Multiple sequence alignment - TraesCS1D01G353200

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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 TraesCS1D01G353200 chr1D 100.000 2245 0 0 1725 3969 438582673 438580429 0.000000e+00 4146.0
1 TraesCS1D01G353200 chr1D 100.000 1524 0 0 1 1524 438584397 438582874 0.000000e+00 2815.0
2 TraesCS1D01G353200 chr1D 94.401 893 39 5 1 889 468393642 468394527 0.000000e+00 1362.0
3 TraesCS1D01G353200 chr1B 96.495 1341 27 6 1821 3156 594493035 594491710 0.000000e+00 2198.0
4 TraesCS1D01G353200 chr1B 96.324 544 7 4 979 1520 594493577 594493045 0.000000e+00 881.0
5 TraesCS1D01G353200 chr1B 94.091 220 8 3 3637 3854 594491647 594491431 2.960000e-86 329.0
6 TraesCS1D01G353200 chr1B 97.391 115 2 1 3856 3969 594491398 594491284 1.130000e-45 195.0
7 TraesCS1D01G353200 chr1B 96.739 92 1 1 891 980 594493833 594493742 6.870000e-33 152.0
8 TraesCS1D01G353200 chr1B 100.000 47 0 0 3604 3650 594491711 594491665 1.960000e-13 87.9
9 TraesCS1D01G353200 chr1B 94.737 38 2 0 892 929 594505317 594505280 4.280000e-05 60.2
10 TraesCS1D01G353200 chr1A 98.018 1211 19 2 1836 3041 535079385 535078175 0.000000e+00 2098.0
11 TraesCS1D01G353200 chr1A 95.122 533 10 7 979 1507 535079903 535079383 0.000000e+00 826.0
12 TraesCS1D01G353200 chr1A 95.808 334 13 1 3050 3383 535076883 535076551 4.510000e-149 538.0
13 TraesCS1D01G353200 chr1A 91.176 204 7 3 3447 3650 535076555 535076363 2.350000e-67 267.0
14 TraesCS1D01G353200 chr1A 75.689 399 54 23 3052 3434 63090340 63089969 4.110000e-35 159.0
15 TraesCS1D01G353200 chr1A 97.778 90 2 0 891 980 535080130 535080041 5.310000e-34 156.0
16 TraesCS1D01G353200 chr7D 98.315 890 12 2 1 887 488123066 488122177 0.000000e+00 1557.0
17 TraesCS1D01G353200 chr7D 87.549 506 42 12 2241 2743 102538539 102539026 2.070000e-157 566.0
18 TraesCS1D01G353200 chr7D 83.397 524 62 13 1727 2239 102537998 102538507 2.790000e-126 462.0
19 TraesCS1D01G353200 chr7D 88.321 137 16 0 1155 1291 102537630 102537766 8.820000e-37 165.0
20 TraesCS1D01G353200 chr7D 85.938 128 12 2 1015 1141 102537454 102537576 8.950000e-27 132.0
21 TraesCS1D01G353200 chr7B 94.111 900 47 5 1 897 365538428 365537532 0.000000e+00 1363.0
22 TraesCS1D01G353200 chr7B 86.364 506 47 13 2241 2743 59743333 59743819 2.100000e-147 532.0
23 TraesCS1D01G353200 chr7B 84.261 521 62 12 1728 2239 59742792 59743301 1.280000e-134 490.0
24 TraesCS1D01G353200 chr7B 90.441 136 13 0 1155 1290 59742404 59742539 3.150000e-41 180.0
25 TraesCS1D01G353200 chr7B 85.938 128 12 2 1015 1141 59742228 59742350 8.950000e-27 132.0
26 TraesCS1D01G353200 chr2A 94.834 871 28 10 42 904 20342620 20341759 0.000000e+00 1343.0
27 TraesCS1D01G353200 chr4B 84.881 1012 121 23 1752 2743 659051856 659052855 0.000000e+00 992.0
