Multiple sequence alignment - TraesCS6A01G391000

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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 TraesCS6A01G391000 chr6A 100.000 3654 0 0 1 3654 605877032 605873379 0.000000e+00 6748.0
1 TraesCS6A01G391000 chr6A 95.556 360 16 0 881 1240 605882347 605881988 8.800000e-161 577.0
2 TraesCS6A01G391000 chr6D 95.706 2422 93 6 1240 3654 459935902 459933485 0.000000e+00 3886.0
3 TraesCS6A01G391000 chr6D 76.860 121 13 10 437 544 38642739 38642857 2.000000e-03 54.7
4 TraesCS6A01G391000 chr2D 96.811 439 12 2 1 438 382430780 382431217 0.000000e+00 732.0
5 TraesCS6A01G391000 chr2D 90.281 391 25 8 873 1252 532444311 532443923 1.960000e-137 499.0
6 TraesCS6A01G391000 chr3A 92.841 447 22 2 436 878 632362644 632363084 1.110000e-179 640.0
7 TraesCS6A01G391000 chr3A 85.641 585 64 13 2322 2898 17270024 17269452 6.750000e-167 597.0
8 TraesCS6A01G391000 chr3A 74.847 1308 283 29 1240 2523 57566440 57567725 5.330000e-153 551.0
9 TraesCS6A01G391000 chr3A 93.048 374 22 1 870 1243 632363129 632363498 8.920000e-151 544.0
10 TraesCS6A01G391000 chr3A 96.457 254 8 1 185 438 632360794 632361046 5.640000e-113 418.0
11 TraesCS6A01G391000 chr3A 87.302 189 8 1 1 189 632305118 632305290 6.190000e-48 202.0
12 TraesCS6A01G391000 chr5D 90.807 446 29 5 436 875 106680429 106680868 1.460000e-163 586.0
13 TraesCS6A01G391000 chr5D 91.870 369 29 1 873 1241 302023251 302022884 7.000000e-142 514.0
14 TraesCS6A01G391000 chr5D 87.200 250 26 5 537 784 10626794 10626549 2.780000e-71 279.0
15 TraesCS6A01G391000 chr5D 85.496 262 26 10 184 438 29885803 29886059 2.800000e-66 263.0
16 TraesCS6A01G391000 chr5D 90.769 195 14 4 245 438 30541937 30542128 1.300000e-64 257.0
17 TraesCS6A01G391000 chr5D 97.260 73 2 0 1 73 275556665 275556737 1.380000e-24 124.0
18 TraesCS6A01G391000 chr6B 93.478 368 24 0 873 1240 49354191 49353824 6.900000e-152 547.0
19 TraesCS6A01G391000 chr6B 95.946 74 2 1 1 73 261844869 261844942 6.410000e-23 119.0
20 TraesCS6A01G391000 chr4A 93.207 368 25 0 873 1240 625204622 625204255 3.210000e-150 542.0
21 TraesCS6A01G391000 chr4A 94.524 347 19 0 894 1240 625227336 625226990 1.490000e-148 536.0
22 TraesCS6A01G391000 chr1B 92.141 369 28 1 873 1240 42163684 42163316 1.500000e-143 520.0
23 TraesCS6A01G391000 chr1A 91.200 375 28 4 873 1245 99196827 99197198 4.210000e-139 505.0
24 TraesCS6A01G391000 chr5A 90.663 332 28 1 550 878 685443027 685442696 4.330000e-119 438.0
25 TraesCS6A01G391000 chr5A 89.811 265 24 3 616 878 567761862 567762125 1.630000e-88 337.0
26 TraesCS6A01G391000 chr7A 85.749 407 27 13 444 834 731024977 731025368 5.680000e-108 401.0
27 TraesCS6A01G391000 chr2A 88.652 282 23 7 487 761 537437710 537437431 5.850000e-88 335.0
28 TraesCS6A01G391000 chr3D 86.620 284 30 6 535 816 486792237 486791960 1.270000e-79 307.0
29 TraesCS6A01G391000 chr3D 86.800 250 27 6 537 784 62914494 62914739 1.290000e-69 274.0
