Multiple sequence alignment - TraesCS1A01G215500

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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 TraesCS1A01G215500 chr1A 100.000 4088 0 0 1 4088 381099446 381095359 0.000000e+00 7550.0
1 TraesCS1A01G215500 chr1A 75.662 604 111 32 2360 2942 254351398 254351986 6.740000e-68 268.0
2 TraesCS1A01G215500 chr1A 74.297 249 44 17 2267 2505 102167826 102168064 2.020000e-13 87.9
3 TraesCS1A01G215500 chr1D 95.900 1951 55 12 1597 3536 303517681 303515745 0.000000e+00 3136.0
4 TraesCS1A01G215500 chr1D 87.898 1603 119 30 41 1592 303519307 303517729 0.000000e+00 1816.0
5 TraesCS1A01G215500 chr1D 92.383 512 31 2 3577 4088 303515751 303515248 0.000000e+00 723.0
6 TraesCS1A01G215500 chr1B 95.033 1671 56 11 1641 3297 411155426 411153769 0.000000e+00 2601.0
7 TraesCS1A01G215500 chr1B 89.719 1245 72 33 340 1553 411156646 411155427 0.000000e+00 1539.0
8 TraesCS1A01G215500 chr1B 83.589 652 77 12 3303 3952 411153506 411152883 5.890000e-163 584.0
9 TraesCS1A01G215500 chr1B 75.405 618 112 35 2360 2954 288757736 288758336 3.130000e-66 263.0
10 TraesCS1A01G215500 chr7A 78.289 304 51 7 2623 2914 718489527 718489827 9.030000e-42 182.0
11 TraesCS1A01G215500 chr7D 85.542 166 23 1 1 165 579132437 579132602 5.430000e-39 172.0
12 TraesCS1A01G215500 chr7D 73.684 171 38 5 1061 1231 618864823 618864986 4.410000e-05 60.2
13 TraesCS1A01G215500 chr2D 82.609 184 25 6 15 196 602654804 602654626 5.470000e-34 156.0
14 TraesCS1A01G215500 chr2D 72.468 316 67 18 2267 2572 71759076 71759381 2.620000e-12 84.2
15 TraesCS1A01G215500 chr5B 84.800 125 18 1 19 143 659587874 659587751 1.540000e-24 124.0
16 TraesCS1A01G215500 chr5B 72.964 307 57 22 2267 2561 319886618 319886326 2.620000e-12 84.2
17 TraesCS1A01G215500 chr2B 82.482 137 21 3 34 169 648630417 648630283 2.580000e-22 117.0
18 TraesCS1A01G215500 chr2B 73.817 317 61 19 2267 2572 108230838 108231143 5.590000e-19 106.0
19 TraesCS1A01G215500 chr2A 73.502 317 62 19 2267 2572 70870136 70870441 2.600000e-17 100.0
20 TraesCS1A01G215500 chr7B 73.896 249 45 17 2267 2505 747591913 747592151 9.420000e-12 82.4
21 TraesCS1A01G215500 chr5A 76.543 162 31 4 3340 3499 7397460 7397616 9.420000e-12 82.4


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 TraesCS1A01G215500 chr1A 381095359 381099446 4087 True 7550.000000 7550 100.000000 1 4088 1 chr1A.!!$R1 4087
1 TraesCS1A01G215500 chr1A 254351398 254351986 588 False 268.000000 268 75.662000 2360 2942 1 chr1A.!!$F2 582
2 TraesCS1A01G215500 chr1D 303515248 303519307 4059 True 1891.666667 3136 92.060333 41 4088 3 chr1D.!!$R1 4047
3 TraesCS1A01G215500 chr1B 411152883 411156646 3763 True 1574.666667 2601 89.447000 340 3952 3 chr1B.!!$R1 3612
