Multiple sequence alignment - TraesCS2A01G503600

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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 TraesCS2A01G503600 chr2A 100.000 3470 0 0 1 3470 732991000 732987531 0.000000e+00 6408.0
1 TraesCS2A01G503600 chr2A 76.058 756 140 29 2661 3388 733039917 733040659 4.260000e-94 355.0
2 TraesCS2A01G503600 chr2B 92.195 1640 86 21 850 2484 727243922 727242320 0.000000e+00 2281.0
3 TraesCS2A01G503600 chr2B 88.605 1641 116 31 850 2484 727317646 727316071 0.000000e+00 1929.0
4 TraesCS2A01G503600 chr2B 95.723 982 35 5 2494 3470 727242037 727241058 0.000000e+00 1574.0
5 TraesCS2A01G503600 chr2B 89.963 269 26 1 2526 2794 727314554 727314287 2.560000e-91 346.0
6 TraesCS2A01G503600 chr2B 94.444 216 12 0 3240 3455 727313996 727313781 2.000000e-87 333.0
7 TraesCS2A01G503600 chr2B 91.322 242 21 0 2849 3090 727314274 727314033 7.180000e-87 331.0
8 TraesCS2A01G503600 chr2B 76.357 571 115 14 2631 3191 727653162 727653722 4.380000e-74 289.0
9 TraesCS2A01G503600 chr2D 91.588 1486 92 10 998 2476 598735167 598733708 0.000000e+00 2021.0
10 TraesCS2A01G503600 chr2D 96.418 977 32 1 2497 3470 598733627 598732651 0.000000e+00 1607.0
11 TraesCS2A01G503600 chr2D 92.380 853 57 3 1 852 623912207 623913052 0.000000e+00 1208.0
12 TraesCS2A01G503600 chr2D 78.142 549 88 21 2847 3388 57258116 57258639 1.550000e-83 320.0
13 TraesCS2A01G503600 chr2D 89.130 92 7 1 3297 3388 57192329 57192417 1.020000e-20 111.0
14 TraesCS2A01G503600 chr6D 92.396 868 61 4 1 865 30534527 30533662 0.000000e+00 1232.0
15 TraesCS2A01G503600 chr6D 77.148 547 95 19 2848 3388 388151914 388152436 1.220000e-74 291.0
16 TraesCS2A01G503600 chr5D 92.623 854 61 2 1 852 534087119 534087972 0.000000e+00 1227.0
17 TraesCS2A01G503600 chr5D 92.182 857 65 2 1 856 376720061 376719206 0.000000e+00 1210.0
18 TraesCS2A01G503600 chr7B 92.697 849 60 2 1 847 634288548 634287700 0.000000e+00 1223.0
19 TraesCS2A01G503600 chr6B 92.479 851 62 2 1 849 57715924 57716774 0.000000e+00 1216.0
20 TraesCS2A01G503600 chr6B 76.374 546 103 16 2847 3388 579887116 579887639 1.590000e-68 270.0
21 TraesCS2A01G503600 chr6A 92.191 858 65 2 1 857 2044936 2044080 0.000000e+00 1212.0
22 TraesCS2A01G503600 chr6A 77.106 546 99 18 2847 3388 534797935 534798458 3.390000e-75 292.0
23 TraesCS2A01G503600 chrUn 92.371 852 62 3 1 850 110780308 110779458 0.000000e+00 1210.0
24 TraesCS2A01G503600 chr7A 91.949 857 68 1 1 856 682327921 682327065 0.000000e+00 1199.0