30 TraesCS6A01G391000 chr3D 91.795 195 12 4 245 438 83876662 83876471 6.010000e-68 268.0
31 TraesCS6A01G391000 chr3D 84.733 262 28 10 184 438 308784210 308784466 6.060000e-63 252.0
32 TraesCS6A01G391000 chr3D 90.206 194 14 5 245 436 32333067 32333257 7.840000e-62 248.0
33 TraesCS6A01G391000 chr3D 96.053 76 3 0 1 76 31879885 31879810 1.380000e-24 124.0
34 TraesCS6A01G391000 chr3D 96.053 76 3 0 1 76 83876932 83876857 1.380000e-24 124.0
35 TraesCS6A01G391000 chr3D 96.875 32 1 0 437 468 41062503 41062534 2.000000e-03 54.7
36 TraesCS6A01G391000 chr7D 85.115 262 27 10 184 438 612700844 612701100 1.300000e-64 257.0
37 TraesCS6A01G391000 chr7D 89.286 196 16 5 245 438 16163365 16163173 1.310000e-59 241.0
38 TraesCS6A01G391000 chr7D 94.805 77 3 1 1 76 420755489 420755413 6.410000e-23 119.0
39 TraesCS6A01G391000 chr4D 94.737 76 4 0 1 76 301520051 301519976 6.410000e-23 119.0
40 TraesCS6A01G391000 chr1D 95.946 74 2 1 1 73 10568457 10568530 6.410000e-23 119.0


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 TraesCS6A01G391000 chr6A 605873379 605877032 3653 True 6748 6748 100.000000 1 3654 1 chr6A.!!$R1 3653
1 TraesCS6A01G391000 chr6D 459933485 459935902 2417 True 3886 3886 95.706000 1240 3654 1 chr6D.!!$R1 2414
2 TraesCS6A01G391000 chr3A 17269452 17270024 572 True 597 597 85.641000 2322 2898 1 chr3A.!!$R1 576
3 TraesCS6A01G391000 chr3A 57566440 57567725 1285 False 551 551 74.847000 1240 2523 1 chr3A.!!$F1 1283
4 TraesCS6A01G391000 chr3A 632360794 632363498 2704 False 534 640 94.115333 185 1243 3 chr3A.!!$F3 1058

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
687 2292 0.317269 CGTGGCTGTTGTGCTCTTTG 60.317 55.0 0.00 0.00 0.00 2.77 F
956 2614 0.733909 TGCTGCAGACGAACTCGATG 60.734 55.0 20.43 5.54 43.02 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1587 3248 0.465460 TGGCTTTCCTGCGTTGAAGT 60.465 50.0 0.0 0.0 0.0 3.01 R
2901 4582 0.378257 CCTTGGTTGATGATTCGGCG 59.622 55.0 0.0 0.0 0.0 6.46 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
68 69 8.776376 TTTGCATTTTCAGAAACTTTTTCTCT 57.224 26.923 0.00 0.00 0.00 3.10
69 70 7.992180 TGCATTTTCAGAAACTTTTTCTCTC 57.008 32.000 0.00 0.00 0.00 3.20
70 71 7.546358 TGCATTTTCAGAAACTTTTTCTCTCA 58.454 30.769 0.00 0.00 0.00 3.27
71 72 7.489113 TGCATTTTCAGAAACTTTTTCTCTCAC 59.511 33.333 0.00 0.00 0.00 3.51
72 73 7.704047 GCATTTTCAGAAACTTTTTCTCTCACT 59.296 33.333 0.00 0.00 0.00 3.41
73 74 9.230932 CATTTTCAGAAACTTTTTCTCTCACTC 57.769 33.333 0.00 0.00 0.00 3.51
74 75 8.567285 TTTTCAGAAACTTTTTCTCTCACTCT 57.433 30.769 0.00 0.00 0.00 3.24
75 76 8.567285 TTTCAGAAACTTTTTCTCTCACTCTT 57.433 30.769 0.00 0.00 0.00 2.85
76 77 7.545362 TCAGAAACTTTTTCTCTCACTCTTG 57.455 36.000 0.00 0.00 0.00 3.02
77 78 7.331026 TCAGAAACTTTTTCTCTCACTCTTGA 58.669 34.615 0.00 0.00 0.00 3.02
78 79 7.824289 TCAGAAACTTTTTCTCTCACTCTTGAA 59.176 33.333 0.00 0.00 0.00 2.69
79 80 8.619546 CAGAAACTTTTTCTCTCACTCTTGAAT 58.380 33.333 0.00 0.00 0.00 2.57
80 81 9.838339 AGAAACTTTTTCTCTCACTCTTGAATA 57.162 29.630 0.00 0.00 0.00 1.75
