Multiple sequence alignment - TraesCS3D01G152300

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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 TraesCS3D01G152300 chr3D 100.000 5315 0 0 1 5315 116398491 116403805 0.000000e+00 9816.0
1 TraesCS3D01G152300 chr3B 92.625 4556 202 58 861 5315 171589457 171593979 0.000000e+00 6429.0
2 TraesCS3D01G152300 chr3B 97.297 37 1 0 1709 1745 171590255 171590291 4.440000e-06 63.9
3 TraesCS3D01G152300 chr3A 93.881 1144 54 9 1678 2807 125484938 125486079 0.000000e+00 1711.0
4 TraesCS3D01G152300 chr3A 94.811 848 33 5 896 1738 125484095 125484936 0.000000e+00 1312.0
5 TraesCS3D01G152300 chr3A 86.499 1111 91 35 4254 5315 125487462 125488562 0.000000e+00 1166.0
6 TraesCS3D01G152300 chr3A 92.225 373 23 3 2878 3248 125486079 125486447 1.700000e-144 523.0
7 TraesCS3D01G152300 chr3A 89.333 225 20 3 3213 3435 125486449 125486671 4.050000e-71 279.0
8 TraesCS3D01G152300 chr3A 85.000 260 23 7 3944 4194 125487180 125487432 3.180000e-62 250.0
9 TraesCS3D01G152300 chr3A 91.608 143 7 3 3439 3576 125486747 125486889 5.430000e-45 193.0
10 TraesCS3D01G152300 chr2D 90.610 852 73 6 1 851 324886876 324887721 0.000000e+00 1123.0
11 TraesCS3D01G152300 chr2D 90.515 854 74 7 1 851 543503851 543504700 0.000000e+00 1122.0
12 TraesCS3D01G152300 chr6D 90.070 856 73 12 1 851 29939388 29938540 0.000000e+00 1099.0
13 TraesCS3D01G152300 chr6D 87.719 855 95 10 1 851 365332177 365333025 0.000000e+00 989.0
14 TraesCS3D01G152300 chr4A 89.413 869 84 8 1 863 276803339 276802473 0.000000e+00 1088.0
15 TraesCS3D01G152300 chr4A 87.237 854 98 10 1 851 246361263 246362108 0.000000e+00 963.0
16 TraesCS3D01G152300 chr4A 82.445 319 38 10 2208 2521 598706230 598706535 4.080000e-66 263.0
17 TraesCS3D01G152300 chr5D 88.929 822 81 9 1 816 464293854 464293037 0.000000e+00 1005.0
18 TraesCS3D01G152300 chr1B 87.967 856 94 8 1 851 401790025 401789174 0.000000e+00 1002.0
19 TraesCS3D01G152300 chr2B 87.734 856 96 9 1 851 760364885 760364034 0.000000e+00 990.0
20 TraesCS3D01G152300 chr4D 91.525 59 5 0 1259 1317 5028759 5028701 1.230000e-11 82.4
21 TraesCS3D01G152300 chr4B 91.525 59 5 0 1259 1317 7873174 7873116 1.230000e-11 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 TraesCS3D01G152300 chr3D 116398491 116403805 5314 False 9816.000000 9816 100.000000 1 5315 1 chr3D.!!$F1 5314
1 TraesCS3D01G152300 chr3B 171589457 171593979 4522 False 3246.450000 6429 94.961000 861 5315 2 chr3B.!!$F1 4454
2 TraesCS3D01G152300 chr3A 125484095 125488562 4467 False 776.285714 1711 90.479571 896 5315 7 chr3A.!!$F1 4419
3 TraesCS3D01G152300 chr2D 324886876 324887721 845 False 1123.000000 1123 90.610000 1 851 1 chr2D.!!$F1 850
4 TraesCS3D01G152300 chr2D 543503851 543504700 849 False 1122.000000 1122 90.515000 1 851 1 chr2D.!!$F2 850
5 TraesCS3D01G152300 chr6D 29938540 29939388 848 True 1099.000000 1099 90.070000 1 851 1 chr6D.!!$R1 850
