Multiple sequence alignment - TraesCS6B01G315300

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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 TraesCS6B01G315300 chr6B 100.000 5616 0 0 1 5616 563148661 563143046 0.000000e+00 10371.0
1 TraesCS6B01G315300 chr6B 94.443 3095 126 22 2456 5542 563134313 563131257 0.000000e+00 4721.0
2 TraesCS6B01G315300 chr6B 94.357 1276 44 5 1 1273 563136866 563135616 0.000000e+00 1932.0
3 TraesCS6B01G315300 chr6B 92.926 1244 42 16 1213 2429 563135634 563134410 0.000000e+00 1768.0
4 TraesCS6B01G315300 chr6B 88.684 1299 89 28 3394 4679 60604074 60602821 0.000000e+00 1531.0
5 TraesCS6B01G315300 chr6B 91.189 908 37 9 2457 3346 60604956 60604074 0.000000e+00 1194.0
6 TraesCS6B01G315300 chr6B 86.100 741 61 9 1322 2046 60606031 60605317 0.000000e+00 760.0
7 TraesCS6B01G315300 chr6B 89.231 585 39 13 1 577 60607362 60606794 0.000000e+00 710.0
8 TraesCS6B01G315300 chr6B 83.875 738 81 14 1326 2046 25376389 25375673 0.000000e+00 669.0
9 TraesCS6B01G315300 chr6B 88.952 525 56 2 2457 2981 25401081 25400559 0.000000e+00 647.0
10 TraesCS6B01G315300 chr6B 93.711 318 19 1 578 894 60606684 60606367 5.090000e-130 475.0
11 TraesCS6B01G315300 chr6B 87.811 402 32 4 917 1318 60606392 60606008 6.630000e-124 455.0
12 TraesCS6B01G315300 chr6B 93.226 310 18 3 2151 2459 60605325 60605018 2.390000e-123 453.0
13 TraesCS6B01G315300 chr6B 92.079 303 22 2 2158 2459 25392168 25391867 5.200000e-115 425.0
14 TraesCS6B01G315300 chr6B 92.079 303 22 2 2158 2459 25398055 25397754 5.200000e-115 425.0
15 TraesCS6B01G315300 chr6B 91.333 300 23 3 2161 2459 25439443 25439146 1.880000e-109 407.0
16 TraesCS6B01G315300 chr6B 91.333 300 23 3 2161 2459 25464910 25464613 1.880000e-109 407.0
17 TraesCS6B01G315300 chr6B 90.099 303 28 2 2158 2459 25375675 25375374 5.270000e-105 392.0
18 TraesCS6B01G315300 chr6B 84.651 215 28 5 132 341 697533180 697533394 5.700000e-50 209.0
19 TraesCS6B01G315300 chr6D 95.304 3173 109 25 2457 5616 376946111 376942966 0.000000e+00 4998.0
20 TraesCS6B01G315300 chr6D 95.189 3180 104 26 2457 5616 376975005 376971855 0.000000e+00 4979.0
21 TraesCS6B01G315300 chr6D 90.849 2251 123 39 2457 4673 29114478 29116679 0.000000e+00 2939.0
22 TraesCS6B01G315300 chr6D 92.740 1281 46 12 1213 2459 376976334 376975067 0.000000e+00 1807.0
23 TraesCS6B01G315300 chr6D 91.176 1360 58 12 1 1350 376948637 376947330 0.000000e+00 1790.0
24 TraesCS6B01G315300 chr6D 93.702 1175 36 8 1301 2459 376947325 376946173 0.000000e+00 1725.0
25 TraesCS6B01G315300 chr6D 92.445 1178 39 6 123 1273 376977470 376976316 0.000000e+00 1637.0
26 TraesCS6B01G315300 chr6D 88.124 741 58 7 1322 2046 29113391 29114117 0.000000e+00 854.0
