Multiple sequence alignment - TraesCS6A01G051000

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 TraesCS6A01G051000 chr6A 100.000 3307 0 0 1 3307 26622839 26619533 0.000000e+00 6107.0
1 TraesCS6A01G051000 chr6A 86.486 333 44 1 1170 1501 57931008 57930676 6.740000e-97 364.0
2 TraesCS6A01G051000 chr6A 84.962 133 20 0 2180 2312 57887265 57887133 5.760000e-28 135.0
3 TraesCS6A01G051000 chrUn 94.121 1684 79 11 839 2510 95233555 95231880 0.000000e+00 2543.0
4 TraesCS6A01G051000 chrUn 84.670 424 55 6 2891 3307 95229580 95229160 6.600000e-112 414.0
5 TraesCS6A01G051000 chrUn 83.747 443 54 11 1075 1500 18917839 18918280 1.430000e-108 403.0
6 TraesCS6A01G051000 chrUn 81.262 523 76 16 1028 1538 95229485 95228973 1.430000e-108 403.0
7 TraesCS6A01G051000 chrUn 93.724 239 11 1 2497 2735 95230349 95230115 4.060000e-94 355.0
8 TraesCS6A01G051000 chrUn 84.326 319 49 1 1178 1495 19066867 19067185 8.910000e-81 311.0
9 TraesCS6A01G051000 chrUn 95.062 81 3 1 2778 2857 95229922 95229842 3.460000e-25 126.0
10 TraesCS6A01G051000 chrUn 85.185 108 14 1 2229 2336 19084637 19084742 3.490000e-20 110.0
11 TraesCS6A01G051000 chrUn 98.387 62 1 0 2689 2750 95230121 95230060 3.490000e-20 110.0
12 TraesCS6A01G051000 chr6B 89.629 1562 117 14 1 1533 45618635 45617090 0.000000e+00 1945.0
13 TraesCS6A01G051000 chr6B 91.076 1199 84 6 1601 2795 45572611 45571432 0.000000e+00 1600.0
14 TraesCS6A01G051000 chr6B 90.121 1235 93 9 1518 2749 45617009 45615801 0.000000e+00 1578.0
15 TraesCS6A01G051000 chr6B 87.785 1359 94 33 6 1298 45600432 45599080 0.000000e+00 1524.0
16 TraesCS6A01G051000 chr6B 88.476 1076 81 9 1 1045 45671432 45670369 0.000000e+00 1260.0
17 TraesCS6A01G051000 chr6B 87.675 1071 82 13 1868 2895 45598501 45597438 0.000000e+00 1201.0
18 TraesCS6A01G051000 chr6B 93.994 616 35 1 1518 2133 45670343 45669730 0.000000e+00 931.0
19 TraesCS6A01G051000 chr6B 90.293 443 23 10 831 1271 45573489 45573065 2.230000e-156 562.0
20 TraesCS6A01G051000 chr6B 95.177 311 14 1 1527 1837 45598806 45598497 1.070000e-134 490.0
21 TraesCS6A01G051000 chr6B 86.957 322 42 0 1170 1491 93840091 93839770 2.430000e-96 363.0
22 TraesCS6A01G051000 chr6B 91.288 264 15 5 2533 2794 45669483 45669226 1.460000e-93 353.0
23 TraesCS6A01G051000 chr6B 82.469 405 63 7 1138 1537 45596960 45596559 6.790000e-92 348.0
24 TraesCS6A01G051000 chr6B 85.714 105 13 1 2238 2342 93837557 93837455 3.490000e-20 110.0