6 TraesCS3D01G152300 chr6D 365332177 365333025 848 False 989.000000 989 87.719000 1 851 1 chr6D.!!$F1 850
7 TraesCS3D01G152300 chr4A 276802473 276803339 866 True 1088.000000 1088 89.413000 1 863 1 chr4A.!!$R1 862
8 TraesCS3D01G152300 chr4A 246361263 246362108 845 False 963.000000 963 87.237000 1 851 1 chr4A.!!$F1 850
9 TraesCS3D01G152300 chr5D 464293037 464293854 817 True 1005.000000 1005 88.929000 1 816 1 chr5D.!!$R1 815
10 TraesCS3D01G152300 chr1B 401789174 401790025 851 True 1002.000000 1002 87.967000 1 851 1 chr1B.!!$R1 850
11 TraesCS3D01G152300 chr2B 760364034 760364885 851 True 990.000000 990 87.734000 1 851 1 chr2B.!!$R1 850

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
470 480 0.108804 GAATGCGGTCGACTCTTCCA 60.109 55.000 16.46 6.11 0.00 3.53 F
1049 1075 0.105039 AGAACCCGATCGGAGCAATC 59.895 55.000 35.42 22.22 37.50 2.67 F
1323 1349 1.134401 CCCTCATGATGCTGGTACGTT 60.134 52.381 0.00 0.00 0.00 3.99 F
1352 1378 1.373497 CCGCCTATGATCTGTCGCC 60.373 63.158 0.00 0.00 0.00 5.54 F
1667 1697 1.937191 TTGCTGGATTTTCCCTTCCC 58.063 50.000 0.00 0.00 35.03 3.97 F
1799 1891 2.770164 TGCCTTCTCTTAGTTGGAGC 57.230 50.000 0.00 0.00 0.00 4.70 F
3682 3910 0.665298 GGATCCGGAAGCAGAAATGC 59.335 55.000 9.01 0.00 0.00 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1667 1697 1.710013 AATGTGACACGAGCTTACCG 58.290 50.000 0.22 0.0 0.00 4.02 R
2553 2652 0.032130 GACCAGAGTCAGAACACGCA 59.968 55.000 0.00 0.0 42.99 5.24 R
3271 3420 2.778299 TCCACTGGTGTATTTGTGCTC 58.222 47.619 0.00 0.0 0.00 4.26 R
3362 3511 5.608449 AGGTCCAACTGTACAAGAAAGTAC 58.392 41.667 0.00 0.0 43.58 2.73 R
3555 3781 1.006922 GCACTTTCAACAGCCCTGC 60.007 57.895 0.00 0.0 0.00 4.85 R
3708 3936 0.464036 ACGGCCACACGATCATACAT 59.536 50.000 2.24 0.0 37.61 2.29 R
5208 5548 0.106519 AGAGCAGAGAGAGAGGGAGC 60.107 60.000 0.00 0.0 0.00 4.70 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
132 136 7.277098 TCGAGGCAAAACATAACTAACATCTAC 59.723 37.037 0.00 0.00 0.00 2.59
312 318 1.107538 AATCCGCCGGAATCTCGAGA 61.108 55.000 19.19 19.19 34.34 4.04
322 328 4.238514 CGGAATCTCGAGAAAACTCAAGT 58.761 43.478 20.91 0.00 0.00 3.16
397 406 3.011144 TGGGATGGAGCATTACCTTCAAA 59.989 43.478 0.00 0.00 34.58 2.69
470 480 0.108804 GAATGCGGTCGACTCTTCCA 60.109 55.000 16.46 6.11 0.00 3.53
475 485 2.637383 GGTCGACTCTTCCACCGCT 61.637 63.158 16.46 0.00 0.00 5.52
518 529 4.437930 GGTTTCTCCTCAATCGAATGCAAG 60.438 45.833 0.00 0.00 0.00 4.01
578 589 1.134907 GGGAGTAAATGAACCGCGAGA 60.135 52.381 8.23 0.00 0.00 4.04
579 590 2.483188 GGGAGTAAATGAACCGCGAGAT 60.483 50.000 8.23 0.00 0.00 2.75
695 710 2.036089 ACCGTTGACCTCAGAGAGAAAC 59.964 50.000 0.00 0.00 0.00 2.78
744 764 2.288825 CCACACACACGACTTGTCCTAT 60.289 50.000 0.00 0.00 35.67 2.57
753 773 2.677902 CGACTTGTCCTATGTGGCACAT 60.678 50.000 33.18 33.18 44.52 3.21
762 782 5.590259 GTCCTATGTGGCACATAAAATCAGT 59.410 40.000 33.04 14.44 44.52 3.41
808 828 0.860618 GGCACTGTACGACGATCGAC 60.861 60.000 24.34 15.51 43.74 4.20
