Multiple sequence alignment - TraesCS7D01G477200

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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 TraesCS7D01G477200 chr7D 100.000 2769 0 0 1 2769 588418911 588421679 0.000000e+00 5114.0
1 TraesCS7D01G477200 chr7D 97.321 112 2 1 1975 2085 588420778 588420889 3.640000e-44 189.0
2 TraesCS7D01G477200 chr7D 97.321 112 2 1 1868 1979 588420885 588420995 3.640000e-44 189.0
3 TraesCS7D01G477200 chr7D 82.353 170 21 7 83 246 582126915 582127081 3.720000e-29 139.0
4 TraesCS7D01G477200 chr3A 93.756 1938 66 30 40 1925 21361213 21359279 0.000000e+00 2857.0
5 TraesCS7D01G477200 chr3A 96.516 287 10 0 2072 2358 21359281 21358995 2.500000e-130 475.0
6 TraesCS7D01G477200 chr3A 94.915 177 9 0 2552 2728 21352824 21352648 7.550000e-71 278.0
7 TraesCS7D01G477200 chr3A 91.803 61 2 3 1975 2032 21359339 21359279 6.360000e-12 82.4
8 TraesCS7D01G477200 chr3B 86.867 1797 161 35 1 1780 781355337 781357075 0.000000e+00 1941.0
9 TraesCS7D01G477200 chr3B 84.487 1199 108 44 802 1984 781494930 781493794 0.000000e+00 1112.0
10 TraesCS7D01G477200 chr3B 84.310 1160 112 34 848 1979 781210449 781211566 0.000000e+00 1070.0
11 TraesCS7D01G477200 chr3B 83.574 1175 124 38 802 1935 781344469 781345615 0.000000e+00 1037.0
12 TraesCS7D01G477200 chr3B 92.432 370 19 7 2004 2369 781362487 781362851 1.140000e-143 520.0
13 TraesCS7D01G477200 chr3B 93.789 161 10 0 2559 2719 781365087 781365247 2.760000e-60 243.0
14 TraesCS7D01G477200 chr3B 87.681 138 15 2 609 745 781342899 781343035 2.850000e-35 159.0
15 TraesCS7D01G477200 chr3B 81.481 189 16 14 1806 1979 781362384 781362568 1.340000e-28 137.0
16 TraesCS7D01G477200 chr3B 83.065 124 7 10 2610 2719 781535287 781535164 1.750000e-17 100.0
17 TraesCS7D01G477200 chr3B 91.667 48 3 1 205 252 781355586 781355632 6.400000e-07 65.8
18 TraesCS7D01G477200 chr3B 90.698 43 4 0 1 43 781533348 781533306 1.070000e-04 58.4
19 TraesCS7D01G477200 chr3D 85.192 1587 136 47 427 1979 584129405 584130926 0.000000e+00 1537.0
20 TraesCS7D01G477200 chr3D 86.295 1131 102 27 830 1935 584048670 584049772 0.000000e+00 1181.0
21 TraesCS7D01G477200 chr3D 86.134 1089 117 22 802 1877 584457005 584455938 0.000000e+00 1144.0
22 TraesCS7D01G477200 chr3D 91.810 232 17 2 2004 2234 584130845 584131075 3.440000e-84 322.0
23 TraesCS7D01G477200 chr3D 85.350 314 34 4 1 307 584128959 584129267 5.760000e-82 315.0
24 TraesCS7D01G477200 chr3D 74.576 767 147 28 1025 1768 584344259 584343518 2.700000e-75 292.0
25 TraesCS7D01G477200 chr3D 87.805 123 7 2 656 774 584048545 584048663 1.340000e-28 137.0
26 TraesCS7D01G477200 chr3D 87.387 111 6 7 2613 2719 584630988 584630882 1.350000e-23 121.0
27 TraesCS7D01G477200 chr3D 83.065 124 7 10 2610 2721 584044971 584045092 1.750000e-17 100.0
