Multiple sequence alignment - TraesCS1A01G258200

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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 TraesCS1A01G258200 chr1A 100.000 5528 0 0 1 5528 449933748 449939275 0.000000e+00 10209.0
1 TraesCS1A01G258200 chr1D 93.684 4956 194 49 616 5528 349743217 349748096 0.000000e+00 7308.0
2 TraesCS1A01G258200 chr1D 90.287 628 52 6 1 623 349716793 349717416 0.000000e+00 813.0
3 TraesCS1A01G258200 chr1B 89.695 2659 171 45 1 2619 471749374 471751969 0.000000e+00 3297.0
4 TraesCS1A01G258200 chr1B 94.765 1299 53 8 2742 4038 471751963 471753248 0.000000e+00 2008.0
5 TraesCS1A01G258200 chr1B 86.594 552 42 14 4292 4831 471753766 471754297 1.030000e-161 580.0
6 TraesCS1A01G258200 chr1B 78.662 553 38 38 5040 5525 471754545 471755084 1.510000e-75 294.0
7 TraesCS1A01G258200 chr1B 88.462 234 19 6 4045 4273 471753327 471753557 5.450000e-70 276.0
8 TraesCS1A01G258200 chr5A 89.883 257 25 1 2161 2416 93734879 93735135 4.130000e-86 329.0
9 TraesCS1A01G258200 chr2A 88.327 257 23 2 2161 2416 256279273 256279523 9.000000e-78 302.0
10 TraesCS1A01G258200 chr2A 100.000 33 0 0 5493 5525 761312672 761312640 1.660000e-05 62.1
11 TraesCS1A01G258200 chr2B 87.121 264 25 3 2161 2416 469354138 469354400 1.950000e-74 291.0
12 TraesCS1A01G258200 chr5B 92.357 157 11 1 2260 2415 202861514 202861670 7.210000e-54 222.0
13 TraesCS1A01G258200 chr3B 91.892 148 12 0 2260 2407 408807118 408806971 2.020000e-49 207.0
14 TraesCS1A01G258200 chr3B 94.595 37 1 1 5493 5528 397668979 397668943 7.740000e-04 56.5
15 TraesCS1A01G258200 chr4D 100.000 29 0 0 5493 5521 138326590 138326618 3.000000e-03 54.7
16 TraesCS1A01G258200 chr6B 83.929 56 8 1 5469 5524 637045952 637045898 1.000000e-02 52.8


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 TraesCS1A01G258200 chr1A 449933748 449939275 5527 False 10209 10209 100.0000 1 5528 1 chr1A.!!$F1 5527
1 TraesCS1A01G258200 chr1D 349743217 349748096 4879 False 7308 7308 93.6840 616 5528 1 chr1D.!!$F2 4912
2 TraesCS1A01G258200 chr1D 349716793 349717416 623 False 813 813 90.2870 1 623 1 chr1D.!!$F1 622
3 TraesCS1A01G258200 chr1B 471749374 471755084 5710 False 1291 3297 87.6356 1 5525 5 chr1B.!!$F1 5524

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
48 49 0.179094 ATGAGCATTGGCAATTGGCG 60.179 50.000 25.00 13.33 46.16 5.69 F
1257 1294 1.653094 CGCCCTGCCTTTAATTCGCA 61.653 55.000 0.00 0.00 0.00 5.10 F
2171 2227 0.539669 AGGGCCAACTTTGTGCCTAC 60.540 55.000 6.18 5.88 41.38 3.18 F
2295 2351 0.337773 TCCTGGATGGAGTGCTCTCT 59.662 55.000 14.98 0.00 40.56 3.10 F
