Multiple sequence alignment - TraesCS3B01G410900

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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 TraesCS3B01G410900 chr3B 100.000 2509 0 0 1 2509 647547250 647544742 0.000000e+00 4634.0
1 TraesCS3B01G410900 chr3A 90.646 1037 51 27 754 1765 627822585 627821570 0.000000e+00 1336.0
2 TraesCS3B01G410900 chr3A 90.108 465 40 5 2046 2507 627820096 627819635 1.280000e-167 599.0
3 TraesCS3B01G410900 chr3A 91.667 312 19 7 238 546 627825272 627824965 2.310000e-115 425.0
4 TraesCS3B01G410900 chr3A 87.138 311 19 6 2039 2348 627707379 627707089 1.440000e-87 333.0
5 TraesCS3B01G410900 chr3A 89.412 170 16 1 2340 2507 627706984 627706815 1.950000e-51 213.0
6 TraesCS3B01G410900 chr3A 100.000 28 0 0 2018 2045 627707409 627707382 5.000000e-03 52.8
7 TraesCS3B01G410900 chr3D 85.526 1292 87 45 766 2015 484809219 484807986 0.000000e+00 1258.0
8 TraesCS3B01G410900 chr3D 90.870 471 40 2 2039 2507 484807881 484807412 1.640000e-176 628.0
9 TraesCS3B01G410900 chr3D 90.415 313 24 6 238 546 484809791 484809481 8.360000e-110 407.0
10 TraesCS3B01G410900 chr3D 93.274 223 11 2 1 220 484810075 484809854 2.410000e-85 326.0
11 TraesCS3B01G410900 chr3D 100.000 28 0 0 2018 2045 484807911 484807884 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 TraesCS3B01G410900 chr3B 647544742 647547250 2508 True 4634.000000 4634 100.000 1 2509 1 chr3B.!!$R1 2508
1 TraesCS3B01G410900 chr3A 627819635 627825272 5637 True 786.666667 1336 90.807 238 2507 3 chr3A.!!$R2 2269
2 TraesCS3B01G410900 chr3D 484807412 484810075 2663 True 534.360000 1258 92.017 1 2507 5 chr3D.!!$R1 2506

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
971 3243 0.16923 CGGAACAGACAGAGACCGAG 59.831 60.0 0.0 0.0 42.4 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 4893 0.240945 GCACGAACCAGGGACATTTG 59.759 55.0 0.0 0.0 0.0 2.32 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
24 25 1.238281 CAACGCACGCTAAAACATCG 58.762 50.000 0.00 0.00 0.00 3.84
81 82 5.048921 GTCATGGATGTCTGGCATTCTTATG 60.049 44.000 1.69 0.00 38.06 1.90
146 147 3.941483 AGTTGTGGGAGCTTTATGATTCG 59.059 43.478 0.00 0.00 0.00 3.34
162 163 5.598416 TGATTCGGATCTAGTGTGATGTT 57.402 39.130 5.06 0.00 33.28 2.71
168 169 8.420374 TTCGGATCTAGTGTGATGTTATTTTC 57.580 34.615 0.00 0.00 0.00 2.29
194 198 6.757237 ACATTTGGTTCTGCAACATAATGAA 58.243 32.000 15.82 1.37 37.18 2.57
200 204 6.867816 TGGTTCTGCAACATAATGAATTGTTC 59.132 34.615 0.00 0.00 33.93 3.18
207 211 6.567050 CAACATAATGAATTGTTCCTGGAGG 58.433 40.000 0.00 0.00 33.93 4.30
225 229 7.453126 TCCTGGAGGAATCTAATTCTATGAGAC 59.547 40.741 0.00 0.00 42.18 3.36
228 232 9.163894 TGGAGGAATCTAATTCTATGAGACAAT 57.836 33.333 0.18 0.00 39.24 2.71
