Multiple sequence alignment - TraesCS2A01G240300

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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 TraesCS2A01G240300 chr2A 100.000 5226 0 0 1 5226 335391972 335397197 0 9651
1 TraesCS2A01G240300 chr2A 87.974 607 65 8 4624 5226 330094540 330095142 0 710
2 TraesCS2A01G240300 chr2D 93.591 5243 296 21 1 5226 269740673 269735454 0 7784
3 TraesCS2A01G240300 chr2B 89.897 2326 215 14 1892 4201 317758930 317756609 0 2976
4 TraesCS2A01G240300 chr2B 91.498 1282 91 10 570 1844 317760301 317759031 0 1748
5 TraesCS2A01G240300 chr1D 88.796 598 59 8 4632 5226 180969311 180969903 0 726
6 TraesCS2A01G240300 chr1D 87.765 613 65 6 4623 5226 181938989 181938378 0 708
7 TraesCS2A01G240300 chr1D 88.167 600 61 9 4632 5226 165153635 165154229 0 706
8 TraesCS2A01G240300 chr1D 87.809 607 66 8 4624 5226 139066070 139066672 0 704
9 TraesCS2A01G240300 chr7D 88.167 600 62 9 4631 5226 331430878 331430284 0 706
10 TraesCS2A01G240300 chr3A 88.167 600 61 10 4632 5226 336342523 336341929 0 706
11 TraesCS2A01G240300 chr6A 87.644 607 67 8 4624 5226 250264913 250265515 0 699


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 TraesCS2A01G240300 chr2A 335391972 335397197 5225 False 9651 9651 100.0000 1 5226 1 chr2A.!!$F2 5225
1 TraesCS2A01G240300 chr2A 330094540 330095142 602 False 710 710 87.9740 4624 5226 1 chr2A.!!$F1 602
2 TraesCS2A01G240300 chr2D 269735454 269740673 5219 True 7784 7784 93.5910 1 5226 1 chr2D.!!$R1 5225
3 TraesCS2A01G240300 chr2B 317756609 317760301 3692 True 2362 2976 90.6975 570 4201 2 chr2B.!!$R1 3631
4 TraesCS2A01G240300 chr1D 180969311 180969903 592 False 726 726 88.7960 4632 5226 1 chr1D.!!$F3 594
5 TraesCS2A01G240300 chr1D 181938378 181938989 611 True 708 708 87.7650 4623 5226 1 chr1D.!!$R1 603
6 TraesCS2A01G240300 chr1D 165153635 165154229 594 False 706 706 88.1670 4632 5226 1 chr1D.!!$F2 594
7 TraesCS2A01G240300 chr1D 139066070 139066672 602 False 704 704 87.8090 4624 5226 1 chr1D.!!$F1 602
8 TraesCS2A01G240300 chr7D 331430284 331430878 594 True 706 706 88.1670 4631 5226 1 chr7D.!!$R1 595
9 TraesCS2A01G240300 chr3A 336341929 336342523 594 True 706 706 88.1670 4632 5226 1 chr3A.!!$R1 594
10 TraesCS2A01G240300 chr6A 250264913 250265515 602 False 699 699 87.6440 4624 5226 1 chr6A.!!$F1 602

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
123 124 0.102120 TTTTGACCAACGCCTGCTTG 59.898 50.000 0.00 0.0 0.00 4.01 F
924 928 0.386476 CCGATGCATGGTTGAATGGG 59.614 55.000 2.46 0.0 31.10 4.00 F
1957 2022 1.135431 TGCGACTTACATTTGCATGGC 60.135 47.619 0.00 0.0 34.27 4.40 F