139 140 5.728637 AAAAGGGGAGAAATAAACTGCAG 57.271 39.130 13.48 13.48 0.00 4.41
140 141 2.728007 AGGGGAGAAATAAACTGCAGC 58.272 47.619 15.27 0.00 0.00 5.25
141 142 2.041620 AGGGGAGAAATAAACTGCAGCA 59.958 45.455 15.27 0.00 0.00 4.41
142 143 3.026694 GGGGAGAAATAAACTGCAGCAT 58.973 45.455 15.27 5.23 0.00 3.79
143 144 4.079787 AGGGGAGAAATAAACTGCAGCATA 60.080 41.667 15.27 7.63 0.00 3.14
144 145 4.276926 GGGGAGAAATAAACTGCAGCATAG 59.723 45.833 15.27 0.00 0.00 2.23
145 146 4.261363 GGGAGAAATAAACTGCAGCATAGC 60.261 45.833 15.27 0.00 0.00 2.97
146 147 4.261363 GGAGAAATAAACTGCAGCATAGCC 60.261 45.833 15.27 0.16 0.00 3.93
147 148 3.313526 AGAAATAAACTGCAGCATAGCCG 59.686 43.478 15.27 0.00 0.00 5.52
148 149 1.597742 ATAAACTGCAGCATAGCCGG 58.402 50.000 15.27 0.00 0.00 6.13
149 150 1.095228 TAAACTGCAGCATAGCCGGC 61.095 55.000 21.89 21.89 0.00 6.13
150 151 4.864334 ACTGCAGCATAGCCGGCC 62.864 66.667 26.15 7.74 0.00 6.13
151 152 4.559063 CTGCAGCATAGCCGGCCT 62.559 66.667 26.15 10.49 0.00 5.19
152 153 4.552365 TGCAGCATAGCCGGCCTC 62.552 66.667 26.15 9.93 0.00 4.70
153 154 4.552365 GCAGCATAGCCGGCCTCA 62.552 66.667 26.15 9.51 0.00 3.86
154 155 2.280660 CAGCATAGCCGGCCTCAG 60.281 66.667 26.15 12.37 0.00 3.35
155 156 4.247380 AGCATAGCCGGCCTCAGC 62.247 66.667 26.15 22.04 38.76 4.26
438 439 4.007644 CCCACTGGCTGAGCACGA 62.008 66.667 6.82 0.00 0.00 4.35
474 2075 0.868406 CGCGAGCACCTTTTCTTCTT 59.132 50.000 0.00 0.00 0.00 2.52
478 2079 3.487207 GCGAGCACCTTTTCTTCTTTTTG 59.513 43.478 0.00 0.00 0.00 2.44
499 2100 4.269183 TGCTTCCTTAGACAGAGAGAGAG 58.731 47.826 0.00 0.00 0.00 3.20
500 2101 4.018870 TGCTTCCTTAGACAGAGAGAGAGA 60.019 45.833 0.00 0.00 0.00 3.10
501 2102 4.576463 GCTTCCTTAGACAGAGAGAGAGAG 59.424 50.000 0.00 0.00 0.00 3.20
502 2103 5.629133 GCTTCCTTAGACAGAGAGAGAGAGA 60.629 48.000 0.00 0.00 0.00 3.10
503 2104 5.614324 TCCTTAGACAGAGAGAGAGAGAG 57.386 47.826 0.00 0.00 0.00 3.20
504 2105 5.277250 TCCTTAGACAGAGAGAGAGAGAGA 58.723 45.833 0.00 0.00 0.00 3.10
548 2149 2.436646 CCTCGCGCCACCTTTCAT 60.437 61.111 0.00 0.00 0.00 2.57
569 2174 2.243810 AGAGAGAGGGAGACACACAAC 58.756 52.381 0.00 0.00 0.00 3.32
585 2190 0.677098 CAACTGCATCCTGCTCTGCT 60.677 55.000 0.34 0.00 45.31 4.24
598 2203 2.182030 CTGCTCCCCTTCGACGAC 59.818 66.667 0.00 0.00 0.00 4.34
606 2211 4.695231 CTTCGACGACGGTGGCGT 62.695 66.667 7.55 0.00 45.79 5.68
625 2230 4.035102 GTTGCCTCCCCTTCGCCT 62.035 66.667 0.00 0.00 0.00 5.52
687 2292 0.317269 CGTGGCTGTTGTGCTCTTTG 60.317 55.000 0.00 0.00 0.00 2.77
710 2315 1.626825 CCTTTCGGGGTAGGTTCTTCA 59.373 52.381 0.00 0.00 0.00 3.02
736 2341 2.437359 GCCTCGGCTTGCAGATGT 60.437 61.111 0.00 0.00 38.26 3.06
762 2367 3.701604 GATCGAGCGGAACAGGCGT 62.702 63.158 0.00 0.00 35.00 5.68
836 2441 7.321034 CAGTGAAAACTTTGTTCTTTTGTTTGC 59.679 33.333 0.00 0.00 32.20 3.68
843 2448 8.153479 ACTTTGTTCTTTTGTTTGCTTTTCTT 57.847 26.923 0.00 0.00 0.00 2.52
956 2614 0.733909 TGCTGCAGACGAACTCGATG 60.734 55.000 20.43 5.54 43.02 3.84
