Multiple sequence alignment - TraesCS6A01G206000

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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 TraesCS6A01G206000 chr6A 100.000 4697 0 0 1 4697 362169821 362165125 0.000000e+00 8674.0
1 TraesCS6A01G206000 chr6A 96.040 707 27 1 3991 4697 296892577 296893282 0.000000e+00 1149.0
2 TraesCS6A01G206000 chr6A 96.040 707 27 1 3991 4697 558018951 558018246 0.000000e+00 1149.0
3 TraesCS6A01G206000 chr5D 95.931 2851 106 7 1146 3991 270485998 270488843 0.000000e+00 4614.0
4 TraesCS6A01G206000 chr5D 92.465 929 66 2 1 925 276038991 276038063 0.000000e+00 1325.0
5 TraesCS6A01G206000 chr5D 92.549 926 64 3 1 925 421821821 421820900 0.000000e+00 1323.0
6 TraesCS6A01G206000 chr3D 96.711 2554 64 10 1446 3991 137630182 137632723 0.000000e+00 4233.0
7 TraesCS6A01G206000 chr3D 93.620 2696 141 19 1302 3991 157824995 157827665 0.000000e+00 3997.0
8 TraesCS6A01G206000 chr3D 92.665 927 65 3 1 925 69415440 69416365 0.000000e+00 1332.0
9 TraesCS6A01G206000 chr3D 92.657 926 67 1 1 925 95976347 95975422 0.000000e+00 1332.0
10 TraesCS6A01G206000 chr3D 94.150 547 30 2 934 1478 137629636 137630182 0.000000e+00 832.0
11 TraesCS6A01G206000 chr6B 91.248 3062 209 44 924 3948 195458571 195461610 0.000000e+00 4115.0
12 TraesCS6A01G206000 chr6B 81.287 342 45 6 2902 3224 611343713 611343372 4.660000e-65 259.0
13 TraesCS6A01G206000 chr2A 95.947 2344 65 7 1650 3991 431666052 431663737 0.000000e+00 3775.0
14 TraesCS6A01G206000 chr2A 96.747 707 23 0 3991 4697 758475760 758476466 0.000000e+00 1179.0
15 TraesCS6A01G206000 chr2A 96.181 707 27 0 3991 4697 447723278 447723984 0.000000e+00 1157.0
16 TraesCS6A01G206000 chr2A 94.444 396 22 0 1083 1478 431666708 431666313 1.120000e-170 610.0
17 TraesCS6A01G206000 chr2A 87.097 434 53 3 924 1356 129754735 129754304 5.460000e-134 488.0
18 TraesCS6A01G206000 chr2A 93.043 230 13 2 1446 1675 431666313 431666087 2.710000e-87 333.0
19 TraesCS6A01G206000 chr2A 94.286 175 9 1 924 1097 431666899 431666725 2.790000e-67 267.0
20 TraesCS6A01G206000 chr5A 97.149 2175 52 7 1446 3617 294708792 294710959 0.000000e+00 3664.0
21 TraesCS6A01G206000 chr5A 92.432 555 33 1 924 1478 294708247 294708792 0.000000e+00 784.0
22 TraesCS6A01G206000 chr5A 97.665 257 5 1 3735 3991 294710978 294711233 1.550000e-119 440.0
23 TraesCS6A01G206000 chr5A 88.119 303 30 5 1883 2183 345359957 345359659 5.780000e-94 355.0
24 TraesCS6A01G206000 chr2B 92.404 2554 153 23 1446 3991 231299025 231296505 0.000000e+00 3603.0
25 TraesCS6A01G206000 chr2B 86.682 443 57 2 924 1366 231301153 231300713 1.520000e-134 490.0
26 TraesCS6A01G206000 chr2B 94.017 117 7 0 1362 1478 231299141 231299025 1.340000e-40 178.0
