Multiple sequence alignment - TraesCS7A01G135800

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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 TraesCS7A01G135800 chr7A 100.000 4949 0 0 1 4949 88808767 88813715 0.000000e+00 9140.0
1 TraesCS7A01G135800 chr7B 94.394 3978 139 43 1002 4945 35667308 35671235 0.000000e+00 6034.0
2 TraesCS7A01G135800 chr7B 98.540 411 6 0 591 1001 743484101 743484511 0.000000e+00 726.0
3 TraesCS7A01G135800 chr7D 93.378 3111 123 35 1874 4947 87228118 87231182 0.000000e+00 4527.0
4 TraesCS7A01G135800 chr7D 93.977 880 42 7 1002 1878 87227168 87228039 0.000000e+00 1321.0
5 TraesCS7A01G135800 chrUn 97.303 1001 27 0 1 1001 40715816 40714816 0.000000e+00 1700.0
6 TraesCS7A01G135800 chrUn 96.825 693 22 0 1 693 220123286 220122594 0.000000e+00 1158.0
7 TraesCS7A01G135800 chr3A 97.194 998 28 0 4 1001 479465867 479464870 0.000000e+00 1688.0
8 TraesCS7A01G135800 chr4B 96.922 1007 25 2 1 1001 57965898 57964892 0.000000e+00 1683.0
9 TraesCS7A01G135800 chr6B 96.903 1001 31 0 1 1001 550744949 550743949 0.000000e+00 1677.0
10 TraesCS7A01G135800 chr6A 96.603 1001 34 0 1 1001 11034766 11033766 0.000000e+00 1661.0
11 TraesCS7A01G135800 chr5B 97.018 570 17 0 1 570 658064582 658064013 0.000000e+00 959.0
12 TraesCS7A01G135800 chr5B 98.081 469 9 0 533 1001 658064013 658063545 0.000000e+00 817.0
13 TraesCS7A01G135800 chr3B 86.818 751 94 5 253 1001 737582617 737583364 0.000000e+00 833.0
14 TraesCS7A01G135800 chr3B 87.273 55 7 0 333 387 3243234 3243180 4.140000e-06 63.9
15 TraesCS7A01G135800 chr1B 87.879 429 47 4 575 1001 14125161 14125586 2.660000e-137 499.0


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 TraesCS7A01G135800 chr7A 88808767 88813715 4948 False 9140 9140 100.0000 1 4949 1 chr7A.!!$F1 4948
1 TraesCS7A01G135800 chr7B 35667308 35671235 3927 False 6034 6034 94.3940 1002 4945 1 chr7B.!!$F1 3943
2 TraesCS7A01G135800 chr7D 87227168 87231182 4014 False 2924 4527 93.6775 1002 4947 2 chr7D.!!$F1 3945
3 TraesCS7A01G135800 chrUn 40714816 40715816 1000 True 1700 1700 97.3030 1 1001 1 chrUn.!!$R1 1000
4 TraesCS7A01G135800 chrUn 220122594 220123286 692 True 1158 1158 96.8250 1 693 1 chrUn.!!$R2 692
5 TraesCS7A01G135800 chr3A 479464870 479465867 997 True 1688 1688 97.1940 4 1001 1 chr3A.!!$R1 997
6 TraesCS7A01G135800 chr4B 57964892 57965898 1006 True 1683 1683 96.9220 1 1001 1 chr4B.!!$R1 1000