28 TraesCS1D01G353200 chr6A 94.118 612 35 1 1 612 396607712 396607102 0.000000e+00 929.0
29 TraesCS1D01G353200 chr7A 94.626 521 23 4 377 893 518147322 518147841 0.000000e+00 802.0
30 TraesCS1D01G353200 chr7A 87.352 506 43 10 2241 2743 106679558 106680045 9.630000e-156 560.0
31 TraesCS1D01G353200 chr7A 83.716 479 56 15 1770 2239 106679061 106679526 2.190000e-117 433.0
32 TraesCS1D01G353200 chr7A 92.414 290 11 3 2 291 518147045 518147323 1.720000e-108 403.0
33 TraesCS1D01G353200 chr7A 85.938 128 12 2 1015 1141 106678404 106678526 8.950000e-27 132.0
34 TraesCS1D01G353200 chr6B 94.942 514 23 2 383 893 46350908 46350395 0.000000e+00 802.0
35 TraesCS1D01G353200 chr6B 94.242 521 25 4 377 893 17408135 17408654 0.000000e+00 791.0
36 TraesCS1D01G353200 chr6B 95.517 290 12 1 2 291 46351201 46350913 2.790000e-126 462.0
37 TraesCS1D01G353200 chr6B 92.414 290 11 3 2 291 17407858 17408136 1.720000e-108 403.0
38 TraesCS1D01G353200 chr6D 96.190 420 16 0 1 420 329532615 329532196 0.000000e+00 688.0
39 TraesCS1D01G353200 chr6D 94.100 339 15 4 565 899 329532117 329531780 9.840000e-141 510.0
40 TraesCS1D01G353200 chr6D 82.374 278 35 9 1 273 458390492 458390224 3.090000e-56 230.0
41 TraesCS1D01G353200 chr6D 100.000 84 0 0 447 530 329532199 329532116 5.310000e-34 156.0
42 TraesCS1D01G353200 chr5D 78.800 250 26 14 3201 3434 388052080 388051842 4.130000e-30 143.0
43 TraesCS1D01G353200 chr4D 87.826 115 10 3 1170 1280 508644411 508644525 8.950000e-27 132.0
44 TraesCS1D01G353200 chr5A 89.552 67 7 0 1168 1234 30215817 30215751 7.070000e-13 86.1
45 TraesCS1D01G353200 chr5A 91.489 47 2 2 861 905 635284761 635284807 3.310000e-06 63.9


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 TraesCS1D01G353200 chr1D 438580429 438584397 3968 True 3480.500000 4146 100.000000 1 3969 2 chr1D.!!$R1 3968
1 TraesCS1D01G353200 chr1D 468393642 468394527 885 False 1362.000000 1362 94.401000 1 889 1 chr1D.!!$F1 888
2 TraesCS1D01G353200 chr1B 594491284 594493833 2549 True 640.483333 2198 96.840000 891 3969 6 chr1B.!!$R2 3078
3 TraesCS1D01G353200 chr1A 535076363 535080130 3767 True 777.000000 2098 95.580400 891 3650 5 chr1A.!!$R2 2759
4 TraesCS1D01G353200 chr7D 488122177 488123066 889 True 1557.000000 1557 98.315000 1 887 1 chr7D.!!$R1 886
5 TraesCS1D01G353200 chr7D 102537454 102539026 1572 False 331.250000 566 86.301250 1015 2743 4 chr7D.!!$F1 1728
6 TraesCS1D01G353200 chr7B 365537532 365538428 896 True 1363.000000 1363 94.111000 1 897 1 chr7B.!!$R1 896
7 TraesCS1D01G353200 chr7B 59742228 59743819 1591 False 333.500000 532 86.751000 1015 2743 4 chr7B.!!$F1 1728
8 TraesCS1D01G353200 chr2A 20341759 20342620 861 True 1343.000000 1343 94.834000 42 904 1 chr2A.!!$R1 862
