 1720 4.684242 TGCTTCGTATGTAGTCACTTGTTG 59.316 41.667 0.00 0.00 0.00 3.33
704 1721 4.921515 GCTTCGTATGTAGTCACTTGTTGA 59.078 41.667 0.00 0.00 0.00 3.18
705 1722 5.404366 GCTTCGTATGTAGTCACTTGTTGAA 59.596 40.000 0.00 0.00 35.39 2.69
706 1723 6.073980 GCTTCGTATGTAGTCACTTGTTGAAA 60.074 38.462 0.00 0.00 35.39 2.69
707 1724 7.360101 GCTTCGTATGTAGTCACTTGTTGAAAT 60.360 37.037 0.00 0.00 35.39 2.17
708 1725 7.576750 TCGTATGTAGTCACTTGTTGAAATC 57.423 36.000 0.00 0.00 35.39 2.17
709 1726 7.375834 TCGTATGTAGTCACTTGTTGAAATCT 58.624 34.615 0.00 0.00 35.39 2.40
710 1727 7.541091 TCGTATGTAGTCACTTGTTGAAATCTC 59.459 37.037 0.00 0.00 35.39 2.75
711 1728 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
712 1729 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
713 1730 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
714 1731 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
715 1732 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
716 1733 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
717 1734 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
718 1735 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
719 1736 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
720 1737 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
721 1738 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
722 1739 9.050601 ACTTGTTGAAATCTCTAGAAAGACAAG 57.949 33.333 17.75 17.75 33.18 3.16
723 1740 8.964476 TTGTTGAAATCTCTAGAAAGACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
759 1776 6.119240 AGGGAGTAGTTTACAGGGTTTTAC 57.881 41.667 0.00 0.00 0.00 2.01
831 1850 2.902846 TTTTGGTGCACCGACCGG 60.903 61.111 30.07 6.94 39.07 5.28
967 1995 3.446161 ACTGCATGCACTATTCAAGCAAT 59.554 39.130 18.46 0.00 42.15 3.56
1012 2047 5.705609 ACACTAACCAATGTGTTCATTCC 57.294 39.130 0.00 0.00 43.88 3.01
1065 2100 1.153469 GCTCTTCTTGGCCTCTCCG 60.153 63.158 3.32 0.00 37.80 4.63
1177 2212 3.848301 AATGGCACGGACTGCTGCA 62.848 57.895 0.88 0.88 46.25 4.41
1322 2360 1.371267 CGCACAACTCGTTCTCCGA 60.371 57.895 0.00 0.00 45.00 4.55
1419 2467 2.359975 CCCGAGCTTCCGCCTTTT 60.360 61.111 0.00 0.00 36.60 2.27
1420 2468 2.399356 CCCGAGCTTCCGCCTTTTC 61.399 63.158 0.00 0.00 36.60 2.29
1679 2727 0.240411 CTCAAAGTGCTCAAGGCTGC 59.760 55.000 0.00 0.00 42.39 5.25
1803 2870 4.437930 GGAGCACATATTGTCAAAGTCAGC 60.438 45.833 0.00 0.00 0.00 4.26
1859 2931 2.028930 GGCAAGATTCCGGAGTCGATAT 60.029 50.000 20.00 2.28 39.00 1.63
1909 2981 6.039270 TGCATTTAGGTAGCAATAACATGTCC 59.961 38.462 0.00 0.00 34.97 4.02
2104 3180 2.736197 AGCAATTTGGCTGCACTGA 58.264 47.368 0.50 0.00 43.89 3.41
2106 3182 0.599558 GCAATTTGGCTGCACTGAGA 59.400 50.000 0.50 0.00 39.69 3.27
2207 3283 7.338196 TGTTAGAAACTCCTTCACAAACATCAA 59.662 33.333 0.00 0.00 36.40 2.57
2340 3417 3.405831 TCTTCAGTTTCTGTCCATGCAG 58.594 45.455 0.00 0.00 37.81 4.41
2572 3655 2.579873 CTGCCATCTATTTGGACCCAG 58.420 52.381 0.00 0.00 39.25 4.45
2653 3759 2.305635 TGGCCTAAAGTGCTGAATCTCA 59.694 45.455 3.32 0.00 0.00 3.27
2736 3842 9.849166 CTTTACCTAAACTTGAGTTTCAACAAA 57.151 29.630 12.05 8.51 44.15 2.83
2770 3876 2.874014 TCCCACAATCAATCTGCAACA 58.126 42.857 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 986 1.215423 AGGTCCTGGAACAAAAGCAGT 59.785 47.619 15.35 0.00 38.70 4.40
95 1063 4.620982 ACTGCTTTATGGTTGTGCTTTTC 58.379 39.130 0.00 0.00 0.00 2.29
100 1072 4.367450 TGAAAACTGCTTTATGGTTGTGC 58.633 39.130 0.00 0.00 0.00 4.57
203 1180 4.497473 TTTGGAAACGTGATTCATGTCC 57.503 40.909 11.80 10.20 31.86 4.02
305 1313 2.354510 GCATGTTTACGGCATGAGCTAA 59.645 45.455 9.17 0.00 44.60 3.09
317 1325 5.166398 ACAGACTTACTACCGCATGTTTAC 58.834 41.667 0.00 0.00 0.00 2.01
358 1367 1.142688 AGATTTGTCCAGGGCCCAGT 61.143 55.000 27.56 0.00 0.00 4.00
395 1404 3.216800 TGCCTGACCTATTCATTGCATC 58.783 45.455 0.00 0.00 37.11 3.91
