Multiple sequence alignment - TraesCS2B01G426300

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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 TraesCS2B01G426300 chr2B 100.000 4319 0 0 1 4319 612691191 612686873 0.000000e+00 7976.0
1 TraesCS2B01G426300 chr2D 91.938 4391 179 62 1 4319 520528491 520524204 0.000000e+00 5986.0
2 TraesCS2B01G426300 chr2A 90.457 2798 111 56 181 2900 665712698 665709979 0.000000e+00 3544.0
3 TraesCS2B01G426300 chr2A 90.721 1401 87 19 2940 4319 665709972 665708594 0.000000e+00 1827.0
4 TraesCS2B01G426300 chr2A 77.812 329 39 17 1731 2039 4115528 4115842 5.740000e-39 172.0
5 TraesCS2B01G426300 chr2A 83.237 173 5 7 32 188 665713103 665712939 2.090000e-28 137.0
6 TraesCS2B01G426300 chr2A 100.000 28 0 0 4 31 665713143 665713116 8.000000e-03 52.8
7 TraesCS2B01G426300 chr6B 88.732 142 14 2 1500 1639 708668041 708667900 5.740000e-39 172.0
8 TraesCS2B01G426300 chr1A 76.694 369 50 20 2562 2897 370109460 370109095 5.740000e-39 172.0
9 TraesCS2B01G426300 chr1A 88.372 129 12 3 1508 1635 478567436 478567562 7.480000e-33 152.0
10 TraesCS2B01G426300 chr1A 91.262 103 9 0 1531 1633 370110215 370110113 1.620000e-29 141.0
11 TraesCS2B01G426300 chr5D 76.471 408 40 26 1683 2052 292676370 292675981 2.070000e-38 171.0
12 TraesCS2B01G426300 chr6D 86.861 137 17 1 1505 1640 464737271 464737135 7.480000e-33 152.0
13 TraesCS2B01G426300 chr6A 90.351 114 11 0 1523 1636 611314563 611314450 2.690000e-32 150.0
14 TraesCS2B01G426300 chr1D 87.597 129 13 3 1508 1635 377973950 377974076 3.480000e-31 147.0
15 TraesCS2B01G426300 chr1D 85.156 128 16 3 2771 2897 297537610 297537485 1.260000e-25 128.0
16 TraesCS2B01G426300 chr1B 87.597 129 13 3 1508 1635 505626339 505626465 3.480000e-31 147.0
17 TraesCS2B01G426300 chr1B 83.594 128 18 3 2771 2897 400312915 400312790 2.730000e-22 117.0
18 TraesCS2B01G426300 chr3B 74.306 432 61 26 1633 2036 573475675 573476084 2.090000e-28 137.0
19 TraesCS2B01G426300 chr7D 88.889 63 3 3 1994 2052 213041799 213041737 1.670000e-09 75.0


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 TraesCS2B01G426300 chr2B 612686873 612691191 4318 True 7976.0 7976 100.00000 1 4319 1 chr2B.!!$R1 4318
1 TraesCS2B01G426300 chr2D 520524204 520528491 4287 True 5986.0 5986 91.93800 1 4319 1 chr2D.!!$R1 4318
2 TraesCS2B01G426300 chr2A 665708594 665713143 4549 True 1390.2 3544 91.10375 4 4319 4 chr2A.!!$R1 4315

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
92 111 0.030638 CAGCAAAGAAACACCCACCG 59.969 55.0 0.00 0.00 0.00 4.94 F
269 551 0.033109 TCCTTCCATGGAGAGAGCGA 60.033 55.0 15.53 6.75 0.00 4.93 F
1920 2301 0.108520 CAGCGCCATGGCTTGAAAAT 60.109 50.0 33.07 9.02 42.53 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1933 2314 0.037447 TTTGCCGGTGACATGGATCA 59.963 50.000 1.9 0.0 0.00 2.92 R
1934 2315 0.734889 CTTTGCCGGTGACATGGATC 59.265 55.000 1.9 0.0 0.00 3.36 R
3421 3831 1.000396 GCCAACTTGAGAGGCCCAT 60.000 57.895 0.0 0.0 42.58 4.00 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
