Multiple sequence alignment - TraesCS2A01G191600

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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 TraesCS2A01G191600 chr2A 100.000 4313 0 0 1 4313 158552436 158556748 0.000000e+00 7965.0
1 TraesCS2A01G191600 chr2A 92.315 1054 62 11 2420 3466 158591718 158592759 0.000000e+00 1480.0
2 TraesCS2A01G191600 chr2A 90.426 940 62 17 719 1649 158589563 158590483 0.000000e+00 1212.0
3 TraesCS2A01G191600 chr2A 85.034 147 17 3 2161 2303 158591542 158591687 1.250000e-30 145.0
4 TraesCS2A01G191600 chr2A 88.496 113 12 1 2041 2152 158591374 158591486 7.520000e-28 135.0
5 TraesCS2A01G191600 chr2D 92.722 2006 115 17 2328 4313 142474225 142472231 0.000000e+00 2867.0
6 TraesCS2A01G191600 chr2D 91.183 1860 104 30 3 1851 142476583 142474773 0.000000e+00 2471.0
7 TraesCS2A01G191600 chr2D 91.119 1126 72 19 2356 3466 142433098 142431986 0.000000e+00 1500.0
8 TraesCS2A01G191600 chr2D 90.265 945 67 12 719 1655 142435858 142434931 0.000000e+00 1212.0
9 TraesCS2A01G191600 chr2D 94.538 476 21 3 1857 2330 142474733 142474261 0.000000e+00 730.0
10 TraesCS2A01G191600 chr2D 84.783 276 29 5 2041 2303 142433382 142433107 9.200000e-67 265.0
11 TraesCS2A01G191600 chr2D 78.022 273 26 14 3 242 601705993 601705722 1.620000e-29 141.0
12 TraesCS2A01G191600 chr2D 100.000 29 0 0 1421 1449 26537573 26537545 2.000000e-03 54.7
13 TraesCS2A01G191600 chr2B 92.503 1974 122 10 2352 4313 200471778 200469819 0.000000e+00 2802.0
14 TraesCS2A01G191600 chr2B 93.843 1072 39 10 566 1632 200473648 200472599 0.000000e+00 1589.0
15 TraesCS2A01G191600 chr2B 93.894 999 56 4 2356 3350 200384467 200385464 0.000000e+00 1502.0
16 TraesCS2A01G191600 chr2B 89.418 945 67 19 719 1649 200382694 200383619 0.000000e+00 1160.0
17 TraesCS2A01G191600 chr2B 90.885 768 25 14 1600 2330 200472600 200471841 0.000000e+00 989.0
18 TraesCS2A01G191600 chr2B 86.042 566 48 13 3 566 200474264 200473728 2.890000e-161 579.0
19 TraesCS2A01G191600 chr2B 84.000 275 30 5 2042 2303 200384185 200384458 7.160000e-63 252.0
20 TraesCS2A01G191600 chr2B 86.047 172 18 4 5 171 89442101 89442271 3.430000e-41 180.0
21 TraesCS2A01G191600 chr2B 82.759 145 14 6 10 146 23244294 23244435 7.580000e-23 119.0
22 TraesCS2A01G191600 chr1B 84.746 177 17 5 3 171 469616292 469616118 7.420000e-38 169.0
23 TraesCS2A01G191600 chr1B 90.541 74 5 2 170 243 279191381 279191452 3.550000e-16 97.1
24 TraesCS2A01G191600 chr3B 83.908 174 22 2 3 171 821011890 821012062 1.240000e-35 161.0
25 TraesCS2A01G191600 chr3B 84.906 159 15 3 3 156 43552920 43553074 7.470000e-33 152.0
26 TraesCS2A01G191600 chr5A 83.721 172 22 2 5 171 493782964 493782794 1.610000e-34 158.0
27 TraesCS2A01G191600 chr3D 83.721 172 22 5 4 171 606572234 606572065 1.610000e-34 158.0
28 TraesCS2A01G191600 chr3D 78.090 178 26 9 487 656 319515928 319515756 2.740000e-17 100.0