7 TraesCS7A01G135800 chr6B 550743949 550744949 1000 True 1677 1677 96.9030 1 1001 1 chr6B.!!$R1 1000
8 TraesCS7A01G135800 chr6A 11033766 11034766 1000 True 1661 1661 96.6030 1 1001 1 chr6A.!!$R1 1000
9 TraesCS7A01G135800 chr5B 658063545 658064582 1037 True 888 959 97.5495 1 1001 2 chr5B.!!$R1 1000
10 TraesCS7A01G135800 chr3B 737582617 737583364 747 False 833 833 86.8180 253 1001 1 chr3B.!!$F1 748

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
634 678 0.319728 CCTCGGCCATCAAGATCGAT 59.680 55.0 2.24 0.00 0.00 3.59 F
1529 1578 1.708341 AGGTGATTTTTGTGCCTGCT 58.292 45.0 0.00 0.00 0.00 4.24 F
2115 2249 2.249413 CTCCCACCTGTGCTGCTAGG 62.249 65.0 17.89 17.89 40.01 3.02 F
3155 3291 0.670546 AACAGAATCTCCGCACCACG 60.671 55.0 0.00 0.00 43.15 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2091 2225 1.242076 CAGCACAGGTGGGAGAAAAG 58.758 55.000 1.10 0.0 0.00 2.27 R
3155 3291 1.972872 CCCATACATGAAGGGAGTGC 58.027 55.000 14.14 0.0 45.80 4.40 R
3825 3961 1.003580 TCTGCGAAGGAAAGGCTCATT 59.996 47.619 0.00 0.0 0.00 2.57 R
4492 4639 0.108615 ATTCTCGAACGGAGGCACTG 60.109 55.000 0.00 0.0 41.55 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
136 137 4.403453 GAAATATGTCAACGACCACTTGC 58.597 43.478 0.00 0.00 0.00 4.01
208 215 4.637977 TGTACTGTTGCAAGATGTGTTTGA 59.362 37.500 0.00 0.00 0.00 2.69
239 246 1.293924 CCAGGATCTTGTCGATGCAC 58.706 55.000 3.93 0.00 42.39 4.57
331 338 2.772568 TCATTCTTGTTGCCACAACG 57.227 45.000 0.00 0.00 38.03 4.10
406 413 2.334838 AGTCCGCTTTCGACATACAAC 58.665 47.619 0.00 0.00 38.10 3.32
448 455 4.067896 GAGAGTTGGAAGATTGCAAGACA 58.932 43.478 4.94 0.00 39.20 3.41
509 516 1.447643 CCAAGATGGGTAGCTCCGG 59.552 63.158 0.00 0.00 37.00 5.14
527 534 1.901464 GCGGAGGGGACAGCAAAAA 60.901 57.895 0.00 0.00 0.00 1.94
562 606 2.237392 GGCAGTTTCCAGAGATGGTAGT 59.763 50.000 0.00 0.00 0.00 2.73
601 645 0.465705 TATGCAGAAGCTCTTCGGGG 59.534 55.000 10.79 4.07 43.97 5.73
634 678 0.319728 CCTCGGCCATCAAGATCGAT 59.680 55.000 2.24 0.00 0.00 3.59
813 857 6.549364 ACCATTAGAGAGATAGTGGAGTCAAG 59.451 42.308 2.70 0.00 36.36 3.02
823 867 7.787028 AGATAGTGGAGTCAAGGAATACTTTC 58.213 38.462 0.00 0.00 37.29 2.62
934 978 4.400529 CCATGTATGGCTTTTAAACCCC 57.599 45.455 0.00 0.00 41.75 4.95
1007 1051 8.129211 AGTGTGTTTAGACTCAAAAATGCTAAC 58.871 33.333 0.00 0.00 31.71 2.34
1022 1066 9.474313 AAAAATGCTAACTGACCATTCCTTATA 57.526 29.630 0.00 0.00 0.00 0.98
