Multiple sequence alignment - TraesCS4A01G285900

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 TraesCS4A01G285900 chr4A 100.000 5987 0 0 1 5987 591716393 591710407 0.000000e+00 11057.0
1 TraesCS4A01G285900 chr4A 100.000 35 0 0 5909 5943 244098897 244098863 1.390000e-06 65.8
2 TraesCS4A01G285900 chr4B 98.104 3534 16 15 2452 5938 20603275 20599746 0.000000e+00 6107.0
3 TraesCS4A01G285900 chr4B 94.097 1135 27 18 769 1886 20605181 20604070 0.000000e+00 1688.0
4 TraesCS4A01G285900 chr4B 96.688 634 21 0 1879 2512 20603917 20603284 0.000000e+00 1055.0
5 TraesCS4A01G285900 chr4B 96.344 547 17 1 215 758 234063067 234063613 0.000000e+00 896.0
6 TraesCS4A01G285900 chr4B 99.083 218 2 0 1 218 234045093 234045310 5.630000e-105 392.0
7 TraesCS4A01G285900 chr4B 93.443 61 3 1 2452 2512 20603309 20603250 8.260000e-14 89.8
8 TraesCS4A01G285900 chr4D 94.051 1849 64 17 3369 5187 10944745 10942913 0.000000e+00 2763.0
9 TraesCS4A01G285900 chr4D 94.917 1751 41 22 769 2512 10947512 10945803 0.000000e+00 2697.0
10 TraesCS4A01G285900 chr4D 95.768 449 16 2 2452 2900 10945726 10945281 0.000000e+00 721.0
11 TraesCS4A01G285900 chr4D 91.313 495 20 10 2890 3373 10945263 10944781 0.000000e+00 654.0
12 TraesCS4A01G285900 chr4D 89.426 331 21 7 5216 5538 10942913 10942589 7.230000e-109 405.0
13 TraesCS4A01G285900 chr4D 80.851 188 18 8 5746 5915 10942592 10942405 1.350000e-26 132.0
14 TraesCS4A01G285900 chr4D 91.803 61 4 1 2452 2512 10945828 10945769 3.850000e-12 84.2
15 TraesCS4A01G285900 chr4D 90.164 61 5 1 2452 2512 10945760 10945701 1.790000e-10 78.7
16 TraesCS4A01G285900 chr4D 92.727 55 3 1 2452 2506 10945794 10945741 1.790000e-10 78.7
17 TraesCS4A01G285900 chr1B 98.318 773 9 2 1 770 33026527 33027298 0.000000e+00 1352.0
18 TraesCS4A01G285900 chr1B 73.460 633 138 20 139 754 310182536 310183155 1.690000e-50 211.0
19 TraesCS4A01G285900 chr6A 98.189 773 11 1 1 770 447166281 447167053 0.000000e+00 1347.0
20 TraesCS4A01G285900 chr6A 95.990 773 28 1 1 770 397198424 397197652 0.000000e+00 1253.0
21 TraesCS4A01G285900 chr5B 97.930 773 13 1 1 770 566690827 566690055 0.000000e+00 1336.0
22 TraesCS4A01G285900 chr5B 96.378 773 21 5 1 770 63843042 63843810 0.000000e+00 1266.0
23 TraesCS4A01G285900 chr5B 97.354 567 15 0 1 567 41887708 41888274 0.000000e+00 965.0
24 TraesCS4A01G285900 chr5B 95.714 210 6 1 564 770 41901532 41901741 9.610000e-88 335.0
25 TraesCS4A01G285900 chr7D 97.028 774 20 1 1 771 5133305 5134078 0.000000e+00 1299.0
