Multiple sequence alignment - TraesCS2A01G339800

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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 TraesCS2A01G339800 chr2A 100.000 3973 0 0 1 3973 574752728 574756700 0.000000e+00 7337.0
1 TraesCS2A01G339800 chr5A 95.474 3822 162 10 154 3973 171517858 171521670 0.000000e+00 6089.0
2 TraesCS2A01G339800 chr5A 87.342 316 23 10 3660 3973 660304344 660304644 2.940000e-91 346.0
3 TraesCS2A01G339800 chr5A 84.196 367 41 10 3610 3973 500028240 500027888 1.370000e-89 340.0
4 TraesCS2A01G339800 chr5A 96.296 81 3 0 234 314 168350061 168350141 2.490000e-27 134.0
5 TraesCS2A01G339800 chr6D 93.471 2175 98 25 1697 3838 440542171 440540008 0.000000e+00 3190.0
6 TraesCS2A01G339800 chr7A 92.528 2168 123 13 1706 3838 1172675 1170512 0.000000e+00 3070.0
7 TraesCS2A01G339800 chr7A 85.013 387 40 11 3589 3973 113112253 113112623 1.040000e-100 377.0
8 TraesCS2A01G339800 chr7D 92.463 2176 118 20 1697 3838 565066912 565069075 0.000000e+00 3068.0
9 TraesCS2A01G339800 chr7D 92.649 1646 91 21 2094 3716 370800774 370802412 0.000000e+00 2342.0
10 TraesCS2A01G339800 chr7D 95.149 268 13 0 422 689 734007 734274 1.320000e-114 424.0
11 TraesCS2A01G339800 chr7D 92.086 278 21 1 1 278 733731 734007 1.340000e-104 390.0
12 TraesCS2A01G339800 chr7D 95.238 42 2 0 1658 1699 755768 755809 2.560000e-07 67.6
13 TraesCS2A01G339800 chr7B 92.198 2166 139 16 1697 3838 629472114 629469955 0.000000e+00 3037.0
14 TraesCS2A01G339800 chr4A 88.913 2336 171 47 1697 3973 697688965 697686659 0.000000e+00 2798.0
15 TraesCS2A01G339800 chr4A 86.849 365 32 5 3610 3973 139726160 139726509 1.030000e-105 394.0
16 TraesCS2A01G339800 chr1A 92.324 1850 98 20 1906 3716 557584607 557582763 0.000000e+00 2590.0
17 TraesCS2A01G339800 chr1A 97.073 205 5 1 756 960 198035832 198036035 1.060000e-90 344.0
18 TraesCS2A01G339800 chr1A 97.073 205 5 1 756 960 198057755 198057958 1.060000e-90 344.0
19 TraesCS2A01G339800 chr1A 100.000 35 0 0 783 817 198035942 198035976 9.220000e-07 65.8
20 TraesCS2A01G339800 chr1A 100.000 35 0 0 783 817 198057865 198057899 9.220000e-07 65.8
21 TraesCS2A01G339800 chr2B 92.412 1331 78 13 2661 3973 535696933 535698258 0.000000e+00 1877.0
22 TraesCS2A01G339800 chr2B 91.922 978 58 6 1706 2665 535685428 535686402 0.000000e+00 1349.0
23 TraesCS2A01G339800 chr5D 94.041 1225 54 11 1697 2904 480174720 480173498 0.000000e+00 1840.0