1037 1081 7.445945 CATTCCTTATATCCTTTCCTCTCGTT 58.554 38.462 0.00 0.00 0.00 3.85
1280 1326 2.042843 GGAAGCGGAGGAGGAGGA 60.043 66.667 0.00 0.00 0.00 3.71
1283 1329 3.687828 AAGCGGAGGAGGAGGAGGG 62.688 68.421 0.00 0.00 0.00 4.30
1484 1533 5.352643 TCGATTCGATCTAATGCGTTCTA 57.647 39.130 4.29 0.00 0.00 2.10
1489 1538 7.061210 CGATTCGATCTAATGCGTTCTAAGATT 59.939 37.037 0.00 0.00 0.00 2.40
1493 1542 8.297426 TCGATCTAATGCGTTCTAAGATTATGT 58.703 33.333 0.00 0.00 0.00 2.29
1494 1543 8.916654 CGATCTAATGCGTTCTAAGATTATGTT 58.083 33.333 0.00 0.00 0.00 2.71
1502 1551 8.900781 TGCGTTCTAAGATTATGTTACTAGTCT 58.099 33.333 0.00 0.00 0.00 3.24
1525 1574 6.024552 TGATTTCTAGGTGATTTTTGTGCC 57.975 37.500 0.00 0.00 0.00 5.01
1529 1578 1.708341 AGGTGATTTTTGTGCCTGCT 58.292 45.000 0.00 0.00 0.00 4.24
1675 1724 5.163612 GGGGCTAATTCAGTTTCTTGCTAAG 60.164 44.000 0.00 0.00 0.00 2.18
1691 1740 3.841845 TGCTAAGTGTGGTAATGGTAGGT 59.158 43.478 0.00 0.00 0.00 3.08
1694 1743 4.482952 AAGTGTGGTAATGGTAGGTAGC 57.517 45.455 0.00 0.00 0.00 3.58
1736 1785 2.883386 GCAGGATCAGGGATGTTTGATC 59.117 50.000 6.03 6.03 45.66 2.92
1809 1859 2.897326 AGCCCCACTGGAAAAATTGTAC 59.103 45.455 0.00 0.00 35.39 2.90
1810 1860 2.897326 GCCCCACTGGAAAAATTGTACT 59.103 45.455 0.00 0.00 35.39 2.73
1811 1861 4.083565 GCCCCACTGGAAAAATTGTACTA 58.916 43.478 0.00 0.00 35.39 1.82
1840 1890 7.498570 ACACCATTTGTTATTGTTCTTTGCATT 59.501 29.630 0.00 0.00 33.09 3.56
1850 1900 3.808726 TGTTCTTTGCATTGCATTTGTCC 59.191 39.130 12.95 0.42 38.76 4.02
1991 2124 6.779860 TGCAACCTTCTTTACTCTCCTTTAT 58.220 36.000 0.00 0.00 0.00 1.40
2046 2179 7.833183 AGAGCTGGATCATCTTTAATTTGAGTT 59.167 33.333 0.00 0.00 0.00 3.01
2047 2180 9.113838 GAGCTGGATCATCTTTAATTTGAGTTA 57.886 33.333 0.00 0.00 0.00 2.24
2074 2207 7.816945 AAGTTGCAATGCTGTATAAATGTTC 57.183 32.000 6.82 0.00 0.00 3.18
2091 2225 4.046938 TGTTCAGTCACTGACTCAGTTC 57.953 45.455 7.12 6.07 42.59 3.01
2115 2249 2.249413 CTCCCACCTGTGCTGCTAGG 62.249 65.000 17.89 17.89 40.01 3.02
2118 2252 3.891817 ACCTGTGCTGCTAGGTGT 58.108 55.556 22.32 5.04 45.30 4.16
2137 2271 4.867608 GGTGTTTAACAACTGCATGTGTTT 59.132 37.500 17.38 5.55 31.84 2.83
2139 2273 6.128418 GGTGTTTAACAACTGCATGTGTTTTT 60.128 34.615 17.38 7.08 31.84 1.94
2516 2652 9.423061 GTATGCTGTTGGTTTTGATTTATTCTT 57.577 29.630 0.00 0.00 0.00 2.52
2564 2700 4.041815 AGGTTTTGGTCTCTCTTAGGTTCC 59.958 45.833 0.00 0.00 0.00 3.62