25 TraesCS6A01G051000 chr7A 79.539 347 65 5 62 403 398906390 398906735 3.300000e-60 243.0
26 TraesCS6A01G051000 chr7A 81.935 155 19 7 64 212 164195386 164195537 4.480000e-24 122.0
27 TraesCS6A01G051000 chr3A 78.019 323 57 10 61 380 728236875 728237186 1.210000e-44 191.0
28 TraesCS6A01G051000 chr3A 81.538 195 34 2 61 255 728098419 728098611 3.420000e-35 159.0
29 TraesCS6A01G051000 chr3A 88.710 62 5 2 2834 2895 482908733 482908674 1.270000e-09 75.0
30 TraesCS6A01G051000 chr3D 77.491 271 49 7 61 326 256986546 256986809 5.720000e-33 152.0
31 TraesCS6A01G051000 chr5D 81.757 148 23 3 67 212 448852249 448852394 1.610000e-23 121.0
32 TraesCS6A01G051000 chr6D 85.000 80 7 5 2827 2904 32658550 32658626 3.540000e-10 76.8
33 TraesCS6A01G051000 chr6D 85.915 71 7 3 2831 2901 361286656 361286723 4.580000e-09 73.1
34 TraesCS6A01G051000 chr2B 87.143 70 6 3 2831 2900 577426524 577426590 3.540000e-10 76.8
35 TraesCS6A01G051000 chr5B 88.710 62 4 1 2831 2892 415125545 415125603 4.580000e-09 73.1
36 TraesCS6A01G051000 chr4D 83.784 74 9 3 2831 2904 83549304 83549234 2.130000e-07 67.6
37 TraesCS6A01G051000 chr4D 83.784 74 9 3 2831 2904 291245586 291245516 2.130000e-07 67.6
38 TraesCS6A01G051000 chr4D 83.784 74 9 3 2831 2904 407485469 407485399 2.130000e-07 67.6


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 TraesCS6A01G051000 chr6A 26619533 26622839 3306 True 6107.00 6107 100.000000 1 3307 1 chr6A.!!$R1 3306
1 TraesCS6A01G051000 chrUn 95228973 95233555 4582 True 658.50 2543 91.204333 839 3307 6 chrUn.!!$R1 2468
2 TraesCS6A01G051000 chr6B 45615801 45618635 2834 True 1761.50 1945 89.875000 1 2749 2 chr6B.!!$R3 2748
3 TraesCS6A01G051000 chr6B 45571432 45573489 2057 True 1081.00 1600 90.684500 831 2795 2 chr6B.!!$R1 1964
4 TraesCS6A01G051000 chr6B 45596559 45600432 3873 True 890.75 1524 88.276500 6 2895 4 chr6B.!!$R2 2889
5 TraesCS6A01G051000 chr6B 45669226 45671432 2206 True 848.00 1260 91.252667 1 2794 3 chr6B.!!$R4 2793
6 TraesCS6A01G051000 chr6B 93837455 93840091 2636 True 236.50 363 86.335500 1170 2342 2 chr6B.!!$R5 1172

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
758 768 0.106268 TGCATGCCAATTATCCGGGT 60.106 50.0 16.68 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2345 4174 0.944386 GTTTGCACGCCTTTGAGAGA 59.056 50.0 0.0 0.0 0.0 3.1 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
28 29 3.173965 TCTTGTCCCTGCTAGCTAGTTT 58.826 45.455 21.62 0.00 0.00 2.66
32 33 2.420372 GTCCCTGCTAGCTAGTTTTTGC 59.580 50.000 21.62 7.97 0.00 3.68
