Multiple sequence alignment - TraesCS4A01G128000

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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 TraesCS4A01G128000 chr4A 100.000 8130 0 0 1 8130 164719504 164711375 0.000000e+00 15014.0
1 TraesCS4A01G128000 chr4D 95.147 7295 200 53 941 8130 309919179 309926424 0.000000e+00 11369.0
2 TraesCS4A01G128000 chr4D 84.615 117 18 0 819 935 343091281 343091397 5.160000e-22 117.0
3 TraesCS4A01G128000 chr4B 95.424 6009 147 29 941 6873 387376748 387382704 0.000000e+00 9455.0
4 TraesCS4A01G128000 chr4B 90.538 539 31 10 7334 7869 387386859 387387380 0.000000e+00 695.0
5 TraesCS4A01G128000 chr4B 89.224 464 24 9 6901 7345 387382959 387383415 2.560000e-154 556.0
6 TraesCS4A01G128000 chr4B 90.341 176 9 5 7958 8130 387387695 387387865 2.950000e-54 224.0
7 TraesCS4A01G128000 chr4B 92.857 70 3 1 7853 7922 387387393 387387460 5.190000e-17 100.0
8 TraesCS4A01G128000 chr2A 98.075 935 8 2 1 935 751506635 751507559 0.000000e+00 1618.0
9 TraesCS4A01G128000 chr7A 95.101 939 41 4 1 939 78522841 78521908 0.000000e+00 1474.0
10 TraesCS4A01G128000 chr7A 90.183 438 38 4 3 438 250692276 250692710 4.260000e-157 566.0
11 TraesCS4A01G128000 chr7A 84.211 95 10 3 5206 5296 35271577 35271670 4.040000e-13 87.9
12 TraesCS4A01G128000 chr7A 84.211 95 10 3 5206 5296 35300222 35300315 4.040000e-13 87.9
13 TraesCS4A01G128000 chr7D 95.150 866 35 6 73 938 113188374 113187516 0.000000e+00 1360.0
14 TraesCS4A01G128000 chr7D 97.531 81 2 0 1 81 113188653 113188573 1.100000e-28 139.0
15 TraesCS4A01G128000 chr5D 95.421 546 23 1 390 935 368822450 368822993 0.000000e+00 869.0
16 TraesCS4A01G128000 chr5D 96.657 359 11 1 1 359 368822096 368822453 5.430000e-166 595.0
17 TraesCS4A01G128000 chr1B 94.567 497 23 4 1 497 41680379 41679887 0.000000e+00 765.0
18 TraesCS4A01G128000 chr5A 81.047 707 56 25 4 661 407774116 407774793 7.330000e-135 492.0
19 TraesCS4A01G128000 chr5A 89.855 276 22 5 168 440 596040254 596040526 4.670000e-92 350.0
20 TraesCS4A01G128000 chr5A 89.640 222 22 1 713 934 407774802 407775022 1.730000e-71 281.0
21 TraesCS4A01G128000 chr5A 93.678 174 11 0 3 176 596039978 596040151 2.250000e-65 261.0
22 TraesCS4A01G128000 chr5A 94.000 50 3 0 5248 5297 493354773 493354822 8.750000e-10 76.8
23 TraesCS4A01G128000 chr3A 89.840 187 14 4 750 935 33141846 33141664 1.360000e-57 235.0
24 TraesCS4A01G128000 chr7B 82.927 123 17 4 817 937 137831456 137831336 3.100000e-19 108.0
25 TraesCS4A01G128000 chr6D 82.500 120 20 1 820 938 450850198 450850079 4.010000e-18 104.0
26 TraesCS4A01G128000 chr3B 82.927 123 14 4 5206 5321 333469003 333469125 4.010000e-18 104.0
27 TraesCS4A01G128000 chrUn 84.211 95 10 3 5206 5296 201313944 201314037 4.040000e-13 87.9