3147 3283 3.691118 TGCTATGCAACAACAGAATCTCC 59.309 43.478 0.00 0.00 34.76 3.71
3155 3291 0.670546 AACAGAATCTCCGCACCACG 60.671 55.000 0.00 0.00 43.15 4.94
3158 3294 2.740714 GAATCTCCGCACCACGCAC 61.741 63.158 0.00 0.00 42.60 5.34
3174 3310 1.811558 CGCACTCCCTTCATGTATGGG 60.812 57.143 12.15 12.15 42.84 4.00
3175 3311 1.972872 CACTCCCTTCATGTATGGGC 58.027 55.000 13.12 0.00 41.51 5.36
3178 3314 2.311542 ACTCCCTTCATGTATGGGCAAA 59.688 45.455 13.12 0.15 41.51 3.68
3231 3367 5.824624 TGAATCTTCTTTGCACCCTCATATC 59.175 40.000 0.00 0.00 0.00 1.63
3238 3374 5.425217 TCTTTGCACCCTCATATCAAGTCTA 59.575 40.000 0.00 0.00 0.00 2.59
3255 3391 3.118629 AGTCTATGATCTTCAAAGCGCCA 60.119 43.478 2.29 0.00 0.00 5.69
3410 3546 5.763088 CAGCATCATCAATGAAGATCAAGG 58.237 41.667 0.00 0.00 40.69 3.61
3466 3602 1.630369 ACATGTATCCTGCACCTGTGT 59.370 47.619 0.00 0.00 0.00 3.72
3659 3795 4.708726 AGGTGTCATTTAGCTTTGATGC 57.291 40.909 0.00 0.00 0.00 3.91
3718 3854 0.882042 ACCTGCACTTGCTGAACTCG 60.882 55.000 9.48 0.00 41.71 4.18
3937 4073 3.052082 CCTGCACACTTCTGCCCG 61.052 66.667 0.00 0.00 36.21 6.13
4006 4142 2.302157 GTGGGCAGGTAGTAACTTCAGT 59.698 50.000 0.00 0.00 0.00 3.41
4007 4143 2.976882 TGGGCAGGTAGTAACTTCAGTT 59.023 45.455 0.00 0.00 41.73 3.16
4008 4144 3.244422 TGGGCAGGTAGTAACTTCAGTTG 60.244 47.826 2.26 0.00 38.90 3.16
4009 4145 3.244457 GGGCAGGTAGTAACTTCAGTTGT 60.244 47.826 2.26 0.00 38.90 3.32
4010 4146 4.386711 GGCAGGTAGTAACTTCAGTTGTT 58.613 43.478 2.26 0.00 38.90 2.83
4011 4147 5.511888 GGGCAGGTAGTAACTTCAGTTGTTA 60.512 44.000 2.26 0.00 38.90 2.41
4012 4148 5.407691 GGCAGGTAGTAACTTCAGTTGTTAC 59.592 44.000 2.26 8.25 45.81 2.50
4020 4156 6.888430 GTAACTTCAGTTGTTACATCAGGTG 58.112 40.000 10.65 0.00 45.19 4.00
4039 4175 1.330213 TGGTGATGATAATGCGCAACG 59.670 47.619 17.11 0.00 0.00 4.10
4066 4203 4.094476 CCCTTAAGTGGGTGTTCTAGAGA 58.906 47.826 0.97 0.00 42.25 3.10
4068 4205 5.189934 CCCTTAAGTGGGTGTTCTAGAGAAT 59.810 44.000 0.97 0.00 42.25 2.40
4069 4206 6.296489 CCCTTAAGTGGGTGTTCTAGAGAATT 60.296 42.308 0.97 0.00 42.25 2.17
4070 4207 7.168905 CCTTAAGTGGGTGTTCTAGAGAATTT 58.831 38.462 0.97 0.00 36.33 1.82
4071 4208 7.665974 CCTTAAGTGGGTGTTCTAGAGAATTTT 59.334 37.037 0.97 0.00 36.33 1.82
4140 4278 5.698089 AGGCAGATGTAAATATGTGTCATCG 59.302 40.000 0.00 0.00 39.54 3.84
4141 4279 5.466728 GGCAGATGTAAATATGTGTCATCGT 59.533 40.000 0.00 0.00 39.54 3.73