1035 2693 4.680237 CTTCCCGTGAGCGCCACA 62.680 66.667 22.90 13.81 45.98 4.17
1049 2707 1.269102 CGCCACACTAACCCTAGATCG 60.269 57.143 0.00 0.00 0.00 3.69
1065 2723 1.605058 ATCGGAAGGGAGTGTCGGTG 61.605 60.000 0.00 0.00 0.00 4.94
1072 2730 1.078426 GGAGTGTCGGTGGGGATTG 60.078 63.158 0.00 0.00 0.00 2.67
1076 2734 2.150719 TGTCGGTGGGGATTGTGGT 61.151 57.895 0.00 0.00 0.00 4.16
1080 2738 1.688811 GGTGGGGATTGTGGTAGCA 59.311 57.895 0.00 0.00 0.00 3.49
1104 2762 2.642254 CCTCGTAAGTCGTGCCCCA 61.642 63.158 0.00 0.00 40.80 4.96
1129 2787 3.326747 CCCACCTCTGTTTATATAGCGC 58.673 50.000 0.00 0.00 0.00 5.92
1189 2847 2.278206 CGATCAGGGCACGAGTCG 60.278 66.667 11.85 11.85 0.00 4.18
1191 2849 1.064946 GATCAGGGCACGAGTCGAG 59.935 63.158 21.50 13.23 0.00 4.04
1227 2885 1.108776 TGGGTTCGAACGGGATAGAG 58.891 55.000 21.34 0.00 0.00 2.43
1254 2912 4.202441 ACCTAACAGCCTTATCAATGCAG 58.798 43.478 0.00 0.00 0.00 4.41
1271 2929 4.340894 TGCAGACAATTTAAGCGATGAC 57.659 40.909 0.00 0.00 0.00 3.06
1282 2940 2.898729 AGCGATGACGAGGATGATTT 57.101 45.000 0.00 0.00 42.66 2.17
1325 2984 1.207089 CACAGATTGGGGAACTCGCTA 59.793 52.381 0.00 0.00 0.00 4.26
1444 3105 5.696270 TGCGTGATCACATTTATATGACCTC 59.304 40.000 24.93 0.00 35.65 3.85
1587 3248 6.852420 ACTAGGTTTATGTAGACAAGCTGA 57.148 37.500 0.00 0.00 30.99 4.26
1603 3264 1.069636 GCTGACTTCAACGCAGGAAAG 60.070 52.381 0.00 0.00 0.00 2.62
1645 3312 0.515564 CGGCAAACCTTTCGAATCGT 59.484 50.000 1.52 0.00 0.00 3.73
1681 3348 0.826256 AGGGCGACACACTCACTGTA 60.826 55.000 0.00 0.00 0.00 2.74
1724 3391 1.000717 TCAGTTCTTCACGCGATGTCA 60.001 47.619 15.93 0.00 0.00 3.58
1750 3417 3.422417 GCTACTGCTCGTGATCTAACA 57.578 47.619 0.00 0.00 36.03 2.41
1806 3473 1.192803 GGTGAAGGACGGGAGAACCT 61.193 60.000 0.00 0.00 40.40 3.50
1813 3480 2.500504 AGGACGGGAGAACCTGATAAAC 59.499 50.000 0.00 0.00 44.87 2.01
1879 3546 4.906065 TGATGCTGGCAAATTCAGTATC 57.094 40.909 13.44 13.44 46.95 2.24
1950 3617 1.742880 CCATGCGTGTGGAGGACAG 60.743 63.158 4.96 0.00 42.02 3.51
1964 3631 1.202770 AGGACAGAAACCCAAACCTCG 60.203 52.381 0.00 0.00 0.00 4.63
2141 3814 8.733458 TCAATCCTTTAGTTGATGATGTTGAAG 58.267 33.333 0.00 0.00 29.93 3.02
2142 3815 6.500684 TCCTTTAGTTGATGATGTTGAAGC 57.499 37.500 0.00 0.00 0.00 3.86
2203 3876 9.500785 TCTTGTAATGTCACAGATTCAACATTA 57.499 29.630 3.38 3.38 41.31 1.90
2209 3882 8.975663 ATGTCACAGATTCAACATTATCATCT 57.024 30.769 0.00 0.00 0.00 2.90
2237 3910 3.206150 AGTACTTGTGTTGTGGCTTCAG 58.794 45.455 0.00 0.00 0.00 3.02
2276 3949 1.135024 CAGCCAACACATGTATTGGGC 60.135 52.381 31.67 24.02 44.76 5.36
2312 3985 5.096443 TGTTGGCACATCTGACATACATA 57.904 39.130 0.00 0.00 34.40 2.29
2354 4027 1.800586 TGCATCAGAAACGTGAAGCTC 59.199 47.619 0.00 0.00 40.90 4.09
2389 4062 7.067494 GGAGATAACCATTGTATTGAAAGCAGT 59.933 37.037 0.00 0.00 0.00 4.40
2403 4076 0.689623 AGCAGTAGCAAAGGCACTCT 59.310 50.000 0.00 0.00 45.49 3.24
2413 4086 3.430374 GCAAAGGCACTCTAGAACCGATA 60.430 47.826 0.00 0.00 38.49 2.92
