Multiple sequence alignment - TraesCS2A01G017200

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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 TraesCS2A01G017200 chr2A 100.000 6591 0 0 1 6591 7929542 7922952 0.000000e+00 12172.0
1 TraesCS2A01G017200 chr2A 93.043 115 8 0 3628 3742 8175943 8176057 1.140000e-37 169.0
2 TraesCS2A01G017200 chr2A 91.304 115 10 0 3628 3742 8349920 8350034 2.460000e-34 158.0
3 TraesCS2A01G017200 chr2A 95.918 49 2 0 703 751 8174028 8174076 5.480000e-11 80.5
4 TraesCS2A01G017200 chr3D 97.998 4246 74 3 1742 5977 563868193 563863949 0.000000e+00 7360.0
5 TraesCS2A01G017200 chr3D 95.620 1644 49 9 105 1744 563869867 563868243 0.000000e+00 2615.0
6 TraesCS2A01G017200 chr3D 97.281 662 18 0 5930 6591 563863886 563863225 0.000000e+00 1123.0
7 TraesCS2A01G017200 chr2B 96.928 586 17 1 2926 3511 12053122 12053706 0.000000e+00 981.0
8 TraesCS2A01G017200 chr2B 87.952 581 33 12 588 1148 12051674 12052237 0.000000e+00 651.0
9 TraesCS2A01G017200 chr2B 89.231 325 14 9 1323 1626 12052303 12052627 2.880000e-103 387.0
10 TraesCS2A01G017200 chr2B 90.508 295 24 2 1454 1744 12053700 12053994 2.880000e-103 387.0
11 TraesCS2A01G017200 chr2B 91.304 115 10 0 3628 3742 12011540 12011654 2.460000e-34 158.0
12 TraesCS2A01G017200 chr2B 93.878 49 3 0 703 751 12008331 12008379 2.550000e-09 75.0
13 TraesCS2A01G017200 chr7A 94.163 651 23 5 323 958 466531068 466530418 0.000000e+00 977.0
14 TraesCS2A01G017200 chr7A 87.583 604 62 9 1742 2339 213096990 213096394 0.000000e+00 688.0
15 TraesCS2A01G017200 chr7A 94.019 418 21 2 1330 1743 466525463 466525046 1.210000e-176 630.0
16 TraesCS2A01G017200 chr7A 88.589 333 32 6 1416 1744 213097393 213097063 3.700000e-107 399.0
17 TraesCS2A01G017200 chr7A 89.098 266 14 10 3 257 466531445 466531184 3.840000e-82 316.0
18 TraesCS2A01G017200 chr7A 96.154 52 2 0 270 321 466531145 466531094 1.180000e-12 86.1
19 TraesCS2A01G017200 chrUn 87.060 796 76 14 2327 3105 100084095 100084880 0.000000e+00 874.0
20 TraesCS2A01G017200 chrUn 90.017 601 54 4 1742 2339 100083269 100083866 0.000000e+00 773.0
21 TraesCS2A01G017200 chr4A 84.677 881 99 23 2327 3186 448519689 448520554 0.000000e+00 846.0
22 TraesCS2A01G017200 chr4A 84.146 820 95 20 2327 3118 572563630 572562818 0.000000e+00 761.0
23 TraesCS2A01G017200 chr4A 89.185 601 58 5 1742 2339 448518868 448519464 0.000000e+00 743.0
24 TraesCS2A01G017200 chr4A 89.851 335 30 4 1413 1744 572564863 572564530 1.700000e-115 427.0
25 TraesCS2A01G017200 chr4D 84.624 878 102 22 2327 3186 122195311 122194449 0.000000e+00 843.0
26 TraesCS2A01G017200 chr4D 84.769 801 78 27 2327 3087 30406820 30407616 0.000000e+00 763.0
