Multiple sequence alignment - TraesCS5A01G414000

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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 TraesCS5A01G414000 chr5A 100.000 3281 0 0 1 3281 602002601 602005881 0.000000e+00 6059
1 TraesCS5A01G414000 chr5A 90.460 1457 124 5 1043 2491 599223819 599222370 0.000000e+00 1906
2 TraesCS5A01G414000 chr5A 96.546 608 20 1 2665 3271 160014908 160014301 0.000000e+00 1005
3 TraesCS5A01G414000 chr5A 95.652 621 25 2 2662 3281 639221525 639222144 0.000000e+00 996
4 TraesCS5A01G414000 chr5A 95.786 617 25 1 2665 3281 552653085 552653700 0.000000e+00 994
5 TraesCS5A01G414000 chr5A 88.000 175 13 2 2492 2662 599222269 599222099 2.000000e-47 200
6 TraesCS5A01G414000 chr5D 92.804 1598 97 13 1038 2624 482298735 482300325 0.000000e+00 2298
7 TraesCS5A01G414000 chr5D 90.942 1391 115 7 1043 2424 480480953 480479565 0.000000e+00 1860
8 TraesCS5A01G414000 chr5D 86.782 174 13 4 2495 2662 480479438 480479269 5.590000e-43 185
9 TraesCS5A01G414000 chr5B 91.413 1514 120 7 1120 2625 591653555 591655066 0.000000e+00 2067
10 TraesCS5A01G414000 chr5B 91.164 1392 114 5 1043 2426 588683399 588682009 0.000000e+00 1881
11 TraesCS5A01G414000 chr5B 93.256 1038 69 1 1 1037 68027133 68026096 0.000000e+00 1528
12 TraesCS5A01G414000 chr5B 93.243 1036 64 4 1 1035 689144089 689143059 0.000000e+00 1520
13 TraesCS5A01G414000 chr5B 84.746 177 19 5 2493 2662 588681877 588681702 1.570000e-38 171
14 TraesCS5A01G414000 chr3A 96.035 1034 41 0 4 1037 101881670 101880637 0.000000e+00 1683
15 TraesCS5A01G414000 chr7A 95.082 1037 51 0 1 1037 7654543 7655579 0.000000e+00 1633
16 TraesCS5A01G414000 chr7A 94.894 1038 52 1 1 1038 543454781 543455817 0.000000e+00 1622
17 TraesCS5A01G414000 chr7A 94.889 1037 53 0 1 1037 726716367 726717403 0.000000e+00 1622
18 TraesCS5A01G414000 chr7A 96.078 612 23 1 2661 3271 31692216 31691605 0.000000e+00 996
19 TraesCS5A01G414000 chr1D 94.615 1040 55 1 1 1039 111696607 111695568 0.000000e+00 1609
20 TraesCS5A01G414000 chr7B 93.353 1038 63 4 1 1037 733818368 733817336 0.000000e+00 1530
21 TraesCS5A01G414000 chr6D 90.144 1045 95 6 1 1038 10506558 10507601 0.000000e+00 1352
22 TraesCS5A01G414000 chr4A 96.602 618 18 3 2665 3281 580983900 580984515 0.000000e+00 1022
23 TraesCS5A01G414000 chr4A 77.155 1160 242 15 1127 2275 31414053 31415200 0.000000e+00 652
24 TraesCS5A01G414000 chr1A 96.117 618 22 2 2665 3281 35065849 35065233 0.000000e+00 1007
