Multiple sequence alignment - TraesCS3B01G256200

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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 TraesCS3B01G256200 chr3B 100.000 2462 0 0 1 2462 413867046 413864585 0.000000e+00 4547.0
1 TraesCS3B01G256200 chr3B 100.000 2249 0 0 2841 5089 413864206 413861958 0.000000e+00 4154.0
2 TraesCS3B01G256200 chr3D 93.159 1871 78 19 606 2462 307879600 307881434 0.000000e+00 2700.0
3 TraesCS3B01G256200 chr3D 94.161 1781 70 12 2841 4594 307881480 307883253 0.000000e+00 2682.0
4 TraesCS3B01G256200 chr3D 89.604 606 52 6 5 604 253555513 253556113 0.000000e+00 760.0
5 TraesCS3B01G256200 chr3D 88.581 613 57 8 1 604 323696799 323697407 0.000000e+00 732.0
6 TraesCS3B01G256200 chr3D 89.961 508 33 5 4582 5088 307899564 307900054 1.540000e-179 640.0
7 TraesCS3B01G256200 chr3A 92.587 1848 81 11 628 2462 427191156 427192960 0.000000e+00 2603.0
8 TraesCS3B01G256200 chr3A 93.488 1336 60 4 2841 4149 427193006 427194341 0.000000e+00 1960.0
9 TraesCS3B01G256200 chr3A 92.760 953 63 4 4141 5088 427197818 427198769 0.000000e+00 1373.0
10 TraesCS3B01G256200 chr3A 80.749 187 28 5 2159 2343 37315488 37315308 6.870000e-29 139.0
11 TraesCS3B01G256200 chr3A 79.474 190 31 7 2159 2343 600645937 600646123 1.490000e-25 128.0
12 TraesCS3B01G256200 chr2D 82.309 944 156 9 2980 3914 174324527 174325468 0.000000e+00 808.0
13 TraesCS3B01G256200 chr2D 81.572 776 129 11 2958 3724 174383078 174383848 3.340000e-176 628.0
14 TraesCS3B01G256200 chr2D 84.191 544 79 7 1026 1566 174322149 174322688 5.840000e-144 521.0
15 TraesCS3B01G256200 chr2D 84.514 381 56 3 1187 1566 174382075 174382453 1.730000e-99 374.0
16 TraesCS3B01G256200 chr2D 84.091 264 37 4 1658 1920 174322798 174323057 3.040000e-62 250.0
17 TraesCS3B01G256200 chr2D 83.019 265 43 2 1657 1920 174382571 174382834 6.580000e-59 239.0
18 TraesCS3B01G256200 chr2D 78.571 196 36 5 2159 2349 533083802 533083608 1.920000e-24 124.0
19 TraesCS3B01G256200 chr2A 82.011 945 158 10 2980 3914 174027289 174028231 0.000000e+00 793.0
20 TraesCS3B01G256200 chr2A 82.726 851 134 10 2958 3800 174245655 174246500 0.000000e+00 745.0
21 TraesCS3B01G256200 chr2A 80.123 810 147 12 3153 3951 174195615 174196421 4.390000e-165 592.0
22 TraesCS3B01G256200 chr2A 82.136 543 92 5 1026 1566 174039100 174039639 1.290000e-125 460.0
23 TraesCS3B01G256200 chr2A 81.400 543 96 5 1026 1566 174244491 174245030 6.050000e-119 438.0
24 TraesCS3B01G256200 chr2A 84.848 264 40 0 1657 1920 174245146 174245409 3.020000e-67 267.0
25 TraesCS3B01G256200 chr2A 84.848 264 35 4 1658 1920 174026488 174026747 1.410000e-65 261.0
26 TraesCS3B01G256200 chr2A 81.132 265 46 4 1657 1920 174039756 174040017 5.160000e-50 209.0
