Multiple sequence alignment - TraesCS3D01G242200

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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 TraesCS3D01G242200 chr3D 100.000 7131 0 0 1 7131 337303212 337310342 0.000000e+00 13169.0
1 TraesCS3D01G242200 chr3B 96.157 4996 125 21 2187 7129 434982457 434987438 0.000000e+00 8100.0
2 TraesCS3D01G242200 chr3B 92.301 2208 84 46 1 2161 434980023 434982191 0.000000e+00 3057.0
3 TraesCS3D01G242200 chr3A 97.383 2828 45 13 4314 7131 454514193 454517001 0.000000e+00 4785.0
4 TraesCS3D01G242200 chr3A 92.718 3131 110 48 1 3096 454510037 454513084 0.000000e+00 4410.0
5 TraesCS3D01G242200 chr3A 95.819 1124 23 7 3154 4259 454513076 454514193 0.000000e+00 1794.0
6 TraesCS3D01G242200 chr3A 83.152 184 25 5 3078 3258 202671091 202671271 5.720000e-36 163.0
7 TraesCS3D01G242200 chr3A 93.750 64 2 2 4255 4316 671630790 671630853 2.120000e-15 95.3
8 TraesCS3D01G242200 chr6A 85.795 176 22 3 3083 3258 52399585 52399413 4.390000e-42 183.0
9 TraesCS3D01G242200 chr6A 90.000 70 4 2 4249 4315 594732807 594732738 3.540000e-13 87.9
10 TraesCS3D01G242200 chr6D 84.916 179 20 6 3085 3260 41929215 41929041 2.640000e-39 174.0
11 TraesCS3D01G242200 chr6D 82.682 179 29 2 3081 3258 393765163 393764986 2.660000e-34 158.0
12 TraesCS3D01G242200 chr6D 92.308 91 5 2 6885 6973 426888235 426888325 2.090000e-25 128.0
13 TraesCS3D01G242200 chr6D 93.103 87 5 1 6888 6973 296196995 296196909 7.510000e-25 126.0
14 TraesCS3D01G242200 chr6B 83.152 184 25 5 3078 3258 84057399 84057579 5.720000e-36 163.0
15 TraesCS3D01G242200 chr6B 97.143 35 0 1 7094 7128 671882969 671883002 2.780000e-04 58.4
16 TraesCS3D01G242200 chr1D 83.152 184 25 5 3078 3258 249720088 249720268 5.720000e-36 163.0
17 TraesCS3D01G242200 chr1B 82.514 183 29 3 3078 3258 165675759 165675940 2.660000e-34 158.0
18 TraesCS3D01G242200 chr1B 82.873 181 25 5 3081 3258 268403574 268403397 2.660000e-34 158.0
19 TraesCS3D01G242200 chr1B 94.186 86 5 0 6888 6973 424083773 424083858 1.610000e-26 132.0
20 TraesCS3D01G242200 chr4A 95.556 90 2 2 6885 6973 485464425 485464337 7.460000e-30 143.0
21 TraesCS3D01G242200 chr4A 93.651 63 2 1 4255 4315 541361216 541361154 7.620000e-15 93.5
22 TraesCS3D01G242200 chr5A 93.333 90 5 1 6885 6973 165328898 165328987 1.610000e-26 132.0