89 108 1.748493 GTGACAGCAAAGAAACACCCA 59.252 47.619 0.00 0.00 0.00 4.51
90 109 1.748493 TGACAGCAAAGAAACACCCAC 59.252 47.619 0.00 0.00 0.00 4.61
91 110 1.067060 GACAGCAAAGAAACACCCACC 59.933 52.381 0.00 0.00 0.00 4.61
92 111 0.030638 CAGCAAAGAAACACCCACCG 59.969 55.000 0.00 0.00 0.00 4.94
93 112 0.395173 AGCAAAGAAACACCCACCGT 60.395 50.000 0.00 0.00 0.00 4.83
106 125 1.542547 CCCACCGTGCTTTTCTGTACT 60.543 52.381 0.00 0.00 0.00 2.73
107 126 2.218603 CCACCGTGCTTTTCTGTACTT 58.781 47.619 0.00 0.00 0.00 2.24
108 127 2.616842 CCACCGTGCTTTTCTGTACTTT 59.383 45.455 0.00 0.00 0.00 2.66
109 128 3.810941 CCACCGTGCTTTTCTGTACTTTA 59.189 43.478 0.00 0.00 0.00 1.85
197 475 8.728596 ATCCTATCCTAGTACTAGTTGCAAAT 57.271 34.615 24.84 4.23 0.00 2.32
208 486 3.980646 AGTTGCAAATGCTAACGAACA 57.019 38.095 0.00 0.00 42.66 3.18
236 518 0.752376 GTACAGGGGACGAGGAGAGG 60.752 65.000 0.00 0.00 0.00 3.69
243 525 0.608640 GGACGAGGAGAGGAAAAGCA 59.391 55.000 0.00 0.00 0.00 3.91
246 528 1.416401 ACGAGGAGAGGAAAAGCAACA 59.584 47.619 0.00 0.00 0.00 3.33
265 547 3.251484 ACAGTTTCCTTCCATGGAGAGA 58.749 45.455 15.53 12.85 37.43 3.10
267 549 2.238395 AGTTTCCTTCCATGGAGAGAGC 59.762 50.000 15.53 11.71 37.43 4.09
269 551 0.033109 TCCTTCCATGGAGAGAGCGA 60.033 55.000 15.53 6.75 0.00 4.93
274 556 1.326213 CCATGGAGAGAGCGAGGTGT 61.326 60.000 5.56 0.00 0.00 4.16
278 560 1.004394 TGGAGAGAGCGAGGTGTAAGA 59.996 52.381 0.00 0.00 0.00 2.10
307 589 4.082523 CGGCTTTGCGAGGAGGGA 62.083 66.667 0.00 0.00 0.00 4.20
308 590 2.351276 GGCTTTGCGAGGAGGGAA 59.649 61.111 0.00 0.00 0.00 3.97
309 591 1.746991 GGCTTTGCGAGGAGGGAAG 60.747 63.158 0.00 0.00 0.00 3.46
310 592 1.746991 GCTTTGCGAGGAGGGAAGG 60.747 63.158 0.00 0.00 0.00 3.46
311 593 1.078143 CTTTGCGAGGAGGGAAGGG 60.078 63.158 0.00 0.00 0.00 3.95
312 594 2.543067 CTTTGCGAGGAGGGAAGGGG 62.543 65.000 0.00 0.00 0.00 4.79
314 596 4.798682 GCGAGGAGGGAAGGGGGA 62.799 72.222 0.00 0.00 0.00 4.81
315 597 2.444895 CGAGGAGGGAAGGGGGAG 60.445 72.222 0.00 0.00 0.00 4.30
316 598 2.040359 GAGGAGGGAAGGGGGAGG 60.040 72.222 0.00 0.00 0.00 4.30
317 599 3.711782 AGGAGGGAAGGGGGAGGG 61.712 72.222 0.00 0.00 0.00 4.30
344 642 3.536917 CGGGCACTATGCTCCGGA 61.537 66.667 17.63 2.93 46.25 5.14
440 739 4.377708 CCCTTTGGGCGCCTTTGC 62.378 66.667 28.56 10.32 35.35 3.68
441 740 3.305516 CCTTTGGGCGCCTTTGCT 61.306 61.111 28.56 0.00 34.43 3.91
458 757 1.937846 CTCGTCCGTAATGTCGCCG 60.938 63.158 0.00 0.00 0.00 6.46
476 776 1.453197 GTTATTGCTCCGGTGGGGG 60.453 63.158 0.00 0.00 36.60 5.40
587 898 0.909623 CGGTGTTTAGGGGGACAGAT 59.090 55.000 0.00 0.00 0.00 2.90
588 899 1.406887 CGGTGTTTAGGGGGACAGATG 60.407 57.143 0.00 0.00 0.00 2.90
596 907 0.251077 GGGGGACAGATGATGATGGC 60.251 60.000 0.00 0.00 0.00 4.40
597 908 0.251077 GGGGACAGATGATGATGGCC 60.251 60.000 0.00 0.00 44.57 5.36
603 914 1.199327 CAGATGATGATGGCCGATTGC 59.801 52.381 0.00 0.00 40.16 3.56
610 921 0.582005 GATGGCCGATTGCTCGTTAC 59.418 55.000 0.00 0.00 43.49 2.50
617 928 2.159841 CCGATTGCTCGTTACTGTGTTG 60.160 50.000 0.00 0.00 43.49 3.33
618 929 2.159841 CGATTGCTCGTTACTGTGTTGG 60.160 50.000 0.00 0.00 40.07 3.77
