Multiple sequence alignment - TraesCS2A01G277000

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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 TraesCS2A01G277000 chr2A 100.000 4685 0 0 1 4685 457945407 457940723 0.000000e+00 8652
1 TraesCS2A01G277000 chr2A 94.797 788 31 6 1 781 557829414 557830198 0.000000e+00 1219
2 TraesCS2A01G277000 chr2A 94.670 788 31 7 1 781 179205335 179206118 0.000000e+00 1212
3 TraesCS2A01G277000 chr2A 90.244 123 11 1 4362 4484 176673420 176673299 4.850000e-35 159
4 TraesCS2A01G277000 chr2D 97.077 3798 90 10 893 4685 345827325 345831106 0.000000e+00 6379
5 TraesCS2A01G277000 chr2B 94.220 3720 179 24 973 4672 411490747 411494450 0.000000e+00 5646
6 TraesCS2A01G277000 chr2B 86.667 210 15 6 792 989 411313001 411313209 2.190000e-53 220
7 TraesCS2A01G277000 chr3A 95.437 789 26 6 1 781 181660833 181661619 0.000000e+00 1249
8 TraesCS2A01G277000 chr3A 94.670 788 33 5 1 781 99646569 99645784 0.000000e+00 1214
9 TraesCS2A01G277000 chr3A 94.677 789 31 7 1 781 544515372 544516157 0.000000e+00 1214
10 TraesCS2A01G277000 chr3A 91.736 121 9 1 4361 4480 602017887 602017767 2.900000e-37 167
11 TraesCS2A01G277000 chr5A 94.797 788 30 7 1 781 29539330 29540113 0.000000e+00 1218
12 TraesCS2A01G277000 chr5A 94.797 788 27 10 1 780 570441874 570442655 0.000000e+00 1216
13 TraesCS2A01G277000 chr5A 92.174 115 8 1 4367 4480 130540662 130540548 1.350000e-35 161
14 TraesCS2A01G277000 chr7A 94.677 789 32 8 1 781 505178463 505177677 0.000000e+00 1216
15 TraesCS2A01G277000 chr7A 89.344 122 12 1 4360 4480 421785163 421785042 8.120000e-33 152
16 TraesCS2A01G277000 chrUn 94.670 788 32 6 2 781 47003435 47002650 0.000000e+00 1214
17 TraesCS2A01G277000 chr7D 93.162 117 7 1 4364 4480 442281471 442281356 2.240000e-38 171
18 TraesCS2A01G277000 chr1B 91.803 122 10 0 4359 4480 667230469 667230590 2.240000e-38 171
19 TraesCS2A01G277000 chr4B 90.984 122 11 0 4359 4480 106227566 106227445 1.040000e-36 165


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 TraesCS2A01G277000 chr2A 457940723 457945407 4684 True 8652 8652 100.000 1 4685 1 chr2A.!!$R2 4684
1 TraesCS2A01G277000 chr2A 557829414 557830198 784 False 1219 1219 94.797 1 781 1 chr2A.!!$F2 780
2 TraesCS2A01G277000 chr2A 179205335 179206118 783 False 1212 1212 94.670 1 781 1 chr2A.!!$F1 780
3 TraesCS2A01G277000 chr2D 345827325 345831106 3781 False 6379 6379 97.077 893 4685 1 chr2D.!!$F1 3792
4 TraesCS2A01G277000 chr2B 411490747 411494450 3703 False 5646 5646 94.220 973 4672 1 chr2B.!!$F2 3699
5 TraesCS2A01G277000 chr3A 181660833 181661619 786 False 1249 1249 95.437 1 781 1 chr3A.!!$F1 780
6 TraesCS2A01G277000 chr3A 99645784 99646569 785 True 1214 1214 94.670 1 781 1 chr3A.!!$R1 780