27 TraesCS3B01G256200 chr2A 83.333 204 30 2 2958 3161 174040262 174040461 8.700000e-43 185.0
28 TraesCS3B01G256200 chr2A 82.781 151 23 3 2159 2308 566474127 566474275 1.150000e-26 132.0
29 TraesCS3B01G256200 chr6B 89.773 616 50 6 1 604 25604744 25604130 0.000000e+00 776.0
30 TraesCS3B01G256200 chr6B 80.941 425 73 8 1146 1566 688469653 688470073 3.800000e-86 329.0
31 TraesCS3B01G256200 chr5B 89.198 611 59 3 1 604 568517368 568517978 0.000000e+00 756.0
32 TraesCS3B01G256200 chr5B 89.180 610 55 6 1 602 353022440 353023046 0.000000e+00 750.0
33 TraesCS3B01G256200 chr5B 80.000 190 31 6 2159 2343 706024790 706024977 3.200000e-27 134.0
34 TraesCS3B01G256200 chr5B 86.667 60 8 0 2372 2431 625125501 625125442 3.290000e-07 67.6
35 TraesCS3B01G256200 chr5B 86.885 61 6 2 2372 2431 628705260 628705201 3.290000e-07 67.6
36 TraesCS3B01G256200 chr1B 88.889 612 58 6 1 604 476347838 476347229 0.000000e+00 745.0
37 TraesCS3B01G256200 chr1B 88.614 606 60 8 1 602 592179296 592178696 0.000000e+00 728.0
38 TraesCS3B01G256200 chr7D 88.980 608 58 8 1 604 577943918 577944520 0.000000e+00 743.0
39 TraesCS3B01G256200 chr7D 81.053 190 30 5 2159 2343 97941096 97940908 4.110000e-31 147.0
40 TraesCS3B01G256200 chr2B 80.912 943 170 7 2980 3914 222143177 222144117 0.000000e+00 736.0
41 TraesCS3B01G256200 chr2B 84.030 263 39 2 1658 1920 222142586 222142845 3.040000e-62 250.0
42 TraesCS3B01G256200 chr4B 88.599 614 56 7 1 607 627248014 627247408 0.000000e+00 734.0
43 TraesCS3B01G256200 chr6D 76.810 815 158 27 1146 1945 453652382 453651584 3.640000e-116 429.0
44 TraesCS3B01G256200 chr6A 82.201 427 64 11 1146 1566 599831943 599831523 1.740000e-94 357.0
45 TraesCS3B01G256200 chr5A 78.836 189 33 6 2159 2343 673179159 673178974 2.490000e-23 121.0


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 TraesCS3B01G256200 chr3B 413861958 413867046 5088 True 4350.500000 4547 100.000000 1 5089 2 chr3B.!!$R1 5088
1 TraesCS3B01G256200 chr3D 307879600 307883253 3653 False 2691.000000 2700 93.660000 606 4594 2 chr3D.!!$F4 3988
2 TraesCS3B01G256200 chr3D 253555513 253556113 600 False 760.000000 760 89.604000 5 604 1 chr3D.!!$F1 599
3 TraesCS3B01G256200 chr3D 323696799 323697407 608 False 732.000000 732 88.581000 1 604 1 chr3D.!!$F3 603
4 TraesCS3B01G256200 chr3A 427191156 427198769 7613 False 1978.666667 2603 92.945000 628 5088 3 chr3A.!!$F2 4460
5 TraesCS3B01G256200 chr2D 174322149 174325468 3319 False 526.333333 808 83.530333 1026 3914 3 chr2D.!!$F1 2888
6 TraesCS3B01G256200 chr2D 174382075 174383848 1773 False 413.666667 628 83.035000 1187 3724 3 chr2D.!!$F2 2537