619 930 0.941542 TTGCTCGTTACTGTGTTGGC 59.058 50.000 0.00 0.00 0.00 4.52
620 931 1.218875 TGCTCGTTACTGTGTTGGCG 61.219 55.000 0.00 0.00 0.00 5.69
622 933 0.782384 CTCGTTACTGTGTTGGCGAC 59.218 55.000 0.00 0.00 0.00 5.19
624 935 1.203313 GTTACTGTGTTGGCGACGC 59.797 57.895 12.43 12.43 39.25 5.19
634 945 3.416382 GGCGACGCCGTTAAGCAA 61.416 61.111 25.24 0.00 39.62 3.91
635 946 2.095843 GCGACGCCGTTAAGCAAG 59.904 61.111 9.14 0.00 38.24 4.01
636 947 2.095843 CGACGCCGTTAAGCAAGC 59.904 61.111 0.00 0.00 0.00 4.01
956 1277 2.500098 GCATGTTCCTACTCCTACACCA 59.500 50.000 0.00 0.00 0.00 4.17
959 1280 2.158279 TGTTCCTACTCCTACACCACCA 60.158 50.000 0.00 0.00 0.00 4.17
965 1305 1.348064 CTCCTACACCACCAGACCAA 58.652 55.000 0.00 0.00 0.00 3.67
1011 1355 4.162690 GCCCGGGCTCGATCACTT 62.163 66.667 38.76 0.00 39.00 3.16
1074 1420 2.778679 CCTGCGCGTGAACTAAGC 59.221 61.111 8.43 0.00 0.00 3.09
1079 1425 3.849953 GCGTGAACTAAGCGGCCG 61.850 66.667 24.05 24.05 0.00 6.13
1080 1426 2.431942 CGTGAACTAAGCGGCCGT 60.432 61.111 28.70 10.76 0.00 5.68
1081 1427 2.442188 CGTGAACTAAGCGGCCGTC 61.442 63.158 28.70 19.09 0.00 4.79
1082 1428 2.126228 TGAACTAAGCGGCCGTCG 60.126 61.111 28.70 14.76 42.76 5.12
1083 1429 2.884207 GAACTAAGCGGCCGTCGG 60.884 66.667 28.70 16.53 39.69 4.79
1184 1539 2.568031 CGACGACGATGACATGCCG 61.568 63.158 0.00 0.00 42.66 5.69
1657 2021 0.903942 TAATTAACCACGCCCGTCCT 59.096 50.000 0.00 0.00 0.00 3.85
1664 2028 3.936203 ACGCCCGTCCTTGCTTGA 61.936 61.111 0.00 0.00 0.00 3.02
1665 2029 2.668212 CGCCCGTCCTTGCTTGAA 60.668 61.111 0.00 0.00 0.00 2.69
1666 2030 2.680913 CGCCCGTCCTTGCTTGAAG 61.681 63.158 0.00 0.00 0.00 3.02
1667 2031 1.302511 GCCCGTCCTTGCTTGAAGA 60.303 57.895 0.00 0.00 32.82 2.87
1701 2074 1.186267 AACAGAGGACGTCCCCTGAC 61.186 60.000 42.15 23.62 36.49 3.51
1725 2106 2.511145 CGCTGCTTCCTCTGCTCC 60.511 66.667 0.00 0.00 0.00 4.70
1730 2111 2.588989 CTTCCTCTGCTCCCAGCC 59.411 66.667 0.00 0.00 41.51 4.85
1903 2284 6.020281 CGAGAGGTAAGAAATCGAAACATCAG 60.020 42.308 0.00 0.00 35.47 2.90
1905 2286 4.330074 AGGTAAGAAATCGAAACATCAGCG 59.670 41.667 0.00 0.00 0.00 5.18
1915 2296 1.940883 AACATCAGCGCCATGGCTTG 61.941 55.000 33.07 28.22 42.53 4.01
1916 2297 2.116533 CATCAGCGCCATGGCTTGA 61.117 57.895 30.82 30.82 42.53 3.02
1920 2301 0.108520 CAGCGCCATGGCTTGAAAAT 60.109 50.000 33.07 9.02 42.53 1.82
1923 2304 2.129607 GCGCCATGGCTTGAAAATATG 58.870 47.619 33.07 15.13 39.32 1.78
1929 2310 5.180271 CCATGGCTTGAAAATATGCAACTT 58.820 37.500 0.00 0.00 0.00 2.66
1930 2311 5.292589 CCATGGCTTGAAAATATGCAACTTC 59.707 40.000 0.00 0.00 0.00 3.01
1931 2312 4.819769 TGGCTTGAAAATATGCAACTTCC 58.180 39.130 0.00 0.00 0.00 3.46
1932 2313 4.282957 TGGCTTGAAAATATGCAACTTCCA 59.717 37.500 0.00 0.00 0.00 3.53
1933 2314 5.046448 TGGCTTGAAAATATGCAACTTCCAT 60.046 36.000 0.00 0.00 0.00 3.41
1934 2315 5.292589 GGCTTGAAAATATGCAACTTCCATG 59.707 40.000 0.00 0.00 0.00 3.66
1935 2316 6.101332 GCTTGAAAATATGCAACTTCCATGA 58.899 36.000 0.00 0.00 0.00 3.07
1946 2327 3.287867 ACTTCCATGATCCATGTCACC 57.712 47.619 0.00 0.00 39.94 4.02
