Multiple sequence alignment - TraesCS2D01G579000

Loading Multiple Alignment...

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 TraesCS2D01G579000 chr2D 100.000 3154 0 0 1 3154 641609472 641606319 0.000000e+00 5825.0
1 TraesCS2D01G579000 chr2D 91.056 805 47 12 764 1559 641959240 641958452 0.000000e+00 1064.0
2 TraesCS2D01G579000 chr2D 91.256 629 37 10 1555 2178 641957919 641957304 0.000000e+00 841.0
3 TraesCS2D01G579000 chr2D 90.506 632 43 10 1555 2181 597904040 597903421 0.000000e+00 819.0
4 TraesCS2D01G579000 chr2D 89.937 477 32 8 764 1238 597922962 597922500 4.500000e-168 601.0
5 TraesCS2D01G579000 chr2D 97.270 293 8 0 1267 1559 597904891 597904599 6.080000e-137 497.0
6 TraesCS2D01G579000 chr2D 94.035 285 16 1 1 284 598020100 598019816 6.250000e-117 431.0
7 TraesCS2D01G579000 chr2D 93.684 285 17 1 1 284 598048291 598048007 2.910000e-115 425.0
8 TraesCS2D01G579000 chr2D 96.063 127 5 0 279 405 598010832 598010706 1.150000e-49 207.0
9 TraesCS2D01G579000 chr2D 96.063 127 5 0 279 405 598039015 598038889 1.150000e-49 207.0
10 TraesCS2D01G579000 chr2D 85.625 160 20 2 475 632 537516387 537516229 7.000000e-37 165.0
11 TraesCS2D01G579000 chr2D 87.000 100 12 1 2 101 597897616 597897714 9.250000e-21 111.0
12 TraesCS2D01G579000 chr2D 85.149 101 13 2 2668 2768 537447243 537447145 5.570000e-18 102.0
13 TraesCS2D01G579000 chr2A 88.836 1890 120 37 689 2529 766710752 766708905 0.000000e+00 2237.0
14 TraesCS2D01G579000 chr2A 91.021 568 28 5 2607 3154 766708639 766708075 0.000000e+00 745.0
15 TraesCS2D01G579000 chr2A 93.207 368 21 4 227 592 766711894 766711529 3.580000e-149 538.0
16 TraesCS2D01G579000 chr2A 91.810 232 17 2 1 230 766712381 766712150 3.920000e-84 322.0
17 TraesCS2D01G579000 chr2A 95.946 74 3 0 2524 2597 766708814 766708741 1.540000e-23 121.0
18 TraesCS2D01G579000 chr2A 85.000 80 8 4 339 418 767558731 767558656 9.380000e-11 78.7
19 TraesCS2D01G579000 chr2A 100.000 28 0 0 638 665 766710779 766710752 6.000000e-03 52.8
20 TraesCS2D01G579000 chr2B 91.480 1561 82 17 689 2230 800026983 800028511 0.000000e+00 2098.0
21 TraesCS2D01G579000 chr2B 90.071 282 24 1 351 632 800025723 800026000 2.310000e-96 363.0
22 TraesCS2D01G579000 chr2B 84.983 293 34 10 2241 2529 800028565 800028851 3.980000e-74 289.0
23 TraesCS2D01G579000 chr2B 89.730 185 14 4 2974 3154 800029420 800029603 6.800000e-57 231.0
