Multiple sequence alignment - TraesCS2B01G401700

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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 TraesCS2B01G401700 chr2B 100.000 2994 0 0 1 2994 570095151 570092158 0.000000e+00 5529
1 TraesCS2B01G401700 chr2B 84.294 694 87 17 4 686 25793190 25793872 0.000000e+00 658
2 TraesCS2B01G401700 chr2B 83.977 699 88 20 2 686 110580390 110581078 0.000000e+00 649
3 TraesCS2B01G401700 chr2B 93.764 433 15 3 255 686 570106708 570106287 9.050000e-180 640
4 TraesCS2B01G401700 chr2B 80.778 437 55 22 9 429 720932667 720933090 6.230000e-82 315
5 TraesCS2B01G401700 chr2A 90.047 1497 84 24 687 2142 630093229 630091757 0.000000e+00 1879
6 TraesCS2B01G401700 chr2A 92.352 863 51 5 2145 2994 231352490 231351630 0.000000e+00 1214
7 TraesCS2B01G401700 chr2A 91.986 861 56 6 2145 2994 69347659 69346801 0.000000e+00 1195
8 TraesCS2B01G401700 chr2D 91.079 1390 75 22 772 2142 485491301 485489942 0.000000e+00 1834
9 TraesCS2B01G401700 chr6D 93.248 859 48 4 2145 2994 465977607 465976750 0.000000e+00 1256
10 TraesCS2B01G401700 chr3D 93.015 859 49 5 2145 2993 132166784 132165927 0.000000e+00 1243
11 TraesCS2B01G401700 chr3D 93.007 858 50 4 2145 2994 246593845 246592990 0.000000e+00 1243
12 TraesCS2B01G401700 chr6A 92.486 865 51 9 2141 2994 122687758 122686897 0.000000e+00 1225
13 TraesCS2B01G401700 chr5D 92.343 862 53 5 2145 2994 210055305 210054445 0.000000e+00 1214
14 TraesCS2B01G401700 chr5D 88.534 689 69 10 4 686 406963351 406962667 0.000000e+00 826
15 TraesCS2B01G401700 chr4A 92.308 858 55 5 2145 2994 327258482 327257628 0.000000e+00 1208
16 TraesCS2B01G401700 chr1D 92.084 859 50 8 2144 2994 30312175 30313023 0.000000e+00 1194
17 TraesCS2B01G401700 chr3B 90.948 696 55 8 1 690 42257952 42257259 0.000000e+00 929
18 TraesCS2B01G401700 chr3B 90.976 410 28 9 283 686 42263181 42262775 7.300000e-151 544
19 TraesCS2B01G401700 chr4B 91.040 692 54 8 1 686 255349768 255349079 0.000000e+00 928
20 TraesCS2B01G401700 chr4B 94.690 113 6 0 574 686 255354687 255354575 3.070000e-40 176
21 TraesCS2B01G401700 chr6B 90.342 673 55 10 1 666 715312178 715311509 0.000000e+00 874
22 TraesCS2B01G401700 chr6B 88.155 439 43 8 254 686 715317017 715316582 5.720000e-142 514
23 TraesCS2B01G401700 chrUn 90.592 574 47 7 1 569 39040562 39041133 0.000000e+00 754
24 TraesCS2B01G401700 chr5B 84.805 691 84 16 7 686 603429812 603429132 0.000000e+00 675