25 TraesCS2A01G503600 chr5B 72.222 504 105 27 2912 3390 682819895 682819402 4.700000e-24 122.0
26 TraesCS2A01G503600 chr3D 79.675 123 21 4 3042 3162 19037865 19037745 6.170000e-13 86.1


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 TraesCS2A01G503600 chr2A 732987531 732991000 3469 True 6408.00 6408 100.0000 1 3470 1 chr2A.!!$R1 3469
1 TraesCS2A01G503600 chr2A 733039917 733040659 742 False 355.00 355 76.0580 2661 3388 1 chr2A.!!$F1 727
2 TraesCS2A01G503600 chr2B 727241058 727243922 2864 True 1927.50 2281 93.9590 850 3470 2 chr2B.!!$R1 2620
3 TraesCS2A01G503600 chr2B 727313781 727317646 3865 True 734.75 1929 91.0835 850 3455 4 chr2B.!!$R2 2605
4 TraesCS2A01G503600 chr2B 727653162 727653722 560 False 289.00 289 76.3570 2631 3191 1 chr2B.!!$F1 560
5 TraesCS2A01G503600 chr2D 598732651 598735167 2516 True 1814.00 2021 94.0030 998 3470 2 chr2D.!!$R1 2472
6 TraesCS2A01G503600 chr2D 623912207 623913052 845 False 1208.00 1208 92.3800 1 852 1 chr2D.!!$F3 851
7 TraesCS2A01G503600 chr2D 57258116 57258639 523 False 320.00 320 78.1420 2847 3388 1 chr2D.!!$F2 541
8 TraesCS2A01G503600 chr6D 30533662 30534527 865 True 1232.00 1232 92.3960 1 865 1 chr6D.!!$R1 864
9 TraesCS2A01G503600 chr6D 388151914 388152436 522 False 291.00 291 77.1480 2848 3388 1 chr6D.!!$F1 540
10 TraesCS2A01G503600 chr5D 534087119 534087972 853 False 1227.00 1227 92.6230 1 852 1 chr5D.!!$F1 851
11 TraesCS2A01G503600 chr5D 376719206 376720061 855 True 1210.00 1210 92.1820 1 856 1 chr5D.!!$R1 855
12 TraesCS2A01G503600 chr7B 634287700 634288548 848 True 1223.00 1223 92.6970 1 847 1 chr7B.!!$R1 846
13 TraesCS2A01G503600 chr6B 57715924 57716774 850 False 1216.00 1216 92.4790 1 849 1 chr6B.!!$F1 848
14 TraesCS2A01G503600 chr6B 579887116 579887639 523 False 270.00 270 76.3740 2847 3388 1 chr6B.!!$F2 541
15 TraesCS2A01G503600 chr6A 2044080 2044936 856 True 1212.00 1212 92.1910 1 857 1 chr6A.!!$R1 856
16 TraesCS2A01G503600 chr6A 534797935 534798458 523 False 292.00 292 77.1060 2847 3388 1 chr6A.!!$F1 541
17 TraesCS2A01G503600 chrUn 110779458 110780308 850 True 1210.00 1210 92.3710 1 850 1 chrUn.!!$R1 849
18 TraesCS2A01G503600 chr7A 682327065 682327921 856 True 1199.00 1199 91.9490 1 856 1 chr7A.!!$R1 855

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
80 81 0.243636 GGGCGCACAGTAAAATTGCT 59.756 50.0 10.83 0.0 33.90 3.91 F
950 963 0.386731 CCAAATTGAACGCACGGGAC 60.387 55.0 0.00 0.0 0.00 4.46 F
1654 1698 0.167908 TTGCTTAACAATGCGCGAGG 59.832 50.0 12.10 0.0 31.73 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1361 1374 0.029300 CCACTGCAACAACAAGTCGG 59.971 55.000 0.0 0.0 0.0 4.79 R
