Multiple sequence alignment - TraesCS6D01G392300

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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 TraesCS6D01G392300 chr6D 100.000 2619 0 0 1 2619 466942844 466945462 0.000000e+00 4837.0
1 TraesCS6D01G392300 chr6A 88.901 1901 142 39 749 2619 613244781 613246642 0.000000e+00 2278.0
2 TraesCS6D01G392300 chr6A 91.176 68 5 1 48 114 592346364 592346297 9.980000e-15 91.6
3 TraesCS6D01G392300 chr6B 93.636 550 26 6 49 593 712123767 712124312 0.000000e+00 813.0
4 TraesCS6D01G392300 chr6B 86.101 554 35 13 625 1150 712124313 712124852 2.280000e-155 558.0
5 TraesCS6D01G392300 chr6B 83.806 599 54 17 1271 1863 712124946 712125507 1.790000e-146 529.0
6 TraesCS6D01G392300 chr6B 82.423 586 73 16 1873 2447 712125601 712126167 3.920000e-133 484.0
7 TraesCS6D01G392300 chr6B 91.176 68 4 2 48 114 508161535 508161469 9.980000e-15 91.6
8 TraesCS6D01G392300 chr6B 97.917 48 1 0 1 48 712123690 712123737 1.670000e-12 84.2
9 TraesCS6D01G392300 chr6B 97.143 35 1 0 1 35 6218649 6218683 2.810000e-05 60.2
10 TraesCS6D01G392300 chr2D 94.118 68 3 1 48 114 430224947 430224880 4.610000e-18 102.0
11 TraesCS6D01G392300 chr2D 91.304 69 5 1 48 115 627039082 627039150 2.780000e-15 93.5
12 TraesCS6D01G392300 chr4A 95.312 64 2 1 48 110 697990077 697990140 1.660000e-17 100.0
13 TraesCS6D01G392300 chr1B 94.030 67 3 1 48 113 58755074 58755008 1.660000e-17 100.0
14 TraesCS6D01G392300 chr1D 92.647 68 4 1 48 114 39864636 39864703 2.150000e-16 97.1
15 TraesCS6D01G392300 chr4D 91.176 68 5 1 48 114 35348706 35348639 9.980000e-15 91.6
16 TraesCS6D01G392300 chr4B 77.953 127 27 1 2466 2592 609492771 609492896 7.770000e-11 78.7
17 TraesCS6D01G392300 chr4B 100.000 29 0 0 2099 2127 195926423 195926451 1.000000e-03 54.7
18 TraesCS6D01G392300 chr5B 93.617 47 3 0 1 47 90957278 90957324 1.300000e-08 71.3
19 TraesCS6D01G392300 chr5B 90.000 50 5 0 2099 2148 235240812 235240861 6.050000e-07 65.8
20 TraesCS6D01G392300 chr2B 93.750 48 1 1 1 48 664456947 664456902 1.300000e-08 71.3
21 TraesCS6D01G392300 chr2A 96.774 31 1 0 1 31 80238828 80238798 5.000000e-03 52.8


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 TraesCS6D01G392300 chr6D 466942844 466945462 2618 False 4837.00 4837 100.0000 1 2619 1 chr6D.!!$F1 2618
1 TraesCS6D01G392300 chr6A 613244781 613246642 1861 False 2278.00 2278 88.9010 749 2619 1 chr6A.!!$F1 1870
2 TraesCS6D01G392300 chr6B 712123690 712126167 2477 False 493.64 813 88.7766 1 2447 5 chr6B.!!$F2 2446

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
723 758 0.107800 TCTCTTGAGATGCAGCTGCC 60.108 55.0 34.64 20.8 41.18 4.85 F
980 1040 0.249868 CAAACTCTCTGTGGTGCCGA 60.250 55.0 0.00 0.0 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1613 1696 1.064017 AGGAGGGAGAGCAGACTACAG 60.064 57.143 0.0 0.0 0.0 2.74 R