28 TraesCS7D01G477200 chr3D 95.745 47 1 1 205 251 584129266 584129311 1.060000e-09 75.0
29 TraesCS7D01G477200 chr3D 84.615 78 8 4 1903 1979 584455929 584455855 1.060000e-09 75.0
30 TraesCS7D01G477200 chrUn 83.842 1213 118 47 802 1971 45483375 45482198 0.000000e+00 1083.0
31 TraesCS7D01G477200 chr7B 91.620 179 14 1 2363 2541 176239239 176239416 2.130000e-61 246.0
32 TraesCS7D01G477200 chr4A 92.169 166 12 1 2364 2528 18657594 18657429 1.660000e-57 233.0
33 TraesCS7D01G477200 chr4A 91.515 165 13 1 2365 2528 18660550 18660386 2.770000e-55 226.0
34 TraesCS7D01G477200 chr4A 90.964 166 14 1 2364 2528 18663503 18663338 3.590000e-54 222.0
35 TraesCS7D01G477200 chr6A 91.975 162 13 0 2371 2532 583002778 583002617 7.710000e-56 228.0
36 TraesCS7D01G477200 chr6A 84.444 90 12 2 1038 1126 601264641 601264553 1.370000e-13 87.9
37 TraesCS7D01G477200 chr5B 91.975 162 13 0 2371 2532 686710565 686710404 7.710000e-56 228.0
38 TraesCS7D01G477200 chr4B 92.500 160 11 1 2371 2529 354785572 354785413 7.710000e-56 228.0
39 TraesCS7D01G477200 chr2B 92.025 163 12 1 2367 2529 406890702 406890863 7.710000e-56 228.0
40 TraesCS7D01G477200 chr2B 83.495 103 12 3 256 354 461746906 461746805 1.060000e-14 91.6
41 TraesCS7D01G477200 chr5D 91.824 159 13 0 2371 2529 468826727 468826885 3.590000e-54 222.0
42 TraesCS7D01G477200 chr2A 85.271 129 14 3 456 580 30569797 30569924 8.050000e-26 128.0
43 TraesCS7D01G477200 chr6D 85.393 89 13 0 1038 1126 454996490 454996402 2.940000e-15 93.5
44 TraesCS7D01G477200 chr6B 86.250 80 11 0 1038 1117 692574489 692574568 1.370000e-13 87.9


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 TraesCS7D01G477200 chr7D 588418911 588421679 2768 False 1830.666667 5114 98.214000 1 2769 3 chr7D.!!$F2 2768
1 TraesCS7D01G477200 chr3A 21358995 21361213 2218 True 1138.133333 2857 94.025000 40 2358 3 chr3A.!!$R2 2318
2 TraesCS7D01G477200 chr3B 781493794 781494930 1136 True 1112.000000 1112 84.487000 802 1984 1 chr3B.!!$R1 1182
3 TraesCS7D01G477200 chr3B 781210449 781211566 1117 False 1070.000000 1070 84.310000 848 1979 1 chr3B.!!$F1 1131
4 TraesCS7D01G477200 chr3B 781355337 781357075 1738 False 1003.400000 1941 89.267000 1 1780 2 chr3B.!!$F3 1779
5 TraesCS7D01G477200 chr3B 781342899 781345615 2716 False 598.000000 1037 85.627500 609 1935 2 chr3B.!!$F2 1326
6 TraesCS7D01G477200 chr3B 781362384 781365247 2863 False 300.000000 520 89.234000 1806 2719 3 chr3B.!!$F4 913
7 TraesCS7D01G477200 chr3D 584455855 584457005 1150 True 609.500000 1144 85.374500 802 1979 2 chr3D.!!$R3 1177
8 TraesCS7D01G477200 chr3D 584128959 584131075 2116 False 562.250000 1537 89.524250 1 2234 4 chr3D.!!$F2 2233
9 TraesCS7D01G477200 chr3D 584044971 584049772 4801 False 472.666667 1181 85.721667 656 2721 3 chr3D.!!$F1 2065