851 872 0.669318 CTCACACGTGTGGGCGTTAT 60.669 55.000 39.88 6.26 45.65 1.89
852 873 0.668096 TCACACGTGTGGGCGTTATC 60.668 55.000 39.88 0.00 45.65 1.75
870 892 6.419771 CGTTATCTTTTCGATTCCCTTTAGC 58.580 40.000 0.00 0.00 33.48 3.09
872 894 3.934068 TCTTTTCGATTCCCTTTAGCGT 58.066 40.909 0.00 0.00 0.00 5.07
894 917 1.016653 GGAACTGCTCGAGTTGCTCC 61.017 60.000 15.13 12.87 46.70 4.70
913 939 1.153086 GCGGATGCTCTCACCCAAT 60.153 57.895 0.00 0.00 38.39 3.16
973 999 2.106683 CGGACGGCCCTGATTTCAC 61.107 63.158 0.00 0.00 0.00 3.18
975 1001 2.746277 ACGGCCCTGATTTCACGC 60.746 61.111 0.00 0.00 0.00 5.34
1049 1075 0.105039 AGAACCCGATCGGAGCAATC 59.895 55.000 35.42 22.22 37.50 2.67
1151 1177 1.437160 CGAAGGCCTCTGCTCTCTC 59.563 63.158 5.23 0.00 37.74 3.20
1323 1349 1.134401 CCCTCATGATGCTGGTACGTT 60.134 52.381 0.00 0.00 0.00 3.99
1352 1378 1.373497 CCGCCTATGATCTGTCGCC 60.373 63.158 0.00 0.00 0.00 5.54
1411 1437 3.751246 CCATGTTGGCTGCCCGTG 61.751 66.667 17.53 12.75 0.00 4.94
1412 1438 4.424566 CATGTTGGCTGCCCGTGC 62.425 66.667 17.53 4.13 38.26 5.34
1413 1439 4.666253 ATGTTGGCTGCCCGTGCT 62.666 61.111 17.53 0.00 38.71 4.40
1568 1594 8.044060 TCAGACATTTAGGATTAACAAAGCTG 57.956 34.615 0.00 0.00 0.00 4.24
1569 1595 6.749118 CAGACATTTAGGATTAACAAAGCTGC 59.251 38.462 0.00 0.00 0.00 5.25
1647 1677 9.349713 ACTTTAGTTAATCCAACACTGATTTCA 57.650 29.630 0.00 0.00 39.81 2.69
1667 1697 1.937191 TTGCTGGATTTTCCCTTCCC 58.063 50.000 0.00 0.00 35.03 3.97
1777 1869 5.243954 TGCTAGTGAACTACTGAACTGATGT 59.756 40.000 0.00 0.00 40.65 3.06
1799 1891 2.770164 TGCCTTCTCTTAGTTGGAGC 57.230 50.000 0.00 0.00 0.00 4.70
1847 1941 5.355596 TGCGAAATTTGTTCTGATTTGGTT 58.644 33.333 0.00 0.00 0.00 3.67
2059 2153 3.563808 TGCAGTCACTTATTGTTTTCGCT 59.436 39.130 0.00 0.00 0.00 4.93
2154 2248 7.775053 TTTAACTCATGGGCTTTCTGTTTAT 57.225 32.000 0.00 0.00 0.00 1.40
2185 2284 4.173594 TCCTCCCTATATCGGTGTCTCTA 58.826 47.826 0.00 0.00 0.00 2.43
2553 2652 6.375455 CAGCTATCAAAACCCAACAGATAACT 59.625 38.462 0.00 0.00 0.00 2.24
2565 2664 3.318017 ACAGATAACTGCGTGTTCTGAC 58.682 45.455 18.67 5.03 46.95 3.51
2567 2666 3.610242 CAGATAACTGCGTGTTCTGACTC 59.390 47.826 11.90 1.20 39.89 3.36
3088 3198 5.047802 GTCCTCTTGCATTTTCAGGAATTGA 60.048 40.000 0.00 0.00 34.98 2.57
3121 3231 4.738252 GTCCTCATTTTTGTCGTTTTGTCC 59.262 41.667 0.00 0.00 0.00 4.02
3271 3420 8.760980 TTATTATTTTAGATTGGAGTGGTGGG 57.239 34.615 0.00 0.00 0.00 4.61
3362 3511 5.051641 GCCTCGACTATGTCTTTTGATAACG 60.052 44.000 0.00 0.00 0.00 3.18
3437 3587 7.938140 AAGAGCACATACCTAAAAATGCTAA 57.062 32.000 0.00 0.00 43.20 3.09
3510 3731 5.750547 CACAGCATCATCTCTGTATAAACGT 59.249 40.000 0.00 0.00 41.19 3.99
3555 3781 3.062763 CAATGACTGGCTATTAGCTCCG 58.937 50.000 15.02 6.72 41.99 4.63
3577 3803 1.142870 AGGGCTGTTGAAAGTGCTGTA 59.857 47.619 0.00 0.00 0.00 2.74
3579 3805 1.946768 GGCTGTTGAAAGTGCTGTACA 59.053 47.619 0.00 0.00 0.00 2.90