7 TraesCS3B01G256200 chr2A 174195615 174196421 806 False 592.000000 592 80.123000 3153 3951 1 chr2A.!!$F1 798
8 TraesCS3B01G256200 chr2A 174026488 174028231 1743 False 527.000000 793 83.429500 1658 3914 2 chr2A.!!$F3 2256
9 TraesCS3B01G256200 chr2A 174244491 174246500 2009 False 483.333333 745 82.991333 1026 3800 3 chr2A.!!$F5 2774
10 TraesCS3B01G256200 chr2A 174039100 174040461 1361 False 284.666667 460 82.200333 1026 3161 3 chr2A.!!$F4 2135
11 TraesCS3B01G256200 chr6B 25604130 25604744 614 True 776.000000 776 89.773000 1 604 1 chr6B.!!$R1 603
12 TraesCS3B01G256200 chr5B 568517368 568517978 610 False 756.000000 756 89.198000 1 604 1 chr5B.!!$F2 603
13 TraesCS3B01G256200 chr5B 353022440 353023046 606 False 750.000000 750 89.180000 1 602 1 chr5B.!!$F1 601
14 TraesCS3B01G256200 chr1B 476347229 476347838 609 True 745.000000 745 88.889000 1 604 1 chr1B.!!$R1 603
15 TraesCS3B01G256200 chr1B 592178696 592179296 600 True 728.000000 728 88.614000 1 602 1 chr1B.!!$R2 601
16 TraesCS3B01G256200 chr7D 577943918 577944520 602 False 743.000000 743 88.980000 1 604 1 chr7D.!!$F1 603
17 TraesCS3B01G256200 chr2B 222142586 222144117 1531 False 493.000000 736 82.471000 1658 3914 2 chr2B.!!$F1 2256
18 TraesCS3B01G256200 chr4B 627247408 627248014 606 True 734.000000 734 88.599000 1 607 1 chr4B.!!$R1 606
19 TraesCS3B01G256200 chr6D 453651584 453652382 798 True 429.000000 429 76.810000 1146 1945 1 chr6D.!!$R1 799

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
492 513 0.033504 CGAAATGGGTCGATCCGGAT 59.966 55.000 19.21 19.21 43.86 4.18 F
611 634 2.361104 GGAGTTGGCCCGAATGCA 60.361 61.111 0.00 0.00 0.00 3.96 F
1559 1582 2.093288 TGCATTCCATCTCGAGAAGCTT 60.093 45.455 20.91 0.00 0.00 3.74 F
3000 4086 0.178992 TTCAGGTCCTTGCCAACCAG 60.179 55.000 0.00 0.00 38.06 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1559 1582 0.245539 GGAGCAGTGCACGTACCTTA 59.754 55.0 19.20 0.00 0.00 2.69 R
1842 1933 0.674895 GCTCGGACTGCAACTGGAAT 60.675 55.0 0.00 0.00 0.00 3.01 R
3495 4592 1.019278 TTCGGATGAAAGCGACAGCC 61.019 55.0 5.34 5.34 46.67 4.85 R
4653 9262 0.038526 TCGAAGGTCTGCCGAGTTTC 60.039 55.0 0.00 0.00 40.50 2.78 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
163 165 4.594854 TGCTTTCCCTTGCGGCCA 62.595 61.111 2.24 0.00 0.00 5.36
176 178 0.035458 GCGGCCATAGTTCCATAGCT 59.965 55.000 2.24 0.00 0.00 3.32
267 276 2.936032 AGGGGCCAGAGTGGGAAC 60.936 66.667 4.39 0.00 38.19 3.62
319 338 0.680618 TTTAAGAAGGACGGCGACCA 59.319 50.000 28.53 6.22 0.00 4.02
371 390 0.522626 CCTGTGCGCATTGATGTTGA 59.477 50.000 15.91 0.00 0.00 3.18
393 412 3.326385 ATGGGAGGTAGGTGGCCGA 62.326 63.158 0.00 0.00 0.00 5.54
462 483 2.098298 CGATTCAAACCAGGCGCG 59.902 61.111 0.00 0.00 0.00 6.86