2644 2716 0.807667 GGATGAGACAGTGCGCGATT 60.808 55.000 12.10 0.0 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1957 2022 0.391661 AATGTGGCTAGTGCGAGTGG 60.392 55.0 0.0 0.0 40.82 4.00 R
2621 2693 0.376152 GCGCACTGTCTCATCCATTG 59.624 55.0 0.3 0.0 0.00 2.82 R
3935 4014 0.037877 AGAGCAGCTTGCCTGTCAAT 59.962 50.0 0.0 0.0 46.52 2.57 R
4307 4389 0.179006 TGGTGCATGGTAGTTGTGCA 60.179 50.0 0.0 0.0 45.69 4.57 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
100 101 6.804677 TCATAACACAACAAAAGATGCAAGT 58.195 32.000 0.00 0.00 0.00 3.16
102 103 5.783100 AACACAACAAAAGATGCAAGTTG 57.217 34.783 0.00 0.00 43.71 3.16
116 117 2.222707 GCAAGTTGTTTTTGACCAACGC 60.223 45.455 4.48 0.00 33.26 4.84
123 124 0.102120 TTTTGACCAACGCCTGCTTG 59.898 50.000 0.00 0.00 0.00 4.01
136 137 7.491048 CCAACGCCTGCTTGTTTATTAAATTAT 59.509 33.333 0.00 0.00 0.00 1.28
198 199 6.512297 ACCATGTCAAAATAAAGTCACAACC 58.488 36.000 0.00 0.00 0.00 3.77
209 210 4.755266 AAGTCACAACCTATAGGCGATT 57.245 40.909 19.25 2.87 39.32 3.34
211 212 3.050619 GTCACAACCTATAGGCGATTCG 58.949 50.000 19.25 0.62 39.32 3.34
224 225 3.002656 AGGCGATTCGAATACATGCTTTG 59.997 43.478 11.38 0.00 0.00 2.77
274 275 1.136500 GGGATCGACCAACTAGACCAC 59.864 57.143 0.00 0.00 41.20 4.16
296 297 6.318900 CCACCTAAACTTATGGCCTCTTTTAG 59.681 42.308 3.32 9.62 0.00 1.85
334 335 9.807921 TGAGGAAATTTGTAGGAGTAAGAATTT 57.192 29.630 0.00 0.00 31.55 1.82
501 502 8.461222 CACATAGAACAAGATAAAAGCCATGAA 58.539 33.333 0.00 0.00 0.00 2.57
508 509 7.107542 ACAAGATAAAAGCCATGAATTGCATT 58.892 30.769 0.00 0.00 34.15 3.56
554 555 9.880064 TTCGTTCGTGATTTAACATTCATTTAA 57.120 25.926 0.00 0.00 0.00 1.52
588 589 2.570415 TGTGTTTTCCTATTCCCGCA 57.430 45.000 0.00 0.00 0.00 5.69
633 635 1.894466 CTGCATTTTCACACCCCATCA 59.106 47.619 0.00 0.00 0.00 3.07
709 711 5.543507 TGTAAGCATCCAAAACAAATGGT 57.456 34.783 0.00 0.00 39.09 3.55
840 844 1.081513 TCTTTAGGCTTACCTCCCCCA 59.918 52.381 0.00 0.00 46.34 4.96
854 858 0.409484 CCCCCACATCCTCCAAACTT 59.591 55.000 0.00 0.00 0.00 2.66
924 928 0.386476 CCGATGCATGGTTGAATGGG 59.614 55.000 2.46 0.00 31.10 4.00
1127 1131 7.703058 AAGAGACAAAGAGAAAAGGAAACAA 57.297 32.000 0.00 0.00 0.00 2.83
1139 1143 3.542969 AGGAAACAAGTTATTGCCCCT 57.457 42.857 0.00 0.00 40.27 4.79
1169 1173 6.187727 AGGAAGTGAGAGAATTGGTTAACA 57.812 37.500 8.10 0.00 0.00 2.41
1170 1174 6.601332 AGGAAGTGAGAGAATTGGTTAACAA 58.399 36.000 8.10 0.00 44.54 2.83
1171 1175 6.712547 AGGAAGTGAGAGAATTGGTTAACAAG 59.287 38.462 8.10 0.00 43.48 3.16
1172 1176 6.072452 GGAAGTGAGAGAATTGGTTAACAAGG 60.072 42.308 8.10 0.00 43.48 3.61
1173 1177 5.941788 AGTGAGAGAATTGGTTAACAAGGT 58.058 37.500 8.10 0.00 43.48 3.50
