Multiple sequence alignment - TraesCS2A01G517600

Loading Multiple Alignment...

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 TraesCS2A01G517600 chr2A 100.000 3965 0 0 1 3965 740876427 740872463 0.000000e+00 7323.0
1 TraesCS2A01G517600 chr2A 91.667 120 10 0 5 124 740885813 740885694 2.450000e-37 167.0
2 TraesCS2A01G517600 chr2A 79.184 245 46 5 5 247 623106861 623106620 8.810000e-37 165.0
3 TraesCS2A01G517600 chr2B 92.753 3091 143 29 5 3061 742895553 742892510 0.000000e+00 4392.0
4 TraesCS2A01G517600 chr2B 93.310 852 53 3 3116 3965 742892499 742891650 0.000000e+00 1254.0
5 TraesCS2A01G517600 chr2B 78.298 235 43 6 7 235 570659593 570659361 1.150000e-30 145.0
6 TraesCS2A01G517600 chr2D 93.880 2206 102 16 1780 3965 608980232 608978040 0.000000e+00 3295.0
7 TraesCS2A01G517600 chr2D 92.727 770 49 7 1017 1784 608981097 608980333 0.000000e+00 1105.0
8 TraesCS2A01G517600 chr2D 96.631 564 17 1 300 863 608982083 608981522 0.000000e+00 935.0
9 TraesCS2A01G517600 chr2D 91.892 296 17 5 5 298 608982416 608982126 1.330000e-109 407.0
10 TraesCS2A01G517600 chr2D 98.077 52 1 0 975 1026 608981163 608981112 1.520000e-14 91.6
11 TraesCS2A01G517600 chr1A 81.739 230 41 1 7 235 554801134 554800905 1.450000e-44 191.0
12 TraesCS2A01G517600 chr3D 79.918 244 46 3 7 248 603112066 603112308 4.070000e-40 176.0
13 TraesCS2A01G517600 chr6A 78.804 184 38 1 6 188 471877351 471877534 5.380000e-24 122.0
14 TraesCS2A01G517600 chr7B 79.444 180 28 6 7 185 498186696 498186525 6.960000e-23 119.0


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 TraesCS2A01G517600 chr2A 740872463 740876427 3964 True 7323.00 7323 100.0000 1 3965 1 chr2A.!!$R2 3964
1 TraesCS2A01G517600 chr2B 742891650 742895553 3903 True 2823.00 4392 93.0315 5 3965 2 chr2B.!!$R2 3960
2 TraesCS2A01G517600 chr2D 608978040 608982416 4376 True 1166.72 3295 94.6414 5 3965 5 chr2D.!!$R1 3960

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
110 111 0.046242 ATGAGGGAGGGGGAATGACA 59.954 55.0 0.0 0.0 0.0 3.58 F
943 1299 0.179113 CTCTCTCTCTTTCCCTGCGC 60.179 60.0 0.0 0.0 0.0 6.09 F
2438 2925 0.253044 GAATACCACCCTCAGCAGCA 59.747 55.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1841 2327 0.251341 ACTGGTGGCAATCAAGGTCC 60.251 55.000 0.00 0.0 0.00 4.46 R
2640 3127 1.071471 CGGGTTCTTGTGGCACTCT 59.929 57.895 19.83 0.0 0.00 3.24 R
3735 4244 0.032952 GGTAGCACCACACGAAGACA 59.967 55.000 0.00 0.0 38.42 3.41 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 2.771943 TCTAGTGCTTTGGTCCTATGGG 59.228 50.000 0.00 0.00 0.00 4.00