492 513 0.033504 CGAAATGGGTCGATCCGGAT 59.966 55.000 19.21 19.21 43.86 4.18
514 535 4.295141 ACAAAACGGATAAGATGGGTCA 57.705 40.909 0.00 0.00 0.00 4.02
549 570 4.629523 GCCACCCGGTTCGTTCCA 62.630 66.667 0.00 0.00 33.28 3.53
611 634 2.361104 GGAGTTGGCCCGAATGCA 60.361 61.111 0.00 0.00 0.00 3.96
684 707 8.600449 GCTAATGCTTAACTCTATCAACTCAT 57.400 34.615 0.00 0.00 36.03 2.90
790 813 2.526873 AGACCGTTGACTGGCCCT 60.527 61.111 0.00 0.00 0.00 5.19
872 895 6.617782 TCAGATCTCCATCTCAGTTTCTTT 57.382 37.500 0.00 0.00 37.25 2.52
876 899 7.064847 CAGATCTCCATCTCAGTTTCTTTTCTG 59.935 40.741 0.00 0.00 37.25 3.02
922 945 2.528818 CCAGAGTTCCCCACAGCCA 61.529 63.158 0.00 0.00 0.00 4.75
954 977 9.828039 TCTCTCCATATATATTGTGATGCATTC 57.172 33.333 0.00 0.00 0.00 2.67
955 978 9.609346 CTCTCCATATATATTGTGATGCATTCA 57.391 33.333 0.00 0.58 0.00 2.57
996 1019 3.694043 TCGAATCAGTCATCCAACCAA 57.306 42.857 0.00 0.00 0.00 3.67
1013 1036 2.654385 ACCAATCTTCCCCCAATCAAGA 59.346 45.455 0.00 0.00 0.00 3.02
1022 1045 2.699846 CCCCCAATCAAGAGAGAGAGAG 59.300 54.545 0.00 0.00 0.00 3.20
1023 1046 3.629539 CCCCCAATCAAGAGAGAGAGAGA 60.630 52.174 0.00 0.00 0.00 3.10
1024 1047 3.638160 CCCCAATCAAGAGAGAGAGAGAG 59.362 52.174 0.00 0.00 0.00 3.20
1559 1582 2.093288 TGCATTCCATCTCGAGAAGCTT 60.093 45.455 20.91 0.00 0.00 3.74
1842 1933 1.264749 ACGCTGAAGGTGCCAGGATA 61.265 55.000 0.00 0.00 32.51 2.59
2013 2140 2.433868 TGGTACACGAGCTCAAGTTC 57.566 50.000 15.40 8.87 0.00 3.01
2015 2142 1.000506 GGTACACGAGCTCAAGTTCCA 59.999 52.381 19.71 0.85 0.00 3.53
2020 2147 4.385825 ACACGAGCTCAAGTTCCAAAATA 58.614 39.130 15.40 0.00 0.00 1.40
2106 2245 4.850680 TCGGCTTACCCAAAATGACTTAT 58.149 39.130 0.00 0.00 0.00 1.73
2114 2253 5.203528 ACCCAAAATGACTTATGCATAGCT 58.796 37.500 6.50 0.00 0.00 3.32
2191 2331 6.524545 TTTAAATAGCTAGCCCCCACTAAT 57.475 37.500 12.13 0.00 0.00 1.73
3000 4086 0.178992 TTCAGGTCCTTGCCAACCAG 60.179 55.000 0.00 0.00 38.06 4.00
3065 4151 5.987953 TCAATTCTGCTCAATCTAATCGGAG 59.012 40.000 0.00 0.00 0.00 4.63
3181 4267 3.552875 CCAATGCATCTCAGGAATGACT 58.447 45.455 0.00 0.00 0.00 3.41
3280 4366 6.202954 GGACAATGGTCATACTAAGTATGCAC 59.797 42.308 1.86 0.00 46.17 4.57
3448 4538 7.078228 GGAAGCATAAGTTGTTTTGTCTACAG 58.922 38.462 0.00 0.00 0.00 2.74
3495 4592 0.677288 TGCTCCGATTATACCCACCG 59.323 55.000 0.00 0.00 0.00 4.94
3525 4622 5.059221 CGCTTTCATCCGAAAAACATACAAC 59.941 40.000 0.00 0.00 40.57 3.32
3602 4699 3.255642 GTGTTGTTAATGCACCATGACCT 59.744 43.478 0.00 0.00 0.00 3.85
3681 4778 1.640149 TCCAAGGCATCCAAGAATCCA 59.360 47.619 0.00 0.00 0.00 3.41
3839 4937 6.697892 GCTCTAGATAACACGAAAATGCTACT 59.302 38.462 0.00 0.00 0.00 2.57
3872 4970 0.811281 GCGCAAATTAAGCTCAGGGT 59.189 50.000 0.30 0.00 0.00 4.34