24 TraesCS2A01G339800 chr3D 96.464 1103 34 4 598 1699 203933249 203934347 0.000000e+00 1816.0
25 TraesCS2A01G339800 chr3D 93.034 1048 62 8 2932 3973 10931891 10930849 0.000000e+00 1520.0
26 TraesCS2A01G339800 chr3D 94.802 404 21 0 1 404 203918264 203918667 7.250000e-177 630.0
27 TraesCS2A01G339800 chr3D 95.930 172 7 0 400 571 203933086 203933257 3.020000e-71 279.0
28 TraesCS2A01G339800 chr5B 90.530 1246 84 25 2714 3952 598670085 598671303 0.000000e+00 1616.0
29 TraesCS2A01G339800 chr5B 90.323 744 61 6 916 1653 561794284 561793546 0.000000e+00 965.0
30 TraesCS2A01G339800 chr5B 94.515 237 13 0 81 317 522046271 522046035 2.260000e-97 366.0
31 TraesCS2A01G339800 chr5B 98.000 50 1 0 476 525 522046036 522045987 1.970000e-13 87.9
32 TraesCS2A01G339800 chr4D 91.373 1136 73 20 2714 3838 446550068 446548947 0.000000e+00 1531.0
33 TraesCS2A01G339800 chr4D 94.093 237 14 0 81 317 142309088 142308852 1.050000e-95 361.0
34 TraesCS2A01G339800 chr1B 89.572 1122 82 26 2860 3973 626315189 626314095 0.000000e+00 1391.0
35 TraesCS2A01G339800 chr1B 93.750 912 50 5 2932 3838 137872514 137873423 0.000000e+00 1362.0
36 TraesCS2A01G339800 chr1B 90.691 752 56 10 909 1653 45050969 45051713 0.000000e+00 989.0
37 TraesCS2A01G339800 chr1B 86.364 198 25 2 154 350 53999793 53999597 8.650000e-52 215.0
38 TraesCS2A01G339800 chr1B 95.000 120 6 0 81 200 337336685 337336566 5.240000e-44 189.0
39 TraesCS2A01G339800 chr1B 95.000 120 6 0 81 200 337425783 337425664 5.240000e-44 189.0
40 TraesCS2A01G339800 chr1B 94.444 54 3 0 476 529 337336485 337336432 2.540000e-12 84.2
41 TraesCS2A01G339800 chr1B 94.444 54 3 0 476 529 337425583 337425530 2.540000e-12 84.2
42 TraesCS2A01G339800 chr1D 92.324 925 53 9 1697 2605 411412194 411413116 0.000000e+00 1299.0
43 TraesCS2A01G339800 chr4B 90.667 750 57 9 916 1658 602166177 602165434 0.000000e+00 985.0
44 TraesCS2A01G339800 chr4B 90.470 745 58 9 916 1653 610015698 610016436 0.000000e+00 970.0
45 TraesCS2A01G339800 chrUn 90.559 752 57 10 909 1653 249824015 249823271 0.000000e+00 983.0
46 TraesCS2A01G339800 chrUn 95.522 268 12 0 422 689 231905670 231905937 2.840000e-116 429.0
47 TraesCS2A01G339800 chrUn 92.086 278 21 1 1 278 231905394 231905670 1.340000e-104 390.0
48 TraesCS2A01G339800 chrUn 100.000 35 0 0 783 817 231906474 231906508 9.220000e-07 65.8
49 TraesCS2A01G339800 chr3B 90.604 745 57 9 916 1653 604554356 604553618 0.000000e+00 976.0
50 TraesCS2A01G339800 chr3B 90.604 745 52 11 916 1653 738229001 738228268 0.000000e+00 972.0