4 TraesCS1A01G215500 chr1B 288757736 288758336 600 False 263.000000 263 75.405000 2360 2954 1 chr1B.!!$F1 594

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
739 793 0.035439 ACTCCACCGTGGCCAATTAG 60.035 55.0 7.24 6.43 37.47 1.73 F
740 794 0.035439 CTCCACCGTGGCCAATTAGT 60.035 55.0 7.24 0.00 37.47 2.24 F
1842 1960 0.109597 CACTTGGACAAGCAATCGGC 60.110 55.0 11.73 0.00 41.99 5.54 F
2009 2141 0.545309 TGGGTTCTGGAGGAGGTGAG 60.545 60.0 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1571 1646 1.561076 AGTCCATGATGCTGGCAAGTA 59.439 47.619 0.00 0.0 36.16 2.24 R
2253 2385 1.749258 GATGCCCGGGAAACTCCAC 60.749 63.158 29.31 3.6 38.64 4.02 R
3009 3150 0.396695 ACCCCACGTACAGATCCGAT 60.397 55.000 0.00 0.0 0.00 4.18 R
3896 4296 0.036952 AGCACACTTCTCCGACCATG 60.037 55.000 0.00 0.0 0.00 3.66 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
51 52 2.454832 ATATGGATGACAGCGGCGGG 62.455 60.000 9.78 0.00 0.00 6.13
70 74 4.248859 CGGGAGCATGATAGATACCTTTG 58.751 47.826 0.00 0.00 0.00 2.77
75 79 7.449704 GGGAGCATGATAGATACCTTTGAATTT 59.550 37.037 0.00 0.00 0.00 1.82
173 177 9.467258 GTCAAAATTGAATCTGAAGAAACATGA 57.533 29.630 0.00 0.00 39.21 3.07
177 181 9.991906 AAATTGAATCTGAAGAAACATGAATGT 57.008 25.926 0.00 0.00 44.20 2.71
257 262 1.232119 GTGTGGGACGTTGGGTTAAG 58.768 55.000 0.00 0.00 0.00 1.85
291 296 1.521681 GCACGCCTTAAGCCGATCT 60.522 57.895 13.42 0.00 38.78 2.75
307 312 2.386249 GATCTAGTCGACCAATCACGC 58.614 52.381 13.01 0.00 0.00 5.34
380 410 1.507174 CTCGTCACCCGACTTCCTC 59.493 63.158 0.00 0.00 41.60 3.71
417 453 1.802069 GGCCAGAGATAATCTTCGCC 58.198 55.000 0.00 0.00 41.46 5.54
427 463 1.265454 AATCTTCGCCTCCCGGTTCT 61.265 55.000 0.00 0.00 37.59 3.01
460 496 3.566523 GCCATGACATAGTACGTCTAGC 58.433 50.000 0.00 0.00 34.37 3.42
482 518 2.440247 CCTTGGCCCAACCGATCC 60.440 66.667 0.00 0.00 43.94 3.36
505 541 3.004002 CACTCACTCACCTACACGTGTTA 59.996 47.826 28.55 11.74 35.18 2.41
528 564 2.033747 CGTGCGGTGCTAATTAGTCATG 60.034 50.000 13.91 9.79 0.00 3.07
530 566 3.621268 GTGCGGTGCTAATTAGTCATGAA 59.379 43.478 13.91 2.63 0.00 2.57
531 567 4.094294 GTGCGGTGCTAATTAGTCATGAAA 59.906 41.667 13.91 0.00 0.00 2.69
532 568 4.094294 TGCGGTGCTAATTAGTCATGAAAC 59.906 41.667 13.91 0.00 0.00 2.78
533 569 4.495844 GCGGTGCTAATTAGTCATGAAACC 60.496 45.833 13.91 9.11 0.00 3.27
535 571 5.220662 CGGTGCTAATTAGTCATGAAACCAG 60.221 44.000 13.91 0.00 0.00 4.00
572 612 2.103263 CCCAACTAATCTCCCCGAGAAG 59.897 54.545 0.00 0.00 42.27 2.85
602 642 6.866480 TGAATCCTTGCAAATGGATAAACTC 58.134 36.000 17.90 12.95 41.76 3.01
632 672 9.211485 CTCAAAAGTGCAAATGGAAAAGATATT 57.789 29.630 0.00 0.00 0.00 1.28
668 722 2.604912 TGGAGTTCTGTGCTCTAGGA 57.395 50.000 0.00 0.00 33.73 2.94
696 750 2.350522 CATGGGAGAGGAAAAGTGTCG 58.649 52.381 0.00 0.00 0.00 4.35