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 TraesCS2B01G401700 chr2B 570092158 570095151 2993 True 5529 5529 100.000 1 2994 1 chr2B.!!$R1 2993
1 TraesCS2B01G401700 chr2B 25793190 25793872 682 False 658 658 84.294 4 686 1 chr2B.!!$F1 682
2 TraesCS2B01G401700 chr2B 110580390 110581078 688 False 649 649 83.977 2 686 1 chr2B.!!$F2 684
3 TraesCS2B01G401700 chr2A 630091757 630093229 1472 True 1879 1879 90.047 687 2142 1 chr2A.!!$R3 1455
4 TraesCS2B01G401700 chr2A 231351630 231352490 860 True 1214 1214 92.352 2145 2994 1 chr2A.!!$R2 849
5 TraesCS2B01G401700 chr2A 69346801 69347659 858 True 1195 1195 91.986 2145 2994 1 chr2A.!!$R1 849
6 TraesCS2B01G401700 chr2D 485489942 485491301 1359 True 1834 1834 91.079 772 2142 1 chr2D.!!$R1 1370
7 TraesCS2B01G401700 chr6D 465976750 465977607 857 True 1256 1256 93.248 2145 2994 1 chr6D.!!$R1 849
8 TraesCS2B01G401700 chr3D 132165927 132166784 857 True 1243 1243 93.015 2145 2993 1 chr3D.!!$R1 848
9 TraesCS2B01G401700 chr3D 246592990 246593845 855 True 1243 1243 93.007 2145 2994 1 chr3D.!!$R2 849
10 TraesCS2B01G401700 chr6A 122686897 122687758 861 True 1225 1225 92.486 2141 2994 1 chr6A.!!$R1 853
11 TraesCS2B01G401700 chr5D 210054445 210055305 860 True 1214 1214 92.343 2145 2994 1 chr5D.!!$R1 849
12 TraesCS2B01G401700 chr5D 406962667 406963351 684 True 826 826 88.534 4 686 1 chr5D.!!$R2 682
13 TraesCS2B01G401700 chr4A 327257628 327258482 854 True 1208 1208 92.308 2145 2994 1 chr4A.!!$R1 849
14 TraesCS2B01G401700 chr1D 30312175 30313023 848 False 1194 1194 92.084 2144 2994 1 chr1D.!!$F1 850
15 TraesCS2B01G401700 chr3B 42257259 42257952 693 True 929 929 90.948 1 690 1 chr3B.!!$R1 689
16 TraesCS2B01G401700 chr4B 255349079 255349768 689 True 928 928 91.040 1 686 1 chr4B.!!$R1 685
17 TraesCS2B01G401700 chr6B 715311509 715312178 669 True 874 874 90.342 1 666 1 chr6B.!!$R1 665
18 TraesCS2B01G401700 chrUn 39040562 39041133 571 False 754 754 90.592 1 569 1 chrUn.!!$F1 568
19 TraesCS2B01G401700 chr5B 603429132 603429812 680 True 675 675 84.805 7 686 1 chr5B.!!$R1 679

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
222 224 0.100682 CGTGGTCAGATCCGATTCGT 59.899 55.0 5.2 0.0 0.0 3.85 F
244 246 0.460987 CCGAGGATTCACTGGCTCAC 60.461 60.0 0.0 0.0 0.0 3.51 F
1700 1765 0.609131 AATCCAACTGCTTCCCACGG 60.609 55.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1651 1715 0.598065 AAAAGGCTAAAGCGGTGCAG 59.402 50.0 0.00 0.0 43.26 4.41 R