3757 3826 1.000359 GTGGCCTACCCCAGCAATT 60.000 57.895 3.32 0.00 35.05 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1323 1360 0.690762 AACGAAGCCCTAGAAGCCAA 59.309 50.000 0.0 0.0 0.00 4.52 R
2274 2330 0.042431 AGAGCACTCCATCCAGGACT 59.958 55.000 0.0 0.0 43.07 3.85 R
3312 3380 0.872388 GTTCGTTTCTGGCAACCGAT 59.128 50.000 0.0 0.0 0.00 4.18 R
4199 4346 1.202348 GCAGCAAACAAGATACCACCC 59.798 52.381 0.0 0.0 0.00 4.61 R
5381 5851 0.032678 AATAGCCCAGACGCTCATCG 59.967 55.000 0.0 0.0 40.39 3.84 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
48 49 0.179094 ATGAGCATTGGCAATTGGCG 60.179 50.000 25.00 13.33 46.16 5.69
72 73 5.569428 GCATGCTTTCCCTAAGTTTGGAAAT 60.569 40.000 11.37 3.74 46.53 2.17
82 83 5.634859 CCTAAGTTTGGAAATGTGACAATGC 59.365 40.000 0.00 0.00 0.00 3.56
142 143 4.308899 ACATGCCTACTCGTATCTTGTC 57.691 45.455 0.00 0.00 0.00 3.18
182 183 8.850454 TTGTTGAGTTAGTTAAATGTCTTTGC 57.150 30.769 0.00 0.00 0.00 3.68
223 224 9.691362 GTATTGTGATGTTTCAAACCTAAATGT 57.309 29.630 0.00 0.00 32.48 2.71
249 250 7.723616 TCACATTTGACCTTCTAAATCCAAAGA 59.276 33.333 0.00 0.00 0.00 2.52
271 272 4.893424 TGTACTTTGAAACTCAAGGTGC 57.107 40.909 12.79 11.94 44.71 5.01
302 303 6.114187 TGGTATATGGATGTCATCACCTTC 57.886 41.667 14.72 0.00 39.74 3.46
333 334 6.473521 TGAACACAAAATGAATTTTCGTTGC 58.526 32.000 13.56 8.61 37.86 4.17
448 449 1.809133 TGTAGGGTTGGACTGTGGAA 58.191 50.000 0.00 0.00 0.00 3.53
487 488 4.152938 TGAAACTCAAGATGCGAATCACTG 59.847 41.667 6.08 2.62 0.00 3.66
512 513 6.040166 GCCACATGAATGTCATCCTCTTAAAT 59.960 38.462 0.00 0.00 39.39 1.40
516 518 9.512588 ACATGAATGTCATCCTCTTAAATATCC 57.487 33.333 0.00 0.00 34.28 2.59
918 946 4.200283 GGAGAGGCAGGCGAGTCG 62.200 72.222 8.54 8.54 0.00 4.18
1217 1254 1.925185 CTATCTCTGTCGTCGTCGTCA 59.075 52.381 1.33 1.79 38.33 4.35
1257 1294 1.653094 CGCCCTGCCTTTAATTCGCA 61.653 55.000 0.00 0.00 0.00 5.10
1320 1357 2.548057 TGCGATTTAGGATTGGATTCGC 59.452 45.455 7.39 7.39 43.22 4.70
1323 1360 2.325583 TTTAGGATTGGATTCGCGCT 57.674 45.000 5.56 0.00 0.00 5.92
1345 1382 1.066071 GGCTTCTAGGGCTTCGTTTCT 60.066 52.381 8.14 0.00 0.00 2.52
1349 1386 1.087501 CTAGGGCTTCGTTTCTTGGC 58.912 55.000 0.00 0.00 0.00 4.52
1381 1418 2.824041 CTGGCGTCGAATTGGGGG 60.824 66.667 0.00 0.00 0.00 5.40
1466 1503 3.972502 CGGGCGAAATTTAATCGAATTCC 59.027 43.478 0.00 0.00 42.76 3.01
1497 1534 3.493524 GCCAATCTCCTAGGCTAGAACAC 60.494 52.174 22.99 0.56 44.92 3.32
1525 1562 1.234615 TGCGCTTCCTTGTTGCTACC 61.235 55.000 9.73 0.00 0.00 3.18
1571 1608 8.079211 TGATTTTGTACTCTCCATTAGCTAGT 57.921 34.615 0.00 0.00 0.00 2.57