50 51 3.766691 GGGGTCTTAGCACGGCGA 61.767 66.667 16.62 0.00 0.00 5.54
51 52 2.499685 GGGTCTTAGCACGGCGAT 59.500 61.111 16.62 0.86 0.00 4.58
55 56 1.467342 GGTCTTAGCACGGCGATTTTT 59.533 47.619 16.62 0.00 0.00 1.94
82 83 6.885922 ACTGTCTACTACAAGAAGGTTTGTT 58.114 36.000 0.00 0.00 41.31 2.83
110 111 0.046242 ATGAGGGAGGGGGAATGACA 59.954 55.000 0.00 0.00 0.00 3.58
112 113 0.621862 GAGGGAGGGGGAATGACAGT 60.622 60.000 0.00 0.00 0.00 3.55
279 282 5.181433 GCTGCCTTTTTAAGTGTAGCTTAGT 59.819 40.000 0.00 0.00 40.41 2.24
403 450 5.492854 CGATCATACATGTTCCGTTTTCTG 58.507 41.667 2.30 0.00 0.00 3.02
529 576 4.313277 AGCTCTTGTTTCTTTTCCAAGC 57.687 40.909 0.00 0.00 36.41 4.01
557 604 0.825410 GCCCACATCAATGGCATCAA 59.175 50.000 0.00 0.00 44.70 2.57
559 606 1.411246 CCCACATCAATGGCATCAAGG 59.589 52.381 0.00 0.00 38.55 3.61
688 735 5.523438 AGTAGCTAGAAGGATGTAACTGC 57.477 43.478 0.00 0.00 0.00 4.40
749 796 5.049405 TCTGAGTTTTCAAAAGATTCGGCTC 60.049 40.000 0.00 0.00 31.69 4.70
797 844 0.832135 ACCAGACGACCAGGTGTCAT 60.832 55.000 18.78 6.45 44.71 3.06
798 845 1.182667 CCAGACGACCAGGTGTCATA 58.817 55.000 18.78 0.00 44.71 2.15
799 846 1.135083 CCAGACGACCAGGTGTCATAC 60.135 57.143 18.78 0.00 44.71 2.39
806 853 3.525537 GACCAGGTGTCATACTGTCATG 58.474 50.000 0.00 0.00 43.85 3.07
807 854 2.906389 ACCAGGTGTCATACTGTCATGT 59.094 45.455 0.00 0.00 32.90 3.21
808 855 3.264947 CCAGGTGTCATACTGTCATGTG 58.735 50.000 0.00 0.00 32.90 3.21
824 871 3.661745 GTGTCAACCACACGAGACT 57.338 52.632 0.00 0.00 46.12 3.24
834 881 2.354704 CCACACGAGACTCTCTCTCTCT 60.355 54.545 4.52 0.00 43.22 3.10
835 882 2.930040 CACACGAGACTCTCTCTCTCTC 59.070 54.545 4.52 0.00 43.22 3.20
836 883 2.832129 ACACGAGACTCTCTCTCTCTCT 59.168 50.000 4.52 0.00 43.22 3.10
916 1272 2.285668 CCCCTCTCTTCCCCTGCA 60.286 66.667 0.00 0.00 0.00 4.41
934 1290 2.308570 TGCACCTCTCTCTCTCTCTCTT 59.691 50.000 0.00 0.00 0.00 2.85
935 1291 3.245229 TGCACCTCTCTCTCTCTCTCTTT 60.245 47.826 0.00 0.00 0.00 2.52
936 1292 3.378427 GCACCTCTCTCTCTCTCTCTTTC 59.622 52.174 0.00 0.00 0.00 2.62
937 1293 3.947834 CACCTCTCTCTCTCTCTCTTTCC 59.052 52.174 0.00 0.00 0.00 3.13
938 1294 3.053619 ACCTCTCTCTCTCTCTCTTTCCC 60.054 52.174 0.00 0.00 0.00 3.97
939 1295 3.203040 CCTCTCTCTCTCTCTCTTTCCCT 59.797 52.174 0.00 0.00 0.00 4.20
940 1296 4.202441 CTCTCTCTCTCTCTCTTTCCCTG 58.798 52.174 0.00 0.00 0.00 4.45
941 1297 2.689983 CTCTCTCTCTCTCTTTCCCTGC 59.310 54.545 0.00 0.00 0.00 4.85
942 1298 1.405105 CTCTCTCTCTCTTTCCCTGCG 59.595 57.143 0.00 0.00 0.00 5.18
943 1299 0.179113 CTCTCTCTCTTTCCCTGCGC 60.179 60.000 0.00 0.00 0.00 6.09
