Multiple sequence alignment - TraesCS5D01G161600

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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 TraesCS5D01G161600 chr5D 100.000 4545 0 0 1 4545 252220611 252216067 0.000000e+00 8394.0
1 TraesCS5D01G161600 chr5D 85.366 410 52 3 102 503 276706014 276706423 7.030000e-113 418.0
2 TraesCS5D01G161600 chr5D 92.920 113 7 1 1 113 50806647 50806758 3.640000e-36 163.0
3 TraesCS5D01G161600 chr5D 93.636 110 5 1 1 110 246618193 246618086 3.640000e-36 163.0
4 TraesCS5D01G161600 chr5D 93.750 96 6 0 3336 3431 420277140 420277235 1.320000e-30 145.0
5 TraesCS5D01G161600 chr5D 93.023 86 6 0 3335 3420 164605953 164606038 4.770000e-25 126.0
6 TraesCS5D01G161600 chr5A 91.948 2459 130 27 918 3336 334760610 334758180 0.000000e+00 3382.0
7 TraesCS5D01G161600 chr5A 93.621 1160 27 14 3418 4545 334758182 334757038 0.000000e+00 1688.0
8 TraesCS5D01G161600 chr5A 85.266 828 68 21 122 933 334761417 334760628 0.000000e+00 804.0
9 TraesCS5D01G161600 chr5A 91.489 94 8 0 3336 3429 302553323 302553416 3.690000e-26 130.0
10 TraesCS5D01G161600 chr5B 96.287 2020 50 4 1855 3874 284833845 284831851 0.000000e+00 3291.0
11 TraesCS5D01G161600 chr5B 96.533 923 24 2 934 1856 284834883 284833969 0.000000e+00 1520.0
12 TraesCS5D01G161600 chr5B 95.946 592 24 0 3954 4545 284830339 284829748 0.000000e+00 961.0
13 TraesCS5D01G161600 chr5B 84.370 595 83 7 3953 4545 560436367 560435781 3.940000e-160 575.0
14 TraesCS5D01G161600 chr5B 92.920 113 7 1 1 113 53693950 53694061 3.640000e-36 163.0
15 TraesCS5D01G161600 chr4A 84.370 595 83 7 3953 4545 705713352 705712766 3.940000e-160 575.0
16 TraesCS5D01G161600 chr4A 86.715 414 51 4 98 507 656848016 656847603 1.490000e-124 457.0
17 TraesCS5D01G161600 chr4A 86.797 409 51 3 102 507 656849731 656849323 1.930000e-123 453.0
18 TraesCS5D01G161600 chr4A 83.855 415 54 11 102 504 683936257 683935844 2.570000e-102 383.0
19 TraesCS5D01G161600 chr4A 97.143 105 3 0 1 105 174504517 174504621 1.300000e-40 178.0
20 TraesCS5D01G161600 chr4A 92.647 68 5 0 552 619 77095634 77095567 1.040000e-16 99.0
21 TraesCS5D01G161600 chr7B 84.034 595 85 7 3953 4545 450597021 450596435 8.540000e-157 564.0
22 TraesCS5D01G161600 chr2B 84.034 595 85 7 3953 4545 338746599 338746013 8.540000e-157 564.0
23 TraesCS5D01G161600 chr2B 84.034 595 85 7 3953 4545 712768643 712768057 8.540000e-157 564.0
24 TraesCS5D01G161600 chr2B 96.190 105 4 0 1 105 525212762 525212866 6.050000e-39 172.0
25 TraesCS5D01G161600 chr2A 83.866 595 86 6 3953 4545 116437903 116438489 3.970000e-155 558.0
26 TraesCS5D01G161600 chr2A 85.372 417 55 6 102 513 49759797 49759382 1.170000e-115 427.0
