Multiple sequence alignment - TraesCS2D01G397700

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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 TraesCS2D01G397700 chr2D 100.000 4557 0 0 1 4557 509742564 509738008 0.000000e+00 8416
1 TraesCS2D01G397700 chr2B 93.178 2360 84 38 235 2574 598966896 598964594 0.000000e+00 3395
2 TraesCS2D01G397700 chr2B 93.544 1611 60 18 2574 4164 598964436 598962850 0.000000e+00 2359
3 TraesCS2D01G397700 chr2B 93.074 231 11 4 1 228 598967180 598966952 2.630000e-87 333
4 TraesCS2D01G397700 chr2B 92.169 166 12 1 4385 4550 598962620 598962456 2.740000e-57 233
5 TraesCS2D01G397700 chr2B 86.432 199 16 5 4231 4418 598962815 598962617 1.660000e-49 207
6 TraesCS2D01G397700 chr2A 95.133 1726 46 13 359 2079 653373701 653372009 0.000000e+00 2687
7 TraesCS2D01G397700 chr2A 92.312 1665 74 22 2907 4544 653370768 653369131 0.000000e+00 2316
8 TraesCS2D01G397700 chr2A 94.990 499 25 0 2076 2574 653371929 653371431 0.000000e+00 784
9 TraesCS2D01G397700 chr2A 87.500 240 18 6 1 228 653374117 653373878 2.700000e-67 267
10 TraesCS2D01G397700 chr2A 91.946 149 4 1 2573 2721 653371275 653371135 7.730000e-48 202


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 TraesCS2D01G397700 chr2D 509738008 509742564 4556 True 8416.0 8416 100.0000 1 4557 1 chr2D.!!$R1 4556
1 TraesCS2D01G397700 chr2B 598962456 598967180 4724 True 1305.4 3395 91.6794 1 4550 5 chr2B.!!$R1 4549
2 TraesCS2D01G397700 chr2A 653369131 653374117 4986 True 1251.2 2687 92.3762 1 4544 5 chr2A.!!$R1 4543

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
586 757 0.105778 CCAGAAATCTCCTCGCCTCC 59.894 60.000 0.00 0.0 0.00 4.30 F
591 762 0.178947 AATCTCCTCGCCTCCCCTAG 60.179 60.000 0.00 0.0 0.00 3.02 F
1927 2112 0.912486 GGAGCCACCTTACCACAGAT 59.088 55.000 0.00 0.0 35.41 2.90 F
2487 2758 1.140852 TGCTGGTTGTGCACTCTAAGT 59.859 47.619 19.41 0.0 35.31 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2174 2443 1.081906 GCACACACCAATGAGCACG 60.082 57.895 0.00 0.00 0.00 5.34 R
2468 2739 1.532868 CACTTAGAGTGCACAACCAGC 59.467 52.381 21.04 0.73 39.62 4.85 R
3268 3896 0.031449 GCTCAGAGTCATAGACCCGC 59.969 60.000 0.00 0.00 32.18 6.13 R
4208 4841 0.958091 CTGCCATGTTCGTGGGAAAA 59.042 50.000 12.23 0.00 39.24 2.29 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
43 45 4.566759 CCTCTTTGCGAAATCGACTGAATA 59.433 41.667 7.06 0.00 43.02 1.75
82 87 4.342772 CCGATGTTTAGTAAATGCACTGC 58.657 43.478 0.00 0.00 0.00 4.40