23 TraesCS3D01G242200 chr5A 93.182 88 5 1 6887 6973 130540656 130540569 2.090000e-25 128.0
24 TraesCS3D01G242200 chr5A 91.045 67 3 2 4255 4319 342045650 342045715 3.540000e-13 87.9
25 TraesCS3D01G242200 chr2D 92.222 90 6 1 6885 6973 602511362 602511451 7.510000e-25 126.0
26 TraesCS3D01G242200 chr7B 98.361 61 1 0 4255 4315 388175900 388175840 2.720000e-19 108.0
27 TraesCS3D01G242200 chr7D 92.188 64 2 2 4253 4315 101475398 101475459 3.540000e-13 87.9
28 TraesCS3D01G242200 chr2B 89.855 69 5 2 4252 4320 17564083 17564149 3.540000e-13 87.9
29 TraesCS3D01G242200 chr5B 90.625 64 6 0 7068 7131 410546804 410546867 1.270000e-12 86.1
30 TraesCS3D01G242200 chr1A 87.671 73 5 3 4256 4326 109577206 109577136 1.650000e-11 82.4


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 TraesCS3D01G242200 chr3D 337303212 337310342 7130 False 13169.0 13169 100.000000 1 7131 1 chr3D.!!$F1 7130
1 TraesCS3D01G242200 chr3B 434980023 434987438 7415 False 5578.5 8100 94.229000 1 7129 2 chr3B.!!$F1 7128
2 TraesCS3D01G242200 chr3A 454510037 454517001 6964 False 3663.0 4785 95.306667 1 7131 3 chr3A.!!$F3 7130

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
692 744 0.179029 GAGACGAGGAGGAGGAGGAG 60.179 65.000 0.00 0.00 0.00 3.69 F
1050 1113 1.079750 GAGGAAGGTGAGACCGTGC 60.080 63.158 0.00 0.00 44.90 5.34 F
2019 2104 0.734942 GTAGCTACCGTCTTTGCGCA 60.735 55.000 13.20 5.66 0.00 6.09 F
2132 2218 2.028476 TGGTCTGTTCGGTATGAAGTGG 60.028 50.000 0.00 0.00 37.23 4.00 F
3984 4318 1.811860 CAATTGCTGGGCAGGCTAC 59.188 57.895 0.00 0.00 40.61 3.58 F
4524 4895 0.249073 CTGATCTCTTGGGTACGCCG 60.249 60.000 7.55 0.00 34.97 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2019 2104 1.135083 CGTAAGCTTCTGGATCACGGT 60.135 52.381 0.00 0.00 0.00 4.83 R
2918 3245 3.512033 AGGACGACAATAGAGAACTGC 57.488 47.619 0.00 0.00 0.00 4.40 R
3944 4278 3.489738 GCATGAGGCATGTTTATGTGGAC 60.490 47.826 8.95 0.00 43.10 4.02 R
4128 4465 6.928520 ACCTTGAATTTGGTCTCATTTCATC 58.071 36.000 0.00 0.00 30.63 2.92 R
5005 5377 7.732140 AGTTGAGGATGATACTCCAATATCTCA 59.268 37.037 1.48 0.00 37.81 3.27 R
6698 7075 0.250124 TACCACGGTTGAGCCAACAG 60.250 55.000 16.55 15.05 45.11 3.16 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
161 162 3.813166 ACCAACCGATAAGATAATTGCGG 59.187 43.478 0.00 0.00 43.95 5.69