27 TraesCS2A01G017200 chr4D 88.945 597 59 4 1742 2334 122196135 122195542 0.000000e+00 730.0
28 TraesCS2A01G017200 chr4D 88.268 358 34 6 1394 1744 122196564 122196208 7.900000e-114 422.0
29 TraesCS2A01G017200 chr4B 89.474 665 60 8 2440 3097 185228949 185228288 0.000000e+00 832.0
30 TraesCS2A01G017200 chr4B 86.693 774 67 16 2327 3082 672237258 672236503 0.000000e+00 826.0
31 TraesCS2A01G017200 chr4B 83.463 901 97 30 2327 3186 43728092 43728981 0.000000e+00 791.0
32 TraesCS2A01G017200 chr4B 89.983 599 56 4 1742 2339 672238073 672237478 0.000000e+00 771.0
33 TraesCS2A01G017200 chr4B 88.870 602 59 6 1742 2339 185229870 185229273 0.000000e+00 734.0
34 TraesCS2A01G017200 chr4B 88.963 598 60 6 1742 2336 599552312 599551718 0.000000e+00 734.0
35 TraesCS2A01G017200 chr4B 88.815 599 58 7 1742 2336 599642961 599642368 0.000000e+00 726.0
36 TraesCS2A01G017200 chr4B 88.136 354 36 6 1394 1744 185230293 185229943 3.680000e-112 416.0
37 TraesCS2A01G017200 chr4B 91.259 286 24 1 1460 1744 599643319 599643034 8.010000e-104 388.0
38 TraesCS2A01G017200 chr7B 90.753 292 23 4 1455 1744 171993108 171993397 2.880000e-103 387.0
39 TraesCS2A01G017200 chr6B 89.308 159 13 4 3584 3742 17227619 17227465 5.210000e-46 196.0
40 TraesCS2A01G017200 chr6A 88.024 167 14 6 3578 3742 11272979 11273141 6.740000e-45 193.0
41 TraesCS2A01G017200 chr6D 88.679 159 14 4 3584 3742 9248777 9248623 2.430000e-44 191.0
42 TraesCS2A01G017200 chr2D 94.495 109 6 0 3634 3742 8776641 8776533 1.140000e-37 169.0
43 TraesCS2A01G017200 chr2D 95.918 49 2 0 703 751 8778622 8778574 5.480000e-11 80.5


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 TraesCS2A01G017200 chr2A 7922952 7929542 6590 True 12172.000000 12172 100.000000 1 6591 1 chr2A.!!$R1 6590
1 TraesCS2A01G017200 chr3D 563863225 563869867 6642 True 3699.333333 7360 96.966333 105 6591 3 chr3D.!!$R1 6486
2 TraesCS2A01G017200 chr2B 12051674 12053994 2320 False 601.500000 981 91.154750 588 3511 4 chr2B.!!$F2 2923
3 TraesCS2A01G017200 chr7A 213096394 213097393 999 True 543.500000 688 88.086000 1416 2339 2 chr7A.!!$R2 923
4 TraesCS2A01G017200 chr7A 466530418 466531445 1027 True 459.700000 977 93.138333 3 958 3 chr7A.!!$R3 955
5 TraesCS2A01G017200 chrUn 100083269 100084880 1611 False 823.500000 874 88.538500 1742 3105 2 chrUn.!!$F1 1363
6 TraesCS2A01G017200 chr4A 448518868 448520554 1686 False 794.500000 846 86.931000 1742 3186 2 chr4A.!!$F1 1444
7 TraesCS2A01G017200 chr4A 572562818 572564863 2045 True 594.000000 761 86.998500 1413 3118 2 chr4A.!!$R1 1705
8 TraesCS2A01G017200 chr4D 30406820 30407616 796 False 763.000000 763 84.769000 2327 3087 1 chr4D.!!$F1 760