3615 3841 5.674525 CAGCAGATAAGGGTGAGTAATCAA 58.325 41.667 0.00 0.00 35.87 2.57
3642 3869 4.814771 CCAAACCTTTTGTCGAGAGTAAGT 59.185 41.667 0.00 0.00 0.00 2.24
3676 3904 1.661341 CTTCAAGGATCCGGAAGCAG 58.339 55.000 26.12 12.04 32.54 4.24
3682 3910 0.665298 GGATCCGGAAGCAGAAATGC 59.335 55.000 9.01 0.00 0.00 3.56
3717 3945 5.354054 CAGCTAAACTGGCATGTATGATC 57.646 43.478 0.00 0.00 43.19 2.92
3764 3992 2.430248 ATCATGGCATGCAGTTCTCA 57.570 45.000 22.56 7.31 0.00 3.27
3775 4003 1.808945 GCAGTTCTCATGTGTCCTTGG 59.191 52.381 0.00 0.00 0.00 3.61
3781 4009 1.808945 CTCATGTGTCCTTGGAACTGC 59.191 52.381 0.00 0.00 0.00 4.40
3798 4030 6.716628 TGGAACTGCTTCTTCTTGTAATCAAT 59.283 34.615 0.00 0.00 32.82 2.57
3811 4043 0.815734 AATCAATGTCCAGCAGCAGC 59.184 50.000 0.00 0.00 42.56 5.25
3854 4086 5.660864 TCTCAGTTTGAACCAAAGGGAAAAT 59.339 36.000 0.00 0.00 33.82 1.82
3888 4120 6.172630 TGCTATATTTGAACACAGAGCTTCA 58.827 36.000 0.00 0.00 0.00 3.02
3889 4121 6.825213 TGCTATATTTGAACACAGAGCTTCAT 59.175 34.615 0.00 0.00 0.00 2.57
3890 4122 7.337689 TGCTATATTTGAACACAGAGCTTCATT 59.662 33.333 0.00 0.00 0.00 2.57
3891 4123 7.642978 GCTATATTTGAACACAGAGCTTCATTG 59.357 37.037 0.00 0.00 0.00 2.82
3892 4124 4.572985 TTTGAACACAGAGCTTCATTGG 57.427 40.909 0.00 0.00 0.00 3.16
3903 4135 3.028850 AGCTTCATTGGATTGGACCATG 58.971 45.455 0.00 0.00 39.82 3.66
3956 4196 0.241749 TGTGTAGCGGTGAACGTAGG 59.758 55.000 0.00 0.00 46.52 3.18
3960 4200 2.531927 TAGCGGTGAACGTAGGTGCG 62.532 60.000 0.00 0.00 46.52 5.34
3961 4201 2.807895 CGGTGAACGTAGGTGCGG 60.808 66.667 0.00 0.00 37.93 5.69
3966 4206 3.243816 AACGTAGGTGCGGGGGTT 61.244 61.111 0.00 0.00 35.98 4.11
3982 4222 3.451540 GGGGGTTTTTGGACACTGTAAAA 59.548 43.478 0.00 0.00 0.00 1.52
3994 4235 5.476945 GGACACTGTAAAATCTCCAACCAAT 59.523 40.000 0.00 0.00 0.00 3.16
3995 4236 6.657541 GGACACTGTAAAATCTCCAACCAATA 59.342 38.462 0.00 0.00 0.00 1.90
4001 4242 9.410556 CTGTAAAATCTCCAACCAATAAAACAG 57.589 33.333 0.00 0.00 0.00 3.16
4005 4246 4.211125 TCTCCAACCAATAAAACAGTGCA 58.789 39.130 0.00 0.00 0.00 4.57
4043 4284 3.508845 TCCTGTTCTTTCCCCTTTCAG 57.491 47.619 0.00 0.00 0.00 3.02
4074 4322 8.190326 TGACAGAATTACCTAGTTTCAGAAGA 57.810 34.615 0.00 0.00 0.00 2.87
4075 4323 8.647796 TGACAGAATTACCTAGTTTCAGAAGAA 58.352 33.333 0.00 0.00 0.00 2.52
4076 4324 9.660180 GACAGAATTACCTAGTTTCAGAAGAAT 57.340 33.333 0.00 0.00 32.89 2.40
4153 4409 1.068474 CTTTCGCTCGACGGATTGTT 58.932 50.000 0.00 0.00 43.89 2.83
4157 4413 1.011968 CGCTCGACGGATTGTTTCCA 61.012 55.000 0.00 0.00 45.78 3.53
4194 4450 1.857217 GTGCGACACTGAGCTATGATG 59.143 52.381 0.00 0.00 0.00 3.07
4201 4460 5.807520 CGACACTGAGCTATGATGTTACTTT 59.192 40.000 0.00 0.00 0.00 2.66
4214 4473 0.037590 TTACTTTGGCGCCTGATGGT 59.962 50.000 29.70 19.74 35.27 3.55
4215 4474 0.392461 TACTTTGGCGCCTGATGGTC 60.392 55.000 29.70 0.00 35.27 4.02
4231 4490 2.161855 TGGTCATTGTCAACATGCTCC 58.838 47.619 0.00 0.00 0.00 4.70