181 182 4.440250 GCGGTATCTTATCATATCACGGCT 60.440 45.833 0.00 0.00 0.00 5.52
186 188 1.545841 TATCATATCACGGCTCGGCT 58.454 50.000 0.00 0.00 0.00 5.52
216 218 2.809601 CTTCCCACGCGAACCGAG 60.810 66.667 15.93 0.58 41.02 4.63
398 433 9.116067 AGCTGAACAAAAGTGTGTTATTAGTAA 57.884 29.630 0.00 0.00 41.78 2.24
399 434 9.724839 GCTGAACAAAAGTGTGTTATTAGTAAA 57.275 29.630 0.00 0.00 41.78 2.01
435 470 4.612412 TTTTGCCGGTCGCCGTCT 62.612 61.111 15.38 0.00 46.80 4.18
583 619 3.443976 GCGGCTGTCAAAAGAAAGAAAA 58.556 40.909 0.00 0.00 0.00 2.29
671 723 0.602106 ACCAGACGAACGAGACGAGA 60.602 55.000 0.14 0.00 34.70 4.04
672 724 0.179220 CCAGACGAACGAGACGAGAC 60.179 60.000 0.14 0.00 34.70 3.36
673 725 0.516727 CAGACGAACGAGACGAGACG 60.517 60.000 0.14 0.00 34.70 4.18
674 726 0.665670 AGACGAACGAGACGAGACGA 60.666 55.000 0.14 0.00 34.70 4.20
675 727 0.246834 GACGAACGAGACGAGACGAG 60.247 60.000 0.14 0.00 34.70 4.18
676 728 0.665670 ACGAACGAGACGAGACGAGA 60.666 55.000 0.14 0.00 34.70 4.04
677 729 0.246834 CGAACGAGACGAGACGAGAC 60.247 60.000 0.00 0.00 0.00 3.36
678 730 0.246834 GAACGAGACGAGACGAGACG 60.247 60.000 0.00 0.00 0.00 4.18
679 731 0.665670 AACGAGACGAGACGAGACGA 60.666 55.000 0.00 0.00 0.00 4.20
680 732 1.072116 ACGAGACGAGACGAGACGAG 61.072 60.000 0.00 0.00 0.00 4.18
681 733 1.744811 CGAGACGAGACGAGACGAGG 61.745 65.000 0.00 0.00 0.00 4.63
682 734 0.458197 GAGACGAGACGAGACGAGGA 60.458 60.000 0.00 0.00 0.00 3.71
683 735 0.458889 AGACGAGACGAGACGAGGAG 60.459 60.000 0.00 0.00 0.00 3.69
684 736 1.422950 GACGAGACGAGACGAGGAGG 61.423 65.000 0.00 0.00 0.00 4.30
685 737 1.153608 CGAGACGAGACGAGGAGGA 60.154 63.158 0.00 0.00 0.00 3.71
686 738 1.149361 CGAGACGAGACGAGGAGGAG 61.149 65.000 0.00 0.00 0.00 3.69
687 739 0.812412 GAGACGAGACGAGGAGGAGG 60.812 65.000 0.00 0.00 0.00 4.30
688 740 1.221293 GACGAGACGAGGAGGAGGA 59.779 63.158 0.00 0.00 0.00 3.71
689 741 0.812412 GACGAGACGAGGAGGAGGAG 60.812 65.000 0.00 0.00 0.00 3.69
690 742 1.525077 CGAGACGAGGAGGAGGAGG 60.525 68.421 0.00 0.00 0.00 4.30
691 743 1.916738 GAGACGAGGAGGAGGAGGA 59.083 63.158 0.00 0.00 0.00 3.71
692 744 0.179029 GAGACGAGGAGGAGGAGGAG 60.179 65.000 0.00 0.00 0.00 3.69
693 745 1.152839 GACGAGGAGGAGGAGGAGG 60.153 68.421 0.00 0.00 0.00 4.30
694 746 2.520741 CGAGGAGGAGGAGGAGGC 60.521 72.222 0.00 0.00 0.00 4.70