9 TraesCS2A01G017200 chr4D 122194449 122196564 2115 True 665.000000 843 87.279000 1394 3186 3 chr4D.!!$R1 1792
10 TraesCS2A01G017200 chr4B 672236503 672238073 1570 True 798.500000 826 88.338000 1742 3082 2 chr4B.!!$R4 1340
11 TraesCS2A01G017200 chr4B 43728092 43728981 889 False 791.000000 791 83.463000 2327 3186 1 chr4B.!!$F1 859
12 TraesCS2A01G017200 chr4B 599551718 599552312 594 True 734.000000 734 88.963000 1742 2336 1 chr4B.!!$R1 594
13 TraesCS2A01G017200 chr4B 185228288 185230293 2005 True 660.666667 832 88.826667 1394 3097 3 chr4B.!!$R2 1703
14 TraesCS2A01G017200 chr4B 599642368 599643319 951 True 557.000000 726 90.037000 1460 2336 2 chr4B.!!$R3 876

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
315 353 0.253394 CCCTTCTCCCCTCCCTTTCT 60.253 60.000 0.00 0.00 0.00 2.52 F
1162 1263 0.925267 CTTGTTCTTGTGTGCACGCG 60.925 55.000 24.30 3.53 0.00 6.01 F
2076 2295 0.758123 AATAGAGGCTGAGCTGGAGC 59.242 55.000 3.72 5.86 42.49 4.70 F
2939 3477 1.197721 GTGTTACTCATGCTGGTGTGC 59.802 52.381 0.00 0.00 0.00 4.57 F
4610 5173 0.042731 TGGGACCTACTTCTCCCCTG 59.957 60.000 0.00 0.00 45.30 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1206 1311 0.733150 CACATGACATGAGCCAGCAG 59.267 55.0 22.19 0.0 0.00 4.24 R
2112 2331 0.737715 GCTCGAAGACCATTCACGCT 60.738 55.0 0.00 0.0 0.00 5.07 R
3612 4175 0.958822 AGAAATGCACAACCCGAACC 59.041 50.0 0.00 0.0 0.00 3.62 R
4746 5318 1.506309 GCGCATTACCATCGGCATCA 61.506 55.0 0.30 0.0 0.00 3.07 R
6351 7033 0.179111 GAGATCCGGTGTTGCGATCA 60.179 55.0 0.00 0.0 35.82 2.92 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
26 27 3.006967 AGACAGTGAACGGTAGAAATGCT 59.993 43.478 0.00 0.00 0.00 3.79
28 29 2.076863 AGTGAACGGTAGAAATGCTGC 58.923 47.619 0.00 0.00 0.00 5.25
29 30 2.076863 GTGAACGGTAGAAATGCTGCT 58.923 47.619 0.00 0.00 0.00 4.24
30 31 3.056107 AGTGAACGGTAGAAATGCTGCTA 60.056 43.478 0.00 0.00 0.00 3.49
35 36 2.483876 GGTAGAAATGCTGCTATCGCA 58.516 47.619 0.00 0.00 45.60 5.10
63 64 1.834188 AAAGCAAATCCTACGGTGGG 58.166 50.000 3.80 3.80 0.00 4.61
96 97 1.889573 GCAAGGAGCCATCGTAGCC 60.890 63.158 0.00 0.00 37.23 3.93
102 103 4.944372 GCCATCGTAGCCGTCCGG 62.944 72.222 0.24 0.24 38.57 5.14
104 105 2.278596 CATCGTAGCCGTCCGGTG 60.279 66.667 7.66 0.00 37.65 4.94
105 106 2.753043 ATCGTAGCCGTCCGGTGT 60.753 61.111 7.66 0.00 37.65 4.16
106 107 1.451927 ATCGTAGCCGTCCGGTGTA 60.452 57.895 7.66 0.00 37.65 2.90
107 108 0.820891 ATCGTAGCCGTCCGGTGTAT 60.821 55.000 7.66 0.00 37.65 2.29
183 195 1.971357 CCACAGGGTAAGACTGACACT 59.029 52.381 0.00 0.00 39.24 3.55
208 220 2.193517 CACCCACGTCCCCAAACA 59.806 61.111 0.00 0.00 0.00 2.83
212 224 1.524165 CCACGTCCCCAAACACGAA 60.524 57.895 0.00 0.00 39.38 3.85
229 241 1.524008 GAAACCCAGCCAACGGAAGG 61.524 60.000 0.00 0.00 0.00 3.46