1955 2128 1.066002 GGCATCGGAACCACATCATTG 59.934 52.381 0.0 0.0 0.0 2.82 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
36 37 3.951332 GCACGCTTGCTACACTGA 58.049 55.556 8.12 0.00 46.17 3.41
138 170 5.167303 AGTCCATAACAGAAAAGAGGTCC 57.833 43.478 0.00 0.00 0.00 4.46
174 206 0.543277 TATGGGAGGCAGAGTGCTTG 59.457 55.000 0.00 0.00 44.28 4.01
177 209 1.673665 GGAGGCAGAGTGCTTGTGG 60.674 63.158 0.00 0.00 44.28 4.17
183 215 0.599991 CAGAGTGCTTGTGGCGTGTA 60.600 55.000 0.00 0.00 45.43 2.90
207 239 6.051717 ACAATGATGCTACTGTAGAATGACC 58.948 40.000 18.64 2.88 0.00 4.02
208 240 5.876651 ATGATGCTACTGTAGAATGACCA 57.123 39.130 18.64 8.34 0.00 4.02
209 241 5.876651 TGATGCTACTGTAGAATGACCAT 57.123 39.130 18.64 10.40 0.00 3.55
210 242 5.604565 TGATGCTACTGTAGAATGACCATG 58.395 41.667 18.64 0.00 0.00 3.66
211 243 3.797039 TGCTACTGTAGAATGACCATGC 58.203 45.455 18.64 0.58 0.00 4.06
250 283 6.483640 GCTAAGGTGAGAAGAGAGAAACAAAA 59.516 38.462 0.00 0.00 0.00 2.44
430 463 7.810658 AGATAAAATATATGCAAACCAGCTCG 58.189 34.615 0.00 0.00 34.99 5.03
497 531 0.878416 CGGTGCCAAATTTTCTCGGA 59.122 50.000 0.00 0.00 0.00 4.55
530 564 2.282701 TTCGGTATGCTGTCGGTTAC 57.717 50.000 0.00 0.00 0.00 2.50
593 628 4.514401 CGTTAGGTGGCTAGAAAGGATTT 58.486 43.478 0.00 0.00 43.98 2.17
594 629 4.941873 CGTTAGGTGGCTAGAAAGGATTTT 59.058 41.667 0.00 0.00 39.27 1.82
595 630 5.163754 CGTTAGGTGGCTAGAAAGGATTTTG 60.164 44.000 0.00 0.00 39.27 2.44
596 631 3.701664 AGGTGGCTAGAAAGGATTTTGG 58.298 45.455 0.00 0.00 39.27 3.28
597 632 3.333680 AGGTGGCTAGAAAGGATTTTGGA 59.666 43.478 0.00 0.00 39.27 3.53
598 633 3.696548 GGTGGCTAGAAAGGATTTTGGAG 59.303 47.826 0.00 0.00 39.27 3.86
599 634 3.696548 GTGGCTAGAAAGGATTTTGGAGG 59.303 47.826 0.00 0.00 39.27 4.30
600 635 3.291584 GGCTAGAAAGGATTTTGGAGGG 58.708 50.000 0.00 0.00 39.27 4.30
601 636 2.690497 GCTAGAAAGGATTTTGGAGGGC 59.310 50.000 0.00 0.00 39.27 5.19
602 637 2.999185 AGAAAGGATTTTGGAGGGCA 57.001 45.000 0.00 0.00 39.27 5.36
603 638 2.529632 AGAAAGGATTTTGGAGGGCAC 58.470 47.619 0.00 0.00 39.27 5.01
604 639 2.158325 AGAAAGGATTTTGGAGGGCACA 60.158 45.455 0.00 0.00 39.27 4.57
605 640 2.397044 AAGGATTTTGGAGGGCACAA 57.603 45.000 0.00 0.00 0.00 3.33
606 641 2.629017 AGGATTTTGGAGGGCACAAT 57.371 45.000 0.00 0.00 0.00 2.71
607 642 2.460669 AGGATTTTGGAGGGCACAATC 58.539 47.619 0.00 0.00 0.00 2.67
608 643 2.178580 GGATTTTGGAGGGCACAATCA 58.821 47.619 0.00 0.00 0.00 2.57
609 644 2.094026 GGATTTTGGAGGGCACAATCAC 60.094 50.000 0.00 0.00 0.00 3.06
610 645 2.079170 TTTTGGAGGGCACAATCACA 57.921 45.000 0.00 0.00 0.00 3.58
611 646 2.079170 TTTGGAGGGCACAATCACAA 57.921 45.000 0.00 0.00 0.00 3.33
612 647 2.307496 TTGGAGGGCACAATCACAAT 57.693 45.000 0.00 0.00 0.00 2.71
613 648 2.307496 TGGAGGGCACAATCACAATT 57.693 45.000 0.00 0.00 0.00 2.32
614 649 2.170166 TGGAGGGCACAATCACAATTC 58.830 47.619 0.00 0.00 0.00 2.17
615 650 2.170166 GGAGGGCACAATCACAATTCA 58.830 47.619 0.00 0.00 0.00 2.57