944 1300 1.153469 CTCTCTCTTTCCCTGCGCC 60.153 63.158 4.18 0.00 0.00 6.53
945 1301 1.610673 TCTCTCTTTCCCTGCGCCT 60.611 57.895 4.18 0.00 0.00 5.52
946 1302 1.153469 CTCTCTTTCCCTGCGCCTC 60.153 63.158 4.18 0.00 0.00 4.70
947 1303 1.610673 TCTCTTTCCCTGCGCCTCT 60.611 57.895 4.18 0.00 0.00 3.69
948 1304 1.153469 CTCTTTCCCTGCGCCTCTC 60.153 63.158 4.18 0.00 0.00 3.20
949 1305 1.610673 TCTTTCCCTGCGCCTCTCT 60.611 57.895 4.18 0.00 0.00 3.10
950 1306 1.153469 CTTTCCCTGCGCCTCTCTC 60.153 63.158 4.18 0.00 0.00 3.20
951 1307 1.610673 TTTCCCTGCGCCTCTCTCT 60.611 57.895 4.18 0.00 0.00 3.10
952 1308 1.608717 TTTCCCTGCGCCTCTCTCTC 61.609 60.000 4.18 0.00 0.00 3.20
953 1309 2.441901 CCCTGCGCCTCTCTCTCT 60.442 66.667 4.18 0.00 0.00 3.10
954 1310 2.489275 CCCTGCGCCTCTCTCTCTC 61.489 68.421 4.18 0.00 0.00 3.20
960 1316 1.871080 CGCCTCTCTCTCTCTCTCTC 58.129 60.000 0.00 0.00 0.00 3.20
963 1319 2.843701 CCTCTCTCTCTCTCTCTCTGC 58.156 57.143 0.00 0.00 0.00 4.26
1064 1444 5.538053 TCTCTCTCTTATTTGCATCCGATCT 59.462 40.000 0.00 0.00 0.00 2.75
1080 1460 4.587684 TCCGATCTGTTCTAGGGTTTATCC 59.412 45.833 0.00 0.00 0.00 2.59
1181 1561 7.995488 AGTTTCTATCTATGCCTGCAAAAGTAT 59.005 33.333 0.00 0.00 0.00 2.12
1310 1690 5.369685 TTTTTGCATGATTTCTGCTCGTA 57.630 34.783 0.00 0.00 40.34 3.43
1316 1696 4.094887 GCATGATTTCTGCTCGTAGGAAAA 59.905 41.667 0.00 0.00 36.68 2.29
1317 1697 5.391950 GCATGATTTCTGCTCGTAGGAAAAA 60.392 40.000 0.00 0.00 36.68 1.94
1348 1728 2.603560 GGTCACTCGGATAAAAGAAGCG 59.396 50.000 0.00 0.00 0.00 4.68
1362 1742 6.817765 AAAAGAAGCGAGACCATCAATTTA 57.182 33.333 0.00 0.00 0.00 1.40
1475 1855 4.535526 AATTTGTATTTGTGCCTCCCAC 57.464 40.909 0.00 0.00 44.90 4.61
1513 1893 8.993121 CACTTCATATTCGCCTACAGAAATTAT 58.007 33.333 0.00 0.00 0.00 1.28
1591 1972 6.613271 AGAGGTCATAACATCTCAACCATACT 59.387 38.462 0.00 0.00 42.67 2.12
1770 2151 9.643693 AAATTAGAAAGTATGCACTGATTTTGG 57.356 29.630 0.00 0.00 34.36 3.28
1795 2281 9.053840 GGGGCTTCATTAGTAACTATTTACTTC 57.946 37.037 10.40 0.00 44.77 3.01
1841 2327 8.310382 CAGATCTCCACTATAATCTTAAGGGTG 58.690 40.741 1.85 3.36 0.00 4.61
2417 2904 4.648626 GCCCACTGAGCAGCCACA 62.649 66.667 0.00 0.00 0.00 4.17
2438 2925 0.253044 GAATACCACCCTCAGCAGCA 59.747 55.000 0.00 0.00 0.00 4.41
2572 3059 4.144727 GGGAGGAGGAGAGGCCGA 62.145 72.222 0.00 0.00 43.43 5.54
2597 3084 3.991536 GACCGGCCGAGCTTGAGAC 62.992 68.421 30.73 4.13 0.00 3.36
2619 3106 1.457346 CAAAGGAGATGCAGGTCCAC 58.543 55.000 17.27 0.00 35.02 4.02
2658 3145 1.071471 AGAGTGCCACAAGAACCCG 59.929 57.895 0.00 0.00 0.00 5.28