27 TraesCS6B01G315300 chr6D 85.753 737 69 8 1326 2046 13947767 13947051 0.000000e+00 747.0
28 TraesCS6B01G315300 chr6D 84.668 737 77 11 1326 2046 13959050 13958334 0.000000e+00 702.0
29 TraesCS6B01G315300 chr6D 92.967 455 28 4 124 577 29112180 29112631 0.000000e+00 660.0
30 TraesCS6B01G315300 chr6D 89.136 405 26 5 917 1321 29113030 29113416 6.540000e-134 488.0
31 TraesCS6B01G315300 chr6D 92.835 321 19 3 575 894 29112738 29113055 3.960000e-126 462.0
32 TraesCS6B01G315300 chr6D 93.750 304 16 3 2151 2453 29114109 29114410 2.390000e-123 453.0
33 TraesCS6B01G315300 chr6D 96.680 241 8 0 1 241 376977697 376977457 8.760000e-108 401.0
34 TraesCS6B01G315300 chr6D 86.760 287 23 8 5258 5542 376942862 376942589 7.070000e-79 305.0
35 TraesCS6B01G315300 chr6D 87.442 215 19 6 124 336 56911327 56911119 2.020000e-59 241.0
36 TraesCS6B01G315300 chr6A 95.361 3169 99 16 2456 5616 518598501 518595373 0.000000e+00 4994.0
37 TraesCS6B01G315300 chr6A 94.180 3196 126 22 2456 5616 518550408 518547238 0.000000e+00 4817.0
38 TraesCS6B01G315300 chr6A 92.976 2463 89 21 1 2431 518601008 518598598 0.000000e+00 3513.0
39 TraesCS6B01G315300 chr6A 90.574 2249 117 40 2456 4679 33293944 33291766 0.000000e+00 2891.0
40 TraesCS6B01G315300 chr6A 91.272 1352 49 6 1 1350 518552917 518551633 0.000000e+00 1779.0
41 TraesCS6B01G315300 chr6A 95.380 1104 31 9 1339 2431 518551599 518550505 0.000000e+00 1738.0
42 TraesCS6B01G315300 chr6A 87.045 741 54 9 1322 2046 33295020 33294306 0.000000e+00 798.0
43 TraesCS6B01G315300 chr6A 90.136 588 41 12 1 577 33296371 33295790 0.000000e+00 749.0
44 TraesCS6B01G315300 chr6A 83.271 807 87 17 2703 3493 14522588 14521814 0.000000e+00 699.0
45 TraesCS6B01G315300 chr6A 83.539 729 85 19 1326 2046 14553979 14553278 0.000000e+00 649.0
46 TraesCS6B01G315300 chr6A 93.146 321 18 3 578 894 33295680 33295360 8.520000e-128 468.0
47 TraesCS6B01G315300 chr6A 93.160 307 18 3 2151 2456 33294314 33294010 1.110000e-121 448.0
48 TraesCS6B01G315300 chr6A 86.797 409 33 7 917 1321 33295385 33294994 2.400000e-118 436.0
49 TraesCS6B01G315300 chr6A 89.389 311 28 4 2151 2459 14599468 14599161 2.450000e-103 387.0
50 TraesCS6B01G315300 chr6A 87.338 308 23 8 5235 5542 518547148 518546857 6.970000e-89 339.0
51 TraesCS6B01G315300 chrUn 86.196 623 65 7 1425 2046 469507769 469507167 0.000000e+00 654.0
52 TraesCS6B01G315300 chrUn 88.952 525 50 6 2457 2981 355298962 355298446 4.740000e-180 641.0
53 TraesCS6B01G315300 chr5A 89.677 155 12 4 730 883 214918580 214918731 1.600000e-45 195.0
54 TraesCS6B01G315300 chr7A 86.517 89 12 0 5261 5349 412553869 412553957 1.290000e-16 99.0
55 TraesCS6B01G315300 chr4A 85.393 89 13 0 5261 5349 496108613 496108701 5.990000e-15 93.5