895 952 3.961197 CATCGTCGATCCGCCCGA 61.961 66.667 4.34 0.00 35.41 5.14
1050 1113 1.079750 GAGGAAGGTGAGACCGTGC 60.080 63.158 0.00 0.00 44.90 5.34
1051 1114 2.432628 GGAAGGTGAGACCGTGCG 60.433 66.667 0.00 0.00 44.90 5.34
1052 1115 3.112709 GAAGGTGAGACCGTGCGC 61.113 66.667 0.00 0.00 44.90 6.09
1053 1116 4.681978 AAGGTGAGACCGTGCGCC 62.682 66.667 4.18 0.00 44.90 6.53
1281 1344 5.591472 TCAGAATTATCTCTTGCCATTGGTG 59.409 40.000 4.26 0.00 32.03 4.17
1326 1389 2.000447 GTCGACAATTCCTTCCTTCCG 59.000 52.381 11.55 0.00 0.00 4.30
1328 1391 2.827322 TCGACAATTCCTTCCTTCCGTA 59.173 45.455 0.00 0.00 0.00 4.02
1329 1392 3.449737 TCGACAATTCCTTCCTTCCGTAT 59.550 43.478 0.00 0.00 0.00 3.06
1330 1393 4.646040 TCGACAATTCCTTCCTTCCGTATA 59.354 41.667 0.00 0.00 0.00 1.47
1357 1423 2.030805 AGGTTGTTGATTTCAGCTTCGC 60.031 45.455 0.00 0.00 0.00 4.70
1364 1430 1.396301 GATTTCAGCTTCGCAGTCCAG 59.604 52.381 0.00 0.00 0.00 3.86
1420 1486 2.573915 AGGGATCCTTTTCACTCCTGTC 59.426 50.000 12.58 0.00 0.00 3.51
1437 1503 3.937706 CCTGTCTCTGGATCACAATTCAC 59.062 47.826 0.00 0.00 0.00 3.18
1515 1581 1.580845 CTTCTTCTGCGGTTGGGCTG 61.581 60.000 0.00 0.00 0.00 4.85
1529 1601 1.654220 GGCTGCGTCTTTTCTTGCA 59.346 52.632 0.00 0.00 35.75 4.08
1552 1624 6.015940 GCATTGTCCCTCTATAAAGGAAATGG 60.016 42.308 12.96 0.00 38.87 3.16
1592 1664 5.282055 TCCATTCCATGCTAGTAGTTGAG 57.718 43.478 0.00 0.00 0.00 3.02
1598 1670 4.575236 TCCATGCTAGTAGTTGAGTACTCG 59.425 45.833 17.85 2.35 38.33 4.18
1616 1688 4.813027 ACTCGTTGCTTCGTAAAGGATTA 58.187 39.130 1.73 0.00 32.39 1.75
1643 1715 4.043435 AGGCCTTTTCAACTCCTGTAATCT 59.957 41.667 0.00 0.00 0.00 2.40
1757 1831 8.877864 ATATGTTTATCTCAACTCAACCCAAA 57.122 30.769 0.00 0.00 0.00 3.28
1778 1852 2.872732 TCTGTGGTCTTCTTACCGTCT 58.127 47.619 0.00 0.00 42.91 4.18
1849 1926 8.210946 TGGATTAGGTTAGGTTGTCATATTCTG 58.789 37.037 0.00 0.00 0.00 3.02
1861 1938 2.575735 TCATATTCTGTGCCCACTTGGA 59.424 45.455 0.00 0.00 37.39 3.53
1962 2041 3.063997 CGATAAGCGCTGTTTTCCTCATT 59.936 43.478 12.58 0.00 0.00 2.57
2019 2104 0.734942 GTAGCTACCGTCTTTGCGCA 60.735 55.000 13.20 5.66 0.00 6.09
2132 2218 2.028476 TGGTCTGTTCGGTATGAAGTGG 60.028 50.000 0.00 0.00 37.23 4.00
2210 2536 5.128171 ACCTGGGTTTAACTTCTTTTTGTCC 59.872 40.000 0.00 0.00 0.00 4.02
2212 2538 6.127168 CCTGGGTTTAACTTCTTTTTGTCCTT 60.127 38.462 0.00 0.00 0.00 3.36