267 279 1.075301 CCCCCAATCATTCACCCCC 60.075 63.158 0.00 0.00 0.00 5.40
315 353 0.253394 CCCTTCTCCCCTCCCTTTCT 60.253 60.000 0.00 0.00 0.00 2.52
321 359 2.759114 CCCTCCCTTTCTGCTGCA 59.241 61.111 0.88 0.88 0.00 4.41
360 422 2.363147 GCTGAGGGAGGTCTCGGT 60.363 66.667 0.00 0.00 41.09 4.69
657 719 2.102357 CACATCGAGCGCTACCGT 59.898 61.111 11.50 2.04 36.67 4.83
675 743 3.124921 CACCACGATGCGGTTCCC 61.125 66.667 0.00 0.00 33.25 3.97
866 949 3.918220 CAAGCGCGACGAGATGCC 61.918 66.667 12.10 0.00 0.00 4.40
1030 1119 1.303317 ATTCCGGTGGCAGTTGGAC 60.303 57.895 0.00 0.00 0.00 4.02
1113 1214 4.051167 CTCCATGCCCCCACTGCA 62.051 66.667 0.00 0.00 43.97 4.41
1151 1252 1.149101 TGGCCTTCTCCCTTGTTCTT 58.851 50.000 3.32 0.00 0.00 2.52
1162 1263 0.925267 CTTGTTCTTGTGTGCACGCG 60.925 55.000 24.30 3.53 0.00 6.01
1206 1311 4.273480 AGTTACAATATGCACCTTCATCGC 59.727 41.667 0.00 0.00 0.00 4.58
1282 1387 2.021380 GTTTATGTGAGCGCGCGG 59.979 61.111 33.06 13.66 0.00 6.46
1366 1474 4.037208 GGATAGTGCATTCCCTTGTTCATG 59.963 45.833 0.00 0.00 0.00 3.07
1451 1563 6.757897 TTCCTTGTTCTATTTCGAATGCAT 57.242 33.333 0.00 0.00 0.00 3.96
1473 1588 5.417754 TCTCTCTTCTGCATGTTTGAGAT 57.582 39.130 0.00 0.00 31.41 2.75
1560 1680 2.508751 GGGAGTATCGAGGGGCCAC 61.509 68.421 4.39 0.00 34.37 5.01
1752 1959 7.930865 TGAAATTTGCTAAATTACCCATATGCC 59.069 33.333 0.00 0.00 40.05 4.40
1754 1961 2.817258 TGCTAAATTACCCATATGCCGC 59.183 45.455 0.00 0.00 0.00 6.53
1934 2147 3.973305 TCTCCCATGGTATGCTGTGATTA 59.027 43.478 11.73 0.00 0.00 1.75
2029 2248 2.886523 CTGTCCAACCAGAAGATTTGCA 59.113 45.455 0.00 0.00 34.23 4.08
2076 2295 0.758123 AATAGAGGCTGAGCTGGAGC 59.242 55.000 3.72 5.86 42.49 4.70
2112 2331 8.519799 AGAAATAAAATTAGCCAATCCGAAGA 57.480 30.769 0.00 0.00 0.00 2.87
2344 2813 8.387190 TGGTTATCTGATATCAATGAAGCAAG 57.613 34.615 16.56 1.14 0.00 4.01
2360 2832 1.876416 GCAAGTAAACTGGACGGAGCA 60.876 52.381 0.00 0.00 0.00 4.26
2934 3472 3.930336 TCTTCTGTGTTACTCATGCTGG 58.070 45.455 0.00 0.00 0.00 4.85
2939 3477 1.197721 GTGTTACTCATGCTGGTGTGC 59.802 52.381 0.00 0.00 0.00 4.57
3768 4331 5.233988 AGCAAACAACAGCTCTTCTACTAG 58.766 41.667 0.00 0.00 36.00 2.57
4260 4823 7.094634 CCTTACTGTAAATTGTGAGCTGAATGT 60.095 37.037 0.00 0.00 0.00 2.71
4402 4965 4.141287 ACATGTTCCCGAAAACTGATTCA 58.859 39.130 0.00 0.00 0.00 2.57
4533 5096 1.029408 TGTTTTGCAGTGCTGGTCGT 61.029 50.000 17.60 0.00 0.00 4.34
4610 5173 0.042731 TGGGACCTACTTCTCCCCTG 59.957 60.000 0.00 0.00 45.30 4.45
4741 5313 3.389002 AGGCTTCACTTCCAAGCAAATTT 59.611 39.130 6.74 0.00 46.94 1.82
4746 5318 6.037500 GCTTCACTTCCAAGCAAATTTTCTTT 59.962 34.615 0.00 0.00 44.87 2.52