2426 4099 7.617225 TCTAGAACCGATAAAAACTCATGGAA 58.383 34.615 0.00 0.00 0.00 3.53
2509 4183 3.266510 AGCTCGGATGTTGATGCTAAA 57.733 42.857 0.00 0.00 0.00 1.85
2542 4216 0.179108 GTGACGAGGTGCCACTATCC 60.179 60.000 0.00 0.00 0.00 2.59
2550 4224 4.523083 GAGGTGCCACTATCCAAAATACA 58.477 43.478 0.00 0.00 0.00 2.29
2572 4246 6.410540 ACATAAGTTGAACCCAAAAAGCAAA 58.589 32.000 0.00 0.00 33.49 3.68
2711 4392 4.540824 GAGCCAAACAATTGAGTCTGAAC 58.459 43.478 13.59 0.39 38.94 3.18
2735 4416 0.179004 TGTCAATTGTTGCCCCGTCT 60.179 50.000 5.13 0.00 0.00 4.18
2787 4468 1.217916 TCTGGGTGGTCAAAGTTCCA 58.782 50.000 0.00 0.00 0.00 3.53
2802 4483 2.513204 CCATGAGTCCAGCCAGCG 60.513 66.667 0.00 0.00 0.00 5.18
2853 4534 7.478667 GCTTACAAACATTATCTGACAAACTCG 59.521 37.037 0.00 0.00 0.00 4.18
2901 4582 3.526534 GTGAGCCAGTTCTCTTGATACC 58.473 50.000 0.00 0.00 34.29 2.73
2922 4603 1.401905 GCCGAATCATCAACCAAGGTC 59.598 52.381 0.00 0.00 0.00 3.85
2930 4611 4.984295 TCATCAACCAAGGTCAGAATTCA 58.016 39.130 8.44 0.00 0.00 2.57
2945 4626 8.302438 GGTCAGAATTCAGAGAAATCATGTTTT 58.698 33.333 8.44 1.33 0.00 2.43
2965 4646 7.326454 TGTTTTTGAACAGGAATTCATTGACA 58.674 30.769 7.93 8.25 38.37 3.58
3093 4774 6.526566 AACAATCGTTAGTTCACTGTCTTC 57.473 37.500 0.00 0.00 32.05 2.87
3096 4777 3.639538 TCGTTAGTTCACTGTCTTCTGC 58.360 45.455 0.00 0.00 0.00 4.26
3116 4797 3.251487 TGCAGATATTCAATGCATCACCG 59.749 43.478 0.00 0.00 44.56 4.94
3121 4802 7.416817 CAGATATTCAATGCATCACCGTTTTA 58.583 34.615 0.00 0.00 0.00 1.52
3122 4803 7.376866 CAGATATTCAATGCATCACCGTTTTAC 59.623 37.037 0.00 0.00 0.00 2.01
3171 4852 3.786635 AGAACTGATGAAGCCATACGAC 58.213 45.455 0.00 0.00 32.09 4.34
3296 4977 4.381398 CGAATCCACTAGAGCCATGATAGG 60.381 50.000 0.00 0.00 0.00 2.57
3302 4983 5.126869 CCACTAGAGCCATGATAGGATAGTG 59.873 48.000 0.00 5.22 39.22 2.74
3348 5029 9.780186 AATAGGGTTATTGAAATGAGTAGCTAC 57.220 33.333 16.43 16.43 0.00 3.58
3417 5098 5.781210 ATCACACATCTCATCGTAGTCAT 57.219 39.130 0.00 0.00 0.00 3.06
3422 5103 4.278419 CACATCTCATCGTAGTCATACCCA 59.722 45.833 0.00 0.00 0.00 4.51
3433 5114 4.380843 AGTCATACCCAATCACCAACAA 57.619 40.909 0.00 0.00 0.00 2.83
3632 5313 3.556999 TGGCCTGTAGCAAAAAGTAACA 58.443 40.909 3.32 0.00 46.50 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 9.387257 AGAGAAAAAGTTTCTGAAAATGCAAAT 57.613 25.926 7.93 0.00 0.00 2.32
43 44 8.776376 AGAGAAAAAGTTTCTGAAAATGCAAA 57.224 26.923 7.93 0.00 0.00 3.68
44 45 8.034215 TGAGAGAAAAAGTTTCTGAAAATGCAA 58.966 29.630 7.93 0.00 0.00 4.08
45 46 7.489113 GTGAGAGAAAAAGTTTCTGAAAATGCA 59.511 33.333 7.93 0.00 0.00 3.96
46 47 7.704047 AGTGAGAGAAAAAGTTTCTGAAAATGC 59.296 33.333 7.93 0.00 0.00 3.56
47 48 9.230932 GAGTGAGAGAAAAAGTTTCTGAAAATG 57.769 33.333 7.93 0.00 0.00 2.32
48 49 9.183368 AGAGTGAGAGAAAAAGTTTCTGAAAAT 57.817 29.630 7.93 0.03 0.00 1.82
49 50 8.567285 AGAGTGAGAGAAAAAGTTTCTGAAAA 57.433 30.769 7.93 0.00 0.00 2.29
50 51 8.454106 CAAGAGTGAGAGAAAAAGTTTCTGAAA 58.546 33.333 7.93 0.00 0.00 2.69