2229 2555 8.925161 TTTGTCCTTTAAGTTGTTTCATTGAG 57.075 30.769 0.00 0.00 0.00 3.02
2282 2609 2.959030 GGGTTTATCCAAAGGATGAGCC 59.041 50.000 13.12 13.12 44.33 4.70
2397 2724 2.446435 TGGGCCTTCTTTTCTGTATGC 58.554 47.619 4.53 0.00 0.00 3.14
2806 3133 2.173519 CACCAAGTCATCAAGGCCAAT 58.826 47.619 5.01 0.00 0.00 3.16
2824 3151 5.047377 GGCCAATGATGACTTAACCAAAGAA 60.047 40.000 0.00 0.00 38.67 2.52
2830 3157 6.068010 TGATGACTTAACCAAAGAACACCAT 58.932 36.000 0.00 0.00 38.67 3.55
2936 3263 5.583495 AGTATGCAGTTCTCTATTGTCGTC 58.417 41.667 0.00 0.00 0.00 4.20
3098 3425 4.556233 CCAAAGTTAAAAAGGCACTAGGC 58.444 43.478 0.00 0.00 38.49 3.93
3420 3754 5.508922 CACTTTGTTTCATGCTTTTTGTTGC 59.491 36.000 0.00 0.00 0.00 4.17
3561 3895 6.312399 TGTTCATTTACCATTGTCTGTGAC 57.688 37.500 0.00 0.00 0.00 3.67
3944 4278 3.377346 AGGATATCTTGTGCGCTACTG 57.623 47.619 9.73 3.47 0.00 2.74
3984 4318 1.811860 CAATTGCTGGGCAGGCTAC 59.188 57.895 0.00 0.00 40.61 3.58
4158 4495 8.599624 AATGAGACCAAATTCAAGGTTCATAT 57.400 30.769 14.82 8.58 38.50 1.78
4306 4676 7.687941 AAAACGCTCTTATATTATGGGATGG 57.312 36.000 0.00 0.00 0.00 3.51
4355 4726 5.568620 TCTTTCACTCCTTAAAAGGCTCT 57.431 39.130 3.73 0.00 46.06 4.09
4390 4761 6.480763 TCAGGATGCTAAATTGGTTGTTCTA 58.519 36.000 0.00 0.00 34.76 2.10
4524 4895 0.249073 CTGATCTCTTGGGTACGCCG 60.249 60.000 7.55 0.00 34.97 6.46
4623 4994 4.079787 AGCATCCTAATCCCTTTGCAACTA 60.080 41.667 0.00 0.00 32.66 2.24
4833 5204 9.366216 AGATTCAAAAACAGGTGTTAAAAACTC 57.634 29.630 0.00 0.00 37.25 3.01
4837 5208 8.145122 TCAAAAACAGGTGTTAAAAACTCTGTT 58.855 29.630 17.69 17.69 47.00 3.16
5086 5458 7.672122 AACGAACTTCCTATATCCTAGGTTT 57.328 36.000 9.08 0.14 36.16 3.27
5263 5638 1.071542 TCGGACAGGAAGCATGTTTCA 59.928 47.619 21.79 0.00 0.00 2.69
6575 6952 4.385358 TTTTCTGGGTTTGAAGCACTTC 57.615 40.909 3.37 3.37 39.91 3.01
6613 6990 5.647589 TGTAGGAGTTCAGCGTTGTAATAG 58.352 41.667 0.00 0.00 0.00 1.73
6616 6993 5.169295 AGGAGTTCAGCGTTGTAATAGTTC 58.831 41.667 0.00 0.00 0.00 3.01
6698 7075 0.888619 GAACTGCTAGTTTTGGGGGC 59.111 55.000 3.56 0.00 38.80 5.80
6738 7115 6.887545 TGGTACTTATTAAACCAGGGTTGATG 59.112 38.462 4.70 0.00 38.36 3.07
7042 7446 7.359014 GGAGTAGAACTTGTATTTGTGAACGAC 60.359 40.741 0.00 0.00 0.00 4.34