27 TraesCS6A01G206000 chr2B 84.314 153 14 8 1681 1830 491568962 491568817 1.760000e-29 141.0
28 TraesCS6A01G206000 chr7D 92.657 926 65 3 1 925 58527873 58528796 0.000000e+00 1330.0
29 TraesCS6A01G206000 chr7D 92.557 927 66 3 1 925 463218619 463217694 0.000000e+00 1327.0
30 TraesCS6A01G206000 chr7D 90.741 54 5 0 1777 1830 436397346 436397399 6.520000e-09 73.1
31 TraesCS6A01G206000 chr2D 92.549 926 67 2 1 925 188535045 188534121 0.000000e+00 1327.0
32 TraesCS6A01G206000 chr2D 93.617 47 3 0 3098 3144 645291712 645291758 2.340000e-08 71.3
33 TraesCS6A01G206000 chr6D 92.449 927 67 3 1 925 155587174 155586249 0.000000e+00 1321.0
34 TraesCS6A01G206000 chr6D 88.532 436 45 4 924 1356 226923700 226923267 1.500000e-144 523.0
35 TraesCS6A01G206000 chr4D 92.441 926 69 1 1 925 403786890 403785965 0.000000e+00 1321.0
36 TraesCS6A01G206000 chr4D 86.570 484 54 9 924 1402 280920443 280920920 1.500000e-144 523.0
37 TraesCS6A01G206000 chr4D 87.986 283 33 1 2374 2656 144438852 144439133 2.710000e-87 333.0
38 TraesCS6A01G206000 chr1A 96.610 708 24 0 3990 4697 501007117 501006410 0.000000e+00 1175.0
39 TraesCS6A01G206000 chr1A 96.181 707 26 1 3991 4697 318621688 318620983 0.000000e+00 1155.0
40 TraesCS6A01G206000 chr1A 88.732 284 32 0 2374 2657 272314319 272314036 9.670000e-92 348.0
41 TraesCS6A01G206000 chr1A 83.193 357 30 12 1828 2183 186719046 186718719 2.750000e-77 300.0
42 TraesCS6A01G206000 chr3A 96.181 707 27 0 3991 4697 386468889 386468183 0.000000e+00 1157.0
43 TraesCS6A01G206000 chr3A 96.040 707 28 0 3991 4697 386493724 386493018 0.000000e+00 1151.0
44 TraesCS6A01G206000 chr7A 96.045 708 26 2 3991 4697 553304159 553303453 0.000000e+00 1151.0
45 TraesCS6A01G206000 chr7A 83.193 357 33 11 1828 2183 287639832 287639502 7.640000e-78 302.0
46 TraesCS6A01G206000 chr3B 85.417 480 63 5 924 1402 271284966 271285439 4.220000e-135 492.0
47 TraesCS6A01G206000 chr5B 83.708 356 32 9 1828 2183 360595123 360595452 3.530000e-81 313.0
48 TraesCS6A01G206000 chr1B 91.026 78 6 1 1398 1475 288551501 288551425 2.310000e-18 104.0
49 TraesCS6A01G206000 chr4A 83.478 115 12 4 1675 1784 319199041 319198929 2.990000e-17 100.0


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 TraesCS6A01G206000 chr6A 362165125 362169821 4696 True 8674.000000 8674 100.000000 1 4697 1 chr6A.!!$R1 4696
1 TraesCS6A01G206000 chr6A 296892577 296893282 705 False 1149.000000 1149 96.040000 3991 4697 1 chr6A.!!$F1 706
2 TraesCS6A01G206000 chr6A 558018246 558018951 705 True 1149.000000 1149 96.040000 3991 4697 1 chr6A.!!$R2 706
3 TraesCS6A01G206000 chr5D 270485998 270488843 2845 False 4614.000000 4614 95.931000 1146 3991 1 chr5D.!!$F1 2845