191 202 5.411781 AGTGACGACCATGATTAAGAGAAC 58.588 41.667 0.00 0.00 0.00 3.01
232 245 5.239359 TGAGCATCAACATTTATGCACTC 57.761 39.130 12.10 4.11 45.97 3.51
354 521 1.741770 CGCACTACTCAACCAGCCC 60.742 63.158 0.00 0.00 0.00 5.19
389 556 1.800805 AGCCACGTTCAGATCACAAG 58.199 50.000 0.00 0.00 0.00 3.16
399 566 2.501723 TCAGATCACAAGCCTACCTTCC 59.498 50.000 0.00 0.00 0.00 3.46
400 567 2.237143 CAGATCACAAGCCTACCTTCCA 59.763 50.000 0.00 0.00 0.00 3.53
401 568 2.912956 AGATCACAAGCCTACCTTCCAA 59.087 45.455 0.00 0.00 0.00 3.53
585 756 1.115467 TCCAGAAATCTCCTCGCCTC 58.885 55.000 0.00 0.00 0.00 4.70
586 757 0.105778 CCAGAAATCTCCTCGCCTCC 59.894 60.000 0.00 0.00 0.00 4.30
587 758 0.105778 CAGAAATCTCCTCGCCTCCC 59.894 60.000 0.00 0.00 0.00 4.30
588 759 1.051556 AGAAATCTCCTCGCCTCCCC 61.052 60.000 0.00 0.00 0.00 4.81
589 760 1.003573 AAATCTCCTCGCCTCCCCT 59.996 57.895 0.00 0.00 0.00 4.79
590 761 0.264955 AAATCTCCTCGCCTCCCCTA 59.735 55.000 0.00 0.00 0.00 3.53
591 762 0.178947 AATCTCCTCGCCTCCCCTAG 60.179 60.000 0.00 0.00 0.00 3.02
592 763 2.723464 ATCTCCTCGCCTCCCCTAGC 62.723 65.000 0.00 0.00 0.00 3.42
593 764 4.541648 TCCTCGCCTCCCCTAGCC 62.542 72.222 0.00 0.00 0.00 3.93
594 765 4.548513 CCTCGCCTCCCCTAGCCT 62.549 72.222 0.00 0.00 0.00 4.58
595 766 2.915137 CTCGCCTCCCCTAGCCTC 60.915 72.222 0.00 0.00 0.00 4.70
596 767 4.541648 TCGCCTCCCCTAGCCTCC 62.542 72.222 0.00 0.00 0.00 4.30
599 770 3.452919 CCTCCCCTAGCCTCCCCT 61.453 72.222 0.00 0.00 0.00 4.79
692 863 2.266554 CTTGTGTCTCAGCTCGATTCC 58.733 52.381 0.00 0.00 0.00 3.01
701 872 3.554692 CTCGATTCCGTGCCGTGC 61.555 66.667 0.00 0.00 37.05 5.34
828 1003 4.135493 GCTTCTTCGCCGCACGTC 62.135 66.667 0.00 0.00 44.19 4.34
880 1055 3.900892 CGTCGCCGCCTGATAGGT 61.901 66.667 0.00 0.00 37.80 3.08
945 1120 1.675641 CTTTTCCGTGCCCTGGAGG 60.676 63.158 0.00 0.00 36.72 4.30
1342 1517 1.307517 AGGCCAACCCCCTTCGATA 60.308 57.895 5.01 0.00 36.11 2.92
1424 1603 5.701290 CCAACTAGTACAGCTTGCTTTAAGT 59.299 40.000 0.00 0.00 38.70 2.24
1490 1670 4.887071 ACCAGTACAGTTTGCTTTCATGAA 59.113 37.500 3.38 3.38 0.00 2.57
1554 1735 4.397481 TTGGTTTGTGTGCAATGAATCA 57.603 36.364 0.00 0.00 34.18 2.57
1562 1743 4.393990 TGTGTGCAATGAATCAGAGATGTC 59.606 41.667 0.00 0.00 0.00 3.06
1570 1751 3.218453 GAATCAGAGATGTCGAGAGGGA 58.782 50.000 0.00 0.00 0.00 4.20
1589 1770 5.193679 AGGGATTTGTTAACTATGACTGGC 58.806 41.667 7.22 0.00 0.00 4.85