7089 7493 0.834612 TACTAGAATGGTTGGGCGGG 59.165 55.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.825308 CATGTGCTGTGGTGTTAATCAC 58.175 45.455 0.00 0.00 45.47 3.06
43 44 3.118702 TGACGCCAAATAACCTAATCGGA 60.119 43.478 0.00 0.00 36.31 4.55
161 162 5.274718 CCGAGCCGTGATATGATAAGATAC 58.725 45.833 0.00 0.00 0.00 2.24
171 172 1.662608 CTGAGCCGAGCCGTGATAT 59.337 57.895 0.00 0.00 0.00 1.63
186 188 1.959226 GGGAAGTTTCGTGCGCTGA 60.959 57.895 9.73 3.44 0.00 4.26
216 218 1.201888 GCAGTAAAAACGAGTAGCGGC 60.202 52.381 0.00 0.00 46.49 6.53
221 223 5.464168 GGAGTACAGCAGTAAAAACGAGTA 58.536 41.667 0.00 0.00 30.67 2.59
222 224 4.304939 GGAGTACAGCAGTAAAAACGAGT 58.695 43.478 0.00 0.00 30.67 4.18
226 232 4.319261 CCAACGGAGTACAGCAGTAAAAAC 60.319 45.833 0.00 0.00 45.00 2.43
411 446 2.613506 CGACCGGCAAAACCACCTC 61.614 63.158 0.00 0.00 39.03 3.85
519 555 6.597280 TGTGATTGACGATGTGGATGATTTTA 59.403 34.615 0.00 0.00 0.00 1.52
583 619 4.798387 CGTTAAAAAGAAGTGCTTGCTTGT 59.202 37.500 0.00 0.00 36.80 3.16
671 723 1.222387 CTCCTCCTCCTCGTCTCGT 59.778 63.158 0.00 0.00 0.00 4.18
672 724 1.525077 CCTCCTCCTCCTCGTCTCG 60.525 68.421 0.00 0.00 0.00 4.04
673 725 0.179029 CTCCTCCTCCTCCTCGTCTC 60.179 65.000 0.00 0.00 0.00 3.36
674 726 1.641552 CCTCCTCCTCCTCCTCGTCT 61.642 65.000 0.00 0.00 0.00 4.18
675 727 1.152839 CCTCCTCCTCCTCCTCGTC 60.153 68.421 0.00 0.00 0.00 4.20
676 728 3.011885 CCTCCTCCTCCTCCTCGT 58.988 66.667 0.00 0.00 0.00 4.18
677 729 2.520741 GCCTCCTCCTCCTCCTCG 60.521 72.222 0.00 0.00 0.00 4.63
678 730 1.760480 GTGCCTCCTCCTCCTCCTC 60.760 68.421 0.00 0.00 0.00 3.71
679 731 2.366570 GTGCCTCCTCCTCCTCCT 59.633 66.667 0.00 0.00 0.00 3.69
680 732 3.151022 CGTGCCTCCTCCTCCTCC 61.151 72.222 0.00 0.00 0.00 4.30
681 733 3.151022 CCGTGCCTCCTCCTCCTC 61.151 72.222 0.00 0.00 0.00 3.71
682 734 3.670629 CTCCGTGCCTCCTCCTCCT 62.671 68.421 0.00 0.00 0.00 3.69
683 735 3.151022 CTCCGTGCCTCCTCCTCC 61.151 72.222 0.00 0.00 0.00 4.30
684 736 3.844090 GCTCCGTGCCTCCTCCTC 61.844 72.222 0.00 0.00 35.15 3.71
685 737 4.390556 AGCTCCGTGCCTCCTCCT 62.391 66.667 0.00 0.00 44.23 3.69
686 738 3.844090 GAGCTCCGTGCCTCCTCC 61.844 72.222 0.87 0.00 44.23 4.30
687 739 3.844090 GGAGCTCCGTGCCTCCTC 61.844 72.222 19.06 0.00 44.23 3.71
688 740 3.914551 AAGGAGCTCCGTGCCTCCT 62.915 63.158 26.95 3.86 44.98 3.69
