Multiple sequence alignment - TraesCS4B01G011100

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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 TraesCS4B01G011100 chr4B 100.000 4544 0 0 1 4544 7352622 7357165 0.000000e+00 8392.0
1 TraesCS4B01G011100 chr4B 94.476 4544 170 32 1 4481 7262177 7266702 0.000000e+00 6926.0
2 TraesCS4B01G011100 chr4B 95.011 4410 142 27 134 4481 7169735 7174128 0.000000e+00 6854.0
3 TraesCS4B01G011100 chr4B 94.696 4412 148 33 135 4481 7216695 7221085 0.000000e+00 6772.0
4 TraesCS4B01G011100 chr4B 94.493 4013 151 24 523 4481 7308198 7312194 0.000000e+00 6122.0
5 TraesCS4B01G011100 chr4B 82.514 692 88 15 826 1492 7381436 7382119 1.100000e-160 577.0
6 TraesCS4B01G011100 chr4B 80.930 645 65 30 58 677 415342086 415342697 1.490000e-124 457.0
7 TraesCS4B01G011100 chr4B 88.047 343 35 5 3405 3742 7378265 7378606 7.080000e-108 401.0
8 TraesCS4B01G011100 chr4B 87.048 332 17 4 134 465 7307995 7308300 7.230000e-93 351.0
9 TraesCS4B01G011100 chr4B 96.667 90 3 0 49 138 7165105 7165194 2.830000e-32 150.0
10 TraesCS4B01G011100 chr4B 96.667 90 3 0 49 138 7212068 7212157 2.830000e-32 150.0
11 TraesCS4B01G011100 chr4B 95.402 87 4 0 49 135 7303367 7303453 6.130000e-29 139.0
12 TraesCS4B01G011100 chr4D 91.291 3812 261 34 705 4481 4416851 4420626 0.000000e+00 5134.0
13 TraesCS4B01G011100 chr4D 86.120 915 88 21 671 1564 4458675 4459571 0.000000e+00 950.0
14 TraesCS4B01G011100 chr4D 100.000 38 0 0 4507 4544 285628907 285628870 2.270000e-08 71.3
15 TraesCS4B01G011100 chr4A 90.562 3486 234 24 734 4191 599179936 599176518 0.000000e+00 4527.0
16 TraesCS4B01G011100 chr4A 90.502 3485 237 27 734 4191 599223363 599219946 0.000000e+00 4516.0
17 TraesCS4B01G011100 chr4A 90.445 3485 239 22 734 4191 599102557 599099140 0.000000e+00 4505.0
18 TraesCS4B01G011100 chr4A 90.794 3172 230 30 1066 4198 598910263 598907115 0.000000e+00 4183.0
19 TraesCS4B01G011100 chr4A 90.602 3171 242 24 1066 4198 598960634 598957482 0.000000e+00 4154.0
20 TraesCS4B01G011100 chr4A 90.433 1317 78 19 734 2021 599126048 599124751 0.000000e+00 1690.0
21 TraesCS4B01G011100 chr4A 90.364 1318 79 16 734 2021 599248088 599246789 0.000000e+00 1687.0
22 TraesCS4B01G011100 chr4A 89.315 730 59 6 3464 4191 599123414 599122702 0.000000e+00 898.0
23 TraesCS4B01G011100 chr4A 81.818 121 17 5 557 674 622794466 622794348 3.740000e-16 97.1
24 TraesCS4B01G011100 chr4A 100.000 38 0 0 4507 4544 295799452 295799415 2.270000e-08 71.3
25 TraesCS4B01G011100 chrUn 89.776 1565 119 14 734 2276 360633173 360631628 0.000000e+00 1965.0