10 TraesCS7D01G477200 chr3D 584343518 584344259 741 True 292.000000 292 74.576000 1025 1768 1 chr3D.!!$R1 743
11 TraesCS7D01G477200 chrUn 45482198 45483375 1177 True 1083.000000 1083 83.842000 802 1971 1 chrUn.!!$R1 1169
12 TraesCS7D01G477200 chr4A 18657429 18663503 6074 True 227.000000 233 91.549333 2364 2528 3 chr4A.!!$R1 164

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
920 5250 0.108207 CATCCAGTCATCCTCAGCCC 59.892 60.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2019 6502 0.037605 CAGTAAAACCGACGAGGCCT 60.038 55.0 3.86 3.86 46.52 5.19 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
30 33 2.167861 GCTGCTAGTCGCCGGAAAG 61.168 63.158 5.05 0.00 38.05 2.62
161 175 1.691976 TGACAAGGAAGAAGGAAGCGA 59.308 47.619 0.00 0.00 0.00 4.93
221 241 1.606601 GGGAAGAAGCAACCCCACC 60.607 63.158 0.00 0.00 38.69 4.61
255 325 1.074775 GGTGGGTGCAGGTTCATCA 59.925 57.895 0.00 0.00 0.00 3.07
479 555 2.348888 GGGCGGTCGAGAGGAAGAA 61.349 63.158 0.00 0.00 0.00 2.52
516 592 1.163554 GCTGGAGGTTGAAGAAGCTG 58.836 55.000 0.00 0.00 40.07 4.24
647 738 0.967887 TTCCTCCTCCAGCTCAGACG 60.968 60.000 0.00 0.00 0.00 4.18
701 3625 3.576118 TGGTATGGTGGTTGACAATTTGG 59.424 43.478 0.78 0.00 0.00 3.28
919 5249 1.070445 CTCATCCAGTCATCCTCAGCC 59.930 57.143 0.00 0.00 0.00 4.85
920 5250 0.108207 CATCCAGTCATCCTCAGCCC 59.892 60.000 0.00 0.00 0.00 5.19
921 5251 0.326904 ATCCAGTCATCCTCAGCCCA 60.327 55.000 0.00 0.00 0.00 5.36
923 5253 1.556373 CCAGTCATCCTCAGCCCACA 61.556 60.000 0.00 0.00 0.00 4.17
926 5256 2.124983 CATCCTCAGCCCACACGG 60.125 66.667 0.00 0.00 0.00 4.94
970 5306 1.285373 ACCACACCAACCAACCAGTTA 59.715 47.619 0.00 0.00 0.00 2.24
1010 5346 2.043652 CTTGACCATGGGGCCCAG 60.044 66.667 31.98 20.77 36.75 4.45
1270 5680 1.004918 CAAGAGGCCGGAGAACGTT 60.005 57.895 5.05 0.00 42.24 3.99
1852 6297 6.203647 ACCACGTAAAAGTGCAGTTTTAATC 58.796 36.000 31.30 21.98 40.59 1.75
1863 6308 5.466393 GTGCAGTTTTAATCCATTTGCTTGT 59.534 36.000 0.00 0.00 0.00 3.16
1941 6424 7.218963 CCTCGTCGGTTTTACTGTTATAACTAC 59.781 40.741 16.33 5.44 0.00 2.73
1944 6427 7.538678 CGTCGGTTTTACTGTTATAACTACTGT 59.461 37.037 16.33 11.61 0.00 3.55
1971 6454 9.695526 TTTTTCTTCATGAACTAATGGTGATTG 57.304 29.630 3.38 0.00 33.88 2.67
1972 6455 8.634335 TTTCTTCATGAACTAATGGTGATTGA 57.366 30.769 3.38 0.00 33.88 2.57
1973 6456 8.812513 TTCTTCATGAACTAATGGTGATTGAT 57.187 30.769 3.38 0.00 0.00 2.57
1974 6457 8.812513 TCTTCATGAACTAATGGTGATTGATT 57.187 30.769 3.38 0.00 0.00 2.57
1975 6458 9.904198 TCTTCATGAACTAATGGTGATTGATTA 57.096 29.630 3.38 0.00 0.00 1.75
1978 6461 9.631257 TCATGAACTAATGGTGATTGATTATGT 57.369 29.630 0.00 0.00 0.00 2.29
2010 6493 9.950496 ACTATATTCTGATTCTTTTGTGTCAGT 57.050 29.630 0.00 0.00 39.22 3.41
2015 6498 8.506168 TTCTGATTCTTTTGTGTCAGTTTAGT 57.494 30.769 0.00 0.00 39.22 2.24
