Multiple sequence alignment - TraesCS2A01G408200

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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 TraesCS2A01G408200 chr2A 100.000 2150 0 0 1864 4013 665843431 665841282 0.000000e+00 3971.0
1 TraesCS2A01G408200 chr2A 100.000 1258 0 0 1 1258 665845294 665844037 0.000000e+00 2324.0
2 TraesCS2A01G408200 chr2A 92.939 1218 40 10 1864 3049 665990447 665989244 0.000000e+00 1731.0
3 TraesCS2A01G408200 chr2A 85.714 931 84 24 342 1258 665991838 665990943 0.000000e+00 937.0
4 TraesCS2A01G408200 chr2A 77.212 452 44 33 3590 4013 569583955 569583535 4.060000e-50 209.0
5 TraesCS2A01G408200 chr5A 97.934 968 20 0 3046 4013 77344682 77345649 0.000000e+00 1677.0
6 TraesCS2A01G408200 chr5A 98.039 969 11 1 3045 4013 706482651 706483611 0.000000e+00 1677.0
7 TraesCS2A01G408200 chr5A 84.672 137 17 3 2831 2963 60524672 60524808 2.520000e-27 134.0
8 TraesCS2A01G408200 chr5A 83.942 137 20 1 2831 2965 599654132 599654268 3.250000e-26 130.0
9 TraesCS2A01G408200 chr5A 96.078 51 2 0 2994 3044 622447437 622447387 2.570000e-12 84.2
10 TraesCS2A01G408200 chr2B 89.796 1225 85 17 43 1258 613038601 613037408 0.000000e+00 1533.0
11 TraesCS2A01G408200 chr2B 87.676 641 38 22 1887 2517 613036890 613036281 0.000000e+00 708.0
12 TraesCS2A01G408200 chr2B 87.581 620 51 15 3047 3641 200575738 200576356 0.000000e+00 695.0
13 TraesCS2A01G408200 chr2B 88.971 408 37 7 3047 3448 607301812 607301407 7.750000e-137 497.0
14 TraesCS2A01G408200 chr2B 86.099 223 10 3 3431 3633 775487689 775487910 1.880000e-53 220.0
15 TraesCS2A01G408200 chr2B 93.023 86 6 0 2964 3049 613035387 613035302 4.210000e-25 126.0
16 TraesCS2A01G408200 chr2D 86.079 1293 91 38 27 1258 520584530 520583266 0.000000e+00 1308.0
17 TraesCS2A01G408200 chr2D 88.318 642 34 18 1864 2495 520583138 520582528 0.000000e+00 732.0
18 TraesCS2A01G408200 chr2D 80.414 531 62 26 3515 4013 310985570 310985050 2.280000e-97 366.0
19 TraesCS2A01G408200 chr2D 84.549 233 13 5 3430 3641 627624785 627624555 4.060000e-50 209.0
20 TraesCS2A01G408200 chr5B 87.981 624 44 6 3047 3641 551672470 551671849 0.000000e+00 708.0
21 TraesCS2A01G408200 chr4A 87.520 625 52 13 3042 3641 717627958 717627335 0.000000e+00 699.0
22 TraesCS2A01G408200 chr4A 80.043 466 53 22 3558 4013 684132292 684131857 3.900000e-80 309.0
23 TraesCS2A01G408200 chr4A 78.097 452 46 27 3588 4013 556534657 556535081 1.860000e-58 237.0
24 TraesCS2A01G408200 chr4A 89.691 97 10 0 3044 3140 616975843 616975747 1.510000e-24 124.0