4250 4509 1.097547 CGGCGCCTGAAATTGGAGAT 61.098 55.000 26.68 0.00 0.00 2.75
4257 4516 3.064545 GCCTGAAATTGGAGATCTGTTCG 59.935 47.826 0.00 0.00 0.00 3.95
4271 4531 2.282958 TTCGTCTCCACCGCTCCT 60.283 61.111 0.00 0.00 0.00 3.69
4299 4559 3.319122 GCATGTATTCCACTCATTTCCCC 59.681 47.826 0.00 0.00 0.00 4.81
4345 4607 4.505313 TCAAGCTCCGTATAGTGCATAG 57.495 45.455 0.00 0.00 0.00 2.23
4514 4781 7.119699 CCATTTTGACAGTATCTTTGCTCTGTA 59.880 37.037 0.00 0.00 40.53 2.74
4524 4791 3.753272 TCTTTGCTCTGTACTTGCATTCC 59.247 43.478 8.35 0.00 36.55 3.01
4526 4793 2.426522 TGCTCTGTACTTGCATTCCAC 58.573 47.619 0.00 0.00 0.00 4.02
4535 4802 0.537828 TTGCATTCCACAGCTGCAGA 60.538 50.000 20.43 8.03 45.72 4.26
4548 4830 3.077359 AGCTGCAGACATTTCCACTTAC 58.923 45.455 20.43 0.00 0.00 2.34
4554 4836 4.563580 GCAGACATTTCCACTTACTCCTGA 60.564 45.833 0.00 0.00 0.00 3.86
4582 4864 0.987294 TCCCCCTCTTGCAGAAGAAG 59.013 55.000 0.00 0.00 37.77 2.85
4586 4868 1.451067 CCTCTTGCAGAAGAAGCTGG 58.549 55.000 0.00 0.00 37.77 4.85
4588 4870 2.355920 CCTCTTGCAGAAGAAGCTGGAT 60.356 50.000 0.00 0.00 37.77 3.41
4597 4884 0.466124 AGAAGCTGGATACCCTTCGC 59.534 55.000 0.00 0.00 44.22 4.70
4600 4887 1.069935 GCTGGATACCCTTCGCTCC 59.930 63.158 0.00 0.00 0.00 4.70
4612 4899 4.767255 CGCTCCTGTCCACTGGCC 62.767 72.222 0.00 0.00 35.24 5.36
5199 5539 1.168714 CCCTTCAACTGGTAAGCTGC 58.831 55.000 0.00 0.00 0.00 5.25
5201 5541 1.808945 CCTTCAACTGGTAAGCTGCTG 59.191 52.381 1.35 0.00 0.00 4.41
5202 5542 2.498167 CTTCAACTGGTAAGCTGCTGT 58.502 47.619 1.35 0.00 0.00 4.40
5203 5543 2.638480 TCAACTGGTAAGCTGCTGTT 57.362 45.000 1.35 0.00 0.00 3.16
5205 5545 1.537202 CAACTGGTAAGCTGCTGTTCC 59.463 52.381 1.35 6.99 0.00 3.62
5208 5548 1.745489 GGTAAGCTGCTGTTCCCCG 60.745 63.158 1.35 0.00 0.00 5.73
5229 5576 1.492176 CTCCCTCTCTCTCTGCTCTCT 59.508 57.143 0.00 0.00 0.00 3.10
5231 5578 1.492176 CCCTCTCTCTCTGCTCTCTCT 59.508 57.143 0.00 0.00 0.00 3.10
5233 5580 2.486191 CCTCTCTCTCTGCTCTCTCTCC 60.486 59.091 0.00 0.00 0.00 3.71
5234 5581 1.490490 TCTCTCTCTGCTCTCTCTCCC 59.510 57.143 0.00 0.00 0.00 4.30
5239 5594 3.071206 TGCTCTCTCTCCCGGTGC 61.071 66.667 0.00 0.00 0.00 5.01
5272 5627 3.727970 GCGGGTCTGTCGATTTGAATTTC 60.728 47.826 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 84 2.158755 GCTATGGCCATCAGTGTAGGTT 60.159 50.000 24.80 0.00 0.00 3.50
82 85 1.417890 GCTATGGCCATCAGTGTAGGT 59.582 52.381 24.80 0.00 0.00 3.08
132 136 1.548986 GATTGAGCGGGCGATTTTTG 58.451 50.000 0.00 0.00 0.00 2.44
312 318 5.930837 TGGTCAATTTCCACTTGAGTTTT 57.069 34.783 0.00 0.00 33.49 2.43
322 328 3.496692 CCTCTCACTGTGGTCAATTTCCA 60.497 47.826 8.11 0.00 0.00 3.53
338 344 2.731571 CGATTTCCGCCCCCTCTCA 61.732 63.158 0.00 0.00 0.00 3.27
475 485 3.706373 GAGGAGAAGGTGGCGGCA 61.706 66.667 7.97 7.97 0.00 5.69
518 529 2.618045 CCAAACCCACTATCCAGACCAC 60.618 54.545 0.00 0.00 0.00 4.16
665 680 2.604174 GGTCAACGGTTGCCAGTCG 61.604 63.158 21.52 0.00 0.00 4.18