1990 2037 0.818040 GCCCACAGGAACTTGACGTT 60.818 55.000 0.0 0.0 34.6 3.99 R
3413 5128 3.357079 GTGGCCGTGAAGGTGCTG 61.357 66.667 0.0 0.0 43.7 4.41 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
35 36 2.260154 CCGTGTGTGGCATGAGCAA 61.260 57.895 0.00 0.00 44.61 3.91
80 81 0.243636 GGGCGCACAGTAAAATTGCT 59.756 50.000 10.83 0.00 33.90 3.91
155 156 3.792736 ACCCCGCACGTATGGCAT 61.793 61.111 4.88 4.88 0.00 4.40
202 204 1.411246 CGCAGCTACATTAGGTACCCA 59.589 52.381 8.74 0.00 34.67 4.51
211 213 2.482414 TTAGGTACCCACGGGATGAT 57.518 50.000 9.72 0.00 38.96 2.45
234 236 1.208706 TTAGTTGCCATCCGGGATGA 58.791 50.000 33.39 15.49 42.09 2.92
248 250 4.899457 TCCGGGATGACAGATGTAGTTATT 59.101 41.667 0.00 0.00 0.00 1.40
283 285 9.153721 CAAATATGGTTGTAAAAGCATGACAAT 57.846 29.630 18.61 3.26 40.64 2.71
341 343 1.021202 TTATGGTAGTTGCCGCATGC 58.979 50.000 7.91 7.91 41.77 4.06
368 370 3.026630 ACCATAGTTGTCGTGTGTGAG 57.973 47.619 0.00 0.00 0.00 3.51
655 661 3.226884 GGCAGAAACTAGTTCGCCA 57.773 52.632 26.73 0.00 46.42 5.69
740 747 1.078426 GCCTTGTCCTACGTGGCAT 60.078 57.895 0.00 0.00 38.41 4.40
840 847 3.720531 CACACGTGTGGGCGTTAA 58.279 55.556 35.65 0.00 43.83 2.01
842 849 1.430479 CACACGTGTGGGCGTTAATA 58.570 50.000 35.65 0.00 43.83 0.98
887 894 4.506654 ACAACAAACTTACTGCAGAGTACG 59.493 41.667 23.35 11.07 34.23 3.67
888 895 4.317671 ACAAACTTACTGCAGAGTACGT 57.682 40.909 23.35 11.69 38.47 3.57
889 896 5.443185 ACAAACTTACTGCAGAGTACGTA 57.557 39.130 23.35 0.00 36.42 3.57
890 897 5.458891 ACAAACTTACTGCAGAGTACGTAG 58.541 41.667 23.35 8.54 36.42 3.51
892 899 6.205464 ACAAACTTACTGCAGAGTACGTAGTA 59.795 38.462 23.35 0.00 45.11 1.82
926 939 5.163854 CCAACAGCGTATACTCCAAGAAAAG 60.164 44.000 0.56 0.00 0.00 2.27
938 951 4.897140 TCCAAGAAAAGCCATCCAAATTG 58.103 39.130 0.00 0.00 0.00 2.32
950 963 0.386731 CCAAATTGAACGCACGGGAC 60.387 55.000 0.00 0.00 0.00 4.46
956 969 1.374252 GAACGCACGGGACAGTGAT 60.374 57.895 6.77 0.00 44.43 3.06
957 970 1.352156 GAACGCACGGGACAGTGATC 61.352 60.000 6.77 0.00 44.43 2.92
958 971 2.880879 CGCACGGGACAGTGATCG 60.881 66.667 6.77 0.00 44.43 3.69
959 972 2.261671 GCACGGGACAGTGATCGT 59.738 61.111 6.77 0.49 44.43 3.73
960 973 4.169102 CACGGGACAGTGATCGTG 57.831 61.111 17.45 17.45 44.43 4.35
961 974 2.094659 CACGGGACAGTGATCGTGC 61.095 63.158 18.39 0.00 44.56 5.34
962 975 2.261361 CGGGACAGTGATCGTGCA 59.739 61.111 0.00 0.00 0.00 4.57
963 976 2.094659 CGGGACAGTGATCGTGCAC 61.095 63.158 6.82 6.82 39.05 4.57