56 TraesCS6B01G315300 chr2A 87.302 63 4 2 4797 4855 737493613 737493675 1.010000e-07 69.4
57 TraesCS6B01G315300 chr1A 87.302 63 4 2 4797 4855 162067298 162067360 1.010000e-07 69.4
58 TraesCS6B01G315300 chr4D 91.304 46 2 2 4894 4939 455480739 455480782 1.690000e-05 62.1
59 TraesCS6B01G315300 chr1B 82.278 79 6 6 4797 4869 634801797 634801721 1.690000e-05 62.1
60 TraesCS6B01G315300 chr4B 80.000 90 9 7 4793 4875 98328095 98328182 2.190000e-04 58.4


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 TraesCS6B01G315300 chr6B 563143046 563148661 5615 True 10371.000000 10371 100.000000 1 5616 1 chr6B.!!$R4 5615
1 TraesCS6B01G315300 chr6B 563131257 563136866 5609 True 2807.000000 4721 93.908667 1 5542 3 chr6B.!!$R8 5541
2 TraesCS6B01G315300 chr6B 60602821 60607362 4541 True 796.857143 1531 89.993143 1 4679 7 chr6B.!!$R7 4678
3 TraesCS6B01G315300 chr6B 25397754 25401081 3327 True 536.000000 647 90.515500 2158 2981 2 chr6B.!!$R6 823
4 TraesCS6B01G315300 chr6B 25375374 25376389 1015 True 530.500000 669 86.987000 1326 2459 2 chr6B.!!$R5 1133
5 TraesCS6B01G315300 chr6D 376971855 376977697 5842 True 2206.000000 4979 94.263500 1 5616 4 chr6D.!!$R5 5615
6 TraesCS6B01G315300 chr6D 376942589 376948637 6048 True 2204.500000 4998 91.735500 1 5616 4 chr6D.!!$R4 5615
7 TraesCS6B01G315300 chr6D 29112180 29116679 4499 False 976.000000 2939 91.276833 124 4673 6 chr6D.!!$F1 4549
8 TraesCS6B01G315300 chr6D 13947051 13947767 716 True 747.000000 747 85.753000 1326 2046 1 chr6D.!!$R1 720
9 TraesCS6B01G315300 chr6D 13958334 13959050 716 True 702.000000 702 84.668000 1326 2046 1 chr6D.!!$R2 720
10 TraesCS6B01G315300 chr6A 518595373 518601008 5635 True 4253.500000 4994 94.168500 1 5616 2 chr6A.!!$R6 5615
11 TraesCS6B01G315300 chr6A 518546857 518552917 6060 True 2168.250000 4817 92.042500 1 5616 4 chr6A.!!$R5 5615
12 TraesCS6B01G315300 chr6A 33291766 33296371 4605 True 965.000000 2891 90.143000 1 4679 6 chr6A.!!$R4 4678
13 TraesCS6B01G315300 chr6A 14521814 14522588 774 True 699.000000 699 83.271000 2703 3493 1 chr6A.!!$R1 790
14 TraesCS6B01G315300 chr6A 14553278 14553979 701 True 649.000000 649 83.539000 1326 2046 1 chr6A.!!$R2 720
15 TraesCS6B01G315300 chrUn 469507167 469507769 602 True 654.000000 654 86.196000 1425 2046 1 chrUn.!!$R2 621
16 TraesCS6B01G315300 chrUn 355298446 355298962 516 True 641.000000 641 88.952000 2457 2981 1 chrUn.!!$R1 524

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
510 727 0.878416 GAACGGCTTACAACATGCCA 59.122 50.000 0.0 0.0 45.72 4.92 F
1299 1847 0.764890 TTCTTCATCCCCCTATGCCG 59.235 55.000 0.0 0.0 0.00 5.69 F
1406 2053 0.179108 GGCAGCTACCTTCACTACCG 60.179 60.000 0.0 0.0 0.00 4.02 F