27 TraesCS5D01G161600 chr2A 83.575 414 58 5 102 507 431581575 431581986 3.320000e-101 379.0
28 TraesCS5D01G161600 chr2A 96.117 103 4 0 1 103 669968212 669968314 7.820000e-38 169.0
29 TraesCS5D01G161600 chr2A 93.023 86 5 1 3334 3419 79308142 79308226 1.720000e-24 124.0
30 TraesCS5D01G161600 chr2A 92.647 68 5 0 552 619 549290360 549290427 1.040000e-16 99.0
31 TraesCS5D01G161600 chr3B 84.909 550 82 1 3997 4545 385477608 385477059 5.140000e-154 555.0
32 TraesCS5D01G161600 chrUn 86.797 409 51 3 102 507 41275439 41275847 1.930000e-123 453.0
33 TraesCS5D01G161600 chr6D 84.951 412 51 5 105 505 119992811 119992400 1.520000e-109 407.0
34 TraesCS5D01G161600 chr6D 95.146 103 5 0 1 103 10398828 10398930 3.640000e-36 163.0
35 TraesCS5D01G161600 chr6D 91.549 71 5 1 552 622 691020 690951 3.740000e-16 97.1
36 TraesCS5D01G161600 chr6D 92.647 68 4 1 552 618 426888295 426888228 3.740000e-16 97.1
37 TraesCS5D01G161600 chr6A 83.374 409 54 11 102 504 374426359 374426759 2.580000e-97 366.0
38 TraesCS5D01G161600 chr6A 96.154 78 3 0 3343 3420 311856916 311856993 1.330000e-25 128.0
39 TraesCS5D01G161600 chr4B 96.190 105 4 0 1 105 380475170 380475066 6.050000e-39 172.0
40 TraesCS5D01G161600 chr4D 95.238 105 5 0 1 105 91605866 91605970 2.810000e-37 167.0
41 TraesCS5D01G161600 chr4D 95.652 69 2 1 552 620 405052856 405052923 4.810000e-20 110.0
42 TraesCS5D01G161600 chr3D 93.023 86 6 0 3335 3420 157099443 157099358 4.770000e-25 126.0
43 TraesCS5D01G161600 chr7A 92.941 85 6 0 3336 3420 562275004 562274920 1.720000e-24 124.0
44 TraesCS5D01G161600 chr7D 88.776 98 11 0 3331 3428 138422057 138422154 2.220000e-23 121.0
45 TraesCS5D01G161600 chr7D 94.030 67 4 0 552 618 623793519 623793585 8.040000e-18 102.0
46 TraesCS5D01G161600 chr6B 92.537 67 5 0 552 618 14076985 14077051 3.740000e-16 97.1
47 TraesCS5D01G161600 chr6B 92.537 67 5 0 552 618 632421351 632421417 3.740000e-16 97.1


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 TraesCS5D01G161600 chr5D 252216067 252220611 4544 True 8394 8394 100.000000 1 4545 1 chr5D.!!$R2 4544
1 TraesCS5D01G161600 chr5A 334757038 334761417 4379 True 1958 3382 90.278333 122 4545 3 chr5A.!!$R1 4423
2 TraesCS5D01G161600 chr5B 284829748 284834883 5135 True 1924 3291 96.255333 934 4545 3 chr5B.!!$R2 3611
3 TraesCS5D01G161600 chr5B 560435781 560436367 586 True 575 575 84.370000 3953 4545 1 chr5B.!!$R1 592
4 TraesCS5D01G161600 chr4A 705712766 705713352 586 True 575 575 84.370000 3953 4545 1 chr4A.!!$R3 592
5 TraesCS5D01G161600 chr4A 656847603 656849731 2128 True 455 457 86.756000 98 507 2 chr4A.!!$R4 409