964 977 1.741770 GGGACAGTGATCGTGCACC 60.742 63.158 12.15 0.00 39.59 5.01
965 978 1.293498 GGACAGTGATCGTGCACCT 59.707 57.895 12.15 0.00 39.59 4.00
966 979 0.530744 GGACAGTGATCGTGCACCTA 59.469 55.000 12.15 0.00 39.59 3.08
967 980 1.630148 GACAGTGATCGTGCACCTAC 58.370 55.000 12.15 5.34 39.59 3.18
971 984 2.805671 CAGTGATCGTGCACCTACAAAA 59.194 45.455 12.15 0.00 39.59 2.44
972 985 2.806244 AGTGATCGTGCACCTACAAAAC 59.194 45.455 12.15 1.06 39.59 2.43
995 1008 0.811616 GAGACGCGCCCAGATCAAAT 60.812 55.000 5.73 0.00 0.00 2.32
1005 1018 3.366679 GCCCAGATCAAATAATCATGGCG 60.367 47.826 0.00 0.00 35.93 5.69
1263 1276 1.677637 CCGACTACCCTGGCTTCTCC 61.678 65.000 0.00 0.00 0.00 3.71
1346 1359 3.757248 AATCACCGGAGATGGCGGC 62.757 63.158 15.53 0.00 0.00 6.53
1372 1385 2.502093 TCGTGGCCGACTTGTTGT 59.498 55.556 0.00 0.00 38.40 3.32
1373 1386 1.153329 TCGTGGCCGACTTGTTGTT 60.153 52.632 0.00 0.00 38.40 2.83
1382 1415 1.102978 GACTTGTTGTTGCAGTGGGT 58.897 50.000 0.00 0.00 0.00 4.51
1524 1557 1.300931 TGAGAGCGCCAACTCACAC 60.301 57.895 20.20 3.40 39.26 3.82
1525 1558 1.300931 GAGAGCGCCAACTCACACA 60.301 57.895 17.69 0.00 39.26 3.72
1526 1559 0.880278 GAGAGCGCCAACTCACACAA 60.880 55.000 17.69 0.00 39.26 3.33
1568 1601 9.761504 ACTAGTGATGAAGTGATGATCTATTTG 57.238 33.333 0.00 0.00 0.00 2.32
1569 1602 9.205719 CTAGTGATGAAGTGATGATCTATTTGG 57.794 37.037 0.00 0.00 0.00 3.28
1570 1603 7.571919 AGTGATGAAGTGATGATCTATTTGGT 58.428 34.615 0.00 0.00 0.00 3.67
1571 1604 7.498239 AGTGATGAAGTGATGATCTATTTGGTG 59.502 37.037 0.00 0.00 0.00 4.17
1572 1605 7.281774 GTGATGAAGTGATGATCTATTTGGTGT 59.718 37.037 0.00 0.00 0.00 4.16
1573 1606 6.990341 TGAAGTGATGATCTATTTGGTGTG 57.010 37.500 0.00 0.00 0.00 3.82
1592 1636 4.146961 GTGTGATTTCGTGTTGCTCAATTG 59.853 41.667 0.00 0.00 0.00 2.32
1633 1677 1.152819 CAGCCCATCCCTGGTCATG 60.153 63.158 0.00 0.00 41.37 3.07
1654 1698 0.167908 TTGCTTAACAATGCGCGAGG 59.832 50.000 12.10 0.00 31.73 4.63
1788 1832 1.064946 CATGGACTCGCTCGTCTCC 59.935 63.158 2.86 0.00 34.38 3.71
1791 1838 2.400402 GACTCGCTCGTCTCCGAC 59.600 66.667 0.00 0.00 38.40 4.79
1929 1976 2.959372 CTGTACGTGTCGCTGGGA 59.041 61.111 0.00 0.00 0.00 4.37
2196 2243 3.195698 GGCGTTCCGATGCTCACC 61.196 66.667 0.00 0.00 37.92 4.02
2276 2327 7.176589 AGATTGGGTACAGTCTTAAAGAGAG 57.823 40.000 0.00 0.00 40.34 3.20
2283 2334 5.083533 ACAGTCTTAAAGAGAGGATGCAG 57.916 43.478 0.00 0.00 34.31 4.41
2286 2337 2.159043 TCTTAAAGAGAGGATGCAGCCG 60.159 50.000 16.75 0.00 0.00 5.52
2445 2496 1.135333 GGATCTTCGTCCACTGACCTC 59.865 57.143 0.00 0.00 38.32 3.85