9 TraesCS1D01G353200 chr4B 659051856 659052855 999 False 992.000000 992 84.881000 1752 2743 1 chr4B.!!$F1 991
10 TraesCS1D01G353200 chr6A 396607102 396607712 610 True 929.000000 929 94.118000 1 612 1 chr6A.!!$R1 611
11 TraesCS1D01G353200 chr7A 518147045 518147841 796 False 602.500000 802 93.520000 2 893 2 chr7A.!!$F2 891
12 TraesCS1D01G353200 chr7A 106678404 106680045 1641 False 375.000000 560 85.668667 1015 2743 3 chr7A.!!$F1 1728
13 TraesCS1D01G353200 chr6B 46350395 46351201 806 True 632.000000 802 95.229500 2 893 2 chr6B.!!$R1 891
14 TraesCS1D01G353200 chr6B 17407858 17408654 796 False 597.000000 791 93.328000 2 893 2 chr6B.!!$F1 891
15 TraesCS1D01G353200 chr6D 329531780 329532615 835 True 451.333333 688 96.763333 1 899 3 chr6D.!!$R2 898

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
423 425 0.606401 CAACCCTCGCTGACCAACAT 60.606 55.000 0.0 0.0 0.0 2.71 F
1520 1860 1.072331 AGATTTTCGGGCTGTCTGTGT 59.928 47.619 0.0 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1814 2254 1.187567 ACAATGGAGCCAAGGTTGCC 61.188 55.0 0.00 0.0 0.0 4.52 R
3409 5196 0.176910 GCTTTTAGAGGCCGAGCTCT 59.823 55.0 12.85 0.0 0.0 4.09 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
56 57 7.954835 ACATCATCTGTTTTTCTTCCATTGAA 58.045 30.769 0.00 0.00 32.90 2.69
196 197 4.616604 CGTCCACAAATTGCATTGTCAGAT 60.617 41.667 2.67 0.00 41.44 2.90
386 388 2.099652 CTCGCCACTCCCAGACACAA 62.100 60.000 0.00 0.00 0.00 3.33
423 425 0.606401 CAACCCTCGCTGACCAACAT 60.606 55.000 0.00 0.00 0.00 2.71
661 700 2.362717 TCGGTATTGCATGTCGGATGTA 59.637 45.455 0.00 0.00 0.00 2.29
847 888 1.418334 ATCTATGCCTTCGAGCCTGT 58.582 50.000 0.00 0.00 0.00 4.00
1293 1557 4.611310 TGTACGTATGCAGACACTACTC 57.389 45.455 12.67 0.00 0.00 2.59
1520 1860 1.072331 AGATTTTCGGGCTGTCTGTGT 59.928 47.619 0.00 0.00 0.00 3.72
1521 1861 1.464997 GATTTTCGGGCTGTCTGTGTC 59.535 52.381 0.00 0.00 0.00 3.67
1766 2204 5.123344 GCCAGTTTGGTGTAGTAATGTAAGG 59.877 44.000 0.00 0.00 40.46 2.69
1808 2248 8.421784 ACTCTTAATCGCCATGTCTTCTAATTA 58.578 33.333 0.00 0.00 0.00 1.40
1814 2254 4.447054 CGCCATGTCTTCTAATTAGCTCAG 59.553 45.833 7.67 4.09 0.00 3.35
1996 2436 0.471780 TCAGTCTCAGGCCCAAGTCA 60.472 55.000 0.00 0.00 0.00 3.41
2245 2719 2.336945 TGGCTAGAACATCCATGCAG 57.663 50.000 0.00 0.00 0.00 4.41
2343 2832 6.000840 GGAATTTGTGGAAGAGAAAGAGAGT 58.999 40.000 0.00 0.00 0.00 3.24
2411 2900 1.815003 GGTGAAAGGTTCAGATGGCAG 59.185 52.381 0.00 0.00 41.01 4.85
2569 3067 7.359514 CCGTTAGTCATATCATGTGCTAATGTG 60.360 40.741 12.46 0.00 36.01 3.21
2784 3282 6.077993 TGGTCTTGGTCTACTATATGCTGAT 58.922 40.000 0.00 0.00 0.00 2.90
3058 4844 9.338622 GAAAAGGGAGAGAATATTCGGAAAATA 57.661 33.333 9.78 0.00 0.00 1.40
3078 4864 2.176273 CAATGAAGGCCGAGCTCCG 61.176 63.158 8.47 2.35 38.18 4.63