29 TraesCS2A01G191600 chr5D 82.857 175 18 8 3 168 442673478 442673307 3.480000e-31 147.0
30 TraesCS2A01G191600 chr6D 91.781 73 6 0 170 242 108148736 108148808 7.630000e-18 102.0
31 TraesCS2A01G191600 chr6B 75.458 273 33 12 3 242 90105874 90106145 7.630000e-18 102.0
32 TraesCS2A01G191600 chr1A 94.444 36 2 0 170 205 250201278 250201313 6.030000e-04 56.5
33 TraesCS2A01G191600 chrUn 100.000 29 0 0 1421 1449 17152116 17152088 2.000000e-03 54.7
34 TraesCS2A01G191600 chrUn 100.000 29 0 0 1421 1449 292609814 292609842 2.000000e-03 54.7


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 TraesCS2A01G191600 chr2A 158552436 158556748 4312 False 7965.000000 7965 100.000000 1 4313 1 chr2A.!!$F1 4312
1 TraesCS2A01G191600 chr2A 158589563 158592759 3196 False 743.000000 1480 89.067750 719 3466 4 chr2A.!!$F2 2747
2 TraesCS2A01G191600 chr2D 142472231 142476583 4352 True 2022.666667 2867 92.814333 3 4313 3 chr2D.!!$R4 4310
3 TraesCS2A01G191600 chr2D 142431986 142435858 3872 True 992.333333 1500 88.722333 719 3466 3 chr2D.!!$R3 2747
4 TraesCS2A01G191600 chr2B 200469819 200474264 4445 True 1489.750000 2802 90.818250 3 4313 4 chr2B.!!$R1 4310
5 TraesCS2A01G191600 chr2B 200382694 200385464 2770 False 971.333333 1502 89.104000 719 3350 3 chr2B.!!$F3 2631

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
923 1014 2.025793 TCACCTCAAAACACAGAACCCA 60.026 45.455 0.00 0.0 0.0 4.51 F
1049 1153 0.301687 CCGTCGCTGATTACACATGC 59.698 55.000 0.00 0.0 0.0 4.06 F
2406 4246 0.042131 ATCACCCCGGGAGTCAGTAA 59.958 55.000 26.32 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2182 3955 0.771127 AGTTTTGGACCCTAGCTGCA 59.229 50.000 1.02 0.0 0.00 4.41 R
2476 4319 1.379843 GGTTCATGGCCAACCCGAT 60.380 57.895 10.96 0.0 37.88 4.18 R
3685 5546 0.248336 CGAAGCGAGTACGTATGCCA 60.248 55.000 12.08 0.0 41.98 4.92 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
61 62 5.532779 GGAGAGTTTGAGAAATTGTTGACCT 59.467 40.000 0.00 0.00 0.00 3.85
67 68 4.136796 TGAGAAATTGTTGACCTGGTCAG 58.863 43.478 26.94 0.00 43.69 3.51
110 111 9.958180 TCTGAATACCTCAATTAATTGTGAAGA 57.042 29.630 24.81 15.81 38.84 2.87
246 249 7.981789 TGAGCTTAGTGTTACAGAGGATTAATG 59.018 37.037 0.00 0.00 0.00 1.90
289 292 3.976654 ACCTAGTGGATATTGCATGAGGT 59.023 43.478 0.00 0.00 33.16 3.85
315 318 7.365426 TGCATGATACTACCTATGATATCCCT 58.635 38.462 0.00 0.00 0.00 4.20
374 377 8.234546 AGCAAGTAAAATAAGGTGATGTAAACG 58.765 33.333 0.00 0.00 0.00 3.60
390 393 9.209048 TGATGTAAACGGGCTATAAGGATATAT 57.791 33.333 0.00 0.00 0.00 0.86
466 469 7.128077 AGAGATGAGAGGAAAGAGAAGAGAAT 58.872 38.462 0.00 0.00 0.00 2.40
470 473 5.782331 TGAGAGGAAAGAGAAGAGAATTGGA 59.218 40.000 0.00 0.00 0.00 3.53
471 474 6.443206 TGAGAGGAAAGAGAAGAGAATTGGAT 59.557 38.462 0.00 0.00 0.00 3.41
472 475 6.888105 AGAGGAAAGAGAAGAGAATTGGATC 58.112 40.000 0.00 0.00 0.00 3.36