6 TraesCS5D01G161600 chr7B 450596435 450597021 586 True 564 564 84.034000 3953 4545 1 chr7B.!!$R1 592
7 TraesCS5D01G161600 chr2B 338746013 338746599 586 True 564 564 84.034000 3953 4545 1 chr2B.!!$R1 592
8 TraesCS5D01G161600 chr2B 712768057 712768643 586 True 564 564 84.034000 3953 4545 1 chr2B.!!$R2 592
9 TraesCS5D01G161600 chr2A 116437903 116438489 586 False 558 558 83.866000 3953 4545 1 chr2A.!!$F2 592
10 TraesCS5D01G161600 chr3B 385477059 385477608 549 True 555 555 84.909000 3997 4545 1 chr3B.!!$R1 548

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
270 271 0.106868 TCCTCCTCCGACGCTATTCA 60.107 55.000 0.00 0.00 0.00 2.57 F
385 388 0.320697 AAAAGAGAACGGGGTCCTCG 59.679 55.000 10.39 10.39 32.52 4.63 F
557 572 0.652592 GCCGACACCGATGATTTGAG 59.347 55.000 0.00 0.00 38.22 3.02 F
892 1344 1.100510 CCCTCCTGTACGAATCGTCA 58.899 55.000 13.00 9.49 41.54 4.35 F
2393 3030 1.541015 GGTATCATGATGCGCAGTGGA 60.541 52.381 18.32 11.27 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 2115 0.874390 TGCCGTTGAAGTGAGAATGC 59.126 50.000 0.0 0.0 0.00 3.56 R
2006 2625 1.133976 AGTGCAGGAAGACAAGCAAGT 60.134 47.619 0.0 0.0 38.91 3.16 R
2406 3043 5.548056 TGGGATTCTGTTCTTAGGAGTCTTT 59.452 40.000 0.0 0.0 0.00 2.52 R
2841 3489 3.532641 AGGCTTCTTCCCAAAGTTCAT 57.467 42.857 0.0 0.0 33.95 2.57 R
4051 6165 0.883833 CAAAGCGACTGGGAGCAAAT 59.116 50.000 0.0 0.0 35.48 2.32 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
39 40 9.632807 TTGCTTGTAAATGTATGTAAAACATCC 57.367 29.630 0.00 0.00 39.88 3.51
40 41 8.797438 TGCTTGTAAATGTATGTAAAACATCCA 58.203 29.630 0.00 0.00 39.88 3.41
41 42 9.632807 GCTTGTAAATGTATGTAAAACATCCAA 57.367 29.630 0.00 0.00 39.88 3.53
64 65 9.685276 CCAAGATTGGTAATATAATAGCATGGA 57.315 33.333 10.08 0.00 43.43 3.41
95 96 7.639162 AAAAATTATAGATACGCTGGAGACG 57.361 36.000 0.00 0.00 0.00 4.18
103 104 0.179134 ACGCTGGAGACGTATCAAGC 60.179 55.000 26.29 26.29 43.02 4.01
104 105 0.179137 CGCTGGAGACGTATCAAGCA 60.179 55.000 32.53 12.83 31.68 3.91
105 106 1.565305 GCTGGAGACGTATCAAGCAG 58.435 55.000 29.97 19.44 31.68 4.24
117 118 3.434319 AAGCAGCAACCATCGCCG 61.434 61.111 0.00 0.00 0.00 6.46
136 137 3.432326 GCCGATGAAGGGAGTTGTAGATT 60.432 47.826 0.00 0.00 0.00 2.40
150 151 7.362142 GGAGTTGTAGATTGGAAAGATCAAACC 60.362 40.741 0.00 0.00 0.00 3.27
162 163 6.206634 GGAAAGATCAAACCTGTAATCACACA 59.793 38.462 0.00 0.00 0.00 3.72
171 172 4.510340 ACCTGTAATCACACAAACGAAGAC 59.490 41.667 0.00 0.00 0.00 3.01
175 176 5.464057 TGTAATCACACAAACGAAGACGAAT 59.536 36.000 0.00 0.00 42.66 3.34
184 185 2.893637 ACGAAGACGAATTGGATCCAG 58.106 47.619 15.53 5.82 42.66 3.86
199 200 3.134081 GGATCCAGATAGTTCCACCGAAA 59.866 47.826 6.95 0.00 0.00 3.46