25 TraesCS5A01G414000 chr6A 95.948 617 24 1 2665 3281 523994947 523994332 0.000000e+00 1000
26 TraesCS5A01G414000 chr6A 95.955 618 20 3 2665 3281 86904320 86903707 0.000000e+00 998
27 TraesCS5A01G414000 chr2A 95.786 617 25 1 2665 3281 123976902 123977517 0.000000e+00 994
28 TraesCS5A01G414000 chr4B 78.224 1171 235 18 1127 2284 538999091 538997928 0.000000e+00 732
29 TraesCS5A01G414000 chr4D 77.502 1169 247 11 1127 2284 437028938 437027775 0.000000e+00 688


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 TraesCS5A01G414000 chr5A 602002601 602005881 3280 False 6059.0 6059 100.000 1 3281 1 chr5A.!!$F2 3280
1 TraesCS5A01G414000 chr5A 599222099 599223819 1720 True 1053.0 1906 89.230 1043 2662 2 chr5A.!!$R2 1619
2 TraesCS5A01G414000 chr5A 160014301 160014908 607 True 1005.0 1005 96.546 2665 3271 1 chr5A.!!$R1 606
3 TraesCS5A01G414000 chr5A 639221525 639222144 619 False 996.0 996 95.652 2662 3281 1 chr5A.!!$F3 619
4 TraesCS5A01G414000 chr5A 552653085 552653700 615 False 994.0 994 95.786 2665 3281 1 chr5A.!!$F1 616
5 TraesCS5A01G414000 chr5D 482298735 482300325 1590 False 2298.0 2298 92.804 1038 2624 1 chr5D.!!$F1 1586
6 TraesCS5A01G414000 chr5D 480479269 480480953 1684 True 1022.5 1860 88.862 1043 2662 2 chr5D.!!$R1 1619
7 TraesCS5A01G414000 chr5B 591653555 591655066 1511 False 2067.0 2067 91.413 1120 2625 1 chr5B.!!$F1 1505
8 TraesCS5A01G414000 chr5B 68026096 68027133 1037 True 1528.0 1528 93.256 1 1037 1 chr5B.!!$R1 1036
9 TraesCS5A01G414000 chr5B 689143059 689144089 1030 True 1520.0 1520 93.243 1 1035 1 chr5B.!!$R2 1034
10 TraesCS5A01G414000 chr5B 588681702 588683399 1697 True 1026.0 1881 87.955 1043 2662 2 chr5B.!!$R3 1619
11 TraesCS5A01G414000 chr3A 101880637 101881670 1033 True 1683.0 1683 96.035 4 1037 1 chr3A.!!$R1 1033
12 TraesCS5A01G414000 chr7A 7654543 7655579 1036 False 1633.0 1633 95.082 1 1037 1 chr7A.!!$F1 1036
13 TraesCS5A01G414000 chr7A 543454781 543455817 1036 False 1622.0 1622 94.894 1 1038 1 chr7A.!!$F2 1037
14 TraesCS5A01G414000 chr7A 726716367 726717403 1036 False 1622.0 1622 94.889 1 1037 1 chr7A.!!$F3 1036
15 TraesCS5A01G414000 chr7A 31691605 31692216 611 True 996.0 996 96.078 2661 3271 1 chr7A.!!$R1 610
16 TraesCS5A01G414000 chr1D 111695568 111696607 1039 True 1609.0 1609 94.615 1 1039 1 chr1D.!!$R1 1038
17 TraesCS5A01G414000 chr7B 733817336 733818368 1032 True 1530.0 1530 93.353 1 1037 1 chr7B.!!$R1 1036
18 TraesCS5A01G414000 chr6D 10506558 10507601 1043 False 1352.0 1352 90.144 1 1038 1 chr6D.!!$F1 1037