3256 5043 4.561326 CGAACAAAAGAAATTGGCCCATCT 60.561 41.667 0.00 0.00 34.56 2.90
3330 5117 8.661257 TGGTTATGAATTTTCACACATACGTAG 58.339 33.333 0.08 0.00 40.49 3.51
3349 5136 3.746045 AGTTCCACGTAAGACACATGT 57.254 42.857 0.00 0.00 43.62 3.21
3395 5182 8.725405 TCACACTGTAGTAATTTGTTCTTTCA 57.275 30.769 0.00 0.00 0.00 2.69
3396 5183 9.168451 TCACACTGTAGTAATTTGTTCTTTCAA 57.832 29.630 0.00 0.00 0.00 2.69
3397 5184 9.781834 CACACTGTAGTAATTTGTTCTTTCAAA 57.218 29.630 0.00 0.00 40.74 2.69
3405 5192 9.952188 AGTAATTTGTTCTTTCAAAACTAGCTC 57.048 29.630 0.00 0.00 40.05 4.09
3406 5193 9.181805 GTAATTTGTTCTTTCAAAACTAGCTCC 57.818 33.333 0.00 0.00 40.05 4.70
3407 5194 5.767816 TTGTTCTTTCAAAACTAGCTCCC 57.232 39.130 0.00 0.00 0.00 4.30
3408 5195 5.048846 TGTTCTTTCAAAACTAGCTCCCT 57.951 39.130 0.00 0.00 0.00 4.20
3409 5196 6.182507 TGTTCTTTCAAAACTAGCTCCCTA 57.817 37.500 0.00 0.00 0.00 3.53
3410 5197 6.231211 TGTTCTTTCAAAACTAGCTCCCTAG 58.769 40.000 0.00 0.00 45.35 3.02
3411 5198 6.042781 TGTTCTTTCAAAACTAGCTCCCTAGA 59.957 38.462 4.86 0.00 43.07 2.43
3412 5199 6.287589 TCTTTCAAAACTAGCTCCCTAGAG 57.712 41.667 4.86 0.00 43.07 2.43
3420 5207 2.197324 CTCCCTAGAGCTCGGCCT 59.803 66.667 8.37 0.00 32.13 5.19
3421 5208 1.901464 CTCCCTAGAGCTCGGCCTC 60.901 68.421 8.37 0.00 32.13 4.70
3422 5209 2.197324 CCCTAGAGCTCGGCCTCT 59.803 66.667 8.37 9.99 44.12 3.69
3423 5210 1.060743 TCCCTAGAGCTCGGCCTCTA 61.061 60.000 8.37 10.96 42.07 2.43
3424 5211 0.178987 CCCTAGAGCTCGGCCTCTAA 60.179 60.000 8.37 0.00 42.24 2.10
3425 5212 1.693627 CCTAGAGCTCGGCCTCTAAA 58.306 55.000 8.37 0.00 42.24 1.85
3426 5213 2.032620 CCTAGAGCTCGGCCTCTAAAA 58.967 52.381 8.37 0.00 42.24 1.52
3427 5214 2.035321 CCTAGAGCTCGGCCTCTAAAAG 59.965 54.545 8.37 5.13 42.24 2.27
3428 5215 0.176910 AGAGCTCGGCCTCTAAAAGC 59.823 55.000 8.37 0.00 40.30 3.51
3429 5216 0.812014 GAGCTCGGCCTCTAAAAGCC 60.812 60.000 0.00 0.00 46.17 4.35
3433 5220 2.045340 GGCCTCTAAAAGCCCGCA 60.045 61.111 0.00 0.00 43.76 5.69
3434 5221 1.677633 GGCCTCTAAAAGCCCGCAA 60.678 57.895 0.00 0.00 43.76 4.85
3435 5222 1.657751 GGCCTCTAAAAGCCCGCAAG 61.658 60.000 0.00 0.00 43.76 4.01
3436 5223 0.676782 GCCTCTAAAAGCCCGCAAGA 60.677 55.000 0.00 0.00 43.02 3.02
3437 5224 1.821216 CCTCTAAAAGCCCGCAAGAA 58.179 50.000 0.00 0.00 43.02 2.52
3438 5225 2.369394 CCTCTAAAAGCCCGCAAGAAT 58.631 47.619 0.00 0.00 43.02 2.40
3439 5226 3.541632 CCTCTAAAAGCCCGCAAGAATA 58.458 45.455 0.00 0.00 43.02 1.75
3440 5227 4.137543 CCTCTAAAAGCCCGCAAGAATAT 58.862 43.478 0.00 0.00 43.02 1.28
3441 5228 4.580580 CCTCTAAAAGCCCGCAAGAATATT 59.419 41.667 0.00 0.00 43.02 1.28
3442 5229 5.499139 TCTAAAAGCCCGCAAGAATATTG 57.501 39.130 0.00 0.00 43.02 1.90
3443 5230 2.584492 AAAGCCCGCAAGAATATTGC 57.416 45.000 2.02 2.02 41.71 3.56
3444 5231 0.746659 AAGCCCGCAAGAATATTGCC 59.253 50.000 7.03 0.00 42.10 4.52