26 TraesCS4A01G285900 chr7D 95.327 214 6 2 560 770 604302690 604302902 2.670000e-88 337.0
27 TraesCS4A01G285900 chr3B 96.903 775 19 2 1 770 672430371 672429597 0.000000e+00 1293.0
28 TraesCS4A01G285900 chr3B 90.909 77 4 2 5913 5986 107132359 107132283 3.820000e-17 100.0
29 TraesCS4A01G285900 chr5D 96.895 773 20 2 1 770 17143710 17142939 0.000000e+00 1291.0
30 TraesCS4A01G285900 chr5D 100.000 35 0 0 5909 5943 315919176 315919142 1.390000e-06 65.8
31 TraesCS4A01G285900 chr6D 96.382 774 24 2 1 770 27470884 27470111 0.000000e+00 1271.0
32 TraesCS4A01G285900 chr6D 98.039 51 1 0 5937 5987 6744185 6744135 8.260000e-14 89.8
33 TraesCS4A01G285900 chr6D 98.039 51 1 0 5937 5987 54491339 54491389 8.260000e-14 89.8
34 TraesCS4A01G285900 chr6D 98.039 51 1 0 5937 5987 63769833 63769783 8.260000e-14 89.8
35 TraesCS4A01G285900 chr6D 98.039 51 1 0 5937 5987 78755851 78755801 8.260000e-14 89.8
36 TraesCS4A01G285900 chr1A 97.207 716 17 1 46 758 99874694 99873979 0.000000e+00 1208.0
37 TraesCS4A01G285900 chr1A 100.000 36 0 0 5908 5943 20415044 20415009 3.870000e-07 67.6
38 TraesCS4A01G285900 chr1A 95.122 41 0 2 5905 5943 154329628 154329668 5.010000e-06 63.9
39 TraesCS4A01G285900 chr7B 96.423 699 22 1 1 696 162328584 162329282 0.000000e+00 1149.0
40 TraesCS4A01G285900 chrUn 100.000 385 0 0 4317 4701 480813983 480813599 0.000000e+00 712.0
41 TraesCS4A01G285900 chrUn 98.039 51 1 0 5937 5987 36485704 36485754 8.260000e-14 89.8
42 TraesCS4A01G285900 chr2B 89.610 77 5 2 5913 5986 563459143 563459067 1.780000e-15 95.3
43 TraesCS4A01G285900 chr2B 98.077 52 1 0 5936 5987 540993483 540993432 2.300000e-14 91.6
44 TraesCS4A01G285900 chr3D 98.077 52 1 0 5936 5987 35441600 35441549 2.300000e-14 91.6
45 TraesCS4A01G285900 chr7A 100.000 34 0 0 5910 5943 336832570 336832537 5.010000e-06 63.9
46 TraesCS4A01G285900 chr3A 90.196 51 1 3 5896 5942 172970076 172970026 5.010000e-06 63.9


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 TraesCS4A01G285900 chr4A 591710407 591716393 5986 True 11057.000000 11057 100.000000 1 5987 1 chr4A.!!$R2 5986
1 TraesCS4A01G285900 chr4B 20599746 20605181 5435 True 2234.950000 6107 95.583000 769 5938 4 chr4B.!!$R1 5169
2 TraesCS4A01G285900 chr4B 234063067 234063613 546 False 896.000000 896 96.344000 215 758 1 chr4B.!!$F2 543
3 TraesCS4A01G285900 chr4D 10942405 10947512 5107 True 845.955556 2763 91.224444 769 5915 9 chr4D.!!$R1 5146