616 651 2.762327 GGAGGGCACAATCACAATTCAT 59.238 45.455 0.00 0.00 0.00 2.57
617 652 3.429822 GGAGGGCACAATCACAATTCATG 60.430 47.826 0.00 0.00 0.00 3.07
618 653 2.498481 AGGGCACAATCACAATTCATGG 59.502 45.455 0.00 0.00 0.00 3.66
619 654 2.419021 GGGCACAATCACAATTCATGGG 60.419 50.000 0.00 0.00 0.00 4.00
620 655 2.419021 GGCACAATCACAATTCATGGGG 60.419 50.000 0.00 0.00 31.35 4.96
621 656 2.234414 GCACAATCACAATTCATGGGGT 59.766 45.455 0.00 0.00 31.35 4.95
622 657 3.676873 GCACAATCACAATTCATGGGGTC 60.677 47.826 0.00 0.00 31.35 4.46
623 658 3.099141 ACAATCACAATTCATGGGGTCC 58.901 45.455 0.00 0.00 31.35 4.46
648 683 2.580815 CTGCAGCGTCATGGGAGA 59.419 61.111 0.00 0.00 0.00 3.71
717 752 2.738846 GCTTTTCGTCTCTTGAGATGCA 59.261 45.455 13.40 0.00 0.00 3.96
719 754 2.001812 TTCGTCTCTTGAGATGCAGC 57.998 50.000 13.40 0.00 0.00 5.25
720 755 1.180907 TCGTCTCTTGAGATGCAGCT 58.819 50.000 2.90 2.90 0.00 4.24
721 756 1.135170 TCGTCTCTTGAGATGCAGCTG 60.135 52.381 10.40 10.11 0.00 4.24
722 757 1.008329 GTCTCTTGAGATGCAGCTGC 58.992 55.000 31.89 31.89 42.50 5.25
723 758 0.107800 TCTCTTGAGATGCAGCTGCC 60.108 55.000 34.64 20.80 41.18 4.85
724 759 1.077930 TCTTGAGATGCAGCTGCCC 60.078 57.895 34.64 25.31 41.18 5.36
725 760 2.437180 TTGAGATGCAGCTGCCCG 60.437 61.111 34.64 0.00 41.18 6.13
726 761 3.258228 TTGAGATGCAGCTGCCCGT 62.258 57.895 34.64 21.01 41.18 5.28
727 762 2.437359 GAGATGCAGCTGCCCGTT 60.437 61.111 34.64 18.05 41.18 4.44
728 763 1.153369 GAGATGCAGCTGCCCGTTA 60.153 57.895 34.64 17.30 41.18 3.18
729 764 1.153289 AGATGCAGCTGCCCGTTAG 60.153 57.895 34.64 0.00 41.18 2.34
730 765 2.124570 ATGCAGCTGCCCGTTAGG 60.125 61.111 34.64 0.00 41.18 2.69
731 766 2.876368 GATGCAGCTGCCCGTTAGGT 62.876 60.000 34.64 10.94 41.18 3.08
732 767 3.127533 GCAGCTGCCCGTTAGGTG 61.128 66.667 28.76 0.00 44.28 4.00
733 768 2.436646 CAGCTGCCCGTTAGGTGG 60.437 66.667 0.00 0.00 39.36 4.61
742 777 2.345991 GTTAGGTGGCCTCACGCA 59.654 61.111 3.32 0.00 44.50 5.24
866 924 3.907130 AAACCCAGGCAGCCAGCT 61.907 61.111 15.80 0.00 44.79 4.24
873 931 2.188994 GGCAGCCAGCTTCTCGAT 59.811 61.111 6.55 0.00 44.79 3.59
921 979 2.043115 TCCTTTCTCTACCTCTGAGCCA 59.957 50.000 0.00 0.00 0.00 4.75
923 981 3.069443 CCTTTCTCTACCTCTGAGCCATC 59.931 52.174 0.00 0.00 0.00 3.51
928 986 1.069823 CTACCTCTGAGCCATCGCATT 59.930 52.381 0.00 0.00 37.52 3.56
937 995 4.260355 CATCGCATTGCAGCCCCG 62.260 66.667 9.69 0.00 0.00 5.73
970 1030 1.722851 TCCTCCCCTACCAAACTCTCT 59.277 52.381 0.00 0.00 0.00 3.10
980 1040 0.249868 CAAACTCTCTGTGGTGCCGA 60.250 55.000 0.00 0.00 0.00 5.54
1044 1104 2.279069 ACCGTCTCTCCTGGCAGTG 61.279 63.158 14.43 6.09 0.00 3.66
1064 1124 1.906824 AGACCTTCCGCGGACAGAA 60.907 57.895 31.19 12.98 0.00 3.02
1116 1179 2.815647 GCTTTCAGAGTCCGGGCG 60.816 66.667 0.00 0.00 0.00 6.13
1152 1215 2.648059 GGAGTAAGTTCCTGCATGCAT 58.352 47.619 22.97 7.74 34.27 3.96