2773 4421 2.579201 CTTCTCCGTGGCGTCCAT 59.421 61.111 1.90 0.00 35.28 3.41
3413 5128 2.811317 CTCCCGAGCGTGCTGTTC 60.811 66.667 0.00 0.00 0.00 3.18
3464 5179 1.375523 GAACCTGCCCCTGTACACG 60.376 63.158 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 3.968096 CACGTGTGAGCAATTTTACTGTG 59.032 43.478 7.58 0.00 0.00 3.66
149 150 2.361789 GCCATTTTTGCTTCATGCCAT 58.638 42.857 0.00 0.00 42.00 4.40
155 156 1.537776 CGTGTGGCCATTTTTGCTTCA 60.538 47.619 9.72 0.00 0.00 3.02
164 165 2.034066 CCAGGACGTGTGGCCATT 59.966 61.111 9.72 0.00 0.00 3.16
202 204 3.214328 GGCAACTAAATCATCATCCCGT 58.786 45.455 0.00 0.00 0.00 5.28
211 213 1.562008 TCCCGGATGGCAACTAAATCA 59.438 47.619 0.73 0.00 37.61 2.57
234 236 4.503296 GCCATCCCGAATAACTACATCTGT 60.503 45.833 0.00 0.00 0.00 3.41
248 250 2.305928 CAACCATATTTGCCATCCCGA 58.694 47.619 0.00 0.00 0.00 5.14
341 343 5.146460 CACACGACAACTATGGTTTGATTG 58.854 41.667 0.00 0.00 32.73 2.67
368 370 8.601476 GTTTGACCATATGTAGCAAGTAGTTAC 58.399 37.037 1.24 0.00 34.81 2.50
618 624 1.480212 CCACACAGCCACCACCTAGA 61.480 60.000 0.00 0.00 0.00 2.43
740 747 2.110213 ACCGAGGCAGTTTTCGCA 59.890 55.556 0.00 0.00 35.58 5.10
840 847 9.862371 TGTTGCACCATAAAATTACGAAAATAT 57.138 25.926 0.00 0.00 0.00 1.28
842 849 8.491950 GTTGTTGCACCATAAAATTACGAAAAT 58.508 29.630 0.00 0.00 0.00 1.82
887 894 3.626217 GCTGTTGGGCCATAAAGTACTAC 59.374 47.826 7.26 0.00 0.00 2.73
888 895 3.680475 CGCTGTTGGGCCATAAAGTACTA 60.680 47.826 7.26 0.00 0.00 1.82
889 896 2.723273 GCTGTTGGGCCATAAAGTACT 58.277 47.619 7.26 0.00 0.00 2.73
890 897 1.400494 CGCTGTTGGGCCATAAAGTAC 59.600 52.381 7.26 1.01 0.00 2.73
891 898 1.003812 ACGCTGTTGGGCCATAAAGTA 59.996 47.619 7.26 0.00 0.00 2.24
892 899 0.251165 ACGCTGTTGGGCCATAAAGT 60.251 50.000 7.26 1.28 0.00 2.66
893 900 1.745232 TACGCTGTTGGGCCATAAAG 58.255 50.000 7.26 6.66 0.00 1.85
926 939 1.349234 GTGCGTTCAATTTGGATGGC 58.651 50.000 0.00 0.00 0.00 4.40
938 951 1.352156 GATCACTGTCCCGTGCGTTC 61.352 60.000 0.00 0.00 34.92 3.95
950 963 2.078849 TTGTAGGTGCACGATCACTG 57.921 50.000 11.45 0.00 37.16 3.66
956 969 3.271729 TCTTTGTTTTGTAGGTGCACGA 58.728 40.909 11.45 0.00 0.00 4.35
957 970 3.311322 TCTCTTTGTTTTGTAGGTGCACG 59.689 43.478 11.45 0.00 0.00 5.34
958 971 4.598062 GTCTCTTTGTTTTGTAGGTGCAC 58.402 43.478 8.80 8.80 0.00 4.57
959 972 3.311322 CGTCTCTTTGTTTTGTAGGTGCA 59.689 43.478 0.00 0.00 0.00 4.57
960 973 3.848554 GCGTCTCTTTGTTTTGTAGGTGC 60.849 47.826 0.00 0.00 0.00 5.01
961 974 3.603857 CGCGTCTCTTTGTTTTGTAGGTG 60.604 47.826 0.00 0.00 0.00 4.00