33 34 2.039746 TCCCTGCTAGCTAGTTTTTGCA 59.960 45.455 21.62 12.15 0.00 4.08
56 58 6.202570 GCATTAAACAAAAGATGAGGTTGCAA 59.797 34.615 0.00 0.00 0.00 4.08
59 61 9.995003 ATTAAACAAAAGATGAGGTTGCAATAA 57.005 25.926 0.59 0.00 0.00 1.40
61 63 8.907222 AAACAAAAGATGAGGTTGCAATAATT 57.093 26.923 0.59 0.00 0.00 1.40
98 108 1.056700 ATAACCCTCGGCCTCTGCAT 61.057 55.000 0.00 0.00 40.13 3.96
218 228 2.413239 CGCTACACCAACAAGCTTGATG 60.413 50.000 32.50 28.58 34.03 3.07
312 322 1.740025 GCATGAACAGGTCTAGCCAAC 59.260 52.381 0.00 0.00 40.61 3.77
331 341 1.233950 CCCACAACACGCACTGCATA 61.234 55.000 1.11 0.00 0.00 3.14
352 362 2.028190 ATGCTCTTCGATCCGCCG 59.972 61.111 0.00 0.00 0.00 6.46
378 388 0.108329 TCTTTCGCCGTCCCATCTTC 60.108 55.000 0.00 0.00 0.00 2.87
406 416 4.096984 GGATCATCACATTGACCTTGGTTC 59.903 45.833 0.00 0.00 0.00 3.62
410 420 1.270550 CACATTGACCTTGGTTCTGCC 59.729 52.381 0.00 0.00 37.90 4.85
433 443 6.627243 CCATTAATTGTGCATGATATCCCAG 58.373 40.000 0.00 0.00 0.00 4.45
455 465 6.204688 CCAGCATATTCTATTGAAACGCCTAA 59.795 38.462 0.00 0.00 35.63 2.69
467 477 5.972935 TGAAACGCCTAATGAGTCAGATTA 58.027 37.500 0.00 0.00 0.00 1.75
471 481 4.890581 ACGCCTAATGAGTCAGATTAGAGT 59.109 41.667 13.01 10.16 36.03 3.24
502 512 3.496131 GGCCCGTGTACATGTGCG 61.496 66.667 15.08 10.19 0.00 5.34
514 524 6.542852 GTGTACATGTGCGAGAAATTTACAT 58.457 36.000 9.11 0.00 32.60 2.29
558 568 4.236147 TGTGGACGAACGAATAAAATCGA 58.764 39.130 3.47 0.00 45.48 3.59
564 574 6.397831 ACGAACGAATAAAATCGAACATGA 57.602 33.333 0.00 0.00 45.48 3.07
584 594 4.148838 TGACGAAATTGGGATTTTGGACT 58.851 39.130 0.00 0.00 39.82 3.85
606 616 8.726988 GGACTTGCTACTATGTGTTTTAATCAA 58.273 33.333 0.00 0.00 0.00 2.57
619 629 8.246871 TGTGTTTTAATCAAGTTTGTGATGACA 58.753 29.630 0.00 0.00 38.28 3.58
634 644 7.477144 TGTGATGACATATATTTGTTCCGAC 57.523 36.000 0.11 0.00 0.00 4.79
657 667 7.358770 ACCATAGGCTAGCAATCTATATCAG 57.641 40.000 18.24 6.72 0.00 2.90
684 694 3.319122 GTGCATCCCAGATTACAAATCCC 59.681 47.826 0.00 0.00 0.00 3.85
705 715 2.724839 CGTTTCTTCTGCATGGCGTAAC 60.725 50.000 0.00 0.00 0.00 2.50
707 717 1.725641 TCTTCTGCATGGCGTAACAG 58.274 50.000 0.00 3.18 0.00 3.16
710 720 2.004583 TCTGCATGGCGTAACAGTAC 57.995 50.000 8.32 0.00 0.00 2.73
740 750 4.396166 GTGTTTGTGATGGTAATCCTCCTG 59.604 45.833 0.00 0.00 34.23 3.86
747 757 0.183492 GGTAATCCTCCTGCATGCCA 59.817 55.000 16.68 2.21 0.00 4.92
758 768 0.106268 TGCATGCCAATTATCCGGGT 60.106 50.000 16.68 0.00 0.00 5.28