2691 3178 2.341543 CCGATGGGAGAGATGCCG 59.658 66.667 0.00 0.00 34.06 5.69
3059 3556 6.486320 TGATTACCAATGATTCGTGTATGCAT 59.514 34.615 3.79 3.79 0.00 3.96
3087 3591 6.643770 GCTATGCATGAATCATTTTTGTAGGG 59.356 38.462 10.16 0.00 0.00 3.53
3105 3609 1.438814 GGGGGCTTTGCATGAATCG 59.561 57.895 0.00 0.00 0.00 3.34
3114 3618 1.062525 GCATGAATCGTCGCCAACC 59.937 57.895 0.00 0.00 0.00 3.77
3298 3805 5.531287 GTGTCTCCTTTTCAACATAGTGGTT 59.469 40.000 0.00 0.00 0.00 3.67
3347 3854 7.384660 GCAAATAAATGGTGTGTGAGAAATTCA 59.615 33.333 0.00 0.00 0.00 2.57
3367 3874 9.862371 AAATTCATACGGTTAAATGCAATACAA 57.138 25.926 0.00 0.00 0.00 2.41
3376 3883 7.642194 CGGTTAAATGCAATACAACAATACGAT 59.358 33.333 0.00 0.00 0.00 3.73
3377 3884 8.742188 GGTTAAATGCAATACAACAATACGATG 58.258 33.333 0.00 0.00 0.00 3.84
3436 3943 8.138712 CCTACATCCTCAACTCTTGACTATAAC 58.861 40.741 0.00 0.00 35.46 1.89
3437 3944 6.565234 ACATCCTCAACTCTTGACTATAACG 58.435 40.000 0.00 0.00 35.46 3.18
3438 3945 4.995124 TCCTCAACTCTTGACTATAACGC 58.005 43.478 0.00 0.00 35.46 4.84
3480 3988 0.528924 CACAATACGGACCGGTCTGA 59.471 55.000 42.84 28.27 39.24 3.27
3484 3992 3.640029 ACAATACGGACCGGTCTGATTAT 59.360 43.478 42.84 29.12 39.24 1.28
3488 3996 0.685660 GGACCGGTCTGATTATCCCC 59.314 60.000 32.52 10.25 0.00 4.81
3517 4025 1.068417 CAACAACGGACCGGTCTGA 59.932 57.895 42.84 0.00 39.24 3.27
3524 4032 1.041447 CGGACCGGTCTGATTACCCT 61.041 60.000 35.70 0.00 38.21 4.34
3526 4034 1.481871 GACCGGTCTGATTACCCTCA 58.518 55.000 27.64 0.00 36.03 3.86
3569 4077 6.849697 ACCCACTCTTACAATCCCATATCTAA 59.150 38.462 0.00 0.00 0.00 2.10
3600 4108 2.486951 TGTCTAGTCTATTTCGCGGC 57.513 50.000 6.13 0.00 0.00 6.53
3602 4110 2.361119 TGTCTAGTCTATTTCGCGGCAT 59.639 45.455 6.13 0.51 0.00 4.40
3735 4244 6.964464 AGTAAAATCCAACCCAAAAACCTTT 58.036 32.000 0.00 0.00 0.00 3.11
3775 4284 2.032528 TCCTGGCTTGGCTGAACG 59.967 61.111 2.86 0.00 0.00 3.95
3799 4309 3.763097 TGATGCTATTTTTGCCGACAG 57.237 42.857 0.00 0.00 0.00 3.51
3800 4310 3.342719 TGATGCTATTTTTGCCGACAGA 58.657 40.909 0.00 0.00 0.00 3.41
3808 4318 4.647424 TTTTTGCCGACAGATTGTTCTT 57.353 36.364 0.00 0.00 0.00 2.52
3842 4352 4.033009 CAATCCCTTTAGCCTCCCAAAAT 58.967 43.478 0.00 0.00 0.00 1.82
3919 4429 1.074405 AGAATGCACCACCATGACAGT 59.926 47.619 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.004734 AGCACTAGAACAACAACCATTGC 59.995 43.478 0.00 0.00 32.47 3.56
1 2 4.836125 AGCACTAGAACAACAACCATTG 57.164 40.909 0.00 0.00 35.59 2.82
2 3 5.451798 CCAAAGCACTAGAACAACAACCATT 60.452 40.000 0.00 0.00 0.00 3.16