263 312 1.723608 TTTGCAGACAACCAGGCGTG 61.724 55.000 0.00 0.00 34.87 5.34
310 359 3.393800 CGATGGTGTCATATTGGTCTCC 58.606 50.000 0.00 0.00 32.98 3.71
346 395 2.601481 CGTGAGCCATGAAGTTTGAC 57.399 50.000 0.00 0.00 0.00 3.18
366 416 1.453669 GGGGATCCTGCTGATGGTC 59.546 63.158 12.58 0.00 32.41 4.02
391 441 2.319136 TGAGTAGTGTGCGTTTGGTT 57.681 45.000 0.00 0.00 0.00 3.67
448 499 2.097110 TCACTGTTGGACTGTAGGGT 57.903 50.000 0.00 0.00 0.00 4.34
496 550 2.818751 ACAACTCCCTGTGTTTGGAA 57.181 45.000 0.00 0.00 0.00 3.53
497 551 2.375146 ACAACTCCCTGTGTTTGGAAC 58.625 47.619 0.00 0.00 0.00 3.62
498 552 2.025321 ACAACTCCCTGTGTTTGGAACT 60.025 45.455 0.00 0.00 0.00 3.01
499 553 2.618709 CAACTCCCTGTGTTTGGAACTC 59.381 50.000 0.00 0.00 0.00 3.01
500 554 1.202651 ACTCCCTGTGTTTGGAACTCG 60.203 52.381 0.00 0.00 0.00 4.18
501 555 0.834612 TCCCTGTGTTTGGAACTCGT 59.165 50.000 0.00 0.00 0.00 4.18
502 556 1.202604 TCCCTGTGTTTGGAACTCGTC 60.203 52.381 0.00 0.00 0.00 4.20
516 570 2.219325 CTCGTCTGACTGAGGTGCCC 62.219 65.000 16.57 0.00 32.81 5.36
530 584 1.448985 GTGCCCGTTTCTTCTATGCA 58.551 50.000 0.00 0.00 0.00 3.96
552 606 9.970395 ATGCAATGTCAAACTAATATATTGGTG 57.030 29.630 14.45 4.51 31.56 4.17
553 607 8.965819 TGCAATGTCAAACTAATATATTGGTGT 58.034 29.630 14.45 7.00 31.56 4.16
554 608 9.236691 GCAATGTCAAACTAATATATTGGTGTG 57.763 33.333 20.70 20.70 37.70 3.82
603 657 6.655425 TGTTTTGGATTAATATGTGGTGTCGA 59.345 34.615 0.00 0.00 0.00 4.20
604 658 7.175119 TGTTTTGGATTAATATGTGGTGTCGAA 59.825 33.333 0.00 0.00 0.00 3.71
611 665 9.646336 GATTAATATGTGGTGTCGAACAATTAC 57.354 33.333 0.00 0.00 0.00 1.89
612 666 8.549338 TTAATATGTGGTGTCGAACAATTACA 57.451 30.769 0.00 0.00 0.00 2.41
621 676 4.814234 TGTCGAACAATTACAAGTGCTCTT 59.186 37.500 0.00 0.00 0.00 2.85
622 677 5.295787 TGTCGAACAATTACAAGTGCTCTTT 59.704 36.000 0.00 0.00 0.00 2.52
624 679 7.172532 TGTCGAACAATTACAAGTGCTCTTTAT 59.827 33.333 0.00 0.00 0.00 1.40
625 680 7.688578 GTCGAACAATTACAAGTGCTCTTTATC 59.311 37.037 0.00 0.00 0.00 1.75
626 681 6.961554 CGAACAATTACAAGTGCTCTTTATCC 59.038 38.462 0.00 0.00 0.00 2.59
637 692 3.910627 TGCTCTTTATCCTCCTATTCCCC 59.089 47.826 0.00 0.00 0.00 4.81
639 694 4.351111 GCTCTTTATCCTCCTATTCCCCAA 59.649 45.833 0.00 0.00 0.00 4.12
640 695 5.746361 GCTCTTTATCCTCCTATTCCCCAAC 60.746 48.000 0.00 0.00 0.00 3.77
677 813 9.793252 GTATGTATGTAAACTATATACACCCGG 57.207 37.037 0.00 0.00 42.76 5.73
678 814 7.838079 TGTATGTAAACTATATACACCCGGT 57.162 36.000 0.00 0.00 37.69 5.28
679 815 8.248904 TGTATGTAAACTATATACACCCGGTT 57.751 34.615 0.00 0.00 37.69 4.44
687 1762 7.133133 ACTATATACACCCGGTTCAGATTTT 57.867 36.000 0.00 0.00 0.00 1.82
688 1763 7.571025 ACTATATACACCCGGTTCAGATTTTT 58.429 34.615 0.00 0.00 0.00 1.94