759 769 0.598065 GCATGCCAATTATCCGGGTC 59.402 55.000 6.36 0.00 0.00 4.46
788 798 3.193263 GCATCGATCAGGCATAGTATGG 58.807 50.000 12.07 0.00 0.00 2.74
798 809 3.073062 AGGCATAGTATGGTTGATGTCCC 59.927 47.826 12.07 1.51 0.00 4.46
808 819 2.420022 GGTTGATGTCCCTGTTCATTCG 59.580 50.000 0.00 0.00 0.00 3.34
809 820 2.401583 TGATGTCCCTGTTCATTCGG 57.598 50.000 0.00 0.00 0.00 4.30
846 881 2.702592 TATGAAGGTCGCCCGAAAAT 57.297 45.000 0.00 0.00 35.12 1.82
860 895 0.657840 GAAAATGTGGATCGGGAGCG 59.342 55.000 0.00 0.00 0.00 5.03
863 898 1.910580 AATGTGGATCGGGAGCGGTT 61.911 55.000 0.00 0.00 0.00 4.44
865 900 2.682136 TGGATCGGGAGCGGTTCA 60.682 61.111 0.00 0.00 0.00 3.18
1026 1069 1.202533 CCACCGATATCGAAGCCAGTT 60.203 52.381 26.32 0.00 43.02 3.16
1222 1299 2.040939 CTGACCTGATCTCCTGCATCT 58.959 52.381 0.00 0.00 0.00 2.90
1353 1430 4.382320 GGCGGCCTGTGGTTCGTA 62.382 66.667 12.87 0.00 0.00 3.43
1499 1576 5.124617 CCAAGCAGTAAGATTTCTTCCTTCC 59.875 44.000 0.00 0.00 37.40 3.46
1731 2126 0.940126 CTCCGATGAAGGATTTGCGG 59.060 55.000 0.00 0.00 39.96 5.69
1965 2360 1.405661 CCTTCGGTAGGGAAGTTCTGC 60.406 57.143 2.25 0.00 41.44 4.26
1968 2363 3.028094 TCGGTAGGGAAGTTCTGCTAT 57.972 47.619 2.25 0.00 0.00 2.97
2070 3860 0.913924 TCTTGCCTGGATGAGCATGA 59.086 50.000 0.00 0.00 39.87 3.07
2089 3879 6.319658 AGCATGAATGACCTTTATTGGTACTG 59.680 38.462 0.00 0.00 41.00 2.74
2103 3893 5.748670 TTGGTACTGGAGCAACTATTACA 57.251 39.130 0.00 0.00 40.60 2.41
2125 3924 9.647797 TTACAATGACTATACTGGTTGTAACTG 57.352 33.333 0.00 0.00 37.21 3.16
2147 3946 1.635817 GCCATCCCTACAAGCCCAGA 61.636 60.000 0.00 0.00 0.00 3.86
2184 3986 4.357918 ACCTGGTCATATCTGCATTACC 57.642 45.455 0.00 0.00 0.00 2.85
2247 4061 2.953648 GGTGATGATGTTGATGATGCCA 59.046 45.455 0.00 0.00 0.00 4.92
2258 4072 4.141233 TGATGATGCCAATCTCGAAGAA 57.859 40.909 0.00 0.00 34.09 2.52
2267 4081 6.528321 TGCCAATCTCGAAGAATATGAGAAT 58.472 36.000 0.00 0.00 41.68 2.40
2319 4148 7.708322 GGTACTTAAGCTAATGTAAGGGTGTAC 59.292 40.741 1.29 0.00 32.60 2.90
2345 4174 5.999205 TGTCAATAATGTTTCAATGCCCT 57.001 34.783 0.00 0.00 0.00 5.19
2354 4183 3.822735 TGTTTCAATGCCCTCTCTCAAAG 59.177 43.478 0.00 0.00 0.00 2.77
2356 4185 1.101331 CAATGCCCTCTCTCAAAGGC 58.899 55.000 0.00 0.00 45.96 4.35
2381 4210 6.074302 CGTGCAAACTCGCTCAATAATATACT 60.074 38.462 0.00 0.00 0.00 2.12
2424 4255 6.811170 TCTTTTGTTTCATTTCGCTCAAAACT 59.189 30.769 0.00 0.00 33.39 2.66
2440 4271 6.414987 GCTCAAAACTAGTTTAAGTGCTTGTG 59.585 38.462 25.11 18.11 30.58 3.33