2016 6499 7.919690 TCTGATTCTTTTGTGTCAGTTTAGTG 58.080 34.615 0.00 0.00 39.22 2.74
2017 6500 7.768582 TCTGATTCTTTTGTGTCAGTTTAGTGA 59.231 33.333 0.00 0.00 39.22 3.41
2018 6501 8.275015 TGATTCTTTTGTGTCAGTTTAGTGAA 57.725 30.769 0.00 0.00 0.00 3.18
2019 6502 8.735315 TGATTCTTTTGTGTCAGTTTAGTGAAA 58.265 29.630 0.00 0.00 0.00 2.69
2020 6503 9.226345 GATTCTTTTGTGTCAGTTTAGTGAAAG 57.774 33.333 0.00 0.00 0.00 2.62
2021 6504 7.083875 TCTTTTGTGTCAGTTTAGTGAAAGG 57.916 36.000 0.00 0.00 0.00 3.11
2022 6505 4.893424 TTGTGTCAGTTTAGTGAAAGGC 57.107 40.909 0.00 0.00 0.00 4.35
2023 6506 3.211045 TGTGTCAGTTTAGTGAAAGGCC 58.789 45.455 0.00 0.00 0.00 5.19
2024 6507 3.118038 TGTGTCAGTTTAGTGAAAGGCCT 60.118 43.478 0.00 0.00 0.00 5.19
2025 6508 3.498777 GTGTCAGTTTAGTGAAAGGCCTC 59.501 47.826 5.23 0.00 0.00 4.70
2026 6509 2.737252 GTCAGTTTAGTGAAAGGCCTCG 59.263 50.000 5.23 0.00 0.00 4.63
2027 6510 2.367567 TCAGTTTAGTGAAAGGCCTCGT 59.632 45.455 5.23 0.00 0.00 4.18
2028 6511 2.737252 CAGTTTAGTGAAAGGCCTCGTC 59.263 50.000 5.23 7.70 0.00 4.20
2029 6512 1.725164 GTTTAGTGAAAGGCCTCGTCG 59.275 52.381 5.23 0.00 0.00 5.12
2030 6513 0.245539 TTAGTGAAAGGCCTCGTCGG 59.754 55.000 5.23 0.00 0.00 4.79
2031 6514 0.896940 TAGTGAAAGGCCTCGTCGGT 60.897 55.000 5.23 0.59 34.25 4.69
2032 6515 1.301479 GTGAAAGGCCTCGTCGGTT 60.301 57.895 5.23 0.00 34.25 4.44
2033 6516 0.883370 GTGAAAGGCCTCGTCGGTTT 60.883 55.000 5.23 0.00 34.25 3.27
2034 6517 0.179040 TGAAAGGCCTCGTCGGTTTT 60.179 50.000 5.23 0.00 34.25 2.43
2035 6518 1.070445 TGAAAGGCCTCGTCGGTTTTA 59.930 47.619 5.23 0.00 34.25 1.52
2036 6519 1.462283 GAAAGGCCTCGTCGGTTTTAC 59.538 52.381 5.23 0.00 34.25 2.01
2037 6520 0.683412 AAGGCCTCGTCGGTTTTACT 59.317 50.000 5.23 0.00 34.25 2.24
2038 6521 0.037605 AGGCCTCGTCGGTTTTACTG 60.038 55.000 0.00 0.00 34.25 2.74
2039 6522 0.320160 GGCCTCGTCGGTTTTACTGT 60.320 55.000 0.00 0.00 34.25 3.55
2040 6523 1.505425 GCCTCGTCGGTTTTACTGTT 58.495 50.000 0.00 0.00 34.25 3.16
2041 6524 2.610232 GGCCTCGTCGGTTTTACTGTTA 60.610 50.000 0.00 0.00 34.25 2.41
2042 6525 3.256558 GCCTCGTCGGTTTTACTGTTAT 58.743 45.455 0.00 0.00 34.25 1.89
2043 6526 4.423732 GCCTCGTCGGTTTTACTGTTATA 58.576 43.478 0.00 0.00 34.25 0.98
2044 6527 4.864247 GCCTCGTCGGTTTTACTGTTATAA 59.136 41.667 0.00 0.00 34.25 0.98
2045 6528 5.220284 GCCTCGTCGGTTTTACTGTTATAAC 60.220 44.000 8.75 8.75 34.25 1.89
2046 6529 6.095377 CCTCGTCGGTTTTACTGTTATAACT 58.905 40.000 16.33 0.09 0.00 2.24
2047 6530 7.250569 CCTCGTCGGTTTTACTGTTATAACTA 58.749 38.462 16.33 0.00 0.00 2.24
2048 6531 7.218963 CCTCGTCGGTTTTACTGTTATAACTAC 59.781 40.741 16.33 5.44 0.00 2.73
2127 6612 6.939132 ATGAATCTACCTGATTGCTTGAAG 57.061 37.500 0.00 0.00 44.70 3.02
2142 6627 7.892778 TTGCTTGAAGTGTCGTTATATTGTA 57.107 32.000 0.00 0.00 0.00 2.41