722 2700 8.616076 AGAACATCTTATAATTCGAAAAGCAGG 58.384 33.333 0.00 0.00 0.00 4.85
723 2701 7.264373 ACATCTTATAATTCGAAAAGCAGGG 57.736 36.000 0.00 0.00 0.00 4.45
724 2702 7.054124 ACATCTTATAATTCGAAAAGCAGGGA 58.946 34.615 0.00 0.00 0.00 4.20
725 2703 7.227512 ACATCTTATAATTCGAAAAGCAGGGAG 59.772 37.037 0.00 0.00 0.00 4.30
726 2704 6.650120 TCTTATAATTCGAAAAGCAGGGAGT 58.350 36.000 0.00 0.00 0.00 3.85
744 2722 4.640647 GGGAGTATGTTGTTCCCTGAAATC 59.359 45.833 1.55 0.00 45.84 2.17
750 2728 0.704076 TGTTCCCTGAAATCCCCCAG 59.296 55.000 0.00 0.00 0.00 4.45
768 3031 5.208121 CCCCAGCCATATAGGAAAGAAAAA 58.792 41.667 0.00 0.00 41.22 1.94
804 3067 4.260702 CGATTCCTAGACCACTACGACTTC 60.261 50.000 0.00 0.00 0.00 3.01
816 3079 5.230942 CACTACGACTTCAGGAAGAACATT 58.769 41.667 15.51 0.00 40.79 2.71
817 3080 5.119279 CACTACGACTTCAGGAAGAACATTG 59.881 44.000 15.51 0.40 40.79 2.82
842 3105 1.134694 GGCAAATTCGTGACTCCGC 59.865 57.895 0.00 0.00 0.00 5.54
843 3106 1.134694 GCAAATTCGTGACTCCGCC 59.865 57.895 0.00 0.00 0.00 6.13
844 3107 1.419922 CAAATTCGTGACTCCGCCG 59.580 57.895 0.00 0.00 0.00 6.46
871 3134 3.185188 CACAGCATCCGAAATATTCTCCG 59.815 47.826 0.00 0.00 0.00 4.63
925 3197 0.179018 AGGCAAGTTGAAAGTCGCCT 60.179 50.000 7.16 0.37 44.89 5.52
928 3200 1.604278 GCAAGTTGAAAGTCGCCTTCT 59.396 47.619 7.16 0.00 0.00 2.85
965 3237 2.125912 CCGCCGGAACAGACAGAG 60.126 66.667 5.05 0.00 0.00 3.35
966 3238 2.636412 CCGCCGGAACAGACAGAGA 61.636 63.158 5.05 0.00 0.00 3.10
967 3239 1.444553 CGCCGGAACAGACAGAGAC 60.445 63.158 5.05 0.00 0.00 3.36
968 3240 1.079750 GCCGGAACAGACAGAGACC 60.080 63.158 5.05 0.00 0.00 3.85
971 3243 0.169230 CGGAACAGACAGAGACCGAG 59.831 60.000 0.00 0.00 42.40 4.63
972 3244 1.535833 GGAACAGACAGAGACCGAGA 58.464 55.000 0.00 0.00 0.00 4.04
973 3245 1.470890 GGAACAGACAGAGACCGAGAG 59.529 57.143 0.00 0.00 0.00 3.20
1078 3371 1.381327 CTCGTAAGCCTCCCTCCCA 60.381 63.158 0.00 0.00 37.18 4.37
1227 3522 2.541999 CGATCTCCCGCAACTTCTACTC 60.542 54.545 0.00 0.00 0.00 2.59
1270 3568 0.796312 CGTTCGATTGGTGGTCTTGG 59.204 55.000 0.00 0.00 0.00 3.61
1331 3629 0.308376 GCTACGAGATCGAGGTGGTC 59.692 60.000 9.58 0.00 43.02 4.02
1442 3740 4.473520 ATCAAGGCGCTCACCCCG 62.474 66.667 7.64 0.00 0.00 5.73
1516 3814 4.828925 GCAGGCCTGACTCGCTCC 62.829 72.222 37.21 12.12 0.00 4.70
1534 3836 3.139029 CGAAGGAAGCACTGGTACC 57.861 57.895 4.43 4.43 0.00 3.34
1544 3846 1.223187 CACTGGTACCGAAACCACAC 58.777 55.000 7.57 0.00 44.68 3.82
1547 3849 0.766131 TGGTACCGAAACCACACCAT 59.234 50.000 7.57 0.00 44.68 3.55
1548 3850 1.161843 GGTACCGAAACCACACCATG 58.838 55.000 0.00 0.00 39.50 3.66
1550 3852 1.802365 GTACCGAAACCACACCATGTC 59.198 52.381 0.00 0.00 0.00 3.06