4144 4282 7.254421 GCAGATGTAAATATGTGTCATCGTTCA 60.254 37.037 0.00 0.00 39.54 3.18
4154 4292 2.241722 GTCATCGTTCACCGCATTTTG 58.758 47.619 0.00 0.00 36.19 2.44
4196 4334 1.293062 ATTCAGGGATGAGTGCTGGT 58.707 50.000 0.00 0.00 0.00 4.00
4224 4362 7.283329 TGCACTATGTAGAGAGATCTGAGTAA 58.717 38.462 0.00 0.00 0.00 2.24
4262 4400 2.301870 TGTTCTCTAGCATTTCGTGGGT 59.698 45.455 0.00 0.00 0.00 4.51
4284 4422 9.045745 TGGGTGATCTGCTGATTATACAATATA 57.954 33.333 7.59 0.00 32.19 0.86
4452 4599 5.482526 TCTCCACTTGTAGGTACATGCTAAA 59.517 40.000 0.00 0.00 35.89 1.85
4469 4616 4.013050 GCTAAATATGCCTCCATTCCCTC 58.987 47.826 0.00 0.00 32.85 4.30
4502 4649 3.436700 AAAAGAAAAACAGTGCCTCCG 57.563 42.857 0.00 0.00 0.00 4.63
4730 4884 9.143631 TCTGTGATTGTTATATATCGCTCAATG 57.856 33.333 0.00 0.00 33.53 2.82
4765 4919 3.058846 CGATATATAGCGCTCGCCTACAT 60.059 47.826 16.34 1.62 43.17 2.29
4767 4921 1.244816 TATAGCGCTCGCCTACATGT 58.755 50.000 16.34 2.69 43.17 3.21
4775 4929 1.101635 TCGCCTACATGTAGCGCTCT 61.102 55.000 29.07 0.00 34.83 4.09
4802 4956 2.669781 CTGGACCACCTATACCGGTAA 58.330 52.381 20.22 7.33 34.94 2.85
4829 4983 3.181458 TGGTTTTGTGTGTAGGGACTCTC 60.181 47.826 0.00 0.00 41.75 3.20
4830 4984 3.071167 GGTTTTGTGTGTAGGGACTCTCT 59.929 47.826 0.00 0.00 41.75 3.10
4831 4985 4.058817 GTTTTGTGTGTAGGGACTCTCTG 58.941 47.826 0.00 0.00 41.75 3.35
4832 4986 1.257743 TGTGTGTAGGGACTCTCTGC 58.742 55.000 0.00 0.00 41.75 4.26
4833 4987 1.203063 TGTGTGTAGGGACTCTCTGCT 60.203 52.381 0.00 0.00 41.75 4.24
4834 4988 1.203523 GTGTGTAGGGACTCTCTGCTG 59.796 57.143 0.00 0.00 41.75 4.41
4836 4990 0.040351 TGTAGGGACTCTCTGCTGCT 59.960 55.000 0.00 0.00 41.75 4.24
4874 5038 6.460781 TCTTCTTTTTCGGCTCTGTGTATAA 58.539 36.000 0.00 0.00 0.00 0.98
4885 5054 2.092968 TCTGTGTATAAGGGCTGCTTGG 60.093 50.000 0.00 0.00 0.00 3.61
4894 5063 3.379445 GCTGCTTGGCCATGCACT 61.379 61.111 35.35 0.00 36.70 4.40
4906 5075 3.144506 GCCATGCACTGACATAAGCTAT 58.855 45.455 0.00 0.00 0.00 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 5.584551 AAGTTTTGGAGGAACATCTACCT 57.415 39.130 0.00 0.00 39.41 3.08
68 69 3.189287 GGTATTGATTGCTGGGCTAATCG 59.811 47.826 0.00 0.00 36.36 3.34
136 137 1.138859 TCCGCTCCACATAATCCACAG 59.861 52.381 0.00 0.00 0.00 3.66
142 143 3.181465 ACGAATCTTCCGCTCCACATAAT 60.181 43.478 0.00 0.00 0.00 1.28
208 215 2.761809 AGATCCTGGTCATGAAGAGCT 58.238 47.619 0.00 0.00 44.98 4.09