19 TraesCS5A01G414000 chr4A 580983900 580984515 615 False 1022.0 1022 96.602 2665 3281 1 chr4A.!!$F2 616
20 TraesCS5A01G414000 chr4A 31414053 31415200 1147 False 652.0 652 77.155 1127 2275 1 chr4A.!!$F1 1148
21 TraesCS5A01G414000 chr1A 35065233 35065849 616 True 1007.0 1007 96.117 2665 3281 1 chr1A.!!$R1 616
22 TraesCS5A01G414000 chr6A 523994332 523994947 615 True 1000.0 1000 95.948 2665 3281 1 chr6A.!!$R2 616
23 TraesCS5A01G414000 chr6A 86903707 86904320 613 True 998.0 998 95.955 2665 3281 1 chr6A.!!$R1 616
24 TraesCS5A01G414000 chr2A 123976902 123977517 615 False 994.0 994 95.786 2665 3281 1 chr2A.!!$F1 616
25 TraesCS5A01G414000 chr4B 538997928 538999091 1163 True 732.0 732 78.224 1127 2284 1 chr4B.!!$R1 1157
26 TraesCS5A01G414000 chr4D 437027775 437028938 1163 True 688.0 688 77.502 1127 2284 1 chr4D.!!$R1 1157

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
553 560 0.320771 GCGTCTGCTCTTCTTTCCCA 60.321 55.0 0.0 0.0 38.39 4.37 F
2084 2103 0.037447 GCTGAAAGGGTTGAGAGGCT 59.963 55.0 0.0 0.0 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2253 2279 0.036388 ATGCGGAAGACACGACCAAT 60.036 50.0 0.00 0.0 0.00 3.16 R
3057 3229 5.853936 TCAGAATAGTGTAAACTGCACTGT 58.146 37.5 7.54 0.0 45.59 3.55 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
88 95 0.329261 CAGATGACTTGAAGCCCCCA 59.671 55.000 0.00 0.00 0.00 4.96
138 145 3.867493 CGCTGATCAAAGTTGCTCATCTA 59.133 43.478 0.00 0.00 33.44 1.98
176 183 3.939837 CTGATGGTGTCGGTGCGCT 62.940 63.158 9.73 0.00 0.00 5.92
177 184 2.742372 GATGGTGTCGGTGCGCTT 60.742 61.111 9.73 0.00 0.00 4.68
235 242 2.106332 CCGGCGGTGATGTAGGAC 59.894 66.667 19.97 0.00 0.00 3.85
313 320 1.592669 CATCTGGGCGAAGTAGGCG 60.593 63.158 0.00 0.00 37.59 5.52
314 321 1.756950 ATCTGGGCGAAGTAGGCGA 60.757 57.895 0.00 0.00 37.59 5.54
326 333 1.001974 AGTAGGCGACAACAGATTGCA 59.998 47.619 0.00 0.00 39.66 4.08
338 345 0.627451 AGATTGCATCCCCTTCTGCA 59.373 50.000 0.00 0.00 46.08 4.41
369 376 0.887933 GCAACCCGGATGTTGTTGAT 59.112 50.000 20.49 0.00 45.80 2.57
553 560 0.320771 GCGTCTGCTCTTCTTTCCCA 60.321 55.000 0.00 0.00 38.39 4.37
582 589 2.099921 CCTTCGTGACGAGGATCTTGAT 59.900 50.000 18.92 0.00 37.14 2.57
924 932 8.840200 TGAGGTACAAGGAAAGTAGAGATAAT 57.160 34.615 0.00 0.00 0.00 1.28
1000 1009 0.104487 TCAACTAAACCGGTGCGTGA 59.896 50.000 8.52 5.16 0.00 4.35
1118 1128 4.021916 AGCTTATTGCAAGCCAAGAATCT 58.978 39.130 17.70 6.68 44.01 2.40
1384 1403 4.636249 CAAAGAACCTACAAGCTCTGAGT 58.364 43.478 6.53 0.00 0.00 3.41