24 TraesCS2D01G579000 chr2B 94.667 75 3 1 2524 2597 800028910 800028984 7.150000e-22 115.0
25 TraesCS2D01G579000 chr6B 86.420 162 17 4 475 632 661519342 661519182 4.180000e-39 172.0
26 TraesCS2D01G579000 chr3D 86.076 158 18 4 475 630 35357486 35357331 1.950000e-37 167.0
27 TraesCS2D01G579000 chr5D 85.535 159 21 2 475 632 493832372 493832529 7.000000e-37 165.0
28 TraesCS2D01G579000 chr4A 85.185 162 18 5 474 632 559353292 559353450 9.050000e-36 161.0
29 TraesCS2D01G579000 chr1D 84.906 159 22 2 475 632 430113407 430113564 3.260000e-35 159.0
30 TraesCS2D01G579000 chrUn 84.810 158 22 2 475 632 86810958 86811113 1.170000e-34 158.0


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 TraesCS2D01G579000 chr2D 641606319 641609472 3153 True 5825.0 5825 100.0000 1 3154 1 chr2D.!!$R8 3153
1 TraesCS2D01G579000 chr2D 641957304 641959240 1936 True 952.5 1064 91.1560 764 2178 2 chr2D.!!$R10 1414
2 TraesCS2D01G579000 chr2D 597903421 597904891 1470 True 658.0 819 93.8880 1267 2181 2 chr2D.!!$R9 914
3 TraesCS2D01G579000 chr2A 766708075 766712381 4306 True 669.3 2237 93.4700 1 3154 6 chr2A.!!$R2 3153
4 TraesCS2D01G579000 chr2B 800025723 800029603 3880 False 619.2 2098 90.1862 351 3154 5 chr2B.!!$F1 2803

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
61 62 0.032130 ATCGACGATGATTCCCACGG 59.968 55.0 10.09 0.00 0.0 4.94 F
666 1917 0.322008 AGGCTCAGCAGTGTAAAGGC 60.322 55.0 0.00 6.33 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1211 2479 0.196118 AGAAGAGGGGGAAGGTTGGA 59.804 55.0 0.0 0.0 0.0 3.53 R
2604 5157 1.402479 CGCCTGTTTTTAATGCCGCG 61.402 55.0 0.0 0.0 0.0 6.46 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
38 39 1.361668 GGTTCACGACGAGCATGCAT 61.362 55.000 21.98 4.40 0.00 3.96
43 44 1.063027 CACGACGAGCATGCATTGAAT 59.937 47.619 21.98 0.00 0.00 2.57
45 46 1.655600 CGACGAGCATGCATTGAATCG 60.656 52.381 21.98 20.48 40.14 3.34
46 47 1.594397 GACGAGCATGCATTGAATCGA 59.406 47.619 25.56 0.00 38.62 3.59
60 61 1.787155 GAATCGACGATGATTCCCACG 59.213 52.381 11.83 0.00 45.46 4.94
61 62 0.032130 ATCGACGATGATTCCCACGG 59.968 55.000 10.09 0.00 0.00 4.94
62 63 2.237751 CGACGATGATTCCCACGGC 61.238 63.158 0.00 0.00 0.00 5.68
63 64 1.153449 GACGATGATTCCCACGGCA 60.153 57.895 0.00 0.00 33.73 5.69
65 66 1.024579 ACGATGATTCCCACGGCAAC 61.025 55.000 0.00 0.00 0.00 4.17
194 197 6.322201 CCAAAATTATATGGCAGAGGAACACT 59.678 38.462 0.00 0.00 0.00 3.55