1745 1926 8.328146 GTTTTCCTTCTTTGTTTATGTTTGCTC 58.672 33.333 0.00 0.00 0.00 4.26
1782 1964 6.817765 TTATTCTTGGCTTTCTGGTACTTG 57.182 37.500 0.00 0.00 0.00 3.16
1793 1975 5.689383 TTCTGGTACTTGTGCTGAAATTC 57.311 39.130 0.00 0.00 0.00 2.17
1794 1976 4.072131 TCTGGTACTTGTGCTGAAATTCC 58.928 43.478 0.00 0.00 0.00 3.01
1795 1977 3.820467 CTGGTACTTGTGCTGAAATTCCA 59.180 43.478 0.00 0.00 0.00 3.53
1927 2112 0.912486 GGAGCCACCTTACCACAGAT 59.088 55.000 0.00 0.00 35.41 2.90
1933 2118 2.417379 CCACCTTACCACAGATGAGTCG 60.417 54.545 0.00 0.00 0.00 4.18
1986 2171 2.683211 AGTTGCTCCATGGGAAGTTT 57.317 45.000 13.02 0.00 0.00 2.66
1999 2184 5.333566 TGGGAAGTTTAGGTTGAATTCCT 57.666 39.130 2.27 0.00 37.08 3.36
2166 2435 3.644966 TTGTGTGGAGGTGAAGTCTTT 57.355 42.857 0.00 0.00 0.00 2.52
2174 2443 1.177401 GGTGAAGTCTTTGGATGCCC 58.823 55.000 0.00 0.00 0.00 5.36
2184 2453 1.314534 TTGGATGCCCGTGCTCATTG 61.315 55.000 0.00 0.00 38.71 2.82
2225 2494 3.142951 TGGTATGACCGTTTCCTTGTTG 58.857 45.455 0.00 0.00 42.58 3.33
2423 2694 5.765677 TCTTGGTGGTTGATTAAAATGTCGA 59.234 36.000 0.00 0.00 0.00 4.20
2468 2739 9.618890 TGGGAAATTAGAGATCATTAGTTTCTG 57.381 33.333 16.60 0.00 30.66 3.02
2487 2758 1.140852 TGCTGGTTGTGCACTCTAAGT 59.859 47.619 19.41 0.00 35.31 2.24
2519 2790 3.887352 AGCTCATAGTCGTAACAGGAGA 58.113 45.455 0.00 0.00 0.00 3.71
2524 2795 6.319141 TCATAGTCGTAACAGGAGATCATG 57.681 41.667 0.00 0.00 0.00 3.07
2577 3007 5.793817 TGTTGCACTAGTATGTCATTGTCT 58.206 37.500 0.00 0.00 0.00 3.41
2596 3026 5.935945 TGTCTTTCCTTTGGTCTTGTGATA 58.064 37.500 0.00 0.00 0.00 2.15
2606 3038 7.989741 CCTTTGGTCTTGTGATAAGATAGTCAT 59.010 37.037 0.00 0.00 0.00 3.06
2609 3041 9.987272 TTGGTCTTGTGATAAGATAGTCATATG 57.013 33.333 0.00 0.00 0.00 1.78
2610 3042 8.588472 TGGTCTTGTGATAAGATAGTCATATGG 58.412 37.037 2.13 0.00 0.00 2.74
2611 3043 8.807118 GGTCTTGTGATAAGATAGTCATATGGA 58.193 37.037 2.13 0.00 0.00 3.41
2612 3044 9.853555 GTCTTGTGATAAGATAGTCATATGGAG 57.146 37.037 2.13 0.00 0.00 3.86
2613 3045 9.593565 TCTTGTGATAAGATAGTCATATGGAGT 57.406 33.333 2.13 0.00 0.00 3.85
2759 3191 7.168469 GCAAATCGTACCACTAAAAACAATGTT 59.832 33.333 0.00 0.00 0.00 2.71
2774 3206 9.985730 AAAAACAATGTTATGATGTGATGAAGT 57.014 25.926 0.00 0.00 0.00 3.01
2775 3207 8.975410 AAACAATGTTATGATGTGATGAAGTG 57.025 30.769 0.00 0.00 0.00 3.16
2776 3208 7.926674 ACAATGTTATGATGTGATGAAGTGA 57.073 32.000 0.00 0.00 0.00 3.41
2777 3209 8.515695 ACAATGTTATGATGTGATGAAGTGAT 57.484 30.769 0.00 0.00 0.00 3.06