4 TraesCS4A01G285900 chr1B 33026527 33027298 771 False 1352.000000 1352 98.318000 1 770 1 chr1B.!!$F1 769
5 TraesCS4A01G285900 chr1B 310182536 310183155 619 False 211.000000 211 73.460000 139 754 1 chr1B.!!$F2 615
6 TraesCS4A01G285900 chr6A 447166281 447167053 772 False 1347.000000 1347 98.189000 1 770 1 chr6A.!!$F1 769
7 TraesCS4A01G285900 chr6A 397197652 397198424 772 True 1253.000000 1253 95.990000 1 770 1 chr6A.!!$R1 769
8 TraesCS4A01G285900 chr5B 566690055 566690827 772 True 1336.000000 1336 97.930000 1 770 1 chr5B.!!$R1 769
9 TraesCS4A01G285900 chr5B 63843042 63843810 768 False 1266.000000 1266 96.378000 1 770 1 chr5B.!!$F3 769
10 TraesCS4A01G285900 chr5B 41887708 41888274 566 False 965.000000 965 97.354000 1 567 1 chr5B.!!$F1 566
11 TraesCS4A01G285900 chr7D 5133305 5134078 773 False 1299.000000 1299 97.028000 1 771 1 chr7D.!!$F1 770
12 TraesCS4A01G285900 chr3B 672429597 672430371 774 True 1293.000000 1293 96.903000 1 770 1 chr3B.!!$R2 769
13 TraesCS4A01G285900 chr5D 17142939 17143710 771 True 1291.000000 1291 96.895000 1 770 1 chr5D.!!$R1 769
14 TraesCS4A01G285900 chr6D 27470111 27470884 773 True 1271.000000 1271 96.382000 1 770 1 chr6D.!!$R2 769
15 TraesCS4A01G285900 chr1A 99873979 99874694 715 True 1208.000000 1208 97.207000 46 758 1 chr1A.!!$R2 712
16 TraesCS4A01G285900 chr7B 162328584 162329282 698 False 1149.000000 1149 96.423000 1 696 1 chr7B.!!$F1 695

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
909 938 0.027063 CACCACACGTTTCACGAACC 59.973 55.000 2.75 0.0 46.05 3.62 F
914 943 0.232303 CACGTTTCACGAACCAGAGC 59.768 55.000 2.75 0.0 46.05 4.09 F
1111 1140 0.759060 GGAGGAGGAGGAGGAAGAGC 60.759 65.000 0.00 0.0 0.00 4.09 F
1946 2157 2.396590 TCGATTTGGTACTCCTTGGC 57.603 50.000 0.00 0.0 34.23 4.52 F
2156 2369 1.403323 GTTAGCATTCTTCTGCAGGGC 59.597 52.381 15.13 8.4 44.77 5.19 F
4315 4813 1.482593 CTCCGAGGTTTCTATGGCTGT 59.517 52.381 0.00 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 2286 1.271108 TGCAGCCGAGTAATTTCCACA 60.271 47.619 0.00 0.00 0.0 4.17 R
2148 2361 2.653234 AAATCCTCATAGCCCTGCAG 57.347 50.000 6.78 6.78 0.0 4.41 R
2156 2369 7.286546 TCTGTCCTCTGAAGTAAATCCTCATAG 59.713 40.741 0.00 0.00 0.0 2.23 R
4315 4813 5.810587 GCTTATTTATGGTTCTGACGTCTCA 59.189 40.000 17.92 7.71 0.0 3.27 R
4704 5202 1.141053 AGATTCAGGGTTCGGTATGCC 59.859 52.381 0.00 0.00 0.0 4.40 R
5544 6085 0.616395 TTATGGAGGTGGACGGAGCA 60.616 55.000 0.00 0.00 0.0 4.26 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
