Multiple sequence alignment - TraesCS3D01G070400

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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 TraesCS3D01G070400 chr3D 100.000 3016 0 0 1 3016 31647340 31650355 0.000000e+00 5570.0
1 TraesCS3D01G070400 chr3D 94.000 700 33 9 2321 3016 31650850 31650156 0.000000e+00 1051.0
2 TraesCS3D01G070400 chr3A 98.030 1015 17 1 1313 2324 51699997 51698983 0.000000e+00 1760.0
3 TraesCS3D01G070400 chr3A 93.510 678 20 4 658 1313 51704924 51704249 0.000000e+00 987.0
4 TraesCS3D01G070400 chr3A 91.456 316 24 2 4 318 51706689 51706376 5.970000e-117 431.0
5 TraesCS3D01G070400 chr3A 90.419 334 10 14 311 627 51705251 51704923 1.290000e-113 420.0
6 TraesCS3D01G070400 chr5B 90.155 193 13 6 1 190 412327533 412327722 2.320000e-61 246.0
7 TraesCS3D01G070400 chr2B 89.691 194 13 6 1 190 214276300 214276490 1.080000e-59 241.0
8 TraesCS3D01G070400 chr2B 89.583 192 14 6 1 190 66609973 66609786 3.890000e-59 239.0
9 TraesCS3D01G070400 chr2B 89.418 189 15 5 4 190 172006338 172006153 1.810000e-57 233.0
10 TraesCS3D01G070400 chr2B 86.603 209 20 8 1 207 495065929 495066131 1.090000e-54 224.0
11 TraesCS3D01G070400 chr2B 92.453 53 2 2 556 606 459477510 459477458 1.160000e-09 75.0
12 TraesCS3D01G070400 chr6B 88.832 197 16 6 1 194 697661131 697660938 1.400000e-58 237.0
13 TraesCS3D01G070400 chr6B 88.265 196 19 4 1 194 270741282 270741089 6.500000e-57 231.0
14 TraesCS3D01G070400 chr7A 88.776 196 17 5 1 194 22104670 22104862 5.030000e-58 235.0
15 TraesCS3D01G070400 chr7A 88.060 67 4 4 557 621 215930470 215930406 3.220000e-10 76.8
16 TraesCS3D01G070400 chr6A 96.000 50 0 2 558 605 17760816 17760767 2.490000e-11 80.5
17 TraesCS3D01G070400 chrUn 91.379 58 3 2 556 611 271622118 271622061 8.960000e-11 78.7
18 TraesCS3D01G070400 chrUn 91.379 58 3 2 556 611 271630241 271630184 8.960000e-11 78.7
19 TraesCS3D01G070400 chr3B 89.062 64 5 2 557 619 598996927 598996865 8.960000e-11 78.7
20 TraesCS3D01G070400 chr4A 92.593 54 2 2 556 607 625489524 625489577 3.220000e-10 76.8
21 TraesCS3D01G070400 chr1B 90.164 61 3 3 556 613 111060032 111060092 3.220000e-10 76.8
22 TraesCS3D01G070400 chr7D 92.308 52 2 2 556 605 587969998 587970049 4.170000e-09 73.1


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 TraesCS3D01G070400 chr3D 31647340 31650355 3015 False 5570.000000 5570 100.000 1 3016 1 chr3D.!!$F1 3015