26 TraesCS4B01G011100 chrUn 91.522 920 52 5 1123 2021 216675822 216674908 0.000000e+00 1243.0
27 TraesCS4B01G011100 chrUn 88.935 479 35 6 734 1207 216652244 216651779 3.940000e-160 575.0
28 TraesCS4B01G011100 chr6A 90.274 730 52 3 3464 4191 593024590 593023878 0.000000e+00 937.0
29 TraesCS4B01G011100 chr3A 85.290 639 62 20 58 670 691379985 691379353 8.300000e-177 630.0
30 TraesCS4B01G011100 chr3A 78.862 123 17 6 554 671 667060967 667061085 1.750000e-09 75.0
31 TraesCS4B01G011100 chr3B 87.562 201 21 3 475 671 154038896 154038696 3.540000e-56 230.0
32 TraesCS4B01G011100 chr3B 84.091 88 10 4 475 558 154039005 154038918 1.050000e-11 82.4
33 TraesCS4B01G011100 chr3B 100.000 38 0 0 4507 4544 294307622 294307659 2.270000e-08 71.3
34 TraesCS4B01G011100 chr3B 100.000 38 0 0 4507 4544 778184411 778184374 2.270000e-08 71.3
35 TraesCS4B01G011100 chr6B 86.735 98 8 5 587 681 21490302 21490397 2.240000e-18 104.0
36 TraesCS4B01G011100 chr6B 86.170 94 10 3 584 675 30511733 30511641 1.040000e-16 99.0
37 TraesCS4B01G011100 chr6B 86.364 66 7 2 495 558 33088076 33088141 2.270000e-08 71.3
38 TraesCS4B01G011100 chr5B 100.000 38 0 0 4507 4544 406752700 406752737 2.270000e-08 71.3
39 TraesCS4B01G011100 chr3D 100.000 38 0 0 4507 4544 141795323 141795360 2.270000e-08 71.3
40 TraesCS4B01G011100 chr2D 100.000 38 0 0 4507 4544 121234046 121234083 2.270000e-08 71.3
41 TraesCS4B01G011100 chr2D 100.000 38 0 0 4507 4544 481947473 481947436 2.270000e-08 71.3
42 TraesCS4B01G011100 chr1B 100.000 38 0 0 4507 4544 298437933 298437970 2.270000e-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 TraesCS4B01G011100 chr4B 7352622 7357165 4543 False 8392.0 8392 100.0000 1 4544 1 chr4B.!!$F7 4543
1 TraesCS4B01G011100 chr4B 7262177 7266702 4525 False 6926.0 6926 94.4760 1 4481 1 chr4B.!!$F5 4480
2 TraesCS4B01G011100 chr4B 7169735 7174128 4393 False 6854.0 6854 95.0110 134 4481 1 chr4B.!!$F2 4347
3 TraesCS4B01G011100 chr4B 7216695 7221085 4390 False 6772.0 6772 94.6960 135 4481 1 chr4B.!!$F4 4346
4 TraesCS4B01G011100 chr4B 7307995 7312194 4199 False 3236.5 6122 90.7705 134 4481 2 chr4B.!!$F9 4347
5 TraesCS4B01G011100 chr4B 7378265 7382119 3854 False 489.0 577 85.2805 826 3742 2 chr4B.!!$F10 2916
6 TraesCS4B01G011100 chr4B 415342086 415342697 611 False 457.0 457 80.9300 58 677 1 chr4B.!!$F8 619
7 TraesCS4B01G011100 chr4D 4416851 4420626 3775 False 5134.0 5134 91.2910 705 4481 1 chr4D.!!$F1 3776
8 TraesCS4B01G011100 chr4D 4458675 4459571 896 False 950.0 950 86.1200 671 1564 1 chr4D.!!$F2 893
9 TraesCS4B01G011100 chr4A 599176518 599179936 3418 True 4527.0 4527 90.5620 734 4191 1 chr4A.!!$R5 3457