212 215 3.201266 ACACTGACAGGGTAAGTTTCCAA 59.799 43.478 9.10 0.00 23.74 3.53
214 217 4.036380 CACTGACAGGGTAAGTTTCCAAAC 59.964 45.833 7.51 0.00 39.17 2.93
250 512 3.449746 TTCCCCACCAAATAACCTCAG 57.550 47.619 0.00 0.00 0.00 3.35
254 516 2.356135 CCACCAAATAACCTCAGTCCG 58.644 52.381 0.00 0.00 0.00 4.79
258 520 2.629051 CAAATAACCTCAGTCCGACCC 58.371 52.381 0.00 0.00 0.00 4.46
316 578 5.605908 TCCAAGAAGAAGCTATCATCTCCAT 59.394 40.000 0.00 0.00 35.11 3.41
320 582 2.977580 AGAAGCTATCATCTCCATGGCA 59.022 45.455 6.96 0.00 0.00 4.92
508 770 9.615295 GCACGGTTTAAGAGATAAAATGTTTTA 57.385 29.630 0.87 0.87 35.33 1.52
556 1061 1.002468 CTTTCAGGTTGCGACAAGTGG 60.002 52.381 6.39 0.00 0.00 4.00
564 1069 4.088762 CGACAAGTGGCGCGCATT 62.089 61.111 34.42 20.92 40.91 3.56
565 1070 2.202349 GACAAGTGGCGCGCATTC 60.202 61.111 34.42 21.16 0.00 2.67
566 1071 2.965147 GACAAGTGGCGCGCATTCA 61.965 57.895 34.42 19.40 0.00 2.57
578 1083 2.749865 GCATTCAGCGCGCCACTTA 61.750 57.895 30.33 9.62 0.00 2.24
581 1086 0.461870 ATTCAGCGCGCCACTTATCA 60.462 50.000 30.33 3.40 0.00 2.15
592 1097 2.554344 GCCACTTATCACAACCTGGGAA 60.554 50.000 0.00 0.00 31.08 3.97
593 1098 3.761897 CCACTTATCACAACCTGGGAAA 58.238 45.455 0.00 0.00 31.08 3.13
594 1099 3.758554 CCACTTATCACAACCTGGGAAAG 59.241 47.826 0.00 0.00 31.08 2.62
595 1100 4.506625 CCACTTATCACAACCTGGGAAAGA 60.507 45.833 0.00 0.00 31.08 2.52
597 1102 5.124457 CACTTATCACAACCTGGGAAAGATG 59.876 44.000 0.00 0.00 31.08 2.90
598 1103 2.584835 TCACAACCTGGGAAAGATGG 57.415 50.000 0.00 0.00 0.00 3.51
599 1104 1.075374 TCACAACCTGGGAAAGATGGG 59.925 52.381 0.00 0.00 0.00 4.00
600 1105 1.075374 CACAACCTGGGAAAGATGGGA 59.925 52.381 0.00 0.00 0.00 4.37
601 1106 1.075536 ACAACCTGGGAAAGATGGGAC 59.924 52.381 0.00 0.00 0.00 4.46
603 1108 0.995024 ACCTGGGAAAGATGGGACTG 59.005 55.000 0.00 0.00 0.00 3.51
604 1109 1.289160 CCTGGGAAAGATGGGACTGA 58.711 55.000 0.00 0.00 0.00 3.41
606 1111 3.048600 CCTGGGAAAGATGGGACTGATA 58.951 50.000 0.00 0.00 0.00 2.15
607 1112 3.654806 CCTGGGAAAGATGGGACTGATAT 59.345 47.826 0.00 0.00 0.00 1.63
610 1817 5.448654 TGGGAAAGATGGGACTGATATTTG 58.551 41.667 0.00 0.00 0.00 2.32
614 1821 7.288621 GGGAAAGATGGGACTGATATTTGAAAT 59.711 37.037 0.00 0.00 0.00 2.17
619 1826 5.508567 TGGGACTGATATTTGAAATGAGCA 58.491 37.500 0.00 0.00 0.00 4.26
622 1829 6.459298 GGGACTGATATTTGAAATGAGCACTG 60.459 42.308 0.00 0.00 0.00 3.66