4763 5335 2.618241 TCTTTGATGCCGATGGTAATGC 59.382 45.455 0.00 0.00 0.00 3.56
4799 5371 5.510430 TGCTCCTCAAGAGTATAGTCAAGA 58.490 41.667 10.21 6.16 45.21 3.02
4812 5384 8.723942 AGTATAGTCAAGAACTTGCCTTATTG 57.276 34.615 9.38 0.00 39.55 1.90
4853 5425 5.924356 TGGAATATTTGACGATGCCTTAGA 58.076 37.500 0.00 0.00 0.00 2.10
4928 5500 5.163426 TGTCAAATTGTCCTGCTGTTGATTT 60.163 36.000 0.00 0.00 0.00 2.17
4966 5538 3.347958 TTGCTTTTGTCACGAATCACC 57.652 42.857 0.00 0.00 0.00 4.02
4967 5539 1.606668 TGCTTTTGTCACGAATCACCC 59.393 47.619 0.00 0.00 0.00 4.61
5038 5610 3.762407 TGTTGCTTACAAGGCTCAGTA 57.238 42.857 0.00 0.00 36.16 2.74
5062 5634 5.901413 AGATGATTCAGAGGCCTTGATAA 57.099 39.130 6.77 0.00 0.00 1.75
5063 5635 6.257994 AGATGATTCAGAGGCCTTGATAAA 57.742 37.500 6.77 0.00 0.00 1.40
5067 5639 7.991084 TGATTCAGAGGCCTTGATAAATATG 57.009 36.000 6.77 0.00 0.00 1.78
5100 5672 1.856873 TTGGGGGAGCAGGTTGGAT 60.857 57.895 0.00 0.00 0.00 3.41
5116 5688 3.737559 TGGATAAGGTTCCTGCAATGT 57.262 42.857 0.00 0.00 36.68 2.71
5129 5701 4.081586 TCCTGCAATGTACCACACGTATTA 60.082 41.667 0.00 0.00 0.00 0.98
5147 5719 5.006358 CGTATTACTTTCACTGGTGGTATGC 59.994 44.000 0.70 0.00 0.00 3.14
5153 5725 3.382083 TCACTGGTGGTATGCTAGAGA 57.618 47.619 0.00 0.00 0.00 3.10
5159 5731 2.564947 GGTGGTATGCTAGAGATGGGAG 59.435 54.545 0.00 0.00 0.00 4.30
5214 5786 5.855395 CAGCTTGCTCAAATTCTCTAACAAC 59.145 40.000 0.00 0.00 0.00 3.32
5220 5792 8.856490 TGCTCAAATTCTCTAACAACTTTTTC 57.144 30.769 0.00 0.00 0.00 2.29
5246 5818 7.928307 AGCATCACAATGTAAGATGTTTAGT 57.072 32.000 13.07 0.00 40.86 2.24
5322 5894 1.222936 CTTCCGATGCAGGGCTTCT 59.777 57.895 1.72 0.00 31.76 2.85
5379 5951 6.345882 GGCGACGAAGCATAAAAACTATCTAG 60.346 42.308 0.00 0.00 39.27 2.43
5686 6258 0.035534 ATGCATGTCTAACACCGGCA 60.036 50.000 0.00 5.68 37.39 5.69
5741 6313 9.722056 GCCTTGTTCAACATTATATAACTGAAG 57.278 33.333 13.09 5.92 0.00 3.02
5872 6444 1.134551 ACTAGCCTAGCTTTGCTCTGC 60.135 52.381 12.40 0.43 40.44 4.26
6026 6708 6.690530 TGAATGGCATTACCTCAAGAAAAAG 58.309 36.000 13.65 0.00 40.22 2.27
6052 6734 7.422465 ACAGGGCATAAACAAATCATTACAT 57.578 32.000 0.00 0.00 0.00 2.29
6099 6781 0.744771 CAAGGCCGCCTTAAGGAGAC 60.745 60.000 26.21 17.11 42.67 3.36
6121 6803 6.593770 AGACGAATTATAGCACACATCACAAA 59.406 34.615 0.00 0.00 0.00 2.83
6129 6811 2.598192 GCACACATCACAAACACAACAC 59.402 45.455 0.00 0.00 0.00 3.32
6241 6923 1.444383 GCCTAAAAGTGCTTGCCGC 60.444 57.895 0.00 0.00 39.77 6.53
6279 6961 4.755411 TGGTCGGTCTTGAGAAATGTATC 58.245 43.478 0.00 0.00 0.00 2.24
6412 7094 4.040461 ACGATACTCCCAACATAGGAATGG 59.960 45.833 0.00 0.00 37.43 3.16
6439 7121 3.202001 CACCGCCATCGCCGATTT 61.202 61.111 0.00 0.00 0.00 2.17