1933 1998 0.673333 TAGGTGCAGGCGTCACAATG 60.673 55.0 12.73 0.0 36.22 2.82 R
2885 2981 0.038618 GTTTTCCCCATGGACAACGC 60.039 55.0 15.22 0.0 40.48 4.84 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
58 59 2.172851 ACGGAATTTTACCACAGCGA 57.827 45.000 0.00 0.00 0.00 4.93
78 79 1.112315 AATTGTTCCAGCCGCAACCA 61.112 50.000 0.00 0.00 0.00 3.67
222 224 0.100682 CGTGGTCAGATCCGATTCGT 59.899 55.000 5.20 0.00 0.00 3.85
244 246 0.460987 CCGAGGATTCACTGGCTCAC 60.461 60.000 0.00 0.00 0.00 3.51
263 265 3.513912 TCACGATACCAATTGACAGGACT 59.486 43.478 7.12 0.00 0.00 3.85
273 275 3.364889 TTGACAGGACTACAACACTCG 57.635 47.619 0.00 0.00 0.00 4.18
275 277 3.154710 TGACAGGACTACAACACTCGAT 58.845 45.455 0.00 0.00 0.00 3.59
278 280 3.057456 ACAGGACTACAACACTCGATCAC 60.057 47.826 0.00 0.00 0.00 3.06
279 281 3.057526 CAGGACTACAACACTCGATCACA 60.058 47.826 0.00 0.00 0.00 3.58
280 282 3.191581 AGGACTACAACACTCGATCACAG 59.808 47.826 0.00 0.00 0.00 3.66
283 285 1.502231 ACAACACTCGATCACAGCAC 58.498 50.000 0.00 0.00 0.00 4.40
284 286 1.202521 ACAACACTCGATCACAGCACA 60.203 47.619 0.00 0.00 0.00 4.57
286 288 2.462456 ACACTCGATCACAGCACAAT 57.538 45.000 0.00 0.00 0.00 2.71
319 322 2.037772 AGCCCCGCTTGTATTATCTCAG 59.962 50.000 0.00 0.00 33.89 3.35
326 329 5.991606 CCGCTTGTATTATCTCAGGATTCAA 59.008 40.000 0.00 0.00 33.71 2.69
328 331 7.348201 CGCTTGTATTATCTCAGGATTCAAAC 58.652 38.462 0.00 0.00 33.71 2.93
330 333 9.547753 GCTTGTATTATCTCAGGATTCAAACTA 57.452 33.333 0.00 0.00 33.71 2.24
378 383 5.168569 TCTGCTCAATTTCTACCAAGTACG 58.831 41.667 0.00 0.00 0.00 3.67
390 396 3.022406 ACCAAGTACGCTAGGGTTCTAG 58.978 50.000 18.45 14.47 44.40 2.43
392 398 3.285484 CAAGTACGCTAGGGTTCTAGGA 58.715 50.000 18.45 0.00 42.41 2.94
393 399 3.880168 AGTACGCTAGGGTTCTAGGAT 57.120 47.619 18.45 0.00 42.41 3.24
394 400 4.989875 AGTACGCTAGGGTTCTAGGATA 57.010 45.455 18.45 0.00 42.41 2.59
396 402 5.699143 AGTACGCTAGGGTTCTAGGATAAA 58.301 41.667 18.45 0.00 42.41 1.40
429 438 2.989571 ACTTGGAGAAGGGGAAAGATGT 59.010 45.455 0.00 0.00 32.95 3.06
557 566 2.227194 GGTTGACGGTGAACAGGAAAT 58.773 47.619 12.39 0.00 0.00 2.17
560 569 3.201353 TGACGGTGAACAGGAAATTGA 57.799 42.857 0.00 0.00 0.00 2.57
690 699 3.596799 TCAGGGTCCTGACGGGGA 61.597 66.667 15.14 0.00 46.80 4.81
691 700 2.606519 CAGGGTCCTGACGGGGAA 60.607 66.667 11.39 0.00 46.30 3.97