624 1831 5.651139 ACTGATATTTGAAATGAGCACTGCT 59.349 36.000 2.22 2.22 43.88 4.24
632 1839 7.686438 TTGAAATGAGCACTGCTTAATTAGA 57.314 32.000 4.67 0.00 39.88 2.10
633 1840 7.076842 TGAAATGAGCACTGCTTAATTAGAC 57.923 36.000 4.67 5.50 39.88 2.59
634 1841 6.654582 TGAAATGAGCACTGCTTAATTAGACA 59.345 34.615 4.67 7.52 39.88 3.41
636 1843 4.893608 TGAGCACTGCTTAATTAGACACA 58.106 39.130 4.67 0.00 39.88 3.72
665 1916 1.446907 CAGGCTCAGCAGTGTAAAGG 58.553 55.000 0.00 0.00 0.00 3.11
666 1917 0.322008 AGGCTCAGCAGTGTAAAGGC 60.322 55.000 0.00 6.33 0.00 4.35
667 1918 0.322008 GGCTCAGCAGTGTAAAGGCT 60.322 55.000 0.00 0.00 38.70 4.58
668 1919 1.528129 GCTCAGCAGTGTAAAGGCTT 58.472 50.000 0.00 0.00 35.27 4.35
669 1920 1.466558 GCTCAGCAGTGTAAAGGCTTC 59.533 52.381 0.00 0.00 35.27 3.86
670 1921 2.079925 CTCAGCAGTGTAAAGGCTTCC 58.920 52.381 0.00 0.00 35.27 3.46
671 1922 1.168714 CAGCAGTGTAAAGGCTTCCC 58.831 55.000 0.00 0.00 35.27 3.97
672 1923 1.068121 AGCAGTGTAAAGGCTTCCCT 58.932 50.000 0.00 0.00 45.77 4.20
673 1924 2.027192 CAGCAGTGTAAAGGCTTCCCTA 60.027 50.000 0.00 0.00 41.90 3.53
674 1925 2.642807 AGCAGTGTAAAGGCTTCCCTAA 59.357 45.455 0.00 0.00 41.90 2.69
675 1926 3.073946 AGCAGTGTAAAGGCTTCCCTAAA 59.926 43.478 0.00 0.00 41.90 1.85
676 1927 3.824443 GCAGTGTAAAGGCTTCCCTAAAA 59.176 43.478 0.00 0.00 41.90 1.52
677 1928 4.279922 GCAGTGTAAAGGCTTCCCTAAAAA 59.720 41.667 0.00 0.00 41.90 1.94
843 2096 3.411351 GCGCCACACGTGTTCGAT 61.411 61.111 31.77 7.01 46.11 3.59
882 2135 1.089920 CGATTTGGAAGTGGCCTCAG 58.910 55.000 3.32 0.00 0.00 3.35
976 2232 1.633915 ATCCCCTTGCTCTGCCTCAG 61.634 60.000 0.00 0.00 0.00 3.35
978 2234 2.438075 CCTTGCTCTGCCTCAGCC 60.438 66.667 0.00 0.00 38.69 4.85
1209 2477 3.547513 GGCCGCCTCCGAGGTATT 61.548 66.667 16.09 0.00 37.80 1.89
1210 2478 2.205152 GGCCGCCTCCGAGGTATTA 61.205 63.158 16.09 0.00 37.80 0.98
1211 2479 1.542187 GGCCGCCTCCGAGGTATTAT 61.542 60.000 16.09 0.00 37.80 1.28
1947 4340 2.071262 AGATCAGCCTGGGAGCAGG 61.071 63.158 0.00 0.00 44.98 4.85
2033 4426 2.984155 CAGGCTGCTGCTGCTGTT 60.984 61.111 26.79 12.97 39.81 3.16
2155 4551 1.591768 AGGCCGGGAAGGAGATAAAA 58.408 50.000 2.18 0.00 45.00 1.52
2202 4613 2.576615 ACTTCAGTTTGTTGGAGCTCC 58.423 47.619 26.78 26.78 0.00 4.70
2203 4614 2.092429 ACTTCAGTTTGTTGGAGCTCCA 60.092 45.455 32.00 32.00 45.94 3.86