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 TraesCS4A01G128000 chr4A 164711375 164719504 8129 True 15014.0 15014 100.0000 1 8130 1 chr4A.!!$R1 8129
1 TraesCS4A01G128000 chr4D 309919179 309926424 7245 False 11369.0 11369 95.1470 941 8130 1 chr4D.!!$F1 7189
2 TraesCS4A01G128000 chr4B 387376748 387387865 11117 False 2206.0 9455 91.6768 941 8130 5 chr4B.!!$F1 7189
3 TraesCS4A01G128000 chr2A 751506635 751507559 924 False 1618.0 1618 98.0750 1 935 1 chr2A.!!$F1 934
4 TraesCS4A01G128000 chr7A 78521908 78522841 933 True 1474.0 1474 95.1010 1 939 1 chr7A.!!$R1 938
5 TraesCS4A01G128000 chr7D 113187516 113188653 1137 True 749.5 1360 96.3405 1 938 2 chr7D.!!$R1 937
6 TraesCS4A01G128000 chr5D 368822096 368822993 897 False 732.0 869 96.0390 1 935 2 chr5D.!!$F1 934
7 TraesCS4A01G128000 chr5A 407774116 407775022 906 False 386.5 492 85.3435 4 934 2 chr5A.!!$F2 930
8 TraesCS4A01G128000 chr5A 596039978 596040526 548 False 305.5 350 91.7665 3 440 2 chr5A.!!$F3 437

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
177 522 1.295357 TTGTGGCACCGAACTATGCG 61.295 55.000 16.26 0.0 43.02 4.73 F
1184 1572 1.687493 CTCCTCTCCACCCCACTCC 60.687 68.421 0.00 0.0 0.00 3.85 F
1837 2240 0.170561 CTGCTGCTTCACATGGCTTC 59.829 55.000 0.00 0.0 0.00 3.86 F
2935 3345 0.388294 CTCCGTCCCCGTTATCTTCC 59.612 60.000 0.00 0.0 0.00 3.46 F
3690 4100 0.846693 AGCCCTGTGAAAGAAGTGGT 59.153 50.000 0.00 0.0 0.00 4.16 F
4769 5181 0.319555 GCAGTCACGCTTCCACACTA 60.320 55.000 0.00 0.0 0.00 2.74 F
5245 5669 2.862541 CATGTGGTGGAAAGTGGAAGA 58.137 47.619 0.00 0.0 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1533 1930 1.182667 TCACGTCGAACCATCCATCT 58.817 50.0 0.00 0.0 0.00 2.90 R
2935 3345 0.098728 GATTGACATGGAAACGCCCG 59.901 55.0 0.00 0.0 34.97 6.13 R
3309 3719 2.091111 TGCTCCCCATCTCTGACATCTA 60.091 50.0 0.00 0.0 0.00 1.98 R
4670 5082 0.106318 ATGCTGCCCCAAGAGGATTC 60.106 55.0 0.00 0.0 38.24 2.52 R
4821 5233 2.597578 AAAGGACCGGCCAAATAAGT 57.402 45.0 15.92 0.0 40.02 2.24 R
6187 6613 0.245539 GGAACTGTGATTCCGACCGA 59.754 55.0 0.00 0.0 38.95 4.69 R
7202 7922 0.170561 TCTTCTCTGGCGAGCGTTAC 59.829 55.0 0.00 0.0 37.19 2.50 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
177 522 1.295357 TTGTGGCACCGAACTATGCG 61.295 55.000 16.26 0.00 43.02 4.73
239 585 9.967451 TGATATAGTTCTGGGTGTTTAAATTCA 57.033 29.630 0.00 0.00 0.00 2.57
686 1056 5.877012 TGATGAGGAGCTTCTACAATCAAAC 59.123 40.000 10.66 0.00 0.00 2.93
915 1285 6.707608 TGAATATGAAGCGCAAGTTCTATGAT 59.292 34.615 11.47 0.00 41.68 2.45
944 1314 9.757227 CTGGTGATATTACCTCTAAAAGAAGAG 57.243 37.037 16.91 0.00 42.30 2.85
1055 1426 2.045131 GCCTCCCTCTACACGTCGT 61.045 63.158 0.00 0.00 0.00 4.34
1184 1572 1.687493 CTCCTCTCCACCCCACTCC 60.687 68.421 0.00 0.00 0.00 3.85
1211 1599 2.439701 TAGTGCCGACCTCCTCCG 60.440 66.667 0.00 0.00 0.00 4.63