1 TraesCS3D01G070400 chr3D 31650156 31650850 694 True 1051.000000 1051 94.000 2321 3016 1 chr3D.!!$R1 695
2 TraesCS3D01G070400 chr3A 51698983 51699997 1014 True 1760.000000 1760 98.030 1313 2324 1 chr3A.!!$R1 1011
3 TraesCS3D01G070400 chr3A 51704249 51706689 2440 True 612.666667 987 91.795 4 1313 3 chr3A.!!$R2 1309

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
656 1806 0.368227 CGTTTGCTCGCTCTAGCTTG 59.632 55.0 0.0 0.0 43.19 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2329 3504 1.303309 CACCTGCATAAGCCTAGTGC 58.697 55.0 0.0 0.0 41.13 4.4 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
100 101 7.857885 GGAAAGTTAGATCTGTGACTTTTTGTG 59.142 37.037 23.13 0.00 41.08 3.33
106 107 2.159448 TCTGTGACTTTTTGTGCGGTTG 60.159 45.455 0.00 0.00 0.00 3.77
112 113 2.232696 ACTTTTTGTGCGGTTGGAAAGT 59.767 40.909 0.00 0.00 33.79 2.66
131 132 8.750298 TGGAAAGTGTTGTTTACAAGGAAATAA 58.250 29.630 0.00 0.00 38.80 1.40
159 160 7.086685 AGAGAAAAATAAACTAGTGGGGTGA 57.913 36.000 0.00 0.00 0.00 4.02
170 171 2.774351 GGGGTGATGGGAGGGGAG 60.774 72.222 0.00 0.00 0.00 4.30
171 172 2.372688 GGGTGATGGGAGGGGAGA 59.627 66.667 0.00 0.00 0.00 3.71
234 236 6.497259 TCATAAAGGCTATCCTACCCAGTAAG 59.503 42.308 0.00 0.00 43.40 2.34
236 238 3.847081 AGGCTATCCTACCCAGTAAGAC 58.153 50.000 0.00 0.00 42.06 3.01
246 248 5.766174 CCTACCCAGTAAGACATCTCTACTC 59.234 48.000 2.62 0.00 0.00 2.59
278 280 4.164988 GGAGAATCTGGGAGAATTTGAGGA 59.835 45.833 0.00 0.00 33.73 3.71
299 301 6.350103 AGGAAGGTCCGATTCTTAAGATTTC 58.650 40.000 5.89 6.00 42.75 2.17
302 304 6.546428 AGGTCCGATTCTTAAGATTTCAGA 57.454 37.500 5.89 2.31 0.00 3.27
324 1458 8.781196 TCAGAAGAATCATTCAAAAGAACAGAG 58.219 33.333 0.00 0.00 0.00 3.35
384 1518 3.712907 GTAGCGGAGTTGGCCCCA 61.713 66.667 0.00 0.00 0.00 4.96
431 1565 2.612212 ACTGCAAGAAGTTACCACAACG 59.388 45.455 0.00 0.00 37.43 4.10
518 1652 4.891168 TGTCAGCTATTGCATTTCATCCAT 59.109 37.500 1.12 0.00 42.74 3.41
578 1724 9.228949 AGAATTCCTCTATCAATGCAATGATAC 57.771 33.333 18.52 8.13 40.44 2.24
583 1729 6.232139 TCTATCAATGCAATGATACGCAAG 57.768 37.500 18.52 11.65 42.37 4.01
584 1730 3.069074 TCAATGCAATGATACGCAAGC 57.931 42.857 0.00 0.00 42.37 4.01
585 1731 2.684374 TCAATGCAATGATACGCAAGCT 59.316 40.909 0.00 0.00 42.37 3.74
586 1732 3.129113 TCAATGCAATGATACGCAAGCTT 59.871 39.130 0.00 0.00 42.37 3.74
587 1733 3.788333 ATGCAATGATACGCAAGCTTT 57.212 38.095 0.00 0.00 42.37 3.51
588 1734 4.898829 ATGCAATGATACGCAAGCTTTA 57.101 36.364 0.00 0.00 42.37 1.85