4 TraesCS6A01G206000 chr5D 276038063 276038991 928 True 1325.000000 1325 92.465000 1 925 1 chr5D.!!$R1 924
5 TraesCS6A01G206000 chr5D 421820900 421821821 921 True 1323.000000 1323 92.549000 1 925 1 chr5D.!!$R2 924
6 TraesCS6A01G206000 chr3D 157824995 157827665 2670 False 3997.000000 3997 93.620000 1302 3991 1 chr3D.!!$F2 2689
7 TraesCS6A01G206000 chr3D 137629636 137632723 3087 False 2532.500000 4233 95.430500 934 3991 2 chr3D.!!$F3 3057
8 TraesCS6A01G206000 chr3D 69415440 69416365 925 False 1332.000000 1332 92.665000 1 925 1 chr3D.!!$F1 924
9 TraesCS6A01G206000 chr3D 95975422 95976347 925 True 1332.000000 1332 92.657000 1 925 1 chr3D.!!$R1 924
10 TraesCS6A01G206000 chr6B 195458571 195461610 3039 False 4115.000000 4115 91.248000 924 3948 1 chr6B.!!$F1 3024
11 TraesCS6A01G206000 chr2A 431663737 431666899 3162 True 1246.250000 3775 94.430000 924 3991 4 chr2A.!!$R2 3067
12 TraesCS6A01G206000 chr2A 758475760 758476466 706 False 1179.000000 1179 96.747000 3991 4697 1 chr2A.!!$F2 706
13 TraesCS6A01G206000 chr2A 447723278 447723984 706 False 1157.000000 1157 96.181000 3991 4697 1 chr2A.!!$F1 706
14 TraesCS6A01G206000 chr5A 294708247 294711233 2986 False 1629.333333 3664 95.748667 924 3991 3 chr5A.!!$F1 3067
15 TraesCS6A01G206000 chr2B 231296505 231301153 4648 True 1423.666667 3603 91.034333 924 3991 3 chr2B.!!$R2 3067
16 TraesCS6A01G206000 chr7D 58527873 58528796 923 False 1330.000000 1330 92.657000 1 925 1 chr7D.!!$F1 924
17 TraesCS6A01G206000 chr7D 463217694 463218619 925 True 1327.000000 1327 92.557000 1 925 1 chr7D.!!$R1 924
18 TraesCS6A01G206000 chr2D 188534121 188535045 924 True 1327.000000 1327 92.549000 1 925 1 chr2D.!!$R1 924
19 TraesCS6A01G206000 chr6D 155586249 155587174 925 True 1321.000000 1321 92.449000 1 925 1 chr6D.!!$R1 924
20 TraesCS6A01G206000 chr4D 403785965 403786890 925 True 1321.000000 1321 92.441000 1 925 1 chr4D.!!$R1 924
21 TraesCS6A01G206000 chr1A 501006410 501007117 707 True 1175.000000 1175 96.610000 3990 4697 1 chr1A.!!$R4 707
22 TraesCS6A01G206000 chr1A 318620983 318621688 705 True 1155.000000 1155 96.181000 3991 4697 1 chr1A.!!$R3 706
23 TraesCS6A01G206000 chr3A 386468183 386468889 706 True 1157.000000 1157 96.181000 3991 4697 1 chr3A.!!$R1 706
24 TraesCS6A01G206000 chr3A 386493018 386493724 706 True 1151.000000 1151 96.040000 3991 4697 1 chr3A.!!$R2 706
25 TraesCS6A01G206000 chr7A 553303453 553304159 706 True 1151.000000 1151 96.045000 3991 4697 1 chr7A.!!$R2 706

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
608 613 0.804989 CTCCGATGCTCAAACCCAAC 59.195 55.000 0.00 0.0 0.0 3.77 F
1254 1301 0.107066 ATCCAATCACTCGCATGCCA 60.107 50.000 13.15 0.0 0.0 4.92 F