1174 1178 6.365520 AGTGAGAGAATTGGTTAACAAGGTT 58.634 36.000 8.10 0.00 43.48 3.50
1175 1179 7.514721 AGTGAGAGAATTGGTTAACAAGGTTA 58.485 34.615 8.10 0.00 43.48 2.85
1176 1180 7.996644 AGTGAGAGAATTGGTTAACAAGGTTAA 59.003 33.333 8.10 0.00 43.48 2.01
1177 1181 8.074370 GTGAGAGAATTGGTTAACAAGGTTAAC 58.926 37.037 18.83 18.83 43.48 2.01
1185 1189 5.045215 GGTTAACAAGGTTAACAAGGTTGC 58.955 41.667 24.87 9.20 36.79 4.17
1393 1405 7.010552 CCGTAATTTGTAGATTCAAGGAGACTG 59.989 40.741 0.00 0.00 42.68 3.51
1403 1415 2.738213 AAGGAGACTGCTTGGGCACG 62.738 60.000 8.62 0.00 44.28 5.34
1405 1417 1.739562 GAGACTGCTTGGGCACGAG 60.740 63.158 0.00 0.00 44.28 4.18
1425 1437 6.805760 CACGAGTAAGTAGAAAAGGGTAGTTC 59.194 42.308 0.00 0.00 0.00 3.01
1531 1543 9.950680 ACTGAGTTATTTGTTAAACACAATCAG 57.049 29.630 11.22 11.22 45.31 2.90
1764 1776 3.393278 AGCACCTAGTTGGGTAAGTTCAA 59.607 43.478 0.00 0.00 41.11 2.69
1768 1780 4.041321 ACCTAGTTGGGTAAGTTCAAGTCC 59.959 45.833 0.00 0.00 41.11 3.85
1956 2021 2.917701 TGCGACTTACATTTGCATGG 57.082 45.000 0.00 0.00 34.27 3.66
1957 2022 1.135431 TGCGACTTACATTTGCATGGC 60.135 47.619 0.00 0.00 34.27 4.40
1984 2050 3.425359 CGCACTAGCCACATTCTCAAAAG 60.425 47.826 0.00 0.00 37.52 2.27
1987 2053 2.299326 AGCCACATTCTCAAAAGGCT 57.701 45.000 0.00 0.00 46.89 4.58
2053 2119 5.046087 GTCACCTAAGGTACCACCAAACTAT 60.046 44.000 15.94 0.00 41.95 2.12
2076 2142 4.139786 CCTACTATACACTTACGAGGGCA 58.860 47.826 0.00 0.00 0.00 5.36
2100 2166 4.081862 TGTGTATGCTAACTGTGTACCCTC 60.082 45.833 0.00 0.00 0.00 4.30
2128 2194 6.098679 GCTATGATGCCAAACACAATTAACA 58.901 36.000 0.00 0.00 0.00 2.41
2152 2218 8.461222 ACACAACATGTAGTCATTTATCAATGG 58.539 33.333 0.00 0.00 40.88 3.16
2154 2220 8.461222 ACAACATGTAGTCATTTATCAATGGTG 58.539 33.333 0.00 0.00 40.41 4.17
2183 2250 3.372025 GGGAGTGCTTGGATACCAAAGAT 60.372 47.826 4.78 0.00 43.44 2.40
2200 2267 6.264067 ACCAAAGATGAGAAAGAGAAACTTGG 59.736 38.462 0.00 0.00 38.98 3.61
2216 2283 2.196595 CTTGGAGGATACCTTGGGTCA 58.803 52.381 0.00 0.00 37.09 4.02
2223 2290 3.011708 AGGATACCTTGGGTCATGCTTTT 59.988 43.478 0.00 0.00 37.09 2.27
2229 2296 2.673775 TGGGTCATGCTTTTTGAGGA 57.326 45.000 0.00 0.00 0.00 3.71
2494 2566 5.710513 TTTCAATGACTTCAATGTCCCAG 57.289 39.130 0.00 0.00 36.21 4.45
2516 2588 5.571741 CAGACATCATTTGTTTCACATGAGC 59.428 40.000 0.00 0.00 39.18 4.26
2642 2714 1.948721 ATGGATGAGACAGTGCGCGA 61.949 55.000 12.10 0.00 0.00 5.87
2643 2715 1.227089 GGATGAGACAGTGCGCGAT 60.227 57.895 12.10 0.00 0.00 4.58
2644 2716 0.807667 GGATGAGACAGTGCGCGATT 60.808 55.000 12.10 0.00 0.00 3.34
2646 2718 2.398498 GATGAGACAGTGCGCGATTAT 58.602 47.619 12.10 0.00 0.00 1.28