589 1735 4.277257 TGCAATGATACGCAAGCTTTAG 57.723 40.909 0.00 0.00 45.62 1.85
632 1782 7.730364 AAACAAGATTAGTATAATCAGGCCG 57.270 36.000 11.10 0.00 0.00 6.13
633 1783 5.794894 ACAAGATTAGTATAATCAGGCCGG 58.205 41.667 0.00 0.00 0.00 6.13
634 1784 4.473477 AGATTAGTATAATCAGGCCGGC 57.527 45.455 21.18 21.18 0.00 6.13
635 1785 4.097418 AGATTAGTATAATCAGGCCGGCT 58.903 43.478 28.56 8.66 0.00 5.52
636 1786 3.955650 TTAGTATAATCAGGCCGGCTC 57.044 47.619 28.56 16.85 0.00 4.70
637 1787 0.977395 AGTATAATCAGGCCGGCTCC 59.023 55.000 28.56 11.04 0.00 4.70
638 1788 0.389948 GTATAATCAGGCCGGCTCCG 60.390 60.000 28.56 15.14 39.44 4.63
639 1789 0.830444 TATAATCAGGCCGGCTCCGT 60.830 55.000 28.56 10.83 37.81 4.69
640 1790 1.696097 ATAATCAGGCCGGCTCCGTT 61.696 55.000 28.56 18.14 37.81 4.44
641 1791 1.906105 TAATCAGGCCGGCTCCGTTT 61.906 55.000 28.56 17.08 37.81 3.60
642 1792 3.976701 ATCAGGCCGGCTCCGTTTG 62.977 63.158 28.56 14.70 37.81 2.93
649 1799 3.491652 GGCTCCGTTTGCTCGCTC 61.492 66.667 0.00 0.00 0.00 5.03
650 1800 2.433318 GCTCCGTTTGCTCGCTCT 60.433 61.111 0.00 0.00 0.00 4.09
651 1801 1.153823 GCTCCGTTTGCTCGCTCTA 60.154 57.895 0.00 0.00 0.00 2.43
652 1802 1.142778 GCTCCGTTTGCTCGCTCTAG 61.143 60.000 0.00 0.00 0.00 2.43
653 1803 1.142778 CTCCGTTTGCTCGCTCTAGC 61.143 60.000 0.00 0.00 43.08 3.42
654 1804 1.153745 CCGTTTGCTCGCTCTAGCT 60.154 57.895 0.00 0.00 43.19 3.32
655 1805 0.737715 CCGTTTGCTCGCTCTAGCTT 60.738 55.000 0.00 0.00 43.19 3.74
656 1806 0.368227 CGTTTGCTCGCTCTAGCTTG 59.632 55.000 0.00 0.00 43.19 4.01
673 1823 1.263217 CTTGTCTCGGTCGTTTTTGGG 59.737 52.381 0.00 0.00 0.00 4.12
677 1827 4.032987 CGGTCGTTTTTGGGCCGG 62.033 66.667 0.00 0.00 38.86 6.13
684 1834 0.898326 GTTTTTGGGCCGGGAGTGAT 60.898 55.000 2.18 0.00 0.00 3.06
926 2088 1.302949 CCTCCCCAATTTCCTCGCA 59.697 57.895 0.00 0.00 0.00 5.10
1013 2185 3.057548 TGCAATGCAGCCTGTCGG 61.058 61.111 2.72 0.00 33.32 4.79
1025 2197 1.068083 CTGTCGGGGACATGGATCG 59.932 63.158 0.00 0.00 41.94 3.69
1183 2355 0.317160 CCAGACGCACCTACACTTGA 59.683 55.000 0.00 0.00 0.00 3.02
1217 2389 6.979238 GTGGTGCCGATCCTAATCTATTATAC 59.021 42.308 0.00 0.00 0.00 1.47
1229 2401 6.763715 AATCTATTATACCAGACAGCCCAA 57.236 37.500 0.00 0.00 0.00 4.12
1297 2469 4.393834 TGGCATTGTTACTGTTTCTGCTA 58.606 39.130 0.00 0.00 0.00 3.49
1346 2518 3.003793 GCAAGGTCACTCTTTCCAAGAAC 59.996 47.826 0.00 0.00 37.02 3.01
1421 2593 3.813166 ACCAGGAACATTGTTGTAGAACG 59.187 43.478 6.80 0.00 34.06 3.95