7 TraesCS2A01G277000 chr3A 544515372 544516157 785 False 1214 1214 94.677 1 781 1 chr3A.!!$F2 780
8 TraesCS2A01G277000 chr5A 29539330 29540113 783 False 1218 1218 94.797 1 781 1 chr5A.!!$F1 780
9 TraesCS2A01G277000 chr5A 570441874 570442655 781 False 1216 1216 94.797 1 780 1 chr5A.!!$F2 779
10 TraesCS2A01G277000 chr7A 505177677 505178463 786 True 1216 1216 94.677 1 781 1 chr7A.!!$R2 780
11 TraesCS2A01G277000 chrUn 47002650 47003435 785 True 1214 1214 94.670 2 781 1 chrUn.!!$R1 779

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
458 463 0.843309 TGGCCTCCTCTTTTGTGTCA 59.157 50.000 3.32 0.0 0.00 3.58 F
1240 1251 0.750546 CCACCTCGTCGATACCCTGA 60.751 60.000 0.00 0.0 0.00 3.86 F
1491 1505 1.379710 AAGCACCAACACCACTGCA 60.380 52.632 0.00 0.0 31.71 4.41 F
1494 1508 1.383456 GCACCAACACCACTGCAGAA 61.383 55.000 23.35 0.0 0.00 3.02 F
1664 1678 1.603739 GGTGCCTCCACTTGTTCCC 60.604 63.158 0.00 0.0 41.75 3.97 F
2439 2464 2.168521 ACCTGACCACATAACATCCTCG 59.831 50.000 0.00 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1452 1463 1.589716 CCCCTTCTTGGCTTCGCAAG 61.590 60.000 0.0 0.00 0.00 4.01 R
2900 2925 2.479566 AGCATCTTCAGCCTTTTCGA 57.520 45.000 0.0 0.00 0.00 3.71 R
2942 2967 3.350833 GAGGAAGATGTTGCCTTGATGT 58.649 45.455 0.0 0.00 30.70 3.06 R
3450 3475 3.417069 TGTCCATTTCGAACCATCTGT 57.583 42.857 0.0 0.00 0.00 3.41 R
3591 3616 5.440610 TCATCCTTCTTTTCCTTCCTATGC 58.559 41.667 0.0 0.00 0.00 3.14 R
3727 3752 5.908831 TGGAGACCATGGTATAACATAAGGT 59.091 40.000 19.8 11.59 31.87 3.50 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
52 53 1.375551 GGTCTCAACAAACACACCGT 58.624 50.000 0.00 0.00 0.00 4.83
257 261 1.557269 ATGGAGCTCCGAAACAGGCT 61.557 55.000 27.43 0.96 39.43 4.58
294 298 1.271108 TGGATACAGAAAGTTGCGGCA 60.271 47.619 0.00 0.00 46.17 5.69
315 319 4.809673 CAGTGGAATTAGGTTTTTGGCTC 58.190 43.478 0.00 0.00 0.00 4.70
341 345 1.078988 TGATCGTTTGGGGGTACGC 60.079 57.895 0.29 0.29 37.66 4.42
458 463 0.843309 TGGCCTCCTCTTTTGTGTCA 59.157 50.000 3.32 0.00 0.00 3.58
619 625 3.897505 GGCCTCCGGTTAATAGGTTAGTA 59.102 47.826 0.00 0.00 32.67 1.82
819 830 8.850156 AGAGAGAAAACTTAAGCTAAAAATGCA 58.150 29.630 1.29 0.00 0.00 3.96
820 831 9.463443 GAGAGAAAACTTAAGCTAAAAATGCAA 57.537 29.630 1.29 0.00 0.00 4.08
821 832 9.249457 AGAGAAAACTTAAGCTAAAAATGCAAC 57.751 29.630 1.29 0.00 0.00 4.17
822 833 8.365399 AGAAAACTTAAGCTAAAAATGCAACC 57.635 30.769 1.29 0.00 0.00 3.77
823 834 7.984617 AGAAAACTTAAGCTAAAAATGCAACCA 59.015 29.630 1.29 0.00 0.00 3.67
824 835 8.499403 AAAACTTAAGCTAAAAATGCAACCAA 57.501 26.923 1.29 0.00 0.00 3.67
825 836 8.499403 AAACTTAAGCTAAAAATGCAACCAAA 57.501 26.923 1.29 0.00 0.00 3.28
826 837 8.499403 AACTTAAGCTAAAAATGCAACCAAAA 57.501 26.923 1.29 0.00 0.00 2.44