2204 4615 2.957402 TCAGTTTGTTGGAGCTCCAT 57.043 45.000 35.42 17.44 46.97 3.41
2232 4645 5.505173 AACGACATTCATTCATTCATCCC 57.495 39.130 0.00 0.00 0.00 3.85
2300 4752 8.418597 TGATGATGATGATCTACTCTGATTGA 57.581 34.615 0.00 0.00 0.00 2.57
2316 4768 5.649395 TCTGATTGAGTTGGTTTGATGATCC 59.351 40.000 0.00 0.00 0.00 3.36
2469 4921 4.912766 TCCGCAAATAAAGTTTAAACAGCG 59.087 37.500 20.06 19.02 40.95 5.18
2475 4927 7.148967 GCAAATAAAGTTTAAACAGCGAGAAGG 60.149 37.037 20.06 3.65 0.00 3.46
2597 5150 1.005156 GCCCGCATCCTCTCTCATC 60.005 63.158 0.00 0.00 0.00 2.92
2599 5152 1.288439 CCGCATCCTCTCTCATCCG 59.712 63.158 0.00 0.00 0.00 4.18
2600 5153 1.372748 CGCATCCTCTCTCATCCGC 60.373 63.158 0.00 0.00 0.00 5.54
2601 5154 1.372748 GCATCCTCTCTCATCCGCG 60.373 63.158 0.00 0.00 0.00 6.46
2604 5157 4.292178 CCTCTCTCATCCGCGCCC 62.292 72.222 0.00 0.00 0.00 6.13
2666 5311 1.451028 CTGCTTGCCCTAGCTGGTC 60.451 63.158 0.00 0.00 41.76 4.02
2693 5338 6.071952 CCGCTATTTTATAATTGTCCATGCCT 60.072 38.462 0.00 0.00 0.00 4.75
2750 5395 2.519622 CCTCACTGCACCACCTCCA 61.520 63.158 0.00 0.00 0.00 3.86
2759 5404 1.463214 ACCACCTCCACCATGACCA 60.463 57.895 0.00 0.00 0.00 4.02
2768 5413 2.124983 CCATGACCACGAGCCCTG 60.125 66.667 0.00 0.00 0.00 4.45
2804 5449 2.514803 ACCTTACGGCAGAGCAAAAAT 58.485 42.857 0.00 0.00 0.00 1.82
2853 5498 8.871125 AGTAAATCATCATTAGAGTAACCCGAT 58.129 33.333 0.00 0.00 0.00 4.18
2871 5516 5.992217 ACCCGATTTACTCTAATTGATCTGC 59.008 40.000 0.00 0.00 0.00 4.26
2914 5559 5.470098 TCAGTGGTTCATGAAGTTTCTAAGC 59.530 40.000 8.80 0.00 0.00 3.09
2977 5672 7.921041 AATGAGATATCCTCTTACCACTTCA 57.079 36.000 0.00 0.00 42.44 3.02
3017 5712 4.574599 AAACAGCAAGTAGAGGCAAAAG 57.425 40.909 0.00 0.00 0.00 2.27
3119 5818 6.373005 TGAAAATCAGGTCACTGGAATCTA 57.627 37.500 0.00 0.00 44.99 1.98
3134 5833 3.282021 GAATCTACTGCCTGCCAAATCA 58.718 45.455 0.00 0.00 0.00 2.57
3135 5834 2.113860 TCTACTGCCTGCCAAATCAC 57.886 50.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.435925 CCGTGGGAATCATCGTCGA 59.564 57.895 0.00 0.00 0.00 4.20
45 46 0.742990 TTGCCGTGGGAATCATCGTC 60.743 55.000 0.00 0.00 0.00 4.20
46 47 1.024579 GTTGCCGTGGGAATCATCGT 61.025 55.000 0.00 0.00 0.00 3.73
60 61 2.746277 AGCCGATTGGTCGTTGCC 60.746 61.111 0.00 0.00 46.25 4.52
61 62 1.696832 GAGAGCCGATTGGTCGTTGC 61.697 60.000 0.00 0.00 46.25 4.17
62 63 0.389817 TGAGAGCCGATTGGTCGTTG 60.390 55.000 0.00 0.00 46.25 4.10