25 TraesCS2A01G408200 chr4A 89.535 86 9 0 3046 3131 177610841 177610926 4.240000e-20 110.0
26 TraesCS2A01G408200 chr7B 87.179 624 47 8 3047 3641 21659229 21659848 0.000000e+00 678.0
27 TraesCS2A01G408200 chr7B 80.962 520 54 22 3515 4013 85989830 85990325 1.760000e-98 370.0
28 TraesCS2A01G408200 chr1A 80.737 950 85 41 3047 3931 493514064 493514980 0.000000e+00 651.0
29 TraesCS2A01G408200 chr1A 80.439 956 89 42 3041 3931 564578546 564579468 1.220000e-179 640.0
30 TraesCS2A01G408200 chr1A 88.889 405 41 4 3047 3448 579649139 579648736 2.790000e-136 496.0
31 TraesCS2A01G408200 chr1A 88.614 404 42 4 3047 3448 569209826 569210227 4.660000e-134 488.0
32 TraesCS2A01G408200 chr6A 80.400 949 89 42 3047 3931 616887475 616886560 2.030000e-177 632.0
33 TraesCS2A01G408200 chr6A 89.050 484 31 19 1867 2334 107701078 107700601 7.480000e-162 580.0
34 TraesCS2A01G408200 chr6A 95.050 303 14 1 956 1258 107798972 107798671 3.630000e-130 475.0
35 TraesCS2A01G408200 chr6A 89.905 317 27 5 943 1257 107692778 107692465 1.740000e-108 403.0
36 TraesCS2A01G408200 chr6A 87.387 333 33 5 31 355 107800351 107800020 1.360000e-99 374.0
37 TraesCS2A01G408200 chr6A 85.350 157 15 5 45 196 91422748 91422901 5.370000e-34 156.0
38 TraesCS2A01G408200 chr6B 87.952 498 39 18 1876 2357 171805205 171804713 5.820000e-158 568.0
39 TraesCS2A01G408200 chr6B 86.667 510 47 17 1864 2357 171768482 171767978 2.730000e-151 545.0
40 TraesCS2A01G408200 chr6B 94.059 303 17 1 956 1258 171972072 171971771 3.650000e-125 459.0
41 TraesCS2A01G408200 chr6B 86.076 395 50 3 866 1258 139894669 139894278 1.720000e-113 420.0
42 TraesCS2A01G408200 chr6B 90.252 318 26 5 943 1258 171805760 171805446 1.040000e-110 411.0
43 TraesCS2A01G408200 chr6B 89.058 329 31 5 932 1258 149055117 149055442 1.740000e-108 403.0
44 TraesCS2A01G408200 chr6B 82.826 460 46 15 31 486 171973027 171972597 8.140000e-102 381.0
45 TraesCS2A01G408200 chr6B 84.865 185 20 2 18 202 171729783 171729607 3.190000e-41 180.0
46 TraesCS2A01G408200 chr6D 86.931 505 44 17 1867 2357 89355621 89355125 7.580000e-152 547.0
47 TraesCS2A01G408200 chr6D 85.972 499 46 18 1864 2345 89365692 89365201 2.770000e-141 512.0
48 TraesCS2A01G408200 chr6D 86.848 441 34 15 1924 2345 89510609 89510174 4.690000e-129 472.0
49 TraesCS2A01G408200 chr6D 84.355 473 52 11 18 486 89512854 89512400 1.020000e-120 444.0
50 TraesCS2A01G408200 chr6D 85.532 235 12 4 3427 3641 454965542 454965774 4.040000e-55 226.0
51 TraesCS2A01G408200 chr6D 84.466 206 13 4 3446 3632 5045872 5046077 6.850000e-43 185.0