827 838 7.915508 ACTTAAGCTAAAAATGCAACCAAAAC 58.084 30.769 1.29 0.00 0.00 2.43
828 839 7.550906 ACTTAAGCTAAAAATGCAACCAAAACA 59.449 29.630 1.29 0.00 0.00 2.83
829 840 6.749923 AAGCTAAAAATGCAACCAAAACAA 57.250 29.167 0.00 0.00 0.00 2.83
830 841 6.940831 AGCTAAAAATGCAACCAAAACAAT 57.059 29.167 0.00 0.00 0.00 2.71
831 842 8.443953 AAGCTAAAAATGCAACCAAAACAATA 57.556 26.923 0.00 0.00 0.00 1.90
832 843 8.443953 AGCTAAAAATGCAACCAAAACAATAA 57.556 26.923 0.00 0.00 0.00 1.40
833 844 8.558700 AGCTAAAAATGCAACCAAAACAATAAG 58.441 29.630 0.00 0.00 0.00 1.73
834 845 8.555361 GCTAAAAATGCAACCAAAACAATAAGA 58.445 29.630 0.00 0.00 0.00 2.10
840 851 9.995003 AATGCAACCAAAACAATAAGAATAAGA 57.005 25.926 0.00 0.00 0.00 2.10
841 852 9.995003 ATGCAACCAAAACAATAAGAATAAGAA 57.005 25.926 0.00 0.00 0.00 2.52
842 853 9.823647 TGCAACCAAAACAATAAGAATAAGAAA 57.176 25.926 0.00 0.00 0.00 2.52
846 857 9.996554 ACCAAAACAATAAGAATAAGAAAAGGG 57.003 29.630 0.00 0.00 0.00 3.95
847 858 9.435688 CCAAAACAATAAGAATAAGAAAAGGGG 57.564 33.333 0.00 0.00 0.00 4.79
852 863 8.903820 ACAATAAGAATAAGAAAAGGGGAATCG 58.096 33.333 0.00 0.00 0.00 3.34
853 864 8.352942 CAATAAGAATAAGAAAAGGGGAATCGG 58.647 37.037 0.00 0.00 0.00 4.18
854 865 5.710409 AGAATAAGAAAAGGGGAATCGGA 57.290 39.130 0.00 0.00 0.00 4.55
855 866 5.685728 AGAATAAGAAAAGGGGAATCGGAG 58.314 41.667 0.00 0.00 0.00 4.63
856 867 5.428783 AGAATAAGAAAAGGGGAATCGGAGA 59.571 40.000 0.00 0.00 45.75 3.71
857 868 5.710409 ATAAGAAAAGGGGAATCGGAGAA 57.290 39.130 0.00 0.00 43.58 2.87
858 869 3.636153 AGAAAAGGGGAATCGGAGAAG 57.364 47.619 0.00 0.00 43.58 2.85
859 870 3.182152 AGAAAAGGGGAATCGGAGAAGA 58.818 45.455 0.00 0.00 43.58 2.87
860 871 3.783082 AGAAAAGGGGAATCGGAGAAGAT 59.217 43.478 0.00 0.00 43.58 2.40
861 872 4.228438 AGAAAAGGGGAATCGGAGAAGATT 59.772 41.667 0.00 0.00 43.58 2.40
862 873 5.428783 AGAAAAGGGGAATCGGAGAAGATTA 59.571 40.000 0.00 0.00 43.58 1.75
863 874 4.691326 AAGGGGAATCGGAGAAGATTAC 57.309 45.455 0.00 0.00 43.58 1.89
867 878 4.939052 GGAATCGGAGAAGATTACCTCA 57.061 45.455 0.00 0.00 43.58 3.86
868 879 5.277857 GGAATCGGAGAAGATTACCTCAA 57.722 43.478 0.00 0.00 43.58 3.02
869 880 5.051153 GGAATCGGAGAAGATTACCTCAAC 58.949 45.833 0.00 0.00 43.58 3.18
870 881 4.674281 ATCGGAGAAGATTACCTCAACC 57.326 45.455 0.00 0.00 43.58 3.77
871 882 3.437213 TCGGAGAAGATTACCTCAACCA 58.563 45.455 0.00 0.00 0.00 3.67
872 883 3.835978 TCGGAGAAGATTACCTCAACCAA 59.164 43.478 0.00 0.00 0.00 3.67
873 884 3.933332 CGGAGAAGATTACCTCAACCAAC 59.067 47.826 0.00 0.00 0.00 3.77
874 885 4.322801 CGGAGAAGATTACCTCAACCAACT 60.323 45.833 0.00 0.00 0.00 3.16
875 886 5.561679 GGAGAAGATTACCTCAACCAACTT 58.438 41.667 0.00 0.00 0.00 2.66
876 887 5.412904 GGAGAAGATTACCTCAACCAACTTG 59.587 44.000 0.00 0.00 0.00 3.16