51 52 7.824289 TCAAGAGTGAGAGAAAAAGTTTCTGAA 59.176 33.333 7.93 0.00 0.00 3.02
52 53 7.331026 TCAAGAGTGAGAGAAAAAGTTTCTGA 58.669 34.615 7.93 0.00 0.00 3.27
53 54 7.545362 TCAAGAGTGAGAGAAAAAGTTTCTG 57.455 36.000 7.93 0.00 0.00 3.02
54 55 8.744568 ATTCAAGAGTGAGAGAAAAAGTTTCT 57.255 30.769 2.94 2.94 34.49 2.52
116 117 5.511373 GCTGCAGTTTATTTCTCCCCTTTTT 60.511 40.000 16.64 0.00 0.00 1.94
117 118 4.021104 GCTGCAGTTTATTTCTCCCCTTTT 60.021 41.667 16.64 0.00 0.00 2.27
118 119 3.511540 GCTGCAGTTTATTTCTCCCCTTT 59.488 43.478 16.64 0.00 0.00 3.11
119 120 3.092301 GCTGCAGTTTATTTCTCCCCTT 58.908 45.455 16.64 0.00 0.00 3.95
120 121 2.041620 TGCTGCAGTTTATTTCTCCCCT 59.958 45.455 16.64 0.00 0.00 4.79
121 122 2.446435 TGCTGCAGTTTATTTCTCCCC 58.554 47.619 16.64 0.00 0.00 4.81
122 123 4.261363 GCTATGCTGCAGTTTATTTCTCCC 60.261 45.833 16.64 0.00 0.00 4.30
123 124 4.261363 GGCTATGCTGCAGTTTATTTCTCC 60.261 45.833 16.64 2.02 34.04 3.71
124 125 4.553547 CGGCTATGCTGCAGTTTATTTCTC 60.554 45.833 16.64 0.00 34.04 2.87
125 126 3.313526 CGGCTATGCTGCAGTTTATTTCT 59.686 43.478 16.64 0.00 34.04 2.52
126 127 3.548818 CCGGCTATGCTGCAGTTTATTTC 60.549 47.826 16.64 0.00 32.89 2.17
127 128 2.358898 CCGGCTATGCTGCAGTTTATTT 59.641 45.455 16.64 0.00 32.89 1.40
128 129 1.949525 CCGGCTATGCTGCAGTTTATT 59.050 47.619 16.64 0.00 32.89 1.40
129 130 1.597742 CCGGCTATGCTGCAGTTTAT 58.402 50.000 16.64 10.19 32.89 1.40
130 131 1.095228 GCCGGCTATGCTGCAGTTTA 61.095 55.000 22.15 6.58 32.89 2.01
131 132 2.409870 GCCGGCTATGCTGCAGTTT 61.410 57.895 22.15 5.66 32.89 2.66
132 133 2.825836 GCCGGCTATGCTGCAGTT 60.826 61.111 22.15 6.05 32.89 3.16
133 134 4.864334 GGCCGGCTATGCTGCAGT 62.864 66.667 28.56 0.00 32.89 4.40
134 135 4.559063 AGGCCGGCTATGCTGCAG 62.559 66.667 28.56 10.11 32.89 4.41
135 136 4.552365 GAGGCCGGCTATGCTGCA 62.552 66.667 28.56 4.13 32.89 4.41
136 137 4.552365 TGAGGCCGGCTATGCTGC 62.552 66.667 28.56 7.55 32.89 5.25
137 138 2.280660 CTGAGGCCGGCTATGCTG 60.281 66.667 28.56 12.85 34.23 4.41
138 139 4.247380 GCTGAGGCCGGCTATGCT 62.247 66.667 28.56 15.32 41.43 3.79
235 236 0.818296 GAAAGAGGAGGCACGAGCTA 59.182 55.000 4.48 0.00 41.70 3.32
297 298 0.608308 TCCGTCGGATCGCTATGGAT 60.608 55.000 10.71 0.00 0.00 3.41
333 334 3.422732 CCGCATCGATCGATTTTGATCAG 60.423 47.826 27.45 14.61 44.02 2.90
397 398 3.179939 GAGAACGAACCGAGCGGC 61.180 66.667 9.14 0.00 39.32 6.53
398 399 2.874780 CGAGAACGAACCGAGCGG 60.875 66.667 7.48 7.48 42.66 5.52
399 400 3.533691 GCGAGAACGAACCGAGCG 61.534 66.667 0.00 0.00 42.66 5.03
471 2072 6.042093 TCTCTCTGTCTAAGGAAGCAAAAAGA 59.958 38.462 0.00 0.00 0.00 2.52
474 2075 5.540337 TCTCTCTCTGTCTAAGGAAGCAAAA 59.460 40.000 0.00 0.00 0.00 2.44
478 2079 4.523083 TCTCTCTCTCTGTCTAAGGAAGC 58.477 47.826 0.00 0.00 0.00 3.86
499 2100 0.593773 GCTTCGACCTCGCATCTCTC 60.594 60.000 0.00 0.00 39.60 3.20
500 2101 1.435515 GCTTCGACCTCGCATCTCT 59.564 57.895 0.00 0.00 39.60 3.10