3445 5232 1.109323 AGCCCGCAAGAATATTGCCC 61.109 55.000 7.03 0.00 42.10 5.36
3446 5233 1.109323 GCCCGCAAGAATATTGCCCT 61.109 55.000 7.03 0.00 42.10 5.19
3447 5234 1.817740 GCCCGCAAGAATATTGCCCTA 60.818 52.381 7.03 0.00 42.10 3.53
3466 5253 5.770417 CCCTATTATCAAGTCGGTAGTGAC 58.230 45.833 0.00 0.00 39.21 3.67
3520 5307 8.848474 AATGCTACTACATCTTTGTAAGTTGT 57.152 30.769 7.90 7.90 42.42 3.32
3531 5318 7.614124 TCTTTGTAAGTTGTAACGGTCTTTT 57.386 32.000 0.00 0.00 0.00 2.27
3533 5320 5.738118 TGTAAGTTGTAACGGTCTTTTGG 57.262 39.130 0.00 0.00 0.00 3.28
3534 5321 4.575645 TGTAAGTTGTAACGGTCTTTTGGG 59.424 41.667 0.00 0.00 0.00 4.12
3535 5322 2.578786 AGTTGTAACGGTCTTTTGGGG 58.421 47.619 0.00 0.00 0.00 4.96
3536 5323 2.092267 AGTTGTAACGGTCTTTTGGGGT 60.092 45.455 0.00 0.00 0.00 4.95
3537 5324 2.689471 GTTGTAACGGTCTTTTGGGGTT 59.311 45.455 0.00 0.00 0.00 4.11
3538 5325 2.574450 TGTAACGGTCTTTTGGGGTTC 58.426 47.619 0.00 0.00 0.00 3.62
3539 5326 2.092538 TGTAACGGTCTTTTGGGGTTCA 60.093 45.455 0.00 0.00 0.00 3.18
3540 5327 2.146920 AACGGTCTTTTGGGGTTCAA 57.853 45.000 0.00 0.00 0.00 2.69
3541 5328 1.687563 ACGGTCTTTTGGGGTTCAAG 58.312 50.000 0.00 0.00 36.62 3.02
3542 5329 0.313987 CGGTCTTTTGGGGTTCAAGC 59.686 55.000 0.00 0.00 36.62 4.01
3543 5330 0.679505 GGTCTTTTGGGGTTCAAGCC 59.320 55.000 0.00 0.00 36.62 4.35
3650 5437 3.003068 CAGAGGAGTTTGAGCAACAAGTG 59.997 47.826 0.00 0.00 39.77 3.16
3651 5438 3.118261 AGAGGAGTTTGAGCAACAAGTGA 60.118 43.478 0.00 0.00 39.77 3.41
3652 5439 3.620488 AGGAGTTTGAGCAACAAGTGAA 58.380 40.909 0.00 0.00 39.77 3.18
3653 5440 3.378427 AGGAGTTTGAGCAACAAGTGAAC 59.622 43.478 0.00 0.00 39.77 3.18
3745 5562 2.392933 TAGCTCAAAACAAAACGCCG 57.607 45.000 0.00 0.00 0.00 6.46
3776 5593 0.038251 CTGTGCGTAAGAGTGAGCCA 60.038 55.000 0.00 0.00 43.02 4.75
3783 5600 2.483877 CGTAAGAGTGAGCCATTTTGCA 59.516 45.455 0.00 0.00 43.02 4.08
3804 5621 4.081420 GCAAGTCAGGTTAGAGATTCAGGA 60.081 45.833 0.00 0.00 0.00 3.86
3828 5645 5.983540 ACACCTCTCCTGAAATCTATGAAC 58.016 41.667 0.00 0.00 0.00 3.18
3841 5658 6.566079 AATCTATGAACAGGACCTCATTGA 57.434 37.500 8.19 8.19 37.91 2.57
3846 5663 3.285484 GAACAGGACCTCATTGATGCAT 58.715 45.455 0.00 0.00 0.00 3.96
3886 5734 6.092670 CCTGTTACCTTGTGATGTGTAATGAG 59.907 42.308 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
386 388 1.485124 TGCGGATGAGTATGGTGTCT 58.515 50.000 0.00 0.00 0.00 3.41
423 425 3.675775 GCTTTTGCACAGGAAGAACAACA 60.676 43.478 0.00 0.00 46.58 3.33
661 700 4.708177 AGATTGTCGCTATAAGCAATGGT 58.292 39.130 0.00 0.00 42.58 3.55
847 888 0.323725 GGGAGAATGCAAGGCCTGAA 60.324 55.000 5.69 0.00 0.00 3.02
1208 1472 4.530857 GGCCACCGACCGATGGAG 62.531 72.222 7.05 0.00 38.34 3.86
1211 1475 2.896854 CATGGCCACCGACCGATG 60.897 66.667 8.16 0.00 0.00 3.84