1435 2607 4.566004 TGTAGAACGAGGAGAAACATTGG 58.434 43.478 0.00 0.00 0.00 3.16
1449 2621 1.412343 ACATTGGCCGCTTTCTTTGTT 59.588 42.857 0.00 0.00 0.00 2.83
1450 2622 2.061028 CATTGGCCGCTTTCTTTGTTC 58.939 47.619 0.00 0.00 0.00 3.18
1456 2628 2.858646 GCCGCTTTCTTTGTTCTTGGTC 60.859 50.000 0.00 0.00 0.00 4.02
1470 2642 3.689347 TCTTGGTCCAATTGGAGATGTG 58.311 45.455 27.73 15.85 46.49 3.21
1706 2881 1.149361 TTTCGACACGACTGCACACC 61.149 55.000 0.00 0.00 34.89 4.16
1873 3048 4.765273 TGAGATGGTATGCGCTTTTCTTA 58.235 39.130 9.73 0.00 0.00 2.10
2144 3319 0.465460 TTTGAAACTCTGCGGCAGGT 60.465 50.000 28.18 21.19 31.51 4.00
2255 3430 6.266558 TGCAAAACCACAAGGATGTAATAGTT 59.733 34.615 0.00 0.00 37.82 2.24
2324 3499 5.398603 TTGAAATATTCATTGCCGTTGGT 57.601 34.783 0.00 0.00 39.84 3.67
2325 3500 5.398603 TGAAATATTCATTGCCGTTGGTT 57.601 34.783 0.00 0.00 34.08 3.67
2326 3501 5.406649 TGAAATATTCATTGCCGTTGGTTC 58.593 37.500 0.00 0.00 34.08 3.62
2327 3502 5.047731 TGAAATATTCATTGCCGTTGGTTCA 60.048 36.000 0.00 0.00 34.08 3.18
2328 3503 2.723124 ATTCATTGCCGTTGGTTCAC 57.277 45.000 0.00 0.00 0.00 3.18
2329 3504 0.309302 TTCATTGCCGTTGGTTCACG 59.691 50.000 0.00 0.00 40.02 4.35
2621 3796 1.507140 TACATCAGCTCCCCGGAAAT 58.493 50.000 0.73 0.00 0.00 2.17
2885 4060 6.515862 GCAAGACACTCTAGATATTCATCGGT 60.516 42.308 0.00 0.00 36.20 4.69
2886 4061 7.308649 GCAAGACACTCTAGATATTCATCGGTA 60.309 40.741 0.00 0.00 36.20 4.02
2887 4062 8.568794 CAAGACACTCTAGATATTCATCGGTAA 58.431 37.037 0.00 0.00 36.20 2.85
2888 4063 8.871629 AGACACTCTAGATATTCATCGGTAAT 57.128 34.615 0.00 0.00 36.20 1.89
2889 4064 9.961264 AGACACTCTAGATATTCATCGGTAATA 57.039 33.333 0.00 0.00 36.20 0.98
2892 4067 9.457110 CACTCTAGATATTCATCGGTAATATGC 57.543 37.037 0.00 0.00 36.20 3.14
2898 4077 9.601217 AGATATTCATCGGTAATATGCTTAACC 57.399 33.333 0.00 0.00 36.20 2.85
2900 4079 4.562082 TCATCGGTAATATGCTTAACCCG 58.438 43.478 8.00 8.00 35.41 5.28
2902 4081 3.719924 TCGGTAATATGCTTAACCCGTG 58.280 45.455 11.87 0.00 35.59 4.94
2905 4084 4.648651 GGTAATATGCTTAACCCGTGGAT 58.351 43.478 0.00 0.00 0.00 3.41
2908 4087 0.751643 ATGCTTAACCCGTGGATGGC 60.752 55.000 0.00 0.00 0.00 4.40
2911 4090 1.921869 CTTAACCCGTGGATGGCCCT 61.922 60.000 0.00 0.00 35.38 5.19
2913 4092 2.833151 TAACCCGTGGATGGCCCTCT 62.833 60.000 8.03 0.00 35.38 3.69
2914 4093 4.181010 CCCGTGGATGGCCCTCTG 62.181 72.222 8.03 0.00 35.38 3.35
2916 4095 3.402681 CGTGGATGGCCCTCTGGT 61.403 66.667 8.03 0.00 35.38 4.00