421 424 4.700213 GGCCTACTTTTCTTACTGATTGCA 59.300 41.667 0.00 0.00 0.00 4.08
443 447 0.103937 TCTTTGGCAAAAACAGCGGG 59.896 50.000 14.43 0.00 0.00 6.13
491 495 2.225117 CCCCTTGGACCATCAGAACTTT 60.225 50.000 0.00 0.00 0.00 2.66
909 938 0.027063 CACCACACGTTTCACGAACC 59.973 55.000 2.75 0.00 46.05 3.62
912 941 1.282817 CACACGTTTCACGAACCAGA 58.717 50.000 2.75 0.00 46.05 3.86
913 942 1.257936 CACACGTTTCACGAACCAGAG 59.742 52.381 2.75 0.00 46.05 3.35
914 943 0.232303 CACGTTTCACGAACCAGAGC 59.768 55.000 2.75 0.00 46.05 4.09
915 944 0.878961 ACGTTTCACGAACCAGAGCC 60.879 55.000 2.75 0.00 46.05 4.70
916 945 1.566018 CGTTTCACGAACCAGAGCCC 61.566 60.000 0.00 0.00 46.05 5.19
917 946 1.301401 TTTCACGAACCAGAGCCCG 60.301 57.895 0.00 0.00 0.00 6.13
918 947 2.725203 TTTCACGAACCAGAGCCCGG 62.725 60.000 0.00 0.00 0.00 5.73
919 948 4.003788 CACGAACCAGAGCCCGGT 62.004 66.667 0.00 0.00 38.85 5.28
921 950 2.742372 CGAACCAGAGCCCGGTTG 60.742 66.667 6.76 0.00 46.80 3.77
922 951 3.056328 GAACCAGAGCCCGGTTGC 61.056 66.667 6.76 0.00 46.80 4.17
923 952 3.842925 GAACCAGAGCCCGGTTGCA 62.843 63.158 6.76 0.00 46.80 4.08
924 953 4.643387 ACCAGAGCCCGGTTGCAC 62.643 66.667 0.00 0.00 30.53 4.57
925 954 4.335647 CCAGAGCCCGGTTGCACT 62.336 66.667 0.00 0.00 32.08 4.40
926 955 2.662596 CAGAGCCCGGTTGCACTA 59.337 61.111 0.00 0.00 30.71 2.74
1107 1136 2.042843 GCGGAGGAGGAGGAGGAA 60.043 66.667 0.00 0.00 0.00 3.36
1111 1140 0.759060 GGAGGAGGAGGAGGAAGAGC 60.759 65.000 0.00 0.00 0.00 4.09
1198 1233 2.995574 CCCCAGAACCGGTCTCGT 60.996 66.667 8.04 0.00 32.70 4.18
1628 1667 7.792374 TGAATAGCCACAGAATTATGAACTC 57.208 36.000 7.16 0.00 0.00 3.01
1915 2126 7.283127 TCCAGGCATATAGAAAAATCTGTTGTC 59.717 37.037 0.00 0.00 0.00 3.18
1946 2157 2.396590 TCGATTTGGTACTCCTTGGC 57.603 50.000 0.00 0.00 34.23 4.52
2075 2286 5.183228 CCAGTCAACGTGAAAATAGGGTAT 58.817 41.667 0.00 0.00 0.00 2.73
2156 2369 1.403323 GTTAGCATTCTTCTGCAGGGC 59.597 52.381 15.13 8.40 44.77 5.19
4315 4813 1.482593 CTCCGAGGTTTCTATGGCTGT 59.517 52.381 0.00 0.00 0.00 4.40
4701 5199 7.761651 TCGTTTCTTCATCATCACTATTGAG 57.238 36.000 0.00 0.00 34.35 3.02
4704 5202 7.408123 GTTTCTTCATCATCACTATTGAGCAG 58.592 38.462 0.00 0.00 34.35 4.24
4705 5203 5.608449 TCTTCATCATCACTATTGAGCAGG 58.392 41.667 0.00 0.00 34.35 4.85
4709 5207 4.961438 TCATCACTATTGAGCAGGCATA 57.039 40.909 0.00 0.00 34.35 3.14
4710 5208 4.635223 TCATCACTATTGAGCAGGCATAC 58.365 43.478 0.00 0.00 34.35 2.39