270 271 0.106868 TCCTCCTCCGACGCTATTCA 60.107 55.000 0.00 0.00 0.00 2.57
284 285 2.318519 TATTCACACCATCGGGGCGG 62.319 60.000 0.00 0.00 42.05 6.13
315 316 5.452255 ACGTGGGAGACATTATTCCTACTA 58.548 41.667 5.66 0.00 41.33 1.82
323 324 7.362802 AGACATTATTCCTACTAAGGGACAC 57.637 40.000 0.00 0.00 43.84 3.67
324 325 7.133483 AGACATTATTCCTACTAAGGGACACT 58.867 38.462 0.00 0.00 43.84 3.55
329 330 2.119495 CCTACTAAGGGACACTGCCAT 58.881 52.381 0.00 0.00 39.48 4.40
330 331 2.505819 CCTACTAAGGGACACTGCCATT 59.494 50.000 0.00 0.00 39.48 3.16
354 355 2.113139 CAGCCCCAACCAAGACGT 59.887 61.111 0.00 0.00 0.00 4.34
370 371 7.252708 ACCAAGACGTTTAACCTAACAAAAAG 58.747 34.615 0.00 0.00 0.00 2.27
371 372 7.121020 ACCAAGACGTTTAACCTAACAAAAAGA 59.879 33.333 0.00 0.00 0.00 2.52
372 373 7.642586 CCAAGACGTTTAACCTAACAAAAAGAG 59.357 37.037 0.00 0.00 0.00 2.85
373 374 8.392612 CAAGACGTTTAACCTAACAAAAAGAGA 58.607 33.333 0.00 0.00 0.00 3.10
375 376 8.393366 AGACGTTTAACCTAACAAAAAGAGAAC 58.607 33.333 0.00 0.00 0.00 3.01
376 377 7.182089 ACGTTTAACCTAACAAAAAGAGAACG 58.818 34.615 0.00 0.00 40.28 3.95
385 388 0.320697 AAAAGAGAACGGGGTCCTCG 59.679 55.000 10.39 10.39 32.52 4.63
443 446 1.318158 CCAAAGGCCATCAGAGGTGC 61.318 60.000 5.01 0.00 0.00 5.01
447 450 4.783621 GCCATCAGAGGTGCGGCA 62.784 66.667 0.00 0.00 40.17 5.69
528 543 2.830923 CCAAATATCTGGTTTGTGGCCA 59.169 45.455 0.00 0.00 35.35 5.36
537 552 1.550072 GGTTTGTGGCCATGCTTACAT 59.450 47.619 9.72 0.00 36.79 2.29
545 560 3.903876 CATGCTTACATGCCGACAC 57.096 52.632 0.00 0.00 46.75 3.67
550 565 0.930310 CTTACATGCCGACACCGATG 59.070 55.000 0.00 0.00 38.22 3.84
557 572 0.652592 GCCGACACCGATGATTTGAG 59.347 55.000 0.00 0.00 38.22 3.02
560 575 2.417379 CCGACACCGATGATTTGAGTCT 60.417 50.000 0.00 0.00 38.22 3.24
641 656 3.551082 TGTGTCCGTTACAACTTACAACG 59.449 43.478 0.00 0.00 40.63 4.10
651 666 3.568007 ACAACTTACAACGCATGGACAAT 59.432 39.130 0.00 0.00 0.00 2.71
777 1229 5.988287 ACACCAAAATGACTCCAATTGTTT 58.012 33.333 4.43 0.00 0.00 2.83
801 1253 7.938140 TTTTTAGAATCGACTCCAATTGGAT 57.062 32.000 27.20 16.89 44.46 3.41
802 1254 7.938140 TTTTAGAATCGACTCCAATTGGATT 57.062 32.000 27.20 21.89 44.46 3.01
803 1255 7.938140 TTTAGAATCGACTCCAATTGGATTT 57.062 32.000 27.20 17.14 44.46 2.17
804 1256 7.938140 TTAGAATCGACTCCAATTGGATTTT 57.062 32.000 27.20 15.23 44.46 1.82
805 1257 6.840780 AGAATCGACTCCAATTGGATTTTT 57.159 33.333 27.20 15.66 44.46 1.94
856 1308 1.730176 CAGCAACAACAACTCGTTCG 58.270 50.000 0.00 0.00 34.86 3.95
864 1316 2.668550 AACTCGTTCGCTTGGGCC 60.669 61.111 0.00 0.00 34.44 5.80
889 1341 1.269998 GATCCCCTCCTGTACGAATCG 59.730 57.143 0.00 0.00 0.00 3.34