3884 4982 8.747538 ATTAAGCTCAGGGTAATTTAATCGTT 57.252 30.769 0.00 0.00 0.00 3.85
3925 5046 5.416083 TGTTCACTATTTACCGTCATCTGG 58.584 41.667 0.00 0.00 0.00 3.86
3930 5051 3.845781 ATTTACCGTCATCTGGCTCAT 57.154 42.857 0.00 0.00 0.00 2.90
3931 5052 3.627395 TTTACCGTCATCTGGCTCATT 57.373 42.857 0.00 0.00 0.00 2.57
4263 8869 3.139397 AGAAGTATGTGTTTTGGTCCCCA 59.861 43.478 0.00 0.00 0.00 4.96
4292 8898 4.431416 TGTCAACCACTACTGGAATTGT 57.569 40.909 0.00 0.00 40.55 2.71
4293 8899 4.787551 TGTCAACCACTACTGGAATTGTT 58.212 39.130 0.00 0.00 40.55 2.83
4305 8911 4.202101 ACTGGAATTGTTGCAATTGTCGAA 60.202 37.500 0.59 0.00 0.00 3.71
4310 8916 4.582701 TTGTTGCAATTGTCGAATTCCT 57.417 36.364 0.59 0.00 28.65 3.36
4316 8922 3.561725 GCAATTGTCGAATTCCTAGGGAG 59.438 47.826 9.46 0.00 31.21 4.30
4371 8977 2.270352 TGCCAAGTTTCATTCTCGGT 57.730 45.000 0.00 0.00 0.00 4.69
4377 8983 5.506649 GCCAAGTTTCATTCTCGGTAAACAA 60.507 40.000 0.00 0.00 34.92 2.83
4388 8994 1.870580 CGGTAAACAACACTCGGCTGA 60.871 52.381 0.00 0.00 0.00 4.26
4501 9110 2.858745 ACTCGGCAAAGTACCATGTTT 58.141 42.857 0.00 0.00 0.00 2.83
4548 9157 1.888512 CATGTGGCTAGCAACCTTTGT 59.111 47.619 19.74 0.00 0.00 2.83
4589 9198 5.072329 CAGTCCAATGATGACTAGGGGTAAT 59.928 44.000 0.00 0.00 41.02 1.89
4600 9209 2.729028 AGGGGTAATATGTGTGGCAC 57.271 50.000 11.55 11.55 34.56 5.01
4637 9246 2.554032 CCCTTTTGCTGAAACTCGTCAT 59.446 45.455 0.00 0.00 0.00 3.06
4645 9254 3.994392 GCTGAAACTCGTCATACCTTTGA 59.006 43.478 0.00 0.00 0.00 2.69
4672 9281 0.038526 GAAACTCGGCAGACCTTCGA 60.039 55.000 0.00 0.00 0.00 3.71
4676 9285 0.734253 CTCGGCAGACCTTCGACAAG 60.734 60.000 0.00 0.00 0.00 3.16
4680 9289 2.271800 GGCAGACCTTCGACAAGTATG 58.728 52.381 0.00 0.00 0.00 2.39
4681 9290 2.353803 GGCAGACCTTCGACAAGTATGT 60.354 50.000 5.50 0.00 44.25 2.29
4703 9312 1.714899 GGGCCACGTGTCATATGTGC 61.715 60.000 15.65 7.70 43.53 4.57
4723 9332 4.442403 GTGCTTGCTTAGTCTTTTCTTTGC 59.558 41.667 0.00 0.00 0.00 3.68
4739 9348 4.742201 GCCGAGCTCCGCACTCAA 62.742 66.667 20.25 0.00 36.84 3.02
4771 9380 3.118482 CCTGGTGATGCTAGTTGATGAGT 60.118 47.826 0.00 0.00 0.00 3.41
4774 9383 3.624861 GGTGATGCTAGTTGATGAGTTGG 59.375 47.826 0.00 0.00 0.00 3.77
4781 9390 5.359576 TGCTAGTTGATGAGTTGGTTTTGTT 59.640 36.000 0.00 0.00 0.00 2.83
4786 9395 4.187694 TGATGAGTTGGTTTTGTTTTGCC 58.812 39.130 0.00 0.00 0.00 4.52
4788 9397 2.303022 TGAGTTGGTTTTGTTTTGCCCA 59.697 40.909 0.00 0.00 0.00 5.36
4815 9424 4.724798 AGTATATCCTGGTGCTAAAACCCA 59.275 41.667 0.00 0.00 39.70 4.51
4828 9437 6.039717 GTGCTAAAACCCATCACATCATGTAT 59.960 38.462 0.00 0.00 0.00 2.29
4830 9439 5.857471 AAAACCCATCACATCATGTATGG 57.143 39.130 14.71 14.71 40.16 2.74