4782 5309 0.736325 GTCAGACCGGAACCGATGTG 60.736 60.000 9.46 6.62 42.83 3.21
5553 6094 0.243095 AAACGAGTACTGCTCCGTCC 59.757 55.000 0.00 0.00 41.10 4.79
5555 6096 1.136984 CGAGTACTGCTCCGTCCAC 59.863 63.158 0.00 0.00 41.10 4.02
5575 6116 7.107542 GTCCACCTCCATAATTGTAGTGTTTA 58.892 38.462 0.00 0.00 0.00 2.01
5576 6117 7.773690 GTCCACCTCCATAATTGTAGTGTTTAT 59.226 37.037 0.00 0.00 0.00 1.40
5602 6143 7.064371 TGTGTCATTTTCAAAAGTCAAACCATG 59.936 33.333 0.00 0.00 0.00 3.66
5940 6501 5.031066 GCCACAATGGGTAGTAACATAGA 57.969 43.478 0.00 0.00 38.19 1.98
5941 6502 4.814771 GCCACAATGGGTAGTAACATAGAC 59.185 45.833 0.00 0.00 38.19 2.59
5942 6503 5.396436 GCCACAATGGGTAGTAACATAGACT 60.396 44.000 0.00 0.00 38.19 3.24
5943 6504 6.281405 CCACAATGGGTAGTAACATAGACTC 58.719 44.000 0.00 0.00 32.67 3.36
5944 6505 6.127168 CCACAATGGGTAGTAACATAGACTCA 60.127 42.308 0.00 0.00 32.67 3.41
5945 6506 7.419057 CCACAATGGGTAGTAACATAGACTCAT 60.419 40.741 0.00 0.00 34.43 2.90
5946 6507 7.653713 CACAATGGGTAGTAACATAGACTCATC 59.346 40.741 0.00 0.00 31.74 2.92
5947 6508 7.565398 ACAATGGGTAGTAACATAGACTCATCT 59.435 37.037 0.00 0.00 31.74 2.90
5948 6509 8.424918 CAATGGGTAGTAACATAGACTCATCTT 58.575 37.037 0.00 0.00 31.74 2.40
5949 6510 7.348080 TGGGTAGTAACATAGACTCATCTTG 57.652 40.000 0.00 0.00 36.29 3.02
5950 6511 6.183360 TGGGTAGTAACATAGACTCATCTTGC 60.183 42.308 0.00 0.00 36.29 4.01
5951 6512 6.217294 GGTAGTAACATAGACTCATCTTGCC 58.783 44.000 0.00 0.00 36.29 4.52
5952 6513 6.041069 GGTAGTAACATAGACTCATCTTGCCT 59.959 42.308 0.00 0.00 36.29 4.75
5953 6514 6.552445 AGTAACATAGACTCATCTTGCCTT 57.448 37.500 0.00 0.00 36.29 4.35
5954 6515 6.344500 AGTAACATAGACTCATCTTGCCTTG 58.656 40.000 0.00 0.00 36.29 3.61
5955 6516 5.426689 AACATAGACTCATCTTGCCTTGA 57.573 39.130 0.00 0.00 36.29 3.02
5956 6517 5.627182 ACATAGACTCATCTTGCCTTGAT 57.373 39.130 0.00 0.00 36.29 2.57
5957 6518 6.737720 ACATAGACTCATCTTGCCTTGATA 57.262 37.500 0.00 0.00 36.29 2.15
5958 6519 7.313740 ACATAGACTCATCTTGCCTTGATAT 57.686 36.000 0.00 0.00 36.29 1.63
5959 6520 7.160049 ACATAGACTCATCTTGCCTTGATATG 58.840 38.462 0.00 0.00 36.29 1.78
5960 6521 5.627182 AGACTCATCTTGCCTTGATATGT 57.373 39.130 0.00 0.00 0.00 2.29
5961 6522 5.366460 AGACTCATCTTGCCTTGATATGTG 58.634 41.667 0.00 0.00 0.00 3.21
5962 6523 5.104610 AGACTCATCTTGCCTTGATATGTGT 60.105 40.000 0.00 0.00 0.00 3.72
5963 6524 4.880120 ACTCATCTTGCCTTGATATGTGTG 59.120 41.667 0.00 0.00 0.00 3.82