1570 3872 1.312371 CGCCGTTGGATGTTGGGAAT 61.312 55.000 0.00 0.00 0.00 3.01
1646 3955 2.417719 GAATCGAGACTTTGCAGTGGT 58.582 47.619 0.00 0.00 31.22 4.16
1658 3967 1.452651 CAGTGGTGCTATGCCTGGG 60.453 63.158 0.00 0.00 0.00 4.45
1684 3994 2.742774 AGATTTTGCTGCGTTTTGTCC 58.257 42.857 0.00 0.00 0.00 4.02
1705 4021 4.337274 TCCATGTGATTGTGATGATTCAGC 59.663 41.667 0.00 0.00 30.85 4.26
1769 4085 6.169094 ACATGTTCCTGAGTTTCTGTCATAG 58.831 40.000 0.00 0.00 0.00 2.23
1770 4086 6.014242 ACATGTTCCTGAGTTTCTGTCATAGA 60.014 38.462 0.00 0.00 0.00 1.98
1772 4088 5.540337 TGTTCCTGAGTTTCTGTCATAGACT 59.460 40.000 0.00 0.00 34.43 3.24
1773 4089 6.719829 TGTTCCTGAGTTTCTGTCATAGACTA 59.280 38.462 0.00 0.00 34.43 2.59
1774 4090 7.232737 TGTTCCTGAGTTTCTGTCATAGACTAA 59.767 37.037 0.00 0.00 34.43 2.24
1777 4093 6.127479 CCTGAGTTTCTGTCATAGACTAAGCT 60.127 42.308 0.00 1.38 34.43 3.74
1831 4459 3.427233 GCTTCTGTTGAATGTGATGGCTC 60.427 47.826 0.00 0.00 0.00 4.70
1873 4501 1.597742 TTCTCTTTGCTGTCTGGCAC 58.402 50.000 0.00 0.00 42.27 5.01
1877 4839 0.309922 CTTTGCTGTCTGGCACACTG 59.690 55.000 0.00 0.00 42.27 3.66
1892 4854 3.016736 CACACTGGCTGTTATTTAGGGG 58.983 50.000 0.00 0.00 0.00 4.79
1896 4858 3.332485 ACTGGCTGTTATTTAGGGGTTCA 59.668 43.478 0.00 0.00 0.00 3.18
1915 4877 4.831674 TCAGATGACAGTTGATCCACAT 57.168 40.909 0.00 0.00 0.00 3.21
1919 4881 5.876460 CAGATGACAGTTGATCCACATTGTA 59.124 40.000 0.00 0.00 30.58 2.41
1921 4883 6.765036 AGATGACAGTTGATCCACATTGTATC 59.235 38.462 0.00 0.00 30.58 2.24
1931 4893 3.388024 TCCACATTGTATCCTCAGCCTAC 59.612 47.826 0.00 0.00 0.00 3.18
1934 4896 5.185454 CACATTGTATCCTCAGCCTACAAA 58.815 41.667 2.47 0.00 38.46 2.83
1939 4901 3.567478 ATCCTCAGCCTACAAATGTCC 57.433 47.619 0.00 0.00 0.00 4.02
1940 4902 1.559682 TCCTCAGCCTACAAATGTCCC 59.440 52.381 0.00 0.00 0.00 4.46
1941 4903 1.561542 CCTCAGCCTACAAATGTCCCT 59.438 52.381 0.00 0.00 0.00 4.20
1965 4927 0.999406 CGTGCTGTCGGTTAGATTGG 59.001 55.000 0.00 0.00 0.00 3.16
1967 4929 0.739462 TGCTGTCGGTTAGATTGGCG 60.739 55.000 0.00 0.00 0.00 5.69
1995 4957 4.460382 TCCAAGGCATCTGAAATCAAGTTC 59.540 41.667 0.00 0.00 0.00 3.01
2015 5524 3.411446 TCGTCTGTTTCAGCCATTGAAT 58.589 40.909 0.00 0.00 44.90 2.57
2052 5642 7.796054 TCCTTCTCTAGAATTTCAATACAGGG 58.204 38.462 0.00 0.00 33.01 4.45
2200 5791 1.670791 ACTGGTACACAAAACACCGG 58.329 50.000 0.00 0.00 43.22 5.28
2221 5812 2.575532 CAAGTCCCTTTGCAGAACTCA 58.424 47.619 0.00 0.00 0.00 3.41
2241 5832 3.264193 TCACATTCATGGTGGTAGAAGCT 59.736 43.478 0.00 0.00 36.90 3.74
2242 5833 3.376234 CACATTCATGGTGGTAGAAGCTG 59.624 47.826 0.00 0.00 32.65 4.24
2283 5874 2.920384 TGGCTCACCACCACGCTA 60.920 61.111 0.00 0.00 42.67 4.26
2289 5880 1.110518 TCACCACCACGCTACACAGA 61.111 55.000 0.00 0.00 0.00 3.41