3 4 4.037923 CCAAAGCACTAGAACAACAACCAT 59.962 41.667 0.00 0.00 0.00 3.55
35 36 1.084289 AAAATCGCCGTGCTAAGACC 58.916 50.000 0.00 0.00 0.00 3.85
50 51 7.599245 CCTTCTTGTAGTAGACAGTCGAAAAAT 59.401 37.037 0.00 0.00 39.88 1.82
51 52 6.921857 CCTTCTTGTAGTAGACAGTCGAAAAA 59.078 38.462 0.00 0.00 39.88 1.94
55 56 4.649692 ACCTTCTTGTAGTAGACAGTCGA 58.350 43.478 0.00 0.00 39.88 4.20
103 104 4.166011 GGCGCGCCACTGTCATTC 62.166 66.667 43.55 13.42 35.81 2.67
194 197 4.265893 TCAACTGTCAAGGTAGCACAAAA 58.734 39.130 0.00 0.00 0.00 2.44
253 256 2.225727 GCTACACTTAAAAAGGCAGCGT 59.774 45.455 0.00 0.00 0.00 5.07
279 282 7.237679 CCTCCCAGGTATCTCCTAAATAAATCA 59.762 40.741 0.00 0.00 46.24 2.57
529 576 1.180456 TTGATGTGGGCTTGGCACAG 61.180 55.000 0.00 0.00 45.08 3.66
557 604 4.772100 TGCCATTAAAGAAGCTTTTAGCCT 59.228 37.500 0.00 0.00 43.77 4.58
559 606 6.389906 TCTTGCCATTAAAGAAGCTTTTAGC 58.610 36.000 0.00 0.00 42.84 3.09
658 705 7.489239 ACATCCTTCTAGCTACTTCTCTTTT 57.511 36.000 0.00 0.00 0.00 2.27
688 735 1.732259 GGCTACACCAAGTCATCAACG 59.268 52.381 0.00 0.00 38.86 4.10
749 796 4.376819 GCAGAAGCTTCGGATGATTTATCG 60.377 45.833 27.75 3.85 35.70 2.92
807 854 1.337071 GAGAGTCTCGTGTGGTTGACA 59.663 52.381 3.95 0.00 32.41 3.58
808 855 1.609555 AGAGAGTCTCGTGTGGTTGAC 59.390 52.381 14.47 0.00 35.36 3.18
823 870 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
824 871 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
834 881 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
835 882 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
836 883 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
881 928 2.624557 GGGGCGGGAGAGAGATATGTAT 60.625 54.545 0.00 0.00 0.00 2.29
892 939 2.042843 GAAGAGAGGGGCGGGAGA 60.043 66.667 0.00 0.00 0.00 3.71
916 1272 3.053619 GGGAAAGAGAGAGAGAGAGAGGT 60.054 52.174 0.00 0.00 0.00 3.85
934 1290 2.038007 AGAGAGAGGCGCAGGGAA 59.962 61.111 10.83 0.00 0.00 3.97
935 1291 2.441164 GAGAGAGAGGCGCAGGGA 60.441 66.667 10.83 0.00 0.00 4.20
936 1292 2.441901 AGAGAGAGAGGCGCAGGG 60.442 66.667 10.83 0.00 0.00 4.45
937 1293 1.447317 GAGAGAGAGAGAGGCGCAGG 61.447 65.000 10.83 0.00 0.00 4.85
938 1294 0.464373 AGAGAGAGAGAGAGGCGCAG 60.464 60.000 10.83 0.00 0.00 5.18
939 1295 0.463654 GAGAGAGAGAGAGAGGCGCA 60.464 60.000 10.83 0.00 0.00 6.09
940 1296 0.179045 AGAGAGAGAGAGAGAGGCGC 60.179 60.000 0.00 0.00 0.00 6.53
941 1297 1.414181 AGAGAGAGAGAGAGAGAGGCG 59.586 57.143 0.00 0.00 0.00 5.52
942 1298 2.843701 CAGAGAGAGAGAGAGAGAGGC 58.156 57.143 0.00 0.00 0.00 4.70
943 1299 2.804572 CGCAGAGAGAGAGAGAGAGAGG 60.805 59.091 0.00 0.00 0.00 3.69