1300 1688 2.774809 AGCCAGGTAATTCTCTTCCCTC 59.225 50.000 0.00 0.00 0.00 4.30
1478 1867 2.841215 TGTTTGCCTTGTTAGTACGCT 58.159 42.857 0.00 0.00 0.00 5.07
1493 1882 2.663826 ACGCTCTCAAGATCAGTTCC 57.336 50.000 0.00 0.00 0.00 3.62
1529 1926 3.374058 CGTTATGGTGTCAATGGAGAACC 59.626 47.826 0.00 0.00 0.00 3.62
1533 1930 2.976185 TGGTGTCAATGGAGAACCTGTA 59.024 45.455 3.98 0.00 37.04 2.74
1542 1939 3.041211 TGGAGAACCTGTAGATGGATGG 58.959 50.000 0.00 0.00 37.04 3.51
1548 1945 2.431057 ACCTGTAGATGGATGGTTCGAC 59.569 50.000 0.00 0.00 0.00 4.20
1567 1967 1.809207 GTGATGGGGCCGTGAATTG 59.191 57.895 0.00 0.00 0.00 2.32
1590 1990 2.359850 GTGGTCGCAATGGGCTGA 60.360 61.111 0.00 0.00 41.67 4.26
1592 1992 2.359850 GGTCGCAATGGGCTGACA 60.360 61.111 11.26 0.00 43.25 3.58
1607 2010 7.011499 TGGGCTGACAGAGTTAATTTTACTA 57.989 36.000 6.65 0.00 0.00 1.82
1639 2042 1.401905 GCCGGATTGGTAAAGCTCAAG 59.598 52.381 5.05 0.00 41.21 3.02
1661 2064 6.364945 AGCTTTTTCCTTCTTATATGCGTC 57.635 37.500 0.00 0.00 0.00 5.19
1680 2083 4.712763 CGTCTTCTTTATTGCTCCACAAC 58.287 43.478 0.00 0.00 42.27 3.32
1717 2120 5.649970 TTAGTCCAAGAGGGTTGGTTTAA 57.350 39.130 3.77 2.33 40.40 1.52
1755 2158 8.208718 TGATCCTTCTAAATAATTTGGACGTG 57.791 34.615 0.00 0.00 29.37 4.49
1788 2191 8.624701 TTAACTTATATTTGAGTTCGGTCTCG 57.375 34.615 0.00 0.00 37.32 4.04
1829 2232 0.654683 CGCCTAATCTGCTGCTTCAC 59.345 55.000 0.00 0.00 0.00 3.18
1837 2240 0.170561 CTGCTGCTTCACATGGCTTC 59.829 55.000 0.00 0.00 0.00 3.86
1883 2286 4.577283 TGGTTAGTTAAGGGATTTATGCGC 59.423 41.667 0.00 0.00 0.00 6.09
1902 2305 2.222678 CGCTGGCTTGATACTGCATAAG 59.777 50.000 0.00 0.00 0.00 1.73
1958 2361 4.528531 GAGACAATCGAGGAATTTGCTC 57.471 45.455 7.79 7.79 0.00 4.26
2047 2454 2.696707 TGTCTGGTCGTTTAAGTGGAGT 59.303 45.455 0.00 0.00 0.00 3.85
2060 2467 2.863809 AGTGGAGTTGGTCATGGTTTC 58.136 47.619 0.00 0.00 0.00 2.78
2071 2481 7.279313 AGTTGGTCATGGTTTCGTTGTATATAC 59.721 37.037 5.89 5.89 0.00 1.47
2098 2508 2.803492 CGTTATGGACTAGGGAAGCAGC 60.803 54.545 0.00 0.00 0.00 5.25
2303 2713 1.138883 TGAGTGACGCATACCGAGC 59.861 57.895 0.00 0.00 41.02 5.03
2385 2795 5.755375 AGACTGAATCTAATTGGTATGCACG 59.245 40.000 0.00 0.00 35.15 5.34
2391 2801 2.113860 AATTGGTATGCACGACTGCT 57.886 45.000 0.00 0.00 44.57 4.24
2402 2812 1.526887 CACGACTGCTGATGAAACGTT 59.473 47.619 0.00 0.00 0.00 3.99
2432 2842 6.764877 TCTTTCTTGTCAGCTAAGTAAACG 57.235 37.500 0.00 0.00 0.00 3.60
2435 2845 6.520792 TTCTTGTCAGCTAAGTAAACGTTC 57.479 37.500 0.00 0.00 0.00 3.95
2620 3030 4.766891 AGAGTGACACACATTAAAATGGGG 59.233 41.667 8.59 3.13 44.11 4.96
2935 3345 0.388294 CTCCGTCCCCGTTATCTTCC 59.612 60.000 0.00 0.00 0.00 3.46
3159 3569 2.416747 TGAGAGCCAGTTGTCATTTCG 58.583 47.619 0.00 0.00 0.00 3.46
3309 3719 2.365617 TCTCGCAACAGGAGAAAACTCT 59.634 45.455 0.00 0.00 37.59 3.24