1309 1574 9.448438 AAAGTTGCATATATGAAAGTAGTGTCA 57.552 29.630 17.10 0.00 28.83 3.58
1310 1575 9.708222 CAAAGTTGCATATATGAAAGTAGTGTC 57.292 33.333 17.10 0.00 28.83 3.67
1311 1576 8.677300 CCAAAGTTGCATATATGAAAGTAGTGT 58.323 33.333 17.10 0.00 28.83 3.55
1312 1577 8.131100 CCCAAAGTTGCATATATGAAAGTAGTG 58.869 37.037 17.10 14.85 28.83 2.74
1313 1578 7.285401 CCCCAAAGTTGCATATATGAAAGTAGT 59.715 37.037 17.10 4.50 28.83 2.73
1314 1579 7.502226 TCCCCAAAGTTGCATATATGAAAGTAG 59.498 37.037 17.10 10.79 28.83 2.57
1315 1580 7.350382 TCCCCAAAGTTGCATATATGAAAGTA 58.650 34.615 17.10 0.00 28.83 2.24
1316 1581 6.194235 TCCCCAAAGTTGCATATATGAAAGT 58.806 36.000 17.10 12.25 30.13 2.66
1317 1582 6.713762 TCCCCAAAGTTGCATATATGAAAG 57.286 37.500 17.10 0.46 0.00 2.62
1318 1583 8.954834 ATATCCCCAAAGTTGCATATATGAAA 57.045 30.769 17.10 9.62 0.00 2.69
1724 2064 9.289303 CAAACTGGCTGTTATAATGTAATGTTC 57.711 33.333 10.29 0.00 38.03 3.18
1725 2065 8.250332 CCAAACTGGCTGTTATAATGTAATGTT 58.750 33.333 10.29 0.00 38.03 2.71
1781 2219 4.688021 AGAAGACATGGCGATTAAGAGTC 58.312 43.478 0.00 0.00 0.00 3.36
1793 2231 4.754114 GCCTGAGCTAATTAGAAGACATGG 59.246 45.833 16.85 8.74 35.50 3.66
1797 2235 4.572795 GGTTGCCTGAGCTAATTAGAAGAC 59.427 45.833 16.85 3.59 40.80 3.01
1808 2248 2.282745 GCCAAGGTTGCCTGAGCT 60.283 61.111 0.00 0.00 40.80 4.09
1814 2254 1.187567 ACAATGGAGCCAAGGTTGCC 61.188 55.000 0.00 0.00 0.00 4.52
1996 2436 1.617947 GCTTCTCATCAGGGGACGGT 61.618 60.000 0.00 0.00 0.00 4.83
2245 2719 3.059325 GGTCAGCAGTAAATCGCATGATC 60.059 47.826 0.00 0.00 32.24 2.92
2343 2832 2.135139 GCGCATCCATCGACTTGATTA 58.865 47.619 0.30 0.00 34.13 1.75
2411 2900 7.518052 GCATCTCAGCAAAGAACATAGTATGTC 60.518 40.741 16.06 9.76 44.07 3.06
2569 3067 8.126074 TGTTGATGCGTGGAAAAATATATGTAC 58.874 33.333 0.00 0.00 0.00 2.90
2784 3282 1.490490 AGGAACTTGCTTGTCAGACCA 59.510 47.619 0.00 0.00 27.25 4.02
2887 3390 9.866936 GTTACAATAATTTATTACGCCGATTCA 57.133 29.630 1.41 0.00 0.00 2.57
3058 4844 1.078143 GAGCTCGGCCTTCATTGGT 60.078 57.895 0.00 0.00 0.00 3.67
3230 5017 2.547855 GGCCAATTTCTTTTGTTCGGCT 60.548 45.455 0.00 0.00 0.00 5.52
3234 5021 4.898320 AGATGGGCCAATTTCTTTTGTTC 58.102 39.130 11.89 0.00 0.00 3.18
3380 5167 9.181805 GGAGCTAGTTTTGAAAGAACAAATTAC 57.818 33.333 0.00 0.00 39.09 1.89
3381 5168 8.357402 GGGAGCTAGTTTTGAAAGAACAAATTA 58.643 33.333 0.00 0.00 39.09 1.40
3382 5169 7.069950 AGGGAGCTAGTTTTGAAAGAACAAATT 59.930 33.333 0.00 0.00 39.09 1.82
3383 5170 6.551227 AGGGAGCTAGTTTTGAAAGAACAAAT 59.449 34.615 0.00 0.00 39.09 2.32
3384 5171 5.891551 AGGGAGCTAGTTTTGAAAGAACAAA 59.108 36.000 0.00 0.00 37.87 2.83
3385 5172 5.445964 AGGGAGCTAGTTTTGAAAGAACAA 58.554 37.500 0.00 0.00 0.00 2.83
3386 5173 5.048846 AGGGAGCTAGTTTTGAAAGAACA 57.951 39.130 0.00 0.00 0.00 3.18