10 TraesCS4B01G011100 chr4A 599219946 599223363 3417 True 4516.0 4516 90.5020 734 4191 1 chr4A.!!$R6 3457
11 TraesCS4B01G011100 chr4A 599099140 599102557 3417 True 4505.0 4505 90.4450 734 4191 1 chr4A.!!$R4 3457
12 TraesCS4B01G011100 chr4A 598907115 598910263 3148 True 4183.0 4183 90.7940 1066 4198 1 chr4A.!!$R2 3132
13 TraesCS4B01G011100 chr4A 598957482 598960634 3152 True 4154.0 4154 90.6020 1066 4198 1 chr4A.!!$R3 3132
14 TraesCS4B01G011100 chr4A 599246789 599248088 1299 True 1687.0 1687 90.3640 734 2021 1 chr4A.!!$R7 1287
15 TraesCS4B01G011100 chr4A 599122702 599126048 3346 True 1294.0 1690 89.8740 734 4191 2 chr4A.!!$R9 3457
16 TraesCS4B01G011100 chrUn 360631628 360633173 1545 True 1965.0 1965 89.7760 734 2276 1 chrUn.!!$R3 1542
17 TraesCS4B01G011100 chrUn 216674908 216675822 914 True 1243.0 1243 91.5220 1123 2021 1 chrUn.!!$R2 898
18 TraesCS4B01G011100 chr6A 593023878 593024590 712 True 937.0 937 90.2740 3464 4191 1 chr6A.!!$R1 727
19 TraesCS4B01G011100 chr3A 691379353 691379985 632 True 630.0 630 85.2900 58 670 1 chr3A.!!$R1 612

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
927 1008 0.324943 CCACCCATCCTCGTTCACTT 59.675 55.0 0.00 0.00 0.0 3.16 F
1373 1475 0.253044 CTGGAAATCGCAGGGAGGAA 59.747 55.0 0.00 0.00 0.0 3.36 F
2191 2446 0.321346 TCAGATTTGTCAGGCGCAGA 59.679 50.0 10.83 3.11 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2170 2424 0.874390 TGCGCCTGACAAATCTGAAC 59.126 50.000 4.18 0.0 0.00 3.18 R
2255 2510 3.005897 ACAATTCTGCTACACGAGACACT 59.994 43.478 0.00 0.0 0.00 3.55 R
3651 3924 0.094046 CTAAGTTTTACGCGCACCCG 59.906 55.000 5.73 0.0 37.57 5.28 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
116 117 3.008375 TGCATAGGCCATCTAGGATTCAC 59.992 47.826 5.01 0.00 41.22 3.18
391 413 3.454858 TGCTAGGACTCTCAGGGATTTT 58.545 45.455 0.00 0.00 0.00 1.82
628 657 9.275398 TGTTAGTTTTGTAGGATTAACGTGATT 57.725 29.630 0.00 0.00 0.00 2.57
927 1008 0.324943 CCACCCATCCTCGTTCACTT 59.675 55.000 0.00 0.00 0.00 3.16
1346 1440 6.325596 TGTCTCGAACTGACTCATCTTAATG 58.674 40.000 5.08 0.00 35.63 1.90
1373 1475 0.253044 CTGGAAATCGCAGGGAGGAA 59.747 55.000 0.00 0.00 0.00 3.36
1430 1532 2.745100 CAGCTCATGCGGTGCACT 60.745 61.111 17.98 0.00 43.04 4.40
1431 1533 1.448365 CAGCTCATGCGGTGCACTA 60.448 57.895 17.98 4.06 43.04 2.74
1475 1577 2.903135 CCTTTCTCTCTCTTCCACCTGT 59.097 50.000 0.00 0.00 0.00 4.00
1540 1651 5.005682 TCGTGCGATTCAGATCTGTTTATTG 59.994 40.000 21.92 16.76 0.00 1.90
1543 1654 7.340699 GTGCGATTCAGATCTGTTTATTGTAG 58.659 38.462 21.92 6.85 0.00 2.74