877 888 5.316987 AGAAGATTACCTCAACCAACTTGG 58.683 41.667 6.24 6.24 45.02 3.61
878 889 4.034285 AGATTACCTCAACCAACTTGGG 57.966 45.455 12.62 0.00 43.37 4.12
879 890 3.655777 AGATTACCTCAACCAACTTGGGA 59.344 43.478 12.62 0.12 43.37 4.37
880 891 3.955524 TTACCTCAACCAACTTGGGAA 57.044 42.857 12.62 0.00 43.37 3.97
881 892 4.463050 TTACCTCAACCAACTTGGGAAT 57.537 40.909 12.62 0.00 43.37 3.01
882 893 3.328535 ACCTCAACCAACTTGGGAATT 57.671 42.857 12.62 0.00 43.37 2.17
883 894 2.965147 ACCTCAACCAACTTGGGAATTG 59.035 45.455 12.62 7.83 43.37 2.32
890 901 4.622260 CCAACTTGGGAATTGGTGATTT 57.378 40.909 0.00 0.00 40.51 2.17
891 902 4.317488 CCAACTTGGGAATTGGTGATTTG 58.683 43.478 0.00 0.00 40.51 2.32
909 920 6.153340 GTGATTTGAGAAATTGGAGATTGGGA 59.847 38.462 0.00 0.00 0.00 4.37
979 990 1.995542 TGAGGAAGGATTTTGGCTCCT 59.004 47.619 0.00 0.00 45.21 3.69
1059 1070 4.011517 GTCGCCTCCCCGAACCAA 62.012 66.667 0.00 0.00 39.17 3.67
1145 1156 2.674084 GGCGACGTAACCAACCAGC 61.674 63.158 0.00 0.00 0.00 4.85
1233 1244 3.148279 GGAGCCCACCTCGTCGAT 61.148 66.667 0.00 0.00 41.71 3.59
1237 1248 3.126528 CCCACCTCGTCGATACCC 58.873 66.667 0.00 0.00 0.00 3.69
1240 1251 0.750546 CCACCTCGTCGATACCCTGA 60.751 60.000 0.00 0.00 0.00 3.86
1260 1271 3.733960 GACGAAAAGGGCGGCCAC 61.734 66.667 31.59 16.47 0.00 5.01
1376 1387 4.357279 GCAGGCCCAGGAACAGCT 62.357 66.667 0.00 0.00 0.00 4.24
1451 1462 2.182030 GCTGGACGCGAGCTACTT 59.818 61.111 15.93 0.00 32.55 2.24
1452 1463 1.874466 GCTGGACGCGAGCTACTTC 60.874 63.158 15.93 0.00 32.55 3.01
1453 1464 1.803943 CTGGACGCGAGCTACTTCT 59.196 57.895 15.93 0.00 0.00 2.85
1491 1505 1.379710 AAGCACCAACACCACTGCA 60.380 52.632 0.00 0.00 31.71 4.41
1493 1507 1.823470 GCACCAACACCACTGCAGA 60.823 57.895 23.35 0.00 0.00 4.26
1494 1508 1.383456 GCACCAACACCACTGCAGAA 61.383 55.000 23.35 0.00 0.00 3.02
1500 1514 2.361757 CAACACCACTGCAGAAATGGAA 59.638 45.455 24.44 0.00 36.94 3.53
1664 1678 1.603739 GGTGCCTCCACTTGTTCCC 60.604 63.158 0.00 0.00 41.75 3.97
1878 1892 2.225019 GTGAGCACTGTCTTGATTGGTG 59.775 50.000 0.00 0.00 0.00 4.17
1885 1899 3.836365 TGTCTTGATTGGTGTGACAGA 57.164 42.857 0.00 0.00 33.45 3.41
1907 1921 8.795513 ACAGAGAGTGATGAGTGATCATATTAG 58.204 37.037 0.00 0.00 43.20 1.73
1939 1953 7.475015 TCATGCTATCACTTTTGCAAGATTAC 58.525 34.615 0.00 0.00 38.96 1.89
1949 1963 8.999431 CACTTTTGCAAGATTACTTAGGAGTTA 58.001 33.333 0.00 0.00 34.23 2.24
2037 2051 7.364673 GGCATTTCCATTAACCTTTTCCTACAT 60.365 37.037 0.00 0.00 34.01 2.29
2111 2126 3.558505 CAAGTCAGTTTGATTTGCTCCG 58.441 45.455 2.12 0.00 37.30 4.63
2217 2242 4.952262 TGTGCTAGCATGAGAATTGTTC 57.048 40.909 22.51 3.55 0.00 3.18
2256 2281 9.476202 GCATAGTTTCAAGTCTTTATGGTTTTT 57.524 29.630 4.26 0.00 0.00 1.94
2391 2416 9.186837 AGATATGATGATGCCTGGAAAATATTC 57.813 33.333 0.00 0.00 34.66 1.75