1608 2285 1.080093 CCGCTACCTTCAGAACGCA 60.080 57.895 0.0 0.0 0.00 5.24 F
3002 3974 1.808411 TCCATTCAAGAGTTGCCGAC 58.192 50.000 0.0 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1406 2053 0.892063 GAGGTATCGGAGATCCTGCC 59.108 60.000 0.00 0.0 45.12 4.85 R
2110 2793 2.048603 GGCATGCCCAGACCAAGTC 61.049 63.158 27.24 0.0 0.00 3.01 R
3103 4106 2.438795 CCTTCCCGCCTTTCCCAA 59.561 61.111 0.00 0.0 0.00 4.12 R
3588 4669 2.038387 AACAGACAGGAACACCACAC 57.962 50.000 0.00 0.0 0.00 3.82 R
4642 5741 0.036022 AAGCTGCACCCAGAAGAGAC 59.964 55.000 1.02 0.0 41.77 3.36 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
75 77 2.934553 GGAAGGTCGGCTGTTAATGTAC 59.065 50.000 0.00 0.00 0.00 2.90
76 78 3.592059 GAAGGTCGGCTGTTAATGTACA 58.408 45.455 0.00 0.00 0.00 2.90
167 360 1.937546 GCCTCACTTTGGATTGCCCG 61.938 60.000 0.00 0.00 37.93 6.13
302 519 4.399303 GCCTAACTTGATATGTGGCAAAGT 59.601 41.667 0.00 0.00 38.79 2.66
303 520 5.677091 GCCTAACTTGATATGTGGCAAAGTG 60.677 44.000 1.09 0.00 38.79 3.16
304 521 5.415701 CCTAACTTGATATGTGGCAAAGTGT 59.584 40.000 1.09 0.00 0.00 3.55
305 522 4.771590 ACTTGATATGTGGCAAAGTGTG 57.228 40.909 0.00 0.00 0.00 3.82
306 523 3.507233 ACTTGATATGTGGCAAAGTGTGG 59.493 43.478 0.00 0.00 0.00 4.17
443 660 7.012704 GCCTATTCTGAAATATCACATGTGTGT 59.987 37.037 24.63 16.75 45.76 3.72
510 727 0.878416 GAACGGCTTACAACATGCCA 59.122 50.000 0.00 0.00 45.72 4.92
608 934 8.640291 GTTATCTATTTCGCAGCATCTTAGTAC 58.360 37.037 0.00 0.00 0.00 2.73
622 948 6.452242 CATCTTAGTACCACACACTACAACA 58.548 40.000 0.00 0.00 0.00 3.33
910 1334 4.143137 GGCACAATTAAAGTGAAATTGCGG 60.143 41.667 13.70 3.47 44.52 5.69
932 1356 4.932799 GGGGCGCAAATAAAGTAAAATTGT 59.067 37.500 10.83 0.00 0.00 2.71
1016 1440 2.348472 TCATCCCACCTCCAACTTTCT 58.652 47.619 0.00 0.00 0.00 2.52
1111 1535 1.129917 TCCGAACACTAACAACCCCA 58.870 50.000 0.00 0.00 0.00 4.96
1122 1546 1.167033 ACAACCCCAATCCTCCCTTT 58.833 50.000 0.00 0.00 0.00 3.11
1128 1552 2.292455 CCCCAATCCTCCCTTTGACATT 60.292 50.000 0.00 0.00 0.00 2.71
1145 1569 5.556915 TGACATTGGTATTCTCTTCGGTTT 58.443 37.500 0.00 0.00 0.00 3.27
1295 1843 1.777272 GCAGGTTCTTCATCCCCCTAT 59.223 52.381 0.00 0.00 0.00 2.57
1296 1844 2.487986 GCAGGTTCTTCATCCCCCTATG 60.488 54.545 0.00 0.00 0.00 2.23
1297 1845 1.777272 AGGTTCTTCATCCCCCTATGC 59.223 52.381 0.00 0.00 0.00 3.14
1298 1846 1.202940 GGTTCTTCATCCCCCTATGCC 60.203 57.143 0.00 0.00 0.00 4.40
1299 1847 0.764890 TTCTTCATCCCCCTATGCCG 59.235 55.000 0.00 0.00 0.00 5.69
1300 1848 1.302832 CTTCATCCCCCTATGCCGC 60.303 63.158 0.00 0.00 0.00 6.53
1301 1849 3.177194 TTCATCCCCCTATGCCGCG 62.177 63.158 0.00 0.00 0.00 6.46
1317 1865 2.825836 CGCCCAGCCATGTCCTTC 60.826 66.667 0.00 0.00 0.00 3.46