1825 1997 2.294233 GCATATTTGGATGTGTCGGCAT 59.706 45.455 0.00 0.00 0.00 4.40
1868 2040 2.158971 GGCCACACAATTGAGGTTTGTT 60.159 45.455 13.59 0.00 35.18 2.83
1951 2124 8.287503 GTGTAACGAAATTGTTGGTATTCTTCT 58.712 33.333 0.00 0.00 33.32 2.85
2035 2208 5.814764 TCTACTATCGTGTCTGTTCTTCC 57.185 43.478 0.00 0.00 0.00 3.46
2042 2215 2.695359 GTGTCTGTTCTTCCGGCAATA 58.305 47.619 0.00 0.00 0.00 1.90
2170 2424 3.371168 CATTGGAACGGTGTTGTTTCTG 58.629 45.455 0.00 0.00 30.75 3.02
2191 2446 0.321346 TCAGATTTGTCAGGCGCAGA 59.679 50.000 10.83 3.11 0.00 4.26
2255 2510 9.667107 CCAAAATTAGAAGACCTGATTGTAGTA 57.333 33.333 0.00 0.00 32.22 1.82
2413 2671 7.315142 TGCTTCATCAAACAATTTATGGAGTC 58.685 34.615 0.00 0.00 29.20 3.36
2502 2762 8.056407 AGTTTGATAAGTTCCTAATTTCCTGC 57.944 34.615 0.00 0.00 0.00 4.85
2688 2951 5.073311 TCTATGTAAACCTGACAGCTCAC 57.927 43.478 0.00 0.00 0.00 3.51
2703 2967 2.159099 AGCTCACGTTGTCTTTCTGTCA 60.159 45.455 0.00 0.00 0.00 3.58
2792 3058 5.874831 TGCAATCACGTTGTTGATATTACC 58.125 37.500 12.51 0.00 40.07 2.85
2818 3084 6.516693 CGGTTCACTATCTGAATATGCTACCA 60.517 42.308 0.00 0.00 41.10 3.25
2851 3117 9.343539 GGTTCTCTTGTAATTTATTGGCTCTAT 57.656 33.333 0.00 0.00 0.00 1.98
3011 3277 2.218953 TTTCAGGTGTCTCGTGTCAC 57.781 50.000 6.35 6.35 34.10 3.67
3126 3392 6.708949 TGATACCAACTTTCCACTAGTTTCAC 59.291 38.462 0.00 0.00 33.73 3.18
3221 3489 8.045176 ACATTTAGATTTGGAGCACTTAGTTC 57.955 34.615 0.00 0.00 0.00 3.01
3609 3881 1.750206 TGCATTATGTGGTCCATGTGC 59.250 47.619 0.00 2.62 42.31 4.57
3638 3911 0.955905 TGTAGCGGTTTTCAAAGGGC 59.044 50.000 0.00 0.00 0.00 5.19
3766 4075 8.053355 TCAGTGTGAAGTCCATATTCTAGAGTA 58.947 37.037 0.00 0.00 0.00 2.59
3985 4296 2.866762 CAGCGTGGCCTTCTTATAAGAC 59.133 50.000 14.85 4.44 34.13 3.01
3987 4298 2.866762 GCGTGGCCTTCTTATAAGACTG 59.133 50.000 14.85 9.87 34.13 3.51
4062 4376 0.390860 GAGGTCACATCCAGGGATCG 59.609 60.000 0.00 0.00 35.27 3.69
4233 4548 7.624077 AGTTATTTAGACTACCCTGAATCACCT 59.376 37.037 0.00 0.00 0.00 4.00
4310 4625 1.608590 CCTGTTGCGAACCATGTTCTT 59.391 47.619 5.53 0.00 0.00 2.52
4378 6027 3.046087 CCATGGCTAGCCGATGCG 61.046 66.667 28.28 19.34 44.33 4.73
4439 6088 0.607489 GGCTCGCCGACTAGGGTATA 60.607 60.000 0.00 0.00 41.48 1.47
4440 6089 1.461559 GCTCGCCGACTAGGGTATAT 58.538 55.000 0.00 0.00 41.48 0.86
4441 6090 1.132643 GCTCGCCGACTAGGGTATATG 59.867 57.143 0.00 0.00 41.48 1.78
4442 6091 2.708051 CTCGCCGACTAGGGTATATGA 58.292 52.381 0.00 0.00 41.48 2.15
4456 6105 9.745018 CTAGGGTATATGATTGGTTGATGAAAT 57.255 33.333 0.00 0.00 0.00 2.17
4465 6117 9.657419 ATGATTGGTTGATGAAATAAAAACTCC 57.343 29.630 0.00 0.00 0.00 3.85