2292 5883 1.738099 CACCACGCTACACAGAGCC 60.738 63.158 0.00 0.00 39.43 4.70
2299 5890 1.517242 GCTACACAGAGCCCATATGC 58.483 55.000 0.00 0.00 36.38 3.14
2311 5902 1.402787 CCATATGCCCAGACCAAACC 58.597 55.000 0.00 0.00 0.00 3.27
2383 5976 4.989797 CAGCCAGATGCAACAATACAAAAA 59.010 37.500 0.00 0.00 44.83 1.94
2476 6069 2.130272 GGAAGGGGTTCCAACTGATC 57.870 55.000 0.00 0.00 40.79 2.92
2480 6073 1.279271 AGGGGTTCCAACTGATCGAAG 59.721 52.381 0.00 0.00 34.83 3.79
2482 6075 2.290071 GGGGTTCCAACTGATCGAAGAA 60.290 50.000 0.00 0.00 43.58 2.52
2507 6100 9.860898 AAAGAAAAATCATTACTCAATACTGCC 57.139 29.630 0.00 0.00 0.00 4.85
2508 6101 7.697691 AGAAAAATCATTACTCAATACTGCCG 58.302 34.615 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.238281 CGATGTTTTAGCGTGCGTTG 58.762 50.000 0.00 0.00 32.58 4.10
24 25 7.569957 GCAATCCATGAGAAAAATGTGTGAAAC 60.570 37.037 0.00 0.00 37.35 2.78
81 82 7.118971 GGTCTGTCCTCTTATGATTATCAATGC 59.881 40.741 0.00 0.00 0.00 3.56
89 90 8.324191 TCAAATAGGTCTGTCCTCTTATGATT 57.676 34.615 0.00 0.00 44.42 2.57
125 126 3.065371 CCGAATCATAAAGCTCCCACAAC 59.935 47.826 0.00 0.00 0.00 3.32
146 147 8.946085 TGTTGAAAATAACATCACACTAGATCC 58.054 33.333 0.00 0.00 35.75 3.36
162 163 7.044181 TGTTGCAGAACCAAATGTTGAAAATA 58.956 30.769 0.00 0.00 37.29 1.40
168 169 6.645827 TCATTATGTTGCAGAACCAAATGTTG 59.354 34.615 10.39 0.00 37.29 3.33
175 176 6.343716 ACAATTCATTATGTTGCAGAACCA 57.656 33.333 0.00 0.00 0.00 3.67
200 204 7.234371 TGTCTCATAGAATTAGATTCCTCCAGG 59.766 40.741 0.00 0.00 40.13 4.45
220 224 8.918202 AAAGGTTCAGTATTACAATTGTCTCA 57.082 30.769 15.85 0.57 0.00 3.27
221 225 9.612620 CAAAAGGTTCAGTATTACAATTGTCTC 57.387 33.333 15.85 4.41 0.00 3.36
225 229 8.081633 TCTGCAAAAGGTTCAGTATTACAATTG 58.918 33.333 3.24 3.24 0.00 2.32
228 232 6.544197 TGTCTGCAAAAGGTTCAGTATTACAA 59.456 34.615 0.00 0.00 0.00 2.41
229 233 6.058833 TGTCTGCAAAAGGTTCAGTATTACA 58.941 36.000 0.00 0.00 0.00 2.41
230 234 6.554334 TGTCTGCAAAAGGTTCAGTATTAC 57.446 37.500 0.00 0.00 0.00 1.89
233 237 4.278419 GGTTGTCTGCAAAAGGTTCAGTAT 59.722 41.667 0.00 0.00 36.22 2.12
234 238 3.630312 GGTTGTCTGCAAAAGGTTCAGTA 59.370 43.478 0.00 0.00 36.22 2.74
235 239 2.427095 GGTTGTCTGCAAAAGGTTCAGT 59.573 45.455 0.00 0.00 36.22 3.41
236 240 2.426738 TGGTTGTCTGCAAAAGGTTCAG 59.573 45.455 0.00 0.00 36.22 3.02
263 312 1.550524 GACAAAAAGGAAGGGGATGGC 59.449 52.381 0.00 0.00 0.00 4.40
346 395 2.429058 CATCAGCAGGATCCCCCG 59.571 66.667 8.55 0.00 40.87 5.73
366 416 2.826979 ACGCACACTACTCATAGTCG 57.173 50.000 0.00 0.00 39.80 4.18
448 499 8.028354 CACAATTGTATCATCACAGGCTAAAAA 58.972 33.333 11.53 0.00 0.00 1.94
485 539 2.540101 GTCAGACGAGTTCCAAACACAG 59.460 50.000 0.00 0.00 0.00 3.66