239 246 3.943381 TCTGGTTCTGCAATGCTATTCAG 59.057 43.478 6.82 8.09 0.00 3.02
251 258 1.427020 GCTTCGCATCTGGTTCTGC 59.573 57.895 0.00 0.00 35.02 4.26
277 284 6.233434 AGATAGCATATCCTGAATCGCAAAA 58.767 36.000 0.00 0.00 0.00 2.44
331 338 3.056107 TCGCATACCAGATAGCCCATAAC 60.056 47.826 0.00 0.00 0.00 1.89
509 516 1.250840 ATTTTTGCTGTCCCCTCCGC 61.251 55.000 0.00 0.00 0.00 5.54
514 521 0.243636 CACGGATTTTTGCTGTCCCC 59.756 55.000 0.00 0.00 0.00 4.81
634 678 0.252761 TCGCTGGATCTGAAATGCCA 59.747 50.000 0.00 0.00 0.00 4.92
813 857 5.059833 AGGAGCAATCATCGAAAGTATTCC 58.940 41.667 0.00 0.00 31.52 3.01
934 978 7.735917 TCATAGGTATACAAGAGATGTTTGGG 58.264 38.462 5.01 0.00 43.63 4.12
1007 1051 7.017056 AGAGGAAAGGATATAAGGAATGGTCAG 59.983 40.741 0.00 0.00 0.00 3.51
1022 1066 5.740290 TGTCTTTAACGAGAGGAAAGGAT 57.260 39.130 0.00 0.00 38.17 3.24
1037 1081 3.630312 GTGGAGCTGTGGTTTTGTCTTTA 59.370 43.478 0.00 0.00 0.00 1.85
1380 1429 4.421554 CCTCCTCTGCCCCTCCCA 62.422 72.222 0.00 0.00 0.00 4.37
1489 1538 9.916360 TCACCTAGAAATCAGACTAGTAACATA 57.084 33.333 0.00 0.00 35.65 2.29
1499 1548 6.803807 GCACAAAAATCACCTAGAAATCAGAC 59.196 38.462 0.00 0.00 0.00 3.51
1500 1549 6.071952 GGCACAAAAATCACCTAGAAATCAGA 60.072 38.462 0.00 0.00 0.00 3.27
1502 1551 5.774690 AGGCACAAAAATCACCTAGAAATCA 59.225 36.000 0.00 0.00 0.00 2.57
1504 1553 5.567423 GCAGGCACAAAAATCACCTAGAAAT 60.567 40.000 0.00 0.00 0.00 2.17
1513 1562 1.413445 AGCAAGCAGGCACAAAAATCA 59.587 42.857 2.37 0.00 35.83 2.57
1525 1574 1.801332 GGAGCATCACAGCAAGCAG 59.199 57.895 0.00 0.00 36.25 4.24
1675 1724 2.482490 CCGCTACCTACCATTACCACAC 60.482 54.545 0.00 0.00 0.00 3.82
1691 1740 3.361281 TCCTTCTCTTCTACACCGCTA 57.639 47.619 0.00 0.00 0.00 4.26
1694 1743 3.839293 CTGTTCCTTCTCTTCTACACCG 58.161 50.000 0.00 0.00 0.00 4.94
1736 1785 4.899502 ACAGCGGATTATTGAATAGAGGG 58.100 43.478 0.00 0.00 0.00 4.30
1742 1791 6.293407 CGGATAACAACAGCGGATTATTGAAT 60.293 38.462 0.00 0.00 0.00 2.57
1809 1859 6.913170 AGAACAATAACAAATGGTGTGCTAG 58.087 36.000 0.00 0.00 40.60 3.42
1810 1860 6.892658 AGAACAATAACAAATGGTGTGCTA 57.107 33.333 0.00 0.00 40.60 3.49
1811 1861 5.789643 AGAACAATAACAAATGGTGTGCT 57.210 34.783 0.00 0.00 40.60 4.40
1840 1890 2.299582 CCATGAAACTGGGACAAATGCA 59.700 45.455 0.00 0.00 38.70 3.96
1850 1900 2.586425 ACAGGTGTTCCATGAAACTGG 58.414 47.619 0.00 0.00 37.66 4.00