1386 1405 6.223852 CAAAGAACCTACAAGCTCTGAGTTA 58.776 40.000 6.53 0.00 0.00 2.24
1389 1408 7.719871 AGAACCTACAAGCTCTGAGTTAATA 57.280 36.000 6.53 0.00 0.00 0.98
1393 1412 7.947282 ACCTACAAGCTCTGAGTTAATATCTC 58.053 38.462 6.53 0.00 0.00 2.75
1403 1422 7.729116 TCTGAGTTAATATCTCACATGCATCA 58.271 34.615 0.00 0.00 37.07 3.07
1435 1454 4.721776 AGATCTGCCCATTCTACAGGTTTA 59.278 41.667 0.00 0.00 32.19 2.01
1509 1528 4.441792 TCGTTCACATCATCGATTTCCAT 58.558 39.130 0.00 0.00 0.00 3.41
1543 1562 4.999950 GGAGCCAGTGGATAACTATCATTG 59.000 45.833 15.20 0.00 36.83 2.82
1593 1612 1.952296 CCATGCCTAAGAATCACTGGC 59.048 52.381 0.00 0.00 43.49 4.85
1681 1700 3.601685 TCTCTGCGTCGTGTGGCA 61.602 61.111 0.00 0.00 37.63 4.92
1752 1771 4.292186 TGAGCATCTTGATATAAGGCCC 57.708 45.455 0.00 0.00 34.92 5.80
1783 1802 6.422223 GTCATTGTAGTGAATTTCGCCTATG 58.578 40.000 6.34 5.61 0.00 2.23
1872 1891 1.386057 GAGCCTATCCCCCAGGGTT 60.386 63.158 4.22 0.00 43.84 4.11
1944 1963 4.770531 TCAAGATACTTGGAGACCTTCGAA 59.229 41.667 10.84 0.00 0.00 3.71
1965 1984 6.757478 TCGAATACTATACGGCAATGTTTGAA 59.243 34.615 0.00 0.00 0.00 2.69
2038 2057 0.524862 GCACTGTCTTGCAAGGGATG 59.475 55.000 25.73 18.45 42.49 3.51
2052 2071 7.894753 TGCAAGGGATGTCATCAATTTAATA 57.105 32.000 14.72 0.00 0.00 0.98
2084 2103 0.037447 GCTGAAAGGGTTGAGAGGCT 59.963 55.000 0.00 0.00 0.00 4.58
2253 2279 4.748701 ACCTTGGTTGGAAGAGTAGAGTA 58.251 43.478 0.00 0.00 0.00 2.59
2268 2294 3.870633 AGAGTATTGGTCGTGTCTTCC 57.129 47.619 0.00 0.00 0.00 3.46
2289 2315 1.131883 GCATGGTGCTGACATGTCTTC 59.868 52.381 25.55 16.96 45.68 2.87
2328 2359 5.236655 TGTGCACTGTTTTTATCGTTGAA 57.763 34.783 19.41 0.00 0.00 2.69
2329 2360 5.641709 TGTGCACTGTTTTTATCGTTGAAA 58.358 33.333 19.41 0.00 0.00 2.69
2330 2361 5.513495 TGTGCACTGTTTTTATCGTTGAAAC 59.487 36.000 19.41 0.00 34.67 2.78
2331 2362 5.741982 GTGCACTGTTTTTATCGTTGAAACT 59.258 36.000 10.32 0.00 35.04 2.66
2332 2363 5.741510 TGCACTGTTTTTATCGTTGAAACTG 59.258 36.000 0.00 0.00 37.86 3.16
2333 2364 5.968848 GCACTGTTTTTATCGTTGAAACTGA 59.031 36.000 14.84 0.00 36.40 3.41
2334 2365 6.470877 GCACTGTTTTTATCGTTGAAACTGAA 59.529 34.615 14.84 0.00 36.40 3.02
2335 2366 7.513041 GCACTGTTTTTATCGTTGAAACTGAAC 60.513 37.037 14.84 0.00 36.40 3.18
2336 2367 6.970613 ACTGTTTTTATCGTTGAAACTGAACC 59.029 34.615 14.84 0.00 36.40 3.62
2337 2368 5.966503 TGTTTTTATCGTTGAAACTGAACCG 59.033 36.000 0.00 0.00 35.04 4.44
2339 2370 4.718858 TTATCGTTGAAACTGAACCGTG 57.281 40.909 0.00 0.00 0.00 4.94