496 550 1.528292 GGCACCTCAGTCAGACGAGT 61.528 60.000 16.35 2.95 0.00 4.18
497 551 1.214062 GGCACCTCAGTCAGACGAG 59.786 63.158 12.76 12.76 0.00 4.18
498 552 3.366629 GGCACCTCAGTCAGACGA 58.633 61.111 0.00 0.00 0.00 4.20
516 570 6.373779 AGTTTGACATTGCATAGAAGAAACG 58.626 36.000 0.00 0.00 0.00 3.60
556 610 7.222000 ACAATATTGCTAGTTTCCGGAAAAA 57.778 32.000 30.49 20.52 31.33 1.94
557 611 6.827586 ACAATATTGCTAGTTTCCGGAAAA 57.172 33.333 30.49 15.71 31.33 2.29
558 612 6.827586 AACAATATTGCTAGTTTCCGGAAA 57.172 33.333 25.67 25.67 0.00 3.13
559 613 6.827586 AAACAATATTGCTAGTTTCCGGAA 57.172 33.333 14.35 14.35 28.81 4.30
560 614 6.349777 CCAAAACAATATTGCTAGTTTCCGGA 60.350 38.462 15.48 0.00 33.45 5.14
561 615 5.804979 CCAAAACAATATTGCTAGTTTCCGG 59.195 40.000 15.48 0.00 33.45 5.14
562 616 6.616947 TCCAAAACAATATTGCTAGTTTCCG 58.383 36.000 15.48 4.20 33.45 4.30
576 630 7.973388 CGACACCACATATTAATCCAAAACAAT 59.027 33.333 0.00 0.00 0.00 2.71
599 653 4.992381 AGAGCACTTGTAATTGTTCGAC 57.008 40.909 0.00 0.00 0.00 4.20
603 657 7.121315 GGAGGATAAAGAGCACTTGTAATTGTT 59.879 37.037 0.00 0.00 36.39 2.83
604 658 6.599638 GGAGGATAAAGAGCACTTGTAATTGT 59.400 38.462 0.00 0.00 36.39 2.71
611 665 5.994668 GGAATAGGAGGATAAAGAGCACTTG 59.005 44.000 0.00 0.00 36.39 3.16
612 666 5.072464 GGGAATAGGAGGATAAAGAGCACTT 59.928 44.000 0.00 0.00 38.05 3.16
621 676 6.606241 AATTGTTGGGGAATAGGAGGATAA 57.394 37.500 0.00 0.00 0.00 1.75
622 677 6.372931 CAAATTGTTGGGGAATAGGAGGATA 58.627 40.000 0.00 0.00 0.00 2.59
624 679 4.609301 CAAATTGTTGGGGAATAGGAGGA 58.391 43.478 0.00 0.00 0.00 3.71
639 694 9.515226 AGTTTACATACATACACTCCAAATTGT 57.485 29.630 0.00 0.00 0.00 2.71
651 787 9.793252 CCGGGTGTATATAGTTTACATACATAC 57.207 37.037 0.00 0.00 37.45 2.39
652 788 9.532494 ACCGGGTGTATATAGTTTACATACATA 57.468 33.333 6.32 0.00 37.45 2.29
654 790 7.838079 ACCGGGTGTATATAGTTTACATACA 57.162 36.000 6.32 0.00 33.80 2.29
657 793 7.288389 TCTGAACCGGGTGTATATAGTTTACAT 59.712 37.037 6.32 0.00 32.56 2.29
700 1775 7.227512 ACTCCCTGCTTTTCGAATTATAAGATG 59.772 37.037 10.73 3.35 0.00 2.90
701 1776 7.283329 ACTCCCTGCTTTTCGAATTATAAGAT 58.717 34.615 10.73 0.00 0.00 2.40
702 1777 6.650120 ACTCCCTGCTTTTCGAATTATAAGA 58.350 36.000 10.73 0.00 0.00 2.10
704 1779 7.990886 ACATACTCCCTGCTTTTCGAATTATAA 59.009 33.333 0.00 0.00 0.00 0.98
705 1780 7.506114 ACATACTCCCTGCTTTTCGAATTATA 58.494 34.615 0.00 0.00 0.00 0.98
713 2691 4.082733 GGAACAACATACTCCCTGCTTTTC 60.083 45.833 0.00 0.00 0.00 2.29
718 2696 1.751437 GGGAACAACATACTCCCTGC 58.249 55.000 0.00 0.00 44.81 4.85
722 2700 4.640647 GGATTTCAGGGAACAACATACTCC 59.359 45.833 0.00 0.00 0.00 3.85
723 2701 4.640647 GGGATTTCAGGGAACAACATACTC 59.359 45.833 0.00 0.00 0.00 2.59
724 2702 4.569865 GGGGATTTCAGGGAACAACATACT 60.570 45.833 0.00 0.00 0.00 2.12