2658 2730 9.582431 ACAGTGCGCGATTATATTACTATTATT 57.418 29.630 12.10 0.00 0.00 1.40
2685 2757 8.885494 TTCTATTTTCAAAACACAATTGGGAG 57.115 30.769 16.31 3.91 0.00 4.30
2721 2793 8.739972 ACTAGCTCGAATCCAATAAAATGTTTT 58.260 29.630 0.00 0.00 0.00 2.43
2872 2949 5.646606 ACGGCATTATTGTGGTAAATGTTC 58.353 37.500 0.00 0.00 33.96 3.18
2888 2965 9.752961 GGTAAATGTTCTAAGTCTAGAGGAATC 57.247 37.037 0.00 0.00 35.55 2.52
2894 2971 9.475620 TGTTCTAAGTCTAGAGGAATCATTACA 57.524 33.333 0.00 0.00 35.55 2.41
2911 2988 7.430992 TCATTACATCAATGCATAGAAGAGC 57.569 36.000 0.00 0.00 43.28 4.09
2931 3008 4.201657 AGCACATCATGAATTCAATCCGA 58.798 39.130 13.09 7.39 0.00 4.55
2951 3028 6.349300 TCCGAATCTTCCTTCCAAGAATAAG 58.651 40.000 0.00 0.00 35.99 1.73
2962 3039 6.659242 CCTTCCAAGAATAAGGTGCTTAAGAA 59.341 38.462 6.67 0.00 37.96 2.52
3049 3126 9.690913 TTCATAGGAATCAAAAAGACAGATCAT 57.309 29.630 0.00 0.00 0.00 2.45
3077 3154 6.660521 AGAATTGTGAGCATTGAATTCTACCA 59.339 34.615 7.05 0.00 41.29 3.25
3134 3211 7.819900 GGGCACGTGAGAAGAGATATATTTTAT 59.180 37.037 22.23 0.00 0.00 1.40
3174 3251 4.201951 CGCATCCGCTACCTTTGT 57.798 55.556 0.00 0.00 35.30 2.83
3189 3266 8.276325 CGCTACCTTTGTGTGAATTAAGATATC 58.724 37.037 0.00 0.00 0.00 1.63
3328 3405 6.134535 TGGGCTTCTCAAGGTTAAATTCTA 57.865 37.500 0.00 0.00 0.00 2.10
3344 3422 9.511272 GTTAAATTCTAACCCTCTTACTTTCCA 57.489 33.333 0.00 0.00 0.00 3.53
3404 3482 5.627780 GTGCAACTTTAATTTAAGTGACCCG 59.372 40.000 10.40 0.20 38.33 5.28
3460 3538 9.625747 TCTACCATCTTTATACAAAATGATGCA 57.374 29.630 0.00 0.00 38.63 3.96
3532 3611 1.418264 GGCCTGGGAGATACCTCTTTC 59.582 57.143 0.00 0.00 39.38 2.62
3553 3632 3.773119 TCGGGGATACTAAAAGTGAAGCT 59.227 43.478 0.00 0.00 0.00 3.74
3666 3745 2.291209 ATGGATGTCACAACAGGCAA 57.709 45.000 0.00 0.00 39.20 4.52
3784 3863 4.631740 TGTCAGGACCTCCCCGCA 62.632 66.667 0.00 0.00 36.42 5.69
3867 3946 1.304282 CCAAGGATGGTGGAGGTGG 59.696 63.158 0.00 0.00 42.18 4.61
3935 4014 8.842358 AGAAAAGGATCACGAATTGTAAACTA 57.158 30.769 0.00 0.00 0.00 2.24
3936 4015 9.449719 AGAAAAGGATCACGAATTGTAAACTAT 57.550 29.630 0.00 0.00 0.00 2.12
4239 4321 2.800985 CGTCTGATATGCCTCACCTGTG 60.801 54.545 0.00 0.00 0.00 3.66
4290 4372 7.424803 TGTGAAAGGACACAAAAGTCAATATG 58.575 34.615 0.00 0.00 45.81 1.78
4291 4373 7.068103 TGTGAAAGGACACAAAAGTCAATATGT 59.932 33.333 0.00 0.00 45.81 2.29
4297 4379 6.183360 GGACACAAAAGTCAATATGTAGACCG 60.183 42.308 0.00 0.00 40.29 4.79
4438 4521 5.179368 GTGCACTTTACAAGAGCTACATCAA 59.821 40.000 10.32 0.00 44.12 2.57
4443 4526 7.959651 CACTTTACAAGAGCTACATCAATCAAC 59.040 37.037 0.00 0.00 0.00 3.18