52 TraesCS2A01G408200 chr5D 84.670 424 33 9 3436 3833 47342340 47341923 1.050000e-105 394.0
53 TraesCS2A01G408200 chr5D 78.947 608 59 29 3446 4013 414019707 414020285 2.300000e-92 350.0
54 TraesCS2A01G408200 chr5D 81.102 127 9 10 3899 4011 47341921 47341796 1.990000e-13 87.9
55 TraesCS2A01G408200 chr7A 80.798 526 49 25 3443 3936 54685546 54685041 8.200000e-97 364.0
56 TraesCS2A01G408200 chr7D 80.088 452 43 31 3588 4013 59736969 59736539 3.920000e-75 292.0
57 TraesCS2A01G408200 chrUn 85.764 288 26 6 3558 3835 45994182 45994464 1.410000e-74 291.0
58 TraesCS2A01G408200 chr3D 85.017 287 28 6 3559 3835 605267358 605267077 1.100000e-70 278.0
59 TraesCS2A01G408200 chr1B 78.330 443 58 31 3588 4013 338433282 338432861 6.660000e-63 252.0
60 TraesCS2A01G408200 chr3B 78.444 450 43 25 3588 4013 70106464 70106045 1.110000e-60 244.0
61 TraesCS2A01G408200 chr1D 82.707 133 12 4 3883 4013 198536324 198536447 1.530000e-19 108.0
62 TraesCS2A01G408200 chr1D 100.000 32 0 0 2705 2736 436968972 436968941 4.330000e-05 60.2
63 TraesCS2A01G408200 chr3A 93.750 48 2 1 3966 4013 750634865 750634911 2.000000e-08 71.3


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 TraesCS2A01G408200 chr2A 665841282 665845294 4012 True 3147.50 3971 100.0000 1 4013 2 chr2A.!!$R2 4012
1 TraesCS2A01G408200 chr2A 665989244 665991838 2594 True 1334.00 1731 89.3265 342 3049 2 chr2A.!!$R3 2707
2 TraesCS2A01G408200 chr5A 77344682 77345649 967 False 1677.00 1677 97.9340 3046 4013 1 chr5A.!!$F2 967
3 TraesCS2A01G408200 chr5A 706482651 706483611 960 False 1677.00 1677 98.0390 3045 4013 1 chr5A.!!$F4 968
4 TraesCS2A01G408200 chr2B 613035302 613038601 3299 True 789.00 1533 90.1650 43 3049 3 chr2B.!!$R2 3006
5 TraesCS2A01G408200 chr2B 200575738 200576356 618 False 695.00 695 87.5810 3047 3641 1 chr2B.!!$F1 594
6 TraesCS2A01G408200 chr2D 520582528 520584530 2002 True 1020.00 1308 87.1985 27 2495 2 chr2D.!!$R3 2468
7 TraesCS2A01G408200 chr2D 310985050 310985570 520 True 366.00 366 80.4140 3515 4013 1 chr2D.!!$R1 498
8 TraesCS2A01G408200 chr5B 551671849 551672470 621 True 708.00 708 87.9810 3047 3641 1 chr5B.!!$R1 594
9 TraesCS2A01G408200 chr4A 717627335 717627958 623 True 699.00 699 87.5200 3042 3641 1 chr4A.!!$R3 599
10 TraesCS2A01G408200 chr7B 21659229 21659848 619 False 678.00 678 87.1790 3047 3641 1 chr7B.!!$F1 594
11 TraesCS2A01G408200 chr1A 493514064 493514980 916 False 651.00 651 80.7370 3047 3931 1 chr1A.!!$F1 884