2800 3232 8.393259 TGATTTATGGGCTGAATCCTTATATGT 58.607 33.333 0.00 0.00 30.66 2.29
2815 3247 5.067805 CCTTATATGTCCCTGAAAAGTTGCC 59.932 44.000 0.00 0.00 0.00 4.52
2818 3250 1.155155 TCCCTGAAAAGTTGCCCCC 59.845 57.895 0.00 0.00 0.00 5.40
2854 3286 2.434336 TGTCTATGACATGTGGGCCTAC 59.566 50.000 13.24 13.24 37.67 3.18
2868 3300 4.454504 GTGGGCCTACGGATATATGTTTTG 59.545 45.833 2.40 0.00 0.00 2.44
2896 3328 3.070429 GCAAAGGCATATGAGGTTTCG 57.930 47.619 6.97 0.04 40.72 3.46
2963 3576 7.288810 TGGTTTTATCTTTGTTCTGCTCAAT 57.711 32.000 0.00 0.00 0.00 2.57
3059 3673 3.056821 CACACATCCGTACTTCTCTTCCA 60.057 47.826 0.00 0.00 0.00 3.53
3068 3682 4.865365 CGTACTTCTCTTCCAATGTCCTTC 59.135 45.833 0.00 0.00 0.00 3.46
3074 3688 7.400339 ACTTCTCTTCCAATGTCCTTCTGTATA 59.600 37.037 0.00 0.00 0.00 1.47
3418 4046 4.439305 CCATGTCGGTGATTTTGTCATT 57.561 40.909 0.00 0.00 39.48 2.57
3592 4220 3.544684 TGTATCACTCCATGTGGCAATC 58.455 45.455 0.00 0.00 46.20 2.67
3628 4256 5.595952 CCTAGCCTTTTTCATAGCCATTCTT 59.404 40.000 0.00 0.00 0.00 2.52
3678 4307 7.670009 TCATTTTTCTAATGGTTTTGCATGG 57.330 32.000 0.00 0.00 0.00 3.66
3729 4358 8.726870 TGTAGTGATAGTTAAATAAGTTGGCC 57.273 34.615 0.00 0.00 0.00 5.36
3950 4580 1.615392 GCTCTTTGCTTCCCATGTGTT 59.385 47.619 0.00 0.00 38.95 3.32
3958 4588 2.095853 GCTTCCCATGTGTTGTGATACG 59.904 50.000 0.00 0.00 0.00 3.06
4004 4635 5.989168 CCAGGTTTTTGTGGGTAAATTCTTC 59.011 40.000 0.00 0.00 0.00 2.87
4077 4708 7.015877 GTCCGAATTATGAGAAGTTTTCACAC 58.984 38.462 0.00 0.00 33.18 3.82
4096 4729 1.484227 CGTGTTCCTCGCGTCAACAA 61.484 55.000 17.50 4.60 43.87 2.83
4108 4741 3.529085 GCGTCAACAACTTCGAAACTAC 58.471 45.455 0.00 0.00 0.00 2.73
4156 4789 3.381272 AGTGTTCTTTCCATGTTGGTGTG 59.619 43.478 0.00 0.00 39.03 3.82
4157 4790 2.100584 TGTTCTTTCCATGTTGGTGTGC 59.899 45.455 0.00 0.00 39.03 4.57
4175 4808 0.788391 GCGTACTTCCAGTTTCGGTG 59.212 55.000 0.00 0.00 0.00 4.94
4208 4841 8.450964 GTGTCAATTTATGTTAGCAGTGTGTAT 58.549 33.333 0.00 0.00 0.00 2.29
4235 4868 2.483877 CACGAACATGGCAGTACACATT 59.516 45.455 0.00 0.00 0.00 2.71
4237 4870 2.095853 CGAACATGGCAGTACACATTCC 59.904 50.000 0.00 0.00 0.00 3.01
4245 4894 5.295950 TGGCAGTACACATTCCAAATTTTG 58.704 37.500 1.99 1.99 0.00 2.44
4375 5034 5.629079 AGCTACATTAAAACCTCTTGCAC 57.371 39.130 0.00 0.00 0.00 4.57
4382 5041 8.504812 ACATTAAAACCTCTTGCACAAAAATT 57.495 26.923 0.00 0.00 0.00 1.82
4398 5057 8.251784 GCACAAAAATTAATTTTCAAAACTGCG 58.748 29.630 22.96 13.08 39.20 5.18