4475 4558 6.015519 TGTTGAATAAAACAAGGGGATCACAG 60.016 38.462 0.00 0.00 37.12 3.66
4485 4568 5.126067 CAAGGGGATCACAGTACCAAATAG 58.874 45.833 0.00 0.00 0.00 1.73
4500 4583 7.985752 AGTACCAAATAGCAGGAGTAAATGTAC 59.014 37.037 0.00 0.00 0.00 2.90
4501 4584 6.958767 ACCAAATAGCAGGAGTAAATGTACT 58.041 36.000 0.00 0.00 43.56 2.73
4502 4585 8.086143 ACCAAATAGCAGGAGTAAATGTACTA 57.914 34.615 0.00 0.00 40.82 1.82
4533 4616 3.576078 TCACAGGTTTATGGGCTATGG 57.424 47.619 0.00 0.00 0.00 2.74
4536 4619 3.632145 CACAGGTTTATGGGCTATGGAAC 59.368 47.826 0.00 0.00 0.00 3.62
4561 4644 7.283127 ACGACCCAAATATTTACGTAGACTAGA 59.717 37.037 15.07 0.00 0.00 2.43
4571 4654 2.613133 ACGTAGACTAGAATCTCCGTGC 59.387 50.000 0.00 0.00 39.49 5.34
4584 4667 2.114670 CCGTGCTTACCATGCCAGG 61.115 63.158 0.00 0.00 0.00 4.45
4588 4671 2.516930 CTTACCATGCCAGGCCCG 60.517 66.667 9.64 0.00 0.00 6.13
4602 4685 3.497763 CCAGGCCCGGTATCAATTGATAA 60.498 47.826 25.95 10.67 38.60 1.75
4604 4687 2.817844 GGCCCGGTATCAATTGATAACC 59.182 50.000 29.33 26.05 40.68 2.85
4609 4692 5.646360 CCCGGTATCAATTGATAACCCATAC 59.354 44.000 29.33 18.30 40.68 2.39
4627 4710 9.528489 AACCCATACAGTTTACAATGAAATACT 57.472 29.630 0.00 0.00 0.00 2.12
4659 4742 1.606668 GCAAATGTGTCCGGTCTTTCA 59.393 47.619 0.00 0.00 0.00 2.69
4696 4779 6.037610 GCTATCATTTTTGGTGGAGTAGACTG 59.962 42.308 0.00 0.00 0.00 3.51
4700 4783 4.336889 TTTTGGTGGAGTAGACTGTGAG 57.663 45.455 0.00 0.00 0.00 3.51
4725 4808 4.556233 TCCGACTACAAACATGTGAGAAG 58.444 43.478 0.00 0.00 0.00 2.85
4796 4879 1.136252 CAAAGCACGATCAACCTGACG 60.136 52.381 0.00 0.00 0.00 4.35
4803 4886 1.467543 CGATCAACCTGACGACGATGT 60.468 52.381 0.00 0.00 0.00 3.06
4851 4935 1.342819 AGCGAGAAAACTGAGACTGCT 59.657 47.619 0.00 0.00 0.00 4.24
4856 4940 5.449314 GCGAGAAAACTGAGACTGCTATCTA 60.449 44.000 0.00 0.00 0.00 1.98
4857 4941 6.734137 CGAGAAAACTGAGACTGCTATCTAT 58.266 40.000 0.00 0.00 0.00 1.98
4932 5016 2.093394 TCTTGGTCTGGTCGTTGAACAA 60.093 45.455 0.00 0.00 37.53 2.83
4974 5059 4.462132 TGCAGCTATGGCAAACTTTAATCA 59.538 37.500 3.10 0.00 38.54 2.57
5084 5177 1.002502 AAACCGGCCCTAACTCTGC 60.003 57.895 0.00 0.00 0.00 4.26
5100 5193 1.702401 TCTGCTTCCCCACACATACAA 59.298 47.619 0.00 0.00 0.00 2.41
5198 5294 8.325046 ACCTATAATAGCCTCTGGATGAAATTC 58.675 37.037 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 5.783100 AACAACTTGCATCTTTTGTTGTG 57.217 34.783 9.96 0.00 46.74 3.33
100 101 1.737363 GCAGGCGTTGGTCAAAAACAA 60.737 47.619 0.00 0.00 0.00 2.83
102 103 0.102300 AGCAGGCGTTGGTCAAAAAC 59.898 50.000 0.00 0.00 29.81 2.43
185 186 5.864418 TCGCCTATAGGTTGTGACTTTAT 57.136 39.130 20.10 0.00 37.57 1.40