1397 3023 1.045911 GCTCCTCCATCCTCCGACTT 61.046 60.000 0.00 0.0 0.0 3.01 F
2878 4613 1.553248 ACAATGCGCCAGGTTCTACTA 59.447 47.619 4.18 0.0 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2263 3995 1.444836 TACATTCGGAAAAGTGGGCG 58.555 50.000 8.81 0.0 0.00 6.13 R
2830 4565 3.382048 ACAGTCGGAGGTTTGTAAGTC 57.618 47.619 0.00 0.0 0.00 3.01 R
3093 4828 5.740513 GCGCCTTCTCCTTAAGTTCATCTAT 60.741 44.000 0.00 0.0 0.00 1.98 R
4055 5800 1.266989 CGTTTGTCTTCAAAGCTCCCC 59.733 52.381 0.00 0.0 43.04 4.81 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
61 62 1.283905 GGGCTTAATACACCACCACCT 59.716 52.381 0.00 0.00 0.00 4.00
82 83 4.405036 CCTCCTAAGGTGGTAGAGGTAAAC 59.595 50.000 0.00 0.00 37.94 2.01
102 103 8.555361 GGTAAACTCTCTTATGAAGATCAATGC 58.445 37.037 0.00 0.00 36.82 3.56
146 147 3.750599 GCACCCTAGCCAATGCCTTTATA 60.751 47.826 0.00 0.00 38.69 0.98
338 339 7.643579 ACAAGTTGCTAAATCTCAAAGAGAAC 58.356 34.615 1.81 0.00 42.27 3.01
343 344 6.701340 TGCTAAATCTCAAAGAGAACTGCTA 58.299 36.000 0.29 0.00 42.27 3.49
423 424 2.292828 ATGACCCAGGAACCACTTTG 57.707 50.000 0.00 0.00 0.00 2.77
564 569 4.899457 TGAACCTGAAGTAGAGAAACCTCA 59.101 41.667 0.00 0.00 33.16 3.86
599 604 3.818210 TGAGACTTCTATCTCCGATGCTC 59.182 47.826 0.53 0.00 43.94 4.26
604 609 3.735237 TCTATCTCCGATGCTCAAACC 57.265 47.619 0.00 0.00 0.00 3.27
608 613 0.804989 CTCCGATGCTCAAACCCAAC 59.195 55.000 0.00 0.00 0.00 3.77
626 631 4.335416 CCAACCTGGTAATGAACACTCAT 58.665 43.478 0.00 0.00 36.97 2.90
664 669 9.947669 GAAAAAGATAATGATGAGGTTCATGAG 57.052 33.333 0.00 0.00 37.20 2.90
665 670 9.690913 AAAAAGATAATGATGAGGTTCATGAGA 57.309 29.630 0.00 0.00 37.20 3.27
800 805 4.312443 TGCTAGAAAACACGGTAAGGAAG 58.688 43.478 0.00 0.00 0.00 3.46
801 806 4.039488 TGCTAGAAAACACGGTAAGGAAGA 59.961 41.667 0.00 0.00 0.00 2.87
887 893 7.201427 CGAAGAATTTGAACACTTTGCTGAAAA 60.201 33.333 0.00 0.00 0.00 2.29
936 942 9.088512 ACTCGCTTGACTGATTTAAAACTATAG 57.911 33.333 0.00 0.00 0.00 1.31
985 991 1.208052 CTCCCTCGATTTCCTGCTTCA 59.792 52.381 0.00 0.00 0.00 3.02
1092 1108 3.823873 TGTGGTAAGTTTACATGGCCAAG 59.176 43.478 10.96 8.43 35.37 3.61
1096 1143 3.525800 AAGTTTACATGGCCAAGGACT 57.474 42.857 10.96 8.84 0.00 3.85
1105 1152 2.846532 CCAAGGACTGGTGGGCTT 59.153 61.111 0.00 0.00 40.78 4.35
1216 1263 1.004200 CGTGGGTAACGCTTCCCTT 60.004 57.895 1.96 0.00 46.99 3.95
1243 1290 0.325484 CCCTTGGCCCAATCCAATCA 60.325 55.000 0.00 0.00 44.39 2.57
1254 1301 0.107066 ATCCAATCACTCGCATGCCA 60.107 50.000 13.15 0.00 0.00 4.92
1274 1321 1.076438 CAACCCTTCCTCCCTCCTTT 58.924 55.000 0.00 0.00 0.00 3.11
1311 1360 3.006728 CACGAACCCCAGCCCCTA 61.007 66.667 0.00 0.00 0.00 3.53