4842 9451 6.149973 CACATCATGTATGGCCGATAATTCTT 59.850 38.462 0.00 0.00 40.16 2.52
4924 9534 6.018262 TGCTAAGTACACATGAAGACACAAAC 60.018 38.462 0.00 0.00 0.00 2.93
4928 9538 6.785191 AGTACACATGAAGACACAAACAAAG 58.215 36.000 0.00 0.00 0.00 2.77
5024 9635 0.853530 AACAAGAGGGGCCAAACTCT 59.146 50.000 15.69 15.69 45.51 3.24
5025 9636 0.402121 ACAAGAGGGGCCAAACTCTC 59.598 55.000 20.05 11.31 42.93 3.20
5056 9667 7.823745 TGAAAAACTTTGAATCCTCTAGCTT 57.176 32.000 0.00 0.00 0.00 3.74
5088 9699 3.620374 CAGTTGGAAGATGTTCATCCTCG 59.380 47.826 4.83 0.00 35.41 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 165 1.001406 GCCGCAGAGCTATGGAACTAT 59.999 52.381 10.92 0.00 0.00 2.12
267 276 1.062685 CGGTCGTCGTCCTCATCAG 59.937 63.158 6.94 0.00 0.00 2.90
319 338 1.683943 CTGTCATCCGGCCATTGAAT 58.316 50.000 2.24 0.00 0.00 2.57
371 390 0.983378 GCCACCTACCTCCCATCTGT 60.983 60.000 0.00 0.00 0.00 3.41
448 469 1.098712 AAACTCGCGCCTGGTTTGAA 61.099 50.000 15.71 0.00 32.84 2.69
449 470 1.525077 AAACTCGCGCCTGGTTTGA 60.525 52.632 15.71 0.00 32.84 2.69
462 483 0.179189 CCCATTTCGAGCGCAAACTC 60.179 55.000 11.47 0.00 0.00 3.01
492 513 5.423704 TGACCCATCTTATCCGTTTTGTA 57.576 39.130 0.00 0.00 0.00 2.41
503 524 1.306654 ACGGCCCTGACCCATCTTA 60.307 57.895 0.00 0.00 0.00 2.10
535 556 1.611410 GGTAAATGGAACGAACCGGGT 60.611 52.381 6.32 0.00 0.00 5.28
543 564 4.052608 GTTTGTTTGGGGTAAATGGAACG 58.947 43.478 0.00 0.00 0.00 3.95
604 627 0.729116 GTGTCCATGACCTGCATTCG 59.271 55.000 0.00 0.00 34.15 3.34
953 976 7.448469 TCGATTGAATGAGTATGGTAGAGATGA 59.552 37.037 0.00 0.00 0.00 2.92
954 977 7.597386 TCGATTGAATGAGTATGGTAGAGATG 58.403 38.462 0.00 0.00 0.00 2.90
955 978 7.767250 TCGATTGAATGAGTATGGTAGAGAT 57.233 36.000 0.00 0.00 0.00 2.75
956 979 7.582667 TTCGATTGAATGAGTATGGTAGAGA 57.417 36.000 0.00 0.00 0.00 3.10
996 1019 3.715834 CTCTCTCTTGATTGGGGGAAGAT 59.284 47.826 0.00 0.00 0.00 2.40
1013 1036 4.614475 TGTCTCTCTCTCTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
1022 1045 6.119536 TCTAAGAACCATGTCTCTCTCTCTC 58.880 44.000 0.00 0.00 0.00 3.20
1023 1046 6.073447 TCTAAGAACCATGTCTCTCTCTCT 57.927 41.667 0.00 0.00 0.00 3.10
1024 1047 5.221048 GCTCTAAGAACCATGTCTCTCTCTC 60.221 48.000 0.00 0.00 0.00 3.20
1262 1285 1.741401 CAGCGGCATCGACCTTGAA 60.741 57.895 1.45 0.00 39.00 2.69
1559 1582 0.245539 GGAGCAGTGCACGTACCTTA 59.754 55.000 19.20 0.00 0.00 2.69
1650 1673 7.028962 TCATGAGCTGCAAATTTAATACACAC 58.971 34.615 1.02 0.00 0.00 3.82
1659 1750 2.235155 TGGCATCATGAGCTGCAAATTT 59.765 40.909 20.02 0.00 38.59 1.82
1761 1852 1.187087 GTCTCTGGAACTCCGGACAT 58.813 55.000 0.00 0.00 46.04 3.06
1842 1933 0.674895 GCTCGGACTGCAACTGGAAT 60.675 55.000 0.00 0.00 0.00 3.01