447 1457 8.349983 TGTTTAAGTTTAAATGCCTGAAGAGAC 58.650 33.333 0.86 0.00 35.35 3.36
464 1474 4.407296 TGCCCCAAGTTTCATGTTTAAGTT 59.593 37.500 0.00 0.00 0.00 2.66
602 1619 9.003658 GTCCATTTGAAATCTCTAGAAAGACAA 57.996 33.333 0.00 0.00 0.00 3.18
603 1620 8.378565 AGTCCATTTGAAATCTCTAGAAAGACA 58.621 33.333 0.00 0.00 0.00 3.41
605 1622 7.335422 GCAGTCCATTTGAAATCTCTAGAAAGA 59.665 37.037 0.00 0.00 0.00 2.52
607 1624 6.942005 TGCAGTCCATTTGAAATCTCTAGAAA 59.058 34.615 0.00 0.00 0.00 2.52
610 1627 5.645067 TGTGCAGTCCATTTGAAATCTCTAG 59.355 40.000 0.00 0.00 0.00 2.43
612 1629 4.401022 TGTGCAGTCCATTTGAAATCTCT 58.599 39.130 0.00 0.00 0.00 3.10
613 1630 4.771590 TGTGCAGTCCATTTGAAATCTC 57.228 40.909 0.00 0.00 0.00 2.75
614 1631 5.163723 CGTATGTGCAGTCCATTTGAAATCT 60.164 40.000 0.00 0.00 0.00 2.40
615 1632 5.030295 CGTATGTGCAGTCCATTTGAAATC 58.970 41.667 0.00 0.00 0.00 2.17
616 1633 4.142403 CCGTATGTGCAGTCCATTTGAAAT 60.142 41.667 0.00 0.00 0.00 2.17
617 1634 3.190327 CCGTATGTGCAGTCCATTTGAAA 59.810 43.478 0.00 0.00 0.00 2.69
618 1635 2.746904 CCGTATGTGCAGTCCATTTGAA 59.253 45.455 0.00 0.00 0.00 2.69
620 1637 2.355197 TCCGTATGTGCAGTCCATTTG 58.645 47.619 0.00 0.00 0.00 2.32
621 1638 2.779755 TCCGTATGTGCAGTCCATTT 57.220 45.000 0.00 0.00 0.00 2.32
623 1640 1.486310 ACATCCGTATGTGCAGTCCAT 59.514 47.619 0.00 0.00 44.79 3.41
625 1642 2.882927 TACATCCGTATGTGCAGTCC 57.117 50.000 3.56 0.00 45.99 3.85
627 1644 6.433093 TGTCTATATACATCCGTATGTGCAGT 59.567 38.462 3.56 0.00 45.99 4.40
628 1645 6.852664 TGTCTATATACATCCGTATGTGCAG 58.147 40.000 3.56 0.00 45.99 4.41
630 1647 9.967346 AATATGTCTATATACATCCGTATGTGC 57.033 33.333 3.56 0.00 45.99 4.57
660 1677 9.214953 CGAAGCAAAATGAGTGAATTTATACTC 57.785 33.333 10.00 10.00 42.77 2.59
661 1678 8.730680 ACGAAGCAAAATGAGTGAATTTATACT 58.269 29.630 0.00 0.00 0.00 2.12
662 1679 8.895932 ACGAAGCAAAATGAGTGAATTTATAC 57.104 30.769 0.00 0.00 0.00 1.47
664 1681 9.507280 CATACGAAGCAAAATGAGTGAATTTAT 57.493 29.630 0.00 0.00 0.00 1.40
665 1682 8.511321 ACATACGAAGCAAAATGAGTGAATTTA 58.489 29.630 0.00 0.00 0.00 1.40
666 1683 7.370383 ACATACGAAGCAAAATGAGTGAATTT 58.630 30.769 0.00 0.00 0.00 1.82
667 1684 6.913170 ACATACGAAGCAAAATGAGTGAATT 58.087 32.000 0.00 0.00 0.00 2.17
668 1685 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
669 1686 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
670 1687 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
671 1688 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
672 1689 6.090898 GTGACTACATACGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
673 1690 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
674 1691 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
675 1692 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
676 1693 6.426937 ACAAGTGACTACATACGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
677 1694 5.756347 ACAAGTGACTACATACGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
678 1695 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
679 1696 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
680 1697 4.514781 ACAAGTGACTACATACGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
681 1698 4.921515 TCAACAAGTGACTACATACGAAGC 59.078 41.667 0.00 0.00 0.00 3.86
682 1699 7.402811 TTTCAACAAGTGACTACATACGAAG 57.597 36.000 0.00 0.00 35.39 3.79
683 1700 7.870954 AGATTTCAACAAGTGACTACATACGAA 59.129 33.333 0.00 0.00 35.39 3.85
684 1701 7.375834 AGATTTCAACAAGTGACTACATACGA 58.624 34.615 0.00 0.00 35.39 3.43
685 1702 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
686 1703 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
688 1705 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
689 1706 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