1676 1713 7.002879 AGATGCTTGCTTATGTGATCCTAAAT 58.997 34.615 0.00 0.00 0.00 1.40
1707 1744 2.037367 TCCCGTGCCTGCTACTCT 59.963 61.111 0.00 0.00 0.00 3.24
1713 1750 2.418746 CCGTGCCTGCTACTCTAATTGT 60.419 50.000 0.00 0.00 0.00 2.71
1824 1863 5.410355 AGTGGCTGTTATTTCGGTAGTTA 57.590 39.130 0.00 0.00 0.00 2.24
1977 2016 3.008485 GGGAGGATGGTGATTAGTGATCC 59.992 52.174 0.00 0.00 33.60 3.36
2064 2106 1.622811 CTGACCTCTCCTTCAACTGCT 59.377 52.381 0.00 0.00 0.00 4.24
2106 2148 5.225642 GTGCCTCATTTCCTTTCTTTTCAG 58.774 41.667 0.00 0.00 0.00 3.02
2164 2220 3.399440 TGCAATTTAGGGCCAACTTTG 57.601 42.857 6.18 5.61 0.00 2.77
2171 2227 0.539669 AGGGCCAACTTTGTGCCTAC 60.540 55.000 6.18 5.88 41.38 3.18
2295 2351 0.337773 TCCTGGATGGAGTGCTCTCT 59.662 55.000 14.98 0.00 40.56 3.10
2336 2392 4.332637 CACACGCACAGCTTGGGC 62.333 66.667 11.13 6.60 44.98 5.36
2361 2420 5.466728 TGTCTAAGTTTGCATCTCTGTCAAC 59.533 40.000 0.00 0.00 0.00 3.18
2492 2555 6.713792 AGTTCTTCTTCTAATTCGTTCAGC 57.286 37.500 0.00 0.00 0.00 4.26
2504 2567 2.771089 TCGTTCAGCTCTCTTGCATTT 58.229 42.857 0.00 0.00 34.99 2.32
2506 2569 4.314961 TCGTTCAGCTCTCTTGCATTTTA 58.685 39.130 0.00 0.00 34.99 1.52
2525 2588 9.533253 GCATTTTATAGTGGTATTTGCAAGAAT 57.467 29.630 0.00 0.00 0.00 2.40
2540 2603 9.729281 ATTTGCAAGAATGAAATGGATTAACTT 57.271 25.926 0.00 0.00 0.00 2.66
2595 2661 3.473625 AGGTGCTGTAACCAGTGTAAAC 58.526 45.455 4.79 0.00 43.20 2.01
2639 2705 9.191479 ACTGTAATAGACTGTATTGAAGCTACT 57.809 33.333 0.00 0.00 38.36 2.57
2654 2720 9.643693 ATTGAAGCTACTTGATTTTGGTTTATG 57.356 29.630 0.00 0.00 0.00 1.90
2655 2721 7.090173 TGAAGCTACTTGATTTTGGTTTATGC 58.910 34.615 0.00 0.00 0.00 3.14
2676 2743 3.671928 GCAGTCAATTTGCAGCTTGTAAG 59.328 43.478 9.37 0.00 41.17 2.34
2686 2753 5.239359 TGCAGCTTGTAAGATTATTGCTG 57.761 39.130 0.00 0.00 46.11 4.41
2706 2773 6.662755 TGCTGGTCATTACAATTTCTATCCT 58.337 36.000 0.00 0.00 0.00 3.24
2782 2850 8.081633 TGTTCAGTTATTCTGGCTTTTTGTATG 58.918 33.333 0.00 0.00 43.76 2.39
2820 2888 9.103861 CATTGTCTAACTCTTCTTTAATCTCCC 57.896 37.037 0.00 0.00 0.00 4.30
2827 2895 6.583562 ACTCTTCTTTAATCTCCCATTACCG 58.416 40.000 0.00 0.00 0.00 4.02
2844 2912 9.458374 CCCATTACCGTATAATCATTTTTGTTC 57.542 33.333 0.00 0.00 0.00 3.18
3060 3128 4.037690 CGAGAAAAACACCTGAAAGCAAG 58.962 43.478 0.00 0.00 0.00 4.01
3273 3341 3.613737 CACGCATTTTCAATGGTTCCATC 59.386 43.478 4.72 0.00 0.00 3.51
3285 3353 1.673168 GTTCCATCCCTGCAGATGTC 58.327 55.000 17.39 1.87 41.79 3.06
3316 3384 5.335127 CAAGTGATTTTGGAGCTTTATCGG 58.665 41.667 0.00 0.00 0.00 4.18