2442 4273 7.693952 TCAAAACTAGTTTAAGTGCTTGTGAG 58.306 34.615 20.83 0.00 30.58 3.51
2580 5955 6.506500 ACTCAGCTTTACATCAAATTCTGG 57.493 37.500 0.00 0.00 32.12 3.86
2620 5995 0.596082 GGCTCGTTTGGCTTGCTTAA 59.404 50.000 0.00 0.00 0.00 1.85
2621 5996 1.202348 GGCTCGTTTGGCTTGCTTAAT 59.798 47.619 0.00 0.00 0.00 1.40
2622 5997 2.352715 GGCTCGTTTGGCTTGCTTAATT 60.353 45.455 0.00 0.00 0.00 1.40
2623 5998 3.119637 GGCTCGTTTGGCTTGCTTAATTA 60.120 43.478 0.00 0.00 0.00 1.40
2667 6043 4.510038 ACTGATGCACCACAAAATTCTC 57.490 40.909 0.00 0.00 0.00 2.87
2712 6088 0.329931 ATGACCCGTAAATGGTGCCA 59.670 50.000 0.00 0.00 35.85 4.92
2816 6343 2.431683 GTGGACAGCTGCCTTGGA 59.568 61.111 22.36 5.18 0.00 3.53
2861 6389 8.163408 AGCATGGTTAATAGTATAGCCAATTGA 58.837 33.333 7.12 0.00 39.25 2.57
2862 6390 8.960591 GCATGGTTAATAGTATAGCCAATTGAT 58.039 33.333 7.12 0.00 39.25 2.57
2882 6429 9.986157 AATTGATGGCTATATATGATGTTTCCT 57.014 29.630 0.00 0.00 0.00 3.36
2902 6659 6.718593 TCCTTGTCATATATAGGCCCATTT 57.281 37.500 0.00 0.00 0.00 2.32
2970 6727 1.410004 CCATGATCAGGCCAGCAAAT 58.590 50.000 5.01 0.00 0.00 2.32
2996 6753 1.227764 CATACTGCCAGCTCGCCAT 60.228 57.895 0.00 0.00 0.00 4.40
3000 6757 3.963687 CTGCCAGCTCGCCATGTCA 62.964 63.158 0.00 0.00 0.00 3.58
3016 6773 2.934801 ATGTCATTCACATCGCAACCGA 60.935 45.455 0.00 0.00 42.62 4.69
3017 6774 4.419260 ATGTCATTCACATCGCAACCGAA 61.419 43.478 0.00 0.00 42.62 4.30
3024 6781 2.357638 TCGCAACCGAAATGCCGA 60.358 55.556 2.23 0.00 41.17 5.54
3026 6783 2.950673 GCAACCGAAATGCCGACA 59.049 55.556 0.00 0.00 37.85 4.35
3032 6789 1.298602 CCGAAATGCCGACATCATCA 58.701 50.000 0.00 0.00 34.62 3.07
3034 6791 1.935873 CGAAATGCCGACATCATCACT 59.064 47.619 0.00 0.00 34.62 3.41
3035 6792 2.286008 CGAAATGCCGACATCATCACTG 60.286 50.000 0.00 0.00 34.62 3.66
3037 6794 0.179702 ATGCCGACATCATCACTGCT 59.820 50.000 0.00 0.00 0.00 4.24
3041 6798 0.176449 CGACATCATCACTGCTGGGA 59.824 55.000 0.00 0.00 0.00 4.37
3116 6964 1.069227 GTCGGTGTTCAAGTTCATGCC 60.069 52.381 0.00 0.00 0.00 4.40
3123 6971 0.107643 TCAAGTTCATGCCCGTGTCA 59.892 50.000 0.00 0.00 0.00 3.58
3143 6991 1.794885 TTGCCGGAAAGGGAATGGGA 61.795 55.000 5.05 0.00 45.90 4.37
3148 6996 1.299939 GGAAAGGGAATGGGAGGAGT 58.700 55.000 0.00 0.00 0.00 3.85
3156 7004 2.484287 AATGGGAGGAGTTGCACCCG 62.484 60.000 3.57 0.00 44.70 5.28
3163 7011 2.847234 AGTTGCACCCGGACCTGA 60.847 61.111 0.73 0.00 0.00 3.86
3165 7013 2.040544 GTTGCACCCGGACCTGATG 61.041 63.158 0.73 0.00 0.00 3.07