744 764 6.040278 TGAAAAGACTGATTTTATGTGCCACA 59.960 34.615 0.00 0.00 32.62 4.17
753 773 7.523293 TCTTGGCATGAAAAGACTGATTTTA 57.477 32.000 0.00 0.00 32.62 1.52
762 782 4.221041 TGCATGAATCTTGGCATGAAAAGA 59.779 37.500 7.20 11.55 43.43 2.52
796 816 0.587985 CACATGCGTCGATCGTCGTA 60.588 55.000 29.51 27.00 41.35 3.43
851 872 3.682858 CACGCTAAAGGGAATCGAAAAGA 59.317 43.478 0.52 0.00 0.00 2.52
852 873 3.181510 CCACGCTAAAGGGAATCGAAAAG 60.182 47.826 0.52 0.00 0.00 2.27
870 892 2.125912 CTCGAGCAGTTCCCCACG 60.126 66.667 0.00 0.00 0.00 4.94
872 894 1.371183 CAACTCGAGCAGTTCCCCA 59.629 57.895 13.61 0.00 44.14 4.96
913 939 2.057922 AGGCTGGGAAGAAGTCAAGAA 58.942 47.619 0.00 0.00 0.00 2.52
965 991 0.874390 GGAGTGCTTGCGTGAAATCA 59.126 50.000 0.00 0.00 0.00 2.57
973 999 2.031012 TGGACAGGAGTGCTTGCG 59.969 61.111 0.00 0.00 36.96 4.85
975 1001 2.320587 GCGTGGACAGGAGTGCTTG 61.321 63.158 0.00 0.00 36.96 4.01
1049 1075 4.838152 CGGGTGAGGGCGTCCATG 62.838 72.222 9.71 0.00 34.83 3.66
1100 1126 1.979693 GTCGTCCTCCTGCCACTCT 60.980 63.158 0.00 0.00 0.00 3.24
1151 1177 0.833949 GCTTTACCTGGAGAGGGGAG 59.166 60.000 0.00 0.00 44.84 4.30
1323 1349 3.552132 TCATAGGCGGAAATTACAGCA 57.448 42.857 0.00 0.00 33.04 4.41
1556 1582 5.772825 TTCTGACTTGCAGCTTTGTTAAT 57.227 34.783 0.00 0.00 44.52 1.40
1568 1594 6.902341 TGTGATACATTTCTTTCTGACTTGC 58.098 36.000 0.00 0.00 0.00 4.01
1569 1595 7.484007 GCATGTGATACATTTCTTTCTGACTTG 59.516 37.037 0.00 0.00 36.53 3.16
1632 1660 4.508461 CAGCAATGAAATCAGTGTTGGA 57.492 40.909 16.57 0.00 45.08 3.53
1647 1677 2.470990 GGGAAGGGAAAATCCAGCAAT 58.529 47.619 0.00 0.00 38.64 3.56
1667 1697 1.710013 AATGTGACACGAGCTTACCG 58.290 50.000 0.22 0.00 0.00 4.02
1777 1869 3.821033 GCTCCAACTAAGAGAAGGCAAAA 59.179 43.478 0.00 0.00 32.86 2.44
1799 1891 6.790285 AAGCATTGCATTTGAAACCTTAAG 57.210 33.333 11.91 0.00 0.00 1.85
1890 1984 4.757149 GCCTAATGATCCAATGTCTACACC 59.243 45.833 0.00 0.00 0.00 4.16
2059 2153 7.624549 ACAAGAGAGCAAATTTGATAGGTCTA 58.375 34.615 22.31 0.00 38.77 2.59
2154 2248 7.676893 ACACCGATATAGGGAGGATTACAAATA 59.323 37.037 6.82 0.00 35.02 1.40
2553 2652 0.032130 GACCAGAGTCAGAACACGCA 59.968 55.000 0.00 0.00 42.99 5.24
2565 2664 4.397481 TGAATCTGCACATAGACCAGAG 57.603 45.455 0.00 0.00 38.82 3.35
2567 2666 4.510711 GTCATGAATCTGCACATAGACCAG 59.489 45.833 0.00 0.00 0.00 4.00
3121 3231 8.567285 AATAACTTGGGTGAAGAGATACAAAG 57.433 34.615 0.00 0.00 35.42 2.77
3271 3420 2.778299 TCCACTGGTGTATTTGTGCTC 58.222 47.619 0.00 0.00 0.00 4.26
3362 3511 5.608449 AGGTCCAACTGTACAAGAAAGTAC 58.392 41.667 0.00 0.00 43.58 2.73
3408 3558 7.698130 GCATTTTTAGGTATGTGCTCTTTACAG 59.302 37.037 0.00 0.00 0.00 2.74
3488 3709 6.643845 CAACGTTTATACAGAGATGATGCTG 58.356 40.000 0.00 0.00 38.10 4.41
3555 3781 1.006922 GCACTTTCAACAGCCCTGC 60.007 57.895 0.00 0.00 0.00 4.85
3577 3803 2.567497 GCTGCCTGCACCATTGTGT 61.567 57.895 0.00 0.00 44.65 3.72
3587 3813 1.099879 CACCCTTATCTGCTGCCTGC 61.100 60.000 0.00 0.00 43.25 4.85