484 487 7.921786 AGAGAATTGGATCGTGAATTTACAA 57.078 32.000 0.95 0.00 0.00 2.41
487 490 7.409697 AGAATTGGATCGTGAATTTACAATCG 58.590 34.615 0.95 0.00 0.00 3.34
522 525 6.596888 TGAGCTCTATGAAATTTTGAGAGTGG 59.403 38.462 16.19 4.01 36.76 4.00
531 534 4.664688 ATTTTGAGAGTGGAAGGTGGAT 57.335 40.909 0.00 0.00 0.00 3.41
625 711 3.949132 TGATAACATGCTACAGCCAACA 58.051 40.909 0.00 0.00 41.18 3.33
626 712 4.331108 TGATAACATGCTACAGCCAACAA 58.669 39.130 0.00 0.00 41.18 2.83
671 757 6.409704 TGCTTTTATAGACTGCTCATGAGTT 58.590 36.000 23.38 8.81 0.00 3.01
672 758 7.555965 TGCTTTTATAGACTGCTCATGAGTTA 58.444 34.615 23.38 12.28 0.00 2.24
679 765 5.599732 AGACTGCTCATGAGTTAATAGCTG 58.400 41.667 23.38 13.90 37.90 4.24
899 985 6.602009 GCTATATAAACACTTCCCCACAAACT 59.398 38.462 0.00 0.00 0.00 2.66
904 990 2.174639 ACACTTCCCCACAAACTCATCA 59.825 45.455 0.00 0.00 0.00 3.07
923 1014 2.025793 TCACCTCAAAACACAGAACCCA 60.026 45.455 0.00 0.00 0.00 4.51
946 1037 4.020128 ACACACCTCCTCTGTATTTTCTCC 60.020 45.833 0.00 0.00 0.00 3.71
969 1062 5.183904 CCCTCTTTAAACCCACAAATCTCTG 59.816 44.000 0.00 0.00 0.00 3.35
977 1077 2.304180 CCCACAAATCTCTGTCTGTCCT 59.696 50.000 0.00 0.00 0.00 3.85
1028 1132 5.125100 AGTGTGCAATACCAACTCAATTG 57.875 39.130 0.00 0.00 38.12 2.32
1032 1136 2.735126 GCAATACCAACTCAATTGCCCG 60.735 50.000 0.00 0.00 46.19 6.13
1034 1138 1.816074 TACCAACTCAATTGCCCGTC 58.184 50.000 0.00 0.00 36.93 4.79
1049 1153 0.301687 CCGTCGCTGATTACACATGC 59.698 55.000 0.00 0.00 0.00 4.06
1068 1172 4.466567 TGCATGTAAACTTTCGTGTCTG 57.533 40.909 0.00 0.00 0.00 3.51
1094 1198 7.642669 ACACTTTCTTCTTGTGTCATGTTATG 58.357 34.615 0.00 0.00 40.39 1.90
1642 1778 3.062909 GCATTAACTGCGTATTTCCGTCA 59.937 43.478 0.00 0.00 41.97 4.35
1658 1794 4.003788 CACCCTCCGTTGCCGAGT 62.004 66.667 0.00 0.00 35.63 4.18
1852 1989 7.579761 AGTATTGGTTGGCTAGTACTACTAC 57.420 40.000 0.00 0.00 29.46 2.73
1853 1990 7.352738 AGTATTGGTTGGCTAGTACTACTACT 58.647 38.462 0.00 0.00 37.04 2.57
1908 3628 3.287222 TGGGGTTGAAAAGTGAGTTCAG 58.713 45.455 0.00 0.00 36.41 3.02
1968 3691 3.396260 TGGTTTCTTCAGTTCTACCCG 57.604 47.619 0.00 0.00 0.00 5.28
1970 3693 2.289506 GGTTTCTTCAGTTCTACCCGCT 60.290 50.000 0.00 0.00 0.00 5.52
2143 3870 4.993584 GCTACCTCATGATACATTGACAGG 59.006 45.833 0.00 0.00 0.00 4.00
2182 3955 5.620738 ACTAATCCAGTCATGTAGTGCAT 57.379 39.130 0.00 0.00 38.60 3.96
2322 4104 6.100004 ACTGTCGATAATGAATTCGAACTGT 58.900 36.000 0.00 0.00 45.03 3.55
2347 4183 7.844653 GTGTAGTTTCTTTGACAAAGTTCGTAG 59.155 37.037 23.78 1.54 39.52 3.51
2350 4186 8.658499 AGTTTCTTTGACAAAGTTCGTAGTAT 57.342 30.769 23.78 3.50 39.52 2.12
2406 4246 0.042131 ATCACCCCGGGAGTCAGTAA 59.958 55.000 26.32 0.00 0.00 2.24
2411 4251 3.054948 CACCCCGGGAGTCAGTAAAATAA 60.055 47.826 26.32 0.00 0.00 1.40
2457 4300 0.110486 ATTCGCAGGTGACCAGGTTT 59.890 50.000 3.63 0.00 0.00 3.27