721 730 2.393768 CCATGCGCTTCGACTTGCT 61.394 57.895 9.73 0.00 0.00 3.91
742 751 4.373116 GCCGGTGACTGGAAGCGA 62.373 66.667 16.12 0.00 40.84 4.93
743 752 2.125912 CCGGTGACTGGAAGCGAG 60.126 66.667 3.85 0.00 40.84 5.03
831 856 1.532078 TGTCTCTGCCCGTGGTACA 60.532 57.895 0.00 0.00 0.00 2.90
1062 1102 2.685380 CCTCCTCCCTTCTGCCGT 60.685 66.667 0.00 0.00 0.00 5.68
1100 1140 2.972819 GCGCTTTCCCCTCCTCCTT 61.973 63.158 0.00 0.00 0.00 3.36
1117 1157 0.674895 CTTCCCCGTCAGAAGCCTTG 60.675 60.000 0.00 0.00 34.77 3.61
1223 1266 3.377485 CGTCCTTTGGATAGTTCGAGAGA 59.623 47.826 0.00 0.00 32.73 3.10
1282 1332 1.001764 CTGCTGCCCAGGTGATGAA 60.002 57.895 0.00 0.00 37.93 2.57
1300 1350 1.893919 AAGAGAGCAAGGCCGTCCTC 61.894 60.000 0.60 0.60 43.40 3.71
1572 1635 4.774124 CAGATAGGCCTGTGAATTCTCAA 58.226 43.478 17.99 0.00 31.88 3.02
1583 1647 5.559770 TGTGAATTCTCAATGCCAACTAGA 58.440 37.500 7.72 0.00 31.88 2.43
1596 1660 4.748102 TGCCAACTAGAAAGTTCTTGTACG 59.252 41.667 8.27 4.13 44.28 3.67
1604 1668 8.142551 ACTAGAAAGTTCTTGTACGTTCAGATT 58.857 33.333 6.39 0.00 40.54 2.40
1608 1672 7.548196 AAGTTCTTGTACGTTCAGATTTCAA 57.452 32.000 0.00 0.00 0.00 2.69
1615 1679 7.079182 TGTACGTTCAGATTTCAAACAACTT 57.921 32.000 0.00 0.00 0.00 2.66
1651 1715 7.066374 GATGTTGTTCTTCTACATCCAGAAC 57.934 40.000 9.83 4.63 46.02 3.01
1666 1731 0.955919 AGAACTGCACCGCTTTAGCC 60.956 55.000 0.00 0.00 37.91 3.93
1694 1759 5.355071 TGATGTCACATAATCCAACTGCTTC 59.645 40.000 0.00 0.00 0.00 3.86
1698 1763 3.129287 CACATAATCCAACTGCTTCCCAC 59.871 47.826 0.00 0.00 0.00 4.61
1700 1765 0.609131 AATCCAACTGCTTCCCACGG 60.609 55.000 0.00 0.00 0.00 4.94
1713 1778 4.819630 GCTTCCCACGGTTAATCATCATTA 59.180 41.667 0.00 0.00 0.00 1.90
1739 1804 7.150783 TGATGACAGCATAGTGTATAGCTAG 57.849 40.000 0.00 0.00 35.19 3.42
1752 1817 8.608844 AGTGTATAGCTAGAATTTATTGTGGC 57.391 34.615 0.00 0.56 37.72 5.01
1756 1821 5.779529 AGCTAGAATTTATTGTGGCCATG 57.220 39.130 9.72 0.00 38.10 3.66
1762 1827 5.876460 AGAATTTATTGTGGCCATGCTTTTC 59.124 36.000 9.72 7.18 0.00 2.29
1763 1828 2.937469 TATTGTGGCCATGCTTTTCG 57.063 45.000 9.72 0.00 0.00 3.46
1775 1840 5.334879 GCCATGCTTTTCGTTTTCTTCTCTA 60.335 40.000 0.00 0.00 0.00 2.43
1783 1848 6.839820 TTCGTTTTCTTCTCTAAACCTCAC 57.160 37.500 0.00 0.00 32.05 3.51
1840 1905 6.296803 GGGGTAATTGTAAATACAGGAGGAG 58.703 44.000 0.00 0.00 37.52 3.69