2919 4098 3.017581 GGATGGCCCTCTGGTGGT 61.018 66.667 8.03 0.00 0.00 4.16
2922 4101 3.586225 ATGGCCCTCTGGTGGTCCT 62.586 63.158 0.00 0.00 34.23 3.85
2925 4104 1.920835 GCCCTCTGGTGGTCCTTCT 60.921 63.158 0.00 0.00 34.23 2.85
2927 4106 1.952621 CCCTCTGGTGGTCCTTCTAA 58.047 55.000 0.00 0.00 34.23 2.10
2929 4108 1.208293 CCTCTGGTGGTCCTTCTAAGC 59.792 57.143 0.00 0.00 34.23 3.09
2930 4109 1.208293 CTCTGGTGGTCCTTCTAAGCC 59.792 57.143 0.00 0.00 34.23 4.35
2933 4112 1.351017 TGGTGGTCCTTCTAAGCCTTG 59.649 52.381 0.00 0.00 34.23 3.61
2935 4114 2.039879 GGTGGTCCTTCTAAGCCTTGAA 59.960 50.000 0.00 0.00 0.00 2.69
2936 4115 3.497942 GGTGGTCCTTCTAAGCCTTGAAA 60.498 47.826 0.00 0.00 0.00 2.69
2937 4116 3.502595 GTGGTCCTTCTAAGCCTTGAAAC 59.497 47.826 0.00 0.00 0.00 2.78
2939 4118 4.141251 TGGTCCTTCTAAGCCTTGAAACTT 60.141 41.667 0.00 0.00 0.00 2.66
2940 4119 4.456222 GGTCCTTCTAAGCCTTGAAACTTC 59.544 45.833 0.00 0.00 0.00 3.01
2941 4120 5.063880 GTCCTTCTAAGCCTTGAAACTTCA 58.936 41.667 0.00 0.00 34.92 3.02
2942 4121 5.180304 GTCCTTCTAAGCCTTGAAACTTCAG 59.820 44.000 0.00 0.00 38.61 3.02
2943 4122 4.457257 CCTTCTAAGCCTTGAAACTTCAGG 59.543 45.833 0.00 0.00 38.61 3.86
2949 4128 1.911057 CTTGAAACTTCAGGGACCCC 58.089 55.000 7.00 1.17 38.61 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 4.694760 AATCAACCGATCCATCTCATCA 57.305 40.909 0.00 0.00 0.00 3.07
42 43 4.214971 CCAAATCAACCGATCCATCTCATC 59.785 45.833 0.00 0.00 0.00 2.92
47 48 2.654863 ACCCAAATCAACCGATCCATC 58.345 47.619 0.00 0.00 0.00 3.51
100 101 2.287393 AAACAACACTTTCCAACCGC 57.713 45.000 0.00 0.00 0.00 5.68
106 107 9.758651 ATTATTTCCTTGTAAACAACACTTTCC 57.241 29.630 0.00 0.00 38.00 3.13
131 132 8.170730 ACCCCACTAGTTTATTTTTCTCTTCAT 58.829 33.333 0.00 0.00 0.00 2.57
134 135 7.523415 TCACCCCACTAGTTTATTTTTCTCTT 58.477 34.615 0.00 0.00 0.00 2.85
138 139 6.127451 CCCATCACCCCACTAGTTTATTTTTC 60.127 42.308 0.00 0.00 0.00 2.29
159 160 1.368374 TTTTTCGTCTCCCCTCCCAT 58.632 50.000 0.00 0.00 0.00 4.00
179 181 0.680061 GTCTCCCACTTTCGTCTGGT 59.320 55.000 0.00 0.00 0.00 4.00
183 185 2.144482 TTTCGTCTCCCACTTTCGTC 57.856 50.000 0.00 0.00 0.00 4.20
228 230 7.422399 GCTTTAGGAGTAGAGATGTCTTACTG 58.578 42.308 0.00 0.00 33.84 2.74
234 236 3.004944 CCCGCTTTAGGAGTAGAGATGTC 59.995 52.174 0.00 0.00 0.00 3.06
236 238 3.223435 TCCCGCTTTAGGAGTAGAGATG 58.777 50.000 0.00 0.00 0.00 2.90
246 248 1.202698 CCCAGATTCTCCCGCTTTAGG 60.203 57.143 0.00 0.00 0.00 2.69