4474 6126 6.723298 TGAAATAAAAACTCCACCACACAT 57.277 33.333 0.00 0.00 0.00 3.21
4482 6134 4.104383 ACTCCACCACACATCAAATTCT 57.896 40.909 0.00 0.00 0.00 2.40
4483 6135 4.473444 ACTCCACCACACATCAAATTCTT 58.527 39.130 0.00 0.00 0.00 2.52
4484 6136 4.895297 ACTCCACCACACATCAAATTCTTT 59.105 37.500 0.00 0.00 0.00 2.52
4485 6137 5.199024 TCCACCACACATCAAATTCTTTG 57.801 39.130 0.00 0.00 41.96 2.77
4487 6139 3.742369 CACCACACATCAAATTCTTTGCC 59.258 43.478 0.00 0.00 40.43 4.52
4488 6140 2.988493 CCACACATCAAATTCTTTGCCG 59.012 45.455 0.00 0.00 40.43 5.69
4492 6144 2.095263 ACATCAAATTCTTTGCCGTCCG 60.095 45.455 0.00 0.00 40.43 4.79
4493 6145 0.239879 TCAAATTCTTTGCCGTCCGC 59.760 50.000 0.00 0.00 40.43 5.54
4495 6147 1.466950 CAAATTCTTTGCCGTCCGCTA 59.533 47.619 0.00 0.00 38.78 4.26
4496 6148 1.369625 AATTCTTTGCCGTCCGCTAG 58.630 50.000 0.00 0.00 38.78 3.42
4497 6149 1.090052 ATTCTTTGCCGTCCGCTAGC 61.090 55.000 4.06 4.06 38.78 3.42
4499 6151 4.367023 TTTGCCGTCCGCTAGCGT 62.367 61.111 33.18 0.00 38.78 5.07
4500 6152 2.877360 CTTTGCCGTCCGCTAGCGTA 62.877 60.000 33.18 18.21 38.78 4.42
4501 6153 3.688475 TTGCCGTCCGCTAGCGTAC 62.688 63.158 33.18 27.44 38.78 3.67
4505 6157 2.787249 GTCCGCTAGCGTACGACA 59.213 61.111 33.18 8.95 37.81 4.35
4506 6158 1.354506 GTCCGCTAGCGTACGACAT 59.645 57.895 33.18 6.37 37.81 3.06
4509 6161 0.725118 CCGCTAGCGTACGACATAGC 60.725 60.000 33.18 25.35 37.79 2.97
4510 6162 0.041576 CGCTAGCGTACGACATAGCA 60.042 55.000 29.96 7.60 40.51 3.49
4511 6163 1.676057 GCTAGCGTACGACATAGCAG 58.324 55.000 27.99 13.33 40.27 4.24
4512 6164 1.263484 GCTAGCGTACGACATAGCAGA 59.737 52.381 27.99 3.74 40.27 4.26
4513 6165 2.906153 CTAGCGTACGACATAGCAGAC 58.094 52.381 21.65 0.00 0.00 3.51
4514 6166 0.027716 AGCGTACGACATAGCAGACG 59.972 55.000 21.65 0.00 0.00 4.18
4515 6167 0.928908 GCGTACGACATAGCAGACGG 60.929 60.000 21.65 0.00 0.00 4.79
4525 6177 2.347490 GCAGACGGCAAAGAGGGA 59.653 61.111 0.00 0.00 43.97 4.20
4526 6178 1.743252 GCAGACGGCAAAGAGGGAG 60.743 63.158 0.00 0.00 43.97 4.30
4532 6184 2.361737 GCAAAGAGGGAGGGTGGC 60.362 66.667 0.00 0.00 0.00 5.01
4533 6185 2.356667 CAAAGAGGGAGGGTGGCC 59.643 66.667 0.00 0.00 0.00 5.36
4534 6186 2.941583 AAAGAGGGAGGGTGGCCC 60.942 66.667 0.00 0.00 45.90 5.80
4543 6195 2.267961 GGGTGGCCCACTAACGAG 59.732 66.667 14.71 0.00 44.65 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 1.152860 TTTGAAGGAGGGCGCACAA 60.153 52.632 14.57 0.00 0.00 3.33
391 413 6.096673 TGAAATATCTGCAGCCGTTAGATA 57.903 37.500 9.47 0.02 37.69 1.98
455 477 5.279056 CCCAAATAAAAAGGGTCACGCTAAA 60.279 40.000 0.00 0.00 37.81 1.85