944 1300 2.101415 TCGCAGAGAGAGAGAGAGAGAG 59.899 54.545 0.00 0.00 0.00 3.20
945 1301 2.107366 TCGCAGAGAGAGAGAGAGAGA 58.893 52.381 0.00 0.00 0.00 3.10
946 1302 2.205074 GTCGCAGAGAGAGAGAGAGAG 58.795 57.143 0.00 0.00 36.95 3.20
947 1303 1.552792 TGTCGCAGAGAGAGAGAGAGA 59.447 52.381 0.00 0.00 36.95 3.10
948 1304 2.022764 TGTCGCAGAGAGAGAGAGAG 57.977 55.000 0.00 0.00 36.95 3.20
949 1305 2.481289 TTGTCGCAGAGAGAGAGAGA 57.519 50.000 0.00 0.00 36.95 3.10
950 1306 2.415357 GGTTTGTCGCAGAGAGAGAGAG 60.415 54.545 0.00 0.00 36.95 3.20
951 1307 1.542030 GGTTTGTCGCAGAGAGAGAGA 59.458 52.381 0.00 0.00 36.95 3.10
952 1308 1.270826 TGGTTTGTCGCAGAGAGAGAG 59.729 52.381 0.00 0.00 36.95 3.20
953 1309 1.328279 TGGTTTGTCGCAGAGAGAGA 58.672 50.000 0.00 0.00 36.95 3.10
954 1310 1.795286 GTTGGTTTGTCGCAGAGAGAG 59.205 52.381 0.00 0.00 36.95 3.20
1080 1460 4.811555 TTGAACGAATCACTCACAAAGG 57.188 40.909 0.00 0.00 37.92 3.11
1181 1561 9.104965 CATGGGTTTTGAATTACGAGAAGTATA 57.895 33.333 0.00 0.00 34.88 1.47
1220 1600 5.324409 AGTCAGAAAATGGGAAGCAACATA 58.676 37.500 0.00 0.00 0.00 2.29
1317 1697 8.411991 TTTTATCCGAGTGACCCTAAATTTTT 57.588 30.769 0.00 0.00 0.00 1.94
1318 1698 7.886446 TCTTTTATCCGAGTGACCCTAAATTTT 59.114 33.333 0.00 0.00 0.00 1.82
1319 1699 7.399634 TCTTTTATCCGAGTGACCCTAAATTT 58.600 34.615 0.00 0.00 0.00 1.82
1320 1700 6.954232 TCTTTTATCCGAGTGACCCTAAATT 58.046 36.000 0.00 0.00 0.00 1.82
1321 1701 6.555463 TCTTTTATCCGAGTGACCCTAAAT 57.445 37.500 0.00 0.00 0.00 1.40
1332 1712 3.117046 GGTCTCGCTTCTTTTATCCGAG 58.883 50.000 0.00 0.00 44.76 4.63
1334 1714 2.888594 TGGTCTCGCTTCTTTTATCCG 58.111 47.619 0.00 0.00 0.00 4.18
1401 1781 6.713731 AGGTGGGGTTTAATCTCTTCTTAA 57.286 37.500 0.00 0.00 0.00 1.85
1411 1791 8.174757 ACTATTTTTCACTAGGTGGGGTTTAAT 58.825 33.333 0.00 0.00 33.87 1.40
1475 1855 6.509199 GCGAATATGAAGTGACAGAAGATGTG 60.509 42.308 0.00 0.00 44.17 3.21
1547 1927 4.325344 CCTCTTTGGTCCATGGGAAACTAT 60.325 45.833 13.02 0.00 31.38 2.12
1549 1929 2.225117 CCTCTTTGGTCCATGGGAAACT 60.225 50.000 13.02 0.00 31.38 2.66
1749 2130 4.463891 CCCCAAAATCAGTGCATACTTTCT 59.536 41.667 0.00 0.00 34.07 2.52
1795 2281 2.874086 TGTGTTGACAGAAGCATCAGTG 59.126 45.455 0.00 0.00 0.00 3.66
1841 2327 0.251341 ACTGGTGGCAATCAAGGTCC 60.251 55.000 0.00 0.00 0.00 4.46
2417 2904 1.207791 CTGCTGAGGGTGGTATTCCT 58.792 55.000 0.00 0.00 35.82 3.36
2438 2925 4.988598 CCGGTTGCTGCTCGGTGT 62.989 66.667 16.90 0.00 39.04 4.16
2457 2944 3.480133 GGCGGCTGAGGGTGGTAT 61.480 66.667 0.00 0.00 0.00 2.73