51 TraesCS2A01G339800 chr3B 93.258 267 17 1 422 688 793785832 793785567 3.720000e-105 392.0
52 TraesCS2A01G339800 chr3B 91.121 214 17 2 41 254 793786048 793785837 5.020000e-74 289.0
53 TraesCS2A01G339800 chr3B 96.000 50 2 0 1650 1699 793784388 793784339 9.150000e-12 82.4
54 TraesCS2A01G339800 chr2D 96.029 277 11 0 1697 1973 598694166 598693890 6.050000e-123 451.0
55 TraesCS2A01G339800 chr6B 92.086 278 21 1 1 278 456578218 456577942 1.340000e-104 390.0
56 TraesCS2A01G339800 chr6B 92.537 268 18 2 422 688 456577942 456577676 2.240000e-102 383.0
57 TraesCS2A01G339800 chr6B 97.115 104 3 0 687 790 456577318 456577215 4.080000e-40 176.0
58 TraesCS2A01G339800 chr6B 97.727 44 1 0 756 799 273028986 273028943 4.260000e-10 76.8


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 TraesCS2A01G339800 chr2A 574752728 574756700 3972 False 7337.000000 7337 100.000000 1 3973 1 chr2A.!!$F1 3972
1 TraesCS2A01G339800 chr5A 171517858 171521670 3812 False 6089.000000 6089 95.474000 154 3973 1 chr5A.!!$F2 3819
2 TraesCS2A01G339800 chr6D 440540008 440542171 2163 True 3190.000000 3190 93.471000 1697 3838 1 chr6D.!!$R1 2141
3 TraesCS2A01G339800 chr7A 1170512 1172675 2163 True 3070.000000 3070 92.528000 1706 3838 1 chr7A.!!$R1 2132
4 TraesCS2A01G339800 chr7D 565066912 565069075 2163 False 3068.000000 3068 92.463000 1697 3838 1 chr7D.!!$F3 2141
5 TraesCS2A01G339800 chr7D 370800774 370802412 1638 False 2342.000000 2342 92.649000 2094 3716 1 chr7D.!!$F2 1622
6 TraesCS2A01G339800 chr7D 733731 734274 543 False 407.000000 424 93.617500 1 689 2 chr7D.!!$F4 688
7 TraesCS2A01G339800 chr7B 629469955 629472114 2159 True 3037.000000 3037 92.198000 1697 3838 1 chr7B.!!$R1 2141
8 TraesCS2A01G339800 chr4A 697686659 697688965 2306 True 2798.000000 2798 88.913000 1697 3973 1 chr4A.!!$R1 2276
9 TraesCS2A01G339800 chr1A 557582763 557584607 1844 True 2590.000000 2590 92.324000 1906 3716 1 chr1A.!!$R1 1810
10 TraesCS2A01G339800 chr2B 535696933 535698258 1325 False 1877.000000 1877 92.412000 2661 3973 1 chr2B.!!$F2 1312
11 TraesCS2A01G339800 chr2B 535685428 535686402 974 False 1349.000000 1349 91.922000 1706 2665 1 chr2B.!!$F1 959
12 TraesCS2A01G339800 chr5D 480173498 480174720 1222 True 1840.000000 1840 94.041000 1697 2904 1 chr5D.!!$R1 1207
13 TraesCS2A01G339800 chr3D 10930849 10931891 1042 True 1520.000000 1520 93.034000 2932 3973 1 chr3D.!!$R1 1041