2476 4319 2.282391 AATGTGGCGGCTTCAGCA 60.282 55.556 11.43 1.93 44.36 4.41
3366 5213 1.061131 CGCTCGGTGTTTCTATGCTTG 59.939 52.381 0.00 0.00 0.00 4.01
3385 5232 5.163913 TGCTTGTTTTGCATGTGTTTGTTAC 60.164 36.000 0.00 0.00 35.31 2.50
3387 5234 6.402011 GCTTGTTTTGCATGTGTTTGTTACTT 60.402 34.615 0.00 0.00 0.00 2.24
3388 5235 6.400579 TGTTTTGCATGTGTTTGTTACTTG 57.599 33.333 0.00 0.00 0.00 3.16
3389 5236 5.928839 TGTTTTGCATGTGTTTGTTACTTGT 59.071 32.000 0.00 0.00 0.00 3.16
3390 5237 6.425114 TGTTTTGCATGTGTTTGTTACTTGTT 59.575 30.769 0.00 0.00 0.00 2.83
3391 5238 7.598869 TGTTTTGCATGTGTTTGTTACTTGTTA 59.401 29.630 0.00 0.00 0.00 2.41
3392 5239 7.748031 TTTGCATGTGTTTGTTACTTGTTAG 57.252 32.000 0.00 0.00 0.00 2.34
3393 5240 5.277825 TGCATGTGTTTGTTACTTGTTAGC 58.722 37.500 0.00 0.00 0.00 3.09
3394 5241 5.163612 TGCATGTGTTTGTTACTTGTTAGCA 60.164 36.000 0.00 0.00 0.00 3.49
3397 5244 5.826586 TGTGTTTGTTACTTGTTAGCATGG 58.173 37.500 0.00 0.00 0.00 3.66
3398 5245 5.358442 TGTGTTTGTTACTTGTTAGCATGGT 59.642 36.000 1.62 1.62 0.00 3.55
3694 5555 5.968528 TTTTTAGACCATTTGGCATACGT 57.031 34.783 0.00 0.00 39.32 3.57
3704 5565 0.248336 TGGCATACGTACTCGCTTCG 60.248 55.000 0.00 0.00 41.18 3.79
3705 5566 0.933509 GGCATACGTACTCGCTTCGG 60.934 60.000 0.00 0.00 41.18 4.30
3706 5567 0.028505 GCATACGTACTCGCTTCGGA 59.971 55.000 0.00 0.00 41.18 4.55
3803 5664 2.878406 CCGGGATAAACAAGGCACTATG 59.122 50.000 0.00 0.00 38.49 2.23
3810 5671 3.340814 AACAAGGCACTATGACAGGAG 57.659 47.619 0.00 0.00 38.49 3.69
3814 5675 2.769209 AGGCACTATGACAGGAGGAAT 58.231 47.619 0.00 0.00 36.02 3.01
3828 5689 1.141053 GAGGAATAGGATGCCAACGGT 59.859 52.381 0.00 0.00 0.00 4.83
3830 5691 2.368875 AGGAATAGGATGCCAACGGTAG 59.631 50.000 0.00 0.00 0.00 3.18
3844 5705 1.814527 GGTAGCCCGTGATTCGAGT 59.185 57.895 0.00 0.00 42.86 4.18
3846 5707 0.527817 GTAGCCCGTGATTCGAGTGG 60.528 60.000 0.00 0.00 42.86 4.00
3848 5709 1.810030 GCCCGTGATTCGAGTGGAC 60.810 63.158 0.00 0.00 42.86 4.02
3863 5724 0.605319 TGGACCGCCAGTTCACAATC 60.605 55.000 0.00 0.00 39.92 2.67
3868 5729 1.154150 GCCAGTTCACAATCTGCGC 60.154 57.895 0.00 0.00 0.00 6.09
3883 5744 2.745281 TCTGCGCACTAACCCAAATAAC 59.255 45.455 5.66 0.00 0.00 1.89
3897 5758 3.060895 CCAAATAACGACGCTCAAGTCTC 59.939 47.826 0.00 0.00 38.90 3.36
3898 5759 2.563471 ATAACGACGCTCAAGTCTCC 57.437 50.000 0.00 0.00 38.90 3.71
3900 5761 2.202492 CGACGCTCAAGTCTCCGG 60.202 66.667 0.00 0.00 38.90 5.14
3906 5767 1.605058 GCTCAAGTCTCCGGGCACTA 61.605 60.000 0.00 0.00 0.00 2.74
3918 5779 2.101249 CCGGGCACTAATTTGATGCAAT 59.899 45.455 0.00 0.00 41.27 3.56
3919 5780 3.374745 CGGGCACTAATTTGATGCAATC 58.625 45.455 13.14 0.00 45.83 2.67
3920 5781 3.721035 GGGCACTAATTTGATGCAATCC 58.279 45.455 13.14 5.36 44.73 3.01
3923 5784 3.038017 CACTAATTTGATGCAATCCGCG 58.962 45.455 0.00 0.00 44.73 6.46
3927 5788 0.726827 TTTGATGCAATCCGCGAGTC 59.273 50.000 8.23 0.00 44.73 3.36