2205 6690 4.837093 TCCATACCCAAGACTTTAGGTG 57.163 45.455 14.46 2.17 30.59 4.00
2409 6894 3.747735 TAGCTCTGCTATAGCCCGT 57.252 52.632 21.84 5.02 41.02 5.28
2415 6900 3.695060 GCTCTGCTATAGCCCGTTATAGA 59.305 47.826 21.84 14.07 41.18 1.98
2441 6926 2.774799 GCAGGGTGCCGCTAAATGG 61.775 63.158 0.00 0.00 37.42 3.16
2451 6936 0.373716 CGCTAAATGGTCGCCTTCAC 59.626 55.000 0.00 0.00 0.00 3.18
2467 8087 4.385825 CCTTCACAAATAGCCCGCTATAA 58.614 43.478 9.56 0.09 38.20 0.98
2471 8092 2.440253 ACAAATAGCCCGCTATAACCCA 59.560 45.455 9.56 0.00 38.20 4.51
2529 8162 6.460953 CCATAGCCCGCTATTTAAAACATTGT 60.461 38.462 6.48 0.00 37.16 2.71
2571 9103 8.962884 AATTGTATTAGTATCTCACATGCACA 57.037 30.769 0.00 0.00 0.00 4.57
2592 9124 6.477742 CACATATGTACGTCCATCTTTGTTG 58.522 40.000 8.32 0.00 0.00 3.33
2600 9132 1.820519 TCCATCTTTGTTGATGCAGCC 59.179 47.619 0.00 0.00 41.65 4.85
2643 9175 5.496133 TCACGAGCTAATTGTACTCCTAC 57.504 43.478 0.00 0.00 0.00 3.18
2671 9203 1.107945 CCGGGCCGGTTGATTTATTT 58.892 50.000 36.52 0.00 42.73 1.40
2699 9231 2.046285 CGGAAATGGTGGCTGGGAC 61.046 63.158 0.00 0.00 0.00 4.46
2719 9251 4.323028 GGACTAGCCATATTCAGCTATGCA 60.323 45.833 0.00 0.00 40.64 3.96
2720 9252 4.573900 ACTAGCCATATTCAGCTATGCAC 58.426 43.478 0.00 0.00 40.64 4.57
2721 9253 3.497103 AGCCATATTCAGCTATGCACA 57.503 42.857 0.00 0.00 37.64 4.57
2722 9254 3.409570 AGCCATATTCAGCTATGCACAG 58.590 45.455 0.00 0.00 37.64 3.66
2723 9255 3.072038 AGCCATATTCAGCTATGCACAGA 59.928 43.478 0.00 0.00 37.64 3.41
2724 9256 4.008330 GCCATATTCAGCTATGCACAGAT 58.992 43.478 0.00 0.00 0.00 2.90
2725 9257 5.046087 AGCCATATTCAGCTATGCACAGATA 60.046 40.000 0.00 0.00 37.64 1.98
2726 9258 5.821470 GCCATATTCAGCTATGCACAGATAT 59.179 40.000 0.00 0.00 0.00 1.63
2727 9259 6.018098 GCCATATTCAGCTATGCACAGATATC 60.018 42.308 0.00 0.00 0.00 1.63
2728 9260 7.046033 CCATATTCAGCTATGCACAGATATCA 58.954 38.462 5.32 0.00 0.00 2.15
2729 9261 7.011202 CCATATTCAGCTATGCACAGATATCAC 59.989 40.741 5.32 0.00 0.00 3.06
2730 9262 4.263018 TCAGCTATGCACAGATATCACC 57.737 45.455 5.32 0.00 0.00 4.02
2731 9263 3.642848 TCAGCTATGCACAGATATCACCA 59.357 43.478 5.32 0.00 0.00 4.17
2732 9264 3.995048 CAGCTATGCACAGATATCACCAG 59.005 47.826 5.32 0.00 0.00 4.00
2733 9265 3.645212 AGCTATGCACAGATATCACCAGT 59.355 43.478 5.32 0.00 0.00 4.00
2734 9266 3.993081 GCTATGCACAGATATCACCAGTC 59.007 47.826 5.32 0.00 0.00 3.51
2735 9267 2.584492 TGCACAGATATCACCAGTCG 57.416 50.000 5.32 0.00 0.00 4.18
2736 9268 1.212616 GCACAGATATCACCAGTCGC 58.787 55.000 5.32 2.12 0.00 5.19
2737 9269 1.471501 GCACAGATATCACCAGTCGCA 60.472 52.381 5.32 0.00 0.00 5.10
2738 9270 2.467838 CACAGATATCACCAGTCGCAG 58.532 52.381 5.32 0.00 0.00 5.18
2739 9271 2.099756 CACAGATATCACCAGTCGCAGA 59.900 50.000 5.32 0.00 0.00 4.26
2740 9272 2.760650 ACAGATATCACCAGTCGCAGAA 59.239 45.455 5.32 0.00 39.69 3.02