892 1344 1.100510 CCCTCCTGTACGAATCGTCA 58.899 55.000 13.00 9.49 41.54 4.35
919 1371 3.557595 CCATGAAGATCGTAAACCAGAGC 59.442 47.826 0.00 0.00 0.00 4.09
1089 1573 3.141488 CTCGAGTCCACTCCGGGG 61.141 72.222 0.00 0.00 39.79 5.73
1129 1613 2.611964 ATCCTCCACCGGCCTCATCT 62.612 60.000 0.00 0.00 0.00 2.90
1190 1674 3.099171 CCTCCTTGCCCAATCCCA 58.901 61.111 0.00 0.00 0.00 4.37
1676 2160 4.213513 GCAAGGATTCAGATTTCTCCCAT 58.786 43.478 0.00 0.00 0.00 4.00
1695 2179 5.127845 TCCCATTGCAAACAAGTTAAAGTGA 59.872 36.000 1.71 0.00 39.69 3.41
1745 2229 4.093514 CGCAATTTCATCTGTAGTTGCAG 58.906 43.478 14.18 6.32 41.31 4.41
1746 2230 3.855950 GCAATTTCATCTGTAGTTGCAGC 59.144 43.478 10.62 0.00 41.01 5.25
1747 2231 4.616604 GCAATTTCATCTGTAGTTGCAGCA 60.617 41.667 2.55 0.00 41.01 4.41
2275 2911 9.709495 ATATTCTCTGCTTGCTCTAAATTCTAG 57.291 33.333 0.00 0.00 0.00 2.43
2276 2912 5.911752 TCTCTGCTTGCTCTAAATTCTAGG 58.088 41.667 0.00 0.00 0.00 3.02
2277 2913 5.028549 TCTGCTTGCTCTAAATTCTAGGG 57.971 43.478 0.00 0.00 0.00 3.53
2278 2914 4.716784 TCTGCTTGCTCTAAATTCTAGGGA 59.283 41.667 0.00 0.00 0.00 4.20
2389 3026 2.486918 TCTTGGTATCATGATGCGCAG 58.513 47.619 18.32 14.81 0.00 5.18
2393 3030 1.541015 GGTATCATGATGCGCAGTGGA 60.541 52.381 18.32 11.27 0.00 4.02
2406 3043 2.628178 CGCAGTGGACCCTTCTATATGA 59.372 50.000 0.00 0.00 0.00 2.15
2421 3058 9.974980 CCTTCTATATGAAAGACTCCTAAGAAC 57.025 37.037 1.58 0.00 33.79 3.01
2610 3248 5.230182 CAGTTTTGCCCCTAATTTGTTCTC 58.770 41.667 0.00 0.00 0.00 2.87
2638 3276 8.224620 AGATGAATTAATATACAGGGAAGCCT 57.775 34.615 0.00 0.00 0.00 4.58
2896 3544 9.579932 AGTAAGAAGTCTTTTTCAAATGAGGAT 57.420 29.630 0.00 0.00 37.40 3.24
3090 3738 3.364964 GGTGAAGCAATTTCAGGTACACG 60.365 47.826 0.00 0.00 46.09 4.49
3108 3756 3.992427 ACACGTTATTTCTTTCTCGGACC 59.008 43.478 0.00 0.00 0.00 4.46
3112 3760 4.619863 CGTTATTTCTTTCTCGGACCTCCA 60.620 45.833 0.00 0.00 35.14 3.86
3223 3871 1.623811 GGTTAGTTCTCCTGTGCTCCA 59.376 52.381 0.00 0.00 0.00 3.86
3241 3889 3.547746 TCCAATGGCGTATTTAACCTCC 58.452 45.455 0.00 0.00 0.00 4.30
3364 4013 2.223249 CCATCCCAAAATAAGTGTCGCG 60.223 50.000 0.00 0.00 0.00 5.87
3384 4033 7.922278 TGTCGCGGATTTAGTACAAAGTTATAT 59.078 33.333 6.13 0.00 0.00 0.86
4046 6160 5.255687 TCCATCTTGTCACATGCAAGTTAT 58.744 37.500 10.24 0.00 42.67 1.89
4051 6165 6.463360 TCTTGTCACATGCAAGTTATAGTCA 58.537 36.000 10.24 0.00 42.67 3.41
4311 6583 4.326826 CAAAGCATCTCACTCAACCCTTA 58.673 43.478 0.00 0.00 0.00 2.69
4412 6684 6.823286 TTCCTCCCACAATCACATAATAGA 57.177 37.500 0.00 0.00 0.00 1.98
4479 6819 8.497745 AGAATCACTATTGTCATCCACCTTAAT 58.502 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.632807 GGATGTTTTACATACATTTACAAGCAA 57.367 29.630 0.00 0.00 39.27 3.91