962 975 2.542595 CGCGTCTCTTTGTTTTGTAGGT 59.457 45.455 0.00 0.00 0.00 3.08
963 976 2.661979 GCGCGTCTCTTTGTTTTGTAGG 60.662 50.000 8.43 0.00 0.00 3.18
964 977 2.560896 GCGCGTCTCTTTGTTTTGTAG 58.439 47.619 8.43 0.00 0.00 2.74
965 978 1.262151 GGCGCGTCTCTTTGTTTTGTA 59.738 47.619 8.43 0.00 0.00 2.41
966 979 0.028902 GGCGCGTCTCTTTGTTTTGT 59.971 50.000 8.43 0.00 0.00 2.83
967 980 0.660300 GGGCGCGTCTCTTTGTTTTG 60.660 55.000 11.94 0.00 0.00 2.44
971 984 2.172483 ATCTGGGCGCGTCTCTTTGT 62.172 55.000 11.94 0.00 0.00 2.83
972 985 1.424493 GATCTGGGCGCGTCTCTTTG 61.424 60.000 11.94 0.00 0.00 2.77
1263 1276 2.377310 CCTGGTGTTAACGGCGTCG 61.377 63.158 15.17 8.42 43.02 5.12
1312 1325 0.883814 GATTGCAGCATCCCCTCGAG 60.884 60.000 5.13 5.13 0.00 4.04
1313 1326 1.146930 GATTGCAGCATCCCCTCGA 59.853 57.895 0.00 0.00 0.00 4.04
1314 1327 1.153107 TGATTGCAGCATCCCCTCG 60.153 57.895 0.00 0.00 0.00 4.63
1315 1328 1.105759 GGTGATTGCAGCATCCCCTC 61.106 60.000 0.00 0.00 42.00 4.30
1316 1329 1.076485 GGTGATTGCAGCATCCCCT 60.076 57.895 0.00 0.00 42.00 4.79
1318 1331 2.484062 CCGGTGATTGCAGCATCCC 61.484 63.158 0.00 0.05 42.53 3.85
1319 1332 1.442526 CTCCGGTGATTGCAGCATCC 61.443 60.000 0.00 0.00 42.53 3.51
1321 1334 0.182061 ATCTCCGGTGATTGCAGCAT 59.818 50.000 13.23 0.00 42.53 3.79
1322 1335 0.745486 CATCTCCGGTGATTGCAGCA 60.745 55.000 16.24 0.00 42.53 4.41
1356 1369 1.010125 CAACAACAAGTCGGCCACG 60.010 57.895 2.24 0.00 42.74 4.94
1357 1370 1.299089 GCAACAACAAGTCGGCCAC 60.299 57.895 2.24 0.00 0.00 5.01
1358 1371 1.723608 CTGCAACAACAAGTCGGCCA 61.724 55.000 2.24 0.00 31.53 5.36
1359 1372 1.008538 CTGCAACAACAAGTCGGCC 60.009 57.895 0.00 0.00 31.53 6.13
1360 1373 0.592247 CACTGCAACAACAAGTCGGC 60.592 55.000 0.00 0.00 0.00 5.54
1361 1374 0.029300 CCACTGCAACAACAAGTCGG 59.971 55.000 0.00 0.00 0.00 4.79
1362 1375 0.029300 CCCACTGCAACAACAAGTCG 59.971 55.000 0.00 0.00 0.00 4.18
1363 1376 1.102978 ACCCACTGCAACAACAAGTC 58.897 50.000 0.00 0.00 0.00 3.01
1364 1377 0.817013 CACCCACTGCAACAACAAGT 59.183 50.000 0.00 0.00 0.00 3.16
1365 1378 0.102844 CCACCCACTGCAACAACAAG 59.897 55.000 0.00 0.00 0.00 3.16
1366 1379 0.613292 ACCACCCACTGCAACAACAA 60.613 50.000 0.00 0.00 0.00 2.83
1367 1380 1.000270 ACCACCCACTGCAACAACA 60.000 52.632 0.00 0.00 0.00 3.33
1368 1381 1.437160 CACCACCCACTGCAACAAC 59.563 57.895 0.00 0.00 0.00 3.32
1369 1382 2.422231 GCACCACCCACTGCAACAA 61.422 57.895 0.00 0.00 33.31 2.83
1370 1383 2.832661 GCACCACCCACTGCAACA 60.833 61.111 0.00 0.00 33.31 3.33
1371 1384 3.605664 GGCACCACCCACTGCAAC 61.606 66.667 0.00 0.00 34.90 4.17