1922 1987 3.523972 GGGACCAAAGACTCTAAAGGGAT 59.476 47.826 0.00 0.00 0.00 3.85
1933 1998 5.561679 ACTCTAAAGGGATCTTCAACAACC 58.438 41.667 0.00 0.00 31.82 3.77
1936 2001 6.552008 TCTAAAGGGATCTTCAACAACCATT 58.448 36.000 0.00 0.00 31.82 3.16
1954 2019 2.034048 TTGTGACGCCTGCACCTACA 62.034 55.000 0.00 0.00 35.43 2.74
1957 2022 3.952628 GACGCCTGCACCTACACCC 62.953 68.421 0.00 0.00 0.00 4.61
1971 2036 0.042881 ACACCCCCTCCTTCTCCTAC 59.957 60.000 0.00 0.00 0.00 3.18
1991 2056 2.578021 ACTATTCCCACACAGGCAGAAT 59.422 45.455 0.00 0.00 34.13 2.40
2003 2068 5.163447 ACACAGGCAGAATAGTTATAAGCGA 60.163 40.000 0.00 0.00 0.00 4.93
2055 2120 4.747810 CACTTTTGTGCTCCAAGAAAGTT 58.252 39.130 0.00 0.00 44.07 2.66
2057 2122 5.743872 CACTTTTGTGCTCCAAGAAAGTTAC 59.256 40.000 0.00 0.00 44.07 2.50
2069 2134 6.996282 TCCAAGAAAGTTACGAAATTCTCCTT 59.004 34.615 0.00 0.00 31.20 3.36
2078 2143 9.892130 AGTTACGAAATTCTCCTTTGAGATATT 57.108 29.630 0.00 0.00 46.75 1.28
2439 2518 3.238232 GACATGCAGCTTGTCCTCA 57.762 52.632 24.60 0.00 38.00 3.86
2472 2551 6.602009 GCCTAACCAACTTATAACCATGACTT 59.398 38.462 0.00 0.00 0.00 3.01
2475 2554 7.687941 AACCAACTTATAACCATGACTTGAG 57.312 36.000 0.00 0.00 0.00 3.02
2572 2651 5.842339 ACTGGGATGATTTATTTTGGACCT 58.158 37.500 0.00 0.00 0.00 3.85
2589 2668 5.701224 TGGACCTCTTAACAAAAAGTGGAT 58.299 37.500 10.70 0.00 40.86 3.41
2646 2725 2.057140 CTGGATCCCATGGACACCATA 58.943 52.381 15.22 0.00 43.15 2.74
2673 2752 2.425143 AAGGAGTGCATGTGTATGGG 57.575 50.000 0.00 0.00 34.79 4.00
2764 2850 1.069090 GCTCTTGTCGGTGACACCA 59.931 57.895 24.18 8.88 42.60 4.17
2821 2907 1.834263 GCACATAGAAGAGTGGAGGGT 59.166 52.381 0.00 0.00 36.29 4.34
2823 2909 3.866651 CACATAGAAGAGTGGAGGGTTG 58.133 50.000 0.00 0.00 32.24 3.77
2824 2910 3.261897 CACATAGAAGAGTGGAGGGTTGT 59.738 47.826 0.00 0.00 32.24 3.32
2832 2918 0.391263 GTGGAGGGTTGTCGATGGAC 60.391 60.000 0.12 0.12 43.71 4.02
2844 2930 0.250038 CGATGGACAATGGCGAGGAT 60.250 55.000 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 3.586430 GTTGCGGCTGGAACAATTT 57.414 47.368 23.46 0.00 44.92 1.82
78 79 2.800250 CTGCAGATTGGGGAGAAACTT 58.200 47.619 8.42 0.00 0.00 2.66
222 224 0.324738 AGCCAGTGAATCCTCGGAGA 60.325 55.000 6.58 0.00 0.00 3.71
244 246 5.006153 TGTAGTCCTGTCAATTGGTATCG 57.994 43.478 5.42 0.00 0.00 2.92
263 265 2.035321 TGTGCTGTGATCGAGTGTTGTA 59.965 45.455 0.00 0.00 0.00 2.41
273 275 5.120830 AGTTCGAGTAAATTGTGCTGTGATC 59.879 40.000 0.00 0.00 0.00 2.92