278 280 6.947464 TCTGAAATCTTAAGAATCGGACCTT 58.053 36.000 20.86 4.14 29.80 3.50
299 301 7.537991 GCTCTGTTCTTTTGAATGATTCTTCTG 59.462 37.037 6.73 0.00 40.94 3.02
302 304 6.492772 AGGCTCTGTTCTTTTGAATGATTCTT 59.507 34.615 6.73 0.00 40.94 2.52
309 311 8.870075 ATACTTTAGGCTCTGTTCTTTTGAAT 57.130 30.769 0.00 0.00 40.94 2.57
342 1476 6.726379 TGGACCAATGACCAAATGAGTAATA 58.274 36.000 0.00 0.00 33.25 0.98
384 1518 3.897239 TGGACCTGAAAGTTGTGAACAT 58.103 40.909 0.00 0.00 0.00 2.71
431 1565 5.555017 ACATGCTGGAGGATATGTACATTC 58.445 41.667 14.77 10.94 32.41 2.67
550 1696 9.803507 ATCATTGCATTGATAGAGGAATTCTTA 57.196 29.630 19.81 0.00 37.36 2.10
559 1705 5.851047 TGCGTATCATTGCATTGATAGAG 57.149 39.130 24.60 21.69 38.83 2.43
578 1724 3.383546 TTGCGAATACTAAAGCTTGCG 57.616 42.857 0.00 0.00 0.00 4.85
608 1758 6.710744 CCGGCCTGATTATACTAATCTTGTTT 59.289 38.462 0.00 0.00 0.00 2.83
622 1772 1.906105 AAACGGAGCCGGCCTGATTA 61.906 55.000 26.15 0.00 44.69 1.75
625 1775 4.697756 CAAACGGAGCCGGCCTGA 62.698 66.667 26.15 0.00 44.69 3.86
632 1782 2.558554 TAGAGCGAGCAAACGGAGCC 62.559 60.000 0.00 0.00 0.00 4.70
633 1783 1.142778 CTAGAGCGAGCAAACGGAGC 61.143 60.000 0.00 0.00 0.00 4.70
634 1784 1.142778 GCTAGAGCGAGCAAACGGAG 61.143 60.000 0.00 0.00 42.36 4.63
635 1785 1.153823 GCTAGAGCGAGCAAACGGA 60.154 57.895 0.00 0.00 42.36 4.69
636 1786 0.737715 AAGCTAGAGCGAGCAAACGG 60.738 55.000 10.35 0.00 45.43 4.44
637 1787 0.368227 CAAGCTAGAGCGAGCAAACG 59.632 55.000 10.35 0.00 45.43 3.60
638 1788 1.391826 GACAAGCTAGAGCGAGCAAAC 59.608 52.381 10.35 0.00 45.43 2.93
639 1789 1.273606 AGACAAGCTAGAGCGAGCAAA 59.726 47.619 10.35 0.00 45.43 3.68
640 1790 0.891373 AGACAAGCTAGAGCGAGCAA 59.109 50.000 10.35 0.00 45.43 3.91
641 1791 0.453793 GAGACAAGCTAGAGCGAGCA 59.546 55.000 10.35 0.00 45.43 4.26
646 1796 0.248296 CGACCGAGACAAGCTAGAGC 60.248 60.000 0.00 0.00 42.49 4.09
647 1797 1.088306 ACGACCGAGACAAGCTAGAG 58.912 55.000 0.00 0.00 0.00 2.43
648 1798 1.531423 AACGACCGAGACAAGCTAGA 58.469 50.000 0.00 0.00 0.00 2.43
649 1799 2.349297 AAACGACCGAGACAAGCTAG 57.651 50.000 0.00 0.00 0.00 3.42
650 1800 2.798283 CAAAAACGACCGAGACAAGCTA 59.202 45.455 0.00 0.00 0.00 3.32
651 1801 1.597663 CAAAAACGACCGAGACAAGCT 59.402 47.619 0.00 0.00 0.00 3.74
652 1802 1.333791 CCAAAAACGACCGAGACAAGC 60.334 52.381 0.00 0.00 0.00 4.01
653 1803 1.263217 CCCAAAAACGACCGAGACAAG 59.737 52.381 0.00 0.00 0.00 3.16