1153 1216 2.615912 GGAGTAAGTTCCTGCATGCATC 59.384 50.000 22.97 12.13 34.27 3.91
1154 1217 2.615912 GAGTAAGTTCCTGCATGCATCC 59.384 50.000 22.97 9.26 0.00 3.51
1155 1218 2.025981 AGTAAGTTCCTGCATGCATCCA 60.026 45.455 22.97 4.95 0.00 3.41
1156 1219 1.927487 AAGTTCCTGCATGCATCCAA 58.073 45.000 22.97 11.26 0.00 3.53
1161 1224 0.466739 CCTGCATGCATCCAAGGCTA 60.467 55.000 22.97 0.00 0.00 3.93
1309 1387 2.737252 GTGTTTCTTTCTGCTAGGTCCG 59.263 50.000 0.00 0.00 0.00 4.79
1406 1484 0.469331 CCTGCATGATGGGCCTCATT 60.469 55.000 13.62 0.00 35.97 2.57
1440 1518 3.265791 GTGGAGCTGGTAAGAACATCTG 58.734 50.000 0.00 0.00 0.00 2.90
1446 1524 4.019860 AGCTGGTAAGAACATCTGTGTCAT 60.020 41.667 0.00 0.00 37.67 3.06
1484 1562 9.214953 CGAAAGCACTGTCATAATTAGAATTTC 57.785 33.333 0.00 0.00 0.00 2.17
1487 1565 8.443953 AGCACTGTCATAATTAGAATTTCCTC 57.556 34.615 0.00 0.00 0.00 3.71
1613 1696 2.495084 GGAAAGGCCTCGATATTCCAC 58.505 52.381 23.01 2.34 39.45 4.02
1641 1726 1.220493 TGCTCTCCCTCCTTGCCTATA 59.780 52.381 0.00 0.00 0.00 1.31
1660 1745 2.322355 AAGATGTTGATGCTCGGGAG 57.678 50.000 0.00 0.00 0.00 4.30
1673 1758 1.757118 CTCGGGAGATAAGAGCCACAA 59.243 52.381 0.00 0.00 38.80 3.33
1678 1763 4.195416 GGGAGATAAGAGCCACAAGAAAG 58.805 47.826 0.00 0.00 0.00 2.62
1679 1764 3.625313 GGAGATAAGAGCCACAAGAAAGC 59.375 47.826 0.00 0.00 0.00 3.51
1683 1771 2.543777 AGAGCCACAAGAAAGCGTTA 57.456 45.000 0.00 0.00 0.00 3.18
1684 1772 2.143925 AGAGCCACAAGAAAGCGTTAC 58.856 47.619 0.00 0.00 0.00 2.50
1685 1773 1.197036 GAGCCACAAGAAAGCGTTACC 59.803 52.381 0.00 0.00 0.00 2.85
1687 1775 1.335496 GCCACAAGAAAGCGTTACCAA 59.665 47.619 0.00 0.00 0.00 3.67
1688 1776 2.030274 GCCACAAGAAAGCGTTACCAAT 60.030 45.455 0.00 0.00 0.00 3.16
1689 1777 3.552068 GCCACAAGAAAGCGTTACCAATT 60.552 43.478 0.00 0.00 0.00 2.32
1690 1778 4.320641 GCCACAAGAAAGCGTTACCAATTA 60.321 41.667 0.00 0.00 0.00 1.40
1691 1779 5.621329 GCCACAAGAAAGCGTTACCAATTAT 60.621 40.000 0.00 0.00 0.00 1.28
1692 1780 5.799936 CCACAAGAAAGCGTTACCAATTATG 59.200 40.000 0.00 0.00 0.00 1.90
1693 1781 5.286082 CACAAGAAAGCGTTACCAATTATGC 59.714 40.000 0.00 0.00 0.00 3.14
1694 1782 4.273005 AGAAAGCGTTACCAATTATGCG 57.727 40.909 0.00 0.00 0.00 4.73
1695 1783 2.468532 AAGCGTTACCAATTATGCGC 57.531 45.000 0.00 0.00 44.36 6.09
1696 1784 1.374560 AGCGTTACCAATTATGCGCA 58.625 45.000 14.96 14.96 46.09 6.09
1697 1785 1.740585 AGCGTTACCAATTATGCGCAA 59.259 42.857 17.11 0.00 46.09 4.85
1698 1786 2.162608 AGCGTTACCAATTATGCGCAAA 59.837 40.909 17.11 10.98 46.09 3.68
1699 1787 2.917971 GCGTTACCAATTATGCGCAAAA 59.082 40.909 17.11 2.00 43.62 2.44
1700 1788 3.365220 GCGTTACCAATTATGCGCAAAAA 59.635 39.130 17.11 13.09 43.62 1.94
1757 1845 9.828039 TCATAGCAAATATATAATGGAGCTCTG 57.172 33.333 14.64 0.01 32.70 3.35
1771 1859 3.181499 GGAGCTCTGAGCATTTCATTGTG 60.181 47.826 29.49 0.00 45.56 3.33