4402 5061 9.701355 AAAAATTAATTTTCAAAACTGCGTCAG 57.299 25.926 22.96 5.47 38.92 3.51
4448 5137 7.136822 TGATATATGTGAGCCCTAGTGTTTT 57.863 36.000 0.00 0.00 0.00 2.43
4449 5138 7.217200 TGATATATGTGAGCCCTAGTGTTTTC 58.783 38.462 0.00 0.00 0.00 2.29
4459 5148 7.504238 TGAGCCCTAGTGTTTTCTTGAATTTTA 59.496 33.333 0.00 0.00 0.00 1.52
4463 5152 8.034804 CCCTAGTGTTTTCTTGAATTTTATGGG 58.965 37.037 0.00 0.00 0.00 4.00
4464 5153 8.802267 CCTAGTGTTTTCTTGAATTTTATGGGA 58.198 33.333 0.00 0.00 0.00 4.37
4536 5225 7.568199 TCCAGACAGTAGAAAAAGAAAAAGG 57.432 36.000 0.00 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 105 8.854117 GTTTCTCATGATTAATAAAGCCTCCAT 58.146 33.333 0.00 0.00 0.00 3.41
101 107 8.225603 TGTTTCTCATGATTAATAAAGCCTCC 57.774 34.615 0.00 0.00 0.00 4.30
191 202 4.207019 GCTCACAATTTTGAGGTTTTGTCG 59.793 41.667 20.34 0.00 42.95 4.35
253 420 9.856488 CAAGTTGTGCGTATTATAGGAGTATAT 57.144 33.333 0.00 0.00 0.00 0.86
354 521 1.446272 GCTTCGAGTCGGGGAACAG 60.446 63.158 13.54 1.07 0.00 3.16
389 556 4.706842 TCTATTGGATTGGAAGGTAGGC 57.293 45.455 0.00 0.00 0.00 3.93
585 756 4.583442 GGGAGGGGAGGCTAGGGG 62.583 77.778 0.00 0.00 0.00 4.79
586 757 4.583442 GGGGAGGGGAGGCTAGGG 62.583 77.778 0.00 0.00 0.00 3.53
587 758 4.583442 GGGGGAGGGGAGGCTAGG 62.583 77.778 0.00 0.00 0.00 3.02
588 759 3.452919 AGGGGGAGGGGAGGCTAG 61.453 72.222 0.00 0.00 0.00 3.42
589 760 3.449126 GAGGGGGAGGGGAGGCTA 61.449 72.222 0.00 0.00 0.00 3.93
592 763 3.369161 ATTGGAGGGGGAGGGGAGG 62.369 68.421 0.00 0.00 0.00 4.30
593 764 1.772156 GATTGGAGGGGGAGGGGAG 60.772 68.421 0.00 0.00 0.00 4.30
594 765 2.376842 GATTGGAGGGGGAGGGGA 59.623 66.667 0.00 0.00 0.00 4.81
595 766 2.778717 GGATTGGAGGGGGAGGGG 60.779 72.222 0.00 0.00 0.00 4.79
596 767 3.171388 CGGATTGGAGGGGGAGGG 61.171 72.222 0.00 0.00 0.00 4.30
597 768 2.040884 TCGGATTGGAGGGGGAGG 60.041 66.667 0.00 0.00 0.00 4.30
598 769 0.691078 TTCTCGGATTGGAGGGGGAG 60.691 60.000 0.00 0.00 34.74 4.30
599 770 0.252974 TTTCTCGGATTGGAGGGGGA 60.253 55.000 0.00 0.00 34.74 4.81
701 872 1.153289 CCACAGATTCTCGGGCAGG 60.153 63.158 0.00 0.00 0.00 4.85
825 1000 2.956964 GCTTCGGATCAGCGGACG 60.957 66.667 0.00 0.00 0.00 4.79
945 1120 1.416813 CGACGACAGATTGCTCCAGC 61.417 60.000 0.00 0.00 42.50 4.85
946 1121 0.171231 TCGACGACAGATTGCTCCAG 59.829 55.000 0.00 0.00 0.00 3.86
947 1122 0.601057 TTCGACGACAGATTGCTCCA 59.399 50.000 0.00 0.00 0.00 3.86