14 TraesCS2A01G339800 chr3D 203933086 203934347 1261 False 1047.500000 1816 96.197000 400 1699 2 chr3D.!!$F2 1299
15 TraesCS2A01G339800 chr5B 598670085 598671303 1218 False 1616.000000 1616 90.530000 2714 3952 1 chr5B.!!$F1 1238
16 TraesCS2A01G339800 chr5B 561793546 561794284 738 True 965.000000 965 90.323000 916 1653 1 chr5B.!!$R1 737
17 TraesCS2A01G339800 chr4D 446548947 446550068 1121 True 1531.000000 1531 91.373000 2714 3838 1 chr4D.!!$R2 1124
18 TraesCS2A01G339800 chr1B 626314095 626315189 1094 True 1391.000000 1391 89.572000 2860 3973 1 chr1B.!!$R2 1113
19 TraesCS2A01G339800 chr1B 137872514 137873423 909 False 1362.000000 1362 93.750000 2932 3838 1 chr1B.!!$F2 906
20 TraesCS2A01G339800 chr1B 45050969 45051713 744 False 989.000000 989 90.691000 909 1653 1 chr1B.!!$F1 744
21 TraesCS2A01G339800 chr1D 411412194 411413116 922 False 1299.000000 1299 92.324000 1697 2605 1 chr1D.!!$F1 908
22 TraesCS2A01G339800 chr4B 602165434 602166177 743 True 985.000000 985 90.667000 916 1658 1 chr4B.!!$R1 742
23 TraesCS2A01G339800 chr4B 610015698 610016436 738 False 970.000000 970 90.470000 916 1653 1 chr4B.!!$F1 737
24 TraesCS2A01G339800 chrUn 249823271 249824015 744 True 983.000000 983 90.559000 909 1653 1 chrUn.!!$R1 744
25 TraesCS2A01G339800 chrUn 231905394 231906508 1114 False 294.933333 429 95.869333 1 817 3 chrUn.!!$F1 816
26 TraesCS2A01G339800 chr3B 604553618 604554356 738 True 976.000000 976 90.604000 916 1653 1 chr3B.!!$R1 737
27 TraesCS2A01G339800 chr3B 738228268 738229001 733 True 972.000000 972 90.604000 916 1653 1 chr3B.!!$R2 737
28 TraesCS2A01G339800 chr3B 793784339 793786048 1709 True 254.466667 392 93.459667 41 1699 3 chr3B.!!$R3 1658
29 TraesCS2A01G339800 chr6B 456577215 456578218 1003 True 316.333333 390 93.912667 1 790 3 chr6B.!!$R2 789

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
54 55 0.107508 CATGCCGACCTCCATCACTT 60.108 55.000 0.00 0.0 0.00 3.16 F
74 75 1.378531 TTGCGGCAGAATACACCATC 58.621 50.000 1.67 0.0 0.00 3.51 F
432 453 1.615392 GCTGTCTTCAGGCCATGTTTT 59.385 47.619 5.01 0.0 41.57 2.43 F
1136 1515 0.398318 GGCTGTGGGAAAGTGTCTCT 59.602 55.000 0.00 0.0 0.00 3.10 F
1431 1814 0.750546 TGCTGCTGATGGGAGAATGC 60.751 55.000 0.00 0.0 35.24 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1035 1413 0.389817 CATCGACGAAGGTCTTGCCA 60.390 55.000 0.00 0.00 41.16 4.92 R
1075 1453 3.059326 ATCCGCCATGCATGTGGGA 62.059 57.895 28.07 28.07 39.73 4.37 R
2322 2726 0.415429 AGCAGAGAAAGAGGGGGAGA 59.585 55.000 0.00 0.00 0.00 3.71 R