1835 1923 4.038042 TCGACAGAGTGATCTTCAACACTT 59.962 41.667 0.00 0.00 45.54 3.16
1866 1954 3.776969 TCTGCTGAGATGGGTGATAGTTT 59.223 43.478 0.00 0.00 0.00 2.66
1947 2120 7.095940 CCATGTTTTGAAAAGTATGCTGACTTG 60.096 37.037 4.82 0.00 39.62 3.16
1955 2128 8.289618 TGAAAAGTATGCTGACTTGTAAATCAC 58.710 33.333 4.82 0.00 39.62 3.06
2027 2200 9.376075 CATATGAGTACAATGTTTCACTCTCTT 57.624 33.333 13.82 4.47 38.56 2.85
2028 2201 9.950496 ATATGAGTACAATGTTTCACTCTCTTT 57.050 29.630 13.82 2.64 38.56 2.52
2133 2315 0.826715 AGCTGCTCGGCTCATTAAGA 59.173 50.000 0.00 0.00 38.24 2.10
2151 2333 3.746045 AGACTTGGCTCGTTAAGTTCA 57.254 42.857 0.00 0.00 37.27 3.18
2206 2397 8.215899 CTTAACTAGCACAAAACTATGTTTGC 57.784 34.615 0.00 0.00 41.33 3.68
2258 2453 2.412089 GACTTTGTGAGCGCTCGTTAAT 59.588 45.455 30.75 15.42 0.00 1.40
2318 2513 3.807071 GGGTGTGATTTTTGCGAACAAAT 59.193 39.130 0.00 0.00 44.96 2.32
2319 2514 4.272261 GGGTGTGATTTTTGCGAACAAATT 59.728 37.500 0.00 0.00 44.96 1.82
2320 2515 5.463724 GGGTGTGATTTTTGCGAACAAATTA 59.536 36.000 0.00 0.00 44.96 1.40
2321 2516 6.018669 GGGTGTGATTTTTGCGAACAAATTAA 60.019 34.615 0.00 0.00 44.96 1.40
2354 2549 2.822561 CAGGAGGAGATGCGCTAGATTA 59.177 50.000 9.73 0.00 0.00 1.75
2386 2581 3.305720 TGAGCTAGGTTGGGTCGATTAT 58.694 45.455 0.00 0.00 34.38 1.28
2418 2613 5.471456 AGATGAGTTGAGGTGTGATGAAAAC 59.529 40.000 0.00 0.00 0.00 2.43
2525 2720 6.880822 TGTTCATTAAGAATCGAACTACCG 57.119 37.500 0.00 0.00 38.76 4.02
2536 2731 1.997606 CGAACTACCGGCTTAACAAGG 59.002 52.381 0.00 0.00 0.00 3.61
2537 2732 2.611224 CGAACTACCGGCTTAACAAGGT 60.611 50.000 0.00 0.00 40.52 3.50
2552 2747 2.639839 ACAAGGTGACCTATCAAGTGCT 59.360 45.455 3.68 0.00 36.31 4.40
2610 2805 2.440147 CCAAGGGCATCCACACCA 59.560 61.111 0.00 0.00 34.83 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 89 8.871629 TGCTCCCTAATGAACAGTAAATTTAA 57.128 30.769 0.00 0.00 0.00 1.52
138 170 7.445945 CCTCCCATATAAAAAGTACTCCTCTG 58.554 42.308 0.00 0.00 0.00 3.35
174 206 1.086696 AGCATCATTGTACACGCCAC 58.913 50.000 0.00 0.00 0.00 5.01
177 209 2.930040 ACAGTAGCATCATTGTACACGC 59.070 45.455 0.00 0.00 0.00 5.34
183 215 6.051717 GGTCATTCTACAGTAGCATCATTGT 58.948 40.000 2.26 0.00 0.00 2.71
207 239 7.806487 CACCTTAGCATTTATTCTACATGCATG 59.194 37.037 25.09 25.09 44.90 4.06
208 240 7.720957 TCACCTTAGCATTTATTCTACATGCAT 59.279 33.333 0.00 0.00 44.90 3.96
209 241 7.053498 TCACCTTAGCATTTATTCTACATGCA 58.947 34.615 6.17 0.00 44.90 3.96
210 242 7.442364 TCTCACCTTAGCATTTATTCTACATGC 59.558 37.037 0.00 0.00 43.15 4.06
211 243 8.893219 TCTCACCTTAGCATTTATTCTACATG 57.107 34.615 0.00 0.00 0.00 3.21
264 297 7.227910 GGATCATATTTTACTTAACGGAAGGCA 59.772 37.037 0.00 0.00 39.74 4.75
265 298 7.308408 GGGATCATATTTTACTTAACGGAAGGC 60.308 40.741 0.00 0.00 39.74 4.35
406 439 7.806690 TCGAGCTGGTTTGCATATATTTTATC 58.193 34.615 0.00 0.00 34.99 1.75
417 450 2.346803 GTCTAATCGAGCTGGTTTGCA 58.653 47.619 0.00 0.00 34.99 4.08