194 195 5.466819 TGTATTCGAATCGCCTATAGGTTG 58.533 41.667 20.10 12.92 37.57 3.77
198 199 5.344066 AGCATGTATTCGAATCGCCTATAG 58.656 41.667 15.25 0.00 0.00 1.31
241 242 5.733676 TGGTCGATCCCATGATAATGTATG 58.266 41.667 0.00 0.00 34.77 2.39
274 275 7.110155 TGACTAAAAGAGGCCATAAGTTTAGG 58.890 38.462 19.73 9.05 34.40 2.69
476 477 8.579850 TTCATGGCTTTTATCTTGTTCTATGT 57.420 30.769 0.00 0.00 0.00 2.29
522 523 9.485591 GAATGTTAAATCACGAACGAATGTAAT 57.514 29.630 0.14 0.00 0.00 1.89
556 557 9.892130 AATAGGAAAACACATAAACCACAAAAA 57.108 25.926 0.00 0.00 0.00 1.94
557 558 9.535878 GAATAGGAAAACACATAAACCACAAAA 57.464 29.630 0.00 0.00 0.00 2.44
558 559 8.145122 GGAATAGGAAAACACATAAACCACAAA 58.855 33.333 0.00 0.00 0.00 2.83
559 560 7.256012 GGGAATAGGAAAACACATAAACCACAA 60.256 37.037 0.00 0.00 0.00 3.33
560 561 6.209788 GGGAATAGGAAAACACATAAACCACA 59.790 38.462 0.00 0.00 0.00 4.17
561 562 6.624204 CGGGAATAGGAAAACACATAAACCAC 60.624 42.308 0.00 0.00 0.00 4.16
588 589 2.363306 TGGAGCACTTGGTGTTTGAT 57.637 45.000 0.00 0.00 35.75 2.57
633 635 5.203528 AGGATAGCATTACCAGTGCAAAAT 58.796 37.500 0.00 0.00 44.87 1.82
840 844 4.453480 TGGAGAAAAGTTTGGAGGATGT 57.547 40.909 0.00 0.00 0.00 3.06
924 928 3.084786 CCAAGAACCATTTGAGTCCTCC 58.915 50.000 0.00 0.00 0.00 4.30
1127 1131 2.024941 CCTCCTCAAAGGGGCAATAACT 60.025 50.000 0.00 0.00 33.28 2.24
1139 1143 5.513788 CCAATTCTCTCACTTCCTCCTCAAA 60.514 44.000 0.00 0.00 0.00 2.69
1169 1173 3.812156 GTTGGCAACCTTGTTAACCTT 57.188 42.857 19.57 0.00 0.00 3.50
1185 1189 5.272397 GCAACAAAAATGAACATTGGTTGG 58.728 37.500 24.00 10.76 37.91 3.77
1337 1349 3.655486 TGCACTGCAAATCTTTCAATGG 58.345 40.909 0.00 0.00 34.76 3.16
1393 1405 1.203994 TCTACTTACTCGTGCCCAAGC 59.796 52.381 0.00 0.00 40.48 4.01
1425 1437 5.885230 TCTTTGTGCTCATGTCCTTTATG 57.115 39.130 0.00 0.00 0.00 1.90
1531 1543 6.892310 AAAATGTGCAAGTCAAAGTTTCTC 57.108 33.333 0.00 0.00 24.35 2.87
1866 1891 5.030295 CACTCACATTAGCCAATTTTAGCG 58.970 41.667 0.00 0.00 0.00 4.26
1956 2021 2.815647 GTGGCTAGTGCGAGTGGC 60.816 66.667 0.00 0.00 40.82 5.01
1957 2022 0.391661 AATGTGGCTAGTGCGAGTGG 60.392 55.000 0.00 0.00 40.82 4.00
1984 2050 2.460757 TACGACAACAAAGGGTAGCC 57.539 50.000 1.60 1.60 0.00 3.93
1987 2053 3.404224 TGCATACGACAACAAAGGGTA 57.596 42.857 0.00 0.00 0.00 3.69
2053 2119 4.141413 TGCCCTCGTAAGTGTATAGTAGGA 60.141 45.833 0.00 0.00 39.48 2.94
2076 2142 4.469945 AGGGTACACAGTTAGCATACACAT 59.530 41.667 0.00 0.00 0.00 3.21
2089 2155 2.623416 TCATAGCATCGAGGGTACACAG 59.377 50.000 11.57 2.74 0.00 3.66
2100 2166 2.355444 TGTGTTTGGCATCATAGCATCG 59.645 45.455 0.00 0.00 35.83 3.84
2128 2194 8.461222 CACCATTGATAAATGACTACATGTTGT 58.539 33.333 12.87 12.87 36.79 3.32