722 776 2.930109 AGTATCCACTCCACTCCACT 57.070 50.000 0.00 0.00 0.00 4.00
736 790 2.034066 CACTCCACCGTGGCCAAT 59.966 61.111 7.24 0.00 37.47 3.16
737 791 1.603455 CACTCCACCGTGGCCAATT 60.603 57.895 7.24 0.00 37.47 2.32
738 792 0.322098 CACTCCACCGTGGCCAATTA 60.322 55.000 7.24 0.00 37.47 1.40
739 793 0.035439 ACTCCACCGTGGCCAATTAG 60.035 55.000 7.24 6.43 37.47 1.73
740 794 0.035439 CTCCACCGTGGCCAATTAGT 60.035 55.000 7.24 0.00 37.47 2.24
741 795 0.402504 TCCACCGTGGCCAATTAGTT 59.597 50.000 7.24 0.00 37.47 2.24
762 816 3.299585 CGATAAGCACTCGCCACG 58.700 61.111 0.00 0.00 39.83 4.94
792 859 3.509659 CCCCCGCGGAAGAAAATC 58.490 61.111 30.73 0.00 0.00 2.17
870 937 1.730064 CATTCATTCCGTTCCGTTCGT 59.270 47.619 0.00 0.00 0.00 3.85
871 938 1.868469 TTCATTCCGTTCCGTTCGTT 58.132 45.000 0.00 0.00 0.00 3.85
874 941 1.126113 CATTCCGTTCCGTTCGTTCAG 59.874 52.381 0.00 0.00 0.00 3.02
894 961 2.110226 GCCGATAGAAAAGTCTCGTCG 58.890 52.381 0.00 0.00 39.77 5.12
896 963 3.242543 GCCGATAGAAAAGTCTCGTCGTA 60.243 47.826 0.00 0.00 39.04 3.43
897 964 4.270102 CCGATAGAAAAGTCTCGTCGTAC 58.730 47.826 0.00 0.00 39.04 3.67
900 967 5.005586 CGATAGAAAAGTCTCGTCGTACTCT 59.994 44.000 3.99 1.58 37.36 3.24
903 970 3.809918 AAAGTCTCGTCGTACTCTCAC 57.190 47.619 3.99 0.00 0.00 3.51
904 971 2.452295 AGTCTCGTCGTACTCTCACA 57.548 50.000 0.00 0.00 0.00 3.58
905 972 2.339418 AGTCTCGTCGTACTCTCACAG 58.661 52.381 0.00 0.00 0.00 3.66
906 973 1.394227 GTCTCGTCGTACTCTCACAGG 59.606 57.143 0.00 0.00 0.00 4.00
907 974 1.274447 TCTCGTCGTACTCTCACAGGA 59.726 52.381 0.00 0.00 0.00 3.86
908 975 1.394227 CTCGTCGTACTCTCACAGGAC 59.606 57.143 0.00 0.00 31.47 3.85
909 976 0.447011 CGTCGTACTCTCACAGGACC 59.553 60.000 0.00 0.00 30.93 4.46
910 977 0.810016 GTCGTACTCTCACAGGACCC 59.190 60.000 0.00 0.00 30.93 4.46
911 978 0.402887 TCGTACTCTCACAGGACCCA 59.597 55.000 0.00 0.00 30.93 4.51
912 979 1.202964 TCGTACTCTCACAGGACCCAA 60.203 52.381 0.00 0.00 30.93 4.12
913 980 1.202582 CGTACTCTCACAGGACCCAAG 59.797 57.143 0.00 0.00 30.93 3.61
938 1005 1.511613 CCAAGCAATCCCCTCTCCTA 58.488 55.000 0.00 0.00 0.00 2.94
939 1006 1.141858 CCAAGCAATCCCCTCTCCTAC 59.858 57.143 0.00 0.00 0.00 3.18
1065 1133 1.381851 CCCTTGCTCCAAGCTCCTT 59.618 57.895 0.11 0.00 42.97 3.36
1181 1255 3.934962 GATGGAGGCTCCCGCTCC 61.935 72.222 30.03 10.98 35.03 4.70
1185 1259 3.984749 GAGGCTCCCGCTCCGATC 61.985 72.222 2.15 0.00 36.09 3.69
1542 1616 2.104792 TGACTCCTGCAAGTAAGCAACT 59.895 45.455 0.00 0.00 45.13 3.16
1544 1618 2.370189 ACTCCTGCAAGTAAGCAACTCT 59.630 45.455 0.00 0.00 45.13 3.24
1545 1619 2.999355 CTCCTGCAAGTAAGCAACTCTC 59.001 50.000 0.00 0.00 45.13 3.20
1555 1629 3.121030 CAACTCTCCGCCTTGCCG 61.121 66.667 0.00 0.00 0.00 5.69