3340 3408 2.690786 CCAGAAACGAACCGGTGAATA 58.309 47.619 8.52 0.00 0.00 1.75
3473 3542 2.890945 ACAAAAGGTTAGCATGTGACCC 59.109 45.455 9.67 0.00 33.89 4.46
3667 3736 1.112315 AGTCTCCTAGCATGCCGAGG 61.112 60.000 24.28 24.28 0.00 4.63
3757 3826 1.000359 GTGGCCTACCCCAGCAATT 60.000 57.895 3.32 0.00 35.05 2.32
3974 4044 5.016173 TCACATGCTTTTAGCCCTTTACAT 58.984 37.500 0.00 0.00 41.51 2.29
4092 4234 3.069729 CCAAGATAGTACTGGTAGTGGCC 59.930 52.174 5.39 0.00 0.00 5.36
4266 4413 4.299586 TCCCTCACAATAACAATGCTCA 57.700 40.909 0.00 0.00 0.00 4.26
4353 4690 0.874390 CACGTGATGGTCCTTTGGTG 59.126 55.000 10.90 0.00 0.00 4.17
4358 4695 3.492337 GTGATGGTCCTTTGGTGGTTTA 58.508 45.455 0.00 0.00 0.00 2.01
4363 4700 3.332485 TGGTCCTTTGGTGGTTTAGCTAT 59.668 43.478 0.00 0.00 0.00 2.97
4369 4706 6.208599 TCCTTTGGTGGTTTAGCTATTTGAAG 59.791 38.462 0.00 0.00 0.00 3.02
4643 4994 3.136763 CCCATCATCGAACTTCTGGATG 58.863 50.000 0.00 0.00 40.61 3.51
4762 5113 7.156673 TGGTTAAGCACTCGTTTACTCTATTT 58.843 34.615 2.54 0.00 0.00 1.40
4773 5124 9.751542 CTCGTTTACTCTATTTGATATTCCTGT 57.248 33.333 0.00 0.00 0.00 4.00
4837 5212 0.815734 AATCCACCGTGAGTAGACCG 59.184 55.000 0.00 0.00 0.00 4.79
4874 5250 3.085533 GGGTGCCACAATGTACATACAA 58.914 45.455 9.21 0.00 39.99 2.41
4876 5252 4.021894 GGGTGCCACAATGTACATACAAAA 60.022 41.667 9.21 0.00 39.99 2.44
4877 5253 5.337169 GGGTGCCACAATGTACATACAAAAT 60.337 40.000 9.21 0.00 39.99 1.82
4880 5256 6.527722 GTGCCACAATGTACATACAAAATCAG 59.472 38.462 9.21 0.00 39.99 2.90
4881 5257 6.208402 TGCCACAATGTACATACAAAATCAGT 59.792 34.615 9.21 0.00 39.99 3.41
4920 5327 9.227490 CAAACAGTATAATTTTGTCGAAACACA 57.773 29.630 0.00 0.00 34.35 3.72
4978 5398 8.821894 CAAGTTACTAGGATTTGTGATTAGCTC 58.178 37.037 0.00 0.00 0.00 4.09
5013 5433 6.439058 AGAAGAAAGAGTAGTCTGCTGGTAAT 59.561 38.462 0.00 0.00 27.82 1.89
5023 5443 2.027192 TCTGCTGGTAATCTGGTTGGTC 60.027 50.000 0.00 0.00 0.00 4.02
5037 5457 3.671716 GGTTGGTCCAAAGAACGATAGT 58.328 45.455 5.69 0.00 44.51 2.12
5111 5532 3.243636 TGACTTGTTGTAGGTTCGAGTCC 60.244 47.826 0.00 1.17 40.12 3.85
5217 5660 8.312896 TGTAAGCAAATTTACAACATCTACGA 57.687 30.769 0.00 0.00 39.78 3.43
5222 5665 3.940209 TTTACAACATCTACGACCGGT 57.060 42.857 6.92 6.92 0.00 5.28
5223 5666 3.940209 TTACAACATCTACGACCGGTT 57.060 42.857 9.42 0.00 0.00 4.44
5242 5685 4.802876 GTTGTCTCAAACCAGTCTCAAG 57.197 45.455 0.00 0.00 0.00 3.02
5246 5689 0.106708 TCAAACCAGTCTCAAGCGCT 59.893 50.000 2.64 2.64 0.00 5.92
5250 5693 2.507992 CAGTCTCAAGCGCTCGGG 60.508 66.667 12.06 0.00 0.00 5.14
5288 5731 1.734655 ATCCGGCACCATTCTAGGAT 58.265 50.000 0.00 0.00 34.02 3.24