1325 1374 1.830071 GCCCCTATTCCTACGATCCCA 60.830 57.143 0.00 0.00 0.00 4.37
1397 3023 1.045911 GCTCCTCCATCCTCCGACTT 61.046 60.000 0.00 0.00 0.00 3.01
1478 3104 3.077556 AAGCCGCGTGAGGAGGAT 61.078 61.111 4.92 0.00 37.92 3.24
1495 3150 2.100989 GGATATACCTCGCCCGAGAAT 58.899 52.381 18.41 13.15 44.53 2.40
1498 3153 2.581216 ATACCTCGCCCGAGAATCTA 57.419 50.000 18.41 3.70 44.53 1.98
1647 3302 3.027170 GCGCATGTGAGTCCCAACG 62.027 63.158 11.26 0.00 0.00 4.10
1667 3332 4.843728 ACGATCTCACTCTCTCTTTCTCT 58.156 43.478 0.00 0.00 0.00 3.10
1811 3542 4.537688 AGAGAGGGATGGAAAAGATGTGAA 59.462 41.667 0.00 0.00 0.00 3.18
1971 3702 6.629515 GCTGTAGTGGGTCAATAGATTGTACA 60.630 42.308 0.00 0.00 38.84 2.90
2193 3925 6.059787 ACCATTAAATTATTTTGGGCTGCA 57.940 33.333 11.65 0.00 0.00 4.41
2236 3968 3.851976 AAGCGTGGTGTGTTTGTTTTA 57.148 38.095 0.00 0.00 0.00 1.52
2263 3995 4.383173 TCCTTTCGAACCCTCAAGTTAAC 58.617 43.478 0.00 0.00 0.00 2.01
2726 4461 6.093495 GCATTCAACTATACTTGGCTACACAA 59.907 38.462 0.00 0.00 0.00 3.33
2736 4471 6.254281 ACTTGGCTACACAAATGTAACATC 57.746 37.500 0.00 0.00 40.84 3.06
2878 4613 1.553248 ACAATGCGCCAGGTTCTACTA 59.447 47.619 4.18 0.00 0.00 1.82
2882 4617 1.553248 TGCGCCAGGTTCTACTACAAT 59.447 47.619 4.18 0.00 0.00 2.71
3077 4812 3.731136 GTGCGACAGGAAGCAACA 58.269 55.556 0.00 0.00 45.61 3.33
3093 4828 5.435686 AGCAACACTGAATATGGTTCCTA 57.564 39.130 0.00 0.00 0.00 2.94
3302 5041 1.202177 GCTGTAATGGTGTGGATTGCG 60.202 52.381 0.00 0.00 0.00 4.85
3317 5056 9.419297 GTGTGGATTGCGATATAAAGTTCTATA 57.581 33.333 0.00 0.00 0.00 1.31
3410 5149 9.277783 GTGATGAAGTAATTATCTTGGCTACAT 57.722 33.333 5.41 0.00 0.00 2.29
3502 5243 9.387123 CAATTGTAGTTTCTAGAAGCTCAAAAC 57.613 33.333 23.25 16.47 33.82 2.43
3639 5380 3.895041 GTGAAAAAGGTGGGATCTTTCCA 59.105 43.478 0.00 0.00 44.60 3.53
3642 5383 4.402616 AAAAGGTGGGATCTTTCCATCA 57.597 40.909 3.01 0.00 44.60 3.07
3652 5394 2.503331 TCTTTCCATCAGCTTTCGCAA 58.497 42.857 0.00 0.00 39.10 4.85
3740 5482 1.021202 CTTTGTGTTGTCGGCCTTGA 58.979 50.000 0.00 0.00 0.00 3.02
3767 5512 1.583556 TCTGGAGCTCTAATTGGCCA 58.416 50.000 14.64 0.00 0.00 5.36
3783 5528 3.936564 TGGCCAATGGACTTTTAAATGC 58.063 40.909 6.71 0.00 0.00 3.56
4061 5806 2.278332 AGTCTTCAAAACAGGGGAGC 57.722 50.000 0.00 0.00 0.00 4.70
4101 5846 8.995027 ATAGAAATGAACCTATAACCATGCAA 57.005 30.769 0.00 0.00 0.00 4.08
4171 5916 5.734855 GTGAAAGCACAAAGACTAACAGA 57.265 39.130 0.00 0.00 44.51 3.41
4362 6107 2.298163 GGTAGACCAGTTCCAACTTCGA 59.702 50.000 0.00 0.00 37.08 3.71
4515 6261 1.194781 ACCTCGCCCAATCACTCTGT 61.195 55.000 0.00 0.00 0.00 3.41
4607 6353 0.523072 TTAGAACGCGACGCCTAACT 59.477 50.000 15.93 10.93 0.00 2.24