5964 6525 5.101648 TCATCTTGCCTTGATATGTGTGA 57.898 39.130 0.00 0.00 0.00 3.58
5965 6526 5.687780 TCATCTTGCCTTGATATGTGTGAT 58.312 37.500 0.00 0.00 0.00 3.06
5966 6527 5.529800 TCATCTTGCCTTGATATGTGTGATG 59.470 40.000 0.00 0.00 0.00 3.07
5967 6528 4.847198 TCTTGCCTTGATATGTGTGATGT 58.153 39.130 0.00 0.00 0.00 3.06
5968 6529 5.255687 TCTTGCCTTGATATGTGTGATGTT 58.744 37.500 0.00 0.00 0.00 2.71
5969 6530 6.413892 TCTTGCCTTGATATGTGTGATGTTA 58.586 36.000 0.00 0.00 0.00 2.41
5970 6531 6.316140 TCTTGCCTTGATATGTGTGATGTTAC 59.684 38.462 0.00 0.00 0.00 2.50
5971 6532 5.744171 TGCCTTGATATGTGTGATGTTACT 58.256 37.500 0.00 0.00 0.00 2.24
5972 6533 5.817296 TGCCTTGATATGTGTGATGTTACTC 59.183 40.000 0.00 0.00 0.00 2.59
5973 6534 5.817296 GCCTTGATATGTGTGATGTTACTCA 59.183 40.000 0.00 0.00 0.00 3.41
5974 6535 6.484643 GCCTTGATATGTGTGATGTTACTCAT 59.515 38.462 0.00 0.00 38.11 2.90
5975 6536 7.519488 GCCTTGATATGTGTGATGTTACTCATG 60.519 40.741 0.00 0.00 36.02 3.07
5976 6537 6.849588 TGATATGTGTGATGTTACTCATGC 57.150 37.500 0.00 0.00 36.02 4.06
5977 6538 6.585416 TGATATGTGTGATGTTACTCATGCT 58.415 36.000 0.00 0.00 36.02 3.79
5978 6539 7.725251 TGATATGTGTGATGTTACTCATGCTA 58.275 34.615 0.00 0.00 36.02 3.49
5979 6540 7.869429 TGATATGTGTGATGTTACTCATGCTAG 59.131 37.037 0.00 0.00 36.02 3.42
5980 6541 5.405935 TGTGTGATGTTACTCATGCTAGT 57.594 39.130 0.00 0.00 36.83 2.57
5981 6542 6.524101 TGTGTGATGTTACTCATGCTAGTA 57.476 37.500 0.00 0.00 36.83 1.82
5982 6543 6.564328 TGTGTGATGTTACTCATGCTAGTAG 58.436 40.000 0.00 0.00 36.83 2.57
5983 6544 6.152831 TGTGTGATGTTACTCATGCTAGTAGT 59.847 38.462 0.00 0.00 36.83 2.73
5984 6545 7.338449 TGTGTGATGTTACTCATGCTAGTAGTA 59.662 37.037 0.00 0.00 36.83 1.82
5985 6546 8.188799 GTGTGATGTTACTCATGCTAGTAGTAA 58.811 37.037 0.00 0.99 36.83 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
421 424 2.288395 CCGCTGTTTTTGCCAAAGAGAT 60.288 45.455 6.77 0.00 0.00 2.75
433 437 1.456705 TTCTTGCCCCCGCTGTTTT 60.457 52.632 0.00 0.00 35.36 2.43
436 440 3.570212 ACTTCTTGCCCCCGCTGT 61.570 61.111 0.00 0.00 35.36 4.40
443 447 1.474077 CTGCCAATACACTTCTTGCCC 59.526 52.381 0.00 0.00 0.00 5.36
491 495 8.918202 TGTAAAGGAGAAAAATTCAGCTAGAA 57.082 30.769 0.00 0.00 41.28 2.10
909 938 1.003839 TTAGTGCAACCGGGCTCTG 60.004 57.895 14.99 4.51 38.05 3.35
912 941 0.889186 CTTGTTAGTGCAACCGGGCT 60.889 55.000 6.32 0.00 37.80 5.19
913 942 1.579429 CTTGTTAGTGCAACCGGGC 59.421 57.895 6.32 0.00 37.80 6.13