2439 2464 2.168521 ACCTGACCACATAACATCCTCG 59.831 50.000 0.00 0.00 0.00 4.63
2443 2468 3.243401 TGACCACATAACATCCTCGATCG 60.243 47.826 9.36 9.36 0.00 3.69
2942 2967 3.520696 TCCTGAGGATGAAGAAAGGTGA 58.479 45.455 0.00 0.00 0.00 4.02
2961 2986 3.084039 TGACATCAAGGCAACATCTTCC 58.916 45.455 0.00 0.00 41.41 3.46
2972 2997 3.684788 GCAACATCTTCCTCGTACACATT 59.315 43.478 0.00 0.00 0.00 2.71
3450 3475 5.972935 TCGAGAGCATTCTATTACCACAAA 58.027 37.500 0.00 0.00 32.53 2.83
3635 3660 9.196552 GGATGAATTTTGGAAGAACAGTAAAAG 57.803 33.333 0.00 0.00 0.00 2.27
3844 3869 7.396540 AAAATTCACTTTGACTGTCTGACTT 57.603 32.000 9.51 2.50 0.00 3.01
3845 3870 5.998454 ATTCACTTTGACTGTCTGACTTG 57.002 39.130 9.51 4.76 0.00 3.16
3875 3900 7.692460 TGATCTGAATACACTTGATTTTGCT 57.308 32.000 0.00 0.00 0.00 3.91
4359 4390 8.131100 CAGTACACATTGAGATTGTTTTCACTT 58.869 33.333 0.00 0.00 0.00 3.16
4506 4539 7.727578 TGAATGAAGGGAGTATTACACAGTA 57.272 36.000 0.00 0.00 0.00 2.74
4571 4604 6.662865 TTTCCTGTTGCCATTGATTTCTTA 57.337 33.333 0.00 0.00 0.00 2.10
4609 4642 2.487762 TCCAGCAATAAGGCAGTTTTCG 59.512 45.455 0.00 0.00 35.83 3.46
4625 4658 6.855914 GCAGTTTTCGTTGATGTAATCTTCAA 59.144 34.615 0.00 0.00 45.81 2.69
4672 4705 6.953520 TCATTTCACCAAACCCATCTATTTCT 59.046 34.615 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 95 7.630242 TTTGGATCTCAATACAATGTTCTCC 57.370 36.000 0.00 0.00 35.60 3.71
257 261 1.123077 CCACGAGATCCCATCTTGGA 58.877 55.000 5.85 0.00 43.70 3.53
294 298 3.832490 GGAGCCAAAAACCTAATTCCACT 59.168 43.478 0.00 0.00 0.00 4.00
315 319 1.540363 CCCCAAACGATCAGATACGGG 60.540 57.143 0.00 0.00 0.00 5.28
341 345 7.716123 CGTACTCCTTCCTCCTATATATACCTG 59.284 44.444 0.00 0.00 0.00 4.00
458 463 2.100989 GAGACTTGGACCCTACGTCAT 58.899 52.381 0.00 0.00 43.95 3.06
793 804 8.850156 TGCATTTTTAGCTTAAGTTTTCTCTCT 58.150 29.630 4.02 0.00 0.00 3.10
794 805 9.463443 TTGCATTTTTAGCTTAAGTTTTCTCTC 57.537 29.630 4.02 0.00 0.00 3.20
795 806 9.249457 GTTGCATTTTTAGCTTAAGTTTTCTCT 57.751 29.630 4.02 0.00 0.00 3.10
796 807 8.487970 GGTTGCATTTTTAGCTTAAGTTTTCTC 58.512 33.333 4.02 0.00 0.00 2.87
797 808 7.984617 TGGTTGCATTTTTAGCTTAAGTTTTCT 59.015 29.630 4.02 0.00 0.00 2.52
798 809 8.137210 TGGTTGCATTTTTAGCTTAAGTTTTC 57.863 30.769 4.02 0.00 0.00 2.29
799 810 8.499403 TTGGTTGCATTTTTAGCTTAAGTTTT 57.501 26.923 4.02 0.00 0.00 2.43
800 811 8.499403 TTTGGTTGCATTTTTAGCTTAAGTTT 57.501 26.923 4.02 0.00 0.00 2.66
801 812 8.394877 GTTTTGGTTGCATTTTTAGCTTAAGTT 58.605 29.630 4.02 0.00 0.00 2.66
802 813 7.550906 TGTTTTGGTTGCATTTTTAGCTTAAGT 59.449 29.630 4.02 0.00 0.00 2.24
803 814 7.914465 TGTTTTGGTTGCATTTTTAGCTTAAG 58.086 30.769 0.00 0.00 0.00 1.85
804 815 7.849804 TGTTTTGGTTGCATTTTTAGCTTAA 57.150 28.000 0.00 0.00 0.00 1.85