1318 1866 2.679716 GCCCAGCCATGTCCTTCT 59.320 61.111 0.00 0.00 0.00 2.85
1319 1867 1.452833 GCCCAGCCATGTCCTTCTC 60.453 63.158 0.00 0.00 0.00 2.87
1406 2053 0.179108 GGCAGCTACCTTCACTACCG 60.179 60.000 0.00 0.00 0.00 4.02
1566 2243 1.961277 AAACCTGAACCTGAGCGCG 60.961 57.895 0.00 0.00 0.00 6.86
1608 2285 1.080093 CCGCTACCTTCAGAACGCA 60.080 57.895 0.00 0.00 0.00 5.24
1668 2345 2.676471 GCCATGCCAAACCGGAGT 60.676 61.111 9.46 0.00 36.56 3.85
1813 2495 8.828644 GTCCTGCTATATGATGATTGATGATTC 58.171 37.037 0.00 0.00 0.00 2.52
2110 2793 7.915508 TCTTATGTTATGTTTTATGTCTGGCG 58.084 34.615 0.00 0.00 0.00 5.69
2203 3073 1.838715 ACAGCTCTGCTCCATGAGAAT 59.161 47.619 0.00 0.00 36.40 2.40
2222 3092 8.225603 TGAGAATATCCTTTGGTATTTGCTTC 57.774 34.615 0.00 0.00 0.00 3.86
2226 3096 5.904362 ATCCTTTGGTATTTGCTTCTGTC 57.096 39.130 0.00 0.00 0.00 3.51
2260 3146 3.254060 CTTGTGTCTGCTAGCACGTTAT 58.746 45.455 14.93 0.00 38.36 1.89
2591 3550 2.866762 GTGAAAGGACACTCCATATCGC 59.133 50.000 0.00 0.00 39.61 4.58
2758 3718 9.774742 GCACTAAAATTTACCAGATAGTTGAAG 57.225 33.333 0.00 0.00 0.00 3.02
2834 3794 6.831976 ACAAGAACCTCATATATCACTTCCC 58.168 40.000 0.00 0.00 0.00 3.97
2901 3872 3.441572 AGTCAAATGGGAAAGCTTCATCG 59.558 43.478 0.00 0.00 0.00 3.84
2926 3898 4.178956 AGCCTAAAAACTGGTGGAAAGA 57.821 40.909 0.00 0.00 0.00 2.52
2969 3941 7.777440 TGGTATGGATGCATCATTTTGTACTTA 59.223 33.333 27.25 7.70 0.00 2.24
3002 3974 1.808411 TCCATTCAAGAGTTGCCGAC 58.192 50.000 0.00 0.00 0.00 4.79
3103 4106 2.279173 AGGAGGGAAGGCATTTAGTGT 58.721 47.619 0.00 0.00 0.00 3.55
3197 4200 3.754965 TGGTCAGTTCCTTCCATTGAAG 58.245 45.455 0.00 0.00 46.29 3.02
3204 4207 6.012508 TCAGTTCCTTCCATTGAAGTATCCTT 60.013 38.462 5.86 0.00 45.45 3.36
3588 4669 8.903570 TGTTATGTTCCGCTAATAATTGTTTG 57.096 30.769 0.00 0.00 0.00 2.93
3600 4681 6.478512 AATAATTGTTTGTGTGGTGTTCCT 57.521 33.333 0.00 0.00 34.23 3.36
3758 4839 7.250445 TCCTTTGTTTCGGTTAAGAACTAAC 57.750 36.000 0.00 0.00 39.45 2.34
3870 4954 7.553044 ACCTCTTAAAGACTATGGTGTTAATGC 59.447 37.037 0.00 0.00 0.00 3.56
3899 4983 3.819337 GGTTCGTAAGCCTTCTTTTCCTT 59.181 43.478 0.00 0.00 33.85 3.36
3917 5001 6.688073 TTCCTTTCACCTTCTTGTATCTCT 57.312 37.500 0.00 0.00 0.00 3.10
3938 5022 7.334090 TCTCTTTTCCCTCATCTCAAACATAG 58.666 38.462 0.00 0.00 0.00 2.23
3943 5027 4.709886 TCCCTCATCTCAAACATAGAACGA 59.290 41.667 0.00 0.00 0.00 3.85
4035 5119 3.017442 CTGATACCGTCTCTCAAGGTCA 58.983 50.000 0.00 0.00 39.31 4.02
4255 5345 0.898320 CCACACCTCTTCCTGATCGT 59.102 55.000 0.00 0.00 0.00 3.73
4335 5426 1.770658 TGATCGGGCAATGAAGGATCT 59.229 47.619 0.00 0.00 35.64 2.75
4422 5516 7.057903 CGAAATCAAGTTGTGTGTATGTAAACG 59.942 37.037 2.11 0.00 0.00 3.60