3186 7034 2.047844 CGTGTCCTCCACAGGCTG 60.048 66.667 14.16 14.16 44.78 4.85
3190 7038 1.915769 GTCCTCCACAGGCTGGACT 60.916 63.158 20.34 0.00 44.99 3.85
3291 7145 1.996786 GCCACATCAATCTGCACGGG 61.997 60.000 0.00 0.00 0.00 5.28
3294 7148 2.108514 CATCAATCTGCACGGGCGT 61.109 57.895 4.58 0.00 45.35 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 7.254727 GCAACCTCATCTTTTGTTTAATGCAAA 60.255 33.333 0.00 2.72 34.47 3.68
32 33 7.712264 TTGCAACCTCATCTTTTGTTTAATG 57.288 32.000 0.00 0.00 0.00 1.90
33 34 9.995003 TTATTGCAACCTCATCTTTTGTTTAAT 57.005 25.926 0.00 0.00 0.00 1.40
158 168 1.273327 GTGGCTTTGGGTTGATCCTTG 59.727 52.381 0.00 0.00 36.25 3.61
206 216 3.190744 CAGAGCACATCATCAAGCTTGTT 59.809 43.478 25.19 15.14 37.48 2.83
295 305 0.690762 GGGTTGGCTAGACCTGTTCA 59.309 55.000 0.00 0.00 40.22 3.18
312 322 1.233950 TATGCAGTGCGTGTTGTGGG 61.234 55.000 20.26 0.00 0.00 4.61
352 362 1.989163 GACGGCGAAAGATGACGTC 59.011 57.895 16.62 9.11 45.42 4.34
378 388 1.942657 GTCAATGTGATGATCCCCGTG 59.057 52.381 0.00 0.00 0.00 4.94
406 416 6.097356 GGATATCATGCACAATTAATGGCAG 58.903 40.000 4.83 7.50 38.20 4.85
410 420 6.097356 GCTGGGATATCATGCACAATTAATG 58.903 40.000 4.83 0.00 0.00 1.90
433 443 7.806690 TCATTAGGCGTTTCAATAGAATATGC 58.193 34.615 0.00 0.00 32.89 3.14
467 477 5.307196 ACGGGCCATAAATGTATCTTACTCT 59.693 40.000 4.39 0.00 0.00 3.24
471 481 5.298989 ACACGGGCCATAAATGTATCTTA 57.701 39.130 4.39 0.00 0.00 2.10
484 494 2.359354 GCACATGTACACGGGCCA 60.359 61.111 4.44 0.00 0.00 5.36
487 497 0.389296 TTCTCGCACATGTACACGGG 60.389 55.000 13.19 10.85 0.00 5.28
514 524 9.256477 CCACAAATAAGATGTAGCTACGATAAA 57.744 33.333 18.74 5.08 0.00 1.40
520 530 6.270815 TCGTCCACAAATAAGATGTAGCTAC 58.729 40.000 17.30 17.30 0.00 3.58
524 534 5.803461 TCGTTCGTCCACAAATAAGATGTAG 59.197 40.000 0.00 0.00 0.00 2.74
526 536 4.562082 TCGTTCGTCCACAAATAAGATGT 58.438 39.130 0.00 0.00 0.00 3.06
527 537 5.524511 TTCGTTCGTCCACAAATAAGATG 57.475 39.130 0.00 0.00 0.00 2.90
558 568 5.011533 TCCAAAATCCCAATTTCGTCATGTT 59.988 36.000 0.00 0.00 33.93 2.71
564 574 4.799255 GCAAGTCCAAAATCCCAATTTCGT 60.799 41.667 0.00 0.00 33.93 3.85
606 616 8.397906 CGGAACAAATATATGTCATCACAAACT 58.602 33.333 0.00 0.00 35.64 2.66
619 629 6.374417 AGCCTATGGTCGGAACAAATATAT 57.626 37.500 0.00 0.00 0.00 0.86
634 644 7.208777 CACTGATATAGATTGCTAGCCTATGG 58.791 42.308 13.29 7.01 0.00 2.74
657 667 0.463654 TAATCTGGGATGCACGCCAC 60.464 55.000 9.44 0.57 0.00 5.01