805 816 7.849804 TTGTTTTGGTTGCATTTTTAGCTTA 57.150 28.000 0.00 0.00 0.00 3.09
806 817 6.749923 TTGTTTTGGTTGCATTTTTAGCTT 57.250 29.167 0.00 0.00 0.00 3.74
807 818 6.940831 ATTGTTTTGGTTGCATTTTTAGCT 57.059 29.167 0.00 0.00 0.00 3.32
808 819 8.555361 TCTTATTGTTTTGGTTGCATTTTTAGC 58.445 29.630 0.00 0.00 0.00 3.09
814 825 9.995003 TCTTATTCTTATTGTTTTGGTTGCATT 57.005 25.926 0.00 0.00 0.00 3.56
815 826 9.995003 TTCTTATTCTTATTGTTTTGGTTGCAT 57.005 25.926 0.00 0.00 0.00 3.96
816 827 9.823647 TTTCTTATTCTTATTGTTTTGGTTGCA 57.176 25.926 0.00 0.00 0.00 4.08
820 831 9.996554 CCCTTTTCTTATTCTTATTGTTTTGGT 57.003 29.630 0.00 0.00 0.00 3.67
821 832 9.435688 CCCCTTTTCTTATTCTTATTGTTTTGG 57.564 33.333 0.00 0.00 0.00 3.28
826 837 8.903820 CGATTCCCCTTTTCTTATTCTTATTGT 58.096 33.333 0.00 0.00 0.00 2.71
827 838 8.352942 CCGATTCCCCTTTTCTTATTCTTATTG 58.647 37.037 0.00 0.00 0.00 1.90
828 839 8.279361 TCCGATTCCCCTTTTCTTATTCTTATT 58.721 33.333 0.00 0.00 0.00 1.40
829 840 7.812306 TCCGATTCCCCTTTTCTTATTCTTAT 58.188 34.615 0.00 0.00 0.00 1.73
830 841 7.126726 TCTCCGATTCCCCTTTTCTTATTCTTA 59.873 37.037 0.00 0.00 0.00 2.10
831 842 6.069615 TCTCCGATTCCCCTTTTCTTATTCTT 60.070 38.462 0.00 0.00 0.00 2.52
832 843 5.428783 TCTCCGATTCCCCTTTTCTTATTCT 59.571 40.000 0.00 0.00 0.00 2.40
833 844 5.681639 TCTCCGATTCCCCTTTTCTTATTC 58.318 41.667 0.00 0.00 0.00 1.75
834 845 5.710409 TCTCCGATTCCCCTTTTCTTATT 57.290 39.130 0.00 0.00 0.00 1.40
835 846 5.428783 TCTTCTCCGATTCCCCTTTTCTTAT 59.571 40.000 0.00 0.00 0.00 1.73
836 847 4.781087 TCTTCTCCGATTCCCCTTTTCTTA 59.219 41.667 0.00 0.00 0.00 2.10
837 848 3.587506 TCTTCTCCGATTCCCCTTTTCTT 59.412 43.478 0.00 0.00 0.00 2.52
838 849 3.182152 TCTTCTCCGATTCCCCTTTTCT 58.818 45.455 0.00 0.00 0.00 2.52
839 850 3.629142 TCTTCTCCGATTCCCCTTTTC 57.371 47.619 0.00 0.00 0.00 2.29
840 851 4.592997 AATCTTCTCCGATTCCCCTTTT 57.407 40.909 0.00 0.00 0.00 2.27
841 852 4.141459 GGTAATCTTCTCCGATTCCCCTTT 60.141 45.833 0.00 0.00 35.40 3.11
842 853 3.391626 GGTAATCTTCTCCGATTCCCCTT 59.608 47.826 0.00 0.00 35.40 3.95
843 854 2.973406 GGTAATCTTCTCCGATTCCCCT 59.027 50.000 0.00 0.00 35.40 4.79
844 855 2.973406 AGGTAATCTTCTCCGATTCCCC 59.027 50.000 0.00 0.00 31.73 4.81
845 856 3.641906 TGAGGTAATCTTCTCCGATTCCC 59.358 47.826 0.00 0.00 35.40 3.97
846 857 4.939052 TGAGGTAATCTTCTCCGATTCC 57.061 45.455 0.00 0.00 35.40 3.01
847 858 5.051153 GGTTGAGGTAATCTTCTCCGATTC 58.949 45.833 0.00 0.00 35.40 2.52
848 859 4.469945 TGGTTGAGGTAATCTTCTCCGATT 59.530 41.667 0.00 0.00 37.40 3.34
849 860 4.030913 TGGTTGAGGTAATCTTCTCCGAT 58.969 43.478 0.00 0.00 0.00 4.18
850 861 3.437213 TGGTTGAGGTAATCTTCTCCGA 58.563 45.455 0.00 0.00 0.00 4.55
851 862 3.887621 TGGTTGAGGTAATCTTCTCCG 57.112 47.619 0.00 0.00 0.00 4.63