63 64 0.320374 TTGAGAGCCGATTGGTCGTT 59.680 50.000 0.00 0.00 46.25 3.85
65 66 0.933097 CATTGAGAGCCGATTGGTCG 59.067 55.000 0.00 0.00 46.24 4.79
66 67 1.667724 CACATTGAGAGCCGATTGGTC 59.332 52.381 0.00 0.00 41.93 4.02
67 68 1.742761 CACATTGAGAGCCGATTGGT 58.257 50.000 0.00 0.00 37.67 3.67
68 69 0.379669 GCACATTGAGAGCCGATTGG 59.620 55.000 0.00 0.00 38.77 3.16
69 70 1.089112 TGCACATTGAGAGCCGATTG 58.911 50.000 0.00 0.00 32.33 2.67
71 72 2.048444 AATGCACATTGAGAGCCGAT 57.952 45.000 0.00 0.00 32.33 4.18
194 197 3.207778 CGTTTGGAAACTTACCCTGTCA 58.792 45.455 1.04 0.00 36.77 3.58
201 204 5.678132 ACACATACCGTTTGGAAACTTAC 57.322 39.130 1.04 0.00 39.21 2.34
212 215 5.045724 TGGGGAAAGTATAACACATACCGTT 60.046 40.000 0.00 0.00 0.00 4.44
214 217 4.812626 GTGGGGAAAGTATAACACATACCG 59.187 45.833 0.00 0.00 0.00 4.02
254 516 0.108756 CGGAGAAGAGAAACCGGGTC 60.109 60.000 6.32 2.17 41.41 4.46
258 520 9.258218 CTCTTAGTAGACGGAGAAGAGAAACCG 62.258 48.148 0.00 0.00 43.80 4.44
267 529 3.522750 AGTCCCTCTTAGTAGACGGAGAA 59.477 47.826 0.00 0.00 36.60 2.87
350 612 1.890489 TCGACGAGTGAAGAAATGGGA 59.110 47.619 0.00 0.00 0.00 4.37
360 622 0.820482 TTGGACAGGTCGACGAGTGA 60.820 55.000 15.05 0.84 0.00 3.41
508 770 9.612066 TTTTCCTTTTTGCAGATCTGTTTATTT 57.388 25.926 23.38 0.00 0.00 1.40
522 784 6.314018 CAACCTGAAAGTTTTTCCTTTTTGC 58.686 36.000 0.00 0.00 34.87 3.68
531 794 3.859411 TGTCGCAACCTGAAAGTTTTT 57.141 38.095 0.00 0.00 0.00 1.94
560 1065 2.051804 ATAAGTGGCGCGCTGAATGC 62.052 55.000 32.29 13.79 38.57 3.56
562 1067 0.461870 TGATAAGTGGCGCGCTGAAT 60.462 50.000 32.29 14.61 0.00 2.57
563 1068 1.079474 TGATAAGTGGCGCGCTGAA 60.079 52.632 32.29 14.50 0.00 3.02
564 1069 1.809619 GTGATAAGTGGCGCGCTGA 60.810 57.895 32.29 15.57 0.00 4.26
565 1070 1.634757 TTGTGATAAGTGGCGCGCTG 61.635 55.000 32.29 0.00 0.00 5.18
566 1071 1.375396 TTGTGATAAGTGGCGCGCT 60.375 52.632 32.29 14.07 0.00 5.92
578 1083 2.291800 CCCATCTTTCCCAGGTTGTGAT 60.292 50.000 0.00 0.00 0.00 3.06
581 1086 1.075536 GTCCCATCTTTCCCAGGTTGT 59.924 52.381 0.00 0.00 0.00 3.32
592 1097 7.014038 GCTCATTTCAAATATCAGTCCCATCTT 59.986 37.037 0.00 0.00 0.00 2.40
593 1098 6.489361 GCTCATTTCAAATATCAGTCCCATCT 59.511 38.462 0.00 0.00 0.00 2.90
594 1099 6.263842 TGCTCATTTCAAATATCAGTCCCATC 59.736 38.462 0.00 0.00 0.00 3.51
595 1100 6.040166 GTGCTCATTTCAAATATCAGTCCCAT 59.960 38.462 0.00 0.00 0.00 4.00