3387 5174 6.465084 TCTAGGGAGCTAGTTTTGAAAGAAC 58.535 40.000 0.00 0.00 0.00 3.01
3388 5175 6.681729 TCTAGGGAGCTAGTTTTGAAAGAA 57.318 37.500 0.00 0.00 0.00 2.52
3389 5176 6.287589 CTCTAGGGAGCTAGTTTTGAAAGA 57.712 41.667 0.00 0.00 32.43 2.52
3403 5190 1.901464 GAGGCCGAGCTCTAGGGAG 60.901 68.421 12.85 0.00 42.18 4.30
3404 5191 1.060743 TAGAGGCCGAGCTCTAGGGA 61.061 60.000 12.85 0.00 0.00 4.20
3405 5192 0.178987 TTAGAGGCCGAGCTCTAGGG 60.179 60.000 12.85 6.98 34.21 3.53
3406 5193 1.693627 TTTAGAGGCCGAGCTCTAGG 58.306 55.000 12.85 7.76 34.21 3.02
3407 5194 2.544903 GCTTTTAGAGGCCGAGCTCTAG 60.545 54.545 12.85 4.09 34.21 2.43
3408 5195 1.409427 GCTTTTAGAGGCCGAGCTCTA 59.591 52.381 12.85 0.00 0.00 2.43
3409 5196 0.176910 GCTTTTAGAGGCCGAGCTCT 59.823 55.000 12.85 0.00 0.00 4.09
3410 5197 0.812014 GGCTTTTAGAGGCCGAGCTC 60.812 60.000 2.73 2.73 44.81 4.09
3411 5198 1.222113 GGCTTTTAGAGGCCGAGCT 59.778 57.895 0.00 0.00 44.81 4.09
3412 5199 3.814991 GGCTTTTAGAGGCCGAGC 58.185 61.111 0.00 1.32 44.81 5.03
3418 5205 1.821216 TTCTTGCGGGCTTTTAGAGG 58.179 50.000 0.00 0.00 0.00 3.69
3419 5206 5.514279 CAATATTCTTGCGGGCTTTTAGAG 58.486 41.667 0.00 0.00 0.00 2.43
3420 5207 4.202010 GCAATATTCTTGCGGGCTTTTAGA 60.202 41.667 0.00 0.00 35.58 2.10
3421 5208 4.044426 GCAATATTCTTGCGGGCTTTTAG 58.956 43.478 0.00 0.00 35.58 1.85
3422 5209 3.181480 GGCAATATTCTTGCGGGCTTTTA 60.181 43.478 4.07 0.00 45.78 1.52
3423 5210 2.418609 GGCAATATTCTTGCGGGCTTTT 60.419 45.455 4.07 0.00 45.78 2.27
3424 5211 1.136891 GGCAATATTCTTGCGGGCTTT 59.863 47.619 4.07 0.00 45.78 3.51
3425 5212 0.746659 GGCAATATTCTTGCGGGCTT 59.253 50.000 4.07 0.00 45.78 4.35
3426 5213 1.109323 GGGCAATATTCTTGCGGGCT 61.109 55.000 4.07 0.00 45.78 5.19
3427 5214 1.109323 AGGGCAATATTCTTGCGGGC 61.109 55.000 4.07 0.00 45.78 6.13
3428 5215 2.270352 TAGGGCAATATTCTTGCGGG 57.730 50.000 4.07 0.00 45.78 6.13
3429 5216 5.647658 TGATAATAGGGCAATATTCTTGCGG 59.352 40.000 4.07 0.00 45.78 5.69
3430 5217 6.741992 TGATAATAGGGCAATATTCTTGCG 57.258 37.500 4.07 0.00 45.78 4.85
3431 5218 8.115490 ACTTGATAATAGGGCAATATTCTTGC 57.885 34.615 1.38 1.38 44.22 4.01
3432 5219 8.446273 CGACTTGATAATAGGGCAATATTCTTG 58.554 37.037 0.00 0.00 0.00 3.02
3433 5220 7.607991 CCGACTTGATAATAGGGCAATATTCTT 59.392 37.037 0.00 0.00 0.00 2.52
3434 5221 7.106239 CCGACTTGATAATAGGGCAATATTCT 58.894 38.462 0.00 0.00 0.00 2.40
3435 5222 6.879458 ACCGACTTGATAATAGGGCAATATTC 59.121 38.462 0.00 0.00 0.00 1.75
3436 5223 6.779860 ACCGACTTGATAATAGGGCAATATT 58.220 36.000 0.00 0.00 0.00 1.28
3437 5224 6.374417 ACCGACTTGATAATAGGGCAATAT 57.626 37.500 0.00 0.00 0.00 1.28
3438 5225 5.818678 ACCGACTTGATAATAGGGCAATA 57.181 39.130 0.00 0.00 0.00 1.90
3439 5226 4.706842 ACCGACTTGATAATAGGGCAAT 57.293 40.909 0.00 0.00 0.00 3.56