1558 1632 2.587194 CTCTCCGCCTTGCCGATG 60.587 66.667 0.00 0.00 0.00 3.84
1565 1639 1.572085 CGCCTTGCCGATGATCCATC 61.572 60.000 0.00 0.00 37.50 3.51
1571 1646 3.497103 TGCCGATGATCCATCTCATTT 57.503 42.857 5.54 0.00 38.59 2.32
1575 1650 4.999950 GCCGATGATCCATCTCATTTACTT 59.000 41.667 5.54 0.00 38.59 2.24
1589 1664 2.804986 TTACTTGCCAGCATCATGGA 57.195 45.000 0.00 0.00 43.57 3.41
1592 1667 0.738975 CTTGCCAGCATCATGGACTG 59.261 55.000 0.00 0.00 43.57 3.51
1594 1669 2.831366 GCCAGCATCATGGACTGCG 61.831 63.158 9.24 5.83 43.57 5.18
1595 1670 2.713770 CAGCATCATGGACTGCGC 59.286 61.111 0.00 0.00 43.17 6.09
1619 1737 6.860023 GCTGCAATAGAATCAATCAACCATAC 59.140 38.462 0.00 0.00 0.00 2.39
1625 1743 1.006086 TCAATCAACCATACAGCGCG 58.994 50.000 0.00 0.00 0.00 6.86
1707 1825 5.003804 AGAAATTTGTCGGTTCAGTATGCT 58.996 37.500 0.00 0.00 34.76 3.79
1840 1958 1.522668 TCCACTTGGACAAGCAATCG 58.477 50.000 11.73 0.00 41.99 3.34
1841 1959 0.523072 CCACTTGGACAAGCAATCGG 59.477 55.000 11.73 2.18 41.99 4.18
1842 1960 0.109597 CACTTGGACAAGCAATCGGC 60.110 55.000 11.73 0.00 41.99 5.54
1915 2044 2.359214 TGTTTGCGTGTGCCAAATTAGA 59.641 40.909 0.00 0.00 41.78 2.10
1917 2046 4.216472 TGTTTGCGTGTGCCAAATTAGATA 59.784 37.500 0.00 0.00 41.78 1.98
2009 2141 0.545309 TGGGTTCTGGAGGAGGTGAG 60.545 60.000 0.00 0.00 0.00 3.51
2459 2594 0.895530 TACGGCCACTTCTTCCTCAG 59.104 55.000 2.24 0.00 0.00 3.35
3415 3813 3.564644 TCGAGAAGGCGAGTTTATAGAGG 59.435 47.826 0.00 0.00 35.01 3.69
3416 3814 3.304794 CGAGAAGGCGAGTTTATAGAGGG 60.305 52.174 0.00 0.00 0.00 4.30
3420 3818 4.120946 AGGCGAGTTTATAGAGGGAGAT 57.879 45.455 0.00 0.00 0.00 2.75
3430 3828 0.902516 AGAGGGAGATGGGCTATCGC 60.903 60.000 6.04 6.04 40.86 4.58
3448 3846 0.733150 GCGCCAAAGGAGGTATTGAC 59.267 55.000 0.00 0.00 0.00 3.18
3547 3947 6.045072 TCTTAATGGTTACATGAACGGAGT 57.955 37.500 0.00 0.00 39.50 3.85
3549 3949 3.973206 ATGGTTACATGAACGGAGTGA 57.027 42.857 0.00 0.00 36.91 3.41
3550 3950 3.034721 TGGTTACATGAACGGAGTGAC 57.965 47.619 0.00 0.00 45.00 3.67
3554 3954 0.391597 ACATGAACGGAGTGACGGTT 59.608 50.000 0.00 0.00 45.00 4.44
3556 3956 4.256813 GAACGGAGTGACGGTTCC 57.743 61.111 0.00 0.00 45.00 3.62
3557 3957 1.373873 GAACGGAGTGACGGTTCCC 60.374 63.158 0.00 0.00 45.00 3.97
3603 4003 2.936498 AGCGGTCAAACCATTTAGATCG 59.064 45.455 0.00 0.00 38.47 3.69
3607 4007 4.390603 CGGTCAAACCATTTAGATCGTCAA 59.609 41.667 0.00 0.00 38.47 3.18
3610 4010 6.581166 GGTCAAACCATTTAGATCGTCAAAAC 59.419 38.462 0.00 0.00 38.42 2.43
3614 4014 4.700213 ACCATTTAGATCGTCAAAACCCTG 59.300 41.667 0.00 0.00 0.00 4.45
3693 4093 8.833231 ATAGGATCGTATCACCATTAACTTTG 57.167 34.615 2.02 0.00 0.00 2.77
3695 4095 5.238650 GGATCGTATCACCATTAACTTTGGG 59.761 44.000 0.00 0.00 38.64 4.12
3744 4144 4.327680 GCTCTGTTGTTCTTTATGACCCT 58.672 43.478 0.00 0.00 0.00 4.34