12 TraesCS2A01G408200 chr1A 564578546 564579468 922 False 640.00 640 80.4390 3041 3931 1 chr1A.!!$F2 890
13 TraesCS2A01G408200 chr6A 616886560 616887475 915 True 632.00 632 80.4000 3047 3931 1 chr6A.!!$R3 884
14 TraesCS2A01G408200 chr6A 107798671 107800351 1680 True 424.50 475 91.2185 31 1258 2 chr6A.!!$R4 1227
15 TraesCS2A01G408200 chr6B 171767978 171768482 504 True 545.00 545 86.6670 1864 2357 1 chr6B.!!$R3 493
16 TraesCS2A01G408200 chr6B 171804713 171805760 1047 True 489.50 568 89.1020 943 2357 2 chr6B.!!$R4 1414
17 TraesCS2A01G408200 chr6B 171971771 171973027 1256 True 420.00 459 88.4425 31 1258 2 chr6B.!!$R5 1227
18 TraesCS2A01G408200 chr6D 89510174 89512854 2680 True 458.00 472 85.6015 18 2345 2 chr6D.!!$R3 2327
19 TraesCS2A01G408200 chr5D 414019707 414020285 578 False 350.00 350 78.9470 3446 4013 1 chr5D.!!$F1 567
20 TraesCS2A01G408200 chr5D 47341796 47342340 544 True 240.95 394 82.8860 3436 4011 2 chr5D.!!$R1 575
21 TraesCS2A01G408200 chr7A 54685041 54685546 505 True 364.00 364 80.7980 3443 3936 1 chr7A.!!$R1 493

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
266 292 0.812811 TTGCTCCGATCTGATGCTGC 60.813 55.0 0.00 0.00 0.00 5.25 F
1904 3835 0.252284 TCCAGAAGGAGTCCACCCTC 60.252 60.0 12.86 2.26 39.61 4.30 F
2447 4406 0.037605 GCTTGAATTGCTTGGCTGCT 60.038 50.0 0.00 0.00 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 3904 0.962489 CAGACGACTCCACCTCAAGT 59.038 55.000 0.00 0.0 0.0 3.16 R
2854 5296 1.234821 TGTTTGCGCTTAGAGTTGGG 58.765 50.000 9.73 0.0 0.0 4.12 R
3328 5825 3.440522 TGTTGTCGATGGAGTCAGTCTAG 59.559 47.826 0.00 0.0 0.0 2.43 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
22 23 4.359434 GATTCCTAATCCTTCTCCACCC 57.641 50.000 0.00 0.00 31.60 4.61
23 24 2.961536 TCCTAATCCTTCTCCACCCA 57.038 50.000 0.00 0.00 0.00 4.51
24 25 2.764269 TCCTAATCCTTCTCCACCCAG 58.236 52.381 0.00 0.00 0.00 4.45
25 26 1.141858 CCTAATCCTTCTCCACCCAGC 59.858 57.143 0.00 0.00 0.00 4.85
26 27 1.839994 CTAATCCTTCTCCACCCAGCA 59.160 52.381 0.00 0.00 0.00 4.41
27 28 1.302907 AATCCTTCTCCACCCAGCAT 58.697 50.000 0.00 0.00 0.00 3.79
28 29 2.196742 ATCCTTCTCCACCCAGCATA 57.803 50.000 0.00 0.00 0.00 3.14
29 30 1.965414 TCCTTCTCCACCCAGCATAA 58.035 50.000 0.00 0.00 0.00 1.90
38 39 7.149202 TCTCCACCCAGCATAAATAAATACT 57.851 36.000 0.00 0.00 0.00 2.12
63 68 1.690219 CCTCCCTCCAATCCTCACCG 61.690 65.000 0.00 0.00 0.00 4.94
87 98 1.964373 CCCAGGAACGGAACCAACG 60.964 63.158 0.00 0.00 37.36 4.10
145 157 2.123425 TCGAATCCTCCTCCCCCG 60.123 66.667 0.00 0.00 0.00 5.73