654 1804 1.301423 CCCAAAAACGACCGAGACAA 58.699 50.000 0.00 0.00 0.00 3.18
655 1805 1.161563 GCCCAAAAACGACCGAGACA 61.162 55.000 0.00 0.00 0.00 3.41
656 1806 1.572941 GCCCAAAAACGACCGAGAC 59.427 57.895 0.00 0.00 0.00 3.36
673 1823 2.592861 GCATGGATCACTCCCGGC 60.593 66.667 0.00 0.00 41.29 6.13
677 1827 1.227674 GGACGGCATGGATCACTCC 60.228 63.158 0.00 0.00 42.45 3.85
684 1834 1.695114 ATCCAATCGGACGGCATGGA 61.695 55.000 13.40 13.40 46.79 3.41
719 1869 3.123620 GCTCACAGGCTCAAGGCG 61.124 66.667 0.00 0.00 46.23 5.52
908 2070 1.032114 GTGCGAGGAAATTGGGGAGG 61.032 60.000 0.00 0.00 0.00 4.30
912 2074 1.376683 TCGGTGCGAGGAAATTGGG 60.377 57.895 0.00 0.00 0.00 4.12
1013 2185 1.447643 CTCACCCGATCCATGTCCC 59.552 63.158 0.00 0.00 0.00 4.46
1025 2197 1.152881 GGGGACATCATGCTCACCC 60.153 63.158 0.00 0.00 36.90 4.61
1072 2244 1.027357 CAGCCGAAATCCCATCCAAG 58.973 55.000 0.00 0.00 0.00 3.61
1118 2290 3.112263 ACGATCTACATGAAAGGGGGAA 58.888 45.455 0.00 0.00 0.00 3.97
1119 2291 2.434336 CACGATCTACATGAAAGGGGGA 59.566 50.000 0.00 0.00 0.00 4.81
1183 2355 1.248785 ATCGGCACCACAGACGTACT 61.249 55.000 0.00 0.00 0.00 2.73
1217 2389 3.909662 CCGATTTGGGCTGTCTGG 58.090 61.111 0.00 0.00 0.00 3.86
1229 2401 4.586841 TCAAATCTTTTGGTTCACCCGATT 59.413 37.500 0.00 0.00 35.15 3.34
1237 2409 5.901552 TGGTTGACTCAAATCTTTTGGTTC 58.098 37.500 0.00 0.00 0.00 3.62
1239 2411 4.202151 GCTGGTTGACTCAAATCTTTTGGT 60.202 41.667 0.00 0.00 0.00 3.67
1297 2469 9.401058 AGCTGCTATTATATGACAAAAGTTTCT 57.599 29.630 0.00 0.00 0.00 2.52
1377 2549 1.003812 TCTACGGTTGTTCCATTGGGG 59.996 52.381 2.09 0.00 35.57 4.96
1421 2593 0.678048 AGCGGCCAATGTTTCTCCTC 60.678 55.000 2.24 0.00 0.00 3.71
1435 2607 1.067060 ACCAAGAACAAAGAAAGCGGC 59.933 47.619 0.00 0.00 0.00 6.53
1449 2621 3.330405 TCACATCTCCAATTGGACCAAGA 59.670 43.478 23.63 18.49 39.78 3.02
1450 2622 3.689347 TCACATCTCCAATTGGACCAAG 58.311 45.455 23.63 13.67 39.78 3.61
1456 2628 5.647589 CACTTCATTCACATCTCCAATTGG 58.352 41.667 19.08 19.08 0.00 3.16
1470 2642 3.347958 TCAACAAACCGCACTTCATTC 57.652 42.857 0.00 0.00 0.00 2.67
1541 2713 2.358195 GGTAGCCTTGGTGGAAATGGAT 60.358 50.000 0.00 0.00 38.35 3.41
1706 2881 3.249320 CCCACGAGCAGAAATATGTGATG 59.751 47.826 0.00 0.00 0.00 3.07
1927 3102 6.957631 TGCAAAATGGACTAGATAGGAAAGA 58.042 36.000 0.00 0.00 0.00 2.52
2329 3504 1.303309 CACCTGCATAAGCCTAGTGC 58.697 55.000 0.00 0.00 41.13 4.40
2881 4056 3.493002 CCACGGGTTAAGCATATTACCGA 60.493 47.826 7.03 0.00 42.19 4.69