3500 3910 2.935201 GCTGCAGATAAGGTTGTCTCAG 59.065 50.000 20.43 9.50 32.42 3.35
3690 4100 0.846693 AGCCCTGTGAAAGAAGTGGT 59.153 50.000 0.00 0.00 0.00 4.16
3754 4164 6.017357 AGGAACCTTTTCGTGATGTTAGAAAC 60.017 38.462 0.00 0.00 34.14 2.78
3787 4197 5.338381 GGACCTGTCTACATCCATGAAAGAA 60.338 44.000 0.00 0.00 0.00 2.52
3893 4303 3.314541 TGCTAACCGAAGAAAGAGGTC 57.685 47.619 0.00 0.00 37.26 3.85
3972 4382 7.867403 TCAAAACAAATGATAGAAAGGTTCTGC 59.133 33.333 0.70 0.00 40.94 4.26
4008 4418 7.823799 TGCAGAACTCATGATGTGAAACTATAA 59.176 33.333 0.00 0.00 38.04 0.98
4064 4475 5.930135 TGCTGTTCCTCTCTTTCTAGTTTT 58.070 37.500 0.00 0.00 0.00 2.43
4065 4476 6.357367 TGCTGTTCCTCTCTTTCTAGTTTTT 58.643 36.000 0.00 0.00 0.00 1.94
4066 4477 7.506114 TGCTGTTCCTCTCTTTCTAGTTTTTA 58.494 34.615 0.00 0.00 0.00 1.52
4067 4478 7.657761 TGCTGTTCCTCTCTTTCTAGTTTTTAG 59.342 37.037 0.00 0.00 0.00 1.85
4316 4728 5.170021 TGAAGCGGCTTATTTTTCTACGTA 58.830 37.500 16.38 0.00 0.00 3.57
4319 4731 3.618150 GCGGCTTATTTTTCTACGTACCA 59.382 43.478 0.00 0.00 0.00 3.25
4473 4885 4.844349 AGGGCATGTCTACAGTTTATGT 57.156 40.909 0.00 0.00 46.45 2.29
4531 4943 9.283420 GCTTTTGCACTTTCTCTAAATAGAATC 57.717 33.333 0.00 0.00 46.58 2.52
4574 4986 3.371595 CCTGTTGTAAATGGTAGGGAGGG 60.372 52.174 0.00 0.00 0.00 4.30
4617 5029 2.738521 CTCCACCACAAGCCGACG 60.739 66.667 0.00 0.00 0.00 5.12
4670 5082 0.994995 CGCACTCTTCGTCATCAAGG 59.005 55.000 0.00 0.00 0.00 3.61
4769 5181 0.319555 GCAGTCACGCTTCCACACTA 60.320 55.000 0.00 0.00 0.00 2.74
4821 5233 6.017109 GCTCTGTGATGAAGTCAAGGTAAAAA 60.017 38.462 0.00 0.00 38.90 1.94
4908 5328 9.542462 TTAAACTAGATATGCGTTGCTAGAAAT 57.458 29.630 16.96 8.30 35.48 2.17
4997 5417 6.785488 TCGTCATATGAATGATAGCAAACC 57.215 37.500 7.07 0.00 43.87 3.27
5245 5669 2.862541 CATGTGGTGGAAAGTGGAAGA 58.137 47.619 0.00 0.00 0.00 2.87
5249 5673 5.055265 TGTGGTGGAAAGTGGAAGATTTA 57.945 39.130 0.00 0.00 0.00 1.40
5658 6084 4.156008 GTGAATTGGTTGACACCTCCATAC 59.844 45.833 0.00 0.00 44.61 2.39
5780 6206 4.463539 ACAATTTGCAGGCAGTATGATGAA 59.536 37.500 0.00 0.00 39.69 2.57
5825 6251 3.013219 GGAATCAAGAGGAGAAAGCCAC 58.987 50.000 0.00 0.00 0.00 5.01
6042 6468 5.857471 TCAATAGGCATTTTCTGGAATGG 57.143 39.130 0.00 0.00 37.47 3.16
6083 6509 9.995003 TTGCTCTTGGTTAAAATATTCACATTT 57.005 25.926 0.00 0.00 0.00 2.32
6187 6613 5.820947 CAGTGGCGGTATAAAGGTCTTAATT 59.179 40.000 0.00 0.00 0.00 1.40
6421 6847 6.095300 CACCCATATTTACAATCTGTGAGCAA 59.905 38.462 0.00 0.00 0.00 3.91
6428 6854 7.936496 TTTACAATCTGTGAGCAATGGATTA 57.064 32.000 0.00 0.00 0.00 1.75
6469 6895 1.420430 TCGAAGACTTGGAAGGTGGT 58.580 50.000 0.00 0.00 0.00 4.16
6547 6973 4.142038 GTGGTGGTTCAAGGTCTACATTT 58.858 43.478 0.00 0.00 0.00 2.32
6598 7024 6.129179 TGAAATGAGGGGAATCCATAGAAAC 58.871 40.000 0.09 0.00 38.24 2.78