4464 5558 1.270907 CTCTAGGTCTGGCTGGTTGT 58.729 55.000 0.00 0.00 0.00 3.32
4642 5741 5.388890 GCTGTTTACTTCTCTGTGAATCGTG 60.389 44.000 0.00 0.00 33.71 4.35
4660 5759 1.123861 TGTCTCTTCTGGGTGCAGCT 61.124 55.000 16.65 0.00 0.00 4.24
4716 5817 2.848691 CTCTGGAGGGCAGAATGAATC 58.151 52.381 0.00 0.00 39.69 2.52
4730 5831 6.227298 AGAATGAATCTGTAGGTTCATCGT 57.773 37.500 17.95 6.36 42.52 3.73
5175 6313 6.461509 CCTGTTTTCCTAGTTTTGCATTGAGT 60.462 38.462 0.00 0.00 0.00 3.41
5176 6314 6.872920 TGTTTTCCTAGTTTTGCATTGAGTT 58.127 32.000 0.00 0.00 0.00 3.01
5177 6315 7.327214 TGTTTTCCTAGTTTTGCATTGAGTTT 58.673 30.769 0.00 0.00 0.00 2.66
5178 6316 7.277539 TGTTTTCCTAGTTTTGCATTGAGTTTG 59.722 33.333 0.00 0.00 0.00 2.93
5179 6317 6.707440 TTCCTAGTTTTGCATTGAGTTTGA 57.293 33.333 0.00 0.00 0.00 2.69
5180 6318 6.899393 TCCTAGTTTTGCATTGAGTTTGAT 57.101 33.333 0.00 0.00 0.00 2.57
5204 6342 7.712204 TTCCTTTCTCTAACCTGTTTGTTTT 57.288 32.000 0.00 0.00 0.00 2.43
5255 6393 4.401202 TCGATTGCCACTGAAGTATGTCTA 59.599 41.667 0.00 0.00 0.00 2.59
5302 6440 6.122277 TGAAAATGGCTCGGATCTAGATTTT 58.878 36.000 6.70 0.76 0.00 1.82
5489 6642 3.387397 CCTCGAAGACTACAAAAACGGT 58.613 45.455 0.00 0.00 0.00 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 77 5.446143 TTAGTTACCAACCAAACATGCTG 57.554 39.130 0.00 0.00 0.00 4.41
76 78 6.454795 CAATTAGTTACCAACCAAACATGCT 58.545 36.000 0.00 0.00 0.00 3.79
167 360 1.305930 AAGTGCGGCGAAATTCCCTC 61.306 55.000 12.98 0.00 0.00 4.30
202 395 7.979115 TTCTTTTGTTCAAAATAAGTCCACG 57.021 32.000 10.46 0.00 0.00 4.94
302 519 3.208383 CAGCCACACGTTGCCACA 61.208 61.111 0.00 0.00 0.00 4.17
303 520 3.964875 CCAGCCACACGTTGCCAC 61.965 66.667 0.00 0.00 0.00 5.01
305 522 4.947147 TCCCAGCCACACGTTGCC 62.947 66.667 0.00 0.00 0.00 4.52
306 523 2.904866 TTCCCAGCCACACGTTGC 60.905 61.111 0.00 0.00 0.00 4.17
307 524 2.551912 GGTTCCCAGCCACACGTTG 61.552 63.158 0.00 0.00 0.00 4.10
308 525 2.203294 GGTTCCCAGCCACACGTT 60.203 61.111 0.00 0.00 0.00 3.99
309 526 2.958578 CTTGGTTCCCAGCCACACGT 62.959 60.000 0.00 0.00 35.46 4.49
310 527 2.203280 TTGGTTCCCAGCCACACG 60.203 61.111 0.00 0.00 35.46 4.49
311 528 2.564721 GCTTGGTTCCCAGCCACAC 61.565 63.158 3.87 0.00 35.46 3.82
443 660 3.610040 ATCACAGAACCACGAGCATAA 57.390 42.857 0.00 0.00 0.00 1.90
559 776 7.334844 ACCTATTACTTCAAATAAGCAAGGC 57.665 36.000 0.00 0.00 0.00 4.35
608 934 4.335315 AGACAACAATGTTGTAGTGTGTGG 59.665 41.667 28.90 1.70 41.31 4.17
622 948 4.503734 CACGCATTTCAACAAGACAACAAT 59.496 37.500 0.00 0.00 0.00 2.71
716 1044 5.355071 TCTTTGGTGATAGTGCTGCTAAATG 59.645 40.000 0.00 0.00 32.72 2.32
796 1124 5.174037 ACCCATAAGATCTCGAAACCAAA 57.826 39.130 0.00 0.00 0.00 3.28
910 1334 5.163903 CCACAATTTTACTTTATTTGCGCCC 60.164 40.000 4.18 0.00 0.00 6.13