1963 2344 0.598065 ACCGGCAAAGCATCTGAAAC 59.402 50.000 0.00 0.00 0.00 2.78
1997 2378 2.094659 GTGTCAGGTGATGGCGACG 61.095 63.158 0.00 0.00 35.76 5.12
2123 2506 1.804151 TGCTGTTCACGTGGCTTAATC 59.196 47.619 17.00 0.26 0.00 1.75
2305 2688 2.358737 GTCACCAAGTCCGGGCTG 60.359 66.667 10.71 0.00 0.00 4.85
2371 2754 2.046023 CAGATCCACAAGGCGGCA 60.046 61.111 13.08 0.00 33.74 5.69
2455 2838 1.836604 CAAGGTGGGTTGGGTTGGG 60.837 63.158 0.00 0.00 0.00 4.12
2466 2849 4.785453 GGTTGGGCAGCCTCCTCG 62.785 72.222 12.43 0.00 0.00 4.63
2520 2903 1.227438 TTTCCCGATCGCGATTCCC 60.227 57.895 24.55 9.72 40.82 3.97
2534 2917 2.814097 CGATTCCCCTGACAAAGGTTGT 60.814 50.000 0.00 0.00 45.78 3.32
2645 3028 0.325577 TGCTGGACTGCCTGGAGATA 60.326 55.000 0.00 0.00 33.99 1.98
2920 3303 3.675348 ATCCATGATCACCACACCAAT 57.325 42.857 0.00 0.00 0.00 3.16
2928 3311 3.751246 CCACACCAATGCCGCCTG 61.751 66.667 0.00 0.00 0.00 4.85
2952 3336 3.626930 ACTGCAACCACCTAAGTTTTCA 58.373 40.909 0.00 0.00 0.00 2.69
2956 3340 4.038642 TGCAACCACCTAAGTTTTCAATCC 59.961 41.667 0.00 0.00 0.00 3.01
2957 3341 4.280929 GCAACCACCTAAGTTTTCAATCCT 59.719 41.667 0.00 0.00 0.00 3.24
2987 3373 5.929992 AGGCTTGAATTGTGAAATTGTGATG 59.070 36.000 0.00 0.00 0.00 3.07
3143 3534 7.063662 CGAGGAAGATCTGATGATGATCATTTC 59.936 40.741 10.14 10.65 41.85 2.17
3174 3571 1.217916 TGGACCTGGACCAGAAAACA 58.782 50.000 23.77 12.72 32.44 2.83
3180 3577 5.303333 GGACCTGGACCAGAAAACAAAAATA 59.697 40.000 23.77 0.00 32.44 1.40
3196 3593 6.489603 ACAAAAATACTGGTCCATACATCCA 58.510 36.000 0.00 0.00 0.00 3.41
3240 3640 4.980434 GCCATAACATGTAGTGGTAGTACG 59.020 45.833 23.08 4.57 32.45 3.67
3282 3685 0.976073 GCACAGTAGGCTACTCCCCA 60.976 60.000 23.95 0.00 36.76 4.96
3288 3691 1.490910 GTAGGCTACTCCCCAAGCATT 59.509 52.381 17.35 0.00 40.61 3.56
3315 3718 2.430694 GTTTGGGGCTACATTCATTCCC 59.569 50.000 0.00 0.00 36.25 3.97
3323 3731 3.688126 GCTACATTCATTCCCATGGTCCA 60.688 47.826 11.73 0.00 0.00 4.02
3327 3735 2.734755 TCATTCCCATGGTCCATCAC 57.265 50.000 11.73 0.00 0.00 3.06
3330 3738 3.785325 TCATTCCCATGGTCCATCACTTA 59.215 43.478 11.73 0.00 0.00 2.24
3421 3831 1.220703 TGTATGTGGATGGGCATGGA 58.779 50.000 0.00 0.00 0.00 3.41
3422 3832 1.782140 TGTATGTGGATGGGCATGGAT 59.218 47.619 0.00 0.00 0.00 3.41
3423 3833 2.165167 GTATGTGGATGGGCATGGATG 58.835 52.381 0.00 0.00 0.00 3.51
3424 3834 0.178944 ATGTGGATGGGCATGGATGG 60.179 55.000 0.00 0.00 0.00 3.51
3467 3877 6.892485 TGACATGATTCACCAGAGTATGAAT 58.108 36.000 0.00 0.00 45.92 2.57
3511 3921 4.978388 AGGGAGAATTATATATCCTGCCCC 59.022 45.833 11.05 0.00 36.21 5.80
3563 3973 5.193728 AGGGAACAATCTATACACACCCAAT 59.806 40.000 0.00 0.00 37.49 3.16
3566 3976 6.828785 GGAACAATCTATACACACCCAATCTT 59.171 38.462 0.00 0.00 0.00 2.40
3569 3979 9.561069 AACAATCTATACACACCCAATCTTATC 57.439 33.333 0.00 0.00 0.00 1.75
3579 3989 8.116026 ACACACCCAATCTTATCTTTCCTATTT 58.884 33.333 0.00 0.00 0.00 1.40
3608 4018 5.359576 ACTTTTACAGCCAACAACATCAAGA 59.640 36.000 0.00 0.00 0.00 3.02