1452 1485 1.421410 GCTCGAAGTGGTACATGGCG 61.421 60.000 0.00 0.00 44.52 5.69
1456 1489 1.153628 GGCGCTCGAAGTGGTACAT 60.154 57.895 7.64 0.00 44.52 2.29
1526 1559 9.670442 TCATCACTAGTAATAATAGGGGAAAGT 57.330 33.333 0.00 0.00 0.00 2.66
1564 1597 3.068024 AGCAACACGAAATCACACCAAAT 59.932 39.130 0.00 0.00 0.00 2.32
1565 1598 2.425312 AGCAACACGAAATCACACCAAA 59.575 40.909 0.00 0.00 0.00 3.28
1566 1599 2.020720 AGCAACACGAAATCACACCAA 58.979 42.857 0.00 0.00 0.00 3.67
1567 1600 1.601903 GAGCAACACGAAATCACACCA 59.398 47.619 0.00 0.00 0.00 4.17
1568 1601 1.601903 TGAGCAACACGAAATCACACC 59.398 47.619 0.00 0.00 0.00 4.16
1569 1602 3.332761 TTGAGCAACACGAAATCACAC 57.667 42.857 0.00 0.00 0.00 3.82
1570 1603 4.202000 ACAATTGAGCAACACGAAATCACA 60.202 37.500 13.59 0.00 0.00 3.58
1571 1604 4.290155 ACAATTGAGCAACACGAAATCAC 58.710 39.130 13.59 0.00 0.00 3.06
1572 1605 4.566545 ACAATTGAGCAACACGAAATCA 57.433 36.364 13.59 0.00 0.00 2.57
1573 1606 5.565259 CAGTACAATTGAGCAACACGAAATC 59.435 40.000 13.59 0.00 0.00 2.17
1592 1636 1.539065 CCCACATCGGATCTGCAGTAC 60.539 57.143 14.67 8.87 36.56 2.73
1633 1677 0.454285 TCGCGCATTGTTAAGCAAGC 60.454 50.000 8.75 0.00 40.86 4.01
1654 1698 1.084370 CCGGACAAGATCGGCTGAAC 61.084 60.000 0.00 0.00 39.78 3.18
1929 1976 2.359230 GGCAGCGAGTGGAAGCTT 60.359 61.111 0.00 0.00 42.52 3.74
1990 2037 0.818040 GCCCACAGGAACTTGACGTT 60.818 55.000 0.00 0.00 34.60 3.99
1991 2038 1.227853 GCCCACAGGAACTTGACGT 60.228 57.895 0.00 0.00 34.60 4.34
2061 2108 2.590575 AGCACCCCGTTGTCGTTG 60.591 61.111 0.00 0.00 35.01 4.10
2062 2109 2.280592 GAGCACCCCGTTGTCGTT 60.281 61.111 0.00 0.00 35.01 3.85
2063 2110 4.657824 CGAGCACCCCGTTGTCGT 62.658 66.667 0.00 0.00 35.01 4.34
2064 2111 4.657824 ACGAGCACCCCGTTGTCG 62.658 66.667 0.00 0.00 36.83 4.35
2065 2112 3.041940 CACGAGCACCCCGTTGTC 61.042 66.667 0.00 0.00 38.29 3.18
2296 2347 1.424493 GCAATCGCCTTCCTCGTGAG 61.424 60.000 0.00 0.00 0.00 3.51
2362 2413 1.828768 CTCTGCTCCTCACCCCATC 59.171 63.158 0.00 0.00 0.00 3.51
2400 2451 1.078918 TTGGATGGCACTGCGAGAG 60.079 57.895 0.00 0.00 0.00 3.20
2488 2539 9.920946 ACTGTATGGAAAAATATACTCCATTGT 57.079 29.630 14.91 10.55 45.73 2.71
2513 2942 6.184015 TCGTTACGTTTATGTGAACAACAAC 58.816 36.000 4.24 0.00 43.61 3.32
2681 4329 3.513225 CCATCCATGGGCAACGTC 58.487 61.111 13.02 0.00 44.31 4.34
2804 4452 4.286320 GCCGGCGAGATGGACGAT 62.286 66.667 12.58 0.00 42.31 3.73
3413 5128 3.357079 GTGGCCGTGAAGGTGCTG 61.357 66.667 0.00 0.00 43.70 4.41


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

AutoCloner maintained by Alex Coulton.