6685 7111 3.911868 TGTTTCAGTGCACAAATATGGC 58.088 40.909 21.04 0.39 0.00 4.40
6762 7236 5.183904 GGTTGCACTAATTTCTGGAGTGAAT 59.816 40.000 9.08 0.00 42.65 2.57
6821 7295 6.827586 ATAAACCGTCCATTGTGTACATTT 57.172 33.333 0.00 0.00 0.00 2.32
6865 7339 5.813672 ACAAATCACTGCCATCATATTTTGC 59.186 36.000 0.00 0.00 0.00 3.68
6869 7343 2.033801 ACTGCCATCATATTTTGCGAGC 59.966 45.455 0.00 0.00 0.00 5.03
6894 7368 0.941963 ATAGTCTAGGGGGACAGGCA 59.058 55.000 0.00 0.00 38.57 4.75
6895 7369 0.941963 TAGTCTAGGGGGACAGGCAT 59.058 55.000 0.00 0.00 38.57 4.40
7016 7717 7.230747 TGGGGGATACAAGATGTATATTTGTG 58.769 38.462 3.15 0.00 43.08 3.33
7053 7755 9.159254 TCAGTATATGATATGAGGTTTCCTGTT 57.841 33.333 0.00 0.00 29.48 3.16
7071 7773 1.270550 GTTCTTCATGTTGGCACCTGG 59.729 52.381 0.00 0.00 0.00 4.45
7081 7783 1.380380 GGCACCTGGGCATAAGCTT 60.380 57.895 3.48 3.48 42.77 3.74
7082 7784 1.669999 GGCACCTGGGCATAAGCTTG 61.670 60.000 9.86 0.00 42.77 4.01
7083 7785 1.669999 GCACCTGGGCATAAGCTTGG 61.670 60.000 9.86 1.80 41.70 3.61
7097 7799 6.571150 GCATAAGCTTGGACTTTTCATTCAGT 60.571 38.462 9.86 0.00 37.91 3.41
7098 7800 4.843220 AGCTTGGACTTTTCATTCAGTG 57.157 40.909 0.00 0.00 0.00 3.66
7099 7801 4.210331 AGCTTGGACTTTTCATTCAGTGT 58.790 39.130 0.00 0.00 0.00 3.55
7129 7849 6.549912 TCTATGATTGCAATTCCATTCTCG 57.450 37.500 14.33 3.93 0.00 4.04
7162 7882 4.989168 GGTCTTATTTAGGCTGGTACGATG 59.011 45.833 0.00 0.00 0.00 3.84
7173 7893 5.944007 AGGCTGGTACGATGTTTCTTATTTT 59.056 36.000 0.00 0.00 0.00 1.82
7241 7961 7.158021 AGAAGAGTAAACTGGATCAAACTCAG 58.842 38.462 3.12 0.00 36.63 3.35
7252 7972 7.993183 ACTGGATCAAACTCAGTAAGAAAGAAA 59.007 33.333 0.00 0.00 39.63 2.52
7276 7996 4.082733 GGAAAGAAACCAATAGACCAGCAC 60.083 45.833 0.00 0.00 0.00 4.40
7277 7997 2.699954 AGAAACCAATAGACCAGCACG 58.300 47.619 0.00 0.00 0.00 5.34
7278 7998 1.737793 GAAACCAATAGACCAGCACGG 59.262 52.381 0.00 0.00 42.50 4.94
7286 8006 2.046892 ACCAGCACGGCAAGCTAG 60.047 61.111 0.00 0.00 41.14 3.42
7325 8045 2.125350 CCTCTTGAGCCAGGCGAC 60.125 66.667 5.55 5.20 0.00 5.19
7329 8049 4.617520 TTGAGCCAGGCGACGCAA 62.618 61.111 23.09 6.87 0.00 4.85
7477 11652 0.905357 TTTCTCCAGGAGTAGCAGGC 59.095 55.000 16.65 0.00 0.00 4.85
7580 11756 5.818136 AATAGTTCCCAAATCATCACACG 57.182 39.130 0.00 0.00 0.00 4.49
7635 11811 4.970662 TCGTAAGGGTCATGTAGTGTAC 57.029 45.455 0.00 0.00 38.47 2.90
7781 11957 3.068560 GGTACCACACGCTCAAACAATA 58.931 45.455 7.15 0.00 0.00 1.90
7812 11988 4.553547 GCACAAACTCAGCTCAGTACAAAG 60.554 45.833 0.00 0.00 0.00 2.77
7818 11994 3.393800 TCAGCTCAGTACAAAGCAGTTC 58.606 45.455 18.30 0.00 41.06 3.01
7897 12102 4.683129 GCCATTAATGAAACATGAACCCCC 60.683 45.833 17.23 0.00 0.00 5.40
7940 12146 1.187567 GGCTGGGTTTGCACAAGGAT 61.188 55.000 0.00 0.00 0.00 3.24
8006 12409 2.295349 AGTCCTGAAACTGCTGCATTTG 59.705 45.455 1.31 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