948 1123 1.855360 GATTCGACGACAGATTGCTCC 59.145 52.381 0.00 0.00 0.00 4.70
949 1124 1.514811 CGATTCGACGACAGATTGCTC 59.485 52.381 0.00 0.00 35.09 4.26
950 1125 1.550065 CGATTCGACGACAGATTGCT 58.450 50.000 0.00 0.00 35.09 3.91
951 1126 0.043822 GCGATTCGACGACAGATTGC 60.044 55.000 10.88 0.31 35.09 3.56
1342 1517 0.549169 TAAGCTACCTTGGTGCCCCT 60.549 55.000 2.03 0.00 32.47 4.79
1424 1603 8.461222 CAAGGAGCAAACTAATCAATCAACATA 58.539 33.333 0.00 0.00 0.00 2.29
1504 1684 4.039124 CCTTCTAGATCCTCTCTTCCAAGC 59.961 50.000 0.00 0.00 35.28 4.01
1554 1735 3.370104 ACAAATCCCTCTCGACATCTCT 58.630 45.455 0.00 0.00 0.00 3.10
1562 1743 6.477033 CAGTCATAGTTAACAAATCCCTCTCG 59.523 42.308 8.61 0.00 0.00 4.04
1570 1751 7.466746 ACATTGCCAGTCATAGTTAACAAAT 57.533 32.000 8.61 0.00 0.00 2.32
1745 1926 5.393461 GCCAAGAATAAACACCATCCAAGAG 60.393 44.000 0.00 0.00 0.00 2.85
1782 1964 4.771590 TTCAGTCATGGAATTTCAGCAC 57.228 40.909 0.00 0.00 0.00 4.40
1793 1975 3.480470 ACAGAGGTGTTTTCAGTCATGG 58.520 45.455 0.00 0.00 30.30 3.66
1794 1976 4.692625 CCTACAGAGGTGTTTTCAGTCATG 59.307 45.833 0.00 0.00 38.16 3.07
1795 1977 4.593206 TCCTACAGAGGTGTTTTCAGTCAT 59.407 41.667 0.00 0.00 44.19 3.06
1927 2112 3.639099 ACGGAAGTACCTCGACTCA 57.361 52.632 7.03 0.00 46.88 3.41
1986 2171 6.996282 AGAAAGTTTCGAAGGAATTCAACCTA 59.004 34.615 9.91 0.00 34.29 3.08
1999 2184 5.630661 TTCCACACAAAGAAAGTTTCGAA 57.369 34.783 9.91 0.00 34.02 3.71
2150 2419 2.930826 TCCAAAGACTTCACCTCCAC 57.069 50.000 0.00 0.00 0.00 4.02
2166 2435 1.750018 CAATGAGCACGGGCATCCA 60.750 57.895 14.57 7.22 44.61 3.41
2174 2443 1.081906 GCACACACCAATGAGCACG 60.082 57.895 0.00 0.00 0.00 5.34
2225 2494 6.047231 ACGCCTGTTATTCCTACTATTCAAC 58.953 40.000 0.00 0.00 0.00 3.18
2257 2528 3.123620 CCTTGTCGGCAGCAGAGC 61.124 66.667 0.00 0.00 0.00 4.09
2423 2694 5.036916 TCCCATCTATGAACTACCAAACCT 58.963 41.667 0.00 0.00 0.00 3.50
2468 2739 1.532868 CACTTAGAGTGCACAACCAGC 59.467 52.381 21.04 0.73 39.62 4.85
2519 2790 9.553064 GAAATAGACCTTTATCACAGACATGAT 57.447 33.333 0.00 0.00 42.13 2.45
2524 2795 6.338937 ACCGAAATAGACCTTTATCACAGAC 58.661 40.000 0.00 0.00 0.00 3.51
2577 3007 8.383175 ACTATCTTATCACAAGACCAAAGGAAA 58.617 33.333 0.00 0.00 0.00 3.13
2606 3038 7.256332 GGCTCCAAGATTGTCTATAACTCCATA 60.256 40.741 0.00 0.00 0.00 2.74
2607 3039 6.465035 GGCTCCAAGATTGTCTATAACTCCAT 60.465 42.308 0.00 0.00 0.00 3.41
2608 3040 5.163301 GGCTCCAAGATTGTCTATAACTCCA 60.163 44.000 0.00 0.00 0.00 3.86