5336 5779 1.514087 TCCGCCACGTTGGACTATC 59.486 57.895 8.04 0.00 40.96 2.08
5339 5809 1.514087 GCCACGTTGGACTATCGGA 59.486 57.895 8.04 0.00 40.96 4.55
5375 5845 1.526455 CGGAAACCCAACGACCCAA 60.526 57.895 0.00 0.00 0.00 4.12
5376 5846 1.788067 CGGAAACCCAACGACCCAAC 61.788 60.000 0.00 0.00 0.00 3.77
5377 5847 0.752376 GGAAACCCAACGACCCAACA 60.752 55.000 0.00 0.00 0.00 3.33
5378 5848 1.104630 GAAACCCAACGACCCAACAA 58.895 50.000 0.00 0.00 0.00 2.83
5379 5849 1.684450 GAAACCCAACGACCCAACAAT 59.316 47.619 0.00 0.00 0.00 2.71
5380 5850 1.324383 AACCCAACGACCCAACAATC 58.676 50.000 0.00 0.00 0.00 2.67
5381 5851 0.538746 ACCCAACGACCCAACAATCC 60.539 55.000 0.00 0.00 0.00 3.01
5405 5875 2.500098 TGAGCGTCTGGGCTATTTAAGT 59.500 45.455 0.00 0.00 44.93 2.24
5429 5899 0.462047 CATCGACCCCCAACACTAGC 60.462 60.000 0.00 0.00 0.00 3.42
5491 5973 1.471327 GCTCTCTGCTCGATCTTTGCT 60.471 52.381 0.00 0.00 38.95 3.91
5495 5977 3.193479 TCTCTGCTCGATCTTTGCTACAA 59.807 43.478 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.674852 CGATGAGGATTGTGGTCAACAG 59.325 50.000 0.00 0.00 40.74 3.16
10 11 3.197549 TCATCGATGAGGATTGTGGTCAA 59.802 43.478 23.99 0.00 33.76 3.18
48 49 2.825532 TCCAAACTTAGGGAAAGCATGC 59.174 45.455 10.51 10.51 38.93 4.06
117 118 5.593095 ACAAGATACGAGTAGGCATGTAAGA 59.407 40.000 0.00 0.00 0.00 2.10
142 143 7.621428 AACTCAACAAGGTATCATCAAGATG 57.379 36.000 3.67 3.67 37.57 2.90
223 224 7.723616 TCTTTGGATTTAGAAGGTCAAATGTGA 59.276 33.333 0.00 0.00 0.00 3.58
249 250 4.278419 GGCACCTTGAGTTTCAAAGTACAT 59.722 41.667 0.00 0.00 35.73 2.29
271 272 7.612633 TGATGACATCCATATACCAATGATTGG 59.387 37.037 22.06 22.06 45.52 3.16
362 363 8.706492 ATGTAATGCACCATGAAAATTAACTG 57.294 30.769 0.00 0.00 0.00 3.16
419 420 3.634910 GTCCAACCCTACAAACAACATGT 59.365 43.478 0.00 0.00 34.81 3.21
420 421 3.888930 AGTCCAACCCTACAAACAACATG 59.111 43.478 0.00 0.00 0.00 3.21
421 422 3.888930 CAGTCCAACCCTACAAACAACAT 59.111 43.478 0.00 0.00 0.00 2.71
423 424 3.066203 CACAGTCCAACCCTACAAACAAC 59.934 47.826 0.00 0.00 0.00 3.32
475 476 0.736636 CATGTGGCAGTGATTCGCAT 59.263 50.000 0.00 0.00 32.61 4.73
487 488 2.928334 AGAGGATGACATTCATGTGGC 58.072 47.619 0.00 0.00 41.95 5.01
512 513 9.004717 TGAGTATTTTCATTTTGTGTTCGGATA 57.995 29.630 0.00 0.00 0.00 2.59
516 518 8.726650 TGATGAGTATTTTCATTTTGTGTTCG 57.273 30.769 0.00 0.00 37.90 3.95
693 708 1.054574 TGATTTCGACCGTTCGTTCG 58.945 50.000 1.29 5.86 46.01 3.95
714 729 1.522569 GGATTGTGGTCGAGGGAGG 59.477 63.158 0.00 0.00 0.00 4.30
717 733 1.153628 GTCGGATTGTGGTCGAGGG 60.154 63.158 0.00 0.00 33.41 4.30