177 522 3.242706 TGCACATAATCATACAACGCAGC 60.243 43.478 0.00 0.00 0.00 5.25
686 1056 4.471904 TTACAGATACACCCTGCTCTTG 57.528 45.455 0.00 0.00 35.14 3.02
894 1264 6.763135 AGAAATCATAGAACTTGCGCTTCATA 59.237 34.615 9.73 0.00 0.00 2.15
939 1309 4.394610 GGCATTTGTTCTCTTCTCCTCTTC 59.605 45.833 0.00 0.00 0.00 2.87
944 1314 2.163211 GCTGGCATTTGTTCTCTTCTCC 59.837 50.000 0.00 0.00 0.00 3.71
1055 1426 3.497115 TGCCTGCTGGTGGGAACA 61.497 61.111 11.69 0.00 38.70 3.18
1184 1572 2.507102 CGGCACTAGCTGGTCGTG 60.507 66.667 0.00 7.10 43.60 4.35
1300 1688 2.697644 AGCAATCCAGGGGAGGGG 60.698 66.667 0.00 0.00 34.05 4.79
1363 1752 3.583882 AATTCACCCACCCCAGCGG 62.584 63.158 0.00 0.00 37.81 5.52
1478 1867 6.043706 AGGAAGAAAAGGAACTGATCTTGAGA 59.956 38.462 0.00 0.00 41.96 3.27
1493 1882 2.351726 CCATAACGCGGAGGAAGAAAAG 59.648 50.000 12.47 0.00 0.00 2.27
1529 1926 2.099263 ACGTCGAACCATCCATCTACAG 59.901 50.000 0.00 0.00 0.00 2.74
1533 1930 1.182667 TCACGTCGAACCATCCATCT 58.817 50.000 0.00 0.00 0.00 2.90
1542 1939 2.818274 GGCCCCATCACGTCGAAC 60.818 66.667 0.00 0.00 0.00 3.95
1548 1945 1.748879 AATTCACGGCCCCATCACG 60.749 57.895 0.00 0.00 0.00 4.35
1567 1967 3.061848 CATTGCGACCACCCACCC 61.062 66.667 0.00 0.00 0.00 4.61
1607 2010 1.750778 CAATCCGGCCAGCAAATAAGT 59.249 47.619 2.24 0.00 0.00 2.24
1639 2042 6.364945 AGACGCATATAAGAAGGAAAAAGC 57.635 37.500 0.00 0.00 0.00 3.51
1661 2064 5.947228 TGAGTTGTGGAGCAATAAAGAAG 57.053 39.130 0.00 0.00 39.55 2.85
1680 2083 4.245660 TGGACTAAACGAGCTCAATTGAG 58.754 43.478 27.82 27.82 44.75 3.02
1717 2120 1.198713 AGGATCAGCACGTCTTGGAT 58.801 50.000 0.00 0.00 0.00 3.41
1755 2158 9.952188 GAACTCAAATATAAGTTAATTCCAGGC 57.048 33.333 0.00 0.00 35.90 4.85
1788 2191 4.437390 CGTTATGGGATTCTCAAACAGCAC 60.437 45.833 0.00 0.00 0.00 4.40
1837 2240 7.536895 CAAGTGTATTCTCTCAATCTTGGAG 57.463 40.000 0.00 0.00 0.00 3.86
1883 2286 5.468072 CCTAACTTATGCAGTATCAAGCCAG 59.532 44.000 0.00 0.00 32.94 4.85
1902 2305 7.611213 TTATAGAAGCAAGCAGAAACCTAAC 57.389 36.000 0.00 0.00 0.00 2.34
1958 2361 9.965824 AATAAACCAATTAAAGAGAACACACAG 57.034 29.630 0.00 0.00 0.00 3.66
2047 2454 7.332557 AGTATATACAACGAAACCATGACCAA 58.667 34.615 15.18 0.00 0.00 3.67
2071 2481 6.377429 TGCTTCCCTAGTCCATAACGATATAG 59.623 42.308 0.00 0.00 0.00 1.31
2078 2488 2.803492 CGCTGCTTCCCTAGTCCATAAC 60.803 54.545 0.00 0.00 0.00 1.89
2098 2508 2.791560 CGATCCTGCATCAACTAGAACG 59.208 50.000 0.00 0.00 0.00 3.95
2385 2795 1.197721 CCCAACGTTTCATCAGCAGTC 59.802 52.381 0.00 0.00 0.00 3.51
2391 2801 6.001460 AGAAAGATAACCCAACGTTTCATCA 58.999 36.000 0.00 0.00 35.79 3.07
2402 2812 4.640771 AGCTGACAAGAAAGATAACCCA 57.359 40.909 0.00 0.00 0.00 4.51
2511 2921 8.442632 TCTTATGGCAGAGAGATGTTTTTATG 57.557 34.615 0.00 0.00 0.00 1.90