852 863 5.167303 AGTTGGTTGAGGTAATCTTCTCC 57.833 43.478 0.00 0.00 0.00 3.71
853 864 5.412904 CCAAGTTGGTTGAGGTAATCTTCTC 59.587 44.000 14.21 0.00 38.60 2.87
854 865 5.316987 CCAAGTTGGTTGAGGTAATCTTCT 58.683 41.667 14.21 0.00 38.60 2.85
855 866 4.459337 CCCAAGTTGGTTGAGGTAATCTTC 59.541 45.833 20.54 0.00 38.60 2.87
856 867 4.105697 TCCCAAGTTGGTTGAGGTAATCTT 59.894 41.667 20.54 0.00 38.60 2.40
857 868 3.655777 TCCCAAGTTGGTTGAGGTAATCT 59.344 43.478 20.54 0.00 38.60 2.40
858 869 4.028993 TCCCAAGTTGGTTGAGGTAATC 57.971 45.455 20.54 0.00 38.60 1.75
859 870 4.463050 TTCCCAAGTTGGTTGAGGTAAT 57.537 40.909 20.54 0.00 38.60 1.89
860 871 3.955524 TTCCCAAGTTGGTTGAGGTAA 57.044 42.857 20.54 1.02 38.60 2.85
861 872 4.148838 CAATTCCCAAGTTGGTTGAGGTA 58.851 43.478 20.54 0.00 38.60 3.08
862 873 2.965147 CAATTCCCAAGTTGGTTGAGGT 59.035 45.455 20.54 2.45 38.60 3.85
863 874 2.299867 CCAATTCCCAAGTTGGTTGAGG 59.700 50.000 20.54 11.37 39.97 3.86
864 875 3.665745 CCAATTCCCAAGTTGGTTGAG 57.334 47.619 20.54 5.39 39.97 3.02
870 881 5.010922 TCTCAAATCACCAATTCCCAAGTTG 59.989 40.000 0.00 0.00 0.00 3.16
871 882 5.147032 TCTCAAATCACCAATTCCCAAGTT 58.853 37.500 0.00 0.00 0.00 2.66
872 883 4.739793 TCTCAAATCACCAATTCCCAAGT 58.260 39.130 0.00 0.00 0.00 3.16
873 884 5.726980 TTCTCAAATCACCAATTCCCAAG 57.273 39.130 0.00 0.00 0.00 3.61
874 885 6.684897 ATTTCTCAAATCACCAATTCCCAA 57.315 33.333 0.00 0.00 0.00 4.12
875 886 6.465948 CAATTTCTCAAATCACCAATTCCCA 58.534 36.000 0.00 0.00 0.00 4.37
876 887 5.876460 CCAATTTCTCAAATCACCAATTCCC 59.124 40.000 0.00 0.00 0.00 3.97
877 888 6.700352 TCCAATTTCTCAAATCACCAATTCC 58.300 36.000 0.00 0.00 0.00 3.01
878 889 7.605449 TCTCCAATTTCTCAAATCACCAATTC 58.395 34.615 0.00 0.00 0.00 2.17
879 890 7.543359 TCTCCAATTTCTCAAATCACCAATT 57.457 32.000 0.00 0.00 0.00 2.32
880 891 7.729124 ATCTCCAATTTCTCAAATCACCAAT 57.271 32.000 0.00 0.00 0.00 3.16
881 892 7.380536 CAATCTCCAATTTCTCAAATCACCAA 58.619 34.615 0.00 0.00 0.00 3.67
882 893 6.071221 CCAATCTCCAATTTCTCAAATCACCA 60.071 38.462 0.00 0.00 0.00 4.17
883 894 6.335777 CCAATCTCCAATTTCTCAAATCACC 58.664 40.000 0.00 0.00 0.00 4.02
884 895 6.153340 TCCCAATCTCCAATTTCTCAAATCAC 59.847 38.462 0.00 0.00 0.00 3.06
885 896 6.255287 TCCCAATCTCCAATTTCTCAAATCA 58.745 36.000 0.00 0.00 0.00 2.57
886 897 6.780457 TCCCAATCTCCAATTTCTCAAATC 57.220 37.500 0.00 0.00 0.00 2.17
887 898 6.155737 CCTTCCCAATCTCCAATTTCTCAAAT 59.844 38.462 0.00 0.00 0.00 2.32
888 899 5.481473 CCTTCCCAATCTCCAATTTCTCAAA 59.519 40.000 0.00 0.00 0.00 2.69
889 900 5.018809 CCTTCCCAATCTCCAATTTCTCAA 58.981 41.667 0.00 0.00 0.00 3.02
890 901 4.292041 TCCTTCCCAATCTCCAATTTCTCA 59.708 41.667 0.00 0.00 0.00 3.27
891 902 4.860022 TCCTTCCCAATCTCCAATTTCTC 58.140 43.478 0.00 0.00 0.00 2.87
909 920 6.070656 TCACTCTCAAATCACCAAATTCCTT 58.929 36.000 0.00 0.00 0.00 3.36