275 277 4.377021 AGTTCGAGTAAATTGTGCTGTGA 58.623 39.130 0.00 0.00 0.00 3.58
278 280 4.201724 GGCTAGTTCGAGTAAATTGTGCTG 60.202 45.833 0.00 0.00 0.00 4.41
279 281 3.933332 GGCTAGTTCGAGTAAATTGTGCT 59.067 43.478 0.00 0.00 0.00 4.40
280 282 3.063588 GGGCTAGTTCGAGTAAATTGTGC 59.936 47.826 0.00 0.00 0.00 4.57
283 285 2.864343 CGGGGCTAGTTCGAGTAAATTG 59.136 50.000 0.00 0.00 0.00 2.32
284 286 2.740904 GCGGGGCTAGTTCGAGTAAATT 60.741 50.000 5.87 0.00 0.00 1.82
286 288 0.174162 GCGGGGCTAGTTCGAGTAAA 59.826 55.000 5.87 0.00 0.00 2.01
319 322 7.177744 TGAACCCCTTATTTGTAGTTTGAATCC 59.822 37.037 0.00 0.00 0.00 3.01
326 329 7.027874 TGATCTGAACCCCTTATTTGTAGTT 57.972 36.000 0.00 0.00 0.00 2.24
328 331 6.543831 CCTTGATCTGAACCCCTTATTTGTAG 59.456 42.308 0.00 0.00 0.00 2.74
330 333 5.015178 TCCTTGATCTGAACCCCTTATTTGT 59.985 40.000 0.00 0.00 0.00 2.83
331 334 5.509498 TCCTTGATCTGAACCCCTTATTTG 58.491 41.667 0.00 0.00 0.00 2.32
332 335 5.796502 TCCTTGATCTGAACCCCTTATTT 57.203 39.130 0.00 0.00 0.00 1.40
334 337 5.230759 AGATCCTTGATCTGAACCCCTTAT 58.769 41.667 5.82 0.00 46.21 1.73
335 338 4.635473 AGATCCTTGATCTGAACCCCTTA 58.365 43.478 5.82 0.00 46.21 2.69
336 339 3.468850 AGATCCTTGATCTGAACCCCTT 58.531 45.455 5.82 0.00 46.21 3.95
360 365 5.394883 CCCTAGCGTACTTGGTAGAAATTGA 60.395 44.000 8.14 0.00 41.36 2.57
378 383 5.776208 AGCTAGTTTATCCTAGAACCCTAGC 59.224 44.000 0.00 0.00 40.78 3.42
390 396 8.639761 TCTCCAAGTGTAATAGCTAGTTTATCC 58.360 37.037 0.00 0.00 0.00 2.59
393 399 8.475639 CCTTCTCCAAGTGTAATAGCTAGTTTA 58.524 37.037 0.00 0.00 0.00 2.01
394 400 7.331791 CCTTCTCCAAGTGTAATAGCTAGTTT 58.668 38.462 0.00 0.00 0.00 2.66
396 402 5.364157 CCCTTCTCCAAGTGTAATAGCTAGT 59.636 44.000 0.00 0.00 0.00 2.57
557 566 0.108804 GACCATCGACGGCTCTTCAA 60.109 55.000 0.00 0.00 0.00 2.69
560 569 1.215647 GTGACCATCGACGGCTCTT 59.784 57.895 0.00 0.00 0.00 2.85
686 695 2.435059 GTCAGCTCGCTGTTCCCC 60.435 66.667 17.53 0.49 43.96 4.81
690 699 2.037136 GCATGGTCAGCTCGCTGTT 61.037 57.895 17.53 0.71 43.96 3.16
691 700 2.435586 GCATGGTCAGCTCGCTGT 60.436 61.111 17.53 0.00 43.96 4.40
747 762 3.118454 CCACTTAGGCACACCGCG 61.118 66.667 0.00 0.00 43.84 6.46
831 856 1.943730 TTTCCCTTGGCTGGTGTGGT 61.944 55.000 0.00 0.00 0.00 4.16
832 857 0.758685 TTTTCCCTTGGCTGGTGTGG 60.759 55.000 0.00 0.00 0.00 4.17
833 858 1.069049 CTTTTTCCCTTGGCTGGTGTG 59.931 52.381 0.00 0.00 0.00 3.82