597 1102 5.591877 AGTGCTCATTTCAAATATCAGTCCC 59.408 40.000 0.00 0.00 0.00 4.46
598 1103 6.493116 CAGTGCTCATTTCAAATATCAGTCC 58.507 40.000 0.00 0.00 0.00 3.85
599 1104 5.970023 GCAGTGCTCATTTCAAATATCAGTC 59.030 40.000 8.18 0.00 0.00 3.51
600 1105 5.651139 AGCAGTGCTCATTTCAAATATCAGT 59.349 36.000 13.14 0.00 30.62 3.41
601 1106 6.132791 AGCAGTGCTCATTTCAAATATCAG 57.867 37.500 13.14 0.00 30.62 2.90
603 1108 9.525409 AATTAAGCAGTGCTCATTTCAAATATC 57.475 29.630 20.03 0.00 38.25 1.63
606 1111 8.742777 TCTAATTAAGCAGTGCTCATTTCAAAT 58.257 29.630 20.03 1.27 38.25 2.32
607 1112 8.023128 GTCTAATTAAGCAGTGCTCATTTCAAA 58.977 33.333 20.03 5.03 38.25 2.69
610 1817 6.963805 GTGTCTAATTAAGCAGTGCTCATTTC 59.036 38.462 20.03 12.96 38.25 2.17
614 1821 4.893608 TGTGTCTAATTAAGCAGTGCTCA 58.106 39.130 20.03 8.89 38.25 4.26
619 1826 5.799213 AGCTCTTGTGTCTAATTAAGCAGT 58.201 37.500 4.77 0.00 0.00 4.40
622 1829 4.268884 CCGAGCTCTTGTGTCTAATTAAGC 59.731 45.833 12.85 0.00 0.00 3.09
624 1831 4.181578 GCCGAGCTCTTGTGTCTAATTAA 58.818 43.478 12.85 0.00 0.00 1.40
632 1839 2.345244 CCTGCCGAGCTCTTGTGT 59.655 61.111 12.85 0.00 0.00 3.72
633 1840 3.123620 GCCTGCCGAGCTCTTGTG 61.124 66.667 12.85 0.00 0.00 3.33
634 1841 3.317571 AGCCTGCCGAGCTCTTGT 61.318 61.111 12.85 0.00 34.91 3.16
678 1929 2.028876 ACGGCCTTTACACTGCTTTTT 58.971 42.857 0.00 0.00 0.00 1.94
679 1930 1.607148 GACGGCCTTTACACTGCTTTT 59.393 47.619 0.00 0.00 0.00 2.27
680 1931 1.235724 GACGGCCTTTACACTGCTTT 58.764 50.000 0.00 0.00 0.00 3.51
681 1932 0.605589 GGACGGCCTTTACACTGCTT 60.606 55.000 0.00 0.00 0.00 3.91
682 1933 1.003718 GGACGGCCTTTACACTGCT 60.004 57.895 0.00 0.00 0.00 4.24
683 1934 2.388232 CGGACGGCCTTTACACTGC 61.388 63.158 5.33 0.00 0.00 4.40
684 1935 1.005394 ACGGACGGCCTTTACACTG 60.005 57.895 5.33 0.00 0.00 3.66
685 1936 1.291272 GACGGACGGCCTTTACACT 59.709 57.895 5.33 0.00 0.00 3.55
686 1937 2.090524 CGACGGACGGCCTTTACAC 61.091 63.158 5.33 0.00 38.46 2.90
687 1938 2.259204 CGACGGACGGCCTTTACA 59.741 61.111 5.33 0.00 38.46 2.41
688 1939 3.184003 GCGACGGACGGCCTTTAC 61.184 66.667 5.33 0.00 42.83 2.01
843 2096 2.422591 GTCGGGTCGGGTGTTTCA 59.577 61.111 0.00 0.00 0.00 2.69
1208 2476 2.680439 AGAGGGGGAAGGTTGGATAA 57.320 50.000 0.00 0.00 0.00 1.75
1209 2477 2.047296 AGAAGAGGGGGAAGGTTGGATA 59.953 50.000 0.00 0.00 0.00 2.59
1210 2478 1.203622 AGAAGAGGGGGAAGGTTGGAT 60.204 52.381 0.00 0.00 0.00 3.41