725 2703 3.699538 GGGGATTTCAGGGAACAACATAC 59.300 47.826 0.00 0.00 0.00 2.39
726 2704 3.309556 GGGGGATTTCAGGGAACAACATA 60.310 47.826 0.00 0.00 0.00 2.29
737 2715 2.986534 ATATGGCTGGGGGATTTCAG 57.013 50.000 0.00 0.00 0.00 3.02
744 2722 2.348472 TCTTTCCTATATGGCTGGGGG 58.652 52.381 0.00 0.00 35.26 5.40
768 3031 6.766467 GGTCTAGGAATCGAATATTTGGTGTT 59.234 38.462 2.78 0.00 0.00 3.32
769 3032 6.126883 TGGTCTAGGAATCGAATATTTGGTGT 60.127 38.462 2.78 0.00 0.00 4.16
804 3067 1.806542 CCGTCACCAATGTTCTTCCTG 59.193 52.381 0.00 0.00 0.00 3.86
816 3079 1.228003 ACGAATTTGCCCGTCACCA 60.228 52.632 0.00 0.00 33.23 4.17
817 3080 1.209127 CACGAATTTGCCCGTCACC 59.791 57.895 0.00 0.00 36.83 4.02
842 3105 2.202797 CGGATGCTGTGGTCTCGG 60.203 66.667 0.00 0.00 0.00 4.63
843 3106 0.389817 TTTCGGATGCTGTGGTCTCG 60.390 55.000 0.00 0.00 0.00 4.04
844 3107 2.029838 ATTTCGGATGCTGTGGTCTC 57.970 50.000 0.00 0.00 0.00 3.36
871 3134 2.745968 TCAATTTATCCCACTTGCCCC 58.254 47.619 0.00 0.00 0.00 5.80
925 3197 1.138661 CCAAGGCAAGGCAAACAAGAA 59.861 47.619 0.00 0.00 0.00 2.52
961 3233 2.477176 CGCCTCCTCTCGGTCTCTG 61.477 68.421 0.00 0.00 0.00 3.35
965 3237 0.249114 GATTTCGCCTCCTCTCGGTC 60.249 60.000 0.00 0.00 0.00 4.79
966 3238 1.817209 GATTTCGCCTCCTCTCGGT 59.183 57.895 0.00 0.00 0.00 4.69
967 3239 1.299468 CGATTTCGCCTCCTCTCGG 60.299 63.158 0.00 0.00 0.00 4.63
968 3240 4.310672 CGATTTCGCCTCCTCTCG 57.689 61.111 0.00 0.00 0.00 4.04
978 3250 0.366871 CTGGTCTGTTCGCGATTTCG 59.633 55.000 10.88 0.00 43.27 3.46
979 3251 0.095417 GCTGGTCTGTTCGCGATTTC 59.905 55.000 10.88 4.47 0.00 2.17
980 3252 1.298859 GGCTGGTCTGTTCGCGATTT 61.299 55.000 10.88 0.00 0.00 2.17
1078 3371 2.200955 GGAAGGGGTTTGGAGAGAGAT 58.799 52.381 0.00 0.00 0.00 2.75
1216 3511 4.287326 AGGGGAGAAAAGGAGTAGAAGTTG 59.713 45.833 0.00 0.00 0.00 3.16
1227 3522 3.084786 CAAGCTTACAGGGGAGAAAAGG 58.915 50.000 0.00 0.00 0.00 3.11
1270 3568 5.105228 ACCAATCACAATCCCATCAATCAAC 60.105 40.000 0.00 0.00 0.00 3.18
1516 3814 0.736325 CGGTACCAGTGCTTCCTTCG 60.736 60.000 13.54 0.00 0.00 3.79
1529 3831 1.161843 CATGGTGTGGTTTCGGTACC 58.838 55.000 0.16 0.16 38.73 3.34
1534 3836 1.866237 CGGACATGGTGTGGTTTCG 59.134 57.895 0.00 0.00 0.00 3.46
1544 3846 2.124736 ATCCAACGGCGGACATGG 60.125 61.111 13.24 14.00 38.07 3.66
1547 3849 1.963855 CAACATCCAACGGCGGACA 60.964 57.895 13.24 0.00 38.07 4.02
1548 3850 2.686816 CCAACATCCAACGGCGGAC 61.687 63.158 13.24 0.00 38.07 4.79
1550 3852 3.439540 CCCAACATCCAACGGCGG 61.440 66.667 13.24 0.00 0.00 6.13
1570 3872 4.498177 GCAGAGAGTACTGTATGATGCGAA 60.498 45.833 17.99 0.00 39.73 4.70
1646 3955 2.407562 TCTTATCACCCAGGCATAGCA 58.592 47.619 0.00 0.00 0.00 3.49