2340 2371 1.292061 TCGTTGAAACTGAACCGTGG 58.708 50.000 0.00 0.00 0.00 4.94
2341 2372 1.134759 TCGTTGAAACTGAACCGTGGA 60.135 47.619 0.00 0.00 0.00 4.02
2343 2374 2.285977 GTTGAAACTGAACCGTGGAGT 58.714 47.619 0.00 0.00 0.00 3.85
2344 2375 1.948104 TGAAACTGAACCGTGGAGTG 58.052 50.000 0.00 0.00 0.00 3.51
2345 2376 1.483004 TGAAACTGAACCGTGGAGTGA 59.517 47.619 0.00 0.00 0.00 3.41
2346 2377 2.104111 TGAAACTGAACCGTGGAGTGAT 59.896 45.455 0.00 0.00 0.00 3.06
2388 2424 7.668469 TCCACGATATTTCTATAGCCTGACTTA 59.332 37.037 0.00 0.00 0.00 2.24
2456 2504 1.202592 TGCTGCTTGTCGGTTCAGTTA 60.203 47.619 0.00 0.00 0.00 2.24
2457 2505 1.194772 GCTGCTTGTCGGTTCAGTTAC 59.805 52.381 0.00 0.00 0.00 2.50
2472 2520 3.506455 TCAGTTACCTGTCTACTCACTGC 59.494 47.826 0.00 0.00 39.82 4.40
2529 2687 0.747852 TGATAATACCGCGACAGCCA 59.252 50.000 8.23 0.00 41.18 4.75
2554 2712 3.065095 ACGTAGAAGAAGGCGTAGTGATC 59.935 47.826 0.00 0.00 35.71 2.92
2555 2713 2.853731 AGAAGAAGGCGTAGTGATCG 57.146 50.000 0.00 0.00 0.00 3.69
2625 2790 2.093181 CCCCGTTGTAGGATTGACATGA 60.093 50.000 0.00 0.00 0.00 3.07
2631 2796 6.238103 CCGTTGTAGGATTGACATGATTGTAC 60.238 42.308 0.00 0.00 35.79 2.90
2632 2797 6.507929 CGTTGTAGGATTGACATGATTGTACG 60.508 42.308 0.00 0.00 35.79 3.67
2633 2798 5.972935 TGTAGGATTGACATGATTGTACGT 58.027 37.500 0.00 0.00 35.79 3.57
2634 2799 7.102847 TGTAGGATTGACATGATTGTACGTA 57.897 36.000 0.00 0.00 35.79 3.57
2663 2835 7.757097 ACTGTACTAATTAGAGCATGTTTCG 57.243 36.000 19.38 6.77 0.00 3.46
2730 2902 2.772077 TTTCAGCCGGCACTAATGTA 57.228 45.000 31.54 8.68 0.00 2.29
2733 2905 4.617253 TTCAGCCGGCACTAATGTATAT 57.383 40.909 31.54 0.00 0.00 0.86
2739 2911 7.123697 TCAGCCGGCACTAATGTATATAATAGT 59.876 37.037 31.54 0.00 0.00 2.12
2769 2941 1.887242 GCGGCGATCAATAGCACCA 60.887 57.895 12.98 0.00 34.54 4.17
2804 2976 3.541632 CTTTACTACCGGTTCATGCCAT 58.458 45.455 15.04 0.00 0.00 4.40
3057 3229 1.809619 GATTGCACGGAGCTACGCA 60.810 57.895 20.78 6.29 45.94 5.24
3231 3404 7.331791 GTTATAACTCCAGACTTTGACCATCT 58.668 38.462 8.41 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 66 1.475280 CAAGTCATCTGCCAATGTGGG 59.525 52.381 0.00 0.00 38.19 4.61
88 95 2.224209 CCTCTACAACAACAACTCGGGT 60.224 50.000 0.00 0.00 0.00 5.28
138 145 1.269309 GCATCGATGACCTCTACGCTT 60.269 52.381 29.20 0.00 0.00 4.68
176 183 0.389817 CTCGTCTCCGCCAATGACAA 60.390 55.000 0.00 0.00 0.00 3.18
177 184 1.215382 CTCGTCTCCGCCAATGACA 59.785 57.895 0.00 0.00 0.00 3.58
235 242 1.913317 TCGATGACGATGAGCTTGTG 58.087 50.000 0.00 0.00 43.81 3.33