684 694 1.075542 TACGCCATGCAGAAGAAACG 58.924 50.000 0.00 0.00 0.00 3.60
705 715 5.635280 CCATCACAAACACACTAGAGTACTG 59.365 44.000 0.00 0.00 0.00 2.74
707 717 5.539048 ACCATCACAAACACACTAGAGTAC 58.461 41.667 0.00 0.00 0.00 2.73
710 720 6.313905 GGATTACCATCACAAACACACTAGAG 59.686 42.308 0.00 0.00 35.97 2.43
740 750 0.598065 GACCCGGATAATTGGCATGC 59.402 55.000 9.90 9.90 0.00 4.06
747 757 1.768870 CACCCAGAGACCCGGATAATT 59.231 52.381 0.73 0.00 0.00 1.40
758 768 0.749049 CTGATCGATGCACCCAGAGA 59.251 55.000 0.54 0.00 0.00 3.10
759 769 0.249784 CCTGATCGATGCACCCAGAG 60.250 60.000 0.54 0.00 0.00 3.35
788 798 2.420022 CCGAATGAACAGGGACATCAAC 59.580 50.000 0.00 0.00 0.00 3.18
798 809 2.030007 ACCAAACATGCCGAATGAACAG 60.030 45.455 5.22 0.00 38.72 3.16
808 819 6.031751 TCATAAAAGGTTACCAAACATGCC 57.968 37.500 3.51 0.00 37.34 4.40
809 820 6.589907 CCTTCATAAAAGGTTACCAAACATGC 59.410 38.462 3.51 0.00 37.34 4.06
846 881 3.000819 AACCGCTCCCGATCCACA 61.001 61.111 0.00 0.00 36.29 4.17
860 895 0.601841 TTTCCGGAGCGACTTGAACC 60.602 55.000 3.34 0.00 0.00 3.62
863 898 1.202604 ACTTTTTCCGGAGCGACTTGA 60.203 47.619 3.34 0.00 0.00 3.02
865 900 1.226746 CACTTTTTCCGGAGCGACTT 58.773 50.000 3.34 0.00 0.00 3.01
1026 1069 2.835701 GAACGATGTGGCGAGCTGGA 62.836 60.000 0.00 0.00 34.83 3.86
1146 1223 1.885388 CGGCGTGAACCAGAACACA 60.885 57.895 0.00 0.00 36.91 3.72
1176 1253 3.670629 CTCCGCCCAGTCCCTCTCT 62.671 68.421 0.00 0.00 0.00 3.10
1203 1280 2.171568 AGATGCAGGAGATCAGGTCA 57.828 50.000 0.00 0.00 0.00 4.02
1731 2126 4.694339 AGAGGTAACATCTTAATCACCGC 58.306 43.478 0.00 0.00 41.41 5.68
2070 3860 5.193679 GCTCCAGTACCAATAAAGGTCATT 58.806 41.667 0.00 0.00 42.06 2.57
2089 3879 9.197694 CAGTATAGTCATTGTAATAGTTGCTCC 57.802 37.037 0.00 0.00 0.00 4.70
2103 3893 6.818644 CAGCAGTTACAACCAGTATAGTCATT 59.181 38.462 0.00 0.00 31.53 2.57
2125 3924 1.825622 GGCTTGTAGGGATGGCAGC 60.826 63.158 0.00 0.00 0.00 5.25
2147 3946 4.338879 ACCAGGTACGACAGTAGTTACAT 58.661 43.478 0.00 0.00 32.77 2.29
2184 3986 7.276658 GCAGTAATCATAATAGGGATCGTCTTG 59.723 40.741 0.00 0.00 0.00 3.02
2319 4148 8.145767 AGGGCATTGAAACATTATTGACATATG 58.854 33.333 0.00 0.00 0.00 1.78
2345 4174 0.944386 GTTTGCACGCCTTTGAGAGA 59.056 50.000 0.00 0.00 0.00 3.10
2356 4185 2.873170 TTATTGAGCGAGTTTGCACG 57.127 45.000 0.00 0.00 37.31 5.34
2394 4225 7.421599 TGAGCGAAATGAAACAAAAGATGTAA 58.578 30.769 0.00 0.00 42.99 2.41
2408 4239 8.067784 CACTTAAACTAGTTTTGAGCGAAATGA 58.932 33.333 25.07 0.70 34.78 2.57