1991 2124 5.241506 CCAAAGGCTCAGTGACAAGATAAAA 59.758 40.000 0.00 0.00 0.00 1.52
1998 2131 1.476833 GGTCCAAAGGCTCAGTGACAA 60.477 52.381 0.00 0.00 0.00 3.18
2047 2180 9.874205 AACATTTATACAGCATTGCAACTTAAT 57.126 25.926 11.91 0.88 0.00 1.40
2074 2207 5.355596 AGAAAAGAACTGAGTCAGTGACTG 58.644 41.667 30.12 18.49 44.62 3.51
2091 2225 1.242076 CAGCACAGGTGGGAGAAAAG 58.758 55.000 1.10 0.00 0.00 2.27
2115 2249 6.401955 AAAACACATGCAGTTGTTAAACAC 57.598 33.333 14.35 0.00 38.88 3.32
2137 2271 9.177608 CTCTTGAGATACCCAATACATTCAAAA 57.822 33.333 0.00 0.00 0.00 2.44
2139 2273 7.770433 CACTCTTGAGATACCCAATACATTCAA 59.230 37.037 4.49 0.00 0.00 2.69
2181 2317 9.313118 GCAGATTCCTTTTAAACAAAAGAAAGA 57.687 29.630 10.62 0.00 41.12 2.52
2516 2652 8.561536 TGATAACCTAGACTGATAAAATCCCA 57.438 34.615 0.00 0.00 0.00 4.37
2564 2700 8.585018 GGTAGGTAATCATGGGGAAATTAATTG 58.415 37.037 0.39 0.00 0.00 2.32
3155 3291 1.972872 CCCATACATGAAGGGAGTGC 58.027 55.000 14.14 0.00 45.80 4.40
3158 3294 2.734755 TTGCCCATACATGAAGGGAG 57.265 50.000 20.82 5.99 45.80 4.30
3231 3367 4.260538 GGCGCTTTGAAGATCATAGACTTG 60.261 45.833 7.64 0.00 28.61 3.16
3238 3374 2.408271 TCTGGCGCTTTGAAGATCAT 57.592 45.000 7.64 0.00 0.00 2.45
3255 3391 3.624861 CCAAGACTTGCGCTTTGATATCT 59.375 43.478 9.73 0.00 0.00 1.98
3410 3546 4.557496 GCTTGACATTGAAAGGTTCAGGAC 60.557 45.833 0.00 0.00 41.38 3.85
3466 3602 7.577361 CATAGAGAATGGAAGCTTTGGCTCAA 61.577 42.308 0.00 0.00 38.75 3.02
3561 3697 1.008995 GGTTGACACGCGTTTGCAT 60.009 52.632 10.22 0.00 42.97 3.96
3571 3707 2.341846 TCAAACTGGAGGGTTGACAC 57.658 50.000 0.00 0.00 45.57 3.67
3659 3795 5.874810 TCAGAGGTAACCGAAATTTCATCAG 59.125 40.000 17.99 6.07 37.17 2.90
3718 3854 5.065988 TGGTAACTGCTTCTCTGTTTTGTTC 59.934 40.000 0.00 0.00 37.84 3.18
3825 3961 1.003580 TCTGCGAAGGAAAGGCTCATT 59.996 47.619 0.00 0.00 0.00 2.57
4013 4149 3.405831 CGCATTATCATCACCACCTGAT 58.594 45.455 0.00 0.00 40.59 2.90
4014 4150 2.837498 CGCATTATCATCACCACCTGA 58.163 47.619 0.00 0.00 0.00 3.86
4015 4151 1.265095 GCGCATTATCATCACCACCTG 59.735 52.381 0.30 0.00 0.00 4.00
4016 4152 1.134128 TGCGCATTATCATCACCACCT 60.134 47.619 5.66 0.00 0.00 4.00
4017 4153 1.308047 TGCGCATTATCATCACCACC 58.692 50.000 5.66 0.00 0.00 4.61
4018 4154 2.719798 GTTGCGCATTATCATCACCAC 58.280 47.619 12.75 0.00 0.00 4.16
4019 4155 1.330213 CGTTGCGCATTATCATCACCA 59.670 47.619 12.75 0.00 0.00 4.17