1077 1114 4.415332 CGGTCGTCCACCTCCGTG 62.415 72.222 0.00 0.00 44.21 4.94
1217 1254 4.587189 GAACCCTAGCGGCGCGAT 62.587 66.667 27.59 13.08 33.26 4.58
1257 1294 0.732880 CGCGAACGACACATCCTCTT 60.733 55.000 0.00 0.00 43.93 2.85
1320 1357 1.078143 AAGCCCTAGAAGCCAAGCG 60.078 57.895 0.00 0.00 0.00 4.68
1323 1360 0.690762 AACGAAGCCCTAGAAGCCAA 59.309 50.000 0.00 0.00 0.00 4.52
1345 1382 0.821711 GGGGCTATGCAATACGCCAA 60.822 55.000 17.08 0.00 41.72 4.52
1349 1386 1.237285 GCCAGGGGCTATGCAATACG 61.237 60.000 0.00 0.00 46.69 3.06
1368 1405 2.644555 ATCGAGCCCCCAATTCGACG 62.645 60.000 0.00 0.00 44.90 5.12
1381 1418 3.193263 TGAAGCATGAGAAGAATCGAGC 58.807 45.455 0.00 0.00 0.00 5.03
1571 1608 1.350684 TGCCTGCAGGAGTATTGTTCA 59.649 47.619 37.21 17.88 37.39 3.18
1676 1713 2.427453 GCACGGGACATCTCTAGAGAAA 59.573 50.000 25.77 4.99 41.36 2.52
1713 1750 6.588204 ACGCAGTATGTCCAAGGATAAATAA 58.412 36.000 0.00 0.00 41.94 1.40
2042 2084 0.980423 AGTTGAAGGAGAGGTCAGCC 59.020 55.000 0.00 0.00 0.00 4.85
2106 2148 7.506114 TGGTCTAATCTATCACCCACATAAAC 58.494 38.462 0.00 0.00 0.00 2.01
2164 2220 1.377333 GGCAGAAGGTGGTAGGCAC 60.377 63.158 0.00 0.00 0.00 5.01
2171 2227 3.831911 TGGAAATAAAAGGCAGAAGGTGG 59.168 43.478 0.00 0.00 0.00 4.61
2248 2304 3.340814 TTTCTGCTAAAGCTCAGAGGG 57.659 47.619 3.26 0.00 40.07 4.30
2274 2330 0.042431 AGAGCACTCCATCCAGGACT 59.958 55.000 0.00 0.00 43.07 3.85
2336 2392 5.233225 TGACAGAGATGCAAACTTAGACAG 58.767 41.667 0.00 0.00 0.00 3.51
2390 2449 9.746457 AGATATGATACTATAGCACTGACAGAA 57.254 33.333 10.08 0.00 0.00 3.02
2471 2531 6.692486 AGAGCTGAACGAATTAGAAGAAGAA 58.308 36.000 0.00 0.00 0.00 2.52
2472 2532 6.151985 AGAGAGCTGAACGAATTAGAAGAAGA 59.848 38.462 0.00 0.00 0.00 2.87
2473 2533 6.329496 AGAGAGCTGAACGAATTAGAAGAAG 58.671 40.000 0.00 0.00 0.00 2.85
2492 2555 9.941664 CAAATACCACTATAAAATGCAAGAGAG 57.058 33.333 0.00 0.00 0.00 3.20
2506 2569 8.199449 CCATTTCATTCTTGCAAATACCACTAT 58.801 33.333 0.00 0.00 0.00 2.12
2525 2588 7.936496 TCATGCAGTAAGTTAATCCATTTCA 57.064 32.000 0.00 0.00 0.00 2.69
2609 2675 8.812329 GCTTCAATACAGTCTATTACAGTTCAG 58.188 37.037 0.00 0.00 0.00 3.02
2611 2677 8.934507 AGCTTCAATACAGTCTATTACAGTTC 57.065 34.615 0.00 0.00 0.00 3.01
2639 2705 8.557864 CAAATTGACTGCATAAACCAAAATCAA 58.442 29.630 0.00 0.00 0.00 2.57
2654 2720 2.144482 ACAAGCTGCAAATTGACTGC 57.856 45.000 15.44 4.35 40.35 4.40
2655 2721 5.112220 TCTTACAAGCTGCAAATTGACTG 57.888 39.130 15.44 6.41 0.00 3.51
2737 2804 9.555727 ACTGAACACATAAAAATACAGTACAGT 57.444 29.630 0.00 0.00 35.95 3.55
2818 2886 9.458374 GAACAAAAATGATTATACGGTAATGGG 57.542 33.333 0.00 0.00 0.00 4.00