6440 7122 1.885388 CACCGCCATCGCCGATTTA 60.885 57.895 0.00 0.00 0.00 1.40
6454 7136 4.743644 CGCCGATTTAGAACTAAACCTAGG 59.256 45.833 7.41 7.41 37.80 3.02
6470 7152 0.818938 TAGGCTTTCACGCGGATACA 59.181 50.000 12.47 0.00 0.00 2.29
6503 7185 1.489649 CAATGTGAGAGGGGAGATGCT 59.510 52.381 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.818961 TCTACCGTTCACTGTCTTACG 57.181 47.619 0.00 0.00 0.00 3.18
1 2 5.163982 GCATTTCTACCGTTCACTGTCTTAC 60.164 44.000 0.00 0.00 0.00 2.34
9 10 2.076863 AGCAGCATTTCTACCGTTCAC 58.923 47.619 0.00 0.00 0.00 3.18
28 29 2.413796 TGCTTTACCGTTGTTGCGATAG 59.586 45.455 0.00 0.00 0.00 2.08
29 30 2.414806 TGCTTTACCGTTGTTGCGATA 58.585 42.857 0.00 0.00 0.00 2.92
30 31 1.231221 TGCTTTACCGTTGTTGCGAT 58.769 45.000 0.00 0.00 0.00 4.58
35 36 4.083696 CGTAGGATTTGCTTTACCGTTGTT 60.084 41.667 0.00 0.00 0.00 2.83
96 97 3.086309 CGGCAAATACACCGGACG 58.914 61.111 9.46 0.00 45.74 4.79
102 103 1.668419 AGCAGATCCGGCAAATACAC 58.332 50.000 9.38 0.00 0.00 2.90
104 105 2.544267 GTGTAGCAGATCCGGCAAATAC 59.456 50.000 9.38 4.44 0.00 1.89
105 106 2.484770 GGTGTAGCAGATCCGGCAAATA 60.485 50.000 9.38 0.00 0.00 1.40
106 107 1.668419 GTGTAGCAGATCCGGCAAAT 58.332 50.000 9.38 0.00 0.00 2.32
107 108 0.392461 GGTGTAGCAGATCCGGCAAA 60.392 55.000 9.38 0.00 0.00 3.68
196 208 1.096967 GGTTTCGTGTTTGGGGACGT 61.097 55.000 0.00 0.00 36.91 4.34
198 210 0.752376 TGGGTTTCGTGTTTGGGGAC 60.752 55.000 0.00 0.00 0.00 4.46
208 220 2.593436 CCGTTGGCTGGGTTTCGT 60.593 61.111 0.00 0.00 0.00 3.85
212 224 2.002018 TTCCTTCCGTTGGCTGGGTT 62.002 55.000 0.00 0.00 0.00 4.11
229 241 0.317519 CGCGGAGTGTTTGGGTTTTC 60.318 55.000 0.00 0.00 0.00 2.29
315 353 3.720601 CCCTACCCAGCTGCAGCA 61.721 66.667 38.24 18.09 45.16 4.41
321 359 1.623542 CCGCTAAACCCTACCCAGCT 61.624 60.000 0.00 0.00 0.00 4.24
484 546 1.142748 CTGACCTGGCCTCGTCATC 59.857 63.158 21.13 4.87 38.29 2.92
486 548 3.695606 GCTGACCTGGCCTCGTCA 61.696 66.667 20.08 20.08 37.44 4.35
657 719 2.047655 GGAACCGCATCGTGGTGA 60.048 61.111 0.00 0.00 46.56 4.02
675 743 4.824166 CGTACAGGGCGTCGACGG 62.824 72.222 36.13 22.86 40.23 4.79
893 976 1.924320 CTCTTCGAAGCCGTCCGAGT 61.924 60.000 20.56 0.00 36.11 4.18
1094 1195 3.736224 CAGTGGGGGCATGGAGCT 61.736 66.667 0.00 0.00 44.79 4.09
1096 1197 4.051167 TGCAGTGGGGGCATGGAG 62.051 66.667 0.00 0.00 36.11 3.86
1097 1198 4.051167 CTGCAGTGGGGGCATGGA 62.051 66.667 5.25 0.00 41.06 3.41
1098 1199 3.369410 ATCTGCAGTGGGGGCATGG 62.369 63.158 14.67 0.00 41.06 3.66
1099 1200 1.826921 GATCTGCAGTGGGGGCATG 60.827 63.158 14.67 0.00 41.06 4.06
1100 1201 2.005266 AGATCTGCAGTGGGGGCAT 61.005 57.895 14.67 0.00 41.06 4.40
1101 1202 2.611800 AGATCTGCAGTGGGGGCA 60.612 61.111 14.67 0.00 39.32 5.36