2013 2140 6.658188 TGGGGTAGAAAGTTTGTATTTTGG 57.342 37.500 0.00 0.00 0.00 3.28
2015 2142 8.764558 AGTTTTGGGGTAGAAAGTTTGTATTTT 58.235 29.630 0.00 0.00 0.00 1.82
2020 2147 7.783119 AGAATAGTTTTGGGGTAGAAAGTTTGT 59.217 33.333 0.00 0.00 0.00 2.83
2106 2245 4.712051 ATTAATCAGGACCAGCTATGCA 57.288 40.909 0.00 0.00 0.00 3.96
2114 2253 7.178573 TGATGTTGGTTTATTAATCAGGACCA 58.821 34.615 0.00 0.00 35.52 4.02
2191 2331 9.103861 TCATGCTCGTATGTTGAAACAAATATA 57.896 29.630 0.00 0.00 43.03 0.86
3181 4267 3.026707 TCCTCCACGACCTCATCAATA 57.973 47.619 0.00 0.00 0.00 1.90
3280 4366 2.202932 CGATCTTGCCACTCGGGG 60.203 66.667 0.00 0.00 37.04 5.73
3316 4402 7.978975 TCAATTTTATTCTTTCCAAATAGGCCG 59.021 33.333 0.00 0.00 37.29 6.13
3361 4448 5.413969 AAACACTACTCACCGTTTTTAGC 57.586 39.130 0.00 0.00 0.00 3.09
3422 4509 5.108385 AGACAAAACAACTTATGCTTCCG 57.892 39.130 0.00 0.00 0.00 4.30
3433 4520 5.813672 TCACCTACACTGTAGACAAAACAAC 59.186 40.000 16.58 0.00 0.00 3.32
3435 4522 5.353938 GTCACCTACACTGTAGACAAAACA 58.646 41.667 16.58 0.00 0.00 2.83
3438 4525 3.962063 TGGTCACCTACACTGTAGACAAA 59.038 43.478 16.58 0.00 0.00 2.83
3439 4526 3.568443 TGGTCACCTACACTGTAGACAA 58.432 45.455 16.58 0.00 0.00 3.18
3448 4538 7.047891 TCATAAAGAATCATGGTCACCTACAC 58.952 38.462 0.00 0.00 0.00 2.90
3495 4592 1.019278 TTCGGATGAAAGCGACAGCC 61.019 55.000 5.34 5.34 46.67 4.85
3525 4622 4.752101 GTGATACCTCCAATCTCCATTTCG 59.248 45.833 0.00 0.00 0.00 3.46
3602 4699 1.611977 CGTCGCTTCCCCATATGTCTA 59.388 52.381 1.24 0.00 0.00 2.59
3648 4745 1.745890 CTTGGATATCCCGTCGGCA 59.254 57.895 19.34 0.00 37.93 5.69
3681 4778 2.091541 CCAAATGGTAGGAACGCACAT 58.908 47.619 0.00 0.00 0.00 3.21
3839 4937 0.679321 TTGCGCACCATGCATAGGAA 60.679 50.000 11.12 5.47 45.36 3.36
3884 4982 4.991687 TGAACATGCATACTTTCGTGTGTA 59.008 37.500 0.00 0.00 35.02 2.90
3925 5046 9.918630 AATTTTATGCCTGATTACATAATGAGC 57.081 29.630 0.00 0.00 38.26 4.26
3931 5052 9.549078 TGTCGTAATTTTATGCCTGATTACATA 57.451 29.630 0.00 0.00 35.66 2.29
4263 8869 5.071250 TCCAGTAGTGGTTGACAATAGTTGT 59.929 40.000 16.36 0.00 45.39 3.32
4292 8898 3.694072 CCCTAGGAATTCGACAATTGCAA 59.306 43.478 11.48 0.00 41.59 4.08
4293 8899 3.054728 TCCCTAGGAATTCGACAATTGCA 60.055 43.478 11.48 0.00 41.59 4.08
4305 8911 1.885049 TTGCTGAGCTCCCTAGGAAT 58.115 50.000 11.48 0.00 0.00 3.01
4310 8916 1.604378 GGCTTTGCTGAGCTCCCTA 59.396 57.895 12.15 0.00 42.32 3.53
4316 8922 0.675633 TTTTCTGGGCTTTGCTGAGC 59.324 50.000 0.00 0.00 41.96 4.26
4371 8977 2.907634 TGTTCAGCCGAGTGTTGTTTA 58.092 42.857 0.00 0.00 0.00 2.01
4377 8983 1.071471 CCCTTGTTCAGCCGAGTGT 59.929 57.895 0.00 0.00 0.00 3.55
4388 8994 1.923356 AATGATTGCCGACCCTTGTT 58.077 45.000 0.00 0.00 0.00 2.83