2152 2218 2.955881 AAGCACTCCCCTACCGCAC 61.956 63.158 0.00 0.00 0.00 5.34
2154 2220 2.125106 CAAGCACTCCCCTACCGC 60.125 66.667 0.00 0.00 0.00 5.68
2183 2250 5.832539 ATCCTCCAAGTTTCTCTTTCTCA 57.167 39.130 0.00 0.00 33.63 3.27
2200 2267 1.771255 AGCATGACCCAAGGTATCCTC 59.229 52.381 0.00 0.00 35.25 3.71
2216 2283 6.839124 TTGTCACATATCCTCAAAAAGCAT 57.161 33.333 0.00 0.00 0.00 3.79
2223 2290 7.629008 GCAATTGACATTGTCACATATCCTCAA 60.629 37.037 18.84 1.19 42.60 3.02
2229 2296 4.096833 AGCGCAATTGACATTGTCACATAT 59.903 37.500 18.84 7.72 42.60 1.78
2297 2364 3.584848 GCATCAGGATATGTAGAACCCCT 59.415 47.826 0.00 0.00 0.00 4.79
2621 2693 0.376152 GCGCACTGTCTCATCCATTG 59.624 55.000 0.30 0.00 0.00 2.82
2626 2698 1.840181 TAATCGCGCACTGTCTCATC 58.160 50.000 8.75 0.00 0.00 2.92
2630 2702 5.122512 AGTAATATAATCGCGCACTGTCT 57.877 39.130 8.75 0.00 0.00 3.41
2670 2742 4.037222 ACTTTCCCTCCCAATTGTGTTTT 58.963 39.130 4.43 0.00 0.00 2.43
2685 2757 3.314541 TTCGAGCTAGTTGACTTTCCC 57.685 47.619 0.00 0.00 0.00 3.97
2721 2793 7.873719 TTCTTGTTTTGGTTCTACTCATCAA 57.126 32.000 0.00 0.00 0.00 2.57
2759 2831 6.855763 AGGGATCTTGCAAATAAATCAACA 57.144 33.333 0.00 0.00 0.00 3.33
2894 2971 5.374071 TGATGTGCTCTTCTATGCATTGAT 58.626 37.500 11.66 0.00 41.45 2.57
2895 2972 4.773013 TGATGTGCTCTTCTATGCATTGA 58.227 39.130 3.54 5.40 41.45 2.57
2899 2976 4.411256 TCATGATGTGCTCTTCTATGCA 57.589 40.909 0.00 0.00 36.79 3.96
2931 3008 5.654209 GCACCTTATTCTTGGAAGGAAGATT 59.346 40.000 7.64 0.00 44.36 2.40
2951 3028 7.010275 CGAACTAGGATTACTTTCTTAAGCACC 59.990 40.741 0.00 0.00 34.60 5.01
3042 3119 6.862711 ATGCTCACAATTCTACATGATCTG 57.137 37.500 0.00 0.00 0.00 2.90
3049 3126 7.692460 AGAATTCAATGCTCACAATTCTACA 57.308 32.000 8.44 0.00 41.62 2.74
3058 3135 7.171508 TCGATTATGGTAGAATTCAATGCTCAC 59.828 37.037 8.44 0.00 0.00 3.51
3223 3300 4.753233 CTGAGTGGTAGTCTTTCATCTGG 58.247 47.826 0.00 0.00 0.00 3.86
3277 3354 1.995626 GGCAGCAGAACCTCCCCTA 60.996 63.158 0.00 0.00 0.00 3.53
3471 3550 4.757799 TCTGTCGTCAGAAGAGAAGAAG 57.242 45.455 10.00 0.00 46.17 2.85
3486 3565 5.918011 GCTCCATCTAGAACTATTTCTGTCG 59.082 44.000 5.63 0.00 42.41 4.35
3532 3611 3.871594 CAGCTTCACTTTTAGTATCCCCG 59.128 47.826 0.00 0.00 0.00 5.73
3553 3632 1.623311 ACAGTGACATCGATTCCACCA 59.377 47.619 18.21 1.85 0.00 4.17
3625 3704 1.911766 GGAGGTGTCAGAACCCCGA 60.912 63.158 0.00 0.00 41.54 5.14
3666 3745 6.439487 TCCTTCTTCTCCAAGATCTCAGTAT 58.561 40.000 0.00 0.00 38.50 2.12
3784 3863 0.178990 GGTTGGACTTCTTGGGCACT 60.179 55.000 0.00 0.00 0.00 4.40
3867 3946 0.618458 TATTGTGCCCACCTCTGGTC 59.382 55.000 0.00 0.00 35.46 4.02