2741 9273 3.195610 ACAGATATCACCAGTCGCAGAAA 59.804 43.478 5.32 0.00 39.69 2.52
2742 9274 4.183865 CAGATATCACCAGTCGCAGAAAA 58.816 43.478 5.32 0.00 39.69 2.29
2743 9275 4.269603 CAGATATCACCAGTCGCAGAAAAG 59.730 45.833 5.32 0.00 39.69 2.27
2744 9276 2.839486 ATCACCAGTCGCAGAAAAGA 57.161 45.000 0.00 0.00 39.69 2.52
2745 9277 2.613026 TCACCAGTCGCAGAAAAGAA 57.387 45.000 0.00 0.00 39.69 2.52
2746 9278 2.912771 TCACCAGTCGCAGAAAAGAAA 58.087 42.857 0.00 0.00 39.69 2.52
2747 9279 3.275143 TCACCAGTCGCAGAAAAGAAAA 58.725 40.909 0.00 0.00 39.69 2.29
2748 9280 3.692101 TCACCAGTCGCAGAAAAGAAAAA 59.308 39.130 0.00 0.00 39.69 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 33 3.182173 CGTTCATTTTGCACATGGTTCAC 59.818 43.478 0.00 0.00 0.00 3.18
161 175 1.215679 TCCCTCTTCCTCTCCCTCGT 61.216 60.000 0.00 0.00 0.00 4.18
221 241 2.037251 CCCACCACCCTAACGATAGATG 59.963 54.545 0.56 0.00 41.38 2.90
430 503 3.083997 CCTAACCGCCAGCCTCCT 61.084 66.667 0.00 0.00 0.00 3.69
479 555 1.707427 AGCCCAACCTCTTGTTCATCT 59.293 47.619 0.00 0.00 34.00 2.90
516 592 0.321122 GTGAGATGGATGGCCGGATC 60.321 60.000 5.05 0.00 36.79 3.36
647 738 1.214062 CTCGTGTGGTCAGAGAGGC 59.786 63.158 0.00 0.00 34.13 4.70
701 3625 3.866651 AGATATGGTTGGATAGCGATGC 58.133 45.455 0.00 0.00 0.00 3.91
923 5253 2.791501 ATAGTTCGTTTGCCGGCCGT 62.792 55.000 26.77 7.19 37.11 5.68
926 5256 0.303796 GCTATAGTTCGTTTGCCGGC 59.696 55.000 22.73 22.73 37.11 6.13
970 5306 4.338879 ACTCAAGTGGCTGCTTAATTGAT 58.661 39.130 16.06 7.94 31.57 2.57
1270 5680 0.957395 AGAAGAACTCGTCCGCCGTA 60.957 55.000 0.00 0.00 37.94 4.02
1732 6154 0.842030 TGGACTTGATGGCCTCCACT 60.842 55.000 3.32 0.00 46.68 4.00
1852 6297 7.424227 ACAAAACATATTGACAAGCAAATGG 57.576 32.000 0.00 0.00 40.48 3.16
1984 6467 9.950496 ACTGACACAAAAGAATCAGAATATAGT 57.050 29.630 7.08 0.00 40.92 2.12
1989 6472 9.125026 ACTAAACTGACACAAAAGAATCAGAAT 57.875 29.630 7.08 0.00 40.92 2.40
1990 6473 8.397906 CACTAAACTGACACAAAAGAATCAGAA 58.602 33.333 7.08 0.00 40.92 3.02
1991 6474 7.768582 TCACTAAACTGACACAAAAGAATCAGA 59.231 33.333 7.08 0.00 40.92 3.27
1992 6475 7.919690 TCACTAAACTGACACAAAAGAATCAG 58.080 34.615 0.00 0.00 43.47 2.90
1993 6476 7.857734 TCACTAAACTGACACAAAAGAATCA 57.142 32.000 0.00 0.00 0.00 2.57
1994 6477 9.226345 CTTTCACTAAACTGACACAAAAGAATC 57.774 33.333 0.00 0.00 0.00 2.52
1995 6478 8.190784 CCTTTCACTAAACTGACACAAAAGAAT 58.809 33.333 0.00 0.00 0.00 2.40
1996 6479 7.535139 CCTTTCACTAAACTGACACAAAAGAA 58.465 34.615 0.00 0.00 0.00 2.52
1997 6480 6.404293 GCCTTTCACTAAACTGACACAAAAGA 60.404 38.462 0.00 0.00 0.00 2.52
1998 6481 5.743872 GCCTTTCACTAAACTGACACAAAAG 59.256 40.000 0.00 0.00 0.00 2.27
1999 6482 5.393678 GGCCTTTCACTAAACTGACACAAAA 60.394 40.000 0.00 0.00 0.00 2.44