2609 3041 5.163301 TGGCTCCAAGATTGTCTATAACTCC 60.163 44.000 0.00 0.00 0.00 3.85
2610 3042 5.918608 TGGCTCCAAGATTGTCTATAACTC 58.081 41.667 0.00 0.00 0.00 3.01
2611 3043 5.957771 TGGCTCCAAGATTGTCTATAACT 57.042 39.130 0.00 0.00 0.00 2.24
2612 3044 6.767902 TGATTGGCTCCAAGATTGTCTATAAC 59.232 38.462 7.47 0.00 39.47 1.89
2613 3045 6.899089 TGATTGGCTCCAAGATTGTCTATAA 58.101 36.000 7.47 0.00 39.47 0.98
2759 3191 7.175467 GCCCATAAATCACTTCATCACATCATA 59.825 37.037 0.00 0.00 0.00 2.15
2770 3202 5.136105 AGGATTCAGCCCATAAATCACTTC 58.864 41.667 0.00 0.00 32.27 3.01
2771 3203 5.134725 AGGATTCAGCCCATAAATCACTT 57.865 39.130 0.00 0.00 32.27 3.16
2772 3204 4.803329 AGGATTCAGCCCATAAATCACT 57.197 40.909 0.00 0.00 32.27 3.41
2773 3205 8.680903 CATATAAGGATTCAGCCCATAAATCAC 58.319 37.037 0.00 0.00 32.27 3.06
2774 3206 8.393259 ACATATAAGGATTCAGCCCATAAATCA 58.607 33.333 0.00 0.00 32.27 2.57
2775 3207 8.814038 ACATATAAGGATTCAGCCCATAAATC 57.186 34.615 0.00 0.00 0.00 2.17
2776 3208 7.836183 GGACATATAAGGATTCAGCCCATAAAT 59.164 37.037 0.00 0.00 0.00 1.40
2777 3209 7.175104 GGACATATAAGGATTCAGCCCATAAA 58.825 38.462 0.00 0.00 0.00 1.40
2800 3232 1.155155 GGGGGCAACTTTTCAGGGA 59.845 57.895 0.00 0.00 0.00 4.20
2825 3257 2.774234 ACATGTCATAGACAGAAGGGGG 59.226 50.000 6.01 0.00 46.04 5.40
2826 3258 3.432749 CCACATGTCATAGACAGAAGGGG 60.433 52.174 0.00 5.23 46.04 4.79
2827 3259 3.432749 CCCACATGTCATAGACAGAAGGG 60.433 52.174 14.81 14.81 46.04 3.95
2828 3260 3.801698 CCCACATGTCATAGACAGAAGG 58.198 50.000 0.00 6.74 46.04 3.46
2829 3261 3.201290 GCCCACATGTCATAGACAGAAG 58.799 50.000 0.00 1.63 46.04 2.85
2896 3328 6.566141 TGTAGACACCAAAAACTAAAAAGGC 58.434 36.000 0.00 0.00 0.00 4.35
2963 3576 2.159531 GCGCAATGAAGCAACTACATGA 60.160 45.455 0.30 0.00 0.00 3.07
3014 3627 0.173708 CTACAAGTGTCGGGAGCTCC 59.826 60.000 25.59 25.59 0.00 4.70
3021 3634 3.191669 TGTGTGAAACTACAAGTGTCGG 58.808 45.455 0.00 0.00 35.17 4.79
3022 3635 4.084537 GGATGTGTGAAACTACAAGTGTCG 60.085 45.833 0.00 0.00 35.17 4.35
3059 3673 6.716934 ACGATGACTATACAGAAGGACATT 57.283 37.500 0.00 0.00 0.00 2.71
3074 3688 9.393512 ACTTATCTAGTAACTGTAACGATGACT 57.606 33.333 0.00 0.00 34.56 3.41
3268 3896 0.031449 GCTCAGAGTCATAGACCCGC 59.969 60.000 0.00 0.00 32.18 6.13
3418 4046 2.352421 GGTCAACTCATCCGAACTCGAA 60.352 50.000 0.00 0.00 43.02 3.71
3628 4256 6.490721 AGAATATTTACAACGGGTTTTGGACA 59.509 34.615 0.00 0.00 0.00 4.02
3664 4293 1.624813 CCAGGTCCATGCAAAACCATT 59.375 47.619 15.43 0.00 35.43 3.16