2844 2912 2.480419 CCGCAAAACTGTTGTAGAGGAG 59.520 50.000 0.00 0.00 0.00 3.69
2845 2913 2.103432 TCCGCAAAACTGTTGTAGAGGA 59.897 45.455 7.96 7.96 0.00 3.71
2846 2914 2.489971 TCCGCAAAACTGTTGTAGAGG 58.510 47.619 0.00 0.00 0.00 3.69
3273 3341 1.227380 GCCTACGACATCTGCAGGG 60.227 63.158 15.13 9.34 0.00 4.45
3285 3353 1.472480 CCAAAATCACTTGGGCCTACG 59.528 52.381 4.53 0.00 41.96 3.51
3312 3380 0.872388 GTTCGTTTCTGGCAACCGAT 59.128 50.000 0.00 0.00 0.00 4.18
3316 3384 1.281656 CCGGTTCGTTTCTGGCAAC 59.718 57.895 0.00 0.00 0.00 4.17
3340 3408 4.564782 TCTCATCAACAGAAGGCTCAAT 57.435 40.909 0.00 0.00 0.00 2.57
3473 3542 5.524646 CCATGGTGGCAGCAAAATTTAATAG 59.475 40.000 24.45 3.78 0.00 1.73
3667 3736 4.036380 CCAAAGTACACAGAAGGTTGGTTC 59.964 45.833 0.00 0.00 31.42 3.62
3757 3826 3.977326 TGTCATAGCAATGGGGGTACATA 59.023 43.478 0.00 0.00 33.61 2.29
3858 3927 9.976511 TTAGACAACCTAACCTTGATATTATCG 57.023 33.333 0.00 0.00 32.67 2.92
3875 3944 2.480845 AGAACACGCACTTAGACAACC 58.519 47.619 0.00 0.00 0.00 3.77
3974 4044 3.010138 ACCAGCCAGATTAAGCCAAGTTA 59.990 43.478 0.00 0.00 0.00 2.24
4092 4234 6.567321 CGGGGTCATAACTCATAACTACTACG 60.567 46.154 0.00 0.00 0.00 3.51
4199 4346 1.202348 GCAGCAAACAAGATACCACCC 59.798 52.381 0.00 0.00 0.00 4.61
4296 4633 8.247562 TGGCAAGCAATATAACGAAATTAAACT 58.752 29.630 0.00 0.00 0.00 2.66
4353 4690 6.894828 TGTTTCGACTTCAAATAGCTAAACC 58.105 36.000 0.00 0.00 0.00 3.27
4358 4695 7.275920 AGGATATGTTTCGACTTCAAATAGCT 58.724 34.615 0.00 0.00 0.00 3.32
4363 4700 5.800296 TGGAGGATATGTTTCGACTTCAAA 58.200 37.500 0.00 0.00 0.00 2.69
4369 4706 4.201822 GCTGTTTGGAGGATATGTTTCGAC 60.202 45.833 0.00 0.00 0.00 4.20
4432 4769 9.758651 ATGAAAATAAAGTTGGGAGTTTGTTAC 57.241 29.630 0.00 0.00 31.69 2.50
4442 4787 6.620678 ACGATGACATGAAAATAAAGTTGGG 58.379 36.000 0.00 0.00 0.00 4.12
4643 4994 5.593679 TTCTTATACACCTAGCTGACACC 57.406 43.478 0.00 0.00 0.00 4.16
4762 5113 5.305386 CAGGGAGTGATGTACAGGAATATCA 59.695 44.000 0.33 0.00 0.00 2.15
4773 5124 0.324368 ACGAGGCAGGGAGTGATGTA 60.324 55.000 0.00 0.00 0.00 2.29
4837 5212 2.767505 CACCCCGAATGCTAAGATACC 58.232 52.381 0.00 0.00 0.00 2.73
4920 5327 5.378230 TGCTCCAGTGGAAATTATGATCT 57.622 39.130 14.17 0.00 0.00 2.75
4973 5393 5.941058 TCTTTCTTCTTTCTCTCTCGAGCTA 59.059 40.000 7.81 0.00 37.19 3.32
4978 5398 7.119262 AGACTACTCTTTCTTCTTTCTCTCTCG 59.881 40.741 0.00 0.00 0.00 4.04
4989 5409 4.529109 ACCAGCAGACTACTCTTTCTTC 57.471 45.455 0.00 0.00 0.00 2.87
5023 5443 4.499183 AGAAGCTGACTATCGTTCTTTGG 58.501 43.478 0.00 0.00 0.00 3.28