3599 3825 6.569127 TTGGCTATTGATTACTCACCCTTA 57.431 37.500 0.00 0.00 0.00 2.69
3603 3829 5.193679 AGGTTTGGCTATTGATTACTCACC 58.806 41.667 0.00 0.00 0.00 4.02
3615 3841 4.003648 CTCTCGACAAAAGGTTTGGCTAT 58.996 43.478 5.12 0.00 0.00 2.97
3642 3869 8.639761 GGATCCTTGAAGCACTACTTATTAGTA 58.360 37.037 3.84 0.00 39.18 1.82
3654 3881 1.373570 CTTCCGGATCCTTGAAGCAC 58.626 55.000 21.18 0.00 30.19 4.40
3659 3886 1.275666 TTCTGCTTCCGGATCCTTGA 58.724 50.000 4.15 3.28 0.00 3.02
3674 3902 3.820467 TGGTAACTCCAGTTGCATTTCTG 59.180 43.478 9.40 0.00 41.93 3.02
3708 3936 0.464036 ACGGCCACACGATCATACAT 59.536 50.000 2.24 0.00 37.61 2.29
3737 3965 1.134936 TGCATGCCATGATTCAGCAAC 60.135 47.619 16.68 2.23 40.46 4.17
3764 3992 2.107204 AGAAGCAGTTCCAAGGACACAT 59.893 45.455 0.00 0.00 32.48 3.21
3775 4003 7.588512 ACATTGATTACAAGAAGAAGCAGTTC 58.411 34.615 0.00 0.00 39.46 3.01
3781 4009 6.149973 TGCTGGACATTGATTACAAGAAGAAG 59.850 38.462 0.00 0.00 39.46 2.85
3798 4030 2.770132 CTACACGCTGCTGCTGGACA 62.770 60.000 14.03 1.51 36.97 4.02
3811 4043 6.879993 ACTGAGATACCATATCCTACTACACG 59.120 42.308 0.00 0.00 0.00 4.49
3815 4047 9.877222 TTCAAACTGAGATACCATATCCTACTA 57.123 33.333 0.00 0.00 0.00 1.82
3888 4120 3.376636 TCATTGCATGGTCCAATCCAAT 58.623 40.909 0.00 2.53 41.09 3.16
3889 4121 2.817665 TCATTGCATGGTCCAATCCAA 58.182 42.857 0.00 0.00 41.09 3.53
3890 4122 2.528673 TCATTGCATGGTCCAATCCA 57.471 45.000 0.00 0.00 42.01 3.41
3891 4123 3.380479 CATCATTGCATGGTCCAATCC 57.620 47.619 0.00 0.00 30.90 3.01
3919 4151 8.547894 CGCTACACATTTTTAAGTGCTATATCA 58.452 33.333 0.00 0.00 39.30 2.15
3925 4157 3.818773 ACCGCTACACATTTTTAAGTGCT 59.181 39.130 0.00 0.00 39.30 4.40
3926 4158 3.911964 CACCGCTACACATTTTTAAGTGC 59.088 43.478 0.00 0.00 39.30 4.40
3935 4167 2.602878 CTACGTTCACCGCTACACATT 58.397 47.619 0.00 0.00 41.42 2.71
3956 4196 2.128507 TGTCCAAAAACCCCCGCAC 61.129 57.895 0.00 0.00 0.00 5.34
3960 4200 2.368311 TACAGTGTCCAAAAACCCCC 57.632 50.000 0.00 0.00 0.00 5.40
3961 4201 4.739587 TTTTACAGTGTCCAAAAACCCC 57.260 40.909 0.00 0.00 0.00 4.95
3966 4206 6.183360 GGTTGGAGATTTTACAGTGTCCAAAA 60.183 38.462 10.86 8.69 45.69 2.44
3982 4222 4.832266 TGCACTGTTTTATTGGTTGGAGAT 59.168 37.500 0.00 0.00 0.00 2.75
3994 4235 7.161404 AGAGATACAATCAGTGCACTGTTTTA 58.839 34.615 38.41 27.89 44.12 1.52
3995 4236 6.000219 AGAGATACAATCAGTGCACTGTTTT 59.000 36.000 38.41 30.07 44.12 2.43
4001 4242 6.989169 AGGAAATAGAGATACAATCAGTGCAC 59.011 38.462 9.40 9.40 0.00 4.57
4005 4246 8.986991 AGAACAGGAAATAGAGATACAATCAGT 58.013 33.333 0.00 0.00 0.00 3.41
4043 4284 7.656137 TGAAACTAGGTAATTCTGTCAGTTGAC 59.344 37.037 5.33 5.33 44.97 3.18
4074 4322 7.582719 TGGTCAGGTAATTCTGCCTTATTATT 58.417 34.615 0.00 0.00 35.03 1.40
4075 4323 7.149202 TGGTCAGGTAATTCTGCCTTATTAT 57.851 36.000 0.00 0.00 35.03 1.28
4076 4324 6.569127 TGGTCAGGTAATTCTGCCTTATTA 57.431 37.500 0.00 0.00 35.03 0.98
4077 4325 5.450818 TGGTCAGGTAATTCTGCCTTATT 57.549 39.130 0.00 0.00 35.03 1.40