932 1356 1.260538 TTTGTTGCTGTTGTGCCCCA 61.261 50.000 0.00 0.00 0.00 4.96
1016 1440 1.437149 TGGAGAAGAGGGGAAGAGGAA 59.563 52.381 0.00 0.00 0.00 3.36
1111 1535 3.833559 ACCAATGTCAAAGGGAGGATT 57.166 42.857 0.00 0.00 0.00 3.01
1122 1546 4.819105 ACCGAAGAGAATACCAATGTCA 57.181 40.909 0.00 0.00 0.00 3.58
1128 1552 2.304761 AGGCAAACCGAAGAGAATACCA 59.695 45.455 0.00 0.00 42.76 3.25
1145 1569 4.096003 GCGCAGGGTTAGGAGGCA 62.096 66.667 0.30 0.00 0.00 4.75
1300 1848 2.825836 GAAGGACATGGCTGGGCG 60.826 66.667 0.00 0.00 0.00 6.13
1301 1849 1.452833 GAGAAGGACATGGCTGGGC 60.453 63.158 0.00 0.00 0.00 5.36
1302 1850 1.225704 GGAGAAGGACATGGCTGGG 59.774 63.158 0.00 0.00 0.00 4.45
1303 1851 0.549950 ATGGAGAAGGACATGGCTGG 59.450 55.000 0.00 0.00 0.00 4.85
1304 1852 1.676746 CATGGAGAAGGACATGGCTG 58.323 55.000 0.00 0.00 40.50 4.85
1305 1853 0.106819 GCATGGAGAAGGACATGGCT 60.107 55.000 0.00 0.00 43.50 4.75
1306 1854 2.412605 GCATGGAGAAGGACATGGC 58.587 57.895 0.00 0.00 43.50 4.40
1307 1855 0.466922 GGGCATGGAGAAGGACATGG 60.467 60.000 0.00 0.00 43.50 3.66
1308 1856 0.466922 GGGGCATGGAGAAGGACATG 60.467 60.000 0.00 0.00 45.49 3.21
1309 1857 1.925888 GGGGCATGGAGAAGGACAT 59.074 57.895 0.00 0.00 0.00 3.06
1310 1858 2.669133 CGGGGCATGGAGAAGGACA 61.669 63.158 0.00 0.00 0.00 4.02
1311 1859 2.190578 CGGGGCATGGAGAAGGAC 59.809 66.667 0.00 0.00 0.00 3.85
1313 1861 4.883354 GGCGGGGCATGGAGAAGG 62.883 72.222 0.00 0.00 0.00 3.46
1314 1862 4.883354 GGGCGGGGCATGGAGAAG 62.883 72.222 0.00 0.00 0.00 2.85
1333 1881 1.226311 GGAATGGGGAAGGAGATGGT 58.774 55.000 0.00 0.00 0.00 3.55
1406 2053 0.892063 GAGGTATCGGAGATCCTGCC 59.108 60.000 0.00 0.00 45.12 4.85
1780 2461 5.604565 TCATCATATAGCAGGACACACAAG 58.395 41.667 0.00 0.00 0.00 3.16
1813 2495 6.472486 CAGCATTCATTTTGATGAAGCTGTAG 59.528 38.462 25.17 13.58 45.12 2.74
2110 2793 2.048603 GGCATGCCCAGACCAAGTC 61.049 63.158 27.24 0.00 0.00 3.01
2203 3073 6.480763 TGACAGAAGCAAATACCAAAGGATA 58.519 36.000 0.00 0.00 0.00 2.59
2222 3092 8.815189 CAGACACAAGTGATATTCTTATGACAG 58.185 37.037 7.28 0.00 0.00 3.51
2226 3096 7.783090 AGCAGACACAAGTGATATTCTTATG 57.217 36.000 7.28 0.46 0.00 1.90
2260 3146 4.891756 TGATCATGTCAGACAGATAGCTCA 59.108 41.667 9.64 3.93 31.80 4.26
2583 3542 3.248602 GCCTTCAACTACAAGCGATATGG 59.751 47.826 0.00 0.00 0.00 2.74
2591 3550 4.024556 CAGTGTCTTGCCTTCAACTACAAG 60.025 45.833 0.00 0.00 40.66 3.16
2747 3707 9.660180 GACTTATTCAGTTTCCTTCAACTATCT 57.340 33.333 0.00 0.00 35.10 1.98
2758 3718 9.774742 GTATTCACATTGACTTATTCAGTTTCC 57.225 33.333 0.00 0.00 35.01 3.13
2901 3872 4.230745 TCCACCAGTTTTTAGGCTATCC 57.769 45.455 0.00 0.00 0.00 2.59
2926 3898 7.872138 TCCATACCATTAGAAAAGGATGAAGT 58.128 34.615 0.00 0.00 0.00 3.01