2480 2887 0.604578 ATCCATGTGGTTGCAGCAAC 59.395 50.000 27.48 27.48 42.89 4.17 R
3195 3805 4.019321 CCTATTGTCCTCCTCCTTCAACAA 60.019 45.833 0.00 0.00 0.00 2.83 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
34 35 1.142748 CTAGCCTCGGTTCCAGCTG 59.857 63.158 6.78 6.78 36.79 4.24
39 40 2.747460 TCGGTTCCAGCTGCATGC 60.747 61.111 11.82 11.82 43.29 4.06
47 48 4.479993 AGCTGCATGCCGACCTCC 62.480 66.667 16.68 0.00 44.23 4.30
54 55 0.107508 CATGCCGACCTCCATCACTT 60.108 55.000 0.00 0.00 0.00 3.16
74 75 1.378531 TTGCGGCAGAATACACCATC 58.621 50.000 1.67 0.00 0.00 3.51
151 152 3.087065 GGCTGGTTTGGCCCTCTA 58.913 61.111 0.00 0.00 43.49 2.43
157 158 3.430453 CTGGTTTGGCCCTCTAAAATGA 58.570 45.455 0.00 0.00 36.04 2.57
195 196 3.119743 GCTGCATTGTATGTTTGCTCTCA 60.120 43.478 0.00 0.00 37.28 3.27
345 366 3.119990 CCCGGTGTTGTTTATGCTAACAG 60.120 47.826 0.00 0.00 39.06 3.16
351 372 6.314784 GTGTTGTTTATGCTAACAGGACATC 58.685 40.000 0.00 0.00 39.06 3.06
432 453 1.615392 GCTGTCTTCAGGCCATGTTTT 59.385 47.619 5.01 0.00 41.57 2.43
463 484 6.615264 TTAAGCGGACACTGTATAGTCTAG 57.385 41.667 0.00 0.00 34.07 2.43
595 618 4.220821 TGCCAAAAGAAACTTGTACCACAA 59.779 37.500 0.00 0.00 36.54 3.33
887 1265 5.188751 AGCTAGCCTCTTTTGTGATTAGTCT 59.811 40.000 12.13 0.00 0.00 3.24
1035 1413 2.488545 CCTCTACAGCTACGACAACTGT 59.511 50.000 9.35 9.35 46.05 3.55
1136 1515 0.398318 GGCTGTGGGAAAGTGTCTCT 59.602 55.000 0.00 0.00 0.00 3.10
1377 1760 6.757237 TGTAAGACGTTTGGTTATGTCCTAA 58.243 36.000 0.00 0.00 35.16 2.69
1431 1814 0.750546 TGCTGCTGATGGGAGAATGC 60.751 55.000 0.00 0.00 35.24 3.56
1703 2087 5.626142 TCAAACTGCTATTTTGGGTGTAGA 58.374 37.500 5.71 0.00 35.12 2.59
1809 2193 6.233905 TGACAATACTCATTAGGCTTGCTA 57.766 37.500 0.00 0.00 0.00 3.49
1847 2231 9.844790 CTTCTTGCACAAATAAAACATCATAGA 57.155 29.630 0.00 0.00 0.00 1.98
1987 2372 4.525487 AGTAACTGATCTCGTGTACCCAAA 59.475 41.667 0.00 0.00 0.00 3.28
2251 2655 2.541466 CTTCTCCTGTTCCCCTAGTGT 58.459 52.381 0.00 0.00 0.00 3.55
2277 2681 1.074926 AGGTCCTGCCCGAGATCAT 60.075 57.895 0.00 0.00 38.26 2.45
2322 2726 1.969923 GCAGGTAGCATCTCCATCTCT 59.030 52.381 0.00 0.00 44.79 3.10
2417 2822 5.595952 AGGAATTCAAGAGGGATTTGTATGC 59.404 40.000 7.93 0.00 0.00 3.14
2476 2883 3.009916 AGAAGATGCAGTCCAGATTGGTT 59.990 43.478 0.00 0.00 39.03 3.67
2480 2887 4.885907 AGATGCAGTCCAGATTGGTTAATG 59.114 41.667 0.00 0.00 39.03 1.90
2488 2895 3.056678 CCAGATTGGTTAATGTTGCTGCA 60.057 43.478 0.00 0.00 31.35 4.41