4078 4326 5.380043 CATGGTCAGGTAATTCTGCCTTAT 58.620 41.667 0.00 0.00 35.03 1.73
4079 4327 4.780815 CATGGTCAGGTAATTCTGCCTTA 58.219 43.478 0.00 0.00 35.03 2.69
4174 4430 1.857217 CATCATAGCTCAGTGTCGCAC 59.143 52.381 0.00 2.28 34.10 5.34
4194 4450 0.451783 CCATCAGGCGCCAAAGTAAC 59.548 55.000 31.54 0.00 0.00 2.50
4201 4460 1.750018 CAATGACCATCAGGCGCCA 60.750 57.895 31.54 9.64 39.06 5.69
4214 4473 1.452110 CCGGAGCATGTTGACAATGA 58.548 50.000 0.00 0.00 0.00 2.57
4215 4474 0.179156 GCCGGAGCATGTTGACAATG 60.179 55.000 5.05 0.00 39.53 2.82
4231 4490 1.097547 ATCTCCAATTTCAGGCGCCG 61.098 55.000 23.20 16.49 0.00 6.46
4239 4498 5.710613 GAGACGAACAGATCTCCAATTTC 57.289 43.478 0.00 0.00 36.18 2.17
4250 4509 1.863662 GAGCGGTGGAGACGAACAGA 61.864 60.000 0.00 0.00 0.00 3.41
4257 4516 3.655810 CTGCAGGAGCGGTGGAGAC 62.656 68.421 5.57 0.00 46.23 3.36
4299 4559 5.097529 CCGTCCATCATTCATCAACAAAAG 58.902 41.667 0.00 0.00 0.00 2.27
4345 4607 0.588252 AGTGTTGCTCGTGTTGCATC 59.412 50.000 0.00 0.00 40.34 3.91
4350 4612 5.034152 CACAAATAAAGTGTTGCTCGTGTT 58.966 37.500 0.00 0.00 32.44 3.32
4359 4621 4.610945 GTGAGCTGCACAAATAAAGTGTT 58.389 39.130 0.25 0.00 46.91 3.32
4461 4728 7.451255 ACAGGTAAACAAATGGAATCTGATTCA 59.549 33.333 26.60 15.70 41.03 2.57
4499 4766 6.428385 AATGCAAGTACAGAGCAAAGATAC 57.572 37.500 10.27 0.00 42.15 2.24
4514 4781 0.824595 TGCAGCTGTGGAATGCAAGT 60.825 50.000 16.64 0.00 46.31 3.16
4524 4791 1.068748 GTGGAAATGTCTGCAGCTGTG 60.069 52.381 16.64 9.01 0.00 3.66
4526 4793 1.531423 AGTGGAAATGTCTGCAGCTG 58.469 50.000 10.11 10.11 0.00 4.24
4535 4802 5.568620 AGTTCAGGAGTAAGTGGAAATGT 57.431 39.130 0.00 0.00 0.00 2.71
4548 4830 2.310052 AGGGGGATGAAAAGTTCAGGAG 59.690 50.000 0.00 0.00 43.98 3.69
4554 4836 2.158325 TGCAAGAGGGGGATGAAAAGTT 60.158 45.455 0.00 0.00 0.00 2.66
4582 4864 1.069935 GGAGCGAAGGGTATCCAGC 59.930 63.158 0.00 0.00 34.83 4.85
4586 4868 0.389757 GGACAGGAGCGAAGGGTATC 59.610 60.000 0.00 0.00 0.00 2.24
4588 4870 1.077805 TGGACAGGAGCGAAGGGTA 59.922 57.895 0.00 0.00 0.00 3.69
4597 4884 2.667418 CAGGCCAGTGGACAGGAG 59.333 66.667 19.84 0.00 29.21 3.69
4902 5236 4.434685 GCTTCCTCAGCTCCATCG 57.565 61.111 0.00 0.00 46.27 3.84
5199 5539 2.685380 AGAGGGAGCGGGGAACAG 60.685 66.667 0.00 0.00 0.00 3.16
5201 5541 2.364448 AGAGAGGGAGCGGGGAAC 60.364 66.667 0.00 0.00 0.00 3.62
5202 5542 2.042843 GAGAGAGGGAGCGGGGAA 60.043 66.667 0.00 0.00 0.00 3.97
5203 5543 3.024356 AGAGAGAGGGAGCGGGGA 61.024 66.667 0.00 0.00 0.00 4.81
5205 5545 1.827789 CAGAGAGAGAGGGAGCGGG 60.828 68.421 0.00 0.00 0.00 6.13
5208 5548 0.106519 AGAGCAGAGAGAGAGGGAGC 60.107 60.000 0.00 0.00 0.00 4.70
5212 5559 2.486191 GGAGAGAGAGCAGAGAGAGAGG 60.486 59.091 0.00 0.00 0.00 3.69
5229 5576 4.758251 CACGCATGCACCGGGAGA 62.758 66.667 19.57 0.00 0.00 3.71
5286 5641 1.732259 CGAAGCGCAGTCCAATTAAGT 59.268 47.619 11.47 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.