2969 3941 8.162085 ACTCTTGAATGGATGAATGTATAGCAT 58.838 33.333 0.00 0.00 40.03 3.79
3103 4106 2.438795 CCTTCCCGCCTTTCCCAA 59.561 61.111 0.00 0.00 0.00 4.12
3365 4395 2.719426 ACGTTTAGACAGAAGGGACG 57.281 50.000 0.00 0.00 35.39 4.79
3588 4669 2.038387 AACAGACAGGAACACCACAC 57.962 50.000 0.00 0.00 0.00 3.82
3600 4681 3.492656 GGAGTCACACAAGCTAACAGACA 60.493 47.826 0.00 0.00 0.00 3.41
3656 4737 5.046448 TGCATATTGAAAGGCCTTGTCAAAT 60.046 36.000 29.95 23.11 35.07 2.32
3744 4825 8.328864 GCAATCTCTAATGTTAGTTCTTAACCG 58.671 37.037 0.16 0.00 40.80 4.44
3758 4839 6.194463 CGTAACCACAATGCAATCTCTAATG 58.806 40.000 0.00 0.00 0.00 1.90
3870 4954 1.810030 GGCTTACGAACCTCGCCAG 60.810 63.158 0.00 0.00 45.12 4.85
3899 4983 6.044404 AGGGAAAAGAGATACAAGAAGGTGAA 59.956 38.462 0.00 0.00 0.00 3.18
3917 5001 6.371548 CGTTCTATGTTTGAGATGAGGGAAAA 59.628 38.462 0.00 0.00 0.00 2.29
3938 5022 6.201425 TCTGTTACAGGTACAACAAATCGTTC 59.799 38.462 12.79 0.00 34.43 3.95
3943 5027 7.609918 TGCATATCTGTTACAGGTACAACAAAT 59.390 33.333 12.79 0.00 34.43 2.32
4007 5091 3.565902 TGAGAGACGGTATCAGTGCATAG 59.434 47.826 5.47 0.00 0.00 2.23
4335 5426 0.470456 ACCACAGAGACCCCGTTACA 60.470 55.000 0.00 0.00 0.00 2.41
4464 5558 7.338449 ACAAGCTAGTTTCCAAAAGTCAAAGTA 59.662 33.333 0.00 0.00 0.00 2.24
4642 5741 0.036022 AAGCTGCACCCAGAAGAGAC 59.964 55.000 1.02 0.00 41.77 3.36
4716 5817 7.033791 TCTAGCTAAAAACGATGAACCTACAG 58.966 38.462 0.00 0.00 0.00 2.74
4730 5831 7.769044 AGGATTGCTAATCGTTCTAGCTAAAAA 59.231 33.333 12.18 0.00 41.96 1.94
4772 5900 8.947055 AACTGCTGAAACTACAAATTCAAATT 57.053 26.923 0.00 0.00 35.31 1.82
5037 6168 4.081642 GCAGATATATCTAAAGGCACCGGA 60.082 45.833 14.92 0.00 34.85 5.14
5039 6170 4.867047 CAGCAGATATATCTAAAGGCACCG 59.133 45.833 14.92 1.24 34.85 4.94
5175 6313 7.559897 ACAAACAGGTTAGAGAAAGGAATCAAA 59.440 33.333 0.00 0.00 0.00 2.69
5176 6314 7.060421 ACAAACAGGTTAGAGAAAGGAATCAA 58.940 34.615 0.00 0.00 0.00 2.57
5177 6315 6.601332 ACAAACAGGTTAGAGAAAGGAATCA 58.399 36.000 0.00 0.00 0.00 2.57
5178 6316 7.511959 AACAAACAGGTTAGAGAAAGGAATC 57.488 36.000 0.00 0.00 0.00 2.52
5179 6317 7.898014 AAACAAACAGGTTAGAGAAAGGAAT 57.102 32.000 0.00 0.00 0.00 3.01
5180 6318 7.394923 TGAAAACAAACAGGTTAGAGAAAGGAA 59.605 33.333 0.00 0.00 0.00 3.36
5255 6393 1.203994 GCAATTGGCTGAAGCATGTCT 59.796 47.619 7.72 0.00 44.36 3.41
5415 6568 7.491682 CAGTTTCCTTCCAGATGAAAGAAAAA 58.508 34.615 1.48 0.00 42.27 1.94
5425 6578 2.560105 GCAAAGCAGTTTCCTTCCAGAT 59.440 45.455 0.00 0.00 0.00 2.90
5489 6642 3.762407 AGTTGCACAGTATACACCACA 57.238 42.857 5.50 0.00 0.00 4.17
5593 6748 4.602340 ACTCCTTCAACTCGCTCTAAAA 57.398 40.909 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.