232 258 3.244770 GGTTGGAGGTGAAGTATTGTGGA 60.245 47.826 0.00 0.00 0.00 4.02
247 273 4.373348 TTGTGGAAATTTCGTCGGTTTT 57.627 36.364 11.95 0.00 0.00 2.43
266 292 0.812811 TTGCTCCGATCTGATGCTGC 60.813 55.000 0.00 0.00 0.00 5.25
268 294 2.279717 TCCGATCTGATGCTGCGC 60.280 61.111 0.00 0.00 0.00 6.09
351 377 5.741011 TCTTAGGGATTTTTGCGTGTAGAT 58.259 37.500 0.00 0.00 0.00 1.98
352 378 6.177610 TCTTAGGGATTTTTGCGTGTAGATT 58.822 36.000 0.00 0.00 0.00 2.40
353 379 4.701956 AGGGATTTTTGCGTGTAGATTG 57.298 40.909 0.00 0.00 0.00 2.67
354 380 4.331968 AGGGATTTTTGCGTGTAGATTGA 58.668 39.130 0.00 0.00 0.00 2.57
355 381 4.949856 AGGGATTTTTGCGTGTAGATTGAT 59.050 37.500 0.00 0.00 0.00 2.57
356 382 6.119536 AGGGATTTTTGCGTGTAGATTGATA 58.880 36.000 0.00 0.00 0.00 2.15
357 383 6.260936 AGGGATTTTTGCGTGTAGATTGATAG 59.739 38.462 0.00 0.00 0.00 2.08
358 384 6.260050 GGGATTTTTGCGTGTAGATTGATAGA 59.740 38.462 0.00 0.00 0.00 1.98
382 416 2.109126 GGGGCAGATCTGTTCGTGC 61.109 63.158 23.38 9.11 35.07 5.34
413 823 7.860872 GGTCAATTAATTCCTTATTAAGCCGTG 59.139 37.037 0.00 0.00 40.91 4.94
449 859 6.037098 GCATGATTTGTCTACTAGTTCGTCT 58.963 40.000 0.00 0.00 0.00 4.18
462 872 2.049156 CGTCTGCTCCTGCGTGAA 60.049 61.111 0.00 0.00 43.34 3.18
530 991 1.135915 CTGCCTGATCTGTAGCTCGTT 59.864 52.381 0.00 0.00 0.00 3.85
539 1000 8.031864 CCTGATCTGTAGCTCGTTATCATATTT 58.968 37.037 0.00 0.00 0.00 1.40
549 1010 9.817809 AGCTCGTTATCATATTTCTTGTTCTAA 57.182 29.630 0.00 0.00 0.00 2.10
570 1031 5.385628 AACGAGATAGTCCTAACCTAGGT 57.614 43.478 9.21 9.21 46.32 3.08
571 1032 4.971939 ACGAGATAGTCCTAACCTAGGTC 58.028 47.826 16.64 1.59 46.32 3.85
628 1146 4.864726 AGGCTTCTTCCTTTGCTTGATAT 58.135 39.130 0.00 0.00 30.82 1.63
629 1147 6.006275 AGGCTTCTTCCTTTGCTTGATATA 57.994 37.500 0.00 0.00 30.82 0.86
630 1148 6.608922 AGGCTTCTTCCTTTGCTTGATATAT 58.391 36.000 0.00 0.00 30.82 0.86
653 1177 3.873952 GACAGCTATGTGGAATCCTTGAC 59.126 47.826 0.00 0.00 40.68 3.18
689 1237 1.973138 CACGTACCGTCTGTTAGGTG 58.027 55.000 0.00 0.00 41.51 4.00
745 1331 9.578439 GTTTGTTTATTATCTACCGTCTGTAGT 57.422 33.333 1.87 0.00 45.99 2.73
809 1414 7.016361 ACAGCTACGTGGAATCATAATTTTC 57.984 36.000 1.81 0.00 0.00 2.29
810 1415 6.129393 CAGCTACGTGGAATCATAATTTTCG 58.871 40.000 1.81 0.00 0.00 3.46
811 1416 5.815740 AGCTACGTGGAATCATAATTTTCGT 59.184 36.000 1.81 0.00 33.69 3.85
901 1555 4.693566 CCTGTTTGTTTAATCTCTACGGCA 59.306 41.667 0.00 0.00 0.00 5.69
965 1653 1.597742 TGCTTGGTCTGCTTCTTGAC 58.402 50.000 0.00 0.00 0.00 3.18
1215 1903 2.046892 CTCCACCTTGTCCTGCGG 60.047 66.667 0.00 0.00 0.00 5.69