3750 4150 7.016268 TCTGTTGTTCTTTATGACCCTCTACTT 59.984 37.037 0.00 0.00 0.00 2.24
3790 4190 5.120830 CACACCAAGAGGATTCTAACTTTCG 59.879 44.000 0.00 0.00 38.69 3.46
3834 4234 5.758784 GGGTCCCTATTAACTCTTGATTTCG 59.241 44.000 0.00 0.00 0.00 3.46
3839 4239 5.588648 CCTATTAACTCTTGATTTCGCCCAA 59.411 40.000 0.00 0.00 0.00 4.12
3892 4292 2.262423 GGCTAAGTAGGCATCTTGGG 57.738 55.000 7.00 0.53 46.94 4.12
3893 4293 1.202818 GGCTAAGTAGGCATCTTGGGG 60.203 57.143 7.00 0.00 46.94 4.96
3894 4294 1.768870 GCTAAGTAGGCATCTTGGGGA 59.231 52.381 4.82 0.00 0.00 4.81
3895 4295 2.172717 GCTAAGTAGGCATCTTGGGGAA 59.827 50.000 4.82 0.00 0.00 3.97
3896 4296 2.808906 AAGTAGGCATCTTGGGGAAC 57.191 50.000 0.00 0.00 0.00 3.62
3916 4316 1.204704 CATGGTCGGAGAAGTGTGCTA 59.795 52.381 0.00 0.00 39.69 3.49
3924 4324 3.381908 CGGAGAAGTGTGCTATAGGAGTT 59.618 47.826 1.04 0.00 0.00 3.01
4059 4459 1.388093 CGACTTGAACACTCTGCATCG 59.612 52.381 0.00 0.00 0.00 3.84
4078 4478 5.449588 GCATCGATTGGTTTGAATGAGATGT 60.450 40.000 0.00 0.00 33.68 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 8.349245 CGCTGTCATCCATATTGGTTAAATTTA 58.651 33.333 0.00 0.00 39.03 1.40
21 22 7.202526 CGCTGTCATCCATATTGGTTAAATTT 58.797 34.615 0.00 0.00 39.03 1.82
22 23 6.239008 CCGCTGTCATCCATATTGGTTAAATT 60.239 38.462 0.00 0.00 39.03 1.82
23 24 5.241506 CCGCTGTCATCCATATTGGTTAAAT 59.758 40.000 0.00 0.00 39.03 1.40
24 25 4.578516 CCGCTGTCATCCATATTGGTTAAA 59.421 41.667 0.00 0.00 39.03 1.52
25 26 4.133820 CCGCTGTCATCCATATTGGTTAA 58.866 43.478 0.00 0.00 39.03 2.01
26 27 3.738982 CCGCTGTCATCCATATTGGTTA 58.261 45.455 0.00 0.00 39.03 2.85
27 28 2.575532 CCGCTGTCATCCATATTGGTT 58.424 47.619 0.00 0.00 39.03 3.67
28 29 1.815408 GCCGCTGTCATCCATATTGGT 60.815 52.381 0.00 0.00 39.03 3.67
29 30 0.877071 GCCGCTGTCATCCATATTGG 59.123 55.000 0.00 0.00 39.43 3.16
30 31 0.514255 CGCCGCTGTCATCCATATTG 59.486 55.000 0.00 0.00 0.00 1.90
31 32 0.603707 CCGCCGCTGTCATCCATATT 60.604 55.000 0.00 0.00 0.00 1.28
32 33 1.004560 CCGCCGCTGTCATCCATAT 60.005 57.895 0.00 0.00 0.00 1.78
33 34 2.421314 CCGCCGCTGTCATCCATA 59.579 61.111 0.00 0.00 0.00 2.74
34 35 4.552365 CCCGCCGCTGTCATCCAT 62.552 66.667 0.00 0.00 0.00 3.41
36 37 4.899239 CTCCCGCCGCTGTCATCC 62.899 72.222 0.00 0.00 0.00 3.51
43 44 3.231889 CTATCATGCTCCCGCCGCT 62.232 63.158 0.00 0.00 34.43 5.52
51 52 8.844244 ACAAATTCAAAGGTATCTATCATGCTC 58.156 33.333 0.00 0.00 0.00 4.26
147 151 9.467258 TCATGTTTCTTCAGATTCAATTTTGAC 57.533 29.630 0.00 0.00 36.83 3.18
175 179 9.675464 ACTTCCTTCGTTCCATAATTTAATACA 57.325 29.630 0.00 0.00 0.00 2.29
182 186 6.039382 GCCAATACTTCCTTCGTTCCATAATT 59.961 38.462 0.00 0.00 0.00 1.40
189 193 4.662145 CATTGCCAATACTTCCTTCGTTC 58.338 43.478 0.00 0.00 0.00 3.95