4020 4156 2.022808 CGTTGCGCATTATCATCACC 57.977 50.000 12.75 0.00 0.00 4.02
4176 4314 2.481441 ACCAGCACTCATCCCTGAATA 58.519 47.619 0.00 0.00 0.00 1.75
4196 4334 7.123397 ACTCAGATCTCTCTACATAGTGCAAAA 59.877 37.037 0.00 0.00 0.00 2.44
4284 4422 1.201647 GCAAACAGTCATGCAGCTGAT 59.798 47.619 20.43 5.31 42.12 2.90
4424 4562 6.327626 AGCATGTACCTACAAGTGGAGATAAT 59.672 38.462 0.00 0.00 39.99 1.28
4425 4563 5.661312 AGCATGTACCTACAAGTGGAGATAA 59.339 40.000 0.00 0.00 39.99 1.75
4452 4599 0.326264 GCGAGGGAATGGAGGCATAT 59.674 55.000 0.00 0.00 0.00 1.78
4483 4630 2.375146 ACGGAGGCACTGTTTTTCTTT 58.625 42.857 0.00 0.00 41.55 2.52
4484 4631 2.052782 ACGGAGGCACTGTTTTTCTT 57.947 45.000 0.00 0.00 41.55 2.52
4486 4633 1.333791 CGAACGGAGGCACTGTTTTTC 60.334 52.381 10.49 0.00 46.60 2.29
4487 4634 0.661020 CGAACGGAGGCACTGTTTTT 59.339 50.000 10.49 0.00 46.60 1.94
4488 4635 0.179067 TCGAACGGAGGCACTGTTTT 60.179 50.000 10.49 0.00 46.60 2.43
4489 4636 0.600255 CTCGAACGGAGGCACTGTTT 60.600 55.000 10.49 0.00 46.60 2.83
4491 4638 1.461091 TTCTCGAACGGAGGCACTGT 61.461 55.000 0.00 0.00 41.55 3.55
4492 4639 0.108615 ATTCTCGAACGGAGGCACTG 60.109 55.000 0.00 0.00 41.55 3.66
4494 4641 0.721718 CAATTCTCGAACGGAGGCAC 59.278 55.000 0.00 0.00 43.34 5.01
4495 4642 0.320374 ACAATTCTCGAACGGAGGCA 59.680 50.000 0.00 0.00 43.34 4.75
4496 4643 0.721718 CACAATTCTCGAACGGAGGC 59.278 55.000 0.00 0.00 43.34 4.70
4497 4644 1.993370 GACACAATTCTCGAACGGAGG 59.007 52.381 0.00 0.00 43.34 4.30
4502 4649 4.084537 ACAACGATGACACAATTCTCGAAC 60.085 41.667 0.00 0.00 33.74 3.95
4640 4789 3.249559 CAGTTTCTTGTCTGGAGAACTGC 59.750 47.826 0.00 0.00 33.15 4.40
4678 4827 0.530870 TGTGGTCGTGAAATGTCGCA 60.531 50.000 0.00 0.00 33.60 5.10
4765 4919 1.379977 AGCCCACTAGAGCGCTACA 60.380 57.895 11.50 0.00 0.00 2.74
4767 4921 2.127869 CCAGCCCACTAGAGCGCTA 61.128 63.158 11.50 0.00 0.00 4.26
4802 4956 3.201266 TCCCTACACACAAAACCAAGACT 59.799 43.478 0.00 0.00 0.00 3.24
4832 4986 1.359459 GAACGGTTTAGGGCGAGCAG 61.359 60.000 0.00 0.00 0.00 4.24
4833 4987 1.375013 GAACGGTTTAGGGCGAGCA 60.375 57.895 0.00 0.00 0.00 4.26
4834 4988 0.672711 AAGAACGGTTTAGGGCGAGC 60.673 55.000 0.00 0.00 0.00 5.03
4836 4990 0.971386 AGAAGAACGGTTTAGGGCGA 59.029 50.000 0.00 0.00 0.00 5.54
4885 5054 1.386533 AGCTTATGTCAGTGCATGGC 58.613 50.000 9.46 11.87 32.96 4.40


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

AutoCloner maintained by Alex Coulton.