459 481 2.954316 CCCAAATAAAAAGGGTCACGC 58.046 47.619 0.00 0.00 37.81 5.34
628 657 0.400213 ATTGAGGCACCAAACGAGGA 59.600 50.000 0.00 0.00 0.00 3.71
950 1033 2.574399 GACTGAGCGGTGGAGACC 59.426 66.667 0.00 0.00 39.14 3.85
1346 1440 1.945387 TGCGATTTCCAGAGCAGATC 58.055 50.000 0.00 0.00 34.39 2.75
1373 1475 0.249741 CGTCAAAGTCCACTTCGGGT 60.250 55.000 0.00 0.00 34.61 5.28
1540 1651 6.151144 ACAAATAAGAATCTGTTGCCCACTAC 59.849 38.462 2.64 0.00 0.00 2.73
1543 1654 5.391312 ACAAATAAGAATCTGTTGCCCAC 57.609 39.130 2.64 0.00 0.00 4.61
1656 1767 7.731688 AGGGCAACAATTTATCCTCATCATAAT 59.268 33.333 0.00 0.00 39.74 1.28
1825 1997 1.152504 TCGTGAGGTACACACCCCA 60.153 57.895 13.95 0.00 46.95 4.96
1868 2040 2.414058 TACGACGCCTGTAAAACGAA 57.586 45.000 0.00 0.00 0.00 3.85
2035 2208 5.995282 TCAACCTAGAATAATGGTATTGCCG 59.005 40.000 0.00 0.00 41.21 5.69
2042 2215 9.753674 TTTTCATTCTCAACCTAGAATAATGGT 57.246 29.630 0.00 0.00 42.90 3.55
2170 2424 0.874390 TGCGCCTGACAAATCTGAAC 59.126 50.000 4.18 0.00 0.00 3.18
2210 2465 4.079980 TGGATATACGACACCCAAATGG 57.920 45.455 0.00 0.00 41.37 3.16
2255 2510 3.005897 ACAATTCTGCTACACGAGACACT 59.994 43.478 0.00 0.00 0.00 3.55
2353 2608 4.441792 TCATTGTCGCTATGTGCAATAGT 58.558 39.130 13.75 0.00 43.06 2.12
2413 2671 4.758674 AGCCATTTCCTATCATGATTGTCG 59.241 41.667 14.65 0.37 0.00 4.35
2625 2887 7.530863 TGTTGCGAATAATTATTGTGTAGCAA 58.469 30.769 15.39 17.97 41.89 3.91
2688 2951 7.059945 GCTGAAAATAATGACAGAAAGACAACG 59.940 37.037 0.00 0.00 32.90 4.10
2934 3200 7.509546 AGAGGTTAACAGAACTGAGATGAAAA 58.490 34.615 8.10 0.00 0.00 2.29
3011 3277 4.213564 ACTCATTCCTAACAAGAGCCAG 57.786 45.455 0.00 0.00 0.00 4.85
3221 3489 3.505464 ATGAGACTTTTCGGTACCTCG 57.495 47.619 10.90 0.00 0.00 4.63
3479 3751 7.761249 GCTGCAACAAAAGATGAATAATAGGTT 59.239 33.333 0.00 0.00 0.00 3.50
3523 3795 4.426704 ACTTAGGAGTTAGGACCACATGT 58.573 43.478 0.00 0.00 29.87 3.21
3609 3881 0.460311 AACCGCTACATCTTCGGAGG 59.540 55.000 6.91 0.00 45.53 4.30
3638 3911 1.226974 CACCCGATAGTGCCAGACG 60.227 63.158 0.00 0.00 0.00 4.18
3651 3924 0.094046 CTAAGTTTTACGCGCACCCG 59.906 55.000 5.73 0.00 37.57 5.28
3766 4075 1.378514 GGGGCAACACATCCACGAT 60.379 57.895 0.00 0.00 42.67 3.73
4062 4376 2.127232 GCGAACCGACAGCTTTGC 60.127 61.111 0.00 0.00 0.00 3.68
4102 4416 5.951747 ACCAATGCAAACATACATAAGTCCT 59.048 36.000 0.00 0.00 34.62 3.85
4110 4424 7.665690 ACTTTTCATACCAATGCAAACATACA 58.334 30.769 0.00 0.00 34.62 2.29
4233 4548 0.111061 ACATGTTCTCTTGCCCAGCA 59.889 50.000 0.00 0.00 36.47 4.41
4310 4625 3.118555 TCAAAGACCCGAAGTTTCACAGA 60.119 43.478 0.00 0.00 0.00 3.41