4608 6354 1.368641 TAGAACGCGACGCCTAACTA 58.631 50.000 15.93 9.97 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 5.267587 GAGTTTACCTCTACCACCTTAGGA 58.732 45.833 4.77 0.00 37.22 2.94
82 83 9.708092 TCATTAGCATTGATCTTCATAAGAGAG 57.292 33.333 0.00 0.00 41.61 3.20
88 89 9.006839 GGATTGTCATTAGCATTGATCTTCATA 57.993 33.333 0.00 0.00 0.00 2.15
95 96 6.124340 TGTGAGGATTGTCATTAGCATTGAT 58.876 36.000 0.00 0.00 0.00 2.57
102 103 7.358066 GTGCATATTGTGAGGATTGTCATTAG 58.642 38.462 0.00 0.00 0.00 1.73
177 178 7.119605 TGTTTCATAACATTTGCATTGAAGC 57.880 32.000 4.32 0.00 39.29 3.86
365 366 4.580167 TGCAACTCTAACAGCAAAGTCATT 59.420 37.500 0.00 0.00 33.48 2.57
514 519 5.298777 AGAAGCATGCAAAGTCCTATCATTC 59.701 40.000 21.98 9.72 0.00 2.67
580 585 4.576216 TTGAGCATCGGAGATAGAAGTC 57.424 45.455 0.00 0.00 45.12 3.01
592 597 0.523072 CAGGTTGGGTTTGAGCATCG 59.477 55.000 0.00 0.00 38.61 3.84
599 604 3.639094 TGTTCATTACCAGGTTGGGTTTG 59.361 43.478 0.00 0.00 43.37 2.93
604 609 3.750371 TGAGTGTTCATTACCAGGTTGG 58.250 45.455 0.00 0.00 45.02 3.77
608 613 6.227298 ACTAGATGAGTGTTCATTACCAGG 57.773 41.667 0.00 0.00 44.01 4.45
800 805 4.776349 AGGTTTTTGAACCCATGGTTTTC 58.224 39.130 11.73 13.10 46.95 2.29
801 806 4.853468 AGGTTTTTGAACCCATGGTTTT 57.147 36.364 11.73 2.95 46.95 2.43
861 867 5.273170 TCAGCAAAGTGTTCAAATTCTTCG 58.727 37.500 0.00 0.00 0.00 3.79
887 893 1.613836 CAAAAAGACTGGCCTCAGCT 58.386 50.000 3.32 0.00 44.59 4.24
936 942 1.227118 GCGAGTTGGCTAGCCTCTC 60.227 63.158 33.07 31.92 37.38 3.20
985 991 0.033208 ACCATGATCCAACGGCCAAT 60.033 50.000 2.24 0.00 0.00 3.16
1092 1108 1.152756 AACACAAGCCCACCAGTCC 60.153 57.895 0.00 0.00 0.00 3.85
1096 1143 0.751277 CACAGAACACAAGCCCACCA 60.751 55.000 0.00 0.00 0.00 4.17
1105 1152 2.792500 CCAACAGGCACAGAACACA 58.208 52.632 0.00 0.00 0.00 3.72
1228 1275 0.394216 CGAGTGATTGGATTGGGCCA 60.394 55.000 0.00 0.00 35.78 5.36
1243 1290 2.672996 GGGTTGTGGCATGCGAGT 60.673 61.111 12.44 0.00 0.00 4.18
1254 1301 0.103876 AAGGAGGGAGGAAGGGTTGT 60.104 55.000 0.00 0.00 0.00 3.32
1274 1321 0.538516 GCGGCTGAGGGAGAGAGATA 60.539 60.000 0.00 0.00 0.00 1.98
1303 1352 1.550976 GGATCGTAGGAATAGGGGCTG 59.449 57.143 0.00 0.00 0.00 4.85
1311 1360 1.038280 GACCGTGGGATCGTAGGAAT 58.962 55.000 2.77 0.00 0.00 3.01
1386 3012 1.196012 GGGAGACAAAGTCGGAGGAT 58.804 55.000 0.00 0.00 37.67 3.24
1397 3023 2.242196 GGAGGATGAATTGGGGAGACAA 59.758 50.000 0.00 0.00 34.41 3.18
1478 3104 2.581216 AGATTCTCGGGCGAGGTATA 57.419 50.000 0.00 0.00 42.20 1.47
1495 3150 3.805145 AGGCCCTCCTCCCATAGA 58.195 61.111 0.00 0.00 38.72 1.98
1514 3169 3.073735 AGCCGCTCCTCTCTGGTG 61.074 66.667 0.00 0.00 37.07 4.17
1647 3302 4.260784 GCGAGAGAAAGAGAGAGTGAGATC 60.261 50.000 0.00 0.00 0.00 2.75