2000 6483 4.097286 GGCCTTTCACTAAACTGACACAAA 59.903 41.667 0.00 0.00 0.00 2.83
2001 6484 3.630312 GGCCTTTCACTAAACTGACACAA 59.370 43.478 0.00 0.00 0.00 3.33
2002 6485 3.118038 AGGCCTTTCACTAAACTGACACA 60.118 43.478 0.00 0.00 0.00 3.72
2003 6486 3.477530 AGGCCTTTCACTAAACTGACAC 58.522 45.455 0.00 0.00 0.00 3.67
2004 6487 3.740115 GAGGCCTTTCACTAAACTGACA 58.260 45.455 6.77 0.00 0.00 3.58
2005 6488 2.737252 CGAGGCCTTTCACTAAACTGAC 59.263 50.000 6.77 0.00 0.00 3.51
2006 6489 2.367567 ACGAGGCCTTTCACTAAACTGA 59.632 45.455 6.77 0.00 0.00 3.41
2007 6490 2.737252 GACGAGGCCTTTCACTAAACTG 59.263 50.000 6.77 0.00 0.00 3.16
2008 6491 2.609737 CGACGAGGCCTTTCACTAAACT 60.610 50.000 6.77 0.00 0.00 2.66
2009 6492 1.725164 CGACGAGGCCTTTCACTAAAC 59.275 52.381 6.77 0.00 0.00 2.01
2010 6493 1.337447 CCGACGAGGCCTTTCACTAAA 60.337 52.381 6.77 0.00 0.00 1.85
2011 6494 0.245539 CCGACGAGGCCTTTCACTAA 59.754 55.000 6.77 0.00 0.00 2.24
2012 6495 0.896940 ACCGACGAGGCCTTTCACTA 60.897 55.000 6.77 0.00 46.52 2.74
2013 6496 1.755393 AACCGACGAGGCCTTTCACT 61.755 55.000 6.77 0.00 46.52 3.41
2014 6497 0.883370 AAACCGACGAGGCCTTTCAC 60.883 55.000 6.77 0.00 46.52 3.18
2015 6498 0.179040 AAAACCGACGAGGCCTTTCA 60.179 50.000 6.77 0.00 46.52 2.69
2016 6499 1.462283 GTAAAACCGACGAGGCCTTTC 59.538 52.381 6.77 5.91 46.52 2.62
2017 6500 1.071228 AGTAAAACCGACGAGGCCTTT 59.929 47.619 6.77 0.00 46.52 3.11
2018 6501 0.683412 AGTAAAACCGACGAGGCCTT 59.317 50.000 6.77 0.00 46.52 4.35
2019 6502 0.037605 CAGTAAAACCGACGAGGCCT 60.038 55.000 3.86 3.86 46.52 5.19
2020 6503 0.320160 ACAGTAAAACCGACGAGGCC 60.320 55.000 0.00 0.00 46.52 5.19
2021 6504 1.505425 AACAGTAAAACCGACGAGGC 58.495 50.000 0.00 0.00 46.52 4.70
2023 6506 7.965107 AGTAGTTATAACAGTAAAACCGACGAG 59.035 37.037 17.65 0.00 0.00 4.18
2024 6507 7.750458 CAGTAGTTATAACAGTAAAACCGACGA 59.250 37.037 17.65 0.00 0.00 4.20
2025 6508 7.461938 GCAGTAGTTATAACAGTAAAACCGACG 60.462 40.741 17.65 0.00 0.00 5.12
2026 6509 7.543520 AGCAGTAGTTATAACAGTAAAACCGAC 59.456 37.037 17.65 0.00 0.00 4.79
2027 6510 7.605449 AGCAGTAGTTATAACAGTAAAACCGA 58.395 34.615 17.65 0.00 0.00 4.69
2028 6511 7.823149 AGCAGTAGTTATAACAGTAAAACCG 57.177 36.000 17.65 0.75 0.00 4.44
2035 6518 9.555727 TGAAGAAAAAGCAGTAGTTATAACAGT 57.444 29.630 17.65 4.34 0.00 3.55
2041 6524 9.289782 AGTTCATGAAGAAAAAGCAGTAGTTAT 57.710 29.630 8.80 0.00 38.13 1.89
2042 6525 8.677148 AGTTCATGAAGAAAAAGCAGTAGTTA 57.323 30.769 8.80 0.00 38.13 2.24
2043 6526 7.573968 AGTTCATGAAGAAAAAGCAGTAGTT 57.426 32.000 8.80 0.00 38.13 2.24
2044 6527 8.677148 TTAGTTCATGAAGAAAAAGCAGTAGT 57.323 30.769 8.80 0.00 38.13 2.73
2045 6528 9.552114 CATTAGTTCATGAAGAAAAAGCAGTAG 57.448 33.333 8.80 0.00 38.13 2.57
2046 6529 8.514594 CCATTAGTTCATGAAGAAAAAGCAGTA 58.485 33.333 8.80 0.00 38.13 2.74