3962 5823 1.710013 ATACAACCGCACTCAAGTCG 58.290 50.000 0.00 0.00 0.00 4.18
3963 5824 0.386476 TACAACCGCACTCAAGTCGT 59.614 50.000 0.00 0.00 0.00 4.34
3964 5825 0.874607 ACAACCGCACTCAAGTCGTC 60.875 55.000 0.00 0.00 0.00 4.20
3965 5826 1.660575 AACCGCACTCAAGTCGTCG 60.661 57.895 0.00 0.00 0.00 5.12
3966 5827 2.067091 AACCGCACTCAAGTCGTCGA 62.067 55.000 0.00 0.00 0.00 4.20
3967 5828 1.797933 CCGCACTCAAGTCGTCGAG 60.798 63.158 0.00 0.00 35.30 4.04
3969 5830 0.385598 CGCACTCAAGTCGTCGAGAA 60.386 55.000 0.00 0.00 33.33 2.87
3970 5831 1.729472 CGCACTCAAGTCGTCGAGAAT 60.729 52.381 0.00 0.00 33.33 2.40
3971 5832 1.651138 GCACTCAAGTCGTCGAGAATG 59.349 52.381 0.00 0.00 33.33 2.67
3972 5833 1.651138 CACTCAAGTCGTCGAGAATGC 59.349 52.381 0.00 0.00 33.33 3.56
3979 5840 1.102978 TCGTCGAGAATGCATCAGGA 58.897 50.000 0.00 0.00 0.00 3.86
3980 5841 1.683385 TCGTCGAGAATGCATCAGGAT 59.317 47.619 0.00 0.00 0.00 3.24
4011 5872 7.507956 TCCACGAGGAATCATAAGAATAAGGTA 59.492 37.037 0.00 0.00 42.23 3.08
4016 5877 9.213799 GAGGAATCATAAGAATAAGGTAGCAAG 57.786 37.037 0.00 0.00 0.00 4.01
4017 5878 8.938883 AGGAATCATAAGAATAAGGTAGCAAGA 58.061 33.333 0.00 0.00 0.00 3.02
4039 5900 5.541868 AGAACTCTCCAATCTCAAGACAAGA 59.458 40.000 0.00 0.00 0.00 3.02
4071 5932 8.598916 TGTTTGTCTATAAAACTAGATGACCCA 58.401 33.333 0.00 0.00 38.17 4.51
4072 5933 9.614792 GTTTGTCTATAAAACTAGATGACCCAT 57.385 33.333 0.00 0.00 35.18 4.00
4075 5936 8.768397 TGTCTATAAAACTAGATGACCCATTGT 58.232 33.333 0.00 0.00 30.75 2.71
4081 5942 0.033796 AGATGACCCATTGTGCCCAG 60.034 55.000 0.00 0.00 0.00 4.45
4083 5944 1.508667 ATGACCCATTGTGCCCAGGA 61.509 55.000 0.00 0.00 0.00 3.86
4086 5947 3.443045 CCATTGTGCCCAGGACGC 61.443 66.667 0.00 0.00 0.00 5.19
4088 5949 2.048023 CATTGTGCCCAGGACGCAT 61.048 57.895 0.00 0.00 38.76 4.73
4089 5950 1.304381 ATTGTGCCCAGGACGCATT 60.304 52.632 0.00 0.00 38.76 3.56
4123 5984 4.719040 ACCGAAAATTTAAGCAAGCTACG 58.281 39.130 0.00 0.00 0.00 3.51
4125 5986 5.123344 ACCGAAAATTTAAGCAAGCTACGAT 59.877 36.000 0.00 0.00 0.00 3.73
4128 5989 6.907212 CGAAAATTTAAGCAAGCTACGATGAT 59.093 34.615 0.00 0.00 0.00 2.45
4135 5996 4.194640 AGCAAGCTACGATGATCATGTTT 58.805 39.130 14.30 0.00 0.00 2.83
4181 6042 7.188834 TGATCTTGATTTATGACATTTCACGC 58.811 34.615 0.00 0.00 33.38 5.34
4270 6131 7.043961 TGTACATGCAAGATGTTTTTACCAA 57.956 32.000 0.00 0.00 33.76 3.67
4276 6137 4.809673 CAAGATGTTTTTACCAAGGGCTC 58.190 43.478 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 8.884124 ATTTCTCAAACTCTCCCATTCAATTA 57.116 30.769 0.00 0.00 0.00 1.40
35 36 5.299279 GTCAACAATTTCTCAAACTCTCCCA 59.701 40.000 0.00 0.00 0.00 4.37
39 40 5.300286 CCAGGTCAACAATTTCTCAAACTCT 59.700 40.000 0.00 0.00 0.00 3.24
197 200 9.178758 CTCACTAGTTTTAAAGAGCCCATATTT 57.821 33.333 0.00 0.00 0.00 1.40
201 204 4.944317 GCTCACTAGTTTTAAAGAGCCCAT 59.056 41.667 16.10 0.00 41.83 4.00