3633 4043 7.428826 AGAGAAGAAAAGCATAACCAAACAAG 58.571 34.615 0.00 0.00 0.00 3.16
3829 4240 6.099269 TCCATTACCTCCTTATAACAGGACAC 59.901 42.308 11.32 0.00 38.11 3.67
3931 4347 0.322997 CCCATACGACCAAAAGGCCA 60.323 55.000 5.01 0.00 0.00 5.36
3950 4366 2.943033 CCAGGTTTGATCCGATGTAACC 59.057 50.000 11.06 11.06 38.78 2.85
3958 4374 3.069586 TGATCCGATGTAACCTCATGGAC 59.930 47.826 0.00 0.00 37.04 4.02
3959 4375 2.462723 TCCGATGTAACCTCATGGACA 58.537 47.619 0.00 0.00 37.04 4.02
4104 4520 4.145052 GGTCCACTTTCCAAGTCTTTCAT 58.855 43.478 0.00 0.00 40.46 2.57
4175 4591 1.066143 CGATGTACTTGGCCACCTCTT 60.066 52.381 3.88 0.00 0.00 2.85
4180 4596 3.136809 TGTACTTGGCCACCTCTTTAACA 59.863 43.478 3.88 0.00 0.00 2.41
4195 4611 2.507407 TAACAAGTTCCATCCCCAGC 57.493 50.000 0.00 0.00 0.00 4.85
4228 4644 3.064820 TCACGTTGTTCTTCAGAAAAGCC 59.935 43.478 0.00 0.00 35.58 4.35
4254 4670 1.305930 GGGTCAGCGCCGAAGAAATT 61.306 55.000 2.29 0.00 0.00 1.82
4265 4681 4.434330 CGCCGAAGAAATTATCGCTTATCC 60.434 45.833 3.45 0.00 37.73 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 108 6.628919 AAATAAAGTACAGAAAAGCACGGT 57.371 33.333 0.00 0.00 0.00 4.83
90 109 7.803724 AGTAAATAAAGTACAGAAAAGCACGG 58.196 34.615 0.00 0.00 0.00 4.94
106 125 4.649692 TGGTGCCGTGGTAAGTAAATAAA 58.350 39.130 0.00 0.00 0.00 1.40
107 126 4.255301 CTGGTGCCGTGGTAAGTAAATAA 58.745 43.478 0.00 0.00 0.00 1.40
108 127 3.369681 CCTGGTGCCGTGGTAAGTAAATA 60.370 47.826 0.00 0.00 0.00 1.40
109 128 2.617021 CCTGGTGCCGTGGTAAGTAAAT 60.617 50.000 0.00 0.00 0.00 1.40
197 475 2.299013 ACACATCCTCTGTTCGTTAGCA 59.701 45.455 0.00 0.00 35.29 3.49
208 486 1.867363 GTCCCCTGTACACATCCTCT 58.133 55.000 0.00 0.00 0.00 3.69
236 518 4.385358 TGGAAGGAAACTGTTGCTTTTC 57.615 40.909 0.00 0.00 44.58 2.29
243 525 3.652869 TCTCTCCATGGAAGGAAACTGTT 59.347 43.478 17.00 0.00 42.68 3.16
265 547 6.204882 GCCATTATTTTATCTTACACCTCGCT 59.795 38.462 0.00 0.00 0.00 4.93
267 549 6.347402 CCGCCATTATTTTATCTTACACCTCG 60.347 42.308 0.00 0.00 0.00 4.63
269 551 5.240844 GCCGCCATTATTTTATCTTACACCT 59.759 40.000 0.00 0.00 0.00 4.00
274 556 6.212955 GCAAAGCCGCCATTATTTTATCTTA 58.787 36.000 0.00 0.00 0.00 2.10
278 560 3.067461 TCGCAAAGCCGCCATTATTTTAT 59.933 39.130 0.00 0.00 0.00 1.40
304 586 1.066585 GTATTCCCCTCCCCCTTCCC 61.067 65.000 0.00 0.00 0.00 3.97
305 587 1.416480 CGTATTCCCCTCCCCCTTCC 61.416 65.000 0.00 0.00 0.00 3.46
306 588 0.399519 TCGTATTCCCCTCCCCCTTC 60.400 60.000 0.00 0.00 0.00 3.46
307 589 0.271005 ATCGTATTCCCCTCCCCCTT 59.729 55.000 0.00 0.00 0.00 3.95
308 590 0.178900 GATCGTATTCCCCTCCCCCT 60.179 60.000 0.00 0.00 0.00 4.79
309 591 1.542187 CGATCGTATTCCCCTCCCCC 61.542 65.000 7.03 0.00 0.00 5.40
310 592 1.542187 CCGATCGTATTCCCCTCCCC 61.542 65.000 15.09 0.00 0.00 4.81
311 593 1.542187 CCCGATCGTATTCCCCTCCC 61.542 65.000 15.09 0.00 0.00 4.30
312 594 1.972978 CCCGATCGTATTCCCCTCC 59.027 63.158 15.09 0.00 0.00 4.30
313 595 1.292541 GCCCGATCGTATTCCCCTC 59.707 63.158 15.09 0.00 0.00 4.30
314 596 1.458777 TGCCCGATCGTATTCCCCT 60.459 57.895 15.09 0.00 0.00 4.79
315 597 1.301479 GTGCCCGATCGTATTCCCC 60.301 63.158 15.09 0.00 0.00 4.81