2620 3030 1.069432 TCACTCGTTGCTCGTGTAGAC 60.069 52.381 8.59 0.00 42.95 2.59
2935 3345 0.098728 GATTGACATGGAAACGCCCG 59.901 55.000 0.00 0.00 34.97 6.13
2979 3389 2.777692 ACCTTTTCCTCAACAGTCCTCA 59.222 45.455 0.00 0.00 0.00 3.86
3159 3569 4.478206 TGACCAGATTCCTTCTCATCAC 57.522 45.455 0.00 0.00 29.93 3.06
3309 3719 2.091111 TGCTCCCCATCTCTGACATCTA 60.091 50.000 0.00 0.00 0.00 1.98
3500 3910 7.170393 AGGCAACCTTATCTACCAAATTTTC 57.830 36.000 0.00 0.00 37.17 2.29
3710 4120 5.857471 TCCTTCGATTTCCCGTTTATAGA 57.143 39.130 0.00 0.00 0.00 1.98
4008 4418 6.964464 TGGTCATGGGTACAAGTAATATTGT 58.036 36.000 0.00 0.00 45.19 2.71
4025 4435 6.319658 AGGAACAGCAAGTAATAATGGTCATG 59.680 38.462 0.00 0.00 28.98 3.07
4574 4986 8.909671 GCTGCAATAAAGCACAAGATATTTATC 58.090 33.333 0.00 0.00 40.11 1.75
4617 5029 2.113860 TGCCAGGTAAGATGCTTCAC 57.886 50.000 2.07 0.00 0.00 3.18
4670 5082 0.106318 ATGCTGCCCCAAGAGGATTC 60.106 55.000 0.00 0.00 38.24 2.52
4769 5181 6.021672 TCTCTCCCATGCATACAATCTATCT 58.978 40.000 0.00 0.00 0.00 1.98
4811 5223 4.926832 CCGGCCAAATAAGTTTTTACCTTG 59.073 41.667 2.24 0.00 0.00 3.61
4821 5233 2.597578 AAAGGACCGGCCAAATAAGT 57.402 45.000 15.92 0.00 40.02 2.24
4997 5417 6.014242 TGCATCCACCATCTATTTACCTCTAG 60.014 42.308 0.00 0.00 0.00 2.43
5245 5669 8.520351 CATCCACATCATCAAGCATATGTAAAT 58.480 33.333 4.29 0.00 31.55 1.40
5249 5673 4.765339 CCATCCACATCATCAAGCATATGT 59.235 41.667 4.29 0.00 32.91 2.29
5780 6206 6.195600 TGGTTTCTCAGGTACCTACATTTT 57.804 37.500 15.80 0.00 33.05 1.82
5825 6251 4.449068 GCACGGGTTCTATCAATACTCATG 59.551 45.833 0.00 0.00 0.00 3.07
6042 6468 8.045176 ACCAAGAGCAAATGATAAACTAAGAC 57.955 34.615 0.00 0.00 0.00 3.01
6083 6509 2.293122 ACATGCGAGTTAAGCTGCAAAA 59.707 40.909 1.02 0.00 41.22 2.44
6187 6613 0.245539 GGAACTGTGATTCCGACCGA 59.754 55.000 0.00 0.00 38.95 4.69
6421 6847 6.543831 GCAACTCATCCAGTAACTTAATCCAT 59.456 38.462 0.00 0.00 32.30 3.41
6428 6854 3.788227 TGGCAACTCATCCAGTAACTT 57.212 42.857 0.00 0.00 32.30 2.66
6547 6973 3.525609 TCAACCCTCCATTAGGTATTGCA 59.474 43.478 0.00 0.00 44.90 4.08
6598 7024 2.719556 CTGTAAATCCGTATGAGCGTCG 59.280 50.000 0.00 0.00 0.00 5.12
6701 7127 8.918202 TCATATTTCTCCTTTGCCGTATTAAT 57.082 30.769 0.00 0.00 0.00 1.40
6786 7260 6.241882 TGGACGGTTTATTTATCCATCTCA 57.758 37.500 0.00 0.00 34.50 3.27
6821 7295 5.079689 TGTGCCTATTAGTTCGATGAACA 57.920 39.130 11.81 0.00 44.11 3.18
6865 7339 2.752354 CCCCTAGACTATCATGAGCTCG 59.248 54.545 9.64 0.00 0.00 5.03
6869 7343 4.085733 CTGTCCCCCTAGACTATCATGAG 58.914 52.174 0.09 0.00 37.66 2.90
6894 7368 6.329197 CCGGATATCTACATATTTACCCCCAT 59.671 42.308 0.00 0.00 0.00 4.00
6895 7369 5.664006 CCGGATATCTACATATTTACCCCCA 59.336 44.000 0.00 0.00 0.00 4.96
6938 7639 5.943349 TTTACATCCCAGATTAAGGTCGA 57.057 39.130 0.00 0.00 0.00 4.20