1102 1203 2.124403 CAGATCTGCAGTGGGGGC 60.124 66.667 14.67 0.00 0.00 5.80
1162 1263 1.154150 AGCAGAATTTGAAGCGCGC 60.154 52.632 26.66 26.66 0.00 6.86
1170 1271 6.694411 GCATATTGTAACTCCAGCAGAATTTG 59.306 38.462 0.00 0.00 0.00 2.32
1206 1311 0.733150 CACATGACATGAGCCAGCAG 59.267 55.000 22.19 0.00 0.00 4.24
1282 1387 6.924060 GGAATGCACGTCCCTCATATATATAC 59.076 42.308 6.97 0.00 0.00 1.47
1388 1498 4.504864 CCTGGAACCACACACAAGATCTAA 60.505 45.833 0.00 0.00 0.00 2.10
1451 1563 4.879197 TCTCAAACATGCAGAAGAGAGA 57.121 40.909 6.80 6.80 0.00 3.10
1560 1680 3.743521 TGTTCACAGTGAAAGATCCAGG 58.256 45.455 17.83 0.00 38.22 4.45
1754 1961 6.206634 TGAAAACATACCCTTAGAGCAAAGTG 59.793 38.462 0.00 0.00 0.00 3.16
1903 2116 6.491062 CAGCATACCATGGGAGAAATCAAATA 59.509 38.462 18.09 0.00 0.00 1.40
2076 2295 9.455847 GGCTAATTTTATTTCTTGTGCAGATAG 57.544 33.333 0.00 0.00 0.00 2.08
2112 2331 0.737715 GCTCGAAGACCATTCACGCT 60.738 55.000 0.00 0.00 0.00 5.07
2344 2813 1.873698 TGTTGCTCCGTCCAGTTTAC 58.126 50.000 0.00 0.00 0.00 2.01
2934 3472 1.726791 CAGTGGTATCAAGACGCACAC 59.273 52.381 0.00 0.00 0.00 3.82
2939 3477 1.002366 GCAGCAGTGGTATCAAGACG 58.998 55.000 0.00 0.00 0.00 4.18
3157 3720 6.009589 TCATTATTGGCAGACTCTGGAAAAA 58.990 36.000 8.17 0.00 31.21 1.94
3595 4158 4.557205 CGAACCAGCTAGTTTTGACTAGT 58.443 43.478 13.38 0.00 41.20 2.57
3612 4175 0.958822 AGAAATGCACAACCCGAACC 59.041 50.000 0.00 0.00 0.00 3.62
3793 4356 2.572290 GGCAGTACCTGAACAGTGTTT 58.428 47.619 10.45 0.00 32.44 2.83
4025 4588 2.902419 CGCACACCGGCAAACATGA 61.902 57.895 0.00 0.00 0.00 3.07
4260 4823 5.825593 ACCAAGAATCAGTACTTCAGGAA 57.174 39.130 10.02 0.00 0.00 3.36
4294 4857 3.828451 ACAGTTAACAGCGGTCTAAGGTA 59.172 43.478 8.61 0.00 0.00 3.08
4416 4979 4.000988 ACAGTTAACAGCAATCTAACGGG 58.999 43.478 8.61 0.00 32.06 5.28
4610 5173 3.188048 CACTTTCATTGCTGGACTCTGAC 59.812 47.826 0.00 0.00 0.00 3.51
4741 5313 3.066621 GCATTACCATCGGCATCAAAGAA 59.933 43.478 0.00 0.00 0.00 2.52
4746 5318 1.506309 GCGCATTACCATCGGCATCA 61.506 55.000 0.30 0.00 0.00 3.07
4799 5371 5.163416 GCACCATAATCCAATAAGGCAAGTT 60.163 40.000 0.00 0.00 37.29 2.66
4812 5384 3.620488 TCCAGAAACTGCACCATAATCC 58.380 45.455 0.00 0.00 0.00 3.01
4853 5425 7.400052 AGGTTGGATATTTGTTAATTCCAGCTT 59.600 33.333 0.00 0.00 35.31 3.74
4898 5470 3.319122 AGCAGGACAATTTGACAGGAAAC 59.681 43.478 2.79 0.00 0.00 2.78
4905 5477 3.988379 TCAACAGCAGGACAATTTGAC 57.012 42.857 2.79 0.00 0.00 3.18
4912 5484 2.844946 TCGAAAATCAACAGCAGGACA 58.155 42.857 0.00 0.00 0.00 4.02
4928 5500 2.742053 GCAATCACAGCCTTACTTCGAA 59.258 45.455 0.00 0.00 0.00 3.71
4966 5538 3.736252 CGAGAATATGTTAACAGCGAGGG 59.264 47.826 14.65 0.00 0.00 4.30