316 598 0.963962 TAGTGCCCGATCGTATTCCC 59.036 55.000 15.09 0.00 0.00 3.97
317 599 2.607187 CATAGTGCCCGATCGTATTCC 58.393 52.381 15.09 0.00 0.00 3.01
440 739 1.937846 CGGCGACATTACGGACGAG 60.938 63.158 0.00 0.00 0.00 4.18
441 740 2.100797 CGGCGACATTACGGACGA 59.899 61.111 0.00 0.00 0.00 4.20
458 757 1.453197 CCCCCACCGGAGCAATAAC 60.453 63.158 9.46 0.00 0.00 1.89
563 874 3.124921 CCCCTAAACACCGCAGCG 61.125 66.667 8.18 8.18 0.00 5.18
564 875 2.750237 CCCCCTAAACACCGCAGC 60.750 66.667 0.00 0.00 0.00 5.25
565 876 1.376812 GTCCCCCTAAACACCGCAG 60.377 63.158 0.00 0.00 0.00 5.18
566 877 2.119484 CTGTCCCCCTAAACACCGCA 62.119 60.000 0.00 0.00 0.00 5.69
567 878 1.376812 CTGTCCCCCTAAACACCGC 60.377 63.158 0.00 0.00 0.00 5.68
568 879 0.909623 ATCTGTCCCCCTAAACACCG 59.090 55.000 0.00 0.00 0.00 4.94
569 880 1.913419 TCATCTGTCCCCCTAAACACC 59.087 52.381 0.00 0.00 0.00 4.16
570 881 3.199946 TCATCATCTGTCCCCCTAAACAC 59.800 47.826 0.00 0.00 0.00 3.32
571 882 3.459828 TCATCATCTGTCCCCCTAAACA 58.540 45.455 0.00 0.00 0.00 2.83
572 883 4.392940 CATCATCATCTGTCCCCCTAAAC 58.607 47.826 0.00 0.00 0.00 2.01
575 886 2.624495 CCATCATCATCTGTCCCCCTA 58.376 52.381 0.00 0.00 0.00 3.53
587 898 0.881600 CGAGCAATCGGCCATCATCA 60.882 55.000 2.24 0.00 46.50 3.07
588 899 0.882042 ACGAGCAATCGGCCATCATC 60.882 55.000 2.24 0.00 46.50 2.92
596 907 1.710013 ACACAGTAACGAGCAATCGG 58.290 50.000 2.46 0.00 37.45 4.18
597 908 2.159841 CCAACACAGTAACGAGCAATCG 60.160 50.000 0.00 0.00 39.31 3.34
603 914 0.782384 GTCGCCAACACAGTAACGAG 59.218 55.000 0.00 0.00 0.00 4.18
617 928 3.362851 CTTGCTTAACGGCGTCGCC 62.363 63.158 26.69 26.69 46.75 5.54
618 929 2.095843 CTTGCTTAACGGCGTCGC 59.904 61.111 15.17 17.01 40.63 5.19
619 930 2.095843 GCTTGCTTAACGGCGTCG 59.904 61.111 15.17 8.42 43.02 5.12
620 931 2.095843 CGCTTGCTTAACGGCGTC 59.904 61.111 15.17 0.09 42.23 5.19
622 933 4.160635 CCCGCTTGCTTAACGGCG 62.161 66.667 4.80 4.80 45.58 6.46
624 935 3.131478 CCCCCGCTTGCTTAACGG 61.131 66.667 0.00 0.00 46.50 4.44
705 1016 3.430929 CCAACTAGGAGTATCACTGTGCC 60.431 52.174 2.12 0.00 41.22 5.01
889 1210 0.613260 ACGAGCAGAAATAGGTGGCA 59.387 50.000 0.00 0.00 0.00 4.92
956 1277 1.139058 GGATAGCGATGTTGGTCTGGT 59.861 52.381 0.00 0.00 0.00 4.00
959 1280 1.496060 TGGGATAGCGATGTTGGTCT 58.504 50.000 0.00 0.00 0.00 3.85
965 1305 1.434188 TGGGAATGGGATAGCGATGT 58.566 50.000 0.00 0.00 0.00 3.06
1402 1766 4.344865 AACCGGCCTTGCGGTCAT 62.345 61.111 0.00 0.00 35.28 3.06
1439 1803 1.633852 GCCAAGAACAGAGAGCAGCG 61.634 60.000 0.00 0.00 0.00 5.18
1512 1876 1.738350 CTTCATCAGCTGCAACTCTGG 59.262 52.381 9.47 0.00 0.00 3.86
1553 1917 1.381327 GGACATGTCCTCCCCGAGA 60.381 63.158 33.47 0.00 46.16 4.04
1601 1965 0.468585 TGATGGCATTGGAGATGGCC 60.469 55.000 0.00 0.00 46.58 5.36
1613 1977 0.249120 CGTAGAGGTTGGTGATGGCA 59.751 55.000 0.00 0.00 0.00 4.92
1642 2006 2.344500 CAAGGACGGGCGTGGTTA 59.656 61.111 0.00 0.00 0.00 2.85
1664 2028 5.790593 TCTGTTTTGTATCGGTAAGCTCTT 58.209 37.500 0.00 0.00 0.00 2.85
1665 2029 5.401531 TCTGTTTTGTATCGGTAAGCTCT 57.598 39.130 0.00 0.00 0.00 4.09