6983 7684 5.163195 ACATCTTGTATCCCCCATCTTACAC 60.163 44.000 0.00 0.00 0.00 2.90
7049 7751 2.030540 CAGGTGCCAACATGAAGAACAG 60.031 50.000 0.00 0.00 40.57 3.16
7053 7755 0.251297 CCCAGGTGCCAACATGAAGA 60.251 55.000 0.00 0.00 40.57 2.87
7071 7773 4.725790 ATGAAAAGTCCAAGCTTATGCC 57.274 40.909 0.00 0.00 40.80 4.40
7079 7781 6.813152 ACAAAACACTGAATGAAAAGTCCAAG 59.187 34.615 0.00 0.00 0.00 3.61
7081 7783 6.279513 ACAAAACACTGAATGAAAAGTCCA 57.720 33.333 0.00 0.00 0.00 4.02
7082 7784 8.352942 AGATACAAAACACTGAATGAAAAGTCC 58.647 33.333 0.00 0.00 0.00 3.85
7097 7799 8.747471 TGGAATTGCAATCATAGATACAAAACA 58.253 29.630 13.38 0.00 0.00 2.83
7098 7800 9.754382 ATGGAATTGCAATCATAGATACAAAAC 57.246 29.630 13.38 0.00 0.00 2.43
7129 7849 7.361799 CCAGCCTAAATAAGACCTAAACAACAC 60.362 40.741 0.00 0.00 0.00 3.32
7183 7903 9.298774 AGCGTTACTCTCAAATAAATACTGTAC 57.701 33.333 0.00 0.00 0.00 2.90
7189 7909 5.461078 GGCGAGCGTTACTCTCAAATAAATA 59.539 40.000 3.23 0.00 43.85 1.40
7190 7910 4.270325 GGCGAGCGTTACTCTCAAATAAAT 59.730 41.667 3.23 0.00 43.85 1.40
7191 7911 3.615496 GGCGAGCGTTACTCTCAAATAAA 59.385 43.478 3.23 0.00 43.85 1.40
7192 7912 3.184541 GGCGAGCGTTACTCTCAAATAA 58.815 45.455 3.23 0.00 43.85 1.40
7202 7922 0.170561 TCTTCTCTGGCGAGCGTTAC 59.829 55.000 0.00 0.00 37.19 2.50
7252 7972 4.202567 TGCTGGTCTATTGGTTTCTTTCCT 60.203 41.667 0.00 0.00 0.00 3.36
7276 7996 1.882167 GCTCTGAGCTAGCTTGCCG 60.882 63.158 20.42 9.46 38.45 5.69
7277 7997 4.123300 GCTCTGAGCTAGCTTGCC 57.877 61.111 20.42 6.84 38.45 4.52
7286 8006 0.179086 GTGCCTAGGAAGCTCTGAGC 60.179 60.000 21.72 21.72 42.84 4.26
7329 8049 3.551259 CCATTAGACGGCAACCTGT 57.449 52.632 0.00 0.00 0.00 4.00
7477 11652 2.194800 TCAAGATAACTCGAGCGCAG 57.805 50.000 13.61 2.69 0.00 5.18
7635 11811 4.991153 TCTACTCTGCTTCACTATGGTG 57.009 45.455 2.16 2.16 44.23 4.17
7659 11835 8.141835 GGCAACAAGAAATCAGTGTTAAAAAT 57.858 30.769 0.00 0.00 33.80 1.82
7761 11937 4.735662 TTATTGTTTGAGCGTGTGGTAC 57.264 40.909 0.00 0.00 0.00 3.34
7781 11957 2.431782 AGCTGAGTTTGTGCACCATTTT 59.568 40.909 15.69 0.00 0.00 1.82
7812 11988 4.434713 AACACCGAAATATTGGAACTGC 57.565 40.909 0.00 0.00 33.82 4.40
7818 11994 9.801873 ATAATCTTCAAAACACCGAAATATTGG 57.198 29.630 0.00 0.00 36.02 3.16
7883 12088 2.696759 CGCCGGGGGTTCATGTTTC 61.697 63.158 11.42 0.00 0.00 2.78
7897 12102 1.644786 GGAAGTTGGTCATTCCGCCG 61.645 60.000 0.00 0.00 35.95 6.46
7962 12365 2.246327 TCTGGTTCCTTCCCCTTGTTTT 59.754 45.455 0.00 0.00 0.00 2.43
8006 12409 8.195436 TGCTAGTTGTAGTGTATTATCACTTCC 58.805 37.037 4.72 0.00 44.92 3.46
8098 12504 9.353999 GTCAAACAAATTCTAGAACAAACACTT 57.646 29.630 7.48 0.00 0.00 3.16
8101 12507 9.134734 GTTGTCAAACAAATTCTAGAACAAACA 57.865 29.630 7.48 1.87 40.15 2.83


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

AutoCloner maintained by Alex Coulton.