4501 9110 3.064682 CGCCATTAATGATCGTTTCACCA 59.935 43.478 17.23 0.00 37.11 4.17
4530 9139 1.604604 GACAAAGGTTGCTAGCCACA 58.395 50.000 19.57 0.00 0.00 4.17
4548 9157 2.357034 GCCAAGTTCCACGCTCGA 60.357 61.111 0.00 0.00 0.00 4.04
4576 9185 3.389983 GCCACACATATTACCCCTAGTCA 59.610 47.826 0.00 0.00 0.00 3.41
4600 9209 5.215160 CAAAAGGGAACTCGACAGAAAATG 58.785 41.667 0.00 0.00 42.68 2.32
4610 9219 2.618709 AGTTTCAGCAAAAGGGAACTCG 59.381 45.455 0.00 0.00 42.68 4.18
4637 9246 4.365723 GAGTTTCACAGTCGTCAAAGGTA 58.634 43.478 0.00 0.00 0.00 3.08
4645 9254 0.597637 CTGCCGAGTTTCACAGTCGT 60.598 55.000 0.00 0.00 45.61 4.34
4653 9262 0.038526 TCGAAGGTCTGCCGAGTTTC 60.039 55.000 0.00 0.00 40.50 2.78
4672 9281 1.674322 GTGGCCCGCACATACTTGT 60.674 57.895 0.00 0.00 36.15 3.16
4676 9285 3.496131 CACGTGGCCCGCACATAC 61.496 66.667 7.95 0.00 41.42 2.39
4680 9289 3.943479 TATGACACGTGGCCCGCAC 62.943 63.158 21.02 1.96 41.42 5.34
4681 9290 3.025189 ATATGACACGTGGCCCGCA 62.025 57.895 21.02 9.23 41.42 5.69
4703 9312 4.024048 TCGGCAAAGAAAAGACTAAGCAAG 60.024 41.667 0.00 0.00 0.00 4.01
4738 9347 0.178953 ATCACCAGGCTGGCTTTGTT 60.179 50.000 33.04 15.87 42.67 2.83
4739 9348 0.896940 CATCACCAGGCTGGCTTTGT 60.897 55.000 33.04 10.91 42.67 2.83
4771 9380 4.407296 ACTCTATGGGCAAAACAAAACCAA 59.593 37.500 0.00 0.00 34.45 3.67
4774 9383 8.135529 GGATATACTCTATGGGCAAAACAAAAC 58.864 37.037 0.00 0.00 0.00 2.43
4781 9390 5.013079 CACCAGGATATACTCTATGGGCAAA 59.987 44.000 0.00 0.00 35.93 3.68
4786 9395 7.482169 TTTAGCACCAGGATATACTCTATGG 57.518 40.000 0.00 0.00 36.99 2.74
4788 9397 7.038231 GGGTTTTAGCACCAGGATATACTCTAT 60.038 40.741 0.00 0.00 38.79 1.98
4815 9424 3.708403 ATCGGCCATACATGATGTGAT 57.292 42.857 8.61 0.00 33.19 3.06
4828 9437 1.286553 ACCCCAAAGAATTATCGGCCA 59.713 47.619 2.24 0.00 0.00 5.36
4830 9439 4.399934 TGTTTACCCCAAAGAATTATCGGC 59.600 41.667 0.00 0.00 0.00 5.54
4842 9451 3.570550 CGAACCAAGAATGTTTACCCCAA 59.429 43.478 0.00 0.00 0.00 4.12
4991 9602 7.229907 GGCCCCTCTTGTTATTTATTCGAAATA 59.770 37.037 0.00 0.00 0.00 1.40
4996 9607 4.204012 TGGCCCCTCTTGTTATTTATTCG 58.796 43.478 0.00 0.00 0.00 3.34
5006 9617 0.402121 GAGAGTTTGGCCCCTCTTGT 59.598 55.000 15.50 0.00 38.15 3.16
5011 9622 0.178961 GGTTTGAGAGTTTGGCCCCT 60.179 55.000 0.00 0.00 0.00 4.79
5014 9625 2.306847 TCAAGGTTTGAGAGTTTGGCC 58.693 47.619 0.00 0.00 34.08 5.36
5024 9635 7.619965 AGGATTCAAAGTTTTTCAAGGTTTGA 58.380 30.769 0.00 0.00 35.78 2.69
5025 9636 7.765819 AGAGGATTCAAAGTTTTTCAAGGTTTG 59.234 33.333 0.00 0.00 0.00 2.93
5056 9667 1.777878 TCTTCCAACTGGCCACCTTTA 59.222 47.619 0.00 0.00 34.44 1.85


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

AutoCloner maintained by Alex Coulton.