1658 3967 5.402270 ACAAAACGCAGCAAAATCTTATCAC 59.598 36.000 0.00 0.00 0.00 3.06
1684 3994 4.279659 CGCTGAATCATCACAATCACATG 58.720 43.478 0.00 0.00 0.00 3.21
1777 4093 6.811170 CCAAAGAAGAAACTAAACTGCAAACA 59.189 34.615 0.00 0.00 0.00 2.83
1831 4459 4.398549 CAAACCAATTTGCAGCAATGAG 57.601 40.909 9.12 1.49 38.92 2.90
1873 4501 3.366052 ACCCCTAAATAACAGCCAGTG 57.634 47.619 0.00 0.00 0.00 3.66
1877 4839 4.230745 TCTGAACCCCTAAATAACAGCC 57.769 45.455 0.00 0.00 0.00 4.85
1892 4854 4.318332 TGTGGATCAACTGTCATCTGAAC 58.682 43.478 1.02 0.00 0.00 3.18
1896 4858 4.914983 ACAATGTGGATCAACTGTCATCT 58.085 39.130 1.02 0.00 0.00 2.90
1915 4877 5.428253 GACATTTGTAGGCTGAGGATACAA 58.572 41.667 0.00 0.00 37.57 2.41
1919 4881 2.173569 GGGACATTTGTAGGCTGAGGAT 59.826 50.000 0.00 0.00 0.00 3.24
1921 4883 1.561542 AGGGACATTTGTAGGCTGAGG 59.438 52.381 0.00 0.00 0.00 3.86
1931 4893 0.240945 GCACGAACCAGGGACATTTG 59.759 55.000 0.00 0.00 0.00 2.32
1934 4896 1.003355 CAGCACGAACCAGGGACAT 60.003 57.895 0.00 0.00 0.00 3.06
1939 4901 2.738521 CCGACAGCACGAACCAGG 60.739 66.667 0.00 0.00 35.09 4.45
1940 4902 0.319211 TAACCGACAGCACGAACCAG 60.319 55.000 0.00 0.00 35.09 4.00
1941 4903 0.319211 CTAACCGACAGCACGAACCA 60.319 55.000 0.00 0.00 35.09 3.67
1965 4927 2.288666 TCAGATGCCTTGGAATTACGC 58.711 47.619 0.00 0.00 0.00 4.42
1967 4929 6.455360 TGATTTCAGATGCCTTGGAATTAC 57.545 37.500 0.00 0.00 0.00 1.89
2048 5638 8.694540 TCATATGTTTTTGGATAACAATCCCTG 58.305 33.333 1.90 0.00 38.82 4.45
2072 5663 4.608170 AGGGATTTTAGAGGGCAATTCA 57.392 40.909 0.00 0.00 0.00 2.57
2146 5737 6.597280 TCATTAGCTTTGTTTTGCAAAAACCT 59.403 30.769 25.40 17.51 45.35 3.50
2221 5812 3.264193 TCAGCTTCTACCACCATGAATGT 59.736 43.478 0.00 0.00 0.00 2.71
2241 5832 2.616634 GCAATCAGCTGAGATCCTCA 57.383 50.000 22.96 0.00 41.15 3.86
2275 5866 2.657237 GGCTCTGTGTAGCGTGGT 59.343 61.111 0.00 0.00 43.74 4.16
2283 5874 1.281199 TGGGCATATGGGCTCTGTGT 61.281 55.000 4.56 0.00 42.84 3.72
2289 5880 1.288508 TTGGTCTGGGCATATGGGCT 61.289 55.000 4.56 0.00 42.84 5.19
2292 5883 1.341877 TGGTTTGGTCTGGGCATATGG 60.342 52.381 4.56 0.00 0.00 2.74
2299 5890 2.672996 CGGCTGGTTTGGTCTGGG 60.673 66.667 0.00 0.00 0.00 4.45
2311 5902 2.046892 CTGAACCCCAGACGGCTG 60.047 66.667 12.69 12.69 45.78 4.85
2322 5913 1.334869 CGATATGCCCTTTGCTGAACC 59.665 52.381 0.00 0.00 42.00 3.62
2352 5943 3.224324 CATCTGGCTGGCCATGGC 61.224 66.667 29.47 29.47 46.15 4.40
2383 5976 2.939103 GCGGTGTCATAGAGCAAGAAAT 59.061 45.455 0.00 0.00 0.00 2.17
2398 5991 1.754803 TGAAATATCCTCTCGCGGTGT 59.245 47.619 6.13 0.00 0.00 4.16
2482 6075 8.184192 CGGCAGTATTGAGTAATGATTTTTCTT 58.816 33.333 0.00 0.00 30.06 2.52


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

AutoCloner maintained by Alex Coulton.