5037 5457 9.561069 AATAAAAGAACAGACTTAAGAAGCTGA 57.439 29.630 22.21 6.95 36.67 4.26
5111 5532 4.816385 ACAGGAGTTTGTTGTCATGTGTAG 59.184 41.667 0.00 0.00 36.40 2.74
5202 5645 3.940209 ACCGGTCGTAGATGTTGTAAA 57.060 42.857 0.00 0.00 40.67 2.01
5217 5660 3.396951 CTGGTTTGAGACAACCGGT 57.603 52.632 0.00 0.00 41.88 5.28
5222 5665 3.206150 GCTTGAGACTGGTTTGAGACAA 58.794 45.455 0.00 0.00 0.00 3.18
5223 5666 2.803133 CGCTTGAGACTGGTTTGAGACA 60.803 50.000 0.00 0.00 0.00 3.41
5234 5677 4.443266 GCCCGAGCGCTTGAGACT 62.443 66.667 26.61 0.00 0.00 3.24
5250 5693 1.113517 TATGAGGGGTGCTAGTCGGC 61.114 60.000 0.00 0.00 0.00 5.54
5252 5695 1.546476 GGATATGAGGGGTGCTAGTCG 59.454 57.143 0.00 0.00 0.00 4.18
5288 5731 2.146724 CCGGGCCACCTCATATCCA 61.147 63.158 4.39 0.00 33.28 3.41
5318 5761 1.514087 GATAGTCCAACGTGGCGGA 59.486 57.895 0.00 0.00 37.47 5.54
5319 5762 1.876714 CGATAGTCCAACGTGGCGG 60.877 63.158 0.00 0.00 37.47 6.13
5322 5765 1.681793 AGATCCGATAGTCCAACGTGG 59.318 52.381 0.00 0.00 39.43 4.94
5324 5767 2.651455 TGAGATCCGATAGTCCAACGT 58.349 47.619 0.00 0.00 0.00 3.99
5325 5768 3.924918 ATGAGATCCGATAGTCCAACG 57.075 47.619 0.00 0.00 0.00 4.10
5326 5769 4.454847 TCGTATGAGATCCGATAGTCCAAC 59.545 45.833 0.00 0.00 0.00 3.77
5330 5773 5.960683 CGATTTCGTATGAGATCCGATAGTC 59.039 44.000 9.30 0.00 33.30 2.59
5331 5774 5.674068 GCGATTTCGTATGAGATCCGATAGT 60.674 44.000 9.30 0.00 42.22 2.12
5332 5775 4.731000 GCGATTTCGTATGAGATCCGATAG 59.269 45.833 9.30 0.00 42.22 2.08
5334 5777 3.191581 AGCGATTTCGTATGAGATCCGAT 59.808 43.478 9.30 2.34 42.22 4.18
5336 5779 2.911723 GAGCGATTTCGTATGAGATCCG 59.088 50.000 9.30 6.47 42.22 4.18
5339 5809 2.552743 TCCGAGCGATTTCGTATGAGAT 59.447 45.455 1.55 0.00 42.22 2.75
5375 5845 0.179100 CCAGACGCTCATCGGATTGT 60.179 55.000 0.00 0.00 43.86 2.71
5376 5846 0.877649 CCCAGACGCTCATCGGATTG 60.878 60.000 0.00 0.00 43.86 2.67
5377 5847 1.443407 CCCAGACGCTCATCGGATT 59.557 57.895 0.00 0.00 43.86 3.01
5378 5848 3.133014 CCCAGACGCTCATCGGAT 58.867 61.111 0.00 0.00 43.86 4.18
5379 5849 2.904178 TAGCCCAGACGCTCATCGGA 62.904 60.000 0.00 0.00 43.86 4.55
5380 5850 1.810606 ATAGCCCAGACGCTCATCGG 61.811 60.000 0.00 0.00 43.86 4.18
5381 5851 0.032678 AATAGCCCAGACGCTCATCG 59.967 55.000 0.00 0.00 40.39 3.84
5405 5875 2.284039 TTGGGGGTCGATGTCCGA 60.284 61.111 0.00 0.00 46.35 4.55
5429 5899 0.534412 AGCGAGAGAAGTGGATGTGG 59.466 55.000 0.00 0.00 0.00 4.17
5491 5973 1.195442 TCTGTCGGGCCATGGTTGTA 61.195 55.000 14.67 0.00 0.00 2.41
5495 5977 3.402681 CCTCTGTCGGGCCATGGT 61.403 66.667 14.67 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.