430 463 4.825085 TGAACAACCAAACAGGGTCTAATC 59.175 41.667 0.00 0.00 41.32 1.75
483 517 6.925610 TCAGTGATATCCGAGAAAATTTGG 57.074 37.500 0.00 0.00 0.00 3.28
497 531 6.258727 CAGCATACCGAAAACTTCAGTGATAT 59.741 38.462 0.00 0.00 0.00 1.63
530 564 1.249407 TTTGGGGTCGGAATTTTCGG 58.751 50.000 0.00 0.00 0.00 4.30
574 609 4.538490 TCCAAAATCCTTTCTAGCCACCTA 59.462 41.667 0.00 0.00 0.00 3.08
575 610 3.333680 TCCAAAATCCTTTCTAGCCACCT 59.666 43.478 0.00 0.00 0.00 4.00
593 628 2.307496 ATTGTGATTGTGCCCTCCAA 57.693 45.000 0.00 0.00 0.00 3.53
594 629 2.170166 GAATTGTGATTGTGCCCTCCA 58.830 47.619 0.00 0.00 0.00 3.86
595 630 2.170166 TGAATTGTGATTGTGCCCTCC 58.830 47.619 0.00 0.00 0.00 4.30
596 631 3.429822 CCATGAATTGTGATTGTGCCCTC 60.430 47.826 0.00 0.00 0.00 4.30
597 632 2.498481 CCATGAATTGTGATTGTGCCCT 59.502 45.455 0.00 0.00 0.00 5.19
598 633 2.419021 CCCATGAATTGTGATTGTGCCC 60.419 50.000 0.00 0.00 0.00 5.36
599 634 2.419021 CCCCATGAATTGTGATTGTGCC 60.419 50.000 0.00 0.00 0.00 5.01
600 635 2.234414 ACCCCATGAATTGTGATTGTGC 59.766 45.455 0.00 0.00 0.00 4.57
601 636 3.119029 GGACCCCATGAATTGTGATTGTG 60.119 47.826 0.00 0.00 0.00 3.33
602 637 3.099141 GGACCCCATGAATTGTGATTGT 58.901 45.455 0.00 0.00 0.00 2.71
603 638 3.098377 TGGACCCCATGAATTGTGATTG 58.902 45.455 0.00 0.00 0.00 2.67
604 639 3.011595 TCTGGACCCCATGAATTGTGATT 59.988 43.478 0.00 0.00 30.82 2.57
605 640 2.582172 TCTGGACCCCATGAATTGTGAT 59.418 45.455 0.00 0.00 30.82 3.06
606 641 1.991813 TCTGGACCCCATGAATTGTGA 59.008 47.619 0.00 0.00 30.82 3.58
607 642 2.512692 TCTGGACCCCATGAATTGTG 57.487 50.000 0.00 0.00 30.82 3.33
608 643 2.582172 TGATCTGGACCCCATGAATTGT 59.418 45.455 0.00 0.00 30.82 2.71
609 644 2.954318 GTGATCTGGACCCCATGAATTG 59.046 50.000 0.00 0.00 30.82 2.32
610 645 2.091665 GGTGATCTGGACCCCATGAATT 60.092 50.000 0.00 0.00 30.82 2.17
611 646 1.496429 GGTGATCTGGACCCCATGAAT 59.504 52.381 0.00 0.00 30.82 2.57
612 647 0.918983 GGTGATCTGGACCCCATGAA 59.081 55.000 0.00 0.00 30.82 2.57
613 648 0.044702 AGGTGATCTGGACCCCATGA 59.955 55.000 0.00 0.00 33.51 3.07
614 649 0.182061 CAGGTGATCTGGACCCCATG 59.818 60.000 0.00 0.00 39.76 3.66
615 650 1.639635 GCAGGTGATCTGGACCCCAT 61.640 60.000 0.00 0.00 43.54 4.00
616 651 2.300967 GCAGGTGATCTGGACCCCA 61.301 63.158 0.00 0.00 43.54 4.96
617 652 2.262774 CTGCAGGTGATCTGGACCCC 62.263 65.000 5.57 0.00 43.54 4.95
618 653 1.222936 CTGCAGGTGATCTGGACCC 59.777 63.158 5.57 0.00 43.54 4.46
619 654 1.451028 GCTGCAGGTGATCTGGACC 60.451 63.158 17.12 0.00 43.54 4.46
620 655 1.812922 CGCTGCAGGTGATCTGGAC 60.813 63.158 17.12 0.00 43.54 4.02
621 656 2.230994 GACGCTGCAGGTGATCTGGA 62.231 60.000 17.12 0.00 43.54 3.86
622 657 1.812922 GACGCTGCAGGTGATCTGG 60.813 63.158 17.12 0.00 43.54 3.86
623 658 0.461516 ATGACGCTGCAGGTGATCTG 60.462 55.000 17.12 0.00 46.03 2.90
648 683 3.005472 TCGAACTTTTGGATCAGACGACT 59.995 43.478 0.00 0.00 0.00 4.18