1904 3835 0.252284 TCCAGAAGGAGTCCACCCTC 60.252 60.000 12.86 2.26 39.61 4.30
1922 3853 1.669115 CCACCTTGTCCTGCGTCTG 60.669 63.158 0.00 0.00 0.00 3.51
1973 3904 1.302431 CACCGGCAAGACCATCACA 60.302 57.895 0.00 0.00 39.03 3.58
2442 4401 1.065358 CTTGCGCTTGAATTGCTTGG 58.935 50.000 9.73 0.00 0.00 3.61
2443 4402 0.945265 TTGCGCTTGAATTGCTTGGC 60.945 50.000 9.73 0.00 0.00 4.52
2444 4403 1.080298 GCGCTTGAATTGCTTGGCT 60.080 52.632 0.00 0.00 0.00 4.75
2445 4404 1.349259 GCGCTTGAATTGCTTGGCTG 61.349 55.000 0.00 0.00 0.00 4.85
2446 4405 1.349259 CGCTTGAATTGCTTGGCTGC 61.349 55.000 0.00 0.00 0.00 5.25
2447 4406 0.037605 GCTTGAATTGCTTGGCTGCT 60.038 50.000 0.00 0.00 0.00 4.24
2448 4407 1.607251 GCTTGAATTGCTTGGCTGCTT 60.607 47.619 0.00 0.00 0.00 3.91
2449 4408 2.066262 CTTGAATTGCTTGGCTGCTTG 58.934 47.619 0.00 0.00 0.00 4.01
2462 4421 2.363683 GCTGCTTGCTTGATCCTACTT 58.636 47.619 0.00 0.00 38.95 2.24
2574 4535 3.155093 GCATCCCTGCTGTGTTAATTG 57.845 47.619 0.00 0.00 45.32 2.32
2678 4664 7.524294 AATTCGAATTGTTGTTATTGCATCC 57.476 32.000 22.16 0.00 0.00 3.51
2854 5296 7.928706 AGTATACAGCCAGTGAGAATAAATGTC 59.071 37.037 5.50 0.00 0.00 3.06
2859 5301 4.142381 GCCAGTGAGAATAAATGTCCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
2888 5330 3.119029 CGCAAACAAAAGGGGATGATGAT 60.119 43.478 0.00 0.00 0.00 2.45
2947 5391 2.605837 TCGCAACTTGAACACCTGTA 57.394 45.000 0.00 0.00 0.00 2.74
3030 5501 8.557864 CATGGATAGCAAGAAAGAAGACTAATG 58.442 37.037 0.00 0.00 0.00 1.90
3328 5825 9.573133 CATGATTACCTCAAATAAGAACCAAAC 57.427 33.333 0.00 0.00 37.44 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.839994 TGCTGGGTGGAGAAGGATTAG 59.160 52.381 0.00 0.00 0.00 1.73
7 8 1.965414 TGCTGGGTGGAGAAGGATTA 58.035 50.000 0.00 0.00 0.00 1.75
8 9 1.302907 ATGCTGGGTGGAGAAGGATT 58.697 50.000 0.00 0.00 0.00 3.01
11 12 2.806945 TTTATGCTGGGTGGAGAAGG 57.193 50.000 0.00 0.00 0.00 3.46
12 13 6.966534 ATTTATTTATGCTGGGTGGAGAAG 57.033 37.500 0.00 0.00 0.00 2.85
13 14 7.502226 CAGTATTTATTTATGCTGGGTGGAGAA 59.498 37.037 0.00 0.00 35.41 2.87
14 15 6.998074 CAGTATTTATTTATGCTGGGTGGAGA 59.002 38.462 0.00 0.00 35.41 3.71
15 16 6.294176 GCAGTATTTATTTATGCTGGGTGGAG 60.294 42.308 0.00 0.00 38.30 3.86
16 17 5.534654 GCAGTATTTATTTATGCTGGGTGGA 59.465 40.000 0.00 0.00 38.30 4.02
17 18 5.278957 GGCAGTATTTATTTATGCTGGGTGG 60.279 44.000 0.00 0.00 38.30 4.61
18 19 5.278957 GGGCAGTATTTATTTATGCTGGGTG 60.279 44.000 0.00 0.00 38.30 4.61
19 20 4.832823 GGGCAGTATTTATTTATGCTGGGT 59.167 41.667 0.00 0.00 38.30 4.51