1667 3332 2.486203 GAGAGAGAGAGAAAGTGTGCGA 59.514 50.000 0.00 0.00 0.00 5.10
1811 3542 8.091449 CAGTTTACTCTTCTCTACTTGTTCCAT 58.909 37.037 0.00 0.00 0.00 3.41
1971 3702 5.972107 ATTTGACAATTAGCAGCTCAAGT 57.028 34.783 0.00 0.00 0.00 3.16
2193 3925 7.809806 GCTTTCATTTGCTACAGACATTAAAGT 59.190 33.333 0.00 0.00 0.00 2.66
2236 3968 4.202472 ACTTGAGGGTTCGAAAGGAAAGAT 60.202 41.667 0.00 0.00 36.14 2.40
2263 3995 1.444836 TACATTCGGAAAAGTGGGCG 58.555 50.000 8.81 0.00 0.00 6.13
2703 4438 8.677300 CATTTGTGTAGCCAAGTATAGTTGAAT 58.323 33.333 19.87 10.98 0.00 2.57
2736 4471 7.874940 TCAATAAACTGGAAGAGAAACACATG 58.125 34.615 0.00 0.00 37.43 3.21
2769 4504 9.753674 ACCAGATAGAACATTCAATCCTTAAAA 57.246 29.630 0.00 0.00 0.00 1.52
2830 4565 3.382048 ACAGTCGGAGGTTTGTAAGTC 57.618 47.619 0.00 0.00 0.00 3.01
2982 4717 5.954150 AGCACAATCTTAGGGAATGATTTGT 59.046 36.000 0.00 0.00 0.00 2.83
3077 4812 9.386122 AGTTCATCTATAGGAACCATATTCAGT 57.614 33.333 14.64 0.00 45.36 3.41
3093 4828 5.740513 GCGCCTTCTCCTTAAGTTCATCTAT 60.741 44.000 0.00 0.00 0.00 1.98
3193 4928 8.857694 TCCTTTATCGGTAAGTTCAAAGAAAT 57.142 30.769 0.00 0.00 0.00 2.17
3317 5056 7.572523 TTTCTGACAACACATCTCTTCAAAT 57.427 32.000 0.00 0.00 0.00 2.32
3403 5142 2.890808 TCGAGATTCACCATGTAGCC 57.109 50.000 0.00 0.00 0.00 3.93
3410 5149 4.223144 TGGGAGATTATCGAGATTCACCA 58.777 43.478 16.55 14.09 0.00 4.17
3479 5219 8.500753 TTGTTTTGAGCTTCTAGAAACTACAA 57.499 30.769 13.97 13.97 32.84 2.41
3652 5394 4.468868 TGCTCTATGATGCATATAGCCAGT 59.531 41.667 16.93 0.00 42.21 4.00
3740 5482 5.826737 CCAATTAGAGCTCCAGAACAATCAT 59.173 40.000 10.93 0.00 0.00 2.45
3767 5512 5.569428 GCAGGGAAGCATTTAAAAGTCCATT 60.569 40.000 10.30 0.00 0.00 3.16
3783 5528 5.567138 AAGAAACGAATATTGCAGGGAAG 57.433 39.130 0.00 0.00 0.00 3.46
3823 5568 5.667539 AGTATAAGAGCAAGCTCACAGAA 57.332 39.130 22.68 4.87 44.99 3.02
4024 5769 8.330466 TGAAGACTTTCATAAAAATCGCCTAA 57.670 30.769 0.00 0.00 38.37 2.69
4055 5800 1.266989 CGTTTGTCTTCAAAGCTCCCC 59.733 52.381 0.00 0.00 43.04 4.81
4061 5806 9.107367 GTTCATTTCTATCGTTTGTCTTCAAAG 57.893 33.333 0.00 0.00 43.04 2.77
4171 5916 1.683917 CTGATCCGTACTGCCTAGCTT 59.316 52.381 0.00 0.00 0.00 3.74
4229 5974 5.913137 TGTCCATTTGTCTTCACTGTTTT 57.087 34.783 0.00 0.00 0.00 2.43
4359 6104 2.095415 CCAGACGTACAACTGTCATCGA 60.095 50.000 12.95 0.00 37.58 3.59
4362 6107 3.746045 AACCAGACGTACAACTGTCAT 57.254 42.857 12.95 0.00 37.58 3.06
4607 6353 4.528076 AGGACTGTGAATCCTCTAGCTA 57.472 45.455 0.00 0.00 43.49 3.32
4608 6354 3.396685 AGGACTGTGAATCCTCTAGCT 57.603 47.619 0.00 0.00 43.49 3.32


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

AutoCloner maintained by Alex Coulton.