234 237 6.932960 TGACATGTCATAGCATTAATCCTCTG 59.067 38.462 24.56 0.00 34.14 3.35
289 292 7.846311 AGGGATATCATAGGTAGTATCATGCAA 59.154 37.037 4.83 0.00 0.00 4.08
410 413 7.846644 ACTCAGCAAAACATCATTTCAAAAA 57.153 28.000 0.00 0.00 0.00 1.94
411 414 7.548427 TCAACTCAGCAAAACATCATTTCAAAA 59.452 29.630 0.00 0.00 0.00 2.44
412 415 7.040494 TCAACTCAGCAAAACATCATTTCAAA 58.960 30.769 0.00 0.00 0.00 2.69
413 416 6.571605 TCAACTCAGCAAAACATCATTTCAA 58.428 32.000 0.00 0.00 0.00 2.69
414 417 6.146601 TCAACTCAGCAAAACATCATTTCA 57.853 33.333 0.00 0.00 0.00 2.69
415 418 7.436080 TCTTTCAACTCAGCAAAACATCATTTC 59.564 33.333 0.00 0.00 0.00 2.17
416 419 7.267128 TCTTTCAACTCAGCAAAACATCATTT 58.733 30.769 0.00 0.00 0.00 2.32
417 420 6.808829 TCTTTCAACTCAGCAAAACATCATT 58.191 32.000 0.00 0.00 0.00 2.57
420 423 6.017605 TCTCTCTTTCAACTCAGCAAAACATC 60.018 38.462 0.00 0.00 0.00 3.06
466 469 4.201871 GCCGATTGTAAATTCACGATCCAA 60.202 41.667 3.70 0.00 36.38 3.53
470 473 3.938963 ACAGCCGATTGTAAATTCACGAT 59.061 39.130 0.00 0.00 0.00 3.73
471 474 3.331150 ACAGCCGATTGTAAATTCACGA 58.669 40.909 0.00 0.00 0.00 4.35
472 475 3.740044 ACAGCCGATTGTAAATTCACG 57.260 42.857 0.00 0.00 0.00 4.35
484 487 4.766970 GCTCATGCTACAGCCGAT 57.233 55.556 0.00 0.00 41.18 4.18
506 509 4.584325 CCACCTTCCACTCTCAAAATTTCA 59.416 41.667 0.00 0.00 0.00 2.69
510 513 4.043310 TGATCCACCTTCCACTCTCAAAAT 59.957 41.667 0.00 0.00 0.00 1.82
567 653 9.534565 AGCTAATGTAATAGTCAACATGTGTAG 57.465 33.333 0.00 0.00 36.47 2.74
607 693 3.501828 CAGTTGTTGGCTGTAGCATGTTA 59.498 43.478 6.18 0.00 44.36 2.41
644 730 6.585416 TCATGAGCAGTCTATAAAAGCATGA 58.415 36.000 0.00 0.00 37.75 3.07
659 745 6.276091 TGTACAGCTATTAACTCATGAGCAG 58.724 40.000 22.83 12.41 35.55 4.24
679 765 8.814235 GGCGTATATGGTTATCATGTTATGTAC 58.186 37.037 0.00 0.00 37.30 2.90
702 788 2.030363 TGTTTAGGAGCAATTGTTGGCG 60.030 45.455 7.40 0.00 34.54 5.69
899 985 3.882888 GGTTCTGTGTTTTGAGGTGATGA 59.117 43.478 0.00 0.00 0.00 2.92
904 990 2.291282 TGTGGGTTCTGTGTTTTGAGGT 60.291 45.455 0.00 0.00 0.00 3.85
923 1014 4.020128 GGAGAAAATACAGAGGAGGTGTGT 60.020 45.833 0.00 0.00 36.43 3.72
946 1037 5.770162 ACAGAGATTTGTGGGTTTAAAGAGG 59.230 40.000 0.00 0.00 0.00 3.69
969 1062 4.155280 GTCTCTCTGAGTGTAAGGACAGAC 59.845 50.000 4.32 3.44 35.82 3.51
977 1077 6.419484 TTTTGATGGTCTCTCTGAGTGTAA 57.581 37.500 4.32 0.00 0.00 2.41
1028 1132 0.810031 ATGTGTAATCAGCGACGGGC 60.810 55.000 0.00 0.00 44.05 6.13
1030 1134 0.301687 GCATGTGTAATCAGCGACGG 59.698 55.000 0.00 0.00 0.00 4.79
1032 1136 2.352651 ACATGCATGTGTAATCAGCGAC 59.647 45.455 30.92 0.00 40.03 5.19
1034 1138 4.534794 TTACATGCATGTGTAATCAGCG 57.465 40.909 36.72 6.64 41.89 5.18
1049 1153 5.432157 GTGTCAGACACGAAAGTTTACATG 58.568 41.667 17.96 0.00 46.40 3.21
1094 1198 4.424430 CGCAACCTGCACGTACGC 62.424 66.667 16.72 0.00 45.36 4.42