4378 6027 4.525949 GGAAGGGAGGCCGTACGC 62.526 72.222 10.49 5.40 0.00 4.42
4439 6088 9.657419 GGAGTTTTTATTTCATCAACCAATCAT 57.343 29.630 0.00 0.00 0.00 2.45
4440 6089 8.646004 TGGAGTTTTTATTTCATCAACCAATCA 58.354 29.630 0.00 0.00 0.00 2.57
4441 6090 8.925700 GTGGAGTTTTTATTTCATCAACCAATC 58.074 33.333 0.00 0.00 0.00 2.67
4442 6091 7.877612 GGTGGAGTTTTTATTTCATCAACCAAT 59.122 33.333 0.00 0.00 0.00 3.16
4456 6105 6.723298 ATTTGATGTGTGGTGGAGTTTTTA 57.277 33.333 0.00 0.00 0.00 1.52
4483 6135 3.688475 GTACGCTAGCGGACGGCAA 62.688 63.158 34.74 11.12 43.67 4.52
4484 6136 4.183686 GTACGCTAGCGGACGGCA 62.184 66.667 34.74 12.53 43.67 5.69
4492 6144 1.263484 TCTGCTATGTCGTACGCTAGC 59.737 52.381 24.83 24.83 34.50 3.42
4493 6145 2.659558 CGTCTGCTATGTCGTACGCTAG 60.660 54.545 11.24 11.91 0.00 3.42
4495 6147 0.027716 CGTCTGCTATGTCGTACGCT 59.972 55.000 11.24 0.00 0.00 5.07
4496 6148 0.928908 CCGTCTGCTATGTCGTACGC 60.929 60.000 11.24 6.57 0.00 4.42
4497 6149 0.928908 GCCGTCTGCTATGTCGTACG 60.929 60.000 9.53 9.53 36.87 3.67
4499 6151 0.812549 TTGCCGTCTGCTATGTCGTA 59.187 50.000 0.00 0.00 42.00 3.43
4500 6152 0.037697 TTTGCCGTCTGCTATGTCGT 60.038 50.000 0.00 0.00 42.00 4.34
4501 6153 0.647410 CTTTGCCGTCTGCTATGTCG 59.353 55.000 0.00 0.00 42.00 4.35
4503 6155 1.406069 CCTCTTTGCCGTCTGCTATGT 60.406 52.381 0.00 0.00 42.00 2.29
4504 6156 1.293924 CCTCTTTGCCGTCTGCTATG 58.706 55.000 0.00 0.00 42.00 2.23
4505 6157 0.179000 CCCTCTTTGCCGTCTGCTAT 59.821 55.000 0.00 0.00 42.00 2.97
4506 6158 0.902984 TCCCTCTTTGCCGTCTGCTA 60.903 55.000 0.00 0.00 42.00 3.49
4509 6161 1.078848 CCTCCCTCTTTGCCGTCTG 60.079 63.158 0.00 0.00 0.00 3.51
4510 6162 2.294078 CCCTCCCTCTTTGCCGTCT 61.294 63.158 0.00 0.00 0.00 4.18
4511 6163 2.269241 CCCTCCCTCTTTGCCGTC 59.731 66.667 0.00 0.00 0.00 4.79
4512 6164 2.529389 ACCCTCCCTCTTTGCCGT 60.529 61.111 0.00 0.00 0.00 5.68
4513 6165 2.045926 CACCCTCCCTCTTTGCCG 60.046 66.667 0.00 0.00 0.00 5.69
4514 6166 2.356667 CCACCCTCCCTCTTTGCC 59.643 66.667 0.00 0.00 0.00 4.52
4515 6167 2.361737 GCCACCCTCCCTCTTTGC 60.362 66.667 0.00 0.00 0.00 3.68
4517 6169 2.941583 GGGCCACCCTCCCTCTTT 60.942 66.667 4.39 0.00 41.34 2.52
4520 6172 3.635869 TAGTGGGCCACCCTCCCTC 62.636 68.421 32.30 5.65 45.70 4.30
4522 6174 2.612746 TTAGTGGGCCACCCTCCC 60.613 66.667 32.30 7.31 45.70 4.30
4524 6176 2.240162 CTCGTTAGTGGGCCACCCTC 62.240 65.000 32.30 20.27 45.70 4.30
4525 6177 2.203877 TCGTTAGTGGGCCACCCT 60.204 61.111 32.30 18.08 45.70 4.34
4526 6178 2.267961 CTCGTTAGTGGGCCACCC 59.732 66.667 32.30 19.21 45.71 4.61


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

AutoCloner maintained by Alex Coulton.