20 21 4.220602 GGGGCAGTATTTATTTATGCTGGG 59.779 45.833 0.00 0.00 38.30 4.45
21 22 4.220602 GGGGGCAGTATTTATTTATGCTGG 59.779 45.833 0.00 0.00 38.30 4.85
22 23 5.391312 GGGGGCAGTATTTATTTATGCTG 57.609 43.478 0.00 0.00 40.09 4.41
63 68 3.254024 TTCCGTTCCTGGGAGCTGC 62.254 63.158 0.00 0.00 34.45 5.25
87 98 0.181350 ACGAGATTGGCTGGGGATTC 59.819 55.000 0.00 0.00 0.00 2.52
164 176 2.602676 CGGGGAGAGGGGAAGCAAA 61.603 63.158 0.00 0.00 0.00 3.68
232 258 3.377439 GGAGCAAAAACCGACGAAATTT 58.623 40.909 0.00 0.00 0.00 1.82
247 273 0.812811 GCAGCATCAGATCGGAGCAA 60.813 55.000 15.46 0.00 0.00 3.91
266 292 1.461888 GGACAACAAGAATCGTTCGCG 60.462 52.381 0.00 0.00 42.98 5.87
268 294 2.055838 TCGGACAACAAGAATCGTTCG 58.944 47.619 0.00 0.00 34.02 3.95
351 377 4.662179 AGATCTGCCCCTTCAATCTATCAA 59.338 41.667 0.00 0.00 0.00 2.57
352 378 4.041321 CAGATCTGCCCCTTCAATCTATCA 59.959 45.833 10.38 0.00 0.00 2.15
353 379 4.041444 ACAGATCTGCCCCTTCAATCTATC 59.959 45.833 22.83 0.00 0.00 2.08
354 380 3.979347 ACAGATCTGCCCCTTCAATCTAT 59.021 43.478 22.83 0.00 0.00 1.98
355 381 3.387962 ACAGATCTGCCCCTTCAATCTA 58.612 45.455 22.83 0.00 0.00 1.98
356 382 2.203584 ACAGATCTGCCCCTTCAATCT 58.796 47.619 22.83 0.00 0.00 2.40
357 383 2.725221 ACAGATCTGCCCCTTCAATC 57.275 50.000 22.83 0.00 0.00 2.67
358 384 2.681976 CGAACAGATCTGCCCCTTCAAT 60.682 50.000 22.83 0.00 0.00 2.57
413 823 3.809832 ACAAATCATGCATACGAGCCTAC 59.190 43.478 0.00 0.00 0.00 3.18
449 859 1.442769 GAATCTTTCACGCAGGAGCA 58.557 50.000 0.00 0.00 42.27 4.26
462 872 9.330063 TCAATCATAAAGAGTTATGCGAATCTT 57.670 29.630 2.26 0.00 44.30 2.40
539 1000 7.066766 GGTTAGGACTATCTCGTTAGAACAAGA 59.933 40.741 0.00 0.00 34.73 3.02
628 1146 5.366477 TCAAGGATTCCACATAGCTGTCATA 59.634 40.000 5.29 0.00 31.62 2.15
629 1147 4.164796 TCAAGGATTCCACATAGCTGTCAT 59.835 41.667 5.29 0.00 31.62 3.06
630 1148 3.519107 TCAAGGATTCCACATAGCTGTCA 59.481 43.478 5.29 0.00 31.62 3.58
653 1177 2.030823 ACGTGCGTGCAGATCAATTATG 59.969 45.455 0.00 0.00 0.00 1.90
710 1296 7.064253 GGTAGATAATAAACAAACGACAGCAGT 59.936 37.037 0.00 0.00 0.00 4.40
745 1331 8.829612 GCTCATCTTTTTCCAAGAAAAATCAAA 58.170 29.630 13.85 3.73 0.00 2.69
766 1353 6.590068 AGCTGTCAGACATTATTTAGCTCAT 58.410 36.000 2.97 0.00 35.54 2.90
768 1355 6.143118 CGTAGCTGTCAGACATTATTTAGCTC 59.857 42.308 13.00 6.38 40.40 4.09
777 1365 1.893137 TCCACGTAGCTGTCAGACATT 59.107 47.619 2.97 0.00 0.00 2.71
873 1523 7.386848 CCGTAGAGATTAAACAAACAGGAGAAA 59.613 37.037 0.00 0.00 0.00 2.52