1666 2030 4.567159 CCTCTGTTTTGTATCGGTAAGCTC 59.433 45.833 0.00 0.00 0.00 4.09
1667 2031 4.222145 TCCTCTGTTTTGTATCGGTAAGCT 59.778 41.667 0.00 0.00 0.00 3.74
1669 2033 4.561606 CGTCCTCTGTTTTGTATCGGTAAG 59.438 45.833 0.00 0.00 0.00 2.34
1670 2034 4.022068 ACGTCCTCTGTTTTGTATCGGTAA 60.022 41.667 0.00 0.00 0.00 2.85
1671 2035 3.507233 ACGTCCTCTGTTTTGTATCGGTA 59.493 43.478 0.00 0.00 0.00 4.02
1673 2037 2.921754 GACGTCCTCTGTTTTGTATCGG 59.078 50.000 3.51 0.00 0.00 4.18
1674 2038 2.921754 GGACGTCCTCTGTTTTGTATCG 59.078 50.000 27.64 0.00 0.00 2.92
1675 2039 3.259902 GGGACGTCCTCTGTTTTGTATC 58.740 50.000 32.52 8.65 35.95 2.24
1676 2040 2.027469 GGGGACGTCCTCTGTTTTGTAT 60.027 50.000 32.52 0.00 32.35 2.29
1677 2041 1.345415 GGGGACGTCCTCTGTTTTGTA 59.655 52.381 32.52 0.00 32.35 2.41
1678 2042 0.108019 GGGGACGTCCTCTGTTTTGT 59.892 55.000 32.52 0.00 32.35 2.83
1679 2043 2.928416 GGGGACGTCCTCTGTTTTG 58.072 57.895 32.52 0.00 32.35 2.44
1701 2074 0.392193 AGAGGAAGCAGCGGATGTTG 60.392 55.000 0.00 0.00 0.00 3.33
1725 2106 3.361977 CCCGAAAACGGTGGCTGG 61.362 66.667 7.83 0.00 0.00 4.85
1730 2111 2.966309 GCAGCTCCCGAAAACGGTG 61.966 63.158 7.83 1.01 0.00 4.94
1763 2144 1.122019 ACTTCTTCTCCACCGGCAGT 61.122 55.000 0.00 0.00 0.00 4.40
1886 2267 2.159517 GGCGCTGATGTTTCGATTTCTT 60.160 45.455 7.64 0.00 0.00 2.52
1889 2270 1.164411 TGGCGCTGATGTTTCGATTT 58.836 45.000 7.64 0.00 0.00 2.17
1905 2286 3.182341 TGCATATTTTCAAGCCATGGC 57.818 42.857 30.12 30.12 42.33 4.40
1915 2296 6.808829 TGGATCATGGAAGTTGCATATTTTC 58.191 36.000 9.77 4.86 0.00 2.29
1916 2297 6.795144 TGGATCATGGAAGTTGCATATTTT 57.205 33.333 9.77 0.00 0.00 1.82
1920 2301 4.795469 ACATGGATCATGGAAGTTGCATA 58.205 39.130 9.77 0.00 45.16 3.14
1923 2304 3.018856 TGACATGGATCATGGAAGTTGC 58.981 45.455 11.85 0.00 45.16 4.17
1929 2310 0.469494 CCGGTGACATGGATCATGGA 59.531 55.000 11.85 0.00 45.16 3.41
1930 2311 1.168407 GCCGGTGACATGGATCATGG 61.168 60.000 1.90 0.82 45.16 3.66
1931 2312 0.464193 TGCCGGTGACATGGATCATG 60.464 55.000 1.90 6.37 46.18 3.07
1932 2313 0.255604 TTGCCGGTGACATGGATCAT 59.744 50.000 1.90 0.00 0.00 2.45
1933 2314 0.037447 TTTGCCGGTGACATGGATCA 59.963 50.000 1.90 0.00 0.00 2.92
1934 2315 0.734889 CTTTGCCGGTGACATGGATC 59.265 55.000 1.90 0.00 0.00 3.36
1935 2316 1.315257 GCTTTGCCGGTGACATGGAT 61.315 55.000 1.90 0.00 0.00 3.41
1946 2327 2.642139 ATGTTTCAGATGCTTTGCCG 57.358 45.000 0.00 0.00 0.00 5.69
1963 2344 4.201980 CCTGACACAACCAGAATGCATATG 60.202 45.833 0.00 1.82 33.65 1.78
1997 2378 1.175983 AGATGTCGGATCTCGGCCTC 61.176 60.000 0.00 5.78 43.91 4.70
2123 2506 2.971261 CGCGCATCATCAATCAAATCAG 59.029 45.455 8.75 0.00 0.00 2.90
2451 2834 2.927856 TTCGAGGAGGCTGCCCAA 60.928 61.111 16.57 0.00 0.00 4.12
2455 2838 2.185608 GAGGTTCGAGGAGGCTGC 59.814 66.667 0.00 0.00 0.00 5.25
2466 2849 0.322546 AGTTTCATGGCGGGAGGTTC 60.323 55.000 0.00 0.00 0.00 3.62
2645 3028 4.194720 GCCTCGTGCTCCGACGAT 62.195 66.667 0.00 0.00 46.72 3.73
2928 3311 1.318576 ACTTAGGTGGTTGCAGTTGC 58.681 50.000 0.00 0.00 42.50 4.17