2518 2925 6.638096 TGGATTTGTATCTATGCAACCATG 57.362 37.500 0.00 0.00 32.15 3.66
2536 2943 3.634448 CCATGTCCCTGTTGTTTGTGTTA 59.366 43.478 0.00 0.00 0.00 2.41
2887 3295 3.486383 CTGGTGGGTTTGACACAACTAT 58.514 45.455 0.00 0.00 40.64 2.12
2913 3321 5.422331 GGATAGTGGATTAGTAGCATGCCTA 59.578 44.000 15.66 6.84 0.00 3.93
2950 3372 4.422057 TGGTGTGACCTACAATTCCTAGA 58.578 43.478 0.00 0.00 41.89 2.43
3097 3519 7.985184 TGACTTACAATCTGTACATGAATACCC 59.015 37.037 0.00 0.00 31.69 3.69
3195 3805 2.629617 CTGCCAGGTGAAGGTTTTCAAT 59.370 45.455 0.00 0.00 44.49 2.57
3226 3836 5.043281 AGGAGGAGGACAATAGGAACTTCTA 60.043 44.000 0.00 0.00 41.75 2.10
3423 4035 6.467677 AGATAGCTTGTAGTGTGATGTGTTT 58.532 36.000 0.00 0.00 0.00 2.83
3429 4041 6.088085 GCTTGTAGTGTGATGTGTTTTAATGC 59.912 38.462 0.00 0.00 0.00 3.56
3550 4163 3.499537 GCAAAGAAATGGCCCAGAAAAAG 59.500 43.478 0.00 0.00 0.00 2.27
3774 4404 0.179100 CAGATTGCCACGTCGGATCT 60.179 55.000 8.04 5.62 36.56 2.75
3855 4503 7.190920 CTTCTGTGAGAAGGTCGTTAATTTT 57.809 36.000 5.57 0.00 46.03 1.82
3935 4584 0.613260 ACTATGACCTTTCAGCGGCA 59.387 50.000 1.45 0.00 34.35 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.649815 CGAGGCTAGCGACGAGATT 59.350 57.895 21.66 0.00 0.00 2.40
34 35 2.182842 GTGATGGAGGTCGGCATGC 61.183 63.158 9.90 9.90 0.00 4.06
39 40 0.804989 GCAAAAGTGATGGAGGTCGG 59.195 55.000 0.00 0.00 0.00 4.79
47 48 2.642139 ATTCTGCCGCAAAAGTGATG 57.358 45.000 0.00 0.00 0.00 3.07
54 55 1.742831 GATGGTGTATTCTGCCGCAAA 59.257 47.619 0.00 0.00 0.00 3.68
74 75 2.037772 ACACCAGTAAGCAGAACCTCAG 59.962 50.000 0.00 0.00 0.00 3.35
173 174 3.119743 TGAGAGCAAACATACAATGCAGC 60.120 43.478 0.00 0.00 42.45 5.25
195 196 3.071602 CCCCACAACAATCTCGATATCCT 59.928 47.826 0.00 0.00 0.00 3.24
275 277 4.706476 CACATAGAGGGGCATTTCTTTTCA 59.294 41.667 0.00 0.00 0.00 2.69
276 278 4.706962 ACACATAGAGGGGCATTTCTTTTC 59.293 41.667 0.00 0.00 0.00 2.29
277 279 4.677182 ACACATAGAGGGGCATTTCTTTT 58.323 39.130 0.00 0.00 0.00 2.27
278 280 4.322057 ACACATAGAGGGGCATTTCTTT 57.678 40.909 0.00 0.00 0.00 2.52
280 282 3.372025 GGAACACATAGAGGGGCATTTCT 60.372 47.826 0.00 0.00 0.00 2.52
281 283 2.952310 GGAACACATAGAGGGGCATTTC 59.048 50.000 0.00 0.00 0.00 2.17
345 366 3.126001 TCACCAACAACAGAGATGTCC 57.874 47.619 0.00 0.00 0.00 4.02
351 372 4.336433 ACAACTGAATCACCAACAACAGAG 59.664 41.667 0.00 0.00 0.00 3.35
420 441 4.326504 AAACAGAAGAAAACATGGCCTG 57.673 40.909 3.32 2.01 0.00 4.85