914 943 0.889186 AGCTTGTTAGTGCAACCGGG 60.889 55.000 6.32 0.00 37.80 5.73
915 944 0.238289 CAGCTTGTTAGTGCAACCGG 59.762 55.000 0.00 0.00 37.80 5.28
916 945 0.385974 GCAGCTTGTTAGTGCAACCG 60.386 55.000 0.00 0.00 37.80 4.44
917 946 0.039165 GGCAGCTTGTTAGTGCAACC 60.039 55.000 0.00 0.00 39.05 3.77
918 947 0.039165 GGGCAGCTTGTTAGTGCAAC 60.039 55.000 0.00 0.00 39.05 4.17
919 948 1.514678 CGGGCAGCTTGTTAGTGCAA 61.515 55.000 0.00 0.00 39.05 4.08
920 949 1.965930 CGGGCAGCTTGTTAGTGCA 60.966 57.895 0.00 0.00 39.05 4.57
921 950 2.870372 CGGGCAGCTTGTTAGTGC 59.130 61.111 0.00 0.00 36.42 4.40
922 951 2.870372 GCGGGCAGCTTGTTAGTG 59.130 61.111 1.25 0.00 44.04 2.74
923 952 2.742372 CGCGGGCAGCTTGTTAGT 60.742 61.111 8.23 0.00 45.59 2.24
924 953 4.166011 GCGCGGGCAGCTTGTTAG 62.166 66.667 20.76 0.00 45.59 2.34
1107 1136 0.534412 CTTCCACCTCATCGTGCTCT 59.466 55.000 0.00 0.00 32.10 4.09
1111 1140 1.135915 CTCCTCTTCCACCTCATCGTG 59.864 57.143 0.00 0.00 0.00 4.35
1581 1620 0.666374 CCCACGTGACCAAGGAAAAC 59.334 55.000 19.30 0.00 0.00 2.43
1628 1667 6.176183 CCTAGTTTCCTATAGGCATCATTGG 58.824 44.000 14.50 6.92 32.60 3.16
1915 2126 8.499162 GGAGTACCAAATCGAAATCTGAATATG 58.501 37.037 0.00 0.00 35.97 1.78
1946 2157 5.119588 TCAACTTAGATAAAACAGAACGGCG 59.880 40.000 4.80 4.80 0.00 6.46
2075 2286 1.271108 TGCAGCCGAGTAATTTCCACA 60.271 47.619 0.00 0.00 0.00 4.17
2114 2325 9.367160 CTAACATTACATCATAAAGGGGGAAAT 57.633 33.333 0.00 0.00 0.00 2.17
2118 2329 6.068010 TGCTAACATTACATCATAAAGGGGG 58.932 40.000 0.00 0.00 0.00 5.40
2119 2330 7.765695 ATGCTAACATTACATCATAAAGGGG 57.234 36.000 0.00 0.00 30.07 4.79
2148 2361 2.653234 AAATCCTCATAGCCCTGCAG 57.347 50.000 6.78 6.78 0.00 4.41
2156 2369 7.286546 TCTGTCCTCTGAAGTAAATCCTCATAG 59.713 40.741 0.00 0.00 0.00 2.23
4315 4813 5.810587 GCTTATTTATGGTTCTGACGTCTCA 59.189 40.000 17.92 7.71 0.00 3.27
4701 5199 1.819632 CAGGGTTCGGTATGCCTGC 60.820 63.158 0.00 0.00 0.00 4.85
4704 5202 1.141053 AGATTCAGGGTTCGGTATGCC 59.859 52.381 0.00 0.00 0.00 4.40
4705 5203 2.622064 AGATTCAGGGTTCGGTATGC 57.378 50.000 0.00 0.00 0.00 3.14
4709 5207 1.358152 TGGAAGATTCAGGGTTCGGT 58.642 50.000 0.00 0.00 0.00 4.69
4710 5208 2.292267 CATGGAAGATTCAGGGTTCGG 58.708 52.381 0.00 0.00 0.00 4.30
4782 5309 1.174712 TTGGAGCTGGCAGTGCTTTC 61.175 55.000 17.16 7.51 41.30 2.62
5538 6079 0.966370 AGGTGGACGGAGCAGTACTC 60.966 60.000 0.00 0.00 45.45 2.59
5542 6083 2.997897 GGAGGTGGACGGAGCAGT 60.998 66.667 0.00 0.00 0.00 4.40