931 1592 7.629222 GCAGACCAAGCAAACTAATATGACAAT 60.629 37.037 0.00 0.00 0.00 2.71
1904 3835 1.669115 CAGACGCAGGACAAGGTGG 60.669 63.158 0.00 0.00 0.00 4.61
1922 3853 3.117175 GATCTGCATGCCACCACGC 62.117 63.158 16.68 0.00 0.00 5.34
1973 3904 0.962489 CAGACGACTCCACCTCAAGT 59.038 55.000 0.00 0.00 0.00 3.16
1986 3917 2.900716 TTGTCAATGGTGTCAGACGA 57.099 45.000 0.00 0.00 33.83 4.20
1987 3918 2.807967 ACATTGTCAATGGTGTCAGACG 59.192 45.455 25.59 1.35 43.21 4.18
1988 3919 3.814842 TGACATTGTCAATGGTGTCAGAC 59.185 43.478 25.59 0.00 44.14 3.51
2337 4296 5.335661 GCACAAGATTTACCCGAAAGTTCAT 60.336 40.000 0.00 0.00 0.00 2.57
2442 4401 2.035530 AGTAGGATCAAGCAAGCAGC 57.964 50.000 0.00 0.00 46.19 5.25
2443 4402 3.341823 ACAAGTAGGATCAAGCAAGCAG 58.658 45.455 0.00 0.00 0.00 4.24
2444 4403 3.423539 ACAAGTAGGATCAAGCAAGCA 57.576 42.857 0.00 0.00 0.00 3.91
2445 4404 4.201861 GCTAACAAGTAGGATCAAGCAAGC 60.202 45.833 0.00 0.00 0.00 4.01
2446 4405 5.064452 CAGCTAACAAGTAGGATCAAGCAAG 59.936 44.000 0.00 0.00 0.00 4.01
2447 4406 4.937620 CAGCTAACAAGTAGGATCAAGCAA 59.062 41.667 0.00 0.00 0.00 3.91
2448 4407 4.020218 ACAGCTAACAAGTAGGATCAAGCA 60.020 41.667 0.00 0.00 0.00 3.91
2449 4408 4.508662 ACAGCTAACAAGTAGGATCAAGC 58.491 43.478 0.00 0.00 0.00 4.01
2462 4421 5.079689 TCATCCAAATCGTACAGCTAACA 57.920 39.130 0.00 0.00 0.00 2.41
2566 4527 9.892130 AAAAATTGGAAGGTTACACAATTAACA 57.108 25.926 0.00 0.00 41.24 2.41
2572 4533 5.734720 TGCAAAAATTGGAAGGTTACACAA 58.265 33.333 0.00 0.00 0.00 3.33
2573 4534 5.344743 TGCAAAAATTGGAAGGTTACACA 57.655 34.783 0.00 0.00 0.00 3.72
2574 4535 4.211164 GCTGCAAAAATTGGAAGGTTACAC 59.789 41.667 0.00 0.00 0.00 2.90
2678 4664 4.318546 GCGGCCTATTGTTTAGTATCAACG 60.319 45.833 0.00 0.00 0.00 4.10
2764 4811 7.131498 GCCAGTTGCATTTGATTGAAAATAA 57.869 32.000 0.00 0.00 40.77 1.40
2854 5296 1.234821 TGTTTGCGCTTAGAGTTGGG 58.765 50.000 9.73 0.00 0.00 4.12
2859 5301 2.351738 CCCCTTTTGTTTGCGCTTAGAG 60.352 50.000 9.73 0.00 0.00 2.43
2888 5330 5.334319 CGATTTGTATTTTCTCATGCTGCA 58.666 37.500 4.13 4.13 0.00 4.41
2947 5391 9.111613 TGCAAAATGAATTTTCAGAACTCAAAT 57.888 25.926 0.00 0.00 41.08 2.32
3030 5501 2.747799 GCCCTGAACTCAATCATCTCCC 60.748 54.545 0.00 0.00 0.00 4.30
3282 5771 9.985730 AATCATGTCATGTTAGTTTCATTTTGT 57.014 25.926 12.54 0.00 0.00 2.83
3328 5825 3.440522 TGTTGTCGATGGAGTCAGTCTAG 59.559 47.826 0.00 0.00 0.00 2.43
3579 6118 4.503714 TGTCTAGGGTTTCAATCATCCC 57.496 45.455 0.00 0.00 40.16 3.85


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

AutoCloner maintained by Alex Coulton.