14 15 8.797438 TGGATGTTTTACATACATTTACAAGCA 58.203 29.630 0.62 0.00 44.09 3.91
71 72 7.208080 ACGTCTCCAGCGTATCTATAATTTTT 58.792 34.615 0.00 0.00 41.06 1.94
72 73 6.746120 ACGTCTCCAGCGTATCTATAATTTT 58.254 36.000 0.00 0.00 41.06 1.82
73 74 6.328641 ACGTCTCCAGCGTATCTATAATTT 57.671 37.500 0.00 0.00 41.06 1.82
74 75 5.961396 ACGTCTCCAGCGTATCTATAATT 57.039 39.130 0.00 0.00 41.06 1.40
83 84 1.065102 GCTTGATACGTCTCCAGCGTA 59.935 52.381 10.58 0.11 46.63 4.42
84 85 0.179134 GCTTGATACGTCTCCAGCGT 60.179 55.000 10.58 0.00 45.11 5.07
85 86 0.179137 TGCTTGATACGTCTCCAGCG 60.179 55.000 18.18 0.00 0.00 5.18
86 87 1.565305 CTGCTTGATACGTCTCCAGC 58.435 55.000 17.06 17.06 0.00 4.85
87 88 1.134995 TGCTGCTTGATACGTCTCCAG 60.135 52.381 0.00 0.00 0.00 3.86
88 89 0.894835 TGCTGCTTGATACGTCTCCA 59.105 50.000 0.00 0.00 0.00 3.86
89 90 1.661112 GTTGCTGCTTGATACGTCTCC 59.339 52.381 0.00 0.00 0.00 3.71
90 91 1.661112 GGTTGCTGCTTGATACGTCTC 59.339 52.381 0.00 0.00 0.00 3.36
91 92 1.001974 TGGTTGCTGCTTGATACGTCT 59.998 47.619 0.00 0.00 0.00 4.18
92 93 1.438651 TGGTTGCTGCTTGATACGTC 58.561 50.000 0.00 0.00 0.00 4.34
93 94 2.009774 GATGGTTGCTGCTTGATACGT 58.990 47.619 0.00 0.00 0.00 3.57
94 95 1.004610 CGATGGTTGCTGCTTGATACG 60.005 52.381 0.00 0.00 0.00 3.06
95 96 1.268234 GCGATGGTTGCTGCTTGATAC 60.268 52.381 0.00 0.00 0.00 2.24
96 97 1.016627 GCGATGGTTGCTGCTTGATA 58.983 50.000 0.00 0.00 0.00 2.15
97 98 1.660560 GGCGATGGTTGCTGCTTGAT 61.661 55.000 0.00 0.00 0.00 2.57
98 99 2.334946 GGCGATGGTTGCTGCTTGA 61.335 57.895 0.00 0.00 0.00 3.02
99 100 2.180017 GGCGATGGTTGCTGCTTG 59.820 61.111 0.00 0.00 0.00 4.01
100 101 3.434319 CGGCGATGGTTGCTGCTT 61.434 61.111 0.00 0.00 30.94 3.91
101 102 3.687321 ATCGGCGATGGTTGCTGCT 62.687 57.895 23.36 0.00 38.62 4.24
102 103 3.204827 ATCGGCGATGGTTGCTGC 61.205 61.111 23.36 0.00 38.62 5.25
103 104 1.368345 TTCATCGGCGATGGTTGCTG 61.368 55.000 39.82 21.57 40.15 4.41
104 105 1.078497 TTCATCGGCGATGGTTGCT 60.078 52.632 39.82 10.60 40.15 3.91
105 106 1.353103 CTTCATCGGCGATGGTTGC 59.647 57.895 39.82 0.00 40.15 4.17
117 118 5.359194 TCCAATCTACAACTCCCTTCATC 57.641 43.478 0.00 0.00 0.00 2.92
136 137 6.206634 GTGTGATTACAGGTTTGATCTTTCCA 59.793 38.462 0.00 0.00 37.52 3.53
150 151 4.443063 TCGTCTTCGTTTGTGTGATTACAG 59.557 41.667 0.00 0.00 36.55 2.74
162 163 3.670625 TGGATCCAATTCGTCTTCGTTT 58.329 40.909 13.46 0.00 38.33 3.60
171 172 4.752101 GTGGAACTATCTGGATCCAATTCG 59.248 45.833 17.00 3.95 43.21 3.34
175 176 2.434336 CGGTGGAACTATCTGGATCCAA 59.566 50.000 17.00 7.48 43.21 3.53
184 185 2.418976 GCTGGTTTTCGGTGGAACTATC 59.581 50.000 0.00 0.00 36.74 2.08