3440 5227 4.652421 ACTACCGACTTGATAATAGGGCAA 59.348 41.667 0.00 0.00 0.00 4.52
3441 5228 4.038763 CACTACCGACTTGATAATAGGGCA 59.961 45.833 0.00 0.00 0.00 5.36
3442 5229 4.280174 TCACTACCGACTTGATAATAGGGC 59.720 45.833 0.00 0.00 0.00 5.19
3443 5230 5.535406 AGTCACTACCGACTTGATAATAGGG 59.465 44.000 0.00 0.00 43.84 3.53
3444 5231 6.636562 AGTCACTACCGACTTGATAATAGG 57.363 41.667 0.00 0.00 43.84 2.57
3445 5232 7.299586 GCTAGTCACTACCGACTTGATAATAG 58.700 42.308 6.69 0.00 43.84 1.73
3446 5233 6.206243 GGCTAGTCACTACCGACTTGATAATA 59.794 42.308 6.69 0.00 43.84 0.98
3447 5234 5.009811 GGCTAGTCACTACCGACTTGATAAT 59.990 44.000 6.69 0.00 43.84 1.28
3471 5258 2.763448 TCCACACCCTTTGTTTTGAAGG 59.237 45.455 0.00 0.00 42.68 3.46
3520 5307 3.215975 CTTGAACCCCAAAAGACCGTTA 58.784 45.455 0.00 0.00 33.76 3.18
3534 5321 0.250770 ACGAAAGAGGGGCTTGAACC 60.251 55.000 0.00 0.00 36.80 3.62
3535 5322 1.266989 CAACGAAAGAGGGGCTTGAAC 59.733 52.381 0.00 0.00 36.80 3.18
3536 5323 1.133915 ACAACGAAAGAGGGGCTTGAA 60.134 47.619 0.00 0.00 36.80 2.69
3537 5324 0.472471 ACAACGAAAGAGGGGCTTGA 59.528 50.000 0.00 0.00 36.80 3.02
3538 5325 2.178912 TACAACGAAAGAGGGGCTTG 57.821 50.000 0.00 0.00 36.80 4.01
3539 5326 2.943036 TTACAACGAAAGAGGGGCTT 57.057 45.000 0.00 0.00 38.88 4.35
3540 5327 3.434940 AATTACAACGAAAGAGGGGCT 57.565 42.857 0.00 0.00 0.00 5.19
3541 5328 5.124936 ACATAAATTACAACGAAAGAGGGGC 59.875 40.000 0.00 0.00 0.00 5.80
3542 5329 6.598064 AGACATAAATTACAACGAAAGAGGGG 59.402 38.462 0.00 0.00 0.00 4.79
3543 5330 7.611213 AGACATAAATTACAACGAAAGAGGG 57.389 36.000 0.00 0.00 0.00 4.30
3650 5437 7.913674 ATTTTGACTGTAATCCTCTCAGTTC 57.086 36.000 0.00 0.00 41.58 3.01
3651 5438 9.965902 ATTATTTTGACTGTAATCCTCTCAGTT 57.034 29.630 0.00 0.00 41.58 3.16
3652 5439 9.606631 GATTATTTTGACTGTAATCCTCTCAGT 57.393 33.333 0.00 0.00 43.72 3.41
3653 5440 9.050601 GGATTATTTTGACTGTAATCCTCTCAG 57.949 37.037 13.45 0.00 45.28 3.35
3687 5502 6.748333 TGCAGATAAAATTCCACTCTTCAG 57.252 37.500 0.00 0.00 0.00 3.02
3745 5562 2.301577 ACGCACAGATAAAGCTCCTC 57.698 50.000 0.00 0.00 0.00 3.71
3776 5593 6.716628 TGAATCTCTAACCTGACTTGCAAAAT 59.283 34.615 0.00 0.00 0.00 1.82
3783 5600 5.544176 TGTTCCTGAATCTCTAACCTGACTT 59.456 40.000 0.00 0.00 0.00 3.01
3804 5621 6.013379 TGTTCATAGATTTCAGGAGAGGTGTT 60.013 38.462 0.00 0.00 0.00 3.32
3828 5645 1.337071 GCATGCATCAATGAGGTCCTG 59.663 52.381 14.21 0.00 0.00 3.86
3841 5658 5.008331 CAGGATTACTAAGATGGCATGCAT 58.992 41.667 21.36 11.12 0.00 3.96
3846 5663 5.665812 AGGTAACAGGATTACTAAGATGGCA 59.334 40.000 0.00 0.00 41.41 4.92
3854 5671 7.038587 ACACATCACAAGGTAACAGGATTACTA 60.039 37.037 0.00 0.00 41.41 1.82
3886 5734 7.222999 GCAAAGCCTATCATATATTCTCGGTAC 59.777 40.741 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.