5544 6085 0.616395 TTATGGAGGTGGACGGAGCA 60.616 55.000 0.00 0.00 0.00 4.26
5553 6094 8.397906 CACATAAACACTACAATTATGGAGGTG 58.602 37.037 8.94 0.00 42.30 4.00
5555 6096 8.506168 ACACATAAACACTACAATTATGGAGG 57.494 34.615 8.94 2.48 42.30 4.30
5575 6116 7.102346 TGGTTTGACTTTTGAAAATGACACAT 58.898 30.769 0.00 0.00 0.00 3.21
5576 6117 6.459066 TGGTTTGACTTTTGAAAATGACACA 58.541 32.000 0.00 0.00 0.00 3.72
5602 6143 7.268586 TCTCAATAAGCCTTGTCAATCTCTAC 58.731 38.462 0.00 0.00 0.00 2.59
5938 6499 5.104610 ACACATATCAAGGCAAGATGAGTCT 60.105 40.000 2.43 0.00 35.82 3.24
5939 6500 5.007430 CACACATATCAAGGCAAGATGAGTC 59.993 44.000 2.43 0.00 0.00 3.36
5940 6501 4.880120 CACACATATCAAGGCAAGATGAGT 59.120 41.667 2.43 0.00 0.00 3.41
5941 6502 5.121105 TCACACATATCAAGGCAAGATGAG 58.879 41.667 2.43 0.00 0.00 2.90
5942 6503 5.101648 TCACACATATCAAGGCAAGATGA 57.898 39.130 2.43 0.00 0.00 2.92
5943 6504 5.298527 ACATCACACATATCAAGGCAAGATG 59.701 40.000 0.00 0.00 36.24 2.90
5944 6505 5.443283 ACATCACACATATCAAGGCAAGAT 58.557 37.500 0.00 0.00 0.00 2.40
5945 6506 4.847198 ACATCACACATATCAAGGCAAGA 58.153 39.130 0.00 0.00 0.00 3.02
5946 6507 5.571784 AACATCACACATATCAAGGCAAG 57.428 39.130 0.00 0.00 0.00 4.01
5947 6508 6.179756 AGTAACATCACACATATCAAGGCAA 58.820 36.000 0.00 0.00 0.00 4.52
5948 6509 5.744171 AGTAACATCACACATATCAAGGCA 58.256 37.500 0.00 0.00 0.00 4.75
5949 6510 5.817296 TGAGTAACATCACACATATCAAGGC 59.183 40.000 0.00 0.00 0.00 4.35
5950 6511 7.519488 GCATGAGTAACATCACACATATCAAGG 60.519 40.741 0.00 0.00 37.07 3.61
5951 6512 7.226128 AGCATGAGTAACATCACACATATCAAG 59.774 37.037 0.00 0.00 37.07 3.02
5952 6513 7.049754 AGCATGAGTAACATCACACATATCAA 58.950 34.615 0.00 0.00 37.07 2.57
5953 6514 6.585416 AGCATGAGTAACATCACACATATCA 58.415 36.000 0.00 0.00 37.07 2.15
5954 6515 7.869937 ACTAGCATGAGTAACATCACACATATC 59.130 37.037 0.00 0.00 37.07 1.63
5955 6516 7.730084 ACTAGCATGAGTAACATCACACATAT 58.270 34.615 0.00 0.00 37.07 1.78
5956 6517 7.112452 ACTAGCATGAGTAACATCACACATA 57.888 36.000 0.00 0.00 37.07 2.29
5957 6518 5.982356 ACTAGCATGAGTAACATCACACAT 58.018 37.500 0.00 0.00 37.07 3.21
5958 6519 5.405935 ACTAGCATGAGTAACATCACACA 57.594 39.130 0.00 0.00 37.07 3.72
5959 6520 6.565234 ACTACTAGCATGAGTAACATCACAC 58.435 40.000 0.00 0.00 37.07 3.82
5960 6521 6.775594 ACTACTAGCATGAGTAACATCACA 57.224 37.500 0.00 0.00 37.07 3.58


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

AutoCloner maintained by Alex Coulton.