192 196 3.070429 GCATTGCCAATACTTCCTTCG 57.930 47.619 0.00 0.00 0.00 3.79
242 246 0.978907 TCCTCTTAACCCAACGTCCC 59.021 55.000 0.00 0.00 0.00 4.46
246 250 3.522553 GAGTGATCCTCTTAACCCAACG 58.477 50.000 4.48 0.00 37.22 4.10
257 262 0.802607 GTGCCGTTCGAGTGATCCTC 60.803 60.000 0.00 0.00 36.80 3.71
287 292 2.033550 AGCGTGATTGGTCGACTAGATC 59.966 50.000 16.46 15.49 0.00 2.75
291 296 1.063027 CGTAGCGTGATTGGTCGACTA 59.937 52.381 16.46 6.50 0.00 2.59
393 429 2.029844 GATTATCTCTGGCCGGCGC 61.030 63.158 22.54 14.37 0.00 6.53
417 453 1.144936 GCCTCATGAGAACCGGGAG 59.855 63.158 24.62 5.66 0.00 4.30
447 483 1.145325 AGGGCCTGCTAGACGTACTAT 59.855 52.381 4.50 0.00 0.00 2.12
482 518 0.959553 ACGTGTAGGTGAGTGAGTGG 59.040 55.000 0.00 0.00 0.00 4.00
505 541 1.997606 GACTAATTAGCACCGCACGTT 59.002 47.619 12.54 0.00 0.00 3.99
511 547 4.634004 TGGTTTCATGACTAATTAGCACCG 59.366 41.667 12.54 6.99 0.00 4.94
528 564 2.401351 GTCGACACCTGTACTGGTTTC 58.599 52.381 20.83 21.43 38.45 2.78
530 566 0.677842 GGTCGACACCTGTACTGGTT 59.322 55.000 20.83 12.71 40.00 3.67
531 567 2.348665 GGTCGACACCTGTACTGGT 58.651 57.895 18.03 18.03 40.00 4.00
572 612 4.696402 TCCATTTGCAAGGATTCAATTTGC 59.304 37.500 3.37 10.86 45.53 3.68
602 642 4.589216 TCCATTTGCACTTTTGAGAAGG 57.411 40.909 0.00 0.00 0.00 3.46
633 673 8.550585 ACAGAACTCCATTCTAGTACTAGTAGT 58.449 37.037 25.58 18.59 46.52 2.73
634 674 8.832521 CACAGAACTCCATTCTAGTACTAGTAG 58.167 40.741 25.58 18.10 46.52 2.57
635 675 7.282675 GCACAGAACTCCATTCTAGTACTAGTA 59.717 40.741 25.58 18.71 46.52 1.82
640 693 5.126384 AGAGCACAGAACTCCATTCTAGTAC 59.874 44.000 0.00 0.00 46.52 2.73
642 695 4.093011 AGAGCACAGAACTCCATTCTAGT 58.907 43.478 0.00 0.00 46.52 2.57
643 696 4.734398 AGAGCACAGAACTCCATTCTAG 57.266 45.455 0.00 0.00 46.52 2.43
655 708 1.479730 CATGCACTCCTAGAGCACAGA 59.520 52.381 1.10 0.00 44.13 3.41
668 722 1.226542 CCTCTCCCATGCATGCACT 59.773 57.895 25.37 9.74 0.00 4.40
696 750 1.136500 GTGGAGTGGATACTTCGGGTC 59.864 57.143 0.00 0.00 37.25 4.46
722 776 0.402504 AACTAATTGGCCACGGTGGA 59.597 50.000 30.65 10.54 40.96 4.02
776 843 1.022451 TTCGATTTTCTTCCGCGGGG 61.022 55.000 27.83 18.63 0.00 5.73
833 900 2.358737 GGAGCTCGGTGTTGTGGG 60.359 66.667 7.83 0.00 0.00 4.61
870 937 3.192844 ACGAGACTTTTCTATCGGCTGAA 59.807 43.478 0.00 0.00 29.47 3.02
871 938 2.753452 ACGAGACTTTTCTATCGGCTGA 59.247 45.455 0.00 0.00 29.47 4.26
874 941 2.110226 CGACGAGACTTTTCTATCGGC 58.890 52.381 0.00 0.00 37.10 5.54
894 961 1.066787 GCTTGGGTCCTGTGAGAGTAC 60.067 57.143 0.00 0.00 0.00 2.73
896 963 1.484444 GGCTTGGGTCCTGTGAGAGT 61.484 60.000 0.00 0.00 0.00 3.24
897 964 1.298014 GGCTTGGGTCCTGTGAGAG 59.702 63.158 0.00 0.00 0.00 3.20
900 967 1.455849 CTTGGCTTGGGTCCTGTGA 59.544 57.895 0.00 0.00 0.00 3.58