3935 4014 0.037877 AGAGCAGCTTGCCTGTCAAT 59.962 50.000 0.00 0.00 46.52 2.57
3936 4015 0.604780 GAGAGCAGCTTGCCTGTCAA 60.605 55.000 0.00 0.00 46.52 3.18
4054 4134 1.965643 ACCTGCATGCTTGTGTCATTT 59.034 42.857 20.33 0.00 0.00 2.32
4290 4372 1.154197 GCACCAACCTTTCGGTCTAC 58.846 55.000 0.00 0.00 44.73 2.59
4291 4373 0.759959 TGCACCAACCTTTCGGTCTA 59.240 50.000 0.00 0.00 44.73 2.59
4307 4389 0.179006 TGGTGCATGGTAGTTGTGCA 60.179 50.000 0.00 0.00 45.69 4.57
4335 4417 2.450609 ACATCCAAGTTTACTCGCGT 57.549 45.000 5.77 0.00 0.00 6.01
4453 4536 5.640147 ACTGTGATCCCCTTGTTTTATTCA 58.360 37.500 0.00 0.00 0.00 2.57
4462 4545 3.433306 TTTGGTACTGTGATCCCCTTG 57.567 47.619 0.00 0.00 0.00 3.61
4475 4558 7.985752 AGTACATTTACTCCTGCTATTTGGTAC 59.014 37.037 0.00 0.00 32.67 3.34
4485 4568 7.119262 ACACACATTTAGTACATTTACTCCTGC 59.881 37.037 0.00 0.00 39.43 4.85
4515 4598 3.684413 CGTTCCATAGCCCATAAACCTGT 60.684 47.826 0.00 0.00 0.00 4.00
4516 4599 2.878406 CGTTCCATAGCCCATAAACCTG 59.122 50.000 0.00 0.00 0.00 4.00
4518 4601 2.876550 GTCGTTCCATAGCCCATAAACC 59.123 50.000 0.00 0.00 0.00 3.27
4533 4616 6.753744 AGTCTACGTAAATATTTGGGTCGTTC 59.246 38.462 19.12 13.42 0.00 3.95
4536 4619 7.642669 TCTAGTCTACGTAAATATTTGGGTCG 58.357 38.462 11.05 11.64 0.00 4.79
4561 4644 1.668419 GCATGGTAAGCACGGAGATT 58.332 50.000 0.00 0.00 0.00 2.40
4566 4649 2.114670 CCTGGCATGGTAAGCACGG 61.115 63.158 0.00 0.00 0.00 4.94
4571 4654 2.516930 CGGGCCTGGCATGGTAAG 60.517 66.667 22.05 0.00 0.00 2.34
4584 4667 2.817844 GGGTTATCAATTGATACCGGGC 59.182 50.000 24.55 13.43 36.81 6.13
4588 4671 8.691661 AACTGTATGGGTTATCAATTGATACC 57.308 34.615 24.55 24.50 36.81 2.73
4627 4710 5.428253 GGACACATTTGCCTCTATCAACTA 58.572 41.667 0.00 0.00 0.00 2.24
4659 4742 1.204146 ATGATAGCCACCGTGTCCTT 58.796 50.000 0.00 0.00 0.00 3.36
4664 4747 2.491693 ACCAAAAATGATAGCCACCGTG 59.508 45.455 0.00 0.00 0.00 4.94
4666 4749 2.159254 CCACCAAAAATGATAGCCACCG 60.159 50.000 0.00 0.00 0.00 4.94
4696 4779 3.587797 TGTTTGTAGTCGGATCCTCAC 57.412 47.619 10.75 6.39 0.00 3.51
4700 4783 3.857052 TCACATGTTTGTAGTCGGATCC 58.143 45.455 0.00 0.00 33.76 3.36
4857 4941 9.944376 AAGCTTTCCTCTTATATTCGCAATATA 57.056 29.630 0.00 5.16 35.72 0.86
4974 5059 9.036671 CATCGTTTATACTTTGGGTTTTGTTTT 57.963 29.630 0.00 0.00 0.00 2.43
5071 5163 1.224870 GGGAAGCAGAGTTAGGGCC 59.775 63.158 0.00 0.00 0.00 5.80
5072 5164 1.224870 GGGGAAGCAGAGTTAGGGC 59.775 63.158 0.00 0.00 0.00 5.19
5084 5177 4.021102 AGAGTTTGTATGTGTGGGGAAG 57.979 45.455 0.00 0.00 0.00 3.46
5198 5294 7.073883 CGAAATATACAAGATGCCACTTCATG 58.926 38.462 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.