2047 6530 7.014615 ACCATTAGTTCATGAAGAAAAAGCAGT 59.985 33.333 8.80 0.00 38.13 4.40
2048 6531 7.327761 CACCATTAGTTCATGAAGAAAAAGCAG 59.672 37.037 8.80 0.00 38.13 4.24
2127 6612 6.742999 TCATCGCTTACAATATAACGACAC 57.257 37.500 0.00 0.00 31.71 3.67
2369 6854 8.755977 AGCTATAGCCGGCTATTTAAAACTATA 58.244 33.333 44.65 25.94 43.38 1.31
2409 6894 4.261801 GCACCCTGCTGAAAAGTCTATAA 58.738 43.478 0.00 0.00 40.96 0.98
2415 6900 4.181051 GGCACCCTGCTGAAAAGT 57.819 55.556 0.00 0.00 44.28 2.66
2441 6926 0.733150 GGGCTATTTGTGAAGGCGAC 59.267 55.000 0.00 0.00 39.08 5.19
2451 6936 2.812011 GTGGGTTATAGCGGGCTATTTG 59.188 50.000 17.49 0.00 39.65 2.32
2467 8087 4.101741 GTCTCCAAATCAGCTATAGTGGGT 59.898 45.833 0.84 0.00 0.00 4.51
2471 8092 3.322254 CGGGTCTCCAAATCAGCTATAGT 59.678 47.826 0.84 0.00 0.00 2.12
2486 8107 1.134907 TGGAAAATAGCGTCGGGTCTC 60.135 52.381 0.00 0.00 0.00 3.36
2550 8183 9.645059 ACATATGTGCATGTGAGATACTAATAC 57.355 33.333 7.78 0.00 37.74 1.89
2552 8185 9.645059 GTACATATGTGCATGTGAGATACTAAT 57.355 33.333 18.81 0.00 39.46 1.73
2553 8186 7.807907 CGTACATATGTGCATGTGAGATACTAA 59.192 37.037 21.64 0.00 39.46 2.24
2554 8187 7.040686 ACGTACATATGTGCATGTGAGATACTA 60.041 37.037 21.64 0.00 39.46 1.82
2556 8189 5.920840 ACGTACATATGTGCATGTGAGATAC 59.079 40.000 21.64 5.95 39.46 2.24
2558 8191 4.948847 ACGTACATATGTGCATGTGAGAT 58.051 39.130 21.64 0.00 39.46 2.75
2560 8193 3.490896 GGACGTACATATGTGCATGTGAG 59.509 47.826 21.64 8.36 39.46 3.51
2563 9095 3.535280 TGGACGTACATATGTGCATGT 57.465 42.857 21.64 12.89 38.39 3.21
2571 9103 6.017934 GCATCAACAAAGATGGACGTACATAT 60.018 38.462 14.70 7.91 44.33 1.78
2574 9106 3.435327 GCATCAACAAAGATGGACGTACA 59.565 43.478 1.10 1.10 44.33 2.90
2600 9132 1.132834 TGCGTATTGATTGGCAAGCAG 59.867 47.619 18.34 8.12 40.42 4.24
2643 9175 4.143333 CCGGCCCGGTACTCTGTG 62.143 72.222 15.86 0.00 42.73 3.66
2662 9194 7.789273 TTTCCGGCGACTAATAAATAAATCA 57.211 32.000 9.30 0.00 0.00 2.57
2671 9203 2.484065 CCACCATTTCCGGCGACTAATA 60.484 50.000 9.30 0.00 0.00 0.98
2699 9231 4.572909 TGTGCATAGCTGAATATGGCTAG 58.427 43.478 0.00 0.00 43.04 3.42
2719 9251 2.379005 TCTGCGACTGGTGATATCTGT 58.621 47.619 3.98 0.00 0.00 3.41
2720 9252 3.443099 TTCTGCGACTGGTGATATCTG 57.557 47.619 3.98 0.00 0.00 2.90
2721 9253 4.160439 TCTTTTCTGCGACTGGTGATATCT 59.840 41.667 3.98 0.00 0.00 1.98
2722 9254 4.433615 TCTTTTCTGCGACTGGTGATATC 58.566 43.478 0.00 0.00 0.00 1.63
2723 9255 4.471904 TCTTTTCTGCGACTGGTGATAT 57.528 40.909 0.00 0.00 0.00 1.63
2724 9256 3.953712 TCTTTTCTGCGACTGGTGATA 57.046 42.857 0.00 0.00 0.00 2.15
2725 9257 2.839486 TCTTTTCTGCGACTGGTGAT 57.161 45.000 0.00 0.00 0.00 3.06
2726 9258 2.613026 TTCTTTTCTGCGACTGGTGA 57.387 45.000 0.00 0.00 0.00 4.02
2727 9259 3.691049 TTTTCTTTTCTGCGACTGGTG 57.309 42.857 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.