313 320 2.134789 AGGGGATGCAATCTGTTGTC 57.865 50.000 0.00 0.00 44.71 3.18
314 321 2.042162 AGAAGGGGATGCAATCTGTTGT 59.958 45.455 0.00 0.00 44.71 3.32
326 333 2.671070 CACGGTGCAGAAGGGGAT 59.329 61.111 0.00 0.00 0.00 3.85
338 345 2.584391 GGGTTGCTCTCTCCACGGT 61.584 63.158 0.00 0.00 0.00 4.83
428 435 0.469917 CAGGTTACCTCCATCGCCAT 59.530 55.000 0.00 0.00 0.00 4.40
553 560 2.352814 CCTCGTCACGAAGGACAAAGAT 60.353 50.000 0.00 0.00 37.66 2.40
582 589 2.908015 GCTCCATGCCGGAACCTA 59.092 61.111 5.05 0.00 45.75 3.08
1000 1009 4.431131 CAGGTCCAAGGGGCGCAT 62.431 66.667 10.83 0.00 0.00 4.73
1118 1128 5.946972 TGTCTCCAGTTACCTTGTTTCAAAA 59.053 36.000 0.00 0.00 0.00 2.44
1144 1154 6.890293 AGTCTCCTGTATTAATTCCCAGAAC 58.110 40.000 0.00 0.00 0.00 3.01
1384 1403 7.557358 ACAAAGGTGATGCATGTGAGATATTAA 59.443 33.333 2.46 0.00 0.00 1.40
1386 1405 5.889853 ACAAAGGTGATGCATGTGAGATATT 59.110 36.000 2.46 0.00 0.00 1.28
1389 1408 3.693807 ACAAAGGTGATGCATGTGAGAT 58.306 40.909 2.46 0.00 0.00 2.75
1403 1422 1.067295 TGGGCAGATCTCACAAAGGT 58.933 50.000 0.00 0.00 0.00 3.50
1435 1454 3.084039 CACCATTGGCTGACATGTAACT 58.916 45.455 0.00 0.00 0.00 2.24
1509 1528 2.364973 TGGCTCCCCTGTGCGATA 60.365 61.111 0.00 0.00 31.76 2.92
1543 1562 2.511145 CCTCGCTGCAAGAGCCTC 60.511 66.667 12.07 0.00 46.01 4.70
1593 1612 7.307278 GCATAAGCAGAGTTTGAGTCATCTATG 60.307 40.741 12.91 12.91 41.58 2.23
1681 1700 2.232941 CAGCATTGAACTCAAAGGGCAT 59.767 45.455 13.22 0.00 39.55 4.40
1749 1768 2.325393 CTACAATGACCTCCCCGGGC 62.325 65.000 17.73 0.30 43.30 6.13
1752 1771 1.191535 TCACTACAATGACCTCCCCG 58.808 55.000 0.00 0.00 0.00 5.73
1783 1802 3.681593 ATCAGGAGTATGATGCAGCTC 57.318 47.619 2.53 0.17 38.49 4.09
1831 1850 9.282569 GCTCTTGATCATTCTTATAATCCTGTT 57.717 33.333 0.00 0.00 0.00 3.16
1872 1891 1.762370 TCCTGCTCAACAAGAGTCACA 59.238 47.619 0.00 0.00 46.47 3.58
1944 1963 8.445275 TTGATTCAAACATTGCCGTATAGTAT 57.555 30.769 0.00 0.00 0.00 2.12
1965 1984 2.158769 TGGGCGAGCAACATCTATTGAT 60.159 45.455 0.00 0.00 0.00 2.57
2038 2057 6.422223 CCTCACACGCTATTAAATTGATGAC 58.578 40.000 0.00 0.00 0.00 3.06
2052 2071 2.324014 TTTCAGCACCCTCACACGCT 62.324 55.000 0.00 0.00 34.29 5.07
2084 2103 0.965439 CCATTTCCCAAACGCCTCAA 59.035 50.000 0.00 0.00 0.00 3.02
2253 2279 0.036388 ATGCGGAAGACACGACCAAT 60.036 50.000 0.00 0.00 0.00 3.16
2289 2315 3.937079 TGCACATACATGAGCTTCTTCTG 59.063 43.478 11.92 0.00 43.41 3.02
2328 2359 2.930826 AATCACTCCACGGTTCAGTT 57.069 45.000 0.00 0.00 0.00 3.16