501 2102 1.590259 GGCTTCGACCTCGCATCTC 60.590 63.158 0.00 0.00 39.60 2.75
502 2103 2.351244 TGGCTTCGACCTCGCATCT 61.351 57.895 0.00 0.00 39.60 2.90
503 2104 2.167861 GTGGCTTCGACCTCGCATC 61.168 63.158 0.00 0.00 39.60 3.91
504 2105 2.125512 GTGGCTTCGACCTCGCAT 60.126 61.111 0.00 0.00 39.60 4.73
548 2149 3.074687 AGTTGTGTGTCTCCCTCTCTCTA 59.925 47.826 0.00 0.00 0.00 2.43
585 2190 3.367743 CACCGTCGTCGAAGGGGA 61.368 66.667 27.35 0.00 36.74 4.81
606 2211 2.282180 GCGAAGGGGAGGCAACAA 60.282 61.111 0.00 0.00 41.41 2.83
625 2230 0.947180 GCTAAGGGAAACGCGTCACA 60.947 55.000 14.44 0.00 0.00 3.58
666 2271 2.947938 AAGAGCACAACAGCCACGCT 62.948 55.000 0.00 0.00 40.77 5.07
731 2336 2.413351 CGATCCCGTCGCACATCT 59.587 61.111 0.00 0.00 44.33 2.90
811 2416 7.226523 AGCAAACAAAAGAACAAAGTTTTCACT 59.773 29.630 0.00 0.00 30.68 3.41
965 2623 1.453928 GCCCCTACTTCACCATGGC 60.454 63.158 13.04 0.00 0.00 4.40
968 2626 2.375345 CCGGCCCCTACTTCACCAT 61.375 63.158 0.00 0.00 0.00 3.55
969 2627 3.006728 CCGGCCCCTACTTCACCA 61.007 66.667 0.00 0.00 0.00 4.17
970 2628 3.007323 ACCGGCCCCTACTTCACC 61.007 66.667 0.00 0.00 0.00 4.02
971 2629 1.623542 ATCACCGGCCCCTACTTCAC 61.624 60.000 0.00 0.00 0.00 3.18
1031 2689 2.662866 TCCGATCTAGGGTTAGTGTGG 58.337 52.381 0.00 0.00 0.00 4.17
1033 2691 3.297736 CCTTCCGATCTAGGGTTAGTGT 58.702 50.000 0.00 0.00 0.00 3.55
1035 2693 2.960163 CCCTTCCGATCTAGGGTTAGT 58.040 52.381 13.56 0.00 45.12 2.24
1049 2707 2.663196 CCACCGACACTCCCTTCC 59.337 66.667 0.00 0.00 0.00 3.46
1065 2723 3.383505 GGTTAATTGCTACCACAATCCCC 59.616 47.826 0.00 0.00 39.32 4.81
1072 2730 5.173664 ACTTACGAGGTTAATTGCTACCAC 58.826 41.667 8.39 2.64 36.87 4.16
1076 2734 5.097529 CACGACTTACGAGGTTAATTGCTA 58.902 41.667 0.00 0.00 45.77 3.49
1080 2738 3.256558 GGCACGACTTACGAGGTTAATT 58.743 45.455 0.00 0.00 45.77 1.40
1104 2762 2.280308 TATAAACAGAGGTGGGGGCT 57.720 50.000 0.00 0.00 0.00 5.19
1117 2775 2.729882 CTGTGACCCGCGCTATATAAAC 59.270 50.000 5.56 0.00 0.00 2.01
1227 2885 6.514048 GCATTGATAAGGCTGTTAGGTTGATC 60.514 42.308 0.00 0.00 34.89 2.92
1254 2912 3.863424 TCCTCGTCATCGCTTAAATTGTC 59.137 43.478 0.00 0.00 36.96 3.18
1271 2929 4.573607 TCTTTGATGCTCAAATCATCCTCG 59.426 41.667 10.45 0.00 44.37 4.63
1282 2940 2.839486 AGTTCGGTCTTTGATGCTCA 57.161 45.000 0.00 0.00 0.00 4.26
1325 2984 0.984995 GCCCCTGTTAGTTCTGGACT 59.015 55.000 0.00 0.00 42.55 3.85
1370 3029 0.746063 TGGCAAGACACAAAAGGCAG 59.254 50.000 0.00 0.00 0.00 4.85
1416 3076 7.166824 GTCATATAAATGTGATCACGCATACG 58.833 38.462 20.54 8.09 44.96 3.06
1460 3121 3.566351 ACATACACTCCATCTCGATCCA 58.434 45.455 0.00 0.00 0.00 3.41
1587 3248 0.465460 TGGCTTTCCTGCGTTGAAGT 60.465 50.000 0.00 0.00 0.00 3.01
1645 3312 2.294074 CCCTTTCTTGTTGTTGACGGA 58.706 47.619 0.00 0.00 0.00 4.69
1681 3348 3.375299 GCAACCTCTCATCGTTATTGCTT 59.625 43.478 0.00 0.00 38.30 3.91
1750 3417 0.623723 AATATGGACGGGCAACACCT 59.376 50.000 0.00 0.00 39.10 4.00
1879 3546 4.172505 CCTCATTGACTTCTGTTCTCTCG 58.827 47.826 0.00 0.00 0.00 4.04