689 741 3.394836 AAGGAGCTCCGTGCCTCC 61.395 66.667 26.95 1.13 44.23 4.30
690 742 2.125350 CAAGGAGCTCCGTGCCTC 60.125 66.667 31.50 5.78 44.23 4.70
916 973 2.421388 CGAGGGAGAGATCTCTGTCTGT 60.421 54.545 29.81 9.42 42.48 3.41
1023 1086 4.400961 ACCTTCCTCCGCTGCTGC 62.401 66.667 5.34 5.34 0.00 5.25
1053 1116 4.954970 ACAGCAACCCCTGGCGTG 62.955 66.667 0.00 0.00 37.16 5.34
1054 1117 3.731766 AAACAGCAACCCCTGGCGT 62.732 57.895 0.00 0.00 37.16 5.68
1200 1263 1.997311 CAGTGCCCCCTCCTCATCA 60.997 63.158 0.00 0.00 0.00 3.07
1281 1344 2.301583 AGGAGAAGAGAAGTTGCAGGAC 59.698 50.000 0.00 0.00 0.00 3.85
1326 1389 7.750903 GCTGAAATCAACAACCTCAACTTATAC 59.249 37.037 0.00 0.00 0.00 1.47
1328 1391 6.491403 AGCTGAAATCAACAACCTCAACTTAT 59.509 34.615 0.00 0.00 0.00 1.73
1329 1392 5.827797 AGCTGAAATCAACAACCTCAACTTA 59.172 36.000 0.00 0.00 0.00 2.24
1330 1393 4.646492 AGCTGAAATCAACAACCTCAACTT 59.354 37.500 0.00 0.00 0.00 2.66
1372 1438 6.677781 TCGCGATAAGAAATGGAAGAAAAT 57.322 33.333 3.71 0.00 0.00 1.82
1420 1486 4.212143 TGAGGTGAATTGTGATCCAGAG 57.788 45.455 0.00 0.00 0.00 3.35
1437 1503 8.454106 CAGAGAACCTTGTGTTAATAATTGAGG 58.546 37.037 0.00 0.00 37.29 3.86
1515 1581 2.319472 GGACAATGCAAGAAAAGACGC 58.681 47.619 0.00 0.00 0.00 5.19
1529 1601 7.226059 ACCATTTCCTTTATAGAGGGACAAT 57.774 36.000 9.36 3.67 37.41 2.71
1592 1664 3.568538 TCCTTTACGAAGCAACGAGTAC 58.431 45.455 9.33 0.00 37.03 2.73
1598 1670 5.063564 CCTCAGTAATCCTTTACGAAGCAAC 59.936 44.000 0.00 0.00 42.14 4.17
1616 1688 1.777272 AGGAGTTGAAAAGGCCTCAGT 59.223 47.619 5.23 0.00 0.00 3.41
1757 1831 3.432378 AGACGGTAAGAAGACCACAGAT 58.568 45.455 0.00 0.00 39.72 2.90
1962 2041 1.719063 AAACTCCTTGGCCTCCAGCA 61.719 55.000 3.32 0.00 46.50 4.41
2019 2104 1.135083 CGTAAGCTTCTGGATCACGGT 60.135 52.381 0.00 0.00 0.00 4.83
2132 2218 8.587952 ACAACAGTCAAATTTTGTATAAAGGC 57.412 30.769 8.89 0.00 30.39 4.35
2180 2266 4.874199 AGAAGTTAAACCCAGGTTTTCCA 58.126 39.130 19.35 0.00 44.84 3.53
2210 2536 6.974965 AGGCTCTCAATGAAACAACTTAAAG 58.025 36.000 0.00 0.00 0.00 1.85
2212 2538 7.665559 ACATAGGCTCTCAATGAAACAACTTAA 59.334 33.333 2.12 0.00 0.00 1.85
2282 2609 4.386711 AGTAAAGGACCAGAAAAGGTTCG 58.613 43.478 0.00 0.00 42.36 3.95
2397 2724 3.851403 CCACAACTGAAACAAAAGACACG 59.149 43.478 0.00 0.00 0.00 4.49
2806 3133 5.441500 TGGTGTTCTTTGGTTAAGTCATCA 58.558 37.500 0.00 0.00 35.28 3.07