199 200 1.375523 GATTCGGTCGGTGCTGGTT 60.376 57.895 0.00 0.00 0.00 3.67
244 245 1.313091 CGTCGGAGGAGGATGTGTGA 61.313 60.000 0.00 0.00 0.00 3.58
284 285 0.396695 TGTCTCCCACGTCCTATCCC 60.397 60.000 0.00 0.00 0.00 3.85
315 316 1.607467 GGCAATGGCAGTGTCCCTT 60.607 57.895 16.96 0.00 43.71 3.95
323 324 2.260434 GCTGTGTGGCAATGGCAG 59.740 61.111 10.55 0.00 43.71 4.85
324 325 3.304721 GGCTGTGTGGCAATGGCA 61.305 61.111 5.05 5.05 43.71 4.92
329 330 2.837291 GTTGGGGCTGTGTGGCAA 60.837 61.111 0.00 0.00 43.83 4.52
330 331 4.912395 GGTTGGGGCTGTGTGGCA 62.912 66.667 0.00 0.00 43.83 4.92
354 355 6.039605 CCCCGTTCTCTTTTTGTTAGGTTAAA 59.960 38.462 0.00 0.00 0.00 1.52
370 371 4.493747 CGCGAGGACCCCGTTCTC 62.494 72.222 0.00 0.00 34.98 2.87
436 439 3.842923 CCGATCTGCCGCACCTCT 61.843 66.667 0.00 0.00 0.00 3.69
462 465 1.203137 TCTCCTTCCTCCTTCCGTTGA 60.203 52.381 0.00 0.00 0.00 3.18
464 467 1.203199 AGTCTCCTTCCTCCTTCCGTT 60.203 52.381 0.00 0.00 0.00 4.44
465 468 0.410270 AGTCTCCTTCCTCCTTCCGT 59.590 55.000 0.00 0.00 0.00 4.69
469 472 4.202514 CCAAGAAAAGTCTCCTTCCTCCTT 60.203 45.833 0.00 0.00 30.70 3.36
528 543 1.089481 CGGTGTCGGCATGTAAGCAT 61.089 55.000 0.00 0.00 35.83 3.79
537 552 0.036858 TCAAATCATCGGTGTCGGCA 60.037 50.000 0.00 0.00 36.95 5.69
545 560 6.507900 ACTACATACAGACTCAAATCATCGG 58.492 40.000 0.00 0.00 0.00 4.18
550 565 9.988815 AATATGGACTACATACAGACTCAAATC 57.011 33.333 0.00 0.00 44.41 2.17
590 605 6.701340 TCCCTCCATTCACGAATATAAGATG 58.299 40.000 0.00 0.00 0.00 2.90
607 622 0.611062 CGGACACACTACTCCCTCCA 60.611 60.000 0.00 0.00 0.00 3.86
641 656 9.555727 TTTATAGAACTAGGTAATTGTCCATGC 57.444 33.333 0.00 0.00 0.00 4.06
754 1206 5.612725 AACAATTGGAGTCATTTTGGTGT 57.387 34.783 10.83 0.00 0.00 4.16
805 1257 2.045561 TGGAGTCGTTGCCTCAAAAA 57.954 45.000 0.00 0.00 0.00 1.94
806 1258 2.045561 TTGGAGTCGTTGCCTCAAAA 57.954 45.000 0.00 0.00 0.00 2.44
807 1259 2.270352 ATTGGAGTCGTTGCCTCAAA 57.730 45.000 0.00 0.00 0.00 2.69
808 1260 1.879380 CAATTGGAGTCGTTGCCTCAA 59.121 47.619 0.00 0.00 0.00 3.02
809 1261 1.522668 CAATTGGAGTCGTTGCCTCA 58.477 50.000 0.00 0.00 0.00 3.86
810 1262 0.804989 CCAATTGGAGTCGTTGCCTC 59.195 55.000 20.50 0.00 37.39 4.70
811 1263 0.400213 TCCAATTGGAGTCGTTGCCT 59.600 50.000 23.63 0.00 39.78 4.75
812 1264 2.941210 TCCAATTGGAGTCGTTGCC 58.059 52.632 23.63 0.00 39.78 4.52
856 1308 2.595754 GGATCATCCGGCCCAAGC 60.596 66.667 0.00 0.00 38.76 4.01
889 1341 1.303309 CGATCTTCATGGGCCTTGAC 58.697 55.000 20.67 9.24 0.00 3.18
892 1344 3.279434 GTTTACGATCTTCATGGGCCTT 58.721 45.455 4.53 0.00 0.00 4.35
919 1371 0.179029 AGACGGTGGTTTCTGTTGGG 60.179 55.000 0.00 0.00 0.00 4.12