432 453 3.181469 ACAGTGTCCGCTTAAACAGAAGA 60.181 43.478 0.00 0.00 0.00 2.87
595 618 3.831911 TGCGAAAGAAATGGGGAAGAAAT 59.168 39.130 0.00 0.00 0.00 2.17
990 1368 2.769621 ATCTCCATGGCCGGCTCA 60.770 61.111 28.56 22.66 0.00 4.26
1035 1413 0.389817 CATCGACGAAGGTCTTGCCA 60.390 55.000 0.00 0.00 41.16 4.92
1075 1453 3.059326 ATCCGCCATGCATGTGGGA 62.059 57.895 28.07 28.07 39.73 4.37
1157 1539 3.734293 CGCTAGAGTAGGCACTGGTAAAC 60.734 52.174 0.00 0.00 41.52 2.01
1398 1781 3.118149 TCAGCAGCAAGGACACATATGAT 60.118 43.478 10.38 0.00 0.00 2.45
1431 1814 6.157211 AGAACAGTCACGTAGTTAGGAATTG 58.843 40.000 0.00 0.00 41.61 2.32
1717 2101 3.510753 TGTGATGCCACCGTTTACTAGTA 59.489 43.478 0.00 0.00 42.53 1.82
1791 2175 6.678568 ATGTCTAGCAAGCCTAATGAGTAT 57.321 37.500 0.00 0.00 0.00 2.12
1796 2180 6.940739 ACCTATATGTCTAGCAAGCCTAATG 58.059 40.000 0.00 0.00 0.00 1.90
2142 2546 1.684248 CCTTTAGCAGGGCAGCATCTT 60.684 52.381 0.00 0.00 39.39 2.40
2193 2597 3.251509 TTGAGCAGAGCAGGGCCA 61.252 61.111 6.18 0.00 0.00 5.36
2239 2643 1.975680 TCTTGGTCACACTAGGGGAAC 59.024 52.381 0.00 0.00 0.00 3.62
2241 2645 1.552486 CCTCTTGGTCACACTAGGGGA 60.552 57.143 0.00 0.00 29.23 4.81
2314 2718 1.324014 AAGAGGGGGAGAGAGATGGA 58.676 55.000 0.00 0.00 0.00 3.41
2322 2726 0.415429 AGCAGAGAAAGAGGGGGAGA 59.585 55.000 0.00 0.00 0.00 3.71
2476 2883 2.029200 CCATGTGGTTGCAGCAACATTA 60.029 45.455 33.86 21.20 45.11 1.90
2480 2887 0.604578 ATCCATGTGGTTGCAGCAAC 59.395 50.000 27.48 27.48 42.89 4.17
2488 2895 6.128486 TGCATAGATACAAATCCATGTGGTT 58.872 36.000 0.00 0.00 34.72 3.67
2518 2925 5.047188 CCAAATAACACAAACAACAGGGAC 58.953 41.667 0.00 0.00 0.00 4.46
2536 2943 8.347035 CAAAACTGAATTTCTTGCAATCCAAAT 58.653 29.630 0.00 2.54 31.94 2.32
2887 3295 5.422331 GGCATGCTACTAATCCACTATCCTA 59.578 44.000 18.92 0.00 0.00 2.94
2913 3321 5.531287 GGTCACACCAGAAACTAAGTCAAAT 59.469 40.000 0.00 0.00 38.42 2.32
2950 3372 8.206867 ACAGTCAACATTCTATAGTATGCACAT 58.793 33.333 16.75 1.83 0.00 3.21
2966 3388 4.628074 GTGTACCACACTACAGTCAACAT 58.372 43.478 2.22 0.00 45.27 2.71
3195 3805 4.019321 CCTATTGTCCTCCTCCTTCAACAA 60.019 45.833 0.00 0.00 0.00 2.83
3429 4041 7.555087 TCCAACTTCTTTTATTATGCCATTGG 58.445 34.615 0.00 0.00 34.35 3.16
3518 4130 1.203994 CATTTCTTTGCTGGGCCTCTG 59.796 52.381 4.53 0.00 0.00 3.35
3568 4189 7.500629 AATTTCTTTGCCTATCCCTTTTGAT 57.499 32.000 0.00 0.00 0.00 2.57
3855 4503 0.604578 AAGCTGGCGGTCGTAAACTA 59.395 50.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.