2824 3151 6.438741 TCTGATAGAGAAAGAACTGATGGTGT 59.561 38.462 0.00 0.00 0.00 4.16
2830 3157 6.788598 AGCATCTGATAGAGAAAGAACTGA 57.211 37.500 0.00 0.00 33.12 3.41
2915 3242 4.645136 AGGACGACAATAGAGAACTGCATA 59.355 41.667 0.00 0.00 0.00 3.14
2918 3245 3.512033 AGGACGACAATAGAGAACTGC 57.488 47.619 0.00 0.00 0.00 4.40
3143 3470 5.107989 CGTATAGTTGCGCTTAAGTGTATGG 60.108 44.000 17.00 1.84 0.00 2.74
3420 3754 9.537848 GGTAAATACAAAGAAGTGTACATTTCG 57.462 33.333 21.19 12.34 36.83 3.46
3561 3895 7.972277 GCTGCAATCATATAAATATTGGTCAGG 59.028 37.037 0.00 0.00 32.44 3.86
3944 4278 3.489738 GCATGAGGCATGTTTATGTGGAC 60.490 47.826 8.95 0.00 43.10 4.02
3984 4318 7.165812 GCAAGAATAATGTGGTATTAAACAGCG 59.834 37.037 0.00 0.00 0.00 5.18
4128 4465 6.928520 ACCTTGAATTTGGTCTCATTTCATC 58.071 36.000 0.00 0.00 30.63 2.92
4133 4470 6.923199 ATGAACCTTGAATTTGGTCTCATT 57.077 33.333 12.37 0.00 34.07 2.57
4170 4507 2.747989 CAAGACCAGCTGACTACGTAGA 59.252 50.000 28.74 6.70 0.00 2.59
4262 4607 0.178984 TGACACTACACTGGGACGGA 60.179 55.000 0.00 0.00 38.67 4.69
4263 4608 0.677288 TTGACACTACACTGGGACGG 59.323 55.000 0.00 0.00 42.99 4.79
4306 4676 9.310449 TCAGGTATTAATGATAACTACTCCCTC 57.690 37.037 0.00 0.00 36.08 4.30
4347 4717 4.461781 CCTGAATTCAACATCAGAGCCTTT 59.538 41.667 9.88 0.00 44.64 3.11
4355 4726 7.649533 ATTTAGCATCCTGAATTCAACATCA 57.350 32.000 9.88 0.00 0.00 3.07
4390 4761 4.818546 GTCAATAGCTGGTGAATACTGCAT 59.181 41.667 0.00 0.00 0.00 3.96
4623 4994 1.139853 GCCTTCTCATTCCGGATCTGT 59.860 52.381 4.15 0.00 0.00 3.41
4833 5204 9.277565 GTGCACATAAACATTGTTAGATAACAG 57.722 33.333 13.17 0.00 45.77 3.16
4837 5208 9.171877 TGATGTGCACATAAACATTGTTAGATA 57.828 29.630 31.45 0.00 37.15 1.98
5005 5377 7.732140 AGTTGAGGATGATACTCCAATATCTCA 59.268 37.037 1.48 0.00 37.81 3.27
5111 5486 7.774625 AGTTATGAAAATTGGCATTTAATGGGG 59.225 33.333 7.08 0.00 31.89 4.96
5112 5487 8.614346 CAGTTATGAAAATTGGCATTTAATGGG 58.386 33.333 7.08 0.00 31.89 4.00
6698 7075 0.250124 TACCACGGTTGAGCCAACAG 60.250 55.000 16.55 15.05 45.11 3.16
6929 7331 8.117988 TGTTTGTTCACTCATTTTAGTTCGTAC 58.882 33.333 0.00 0.00 0.00 3.67
7042 7446 3.369546 AAGTTTTCAAATGCACTCCCG 57.630 42.857 0.00 0.00 0.00 5.14
7101 7505 4.855715 TGAAAACTCAACAACACCAACA 57.144 36.364 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.