1679 1815 3.730761 CAGCTCAGGGCAACGCAC 61.731 66.667 0.00 0.00 44.79 5.34
1852 1989 5.906073 ACTCAAATTTGTTCAACCCTTGAG 58.094 37.500 17.47 18.43 42.44 3.02
1853 1990 5.930837 ACTCAAATTTGTTCAACCCTTGA 57.069 34.783 17.47 0.00 38.04 3.02
1887 3606 3.287222 CTGAACTCACTTTTCAACCCCA 58.713 45.455 0.00 0.00 32.61 4.96
1908 3628 1.035139 CATATTTCTGGCTGCCCCAC 58.965 55.000 17.53 0.00 39.18 4.61
1968 3691 9.154847 AGAAAACATATTTGGATTTAGCAAAGC 57.845 29.630 0.00 0.00 0.00 3.51
2040 3767 5.957842 TGGGCTAACAATGTAGAACAAAG 57.042 39.130 0.00 0.00 0.00 2.77
2043 3770 4.076394 GGTTGGGCTAACAATGTAGAACA 58.924 43.478 15.85 0.00 41.18 3.18
2143 3870 6.316140 TGGATTAGTTAGTGAATGACATGTGC 59.684 38.462 1.15 0.00 0.00 4.57
2182 3955 0.771127 AGTTTTGGACCCTAGCTGCA 59.229 50.000 1.02 0.00 0.00 4.41
2322 4104 6.730960 ACGAACTTTGTCAAAGAAACTACA 57.269 33.333 28.07 0.00 41.02 2.74
2457 4300 2.334946 GCTGAAGCCGCCACATTCA 61.335 57.895 0.00 0.00 34.31 2.57
2476 4319 1.379843 GGTTCATGGCCAACCCGAT 60.380 57.895 10.96 0.00 37.88 4.18
3366 5213 6.401955 ACAAGTAACAAACACATGCAAAAC 57.598 33.333 0.00 0.00 0.00 2.43
3675 5536 5.347620 AGTACGTATGCCAAATGGTCTAA 57.652 39.130 0.00 0.00 37.57 2.10
3676 5537 4.498513 CGAGTACGTATGCCAAATGGTCTA 60.499 45.833 0.00 0.00 34.47 2.59
3677 5538 3.737047 CGAGTACGTATGCCAAATGGTCT 60.737 47.826 0.00 0.00 34.47 3.85
3685 5546 0.248336 CGAAGCGAGTACGTATGCCA 60.248 55.000 12.08 0.00 41.98 4.92
3691 5552 0.390866 TCTCTCCGAAGCGAGTACGT 60.391 55.000 0.00 0.00 41.98 3.57
3692 5553 0.302288 CTCTCTCCGAAGCGAGTACG 59.698 60.000 0.00 0.00 42.93 3.67
3694 5555 0.252479 ACCTCTCTCCGAAGCGAGTA 59.748 55.000 0.00 0.00 33.33 2.59
3704 5565 1.743252 CCTTTGCGCACCTCTCTCC 60.743 63.158 11.12 0.00 0.00 3.71
3705 5566 1.743252 CCCTTTGCGCACCTCTCTC 60.743 63.158 11.12 0.00 0.00 3.20
3706 5567 2.348998 CCCTTTGCGCACCTCTCT 59.651 61.111 11.12 0.00 0.00 3.10
3726 5587 3.620488 TCCTACAACATGAAGATTGGGC 58.380 45.455 0.00 0.00 0.00 5.36
3766 5627 1.308998 CCGGCTACCCACAATTGATC 58.691 55.000 13.59 0.00 0.00 2.92
3770 5631 1.513858 TATCCCGGCTACCCACAATT 58.486 50.000 0.00 0.00 0.00 2.32
3777 5638 1.963172 CCTTGTTTATCCCGGCTACC 58.037 55.000 0.00 0.00 0.00 3.18
3803 5664 2.050144 TGGCATCCTATTCCTCCTGTC 58.950 52.381 0.00 0.00 0.00 3.51
3810 5671 2.767505 CTACCGTTGGCATCCTATTCC 58.232 52.381 0.00 0.00 0.00 3.01
3814 5675 1.692173 GGGCTACCGTTGGCATCCTA 61.692 60.000 8.67 0.00 0.00 2.94
3835 5696 2.225791 CTGGCGGTCCACTCGAATCA 62.226 60.000 0.00 0.00 37.47 2.57
3839 5700 2.915659 AACTGGCGGTCCACTCGA 60.916 61.111 0.00 0.00 37.47 4.04
3841 5702 1.668151 GTGAACTGGCGGTCCACTC 60.668 63.158 8.76 0.00 37.47 3.51
3844 5705 0.605319 GATTGTGAACTGGCGGTCCA 60.605 55.000 0.00 0.00 40.85 4.02
3846 5707 0.798776 CAGATTGTGAACTGGCGGTC 59.201 55.000 0.00 0.00 0.00 4.79
3848 5709 1.503542 GCAGATTGTGAACTGGCGG 59.496 57.895 0.00 0.00 35.05 6.13