690 1707 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
691 1708 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
692 1709 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
693 1710 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
694 1711 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
695 1712 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
696 1713 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
697 1714 9.050601 ACTTGTCTTTCTAGAGATTTCAACAAG 57.949 33.333 18.42 18.42 32.73 3.16
698 1715 8.964476 ACTTGTCTTTCTAGAGATTTCAACAA 57.036 30.769 0.00 0.00 0.00 2.83
708 1725 9.291664 CGTTCCTAAATACTTGTCTTTCTAGAG 57.708 37.037 0.00 0.00 0.00 2.43
709 1726 8.248945 CCGTTCCTAAATACTTGTCTTTCTAGA 58.751 37.037 0.00 0.00 0.00 2.43
710 1727 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
711 1728 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
712 1729 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
713 1730 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
714 1731 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
715 1732 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
716 1733 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
717 1734 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
718 1735 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
719 1736 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
720 1737 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
721 1738 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
722 1739 4.892345 ACTACTCCCTCCGTTCCTAAATAC 59.108 45.833 0.00 0.00 0.00 1.89
723 1740 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
724 1741 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
725 1742 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
726 1743 3.463048 AACTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
727 1744 3.463048 AAACTACTCCCTCCGTTCCTA 57.537 47.619 0.00 0.00 0.00 2.94
728 1745 2.322339 AAACTACTCCCTCCGTTCCT 57.678 50.000 0.00 0.00 0.00 3.36
729 1746 2.827921 TGTAAACTACTCCCTCCGTTCC 59.172 50.000 0.00 0.00 0.00 3.62
730 1747 3.119209 CCTGTAAACTACTCCCTCCGTTC 60.119 52.174 0.00 0.00 0.00 3.95
731 1748 2.830321 CCTGTAAACTACTCCCTCCGTT 59.170 50.000 0.00 0.00 0.00 4.44
759 1776 9.830186 ATCCATACCTACCCATTATAGCTATAG 57.170 37.037 13.07 5.07 0.00 1.31
967 1995 3.139397 TCTTCCCCCTTCTTGTTTTGCTA 59.861 43.478 0.00 0.00 0.00 3.49
1322 2360 4.162690 GCTCCGCCGGAAGACCAT 62.163 66.667 7.50 0.00 35.59 3.55
1372 2412 0.603707 TTGAGCCGGTTGAAGCTGAG 60.604 55.000 1.90 0.00 40.11 3.35
1419 2467 3.384532 GGCCGGTCGGTGGTAAGA 61.385 66.667 11.25 0.00 37.65 2.10
1420 2468 3.366739 GAGGCCGGTCGGTGGTAAG 62.367 68.421 11.25 0.00 37.65 2.34
1506 2554 1.882912 TGAGCGCAATCAGACTGTTT 58.117 45.000 11.47 0.00 0.00 2.83
1557 2605 1.666054 CAAGGCAGAGAGAAGATGGC 58.334 55.000 0.00 0.00 39.62 4.40
1679 2727 2.938838 TCCCACTTAGGTTGTTGTTGG 58.061 47.619 0.00 0.00 34.66 3.77
1803 2870 3.323403 CCCTCCAAGGAGTAGCTAGATTG 59.677 52.174 14.65 0.00 37.67 2.67
1909 2981 1.817099 GAGTTGATGGCAGCTCCCG 60.817 63.158 3.69 0.00 43.96 5.14
2104 3180 0.110486 AAATGGTTGGCCGACAGTCT 59.890 50.000 24.82 3.38 37.67 3.24
2106 3182 0.893727 GGAAATGGTTGGCCGACAGT 60.894 55.000 24.82 9.50 37.67 3.55
2207 3283 0.177836 AAGGGCGTGCAAAGCTTTTT 59.822 45.000 9.53 0.00 42.50 1.94
2220 3296 1.817099 CCTGCAGCTCTTAAGGGCG 60.817 63.158 21.42 16.61 0.00 6.13
2340 3417 2.223377 CCTTCCAGTAAACGAACACTGC 59.777 50.000 8.78 0.00 40.69 4.40
2572 3655 8.865090 CATATATATTGGTAGATCAGGGAGGTC 58.135 40.741 0.00 0.00 0.00 3.85
2736 3842 6.914665 TGATTGTGGGATCTCTCCATAAAAT 58.085 36.000 0.00 0.00 44.08 1.82


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

AutoCloner maintained by Alex Coulton.