2937 3320 6.884836 GTGATAGGATTGAAAACTTAGGTGGT 59.115 38.462 0.00 0.00 0.00 4.16
2942 3325 6.825721 AGCCTGTGATAGGATTGAAAACTTAG 59.174 38.462 0.00 0.00 44.62 2.18
2943 3326 6.721318 AGCCTGTGATAGGATTGAAAACTTA 58.279 36.000 0.00 0.00 44.62 2.24
2956 3340 5.885230 TTCACAATTCAAGCCTGTGATAG 57.115 39.130 5.07 0.00 46.45 2.08
2957 3341 6.839124 ATTTCACAATTCAAGCCTGTGATA 57.161 33.333 5.07 1.66 46.45 2.15
2987 3373 3.755378 AGCACAAGAACAGATTCATCACC 59.245 43.478 0.00 0.00 37.29 4.02
3174 3571 6.777580 GGATGGATGTATGGACCAGTATTTTT 59.222 38.462 0.00 0.00 37.12 1.94
3180 3577 2.775418 TGGATGGATGTATGGACCAGT 58.225 47.619 0.00 0.00 37.12 4.00
3196 3593 8.654485 ATGGCATAATGTACATATTGTTGGAT 57.346 30.769 9.21 0.00 0.00 3.41
3240 3640 4.321718 TCATGCTGCTATCTTCCATTAGC 58.678 43.478 0.00 0.00 40.97 3.09
3282 3685 1.207811 GCCCCAAACATAGCAATGCTT 59.792 47.619 14.85 0.00 40.44 3.91
3288 3691 3.287222 GAATGTAGCCCCAAACATAGCA 58.713 45.455 0.00 0.00 35.30 3.49
3291 3694 4.892934 GGAATGAATGTAGCCCCAAACATA 59.107 41.667 0.00 0.00 35.30 2.29
3295 3698 2.043664 TGGGAATGAATGTAGCCCCAAA 59.956 45.455 0.00 0.00 40.56 3.28
3315 3718 3.695556 TGCAATGTAAGTGATGGACCATG 59.304 43.478 12.99 0.00 30.28 3.66
3323 3731 7.117285 TGATAGAGAGTGCAATGTAAGTGAT 57.883 36.000 0.00 0.00 30.28 3.06
3327 3735 6.982724 TGTCATGATAGAGAGTGCAATGTAAG 59.017 38.462 0.00 0.00 0.00 2.34
3330 3738 5.349061 TGTCATGATAGAGAGTGCAATGT 57.651 39.130 0.00 0.00 0.00 2.71
3363 3773 7.447545 ACAAGTGACAAGTGATACTGTACTCTA 59.552 37.037 0.00 0.00 0.00 2.43
3421 3831 1.000396 GCCAACTTGAGAGGCCCAT 60.000 57.895 0.00 0.00 42.58 4.00
3422 3832 2.436109 GCCAACTTGAGAGGCCCA 59.564 61.111 0.00 0.00 42.58 5.36
3511 3921 7.108847 ACTGTCTGAAGAATAATTTCCCTCAG 58.891 38.462 8.21 8.21 40.45 3.35
3569 3979 7.595130 GGCTGTAAAAGTGTGAAAATAGGAAAG 59.405 37.037 0.00 0.00 0.00 2.62
3579 3989 4.218635 TGTTGTTGGCTGTAAAAGTGTGAA 59.781 37.500 0.00 0.00 0.00 3.18
3586 3996 5.592282 TCTCTTGATGTTGTTGGCTGTAAAA 59.408 36.000 0.00 0.00 0.00 1.52
3608 4018 6.959639 TGTTTGGTTATGCTTTTCTTCTCT 57.040 33.333 0.00 0.00 0.00 3.10
3633 4043 3.202829 TGTGGTTCCAAACACTAGGAC 57.797 47.619 8.88 0.00 38.39 3.85
3716 4126 2.829120 GGTTGAATCCCATTTTCCGGAA 59.171 45.455 14.35 14.35 0.00 4.30
3782 4193 9.838339 ATGGAAAAGTAAAGTGAGTATGATAGG 57.162 33.333 0.00 0.00 0.00 2.57
3829 4240 7.394077 TCTTCTATAGAGATGAGGATTCAGCAG 59.606 40.741 2.02 0.00 42.14 4.24
3856 4270 8.379457 AGGATTTAATAGATTTAGCGGTGTTC 57.621 34.615 0.00 0.00 0.00 3.18
3950 4366 7.323420 TGTAGATCTTTGTAGTTGTCCATGAG 58.677 38.462 0.00 0.00 0.00 2.90
4104 4520 4.574674 AAAGCATTAGATGAGGTGGTGA 57.425 40.909 0.00 0.00 0.00 4.02
4160 4576 4.141344 ACTTGTTAAAGAGGTGGCCAAGTA 60.141 41.667 7.24 0.00 39.23 2.24
4175 4591 2.802719 GCTGGGGATGGAACTTGTTAA 58.197 47.619 0.00 0.00 0.00 2.01
4180 4596 2.231380 ACCGCTGGGGATGGAACTT 61.231 57.895 18.53 0.00 39.97 2.66
4195 4611 2.029073 AACGTGAGACCAGCACCG 59.971 61.111 0.00 0.00 32.74 4.94


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

AutoCloner maintained by Alex Coulton.