979 990 4.337060 CGACGCCGTGTCTCACCA 62.337 66.667 10.27 0.00 45.87 4.17
1216 1227 1.826921 TATCGACGAGGTGGGCTCC 60.827 63.158 3.01 0.00 0.00 4.70
1233 1244 2.617021 GCCCTTTTCGTCATTCAGGGTA 60.617 50.000 4.49 0.00 45.55 3.69
1237 1248 0.447801 CCGCCCTTTTCGTCATTCAG 59.552 55.000 0.00 0.00 0.00 3.02
1240 1251 2.340328 GGCCGCCCTTTTCGTCATT 61.340 57.895 0.00 0.00 0.00 2.57
1376 1387 1.617263 CCTCCTCCTCCTCTTGTCGAA 60.617 57.143 0.00 0.00 0.00 3.71
1452 1463 1.589716 CCCCTTCTTGGCTTCGCAAG 61.590 60.000 0.00 0.00 0.00 4.01
1453 1464 1.603455 CCCCTTCTTGGCTTCGCAA 60.603 57.895 0.00 0.00 0.00 4.85
1491 1505 4.593956 AGGCGAGAATTTCTTCCATTTCT 58.406 39.130 16.23 0.00 31.27 2.52
1493 1507 5.473039 CAAAGGCGAGAATTTCTTCCATTT 58.527 37.500 16.23 10.65 31.27 2.32
1494 1508 4.619160 GCAAAGGCGAGAATTTCTTCCATT 60.619 41.667 16.23 10.42 31.27 3.16
1878 1892 4.157472 TGATCACTCATCACTCTCTGTCAC 59.843 45.833 0.00 0.00 36.51 3.67
1885 1899 9.979578 GAAACTAATATGATCACTCATCACTCT 57.020 33.333 0.00 0.00 44.70 3.24
1907 1921 6.587226 TGCAAAAGTGATAGCATGAATGAAAC 59.413 34.615 0.00 0.00 31.05 2.78
1949 1963 8.798859 TCTAAGTCGGTCAATAAGTAACTACT 57.201 34.615 0.00 0.00 38.39 2.57
2111 2126 9.937175 GTTCATACCAAAGAATTTACAGATAGC 57.063 33.333 0.00 0.00 35.03 2.97
2217 2242 8.246180 ACTTGAAACTATGCAAACCTATCAATG 58.754 33.333 0.00 0.00 0.00 2.82
2256 2281 3.769300 TCATGCTTAGTTAGGACAGAGCA 59.231 43.478 8.54 8.54 44.44 4.26
2391 2416 5.655488 ACATTGTTCTTCTCCATACTCTCG 58.345 41.667 0.00 0.00 0.00 4.04
2439 2464 6.292919 GCCTCTTCATTACCATTAACACGATC 60.293 42.308 0.00 0.00 0.00 3.69
2443 2468 4.495844 GCGCCTCTTCATTACCATTAACAC 60.496 45.833 0.00 0.00 0.00 3.32
2726 2751 2.963101 ACCCTTGTTGGTTTTAAGCCTC 59.037 45.455 0.00 0.00 33.91 4.70
2900 2925 2.479566 AGCATCTTCAGCCTTTTCGA 57.520 45.000 0.00 0.00 0.00 3.71
2942 2967 3.350833 GAGGAAGATGTTGCCTTGATGT 58.649 45.455 0.00 0.00 30.70 3.06
2961 2986 5.120053 TGCACAAATCAGTAATGTGTACGAG 59.880 40.000 6.95 0.00 44.79 4.18
3450 3475 3.417069 TGTCCATTTCGAACCATCTGT 57.583 42.857 0.00 0.00 0.00 3.41
3591 3616 5.440610 TCATCCTTCTTTTCCTTCCTATGC 58.559 41.667 0.00 0.00 0.00 3.14
3727 3752 5.908831 TGGAGACCATGGTATAACATAAGGT 59.091 40.000 19.80 11.59 31.87 3.50
3953 3978 6.428159 TCAGAAAGCCTAAAAGAGCAGTTTAG 59.572 38.462 6.77 6.77 38.00 1.85
4486 4517 5.776208 TGTGTACTGTGTAATACTCCCTTCA 59.224 40.000 0.00 0.00 0.00 3.02
4506 4539 2.198827 TTCAAATGAGGCCGATGTGT 57.801 45.000 0.00 0.00 0.00 3.72
4571 4604 1.774254 TGGACTTTCCACCATGACTGT 59.226 47.619 0.00 0.00 42.67 3.55
4609 4642 7.331791 AGGAGTACCTTGAAGATTACATCAAC 58.668 38.462 0.00 0.00 45.36 3.18


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

AutoCloner maintained by Alex Coulton.