2882 4057 2.803956 CCACGGGTTAAGCATATTACCG 59.196 50.000 7.03 0.00 44.86 4.02
2885 4060 4.647611 CCATCCACGGGTTAAGCATATTA 58.352 43.478 7.03 0.00 0.00 0.98
2886 4061 3.486383 CCATCCACGGGTTAAGCATATT 58.514 45.455 7.03 0.00 0.00 1.28
2887 4062 2.814097 GCCATCCACGGGTTAAGCATAT 60.814 50.000 7.03 0.00 0.00 1.78
2888 4063 1.476110 GCCATCCACGGGTTAAGCATA 60.476 52.381 7.03 0.00 0.00 3.14
2889 4064 0.751643 GCCATCCACGGGTTAAGCAT 60.752 55.000 7.03 0.00 0.00 3.79
2892 4067 1.453197 GGGCCATCCACGGGTTAAG 60.453 63.158 4.39 0.00 35.00 1.85
2894 4073 2.285818 AGGGCCATCCACGGGTTA 60.286 61.111 6.18 0.00 38.24 2.85
2897 4076 4.181010 CAGAGGGCCATCCACGGG 62.181 72.222 15.12 0.00 38.24 5.28
2898 4077 4.181010 CCAGAGGGCCATCCACGG 62.181 72.222 15.12 8.83 38.24 4.94
2900 4079 2.273449 CACCAGAGGGCCATCCAC 59.727 66.667 15.12 0.00 37.90 4.02
2902 4081 3.017581 ACCACCAGAGGGCCATCC 61.018 66.667 15.12 0.00 37.90 3.51
2908 4087 1.834263 CTTAGAAGGACCACCAGAGGG 59.166 57.143 0.00 0.00 38.94 4.30
2911 4090 1.203313 AGGCTTAGAAGGACCACCAGA 60.203 52.381 0.00 0.00 38.94 3.86
2913 4092 1.351017 CAAGGCTTAGAAGGACCACCA 59.649 52.381 0.00 0.00 38.94 4.17
2914 4093 1.628846 TCAAGGCTTAGAAGGACCACC 59.371 52.381 0.00 0.00 0.00 4.61
2916 4095 3.394606 AGTTTCAAGGCTTAGAAGGACCA 59.605 43.478 0.00 0.00 0.00 4.02
2919 4098 5.304686 TGAAGTTTCAAGGCTTAGAAGGA 57.695 39.130 0.00 0.00 33.55 3.36
2922 4101 4.104102 TCCCTGAAGTTTCAAGGCTTAGAA 59.896 41.667 0.00 3.74 38.42 2.10
2925 4104 3.497942 GGTCCCTGAAGTTTCAAGGCTTA 60.498 47.826 0.00 0.00 38.42 3.09
2927 4106 1.202940 GGTCCCTGAAGTTTCAAGGCT 60.203 52.381 4.89 0.00 38.42 4.58
2929 4108 1.547901 GGGGTCCCTGAAGTTTCAAGG 60.548 57.143 8.15 3.56 39.61 3.61
2930 4109 1.425448 AGGGGTCCCTGAAGTTTCAAG 59.575 52.381 7.93 0.00 46.22 3.02
2942 4121 4.284746 CACTCTAGATATTCAAGGGGTCCC 59.715 50.000 0.00 0.00 0.00 4.46
2943 4122 4.902448 ACACTCTAGATATTCAAGGGGTCC 59.098 45.833 0.00 0.00 0.00 4.46
2944 4123 5.836358 AGACACTCTAGATATTCAAGGGGTC 59.164 44.000 0.00 0.00 0.00 4.46
2945 4124 5.782925 AGACACTCTAGATATTCAAGGGGT 58.217 41.667 0.00 0.00 0.00 4.95
2946 4125 6.520272 CAAGACACTCTAGATATTCAAGGGG 58.480 44.000 0.00 0.00 0.00 4.79
2947 4126 5.988561 GCAAGACACTCTAGATATTCAAGGG 59.011 44.000 0.00 0.00 0.00 3.95
2948 4127 6.815089 AGCAAGACACTCTAGATATTCAAGG 58.185 40.000 0.00 0.00 0.00 3.61
2949 4128 9.979578 ATTAGCAAGACACTCTAGATATTCAAG 57.020 33.333 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.