1950 3617 1.670791 TGTCACGAGGTTTGGGTTTC 58.329 50.000 0.00 0.00 0.00 2.78
1964 3631 5.516339 CAGAGATTTGGTGTTGTTTTGTCAC 59.484 40.000 0.00 0.00 0.00 3.67
2115 3788 8.634335 TTCAACATCATCAACTAAAGGATTGA 57.366 30.769 0.00 0.00 39.09 2.57
2141 3814 1.360192 GTTGACACCCAAGCACTGC 59.640 57.895 0.00 0.00 35.03 4.40
2142 3815 0.664761 CTGTTGACACCCAAGCACTG 59.335 55.000 0.00 0.00 35.03 3.66
2203 3876 7.124901 ACAACACAAGTACTCTGGATAGATGAT 59.875 37.037 0.00 0.00 31.21 2.45
2209 3882 4.562757 GCCACAACACAAGTACTCTGGATA 60.563 45.833 0.00 0.00 0.00 2.59
2237 3910 3.367395 GCTGGAACTTTAGGTGAATTGCC 60.367 47.826 0.00 0.00 0.00 4.52
2276 3949 6.355397 TGTGCCAACATTTACATTTTGTTG 57.645 33.333 7.80 7.80 46.13 3.33
2312 3985 1.065551 GCCGTCTGCTTTGTTGTTTCT 59.934 47.619 0.00 0.00 36.87 2.52
2354 4027 1.200519 TGGTTATCTCCCCCAGTTCG 58.799 55.000 0.00 0.00 0.00 3.95
2389 4062 2.094182 CGGTTCTAGAGTGCCTTTGCTA 60.094 50.000 0.00 0.00 38.71 3.49
2403 4076 7.333423 CAGTTCCATGAGTTTTTATCGGTTCTA 59.667 37.037 0.00 0.00 0.00 2.10
2413 4086 3.896888 TGCCATCAGTTCCATGAGTTTTT 59.103 39.130 0.00 0.00 31.44 1.94
2426 4099 2.157738 GTCAGCTTCTTTGCCATCAGT 58.842 47.619 0.00 0.00 0.00 3.41
2509 4183 5.236478 CACCTCGTCACTGTTAACTTCATTT 59.764 40.000 7.22 0.00 0.00 2.32
2681 4362 5.774690 ACTCAATTGTTTGGCTCCAGATTTA 59.225 36.000 5.13 0.00 33.44 1.40
2711 4392 0.737019 GGGCAACAATTGACATGCGG 60.737 55.000 13.59 0.00 41.76 5.69
2735 4416 2.100197 AGCTCTGATACGCTTGTACCA 58.900 47.619 0.00 0.00 31.17 3.25
2787 4468 2.596851 AACCGCTGGCTGGACTCAT 61.597 57.895 9.58 0.00 0.00 2.90
2836 4517 5.578336 TGAGCTTCGAGTTTGTCAGATAATG 59.422 40.000 0.00 0.00 0.00 1.90
2842 4523 2.064762 CCTGAGCTTCGAGTTTGTCAG 58.935 52.381 0.00 5.73 32.81 3.51
2853 4534 3.744660 TCTTTTTGACCTCCTGAGCTTC 58.255 45.455 0.00 0.00 0.00 3.86
2901 4582 0.378257 CCTTGGTTGATGATTCGGCG 59.622 55.000 0.00 0.00 0.00 6.46
2922 4603 9.687210 TCAAAAACATGATTTCTCTGAATTCTG 57.313 29.630 7.05 6.50 0.00 3.02
2930 4611 7.587037 TCCTGTTCAAAAACATGATTTCTCT 57.413 32.000 0.00 0.00 44.18 3.10
2945 4626 5.244402 AGCATGTCAATGAATTCCTGTTCAA 59.756 36.000 2.27 0.00 41.09 2.69
2987 4668 5.948742 AACCATTGGAAGTTCCTTTCAAA 57.051 34.783 22.41 8.64 41.54 2.69
3096 4777 5.428496 AACGGTGATGCATTGAATATCTG 57.572 39.130 0.00 0.00 0.00 2.90
3114 4795 4.812626 AGTACTTGGTTGACAGTAAAACGG 59.187 41.667 0.00 0.00 0.00 4.44
3116 4797 6.673154 ACAGTACTTGGTTGACAGTAAAAC 57.327 37.500 0.00 0.00 0.00 2.43
3121 4802 6.655848 TGTAAAAACAGTACTTGGTTGACAGT 59.344 34.615 0.00 0.00 36.64 3.55
3122 4803 7.079182 TGTAAAAACAGTACTTGGTTGACAG 57.921 36.000 0.00 0.00 36.64 3.51
3302 4983 9.367444 CCCTATTGGTCTTGTAATCGATATAAC 57.633 37.037 0.00 0.00 0.00 1.89
3417 5098 2.666272 TGCTTGTTGGTGATTGGGTA 57.334 45.000 0.00 0.00 0.00 3.69
3460 5141 1.871039 GGCACGAGTTTGCAGAAGTAA 59.129 47.619 0.00 0.00 44.94 2.24
3586 5267 4.761739 CCAAGTTGCCATAGTCAGAGAAAA 59.238 41.667 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.