3678 4307 6.821388 AGAATACATAACATGACTCCAGGTC 58.179 40.000 0.00 0.00 44.70 3.85
3729 4358 5.011533 CCACCTACATCTAAATCCTCCTGAG 59.988 48.000 0.00 0.00 0.00 3.35
3915 4544 2.865343 AGAGCGGGTTACACTTATCG 57.135 50.000 0.00 0.00 0.00 2.92
3950 4580 1.805943 TCTCCGTTTCGTCGTATCACA 59.194 47.619 0.00 0.00 0.00 3.58
3958 4588 1.641577 CTCCCAATCTCCGTTTCGTC 58.358 55.000 0.00 0.00 0.00 4.20
3985 4616 6.210287 ACACGAAGAATTTACCCACAAAAA 57.790 33.333 0.00 0.00 0.00 1.94
4004 4635 7.432252 AGCTTGAACTCTCATTTTTAAAACACG 59.568 33.333 0.00 0.00 0.00 4.49
4022 4653 6.402816 GTTCGAAAAACATTTCAGCTTGAAC 58.597 36.000 0.00 3.71 35.89 3.18
4053 4684 6.128661 CGTGTGAAAACTTCTCATAATTCGGA 60.129 38.462 0.00 0.00 35.84 4.55
4091 4724 4.741676 ACCTACGTAGTTTCGAAGTTGTTG 59.258 41.667 20.73 3.36 37.78 3.33
4096 4729 4.741676 CACAAACCTACGTAGTTTCGAAGT 59.258 41.667 20.73 7.16 37.78 3.01
4108 4741 5.567534 GCATGTACAAAATCACAAACCTACG 59.432 40.000 0.00 0.00 0.00 3.51
4157 4790 3.478082 CGACACCGAAACTGGAAGTACG 61.478 54.545 0.00 0.00 43.00 3.67
4175 4808 4.419522 AACATAAATTGACACAGGCGAC 57.580 40.909 0.00 0.00 0.00 5.19
4208 4841 0.958091 CTGCCATGTTCGTGGGAAAA 59.042 50.000 12.23 0.00 39.24 2.29
4245 4894 4.942852 TGTCATGTTCACAACCAAATTCC 58.057 39.130 0.00 0.00 0.00 3.01
4246 4895 6.700960 TGAATGTCATGTTCACAACCAAATTC 59.299 34.615 0.00 0.00 31.07 2.17
4284 4933 8.907222 AATTAATTCCAAAATGCACTGAAACT 57.093 26.923 0.00 0.00 0.00 2.66
4285 4934 9.384682 CAAATTAATTCCAAAATGCACTGAAAC 57.615 29.630 0.10 0.00 0.00 2.78
4356 5015 9.606631 AATTTTTGTGCAAGAGGTTTTAATGTA 57.393 25.926 0.00 0.00 0.00 2.29
4364 5023 9.171877 TGAAAATTAATTTTTGTGCAAGAGGTT 57.828 25.926 23.44 0.43 39.86 3.50
4394 5053 2.826777 ATTTCCAGCCCCTGACGCAG 62.827 60.000 0.52 0.52 32.44 5.18
4398 5057 4.466015 TGAAAAATATTTCCAGCCCCTGAC 59.534 41.667 0.10 0.00 43.54 3.51
4402 5061 7.301868 TCATATGAAAAATATTTCCAGCCCC 57.698 36.000 1.98 0.00 43.54 5.80
4448 5137 8.663209 TTCTTTGGATCCCATAAAATTCAAGA 57.337 30.769 9.90 0.00 31.53 3.02
4449 5138 9.895138 ATTTCTTTGGATCCCATAAAATTCAAG 57.105 29.630 9.90 0.00 31.53 3.02
4459 5148 5.188359 CCAGTTCAATTTCTTTGGATCCCAT 59.812 40.000 9.90 0.00 35.92 4.00
4463 5152 7.605449 TCATTCCAGTTCAATTTCTTTGGATC 58.395 34.615 0.00 0.00 34.91 3.36
4464 5153 7.543359 TCATTCCAGTTCAATTTCTTTGGAT 57.457 32.000 0.00 0.00 34.91 3.41


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

AutoCloner maintained by Alex Coulton.