1039 1079 3.855853 GAAGGGAGGAGGAGCCGC 61.856 72.222 0.00 0.00 43.43 6.53
1040 1080 2.042435 AGAAGGGAGGAGGAGCCG 60.042 66.667 0.00 0.00 43.43 5.52
1041 1081 2.741055 GCAGAAGGGAGGAGGAGCC 61.741 68.421 0.00 0.00 0.00 4.70
1042 1082 2.741055 GGCAGAAGGGAGGAGGAGC 61.741 68.421 0.00 0.00 0.00 4.70
1043 1083 2.430610 CGGCAGAAGGGAGGAGGAG 61.431 68.421 0.00 0.00 0.00 3.69
1050 1090 1.228894 AGAGACACGGCAGAAGGGA 60.229 57.895 0.00 0.00 0.00 4.20
1051 1091 1.216710 GAGAGACACGGCAGAAGGG 59.783 63.158 0.00 0.00 0.00 3.95
1100 1140 2.592993 CCAAGGCTTCTGACGGGGA 61.593 63.158 0.00 0.00 0.00 4.81
1223 1266 3.645268 GACCCAGCCCGAAATGCCT 62.645 63.158 0.00 0.00 0.00 4.75
1282 1332 2.284258 AGGACGGCCTTGCTCTCT 60.284 61.111 2.12 0.00 43.90 3.10
1300 1350 2.202623 CCGAGGAAGAAGGCGTCG 60.203 66.667 0.00 0.00 41.65 5.12
1474 1524 8.868103 GGTAAAGCTAAACACTAGTATATCCCT 58.132 37.037 0.00 0.00 0.00 4.20
1475 1525 8.868103 AGGTAAAGCTAAACACTAGTATATCCC 58.132 37.037 0.00 0.00 0.00 3.85
1572 1635 5.408604 CGTACAAGAACTTTCTAGTTGGCAT 59.591 40.000 0.00 0.00 44.51 4.40
1583 1647 7.548196 TGAAATCTGAACGTACAAGAACTTT 57.452 32.000 0.00 0.00 0.00 2.66
1633 1697 4.390297 GTGCAGTTCTGGATGTAGAAGAAC 59.610 45.833 6.66 6.66 46.59 3.01
1651 1715 0.598065 AAAAGGCTAAAGCGGTGCAG 59.402 50.000 0.00 0.00 43.26 4.41
1666 1731 6.529125 GCAGTTGGATTATGTGACATCAAAAG 59.471 38.462 0.00 0.00 0.00 2.27
1694 1759 6.875948 TCAATAATGATGATTAACCGTGGG 57.124 37.500 0.00 0.00 0.00 4.61
1713 1778 7.002250 AGCTATACACTATGCTGTCATCAAT 57.998 36.000 0.00 0.00 34.19 2.57
1730 1795 7.979444 TGGCCACAATAAATTCTAGCTATAC 57.021 36.000 0.00 0.00 0.00 1.47
1739 1804 5.220453 CGAAAAGCATGGCCACAATAAATTC 60.220 40.000 8.16 6.52 0.00 2.17
1752 1817 5.113502 AGAGAAGAAAACGAAAAGCATGG 57.886 39.130 0.00 0.00 0.00 3.66
1756 1821 6.726230 AGGTTTAGAGAAGAAAACGAAAAGC 58.274 36.000 0.00 0.00 36.63 3.51
1762 1827 5.983720 TCTGTGAGGTTTAGAGAAGAAAACG 59.016 40.000 0.00 0.00 36.63 3.60
1763 1828 7.787725 TTCTGTGAGGTTTAGAGAAGAAAAC 57.212 36.000 0.00 0.00 35.34 2.43
1775 1840 8.157476 AGAAGTGTGTATAATTCTGTGAGGTTT 58.843 33.333 0.00 0.00 31.00 3.27
1790 1855 7.094205 CCCAAAGAGCAATTTAGAAGTGTGTAT 60.094 37.037 0.00 0.00 0.00 2.29
1791 1856 6.206634 CCCAAAGAGCAATTTAGAAGTGTGTA 59.793 38.462 0.00 0.00 0.00 2.90
1794 1859 4.524328 CCCCAAAGAGCAATTTAGAAGTGT 59.476 41.667 0.00 0.00 0.00 3.55