722 757 2.267961 GTGAGGCCACCTAACGGG 59.732 66.667 5.01 0.00 37.33 5.28
725 760 0.177141 TATGCGTGAGGCCACCTAAC 59.823 55.000 5.01 0.00 42.61 2.34
726 761 0.906066 TTATGCGTGAGGCCACCTAA 59.094 50.000 5.01 0.00 42.61 2.69
727 762 0.177141 GTTATGCGTGAGGCCACCTA 59.823 55.000 5.01 0.00 42.61 3.08
728 763 1.078426 GTTATGCGTGAGGCCACCT 60.078 57.895 5.01 0.00 42.61 4.00
729 764 0.748005 ATGTTATGCGTGAGGCCACC 60.748 55.000 5.01 0.00 42.61 4.61
730 765 1.094785 AATGTTATGCGTGAGGCCAC 58.905 50.000 5.01 0.00 42.61 5.01
731 766 1.472082 CAAATGTTATGCGTGAGGCCA 59.528 47.619 5.01 0.00 42.61 5.36
732 767 1.742831 TCAAATGTTATGCGTGAGGCC 59.257 47.619 0.00 0.00 42.61 5.19
733 768 2.792542 GCTCAAATGTTATGCGTGAGGC 60.793 50.000 0.00 0.00 43.96 4.70
742 777 1.133025 GCTGCGTGGCTCAAATGTTAT 59.867 47.619 0.00 0.00 0.00 1.89
849 907 3.457329 AAGCTGGCTGCCTGGGTTT 62.457 57.895 24.37 13.53 44.23 3.27
852 910 3.991725 GAGAAGCTGGCTGCCTGGG 62.992 68.421 24.37 13.60 44.23 4.45
866 924 1.582937 GCGAACGAGCGATCGAGAA 60.583 57.895 31.66 0.00 41.82 2.87
873 931 4.189188 GGGCTAGCGAACGAGCGA 62.189 66.667 9.00 0.00 44.70 4.93
937 995 1.148048 GGAGGAAGATGAGCAGGCC 59.852 63.158 0.00 0.00 0.00 5.19
946 1004 3.116174 GAGTTTGGTAGGGGAGGAAGAT 58.884 50.000 0.00 0.00 0.00 2.40
970 1030 0.687920 TGATTAACCTCGGCACCACA 59.312 50.000 0.00 0.00 0.00 4.17
980 1040 4.943705 CCATTGCTGTACACTGATTAACCT 59.056 41.667 0.00 0.00 30.70 3.50
1018 1078 0.247736 AGGAGAGACGGTGCATGAAC 59.752 55.000 0.00 0.00 0.00 3.18
1044 1104 4.373116 TGTCCGCGGAAGGTCTGC 62.373 66.667 32.93 16.47 45.04 4.26
1152 1215 1.381327 CGAGGGAGGTAGCCTTGGA 60.381 63.158 0.00 0.00 31.76 3.53
1153 1216 3.095347 GCGAGGGAGGTAGCCTTGG 62.095 68.421 0.00 0.00 31.76 3.61
1154 1217 1.617947 AAGCGAGGGAGGTAGCCTTG 61.618 60.000 0.00 0.00 31.76 3.61
1155 1218 1.306226 AAGCGAGGGAGGTAGCCTT 60.306 57.895 0.00 0.00 31.76 4.35
1156 1219 1.758906 GAAGCGAGGGAGGTAGCCT 60.759 63.158 0.00 0.00 36.03 4.58
1161 1224 2.352032 CGAAGGAAGCGAGGGAGGT 61.352 63.158 0.00 0.00 0.00 3.85
1406 1484 1.899437 GCTCCACGATGAAGGTCCCA 61.899 60.000 0.00 0.00 0.00 4.37
1440 1518 0.025001 CGCGATTGAACGGATGACAC 59.975 55.000 0.00 0.00 0.00 3.67
1446 1524 0.946700 TGCTTTCGCGATTGAACGGA 60.947 50.000 10.88 0.00 39.65 4.69
1477 1555 7.062322 TGCATGTATACAATGGAGGAAATTCT 58.938 34.615 10.14 0.00 0.00 2.40
1484 1562 6.039605 TCACAAATGCATGTATACAATGGAGG 59.960 38.462 10.14 6.90 30.84 4.30
1487 1565 9.917129 ATAATCACAAATGCATGTATACAATGG 57.083 29.630 10.14 4.04 30.84 3.16
1497 1575 5.460748 ACGCATCAATAATCACAAATGCATG 59.539 36.000 0.00 0.00 39.49 4.06
1613 1696 1.064017 AGGAGGGAGAGCAGACTACAG 60.064 57.143 0.00 0.00 0.00 2.74
1641 1726 1.833630 TCTCCCGAGCATCAACATCTT 59.166 47.619 0.00 0.00 33.17 2.40
1660 1745 3.003480 ACGCTTTCTTGTGGCTCTTATC 58.997 45.455 0.00 0.00 0.00 1.75