4967 5539 4.607955 TCGAGAATATGTTAACAGCGAGG 58.392 43.478 14.65 0.64 0.00 4.63
5038 5610 4.581309 TCAAGGCCTCTGAATCATCTTT 57.419 40.909 5.23 0.00 0.00 2.52
5062 5634 7.333323 CCCCAAGAGAAATTTTCAAGCATATT 58.667 34.615 11.53 0.00 0.00 1.28
5063 5635 6.126968 CCCCCAAGAGAAATTTTCAAGCATAT 60.127 38.462 11.53 0.00 0.00 1.78
5067 5639 3.578282 TCCCCCAAGAGAAATTTTCAAGC 59.422 43.478 11.53 1.12 0.00 4.01
5081 5653 1.867595 ATCCAACCTGCTCCCCCAAG 61.868 60.000 0.00 0.00 0.00 3.61
5100 5672 3.073209 TGTGGTACATTGCAGGAACCTTA 59.927 43.478 9.94 0.00 44.52 2.69
5116 5688 5.010922 ACCAGTGAAAGTAATACGTGTGGTA 59.989 40.000 0.00 0.00 32.81 3.25
5129 5701 3.838317 TCTAGCATACCACCAGTGAAAGT 59.162 43.478 0.00 0.00 0.00 2.66
5147 5719 4.404073 GGGTACATATGCTCCCATCTCTAG 59.596 50.000 23.05 0.00 39.68 2.43
5153 5725 2.440494 AGGGGTACATATGCTCCCAT 57.560 50.000 26.67 21.13 41.51 4.00
5159 5731 9.561069 CATTATCCTTATAAGGGGTACATATGC 57.439 37.037 27.65 0.00 46.47 3.14
5214 5786 8.644619 CATCTTACATTGTGATGCTTGAAAAAG 58.355 33.333 0.00 0.00 36.72 2.27
5220 5792 8.239314 ACTAAACATCTTACATTGTGATGCTTG 58.761 33.333 14.01 7.72 40.66 4.01
5246 5818 3.194968 GGGTGTGTATCCGAAGAGAAAGA 59.805 47.826 0.00 0.00 0.00 2.52
5322 5894 1.323412 GCATCCCGCTCTTCTAGAGA 58.677 55.000 7.85 0.00 45.07 3.10
5331 5903 3.127533 AAACGCTGCATCCCGCTC 61.128 61.111 0.00 0.00 43.06 5.03
5379 5951 4.006319 AGAATGGAAAACAGTAGCTGAGC 58.994 43.478 0.00 0.00 35.18 4.26
5686 6258 4.501400 GGCTTACAACAACAGCAATTTCCT 60.501 41.667 0.00 0.00 35.05 3.36
6026 6708 7.319646 TGTAATGATTTGTTTATGCCCTGTTC 58.680 34.615 0.00 0.00 0.00 3.18
6052 6734 3.829886 GCTTGTGCTATGCTTGTTGTA 57.170 42.857 0.00 0.00 36.03 2.41
6099 6781 6.465781 GTGTTTGTGATGTGTGCTATAATTCG 59.534 38.462 0.00 0.00 0.00 3.34
6121 6803 1.346722 GGTAGGCACCTAGTGTTGTGT 59.653 52.381 0.00 0.00 42.11 3.72
6129 6811 2.474112 TGGTTTAGGGTAGGCACCTAG 58.526 52.381 0.00 0.00 45.04 3.02
6183 6865 4.500127 TGATTACATAAGTCACGGTGGTG 58.500 43.478 8.50 3.11 45.78 4.17
6241 6923 3.491619 CCGACCAAGTCCTGACATCTATG 60.492 52.174 0.00 0.00 0.00 2.23
6279 6961 0.320683 TCACTGGTGCATCCAAGACG 60.321 55.000 8.96 1.53 46.59 4.18
6351 7033 0.179111 GAGATCCGGTGTTGCGATCA 60.179 55.000 0.00 0.00 35.82 2.92
6391 7073 4.327680 GCCATTCCTATGTTGGGAGTATC 58.672 47.826 0.00 0.00 34.06 2.24
6439 7121 5.717119 CGTGAAAGCCTAGGTTTAGTTCTA 58.283 41.667 11.70 0.00 33.25 2.10
6440 7122 4.566987 CGTGAAAGCCTAGGTTTAGTTCT 58.433 43.478 11.70 0.00 33.25 3.01
6454 7136 0.793861 TGTTGTATCCGCGTGAAAGC 59.206 50.000 4.92 0.00 0.00 3.51
6470 7152 3.766591 TCTCACATTGGTGTTTGGTTGTT 59.233 39.130 0.00 0.00 45.45 2.83


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

AutoCloner maintained by Alex Coulton.