2489 2976 1.584724 CTGAGGGTGGTGGTATTCCT 58.415 55.000 0.00 0.00 34.23 3.36
2572 3059 3.007973 GCTCGGCCGGTCTCTCTTT 62.008 63.158 27.83 0.00 0.00 2.52
2597 3084 1.372087 GACCTGCATCTCCTTTGGCG 61.372 60.000 0.00 0.00 0.00 5.69
2640 3127 1.071471 CGGGTTCTTGTGGCACTCT 59.929 57.895 19.83 0.00 0.00 3.24
2658 3145 2.766229 GGGTGCCTCCTCTCCCTC 60.766 72.222 0.00 0.00 36.94 4.30
3012 3499 1.923204 GACACGCAAAACACATGCAAA 59.077 42.857 0.00 0.00 44.01 3.68
3059 3556 6.869695 ACAAAAATGATTCATGCATAGCAGA 58.130 32.000 0.00 0.00 43.65 4.26
3087 3591 1.322538 ACGATTCATGCAAAGCCCCC 61.323 55.000 0.00 0.00 0.00 5.40
3105 3609 2.125512 AGAGCATCGGTTGGCGAC 60.126 61.111 0.00 0.00 42.67 5.19
3114 3618 2.141517 GATGTGAATGGGAGAGCATCG 58.858 52.381 0.00 0.00 42.67 3.84
3153 3660 2.606795 GGAAGGCATCGATTCTCTCTCG 60.607 54.545 0.00 0.00 37.47 4.04
3154 3661 2.288763 GGGAAGGCATCGATTCTCTCTC 60.289 54.545 0.00 0.00 0.00 3.20
3298 3805 6.372659 TGCCAAAGTGCTAAAAATTGTTTCAA 59.627 30.769 0.00 0.00 0.00 2.69
3347 3854 9.724839 GTATTGTTGTATTGCATTTAACCGTAT 57.275 29.630 0.00 0.00 0.00 3.06
3352 3859 8.259194 GCATCGTATTGTTGTATTGCATTTAAC 58.741 33.333 0.00 0.00 0.00 2.01
3367 3874 7.609760 TTAACAAATCTGAGCATCGTATTGT 57.390 32.000 0.00 0.00 38.61 2.71
3376 3883 7.994425 TGAACCTTATTAACAAATCTGAGCA 57.006 32.000 0.00 0.00 0.00 4.26
3377 3884 8.296713 TGTTGAACCTTATTAACAAATCTGAGC 58.703 33.333 0.00 0.00 30.81 4.26
3436 3943 1.102154 TTAATGCATGTTGAGGGGCG 58.898 50.000 0.00 0.00 0.00 6.13
3437 3944 3.825143 ATTTAATGCATGTTGAGGGGC 57.175 42.857 0.00 0.00 0.00 5.80
3438 3945 6.534793 GTGTTAATTTAATGCATGTTGAGGGG 59.465 38.462 0.00 0.00 0.00 4.79
3500 4008 0.395312 AATCAGACCGGTCCGTTGTT 59.605 50.000 30.82 14.70 0.00 2.83
3517 4025 1.406887 GGCACACGACATGAGGGTAAT 60.407 52.381 0.00 0.00 0.00 1.89
3569 4077 9.209175 GAAATAGACTAGACAAAGTTGATGTGT 57.791 33.333 0.00 0.00 0.00 3.72
3600 4108 4.999311 TGAAGATTGTGGAGTTGACTGATG 59.001 41.667 0.00 0.00 0.00 3.07
3602 4110 4.687901 TGAAGATTGTGGAGTTGACTGA 57.312 40.909 0.00 0.00 0.00 3.41
3735 4244 0.032952 GGTAGCACCACACGAAGACA 59.967 55.000 0.00 0.00 38.42 3.41
3775 4284 3.304293 GTCGGCAAAAATAGCATCAAAGC 59.696 43.478 0.00 0.00 0.00 3.51
3824 4334 2.760650 GACATTTTGGGAGGCTAAAGGG 59.239 50.000 0.00 0.00 0.00 3.95
3830 4340 7.785033 CAAAATATAAGACATTTTGGGAGGCT 58.215 34.615 11.05 0.00 44.25 4.58
3842 4352 8.752187 AGTACTTCCGTACCAAAATATAAGACA 58.248 33.333 0.00 0.00 45.68 3.41
3878 4388 5.216648 TCTAGCGGCAACAACAAATTAAAC 58.783 37.500 1.45 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.