1819 1884 8.702819 ACTACCTCCTCCTGTATTTACAATTAC 58.297 37.037 0.00 0.00 35.50 1.89
1829 1894 4.479056 TCTCTGAACTACCTCCTCCTGTAT 59.521 45.833 0.00 0.00 0.00 2.29
1840 1905 3.339141 CTTTTGGGCTCTCTGAACTACC 58.661 50.000 0.00 0.00 0.00 3.18
1922 1987 2.032799 GCGTCACAATGGTTGTTGAAGA 59.967 45.455 0.00 0.00 43.23 2.87
1933 1998 0.673333 TAGGTGCAGGCGTCACAATG 60.673 55.000 12.73 0.00 36.22 2.82
1936 2001 2.342279 GTAGGTGCAGGCGTCACA 59.658 61.111 12.73 0.00 36.22 3.58
1954 2019 2.012168 TAGTAGGAGAAGGAGGGGGT 57.988 55.000 0.00 0.00 0.00 4.95
1957 2022 3.116707 TGGGAATAGTAGGAGAAGGAGGG 60.117 52.174 0.00 0.00 0.00 4.30
1971 2036 2.787473 TTCTGCCTGTGTGGGAATAG 57.213 50.000 0.00 0.00 35.09 1.73
1991 2056 6.615264 ACTCTTCATCGTCGCTTATAACTA 57.385 37.500 0.00 0.00 0.00 2.24
2003 2068 2.029020 TGCAGCACTAACTCTTCATCGT 60.029 45.455 0.00 0.00 0.00 3.73
2078 2143 9.130661 TCAAAGAAAGGACAACTTGATCAATAA 57.869 29.630 8.96 0.00 39.96 1.40
2122 2187 7.617041 ACAGGCATAGATTTTTCTAGTTGAC 57.383 36.000 0.00 0.00 0.00 3.18
2315 2385 4.287552 AGATAAGGGTCGCTTTCTTAGGA 58.712 43.478 7.54 0.00 0.00 2.94
2322 2392 6.990939 GGTTAATTAGAGATAAGGGTCGCTTT 59.009 38.462 7.54 0.00 30.69 3.51
2439 2518 0.111253 AGTTGGTTAGGCTGCAGCTT 59.889 50.000 35.82 31.71 41.70 3.74
2472 2551 4.164604 AGGTGTTAGGTTTGTGTTACCTCA 59.835 41.667 0.00 0.00 44.74 3.86
2475 2554 6.940831 TTTAGGTGTTAGGTTTGTGTTACC 57.059 37.500 0.00 0.00 35.85 2.85
2646 2725 2.559668 CACATGCACTCCTTTTGTCCAT 59.440 45.455 0.00 0.00 0.00 3.41
2673 2752 1.391157 TTGCAACCACTTCCAGGTGC 61.391 55.000 0.00 0.00 39.86 5.01
2688 2767 0.601046 CTCTGTTGGTCGCTCTTGCA 60.601 55.000 0.00 0.00 39.64 4.08
2750 2836 1.599518 GGCATGGTGTCACCGACAA 60.600 57.895 17.27 0.00 44.49 3.18
2795 2881 0.108138 ACTCTTCTATGTGCGGTGCC 60.108 55.000 0.00 0.00 0.00 5.01
2806 2892 2.168496 CGACAACCCTCCACTCTTCTA 58.832 52.381 0.00 0.00 0.00 2.10
2823 2909 1.154205 CCTCGCCATTGTCCATCGAC 61.154 60.000 0.00 0.00 39.66 4.20
2824 2910 1.143838 CCTCGCCATTGTCCATCGA 59.856 57.895 0.00 0.00 0.00 3.59
2832 2918 2.484062 GCACCCATCCTCGCCATTG 61.484 63.158 0.00 0.00 0.00 2.82
2868 2964 2.383527 GCCCTCAAAGTCTGCGACG 61.384 63.158 0.00 0.00 37.67 5.12
2885 2981 0.038618 GTTTTCCCCATGGACAACGC 60.039 55.000 15.22 0.00 40.48 4.84
2930 3026 4.237445 GGACCTCGATCTCGTCCA 57.763 61.111 14.53 0.00 44.60 4.02


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

AutoCloner maintained by Alex Coulton.