1211 2479 0.196118 AGAAGAGGGGGAAGGTTGGA 59.804 55.000 0.00 0.00 0.00 3.53
1379 2668 3.786101 CAGCCGAACTGGATCGTG 58.214 61.111 4.78 0.00 43.19 4.35
1922 4315 1.617018 CCCAGGCTGATCTGTTCGGA 61.617 60.000 17.94 0.00 31.81 4.55
1973 4366 2.281276 TGCTGCTGCTGAGGTGTG 60.281 61.111 17.00 0.00 40.48 3.82
2033 4426 1.982395 CTGTGTCTGTCCCGCCCTA 60.982 63.158 0.00 0.00 0.00 3.53
2136 4532 1.591768 TTTTATCTCCTTCCCGGCCT 58.408 50.000 0.00 0.00 0.00 5.19
2202 4613 9.934190 TGAATGAATGAATGTCGTTAATACATG 57.066 29.630 7.06 0.00 37.62 3.21
2265 4717 9.872721 GTAGATCATCATCATCAATGTACTCAT 57.127 33.333 0.00 0.00 36.68 2.90
2266 4718 9.086758 AGTAGATCATCATCATCAATGTACTCA 57.913 33.333 0.00 0.00 36.68 3.41
2267 4719 9.571810 GAGTAGATCATCATCATCAATGTACTC 57.428 37.037 0.00 0.00 36.68 2.59
2268 4720 9.311676 AGAGTAGATCATCATCATCAATGTACT 57.688 33.333 0.00 0.00 36.68 2.73
2274 4726 8.867097 TCAATCAGAGTAGATCATCATCATCAA 58.133 33.333 0.00 0.00 0.00 2.57
2300 4752 5.241403 TGTAGTGGATCATCAAACCAACT 57.759 39.130 0.00 0.00 35.40 3.16
2316 4768 1.935873 CATGAGCCACGGATTGTAGTG 59.064 52.381 0.00 0.00 38.05 2.74
2469 4921 1.420138 TCAAGGAACACACCCCTTCTC 59.580 52.381 0.00 0.00 40.57 2.87
2475 4927 4.280677 TGAATTGAATCAAGGAACACACCC 59.719 41.667 1.10 0.00 0.00 4.61
2585 5138 2.569354 GGCGCGGATGAGAGAGGAT 61.569 63.158 8.83 0.00 0.00 3.24
2604 5157 1.402479 CGCCTGTTTTTAATGCCGCG 61.402 55.000 0.00 0.00 0.00 6.46
2666 5311 6.620678 CATGGACAATTATAAAATAGCGGGG 58.379 40.000 0.00 0.00 0.00 5.73
2693 5338 3.047280 GCGGTGCGGATTGTGTCA 61.047 61.111 0.00 0.00 0.00 3.58
2750 5395 2.607750 AGGGCTCGTGGTCATGGT 60.608 61.111 0.00 0.00 0.00 3.55
2759 5404 1.534235 AGGTCACTTCAGGGCTCGT 60.534 57.895 0.00 0.00 0.00 4.18
2768 5413 4.679905 CGTAAGGTTATCCCAGGTCACTTC 60.680 50.000 0.00 0.00 34.66 3.01
2845 5490 7.656137 GCAGATCAATTAGAGTAAATCGGGTTA 59.344 37.037 0.00 0.00 0.00 2.85
2862 5507 7.049133 GGAGCTGATCATTATAGCAGATCAAT 58.951 38.462 9.23 6.70 45.18 2.57
2871 5516 7.598189 CACTGATTGGAGCTGATCATTATAG 57.402 40.000 0.00 0.00 32.31 1.31
2977 5672 6.806739 GCTGTTTAAACTTTATTTCTGCCGAT 59.193 34.615 18.72 0.00 0.00 4.18
3017 5712 7.500227 TCAAGTCCACATGAGATCATTAATTCC 59.500 37.037 0.00 0.00 33.61 3.01
3110 5809 0.543277 TGGCAGGCAGTAGATTCCAG 59.457 55.000 0.00 0.00 0.00 3.86
3119 5818 0.251922 ATGGTGATTTGGCAGGCAGT 60.252 50.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.