903 970 2.677875 GGCTTGGCTTGGGTCCTG 60.678 66.667 0.00 0.00 0.00 3.86
904 971 2.720144 CTTGGCTTGGCTTGGGTCCT 62.720 60.000 0.00 0.00 0.00 3.85
905 972 2.203625 TTGGCTTGGCTTGGGTCC 60.204 61.111 0.00 0.00 0.00 4.46
906 973 2.935740 GCTTGGCTTGGCTTGGGTC 61.936 63.158 0.00 0.00 0.00 4.46
907 974 2.919328 GCTTGGCTTGGCTTGGGT 60.919 61.111 0.00 0.00 0.00 4.51
908 975 1.833787 ATTGCTTGGCTTGGCTTGGG 61.834 55.000 0.00 0.00 0.00 4.12
909 976 0.390735 GATTGCTTGGCTTGGCTTGG 60.391 55.000 0.00 0.00 0.00 3.61
910 977 0.390735 GGATTGCTTGGCTTGGCTTG 60.391 55.000 0.00 0.00 0.00 4.01
911 978 1.547472 GGGATTGCTTGGCTTGGCTT 61.547 55.000 0.00 0.00 0.00 4.35
912 979 1.986210 GGGATTGCTTGGCTTGGCT 60.986 57.895 0.00 0.00 0.00 4.75
913 980 2.580815 GGGATTGCTTGGCTTGGC 59.419 61.111 0.00 0.00 0.00 4.52
938 1005 0.325602 AGTCGTCGGAGGAAGAGAGT 59.674 55.000 1.41 0.00 31.18 3.24
939 1006 1.011333 GAGTCGTCGGAGGAAGAGAG 58.989 60.000 1.41 0.00 31.18 3.20
1050 1118 0.473755 TGTGAAGGAGCTTGGAGCAA 59.526 50.000 2.47 0.00 45.56 3.91
1521 1595 2.104792 AGTTGCTTACTTGCAGGAGTCA 59.895 45.455 1.40 0.00 44.27 3.41
1542 1616 2.369257 GATCATCGGCAAGGCGGAGA 62.369 60.000 16.03 13.66 40.90 3.71
1544 1618 2.108976 GATCATCGGCAAGGCGGA 59.891 61.111 16.03 7.40 41.73 5.54
1545 1619 2.974698 GGATCATCGGCAAGGCGG 60.975 66.667 16.03 1.45 0.00 6.13
1555 1629 5.766670 TGGCAAGTAAATGAGATGGATCATC 59.233 40.000 0.00 0.00 39.00 2.92
1558 1632 4.023365 GCTGGCAAGTAAATGAGATGGATC 60.023 45.833 0.00 0.00 0.00 3.36
1565 1639 4.499188 CCATGATGCTGGCAAGTAAATGAG 60.499 45.833 6.76 0.00 0.00 2.90
1571 1646 1.561076 AGTCCATGATGCTGGCAAGTA 59.439 47.619 0.00 0.00 36.16 2.24
1575 1650 1.751544 GCAGTCCATGATGCTGGCA 60.752 57.895 9.45 0.00 39.38 4.92
1589 1664 2.028420 TGATTCTATTGCAGCGCAGT 57.972 45.000 11.47 3.97 40.61 4.40
1592 1667 3.614159 TGATTGATTCTATTGCAGCGC 57.386 42.857 0.00 0.00 0.00 5.92
1594 1669 5.252969 TGGTTGATTGATTCTATTGCAGC 57.747 39.130 0.00 0.00 0.00 5.25
1595 1670 7.933396 TGTATGGTTGATTGATTCTATTGCAG 58.067 34.615 0.00 0.00 0.00 4.41
1635 1753 6.087522 TCGAATTAAACCAATTTAACTGCGG 58.912 36.000 0.00 0.00 41.84 5.69
1679 1797 3.146066 TGAACCGACAAATTTCTCCCAG 58.854 45.455 0.00 0.00 0.00 4.45
1707 1825 2.016318 CAGAACACTTGCACAACCAGA 58.984 47.619 0.00 0.00 0.00 3.86
1840 1958 9.694137 ATAGAGAACTATTTTTGTATACTCGCC 57.306 33.333 4.17 0.00 36.05 5.54
1873 2002 5.691896 ACAATAACCTAATCAGCTAACCCC 58.308 41.667 0.00 0.00 0.00 4.95
1915 2044 7.120285 CCCAATTCTCATTCGCTAATCATGTAT 59.880 37.037 0.00 0.00 0.00 2.29
1917 2046 5.240183 CCCAATTCTCATTCGCTAATCATGT 59.760 40.000 0.00 0.00 0.00 3.21
2085 2217 4.335647 CCCTTGAGCACCGGCAGT 62.336 66.667 0.00 0.00 44.61 4.40
2253 2385 1.749258 GATGCCCGGGAAACTCCAC 60.749 63.158 29.31 3.60 38.64 4.02