2329 2360 2.878406 CAAAATCACTCCACGGTTCAGT 59.122 45.455 0.00 0.00 0.00 3.41
2330 2361 2.878406 ACAAAATCACTCCACGGTTCAG 59.122 45.455 0.00 0.00 0.00 3.02
2331 2362 2.616376 CACAAAATCACTCCACGGTTCA 59.384 45.455 0.00 0.00 0.00 3.18
2332 2363 2.616842 ACACAAAATCACTCCACGGTTC 59.383 45.455 0.00 0.00 0.00 3.62
2333 2364 2.650322 ACACAAAATCACTCCACGGTT 58.350 42.857 0.00 0.00 0.00 4.44
2334 2365 2.341846 ACACAAAATCACTCCACGGT 57.658 45.000 0.00 0.00 0.00 4.83
2335 2366 3.363575 CGTAACACAAAATCACTCCACGG 60.364 47.826 0.00 0.00 0.00 4.94
2336 2367 3.246699 ACGTAACACAAAATCACTCCACG 59.753 43.478 0.00 0.00 0.00 4.94
2337 2368 4.806342 ACGTAACACAAAATCACTCCAC 57.194 40.909 0.00 0.00 0.00 4.02
2339 2370 5.412526 TCAACGTAACACAAAATCACTCC 57.587 39.130 0.00 0.00 0.00 3.85
2340 2371 6.077838 GGATCAACGTAACACAAAATCACTC 58.922 40.000 0.00 0.00 0.00 3.51
2341 2372 5.529430 TGGATCAACGTAACACAAAATCACT 59.471 36.000 0.00 0.00 0.00 3.41
2343 2374 5.559225 CGTGGATCAACGTAACACAAAATCA 60.559 40.000 14.75 0.00 38.74 2.57
2344 2375 4.843984 CGTGGATCAACGTAACACAAAATC 59.156 41.667 14.75 0.00 38.74 2.17
2345 2376 4.512198 TCGTGGATCAACGTAACACAAAAT 59.488 37.500 21.66 0.00 43.96 1.82
2346 2377 3.869832 TCGTGGATCAACGTAACACAAAA 59.130 39.130 21.66 0.00 43.96 2.44
2388 2424 0.846427 TCTGAAACTGGGGGCAGGAT 60.846 55.000 0.00 0.00 0.00 3.24
2456 2504 2.294449 TGAGCAGTGAGTAGACAGGT 57.706 50.000 0.00 0.00 0.00 4.00
2457 2505 3.023119 AGATGAGCAGTGAGTAGACAGG 58.977 50.000 0.00 0.00 0.00 4.00
2472 2520 4.928615 GCCGATTCCTCTGAATTAGATGAG 59.071 45.833 0.00 0.00 41.30 2.90
2529 2687 4.637534 TCACTACGCCTTCTTCTACGTTAT 59.362 41.667 0.00 0.00 39.78 1.89
2676 2848 6.238211 GCACTATTATGCTTCACGTTTGATCT 60.238 38.462 0.00 0.00 42.62 2.75
2678 2850 5.220854 GGCACTATTATGCTTCACGTTTGAT 60.221 40.000 0.00 0.00 45.38 2.57
2693 2865 5.392595 GCTGAAATTCAAACCGGCACTATTA 60.393 40.000 0.00 0.00 0.00 0.98
2730 2902 4.379813 CGCCACGAACCGGTACTATTATAT 60.380 45.833 8.00 0.00 0.00 0.86
2733 2905 1.065401 CGCCACGAACCGGTACTATTA 59.935 52.381 8.00 0.00 0.00 0.98
2788 2960 2.036958 TTCATGGCATGAACCGGTAG 57.963 50.000 33.06 4.14 43.84 3.18
2804 2976 2.232941 CAGCCTCTTTAGTACCGGTTCA 59.767 50.000 15.04 0.00 0.00 3.18
2852 3024 2.722094 GGCACTAAATGGTGATGGTGA 58.278 47.619 0.67 0.00 39.34 4.02
3057 3229 5.853936 TCAGAATAGTGTAAACTGCACTGT 58.146 37.500 7.54 0.00 45.59 3.55
3128 3300 7.545489 AGAAGTCCGGAGTTGTAATAAGTTAG 58.455 38.462 29.05 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.