2424 4255 5.284861 TCACCTCACAAGCACTTAAACTA 57.715 39.130 0.00 0.00 0.00 2.24
2440 4271 3.243839 ACACAATTTGGCACATTCACCTC 60.244 43.478 0.00 0.00 39.30 3.85
2442 4273 3.110447 ACACAATTTGGCACATTCACC 57.890 42.857 0.00 0.00 39.30 4.02
2489 4320 7.199541 AGAAGATGACAAATGTTTCAGTCAG 57.800 36.000 0.00 0.00 43.39 3.51
2555 5930 7.882791 TCCAGAATTTGATGTAAAGCTGAGTTA 59.117 33.333 0.00 0.00 37.05 2.24
2562 5937 7.274250 GTGTGATTCCAGAATTTGATGTAAAGC 59.726 37.037 0.00 0.00 0.00 3.51
2580 5955 4.555511 GCCTCTCTTTGTTGTGTGTGATTC 60.556 45.833 0.00 0.00 0.00 2.52
2667 6043 1.737793 GCAAACTGAACGGGTCTATGG 59.262 52.381 0.00 0.00 0.00 2.74
2712 6088 6.430000 AGAATTGGCATTTTGTACTTCTACGT 59.570 34.615 0.00 0.00 0.00 3.57
2816 6343 4.408276 TGCTCTAACGGGCTATAGAGATT 58.592 43.478 19.00 0.00 45.17 2.40
2861 6389 8.385491 TGACAAGGAAACATCATATATAGCCAT 58.615 33.333 0.00 0.00 0.00 4.40
2862 6390 7.744733 TGACAAGGAAACATCATATATAGCCA 58.255 34.615 0.00 0.00 0.00 4.75
2863 6391 8.798859 ATGACAAGGAAACATCATATATAGCC 57.201 34.615 0.00 0.00 30.64 3.93
2879 6426 6.718593 AAATGGGCCTATATATGACAAGGA 57.281 37.500 0.24 0.00 0.00 3.36
2882 6429 9.073475 GTACAAAAATGGGCCTATATATGACAA 57.927 33.333 0.24 0.00 0.00 3.18
2932 6689 2.039216 TGGCCCGTCTAAAATGTTGAGA 59.961 45.455 0.00 0.00 0.00 3.27
2970 6727 0.744874 GCTGGCAGTATGTAGGTCGA 59.255 55.000 17.16 0.00 39.31 4.20
2996 6753 0.795698 CGGTTGCGATGTGAATGACA 59.204 50.000 0.00 0.00 39.53 3.58
3000 6757 2.731968 GCATTTCGGTTGCGATGTGAAT 60.732 45.455 0.00 0.00 0.00 2.57
3016 6773 1.402968 GCAGTGATGATGTCGGCATTT 59.597 47.619 2.92 0.00 35.07 2.32
3017 6774 1.019673 GCAGTGATGATGTCGGCATT 58.980 50.000 2.92 0.00 35.07 3.56
3024 6781 0.545171 CCTCCCAGCAGTGATGATGT 59.455 55.000 10.64 0.00 0.00 3.06
3026 6783 0.622738 ACCCTCCCAGCAGTGATGAT 60.623 55.000 10.64 0.00 0.00 2.45
3123 6971 0.687427 CCCATTCCCTTTCCGGCAAT 60.687 55.000 0.00 0.00 0.00 3.56
3138 6986 2.971598 CGGGTGCAACTCCTCCCAT 61.972 63.158 0.00 0.00 39.87 4.00
3143 6991 3.637273 GGTCCGGGTGCAACTCCT 61.637 66.667 0.00 0.00 28.69 3.69
3148 6996 2.350895 CATCAGGTCCGGGTGCAA 59.649 61.111 0.00 0.00 0.00 4.08
3163 7011 3.388841 GTGGAGGACACGGGACAT 58.611 61.111 0.00 0.00 40.85 3.06
3186 7034 2.123640 AGGAGCTCGGCCTAGTCC 60.124 66.667 7.83 14.32 32.92 3.85
3282 7136 4.662961 CACAGACGCCCGTGCAGA 62.663 66.667 0.00 0.00 37.32 4.26


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

AutoCloner maintained by Alex Coulton.