2373 2505 2.811431 CGGAAACTGCTTGTATTCACCA 59.189 45.455 0.00 0.00 0.00 4.17
2379 2511 1.906574 TCCTCCGGAAACTGCTTGTAT 59.093 47.619 5.23 0.00 0.00 2.29
2459 2594 2.029307 GAGCATCCCGGAGTACCACC 62.029 65.000 0.73 0.00 35.59 4.61
3003 3144 0.939577 CGTACAGATCCGATTGCCCG 60.940 60.000 0.00 0.00 0.00 6.13
3009 3150 0.396695 ACCCCACGTACAGATCCGAT 60.397 55.000 0.00 0.00 0.00 4.18
3171 3312 1.139654 ACCTGCACGCACAGATCATAT 59.860 47.619 6.84 0.00 40.25 1.78
3313 3711 5.588648 AGAAATTGTTTTGAGTCCTTGACGA 59.411 36.000 0.00 0.00 37.67 4.20
3347 3745 3.866582 GCCTCTCCCCGGGTGATG 61.867 72.222 21.85 14.78 0.00 3.07
3410 3808 2.516227 CGATAGCCCATCTCCCTCTA 57.484 55.000 0.00 0.00 0.00 2.43
3430 3828 1.006832 CGTCAATACCTCCTTTGGCG 58.993 55.000 0.00 0.00 43.38 5.69
3433 3831 2.107950 TGGCGTCAATACCTCCTTTG 57.892 50.000 0.00 0.00 0.00 2.77
3436 3834 1.139058 GTCATGGCGTCAATACCTCCT 59.861 52.381 0.00 0.00 0.00 3.69
3525 3925 5.872617 TCACTCCGTTCATGTAACCATTAAG 59.127 40.000 0.00 0.00 34.33 1.85
3529 3929 3.596214 GTCACTCCGTTCATGTAACCAT 58.404 45.455 0.00 0.00 34.33 3.55
3554 3954 1.639722 TGTTCATGACTTCCGAGGGA 58.360 50.000 0.00 0.00 0.00 4.20
3556 3956 5.118990 ACATATTGTTCATGACTTCCGAGG 58.881 41.667 0.00 0.00 0.00 4.63
3557 3957 6.668541 AACATATTGTTCATGACTTCCGAG 57.331 37.500 0.00 0.00 35.27 4.63
3603 4003 6.216801 AGTTTTAAAGTCCAGGGTTTTGAC 57.783 37.500 0.00 0.00 0.00 3.18
3607 4007 6.839134 AGATCAAGTTTTAAAGTCCAGGGTTT 59.161 34.615 0.00 0.00 0.00 3.27
3610 4010 6.901081 AAGATCAAGTTTTAAAGTCCAGGG 57.099 37.500 0.00 0.00 0.00 4.45
3658 4058 6.692486 GTGATACGATCCTATCACCATTCTT 58.308 40.000 23.70 0.00 43.86 2.52
3693 4093 4.147449 GCCCAAAGGATTGCGCCC 62.147 66.667 4.18 0.00 34.88 6.13
3695 4095 1.737735 GTTGCCCAAAGGATTGCGC 60.738 57.895 0.00 0.00 40.09 6.09
3744 4144 8.467598 GTGTGGACTATCTTACAATCAAGTAGA 58.532 37.037 0.00 0.00 0.00 2.59
3750 4150 6.212589 TCTTGGTGTGGACTATCTTACAATCA 59.787 38.462 0.00 0.00 0.00 2.57
3790 4190 4.010349 CCCTCTCAACATAAACCAACTCC 58.990 47.826 0.00 0.00 0.00 3.85
3850 4250 3.243771 ACGCTTCAAGTACTAGTTGCTGT 60.244 43.478 0.00 0.19 0.00 4.40
3853 4253 2.412089 CCACGCTTCAAGTACTAGTTGC 59.588 50.000 0.00 0.00 0.00 4.17
3892 4292 1.002087 ACACTTCTCCGACCATGTTCC 59.998 52.381 0.00 0.00 0.00 3.62
3893 4293 2.069273 CACACTTCTCCGACCATGTTC 58.931 52.381 0.00 0.00 0.00 3.18
3894 4294 1.878102 GCACACTTCTCCGACCATGTT 60.878 52.381 0.00 0.00 0.00 2.71
3895 4295 0.320771 GCACACTTCTCCGACCATGT 60.321 55.000 0.00 0.00 0.00 3.21
3896 4296 0.036952 AGCACACTTCTCCGACCATG 60.037 55.000 0.00 0.00 0.00 3.66
3924 4324 7.805163 TGAAGAAGGCAGGAGATCAATAAATA 58.195 34.615 0.00 0.00 0.00 1.40
4059 4459 7.148689 GCTTTCAACATCTCATTCAAACCAATC 60.149 37.037 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.