3854 5715 2.412847 GGTTAGTGCGCAGATTGTGAAC 60.413 50.000 12.22 7.34 36.67 3.18
3863 5724 2.475519 CGTTATTTGGGTTAGTGCGCAG 60.476 50.000 12.22 0.00 32.94 5.18
3868 5729 2.997986 AGCGTCGTTATTTGGGTTAGTG 59.002 45.455 0.00 0.00 0.00 2.74
3883 5744 2.202492 CCGGAGACTTGAGCGTCG 60.202 66.667 0.00 0.00 38.90 5.12
3897 5758 1.102154 TGCATCAAATTAGTGCCCGG 58.898 50.000 0.00 0.00 38.06 5.73
3898 5759 2.937469 TTGCATCAAATTAGTGCCCG 57.063 45.000 7.04 0.00 38.06 6.13
3900 5761 3.374745 CGGATTGCATCAAATTAGTGCC 58.625 45.455 7.04 0.00 38.06 5.01
3906 5767 1.745087 ACTCGCGGATTGCATCAAATT 59.255 42.857 6.13 0.00 46.97 1.82
3918 5779 0.454196 TTTCATGATCGACTCGCGGA 59.546 50.000 6.13 0.00 41.33 5.54
3919 5780 1.277326 TTTTCATGATCGACTCGCGG 58.723 50.000 6.13 0.00 41.33 6.46
3942 5803 2.229543 ACGACTTGAGTGCGGTTGTATA 59.770 45.455 0.00 0.00 0.00 1.47
3951 5812 1.651138 CATTCTCGACGACTTGAGTGC 59.349 52.381 0.00 0.00 33.88 4.40
3962 5823 3.103447 TCATCCTGATGCATTCTCGAC 57.897 47.619 0.00 0.00 38.65 4.20
3963 5824 3.133542 AGTTCATCCTGATGCATTCTCGA 59.866 43.478 0.00 0.00 38.65 4.04
3964 5825 3.464907 AGTTCATCCTGATGCATTCTCG 58.535 45.455 0.00 0.00 38.65 4.04
3965 5826 3.814283 GGAGTTCATCCTGATGCATTCTC 59.186 47.826 0.00 7.04 45.64 2.87
3966 5827 3.818180 GGAGTTCATCCTGATGCATTCT 58.182 45.455 0.00 0.00 45.64 2.40
3979 5840 5.363868 TCTTATGATTCCTCGTGGAGTTCAT 59.636 40.000 24.90 24.90 44.24 2.57
3980 5841 4.709886 TCTTATGATTCCTCGTGGAGTTCA 59.290 41.667 17.99 17.99 44.24 3.18
4011 5872 4.285517 TCTTGAGATTGGAGAGTTCTTGCT 59.714 41.667 0.00 0.00 0.00 3.91
4016 5877 5.637387 GTCTTGTCTTGAGATTGGAGAGTTC 59.363 44.000 0.00 0.00 0.00 3.01
4017 5878 5.306678 AGTCTTGTCTTGAGATTGGAGAGTT 59.693 40.000 0.00 0.00 0.00 3.01
4071 5932 1.304381 AATGCGTCCTGGGCACAAT 60.304 52.632 0.00 0.00 44.23 2.71
4072 5933 2.115052 AATGCGTCCTGGGCACAA 59.885 55.556 0.00 0.00 44.23 3.33
4081 5942 0.669932 TGCAATTTGCCAATGCGTCC 60.670 50.000 18.27 0.00 44.23 4.79
4083 5944 0.867086 GTTGCAATTTGCCAATGCGT 59.133 45.000 18.27 0.00 44.23 5.24
4086 5947 1.793258 TCGGTTGCAATTTGCCAATG 58.207 45.000 18.27 6.67 44.23 2.82
4088 5949 2.315925 TTTCGGTTGCAATTTGCCAA 57.684 40.000 18.27 9.92 44.23 4.52
4089 5950 2.315925 TTTTCGGTTGCAATTTGCCA 57.684 40.000 18.27 4.91 44.23 4.92
4109 5970 5.817296 ACATGATCATCGTAGCTTGCTTAAA 59.183 36.000 4.86 0.00 0.00 1.52
4128 5989 9.681692 GCTATGTGCATAATTCATAAAACATGA 57.318 29.630 0.00 0.00 42.31 3.07
4213 6074 9.612066 TTGCCTCATTTATCGAATGCATATATA 57.388 29.630 0.00 0.00 43.93 0.86
4217 6078 6.822667 ATTGCCTCATTTATCGAATGCATA 57.177 33.333 0.00 0.00 43.93 3.14
4231 6092 6.876155 TGCATGTACAAATTAATTGCCTCAT 58.124 32.000 11.66 3.03 43.13 2.90
4270 6131 1.356124 ACTCACAAGACATGAGCCCT 58.644 50.000 0.00 0.00 46.33 5.19
4276 6137 6.201615 ACAATATGCGATACTCACAAGACATG 59.798 38.462 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.