1673 1758 3.486875 GCGCATAATTGGTAACGCTTTCT 60.487 43.478 0.30 0.00 37.97 2.52
1678 1763 2.181426 TTGCGCATAATTGGTAACGC 57.819 45.000 12.75 0.00 40.13 4.84
1701 1789 4.619628 GCATAGCCATTGGTAACGGTTTTT 60.620 41.667 4.26 0.00 42.51 1.94
1702 1790 3.119280 GCATAGCCATTGGTAACGGTTTT 60.119 43.478 4.26 0.00 42.51 2.43
1703 1791 2.425668 GCATAGCCATTGGTAACGGTTT 59.574 45.455 4.26 0.00 42.51 3.27
1704 1792 2.021457 GCATAGCCATTGGTAACGGTT 58.979 47.619 4.26 0.00 42.51 4.44
1705 1793 1.211949 AGCATAGCCATTGGTAACGGT 59.788 47.619 4.26 0.00 42.51 4.83
1706 1794 1.967319 AGCATAGCCATTGGTAACGG 58.033 50.000 4.26 0.00 42.51 4.44
1707 1795 3.120199 GCATAGCATAGCCATTGGTAACG 60.120 47.826 4.26 0.00 42.51 3.18
1708 1796 3.820467 TGCATAGCATAGCCATTGGTAAC 59.180 43.478 4.26 0.00 31.71 2.50
1709 1797 4.097551 TGCATAGCATAGCCATTGGTAA 57.902 40.909 4.26 0.00 31.71 2.85
1710 1798 3.786368 TGCATAGCATAGCCATTGGTA 57.214 42.857 4.26 0.00 31.71 3.25
1737 1825 8.734218 ATGCTCAGAGCTCCATTATATATTTG 57.266 34.615 23.15 0.00 42.97 2.32
1748 1836 3.014623 CAATGAAATGCTCAGAGCTCCA 58.985 45.455 23.15 14.66 42.97 3.86
1749 1837 3.015327 ACAATGAAATGCTCAGAGCTCC 58.985 45.455 23.15 9.86 42.97 4.70
1771 1859 8.155923 CGAGTGTAAAAATGAAAAATAGCAAGC 58.844 33.333 0.00 0.00 0.00 4.01
1835 1923 4.164796 ACCCATCTCAGCAGAATATTGTCA 59.835 41.667 0.00 0.00 30.24 3.58
1866 1954 8.222433 CGAACAAGTTTTCATATTAACGGTACA 58.778 33.333 0.00 0.00 0.00 2.90
1955 2128 1.066002 GGCATCGGAACCACATCATTG 59.934 52.381 0.00 0.00 0.00 2.82
1969 2142 6.090493 CACTAGTTCAGAATATCATGGCATCG 59.910 42.308 0.00 0.00 0.00 3.84
2133 2315 5.148651 AGTATGAACTTAACGAGCCAAGT 57.851 39.130 0.00 0.00 36.56 3.16
2206 2397 4.555348 ACGAGCTTTAGACGAATAGAGG 57.445 45.455 0.00 0.00 0.00 3.69
2258 2453 9.445878 CCATAGGTAGTAAATCATCGTAGTCTA 57.554 37.037 0.00 0.00 0.00 2.59
2286 2481 3.576078 AAATCACACCCACACTCTCAA 57.424 42.857 0.00 0.00 0.00 3.02
2318 2513 4.942944 TCCTCCTGTAGTCACCATCTTAA 58.057 43.478 0.00 0.00 0.00 1.85
2319 2514 4.229812 TCTCCTCCTGTAGTCACCATCTTA 59.770 45.833 0.00 0.00 0.00 2.10
2320 2515 3.011821 TCTCCTCCTGTAGTCACCATCTT 59.988 47.826 0.00 0.00 0.00 2.40
2321 2516 2.583101 TCTCCTCCTGTAGTCACCATCT 59.417 50.000 0.00 0.00 0.00 2.90
2354 2549 4.445448 CCAACCTAGCTCATAAGAGGCAAT 60.445 45.833 0.00 0.00 42.33 3.56
2386 2581 8.078060 TCACACCTCAACTCATCTATTCAATA 57.922 34.615 0.00 0.00 0.00 1.90
2492 2687 8.998377 TCGATTCTTAATGAACAAAGTCAATCA 58.002 29.630 0.00 0.00 37.52 2.57
2499 2694 7.898309 CGGTAGTTCGATTCTTAATGAACAAAG 59.102 37.037 6.70 0.00 42.35 2.77
2515 2710 2.353011 CCTTGTTAAGCCGGTAGTTCGA 60.353 50.000 1.90 0.00 0.00 3.71
2525 2720 4.216411 TGATAGGTCACCTTGTTAAGCC 57.784 45.455 0.00 0.00 34.61 4.35
2536 2731 6.595772 CTTAATGAGCACTTGATAGGTCAC 57.404 41.667 0.00 0.00 43.96 3.67


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

AutoCloner maintained by Alex Coulton.