980 1464 4.527816 ACATGGCTTTTGCTGAGGAAATTA 59.472 37.500 0.00 0.00 46.54 1.40
1631 2115 0.874390 TGCCGTTGAAGTGAGAATGC 59.126 50.000 0.00 0.00 0.00 3.56
1676 2160 9.477484 TTTAGTTTCACTTTAACTTGTTTGCAA 57.523 25.926 0.00 0.00 37.12 4.08
1695 2179 7.125963 TCCAATTTTAGGTGGGTTGTTTAGTTT 59.874 33.333 0.00 0.00 35.46 2.66
1745 2229 1.142474 GCCTTTCACTTGTGCATTGC 58.858 50.000 0.46 0.46 0.00 3.56
1746 2230 2.512485 TGCCTTTCACTTGTGCATTG 57.488 45.000 0.00 0.00 0.00 2.82
1747 2231 3.322828 AGATTGCCTTTCACTTGTGCATT 59.677 39.130 0.00 0.00 0.00 3.56
2006 2625 1.133976 AGTGCAGGAAGACAAGCAAGT 60.134 47.619 0.00 0.00 38.91 3.16
2275 2911 5.827797 TGGTCATTTATACAAAGAGCATCCC 59.172 40.000 0.00 0.00 33.66 3.85
2276 2912 6.767902 TCTGGTCATTTATACAAAGAGCATCC 59.232 38.462 0.00 0.00 33.24 3.51
2277 2913 7.792374 TCTGGTCATTTATACAAAGAGCATC 57.208 36.000 0.00 0.00 33.24 3.91
2278 2914 9.499479 CTATCTGGTCATTTATACAAAGAGCAT 57.501 33.333 0.00 0.00 33.24 3.79
2389 3026 6.463190 GGAGTCTTTCATATAGAAGGGTCCAC 60.463 46.154 0.00 0.00 37.09 4.02
2393 3030 8.290277 TCTTAGGAGTCTTTCATATAGAAGGGT 58.710 37.037 0.00 0.00 37.57 4.34
2406 3043 5.548056 TGGGATTCTGTTCTTAGGAGTCTTT 59.452 40.000 0.00 0.00 0.00 2.52
2421 3058 7.040062 TGGTTTGTTAATACAGTTGGGATTCTG 60.040 37.037 0.00 0.00 35.28 3.02
2610 3248 9.160496 GCTTCCCTGTATATTAATTCATCTCAG 57.840 37.037 0.00 0.00 0.00 3.35
2841 3489 3.532641 AGGCTTCTTCCCAAAGTTCAT 57.467 42.857 0.00 0.00 33.95 2.57
2896 3544 1.059098 ATGTCTCAGCAGGGACACAA 58.941 50.000 14.72 0.00 43.79 3.33
3090 3738 4.630505 GTGGAGGTCCGAGAAAGAAATAAC 59.369 45.833 0.00 0.00 39.43 1.89
3108 3756 6.851222 ATCGCAGAAAATATAACTGTGGAG 57.149 37.500 0.00 0.00 43.58 3.86
3223 3871 5.072600 TGGATAGGAGGTTAAATACGCCATT 59.927 40.000 0.00 0.00 0.00 3.16
3341 3990 3.065371 GCGACACTTATTTTGGGATGGAG 59.935 47.826 0.00 0.00 0.00 3.86
3384 4033 6.431543 TCCCAAAATAAGTGTCGCTGATTTAA 59.568 34.615 8.84 0.00 37.29 1.52
3397 4046 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
3625 4274 6.535508 GTCTCGGCAAAACATAAGATAAGAGT 59.464 38.462 0.00 0.00 0.00 3.24
3628 4277 6.018669 GGAGTCTCGGCAAAACATAAGATAAG 60.019 42.308 0.00 0.00 0.00 1.73
3645 4294 6.585322 ACGAATTACTTTGTAAAGGAGTCTCG 59.415 38.462 9.00 10.75 40.31 4.04
4046 6160 1.405526 GCGACTGGGAGCAAATGACTA 60.406 52.381 0.00 0.00 0.00 2.59
4051 6165 0.883833 CAAAGCGACTGGGAGCAAAT 59.116 50.000 0.00 0.00 35.48 2.32
4311 6583 8.879227 AGGAAGCTAAGATTAGAGCATTATCTT 58.121 33.333 3.77 7.89 41.36 2.40
4412 6684 8.316946 TCAAGATGACAGAATATCAACTTCAGT 58.683 33.333 0.00 0.00 37.16 3.41
4479 6819 2.037902 TGGTTTGCGAAGAGTGGACATA 59.962 45.455 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.